diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 647a04254f819..8d674f94d61ad 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -13,6 +13,7 @@ jobs: max-parallel: 6 matrix: runner: [0, 1, 2, 3, 4, 5] + # runner: [0] steps: - uses: actions/checkout@v4 with: @@ -58,7 +59,7 @@ jobs: --worker-offset ${{ matrix.runner }} --n-workers 6 \ --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \ --lint --record-build-failures --skiplist-leafs \ - --exclude bioconda-repodata-patches + --exclude bioconda-repodata-patches # --subdag-depth 5 conda clean -y --all build-osx: @@ -67,9 +68,9 @@ jobs: runs-on: macos-13 strategy: fail-fast: false - max-parallel: 4 + max-parallel: 3 matrix: - runner: [0, 1, 2, 3] + runner: [0, 1, 2] steps: - uses: actions/checkout@v4 with: @@ -117,9 +118,9 @@ jobs: python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")' echo '============' bioconda-utils build recipes config.yml \ - --worker-offset ${{ matrix.runner }} --n-workers 4 \ + --worker-offset ${{ matrix.runner }} --n-workers 3 \ --lint --anaconda-upload --record-build-failures --skiplist-leafs \ - --exclude bioconda-repodata-patches + --exclude bioconda-repodata-patches # --subdag-depth 5 conda clean -y --all build-osx-arm: diff --git a/recipes/10x_bamtofastq/meta.yaml b/recipes/10x_bamtofastq/meta.yaml index 486958290de0a..9da8f55737aa9 100644 --- a/recipes/10x_bamtofastq/meta.yaml +++ b/recipes/10x_bamtofastq/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 source: url: https://github.com/10XGenomics/bamtofastq/archive/refs/tags/v{{ version }}.tar.gz diff --git a/recipes/2pg_cartesian/meta.yaml b/recipes/2pg_cartesian/meta.yaml index cf8a9e16d0f44..855f8d25d0e69 100644 --- a/recipes/2pg_cartesian/meta.yaml +++ b/recipes/2pg_cartesian/meta.yaml @@ -10,7 +10,7 @@ source: build: skip: True #[osx] - number: 7 + number: 8 requirements: build: diff --git a/recipes/3seq/build_failure.linux-aarch64.yaml b/recipes/3seq/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..fbd9d2d7dbfe3 --- /dev/null +++ b/recipes/3seq/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 482ec77add88952c9953d6e21d2a0ca92d37689cd8dc5aafb1e998e5f1749d35 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Configuring done (0.4s) + -- Generating done (0.0s) + -- Build files have been written to: $SRC_DIR/build + [ 3%] Building CXX object CMakeFiles/3seq.dir/source/3Seq.cpp.o + [ 7%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/CheckPRun.cpp.o + [ 10%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/FullRun.cpp.o + [ 14%] Building CXX object CMakeFiles/3seq.dir/source/data/bio/Genome.cpp.o + [ 17%] Building CXX object CMakeFiles/3seq.dir/source/data/bio/GenomeSet.cpp.o + [ 21%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/GenPRun.cpp.o + [ 25%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/HelpRun.cpp.o + [ 28%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/InfoRun.cpp.o + [ 32%] Building CXX object CMakeFiles/3seq.dir/source/Interface.cpp.o + [ 35%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/MatchRun.cpp.o + [ 39%] Building CXX object CMakeFiles/3seq.dir/source/data/bio/Nucleotide.cpp.o + [ 42%] Building CXX object CMakeFiles/3seq.dir/source/stat/PTable.cpp.o + [ 46%] Building CXX object CMakeFiles/3seq.dir/source/stat/PTableFile.cpp.o + [ 50%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/Run.cpp.o + [ 53%] Building CXX object CMakeFiles/3seq.dir/source/data/bio/Sequence.cpp.o + [ 57%] Building CXX object CMakeFiles/3seq.dir/source/data/file/SequenceFile.cpp.o + [ 60%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/SingleBpRun.cpp.o + [ 64%] Building CXX object CMakeFiles/3seq.dir/source/stat/stat.cpp.o + [ 67%] Building CXX object CMakeFiles/3seq.dir/source/util/String.cpp.o + [ 71%] Building CXX object CMakeFiles/3seq.dir/source/data/file/TextFile.cpp.o + [ 75%] Building CXX object CMakeFiles/3seq.dir/source/data/bio/Triplet.cpp.o + [ 78%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/TripletRun.cpp.o + [ 82%] Building CXX object CMakeFiles/3seq.dir/source/util/Util.cpp.o + [ 85%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/VersionRun.cpp.o + [ 89%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/WriteRun.cpp.o + [ 92%] Building CXX object CMakeFiles/3seq.dir/source/AppInfo.cpp.o + [ 96%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/RFullRun.cpp.o + [100%] Linking CXX executable 3seq + [100%] Built target 3seq + --2024-12-13 03:19:32-- https://www.dropbox.com/s/zac4wotgdmm3mvb/pvaluetable.2017.700.tgz + Resolving www.dropbox.com (www.dropbox.com)... 162.125.6.18, 2620:100:601c:18::a27d:612 + Connecting to www.dropbox.com (www.dropbox.com)|162.125.6.18|:443... connected. + HTTP request sent, awaiting response... 302 Found + Location: https://www.dropbox.com/scl/fi/vss650bd06nfjfjs2chw5/pvaluetable.2017.700.tgz?rlkey=tgnqupam50kv57ckl7fbdbgtm [following] + --2024-12-13 03:19:32-- https://www.dropbox.com/scl/fi/vss650bd06nfjfjs2chw5/pvaluetable.2017.700.tgz?rlkey=tgnqupam50kv57ckl7fbdbgtm + Reusing existing connection to www.dropbox.com:443. + HTTP request sent, awaiting response... 302 Found + Location: https://ucdc0812fd3f0d759ad1863f8deb.dl.dropboxusercontent.com/cd/0/inline/CgKT93TYemZCjT--ige0eEZpvkGsxchqZlmk5pGYcMW2d1oWMutdGgNm4xrQLdwCgCYTUYgrKgGxZodi88k1PpY65F5q8bFbL82b1xO8AyXgEuQccS_yGU4NU6SNxHPQ494/file# [following] + --2024-12-13 03:19:33-- https://ucdc0812fd3f0d759ad1863f8deb.dl.dropboxusercontent.com/cd/0/inline/CgKT93TYemZCjT--ige0eEZpvkGsxchqZlmk5pGYcMW2d1oWMutdGgNm4xrQLdwCgCYTUYgrKgGxZodi88k1PpY65F5q8bFbL82b1xO8AyXgEuQccS_yGU4NU6SNxHPQ494/file + Resolving ucdc0812fd3f0d759ad1863f8deb.dl.dropboxusercontent.com (ucdc0812fd3f0d759ad1863f8deb.dl.dropboxusercontent.com)... 162.125.6.15, 2620:100:601c:15::a27d:60f + Connecting to ucdc0812fd3f0d759ad1863f8deb.dl.dropboxusercontent.com (ucdc0812fd3f0d759ad1863f8deb.dl.dropboxusercontent.com)|162.125.6.15|:443... connected. + HTTP request sent, awaiting response... 302 Found + Location: /cd/0/inline2/CgKpK5UQm_6483X6-NYh7sC9Gwp1gRPAvs9-22s4_owWzC92xAKPn0by2RukudDuwqSN9LKsBJAeDlC_OUNFZG1peOoCGBhynPjHsC8cMgV_f4T-xxklkS1RpY0FbAGyQxYPBj23jT-hjK3e9X4uoWcyuA_rj9YXu5htQXE52472Mm5MA0B0C3pgZgyrPdwU9jbbf-WVSM5SvZnWWCY8ZOU4eFmVVhidGdRGkgmWN6NpGBJxs09LLDcs-cSX_zMLRiG6Pdj6fI-Qa_Zauxx_PCWtmRwxY3yKwClN4S6ZUXBfqNbVIgQ9Ztg7csOagUFQRnFVQE4EgUlUy8v1-nbb9_iURbSjzQXbA5Ul_mXzV4MfsA/file [following] + --2024-12-13 03:19:33-- https://ucdc0812fd3f0d759ad1863f8deb.dl.dropboxusercontent.com/cd/0/inline2/CgKpK5UQm_6483X6-NYh7sC9Gwp1gRPAvs9-22s4_owWzC92xAKPn0by2RukudDuwqSN9LKsBJAeDlC_OUNFZG1peOoCGBhynPjHsC8cMgV_f4T-xxklkS1RpY0FbAGyQxYPBj23jT-hjK3e9X4uoWcyuA_rj9YXu5htQXE52472Mm5MA0B0C3pgZgyrPdwU9jbbf-WVSM5SvZnWWCY8ZOU4eFmVVhidGdRGkgmWN6NpGBJxs09LLDcs-cSX_zMLRiG6Pdj6fI-Qa_Zauxx_PCWtmRwxY3yKwClN4S6ZUXBfqNbVIgQ9Ztg7csOagUFQRnFVQE4EgUlUy8v1-nbb9_iURbSjzQXbA5Ul_mXzV4MfsA/file + Reusing existing connection to ucdc0812fd3f0d759ad1863f8deb.dl.dropboxusercontent.com:443. + HTTP request sent, awaiting response... 200 OK + Length: 205243295 (196M) [application/x-gtar] + Saving to: '/opt/conda/conda-bld/3seq_1734059853486/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/share/3seq/pvaluetable.2017.700.tgz' + + pvaluetable.2017.70 0%[ ] 0 --.-KB/s pvaluetable.2017.70 4%[ ] 8.00M --.-KB/s pvaluetable.2017.70 4%[ ] 8.02M 5.50MB/s pvaluetable.2017.70 22%[===> ] 44.92M 27.1MB/s pvaluetable.2017.70 31%[=====> ] 60.77M 32.7MB/s pvaluetable.2017.70 41%[=======> ] 82.02M 39.8MB/s pvaluetable.2017.70 52%[=========> ] 102.64M 45.2MB/s pvaluetable.2017.70 63%[===========> ] 123.52M 49.8MB/s pvaluetable.2017.70 71%[=============> ] 139.77M 52.1MB/s pvaluetable.2017.70 86%[================> ] 169.27M 58.7MB/s pvaluetable.2017.70 100%[===================>] 195.73M 65.1MB/s in 3.0s + + 2024-12-13 03:19:37 (65.1 MB/s) - '/opt/conda/conda-bld/3seq_1734059853486/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/share/3seq/pvaluetable.2017.700.tgz' saved [205243295/205243295] + + + Resource usage statistics from building 3seq: + Process count: 10 + CPU time: Sys=0:00:00.9, User=0:00:08.8 + Memory: 159.3M + Disk usage: 20.4K + Time elapsed: 0:00:34.1 + + + Packaging 3seq + Packaging 3seq-1.8-h163da20_5 + number of files: 3 + Warning: rpath /opt/conda/conda-bld/3seq_1734059853486/_build_env/lib is outside prefix /opt/conda/conda-bld/3seq_1734059853486/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol (removing it) + patchelf: open: Text file busy + INFO: sysroot: '/opt/conda/conda-bld/3seq_1734059853486/_build_env/aarch64-conda-linux-gnu/sysroot/' files: '['usr/share/zoneinfo', 'usr/share/locale/zh_TW/LC_MESSAGES/libc.mo', 'usr/share/locale/zh_CN/LC_MESSAGES/libc.mo', 'usr/share/locale/vi/LC_MESSAGES/libc.mo']' + INFO (3seq,bin/3seq): Needed DSO lib/libstdc.so.6 found in conda-forge/linux-aarch64::libstdcxx==14.2.0=h3f4de04_1 + INFO (3seq,bin/3seq): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_18 + INFO (3seq,bin/3seq): Needed DSO lib/libgcc_s.so.1 found in conda-forge/linux-aarch64::libgcc==14.2.0=he277a41_1 + INFO (3seq,bin/3seq): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_18 + INFO (3seq,bin/3seq): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/ld-linux-aarch64.so.1 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_18 + Fixing permissions + Packaged license file/s. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2765, in build + newly_built_packages = bundlers[pkg_type]( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 1889, in bundle_conda + output["checksums"] = create_info_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 1417, in create_info_files + files_with_prefix = get_files_with_prefix(m, replacements, files, prefix) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 1016, in get_files_with_prefix + files_with_prefix = [ + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 1020, in + if open(os.path.join(prefix, f), "rb").read().find(b"\x00") != -1 + OSError: [Errno 26] Text file busy: '/opt/conda/conda-bld/3seq_1734059853486/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/3seq' +# Last 100 lines of the build log. diff --git a/recipes/3seq/meta.yaml b/recipes/3seq/meta.yaml index 00113808e3473..6f92dfb65cccc 100644 --- a/recipes/3seq/meta.yaml +++ b/recipes/3seq/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage("3seq", max_pin="x") }} diff --git a/recipes/abawaca/meta.yaml b/recipes/abawaca/meta.yaml index 22c0eb47290e3..9ff2edccc8336 100644 --- a/recipes/abawaca/meta.yaml +++ b/recipes/abawaca/meta.yaml @@ -11,7 +11,7 @@ source: - 0001-Use-CXX-and-flags.patch build: - number: 7 + number: 8 run_exports: - {{ pin_subpackage("abawaca", max_pin="x") }} @@ -37,4 +37,4 @@ extra: identifiers: - doi:10.1038/nature14486 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/abismal/meta.yaml b/recipes/abismal/meta.yaml index 0960ba5728525..bcec5fe4fcbbb 100644 --- a/recipes/abismal/meta.yaml +++ b/recipes/abismal/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: # abismal is currently not intended to be stable between minor versions (x.x). - {{ pin_subpackage('abismal', max_pin="x.x") }} diff --git a/recipes/abpoa/meta.yaml b/recipes/abpoa/meta.yaml index 069ecd8444e2e..10b15ae4aaba8 100644 --- a/recipes/abpoa/meta.yaml +++ b/recipes/abpoa/meta.yaml @@ -10,7 +10,7 @@ source: sha256: bb97de2dbdec014f2fb24beb0c85fa0b2073f717f3b68639e1edd89239729e6c build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name | lower, max_pin="x") }} diff --git a/recipes/abra2/build_failure.linux-64.yaml b/recipes/abra2/build_failure.linux-64.yaml index 0b7415e682a8b..18980ec23b251 100644 --- a/recipes/abra2/build_failure.linux-64.yaml +++ b/recipes/abra2/build_failure.linux-64.yaml @@ -1,80 +1,75 @@ -recipe_sha: 7d02a5f3ffd8dd4df36a0f29b598051278f04d8b0f511c225cc3ddf098885eea # The commit at which this recipe failed to build. +recipe_sha: 52ab7095cf3815703b163ecd676f6a534aa78617bf24a551652f0d8cf3a313ab # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- - Progress (2): 197/358 kB | 115/640 kB - Progress (2): 197/358 kB | 131/640 kB - Progress (2): 213/358 kB | 131/640 kB - Progress (2): 213/358 kB | 147/640 kB - Progress (2): 229/358 kB | 147/640 kB - Progress (2): 246/358 kB | 147/640 kB - Progress (2): 262/358 kB | 147/640 kB - Progress (2): 279/358 kB | 147/640 kB - Progress (2): 295/358 kB | 147/640 kB - Progress (2): 295/358 kB | 164/640 kB - Progress (2): 311/358 kB | 164/640 kB - Progress (2): 328/358 kB | 164/640 kB - Progress (2): 344/358 kB | 164/640 kB - Progress (2): 344/358 kB | 180/640 kB - Progress (2): 358 kB | 180/640 kB + Progress (3): 310/358 kB | 49/640 kB | 66/121 kB + Progress (3): 310/358 kB | 62/640 kB | 66/121 kB + Progress (3): 310/358 kB | 78/640 kB | 66/121 kB + Progress (3): 310/358 kB | 78/640 kB | 82/121 kB + Progress (3): 310/358 kB | 94/640 kB | 82/121 kB + Progress (3): 310/358 kB | 94/640 kB | 98/121 kB + Progress (3): 310/358 kB | 111/640 kB | 98/121 kB + Progress (3): 310/358 kB | 111/640 kB | 115/121 kB + Progress (3): 310/358 kB | 127/640 kB | 115/121 kB + Progress (3): 310/358 kB | 127/640 kB | 121 kB + Progress (3): 310/358 kB | 144/640 kB | 121 kB - Downloaded from central: https://repo.maven.apache.org/maven2/log4j/log4j/1.2.12/log4j-1.2.12.jar (358 kB at 2.4 MB/s) - Progress (1): 197/640 kB - Progress (1): 213/640 kB - Progress (1): 229/640 kB - Progress (1): 246/640 kB - Progress (1): 262/640 kB - Progress (1): 279/640 kB - Progress (1): 295/640 kB - Progress (1): 311/640 kB - Progress (1): 328/640 kB - Progress (1): 344/640 kB - Progress (1): 360/640 kB - Progress (1): 377/640 kB - Progress (1): 393/640 kB - Progress (1): 410/640 kB - Progress (1): 426/640 kB - Progress (1): 442/640 kB - Progress (1): 459/640 kB - Progress (1): 475/640 kB - Progress (1): 492/640 kB - Progress (1): 508/640 kB - Progress (1): 524/640 kB - Progress (1): 541/640 kB - Progress (1): 557/640 kB - Progress (1): 573/640 kB - Progress (1): 590/640 kB - Progress (1): 606/640 kB - Progress (1): 623/640 kB - Progress (1): 639/640 kB + Downloaded from central: https://repo.maven.apache.org/maven2/junit/junit/3.8.2/junit-3.8.2.jar (121 kB at 2.5 MB/s) + Progress (2): 310/358 kB | 160/640 kB + Progress (2): 310/358 kB | 176/640 kB + Progress (2): 327/358 kB | 176/640 kB + Progress (2): 327/358 kB | 193/640 kB + Progress (2): 343/358 kB | 193/640 kB + Progress (2): 358 kB | 193/640 kB + Progress (2): 358 kB | 209/640 kB + Progress (2): 358 kB | 226/640 kB + + Downloaded from central: https://repo.maven.apache.org/maven2/log4j/log4j/1.2.12/log4j-1.2.12.jar (358 kB at 7.0 MB/s) + Progress (1): 242/640 kB + Progress (1): 258/640 kB + Progress (1): 275/640 kB + Progress (1): 291/640 kB + Progress (1): 307/640 kB + Progress (1): 324/640 kB + Progress (1): 340/640 kB + Progress (1): 357/640 kB + Progress (1): 373/640 kB + Progress (1): 389/640 kB + Progress (1): 406/640 kB + Progress (1): 422/640 kB + Progress (1): 439/640 kB + Progress (1): 455/640 kB + Progress (1): 471/640 kB + Progress (1): 488/640 kB + Progress (1): 504/640 kB + Progress (1): 520/640 kB + Progress (1): 537/640 kB + Progress (1): 553/640 kB + Progress (1): 570/640 kB + Progress (1): 586/640 kB + Progress (1): 602/640 kB + Progress (1): 619/640 kB + Progress (1): 635/640 kB Progress (1): 640 kB - Downloaded from central: https://repo.maven.apache.org/maven2/com/google/collections/google-collections/1.0/google-collections-1.0.jar (640 kB at 2.5 MB/s) + Downloaded from central: https://repo.maven.apache.org/maven2/com/google/collections/google-collections/1.0/google-collections-1.0.jar (640 kB at 11 MB/s) [INFO] Changes detected - recompiling the module! [INFO] Compiling 62 source files to $SRC_DIR/target/classes [INFO] ------------------------------------------------------------- [ERROR] COMPILATION ERROR : [INFO] ------------------------------------------------------------- - [ERROR] Source option 6 is no longer supported. Use 7 or later. - [ERROR] Target option 6 is no longer supported. Use 7 or later. + [ERROR] Source option 6 is no longer supported. Use 8 or later. + [ERROR] Target option 6 is no longer supported. Use 8 or later. [INFO] 2 errors [INFO] ------------------------------------------------------------- [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ - [INFO] Total time: 4.686 s - [INFO] Finished at: 2023-05-29T09:12:47Z + [INFO] Total time: 3.617 s + [INFO] Finished at: 2024-12-13T10:49:42Z [INFO] ------------------------------------------------------------------------ - [WARNING] - [WARNING] Plugin validation issues were detected in 2 plugin(s) - [WARNING] - [WARNING] * org.apache.maven.plugins:maven-compiler-plugin:3.1 - [WARNING] * org.apache.maven.plugins:maven-resources-plugin:3.3.0 - [WARNING] - [WARNING] For more or less details, use 'maven.plugin.validation' property with one of the values (case insensitive): [BRIEF, DEFAULT, VERBOSE] - [WARNING] [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project abra2: Compilation failure: Compilation failure: - [ERROR] Source option 6 is no longer supported. Use 7 or later. - [0m[ERROR] Target option 6 is no longer supported. Use 7 or later. + [ERROR] Source option 6 is no longer supported. Use 8 or later. + [ERROR] Target option 6 is no longer supported. Use 8 or later. [ERROR] -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. @@ -82,23 +77,28 @@ log: |- [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException - make: *** [Makefile:9: java] Error 1 + [0mmake: *** [Makefile:9: java] Error 1 Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/abra2_1685351354756/work/conda_build.sh']' returned non-zero exit status 2. + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/abra2_1734086863283/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/abra2_1734086863283/work/conda_build.sh']' returned non-zero exit status 2. # Last 100 lines of the build log. diff --git a/recipes/abra2/build_failure.linux-aarch64.yaml b/recipes/abra2/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..35b8ebd98bc65 --- /dev/null +++ b/recipes/abra2/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 52ab7095cf3815703b163ecd676f6a534aa78617bf24a551652f0d8cf3a313ab # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Progress (3): 209/640 kB | 244/358 kB | 45 kB + Progress (3): 209/640 kB | 261/358 kB | 45 kB + Progress (3): 225/640 kB | 261/358 kB | 45 kB + Progress (3): 225/640 kB | 277/358 kB | 45 kB + Progress (3): 225/640 kB | 294/358 kB | 45 kB + Progress (3): 225/640 kB | 310/358 kB | 45 kB + Progress (3): 242/640 kB | 310/358 kB | 45 kB + Progress (3): 242/640 kB | 326/358 kB | 45 kB + Progress (3): 258/640 kB | 326/358 kB | 45 kB + + Downloaded from central: https://repo.maven.apache.org/maven2/commons-logging/commons-logging-api/1.1/commons-logging-api-1.1.jar (45 kB at 910 kB/s) + Progress (2): 258/640 kB | 343/358 kB + Progress (2): 258/640 kB | 358 kB + Progress (2): 275/640 kB | 358 kB + Progress (2): 291/640 kB | 358 kB + Progress (2): 307/640 kB | 358 kB + + Downloaded from central: https://repo.maven.apache.org/maven2/log4j/log4j/1.2.12/log4j-1.2.12.jar (358 kB at 6.9 MB/s) + Progress (1): 324/640 kB + Progress (1): 340/640 kB + Progress (1): 357/640 kB + Progress (2): 357/640 kB | 16/121 kB + Progress (2): 373/640 kB | 16/121 kB + Progress (2): 373/640 kB | 33/121 kB + Progress (2): 389/640 kB | 33/121 kB + Progress (2): 389/640 kB | 49/121 kB + Progress (2): 389/640 kB | 66/121 kB + Progress (2): 389/640 kB | 82/121 kB + Progress (2): 406/640 kB | 82/121 kB + Progress (2): 406/640 kB | 98/121 kB + Progress (2): 406/640 kB | 115/121 kB + Progress (2): 406/640 kB | 121 kB + Progress (2): 422/640 kB | 121 kB + + Downloaded from central: https://repo.maven.apache.org/maven2/junit/junit/3.8.2/junit-3.8.2.jar (121 kB at 2.2 MB/s) + Progress (1): 438/640 kB + Progress (1): 455/640 kB + Progress (1): 471/640 kB + Progress (1): 488/640 kB + Progress (1): 504/640 kB + Progress (1): 520/640 kB + Progress (1): 537/640 kB + Progress (1): 553/640 kB + Progress (1): 570/640 kB + Progress (1): 586/640 kB + Progress (1): 602/640 kB + Progress (1): 619/640 kB + Progress (1): 635/640 kB + Progress (1): 640 kB + + Downloaded from central: https://repo.maven.apache.org/maven2/com/google/collections/google-collections/1.0/google-collections-1.0.jar (640 kB at 11 MB/s) + [INFO] Changes detected - recompiling the module! + [INFO] Compiling 62 source files to $SRC_DIR/target/classes + [INFO] ------------------------------------------------------------- + [ERROR] COMPILATION ERROR : + [INFO] ------------------------------------------------------------- + [ERROR] Source option 6 is no longer supported. Use 8 or later. + [ERROR] Target option 6 is no longer supported. Use 8 or later. + [INFO] 2 errors + [INFO] ------------------------------------------------------------- + [INFO] ------------------------------------------------------------------------ + [INFO] BUILD FAILURE + [INFO] ------------------------------------------------------------------------ + [INFO] Total time: 2.951 s + [INFO] Finished at: 2024-12-12T15:18:22Z + [INFO] ------------------------------------------------------------------------ + [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project abra2: Compilation failure: Compilation failure: + [ERROR] Source option 6 is no longer supported. Use 8 or later. + [ERROR] Target option 6 is no longer supported. Use 8 or later. + [0m[ERROR] -> [Help 1] + [ERROR] + [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. + [ERROR] Re-run Maven using the -X switch to enable full debug logging. + [ERROR] + [ERROR] For more information about the errors and possible solutions, please read the following articles: + [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException + make: *** [Makefile:9: java] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/abra2_1734016603311/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/abra2_1734016603311/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/abra2/meta.yaml b/recipes/abra2/meta.yaml index 342af9bad048e..0e5f5392cd790 100644 --- a/recipes/abra2/meta.yaml +++ b/recipes/abra2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: edb35fb6ff318239353a573d1abad148073b8ac0bb2cd44a18e561abe08aef32 build: - number: 3 + number: 4 skip: true # [osx] run_exports: - pin_subpackage(name, max_pin="x") diff --git a/recipes/abricate/meta.yaml b/recipes/abricate/meta.yaml index f2370a576149a..84cd844970d70 100644 --- a/recipes/abricate/meta.yaml +++ b/recipes/abricate/meta.yaml @@ -8,7 +8,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 noarch: generic run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/abundancebin/meta.yaml b/recipes/abundancebin/meta.yaml index 1fc298ebc42e5..ee22c310302aa 100644 --- a/recipes/abundancebin/meta.yaml +++ b/recipes/abundancebin/meta.yaml @@ -14,7 +14,7 @@ source: - 0001-Use-CXX-and-flags.patch build: - number: 7 + number: 8 run_exports: - {{ pin_subpackage("abundancebin", max_pin="x.x.x") }} skip: True # [osx] diff --git a/recipes/abyss/meta.yaml b/recipes/abyss/meta.yaml index d1fc364dca7f9..a38fce82295f8 100644 --- a/recipes/abyss/meta.yaml +++ b/recipes/abyss/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/ac/meta.yaml b/recipes/ac/meta.yaml index 17b4fbc7a327c..481b037c9eb76 100644 --- a/recipes/ac/meta.yaml +++ b/recipes/ac/meta.yaml @@ -7,7 +7,7 @@ package: build: # Passes some invalid flags for clang skip: True # [osx] - number: 5 + number: 6 run_exports: - {{ pin_subpackage("ac", max_pin="x.x") }} diff --git a/recipes/acdc/build_failure.linux-64.yaml b/recipes/acdc/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..c237a95c6bf22 --- /dev/null +++ b/recipes/acdc/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 34c22041caa4c8c48016dd2e0b755ee806d629da17f602fc8ca29ea508b56b9b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + policies are deprecated and that a policy should be set to OLD only under + specific short-term circumstances. Projects should be ported to the NEW + behavior and not rely on setting a policy to OLD. + + + CMake Deprecation Warning at libyamlcpp/CMakeLists.txt:13 (cmake_policy): + The OLD behavior for policy CMP0015 will be removed from a future version + of CMake. + + The cmake-policies(7) manual explains that the OLD behaviors of all + policies are deprecated and that a policy should be set to OLD only under + specific short-term circumstances. Projects should be ported to the NEW + behavior and not rely on setting a policy to OLD. + + + -- Performing Test FLAG_WEXTRA + -- Performing Test FLAG_WEXTRA - Success + -- Found OpenMP_C: -fopenmp (found version "4.5") + -- Found OpenMP_CXX: -fopenmp (found version "4.5") + -- Found OpenMP: TRUE (found version "4.5") + -- $SRC_DIR + -- CMAKE_INSTALL_PREFIX: $PREFIX + -- Configuring done (1.0s) + -- Generating done (0.0s) + -- Build files have been written to: $SRC_DIR/build + [ 1%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o + [ 2%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o + [ 4%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o + [ 5%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o + [ 7%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o + [ 8%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o + [ 10%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o + [ 11%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o + [ 13%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o + [ 14%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o + [ 16%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o + [ 17%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o + [ 19%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o + [ 20%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o + [ 22%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o + [ 23%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o + [ 25%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o + [ 26%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o + [ 28%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o + [ 29%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o + [ 31%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o + [ 32%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o + [ 34%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o + [ 35%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o + [ 37%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o + [ 38%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o + [ 40%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o + [ 41%] Building CXX object libyamlcpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o + [ 43%] Linking CXX static library libyaml-cpp.a + [ 43%] Built target yaml-cpp + [ 44%] Building C object libdip/CMakeFiles/dip.dir/dip.c.o + [ 46%] Building CXX object libdip/CMakeFiles/dip.dir/DipStatistic.cpp.o + [ 47%] Linking CXX static library libdip.a + [ 47%] Built target dip + [ 49%] Building CXX object libtsne/CMakeFiles/tsne.dir/sptree.cpp.o + [ 50%] Building CXX object libtsne/CMakeFiles/tsne.dir/tsne.cpp.o + [ 52%] Linking CXX static library libtsne.a + [ 52%] Built target tsne + [ 53%] Building CXX object libfastcluster/CMakeFiles/fastcluster.dir/fastclusterAcdc.cpp.o + [ 55%] Linking CXX static library libfastcluster.a + [ 55%] Built target fastcluster + [ 56%] Building CXX object src/CMakeFiles/mainprog.dir/Opts.cpp.o + [ 58%] Building CXX object src/CMakeFiles/mainprog.dir/SequenceUtil.cpp.o + [ 59%] Building CXX object src/CMakeFiles/mainprog.dir/MatrixUtil.cpp.o + [ 61%] Building CXX object src/CMakeFiles/mainprog.dir/IOUtil.cpp.o + /opt/conda/conda-bld/acdc_1734252074859/work/src/IOUtil.cpp: In static member function 'static void IOUtil::copyDir(const boost::filesystem::path&, const boost::filesystem::path&, bool)': + /opt/conda/conda-bld/acdc_1734252074859/work/src/IOUtil.cpp:29:78: error: 'fs::copy_option' has not been declared + 29 | fs::copy_file(current, destination / current.filename(), fs::copy_option::overwrite_if_exists); + | ^~~~~~~~~~~ + make[2]: *** [src/CMakeFiles/mainprog.dir/build.make:121: src/CMakeFiles/mainprog.dir/IOUtil.cpp.o] Error 1 + make[1]: *** [CMakeFiles/Makefile2:444: src/CMakeFiles/mainprog.dir/all] Error 2 + make: *** [Makefile:136: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/acdc_1734252074859/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/acdc_1734252074859/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/acdc/meta.yaml b/recipes/acdc/meta.yaml index 474867b567bb1..2bafdf75f8c33 100644 --- a/recipes/acdc/meta.yaml +++ b/recipes/acdc/meta.yaml @@ -10,7 +10,7 @@ source: sha256: dc44d77abcbccd0fac4e99754f1f4987fad40930c3a21013cfc36a6df089a425 build: - number: 0 + number: 1 skip: true # [osx] requirements: diff --git a/recipes/acms/meta.yaml b/recipes/acms/meta.yaml index 3c3dfbe30c7fd..fe7a22dc99e13 100644 --- a/recipes/acms/meta.yaml +++ b/recipes/acms/meta.yaml @@ -15,7 +15,7 @@ source: url: https://github.com/jlab/fold-grammars/archive/refs/tags/{{ fold_grammars_version }}.tar.gz build: - number: 1 + number: 2 skip: True # [osx] run_exports: - {{ pin_subpackage('acms', max_pin="x") }} diff --git a/recipes/adapterremoval/meta.yaml b/recipes/adapterremoval/meta.yaml index 7f369ac53924a..4685c5a8367c5 100644 --- a/recipes/adapterremoval/meta.yaml +++ b/recipes/adapterremoval/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("adapterremoval", max_pin="x") }} diff --git a/recipes/addrg/meta.yaml b/recipes/addrg/meta.yaml index 6b55770d98737..dcec868ec1110 100644 --- a/recipes/addrg/meta.yaml +++ b/recipes/addrg/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 12 + number: 13 run_exports: - {{ pin_subpackage("addrg", max_pin="x.x") }} diff --git a/recipes/admixtools/build_failure.osx-64.yaml b/recipes/admixtools/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..42e426f1b8690 --- /dev/null +++ b/recipes/admixtools/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 07fb317fc7518a6604b12e7055f53f51460ac1442c2a81052edb9405f4350820 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - libzlib 1.3.1 hd23fc13_2 + - ca-certificates 2024.12.14 h8857fd0_0 + - zstd 1.5.6 h915ae27_0 + - libllvm18 18.1.8 h9ce406d_2 + - libcxx 19.1.5 hf95d169_0 + - sigtool 0.1.3 h88f4db0_0 + host: + - llvm-openmp 19.1.5 ha54dae1_0 + - libgfortran5 13.2.0 h2873a65_3 + - libgfortran 5.0.0 13_2_0_h97931a8_3 + - libopenblas 0.3.28 openmp_hbf64a52_1 + - libblas 3.9.0 25_osx64_openblas + - openblas 0.3.28 openmp_h30af337_1 + - libcblas 3.9.0 25_osx64_openblas + - gsl 2.7 h93259b0_0 + run: + - gsl >=2.7,<2.8.0a0 + - openblas + test: + commands: + - qp3Pop 2>&1 | grep Usage + about: + home: https://github.com/DReichLab/AdmixTools + license: Free for Academic Use + summary: ADMIXTOOLS (Patterson et al. 2012) is a software package that supports + formal tests of whether admixture occurred, and makes it possible to infer admixture + proportions and dates. + extra: + copy_test_source_files: true + final: true + identifiers: + - biotools:AdmixTools + - doi:10.1534/genetics.112.145037 + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/admixtools_1734401318458/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/admixtools_1734401318458/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/admixtools_1734401318458/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/admixtools_1734401318458/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/admixtools-7.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/admixtools-7.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + rm -f *.o + rm -f *junk* + rm -f core + make -C nicksrc clean + make[1]: Entering directory '$SRC_DIR/src/nicksrc' + rm -f *.o + rm -f libnick.a + make[1]: Leaving directory '$SRC_DIR/src/nicksrc' + rm -f qp3Pop qpDstat qpF4ratio qpAdm qpWave qp4diff qpdslow dowtjack expfit.sh qpBound qpGraph qpreroot qpff3base qpDpart qpfstats qpfmv qpmix + rm -f rolloff rolloffp convertf mergeit simpjack2 grabpars kimf gcount + rm -rf $SRC_DIR/src/admixtables + rm -f tables + rm -f ../bin/* + make -C nicksrc + make[1]: Entering directory '$SRC_DIR/src/nicksrc' + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/admixtools-7.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c -g -p -Wimplicit -I./ -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o strsubs.o strsubs.c + make[1]: Leaving directory '$SRC_DIR/src/nicksrc' +# Last 100 lines of the build log. diff --git a/recipes/admixtools/meta.yaml b/recipes/admixtools/meta.yaml index 34cb5ebf46837..f8f51f1936f34 100644 --- a/recipes/admixtools/meta.yaml +++ b/recipes/admixtools/meta.yaml @@ -10,7 +10,7 @@ source: - makefile-compiler.patch build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/aegean/meta.yaml b/recipes/aegean/meta.yaml index d79f901b835d4..802f42ddfbbb4 100644 --- a/recipes/aegean/meta.yaml +++ b/recipes/aegean/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 skip: True # [osx] requirements: diff --git a/recipes/age-metasv/meta.yaml b/recipes/age-metasv/meta.yaml index 212bb76c1a0d5..7802e706878b6 100644 --- a/recipes/age-metasv/meta.yaml +++ b/recipes/age-metasv/meta.yaml @@ -10,7 +10,7 @@ source: build: skip: True # [osx] - number: 8 + number: 9 run_exports: - {{ pin_subpackage("age-metasv", max_pin="x.x.x") }} diff --git a/recipes/akt/build_failure.osx-64.yaml b/recipes/akt/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..9371789cf58b7 --- /dev/null +++ b/recipes/akt/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: fb3d75f3d589d4629034778f293c91d970cfa6fad627aac925f8f62a43dd937b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + description: Ancestry and Kinship Tools (AKT) provides a handful of useful statistical + genetics routines using the htslib API for input/output. This means it can seamlessly + read BCF/VCF files and play nicely with bcftools. + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/akt_1734461875937/work/conda_build.sh']' returned non-zero exit status 2. + home: https://github.com/Illumina/akt + license: GPL3 + license_file: LICENSE + summary: Ancestry and Kinship Tools (AKT) + extra: + additional-platforms: + - linux-aarch64 + copy_test_source_files: true + final: true + identifiers: + - doi:10.1093/bioinformatics/btw576 + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/akt_1734461875937/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/akt_1734461875937/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/akt_1734461875937/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/akt_1734461875937/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + echo '#define AKT_VERSION "0.3.3"' > version.hh + echo '#define BCFTOOLS_VERSION "1.6"' >> version.hh + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -O2 -fopenmp -mpopcnt -Ihtslib-1.6 -I./ -c -o utils.o utils.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -O2 -fopenmp -mpopcnt -Ihtslib-1.6 -I./ -c -o HaplotypeBuffer.o HaplotypeBuffer.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -O2 -fopenmp -mpopcnt -Ihtslib-1.6 -I./ -c -o pedphase.o pedphase.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -O2 -fopenmp -mpopcnt -Ihtslib-1.6 -I./ -c -o family.o family.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -O2 -fopenmp -mpopcnt -Ihtslib-1.6 -I./ -c -o reader.o reader.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -O2 -fopenmp -mpopcnt -Ihtslib-1.6 -I./ -c -o vcfpca.o vcfpca.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -O2 -fopenmp -mpopcnt -Ihtslib-1.6 -I./ -c -o relatives.o relatives.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -O2 -fopenmp -mpopcnt -Ihtslib-1.6 -I./ -c -o kin.o kin.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -O2 -fopenmp -mpopcnt -Ihtslib-1.6 -I./ -c -o pedigree.o pedigree.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -O2 -fopenmp -mpopcnt -Ihtslib-1.6 -I./ -c -o unrelated.o unrelated.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -O2 -fopenmp -mpopcnt -Ihtslib-1.6 -I./ -c -o cluster.o cluster.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -O2 -fopenmp -mpopcnt -Ihtslib-1.6 -I./ -c -o Genotype.o Genotype.cpp + cd htslib-1.6 && make lib-static + make[1]: Entering directory '$SRC_DIR/htslib-1.6' + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -O2 -I. -c -o kfunc.o kfunc.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -O2 -I. -c -o knetfile.o knetfile.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -O2 -I. -c -o kstring.o kstring.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -O2 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -O2 -I. -c -o bgzf.o bgzf.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -O2 -I. -c -o errmod.o errmod.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -O2 -I. -c -o faidx.o faidx.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/akt-0.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -O2 -I. -c -o hfile.o hfile.c + make[1]: Leaving directory '$SRC_DIR/htslib-1.6' +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/akt/meta.yaml b/recipes/akt/meta.yaml index fe1cfb1e46ba5..c76f00b9265e4 100644 --- a/recipes/akt/meta.yaml +++ b/recipes/akt/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage("akt", max_pin="x.x.x") }} diff --git a/recipes/alcor/meta.yaml b/recipes/alcor/meta.yaml index 5a5432b3db1a5..fc78eb070ecff 100644 --- a/recipes/alcor/meta.yaml +++ b/recipes/alcor/meta.yaml @@ -10,7 +10,7 @@ package: build: # Passes some invalid flags for clang skip: True # [osx] - number: 4 + number: 5 run_exports: - {{ pin_subpackage("alcor", max_pin="x.x") }} diff --git a/recipes/alder/meta.yaml b/recipes/alder/meta.yaml index 158c7f105e945..877346442cfec 100644 --- a/recipes/alder/meta.yaml +++ b/recipes/alder/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.03" build: - number: 6 + number: 7 source: url: http://cb.csail.mit.edu/cb/alder/alder_v1.03.tar.gz diff --git a/recipes/ale-core/meta.yaml b/recipes/ale-core/meta.yaml index 7ce9aa4e5e075..8be1697c58d29 100644 --- a/recipes/ale-core/meta.yaml +++ b/recipes/ale-core/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("ale-core", max_pin=None) }} diff --git a/recipes/aletsch/meta.yaml b/recipes/aletsch/meta.yaml index 036c9fa58682e..32240762a06a7 100644 --- a/recipes/aletsch/meta.yaml +++ b/recipes/aletsch/meta.yaml @@ -10,7 +10,7 @@ source: sha256: "74e1b7e2ff2cb065d02f1e0d45d7e87ae332ccfcef86b6a32af88b2a7005c9f7" build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('aletsch', max_pin="x") }} diff --git a/recipes/alfred/build_failure.osx-64.yaml b/recipes/alfred/build_failure.osx-64.yaml deleted file mode 100644 index 6087a3ba4fc99..0000000000000 --- a/recipes/alfred/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: d46af4deecffe4a1440fa36938c99ce9ef54cdde43c41212907669264297e79e # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - /opt/mambaforge/envs/bioconda/conda-bld/alfred_1717637017535/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/htslib/sam.h:1160:41: note: expanded from macro 'bam_index_build' - #define bam_index_build(fn, min_shift) (sam_index_build((fn), (min_shift))) - ^~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ - src/split.h:454:12: note: in instantiation of function template specialization 'bamstats::phaseBamRun' requested here - return phaseBamRun(c); - ^ - src/split.h:319:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] - bam_index_build(c.h2bam.string().c_str(), 0); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/alfred_1717637017535/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/htslib/sam.h:1160:41: note: expanded from macro 'bam_index_build' - #define bam_index_build(fn, min_shift) (sam_index_build((fn), (min_shift))) - ^~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ - In file included from src/alfred.cpp:28: - In file included from src/bamstats.h:20: - src/json.h:31:24: warning: equality comparison result unused [-Wunused-comparison] - meta["regionFile"] == c.regionFile.string(); - ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ - src/bamstats.h:581:23: note: in instantiation of function template specialization 'bamstats::qcJsonOut>' requested here - if (c.hasJsonOut) qcJsonOut(c, hdr, rgMap, be, rf); - ^ - src/qc.h:269:10: note: in instantiation of function template specialization 'bamstats::bamStatsRun' requested here - return bamStatsRun(c); - ^ - src/json.h:31:24: note: use '=' to turn this equality comparison into an assignment - meta["regionFile"] == c.regionFile.string(); - ^~ - = - 9 warnings and 1 error generated. - make: *** [Makefile:54: src/alfred] Error 1 - Extracting download - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/alfred_1717637017535/work - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/alfred_1717637017535/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/alfred_1717637017535/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/alfred_1717637017535/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/alfred-0.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/alfred_1717637017535/work/conda_build.sh']' returned non-zero exit status 2. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/alfred-0.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/alfred-0.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/alfred-0.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - if [ -r src/htslib/Makefile ]; then cd src/htslib && autoreconf -i && ./configure --disable-s3 --disable-gcs --disable-libcurl --disable-plugins && make && make lib-static && cd ../../ && touch .htslib; fi - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/alfred-0.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D__STDC_FORMAT_MACROS -std=c11 -isystem $SRC_DIR/src/jlib/ -isystem $SRC_DIR/src/htslib/ -pedantic -W -Wall -O3 -fno-tree-vectorize -DNDEBUG src/alfred.cpp src/edlib.cpp -o src/alfred -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$SRC_DIR/src/htslib/ -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -lhts -lz -llzma -lbz2 -Wl,-rpath,$SRC_DIR/src/htslib/ -# Last 100 lines of the build log. diff --git a/recipes/alfred/meta.yaml b/recipes/alfred/meta.yaml index d7ea18f44fdf3..57db873c4f669 100644 --- a/recipes/alfred/meta.yaml +++ b/recipes/alfred/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('alfred', max_pin="x.x") }} diff --git a/recipes/align_it/meta.yaml b/recipes/align_it/meta.yaml index fc664d95eed18..108e8242ec7e8 100644 --- a/recipes/align_it/meta.yaml +++ b/recipes/align_it/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 skip: True # [osx] requirements: diff --git a/recipes/alignoth/meta.yaml b/recipes/alignoth/meta.yaml index cc6001b85a7db..c1c13797b0ce5 100644 --- a/recipes/alignoth/meta.yaml +++ b/recipes/alignoth/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 # TODO fails to build on osx with # Undefined symbols for architecture x86_64: "_SSLCopyALPNProtocols", referenced from: _sectransp_connect_step2 in libcurl_sys-1f07db570920ba9f.rlib(sectransp.o) skip: true #[osx] diff --git a/recipes/allegro/meta.yaml b/recipes/allegro/meta.yaml index 8a98f890cce1a..38057b919fb09 100644 --- a/recipes/allegro/meta.yaml +++ b/recipes/allegro/meta.yaml @@ -18,7 +18,7 @@ source: build: skip: True # [osx] - number: 8 + number: 9 run_exports: - {{ pin_subpackage("allegro", max_pin="x.x.x") }} diff --git a/recipes/altair-mf/meta.yaml b/recipes/altair-mf/meta.yaml index 0deed9c024b96..9cee402409116 100644 --- a/recipes/altair-mf/meta.yaml +++ b/recipes/altair-mf/meta.yaml @@ -10,7 +10,7 @@ package: build: # Passes some invalid flags for clang skip: True # [osx] - number: 3 + number: 4 run_exports: - {{ pin_subpackage("altair-mf", max_pin="x.x.x") }} diff --git a/recipes/amplici/meta.yaml b/recipes/amplici/meta.yaml index 5949ed9ee80c6..09d8b97feb454 100644 --- a/recipes/amplici/meta.yaml +++ b/recipes/amplici/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 273362b5449ec29ff411d4c1aa5f89b1ec1eb361c8a9b69a4d89f4409fbdb70e build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("amplici", max_pin="x") }} diff --git a/recipes/amplisim/meta.yaml b/recipes/amplisim/meta.yaml index 567f3e3f1e413..4a875fbef41b6 100644 --- a/recipes/amplisim/meta.yaml +++ b/recipes/amplisim/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 skip: True # [osx] run_exports: - {{ pin_subpackage('amplisim', max_pin="x") }} diff --git a/recipes/ancestry_hmm-s/meta.yaml b/recipes/ancestry_hmm-s/meta.yaml index 27e8fb91c3ef8..1b8352f59e173 100644 --- a/recipes/ancestry_hmm-s/meta.yaml +++ b/recipes/ancestry_hmm-s/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 3bbee77945f7c90b6aeddb27ca388411d91bc61c4b770dd1750492beeee9583f build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage(name, max_pin="x.x.x") }} diff --git a/recipes/ancestry_hmm/meta.yaml b/recipes/ancestry_hmm/meta.yaml index c1dc3d738c45c..daeb198782a6a 100644 --- a/recipes/ancestry_hmm/meta.yaml +++ b/recipes/ancestry_hmm/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{sha256}} build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage("ancestry_hmm", max_pin="x.x.x") }} diff --git a/recipes/anchorwave/meta.yaml b/recipes/anchorwave/meta.yaml index 7e9ee0a0d0817..6a2f6e7a22d6d 100644 --- a/recipes/anchorwave/meta.yaml +++ b/recipes/anchorwave/meta.yaml @@ -12,7 +12,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 script_env: - TARGET_PLATFORM=macOS # [osx] - TARGET_PLATFORM=Linux # [linux] diff --git a/recipes/andi/meta.yaml b/recipes/andi/meta.yaml index a2ce906cfcea7..5b9eadfdad90f 100644 --- a/recipes/andi/meta.yaml +++ b/recipes/andi/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage("andi", max_pin="x.x") }} diff --git a/recipes/angsd/meta.yaml b/recipes/angsd/meta.yaml index ada38cb647493..7838046a90be9 100644 --- a/recipes/angsd/meta.yaml +++ b/recipes/angsd/meta.yaml @@ -12,7 +12,7 @@ source: build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage("angsd", max_pin="x.x") }} skip: True # [osx] diff --git a/recipes/anise_basil/meta.yaml b/recipes/anise_basil/meta.yaml index 3aa97ab6fb860..e9006f85c7c38 100644 --- a/recipes/anise_basil/meta.yaml +++ b/recipes/anise_basil/meta.yaml @@ -18,7 +18,7 @@ source: build: skip: True # [py27] - number: 8 + number: 9 run_exports: - {{ pin_subpackage("anise_basil", max_pin="x.x.x") }} diff --git a/recipes/annembed/meta.yaml b/recipes/annembed/meta.yaml index d6a1f2f98852c..0ee6118674fb5 100644 --- a/recipes/annembed/meta.yaml +++ b/recipes/annembed/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('annembed', max_pin="x.x") }} skip: True # [osx] diff --git a/recipes/annonars/build_failure.linux-64.yaml b/recipes/annonars/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..380e72b7b9817 --- /dev/null +++ b/recipes/annonars/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: dd005183eef6d5b7e62d6d8abd08a13f7a13f58f2b2385aea0ac45c40bebaac1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + Running rustc --crate-name env_filter --edition=2021 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/env_filter-0.1.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no '--warn=clippy::zero_sized_map_values' '--warn=clippy::wildcard_imports' '--warn=clippy::verbose_file_reads' --warn=unused_qualifications --warn=unused_macro_rules --warn=unused_lifetimes --warn=unsafe_op_in_unsafe_fn --warn=unreachable_pub '--warn=clippy::trait_duplication_in_bounds' '--warn=clippy::todo' '--warn=clippy::string_to_string' '--warn=clippy::string_lit_as_bytes' '--warn=clippy::string_add_assign' '--warn=clippy::string_add' '--warn=clippy::str_to_string' '--warn=clippy::single_match_else' '--warn=clippy::semicolon_if_nothing_returned' '--warn=clippy::self_named_module_files' '--warn=clippy::same_functions_in_if_condition' --warn=rust_2018_idioms '--warn=clippy::rest_pat_in_fully_bound_structs' '--warn=clippy::ref_option_ref' '--warn=clippy::redundant_feature_names' '--warn=clippy::rc_mutex' '--warn=clippy::ptr_as_ptr' '--warn=clippy::path_buf_push_overwrite' '--warn=clippy::negative_feature_names' '--warn=clippy::needless_for_each' '--warn=clippy::needless_continue' '--warn=clippy::mutex_integer' '--warn=clippy::mem_forget' '--warn=clippy::match_wildcard_for_single_variants' '--warn=clippy::macro_use_imports' '--warn=clippy::lossy_float_literal' '--warn=clippy::linkedlist' '--allow=clippy::let_and_return' '--warn=clippy::large_types_passed_by_value' '--warn=clippy::large_stack_arrays' '--warn=clippy::large_digit_groups' '--warn=clippy::invalid_upcast_comparisons' '--warn=clippy::infinite_loop' '--warn=clippy::inefficient_to_string' '--warn=clippy::inconsistent_struct_constructor' '--warn=clippy::imprecise_flops' '--warn=clippy::implicit_clone' '--allow=clippy::if_same_then_else' '--warn=clippy::from_iter_instead_of_collect' '--warn=clippy::fn_params_excessive_bools' '--warn=clippy::float_cmp_const' '--warn=clippy::flat_map_option' '--warn=clippy::filter_map_next' '--warn=clippy::fallible_impl_from' '--warn=clippy::explicit_into_iter_loop' '--warn=clippy::explicit_deref_methods' '--warn=clippy::expl_impl_clone_on_copy' '--warn=clippy::enum_glob_use' '--warn=clippy::empty_enum' '--warn=clippy::doc_markdown' '--warn=clippy::debug_assert_with_mut_call' '--warn=clippy::dbg_macro' '--warn=clippy::create_dir' '--allow=clippy::collapsible_else_if' '--warn=clippy::checked_conversions' '--allow=clippy::branches_sharing_code' '--allow=clippy::bool_assert_comparison' --cfg 'feature="regex"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "regex"))' -C metadata=41a6f91a551ca137 -C extra-filename=-41a6f91a551ca137 --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --extern log=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/liblog-054a084181905fb9.rmeta --extern regex=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libregex-8c520ba8846f7e23.rmeta --cap-lints allow + Running rustc --crate-name prost --edition=2021 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/prost-0.13.4/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="derive"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "derive", "no-recursion-limit", "prost-derive", "std"))' -C metadata=15b98fa9c74e6f8c -C extra-filename=-15b98fa9c74e6f8c --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --extern bytes=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libbytes-873411b0e6be0e8c.rmeta --extern prost_derive=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libprost_derive-098d1b34d18be86c.so --cap-lints allow + Compiling tracing-log v0.2.0 + Running rustc --crate-name tracing_log --edition=2018 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/tracing-log-0.2.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="log-tracer"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("ahash", "default", "interest-cache", "log-tracer", "lru", "std"))' -C metadata=42b9cd47db02dda6 -C extra-filename=-42b9cd47db02dda6 --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --extern log=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/liblog-054a084181905fb9.rmeta --extern once_cell=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libonce_cell-121a82602af2947b.rmeta --extern tracing_core=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libtracing_core-120b59859caaa323.rmeta --cap-lints allow + Compiling vec_map v0.8.2 + Running rustc --crate-name vec_map --edition=2015 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/vec_map-0.8.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="eders"' --cfg 'feature="serde"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("eders", "serde"))' -C metadata=6820348c35fe77b2 -C extra-filename=-6820348c35fe77b2 --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --extern serde=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libserde-fc59797db66b78e9.rmeta --cap-lints allow + Running rustc --crate-name multimap --edition=2015 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/multimap-0.10.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="serde"' --cfg 'feature="serde_impl"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "serde", "serde_impl"))' -C metadata=428c9b2a0ea4998c -C extra-filename=-428c9b2a0ea4998c --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --extern serde=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libserde-fc59797db66b78e9.rmeta --cap-lints allow + Compiling ordered-float v4.5.0 + Running rustc --crate-name ordered_float --edition=2021 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/ordered-float-4.5.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("arbitrary", "borsh", "bytemuck", "default", "derive-visitor", "num-cmp", "proptest", "rand", "randtest", "rkyv", "rkyv_16", "rkyv_32", "rkyv_64", "rkyv_ck", "schemars", "serde", "speedy", "std"))' -C metadata=575dab606737764a -C extra-filename=-575dab606737764a --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --extern num_traits=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libnum_traits-aecc12c36341049b.rmeta --cap-lints allow + Compiling itertools-num v0.1.3 + Running rustc --crate-name itertools_num --edition=2015 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/itertools-num-0.1.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=1f8b4515fa815d82 -C extra-filename=-1f8b4515fa815d82 --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --extern num_traits=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libnum_traits-aecc12c36341049b.rmeta --cap-lints allow + Compiling thread_local v1.1.8 + Running rustc --crate-name thread_local --edition=2021 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/thread_local-1.1.8/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("nightly"))' -C metadata=ad9589d461652178 -C extra-filename=-ad9589d461652178 --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --extern cfg_if=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libcfg_if-683714872c84c8c9.rmeta --extern once_cell=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libonce_cell-121a82602af2947b.rmeta --cap-lints allow + Compiling fxhash v0.2.1 + Running rustc --crate-name fxhash --edition=2015 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/fxhash-0.2.1/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=9cb90fd7e09b01a5 -C extra-filename=-9cb90fd7e09b01a5 --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --extern byteorder=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libbyteorder-b4135b9eba9ebb4c.rmeta --cap-lints allow + Compiling custom_derive v0.1.7 + Running rustc --crate-name custom_derive --edition=2015 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/custom_derive-0.1.7/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "std"))' -C metadata=4d2d6eed4a82340f -C extra-filename=-4d2d6eed4a82340f --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --cap-lints allow + Compiling triple_accel v0.4.0 + Running rustc --crate-name triple_accel --edition=2018 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/triple_accel-0.4.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="jewel-16bit"' --cfg 'feature="jewel-32bit"' --cfg 'feature="jewel-8bit"' --cfg 'feature="jewel-avx"' --cfg 'feature="jewel-sse"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("debug", "default", "jewel-16bit", "jewel-32bit", "jewel-8bit", "jewel-avx", "jewel-sse"))' -C metadata=3765e75a5345b6e9 -C extra-filename=-3765e75a5345b6e9 --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --cap-lints allow + Compiling bytecount v0.6.8 + Running rustc --crate-name bytecount --edition=2018 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/bytecount-0.6.8/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("generic-simd", "html_report", "runtime-dispatch-simd"))' -C metadata=d69d77d47b69b25a -C extra-filename=-d69d77d47b69b25a --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --cap-lints allow + Compiling number_prefix v0.4.0 + Running rustc --crate-name number_prefix --edition=2015 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/number_prefix-0.4.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "std"))' -C metadata=3538600420e6fe66 -C extra-filename=-3538600420e6fe66 --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --cap-lints allow + Compiling humantime v2.1.0 + Running rustc --crate-name humantime --edition=2018 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/humantime-2.1.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=d7d35d4942a3f070 -C extra-filename=-d7d35d4942a3f070 --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --cap-lints allow + Compiling editdistancek v1.0.2 + Running rustc --crate-name editdistancek --edition=2018 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/editdistancek-1.0.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=fbcabf80324f8ce3 -C extra-filename=-fbcabf80324f8ce3 --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --cap-lints allow + Compiling unicode-width v0.2.0 + Running rustc --crate-name unicode_width --edition=2021 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/unicode-width-0.2.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="cjk"' --cfg 'feature="default"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("cjk", "compiler_builtins", "core", "default", "no_std", "rustc-dep-of-std", "std"))' -C metadata=afb744becaf5cbee -C extra-filename=-afb744becaf5cbee --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --cap-lints allow + Compiling env_logger v0.11.5 + Running rustc --crate-name env_logger --edition=2021 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/env_logger-0.11.5/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no '--warn=clippy::zero_sized_map_values' '--warn=clippy::wildcard_imports' '--warn=clippy::verbose_file_reads' --warn=unused_qualifications --warn=unused_macro_rules --warn=unused_lifetimes --warn=unsafe_op_in_unsafe_fn --warn=unreachable_pub '--warn=clippy::trait_duplication_in_bounds' '--warn=clippy::todo' '--warn=clippy::string_to_string' '--warn=clippy::string_lit_as_bytes' '--warn=clippy::string_add_assign' '--warn=clippy::string_add' '--warn=clippy::str_to_string' '--warn=clippy::single_match_else' '--warn=clippy::semicolon_if_nothing_returned' '--warn=clippy::self_named_module_files' '--warn=clippy::same_functions_in_if_condition' --warn=rust_2018_idioms '--warn=clippy::rest_pat_in_fully_bound_structs' '--warn=clippy::ref_option_ref' '--warn=clippy::redundant_feature_names' '--warn=clippy::rc_mutex' '--warn=clippy::ptr_as_ptr' '--warn=clippy::path_buf_push_overwrite' '--warn=clippy::negative_feature_names' '--warn=clippy::needless_for_each' '--warn=clippy::needless_continue' '--warn=clippy::mutex_integer' '--warn=clippy::mem_forget' '--warn=clippy::match_wildcard_for_single_variants' '--warn=clippy::macro_use_imports' '--warn=clippy::lossy_float_literal' '--warn=clippy::linkedlist' '--allow=clippy::let_and_return' '--warn=clippy::large_types_passed_by_value' '--warn=clippy::large_stack_arrays' '--warn=clippy::large_digit_groups' '--warn=clippy::invalid_upcast_comparisons' '--warn=clippy::infinite_loop' '--warn=clippy::inefficient_to_string' '--warn=clippy::inconsistent_struct_constructor' '--warn=clippy::imprecise_flops' '--warn=clippy::implicit_clone' '--allow=clippy::if_same_then_else' '--warn=clippy::from_iter_instead_of_collect' '--warn=clippy::fn_params_excessive_bools' '--warn=clippy::float_cmp_const' '--warn=clippy::flat_map_option' '--warn=clippy::filter_map_next' '--warn=clippy::fallible_impl_from' '--warn=clippy::explicit_into_iter_loop' '--warn=clippy::explicit_deref_methods' '--warn=clippy::expl_impl_clone_on_copy' '--warn=clippy::enum_glob_use' '--warn=clippy::empty_enum' '--warn=clippy::doc_markdown' '--warn=clippy::debug_assert_with_mut_call' '--warn=clippy::dbg_macro' '--warn=clippy::create_dir' '--allow=clippy::collapsible_else_if' '--warn=clippy::checked_conversions' '--allow=clippy::branches_sharing_code' '--allow=clippy::bool_assert_comparison' --cfg 'feature="auto-color"' --cfg 'feature="color"' --cfg 'feature="default"' --cfg 'feature="humantime"' --cfg 'feature="regex"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("auto-color", "color", "default", "humantime", "regex", "unstable-kv"))' -C metadata=e4b5cc29465532f1 -C extra-filename=-e4b5cc29465532f1 --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --extern anstream=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libanstream-3e95e9c03093f011.rmeta --extern anstyle=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libanstyle-76780ac0e3caa841.rmeta --extern env_filter=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libenv_filter-41a6f91a551ca137.rmeta --extern humantime=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libhumantime-d7d35d4942a3f070.rmeta --extern log=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/liblog-054a084181905fb9.rmeta --cap-lints allow + Compiling indicatif v0.17.9 + Running rustc --crate-name indicatif --edition=2021 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/indicatif-0.17.9/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="rayon"' --cfg 'feature="unicode-width"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "futures", "improved_unicode", "in_memory", "rayon", "tokio", "unicode-segmentation", "unicode-width", "vt100"))' -C metadata=2721336661eaeb4b -C extra-filename=-2721336661eaeb4b --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --extern console=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libconsole-5c7ca505e6d280a8.rmeta --extern number_prefix=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libnumber_prefix-3538600420e6fe66.rmeta --extern portable_atomic=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libportable_atomic-f295aa83c34fc75c.rmeta --extern rayon=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/librayon-c7dc6d7867e2551f.rmeta --extern unicode_width=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libunicode_width-afb744becaf5cbee.rmeta --cap-lints allow + Compiling bio v2.0.3 + Running rustc --crate-name bio --edition=2018 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/bio-2.0.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("generic-simd", "pest", "pest_derive", "phylogeny", "runtime-dispatch-simd"))' -C metadata=b91e85ef64514672 -C extra-filename=-b91e85ef64514672 --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --extern anyhow=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libanyhow-2cb14037eccbaced.rmeta --extern approx=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libapprox-4aba898dd4c68aff.rmeta --extern bio_types=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libbio_types-0366d3f6fd4da0f5.rmeta --extern bit_set=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libbit_set-4e10d7ad6efb77fb.rmeta --extern bv=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libbv-20eeb54a9811cd90.rmeta --extern bytecount=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libbytecount-d69d77d47b69b25a.rmeta --extern csv=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libcsv-832cbbc42ad66b35.rmeta --extern custom_derive=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libcustom_derive-4d2d6eed4a82340f.rmeta --extern editdistancek=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libeditdistancek-fbcabf80324f8ce3.rmeta --extern enum_map=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libenum_map-7ef4719bfc438ce4.rmeta --extern fxhash=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libfxhash-9cb90fd7e09b01a5.rmeta --extern itertools=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libitertools-c92793cdbc6b4ef2.rmeta --extern itertools_num=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libitertools_num-1f8b4515fa815d82.rmeta --extern lazy_static=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/liblazy_static-5690c89ce0b7662a.rmeta --extern multimap=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libmultimap-428c9b2a0ea4998c.rmeta --extern ndarray=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libndarray-649275f66e144d30.rmeta --extern newtype_derive=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libnewtype_derive-5d9e9cf2d1b29ac9.rmeta --extern num_integer=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libnum_integer-fc9f7b7015fd54df.rmeta --extern num_traits=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libnum_traits-aecc12c36341049b.rmeta --extern ordered_float=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libordered_float-575dab606737764a.rmeta --extern petgraph=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libpetgraph-9cc18fbfc8b4772d.rmeta --extern rand=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/librand-6810d8953c6014c9.rmeta --extern regex=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libregex-8c520ba8846f7e23.rmeta --extern serde=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libserde-fc59797db66b78e9.rmeta --extern serde_derive=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libserde_derive-c5359619a68902d0.so --extern statrs=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libstatrs-5e67c33d7d0d360b.rmeta --extern strum=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libstrum-9d1affc7cb3937a4.rmeta --extern strum_macros=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libstrum_macros-8fead3aa178080db.so --extern thiserror=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libthiserror-e3c3f060f769fd8f.rmeta --extern triple_accel=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libtriple_accel-3765e75a5345b6e9.rmeta --extern vec_map=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libvec_map-6820348c35fe77b2.rmeta --cap-lints allow + Compiling tracing-subscriber v0.3.19 + Running rustc --crate-name tracing_subscriber --edition=2018 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/tracing-subscriber-0.3.19/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --warn=unexpected_cfgs --check-cfg 'cfg(flaky_tests)' --check-cfg 'cfg(tracing_unstable)' --cfg 'feature="alloc"' --cfg 'feature="ansi"' --cfg 'feature="default"' --cfg 'feature="fmt"' --cfg 'feature="nu-ansi-term"' --cfg 'feature="registry"' --cfg 'feature="sharded-slab"' --cfg 'feature="smallvec"' --cfg 'feature="std"' --cfg 'feature="thread_local"' --cfg 'feature="tracing-log"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "ansi", "chrono", "default", "env-filter", "fmt", "json", "local-time", "matchers", "nu-ansi-term", "once_cell", "parking_lot", "regex", "registry", "serde", "serde_json", "sharded-slab", "smallvec", "std", "thread_local", "time", "tracing", "tracing-log", "tracing-serde", "valuable", "valuable-serde", "valuable_crate"))' -C metadata=db912714a97cad3e -C extra-filename=-db912714a97cad3e --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --extern nu_ansi_term=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libnu_ansi_term-2b39384a1239e058.rmeta --extern sharded_slab=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libsharded_slab-5671e201184ded46.rmeta --extern smallvec=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libsmallvec-e8446a3a0bea045f.rmeta --extern thread_local=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libthread_local-ad9589d461652178.rmeta --extern tracing_core=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libtracing_core-120b59859caaa323.rmeta --extern tracing_log=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libtracing_log-42b9cd47db02dda6.rmeta --cap-lints allow + Running rustc --crate-name pbjson_types --edition=2021 /opt/conda/conda-bld/annonars_1734198454343/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/pbjson-types-0.7.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=da0cae19a1753bc2 -C extra-filename=-da0cae19a1753bc2 --out-dir /opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734198454343/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps --extern bytes=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libbytes-873411b0e6be0e8c.rmeta --extern chrono=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libchrono-b8ac2e5b14e4ce97.rmeta --extern pbjson=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libpbjson-18cd64d5b206be69.rmeta --extern prost=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libprost-15b98fa9c74e6f8c.rmeta --extern serde=/opt/conda/conda-bld/annonars_1734198454343/work/target/release/deps/libserde-fc59797db66b78e9.rmeta --cap-lints allow + Running /opt/conda/conda-bld/annonars_1734198454343/work/target/release/build/annonars-b8e96e9c79d6eced/build-script-build + error: failed to run custom build command for annonars v0.41.0 (/opt/conda/conda-bld/annonars_1734198454343/work) + + Caused by: + process didn't exit successfully: /opt/conda/conda-bld/annonars_1734198454343/work/target/release/build/annonars-b8e96e9c79d6eced/build-script-build (exit status: 1) + --- stdout + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/clinvar_data/class_by_freq.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/clinvar_data/clinvar_public.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/clinvar_data/extracted_vars.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/clinvar_data/gene_impact.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/clinvar_data/phenotype_link.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/clinvar/minimal.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/clinvar/per_gene.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/clinvar/sv.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/common/versions.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/cons/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/dbsnp/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/functional/refseq.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/genes/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/gnomad/exac_cnv.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/gnomad/gnomad2.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/gnomad/gnomad3.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/gnomad/gnomad4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/gnomad/gnomad_cnv4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/gnomad/gnomad_sv2.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/gnomad/gnomad_sv4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/gnomad/mtdna.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/gnomad/vep_common.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/gnomad/vep_gnomad2.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/gnomad/vep_gnomad3.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/gnomad/vep_gnomad4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/helixmtdb/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734198454343/work/protos/annonars/regions/clingen.proto + + --- stderr + Error: Could not find protoc. If protoc is installed, try setting the PROTOC environment variable to the path of the protoc binary. To install it on Debian, run apt-get install protobuf-compiler. It is also available at https://github.com/protocolbuffers/protobuf/releases For more information: https://docs.rs/prost-build/#sourcing-protoc + warning: build failed, waiting for other jobs to finish... + error: failed to compile annonars v0.41.0 (/opt/conda/conda-bld/annonars_1734198454343/work), intermediate artifacts can be found at /opt/conda/conda-bld/annonars_1734198454343/work/target. + To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/annonars_1734198454343/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/annonars_1734198454343/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. diff --git a/recipes/annonars/build_failure.linux-aarch64.yaml b/recipes/annonars/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..a2d42bc53c1c2 --- /dev/null +++ b/recipes/annonars/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: dd005183eef6d5b7e62d6d8abd08a13f7a13f58f2b2385aea0ac45c40bebaac1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + Running rustc --crate-name env_filter --edition=2021 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/env_filter-0.1.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no '--warn=clippy::zero_sized_map_values' '--warn=clippy::wildcard_imports' '--warn=clippy::verbose_file_reads' --warn=unused_qualifications --warn=unused_macro_rules --warn=unused_lifetimes --warn=unsafe_op_in_unsafe_fn --warn=unreachable_pub '--warn=clippy::trait_duplication_in_bounds' '--warn=clippy::todo' '--warn=clippy::string_to_string' '--warn=clippy::string_lit_as_bytes' '--warn=clippy::string_add_assign' '--warn=clippy::string_add' '--warn=clippy::str_to_string' '--warn=clippy::single_match_else' '--warn=clippy::semicolon_if_nothing_returned' '--warn=clippy::self_named_module_files' '--warn=clippy::same_functions_in_if_condition' --warn=rust_2018_idioms '--warn=clippy::rest_pat_in_fully_bound_structs' '--warn=clippy::ref_option_ref' '--warn=clippy::redundant_feature_names' '--warn=clippy::rc_mutex' '--warn=clippy::ptr_as_ptr' '--warn=clippy::path_buf_push_overwrite' '--warn=clippy::negative_feature_names' '--warn=clippy::needless_for_each' '--warn=clippy::needless_continue' '--warn=clippy::mutex_integer' '--warn=clippy::mem_forget' '--warn=clippy::match_wildcard_for_single_variants' '--warn=clippy::macro_use_imports' '--warn=clippy::lossy_float_literal' '--warn=clippy::linkedlist' '--allow=clippy::let_and_return' '--warn=clippy::large_types_passed_by_value' '--warn=clippy::large_stack_arrays' '--warn=clippy::large_digit_groups' '--warn=clippy::invalid_upcast_comparisons' '--warn=clippy::infinite_loop' '--warn=clippy::inefficient_to_string' '--warn=clippy::inconsistent_struct_constructor' '--warn=clippy::imprecise_flops' '--warn=clippy::implicit_clone' '--allow=clippy::if_same_then_else' '--warn=clippy::from_iter_instead_of_collect' '--warn=clippy::fn_params_excessive_bools' '--warn=clippy::float_cmp_const' '--warn=clippy::flat_map_option' '--warn=clippy::filter_map_next' '--warn=clippy::fallible_impl_from' '--warn=clippy::explicit_into_iter_loop' '--warn=clippy::explicit_deref_methods' '--warn=clippy::expl_impl_clone_on_copy' '--warn=clippy::enum_glob_use' '--warn=clippy::empty_enum' '--warn=clippy::doc_markdown' '--warn=clippy::debug_assert_with_mut_call' '--warn=clippy::dbg_macro' '--warn=clippy::create_dir' '--allow=clippy::collapsible_else_if' '--warn=clippy::checked_conversions' '--allow=clippy::branches_sharing_code' '--allow=clippy::bool_assert_comparison' --cfg 'feature="regex"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "regex"))' -C metadata=e77b5133da392c9f -C extra-filename=-e77b5133da392c9f --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --extern log=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/liblog-04ec5d9c8611df36.rmeta --extern regex=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libregex-7d3b53a375782bb5.rmeta --cap-lints allow + Running rustc --crate-name prost --edition=2021 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/prost-0.13.4/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="derive"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "derive", "no-recursion-limit", "prost-derive", "std"))' -C metadata=df970c184a6591f1 -C extra-filename=-df970c184a6591f1 --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --extern bytes=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libbytes-e696f34443ff21df.rmeta --extern prost_derive=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libprost_derive-640ee1edf78aa4ed.so --cap-lints allow + Compiling tracing-log v0.2.0 + Running rustc --crate-name tracing_log --edition=2018 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/tracing-log-0.2.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="log-tracer"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("ahash", "default", "interest-cache", "log-tracer", "lru", "std"))' -C metadata=8d5800c18539b346 -C extra-filename=-8d5800c18539b346 --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --extern log=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/liblog-04ec5d9c8611df36.rmeta --extern once_cell=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libonce_cell-c199536a47bd18dd.rmeta --extern tracing_core=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libtracing_core-a26c24b3de00f66a.rmeta --cap-lints allow + Compiling vec_map v0.8.2 + Running rustc --crate-name vec_map --edition=2015 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/vec_map-0.8.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="eders"' --cfg 'feature="serde"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("eders", "serde"))' -C metadata=c39c40d3a8a5527b -C extra-filename=-c39c40d3a8a5527b --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --extern serde=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libserde-19592f145aaec510.rmeta --cap-lints allow + Running rustc --crate-name multimap --edition=2015 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/multimap-0.10.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="serde"' --cfg 'feature="serde_impl"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "serde", "serde_impl"))' -C metadata=1cd7f9f2cc08342c -C extra-filename=-1cd7f9f2cc08342c --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --extern serde=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libserde-19592f145aaec510.rmeta --cap-lints allow + Compiling itertools-num v0.1.3 + Running rustc --crate-name itertools_num --edition=2015 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/itertools-num-0.1.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=ec0f49d83ac1fb43 -C extra-filename=-ec0f49d83ac1fb43 --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --extern num_traits=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libnum_traits-111eb85696e7d6e8.rmeta --cap-lints allow + Compiling ordered-float v4.5.0 + Running rustc --crate-name ordered_float --edition=2021 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/ordered-float-4.5.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("arbitrary", "borsh", "bytemuck", "default", "derive-visitor", "num-cmp", "proptest", "rand", "randtest", "rkyv", "rkyv_16", "rkyv_32", "rkyv_64", "rkyv_ck", "schemars", "serde", "speedy", "std"))' -C metadata=b652a9d362bdb415 -C extra-filename=-b652a9d362bdb415 --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --extern num_traits=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libnum_traits-111eb85696e7d6e8.rmeta --cap-lints allow + Compiling thread_local v1.1.8 + Running rustc --crate-name thread_local --edition=2021 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/thread_local-1.1.8/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("nightly"))' -C metadata=281ce0d837fae246 -C extra-filename=-281ce0d837fae246 --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --extern cfg_if=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libcfg_if-d04d46819c96fdff.rmeta --extern once_cell=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libonce_cell-c199536a47bd18dd.rmeta --cap-lints allow + Compiling fxhash v0.2.1 + Running rustc --crate-name fxhash --edition=2015 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/fxhash-0.2.1/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=f9b3f904cfc87941 -C extra-filename=-f9b3f904cfc87941 --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --extern byteorder=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libbyteorder-35ab6b9c20886704.rmeta --cap-lints allow + Compiling number_prefix v0.4.0 + Running rustc --crate-name number_prefix --edition=2015 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/number_prefix-0.4.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "std"))' -C metadata=dc010896d8325d3c -C extra-filename=-dc010896d8325d3c --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --cap-lints allow + Compiling unicode-width v0.2.0 + Running rustc --crate-name unicode_width --edition=2021 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/unicode-width-0.2.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="cjk"' --cfg 'feature="default"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("cjk", "compiler_builtins", "core", "default", "no_std", "rustc-dep-of-std", "std"))' -C metadata=a6720db83dda571f -C extra-filename=-a6720db83dda571f --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --cap-lints allow + Compiling humantime v2.1.0 + Running rustc --crate-name humantime --edition=2018 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/humantime-2.1.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=56d1b7526da0c836 -C extra-filename=-56d1b7526da0c836 --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --cap-lints allow + Compiling bytecount v0.6.8 + Running rustc --crate-name bytecount --edition=2018 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/bytecount-0.6.8/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("generic-simd", "html_report", "runtime-dispatch-simd"))' -C metadata=8690a159f4091572 -C extra-filename=-8690a159f4091572 --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --cap-lints allow + Compiling triple_accel v0.4.0 + Running rustc --crate-name triple_accel --edition=2018 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/triple_accel-0.4.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="jewel-16bit"' --cfg 'feature="jewel-32bit"' --cfg 'feature="jewel-8bit"' --cfg 'feature="jewel-avx"' --cfg 'feature="jewel-sse"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("debug", "default", "jewel-16bit", "jewel-32bit", "jewel-8bit", "jewel-avx", "jewel-sse"))' -C metadata=2b16dffb20dc2e4a -C extra-filename=-2b16dffb20dc2e4a --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --cap-lints allow + Compiling editdistancek v1.0.2 + Running rustc --crate-name editdistancek --edition=2018 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/editdistancek-1.0.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=50555f000fff8bda -C extra-filename=-50555f000fff8bda --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --cap-lints allow + Compiling custom_derive v0.1.7 + Running rustc --crate-name custom_derive --edition=2015 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/custom_derive-0.1.7/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "std"))' -C metadata=4a6a573099d7bb37 -C extra-filename=-4a6a573099d7bb37 --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --cap-lints allow + Compiling env_logger v0.11.5 + Running rustc --crate-name env_logger --edition=2021 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/env_logger-0.11.5/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no '--warn=clippy::zero_sized_map_values' '--warn=clippy::wildcard_imports' '--warn=clippy::verbose_file_reads' --warn=unused_qualifications --warn=unused_macro_rules --warn=unused_lifetimes --warn=unsafe_op_in_unsafe_fn --warn=unreachable_pub '--warn=clippy::trait_duplication_in_bounds' '--warn=clippy::todo' '--warn=clippy::string_to_string' '--warn=clippy::string_lit_as_bytes' '--warn=clippy::string_add_assign' '--warn=clippy::string_add' '--warn=clippy::str_to_string' '--warn=clippy::single_match_else' '--warn=clippy::semicolon_if_nothing_returned' '--warn=clippy::self_named_module_files' '--warn=clippy::same_functions_in_if_condition' --warn=rust_2018_idioms '--warn=clippy::rest_pat_in_fully_bound_structs' '--warn=clippy::ref_option_ref' '--warn=clippy::redundant_feature_names' '--warn=clippy::rc_mutex' '--warn=clippy::ptr_as_ptr' '--warn=clippy::path_buf_push_overwrite' '--warn=clippy::negative_feature_names' '--warn=clippy::needless_for_each' '--warn=clippy::needless_continue' '--warn=clippy::mutex_integer' '--warn=clippy::mem_forget' '--warn=clippy::match_wildcard_for_single_variants' '--warn=clippy::macro_use_imports' '--warn=clippy::lossy_float_literal' '--warn=clippy::linkedlist' '--allow=clippy::let_and_return' '--warn=clippy::large_types_passed_by_value' '--warn=clippy::large_stack_arrays' '--warn=clippy::large_digit_groups' '--warn=clippy::invalid_upcast_comparisons' '--warn=clippy::infinite_loop' '--warn=clippy::inefficient_to_string' '--warn=clippy::inconsistent_struct_constructor' '--warn=clippy::imprecise_flops' '--warn=clippy::implicit_clone' '--allow=clippy::if_same_then_else' '--warn=clippy::from_iter_instead_of_collect' '--warn=clippy::fn_params_excessive_bools' '--warn=clippy::float_cmp_const' '--warn=clippy::flat_map_option' '--warn=clippy::filter_map_next' '--warn=clippy::fallible_impl_from' '--warn=clippy::explicit_into_iter_loop' '--warn=clippy::explicit_deref_methods' '--warn=clippy::expl_impl_clone_on_copy' '--warn=clippy::enum_glob_use' '--warn=clippy::empty_enum' '--warn=clippy::doc_markdown' '--warn=clippy::debug_assert_with_mut_call' '--warn=clippy::dbg_macro' '--warn=clippy::create_dir' '--allow=clippy::collapsible_else_if' '--warn=clippy::checked_conversions' '--allow=clippy::branches_sharing_code' '--allow=clippy::bool_assert_comparison' --cfg 'feature="auto-color"' --cfg 'feature="color"' --cfg 'feature="default"' --cfg 'feature="humantime"' --cfg 'feature="regex"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("auto-color", "color", "default", "humantime", "regex", "unstable-kv"))' -C metadata=42ec598147f5ee70 -C extra-filename=-42ec598147f5ee70 --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --extern anstream=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libanstream-820b70288d18f5bd.rmeta --extern anstyle=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libanstyle-074306b3f8752148.rmeta --extern env_filter=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libenv_filter-e77b5133da392c9f.rmeta --extern humantime=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libhumantime-56d1b7526da0c836.rmeta --extern log=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/liblog-04ec5d9c8611df36.rmeta --cap-lints allow + Compiling bio v2.0.3 + Running rustc --crate-name bio --edition=2018 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/bio-2.0.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("generic-simd", "pest", "pest_derive", "phylogeny", "runtime-dispatch-simd"))' -C metadata=b7beb55aab49917a -C extra-filename=-b7beb55aab49917a --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --extern anyhow=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libanyhow-a486a108fb06f70e.rmeta --extern approx=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libapprox-023d2a78cbada9d9.rmeta --extern bio_types=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libbio_types-312d0e9cae3ace72.rmeta --extern bit_set=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libbit_set-d31f4255ca684ef9.rmeta --extern bv=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libbv-84913e5a15ff45f1.rmeta --extern bytecount=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libbytecount-8690a159f4091572.rmeta --extern csv=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libcsv-f91fb0ec20669d70.rmeta --extern custom_derive=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libcustom_derive-4a6a573099d7bb37.rmeta --extern editdistancek=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libeditdistancek-50555f000fff8bda.rmeta --extern enum_map=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libenum_map-e7763b964733aa74.rmeta --extern fxhash=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libfxhash-f9b3f904cfc87941.rmeta --extern itertools=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libitertools-7947b004be9e2539.rmeta --extern itertools_num=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libitertools_num-ec0f49d83ac1fb43.rmeta --extern lazy_static=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/liblazy_static-09f0c2f76d110bc7.rmeta --extern multimap=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libmultimap-1cd7f9f2cc08342c.rmeta --extern ndarray=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libndarray-cef427f06177cf43.rmeta --extern newtype_derive=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libnewtype_derive-b8698437b56c9c15.rmeta --extern num_integer=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libnum_integer-3016ce68296898e2.rmeta --extern num_traits=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libnum_traits-111eb85696e7d6e8.rmeta --extern ordered_float=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libordered_float-b652a9d362bdb415.rmeta --extern petgraph=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libpetgraph-26665bbd56506f0d.rmeta --extern rand=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/librand-eddf2078bb3a022c.rmeta --extern regex=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libregex-7d3b53a375782bb5.rmeta --extern serde=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libserde-19592f145aaec510.rmeta --extern serde_derive=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libserde_derive-af64b1abf29386ef.so --extern statrs=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libstatrs-e61a04a035eb63a8.rmeta --extern strum=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libstrum-e34699998247f339.rmeta --extern strum_macros=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libstrum_macros-ec3c28e5a4e3c963.so --extern thiserror=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libthiserror-4503d0f721896523.rmeta --extern triple_accel=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libtriple_accel-2b16dffb20dc2e4a.rmeta --extern vec_map=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libvec_map-c39c40d3a8a5527b.rmeta --cap-lints allow + Compiling indicatif v0.17.9 + Running rustc --crate-name indicatif --edition=2021 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/indicatif-0.17.9/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="rayon"' --cfg 'feature="unicode-width"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "futures", "improved_unicode", "in_memory", "rayon", "tokio", "unicode-segmentation", "unicode-width", "vt100"))' -C metadata=f6a00bebfba569ca -C extra-filename=-f6a00bebfba569ca --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --extern console=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libconsole-c65f2483b8d5026d.rmeta --extern number_prefix=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libnumber_prefix-dc010896d8325d3c.rmeta --extern portable_atomic=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libportable_atomic-0a1524879fdcf0f4.rmeta --extern rayon=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/librayon-eb0fed77d241d03c.rmeta --extern unicode_width=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libunicode_width-a6720db83dda571f.rmeta --cap-lints allow + Compiling tracing-subscriber v0.3.19 + Running rustc --crate-name tracing_subscriber --edition=2018 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/tracing-subscriber-0.3.19/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --warn=unexpected_cfgs --check-cfg 'cfg(flaky_tests)' --check-cfg 'cfg(tracing_unstable)' --cfg 'feature="alloc"' --cfg 'feature="ansi"' --cfg 'feature="default"' --cfg 'feature="fmt"' --cfg 'feature="nu-ansi-term"' --cfg 'feature="registry"' --cfg 'feature="sharded-slab"' --cfg 'feature="smallvec"' --cfg 'feature="std"' --cfg 'feature="thread_local"' --cfg 'feature="tracing-log"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "ansi", "chrono", "default", "env-filter", "fmt", "json", "local-time", "matchers", "nu-ansi-term", "once_cell", "parking_lot", "regex", "registry", "serde", "serde_json", "sharded-slab", "smallvec", "std", "thread_local", "time", "tracing", "tracing-log", "tracing-serde", "valuable", "valuable-serde", "valuable_crate"))' -C metadata=4eef18d6c64cdb52 -C extra-filename=-4eef18d6c64cdb52 --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --extern nu_ansi_term=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libnu_ansi_term-f82b34c4f7db080d.rmeta --extern sharded_slab=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libsharded_slab-69f8d9850e16d26f.rmeta --extern smallvec=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libsmallvec-5300ad5268eb1c92.rmeta --extern thread_local=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libthread_local-281ce0d837fae246.rmeta --extern tracing_core=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libtracing_core-a26c24b3de00f66a.rmeta --extern tracing_log=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libtracing_log-8d5800c18539b346.rmeta --cap-lints allow + Running rustc --crate-name pbjson_types --edition=2021 /opt/conda/conda-bld/annonars_1734143469563/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/pbjson-types-0.7.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=13559bc03782c2d7 -C extra-filename=-13559bc03782c2d7 --out-dir /opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps -C linker=/opt/conda/conda-bld/annonars_1734143469563/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps --extern bytes=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libbytes-e696f34443ff21df.rmeta --extern chrono=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libchrono-ee4521c3aa513ce0.rmeta --extern pbjson=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libpbjson-df0be0ee730bd7d9.rmeta --extern prost=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libprost-df970c184a6591f1.rmeta --extern serde=/opt/conda/conda-bld/annonars_1734143469563/work/target/release/deps/libserde-19592f145aaec510.rmeta --cap-lints allow + Running /opt/conda/conda-bld/annonars_1734143469563/work/target/release/build/annonars-c910b98a15d8d3c3/build-script-build + error: failed to run custom build command for annonars v0.41.0 (/opt/conda/conda-bld/annonars_1734143469563/work) + + Caused by: + process didn't exit successfully: /opt/conda/conda-bld/annonars_1734143469563/work/target/release/build/annonars-c910b98a15d8d3c3/build-script-build (exit status: 1) + --- stdout + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/clinvar_data/class_by_freq.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/clinvar_data/clinvar_public.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/clinvar_data/extracted_vars.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/clinvar_data/gene_impact.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/clinvar_data/phenotype_link.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/clinvar/minimal.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/clinvar/per_gene.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/clinvar/sv.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/common/versions.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/cons/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/dbsnp/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/functional/refseq.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/genes/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/gnomad/exac_cnv.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/gnomad/gnomad2.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/gnomad/gnomad3.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/gnomad/gnomad4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/gnomad/gnomad_cnv4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/gnomad/gnomad_sv2.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/gnomad/gnomad_sv4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/gnomad/mtdna.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/gnomad/vep_common.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/gnomad/vep_gnomad2.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/gnomad/vep_gnomad3.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/gnomad/vep_gnomad4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/helixmtdb/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/annonars_1734143469563/work/protos/annonars/regions/clingen.proto + + --- stderr + Error: Could not find protoc. If protoc is installed, try setting the PROTOC environment variable to the path of the protoc binary. To install it on Debian, run apt-get install protobuf-compiler. It is also available at https://github.com/protocolbuffers/protobuf/releases For more information: https://docs.rs/prost-build/#sourcing-protoc + warning: build failed, waiting for other jobs to finish... + error: failed to compile annonars v0.41.0 (/opt/conda/conda-bld/annonars_1734143469563/work), intermediate artifacts can be found at /opt/conda/conda-bld/annonars_1734143469563/work/target. + To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/annonars_1734143469563/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/annonars_1734143469563/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index c6fd696b3a026..d74a25e120f1f 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage("annonars", max_pin="x.x") }} diff --git a/recipes/aprfinder/meta.yaml b/recipes/aprfinder/meta.yaml index 9003d44d897ee..b6351f3cd212e 100644 --- a/recipes/aprfinder/meta.yaml +++ b/recipes/aprfinder/meta.yaml @@ -6,7 +6,7 @@ package : version : {{ version }} build: - number: 2 + number: 3 source: url: https://github.com/jaroslav-kubin/aprfinder/releases/download/v{{version}}/aprfinder-{{version}}.tar.gz diff --git a/recipes/apt-probeset-summarize/meta.yaml b/recipes/apt-probeset-summarize/meta.yaml index 6eada9003177d..d86128faaa6f8 100644 --- a/recipes/apt-probeset-summarize/meta.yaml +++ b/recipes/apt-probeset-summarize/meta.yaml @@ -4,7 +4,7 @@ package: build: skip: True #[osx] - number: 5 + number: 6 source: md5: 1a384def6f633c1ad24296e0fc677ec3 diff --git a/recipes/apu-label-propagation/meta.yaml b/recipes/apu-label-propagation/meta.yaml index d8e15873d5b8d..88451692c61bd 100644 --- a/recipes/apu-label-propagation/meta.yaml +++ b/recipes/apu-label-propagation/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 50424bf7df99b51dc71a4121beae89ef69b2bb4eaba559c99643baecb8544806 build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('apu-label-propagation', max_pin="x.x") }} diff --git a/recipes/aragorn/meta.yaml b/recipes/aragorn/meta.yaml index 986a8e82e22af..29b12e40431d3 100644 --- a/recipes/aragorn/meta.yaml +++ b/recipes/aragorn/meta.yaml @@ -7,7 +7,7 @@ source: url: http://www.ansikte.se/ARAGORN/Downloads/aragorn1.2.41.c build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage("aragorn", max_pin="x.x.x") }} diff --git a/recipes/arcs/build_failure.linux-64.yaml b/recipes/arcs/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..1e3f5f4b5afc7 --- /dev/null +++ b/recipes/arcs/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 8d723074ba4dec2549af43d0d0d72cac669877495074141fb65f4819bb63fac2 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + config.status: creating Common/Makefile + config.status: creating DataLayer/Makefile + config.status: creating Graph/Makefile + config.status: creating Test/Makefile + config.status: creating src/Makefile + config.status: creating config.h + config.status: executing depfiles commands + Making install in Common + make[1]: Entering directory '$SRC_DIR/Common' + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-BloomFilter.o -MD -MP -MF .deps/libcommon_a-BloomFilter.Tpo -c -o libcommon_a-BloomFilter.o test -f 'BloomFilter.cpp' || echo '$SRC_DIR/Common/'BloomFilter.cpp + mv -f .deps/libcommon_a-BloomFilter.Tpo .deps/libcommon_a-BloomFilter.Po + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-BloomFilterInfo.o -MD -MP -MF .deps/libcommon_a-BloomFilterInfo.Tpo -c -o libcommon_a-BloomFilterInfo.o test -f 'BloomFilterInfo.cpp' || echo '$SRC_DIR/Common/'BloomFilterInfo.cpp + mv -f .deps/libcommon_a-BloomFilterInfo.Tpo .deps/libcommon_a-BloomFilterInfo.Po + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-city.o -MD -MP -MF .deps/libcommon_a-city.Tpo -c -o libcommon_a-city.o test -f 'city.cc' || echo '$SRC_DIR/Common/'city.cc + mv -f .deps/libcommon_a-city.Tpo .deps/libcommon_a-city.Po + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-Dynamicofstream.o -MD -MP -MF .deps/libcommon_a-Dynamicofstream.Tpo -c -o libcommon_a-Dynamicofstream.o test -f 'Dynamicofstream.cpp' || echo '$SRC_DIR/Common/'Dynamicofstream.cpp + mv -f .deps/libcommon_a-Dynamicofstream.Tpo .deps/libcommon_a-Dynamicofstream.Po + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-Fcontrol.o -MD -MP -MF .deps/libcommon_a-Fcontrol.Tpo -c -o libcommon_a-Fcontrol.o test -f 'Fcontrol.cpp' || echo '$SRC_DIR/Common/'Fcontrol.cpp + mv -f .deps/libcommon_a-Fcontrol.Tpo .deps/libcommon_a-Fcontrol.Po + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-gzstream.o -MD -MP -MF .deps/libcommon_a-gzstream.Tpo -c -o libcommon_a-gzstream.o test -f 'gzstream.C' || echo '$SRC_DIR/Common/'gzstream.C + mv -f .deps/libcommon_a-gzstream.Tpo .deps/libcommon_a-gzstream.Po + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-Options.o -MD -MP -MF .deps/libcommon_a-Options.Tpo -c -o libcommon_a-Options.o test -f 'Options.cpp' || echo '$SRC_DIR/Common/'Options.cpp + mv -f .deps/libcommon_a-Options.Tpo .deps/libcommon_a-Options.Po + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-ReadsProcessor.o -MD -MP -MF .deps/libcommon_a-ReadsProcessor.Tpo -c -o libcommon_a-ReadsProcessor.o test -f 'ReadsProcessor.cpp' || echo '$SRC_DIR/Common/'ReadsProcessor.cpp + mv -f .deps/libcommon_a-ReadsProcessor.Tpo .deps/libcommon_a-ReadsProcessor.Po + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-Sequence.o -MD -MP -MF .deps/libcommon_a-Sequence.Tpo -c -o libcommon_a-Sequence.o test -f 'Sequence.cpp' || echo '$SRC_DIR/Common/'Sequence.cpp + mv -f .deps/libcommon_a-Sequence.Tpo .deps/libcommon_a-Sequence.Po + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-SignalHandler.o -MD -MP -MF .deps/libcommon_a-SignalHandler.Tpo -c -o libcommon_a-SignalHandler.o test -f 'SignalHandler.cpp' || echo '$SRC_DIR/Common/'SignalHandler.cpp + mv -f .deps/libcommon_a-SignalHandler.Tpo .deps/libcommon_a-SignalHandler.Po + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-Uncompress.o -MD -MP -MF .deps/libcommon_a-Uncompress.Tpo -c -o libcommon_a-Uncompress.o test -f 'Uncompress.cpp' || echo '$SRC_DIR/Common/'Uncompress.cpp + mv -f .deps/libcommon_a-Uncompress.Tpo .deps/libcommon_a-Uncompress.Po + rm -f libcommon.a + ar cru libcommon.a libcommon_a-BloomFilter.o libcommon_a-BloomFilterInfo.o libcommon_a-city.o libcommon_a-Dynamicofstream.o libcommon_a-Fcontrol.o libcommon_a-gzstream.o libcommon_a-Options.o libcommon_a-ReadsProcessor.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Uncompress.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib libcommon.a + make[2]: Entering directory '$SRC_DIR/Common' + make[2]: Nothing to be done for 'install-exec-am'. + make[2]: Nothing to be done for 'install-data-am'. + make[2]: Leaving directory '$SRC_DIR/Common' + make[1]: Leaving directory '$SRC_DIR/Common' + Making install in DataLayer + make[1]: Entering directory '$SRC_DIR/DataLayer' + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -I$SRC_DIR/Common -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libdatalayer_a-FastaReader.o -MD -MP -MF .deps/libdatalayer_a-FastaReader.Tpo -c -o libdatalayer_a-FastaReader.o test -f 'FastaReader.cpp' || echo '$SRC_DIR/DataLayer/'FastaReader.cpp + mv -f .deps/libdatalayer_a-FastaReader.Tpo .deps/libdatalayer_a-FastaReader.Po + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -I$SRC_DIR/Common -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libdatalayer_a-FastaWriter.o -MD -MP -MF .deps/libdatalayer_a-FastaWriter.Tpo -c -o libdatalayer_a-FastaWriter.o test -f 'FastaWriter.cpp' || echo '$SRC_DIR/DataLayer/'FastaWriter.cpp + mv -f .deps/libdatalayer_a-FastaWriter.Tpo .deps/libdatalayer_a-FastaWriter.Po + rm -f libdatalayer.a + ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib libdatalayer.a + make[2]: Entering directory '$SRC_DIR/DataLayer' + make[2]: Nothing to be done for 'install-exec-am'. + make[2]: Nothing to be done for 'install-data-am'. + make[2]: Leaving directory '$SRC_DIR/DataLayer' + make[1]: Leaving directory '$SRC_DIR/DataLayer' + Making install in Graph + make[1]: Entering directory '$SRC_DIR/Graph' + make[2]: Entering directory '$SRC_DIR/Graph' + make[2]: Nothing to be done for 'install-exec-am'. + make[2]: Nothing to be done for 'install-data-am'. + make[2]: Leaving directory '$SRC_DIR/Graph' + make[1]: Leaving directory '$SRC_DIR/Graph' + Making install in Arcs + make[1]: Entering directory '$SRC_DIR/Arcs' + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR/Arcs -I$SRC_DIR/Common -I$SRC_DIR/DataLayer -I$SRC_DIR -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -Wno-unknown-pragmas -Wno-error=unused-but-set-variable -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT arcs-Arcs.o -MD -MP -MF .deps/arcs-Arcs.Tpo -c -o arcs-Arcs.o test -f 'Arcs.cpp' || echo '$SRC_DIR/Arcs/'Arcs.cpp + In file included from Arcs.cpp:9: + ../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = DistanceEst; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]': + ../Graph/DotIO.h:110:14: required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' + Arcs.cpp:1670:11: required from here + ../Graph/DotIO.h:44:43: error: possibly dangling reference to a temporary [-Werror=dangling-reference] + 44 | const edge_property_type& ep = get(edge_bundle, g, e); + | ^~ + ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))' + 44 | const edge_property_type& ep = get(edge_bundle, g, e); + | ~~~^~~~~~~~~~~~~~~~~~~ + cc1plus: all warnings being treated as errors + make[1]: *** [Makefile:385: arcs-Arcs.o] Error 1 + make[1]: Leaving directory '$SRC_DIR/Arcs' + make: *** [Makefile:413: install-recursive] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/arcs_1734306143692/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/arcs_1734306143692/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/arcs/build_failure.linux-aarch64.yaml b/recipes/arcs/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..9860e1c5a13f7 --- /dev/null +++ b/recipes/arcs/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 8d723074ba4dec2549af43d0d0d72cac669877495074141fb65f4819bb63fac2 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + config.status: creating Common/Makefile + config.status: creating DataLayer/Makefile + config.status: creating Graph/Makefile + config.status: creating Test/Makefile + config.status: creating src/Makefile + config.status: creating config.h + config.status: executing depfiles commands + Making install in Common + make[1]: Entering directory '$SRC_DIR/Common' + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-BloomFilter.o -MD -MP -MF .deps/libcommon_a-BloomFilter.Tpo -c -o libcommon_a-BloomFilter.o test -f 'BloomFilter.cpp' || echo '$SRC_DIR/Common/'BloomFilter.cpp + mv -f .deps/libcommon_a-BloomFilter.Tpo .deps/libcommon_a-BloomFilter.Po + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-BloomFilterInfo.o -MD -MP -MF .deps/libcommon_a-BloomFilterInfo.Tpo -c -o libcommon_a-BloomFilterInfo.o test -f 'BloomFilterInfo.cpp' || echo '$SRC_DIR/Common/'BloomFilterInfo.cpp + mv -f .deps/libcommon_a-BloomFilterInfo.Tpo .deps/libcommon_a-BloomFilterInfo.Po + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-city.o -MD -MP -MF .deps/libcommon_a-city.Tpo -c -o libcommon_a-city.o test -f 'city.cc' || echo '$SRC_DIR/Common/'city.cc + mv -f .deps/libcommon_a-city.Tpo .deps/libcommon_a-city.Po + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-Dynamicofstream.o -MD -MP -MF .deps/libcommon_a-Dynamicofstream.Tpo -c -o libcommon_a-Dynamicofstream.o test -f 'Dynamicofstream.cpp' || echo '$SRC_DIR/Common/'Dynamicofstream.cpp + mv -f .deps/libcommon_a-Dynamicofstream.Tpo .deps/libcommon_a-Dynamicofstream.Po + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-Fcontrol.o -MD -MP -MF .deps/libcommon_a-Fcontrol.Tpo -c -o libcommon_a-Fcontrol.o test -f 'Fcontrol.cpp' || echo '$SRC_DIR/Common/'Fcontrol.cpp + mv -f .deps/libcommon_a-Fcontrol.Tpo .deps/libcommon_a-Fcontrol.Po + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-gzstream.o -MD -MP -MF .deps/libcommon_a-gzstream.Tpo -c -o libcommon_a-gzstream.o test -f 'gzstream.C' || echo '$SRC_DIR/Common/'gzstream.C + mv -f .deps/libcommon_a-gzstream.Tpo .deps/libcommon_a-gzstream.Po + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-Options.o -MD -MP -MF .deps/libcommon_a-Options.Tpo -c -o libcommon_a-Options.o test -f 'Options.cpp' || echo '$SRC_DIR/Common/'Options.cpp + mv -f .deps/libcommon_a-Options.Tpo .deps/libcommon_a-Options.Po + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-ReadsProcessor.o -MD -MP -MF .deps/libcommon_a-ReadsProcessor.Tpo -c -o libcommon_a-ReadsProcessor.o test -f 'ReadsProcessor.cpp' || echo '$SRC_DIR/Common/'ReadsProcessor.cpp + mv -f .deps/libcommon_a-ReadsProcessor.Tpo .deps/libcommon_a-ReadsProcessor.Po + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-Sequence.o -MD -MP -MF .deps/libcommon_a-Sequence.Tpo -c -o libcommon_a-Sequence.o test -f 'Sequence.cpp' || echo '$SRC_DIR/Common/'Sequence.cpp + mv -f .deps/libcommon_a-Sequence.Tpo .deps/libcommon_a-Sequence.Po + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-SignalHandler.o -MD -MP -MF .deps/libcommon_a-SignalHandler.Tpo -c -o libcommon_a-SignalHandler.o test -f 'SignalHandler.cpp' || echo '$SRC_DIR/Common/'SignalHandler.cpp + mv -f .deps/libcommon_a-SignalHandler.Tpo .deps/libcommon_a-SignalHandler.Po + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -Wno-error=unused-result -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libcommon_a-Uncompress.o -MD -MP -MF .deps/libcommon_a-Uncompress.Tpo -c -o libcommon_a-Uncompress.o test -f 'Uncompress.cpp' || echo '$SRC_DIR/Common/'Uncompress.cpp + mv -f .deps/libcommon_a-Uncompress.Tpo .deps/libcommon_a-Uncompress.Po + rm -f libcommon.a + ar cru libcommon.a libcommon_a-BloomFilter.o libcommon_a-BloomFilterInfo.o libcommon_a-city.o libcommon_a-Dynamicofstream.o libcommon_a-Fcontrol.o libcommon_a-gzstream.o libcommon_a-Options.o libcommon_a-ReadsProcessor.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Uncompress.o + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib libcommon.a + make[2]: Entering directory '$SRC_DIR/Common' + make[2]: Nothing to be done for 'install-exec-am'. + make[2]: Nothing to be done for 'install-data-am'. + make[2]: Leaving directory '$SRC_DIR/Common' + make[1]: Leaving directory '$SRC_DIR/Common' + Making install in DataLayer + make[1]: Entering directory '$SRC_DIR/DataLayer' + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -I$SRC_DIR/Common -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libdatalayer_a-FastaReader.o -MD -MP -MF .deps/libdatalayer_a-FastaReader.Tpo -c -o libdatalayer_a-FastaReader.o test -f 'FastaReader.cpp' || echo '$SRC_DIR/DataLayer/'FastaReader.cpp + mv -f .deps/libdatalayer_a-FastaReader.Tpo .deps/libdatalayer_a-FastaReader.Po + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR -I$SRC_DIR/Common -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT libdatalayer_a-FastaWriter.o -MD -MP -MF .deps/libdatalayer_a-FastaWriter.Tpo -c -o libdatalayer_a-FastaWriter.o test -f 'FastaWriter.cpp' || echo '$SRC_DIR/DataLayer/'FastaWriter.cpp + mv -f .deps/libdatalayer_a-FastaWriter.Tpo .deps/libdatalayer_a-FastaWriter.Po + rm -f libdatalayer.a + ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib libdatalayer.a + make[2]: Entering directory '$SRC_DIR/DataLayer' + make[2]: Nothing to be done for 'install-exec-am'. + make[2]: Nothing to be done for 'install-data-am'. + make[2]: Leaving directory '$SRC_DIR/DataLayer' + make[1]: Leaving directory '$SRC_DIR/DataLayer' + Making install in Graph + make[1]: Entering directory '$SRC_DIR/Graph' + make[2]: Entering directory '$SRC_DIR/Graph' + make[2]: Nothing to be done for 'install-exec-am'. + make[2]: Nothing to be done for 'install-data-am'. + make[2]: Leaving directory '$SRC_DIR/Graph' + make[1]: Leaving directory '$SRC_DIR/Graph' + Making install in Arcs + make[1]: Entering directory '$SRC_DIR/Arcs' + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR/Arcs -I$SRC_DIR/Common -I$SRC_DIR/DataLayer -I$SRC_DIR -I$SRC_DIR -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -isystem$SRC_DIR/1_58_0 -Wall -Wextra -Werror -std=c0x -Wno-unknown-pragmas -Wno-error=unused-but-set-variable -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arcs-1.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-error=unused-result -fopenmp -MT arcs-Arcs.o -MD -MP -MF .deps/arcs-Arcs.Tpo -c -o arcs-Arcs.o test -f 'Arcs.cpp' || echo '$SRC_DIR/Arcs/'Arcs.cpp + In file included from Arcs.cpp:9: + ../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = DistanceEst; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]': + ../Graph/DotIO.h:110:14: required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]' + Arcs.cpp:1670:11: required from here + ../Graph/DotIO.h:44:43: error: possibly dangling reference to a temporary [-Werror=dangling-reference] + 44 | const edge_property_type& ep = get(edge_bundle, g, e); + | ^~ + ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))' + 44 | const edge_property_type& ep = get(edge_bundle, g, e); + | ~~~^~~~~~~~~~~~~~~~~~~ + cc1plus: all warnings being treated as errors + make[1]: *** [Makefile:385: arcs-Arcs.o] Error 1 + make[1]: Leaving directory '$SRC_DIR/Arcs' + make: *** [Makefile:413: install-recursive] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/arcs_1734607935138/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/arcs_1734607935138/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/arcs/meta.yaml b/recipes/arcs/meta.yaml index 21f64964882dd..826be0adcfcea 100644 --- a/recipes/arcs/meta.yaml +++ b/recipes/arcs/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('arcs', max_pin="x") }} diff --git a/recipes/ariba/build_failure.linux-64.yaml b/recipes/ariba/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..45b8215451a35 --- /dev/null +++ b/recipes/ariba/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: c64f52ae984e507c666152f84058ae6e8dd344731ee53981fd6f30a26768db32 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("pysam==0.15.3=py27hbcae180_3"), MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']")} + Encountered problems while solving: + - package pysam-0.15.3-py27hbcae180_3 requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mlibzlib >=1.3.1,<2.0a0 [0m is installable with the potential options + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_0[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [31mpysam >=0.15.3,<=0.18.0 [0m is not installable because there are no viable options + [31mpysam 0.15.3[0m would require + [31mlibdeflate >=1.0,<1.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mpysam [0.15.3|0.15.4|...|0.18.0][0m would require + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("pysam==0.15.3=py27hbcae180_3"), MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']")} + Encountered problems while solving: + - package pysam-0.15.3-py27hbcae180_3 requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mlibzlib >=1.3.1,<2.0a0 [0m is installable with the potential options + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_0[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [31mpysam >=0.15.3,<=0.18.0 [0m is not installable because there are no viable options + [31mpysam 0.15.3[0m would require + [31mlibdeflate >=1.0,<1.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mpysam [0.15.3|0.15.4|...|0.18.0][0m would require + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. +category: |- + dependency issue diff --git a/recipes/ariba/meta.yaml b/recipes/ariba/meta.yaml index 483b0162b5ee2..4146f9cdc0e33 100644 --- a/recipes/ariba/meta.yaml +++ b/recipes/ariba/meta.yaml @@ -14,7 +14,7 @@ source: - ref_genes_getter.patch build: - number: 6 + number: 7 # Skipping py>=36 on osx because the bowtie2 <2.4.0 recipes are currently skipped on osx. skip: True # [py<30 or (py>=36 and osx) or py > 39] script: python -m pip install --no-deps --ignore-installed . diff --git a/recipes/arriba/build_failure.linux-64.yaml b/recipes/arriba/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..2ff1f52bca698 --- /dev/null +++ b/recipes/arriba/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c4bcdfa938383de1e9b4274f21dc4f583881117f4bac7e5415252a0fca3fbcf5 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arriba-2.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arriba-2.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + make -j 4 'CPPFLAGS=-I/opt/conda/conda-bld/arriba_1735034454847/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include -I/opt/conda/conda-bld/arriba_1735034454847/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include/htslib' 'LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/arriba_1735034454847/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -Wl,-rpath-link,/opt/conda/conda-bld/arriba_1735034454847/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -L/opt/conda/conda-bld/arriba_1735034454847/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' CXX=/opt/conda/conda-bld/arriba_1735034454847/_build_env/bin/x86_64-conda-linux-gnu-c bioconda + make LIBS_SO="-ldl -lhts -ldeflate -lz -lbz2 -llzma -lm" arriba + make[1]: Entering directory '$SRC_DIR' + $BUILD_PREFIX/bin/wget --no-check-certificate -O - 'https://github.com/Tessil/hat-trie/archive/v0.6.0.tar.gz' | tar -xzf - -C libraries && \ + cp -r libraries/hat-trie-*/include/tsl libraries + --2024-12-24 10:02:48-- https://github.com/Tessil/hat-trie/archive/v0.6.0.tar.gz + Resolving github.com (github.com)... 140.82.113.3 + Connecting to github.com (github.com)|140.82.113.3|:443... connected. + HTTP request sent, awaiting response... 302 Found + Location: https://codeload.github.com/Tessil/hat-trie/tar.gz/refs/tags/v0.6.0 [following] + --2024-12-24 10:02:48-- https://codeload.github.com/Tessil/hat-trie/tar.gz/refs/tags/v0.6.0 + Resolving codeload.github.com (codeload.github.com)... 140.82.113.10 + Connecting to codeload.github.com (codeload.github.com)|140.82.113.10|:443... connected. + HTTP request sent, awaiting response... 200 OK + Length: unspecified [application/x-gzip] + Saving to: 'STDOUT' + + - [<=> ] 0 --.-KB/s - [ <=> ] 77.75K --.-KB/s in 0.004s + + 2024-12-24 10:02:48 (19.5 MB/s) - written to stdout [79611] + + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/annotation.o source/annotation.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/assembly.o source/assembly.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/options.o source/options.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/read_chimeric_alignments.o source/read_chimeric_alignments.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_duplicates.o source/filter_duplicates.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_uninteresting_contigs.o source/filter_uninteresting_contigs.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_viral_contigs.o source/filter_viral_contigs.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_top_expressed_viral_contigs.o source/filter_top_expressed_viral_contigs.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_low_coverage_viral_contigs.o source/filter_low_coverage_viral_contigs.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_inconsistently_clipped.o source/filter_inconsistently_clipped.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_homopolymer.o source/filter_homopolymer.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/read_stats.o source/read_stats.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/fusions.o source/fusions.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_proximal_read_through.o source/filter_proximal_read_through.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_same_gene.o source/filter_same_gene.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_small_insert_size.o source/filter_small_insert_size.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_long_gap.o source/filter_long_gap.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_hairpin.o source/filter_hairpin.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_multimappers.o source/filter_multimappers.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_mismatches.o source/filter_mismatches.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_low_entropy.o source/filter_low_entropy.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_relative_support.o source/filter_relative_support.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_both_intronic.o source/filter_both_intronic.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_non_coding_neighbors.o source/filter_non_coding_neighbors.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_intragenic_both_exonic.o source/filter_intragenic_both_exonic.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/recover_internal_tandem_duplication.o source/recover_internal_tandem_duplication.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_min_support.o source/filter_min_support.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/recover_known_fusions.o source/recover_known_fusions.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/recover_both_spliced.o source/recover_both_spliced.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_blacklisted_ranges.o source/filter_blacklisted_ranges.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_end_to_end.o source/filter_end_to_end.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_in_vitro.o source/filter_in_vitro.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/merge_adjacent_fusions.o source/merge_adjacent_fusions.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/select_best.o source/select_best.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_marginal_read_through.o source/filter_marginal_read_through.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_short_anchor.o source/filter_short_anchor.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_no_coverage.o source/filter_no_coverage.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_homologs.o source/filter_homologs.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_mismappers.o source/filter_mismappers.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/recover_many_spliced.o source/recover_many_spliced.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_genomic_support.o source/filter_genomic_support.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/recover_isoforms.o source/recover_isoforms.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/annotate_tags.o source/annotate_tags.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/annotate_protein_domains.o source/annotate_protein_domains.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/output_fusions.o source/output_fusions.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/read_compressed_file.o source/read_compressed_file.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Isource -Ilibraries/htslib -Ilibraries/tsl -o arriba source/arriba.cpp source/annotation.o source/assembly.o source/options.o source/read_chimeric_alignments.o source/filter_duplicates.o source/filter_uninteresting_contigs.o source/filter_viral_contigs.o source/filter_top_expressed_viral_contigs.o source/filter_low_coverage_viral_contigs.o source/filter_inconsistently_clipped.o source/filter_homopolymer.o source/read_stats.o source/fusions.o source/filter_proximal_read_through.o source/filter_same_gene.o source/filter_small_insert_size.o source/filter_long_gap.o source/filter_hairpin.o source/filter_multimappers.o source/filter_mismatches.o source/filter_low_entropy.o source/filter_relative_support.o source/filter_both_intronic.o source/filter_non_coding_neighbors.o source/filter_intragenic_both_exonic.o source/recover_internal_tandem_duplication.o source/filter_min_support.o source/recover_known_fusions.o source/recover_both_spliced.o source/filter_blacklisted_ranges.o source/filter_end_to_end.o source/filter_in_vitro.o source/merge_adjacent_fusions.o source/select_best.o source/filter_marginal_read_through.o source/filter_short_anchor.o source/filter_no_coverage.o source/filter_homologs.o source/filter_mismappers.o source/recover_many_spliced.o source/filter_genomic_support.o source/recover_isoforms.o source/annotate_tags.o source/annotate_protein_domains.o source/output_fusions.o source/read_compressed_file.o -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -ldl -lhts -ldeflate -lz -lbz2 -llzma -lm + /opt/conda/conda-bld/arriba_1735034454847/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -llzma: No such file or directory + collect2: error: ld returned 1 exit status + make[1]: *** [Makefile:17: arriba] Error 1 + make[1]: Leaving directory '$SRC_DIR' + make: *** [Makefile:13: bioconda] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/arriba_1735034454847/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/arriba_1735034454847/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/arriba/build_failure.linux-aarch64.yaml b/recipes/arriba/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..568947a9a61a7 --- /dev/null +++ b/recipes/arriba/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c4bcdfa938383de1e9b4274f21dc4f583881117f4bac7e5415252a0fca3fbcf5 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arriba-2.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arriba-2.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-g + make -j 4 'CPPFLAGS=-I/opt/conda/conda-bld/arriba_1735342585836/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include -I/opt/conda/conda-bld/arriba_1735342585836/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include/htslib' 'LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/arriba_1735342585836/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -Wl,-rpath-link,/opt/conda/conda-bld/arriba_1735342585836/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -L/opt/conda/conda-bld/arriba_1735342585836/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' CXX=/opt/conda/conda-bld/arriba_1735342585836/_build_env/bin/aarch64-conda-linux-gnu-c bioconda + make LIBS_SO="-ldl -lhts -ldeflate -lz -lbz2 -llzma -lm" arriba + make[1]: Entering directory '$SRC_DIR' + $BUILD_PREFIX/bin/wget --no-check-certificate -O - 'https://github.com/Tessil/hat-trie/archive/v0.6.0.tar.gz' | tar -xzf - -C libraries && \ + cp -r libraries/hat-trie-*/include/tsl libraries + --2024-12-27 23:38:10-- https://github.com/Tessil/hat-trie/archive/v0.6.0.tar.gz + Resolving github.com (github.com)... 140.82.114.4 + Connecting to github.com (github.com)|140.82.114.4|:443... connected. + HTTP request sent, awaiting response... 302 Found + Location: https://codeload.github.com/Tessil/hat-trie/tar.gz/refs/tags/v0.6.0 [following] + --2024-12-27 23:38:10-- https://codeload.github.com/Tessil/hat-trie/tar.gz/refs/tags/v0.6.0 + Resolving codeload.github.com (codeload.github.com)... 140.82.113.9 + Connecting to codeload.github.com (codeload.github.com)|140.82.113.9|:443... connected. + HTTP request sent, awaiting response... 200 OK + Length: unspecified [application/x-gzip] + Saving to: 'STDOUT' + + - [<=> ] 0 --.-KB/s - [ <=> ] 77.75K --.-KB/s in 0.003s + + 2024-12-27 23:38:10 (26.0 MB/s) - written to stdout [79611] + + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/annotation.o source/annotation.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/assembly.o source/assembly.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/options.o source/options.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/read_chimeric_alignments.o source/read_chimeric_alignments.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_duplicates.o source/filter_duplicates.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_uninteresting_contigs.o source/filter_uninteresting_contigs.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_viral_contigs.o source/filter_viral_contigs.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_top_expressed_viral_contigs.o source/filter_top_expressed_viral_contigs.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_low_coverage_viral_contigs.o source/filter_low_coverage_viral_contigs.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_inconsistently_clipped.o source/filter_inconsistently_clipped.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_homopolymer.o source/filter_homopolymer.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/read_stats.o source/read_stats.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/fusions.o source/fusions.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_proximal_read_through.o source/filter_proximal_read_through.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_same_gene.o source/filter_same_gene.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_small_insert_size.o source/filter_small_insert_size.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_long_gap.o source/filter_long_gap.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_hairpin.o source/filter_hairpin.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_multimappers.o source/filter_multimappers.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_mismatches.o source/filter_mismatches.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_low_entropy.o source/filter_low_entropy.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_relative_support.o source/filter_relative_support.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_both_intronic.o source/filter_both_intronic.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_non_coding_neighbors.o source/filter_non_coding_neighbors.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_intragenic_both_exonic.o source/filter_intragenic_both_exonic.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/recover_internal_tandem_duplication.o source/recover_internal_tandem_duplication.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_min_support.o source/filter_min_support.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/recover_known_fusions.o source/recover_known_fusions.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/recover_both_spliced.o source/recover_both_spliced.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_blacklisted_ranges.o source/filter_blacklisted_ranges.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_end_to_end.o source/filter_end_to_end.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_in_vitro.o source/filter_in_vitro.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/merge_adjacent_fusions.o source/merge_adjacent_fusions.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/select_best.o source/select_best.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_marginal_read_through.o source/filter_marginal_read_through.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_short_anchor.o source/filter_short_anchor.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_no_coverage.o source/filter_no_coverage.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_homologs.o source/filter_homologs.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_mismappers.o source/filter_mismappers.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/recover_many_spliced.o source/recover_many_spliced.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_genomic_support.o source/filter_genomic_support.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/recover_isoforms.o source/recover_isoforms.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/annotate_tags.o source/annotate_tags.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/annotate_protein_domains.o source/annotate_protein_domains.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/output_fusions.o source/output_fusions.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/read_compressed_file.o source/read_compressed_file.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Isource -Ilibraries/htslib -Ilibraries/tsl -o arriba source/arriba.cpp source/annotation.o source/assembly.o source/options.o source/read_chimeric_alignments.o source/filter_duplicates.o source/filter_uninteresting_contigs.o source/filter_viral_contigs.o source/filter_top_expressed_viral_contigs.o source/filter_low_coverage_viral_contigs.o source/filter_inconsistently_clipped.o source/filter_homopolymer.o source/read_stats.o source/fusions.o source/filter_proximal_read_through.o source/filter_same_gene.o source/filter_small_insert_size.o source/filter_long_gap.o source/filter_hairpin.o source/filter_multimappers.o source/filter_mismatches.o source/filter_low_entropy.o source/filter_relative_support.o source/filter_both_intronic.o source/filter_non_coding_neighbors.o source/filter_intragenic_both_exonic.o source/recover_internal_tandem_duplication.o source/filter_min_support.o source/recover_known_fusions.o source/recover_both_spliced.o source/filter_blacklisted_ranges.o source/filter_end_to_end.o source/filter_in_vitro.o source/merge_adjacent_fusions.o source/select_best.o source/filter_marginal_read_through.o source/filter_short_anchor.o source/filter_no_coverage.o source/filter_homologs.o source/filter_mismappers.o source/recover_many_spliced.o source/filter_genomic_support.o source/recover_isoforms.o source/annotate_tags.o source/annotate_protein_domains.o source/output_fusions.o source/read_compressed_file.o -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -ldl -lhts -ldeflate -lz -lbz2 -llzma -lm + /opt/conda/conda-bld/arriba_1735342585836/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: cannot find -llzma: No such file or directory + collect2: error: ld returned 1 exit status + make[1]: *** [Makefile:17: arriba] Error 1 + make[1]: Leaving directory '$SRC_DIR' + make: *** [Makefile:13: bioconda] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/arriba_1735342585836/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/arriba_1735342585836/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/arriba/build_failure.osx-64.yaml b/recipes/arriba/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..43e09561f32c9 --- /dev/null +++ b/recipes/arriba/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c4bcdfa938383de1e9b4274f21dc4f583881117f4bac7e5415252a0fca3fbcf5 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arriba-2.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arriba-2.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arriba-2.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/arriba-2.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + make LIBS_SO="-ldl -lhts -ldeflate -lz -lbz2 -llzma -lm" arriba + make[1]: Entering directory '$SRC_DIR' + $BUILD_PREFIX/bin/wget --no-check-certificate -O - 'https://github.com/Tessil/hat-trie/archive/v0.6.0.tar.gz' | tar -xzf - -C libraries && \ + cp -r libraries/hat-trie-*/include/tsl libraries + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/annotation.o source/annotation.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/assembly.o source/assembly.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/options.o source/options.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/read_chimeric_alignments.o source/read_chimeric_alignments.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_duplicates.o source/filter_duplicates.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_uninteresting_contigs.o source/filter_uninteresting_contigs.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_viral_contigs.o source/filter_viral_contigs.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_top_expressed_viral_contigs.o source/filter_top_expressed_viral_contigs.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_low_coverage_viral_contigs.o source/filter_low_coverage_viral_contigs.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_inconsistently_clipped.o source/filter_inconsistently_clipped.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_homopolymer.o source/filter_homopolymer.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/read_stats.o source/read_stats.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/fusions.o source/fusions.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_proximal_read_through.o source/filter_proximal_read_through.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_same_gene.o source/filter_same_gene.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_small_insert_size.o source/filter_small_insert_size.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_long_gap.o source/filter_long_gap.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_hairpin.o source/filter_hairpin.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_multimappers.o source/filter_multimappers.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_mismatches.o source/filter_mismatches.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_low_entropy.o source/filter_low_entropy.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_relative_support.o source/filter_relative_support.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_both_intronic.o source/filter_both_intronic.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_non_coding_neighbors.o source/filter_non_coding_neighbors.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_intragenic_both_exonic.o source/filter_intragenic_both_exonic.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/recover_internal_tandem_duplication.o source/recover_internal_tandem_duplication.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_min_support.o source/filter_min_support.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/recover_known_fusions.o source/recover_known_fusions.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/recover_both_spliced.o source/recover_both_spliced.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_blacklisted_ranges.o source/filter_blacklisted_ranges.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_end_to_end.o source/filter_end_to_end.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_in_vitro.o source/filter_in_vitro.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/merge_adjacent_fusions.o source/merge_adjacent_fusions.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/select_best.o source/select_best.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_marginal_read_through.o source/filter_marginal_read_through.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_short_anchor.o source/filter_short_anchor.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_no_coverage.o source/filter_no_coverage.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_homologs.o source/filter_homologs.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_mismappers.o source/filter_mismappers.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/recover_many_spliced.o source/recover_many_spliced.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/filter_genomic_support.o source/filter_genomic_support.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/recover_isoforms.o source/recover_isoforms.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/annotate_tags.o source/annotate_tags.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/annotate_protein_domains.o source/annotate_protein_domains.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/output_fusions.o source/output_fusions.cpp + x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Ilibraries/htslib -Ilibraries/tsl -o source/read_compressed_file.o source/read_compressed_file.cpp + x86_64-apple-darwin13.4.0-clang -Wall -Wno-parentheses -pthread -std=c0x -O2 -I$PREFIX/include -I$PREFIX/include/htslib -Isource -Ilibraries/htslib -Ilibraries/tsl -o arriba source/arriba.cpp source/annotation.o source/assembly.o source/options.o source/read_chimeric_alignments.o source/filter_duplicates.o source/filter_uninteresting_contigs.o source/filter_viral_contigs.o source/filter_top_expressed_viral_contigs.o source/filter_low_coverage_viral_contigs.o source/filter_inconsistently_clipped.o source/filter_homopolymer.o source/read_stats.o source/fusions.o source/filter_proximal_read_through.o source/filter_same_gene.o source/filter_small_insert_size.o source/filter_long_gap.o source/filter_hairpin.o source/filter_multimappers.o source/filter_mismatches.o source/filter_low_entropy.o source/filter_relative_support.o source/filter_both_intronic.o source/filter_non_coding_neighbors.o source/filter_intragenic_both_exonic.o source/recover_internal_tandem_duplication.o source/filter_min_support.o source/recover_known_fusions.o source/recover_both_spliced.o source/filter_blacklisted_ranges.o source/filter_end_to_end.o source/filter_in_vitro.o source/merge_adjacent_fusions.o source/select_best.o source/filter_marginal_read_through.o source/filter_short_anchor.o source/filter_no_coverage.o source/filter_homologs.o source/filter_mismappers.o source/recover_many_spliced.o source/filter_genomic_support.o source/recover_isoforms.o source/annotate_tags.o source/annotate_protein_domains.o source/output_fusions.o source/read_compressed_file.o -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -ldl -lhts -ldeflate -lz -lbz2 -llzma -lm + make[1]: Leaving directory '$SRC_DIR' +# Last 100 lines of the build log. diff --git a/recipes/arriba/meta.yaml b/recipes/arriba/meta.yaml index 126939ca54892..27b8c9b5ec406 100644 --- a/recipes/arriba/meta.yaml +++ b/recipes/arriba/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage('arriba', max_pin="x") }} diff --git a/recipes/art/meta.yaml b/recipes/art/meta.yaml index 84123e4e38846..8a272a0dc70bf 100644 --- a/recipes/art/meta.yaml +++ b/recipes/art/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 12 + number: 13 run_exports: - {{ pin_subpackage(name, max_pin=None) }} diff --git a/recipes/artic-porechop/meta.yaml b/recipes/artic-porechop/meta.yaml index 14c8c5cefb6f0..54eb500a717d1 100644 --- a/recipes/artic-porechop/meta.yaml +++ b/recipes/artic-porechop/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 6 + number: 7 skip: True # [py27] entry_points: - porechop = porechop.porechop:main diff --git a/recipes/artic-tools/build_failure.linux-64.yaml b/recipes/artic-tools/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..5730b9cd2c056 --- /dev/null +++ b/recipes/artic-tools/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 08d589a4ee57a9a07d0a936669b29d4fb0c7fe39285d74ae0f2d4ad11fdf9801 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:21:30: error: 'i' was not declared in this scope + 21 | for (uint32_t i = 0; i < seqLen; i) + | ^ + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:25:13: error: 'uint8_t' was not declared in this scope + 25 | uint8_t base = (uint8_t)seq[i] < 128 ? nt2char[static_cast(seq[i])] : 4; + | ^~~~~~~ + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:25:13: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:28:17: error: 'base' was not declared in this scope + 28 | if (base > 3) + | ^~~~ + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:32:33: error: 'base' was not declared in this scope + 32 | x[0] = (x[0] << 2 | base) & kmerMask; + | ^~~~ + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:32:41: error: 'kmerMask' was not declared in this scope; did you mean 'kmers'? + 32 | x[0] = (x[0] << 2 | base) & kmerMask; + | ^~~~~~~~ + | kmers + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:33:59: error: 'bitShift' was not declared in this scope + 33 | x[1] = x[1] >> 2 | (uint64_t)(3ULL - base) << bitShift; + | ^~~~~~~~ + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:36:19: error: 'l' was not declared in this scope + 36 | if (l >= kSize) + | ^ + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:37:40: error: request for member 'emplace_back' in 'kmers', which is of non-class type 'artic::kmerset_t' {aka 'int'} + 37 | (x[0] <= x[1]) ? kmers.emplace_back(x[0]) : kmers.emplace_back(x[1]); + | ^~~~~~~~~~~~ + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:37:67: error: request for member 'emplace_back' in 'kmers', which is of non-class type 'artic::kmerset_t' {aka 'int'} + 37 | (x[0] <= x[1]) ? kmers.emplace_back(x[0]) : kmers.emplace_back(x[1]); + | ^~~~~~~~~~~~ + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:10:38: warning: unused parameter 'seq' [-Wunused-parameter] + 10 | void GetEncodedKmers(const char* seq, uint32_t seqLen, uint32_t kSize, kmerset_t& kmers) + | ~~~~~~~~~~~~^~~ + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp: At global scope: + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:43:5: error: 'kmer_t' does not name a type; did you mean 'timer_t'? + 43 | kmer_t GetRCencoding(kmer_t encodedKmer, uint32_t kSize) + | ^~~~~~ + | timer_t + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:55:10: error: variable or field 'DecodeKmer' declared void + 55 | void DecodeKmer(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^~~~~~~~~~ + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:55:21: error: 'kmer_t' was not declared in this scope; did you mean 'timer_t'? + 55 | void DecodeKmer(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^~~~~~ + | timer_t + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:55:41: error: 'uint32_t' was not declared in this scope + 55 | void DecodeKmer(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^~~~~~~~ + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:55:41: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:55:68: error: expected primary-expression before '&' token + 55 | void DecodeKmer(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^ + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:55:70: error: 'decodedKmer' was not declared in this scope; did you mean 'GetEncodedKmers'? + 55 | void DecodeKmer(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^~~~~~~~~~~ + | GetEncodedKmers + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:70:10: error: variable or field 'DecodeKmer_rc' declared void + 70 | void DecodeKmer_rc(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:70:24: error: 'kmer_t' was not declared in this scope; did you mean 'timer_t'? + 70 | void DecodeKmer_rc(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^~~~~~ + | timer_t + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:70:44: error: 'uint32_t' was not declared in this scope + 70 | void DecodeKmer_rc(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^~~~~~~~ + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:70:44: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:70:71: error: expected primary-expression before '&' token + 70 | void DecodeKmer_rc(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^ + /opt/conda/conda-bld/artic-tools_1734277767281/work/artic/kmers.cpp:70:73: error: 'decodedKmer' was not declared in this scope; did you mean 'GetEncodedKmers'? + 70 | void DecodeKmer_rc(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^~~~~~~~~~~ + | GetEncodedKmers + make[2]: *** [artic/CMakeFiles/artic_static.dir/build.make:107: artic/CMakeFiles/artic_static.dir/kmers.cpp.o] Error 1 + make[2]: *** Waiting for unfinished jobs.... + make[1]: *** [CMakeFiles/Makefile2:1342: artic/CMakeFiles/artic_static.dir/all] Error 2 + make: *** [Makefile:166: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/artic-tools_1734277767281/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/artic-tools_1734277767281/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/artic-tools/build_failure.linux-aarch64.yaml b/recipes/artic-tools/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..0087ed1fbafd3 --- /dev/null +++ b/recipes/artic-tools/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 08d589a4ee57a9a07d0a936669b29d4fb0c7fe39285d74ae0f2d4ad11fdf9801 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:21:30: error: 'i' was not declared in this scope + 21 | for (uint32_t i = 0; i < seqLen; i) + | ^ + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:25:13: error: 'uint8_t' was not declared in this scope + 25 | uint8_t base = (uint8_t)seq[i] < 128 ? nt2char[static_cast(seq[i])] : 4; + | ^~~~~~~ + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:25:13: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:28:17: error: 'base' was not declared in this scope + 28 | if (base > 3) + | ^~~~ + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:32:33: error: 'base' was not declared in this scope + 32 | x[0] = (x[0] << 2 | base) & kmerMask; + | ^~~~ + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:32:41: error: 'kmerMask' was not declared in this scope; did you mean 'kmers'? + 32 | x[0] = (x[0] << 2 | base) & kmerMask; + | ^~~~~~~~ + | kmers + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:33:59: error: 'bitShift' was not declared in this scope + 33 | x[1] = x[1] >> 2 | (uint64_t)(3ULL - base) << bitShift; + | ^~~~~~~~ + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:36:19: error: 'l' was not declared in this scope + 36 | if (l >= kSize) + | ^ + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:37:40: error: request for member 'emplace_back' in 'kmers', which is of non-class type 'artic::kmerset_t' {aka 'int'} + 37 | (x[0] <= x[1]) ? kmers.emplace_back(x[0]) : kmers.emplace_back(x[1]); + | ^~~~~~~~~~~~ + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:37:67: error: request for member 'emplace_back' in 'kmers', which is of non-class type 'artic::kmerset_t' {aka 'int'} + 37 | (x[0] <= x[1]) ? kmers.emplace_back(x[0]) : kmers.emplace_back(x[1]); + | ^~~~~~~~~~~~ + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:10:38: warning: unused parameter 'seq' [-Wunused-parameter] + 10 | void GetEncodedKmers(const char* seq, uint32_t seqLen, uint32_t kSize, kmerset_t& kmers) + | ~~~~~~~~~~~~^~~ + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp: At global scope: + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:43:5: error: 'kmer_t' does not name a type; did you mean 'timer_t'? + 43 | kmer_t GetRCencoding(kmer_t encodedKmer, uint32_t kSize) + | ^~~~~~ + | timer_t + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:55:10: error: variable or field 'DecodeKmer' declared void + 55 | void DecodeKmer(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^~~~~~~~~~ + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:55:21: error: 'kmer_t' was not declared in this scope; did you mean 'timer_t'? + 55 | void DecodeKmer(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^~~~~~ + | timer_t + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:55:41: error: 'uint32_t' was not declared in this scope + 55 | void DecodeKmer(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^~~~~~~~ + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:55:41: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:55:68: error: expected primary-expression before '&' token + 55 | void DecodeKmer(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^ + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:55:70: error: 'decodedKmer' was not declared in this scope; did you mean 'GetEncodedKmers'? + 55 | void DecodeKmer(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^~~~~~~~~~~ + | GetEncodedKmers + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:70:10: error: variable or field 'DecodeKmer_rc' declared void + 70 | void DecodeKmer_rc(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:70:24: error: 'kmer_t' was not declared in this scope; did you mean 'timer_t'? + 70 | void DecodeKmer_rc(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^~~~~~ + | timer_t + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:70:44: error: 'uint32_t' was not declared in this scope + 70 | void DecodeKmer_rc(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^~~~~~~~ + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:70:44: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:70:71: error: expected primary-expression before '&' token + 70 | void DecodeKmer_rc(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^ + /opt/conda/conda-bld/artic-tools_1734364875168/work/artic/kmers.cpp:70:73: error: 'decodedKmer' was not declared in this scope; did you mean 'GetEncodedKmers'? + 70 | void DecodeKmer_rc(kmer_t encodedKmer, uint32_t kSize, std::string& decodedKmer) + | ^~~~~~~~~~~ + | GetEncodedKmers + make[2]: *** [artic/CMakeFiles/artic_static.dir/build.make:107: artic/CMakeFiles/artic_static.dir/kmers.cpp.o] Error 1 + make[2]: *** Waiting for unfinished jobs.... + make[1]: *** [CMakeFiles/Makefile2:1342: artic/CMakeFiles/artic_static.dir/all] Error 2 + make: *** [Makefile:166: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/artic-tools_1734364875168/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/artic-tools_1734364875168/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/artic-tools/meta.yaml b/recipes/artic-tools/meta.yaml index 931a621ad0ae8..520e643dd2f46 100644 --- a/recipes/artic-tools/meta.yaml +++ b/recipes/artic-tools/meta.yaml @@ -27,7 +27,7 @@ source: build: skip: True # [osx] - number: 7 + number: 8 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/ascat/meta.yaml b/recipes/ascat/meta.yaml index 227ee1e9efa68..423331bddcd27 100644 --- a/recipes/ascat/meta.yaml +++ b/recipes/ascat/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/asgal/meta.yaml b/recipes/asgal/meta.yaml index 8791ec36c1548..95b3272ed1894 100644 --- a/recipes/asgal/meta.yaml +++ b/recipes/asgal/meta.yaml @@ -15,7 +15,7 @@ source: - galig.formatSAM.patch build: - number: 1 + number: 2 skip: True # [osx] requirements: diff --git a/recipes/assembly-stats/build_failure.osx-64.yaml b/recipes/assembly-stats/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..ab67e6176c667 --- /dev/null +++ b/recipes/assembly-stats/build_failure.osx-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: 451a18d20c15fd6308d14d27734b055a3c87b5a2b3f72fd3f016961c6b035670 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/assembly-stats-1.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/assembly-stats-1.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -- The C compiler identification is Clang 18.1.8 + -- The CXX compiler identification is Clang 18.1.8 + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped + -- Detecting C compile features + -- Detecting C compile features - done + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Found PythonInterp: /opt/mambaforge/envs/bioconda/bin/python (found version "3.10.16") + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success + -- Found Threads: TRUE + -- Configuring done (2.3s) + -- Generating done (0.1s) + -- Build files have been written to: $SRC_DIR/build + [ 5%] Building CXX object gtest-1.7.0/CMakeFiles/gtest.dir/src/gtest-all.cc.o + [ 10%] Linking CXX static library libgtest.a + [ 10%] Built target gtest + [ 15%] Building CXX object gtest-1.7.0/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o + [ 21%] Linking CXX static library libgtest_main.a + [ 21%] Built target gtest_main + [ 26%] Building CXX object CMakeFiles/fasta.dir/fasta.cpp.o + [ 31%] Linking CXX static library libfasta.a + [ 31%] Built target fasta + [ 36%] Building CXX object CMakeFiles/fastq.dir/fastq.cpp.o + [ 42%] Linking CXX static library libfastq.a + [ 42%] Built target fastq + [ 47%] Building CXX object CMakeFiles/filetype.dir/filetype.cpp.o + [ 52%] Linking CXX static library libfiletype.a + [ 52%] Built target filetype + [ 57%] Building CXX object CMakeFiles/stats.dir/stats.cpp.o + [ 63%] Linking CXX static library libstats.a + [ 63%] Built target stats + [ 68%] Building CXX object CMakeFiles/runUnitTests.dir/fasta_unittest.cpp.o + [ 73%] Building CXX object CMakeFiles/runUnitTests.dir/fastq_unittest.cpp.o + [ 78%] Building CXX object CMakeFiles/runUnitTests.dir/filetype_unittest.cpp.o + [ 84%] Building CXX object CMakeFiles/runUnitTests.dir/stats_unittest.cpp.o + [ 89%] Linking CXX executable runUnitTests + [ 89%] Built target runUnitTests + [ 94%] Building CXX object CMakeFiles/assembly-stats.dir/assembly-stats.cpp.o + [100%] Linking CXX executable assembly-stats + [100%] Built target assembly-stats + + Resource usage statistics from building assembly-stats: + Process count: 8 + CPU time: Sys=0:00:01.0, User=0:00:10.1 + Memory: 140.3M + Disk usage: 18.3K + Time elapsed: 0:00:31.9 + + + Packaging assembly-stats + Packaging assembly-stats-1.0.1-h5fa12a8_9 + number of files: 1 + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2765, in build + newly_built_packages = bundlers[pkg_type]( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1874, in bundle_conda + files = post_process_files(metadata, initial_files) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1653, in post_process_files + post_build(m, new_files, build_python=python) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1759, in post_build + post_process_shared_lib(m, f, prefix_files, host_prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1635, in post_process_shared_lib + mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 488, in mk_relative_osx + existing_rpaths = macho.get_rpaths(path, build_prefix=prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 252, in get_rpaths + dylib_loads = otool(path, build_prefix, is_rpath) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 221, in otool + lines = check_output([otool, "-l", path], stderr=STDOUT).decode("utf-8") + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 421, in check_output + return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 526, in run + raise CalledProcessError(retcode, process.args, + subprocess.CalledProcessError: Command '['/opt/mambaforge/envs/bioconda/conda-bld/assembly-stats_1734455441579/_build_env/bin/llvm-otool', '-l', '/opt/mambaforge/envs/bioconda/conda-bld/assembly-stats_1734455441579/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/assembly-stats']' died with . +# Last 100 lines of the build log. +reason: |- + see https://github.com/conda/conda-build/issues/5429 +category: |- + conda/mamba bug diff --git a/recipes/assembly-stats/meta.yaml b/recipes/assembly-stats/meta.yaml index 9513521d7e277..046ea9c52fd02 100644 --- a/recipes/assembly-stats/meta.yaml +++ b/recipes/assembly-stats/meta.yaml @@ -12,7 +12,7 @@ source: - 0001-Fix-macOS-compilation.patch build: - number: 8 + number: 9 run_exports: - {{ pin_subpackage("assembly-stats", max_pin="x") }} diff --git a/recipes/assemblyutility/meta.yaml b/recipes/assemblyutility/meta.yaml index 845d86df5c252..95c580156fec4 100644 --- a/recipes/assemblyutility/meta.yaml +++ b/recipes/assemblyutility/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 7 + number: 8 source: url: https://github.com/yechengxi/AssemblyUtility/archive/8e476764eb67ebb486e673ecbd8a0fa5d8eae22c.tar.gz diff --git a/recipes/aster/meta.yaml b/recipes/aster/meta.yaml index 6d7dce2306868..9ae9c4cce7c45 100644 --- a/recipes/aster/meta.yaml +++ b/recipes/aster/meta.yaml @@ -7,7 +7,7 @@ package: version: "{{ version }}" build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('aster', max_pin="x") }} diff --git a/recipes/atac/meta.yaml b/recipes/atac/meta.yaml index 461a57b0f11a1..27f81d9df1ff4 100644 --- a/recipes/atac/meta.yaml +++ b/recipes/atac/meta.yaml @@ -9,7 +9,7 @@ source: md5: e23ef1d41836b29332b70271b7c9eb74 build: - number: 6 + number: 7 run_exports: - {{ pin_subpackage("atac", max_pin=None) }} diff --git a/recipes/ataqv/meta.yaml b/recipes/ataqv/meta.yaml index 58f8c7bb4ecaf..debc32d95b1db 100644 --- a/recipes/ataqv/meta.yaml +++ b/recipes/ataqv/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -52,4 +52,4 @@ about: extra: additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 diff --git a/recipes/atlas/meta.yaml b/recipes/atlas/meta.yaml index fdf92201097e6..e0e60dc311917 100644 --- a/recipes/atlas/meta.yaml +++ b/recipes/atlas/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 017235049dddfac88fedf16bfc444cf38aed25ac84df084dc555736b5d48d6a3 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("atlas", max_pin="x") }} diff --git a/recipes/atropos/meta.yaml b/recipes/atropos/meta.yaml index 3465bbd568dd6..792e46e5d7f27 100644 --- a/recipes/atropos/meta.yaml +++ b/recipes/atropos/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 # Ensure Cython is rerun by removing *.c output files and PKG-INFO (checked for by setup.py) script: find . "(" -name "*.c" -o -name PKG-INFO ")" -exec rm {} ";" && {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv run_exports: @@ -23,6 +23,7 @@ requirements: host: - python - pip + - setuptools - cython >=0.25.2 run: - python diff --git a/recipes/augustus/3.3.3/build_failure.linux-64.yaml b/recipes/augustus/3.3.3/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..72bafec99c94c --- /dev/null +++ b/recipes/augustus/3.3.3/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 1f27a21b2f4143d04dce0a1774e00273fd66de8d5a0d68a49a2cb9b8ec1b07a7 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + '[' Linux = Darwin ']' + sqlite=SQLITE=true + make CC=/opt/conda/conda-bld/augustus_1734294070029/_build_env/bin/x86_64-conda-linux-gnu-cc CXX=/opt/conda/conda-bld/augustus_1734294070029/_build_env/bin/x86_64-conda-linux-gnu-c BAMTOOLS_CC=/opt/conda/conda-bld/augustus_1734294070029/_build_env/bin/x86_64-conda-linux-gnu-cc BAMTOOLS_CXX=/opt/conda/conda-bld/augustus_1734294070029/_build_env/bin/x86_64-conda-linux-gnu-c BAMTOOLS=/opt/conda/conda-bld/augustus_1734294070029/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac COMPGENPRED=true SQLITE=true + mkdir -p bin + cd src && make + make[1]: Entering directory '$SRC_DIR/src' + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o genbank.o genbank.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o properties.o properties.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o pp_profile.o pp_profile.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o pp_hitseq.o pp_hitseq.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o pp_scoring.o pp_scoring.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o statemodel.o statemodel.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o namgene.o namgene.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o types.o types.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o gene.o gene.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o evaluation.o evaluation.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o motif.o motif.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o geneticcode.o geneticcode.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o hints.o hints.cc -I../include -I$PREFIX/include/lpsolve + hints.cc: In function 'std::istream& operator>>(std::istream&, Feature&)': + hints.cc:82:16: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation] + 82 | strncpy(copybuff, buff, 1014); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o extrinsicinfo.o extrinsicinfo.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o projectio.o projectio.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o intronmodel.o intronmodel.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o exonmodel.o exonmodel.cc -I../include -I$PREFIX/include/lpsolve + exonmodel.cc: In static member function 'static void ExonModel::readAllParameters()': + exonmodel.cc:671:28: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] + 671 | sprintf(zusString, "[%d]", idx1); + | ^~ + exonmodel.cc:671:26: note: directive argument in the range [1, 2147483647] + 671 | sprintf(zusString, "[%d]", idx1); + | ^~~~~~ + exonmodel.cc:671:14: note: 'sprintf' output between 4 and 13 bytes into a destination of size 6 + 671 | sprintf(zusString, "[%d]", idx1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o igenicmodel.o igenicmodel.cc -I../include -I$PREFIX/include/lpsolve + igenicmodel.cc: In static member function 'static void IGenicModel::readAllParameters()': + igenicmodel.cc:162:32: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] + 162 | sprintf(zusString, "[%d]", idx1); + | ^~ + igenicmodel.cc:162:30: note: directive argument in the range [1, 2147483647] + 162 | sprintf(zusString, "[%d]", idx1); + | ^~~~~~ + igenicmodel.cc:162:18: note: 'sprintf' output between 4 and 13 bytes into a destination of size 6 + 162 | sprintf(zusString, "[%d]", idx1); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o utrmodel.o utrmodel.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o merkmal.o merkmal.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o vitmatrix.o vitmatrix.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o lldouble.o lldouble.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o mea.o mea.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o graph.o graph.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o meaPath.o meaPath.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o exoncand.o exoncand.cc -I../include -I$PREFIX/include/lpsolve + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -std=c11 -DCOMPGENEPRED -DSQLITE -o randseqaccess.o randseqaccess.cc -I../include -I$PREFIX/include/lpsolve + In file included from ../include/randseqaccess.hh:25, + from randseqaccess.cc:10: + ../include/sqliteDB.hh:93:29: error: 'uint64_t' has not been declared + 93 | void bindInt64(int idx, uint64_t x); + | ^~~~~~~~ + ../include/sqliteDB.hh:102:12: error: 'uint64_t' does not name a type + 102 | inline uint64_t int64Column(int colNum){return (uint64_t)sqlite3_column_int64(stmt,colNum);} + | ^~~~~~~~ + ../include/sqliteDB.hh:14:1: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + 13 | #include + |#include + 14 | + randseqaccess.cc: In member function 'virtual AnnoSequence* SQLiteAccess::getSeq(std::string, std::string, int, int, Strand)': + randseqaccess.cc:772:47: error: 'class Statement' has no member named 'int64Column'; did you mean 'intColumn'? + 772 | file_start = (std::streampos)stmt.int64Column(2); + | ^~~~~~~~~~~ + | intColumn + make[1]: *** [Makefile:72: randseqaccess.o] Error 1 + make[1]: Leaving directory '$SRC_DIR/src' + make: *** [Makefile:8: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/augustus_1734294070029/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/augustus_1734294070029/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/augustus/3.3.3/build_failure.osx-64.yaml b/recipes/augustus/3.3.3/build_failure.osx-64.yaml index 7d8410da8f38d..8f6b1c3d21240 100644 --- a/recipes/augustus/3.3.3/build_failure.osx-64.yaml +++ b/recipes/augustus/3.3.3/build_failure.osx-64.yaml @@ -1,105 +1,106 @@ -recipe_sha: be13d36eb1c14158ca987c33153650e289a0b64ea14456830f65ae7c8cb58b9b # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 1f27a21b2f4143d04dce0a1774e00273fd66de8d5a0d68a49a2cb9b8ec1b07a7 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: compiler error -log: |- - ../src/Coord_Transform.cpp:77:7: error: use of undeclared identifier 'bind2nd' - bind2nd(finding_intron_greater_s(), i)); - ^ - ../src/Coord_Transform.cpp:81:7: error: use of undeclared identifier 'bind2nd' - bind2nd(finding_intron_greater_e(), i)); - ^ - ../src/Coord_Transform.cpp:89:7: error: use of undeclared identifier 'bind2nd' - bind2nd(finding_intron_lesser_e(), i)); - ^ - ../src/Coord_Transform.cpp:93:7: error: use of undeclared identifier 'bind2nd' - bind2nd(finding_intron_lesser_s(), i)); - ^ - 8 errors generated. - make[2]: *** [src/subdir.mk:41: src/Coord_Transform.o] Error 1 - make[1]: *** [Makefile:13: all] Error 2 - make: *** [Makefile:9: all] Error 2 +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("libzlib[version='>=1.3.1,<2.0a0']"), MatchSpec("libsqlite==3.47.2=hdb6dae5_0")} + Encountered problems while solving: + - package libsqlite-3.47.2-hdb6dae5_0 requires libzlib >=1.3.1,<2.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + cdbtools is installable with the potential options + cdbtools 0.99 would require + zlib >=1.2.11,<1.3.0a0 , which can be installed; + cdbtools 0.99 would require + zlib >=1.2.13,<1.3.0a0 , which can be installed; + cdbtools 0.99 would require + libzlib >=1.2.13,<1.3.0a0 , which can be installed; + libsqlite >=3.47.2,<4.0a0 is not installable because it requires + libzlib >=1.3.1,<2.0a0 but there are no viable options + libzlib 1.3.1 would require + zlib 1.3.1 *_0, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_1, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_2, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + Traceback (most recent call last): File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -Wall -O2 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -c bam2hints.cc -o bam2hints.o -I$PREFIX/include/bamtools - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -Wall -O2 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o bam2hints bam2hints.o -L$PREFIX/lib/ -lbamtools -lz - mkdir -p ../../bin - cp bam2hints ../../bin - make[2]: Leaving directory '$SRC_DIR/auxprogs/bam2hints' - cd compileSpliceCands; make; + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - make[2]: Entering directory '$SRC_DIR/auxprogs/compileSpliceCands' - x86_64-apple-darwin13.4.0-clang -Wall -pedantic -ansi -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c compileSpliceCands.c + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o list.o list.c - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - x86_64-apple-darwin13.4.0-clang -o compileSpliceCands compileSpliceCands.o list.o; - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/augustus_1718124280585/work/conda_build.sh']' returned non-zero exit status 2. - cp compileSpliceCands ../../bin/compileSpliceCands - make[2]: Leaving directory '$SRC_DIR/auxprogs/compileSpliceCands' - cd filterBam; make; - make[2]: Entering directory '$SRC_DIR/auxprogs/filterBam' - (cd src;make) - make[3]: Entering directory '$SRC_DIR/auxprogs/filterBam/src' - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -Wall -O2 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c filterBam.cc -o filterBam.o -I$PREFIX/include/bamtools -Iheaders -I./bamtools - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -Wall -O2 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c functions/MatePairs.cc -o MatePairs.o -I$PREFIX/include/bamtools -Iheaders -I./bamtools - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -Wall -O2 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c functions/getReferenceName.cc -o getReferenceName.o -I$PREFIX/include/bamtools -Iheaders -I./bamtools - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -Wall -O2 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c functions/initOptions.cc -o initOptions.o -I$PREFIX/include/bamtools -Iheaders -I./bamtools - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -Wall -O2 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c functions/SingleAlignment.cc -o SingleAlignment.o -I$PREFIX/include/bamtools -Iheaders -I./bamtools - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -Wall -O2 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c functions/printElapsedTime.cc -o printElapsedTime.o -I$PREFIX/include/bamtools -Iheaders -I./bamtools - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -Wall -O2 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c functions/sumMandIOperations.cc -o sumMandIOperations.o -I$PREFIX/include/bamtools -Iheaders -I./bamtools - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -Wall -O2 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c functions/sumDandIOperations.cc -o sumDandIOperations.o -I$PREFIX/include/bamtools -Iheaders -I./bamtools - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -Wall -O2 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c functions/PairednessCoverage.cc -o PairednessCoverage.o -I$PREFIX/include/bamtools -Iheaders -I./bamtools - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -Wall -O2 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -L$PREFIX/lib/ -lbamtools -lz - filterBam compiled with BAMTOOLS=$PREFIX - mv filterBam ../../../bin/filterBam - make[3]: Leaving directory '$SRC_DIR/auxprogs/filterBam/src' - make[2]: Leaving directory '$SRC_DIR/auxprogs/filterBam' - cd homGeneMapping; make; - make[2]: Entering directory '$SRC_DIR/auxprogs/homGeneMapping' - (cd src; make) - make[3]: Entering directory '$SRC_DIR/auxprogs/homGeneMapping/src' - x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-sign-compare -ansi -pedantic -std=c0x -pthread -O2 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o gene.o gene.cc -I../include -I$PREFIX/include - x86_64-apple-darwin13.4.0-clang -c -Wall -Wno-sign-compare -ansi -pedantic -std=c0x -pthread -O2 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o genome.o genome.cc -I../include -I$PREFIX/include - x86_64-apple-darwin13.4.0-clang -Wall -Wno-sign-compare -ansi -pedantic -std=c0x -pthread -O2 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -o homGeneMapping main.cc gene.o genome.o -I../include -I$PREFIX/include - mkdir -p ../../../bin/ - cp homGeneMapping ../../../bin/homGeneMapping - make[3]: Leaving directory '$SRC_DIR/auxprogs/homGeneMapping/src' - make[2]: Leaving directory '$SRC_DIR/auxprogs/homGeneMapping' - cd joingenes; make; - make[2]: Entering directory '$SRC_DIR/auxprogs/joingenes' - x86_64-apple-darwin13.4.0-clang -c -Wall -std=gnu0x -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib joingenes.cpp - x86_64-apple-darwin13.4.0-clang -c -Wall -std=gnu0x -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib jg_transcript.cpp - x86_64-apple-darwin13.4.0-clang -c -Wall -std=gnu0x -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib jg_ios.cpp - x86_64-apple-darwin13.4.0-clang -Wall -std=gnu0x -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -DUSE_BOOST -I$PREFIX/include/bamtools -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib joingenes.o jg_transcript.o jg_ios.o -o joingenes - cp joingenes ../../bin/ - make[2]: Leaving directory '$SRC_DIR/auxprogs/joingenes' - cd bam2wig; make; - make[2]: Entering directory '$SRC_DIR/auxprogs/bam2wig' - x86_64-apple-darwin13.4.0-clang -Wall -O2 -I$PREFIX/include/samtools -I. -I$PREFIX/include/bam -I$PREFIX/include -c bam2wig.c -o bam2wig.o - x86_64-apple-darwin13.4.0-clang -Wall -O2 -I$PREFIX/include/samtools -I. -I$PREFIX/include/bam -I$PREFIX/include bam2wig.o -o bam2wig -lbam -lhts -lncurses -lm -lz -lpthread -lcurl -lbz2 -llzma -L$PREFIX/lib/ - mkdir -p ../../bin - cp bam2wig ../../bin/bam2wig - make[2]: Leaving directory '$SRC_DIR/auxprogs/bam2wig' - cd utrrnaseq/Debug; make all; - make[2]: Entering directory '$SRC_DIR/auxprogs/utrrnaseq/Debug' - Building file: ../src/Compute_UTRs.cpp - Invoking: GCC C Compiler - x86_64-apple-darwin13.4.0-clang -I$PREFIX/include -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Compute_UTRs.d" -MT"src/Compute_UTRs.o" -o "src/Compute_UTRs.o" "../src/Compute_UTRs.cpp" - Finished building: ../src/Compute_UTRs.cpp + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("libzlib[version='>=1.3.1,<2.0a0']"), MatchSpec("libsqlite==3.47.2=hdb6dae5_0")} + Encountered problems while solving: + - package libsqlite-3.47.2-hdb6dae5_0 requires libzlib >=1.3.1,<2.0a0, but none of the providers can be installed - Building file: ../src/Coord_Transform.cpp - Invoking: GCC C Compiler - x86_64-apple-darwin13.4.0-clang -I$PREFIX/include -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Coord_Transform.d" -MT"src/Coord_Transform.o" -o "src/Coord_Transform.o" "../src/Coord_Transform.cpp" - make[2]: Leaving directory '$SRC_DIR/auxprogs/utrrnaseq/Debug' - make[1]: Leaving directory '$SRC_DIR/auxprogs' + Could not solve for environment specs + The following packages are incompatible + cdbtools is installable with the potential options + cdbtools 0.99 would require + zlib >=1.2.11,<1.3.0a0 , which can be installed; + cdbtools 0.99 would require + zlib >=1.2.13,<1.3.0a0 , which can be installed; + cdbtools 0.99 would require + libzlib >=1.2.13,<1.3.0a0 , which can be installed; + libsqlite >=3.47.2,<4.0a0 is not installable because it requires + libzlib >=1.3.1,<2.0a0 but there are no viable options + libzlib 1.3.1 would require + zlib 1.3.1 *_0, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_1, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_2, which conflicts with any installable versions previously reported. # Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/augustus/3.3.3/meta.yaml b/recipes/augustus/3.3.3/meta.yaml index b8348d67a24f7..cfa9093c2eeda 100644 --- a/recipes/augustus/3.3.3/meta.yaml +++ b/recipes/augustus/3.3.3/meta.yaml @@ -22,7 +22,7 @@ source: - patches/src.makefile.patch build: - number: 13 + number: 14 requirements: build: diff --git a/recipes/augustus/build_failure.linux-64.yaml b/recipes/augustus/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..a21b680f013bd --- /dev/null +++ b/recipes/augustus/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 91ece91f678ab0b9d08ad8813609b1a7376faa5ad75d16389d6c4d7996b14482 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -DUSE_BOOST -I$PREFIX/include -I../include -I$PREFIX/include/lpsolve -c -o compgenepred.o compgenepred.cc + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -DUSE_BOOST -I$PREFIX/include -I../include -I$PREFIX/include/lpsolve -c -o phylotree.o phylotree.cc + In file included from /opt/conda/conda-bld/augustus_1734294352918/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/x86_64-conda-linux-gnu/bits/callocator.h:33, + from /opt/conda/conda-bld/augustus_1734294352918/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/allocator.h:46, + from /opt/conda/conda-bld/augustus_1734294352918/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/string:43, + from /opt/conda/conda-bld/augustus_1734294352918/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/locale_classes.h:40, + from /opt/conda/conda-bld/augustus_1734294352918/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/ios_base.h:41, + from /opt/conda/conda-bld/augustus_1734294352918/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/ios:44, + from /opt/conda/conda-bld/augustus_1734294352918/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/istream:40, + from /opt/conda/conda-bld/augustus_1734294352918/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/sstream:40, + from ../include/lldouble.hh:13, + from ../include/types.hh:12, + from ../include/alignment.hh:11, + from ../include/genomicMSA.hh:11, + from genomicMSA.cc:10: + In member function 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = boost::list_edge >; _Args = {const boost::list_edge >&}; _Tp = std::_List_node > >]', + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = boost::list_edge >; _Args = {const boost::list_edge >&}; _Tp = std::_List_node > >]' at /opt/conda/conda-bld/augustus_1734294352918/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/alloc_traits.h:538:17, + inlined from 'std::__cxx11::list<_Tp, _Alloc>::_Node* std::__cxx11::list<_Tp, _Alloc>::_M_create_node(_Args&& ...) [with _Args = {const boost::list_edge >&}; _Tp = boost::list_edge >; _Alloc = std::allocator > >]' at /opt/conda/conda-bld/augustus_1734294352918/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_list.h:713:33, + inlined from 'void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const boost::list_edge >&}; _Tp = boost::list_edge >; _Alloc = std::allocator > >]' at /opt/conda/conda-bld/augustus_1734294352918/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_list.h:2005:32, + inlined from 'void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = boost::list_edge >; _Alloc = std::allocator > >]' at /opt/conda/conda-bld/augustus_1734294352918/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_list.h:1306:24, + inlined from 'std::pair boost::graph_detail::push_dispatch(Container&, T&&, back_insertion_sequence_tag) [with Container = std::__cxx11::list >, std::allocator > > >; T = boost::list_edge >&]' at /opt/conda/conda-bld/augustus_1734294352918/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/boost/pending/container_traits.hpp:574:20, + inlined from 'std::pair boost::graph_detail::push(Container&, T&&) [with Container = std::__cxx11::list >, std::allocator > > >; T = boost::list_edge >&]' at /opt/conda/conda-bld/augustus_1734294352918/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/boost/pending/container_traits.hpp:606:29, + inlined from 'std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, bidirectional_graph_helper_with_property&) [with Config = detail::adj_list_gen, AliGraph>, vecS, setS, bidirectionalS, AliNode, property, AliGraph, listS>::config]' at /opt/conda/conda-bld/augustus_1734294352918/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/boost/graph/detail/adjacency_list.hpp:1498:29, + inlined from 'std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, const typename Config::edge_property_type&, vec_adj_list_impl&) [with Graph = adjacency_list, AliGraph>; Config = detail::adj_list_gen, AliGraph>, vecS, setS, bidirectionalS, AliNode, property, AliGraph, listS>::config; Base = bidirectional_graph_helper_with_property, AliGraph>, vecS, setS, bidirectionalS, AliNode, property, AliGraph, listS>::config>]' at /opt/conda/conda-bld/augustus_1734294352918/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/boost/graph/detail/adjacency_list.hpp:2263:20, + inlined from 'std::pair boost::add_edge(typename Config::vertex_descriptor, typename Config::vertex_descriptor, vec_adj_list_impl&) [with Graph = adjacency_list, AliGraph>; Config = detail::adj_list_gen, AliGraph>, vecS, setS, bidirectionalS, AliNode, property, AliGraph, listS>::config; Base = bidirectional_graph_helper_with_property, AliGraph>, vecS, setS, bidirectionalS, AliNode, property, AliGraph, listS>::config>]' at /opt/conda/conda-bld/augustus_1734294352918/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/boost/graph/detail/adjacency_list.hpp:2271:20, + inlined from 'void GenomicMSA::findGeneRanges()' at genomicMSA.cc:469:17: + /opt/conda/conda-bld/augustus_1734294352918/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/new_allocator.h:191:11: warning: 'p.boost::property::m_base.AliEdge::weight' may be used uninitialized [-Wmaybe-uninitialized] + 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + In file included from /opt/conda/conda-bld/augustus_1734294352918/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/boost/graph/adjacency_list.hpp:255, + from ../include/genomicMSA.hh:15: + /opt/conda/conda-bld/augustus_1734294352918/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/boost/graph/detail/adjacency_list.hpp: In member function 'void GenomicMSA::findGeneRanges()': + /opt/conda/conda-bld/augustus_1734294352918/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/boost/graph/detail/adjacency_list.hpp:2270:41: note: 'p.boost::property::m_base.AliEdge::weight' was declared here + 2270 | typename Config::edge_property_type p; + | ^ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -DUSE_BOOST -I$PREFIX/include -I../include -I$PREFIX/include/lpsolve -c -o orthograph.o orthograph.cc + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -DUSE_BOOST -I$PREFIX/include -I../include -I$PREFIX/include/lpsolve -c -o orthoexon.o orthoexon.cc + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -DUSE_BOOST -I$PREFIX/include -I../include -I$PREFIX/include/lpsolve -c -o alignment.o alignment.cc + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -DUSE_BOOST -I$PREFIX/include -I../include -I$PREFIX/include/lpsolve -c -o speciesgraph.o speciesgraph.cc + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -DUSE_BOOST -I$PREFIX/include -I../include -I$PREFIX/include/lpsolve -c -o codonMSA.o codonMSA.cc + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -DUSE_BOOST -I$PREFIX/include -I../include -I$PREFIX/include/lpsolve -c -o train_logReg_param.o train_logReg_param.cc + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -DUSE_BOOST -I$PREFIX/include -I../include -I$PREFIX/include/lpsolve -c -o tokenizer.o tokenizer.cc + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -DUSE_BOOST -I$PREFIX/include -I../include -I$PREFIX/include/lpsolve -c -o sqliteDB.o sqliteDB.cc + train_logReg_param.cc: In function 'void sgd(std::vector > >*, gsl_vector*, int)': + train_logReg_param.cc:490:18: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >*, vector > > >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] + 490 | random_shuffle ( samples->begin(), samples->end() ); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + In file included from /opt/conda/conda-bld/augustus_1734294352918/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/regex:52, + from train_logReg_param.cc:14: + /opt/conda/conda-bld/augustus_1734294352918/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:4581:5: note: declared here + 4581 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) + | ^~~~~~~~~~~~~~ + In file included from sqliteDB.cc:10: + ../include/sqliteDB.hh:93:29: error: 'uint64_t' has not been declared + 93 | void bindInt64(int idx, uint64_t x); + | ^~~~~~~~ + ../include/sqliteDB.hh:102:12: error: 'uint64_t' does not name a type + 102 | inline uint64_t int64Column(int colNum){return (uint64_t)sqlite3_column_int64(stmt,colNum);} + | ^~~~~~~~ + ../include/sqliteDB.hh:14:1: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + 13 | #include + |#include + 14 | + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c11 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/augustus-3.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -DUSE_BOOST -I$PREFIX/include -I../include -I$PREFIX/include/lpsolve -c -o commontrain.o commontrain.cc + sqliteDB.cc:210:6: error: no declaration matches 'void Statement::bindInt64(int, uint64_t)' + 210 | void Statement::bindInt64(int idx, uint64_t x){ + | ^~~~~~~~~ + ../include/sqliteDB.hh:93:10: note: candidate is: 'void Statement::bindInt64(int, int)' + 93 | void bindInt64(int idx, uint64_t x); + | ^~~~~~~~~ + ../include/sqliteDB.hh:83:7: note: 'class Statement' defined here + 83 | class Statement + | ^~~~~~~~~ + make[1]: *** [Makefile:85: sqliteDB.o] Error 1 + make[1]: *** Waiting for unfinished jobs.... + make[1]: Leaving directory '$SRC_DIR/src' + make: *** [Makefile:12: augustus] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/augustus_1734294352918/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/augustus_1734294352918/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/augustus/build_failure.osx-64.yaml b/recipes/augustus/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..14b433e190281 --- /dev/null +++ b/recipes/augustus/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 91ece91f678ab0b9d08ad8813609b1a7376faa5ad75d16389d6c4d7996b14482 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("libzlib[version='>=1.3.1,<2.0a0']"), MatchSpec("libsqlite==3.47.2=hdb6dae5_0")} + Encountered problems while solving: + - package libsqlite-3.47.2-hdb6dae5_0 requires libzlib >=1.3.1,<2.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + cdbtools is installable with the potential options + cdbtools 0.99 would require + zlib >=1.2.11,<1.3.0a0 , which can be installed; + cdbtools 0.99 would require + zlib >=1.2.13,<1.3.0a0 , which can be installed; + cdbtools 0.99 would require + libzlib >=1.2.13,<1.3.0a0 , which can be installed; + libsqlite >=3.47.2,<4.0a0 is not installable because it requires + libzlib >=1.3.1,<2.0a0 but there are no viable options + libzlib 1.3.1 would require + zlib 1.3.1 *_0, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_1, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_2, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("libzlib[version='>=1.3.1,<2.0a0']"), MatchSpec("libsqlite==3.47.2=hdb6dae5_0")} + Encountered problems while solving: + - package libsqlite-3.47.2-hdb6dae5_0 requires libzlib >=1.3.1,<2.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + cdbtools is installable with the potential options + cdbtools 0.99 would require + zlib >=1.2.11,<1.3.0a0 , which can be installed; + cdbtools 0.99 would require + zlib >=1.2.13,<1.3.0a0 , which can be installed; + cdbtools 0.99 would require + libzlib >=1.2.13,<1.3.0a0 , which can be installed; + libsqlite >=3.47.2,<4.0a0 is not installable because it requires + libzlib >=1.3.1,<2.0a0 but there are no viable options + libzlib 1.3.1 would require + zlib 1.3.1 *_0, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_1, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_2, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/augustus/meta.yaml b/recipes/augustus/meta.yaml index 6eec34c826555..3d4343a2204d0 100644 --- a/recipes/augustus/meta.yaml +++ b/recipes/augustus/meta.yaml @@ -15,7 +15,7 @@ source: - patches/utrrnaseq.patch build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('augustus', max_pin="x") }} diff --git a/recipes/auspice/meta.yaml b/recipes/auspice/meta.yaml index f9d27847244f7..0f74ded437694 100644 --- a/recipes/auspice/meta.yaml +++ b/recipes/auspice/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 828bc00e27ca3d403332686ab041dd3171c999a1a942b9fe89ba8256daedfecc build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/autodock/build_failure.osx-64.yaml b/recipes/autodock/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..94d59645d2d01 --- /dev/null +++ b/recipes/autodock/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 8199b7f13211047a7763a031a7dddd2dc20129839e537a6e504c8cfbbcfcf855 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/autodock-4.2.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/autodock-4.2.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + $SRC_DIR/autodock $SRC_DIR + checking for a BSD-compatible install... /usr/bin/install -c + checking whether build environment is sane... yes + checking for a thread-safe mkdir -p... ./install-sh -c -d + checking for gawk... no + checking for mawk... no + checking for nawk... no + checking for awk... awk + checking whether make sets $(MAKE)... yes + checking for gawk... (cached) awk + checking whether the C compiler works... yes + checking for C compiler default output file name... a.out + checking for suffix of executables... + checking whether we are cross compiling... no + checking for suffix of object files... o + checking whether we are using the GNU C compiler... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking for style of include used by make... GNU + checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 + checking for x86_64-apple-darwin13.4.0-ranlib... x86_64-apple-darwin13.4.0-ranlib + checking build system type... x86_64-apple-darwin13.4.0 + checking host system type... x86_64-apple-darwin13.4.0 + checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang + checking whether we are using the GNU C compiler... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking for x86_64-apple-darwin13.4.0-clang option to accept ISO C89... none needed + checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 + checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang-cpp + checking for grep that handles long lines and -e... /usr/bin/grep + checking for egrep... /usr/bin/grep -E + checking for ANSI C header files... yes + checking for sys/types.h... yes + checking for sys/stat.h... yes + checking for stdlib.h... yes + checking for string.h... yes + checking for memory.h... yes + checking for strings.h... yes + checking for inttypes.h... yes + checking for stdint.h... yes + checking for unistd.h... yes + checking for stdbool.h that conforms to C99... yes + checking for _Bool... yes + checking for an ANSI C-conforming const... yes + checking for inline... inline + checking for size_t... yes + checking whether struct tm is in sys/time.h or time.h... time.h + checking for stdlib.h... (cached) yes + checking for GNU libc compatible malloc... (cached) yes + checking for gethostname... yes + checking for getpid... yes + checking for GetProcessId... no + checking for fchmod... yes + checking for setlinebuf... yes + checking for sysconf... yes + checking for times... yes + checking for getrusage... yes + checking for pow... yes + checking for sqrt... yes + checking for strncasecmp... yes + checking whether we are using the GNU C compiler... (cached) yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... (cached) yes + checking dependency style of x86_64-apple-darwin13.4.0-clang... (cached) gcc3 + checking for x86_64-apple-darwin13.4.0-clang option to support OpenMP... -fopenmp + checking that generated files are newer than configure... done + configure: creating ./config.status + config.status: creating Makefile + config.status: executing depfiles commands + rm -f default_parameters.h + csh ./paramdat2h.csh ./AD4_parameters.dat ./AD4.1_bound.dat > default_parameters.h + make all-am + make[1]: Entering directory '$SRC_DIR/autodock' + x86_64-apple-darwin13.4.0-clang -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.2.6\" -DPACKAGE_STRING=\"autodock\ 4.2.6\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autodock\" -DVERSION=\"4.2.6\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -DNOSQRT -DUSE_DOUBLE -DUSE_8A_NBCUTOFF -DUSE_INT_AS_FOURBYTELONG -O3 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wall -Wno-write-strings -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/autodock-4.2.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT autodock4-main.o -MD -MP -MF .deps/autodock4-main.Tpo -c -o autodock4-main.o test -f 'main.cc' || echo './'main.cc + make[1]: Leaving directory '$SRC_DIR/autodock' +# Last 100 lines of the build log. diff --git a/recipes/autodock/meta.yaml b/recipes/autodock/meta.yaml index b1e82ef22a3c2..5f7f78e621615 100644 --- a/recipes/autodock/meta.yaml +++ b/recipes/autodock/meta.yaml @@ -6,7 +6,7 @@ package: build: version: {{ version }} - number: 3 + number: 4 source: url: https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/autodocksuite-{{ version }}-src.tar.gz diff --git a/recipes/autogrid/build_failure.osx-64.yaml b/recipes/autogrid/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..76431bcbf53b1 --- /dev/null +++ b/recipes/autogrid/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: ff3af9b5c7fc880242cba9c0c3178908829133a22060a78d7d728ac194576c39 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/autogrid-4.2.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/autogrid-4.2.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + $SRC_DIR/autogrid $SRC_DIR + checking for a BSD-compatible install... /usr/bin/install -c + checking whether build environment is sane... yes + checking for a thread-safe mkdir -p... ./install-sh -c -d + checking for gawk... no + checking for mawk... no + checking for nawk... no + checking for awk... awk + checking whether make sets $(MAKE)... yes + checking whether the C compiler works... yes + checking for C compiler default output file name... a.out + checking for suffix of executables... + checking whether we are cross compiling... no + checking for suffix of object files... o + checking whether we are using the GNU C compiler... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking for style of include used by make... GNU + checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 + checking build system type... x86_64-apple-darwin13.4.0 + checking host system type... x86_64-apple-darwin13.4.0 + checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang + checking whether we are using the GNU C compiler... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking for x86_64-apple-darwin13.4.0-clang option to accept ISO C89... none needed + checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 + checking for sqrt in -lm... yes + checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang-cpp + checking for grep that handles long lines and -e... /usr/bin/grep + checking for egrep... /usr/bin/grep -E + checking for ANSI C header files... yes + checking for sys/types.h... yes + checking for sys/stat.h... yes + checking for stdlib.h... yes + checking for string.h... yes + checking for memory.h... yes + checking for strings.h... yes + checking for inttypes.h... yes + checking for stdint.h... yes + checking for unistd.h... yes + checking for stdbool.h that conforms to C99... yes + checking for _Bool... yes + checking for an ANSI C-conforming const... yes + checking whether struct tm is in sys/time.h or time.h... time.h + checking for stdlib.h... (cached) yes + checking for GNU libc compatible malloc... (cached) yes + checking for gethostname... yes + checking for getpid... yes + checking for GetProcessId... no + checking for fchmod... yes + checking for setlinebuf... yes + checking for sysconf... yes + checking for times... yes + checking for getrusage... yes + checking for pow... yes + checking for sqrt... yes + checking for strncasecmp... yes + checking that generated files are newer than configure... done + configure: creating ./config.status + config.status: creating Makefile + config.status: executing depfiles commands + rm -f default_parameters.h + csh ./../autodock/paramdat2h.csh ./../autodock/AD4_parameters.dat ./../autodock/AD4.1_bound.dat > default_parameters.h + sh ./copyfilesfromAD + make all-am + make[1]: Entering directory '$SRC_DIR/autogrid' + x86_64-apple-darwin13.4.0-clang -DPACKAGE_NAME=\"autogrid\" -DPACKAGE_TARNAME=\"autogrid\" -DPACKAGE_VERSION=\"4.2.6\" -DPACKAGE_STRING=\"autogrid\ 4.2.6\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE_URL=\"\" -DPACKAGE=\"autogrid\" -DVERSION=\"4.2.6\" -DHAVE_LIBM=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPID=1 -DHAVE_FCHMOD=1 -DHAVE_SETLINEBUF=1 -DHAVE_SYSCONF=1 -DHAVE_TIMES=1 -DHAVE_GETRUSAGE=1 -DHAVE_POW=1 -DHAVE_SQRT=1 -DHAVE_STRNCASECMP=1 -I. -Wall -O3 -I . -I./../autodock -Wno-write-strings -DUSE_8A_NBCUTOFF -DUSE_DOUBLE -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/autogrid-4.2.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT autogrid4-main.o -MD -MP -MF .deps/autogrid4-main.Tpo -c -o autogrid4-main.o test -f 'main.cpp' || echo './'main.cpp + make[1]: Leaving directory '$SRC_DIR/autogrid' +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/autogrid/meta.yaml b/recipes/autogrid/meta.yaml index fc06551e99220..a1292beb2e445 100644 --- a/recipes/autogrid/meta.yaml +++ b/recipes/autogrid/meta.yaml @@ -6,7 +6,8 @@ package: build: version: {{ version }} - number: 3 + number: 4 + run_exports: '{{ pin_subpackage("autogrid", max_pin="x") }}' source: url: https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/autodocksuite-{{ version }}-src.tar.gz diff --git a/recipes/bali-phy/meta.yaml b/recipes/bali-phy/meta.yaml index 99cc303ea2098..3702961e9537e 100644 --- a/recipes/bali-phy/meta.yaml +++ b/recipes/bali-phy/meta.yaml @@ -7,7 +7,7 @@ source: sha256: f7819b0f68043abbadc3df19adc9a590d0bab6c2fbbf4ddb0feeb44165796c03 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('bali-phy', max_pin='x') }} diff --git a/recipes/balrog/build_failure.osx-64.yaml b/recipes/balrog/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..bb0d673bc8764 --- /dev/null +++ b/recipes/balrog/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5fb41089f54652976358a1c05552ff12bd0a02d5071c4b51ba393987d0a882ad # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/balrog_1733861115484/work/conda_build.sh']' returned non-zero exit status 2. + - zlib 1.3.1 hd23fc13_2 + run: + - libzlib >=1.3.1,<2.0a0 + - zlib + - scipy + - libcxx >=14.0.6 + - llvm-openmp >=18.1.8 + - llvm-openmp >=19.1.5 + test: + commands: + - balrog --help + about: + home: https://github.com/Markusjsommer/BalrogCPP + license: MIT + license_file: LICENSE + summary: 'Balrog: A universal protein model for prokaryotic gene prediction' + extra: + additional-platforms: + - linux-aarch64 + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/balrog_1733861115484/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/balrog_1733861115484/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/balrog_1733861115484/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/balrog_1733861115484/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/balrog-0.5.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/balrog-0.5.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/balrog-0.5.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/balrog-0.5.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -- The C compiler identification is Clang 14.0.6 + -- The CXX compiler identification is Clang 14.0.6 + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped + -- Detecting C compile features + -- Detecting C compile features - done + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Found ZLIB: $PREFIX/lib/libz.dylib (found version "1.3.1") + -- Configuring done (2.4s) + -- Generating done (0.0s) + -- Build files have been written to: $SRC_DIR/build + [ 15%] Generating cmakeresources resource loader + [ 15%] Generating intermediate file for $SRC_DIR/data/TIS_model_v1.0.pt + [ 23%] Generating intermediate file for $SRC_DIR/data/gene_model_v1.0.pt + [ 30%] Generating intermediate file for $SRC_DIR/data/reference_genes.fasta + [ 46%] Building CXX object CMakeFiles/cmakeresources.dir/__cmrc_cmakeresources/intermediate/gene_model_v1.0.pt.cpp.o + [ 46%] Building CXX object CMakeFiles/cmakeresources.dir/__cmrc_cmakeresources/lib.cpp.o +# Last 100 lines of the build log. diff --git a/recipes/balrog/meta.yaml b/recipes/balrog/meta.yaml index b9157d536a298..1dab1f5fa8266 100644 --- a/recipes/balrog/meta.yaml +++ b/recipes/balrog/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage("balrog", max_pin="x.x") }} @@ -40,4 +40,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/bam-readcount/build_failure.linux-64.yaml b/recipes/bam-readcount/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..ccfc5a2c3c29a --- /dev/null +++ b/recipes/bam-readcount/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 7912943d91e9bbca70cf5329534ead53618ac3d3c42509ec94f6ec5160db4c94 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + -- extracting... + src='$SRC_DIR/vendor/boost-1.55-bamrc.tar.gz' + dst='$SRC_DIR/build/vendor/boost-src' + -- extracting... [tar xfz] + -- extracting... [analysis] + -- extracting... [rename] + -- extracting... [clean up] + -- extracting... done + [ 14%] No update step for 'boost-1.55' + [ 16%] No patch step for 'boost-1.55' + [ 17%] Performing configure step for 'boost-1.55' + + Could not find a suitable toolset. + + You can specify the toolset as the argument, i.e.: + ./build.sh [options] gcc + + Toolsets supported by this script are: + acc, clang, como, gcc, intel-darwin, intel-linux, kcc, kylix, mipspro, + pathscale, pgi, qcc, sun, sunpro, tru64cxx, vacpp + + For any toolset you can override the path to the compiler with the '--cxx' + option. You can also use additional flags for the compiler with the + '--cxxflags' option. + + A special toolset; cxx, is available which is used as a fallback when a more + specific toolset is not found and the cxx command is detected. The 'cxx' + toolset will use the '--cxx' and '--cxxflags' options, if present. + + Options: + --help Show this help message. + --verbose Show messages about what this script is doing. + --debug Build b2 with debug information, and no + optimizations. + --guess-toolset Print the toolset we can detect for building. + --cxx=CXX The compiler exec to use instead of the detected + compiler exec. + --cxxflags=CXXFLAGS The compiler flags to use in addition to the + flags for the detected compiler. + + + Building B2 engine.. + + Could not find a suitable toolset. + + You can specify the toolset as the argument, i.e.: + ./build.sh [options] gcc + + Toolsets supported by this script are: + acc, clang, como, gcc, intel-darwin, intel-linux, kcc, kylix, mipspro, + pathscale, pgi, qcc, sun, sunpro, tru64cxx, vacpp + + For any toolset you can override the path to the compiler with the '--cxx' + option. You can also use additional flags for the compiler with the + '--cxxflags' option. + + A special toolset; cxx, is available which is used as a fallback when a more + specific toolset is not found and the cxx command is detected. The 'cxx' + toolset will use the '--cxx' and '--cxxflags' options, if present. + + Options: + --help Show this help message. + --verbose Show messages about what this script is doing. + --debug Build b2 with debug information, and no + optimizations. + --guess-toolset Print the toolset we can detect for building. + --cxx=CXX The compiler exec to use instead of the detected + compiler exec. + --cxxflags=CXXFLAGS The compiler flags to use in addition to the + flags for the detected compiler. + + + + Failed to build B2 build engine + make[2]: *** [CMakeFiles/boost-1.55.dir/build.make:92: vendor/src/boost-1.55-stamp/boost-1.55-configure] Error 1 + make[1]: *** [CMakeFiles/Makefile2:264: CMakeFiles/boost-1.55.dir/all] Error 2 + make: *** [Makefile:166: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bam-readcount_1734293648433/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bam-readcount_1734293648433/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/bam-readcount/build_failure.linux-aarch64.yaml b/recipes/bam-readcount/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..fa7e5a78880b6 --- /dev/null +++ b/recipes/bam-readcount/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 7912943d91e9bbca70cf5329534ead53618ac3d3c42509ec94f6ec5160db4c94 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + -- extracting... + src='$SRC_DIR/vendor/boost-1.55-bamrc.tar.gz' + dst='$SRC_DIR/build/vendor/boost-src' + -- extracting... [tar xfz] + -- extracting... [analysis] + -- extracting... [rename] + -- extracting... [clean up] + -- extracting... done + [ 14%] No update step for 'boost-1.55' + [ 16%] No patch step for 'boost-1.55' + [ 17%] Performing configure step for 'boost-1.55' + + Could not find a suitable toolset. + + You can specify the toolset as the argument, i.e.: + ./build.sh [options] gcc + + Toolsets supported by this script are: + acc, clang, como, gcc, intel-darwin, intel-linux, kcc, kylix, mipspro, + pathscale, pgi, qcc, sun, sunpro, tru64cxx, vacpp + + For any toolset you can override the path to the compiler with the '--cxx' + option. You can also use additional flags for the compiler with the + '--cxxflags' option. + + A special toolset; cxx, is available which is used as a fallback when a more + specific toolset is not found and the cxx command is detected. The 'cxx' + toolset will use the '--cxx' and '--cxxflags' options, if present. + + Options: + --help Show this help message. + --verbose Show messages about what this script is doing. + --debug Build b2 with debug information, and no + optimizations. + --guess-toolset Print the toolset we can detect for building. + --cxx=CXX The compiler exec to use instead of the detected + compiler exec. + --cxxflags=CXXFLAGS The compiler flags to use in addition to the + flags for the detected compiler. + + + Building B2 engine.. + + Could not find a suitable toolset. + + You can specify the toolset as the argument, i.e.: + ./build.sh [options] gcc + + Toolsets supported by this script are: + acc, clang, como, gcc, intel-darwin, intel-linux, kcc, kylix, mipspro, + pathscale, pgi, qcc, sun, sunpro, tru64cxx, vacpp + + For any toolset you can override the path to the compiler with the '--cxx' + option. You can also use additional flags for the compiler with the + '--cxxflags' option. + + A special toolset; cxx, is available which is used as a fallback when a more + specific toolset is not found and the cxx command is detected. The 'cxx' + toolset will use the '--cxx' and '--cxxflags' options, if present. + + Options: + --help Show this help message. + --verbose Show messages about what this script is doing. + --debug Build b2 with debug information, and no + optimizations. + --guess-toolset Print the toolset we can detect for building. + --cxx=CXX The compiler exec to use instead of the detected + compiler exec. + --cxxflags=CXXFLAGS The compiler flags to use in addition to the + flags for the detected compiler. + + + + Failed to build B2 build engine + make[2]: *** [CMakeFiles/boost-1.55.dir/build.make:92: vendor/src/boost-1.55-stamp/boost-1.55-configure] Error 1 + make[1]: *** [CMakeFiles/Makefile2:264: CMakeFiles/boost-1.55.dir/all] Error 2 + make: *** [Makefile:166: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bam-readcount_1734270976436/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bam-readcount_1734270976436/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/bam-readcount/build_failure.osx-64.yaml b/recipes/bam-readcount/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..b8f031422fc24 --- /dev/null +++ b/recipes/bam-readcount/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 7912943d91e9bbca70cf5329534ead53618ac3d3c42509ec94f6ec5160db4c94 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [ 25%] Building CXX object CMakeFiles/gtest.dir/src/gtest-all.cc.o + [ 50%] Linking CXX static library libgtest.a + [ 50%] Built target gtest + [ 75%] Building CXX object CMakeFiles/gtest_main.dir/src/gtest_main.cc.o + [100%] Linking CXX static library libgtest_main.a + [100%] Built target gtest_main + [ 9%] No install step for 'gtest160' + [ 10%] Completed 'gtest160' + [ 10%] Built target gtest160 + [ 12%] Creating directories for 'boost-1.55' + [ 13%] Performing download step (verify and extract) for 'boost-1.55' + -- extracting... + src='$SRC_DIR/vendor/boost-1.55-bamrc.tar.gz' + dst='$SRC_DIR/build/vendor/boost-src' + -- extracting... [tar xfz] + -- extracting... [analysis] + -- extracting... [rename] + -- extracting... [clean up] + -- extracting... done + [ 14%] No update step for 'boost-1.55' + [ 16%] No patch step for 'boost-1.55' + [ 17%] Performing configure step for 'boost-1.55' + Building B2 engine.. + + ### + ### + ### Using 'clang' toolset. + ### + ### + + clang version 18.1.8 + Target: x86_64-apple-darwin22.6.0 + Thread model: posix + InstalledDir: $BUILD_PREFIX/bin + + ### + ### + + > clang -x c -std=c11 -O3 -s -Wno-deprecated-declarations -DNDEBUG bindjam.cpp builtins.cpp class.cpp command.cpp compile.cpp constants.cpp cwd.cpp debug.cpp debugger.cpp execcmd.cpp execnt.cpp execunix.cpp filent.cpp filesys.cpp fileunix.cpp frames.cpp function.cpp glob.cpp hash.cpp hcache.cpp hdrmacro.cpp headers.cpp jam_strings.cpp jam.cpp jamgram.cpp lists.cpp make.cpp make1.cpp md5.cpp mem.cpp modules.cpp native.cpp option.cpp output.cpp parse.cpp pathnt.cpp pathsys.cpp pathunix.cpp regexp.cpp rules.cpp scan.cpp search.cpp startup.cpp tasks.cpp timestamp.cpp value.cpp variable.cpp w32_getreg.cpp mod_jam_builtin.cpp mod_jam_class.cpp mod_jam_errors.cpp mod_jam_modules.cpp mod_order.cpp mod_path.cpp mod_property_set.cpp mod_regex.cpp mod_sequence.cpp mod_set.cpp mod_string.cpp mod_summary.cpp mod_sysinfo.cpp mod_version.cpp -o b2 + tools/build/src/engine/b2 + Detecting Python version... 3.10 + Detecting Python root... /opt/mambaforge/envs/bioconda + Unicode/ICU support for Boost.Regex?... not found. + Generating B2 configuration in project-config.jam for clang... + + Bootstrapping is done. To build, run: + + ./b2 + + To generate header files, run: + + ./b2 headers + + The configuration generated uses clang to build by default. If that is + unintended either use the --with-toolset option or adjust configuration, by + editing 'project-config.jam'. + + Further information: + + - Command line help: + ./b2 --help + + - Getting started guide: + http://www.boost.org/more/getting_started/unix-variants.html + + - B2 documentation: + http://www.boost.org/build/ + + [ 18%] Performing build step for 'boost-1.55' + Building boost, build log is $SRC_DIR/build/vendor/boost-src/build.log + [ 20%] Performing install step for 'boost-1.55' + [ 21%] Completed 'boost-1.55' + [ 21%] Built target boost-1.55 + [ 21%] Built target __bc_predepends + [ 22%] Creating directories for 'zlib' + [ 24%] Performing download step (verify and extract) for 'zlib' + -- extracting... + src='$SRC_DIR/vendor/zlib-1.2.11.tar.gz' + dst='$SRC_DIR/build/vendor/zlib-src' + -- extracting... [tar xfz] + -- extracting... [analysis] + -- extracting... [rename] + -- extracting... [clean up] + -- extracting... done + [ 25%] No update step for 'zlib' + [ 26%] No patch step for 'zlib' + [ 28%] Performing configure step for 'zlib' + Checking for shared library support... + Building shared library libz.1.2.11.dylib with x86_64-apple-darwin13.4.0-clang. + Checking for size_t... Yes. + Checking for off64_t... No. + Checking for fseeko... Yes. + Checking for strerror... Yes. + Checking for unistd.h... Yes. + Checking for stdarg.h... Yes. + Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf(). + Checking for vsnprintf() in stdio.h... Yes. + Checking for return value of vsnprintf()... Yes. + Checking for attribute(visibility) support... Yes. + [ 29%] Performing build step for 'zlib' +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/bam-readcount/meta.yaml b/recipes/bam-readcount/meta.yaml index fa49a617952da..4d553713e95bf 100644 --- a/recipes/bam-readcount/meta.yaml +++ b/recipes/bam-readcount/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 8ebf84d9efee0f2d3b43f0452dbf16b27337c960e25128f6a7173119e62588b8 build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('bam-readcount', max_pin="x") }} diff --git a/recipes/bambamc/meta.yaml b/recipes/bambamc/meta.yaml index 113f9b83fe42e..50903e5153653 100644 --- a/recipes/bambamc/meta.yaml +++ b/recipes/bambamc/meta.yaml @@ -7,7 +7,7 @@ source: md5: 4de1f030fab1de54387f68e4fbd2cd35 build: - number: 8 + number: 9 run_exports: - {{ pin_subpackage('bambamc', max_pin="x.x.x") }} diff --git a/recipes/bamcmp/meta.yaml b/recipes/bamcmp/meta.yaml index 6972f19620ab3..68cf108f8ef7f 100644 --- a/recipes/bamcmp/meta.yaml +++ b/recipes/bamcmp/meta.yaml @@ -7,7 +7,7 @@ source: md5: 05e583af007f86b275bcf95eceea7ba7 build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage("bamcmp", max_pin="x") }} script_env: diff --git a/recipes/bamhash/1.0/build_failure.osx-64.yaml b/recipes/bamhash/1.0/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c10d8e97bf7f7 --- /dev/null +++ b/recipes/bamhash/1.0/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 0bfbf30dc72ef0ed1b02d441d4825305207395badfdac7fff61481c1bb918bd2 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - libcxx-devel 18.1.8 h7c275be_7 + - libllvm18 18.1.8 h9ce406d_2 + - clang 18.1.8 default_h179603d_5 + - clangxx_osx-64 18.1.8 h7e5c614_23 + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + - make 4.4.1 h00291cd_2 + host: + - libcxx 19.1.5 hf95d169_0 + - ca-certificates 2024.8.30 h8857fd0_0 + - libzlib 1.3.1 hd23fc13_2 + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + - openssl 3.4.0 hd471939_0 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + - zlib 1.3.1 hd23fc13_2 + run: + - openssl >=3.4.0,<4.0a0 + - zlib + - libcxx >=18 + - libzlib >=1.3.1,<2.0a0 + test: + commands: + return build_tree( + - bamhash_checksum_bam --version + - bamhash_checksum_fastq --version + about: + home: https://github.com/DecodeGenetics/BamHash + license: GPL-3-0 + license_file: LICENSE + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + summary: Hash BAM and FASTQ files to verify data integrity + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/bamhash_1733952618101/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bamhash_1733952618101/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bamhash_1733952618101/_build_env + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bamhash_1733952618101/work/conda_build.sh']' returned non-zero exit status 2. + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/bamhash_1733952618101/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamhash-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamhash-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamhash-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamhash-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + x86_64-apple-darwin13.4.0-clang -I$PREFIX/include -I. -Wno-deprecated-declarations -O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 -DSEQAN_HAS_ZLIB=1 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o bamhash_checksum_common.o bamhash_checksum_common.cpp + x86_64-apple-darwin13.4.0-clang -I$PREFIX/include -I. -Wno-deprecated-declarations -O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 -DSEQAN_HAS_ZLIB=1 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o bamhash_checksum_bam.o bamhash_checksum_bam.cpp +# Last 100 lines of the build log. diff --git a/recipes/bamhash/1.0/meta.yaml b/recipes/bamhash/1.0/meta.yaml index 0d8ee636f7bc5..ec900fd6b0723 100644 --- a/recipes/bamhash/1.0/meta.yaml +++ b/recipes/bamhash/1.0/meta.yaml @@ -7,7 +7,7 @@ source: sha256: af1c939901afe8666ba300c66e9538d79bb48b5e9dd665f4bf575376d288189e build: - number: 7 + number: 8 requirements: build: diff --git a/recipes/bamhash/1.1/build_failure.osx-64.yaml b/recipes/bamhash/1.1/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..fb31b157b7ac3 --- /dev/null +++ b/recipes/bamhash/1.1/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 22dc5111bff023908bf7e8dcaec5db32e3ec9dbb003a4b07d2cdd032228ce2b1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - ca-certificates 2024.8.30 h8857fd0_0 + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bamhash_1733952277944/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + - clangxx_impl_osx-64 18.1.8 h4b7810f_23 + host: + - libcxx 19.1.5 hf95d169_0 + - ca-certificates 2024.8.30 h8857fd0_0 + - libzlib 1.3.1 hd23fc13_2 + - openssl 3.4.0 hd471939_0 + - zlib 1.3.1 hd23fc13_2 + run: + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + - libzlib >=1.3.1,<2.0a0 + - libcxx >=18 + - openssl >=3.4.0,<4.0a0 + - zlib + test: + commands: + - bamhash_checksum_bam --version + - bamhash_checksum_fastq --version + - bamhash_checksum_fasta --version + about: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + home: https://github.com/DecodeGenetics/BamHash + license: GPL-3-0 + license_file: LICENSE + summary: Hash BAM and FASTQ files to verify data integrity + extra: + copy_test_source_files: true + final: true + + + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/bamhash_1733952277944/work + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bamhash_1733952277944/work/conda_build.sh']' returned non-zero exit status 2. + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bamhash_1733952277944/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bamhash_1733952277944/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/bamhash_1733952277944/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamhash-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamhash-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamhash-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamhash-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + x86_64-apple-darwin13.4.0-clang -I$PREFIX/include -I. -Wno-deprecated-declarations -O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 -DSEQAN_HAS_ZLIB=1 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o bamhash_checksum_common.o bamhash_checksum_common.cpp + x86_64-apple-darwin13.4.0-clang -I$PREFIX/include -I. -Wno-deprecated-declarations -O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 -DSEQAN_HAS_ZLIB=1 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o bamhash_checksum_bam.o bamhash_checksum_bam.cpp +# Last 100 lines of the build log. diff --git a/recipes/bamhash/1.1/meta.yaml b/recipes/bamhash/1.1/meta.yaml index e5866f2488d26..8b5d9302a08dd 100644 --- a/recipes/bamhash/1.1/meta.yaml +++ b/recipes/bamhash/1.1/meta.yaml @@ -7,7 +7,7 @@ source: sha256: c1598f71c3662e199bd4853884082eecdd7f69099a3514476aee3485bb0c298c build: - number: 8 + number: 9 requirements: build: diff --git a/recipes/bamread/build_failure.osx-64.yaml b/recipes/bamread/build_failure.osx-64.yaml deleted file mode 100644 index 44897c6af34d3..0000000000000 --- a/recipes/bamread/build_failure.osx-64.yaml +++ /dev/null @@ -1,105 +0,0 @@ -recipe_sha: 8f26375d8b5482a572de19471f95b0c74d50dea5df302d8ab63ff1f5fd6927b9 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: compiler error -log: |2- - Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-711-ha20a434_0/bin/../lib/libtapi.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-711-ha20a434_0/bin/../lib/libtapi.dylib' (no such file), '/usr/local/lib/libtapi.dylib' (no such file), '/usr/lib/libtapi.dylib' (no such file, not in dyld cache) - clang-16: error: unable to execute command: Abort trap: 6 - clang-16: error: linker command failed due to signal (use -v to see invocation) - error: command '/opt/mambaforge/envs/bioconda/conda-bld/bamread_1718324170755/_build_env/bin/x86_64-apple-darwin13.4.0-clang' failed with exit code 1 - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/bamread_1718324170755/work - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bamread_1718324170755/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bamread_1718324170755/_build_env - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bamread_1718324170755/work/conda_build.sh']' returned non-zero exit status 1. - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/bamread_1718324170755/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamread-0.0.16 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamread-0.0.16 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - Compiling bamread/src/bamread.pyx because it changed. - [1/1] Cythonizing bamread/src/bamread.pyx - running install - running build - running build_py - creating build - creating build/lib.macosx-10.9-x86_64-cpython-312 - creating build/lib.macosx-10.9-x86_64-cpython-312/bamread - copying bamread/__init__.py -> build/lib.macosx-10.9-x86_64-cpython-312/bamread - copying bamread/read.py -> build/lib.macosx-10.9-x86_64-cpython-312/bamread - creating build/lib.macosx-10.9-x86_64-cpython-312/bamread/src - copying bamread/src/__init__.py -> build/lib.macosx-10.9-x86_64-cpython-312/bamread/src - running egg_info - writing bamread.egg-info/PKG-INFO - writing dependency_links to bamread.egg-info/dependency_links.txt - writing requirements to bamread.egg-info/requires.txt - writing top-level names to bamread.egg-info/top_level.txt - reading manifest file 'bamread.egg-info/SOURCES.txt' - writing manifest file 'bamread.egg-info/SOURCES.txt' - creating build/lib.macosx-10.9-x86_64-cpython-312/bin - copying bin/bamread -> build/lib.macosx-10.9-x86_64-cpython-312/bin - creating build/lib.macosx-10.9-x86_64-cpython-312/tests - copying tests/control.bam -> build/lib.macosx-10.9-x86_64-cpython-312/tests - copying bamread/src/bamread.c -> build/lib.macosx-10.9-x86_64-cpython-312/bamread/src - copying bamread/src/bamread.pyx -> build/lib.macosx-10.9-x86_64-cpython-312/bamread/src - copying bamread/src/bamwrite.pyx -> build/lib.macosx-10.9-x86_64-cpython-312/bamread/src - running build_ext - building 'bamread.src.bamread' extension - creating build/temp.macosx-10.9-x86_64-cpython-312 - creating build/temp.macosx-10.9-x86_64-cpython-312/bamread - creating build/temp.macosx-10.9-x86_64-cpython-312/bamread/src - x86_64-apple-darwin13.4.0-clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamread-0.0.16 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include/python3.12 -c bamread/src/bamread.c -o build/temp.macosx-10.9-x86_64-cpython-312/bamread/src/bamread.o - x86_64-apple-darwin13.4.0-clang -bundle -undefined dynamic_lookup -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamread-0.0.16 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 build/temp.macosx-10.9-x86_64-cpython-312/bamread/src/bamread.o -o build/lib.macosx-10.9-x86_64-cpython-312/bamread/src/bamread.cpython-312-darwin.so -# Last 100 lines of the build log. diff --git a/recipes/bamread/meta.yaml b/recipes/bamread/meta.yaml index db3f3aca49d74..e713c64ae35ff 100644 --- a/recipes/bamread/meta.yaml +++ b/recipes/bamread/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 913ae7d433592aa9bfad8699da93e74b5dfe8f567a1ebf4147f0da61baaf2b70 build: - number: 4 + number: 5 script: python setup.py install --single-version-externally-managed --record=record.txt run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/bamtocov/build_failure.linux-64.yaml b/recipes/bamtocov/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..42e767ebfa781 --- /dev/null +++ b/recipes/bamtocov/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 440bd585acf3fae3bb8f9ae7deb902925f8a1236a5171c9ffee3c855118a3c33 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + Verifying dependencies for unicodedb@0.13.0 + Installing unicodedb@0.13.0 + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/segmentation_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/segmentation_data.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/types.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/types.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/names.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/names.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/segmentation.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/segmentation.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/scripts_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/scripts_data.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/widths.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/widths.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/names_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/names_data.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/properties.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/properties.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/casing.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/casing.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/casing_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/casing_data.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/types_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/types_data.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/decompositions_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/decompositions_data.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/collation_mk_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/collation_mk_data.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/decompositions.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/decompositions.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/blocks.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/blocks.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/widths_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/widths_data.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/blocks_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/blocks_data.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/properties_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/properties_data.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/scripts.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/scripts.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/compositions.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/compositions.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/compositions_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/compositions_data.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/collation.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/collation.nim + Copying file /tmp/nimble_564/githubcom_nitelynimunicodedb_0.7.2/unicodedb.nimble to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb.nimble + Success: unicodedb installed successfully. + Installing regex@0.26.0 + Copying file /tmp/nimble_564/githubcom_nitelynimregex_0.11.1/src/regex.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex.nim + Copying file /tmp/nimble_564/githubcom_nitelynimregex_0.11.1/src/regex/parser.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/parser.nim + Copying file /tmp/nimble_564/githubcom_nitelynimregex_0.11.1/src/regex/nfamacro.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfamacro.nim + Copying file /tmp/nimble_564/githubcom_nitelynimregex_0.11.1/src/regex/types.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/types.nim + Copying file /tmp/nimble_564/githubcom_nitelynimregex_0.11.1/src/regex/exptype.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/exptype.nim + Copying file /tmp/nimble_564/githubcom_nitelynimregex_0.11.1/src/regex/exptransformation.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/exptransformation.nim + Copying file /tmp/nimble_564/githubcom_nitelynimregex_0.11.1/src/regex/nfatype.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfatype.nim + Copying file /tmp/nimble_564/githubcom_nitelynimregex_0.11.1/src/regex/nodematch.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nodematch.nim + Copying file /tmp/nimble_564/githubcom_nitelynimregex_0.11.1/src/regex/nfamatch2.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfamatch2.nim + Copying file /tmp/nimble_564/githubcom_nitelynimregex_0.11.1/src/regex/litopt.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/litopt.nim + Copying file /tmp/nimble_564/githubcom_nitelynimregex_0.11.1/src/regex/nfa.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfa.nim + Copying file /tmp/nimble_564/githubcom_nitelynimregex_0.11.1/src/regex/nfafindall2.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfafindall2.nim + Copying file /tmp/nimble_564/githubcom_nitelynimregex_0.11.1/src/regex/common.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/common.nim + Copying file /tmp/nimble_564/githubcom_nitelynimregex_0.11.1/src/regex/nfafindall.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfafindall.nim + Copying file /tmp/nimble_564/githubcom_nitelynimregex_0.11.1/src/regex/compiler.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/compiler.nim + Copying file /tmp/nimble_564/githubcom_nitelynimregex_0.11.1/src/regex/nfamatch.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfamatch.nim + Copying file /tmp/nimble_564/githubcom_nitelynimregex_0.11.1/src/regex/dotgraph.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/dotgraph.nim + Copying file /tmp/nimble_564/githubcom_nitelynimregex_0.11.1/src/regex/scanner.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/scanner.nim + Copying file /tmp/nimble_564/githubcom_nitelynimregex_0.11.1/regex.nimble to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex.nimble + Success: regex installed successfully. + Installing docopt@0.7.1 + Copying file /tmp/nimble_564/githubcom_docoptdocoptnim_0.6.8/src/docopt/util.nim to /home/conda/.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9/docopt/util.nim + Copying file /tmp/nimble_564/githubcom_docoptdocoptnim_0.6.8/src/docopt/value.nim to /home/conda/.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9/docopt/value.nim + Copying file /tmp/nimble_564/githubcom_docoptdocoptnim_0.6.8/src/docopt/dispatch.nim to /home/conda/.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9/docopt/dispatch.nim + Copying file /tmp/nimble_564/githubcom_docoptdocoptnim_0.6.8/src/docopt.nim to /home/conda/.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9/docopt.nim + Copying file /tmp/nimble_564/githubcom_docoptdocoptnim_0.6.8/docopt.nimble to /home/conda/.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9/docopt.nimble + Success: docopt installed successfully. + Reading official package list + Checking for lapper@any version + Installing lapper@any version + Reading official package list + Downloading https://github.com/brentp/nim-lapper using git + Cloning latest tagged version: v0.1.7 + Verifying dependencies for lapper@0.1.7 + Installing lapper@0.1.7 + Copying file /tmp/nimble_564/githubcom_brentpnimlapper/src/lapper.nim to /home/conda/.nimble/pkgs2/lapper-0.1.7-d6b2a932f7b8f786a40c452e763a837603c119ea/lapper.nim + Copying file /tmp/nimble_564/githubcom_brentpnimlapper/lapper.nimble to /home/conda/.nimble/pkgs2/lapper-0.1.7-d6b2a932f7b8f786a40c452e763a837603c119ea/lapper.nimble + Success: lapper installed successfully. + Building bamtocov/covtotarget using c backend + Executing $BUILD_PREFIX/nim/bin/nim c --colors:off --noNimblePath -d:release --opt:speed -d:NimblePkgVersion=2.7.0 --path:/home/conda/.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9 --path:/home/conda/.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611 --path:/home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d --path:/home/conda/.nimble/pkgs2/lapper-0.1.7-d6b2a932f7b8f786a40c452e763a837603c119ea --path:/home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a --colors:off -o:$SRC_DIR/bin/covtotarget $SRC_DIR/src/covtotarget.nim + Hint: used config file '/opt/conda/conda-bld/bamtocov_1734278094423/_build_env/nim/config/nim.cfg' [Conf] + Hint: used config file '/opt/conda/conda-bld/bamtocov_1734278094423/_build_env/nim/config/config.nims' [Conf] + Hint: used config file '/opt/conda/conda-bld/bamtocov_1734278094423/work/nim.cfg' [Conf] + .................................................................................................................................................... + /home/conda/.nimble/pkgs2/lapper-0.1.7-d6b2a932f7b8f786a40c452e763a837603c119ea/lapper.nim(132, 10) Error: undeclared identifier: 'shallow' + nimble.nim(304) buildFromDir + + Error: Build failed for the package: bamtocov + Info: Nimble data file "/home/conda/.nimble/nimbledata2.json" has been saved. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bamtocov_1734278094423/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bamtocov_1734278094423/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bamtocov/build_failure.osx-64.yaml b/recipes/bamtocov/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..04dede945a51c --- /dev/null +++ b/recipes/bamtocov/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 440bd585acf3fae3bb8f9ae7deb902925f8a1236a5171c9ffee3c855118a3c33 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + Copying file /tmp/nimble_85589/githubcom_brentphtsnim_0.3.1/src/hts/utils.nim to $SRC_DIR/.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/utils.nim + Copying file /tmp/nimble_85589/githubcom_brentphtsnim_0.3.1/src/hts/private/hts_concat.nim to $SRC_DIR/.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/private/hts_concat.nim + Copying file /tmp/nimble_85589/githubcom_brentphtsnim_0.3.1/src/hts/private/hts_concat.h to $SRC_DIR/.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/private/hts_concat.h + Copying file /tmp/nimble_85589/githubcom_brentphtsnim_0.3.1/src/hts/vcf.nim to $SRC_DIR/.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/vcf.nim + Copying file /tmp/nimble_85589/githubcom_brentphtsnim_0.3.1/src/hts/stats.nim to $SRC_DIR/.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/stats.nim + Copying file /tmp/nimble_85589/githubcom_brentphtsnim_0.3.1/src/hts/bgzf/bgzi.nim to $SRC_DIR/.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts/bgzf/bgzi.nim + Copying file /tmp/nimble_85589/githubcom_brentphtsnim_0.3.1/hts.nimble to $SRC_DIR/.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611/hts.nimble + Success: hts installed successfully. + Reading official package list + Checking for docopt@>= 0.6.8 + Installing docopt@>= 0.6.8 + Reading official package list + Downloading https://github.com/docopt/docopt.nim using git + Cloning latest tagged version: v0.7.1 + Verifying dependencies for docopt@0.7.1 + Reading official package list + Checking for regex@>= 0.11.1 + Installing regex@>= 0.11.1 + Reading official package list + Downloading https://github.com/nitely/nim-regex using git + Cloning latest tagged version: v0.26.0 + Verifying dependencies for regex@0.26.0 + Reading official package list + Checking for unicodedb@>= 0.7.2 + Installing unicodedb@>= 0.7.2 + Reading official package list + Downloading https://github.com/nitely/nim-unicodedb using git + Cloning latest tagged version: v0.13.0 + Verifying dependencies for unicodedb@0.13.0 + Installing unicodedb@0.13.0 + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/names.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/names.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/types_data.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/types_data.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/properties.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/properties.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/properties_data.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/properties_data.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/segmentation_data.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/segmentation_data.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/collation_mk_data.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/collation_mk_data.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/widths.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/widths.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/blocks.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/blocks.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/scripts.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/scripts.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/casing.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/casing.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/collation.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/collation.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/blocks_data.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/blocks_data.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/types.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/types.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/compositions.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/compositions.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/compositions_data.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/compositions_data.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/scripts_data.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/scripts_data.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/casing_data.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/casing_data.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/decompositions.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/decompositions.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/segmentation.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/segmentation.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/decompositions_data.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/decompositions_data.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/widths_data.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/widths_data.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/names_data.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/names_data.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb.nim to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimunicodedb_0.7.2/unicodedb.nimble to $SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb.nimble + Success: unicodedb installed successfully. + Installing regex@0.26.0 + Copying file /tmp/nimble_85589/githubcom_nitelynimregex_0.11.1/src/regex/dotgraph.nim to $SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/dotgraph.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimregex_0.11.1/src/regex/nfatype.nim to $SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfatype.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimregex_0.11.1/src/regex/nfa.nim to $SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfa.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimregex_0.11.1/src/regex/nodematch.nim to $SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nodematch.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimregex_0.11.1/src/regex/parser.nim to $SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/parser.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimregex_0.11.1/src/regex/nfafindall.nim to $SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfafindall.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimregex_0.11.1/src/regex/nfamacro.nim to $SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfamacro.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimregex_0.11.1/src/regex/types.nim to $SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/types.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimregex_0.11.1/src/regex/common.nim to $SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/common.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimregex_0.11.1/src/regex/nfafindall2.nim to $SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfafindall2.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimregex_0.11.1/src/regex/compiler.nim to $SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/compiler.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimregex_0.11.1/src/regex/nfamatch.nim to $SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfamatch.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimregex_0.11.1/src/regex/litopt.nim to $SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/litopt.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimregex_0.11.1/src/regex/exptransformation.nim to $SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/exptransformation.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimregex_0.11.1/src/regex/exptype.nim to $SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/exptype.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimregex_0.11.1/src/regex/nfamatch2.nim to $SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfamatch2.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimregex_0.11.1/src/regex/scanner.nim to $SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/scanner.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimregex_0.11.1/src/regex.nim to $SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex.nim + Copying file /tmp/nimble_85589/githubcom_nitelynimregex_0.11.1/regex.nimble to $SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex.nimble + Success: regex installed successfully. + Installing docopt@0.7.1 + Copying file /tmp/nimble_85589/githubcom_docoptdocoptnim_0.6.8/src/docopt.nim to $SRC_DIR/.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9/docopt.nim + Copying file /tmp/nimble_85589/githubcom_docoptdocoptnim_0.6.8/src/docopt/value.nim to $SRC_DIR/.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9/docopt/value.nim + Copying file /tmp/nimble_85589/githubcom_docoptdocoptnim_0.6.8/src/docopt/dispatch.nim to $SRC_DIR/.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9/docopt/dispatch.nim + Copying file /tmp/nimble_85589/githubcom_docoptdocoptnim_0.6.8/src/docopt/util.nim to $SRC_DIR/.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9/docopt/util.nim + Copying file /tmp/nimble_85589/githubcom_docoptdocoptnim_0.6.8/docopt.nimble to $SRC_DIR/.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9/docopt.nimble + Success: docopt installed successfully. + Reading official package list + Checking for lapper@any version + Installing lapper@any version + Reading official package list + Downloading https://github.com/brentp/nim-lapper using git + Cloning latest tagged version: v0.1.7 + Verifying dependencies for lapper@0.1.7 + Installing lapper@0.1.7 + Copying file /tmp/nimble_85589/githubcom_brentpnimlapper/src/lapper.nim to $SRC_DIR/.nimble/pkgs2/lapper-0.1.7-d6b2a932f7b8f786a40c452e763a837603c119ea/lapper.nim + Copying file /tmp/nimble_85589/githubcom_brentpnimlapper/lapper.nimble to $SRC_DIR/.nimble/pkgs2/lapper-0.1.7-d6b2a932f7b8f786a40c452e763a837603c119ea/lapper.nimble + Success: lapper installed successfully. + Building bamtocov/covtotarget using c backend + Executing $BUILD_PREFIX/nim/bin/nim c --colors:off --noNimblePath -d:release --opt:speed -d:NimblePkgVersion=2.7.0 --path:$SRC_DIR/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a --path:$SRC_DIR/.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9 --path:$SRC_DIR/.nimble/pkgs2/lapper-0.1.7-d6b2a932f7b8f786a40c452e763a837603c119ea --path:$SRC_DIR/.nimble/pkgs2/hts-0.3.25-c05c9adf6b2e10a7f07edfef29110ea14bb66611 --path:$SRC_DIR/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d --colors:off -o:$SRC_DIR/bin/covtotarget $SRC_DIR/src/covtotarget.nim + nimble.nim(304) buildFromDir + + Error: Build failed for the package: bamtocov + Info: Nimble data file "$SRC_DIR/.nimble/nimbledata2.json" has been saved. +# Last 100 lines of the build log. diff --git a/recipes/bamtocov/meta.yaml b/recipes/bamtocov/meta.yaml index 8dcba8e178e85..b7bf3f9cb0ca1 100755 --- a/recipes/bamtocov/meta.yaml +++ b/recipes/bamtocov/meta.yaml @@ -12,7 +12,7 @@ source: build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/bamtools/meta.yaml b/recipes/bamtools/meta.yaml index 0f5b309f2a25e..aa262d2797265 100644 --- a/recipes/bamtools/meta.yaml +++ b/recipes/bamtools/meta.yaml @@ -12,7 +12,7 @@ source: # - 0001-Const-qualify-all-functors-operator-member-functions.patch build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} diff --git a/recipes/bamutil/build_failure.osx-64.yaml b/recipes/bamutil/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..5b4e5528a12f2 --- /dev/null +++ b/recipes/bamutil/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 8bb7bd24b57d2e88ef72d26256526f1ee30d6845369937448e45d6d0495c2b1f # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + "SamRecord::getString(char const*)", referenced from: + Bam2FastQ::writeFastQ(SamRecord&, InputFile*, std::__1::basic_string, std::__1::allocator> const&, char const*) in Bam2FastQ.o + Recab::processReadBuildTable(SamRecord&) in Recab.o + Recab::processReadApplyTable(SamRecord&) in Recab.o + "SamRecord::SamRecord(ErrorHandler::HandlingType)", referenced from: + Validate::execute(int, char**) in Validate.o + "SamRecord::SamRecord()", referenced from: + Convert::execute(int, char**) in Convert.o + Diff::getSamRecord() in Diff.o + SplitChromosome::execute(int, char**) in SplitChromosome.o + WriteRegion::execute(int, char**) in WriteRegion.o + ReadIndexedBam::readIndexedBam(char const*, char const*, char const*) in ReadIndexedBam.o + DumpRefInfo::execute(int, char**) in DumpRefInfo.o + Filter::execute(int, char**) in Filter.o + ... + "SamRecord::~SamRecord()", referenced from: + Validate::execute(int, char**) in Validate.o + Convert::execute(int, char**) in Convert.o + SplitChromosome::execute(int, char**) in SplitChromosome.o + WriteRegion::execute(int, char**) in WriteRegion.o + ReadIndexedBam::readIndexedBam(char const*, char const*, char const*) in ReadIndexedBam.o + DumpRefInfo::execute(int, char**) in DumpRefInfo.o + Filter::execute(int, char**) in Filter.o + ... + "SamFileHeader::getHeaderString(std::__1::basic_string, std::__1::allocator>&) const", referenced from: + DumpHeader::dumpHeader(char const*) in DumpHeader.o + "SamFileHeader::getReferenceInfo() const", referenced from: + ReadIndexedBam::readIndexedBam(char const*, char const*, char const*) in ReadIndexedBam.o + DumpRefInfo::execute(int, char**) in DumpRefInfo.o + Stats::execute(int, char**) in Stats.o + MergeBam::execute(int, char**) in MergeBam.o + "SamFileHeader::getReferenceLabel(int) const", referenced from: + SplitChromosome::execute(int, char**) in SplitChromosome.o + "SamHeaderRecord::getTagValue(char const*) const", referenced from: + SplitBam::execute(int, char**) in SplitBam.o + parseOutRG(SamFileHeader&, std::__1::basic_string, std::__1::allocator>&, SamFileHeader*, bool) in MergeBam.o + PolishBam::execute(int, char**) in PolishBam.o + Dedup::buildReadGroupLibraryMap(SamFileHeader&) in Dedup.o + Dedup_LowMem::buildReadGroupLibraryMap(SamFileHeader&) in Dedup_LowMem.o + "SamReferenceInfo::getNumEntries() const", referenced from: + ReadIndexedBam::readIndexedBam(char const*, char const*, char const*) in ReadIndexedBam.o + DumpRefInfo::execute(int, char**) in DumpRefInfo.o + Stats::execute(int, char**) in Stats.o + "SamReferenceInfo::getReferenceName(int) const", referenced from: + DumpRefInfo::execute(int, char**) in DumpRefInfo.o + "SamReferenceInfo::getReferenceLength(int) const", referenced from: + Stats::execute(int, char**) in Stats.o + "SamReferenceInfo::operator==(SamReferenceInfo const&) const", referenced from: + MergeBam::execute(int, char**) in MergeBam.o + "SamValidationError::getType() const", referenced from: + Validate::execute(int, char**) in Validate.o + "SamValidationErrors::getErrorString(std::__1::basic_string, std::__1::allocator>&) const", referenced from: + Validate::execute(int, char**) in Validate.o + "typeinfo for PileupElement", referenced from: + typeinfo for PileupElementBaseQCStats in PileupElementBaseQCStats.o + ld: symbol(s) not found for architecture x86_64 + x86_64-apple-darwin13.4: error: linker command failed with exit code 1 (use -v to see invocation) + make[1]: *** [../../libStatGen/Makefiles/Makefile.ext:46: ../bin/profile/bam] Error 1 + make: *** [../libStatGen/Makefiles/Makefile.base:15: src] Error 2 + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-strict-overflow -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Tue Dec 10 22:00:02 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"runner\"" -o ../obj/profile/Dedup.o -c Dedup.cpp -DVERSION="\"1.0.15\"" + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bamutil_1733867527964/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-strict-overflow -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Tue Dec 10 22:00:02 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"runner\"" -o ../obj/profile/Dedup_LowMem.o -c Dedup_LowMem.cpp -DVERSION="\"1.0.15\"" + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-strict-overflow -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Tue Dec 10 22:00:04 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"runner\"" -o ../obj/profile/Prediction.o -c Prediction.cpp -DVERSION="\"1.0.15\"" + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bamutil_1733867527964/work/conda_build.sh']' returned non-zero exit status 2. + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-strict-overflow -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Tue Dec 10 22:00:05 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"runner\"" -o ../obj/profile/LogisticRegression.o -c LogisticRegression.cpp -DVERSION="\"1.0.15\"" + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-strict-overflow -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Tue Dec 10 22:00:06 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"runner\"" -o ../obj/profile/MathCholesky.o -c MathCholesky.cpp -DVERSION="\"1.0.15\"" + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-strict-overflow -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Tue Dec 10 22:00:07 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"runner\"" -o ../obj/profile/HashErrorModel.o -c HashErrorModel.cpp -DVERSION="\"1.0.15\"" + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-strict-overflow -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Tue Dec 10 22:00:08 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"runner\"" -o ../obj/profile/Recab.o -c Recab.cpp -DVERSION="\"1.0.15\"" + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-strict-overflow -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Tue Dec 10 22:00:08 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"runner\"" -o ../obj/profile/OverlapHandler.o -c OverlapHandler.cpp -DVERSION="\"1.0.15\"" + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-strict-overflow -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Tue Dec 10 22:00:09 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"runner\"" -o ../obj/profile/OverlapClipLowerBaseQual.o -c OverlapClipLowerBaseQual.cpp -DVERSION="\"1.0.15\"" + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-strict-overflow -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Tue Dec 10 22:00:10 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"runner\"" -o ../obj/profile/ExplainFlags.o -c ExplainFlags.cpp -DVERSION="\"1.0.15\"" + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-strict-overflow -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Tue Dec 10 22:00:11 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"runner\"" -o ../obj/profile/Main.o -c Main.cpp -DVERSION="\"1.0.15\"" + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-strict-overflow -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Tue Dec 10 22:00:12 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"runner\"" -o ../obj/BamExecutable.o -c BamExecutable.cpp -DVERSION="\"1.0.15\"" + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-strict-overflow -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Tue Dec 10 22:00:13 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"runner\"" -o ../obj/debug/BamExecutable.o -c BamExecutable.cpp -DVERSION="\"1.0.15\"" + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-strict-overflow -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Tue Dec 10 22:00:14 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"runner\"" -o ../bin/bam ../obj/BamExecutable.o ../obj/Validate.o ../obj/Convert.o ../obj/Diff.o ../obj/DumpHeader.o ../obj/SplitChromosome.o ../obj/WriteRegion.o ../obj/DumpIndex.o ../obj/ReadIndexedBam.o ../obj/DumpRefInfo.o ../obj/Filter.o ../obj/ReadReference.o ../obj/Revert.o ../obj/Squeeze.o ../obj/FindCigars.o ../obj/Stats.o ../obj/PileupElementBaseQCStats.o ../obj/ClipOverlap.o ../obj/MateMapByCoord.o ../obj/SplitBam.o ../obj/TrimBam.o ../obj/MergeBam.o ../obj/PolishBam.o ../obj/GapInfo.o ../obj/Logger.o ../obj/Bam2FastQ.o ../obj/Dedup.o ../obj/Dedup_LowMem.o ../obj/Prediction.o ../obj/LogisticRegression.o ../obj/MathCholesky.o ../obj/HashErrorModel.o ../obj/Recab.o ../obj/OverlapHandler.o ../obj/OverlapClipLowerBaseQual.o ../obj/ExplainFlags.o ../obj/Main.o ../../libStatGen/libStatGen.a -lm -lz + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-strict-overflow -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Tue Dec 10 22:00:14 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"runner\"" -o ../obj/profile/BamExecutable.o -c BamExecutable.cpp -DVERSION="\"1.0.15\"" + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-strict-overflow -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Tue Dec 10 22:00:15 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"runner\"" -o ../bin/debug/bam ../obj/debug/BamExecutable.o ../obj/debug/Validate.o ../obj/debug/Convert.o ../obj/debug/Diff.o ../obj/debug/DumpHeader.o ../obj/debug/SplitChromosome.o ../obj/debug/WriteRegion.o ../obj/debug/DumpIndex.o ../obj/debug/ReadIndexedBam.o ../obj/debug/DumpRefInfo.o ../obj/debug/Filter.o ../obj/debug/ReadReference.o ../obj/debug/Revert.o ../obj/debug/Squeeze.o ../obj/debug/FindCigars.o ../obj/debug/Stats.o ../obj/debug/PileupElementBaseQCStats.o ../obj/debug/ClipOverlap.o ../obj/debug/MateMapByCoord.o ../obj/debug/SplitBam.o ../obj/debug/TrimBam.o ../obj/debug/MergeBam.o ../obj/debug/PolishBam.o ../obj/debug/GapInfo.o ../obj/debug/Logger.o ../obj/debug/Bam2FastQ.o ../obj/debug/Dedup.o ../obj/debug/Dedup_LowMem.o ../obj/debug/Prediction.o ../obj/debug/LogisticRegression.o ../obj/debug/MathCholesky.o ../obj/debug/HashErrorModel.o ../obj/debug/Recab.o ../obj/debug/OverlapHandler.o ../obj/debug/OverlapClipLowerBaseQual.o ../obj/debug/ExplainFlags.o ../obj/debug/Main.o ../../libStatGen/libStatGen_debug.a -lm -lz + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamutil-1.0.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-strict-overflow -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Tue Dec 10 22:00:16 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"runner\"" -o ../bin/profile/bam ../obj/profile/BamExecutable.o ../obj/profile/Validate.o ../obj/profile/Convert.o ../obj/profile/Diff.o ../obj/profile/DumpHeader.o ../obj/profile/SplitChromosome.o ../obj/profile/WriteRegion.o ../obj/profile/DumpIndex.o ../obj/profile/ReadIndexedBam.o ../obj/profile/DumpRefInfo.o ../obj/profile/Filter.o ../obj/profile/ReadReference.o ../obj/profile/Revert.o ../obj/profile/Squeeze.o ../obj/profile/FindCigars.o ../obj/profile/Stats.o ../obj/profile/PileupElementBaseQCStats.o ../obj/profile/ClipOverlap.o ../obj/profile/MateMapByCoord.o ../obj/profile/SplitBam.o ../obj/profile/TrimBam.o ../obj/profile/MergeBam.o ../obj/profile/PolishBam.o ../obj/profile/GapInfo.o ../obj/profile/Logger.o ../obj/profile/Bam2FastQ.o ../obj/profile/Dedup.o ../obj/profile/Dedup_LowMem.o ../obj/profile/Prediction.o ../obj/profile/LogisticRegression.o ../obj/profile/MathCholesky.o ../obj/profile/HashErrorModel.o ../obj/profile/Recab.o ../obj/profile/OverlapHandler.o ../obj/profile/OverlapClipLowerBaseQual.o ../obj/profile/ExplainFlags.o ../obj/profile/Main.o ../../libStatGen/libStatGen_profile.a -lm -lz + make[1]: Leaving directory '$SRC_DIR/bamUtil/src' +# Last 100 lines of the build log. diff --git a/recipes/bamutil/meta.yaml b/recipes/bamutil/meta.yaml index 68fad40c1b808..b482b48b8992f 100644 --- a/recipes/bamutil/meta.yaml +++ b/recipes/bamutil/meta.yaml @@ -13,7 +13,7 @@ source: folder: libStatGen build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('bamutil', max_pin="x") }} diff --git a/recipes/bandage_ng/build_failure.linux-64.yaml b/recipes/bandage_ng/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..cac8154356b7e --- /dev/null +++ b/recipes/bandage_ng/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 3b659a35a90407fa515cca081bd5bebe38c01d6e0d8151ebe06678b13791093a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bandage_ng-2022.09 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bandage_ng-2022.09 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bandage_ng-2022.09 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bandage_ng-2022.09 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + mkdir -p build + cd build + uname + [[ Linux == \L\i\n\u\x ]] + CMAKE_ARGS='-DCMAKE_AR=/opt/conda/conda-bld/bandage_ng_1734144258533/_build_env/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=/opt/conda/conda-bld/bandage_ng_1734144258533/_build_env/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=/opt/conda/conda-bld/bandage_ng_1734144258533/_build_env/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=/opt/conda/conda-bld/bandage_ng_1734144258533/_build_env/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=/opt/conda/conda-bld/bandage_ng_1734144258533/_build_env/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=/opt/conda/conda-bld/bandage_ng_1734144258533/_build_env/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=/opt/conda/conda-bld/bandage_ng_1734144258533/_build_env/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=/opt/conda/conda-bld/bandage_ng_1734144258533/_build_env/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=/opt/conda/conda-bld/bandage_ng_1734144258533/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl;/opt/conda/conda-bld/bandage_ng_1734144258533/_build_env/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=/opt/conda/conda-bld/bandage_ng_1734144258533/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=/opt/conda/conda-bld/bandage_ng_1734144258533/_build_env/bin;/opt/conda/conda-bld/bandage_ng_1734144258533/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/bin -DFEATURE_egl=ON -DFEATURE_eglfs=ON' + cmake -DCMAKE_PREFIX_PATH=/opt/conda/conda-bld/bandage_ng_1734144258533/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl '-DCMAKE_CXX_FLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/conda-bld/bandage_ng_1734144258533/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include -fdebug-prefix-map=/opt/conda/conda-bld/bandage_ng_1734144258533/work=/usr/local/src/conda/bandage_ng-2022.09 -fdebug-prefix-map=/opt/conda/conda-bld/bandage_ng_1734144258533/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl=/usr/local/src/conda-prefix -D__STDC_FORMAT_MACROS' -DEGL_INCLUDE_DIR:PATH=/opt/conda/conda-bld/bandage_ng_1734144258533/_build_env/x86_64-conda-linux-gnu/sysroot/usr/include -DEGL_LIBRARY:FILEPATH=/opt/conda/conda-bld/bandage_ng_1734144258533/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib/libEGL.so.1 -DOPENGL_egl_LIBRARY:FILEPATH=/opt/conda/conda-bld/bandage_ng_1734144258533/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib/libEGL.so.1 -DEGL_opengl_LIBRARY:FILEPATH=/opt/conda/conda-bld/bandage_ng_1734144258533/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib64/libGL.so -DOPENGL_opengl_LIBRARY:FILEPATH=/opt/conda/conda-bld/bandage_ng_1734144258533/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib64/libGL.so .. + -- The CXX compiler identification is GNU 13.3.0 + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed + -- Check if compiler accepts -pthread + -- Check if compiler accepts -pthread - yes + -- Found Threads: TRUE + -- Performing Test HAVE_STDATOMIC + -- Performing Test HAVE_STDATOMIC - Success + -- Found WrapAtomic: TRUE + -- Found OpenGL: $BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr/lib64/libGL.so + -- Found WrapOpenGL: TRUE + -- Found XKB: $PREFIX/lib/libxkbcommon.so (found suitable version "1.7.0", minimum required is "0.5.0") + -- Could NOT find WrapVulkanHeaders (missing: Vulkan_INCLUDE_DIR) + CMake Error at /opt/conda/conda-bld/bandage_ng_1734144258533/_build_env/share/cmake-3.31/Modules/FindPackageHandleStandardArgs.cmake:233 (message): + Could NOT find ZLIB (missing: ZLIB_LIBRARY ZLIB_INCLUDE_DIR) + Call Stack (most recent call first): + /opt/conda/conda-bld/bandage_ng_1734144258533/_build_env/share/cmake-3.31/Modules/FindPackageHandleStandardArgs.cmake:603 (_FPHSA_FAILURE_MESSAGE) + /opt/conda/conda-bld/bandage_ng_1734144258533/_build_env/share/cmake-3.31/Modules/FindZLIB.cmake:202 (FIND_PACKAGE_HANDLE_STANDARD_ARGS) + CMakeLists.txt:14 (find_package) + + + -- Configuring incomplete, errors occurred! + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bandage_ng_1734144258533/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bandage_ng_1734144258533/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bandage_ng/meta.yaml b/recipes/bandage_ng/meta.yaml index ca560807e8f66..91c11e0066c56 100644 --- a/recipes/bandage_ng/meta.yaml +++ b/recipes/bandage_ng/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 892c36350ee0eb8a58ec7187cf08b6b5b288915bd74f6d69e68c7aa2fdd704f0 build: - number: 4 + number: 5 skip: True # [osx] run_exports: - {{ pin_subpackage("bandage_ng", max_pin=None) }} diff --git a/recipes/batvi/build_failure.osx-64.yaml b/recipes/batvi/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..5dc31c6d8e42e --- /dev/null +++ b/recipes/batvi/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 6dd0174d0114fc400bf1dfa6ec15d88b296989e43ffdc89efc9d10039bddd5b4 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + checking for suffix of executables... + checking whether we are cross compiling... no + checking for suffix of object files... o + checking whether the compiler supports GNU C... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking for x86_64-apple-darwin13.4.0-clang option to enable C11 features... none needed + checking whether make supports the include directive... yes (GNU style) + checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 + checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang + checking whether the compiler supports GNU C... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking for x86_64-apple-darwin13.4.0-clang option to enable C11 features... none needed + checking whether x86_64-apple-darwin13.4.0-clang understands -c and -o together... yes + checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 + checking for stdio.h... yes + checking for stdlib.h... yes + checking for string.h... yes + checking for inttypes.h... yes + checking for stdint.h... yes + checking for strings.h... yes + checking for sys/stat.h... yes + checking for sys/types.h... yes + checking for unistd.h... yes + checking for sys/time.h... yes + checking for grep that handles long lines and -e... /usr/bin/grep + checking for egrep... /usr/bin/grep -E + checking for limits.h... yes + checking for malloc.h... no + checking for stddef.h... yes + checking for stdint.h... (cached) yes + checking for stdlib.h... (cached) yes + checking for string.h... (cached) yes + checking for sys/socket.h... yes + checking for sys/time.h... (cached) yes + checking for unistd.h... (cached) yes + checking for an ANSI C-conforming const... yes + checking for size_t... yes + checking for working volatile... yes + checking for ptrdiff_t... yes + checking build system type... x86_64-apple-darwin13.4.0 + checking host system type... x86_64-apple-darwin13.4.0 + checking for GNU libc compatible malloc... (cached) yes + checking for GNU libc compatible realloc... (cached) yes + checking for vprintf... yes + checking for floor... yes + checking for gettimeofday... yes + checking for memmove... yes + checking for memset... yes + checking for pow... yes + checking for socket... yes + checking for sqrt... yes + checking for strchr... yes + checking for strdup... yes + checking for strtoul... yes + checking Checking for SIMD support and for a gcc bug...... OK... + checking that generated files are newer than configure... done + configure: creating ./config.status + config.status: creating Makefile + config.status: creating src/Makefile + config.status: creating scripts/Makefile + config.status: creating doc/Makefile + config.status: creating config.h + config.status: executing depfiles commands + make all-recursive + make[1]: Entering directory '$SRC_DIR/source/BatMis-3.00' + Making all in scripts + make[2]: Entering directory '$SRC_DIR/source/BatMis-3.00/scripts' + make[2]: Nothing to be done for 'all'. + make[2]: Leaving directory '$SRC_DIR/source/BatMis-3.00/scripts' + Making all in src + make[2]: Entering directory '$SRC_DIR/source/BatMis-3.00/src' + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -w -O3 -funroll-loops -Dfopen64=fopen -Dfseeko64=fseeko -Dftello64=ftello -Dlseek64=lseek -Doff64_t=off_t -msse2 -lm -lz -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/batvi-1.04 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT bwtformatdb.o -MD -MP -MF .deps/bwtformatdb.Tpo -c -o bwtformatdb.o bwtformatdb.c + mv -f .deps/bwtformatdb.Tpo .deps/bwtformatdb.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -w -O3 -funroll-loops -Dfopen64=fopen -Dfseeko64=fseeko -Dftello64=ftello -Dlseek64=lseek -Doff64_t=off_t -msse2 -lm -lz -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/batvi-1.04 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT BWT.o -MD -MP -MF .deps/BWT.Tpo -c -o BWT.o BWT.c + mv -f .deps/BWT.Tpo .deps/BWT.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -w -O3 -funroll-loops -Dfopen64=fopen -Dfseeko64=fseeko -Dftello64=ftello -Dlseek64=lseek -Doff64_t=off_t -msse2 -lm -lz -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/batvi-1.04 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT BWTConstruct.o -MD -MP -MF .deps/BWTConstruct.Tpo -c -o BWTConstruct.o BWTConstruct.c + mv -f .deps/BWTConstruct.Tpo .deps/BWTConstruct.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -w -O3 -funroll-loops -Dfopen64=fopen -Dfseeko64=fseeko -Dftello64=ftello -Dlseek64=lseek -Doff64_t=off_t -msse2 -lm -lz -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/batvi-1.04 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT MiscUtilities.o -MD -MP -MF .deps/MiscUtilities.Tpo -c -o MiscUtilities.o MiscUtilities.c + mv -f .deps/MiscUtilities.Tpo .deps/MiscUtilities.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -w -O3 -funroll-loops -Dfopen64=fopen -Dfseeko64=fseeko -Dftello64=ftello -Dlseek64=lseek -Doff64_t=off_t -msse2 -lm -lz -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/batvi-1.04 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT MemManager.o -MD -MP -MF .deps/MemManager.Tpo -c -o MemManager.o MemManager.c + mv -f .deps/MemManager.Tpo .deps/MemManager.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -w -O3 -funroll-loops -Dfopen64=fopen -Dfseeko64=fseeko -Dftello64=ftello -Dlseek64=lseek -Doff64_t=off_t -msse2 -lm -lz -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/batvi-1.04 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT TextConverter.o -MD -MP -MF .deps/TextConverter.Tpo -c -o TextConverter.o TextConverter.c + mv -f .deps/TextConverter.Tpo .deps/TextConverter.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -w -O3 -funroll-loops -Dfopen64=fopen -Dfseeko64=fseeko -Dftello64=ftello -Dlseek64=lseek -Doff64_t=off_t -msse2 -lm -lz -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/batvi-1.04 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT r250.o -MD -MP -MF .deps/r250.Tpo -c -o r250.o r250.c + mv -f .deps/r250.Tpo .deps/r250.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -w -O3 -funroll-loops -Dfopen64=fopen -Dfseeko64=fseeko -Dftello64=ftello -Dlseek64=lseek -Doff64_t=off_t -msse2 -lm -lz -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/batvi-1.04 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT QSufSort.o -MD -MP -MF .deps/QSufSort.Tpo -c -o QSufSort.o QSufSort.c + mv -f .deps/QSufSort.Tpo .deps/QSufSort.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -w -O3 -funroll-loops -Dfopen64=fopen -Dfseeko64=fseeko -Dftello64=ftello -Dlseek64=lseek -Doff64_t=off_t -msse2 -lm -lz -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/batvi-1.04 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT iniparser.o -MD -MP -MF .deps/iniparser.Tpo -c -o iniparser.o iniparser.c + mv -f .deps/iniparser.Tpo .deps/iniparser.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -w -O3 -funroll-loops -Dfopen64=fopen -Dfseeko64=fseeko -Dftello64=ftello -Dlseek64=lseek -Doff64_t=off_t -msse2 -lm -lz -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/batvi-1.04 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT inistrlib.o -MD -MP -MF .deps/inistrlib.Tpo -c -o inistrlib.o inistrlib.c + mv -f .deps/inistrlib.Tpo .deps/inistrlib.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -w -O3 -funroll-loops -Dfopen64=fopen -Dfseeko64=fseeko -Dftello64=ftello -Dlseek64=lseek -Doff64_t=off_t -msse2 -lm -lz -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/batvi-1.04 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT dictionary.o -MD -MP -MF .deps/dictionary.Tpo -c -o dictionary.o dictionary.c + mv -f .deps/dictionary.Tpo .deps/dictionary.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -w -O3 -funroll-loops -Dfopen64=fopen -Dfseeko64=fseeko -Dftello64=ftello -Dlseek64=lseek -Doff64_t=off_t -msse2 -lm -lz -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/batvi-1.04 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT DNACount.o -MD -MP -MF .deps/DNACount.Tpo -c -o DNACount.o DNACount.c + mv -f .deps/DNACount.Tpo .deps/DNACount.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -w -O3 -funroll-loops -Dfopen64=fopen -Dfseeko64=fseeko -Dftello64=ftello -Dlseek64=lseek -Doff64_t=off_t -msse2 -lm -lz -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/batvi-1.04 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT Timing.o -MD -MP -MF .deps/Timing.Tpo -c -o Timing.o Timing.c + mv -f .deps/Timing.Tpo .deps/Timing.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -w -O3 -funroll-loops -Dfopen64=fopen -Dfseeko64=fseeko -Dftello64=ftello -Dlseek64=lseek -Doff64_t=off_t -msse2 -lm -lz -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/batvi-1.04 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT Socket.o -MD -MP -MF .deps/Socket.Tpo -c -o Socket.o Socket.c + make[2]: Leaving directory '$SRC_DIR/source/BatMis-3.00/src' + make[1]: Leaving directory '$SRC_DIR/source/BatMis-3.00' +# Last 100 lines of the build log. diff --git a/recipes/batvi/meta.yaml b/recipes/batvi/meta.yaml index 2e23293867158..b8be3c998edf3 100644 --- a/recipes/batvi/meta.yaml +++ b/recipes/batvi/meta.yaml @@ -19,7 +19,7 @@ source: # sha256: 0072a56055998d0d67822d66128de1e84ea9d34770fd3752192ca1f93bf6569d build: - number: 8 + number: 9 requirements: build: diff --git a/recipes/bayescan/meta.yaml b/recipes/bayescan/meta.yaml index 3f66b41aaf9e3..b42166d048856 100644 --- a/recipes/bayescan/meta.yaml +++ b/recipes/bayescan/meta.yaml @@ -3,7 +3,7 @@ package: version: 2.0.1 build: - number: 6 + number: 7 skip: True # [osx] source: diff --git a/recipes/bayescode/meta.yaml b/recipes/bayescode/meta.yaml index 92815ce859119..5763605456d14 100644 --- a/recipes/bayescode/meta.yaml +++ b/recipes/bayescode/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('bayescode', max_pin="x") }} diff --git a/recipes/bayestyper/meta.yaml b/recipes/bayestyper/meta.yaml index 88a72501f760c..817848891b8f9 100644 --- a/recipes/bayestyper/meta.yaml +++ b/recipes/bayestyper/meta.yaml @@ -15,7 +15,7 @@ source: - stdafx.patch # [osx] build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage('bayestyper', max_pin="x") }} diff --git a/recipes/baypass/build_failure.linux-64.yaml b/recipes/baypass/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..566a1b6bbfd81 --- /dev/null +++ b/recipes/baypass/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c44cea1f603a6d35fec94e6a557adcb2870a38c55e97b7542188eb709917e068 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + 2024-12-14T02:34:10 noarch Building current_repodata subset + 2024-12-14T02:34:10 noarch Writing current_repodata subset + 2024-12-14T02:34:10 noarch Writing index HTML + /opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (/opt/recipe/meta.yaml). + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml + Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for baypass + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['baypass-2.31-h8d36177_3.tar.bz2'] + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/baypass_1734143651312/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgfortran: 14.2.0-h69a702a_1 conda-forge + libgfortran5: 14.2.0-hd5240d6_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/baypass_1734143651312/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.43-h4bf12b8_2 conda-forge + binutils_linux-64: 2.43-h4852527_2 conda-forge + gcc_impl_linux-64: 13.3.0-hfea6d02_1 conda-forge + gcc_linux-64: 13.3.0-hc28eda2_7 conda-forge + gfortran_impl_linux-64: 13.3.0-h10434e7_1 conda-forge + gfortran_linux-64: 13.3.0-hb919d3a_7 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libgfortran5: 14.2.0-hd5240d6_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libsanitizer: 13.3.0-heb74ff8_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + make: 4.4.1-hb9d3cd8_2 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: baypass_2.31_3b4ff4c86c.tar.gz + Downloading http://www1.montpellier.inra.fr/CBGP/software/baypass/files/baypass_2.31.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.752463 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download http://www1.montpellier.inra.fr/CBGP/software/baypass/files/baypass_2.31.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/baypass/meta.yaml b/recipes/baypass/meta.yaml index 9ceb5a46577e9..d767f611b5bd5 100644 --- a/recipes/baypass/meta.yaml +++ b/recipes/baypass/meta.yaml @@ -10,7 +10,7 @@ source: md5: 3b4ff4c86cf3cab0b0fdd126f35852b5 build: - number: 2 + number: 3 skip: True # [osx] requirements: diff --git a/recipes/bbknn/meta.yaml b/recipes/bbknn/meta.yaml index 1234e90ae2c9f..3ce4ea3da7845 100644 --- a/recipes/bbknn/meta.yaml +++ b/recipes/bbknn/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 1c01a9d6df2fc52a527de8a403617897a4b672724863299a7026f2132f1b041b build: - number: 3 + number: 4 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " run_exports: - {{ pin_subpackage('bbknn', max_pin="x") }} diff --git a/recipes/bbmap/meta.yaml b/recipes/bbmap/meta.yaml index f49885f19c247..554cf6e1792b8 100644 --- a/recipes/bbmap/meta.yaml +++ b/recipes/bbmap/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} diff --git a/recipes/bcalm/build_failure.osx-64.yaml b/recipes/bcalm/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..f094fcee82b1f --- /dev/null +++ b/recipes/bcalm/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 698d7102ae8eb52bf9d7b3733c8db84faf76abc6457ad60522da7524ce955270 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [ 26%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FDtest.c.o + [ 26%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FDwindows.c.o + [ 26%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FL.c.o + [ 26%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FO.c.o + [ 27%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FS.c.o + [ 27%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FScache.c.o + [ 27%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FSdbg.c.o + [ 27%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FSint.c.o + [ 28%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FSsection.c.o + [ 28%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FSstat.c.o + [ 28%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FStest.c.o + [ 28%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5G.c.o + [ 28%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gbtree2.c.o + [ 29%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gcache.c.o + [ 29%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gcompact.c.o + [ 29%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gdense.c.o + [ 29%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gdeprec.c.o + [ 30%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gent.c.o + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + [ 30%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gint.c.o + [ 30%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Glink.c.o + raise subprocess.CalledProcessError(proc.returncode, _args) + [ 30%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gloc.c.o + [ 30%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gname.c.o + [ 31%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gnode.c.o + [ 31%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gobj.c.o + [ 31%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Goh.c.o + [ 31%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Groot.c.o + [ 31%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gstab.c.o + [ 32%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gtest.c.o + [ 32%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gtraverse.c.o + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bcalm_1734475859300/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + [ 32%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HF.c.o + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + [ 32%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFbtree2.c.o + [ 33%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFcache.c.o + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + [ 33%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFdbg.c.o + [ 33%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFdblock.c.o + [ 33%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFdtable.c.o + [ 33%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFhdr.c.o + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bcalm_1734475859300/work/conda_build.sh']' returned non-zero exit status 2. + [ 34%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFhuge.c.o + [ 34%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFiblock.c.o + [ 34%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFiter.c.o + [ 34%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFman.c.o + [ 35%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFsection.c.o + [ 35%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFspace.c.o + [ 35%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFstat.c.o + [ 35%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFtest.c.o + [ 35%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFtiny.c.o + [ 36%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HG.c.o + [ 36%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HGcache.c.o + [ 36%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HGdbg.c.o + [ 36%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HGquery.c.o + [ 37%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HL.c.o + [ 37%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HLcache.c.o + [ 37%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HLdbg.c.o + [ 37%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HLdblk.c.o + [ 37%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HLint.c.o + [ 38%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HLprfx.c.o + [ 38%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HP.c.o + [ 38%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5I.c.o + [ 38%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Itest.c.o + [ 39%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5L.c.o + [ 39%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Lexternal.c.o + [ 39%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MF.c.o + [ 39%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MFaggr.c.o + [ 39%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MFdbg.c.o + [ 40%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MFsection.c.o + [ 40%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MM.c.o + [ 40%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MP.c.o + [ 40%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MPtest.c.o + [ 40%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5O.c.o + [ 41%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Oainfo.c.o + [ 41%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Oalloc.c.o + [ 41%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Oattr.c.o + [ 41%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Oattribute.c.o + [ 42%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Obogus.c.o + [ 42%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Obtreek.c.o + [ 42%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Ocache.c.o + [ 42%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Ocache_image.c.o + [ 42%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Ochunk.c.o + [ 43%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Ocont.c.o + [ 43%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Ocopy.c.o + [ 43%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Odbg.c.o + [ 43%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Odeprec.c.o +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/bcalm/meta.yaml b/recipes/bcalm/meta.yaml index 225521b463c93..5ef373a7ba422 100644 --- a/recipes/bcalm/meta.yaml +++ b/recipes/bcalm/meta.yaml @@ -11,7 +11,7 @@ source: sha256: '{{sha256}}' build: - number: 6 + number: 7 run_exports: - {{ pin_subpackage("bcalm", max_pin="x.x.x") }} diff --git a/recipes/bcftools/1.3/meta.yaml b/recipes/bcftools/1.3/meta.yaml index 3f153aca1164b..44063ec9aff47 100644 --- a/recipes/bcftools/1.3/meta.yaml +++ b/recipes/bcftools/1.3/meta.yaml @@ -7,7 +7,7 @@ source: url: https://github.com/samtools/bcftools/releases/download/1.3/bcftools-1.3.tar.bz2 build: - number: 8 + number: 9 requirements: build: diff --git a/recipes/bcftools/meta.yaml b/recipes/bcftools/meta.yaml index c2d6bc3961469..de359ecb191dd 100644 --- a/recipes/bcftools/meta.yaml +++ b/recipes/bcftools/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("bcftools", max_pin="x") }} diff --git a/recipes/bcov/build_failure.osx-64.yaml b/recipes/bcov/build_failure.osx-64.yaml index 4a52bda41095a..e67338c382bc5 100644 --- a/recipes/bcov/build_failure.osx-64.yaml +++ b/recipes/bcov/build_failure.osx-64.yaml @@ -1,29 +1,7 @@ -recipe_sha: 22c66601a735ae21975313b1d7913f6ded1f2e5b4c41bfcda0f832817b9f6f06 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: fc5623dbe1d8ae87375ad4b7f4bec5c75fad6da18c691708088a1577e37a78bc # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- - GFORTRAN=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bcov-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bcov-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -32,27 +10,49 @@ log: |- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack SIZE=x86_64-apple-darwin13.4.0-size + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bcov_1733962369132/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( STRINGS=x86_64-apple-darwin13.4.0-strings STRIP=x86_64-apple-darwin13.4.0-strip _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 ac_cv_func_malloc_0_nonnull=yes ac_cv_func_realloc_0_nonnull=yes build_alias=x86_64-apple-darwin13.4.0 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc host_alias=x86_64-apple-darwin13.4.0 checking for a BSD-compatible install... /usr/bin/install -c + checking whether sleep supports fractional seconds... yes + checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bcov_1733962369132/work/conda_build.sh']' returned non-zero exit status 2. checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes + checking xargs -n works... yes checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang checking whether the C compiler works... yes checking for C compiler default output file name... a.out @@ -98,7 +98,7 @@ log: |- make[1]: Entering directory '$SRC_DIR' Making all in src make[2]: Entering directory '$SRC_DIR/src' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bcov-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bcov-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c make[2]: Leaving directory '$SRC_DIR/src' make[1]: Leaving directory '$SRC_DIR' # Last 100 lines of the build log. diff --git a/recipes/bcov/meta.yaml b/recipes/bcov/meta.yaml index 7875a0390f4f8..5ecf7e7094e84 100644 --- a/recipes/bcov/meta.yaml +++ b/recipes/bcov/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 9 + number: 10 run_exports: - {{ pin_subpackage("bcov", max_pin="x.x.x") }} diff --git a/recipes/beagle-lib/meta.yaml b/recipes/beagle-lib/meta.yaml index 4d711fca88a13..1a2dc5ea6d4ed 100644 --- a/recipes/beagle-lib/meta.yaml +++ b/recipes/beagle-lib/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 9d258cd9bedd86d7c28b91587acd1132f4e01d4f095c657ad4dc93bd83d4f120 build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('beagle-lib', max_pin="x") }} diff --git a/recipes/bed2gff/meta.yaml b/recipes/bed2gff/meta.yaml index 43a1e954c68bf..c528b0ebca25c 100644 --- a/recipes/bed2gff/meta.yaml +++ b/recipes/bed2gff/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 250333a3388a90d0a2f5a927eef220def95f7556e0c7d2344f0f7a37b3efa327 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('bed2gff', max_pin="x.x") }} diff --git a/recipes/bed2gtf/meta.yaml b/recipes/bed2gtf/meta.yaml index 544347765bd27..db746c42bb012 100644 --- a/recipes/bed2gtf/meta.yaml +++ b/recipes/bed2gtf/meta.yaml @@ -10,7 +10,7 @@ source: sha256: c6a0b2ea31719932ef6cf002e68d72579daaa327d993da0069b302b51b1b7439 build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('bed2gtf', max_pin="x.x") }} diff --git a/recipes/bedops/build_failure.osx-64.yaml b/recipes/bedops/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..4763ceaa2edca --- /dev/null +++ b/recipes/bedops/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: f6f36dc0235be8810e8c432174bb74485d4a7099dd82f08431e511b25420caa3 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + make[8]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test/suites/api' + make[8]: Nothing to be done for 'all'. + make[8]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test/suites/api' + make[8]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test/suites' + make[8]: Nothing to be done for 'all-am'. + make[8]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test/suites' + make[7]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test/suites' + make[7]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test' + make[7]: Nothing to be done for 'all-am'. + make[7]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test' + make[6]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test' + make[6]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6' + make[6]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6' + make[5]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6' + make[4]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6' + make[4]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6' + Making install in doc + make[5]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/doc' + make[6]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/doc' + make[6]: Nothing to be done for 'install-exec-am'. + make[6]: Nothing to be done for 'install-data-am'. + make[6]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/doc' + make[5]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/doc' + Making install in src + make[5]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/src' + make[6]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/src' + .././install-sh -c -d '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/lib' + .././install-sh -c -d '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/include' + /bin/sh ../libtool --mode=install /usr/bin/install -c libjansson.la '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/lib' + /usr/bin/install -c -m 644 jansson.h jansson_config.h '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/include' + libtool: install: /usr/bin/install -c .libs/libjansson.4.dylib $SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/lib/libjansson.4.dylib + libtool: install: (cd $SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/lib && { ln -s -f libjansson.4.dylib libjansson.dylib || { rm -f libjansson.dylib && ln -s libjansson.4.dylib libjansson.dylib; }; }) + libtool: install: /usr/bin/install -c .libs/libjansson.lai $SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/lib/libjansson.la + libtool: install: /usr/bin/install -c .libs/libjansson.a $SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/lib/libjansson.a + libtool: install: chmod 644 $SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/lib/libjansson.a + libtool: install: x86_64-apple-darwin13.4.0-ranlib $SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/lib/libjansson.a + make[6]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/src' + make[5]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/src' + Making install in test + make[5]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test' + Making install in bin + make[6]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test/bin' + make[7]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test/bin' + make[7]: Nothing to be done for 'install-exec-am'. + make[7]: Nothing to be done for 'install-data-am'. + make[7]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test/bin' + make[6]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test/bin' + Making install in suites + make[6]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test/suites' + Making install in api + make[7]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test/suites/api' + make[8]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test/suites/api' + make[8]: Nothing to be done for 'install-exec-am'. + make[8]: Nothing to be done for 'install-data-am'. + make[8]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test/suites/api' + make[7]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test/suites/api' + make[7]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test/suites' + make[8]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test/suites' + make[8]: Nothing to be done for 'install-exec-am'. + make[8]: Nothing to be done for 'install-data-am'. + make[8]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test/suites' + make[7]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test/suites' + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + make[6]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test/suites' + make[6]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test' + make[7]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test' + make[7]: Nothing to be done for 'install-exec-am'. + make[7]: Nothing to be done for 'install-data-am'. + make[7]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test' + make[6]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test' + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + make[5]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/test' + make[5]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6' + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bedops_1734795285806/work/conda_build.sh']' returned non-zero exit status 2. + + make[6]: Entering directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6' + make[6]: Nothing to be done for 'install-exec-am'. + ./install-sh -c -d '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/lib/pkgconfig' + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + /usr/bin/install -c -m 644 jansson.pc '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6/lib/pkgconfig' + make[6]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6' + make[5]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6' + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + make[4]: Leaving directory '$SRC_DIR/third-party/darwin_intel_x86_64/jansson-2.6' + make[3]: Leaving directory '$SRC_DIR' + make[2]: Leaving directory '$SRC_DIR' + make[1]: Leaving directory '$SRC_DIR' + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bedops_1734795285806/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/bedops/meta.yaml b/recipes/bedops/meta.yaml index 8224cdd389f9a..cce8fe1679835 100644 --- a/recipes/bedops/meta.yaml +++ b/recipes/bedops/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage("bedops", max_pin="x.x.x") }} diff --git a/recipes/bedtk/meta.yaml b/recipes/bedtk/meta.yaml index 13e1ffd1868b4..2900dcc271327 100644 --- a/recipes/bedtk/meta.yaml +++ b/recipes/bedtk/meta.yaml @@ -14,7 +14,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage("bedtk", max_pin="x.x.x") }} diff --git a/recipes/bedtools/2.27.1/meta.yaml b/recipes/bedtools/2.27.1/meta.yaml index 71274ad80b12d..090531aaf694e 100644 --- a/recipes/bedtools/2.27.1/meta.yaml +++ b/recipes/bedtools/2.27.1/meta.yaml @@ -12,7 +12,7 @@ source: - 0001-Makefile-append-CXXFLAGS.patch build: - number: 8 + number: 9 requirements: build: diff --git a/recipes/bedtools/meta.yaml b/recipes/bedtools/meta.yaml index bf08c71d3d5ed..ebb05ca172bfb 100644 --- a/recipes/bedtools/meta.yaml +++ b/recipes/bedtools/meta.yaml @@ -10,7 +10,7 @@ source: sha256: fc7e660c2279b1e008b80aca0165a4a157daf4994d08a533ee925d73ce732b97 build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('bedtools', max_pin="x") }} diff --git a/recipes/bellmans-gapc/build_failure.linux-aarch64.yaml b/recipes/bellmans-gapc/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..c3b53114a9822 --- /dev/null +++ b/recipes/bellmans-gapc/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 3f2a263ec2187db34d03e96a3fdfbb4d58286c7f4195dd7da4081ddf7bdcc5ff # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + checking for $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc option to enable C11 features... none needed + checking for stdio.h... yes + checking for stdlib.h... yes + checking for string.h... yes + checking for inttypes.h... yes + checking for stdint.h... yes + checking for strings.h... yes + checking for sys/stat.h... yes + checking for sys/types.h... yes + checking for unistd.h... yes + checking for wchar.h... yes + checking for minix/config.h... no + checking whether it is safe to define __EXTENSIONS__... yes + checking whether _XOPEN_SOURCE should be defined... no + checking for strdup... yes + configure: creating ./config.status + config.status: creating config.h + uname + '[' xLinux == xDarwin ']' + make -j 4 CC=/opt/conda/conda-bld/bellmans-gapc_1734538923826/_build_env/bin/aarch64-conda-linux-gnu-cc CXX=/opt/conda/conda-bld/bellmans-gapc_1734538923826/_build_env/bin/aarch64-conda-linux-gnu-c + ################################################################################ + Using user supplied build config from config.mf + ################################################################################ + make -C testdata/config-tests -f config.mf clean + make[1]: Entering directory '$SRC_DIR/testdata/config-tests' + tput: No value for $TERM and no -T specified + tput: No value for $TERM and no -T specified + rm -f cc.succ cxx.succ boost.succ boost_test.succ boost_program.succ flex.succ bison.succ ksh.succ openmpxx.succ sed.succ mmap.succ cc_test cc_exec cc_pre cc_post cxx_test cxx_exec cxx_pre cxx_post boost_test boost_exec boost_pre boost_post boost_test_exec boost_test_pre boost_test_post boost_program_test boost_program_exec boost_program_pre boost_program_post flex_test flex_test.cc flex_exec flex_pre flex_post bison_test bison_test.cc bison_exec bison_pre bison_post position.hh stack.hh bison_test.output bison_test.hh location.hh ksh_exec ksh_pre ksh_post openmpxx_test openmpxx_exec openmpxx_pre openmpxx_post sed_pre ser_exec sed_post mmap_pre mmap_test mmap_post mmap_exec config.finished + make[1]: Leaving directory '$SRC_DIR/testdata/config-tests' + make -C testdata/config-tests -f config.mf + make[1]: Entering directory '$SRC_DIR/testdata/config-tests' + tput: No value for $TERM and no -T specified + tput: No value for $TERM and no -T specified + >>> Checking for C99 compiler ... + >>> Checking for ISO C compiler ... + >>> Checking for boost unit test framework ... OK + $PREFIX/bin/flex -o flex_test.cc flex_test.l + >>> Creating parser via bison ... + # make a copy of the original file + >>> Checking for ksh compatible shell ... + cp bison_test.y bison_test.y.orig + # create a new temporary directory + # copy input file into temporary directory + >>> Checking OpenMP with C compilation ... + cp bison_test.y /tmp/tmp.cJ3aUFhBrR/ + # use bison to generate parser source files + # we have a breaking change since Bison 3.3.2, which only effects src/parser.y + >>> Checking for sed ... + # if first bison attempt fails, we will try to apply a patch to the input in the tmpdir and rerun the code generation + cd /tmp/tmp.cJ3aUFhBrR; $PREFIX/bin/bison -o bison_test.cc bison_test.y 2>&1 \ + || (echo "failed to generate parser, trying to patch input bison_test.y file..." && (patch bison_test.y < $SRC_DIR/testdata/config-tests/bison_test.y_apiparserclass.patch && $PREFIX/bin/bison -o bison_test.cc bison_test.y 2>&1)) \ + || (echo "failed to generate parser, trying another patch on input bison_test.y file..." && cp $SRC_DIR/testdata/config-tests/bison_test.y . && (patch bison_test.y < $SRC_DIR/testdata/config-tests/bison_test.y_osx.patch && $PREFIX/bin/bison -o bison_test.cc bison_test.y 2>&1)) + bison_test.y:21.1-14: warning: deprecated directive: '%error-verbose', use '%define parse.error verbose' [-Wdeprecated] + 21 | %error-verbose + | ^~~~~~~~~~~~~~ + | %define parse.error verbose + >>> Checking mmap ... + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bellmans-gapc-2024.01.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -I librna/ -std=c11 -DHAVE_CONFIG_H -DNDEBUG cc_test.c -L$PREFIX/lib/ -Xlinker -rpath -Xlinker $PREFIX/lib/ -o cc_test + bison_test.y: warning: fix-its can be applied. Rerun with option '--update'. [-Wother] + # remove source file from temporary directiry + rm /tmp/tmp.cJ3aUFhBrR/bison_test.y + # copy all generated files into working directory + cp /tmp/tmp.cJ3aUFhBrR/* ./ + # clean up temporary directory + rm /tmp/tmp.cJ3aUFhBrR/* + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bellmans-gapc-2024.01.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c17 -D_XOPEN_SOURCE=500 -MMD -MP -Wall -Wnon-virtual-dtor -Wno-unused-variable -Wno-parentheses -DNDEBUG -DBISONNEW cxx_test.cc -L$PREFIX/lib/ -Xlinker -rpath -Xlinker $PREFIX/lib/ -o cxx_test + rmdir /tmp/tmp.cJ3aUFhBrR + # revert patch + mv bison_test.y.orig bison_test.y + touch boost_test.succ + /bin/sh ksh_test.sh 1 2 3 > ksh_exec + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bellmans-gapc-2024.01.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c17 -D_XOPEN_SOURCE=500 -MMD -MP -Wall -Wnon-virtual-dtor -Wno-unused-variable -Wno-parentheses -DNDEBUG -DBISONNEW -fopenmp openmpxx_test.cc -L$PREFIX/lib/ -Xlinker -rpath -Xlinker $PREFIX/lib/ -o openmpxx_test + ./sed_test.sh sed + make[1]: *** [config.mf:203: sed_exec] Error 127 + make[1]: *** Waiting for unfinished jobs.... + make[1]: Leaving directory '$SRC_DIR/testdata/config-tests' + make: *** No rule to make target 'testdata/config-tests/config.finished', needed by 'src/location.hh'. Stop. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bellmans-gapc_1734538923826/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bellmans-gapc_1734538923826/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/bellmans-gapc/meta.yaml b/recipes/bellmans-gapc/meta.yaml index 5aac7f2d5df62..d7195960a5fa3 100644 --- a/recipes/bellmans-gapc/meta.yaml +++ b/recipes/bellmans-gapc/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 590b62d5fc39b1deb45855b0586d7ca3674ef17c59fc84ef445d2760a480f7ba build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage('bellmans-gapc', max_pin=None) }} diff --git a/recipes/bfc/meta.yaml b/recipes/bfc/meta.yaml index 48efced8289a0..d311092fbc106 100644 --- a/recipes/bfc/meta.yaml +++ b/recipes/bfc/meta.yaml @@ -3,7 +3,7 @@ package: version: "r181" build: - number: 10 + number: 11 run_exports: - {{ pin_subpackage("bfc", max_pin="x.x.x") }} diff --git a/recipes/bgreat/meta.yaml b/recipes/bgreat/meta.yaml index 586688e1e95e1..8a6426ab235ec 100644 --- a/recipes/bgreat/meta.yaml +++ b/recipes/bgreat/meta.yaml @@ -10,7 +10,7 @@ source: sha256: bc60e755a3205b725834f37d7509062879415f03730b424cbac06b776eb977cc build: - number: 7 + number: 8 run_exports: - {{ pin_subpackage("bgreat", max_pin="x.x.x") }} skip: true # [osx] diff --git a/recipes/bgt/meta.yaml b/recipes/bgt/meta.yaml index aa4a6ac4d4fb5..1f6bff2f50b59 100644 --- a/recipes/bgt/meta.yaml +++ b/recipes/bgt/meta.yaml @@ -3,7 +3,7 @@ package: version: "r283" build: - number: 6 + number: 7 source: url: https://github.com/lh3/bgt/archive/7c66cc885df74328a191b943140e3db96a3c7de6.tar.gz diff --git a/recipes/bicseq2-norm/meta.yaml b/recipes/bicseq2-norm/meta.yaml index 9ab60958085a9..7e5d8f6b71dcd 100644 --- a/recipes/bicseq2-norm/meta.yaml +++ b/recipes/bicseq2-norm/meta.yaml @@ -14,7 +14,7 @@ source: - paths.patch build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/bicseq2-seg/meta.yaml b/recipes/bicseq2-seg/meta.yaml index 70fc1109d855c..9a59cc8cf8e09 100644 --- a/recipes/bicseq2-seg/meta.yaml +++ b/recipes/bicseq2-seg/meta.yaml @@ -13,7 +13,7 @@ source: - paths.patch build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/bifrost/build_failure.osx-arm64.yaml b/recipes/bifrost/build_failure.osx-arm64.yaml new file mode 100644 index 0000000000000..e90dc74d58605 --- /dev/null +++ b/recipes/bifrost/build_failure.osx-arm64.yaml @@ -0,0 +1,106 @@ +recipe_sha: f52add991f649897983aef31eaaa2f4c237c87776d7bfc1ad960a034a1ed8a6a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + LIBTOOL=arm64-apple-darwin20.0.0-libtool + LIPO=arm64-apple-darwin20.0.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=arm64-apple-darwin20.0.0-nm + NMEDIT=arm64-apple-darwin20.0.0-nmedit + OBJC=arm64-apple-darwin20.0.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang + OTOOL=arm64-apple-darwin20.0.0-otool + PAGESTUFF=arm64-apple-darwin20.0.0-pagestuff + RANLIB=arm64-apple-darwin20.0.0-ranlib + REDO_PREBINDING=arm64-apple-darwin20.0.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk + SEGEDIT=arm64-apple-darwin20.0.0-segedit + SEG_ADDR_TABLE=arm64-apple-darwin20.0.0-seg_addr_table + SEG_HACK=arm64-apple-darwin20.0.0-seg_hack + SIZE=arm64-apple-darwin20.0.0-size + STRINGS=arm64-apple-darwin20.0.0-strings + STRIP=arm64-apple-darwin20.0.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_arm64_apple_darwin20_0_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=arm64-apple-darwin20.0.0 + host_alias=arm64-apple-darwin20.0.0 + INFO: activate_clangxx_osx-arm64.sh made the following environmental changes: + CLANGXX=arm64-apple-darwin20.0.0-clang + CXX=arm64-apple-darwin20.0.0-clang + CXXFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bifrost-1.3.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang + DEBUG_CXXFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bifrost-1.3.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -- The C compiler identification is Clang 18.1.8 + -- The CXX compiler identification is Clang 18.1.8 + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang - skipped + -- Detecting C compile features + -- Detecting C compile features - done + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success + -- Found Threads: TRUE + -- Found ZLIB: $PREFIX/lib/libz.dylib (found version "1.3.1") + -- Configuring done (11.2s) + -- Generating done (0.0s) + -- Build files have been written to: $SRC_DIR/build + Change Dir: '$SRC_DIR/build' + + Run Build Command(s): $BUILD_PREFIX/bin/cmake -E env VERBOSE=1 $BUILD_PREFIX/bin/make -f Makefile -j2 install + $BUILD_PREFIX/bin/cmake -S$SRC_DIR -B$SRC_DIR/build --check-build-system CMakeFiles/Makefile.cmake 0 + $BUILD_PREFIX/bin/cmake -E cmake_progress_start $SRC_DIR/build/CMakeFiles $SRC_DIR/build//CMakeFiles/progress.marks + $BUILD_PREFIX/bin/make -f CMakeFiles/Makefile2 all + make[1]: Entering directory '$SRC_DIR/build' + $BUILD_PREFIX/bin/make -f src/CMakeFiles/bifrost_static.dir/build.make src/CMakeFiles/bifrost_static.dir/depend + $BUILD_PREFIX/bin/make -f src/CMakeFiles/bifrost_dynamic.dir/build.make src/CMakeFiles/bifrost_dynamic.dir/depend + make[2]: Entering directory '$SRC_DIR/build' + cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR/src $SRC_DIR/build $SRC_DIR/build/src $SRC_DIR/build/src/CMakeFiles/bifrost_static.dir/DependInfo.cmake "--color=" + make[2]: Entering directory '$SRC_DIR/build' + cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR/src $SRC_DIR/build $SRC_DIR/build/src $SRC_DIR/build/src/CMakeFiles/bifrost_dynamic.dir/DependInfo.cmake "--color=" + Dependee "$SRC_DIR/build/src/CMakeFiles/bifrost_dynamic.dir/DependInfo.cmake" is newer than depender "$SRC_DIR/build/src/CMakeFiles/bifrost_dynamic.dir/depend.internal". + Dependee "$SRC_DIR/build/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "$SRC_DIR/build/src/CMakeFiles/bifrost_dynamic.dir/depend.internal". + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bifrost_1734391278452/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bifrost_1734391278452/work/conda_build.sh']' returned non-zero exit status 2. + Dependee "$SRC_DIR/build/src/CMakeFiles/bifrost_static.dir/DependInfo.cmake" is newer than depender "$SRC_DIR/build/src/CMakeFiles/bifrost_static.dir/depend.internal". + Dependee "$SRC_DIR/build/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "$SRC_DIR/build/src/CMakeFiles/bifrost_static.dir/depend.internal". + Scanning dependencies of target bifrost_static + Scanning dependencies of target bifrost_dynamic + make[2]: Leaving directory '$SRC_DIR/build' + $BUILD_PREFIX/bin/make -f src/CMakeFiles/bifrost_static.dir/build.make src/CMakeFiles/bifrost_static.dir/build + make[2]: Leaving directory '$SRC_DIR/build' + $BUILD_PREFIX/bin/make -f src/CMakeFiles/bifrost_dynamic.dir/build.make src/CMakeFiles/bifrost_dynamic.dir/build + make[2]: Entering directory '$SRC_DIR/build' + make[2]: Entering directory '$SRC_DIR/build' + [ 3%] Building CXX object src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o + cd $SRC_DIR/build/src && $BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I$SRC_DIR/src -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bifrost-1.3.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -D_FILE_OFFSET_BITS=64 -I$PREFIX/include -std=c11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -mmacosx-version-min=11.0 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -MF CMakeFiles/bifrost_static.dir/Bifrost.cpp.o.d -o CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -c $SRC_DIR/src/Bifrost.cpp + [ 6%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o + cd $SRC_DIR/build/src && $BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I$SRC_DIR/src -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bifrost-1.3.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -D_FILE_OFFSET_BITS=64 -I$PREFIX/include -std=c11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -mmacosx-version-min=11.0 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o -c $SRC_DIR/src/Bifrost.cpp + make[2]: Leaving directory '$SRC_DIR/build' + [ 9%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o + cd $SRC_DIR/build/src && $BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I$SRC_DIR/src -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bifrost-1.3.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -D_FILE_OFFSET_BITS=64 -I$PREFIX/include -std=c11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -mmacosx-version-min=11.0 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o -c $SRC_DIR/src/BitContainer.cpp + make[2]: Leaving directory '$SRC_DIR/build' + make[1]: Leaving directory '$SRC_DIR/build' +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/bifrost/meta.yaml b/recipes/bifrost/meta.yaml index 1dc9bb202eea2..02163a813e04e 100644 --- a/recipes/bifrost/meta.yaml +++ b/recipes/bifrost/meta.yaml @@ -10,7 +10,7 @@ source: sha256: e1b2491328b0cc1a32e433a8a9780f05547fa4b8d674b58abdda9ac8809f5341 build: - number: 1 + number: 2 # v1.3.0 breaks Bifrost Index File (.bfi) compatibility with previous Bifrost versions run_exports: - {{ pin_subpackage('bifrost', max_pin="x.x") }} diff --git a/recipes/bigtools/meta.yaml b/recipes/bigtools/meta.yaml index 6928b2c7a780a..629d46725e5db 100644 --- a/recipes/bigtools/meta.yaml +++ b/recipes/bigtools/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('bigtools', max_pin="x.x") }} diff --git a/recipes/bindash/meta.yaml b/recipes/bindash/meta.yaml index fbfd4d1282bb2..cf57427ba0442 100644 --- a/recipes/bindash/meta.yaml +++ b/recipes/bindash/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 6e4bf36fd04195ed0738ea8bf835eca1e400b5ce6eef3902bdf0673955d15166 build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage('bindash', max_pin="x") }} diff --git a/recipes/binspreader/build_failure.linux-64.yaml b/recipes/binspreader/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..aae165f3c33f9 --- /dev/null +++ b/recipes/binspreader/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 72eff078250ab1ca53b63c1ced095db4bf4259e0941cbbee62599fb8cfa43bd9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + libzlib: 1.3.1-hb9d3cd8_2 conda-forge + llvm-openmp: 8.0.1-hc9558a2_0 conda-forge + openmp: 8.0.1-0 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + zlib: 1.3.1-hb9d3cd8_2 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/binspreader_1733932373560/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.39-he00db2b_1 conda-forge + binutils_linux-64: 2.39-h5fc0e48_13 conda-forge + bzip2: 1.0.8-h4bc722e_7 conda-forge + c-ares: 1.34.3-hb9d3cd8_1 conda-forge + ca-certificates: 2024.8.30-hbcca054_0 conda-forge + cmake: 3.31.2-h74e3db0_1 conda-forge + gcc_impl_linux-64: 9.5.0-h99780fb_19 conda-forge + gcc_linux-64: 9.5.0-h4258300_13 conda-forge + gxx_impl_linux-64: 9.5.0-h99780fb_19 conda-forge + gxx_linux-64: 9.5.0-h43f449f_13 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + keyutils: 1.6.1-h166bdaf_0 conda-forge + krb5: 1.21.3-h659f571_0 conda-forge + ld_impl_linux-64: 2.39-hcc3a1bd_1 conda-forge + libcurl: 8.10.1-hbbe4b11_0 conda-forge + libedit: 3.1.20191231-he28a2e2_2 conda-forge + libev: 4.33-hd590300_2 conda-forge + libexpat: 2.6.4-h5888daf_0 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 9.5.0-h0a57e50_19 conda-forge + libgcc-ng: 14.2.0-h69a702a_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + liblzma: 5.6.3-hb9d3cd8_1 conda-forge + libnghttp2: 1.64.0-h161d5f1_0 conda-forge + libsanitizer: 9.5.0-h2f262e1_19 conda-forge + libssh2: 1.11.1-hf672d98_0 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-devel_linux-64: 9.5.0-h0a57e50_19 conda-forge + libstdcxx-ng: 14.2.0-h4852527_1 conda-forge + libuv: 1.49.2-hb9d3cd8_0 conda-forge + libzlib: 1.3.1-hb9d3cd8_2 conda-forge + llvm-openmp: 8.0.1-hc9558a2_0 conda-forge + make: 4.4.1-hb9d3cd8_2 conda-forge + ncurses: 6.5-he02047a_1 conda-forge + openmp: 8.0.1-0 conda-forge + openssl: 3.4.0-hb9d3cd8_0 conda-forge + pkg-config: 0.29.2-h4bc722e_1009 conda-forge + rhash: 1.4.5-hb9d3cd8_0 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: BinSPreader-3.16.0-dev_c4e2520879.tar.gz + Downloading https://cab.spbu.ru/files/binspreader/BinSPreader-3.16.0-dev.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NameResolutionError(": Failed to resolve 'cab.spbu.ru' ([Errno -2] Name or service not known)")': /files/binspreader/BinSPreader-3.16.0-dev.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NameResolutionError(": Failed to resolve 'cab.spbu.ru' ([Errno -2] Name or service not known)")': /files/binspreader/BinSPreader-3.16.0-dev.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NameResolutionError(": Failed to resolve 'cab.spbu.ru' ([Errno -2] Name or service not known)")': /files/binspreader/BinSPreader-3.16.0-dev.tar.gz + WARNING: Error: HTTP 000 CONNECTION FAILED for url + Elapsed: - + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download https://cab.spbu.ru/files/binspreader/BinSPreader-3.16.0-dev.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/binspreader/build_failure.osx-64.yaml b/recipes/binspreader/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..303897c6f1ea2 --- /dev/null +++ b/recipes/binspreader/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 72eff078250ab1ca53b63c1ced095db4bf4259e0941cbbee62599fb8cfa43bd9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (local): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (local): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/binspreader_1733870805574/_build_env + + + The following NEW packages will be INSTALLED: + + bzip2: 1.0.8-hfdf4475_7 conda-forge + c-ares: 1.34.3-hf13058a_1 conda-forge + ca-certificates: 2024.8.30-h8857fd0_0 conda-forge + cctools_osx-64: 1010.6-h00edd4c_2 conda-forge + clang: 18.1.8-default_h179603d_5 conda-forge + clang-18: 18.1.8-default_h0c94c6a_5 conda-forge + clang-format: 18.1.8-default_h0c94c6a_5 conda-forge + clang-format-18: 18.1.8-default_h0c94c6a_5 conda-forge + clang-tools: 18.1.8-default_h0c94c6a_5 conda-forge + clang_impl_osx-64: 18.1.8-h6a44ed1_23 conda-forge + clang_osx-64: 18.1.8-h7e5c614_23 conda-forge + clangdev: 18.1.8-default_h0c94c6a_5 conda-forge + clangxx: 18.1.8-default_h179603d_5 conda-forge + clangxx_impl_osx-64: 18.1.8-h4b7810f_23 conda-forge + clangxx_osx-64: 18.1.8-h7e5c614_23 conda-forge + cmake: 3.31.2-heacca2f_0 conda-forge + compiler-rt: 18.1.8-h1020d70_1 conda-forge + compiler-rt_osx-64: 18.1.8-hf2b8a54_1 conda-forge + krb5: 1.21.3-h37d8d59_0 conda-forge + ld64_osx-64: 951.9-hc8d1a19_2 conda-forge + libclang: 18.1.8-default_h0c94c6a_5 conda-forge + libclang-cpp: 18.1.8-default_h0c94c6a_5 conda-forge + libclang-cpp18.1: 18.1.8-default_h0c94c6a_5 conda-forge + libclang13: 18.1.8-default_h9ff962c_5 conda-forge + libcurl: 8.10.1-h58e7537_0 conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libcxx-devel: 18.1.8-h7c275be_7 conda-forge + libedit: 3.1.20191231-h0678c8f_2 conda-forge + libev: 4.33-h10d778d_2 conda-forge + libexpat: 2.6.4-h240833e_0 conda-forge + libiconv: 1.17-hd75f5a5_2 conda-forge + libllvm18: 18.1.8-h9ce406d_2 conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libnghttp2: 1.64.0-hc7306c3_0 conda-forge + libssh2: 1.11.1-h3dc7d44_0 conda-forge + libuv: 1.49.2-hd79239c_0 conda-forge + libxml2: 2.13.5-he8ee3e7_1 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-openmp: 18.1.8-h15ab845_1 conda-forge + llvm-tools: 18.1.8-h9ce406d_2 conda-forge + llvm-tools-18: 18.1.8-h9ce406d_2 conda-forge + llvmdev: 18.1.8-h9ce406d_2 conda-forge + make: 4.4.1-h00291cd_2 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + pkg-config: 0.29.2-hf7e621a_1009 conda-forge + rhash: 1.4.5-ha44c9a9_0 conda-forge + sigtool: 0.1.3-h88f4db0_0 conda-forge + tapi: 1300.6.5-h390ca13_0 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache + Downloading source to cache: BinSPreader-3.16.0-dev_c4e2520879.tar.gz + Downloading https://cab.spbu.ru/files/binspreader/BinSPreader-3.16.0-dev.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NameResolutionError(": Failed to resolve 'cab.spbu.ru' ([Errno 8] nodename nor servname provided, or not known)")': /files/binspreader/BinSPreader-3.16.0-dev.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NameResolutionError(": Failed to resolve 'cab.spbu.ru' ([Errno 8] nodename nor servname provided, or not known)")': /files/binspreader/BinSPreader-3.16.0-dev.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NameResolutionError(": Failed to resolve 'cab.spbu.ru' ([Errno 8] nodename nor servname provided, or not known)")': /files/binspreader/BinSPreader-3.16.0-dev.tar.gz + WARNING: Error: HTTP 000 CONNECTION FAILED for url + Elapsed: - + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download https://cab.spbu.ru/files/binspreader/BinSPreader-3.16.0-dev.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/binspreader/meta.yaml b/recipes/binspreader/meta.yaml index a3e44865c1a69..46eead9588203 100644 --- a/recipes/binspreader/meta.yaml +++ b/recipes/binspreader/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/bioawk/meta.yaml b/recipes/bioawk/meta.yaml index 70ec45f58e648..bfe64f07d70f2 100644 --- a/recipes/bioawk/meta.yaml +++ b/recipes/bioawk/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 5cbef3f39b085daba45510ff450afcf943cfdfdd483a546c8a509d3075ff51b5 build: - number: 12 + number: 13 run_exports: - {{ pin_subpackage("bioawk", max_pin="x.x.x") }} diff --git a/recipes/biobambam/build_failure.linux-aarch64.yaml b/recipes/biobambam/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..ec88779afbe52 --- /dev/null +++ b/recipes/biobambam/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 58179d769e41c88f6906267b814a922be99028500b080706e1c976a986b20ac3 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + INFO (biobambam,bin/bamfiltermc): Needed DSO lib/libstdc.so.6 found in conda-forge/linux-aarch64::libstdcxx==14.2.0=h3f4de04_1 + WARNING (biobambam,bin/bamfiltermc): Needed DSO lib/libgomp.so.1 found in ['conda-forge/linux-aarch64::_openmp_mutex==4.5=2_gnu'] + WARNING (biobambam,bin/bamfiltermc): .. but ['conda-forge/linux-aarch64::_openmp_mutex==4.5=2_gnu'] not in reqs/run, (i.e. it is overlinking) (likely) or a missing dependency (less likely) + INFO (biobambam,bin/bamfiltermc): Needed DSO lib/libgcc_s.so.1 found in conda-forge/linux-aarch64::libgcc==14.2.0=he277a41_1 + INFO (biobambam,bin/bamfiltermc): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libpthread.so.0 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_18 + INFO (biobambam,bin/bamfiltermc): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_18 + INFO (biobambam,bin/bamfiltermc): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/ld-linux-aarch64.so.1 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_18 + WARNING (biobambam): run-exports library package conda-forge/linux-aarch64::gmp==6.3.0=h0a1ffab_2 in requirements/run but it is not used (i.e. it is overdepending or perhaps statically linked? If that is what you want then add it to build/ignore_run_exports) + WARNING (biobambam): run-exports library package conda-forge/linux-aarch64::xerces-c==3.2.5=h595f43b_2 in requirements/run but it is not used (i.e. it is overdepending or perhaps statically linked? If that is what you want then add it to build/ignore_run_exports) + Fixing permissions + Packaged license file/s. + INFO :: Time taken to mark (prefix) + 0 replacements in 0 files was 0.05 seconds + WARNING: Importing conda-verify failed. Please be sure to test your packages. conda install conda-verify to make this message go away. + TEST START: /opt/conda/conda-bld/linux-aarch64/biobambam-2.0.185-h7d28f73_1.tar.bz2 + Renaming work directory '/opt/conda/conda-bld/biobambam_1734549481365/work' to '/opt/conda/conda-bld/biobambam_1734549481365/work_moved_biobambam-2.0.185-h7d28f73_1_linux-aarch64' + shutil.move(work)=/opt/conda/conda-bld/biobambam_1734549481365/work, dest=/opt/conda/conda-bld/biobambam_1734549481365/work_moved_biobambam-2.0.185-h7d28f73_1_linux-aarch64) + Reloading output folder (local): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/biobambam_1734549481365/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + + + The following NEW packages will be INSTALLED: + + _openmp_mutex: 4.5-2_gnu conda-forge + biobambam: 2.0.185-h7d28f73_1 local + boost-cpp: 1.85.0-hdad291f_4 conda-forge + bzip2: 1.0.8-h68df207_7 conda-forge + c-ares: 1.34.4-h86ecc28_0 conda-forge + ca-certificates: 2024.12.14-hcefe29a_0 conda-forge + gmp: 6.3.0-h0a1ffab_2 conda-forge + icu: 75.1-hf9b3779_0 conda-forge + keyutils: 1.6.1-h4e544f5_0 conda-forge + krb5: 1.21.3-h50a48e9_0 conda-forge + libboost: 1.85.0-h9fa81b4_4 conda-forge + libboost-devel: 1.85.0-h37bb5a9_4 conda-forge + libboost-headers: 1.85.0-h8af1aa0_4 conda-forge + libcurl: 8.11.1-h6702fde_0 conda-forge + libdeflate: 1.22-h86ecc28_0 conda-forge + libedit: 3.1.20191231-he28a2e2_2 conda-forge + libev: 4.33-h31becfc_2 conda-forge + libgcc: 14.2.0-he277a41_1 conda-forge + libgcc-ng: 14.2.0-he9431aa_1 conda-forge + libgomp: 14.2.0-he277a41_1 conda-forge + liblzma: 5.6.3-h86ecc28_1 conda-forge + liblzma-devel: 5.6.3-h86ecc28_1 conda-forge + libmaus2: 2.0.813-h3f813d2_1 bioconda + libnghttp2: 1.64.0-hc8609a4_0 conda-forge + libnsl: 2.0.1-h31becfc_0 conda-forge + libssh2: 1.11.1-ha41c0db_0 conda-forge + libstdcxx: 14.2.0-h3f4de04_1 conda-forge + libstdcxx-ng: 14.2.0-hf1166c9_1 conda-forge + libzlib: 1.3.1-h86ecc28_2 conda-forge + ncurses: 6.5-hcccb83c_1 conda-forge + nettle: 3.9.1-h9d1147b_0 conda-forge + openssl: 3.4.0-h86ecc28_0 conda-forge + snappy: 1.1.8-h54f1f3f_3 conda-forge + staden_io_lib: 1.15.0-h346a1c6_3 bioconda + xerces-c: 3.2.5-h595f43b_2 conda-forge + xz: 5.6.3-h2dbfc1b_1 conda-forge + xz-gpl-tools: 5.6.3-h2dbfc1b_1 conda-forge + xz-tools: 5.6.3-h86ecc28_1 conda-forge + zstd: 1.5.6-h02f22dd_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + export PREFIX=/opt/conda/conda-bld/biobambam_1734549481365/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export SRC_DIR=/opt/conda/conda-bld/biobambam_1734549481365/test_tmp + bamsormadup --help + bamsormadup: error while loading shared libraries: libstaden-read.so.14: cannot open shared object file: No such file or directory + WARNING: Tests failed for biobambam-2.0.185-h7d28f73_1.tar.bz2 - moving package to /opt/conda/conda-bld/broken + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/biobambam_1734549481365/test_tmp/conda_test_runner.sh']' returned non-zero exit status 127. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: biobambam-2.0.185-h7d28f73_1.tar.bz2 +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/biobambam/meta.yaml b/recipes/biobambam/meta.yaml index 69ad250229d2e..e21ae3826e86d 100644 --- a/recipes/biobambam/meta.yaml +++ b/recipes/biobambam/meta.yaml @@ -12,7 +12,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin='x') }} diff --git a/recipes/biobb_mem/meta.yaml b/recipes/biobb_mem/meta.yaml index ab0aa0c792ca8..2c72d104c8302 100644 --- a/recipes/biobb_mem/meta.yaml +++ b/recipes/biobb_mem/meta.yaml @@ -69,4 +69,4 @@ about: extra: recipe-maintainers: - - RubenChM \ No newline at end of file + - RubenChM diff --git a/recipes/biobloomtools/meta.yaml b/recipes/biobloomtools/meta.yaml index c3805666e6ca3..261b1779a8ab9 100644 --- a/recipes/biobloomtools/meta.yaml +++ b/recipes/biobloomtools/meta.yaml @@ -10,7 +10,7 @@ source: build: skip: true # [osx or win] - number: 5 + number: 6 run_exports: - {{ pin_subpackage("biobloomtools", max_pin="x") }} @@ -45,4 +45,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/bioconda-repodata-patches/meta.yaml b/recipes/bioconda-repodata-patches/meta.yaml index 5179e4331acad..edb4691f6e8b2 100644 --- a/recipes/bioconda-repodata-patches/meta.yaml +++ b/recipes/bioconda-repodata-patches/meta.yaml @@ -7,7 +7,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage("bioconda-repodata-patches", max_pin=None) }} diff --git a/recipes/bioconductor-a4/meta.yaml b/recipes/bioconductor-a4/meta.yaml index 5ce9102925ae3..077f2b5d54a5c 100644 --- a/recipes/bioconductor-a4/meta.yaml +++ b/recipes/bioconductor-a4/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "a4" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Umbrella package is available for the entire Automated Affymetrix Array Analysis suite of package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Automated Affymetrix Array Analysis Umbrella Package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 54c9c4300db0c04edd9b531bb0f121a0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-a4", max_pin="x.x") }}' - noarch: generic -# Suggests: MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats, hgu95av2.db requirements: host: - - 'bioconductor-a4base >=1.50.0,<1.51.0' - - 'bioconductor-a4classif >=1.50.0,<1.51.0' - - 'bioconductor-a4core >=1.50.0,<1.51.0' - - 'bioconductor-a4preproc >=1.50.0,<1.51.0' - - 'bioconductor-a4reporting >=1.50.0,<1.51.0' + - bioconductor-a4base >=1.54.0,<1.55.0 + - bioconductor-a4classif >=1.54.0,<1.55.0 + - bioconductor-a4core >=1.54.0,<1.55.0 + - bioconductor-a4preproc >=1.54.0,<1.55.0 + - bioconductor-a4reporting >=1.54.0,<1.55.0 - r-base run: - - 'bioconductor-a4base >=1.50.0,<1.51.0' - - 'bioconductor-a4classif >=1.50.0,<1.51.0' - - 'bioconductor-a4core >=1.50.0,<1.51.0' - - 'bioconductor-a4preproc >=1.50.0,<1.51.0' - - 'bioconductor-a4reporting >=1.50.0,<1.51.0' + - bioconductor-a4base >=1.54.0,<1.55.0 + - bioconductor-a4classif >=1.54.0,<1.55.0 + - bioconductor-a4core >=1.54.0,<1.55.0 + - bioconductor-a4preproc >=1.54.0,<1.55.0 + - bioconductor-a4reporting >=1.54.0,<1.55.0 - r-base + +source: + md5: 40f370dbf39df0f5d4182463c5bbd9d7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Automated Affymetrix Array Analysis Umbrella Package' - description: 'Umbrella package is available for the entire Automated Affymetrix Array Analysis suite of package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-a4base/meta.yaml b/recipes/bioconductor-a4base/meta.yaml index 8d52ef862f80d..1ec0e0dc9025f 100644 --- a/recipes/bioconductor-a4base/meta.yaml +++ b/recipes/bioconductor-a4base/meta.yaml @@ -1,65 +1,71 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "a4Base" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Base utility functions are available for the Automated Affymetrix Array Analysis set of packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Automated Affymetrix Array Analysis Base Package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 927ee5147653a1ee4df6380f52ad055a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-a4base", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:a4base + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-a4base + path: recipes/bioconductor-a4base + version: 1.28.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Cairo, ALL, hgu95av2.db, nlcv requirements: host: - - 'bioconductor-a4core >=1.50.0,<1.51.0' - - 'bioconductor-a4preproc >=1.50.0,<1.51.0' - - 'bioconductor-annaffy >=1.74.0,<1.75.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-a4core >=1.54.0,<1.55.0 + - bioconductor-a4preproc >=1.54.0,<1.55.0 + - bioconductor-annaffy >=1.78.0,<1.79.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base - r-glmnet - r-gplots - r-mpm run: - - 'bioconductor-a4core >=1.50.0,<1.51.0' - - 'bioconductor-a4preproc >=1.50.0,<1.51.0' - - 'bioconductor-annaffy >=1.74.0,<1.75.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-a4core >=1.54.0,<1.55.0 + - bioconductor-a4preproc >=1.54.0,<1.55.0 + - bioconductor-annaffy >=1.78.0,<1.79.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base - r-glmnet - r-gplots - r-mpm + +source: + md5: 4771171aad0490cd8cbde8837845b9a7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Automated Affymetrix Array Analysis Base Package' - description: 'Base utility functions are available for the Automated Affymetrix Array Analysis set of packages.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:a4base - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-a4base - path: recipes/bioconductor-a4base - version: 1.28.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-a4classif/meta.yaml b/recipes/bioconductor-a4classif/meta.yaml index c519e2749143a..fdd94d1b7805d 100644 --- a/recipes/bioconductor-a4classif/meta.yaml +++ b/recipes/bioconductor-a4classif/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "a4Classif" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functionalities for classification of Affymetrix microarray data, integrating within the Automated Affymetrix Array Analysis set of packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Automated Affymetrix Array Analysis Classification Package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2af82160c9909dd6fdec620de5710cfa build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-a4classif", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ALL, hgu95av2.db, knitr, rmarkdown requirements: host: - - 'bioconductor-a4core >=1.50.0,<1.51.0' - - 'bioconductor-a4preproc >=1.50.0,<1.51.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-a4core >=1.54.0,<1.55.0 + - bioconductor-a4preproc >=1.54.0,<1.55.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-glmnet - r-pamr - r-rocr - r-varselrf run: - - 'bioconductor-a4core >=1.50.0,<1.51.0' - - 'bioconductor-a4preproc >=1.50.0,<1.51.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-a4core >=1.54.0,<1.55.0 + - bioconductor-a4preproc >=1.54.0,<1.55.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-glmnet - r-pamr - r-rocr - r-varselrf + +source: + md5: 05f58ff9cc5356d54f099b548556f1de + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Automated Affymetrix Array Analysis Classification Package' - description: 'Functionalities for classification of Affymetrix microarray data, integrating within the Automated Affymetrix Array Analysis set of packages.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-a4core/meta.yaml b/recipes/bioconductor-a4core/meta.yaml index 581eed71adc05..f458676f69dd9 100644 --- a/recipes/bioconductor-a4core/meta.yaml +++ b/recipes/bioconductor-a4core/meta.yaml @@ -1,49 +1,55 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "a4Core" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Utility functions for the Automated Affymetrix Array Analysis set of packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Automated Affymetrix Array Analysis Core Package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fdca418afe3a74d9114d8d28afca2037 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-a4core", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:a4core + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-a4core + path: recipes/bioconductor-a4core + version: 1.28.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-glmnet run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-glmnet + +source: + md5: 5d5ce981344b7e509946fdf02ac78498 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Automated Affymetrix Array Analysis Core Package' - description: 'Utility functions for the Automated Affymetrix Array Analysis set of packages.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:a4core - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-a4core - path: recipes/bioconductor-a4core - version: 1.28.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-a4preproc/meta.yaml b/recipes/bioconductor-a4preproc/meta.yaml index 06b428d18d822..6a80419f22457 100644 --- a/recipes/bioconductor-a4preproc/meta.yaml +++ b/recipes/bioconductor-a4preproc/meta.yaml @@ -1,43 +1,22 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "a4Preproc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Utility functions to pre-process data for the Automated Affymetrix Array Analysis set of packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Automated Affymetrix Array Analysis Preprocessing Package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d9eea3d9957fc99156115052398f0cb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-a4preproc", max_pin="x.x") }}' - noarch: generic -# Suggests: ALL, hgu95av2.db, knitr, rmarkdown -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Automated Affymetrix Array Analysis Preprocessing Package' - description: 'Utility functions to pre-process data for the Automated Affymetrix Array Analysis set of packages.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:a4preproc @@ -47,3 +26,30 @@ extra: path: recipes/bioconductor-a4preproc version: 1.28.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: ALL, hgu95av2.db, knitr, rmarkdown +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - r-base + +source: + md5: b3655d08032f31ffc898cb0904221173 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-a4reporting/meta.yaml b/recipes/bioconductor-a4reporting/meta.yaml index 2da455e03ce4c..18272e6e66940 100644 --- a/recipes/bioconductor-a4reporting/meta.yaml +++ b/recipes/bioconductor-a4reporting/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "a4Reporting" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Utility functions to facilitate the reporting of the Automated Affymetrix Array Analysis Reporting set of packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Automated Affymetrix Array Analysis Reporting Package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ba7f3c5606c2f898d84314ba63208fa build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-a4reporting", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:a4reporting + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-a4reporting + path: recipes/bioconductor-a4reporting + version: 1.28.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: @@ -27,21 +38,16 @@ requirements: run: - r-base - r-xtable + +source: + md5: 9c1304a0bcbb5f174e3d4d3a59870d87 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Automated Affymetrix Array Analysis Reporting Package' - description: 'Utility functions to facilitate the reporting of the Automated Affymetrix Array Analysis Reporting set of packages.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:a4reporting - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-a4reporting - path: recipes/bioconductor-a4reporting - version: 1.28.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-abarray/meta.yaml b/recipes/bioconductor-abarray/meta.yaml index 7e528a9709f81..9875aee02a753 100644 --- a/recipes/bioconductor-abarray/meta.yaml +++ b/recipes/bioconductor-abarray/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.70.0" %} +{% set version = "1.74.0" %} {% set name = "ABarray" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 59e686f9daf6990fbe6e1594b8676197 +about: + description: Automated pipline to perform gene expression analysis for Applied Biosystems Genome Survey Microarray (AB1700) data format. Functions include data preprocessing, filtering, control probe analysis, statistical analysis in one single function. A GUI interface is also provided. The raw data, processed data, graphics output and statistical results are organized into folders according to the analysis settings used. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-abarray", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: limma, LPE requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base +source: + md5: 429b9e4d49fd5fba698e47e172f4fb76 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL - summary: 'Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.' - description: 'Automated pipline to perform gene expression analysis for Applied Biosystems Genome Survey Microarray (AB1700) data format. Functions include data preprocessing, filtering, control probe analysis, statistical analysis in one single function. A GUI interface is also provided. The raw data, processed data, graphics output and statistical results are organized into folders according to the analysis settings used.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-abseqr/meta.yaml b/recipes/bioconductor-abseqr/meta.yaml index da20a9a3cd15d..232f945dcede0 100644 --- a/recipes/bioconductor-abseqr/meta.yaml +++ b/recipes/bioconductor-abseqr/meta.yaml @@ -1,30 +1,33 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "abseqR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: AbSeq is a comprehensive bioinformatic pipeline for the analysis of sequencing datasets generated from antibody libraries and abseqR is one of its packages. abseqR empowers the users of abseqPy (https://github.com/malhamdoosh/abseqPy) with plotting and reporting capabilities and allows them to generate interactive HTML reports for the convenience of viewing and sharing with other researchers. Additionally, abseqR extends abseqPy to compare multiple repertoire analyses and perform further downstream analysis on its output. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 | file LICENSE + license_file: LICENSE + summary: Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f35214f635511b611297a3730386b205 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-abseqr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat # SystemRequirements: pandoc (>= 1.19.2.1) requirements: + host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 - r-base - r-circlize - r-flexdashboard @@ -42,10 +45,11 @@ requirements: - r-stringr - r-vegan - r-venndiagram - - 'pandoc >=1.19.2.1' + - pandoc >=1.19.2.1 + run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 - r-base - r-circlize - r-flexdashboard @@ -63,14 +67,17 @@ requirements: - r-stringr - r-vegan - r-venndiagram - - 'pandoc >=1.19.2.1' + - pandoc >=1.19.2.1 + +source: + md5: b5c8029b788cd97456e272dc515fd35e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 | file LICENSE' - summary: 'Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries' - description: 'AbSeq is a comprehensive bioinformatic pipeline for the analysis of sequencing datasets generated from antibody libraries and abseqR is one of its packages. abseqR empowers the users of abseqPy (https://github.com/malhamdoosh/abseqPy) with plotting and reporting capabilities and allows them to generate interactive HTML reports for the convenience of viewing and sharing with other researchers. Additionally, abseqR extends abseqPy to compare multiple repertoire analyses and perform further downstream analysis on its output.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-absseq/meta.yaml b/recipes/bioconductor-absseq/meta.yaml index 7b51b8e054377..f88c28fe20133 100644 --- a/recipes/bioconductor-absseq/meta.yaml +++ b/recipes/bioconductor-absseq/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "1.56.0" %} +{% set version = "1.60.0" %} {% set name = "ABSSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Inferring differential expression genes by absolute counts difference between two groups, utilizing Negative binomial distribution and moderating fold-change according to heterogeneity of dispersion across expression level. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d170bf2f9a37dcdffd2d91e233ce5132 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-absseq", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:absseq + parent_recipe: + name: bioconductor-absseq + path: recipes/bioconductor-absseq + version: 1.34.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: edgeR requirements: host: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-locfit run: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-locfit + +source: + md5: f3c08b1ca4057368a9697c1c4b457ad2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences' - description: 'Inferring differential expression genes by absolute counts difference between two groups, utilizing Negative binomial distribution and moderating fold-change according to heterogeneity of dispersion across expression level.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:absseq - parent_recipe: - name: bioconductor-absseq - path: recipes/bioconductor-absseq - version: 1.34.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-acde/meta.yaml b/recipes/bioconductor-acde/meta.yaml index 2d4644f22d888..21231ae52be5e 100644 --- a/recipes/bioconductor-acde/meta.yaml +++ b/recipes/bioconductor-acde/meta.yaml @@ -1,41 +1,22 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "acde" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a multivariate inferential analysis method for detecting differentially expressed genes in gene expression data. It uses artificial components, close to the data's principal components but with an exact interpretation in terms of differential genetic expression, to identify differentially expressed genes while controlling the false discovery rate (FDR). The methods on this package are described in the vignette or in the article 'Multivariate Method for Inferential Identification of Differentially Expressed Genes in Gene Expression Experiments' by J. P. Acosta, L. Lopez-Kleine and S. Restrepo (2015, pending publication). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Artificial Components Detection of Differentially Expressed Genes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9a324caddfceb2aa977e0fc9e7e41615 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-acde", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocGenerics, RUnit -requirements: - host: - - r-base - - 'r-boot >=1.3' - run: - - r-base - - 'r-boot >=1.3' -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Artificial Components Detection of Differentially Expressed Genes' - description: 'This package provides a multivariate inferential analysis method for detecting differentially expressed genes in gene expression data. It uses artificial components, close to the data''s principal components but with an exact interpretation in terms of differential genetic expression, to identify differentially expressed genes while controlling the false discovery rate (FDR). The methods on this package are described in the vignette or in the article ''Multivariate Method for Inferential Identification of Differentially Expressed Genes in Gene Expression Experiments'' by J. P. Acosta, L. Lopez-Kleine and S. Restrepo (2015, pending publication).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:acde @@ -45,3 +26,28 @@ extra: path: recipes/bioconductor-acde version: 1.10.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocGenerics, RUnit +requirements: + host: + - r-base + - r-boot >=1.3 + run: + - r-base + - r-boot >=1.3 + +source: + md5: df39a71c8b906769d5894ea2ffab69cb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-ace/meta.yaml b/recipes/bioconductor-ace/meta.yaml index 9befebeb13c7e..2a0609b757f6f 100644 --- a/recipes/bioconductor-ace/meta.yaml +++ b/recipes/bioconductor-ace/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "ACE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dd177150c01a5547ca8edabf82ef85d6 +about: + description: Uses segmented copy number data to estimate tumor cell percentage and produce copy number plots displaying absolute copy numbers. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ace", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-qdnaseq >=1.42.0,<1.43.0 - r-base - r-ggplot2 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-qdnaseq >=1.42.0,<1.43.0 - r-base - r-ggplot2 +source: + md5: 046bdc85e9ed95204bb696c7f0a14700 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing' - description: 'Uses segmented copy number data to estimate tumor cell percentage and produce copy number plots displaying absolute copy numbers.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-acgh/meta.yaml b/recipes/bioconductor-acgh/meta.yaml index 480a44e57a521..def2cd2ff51ed 100644 --- a/recipes/bioconductor-acgh/meta.yaml +++ b/recipes/bioconductor-acgh/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "1.80.0" %} +{% set version = "1.84.0" %} {% set name = "aCGH" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Classes and functions for Array Comparative Genomic Hybridization data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 137af76dc5756a83094da18eb0bededa build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-acgh", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:acgh + - doi:10.1093/bioinformatics/bti677 + parent_recipe: + name: bioconductor-acgh + path: recipes/bioconductor-acgh + version: 1.58.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base - r-cluster - r-survival - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base - r-cluster - r-survival - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: c2acef2cc478e54d29de890b7d12c146 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2.0-only - summary: 'Classes and functions for Array Comparative Genomic Hybridization data' - description: 'Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:acgh - - doi:10.1093/bioinformatics/bti677 - parent_recipe: - name: bioconductor-acgh - path: recipes/bioconductor-acgh - version: 1.58.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-acme/build_failure.osx-64.yaml b/recipes/bioconductor-acme/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..151e2aa804d42 --- /dev/null +++ b/recipes/bioconductor-acme/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 48ad0e196843735c5b1468d74a927a6ee81cd72f47963d8f9122626a3b95ffc3 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + license_file: /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-acme_1734487385093/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/R/share/licenses/GPL-3 + summary: Algorithms for Calculating Microarray Enrichment (ACME) + extra: + additional-platforms: + - linux-aarch64 + copy_test_source_files: true + final: true + identifiers: + - biotools:acme + parent_recipe: + name: bioconductor-acme + path: recipes/bioconductor-acme + version: 2.36.0 + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-acme_1734487385093/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-acme_1734487385093/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-acme_1734487385093/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-acme_1734487385093/work + INFO: activate-gfortran_osx-64.sh made the following environmental changes: + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-acme-2.62.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-acme-2.62.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-acme-2.62.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-acme-2.62.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-acme-2.62.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-acme-2.62.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-acme-2.62.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-acme-2.62.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-acme-2.62.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-acme-2.62.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-acme-2.62.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-acme-2.62.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-acme-2.62.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-acme-2.62.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -I"$PREFIX/lib/R/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c windowChisq.c -o windowChisq.o +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-acme/meta.yaml b/recipes/bioconductor-acme/meta.yaml index 47fd7e89692ed..2885c22d2cee5 100644 --- a/recipes/bioconductor-acme/meta.yaml +++ b/recipes/bioconductor-acme/meta.yaml @@ -1,46 +1,21 @@ -{% set version = "2.58.0" %} +{% set version = "2.62.0" %} {% set name = "ACME" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Algorithms for Calculating Microarray Enrichment (ACME) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6668a82e0a26ac03c9697e2cf22eb75e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-acme", max_pin="x.x") }}' -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - r-base - - libblas - - liblapack - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - r-base - build: - - {{ compiler('c') }} - - make -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3-only' - summary: 'Algorithms for Calculating Microarray Enrichment (ACME)' - description: 'ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: additional-platforms: - linux-aarch64 @@ -51,3 +26,34 @@ extra: path: recipes/bioconductor-acme version: 2.36.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + build: + - {{ compiler('c') }} + - make + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - r-base + - libblas + - liblapack + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - r-base + +source: + md5: daf938706b80e3ef74ee6d3aa5b4e247 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-adacgh2/build_failure.linux-64.yaml b/recipes/bioconductor-adacgh2/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..eb9cdc3f640cb --- /dev/null +++ b/recipes/bioconductor-adacgh2/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a1e9b48f8e4acc8474beadc47e5e81908493eb592a4453e282bd7776d66f98f9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + copy_test_source_files: true + final: true + + + source tree in: /opt/conda/conda-bld/bioconductor-adacgh2_1736183818755/work + export PREFIX=/opt/conda/conda-bld/bioconductor-adacgh2_1736183818755/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-adacgh2_1736183818755/_build_env + export SRC_DIR=/opt/conda/conda-bld/bioconductor-adacgh2_1736183818755/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adacgh2-2.46.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adacgh2-2.46.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-adacgh2_1736183818755/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library + * installing *source* package ADaCGH2 ... + ** package ADaCGH2 successfully unpacked and MD5 sums checked + ** using staged installation + ** libs + using C compiler: x86_64-conda-linux-gnu-cc (conda-forge gcc 13.3.0-1) 13.3.0 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c init.c -o init.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c r_haarseg.c -o r_haarseg.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -shared -L$PREFIX/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -o ADaCGH2.so init.o r_haarseg.o -L$PREFIX/lib/R/lib -lR + installing to /opt/conda/conda-bld/bioconductor-adacgh2_1736183818755/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/00LOCK-work/00new/ADaCGH2/libs + ** R + ** data + ** inst + ** byte-compile and prepare package for lazy loading + During startup - Warning message: + Setting LC_TIME failed, using "C" + Error in dyn.load(file, DLLpath = DLLpath, ...) : + unable to load shared object '$PREFIX/lib/R/library/multitaper/libs/multitaper.so': + libopenblas.so.0: cannot open shared object file: No such file or directory + Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load + Execution halted + ERROR: lazy loading failed for package ADaCGH2 + * removing /opt/conda/conda-bld/bioconductor-adacgh2_1736183818755/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/ADaCGH2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-adacgh2_1736183818755/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-adacgh2_1736183818755/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-adacgh2/build_failure.osx-64.yaml b/recipes/bioconductor-adacgh2/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..ca89df3681edb --- /dev/null +++ b/recipes/bioconductor-adacgh2/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a1e9b48f8e4acc8474beadc47e5e81908493eb592a4453e282bd7776d66f98f9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + utils.check_call_env( + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adacgh2-2.46.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-adacgh2_1736184569908/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adacgh2-2.46.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-adacgh2_1736184569908/work/conda_build.sh']' returned non-zero exit status 1. + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adacgh2-2.46.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adacgh2-2.46.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adacgh2-2.46.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adacgh2-2.46.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adacgh2-2.46.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adacgh2-2.46.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adacgh2-2.46.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adacgh2-2.46.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -I"$PREFIX/lib/R/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c init.c -o init.o + x86_64-apple-darwin13.4.0-clang -I"$PREFIX/lib/R/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c r_haarseg.c -o r_haarseg.o + x86_64-apple-darwin13.4.0-clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L$PREFIX/lib/R/lib -Wl,-dead_strip_dylibs -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o ADaCGH2.so init.o r_haarseg.o -L$PREFIX/lib/R/lib -lR -Wl,-framework -Wl,CoreFoundation + Error in dyn.load(file, DLLpath = DLLpath, ...) : + unable to load shared object '$PREFIX/lib/R/library/multitaper/libs/multitaper.so': + dlopen($PREFIX/lib/R/library/multitaper/libs/multitaper.so, 0x0006): Library not loaded: @rpath/libopenblas.0.dylib + Referenced from: <1E0AAECC-7EB6-3F03-B536-F23221EE27C1> /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-adacgh2_1736184569908/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load + Execution halted +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-adacgh2/meta.yaml b/recipes/bioconductor-adacgh2/meta.yaml index 1c71ce07f7657..9c6bfc72ad675 100644 --- a/recipes/bioconductor-adacgh2/meta.yaml +++ b/recipes/bioconductor-adacgh2/meta.yaml @@ -1,31 +1,35 @@ -{% set version = "2.42.0" %} +{% set version = "2.46.0" %} {% set name = "ADaCGH2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Analysis of big data from aCGH experiments using parallel computing and ff objects -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ce28a95b156205f60eeda851b36c958 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-adacgh2", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: CGHregions, Cairo, limma requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-acgh >=1.80.0,<1.81.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-glad >=2.66.0,<2.67.0' - - 'bioconductor-snapcgh >=1.72.0,<1.73.0' - - 'bioconductor-tilingarray >=1.80.0,<1.81.0' + - bioconductor-acgh >=1.84.0,<1.85.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-glad >=2.70.0,<2.71.0 + - bioconductor-tilingarray >=1.84.0,<1.85.0 - r-base - r-bit - r-cluster @@ -34,26 +38,25 @@ requirements: - libblas - liblapack run: - - 'bioconductor-acgh >=1.80.0,<1.81.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-glad >=2.66.0,<2.67.0' - - 'bioconductor-snapcgh >=1.72.0,<1.73.0' - - 'bioconductor-tilingarray >=1.80.0,<1.81.0' + - bioconductor-acgh >=1.84.0,<1.85.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-glad >=2.70.0,<2.71.0 + - bioconductor-tilingarray >=1.84.0,<1.85.0 - r-base - r-bit - r-cluster - r-ff - r-waveslim - build: - - {{ compiler('c') }} - - make + +source: + md5: 329f00761ec18e4670f9f057caa37556 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Analysis of big data from aCGH experiments using parallel computing and ff objects' - description: 'Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-adam/meta.yaml b/recipes/bioconductor-adam/meta.yaml index ecee8bcc2ce80..3ca50649b0ed2 100644 --- a/recipes/bioconductor-adam/meta.yaml +++ b/recipes/bioconductor-adam/meta.yaml @@ -1,61 +1,66 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "ADAM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ADAM is a GSEA R package created to group a set of genes from comparative samples (control versus experiment) belonging to different species according to their respective functions (Gene Ontology and KEGG pathways as default) and show their significance by calculating p-values referring togene diversity and activity. Each group of genes is called GFAG (Group of Functionally Associated Genes). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'ADAM: Activity and Diversity Analysis Module' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7f051085afca603520dbb5cb010e58fe build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-adam", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, rmarkdown, BiocStyle # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-dplyr >=0.7.6' - - 'r-dt >=0.4' + - r-dplyr >=0.7.6 + - r-dt >=0.4 - r-knitr - - 'r-pbapply >=1.3-4' - - 'r-rcpp >=0.12.18' - - 'r-stringr >=1.3.1' + - r-pbapply >=1.3-4 + - r-rcpp >=0.12.18 + - r-stringr >=1.3.1 - libblas - liblapack run: - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-dplyr >=0.7.6' - - 'r-dt >=0.4' + - r-dplyr >=0.7.6 + - r-dt >=0.4 - r-knitr - - 'r-pbapply >=1.3-4' - - 'r-rcpp >=0.12.18' - - 'r-stringr >=1.3.1' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-pbapply >=1.3-4 + - r-rcpp >=0.12.18 + - r-stringr >=1.3.1 + +source: + md5: 7f115ef3a54bf9fdc0100faa1ca78650 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'ADAM: Activity and Diversity Analysis Module' - description: 'ADAM is a GSEA R package created to group a set of genes from comparative samples (control versus experiment) belonging to different species according to their respective functions (Gene Ontology and KEGG pathways as default) and show their significance by calculating p-values referring togene diversity and activity. Each group of genes is called GFAG (Group of Functionally Associated Genes).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-adamgui/meta.yaml b/recipes/bioconductor-adamgui/meta.yaml index d9cd81c8fabd7..ad18d4b583542 100644 --- a/recipes/bioconductor-adamgui/meta.yaml +++ b/recipes/bioconductor-adamgui/meta.yaml @@ -1,77 +1,84 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "ADAMgui" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ADAMgui is a Graphical User Interface for the ADAM package. The ADAMgui package provides 2 shiny-based applications that allows the user to study the output of the ADAM package files through different plots. It's possible, for example, to choose a specific GFAG and observe the gene expression behavior with the plots created with the GFAGtargetUi function. Features such as differential expression and foldchange can be easily seen with aid of the plots made with GFAGpathUi function. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Activity and Diversity Analysis Module Graphical User Interface -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d6b76d93be7f193cd913f44f6ff41a64 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-adamgui", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: markdown, BiocStyle requirements: + host: - - 'bioconductor-adam >=1.18.0,<1.19.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' + - bioconductor-adam >=1.22.0,<1.23.0 + - bioconductor-go.db >=3.20.0,<3.21.0 - r-base - - 'r-colorramps >=2.3' - - 'r-data.table >=1.11.4' - - 'r-dplyr >=0.7.6' - - 'r-dt >=0.4' - - 'r-ggplot2 >=3.0.0' - - 'r-ggpubr >=0.1.8' - - 'r-ggrepel >=0.8.0' - - 'r-ggsignif >=0.4.0' - - 'r-gridextra >=2.3' + - r-colorramps >=2.3 + - r-data.table >=1.11.4 + - r-dplyr >=0.7.6 + - r-dt >=0.4 + - r-ggplot2 >=3.0.0 + - r-ggpubr >=0.1.8 + - r-ggrepel >=0.8.0 + - r-ggsignif >=0.4.0 + - r-gridextra >=2.3 - r-knitr - - 'r-rcolorbrewer >=1.1-2' - - 'r-reshape2 >=1.4.3' - - 'r-shiny >=1.1.0' - - 'r-shinyjs >=1.0' - - 'r-stringi >=1.2.4' - - 'r-stringr >=1.3.1' + - r-rcolorbrewer >=1.1-2 + - r-reshape2 >=1.4.3 + - r-shiny >=1.1.0 + - r-shinyjs >=1.0 + - r-stringi >=1.2.4 + - r-stringr >=1.3.1 - r-testthat - - 'r-varhandle >=2.0.3' + - r-varhandle >=2.0.3 + run: - - 'bioconductor-adam >=1.18.0,<1.19.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' + - bioconductor-adam >=1.22.0,<1.23.0 + - bioconductor-go.db >=3.20.0,<3.21.0 - r-base - - 'r-colorramps >=2.3' - - 'r-data.table >=1.11.4' - - 'r-dplyr >=0.7.6' - - 'r-dt >=0.4' - - 'r-ggplot2 >=3.0.0' - - 'r-ggpubr >=0.1.8' - - 'r-ggrepel >=0.8.0' - - 'r-ggsignif >=0.4.0' - - 'r-gridextra >=2.3' + - r-colorramps >=2.3 + - r-data.table >=1.11.4 + - r-dplyr >=0.7.6 + - r-dt >=0.4 + - r-ggplot2 >=3.0.0 + - r-ggpubr >=0.1.8 + - r-ggrepel >=0.8.0 + - r-ggsignif >=0.4.0 + - r-gridextra >=2.3 - r-knitr - - 'r-rcolorbrewer >=1.1-2' - - 'r-reshape2 >=1.4.3' - - 'r-shiny >=1.1.0' - - 'r-shinyjs >=1.0' - - 'r-stringi >=1.2.4' - - 'r-stringr >=1.3.1' + - r-rcolorbrewer >=1.1-2 + - r-reshape2 >=1.4.3 + - r-shiny >=1.1.0 + - r-shinyjs >=1.0 + - r-stringi >=1.2.4 + - r-stringr >=1.3.1 - r-testthat - - 'r-varhandle >=2.0.3' + - r-varhandle >=2.0.3 + +source: + md5: a136c41aed3a65f212e744caf5c8d9db + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Activity and Diversity Analysis Module Graphical User Interface' - description: 'ADAMgui is a Graphical User Interface for the ADAM package. The ADAMgui package provides 2 shiny-based applications that allows the user to study the output of the ADAM package files through different plots. It''s possible, for example, to choose a specific GFAG and observe the gene expression behavior with the plots created with the GFAGtargetUi function. Features such as differential expression and foldchange can be easily seen with aid of the plots made with GFAGpathUi function.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-adapt/build.sh b/recipes/bioconductor-adapt/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-adapt/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-adapt/build_failure.osx-64.yaml b/recipes/bioconductor-adapt/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..8afb18b8b3325 --- /dev/null +++ b/recipes/bioconductor-adapt/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 9c69932d7f304c8ceb6420dcab7eea831d4c344d8f5bd187a00e7182d93d4d72 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-adapt_1734711592278/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adapt-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adapt-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + packages_from_this = build( + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adapt-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-adapt_1734711592278/work/conda_build.sh']' returned non-zero exit status 1. + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adapt-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adapt-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adapt-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adapt-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adapt-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adapt-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adapt-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adapt-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-adapt-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/RcppParallel/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c CR_LRT.cpp -o CR_LRT.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/RcppParallel/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/RcppParallel/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c Tobit.cpp -o Tobit.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L$PREFIX/lib/R/lib -Wl,-dead_strip_dylibs -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o ADAPT.so CR_LRT.o RcppExports.o Tobit.o -llapack -lblas -L$PREFIX/lib/gcc/x86_64-apple-darwin13.4.0/13.2.0 -L/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/_build_env/lib -lgfortran -lquadmath -lm -L$PREFIX/lib/R/lib -lR -Wl,-framework -Wl,CoreFoundation + if test -e "/usr/bin/strip"; then /usr/bin/strip --strip-debug ADAPT.so; fi +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-adapt/meta.yaml b/recipes/bioconductor-adapt/meta.yaml new file mode 100644 index 0000000000000..84a40f219c5b5 --- /dev/null +++ b/recipes/bioconductor-adapt/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.0.0" %} +{% set name = "ADAPT" %} +{% set bioc = "3.20" %} + +about: + description: ADAPT carries out differential abundance analysis for microbiome metagenomics data in phyloseq format. It has two innovations. One is to treat zero counts as left censored and use Tobit models for log count ratios. The other is an innovative way to find non-differentially abundant taxa as reference, then use the reference taxa to find the differentially abundant ones. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Analysis of Microbiome Differential Abundance by Pooling Tobit Models + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-adapt", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: rmarkdown (>= 2.11), knitr (>= 1.37), testthat (>= 3.0.0) +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: + - bioconductor-phyloseq >=1.50.0,<1.51.0 + - r-base + - r-ggplot2 >=3.4.1 + - r-ggrepel >=0.9.1 + - r-rcpp >=1.0.8 + - r-rcpparmadillo >=0.10.8 + - r-rcppparallel >=5.1.5 + - libblas + - liblapack + run: + - bioconductor-phyloseq >=1.50.0,<1.51.0 + - r-base + - r-ggplot2 >=3.4.1 + - r-ggrepel >=0.9.1 + - r-rcpp >=1.0.8 + - r-rcpparmadillo >=0.10.8 + - r-rcppparallel >=5.1.5 + +source: + md5: 707165726b7a8d2cbc4e1aca5c663318 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-adductdata/meta.yaml b/recipes/bioconductor-adductdata/meta.yaml index ad2a3978ce00b..604ec99394ca5 100644 --- a/recipes/bioconductor-adductdata/meta.yaml +++ b/recipes/bioconductor-adductdata/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "adductData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bf0e3549ee672a31f32759f0535f360a +about: + description: mzXML files from Grigoryan et al 2016 (Anal Chem). + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Data from untargeted MS of modifications to Cys34 of serum albumin build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-adductdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr (>= 1.15.1), rmarkdown (>= 1.5) requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ed236e56217a786e98246e4db03eda1e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Data from untargeted MS of modifications to Cys34 of serum albumin' - description: 'mzXML files from Grigoryan et al 2016 (Anal Chem).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-adductdata/post-link.sh b/recipes/bioconductor-adductdata/post-link.sh index d3605c39b51d2..a674bdf1d2472 100644 --- a/recipes/bioconductor-adductdata/post-link.sh +++ b/recipes/bioconductor-adductdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "adductdata-1.18.0" +installBiocDataPackage.sh "adductdata-1.22.0" diff --git a/recipes/bioconductor-adductomicsr/meta.yaml b/recipes/bioconductor-adductomicsr/meta.yaml index 0dae0b1138261..a7f1614b40c6d 100644 --- a/recipes/bioconductor-adductomicsr/meta.yaml +++ b/recipes/bioconductor-adductomicsr/meta.yaml @@ -1,78 +1,85 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "adductomicsR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Processes MS2 data to identify potentially adducted peptides from spectra that has been corrected for mass drift and retention time drift and quantifies MS1 level mass spectral peaks. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Processing of adductomic mass spectral datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 82e24a09ba891b76e9497a6725b96fe0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-adductomicsr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr (>= 1.15.1), rmarkdown (>= 1.5), Rdisop (>= 1.34.0), testthat requirements: + host: - - 'bioconductor-adductdata >=1.18.0,<1.19.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' - - 'r-ade4 >=1.7.6' + - bioconductor-adductdata >=1.22.0,<1.23.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-mzr >=2.40.0,<2.41.0 + - r-ade4 >=1.7.6 - r-base - - 'r-bootstrap >=2017.2' - - 'r-data.table >=1.10.4' - - 'r-dosnow >=1.0.14' - - 'r-dplyr >=0.7.5' - - 'r-dt >=0.2' - - 'r-fastcluster >=1.1.22' - - 'r-foreach >=1.4.3' - - 'r-fpc >=2.1.10' - - 'r-orgmassspecr >=0.4.6' - - 'r-pastecs >=1.3.18' - - 'r-pracma >=2.0.4' - - 'r-rcppeigen >=0.3.3.3.0' - - 'r-reshape2 >=1.4.2' - - 'r-rvest >=0.3.2' - - 'r-smoother >=1.1' - - 'r-zoo >=1.8' + - r-bootstrap >=2017.2 + - r-data.table >=1.10.4 + - r-dosnow >=1.0.14 + - r-dplyr >=0.7.5 + - r-dt >=0.2 + - r-fastcluster >=1.1.22 + - r-foreach >=1.4.3 + - r-fpc >=2.1.10 + - r-orgmassspecr >=0.4.6 + - r-pastecs >=1.3.18 + - r-pracma >=2.0.4 + - r-rcppeigen >=0.3.3.3.0 + - r-reshape2 >=1.4.2 + - r-rvest >=0.3.2 + - r-smoother >=1.1 + - r-zoo >=1.8 + run: - - 'bioconductor-adductdata >=1.18.0,<1.19.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' - - 'r-ade4 >=1.7.6' + - bioconductor-adductdata >=1.22.0,<1.23.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-mzr >=2.40.0,<2.41.0 + - r-ade4 >=1.7.6 - r-base - - 'r-bootstrap >=2017.2' - - 'r-data.table >=1.10.4' - - 'r-dosnow >=1.0.14' - - 'r-dplyr >=0.7.5' - - 'r-dt >=0.2' - - 'r-fastcluster >=1.1.22' - - 'r-foreach >=1.4.3' - - 'r-fpc >=2.1.10' - - 'r-orgmassspecr >=0.4.6' - - 'r-pastecs >=1.3.18' - - 'r-pracma >=2.0.4' - - 'r-rcppeigen >=0.3.3.3.0' - - 'r-reshape2 >=1.4.2' - - 'r-rvest >=0.3.2' - - 'r-smoother >=1.1' - - 'r-zoo >=1.8' + - r-bootstrap >=2017.2 + - r-data.table >=1.10.4 + - r-dosnow >=1.0.14 + - r-dplyr >=0.7.5 + - r-dt >=0.2 + - r-fastcluster >=1.1.22 + - r-foreach >=1.4.3 + - r-fpc >=2.1.10 + - r-orgmassspecr >=0.4.6 + - r-pastecs >=1.3.18 + - r-pracma >=2.0.4 + - r-rcppeigen >=0.3.3.3.0 + - r-reshape2 >=1.4.2 + - r-rvest >=0.3.2 + - r-smoother >=1.1 + - r-zoo >=1.8 + +source: + md5: c5599996505f3e49b095bd755f11fbed + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Processing of adductomic mass spectral datasets' - description: 'Processes MS2 data to identify potentially adducted peptides from spectra that has been corrected for mass drift and retention time drift and quantifies MS1 level mass spectral peaks.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-adimpute/meta.yaml b/recipes/bioconductor-adimpute/meta.yaml index dc9e7cde8ce66..9ecae58136eb1 100644 --- a/recipes/bioconductor-adimpute/meta.yaml +++ b/recipes/bioconductor-adimpute/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "ADImpute" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Single-cell RNA sequencing (scRNA-seq) methods are typically unable to quantify the expression levels of all genes in a cell, creating a need for the computational prediction of missing values (‘dropout imputation’). Most existing dropout imputation methods are limited in the sense that they exclusively use the scRNA-seq dataset at hand and do not exploit external gene-gene relationship information. Here we propose two novel methods: a gene regulatory network-based approach using gene-gene relationships learnt from external data and a baseline approach corresponding to a sample-wide average. ADImpute can implement these novel methods and also combine them with existing imputation methods (currently supported: DrImpute, SAVER). ADImpute can learn the best performing method per gene and combine the results from different methods into an ensemble.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Adaptive Dropout Imputer (ADImpute) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 488025707dc1ae48d36b1e936cd86e18 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-adimpute", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-checkmate - r-data.table @@ -36,10 +38,10 @@ requirements: - r-rsvd - r-saver run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-checkmate - r-data.table @@ -49,13 +51,16 @@ requirements: - r-matrix - r-rsvd - r-saver + +source: + md5: 412ef2483765b22093eb394039ff6c20 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Adaptive Dropout Imputer (ADImpute)' - description: 'Single-cell RNA sequencing (scRNA-seq) methods are typically unable to quantify the expression levels of all genes in a cell, creating a need for the computational prediction of missing values (‘dropout imputation’). Most existing dropout imputation methods are limited in the sense that they exclusively use the scRNA-seq dataset at hand and do not exploit external gene-gene relationship information. Here we propose two novel methods: a gene regulatory network-based approach using gene-gene relationships learnt from external data and a baseline approach corresponding to a sample-wide average. ADImpute can implement these novel methods and also combine them with existing imputation methods (currently supported: DrImpute, SAVER). ADImpute can learn the best performing method per gene and combine the results from different methods into an ensemble.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-adme16cod.db/meta.yaml b/recipes/bioconductor-adme16cod.db/meta.yaml index e4dce7a0d51e4..bdd438f4cd4b8 100644 --- a/recipes/bioconductor-adme16cod.db/meta.yaml +++ b/recipes/bioconductor-adme16cod.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.4.0" %} {% set name = "adme16cod.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3902516a40a503302ef732143b2394b9 +about: + description: Codelink ADME Rat 16-Assay Bioarray annotation data (chip adme16cod) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Codelink ADME Rat 16-Assay Bioarray annotation data (chip adme16cod) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-adme16cod.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3902516a40a503302ef732143b2394b9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Codelink ADME Rat 16-Assay Bioarray annotation data (chip adme16cod)' - description: 'Codelink ADME Rat 16-Assay Bioarray annotation data (chip adme16cod) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-adsplit/meta.yaml b/recipes/bioconductor-adsplit/meta.yaml index 63e85226e64ef..edf6582acdf8a 100644 --- a/recipes/bioconductor-adsplit/meta.yaml +++ b/recipes/bioconductor-adsplit/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "1.72.0" %} +{% set version = "1.76.0" %} {% set name = "adSplit" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Annotation-Driven Clustering -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d50affb50e6f6a11d8c4e379b6116d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-adsplit", max_pin="x.x") }}' + +extra: + parent_recipe: + name: bioconductor-adsplit + path: recipes/bioconductor-adsplit + version: 1.50.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: golubEsets (>= 1.0), vsn (>= 1.5.0), hu6800.db (>= 1.8.1) requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base - - 'r-cluster >=1.9.1' + - r-cluster >=1.9.1 - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base - - 'r-cluster >=1.9.1' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-cluster >=1.9.1 + +source: + md5: 4dba31266eac16ec5639cc0fa671532c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Annotation-Driven Clustering' - description: 'This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-adsplit - path: recipes/bioconductor-adsplit - version: 1.50.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-adverscarial/meta.yaml b/recipes/bioconductor-adverscarial/meta.yaml index 4a8c254b26e82..b62cbef29fb64 100644 --- a/recipes/bioconductor-adverscarial/meta.yaml +++ b/recipes/bioconductor-adverscarial/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "adverSCarial" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 196840790cf7fd0a0cbfe6d1aeb60e07 +about: + description: adverSCarial is an R Package designed for generating and analyzing the vulnerability of scRNA-seq classifiers to adversarial attacks. The package is versatile and provides a format for integrating any type of classifier. It offers functions for studying and generating two types of attacks, single gene attack and max change attack. The single-gene attack involves making a small modification to the input to alter the classification. The max-change attack involves making a large modification to the input without changing its classification. The package provides a comprehensive solution for evaluating the robustness of scRNA-seq classifiers against adversarial attacks. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: adverSCarial, generate and analyze the vulnerability of scRNA-seq classifier to adversarial attacks build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-adverscarial", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, RUnit, BiocGenerics, TENxPBMCData, CHETAH, stringr, LoomExperiment requirements: host: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-gtools run: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-gtools +source: + md5: 2c56a48a86bb4ee673b7db23b852d94e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'adverSCarial, generate and analyze the vulnerability of scRNA-seq classifiers to adversarial attacks' - description: 'adverSCarial is an R Package designed for generating and analyzing the vulnerability of scRNA-seq classifiers to adversarial attacks. The package is versatile and provides a format for integrating any type of classifier. It offers functions for studying and generating two types of attacks, single gene attack and max change attack. The single gene attack involves making a small modification to the input to alter the classification. The max change attack involves making a large modification to the input without changing its classification. The package provides a comprehensive solution for evaluating the robustness of scRNA-seq classifiers against adversarial attacks.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-affixcan/meta.yaml b/recipes/bioconductor-affixcan/meta.yaml index 239059a2abf23..3494760861339 100644 --- a/recipes/bioconductor-affixcan/meta.yaml +++ b/recipes/bioconductor-affixcan/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "AffiXcan" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0fdb85714a4ee94e3c04117e56d35724 +about: + description: Impute a GReX (Genetically Regulated Expression) for a set of genes in a sample of individuals, using a method based on the Total Binding Affinity (TBA). Statistical models to impute GReX can be trained with a training dataset where the real total expression values are known. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A Functional Approach To Impute Genetically Regulated Expression build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-affixcan", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-crayon run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-crayon +source: + md5: 9a5927d91abde2bc1c6f49c20372855a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'A Functional Approach To Impute Genetically Regulated Expression' - description: 'Impute a GReX (Genetically Regulated Expression) for a set of genes in a sample of individuals, using a method based on the Total Binding Affinity (TBA). Statistical models to impute GReX can be trained with a training dataset where the real total expression values are known.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-affxparser/meta.yaml b/recipes/bioconductor-affxparser/meta.yaml index b14c8b9d06485..f394ebfe8681d 100644 --- a/recipes/bioconductor-affxparser/meta.yaml +++ b/recipes/bioconductor-affxparser/meta.yaml @@ -1,49 +1,55 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "affxparser" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Affymetrix File Parsing SDK -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2b6b9373d749a0ccbf930f834df90b92 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-affxparser", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + parent_recipe: + name: bioconductor-affxparser + path: recipes/bioconductor-affxparser + version: 1.52.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: R.oo (>= 1.22.0), R.utils (>= 2.7.0), AffymetrixDataTestFiles requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 594e4fd69853dece7646c5356fabc31a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'Affymetrix File Parsing SDK' - description: 'Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix'' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - additional-platforms: - - linux-aarch64 - parent_recipe: - name: bioconductor-affxparser - path: recipes/bioconductor-affxparser - version: 1.52.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-affy/meta.yaml b/recipes/bioconductor-affy/meta.yaml index d7bd0340a6b27..aa8dfa34ef2ed 100644 --- a/recipes/bioconductor-affy/meta.yaml +++ b/recipes/bioconductor-affy/meta.yaml @@ -1,63 +1,69 @@ -{% set version = "1.80.0" %} +{% set version = "1.84.0" %} {% set name = "affy" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2.0) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Methods for Affymetrix Oligonucleotide Arrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 09376016b32f86f707ff9b8f8cb8a1a5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-affy", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:affy + parent_recipe: + name: bioconductor-affy + path: recipes/bioconductor-affy + version: 1.58.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools, hgu95av2cdf requirements: + build: + - {{ compiler('c') }} + - automake + - make host: - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-biocmanager - libblas - liblapack run: - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-biocmanager - build: - - {{ compiler('c') }} - - automake - - make + +source: + md5: 82c2e7dafd9b513f793df8455b53570c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL-3-only' - summary: 'Methods for Affymetrix Oligonucleotide Arrays' - description: 'The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. ''affy'' is fully functional without it.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:affy - parent_recipe: - name: bioconductor-affy - path: recipes/bioconductor-affy - version: 1.58.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-affycomp/meta.yaml b/recipes/bioconductor-affycomp/meta.yaml index 8637840fed6df..17cd83721c38b 100644 --- a/recipes/bioconductor-affycomp/meta.yaml +++ b/recipes/bioconductor-affycomp/meta.yaml @@ -1,41 +1,22 @@ -{% set version = "1.78.0" %} +{% set version = "1.82.0" %} {% set name = "affycomp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Graphics Toolbox for Assessment of Affymetrix Expression Measures -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f80b53dc57dcb88730eda3c0506b9df1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-affycomp", max_pin="x.x") }}' - noarch: generic -# Suggests: splines, affycompData -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Graphics Toolbox for Assessment of Affymetrix Expression Measures' - description: 'The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:affycomp @@ -45,3 +26,28 @@ extra: path: recipes/bioconductor-affycomp version: 1.56.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: splines, affycompData +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + +source: + md5: 9dd57ca955c7b4b9bf7e5787e060de4a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-affycompdata/meta.yaml b/recipes/bioconductor-affycompdata/meta.yaml index 0095e5b77d597..1890c16d62573 100644 --- a/recipes/bioconductor-affycompdata/meta.yaml +++ b/recipes/bioconductor-affycompdata/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "affycompData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 205391e19fb160dcff1531892f28b006 +about: + description: Data needed by the affycomp package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: affycomp data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-affycompdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-affycomp >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-affycomp >=1.82.0,<1.83.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-affycomp >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-affycomp >=1.82.0,<1.83.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5c7cbe480087fc6f1fd20a85c954f9fc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'affycomp data' - description: 'Data needed by the affycomp package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-affycompdata/post-link.sh b/recipes/bioconductor-affycompdata/post-link.sh index 8afa441ea7552..f4f5f33ab53c2 100644 --- a/recipes/bioconductor-affycompdata/post-link.sh +++ b/recipes/bioconductor-affycompdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affycompdata-1.40.0" +installBiocDataPackage.sh "affycompdata-1.44.0" diff --git a/recipes/bioconductor-affycontam/meta.yaml b/recipes/bioconductor-affycontam/meta.yaml index 5b27747fc443e..316056be2c562 100644 --- a/recipes/bioconductor-affycontam/meta.yaml +++ b/recipes/bioconductor-affycontam/meta.yaml @@ -1,44 +1,21 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "affyContam" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: structured corruption of cel file data to demonstrate QA effectiveness + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: structured corruption of affymetrix cel file data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eb7e98d31e923d77d4e6197e5cf8b02d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-affycontam", max_pin="x.x") }}' - noarch: generic -# Suggests: hgu95av2cdf -requirements: - host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affydata >=1.50.0,<1.51.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base - run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affydata >=1.50.0,<1.51.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'structured corruption of affymetrix cel file data' - description: 'structured corruption of cel file data to demonstrate QA effectiveness' + extra: identifiers: - biotools:affycontam @@ -48,3 +25,32 @@ extra: path: recipes/bioconductor-affycontam version: 1.38.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: hgu95av2cdf +requirements: + host: + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affydata >=1.54.0,<1.55.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + run: + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affydata >=1.54.0,<1.55.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + +source: + md5: 54580b1d9c057863579b3cb9582366ba + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-affycoretools/meta.yaml b/recipes/bioconductor-affycoretools/meta.yaml index a986df1b11158..d0fc284d0b1bd 100644 --- a/recipes/bioconductor-affycoretools/meta.yaml +++ b/recipes/bioconductor-affycoretools/meta.yaml @@ -1,39 +1,50 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "affycoretools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Functions useful for those doing repetitive analyses with Affymetrix GeneChips -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0e35c33fb3f3a4cdc7778efacbc45441 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-affycoretools", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:affycoretools + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-affycoretools + path: recipes/bioconductor-affycoretools + version: 1.52.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl, rmarkdown requirements: + host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-gcrma >=2.74.0,<2.75.0' - - 'bioconductor-glimma >=2.12.0,<2.13.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-reportingtools >=2.42.0,<2.43.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-gcrma >=2.78.0,<2.79.0 + - bioconductor-glimma >=2.16.0,<2.17.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-reportingtools >=2.46.0,<2.47.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dbi - r-ggplot2 @@ -42,19 +53,20 @@ requirements: - r-lattice - r-rsqlite - r-xtable + run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-gcrma >=2.74.0,<2.75.0' - - 'bioconductor-glimma >=2.12.0,<2.13.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-reportingtools >=2.42.0,<2.43.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-gcrma >=2.78.0,<2.79.0 + - bioconductor-glimma >=2.16.0,<2.17.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-reportingtools >=2.46.0,<2.47.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dbi - r-ggplot2 @@ -63,20 +75,16 @@ requirements: - r-lattice - r-rsqlite - r-xtable + +source: + md5: 89eb1dc5c507584e34f3b67322d9b455 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Functions useful for those doing repetitive analyses with Affymetrix GeneChips' - description: 'Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.' -extra: - identifiers: - - biotools:affycoretools - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-affycoretools - path: recipes/bioconductor-affycoretools - version: 1.52.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-affydata/meta.yaml b/recipes/bioconductor-affydata/meta.yaml index 2f929ae9839ca..523a9365e6c4f 100644 --- a/recipes/bioconductor-affydata/meta.yaml +++ b/recipes/bioconductor-affydata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "affydata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 29caf389ca94d4c0c0b27d993f33354c +about: + description: Example datasets of a slightly large size. They represent 'real world examples', unlike the artificial examples included in the package affy. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Affymetrix Data for Demonstration Purpose build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-affydata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: hgu95av2cdf, hgu133acdf requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' + - bioconductor-affy >=1.84.0,<1.85.0 - r-base run: - - 'bioconductor-affy >=1.80.0,<1.81.0' + - bioconductor-affy >=1.84.0,<1.85.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: dfb8275fc3bb96847e867ddcdced9c52 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Affymetrix Data for Demonstration Purpose' - description: 'Example datasets of a slightly large size. They represent ''real world examples'', unlike the artificial examples included in the package affy.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-affydata/post-link.sh b/recipes/bioconductor-affydata/post-link.sh index d1076767bb073..3dcb35ee8de83 100644 --- a/recipes/bioconductor-affydata/post-link.sh +++ b/recipes/bioconductor-affydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affydata-1.50.0" +installBiocDataPackage.sh "affydata-1.54.0" diff --git a/recipes/bioconductor-affyhgu133a2expr/meta.yaml b/recipes/bioconductor-affyhgu133a2expr/meta.yaml index c8a6b90c26c8e..fe28d60f1f0ce 100644 --- a/recipes/bioconductor-affyhgu133a2expr/meta.yaml +++ b/recipes/bioconductor-affyhgu133a2expr/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "Affyhgu133A2Expr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 56296960e5539a4fd84724344f30aaaa +about: + description: Contains pre-built human (GPL571) databases of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Affymetrix Human Genome U133A 2.0 Array (GPL571) Expression Data Package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-affyhgu133a2expr", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 92f8f2e7fad2450606a57456cff8f5c1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Affymetrix Human Genome U133A 2.0 Array (GPL571) Expression Data Package' - description: 'Contains pre-built human (GPL571) databases of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-affyhgu133a2expr/post-link.sh b/recipes/bioconductor-affyhgu133a2expr/post-link.sh index 51c44933e7561..0a7dc9113f768 100644 --- a/recipes/bioconductor-affyhgu133a2expr/post-link.sh +++ b/recipes/bioconductor-affyhgu133a2expr/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affyhgu133a2expr-1.38.0" +installBiocDataPackage.sh "affyhgu133a2expr-1.42.0" diff --git a/recipes/bioconductor-affyhgu133aexpr/meta.yaml b/recipes/bioconductor-affyhgu133aexpr/meta.yaml index cb49ec76a1c59..e7b547fcce637 100644 --- a/recipes/bioconductor-affyhgu133aexpr/meta.yaml +++ b/recipes/bioconductor-affyhgu133aexpr/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "Affyhgu133aExpr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2cf458278c574450a3a5ffe64a2aa72b +about: + description: Contains pre-built human (GPL96) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Affymetrix Human hgu133a Array (GPL96) Expression Data Package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-affyhgu133aexpr", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4127126e7740a9c964f667637c67e5c9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Affymetrix Human hgu133a Array (GPL96) Expression Data Package' - description: 'Contains pre-built human (GPL96) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-affyhgu133aexpr/post-link.sh b/recipes/bioconductor-affyhgu133aexpr/post-link.sh index 340a6ec306e19..ba1503bce4743 100644 --- a/recipes/bioconductor-affyhgu133aexpr/post-link.sh +++ b/recipes/bioconductor-affyhgu133aexpr/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affyhgu133aexpr-1.40.0" +installBiocDataPackage.sh "affyhgu133aexpr-1.44.0" diff --git a/recipes/bioconductor-affyhgu133plus2expr/meta.yaml b/recipes/bioconductor-affyhgu133plus2expr/meta.yaml index 34d5b6c564a12..1c51db1f5304f 100644 --- a/recipes/bioconductor-affyhgu133plus2expr/meta.yaml +++ b/recipes/bioconductor-affyhgu133plus2expr/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "Affyhgu133Plus2Expr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f8baac83db4de07f941552d7b62c8d62 +about: + description: Contains pre-built human (GPL570) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Affyhgu133Plus2Expr (GPL570) Expression Data Package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-affyhgu133plus2expr", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 026699f8f4eba1143c4ca44dc773a48d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Affyhgu133Plus2Expr (GPL570) Expression Data Package' - description: 'Contains pre-built human (GPL570) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-affyhgu133plus2expr/post-link.sh b/recipes/bioconductor-affyhgu133plus2expr/post-link.sh index 61b0c8692f259..3d9ae42360e98 100644 --- a/recipes/bioconductor-affyhgu133plus2expr/post-link.sh +++ b/recipes/bioconductor-affyhgu133plus2expr/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affyhgu133plus2expr-1.36.0" +installBiocDataPackage.sh "affyhgu133plus2expr-1.40.0" diff --git a/recipes/bioconductor-affyilm/meta.yaml b/recipes/bioconductor-affyilm/meta.yaml index 6433bba0da600..ba4f2a27d9549 100644 --- a/recipes/bioconductor-affyilm/meta.yaml +++ b/recipes/bioconductor-affyilm/meta.yaml @@ -1,47 +1,22 @@ -{% set version = "1.54.0" %} +{% set version = "1.58.0" %} {% set name = "affyILM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: affyILM is a preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behalf of the Langmuir model. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Linear Model of background subtraction and the Langmuir isotherm -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96d1989fb75742f6a9b0f9d8df1c3fc0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-affyilm", max_pin="x.x") }}' - noarch: generic -# Suggests: AffymetrixDataTestFiles, hgfocusprobe -requirements: - host: - - 'bioconductor-affxparser >=1.74.0,<1.75.0' - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gcrma >=2.74.0,<2.75.0' - - r-base - run: - - 'bioconductor-affxparser >=1.74.0,<1.75.0' - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gcrma >=2.74.0,<2.75.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Linear Model of background subtraction and the Langmuir isotherm' - description: 'affyILM is a preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behalf of the Langmuir model.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:affyilm @@ -51,3 +26,34 @@ extra: path: recipes/bioconductor-affyilm version: 1.32.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: AffymetrixDataTestFiles, hgfocusprobe +requirements: + host: + - bioconductor-affxparser >=1.78.0,<1.79.0 + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gcrma >=2.78.0,<2.79.0 + - r-base + run: + - bioconductor-affxparser >=1.78.0,<1.79.0 + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gcrma >=2.78.0,<2.79.0 + - r-base + +source: + md5: 0ce1033e222cfc11db61d1a6fb09c4f3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-affyio/meta.yaml b/recipes/bioconductor-affyio/meta.yaml index 7e1bef9f6ac34..a5e0662da8664 100644 --- a/recipes/bioconductor-affyio/meta.yaml +++ b/recipes/bioconductor-affyio/meta.yaml @@ -1,45 +1,21 @@ -{% set version = "1.72.0" %} +{% set version = "1.76.0" %} {% set name = "affyio" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Tools for parsing Affymetrix data files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9bd1e4acedbf756386f96d4c1ebb21f3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-affyio", max_pin="x.x") }}' -requirements: - host: - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - - r-base - - libblas - - liblapack - run: - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - - r-base - build: - - {{ compiler('c') }} - - automake - - make -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL-3.0-or-later' - summary: 'Tools for parsing Affymetrix data files' - description: 'Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + extra: additional-platforms: - linux-aarch64 @@ -51,3 +27,34 @@ extra: path: recipes/bioconductor-affyio version: 1.50.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + build: + - {{ compiler('c') }} + - automake + - make + host: + - bioconductor-zlibbioc >=1.52.0,<1.53.0 + - r-base + - libblas + - liblapack + - zlib + run: + - bioconductor-zlibbioc >=1.52.0,<1.53.0 + - r-base + +source: + md5: c1504546527ab09831f56b7d34ba4a34 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-affylmgui/meta.yaml b/recipes/bioconductor-affylmgui/meta.yaml index a22190a4e1974..6c4913037d634 100644 --- a/recipes/bioconductor-affylmgui/meta.yaml +++ b/recipes/bioconductor-affylmgui/meta.yaml @@ -1,58 +1,63 @@ -{% set version = "1.76.0" %} +{% set version = "1.80.0" %} {% set name = "affylmGUI" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A Graphical User Interface (GUI) for analysis of Affymetrix microarray gene expression data using the affy and limma packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: GUI for limma Package with Affymetrix Microarrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 22d9ba796444840fc24cf9b7384f81c9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-affylmgui", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-affyplm >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-gcrma >=2.74.0,<2.75.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-affyplm >=1.82.0,<1.83.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-gcrma >=2.78.0,<2.79.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-biocmanager - r-r2html - r-tkrplot - r-xtable run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-affyplm >=1.78.0,<1.79.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-gcrma >=2.74.0,<2.75.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-affyplm >=1.82.0,<1.83.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-gcrma >=2.78.0,<2.79.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-biocmanager - r-r2html - r-tkrplot - r-xtable + +source: + md5: 46c5dbc922f7355302276f37495a7cee + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'GUI for limma Package with Affymetrix Microarrays' - description: 'A Graphical User Interface (GUI) for analysis of Affymetrix microarray gene expression data using the affy and limma packages.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-affymetrixdatatestfiles/meta.yaml b/recipes/bioconductor-affymetrixdatatestfiles/meta.yaml index 66437faa2f9b4..ce763390600af 100644 --- a/recipes/bioconductor-affymetrixdatatestfiles/meta.yaml +++ b/recipes/bioconductor-affymetrixdatatestfiles/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "0.40.0" %} +{% set version = "0.44.0" %} {% set name = "AffymetrixDataTestFiles" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 57ecb8e4d3f0d7a9cdcedb2a9648dd1e +about: + description: This package contains annotation data files and sample data files of Affymetrix file formats. The files originate from the Affymetrix' Fusion SDK distribution and other official sources. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL-2.1 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2.1' + summary: Affymetrix Data Files (CEL, CDF, CHP, EXP, PGF, PSI) for Testing build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-affymetrixdatatestfiles", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7a7a9f89c31c1628a0d1e7c34dca730a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL-2.1 - summary: 'Affymetrix Data Files (CEL, CDF, CHP, EXP, PGF, PSI) for Testing' - description: 'This package contains annotation data files and sample data files of Affymetrix file formats. The files originate from the Affymetrix'' Fusion SDK distribution and other official sources.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2.1' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-affymetrixdatatestfiles/post-link.sh b/recipes/bioconductor-affymetrixdatatestfiles/post-link.sh index e2ba7cf5c205a..5feabd8630e26 100644 --- a/recipes/bioconductor-affymetrixdatatestfiles/post-link.sh +++ b/recipes/bioconductor-affymetrixdatatestfiles/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affymetrixdatatestfiles-0.40.0" +installBiocDataPackage.sh "affymetrixdatatestfiles-0.44.0" diff --git a/recipes/bioconductor-affymoe4302expr/meta.yaml b/recipes/bioconductor-affymoe4302expr/meta.yaml index 2c17903299ff0..902733fb547fa 100644 --- a/recipes/bioconductor-affymoe4302expr/meta.yaml +++ b/recipes/bioconductor-affymoe4302expr/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "Affymoe4302Expr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4dcd432d350cf2f8000f67774d95481c +about: + description: Contains pre-built mouse (GPL1261) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Affymetrix Mouse Genome 430 2.0 Array (GPL1261) Expression Data Package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-affymoe4302expr", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 295950e1bd7dcc3617cd3de48e7187ec + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Affymetrix Mouse Genome 430 2.0 Array (GPL1261) Expression Data Package' - description: 'Contains pre-built mouse (GPL1261) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-affymoe4302expr/post-link.sh b/recipes/bioconductor-affymoe4302expr/post-link.sh index 1c18e0a13e6be..5b2719401c306 100644 --- a/recipes/bioconductor-affymoe4302expr/post-link.sh +++ b/recipes/bioconductor-affymoe4302expr/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "affymoe4302expr-1.40.0" +installBiocDataPackage.sh "affymoe4302expr-1.44.0" diff --git a/recipes/bioconductor-affyplm/meta.yaml b/recipes/bioconductor-affyplm/meta.yaml index 6f6f1faaf8e41..c1a9fbc12c078 100644 --- a/recipes/bioconductor-affyplm/meta.yaml +++ b/recipes/bioconductor-affyplm/meta.yaml @@ -1,60 +1,67 @@ -{% set version = "1.78.0" %} +{% set version = "1.82.0" %} {% set name = "affyPLM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Methods for fitting probe-level models -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cdfd69bc9c54f3c03b52b3fd6e9f86b7 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-affyplm", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:affyplm + parent_recipe: + name: bioconductor-affyplm + path: recipes/bioconductor-affyplm + version: 1.56.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: affydata, MASS, hgu95av2cdf requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-gcrma >=2.74.0,<2.75.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-gcrma >=2.78.0,<2.79.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - libblas - liblapack + - zlib run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-gcrma >=2.74.0,<2.75.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-gcrma >=2.78.0,<2.79.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: 0f9e6db33cf6d5d8ed16a0885d59ffe0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Methods for fitting probe-level models' - description: 'A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:affyplm - parent_recipe: - name: bioconductor-affyplm - path: recipes/bioconductor-affyplm - version: 1.56.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-affyrnadegradation/meta.yaml b/recipes/bioconductor-affyrnadegradation/meta.yaml index 0cc0bd45177a2..c50e1a6201051 100644 --- a/recipes/bioconductor-affyrnadegradation/meta.yaml +++ b/recipes/bioconductor-affyrnadegradation/meta.yaml @@ -1,46 +1,52 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "AffyRNADegradation" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Analyze and correct probe positional bias in microarray data due to RNA degradation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4affd7f48b178750311671c1f2ac8c4f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-affyrnadegradation", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:affyrnadegradation + parent_recipe: + name: bioconductor-affyrnadegradation + path: recipes/bioconductor-affyrnadegradation + version: 1.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AmpAffyExample, hgu133acdf requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' + - bioconductor-affy >=1.84.0,<1.85.0 - r-base run: - - 'bioconductor-affy >=1.80.0,<1.81.0' + - bioconductor-affy >=1.84.0,<1.85.0 - r-base + +source: + md5: cadf0ca1b06dd4db0aad5357277b3967 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Analyze and correct probe positional bias in microarray data due to RNA degradation' - description: 'The package helps with the assessment and correction of RNA degradation effects in Affymetrix 3'' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:affyrnadegradation - parent_recipe: - name: bioconductor-affyrnadegradation - path: recipes/bioconductor-affyrnadegradation - version: 1.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ag.db/meta.yaml b/recipes/bioconductor-ag.db/meta.yaml index 7b597e80ef24d..61e65c764a9b2 100644 --- a/recipes/bioconductor-ag.db/meta.yaml +++ b/recipes/bioconductor-ag.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "ag.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 925e808d2c9b21a11ed131d483e75ab6 +about: + description: Affymetrix Affymetrix AG Array annotation data (chip ag) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix AG Array annotation data (chip ag) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ag.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.at.tair.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.at.tair.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.at.tair.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.at.tair.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 925e808d2c9b21a11ed131d483e75ab6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix AG Array annotation data (chip ag)' - description: 'Affymetrix Affymetrix AG Array annotation data (chip ag) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-agcdf/meta.yaml b/recipes/bioconductor-agcdf/meta.yaml index 312952757082a..5047f6d07d3f5 100644 --- a/recipes/bioconductor-agcdf/meta.yaml +++ b/recipes/bioconductor-agcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "agcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5dd14bc6a6d2729f5e7b170105c78e48 +about: + description: A package containing an environment representing the AG.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: agcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-agcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5dd14bc6a6d2729f5e7b170105c78e48 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: agcdf - description: 'A package containing an environment representing the AG.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-agdex/meta.yaml b/recipes/bioconductor-agdex/meta.yaml index 4304a5d0cccc5..8c6a77470d57c 100644 --- a/recipes/bioconductor-agdex/meta.yaml +++ b/recipes/bioconductor-agdex/meta.yaml @@ -1,42 +1,22 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "AGDEX" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A tool to evaluate agreement of differential expression for cross-species genomics + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL Version 2 or later + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Agreement of Differential Expression Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e74a7202bdc2e422e2213f1fb7a23f1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-agdex", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL Version 2 or later' - summary: 'Agreement of Differential Expression Analysis' - description: 'A tool to evaluate agreement of differential expression for cross-species genomics' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:agdex @@ -46,3 +26,29 @@ extra: path: recipes/bioconductor-agdex version: 1.28.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - r-base + +source: + md5: a4c17a430f2da1e099c8358960401e6a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-aggregatebiovar/meta.yaml b/recipes/bioconductor-aggregatebiovar/meta.yaml index a32ad85909c4c..06af8fbd1ab82 100644 --- a/recipes/bioconductor-aggregatebiovar/meta.yaml +++ b/recipes/bioconductor-aggregatebiovar/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "aggregateBioVar" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: For single cell RNA-seq data collected from more than one subject (e.g. biological sample or technical replicates), this package contains tools to summarize single cell gene expression profiles at the level of subject. A SingleCellExperiment object is taken as input and converted to a list of SummarizedExperiment objects, where each list element corresponds to an assigned cell type. The SummarizedExperiment objects contain aggregate gene-by-subject count matrices and inter-subject column metadata for individual subjects that can be processed using downstream bulk RNA-seq tools. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Differential Gene Expression Analysis for Multi-subject scRNA-seq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f389a909fab4bbc4cb526505c68f22e1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-aggregatebiovar", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, magick, knitr, rmarkdown, testthat, BiocGenerics, DESeq2, magrittr, dplyr, ggplot2, cowplot, ggtext, RColorBrewer, pheatmap, viridis requirements: host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-rlang - r-tibble run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-rlang - r-tibble + +source: + md5: 9290129272eae2c83034ff774bdc1aba + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Differential Gene Expression Analysis for Multi-subject scRNA-seq' - description: 'For single cell RNA-seq data collected from more than one subject (e.g. biological sample or technical replicates), this package contains tools to summarize single cell gene expression profiles at the level of subject. A SingleCellExperiment object is taken as input and converted to a list of SummarizedExperiment objects, where each list element corresponds to an assigned cell type. The SummarizedExperiment objects contain aggregate gene-by-subject count matrices and inter-subject column metadata for individual subjects that can be processed using downstream bulk RNA-seq tools.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-agilp/meta.yaml b/recipes/bioconductor-agilp/meta.yaml index e3c5bbb5a3261..b50b4a1bff87f 100644 --- a/recipes/bioconductor-agilp/meta.yaml +++ b/recipes/bioconductor-agilp/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "3.34.0" %} +{% set version = "3.38.0" %} {% set name = "agilp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 21b54a703747520483657dd63288f403 +about: + description: More about what it does (maybe more than one line) + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Agilent expression array processing package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-agilp", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-agilp + path: recipes/bioconductor-agilp + version: 3.12.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base +source: + md5: dbf0be42e3149d23acd29c60631252ca + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Agilent expression array processing package' - description: 'More about what it does (maybe more than one line)' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-agilp - path: recipes/bioconductor-agilp - version: 3.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-agimicrorna/meta.yaml b/recipes/bioconductor-agimicrorna/meta.yaml index 5030fc363a442..1031e5d6dbe89 100644 --- a/recipes/bioconductor-agimicrorna/meta.yaml +++ b/recipes/bioconductor-agimicrorna/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "2.52.0" %} +{% set version = "2.56.0" %} {% set name = "AgiMicroRna" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Processing and Analysis of Agilent microRNA data + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Processing and Differential Expression Analysis of Agilent microRNA chips -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c1046ab29a7766af0c602c974b4ec21 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-agimicrorna", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: geneplotter,marray,gplots,gtools,gdata,codelink requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affycoretools >=1.74.0,<1.75.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affycoretools >=1.78.0,<1.79.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affycoretools >=1.74.0,<1.75.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affycoretools >=1.78.0,<1.79.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base + +source: + md5: 9a533477c8c2c1ad03148f5a1f3dd8bf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Processing and Differential Expression Analysis of Agilent microRNA chips' - description: 'Processing and Analysis of Agilent microRNA data' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-agprobe/meta.yaml b/recipes/bioconductor-agprobe/meta.yaml index c2ba8fe20c5c7..ec2d911bf1d5e 100644 --- a/recipes/bioconductor-agprobe/meta.yaml +++ b/recipes/bioconductor-agprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "agprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 08f7527d4c8a30d8b2f86016a53f075a +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was AG\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type ag build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-agprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 08f7527d4c8a30d8b2f86016a53f075a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type ag' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was AG\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ahcytobands/meta.yaml b/recipes/bioconductor-ahcytobands/meta.yaml index 1fd99874310a1..8c652e9845a6e 100644 --- a/recipes/bioconductor-ahcytobands/meta.yaml +++ b/recipes/bioconductor-ahcytobands/meta.yaml @@ -1,37 +1,37 @@ {% set version = "0.99.1" %} {% set name = "AHCytoBands" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3dd85d02e7ed3fca4c7898b5e395edeb +about: + description: Supplies AnnotationHub with CytoBand information from UCSC. There is a track for each major organism. Giemsa-stained bands are commonly used to decorate chromosomal overviews in visualizations of genomic data. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: CytoBands for AnnotationHub build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ahcytobands", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3dd85d02e7ed3fca4c7898b5e395edeb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'CytoBands for AnnotationHub' - description: 'Supplies AnnotationHub with CytoBand information from UCSC. There is a track for each major organism. Giemsa-stained bands are commonly used to decorate chromosomal overviews in visualizations of genomic data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ahensdbs/build_failure.linux-64.yaml b/recipes/bioconductor-ahensdbs/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..81725921604be --- /dev/null +++ b/recipes/bioconductor-ahensdbs/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 0f6541c63494c920fb3ed686c1e9b41e85911787c300da23d97f8235674e1ed5 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-ps: 1.8.1-r44h2b5f3a1_0 conda-forge + r-purrr: 1.0.2-r44hdb488b9_1 conda-forge + r-r6: 2.5.1-r44hc72bb7e_3 conda-forge + r-rappdirs: 0.3.3-r44hb1dbf0f_3 conda-forge + r-rcurl: 1.98_1.16-r44he8228da_1 conda-forge + r-restfulr: 0.0.15-r44h5ef9028_5 bioconda + r-rjson: 0.2.23-r44h93ab643_0 conda-forge + r-rlang: 1.1.4-r44ha18555a_1 conda-forge + r-rsqlite: 2.3.9-r44h93ab643_0 conda-forge + r-runit: 0.4.33-r44hc72bb7e_1 conda-forge + r-rvest: 1.0.4-r44hc72bb7e_1 conda-forge + r-selectr: 0.4_2-r44hc72bb7e_4 conda-forge + r-snow: 0.4_4-r44hc72bb7e_3 conda-forge + r-stringdist: 0.9.14-r44h2b5f3a1_0 conda-forge + r-stringi: 1.8.4-r44h33cde33_3 conda-forge + r-stringr: 1.5.1-r44h785f33e_1 conda-forge + r-sys: 3.4.3-r44h2b5f3a1_0 conda-forge + r-tibble: 3.2.1-r44hdb488b9_3 conda-forge + r-tidyr: 1.3.1-r44h0d4f4ea_1 conda-forge + r-tidyselect: 1.2.1-r44hc72bb7e_1 conda-forge + r-utf8: 1.2.4-r44hb1dbf0f_1 conda-forge + r-vctrs: 0.6.5-r44h0d4f4ea_1 conda-forge + r-withr: 3.0.2-r44hc72bb7e_0 conda-forge + r-xfun: 0.49-r44h93ab643_0 conda-forge + r-xml: 3.99_0.17-r44h5bae778_2 conda-forge + r-xml2: 1.3.6-r44h8194278_2 conda-forge + r-yaml: 2.3.10-r44hdb488b9_0 conda-forge + readline: 8.2-h8228510_1 conda-forge + sed: 4.8-he412f7d_0 conda-forge + setuptools: 75.6.0-pyhff2d567_1 conda-forge + sysroot_linux-64: 2.17-h0157908_18 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tktable: 2.10-h8bc8fbc_6 conda-forge + toml: 0.10.2-pyhd8ed1ab_1 conda-forge + tomlkit: 0.13.2-pyha770c72_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + xmltodict: 0.14.2-pyhd8ed1ab_1 conda-forge + xorg-libice: 1.1.2-hb9d3cd8_0 conda-forge + xorg-libsm: 1.2.5-he73a12e_0 conda-forge + xorg-libx11: 1.8.10-h4f16b4b_1 conda-forge + xorg-libxau: 1.0.12-hb9d3cd8_0 conda-forge + xorg-libxdmcp: 1.1.5-hb9d3cd8_0 conda-forge + xorg-libxext: 1.3.6-hb9d3cd8_0 conda-forge + xorg-libxrender: 0.9.12-hb9d3cd8_0 conda-forge + xorg-libxt: 1.3.1-hb9d3cd8_0 conda-forge + yaml: 0.2.5-h7f98852_2 conda-forge + yq: 3.4.3-pyhd8ed1ab_1 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: AHEnsDbs_1.5.1_be76ea8794.tar.gz + Downloading https://bioconductor.org/packages/3.20/data/annotation/src/contrib/AHEnsDbs_1.5.1.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.073553 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioconductor.org/packages/3.20/bioc/src/contrib/Archive/AHEnsDbs/AHEnsDbs_1.5.1.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.044127 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioarchive.galaxyproject.org/AHEnsDbs_1.5.1.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.602924 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://depot.galaxyproject.org/software/bioconductor-ahensdbs/bioconductor-ahensdbs_1.5.1_src_all.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.475987 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download https://depot.galaxyproject.org/software/bioconductor-ahensdbs/bioconductor-ahensdbs_1.5.1_src_all.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-ahensdbs/meta.yaml b/recipes/bioconductor-ahensdbs/meta.yaml index 117aeb2c7ff6a..6bf7bcea508f5 100644 --- a/recipes/bioconductor-ahensdbs/meta.yaml +++ b/recipes/bioconductor-ahensdbs/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.1.10" %} +{% set version = "1.5.1" %} {% set name = "AHEnsDbs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 63aa3efc1c85d5a26e4d69d50f781a2a +about: + description: Supplies AnnotationHub with EnsDb Ensembl-based annotation databases for all species. EnsDb SQLite databases are generated separately from Ensembl MySQL databases using functions from the ensembldb package employing the Ensembl Perl API. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: EnsDbs for AnnotationHub build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ahensdbs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, AnnotationHub (>= 2.7.13), rmarkdown requirements: host: - - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - bioconductor-annotationhubdata >=1.36.0,<1.37.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 - r-base run: - - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - bioconductor-annotationhubdata >=1.36.0,<1.37.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: be76ea879496d8b031f8996cff09c6c0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'EnsDbs for AnnotationHub' - description: 'Supplies AnnotationHub with EnsDb Ensembl-based annotation databases for all species. EnsDb SQLite databases are generated separately from Ensembl MySQL databases using functions from the ensembldb package employing the Ensembl Perl API.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ahensdbs/post-link.sh b/recipes/bioconductor-ahensdbs/post-link.sh index e004d994abd34..55ad70fa66943 100644 --- a/recipes/bioconductor-ahensdbs/post-link.sh +++ b/recipes/bioconductor-ahensdbs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ahensdbs-1.1.10" +installBiocDataPackage.sh "ahensdbs-1.5.1" diff --git a/recipes/bioconductor-ahlrbasedbs/meta.yaml b/recipes/bioconductor-ahlrbasedbs/meta.yaml index 29db9f49d2eb6..8b4c049e544d5 100644 --- a/recipes/bioconductor-ahlrbasedbs/meta.yaml +++ b/recipes/bioconductor-ahlrbasedbs/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.7.0" %} +{% set version = "1.8.0" %} {% set name = "AHLRBaseDbs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5df6ef84988477d6262e54abd07c82da +about: + description: Supplies AnnotationHub with `LRbaseDb` Ligand-Receptor annotation databases for many species. All the SQLite files are generated by our Snakemake workflow [lrbase-workflow](https://github.com/rikenbit/lrbase-workflow). For the details, see the README.md of lrbase-workflow. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: LRBaseDbs for AnnotationHub build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ahlrbasedbs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a6628fab5cc4b0b8b129b20082e14380 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'LRBaseDbs for AnnotationHub' - description: 'Supplies AnnotationHub with `LRbaseDb` Ligand-Receptor annotation databases for many species. All the SQLite files are generated by our Snakemake workflow [lrbase-workflow](https://github.com/rikenbit/lrbase-workflow). For the details, see the README.md of lrbase-workflow.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ahlrbasedbs/post-link.sh b/recipes/bioconductor-ahlrbasedbs/post-link.sh index b59c08f98bc83..d17e3d1a7dab3 100644 --- a/recipes/bioconductor-ahlrbasedbs/post-link.sh +++ b/recipes/bioconductor-ahlrbasedbs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ahlrbasedbs-1.7.0" +installBiocDataPackage.sh "ahlrbasedbs-1.8.0" diff --git a/recipes/bioconductor-ahmassbank/meta.yaml b/recipes/bioconductor-ahmassbank/meta.yaml index 6db48bd579837..781af312821a4 100644 --- a/recipes/bioconductor-ahmassbank/meta.yaml +++ b/recipes/bioconductor-ahmassbank/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "AHMassBank" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b9ddc7dff0cabd4b170bc750cc3c47d3 +about: + description: Supplies AnnotationHub with MassBank metabolite/compound annotations bundled in CompDb SQLite databases. CompDb SQLite databases contain general compound annotation as well as fragment spectra representing fragmentation patterns of compounds' ions. MassBank data is retrieved from https://massbank.eu/MassBank and processed using helper functions from the CompoundDb Bioconductor package into redistributable SQLite databases. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: MassBank Annotation Resources for AnnotationHub build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ahmassbank", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, AnnotationHub (>= 2.7.13), rmarkdown, methods, CompoundDb (>= 1.1.4) requirements: host: - - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' + - bioconductor-annotationhubdata >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' + - bioconductor-annotationhubdata >=1.36.0,<1.37.0 - r-base +source: + md5: 771a7ffcb78436003de5c057e9c665de + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'MassBank Annotation Resources for AnnotationHub' - description: 'Supplies AnnotationHub with MassBank metabolite/compound annotations bundled in CompDb SQLite databases. CompDb SQLite databases contain general compound annotation as well as fragment spectra representing fragmentation patterns of compounds'' ions. MassBank data is retrieved from https://massbank.eu/MassBank and processed using helper functions from the CompoundDb Bioconductor package into redistributable SQLite databases.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ahmeshdbs/meta.yaml b/recipes/bioconductor-ahmeshdbs/meta.yaml index f7efca97a5554..79a1e7f105ab9 100644 --- a/recipes/bioconductor-ahmeshdbs/meta.yaml +++ b/recipes/bioconductor-ahmeshdbs/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.7.0" %} +{% set version = "1.8.0" %} {% set name = "AHMeSHDbs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9bbcae25794d2f854a122ba36a4e4c5c +about: + description: Supplies AnnotationHub with `MeSHDb` NIH MeSH annotation databases for many species. All the SQLite files and metadata.csv are generated by our Snakemake workflow [mesh-workflow](https://github.com/rikenbit/mesh-workflow). + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: MeSHDbs for AnnotationHub build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ahmeshdbs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4c370cd555a57e564b65d83106d7a7b0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'MeSHDbs for AnnotationHub' - description: 'Supplies AnnotationHub with `MeSHDb` NIH MeSH annotation databases for many species. All the SQLite files and metadata.csv are generated by our Snakemake workflow [mesh-workflow](https://github.com/rikenbit/mesh-workflow).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ahmeshdbs/post-link.sh b/recipes/bioconductor-ahmeshdbs/post-link.sh index 4b406789a1680..464554ad58f24 100644 --- a/recipes/bioconductor-ahmeshdbs/post-link.sh +++ b/recipes/bioconductor-ahmeshdbs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ahmeshdbs-1.7.0" +installBiocDataPackage.sh "ahmeshdbs-1.8.0" diff --git a/recipes/bioconductor-ahpathbankdbs/meta.yaml b/recipes/bioconductor-ahpathbankdbs/meta.yaml index aa5554f14038d..0bcc3a6f7f8ed 100644 --- a/recipes/bioconductor-ahpathbankdbs/meta.yaml +++ b/recipes/bioconductor-ahpathbankdbs/meta.yaml @@ -1,40 +1,40 @@ {% set version = "0.99.5" %} {% set name = "AHPathbankDbs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 70339eae8c03c47248b612b365bda4ff +about: + description: The package provides a comprehensive mapping table of metabolites and proteins linked to PathBank pathways. The tables include HMDB, KEGG, ChEBI, CAS, Drugbank, Uniprot IDs. The tables are provided for each of the 10 species ("Homo sapiens", "Escherichia coli", "Mus musculus", "Arabidopsis thaliana", "Saccharomyces cerevisiae", "Bos taurus", "Caenorhabditis elegans", "Rattus norvegicus", "Drosophila melanogaster", and "Pseudomonas aeruginosa"). These table information can be used for Metabolite Set (and other) Enrichment Analysis. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Metabolites and proteins linked to PathBank pathways (for AnnotationHub) build: - number: 5 + noarch: generic + number: 6 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ahpathbankdbs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, magrittr, dplyr, tibble, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 70339eae8c03c47248b612b365bda4ff + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Metabolites and proteins linked to PathBank pathways (for AnnotationHub)' - description: 'The package provides a comprehensive mapping table of metabolites and proteins linked to PathBank pathways. The tables include HMDB, KEGG, ChEBI, CAS, Drugbank, Uniprot IDs. The tables are provided for each of the 10 species ("Homo sapiens", "Escherichia coli", "Mus musculus", "Arabidopsis thaliana", "Saccharomyces cerevisiae", "Bos taurus", "Caenorhabditis elegans", "Rattus norvegicus", "Drosophila melanogaster", and "Pseudomonas aeruginosa"). These table information can be used for Metabolite Set (and other) Enrichment Analysis.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ahpubmeddbs/meta.yaml b/recipes/bioconductor-ahpubmeddbs/meta.yaml index 8692df0e1a8d1..6802ea4e3c80d 100644 --- a/recipes/bioconductor-ahpubmeddbs/meta.yaml +++ b/recipes/bioconductor-ahpubmeddbs/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.7.0" %} +{% set version = "1.8.0" %} {% set name = "AHPubMedDbs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b2db2eda6009bc9cdec579c4ab579f25 +about: + description: Supplies AnnotationHub with some preprocessed sqlite, tibble, and data.table datasets of PubMed. All the datasets are generated by our Snakemake workflow [pubmed-workflow](https://github.com/rikenbit/pubmed-workflow). For the details, see the README.md of pubmed-workflow. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: SQLites, tibbles, and data.tables for AnnotationHub build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ahpubmeddbs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a5c32ec183a48fc624a5a09cf2472196 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'SQLites, tibbles, and data.tables for AnnotationHub' - description: 'Supplies AnnotationHub with some preprocessed sqlite, tibble, and data.table datasets of PubMed. All the datasets are generated by our Snakemake workflow [pubmed-workflow](https://github.com/rikenbit/pubmed-workflow). For the details, see the README.md of pubmed-workflow.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ahpubmeddbs/post-link.sh b/recipes/bioconductor-ahpubmeddbs/post-link.sh index 42e051ec75f48..67d83c40cddbd 100644 --- a/recipes/bioconductor-ahpubmeddbs/post-link.sh +++ b/recipes/bioconductor-ahpubmeddbs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ahpubmeddbs-1.7.0" +installBiocDataPackage.sh "ahpubmeddbs-1.8.0" diff --git a/recipes/bioconductor-ahwikipathwaysdbs/meta.yaml b/recipes/bioconductor-ahwikipathwaysdbs/meta.yaml index 73c928b6ecca4..82dfa31532b44 100644 --- a/recipes/bioconductor-ahwikipathwaysdbs/meta.yaml +++ b/recipes/bioconductor-ahwikipathwaysdbs/meta.yaml @@ -1,40 +1,40 @@ {% set version = "0.99.4" %} {% set name = "AHWikipathwaysDbs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ffa90f6d6e8832ae6f4b5bf8b151cd46 +about: + description: The package provides a comprehensive mapping table of metabolites linked to Wikipathways pathways. The tables include HMDB, KEGG, ChEBI, Drugbank, PubChem compound, ChemSpider, KNApSAcK, and Wikidata IDs plus CAS and InChIKey. The tables are provided for each of the 25 species ("Anopheles gambiae", "Arabidopsis thaliana", "Bacillus subtilis", "Bos taurus", "Caenorhabditis elegans", "Canis familiaris", "Danio rerio", "Drosophila melanogaster", "Equus caballus", "Escherichia coli", "Gallus gallus", "Gibberella zeae", "Homo sapiens", "Hordeum vulgare", "Mus musculus", "Mycobacterium tuberculosis", "Oryza sativa", "Pan troglodytes", "Plasmodium falciparum", "Populus trichocarpa", "Rattus norvegicus", "Saccharomyces cerevisiae", "Solanum lycopersicum", "Sus scrofa", "Zea mays"). These table information can be used for Metabolite Set Enrichment Analysis. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Metabolites linked to WikiPathways pathways (for AnnotationHub) build: - number: 5 + noarch: generic + number: 6 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ahwikipathwaysdbs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, magrittr, dplyr, tibble, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ffa90f6d6e8832ae6f4b5bf8b151cd46 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Metabolites linked to WikiPathways pathways (for AnnotationHub)' - description: 'The package provides a comprehensive mapping table of metabolites linked to Wikipathways pathways. The tables include HMDB, KEGG, ChEBI, Drugbank, PubChem compound, ChemSpider, KNApSAcK, and Wikidata IDs plus CAS and InChIKey. The tables are provided for each of the 25 species ("Anopheles gambiae", "Arabidopsis thaliana", "Bacillus subtilis", "Bos taurus", "Caenorhabditis elegans", "Canis familiaris", "Danio rerio", "Drosophila melanogaster", "Equus caballus", "Escherichia coli", "Gallus gallus", "Gibberella zeae", "Homo sapiens", "Hordeum vulgare", "Mus musculus", "Mycobacterium tuberculosis", "Oryza sativa", "Pan troglodytes", "Plasmodium falciparum", "Populus trichocarpa", "Rattus norvegicus", "Saccharomyces cerevisiae", "Solanum lycopersicum", "Sus scrofa", "Zea mays"). These table information can be used for Metabolite Set Enrichment Analysis.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-aims/meta.yaml b/recipes/bioconductor-aims/meta.yaml index 4e9667789a111..2bdc15c218151 100644 --- a/recipes/bioconductor-aims/meta.yaml +++ b/recipes/bioconductor-aims/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "AIMS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains the AIMS implementation. It contains necessary functions to assign the five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, Basal-like, Normal-like). Assignments could be done on individual samples as well as on dataset of gene expression data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 23ef11145babcac9430b2c94db4dfae3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-aims", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:aims + - doi:10.1093/jnci/dju357 + parent_recipe: + name: bioconductor-aims + path: recipes/bioconductor-aims + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: breastCancerVDX, hgu133a.db, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-e1071 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-e1071 + +source: + md5: 9b22b78928bb98883fb3948fba2b40f8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype' - description: 'This package contains the AIMS implementation. It contains necessary functions to assign the five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, Basal-like, Normal-like). Assignments could be done on individual samples as well as on dataset of gene expression data.' -extra: - identifiers: - - biotools:aims - - doi:10.1093/jnci/dju357 - parent_recipe: - name: bioconductor-aims - path: recipes/bioconductor-aims - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-airpart/meta.yaml b/recipes/bioconductor-airpart/meta.yaml index c343eeefb76a6..88b206e4c6fb2 100644 --- a/recipes/bioconductor-airpart/meta.yaml +++ b/recipes/bioconductor-airpart/meta.yaml @@ -1,33 +1,36 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "airpart" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Airpart identifies sets of genes displaying differential cell-type-specific allelic imbalance across cell types or states, utilizing single-cell allelic counts. It makes use of a generalized fused lasso with binomial observations of allelic counts to partition cell types by their allelic imbalance. Alternatively, a nonparametric method for partitioning cell types is offered. The package includes a number of visualizations and quality control functions for examining single cell allelic imbalance datasets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Differential cell-type-specific allelic imbalance -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 59977674a0dc5eb9f4bd03ef89a73630 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-airpart", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, roxygen2 (>= 6.0.0), testthat (>= 3.0.0), gplots, tidyr requirements: + host: - - 'bioconductor-apeglm >=1.24.0,<1.25.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-apeglm >=1.28.0,<1.29.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-clue - r-dplyr @@ -43,13 +46,14 @@ requirements: - r-rcolorbrewer - r-rlang - r-smurf + run: - - 'bioconductor-apeglm >=1.24.0,<1.25.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-apeglm >=1.28.0,<1.29.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-clue - r-dplyr @@ -65,13 +69,16 @@ requirements: - r-rcolorbrewer - r-rlang - r-smurf + +source: + md5: 44e2b628fbf8a160a72cc01685deee2f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Differential cell-type-specific allelic imbalance' - description: 'Airpart identifies sets of genes displaying differential cell-type-specific allelic imbalance across cell types or states, utilizing single-cell allelic counts. It makes use of a generalized fused lasso with binomial observations of allelic counts to partition cell types by their allelic imbalance. Alternatively, a nonparametric method for partitioning cell types is offered. The package includes a number of visualizations and quality control functions for examining single cell allelic imbalance datasets.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-airway/meta.yaml b/recipes/bioconductor-airway/meta.yaml index ba924b9263df0..431594257e756 100644 --- a/recipes/bioconductor-airway/meta.yaml +++ b/recipes/bioconductor-airway/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "airway" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ffed4ae3349ebeeeabff9f1456b8ba1d +about: + description: 'This package provides a RangedSummarizedExperiment object of read counts in genes for an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. Details on the gene model and read counting procedure are provided in the package vignette. The citation for the experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST, Lu Q. ''RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells.'' PLoS One. 2014 Jun 13;9(6):e99625. PMID: 24926665. GEO: GSE52778.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-airway", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, GEOquery, markdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 46b3c23c9c6d6fcf5973d6dcee659f94 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014' - description: 'This package provides a RangedSummarizedExperiment object of read counts in genes for an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. Details on the gene model and read counting procedure are provided in the package vignette. The citation for the experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST, Lu Q. ''RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells.'' PLoS One. 2014 Jun 13;9(6):e99625. PMID: 24926665. GEO: GSE52778.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-airway/post-link.sh b/recipes/bioconductor-airway/post-link.sh index a8e50bfc60ff3..892c58c20ecb1 100644 --- a/recipes/bioconductor-airway/post-link.sh +++ b/recipes/bioconductor-airway/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "airway-1.22.0" +installBiocDataPackage.sh "airway-1.26.0" diff --git a/recipes/bioconductor-alabaster.base/build.sh b/recipes/bioconductor-alabaster.base/build.sh index c1d13421f5f1e..3e0e95a487bc9 100644 --- a/recipes/bioconductor-alabaster.base/build.sh +++ b/recipes/bioconductor-alabaster.base/build.sh @@ -8,4 +8,5 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars +export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-alabaster.base/build_failure.osx-64.yaml b/recipes/bioconductor-alabaster.base/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..edd14f117dc68 --- /dev/null +++ b/recipes/bioconductor-alabaster.base/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: d39385cb1d5f629d0aa570d4a326ce35bc254dd4e494c613fe345e497f92e949 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + of such objects into RDS files. Each artifact is associated with metadata for + further interpretation; downstream applications can enrich this metadata with + context-specific properties. + home: https://bioconductor.org/packages/3.20/bioc/html/alabaster.base.html + license: MIT file LICENSE + license_file: LICENSE + summary: Save Bioconductor Objects To File + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-alabaster.base_1736090045496/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-alabaster.base_1736090045496/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-alabaster.base_1736090045496/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-alabaster.base_1736090045496/work + INFO: activate-gfortran_osx-64.sh made the following environmental changes: + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I../inst/include -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1720307552622/work=/usr/local/src/conda/r-base-4.4.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I../inst/include -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1720307552622/work=/usr/local/src/conda/r-base-4.4.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c check_csv.cpp -o check_csv.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I../inst/include -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1720307552622/work=/usr/local/src/conda/r-base-4.4.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c check_list.cpp -o check_list.o +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-alabaster.base/conda_build_config.yaml b/recipes/bioconductor-alabaster.base/conda_build_config.yaml new file mode 100644 index 0000000000000..dfa107c97cb62 --- /dev/null +++ b/recipes/bioconductor-alabaster.base/conda_build_config.yaml @@ -0,0 +1,8 @@ +MACOSX_DEPLOYMENT_TARGET: # [osx and x86_64] + - "10.15" # [osx and x86_64] + +MACOSX_SDK_VERSION: # [osx and x86_64] + - "10.15" # [osx and x86_64] + +c_stdlib_version: + - 10.15 # [osx and x86_64] \ No newline at end of file diff --git a/recipes/bioconductor-alabaster.base/meta.yaml b/recipes/bioconductor-alabaster.base/meta.yaml index 22787eb448ec7..d172f478fc099 100644 --- a/recipes/bioconductor-alabaster.base/meta.yaml +++ b/recipes/bioconductor-alabaster.base/meta.yaml @@ -1,31 +1,37 @@ -{% set version = "1.2.1" %} +{% set version = "1.6.0" %} {% set name = "alabaster.base" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Save Bioconductor data structures into file artifacts, and load them back into memory. This is a more robust and portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Save Bioconductor Objects To File -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2d6215dfe9b8412438f9b05b54be2331 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alabaster.base", max_pin="x.x") }}' -# Suggests: BiocStyle, rmarkdown, knitr, testthat, digest, Matrix + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, rmarkdown, knitr, testthat, digest, Matrix, alabaster.matrix # SystemRequirements: C++17, GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-alabaster.schemas >=1.2.0,<1.3.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-alabaster.schemas >=1.6.0,<1.7.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-jsonlite - r-jsonvalidate @@ -33,25 +39,24 @@ requirements: - libblas - liblapack run: - - 'bioconductor-alabaster.schemas >=1.2.0,<1.3.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-alabaster.schemas >=1.6.0,<1.7.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-jsonlite - r-jsonvalidate - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: caec8d8c552e814f0d2d38c30a947286 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Save Bioconductor Objects To File' - description: 'Save Bioconductor data structures into file artifacts, and load them back into memory. This is a more robust and portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-alabaster.bumpy/build_failure.osx-64.yaml b/recipes/bioconductor-alabaster.bumpy/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..1c27dba502c1b --- /dev/null +++ b/recipes/bioconductor-alabaster.bumpy/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 539ee2afd81fd2259f5fd1585c1d10d678b4240c401fb35c1ef2f794df0988a5 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bioconductor-alabaster.base needs to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-alabaster.bumpy/meta.yaml b/recipes/bioconductor-alabaster.bumpy/meta.yaml index ab61aee778ded..ed837188b4596 100644 --- a/recipes/bioconductor-alabaster.bumpy/meta.yaml +++ b/recipes/bioconductor-alabaster.bumpy/meta.yaml @@ -1,49 +1,56 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "alabaster.bumpy" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Save BumpyMatrix objects into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Save and Load BumpyMatrices to/from file -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0d5111cd74d5b72fc88eb66ac5b670c3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alabaster.bumpy", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, rmarkdown, knitr, testthat, jsonlite requirements: host: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bumpymatrix >=1.14.0,<1.15.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-matrix run: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bumpymatrix >=1.14.0,<1.15.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-matrix + +source: + md5: 57b7d691a5513b65c5b6867154af3d3b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Save and Load BumpyMatrices to/from file' - description: 'Save BumpyMatrix objects into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-alabaster.files/build_failure.osx-64.yaml b/recipes/bioconductor-alabaster.files/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..eaaead02d1cb3 --- /dev/null +++ b/recipes/bioconductor-alabaster.files/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 0b8840ac8f54983081b75f086912870a63c5c119d5784980a3afa43541975048 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bioconductor-alabaster.base needs to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-alabaster.files/meta.yaml b/recipes/bioconductor-alabaster.files/meta.yaml index a91a9a98a4880..7c847aac6efc8 100644 --- a/recipes/bioconductor-alabaster.files/meta.yaml +++ b/recipes/bioconductor-alabaster.files/meta.yaml @@ -1,49 +1,45 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "alabaster.files" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ea12d81dadbad7340c5f2d6be276a697 +about: + description: Save common bioinformatics file formats within the alabaster framework. This includes BAM, BED, VCF, bigWig, bigBed, FASTQ, FASTA and so on. We save and load additional metadata for each file, and we support linkage between each file and its corresponding index. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Wrappers to Save Common File Formats build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alabaster.files", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, rmarkdown, knitr, testthat, VariantAnnotation +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: BiocStyle, rmarkdown, knitr, testthat, VariantAnnotation, rtracklayer, Biostrings requirements: host: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base +source: + md5: 64bb711a5c17a08b033e7f8ff7fc36a2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Wrappers to Save Common File Formats' - description: 'Save common bioinformatics file formats within the alabaster framework. This includes BAM, BED, VCF, bigWig, bigBed, FASTQ, FASTA and so on. We save and load additional metadata for each file, and we support linkage between each file and its corresponding index.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-alabaster.mae/build_failure.osx-64.yaml b/recipes/bioconductor-alabaster.mae/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..f58f526c38b4d --- /dev/null +++ b/recipes/bioconductor-alabaster.mae/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 93d8c7574f21cd60cb4decdd13c5ed0d0ede0fff13edf50e6cd8fb014dfbadb9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bioconductor-alabaster.base needs to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-alabaster.mae/meta.yaml b/recipes/bioconductor-alabaster.mae/meta.yaml index 15bed2c113976..cbb1640e012de 100644 --- a/recipes/bioconductor-alabaster.mae/meta.yaml +++ b/recipes/bioconductor-alabaster.mae/meta.yaml @@ -1,45 +1,54 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "alabaster.mae" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Save MultiAssayExperiments into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Load and Save MultiAssayExperiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 43abcdda61fc9d69dbc24dbd1c91664d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alabaster.mae", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, SummarizedExperiment, BiocParallel, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-alabaster.se >=1.6.0,<1.7.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base + - r-jsonlite run: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-alabaster.se >=1.6.0,<1.7.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base + - r-jsonlite + +source: + md5: 3dde2c4194478c89d796cec1bb5b8a31 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Load and Save MultiAssayExperiments' - description: 'Save MultiAssayExperiments into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-alabaster.matrix/build_failure.osx-64.yaml b/recipes/bioconductor-alabaster.matrix/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..5a2771d039bf2 --- /dev/null +++ b/recipes/bioconductor-alabaster.matrix/build_failure.osx-64.yaml @@ -0,0 +1,107 @@ +recipe_sha: 0aaa4e891ecb1e9064d6cf264dcf57259ece1084fd5887807376afcb7d3c87a8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + of such objects into RDS files. Each artifact is associated with metadata for + further interpretation; downstream applications can enrich this metadata with + context-specific properties. + home: https://bioconductor.org/packages/3.20/bioc/html/alabaster.base.html + license: MIT file LICENSE + license_file: LICENSE + summary: Save Bioconductor Objects To File + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-alabaster.base_1735857573424/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-alabaster.base_1735857573424/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-alabaster.base_1735857573424/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-alabaster.base_1735857573424/work + INFO: activate-gfortran_osx-64.sh made the following environmental changes: + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-alabaster.base-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I../inst/include -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1720307552622/work=/usr/local/src/conda/r-base-4.4.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I../inst/include -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1720307552622/work=/usr/local/src/conda/r-base-4.4.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c check_csv.cpp -o check_csv.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I../inst/include -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1720307552622/work=/usr/local/src/conda/r-base-4.4.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c check_list.cpp -o check_list.o +# Last 100 lines of the build log. +category: |- + dependency issue + diff --git a/recipes/bioconductor-alabaster.matrix/meta.yaml b/recipes/bioconductor-alabaster.matrix/meta.yaml index 73ee0d6404f07..641cdd795f5c1 100644 --- a/recipes/bioconductor-alabaster.matrix/meta.yaml +++ b/recipes/bioconductor-alabaster.matrix/meta.yaml @@ -1,53 +1,67 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "alabaster.matrix" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Save matrices, arrays and similar objects into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Load and Save Artifacts from File -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 099a01bbb4a95bdaf0f91ffd2b89653d build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alabaster.matrix", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, knitr, BiocStyle, chihaya + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, knitr, BiocStyle, chihaya, BiocSingular, ResidualMatrix requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-sparsearray >=1.2.0,<1.3.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4arrays >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 - r-base - r-matrix + - r-rcpp + - libblas + - liblapack run: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-sparsearray >=1.2.0,<1.3.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4arrays >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 - r-base - r-matrix + - r-rcpp + +source: + md5: 7fa595f12999ab54198984422d573890 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Load and Save Artifacts from File' - description: 'Save matrices, arrays and similar objects into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-alabaster.ranges/build_failure.osx-64.yaml b/recipes/bioconductor-alabaster.ranges/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..8e85823e9283f --- /dev/null +++ b/recipes/bioconductor-alabaster.ranges/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 1e90ce89d2d62c2c3e959af38cad77baa6d030ebb6061f734193ea3530cbca69 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bioconductor-alabaster.base needs to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-alabaster.ranges/meta.yaml b/recipes/bioconductor-alabaster.ranges/meta.yaml index d912501aceef5..916b415ae1811 100644 --- a/recipes/bioconductor-alabaster.ranges/meta.yaml +++ b/recipes/bioconductor-alabaster.ranges/meta.yaml @@ -1,49 +1,56 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "alabaster.ranges" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Save GenomicRanges, IRanges and related data structures into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Load and Save Ranges-related Artifacts from File -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: af5d849080999b0167cc39fc182721e9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alabaster.ranges", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, BiocStyle, jsonlite requirements: host: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base + +source: + md5: 91f5afc229776f80c91244592f138ed1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Load and Save Ranges-related Artifacts from File' - description: 'Save GenomicRanges, IRanges and related data structures into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-alabaster.sce/build_failure.osx-64.yaml b/recipes/bioconductor-alabaster.sce/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..146373986b82d --- /dev/null +++ b/recipes/bioconductor-alabaster.sce/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 38f3ef22e9bfbb896d1692a8c4961ac7bd0ad209b28151a029b63648f50e54f4 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bioconductor-alabaster.base needs to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-alabaster.sce/meta.yaml b/recipes/bioconductor-alabaster.sce/meta.yaml index dbb5845379eba..67796089ec138 100644 --- a/recipes/bioconductor-alabaster.sce/meta.yaml +++ b/recipes/bioconductor-alabaster.sce/meta.yaml @@ -1,43 +1,45 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "alabaster.sce" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e508f30fb84947c7246b093b63a5aea3 +about: + description: Save SingleCellExperiment into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Load and Save SingleCellExperiment from File build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alabaster.sce", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, testthat, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-alabaster.se >=1.6.0,<1.7.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base + - r-jsonlite run: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-alabaster.se >=1.6.0,<1.7.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base + - r-jsonlite +source: + md5: 4efd5d1f6bdb1715cbdba9bf43d9f3b7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Load and Save SingleCellExperiment from File' - description: 'Save SingleCellExperiment into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-alabaster.schemas/meta.yaml b/recipes/bioconductor-alabaster.schemas/meta.yaml index 6a45f9d6cc290..0e9d124862fc4 100644 --- a/recipes/bioconductor-alabaster.schemas/meta.yaml +++ b/recipes/bioconductor-alabaster.schemas/meta.yaml @@ -1,37 +1,37 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "alabaster.schemas" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 308883d85ab416d45eaa55428463d308 +about: + description: Stores all schemas required by various alabaster.* packages. No computation should be performed by this package, as that is handled by alabaster.base. We use a separate package instead of storing the schemas in alabaster.base itself, to avoid conflating management of the schemas with code maintenence. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Schemas for the Alabaster Framework build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alabaster.schemas", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - r-base run: - r-base +source: + md5: ad4e4e98115922e6f1f141801c65c97d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Schemas for the Alabaster Framework' - description: 'Stores all schemas required by various alabaster.* packages. No computation should be performed by this package, as that is handled by alabaster.base. We use a separate package instead of storing the schemas in alabaster.base itself, to avoid conflating management of the schemas with code maintenence.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-alabaster.se/build_failure.osx-64.yaml b/recipes/bioconductor-alabaster.se/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..1978f9054d263 --- /dev/null +++ b/recipes/bioconductor-alabaster.se/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 3e28ec88f6f45acadef755d05067117420f933fcdd53544bb189834bdcebf459 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bioconductor-alabaster.base needs to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-alabaster.se/meta.yaml b/recipes/bioconductor-alabaster.se/meta.yaml index 6a54ef0e020fa..15e996a33a444 100644 --- a/recipes/bioconductor-alabaster.se/meta.yaml +++ b/recipes/bioconductor-alabaster.se/meta.yaml @@ -1,53 +1,60 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "alabaster.se" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Save SummarizedExperiments into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Load and Save SummarizedExperiments from File -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 25133d88cc71ec6029229772a1eee0e8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alabaster.se", max_pin="x.x") }}' - noarch: generic -# Suggests: rmarkdown, knitr, testthat, BiocStyle, jsonlite + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: rmarkdown, knitr, testthat, BiocStyle requirements: host: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.matrix >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.ranges >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-alabaster.matrix >=1.6.0,<1.7.0 + - bioconductor-alabaster.ranges >=1.6.0,<1.7.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + - r-jsonlite run: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.matrix >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.ranges >=1.2.0,<1.3.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-alabaster.matrix >=1.6.0,<1.7.0 + - bioconductor-alabaster.ranges >=1.6.0,<1.7.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + - r-jsonlite + +source: + md5: e649779f0e179554bbb4091e7d000bff + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Load and Save SummarizedExperiments from File' - description: 'Save SummarizedExperiments into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-alabaster.spatial/build_failure.osx-64.yaml b/recipes/bioconductor-alabaster.spatial/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..92aec1e30a769 --- /dev/null +++ b/recipes/bioconductor-alabaster.spatial/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: d4ab66d4b8fa84ad6f84a880d4566b1cc9f6a29fa2a9a9f6bc21c38efb236344 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bioconductor-alabaster.base needs to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-alabaster.spatial/meta.yaml b/recipes/bioconductor-alabaster.spatial/meta.yaml index fa129e7aa9045..b11b997e551d2 100644 --- a/recipes/bioconductor-alabaster.spatial/meta.yaml +++ b/recipes/bioconductor-alabaster.spatial/meta.yaml @@ -1,49 +1,52 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "alabaster.spatial" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Save SpatialExperiment objects and their images into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Save and Load Spatial 'Omics Data to/from File -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 906d73c492ba97e8eda563055c51bbfc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alabaster.spatial", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocStyle, DropletUtils, magick, png, digest requirements: host: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.sce >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-alabaster.sce >=1.6.0,<1.7.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 - r-base - - r-jsonlite run: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.sce >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-alabaster.sce >=1.6.0,<1.7.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 - r-base - - r-jsonlite + +source: + md5: af2730bd012615de011fb86a4af44804 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Save and Load Spatial ''Omics Data to/from File' - description: 'Save SpatialExperiment objects and their images into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-alabaster.string/build_failure.osx-64.yaml b/recipes/bioconductor-alabaster.string/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..17e8aae9aa76a --- /dev/null +++ b/recipes/bioconductor-alabaster.string/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: f35af6e3bf3a96d1107b11019925879572d221e362a99ea3b9f32e745188e9c1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bioconductor-alabaster.base needs to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-alabaster.string/meta.yaml b/recipes/bioconductor-alabaster.string/meta.yaml index 3ab554683fc97..b952e03500a16 100644 --- a/recipes/bioconductor-alabaster.string/meta.yaml +++ b/recipes/bioconductor-alabaster.string/meta.yaml @@ -1,41 +1,43 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "alabaster.string" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b7add7aa52b8835471b04038842da095 +about: + description: Save Biostrings objects to file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Save and Load Biostrings to/from File build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alabaster.string", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, rmarkdown, knitr, testthat requirements: host: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base +source: + md5: 40407640753273dadcc3d008a65691a2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Save and Load Biostrings to/from File' - description: 'Save Biostrings objects to file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-alabaster.vcf/build_failure.osx-64.yaml b/recipes/bioconductor-alabaster.vcf/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..511dd53f1c2a4 --- /dev/null +++ b/recipes/bioconductor-alabaster.vcf/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 2bb9b4b6bfe59c17e1c135f7a34a39fb522a4903e5e4eff030a859306e56e2bd # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bioconductor-alabaster.base needs to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-alabaster.vcf/meta.yaml b/recipes/bioconductor-alabaster.vcf/meta.yaml index 191429828c512..99d6f32da0515 100644 --- a/recipes/bioconductor-alabaster.vcf/meta.yaml +++ b/recipes/bioconductor-alabaster.vcf/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "alabaster.vcf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Save variant calling SummarizedExperiment to file and load them back as VCF objects. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Save and Load Variant Data to/from File -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e0873ba68051843f6a35b01fef673423 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alabaster.vcf", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.string >=1.2.0,<1.3.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-alabaster.se >=1.6.0,<1.7.0 + - bioconductor-alabaster.string >=1.6.0,<1.7.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.string >=1.2.0,<1.3.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-alabaster.se >=1.6.0,<1.7.0 + - bioconductor-alabaster.string >=1.6.0,<1.7.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base + +source: + md5: 39e2ae0051549a4dcd29a8baf6b3c800 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Save and Load Variant Data to/from File' - description: 'Save variant calling SummarizedExperiment to file and load them back as VCF objects. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-alabaster/build_failure.osx-64.yaml b/recipes/bioconductor-alabaster/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..7ac3467e19cd2 --- /dev/null +++ b/recipes/bioconductor-alabaster/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 095f279dc8310e9a787eafcb34f0f21e1a4b634f1dba13a09d4b1c142f569e4e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bioconductor-alabaster.base needs to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-alabaster/meta.yaml b/recipes/bioconductor-alabaster/meta.yaml index 2189836f4b577..41f89a9830ba4 100644 --- a/recipes/bioconductor-alabaster/meta.yaml +++ b/recipes/bioconductor-alabaster/meta.yaml @@ -1,57 +1,62 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "alabaster" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Umbrella for the alabaster suite, providing a single-line import for all alabaster.* packages. Installing this package ensures that all known alabaster.* packages are also installed, avoiding problems with missing packages when a staging method or loading function is dynamically requested. Obviously, this comes at the cost of needing to install more packages, so advanced users and application developers may prefer to install the required alabaster.* packages individually. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Umbrella for the Alabaster Framework -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 359d26d34b8867dd418d0d277b0228c9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alabaster", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.bumpy >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.mae >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.matrix >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.ranges >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.sce >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.spatial >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.string >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.vcf >=1.2.0,<1.3.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-alabaster.bumpy >=1.6.0,<1.7.0 + - bioconductor-alabaster.mae >=1.6.0,<1.7.0 + - bioconductor-alabaster.matrix >=1.6.0,<1.7.0 + - bioconductor-alabaster.ranges >=1.6.0,<1.7.0 + - bioconductor-alabaster.sce >=1.6.0,<1.7.0 + - bioconductor-alabaster.se >=1.6.0,<1.7.0 + - bioconductor-alabaster.spatial >=1.6.0,<1.7.0 + - bioconductor-alabaster.string >=1.6.0,<1.7.0 + - bioconductor-alabaster.vcf >=1.6.0,<1.7.0 - r-base run: - - 'bioconductor-alabaster.base >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.bumpy >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.mae >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.matrix >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.ranges >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.sce >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.se >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.spatial >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.string >=1.2.0,<1.3.0' - - 'bioconductor-alabaster.vcf >=1.2.0,<1.3.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-alabaster.bumpy >=1.6.0,<1.7.0 + - bioconductor-alabaster.mae >=1.6.0,<1.7.0 + - bioconductor-alabaster.matrix >=1.6.0,<1.7.0 + - bioconductor-alabaster.ranges >=1.6.0,<1.7.0 + - bioconductor-alabaster.sce >=1.6.0,<1.7.0 + - bioconductor-alabaster.se >=1.6.0,<1.7.0 + - bioconductor-alabaster.spatial >=1.6.0,<1.7.0 + - bioconductor-alabaster.string >=1.6.0,<1.7.0 + - bioconductor-alabaster.vcf >=1.6.0,<1.7.0 - r-base + +source: + md5: dcb396e0287261019fe05475bdb03c70 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Umbrella for the Alabaster Framework' - description: 'Umbrella for the alabaster suite, providing a single-line import for all alabaster.* packages. Installing this package ensures that all known alabaster.* packages are also installed, avoiding problems with missing packages when a staging method or loading function is dynamically requested. Obviously, this comes at the cost of needing to install more packages, so advanced users and application developers may prefer to install the required alabaster.* packages individually.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-aldex2/meta.yaml b/recipes/bioconductor-aldex2/meta.yaml index 70392f9f4f9ec..1d8d6b04a8c64 100644 --- a/recipes/bioconductor-aldex2/meta.yaml +++ b/recipes/bioconductor-aldex2/meta.yaml @@ -1,33 +1,43 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "ALDEx2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcoxon Rank Sum test and Welch's t-test (via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear model (via aldex.glm), or a correlation test (via aldex.corr). All tests report predicted p-values and posterior Benjamini-Hochberg corrected p-values. ALDEx2 also calculates expected standardized effect sizes for paired or unpaired study designs. ALDEx2 can now be used to estimate the effect of scale on the results and report on the scale-dependent robustness of results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 359e47382b7cac1093aa1a5c24307cec build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-aldex2", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:aldex2 + parent_recipe: + name: bioconductor-aldex2 + path: recipes/bioconductor-aldex2 + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr, rmarkdown, purrr, ggpattern, ggplot2, cowplot, tidyverse, magick requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-directlabels - r-lattice @@ -35,32 +45,28 @@ requirements: - r-rfast - r-zcompositions run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-directlabels - r-lattice - r-latticeextra - r-rfast - r-zcompositions + +source: + md5: 8825241132d974416136aff59d855306 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=3)' - summary: 'Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account' - description: 'A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcoxon Rank Sum test and Welch''s t-test (via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear model (via aldex.glm), or a correlation test (via aldex.corr). All tests report predicted p-values and posterior Benjamini-Hochberg corrected p-values. ALDEx2 also calculates expected standardized effect sizes for paired or unpaired study designs. ALDEx2 can now be used to estimate the effect of scale on the results and report on the scale-dependent robustness of results.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:aldex2 - parent_recipe: - name: bioconductor-aldex2 - path: recipes/bioconductor-aldex2 - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-alevinqc/meta.yaml b/recipes/bioconductor-alevinqc/meta.yaml index 619d9e458faed..f3f7048460f8d 100644 --- a/recipes/bioconductor-alevinqc/meta.yaml +++ b/recipes/bioconductor-alevinqc/meta.yaml @@ -1,67 +1,72 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "alevinQC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Generate QC reports summarizing the output from an alevin, alevin-fry, or simpleaf run. Reports can be generated as html or pdf files, or as shiny applications. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Generate QC Reports For Alevin Output -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fa79ac8ac72e4d6d16c096886e9f759d build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alevinqc", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, testthat (>= 3.0.0), BiocManager # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-tximport >=1.30.0,<1.31.0' + - bioconductor-tximport >=1.34.0,<1.35.0 - r-base - r-cowplot - r-dplyr - r-dt - r-ggally - - 'r-ggplot2 >=3.4.0' + - r-ggplot2 >=3.4.0 - r-rcpp - r-rjson - r-rlang - - 'r-rmarkdown >=2.5' + - r-rmarkdown >=2.5 - r-shiny - r-shinydashboard - libblas - liblapack run: - - 'bioconductor-tximport >=1.30.0,<1.31.0' + - bioconductor-tximport >=1.34.0,<1.35.0 - r-base - r-cowplot - r-dplyr - r-dt - r-ggally - - 'r-ggplot2 >=3.4.0' + - r-ggplot2 >=3.4.0 - r-rcpp - r-rjson - r-rlang - - 'r-rmarkdown >=2.5' + - r-rmarkdown >=2.5 - r-shiny - r-shinydashboard - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 598d1fb1c071731ccf24c63d27467fcf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Generate QC Reports For Alevin Output' - description: 'Generate QC reports summarizing the output from an alevin, alevin-fry, or simpleaf run. Reports can be generated as html or pdf files, or as shiny applications.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-all/meta.yaml b/recipes/bioconductor-all/meta.yaml index 21dff1b6d6ed1..6433f9d160a03 100644 --- a/recipes/bioconductor-all/meta.yaml +++ b/recipes/bioconductor-all/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "ALL" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_{{ name|lower }}.tar.gz' - md5: b80eb482b4937ef4eac01027ac95a61a +about: + description: Data of T- and B-cell Acute Lymphocytic Leukemia from the Ritz Laboratory at the DFCI (includes Apr 2004 versions) + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: A data package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-all", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-all + path: recipes/bioconductor-all + version: 1.22.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: rpart requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5580b83d2affbc83bfe4d3c7c090ceff + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_{{ name|lower }}.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A data package' - description: 'Data of T- and B-cell Acute Lymphocytic Leukemia from the Ritz Laboratory at the DFCI (includes Apr 2004 versions)' -extra: - parent_recipe: - name: bioconductor-all - path: recipes/bioconductor-all - version: 1.22.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-all/post-link.sh b/recipes/bioconductor-all/post-link.sh index 2c5b04230e97b..abe279d166c33 100644 --- a/recipes/bioconductor-all/post-link.sh +++ b/recipes/bioconductor-all/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "all-1.44.0" +installBiocDataPackage.sh "all-1.48.0" diff --git a/recipes/bioconductor-allelicimbalance/meta.yaml b/recipes/bioconductor-allelicimbalance/meta.yaml index bcbc7a1991cf6..4d9048d3e5708 100644 --- a/recipes/bioconductor-allelicimbalance/meta.yaml +++ b/recipes/bioconductor-allelicimbalance/meta.yaml @@ -1,75 +1,82 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "AllelicImbalance" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides a framework for allelic specific expression investigation using RNA-seq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Investigates Allele Specific Expression -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9eb6991f47f1337aef63f9ce750db08a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-allelicimbalance", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, BiocStyle, knitr, rmarkdown requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-gridextra - r-lattice - r-latticeextra - r-nlme - r-seqinr + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-gridextra - r-lattice - r-latticeextra - r-nlme - r-seqinr + +source: + md5: d9c3a43fb911b080f918f3316022cefc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Investigates Allele Specific Expression' - description: 'Provides a framework for allelic specific expression investigation using RNA-seq data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-allmll/meta.yaml b/recipes/bioconductor-allmll/meta.yaml index e181a78da8504..3d66f4ec461f7 100644 --- a/recipes/bioconductor-allmll/meta.yaml +++ b/recipes/bioconductor-allmll/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "ALLMLL" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 669e7ff030b6fea51c8013816bd6fae7 +about: + description: 'This package provides probe-level data for 20 HGU133A and 20 HGU133B arrays which are a subset of arrays from a large ALL study. The data is for the MLL arrays. This data was published in Mary E. Ross, Xiaodong Zhou, Guangchun Song, Sheila A. Shurtleff, Kevin Girtman, W. Kent Williams, Hsi-Che Liu, Rami Mahfouz, Susana C. Raimondi, Noel Lenny, Anami Patel, and James R. Downing (2003) Classification of pediatric acute lymphoblastic leukemia by gene expression profiling Blood 102: 2951-2959' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A subset of arrays from a large acute lymphoblastic leukemia (ALL) study build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-allmll", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' + - bioconductor-affy >=1.84.0,<1.85.0 - r-base run: - - 'bioconductor-affy >=1.80.0,<1.81.0' + - bioconductor-affy >=1.84.0,<1.85.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b97903b1c1a6e0333549512656ede245 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'A subset of arrays from a large acute lymphoblastic leukemia (ALL) study' - description: 'This package provides probe-level data for 20 HGU133A and 20 HGU133B arrays which are a subset of arrays from a large ALL study. The data is for the MLL arrays. This data was published in Mary E. Ross, Xiaodong Zhou, Guangchun Song, Sheila A. Shurtleff, Kevin Girtman, W. Kent Williams, Hsi-Che Liu, Rami Mahfouz, Susana C. Raimondi, Noel Lenny, Anami Patel, and James R. Downing (2003) Classification of pediatric acute lymphoblastic leukemia by gene expression profiling Blood 102: 2951-2959' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-allmll/post-link.sh b/recipes/bioconductor-allmll/post-link.sh index f9958cf78ac2a..d61d2d6474856 100644 --- a/recipes/bioconductor-allmll/post-link.sh +++ b/recipes/bioconductor-allmll/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "allmll-1.42.0" +installBiocDataPackage.sh "allmll-1.46.0" diff --git a/recipes/bioconductor-alphabeta/meta.yaml b/recipes/bioconductor-alphabeta/meta.yaml index a5240ce1ab0a6..2a2c76c12228d 100644 --- a/recipes/bioconductor-alphabeta/meta.yaml +++ b/recipes/bioconductor-alphabeta/meta.yaml @@ -1,57 +1,62 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "AlphaBeta" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'AlphaBeta is a computational method for estimating epimutation rates and spectra from high-throughput DNA methylation data in plants. The method has been specifically designed to: 1. analyze ''germline'' epimutations in the context of multi-generational mutation accumulation lines (MA-lines). 2. analyze ''somatic'' epimutations in the context of plant development and aging.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b03e94ae649db2b4141f97a7859e0683 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alphabeta", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - - 'r-data.table >=1.10' - - 'r-dplyr >=0.7' - - 'r-expm >=0.999-4' - - 'r-ggplot2 >=3.2' - - 'r-gtools >=3.8.0' - - 'r-igraph >=1.2.4' - - 'r-optimx >=2018-7.10' - - 'r-plotly >=4.9' - - 'r-stringr >=1.3' + - r-data.table >=1.10 + - r-dplyr >=0.7 + - r-expm >=0.999-4 + - r-ggplot2 >=3.2 + - r-gtools >=3.8.0 + - r-igraph >=1.2.4 + - r-optimx >=2018-7.10 + - r-plotly >=4.9 + - r-stringr >=1.3 run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - - 'r-data.table >=1.10' - - 'r-dplyr >=0.7' - - 'r-expm >=0.999-4' - - 'r-ggplot2 >=3.2' - - 'r-gtools >=3.8.0' - - 'r-igraph >=1.2.4' - - 'r-optimx >=2018-7.10' - - 'r-plotly >=4.9' - - 'r-stringr >=1.3' + - r-data.table >=1.10 + - r-dplyr >=0.7 + - r-expm >=0.999-4 + - r-ggplot2 >=3.2 + - r-gtools >=3.8.0 + - r-igraph >=1.2.4 + - r-optimx >=2018-7.10 + - r-plotly >=4.9 + - r-stringr >=1.3 + +source: + md5: 86a786c66cba570f3f556cf9b8125dbb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants' - description: 'AlphaBeta is a computational method for estimating epimutation rates and spectra from high-throughput DNA methylation data in plants. The method has been specifically designed to: 1. analyze ''germline'' epimutations in the context of multi-generational mutation accumulation lines (MA-lines). 2. analyze ''somatic'' epimutations in the context of plant development and aging.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-alphamissense.v2023.hg19/meta.yaml b/recipes/bioconductor-alphamissense.v2023.hg19/meta.yaml index c4e4b98feb206..1c88b09da3780 100644 --- a/recipes/bioconductor-alphamissense.v2023.hg19/meta.yaml +++ b/recipes/bioconductor-alphamissense.v2023.hg19/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.18.2" %} {% set name = "AlphaMissense.v2023.hg19" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e8784ad000be637321f432188a5a3f45 +about: + description: Store Google DeepMind AlphaMissense v2023 hg19 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for Google DeepMind AlphaMissense v2023 hg19 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: AlphaMissense v2023 Pathogenicity Scores AnnotationHub Resource Metadata for hg19 build: - number: 0 + noarch: generic + number: 1 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alphamissense.v2023.hg19", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e8784ad000be637321f432188a5a3f45 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'AlphaMissense v2023 Pathogenicity Scores AnnotationHub Resource Metadata for hg19' - description: 'Store Google DeepMind AlphaMissense v2023 hg19 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for Google DeepMind AlphaMissense v2023 hg19 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-alphamissense.v2023.hg38/meta.yaml b/recipes/bioconductor-alphamissense.v2023.hg38/meta.yaml index 5974912274231..e28dd01d0d9fc 100644 --- a/recipes/bioconductor-alphamissense.v2023.hg38/meta.yaml +++ b/recipes/bioconductor-alphamissense.v2023.hg38/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.18.2" %} {% set name = "AlphaMissense.v2023.hg38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bedac9523e18829c5067dec1ebf801d4 +about: + description: Store Google DeepMind AlphaMissense v2023 hg38 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for Google DeepMind AlphaMissense v2023 hg38 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: AlphaMissense v2023 Pathogenicity Scores AnnotationHub Resource Metadata for hg38 build: - number: 0 + noarch: generic + number: 1 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alphamissense.v2023.hg38", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bedac9523e18829c5067dec1ebf801d4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'AlphaMissense v2023 Pathogenicity Scores AnnotationHub Resource Metadata for hg38' - description: 'Store Google DeepMind AlphaMissense v2023 hg38 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for Google DeepMind AlphaMissense v2023 hg38 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-alphamissenser/build.sh b/recipes/bioconductor-alphamissenser/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-alphamissenser/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-alphamissenser/meta.yaml b/recipes/bioconductor-alphamissenser/meta.yaml new file mode 100644 index 0000000000000..72180bcad17e6 --- /dev/null +++ b/recipes/bioconductor-alphamissenser/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.2.0" %} +{% set name = "AlphaMissenseR" %} +{% set bioc = "3.20" %} + +about: + description: The AlphaMissense publication outlines how a variant of AlphaFold / DeepMind was used to predict missense variant pathogenicity. Supporting data on Zenodo include, for instance, 71M variants across hg19 and hg38 genome builds. The 'AlphaMissenseR' package allows ready access to the data, downloading individual files to DuckDB databases for exploration and integration into *R* and *Bioconductor* workflows. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Accessing AlphaMissense Data Resources in R + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-alphamissenser", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocManager, BiocGenerics, GenomicRanges, GenomeInfoDb, AnnotationHub, ExperimentHub, ensembldb, httr, tidyr, r3dmol, bio3d, shiny, shiny.gosling, ggdist, gghalves, colorspace, knitr, rmarkdown, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - r-base + - r-curl + - r-dbi + - r-dplyr + - r-duckdb >=0.9.1 + - r-ggplot2 + - r-memoise + - r-rjsoncons >=1.0.1 + - r-rlang + - r-spdl + - r-whisker + run: + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - r-base + - r-curl + - r-dbi + - r-dplyr + - r-duckdb >=0.9.1 + - r-ggplot2 + - r-memoise + - r-rjsoncons >=1.0.1 + - r-rlang + - r-spdl + - r-whisker + +source: + md5: ac4ca4151be8a0e1870c53b79d7d3daf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-alpsnmr/meta.yaml b/recipes/bioconductor-alpsnmr/meta.yaml index 6ae5496aa23be..533141617cfaf 100644 --- a/recipes/bioconductor-alpsnmr/meta.yaml +++ b/recipes/bioconductor-alpsnmr/meta.yaml @@ -1,101 +1,108 @@ -{% set version = "4.4.0" %} +{% set version = "4.8.0" %} {% set name = "AlpsNMR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Reads Bruker NMR data directories both zipped and unzipped. It provides automated and efficient signal processing for untargeted NMR metabolomics. It is able to interpolate the samples, detect outliers, exclude regions, normalize, detect peaks, align the spectra, integrate peaks, manage metadata and visualize the spectra. After spectra proccessing, it can apply multivariate analysis on extracted data. Efficient plotting with 1-D data is also available. Basic reading of 1D ACD/Labs exported JDX samples is also available. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Automated spectraL Processing System for NMR -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 938d77895e6337a35d98b6a57fa90303 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alpsnmr", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, ChemoSpec, cowplot, curl, DT (>= 0.5), GGally (>= 1.4.0), ggrepel (>= 0.8.0), gridExtra, knitr, plotly (>= 4.7.1), progressr, SummarizedExperiment, S4Vectors, testthat (>= 2.0.0), writexl (>= 1.0), zip (>= 2.0.4) + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: ASICS, BiocStyle, ChemoSpec, cowplot, curl, DT (>= 0.5), GGally (>= 1.4.0), ggrepel (>= 0.8.0), gridExtra, knitr, NMRphasing, plotly (>= 4.7.1), progressr, SummarizedExperiment, S4Vectors, testthat (>= 2.0.0), writexl (>= 1.0), zip (>= 2.0.4) requirements: + + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] + host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-mixomics >=6.26.0,<6.27.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-mixomics >=6.30.0,<6.31.0 - r-base - - 'r-baseline >=1.2-1' + - r-baseline >=1.2-1 - r-cli - - 'r-dplyr >=1.1.0' - - 'r-fs >=1.2.6' - - 'r-future >=1.10.0' + - r-dplyr >=1.1.0 + - r-fs >=1.2.6 - r-generics - - 'r-ggplot2 >=3.1.0' - - 'r-glue >=1.2.0' - - 'r-htmltools >=0.3.6' - - 'r-magrittr >=1.5' - - 'r-matrixstats >=0.54.0' - - 'r-pcapp >=1.9-73' - - 'r-purrr >=0.2.5' - - 'r-readxl >=1.1.0' - - 'r-reshape2 >=1.4.3' - - 'r-rlang >=0.3.0.1' - - 'r-rmarkdown >=1.10' - - 'r-scales >=1.2.0' - - 'r-signal >=0.7-6' - - 'r-speaq >=2.4.0' - - 'r-stringr >=1.3.1' - - 'r-tibble >=1.3.4' - - 'r-tidyr >=1.0.0' + - r-ggplot2 >=3.1.0 + - r-glue >=1.2.0 + - r-htmltools >=0.3.6 + - r-magrittr >=1.5 + - r-matrixstats >=0.54.0 + - r-pcapp >=1.9-73 + - r-purrr >=0.2.5 + - r-readxl >=1.1.0 + - r-reshape2 >=1.4.3 + - r-rlang >=0.3.0.1 + - r-rmarkdown >=1.10 + - r-scales >=1.2.0 + - r-signal >=0.7-6 + - r-speaq >=2.4.0 + - r-stringr >=1.3.1 + - r-tibble >=1.3.4 + - r-tidyr >=1.0.0 - r-tidyselect - - 'r-vctrs >=0.3.0' + - r-vctrs >=0.3.0 + run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-mixomics >=6.26.0,<6.27.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-mixomics >=6.30.0,<6.31.0 - r-base - - 'r-baseline >=1.2-1' + - r-baseline >=1.2-1 - r-cli - - 'r-dplyr >=1.1.0' - - 'r-fs >=1.2.6' - - 'r-future >=1.10.0' + - r-dplyr >=1.1.0 + - r-fs >=1.2.6 - r-generics - - 'r-ggplot2 >=3.1.0' - - 'r-glue >=1.2.0' - - 'r-htmltools >=0.3.6' - - 'r-magrittr >=1.5' - - 'r-matrixstats >=0.54.0' - - 'r-pcapp >=1.9-73' - - 'r-purrr >=0.2.5' - - 'r-readxl >=1.1.0' - - 'r-reshape2 >=1.4.3' - - 'r-rlang >=0.3.0.1' - - 'r-rmarkdown >=1.10' - - 'r-scales >=1.2.0' - - 'r-signal >=0.7-6' - - 'r-speaq >=2.4.0' - - 'r-stringr >=1.3.1' - - 'r-tibble >=1.3.4' - - 'r-tidyr >=1.0.0' + - r-ggplot2 >=3.1.0 + - r-glue >=1.2.0 + - r-htmltools >=0.3.6 + - r-magrittr >=1.5 + - r-matrixstats >=0.54.0 + - r-pcapp >=1.9-73 + - r-purrr >=0.2.5 + - r-readxl >=1.1.0 + - r-reshape2 >=1.4.3 + - r-rlang >=0.3.0.1 + - r-rmarkdown >=1.10 + - r-scales >=1.2.0 + - r-signal >=0.7-6 + - r-speaq >=2.4.0 + - r-stringr >=1.3.1 + - r-tibble >=1.3.4 + - r-tidyr >=1.0.0 - r-tidyselect - - 'r-vctrs >=0.3.0' - build: - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - xorg-libxfixes # [linux] + - r-vctrs >=0.3.0 + +source: + md5: cbc977c0ded1aff49e34e463eecc0730 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Automated spectraL Processing System for NMR' - description: 'Reads Bruker NMR data directories both zipped and unzipped. It provides automated and efficient signal processing for untargeted NMR metabolomics. It is able to interpolate the samples, detect outliers, exclude regions, normalize, detect peaks, align the spectra, integrate peaks, manage metadata and visualize the spectra. After spectra proccessing, it can apply multivariate analysis on extracted data. Efficient plotting with 1-D data is also available. Basic reading of 1D ACD/Labs exported JDX samples is also available.' - license_file: LICENSE -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-altcdfenvs/meta.yaml b/recipes/bioconductor-altcdfenvs/meta.yaml index 2f56521289f0e..e5aa9f13fa548 100644 --- a/recipes/bioconductor-altcdfenvs/meta.yaml +++ b/recipes/bioconductor-altcdfenvs/meta.yaml @@ -1,58 +1,64 @@ -{% set version = "2.64.0" %} +{% set version = "2.68.0" %} {% set name = "altcdfenvs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Convenience data structures and functions to handle cdfenvs + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: alternative CDF environments (aka probeset mappings) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8bd83d29c11857ae73a4046289748f90 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-altcdfenvs", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:altcdfenvs + parent_recipe: + name: bioconductor-altcdfenvs + path: recipes/bioconductor-altcdfenvs + version: 2.42.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db, hgu133acdf, Rgraphviz, RColorBrewer requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-hypergraph >=1.74.0,<1.75.0' - - 'bioconductor-makecdfenv >=1.78.0,<1.79.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-hypergraph >=1.78.0,<1.79.0 + - bioconductor-makecdfenv >=1.82.0,<1.83.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-hypergraph >=1.74.0,<1.75.0' - - 'bioconductor-makecdfenv >=1.78.0,<1.79.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-hypergraph >=1.78.0,<1.79.0 + - bioconductor-makecdfenv >=1.82.0,<1.83.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base + +source: + md5: 9efb851f488b8e78f0b1b38fa8a24090 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'alternative CDF environments (aka probeset mappings)' - description: 'Convenience data structures and functions to handle cdfenvs' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:altcdfenvs - parent_recipe: - name: bioconductor-altcdfenvs - path: recipes/bioconductor-altcdfenvs - version: 2.42.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-alternativesplicingevents.hg19/meta.yaml b/recipes/bioconductor-alternativesplicingevents.hg19/meta.yaml index 7d1ab3e0251b4..91a3c99801972 100644 --- a/recipes/bioconductor-alternativesplicingevents.hg19/meta.yaml +++ b/recipes/bioconductor-alternativesplicingevents.hg19/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.1.0" %} {% set name = "alternativeSplicingEvents.hg19" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b1acae776c9e9c5d961cf4884cadc58f +about: + description: Data frame containing alternative splicing events. The splicing events were compiled from the annotation files used by the alternative splicing quantification tools MISO, VAST-TOOLS, SUPPA and rMATS. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Alternative splicing event annotation for Human (hg19) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alternativesplicingevents.hg19", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: data.frame, dplyr, GenomicRanges, S4Vectors requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b1acae776c9e9c5d961cf4884cadc58f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Alternative splicing event annotation for Human (hg19)' - description: 'Data frame containing alternative splicing events. The splicing events were compiled from the annotation files used by the alternative splicing quantification tools MISO, VAST-TOOLS, SUPPA and rMATS.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml b/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml index 30e73e4117234..865f8b464db7c 100644 --- a/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml +++ b/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.1.0" %} {% set name = "alternativeSplicingEvents.hg38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d49710eebd62fb15a48cab252ff3eca +about: + description: Data frame containing alternative splicing events. The splicing events were compiled from the annotation files used by the alternative splicing quantification tools MISO, VAST-TOOLS, SUPPA and rMATS. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Alternative splicing event annotation for Human (hg38) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-alternativesplicingevents.hg38", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: dplyr, GenomicRanges, S4Vectors requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8d49710eebd62fb15a48cab252ff3eca + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Alternative splicing event annotation for Human (hg38)' - description: 'Data frame containing alternative splicing events. The splicing events were compiled from the annotation files used by the alternative splicing quantification tools MISO, VAST-TOOLS, SUPPA and rMATS.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-amaretto/build_failure.osx-64.yaml b/recipes/bioconductor-amaretto/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..017fd50040a11 --- /dev/null +++ b/recipes/bioconductor-amaretto/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: d1d6c9195558f9080803c5d4e23d297cec84af97d67b3cf10838a7bcd1372186 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-fansi: 1.0.6-r44h6b9d099_1 conda-forge + r-fastmap: 1.2.0-r44h25d921d_1 conda-forge + r-filelock: 1.0.3-r44h6b9d099_1 conda-forge + r-generics: 0.1.3-r44hc72bb7e_3 conda-forge + r-glue: 1.8.0-r44h199b6f9_0 conda-forge + r-httr: 1.4.7-r44hc72bb7e_1 conda-forge + r-jsonlite: 1.8.9-r44h199b6f9_0 conda-forge + r-lattice: 0.22_6-r44h6b9d099_1 conda-forge + r-lifecycle: 1.0.4-r44hc72bb7e_1 conda-forge + r-magrittr: 2.0.3-r44h6b9d099_3 conda-forge + r-matrix: 1.6_5-r44h9cf22e7_1 conda-forge + r-matrixstats: 1.4.1-r44h199b6f9_0 conda-forge + r-memoise: 2.0.1-r44hc72bb7e_3 conda-forge + r-mime: 0.12-r44h6b9d099_3 conda-forge + r-openssl: 2.2.2-r44h83cc2e4_0 conda-forge + r-pillar: 1.10.0-r44hc72bb7e_0 conda-forge + r-pkgconfig: 2.0.3-r44hc72bb7e_4 conda-forge + r-plogr: 0.2.0-r44hc72bb7e_1006 conda-forge + r-png: 0.1_8-r44h9a19d2a_2 conda-forge + r-purrr: 1.0.2-r44h6b9d099_1 conda-forge + r-r6: 2.5.1-r44hc72bb7e_3 conda-forge + r-rappdirs: 0.3.3-r44h6b9d099_3 conda-forge + r-rlang: 1.1.4-r44h25d921d_1 conda-forge + r-rsqlite: 2.3.9-r44h2711daa_0 conda-forge + r-stringi: 1.8.4-r44hf60abff_3 conda-forge + r-stringr: 1.5.1-r44h785f33e_1 conda-forge + r-sys: 3.4.3-r44h199b6f9_0 conda-forge + r-tibble: 3.2.1-r44h6b9d099_3 conda-forge + r-tidyr: 1.3.1-r44h25d921d_1 conda-forge + r-tidyselect: 1.2.1-r44hc72bb7e_1 conda-forge + r-utf8: 1.2.4-r44h6b9d099_1 conda-forge + r-vctrs: 0.6.5-r44h25d921d_1 conda-forge + r-withr: 3.0.2-r44hc72bb7e_0 conda-forge + r-yaml: 2.3.10-r44h6b9d099_0 conda-forge + readline: 8.2-h9e318b2_1 conda-forge + setuptools: 75.6.0-pyhff2d567_1 conda-forge + sigtool: 0.1.3-h88f4db0_0 conda-forge + tapi: 1300.6.5-h390ca13_0 conda-forge + tk: 8.6.13-h1abcd95_1 conda-forge + tktable: 2.10-hba9d6f1_6 conda-forge + toml: 0.10.2-pyhd8ed1ab_1 conda-forge + tomlkit: 0.13.2-pyha770c72_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + xmltodict: 0.14.2-pyhd8ed1ab_1 conda-forge + yaml: 0.2.5-h0d85af4_2 conda-forge + yq: 3.4.3-pyhd8ed1ab_1 conda-forge + zlib: 1.3.1-hd23fc13_2 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (local): ...working... done + Solving environment (_test_env): ...working... done + Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache + Downloading source to cache: curatedTCGAData_1.28.0_081d2bb849.tar.gz + Downloading https://bioconductor.org/packages/3.20/data/experiment/src/contrib/curatedTCGAData_1.28.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.039116 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioconductor.org/packages/3.20/bioc/src/contrib/Archive/curatedTCGAData/curatedTCGAData_1.28.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Downloading https://bioarchive.galaxyproject.org/curatedTCGAData_1.28.0.tar.gz + Elapsed: 00:00.021221 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.076035 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://depot.galaxyproject.org/software/bioconductor-curatedtcgadata/bioconductor-curatedtcgadata_1.28.0_src_all.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.135389 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download https://depot.galaxyproject.org/software/bioconductor-curatedtcgadata/bioconductor-curatedtcgadata_1.28.0_src_all.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-amaretto/meta.yaml b/recipes/bioconductor-amaretto/meta.yaml index 687714cb9991a..1cc89a19dafac 100644 --- a/recipes/bioconductor-amaretto/meta.yaml +++ b/recipes/bioconductor-amaretto/meta.yaml @@ -1,34 +1,41 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "AMARETTO" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Integrating an increasing number of available multi-omics cancer data remains one of the main challenges to improve our understanding of cancer. One of the main challenges is using multi-omics data for identifying novel cancer driver genes. We have developed an algorithm, called AMARETTO, that integrates copy number, DNA methylation and gene expression data to identify a set of driver genes by analyzing cancer samples and connects them to clusters of co-expressed genes, which we define as modules. We applied AMARETTO in a pancancer setting to identify cancer driver genes and their modules on multiple cancer sites. AMARETTO captures modules enriched in angiogenesis, cell cycle and EMT, and modules that accurately predict survival and molecular subtypes. This allows AMARETTO to identify novel cancer driver genes directing canonical cancer pathways. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Apache License (== 2.0) + file LICENSE + license_file: LICENSE + summary: Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d6b16e06e3eb15ba4cac645265a43db1 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-amaretto", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, MASS, knitr, BiocStyle requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-curatedtcgadata >=1.24.0,<1.25.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-curatedtcgadata >=1.28.0,<1.29.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 - r-base - - 'r-callr >=3.0.0.9001' + - r-callr >=3.0.0.9001 - r-circlize - r-doparallel - r-dplyr @@ -48,15 +55,16 @@ requirements: - r-tibble - libblas - liblapack + run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-curatedtcgadata >=1.24.0,<1.25.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-curatedtcgadata >=1.28.0,<1.29.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 - r-base - - 'r-callr >=3.0.0.9001' + - r-callr >=3.0.0.9001 - r-circlize - r-doparallel - r-dplyr @@ -74,16 +82,16 @@ requirements: - r-reshape2 - r-rmarkdown - r-tibble - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} + +source: + md5: 7fae894cf9503fe495c581a1cdfd0b1e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Apache License (== 2.0) + file LICENSE' - summary: 'Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression' - description: 'Integrating an increasing number of available multi-omics cancer data remains one of the main challenges to improve our understanding of cancer. One of the main challenges is using multi-omics data for identifying novel cancer driver genes. We have developed an algorithm, called AMARETTO, that integrates copy number, DNA methylation and gene expression data to identify a set of driver genes by analyzing cancer samples and connects them to clusters of co-expressed genes, which we define as modules. We applied AMARETTO in a pancancer setting to identify cancer driver genes and their modules on multiple cancer sites. AMARETTO captures modules enriched in angiogenesis, cell cycle and EMT, and modules that accurately predict survival and molecular subtypes. This allows AMARETTO to identify novel cancer driver genes directing canonical cancer pathways.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-amountain/meta.yaml b/recipes/bioconductor-amountain/meta.yaml index dd5d22ebd6e60..6aefffcdbb079 100644 --- a/recipes/bioconductor-amountain/meta.yaml +++ b/recipes/bioconductor-amountain/meta.yaml @@ -1,26 +1,42 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "AMOUNTAIN" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A pure data-driven gene network, weighted gene co-expression network (WGCN) could be constructed only from expression profile. Different layers in such networks may represent different time points, multiple conditions or various species. AMOUNTAIN aims to search active modules in multi-layer WGCN using a continuous optimization approach. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: acf007b4bceaa196843cbcf221b762ba build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-amountain", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:amountain + - doi:10.1101/056952 + parent_recipe: + name: bioconductor-amountain + path: recipes/bioconductor-amountain + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, qgraph, knitr, rmarkdown # SystemRequirements: gsl requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - libblas @@ -29,26 +45,16 @@ requirements: run: - r-base - gsl - build: - - {{ compiler('c') }} - - make + +source: + md5: 7c1d2a6ea5ea79a745fa9b4d03fa1e91 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach' - description: 'A pure data-driven gene network, weighted gene co-expression network (WGCN) could be constructed only from expression profile. Different layers in such networks may represent different time points, multiple conditions or various species. AMOUNTAIN aims to search active modules in multi-layer WGCN using a continuous optimization approach.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:amountain - - doi:10.1101/056952 - parent_recipe: - name: bioconductor-amountain - path: recipes/bioconductor-amountain - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ampaffyexample/meta.yaml b/recipes/bioconductor-ampaffyexample/meta.yaml index a4124743b758b..17eae589d37e3 100644 --- a/recipes/bioconductor-ampaffyexample/meta.yaml +++ b/recipes/bioconductor-ampaffyexample/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "AmpAffyExample" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3277d6d26f145ddbb45c3808273cd150 +about: + description: Six arrays. Three from amplified RNA, three from the typical procedure. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Example of Amplified Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ampaffyexample", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: hgu133acdf requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' + - bioconductor-affy >=1.84.0,<1.85.0 - r-base run: - - 'bioconductor-affy >=1.80.0,<1.81.0' + - bioconductor-affy >=1.84.0,<1.85.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f4bcd408e003773b8dd09c6299c5a7c6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'Example of Amplified Data' - description: 'Six arrays. Three from amplified RNA, three from the typical procedure.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ampaffyexample/post-link.sh b/recipes/bioconductor-ampaffyexample/post-link.sh index 2d12c440e0cea..bdfa9a84b1d78 100644 --- a/recipes/bioconductor-ampaffyexample/post-link.sh +++ b/recipes/bioconductor-ampaffyexample/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ampaffyexample-1.42.0" +installBiocDataPackage.sh "ampaffyexample-1.46.0" diff --git a/recipes/bioconductor-amplican/meta.yaml b/recipes/bioconductor-amplican/meta.yaml index 80fb494e2eb87..4e2816d82da4f 100644 --- a/recipes/bioconductor-amplican/meta.yaml +++ b/recipes/bioconductor-amplican/meta.yaml @@ -1,91 +1,102 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "amplican" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: '`amplican` performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Automated analysis of CRISPR experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 73fd9acdf5066ee76b1157068151f1f4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-amplican", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:amplican + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, GenomicAlignments requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - - 'r-cluster >=2.1.4' - - 'r-data.table >=1.10.4-3' - - 'r-dplyr >=0.7.2' - - 'r-ggplot2 >=3.3.4' - - 'r-ggthemes >=3.4.0' - - 'r-gridextra >=2.2.1' - - 'r-gtable >=0.2.0' - - 'r-knitr >=1.16' - - 'r-matrix >=1.2-10' - - 'r-matrixstats >=0.52.2' + - r-cluster >=2.1.4 + - r-data.table >=1.10.4-3 + - r-dplyr >=0.7.2 + - r-ggplot2 >=3.3.4 + - r-ggthemes >=3.4.0 + - r-gridextra >=2.2.1 + - r-gtable >=0.2.0 + - r-knitr >=1.16 + - r-matrix >=1.2-10 + - r-matrixstats >=0.52.2 - r-rcpp - - 'r-rmarkdown >=1.6' - - 'r-stringr >=1.2.0' - - 'r-waffle >=0.7.0' + - r-rmarkdown >=1.6 + - r-stringr >=1.2.0 + - r-waffle >=0.7.0 - libblas - liblapack + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - - 'r-cluster >=2.1.4' - - 'r-data.table >=1.10.4-3' - - 'r-dplyr >=0.7.2' - - 'r-ggplot2 >=3.3.4' - - 'r-ggthemes >=3.4.0' - - 'r-gridextra >=2.2.1' - - 'r-gtable >=0.2.0' - - 'r-knitr >=1.16' - - 'r-matrix >=1.2-10' - - 'r-matrixstats >=0.52.2' + - r-cluster >=2.1.4 + - r-data.table >=1.10.4-3 + - r-dplyr >=0.7.2 + - r-ggplot2 >=3.3.4 + - r-ggthemes >=3.4.0 + - r-gridextra >=2.2.1 + - r-gtable >=0.2.0 + - r-knitr >=1.16 + - r-matrix >=1.2-10 + - r-matrixstats >=0.52.2 - r-rcpp - - 'r-rmarkdown >=1.6' - - 'r-stringr >=1.2.0' - - 'r-waffle >=0.7.0' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rmarkdown >=1.6 + - r-stringr >=1.2.0 + - r-waffle >=0.7.0 + +source: + md5: 5559c78c0eb1594ce6a7ce3c57aaf3e4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'Automated analysis of CRISPR experiments' - description: '`amplican` performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name }} diff --git a/recipes/bioconductor-anaquin/meta.yaml b/recipes/bioconductor-anaquin/meta.yaml index aa5132a62ebf8..baa989f09d5fc 100644 --- a/recipes/bioconductor-anaquin/meta.yaml +++ b/recipes/bioconductor-anaquin/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "2.26.0" %} +{% set version = "2.30.0" %} {% set name = "Anaquin" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The project is intended to support the use of sequins (synthetic sequencing spike-in controls) owned and made available by the Garvan Institute of Medical Research. The goal is to provide a standard open source library for quantitative analysis, modelling and visualization of spike-in controls. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_3_clause + file LICENSE + license_file: LICENSE + summary: Statistical analysis of sequins -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a0b480fdac1e56d9b308c2c23518b4a0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-anaquin", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, rmarkdown requirements: host: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - - 'r-ggplot2 >=2.2.0' + - r-ggplot2 >=2.2.0 - r-knitr - r-locfit - r-plyr - r-rocr run: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - - 'r-ggplot2 >=2.2.0' + - r-ggplot2 >=2.2.0 - r-knitr - r-locfit - r-plyr - r-rocr + +source: + md5: 26e5fa0bd8c5775553748265b4820dd2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_3_clause + file LICENSE' - summary: 'Statistical analysis of sequins' - description: 'The project is intended to support the use of sequins (synthetic sequencing spike-in controls) owned and made available by the Garvan Institute of Medical Research. The goal is to provide a standard open source library for quantitative analysis, modelling and visualization of spike-in controls.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ancombc/meta.yaml b/recipes/bioconductor-ancombc/meta.yaml index 25c2d9638dbc9..6133472bbc46a 100644 --- a/recipes/bioconductor-ancombc/meta.yaml +++ b/recipes/bioconductor-ancombc/meta.yaml @@ -1,32 +1,28 @@ -{% set version = "2.4.0" %} +{% set version = "2.8.0" %} {% set name = "ANCOMBC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'ANCOMBC is a package containing differential abundance (DA) and correlation analyses for microbiome data. Specifically, the package includes Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2), Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC), and Analysis of Composition of Microbiomes (ANCOM) for DA analysis, and Sparse Estimation of Correlations among Microbiomes (SECOM) for correlation analysis. Microbiome data are typically subject to two sources of biases: unequal sampling fractions (sample-specific biases) and differential sequencing efficiencies (taxon-specific biases). Methodologies included in the ANCOMBC package are designed to correct these biases and construct statistically consistent estimators.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Microbiome differential abudance and correlation analyses with bias correction -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 42059f62faa03e818d0cd15b7bcf0094 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ancombc", max_pin="x.x") }}' - noarch: generic -# Suggests: dplyr, knitr, rmarkdown, testthat, DT, tidyr, tidyverse, microbiome, magrittr + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: mia (>= 1.6.0), DT, S4Vectors, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, dplyr, knitr, magrittr, microbiome, phyloseq, rmarkdown, testthat, tidyr, tidyverse requirements: host: - - 'bioconductor-mia >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-cvxr - r-desctools @@ -44,11 +40,6 @@ requirements: - r-nloptr - r-rdpack run: - - 'bioconductor-mia >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' - r-base - r-cvxr - r-desctools @@ -65,12 +56,16 @@ requirements: - r-multcomp - r-nloptr - r-rdpack + +source: + md5: 4b876fab332f19e7fc9bbbfe070e53f8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Microbiome differential abudance and correlation analyses with bias correction' - description: 'ANCOMBC is a package containing differential abundance (DA) and correlation analyses for microbiome data. Specifically, the package includes Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2), Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC), and Analysis of Composition of Microbiomes (ANCOM) for DA analysis, and Sparse Estimation of Correlations among Microbiomes (SECOM) for correlation analysis. Microbiome data are typically subject to two sources of biases: unequal sampling fractions (sample-specific biases) and differential sequencing efficiencies (taxon-specific biases). Methodologies included in the ANCOMBC package are designed to correct these biases and construct statistically consistent estimators.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-aneufinder/build_failure.osx-64.yaml b/recipes/bioconductor-aneufinder/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c206ea025d461 --- /dev/null +++ b/recipes/bioconductor-aneufinder/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a5867be56a719b8b6041150fd688c6561bca9244e7ffe3caf0990e198cef9060 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-aneufinder-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-aneufinder-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-aneufinder_1734827582271/work/conda_build.sh']' returned non-zero exit status 1. + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-aneufinder-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-aneufinder-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-aneufinder-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-aneufinder-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-aneufinder-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-aneufinder-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-aneufinder-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-aneufinder-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-aneufinder-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-aneufinder-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-aneufinder-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-aneufinder-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c R_interface.cpp -o R_interface.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c densities.cpp -o densities.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c init.cpp -o init.o +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-aneufinder/meta.yaml b/recipes/bioconductor-aneufinder/meta.yaml index c0989067c743b..ac72d96ea436a 100644 --- a/recipes/bioconductor-aneufinder/meta.yaml +++ b/recipes/bioconductor-aneufinder/meta.yaml @@ -1,37 +1,44 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "AneuFinder" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: AneuFinder implements functions for copy-number detection, breakpoint detection, and karyotype and heterogeneity analysis in single-cell whole genome sequencing and strand-seq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Analysis of Copy Number Variation in Single-Cell-Sequencing Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 421efa90a617606c8db2c947d302c6b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-aneufinder", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-aneufinderdata >=1.30.0,<1.31.0' - - 'bioconductor-bamsignals >=1.34.0,<1.35.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-aneufinderdata >=1.34.0,<1.35.0 + - bioconductor-bamsignals >=1.38.0,<1.39.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cowplot - r-doparallel @@ -44,18 +51,19 @@ requirements: - r-reshape2 - libblas - liblapack + run: - - 'bioconductor-aneufinderdata >=1.30.0,<1.31.0' - - 'bioconductor-bamsignals >=1.34.0,<1.35.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-aneufinderdata >=1.34.0,<1.35.0 + - bioconductor-bamsignals >=1.38.0,<1.39.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cowplot - r-doparallel @@ -66,16 +74,16 @@ requirements: - r-ggrepel - r-mclust - r-reshape2 - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: ed103ff2f579686b2671c28913a4dddb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Analysis of Copy Number Variation in Single-Cell-Sequencing Data' - description: 'AneuFinder implements functions for copy-number detection, breakpoint detection, and karyotype and heterogeneity analysis in single-cell whole genome sequencing and strand-seq data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-aneufinderdata/meta.yaml b/recipes/bioconductor-aneufinderdata/meta.yaml index 7556ff6e34b2c..89b3cc2dece50 100644 --- a/recipes/bioconductor-aneufinderdata/meta.yaml +++ b/recipes/bioconductor-aneufinderdata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "AneuFinderData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 895230cd9b780dbb286a012f3c8777eb +about: + description: Whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: WGSCS Data for Demonstration Purposes build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-aneufinderdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e003f8236f1f1b4e2c1049ca787bdab2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'WGSCS Data for Demonstration Purposes' - description: 'Whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-aneufinderdata/post-link.sh b/recipes/bioconductor-aneufinderdata/post-link.sh index 25c0a75eda265..c0d6e6c4ffaa2 100644 --- a/recipes/bioconductor-aneufinderdata/post-link.sh +++ b/recipes/bioconductor-aneufinderdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "aneufinderdata-1.30.0" +installBiocDataPackage.sh "aneufinderdata-1.34.0" diff --git a/recipes/bioconductor-anf/meta.yaml b/recipes/bioconductor-anf/meta.yaml index 2b25857f8023a..b8d3156b29a22 100644 --- a/recipes/bioconductor-anf/meta.yaml +++ b/recipes/bioconductor-anf/meta.yaml @@ -1,46 +1,52 @@ -{% set version = "1.22.0" %} +{% set version = "1.28.0" %} {% set name = "ANF" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: This package is used for complex patient clustering by integrating multi-omic data through affinity network fusion. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Affinity Network Fusion for Complex Patient Clustering -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d075ac90f30a9d8b2d98ed483ae8012 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic + run_exports: '{{ pin_subpackage("bioconductor-anf", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ExperimentHub, SNFtool, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-igraph - r-mass - r-rcolorbrewer - r-survival run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-igraph - r-mass - r-rcolorbrewer - r-survival + +source: + md5: 9f597355f1b3399b66316f456272f316 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Affinity Network Fusion for Complex Patient Clustering' - description: 'This package is used for complex patient clustering by integrating multi-omic data through affinity network fusion.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-animalcules/meta.yaml b/recipes/bioconductor-animalcules/meta.yaml index af2a1126144e5..240f4ab2d6d82 100644 --- a/recipes/bioconductor-animalcules/meta.yaml +++ b/recipes/bioconductor-animalcules/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.16.0" %} +{% set version = "1.22.0" %} {% set name = "animalcules" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: animalcules is an R package for utilizing up-to-date data analytics, visualization methods, and machine learning models to provide users an easy-to-use interactive microbiome analysis framework. It can be used as a standalone software package or users can explore their data with the accompanying interactive R Shiny application. Traditional microbiome analysis such as alpha/beta diversity and differential abundance analysis are enhanced, while new methods like biomarker identification are introduced by animalcules. Powerful interactive and dynamic figures generated by animalcules enable users to understand their data better and discover new insights. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Interactive microbiome analysis toolkit -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b16939076d7ca77f0254c70e6fd35029 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis + run_exports: '{{ pin_subpackage("bioconductor-animalcules", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, biomformat, devtools, glmnet, knitr, rmarkdown, testthat, usethis requirements: + host: - - 'bioconductor-biomformat >=1.28.0,<1.29.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-ape - r-assertthat - r-base @@ -35,31 +37,32 @@ requirements: - r-dplyr - r-dt - r-forcats + - r-ggforce - r-ggplot2 - - r-glmnet - r-gunifrac - r-lattice - r-magrittr - r-matrix - r-plotly - - r-plotroc - r-rentrez - r-reshape2 + - r-rocit - r-scales - r-shiny - r-shinyjs - r-tibble + - r-tidyr - r-tsne - r-umap - r-vegan - r-xml + run: - - 'bioconductor-biomformat >=1.28.0,<1.29.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-multiassayexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-ape - r-assertthat - r-base @@ -68,30 +71,35 @@ requirements: - r-dplyr - r-dt - r-forcats + - r-ggforce - r-ggplot2 - - r-glmnet - r-gunifrac - r-lattice - r-magrittr - r-matrix - r-plotly - - r-plotroc - r-rentrez - r-reshape2 + - r-rocit - r-scales - r-shiny - r-shinyjs - r-tibble + - r-tidyr - r-tsne - r-umap - r-vegan - r-xml + +source: + md5: b83ed641e1cda8184dcd9d7616199043 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Interactive microbiome analysis toolkit' - description: 'animalcules is an R package for utilizing up-to-date data analytics, visualization methods, and machine learning models to provide users an easy-to-use interactive microbiome analysis framework. It can be used as a standalone software package or users can explore their data with the accompanying interactive R Shiny application. Traditional microbiome analysis such as alpha/beta diversity and differential abundance analysis are enhanced, while new methods like biomarker identification are introduced by animalcules. Powerful interactive and dynamic figures generated by animalcules enable users to understand their data better and discover new insights.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-annaffy/meta.yaml b/recipes/bioconductor-annaffy/meta.yaml index 843f2adced6d4..daf13ee0cc91b 100644 --- a/recipes/bioconductor-annaffy/meta.yaml +++ b/recipes/bioconductor-annaffy/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "annaffy" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Annotation tools for Affymetrix biological metadata -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a590578d3e87dbab236a5531f0a5bce0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-annaffy", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:annaffy + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-annaffy + path: recipes/bioconductor-annaffy + version: 1.52.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: hgu95av2.db, multtest, tcltk requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-go.db >=3.20.0,<3.21.0 - r-base - r-biocmanager - r-dbi run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-go.db >=3.20.0,<3.21.0 - r-base - r-biocmanager - r-dbi + +source: + md5: 276ba25b848eb8109a19c09c54a11e76 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Annotation tools for Affymetrix biological metadata' - description: 'Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:annaffy - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-annaffy - path: recipes/bioconductor-annaffy - version: 1.52.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-annmap/meta.yaml b/recipes/bioconductor-annmap/meta.yaml index 54d7f473f442b..065654076b280 100644 --- a/recipes/bioconductor-annmap/meta.yaml +++ b/recipes/bioconductor-annmap/meta.yaml @@ -1,65 +1,71 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "annmap" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl. The annmap database can be downloaded from: https://figshare.manchester.ac.uk/account/articles/16685071' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis. -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4e793a7c30de8248f566e7c14bf3fa90 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-annmap", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:annmap + - doi:10.1093/nar/gkm779 + parent_recipe: + name: bioconductor-annmap + path: recipes/bioconductor-annmap + version: 1.22.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, rjson, Gviz requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-dbi - r-digest - r-lattice - - 'r-rmysql >=0.6-0' + - r-rmysql >=0.6-0 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-dbi - r-digest - r-lattice - - 'r-rmysql >=0.6-0' + - r-rmysql >=0.6-0 + +source: + md5: 42021c12b144cf00a450a58d0767337c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.' - description: 'annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl. The annmap database can be downloaded from: https://figshare.manchester.ac.uk/account/articles/16685071' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:annmap - - doi:10.1093/nar/gkm779 - parent_recipe: - name: bioconductor-annmap - path: recipes/bioconductor-annmap - version: 1.22.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-annotate/meta.yaml b/recipes/bioconductor-annotate/meta.yaml index 0e27f09050df3..db517541e3d01 100644 --- a/recipes/bioconductor-annotate/meta.yaml +++ b/recipes/bioconductor-annotate/meta.yaml @@ -1,58 +1,64 @@ -{% set version = "1.80.0" %} +{% set version = "1.84.0" %} {% set name = "annotate" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Using R enviroments for annotation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation for microarrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 04d25cadc03401556364f8ca9c3b2a61 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-annotate", max_pin="x.x") }}' - noarch: generic -# Suggests: hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit, + +extra: + identifiers: + - biotools:annotate + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-annotate + path: recipes/bioconductor-annotate + version: 1.58.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit, BiocStyle, knitr requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-dbi - r-httr - r-xml - r-xtable run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-dbi - r-httr - r-xml - r-xtable + +source: + md5: b23b95c735b6e0dc9306a9a1b4a032f3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation for microarrays' - description: 'Using R enviroments for annotation.' -extra: - identifiers: - - biotools:annotate - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-annotate - path: recipes/bioconductor-annotate - version: 1.58.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-annotationdbi/meta.yaml b/recipes/bioconductor-annotationdbi/meta.yaml index 092d59455da59..2bb6487da4624 100644 --- a/recipes/bioconductor-annotationdbi/meta.yaml +++ b/recipes/bioconductor-annotationdbi/meta.yaml @@ -1,58 +1,64 @@ -{% set version = "1.64.1" %} +{% set version = "1.68.0" %} {% set name = "AnnotationDbi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implements a user-friendly interface for querying SQLite-based annotation data packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Manipulation of SQLite-based annotations in Bioconductor -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 965300db0b7a8b527ed3eb00fdd6d10f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-annotationdbi", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:annotationdbi + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-annotationdbi + path: recipes/bioconductor-annotationdbi + version: 1.42.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: utils, hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dbi - r-rsqlite + +source: + md5: 0f0e70eecd93f528f954d8d9fb4c8a8e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Manipulation of SQLite-based annotations in Bioconductor' - description: 'Implements a user-friendly interface for querying SQLite-based annotation data packages.' -extra: - identifiers: - - biotools:annotationdbi - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-annotationdbi - path: recipes/bioconductor-annotationdbi - version: 1.42.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-annotationfilter/meta.yaml b/recipes/bioconductor-annotationfilter/meta.yaml index 72a8de6d1d3e4..e423a5a92d448 100644 --- a/recipes/bioconductor-annotationfilter/meta.yaml +++ b/recipes/bioconductor-annotationfilter/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "AnnotationFilter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 512eececc247990236fd09aa1fc46966 +about: + description: This package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Facilities for Filtering Bioconductor Annotation Resources build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-annotationfilter", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-annotationfilter + path: recipes/bioconductor-annotationfilter + version: 1.4.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-lazyeval run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-lazyeval +source: + md5: da4a64897ad46309b7668de0fbacd487 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Facilities for Filtering Bioconductor Annotation Resources' - description: 'This package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.' -extra: - parent_recipe: - name: bioconductor-annotationfilter - path: recipes/bioconductor-annotationfilter - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-annotationforge/meta.yaml b/recipes/bioconductor-annotationforge/meta.yaml index 0ff1070736cfa..ee95be722bd60 100644 --- a/recipes/bioconductor-annotationforge/meta.yaml +++ b/recipes/bioconductor-annotationforge/meta.yaml @@ -1,60 +1,66 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "AnnotationForge" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Tools for building SQLite-based annotation data packages -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4aa011cdbdc464bbfe1542ec418e7749 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-annotationforge", max_pin="x.x") }}' - noarch: generic -# Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db, markdown, BiocStyle, knitr, BiocManager, BiocFileCache, RUnit + +extra: + identifiers: + - biotools:annotationforge + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-annotationforge + path: recipes/bioconductor-annotationforge + version: 1.22.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db, rmarkdown, BiocStyle, knitr, BiocManager, BiocFileCache, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dbi - r-rcurl - r-rsqlite - r-xml run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dbi - r-rcurl - r-rsqlite - r-xml + +source: + md5: af0c7c1445b51177250c4101e2efc1a3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Tools for building SQLite-based annotation data packages' - description: 'Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.' -extra: - identifiers: - - biotools:annotationforge - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-annotationforge - path: recipes/bioconductor-annotationforge - version: 1.22.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-annotationhub/meta.yaml b/recipes/bioconductor-annotationhub/meta.yaml index 06f8f353cee10..c55a33c55654b 100644 --- a/recipes/bioconductor-annotationhub/meta.yaml +++ b/recipes/bioconductor-annotationhub/meta.yaml @@ -1,33 +1,42 @@ -{% set version = "3.10.0" %} +{% set version = "3.14.0" %} {% set name = "AnnotationHub" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Client to access AnnotationHub resources -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9dcc8ea705c0e7f8ac8e9af262de876f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-annotationhub", max_pin="x.x") }}' - noarch: generic -# Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub + +extra: + identifiers: + - biotools:annotationhub + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-annotationhub + path: recipes/bioconductor-annotationhub + version: 2.12.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, txdbmaker, MSnbase, mzR, Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocversion >=3.18.0,<3.19.0' - - 'bioconductor-interactivedisplaybase >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocversion >=3.20.0,<3.21.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-biocmanager - r-curl @@ -37,12 +46,11 @@ requirements: - r-rsqlite - r-yaml run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocversion >=3.18.0,<3.19.0' - - 'bioconductor-interactivedisplaybase >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocversion >=3.20.0,<3.21.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-biocmanager - r-curl @@ -51,20 +59,16 @@ requirements: - r-rappdirs - r-rsqlite - r-yaml + +source: + md5: b637981ca6631a32c25266604141b11d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Client to access AnnotationHub resources' - description: 'This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.' -extra: - identifiers: - - biotools:annotationhub - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-annotationhub - path: recipes/bioconductor-annotationhub - version: 2.12.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-annotationhubdata/meta.yaml b/recipes/bioconductor-annotationhubdata/meta.yaml index 712e0387d8f7f..31f54d0cfb812 100644 --- a/recipes/bioconductor-annotationhubdata/meta.yaml +++ b/recipes/bioconductor-annotationhubdata/meta.yaml @@ -1,92 +1,100 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "AnnotationHubData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard Bioconductor data structures. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Transform public data resources into Bioconductor Data Structures -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0c08db64bda6298ca0d673b190a90dee build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-annotationhubdata", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:annotationhubdata + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-annotationhubdata + path: recipes/bioconductor-annotationhubdata + version: 1.10.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData, rmarkdown, HubPub requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationforge >=1.44.0,<1.45.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-bioccheck >=1.38.0,<1.39.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocviews >=1.70.0,<1.71.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationforge >=1.48.0,<1.49.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-bioccheck >=1.42.0,<1.43.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocviews >=1.74.0,<1.75.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-organismdbi >=1.48.0,<1.49.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-biocmanager - r-dbi - - 'r-futile.logger >=1.3.0' + - r-futile.logger >=1.3.0 - r-jsonlite - r-rcurl - r-rsqlite - r-xml + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationforge >=1.44.0,<1.45.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-bioccheck >=1.38.0,<1.39.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocviews >=1.70.0,<1.71.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationforge >=1.48.0,<1.49.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-bioccheck >=1.42.0,<1.43.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocviews >=1.74.0,<1.75.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-organismdbi >=1.48.0,<1.49.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-biocmanager - r-dbi - - 'r-futile.logger >=1.3.0' + - r-futile.logger >=1.3.0 - r-jsonlite - r-rcurl - r-rsqlite - r-xml + +source: + md5: b1ea7de5d95a49f8b0d925623384e10b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Transform public data resources into Bioconductor Data Structures' - description: 'These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard Bioconductor data structures.' -extra: - identifiers: - - biotools:annotationhubdata - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-annotationhubdata - path: recipes/bioconductor-annotationhubdata - version: 1.10.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-annotationtools/meta.yaml b/recipes/bioconductor-annotationtools/meta.yaml index e72898bc9a532..a1ab8d6cab4cb 100644 --- a/recipes/bioconductor-annotationtools/meta.yaml +++ b/recipes/bioconductor-annotationtools/meta.yaml @@ -1,46 +1,52 @@ -{% set version = "1.76.0" %} +{% set version = "1.80.0" %} {% set name = "annotationTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Annotate microarrays and perform cross-species gene expression analyses using flat file databases -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3b0a795d7898c0b6112ed596f9d2de27 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-annotationtools", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:annotationtools + parent_recipe: + name: bioconductor-annotationtools + path: recipes/bioconductor-annotationtools + version: 1.54.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base + +source: + md5: 54e53adce6ba517f69348253baeac061 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL - summary: 'Annotate microarrays and perform cross-species gene expression analyses using flat file databases' - description: 'Functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:annotationtools - parent_recipe: - name: bioconductor-annotationtools - path: recipes/bioconductor-annotationtools - version: 1.54.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-annotatr/meta.yaml b/recipes/bioconductor-annotatr/meta.yaml index a2faf6e30caba..7f8cfadd1b4e9 100644 --- a/recipes/bioconductor-annotatr/meta.yaml +++ b/recipes/bioconductor-annotatr/meta.yaml @@ -1,63 +1,68 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "annotatr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic sites/regions with genomic annotations. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Annotation of Genomic Regions to Genomic Annotations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 433372717ce78a1ae23a91a80601f2b6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-annotatr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, devtools, knitr, org.Dm.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2, testthat, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Ggallus.UCSC.galGal5.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-regioner >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-regioner >=1.38.0,<1.39.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-ggplot2 - r-readr - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-regioner >=1.34.0,<1.35.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-regioner >=1.38.0,<1.39.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-ggplot2 - r-readr - r-reshape2 + +source: + md5: 9b86eaf14c7da6e5baba946ff893bede + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Annotation of Genomic Regions to Genomic Annotations' - description: 'Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5''UTRs, exons, introns, and 3''UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic sites/regions with genomic annotations.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-anopheles.db0/meta.yaml b/recipes/bioconductor-anopheles.db0/meta.yaml index df8ab3def33f1..3714f89f742ec 100644 --- a/recipes/bioconductor-anopheles.db0/meta.yaml +++ b/recipes/bioconductor-anopheles.db0/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "anopheles.db0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cd7b03fffb4ffd0cf0877a55a3636d93 +about: + description: Base annotation databases for anopheles, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Level Annotation databases for anopheles build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-anopheles.db0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 947db8d7057679f9f1340dc883cc7e1c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Level Annotation databases for anopheles' - description: 'Base annotation databases for anopheles, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-anopheles.db0/post-link.sh b/recipes/bioconductor-anopheles.db0/post-link.sh index 9febec5c61f5f..505b8b8a8b45d 100644 --- a/recipes/bioconductor-anopheles.db0/post-link.sh +++ b/recipes/bioconductor-anopheles.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "anopheles.db0-3.18.0" +installBiocDataPackage.sh "anopheles.db0-3.20.0" diff --git a/recipes/bioconductor-anota/meta.yaml b/recipes/bioconductor-anota/meta.yaml index eabf4ab9ea756..025372657111d 100644 --- a/recipes/bioconductor-anota/meta.yaml +++ b/recipes/bioconductor-anota/meta.yaml @@ -1,42 +1,22 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "anota" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Genome wide studies of translational control is emerging as a tool to study verious biological conditions. The output from such analysis is both the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively involved in translation (the actively translating mRNA level) for each mRNA. The standard analysis of such data strives towards identifying differential translational between two or more sample classes - i.e. differences in actively translated mRNA levels that are independent of underlying differences in cytosolic mRNA levels. This package allows for such analysis using partial variances and the random variance model. As 10s of thousands of mRNAs are analyzed in parallell the library performs a number of tests to assure that the data set is suitable for such analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: ANalysis Of Translational Activity (ANOTA). -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dc1461d1c43ffdfedc8e0f49a2b4ac6b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-anota", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - r-base - run: - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'ANalysis Of Translational Activity (ANOTA).' - description: 'Genome wide studies of translational control is emerging as a tool to study verious biological conditions. The output from such analysis is both the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively involved in translation (the actively translating mRNA level) for each mRNA. The standard analysis of such data strives towards identifying differential translational between two or more sample classes - i.e. differences in actively translated mRNA levels that are independent of underlying differences in cytosolic mRNA levels. This package allows for such analysis using partial variances and the random variance model. As 10s of thousands of mRNAs are analyzed in parallell the library performs a number of tests to assure that the data set is suitable for such analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:anota @@ -46,3 +26,29 @@ extra: path: recipes/bioconductor-anota version: 1.28.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - r-base + run: + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - r-base + +source: + md5: 0a28d2588bcff721d1b6e4d179c5204e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-anota2seq/meta.yaml b/recipes/bioconductor-anota2seq/meta.yaml index 295afda5304e6..089b749c75b2c 100644 --- a/recipes/bioconductor-anota2seq/meta.yaml +++ b/recipes/bioconductor-anota2seq/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "anota2seq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: anota2seq provides analysis of translational efficiency and differential expression analysis for polysome-profiling and ribosome-profiling studies (two or more sample classes) quantified by RNA sequencing or DNA-microarray. Polysome-profiling and ribosome-profiling typically generate data for two RNA sources; translated mRNA and total mRNA. Analysis of differential expression is used to estimate changes within each RNA source (i.e. translated mRNA or total mRNA). Analysis of translational efficiency aims to identify changes in translation efficiency leading to altered protein levels that are independent of total mRNA levels (i.e. changes in translated mRNA that are independent of levels of total mRNA) or buffering, a mechanism regulating translational efficiency so that protein levels remain constant despite fluctuating total mRNA levels (i.e. changes in total mRNA that are independent of levels of translated mRNA). anota2seq applies analysis of partial variance and the random variance model to fulfill these tasks. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c14a5f4c2cd7c51fbc9c7ecd844ad0be build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-anota2seq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle,knitr requirements: host: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-rcolorbrewer run: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-rcolorbrewer + +source: + md5: ea94d12f3010127e0fc8add4930650f8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq' - description: 'anota2seq provides analysis of translational efficiency and differential expression analysis for polysome-profiling and ribosome-profiling studies (two or more sample classes) quantified by RNA sequencing or DNA-microarray. Polysome-profiling and ribosome-profiling typically generate data for two RNA sources; translated mRNA and total mRNA. Analysis of differential expression is used to estimate changes within each RNA source (i.e. translated mRNA or total mRNA). Analysis of translational efficiency aims to identify changes in translation efficiency leading to altered protein levels that are independent of total mRNA levels (i.e. changes in translated mRNA that are independent of levels of total mRNA) or buffering, a mechanism regulating translational efficiency so that protein levels remain constant despite fluctuating total mRNA levels (i.e. changes in total mRNA that are independent of levels of translated mRNA). anota2seq applies analysis of partial variance and the random variance model to fulfill these tasks.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-antiprofiles/meta.yaml b/recipes/bioconductor-antiprofiles/meta.yaml index b885a849653a4..a64fd6ffcb914 100644 --- a/recipes/bioconductor-antiprofiles/meta.yaml +++ b/recipes/bioconductor-antiprofiles/meta.yaml @@ -1,42 +1,21 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "antiProfiles" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implements gene expression anti-profiles as described in Corrada Bravo et al., BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Implementation of gene expression anti-profiles -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80b3c1174d02d3b00b3ebf5d14a75b90 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-antiprofiles", max_pin="x.x") }}' - noarch: generic -# Suggests: antiProfilesData, RColorBrewer -requirements: - host: - - r-base - - 'r-locfit >=1.5' - - 'r-matrixstats >=0.50.0' - run: - - r-base - - 'r-locfit >=1.5' - - 'r-matrixstats >=0.50.0' -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Implementation of gene expression anti-profiles' - description: 'Implements gene expression anti-profiles as described in Corrada Bravo et al., BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272.' + extra: identifiers: - biotools:antiprofiles @@ -46,3 +25,30 @@ extra: path: recipes/bioconductor-antiprofiles version: 1.20.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: antiProfilesData, RColorBrewer +requirements: + host: + - r-base + - r-locfit >=1.5 + - r-matrixstats >=0.50.0 + run: + - r-base + - r-locfit >=1.5 + - r-matrixstats >=0.50.0 + +source: + md5: 64a8a17ea0a8452fe4b9b8ee33789d3a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-antiprofilesdata/build_failure.linux-64.yaml b/recipes/bioconductor-antiprofilesdata/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..8287bcc297798 --- /dev/null +++ b/recipes/bioconductor-antiprofilesdata/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: b4578a9e3a50d2d95e6dab615802e53d40d5560de5c0e0c8d6e04aa8efa1fbc6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 14.2.0-h41c2201_101 conda-forge + libgcc-ng: 14.2.0-h69a702a_1 conda-forge + libgfortran: 14.2.0-h69a702a_1 conda-forge + libgfortran-ng: 14.2.0-h69a702a_1 conda-forge + libgfortran5: 14.2.0-hd5240d6_1 conda-forge + libglib: 2.82.2-h2ff4ddf_0 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libiconv: 1.17-hd590300_2 conda-forge + libjpeg-turbo: 3.0.0-hd590300_1 conda-forge + liblapack: 3.9.0-26_linux64_openblas conda-forge + liblzma: 5.6.3-hb9d3cd8_1 conda-forge + libnghttp2: 1.64.0-h161d5f1_0 conda-forge + libopenblas: 0.3.28-pthreads_h94d23a6_1 conda-forge + libpng: 1.6.44-hadc24fc_0 conda-forge + libsanitizer: 14.2.0-h2a3dede_1 conda-forge + libssh2: 1.11.1-hf672d98_0 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-devel_linux-64: 14.2.0-h41c2201_101 conda-forge + libstdcxx-ng: 14.2.0-h4852527_1 conda-forge + libtiff: 4.7.0-hd9ff511_3 conda-forge + libuuid: 2.38.1-h0b41bf4_0 conda-forge + libwebp-base: 1.4.0-hd590300_0 conda-forge + libxcb: 1.17.0-h8a09558_0 conda-forge + libzlib: 1.3.1-hb9d3cd8_2 conda-forge + make: 4.4.1-hb9d3cd8_2 conda-forge + ncurses: 6.5-he02047a_1 conda-forge + openssl: 3.4.0-hb9d3cd8_0 conda-forge + pango: 1.54.0-h3a902e7_3 conda-forge + pcre2: 10.44-hba22ea6_2 conda-forge + pixman: 0.44.2-h29eaf8c_0 conda-forge + pthread-stubs: 0.4-hb9d3cd8_1002 conda-forge + r-base: 4.4.2-hc737e89_2 conda-forge + readline: 8.2-h8228510_1 conda-forge + sed: 4.8-he412f7d_0 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tktable: 2.10-h8bc8fbc_6 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + xorg-libice: 1.1.2-hb9d3cd8_0 conda-forge + xorg-libsm: 1.2.5-he73a12e_0 conda-forge + xorg-libx11: 1.8.10-h4f16b4b_1 conda-forge + xorg-libxau: 1.0.12-hb9d3cd8_0 conda-forge + xorg-libxdmcp: 1.1.5-hb9d3cd8_0 conda-forge + xorg-libxext: 1.3.6-hb9d3cd8_0 conda-forge + xorg-libxrender: 0.9.12-hb9d3cd8_0 conda-forge + xorg-libxt: 1.3.1-hb9d3cd8_0 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: antiProfilesData_1.41.0_78cdf58c93.tar.gz + Downloading https://bioconductor.org/packages/3.20/data/experiment/src/contrib/antiProfilesData_1.41.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.244086 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioconductor.org/packages/3.20/bioc/src/contrib/Archive/antiProfilesData/antiProfilesData_1.41.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.028778 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioarchive.galaxyproject.org/antiProfilesData_1.41.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.313277 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://depot.galaxyproject.org/software/bioconductor-antiprofilesdata/bioconductor-antiprofilesdata_1.41.0_src_all.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.367239 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download https://depot.galaxyproject.org/software/bioconductor-antiprofilesdata/bioconductor-antiprofilesdata_1.41.0_src_all.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-antiprofilesdata/meta.yaml b/recipes/bioconductor-antiprofilesdata/meta.yaml index 4803d0b345804..49a64838fa114 100644 --- a/recipes/bioconductor-antiprofilesdata/meta.yaml +++ b/recipes/bioconductor-antiprofilesdata/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.38.0" %} +{% set version = "1.41.0" %} {% set name = "antiProfilesData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dc40c00fb296b31cf65369e801d6f2f8 +about: + description: 'Colon normal tissue and cancer samples used in Corrada Bravo, et al. gene expression anti-profiles paper: BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272. Measurements are z-scores obtained from the GeneExpression Barcode in the ''frma'' package' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Normal colon and cancer preprocessed affy data for antiProfile building. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-antiprofilesdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: frma, GEOquery, GEOmetadb requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 78cdf58c935b2e6d2bbd053938d45092 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Normal colon and cancer preprocessed affy data for antiProfile building.' - description: 'Colon normal tissue and cancer samples used in Corrada Bravo, et al. gene expression anti-profiles paper: BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272. Measurements are z-scores obtained from the GeneExpression Barcode in the ''frma'' package' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-antiprofilesdata/post-link.sh b/recipes/bioconductor-antiprofilesdata/post-link.sh index 7de926d0707ed..2df7614e3cd51 100644 --- a/recipes/bioconductor-antiprofilesdata/post-link.sh +++ b/recipes/bioconductor-antiprofilesdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "antiprofilesdata-1.38.0" +installBiocDataPackage.sh "antiprofilesdata-1.41.0" diff --git a/recipes/bioconductor-anvil/meta.yaml b/recipes/bioconductor-anvil/meta.yaml index 27898e91b994e..64eb67bd2a28b 100644 --- a/recipes/bioconductor-anvil/meta.yaml +++ b/recipes/bioconductor-anvil/meta.yaml @@ -1,27 +1,30 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "AnVIL" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVIL package provides end-user and developer functionality. For the end-user, AnVIL provides fast binary package installation, utitlities for working with Terra / AnVIL table and data resources, and convenient functions for file movement to and from Google cloud storage. For developers, AnVIL provides programatic access to the Terra, Leonardo, Rawls, and Dockstore RESTful programming interface, including helper functions to transform JSON responses to formats more amenable to manipulation in R. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Bioconductor on the AnVIL compute environment -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 960614983c195ba60dca0a63a0fbf352 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-anvil", max_pin="x.x") }}' - noarch: generic -# Suggests: parallel, knitr, rmarkdown, testthat, withr, readr, BiocStyle, devtools + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: parallel, knitr, rmarkdown, testthat, withr, readr, BiocStyle, devtools, AnVILAz, AnVILGCP, lifecycle requirements: host: + - bioconductor-anvilbase >=1.0.0,<1.1.0 + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 - r-base - r-biocmanager - r-dplyr @@ -31,13 +34,16 @@ requirements: - r-httr - r-jsonlite - r-miniui - - 'r-rapiclient >=0.1.3' + - r-rapiclient >=0.1.3 - r-rlang - r-shiny - r-tibble - r-tidyr - r-tidyselect + - r-yaml run: + - bioconductor-anvilbase >=1.0.0,<1.1.0 + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 - r-base - r-biocmanager - r-dplyr @@ -47,18 +53,23 @@ requirements: - r-httr - r-jsonlite - r-miniui - - 'r-rapiclient >=0.1.3' + - r-rapiclient >=0.1.3 - r-rlang - r-shiny - r-tibble - r-tidyr - r-tidyselect + - r-yaml + +source: + md5: 8511366a69476b2e246ec3f6d6ea54fe + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Bioconductor on the AnVIL compute environment' - description: 'The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVIL package provides end-user and developer functionality. For the end-user, AnVIL provides fast binary package installation, utitlities for working with Terra / AnVIL table and data resources, and convenient functions for file movement to and from Google cloud storage. For developers, AnVIL provides programatic access to the Terra, Leonardo, Rawls, and Dockstore RESTful programming interface, including helper functions to transform JSON responses to formats more amenable to manipulation in R.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-anvilaz/build.sh b/recipes/bioconductor-anvilaz/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-anvilaz/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-anvilaz/meta.yaml b/recipes/bioconductor-anvilaz/meta.yaml new file mode 100644 index 0000000000000..6bc62814c60df --- /dev/null +++ b/recipes/bioconductor-anvilaz/meta.yaml @@ -0,0 +1,56 @@ +{% set version = "1.0.0" %} +{% set name = "AnVILAz" %} +{% set bioc = "3.20" %} + +about: + description: The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVILAz package supports end-users and developers using the AnVIL platform in the Azure cloud. The package provides a programmatic interface to AnVIL resources, including workspaces, notebooks, tables, and workflows. The package also provides utilities for managing resources, including copying files to and from Azure Blob Storage, and creating shared access signatures (SAS) for secure access to Azure resources. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: R / Bioconductor Support for the AnVIL Azure Platform + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-anvilaz", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, dplyr, knitr, readr, rmarkdown, tinytest +# SystemRequirements: az, azcopy +requirements: + host: + - bioconductor-anvilbase >=1.0.0,<1.1.0 + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - r-base + - r-curl + - r-httr2 + - r-jsonlite + - r-rjsoncons + - r-tibble + run: + - bioconductor-anvilbase >=1.0.0,<1.1.0 + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - r-base + - r-curl + - r-httr2 + - r-jsonlite + - r-rjsoncons + - r-tibble + +source: + md5: dd38a856f187e15cbd9c25c92019a1ee + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-anvilbase/build.sh b/recipes/bioconductor-anvilbase/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-anvilbase/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-anvilbase/meta.yaml b/recipes/bioconductor-anvilbase/meta.yaml new file mode 100644 index 0000000000000..2ea1a45d90f77 --- /dev/null +++ b/recipes/bioconductor-anvilbase/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.0.0" %} +{% set name = "AnVILBase" %} +{% set bioc = "3.20" %} + +about: + description: Provides generic functions for interacting with the AnVIL ecosystem. Packages that use either GCP or Azure in AnVIL are built on top of AnVILBase. Extension packages will provide methods for interacting with other cloud providers. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Generic functions for interacting with the AnVIL ecosystem + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-anvilbase", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: AnVIL, AnVILAz, AnVILGCP, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), tinytest +requirements: + host: + - r-base + - r-dplyr + - r-httr + - r-httr2 + - r-jsonlite + - r-tibble + run: + - r-base + - r-dplyr + - r-httr + - r-httr2 + - r-jsonlite + - r-tibble + +source: + md5: fd6e6ce4ae5c1c8c9a72b1a72cda36a8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-anvilbilling/meta.yaml b/recipes/bioconductor-anvilbilling/meta.yaml index a68235d62783f..408f8f1836fd4 100644 --- a/recipes/bioconductor-anvilbilling/meta.yaml +++ b/recipes/bioconductor-anvilbilling/meta.yaml @@ -1,24 +1,25 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "AnVILBilling" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: AnVILBilling helps monitor AnVIL-related costs in R, using queries to a BigQuery table to which costs are exported daily. Functions are defined to help categorize tasks and associated expenditures, and to visualize and explore expense profiles over time. This package will be expanded to help users estimate costs for specific task sets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Provide functions to retrieve and report on usage expenses in NHGRI AnVIL (anvilproject.org). -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e6cd90c2e4e31067dfab860b5130cf8 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-anvilbilling", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, BiocStyle, rmarkdown requirements: host: @@ -45,12 +46,16 @@ requirements: - r-plotly - r-shiny - r-shinytoastr + +source: + md5: 42b4e30f729b87f6a3b4f8b2628d2ccd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Provide functions to retrieve and report on usage expenses in NHGRI AnVIL (anvilproject.org).' - description: 'AnVILBilling helps monitor AnVIL-related costs in R, using queries to a BigQuery table to which costs are exported daily. Functions are defined to help categorize tasks and associated expenditures, and to visualize and explore expense profiles over time. This package will be expanded to help users estimate costs for specific task sets.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-anvilgcp/build.sh b/recipes/bioconductor-anvilgcp/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-anvilgcp/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-anvilgcp/meta.yaml b/recipes/bioconductor-anvilgcp/meta.yaml new file mode 100644 index 0000000000000..103f11cae9817 --- /dev/null +++ b/recipes/bioconductor-anvilgcp/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.0.0" %} +{% set name = "AnVILGCP" %} +{% set bioc = "3.20" %} + +about: + description: The package provides a set of functions to interact with the Google Cloud Platform (GCP) services on the AnVIL platform. The package is designed to work with the AnVIL package. User-level interaction with this package should be minimal. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: The GCP R Client for the AnVIL + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-anvilgcp", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: AnVIL, BiocStyle, httr2, knitr, rmarkdown, testthat, withr +# SystemRequirements: gsutil, gcloud +requirements: + host: + - bioconductor-anvilbase >=1.0.0,<1.1.0 + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - r-base + - r-dplyr + - r-httr + - r-jsonlite + - r-rlang + - r-tibble + - r-tidyr + run: + - bioconductor-anvilbase >=1.0.0,<1.1.0 + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - r-base + - r-dplyr + - r-httr + - r-jsonlite + - r-rlang + - r-tibble + - r-tidyr + +source: + md5: faa94033f8fdd6320dbc8d157fbaf290 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-anvilpublish/meta.yaml b/recipes/bioconductor-anvilpublish/meta.yaml index 60a805d1f9759..f59d4dca65886 100644 --- a/recipes/bioconductor-anvilpublish/meta.yaml +++ b/recipes/bioconductor-anvilpublish/meta.yaml @@ -1,29 +1,33 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "AnVILPublish" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Use this package to create or update AnVIL workspaces from resources such as R / Bioconductor packages. The metadata about the package (e.g., select information from the package DESCRIPTION file and from vignette YAML headings) are used to populate the 'DASHBOARD'. Vignettes are translated to python notebooks ready for evaluation in AnVIL. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Publish Packages and Other Resources to AnVIL Workspaces -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bbd5bd8ab36e2563e7b4b01e2b11295d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-anvilpublish", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, BiocStyle, BiocManager, testthat (>= 3.0.0) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-anvil >=1.14.0,<1.15.0' + - bioconductor-anvil >=1.18.0,<1.19.0 + - bioconductor-anvilgcp >=1.0.0,<1.1.0 + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 - r-base + - r-biocmanager - r-httr - r-jsonlite - r-readr @@ -31,20 +35,27 @@ requirements: - r-whisker - r-yaml run: - - 'bioconductor-anvil >=1.14.0,<1.15.0' + - bioconductor-anvil >=1.18.0,<1.19.0 + - bioconductor-anvilgcp >=1.0.0,<1.1.0 + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 - r-base + - r-biocmanager - r-httr - r-jsonlite - r-readr - r-rmarkdown - r-whisker - r-yaml + +source: + md5: 06c30bb2a89c9c9eb420ec131caba7ab + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Publish Packages and Other Resources to AnVIL Workspaces' - description: 'Use this package to create or update AnVIL workspaces from resources such as R / Bioconductor packages. The metadata about the package (e.g., select information from the package DESCRIPTION file and from vignette YAML headings) are used to populate the ''DASHBOARD''. Vignettes are translated to python notebooks ready for evaluation in AnVIL.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-anvilworkflow/meta.yaml b/recipes/bioconductor-anvilworkflow/meta.yaml index de05da6b61a56..f849bbec7de5c 100644 --- a/recipes/bioconductor-anvilworkflow/meta.yaml +++ b/recipes/bioconductor-anvilworkflow/meta.yaml @@ -1,42 +1,63 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "AnVILWorkflow" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The main cloud-based genomics platform deported by the AnVIL project is Terra. The AnVILWorkflow package allows remote access to Terra implemented workflows, enabling end-user to utilize Terra/ AnVIL provided resources - such as data, workflows, and flexible/scalble computing resources - through the conventional R functions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Run workflows implemented in Terra/AnVIL workspace -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af890e3cea3c42346ec887603ba12e40 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-anvilworkflow", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, tibble, BiocStyle + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, BiocStyle requirements: host: - - 'bioconductor-anvil >=1.14.0,<1.15.0' + - bioconductor-anvil >=1.18.0,<1.19.0 + - bioconductor-anvilbase >=1.0.0,<1.1.0 + - bioconductor-anvilgcp >=1.0.0,<1.1.0 - r-base + - r-dplyr - r-httr - r-jsonlite + - r-plyr + - r-rlang + - r-stringr + - r-tibble + - r-tidyr run: - - 'bioconductor-anvil >=1.14.0,<1.15.0' + - bioconductor-anvil >=1.18.0,<1.19.0 + - bioconductor-anvilbase >=1.0.0,<1.1.0 + - bioconductor-anvilgcp >=1.0.0,<1.1.0 - r-base + - r-dplyr - r-httr - r-jsonlite + - r-plyr + - r-rlang + - r-stringr + - r-tibble + - r-tidyr + +source: + md5: 7a0d2a5b63a89a86ca0cbeaada7dcc6e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Run workflows implemented in Terra/AnVIL workspace' - description: 'The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The main cloud-based genomics platform deported by the AnVIL project is Terra. The AnVILWorkflow package allows remote access to Terra implemented workflows, enabling end-user to utilize Terra/ AnVIL provided resources - such as data, workflows, and flexible/scalble computing resources - through the conventional R functions.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-apalyzer/meta.yaml b/recipes/bioconductor-apalyzer/meta.yaml index 744b59ec3073e..6bdda3a248dcd 100644 --- a/recipes/bioconductor-apalyzer/meta.yaml +++ b/recipes/bioconductor-apalyzer/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "APAlyzer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Perform 3'UTR APA, Intronic APA and gene expression analysis using RNA-seq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: A toolkit for APA analysis using RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 88aebb2681d07ad9bc8b7e3499339d51 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-apalyzer", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, testthat, pasillaBamSubset requirements: host: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hybridmtest >=1.46.0,<1.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rsubread >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hybridmtest >=1.50.0,<1.51.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rsubread >=2.20.0,<2.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-dplyr - r-ggplot2 @@ -39,29 +41,32 @@ requirements: - r-repmis - r-tidyr run: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hybridmtest >=1.46.0,<1.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rsubread >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hybridmtest >=1.50.0,<1.51.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rsubread >=2.20.0,<2.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-dplyr - r-ggplot2 - r-ggrepel - r-repmis - r-tidyr + +source: + md5: 8778e7b93e0dec42f1bdc978085ae254 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'A toolkit for APA analysis using RNA-seq data' - description: 'Perform 3''UTR APA, Intronic APA and gene expression analysis using RNA-seq data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-apcomplex/meta.yaml b/recipes/bioconductor-apcomplex/meta.yaml index 78e15d595cd68..997bb9a8c77cc 100644 --- a/recipes/bioconductor-apcomplex/meta.yaml +++ b/recipes/bioconductor-apcomplex/meta.yaml @@ -1,46 +1,22 @@ -{% set version = "2.68.0" %} +{% set version = "2.72.0" %} {% set name = "apComplex" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions to estimate a bipartite graph of protein complex membership using AP-MS data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Estimate protein complex membership using AP-MS protein data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 03418539dfa5904bf05f430718789fde build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-apcomplex", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - r-base - run: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Estimate protein complex membership using AP-MS protein data' - description: 'Functions to estimate a bipartite graph of protein complex membership using AP-MS data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + extra: identifiers: - biotools:apcomplex @@ -50,3 +26,33 @@ extra: path: recipes/bioconductor-apcomplex version: 2.46.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-org.sc.sgd.db >=3.20.0,<3.21.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - r-base + run: + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-org.sc.sgd.db >=3.20.0,<3.21.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - r-base + +source: + md5: c355c45f983cd44ccd52914938f375f2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-apeglm/meta.yaml b/recipes/bioconductor-apeglm/meta.yaml index 78fd5a84b9c6b..9fade3509a11d 100644 --- a/recipes/bioconductor-apeglm/meta.yaml +++ b/recipes/bioconductor-apeglm/meta.yaml @@ -1,28 +1,42 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "apeglm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Approximate posterior estimation for GLM coefficients -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0f8e64bdd8eec2566238fdc487afabb8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-apeglm", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + parent_recipe: + name: bioconductor-apeglm + path: recipes/bioconductor-apeglm + version: 1.2.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: DESeq2, airway, knitr, rmarkdown, testthat requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-emdbook - r-rcpp @@ -31,31 +45,23 @@ requirements: - libblas - liblapack run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-emdbook - r-rcpp - r-rcppeigen - r-rcppnumerical - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: f1121b16b6271d8102ccce697b1bd9ff + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Approximate posterior estimation for GLM coefficients' - description: 'apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - additional-platforms: - - linux-aarch64 - parent_recipe: - name: bioconductor-apeglm - path: recipes/bioconductor-apeglm - version: 1.2.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-appreci8r/meta.yaml b/recipes/bioconductor-appreci8r/meta.yaml index fdbd9dac892ba..f64624169cce5 100644 --- a/recipes/bioconductor-appreci8r/meta.yaml +++ b/recipes/bioconductor-appreci8r/meta.yaml @@ -1,48 +1,51 @@ -{% set version = "1.20.1" %} +{% set version = "1.24.0" %} {% set name = "appreci8R" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The appreci8R is an R version of our appreci8-algorithm - A Pipeline for PREcise variant Calling Integrating 8 tools. Variant calling results of our standard appreci8-tools (GATK, Platypus, VarScan, FreeBayes, LoFreq, SNVer, samtools and VarDict), as well as up to 5 additional tools is combined, evaluated and filtered. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: 'appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9165459dd4a98c9645928c87b934c081 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-appreci8r", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: GO.db, org.Hs.eg.db, utils requirements: + host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-cosmic.67 >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mafdb.1kgenomes.phase3.hs37d5 >=3.10.0,<3.11.0' - - 'bioconductor-mafdb.exac.r1.0.hs37d5 >=3.10.0,<3.11.0' - - 'bioconductor-mafdb.gnomadex.r2.1.hs37d5 >=3.10.0,<3.11.0' - - 'bioconductor-polyphen.hsapiens.dbsnp131 >=1.0.0,<1.1.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-sift.hsapiens.dbsnp137 >=1.0.0,<1.1.0' - - 'bioconductor-snplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - - 'bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-cosmic.67 >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-homo.sapiens >=1.3.0,<1.4.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mafdb.1kgenomes.phase3.hs37d5 >=3.10.0,<3.11.0 + - bioconductor-mafdb.exac.r1.0.hs37d5 >=3.10.0,<3.11.0 + - bioconductor-mafdb.gnomadex.r2.1.hs37d5 >=3.10.0,<3.11.0 + - bioconductor-polyphen.hsapiens.dbsnp131 >=1.0.0,<1.1.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sift.hsapiens.dbsnp137 >=1.0.0,<1.1.0 + - bioconductor-snplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0 - r-base - r-dt - r-openxlsx @@ -51,28 +54,29 @@ requirements: - r-shiny - r-shinyjs - r-stringr + run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-cosmic.67 >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mafdb.1kgenomes.phase3.hs37d5 >=3.10.0,<3.11.0' - - 'bioconductor-mafdb.exac.r1.0.hs37d5 >=3.10.0,<3.11.0' - - 'bioconductor-mafdb.gnomadex.r2.1.hs37d5 >=3.10.0,<3.11.0' - - 'bioconductor-polyphen.hsapiens.dbsnp131 >=1.0.0,<1.1.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-sift.hsapiens.dbsnp137 >=1.0.0,<1.1.0' - - 'bioconductor-snplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - - 'bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-cosmic.67 >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-homo.sapiens >=1.3.0,<1.4.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mafdb.1kgenomes.phase3.hs37d5 >=3.10.0,<3.11.0 + - bioconductor-mafdb.exac.r1.0.hs37d5 >=3.10.0,<3.11.0 + - bioconductor-mafdb.gnomadex.r2.1.hs37d5 >=3.10.0,<3.11.0 + - bioconductor-polyphen.hsapiens.dbsnp131 >=1.0.0,<1.1.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sift.hsapiens.dbsnp137 >=1.0.0,<1.1.0 + - bioconductor-snplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0 - r-base - r-dt - r-openxlsx @@ -81,13 +85,16 @@ requirements: - r-shiny - r-shinyjs - r-stringr + +source: + md5: 99584620659f94fbb38d19829e144235 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV' - description: 'The appreci8R is an R version of our appreci8-algorithm - A Pipeline for PREcise variant Calling Integrating 8 tools. Variant calling results of our standard appreci8-tools (GATK, Platypus, VarScan, FreeBayes, LoFreq, SNVer, samtools and VarDict), as well as up to 5 additional tools is combined, evaluated and filtered.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-arabidopsis.db0/meta.yaml b/recipes/bioconductor-arabidopsis.db0/meta.yaml index a353a6fe036e9..ea5ba859eab9d 100644 --- a/recipes/bioconductor-arabidopsis.db0/meta.yaml +++ b/recipes/bioconductor-arabidopsis.db0/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "arabidopsis.db0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5896dbae0f9f8fdc87712dba0bb6cbd1 +about: + description: Base annotation databases for arabidopsis, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Level Annotation databases for arabidopsis build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-arabidopsis.db0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1c09bf13aaf74707cae7583fb4cef467 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Level Annotation databases for arabidopsis' - description: 'Base annotation databases for arabidopsis, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-arabidopsis.db0/post-link.sh b/recipes/bioconductor-arabidopsis.db0/post-link.sh index 45f1d087e4fb9..a7e2c95e2e40d 100644 --- a/recipes/bioconductor-arabidopsis.db0/post-link.sh +++ b/recipes/bioconductor-arabidopsis.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "arabidopsis.db0-3.18.0" +installBiocDataPackage.sh "arabidopsis.db0-3.20.0" diff --git a/recipes/bioconductor-aracne.networks/meta.yaml b/recipes/bioconductor-aracne.networks/meta.yaml index a1725ffbcf2bf..6e944457bd14a 100644 --- a/recipes/bioconductor-aracne.networks/meta.yaml +++ b/recipes/bioconductor-aracne.networks/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "aracne.networks" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 42657d0acf4c1ba54aa2057fa4525d51 +about: + description: This package contains ARACNe-inferred networks from TCGA tumor datasets. It also contains a function to export them into plain-text format. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: ARACNe-inferred gene networks from TCGA tumor datasets build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-aracne.networks", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-viper >=1.36.0,<1.37.0' + - bioconductor-viper >=1.40.0,<1.41.0 - r-base run: - - 'bioconductor-viper >=1.36.0,<1.37.0' + - bioconductor-viper >=1.40.0,<1.41.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5f2866bb8b3db3bf6e87a9773d76da17 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'ARACNe-inferred gene networks from TCGA tumor datasets' - description: 'This package contains ARACNe-inferred networks from TCGA tumor datasets. It also contains a function to export them into plain-text format.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-aracne.networks/post-link.sh b/recipes/bioconductor-aracne.networks/post-link.sh index a25ee53fa9383..61170218359e6 100644 --- a/recipes/bioconductor-aracne.networks/post-link.sh +++ b/recipes/bioconductor-aracne.networks/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "aracne.networks-1.28.0" +installBiocDataPackage.sh "aracne.networks-1.32.0" diff --git a/recipes/bioconductor-aroma.light/meta.yaml b/recipes/bioconductor-aroma.light/meta.yaml index 30e404c5a01cf..276db8f1894ae 100644 --- a/recipes/bioconductor-aroma.light/meta.yaml +++ b/recipes/bioconductor-aroma.light/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "3.32.0" %} +{% set version = "3.36.0" %} {% set name = "aroma.light" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 07d98bcf8be950a16c1d6aaae375f17d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-aroma.light", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:aroma.light + parent_recipe: + name: bioconductor-aroma.light + path: recipes/bioconductor-aroma.light + version: 3.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: princurve (>= 2.1.4) requirements: host: - r-base - - 'r-matrixstats >=0.55.0' - - 'r-r.methodss3 >=1.7.1' - - 'r-r.oo >=1.23.0' - - 'r-r.utils >=2.9.0' + - r-matrixstats >=0.55.0 + - r-r.methodss3 >=1.7.1 + - r-r.oo >=1.23.0 + - r-r.utils >=2.9.0 run: - r-base - - 'r-matrixstats >=0.55.0' - - 'r-r.methodss3 >=1.7.1' - - 'r-r.oo >=1.23.0' - - 'r-r.utils >=2.9.0' + - r-matrixstats >=0.55.0 + - r-r.methodss3 >=1.7.1 + - r-r.oo >=1.23.0 + - r-r.utils >=2.9.0 + +source: + md5: 65fab39e6270885aa65b48a528136b14 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types' - description: 'Methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:aroma.light - parent_recipe: - name: bioconductor-aroma.light - path: recipes/bioconductor-aroma.light - version: 3.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-arrayexpress/meta.yaml b/recipes/bioconductor-arrayexpress/meta.yaml index 6efa3dbf50684..46bfc1dcf60f9 100644 --- a/recipes/bioconductor-arrayexpress/meta.yaml +++ b/recipes/bioconductor-arrayexpress/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "1.62.0" %} +{% set version = "1.66.0" %} {% set name = "ArrayExpress" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6232db8158e5ba9cde38da322b0c5163 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-arrayexpress", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-arrayexpress + path: recipes/bioconductor-arrayexpress + version: 1.40.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: affy requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-oligo >=1.70.0,<1.71.0 - r-base - r-httr - r-jsonlite - r-rlang run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-oligo >=1.70.0,<1.71.0 - r-base - r-httr - r-jsonlite - r-rlang + +source: + md5: 82a4dac2aeb99c9019adf6a234917b2b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet' - description: 'Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet.' -extra: - parent_recipe: - name: bioconductor-arrayexpress - path: recipes/bioconductor-arrayexpress - version: 1.40.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-arraymvout/meta.yaml b/recipes/bioconductor-arraymvout/meta.yaml index 612d3124a7a6b..a7dd2ce3717ae 100644 --- a/recipes/bioconductor-arraymvout/meta.yaml +++ b/recipes/bioconductor-arraymvout/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "arrayMvout" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: multivariate outlier detection for expression array QA -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7aa46c496dbe47218ea774cb02108800 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-arraymvout", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affycontam >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' - - 'bioconductor-mdqc >=1.64.0,<1.65.0' - - 'bioconductor-parody >=1.60.0,<1.61.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affycontam >=1.64.0,<1.65.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-lumi >=2.58.0,<2.59.0 + - bioconductor-mdqc >=1.68.0,<1.69.0 + - bioconductor-parody >=1.64.0,<1.65.0 - r-base run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affycontam >=1.60.0,<1.61.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' - - 'bioconductor-mdqc >=1.64.0,<1.65.0' - - 'bioconductor-parody >=1.60.0,<1.61.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affycontam >=1.64.0,<1.65.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-lumi >=2.58.0,<2.59.0 + - bioconductor-mdqc >=1.68.0,<1.69.0 + - bioconductor-parody >=1.64.0,<1.65.0 - r-base + +source: + md5: 1a220831639a56bbe6cd97eece9b1d1f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'multivariate outlier detection for expression array QA' - description: 'This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-arrayquality/meta.yaml b/recipes/bioconductor-arrayquality/meta.yaml index c3c33beb6b5c6..bef48694166a0 100644 --- a/recipes/bioconductor-arrayquality/meta.yaml +++ b/recipes/bioconductor-arrayquality/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.80.0" %} +{% set version = "1.84.0" %} {% set name = "arrayQuality" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions for performing print-run and array level quality assessment. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Assessing array quality on spotted arrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9d875e31dc2f51e4c476d1a13330ad18 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-arrayquality", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:arrayquality + - doi:10.1093/bioinformatics/btn647 + parent_recipe: + name: bioconductor-arrayquality + path: recipes/bioconductor-arrayquality + version: 1.58.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: mclust, MEEBOdata, HEEBOdata requirements: host: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-marray >=1.84.0,<1.85.0 - r-base - r-gridbase - r-hexbin - r-rcolorbrewer run: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-marray >=1.84.0,<1.85.0 - r-base - r-gridbase - r-hexbin - r-rcolorbrewer + +source: + md5: 9c1faf2d4271c228c2c4b8d1f8b69dce + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Assessing array quality on spotted arrays' - description: 'Functions for performing print-run and array level quality assessment.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:arrayquality - - doi:10.1093/bioinformatics/btn647 - parent_recipe: - name: bioconductor-arrayquality - path: recipes/bioconductor-arrayquality - version: 1.58.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-arrayqualitymetrics/meta.yaml b/recipes/bioconductor-arrayqualitymetrics/meta.yaml index 46f59c2bc01a2..7001dc586a672 100644 --- a/recipes/bioconductor-arrayqualitymetrics/meta.yaml +++ b/recipes/bioconductor-arrayqualitymetrics/meta.yaml @@ -1,36 +1,46 @@ -{% set version = "3.58.0" %} +{% set version = "3.62.0" %} {% set name = "arrayQualityMetrics" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Quality metrics report for microarray data sets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 65128c55b6181bdadb73d256e399091e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-arrayqualitymetrics", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:arrayqualitymetrics + parent_recipe: + name: bioconductor-arrayqualitymetrics + path: recipes/bioconductor-arrayqualitymetrics + version: 3.36.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ALLMLL, CCl4, BiocStyle, knitr requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affyplm >=1.78.0,<1.79.0' - - 'bioconductor-beadarray >=2.52.0,<2.53.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affyplm >=1.82.0,<1.83.0 + - bioconductor-beadarray >=2.56.0,<2.57.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-base - - 'r-gridsvg >=1.4-3' + - r-gridsvg >=1.4-3 - r-hmisc - r-hwriter - r-lattice @@ -40,15 +50,15 @@ requirements: - r-svglite - r-xml run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affyplm >=1.78.0,<1.79.0' - - 'bioconductor-beadarray >=2.52.0,<2.53.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affyplm >=1.82.0,<1.83.0 + - bioconductor-beadarray >=2.56.0,<2.57.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-base - - 'r-gridsvg >=1.4-3' + - r-gridsvg >=1.4-3 - r-hmisc - r-hwriter - r-lattice @@ -57,20 +67,16 @@ requirements: - r-setrng - r-svglite - r-xml + +source: + md5: 00d3779f4daae37b1229b8b81912621b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'Quality metrics report for microarray data sets' - description: 'This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:arrayqualitymetrics - parent_recipe: - name: bioconductor-arrayqualitymetrics - path: recipes/bioconductor-arrayqualitymetrics - version: 3.36.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-arrmdata/meta.yaml b/recipes/bioconductor-arrmdata/meta.yaml index a7fe1357a1d0d..847a9580a4feb 100644 --- a/recipes/bioconductor-arrmdata/meta.yaml +++ b/recipes/bioconductor-arrmdata/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "ARRmData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 95475f869b8ff3d6344c0f45f2e616c9 +about: + description: Raw Beta values from 36 samples across 3 groups from Illumina 450k methylation arrays + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Example dataset for normalization of Illumina 450k Methylation data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-arrmdata", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-arrmdata + path: recipes/bioconductor-arrmdata + version: 1.16.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 372caa2484b4a15568d1afd7574d16b1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Example dataset for normalization of Illumina 450k Methylation data' - description: 'Raw Beta values from 36 samples across 3 groups from Illumina 450k methylation arrays' -extra: - parent_recipe: - name: bioconductor-arrmdata - path: recipes/bioconductor-arrmdata - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-arrmdata/post-link.sh b/recipes/bioconductor-arrmdata/post-link.sh index 92579cc4ac064..ed4c8b62a1fb7 100644 --- a/recipes/bioconductor-arrmdata/post-link.sh +++ b/recipes/bioconductor-arrmdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "arrmdata-1.38.0" +installBiocDataPackage.sh "arrmdata-1.42.0" diff --git a/recipes/bioconductor-arrmnormalization/meta.yaml b/recipes/bioconductor-arrmnormalization/meta.yaml index 437968da022a4..d94187e8e49a1 100644 --- a/recipes/bioconductor-arrmnormalization/meta.yaml +++ b/recipes/bioconductor-arrmnormalization/meta.yaml @@ -1,39 +1,21 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "ARRmNormalization" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Adaptive Robust Regression normalization for Illumina methylation data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a6223cb64b7077670d38fb437638e0fe build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-arrmnormalization", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-arrmdata >=1.38.0,<1.39.0' - - r-base - run: - - 'bioconductor-arrmdata >=1.38.0,<1.39.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Adaptive Robust Regression normalization for Illumina methylation data' - description: 'Perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.' + extra: identifiers: - biotools:arrmnormalization @@ -43,3 +25,27 @@ extra: path: recipes/bioconductor-arrmnormalization version: 1.20.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-arrmdata >=1.42.0,<1.43.0 + - r-base + run: + - bioconductor-arrmdata >=1.42.0,<1.43.0 + - r-base + +source: + md5: 0af955b7b98040954d6f8bfb2407ae2a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-artms/meta.yaml b/recipes/bioconductor-artms/meta.yaml index 25f17daed6675..ddd3221b4702d 100644 --- a/recipes/bioconductor-artms/meta.yaml +++ b/recipes/bioconductor-artms/meta.yaml @@ -1,31 +1,34 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "artMS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON. Check [http://artms.org](http://artms.org) for details. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + file LICENSE + license_file: LICENSE + summary: Analytical R tools for Mass Spectrometry -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d52a9405bcf6f4a3920ecb70be49c1d9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-artms", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR, knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-msstats >=4.10.0,<4.11.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-msstats >=4.14.0,<4.15.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - r-bit64 - r-circlize @@ -50,11 +53,12 @@ requirements: - r-upsetr - r-venndiagram - r-yaml + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-msstats >=4.10.0,<4.11.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-msstats >=4.14.0,<4.15.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - r-bit64 - r-circlize @@ -79,13 +83,16 @@ requirements: - r-upsetr - r-venndiagram - r-yaml + +source: + md5: bb8230343feec9d22b0b9ce66645aad3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3) + file LICENSE' - summary: 'Analytical R tools for Mass Spectrometry' - description: 'artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON. Check [http://artms.org](http://artms.org) for details.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-asafe/meta.yaml b/recipes/bioconductor-asafe/meta.yaml index 46bae4e0a4f2d..df79b927d0190 100644 --- a/recipes/bioconductor-asafe/meta.yaml +++ b/recipes/bioconductor-asafe/meta.yaml @@ -1,38 +1,19 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "ASAFE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e054d986c3b6f2574c26498eaf6e4f7c +about: + description: Given admixed individuals' bi-allelic SNP genotypes and ancestry pairs (where each ancestry can take one of three values) for multiple SNPs, perform an EM algorithm to deal with the fact that SNP genotypes are unphased with respect to ancestry pairs, in order to estimate ancestry-specific allele frequencies for all SNPs. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Ancestry Specific Allele Frequency Estimation build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-asafe", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, testthat -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Ancestry Specific Allele Frequency Estimation' - description: 'Given admixed individuals'' bi-allelic SNP genotypes and ancestry pairs (where each ancestry can take one of three values) for multiple SNPs, perform an EM algorithm to deal with the fact that SNP genotypes are unphased with respect to ancestry pairs, in order to estimate ancestry-specific allele frequencies for all SNPs.' extra: identifiers: - biotools:asafe @@ -41,4 +22,23 @@ extra: name: bioconductor-asafe path: recipes/bioconductor-asafe version: 1.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: knitr, testthat +requirements: + host: + - r-base + run: + - r-base +source: + md5: f0b5ce85ed013abf23384cc62c077325 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-aseb/meta.yaml b/recipes/bioconductor-aseb/meta.yaml index 185e0ab4c1db4..696d6cb7f81e4 100644 --- a/recipes/bioconductor-aseb/meta.yaml +++ b/recipes/bioconductor-aseb/meta.yaml @@ -1,49 +1,55 @@ -{% set version = "1.46.3" %} +{% set version = "1.50.0" %} {% set name = "ASEB" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ASEB is an R package to predict lysine sites that can be acetylated by a specific KAT-family. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Predict Acetylated Lysine Sites -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e9312371523d44d7f1cb759af2d150e build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-aseb", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:aseb + - doi:10.1093/nar/gks437 + parent_recipe: + name: bioconductor-aseb + path: recipes/bioconductor-aseb + version: 1.24.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: e3cd7166e35309e339b37d48d5f076a2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Predict Acetylated Lysine Sites' - description: 'ASEB is an R package to predict lysine sites that can be acetylated by a specific KAT-family.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:aseb - - doi:10.1093/nar/gks437 - parent_recipe: - name: bioconductor-aseb - path: recipes/bioconductor-aseb - version: 1.24.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-asgsca/meta.yaml b/recipes/bioconductor-asgsca/meta.yaml index 2fd57fbdec08e..0cec5e2a80868 100644 --- a/recipes/bioconductor-asgsca/meta.yaml +++ b/recipes/bioconductor-asgsca/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "ASGSCA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package provides tools to model and test the association between multiple genotypes and multiple traits, taking into account the prior biological knowledge. Genes, and clinical pathways are incorporated in the model as latent variables. The method is based on Generalized Structured Component Analysis (GSCA). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Association Studies for multiple SNPs and multiple traits using Generalized Structured Equation Models -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c0e60b4fa228444ab7863044881fa8bb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-asgsca", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:asgsca + - doi:10.1002/gepi.21872 + parent_recipe: + name: bioconductor-asgsca + path: recipes/bioconductor-asgsca + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle requirements: host: @@ -29,21 +40,16 @@ requirements: - r-base - r-mass - r-matrix + +source: + md5: 90ef625503107f317b94142820c3689d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Association Studies for multiple SNPs and multiple traits using Generalized Structured Equation Models' - description: 'The package provides tools to model and test the association between multiple genotypes and multiple traits, taking into account the prior biological knowledge. Genes, and clinical pathways are incorporated in the model as latent variables. The method is based on Generalized Structured Component Analysis (GSCA).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:asgsca - - doi:10.1002/gepi.21872 - parent_recipe: - name: bioconductor-asgsca - path: recipes/bioconductor-asgsca - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ashkenazimsonchr21/meta.yaml b/recipes/bioconductor-ashkenazimsonchr21/meta.yaml index e111494e14c2a..40c7f96b65e7e 100644 --- a/recipes/bioconductor-ashkenazimsonchr21/meta.yaml +++ b/recipes/bioconductor-ashkenazimsonchr21/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "AshkenazimSonChr21" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a4455fab1d47dcf8dc2411fec1066a2c +about: + description: SonVariantsChr21 is a dataset of annotated genomic variants coming from Complete Genomics whole genome sequencing. Data comes from GIAB project, Ashkenazim Trio, sample HG002 run 1. Both vcf and annotated data frame are provided. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotated variants on the chromosome 21, human genome 19, Ashkenazim Trio son sample build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ashkenazimsonchr21", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, VariantAnnotation requirements: host: @@ -26,13 +24,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c7fe6ce4801ab4d0d7f3405b03a1b605 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotated variants on the chromosome 21, human genome 19, Ashkenazim Trio son sample' - description: 'SonVariantsChr21 is a dataset of annotated genomic variants coming from Complete Genomics whole genome sequencing. Data comes from GIAB project, Ashkenazim Trio, sample HG002 run 1. Both vcf and annotated data frame are provided.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ashkenazimsonchr21/post-link.sh b/recipes/bioconductor-ashkenazimsonchr21/post-link.sh index 20f8d2ad38a7e..d7afaa8a1aa9c 100644 --- a/recipes/bioconductor-ashkenazimsonchr21/post-link.sh +++ b/recipes/bioconductor-ashkenazimsonchr21/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ashkenazimsonchr21-1.32.0" +installBiocDataPackage.sh "ashkenazimsonchr21-1.36.0" diff --git a/recipes/bioconductor-asics/meta.yaml b/recipes/bioconductor-asics/meta.yaml index 49a962cda7e85..49a40fa2eae90 100644 --- a/recipes/bioconductor-asics/meta.yaml +++ b/recipes/bioconductor-asics/meta.yaml @@ -1,31 +1,37 @@ -{% set version = "2.18.0" %} +{% set version = "2.22.0" %} {% set name = "ASICS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: With a set of pure metabolite reference spectra, ASICS quantifies concentration of metabolites in a complex spectrum. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty. The method and its statistical properties are described in Tardivel et al. (2017) . + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Automatic Statistical Identification in Complex Spectra -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 526bfb1ebf38574a4914a434cd159769 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-asics", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat, ASICSdata requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-pepsnmr >=1.20.0,<1.21.0' - - 'bioconductor-ropls >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-pepsnmr >=1.24.0,<1.25.0 + - bioconductor-ropls >=1.38.0,<1.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-glmnet @@ -36,10 +42,10 @@ requirements: - r-quadprog - r-zoo run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-pepsnmr >=1.20.0,<1.21.0' - - 'bioconductor-ropls >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-pepsnmr >=1.24.0,<1.25.0 + - bioconductor-ropls >=1.38.0,<1.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-glmnet @@ -49,16 +55,16 @@ requirements: - r-plyr - r-quadprog - r-zoo + +source: + md5: 5e56f9ee7c4ecc30c1ba38c947b0c14c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Automatic Statistical Identification in Complex Spectra' - description: 'With a set of pure metabolite reference spectra, ASICS quantifies concentration of metabolites in a complex spectrum. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty. The method and its statistical properties are described in Tardivel et al. (2017) .' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - container: - extended-base: true + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-asicsdata/meta.yaml b/recipes/bioconductor-asicsdata/meta.yaml index 6863b79647e76..7f7fc3d1bf99c 100644 --- a/recipes/bioconductor-asicsdata/meta.yaml +++ b/recipes/bioconductor-asicsdata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "ASICSdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: afb117c0db733e23239bf2cf4e18d364 +about: + description: 1D NMR example spectra and additional data for use with the ASICS package. Raw 1D Bruker spectral data files were found in the MetaboLights database (https://www.ebi.ac.uk/metabolights/, study MTBLS1). + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Example of 1D NMR spectra data for ASICS package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-asicsdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d2a2fba95d9d2d4edf0fbeca46cc7bef + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Example of 1D NMR spectra data for ASICS package' - description: '1D NMR example spectra and additional data for use with the ASICS package. Raw 1D Bruker spectral data files were found in the MetaboLights database (https://www.ebi.ac.uk/metabolights/, study MTBLS1).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-asicsdata/post-link.sh b/recipes/bioconductor-asicsdata/post-link.sh index cacabdb1a734e..dd9379d40c350 100644 --- a/recipes/bioconductor-asicsdata/post-link.sh +++ b/recipes/bioconductor-asicsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "asicsdata-1.22.0" +installBiocDataPackage.sh "asicsdata-1.26.0" diff --git a/recipes/bioconductor-aspli/meta.yaml b/recipes/bioconductor-aspli/meta.yaml index 7b9d0fd06dfdf..6d5630645f682 100644 --- a/recipes/bioconductor-aspli/meta.yaml +++ b/recipes/bioconductor-aspli/meta.yaml @@ -1,38 +1,51 @@ -{% set version = "2.12.0" %} +{% set version = "2.16.0" %} {% set name = "ASpli" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Integrative pipeline for the analysis of alternative splicing using RNAseq. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Analysis of Alternative Splicing Using RNA-Seq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: abf86e5478e3191f21892ba2eb35e442 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-aspli", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:aspli + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-aspli + path: recipes/bioconductor-aspli + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-data.table - r-dt @@ -42,19 +55,21 @@ requirements: - r-pbmcapply - r-tidyr - r-upsetr + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-data.table - r-dt @@ -64,21 +79,16 @@ requirements: - r-pbmcapply - r-tidyr - r-upsetr + +source: + md5: 4a8a46161468892eed33896cd0be8970 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL - summary: 'Analysis of Alternative Splicing Using RNA-Seq' - description: 'Integrative pipeline for the analysis of alternative splicing using RNAseq.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:aspli - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-aspli - path: recipes/bioconductor-aspli - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-assessorf/meta.yaml b/recipes/bioconductor-assessorf/meta.yaml index b03bbb0dcf99d..5b58f435ca1e0 100644 --- a/recipes/bioconductor-assessorf/meta.yaml +++ b/recipes/bioconductor-assessorf/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "AssessORF" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b11ca260fff21c6afe98ee471d79b3ec +about: + description: In order to assess the quality of a set of predicted genes for a genome, evidence must first be mapped to that genome. Next, each gene must be categorized based on how strong the evidence is for or against that gene. The AssessORF package provides the functions and class structures necessary for accomplishing those tasks, using proteomic hits and evolutionarily conserved start codons as the forms of evidence. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Assess Gene Predictions Using Proteomics and Evolutionary Conservation build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-assessorf", max_pin="x.x") }}' - noarch: generic -# Suggests: AssessORFData, BiocStyle, knitr, rmarkdown +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: AssessORFData, BiocStyle, knitr, rmarkdown, RSQLite (>= 1.1) requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-decipher >=2.30.0,<2.31.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-decipher >=3.2.0,<3.3.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-decipher >=2.30.0,<2.31.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-decipher >=3.2.0,<3.3.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base +source: + md5: 1adeb28ba820670c4e143a4e5749f7d6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Assess Gene Predictions Using Proteomics and Evolutionary Conservation' - description: 'In order to assess the quality of a set of predicted genes for a genome, evidence must first be mapped to that genome. Next, each gene must be categorized based on how strong the evidence is for or against that gene. The AssessORF package provides the functions and class structures necessary for accomplishing those tasks, using proteomic hits and evolutionarily conserved start codons as the forms of evidence.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-asset/meta.yaml b/recipes/bioconductor-asset/meta.yaml index fe7f5b9cdda56..c3853cf2ba5c8 100644 --- a/recipes/bioconductor-asset/meta.yaml +++ b/recipes/bioconductor-asset/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "2.20.0" %} +{% set version = "2.24.0" %} {% set name = "ASSET" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 395bcc1b0256acc248c5d3440bf5dfeb +about: + description: An R package for subset-based analysis of heterogeneous traits and disease subtypes. The package allows the user to search through all possible subsets of z-scores to identify the subset of traits giving the best meta-analyzed z-score. Further, it returns a p-value adjusting for the multiple-testing involved in the search. It also allows for searching for the best combination of disease subtypes associated with each variant. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + file LICENSE + license_file: LICENSE + summary: An R package for subset-based association analysis of heterogeneous traits and subtypes build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-asset", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: RUnit, BiocGenerics, knitr requirements: host: @@ -31,13 +30,14 @@ requirements: - r-mass - r-msm - r-rmeta +source: + md5: 88f9ff419ff944d16089a40d67dc6be5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-2 + file LICENSE' - summary: 'An R package for subset-based association analysis of heterogeneous traits and subtypes' - description: 'An R package for subset-based analysis of heterogeneous traits and disease subtypes. The package allows the user to search through all possible subsets of z-scores to identify the subset of traits giving the best meta-analyzed z-score. Further, it returns a p-value adjusting for the multiple-testing involved in the search. It also allows for searching for the best combination of disease subtypes associated with each variant.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-assign/meta.yaml b/recipes/bioconductor-assign/meta.yaml index ce78d053d88c9..90ce8e3bc5ed8 100644 --- a/recipes/bioconductor-assign/meta.yaml +++ b/recipes/bioconductor-assign/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "ASSIGN" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ASSIGN is a computational tool to evaluate the pathway deregulation/activation status in individual patient samples. ASSIGN employs a flexible Bayesian factor analysis approach that adapts predetermined pathway signatures derived either from knowledge-based literature or from perturbation experiments to the cell-/tissue-specific pathway signatures. The deregulation/activation level of each context-specific pathway is quantified to a score, which represents the extent to which a patient sample encompasses the pathway deregulation/activation signature. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Adaptive Signature Selection and InteGratioN (ASSIGN) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c03c8eedec6379aa0fac65d11377fdf8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-assign", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, lintr, knitr, rmarkdown requirements: host: - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-ggplot2 - r-gplots @@ -30,20 +32,23 @@ requirements: - r-rlab - r-yaml run: - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-ggplot2 - r-gplots - r-msm - r-rlab - r-yaml + +source: + md5: de3418c360df75b32474cdc6815a3a88 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Adaptive Signature Selection and InteGratioN (ASSIGN)' - description: 'ASSIGN is a computational tool to evaluate the pathway deregulation/activation status in individual patient samples. ASSIGN employs a flexible Bayesian factor analysis approach that adapts predetermined pathway signatures derived either from knowledge-based literature or from perturbation experiments to the cell-/tissue-specific pathway signatures. The deregulation/activation level of each context-specific pathway is quantified to a score, which represents the extent to which a patient sample encompasses the pathway deregulation/activation signature.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-assorthead/build.sh b/recipes/bioconductor-assorthead/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-assorthead/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-assorthead/meta.yaml b/recipes/bioconductor-assorthead/meta.yaml new file mode 100644 index 0000000000000..2cd6ed5b58e38 --- /dev/null +++ b/recipes/bioconductor-assorthead/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.0.0" %} +{% set name = "assorthead" %} +{% set bioc = "3.20" %} + +about: + description: Vendors an assortment of useful header-only C++ libraries. Bioconductor packages can use these libraries in their own C++ code by LinkingTo this package without introducing any additional dependencies. The use of a central repository avoids duplicate vendoring of libraries across multiple R packages, and enables better coordination of version updates across cohorts of interdependent C++ libraries. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Assorted Header-Only C++ Libraries +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-assorthead", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: knitr, rmarkdown, BiocStyle +requirements: + host: + - r-base + run: + - r-base +source: + md5: 35eb53af6a3e3ba00798ad551c1d0800 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-asurat/meta.yaml b/recipes/bioconductor-asurat/meta.yaml index 79307284cafc7..0ea7f686d6642 100644 --- a/recipes/bioconductor-asurat/meta.yaml +++ b/recipes/bioconductor-asurat/meta.yaml @@ -1,58 +1,63 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "ASURAT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity. Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign-by-sample matrices (SSMs). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Functional annotation-driven unsupervised clustering for single-cell data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a1cb615f6ddab8cb8b9ccb1a73ba39de build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-asurat", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi, BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat (>= 3.0.0) requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-cluster - r-plot3d - - 'r-rcpp >=1.0.7' + - r-rcpp >=1.0.7 - libblas - liblapack run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-cluster - r-plot3d - - 'r-rcpp >=1.0.7' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=1.0.7 + +source: + md5: 982b35bc493bed92ff26988b1bd9224e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Functional annotation-driven unsupervised clustering for single-cell data' - description: 'ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity. Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign-by-sample matrices (SSMs).' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-atacseqqc/meta.yaml b/recipes/bioconductor-atacseqqc/meta.yaml index 46ba87f49caf2..5ba6c48f6e17c 100644 --- a/recipes/bioconductor-atacseqqc/meta.yaml +++ b/recipes/bioconductor-atacseqqc/meta.yaml @@ -1,78 +1,88 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "ATACseqQC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. Comparing to the other methods, ATAC-seq requires less amount of the biological samples and time to process. In the process of analyzing several ATAC-seq dataset produced in our labs, we learned some of the unique aspects of the quality assessment for ATAC-seq data.To help users to quickly assess whether their ATAC-seq experiment is successful, we developed ATACseqQC package partially following the guideline published in Nature Method 2013 (Greenleaf et al.), including diagnostic plot of fragment size distribution, proportion of mitochondria reads, nucleosome positioning pattern, and CTCF or other Transcript Factor footprints. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: ATAC-seq Quality Control -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6742da3bbb4073be7aa5f2544b65df23 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-atacseqqc", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-atacseqqc + path: recipes/bioconductor-atacseqqc + version: 1.4.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat, rmarkdown requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-motifstack >=1.46.0,<1.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-chippeakanno >=3.40.0,<3.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-motifstack >=1.50.0,<1.51.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-kernsmooth - r-preseqr - r-randomforest + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-motifstack >=1.46.0,<1.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-chippeakanno >=3.40.0,<3.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-motifstack >=1.50.0,<1.51.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-kernsmooth - r-preseqr - r-randomforest + +source: + md5: 3396042fcbd4c5e18725c1e9c33c0199 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'ATAC-seq Quality Control' - description: 'ATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. Comparing to the other methods, ATAC-seq requires less amount of the biological samples and time to process. In the process of analyzing several ATAC-seq dataset produced in our labs, we learned some of the unique aspects of the quality assessment for ATAC-seq data.To help users to quickly assess whether their ATAC-seq experiment is successful, we developed ATACseqQC package partially following the guideline published in Nature Method 2013 (Greenleaf et al.), including diagnostic plot of fragment size distribution, proportion of mitochondria reads, nucleosome positioning pattern, and CTCF or other Transcript Factor footprints.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-atacseqqc - path: recipes/bioconductor-atacseqqc - version: 1.4.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-atacseqtfea/meta.yaml b/recipes/bioconductor-atacseqtfea/meta.yaml index e11f613d103a9..2c53da486ed31 100644 --- a/recipes/bioconductor-atacseqtfea/meta.yaml +++ b/recipes/bioconductor-atacseqtfea/meta.yaml @@ -1,38 +1,41 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "ATACseqTFEA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Assay for Transpose-Accessible Chromatin using sequencing (ATAC-seq) is a technique to assess genome-wide chromatin accessibility by probing open chromatin with hyperactive mutant Tn5 Transposase that inserts sequencing adapters into open regions of the genome. ATACseqTFEA is an improvement of the current computational method that detects differential activity of transcription factors (TFs). ATACseqTFEA not only uses the difference of open region information, but also (or emphasizes) the difference of TFs footprints (cutting sites or insertion sites). ATACseqTFEA provides an easy, rigorous way to broadly assess TF activity changes between two conditions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Transcription Factor Enrichment Analysis for ATAC-seq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 30284cc31687d97f23d2a7c023e8561d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-atacseqtfea", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Drerio.UCSC.danRer10, knitr, testthat, ATACseqQC, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-motifmatchr >=1.28.0,<1.29.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tfbstools >=1.44.0,<1.45.0 - r-base - r-dplyr - r-ggplot2 @@ -40,30 +43,34 @@ requirements: - r-matrix - r-pracma run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-motifmatchr >=1.28.0,<1.29.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tfbstools >=1.44.0,<1.45.0 - r-base - r-dplyr - r-ggplot2 - r-ggrepel - r-matrix - r-pracma + +source: + md5: ddd2599383dc600b5a673bbf4b6b9ba5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Transcription Factor Enrichment Analysis for ATAC-seq' - description: 'Assay for Transpose-Accessible Chromatin using sequencing (ATAC-seq) is a technique to assess genome-wide chromatin accessibility by probing open chromatin with hyperactive mutant Tn5 Transposase that inserts sequencing adapters into open regions of the genome. ATACseqTFEA is an improvement of the current computational method that detects differential activity of transcription factors (TFs). ATACseqTFEA not only uses the difference of open region information, but also (or emphasizes) the difference of TFs footprints (cutting sites or insertion sites). ATACseqTFEA provides an easy, rigorous way to broadly assess TF activity changes between two conditions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-atena/meta.yaml b/recipes/bioconductor-atena/meta.yaml index f34d851d4bc20..163aeb091cd81 100644 --- a/recipes/bioconductor-atena/meta.yaml +++ b/recipes/bioconductor-atena/meta.yaml @@ -1,64 +1,75 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "atena" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Quantify expression of transposable elements (TEs) from RNA-seq data through different methods, including ERVmap, TEtranscripts and Telescope. A common interface is provided to use each of these methods, which consists of building a parameter object, calling the quantification function with this object and getting a SummarizedExperiment object as output container of the quantified expression profiles. The implementation allows one to quantify TEs and gene transcripts in an integrated manner. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Analysis of Transposable Elements -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c7ae11b12240ed1d848301b4c40b019e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-atena", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: covr, BiocStyle, knitr, rmarkdown, RUnit, TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + - r-cli - r-matrix - r-matrixstats - r-squarem run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + - r-cli - r-matrix - r-matrixstats - r-squarem + +source: + md5: 57c4c4a007244cf697982945cf46e75b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Analysis of Transposable Elements' - description: 'Quantify expression of transposable elements (TEs) from RNA-seq data through different methods, including ERVmap, TEtranscripts and Telescope. A common interface is provided to use each of these methods, which consists of building a parameter object, calling the quantification function with this object and getting a SummarizedExperiment object as output container of the quantified expression profiles. The implementation allows one to quantify TEs and gene transcripts in an integrated manner.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ath1121501.db/meta.yaml b/recipes/bioconductor-ath1121501.db/meta.yaml index ad07150ccead6..f1bab6f222acc 100644 --- a/recipes/bioconductor-ath1121501.db/meta.yaml +++ b/recipes/bioconductor-ath1121501.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "ath1121501.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c5d937ca9c6bcbb4385fb37a3b14ad15 +about: + description: Affymetrix Affymetrix ATH1-121501 Array annotation data (chip ath1121501) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix ATH1-121501 Array annotation data (chip ath1121501) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ath1121501.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.at.tair.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.at.tair.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.at.tair.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.at.tair.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c5d937ca9c6bcbb4385fb37a3b14ad15 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix ATH1-121501 Array annotation data (chip ath1121501)' - description: 'Affymetrix Affymetrix ATH1-121501 Array annotation data (chip ath1121501) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ath1121501cdf/meta.yaml b/recipes/bioconductor-ath1121501cdf/meta.yaml index 24a018cde9f47..b7956c12aed86 100644 --- a/recipes/bioconductor-ath1121501cdf/meta.yaml +++ b/recipes/bioconductor-ath1121501cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "ath1121501cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8b63798143219b7c1c2666a91a1a2440 +about: + description: A package containing an environment representing the ATH1-121501.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: ath1121501cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ath1121501cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8b63798143219b7c1c2666a91a1a2440 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: ath1121501cdf - description: 'A package containing an environment representing the ATH1-121501.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ath1121501frmavecs/meta.yaml b/recipes/bioconductor-ath1121501frmavecs/meta.yaml new file mode 100644 index 0000000000000..c1b68fe3770cb --- /dev/null +++ b/recipes/bioconductor-ath1121501frmavecs/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.0" %} +{% set name = "ath1121501frmavecs" %} +{% set bioc = "3.20" %} + +about: + description: Annotation package for the implementation of the frozen Robust Multiarray Analysis procedure for Arabidopsis thaliana. This package was generated on the basis of frmaTools version 1.52.0. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Vectors used by frma for microarrays of type ath1121501 +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ath1121501frmavecs", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: frma, GEOquery, affy, ath1121501.db, BiocStyle, knitr, rmarkdown +requirements: + host: + - r-base + run: + - r-base + - curl + - bioconductor-data-packages >=20241103 +source: + md5: e77c631160730a18037caf3f656e82c5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-ath1121501frmavecs/post-link.sh b/recipes/bioconductor-ath1121501frmavecs/post-link.sh new file mode 100644 index 0000000000000..2bdbad1aeac4d --- /dev/null +++ b/recipes/bioconductor-ath1121501frmavecs/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "ath1121501frmavecs-1.0.0" diff --git a/recipes/bioconductor-ath1121501frmavecs/pre-unlink.sh b/recipes/bioconductor-ath1121501frmavecs/pre-unlink.sh new file mode 100644 index 0000000000000..6ae65e60e2875 --- /dev/null +++ b/recipes/bioconductor-ath1121501frmavecs/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ath1121501frmavecs diff --git a/recipes/bioconductor-ath1121501probe/meta.yaml b/recipes/bioconductor-ath1121501probe/meta.yaml index b5f881e5be459..7b54a4bb572fb 100644 --- a/recipes/bioconductor-ath1121501probe/meta.yaml +++ b/recipes/bioconductor-ath1121501probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "ath1121501probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eeeae5e6550bb472ba3419d71bbd7dfb +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was ATH1-121501\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type ath1121501 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ath1121501probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: eeeae5e6550bb472ba3419d71bbd7dfb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type ath1121501' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was ATH1-121501\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-atsnp/meta.yaml b/recipes/bioconductor-atsnp/meta.yaml index 22b2497f49120..fd354818cdea5 100644 --- a/recipes/bioconductor-atsnp/meta.yaml +++ b/recipes/bioconductor-atsnp/meta.yaml @@ -1,30 +1,36 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "atSNP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: atSNP performs affinity tests of motif matches with the SNP or the reference genomes and SNP-led changes in motif matches. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Affinity test for identifying regulatory SNPs -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e7de15cd417026f8449b14841ff89bd2 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-atsnp", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-motifstack >=1.46.0,<1.47.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-motifstack >=1.50.0,<1.51.0 - r-base - r-data.table - r-ggplot2 @@ -35,10 +41,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-motifstack >=1.46.0,<1.47.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-motifstack >=1.50.0,<1.51.0 - r-base - r-data.table - r-ggplot2 @@ -46,17 +52,16 @@ requirements: - r-rappdirs - r-rcpp - r-testthat - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: b41daf45073e69401646e56c91044e9d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Affinity test for identifying regulatory SNPs' - description: 'atSNP performs affinity tests of motif matches with the SNP or the reference genomes and SNP-led changes in motif matches.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-attract/meta.yaml b/recipes/bioconductor-attract/meta.yaml index 8bf0a00a35862..77461f91f98b4 100644 --- a/recipes/bioconductor-attract/meta.yaml +++ b/recipes/bioconductor-attract/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.54.0" %} +{% set version = "1.58.0" %} {% set name = "attract" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains the functions to find the gene expression modules that represent the drivers of Kauffman's attractor landscape. The modules are the core attractor pathways that discriminate between different cell types of groups of interest. Each pathway has a set of synexpression groups, which show transcriptionally-coordinated changes in gene expression. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2.0) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e7d563026d5d00b5dd3bd906268af221 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-attract", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: illuminaHumanv1.db requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-reactome.db >=1.89.0,<1.90.0 - r-base - r-cluster run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-reactome.db >=1.89.0,<1.90.0 - r-base - r-cluster + +source: + md5: d2537505966a09c9f55c075123193a6e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2.0)' - summary: 'Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman''s Attractor Landscape' - description: 'This package contains the functions to find the gene expression modules that represent the drivers of Kauffman''s attractor landscape. The modules are the core attractor pathways that discriminate between different cell types of groups of interest. Each pathway has a set of synexpression groups, which show transcriptionally-coordinated changes in gene expression.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-aucell/meta.yaml b/recipes/bioconductor-aucell/meta.yaml index 806723573eb1a..976dca88c1204 100644 --- a/recipes/bioconductor-aucell/meta.yaml +++ b/recipes/bioconductor-aucell/meta.yaml @@ -1,57 +1,60 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "AUCell" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: AUCell allows to identify cells with active gene sets (e.g. signatures, gene modules...) in single-cell RNA-seq data. AUCell uses the "Area Under the Curve" (AUC) to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell. The distribution of AUC scores across all the cells allows exploring the relative expression of the signature. Since the scoring method is ranking-based, AUCell is independent of the gene expression units and the normalization procedure. In addition, since the cells are evaluated individually, it can easily be applied to bigger datasets, subsetting the expression matrix if needed. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'AUCell: Analysis of ''gene set'' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d095823da2fd13bf83c831c037564ff build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-aucell", max_pin="x.x") }}' - noarch: generic -# Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, rbokeh, Rtsne, testthat, zoo + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, Rtsne, testthat, zoo requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-matrix - r-mixtools - r-r.utils - - r-shiny run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-matrix - r-mixtools - r-r.utils - - r-shiny + +source: + md5: b9c51a392e6fc3b41974a49ed01d1568 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'AUCell: Analysis of ''gene set'' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)' - description: 'AUCell allows to identify cells with active gene sets (e.g. signatures, gene modules...) in single-cell RNA-seq data. AUCell uses the "Area Under the Curve" (AUC) to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell. The distribution of AUC scores across all the cells allows exploring the relative expression of the signature. Since the scoring method is ranking-based, AUCell is independent of the gene expression units and the normalization procedure. In addition, since the cells are evaluated individually, it can easily be applied to bigger datasets, subsetting the expression matrix if needed.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-autonomics/build_failure.linux-64.yaml b/recipes/bioconductor-autonomics/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..9636b54076df1 --- /dev/null +++ b/recipes/bioconductor-autonomics/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c91b70831e85c98a5321ad7e8d3d646ca5fd009272af83531a1851eb3b9d9107 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-codingmatrices")} + Encountered problems while solving: + - nothing provides requested r-codingmatrices + + Could not solve for environment specs + The following package could not be installed + [31mr-codingmatrices[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-codingmatrices")} + Encountered problems while solving: + - nothing provides requested r-codingmatrices + + Could not solve for environment specs + The following package could not be installed + [31mr-codingmatrices[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-codingmatrices")} + Encountered problems while solving: + - nothing provides requested r-codingmatrices + + Could not solve for environment specs + The following package could not be installed + [31mr-codingmatrices[0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-autonomics/meta.yaml b/recipes/bioconductor-autonomics/meta.yaml index 506a4b040c9ad..c96a45b5226cd 100644 --- a/recipes/bioconductor-autonomics/meta.yaml +++ b/recipes/bioconductor-autonomics/meta.yaml @@ -1,95 +1,102 @@ -{% set version = "1.10.2" %} +{% set version = "1.14.0" %} {% set name = "autonomics" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package unifies access to Statistal Modeling of Omics Data. Across linear modeling engines (lm, lme, lmer, limma, and wilcoxon). Across coding systems (treatment, difference, deviation, etc). Across model formulae (with/without intercept, random effect, interaction or nesting). Across omics platforms (microarray, rnaseq, msproteomics, affinity proteomics, metabolomics). Across projection methods (pca, pls, sma, lda, spls, opls). Across clustering methods (hclust, pam, cmeans). It provides a fast enrichment analysis implementation. And an intuitive contrastogram visualisation to summarize contrast effects in complex designs. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Unified statistal Modeling of Omics Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9034c755764d54d8bf0eb0e330f4e54f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-autonomics", max_pin="x.x") }}' - noarch: generic -# Suggests: affy, AnnotationDbi, BiocManager, BiocStyle, diagram, GenomicRanges, GEOquery, hgu95av2.db, ICSNP, knitr, lme4, lmerTest, MASS, mixOmics, mpm, nlme, org.Hs.eg.db, org.Mm.eg.db, RCurl, remotes, rmarkdown, ropls, Rsubread, rtracklayer, seqinr, statmod, testthat + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: affy, AnnotationDbi, AnnotationHub, apcluster, Biobase, BiocManager, BiocStyle, Biostrings, diagram, DBI, e1071, ensembldb, GenomicDataCommons, GenomicRanges, GEOquery, hgu95av2.db, ICSNP, jsonlite, knitr, lme4, lmerTest, MASS, patchwork, mixOmics, mpm, nlme, OlinkAnalyze, org.Hs.eg.db, org.Mm.eg.db, pcaMethods, pheatmap, progeny, propagate, RCurl, RSQLite, remotes, rmarkdown, ropls, Rsubread, readODS, rtracklayer, statmod, survival, survminer, testthat, UniProt.ws, writexl, XML requirements: + host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-abind - - r-assertive.base - - r-assertive.files - - r-assertive.numbers - - r-assertive.sets - r-base - r-bit64 + - r-cluster + - r-codingmatrices - r-colorspace - r-data.table - r-dplyr + - r-ggforce - r-ggplot2 - r-ggrepel - r-gridextra - r-magrittr - r-matrixstats - r-r.utils - - r-rappdirs + - r-rcolorbrewer - r-readxl - r-rlang - r-scales - r-stringi - r-tidyr + - r-tidyselect + run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-abind - - r-assertive.base - - r-assertive.files - - r-assertive.numbers - - r-assertive.sets - r-base - r-bit64 + - r-cluster + - r-codingmatrices - r-colorspace - r-data.table - r-dplyr + - r-ggforce - r-ggplot2 - r-ggrepel - r-gridextra - r-magrittr - r-matrixstats - r-r.utils - - r-rappdirs + - r-rcolorbrewer - r-readxl - r-rlang - r-scales - r-stringi - r-tidyr + - r-tidyselect + +source: + md5: e0bcbda4df1a046e40aaf140d53d8ab7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Generifying and intuifying cross-platform omics analysis' - description: 'This package offers a generic and intuitive solution for cross-platform omics data analysis. It has functions for import, preprocessing, exploration, contrast analysis and visualization of omics data. It follows a tidy, functional programming paradigm.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-awfisher/meta.yaml b/recipes/bioconductor-awfisher/meta.yaml index cc019247c8442..795a97486be99 100644 --- a/recipes/bioconductor-awfisher/meta.yaml +++ b/recipes/bioconductor-awfisher/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "AWFisher" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implementation of the adaptively weighted fisher's method, including fast p-value computing, variability index, and meta-pattern. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: An R package for fast computing for adaptively weighted fisher's method -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ba9b2824782018cc7626ebc72b6bb81e build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-awfisher", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, tightClust requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - libblas - liblapack run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: c7f62af9f37de3f5a7e29e53b93d2f04 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'An R package for fast computing for adaptively weighted fisher''s method' - description: 'Implementation of the adaptively weighted fisher''s method, including fast p-value computing, variability index, and meta-pattern.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-awst/meta.yaml b/recipes/bioconductor-awst/meta.yaml index c735340e61235..8841640994ee2 100644 --- a/recipes/bioconductor-awst/meta.yaml +++ b/recipes/bioconductor-awst/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "awst" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a7ca0636a8f728b63d6cf56729b856eb +about: + description: 'We propose an Asymmetric Within-Sample Transformation (AWST) to regularize RNA-seq read counts and reduce the effect of noise on the classification of samples. AWST comprises two main steps: standardization and smoothing. These steps transform gene expression data to reduce the noise of the lowly expressed features, which suffer from background effects and low signal-to-noise ratio, and the influence of the highly expressed features, which may be the result of amplification bias and other experimental artifacts.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Asymmetric Within-Sample Transformation build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-awst", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: airway, ggplot2, testthat, EDASeq, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base +source: + md5: 7a099402976fd103a22969c4cb2c6895 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Asymmetric Within-Sample Transformation' - description: 'We propose an Asymmetric Within-Sample Transformation (AWST) to regularize RNA-seq read counts and reduce the effect of noise on the classification of samples. AWST comprises two main steps: standardization and smoothing. These steps transform gene expression data to reduce the noise of the lowly expressed features, which suffer from background effects and low signal-to-noise ratio, and the influence of the highly expressed features, which may be the result of amplification bias and other experimental artifacts.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-baalchip/meta.yaml b/recipes/bioconductor-baalchip/meta.yaml index 4596a55c8a87c..135fd21a71912 100644 --- a/recipes/bioconductor-baalchip/meta.yaml +++ b/recipes/bioconductor-baalchip/meta.yaml @@ -1,32 +1,42 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "BaalChIP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package offers functions to process multiple ChIP-seq BAM files and detect allele-specific events. Computes allele counts at individual variants (SNPs/SNVs), implements extensive QC steps to remove problematic variants, and utilizes a bayesian framework to identify statistically significant allele- specific events. BaalChIP is able to account for copy number differences between the two alleles, a known phenotypical feature of cancer samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f2cf6dd86b26982d4d7ed693f961246 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-baalchip", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:baalchip + - doi:10.1186/s13059-017-1165-7 + parent_recipe: + name: bioconductor-baalchip + path: recipes/bioconductor-baalchip + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-coda - r-doby @@ -36,11 +46,11 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-coda - r-doby @@ -49,20 +59,16 @@ requirements: - r-ggplot2 - r-reshape2 - r-scales + +source: + md5: 40ecb0da98e64425999851a52ea9a915 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes' - description: 'The package offers functions to process multiple ChIP-seq BAM files and detect allele-specific events. Computes allele counts at individual variants (SNPs/SNVs), implements extensive QC steps to remove problematic variants, and utilizes a bayesian framework to identify statistically significant allele- specific events. BaalChIP is able to account for copy number differences between the two alleles, a known phenotypical feature of cancer samples.' -extra: - identifiers: - - biotools:baalchip - - doi:10.1186/s13059-017-1165-7 - parent_recipe: - name: bioconductor-baalchip - path: recipes/bioconductor-baalchip - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bacon/meta.yaml b/recipes/bioconductor-bacon/meta.yaml index 350eb69311bf0..73371ffbddf17 100644 --- a/recipes/bioconductor-bacon/meta.yaml +++ b/recipes/bioconductor-bacon/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "bacon" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Bacon can be used to remove inflation and bias often observed in epigenome- and transcriptome-wide association studies. To this end bacon constructs an empirical null distribution using a Gibbs Sampling algorithm by fitting a three-component normal mixture on z-scores. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Controlling bias and inflation in association studies using the empirical null distribution -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3757e896d5a8253845a21e37e555044a build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bacon", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:bacon + parent_recipe: + name: bioconductor-bacon + path: recipes/bioconductor-bacon + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, roxygen2 requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-ellipse - r-ggplot2 - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-ellipse - r-ggplot2 - build: - - {{ compiler('c') }} - - make + +source: + md5: 76ba7c4a2a1d8c6517abf620dd859282 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Controlling bias and inflation in association studies using the empirical null distribution' - description: 'Bacon can be used to remove inflation and bias often observed in epigenome- and transcriptome-wide association studies. To this end bacon constructs an empirical null distribution using a Gibbs Sampling algorithm by fitting a three-component normal mixture on z-scores.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:bacon - parent_recipe: - name: bioconductor-bacon - path: recipes/bioconductor-bacon - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bader/meta.yaml b/recipes/bioconductor-bader/meta.yaml index 346caafa84021..3a988e9f9c425 100644 --- a/recipes/bioconductor-bader/meta.yaml +++ b/recipes/bioconductor-bader/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "BADER" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: For RNA sequencing count data, BADER fits a Bayesian hierarchical model. The algorithm returns the posterior probability of differential expression for each gene between two groups A and B. The joint posterior distribution of the variables in the model can be returned in the form of posterior samples, which can be used for further down-stream analyses such as gene set enrichment. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Bayesian Analysis of Differential Expression in RNA Sequencing Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 10d4e5e231ff178df7922078024f9d89 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bader", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:bader + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-bader + path: recipes/bioconductor-bader + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: pasilla (>= 0.2.10) requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: c36f487fbf82133999f70537d6627ae4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Bayesian Analysis of Differential Expression in RNA Sequencing Data' - description: 'For RNA sequencing count data, BADER fits a Bayesian hierarchical model. The algorithm returns the posterior probability of differential expression for each gene between two groups A and B. The joint posterior distribution of the variables in the model can be returned in the form of posterior samples, which can be used for further down-stream analyses such as gene set enrichment.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:bader - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-bader - path: recipes/bioconductor-bader - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-badregionfinder/meta.yaml b/recipes/bioconductor-badregionfinder/meta.yaml index 18612ea8cae65..4ef2f3b267fa7 100644 --- a/recipes/bioconductor-badregionfinder/meta.yaml +++ b/recipes/bioconductor-badregionfinder/meta.yaml @@ -1,49 +1,22 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "BadRegionFinder" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: BadRegionFinder is a package for identifying regions with a bad, acceptable and good coverage in sequence alignment data available as bam files. The whole genome may be considered as well as a set of target regions. Various visual and textual types of output are available. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: 'BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c492af1d6b1297cd322a79355e3d3664 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-badregionfinder", max_pin="x.x") }}' - noarch: generic -# Suggests: BSgenome.Hsapiens.UCSC.hg19 -requirements: - host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - - r-base - run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage' - description: 'BadRegionFinder is a package for identifying regions with a bad, acceptable and good coverage in sequence alignment data available as bam files. The whole genome may be considered as well as a set of target regions. Various visual and textual types of output are available.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + extra: identifiers: - biotools:badregionfinder @@ -53,3 +26,36 @@ extra: path: recipes/bioconductor-badregionfinder version: 1.8.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BSgenome.Hsapiens.UCSC.hg19 +requirements: + host: + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - r-base + run: + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - r-base + +source: + md5: c6ef5317cc7794b619ec51a602e8dca3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-bags/meta.yaml b/recipes/bioconductor-bags/meta.yaml index 9aa67ffe4f606..5b3487cf96b15 100644 --- a/recipes/bioconductor-bags/meta.yaml +++ b/recipes/bioconductor-bags/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "2.42.0" %} +{% set version = "2.46.0" %} {% set name = "BAGS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 42c7a57422ddbb5c2d5263703a7e22d0 +about: + description: R package providing functions to perform geneset significance analysis over simple cross-sectional data between 2 and 5 phenotypes of interest. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: A Bayesian Approach for Geneset Selection build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bags", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-breastcancervdx >=1.40.0,<1.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-breastcancervdx >=1.44.0,<1.45.0 - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-breastcancervdx >=1.40.0,<1.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-breastcancervdx >=1.44.0,<1.45.0 - r-base - build: - - {{ compiler('c') }} - - make +source: + md5: 738eda14cf8c51b1f968e287529b0721 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A Bayesian Approach for Geneset Selection' - description: 'R package providing functions to perform geneset significance analysis over simple cross-sectional data between 2 and 5 phenotypes of interest.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ballgown/meta.yaml b/recipes/bioconductor-ballgown/meta.yaml index a9d3e0017fa92..0e284c0133d4f 100644 --- a/recipes/bioconductor-ballgown/meta.yaml +++ b/recipes/bioconductor-ballgown/meta.yaml @@ -1,62 +1,68 @@ -{% set version = "2.34.0" %} +{% set version = "2.38.0" %} {% set name = "ballgown" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Flexible, isoform-level differential expression analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 805a1514b4080a8b00b4bdfce051dcda build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ballgown", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:ballgown + - doi:10.1038/nbt.3172 + parent_recipe: + name: bioconductor-ballgown + path: recipes/bioconductor-ballgown + version: 2.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, markdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-rcolorbrewer + +source: + md5: 761ad5b9df7c3ee5c702f2826c2ba9ea + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Flexible, isoform-level differential expression analysis' - description: 'Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation.' -extra: - identifiers: - - biotools:ballgown - - doi:10.1038/nbt.3172 - parent_recipe: - name: bioconductor-ballgown - path: recipes/bioconductor-ballgown - version: 2.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bambu/build_failure.linux-64.yaml b/recipes/bioconductor-bambu/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..c71ce58b0a72a --- /dev/null +++ b/recipes/bioconductor-bambu/build_failure.linux-64.yaml @@ -0,0 +1,105 @@ +recipe_sha: 25f4f0770f51650bc526f22676f81e1b8c3bac4792877b28af96c180776ca247 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [32mbioconductor-summarizedexperiment >=1.36.0,<1.37.0 [0m is installable and it requires + [32mbioconductor-delayedarray >=0.32.0,<0.33.0 [0m, which requires + [32mbioconductor-sparsearray >=1.6.0,<1.7.0 [0m, which requires + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [31mr-xgboost[0m is not installable because there are no viable options + [31mr-xgboost 0.80[0m would require + [31mmro-base >=3.5.0,<3.5.1.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-xgboost [0.80|0.81|0.82|0.90|1.0.2][0m would require + [31mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [0.82|0.90|...|1.4.0][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.0.2|1.1.1|...|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.4.0|1.4.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-xgboost==0.80=mro350h255eb88_1"), MatchSpec(">=3.5.0,<3.5.1.0a0")} + Encountered problems while solving: + - nothing provides mro-base >=3.5.0,<3.5.1.0a0 needed by r-xgboost-0.80-mro350h255eb88_1 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-summarizedexperiment >=1.36.0,<1.37.0 [0m is installable and it requires + [32mbioconductor-delayedarray >=0.32.0,<0.33.0 [0m, which requires + [32mbioconductor-sparsearray >=1.6.0,<1.7.0 [0m, which requires + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [31mr-xgboost[0m is not installable because there are no viable options + [31mr-xgboost 0.80[0m would require + [31mmro-base >=3.5.0,<3.5.1.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-xgboost [0.80|0.81|0.82|0.90|1.0.2][0m would require + [31mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [0.82|0.90|...|1.4.0][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.0.2|1.1.1|...|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.4.0|1.4.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. +reason: waiting for r-xgboost R 4.4 migration on conda-forge https://github.com/conda-forge/xgboost-feedstock/pull/196 diff --git a/recipes/bioconductor-bambu/build_failure.linux-aarch64.yaml b/recipes/bioconductor-bambu/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..e94676babe1ac --- /dev/null +++ b/recipes/bioconductor-bambu/build_failure.linux-aarch64.yaml @@ -0,0 +1,105 @@ +recipe_sha: 25f4f0770f51650bc526f22676f81e1b8c3bac4792877b28af96c180776ca247 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - nothing provides __cuda needed by r-xgboost-1.7.4-cuda112_r41hb1b98f1_1 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-bsgenome >=1.74.0,<1.75.0 [0m is installable and it requires + [32mbioconductor-rtracklayer >=1.66.0,<1.67.0 [0m, which requires + [32mr-restfulr >=0.0.13 [0m with the potential options + [32mr-restfulr 0.0.15[0m would require + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [32mr-restfulr 0.0.15[0m would require + [32mbioconductor-s4vectors >=0.40.2,<0.41.0a0 [0m, which can be installed; + [31mbioconductor-s4vectors >=0.44.0,<0.45.0 [0m is not installable because it conflicts with any installable versions previously reported; + [31mr-xgboost[0m is not installable because there are no viable options + [31mr-xgboost [1.5.1|1.6.1|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec("r-xgboost==1.7.4=cuda112_r41hb1b98f1_1"), MatchSpec("__cuda")} + Encountered problems while solving: + - nothing provides __cuda needed by r-xgboost-1.7.4-cuda112_r41hb1b98f1_1 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-bsgenome >=1.74.0,<1.75.0 [0m is installable and it requires + [32mbioconductor-rtracklayer >=1.66.0,<1.67.0 [0m, which requires + [32mr-restfulr >=0.0.13 [0m with the potential options + [32mr-restfulr 0.0.15[0m would require + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [32mr-restfulr 0.0.15[0m would require + [32mbioconductor-s4vectors >=0.40.2,<0.41.0a0 [0m, which can be installed; + [31mbioconductor-s4vectors >=0.44.0,<0.45.0 [0m is not installable because it conflicts with any installable versions previously reported; + [31mr-xgboost[0m is not installable because there are no viable options + [31mr-xgboost [1.5.1|1.6.1|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system. +# Last 100 lines of the build log. +category: dependency issue diff --git a/recipes/bioconductor-bambu/build_failure.osx-64.yaml b/recipes/bioconductor-bambu/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..027a012731a40 --- /dev/null +++ b/recipes/bioconductor-bambu/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 25f4f0770f51650bc526f22676f81e1b8c3bac4792877b28af96c180776ca247 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1 conflicts with any installable versions previously reported; + r-xgboost [0.82|0.90|...|1.4.0] would require + r-base >=3.6,<3.7.0a0 but there are no viable options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3] conflicts with any installable versions previously reported; + r-xgboost [1.0.2|1.1.1|...|1.6.2] would require + r-base >=4.0,<4.1.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.4.0|1.4.1|...|1.7.4] would require + r-base >=4.1,<4.2.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.6.2|1.7.0|...|2.0.3] would require + r-base >=4.2,<4.3.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.7.4|1.7.6|...|2.1.3] would require + r-base >=4.3,<4.4.0a0 , which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("4.0.1==hcfea43d_1"), MatchSpec("clang==4.0.1=1")} + Encountered problems while solving: + - nothing provides compiler-rt 4.0.1 hcfea43d_1 needed by clang-4.0.1-1 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-summarizedexperiment >=1.36.0,<1.37.0 is installable and it requires + bioconductor-delayedarray >=0.32.0,<0.33.0 , which requires + bioconductor-sparsearray >=1.6.0,<1.7.0 , which requires + r-base >=4.4,<4.5.0a0 , which can be installed; + r-xgboost is not installable because there are no viable options + r-xgboost [0.80|0.81|0.82|0.90|1.0.2] would require + r-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ] but there are no viable options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1 conflicts with any installable versions previously reported; + r-xgboost [0.82|0.90|...|1.4.0] would require + r-base >=3.6,<3.7.0a0 but there are no viable options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3] conflicts with any installable versions previously reported; + r-xgboost [1.0.2|1.1.1|...|1.6.2] would require + r-base >=4.0,<4.1.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.4.0|1.4.1|...|1.7.4] would require + r-base >=4.1,<4.2.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.6.2|1.7.0|...|2.0.3] would require + r-base >=4.2,<4.3.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.7.4|1.7.6|...|2.1.3] would require + r-base >=4.3,<4.4.0a0 , which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-bambu/meta.yaml b/recipes/bioconductor-bambu/meta.yaml index 9eb6587182a64..889d80819e95b 100644 --- a/recipes/bioconductor-bambu/meta.yaml +++ b/recipes/bioconductor-bambu/meta.yaml @@ -1,37 +1,45 @@ -{% set version = "3.4.0" %} +{% set version = "3.8.0" %} {% set name = "bambu" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis such as differential gene expression or transcript usage. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Context-Aware Transcript Quantification from Long Read RNA-Seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 900e0e67c251f12989154113c54d2b32 build: number: 1 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bambu", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationDbi, Biostrings, rmarkdown, BiocFileCache, ggplot2, ComplexHeatmap, circlize, ggbio, gridExtra, knitr, testthat, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3), DESeq2, NanoporeRNASeq, purrr, apeglm, utils, DEXSeq requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-dplyr @@ -41,18 +49,19 @@ requirements: - r-xgboost - libblas - liblapack + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-dplyr @@ -60,19 +69,18 @@ requirements: - r-rcpparmadillo - r-tidyr - r-xgboost - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 91905c0b974b39b990bf3fe3c42c0937 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Context-Aware Transcript Quantification from Long Read RNA-Seq data' - description: 'bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis such as differential gene expression or transcript usage.' - license_file: LICENSE + - $R -e "library('{{ name }}')" extra: additional-platforms: diff --git a/recipes/bioconductor-bamsignals/meta.yaml b/recipes/bioconductor-bamsignals/meta.yaml index aa4d6567aedc3..d071c2f48c075 100644 --- a/recipes/bioconductor-bamsignals/meta.yaml +++ b/recipes/bioconductor-bamsignals/meta.yaml @@ -1,65 +1,73 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "bamsignals" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Extract read count signals from bam files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e7b42351aa9651bdf7d429a6377143f5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bamsignals", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:bamsignals + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-bamsignals + path: recipes/bioconductor-bamsignals + version: 1.12.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - - 'r-rcpp >=0.10.6' + - r-rcpp >=0.10.6 - libblas - liblapack + - zlib + - liblzma-devel run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - - 'r-rcpp >=0.10.6' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=0.10.6 + +source: + md5: 5a5aa95943909f70466d770764923ba8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2.0-only - summary: 'Extract read count signals from bam files' - description: 'This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:bamsignals - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-bamsignals - path: recipes/bioconductor-bamsignals - version: 1.12.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bandits/meta.yaml b/recipes/bioconductor-bandits/meta.yaml index 7ad9f0390a7b8..1e77360ec3339 100644 --- a/recipes/bioconductor-bandits/meta.yaml +++ b/recipes/bioconductor-bandits/meta.yaml @@ -1,29 +1,35 @@ -{% set version = "1.18.1" %} +{% set version = "1.22.0" %} {% set name = "BANDITS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: BANDITS is a Bayesian hierarchical model for detecting differential splicing of genes and transcripts, via differential transcript usage (DTU), between two or more conditions. The method uses a Bayesian hierarchical framework, which allows for sample specific proportions in a Dirichlet-Multinomial model, and samples the allocation of fragments to the transcripts. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques and a DTU test is performed via a multivariate Wald test on the posterior densities for the average relative abundance of transcripts. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'BANDITS: Bayesian ANalysis of DIfferenTial Splicing' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2a65b9a4669d4075f5882047445491eb build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bandits", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, tximport, BiocStyle, GenomicFeatures, Biostrings # SystemRequirements: C++17 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-drimseq >=1.30.0,<1.31.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-drimseq >=1.34.0,<1.35.0 - r-base - r-data.table - r-doparallel @@ -37,8 +43,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-drimseq >=1.30.0,<1.31.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-drimseq >=1.34.0,<1.35.0 - r-base - r-data.table - r-doparallel @@ -49,17 +55,16 @@ requirements: - r-r.utils - r-rcpp - r-rcpparmadillo - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: cf2e2efd7899760d785cd521ba2d3f1f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'BANDITS: Bayesian ANalysis of DIfferenTial Splicing' - description: 'BANDITS is a Bayesian hierarchical model for detecting differential splicing of genes and transcripts, via differential transcript usage (DTU), between two or more conditions. The method uses a Bayesian hierarchical framework, which allows for sample specific proportions in a Dirichlet-Multinomial model, and samples the allocation of fragments to the transcripts. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques and a DTU test is performed via a multivariate Wald test on the posterior densities for the average relative abundance of transcripts.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bandle/build_failure.linux-64.yaml b/recipes/bioconductor-bandle/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..90b2a1041e4a9 --- /dev/null +++ b/recipes/bioconductor-bandle/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: 1b44810561201bbd0eafb438197ac935091631d0410548b8318b9f92c9cd44af # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + | ^~~~~~~~~~~ + | enable_if + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/trunc.hpp:339:44: error: 'enable_if_t' in namespace 'boost::math' does not name a template type; did you mean 'enable_if'? + 339 | BOOST_MATH_GPU_ENABLED inline boost::math::enable_if_t, long> + | ^~~~~~~~~~~ + | enable_if + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/trunc.hpp:346:44: error: 'enable_if_t' in namespace 'boost::math' does not name a template type; did you mean 'enable_if'? + 346 | BOOST_MATH_GPU_ENABLED inline boost::math::enable_if_t, long> + | ^~~~~~~~~~~ + | enable_if + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/trunc.hpp:354:44: error: 'enable_if_t' in namespace 'boost::math' does not name a template type; did you mean 'enable_if'? + 354 | BOOST_MATH_GPU_ENABLED inline boost::math::enable_if_t, long long> + | ^~~~~~~~~~~ + | enable_if + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/trunc.hpp:361:53: error: 'enable_if_t' in namespace 'boost::math' does not name a template type; did you mean 'enable_if'? + 361 | BOOST_MATH_GPU_ENABLED inline typename boost::math::enable_if_t, long long> + | ^~~~~~~~~~~ + | enable_if + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/trunc.hpp:361:64: error: expected unqualified-id before '<' token + 361 | BOOST_MATH_GPU_ENABLED inline typename boost::math::enable_if_t, long long> + | ^ + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/trunc.hpp:369:76: error: 'enable_if_t' in namespace 'boost::math' does not name a template type; did you mean 'enable_if'? + 369 | BOOST_MATH_GPU_ENABLED [[deprecated("Use llconvert")]] inline boost::math::enable_if_t, long long> + | ^~~~~~~~~~~ + | enable_if + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/trunc.hpp:376:85: error: 'enable_if_t' in namespace 'boost::math' does not name a template type; did you mean 'enable_if'? + 376 | BOOST_MATH_GPU_ENABLED [[deprecated("Use llconvert")]] inline typename boost::math::enable_if_t, long long> + | ^~~~~~~~~~~ + | enable_if + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/trunc.hpp:376:96: error: expected unqualified-id before '<' token + 376 | BOOST_MATH_GPU_ENABLED [[deprecated("Use llconvert")]] inline typename boost::math::enable_if_t, long long> + | ^ + In file included from /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/detail/polygamma.hpp:24, + from /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/polygamma.hpp:15, + from /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/gamma.hpp:42, + from /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:16, + from /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/bessel.hpp:26: + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/pow.hpp:126:79: error: redeclaration 'constexpr typename boost::math::tools::promote_args::type boost::math::pow(T, const Policy&)' differs in 'constexpr' from previous declaration + 126 | BOOST_MATH_GPU_ENABLED constexpr inline typename tools::promote_args::type pow(T base, const Policy& policy) + | ^~~ + In file included from /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/sign.hpp:20, + from /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/tools/roots.hpp:20: + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:1173:79: note: previous declaration 'boost::math::tools::promote_args_t boost::math::pow(T, const Policy&)' + 1173 | BOOST_MATH_GPU_ENABLED BOOST_MATH_CXX14_CONSTEXPR tools::promote_args_t pow(T base, const Policy& policy); + | ^~~ + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/pow.hpp:133:79: error: redeclaration 'constexpr typename boost::math::tools::promote_args::type boost::math::pow(T)' differs in 'constexpr' from previous declaration + 133 | BOOST_MATH_GPU_ENABLED constexpr inline typename tools::promote_args::type pow(T base) + | ^~~ + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:1176:79: note: previous declaration 'boost::math::tools::promote_args_t boost::math::pow(T)' + 1176 | BOOST_MATH_GPU_ENABLED BOOST_MATH_CXX14_CONSTEXPR tools::promote_args_t pow(T base); + | ^~~ + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/tools/promotion.hpp: In instantiation of 'struct boost::math::tools::promote_args_permissive': + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/tools/promotion.hpp:119:16: required from 'struct boost::math::tools::promote_args' + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:728:16: required from 'struct boost::math::detail::bessel_traits >' + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/bessel.hpp:616:104: required by substitution of 'template typename boost::math::detail::bessel_traits >::result_type boost::math::cyl_bessel_k(T1, T2) [with T1 = double; T2 = double]' + Bessel2ndKind.cpp:16:37: required from here + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/tools/promotion.hpp:105:16: error: no type named 'type' in 'struct boost::math::tools::pa2_integral_already_removed' + 105 | using type = typename pa2_integral_already_removed< + | ^~~~ + Bessel2ndKind.cpp: In function 'double besselK_boost(double, double)': + Bessel2ndKind.cpp:16:37: error: no matching function for call to 'cyl_bessel_k(double&, double&)' + 16 | return boost::math::cyl_bessel_k(v, x); + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/bessel.hpp:600:91: note: candidate: 'template typename boost::math::detail::bessel_traits::result_type boost::math::cyl_bessel_k(T1, T2, const Policy&)' + 600 | BOOST_MATH_GPU_ENABLED inline typename detail::bessel_traits::result_type cyl_bessel_k(T1 v, T2 x, const Policy& /* pol */) + | ^~~~~~~~~~~~ + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/bessel.hpp:600:91: note: template argument deduction/substitution failed: + Bessel2ndKind.cpp:16:37: note: candidate expects 3 arguments, 2 provided + 16 | return boost::math::cyl_bessel_k(v, x); + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/bessel.hpp:616:104: note: candidate: 'template typename boost::math::detail::bessel_traits >::result_type boost::math::cyl_bessel_k(T1, T2)' + 616 | BOOST_MATH_GPU_ENABLED inline typename detail::bessel_traits >::result_type cyl_bessel_k(T1 v, T2 x) + | ^~~~~~~~~~~~ + /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/BH/include/boost/math/special_functions/bessel.hpp:616:104: note: substitution of deduced template arguments resulted in errors seen above + make: *** [/opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/etc/Makeconf:204: Bessel2ndKind.o] Error 1 + ERROR: compilation failed for package bandle + * removing /opt/conda/conda-bld/bioconductor-bandle_1736182811019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/bandle + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-bandle_1736182811019/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-bandle_1736182811019/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + compiler error +reason: |- + 'enable_if_t' in namespace 'boost::math' does not name a template type diff --git a/recipes/bioconductor-bandle/build_failure.osx-64.yaml b/recipes/bioconductor-bandle/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..4e19c7dc7c86e --- /dev/null +++ b/recipes/bioconductor-bandle/build_failure.osx-64.yaml @@ -0,0 +1,109 @@ +recipe_sha: 1b44810561201bbd0eafb438197ac935091631d0410548b8318b9f92c9cd44af # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-bandle-1.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-bandle-1.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-bandle_1736185276388/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + api.build( + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-bandle-1.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-bandle_1736185276388/work/conda_build.sh']' returned non-zero exit status 1. + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-bandle-1.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-bandle-1.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-bandle-1.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-bandle-1.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-bandle-1.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-bandle-1.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-bandle-1.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-bandle-1.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-bandle-1.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/BH/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fopenmp -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c Bessel2ndKind.cpp -o Bessel2ndKind.o +# Last 100 lines of the build log. +category: |- + compiler error +reason: |- + 'enable_if_t' in namespace 'boost::math' does not name a template type + diff --git a/recipes/bioconductor-bandle/meta.yaml b/recipes/bioconductor-bandle/meta.yaml index c2bea3dd5035c..a9b5422f0afb3 100644 --- a/recipes/bioconductor-bandle/meta.yaml +++ b/recipes/bioconductor-bandle/meta.yaml @@ -1,33 +1,40 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "bandle" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data. Experimental methods supported include dynamic LOPIT-DC, hyperLOPIT, Dynamic Organellar Maps, Dynamic PCP. It provides Bioconductor infrastructure to analyse these data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: An R package for the Bayesian analysis of differential subcellular localisation experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9c8dd928dd2b7900ff453ddc590ad6e4 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bandle", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: coda (>= 0.19-4), testthat, interp, fields, pheatmap, viridis, rmarkdown, spelling requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-proloc >=1.42.0,<1.43.0' - - 'bioconductor-prolocdata >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-proloc >=1.46.0,<1.47.0 + - bioconductor-prolocdata >=1.44.0,<1.45.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-bh - r-circlize @@ -38,21 +45,24 @@ requirements: - r-knitr - r-lbfgs - r-plyr - - 'r-rcpp >=1.0.4.6' + - r-rcpp >=1.0.4.6 - r-rcpparmadillo - r-rlang - r-robustbase - r-tidyr - libblas - liblapack + - zlib + - liblzma-devel + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-proloc >=1.42.0,<1.43.0' - - 'bioconductor-prolocdata >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-proloc >=1.46.0,<1.47.0 + - bioconductor-prolocdata >=1.44.0,<1.45.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-bh - r-circlize @@ -63,21 +73,21 @@ requirements: - r-knitr - r-lbfgs - r-plyr - - 'r-rcpp >=1.0.4.6' + - r-rcpp >=1.0.4.6 - r-rcpparmadillo - r-rlang - r-robustbase - r-tidyr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: ed95c12dfed9d5e8deca400016c048f6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'An R package for the Bayesian analysis of differential subcellular localisation experiments' - description: 'The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data. Experimental methods supported include dynamic LOPIT-DC, hyperLOPIT, Dynamic Organellar Maps, Dynamic PCP. It provides Bioconductor infrastructure to analyse these data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-banksy/build.sh b/recipes/bioconductor-banksy/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-banksy/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-banksy/build_failure.linux-64.yaml b/recipes/bioconductor-banksy/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..4570aa9a192c4 --- /dev/null +++ b/recipes/bioconductor-banksy/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5f9fc8cdc0a31c8fe34da19538c68f38c2dfb4b444ae051f2a07df0b6c8e8e3e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-rcpphungarian")} + Encountered problems while solving: + - nothing provides requested r-rcpphungarian + + Could not solve for environment specs + The following package could not be installed + [31mr-rcpphungarian[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-rcpphungarian")} + Encountered problems while solving: + - nothing provides requested r-rcpphungarian + + Could not solve for environment specs + The following package could not be installed + [31mr-rcpphungarian[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-rcpphungarian")} + Encountered problems while solving: + - nothing provides requested r-rcpphungarian + + Could not solve for environment specs + The following package could not be installed + [31mr-rcpphungarian[0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-banksy/meta.yaml b/recipes/bioconductor-banksy/meta.yaml new file mode 100644 index 0000000000000..af7be7382e665 --- /dev/null +++ b/recipes/bioconductor-banksy/meta.yaml @@ -0,0 +1,70 @@ +{% set version = "1.2.0" %} +{% set name = "Banksy" %} +{% set bioc = "3.20" %} + +about: + description: Banksy is an R package that incorporates spatial information to cluster cells in a feature space (e.g. gene expression). To incorporate spatial information, BANKSY computes the mean neighborhood expression and azimuthal Gabor filters that capture gene expression gradients. These features are combined with the cell's own expression to embed cells in a neighbor-augmented product space which can then be clustered, allowing for accurate and spatially-aware cell typing and tissue domain segmentation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Spatial transcriptomic clustering + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-banksy", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, pals, scuttle, scater, scran, cowplot, ggplot2, testthat (>= 3.0.0), harmony, Seurat, ExperimentHub, spatialLIBD, BiocStyle +requirements: + host: + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-aricode + - r-base + - r-data.table + - r-dbscan + - r-igraph + - r-irlba + - r-leidenalg >=1.1.0 + - r-matrixstats + - r-mclust + - r-rcpphungarian + - r-uwot + run: + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-aricode + - r-base + - r-data.table + - r-dbscan + - r-igraph + - r-irlba + - r-leidenalg >=1.1.0 + - r-matrixstats + - r-mclust + - r-rcpphungarian + - r-uwot + +source: + md5: 93df59b263b0be76ca53c924154f6c04 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-banocc/meta.yaml b/recipes/bioconductor-banocc/meta.yaml index 6c42e52f10707..737c66430a234 100644 --- a/recipes/bioconductor-banocc/meta.yaml +++ b/recipes/bioconductor-banocc/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "banocc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: BAnOCC is a package designed for compositional data, where each sample sums to one. It infers the approximate covariance of the unconstrained data using a Bayesian model coded with `rstan`. It provides as output the `stanfit` object as well as posterior median and credible interval estimates for each correlation element. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Bayesian ANalysis Of Compositional Covariance -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5a73975945814e725991bd67552349e6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-banocc", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-banocc + path: recipes/bioconductor-banocc + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, methods, testthat, BiocStyle requirements: host: - r-base - - 'r-coda >=0.18.1' + - r-coda >=0.18.1 - r-mvtnorm - - 'r-rstan >=2.17.4' + - r-rstan >=2.17.4 - r-stringr run: - r-base - - 'r-coda >=0.18.1' + - r-coda >=0.18.1 - r-mvtnorm - - 'r-rstan >=2.17.4' + - r-rstan >=2.17.4 - r-stringr + +source: + md5: 70d1a1d5bff0cd4560145ac38c1420b5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Bayesian ANalysis Of Compositional Covariance' - description: 'BAnOCC is a package designed for compositional data, where each sample sums to one. It infers the approximate covariance of the unconstrained data using a Bayesian model coded with `rstan`. It provides as output the `stanfit` object as well as posterior median and credible interval estimates for each correlation element.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-banocc - path: recipes/bioconductor-banocc - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-barcodetrackr/meta.yaml b/recipes/bioconductor-barcodetrackr/meta.yaml index c001ab2392527..c1737207211b5 100644 --- a/recipes/bioconductor-barcodetrackr/meta.yaml +++ b/recipes/bioconductor-barcodetrackr/meta.yaml @@ -1,29 +1,32 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "barcodetrackR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: barcodetrackR is an R package developed for the analysis and visualization of clonal tracking data. Data required is samples and tag abundances in matrix form. Usually from cellular barcoding experiments, integration site retrieval analyses, or similar technologies. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Functions for Analyzing Cellular Barcoding Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 34e3b62fbe85f743278fba96cfc8c618 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-barcodetrackr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, magick, rmarkdown, testthat requirements: + host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-cowplot @@ -42,9 +45,10 @@ requirements: - r-tidyr - r-vegan - r-viridis + run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-cowplot @@ -63,13 +67,16 @@ requirements: - r-tidyr - r-vegan - r-viridis + +source: + md5: 1ff7c7f592ec978c0ab7f50babd89c21 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Functions for Analyzing Cellular Barcoding Data' - description: 'barcodetrackR is an R package developed for the analysis and visualization of clonal tracking data. Data required is samples and tag abundances in matrix form. Usually from cellular barcoding experiments, integration site retrieval analyses, or similar technologies.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-barley1cdf/meta.yaml b/recipes/bioconductor-barley1cdf/meta.yaml index 462dda51f3f36..93d74111846ba 100644 --- a/recipes/bioconductor-barley1cdf/meta.yaml +++ b/recipes/bioconductor-barley1cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "barley1cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 16a2ca83f550518756d9fa3273672157 +about: + description: A package containing an environment representing the Barley1.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: barley1cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-barley1cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 16a2ca83f550518756d9fa3273672157 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: barley1cdf - description: 'A package containing an environment representing the Barley1.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-barley1probe/meta.yaml b/recipes/bioconductor-barley1probe/meta.yaml index 851b639c63da9..99f4634efda5a 100644 --- a/recipes/bioconductor-barley1probe/meta.yaml +++ b/recipes/bioconductor-barley1probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "barley1probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 80595d8ecf83ba83ea84a722a24ab474 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Barley1\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type barley1 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-barley1probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 80595d8ecf83ba83ea84a722a24ab474 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type barley1' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Barley1\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-basecallqc/meta.yaml b/recipes/bioconductor-basecallqc/meta.yaml index a9a2496602e83..b858257c82b4b 100644 --- a/recipes/bioconductor-basecallqc/meta.yaml +++ b/recipes/bioconductor-basecallqc/meta.yaml @@ -1,29 +1,40 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "basecallQC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Working with Illumina Basecalling and Demultiplexing input and output files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad61b901f8e533f817dccfb4830b222a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-basecallqc", max_pin="x.x") }}' - noarch: generic + +extra: + notes: | + 'This package relies on bcl2fastq being available in the system PATH. Due to licensing + restrictions Bioconda does not provide this package.' + parent_recipe: + name: bioconductor-basecallqc + path: recipes/bioconductor-basecallqc + version: 1.4.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle # SystemRequirements: bcl2Fastq (versions >= 2.1.7) requirements: host: - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-data.table - r-dplyr @@ -40,7 +51,7 @@ requirements: - r-xml - r-yaml run: - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-data.table - r-dplyr @@ -56,21 +67,16 @@ requirements: - r-tidyr - r-xml - r-yaml + +source: + md5: c009b07124d15d2dcb83f63e78afa775 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Working with Illumina Basecalling and Demultiplexing input and output files' - description: 'The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - notes: | - 'This package relies on bcl2fastq being available in the system PATH. Due to licensing - restrictions Bioconda does not provide this package.' - parent_recipe: - name: bioconductor-basecallqc - path: recipes/bioconductor-basecallqc - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-basespacer/meta.yaml b/recipes/bioconductor-basespacer/meta.yaml index d19b37977de6b..6ab0b944c66d6 100644 --- a/recipes/bioconductor-basespacer/meta.yaml +++ b/recipes/bioconductor-basespacer/meta.yaml @@ -1,24 +1,34 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "BaseSpaceR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A rich R interface to Illumina's BaseSpace cloud computing environment, enabling the fast development of data analysis and visualisation tools. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Apache License 2.0 + summary: R SDK for BaseSpace RESTful API -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b141511c6e978d4f26c8ec4c42c078c2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-basespacer", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:basespacer + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-basespacer + path: recipes/bioconductor-basespacer + version: 1.24.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, IRanges, Rsamtools requirements: host: @@ -29,20 +39,16 @@ requirements: - r-base - r-rcurl - r-rjsonio + +source: + md5: 85e110d6473c2758a06e1703565fb1f4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Apache License 2.0' - summary: 'R SDK for BaseSpace RESTful API' - description: 'A rich R interface to Illumina''s BaseSpace cloud computing environment, enabling the fast development of data analysis and visualisation tools.' -extra: - identifiers: - - biotools:basespacer - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-basespacer - path: recipes/bioconductor-basespacer - version: 1.24.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-basic4cseq/meta.yaml b/recipes/bioconductor-basic4cseq/meta.yaml index 1a5adc44f4e62..7bfcf374bb97b 100644 --- a/recipes/bioconductor-basic4cseq/meta.yaml +++ b/recipes/bioconductor-basic4cseq/meta.yaml @@ -1,57 +1,63 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "Basic4Cseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: 'Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b6e8e624b34a0626cfa015e9814d017b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-basic4cseq", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:basic4cseq + - doi:10.1093/bioinformatics/btu497 + parent_recipe: + name: bioconductor-basic4cseq + path: recipes/bioconductor-basic4cseq + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.ecoli.ncbi.20080805 >=1.3.0,<1.4.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.ecoli.ncbi.20080805 >=1.3.0,<1.4.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-catools - r-rcircos run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.ecoli.ncbi.20080805 >=1.3.0,<1.4.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.ecoli.ncbi.20080805 >=1.3.0,<1.4.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-catools - r-rcircos + +source: + md5: 936c1f2f0d2924f8387e9cf8bb312ade + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data' - description: 'Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment''s viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:basic4cseq - - doi:10.1093/bioinformatics/btu497 - parent_recipe: - name: bioconductor-basic4cseq - path: recipes/bioconductor-basic4cseq - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-basics/meta.yaml b/recipes/bioconductor-basics/meta.yaml index 71548c210ade6..26db8d1acb4be 100644 --- a/recipes/bioconductor-basics/meta.yaml +++ b/recipes/bioconductor-basics/meta.yaml @@ -1,35 +1,43 @@ -{% set version = "2.14.0" %} +{% set version = "2.18.0" %} {% set name = "BASiCS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Single-cell mRNA sequencing can uncover novel cell-to-cell heterogeneity in gene expression levels in seemingly homogeneous populations of cells. However, these experiments are prone to high levels of technical noise, creating new challenges for identifying genes that show genuine heterogeneous expression within the population of cells under study. BASiCS (Bayesian Analysis of Single-Cell Sequencing data) is an integrated Bayesian hierarchical model to perform statistical analyses of single-cell RNA sequencing datasets in the context of supervised experiments (where the groups of cells of interest are known a priori, e.g. experimental conditions or cell types). BASiCS performs built-in data normalisation (global scaling) and technical noise quantification (based on spike-in genes). BASiCS provides an intuitive detection criterion for highly (or lowly) variable genes within a single group of cells. Additionally, BASiCS can compare gene expression patterns between two or more pre-specified groups of cells. Unlike traditional differential expression tools, BASiCS quantifies changes in expression that lie beyond comparisons of means, also allowing the study of changes in cell-to-cell heterogeneity. The latter can be quantified via a biological over-dispersion parameter that measures the excess of variability that is observed with respect to Poisson sampling noise, after normalisation and technical noise removal. Due to the strong mean/over-dispersion confounding that is typically observed for scRNA-seq datasets, BASiCS also tests for changes in residual over-dispersion, defined by residual values with respect to a global mean/over-dispersion trend. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Bayesian Analysis of Single-Cell Sequencing data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1252fa180b0da21a4a22e3400550ab93 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-basics", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, magick # SystemRequirements: C++11 requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-coda @@ -38,24 +46,25 @@ requirements: - r-ggplot2 - r-hexbin - r-mass - - 'r-matrix >=1.5.0' + - r-matrix >=1.5.0 - r-matrixstats - r-posterior - - 'r-rcpp >=0.11.3' + - r-rcpp >=0.11.3 - r-rcpparmadillo - r-reshape2 - r-viridis - libblas - liblapack + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-coda @@ -64,24 +73,23 @@ requirements: - r-ggplot2 - r-hexbin - r-mass - - 'r-matrix >=1.5.0' + - r-matrix >=1.5.0 - r-matrixstats - r-posterior - - 'r-rcpp >=0.11.3' + - r-rcpp >=0.11.3 - r-rcpparmadillo - r-reshape2 - r-viridis - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 075730ceccc669baaff1bc0649dbe0b7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Bayesian Analysis of Single-Cell Sequencing data' - description: 'Single-cell mRNA sequencing can uncover novel cell-to-cell heterogeneity in gene expression levels in seemingly homogeneous populations of cells. However, these experiments are prone to high levels of technical noise, creating new challenges for identifying genes that show genuine heterogeneous expression within the population of cells under study. BASiCS (Bayesian Analysis of Single-Cell Sequencing data) is an integrated Bayesian hierarchical model to perform statistical analyses of single-cell RNA sequencing datasets in the context of supervised experiments (where the groups of cells of interest are known a priori, e.g. experimental conditions or cell types). BASiCS performs built-in data normalisation (global scaling) and technical noise quantification (based on spike-in genes). BASiCS provides an intuitive detection criterion for highly (or lowly) variable genes within a single group of cells. Additionally, BASiCS can compare gene expression patterns between two or more pre-specified groups of cells. Unlike traditional differential expression tools, BASiCS quantifies changes in expression that lie beyond comparisons of means, also allowing the study of changes in cell-to-cell heterogeneity. The latter can be quantified via a biological over-dispersion parameter that measures the excess of variability that is observed with respect to Poisson sampling noise, after normalisation and technical noise removal. Due to the strong mean/over-dispersion confounding that is typically observed for scRNA-seq datasets, BASiCS also tests for changes in residual over-dispersion, defined by residual values with respect to a global mean/over-dispersion trend.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-basicstan/meta.yaml b/recipes/bioconductor-basicstan/meta.yaml index 5e7eecf766f1d..3147e22abb831 100644 --- a/recipes/bioconductor-basicstan/meta.yaml +++ b/recipes/bioconductor-basicstan/meta.yaml @@ -1,70 +1,75 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "BASiCStan" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides an interface to infer the parameters of BASiCS using the variational inference (ADVI), Markov chain Monte Carlo (NUTS), and maximum a posteriori (BFGS) inference engines in the Stan programming language. BASiCS is a Bayesian hierarchical model that uses an adaptive Metropolis within Gibbs sampling scheme. Alternative inference methods provided by Stan may be preferable in some situations, for example for particularly large data or posterior distributions with difficult geometries. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Stan implementation of BASiCS -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7179ffcf510240c0c3cc6e8e31b60d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-basicstan", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.0.0), knitr, rmarkdown # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - - 'bioconductor-basics >=2.14.0,<2.15.0' - - 'bioconductor-glmgampoi >=1.14.0,<1.15.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-basics >=2.18.0,<2.19.0 + - bioconductor-glmgampoi >=1.18.0,<1.19.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-bh >=1.66.0' - - 'r-rcpp >=0.12.0' - - 'r-rcppeigen >=0.3.3.3.0' - - 'r-rcppparallel >=5.0.1' - - 'r-rstan >=2.18.1' - - 'r-rstantools >=2.1.1' - - 'r-stanheaders >=2.18.0' + - r-bh >=1.66.0 + - r-rcpp >=0.12.0 + - r-rcppeigen >=0.3.3.3.0 + - r-rcppparallel >=5.0.1 + - r-rstan >=2.18.1 + - r-rstantools >=2.1.1 + - r-stanheaders >=2.18.0 - libblas - liblapack run: - - 'bioconductor-basics >=2.14.0,<2.15.0' - - 'bioconductor-glmgampoi >=1.14.0,<1.15.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-basics >=2.18.0,<2.19.0 + - bioconductor-glmgampoi >=1.18.0,<1.19.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-bh >=1.66.0' - - 'r-rcpp >=0.12.0' - - 'r-rcppeigen >=0.3.3.3.0' - - 'r-rcppparallel >=5.0.1' - - 'r-rstan >=2.18.1' - - 'r-rstantools >=2.1.1' - - 'r-stanheaders >=2.18.0' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + - r-bh >=1.66.0 + - r-rcpp >=0.12.0 + - r-rcppeigen >=0.3.3.3.0 + - r-rcppparallel >=5.0.1 + - r-rstan >=2.18.1 + - r-rstantools >=2.1.1 + - r-stanheaders >=2.18.0 + +source: + md5: a4186cc4e1dc5ff03d112a63c06acc09 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Stan implementation of BASiCS' - description: 'Provides an interface to infer the parameters of BASiCS using the variational inference (ADVI), Markov chain Monte Carlo (NUTS), and maximum a posteriori (BFGS) inference engines in the Stan programming language. BASiCS is a Bayesian hierarchical model that uses an adaptive Metropolis within Gibbs sampling scheme. Alternative inference methods provided by Stan may be preferable in some situations, for example for particularly large data or posterior distributions with difficult geometries.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-basicstarrseq/meta.yaml b/recipes/bioconductor-basicstarrseq/meta.yaml index 0962d27074600..f96b32cc01c02 100644 --- a/recipes/bioconductor-basicstarrseq/meta.yaml +++ b/recipes/bioconductor-basicstarrseq/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "BasicSTARRseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Basic peak calling on STARR-seq data based on a method introduced in "Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq" Arnold et al. Science. 2013 Mar 1;339(6123):1074-7. doi: 10.1126/science. 1232542. Epub 2013 Jan 17.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Basic peak calling on STARR-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45c21fe93b28467ae466fd4017792494 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-basicstarrseq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: host: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base + +source: + md5: 1f30b4542e5e7f62e34207237c972f43 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'Basic peak calling on STARR-seq data' - description: 'Basic peak calling on STARR-seq data based on a method introduced in "Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq" Arnold et al. Science. 2013 Mar 1;339(6123):1074-7. doi: 10.1126/science. 1232542. Epub 2013 Jan 17.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-basilisk.utils/meta.yaml b/recipes/bioconductor-basilisk.utils/meta.yaml index 50279f87793f9..357bf1825a676 100644 --- a/recipes/bioconductor-basilisk.utils/meta.yaml +++ b/recipes/bioconductor-basilisk.utils/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.14.1" %} +{% set version = "1.18.0" %} {% set name = "basilisk.utils" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d5e61359283886e8653f772e65b0a898 +about: + description: Implements utilities for installation of the basilisk package, primarily for creation of the underlying Conda instance. This allows us to avoid re-writing the same R code in both the configure script (for centrally administered R installations) and in the lazy installation mechanism (for distributed package binaries). It is highly unlikely that developers - or, heaven forbid, end-users! - will need to interact with this package directly; they should be using the basilisk package instead. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Basilisk Installation Utilities build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-basilisk.utils", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: reticulate, knitr, rmarkdown, BiocStyle, testthat, basilisk requirements: host: - - 'bioconductor-dir.expiry >=1.10.0,<1.11.0' + - bioconductor-dir.expiry >=1.14.0,<1.15.0 - r-base run: - - 'bioconductor-dir.expiry >=1.10.0,<1.11.0' + - bioconductor-dir.expiry >=1.14.0,<1.15.0 - r-base +source: + md5: 89953864457a1974b657ed7dc01f8d50 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Basilisk Installation Utilities' - description: 'Implements utilities for installation of the basilisk package, primarily for creation of the underlying Conda instance. This allows us to avoid re-writing the same R code in both the configure script (for centrally administered R installations) and in the lazy installation mechanism (for distributed package binaries). It is highly unlikely that developers - or, heaven forbid, end-users! - will need to interact with this package directly; they should be using the basilisk package instead.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-basilisk/meta.yaml b/recipes/bioconductor-basilisk/meta.yaml index 8e6089e3f742c..e054adaa98bc2 100644 --- a/recipes/bioconductor-basilisk/meta.yaml +++ b/recipes/bioconductor-basilisk/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.14.1" %} +{% set version = "1.18.0" %} {% set name = "basilisk" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b47dde22cc3bb45ec9c785fe025241a0 +about: + description: Installs a self-contained conda instance that is managed by the R/Bioconductor installation machinery. This aims to provide a consistent Python environment that can be used reliably by Bioconductor packages. Functions are also provided to enable smooth interoperability of multiple Python environments in a single R session. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Freezing Python Dependencies Inside Bioconductor Packages build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-basilisk", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle, testthat, callr requirements: host: - - 'bioconductor-basilisk.utils >=1.14.0,<1.15.0' - - 'bioconductor-dir.expiry >=1.10.0,<1.11.0' + - bioconductor-basilisk.utils >=1.18.0,<1.19.0 + - bioconductor-dir.expiry >=1.14.0,<1.15.0 - r-base - r-reticulate run: - - 'bioconductor-basilisk.utils >=1.14.0,<1.15.0' - - 'bioconductor-dir.expiry >=1.10.0,<1.11.0' + - bioconductor-basilisk.utils >=1.18.0,<1.19.0 + - bioconductor-dir.expiry >=1.14.0,<1.15.0 - r-base - r-reticulate +source: + md5: d75135397396224a3d7e2fe691aadb33 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Freezing Python Dependencies Inside Bioconductor Packages' - description: 'Installs a self-contained conda instance that is managed by the R/Bioconductor installation machinery. This aims to provide a consistent Python environment that can be used reliably by Bioconductor packages. Functions are also provided to enable smooth interoperability of multiple Python environments in a single R session.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-batchelor/meta.yaml b/recipes/bioconductor-batchelor/meta.yaml index 1bf33aba12c89..1de95db3f8133 100644 --- a/recipes/bioconductor-batchelor/meta.yaml +++ b/recipes/bioconductor-batchelor/meta.yaml @@ -1,80 +1,91 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "batchelor" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implements a variety of methods for batch correction of single-cell (RNA sequencing) data. This includes methods based on detecting mutually nearest neighbors, as well as several efficient variants of linear regression of the log-expression values. Functions are also provided to perform global rescaling to remove differences in depth between batches, and to perform a principal components analysis that is robust to differences in the numbers of cells across batches. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Single-Cell Batch Correction Methods -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e78aa00a2e343b79e7ad7aeb0fde1196 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-batchelor", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:batchelor + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr, rmarkdown, scran, scater, bluster, scRNAseq # SystemRequirements: C++11 requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-residualmatrix >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-residualmatrix >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scaledmatrix >=1.14.0,<1.15.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-igraph - r-matrix - r-rcpp - libblas - liblapack + run: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-residualmatrix >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-residualmatrix >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scaledmatrix >=1.14.0,<1.15.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-igraph - r-matrix - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: d94a18149110a29fb790ade3b086411c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'Single-Cell Batch Correction Methods' - description: 'Implements a variety of methods for batch correction of single-cell (RNA sequencing) data. This includes methods based on detecting mutually nearest neighbors, as well as several efficient variants of linear regression of the log-expression values. Functions are also provided to perform global rescaling to remove differences in depth between batches, and to perform a principal components analysis that is robust to differences in the numbers of cells across batches.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-batchqc/meta.yaml b/recipes/bioconductor-batchqc/meta.yaml index b8c5d00be9898..7c3967e17ddbb 100644 --- a/recipes/bioconductor-batchqc/meta.yaml +++ b/recipes/bioconductor-batchqc/meta.yaml @@ -1,77 +1,98 @@ -{% set version = "1.30.0" %} +{% set version = "2.2.0" %} {% set name = "BatchQC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This often produces technical biases that can lead to incorrect results in the downstream analysis. BatchQC is a software tool that streamlines batch preprocessing and evaluation by providing interactive diagnostics, visualizations, and statistical analyses to explore the extent to which batch variation impacts the data. BatchQC diagnostics help determine whether batch adjustment needs to be done, and how correction should be applied before proceeding with a downstream analysis. Moreover, BatchQC interactively applies multiple common batch effect approaches to the data and the user can quickly see the benefits of each method. BatchQC is developed as a Shiny App. The output is organized into multiple tabs and each tab features an important part of the batch effect analysis and visualization of the data. The BatchQC interface has the following analysis groups: Summary, Differential Expression, Median Correlations, Heatmaps, Circular Dendrogram, PCA Analysis, Shape, ComBat and SVA.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Batch Effects Quality Control Software -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8940666878af6ea1981e6d90095bc98 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-batchqc", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat -# SystemRequirements: pandoc (http://pandoc.org/installing.html) for generating reports from markdown files. + +extra: + identifiers: + - biotools:batchqc + parent_recipe: + name: bioconductor-batchqc + path: recipes/bioconductor-batchqc + version: 1.8.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocManager, BiocStyle, bladderbatch, devtools, knitr, lintr, plotly, rmarkdown, spelling, testthat (>= 3.0.0) requirements: + host: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-ebseq >=2.4.0,<2.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - - r-corpcor - - r-ggvis - - r-gplots - - r-heatmaply - - r-knitr - - r-matrix + - r-data.table + - r-dplyr + - r-ggdendro + - r-ggnewscale + - r-ggplot2 - r-matrixstats - - r-mcmcpack - - r-moments - - r-pander + - r-pheatmap + - r-rcolorbrewer + - r-reader - r-reshape2 - - r-rmarkdown - r-shiny - - pandoc + - r-shinyjs + - r-shinythemes + - r-tibble + - r-tidyr + - r-tidyverse + run: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-ebseq >=2.4.0,<2.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - - r-corpcor - - r-ggvis - - r-gplots - - r-heatmaply - - r-knitr - - r-matrix + - r-data.table + - r-dplyr + - r-ggdendro + - r-ggnewscale + - r-ggplot2 - r-matrixstats - - r-mcmcpack - - r-moments - - r-pander + - r-pheatmap + - r-rcolorbrewer + - r-reader - r-reshape2 - - r-rmarkdown - r-shiny - - pandoc + - r-shinyjs + - r-shinythemes + - r-tibble + - r-tidyr + - r-tidyverse + +source: + md5: d0a36d52c86f8622c51921a5684684ef + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Batch Effects Quality Control Software' - description: 'Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This often produces technical biases that can lead to incorrect results in the downstream analysis. BatchQC is a software tool that streamlines batch preprocessing and evaluation by providing interactive diagnostics, visualizations, and statistical analyses to explore the extent to which batch variation impacts the data. BatchQC diagnostics help determine whether batch adjustment needs to be done, and how correction should be applied before proceeding with a downstream analysis. Moreover, BatchQC interactively applies multiple common batch effect approaches to the data, and the user can quickly see the benefits of each method. BatchQC is developed as a Shiny App. The output is organized into multiple tabs, and each tab features an important part of the batch effect analysis and visualization of the data. The BatchQC interface has the following analysis groups: Summary, Differential Expression, Median Correlations, Heatmaps, Circular Dendrogram, PCA Analysis, Shape, ComBat and SVA.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:batchqc - parent_recipe: - name: bioconductor-batchqc - path: recipes/bioconductor-batchqc - version: 1.8.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bayesknockdown/meta.yaml b/recipes/bioconductor-bayesknockdown/meta.yaml index 34fc090aa009a..e74b463001474 100644 --- a/recipes/bioconductor-bayesknockdown/meta.yaml +++ b/recipes/bioconductor-bayesknockdown/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "BayesKnockdown" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6efc97e1bf0448a97ca0b3d595096a3d +about: + description: A simple, fast Bayesian method for computing posterior probabilities for relationships between a single predictor variable and multiple potential outcome variables, incorporating prior probabilities of relationships. In the context of knockdown experiments, the predictor variable is the knocked-down gene, while the other genes are potential targets. Can also be used for differential expression/2-class data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bayesknockdown", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base +source: + md5: 1fde1dce499b8d8bfcfce801c7c52317 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data' - description: 'A simple, fast Bayesian method for computing posterior probabilities for relationships between a single predictor variable and multiple potential outcome variables, incorporating prior probabilities of relationships. In the context of knockdown experiments, the predictor variable is the knocked-down gene, while the other genes are potential targets. Can also be used for differential expression/2-class data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bayesspace/build_failure.linux-64.yaml b/recipes/bioconductor-bayesspace/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0cadff04257f6 --- /dev/null +++ b/recipes/bioconductor-bayesspace/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: fdc536d73e8f6085a7dbcfecb3eb9a5358215bb7d3d5d202103f9264f0b2643b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [32mbioconductor-xvector >=0.46.0,<0.47.0 [0m, which requires + [32mbioconductor-zlibbioc >=1.52.0,<1.53.0 [0m, which requires + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [31mr-xgboost[0m is not installable because there are no viable options + [31mr-xgboost 0.80[0m would require + [31mmro-base >=3.5.0,<3.5.1.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-xgboost [0.80|0.81|0.82|0.90|1.0.2][0m would require + [31mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [0.82|0.90|...|1.4.0][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.0.2|1.1.1|...|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.4.0|1.4.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-xgboost==0.80=mro350h255eb88_1"), MatchSpec(">=3.5.0,<3.5.1.0a0")} + Encountered problems while solving: + - nothing provides mro-base >=3.5.0,<3.5.1.0a0 needed by r-xgboost-0.80-mro350h255eb88_1 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-scater >=1.34.0,<1.35.0 [0m is installable and it requires + [32mbioconductor-sparsearray >=1.6.0,<1.7.0 [0m, which requires + [32mbioconductor-xvector >=0.46.0,<0.47.0 [0m, which requires + [32mbioconductor-zlibbioc >=1.52.0,<1.53.0 [0m, which requires + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [31mr-xgboost[0m is not installable because there are no viable options + [31mr-xgboost 0.80[0m would require + [31mmro-base >=3.5.0,<3.5.1.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-xgboost [0.80|0.81|0.82|0.90|1.0.2][0m would require + [31mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [0.82|0.90|...|1.4.0][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.0.2|1.1.1|...|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.4.0|1.4.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. +category: |- + dependency issue diff --git a/recipes/bioconductor-bayesspace/build_failure.osx-64.yaml b/recipes/bioconductor-bayesspace/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..7257eefa03868 --- /dev/null +++ b/recipes/bioconductor-bayesspace/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: fdc536d73e8f6085a7dbcfecb3eb9a5358215bb7d3d5d202103f9264f0b2643b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1 conflicts with any installable versions previously reported; + r-xgboost [0.82|0.90|...|1.4.0] would require + r-base >=3.6,<3.7.0a0 but there are no viable options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3] conflicts with any installable versions previously reported; + r-xgboost [1.0.2|1.1.1|...|1.6.2] would require + r-base >=4.0,<4.1.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.4.0|1.4.1|...|1.7.4] would require + r-base >=4.1,<4.2.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.6.2|1.7.0|...|2.0.3] would require + r-base >=4.2,<4.3.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.7.4|1.7.6|...|2.1.3] would require + r-base >=4.3,<4.4.0a0 , which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("4.0.1==hcfea43d_1"), MatchSpec("clang==4.0.1=1")} + Encountered problems while solving: + - nothing provides compiler-rt 4.0.1 hcfea43d_1 needed by clang-4.0.1-1 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-scater >=1.34.0,<1.35.0 is installable and it requires + bioconductor-sparsearray >=1.6.0,<1.7.0 , which requires + bioconductor-xvector >=0.46.0,<0.47.0 , which requires + bioconductor-zlibbioc >=1.52.0,<1.53.0 , which requires + r-base >=4.4,<4.5.0a0 , which can be installed; + r-xgboost is not installable because there are no viable options + r-xgboost [0.80|0.81|0.82|0.90|1.0.2] would require + r-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ] but there are no viable options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1 conflicts with any installable versions previously reported; + r-xgboost [0.82|0.90|...|1.4.0] would require + r-base >=3.6,<3.7.0a0 but there are no viable options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3] conflicts with any installable versions previously reported; + r-xgboost [1.0.2|1.1.1|...|1.6.2] would require + r-base >=4.0,<4.1.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.4.0|1.4.1|...|1.7.4] would require + r-base >=4.1,<4.2.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.6.2|1.7.0|...|2.0.3] would require + r-base >=4.2,<4.3.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.7.4|1.7.6|...|2.1.3] would require + r-base >=4.3,<4.4.0a0 , which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. +category: |- + dependency issue diff --git a/recipes/bioconductor-bayesspace/meta.yaml b/recipes/bioconductor-bayesspace/meta.yaml index 8c53962e97f47..07deae3e46c17 100644 --- a/recipes/bioconductor-bayesspace/meta.yaml +++ b/recipes/bioconductor-bayesspace/meta.yaml @@ -1,87 +1,114 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "BayesSpace" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for clustering and enhancing the resolution of spatial gene expression experiments. BayesSpace clusters a low-dimensional representation of the gene expression matrix, incorporating a spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into "sub-spots", for which features such as gene expression or cell type composition can be imputed. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Clustering and Resolution Enhancement of Spatial Transcriptomes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5505178450768dc45884632e3e0a3baf build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bayesspace", max_pin="x.x") }}' -# Suggests: testthat, knitr, rmarkdown, igraph, spatialLIBD, dplyr, viridis, patchwork, RColorBrewer, Seurat -# SystemRequirements: C++11 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, knitr, rmarkdown, igraph, spatialLIBD, viridis, patchwork, RColorBrewer, Seurat +# SystemRequirements: C++17 requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make + host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-arrow - r-assertthat - r-base - r-coda - r-dirichletreg + - r-dplyr - r-ggplot2 + - r-magrittr - r-matrix - r-mclust + - r-microbenchmark - r-purrr - - 'r-rcpp >=1.0.4.6' + - r-rcpp >=1.0.4.6 - r-rcpparmadillo - r-rcppdist - r-rcppprogress - r-rcurl + - r-rjson + - r-rlang - r-scales + - r-tibble + - r-tidyr - r-xgboost - libblas - liblapack + run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-arrow - r-assertthat - r-base - r-coda - r-dirichletreg + - r-dplyr - r-ggplot2 + - r-magrittr - r-matrix - r-mclust + - r-microbenchmark - r-purrr - - 'r-rcpp >=1.0.4.6' + - r-rcpp >=1.0.4.6 - r-rcpparmadillo - r-rcppdist - r-rcppprogress - r-rcurl + - r-rjson + - r-rlang - r-scales + - r-tibble + - r-tidyr - r-xgboost - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 54c0fce8afc2730a26310b710fc67951 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Clustering and Resolution Enhancement of Spatial Transcriptomes' - description: 'Tools for clustering and enhancing the resolution of spatial gene expression experiments. BayesSpace clusters a low-dimensional representation of the gene expression matrix, incorporating a spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into "sub-spots", for which features such as gene expression or cell type composition can be imputed.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-baynorm/meta.yaml b/recipes/bioconductor-baynorm/meta.yaml index 32927dab2124f..13a9cc0bbb2d6 100644 --- a/recipes/bioconductor-baynorm/meta.yaml +++ b/recipes/bioconductor-baynorm/meta.yaml @@ -1,29 +1,35 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "bayNorm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: bayNorm is used for normalizing single-cell RNA-seq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Single-cell RNA sequencing data normalization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fda25f54086787e9a038cc59f0660a58 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-baynorm", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bb - r-dosnow @@ -33,15 +39,15 @@ requirements: - r-locfit - r-mass - r-matrix - - 'r-rcpp >=0.12.12' + - r-rcpp >=0.12.12 - r-rcpparmadillo - r-rcppprogress - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bb - r-dosnow @@ -51,20 +57,19 @@ requirements: - r-locfit - r-mass - r-matrix - - 'r-rcpp >=0.12.12' + - r-rcpp >=0.12.12 - r-rcpparmadillo - r-rcppprogress - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 6bf2ec12971ed9837cabe1a3225f95c0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Single-cell RNA sequencing data normalization' - description: 'bayNorm is used for normalizing single-cell RNA-seq data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bayseq/meta.yaml b/recipes/bioconductor-bayseq/meta.yaml index 1060cb2108ad2..952726fa6e93d 100644 --- a/recipes/bioconductor-bayseq/meta.yaml +++ b/recipes/bioconductor-bayseq/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "2.36.0" %} +{% set version = "2.40.0" %} {% set name = "baySeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f46b63ebca2bda7c124133149aa7e552 +about: + description: This package identifies differential expression in high-throughput 'count' data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Empirical Bayesian analysis of patterns of differential expression in count data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bayseq", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, BiocGenerics requirements: host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-abind - r-base run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-abind - r-base +source: + md5: a0f89002a2588eb4707bbee8bf64703a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Empirical Bayesian analysis of patterns of differential expression in count data' - description: 'This package identifies differential expression in high-throughput ''count'' data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bbcanalyzer/meta.yaml b/recipes/bioconductor-bbcanalyzer/meta.yaml index 953c2118d4578..436ecd8aaec1f 100644 --- a/recipes/bioconductor-bbcanalyzer/meta.yaml +++ b/recipes/bioconductor-bbcanalyzer/meta.yaml @@ -1,51 +1,22 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "BBCAnalyzer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: BBCAnalyzer is a package for visualizing the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: 'BBCAnalyzer: an R/Bioconductor package for visualizing base counts' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 33b123d417f53ee03c547220dfdb1612 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bbcanalyzer", max_pin="x.x") }}' - noarch: generic -# Suggests: BSgenome.Hsapiens.UCSC.hg19 -requirements: - host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - - r-base - run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'BBCAnalyzer: an R/Bioconductor package for visualizing base counts' - description: 'BBCAnalyzer is a package for visualizing the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + extra: identifiers: - biotools:bbcanalyzer @@ -55,3 +26,38 @@ extra: path: recipes/bioconductor-bbcanalyzer version: 1.10.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BSgenome.Hsapiens.UCSC.hg19 +requirements: + host: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - r-base + run: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - r-base + +source: + md5: bcd7378834e0897f6415fdcb5e069869 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-bcellviper/meta.yaml b/recipes/bioconductor-bcellviper/meta.yaml index 62edc4c0af227..2846ea4690848 100644 --- a/recipes/bioconductor-bcellviper/meta.yaml +++ b/recipes/bioconductor-bcellviper/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "bcellViper" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e93bbaa204826358c77282e2a370074 +about: + description: This package provides a human B-cell context-specific transcriptional regulatory network and a human normal B-cells dataset for the examples in package viper. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Human B-cell transcriptional interactome and normal human B-cell expression data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bcellviper", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 72732d35e21a870acb5095bf03b05128 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Human B-cell transcriptional interactome and normal human B-cell expression data' - description: 'This package provides a human B-cell context-specific transcriptional regulatory network and a human normal B-cells dataset for the examples in package viper.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bcellviper/post-link.sh b/recipes/bioconductor-bcellviper/post-link.sh index 00b243486be7d..f8a89e7890e93 100644 --- a/recipes/bioconductor-bcellviper/post-link.sh +++ b/recipes/bioconductor-bcellviper/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bcellviper-1.38.0" +installBiocDataPackage.sh "bcellviper-1.42.0" diff --git a/recipes/bioconductor-bcrank/meta.yaml b/recipes/bioconductor-bcrank/meta.yaml index 52d59782460fa..2f0d4a4ed7a1d 100644 --- a/recipes/bioconductor-bcrank/meta.yaml +++ b/recipes/bioconductor-bcrank/meta.yaml @@ -1,45 +1,21 @@ -{% set version = "1.64.0" %} +{% set version = "1.68.0" %} {% set name = "BCRANK" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Predicting binding site consensus from ranked DNA sequences -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6c551ab389af456ab76449642c01881a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bcrank", max_pin="x.x") }}' -# Suggests: seqLogo -requirements: - host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - r-base - - libblas - - liblapack - run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - r-base - build: - - {{ compiler('c') }} - - make -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2.0-only - summary: 'Predicting binding site consensus from ranked DNA sequences' - description: 'Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + extra: additional-platforms: - linux-aarch64 @@ -51,3 +27,33 @@ extra: path: recipes/bioconductor-bcrank version: 1.42.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: seqLogo +requirements: + build: + - {{ compiler('c') }} + - make + host: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - r-base + - libblas + - liblapack + run: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - r-base + +source: + md5: 79c2594e60ea105c143574ce699c10b1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-bcseq/meta.yaml b/recipes/bioconductor-bcseq/meta.yaml index 523746769460e..a7943f9f7ca17 100644 --- a/recipes/bioconductor-bcseq/meta.yaml +++ b/recipes/bioconductor-bcseq/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "bcSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This Rcpp-based package implements a highly efficient data structure and algorithm for performing alignment of short reads from CRISPR or shRNA screens to reference barcode library. Sequencing error are considered and matching qualities are evaluated based on Phred scores. A Bayes' classifier is employed to predict the originating barcode of a read. The package supports provision of user-defined probability models for evaluating matching qualities. The package also supports multi-threading. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e582b114bc4743a328b6ada2953a74da build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bcseq", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:bcSeq + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - r-matrix - - 'r-rcpp >=0.12.12' + - r-rcpp >=0.12.12 - libblas - liblapack run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - r-matrix - - 'r-rcpp >=0.12.12' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=0.12.12 + +source: + md5: 8628fcba235199af4969c5fa6912e8db + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens' - description: 'This Rcpp-based package implements a highly efficient data structure and algorithm for performing alignment of short reads from CRISPR or shRNA screens to reference barcode library. Sequencing error are considered and matching qualities are evaluated based on Phred scores. A Bayes'' classifier is employed to predict the originating barcode of a read. The package supports provision of user-defined probability models for evaluating matching qualities. The package also supports multi-threading.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name }} diff --git a/recipes/bioconductor-beachmat.hdf5/meta.yaml b/recipes/bioconductor-beachmat.hdf5/meta.yaml index d26114501a536..30a3321cfa114 100644 --- a/recipes/bioconductor-beachmat.hdf5/meta.yaml +++ b/recipes/bioconductor-beachmat.hdf5/meta.yaml @@ -1,53 +1,61 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "beachmat.hdf5" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Extends beachmat to support initialization of tatami matrices from HDF5-backed arrays. This allows C++ code in downstream packages to directly call the HDF5 C/C++ library to access array data, without the need for block processing via DelayedArray. Some utilities are also provided for direct creation of an in-memory tatami matrix from a HDF5 file. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: beachmat bindings for HDF5-backed matrices -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b2ca9b6358fb05895101e6a911ca0e39 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-beachmat.hdf5", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr, rmarkdown, rhdf5, Matrix # SystemRequirements: C++17, GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - bioconductor-assorthead >=1.0.0,<1.1.0 + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 - r-base - r-rcpp - libblas - liblapack + - zlib run: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - bioconductor-assorthead >=1.0.0,<1.1.0 + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 - r-base - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 92056406f63cce411dad2a915b700533 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'beachmat bindings for HDF5-backed matrices' - description: 'Extends beachmat to support initialization of tatami matrices from HDF5-backed arrays. This allows C++ code in downstream packages to directly call the HDF5 C/C++ library to access array data, without the need for block processing via DelayedArray. Some utilities are also provided for direct creation of an in-memory tatami matrix from a HDF5 file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-beachmat/meta.yaml b/recipes/bioconductor-beachmat/meta.yaml index 3f65c0a6c6a2f..5846949ac3ece 100644 --- a/recipes/bioconductor-beachmat/meta.yaml +++ b/recipes/bioconductor-beachmat/meta.yaml @@ -1,65 +1,70 @@ -{% set version = "2.18.0" %} +{% set version = "2.22.0" %} {% set name = "beachmat" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides a consistent C++ class interface for reading from a variety of commonly used matrix types. Ordinary matrices and several sparse/dense Matrix classes are directly supported, along with a subset of the delayed operations implemented in the DelayedArray package. All other matrix-like objects are supported by calling back into R. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Compiling Bioconductor to Handle Each Matrix Type -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ec47172a09aba997192731b4a5f2f284 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-beachmat", max_pin="x.x") }}' -# Suggests: testthat, BiocStyle, knitr, rmarkdown, rcmdcheck, BiocParallel, HDF5Array + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:beachmat + parent_recipe: + name: bioconductor-beachmat + path: recipes/bioconductor-beachmat + version: 1.2.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, BiocStyle, knitr, rmarkdown, rcmdcheck, BiocParallel, HDF5Array, beachmat.hdf5 # SystemRequirements: C++17 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-sparsearray >=1.2.0,<1.3.0' + - bioconductor-assorthead >=1.0.0,<1.1.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 - r-base - r-matrix - r-rcpp - libblas - liblapack - - tapi # [osx] run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-sparsearray >=1.2.0,<1.3.0' + - bioconductor-assorthead >=1.0.0,<1.1.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 - r-base - r-matrix - r-rcpp - - tapi - - tapi # [osx] - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 3e11f4224ff4e9cfa1ebffae6f9bfee4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'Compiling Bioconductor to Handle Each Matrix Type' - description: 'Provides a consistent C++ class interface for reading from a variety of commonly used matrix types. Ordinary matrices and several sparse/dense Matrix classes are directly supported, along with a subset of the delayed operations implemented in the DelayedArray package. All other matrix-like objects are supported by calling back into R.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} - parent_recipe: - name: bioconductor-beachmat - path: recipes/bioconductor-beachmat - version: 1.2.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-beadarray/meta.yaml b/recipes/bioconductor-beadarray/meta.yaml index 16d2467732896..5b023e11b3c43 100644 --- a/recipes/bioconductor-beadarray/meta.yaml +++ b/recipes/bioconductor-beadarray/meta.yaml @@ -1,34 +1,47 @@ -{% set version = "2.52.0" %} +{% set version = "2.56.0" %} {% set name = "beadarray" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Quality assessment and low-level analysis for Illumina BeadArray data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ed1729be533d0731833e523174b9dbb4 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-beadarray", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:beadarray + parent_recipe: + name: bioconductor-beadarray + path: recipes/bioconductor-beadarray + version: 2.30.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-beaddatapackr >=1.54.0,<1.55.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-beaddatapackr >=1.58.0,<1.59.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-ggplot2 - r-hexbin @@ -36,35 +49,28 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-beaddatapackr >=1.54.0,<1.55.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-beaddatapackr >=1.58.0,<1.59.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-ggplot2 - r-hexbin - r-reshape2 - build: - - {{ compiler('c') }} - - make + +source: + md5: 5efd39d338403e9b6dbddfa3561d8b71 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Quality assessment and low-level analysis for Illumina BeadArray data' - description: 'The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.' - license_file: LICENSE -extra: - identifiers: - - biotools:beadarray - parent_recipe: - name: bioconductor-beadarray - path: recipes/bioconductor-beadarray - version: 2.30.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-beadarrayexampledata/meta.yaml b/recipes/bioconductor-beadarrayexampledata/meta.yaml index 8a5709c7d1053..fe8292315005f 100644 --- a/recipes/bioconductor-beadarrayexampledata/meta.yaml +++ b/recipes/bioconductor-beadarrayexampledata/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "beadarrayExampleData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d327e659adc868f1e3c7ae457c60087b +about: + description: An small dataset that can be used to run examples from the beadarray vignette and examples + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Example data for the beadarray package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-beadarrayexampledata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-beadarray >=2.52.0,<2.53.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-beadarray >=2.56.0,<2.57.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-beadarray >=2.52.0,<2.53.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-beadarray >=2.56.0,<2.57.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 435c0cf9624aef923febb8c90a8bcc6a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Example data for the beadarray package' - description: 'An small dataset that can be used to run examples from the beadarray vignette and examples' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-beadarrayexampledata/post-link.sh b/recipes/bioconductor-beadarrayexampledata/post-link.sh index 42281c8dc3e00..3e85019a8d022 100644 --- a/recipes/bioconductor-beadarrayexampledata/post-link.sh +++ b/recipes/bioconductor-beadarrayexampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "beadarrayexampledata-1.40.0" +installBiocDataPackage.sh "beadarrayexampledata-1.44.0" diff --git a/recipes/bioconductor-beadarrayusecases/build_failure.linux-64.yaml b/recipes/bioconductor-beadarrayusecases/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..c81eb73c9e971 --- /dev/null +++ b/recipes/bioconductor-beadarrayusecases/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: ce3ac5bc6d31563363e77f65a1edc6639a7c938aec62e3b77d5e50ff7c894889 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-r6: 2.5.1-r44hc72bb7e_3 conda-forge + r-rappdirs: 0.3.3-r44hb1dbf0f_3 conda-forge + r-rcolorbrewer: 1.1_3-r44h785f33e_3 conda-forge + r-rcpp: 1.0.13_1-r44h93ab643_0 conda-forge + r-readr: 2.1.5-r44h0d4f4ea_1 conda-forge + r-rentrez: 1.2.3-r44h785f33e_3 conda-forge + r-reshape2: 1.4.4-r44h0d4f4ea_4 conda-forge + r-rlang: 1.1.4-r44ha18555a_1 conda-forge + r-rsqlite: 2.3.9-r44h93ab643_0 conda-forge + r-rvest: 1.0.4-r44hc72bb7e_1 conda-forge + r-scales: 1.3.0-r44hc72bb7e_1 conda-forge + r-selectr: 0.4_2-r44hc72bb7e_4 conda-forge + r-statmod: 1.5.0-r44ha36c22a_2 conda-forge + r-stringi: 1.8.4-r44h33cde33_3 conda-forge + r-stringr: 1.5.1-r44h785f33e_1 conda-forge + r-sys: 3.4.3-r44h2b5f3a1_0 conda-forge + r-tibble: 3.2.1-r44hdb488b9_3 conda-forge + r-tidyr: 1.3.1-r44h0d4f4ea_1 conda-forge + r-tidyselect: 1.2.1-r44hc72bb7e_1 conda-forge + r-tzdb: 0.4.0-r44ha18555a_2 conda-forge + r-utf8: 1.2.4-r44hb1dbf0f_1 conda-forge + r-vctrs: 0.6.5-r44h0d4f4ea_1 conda-forge + r-viridislite: 0.4.2-r44hc72bb7e_2 conda-forge + r-vroom: 1.6.5-r44h0d4f4ea_1 conda-forge + r-withr: 3.0.2-r44hc72bb7e_0 conda-forge + r-xml: 3.99_0.17-r44h5bae778_2 conda-forge + r-xml2: 1.3.6-r44h8194278_2 conda-forge + readline: 8.2-h8228510_1 conda-forge + sed: 4.8-he412f7d_0 conda-forge + setuptools: 75.6.0-pyhff2d567_1 conda-forge + sysroot_linux-64: 2.17-h0157908_18 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tktable: 2.10-h8bc8fbc_6 conda-forge + toml: 0.10.2-pyhd8ed1ab_1 conda-forge + tomlkit: 0.13.2-pyha770c72_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + xmltodict: 0.14.2-pyhd8ed1ab_1 conda-forge + xorg-libice: 1.1.2-hb9d3cd8_0 conda-forge + xorg-libsm: 1.2.5-he73a12e_0 conda-forge + xorg-libx11: 1.8.10-h4f16b4b_1 conda-forge + xorg-libxau: 1.0.12-hb9d3cd8_0 conda-forge + xorg-libxdmcp: 1.1.5-hb9d3cd8_0 conda-forge + xorg-libxext: 1.3.6-hb9d3cd8_0 conda-forge + xorg-libxrender: 0.9.12-hb9d3cd8_0 conda-forge + xorg-libxt: 1.3.1-hb9d3cd8_0 conda-forge + yaml: 0.2.5-h7f98852_2 conda-forge + yq: 3.4.3-pyhd8ed1ab_1 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: BeadArrayUseCases_1.43.0_6540429ac7.tar.gz + Downloading https://bioconductor.org/packages/3.20/data/experiment/src/contrib/BeadArrayUseCases_1.43.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.066406 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioconductor.org/packages/3.20/bioc/src/contrib/Archive/BeadArrayUseCases/BeadArrayUseCases_1.43.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.017083 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioarchive.galaxyproject.org/BeadArrayUseCases_1.43.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.310888 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://depot.galaxyproject.org/software/bioconductor-beadarrayusecases/bioconductor-beadarrayusecases_1.43.0_src_all.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.108233 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download https://depot.galaxyproject.org/software/bioconductor-beadarrayusecases/bioconductor-beadarrayusecases_1.43.0_src_all.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-beadarrayusecases/meta.yaml b/recipes/bioconductor-beadarrayusecases/meta.yaml index 29e716cd61f24..fac2099034d22 100644 --- a/recipes/bioconductor-beadarrayusecases/meta.yaml +++ b/recipes/bioconductor-beadarrayusecases/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.40.0" %} +{% set version = "1.43.0" %} {% set name = "BeadArrayUseCases" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a939c03744773755b9a80de63a925c3e +about: + description: Example data files and use cases for processing Illumina BeadArray expression data using Bioconductor + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Analysing Illumina BeadArray expression data using Bioconductor build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-beadarrayusecases", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db requirements: host: - - 'bioconductor-beadarray >=2.52.0,<2.53.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-beadarray >=2.56.0,<2.57.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base run: - - 'bioconductor-beadarray >=2.52.0,<2.53.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-beadarray >=2.56.0,<2.57.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6540429ac7c52046a6bf1aa3c7eb2100 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Analysing Illumina BeadArray expression data using Bioconductor' - description: 'Example data files and use cases for processing Illumina BeadArray expression data using Bioconductor' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-beadarrayusecases/post-link.sh b/recipes/bioconductor-beadarrayusecases/post-link.sh index 60fda081d37d8..abaf927bdd7d7 100644 --- a/recipes/bioconductor-beadarrayusecases/post-link.sh +++ b/recipes/bioconductor-beadarrayusecases/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "beadarrayusecases-1.40.0" +installBiocDataPackage.sh "beadarrayusecases-1.43.0" diff --git a/recipes/bioconductor-beaddatapackr/meta.yaml b/recipes/bioconductor-beaddatapackr/meta.yaml index 6613cebb430b6..2e6b2fdc88e28 100644 --- a/recipes/bioconductor-beaddatapackr/meta.yaml +++ b/recipes/bioconductor-beaddatapackr/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "1.54.0" %} +{% set version = "1.58.0" %} {% set name = "BeadDataPackR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Compression of Illumina BeadArray data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b1e73395e4f18af4b799a1f447487a87 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-beaddatapackr", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:beaddatapackr + parent_recipe: + name: bioconductor-beaddatapackr + path: recipes/bioconductor-beaddatapackr + version: 1.32.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: 63023a2f3a4e09ca1f357570eda58adf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Compression of Illumina BeadArray data' - description: 'Provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:beaddatapackr - parent_recipe: - name: bioconductor-beaddatapackr - path: recipes/bioconductor-beaddatapackr - version: 1.32.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-beadsorted.saliva.epic/meta.yaml b/recipes/bioconductor-beadsorted.saliva.epic/meta.yaml index c39f60e6e07de..299bfd9ae6751 100644 --- a/recipes/bioconductor-beadsorted.saliva.epic/meta.yaml +++ b/recipes/bioconductor-beadsorted.saliva.epic/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "BeadSorted.Saliva.EPIC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ca080a144452fad8ce1bdf8e86d88c74 +about: + description: Raw data objects used to estimate saliva cell proportion estimates in ewastools. The FlowSorted.Saliva.EPIC object is constructed from samples assayed by Lauren Middleton et. al. (2021). + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Illumina EPIC data on BeadSorted child saliva cells build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-beadsorted.saliva.epic", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 10b9f6f46be07aa4e2b5fd5ff4dae4ff + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Illumina EPIC data on BeadSorted child saliva cells' - description: 'Raw data objects used to estimate saliva cell proportion estimates in ewastools. The FlowSorted.Saliva.EPIC object is constructed from samples assayed by Lauren Middleton et. al. (2021).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-beadsorted.saliva.epic/post-link.sh b/recipes/bioconductor-beadsorted.saliva.epic/post-link.sh index 4ce7d05773879..936fcc5937bea 100644 --- a/recipes/bioconductor-beadsorted.saliva.epic/post-link.sh +++ b/recipes/bioconductor-beadsorted.saliva.epic/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "beadsorted.saliva.epic-1.10.0" +installBiocDataPackage.sh "beadsorted.saliva.epic-1.14.0" diff --git a/recipes/bioconductor-beat/meta.yaml b/recipes/bioconductor-beat/meta.yaml index 3305424e4dae2..4b2a644b9820d 100644 --- a/recipes/bioconductor-beat/meta.yaml +++ b/recipes/bioconductor-beat/meta.yaml @@ -1,46 +1,22 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "BEAT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Model-based analysis of single-cell methylation data + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 3.0) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: BEAT - BS-Seq Epimutation Analysis Toolkit -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46e0caf216c816dbe7323a1b0117fbf6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-beat", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - r-base - run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 3.0)' - summary: 'BEAT - BS-Seq Epimutation Analysis Toolkit' - description: 'Model-based analysis of single-cell methylation data' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + extra: identifiers: - biotools:beat @@ -50,3 +26,33 @@ extra: path: recipes/bioconductor-beat version: 1.18.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - r-base + run: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - r-base + +source: + md5: 17acde8cfa4a9e16817cd68309f30051 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-beclear/meta.yaml b/recipes/bioconductor-beclear/meta.yaml index 5c7b037c6d71c..5ae56658c59b7 100644 --- a/recipes/bioconductor-beclear/meta.yaml +++ b/recipes/bioconductor-beclear/meta.yaml @@ -1,31 +1,48 @@ -{% set version = "2.18.0" %} +{% set version = "2.22.0" %} {% set name = "BEclear" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Correction of batch effects in DNA methylation data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bd34703e5a35dfc888f0029395df2c80 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-beclear", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:beclear + - doi:10.1371/journal.pone.0159921 + parent_recipe: + name: bioconductor-beclear + path: recipes/bioconductor-beclear + version: 1.12.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr, rmarkdown, pander, seewave # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-abind - r-base - - 'r-data.table >=1.11.8' + - r-data.table >=1.11.8 - r-dixontest - r-futile.logger - r-ids @@ -35,37 +52,26 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-abind - r-base - - 'r-data.table >=1.11.8' + - r-data.table >=1.11.8 - r-dixontest - r-futile.logger - r-ids - r-matrix - r-rcpp - r-rdpack - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: d8de2e2efc4f8bb25d2a9462d2e23f86 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-only' - summary: 'Correction of batch effects in DNA methylation data' - description: 'Provides functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:beclear - - doi:10.1371/journal.pone.0159921 - parent_recipe: - name: bioconductor-beclear - path: recipes/bioconductor-beclear - version: 1.12.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-beer/meta.yaml b/recipes/bioconductor-beer/meta.yaml index db26d4c26e576..71a70ac4c76be 100644 --- a/recipes/bioconductor-beer/meta.yaml +++ b/recipes/bioconductor-beer/meta.yaml @@ -1,52 +1,57 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "beer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: BEER implements a Bayesian model for analyzing phage-immunoprecipitation sequencing (PhIP-seq) data. Given a PhIPData object, BEER returns posterior probabilities of enriched antibody responses, point estimates for the relative fold-change in comparison to negative control samples, and more. Additionally, BEER provides a convenient implementation for using edgeR to identify enriched antibody responses. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Bayesian Enrichment Estimation in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c8e6192a3f9bd04b62ed564c8164ba00 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-beer", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr, rmarkdown, dplyr, ggplot2, spelling # SystemRequirements: JAGS (4.3.0) requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-phipdata >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-phipdata >=1.14.0,<1.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cli - r-progressr - r-rjags run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-phipdata >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-phipdata >=1.14.0,<1.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cli - r-progressr - r-rjags + +source: + md5: e2b2b44d638bb6b8a99e37fcdfe0bc67 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Bayesian Enrichment Estimation in R' - description: 'BEER implements a Bayesian model for analyzing phage-immunoprecipitation sequencing (PhIP-seq) data. Given a PhIPData object, BEER returns posterior probabilities of enriched antibody responses, point estimates for the relative fold-change in comparison to negative control samples, and more. Additionally, BEER provides a convenient implementation for using edgeR to identify enriched antibody responses.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-benchmarkfdrdata2019/meta.yaml b/recipes/bioconductor-benchmarkfdrdata2019/meta.yaml index 2b84b56cb70ce..10a30b2c4dda9 100644 --- a/recipes/bioconductor-benchmarkfdrdata2019/meta.yaml +++ b/recipes/bioconductor-benchmarkfdrdata2019/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "benchmarkfdrData2019" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 50ce7eb4100da1909ddd6c71c31e7e0c +about: + description: Benchmarking results for experimental and simulated data sets used in Korthauer and Kimes et al. (2019) to compare methods for controlling the false discovery rate. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Data and Benchmarking Results from Korthauer and Kimes et al. (2019) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-benchmarkfdrdata2019", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: rmarkdown, knitr, BiocStyle, testthat, SummarizedBenchmark, dplyr, ggplot2, rlang requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 93fd3ecc26e32fdc7f4086ddd4a06a02 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Data and Benchmarking Results from Korthauer and Kimes et al. (2019)' - description: 'Benchmarking results for experimental and simulated data sets used in Korthauer and Kimes et al. (2019) to compare methods for controlling the false discovery rate.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-benchmarkfdrdata2019/post-link.sh b/recipes/bioconductor-benchmarkfdrdata2019/post-link.sh index 1129bed5479d6..17fff9c58d30c 100644 --- a/recipes/bioconductor-benchmarkfdrdata2019/post-link.sh +++ b/recipes/bioconductor-benchmarkfdrdata2019/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "benchmarkfdrdata2019-1.16.0" +installBiocDataPackage.sh "benchmarkfdrdata2019-1.20.0" diff --git a/recipes/bioconductor-bert/build.sh b/recipes/bioconductor-bert/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bert/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bert/build_failure.linux-64.yaml b/recipes/bioconductor-bert/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..4ec5211977fd9 --- /dev/null +++ b/recipes/bioconductor-bert/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: dfb0a1087d91c859a89c20208845e70b4dcbf38a7b979c4c275bf9ff54bcb293 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-comprehenr")} + Encountered problems while solving: + - nothing provides requested r-comprehenr + + Could not solve for environment specs + The following package could not be installed + [31mr-comprehenr[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-comprehenr")} + Encountered problems while solving: + - nothing provides requested r-comprehenr + + Could not solve for environment specs + The following package could not be installed + [31mr-comprehenr[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-comprehenr")} + Encountered problems while solving: + - nothing provides requested r-comprehenr + + Could not solve for environment specs + The following package could not be installed + [31mr-comprehenr[0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. +reason: |- + needs r-comprehenr to be in conda-forge +category: |- + dependency issue diff --git a/recipes/bioconductor-bert/build_failure.osx-64.yaml b/recipes/bioconductor-bert/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..0bd88583c1271 --- /dev/null +++ b/recipes/bioconductor-bert/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: dfb0a1087d91c859a89c20208845e70b4dcbf38a7b979c4c275bf9ff54bcb293 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + needs r-comprehenr to be in conda-forge +category: |- + dependency issue diff --git a/recipes/bioconductor-bert/meta.yaml b/recipes/bioconductor-bert/meta.yaml new file mode 100644 index 0000000000000..997c8e73ae1e3 --- /dev/null +++ b/recipes/bioconductor-bert/meta.yaml @@ -0,0 +1,64 @@ +{% set version = "1.2.0" %} +{% set name = "BERT" %} +{% set bioc = "3.20" %} + +about: + description: Provides efficient batch-effect adjustment of data with missing values. BERT orders all batch effect correction to a tree of pairwise computations. BERT allows parallelization over sub-trees. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: High Performance Data Integration for Large-Scale Analyses of Incomplete Omic Profiles Using Batch-Effect Reduction Trees (BERT) + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bert", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle +requirements: + host: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 + - r-base + - r-cluster + - r-comprehenr + - r-foreach >=1.5.2 + - r-invgamma + - r-iterators >=1.0.14 + - r-janitor >=2.2.0 + - r-logging >=0.10-108 + run: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 + - r-base + - r-cluster + - r-comprehenr + - r-foreach >=1.5.2 + - r-invgamma + - r-iterators >=1.0.14 + - r-janitor >=2.2.0 + - r-logging >=0.10-108 + +source: + md5: 12e279dc220c5b5d8d327189c37dfdcd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-beta7/meta.yaml b/recipes/bioconductor-beta7/meta.yaml index 47ad27c91e376..cc87b2b3a082b 100644 --- a/recipes/bioconductor-beta7/meta.yaml +++ b/recipes/bioconductor-beta7/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "beta7" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7beee3699282a97c765cf418036fc0ed +about: + description: Data from 6 gpr files aims to identify differential expressed genes between the beta 7+ and beta 7- memory T helper cells. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Rodriguez et al. (2004) Differential Gene Expression by Memory/Effector T Helper Cells Bearing the Gut-Homing Receptor Integrin alpha4 beta7. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-beta7", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-marray >=1.84.0,<1.85.0 - r-base run: - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-marray >=1.84.0,<1.85.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b3f1aa522feccc463e3d7aca2da3c03f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Rodriguez et al. (2004) Differential Gene Expression by Memory/Effector T Helper Cells Bearing the Gut-Homing Receptor Integrin alpha4 beta7.' - description: 'Data from 6 gpr files aims to identify differential expressed genes between the beta 7+ and beta 7- memory T helper cells.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-beta7/post-link.sh b/recipes/bioconductor-beta7/post-link.sh index 8c038bab630b5..b74ea32c18953 100644 --- a/recipes/bioconductor-beta7/post-link.sh +++ b/recipes/bioconductor-beta7/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "beta7-1.40.0" +installBiocDataPackage.sh "beta7-1.44.0" diff --git a/recipes/bioconductor-betahmm/build.sh b/recipes/bioconductor-betahmm/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-betahmm/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-betahmm/meta.yaml b/recipes/bioconductor-betahmm/meta.yaml new file mode 100644 index 0000000000000..75677ae4408f9 --- /dev/null +++ b/recipes/bioconductor-betahmm/meta.yaml @@ -0,0 +1,68 @@ +{% set version = "1.2.0" %} +{% set name = "betaHMM" %} +{% set bioc = "3.20" %} + +about: + description: A novel approach utilizing a homogeneous hidden Markov model. And effectively model untransformed beta values. To identify DMCs while considering the spatial. Correlation of the adjacent CpG sites. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Beta-Valued DNA Methylation Data + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-betahmm", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle +requirements: + host: + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-cowplot + - r-doparallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-proc + - r-scales + - r-stringr + - r-tidyr + - r-tidyselect + run: + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-cowplot + - r-doparallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-proc + - r-scales + - r-stringr + - r-tidyr + - r-tidyselect + +source: + md5: 26447f2f3e79b0dbb7e341094601d325 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-bettr/build.sh b/recipes/bioconductor-bettr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bettr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bettr/meta.yaml b/recipes/bioconductor-bettr/meta.yaml new file mode 100644 index 0000000000000..5aa17eb269f6d --- /dev/null +++ b/recipes/bioconductor-bettr/meta.yaml @@ -0,0 +1,76 @@ +{% set version = "1.2.0" %} +{% set name = "bettr" %} +{% set bioc = "3.20" %} + +about: + description: bettr provides a set of interactive visualization methods to explore the results of a benchmarking study, where typically more than a single performance measures are computed. The user can weight the performance measures according to their preferences. Performance measures can also be grouped and aggregated according to additional annotations. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: A Better Way To Explore What Is Best + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bettr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle +requirements: + host: + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-bslib + - r-circlize + - r-cowplot + - r-dplyr >=1.0 + - r-dt + - r-ggplot2 >=3.4.1 + - r-hmisc + - r-rlang + - r-scales + - r-shiny >=1.6 + - r-shinyjqui + - r-sortable + - r-tibble + - r-tidyr + run: + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-bslib + - r-circlize + - r-cowplot + - r-dplyr >=1.0 + - r-dt + - r-ggplot2 >=3.4.1 + - r-hmisc + - r-rlang + - r-scales + - r-shiny >=1.6 + - r-shinyjqui + - r-sortable + - r-tibble + - r-tidyr + +source: + md5: 07fe79bca7bad892bdaebcc261cf33ec + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-bg2/meta.yaml b/recipes/bioconductor-bg2/meta.yaml index 707795e15d457..7306dfa14ecaa 100644 --- a/recipes/bioconductor-bg2/meta.yaml +++ b/recipes/bioconductor-bg2/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "BG2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is built to perform GWAS analysis for non-Gaussian data using BG2. The BG2 method uses penalized quasi-likelihood along with nonlocal priors in a two step manner to identify SNPs in GWAS analysis. The research related to this package was supported in part by National Science Foundation awards DMS 1853549 and DMS 2054173. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Performs Bayesian GWAS analysis for non-Gaussian data using BG2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: da6ea59dda3c728bdce70a5b43e4541e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bg2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP, testthat (>= 3.0.0) requirements: host: - r-base - - 'r-caret >=6.0-86' - - 'r-ga >=3.2' - - 'r-mass >=7.3-58.1' - - 'r-matrix >=1.2-18' - - 'r-memoise >=1.1.0' + - r-caret >=6.0-86 + - r-ga >=3.2 + - r-mass >=7.3-58.1 + - r-matrix >=1.2-18 + - r-memoise >=1.1.0 run: - r-base - - 'r-caret >=6.0-86' - - 'r-ga >=3.2' - - 'r-mass >=7.3-58.1' - - 'r-matrix >=1.2-18' - - 'r-memoise >=1.1.0' + - r-caret >=6.0-86 + - r-ga >=3.2 + - r-mass >=7.3-58.1 + - r-matrix >=1.2-18 + - r-memoise >=1.1.0 + +source: + md5: 6a60a5d3010345c4b5559006b403c640 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Performs Bayesian GWAS analysis for non-Gaussian data using BG2' - description: 'This package is built to perform GWAS analysis for non-Gaussian data using BG2. The BG2 method uses penalized quasi-likelihood along with nonlocal priors in a two step manner to identify SNPs in GWAS analysis. The research related to this package was supported in part by National Science Foundation awards DMS 1853549 and DMS 2054173.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bgeecall/meta.yaml b/recipes/bioconductor-bgeecall/meta.yaml index 75110cb7b2571..78d6814563ff4 100644 --- a/recipes/bioconductor-bgeecall/meta.yaml +++ b/recipes/bioconductor-bgeecall/meta.yaml @@ -1,34 +1,37 @@ -{% set version = "1.18.1" %} +{% set version = "1.22.0" %} {% set name = "BgeeCall" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: BgeeCall allows to generate present/absent gene expression calls without using an arbitrary cutoff like TPM<1. Calls are generated based on reference intergenic sequences. These sequences are generated based on expression of all RNA-Seq libraries of each species integrated in Bgee (https://bgee.org). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Automatic RNA-Seq present/absent gene expression calls generation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d6ffd11b71faf135832b99515c7ba4cd build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bgeecall", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, rmarkdown, AnnotationHub, httr # SystemRequirements: kallisto requirements: host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-tximport >=1.30.0,<1.31.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 + - bioconductor-tximport >=1.34.0,<1.35.0 - r-base - r-data.table - r-dplyr @@ -36,25 +39,29 @@ requirements: - r-rslurm - r-sjmisc run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-tximport >=1.30.0,<1.31.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 + - bioconductor-tximport >=1.34.0,<1.35.0 - r-base - r-data.table - r-dplyr - r-jsonlite - r-rslurm - r-sjmisc + +source: + md5: 4c2e44c5068cb6d4f72ce57b41232eba + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Automatic RNA-Seq present/absent gene expression calls generation' - description: 'BgeeCall allows to generate present/absent gene expression calls without using an arbitrary cutoff like TPM<1. Calls are generated based on reference intergenic sequences. These sequences are generated based on expression of all RNA-Seq libraries of each species integrated in Bgee (https://bgee.org).' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bgeedb/build_failure.linux-64.yaml b/recipes/bioconductor-bgeedb/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0829cc579d3c1 --- /dev/null +++ b/recipes/bioconductor-bgeedb/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: dd423d6b2c63ee0f422c1c760508456ef526fb75fbdf33a0b7bc25616f764ab8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-bread")} + Encountered problems while solving: + - nothing provides requested r-bread + + Could not solve for environment specs + The following package could not be installed + [31mr-bread[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-bread")} + Encountered problems while solving: + - nothing provides requested r-bread + + Could not solve for environment specs + The following package could not be installed + [31mr-bread[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-bread")} + Encountered problems while solving: + - nothing provides requested r-bread + + Could not solve for environment specs + The following package could not be installed + [31mr-bread[0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. +reason: |- + needs r-bread package to be added to conda-forge +category: |- + dependency issue diff --git a/recipes/bioconductor-bgeedb/build_failure.osx-64.yaml b/recipes/bioconductor-bgeedb/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..f41b98b7799ef --- /dev/null +++ b/recipes/bioconductor-bgeedb/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: dd423d6b2c63ee0f422c1c760508456ef526fb75fbdf33a0b7bc25616f764ab8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + needs r-bread package to be added to conda-forge +category: |- + dependency issue diff --git a/recipes/bioconductor-bgeedb/meta.yaml b/recipes/bioconductor-bgeedb/meta.yaml index c84ee3e31ee05..7c8bbc1766c33 100644 --- a/recipes/bioconductor-bgeedb/meta.yaml +++ b/recipes/bioconductor-bgeedb/meta.yaml @@ -1,31 +1,46 @@ -{% set version = "2.28.0" %} +{% set version = "2.32.0" %} {% set name = "BgeeDB" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'A package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9b8f5e9e829bd05d9a8322b3ff3408dd build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bgeedb", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:bgeedb + - doi:10.12688/f1000research.9973.1 + parent_recipe: + name: bioconductor-bgeedb + path: recipes/bioconductor-bgeedb + version: 2.6.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, testthat, rmarkdown, markdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-topgo >=2.58.0,<2.59.0 + - bioconductor-zellkonverter >=1.16.0,<1.17.0 + - r-anndata - r-base + - r-bread - r-curl - r-data.table - r-digest @@ -35,10 +50,14 @@ requirements: - r-rsqlite - r-tidyr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-topgo >=2.58.0,<2.59.0 + - bioconductor-zellkonverter >=1.16.0,<1.17.0 + - r-anndata - r-base + - r-bread - r-curl - r-data.table - r-digest @@ -47,21 +66,16 @@ requirements: - r-rcurl - r-rsqlite - r-tidyr + +source: + md5: cc657beb492269eb151c26a813026b64 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology' - description: 'A package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.' - license_file: LICENSE -extra: - identifiers: - - biotools:bgeedb - - doi:10.12688/f1000research.9973.1 - parent_recipe: - name: bioconductor-bgeedb - path: recipes/bioconductor-bgeedb - version: 2.6.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bicare/meta.yaml b/recipes/bioconductor-bicare/meta.yaml index e703872a25ea2..9661440d63b1e 100644 --- a/recipes/bioconductor-bicare/meta.yaml +++ b/recipes/bioconductor-bicare/meta.yaml @@ -1,57 +1,63 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "BicARE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Biclustering Analysis and Results Exploration. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Biclustering Analysis and Results Exploration -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d2498da49d01723934f42b4bf235fa05 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bicare", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:bicare + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-bicare + path: recipes/bioconductor-bicare + version: 1.38.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: hgu95av2 requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: 139bdada55b8e0f1c8c2cab35daf8962 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Biclustering Analysis and Results Exploration' - description: 'Biclustering Analysis and Results Exploration.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:bicare - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-bicare - path: recipes/bioconductor-bicare - version: 1.38.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bifet/meta.yaml b/recipes/bioconductor-bifet/meta.yaml index 9355f41630d56..41acf3eea7dfc 100644 --- a/recipes/bioconductor-bifet/meta.yaml +++ b/recipes/bioconductor-bifet/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "BiFET" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11fcc80fc0c2745e5a15524fd2279bed +about: + description: BiFET identifies TFs whose footprints are over-represented in target regions compared to background regions after correcting for the bias arising from the imbalance in read counts and GC contents between the target and background regions. For a given TF k, BiFET tests the null hypothesis that the target regions have the same probability of having footprints for the TF k as the background regions while correcting for the read count and GC content bias. For this, we use the number of target regions with footprints for TF k, t_k as a test statistic and calculate the p-value as the probability of observing t_k or more target regions with footprints under the null hypothesis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Bias-free Footprint Enrichment Test build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bifet", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: rmarkdown, testthat, knitr requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-poibin run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-poibin +source: + md5: dd89b71d4770cb7e547808c5d5ea8cba + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Bias-free Footprint Enrichment Test' - description: 'BiFET identifies TFs whose footprints are over-represented in target regions compared to background regions after correcting for the bias arising from the imbalance in read counts and GC contents between the target and background regions. For a given TF k, BiFET tests the null hypothesis that the target regions have the same probability of having footprints for the TF k as the background regions while correcting for the read count and GC content bias. For this, we use the number of target regions with footprints for TF k, t_k as a test statistic and calculate the p-value as the probability of observing t_k or more target regions with footprints under the null hypothesis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biggr/build_failure.linux-64.yaml b/recipes/bioconductor-biggr/build_failure.linux-64.yaml index 1f88c079d088c..39555bd9026d1 100644 --- a/recipes/bioconductor-biggr/build_failure.linux-64.yaml +++ b/recipes/bioconductor-biggr/build_failure.linux-64.yaml @@ -1,106 +1,104 @@ -recipe_sha: b7766d035130ae790cea751e3ffdd9b9db7a9ee165bdd6eac0deefe15615c9f1 # The commit at which this recipe failed to build. +recipe_sha: 0e19f0415c39de2f9051732170340995d4657954b58098897a982b00c87eb092 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: |- - dependency issue -log: |- - conda-forge/linux-64 100%[2K[1A[2K[0Gconda-forge/linux-64 - [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m - [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 2.2MB/s 0.0s - [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m - [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 2.2MB/s 0.0s - [?25hMamba failed to solve: - - bioconductor-rsbml >=2.60.0,<2.61.0 - - r-stringr - - bioconductor-hyperdraw >=1.54.0,<1.55.0 - - r-lim - - r-base 4.3.* - - bioconductor-hypergraph >=1.74.0,<1.75.0 - - r-limsolve +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rsbml[version='>=2.64.0,<2.65.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rsbml >=2.64.0,<2.65.0 - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - package bioconductor-hyperdraw-1.54.0-r43hba55f59_0 requires graphviz >=8.1.0,<9.0a0, but none of the providers can be installed - - - - Leaving build/test directories: - Work: - /opt/conda/conda-bld/work - Test: - /opt/conda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl - Build: - source activate /opt/conda/conda-bld/_build_env + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rsbml >=2.64.0,<2.65.0 [0m does not exist (perhaps a typo or a missing channel). + During handling of the above exception, another exception occurred: Traceback (most recent call last): - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action - t = self.solve(specs) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - bioconductor-rsbml >=2.60.0,<2.61.0 - - r-stringr - - bioconductor-hyperdraw >=1.54.0,<1.55.0 - - r-lim - - r-base 4.3.* - - bioconductor-hypergraph >=1.74.0,<1.75.0 - - r-limsolve + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rsbml[version='>=2.64.0,<2.65.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rsbml >=2.64.0,<2.65.0 - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - package bioconductor-hyperdraw-1.54.0-r43hba55f59_0 requires graphviz >=8.1.0,<9.0a0, but none of the providers can be installed - - + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rsbml >=2.64.0,<2.65.0 [0m does not exist (perhaps a typo or a missing channel). During handling of the above exception, another exception occurred: Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs - for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set conda_packages = finalize_outputs_pass( - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass fm = finalize_metadata( - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata - build_unsat, host_unsat = add_upstream_pins(m, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins - host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files - deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies - actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-hyperdraw==1.54.0=r43hba55f59_0"), MatchSpec("graphviz[version='>=8.1.0,<9.0a0']")} + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rsbml[version='>=2.64.0,<2.65.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rsbml >=2.64.0,<2.65.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rsbml >=2.64.0,<2.65.0 [0m does not exist (perhaps a typo or a missing channel). # Last 100 lines of the build log. diff --git a/recipes/bioconductor-biggr/meta.yaml b/recipes/bioconductor-biggr/meta.yaml index 4ea339b2a2ef1..ea0a155580e0f 100644 --- a/recipes/bioconductor-biggr/meta.yaml +++ b/recipes/bioconductor-biggr/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "BiGGR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides an interface to simulate metabolic reconstruction from the BiGG database(http://bigg.ucsd.edu/) and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Constraint based modeling in R using metabolic reconstruction databases -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 16eeec0ca7502101425cbb568e6eef15 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biggr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-hyperdraw >=1.54.0,<1.55.0' - - 'bioconductor-hypergraph >=1.74.0,<1.75.0' - - 'bioconductor-rsbml >=2.60.0,<2.61.0' + - bioconductor-hyperdraw >=1.58.0,<1.59.0 + - bioconductor-hypergraph >=1.78.0,<1.79.0 + - bioconductor-rsbml >=2.64.0,<2.65.0 - r-base - r-lim - r-limsolve - r-stringr run: - - 'bioconductor-hyperdraw >=1.54.0,<1.55.0' - - 'bioconductor-hypergraph >=1.74.0,<1.75.0' - - 'bioconductor-rsbml >=2.60.0,<2.61.0' + - bioconductor-hyperdraw >=1.58.0,<1.59.0 + - bioconductor-hypergraph >=1.78.0,<1.79.0 + - bioconductor-rsbml >=2.64.0,<2.65.0 - r-base - r-lim - r-limsolve - r-stringr + +source: + md5: 35ba1a1c22de3f2c7e971f2a0bba0a4b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Constraint based modeling in R using metabolic reconstruction databases' - description: 'This package provides an interface to simulate metabolic reconstruction from the BiGG database(http://bigg.ucsd.edu/) and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bigmelon/meta.yaml b/recipes/bioconductor-bigmelon/meta.yaml index 0f7c8a2a7a8ee..d5ece8511e2aa 100644 --- a/recipes/bioconductor-bigmelon/meta.yaml +++ b/recipes/bioconductor-bigmelon/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "bigmelon" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Methods for working with Illumina arrays using gdsfmt. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Illumina methylation array analysis for large experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1c6944989ec4f16b1903143a34296bf0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bigmelon", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, RUnit, BiocStyle, minfiData, parallel, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - - 'bioconductor-methylumi >=2.48.0,<2.49.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-watermelon >=2.8.0,<2.9.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 + - bioconductor-methylumi >=2.52.0,<2.53.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-watermelon >=2.12.0,<2.13.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - - 'bioconductor-methylumi >=2.48.0,<2.49.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-watermelon >=2.8.0,<2.9.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 + - bioconductor-methylumi >=2.52.0,<2.53.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-watermelon >=2.12.0,<2.13.0 - r-base + +source: + md5: 423b0bad7fa00435f8be661b0dc6f75f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Illumina methylation array analysis for large experiments' - description: 'Methods for working with Illumina arrays using gdsfmt.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bindingsitefinder/meta.yaml b/recipes/bioconductor-bindingsitefinder/meta.yaml index 0d45dbb551c79..571ddaa0030dc 100644 --- a/recipes/bioconductor-bindingsitefinder/meta.yaml +++ b/recipes/bioconductor-bindingsitefinder/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "2.0.0" %} +{% set version = "2.4.0" %} {% set name = "BindingSiteFinder" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understand (post-) transcriptional regulatory processes. Here we present a workflow that describes how exact binding sites can be defined from iCLIP data. The package provides functions for binding site definition and result visualization. For details please see the vignette. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Binding site defintion based on iCLIP data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b54f11a27c1f6f55b4cc60ad8986e029 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bindingsitefinder", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicAlignments, scales, Gviz, xlsx, GGally, patchwork, viridis, ggplotify, SummarizedExperiment, DESeq2, ggpointdensity, ggrastr, ashr requirements: + host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-forcats @@ -43,14 +45,15 @@ requirements: - r-rlang - r-tibble - r-tidyr + run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-forcats @@ -65,12 +68,16 @@ requirements: - r-rlang - r-tibble - r-tidyr + +source: + md5: 5391da35eacee94b739cd6b45d4e4a1b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Binding site defintion based on iCLIP data' - description: 'Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understand (post-) transcriptional regulatory processes. Here we present a workflow that describes how exact binding sites can be defined from iCLIP data. The package provides functions for binding site definition and result visualization. For details please see the vignette.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bioassayr/meta.yaml b/recipes/bioconductor-bioassayr/meta.yaml index af54b2e1f736c..e1fc98ab64adb 100644 --- a/recipes/bioconductor-bioassayr/meta.yaml +++ b/recipes/bioconductor-bioassayr/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "bioassayR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: bioassayR is a computational tool that enables simultaneous analysis of thousands of bioassay experiments performed over a diverse set of compounds and biological targets. Unique features include support for large-scale cross-target analyses of both public and custom bioassays, generation of high throughput screening fingerprints (HTSFPs), and an optional preloaded database that provides access to a substantial portion of publicly available bioactivity data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Cross-target analysis of small molecule bioactivity -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94ac7a2ff2a9de7b65d8ebd864513a31 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bioassayr", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, RCurl, biomaRt, cellHTS2, knitr, knitcitations, knitrBootstrap, testthat, ggplot2, rmarkdown + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, RCurl, biomaRt, knitr, knitcitations, knitrBootstrap, testthat, ggplot2, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-chemminer >=3.58.0,<3.59.0 - r-base - - 'r-dbi >=0.3.1' + - r-dbi >=0.3.1 - r-matrix - r-rjson - - 'r-rsqlite >=1.0.0' + - r-rsqlite >=1.0.0 - r-xml run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-chemminer >=3.58.0,<3.59.0 - r-base - - 'r-dbi >=0.3.1' + - r-dbi >=0.3.1 - r-matrix - r-rjson - - 'r-rsqlite >=1.0.0' + - r-rsqlite >=1.0.0 - r-xml + +source: + md5: eff797f2b472054d3ceda0df1abd6cef + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Cross-target analysis of small molecule bioactivity' - description: 'bioassayR is a computational tool that enables simultaneous analysis of thousands of bioassay experiments performed over a diverse set of compounds and biological targets. Unique features include support for large-scale cross-target analyses of both public and custom bioassays, generation of high throughput screening fingerprints (HTSFPs), and an optional preloaded database that provides access to a substantial portion of publicly available bioactivity data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biobase/meta.yaml b/recipes/bioconductor-biobase/meta.yaml index d70e8f10c58aa..6b18f80ad5be7 100644 --- a/recipes/bioconductor-biobase/meta.yaml +++ b/recipes/bioconductor-biobase/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "2.62.0" %} +{% set version = "2.66.0" %} {% set name = "Biobase" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 75a65eb015d58ca611f2bebca41f9d2d build: - number: 3 + number: 0 + rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biobase", max_pin="x.x") }}' -# Suggests: tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr, limma requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: 3782a10ac7f920542aa3265b8253746b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - '$R -e "library(''{{ name }}'')"' + about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Biobase: Base functions for Bioconductor' description: 'Functions that are needed by many other packages or which replace R functions.' + extra: additional-platforms: - linux-aarch64 - osx-arm64 identifiers: - biotools:biobase - diff --git a/recipes/bioconductor-biobroom/meta.yaml b/recipes/bioconductor-biobroom/meta.yaml index 629191ae0ef98..5354e4a74e9a2 100644 --- a/recipes/bioconductor-biobroom/meta.yaml +++ b/recipes/bioconductor-biobroom/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "biobroom" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b0a4b29e9aa3bbb99f42cd2cd19ca4d7 +about: + description: This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to tidy data. It thus serves as a complement to the broom package, and follows the same the tidy, augment, glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Turn Bioconductor objects into tidy data frames build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biobroom", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: limma, DESeq2, airway, ggplot2, plyr, GenomicRanges, testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase, rmarkdown, SummarizedExperiment requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-broom - r-dplyr - r-tidyr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-broom - r-dplyr - r-tidyr +source: + md5: c5003dfa490d449f3cb5498fde138cb6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Turn Bioconductor objects into tidy data frames' - description: 'This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to tidy data. It thus serves as a complement to the broom package, and follows the same the tidy, augment, glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biobtreer/meta.yaml b/recipes/bioconductor-biobtreer/meta.yaml index c14de14924e0e..00fc1545b689a 100644 --- a/recipes/bioconductor-biobtreer/meta.yaml +++ b/recipes/bioconductor-biobtreer/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "biobtreeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c341e537e79161abfd6f1f3382d3eb90 +about: + description: The biobtreeR package provides an interface to [biobtree](https://github.com/tamerh/biobtree) tool which covers large set of bioinformatics datasets and allows search and chain mappings functionalities. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Using biobtree tool from R build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biobtreer", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr,testthat,rmarkdown,markdown requirements: host: @@ -33,13 +32,14 @@ requirements: - r-httr - r-jsonlite - r-stringi +source: + md5: bd9bf70b1229e72787df6a1fc5646118 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Using biobtree tool from R' - description: 'The biobtreeR package provides an interface to [biobtree](https://github.com/tamerh/biobtree) tool which covers large set of bioinformatics datasets and allows search and chain mappings functionalities.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biocancer/meta.yaml b/recipes/bioconductor-biocancer/meta.yaml index ff3219486924f..876f52f721471 100644 --- a/recipes/bioconductor-biocancer/meta.yaml +++ b/recipes/bioconductor-biocancer/meta.yaml @@ -1,89 +1,98 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "bioCancer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is a Shiny App to visualize and analyse interactively Multi-Assays of Cancer Genomic Data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 | file LICENSE + license_file: LICENSE + summary: Interactive Multi-Omics Cancers Data Visualization and Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2eff081b55d8bda988f08f1836420b24 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocancer", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, prettydoc, rmarkdown, knitr, testthat (>= 0.10.0) requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-genetclassifier >=1.42.0,<1.43.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-org.bt.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - - 'bioconductor-reactomepa >=1.46.0,<1.47.0' - - 'r-algdesign >=1.1.7.3' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-cbioportaldata >=2.18.0,<2.19.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-genetclassifier >=1.46.0,<1.47.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-org.bt.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-reactome.db >=1.89.0,<1.90.0 + - bioconductor-reactomepa >=1.50.0,<1.51.0 + - r-algdesign >=1.1.7.3 - r-base - - 'r-diagrammer <=1.01' - - 'r-dplyr >=0.7.2' - - 'r-dt >=0.3' + - r-diagrammer <=1.01 + - r-dplyr >=0.7.2 + - r-dt >=0.3 - r-htmlwidgets - - r-httr - - 'r-import >=1.1.0' + - r-import >=1.1.0 - r-plyr - r-r.methodss3 - r-r.oo - - 'r-radiant.data >=0.9.1' - - 'r-shiny >=1.0.5' + - r-radiant.data >=0.9.1 + - r-shiny >=1.0.5 - r-shinythemes - r-tibble + - r-tidyr - r-visnetwork - - 'r-xml >=3.98' + - r-xml >=3.98 + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-genetclassifier >=1.42.0,<1.43.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-org.bt.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - - 'bioconductor-reactomepa >=1.46.0,<1.47.0' - - 'r-algdesign >=1.1.7.3' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-cbioportaldata >=2.18.0,<2.19.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-genetclassifier >=1.46.0,<1.47.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-org.bt.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-reactome.db >=1.89.0,<1.90.0 + - bioconductor-reactomepa >=1.50.0,<1.51.0 + - r-algdesign >=1.1.7.3 - r-base - - 'r-diagrammer <=1.01' - - 'r-dplyr >=0.7.2' - - 'r-dt >=0.3' + - r-diagrammer <=1.01 + - r-dplyr >=0.7.2 + - r-dt >=0.3 - r-htmlwidgets - - r-httr - - 'r-import >=1.1.0' + - r-import >=1.1.0 - r-plyr - r-r.methodss3 - r-r.oo - - 'r-radiant.data >=0.9.1' - - 'r-shiny >=1.0.5' + - r-radiant.data >=0.9.1 + - r-shiny >=1.0.5 - r-shinythemes - r-tibble + - r-tidyr - r-visnetwork - - 'r-xml >=3.98' + - r-xml >=3.98 + +source: + md5: 5850a568e20fd8958a7ad1463f4644cb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'AGPL-3 | file LICENSE' - summary: 'Interactive Multi-Omics Cancers Data Visualization and Analysis' - description: 'This package is a Shiny App to visualize and analyse interactively Multi-Assays of Cancer Genomic Data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biocartaimage/meta.yaml b/recipes/bioconductor-biocartaimage/meta.yaml index 61d3f51296c03..4113bace1c6f1 100644 --- a/recipes/bioconductor-biocartaimage/meta.yaml +++ b/recipes/bioconductor-biocartaimage/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "BioCartaImage" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8190c93a49f3d53085b3e6e44d482ffa +about: + description: The core functionality of the package is to provide coordinates of genes on the BioCarta pathway images and to provide methods to add self-defined graphics to the genes of interest. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: BioCarta Pathway Images build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocartaimage", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat, knitr, BiocStyle, ragg requirements: host: @@ -27,13 +26,14 @@ requirements: run: - r-base - r-magick +source: + md5: 6aad111e37fc2ff3af5ef2c8847bef6d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'BioCarta Pathway Images' - description: 'The core functionality of the package is to provide coordinates of genes on the BioCarta pathway images and to provide methods to add self-defined graphics to the genes of interest.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biocbaseutils/meta.yaml b/recipes/bioconductor-biocbaseutils/meta.yaml index 66db86820aac2..6b87a426bedbc 100644 --- a/recipes/bioconductor-biocbaseutils/meta.yaml +++ b/recipes/bioconductor-biocbaseutils/meta.yaml @@ -1,36 +1,36 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "BiocBaseUtils" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 23ed1406ff70165a763ca2040c46353e +about: + description: The package provides utility functions related to package development. These include functions that replace slots, and selectors for show methods. It aims to coalesce the various helper functions often re-used throughout the Bioconductor ecosystem. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: General utility functions for developing Bioconductor packages build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocbaseutils", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle, tinytest requirements: host: - r-base run: - r-base +source: + md5: 23940f43a8e0ce95c6cf8780524dcaea + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'General utility functions for developing Bioconductor packages' - description: 'The package provides utility functions related to package development. These include functions that replace slots, and selectors for show methods. It aims to coalesce the various helper functions often re-used throughout the Bioconductor ecosystem.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biocbook/meta.yaml b/recipes/bioconductor-biocbook/meta.yaml index 03d10aeca7f90..414e73301f23f 100644 --- a/recipes/bioconductor-biocbook/meta.yaml +++ b/recipes/bioconductor-biocbook/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "BiocBook" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A BiocBook can be created by authors (e.g. R developers, but also scientists, teachers, communicators, ...) who wish to 1) write (compile a body of biological and/or bioinformatics knowledge), 2) containerize (provide Docker images to reproduce the examples illustrated in the compendium), 3) publish (deploy an online book to disseminate the compendium), and 4) version (automatically generate specific online book versions and Docker images for specific Bioconductor releases). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Write, containerize, publish and version Quarto books with Bioconductor -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6bcb226068f30b135b705960de603ff0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocbook", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, testthat (>= 3.0.0), rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-available - r-base - r-cli @@ -42,7 +44,7 @@ requirements: - r-usethis - r-yaml run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-available - r-base - r-cli @@ -61,13 +63,16 @@ requirements: - r-tibble - r-usethis - r-yaml + +source: + md5: e026613850b65685d6d8c5af7b314a6d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Write, containerize, publish and version Quarto books with Bioconductor' - description: 'A BiocBook can be created by authors (e.g. R developers, but also scientists, teachers, communicators, ...) who wish to 1) write (compile a body of biological and/or bioinformatics knowledge), 2) containerize (provide Docker images to reproduce the examples illustrated in the compendium), 3) publish (deploy an online book to disseminate the compendium), and 4) version (automatically generate specific online book versions and Docker images for specific Bioconductor releases).' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bioccheck/meta.yaml b/recipes/bioconductor-bioccheck/meta.yaml index 2512f02beb7da..e5445f785f1ef 100644 --- a/recipes/bioconductor-bioccheck/meta.yaml +++ b/recipes/bioconductor-bioccheck/meta.yaml @@ -1,56 +1,65 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "BiocCheck" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: BiocCheck guides maintainers through Bioconductor best practicies. It runs Bioconductor-specific package checks by searching through package code, examples, and vignettes. Maintainers are required to address all errors, warnings, and most notes produced. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Bioconductor-specific package checks -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d003f035a6c197261bed5fa4cd989738 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bioccheck", max_pin="x.x") }}' - noarch: generic -# Suggests: RUnit, BiocGenerics, Biobase, jsonlite, rmarkdown, downloader, devtools (>= 1.4.1), usethis, BiocStyle, GenomicRanges, gert + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, devtools, gert, jsonlite, rmarkdown, tinytest, usethis requirements: host: - - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocviews >=1.70.0,<1.71.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocviews >=1.74.0,<1.75.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-biocmanager - r-callr + - r-cli - r-codetools - - r-httr + - r-httr2 - r-knitr + - r-rvest - r-stringdist run: - - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocviews >=1.70.0,<1.71.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocviews >=1.74.0,<1.75.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-biocmanager - r-callr + - r-cli - r-codetools - - r-httr + - r-httr2 - r-knitr + - r-rvest - r-stringdist + +source: + md5: 8c3893efe1dd51dc71e73985b8b7d7ce + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Bioconductor-specific package checks' - description: 'BiocCheck guides maintainers through Bioconductor best practicies. It runs Bioconductor-specific package checks by searching through package code, examples, and vignettes. Maintainers are required to address all errors, warnings, and most notes produced.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biocfhir/meta.yaml b/recipes/bioconductor-biocfhir/meta.yaml index 10c51d83594e6..ac2f96a4e1e0a 100644 --- a/recipes/bioconductor-biocfhir/meta.yaml +++ b/recipes/bioconductor-biocfhir/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "BiocFHIR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: FHIR R4 bundles in JSON format are derived from https://synthea.mitre.org/downloads. Transformation inspired by a kaggle notebook published by Dr Alexander Scarlat, https://www.kaggle.com/code/drscarlat/fhir-starter-parse-healthcare-bundles-into-tables. This is a very limited illustration of some basic parsing and reorganization processes. Additional tooling will be required to move beyond the Synthea data illustrations. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Illustration of FHIR ingestion and transformation using R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 788951417cde10ad9434dd443db47f80 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocfhir", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, rjsoncons, igraph, BiocStyle requirements: host: - - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-dplyr - r-dt @@ -32,8 +33,8 @@ requirements: - r-tidyr - r-visnetwork run: - - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-dplyr - r-dt @@ -41,12 +42,16 @@ requirements: - r-shiny - r-tidyr - r-visnetwork + +source: + md5: eb92ae6530e91900d382a7ef1e148343 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illustration of FHIR ingestion and transformation using R' - description: 'FHIR R4 bundles in JSON format are derived from https://synthea.mitre.org/downloads. Transformation inspired by a kaggle notebook published by Dr Alexander Scarlat, https://www.kaggle.com/code/drscarlat/fhir-starter-parse-healthcare-bundles-into-tables. This is a very limited illustration of some basic parsing and reorganization processes. Additional tooling will be required to move beyond the Synthea data illustrations.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biocfilecache/meta.yaml b/recipes/bioconductor-biocfilecache/meta.yaml index f7dcc3d5468c6..3c964a9fe7de6 100644 --- a/recipes/bioconductor-biocfilecache/meta.yaml +++ b/recipes/bioconductor-biocfilecache/meta.yaml @@ -1,31 +1,38 @@ -{% set version = "2.10.1" %} +{% set version = "2.14.0" %} {% set name = "BiocFileCache" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Manage Files Across Sessions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80f9b9c7ef6f3fcb9aaff7125b409137 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocfilecache", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-biocfilecache + path: recipes/bioconductor-biocfilecache + version: 1.4.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, BiocStyle, rmarkdown, rtracklayer requirements: host: - r-base - r-curl - r-dbi - - 'r-dbplyr >=1.0.0' + - r-dbplyr >=1.0.0 - r-dplyr - r-filelock - r-httr @@ -34,22 +41,21 @@ requirements: - r-base - r-curl - r-dbi - - 'r-dbplyr >=1.0.0' + - r-dbplyr >=1.0.0 - r-dplyr - r-filelock - r-httr - r-rsqlite + +source: + md5: 42f28ab40124ed8865fd2bfc6bd96de0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Manage Files Across Sessions' - description: 'This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.' -extra: - parent_recipe: - name: bioconductor-biocfilecache - path: recipes/bioconductor-biocfilecache - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biocgenerics/meta.yaml b/recipes/bioconductor-biocgenerics/meta.yaml index d2b4a7afa324d..e5d48fe99f440 100644 --- a/recipes/bioconductor-biocgenerics/meta.yaml +++ b/recipes/bioconductor-biocgenerics/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "0.48.1" %} +{% set version = "0.52.0" %} {% set name = "BiocGenerics" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 77629e64c2a9a0324eb11bb59b53b126 +about: + description: The package defines many S4 generic functions used in Bioconductor. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: S4 generic functions used in Bioconductor build: - number: 2 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocgenerics", max_pin="x.x") }}' - noarch: generic -# Suggests: Biobase, S4Vectors, IRanges, GenomicRanges, DelayedArray, Biostrings, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2, flowClust, MSnbase, annotate, RUnit +extra: + identifiers: + - biotools:biocgenerics +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: Biobase, S4Vectors, IRanges, S4Arrays, SparseArray, DelayedArray, HDF5Array, GenomicRanges, pwalign, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2, flowClust, MSnbase, annotate, RUnit requirements: host: - r-base run: - r-base +source: + md5: 17433e48365e2cb89bc5e59de7ead46b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'S4 generic functions used in Bioconductor' - description: 'The package defines many S4 generic functions used in Bioconductor.' -extra: - identifiers: - - biotools:biocgenerics + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biocgraph/meta.yaml b/recipes/bioconductor-biocgraph/meta.yaml index e66a514e3c4a8..2e64a4941392c 100644 --- a/recipes/bioconductor-biocgraph/meta.yaml +++ b/recipes/bioconductor-biocgraph/meta.yaml @@ -1,46 +1,21 @@ -{% set version = "1.64.0" %} +{% set version = "1.68.0" %} {% set name = "biocGraph" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides examples and code that make use of the different graph related packages produced by Bioconductor. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Graph examples and use cases in Bioinformatics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5deb3ff8596eaf678592ad9ae15defe2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocgraph", max_pin="x.x") }}' - noarch: generic -# Suggests: fibroEset, geneplotter, hgu95av2.db -requirements: - host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-geneplotter >=1.80.0,<1.81.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - r-base - run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-geneplotter >=1.80.0,<1.81.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Graph examples and use cases in Bioinformatics' - description: 'This package provides examples and code that make use of the different graph related packages produced by Bioconductor.' + extra: identifiers: - biotools:biocgraph @@ -50,3 +25,34 @@ extra: path: recipes/bioconductor-biocgraph version: 1.42.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: fibroEset, geneplotter, hgu95av2.db +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-geneplotter >=1.84.0,<1.85.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - r-base + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-geneplotter >=1.84.0,<1.85.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - r-base + +source: + md5: 742f69229f19a7c626ba3ecb3c52acca + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-biochubsshiny/meta.yaml b/recipes/bioconductor-biochubsshiny/meta.yaml index eda08864d20d6..a7d58bb36b755 100644 --- a/recipes/bioconductor-biochubsshiny/meta.yaml +++ b/recipes/bioconductor-biochubsshiny/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "BiocHubsShiny" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package that allows interactive exploration of AnnotationHub and ExperimentHub resources. It uses DT / DataTable to display resources for multiple organisms. It provides template code for reproducibility and for downloading resources via the indicated Hub package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: View AnnotationHub and ExperimentHub Resources Interactively -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bc7ef9bc6285eb045f191b7c72846d68 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biochubsshiny", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocManager, BiocStyle, knitr, rmarkdown, sessioninfo, shinytest2 requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dt - r-htmlwidgets @@ -34,9 +35,9 @@ requirements: - r-shinythemes - r-shinytoastr run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dt - r-htmlwidgets @@ -45,12 +46,16 @@ requirements: - r-shinyjs - r-shinythemes - r-shinytoastr + +source: + md5: c7135fde8c3a9a8604e4ba7890a3380c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'View AnnotationHub and ExperimentHub Resources Interactively' - description: 'A package that allows interactive exploration of AnnotationHub and ExperimentHub resources. It uses DT / DataTable to display resources for multiple organisms. It provides template code for reproducibility and for downloading resources via the indicated Hub package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biocio/meta.yaml b/recipes/bioconductor-biocio/meta.yaml index 71881e468ca28..e5708137f8685 100644 --- a/recipes/bioconductor-biocio/meta.yaml +++ b/recipes/bioconductor-biocio/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "BiocIO" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6e0c18bdf6d9f707f9d1e431400fa1c7 +about: + description: The `BiocIO` package contains high-level abstract classes and generics used by developers to build IO funcionality within the Bioconductor suite of packages. Implements `import()` and `export()` standard generics for importing and exporting biological data formats. `import()` supports whole-file as well as chunk-wise iterative import. The `import()` interface optionally provides a standard mechanism for 'lazy' access via `filter()` (on row or element-like components of the file resource), `select()` (on column-like components of the file resource) and `collect()`. The `import()` interface optionally provides transparent access to remote (e.g. via https) as well as local access. Developers can register a file extension, e.g., `.loom` for dispatch from character-based URIs to specific `import()` / `export()` methods based on classes representing file types, e.g., `LoomFile()`. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Standard Input and Output for Bioconductor Packages build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocio", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base +source: + md5: e5e7286586833da1f558a800f4e2bcd2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Standard Input and Output for Bioconductor Packages' - description: 'The `BiocIO` package contains high-level abstract classes and generics used by developers to build IO funcionality within the Bioconductor suite of packages. Implements `import()` and `export()` standard generics for importing and exporting biological data formats. `import()` supports whole-file as well as chunk-wise iterative import. The `import()` interface optionally provides a standard mechanism for ''lazy'' access via `filter()` (on row or element-like components of the file resource), `select()` (on column-like components of the file resource) and `collect()`. The `import()` interface optionally provides transparent access to remote (e.g. via https) as well as local access. Developers can register a file extension, e.g., `.loom` for dispatch from character-based URIs to specific `import()` / `export()` methods based on classes representing file types, e.g., `LoomFile()`.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biocneighbors/meta.yaml b/recipes/bioconductor-biocneighbors/meta.yaml index ed7fc9a00824d..a4ce3ed2a29e3 100644 --- a/recipes/bioconductor-biocneighbors/meta.yaml +++ b/recipes/bioconductor-biocneighbors/meta.yaml @@ -1,58 +1,59 @@ -{% set version = "1.20.0" %} +{% set version = "2.0.0" %} {% set name = "BiocNeighbors" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Exact searches can be performed using the k-means for k-nearest neighbors algorithm or with vantage point trees. Approximate searches can be performed using the Annoy or HNSW libraries. Searching on either Euclidean or Manhattan distances is supported. Parallelization is achieved for all methods by using BiocParallel. Functions are also provided to search for all neighbors within a given distance. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Nearest Neighbor Detection for Bioconductor Packages -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3cfb96ab6d42068c5b875fa6fcefd779 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocneighbors", max_pin="x.x") }}' -# Suggests: testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy, RcppHNSW -# SystemRequirements: C++11 + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:biocneighbors + - usegalaxy-eu:biocneighbors + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocParallel, testthat, BiocStyle, knitr, rmarkdown +# SystemRequirements: C++17 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-assorthead >=1.0.0,<1.1.0 - r-base - - r-matrix - r-rcpp - - r-rcpphnsw - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-assorthead >=1.0.0,<1.1.0 - r-base - - r-matrix - r-rcpp - - r-rcpphnsw - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 34c48c38ec004879dd3bc6757cf428d0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3-only - summary: 'Nearest Neighbor Detection for Bioconductor Packages' - description: 'Implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Exact searches can be performed using the k-means for k-nearest neighbors algorithm or with vantage point trees. Approximate searches can be performed using the Annoy or HNSW libraries. Searching on either Euclidean or Manhattan distances is supported. Parallelization is achieved for all methods by using BiocParallel. Functions are also provided to search for all neighbors within a given distance.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} - - usegalaxy-eu:{{ name|lower }} + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-biocor/meta.yaml b/recipes/bioconductor-biocor/meta.yaml index 4f9b1efe69ee1..24cebffc77f2f 100644 --- a/recipes/bioconductor-biocor/meta.yaml +++ b/recipes/bioconductor-biocor/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "BioCor" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d061581890948dc4341346b82f8d170 +about: + description: Calculates functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships... + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Functional similarities build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocor", max_pin="x.x") }}' - noarch: generic -# Suggests: airway, BiocStyle, boot, DESeq2, ggplot2 (>= 3.4.1), GOSemSim, Hmisc, knitr (>= 1.35), org.Hs.eg.db, reactome.db, rmarkdown, spelling, targetscan.Hs.eg.db, testthat, WGCNA +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: airway, BiocStyle, boot, DESeq2, ggplot2 (>= 3.4.1), GOSemSim, Hmisc, knitr (>= 1.35), org.Hs.eg.db, reactome.db, rmarkdown, spelling, targetscan.Hs.eg.db, testthat (>= 3.0.0), WGCNA requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 - r-base - r-matrix run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 - r-base - r-matrix +source: + md5: 4daca28f480099a769178e0bd4e60386 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Functional similarities' - description: 'Calculates functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships...' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biocparallel/meta.yaml b/recipes/bioconductor-biocparallel/meta.yaml index 29a36dc28da04..aabc9404fb11d 100644 --- a/recipes/bioconductor-biocparallel/meta.yaml +++ b/recipes/bioconductor-biocparallel/meta.yaml @@ -1,26 +1,44 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "BiocParallel" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 | GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Bioconductor facilities for parallel evaluation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a6a331ac453920e713836ddd0de38e25 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocparallel", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:biocparallel + - doi:10.1214/14-STS476 + parent_recipe: + name: bioconductor-biocparallel + path: recipes/bioconductor-biocparallel + version: 1.14.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, tools, foreach, BBmisc, doParallel, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle, knitr, batchtools, data.table # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - r-base - r-bh @@ -37,28 +55,16 @@ requirements: - r-cpp11 - r-futile.logger - r-snow - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: f2801ca5ef796a79de667cab673a4603 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-2 | GPL-3' - summary: 'Bioconductor facilities for parallel evaluation' - description: 'This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:biocparallel - - doi:10.1214/14-STS476 - parent_recipe: - name: bioconductor-biocparallel - path: recipes/bioconductor-biocparallel - version: 1.14.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biocpkgtools/meta.yaml b/recipes/bioconductor-biocpkgtools/meta.yaml index 4c6bab59e87ca..8fc18b43ed740 100644 --- a/recipes/bioconductor-biocpkgtools/meta.yaml +++ b/recipes/bioconductor-biocpkgtools/meta.yaml @@ -1,32 +1,41 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "BiocPkgTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Bioconductor has a rich ecosystem of metadata around packages, usage, and build status. This package is a simple collection of functions to access that metadata from R. The goal is to expose metadata for data mining and value-added functionality such as package searching, text mining, and analytics on packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Collection of simple tools for learning about Bioconductor Packages -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a0ab7353a78b22b286d22520faff6142 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocpkgtools", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, testthat, tm, lubridate, visNetwork, clipr, blastula, kableExtra, DiagrammeR, SummarizedExperiment + +extra: + parent_recipe: + name: bioconductor-biocpkgtools + path: recipes/bioconductor-biocpkgtools + version: 1.0.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, testthat, tm, lubridate, networkD3, visNetwork, clipr, blastula, kableExtra, DiagrammeR, SummarizedExperiment # SystemRequirements: mailsend-go requirements: + host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocviews >=1.70.0,<1.71.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocviews >=1.74.0,<1.75.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 - r-base - r-biocmanager - r-dplyr @@ -45,11 +54,12 @@ requirements: - r-stringr - r-tibble - r-xml2 + run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocviews >=1.70.0,<1.71.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocviews >=1.74.0,<1.75.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 - r-base - r-biocmanager - r-dplyr @@ -68,18 +78,16 @@ requirements: - r-stringr - r-tibble - r-xml2 + +source: + md5: b57e41fe56993ef09ebd46bcd8c97435 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Collection of simple tools for learning about Bioconductor Packages' - description: 'Bioconductor has a rich ecosystem of metadata around packages, usage, and build status. This package is a simple collection of functions to access that metadata from R. The goal is to expose metadata for data mining and value-added functionality such as package searching, text mining, and analytics on packages.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-biocpkgtools - path: recipes/bioconductor-biocpkgtools - version: 1.0.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biocroxytest/build.sh b/recipes/bioconductor-biocroxytest/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-biocroxytest/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocroxytest/meta.yaml b/recipes/bioconductor-biocroxytest/meta.yaml new file mode 100644 index 0000000000000..46e3fe38fba9c --- /dev/null +++ b/recipes/bioconductor-biocroxytest/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.2.0" %} +{% set name = "biocroxytest" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a roclet for roxygen2 that identifies and processes code blocks in your documentation marked with `@longtests`. These blocks should contain tests that take a long time to run and thus cannot be included in the regular test suite of the package. When you run `roxygen2::roxygenise` with the `longtests_roclet`, it will extract these long tests from your documentation and save them in a separate directory. This allows you to run these long tests separately from the rest of your tests, for example, on a continuous integration server that is set up to run long tests. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Handle Long Tests in Bioconductor Packages +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-biocroxytest", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: BiocStyle, here, knitr, rmarkdown, testthat (>= 3.0.0) +requirements: + host: + - r-base + - r-cli + - r-glue + - r-roxygen2 + - r-stringr + run: + - r-base + - r-cli + - r-glue + - r-roxygen2 + - r-stringr +source: + md5: 5fb89e73aaa2844888086004a9b06a0f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-biocset/meta.yaml b/recipes/bioconductor-biocset/meta.yaml index e2086fa5fd45a..9d5b170154f2a 100644 --- a/recipes/bioconductor-biocset/meta.yaml +++ b/recipes/bioconductor-biocset/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "BiocSet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: BiocSet displays different biological sets in a triple tibble format. These three tibbles are `element`, `set`, and `elementset`. The user has the abilty to activate one of these three tibbles to perform common functions from the dplyr package. Mapping functionality and accessing web references for elements/sets are also available in BiocSet. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Representing Different Biological Sets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 69ab960333325b038fb2379781fe36c3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocset", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: GSEABase, airway, org.Hs.eg.db, DESeq2, limma, BiocFileCache, GO.db, testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-ontologyindex @@ -34,10 +35,10 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-ontologyindex @@ -45,12 +46,16 @@ requirements: - r-rlang - r-tibble - r-tidyr + +source: + md5: 37ddc4adbc2908bc87de735cd4c20a12 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Representing Different Biological Sets' - description: 'BiocSet displays different biological sets in a triple tibble format. These three tibbles are `element`, `set`, and `elementset`. The user has the abilty to activate one of these three tibbles to perform common functions from the dplyr package. Mapping functionality and accessing web references for elements/sets are also available in BiocSet.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biocsingular/meta.yaml b/recipes/bioconductor-biocsingular/meta.yaml index 45a90cc65e135..5c5ab734458d6 100644 --- a/recipes/bioconductor-biocsingular/meta.yaml +++ b/recipes/bioconductor-biocsingular/meta.yaml @@ -1,33 +1,46 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "BiocSingular" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implements exact and approximate methods for singular value decomposition and principal components analysis, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Where possible, parallelization is achieved using the BiocParallel framework. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Singular Value Decomposition for Bioconductor Packages -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9b4158e143f2cbefc140228c13090b35 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocsingular", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:biocsingular + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix # SystemRequirements: C++17 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' + - bioconductor-assorthead >=1.0.0,<1.1.0 + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scaledmatrix >=1.14.0,<1.15.0 - r-base - r-irlba - r-matrix @@ -36,33 +49,28 @@ requirements: - libblas - liblapack run: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' + - bioconductor-assorthead >=1.0.0,<1.1.0 + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scaledmatrix >=1.14.0,<1.15.0 - r-base - r-irlba - r-matrix - r-rcpp - r-rsvd - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: bb704ac1d36b56a1b8ea141ffad65ab6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'Singular Value Decomposition for Bioconductor Packages' - description: 'Implements exact and approximate methods for singular value decomposition and principal components analysis, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Where possible, parallelization is achieved using the BiocParallel framework.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-biocsklearn/meta.yaml b/recipes/bioconductor-biocsklearn/meta.yaml index 5974e5fdc00d4..da7cfa001c9f9 100644 --- a/recipes/bioconductor-biocsklearn/meta.yaml +++ b/recipes/bioconductor-biocsklearn/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "BiocSklearn" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3df49031172bfd2b2a3b1c242b7dd40 +about: + description: This package provides interfaces to selected sklearn elements, and demonstrates fault tolerant use of python modules requiring extensive iteration. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: interface to python sklearn via Rstudio reticulate build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocsklearn", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, restfulSE, HDF5Array, BiocStyle, rmarkdown, knitr +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: testthat, HDF5Array, BiocStyle, rmarkdown, knitr # SystemRequirements: python (>= 2.7), sklearn, numpy, pandas, h5py requirements: host: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-reticulate - - 'python >=2.7' + - python >=2.7 run: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-reticulate - - 'python >=2.7' + - python >=2.7 +source: + md5: 3b8803f511bbfa480a9b39faa6d10434 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'interface to python sklearn via Rstudio reticulate' - description: 'This package provides interfaces to selected sklearn elements, and demonstrates fault tolerant use of python modules requiring extensive iteration.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biocstyle/meta.yaml b/recipes/bioconductor-biocstyle/meta.yaml index 0f8df92a25fe6..b2e1f2aa9a689 100644 --- a/recipes/bioconductor-biocstyle/meta.yaml +++ b/recipes/bioconductor-biocstyle/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "2.30.0" %} +{% set version = "2.34.0" %} {% set name = "BiocStyle" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Standard styles for vignettes and other Bioconductor documents -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 22ceacb6ab374657de48283e78dedbb5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocstyle", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:biocstyle + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-biocstyle + path: recipes/bioconductor-biocstyle + version: 2.8.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, RUnit, htmltools requirements: host: - r-base - r-biocmanager - r-bookdown - - 'r-knitr >=1.30' - - 'r-rmarkdown >=1.2' + - r-knitr >=1.30 + - r-rmarkdown >=1.2 - r-yaml run: - r-base - r-biocmanager - r-bookdown - - 'r-knitr >=1.30' - - 'r-rmarkdown >=1.2' + - r-knitr >=1.30 + - r-rmarkdown >=1.2 - r-yaml + +source: + md5: 7a5cd7607712007cf0a0d7f99725d3e7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Standard styles for vignettes and other Bioconductor documents' - description: 'Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.' -extra: - identifiers: - - biotools:biocstyle - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-biocstyle - path: recipes/bioconductor-biocstyle - version: 2.8.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biocthis/meta.yaml b/recipes/bioconductor-biocthis/meta.yaml index 6e1853af5c371..59d6b16d6b987 100644 --- a/recipes/bioconductor-biocthis/meta.yaml +++ b/recipes/bioconductor-biocthis/meta.yaml @@ -1,24 +1,25 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "biocthis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package expands the usethis package with the goal of helping automate the process of creating R packages for Bioconductor or making them Bioconductor-friendly. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Automate package and project setup for Bioconductor packages -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7ebf8e46d2b20a3a2bae3cc7a36264d5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocthis", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, covr, devtools, knitr, pkgdown, RefManageR, rmarkdown, sessioninfo, testthat, utils requirements: host: @@ -28,7 +29,7 @@ requirements: - r-glue - r-rlang - r-styler - - 'r-usethis >=2.0.1' + - r-usethis >=2.0.1 run: - r-base - r-biocmanager @@ -36,13 +37,17 @@ requirements: - r-glue - r-rlang - r-styler - - 'r-usethis >=2.0.1' + - r-usethis >=2.0.1 + +source: + md5: b41b21d9b5c008ad5b1bc6814e739103 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Automate package and project setup for Bioconductor packages' - description: 'This package expands the usethis package with the goal of helping automate the process of creating R packages for Bioconductor or making them Bioconductor-friendly.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biocversion/meta.yaml b/recipes/bioconductor-biocversion/meta.yaml index 2f6a6eaf4f1d2..3a396797ca895 100644 --- a/recipes/bioconductor-biocversion/meta.yaml +++ b/recipes/bioconductor-biocversion/meta.yaml @@ -1,35 +1,35 @@ -{% set version = "3.18.1" %} +{% set version = "3.20.0" %} {% set name = "BiocVersion" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46dbe2f6ca9c058b24da1bd98f79631e +about: + description: This package provides repository information for the appropriate version of Bioconductor. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Set the appropriate version of Bioconductor packages build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocversion", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base +source: + md5: 118dd948af617820eab08b946fb28cbf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Set the appropriate version of Bioconductor packages' - description: 'This package provides repository information for the appropriate version of Bioconductor.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biocviews/meta.yaml b/recipes/bioconductor-biocviews/meta.yaml index 0627cb2e4f0f5..fac7dd79c8ea2 100644 --- a/recipes/bioconductor-biocviews/meta.yaml +++ b/recipes/bioconductor-biocviews/meta.yaml @@ -1,58 +1,64 @@ -{% set version = "1.70.0" %} +{% set version = "1.74.0" %} {% set name = "biocViews" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Infrastructure to support 'views' used to classify Bioconductor packages. 'biocViews' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to 'software', 'annotation', and 'experiment data' packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Categorized views of R package repositories -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e258342a57f06fa23f3732c75539c58d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocviews", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:biocviews + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-biocviews + path: recipes/bioconductor-biocviews + version: 1.48.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, knitr, commonmark, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 - r-base - r-biocmanager - r-rcurl - r-runit - r-xml run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 - r-base - r-biocmanager - r-rcurl - r-runit - r-xml + +source: + md5: 2eb20c70e91cd16fd7bda9e43ecdd44f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Categorized views of R package repositories' - description: 'Infrastructure to support ''views'' used to classify Bioconductor packages. ''biocViews'' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to ''software'', ''annotation'', and ''experiment data'' packages.' -extra: - identifiers: - - biotools:biocviews - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-biocviews - path: recipes/bioconductor-biocviews - version: 1.48.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biocworkflowtools/meta.yaml b/recipes/bioconductor-biocworkflowtools/meta.yaml index 800ffd008347d..c96ad19e445f2 100644 --- a/recipes/bioconductor-biocworkflowtools/meta.yaml +++ b/recipes/bioconductor-biocworkflowtools/meta.yaml @@ -1,27 +1,37 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "BiocWorkflowTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Tools to aid the development of Bioconductor Workflow packages -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 412d30d47953d51e35e9fa188e28841e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biocworkflowtools", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:BiocWorkflowTools + parent_recipe: + name: bioconductor-biocworkflowtools + path: recipes/bioconductor-biocworkflowtools + version: 1.6.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 - r-base - r-bookdown - r-git2r @@ -32,7 +42,7 @@ requirements: - r-stringr - r-usethis run: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 - r-base - r-bookdown - r-git2r @@ -42,20 +52,16 @@ requirements: - r-rstudioapi - r-stringr - r-usethis + +source: + md5: 40aa2f7806fa4ef97cba57498f9a1af7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Tools to aid the development of Bioconductor Workflow packages' - description: 'Provides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.' - license_file: LICENSE -extra: - identifiers: - - biotools:BiocWorkflowTools - parent_recipe: - name: bioconductor-biocworkflowtools - path: recipes/bioconductor-biocworkflowtools - version: 1.6.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biodb/meta.yaml b/recipes/bioconductor-biodb/meta.yaml index ad39c52b330b1..9a67b5c810221 100644 --- a/recipes/bioconductor-biodb/meta.yaml +++ b/recipes/bioconductor-biodb/meta.yaml @@ -1,27 +1,35 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "biodb" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local database files (CSV, SQLite), with easy retrieval of entries, access to web services, search of compounds by mass and/or name, and mass spectra matching for LCMS and MSMS. Its architecture as a development framework facilitates the development of new database connectors for local projects or inside separate published packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + summary: biodb, a library and a development framework for connecting to chemical and biological databases -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0716a73291fb80cc3d1f0909549cbaa8 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biodb", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, xml2 requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base - r-chk - r-git2r @@ -43,8 +51,9 @@ requirements: - r-yaml - libblas - liblapack + run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base - r-chk - r-git2r @@ -64,17 +73,16 @@ requirements: - r-withr - r-xml - r-yaml - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: a1b7adef44ebc05598d5e45645d6571e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3 - summary: 'biodb, a library and a development framework for connecting to chemical and biological databases' - description: 'The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local database files (CSV, SQLite), with easy retrieval of entries, access to web services, search of compounds by mass and/or name, and mass spectra matching for LCMS and MSMS. Its architecture as a development framework facilitates the development of new database connectors for local projects or inside separate published packages.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biodbchebi/meta.yaml b/recipes/bioconductor-biodbchebi/meta.yaml index 4371bc0a4a43f..a28c5849db8db 100644 --- a/recipes/bioconductor-biodbchebi/meta.yaml +++ b/recipes/bioconductor-biodbchebi/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "biodbChebi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 31f6ed155e1126b62c5a6cd7fbd6c742 +about: + description: The biodbChebi library provides access to the ChEBI Database, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name, mass or other fields. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + summary: biodbChebi, a library for connecting to the ChEBI Database build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biodbchebi", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, lgr requirements: host: - - 'bioconductor-biodb >=1.10.0,<1.11.0' + - bioconductor-biodb >=1.14.0,<1.15.0 - r-base - r-r6 run: - - 'bioconductor-biodb >=1.10.0,<1.11.0' + - bioconductor-biodb >=1.14.0,<1.15.0 - r-base - r-r6 +source: + md5: 60d18795d94f834ec183ef0ccfaf4b3d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3 - summary: 'biodbChebi, a library for connecting to the ChEBI Database' - description: 'The biodbChebi library provides access to the ChEBI Database, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name, mass or other fields.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biodbhmdb/meta.yaml b/recipes/bioconductor-biodbhmdb/meta.yaml index 43819b75e957a..3c7d68827ec95 100644 --- a/recipes/bioconductor-biodbhmdb/meta.yaml +++ b/recipes/bioconductor-biodbhmdb/meta.yaml @@ -1,27 +1,33 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "biodbHmdb" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The biodbHmdb library is an extension of the biodb framework package that provides access to the HMDB Metabolites database. It allows to download the whole HMDB Metabolites database locally, access entries and search for entries by name or description. A future version of this package will also include a search by mass and mass spectra annotation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + summary: biodbHmdb, a library for connecting to the HMDB Database -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b34c06c2ce8865b7eebedb869a1ab505 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biodbhmdb", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, lgr requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biodb >=1.10.0,<1.11.0' + - bioconductor-biodb >=1.14.0,<1.15.0 - r-base - r-r6 - r-rcpp @@ -30,23 +36,22 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biodb >=1.10.0,<1.11.0' + - bioconductor-biodb >=1.14.0,<1.15.0 - r-base - r-r6 - r-rcpp - r-testthat - r-zip - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 0333d0ac49b6de03426e7709fa2ca1ac + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3 - summary: 'biodbHmdb, a library for connecting to the HMDB Database' - description: 'The biodbHmdb library is an extension of the biodb framework package that provides access to the HMDB Metabolites database. It allows to download the whole HMDB Metabolites database locally, access entries and search for entries by name or description. A future version of this package will also include a search by mass and mass spectra annotation.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biodbncbi/meta.yaml b/recipes/bioconductor-biodbncbi/meta.yaml index 95b4d06ff4236..13e81db33830f 100644 --- a/recipes/bioconductor-biodbncbi/meta.yaml +++ b/recipes/bioconductor-biodbncbi/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "biodbNcbi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d2c3e8eade431a86e13d54be468832e +about: + description: The biodbNcbi library provides access to the NCBI databases CCDS, Gene, Pubchem Comp and Pubchem Subst, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name or mass. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + summary: biodbNcbi, a library for connecting to NCBI Databases. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biodbncbi", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr requirements: host: - - 'bioconductor-biodb >=1.10.0,<1.11.0' + - bioconductor-biodb >=1.14.0,<1.15.0 - r-base - r-chk - r-r6 - r-xml run: - - 'bioconductor-biodb >=1.10.0,<1.11.0' + - bioconductor-biodb >=1.14.0,<1.15.0 - r-base - r-chk - r-r6 - r-xml +source: + md5: c17c1f48c74070ec3e73b877f580c4c9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3 - summary: 'biodbNcbi, a library for connecting to NCBI Databases.' - description: 'The biodbNcbi library provides access to the NCBI databases CCDS, Gene, Pubchem Comp and Pubchem Subst, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name or mass.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biodbnci/meta.yaml b/recipes/bioconductor-biodbnci/meta.yaml index cc1d3f3405d9c..ff0c492ac871d 100644 --- a/recipes/bioconductor-biodbnci/meta.yaml +++ b/recipes/bioconductor-biodbnci/meta.yaml @@ -1,27 +1,33 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "biodbNci" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The biodbNci library is an extension of the biodb framework package. It provides access to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database. It allows to retrieve entries by their accession number, and run specific web services. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + summary: biodbNci, a library for connecting to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6dcd43d5c282054f4edfef08a2f597cd build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biodbnci", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr, rmarkdown, covr, lgr requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biodb >=1.10.0,<1.11.0' + - bioconductor-biodb >=1.14.0,<1.15.0 - r-base - r-chk - r-r6 @@ -30,23 +36,22 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biodb >=1.10.0,<1.11.0' + - bioconductor-biodb >=1.14.0,<1.15.0 - r-base - r-chk - r-r6 - r-rcpp - r-testthat - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: c60bde3f0881c284dbc9dc6089338b64 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3 - summary: 'biodbNci, a library for connecting to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database' - description: 'The biodbNci library is an extension of the biodb framework package. It provides access to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database. It allows to retrieve entries by their accession number, and run specific web services.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biodbuniprot/meta.yaml b/recipes/bioconductor-biodbuniprot/meta.yaml index a4e0d9a6b658e..cefd357900d2d 100644 --- a/recipes/bioconductor-biodbuniprot/meta.yaml +++ b/recipes/bioconductor-biodbuniprot/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "biodbUniprot" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4f5bcc32018b6472836efcc8c82671c +about: + description: The biodbUniprot library is an extension of the biodb framework package. It provides access to the UniProt database. It allows to retrieve entries by their accession number, and run web service queries for searching for entries. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + summary: biodbUniprot, a library for connecting to the Uniprot Database build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biodbuniprot", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, lgr, covr requirements: host: - - 'bioconductor-biodb >=1.10.0,<1.11.0' + - bioconductor-biodb >=1.14.0,<1.15.0 - r-base - r-r6 run: - - 'bioconductor-biodb >=1.10.0,<1.11.0' + - bioconductor-biodb >=1.14.0,<1.15.0 - r-base - r-r6 +source: + md5: 964a9897ac1aecbe5f798ea706d1d74c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3 - summary: 'biodbUniprot, a library for connecting to the Uniprot Database' - description: 'The biodbUniprot library is an extension of the biodb framework package. It provides access to the UniProt database. It allows to retrieve entries by their accession number, and run web service queries for searching for entries.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biodist/meta.yaml b/recipes/bioconductor-biodist/meta.yaml index 638ca746d888c..6fe425b88507c 100644 --- a/recipes/bioconductor-biodist/meta.yaml +++ b/recipes/bioconductor-biodist/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "bioDist" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A collection of software tools for calculating distance measures. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Different distance measures -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a0c907dc82834b4771074cd8164cf773 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biodist", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:biodist + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-biodist + path: recipes/bioconductor-biodist + version: 1.52.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: locfit requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-kernsmooth run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-kernsmooth + +source: + md5: 85ab92d68c01525dc662ffc42dc68aed + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Different distance measures' - description: 'A collection of software tools for calculating distance measures.' -extra: - identifiers: - - biotools:biodist - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-biodist - path: recipes/bioconductor-biodist - version: 1.52.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bioga/build.sh b/recipes/bioconductor-bioga/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bioga/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bioga/build_failure.osx-64.yaml b/recipes/bioconductor-bioga/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..b3e1d7f154a80 --- /dev/null +++ b/recipes/bioconductor-bioga/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: aebb878f4c680fd932083d3ef2ee46051a3fadbbfcf9d0ff19a987c130f585db # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec(">=1.84.0,<1.85.0"), MatchSpec("bioconductor-biocviews==1.74.0=r44hdfd78af_0")} + Encountered problems while solving: + - nothing provides bioconductor-graph >=1.84.0,<1.85.0 needed by bioconductor-biocviews-1.74.0-r44hdfd78af_0 + + Could not solve for environment specs + The following package could not be installed + bioconductor-biocviews >=1.74.0,<1.75.0 is not installable because it requires + bioconductor-graph >=1.84.0,<1.85.0 , which does not exist (perhaps a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec(">=1.84.0,<1.85.0"), MatchSpec("bioconductor-biocviews==1.74.0=r44hdfd78af_0")} + Encountered problems while solving: + - nothing provides bioconductor-graph >=1.84.0,<1.85.0 needed by bioconductor-biocviews-1.74.0-r44hdfd78af_0 + + Could not solve for environment specs + The following package could not be installed + bioconductor-biocviews >=1.74.0,<1.75.0 is not installable because it requires + bioconductor-graph >=1.84.0,<1.85.0 , which does not exist (perhaps a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec(">=1.84.0,<1.85.0"), MatchSpec("bioconductor-biocviews==1.74.0=r44hdfd78af_0")} + Encountered problems while solving: + - nothing provides bioconductor-graph >=1.84.0,<1.85.0 needed by bioconductor-biocviews-1.74.0-r44hdfd78af_0 + + Could not solve for environment specs + The following package could not be installed + bioconductor-biocviews >=1.74.0,<1.75.0 is not installable because it requires + bioconductor-graph >=1.84.0,<1.85.0 , which does not exist (perhaps a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-bioga/meta.yaml b/recipes/bioconductor-bioga/meta.yaml new file mode 100644 index 0000000000000..74ef10a9f6438 --- /dev/null +++ b/recipes/bioconductor-bioga/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.0.0" %} +{% set name = "BioGA" %} +{% set bioc = "3.20" %} + +about: + description: Genetic algorithm are a class of optimization algorithms inspired by the process of natural selection and genetics. This package allows users to analyze and optimize high throughput genomic data using genetic algorithms. The functions provided are implemented in C++ for improved speed and efficiency, with an easy-to-use interface for use within R. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Bioinformatics Genetic Algorithm (BioGA) + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bioga", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, testthat (>= 3.0.0) +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-biocviews >=1.74.0,<1.75.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-animation + - r-base + - r-ggplot2 + - r-rcpp + - r-rlang + - r-sessioninfo + - libblas + - liblapack + run: + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-biocviews >=1.74.0,<1.75.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-animation + - r-base + - r-ggplot2 + - r-rcpp + - r-rlang + - r-sessioninfo + +source: + md5: 3b1aaf87addc00db6a311f84704987be + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-bioimagedbs/meta.yaml b/recipes/bioconductor-bioimagedbs/meta.yaml index f7ebe42cadf2b..c1f4e68ffb01c 100644 --- a/recipes/bioconductor-bioimagedbs/meta.yaml +++ b/recipes/bioconductor-bioimagedbs/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "BioImageDbs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package provides a bioimage dataset for the image analysis using machine learning and deep learning. The dataset includes microscopy imaging data with supervised labels. The data is provided as R list data that can be loaded to Keras/tensorflow in R. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Bio- and biomedical imaging dataset for machine learning and deep learning (for ExperimentHub) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 785e9ea81ef5699d70af969fd8d4703d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bioimagedbs", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, purrr requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-animation - r-base - r-einsum @@ -34,9 +35,9 @@ requirements: - r-markdown - r-rmarkdown run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-animation - r-base - r-einsum @@ -46,13 +47,17 @@ requirements: - r-markdown - r-rmarkdown - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 3cc77545922812f009e5c6444f20b985 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Bio- and biomedical imaging dataset for machine learning and deep learning (for ExperimentHub)' - description: 'The package provides a bioimage dataset for the image analysis using machine learning and deep learning. The dataset includes microscopy imaging data with supervised labels. The data is provided as R list data that can be loaded to Keras/tensorflow in R.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bioimagedbs/post-link.sh b/recipes/bioconductor-bioimagedbs/post-link.sh index 908f4e675bd43..a6cf52b3790b1 100644 --- a/recipes/bioconductor-bioimagedbs/post-link.sh +++ b/recipes/bioconductor-bioimagedbs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bioimagedbs-1.10.0" +installBiocDataPackage.sh "bioimagedbs-1.14.0" diff --git a/recipes/bioconductor-biomart/meta.yaml b/recipes/bioconductor-biomart/meta.yaml index 9682b4d2750eb..d8a6e8a78dad4 100644 --- a/recipes/bioconductor-biomart/meta.yaml +++ b/recipes/bioconductor-biomart/meta.yaml @@ -1,62 +1,68 @@ -{% set version = "2.58.0" %} +{% set version = "2.62.0" %} {% set name = "biomaRt" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are maintain by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Interface to BioMart databases (i.e. Ensembl) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dd18037fef27f7c50af56f5da2086e04 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biomart", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, knitr, mockery, rmarkdown, testthat, webmockr + +extra: + identifiers: + - biotools:biomaRt + - doi:10.1038/nprot.2009.97 + parent_recipe: + name: bioconductor-biomart + path: recipes/bioconductor-biomart + version: 2.36.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, mockery, rmarkdown, testthat, httptest2 requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base + - r-curl - r-digest - - r-httr + - r-httr2 - r-progress - r-rappdirs - r-stringr - - 'r-xml >=3.99-0.7' - r-xml2 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base + - r-curl - r-digest - - r-httr + - r-httr2 - r-progress - r-rappdirs - r-stringr - - 'r-xml >=3.99-0.7' - r-xml2 + +source: + md5: 405174e4e9aaafe96f14c5c3f4d43dcb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Interface to BioMart databases (i.e. Ensembl)' - description: 'In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are maintain by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.' -extra: - identifiers: - - biotools:biomaRt - - doi:10.1038/nprot.2009.97 - parent_recipe: - name: bioconductor-biomart - path: recipes/bioconductor-biomart - version: 2.36.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biomartgogenesets/meta.yaml b/recipes/bioconductor-biomartgogenesets/meta.yaml index df4009848c019..543b40ff718d0 100644 --- a/recipes/bioconductor-biomartgogenesets/meta.yaml +++ b/recipes/bioconductor-biomartgogenesets/meta.yaml @@ -1,43 +1,43 @@ {% set version = "0.99.11" %} {% set name = "BioMartGOGeneSets" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f96a12703fd2f9c357442a60e5f2c764 +about: + description: It contains pre-compiled Gene Ontology gene sets for all organisms available on the Ensembl database. It also includes GO gene sets for organisms on Ensembl Plants, Ensembl Metazoa, Ensembl Fungi and Ensembl Protists. The data was collected with the biomaRt package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Gene Ontology Gene Sets from BioMart build: - number: 0 + noarch: generic + number: 1 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biomartgogenesets", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: biomaRt, GO.db, GenomeInfoDb, knitr, testthat, GetoptLong, DT requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f96a12703fd2f9c357442a60e5f2c764 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Gene Ontology Gene Sets from BioMart' - description: 'It contains pre-compiled Gene Ontology gene sets for all organisms available on the Ensembl database. It also includes GO gene sets for organisms on Ensembl Plants, Ensembl Metazoa, Ensembl Fungi and Ensembl Protists. The data was collected with the biomaRt package.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biomformat/meta.yaml b/recipes/bioconductor-biomformat/meta.yaml index 9baeccbf7f291..52c718eb8220c 100644 --- a/recipes/bioconductor-biomformat/meta.yaml +++ b/recipes/bioconductor-biomformat/meta.yaml @@ -1,47 +1,22 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "biomformat" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: An interface package for the BIOM file format -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f35aaf72b454bc1872f1247642029006 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biomformat", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6), rmarkdown (>= 0.7) -requirements: - host: - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - r-base - - 'r-jsonlite >=0.9.16' - - 'r-matrix >=1.2' - - 'r-plyr >=1.8' - run: - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - r-base - - 'r-jsonlite >=0.9.16' - - 'r-matrix >=1.2' - - 'r-plyr >=1.8' -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'An interface package for the BIOM file format' - description: 'This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + extra: identifiers: - biotools:biomformat @@ -51,3 +26,34 @@ extra: path: recipes/bioconductor-biomformat version: 1.8.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6), rmarkdown (>= 0.7) +requirements: + host: + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - r-base + - r-jsonlite >=0.9.16 + - r-matrix >=1.2 + - r-plyr >=1.8 + run: + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - r-base + - r-jsonlite >=0.9.16 + - r-matrix >=1.2 + - r-plyr >=1.8 + +source: + md5: bbdd408a1360bceaf000d7004915b0e0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-biomvcclass/meta.yaml b/recipes/bioconductor-biomvcclass/meta.yaml index 63e1563014b71..0f25d1d0eee48 100644 --- a/recipes/bioconductor-biomvcclass/meta.yaml +++ b/recipes/bioconductor-biomvcclass/meta.yaml @@ -1,46 +1,22 @@ -{% set version = "1.70.0" %} +{% set version = "1.74.0" %} {% set name = "BioMVCClass" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Creates classes used in model-view-controller (MVC) design + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Model-View-Controller (MVC) Classes That Use Biobase -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 72d762b9a59c4b75d79c378792250b48 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biomvcclass", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-mvcclass >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-mvcclass >=1.76.0,<1.77.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Model-View-Controller (MVC) Classes That Use Biobase' - description: 'Creates classes used in model-view-controller (MVC) design' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + extra: identifiers: - biotools:biomvcclass @@ -50,3 +26,33 @@ extra: path: recipes/bioconductor-biomvcclass version: 1.48.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-mvcclass >=1.80.0,<1.81.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-mvcclass >=1.80.0,<1.81.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - r-base + +source: + md5: 014dcb2009fc78bb10f71f66b0b50443 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-biomvrcns/meta.yaml b/recipes/bioconductor-biomvrcns/meta.yaml index 29c5079d7968d..16e0de349cc7a 100644 --- a/recipes/bioconductor-biomvrcns/meta.yaml +++ b/recipes/bioconductor-biomvrcns/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.42.1" %} +{% set version = "1.46.0" %} {% set name = "biomvRCNS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: In this package, a Hidden Semi Markov Model (HSMM) and one homogeneous segmentation model are designed and implemented for segmentation genomic data, with the aim of assisting in transcripts detection using high throughput technology like RNA-seq or tiling array, and copy number analysis using aCGH or sequencing. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Copy Number study and Segmentation for multivariate biological data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 592c6d6f34e855eed52b4591b6b065e1 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biomvrcns", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: cluster, parallel, GenomicFeatures, dynamicTreeCut, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-mvtnorm - libblas - liblapack run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-mvtnorm - build: - - {{ compiler('c') }} - - make + +source: + md5: 13b55aa2b6d539c30280f7e7e948e1f5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Copy Number study and Segmentation for multivariate biological data' - description: 'In this package, a Hidden Semi Markov Model (HSMM) and one homogeneous segmentation model are designed and implemented for segmentation genomic data, with the aim of assisting in transcripts detection using high throughput technology like RNA-seq or tiling array, and copy number analysis using aCGH or sequencing.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bionar/meta.yaml b/recipes/bioconductor-bionar/meta.yaml index a1ef1fc42337d..9e893c24518a5 100644 --- a/recipes/bioconductor-bionar/meta.yaml +++ b/recipes/bioconductor-bionar/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "BioNAR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: the R package BioNAR, developed to step by step analysis of PPI network. The aim is to quantify and rank each protein’s simultaneous impact into multiple complexes based on network topology and clustering. Package also enables estimating of co-occurrence of diseases across the network and specific clusters pointing towards shared/common mechanisms. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Biological Network Analysis in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4cbc1fe5bd753444b3470a317029a885 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bionar", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, magick, rmarkdown, igraphdata, testthat (>= 3.0.0), vdiffr, devtools, pander, plotly, randomcoloR requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - r-clustercons - r-cowplot @@ -33,7 +35,7 @@ requirements: - r-dplyr - r-ggplot2 - r-ggrepel - - 'r-igraph >=1.4.0' + - r-igraph >=2.0.1.1 - r-latex2exp - r-matrix - r-minpack.lm @@ -45,11 +47,12 @@ requirements: - r-stringr - r-viridis - r-wgcna + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - r-clustercons - r-cowplot @@ -57,7 +60,7 @@ requirements: - r-dplyr - r-ggplot2 - r-ggrepel - - 'r-igraph >=1.4.0' + - r-igraph >=2.0.1.1 - r-latex2exp - r-matrix - r-minpack.lm @@ -69,12 +72,16 @@ requirements: - r-stringr - r-viridis - r-wgcna + +source: + md5: 6d871ed023436cf01a3eda576b888423 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Biological Network Analysis in R' - description: 'the R package BioNAR, developed to step by step analysis of PPI network. The aim is to quantify and rank each protein’s simultaneous impact into multiple complexes based on network topology and clustering. Package also enables estimating of co-occurrence of diseases across the network and specific clusters pointing towards shared/common mechanisms.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bionero/meta.yaml b/recipes/bioconductor-bionero/meta.yaml index 2ebcf257d05b5..d052aba6ca0f0 100644 --- a/recipes/bioconductor-bionero/meta.yaml +++ b/recipes/bioconductor-bionero/meta.yaml @@ -1,33 +1,36 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "BioNERO" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses for biological interpretations. BioNERO can be used to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs) from gene expression data. Additionally, it can be used to explore topological properties of protein-protein interaction (PPI) networks. GCN inference relies on the popular WGCNA algorithm. GRN inference is based on the "wisdom of the crowds" principle, which consists in inferring GRNs with multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average rank for each interaction pair. As all steps of network analyses are included in this package, BioNERO makes users avoid having to learn the syntaxes of several packages and how to communicate between them. Finally, users can also identify consensus modules across independent expression sets and calculate intra and interspecies module preservation statistics between different networks. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Biological Network Reconstruction Omnibus -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4cc77a8b8eb3cff071fbe5df15a6eb67 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bionero", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle, DESeq2, networkD3, covr requirements: + host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genie3 >=1.24.0,<1.25.0' - - 'bioconductor-minet >=3.60.0,<3.61.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genie3 >=1.28.0,<1.29.0 + - bioconductor-minet >=3.64.0,<3.65.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-dynamictreecut - r-ggdendro @@ -43,13 +46,14 @@ requirements: - r-reshape2 - r-rlang - r-wgcna + run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genie3 >=1.24.0,<1.25.0' - - 'bioconductor-minet >=3.60.0,<3.61.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genie3 >=1.28.0,<1.29.0 + - bioconductor-minet >=3.64.0,<3.65.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-dynamictreecut - r-ggdendro @@ -65,13 +69,16 @@ requirements: - r-reshape2 - r-rlang - r-wgcna + +source: + md5: bd8a627c25eb9e60f504ca4b30c01a56 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Biological Network Reconstruction Omnibus' - description: 'BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses for biological interpretations. BioNERO can be used to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs) from gene expression data. Additionally, it can be used to explore topological properties of protein-protein interaction (PPI) networks. GCN inference relies on the popular WGCNA algorithm. GRN inference is based on the "wisdom of the crowds" principle, which consists in inferring GRNs with multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average rank for each interaction pair. As all steps of network analyses are included in this package, BioNERO makes users avoid having to learn the syntaxes of several packages and how to communicate between them. Finally, users can also identify consensus modules across independent expression sets and calculate intra and interspecies module preservation statistics between different networks.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bionet/meta.yaml b/recipes/bioconductor-bionet/meta.yaml index ba12d6bab333a..9cadb1e43d3da 100644 --- a/recipes/bioconductor-bionet/meta.yaml +++ b/recipes/bioconductor-bionet/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "1.62.0" %} +{% set version = "1.66.0" %} {% set name = "BioNet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. E.g. p-values obtained from the differential expression of the genes from an Affymetrix array are assigned to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from the p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Routines for the functional analysis of biological networks -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7f2fb01406a2c73946981af9fa9c86c8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bionet", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:bionet + parent_recipe: + name: bioconductor-bionet + path: recipes/bioconductor-bionet + version: 1.40.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 - r-base - - 'r-igraph >=1.0.1' + - r-igraph >=1.0.1 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 - r-base - - 'r-igraph >=1.0.1' + - r-igraph >=1.0.1 + +source: + md5: 8bc51fd946d2646ec224f2b823ebdae1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Routines for the functional analysis of biological networks' - description: 'This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. E.g. p-values obtained from the differential expression of the genes from an Affymetrix array are assigned to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from the p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:bionet - parent_recipe: - name: bioconductor-bionet - path: recipes/bioconductor-bionet - version: 1.40.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bioplex/meta.yaml b/recipes/bioconductor-bioplex/meta.yaml index 2861b800c834c..1da48be2aed8b 100644 --- a/recipes/bioconductor-bioplex/meta.yaml +++ b/recipes/bioconductor-bioplex/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "BioPlex" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The BioPlex package implements access to the BioPlex protein-protein interaction networks and related resources from within R. Besides protein-protein interaction networks for HEK293 and HCT116 cells, this includes access to CORUM protein complex data, and transcriptome and proteome data for the two cell lines. Functionality focuses on importing the various data resources and storing them in dedicated Bioconductor data structures, as a foundation for integrative downstream analysis of the data. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: R-side access to BioPlex protein-protein interaction data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 77e38da3b194e7776fa7007a2cef42bf build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bioplex", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationDbi, AnnotationHub, BiocStyle, DEXSeq, ExperimentHub, GenomicFeatures, S4Vectors, depmap, knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 6082010a89fc4adbb51185459ab189f5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'R-side access to BioPlex protein-protein interaction data' - description: 'The BioPlex package implements access to the BioPlex protein-protein interaction networks and related resources from within R. Besides protein-protein interaction networks for HEK293 and HCT116 cells, this includes access to CORUM protein complex data, and transcriptome and proteome data for the two cell lines. Functionality focuses on importing the various data resources and storing them in dedicated Bioconductor data structures, as a foundation for integrative downstream analysis of the data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bioplex/post-link.sh b/recipes/bioconductor-bioplex/post-link.sh index fbbc180637819..b2adb42286944 100644 --- a/recipes/bioconductor-bioplex/post-link.sh +++ b/recipes/bioconductor-bioplex/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bioplex-1.8.0" +installBiocDataPackage.sh "bioplex-1.12.0" diff --git a/recipes/bioconductor-bioqc/meta.yaml b/recipes/bioconductor-bioqc/meta.yaml index 857cec979ea61..fd679b347216b 100644 --- a/recipes/bioconductor-bioqc/meta.yaml +++ b/recipes/bioconductor-bioqc/meta.yaml @@ -1,58 +1,64 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "BioQC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: BioQC performs quality control of high-throughput expression data based on tissue gene signatures. It can detect tissue heterogeneity in gene expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is optimised for high performance. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=3) + file LICENSE + license_file: LICENSE + summary: Detect tissue heterogeneity in expression profiles with gene sets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e9b338e001fdeb614091e4fa0cf50cd build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bioqc", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:bioqc + - doi:10.1186/s12864-017-3661-2 + parent_recipe: + name: bioconductor-bioqc + path: recipes/bioconductor-bioqc + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, lattice, latticeExtra, rbenchmark, gplots, gridExtra, org.Hs.eg.db, hgu133plus2.db, ggplot2, reshape2, plyr, ineq, covr, limma, RColorBrewer requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-edger >=4.4.0,<4.5.0 - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-edger >=4.4.0,<4.5.0 - r-base - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: ebefc9755aefc0a29ad7bd459db71ae3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later + file LICENSE' - summary: 'Detect tissue heterogeneity in expression profiles with gene sets' - description: 'BioQC performs quality control of high-throughput expression data based on tissue gene signatures. It can detect tissue heterogeneity in gene expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is optimised for high performance.' - license_file: LICENSE -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:bioqc - - doi:10.1186/s12864-017-3661-2 - parent_recipe: - name: bioconductor-bioqc - path: recipes/bioconductor-bioqc - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biosigner/meta.yaml b/recipes/bioconductor-biosigner/meta.yaml index 459f194a9ee3b..5aa39ff42d0e3 100644 --- a/recipes/bioconductor-biosigner/meta.yaml +++ b/recipes/bioconductor-biosigner/meta.yaml @@ -1,58 +1,64 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "biosigner" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Feature selection is critical in omics data analysis to extract restricted and meaningful molecular signatures from complex and high-dimension data, and to build robust classifiers. This package implements a new method to assess the relevance of the variables for the prediction performances of the classifier. The approach can be run in parallel with the PLS-DA, Random Forest, and SVM binary classifiers. The signatures and the corresponding 'restricted' models are returned, enabling future predictions on new datasets. A Galaxy implementation of the package is available within the Workflow4metabolomics.org online infrastructure for computational metabolomics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: CeCILL + summary: Signature discovery from omics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 33d853127b5e108b0fa1c5dfea22517d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biosigner", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:biosigner + - doi:10.3389/fmolb.2016.00026 + parent_recipe: + name: bioconductor-biosigner + path: recipes/bioconductor-biosigner + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BioMark, BiocGenerics, BiocStyle, golubEsets, hu6800.db, knitr, omicade4, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-multidataset >=1.30.0,<1.31.0' - - 'bioconductor-ropls >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-multidataset >=1.34.0,<1.35.0 + - bioconductor-ropls >=1.38.0,<1.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-e1071 - r-randomforest run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-multidataset >=1.30.0,<1.31.0' - - 'bioconductor-ropls >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-multidataset >=1.34.0,<1.35.0 + - bioconductor-ropls >=1.38.0,<1.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-e1071 - r-randomforest + +source: + md5: 520d3316884f94a15696c3d91fbc3a6f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: CeCILL - summary: 'Signature discovery from omics data' - description: 'Feature selection is critical in omics data analysis to extract restricted and meaningful molecular signatures from complex and high-dimension data, and to build robust classifiers. This package implements a new method to assess the relevance of the variables for the prediction performances of the classifier. The approach can be run in parallel with the PLS-DA, Random Forest, and SVM binary classifiers. The signatures and the corresponding ''restricted'' models are returned, enabling future predictions on new datasets. A Galaxy implementation of the package is available within the Workflow4metabolomics.org online infrastructure for computational metabolomics.' -extra: - identifiers: - - biotools:biosigner - - doi:10.3389/fmolb.2016.00026 - parent_recipe: - name: bioconductor-biosigner - path: recipes/bioconductor-biosigner - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biostrings/meta.yaml b/recipes/bioconductor-biostrings/meta.yaml index 7edb20f32cd62..50bc730633c7f 100644 --- a/recipes/bioconductor-biostrings/meta.yaml +++ b/recipes/bioconductor-biostrings/meta.yaml @@ -1,62 +1,68 @@ -{% set version = "2.70.1" %} +{% set version = "2.74.0" %} {% set name = "Biostrings" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Efficient manipulation of biological strings -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 998fdd127f3613ca157917c847e22ac3 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biostrings", max_pin="x.x") }}' -# Suggests: BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit, BiocStyle, knitr + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:biostrings + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-biostrings + path: recipes/bioconductor-biostrings + version: 2.48.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: graphics, pwalign, BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit, BiocStyle, knitr, testthat (>= 3.0.0), covr requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-crayon - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-crayon - build: - - {{ compiler('c') }} - - make + +source: + md5: 9c1fa1b00da834f1dc7c2976af36b00c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Efficient manipulation of biological strings' - description: 'Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:biostrings - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-biostrings - path: recipes/bioconductor-biostrings - version: 2.48.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biotip/meta.yaml b/recipes/bioconductor-biotip/meta.yaml index 89e01b63d03be..803b3600de3bc 100644 --- a/recipes/bioconductor-biotip/meta.yaml +++ b/recipes/bioconductor-biotip/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "BioTIP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Adopting tipping-point theory to transcriptome profiles to unravel disease regulatory trajectory. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'BioTIP: An R package for characterization of Biological Tipping-Point' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9a7765bd55ed7e2d7d09d4eff3b2127c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biotip", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, markdown, base, rmarkdown, ggplot2 requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-scran >=1.34.0,<1.35.0 - r-base - r-cluster - r-igraph @@ -31,21 +33,24 @@ requirements: - r-psych - r-stringr run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-scran >=1.34.0,<1.35.0 - r-base - r-cluster - r-igraph - r-mass - r-psych - r-stringr + +source: + md5: 3361614ccd89db9170a5a239ef6f5006 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'BioTIP: An R package for characterization of Biological Tipping-Point' - description: 'Adopting tipping-point theory to transcriptome profiles to unravel disease regulatory trajectory.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biotmle/meta.yaml b/recipes/bioconductor-biotmle/meta.yaml index b7e9320cef7ee..7a015608935ee 100644 --- a/recipes/bioconductor-biotmle/meta.yaml +++ b/recipes/bioconductor-biotmle/meta.yaml @@ -1,61 +1,66 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "biotmle" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for differential expression biomarker discovery based on microarray and next-generation sequencing data that leverage efficient semiparametric estimators of the average treatment effect for variable importance analysis. Estimation and inference of the (marginal) average treatment effects of potential biomarkers are computed by targeted minimum loss-based estimation, with joint, stable inference constructed across all biomarkers using a generalization of moderated statistics for use with the estimated efficient influence function. The procedure accommodates the use of ensemble machine learning for the estimation of nuisance functions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Targeted Learning with Moderated Statistics for Biomarker Discovery -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 10fcb7a34336492cbd49f3170a2f81ba build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biotmle", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocStyle, arm, earth, ranger, SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1) requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-dplyr - - 'r-drtmle >=1.0.4' + - r-drtmle >=1.0.4 - r-ggplot2 - r-ggsci - r-superheat - r-tibble run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-dplyr - - 'r-drtmle >=1.0.4' + - r-drtmle >=1.0.4 - r-ggplot2 - r-ggsci - r-superheat - r-tibble + +source: + md5: 5badccc0ebe373d912aa5b62508a5539 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Targeted Learning with Moderated Statistics for Biomarker Discovery' - description: 'Tools for differential expression biomarker discovery based on microarray and next-generation sequencing data that leverage efficient semiparametric estimators of the average treatment effect for variable importance analysis. Estimation and inference of the (marginal) average treatment effects of potential biomarkers are computed by targeted minimum loss-based estimation, with joint, stable inference constructed across all biomarkers using a generalization of moderated statistics for use with the estimated efficient influence function. The procedure accommodates the use of ensemble machine learning for the estimation of nuisance functions.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biotmledata/meta.yaml b/recipes/bioconductor-biotmledata/meta.yaml index 2413693fa7bec..b6379e650302c 100644 --- a/recipes/bioconductor-biotmledata/meta.yaml +++ b/recipes/bioconductor-biotmledata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "biotmleData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8c725d5c496f9bfe7ed4b5d5c538244a +about: + description: Microarray data (from the Illumina Ref-8 BeadChips platform) and phenotype-level data from an epidemiological investigation of benzene exposure, packaged using "SummarizedExperiemnt", for use as an example with the "biotmle" R package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Example experimental microarray data set for the "biotmle" R package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biotmledata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: Biobase, SummarizedExperiment requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ebc2c473d76e484b65b601f4be16190b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Example experimental microarray data set for the "biotmle" R package' - description: 'Microarray data (from the Illumina Ref-8 BeadChips platform) and phenotype-level data from an epidemiological investigation of benzene exposure, packaged using "SummarizedExperiemnt", for use as an example with the "biotmle" R package.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biotmledata/post-link.sh b/recipes/bioconductor-biotmledata/post-link.sh index f4cbb02679956..f56cfa6a0522c 100644 --- a/recipes/bioconductor-biotmledata/post-link.sh +++ b/recipes/bioconductor-biotmledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "biotmledata-1.26.0" +installBiocDataPackage.sh "biotmledata-1.30.0" diff --git a/recipes/bioconductor-biovizbase/meta.yaml b/recipes/bioconductor-biovizbase/meta.yaml index 441d67f46f122..fd2a819c40142 100644 --- a/recipes/bioconductor-biovizbase/meta.yaml +++ b/recipes/bioconductor-biovizbase/meta.yaml @@ -1,40 +1,57 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "biovizBase" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Basic graphic utilities for visualization of genomic data. -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8430b2a7913fdcfe27b9bf52ba9aff7e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biovizbase", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:biovizbase + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-biovizbase + path: recipes/bioconductor-biovizbase + version: 1.28.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit requirements: + + build: + - {{ compiler('c') }} + - make + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-dichromat - r-hmisc @@ -43,46 +60,38 @@ requirements: - r-scales - libblas - liblapack + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-dichromat - r-hmisc - r-rcolorbrewer - r-rlang - r-scales - build: - - {{ compiler('c') }} - - make + +source: + md5: 8c46d5b8947d56ba506dd9fcb1e8363b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Basic graphic utilities for visualization of genomic data.' - description: 'The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:biovizbase - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-biovizbase - path: recipes/bioconductor-biovizbase - version: 1.28.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-birewire/meta.yaml b/recipes/bioconductor-birewire/meta.yaml index 94f5cee0bbfa8..997a123153b52 100644 --- a/recipes/bioconductor-birewire/meta.yaml +++ b/recipes/bioconductor-birewire/meta.yaml @@ -1,25 +1,38 @@ -{% set version = "3.34.0" %} +{% set version = "3.38.0" %} {% set name = "BiRewire" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Fast functions for bipartite network rewiring through N consecutive switching steps (See References) and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. Includes functions for the analysis of the introduced randomness across the switching steps and several other routines to analyse the resulting networks and their natural projections. Extension to undirected networks and directed signed networks is also provided. Starting from version 1.9.7 a more precise bound (especially for small network) has been implemented. Starting from version 2.2.0 the analysis routine is more complete and a visual montioring of the underlying Markov Chain has been implemented. Starting from 3.6.0 the library can handle also matrices with NA (not for the directed signed graphs). Since version 3.27.1 it is possible to add a constraint for dsg generation: usually positive and negative arc between two nodes could be not accepted.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2539b609076f98e95e044f33fe443bdf build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-birewire", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:birewire + parent_recipe: + name: bioconductor-birewire + path: recipes/bioconductor-birewire + version: 3.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - r-igraph @@ -34,23 +47,16 @@ requirements: - r-matrix - r-rtsne - r-slam - build: - - {{ compiler('c') }} - - make + +source: + md5: 82b6218fb208981decfce9c06efb5951 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals)' - description: 'Fast functions for bipartite network rewiring through N consecutive switching steps (See References) and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. Includes functions for the analysis of the introduced randomness across the switching steps and several other routines to analyse the resulting networks and their natural projections. Extension to undirected networks and directed signed networks is also provided. Starting from version 1.9.7 a more precise bound (especially for small network) has been implemented. Starting from version 2.2.0 the analysis routine is more complete and a visual montioring of the underlying Markov Chain has been implemented. Starting from 3.6.0 the library can handle also matrices with NA (not for the directed signed graphs). Since version 3.27.1 it is possible to add a constraint for dsg generation: usually positive and negative arc between two nodes could be not accepted.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:birewire - parent_recipe: - name: bioconductor-birewire - path: recipes/bioconductor-birewire - version: 3.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biscuiteer/meta.yaml b/recipes/bioconductor-biscuiteer/meta.yaml index ab11d6d9b3f44..7e4e3f750dcfd 100644 --- a/recipes/bioconductor-biscuiteer/meta.yaml +++ b/recipes/bioconductor-biscuiteer/meta.yaml @@ -1,47 +1,50 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "biscuiteer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A test harness for bsseq loading of Biscuit output, summarization of WGBS data over defined regions and in mappable samples, with or without imputation, dropping of mostly-NA rows, age estimates, etc. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Convenience Functions for Biscuit -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a38a486daf7d4c4dd682f20658039234 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biscuiteer", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: DSS, covr, knitr, rmarkdown, markdown, rlang, scmeth, pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10, BiocStyle requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biscuiteerdata >=1.16.0,<1.17.0' - - 'bioconductor-bsseq >=1.38.0,<1.39.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-dmrseq >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mus.musculus >=1.3.0,<1.4.0' - - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biscuiteerdata >=1.20.0,<1.21.0 + - bioconductor-bsseq >=1.42.0,<1.43.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-dmrseq >=1.26.0,<1.27.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-homo.sapiens >=1.3.0,<1.4.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mus.musculus >=1.3.0,<1.4.0 + - bioconductor-qdnaseq >=1.42.0,<1.43.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-data.table - r-gtools @@ -50,27 +53,28 @@ requirements: - r-qualv - r-r.utils - r-readr + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biscuiteerdata >=1.16.0,<1.17.0' - - 'bioconductor-bsseq >=1.38.0,<1.39.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-dmrseq >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mus.musculus >=1.3.0,<1.4.0' - - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biscuiteerdata >=1.20.0,<1.21.0 + - bioconductor-bsseq >=1.42.0,<1.43.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-dmrseq >=1.26.0,<1.27.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-homo.sapiens >=1.3.0,<1.4.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mus.musculus >=1.3.0,<1.4.0 + - bioconductor-qdnaseq >=1.42.0,<1.43.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-data.table - r-gtools @@ -79,13 +83,16 @@ requirements: - r-qualv - r-r.utils - r-readr + +source: + md5: 1cc57297b85e930acac1cd5060d566fc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Convenience Functions for Biscuit' - description: 'A test harness for bsseq loading of Biscuit output, summarization of WGBS data over defined regions and in mappable samples, with or without imputation, dropping of mostly-NA rows, age estimates, etc.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biscuiteerdata/meta.yaml b/recipes/bioconductor-biscuiteerdata/meta.yaml index c4cfffd5a8b7c..2674b4a1a1972 100644 --- a/recipes/bioconductor-biscuiteerdata/meta.yaml +++ b/recipes/bioconductor-biscuiteerdata/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "biscuiteerData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Contains default datasets used by the Bioconductor package biscuiteer. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Data Package for Biscuiteer -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9610f1ea2c2e8303acbb0b52204f8d3e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biscuiteerdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, markdown requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-curl run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-curl - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 71b2c48b7e095c2546f3ebfc8331b7a5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Data Package for Biscuiteer' - description: 'Contains default datasets used by the Bioconductor package biscuiteer.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-biscuiteerdata/post-link.sh b/recipes/bioconductor-biscuiteerdata/post-link.sh index 6c22e115a9ff9..6f2953d19ae13 100644 --- a/recipes/bioconductor-biscuiteerdata/post-link.sh +++ b/recipes/bioconductor-biscuiteerdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "biscuiteerdata-1.16.0" +installBiocDataPackage.sh "biscuiteerdata-1.20.0" diff --git a/recipes/bioconductor-biseq/meta.yaml b/recipes/bioconductor-biseq/meta.yaml index 93bf96e0a6e37..b9088c713811e 100644 --- a/recipes/bioconductor-biseq/meta.yaml +++ b/recipes/bioconductor-biseq/meta.yaml @@ -1,68 +1,74 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "BiSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The BiSeq package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs). The package takes already aligned BS data from one or multiple samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Processing and analyzing bisulfite sequencing data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 76a46bdea0a83b3ead6a8ee87d6000ac build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-biseq", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:biseq + - doi:10.1093/bib/bbv095 + parent_recipe: + name: bioconductor-biseq + path: recipes/bioconductor-biseq + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-globaltest >=5.56.0,<5.57.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-globaltest >=5.60.0,<5.61.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-betareg - r-formula - r-lokern run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-globaltest >=5.56.0,<5.57.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-globaltest >=5.60.0,<5.61.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-betareg - r-formula - r-lokern + +source: + md5: f103ea3789e9930284f04a8a5bdd02db + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'Processing and analyzing bisulfite sequencing data' - description: 'The BiSeq package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs). The package takes already aligned BS data from one or multiple samples.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:biseq - - doi:10.1093/bib/bbv095 - parent_recipe: - name: bioconductor-biseq - path: recipes/bioconductor-biseq - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-blacksheepr/meta.yaml b/recipes/bioconductor-blacksheepr/meta.yaml index 956002139ea7c..e2814f299ef45 100644 --- a/recipes/bioconductor-blacksheepr/meta.yaml +++ b/recipes/bioconductor-blacksheepr/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "blacksheepr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Blacksheep is a tool designed for outlier analysis in the context of pairwise comparisons in an effort to find distinguishing characteristics from two groups. This tool was designed to be applied for biological applications such as phosphoproteomics or transcriptomics, but it can be used for any data that can be represented by a 2D table, and has two sub populations within the table to compare. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Outlier Analysis for pairwise differential comparison -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 464b853300f0d97e2ad8f0a4188701c4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-blacksheepr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, curl requirements: host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-pasilla >=1.30.0,<1.31.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-pasilla >=1.34.0,<1.35.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-rcolorbrewer - r-viridis run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-pasilla >=1.30.0,<1.31.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-pasilla >=1.34.0,<1.35.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-rcolorbrewer - r-viridis + +source: + md5: bbd3a0bb03fc8ba8f6468f035fe45cb5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Outlier Analysis for pairwise differential comparison' - description: 'Blacksheep is a tool designed for outlier analysis in the context of pairwise comparisons in an effort to find distinguishing characteristics from two groups. This tool was designed to be applied for biological applications such as phosphoproteomics or transcriptomics, but it can be used for any data that can be represented by a 2D table, and has two sub populations within the table to compare.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bladderbatch/meta.yaml b/recipes/bioconductor-bladderbatch/meta.yaml index 9eafff22e508e..e64441c695a3e 100644 --- a/recipes/bioconductor-bladderbatch/meta.yaml +++ b/recipes/bioconductor-bladderbatch/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "bladderbatch" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d59d10a87e8d62c6ba10f7e9c0160a44 +about: + description: This package contains microarray gene expression data on 57 bladder samples from 5 batches. The data are used as an illustrative example for the sva package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Bladder gene expression data illustrating batch effects build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bladderbatch", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-bladderbatch + path: recipes/bioconductor-bladderbatch + version: 1.18.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3447e61de0537a4b0541b25a3aadc0b4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Bladder gene expression data illustrating batch effects' - description: 'This package contains microarray gene expression data on 57 bladder samples from 5 batches. The data are used as an illustrative example for the sva package.' -extra: - parent_recipe: - name: bioconductor-bladderbatch - path: recipes/bioconductor-bladderbatch - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bladderbatch/post-link.sh b/recipes/bioconductor-bladderbatch/post-link.sh index fac44e79b40e2..95f3ca83a9861 100644 --- a/recipes/bioconductor-bladderbatch/post-link.sh +++ b/recipes/bioconductor-bladderbatch/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bladderbatch-1.40.0" +installBiocDataPackage.sh "bladderbatch-1.44.0" diff --git a/recipes/bioconductor-blima/meta.yaml b/recipes/bioconductor-blima/meta.yaml index dee6d37139ead..ddfeeec9d56e9 100644 --- a/recipes/bioconductor-blima/meta.yaml +++ b/recipes/bioconductor-blima/meta.yaml @@ -1,58 +1,64 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "blima" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package blima includes several algorithms for the preprocessing of Illumina microarray data. It focuses to the bead level analysis and provides novel approach to the quantile normalization of the vectors of unequal lengths. It provides variety of the methods for background correction including background subtraction, RMA like convolution and background outlier removal. It also implements variance stabilizing transformation on the bead level. There are also implemented methods for data summarization. It also provides the methods for performing T-tests on the detector (bead) level and on the probe level for differential expression testing. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a0d7cbb46b78eabdbc06c4ee1b417bcb build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-blima", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:blima + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-blima + path: recipes/bioconductor-blima + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db, lumi, knitr requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-beadarray >=2.52.0,<2.53.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-beadarray >=2.56.0,<2.57.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - - 'r-rcpp >=0.12.8' + - r-rcpp >=0.12.8 - libblas - liblapack run: - - 'bioconductor-beadarray >=2.52.0,<2.53.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-beadarray >=2.56.0,<2.57.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - - 'r-rcpp >=0.12.8' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=0.12.8 + +source: + md5: 313563f0d686af24c388b30517a271d4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level' - description: 'Package blima includes several algorithms for the preprocessing of Illumina microarray data. It focuses to the bead level analysis and provides novel approach to the quantile normalization of the vectors of unequal lengths. It provides variety of the methods for background correction including background subtraction, RMA like convolution and background outlier removal. It also implements variance stabilizing transformation on the bead level. There are also implemented methods for data summarization. It also provides the methods for performing T-tests on the detector (bead) level and on the probe level for differential expression testing.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:blima - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-blima - path: recipes/bioconductor-blima - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-blimatestingdata/meta.yaml b/recipes/bioconductor-blimatestingdata/meta.yaml index 6d25e2e3e3f9e..54a95faed7977 100644 --- a/recipes/bioconductor-blimatestingdata/meta.yaml +++ b/recipes/bioconductor-blimatestingdata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "blimaTestingData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ae3da97d0d020e16feee29b93c24825 +about: + description: Experiment data package. The set were prepared using microarray images of human mesenchymal cells treated with various supplements. This package is intended to provide example data to test functionality provided by blima. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Data for testing of the package blima. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-blimatestingdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: blima, beadarray, illuminaHumanv4.db, BiocStyle requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2e6d3952baeb1a16f51291872a56e932 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Data for testing of the package blima.' - description: 'Experiment data package. The set were prepared using microarray images of human mesenchymal cells treated with various supplements. This package is intended to provide example data to test functionality provided by blima.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-blimatestingdata/post-link.sh b/recipes/bioconductor-blimatestingdata/post-link.sh index 1418b77f265e3..00497a0bf9622 100644 --- a/recipes/bioconductor-blimatestingdata/post-link.sh +++ b/recipes/bioconductor-blimatestingdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "blimatestingdata-1.22.0" +installBiocDataPackage.sh "blimatestingdata-1.26.0" diff --git a/recipes/bioconductor-blma/meta.yaml b/recipes/bioconductor-blma/meta.yaml index acbf15edf9540..267ca937c8d94 100644 --- a/recipes/bioconductor-blma/meta.yaml +++ b/recipes/bioconductor-blma/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "BLMA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Suit of tools for bi-level meta-analysis. The package can be used in a wide range of applications, including general hypothesis testings, differential expression analysis, functional analysis, and pathway analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'BLMA: A package for bi-level meta-analysis' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a09cb94872d4a064b9b6300945795cdf build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-blma", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-padog >=1.44.0,<1.45.0' - - 'bioconductor-rontotools >=2.30.0,<2.31.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-padog >=1.48.0,<1.49.0 + - bioconductor-rontotools >=2.34.0,<2.35.0 - r-base - r-gsa - r-metafor run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-padog >=1.44.0,<1.45.0' - - 'bioconductor-rontotools >=2.30.0,<2.31.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-padog >=1.48.0,<1.49.0 + - bioconductor-rontotools >=2.34.0,<2.35.0 - r-base - r-gsa - r-metafor + +source: + md5: 4f33acc810f848d50529b5d02b2046d5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'BLMA: A package for bi-level meta-analysis' - description: 'Suit of tools for bi-level meta-analysis. The package can be used in a wide range of applications, including general hypothesis testings, differential expression analysis, functional analysis, and pathway analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bloodcancermultiomics2017/meta.yaml b/recipes/bioconductor-bloodcancermultiomics2017/meta.yaml index d6fbe40747131..a998c056450ad 100644 --- a/recipes/bioconductor-bloodcancermultiomics2017/meta.yaml +++ b/recipes/bioconductor-bloodcancermultiomics2017/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "BloodCancerMultiOmics2017" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package contains data of the Primary Blood Cancer Encyclopedia (PACE) project together with a complete executable transcript of the statistical analysis and reproduces figures presented in the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) 128(1):427-445. doi:10.1172/JCI93801. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: '"Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al. - experimental data and complete analysis' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d2b2dcb147bf904df505fedca2d1ea9e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bloodcancermultiomics2017", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, abind, AnnotationDbi, biomaRt, broom, colorspace, cowplot, dendsort, doParallel, foreach, forestplot, genefilter, ggbeeswarm, ggtern, gridExtra, hexbin, IHW, limma, magrittr, Matrix, maxstat, nat, org.Hs.eg.db, pheatmap, piano, readxl, Rtsne, tidyr, xtable requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-beeswarm - r-devtools @@ -40,9 +42,9 @@ requirements: - r-survival - r-tibble run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-beeswarm - r-devtools @@ -58,14 +60,17 @@ requirements: - r-survival - r-tibble - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: b3f8ec1359432e60d43fd88217e07889 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'LGPL (>= 3)' - summary: '"Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al. - experimental data and complete analysis' - description: 'The package contains data of the Primary Blood Cancer Encyclopedia (PACE) project together with a complete executable transcript of the statistical analysis and reproduces figures presented in the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) 128(1):427-445. doi:10.1172/JCI93801.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bloodcancermultiomics2017/post-link.sh b/recipes/bioconductor-bloodcancermultiomics2017/post-link.sh index 84e46bc91c92a..da4cecb3c878a 100644 --- a/recipes/bioconductor-bloodcancermultiomics2017/post-link.sh +++ b/recipes/bioconductor-bloodcancermultiomics2017/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bloodcancermultiomics2017-1.22.0" +installBiocDataPackage.sh "bloodcancermultiomics2017-1.26.0" diff --git a/recipes/bioconductor-bloodgen3module/meta.yaml b/recipes/bioconductor-bloodgen3module/meta.yaml index aad99351531e3..2a36e25dd91e5 100644 --- a/recipes/bioconductor-bloodgen3module/meta.yaml +++ b/recipes/bioconductor-bloodgen3module/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "BloodGen3Module" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The BloodGen3Module package provides functions for R user performing module repertoire analyses and generating fingerprint representations. Functions can perform group comparison or individual sample analysis and visualization by fingerprint grid plot or fingerprint heatmap. Module repertoire analyses typically involve determining the percentage of the constitutive genes for each module that are significantly increased or decreased. As we describe in details;https://www.biorxiv.org/content/10.1101/525709v2 and https://pubmed.ncbi.nlm.nih.gov/33624743/, the results of module repertoire analyses can be represented in a fingerprint format, where red and blue spots indicate increases or decreases in module activity. These spots are subsequently represented either on a grid, with each position being assigned to a given module, or in a heatmap where the samples are arranged in columns and the modules in rows. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: This R package for performing module repertoire analyses and generating fingerprint representations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c9957080f8c55f99ebcc89cdc652deb9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bloodgen3module", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, devtools, BiocGenerics, knitr, rmarkdown requirements: host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-ggplot2 @@ -37,11 +39,11 @@ requirements: - r-testthat - r-v8 run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-ggplot2 @@ -51,13 +53,16 @@ requirements: - r-reshape2 - r-testthat - r-v8 + +source: + md5: f85a417ca0010c2678a201a37a2e3391 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'This R package for performing module repertoire analyses and generating fingerprint representations' - description: 'The BloodGen3Module package provides functions for R user performing module repertoire analyses and generating fingerprint representations. Functions can perform group comparison or individual sample analysis and visualization by fingerprint grid plot or fingerprint heatmap. Module repertoire analyses typically involve determining the percentage of the constitutive genes for each module that are significantly increased or decreased. As we describe in details;https://www.biorxiv.org/content/10.1101/525709v2 and https://pubmed.ncbi.nlm.nih.gov/33624743/, the results of module repertoire analyses can be represented in a fingerprint format, where red and blue spots indicate increases or decreases in module activity. These spots are subsequently represented either on a grid, with each position being assigned to a given module, or in a heatmap where the samples are arranged in columns and the modules in rows.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bluster/meta.yaml b/recipes/bioconductor-bluster/meta.yaml index 672e737816913..6781e4d2e1b87 100644 --- a/recipes/bioconductor-bluster/meta.yaml +++ b/recipes/bioconductor-bluster/meta.yaml @@ -1,30 +1,43 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "bluster" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. Several utilities are also provided to compare and evaluate clustering results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Clustering Algorithms for Bioconductor -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: baf91e0700b1f49eb80522be9eb8204d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bluster", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:bluster + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut, scRNAseq, scuttle, scater, scran, pheatmap, viridis, mbkmeans, kohonen, apcluster, DirichletMultinomial, vegan, fastcluster -# SystemRequirements: C++11 +# SystemRequirements: C++17 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-assorthead >=1.0.0,<1.1.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cluster - r-igraph @@ -33,30 +46,25 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-assorthead >=1.0.0,<1.1.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cluster - r-igraph - r-matrix - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 641f8217b19175b751769f6e4272743a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'Clustering Algorithms for Bioconductor' - description: 'Wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. Several utilities are also provided to compare and evaluate clustering results.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-bnbc/meta.yaml b/recipes/bioconductor-bnbc/meta.yaml index b54e5916ff3f5..22e2b72f70b67 100644 --- a/recipes/bioconductor-bnbc/meta.yaml +++ b/recipes/bioconductor-bnbc/meta.yaml @@ -1,73 +1,80 @@ -{% set version = "1.23.0" %} +{% set version = "1.28.0" %} {% set name = "bnbc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools to normalize (several) Hi-C data from replicates. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Bandwise normalization and batch correction of Hi-C data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 201f8c694f60da1dfa8112194f29ca18 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bnbc", max_pin="x.x") }}' -# Suggests: BiocStyle, knitr, rmarkdown, RUnit + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:bnbc + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, RUnit, BSgenome.Hsapiens.UCSC.hg19 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hicbricks >=1.24.0,<1.25.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-data.table - r-matrixstats - - 'r-rcpp >=0.12.12' + - r-rcpp >=0.12.12 - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hicbricks >=1.24.0,<1.25.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-data.table - r-matrixstats - - 'r-rcpp >=0.12.12' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make - - libcxx <17 # [osx] + - r-rcpp >=0.12.12 + +source: + md5: 04ca83e01ed5fa40260e072e2edda12a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Bandwise normalization and batch correction of Hi-C data' - description: 'Tools to normalize (several) Hi-C data from replicates.' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name}} diff --git a/recipes/bioconductor-bnem/build_failure.linux-64.yaml b/recipes/bioconductor-bnem/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..c3dbbb403c474 --- /dev/null +++ b/recipes/bioconductor-bnem/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 012013e4f840cae3566ca7e05ac7e82ed00384a6ce47c0e04c4476880a59f964 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-epinem[version='>=1.30.0,<1.31.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-epinem >=1.30.0,<1.31.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-epinem >=1.30.0,<1.31.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-epinem[version='>=1.30.0,<1.31.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-epinem >=1.30.0,<1.31.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-epinem >=1.30.0,<1.31.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-epinem[version='>=1.30.0,<1.31.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-epinem >=1.30.0,<1.31.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-epinem >=1.30.0,<1.31.0 [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-bnem/meta.yaml b/recipes/bioconductor-bnem/meta.yaml index c24854a74af32..06cd44fef9fb4 100644 --- a/recipes/bioconductor-bnem/meta.yaml +++ b/recipes/bioconductor-bnem/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "bnem" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: bnem combines the use of indirect measurements of Nested Effects Models (package mnem) with the Boolean networks of CellNOptR. Perturbation experiments of signalling nodes in cells are analysed for their effect on the global gene expression profile. Those profiles give evidence for the Boolean regulation of down-stream nodes in the network, e.g., whether two parents activate their child independently (OR-gate) or jointly (AND-gate). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Training of logical models from indirect measurements of perturbation experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 84eb035082edc5cefe35763abde3093f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bnem", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocGenerics, MatrixGenerics, BiocStyle, RUnit requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' - - 'bioconductor-epinem >=1.26.0,<1.27.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-mnem >=1.18.0,<1.19.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-cellnoptr >=1.52.0,<1.53.0 + - bioconductor-epinem >=1.30.0,<1.31.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-mnem >=1.22.0,<1.23.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-sva >=3.54.0,<3.55.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-base - r-binom - r-cluster @@ -41,16 +43,16 @@ requirements: - r-rmarkdown - r-snowfall run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' - - 'bioconductor-epinem >=1.26.0,<1.27.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-mnem >=1.18.0,<1.19.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-cellnoptr >=1.52.0,<1.53.0 + - bioconductor-epinem >=1.30.0,<1.31.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-mnem >=1.22.0,<1.23.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-sva >=3.54.0,<3.55.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-base - r-binom - r-cluster @@ -59,13 +61,16 @@ requirements: - r-rcolorbrewer - r-rmarkdown - r-snowfall + +source: + md5: 853a3dbaebca6e75a1cca0bedcb820c0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Training of logical models from indirect measurements of perturbation experiments' - description: 'bnem combines the use of indirect measurements of Nested Effects Models (package mnem) with the Boolean networks of CellNOptR. Perturbation experiments of signalling nodes in cells are analysed for their effect on the global gene expression profile. Those profiles give evidence for the Boolean regulation of down-stream nodes in the network, e.g., whether two parents activate their child independently (OR-gate) or jointly (AND-gate).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bobafit/meta.yaml b/recipes/bioconductor-bobafit/meta.yaml index 4b504236c4870..ecc0dfe3efe5c 100644 --- a/recipes/bioconductor-bobafit/meta.yaml +++ b/recipes/bioconductor-bobafit/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "BOBaFIT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'This package provides a method to refit and correct the diploid region in copy number profiles. It uses a clustering algorithm to identify pathology-specific normal (diploid) chromosomes and then use their copy number signal to refit the whole profile. The package is composed by three functions: DRrefit (the main function), ComputeNormalChromosome and PlotCluster.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Refitting diploid region profiles using a clustering procedure -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 48b9cc5c35adf6469bd1dc2ca566bed1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bobafit", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, markdown, BiocStyle, knitr, testthat (>= 3.0.0), utils, testthat requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 - r-base - r-dplyr - r-ggforce @@ -34,9 +36,9 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 - r-base - r-dplyr - r-ggforce @@ -45,13 +47,16 @@ requirements: - r-nbclust - r-stringr - r-tidyr + +source: + md5: 05eeacc049e8d4eb8ae3918b85ac3963 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Refitting diploid region profiles using a clustering procedure' - description: 'This package provides a method to refit and correct the diploid region in copy number profiles. It uses a clustering algorithm to identify pathology-specific normal (diploid) chromosomes and then use their copy number signal to refit the whole profile. The package is composed by three functions: DRrefit (the main function), ComputeNormalChromosome and PlotCluster.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bodymaprat/meta.yaml b/recipes/bioconductor-bodymaprat/meta.yaml index a13f963c7a9e9..0251f70a088e7 100644 --- a/recipes/bioconductor-bodymaprat/meta.yaml +++ b/recipes/bioconductor-bodymaprat/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "bodymapRat" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fc575d7f33dd1ee73f1860fb076a840b +about: + description: This package contains a SummarizedExperiment from the Yu et al. (2013) paper that performed the rat BodyMap across 11 organs and 4 developmental stages. Raw FASTQ files were downloaded and mapped using STAR. Data is available on ExperimentHub as a data package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: CC BY 4.0 + summary: Experimental dataset from the rat BodyMap project build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bodymaprat", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: rmarkdown, knitr, BiocStyle, testthat requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bb02b15c5ef09829d18834e0f7e37440 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'CC BY 4.0' - summary: 'Experimental dataset from the rat BodyMap project' - description: 'This package contains a SummarizedExperiment from the Yu et al. (2013) paper that performed the rat BodyMap across 11 organs and 4 developmental stages. Raw FASTQ files were downloaded and mapped using STAR. Data is available on ExperimentHub as a data package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bodymaprat/post-link.sh b/recipes/bioconductor-bodymaprat/post-link.sh index d4ee9d2550175..ff7a938bdfd7b 100644 --- a/recipes/bioconductor-bodymaprat/post-link.sh +++ b/recipes/bioconductor-bodymaprat/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bodymaprat-1.18.0" +installBiocDataPackage.sh "bodymaprat-1.22.0" diff --git a/recipes/bioconductor-borealis/meta.yaml b/recipes/bioconductor-borealis/meta.yaml index 207f890f9427c..a69516fde241b 100644 --- a/recipes/bioconductor-borealis/meta.yaml +++ b/recipes/bioconductor-borealis/meta.yaml @@ -1,30 +1,33 @@ -{% set version = "1.4.0" %} +{% set version = "1.10.0" %} {% set name = "borealis" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: Borealis is an R library performing outlier analysis for count-based bisulfite sequencing data. It detectes outlier methylated CpG sites from bisulfite sequencing (BS-seq). The core of Borealis is modeling Beta-Binomial distributions. This can be useful for rare disease diagnoses. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a49d811ecb46b4fa88ff125fc5ff8486 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic + run_exports: '{{ pin_subpackage("bioconductor-borealis", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, annotatr, tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db requirements: host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-dss >=2.48.0,<2.49.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-bsseq >=1.42.0,<1.43.0 + - bioconductor-dss >=2.54.0,<2.55.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-cowplot - r-doparallel @@ -39,10 +42,10 @@ requirements: - r-rlang - r-snow run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-dss >=2.48.0,<2.49.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-bsseq >=1.42.0,<1.43.0 + - bioconductor-dss >=2.54.0,<2.55.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-cowplot - r-doparallel @@ -56,13 +59,16 @@ requirements: - r-r.utils - r-rlang - r-snow + +source: + md5: 284017a6199bf885961cfe4a246bb7fc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution' - description: 'Borealis is an R library performing outlier analysis for count-based bisulfite sequencing data. It detectes outlier methylated CpG sites from bisulfite sequencing (BS-seq). The core of Borealis is modeling Beta-Binomial distributions. This can be useful for rare disease diagnoses.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bovine.db/meta.yaml b/recipes/bioconductor-bovine.db/meta.yaml index 29be66b899563..9df31bbeb3de5 100644 --- a/recipes/bioconductor-bovine.db/meta.yaml +++ b/recipes/bioconductor-bovine.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "bovine.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dcc1180e8ac11247f9899f140082647e +about: + description: Affymetrix Affymetrix Bovine Array annotation data (chip bovine) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Bovine Array annotation data (chip bovine) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bovine.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.bt.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.bt.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.bt.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.bt.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: dcc1180e8ac11247f9899f140082647e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Bovine Array annotation data (chip bovine)' - description: 'Affymetrix Affymetrix Bovine Array annotation data (chip bovine) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bovine.db0/meta.yaml b/recipes/bioconductor-bovine.db0/meta.yaml index 7014ea409a9c4..bab7ccadb46fa 100644 --- a/recipes/bioconductor-bovine.db0/meta.yaml +++ b/recipes/bioconductor-bovine.db0/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "bovine.db0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 658829797db74aec87af1914483d1af7 +about: + description: Base annotation databases for bovine, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Level Annotation databases for bovine build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bovine.db0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8a8cd59df5a98057def6c71806cd5f68 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Level Annotation databases for bovine' - description: 'Base annotation databases for bovine, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bovine.db0/post-link.sh b/recipes/bioconductor-bovine.db0/post-link.sh index 0c3dc1fc3f167..0382df6de206c 100644 --- a/recipes/bioconductor-bovine.db0/post-link.sh +++ b/recipes/bioconductor-bovine.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bovine.db0-3.18.0" +installBiocDataPackage.sh "bovine.db0-3.20.0" diff --git a/recipes/bioconductor-bovinecdf/meta.yaml b/recipes/bioconductor-bovinecdf/meta.yaml index 3a8ad02076f2f..b18cb95985e95 100644 --- a/recipes/bioconductor-bovinecdf/meta.yaml +++ b/recipes/bioconductor-bovinecdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "bovinecdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e155fc7d5f84ee420d9b250a639af305 +about: + description: A package containing an environment representing the Bovine.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: bovinecdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bovinecdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e155fc7d5f84ee420d9b250a639af305 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: bovinecdf - description: 'A package containing an environment representing the Bovine.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bovineprobe/meta.yaml b/recipes/bioconductor-bovineprobe/meta.yaml index d4af93a9c72d3..18395e30955d4 100644 --- a/recipes/bioconductor-bovineprobe/meta.yaml +++ b/recipes/bioconductor-bovineprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "bovineprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9f9e25fc8c7a76acf541745b7c09748b +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Bovine\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type bovine build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bovineprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9f9e25fc8c7a76acf541745b7c09748b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type bovine' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Bovine\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bprmeth/meta.yaml b/recipes/bioconductor-bprmeth/meta.yaml index 6a3d18505b240..5cb5a76ea8b40 100644 --- a/recipes/bioconductor-bprmeth/meta.yaml +++ b/recipes/bioconductor-bprmeth/meta.yaml @@ -1,30 +1,44 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "BPRMeth" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The BPRMeth package is a probabilistic method to quantify explicit features of methylation profiles, in a way that would make it easier to formally use such profiles in downstream modelling efforts, such as predicting gene expression levels or clustering genomic regions or cells according to their methylation profiles. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 | file LICENSE + license_file: LICENSE + summary: Model higher-order methylation profiles -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8229c7c5175e3888c86a5a3a42eb7a8c build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bprmeth", max_pin="x.x") }}' + +extra: + parent_recipe: + name: bioconductor-bprmeth + path: recipes/bioconductor-bprmeth + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-assertthat - r-base - r-cowplot @@ -40,16 +54,17 @@ requirements: - r-matrixcalc - r-mvtnorm - r-randomforest - - 'r-rcpp >=0.12.14' + - r-rcpp >=0.12.14 - r-rcpparmadillo - r-truncnorm - libblas - liblapack + run: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-assertthat - r-base - r-cowplot @@ -65,25 +80,19 @@ requirements: - r-matrixcalc - r-mvtnorm - r-randomforest - - 'r-rcpp >=0.12.14' + - r-rcpp >=0.12.14 - r-rcpparmadillo - r-truncnorm - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: ddcbd96422007aa7889349a9626589f3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 | file LICENSE' - summary: 'Model higher-order methylation profiles' - description: 'The BPRMeth package is a probabilistic method to quantify explicit features of methylation profiles, in a way that would make it easier to formally use such profiles in downstream modelling efforts, such as predicting gene expression levels or clustering genomic regions or cells according to their methylation profiles.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-bprmeth - path: recipes/bioconductor-bprmeth - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-brain/meta.yaml b/recipes/bioconductor-brain/meta.yaml index f5e9400cafc79..e8a5d4c33a86f 100644 --- a/recipes/bioconductor-brain/meta.yaml +++ b/recipes/bioconductor-brain/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "BRAIN" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S). This is an implementation of the BRAIN algorithm described in the paper by J. Claesen, P. Dittwald, T. Burzykowski and D. Valkenborg. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Baffling Recursive Algorithm for Isotope distributioN calculations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 575b879f058d01202c3bc33b0ff8e3f1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-brain", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:brain + - doi:10.1021/ac303439m + parent_recipe: + name: bioconductor-brain + path: recipes/bioconductor-brain + version: 1.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - r-lattice - r-polynomf run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - r-lattice - r-polynomf + +source: + md5: 1ff55402202da07c9e0bf79088fd000c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Baffling Recursive Algorithm for Isotope distributioN calculations' - description: 'Package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S). This is an implementation of the BRAIN algorithm described in the paper by J. Claesen, P. Dittwald, T. Burzykowski and D. Valkenborg.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:brain - - doi:10.1021/ac303439m - parent_recipe: - name: bioconductor-brain - path: recipes/bioconductor-brain - version: 1.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-branchpointer/meta.yaml b/recipes/bioconductor-branchpointer/meta.yaml index b5aa55175fda0..07e402d3756ac 100644 --- a/recipes/bioconductor-branchpointer/meta.yaml +++ b/recipes/bioconductor-branchpointer/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "branchpointer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_3_clause + file LICENSE + license_file: LICENSE + summary: Prediction of intronic splicing branchpoints -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7a62abd020843736b7ea125ffc4a56e0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-branchpointer", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle requirements: host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-caret - r-cowplot @@ -40,14 +42,14 @@ requirements: - r-plyr - r-stringr run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-caret - r-cowplot @@ -57,13 +59,16 @@ requirements: - r-kernlab - r-plyr - r-stringr + +source: + md5: 3869a4014bf47b43df8c1c581e04bdb8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_3_clause + file LICENSE' - summary: 'Prediction of intronic splicing branchpoints' - description: 'Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-breakpointr/meta.yaml b/recipes/bioconductor-breakpointr/meta.yaml index f401d66f805fd..cd18d984777b0 100644 --- a/recipes/bioconductor-breakpointr/meta.yaml +++ b/recipes/bioconductor-breakpointr/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "breakpointR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements functions for finding breakpoints, plotting and export of Strand-seq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Find breakpoints in Strand-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96dddc1e7bbd8b880a89f8f1be145e66 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-breakpointr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-breakpointrdata >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-breakpointrdata >=1.24.0,<1.25.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cowplot - r-doparallel @@ -37,27 +39,30 @@ requirements: - r-ggplot2 - r-gtools run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-breakpointrdata >=1.20.0,<1.21.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-breakpointrdata >=1.24.0,<1.25.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cowplot - r-doparallel - r-foreach - r-ggplot2 - r-gtools + +source: + md5: dd315aa4292112edd33826eafa57754a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Find breakpoints in Strand-seq data' - description: 'This package implements functions for finding breakpoints, plotting and export of Strand-seq data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-breakpointrdata/meta.yaml b/recipes/bioconductor-breakpointrdata/meta.yaml index 904bd544168f7..f0134201539fb 100644 --- a/recipes/bioconductor-breakpointrdata/meta.yaml +++ b/recipes/bioconductor-breakpointrdata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "breakpointRdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e3f74132513d150cb5d5cc62bfd49586 +about: + description: Strand-seq data to demonstrate functionalities of breakpointR package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Strand-seq data for demonstration purposes build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-breakpointrdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, BiocStyle, requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 11f2cc0f64846cce27286f3cb0e3aea5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Strand-seq data for demonstration purposes' - description: 'Strand-seq data to demonstrate functionalities of breakpointR package.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-breakpointrdata/post-link.sh b/recipes/bioconductor-breakpointrdata/post-link.sh index 726ec7f9888bf..255ec28e4d064 100644 --- a/recipes/bioconductor-breakpointrdata/post-link.sh +++ b/recipes/bioconductor-breakpointrdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breakpointrdata-1.20.0" +installBiocDataPackage.sh "breakpointrdata-1.24.0" diff --git a/recipes/bioconductor-breastcancermainz/meta.yaml b/recipes/bioconductor-breastcancermainz/meta.yaml index e073dd94ff14c..b4f7dda2fa39d 100644 --- a/recipes/bioconductor-breastcancermainz/meta.yaml +++ b/recipes/bioconductor-breastcancermainz/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "breastCancerMAINZ" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2b8df5af87b71c6706f909129212b504 +about: + description: Gene expression data from the breast cancer study published by Schmidt et al. in 2008, provided as an eSet. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Gene expression dataset published by Schmidt et al. [2008] (MAINZ). build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-breastcancermainz", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: survcomp, genefu, Biobase requirements: host: @@ -26,13 +24,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 22952cca74ba799453172c26a1b9e095 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Gene expression dataset published by Schmidt et al. [2008] (MAINZ).' - description: 'Gene expression data from the breast cancer study published by Schmidt et al. in 2008, provided as an eSet.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-breastcancermainz/post-link.sh b/recipes/bioconductor-breastcancermainz/post-link.sh index 4570fff6a22f3..db94683c9ec1f 100644 --- a/recipes/bioconductor-breastcancermainz/post-link.sh +++ b/recipes/bioconductor-breastcancermainz/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breastcancermainz-1.40.0" +installBiocDataPackage.sh "breastcancermainz-1.44.0" diff --git a/recipes/bioconductor-breastcancernki/meta.yaml b/recipes/bioconductor-breastcancernki/meta.yaml index 38686c35da078..9a08d9ec77204 100644 --- a/recipes/bioconductor-breastcancernki/meta.yaml +++ b/recipes/bioconductor-breastcancernki/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "breastCancerNKI" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0a0940593d75deaed0aa6f01954cf61c +about: + description: Genexpression data from a breast cancer study published by van't Veer et al. in 2002 and van de Vijver et al. in 2002, provided as an eSet. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Genexpression dataset published by van't Veer et al. [2002] and van de Vijver et al. [2002] (NKI). build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-breastcancernki", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: survcomp, genefu, Biobase requirements: host: @@ -26,13 +24,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d33d1f8a22c9a9c46a2d3d0979e73a43 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genexpression dataset published by van''t Veer et al. [2002] and van de Vijver et al. [2002] (NKI).' - description: 'Genexpression data from a breast cancer study published by van''t Veer et al. in 2002 and van de Vijver et al. in 2002, provided as an eSet.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-breastcancernki/post-link.sh b/recipes/bioconductor-breastcancernki/post-link.sh index e92a07580eac6..bed4af043a74e 100644 --- a/recipes/bioconductor-breastcancernki/post-link.sh +++ b/recipes/bioconductor-breastcancernki/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breastcancernki-1.40.0" +installBiocDataPackage.sh "breastcancernki-1.44.0" diff --git a/recipes/bioconductor-breastcancertransbig/meta.yaml b/recipes/bioconductor-breastcancertransbig/meta.yaml index 80be8500b3982..1671fbbd62112 100644 --- a/recipes/bioconductor-breastcancertransbig/meta.yaml +++ b/recipes/bioconductor-breastcancertransbig/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "breastCancerTRANSBIG" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 170d89ddd3e554da50a0b2b5d040a96e +about: + description: Gene expression data from a breast cancer study published by Desmedt et al. in 2007, provided as an eSet. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Gene expression dataset published by Desmedt et al. [2007] (TRANSBIG). build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-breastcancertransbig", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: survcomp, genefu, Biobase requirements: host: @@ -26,13 +24,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fc586508a997c8c11e7597e313af8656 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Gene expression dataset published by Desmedt et al. [2007] (TRANSBIG).' - description: 'Gene expression data from a breast cancer study published by Desmedt et al. in 2007, provided as an eSet.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-breastcancertransbig/post-link.sh b/recipes/bioconductor-breastcancertransbig/post-link.sh index 819f5330c62a7..bd1b030f0c3f9 100644 --- a/recipes/bioconductor-breastcancertransbig/post-link.sh +++ b/recipes/bioconductor-breastcancertransbig/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breastcancertransbig-1.40.0" +installBiocDataPackage.sh "breastcancertransbig-1.44.0" diff --git a/recipes/bioconductor-breastcancerunt/meta.yaml b/recipes/bioconductor-breastcancerunt/meta.yaml index 938bc94e4da08..e77742f013f7f 100644 --- a/recipes/bioconductor-breastcancerunt/meta.yaml +++ b/recipes/bioconductor-breastcancerunt/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "breastCancerUNT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 31e1b6d7e34b4acb9207e3e152539166 +about: + description: Gene expression data from a breast cancer study published by Sotiriou et al. in 2007, provided as an eSet. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Gene expression dataset published by Sotiriou et al. [2007] (UNT). build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-breastcancerunt", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: survcomp, genefu, Biobase requirements: host: @@ -26,13 +24,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 59b7e8804b56e38b43e6fdbe27c7467d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Gene expression dataset published by Sotiriou et al. [2007] (UNT).' - description: 'Gene expression data from a breast cancer study published by Sotiriou et al. in 2007, provided as an eSet.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-breastcancerunt/post-link.sh b/recipes/bioconductor-breastcancerunt/post-link.sh index 0b186b89bdffc..0d760cca9daf8 100644 --- a/recipes/bioconductor-breastcancerunt/post-link.sh +++ b/recipes/bioconductor-breastcancerunt/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breastcancerunt-1.40.0" +installBiocDataPackage.sh "breastcancerunt-1.44.0" diff --git a/recipes/bioconductor-breastcancerupp/meta.yaml b/recipes/bioconductor-breastcancerupp/meta.yaml index 0bdf776792724..18bf92987119b 100644 --- a/recipes/bioconductor-breastcancerupp/meta.yaml +++ b/recipes/bioconductor-breastcancerupp/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "breastCancerUPP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c5c10989a8a2dbfd20c228522474fac1 +about: + description: Gene expression data from a breast cancer study published by Miller et al. in 2005, provided as an eSet. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Gene expression dataset published by Miller et al. [2005] (UPP). build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-breastcancerupp", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: survcomp, genefu, Biobase requirements: host: @@ -26,13 +24,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 164ea026b64aa6ed9c09feedd1b9b348 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Gene expression dataset published by Miller et al. [2005] (UPP).' - description: 'Gene expression data from a breast cancer study published by Miller et al. in 2005, provided as an eSet.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-breastcancerupp/post-link.sh b/recipes/bioconductor-breastcancerupp/post-link.sh index 7abd029d8fdcd..57bb9f04f3f7e 100644 --- a/recipes/bioconductor-breastcancerupp/post-link.sh +++ b/recipes/bioconductor-breastcancerupp/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breastcancerupp-1.40.0" +installBiocDataPackage.sh "breastcancerupp-1.44.0" diff --git a/recipes/bioconductor-breastcancervdx/meta.yaml b/recipes/bioconductor-breastcancervdx/meta.yaml index ed8c49c9a563f..9ea7b61649e44 100644 --- a/recipes/bioconductor-breastcancervdx/meta.yaml +++ b/recipes/bioconductor-breastcancervdx/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "breastCancerVDX" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 446ef46e0bdd1480e12de21ded7b58f0 +about: + description: Gene expression data from a breast cancer study published by Wang et al. in 2005 and Minn et al. in 2007, provided as an eSet. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Gene expression datasets published by Wang et al. [2005] and Minn et al. [2007] (VDX). build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-breastcancervdx", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: survcomp, genefu, Biobase requirements: host: @@ -26,13 +24,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b9c4ab9d76d527bef300fa0cfc0f7786 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Gene expression datasets published by Wang et al. [2005] and Minn et al. [2007] (VDX).' - description: 'Gene expression data from a breast cancer study published by Wang et al. in 2005 and Minn et al. in 2007, provided as an eSet.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-breastcancervdx/post-link.sh b/recipes/bioconductor-breastcancervdx/post-link.sh index 1269d20e15959..e8b2454563e3a 100644 --- a/recipes/bioconductor-breastcancervdx/post-link.sh +++ b/recipes/bioconductor-breastcancervdx/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "breastcancervdx-1.40.0" +installBiocDataPackage.sh "breastcancervdx-1.44.0" diff --git a/recipes/bioconductor-brendadb/meta.yaml b/recipes/bioconductor-brendadb/meta.yaml index b084097d11c03..c346e4901efda 100644 --- a/recipes/bioconductor-brendadb/meta.yaml +++ b/recipes/bioconductor-brendadb/meta.yaml @@ -1,29 +1,35 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "brendaDb" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: R interface for importing and analyzing enzyme information from the BRENDA database. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: The BRENDA Enzyme Database -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 35e521feef3f87b0122ac00ad0deae5b build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-brendadb", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr, rmarkdown, devtools # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-crayon - r-dplyr @@ -38,8 +44,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-crayon - r-dplyr @@ -51,17 +57,16 @@ requirements: - r-stringr - r-tibble - r-tidyr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: d60603b98537df788d499fbd84837974 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'The BRENDA Enzyme Database' - description: 'R interface for importing and analyzing enzyme information from the BRENDA database.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-brew3r.r/build.sh b/recipes/bioconductor-brew3r.r/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-brew3r.r/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-brew3r.r/meta.yaml b/recipes/bioconductor-brew3r.r/meta.yaml new file mode 100644 index 0000000000000..79c98f13a8ff3 --- /dev/null +++ b/recipes/bioconductor-brew3r.r/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.2.0" %} +{% set name = "BREW3R.r" %} +{% set bioc = "3.20" %} + +about: + description: This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: R package associated to BREW3R +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-brew3r.r", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: testthat (>= 3.0.0), IRanges, knitr, rmarkdown, BiocStyle, rtracklayer +requirements: + host: + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-rlang + run: + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-rlang +source: + md5: ac38ec812219d763381c8554a9a5cdf3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-brgedata/meta.yaml b/recipes/bioconductor-brgedata/meta.yaml index 39687c989b37a..2ce26f5114413 100644 --- a/recipes/bioconductor-brgedata/meta.yaml +++ b/recipes/bioconductor-brgedata/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "brgedata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b8d26c8dfa756e9eb556e4662e3b3302 +about: + description: This package contains several sets of omics data including Gene Expression (ExpressionSet), Methylation (GenomicRatioSet), Proteome and Exposome (ExposomeSet). This data is used in vignettes and exaples at MEAL, MultiDataSet and omicRexposome. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Exposures, Gene Expression and Methylation data for ilustration purpouses build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-brgedata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: minfi, MultiAssayExperiment, knitr, rmarkdown, rexposome, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 576c30227addd3d7feda172a74c0b869 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Exposures, Gene Expression and Methylation data for ilustration purpouses' - description: 'This package contains several sets of omics data including Gene Expression (ExpressionSet), Methylation (GenomicRatioSet), Proteome and Exposome (ExposomeSet). This data is used in vignettes and exaples at MEAL, MultiDataSet and omicRexposome.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-brgedata/post-link.sh b/recipes/bioconductor-brgedata/post-link.sh index 267b22a18da9f..4d4f576e39e0f 100644 --- a/recipes/bioconductor-brgedata/post-link.sh +++ b/recipes/bioconductor-brgedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "brgedata-1.24.0" +installBiocDataPackage.sh "brgedata-1.28.0" diff --git a/recipes/bioconductor-bridgedbr/meta.yaml b/recipes/bioconductor-bridgedbr/meta.yaml index f48e3b4fbacd2..82e6fe6f8b026 100644 --- a/recipes/bioconductor-bridgedbr/meta.yaml +++ b/recipes/bioconductor-bridgedbr/meta.yaml @@ -1,24 +1,32 @@ -{% set version = "2.12.0" %} +{% set version = "2.16.0" %} {% set name = "BridgeDbR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Use BridgeDb functions and load identifier mapping databases in R. It uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + summary: Code for using BridgeDb identifier mapping framework from within R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2c155c28cb8d117e2dc1b69873b91d84 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bridgedbr", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-bridgedbr + path: recipes/bioconductor-bridgedbr + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: @@ -29,18 +37,16 @@ requirements: - r-base - r-curl - r-rjava + +source: + md5: 40d8122a411aace02a4c0a426baa83ec + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3 - summary: 'Code for using BridgeDb identifier mapping framework from within R' - description: 'Use BridgeDb functions and load identifier mapping databases in R. It uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' -extra: - parent_recipe: - name: bioconductor-bridgedbr - path: recipes/bioconductor-bridgedbr - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-broadseq/build.sh b/recipes/bioconductor-broadseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-broadseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-broadseq/meta.yaml b/recipes/bioconductor-broadseq/meta.yaml new file mode 100644 index 0000000000000..46d443e2dfa7d --- /dev/null +++ b/recipes/bioconductor-broadseq/meta.yaml @@ -0,0 +1,82 @@ +{% set version = "1.0.0" %} +{% set name = "broadSeq" %} +{% set bioc = "3.20" %} + +about: + description: This package helps user to do easily RNA-seq data analysis with multiple methods (usually which needs many different input formats). Here the user will provid the expression data as a SummarizedExperiment object and will get results from different methods. It will help user to quickly evaluate different methods. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 'broadSeq : for streamlined exploration of RNA-seq data' + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-broadseq", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, limma (>= 3.54.0), rmarkdown, stats (>= 4.2.2), samr +requirements: + + host: + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-delocal >=1.6.0,<1.7.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-ebseq >=2.4.0,<2.5.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-noiseq >=2.50.0,<2.51.0 + - bioconductor-sechm >=1.14.0,<1.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-dplyr + - r-forcats >=1.0.0 + - r-ggplot2 + - r-ggplotify + - r-ggpubr + - r-pheatmap + - r-plyr + - r-purrr >=0.3.5 + - r-stringr + + run: + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-delocal >=1.6.0,<1.7.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-ebseq >=2.4.0,<2.5.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-noiseq >=2.50.0,<2.51.0 + - bioconductor-sechm >=1.14.0,<1.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-dplyr + - r-forcats >=1.0.0 + - r-ggplot2 + - r-ggplotify + - r-ggpubr + - r-pheatmap + - r-plyr + - r-purrr >=0.3.5 + - r-stringr + +source: + md5: fbf7fd027ead86d2350bb975955aab99 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-bronchialil13/meta.yaml b/recipes/bioconductor-bronchialil13/meta.yaml index 4084cc6bf0bff..a7a48041a6aaf 100644 --- a/recipes/bioconductor-bronchialil13/meta.yaml +++ b/recipes/bioconductor-bronchialil13/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "bronchialIL13" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: be303e29450fb15b03a10f6caaf30159 +about: + description: derived from CNMC (pepr.cnmcresearch.org) http://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=95 Human Bronchial Cell line A549 + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: time course experiment involving il13 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bronchialil13", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' + - bioconductor-affy >=1.84.0,<1.85.0 - r-base run: - - 'bioconductor-affy >=1.80.0,<1.81.0' + - bioconductor-affy >=1.84.0,<1.85.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 00ffcfd4e6583e294b378101c011efd7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'time course experiment involving il13' - description: 'derived from CNMC (pepr.cnmcresearch.org) http://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=95 Human Bronchial Cell line A549' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bronchialil13/post-link.sh b/recipes/bioconductor-bronchialil13/post-link.sh index 6ec47d8303721..c3afcf5edf826 100644 --- a/recipes/bioconductor-bronchialil13/post-link.sh +++ b/recipes/bioconductor-bronchialil13/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bronchialil13-1.40.0" +installBiocDataPackage.sh "bronchialil13-1.44.0" diff --git a/recipes/bioconductor-browserviz/meta.yaml b/recipes/bioconductor-browserviz/meta.yaml index a84be67b166ab..babd923bf6fff 100644 --- a/recipes/bioconductor-browserviz/meta.yaml +++ b/recipes/bioconductor-browserviz/meta.yaml @@ -1,45 +1,22 @@ -{% set version = "2.24.0" %} +{% set version = "2.28.0" %} {% set name = "BrowserViz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Interactvive graphics in a web browser from R, using websockets and JSON. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'BrowserViz: interactive R/browser graphics using websockets and JSON' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ae6366903bd754cbe0ca0d21168c6883 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-browserviz", max_pin="x.x") }}' - noarch: generic -# Suggests: RUnit, BiocStyle, knitr, rmarkdown -requirements: - host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - r-base - - 'r-httpuv >=1.5.0' - - 'r-jsonlite >=1.5' - run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - r-base - - 'r-httpuv >=1.5.0' - - 'r-jsonlite >=1.5' -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'BrowserViz: interactive R/browser graphics using websockets and JSON' - description: 'Interactvive graphics in a web browser from R, using websockets and JSON.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + extra: identifiers: - biotools:browserviz @@ -49,3 +26,32 @@ extra: path: recipes/bioconductor-browserviz version: 2.2.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RUnit, BiocStyle, knitr, rmarkdown +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - r-base + - r-httpuv >=1.5.0 + - r-jsonlite >=1.5 + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - r-base + - r-httpuv >=1.5.0 + - r-jsonlite >=1.5 + +source: + md5: 2732179787359af166be88c9d1265bda + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-bsgenome.alyrata.jgi.v1/meta.yaml b/recipes/bioconductor-bsgenome.alyrata.jgi.v1/meta.yaml index 8b13956ebc368..c79cdf5e231ae 100644 --- a/recipes/bioconductor-bsgenome.alyrata.jgi.v1/meta.yaml +++ b/recipes/bioconductor-bsgenome.alyrata.jgi.v1/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.0.1" %} {% set name = "BSgenome.Alyrata.JGI.v1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 64878499c633de66ccf4c5abc32c0aeb +about: + description: Arabidopsis lyrata 8x Release [project ID 4002920] as provided by JGI ( snapshot from March 24, 2011) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Arabidopsis lyrata full genome (JGI version V1.0) build: - number: 5 + noarch: generic + number: 6 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.alyrata.jgi.v1", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 64878499c633de66ccf4c5abc32c0aeb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Arabidopsis lyrata full genome (JGI version V1.0)' - description: 'Arabidopsis lyrata 8x Release [project ID 4002920] as provided by JGI ( snapshot from March 24, 2011) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/meta.yaml b/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/meta.yaml index ab05d12803a09..000d1d166c83c 100644 --- a/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/meta.yaml +++ b/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Amellifera.BeeBase.assembly4" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 77495ee5eba48fe52902c9cc4f9ba7cc +about: + description: iFull genome sequences for Apis mellifera (Honey Bee) as provided by BeeBase (assembly4, Feb. 2008) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Apis mellifera (BeeBase assembly4) build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.amellifera.beebase.assembly4", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 77495ee5eba48fe52902c9cc4f9ba7cc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Apis mellifera (BeeBase assembly4)' - description: 'iFull genome sequences for Apis mellifera (Honey Bee) as provided by BeeBase (assembly4, Feb. 2008) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1/meta.yaml b/recipes/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1/meta.yaml index be19401c6fca5..66ec56b6507e7 100644 --- a/recipes/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1/meta.yaml +++ b/recipes/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.5.0" %} {% set name = "BSgenome.Amellifera.NCBI.AmelHAv3.1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b119087dfe54805c90cb6bf901e8237e +about: + description: Full genome sequences for Apis mellifera as provided by NCBI (assembly Amel_HAv3.1, assembly accession GCF_003254395.2) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Apis mellifera (Amel_HAv3.1) build: - number: 5 + noarch: generic + number: 6 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.amellifera.ncbi.amelhav3.1", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b119087dfe54805c90cb6bf901e8237e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Apis mellifera (Amel_HAv3.1)' - description: 'Full genome sequences for Apis mellifera as provided by NCBI (assembly Amel_HAv3.1, assembly accession GCF_003254395.2) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/meta.yaml b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/meta.yaml index 5ad72a039a442..75bd27c1d231e 100644 --- a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Amellifera.UCSC.apiMel2.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e7a7ff8cfce8e239b22116855456f23d +about: + description: 'Full genome sequences for Apis mellifera (Honey Bee) as provided by UCSC (apiMel2, Jan. 2005) and stored in Biostrings objects. The sequences are the same as in BSgenome.Amellifera.UCSC.apiMel2, except that each of them has the 3 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), and (3) the mask of repeats from RepeatMasker (RM mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Apis mellifera (UCSC version apiMel2) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.amellifera.ucsc.apimel2.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.amellifera.ucsc.apimel2 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.amellifera.ucsc.apimel2 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.amellifera.ucsc.apimel2 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.amellifera.ucsc.apimel2 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e7a7ff8cfce8e239b22116855456f23d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Apis mellifera (UCSC version apiMel2)' - description: 'Full genome sequences for Apis mellifera (Honey Bee) as provided by UCSC (apiMel2, Jan. 2005) and stored in Biostrings objects. The sequences are the same as in BSgenome.Amellifera.UCSC.apiMel2, except that each of them has the 3 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), and (3) the mask of repeats from RepeatMasker (RM mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/meta.yaml b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/meta.yaml index 03cf1f3dc82a3..2f1e46889f0e9 100644 --- a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/meta.yaml +++ b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Amellifera.UCSC.apiMel2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 436ddf54868906e7d1135369d41a2ffe +about: + description: Full genome sequences for Apis mellifera (Honey Bee) as provided by UCSC (apiMel2, Jan. 2005) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Apis mellifera (UCSC version apiMel2) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.amellifera.ucsc.apimel2", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 436ddf54868906e7d1135369d41a2ffe + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Apis mellifera (UCSC version apiMel2)' - description: 'Full genome sequences for Apis mellifera (Honey Bee) as provided by UCSC (apiMel2, Jan. 2005) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/meta.yaml b/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/meta.yaml index cd38ff3980573..4fb36d1e2f0e4 100644 --- a/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/meta.yaml +++ b/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.0.0" %} {% set name = "BSgenome.Aofficinalis.NCBI.V1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f8fd13e74eee63895a5ef528004b60b +about: + description: Full genome sequences for Asparagus officinalis (Garden asparagus) as provided by NCBI (Aspof.V1, Feb. 2017) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Asparagus officinalis (Garden asparagus) full genome (NCBI version Aspof.V1) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.aofficinalis.ncbi.v1", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3f8fd13e74eee63895a5ef528004b60b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: GPL-3 - summary: 'Asparagus officinalis (Garden asparagus) full genome (NCBI version Aspof.V1)' - description: 'Full genome sequences for Asparagus officinalis (Garden asparagus) as provided by NCBI (Aspof.V1, Feb. 2017) and stored in Biostrings objects.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.athaliana.tair.04232008/meta.yaml b/recipes/bioconductor-bsgenome.athaliana.tair.04232008/meta.yaml index 4fdd444fe0fb6..1b3b3d45f61c3 100644 --- a/recipes/bioconductor-bsgenome.athaliana.tair.04232008/meta.yaml +++ b/recipes/bioconductor-bsgenome.athaliana.tair.04232008/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Athaliana.TAIR.04232008" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b8a31a228dbcf4468974f5ec1d98467 +about: + description: Full genome sequences for Arabidopsis thaliana as provided by TAIR (snapshot from April 23, 2008) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Arabidopsis thaliana (TAIR version from April 23, 2008) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.athaliana.tair.04232008", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6b8a31a228dbcf4468974f5ec1d98467 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Arabidopsis thaliana (TAIR version from April 23, 2008)' - description: 'Full genome sequences for Arabidopsis thaliana as provided by TAIR (snapshot from April 23, 2008) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.athaliana.tair.tair9/meta.yaml b/recipes/bioconductor-bsgenome.athaliana.tair.tair9/meta.yaml index 5829649a04069..d293bfedbb337 100644 --- a/recipes/bioconductor-bsgenome.athaliana.tair.tair9/meta.yaml +++ b/recipes/bioconductor-bsgenome.athaliana.tair.tair9/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Athaliana.TAIR.TAIR9" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8c6709a5f544616d59f4d39aac5787a7 +about: + description: Full genome sequences for Arabidopsis thaliana as provided by TAIR (TAIR9 Genome Release) and stored in Biostrings objects. Note that TAIR10 is an "annotation release" based on the same genome assembly as TAIR9. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Arabidopsis thaliana (TAIR9) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.athaliana.tair.tair9", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8c6709a5f544616d59f4d39aac5787a7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Arabidopsis thaliana (TAIR9)' - description: 'Full genome sequences for Arabidopsis thaliana as provided by TAIR (TAIR9 Genome Release) and stored in Biostrings objects. Note that TAIR10 is an "annotation release" based on the same genome assembly as TAIR9.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/meta.yaml index 5e00c72c1eb23..dfd78ae44c8f7 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau3.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 50f7da5907cbe0d08183dc7161a8ca56 +about: + description: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau3, Aug. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Bos taurus (UCSC version bosTau3) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau3.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.btaurus.ucsc.bostau3 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.btaurus.ucsc.bostau3 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.btaurus.ucsc.bostau3 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.btaurus.ucsc.bostau3 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 50f7da5907cbe0d08183dc7161a8ca56 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Bos taurus (UCSC version bosTau3)' - description: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau3, Aug. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/meta.yaml index cf3656257eb57..5cf7aaac9da04 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau3" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fe6c4d5853f91c3db3e716ddbc773580 +about: + description: Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau3, Aug. 2006) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Bos taurus (UCSC version bosTau3) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau3", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fe6c4d5853f91c3db3e716ddbc773580 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Bos taurus (UCSC version bosTau3)' - description: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau3, Aug. 2006) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/meta.yaml index 27d7dfefcbef2..4e3bc24feac2a 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau4.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c5294349c7061adfb3948bc5659afeb +about: + description: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau4, Oct. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau4, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Bos taurus (UCSC version bosTau4) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau4.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.btaurus.ucsc.bostau4 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.btaurus.ucsc.bostau4 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.btaurus.ucsc.bostau4 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.btaurus.ucsc.bostau4 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7c5294349c7061adfb3948bc5659afeb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Bos taurus (UCSC version bosTau4)' - description: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau4, Oct. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau4, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/meta.yaml index eab5a9891ec02..b8e9ab5def512 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau4" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 162cd253c719e347df5748ebb407a191 +about: + description: Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau4, Oct. 2007) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Bos taurus (UCSC version bosTau4) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau4", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 162cd253c719e347df5748ebb407a191 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Bos taurus (UCSC version bosTau4)' - description: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau4, Oct. 2007) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/meta.yaml index bbfbee0affde2..519427b08180f 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau6.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a176de6b1b91854d47e783b8249dbf58 +about: + description: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau6, Nov. 2009) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau6, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Bos taurus (UCSC version bosTau6) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau6.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.btaurus.ucsc.bostau6 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.btaurus.ucsc.bostau6 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.btaurus.ucsc.bostau6 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.btaurus.ucsc.bostau6 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a176de6b1b91854d47e783b8249dbf58 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Bos taurus (UCSC version bosTau6)' - description: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau6, Nov. 2009) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau6, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/meta.yaml index ce246f321d24a..52b6ed773f75f 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau6" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b22391e0678fc3743daa4b77ecc55f66 +about: + description: Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau6, Nov. 2009) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Bos taurus (UCSC version bosTau6) build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau6", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b22391e0678fc3743daa4b77ecc55f66 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Bos taurus (UCSC version bosTau6)' - description: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau6, Nov. 2009) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/meta.yaml index 682d89e7f4c24..61a77044d0e5f 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau8" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61ababa7b2b5360fceeb06f0bf49b208 +about: + description: Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau8, Jun. 2014) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Bos taurus (UCSC version bosTau8) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau8", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 61ababa7b2b5360fceeb06f0bf49b208 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Bos taurus (UCSC version bosTau8)' - description: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau8, Jun. 2014) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9.masked/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9.masked/meta.yaml index 62f59fbac5296..e63895ef9ee6d 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.4.4" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau9.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c96bd95c3b791d712aa5cb8c96f9c937 +about: + description: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (genome bosTau9) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau9, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Bos taurus (UCSC version bosTau9) build: - number: 2 + noarch: generic + number: 3 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau9.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.btaurus.ucsc.bostau9 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.btaurus.ucsc.bostau9 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.btaurus.ucsc.bostau9 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.btaurus.ucsc.bostau9 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c96bd95c3b791d712aa5cb8c96f9c937 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Bos taurus (UCSC version bosTau9)' - description: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (genome bosTau9) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau9, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9/meta.yaml index 3f586fcdbffff..2763acda6856d 100644 --- a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9/meta.yaml +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau9/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Btaurus.UCSC.bosTau9" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9b3343725d85c093999413d91218079d +about: + description: Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau9, Apr. 2018) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Bos taurus (UCSC version bosTau9) build: - number: 8 + noarch: generic + number: 9 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.btaurus.ucsc.bostau9", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9b3343725d85c093999413d91218079d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Bos taurus (UCSC version bosTau9)' - description: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau9, Apr. 2018) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/meta.yaml b/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/meta.yaml index 648f18fbe0f64..53fe71f7d83f3 100644 --- a/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/meta.yaml +++ b/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.0.0" %} {% set name = "BSgenome.Carietinum.NCBI.v1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eef018ecce6d32852aa18ac39cf377c6 +about: + description: Full genome sequences for Cicer arietinum (Chickpea) as provided by NCBI (ASM33114v1, Jan. 2013) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Cicer arietinum (Chickpea) full genome (NCBI version ASM33114v1) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.carietinum.ncbi.v1", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: eef018ecce6d32852aa18ac39cf377c6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: GPL-3 - summary: 'Cicer arietinum (Chickpea) full genome (NCBI version ASM33114v1)' - description: 'Full genome sequences for Cicer arietinum (Chickpea) as provided by NCBI (ASM33114v1, Jan. 2013) and stored in Biostrings objects.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml index 7f4da58f4e64f..b878a07a432ac 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml @@ -1,45 +1,45 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Celegans.UCSC.ce10" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98a8ca836d6db23e46674552669d7942 +about: + description: Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce10, Oct. 2010) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Caenorhabditis elegans (UCSC version ce10) build: - number: 17 + noarch: generic + number: 18 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.celegans.ucsc.ce10", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-bsgenome.celegans.ucsc.ce10 + path: recipes/bioconductor-bsgenome.celegans.ucsc.ce10 + version: 1.4.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 98a8ca836d6db23e46674552669d7942 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Caenorhabditis elegans (UCSC version ce10)' - description: 'Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce10, Oct. 2010) and stored in Biostrings objects.' -extra: - parent_recipe: - name: bioconductor-bsgenome.celegans.ucsc.ce10 - path: recipes/bioconductor-bsgenome.celegans.ucsc.ce10 - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/meta.yaml index c2b220fe98a18..6325b989996e8 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Celegans.UCSC.ce11" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b80e24149a0c6ed323d0c9a6d112ef52 +about: + description: Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce11, Feb. 2013) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Caenorhabditis elegans (UCSC version ce11) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.celegans.ucsc.ce11", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b80e24149a0c6ed323d0c9a6d112ef52 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Caenorhabditis elegans (UCSC version ce11)' - description: 'Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce11, Feb. 2013) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/meta.yaml index 32235e1365fe1..878b3251adf4a 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Celegans.UCSC.ce2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b2bf7eec2b07685cf9dcdf42840db208 +about: + description: Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce2, Mar. 2004) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Caenorhabditis elegans (UCSC version ce2) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.celegans.ucsc.ce2", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b2bf7eec2b07685cf9dcdf42840db208 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Caenorhabditis elegans (UCSC version ce2)' - description: 'Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce2, Mar. 2004) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml index e42da8e5488ee..75cc9baf4efe1 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml @@ -1,45 +1,45 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Celegans.UCSC.ce6" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cb86ff861d8f660c2abd8fc1907d84a6 +about: + description: Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Caenorhabditis elegans (UCSC version ce6) build: - number: 17 + noarch: generic + number: 18 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.celegans.ucsc.ce6", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-bsgenome.celegans.ucsc.ce6 + path: recipes/bioconductor-bsgenome.celegans.ucsc.ce6 + version: 1.4.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: TxDb.Celegans.UCSC.ce6.ensGene requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: cb86ff861d8f660c2abd8fc1907d84a6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Caenorhabditis elegans (UCSC version ce6)' - description: 'Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings objects.' -extra: - parent_recipe: - name: bioconductor-bsgenome.celegans.ucsc.ce6 - path: recipes/bioconductor-bsgenome.celegans.ucsc.ce6 - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/meta.yaml index 069fc1c59c867..22c6f10380ae0 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Cfamiliaris.UCSC.canFam2.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6f921533bb83f83f43b8d227b00a48cb +about: + description: 'Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam2, May 2005) and stored in Biostrings objects. The sequences are the same as in BSgenome.Cfamiliaris.UCSC.canFam2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Canis lupus familiaris (UCSC version canFam2) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam2 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.cfamiliaris.ucsc.canfam2 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam2 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.cfamiliaris.ucsc.canfam2 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6f921533bb83f83f43b8d227b00a48cb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Canis lupus familiaris (UCSC version canFam2)' - description: 'Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam2, May 2005) and stored in Biostrings objects. The sequences are the same as in BSgenome.Cfamiliaris.UCSC.canFam2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/meta.yaml index 982e9034314f8..fe3795ee9061f 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/meta.yaml +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Cfamiliaris.UCSC.canFam2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b98f5289ed5d362cd815db9352598634 +about: + description: Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam2, May 2005) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Canis lupus familiaris (UCSC version canFam2) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cfamiliaris.ucsc.canfam2", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b98f5289ed5d362cd815db9352598634 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Canis lupus familiaris (UCSC version canFam2)' - description: 'Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam2, May 2005) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/meta.yaml index 0261f9eff5a17..49a138da82db5 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Cfamiliaris.UCSC.canFam3.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e2246f51fc967dc2ed748cf967a7649 +about: + description: 'Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam3, Sep. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Cfamiliaris.UCSC.canFam3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Canis lupus familiaris (UCSC version canFam3) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam3 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.cfamiliaris.ucsc.canfam3 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam3 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.cfamiliaris.ucsc.canfam3 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8e2246f51fc967dc2ed748cf967a7649 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Canis lupus familiaris (UCSC version canFam3)' - description: 'Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam3, Sep. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Cfamiliaris.UCSC.canFam3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/meta.yaml index 89560db448749..2780ee55766e5 100644 --- a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/meta.yaml +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Cfamiliaris.UCSC.canFam3" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: efcdc531042be86f99a734cd69c0688c +about: + description: Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam3, Sep. 2011) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Canis lupus familiaris (UCSC version canFam3) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cfamiliaris.ucsc.canfam3", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: efcdc531042be86f99a734cd69c0688c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Canis lupus familiaris (UCSC version canFam3)' - description: 'Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam3, Sep. 2011) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/meta.yaml b/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/meta.yaml index 10417581a99fc..d0936fb844e91 100644 --- a/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/meta.yaml +++ b/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac3/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Cjacchus.UCSC.calJac3" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 41f927aa0d6ffbdaa6ad93c9135409e6 +about: + description: Full genome sequences for Callithrix jacchus (Marmoset) as provided by UCSC (calJac3, Mar. 2009) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Callithrix jacchus (UCSC version calJac3) build: - number: 11 + noarch: generic + number: 12 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cjacchus.ucsc.caljac3", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 41f927aa0d6ffbdaa6ad93c9135409e6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Callithrix jacchus (UCSC version calJac3)' - description: 'Full genome sequences for Callithrix jacchus (Marmoset) as provided by UCSC (calJac3, Mar. 2009) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac4/meta.yaml b/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac4/meta.yaml index 516f9eb1efe23..c2f68ff5a45ab 100644 --- a/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac4/meta.yaml +++ b/recipes/bioconductor-bsgenome.cjacchus.ucsc.caljac4/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.5.0" %} {% set name = "BSgenome.Cjacchus.UCSC.calJac4" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b11d16ac2cfa81e04af74e2049e52670 +about: + description: Full genome sequences for Callithrix jacchus (Marmoset) as provided by UCSC (calJac4, May 2020) and wrapped in a BSgenome object. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Callithrix jacchus (UCSC version calJac4) build: - number: 2 + noarch: generic + number: 3 rpaths: - lib/R/lib/ - lib/ - run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cjacchus.ucsc.caljac4", max_pin="x") }}' - noarch: generic + run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cjacchus.ucsc.caljac4", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - bioconductor-data-packages >=20231202 + - bioconductor-data-packages >=20241103 +source: + md5: b11d16ac2cfa81e04af74e2049e52670 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Callithrix jacchus (UCSC version calJac4)' - description: 'Full genome sequences for Callithrix jacchus (Marmoset) as provided by UCSC (calJac4, May 2020) and wrapped in a BSgenome object.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1/meta.yaml b/recipes/bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1/meta.yaml index 462035d069539..e7323a0ce8e1c 100644 --- a/recipes/bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1/meta.yaml +++ b/recipes/bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.0.0" %} {% set name = "BSgenome.CneoformansVarGrubiiKN99.NCBI.ASM221672v1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea536a15bd932af794f672d9b204c141 +about: + description: Full genome sequences for Cryptococcus neoformans var. grubii KN99 (assembly ASM221672v1 assembly accession GCA_002216725.1). + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full Genome Sequence for Cryptococcus neoformans var. grubii KN99 (ASM221672v1) build: - number: 2 + noarch: generic + number: 3 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ea536a15bd932af794f672d9b204c141 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full Genome Sequence for Cryptococcus neoformans var. grubii KN99 (ASM221672v1)' - description: 'Full genome sequences for Cryptococcus neoformans var. grubii KN99 (assembly ASM221672v1 assembly accession GCA_002216725.1).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.creinhardtii.jgi.v5.6/meta.yaml b/recipes/bioconductor-bsgenome.creinhardtii.jgi.v5.6/meta.yaml index c415b873854e9..eb38c9fa6a0bc 100644 --- a/recipes/bioconductor-bsgenome.creinhardtii.jgi.v5.6/meta.yaml +++ b/recipes/bioconductor-bsgenome.creinhardtii.jgi.v5.6/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.5.0" %} {% set name = "BSgenome.Creinhardtii.JGI.v5.6" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2bd1be53d19249ac14ad7f39dc00af0e +about: + description: Full genome sequences for Chlamydomonas reinhardtii (v5.6) as provided by JGI and stored in Biostrings objects. The data in this package is public. See 'citation("BSgenome.Creinhardtii.JGI.v5.6")' for how to cite in publications. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Chlamydomonas reinhardtii (v5.6) build: - number: 5 + noarch: generic + number: 6 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.creinhardtii.jgi.v5.6", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2bd1be53d19249ac14ad7f39dc00af0e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Chlamydomonas reinhardtii (v5.6)' - description: 'Full genome sequences for Chlamydomonas reinhardtii (v5.6) as provided by JGI and stored in Biostrings objects. The data in this package is public. See ''citation("BSgenome.Creinhardtii.JGI.v5.6")'' for how to cite in publications.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/meta.yaml index 62a0b17986a8d..0cbf543671b88 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm2.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ae7ca3053e97a0d6bd20bc2b9635ecce +about: + description: 'Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm2, Apr. 2004) and stored in Biostrings objects. The sequences are the same as in BSgenome.Dmelanogaster.UCSC.dm2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Drosophila melanogaster (UCSC version dm2) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm2 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.dmelanogaster.ucsc.dm2 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm2 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.dmelanogaster.ucsc.dm2 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ae7ca3053e97a0d6bd20bc2b9635ecce + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Drosophila melanogaster (UCSC version dm2)' - description: 'Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm2, Apr. 2004) and stored in Biostrings objects. The sequences are the same as in BSgenome.Dmelanogaster.UCSC.dm2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/meta.yaml index 7b1927e47450e..e8d991808ae4b 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ebc88df5595fc7aad588b8f3f7de4784 +about: + description: Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm2, Apr. 2004) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Drosophila melanogaster (UCSC version dm2) build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.dmelanogaster.ucsc.dm2", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ebc88df5595fc7aad588b8f3f7de4784 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Drosophila melanogaster (UCSC version dm2)' - description: 'Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm2, Apr. 2004) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/meta.yaml index 6067d2d13f90e..cab0c29d36f55 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm3.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 592e7ec451d126b2d314ab6c75d86830 +about: + description: 'Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, Apr. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Drosophila melanogaster (UCSC version dm3) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm3 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.dmelanogaster.ucsc.dm3 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm3 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.dmelanogaster.ucsc.dm3 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 592e7ec451d126b2d314ab6c75d86830 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Drosophila melanogaster (UCSC version dm3)' - description: 'Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, Apr. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml index c68d6516cefb1..6e2f1704f4877 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml @@ -1,45 +1,45 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm3" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7ceebf7bfee766596f602f9e808d069 +about: + description: Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, Apr. 2006) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Drosophila melanogaster (UCSC version dm3) build: - number: 17 + noarch: generic + number: 18 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.dmelanogaster.ucsc.dm3", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-bsgenome.dmelanogaster.ucsc.dm3 + path: recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3 + version: 1.4.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: TxDb.Dmelanogaster.UCSC.dm3.ensGene requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b7ceebf7bfee766596f602f9e808d069 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Drosophila melanogaster (UCSC version dm3)' - description: 'Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, Apr. 2006) and stored in Biostrings objects.' -extra: - parent_recipe: - name: bioconductor-bsgenome.dmelanogaster.ucsc.dm3 - path: recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3 - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/meta.yaml index feaea65b5861e..c14c27267aa8a 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.1" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm6" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f9d6e406b7893a17c08edd4521c2802f +about: + description: Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm6, Aug. 2014) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Drosophila melanogaster (UCSC version dm6) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.dmelanogaster.ucsc.dm6", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f9d6e406b7893a17c08edd4521c2802f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Drosophila melanogaster (UCSC version dm6)' - description: 'Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm6, Aug. 2014) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/meta.yaml index 87a3b044b538d..1084feb911684 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Drerio.UCSC.danRer10" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b8dbcc8a338a021ed35656b27b3dd4c0 +about: + description: Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer10, Sep. 2014) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Danio rerio (UCSC version danRer10) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer10", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b8dbcc8a338a021ed35656b27b3dd4c0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Danio rerio (UCSC version danRer10)' - description: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer10, Sep. 2014) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer11/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer11/meta.yaml index 95822ca277bba..3153c427daff7 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer11/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer11/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Drerio.UCSC.danRer11" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd586da56ca88ccebb85804f992ba204 +about: + description: Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Danio rerio (UCSC version danRer11) build: - number: 8 + noarch: generic + number: 9 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer11", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: cd586da56ca88ccebb85804f992ba204 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Danio rerio (UCSC version danRer11)' - description: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/meta.yaml index 64e298e1c21eb..f74f27c049b5c 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Drerio.UCSC.danRer5.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f0623bcbe1743754a56c55599b535f3 +about: + description: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer5, Jul. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Drerio.UCSC.danRer5, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Danio rerio (UCSC version danRer5) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer5.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.drerio.ucsc.danrer5 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.drerio.ucsc.danrer5 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.drerio.ucsc.danrer5 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.drerio.ucsc.danrer5 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8f0623bcbe1743754a56c55599b535f3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Danio rerio (UCSC version danRer5)' - description: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer5, Jul. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Drerio.UCSC.danRer5, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/meta.yaml index bf6871a4d5a7d..b790e829098b4 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Drerio.UCSC.danRer5" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b1fee4bcc0d9cebb2bbdec5cb851f00d +about: + description: Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer5, Jul. 2007) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Danio rerio (UCSC version danRer5) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer5", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b1fee4bcc0d9cebb2bbdec5cb851f00d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Danio rerio (UCSC version danRer5)' - description: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer5, Jul. 2007) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/meta.yaml index 6b526c573e5c6..d61e2dd160379 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Drerio.UCSC.danRer6.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71c9b05c27b8d2e05735e6494a8f17ba +about: + description: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer6, Dec. 2008) and stored in Biostrings objects. The sequences are the same as in BSgenome.Drerio.UCSC.danRer6, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Danio rerio (UCSC version danRer6) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer6.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.drerio.ucsc.danrer6 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.drerio.ucsc.danrer6 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.drerio.ucsc.danrer6 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.drerio.ucsc.danrer6 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 71c9b05c27b8d2e05735e6494a8f17ba + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Danio rerio (UCSC version danRer6)' - description: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer6, Dec. 2008) and stored in Biostrings objects. The sequences are the same as in BSgenome.Drerio.UCSC.danRer6, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/meta.yaml index 478b3e1bddeff..339186459762a 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Drerio.UCSC.danRer6" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 537d37d29d97ae0c31d77decc67b25b0 +about: + description: Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer6, Dec. 2008) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Danio rerio (UCSC version danRer6) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer6", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 537d37d29d97ae0c31d77decc67b25b0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Danio rerio (UCSC version danRer6)' - description: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer6, Dec. 2008) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/meta.yaml index 019514752ee1c..4dde9e817e4c7 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Drerio.UCSC.danRer7.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d68af24477d006ed22e7342ff97ac16 +about: + description: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer7, Jul. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Drerio.UCSC.danRer7, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Danio rerio (UCSC version danRer7) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer7.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5d68af24477d006ed22e7342ff97ac16 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Danio rerio (UCSC version danRer7)' - description: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer7, Jul. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Drerio.UCSC.danRer7, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml index 6c1a8c0e62b9d..c2b92aa0ee944 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml @@ -1,45 +1,45 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Drerio.UCSC.danRer7" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 766b407a46f20d69a143eab0809eb10a +about: + description: Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer7, Jul. 2010) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Danio rerio (UCSC version danRer7) build: - number: 16 + noarch: generic + number: 17 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.drerio.ucsc.danrer7", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-bsgenome.drerio.ucsc.danrer7 + path: recipes/bioconductor-bsgenome.drerio.ucsc.danrer7 + version: 1.4.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 766b407a46f20d69a143eab0809eb10a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Danio rerio (UCSC version danRer7)' - description: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer7, Jul. 2010) and stored in Biostrings objects.' -extra: - parent_recipe: - name: bioconductor-bsgenome.drerio.ucsc.danrer7 - path: recipes/bioconductor-bsgenome.drerio.ucsc.danrer7 - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1/meta.yaml b/recipes/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1/meta.yaml index 0ce3c6e24705b..d861548c6137b 100644 --- a/recipes/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1/meta.yaml +++ b/recipes/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Dvirilis.Ensembl.dvircaf1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a6a6dc7b2d68a741c85525045a67890 +about: + description: Full genome sequences for Drosophila virilis (assembly dvir_caf1, GenBank assembly accession GCA_000005245.1) as provided by Ensembl and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Drosophila virilis (assembly dvir_caf1) build: - number: 8 + noarch: generic + number: 9 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.dvirilis.ensembl.dvircaf1", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6a6a6dc7b2d68a741c85525045a67890 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Drosophila virilis (assembly dvir_caf1)' - description: 'Full genome sequences for Drosophila virilis (assembly dvir_caf1, GenBank assembly accession GCA_000005245.1) as provided by Ensembl and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml index 2f3ba681a1364..9a066b5eec91a 100644 --- a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml +++ b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml @@ -1,44 +1,44 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Ecoli.NCBI.20080805" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c653e9cbee3faeb6fd5759b7575f234d +about: + description: Escherichia coli full genomes for several strains as provided by NCBI on 2008/08/05 and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Escherichia coli full genomes build: - number: 17 + noarch: generic + number: 18 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ecoli.ncbi.20080805", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-bsgenome.ecoli.ncbi.20080805 + path: recipes/bioconductor-bsgenome.ecoli.ncbi.20080805 + version: 1.3.1000 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c653e9cbee3faeb6fd5759b7575f234d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Escherichia coli full genomes' - description: 'Escherichia coli full genomes for several strains as provided by NCBI on 2008/08/05 and stored in Biostrings objects.' -extra: - parent_recipe: - name: bioconductor-bsgenome.ecoli.ncbi.20080805 - path: recipes/bioconductor-bsgenome.ecoli.ncbi.20080805 - version: 1.3.1000 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/meta.yaml b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/meta.yaml index 3a5920d510aaa..fa99975dfc767 100644 --- a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Gaculeatus.UCSC.gasAcu1.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9d9b9e70f4f4624ee4a2b09a59d44510 +about: + description: 'Full genome sequences for Gasterosteus aculeatus (Stickleback) as provided by UCSC (gasAcu1, Feb. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Gaculeatus.UCSC.gasAcu1, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Gasterosteus aculeatus (UCSC version gasAcu1) build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.gaculeatus.ucsc.gasacu1 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.gaculeatus.ucsc.gasacu1 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.gaculeatus.ucsc.gasacu1 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.gaculeatus.ucsc.gasacu1 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9d9b9e70f4f4624ee4a2b09a59d44510 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Gasterosteus aculeatus (UCSC version gasAcu1)' - description: 'Full genome sequences for Gasterosteus aculeatus (Stickleback) as provided by UCSC (gasAcu1, Feb. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Gaculeatus.UCSC.gasAcu1, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/meta.yaml b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/meta.yaml index 6a6732255be3d..e8a39d9bfae0f 100644 --- a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/meta.yaml +++ b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Gaculeatus.UCSC.gasAcu1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 412aa0570d9c556861b7bb9a5bbc2007 +about: + description: Full genome sequences for Gasterosteus aculeatus (Stickleback) as provided by UCSC (gasAcu1, Feb. 2006) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Gasterosteus aculeatus (UCSC version gasAcu1) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.gaculeatus.ucsc.gasacu1", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 412aa0570d9c556861b7bb9a5bbc2007 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Gasterosteus aculeatus (UCSC version gasAcu1)' - description: 'Full genome sequences for Gasterosteus aculeatus (Stickleback) as provided by UCSC (gasAcu1, Feb. 2006) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/meta.yaml index cf7403c1a2f0a..b106fbe513919 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Ggallus.UCSC.galGal3.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b3224e3a2b15de379c068e61cedfefa6 +about: + description: 'Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal3, May 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ggallus.UCSC.galGal3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Gallus gallus (UCSC version galGal3) build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ggallus.ucsc.galgal3.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.ggallus.ucsc.galgal3 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.ggallus.ucsc.galgal3 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.ggallus.ucsc.galgal3 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.ggallus.ucsc.galgal3 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b3224e3a2b15de379c068e61cedfefa6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Gallus gallus (UCSC version galGal3)' - description: 'Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal3, May 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ggallus.UCSC.galGal3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/meta.yaml index e8b20a1070d3b..11339f4ebc581 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Ggallus.UCSC.galGal3" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a463e5ccfc8c6d2c62a6ade0da65dbc4 +about: + description: Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal3, May 2006) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Gallus gallus (UCSC version galGal3) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ggallus.ucsc.galgal3", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a463e5ccfc8c6d2c62a6ade0da65dbc4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Gallus gallus (UCSC version galGal3)' - description: 'Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal3, May 2006) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/meta.yaml index 4b54412a74eac..8c9035e83385b 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Ggallus.UCSC.galGal4.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0166121ebd8d0b6a4d24d67e175cfe81 +about: + description: 'Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal4, Nov. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ggallus.UCSC.galGal4, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Gallus gallus (UCSC version galGal4) build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ggallus.ucsc.galgal4.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.ggallus.ucsc.galgal4 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.ggallus.ucsc.galgal4 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.ggallus.ucsc.galgal4 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.ggallus.ucsc.galgal4 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0166121ebd8d0b6a4d24d67e175cfe81 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Gallus gallus (UCSC version galGal4)' - description: 'Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal4, Nov. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ggallus.UCSC.galGal4, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/meta.yaml index d54b800d51b31..5be03b83ea8f9 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Ggallus.UCSC.galGal4" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c2cb4bfc39db93c060e78d8d12542c11 +about: + description: Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal4, Nov. 2011) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Gallus gallus (UCSC version galGal4) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ggallus.ucsc.galgal4", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c2cb4bfc39db93c060e78d8d12542c11 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Gallus gallus (UCSC version galGal4)' - description: 'Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal4, Nov. 2011) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/meta.yaml index 18a560405740b..60a68c4f6d528 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Ggallus.UCSC.galGal5" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 93b42354404edd848b21ea6781ca135c +about: + description: Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal5, Dec. 2015) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Gallus gallus (UCSC version galGal5) build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ggallus.ucsc.galgal5", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 93b42354404edd848b21ea6781ca135c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Gallus gallus (UCSC version galGal5)' - description: 'Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal5, Dec. 2015) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal6/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal6/meta.yaml index a44fab45df53d..550172fcbbe92 100644 --- a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal6/meta.yaml +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal6/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Ggallus.UCSC.galGal6" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 25ef08a5430fb337dbf752ca3378ea3e +about: + description: Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal6, Mar. 2018) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Gallus gallus (UCSC version galGal6) build: - number: 8 + noarch: generic + number: 9 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ggallus.ucsc.galgal6", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 25ef08a5430fb337dbf752ca3378ea3e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Gallus gallus (UCSC version galGal6)' - description: 'Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal6, Mar. 2018) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.gmax.ncbi.gmv40/meta.yaml b/recipes/bioconductor-bsgenome.gmax.ncbi.gmv40/meta.yaml index fe9c07be232c6..f4be2ddb115f7 100644 --- a/recipes/bioconductor-bsgenome.gmax.ncbi.gmv40/meta.yaml +++ b/recipes/bioconductor-bsgenome.gmax.ncbi.gmv40/meta.yaml @@ -1,40 +1,40 @@ {% set version = "4.0" %} {% set name = "BSgenome.Gmax.NCBI.Gmv40" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 421c045b993b2cfbc2b08c8103835c56 +about: + description: Full genome sequences for Glycine max as provided by NCBI (assembly Glycine_max_v4.0, assembly accession GCF_000004515.5) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Creative Commons Legal Code + file LICENSE + license_file: LICENSE + summary: Full genome sequences for Glycine max (Gmv40) build: - number: 2 + noarch: generic + number: 3 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.gmax.ncbi.gmv40", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 421c045b993b2cfbc2b08c8103835c56 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'Creative Commons Legal Code + file LICENSE' - summary: 'Full genome sequences for Glycine max (Gmv40)' - description: 'Full genome sequences for Glycine max as provided by NCBI (assembly Glycine_max_v4.0, assembly accession GCF_000004515.5) and stored in Biostrings objects.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/meta.yaml index 7fb6b93796e7d..0b3d2f5b6ebc8 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/meta.yaml @@ -1,39 +1,39 @@ {% set version = "0.99.1" %} {% set name = "BSgenome.Hsapiens.1000genomes.hs37d5" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 164e1692d38fefa499c2c8ac5fc22793 +about: + description: 1000genomes Phase2 Reference Genome Sequence (hs37d5), based on NCBI GRCh37. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: 1000genomes Reference Genome Sequence (hs37d5) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.1000genomes.hs37d5", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 164e1692d38fefa499c2c8ac5fc22793 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: '1000genomes Reference Genome Sequence (hs37d5)' - description: '1000genomes Phase2 Reference Genome Sequence (hs37d5), based on NCBI GRCh37.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/meta.yaml index 04da6b9994ab5..0aed8f9d735fc 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Hsapiens.NCBI.GRCh38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 733d324b34d34d7da8c4bf38459f4fae +about: + description: Full genome sequences for Homo sapiens (Human) as provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Homo sapiens (GRCh38) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ncbi.grch38", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 733d324b34d34d7da8c4bf38459f4fae + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Homo sapiens (GRCh38)' - description: 'Full genome sequences for Homo sapiens (Human) as provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0/meta.yaml index 4f0ef091db55a..41d6e611b186c 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.5.0" %} {% set name = "BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 22a99174e1e17718e0b4f8b66f32fd9b +about: + description: 'The T2T-CHM13v2.0 assembly (accession GCA_009914755.4), as submitted to NCBI by the T2T Consortium, and wrapped in a BSgenome object. Companion paper: "The complete sequence of a human genome" by Nurk S, Koren S, Rhie A, Rautiainen M, et al. Science, 2022.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: T2T-CHM13v2.0 assembly (Homo sapiens) wrapped in a BSgenome object build: - number: 2 + noarch: generic + number: 3 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 22a99174e1e17718e0b4f8b66f32fd9b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'T2T-CHM13v2.0 assembly (Homo sapiens) wrapped in a BSgenome object' - description: 'The T2T-CHM13v2.0 assembly (accession GCA_009914755.4), as submitted to NCBI by the T2T Consortium, and wrapped in a BSgenome object. Companion paper: "The complete sequence of a human genome" by Nurk S, Koren S, Rhie A, Rautiainen M, et al. Science, 2022.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/meta.yaml index 7fb6eb6c52a75..01410ab7abc21 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.3.99" %} +{% set version = "1.3.999" %} {% set name = "BSgenome.Hsapiens.UCSC.hg17.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ff6ee5196f234c5a2a3bcdd052c3c08e +about: + description: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg17, May 2004) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg17, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Homo sapiens (UCSC version hg17) build: - number: 12 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg17.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg17 >=1.3.0,<1.4.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg17 >=1.3.0,<1.4.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg17 >=1.3.0,<1.4.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg17 >=1.3.0,<1.4.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e3257cb973663f54841fd62a643ecaa7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Homo sapiens (UCSC version hg17)' - description: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg17, May 2004) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg17, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/post-link.sh index 6885f219a10b3..57e037eed52c7 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/post-link.sh +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bsgenome.hsapiens.ucsc.hg17.masked-1.3.99" +installBiocDataPackage.sh "bsgenome.hsapiens.ucsc.hg17.masked-1.3.999" diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/meta.yaml index eb46af4af2e48..78f4d1472d936 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.3.1000" %} +{% set version = "1.3.1001" %} {% set name = "BSgenome.Hsapiens.UCSC.hg17" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cbea3029c3d3125a88e6c061c3d3abde +about: + description: Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg17, May 2004) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Homo sapiens (UCSC version hg17) build: - number: 12 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg17", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9568b8979caae68531475136ed71316d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Homo sapiens (UCSC version hg17)' - description: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg17, May 2004) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/post-link.sh index c2e8be2201ba9..18f2ad426e247 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/post-link.sh +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bsgenome.hsapiens.ucsc.hg17-1.3.1000" +installBiocDataPackage.sh "bsgenome.hsapiens.ucsc.hg17-1.3.1001" diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/meta.yaml index e950d5f76a8de..b3c037baae440 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Hsapiens.UCSC.hg18.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e6a31e3cba34ce5e0eb6f76d2c19870c +about: + description: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg18, Mar. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg18, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Homo sapiens (UCSC version hg18) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg18.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e6a31e3cba34ce5e0eb6f76d2c19870c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Homo sapiens (UCSC version hg18)' - description: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg18, Mar. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg18, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml index 33e4cdff26eae..c02a4f0fc2fed 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml @@ -1,45 +1,45 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Hsapiens.UCSC.hg18" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 51bb2e1ed4009860bb21aaac32fffd9c +about: + description: Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg18, Mar. 2006) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Homo sapiens (UCSC version hg18) build: - number: 15 + noarch: generic + number: 16 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg18", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-bsgenome.hsapiens.ucsc.hg18 + path: recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18 + version: 1.3.1000 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: TxDb.Hsapiens.UCSC.hg18.knownGene requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 51bb2e1ed4009860bb21aaac32fffd9c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Homo sapiens (UCSC version hg18)' - description: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg18, Mar. 2006) and stored in Biostrings objects.' -extra: - parent_recipe: - name: bioconductor-bsgenome.hsapiens.ucsc.hg18 - path: recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18 - version: 1.3.1000 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/meta.yaml index 5664f8236fb7e..12cce4970b2d9 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.993" %} {% set name = "BSgenome.Hsapiens.UCSC.hg19.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4424e1bda9cc005d75f5f05ba4a50c77 +about: + description: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, based on GRCh37.p13) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13) build: - number: 8 + noarch: generic + number: 9 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg19.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4424e1bda9cc005d75f5f05ba4a50c77 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13)' - description: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, based on GRCh37.p13) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml index 4280e60fd61df..4efb07fe22ab8 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml @@ -1,44 +1,44 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Hsapiens.UCSC.hg19" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bb3f864ab32450d895816b45f6105f4f +about: + description: Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, based on GRCh37.p13) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13) build: - number: 8 + noarch: generic + number: 9 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg19", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-bsgenome.hsapiens.ucsc.hg19 + path: recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19 + version: 1.4.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bb3f864ab32450d895816b45f6105f4f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13)' - description: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, based on GRCh37.p13) and stored in Biostrings objects.' -extra: - parent_recipe: - name: bioconductor-bsgenome.hsapiens.ucsc.hg19 - path: recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19 - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major/meta.yaml index 2c99c40050795..74e996d9f6c20 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major/meta.yaml @@ -1,40 +1,40 @@ {% set version = "0.0.9999" %} {% set name = "BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c59f66e52d4982942bea2254223d58df +about: + description: Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with major allele injected from dbSNP151, and stored in Biostrings objects. Only single nucleotide variants (SNVs) were considered. At each SNV, the most frequent allele was chosen at the major allele to be injected into the reference genome. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: CC BY-NC-ND 4.0 + summary: Full genome sequences for Homo sapiens (UCSC version hg38, based on GRCh38.p12) with injected major alleles (dbSNP151) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor, testthat requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c59f66e52d4982942bea2254223d58df + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'CC BY-NC-ND 4.0' - summary: 'Full genome sequences for Homo sapiens (UCSC version hg38, based on GRCh38.p12) with injected major alleles (dbSNP151)' - description: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with major allele injected from dbSNP151, and stored in Biostrings objects. Only single nucleotide variants (SNVs) were considered. At each SNV, the most frequent allele was chosen at the major allele to be injected into the reference genome.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor/meta.yaml index 9c2021c5d0a73..729a7258128db 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor/meta.yaml @@ -1,40 +1,40 @@ {% set version = "0.0.9999" %} {% set name = "BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2cc3a612a2064624735d6a92910be7f3 +about: + description: Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with minor alleles injected from dbSNP151, and stored in Biostrings objects. Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with minor alleles injected from dbSNP151, and stored in Biostrings objects. Only common single nucleotide variants (SNVs) with at least one alternate allele with frequency greater than 0.01 were considered. For SNVs with more than 1 alternate allele, the most frequent allele was chosen as the minor allele to be injected into the reference genome. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: CC BY-NC-ND 4.0 + summary: Full genome sequences for Homo sapiens (UCSC version hg38, based on GRCh38.p12) with injected minor alleles (dbSNP151) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major, testthat requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2cc3a612a2064624735d6a92910be7f3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'CC BY-NC-ND 4.0' - summary: 'Full genome sequences for Homo sapiens (UCSC version hg38, based on GRCh38.p12) with injected minor alleles (dbSNP151)' - description: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with minor alleles injected from dbSNP151, and stored in Biostrings objects. Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with minor alleles injected from dbSNP151, and stored in Biostrings objects. Only common single nucleotide variants (SNVs) with at least one alternate allele with frequency greater than 0.01 were considered. For SNVs with more than 1 alternate allele, the most frequent allele was chosen as the minor allele to be injected into the reference genome.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/meta.yaml index 5a69152654b1b..760fcbbd86c40 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/meta.yaml @@ -1,43 +1,43 @@ {% set version = "1.4.5" %} {% set name = "BSgenome.Hsapiens.UCSC.hg38.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7570dd1b4f013b3c6acecd68602180b4 +about: + description: 'Full genomic sequences for Homo sapiens as provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31). The sequences are the same as in BSgenome.Hsapiens.UCSC.hg38, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default. The sequences are stored in MaskedDNAString objects.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genomic sequences for Homo sapiens (UCSC version hg38) build: - number: 1 + noarch: generic + number: 2 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg38.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7570dd1b4f013b3c6acecd68602180b4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genomic sequences for Homo sapiens (UCSC version hg38)' - description: 'Full genomic sequences for Homo sapiens as provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31). The sequences are the same as in BSgenome.Hsapiens.UCSC.hg38, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default. The sequences are stored in MaskedDNAString objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml index caafd0d4f2854..3c63638e5241d 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml @@ -1,46 +1,52 @@ {% set version = "1.4.5" %} {% set name = "BSgenome.Hsapiens.UCSC.hg38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Full genomic sequences for Homo sapiens as provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31). The sequences are stored in DNAString objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genomic sequences for Homo sapiens (UCSC genome hg38) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b2e670c27944eed77fbe9a9b55be40d2 build: - number: 2 + noarch: generic + number: 3 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hg38", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-bsgenome.hsapiens.ucsc.hg38 + path: recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38 + version: 1.4.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: b2e670c27944eed77fbe9a9b55be40d2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genomic sequences for Homo sapiens (UCSC genome hg38)' - description: 'Full genomic sequences for Homo sapiens as provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31). The sequences are stored in DNAString objects.' -extra: - parent_recipe: - name: bioconductor-bsgenome.hsapiens.ucsc.hg38 - path: recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38 - version: 1.4.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hs1/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hs1/meta.yaml index 6e76b23734749..f8457e0cbce75 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hs1/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hs1/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.4" %} {% set name = "BSgenome.Hsapiens.UCSC.hs1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5812c5670f51a5c58a9da9e042e7e440 +about: + description: Full genomic sequences for UCSC genome hs1 (the hs1 genome is based on assembly T2T-CHM13v2.0, with GenBank assembly accession GCA_009914755.4). The sequences are stored in DNAString objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genomic sequences for UCSC genome hs1 (Homo sapiens) build: - number: 1 + noarch: generic + number: 2 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.hsapiens.ucsc.hs1", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5812c5670f51a5c58a9da9e042e7e440 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genomic sequences for UCSC genome hs1 (Homo sapiens)' - description: 'Full genomic sequences for UCSC genome hs1 (the hs1 genome is based on assembly T2T-CHM13v2.0, with GenBank assembly accession GCA_009914755.4). The sequences are stored in DNAString objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/meta.yaml b/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/meta.yaml index c4ab4bc879512..a56b1acca06f6 100644 --- a/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/meta.yaml +++ b/recipes/bioconductor-bsgenome.mdomestica.ucsc.mondom5/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Mdomestica.UCSC.monDom5" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ff940f7446a275962f69a6f4cb84724c +about: + description: Full genome sequences for Monodelphis domestica (Opossum) as provided by UCSC (monDom5, Oct. 2006) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Monodelphis domestica (UCSC version monDom5) build: - number: 11 + noarch: generic + number: 12 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mdomestica.ucsc.mondom5", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ff940f7446a275962f69a6f4cb84724c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Monodelphis domestica (UCSC version monDom5)' - description: 'Full genome sequences for Monodelphis domestica (Opossum) as provided by UCSC (monDom5, Oct. 2006) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/meta.yaml b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/meta.yaml index c888f310c4025..fadbb519a8a9a 100644 --- a/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/meta.yaml +++ b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Mfascicularis.NCBI.5.0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dba6ade39dc6b4f6d06f488141b5550b +about: + description: Full genome sequences for Macaca fascicularis (long-tailed macaque) as provided by NCBI (Macaca_fascicularis_5.0, 2013-06-12) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Macaca fascicularis (Macaca_fascicularis_5.0) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mfascicularis.ncbi.5.0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: dba6ade39dc6b4f6d06f488141b5550b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Macaca fascicularis (Macaca_fascicularis_5.0)' - description: 'Full genome sequences for Macaca fascicularis (long-tailed macaque) as provided by NCBI (Macaca_fascicularis_5.0, 2013-06-12) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.mfascicularis.ncbi.6.0/meta.yaml b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.6.0/meta.yaml index d6051b0d89c9a..2f84676221863 100644 --- a/recipes/bioconductor-bsgenome.mfascicularis.ncbi.6.0/meta.yaml +++ b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.6.0/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.5.0" %} {% set name = "BSgenome.Mfascicularis.NCBI.6.0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67272a96950f485d3c0770265f59c85c +about: + description: Full genome sequences for Macaca fascicularis (Crab-eating macaque) as provided by NCBI (assembly Macaca_fascicularis_6.0, assembly accession GCA_011100615.1) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Macaca fascicularis (Macaca_fascicularis_6.0) build: - number: 2 + noarch: generic + number: 3 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mfascicularis.ncbi.6.0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 67272a96950f485d3c0770265f59c85c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Macaca fascicularis (Macaca_fascicularis_6.0)' - description: 'Full genome sequences for Macaca fascicularis (Crab-eating macaque) as provided by NCBI (assembly Macaca_fascicularis_6.0, assembly accession GCA_011100615.1) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/meta.yaml b/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/meta.yaml index 561159c626803..5c4fae6057db1 100644 --- a/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/meta.yaml +++ b/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.1" %} {% set name = "BSgenome.Mfuro.UCSC.musFur1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c33e71746ce551bcbcd22be1979aee63 +about: + description: Full genome sequences for Mustela putorius furo (Ferret) as provided by UCSC (musFur1, Apr. 2011) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Mustela putorius furo (UCSC version musFur1) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mfuro.ucsc.musfur1", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c33e71746ce551bcbcd22be1979aee63 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Mustela putorius furo (UCSC version musFur1)' - description: 'Full genome sequences for Mustela putorius furo (Ferret) as provided by UCSC (musFur1, Apr. 2011) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac10/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac10/meta.yaml index 075e65553bbe0..2be8001d5b308 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac10/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac10/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac10" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f2afe40d5dcf8d8620aa5e12e311fbc +about: + description: Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac10, Feb. 2019) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Macaca mulatta (UCSC version rheMac10) build: - number: 8 + noarch: generic + number: 9 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmulatta.ucsc.rhemac10", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2f2afe40d5dcf8d8620aa5e12e311fbc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Macaca mulatta (UCSC version rheMac10)' - description: 'Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac10, Feb. 2019) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/meta.yaml index 0f176b99d2e61..6725e88448356 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac2.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7602d86b68df7e4c8d336fede4090a62 +about: + description: 'Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac2, Jan. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmulatta.UCSC.rheMac2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default. NOTE: In most assemblies available at UCSC, Tandem Repeats Finder repeats were filtered to retain only the repeats with period <= 12. However, the filtering was omitted for this assembly, so the TRF masks contain all Tandem Repeats Finder results.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Macaca mulatta (UCSC version rheMac2) build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac2 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.mmulatta.ucsc.rhemac2 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac2 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.mmulatta.ucsc.rhemac2 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7602d86b68df7e4c8d336fede4090a62 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Macaca mulatta (UCSC version rheMac2)' - description: 'Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac2, Jan. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmulatta.UCSC.rheMac2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default. NOTE: In most assemblies available at UCSC, Tandem Repeats Finder repeats were filtered to retain only the repeats with period <= 12. However, the filtering was omitted for this assembly, so the TRF masks contain all Tandem Repeats Finder results.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/meta.yaml index 775d3ae08031f..38c4f6b573c15 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90c43e127e76dfd7cea90de9e1af9a50 +about: + description: Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac2, Jan. 2006) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Macaca mulatta (UCSC version rheMac2) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmulatta.ucsc.rhemac2", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 90c43e127e76dfd7cea90de9e1af9a50 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Macaca mulatta (UCSC version rheMac2)' - description: 'Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac2, Jan. 2006) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/meta.yaml index e99cfc364553a..d9e842212e815 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac3.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94f8714865655d3144e14f6fc5c24e76 +about: + description: 'Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac3, Oct. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmulatta.UCSC.rheMac3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Macaca mulatta (UCSC version rheMac3) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac3 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.mmulatta.ucsc.rhemac3 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac3 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.mmulatta.ucsc.rhemac3 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 94f8714865655d3144e14f6fc5c24e76 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Macaca mulatta (UCSC version rheMac3)' - description: 'Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac3, Oct. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmulatta.UCSC.rheMac3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/meta.yaml index b7f2e7e8cd0b3..e4efb315c202c 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac3" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dfa1ecb9d0bb7a5d9fa628092fb1c354 +about: + description: Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac3, Oct. 2010) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Macaca mulatta (UCSC version rheMac3) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmulatta.ucsc.rhemac3", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: dfa1ecb9d0bb7a5d9fa628092fb1c354 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Macaca mulatta (UCSC version rheMac3)' - description: 'Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac3, Oct. 2010) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/meta.yaml index 1e79bebdc1783..1acacd078fe65 100644 --- a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Mmulatta.UCSC.rheMac8" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e9ad1f70f652c62554e2c5af7638c015 +about: + description: Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac8, Nov. 2015) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Macaca mulatta (UCSC version rheMac8) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmulatta.ucsc.rhemac8", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e9ad1f70f652c62554e2c5af7638c015 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Macaca mulatta (UCSC version rheMac8)' - description: 'Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac8, Nov. 2015) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/meta.yaml index 82ebb44b2a53d..505e3ac9d7488 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Mmusculus.UCSC.mm10.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 40d51fb428a5fda8c05101a3dddb8957 +about: + description: 'Full genome sequences for Mus musculus (Mouse) as provided by UCSC (genome mm10, based on GRCm38.p6) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm10, except that each of them has the 2 following masks on top: (1) the mask of assembly gaps (AGAPS mask), and (2) the mask of intra-contig ambiguities (AMB mask).' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Mus musculus (UCSC genome mm10, based on GRCm38.p6) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm10.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 40d51fb428a5fda8c05101a3dddb8957 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Mus musculus (UCSC genome mm10, based on GRCm38.p6)' - description: 'Full genome sequences for Mus musculus (Mouse) as provided by UCSC (genome mm10, based on GRCm38.p6) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm10, except that each of them has the 2 following masks on top: (1) the mask of assembly gaps (AGAPS mask), and (2) the mask of intra-contig ambiguities (AMB mask).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml index 8d717d8f96f31..229eacc48e225 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml @@ -1,44 +1,44 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Mmusculus.UCSC.mm10" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ffddc2e035527ed1a1e201ac4cc0b1f3 +about: + description: Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm10, based on GRCm38.p6) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Mus musculus (UCSC version mm10, based on GRCm38.p6) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm10", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-bsgenome.mmusculus.ucsc.mm10 + path: recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10 + version: 1.4.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ffddc2e035527ed1a1e201ac4cc0b1f3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Mus musculus (UCSC version mm10, based on GRCm38.p6)' - description: 'Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm10, based on GRCm38.p6) and stored in Biostrings objects.' -extra: - parent_recipe: - name: bioconductor-bsgenome.mmusculus.ucsc.mm10 - path: recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10 - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm39/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm39/meta.yaml index 935b7d6e381f3..f8c6f992ee0a2 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm39/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm39/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Mmusculus.UCSC.mm39" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a130ef50dd55da9fd341e6c90b22637b +about: + description: Full genome sequences for Mus musculus (Mouse) as provided by UCSC (genome mm39, based on assembly GRCm39) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Mus musculus (UCSC genome mm39, based on GRCm39) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm39", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a130ef50dd55da9fd341e6c90b22637b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Mus musculus (UCSC genome mm39, based on GRCm39)' - description: 'Full genome sequences for Mus musculus (Mouse) as provided by UCSC (genome mm39, based on assembly GRCm39) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/meta.yaml index 7f6fd1ee3b55f..c3b1c72910da3 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Mmusculus.UCSC.mm8.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5809f925e0fe7c4b73b78a90c9a36fdd +about: + description: 'Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm8, Feb. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm8, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Mus musculus (UCSC version mm8) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm8.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm8 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.mmusculus.ucsc.mm8 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm8 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.mmusculus.ucsc.mm8 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5809f925e0fe7c4b73b78a90c9a36fdd + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Mus musculus (UCSC version mm8)' - description: 'Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm8, Feb. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm8, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/meta.yaml index 1015d037ec13c..f848a6f0ab431 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmusculus.UCSC.mm8" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f6aa91cdce2607f30a34f6dd0d678aff +about: + description: Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm8, Feb. 2006) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Mus musculus (UCSC version mm8) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm8", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f6aa91cdce2607f30a34f6dd0d678aff + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Mus musculus (UCSC version mm8)' - description: 'Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm8, Feb. 2006) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/meta.yaml index a388770cefc1a..3a913b3f47cd0 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Mmusculus.UCSC.mm9.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a5dadab14e55cdfc39649ede7a8483d5 +about: + description: 'Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Mus musculus (UCSC version mm9) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm9.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a5dadab14e55cdfc39649ede7a8483d5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Mus musculus (UCSC version mm9)' - description: 'Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml index c84701d12370e..50303f12a7fa4 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml @@ -1,45 +1,45 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmusculus.UCSC.mm9" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a30ba2b4481a17e8e6979eb69eabf78 +about: + description: Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Mus musculus (UCSC version mm9) build: - number: 17 + noarch: generic + number: 18 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.mmusculus.ucsc.mm9", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-bsgenome.mmusculus.ucsc.mm9 + path: recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9 + version: 1.4.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: TxDb.Mmusculus.UCSC.mm9.knownGene requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5a30ba2b4481a17e8e6979eb69eabf78 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Mus musculus (UCSC version mm9)' - description: 'Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects.' -extra: - parent_recipe: - name: bioconductor-bsgenome.mmusculus.ucsc.mm9 - path: recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9 - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.osativa.msu.msu7/meta.yaml b/recipes/bioconductor-bsgenome.osativa.msu.msu7/meta.yaml index 163678ae1635a..0cb40bbb08dbf 100644 --- a/recipes/bioconductor-bsgenome.osativa.msu.msu7/meta.yaml +++ b/recipes/bioconductor-bsgenome.osativa.msu.msu7/meta.yaml @@ -1,39 +1,39 @@ {% set version = "0.99.2" %} {% set name = "BSgenome.Osativa.MSU.MSU7" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80648058756a2f74aa5a246d38ecf576 +about: + description: Oryza sativa full genome as provided by MSU (MSU7 Genome Release) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Oryza sativa full genome (MSU7) build: - number: 5 + noarch: generic + number: 6 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.osativa.msu.msu7", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 80648058756a2f74aa5a246d38ecf576 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Oryza sativa full genome (MSU7)' - description: 'Oryza sativa full genome as provided by MSU (MSU7 Genome Release) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan1/meta.yaml b/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan1/meta.yaml index 85411a3df2b2e..530bb1d2d1f6c 100644 --- a/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan1/meta.yaml +++ b/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan1/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Ppaniscus.UCSC.panPan1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 186adb59264d468d17c0f6374e2eb1f6 +about: + description: Full genome sequences for Pan paniscus (Bonobo) as provided by UCSC (panPan1, May 2012) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Pan paniscus (UCSC version panPan1) build: - number: 7 + noarch: generic + number: 8 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ppaniscus.ucsc.panpan1", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 186adb59264d468d17c0f6374e2eb1f6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Pan paniscus (UCSC version panPan1)' - description: 'Full genome sequences for Pan paniscus (Bonobo) as provided by UCSC (panPan1, May 2012) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan2/meta.yaml b/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan2/meta.yaml index f6c6a0c21e800..6f0cd05c04d8b 100644 --- a/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan2/meta.yaml +++ b/recipes/bioconductor-bsgenome.ppaniscus.ucsc.panpan2/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Ppaniscus.UCSC.panPan2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 74973376a6377d6820d6cd7fb3655a19 +about: + description: Full genome sequences for Pan paniscus (Bonobo) as provided by UCSC (panPan2, Dec. 2015) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Pan paniscus (UCSC version panPan2) build: - number: 7 + noarch: generic + number: 8 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ppaniscus.ucsc.panpan2", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 74973376a6377d6820d6cd7fb3655a19 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Pan paniscus (UCSC version panPan2)' - description: 'Full genome sequences for Pan paniscus (Bonobo) as provided by UCSC (panPan2, Dec. 2015) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/meta.yaml index 456bbdeda57f3..ecd8ce7f940c1 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro2.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e6d069be23712b483b4e4c71554594cf +about: + description: 'Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro2, Mar. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ptroglodytes.UCSC.panTro2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Pan troglodytes (UCSC version panTro2) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro2 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.ptroglodytes.ucsc.pantro2 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro2 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.ptroglodytes.ucsc.pantro2 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e6d069be23712b483b4e4c71554594cf + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Pan troglodytes (UCSC version panTro2)' - description: 'Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro2, Mar. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ptroglodytes.UCSC.panTro2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/meta.yaml index 13287c4def47d..50a5720dc8de3 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 780200c315779ac75fcf0bdeb9a2eb8c +about: + description: Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro2, Mar. 2006) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Pan troglodytes (UCSC version panTro2) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ptroglodytes.ucsc.pantro2", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 780200c315779ac75fcf0bdeb9a2eb8c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Pan troglodytes (UCSC version panTro2)' - description: 'Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro2, Mar. 2006) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/meta.yaml index ccedb52acf0fe..60dd45100d7fa 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro3.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 89e96b3796d3b8e8793146597506e3f5 +about: + description: 'Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro3, Oct. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ptroglodytes.UCSC.panTro3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Pan troglodytes (UCSC version panTro3) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro3 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.ptroglodytes.ucsc.pantro3 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro3 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.ptroglodytes.ucsc.pantro3 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 89e96b3796d3b8e8793146597506e3f5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Pan troglodytes (UCSC version panTro3)' - description: 'Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro3, Oct. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ptroglodytes.UCSC.panTro3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/meta.yaml index 4cced5a9b52a6..9d18bcf4ae7b7 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro3" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4677c75befd60742f3fc2a54c7f60666 +about: + description: Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro3, Oct. 2010) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Pan troglodytes (UCSC version panTro3) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ptroglodytes.ucsc.pantro3", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4677c75befd60742f3fc2a54c7f60666 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Pan troglodytes (UCSC version panTro3)' - description: 'Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro3, Oct. 2010) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/meta.yaml index e2c5ae5f72aaa..4a53bb276030e 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro5" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b88573dd9c3ef838699b65934f8abe3 +about: + description: Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro5, May 2016) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Pan troglodytes (UCSC version panTro5) build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ptroglodytes.ucsc.pantro5", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5b88573dd9c3ef838699b65934f8abe3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Pan troglodytes (UCSC version panTro5)' - description: 'Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro5, May 2016) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/meta.yaml index 12604327f1864..8ab79b0327312 100644 --- a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/meta.yaml +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Ptroglodytes.UCSC.panTro6" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1df05d985374e9edc1dd7c3df5118338 +about: + description: Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro6, Jan. 2018) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Pan troglodytes (UCSC version panTro6) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.ptroglodytes.ucsc.pantro6", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1df05d985374e9edc1dd7c3df5118338 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Pan troglodytes (UCSC version panTro6)' - description: 'Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro6, Jan. 2018) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/meta.yaml index c583c872ec589..4737e34395fd4 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn4.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e2ea7df588b6b10515e07ea3868c568 +about: + description: 'Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn4, Nov. 2004) and stored in Biostrings objects. The sequences are the same as in BSgenome.Rnorvegicus.UCSC.rn4, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Rattus norvegicus (UCSC version rn4) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn4 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.rnorvegicus.ucsc.rn4 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn4 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.rnorvegicus.ucsc.rn4 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7e2ea7df588b6b10515e07ea3868c568 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Rattus norvegicus (UCSC version rn4)' - description: 'Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn4, Nov. 2004) and stored in Biostrings objects. The sequences are the same as in BSgenome.Rnorvegicus.UCSC.rn4, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/meta.yaml index 1c86c50cd4dae..b247844ef82e7 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn4" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3afe6729237781445d99ec38228ee1a8 +about: + description: Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn4, Nov. 2004) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Rattus norvegicus (UCSC version rn4) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.rnorvegicus.ucsc.rn4", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: TxDb.Rnorvegicus.UCSC.rn4.ensGene requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3afe6729237781445d99ec38228ee1a8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Rattus norvegicus (UCSC version rn4)' - description: 'Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn4, Nov. 2004) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/meta.yaml index 89dbbafe4e2e5..646ce34da1433 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn5.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 663233774b79012cb2cc08224ac275ed +about: + description: 'Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn5, Mar. 2012) and stored in Biostrings objects. The sequences are the same as in BSgenome.Rnorvegicus.UCSC.rn5, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Rattus norvegicus (UCSC version rn5) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn5 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.rnorvegicus.ucsc.rn5 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn5 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.rnorvegicus.ucsc.rn5 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 663233774b79012cb2cc08224ac275ed + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Rattus norvegicus (UCSC version rn5)' - description: 'Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn5, Mar. 2012) and stored in Biostrings objects. The sequences are the same as in BSgenome.Rnorvegicus.UCSC.rn5, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/meta.yaml index 4297c1fcfc716..d48c0e5cd7825 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn5" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 723b1f3ced395ef638b2d68053b05c86 +about: + description: Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn5, Mar. 2012) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Rattus norvegicus (UCSC version rn5) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.rnorvegicus.ucsc.rn5", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: TxDb.Rnorvegicus.UCSC.rn5.refGene requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 723b1f3ced395ef638b2d68053b05c86 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Rattus norvegicus (UCSC version rn5)' - description: 'Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn5, Mar. 2012) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/meta.yaml index 1ee39156f2de8..52188c5a18a9e 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.4.1" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn6" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 60d3fb201e0b1475912aaf681927096d +about: + description: Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn6, Jul. 2014) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Rattus norvegicus (UCSC version rn6) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.rnorvegicus.ucsc.rn6", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 60d3fb201e0b1475912aaf681927096d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Rattus norvegicus (UCSC version rn6)' - description: 'Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn6, Jul. 2014) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn7/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn7/meta.yaml index 07102a354264c..9c3b504607d75 100644 --- a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn7/meta.yaml +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn7/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.3" %} {% set name = "BSgenome.Rnorvegicus.UCSC.rn7" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c64f7dd9e30ff88ce02ecd3712e4c454 +about: + description: Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (genome rn7) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Rattus norvegicus (UCSC genome rn7) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.rnorvegicus.ucsc.rn7", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c64f7dd9e30ff88ce02ecd3712e4c454 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Rattus norvegicus (UCSC genome rn7)' - description: 'Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (genome rn7) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/meta.yaml b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/meta.yaml index 725432e3a6292..aa51c8b288dee 100644 --- a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/meta.yaml +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Scerevisiae.UCSC.sacCer1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad4c29c16a9635088bf13872b4a02ed4 +about: + description: Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer1, Oct. 2003) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer1) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.scerevisiae.ucsc.saccer1", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ad4c29c16a9635088bf13872b4a02ed4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer1)' - description: 'Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer1, Oct. 2003) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/meta.yaml b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/meta.yaml index f65fa66ad4026..750ea692d863b 100644 --- a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/meta.yaml +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Scerevisiae.UCSC.sacCer2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f1025b4d0fa7891dc46301550163753e +about: + description: Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer2, June 2008) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer2) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.scerevisiae.ucsc.saccer2", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f1025b4d0fa7891dc46301550163753e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer2)' - description: 'Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer2, June 2008) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/meta.yaml b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/meta.yaml index b386b9c86ea88..45778ef17e899 100644 --- a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/meta.yaml +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Scerevisiae.UCSC.sacCer3" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7f2d8bba69c3dcebf426d9b19a6bed30 +about: + description: Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer3, April 2011) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer3) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.scerevisiae.ucsc.saccer3", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7f2d8bba69c3dcebf426d9b19a6bed30 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer3)' - description: 'Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer3, April 2011) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/meta.yaml b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/meta.yaml index e2ac5d79e3f68..e2c5c87049f0c 100644 --- a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/meta.yaml +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Sscrofa.UCSC.susScr11" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: db22832229e31e1a629d107df522dff9 +about: + description: Full genome sequences for Sus scrofa (Pig) as provided by UCSC (susScr11, Feb. 2017) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Sus scrofa (UCSC version susScr11) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.sscrofa.ucsc.susscr11", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: db22832229e31e1a629d107df522dff9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Sus scrofa (UCSC version susScr11)' - description: 'Full genome sequences for Sus scrofa (Pig) as provided by UCSC (susScr11, Feb. 2017) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/meta.yaml b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/meta.yaml index c116c67adf671..b935f341a742e 100644 --- a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Sscrofa.UCSC.susScr3.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fd240651d22d169fd1e27a2b66e40dd7 +about: + description: 'Full genome sequences for Sus scrofa (Pig) as provided by UCSC (susScr3, Aug. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Sscrofa.UCSC.susScr3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Sus scrofa (UCSC version susScr3) build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.sscrofa.ucsc.susscr3 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.sscrofa.ucsc.susscr3 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.sscrofa.ucsc.susscr3 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.sscrofa.ucsc.susscr3 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fd240651d22d169fd1e27a2b66e40dd7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Sus scrofa (UCSC version susScr3)' - description: 'Full genome sequences for Sus scrofa (Pig) as provided by UCSC (susScr3, Aug. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Sscrofa.UCSC.susScr3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/meta.yaml b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/meta.yaml index 2903b8432bb02..64d55a7b10182 100644 --- a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/meta.yaml +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Sscrofa.UCSC.susScr3" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0457ca52a81c9d7ceadad5830169e6cf +about: + description: Full genome sequences for Sus scrofa (Pig) as provided by UCSC (susScr3, Aug. 2011) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Sus scrofa (UCSC version susScr3) build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.sscrofa.ucsc.susscr3", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0457ca52a81c9d7ceadad5830169e6cf + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Sus scrofa (UCSC version susScr3)' - description: 'Full genome sequences for Sus scrofa (Pig) as provided by UCSC (susScr3, Aug. 2011) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/meta.yaml b/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/meta.yaml index c22953ef89cf7..b69461518dadc 100644 --- a/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/meta.yaml +++ b/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/meta.yaml @@ -1,40 +1,40 @@ {% set version = "0.99.1" %} {% set name = "BSgenome.Tgondii.ToxoDB.7.0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f67644d1a897fe2ff4139832d4ceaf80 +about: + description: Toxoplasma gondii ME49 genome Release 7.0 available at http://www.toxodb.org + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL 3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Toxoplasma gondii ME49 (ToxoDB-7.0) build: - number: 5 + noarch: generic + number: 6 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.tgondii.toxodb.7.0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f67644d1a897fe2ff4139832d4ceaf80 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'GPL 3' - summary: 'Toxoplasma gondii ME49 (ToxoDB-7.0)' - description: 'Toxoplasma gondii ME49 genome Release 7.0 available at http://www.toxodb.org' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/meta.yaml b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/meta.yaml index 44e84dd6f5b29..085a5fc119b82 100644 --- a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/meta.yaml +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.3.99" %} {% set name = "BSgenome.Tguttata.UCSC.taeGut1.masked" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 63684abb5b330bb54ff89fe78f2e6444 +about: + description: 'Full genome sequences for Taeniopygia guttata (Zebra finch) as provided by UCSC (taeGut1, Jul. 2008) and stored in Biostrings objects. The sequences are the same as in BSgenome.Tguttata.UCSC.taeGut1, except that each of them has the 2 following masks on top: (1) the mask of assembly gaps (AGAPS mask), and (2) the mask of intra-contig ambiguities (AMB mask). Both masks are "active" by default.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full masked genome sequences for Taeniopygia guttata (UCSC version taeGut1) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.tguttata.ucsc.taegut1.masked", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.tguttata.ucsc.taegut1 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.tguttata.ucsc.taegut1 >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.tguttata.ucsc.taegut1 >=1.4.0,<1.5.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.tguttata.ucsc.taegut1 >=1.4.0,<1.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 63684abb5b330bb54ff89fe78f2e6444 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full masked genome sequences for Taeniopygia guttata (UCSC version taeGut1)' - description: 'Full genome sequences for Taeniopygia guttata (Zebra finch) as provided by UCSC (taeGut1, Jul. 2008) and stored in Biostrings objects. The sequences are the same as in BSgenome.Tguttata.UCSC.taeGut1, except that each of them has the 2 following masks on top: (1) the mask of assembly gaps (AGAPS mask), and (2) the mask of intra-contig ambiguities (AMB mask). Both masks are "active" by default.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/meta.yaml b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/meta.yaml index 086df25bd94c0..53b6c671bf665 100644 --- a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/meta.yaml +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Tguttata.UCSC.taeGut1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9753d9568d2a866a627673a518a1dd8a +about: + description: Full genome sequences for Taeniopygia guttata (Zebra finch) as provided by UCSC (taeGut1, Jul. 2008) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Taeniopygia guttata (UCSC version taeGut1) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.tguttata.ucsc.taegut1", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9753d9568d2a866a627673a518a1dd8a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Taeniopygia guttata (UCSC version taeGut1)' - description: 'Full genome sequences for Taeniopygia guttata (Zebra finch) as provided by UCSC (taeGut1, Jul. 2008) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/meta.yaml b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/meta.yaml index fbca5f56adb3d..29d45f53236c9 100644 --- a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/meta.yaml +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/meta.yaml @@ -1,39 +1,39 @@ {% set version = "1.4.2" %} {% set name = "BSgenome.Tguttata.UCSC.taeGut2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d39678fb060e643f7e9c4ec25e828c0 +about: + description: Full genome sequences for Taeniopygia guttata (Zebra finch) as provided by UCSC (taeGut2, Feb. 2013) and stored in Biostrings objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Full genome sequences for Taeniopygia guttata (UCSC version taeGut2) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.tguttata.ucsc.taegut2", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1d39678fb060e643f7e9c4ec25e828c0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Full genome sequences for Taeniopygia guttata (UCSC version taeGut2)' - description: 'Full genome sequences for Taeniopygia guttata (Zebra finch) as provided by UCSC (taeGut2, Feb. 2013) and stored in Biostrings objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/meta.yaml b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/meta.yaml index ef55869bfb77c..e8606390985be 100644 --- a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/meta.yaml +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/meta.yaml @@ -1,39 +1,39 @@ {% set version = "0.1" %} {% set name = "BSgenome.Vvinifera.URGI.IGGP12Xv0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f791de6d699325a97080cd98be86d89 +about: + description: Full reference nuclear genome sequences for Vitis vinifera subsp. vinifera PN40024 (derived from Pinot Noir and close to homozygosity after 6-9 rounds of selfing) as assembled by the IGGP (version 12Xv0) and available at the URGI (INRA) + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: CC0 + summary: Full reference nuclear genome sequences for Vitis vinifera subsp. vinifera PN40024 (IGGP version 12Xv0) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.vvinifera.urgi.iggp12xv0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3f791de6d699325a97080cd98be86d89 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: CC0 - summary: 'Full reference nuclear genome sequences for Vitis vinifera subsp. vinifera PN40024 (IGGP version 12Xv0)' - description: 'Full reference nuclear genome sequences for Vitis vinifera subsp. vinifera PN40024 (derived from Pinot Noir and close to homozygosity after 6-9 rounds of selfing) as assembled by the IGGP (version 12Xv0) and available at the URGI (INRA)' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/meta.yaml b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/meta.yaml index 32841939100f7..607eaf30166af 100644 --- a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/meta.yaml +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/meta.yaml @@ -1,39 +1,39 @@ {% set version = "0.1" %} {% set name = "BSgenome.Vvinifera.URGI.IGGP12Xv2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 95472e574ab46327c19e241c381b26a2 +about: + description: Full reference nuclear genome sequences for Vitis vinifera subsp. vinifera PN40024 (derived from Pinot Noir and close to homozygosity after 6-9 rounds of selfing) as assembled by the IGGP (version 12Xv2) and available at the URGI (INRA) + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: CC0 + summary: Full reference nuclear genome sequences for Vitis vinifera subsp. vinifera PN40024 (IGGP version 12Xv2) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.vvinifera.urgi.iggp12xv2", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 95472e574ab46327c19e241c381b26a2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: CC0 - summary: 'Full reference nuclear genome sequences for Vitis vinifera subsp. vinifera PN40024 (IGGP version 12Xv2)' - description: 'Full reference nuclear genome sequences for Vitis vinifera subsp. vinifera PN40024 (derived from Pinot Noir and close to homozygosity after 6-9 rounds of selfing) as assembled by the IGGP (version 12Xv2) and available at the URGI (INRA)' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/meta.yaml b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/meta.yaml index 34e0332d217bc..7f3cf116e1285 100644 --- a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/meta.yaml +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/meta.yaml @@ -1,39 +1,39 @@ {% set version = "0.1" %} {% set name = "BSgenome.Vvinifera.URGI.IGGP8X" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fccaf60e5c9352b9c454f7a8ecac2a20 +about: + description: Full reference nuclear genome sequences for Vitis vinifera subsp. vinifera PN40024 (derived from Pinot Noir and close to homozygosity after 6-9 rounds of selfing) as assembled by the IGGP (version 8X) and available at the URGI (INRA). More details in Jaillon et al (Nature, 2007). + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: CC0 + summary: Full reference nuclear genome sequences for Vitis vinifera subsp. vinifera PN40024 (IGGP version 8X) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome.vvinifera.urgi.iggp8x", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fccaf60e5c9352b9c454f7a8ecac2a20 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: CC0 - summary: 'Full reference nuclear genome sequences for Vitis vinifera subsp. vinifera PN40024 (IGGP version 8X)' - description: 'Full reference nuclear genome sequences for Vitis vinifera subsp. vinifera PN40024 (derived from Pinot Noir and close to homozygosity after 6-9 rounds of selfing) as assembled by the IGGP (version 8X) and available at the URGI (INRA). More details in Jaillon et al (Nature, 2007).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenome/meta.yaml b/recipes/bioconductor-bsgenome/meta.yaml index 0958486077c61..9cea0fd233ce9 100644 --- a/recipes/bioconductor-bsgenome/meta.yaml +++ b/recipes/bioconductor-bsgenome/meta.yaml @@ -1,66 +1,72 @@ -{% set version = "1.70.1" %} +{% set version = "1.74.0" %} {% set name = "BSgenome" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Infrastructure shared by all the Biostrings-based genome data packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Software infrastructure for efficient representation of full genomes and their SNPs -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a94697b953c4fc9bb0ba15daf35a884d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenome", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit, BSgenomeForge + +extra: + identifiers: + - biotools:bsgenome + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-bsgenome + path: recipes/bioconductor-bsgenome + version: 1.48.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocManager, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit, BSgenomeForge requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-matrixstats run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-matrixstats + +source: + md5: d5a0e768ab5eebb73116c59b50afb921 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Software infrastructure for efficient representation of full genomes and their SNPs' - description: 'Infrastructure shared by all the Biostrings-based genome data packages.' -extra: - identifiers: - - biotools:bsgenome - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-bsgenome - path: recipes/bioconductor-bsgenome - version: 1.48.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsgenomeforge/meta.yaml b/recipes/bioconductor-bsgenomeforge/meta.yaml index 0c189d94200e2..40367fe38a400 100644 --- a/recipes/bioconductor-bsgenomeforge/meta.yaml +++ b/recipes/bioconductor-bsgenomeforge/meta.yaml @@ -1,52 +1,61 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "BSgenomeForge" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A set of tools to forge BSgenome data packages. Supersedes the old seed-based tools from the BSgenome software package. This package allows the user to create a BSgenome data package in one function call, simplifying the old seed-based process. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Forge your own BSgenome data package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed03f4628533403765aae28991855bca build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsgenomeforge", max_pin="x.x") }}' - noarch: generic -# Suggests: GenomicRanges, GenomicFeatures, testthat, knitr, rmarkdown, BiocStyle, devtools + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: GenomicFeatures, Rsamtools, testthat, knitr, rmarkdown, BiocStyle, devtools, BSgenome.Celegans.UCSC.ce2 requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base + +source: + md5: ca1e4c6acfa4a7ac708711f952607ad1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Forge BSgenome data packages' - description: 'A set of tools to forge BSgenome data packages. Supersedes the old seed-based tools from the BSgenome software package. This package allows the user to create a BSgenome data package in one function call, simplifying the old seed-based process.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsseq/meta.yaml b/recipes/bioconductor-bsseq/meta.yaml index 70bb7392726a0..57088e35840e6 100644 --- a/recipes/bioconductor-bsseq/meta.yaml +++ b/recipes/bioconductor-bsseq/meta.yaml @@ -1,96 +1,105 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "bsseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A collection of tools for analyzing and visualizing whole-genome methylation data from sequencing. This includes whole-genome bisulfite sequencing and Oxford nanopore data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Analyze, manage and store whole-genome methylation data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0fee416655d94a260bf4a613b4a6321e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsseq", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:bsseq + parent_recipe: + name: bioconductor-bsseq + path: recipes/bioconductor-bsseq + version: 1.16.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat (>= 1.5.2), batchtools requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-data.table >=1.11.8' + - r-data.table >=1.11.8 - r-gtools - r-locfit - r-permute - - 'r-r.utils >=2.0.0' + - r-r.utils >=2.0.0 - r-rcpp - r-scales - libblas - liblapack + run: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-data.table >=1.11.8' + - r-data.table >=1.11.8 - r-gtools - r-locfit - r-permute - - 'r-r.utils >=2.0.0' + - r-r.utils >=2.0.0 - r-rcpp - r-scales - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: f1b8ff8a8f192525c809624b3ad357ad + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Analyze, manage and store bisulfite sequencing data' - description: 'A collection of tools for analyzing and visualizing bisulfite sequencing data.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:bsseq - parent_recipe: - name: bioconductor-bsseq - path: recipes/bioconductor-bsseq - version: 1.16.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsseqdata/meta.yaml b/recipes/bioconductor-bsseqdata/meta.yaml index 2c014a22b1551..054979d59e823 100644 --- a/recipes/bioconductor-bsseqdata/meta.yaml +++ b/recipes/bioconductor-bsseqdata/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "0.40.0" %} +{% set version = "0.44.0" %} {% set name = "bsseqData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 514171e8133c8d38e6b1ad31eff722a8 +about: + description: Example whole genome bisulfite data for the bsseq package + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Example whole genome bisulfite data for the bsseq package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsseqdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - bioconductor-bsseq >=1.42.0,<1.43.0 - r-base run: - - 'bioconductor-bsseq >=1.38.0,<1.39.0' + - bioconductor-bsseq >=1.42.0,<1.43.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 759f2d070264c33866572d991c5723af + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Example whole genome bisulfite data for the bsseq package' - description: 'Example whole genome bisulfite data for the bsseq package' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsseqdata/post-link.sh b/recipes/bioconductor-bsseqdata/post-link.sh index 6f79c30564302..c7ad431547510 100644 --- a/recipes/bioconductor-bsseqdata/post-link.sh +++ b/recipes/bioconductor-bsseqdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "bsseqdata-0.40.0" +installBiocDataPackage.sh "bsseqdata-0.44.0" diff --git a/recipes/bioconductor-bsubtiliscdf/meta.yaml b/recipes/bioconductor-bsubtiliscdf/meta.yaml index d9da46bade688..e43c18e79e281 100644 --- a/recipes/bioconductor-bsubtiliscdf/meta.yaml +++ b/recipes/bioconductor-bsubtiliscdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "bsubtiliscdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7d7893d28c601206805819ae0e49b31b +about: + description: A package containing an environment representing the Bsubtilis.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: bsubtiliscdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsubtiliscdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7d7893d28c601206805819ae0e49b31b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: bsubtiliscdf - description: 'A package containing an environment representing the Bsubtilis.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bsubtilisprobe/meta.yaml b/recipes/bioconductor-bsubtilisprobe/meta.yaml index 7cfe3dece2b39..5214553c45006 100644 --- a/recipes/bioconductor-bsubtilisprobe/meta.yaml +++ b/recipes/bioconductor-bsubtilisprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "bsubtilisprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 83568fcea2122350b7ce982e79b7ec53 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Bsubtilis\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type bsubtilis build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bsubtilisprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 83568fcea2122350b7ce982e79b7ec53 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type bsubtilis' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Bsubtilis\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bubbletree/meta.yaml b/recipes/bioconductor-bubbletree/meta.yaml index 23898ead413c9..9079596ade7b3 100644 --- a/recipes/bioconductor-bubbletree/meta.yaml +++ b/recipes/bioconductor-bubbletree/meta.yaml @@ -1,34 +1,45 @@ -{% set version = "2.32.0" %} +{% set version = "2.36.0" %} {% set name = "BubbleTree" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CNV analysis in groups of tumor samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: 'BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84649d9271ce193051e18a7bb56ff58e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bubbletree", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:bubbletree + - doi:10.1093/nar/gkv1102 + parent_recipe: + name: bioconductor-bubbletree + path: recipes/bioconductor-bubbletree + version: 2.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-biovizbase >=1.50.0,<1.51.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-biovizbase >=1.54.0,<1.55.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-dplyr - r-e1071 @@ -41,13 +52,13 @@ requirements: - r-rcolorbrewer - r-writexls run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-biovizbase >=1.50.0,<1.51.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-biovizbase >=1.54.0,<1.55.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-dplyr - r-e1071 @@ -59,21 +70,16 @@ requirements: - r-plyr - r-rcolorbrewer - r-writexls + +source: + md5: acf0e813b99cba417798d192588822e0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 3)' - summary: 'BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data' - description: 'CNV analysis in groups of tumor samples.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:bubbletree - - doi:10.1093/nar/gkv1102 - parent_recipe: - name: bioconductor-bubbletree - path: recipes/bioconductor-bubbletree - version: 2.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bufferedmatrix/meta.yaml b/recipes/bioconductor-bufferedmatrix/meta.yaml index dbb18ad6dfccf..f695c5648e451 100644 --- a/recipes/bioconductor-bufferedmatrix/meta.yaml +++ b/recipes/bioconductor-bufferedmatrix/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "1.66.0" %} +{% set version = "1.70.0" %} {% set name = "BufferedMatrix" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: A matrix data storage object held in temporary files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a4ad95db528526463e6dfca80975815e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bufferedmatrix", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:bufferedmatrix + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-bufferedmatrix + path: recipes/bioconductor-bufferedmatrix + version: 1.44.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: f6e6592cef55d8c83e92b5fa3e2ea41d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'A matrix data storage object held in temporary files' - description: 'A tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:bufferedmatrix - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-bufferedmatrix - path: recipes/bioconductor-bufferedmatrix - version: 1.44.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bufferedmatrixmethods/meta.yaml b/recipes/bioconductor-bufferedmatrixmethods/meta.yaml index 55a8f987f77dc..440d414904f76 100644 --- a/recipes/bioconductor-bufferedmatrixmethods/meta.yaml +++ b/recipes/bioconductor-bufferedmatrixmethods/meta.yaml @@ -1,51 +1,57 @@ -{% set version = "1.66.0" %} +{% set version = "1.70.0" %} {% set name = "BufferedMatrixMethods" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Microarray analysis methods that use BufferedMatrix objects + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Microarray Data related methods that utlize BufferedMatrix objects -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 57eb9e8db5a9dc58db25b88bbe5d2436 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bufferedmatrixmethods", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:bufferedmatrixmethods + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-bufferedmatrixmethods + path: recipes/bioconductor-bufferedmatrixmethods + version: 1.44.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: affyio, affy requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-bufferedmatrix >=1.66.0,<1.67.0' + - bioconductor-bufferedmatrix >=1.70.0,<1.71.0 - r-base - libblas - liblapack run: - - 'bioconductor-bufferedmatrix >=1.66.0,<1.67.0' + - bioconductor-bufferedmatrix >=1.70.0,<1.71.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: 63ef3df515379903325382cdf999e38a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Microarray Data related methods that utlize BufferedMatrix objects' - description: 'Microarray analysis methods that use BufferedMatrix objects' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:bufferedmatrixmethods - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-bufferedmatrixmethods - path: recipes/bioconductor-bufferedmatrixmethods - version: 1.44.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bugphyzz/meta.yaml b/recipes/bioconductor-bugphyzz/meta.yaml new file mode 100644 index 0000000000000..ec76c4cb3f04a --- /dev/null +++ b/recipes/bioconductor-bugphyzz/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.0.0" %} +{% set name = "bugphyzz" %} +{% set bioc = "3.20" %} + +about: + description: bugphyzz is an electronic database of standardized microbial annotations. It facilitates the creation of microbial signatures based on shared attributes, which are utilized for bug set enrichment analysis. The data also includes annotations imputed with ancestra state reconstruction methods. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: A harmonized data resource and software for enrichment analysis of microbial physiologies + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-bugphyzz", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: DT, forcats, ggplot2, htmltools, knitr, rmarkdown, sessioninfo, testthat, EnrichmentBrowser, MicrobiomeBenchmarkData, mia, stats, rlang, limma, mgsub, methods, readr, crayon, tibble, magrittr, tidytext, BiocStyle +requirements: + host: + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-dplyr + - r-httr2 + - r-purrr + - r-stringr + - r-tidyr + - r-tidyselect + run: + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-dplyr + - r-httr2 + - r-purrr + - r-stringr + - r-tidyr + - r-tidyselect + - curl + - bioconductor-data-packages >=20241103 + +source: + md5: b29c65abe5333278bea9cbd13db6dc77 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-bugphyzz/post-link.sh b/recipes/bioconductor-bugphyzz/post-link.sh new file mode 100644 index 0000000000000..c00017416e3f0 --- /dev/null +++ b/recipes/bioconductor-bugphyzz/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "bugphyzz-1.0.0" diff --git a/recipes/bioconductor-bugphyzz/pre-unlink.sh b/recipes/bioconductor-bugphyzz/pre-unlink.sh new file mode 100644 index 0000000000000..c21f579be4406 --- /dev/null +++ b/recipes/bioconductor-bugphyzz/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ bugphyzz diff --git a/recipes/bioconductor-bugsigdbr/meta.yaml b/recipes/bioconductor-bugsigdbr/meta.yaml index 345d5d5fb9b45..4657a795c01a8 100644 --- a/recipes/bioconductor-bugsigdbr/meta.yaml +++ b/recipes/bioconductor-bugsigdbr/meta.yaml @@ -1,39 +1,41 @@ -{% set version = "1.8.1" %} +{% set version = "1.12.0" %} {% set name = "bugsigdbr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 35aebe840ca55cd93f16af9d239ea806 +about: + description: The bugsigdbr package implements convenient access to bugsigdb.org from within R/Bioconductor. The goal of the package is to facilitate import of BugSigDB data into R/Bioconductor, provide utilities for extracting microbe signatures, and enable export of the extracted signatures to plain text files in standard file formats such as GMT. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: R-side access to published microbial signatures from BugSigDB build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bugsigdbr", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, ontologyIndex, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base + - r-vroom run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base + - r-vroom +source: + md5: 497ef05e5eb6f51b0eb9f150f7f61565 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'R-side access to published microbial signatures from BugSigDB' - description: 'The bugsigdbr package implements convenient access to bugsigdb.org from within R/Bioconductor. The goal of the package is to facilitate import of BugSigDB data into R/Bioconductor, provide utilities for extracting microbe signatures, and enable export of the extracted signatures to plain text files in standard file formats such as GMT.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bumhmm/meta.yaml b/recipes/bioconductor-bumhmm/meta.yaml index 853c6756464b6..9de7eeb6b9644 100644 --- a/recipes/bioconductor-bumhmm/meta.yaml +++ b/recipes/bioconductor-bumhmm/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "BUMHMM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This is a probabilistic modelling pipeline for computing per- nucleotide posterior probabilities of modification from the data collected in structure probing experiments. The model supports multiple experimental replicates and empirically corrects coverage- and sequence-dependent biases. The model utilises the measure of a "drop-off rate" for each nucleotide, which is compared between replicates through a log-ratio (LDR). The LDRs between control replicates define a null distribution of variability in drop-off rate observed by chance and LDRs between treatment and control replicates gets compared to this distribution. Resulting empirical p-values (probability of being "drawn" from the null distribution) are used as observations in a Hidden Markov Model with a Beta-Uniform Mixture model used as an emission model. The resulting posterior probabilities indicate the probability of a nucleotide of having being modified in a structure probing experiment. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Computational pipeline for computing probability of modification from structure probing experiment data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c70dbfec58330fd1fa6cd1aca5e16912 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bumhmm", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-devtools - r-gtools - r-stringi run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-devtools - r-gtools - r-stringi + +source: + md5: 0ad6f721f6976cbc5d8df86870e391e1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Computational pipeline for computing probability of modification from structure probing experiment data' - description: 'This is a probabilistic modelling pipeline for computing per- nucleotide posterior probabilities of modification from the data collected in structure probing experiments. The model supports multiple experimental replicates and empirically corrects coverage- and sequence-dependent biases. The model utilises the measure of a "drop-off rate" for each nucleotide, which is compared between replicates through a log-ratio (LDR). The LDRs between control replicates define a null distribution of variability in drop-off rate observed by chance and LDRs between treatment and control replicates gets compared to this distribution. Resulting empirical p-values (probability of being "drawn" from the null distribution) are used as observations in a Hidden Markov Model with a Beta-Uniform Mixture model used as an emission model. The resulting posterior probabilities indicate the probability of a nucleotide of having being modified in a structure probing experiment.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bumphunter/meta.yaml b/recipes/bioconductor-bumphunter/meta.yaml index 44699549646a5..41c383e2af3ff 100644 --- a/recipes/bioconductor-bumphunter/meta.yaml +++ b/recipes/bioconductor-bumphunter/meta.yaml @@ -1,35 +1,44 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "bumphunter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for finding bumps in genomic data + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Bump Hunter -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fea93f84b54daabaaf1686d658aeedfc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bumphunter", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, RUnit, doParallel, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene + +extra: + identifiers: + - biotools:bumphunter + parent_recipe: + name: bioconductor-bumphunter + path: recipes/bioconductor-bumphunter + version: 1.22.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, RUnit, doParallel, txdbmaker, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dorng - r-foreach @@ -37,33 +46,30 @@ requirements: - r-locfit - r-matrixstats run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dorng - r-foreach - r-iterators - r-locfit - r-matrixstats + +source: + md5: 94f5d4d153ee1074d241159ce20e1376 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Bump Hunter' - description: 'Tools for finding bumps in genomic data' -extra: - identifiers: - - biotools:bumphunter - parent_recipe: - name: bioconductor-bumphunter - path: recipes/bioconductor-bumphunter - version: 1.22.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bumpymatrix/meta.yaml b/recipes/bioconductor-bumpymatrix/meta.yaml index 3087aebf5c9a1..32f1aea79adbd 100644 --- a/recipes/bioconductor-bumpymatrix/meta.yaml +++ b/recipes/bioconductor-bumpymatrix/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "BumpyMatrix" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6069ae96659170c765102c2513e44b58 +about: + description: Implements the BumpyMatrix class and several subclasses for holding non-scalar objects in each entry of the matrix. This is akin to a ragged array but the raggedness is in the third dimension, much like a bumpy surface - hence the name. Of particular interest is the BumpyDataFrameMatrix, where each entry is a Bioconductor data frame. This allows us to naturally represent multivariate data in a format that is compatible with two-dimensional containers like the SummarizedExperiment and MultiAssayExperiment objects. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Bumpy Matrix of Non-Scalar Objects build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bumpymatrix", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-matrix run: - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-matrix +source: + md5: 1b8c1a220002a9495d39e0300fe75085 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Bumpy Matrix of Non-Scalar Objects' - description: 'Implements the BumpyMatrix class and several subclasses for holding non-scalar objects in each entry of the matrix. This is akin to a ragged array but the raggedness is in the third dimension, much like a bumpy surface - hence the name. Of particular interest is the BumpyDataFrameMatrix, where each entry is a Bioconductor data frame. This allows us to naturally represent multivariate data in a format that is compatible with two-dimensional containers like the SummarizedExperiment and MultiAssayExperiment objects.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-bus/meta.yaml b/recipes/bioconductor-bus/meta.yaml index ba7572a435302..322206f012c72 100644 --- a/recipes/bioconductor-bus/meta.yaml +++ b/recipes/bioconductor-bus/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.58.0" %} +{% set version = "1.62.0" %} {% set name = "BUS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package can be used to compute associations among genes (gene-networks) or between genes and some external traits (i.e. clinical). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Gene network reconstruction -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 788ab26ecf05f0df93667a7c37f564ff build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-bus", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:bus + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-bus + path: recipes/bioconductor-bus + version: 1.36.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-minet >=3.60.0,<3.61.0' + - bioconductor-minet >=3.64.0,<3.65.0 - r-base - r-infotheo - libblas - liblapack run: - - 'bioconductor-minet >=3.60.0,<3.61.0' + - bioconductor-minet >=3.64.0,<3.65.0 - r-base - r-infotheo - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: f27cadc9aa3bb2c0b0b07e06dc6dd118 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-only' - summary: 'Gene network reconstruction' - description: 'This package can be used to compute associations among genes (gene-networks) or between genes and some external traits (i.e. clinical).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:bus - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-bus - path: recipes/bioconductor-bus - version: 1.36.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-buscorrect/meta.yaml b/recipes/bioconductor-buscorrect/meta.yaml index 6758c04e142f8..3b3938b96c5c2 100644 --- a/recipes/bioconductor-buscorrect/meta.yaml +++ b/recipes/bioconductor-buscorrect/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "BUScorrect" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: High-throughput experimental data are accumulating exponentially in public databases. However, mining valid scientific discoveries from these abundant resources is hampered by technical artifacts and inherent biological heterogeneity. The former are usually termed "batch effects," and the latter is often modelled by "subtypes." The R package BUScorrect fits a Bayesian hierarchical model, the Batch-effects-correction-with-Unknown-Subtypes model (BUS), to correct batch effects in the presence of unknown subtypes. BUS is capable of (a) correcting batch effects explicitly, (b) grouping samples that share similar characteristics into subtypes, (c) identifying features that distinguish subtypes, and (d) enjoying a linear-order computation complexity. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Batch Effects Correction with Unknown Subtypes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d24bece1ac7982a2a157e5cccc01b99 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-buscorrect", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:buscorrect + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, RUnit, BiocGenerics requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-gplots - libblas - liblapack run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-gplots - build: - - {{ compiler('c') }} - - make + +source: + md5: c8e9340a9183bd8776e7ad149dad395e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'Batch Effects Correction with Unknown Subtypes' - description: 'High-throughput experimental data are accumulating exponentially in public databases. However, mining valid scientific discoveries from these abundant resources is hampered by technical artifacts and inherent biological heterogeneity. The former are usually termed "batch effects," and the latter is often modelled by "subtypes." The R package BUScorrect fits a Bayesian hierarchical model, the Batch-effects-correction-with-Unknown-Subtypes model (BUS), to correct batch effects in the presence of unknown subtypes. BUS is capable of (a) correcting batch effects explicitly, (b) grouping samples that share similar characteristics into subtypes, (c) identifying features that distinguish subtypes, and (d) enjoying a linear-order computation complexity.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-busparse/meta.yaml b/recipes/bioconductor-busparse/meta.yaml index 6946225b5c956..bcc820e90662d 100644 --- a/recipes/bioconductor-busparse/meta.yaml +++ b/recipes/bioconductor-busparse/meta.yaml @@ -1,40 +1,48 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "BUSpaRse" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The kallisto | bustools pipeline is a fast and modular set of tools to convert single cell RNA-seq reads in fastq files into gene count or transcript compatibility counts (TCC) matrices for downstream analysis. Central to this pipeline is the barcode, UMI, and set (BUS) file format. This package serves the following purposes: First, this package allows users to manipulate BUS format files as data frames in R and then convert them into gene count or TCC matrices. Furthermore, since R and Rcpp code is easier to handle than pure C++ code, users are encouraged to tweak the source code of this package to experiment with new uses of BUS format and different ways to convert the BUS file into gene count matrix. Second, this package can conveniently generate files required to generate gene count matrices for spliced and unspliced transcripts for RNA velocity. Here biotypes can be filtered and scaffolds and haplotypes can be removed, and the filtered transcriptome can be extracted and written to disk. Third, this package implements utility functions to get transcripts and associated genes required to convert BUS files to gene count matrices, to write the transcript to gene information in the format required by bustools, and to read output of bustools into R as sparses matrices.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_2_clause + file LICENSE + license_file: LICENSE + summary: kallisto | bustools R utilities -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7d2decd570fd518ad9a06c10a5ecffb3 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-busparse", max_pin="x.x") }}' -# Suggests: knitr, rmarkdown, testthat, BiocStyle, TENxBUSData, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, testthat, BiocStyle, txdbmaker, TENxBUSData, TxDb.Hsapiens.UCSC.hg38.knownGene, txdbmaker, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 # SystemRequirements: GNU make requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-bh - r-dplyr @@ -50,20 +58,21 @@ requirements: - r-zeallot - libblas - liblapack + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-bh - r-dplyr @@ -77,17 +86,16 @@ requirements: - r-tibble - r-tidyr - r-zeallot - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: e79fe5b2e7c9decd8d072e3e0d5c0bec + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_2_clause + file LICENSE' - summary: 'kallisto | bustools R utilities' - description: 'The kallisto | bustools pipeline is a fast and modular set of tools to convert single cell RNA-seq reads in fastq files into gene count or transcript compatibility counts (TCC) matrices for downstream analysis. Central to this pipeline is the barcode, UMI, and set (BUS) file format. This package serves the following purposes: First, this package allows users to manipulate BUS format files as data frames in R and then convert them into gene count or TCC matrices. Furthermore, since R and Rcpp code is easier to handle than pure C++ code, users are encouraged to tweak the source code of this package to experiment with new uses of BUS format and different ways to convert the BUS file into gene count matrix. Second, this package can conveniently generate files required to generate gene count matrices for spliced and unspliced transcripts for RNA velocity. Here biotypes can be filtered and scaffolds and haplotypes can be removed, and the filtered transcriptome can be extracted and written to disk. Third, this package implements utility functions to get transcripts and associated genes required to convert BUS files to gene count matrices, to write the transcript to gene information in the format required by bustools, and to read output of bustools into R as sparses matrices.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-busseq/meta.yaml b/recipes/bioconductor-busseq/meta.yaml index 1efe83d6f0fd2..2d9f3b540a2ed 100644 --- a/recipes/bioconductor-busseq/meta.yaml +++ b/recipes/bioconductor-busseq/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "BUSseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: BUSseq R package fits an interpretable Bayesian hierarchical model---the Batch Effects Correction with Unknown Subtypes for scRNA seq Data (BUSseq)---to correct batch effects in the presence of unknown cell types. BUSseq is able to simultaneously correct batch effects, clusters cell types, and takes care of the count data nature, the overdispersion, the dropout events, and the cell-specific sequencing depth of scRNA-seq data. After correcting the batch effects with BUSseq, the corrected value can be used for downstream analysis as if all cells were sequenced in a single batch. BUSseq can integrate read count matrices obtained from different scRNA-seq platforms and allow cell types to be measured in some but not all of the batches as long as the experimental design fulfills the conditions listed in our manuscript. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Batch Effect Correction with Unknow Subtypes for scRNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ba606db2bfb17a5958ba686639ecefbe build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-busseq", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, BiocGenerics requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-gplots - libblas - liblapack run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-gplots - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 64c3fd5cab0f930157fe424019a64cda + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Batch Effect Correction with Unknow Subtypes for scRNA-seq data' - description: 'BUSseq R package fits an interpretable Bayesian hierarchical model---the Batch Effects Correction with Unknown Subtypes for scRNA seq Data (BUSseq)---to correct batch effects in the presence of unknown cell types. BUSseq is able to simultaneously correct batch effects, clusters cell types, and takes care of the count data nature, the overdispersion, the dropout events, and the cell-specific sequencing depth of scRNA-seq data. After correcting the batch effects with BUSseq, the corrected value can be used for downstream analysis as if all cells were sequenced in a single batch. BUSseq can integrate read count matrices obtained from different scRNA-seq platforms and allow cell types to be measured in some but not all of the batches as long as the experimental design fulfills the conditions listed in our manuscript.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cadd.v1.6.hg19/meta.yaml b/recipes/bioconductor-cadd.v1.6.hg19/meta.yaml index 446a23d0973bb..f6a4121e9765f 100644 --- a/recipes/bioconductor-cadd.v1.6.hg19/meta.yaml +++ b/recipes/bioconductor-cadd.v1.6.hg19/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.18.1" %} {% set name = "cadd.v1.6.hg19" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 10cc50d17dbca89406a2290f37d5203c +about: + description: Store University of Washington CADD v1.6 hg19 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for University of Washington CADD v1.6 hg19 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: CADD v1.6 Pathogenicity Scores AnnotationHub Resource Metadata for hg19 build: - number: 0 + noarch: generic + number: 1 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cadd.v1.6.hg19", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 10cc50d17dbca89406a2290f37d5203c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'CADD v1.6 Pathogenicity Scores AnnotationHub Resource Metadata for hg19' - description: 'Store University of Washington CADD v1.6 hg19 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for University of Washington CADD v1.6 hg19 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cadd.v1.6.hg38/meta.yaml b/recipes/bioconductor-cadd.v1.6.hg38/meta.yaml index 1136468b55f7b..0237df5c1b36f 100644 --- a/recipes/bioconductor-cadd.v1.6.hg38/meta.yaml +++ b/recipes/bioconductor-cadd.v1.6.hg38/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.18.1" %} {% set name = "cadd.v1.6.hg38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 620a889ea8bc55f98811a80a3aec814d +about: + description: Store University of Washington CADD v1.6 hg38 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for University of Washington CADD v1.6 hg38 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: CADD v1.6 Pathogenicity Scores AnnotationHub Resource Metadata for hg38 build: - number: 0 + noarch: generic + number: 1 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cadd.v1.6.hg38", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 620a889ea8bc55f98811a80a3aec814d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'CADD v1.6 Pathogenicity Scores AnnotationHub Resource Metadata for hg38' - description: 'Store University of Washington CADD v1.6 hg38 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for University of Washington CADD v1.6 hg38 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cadra/build_failure.linux-64.yaml b/recipes/bioconductor-cadra/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0bd261b8b16ec --- /dev/null +++ b/recipes/bioconductor-cadra/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a1e8b3f620ab35cea1240408f113046fcf71996bf7dbc981705e38371a95bbec # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-knnmi")} + Encountered problems while solving: + - nothing provides requested r-knnmi + + Could not solve for environment specs + The following package could not be installed + [31mr-knnmi[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-knnmi")} + Encountered problems while solving: + - nothing provides requested r-knnmi + + Could not solve for environment specs + The following package could not be installed + [31mr-knnmi[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-knnmi")} + Encountered problems while solving: + - nothing provides requested r-knnmi + + Could not solve for environment specs + The following package could not be installed + [31mr-knnmi[0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-cadra/build_failure.osx-64.yaml b/recipes/bioconductor-cadra/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..689ffa94fbd43 --- /dev/null +++ b/recipes/bioconductor-cadra/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a1e8b3f620ab35cea1240408f113046fcf71996bf7dbc981705e38371a95bbec # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("r-knnmi")} + Encountered problems while solving: + - nothing provides requested r-knnmi + + Could not solve for environment specs + The following package could not be installed + r-knnmi does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("r-knnmi")} + Encountered problems while solving: + - nothing provides requested r-knnmi + + Could not solve for environment specs + The following package could not be installed + r-knnmi does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("r-knnmi")} + Encountered problems while solving: + - nothing provides requested r-knnmi + + Could not solve for environment specs + The following package could not be installed + r-knnmi does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-cadra/meta.yaml b/recipes/bioconductor-cadra/meta.yaml index 72f0b311f64e6..44e04589c7b27 100644 --- a/recipes/bioconductor-cadra/meta.yaml +++ b/recipes/bioconductor-cadra/meta.yaml @@ -1,32 +1,38 @@ -{% set version = "1.0.1" %} +{% set version = "1.4.0" %} {% set name = "CaDrA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Performs both stepwise and backward heuristic search for candidate (epi)genetic drivers based on a binary multi-omics dataset. CaDrA's main objective is to identify features which, together, are significantly skewed or enriched pertaining to a given vector of continuous scores (e.g. sample-specific scores representing a phenotypic readout of interest, such as protein expression, pathway activity, etc.), based on the union occurence (i.e. logical OR) of the events. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Candidate Driver Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ac2bc6afe6632e5fbd00c687ca19bba build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cadra", max_pin="x.x") }}' -# Suggests: BiocManager, BiocStyle, devtools, knitr, magick, pheatmap, rmarkdown, testthat (>= 3.1.6) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocManager, devtools, knitr, pheatmap, rmarkdown, testthat (>= 3.1.6) requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-doparallel - r-ggplot2 - r-gplots - r-gtable + - r-knnmi - r-mass - r-misc3d - r-plyr @@ -36,28 +42,29 @@ requirements: - libblas - liblapack run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-doparallel - r-ggplot2 - r-gplots - r-gtable + - r-knnmi - r-mass - r-misc3d - r-plyr - r-ppcor - r-r.cache - r-reshape2 - build: - - {{ compiler('c') }} - - make + +source: + md5: cab1dab6ad03235b3aa01ad002fdd406 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Candidate Driver Analysis' - description: 'Performs both stepwise and backward heuristic search for candidate (epi)genetic drivers based on a binary multi-omics dataset. CaDrA''s main objective is to identify features which, together, are significantly skewed or enriched pertaining to a given vector of continuous scores (e.g. sample-specific scores representing a phenotypic readout of interest, such as protein expression, pathway activity, etc.), based on the union occurence (i.e. logical OR) of the events.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-caen/meta.yaml b/recipes/bioconductor-caen/meta.yaml index 9430206502ac5..27ef3c3599387 100644 --- a/recipes/bioconductor-caen/meta.yaml +++ b/recipes/bioconductor-caen/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "CAEN" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 66decd595d2315a90c09b7d52df606c5 +about: + description: With the development of high-throughput techniques, more and more gene expression analysis tend to replace hybridization-based microarrays with the revolutionary technology.The novel method encodes the category again by employing the rank of samples for each gene in each class. We then consider the correlation coefficient of gene and class with rank of sample and new rank of category. The highest correlation coefficient genes are considered as the feature genes which are most effective to classify the samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Category encoding method for selecting feature genes for the classification of single-cell RNA-seq build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-caen", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr,rmarkdown,BiocManager,SummarizedExperiment,BiocStyle requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-poiclaclu run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-poiclaclu +source: + md5: ff95eb63dae6ed8bc55d4da921199c8d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Category encoding method for selecting feature genes for the classification of single-cell RNA-seq' - description: 'With the development of high-throughput techniques, more and more gene expression analysis tend to replace hybridization-based microarrays with the revolutionary technology.The novel method encodes the category again by employing the rank of samples for each gene in each class. We then consider the correlation coefficient of gene and class with rank of sample and new rank of category. The highest correlation coefficient genes are considered as the feature genes which are most effective to classify the samples.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cafe/meta.yaml b/recipes/bioconductor-cafe/meta.yaml index 38e52b776a3fc..8b60e237b0d00 100644 --- a/recipes/bioconductor-cafe/meta.yaml +++ b/recipes/bioconductor-cafe/meta.yaml @@ -1,55 +1,60 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "CAFE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Detection and visualizations of gross chromosomal aberrations using Affymetrix expression microarrays as input + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Chromosmal Aberrations Finder in Expression data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a64370f203f198ad86163715decbebb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cafe", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biovizbase >=1.50.0,<1.51.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biovizbase >=1.54.0,<1.55.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-ggplot2 - r-gridextra run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biovizbase >=1.50.0,<1.51.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biovizbase >=1.54.0,<1.55.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-ggplot2 - r-gridextra + +source: + md5: 9689cfdc79ee19a10d8c0c095e33eae3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Chromosmal Aberrations Finder in Expression data' - description: 'Detection and visualizations of gross chromosomal aberrations using Affymetrix expression microarrays as input' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cagefightr/meta.yaml b/recipes/bioconductor-cagefightr/meta.yaml index 7c7717aa940e4..c8e3f02793885 100644 --- a/recipes/bioconductor-cagefightr/meta.yaml +++ b/recipes/bioconductor-cagefightr/meta.yaml @@ -1,71 +1,76 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "CAGEfightR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5''-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 86c87a4bec49d7c37ef74a6a6081a685 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cagefightr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm9.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' - - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'r-assertthat >=0.2.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicfiles >=1.42.0,<1.43.0 + - bioconductor-genomicinteractions >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-assertthat >=0.2.0 - r-base - - 'r-matrix >=1.2-12' - - 'r-pryr >=0.1.3' + - r-matrix >=1.2-12 + - r-pryr >=0.1.3 run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' - - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'r-assertthat >=0.2.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicfiles >=1.42.0,<1.43.0 + - bioconductor-genomicinteractions >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-assertthat >=0.2.0 - r-base - - 'r-matrix >=1.2-12' - - 'r-pryr >=0.1.3' + - r-matrix >=1.2-12 + - r-pryr >=0.1.3 + +source: + md5: 9c31a19923b66f0d794f9e75aa9be16f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor' - description: 'CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5''-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cageminer/meta.yaml b/recipes/bioconductor-cageminer/meta.yaml index f6b6d7035888b..5c8bdb3e10b52 100644 --- a/recipes/bioconductor-cageminer/meta.yaml +++ b/recipes/bioconductor-cageminer/meta.yaml @@ -1,55 +1,60 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "cageminer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users must define a set of guide genes, which are known genes involved in the studied phenotype. Additionally, the mined candidates can be given a score that favor candidates that are hubs and/or transcription factors. The scores can then be used to rank and select the top n most promising genes for downstream experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Candidate Gene Miner -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 02b96b12bfe145c4c9deefff49cd1015 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cageminer", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle, rmarkdown, covr, sessioninfo requirements: host: - - 'bioconductor-bionero >=1.10.0,<1.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-bionero >=1.14.0,<1.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-ggplot2 - r-ggtext - r-reshape2 - r-rlang run: - - 'bioconductor-bionero >=1.10.0,<1.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-bionero >=1.14.0,<1.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-ggplot2 - r-ggtext - r-reshape2 - r-rlang + +source: + md5: e69419f705e3604dfbbff8c7b383dcf5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Candidate Gene Miner' - description: 'This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users must define a set of guide genes, which are known genes involved in the studied phenotype. Additionally, the mined candidates can be given a score that favor candidates that are hubs and/or transcription factors. The scores can then be used to rank and select the top n most promising genes for downstream experiments.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cager/meta.yaml b/recipes/bioconductor-cager/meta.yaml index 760142e82ee20..6803bdda38770 100644 --- a/recipes/bioconductor-cager/meta.yaml +++ b/recipes/bioconductor-cager/meta.yaml @@ -1,100 +1,112 @@ -{% set version = "2.8.0" %} +{% set version = "2.12.0" %} {% set name = "CAGEr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The _CAGEr_ package identifies transcription start sites (TSS) and their usage frequency from CAGE (Cap Analysis Gene Expression) sequencing data. It normalises raw CAGE tag count, clusters TSSs into tag clusters (TC) and aggregates them across multiple CAGE experiments to construct consensus clusters (CC) representing the promoterome. CAGEr provides functions to profile expression levels of these clusters by cumulative expression and rarefaction analysis, and outputs the plots in ggplot2 format for further facetting and customisation. After clustering, CAGEr performs analyses of promoter width and detects differential usage of TSSs (promoter shifting) between samples. CAGEr also exports its data as genome browser tracks, and as R objects for downsteam expression analysis by other Bioconductor packages such as DESeq2, CAGEfightR, or seqArchR. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 845c3a47631734b6fe7209f173e24100 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cager", max_pin="x.x") }}' - noarch: generic -# Suggests: BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE, BiocStyle, knitr, rmarkdown + +extra: + identifiers: + - biotools:cager + parent_recipe: + name: bioconductor-cager + path: recipes/bioconductor-cager + version: 1.22.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9, DESeq2, FANTOM3and4CAGE, ggseqlogo, BiocStyle, knitr, rmarkdown requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-cagefightr >=1.22.0,<1.23.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-cagefightr >=1.26.0,<1.27.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-formula.tools - - 'r-ggplot2 >=2.2.0' + - r-ggplot2 >=2.2.0 - r-gtools - r-kernsmooth - r-memoise - r-plyr - r-reshape2 + - r-rlang + - r-scales - r-som - r-stringdist - r-stringi - r-vegan - r-vgam + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-cagefightr >=1.22.0,<1.23.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-cagefightr >=1.26.0,<1.27.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-formula.tools - - 'r-ggplot2 >=2.2.0' + - r-ggplot2 >=2.2.0 - r-gtools - r-kernsmooth - r-memoise - r-plyr - r-reshape2 + - r-rlang + - r-scales - r-som - r-stringdist - r-stringi - r-vegan - r-vgam + +source: + md5: 056b2f3234240143e260fe91edf2db85 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining' - description: 'Preprocessing of CAGE sequencing data, identification and normalization of transcription start sites and downstream analysis of transcription start sites clusters (promoters).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:cager - parent_recipe: - name: bioconductor-cager - path: recipes/bioconductor-cager - version: 1.22.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-calm/meta.yaml b/recipes/bioconductor-calm/meta.yaml index d544112473d73..40e5848e641b5 100644 --- a/recipes/bioconductor-calm/meta.yaml +++ b/recipes/bioconductor-calm/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "calm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9a2b4c48021193636c88c997331ede2d +about: + description: Statistical methods for multiple testing with covariate information. Traditional multiple testing methods only consider a list of test statistics, such as p-values. Our methods incorporate the auxiliary information, such as the lengths of gene coding regions or the minor allele frequencies of SNPs, to improve power. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Covariate Assisted Large-scale Multiple testing build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-calm", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: @@ -27,13 +26,14 @@ requirements: run: - r-base - r-mgcv +source: + md5: 9fe2eb9aa8aa3db12074fee808438ef0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Covariate Assisted Large-scale Multiple testing' - description: 'Statistical methods for multiple testing with covariate information. Traditional multiple testing methods only consider a list of test statistics, such as p-values. Our methods incorporate the auxiliary information, such as the lengths of gene coding regions or the minor allele frequencies of SNPs, to improve power.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-camera/meta.yaml b/recipes/bioconductor-camera/meta.yaml index 420d36ddcad2f..32eb7defc481e 100644 --- a/recipes/bioconductor-camera/meta.yaml +++ b/recipes/bioconductor-camera/meta.yaml @@ -1,62 +1,68 @@ -{% set version = "1.58.0" %} +{% set version = "1.62.0" %} {% set name = "CAMERA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Collection of annotation related methods for mass spectrometry data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1958cafb2c9dd92fa44a35cfc607f894 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-camera", max_pin="x.x") }}' -# Suggests: faahKO, RUnit, BiocGenerics + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:camera + parent_recipe: + name: bioconductor-camera + path: recipes/bioconductor-camera + version: 1.38.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: faahKO, RUnit, BiocGenerics, multtest requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base - r-hmisc - r-igraph - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base - r-hmisc - r-igraph - build: - - {{ compiler('c') }} - - make + +source: + md5: e092282c76a9381310b1afc1e425b66c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'Collection of annotation related methods for mass spectrometry data' - description: 'Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:camera - parent_recipe: - name: bioconductor-camera - path: recipes/bioconductor-camera - version: 1.38.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-camutqc/build.sh b/recipes/bioconductor-camutqc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-camutqc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-camutqc/meta.yaml b/recipes/bioconductor-camutqc/meta.yaml new file mode 100644 index 0000000000000..6d50506b63615 --- /dev/null +++ b/recipes/bioconductor-camutqc/meta.yaml @@ -0,0 +1,64 @@ +{% set version = "1.2.0" %} +{% set name = "CaMutQC" %} +{% set bioc = "3.20" %} + +about: + description: CaMutQC is able to filter false positive mutations generated due to technical issues, as well as to select candidate cancer mutations through a series of well-structured functions by labeling mutations with various flags. And a detailed and vivid filter report will be offered after completing a whole filtration or selection section. Also, CaMutQC integrates serveral methods and gene panels for Tumor Mutational Burden (TMB) estimation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-camutqc", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, BiocStyle +requirements: + host: + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-maftools >=2.22.0,<2.23.0 + - bioconductor-meskit >=1.16.0,<1.17.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - r-base + - r-data.table + - r-dplyr + - r-dt + - r-ggplot2 + - r-stringr + - r-tidyr + - r-vcfr + run: + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-maftools >=2.22.0,<2.23.0 + - bioconductor-meskit >=1.16.0,<1.17.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - r-base + - r-data.table + - r-dplyr + - r-dt + - r-ggplot2 + - r-stringr + - r-tidyr + - r-vcfr + +source: + md5: 2f0df30bdb243447767a9f1409f7a240 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-cancer/meta.yaml b/recipes/bioconductor-cancer/meta.yaml index 1498a00e3bb28..57086774e36d5 100644 --- a/recipes/bioconductor-cancer/meta.yaml +++ b/recipes/bioconductor-cancer/meta.yaml @@ -1,66 +1,75 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "canceR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package is user friendly interface based on the cgdsr and other modeling packages to explore, compare, and analyse all available Cancer Data (Clinical data, Gene Mutation, Gene Methylation, Gene Expression, Protein Phosphorylation, Copy Number Alteration) hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4311164fc68969a40252dc3761583f24 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cancer", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.1), knitr, rmarkdown, BiocStyle # SystemRequirements: Tktable, BWidget requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genetclassifier >=1.42.0,<1.43.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-phenotest >=1.50.0,<1.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-cbioportaldata >=2.18.0,<2.19.0 + - bioconductor-genetclassifier >=1.46.0,<1.47.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-phenotest >=1.54.0,<1.55.0 - r-base - r-circlize + - r-dplyr - r-formula - - r-httr - r-plyr - r-r.methodss3 - r-r.oo - r-rpart - r-runit - r-survival + - r-tidyr - r-tkrplot run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genetclassifier >=1.42.0,<1.43.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-phenotest >=1.50.0,<1.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-cbioportaldata >=2.18.0,<2.19.0 + - bioconductor-genetclassifier >=1.46.0,<1.47.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-phenotest >=1.54.0,<1.55.0 - r-base - r-circlize + - r-dplyr - r-formula - - r-httr - r-plyr - r-r.methodss3 - r-r.oo - r-rpart - r-runit - r-survival + - r-tidyr - r-tkrplot + +source: + md5: ea3e99cc592c53d219a6955ef969533d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC' - description: 'The package is user friendly interface based on the cgdsr and other modeling packages to explore, compare, and analyse all available Cancer Data (Clinical data, Gene Mutation, Gene Methylation, Gene Expression, Protein Phosphorylation, Copy Number Alteration) hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cancerclass/meta.yaml b/recipes/bioconductor-cancerclass/meta.yaml index ee3fb82ad436d..9f1cd65388832 100644 --- a/recipes/bioconductor-cancerclass/meta.yaml +++ b/recipes/bioconductor-cancerclass/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "cancerclass" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b2e5d6ec200ee08476480fa1f0a1577d +about: + description: The classification protocol starts with a feature selection step and continues with nearest-centroid classification. The accurarcy of the predictor can be evaluated using training and test set validation, leave-one-out cross-validation or in a multiple random validation protocol. Methods for calculation and visualization of continuous prediction scores allow to balance sensitivity and specificity and define a cutoff value according to clinical requirements. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL 3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Development and validation of diagnostic tests from high-dimensional molecular data build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cancerclass", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: cancerdata requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-binom - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-binom - build: - - {{ compiler('c') }} - - make +source: + md5: 116324a4bf732430c8280593e5eec0ab + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL 3' - summary: 'Development and validation of diagnostic tests from high-dimensional molecular data' - description: 'The classification protocol starts with a feature selection step and continues with nearest-centroid classification. The accurarcy of the predictor can be evaluated using training and test set validation, leave-one-out cross-validation or in a multiple random validation protocol. Methods for calculation and visualization of continuous prediction scores allow to balance sensitivity and specificity and define a cutoff value according to clinical requirements.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cancerdata/meta.yaml b/recipes/bioconductor-cancerdata/meta.yaml index 8b5aaa6fb459c..c0f3ab070ec15 100644 --- a/recipes/bioconductor-cancerdata/meta.yaml +++ b/recipes/bioconductor-cancerdata/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "cancerdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7baa088ef320a0222a897987ea8c3e8b +about: + description: Dataset for the R package cancerclass + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'Development and validation of diagnostic tests from high-dimensional molecular data: Datasets' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cancerdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0765bb89fc39828f03110a42851e1a02 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Development and validation of diagnostic tests from high-dimensional molecular data: Datasets' - description: 'Dataset for the R package cancerclass' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cancerdata/post-link.sh b/recipes/bioconductor-cancerdata/post-link.sh index f48bb85329be6..752b9fd1a26ef 100644 --- a/recipes/bioconductor-cancerdata/post-link.sh +++ b/recipes/bioconductor-cancerdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cancerdata-1.40.0" +installBiocDataPackage.sh "cancerdata-1.44.0" diff --git a/recipes/bioconductor-canine.db/meta.yaml b/recipes/bioconductor-canine.db/meta.yaml index 9afadfb4280f1..f016c878c5f7a 100644 --- a/recipes/bioconductor-canine.db/meta.yaml +++ b/recipes/bioconductor-canine.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "canine.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a876bb01eda62604a32a96b46e34162b +about: + description: Affymetrix Affymetrix Canine Array annotation data (chip canine) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Canine Array annotation data (chip canine) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-canine.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.cf.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.cf.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.cf.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.cf.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a876bb01eda62604a32a96b46e34162b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Canine Array annotation data (chip canine)' - description: 'Affymetrix Affymetrix Canine Array annotation data (chip canine) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-canine.db0/meta.yaml b/recipes/bioconductor-canine.db0/meta.yaml index 9e295898ab473..48e3851d78595 100644 --- a/recipes/bioconductor-canine.db0/meta.yaml +++ b/recipes/bioconductor-canine.db0/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "canine.db0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dc4fff8ed0a758ddff3f52aa0e8652c6 +about: + description: Base annotation databases for canine, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Level Annotation databases for canine build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-canine.db0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 26d30a229ee9309b9f473dba4d1a61eb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Level Annotation databases for canine' - description: 'Base annotation databases for canine, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-canine.db0/post-link.sh b/recipes/bioconductor-canine.db0/post-link.sh index e5e86dee05068..5a95800e7e380 100644 --- a/recipes/bioconductor-canine.db0/post-link.sh +++ b/recipes/bioconductor-canine.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "canine.db0-3.18.0" +installBiocDataPackage.sh "canine.db0-3.20.0" diff --git a/recipes/bioconductor-canine2.db/meta.yaml b/recipes/bioconductor-canine2.db/meta.yaml index 6b4c2bc532688..4e3e826aab1e6 100644 --- a/recipes/bioconductor-canine2.db/meta.yaml +++ b/recipes/bioconductor-canine2.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "canine2.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 24727f27cdf1e324f097a76db81dfc1d +about: + description: Affymetrix Affymetrix Canine_2 Array annotation data (chip canine2) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Canine_2 Array annotation data (chip canine2) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-canine2.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.cf.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.cf.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.cf.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.cf.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 24727f27cdf1e324f097a76db81dfc1d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Canine_2 Array annotation data (chip canine2)' - description: 'Affymetrix Affymetrix Canine_2 Array annotation data (chip canine2) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-canine2cdf/meta.yaml b/recipes/bioconductor-canine2cdf/meta.yaml index 9d689a5971930..71abe881e842a 100644 --- a/recipes/bioconductor-canine2cdf/meta.yaml +++ b/recipes/bioconductor-canine2cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "canine2cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 78740cde98c75e6680470564a4df74c3 +about: + description: A package containing an environment representing the Canine_2.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: canine2cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-canine2cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 78740cde98c75e6680470564a4df74c3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: canine2cdf - description: 'A package containing an environment representing the Canine_2.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-canine2probe/meta.yaml b/recipes/bioconductor-canine2probe/meta.yaml index 6f54871ac6b19..35fcf98131af4 100644 --- a/recipes/bioconductor-canine2probe/meta.yaml +++ b/recipes/bioconductor-canine2probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "canine2probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7de0f4ea616e8662dc2eaa9ab78d1f13 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Canine\_2\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type canine2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-canine2probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7de0f4ea616e8662dc2eaa9ab78d1f13 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type canine2' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Canine\_2\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-caninecdf/meta.yaml b/recipes/bioconductor-caninecdf/meta.yaml index f80e3709dcb35..2973bb4d7e6c4 100644 --- a/recipes/bioconductor-caninecdf/meta.yaml +++ b/recipes/bioconductor-caninecdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "caninecdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 656f845cc66890015a4e13c5304ec262 +about: + description: A package containing an environment representing the Canine.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: caninecdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-caninecdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 656f845cc66890015a4e13c5304ec262 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: caninecdf - description: 'A package containing an environment representing the Canine.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-canineprobe/meta.yaml b/recipes/bioconductor-canineprobe/meta.yaml index a85ebdab28fe3..1d0b76f94de22 100644 --- a/recipes/bioconductor-canineprobe/meta.yaml +++ b/recipes/bioconductor-canineprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "canineprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e5467bc9b7e54c5adce6b409ba7df767 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Canine\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type canine build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-canineprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e5467bc9b7e54c5adce6b409ba7df767 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type canine' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Canine\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cardelino/meta.yaml b/recipes/bioconductor-cardelino/meta.yaml index 684c1386c8a20..3229ca5e89bb2 100644 --- a/recipes/bioconductor-cardelino/meta.yaml +++ b/recipes/bioconductor-cardelino/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "cardelino" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Methods to infer clonal tree configuration for a population of cells using single-cell RNA-seq data (scRNA-seq), and possibly other data modalities. Methods are also provided to assign cells to inferred clones and explore differences in gene expression between clones. These methods can flexibly integrate information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. A flexible beta-binomial error model that accounts for stochastic dropout events as well as systematic allelic imbalance is used. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Clone Identification from Single Cell Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 363c06547419f29e1cdfe473651e1861 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cardelino", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, foreach, knitr, pcaMethods, rmarkdown, testthat, VGAM requirements: host: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-snpstats >=1.52.0,<1.53.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-snpstats >=1.56.0,<1.57.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-combinat - r-ggplot2 @@ -36,12 +38,12 @@ requirements: - r-pheatmap - r-vcfr run: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-snpstats >=1.52.0,<1.53.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-snpstats >=1.56.0,<1.57.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-combinat - r-ggplot2 @@ -49,13 +51,16 @@ requirements: - r-matrixstats - r-pheatmap - r-vcfr + +source: + md5: cd0a4c4ec8ded3c833d1e32aeb2af021 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Clone Identification from Single Cell Data' - description: 'Methods to infer clonal tree configuration for a population of cells using single-cell RNA-seq data (scRNA-seq), and possibly other data modalities. Methods are also provided to assign cells to inferred clones and explore differences in gene expression between clones. These methods can flexibly integrate information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. A flexible beta-binomial error model that accounts for stochastic dropout events as well as systematic allelic imbalance is used.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cardinal/meta.yaml b/recipes/bioconductor-cardinal/meta.yaml index ebb5c8fde4502..15098f685b5ff 100644 --- a/recipes/bioconductor-cardinal/meta.yaml +++ b/recipes/bioconductor-cardinal/meta.yaml @@ -1,79 +1,73 @@ -{% set version = "3.4.3" %} +{% set version = "3.8.0" %} {% set name = "Cardinal" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 | file LICENSE + license_file: LICENSE + summary: A mass spectrometry imaging toolbox for statistical analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee7f799a94a4c3cd1946feb2b1db9dd4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cardinal", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:cardinal + - usegalaxy-eu:cardinal_segmentations + parent_recipe: + name: bioconductor-cardinal + path: recipes/bioconductor-cardinal + version: 1.12.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-cardinalio >=1.0.0,<1.1.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-matter >=2.4.0,<2.5.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-cardinalio >=1.4.0,<1.5.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-matter >=2.8.0,<2.9.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-irlba - - r-magrittr - r-matrix - - r-mclust - r-nlme - - r-signal - - r-viridislite - - libblas - - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-cardinalio >=1.0.0,<1.1.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-matter >=2.4.0,<2.5.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-cardinalio >=1.4.0,<1.5.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-matter >=2.8.0,<2.9.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-irlba - - r-magrittr - r-matrix - - r-mclust - r-nlme - - r-signal - - r-viridislite - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: d41a53e6890b0f7cd69fb75226b18edd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A mass spectrometry imaging toolbox for statistical analysis' - description: 'Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.' -extra: - identifiers: - - biotools:cardinal - - usegalaxy-eu:cardinal_segmentations - parent_recipe: - name: bioconductor-cardinal - path: recipes/bioconductor-cardinal - version: 1.12.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cardinalio/meta.yaml b/recipes/bioconductor-cardinalio/meta.yaml index e51480d5e4ba8..763450843fa65 100644 --- a/recipes/bioconductor-cardinalio/meta.yaml +++ b/recipes/bioconductor-cardinalio/meta.yaml @@ -1,47 +1,55 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "CardinalIO" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Fast and efficient reading and writing of mass spectrometry imaging data files. Supports imzML and Analyze 7.5 formats. Provides ontologies for mass spectrometry imaging. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 | file LICENSE + license_file: LICENSE + summary: Read and write mass spectrometry imaging files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 746846f9fda38de9fe2c3dd4c49c18e1 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cardinalio", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-matter >=2.4.0,<2.5.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-matter >=2.8.0,<2.9.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ontologyindex - libblas - liblapack run: - - 'bioconductor-matter >=2.4.0,<2.5.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-matter >=2.8.0,<2.9.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ontologyindex - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 5a03247fab3dbcef8a70a86c536d0a79 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Read and write mass spectrometry imaging files' - description: 'Fast and efficient reading and writing of mass spectrometry imaging data files. Supports imzML and Analyze 7.5 formats. Provides ontologies for mass spectrometry imaging.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cardinalworkflows/meta.yaml b/recipes/bioconductor-cardinalworkflows/meta.yaml index 9935acb2c639a..461f6ee998ea7 100644 --- a/recipes/bioconductor-cardinalworkflows/meta.yaml +++ b/recipes/bioconductor-cardinalworkflows/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "CardinalWorkflows" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54c51a2ec2f20f96ad9e60c16eeb2ccb +about: + description: 'Datasets and workflows for Cardinal: DESI and MALDI examples including pig fetus, cardinal painting, and human RCC.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Datasets and workflows for the Cardinal MSI build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cardinalworkflows", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-cardinal >=3.4.0,<3.5.0' + - bioconductor-cardinal >=3.8.0,<3.9.0 - r-base run: - - 'bioconductor-cardinal >=3.4.0,<3.5.0' + - bioconductor-cardinal >=3.8.0,<3.9.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d245d4c9f068e8618542e73c1ccb4973 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Datasets and workflows for the Cardinal mass spectrometry imaging package' - description: 'Datasets and workflows for Cardinal: DESI and MALDI examples including pig fetus, cardinal painting, and human RCC.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cardinalworkflows/post-link.sh b/recipes/bioconductor-cardinalworkflows/post-link.sh index d557ce84baab0..19d59d62eb30b 100644 --- a/recipes/bioconductor-cardinalworkflows/post-link.sh +++ b/recipes/bioconductor-cardinalworkflows/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cardinalworkflows-1.34.0" +installBiocDataPackage.sh "cardinalworkflows-1.38.0" diff --git a/recipes/bioconductor-carnival/meta.yaml b/recipes/bioconductor-carnival/meta.yaml index 565eefdb379a4..a195d07dae6d7 100644 --- a/recipes/bioconductor-carnival/meta.yaml +++ b/recipes/bioconductor-carnival/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "2.12.0" %} +{% set version = "2.16.0" %} {% set name = "CARNIVAL" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An upgraded causal reasoning tool from Melas et al in R with updated assignments of TFs' weights from PROGENy scores. Optimization parameters can be freely adjusted and multiple solutions can be obtained and aggregated. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c5457d5d859c16cbec56532338f64fb0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-carnival", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0), sessioninfo requirements: host: @@ -43,13 +45,16 @@ requirements: - r-stringr - r-tibble - r-tidyr + +source: + md5: d2dd4eea47a8e994cc4ea365de7889ed + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming' - description: 'An upgraded causal reasoning tool from Melas et al in R with updated assignments of TFs'' weights from PROGENy scores. Optimization parameters can be freely adjusted and multiple solutions can be obtained and aggregated.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-casper/meta.yaml b/recipes/bioconductor-casper/meta.yaml index d76b691030941..8dc279c4b2daf 100644 --- a/recipes/bioconductor-casper/meta.yaml +++ b/recipes/bioconductor-casper/meta.yaml @@ -1,37 +1,51 @@ -{% set version = "2.36.0" %} +{% set version = "2.40.0" %} {% set name = "casper" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Characterization of Alternative Splicing based on Paired-End Reads -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4c9fc29e3b92d5b493953ea97436556a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-casper", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:casper + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-ebarrays >=2.66.0,<2.67.0' - - 'bioconductor-gaga >=2.48.0,<2.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-ebarrays >=2.70.0,<2.71.0 + - bioconductor-gaga >=2.52.0,<2.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-coda - r-gtools @@ -41,19 +55,20 @@ requirements: - r-vgam - libblas - liblapack + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-ebarrays >=2.66.0,<2.67.0' - - 'bioconductor-gaga >=2.48.0,<2.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-ebarrays >=2.70.0,<2.71.0 + - bioconductor-gaga >=2.52.0,<2.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-coda - r-gtools @@ -61,23 +76,16 @@ requirements: - r-sqldf - r-survival - r-vgam - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make - - libcxx <17 # [osx] + +source: + md5: fd3a5c749266a829e4f0a06d339806be + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'Characterization of Alternative Splicing based on Paired-End Reads' - description: 'Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-catalyst/meta.yaml b/recipes/bioconductor-catalyst/meta.yaml index 42b526eec0739..d32d97dc4d888 100644 --- a/recipes/bioconductor-catalyst/meta.yaml +++ b/recipes/bioconductor-catalyst/meta.yaml @@ -1,35 +1,38 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "CATALYST" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CATALYST provides tools for preprocessing of and differential discovery in cytometry data such as FACS, CyTOF, and IMC. Preprocessing includes i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation. For differential discovery, the package provides a number of convenient functions for data processing (e.g., clustering, dimension reduction), as well as a suite of visualizations for exploratory data analysis and exploration of results from differential abundance (DA) and state (DS) analysis in order to identify differences in composition and expression profiles at the subpopulation-level, respectively. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Cytometry dATa anALYSis Tools -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ce647576b86ebdf9fe0933fd87b79ce build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-catalyst", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto, rmarkdown, testthat, uwot requirements: + host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowsom >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-consensusclusterplus >=1.70.0,<1.71.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowsom >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-cowplot @@ -48,15 +51,16 @@ requirements: - r-reshape2 - r-rtsne - r-scales + run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowsom >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-consensusclusterplus >=1.70.0,<1.71.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowsom >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-cowplot @@ -75,13 +79,16 @@ requirements: - r-reshape2 - r-rtsne - r-scales + +source: + md5: 3d28b77bb5f2fc0bb9ebe0ef26fc460f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Cytometry dATa anALYSis Tools' - description: 'CATALYST provides tools for preprocessing of and differential discovery in cytometry data such as FACS, CyTOF, and IMC. Preprocessing includes i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation. For differential discovery, the package provides a number of convenient functions for data processing (e.g., clustering, dimension reduction), as well as a suite of visualizations for exploratory data analysis and exploration of results from differential abundance (DA) and state (DS) analysis in order to identify differences in composition and expression profiles at the subpopulation-level, respectively.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-category/meta.yaml b/recipes/bioconductor-category/meta.yaml index a746fe351958e..82d2b2b12b70d 100644 --- a/recipes/bioconductor-category/meta.yaml +++ b/recipes/bioconductor-category/meta.yaml @@ -1,64 +1,70 @@ -{% set version = "2.68.0" %} +{% set version = "2.72.0" %} {% set name = "Category" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A collection of tools for performing category (gene set enrichment) analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Category Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d84fb36419834bb84721436d7f956932 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-category", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:category + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-category + path: recipes/bioconductor-category + version: 2.46.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGGREST, karyoploteR, geneplotter, limma, lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db requirements: host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 - r-base - r-dbi - r-matrix run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 - r-base - r-dbi - r-matrix + +source: + md5: 2784fd82b32eca8f0e0da92fe8bee5ed + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Category Analysis' - description: 'A collection of tools for performing category (gene set enrichment) analysis.' -extra: - identifiers: - - biotools:category - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-category - path: recipes/bioconductor-category - version: 2.46.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-categorycompare/meta.yaml b/recipes/bioconductor-categorycompare/meta.yaml index 1a04329db5a0c..bb3cd06b9d206 100644 --- a/recipes/bioconductor-categorycompare/meta.yaml +++ b/recipes/bioconductor-categorycompare/meta.yaml @@ -1,62 +1,67 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "categoryCompare" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Meta-analysis of high-throughput experiments using feature annotations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9809c7142b4af81d181bf8d8f7e0f815 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-categorycompare", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter, rmarkdown # SystemRequirements: Cytoscape (>= 3.6.1) (if used for visualization of results, heavily suggested) requirements: host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-category >=2.68.0,<2.69.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-category >=2.72.0,<2.73.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 - r-base - r-colorspace - r-hwriter - - 'cytoscape >=3.6.1' + - cytoscape >=3.6.1 run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-category >=2.68.0,<2.69.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-category >=2.72.0,<2.73.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 - r-base - r-colorspace - r-hwriter - - 'cytoscape >=3.6.1' + - cytoscape >=3.6.1 + +source: + md5: 698bd62c3b933e00e072bf741fd1bbb4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Meta-analysis of high-throughput experiments using feature annotations' - description: 'Calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-catscradle/build.sh b/recipes/bioconductor-catscradle/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-catscradle/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-catscradle/meta.yaml b/recipes/bioconductor-catscradle/meta.yaml new file mode 100644 index 0000000000000..64bc9832bc498 --- /dev/null +++ b/recipes/bioconductor-catscradle/meta.yaml @@ -0,0 +1,86 @@ +{% set version = "1.0.0" %} +{% set name = "CatsCradle" %} +{% set bioc = "3.20" %} + +about: + description: This package addresses two broad areas. It allows for in-depth analysis of spatial transcriptomic data by identifying tissue neighbourhoods. These are contiguous regions of tissue surrounding individual cells. 'CatsCradle' allows for the categorisation of neighbourhoods by the cell types contained in them and the genes expressed in them. In particular, it produces Seurat objects whose individual elements are neighbourhoods rather than cells. In addition, it enables the categorisation and annotation of genes by producing Seurat objects whose elements are genes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-catscradle", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: fossil, interp, knitr, BiocStyle, tictoc +requirements: + + host: + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-abind + - r-base + - r-data.table + - r-geometry + - r-ggplot2 + - r-igraph + - r-matrix + - r-msigdbr + - r-networkd3 + - r-pheatmap + - r-pracma + - r-rdist + - r-reshape2 + - r-rfast + - r-seurat >=5.0.1 + - r-seuratobject + - r-stringr + + run: + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-abind + - r-base + - r-data.table + - r-geometry + - r-ggplot2 + - r-igraph + - r-matrix + - r-msigdbr + - r-networkd3 + - r-pheatmap + - r-pracma + - r-rdist + - r-reshape2 + - r-rfast + - r-seurat >=5.0.1 + - r-seuratobject + - r-stringr + +source: + md5: a7c7b9e66686e0df39d6641658e7b387 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-causalr/meta.yaml b/recipes/bioconductor-causalr/meta.yaml index 19336b1df1182..5fba6e679241a 100644 --- a/recipes/bioconductor-causalr/meta.yaml +++ b/recipes/bioconductor-causalr/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "CausalR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Causal network analysis methods for regulator prediction and network reconstruction from genome scale data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Causal network analysis methods -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 408b3cc6bc7a45715e6c07095f61ca2b build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-causalr", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:causalr + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-causalr + path: recipes/bioconductor-causalr + version: 1.14.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, RUnit, BiocGenerics requirements: host: @@ -27,21 +38,16 @@ requirements: run: - r-base - r-igraph + +source: + md5: ad152d4f41605f4c7784494641686fd3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Causal network analysis methods' - description: 'Causal network analysis methods for regulator prediction and network reconstruction from genome scale data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:causalr - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-causalr - path: recipes/bioconductor-causalr - version: 1.14.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cbaf/meta.yaml b/recipes/bioconductor-cbaf/meta.yaml index 8e99a667fb4cb..4069be119e2a7 100644 --- a/recipes/bioconductor-cbaf/meta.yaml +++ b/recipes/bioconductor-cbaf/meta.yaml @@ -1,48 +1,55 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "cbaf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains functions that allow analysing and comparing omic data across various cancers/cancer subgroups easily. So far, it is compatible with RNA-seq, microRNA-seq, microarray and methylation datasets that are stored on cbioportal.org. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Automated functions for comparing various omic data from cbioportal.org -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e3c093194c8fdcbd04ca035dddeaf5f5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cbaf", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-cbioportaldata >=2.14.0,<2.15.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-cbioportaldata >=2.18.0,<2.19.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 - r-base - r-gplots - r-openxlsx - r-rcolorbrewer + - r-zip run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-cbioportaldata >=2.14.0,<2.15.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-cbioportaldata >=2.18.0,<2.19.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 - r-base - r-gplots - r-openxlsx - r-rcolorbrewer + - r-zip + +source: + md5: 718fd18e73d785240a766ca4282ff05c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Automated functions for comparing various omic data from cbioportal.org' - description: 'This package contains functions that allow analysing and comparing omic data across various cancers/cancer subgroups easily. So far, it is compatible with RNA-seq, microRNA-seq, microarray and methylation datasets that are stored on cbioportal.org.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cbea/meta.yaml b/recipes/bioconductor-cbea/meta.yaml index 63e685b38f7f5..f6ad976461e1f 100644 --- a/recipes/bioconductor-cbea/meta.yaml +++ b/recipes/bioconductor-cbea/meta.yaml @@ -1,30 +1,38 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "CBEA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements CBEA, a method to perform set-based analysis for microbiome relative abundance data. This approach constructs a competitive balance between taxa within the set and remainder taxa per sample. More details can be found in the Nguyen et al. 2021+ manuscript. Additionally, this package adds support functions to help users perform taxa-set enrichment analyses using existing gene set analysis methods. In the future we hope to also provide curated knowledge driven taxa sets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Competitive Balances for Taxonomic Enrichment Analysis in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20761b06df9cf37c59172508ff8cd01d build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cbea", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: phyloseq, BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), tidyverse, roxygen2, mia, purrr requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocset >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocset >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 - r-base - r-dplyr - r-fitdistrplus @@ -34,17 +42,18 @@ requirements: - r-lmom - r-magrittr - r-mixtools - - 'r-rcpp >=1.0.7' + - r-rcpp >=1.0.7 - r-rlang - r-tibble - r-tidyr - libblas - liblapack + run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocset >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocset >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 - r-base - r-dplyr - r-fitdistrplus @@ -54,21 +63,20 @@ requirements: - r-lmom - r-magrittr - r-mixtools - - 'r-rcpp >=1.0.7' + - r-rcpp >=1.0.7 - r-rlang - r-tibble - r-tidyr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 30daf429eb8568948239698ba7f06989 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Competitive Balances for Taxonomic Enrichment Analysis in R' - description: 'This package implements CBEA, a method to perform set-based analysis for microbiome relative abundance data. This approach constructs a competitive balance between taxa within the set and remainder taxa per sample. More details can be found in the Nguyen et al. 2021+ manuscript. Additionally, this package adds support functions to help users perform taxa-set enrichment analyses using existing gene set analysis methods. In the future we hope to also provide curated knowledge driven taxa sets.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cbioportaldata/meta.yaml b/recipes/bioconductor-cbioportaldata/meta.yaml index 4508b5319a9db..bcd689ed04db5 100644 --- a/recipes/bioconductor-cbioportaldata/meta.yaml +++ b/recipes/bioconductor-cbioportaldata/meta.yaml @@ -1,38 +1,40 @@ -{% set version = "2.14.0" %} +{% set version = "2.18.0" %} {% set name = "cBioPortalData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The cBioPortalData R package accesses study datasets from the cBio Cancer Genomics Portal. It accesses the data either from the pre-packaged zip / tar files or from the API interface that was recently implemented by the cBioPortal Data Team. The package can provide data in either tabular format or with MultiAssayExperiment object that uses familiar Bioconductor data representations. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + summary: Exposes and Makes Available Data from the cBioPortal Web Resources -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fc51f3b952b9c31900365adc94f85585 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cbioportaldata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, survival, survminer, rmarkdown, testthat requirements: host: - - 'bioconductor-anvil >=1.14.0,<1.15.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rtcgatoolbox >=2.32.0,<2.33.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tcgautils >=1.22.0,<1.23.0' + - bioconductor-anvil >=1.18.0,<1.19.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-raggedexperiment >=1.30.0,<1.31.0 + - bioconductor-rtcgatoolbox >=2.36.0,<2.37.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tcgautils >=1.26.0,<1.27.0 - r-base - r-digest - r-dplyr @@ -41,17 +43,17 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-anvil >=1.14.0,<1.15.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' - - 'bioconductor-rtcgatoolbox >=2.32.0,<2.33.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tcgautils >=1.22.0,<1.23.0' + - bioconductor-anvil >=1.18.0,<1.19.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-raggedexperiment >=1.30.0,<1.31.0 + - bioconductor-rtcgatoolbox >=2.36.0,<2.37.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tcgautils >=1.26.0,<1.27.0 - r-base - r-digest - r-dplyr @@ -59,13 +61,16 @@ requirements: - r-readr - r-tibble - r-tidyr + +source: + md5: 5250bc58eda55ea9f78d7b6e775c4a20 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3 - summary: 'Exposes and makes available data from the cBioPortal web resources' - description: 'The cBioPortalData R package accesses study datasets from the cBio Cancer Genomics Portal. It accesses the data either from the pre-packaged zip / tar files or from the API interface that was recently implemented by the cBioPortal Data Team. The package can provide data in either tabular format or with MultiAssayExperiment object that uses familiar Bioconductor data representations.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cbnplot/meta.yaml b/recipes/bioconductor-cbnplot/meta.yaml index 8ca2a36fb2135..ed7aaa4cd32bb 100644 --- a/recipes/bioconductor-cbnplot/meta.yaml +++ b/recipes/bioconductor-cbnplot/meta.yaml @@ -1,36 +1,38 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "CBNplot" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides the visualization of bayesian network inferred from gene expression data. The networks are based on enrichment analysis results inferred from packages including clusterProfiler and ReactomePA. The networks between pathways and genes inside the pathways can be inferred and visualized. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: plot bayesian network inferred from gene expression data based on enrichment analysis results -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d589e9361caf3409d65345cc48e5ccee build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cbnplot", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, arules, concaveman, ReactomePA, bnviewer, DESeq2, GEOquery, rmarkdown, withr, BiocStyle, testthat (>= 3.0.0) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, arules, concaveman, ReactomePA, bnviewer, rmarkdown, withr, BiocStyle, testthat (>= 3.0.0) requirements: + host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-depmap >=1.16.0,<1.17.0' - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-graphite >=1.48.0,<1.49.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-depmap >=1.20.0,<1.21.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-graphite >=1.52.0,<1.53.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - - 'r-bnlearn >=4.7' + - r-bnlearn >=4.7 - r-dplyr - r-ggdist - r-ggforce @@ -39,7 +41,6 @@ requirements: - r-graphlayouts - r-igraph - r-magrittr - - r-oaqc - r-patchwork - r-purrr - r-pvclust @@ -48,16 +49,17 @@ requirements: - r-rmpfr - r-stringr - r-tidyr + run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-depmap >=1.16.0,<1.17.0' - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-graphite >=1.48.0,<1.49.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-depmap >=1.20.0,<1.21.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-graphite >=1.52.0,<1.53.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - - 'r-bnlearn >=4.7' + - r-bnlearn >=4.7 - r-dplyr - r-ggdist - r-ggforce @@ -66,7 +68,6 @@ requirements: - r-graphlayouts - r-igraph - r-magrittr - - r-oaqc - r-patchwork - r-purrr - r-pvclust @@ -75,12 +76,16 @@ requirements: - r-rmpfr - r-stringr - r-tidyr + +source: + md5: 1b6998ff402119e2e1bd5d0fde10175a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'plot bayesian network inferred from gene expression data based on enrichment analysis results' - description: 'This package provides the visualization of bayesian network inferred from gene expression data. The networks are based on enrichment analysis results inferred from packages including clusterProfiler and ReactomePA. The networks between pathways and genes inside the pathways can be inferred and visualized.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cbpmanager/meta.yaml b/recipes/bioconductor-cbpmanager/meta.yaml index e35ef4a737405..80e68b0f3cc81 100644 --- a/recipes/bioconductor-cbpmanager/meta.yaml +++ b/recipes/bioconductor-cbpmanager/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "cbpManager" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This R package provides an R Shiny application that enables the user to generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics. Create cancer studies and edit its metadata. Upload mutation data of a patient that will be concatenated to the data_mutation_extended.txt file of the study. Create and edit clinical patient data, sample data, and timeline data. Create custom timeline tracks for patients. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + file LICENSE + license_file: LICENSE + summary: Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6567afab9427e6ee44a029fa5be314e7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cbpmanager", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 - r-base - r-dplyr - r-dt @@ -41,7 +43,7 @@ requirements: - r-shinydashboard - r-vroom run: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 - r-base - r-dplyr - r-dt @@ -59,13 +61,16 @@ requirements: - r-shinycssloaders - r-shinydashboard - r-vroom + +source: + md5: 0b499c0dabec8c6f39df576b789c1dbb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'AGPL-3 + file LICENSE' - summary: 'Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics' - description: 'This R package provides an R Shiny application that enables the user to generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics. Create cancer studies and edit its metadata. Upload mutation data of a patient that will be concatenated to the data_mutation_extended.txt file of the study. Create and edit clinical patient data, sample data, and timeline data. Create custom timeline tracks for patients.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ccdata/meta.yaml b/recipes/bioconductor-ccdata/meta.yaml index e552cec2d123c..f31e56c59f094 100644 --- a/recipes/bioconductor-ccdata/meta.yaml +++ b/recipes/bioconductor-ccdata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "ccdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 60cbd595e53467fd61e1edc4f8ea47e7 +about: + description: This package contains microarray gene expression data generated from the Connectivity Map build 02 and LINCS l1000. The data are used by the ccmap package to find drugs and drug combinations to mimic or reverse a gene expression signature. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Data for Combination Connectivity Mapping (ccmap) Package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ccdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 310ec3465e4b2c78427eff60b91aeaae + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Data for Combination Connectivity Mapping (ccmap) Package' - description: 'This package contains microarray gene expression data generated from the Connectivity Map build 02 and LINCS l1000. The data are used by the ccmap package to find drugs and drug combinations to mimic or reverse a gene expression signature.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ccdata/post-link.sh b/recipes/bioconductor-ccdata/post-link.sh index 3c5a6ff31dcdd..e3d5ddfbb81f7 100644 --- a/recipes/bioconductor-ccdata/post-link.sh +++ b/recipes/bioconductor-ccdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ccdata-1.28.0" +installBiocDataPackage.sh "ccdata-1.32.0" diff --git a/recipes/bioconductor-ccfindr/build_failure.linux-64.yaml b/recipes/bioconductor-ccfindr/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..3d677660e9fb9 --- /dev/null +++ b/recipes/bioconductor-ccfindr/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a2e98af63e16ef347fe96478b5168bda98611505a6bc7af527460be2e032d328 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-genomicranges[version='>=1.58.0,<1.59.0']"), MatchSpec("bioconductor-singlecellexperiment==1.28.0=r44hdfd78af_0")} + Encountered problems while solving: + - package bioconductor-singlecellexperiment-1.28.0-r44hdfd78af_0 requires bioconductor-genomicranges >=1.58.0,<1.59.0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-singlecellexperiment >=1.28.0,<1.29.0 [0m is installable and it requires + [32mbioconductor-genomicranges >=1.58.0,<1.59.0 [0m, which requires + [32mbioconductor-xvector >=0.46.0,<0.47.0 [0m, which requires + [32mbioconductor-zlibbioc >=1.52.0,<1.53.0 [0m, which requires + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [31mr-rmpi[0m is not installable because there are no viable options + [31mr-rmpi 0.6_9[0m would require + [31mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which conflicts with any installable versions previously reported; + [31mr-rmpi [0.6_9|0.6_9.1][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-rmpi [0.6_9|0.6_9.1|0.6_9.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-rmpi [0.6_9.1|0.6_9.2|0.7_1][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-rmpi [0.6_9.2|0.7_1|0.7_2][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-rmpi [0.7_1|0.7_2|0.7_2.1][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-genomicranges[version='>=1.58.0,<1.59.0']"), MatchSpec("bioconductor-singlecellexperiment==1.28.0=r44hdfd78af_0")} + Encountered problems while solving: + - package bioconductor-singlecellexperiment-1.28.0-r44hdfd78af_0 requires bioconductor-genomicranges >=1.58.0,<1.59.0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-singlecellexperiment >=1.28.0,<1.29.0 [0m is installable and it requires + [32mbioconductor-genomicranges >=1.58.0,<1.59.0 [0m, which requires + [32mbioconductor-xvector >=0.46.0,<0.47.0 [0m, which requires + [32mbioconductor-zlibbioc >=1.52.0,<1.53.0 [0m, which requires + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [31mr-rmpi[0m is not installable because there are no viable options + [31mr-rmpi 0.6_9[0m would require + [31mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which conflicts with any installable versions previously reported; + [31mr-rmpi [0.6_9|0.6_9.1][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-rmpi [0.6_9|0.6_9.1|0.6_9.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-rmpi [0.6_9.1|0.6_9.2|0.7_1][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-rmpi [0.6_9.2|0.7_1|0.7_2][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-rmpi [0.7_1|0.7_2|0.7_2.1][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-ccfindr/build_failure.osx-64.yaml b/recipes/bioconductor-ccfindr/build_failure.osx-64.yaml index f96432c2ea200..ff04b78860d2e 100644 --- a/recipes/bioconductor-ccfindr/build_failure.osx-64.yaml +++ b/recipes/bioconductor-ccfindr/build_failure.osx-64.yaml @@ -1,104 +1,104 @@ -recipe_sha: 284d8b5d60d001aad42c11aa0f88615ff84ff828b15ac43defb45c3fd2d1f416 # The commit at which this recipe failed to build. +recipe_sha: a2e98af63e16ef347fe96478b5168bda98611505a6bc7af527460be2e032d328 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-ccfindr-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-ccfindr-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-ccfindr-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-ccfindr-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-ccfindr-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-ccfindr-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - INFO: activate_clang_osx-64.sh made the following environmental changes: - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - * installing to library /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library - * installing *source* package ccfindR ... - ** using staged installation - ** libs - dyld[12683]: Library not loaded: '@rpath/libclang-cpp.15.dylib' - Referenced from: '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/clang-15' - Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/libclang-cpp.15.dylib' (no such file), '/Users/runner/miniforge3/conda-bld/r-base-split_1700316070281/_build_env/lib/jvm/lib/server/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/libclang-cpp.15.dylib' (no such file), '/Users/runner/miniforge3/conda-bld/r-base-split_1700316070281/_build_env/lib/jvm/lib/server/libclang-cpp.15.dylib' (no such file) - using C compiler: NA - using C11 - using SDK: - x86_64-apple-darwin13.4.0-clang -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1700316070281/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o - dyld[12689]: Library not loaded: '@rpath/libclang-cpp.15.dylib' - Referenced from: '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/clang-15' - Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-15-15.0.7-default_h6b1ee41_4/bin/../lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/libclang-cpp.15.dylib' (no such file), '/Users/runner/miniforge3/conda-bld/r-base-split_1700316070281/_build_env/lib/jvm/lib/server/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/lib/libclang-cpp.15.dylib' (no such file), '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/libclang-cpp.15.dylib' (no such file), '/Users/runner/miniforge3/conda-bld/r-base-split_1700316070281/_build_env/lib/jvm/lib/server/libclang-cpp.15.dylib' (no such file) - make: *** [/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/etc/Makeconf:200: RcppExports.o] Abort trap: 6 - ERROR: compilation failed for package ccfindR - * removing /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/ccfindR +log: |2- + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1 conflicts with any installable versions previously reported; + r-rmpi [0.6_9|0.6_9.1] would require + r-base >=3.6,<3.7.0a0 but there are no viable options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3] conflicts with any installable versions previously reported; + r-rmpi [0.6_9|0.6_9.1|0.6_9.2] would require + r-base >=4.0,<4.1.0a0 , which conflicts with any installable versions previously reported; + r-rmpi [0.6_9.1|0.6_9.2|0.7_1] would require + r-base >=4.1,<4.2.0a0 , which conflicts with any installable versions previously reported; + r-rmpi [0.6_9.2|0.7_1|0.7_2] would require + r-base >=4.2,<4.3.0a0 , which conflicts with any installable versions previously reported; + r-rmpi [0.7_1|0.7_2|0.7_2.1] would require + r-base >=4.3,<4.4.0a0 , which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-ccfindr_1703622619603/work/conda_build.sh']' returned non-zero exit status 1. + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("clang==4.0.1=1"), MatchSpec("4.0.1==hcfea43d_1")} + Encountered problems while solving: + - nothing provides compiler-rt 4.0.1 hcfea43d_1 needed by clang-4.0.1-1 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-singlecellexperiment >=1.28.0,<1.29.0 is installable and it requires + bioconductor-genomicranges >=1.58.0,<1.59.0 , which requires + bioconductor-xvector >=0.46.0,<0.47.0 , which requires + bioconductor-zlibbioc >=1.52.0,<1.53.0 , which requires + r-base >=4.4,<4.5.0a0 , which can be installed; + r-rmpi is not installable because there are no viable options + r-rmpi 0.6_9 would require + r-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ] but there are no viable options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1 conflicts with any installable versions previously reported; + r-rmpi [0.6_9|0.6_9.1] would require + r-base >=3.6,<3.7.0a0 but there are no viable options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3] conflicts with any installable versions previously reported; + r-rmpi [0.6_9|0.6_9.1|0.6_9.2] would require + r-base >=4.0,<4.1.0a0 , which conflicts with any installable versions previously reported; + r-rmpi [0.6_9.1|0.6_9.2|0.7_1] would require + r-base >=4.1,<4.2.0a0 , which conflicts with any installable versions previously reported; + r-rmpi [0.6_9.2|0.7_1|0.7_2] would require + r-base >=4.2,<4.3.0a0 , which conflicts with any installable versions previously reported; + r-rmpi [0.7_1|0.7_2|0.7_2.1] would require + r-base >=4.3,<4.4.0a0 , which conflicts with any installable versions previously reported. # Last 100 lines of the build log. diff --git a/recipes/bioconductor-ccfindr/meta.yaml b/recipes/bioconductor-ccfindr/meta.yaml index 885a9ad43f114..9f0c48d3615f6 100644 --- a/recipes/bioconductor-ccfindr/meta.yaml +++ b/recipes/bioconductor-ccfindr/meta.yaml @@ -1,30 +1,35 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "ccfindR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A collection of tools for cancer genomic data clustering analyses, including those for single cell RNA-seq. Cell clustering and feature gene selection analysis employ Bayesian (and maximum likelihood) non-negative matrix factorization (NMF) algorithm. Input data set consists of RNA count matrix, gene, and cell bar code annotations. Analysis outputs are factor matrices for multiple ranks and marginal likelihood values for each rank. The package includes utilities for downstream analyses, including meta-gene identification, visualization, and construction of rank-based trees for clusters. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Cancer Clone Finder -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0a0dd7c35273c39673f992bed7fa952d build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ccfindr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown -# SystemRequirements: gsl requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-ape - r-base - r-gtools @@ -33,16 +38,15 @@ requirements: - r-rcolorbrewer - r-rcpp - r-rcppeigen - - 'r-rdpack >=0.7' + - r-rdpack >=0.7 - r-rmpi - r-rtsne - libblas - liblapack - - gsl run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-ape - r-base - r-gtools @@ -51,21 +55,19 @@ requirements: - r-rcolorbrewer - r-rcpp - r-rcppeigen - - 'r-rdpack >=0.7' + - r-rdpack >=0.7 - r-rmpi - r-rtsne - - gsl - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 5867f5ce4db69f5458c4bd2ff520d6f4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Cancer Clone Finder' - description: 'A collection of tools for cancer genomic data clustering analyses, including those for single cell RNA-seq. Cell clustering and feature gene selection analysis employ Bayesian (and maximum likelihood) non-negative matrix factorization (NMF) algorithm. Input data set consists of RNA count matrix, gene, and cell bar code annotations. Analysis outputs are factor matrices for multiple ranks and marginal likelihood values for each rank. The package includes utilities for downstream analyses, including meta-gene identification, visualization, and construction of rank-based trees for clusters.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ccimpute/meta.yaml b/recipes/bioconductor-ccimpute/meta.yaml index 14e1190d5d502..60d137086089d 100644 --- a/recipes/bioconductor-ccimpute/meta.yaml +++ b/recipes/bioconductor-ccimpute/meta.yaml @@ -1,52 +1,63 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "ccImpute" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Dropout events make the lowly expressed genes indistinguishable from true zero expression and different than the low expression present in cells of the same type. This issue makes any subsequent downstream analysis difficult. ccImpute is an imputation algorithm that uses cell similarity established by consensus clustering to impute the most probable dropout events in the scRNA-seq datasets. ccImpute demonstrated performance which exceeds the performance of existing imputation approaches while introducing the least amount of new noise as measured by clustering performance characteristics on datasets with known cell identities. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data (https://doi.org/10.1186/s12859-022-04814-8)' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f402177e3fc7bbbcac504c956889dfa9 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ccimpute", max_pin="x.x") }}' -# Suggests: knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater, SingleCellExperiment, mclust, testthat (>= 3.0.0) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater, mclust, testthat (>= 3.0.0), splatter requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-simlr >=1.28.0,<1.29.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - r-matrixstats + - r-irlba + - r-matrix - r-rcpp - r-rcppeigen - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-simlr >=1.28.0,<1.29.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - r-matrixstats + - r-irlba + - r-matrix - r-rcpp - r-rcppeigen - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 1f2214b009e55a529068e1618e30b81f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data (https://doi.org/10.1186/s12859-022-04814-8)' - description: 'Dropout events make the lowly expressed genes indistinguishable from true zero expression and different than the low expression present in cells of the same type. This issue makes any subsequent downstream analysis difficult. ccImpute is an imputation algorithm that uses cell similarity established by consensus clustering to impute the most probable dropout events in the scRNA-seq datasets. ccImpute demonstrated performance which exceeds the performance of existing imputation approaches while introducing the least amount of new noise as measured by clustering performance characteristics on datasets with known cell identities.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ccl4/meta.yaml b/recipes/bioconductor-ccl4/meta.yaml index 6179644dbc14d..45415b149021d 100644 --- a/recipes/bioconductor-ccl4/meta.yaml +++ b/recipes/bioconductor-ccl4/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "CCl4" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3247cf1db347f959d908e88b5e8febb5 +about: + description: NChannelSet for rat hepatocytes treated with Carbon Tetrachloride (CCl4) data from LGC company. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Carbon Tetrachloride (CCl4) treated hepatocytes build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ccl4", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fb2ae341e4ce02f9252126a652638004 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Carbon Tetrachloride (CCl4) treated hepatocytes' - description: 'NChannelSet for rat hepatocytes treated with Carbon Tetrachloride (CCl4) data from LGC company.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ccl4/post-link.sh b/recipes/bioconductor-ccl4/post-link.sh index 8bd8b92dae2ca..5d963dfa1443f 100644 --- a/recipes/bioconductor-ccl4/post-link.sh +++ b/recipes/bioconductor-ccl4/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ccl4-1.40.0" +installBiocDataPackage.sh "ccl4-1.44.0" diff --git a/recipes/bioconductor-ccmap/build_failure.linux-64.yaml b/recipes/bioconductor-ccmap/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0b1c52ff25056 --- /dev/null +++ b/recipes/bioconductor-ccmap/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 02e1b41006d7ee68ffd9cbb50ef5635c4544ce384f08086581e9abebf01d960a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec(">=3.5.0,<3.5.1.0a0"), MatchSpec("r-xgboost==0.80=mro350h255eb88_1")} + Encountered problems while solving: + - nothing provides mro-base >=3.5.0,<3.5.1.0a0 needed by r-xgboost-0.80-mro350h255eb88_1 + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-xgboost >=0.6.4 [0m is not installable because there are no viable options + [31mr-xgboost 0.80[0m would require + [31mmro-base >=3.5.0,<3.5.1.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-xgboost [0.80|0.81|0.82|0.90|1.0.2][0m would require + [31mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [0.82|0.90|...|1.4.0][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.0.2|1.1.1|...|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.4.0|1.4.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec(">=3.5.0,<3.5.1.0a0"), MatchSpec("r-xgboost==0.80=mro350h255eb88_1")} + Encountered problems while solving: + - nothing provides mro-base >=3.5.0,<3.5.1.0a0 needed by r-xgboost-0.80-mro350h255eb88_1 + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-xgboost >=0.6.4 [0m is not installable because there are no viable options + [31mr-xgboost 0.80[0m would require + [31mmro-base >=3.5.0,<3.5.1.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-xgboost [0.80|0.81|0.82|0.90|1.0.2][0m would require + [31mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [0.82|0.90|...|1.4.0][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.0.2|1.1.1|...|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.4.0|1.4.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-ccmap/meta.yaml b/recipes/bioconductor-ccmap/meta.yaml index 765e1c9c198f5..f9851c249d34e 100644 --- a/recipes/bioconductor-ccmap/meta.yaml +++ b/recipes/bioconductor-ccmap/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "ccmap" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Finds drugs and drug combinations that are predicted to reverse or mimic gene expression signatures. These drugs might reverse diseases or mimic healthy lifestyles. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Combination Connectivity Mapping -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d01f3e9dca6ce3403096f8fc00766755 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ccmap", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: crossmeta, knitr, rmarkdown, testthat, lydata requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-ccdata >=1.28.0,<1.29.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-ccdata >=1.32.0,<1.33.0 - r-base - - 'r-biocmanager >=1.30.4' - - 'r-data.table >=1.10.4' - - 'r-doparallel >=1.0.10' - - 'r-foreach >=1.4.3' - - 'r-lsa >=0.73.1' - - 'r-xgboost >=0.6.4' + - r-biocmanager >=1.30.4 + - r-data.table >=1.10.4 + - r-doparallel >=1.0.10 + - r-foreach >=1.4.3 + - r-lsa >=0.73.1 + - r-xgboost >=0.6.4 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-ccdata >=1.28.0,<1.29.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-ccdata >=1.32.0,<1.33.0 - r-base - - 'r-biocmanager >=1.30.4' - - 'r-data.table >=1.10.4' - - 'r-doparallel >=1.0.10' - - 'r-foreach >=1.4.3' - - 'r-lsa >=0.73.1' - - 'r-xgboost >=0.6.4' + - r-biocmanager >=1.30.4 + - r-data.table >=1.10.4 + - r-doparallel >=1.0.10 + - r-foreach >=1.4.3 + - r-lsa >=0.73.1 + - r-xgboost >=0.6.4 + +source: + md5: 350b860cb1123cd82d554b834566c29a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Combination Connectivity Mapping' - description: 'Finds drugs and drug combinations that are predicted to reverse or mimic gene expression signatures. These drugs might reverse diseases or mimic healthy lifestyles.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ccplotr/meta.yaml b/recipes/bioconductor-ccplotr/meta.yaml index 550ccfa7556d0..354d235a223d0 100644 --- a/recipes/bioconductor-ccplotr/meta.yaml +++ b/recipes/bioconductor-ccplotr/meta.yaml @@ -1,28 +1,31 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "CCPlotR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CCPlotR is an R package for visualising results from tools that predict cell-cell interactions from single-cell RNA-seq data. These plots are generic and can be used to visualise results from multiple tools such as Liana, CellPhoneDB, NATMI etc. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Plots For Visualising Cell-Cell Interactions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 913896518f29cd88d7ac9d57298f44de build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ccplotr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) requirements: + host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 - r-base - r-circlize - r-dplyr @@ -42,8 +45,9 @@ requirements: - r-tibble - r-tidyr - r-viridis + run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 - r-base - r-circlize - r-dplyr @@ -63,13 +67,16 @@ requirements: - r-tibble - r-tidyr - r-viridis + +source: + md5: 568a1409688bbdcbd8041e911f45147e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Plots For Visualising Cell-Cell Interactions' - description: 'CCPlotR is an R package for visualising results from tools that predict cell-cell interactions from single-cell RNA-seq data. These plots are generic and can be used to visualise results from multiple tools such as Liana, CellPhoneDB, NATMI etc.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ccpromise/build_failure.linux-64.yaml b/recipes/bioconductor-ccpromise/build_failure.linux-64.yaml deleted file mode 100644 index 72fc0dc3a0c09..0000000000000 --- a/recipes/bioconductor-ccpromise/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 722fb617600a55303b535b784f5387ef700db6e8486e427c054d57fb5deff1b6 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.1s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.2s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.3s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.4s - [2K[1A[2K[0Gconda-forge/linux-64 - [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m - [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 2.2MB/s 0.0s - [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m - [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 2.1MB/s 0.0s - [?25hMamba failed to solve: - - r-base 4.3.* - - r-ccp - - bioconductor-biobase >=2.62.0,<2.63.0 - - bioconductor-gseabase >=1.64.0,<1.65.0 - - bioconductor-promise >=1.54.0,<1.55.0 - - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested bioconductor-promise >=1.54.0,<1.55.0 - - - - Leaving build/test directories: - Work: - /opt/conda/conda-bld/work - Test: - /opt/conda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl - Build: - source activate /opt/conda/conda-bld/_build_env - - - Traceback (most recent call last): - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action - t = self.solve(specs) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - r-base 4.3.* - - r-ccp - - bioconductor-biobase >=2.62.0,<2.63.0 - - bioconductor-gseabase >=1.64.0,<1.65.0 - - bioconductor-promise >=1.54.0,<1.55.0 - - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested bioconductor-promise >=1.54.0,<1.55.0 - - - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build - output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs - for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set - conda_packages = finalize_outputs_pass( - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass - fm = finalize_metadata( - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata - build_unsat, host_unsat = add_upstream_pins(m, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins - host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files - deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies - actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-promise[version='>=1.54.0,<1.55.0']")} -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-ccpromise/meta.yaml b/recipes/bioconductor-ccpromise/meta.yaml index a9de2cd528f55..ebdb6e03eea26 100644 --- a/recipes/bioconductor-ccpromise/meta.yaml +++ b/recipes/bioconductor-ccpromise/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "CCPROMISE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b85c7bbed3be474abf4e4591882abdf +about: + description: Perform Canonical correlation between two forms of high demensional genetic data, and associate the first compoent of each form of data with a specific biologically interesting pattern of associations with multiple endpoints. A probe level analysis is also implemented. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ccpromise", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-promise >=1.54.0,<1.55.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-promise >=1.58.0,<1.59.0 - r-base - r-ccp run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-promise >=1.54.0,<1.55.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-promise >=1.58.0,<1.59.0 - r-base - r-ccp +source: + md5: 07f93a5a9f5eeb58a89cc2ccd4f8156a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data' - description: 'Perform Canonical correlation between two forms of high demensional genetic data, and associate the first compoent of each form of data with a specific biologically interesting pattern of associations with multiple endpoints. A probe level analysis is also implemented.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ccrepe/meta.yaml b/recipes/bioconductor-ccrepe/meta.yaml index c3c4ac81e4a32..d9608a1e33b30 100644 --- a/recipes/bioconductor-ccrepe/meta.yaml +++ b/recipes/bioconductor-ccrepe/meta.yaml @@ -1,43 +1,44 @@ -{% set version = "1.36.0" %} +{% set version = "1.42.0" %} {% set name = "ccrepe" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e7eede47c35843ca92b83c8069a1d606 +about: + description: 'The CCREPE (Compositionality Corrected by REnormalizaion and PErmutation) package is designed to assess the significance of general similarity measures in compositional datasets. In microbial abundance data, for example, the total abundances of all microbes sum to one; CCREPE is designed to take this constraint into account when assigning p-values to similarity measures between the microbes. The package has two functions: ccrepe: Calculates similarity measures, p-values and q-values for relative abundances of bugs in one or two body sites using bootstrap and permutation matrices of the data. nc.score: Calculates species-level co-variation and co-exclusion patterns based on an extension of the checkerboard score to ordinal data.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: ccrepe_and_nc.score build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic -# Suggests: knitr, BiocStyle, BiocGenerics, testthat + run_exports: '{{ pin_subpackage("bioconductor-ccrepe", max_pin="x.x") }}' +extra: + parent_recipe: + name: bioconductor-ccrepe + path: recipes/bioconductor-ccrepe + version: 1.18.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: knitr, BiocStyle, BiocGenerics, testthat, RUnit requirements: host: - r-base - - 'r-infotheo >=1.1' + - r-infotheo >=1.1 run: - r-base - - 'r-infotheo >=1.1' + - r-infotheo >=1.1 +source: + md5: fa406df6f23f3e0f98ceb330645cf3cf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: ccrepe_and_nc.score - description: 'The CCREPE (Compositionality Corrected by REnormalizaion and PErmutation) package is designed to assess the significance of general similarity measures in compositional datasets. In microbial abundance data, for example, the total abundances of all microbes sum to one; CCREPE is designed to take this constraint into account when assigning p-values to similarity measures between the microbes. The package has two functions: ccrepe: Calculates similarity measures, p-values and q-values for relative abundances of bugs in one or two body sites using bootstrap and permutation matrices of the data. nc.score: Calculates species-level co-variation and co-exclusion patterns based on an extension of the checkerboard score to ordinal data.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-ccrepe - path: recipes/bioconductor-ccrepe - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cdi/meta.yaml b/recipes/bioconductor-cdi/meta.yaml index 10184abeabdbc..298d198d927af 100644 --- a/recipes/bioconductor-cdi/meta.yaml +++ b/recipes/bioconductor-cdi/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.0.2" %} +{% set version = "1.4.0" %} {% set name = "CDI" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Single-cell RNA-sequencing (scRNA-seq) is widely used to explore cellular variation. The analysis of scRNA-seq data often starts from clustering cells into subpopulations. This initial step has a high impact on downstream analyses, and hence it is important to be accurate. However, there have not been unsupervised metric designed for scRNA-seq to evaluate clustering performance. Hence, we propose clustering deviation index (CDI), an unsupervised metric based on the modeling of scRNA-seq UMI counts to evaluate clustering of cells. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Clustering Deviation Index (CDI) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 64ebd520b0ba4613c3bddf06bb82dbc0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cdi", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, RUnit, BiocGenerics, magick, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-ggsci @@ -33,9 +35,9 @@ requirements: - r-seurat - r-seuratobject run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-ggsci @@ -43,13 +45,16 @@ requirements: - r-reshape2 - r-seurat - r-seuratobject + +source: + md5: 19e4c824c0177090307638f483e15173 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Clustering Deviation Index (CDI)' - description: 'Single-cell RNA-sequencing (scRNA-seq) is widely used to explore cellular variation. The analysis of scRNA-seq data often starts from clustering cells into subpopulations. This initial step has a high impact on downstream analyses, and hence it is important to be accurate. However, there have not been unsupervised metric designed for scRNA-seq to evaluate clustering performance. Hence, we propose clustering deviation index (CDI), an unsupervised metric based on the modeling of scRNA-seq UMI counts to evaluate clustering of cells.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-celaref/meta.yaml b/recipes/bioconductor-celaref/meta.yaml index f3530a6b4cb5d..d24c6474b4d8b 100644 --- a/recipes/bioconductor-celaref/meta.yaml +++ b/recipes/bioconductor-celaref/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "celaref" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: After the clustering step of a single-cell RNAseq experiment, this package aims to suggest labels/cell types for the clusters, on the basis of similarity to a reference dataset. It requires a table of read counts per cell per gene, and a list of the cells belonging to each of the clusters, (for both test and reference data). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Single-cell RNAseq cell cluster labelling by reference -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8c168c1e505d63f6372d6baac7051a06 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-celaref", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: limma, parallel, knitr, rmarkdown, ExperimentHub, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-mast >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-mast >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -36,11 +38,11 @@ requirements: - r-rlang - r-tibble run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-mast >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-mast >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -49,13 +51,16 @@ requirements: - r-readr - r-rlang - r-tibble + +source: + md5: 445dc9fc9201b8b1eb4978c80c0b4171 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Single-cell RNAseq cell cluster labelling by reference' - description: 'After the clustering step of a single-cell RNAseq experiment, this package aims to suggest labels/cell types for the clusters, on the basis of similarity to a reference dataset. It requires a table of read counts per cell per gene, and a list of the cells belonging to each of the clusters, (for both test and reference data).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-celarefdata/meta.yaml b/recipes/bioconductor-celarefdata/meta.yaml index 5babbe3604e80..03df6e61d6ff4 100644 --- a/recipes/bioconductor-celarefdata/meta.yaml +++ b/recipes/bioconductor-celarefdata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "celarefData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6864c27f1d574314fe10612b37f6c433 +about: + description: This experiment data contains some processed data used in the celaref package vignette. These are publically available datasets, that have been processed by celaref package, and can be manipulated further with it. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Processed scRNA data for celaref Vignette - cell labelling by reference build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-celarefdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: ExperimentHub, knitr, rmarkdown requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 53757d12a0a75e5220f8a1ceac494942 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Processed scRNA data for celaref Vignette - cell labelling by reference' - description: 'This experiment data contains some processed data used in the celaref package vignette. These are publically available datasets, that have been processed by celaref package, and can be manipulated further with it.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-celarefdata/post-link.sh b/recipes/bioconductor-celarefdata/post-link.sh index da558cc839610..419674d8ae77d 100644 --- a/recipes/bioconductor-celarefdata/post-link.sh +++ b/recipes/bioconductor-celarefdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "celarefdata-1.20.0" +installBiocDataPackage.sh "celarefdata-1.24.0" diff --git a/recipes/bioconductor-celda/meta.yaml b/recipes/bioconductor-celda/meta.yaml index 921775f6f1896..920af0704d6a0 100644 --- a/recipes/bioconductor-celda/meta.yaml +++ b/recipes/bioconductor-celda/meta.yaml @@ -1,33 +1,41 @@ -{% set version = "1.18.1" %} +{% set version = "1.22.0" %} {% set name = "celda" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Celda is a suite of Bayesian hierarchical models for clustering single-cell RNA-sequencing (scRNA-seq) data. It is able to perform "bi-clustering" and simultaneously cluster genes into gene modules and cells into cell subpopulations. It also contains DecontX, a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. A variety of scRNA-seq data visualization functions is also included. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: CEllular Latent Dirichlet Allocation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5b60cdee9ee9cbb13f4af0a40abdd177 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-celda", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-data.table @@ -55,14 +63,15 @@ requirements: - r-withr - libblas - liblapack + run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-data.table @@ -88,17 +97,16 @@ requirements: - r-stringr - r-uwot - r-withr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 634d074a852e468ae51c3bf34d740134 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'CEllular Latent Dirichlet Allocation' - description: 'Celda is a suite of Bayesian hierarchical models for clustering single-cell RNA-sequencing (scRNA-seq) data. It is able to perform "bi-clustering" and simultaneously cluster genes into gene modules and cells into cell subpopulations. It also contains DecontX, a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. A variety of scRNA-seq data visualization functions is also included.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-celegans.db/meta.yaml b/recipes/bioconductor-celegans.db/meta.yaml index ea39dc2bada5e..14443380cb770 100644 --- a/recipes/bioconductor-celegans.db/meta.yaml +++ b/recipes/bioconductor-celegans.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "celegans.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3cfa9df5a81ef538a890ed8c5d5a98ad +about: + description: Affymetrix Affymetrix Celegans Array annotation data (chip celegans) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Celegans Array annotation data (chip celegans) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-celegans.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.ce.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.ce.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.ce.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.ce.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3cfa9df5a81ef538a890ed8c5d5a98ad + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Celegans Array annotation data (chip celegans)' - description: 'Affymetrix Affymetrix Celegans Array annotation data (chip celegans) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-celeganscdf/meta.yaml b/recipes/bioconductor-celeganscdf/meta.yaml index 3e1337bd905c5..9ba7d27170ae8 100644 --- a/recipes/bioconductor-celeganscdf/meta.yaml +++ b/recipes/bioconductor-celeganscdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "celeganscdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1098cd99bfc5000bf9858e4a3acaf452 +about: + description: A package containing an environment representing the Celegans.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: celeganscdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-celeganscdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1098cd99bfc5000bf9858e4a3acaf452 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: celeganscdf - description: 'A package containing an environment representing the Celegans.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-celegansprobe/meta.yaml b/recipes/bioconductor-celegansprobe/meta.yaml index b1c063a28735f..8b21fb954d3bb 100644 --- a/recipes/bioconductor-celegansprobe/meta.yaml +++ b/recipes/bioconductor-celegansprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "celegansprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7454bba10ff2dd7c03bfe0f9d450f148 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was C\_elegans\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type celegans build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-celegansprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7454bba10ff2dd7c03bfe0f9d450f148 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type celegans' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was C\_elegans\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cellbarcode/meta.yaml b/recipes/bioconductor-cellbarcode/meta.yaml index 27da6a1d0c2b9..c7059271844de 100644 --- a/recipes/bioconductor-cellbarcode/meta.yaml +++ b/recipes/bioconductor-cellbarcode/meta.yaml @@ -1,70 +1,77 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "CellBarcode" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package CellBarcode performs Cellular DNA Barcode analysis. It can handle all kinds of DNA barcodes, as long as the barcode is within a single sequencing read and has a pattern that can be matched by a regular expression. \code{CellBarcode} can handle barcodes with flexible lengths, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing some amplicon data such as CRISPR gRNA screening, immune repertoire sequencing, and metagenome data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Cellular DNA Barcode Analysis toolkit -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d219d9d5c998fda5f5c02f817361c56a build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cellbarcode", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-bh - r-ckmeans.1d.dp - - 'r-data.table >=1.12.6' + - r-data.table >=1.12.6 - r-egg - r-ggplot2 - r-magrittr - r-plyr - - 'r-rcpp >=1.0.5' + - r-rcpp >=1.0.5 - r-seqinr - r-stringr - libblas - liblapack + - zlib run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-bh - r-ckmeans.1d.dp - - 'r-data.table >=1.12.6' + - r-data.table >=1.12.6 - r-egg - r-ggplot2 - r-magrittr - r-plyr - - 'r-rcpp >=1.0.5' + - r-rcpp >=1.0.5 - r-seqinr - r-stringr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 033800efd6a20b732a66ea8993054ca6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Cellular DNA Barcode Analysis toolkit' - description: 'The package CellBarcode performs Cellular DNA Barcode analysis. It can handle all kinds of DNA barcodes, as long as the barcode is within a single sequencing read and has a pattern that can be matched by a regular expression. \code{CellBarcode} can handle barcodes with flexible lengths, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing some amplicon data such as CRISPR gRNA screening, immune repertoire sequencing, and metagenome data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cellbaser/meta.yaml b/recipes/bioconductor-cellbaser/meta.yaml index a80228b09d7cc..0ed1b9aa39afe 100644 --- a/recipes/bioconductor-cellbaser/meta.yaml +++ b/recipes/bioconductor-cellbaser/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "cellbaseR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This R package makes use of the exhaustive RESTful Web service API that has been implemented for the Cellabase database. It enable researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Apache License (== 2.0) + summary: Querying annotation data from the high performance Cellbase web -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1540f788e9e1fba133da3a369fe2c8b4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cellbaser", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-data.table - r-doparallel @@ -34,8 +35,8 @@ requirements: - r-r.utils - r-tidyr run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-data.table - r-doparallel @@ -45,12 +46,16 @@ requirements: - r-pbapply - r-r.utils - r-tidyr + +source: + md5: d859f87b16f32b7735d9672440e1f095 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Apache License (== 2.0)' - summary: 'Querying annotation data from the high performance Cellbase web' - description: 'This R package makes use of the exhaustive RESTful Web service API that has been implemented for the Cellabase database. It enable researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cellbench/meta.yaml b/recipes/bioconductor-cellbench/meta.yaml index 6dbd1f801f5e5..08b7514ca0ded 100644 --- a/recipes/bioconductor-cellbench/meta.yaml +++ b/recipes/bioconductor-cellbench/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "CellBench" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains infrastructure for benchmarking analysis methods and access to single cell mixture benchmarking data. It provides a framework for organising analysis methods and testing combinations of methods in a pipeline without explicitly laying out each combination. It also provides utilities for sampling and filtering SingleCellExperiment objects, constructing lists of functions with varying parameters, and multithreaded evaluation of analysis methods. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Construct Benchmarks for Single Cell Analysis Methods -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 21b854517881e111491fd4b6dba0857c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cellbench", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2 requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-assertthat - r-base - r-dplyr @@ -33,17 +35,17 @@ requirements: - r-lubridate - r-magrittr - r-memoise - - 'r-purrr >=0.3.0' + - r-purrr >=0.3.0 - r-rappdirs - r-rlang - r-tibble - r-tidyr - r-tidyselect run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-assertthat - r-base - r-dplyr @@ -51,19 +53,22 @@ requirements: - r-lubridate - r-magrittr - r-memoise - - 'r-purrr >=0.3.0' + - r-purrr >=0.3.0 - r-rappdirs - r-rlang - r-tibble - r-tidyr - r-tidyselect + +source: + md5: 4da39f8bcdb9a8031bbddae19ae13c04 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Construct Benchmarks for Single Cell Analysis Methods' - description: 'This package contains infrastructure for benchmarking analysis methods and access to single cell mixture benchmarking data. It provides a framework for organising analysis methods and testing combinations of methods in a pipeline without explicitly laying out each combination. It also provides utilities for sampling and filtering SingleCellExperiment objects, constructing lists of functions with varying parameters, and multithreaded evaluation of analysis methods.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-celldex/build_failure.osx-64.yaml b/recipes/bioconductor-celldex/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..ed298296dbbd5 --- /dev/null +++ b/recipes/bioconductor-celldex/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 539da9a065b3f7f65af68a953c1840d6fb1ff7beef430942f29691b4c8e63d49 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bioconductor-alabaster.base needs to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-celldex/meta.yaml b/recipes/bioconductor-celldex/meta.yaml index 36ae84f27c872..a02331aa0f1b5 100644 --- a/recipes/bioconductor-celldex/meta.yaml +++ b/recipes/bioconductor-celldex/meta.yaml @@ -1,53 +1,74 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "celldex" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides a collection of reference expression datasets with curated cell type labels, for use in procedures like automated annotation of single-cell data or deconvolution of bulk RNA-seq. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Index of Reference Cell Type Datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 62419c915beb91f7c228e1a125df68f8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-celldex", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, knitr, rmarkdown, BiocStyle, DT, ensembldb + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, knitr, rmarkdown, BiocStyle, DT, jsonvalidate, BiocManager, ensembldb requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-alabaster.matrix >=1.6.0,<1.7.0 + - bioconductor-alabaster.se >=1.6.0,<1.7.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-gypsum >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + - r-dbi + - r-jsonlite + - r-matrix + - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-alabaster.matrix >=1.6.0,<1.7.0 + - bioconductor-alabaster.se >=1.6.0,<1.7.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-gypsum >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + - r-dbi + - r-jsonlite + - r-matrix + - r-rsqlite - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: ba3dc1f475b673ee0303293d6d997194 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Reference Index for Cell Types' - description: 'Provides a collection of reference expression datasets with curated cell type labels, for use in procedures like automated annotation of single-cell data or deconvolution of bulk RNA-seq.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-celldex/post-link.sh b/recipes/bioconductor-celldex/post-link.sh index d36c9de2e3d47..9d3e945d9e5f7 100644 --- a/recipes/bioconductor-celldex/post-link.sh +++ b/recipes/bioconductor-celldex/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "celldex-1.12.0" +installBiocDataPackage.sh "celldex-1.16.0" diff --git a/recipes/bioconductor-cellid/meta.yaml b/recipes/bioconductor-cellid/meta.yaml index 7aff6e471d46e..c3c90b244282c 100644 --- a/recipes/bioconductor-cellid/meta.yaml +++ b/recipes/bioconductor-cellid/meta.yaml @@ -1,31 +1,39 @@ -{% set version = "1.10.1" %} +{% set version = "1.14.0" %} {% set name = "CelliD" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CelliD is a clustering-free multivariate statistical method for the robust extraction of per-cell gene signatures from single-cell RNA-seq. CelliD allows unbiased cell identity recognition across different donors, tissues-of-origin, model organisms and single-cell omics protocols. The package can also be used to explore functional pathways enrichment in single cell data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91ef83db3f348575f3b90cf4c3753806 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cellid", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat, tidyverse, ggpubr, destiny, ggrepel requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-fastmatch @@ -39,18 +47,19 @@ requirements: - r-rcpparmadillo - r-reticulate - r-rtsne - - 'r-seurat >=4.0.1' + - r-seurat >=4.0.1 - r-stringr - r-tictoc - r-umap - libblas - liblapack + run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-fastmatch @@ -64,21 +73,20 @@ requirements: - r-rcpparmadillo - r-reticulate - r-rtsne - - 'r-seurat >=4.0.1' + - r-seurat >=4.0.1 - r-stringr - r-tictoc - r-umap - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 4e1bf3f329f4b7d8459d632fa21c0a61 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis' - description: 'CelliD is a clustering-free multivariate statistical method for the robust extraction of per-cell gene signatures from single-cell RNA-seq. CelliD allows unbiased cell identity recognition across different donors, tissues-of-origin, model organisms and single-cell omics protocols. The package can also be used to explore functional pathways enrichment in single cell data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cellity/meta.yaml b/recipes/bioconductor-cellity/meta.yaml index 3f533b5866143..39e83d5d68130 100644 --- a/recipes/bioconductor-cellity/meta.yaml +++ b/recipes/bioconductor-cellity/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "cellity" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A support vector machine approach to identifying and filtering low quality cells from single-cell RNA-seq datasets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Quality Control for Single-Cell RNA-seq Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c6680442e176cef832fc19d82d49815a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cellity", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, caret, knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-base - r-e1071 - r-ggplot2 - r-mvoutlier - r-robustbase run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-base - r-e1071 - r-ggplot2 - r-mvoutlier - r-robustbase + +source: + md5: b1b85755cfcbf44ae791e0f294954c5c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Quality Control for Single-Cell RNA-seq Data' - description: 'A support vector machine approach to identifying and filtering low quality cells from single-cell RNA-seq datasets.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cellmapper/meta.yaml b/recipes/bioconductor-cellmapper/meta.yaml index 6cfb167524086..7cfd443e0f857 100644 --- a/recipes/bioconductor-cellmapper/meta.yaml +++ b/recipes/bioconductor-cellmapper/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "CellMapper" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ca94af55dbc55bb2bf40c69f4965b553 +about: + description: Infers cell type-specific expression based on co-expression similarity with known cell type marker genes. Can make accurate predictions using publicly available expression data, even when a cell type has not been isolated before. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Predict genes expressed selectively in specific cell types build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cellmapper", max_pin="x.x") }}' - noarch: generic +extra: + identifiers: + - biotools:cellmapper + parent_recipe: + name: bioconductor-cellmapper + path: recipes/bioconductor-cellmapper + version: 1.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub requirements: host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base +source: + md5: d058499d206f6f466386a4930bfca89e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Predict genes expressed selectively in specific cell types' - description: 'Infers cell type-specific expression based on co-expression similarity with known cell type marker genes. Can make accurate predictions using publicly available expression data, even when a cell type has not been isolated before.' -extra: - identifiers: - - biotools:cellmapper - parent_recipe: - name: bioconductor-cellmapper - path: recipes/bioconductor-cellmapper - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cellmapperdata/meta.yaml b/recipes/bioconductor-cellmapperdata/meta.yaml index 694aa257b25ef..771a0a7ae1365 100644 --- a/recipes/bioconductor-cellmapperdata/meta.yaml +++ b/recipes/bioconductor-cellmapperdata/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "CellMapperData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5db37729dd49f26b6cba9ff4aff80b1d +about: + description: Experiment data package. Contains microarray data from several large expression compendia that have been pre-processed for use with the CellMapper package. This pre-processed data is recommended for routine searches using the CellMapper package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Pre-processed data for use with the CellMapper package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cellmapperdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle requirements: host: - - 'bioconductor-cellmapper >=1.28.0,<1.29.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-cellmapper >=1.32.0,<1.33.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-cellmapper >=1.28.0,<1.29.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-cellmapper >=1.32.0,<1.33.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0ddd6a344cf219cebb22142890c1b2d3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Pre-processed data for use with the CellMapper package' - description: 'Experiment data package. Contains microarray data from several large expression compendia that have been pre-processed for use with the CellMapper package. This pre-processed data is recommended for routine searches using the CellMapper package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cellmapperdata/post-link.sh b/recipes/bioconductor-cellmapperdata/post-link.sh index a5db39ff29df7..2e8059fc93882 100644 --- a/recipes/bioconductor-cellmapperdata/post-link.sh +++ b/recipes/bioconductor-cellmapperdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cellmapperdata-1.28.0" +installBiocDataPackage.sh "cellmapperdata-1.32.0" diff --git a/recipes/bioconductor-cellmigration/meta.yaml b/recipes/bioconductor-cellmigration/meta.yaml index c4b413d5dc107..b85c16333ea41 100644 --- a/recipes/bioconductor-cellmigration/meta.yaml +++ b/recipes/bioconductor-cellmigration/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "cellmigRation" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Import TIFF images of fluorescently labeled cells, and track cell movements over time. Parallelization is supported for image processing and for fast computation of cell trajectories. In-depth analysis of cell trajectories is enabled by 15 trajectory analysis functions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Track Cells, Analyze Cell Trajectories and Compute Migration Statistics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61fc4a74a41e132fc3b760bc444ee5d4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cellmigration", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics, BiocManager, kableExtra, rgl requirements: host: @@ -47,13 +49,16 @@ requirements: - r-spatialtools - r-tiff - r-vioplot + +source: + md5: a27b199ad5e9a18cbcf97135a2c7c2ff + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Track Cells, Analyze Cell Trajectories and Compute Migration Statistics' - description: 'Import TIFF images of fluorescently labeled cells, and track cell movements over time. Parallelization is supported for image processing and for fast computation of cell trajectories. In-depth analysis of cell trajectories is enabled by 15 trajectory analysis functions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cellmixs/meta.yaml b/recipes/bioconductor-cellmixs/meta.yaml index fbf1f4f06dd59..b0cb32af7bd60 100644 --- a/recipes/bioconductor-cellmixs/meta.yaml +++ b/recipes/bioconductor-cellmixs/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "CellMixS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CellMixS provides metrics and functions to evaluate batch effects, data integration and batch effect correction in single cell trancriptome data with single cell resolution. Results can be visualized and summarised on different levels, e.g. on cell, celltype or dataset level. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Evaluate Cellspecific Mixing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67910c3dc01e01dc6be6ca3bb76d7794 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cellmixs", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cowplot - r-dplyr @@ -39,12 +41,12 @@ requirements: - r-tidyr - r-viridis run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cowplot - r-dplyr @@ -55,13 +57,16 @@ requirements: - r-purrr - r-tidyr - r-viridis + +source: + md5: 274b4331924cc46953bff81435ea5504 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Evaluate Cellspecific Mixing' - description: 'CellMixS provides metrics and functions to evaluate batch effects, data integration and batch effect correction in single cell trancriptome data with single cell resolution. Results can be visualized and summarised on different levels, e.g. on cell, celltype or dataset level.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cellnoptr/meta.yaml b/recipes/bioconductor-cellnoptr/meta.yaml index c4a20e64f1c8a..dee3c2b7a6241 100644 --- a/recipes/bioconductor-cellnoptr/meta.yaml +++ b/recipes/bioconductor-cellnoptr/meta.yaml @@ -1,30 +1,44 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "CellNOptR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 22ea1e446726e7b83f26f1f5f614d74f build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cellnoptr", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:cellnoptr + - doi:10.1186/1752-0509-6-133 + parent_recipe: + name: bioconductor-cellnoptr + path: recipes/bioconductor-cellnoptr + version: 1.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics, # SystemRequirements: Graphviz version >= 2.2 requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-ggplot2 - r-igraph @@ -35,11 +49,11 @@ requirements: - r-xml - libblas - liblapack - - 'graphviz >=2.2' + - graphviz >=2.2 run: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-ggplot2 - r-igraph @@ -48,25 +62,17 @@ requirements: - r-stringi - r-stringr - r-xml - - 'graphviz >=2.2' - build: - - {{ compiler('c') }} - - make + - graphviz >=2.2 + +source: + md5: 4e04f8ff6b1bd740c8550feb529780a5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data' - description: 'This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:cellnoptr - - doi:10.1186/1752-0509-6-133 - parent_recipe: - name: bioconductor-cellnoptr - path: recipes/bioconductor-cellnoptr - version: 1.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cellscape/meta.yaml b/recipes/bioconductor-cellscape/meta.yaml index 6e92e1f34a829..7c4577cc29783 100644 --- a/recipes/bioconductor-cellscape/meta.yaml +++ b/recipes/bioconductor-cellscape/meta.yaml @@ -1,50 +1,54 @@ -{% set version = "1.24.0" %} +{% set version = "1.30.0" %} {% set name = "cellscape" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: 'CellScape facilitates interactive browsing of single cell clonal evolution datasets. The tool requires two main inputs: (i) the genomic content of each single cell in the form of either copy number segments or targeted mutation values, and (ii) a single cell phylogeny. Phylogenetic formats can vary from dendrogram-like phylogenies with leaf nodes to evolutionary model-derived phylogenies with observed or latent internal nodes. The CellScape phylogeny is flexibly input as a table of source-target edges to support arbitrary representations, where each node may or may not have associated genomic data. The output of CellScape is an interactive interface displaying a single cell phylogeny and a cell-by-locus genomic heatmap representing the mutation status in each cell for each locus.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Explores single cell copy number profiles in the context of a single cell tree -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7df865c4752c43a3745b01f93654a00a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic + run_exports: '{{ pin_subpackage("bioconductor-cellscape", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - r-base - - 'r-dplyr >=0.4.3' - - 'r-gtools >=3.5.0' - - 'r-htmlwidgets >=0.5' - - 'r-jsonlite >=0.9.19' - - 'r-plyr >=1.8.3' - - 'r-reshape2 >=1.4.1' - - 'r-stringr >=1.0.0' + - r-dplyr >=0.4.3 + - r-gtools >=3.5.0 + - r-htmlwidgets >=0.5 + - r-jsonlite >=0.9.19 + - r-reshape2 >=1.4.1 + - r-stringr >=1.0.0 run: - r-base - - 'r-dplyr >=0.4.3' - - 'r-gtools >=3.5.0' - - 'r-htmlwidgets >=0.5' - - 'r-jsonlite >=0.9.19' - - 'r-plyr >=1.8.3' - - 'r-reshape2 >=1.4.1' - - 'r-stringr >=1.0.0' + - r-dplyr >=0.4.3 + - r-gtools >=3.5.0 + - r-htmlwidgets >=0.5 + - r-jsonlite >=0.9.19 + - r-reshape2 >=1.4.1 + - r-stringr >=1.0.0 + +source: + md5: 9dc56beae183f99fae4f3da0c4f63e3e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Explores single cell copy number profiles in the context of a single cell tree' - description: 'CellScape facilitates interactive browsing of single cell clonal evolution datasets. The tool requires two main inputs: (i) the genomic content of each single cell in the form of either copy number segments or targeted mutation values, and (ii) a single cell phylogeny. Phylogenetic formats can vary from dendrogram-like phylogenies with leaf nodes to evolutionary model-derived phylogenies with observed or latent internal nodes. The CellScape phylogeny is flexibly input as a table of source-target edges to support arbitrary representations, where each node may or may not have associated genomic data. The output of CellScape is an interactive interface displaying a single cell phylogeny and a cell-by-locus genomic heatmap representing the mutation status in each cell for each locus.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cellscore/meta.yaml b/recipes/bioconductor-cellscore/meta.yaml index 91e7ab9ca06b4..790aa0e5c9bf8 100644 --- a/recipes/bioconductor-cellscore/meta.yaml +++ b/recipes/bioconductor-cellscore/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "CellScore" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The CellScore package contains functions to evaluate the cell identity of a test sample, given a cell transition defined with a starting (donor) cell type and a desired target cell type. The evaluation is based upon a scoring system, which uses a set of standard samples of known cell types, as the reference set. The functions have been carried out on a large set of microarray data from one platform (Affymetrix Human Genome U133 Plus 2.0). In principle, the method could be applied to any expression dataset, provided that there are a sufficient number of standard samples and that the data are normalized. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Tool for Evaluation of Cell Identity from Transcription Profiles -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c842a56a0f5067b891a0ab7c9f9b1e21 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cellscore", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: hgu133plus2CellScore, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-gplots >=3.0.1' - - 'r-lsa >=0.73.1' - - 'r-rcolorbrewer >=1.1-2' - - 'r-squash >=1.0.8' + - r-gplots >=3.0.1 + - r-lsa >=0.73.1 + - r-rcolorbrewer >=1.1-2 + - r-squash >=1.0.8 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-gplots >=3.0.1' - - 'r-lsa >=0.73.1' - - 'r-rcolorbrewer >=1.1-2' - - 'r-squash >=1.0.8' + - r-gplots >=3.0.1 + - r-lsa >=0.73.1 + - r-rcolorbrewer >=1.1-2 + - r-squash >=1.0.8 + +source: + md5: 9c03f94a8230fff9efc0da6ef09c1513 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Tool for Evaluation of Cell Identity from Transcription Profiles' - description: 'The CellScore package contains functions to evaluate the cell identity of a test sample, given a cell transition defined with a starting (donor) cell type and a desired target cell type. The evaluation is based upon a scoring system, which uses a set of standard samples of known cell types, as the reference set. The functions have been carried out on a large set of microarray data from one platform (Affymetrix Human Genome U133 Plus 2.0). In principle, the method could be applied to any expression dataset, provided that there are a sufficient number of standard samples and that the data are normalized.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-celltrails/meta.yaml b/recipes/bioconductor-celltrails/meta.yaml index 81e50c10fe30a..c688a986a1768 100644 --- a/recipes/bioconductor-celltrails/meta.yaml +++ b/recipes/bioconductor-celltrails/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "CellTrails" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CellTrails is an unsupervised algorithm for the de novo chronological ordering, visualization and analysis of single-cell expression data. CellTrails makes use of a geometrically motivated concept of lower-dimensional manifold learning, which exhibits a multitude of virtues that counteract intrinsic noise of single cell data caused by drop-outs, technical variance, and redundancy of predictive variables. CellTrails enables the reconstruction of branching trajectories and provides an intuitive graphical representation of expression patterns along all branches simultaneously. It allows the user to define and infer the expression dynamics of individual and multiple pathways towards distinct phenotypes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Reconstruction, visualization and analysis of branching trajectories -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 87b23b653d772f9b436b655e5e8af5ae build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-celltrails", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cba - r-dendextend @@ -39,10 +40,10 @@ requirements: - r-reshape2 - r-rtsne run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cba - r-dendextend @@ -55,12 +56,16 @@ requirements: - r-mgcv - r-reshape2 - r-rtsne + +source: + md5: caa233600a24e15c19349f3b61f2b12d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Reconstruction, visualization and analysis of branching trajectories' - description: 'CellTrails is an unsupervised algorithm for the de novo chronological ordering, visualization and analysis of single-cell expression data. CellTrails makes use of a geometrically motivated concept of lower-dimensional manifold learning, which exhibits a multitude of virtues that counteract intrinsic noise of single cell data caused by drop-outs, technical variance, and redundancy of predictive variables. CellTrails enables the reconstruction of branching trajectories and provides an intuitive graphical representation of expression patterns along all branches simultaneously. It allows the user to define and infer the expression dynamics of individual and multiple pathways towards distinct phenotypes.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cellxgenedp/meta.yaml b/recipes/bioconductor-cellxgenedp/meta.yaml index 52a8b40eb76cb..ece19799e01d8 100644 --- a/recipes/bioconductor-cellxgenedp/meta.yaml +++ b/recipes/bioconductor-cellxgenedp/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.6.1" %} +{% set version = "1.10.0" %} {% set name = "cellxgenedp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The cellxgene data portal (https://cellxgene.cziscience.com/) provides a graphical user interface to collections of single-cell sequence data processed in standard ways to 'count matrix' summaries. The cellxgenedp package provides an alternative, R-based inteface, allowind data discovery, viewing, and downloading. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Discover and Access Single Cell Data Sets in the CELLxGENE Data Portal -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dc1730a545f49b0b8c14991289f29a6b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cellxgenedp", max_pin="x.x") }}' - noarch: generic -# Suggests: zellkonverter, SingleCellExperiment, HDF5Array, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), mockery + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: zellkonverter, SingleCellExperiment, HDF5Array, tidyr, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), mockery requirements: host: - r-base + - r-cli - r-curl - r-dplyr - r-dt - r-httr - - r-jsonlite - r-rjsoncons - r-shiny run: - r-base + - r-cli - r-curl - r-dplyr - r-dt - r-httr - - r-jsonlite - r-rjsoncons - r-shiny + +source: + md5: b0e6fa300e7472503bf39a8fba813510 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Discover and Access Single Cell Data Sets in the cellxgene Data Portal' - description: 'The cellxgene data portal (https://cellxgene.cziscience.com/) provides a graphical user interface to collections of single-cell sequence data processed in standard ways to ''count matrix'' summaries. The cellxgenedp package provides an alternative, R-based inteface, allowind data discovery, viewing, and downloading.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cemitool/meta.yaml b/recipes/bioconductor-cemitool/meta.yaml index 0b2b39b75ff26..ee0a81155d672 100644 --- a/recipes/bioconductor-cemitool/meta.yaml +++ b/recipes/bioconductor-cemitool/meta.yaml @@ -1,31 +1,34 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "CEMiTool" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The CEMiTool package unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Co-expression Modules identification Tool -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: df823e2602a3b994f889644e39e0eb8f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cemitool", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocManager requirements: + host: - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 - r-base - - 'r-data.table >=1.9.4' + - r-data.table >=1.9.4 - r-dplyr - r-dt - r-fastcluster @@ -48,11 +51,12 @@ requirements: - r-sna - r-stringr - r-wgcna + run: - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 - r-base - - 'r-data.table >=1.9.4' + - r-data.table >=1.9.4 - r-dplyr - r-dt - r-fastcluster @@ -75,13 +79,16 @@ requirements: - r-sna - r-stringr - r-wgcna + +source: + md5: 9f4c1e81bd0375316d1faa8fefdd090f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Co-expression Modules identification Tool' - description: 'The CEMiTool package unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-censcyt/meta.yaml b/recipes/bioconductor-censcyt/meta.yaml index 5ed00b98241a1..f3639b0c24973 100644 --- a/recipes/bioconductor-censcyt/meta.yaml +++ b/recipes/bioconductor-censcyt/meta.yaml @@ -1,32 +1,35 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "censcyt" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Methods for differential abundance analysis in high-dimensional cytometry data when a covariate is subject to right censoring (e.g. survival time) based on multiple imputation and generalized linear mixed models. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Differential abundance analysis with a right censored covariate in high-dimensional cytometry -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e5f2a60dcafc6d878e1e97e85768f078 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-censcyt", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2 requirements: + host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-diffcyt >=1.22.0,<1.23.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-diffcyt >=1.26.0,<1.27.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-broom.mixed - r-dirmult @@ -43,12 +46,13 @@ requirements: - r-survival - r-tibble - r-tidyr + run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-diffcyt >=1.22.0,<1.23.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-diffcyt >=1.26.0,<1.27.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-broom.mixed - r-dirmult @@ -65,13 +69,16 @@ requirements: - r-survival - r-tibble - r-tidyr + +source: + md5: 5aee854e0307906870749c17f9e558a3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Differential abundance analysis with a right censored covariate in high-dimensional cytometry' - description: 'Methods for differential abundance analysis in high-dimensional cytometry data when a covariate is subject to right censoring (e.g. survival time) based on multiple imputation and generalized linear mixed models.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cepo/build_failure.linux-64.yaml b/recipes/bioconductor-cepo/build_failure.linux-64.yaml deleted file mode 100644 index 5ac0014c0d22a..0000000000000 --- a/recipes/bioconductor-cepo/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: b904f129759930c0079c8f1858105b52b54ce300d7c837bd4c417f305be8d2d0 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - yaml: 0.2.5-h7f98852_2 conda-forge - yq: 3.2.3-pyhd8ed1ab_0 conda-forge - zlib: 1.2.13-hd590300_5 conda-forge - zstd: 1.5.5-hfc55251_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - [34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m - [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.1MB/s 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 2.4MB/s 0.0s - [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m - [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.0MB/s 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 2.9MB/s 0.0s - [?25h - ## Package Plan ## - - environment location: /opt/conda/conda-bld/bioconductor-cepo_1703278295981/_build_env - - - Source cache directory is: /opt/conda/conda-bld/src_cache - INFO:conda_build.source:Source cache directory is: /opt/conda/conda-bld/src_cache - Downloading source to cache: Cepo_1.8.0_9eee9f73ec.tar.gz - INFO:conda_build.source:Downloading source to cache: Cepo_1.8.0_9eee9f73ec.tar.gz - Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/Cepo_1.8.0.tar.gz - INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/Cepo_1.8.0.tar.gz - Success - INFO:conda_build.source:Success - Extracting download - source tree in: /opt/conda/conda-bld/bioconductor-cepo_1703278295981/work - export PREFIX=/opt/conda/conda-bld/bioconductor-cepo_1703278295981/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place - export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-cepo_1703278295981/_build_env - export SRC_DIR=/opt/conda/conda-bld/bioconductor-cepo_1703278295981/work - During startup - Warning message: - Setting LC_TIME failed, using "C" - * installing to library /opt/conda/conda-bld/bioconductor-cepo_1703278295981/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/R/library - * installing *source* package Cepo ... - ** using staged installation - ** R - ** data - ** inst - ** byte-compile and prepare package for lazy loading - During startup - Warning message: - Setting LC_TIME failed, using "C" - ** help - *** installing help indices - *** copying figures - ** building package indices - During startup - Warning message: - Setting LC_TIME failed, using "C" - ** installing vignettes - ** testing if installed package can be loaded from temporary location - During startup - Warning message: - Setting LC_TIME failed, using "C" - ** testing if installed package can be loaded from final location - During startup - Warning message: - Setting LC_TIME failed, using "C" - ** testing if installed package keeps a record of temporary installation path - * creating tarball - packaged installation of Cepo as Cepo_1.8.0_R_x86_64-conda-linux-gnu.tar.gz - * DONE (Cepo) - - Resource usage statistics from building bioconductor-cepo: - Process count: 6 - CPU time: Sys=0:00:02.4, User=0:00:20.2 - Memory: 733.9M - Disk usage: 6.8K - Time elapsed: 0:00:27.8 - - - Packaging bioconductor-cepo - INFO:conda_build.build:Packaging bioconductor-cepo - Packaging bioconductor-cepo-1.8.0-r43hdfd78af_0 - INFO:conda_build.build:Packaging bioconductor-cepo-1.8.0-r43hdfd78af_0 - number of files: 30 - Fixing permissions - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2358, in build - newly_built_packages = bundlers[pkg_type](output_d, m, env, stats) - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 1672, in bundle_conda - output['checksums'] = create_info_files(metadata, replacements, files, prefix=metadata.config.host_prefix) - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 1272, in create_info_files - copy_license(m) - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 762, in copy_license - generic_copy(m, "license", "license_file") - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 800, in generic_copy - raise ValueError( - ValueError: License file given in about/license_file (/opt/recipe/LICENSE) does not exist in source root dir or in recipe root dir (with meta.yaml) -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-cepo/meta.yaml b/recipes/bioconductor-cepo/meta.yaml index 3e7d32bc32c6d..8c344a1b95628 100644 --- a/recipes/bioconductor-cepo/meta.yaml +++ b/recipes/bioconductor-cepo/meta.yaml @@ -1,63 +1,70 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "Cepo" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Defining the identity of a cell is fundamental to understand the heterogeneity of cells to various environmental signals and perturbations. We present Cepo, a new method to explore cell identities from single-cell RNA-sequencing data using differential stability as a new metric to define cell identity genes. Cepo computes cell-type specific gene statistics pertaining to differential stable gene expression. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Cepo for the identification of differentially stable genes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9eee9f73ecd4d7dd782d14db0f60bd1f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cepo", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater, scMerge, fgsea, escape, pheatmap, patchwork + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater, scMerge, fgsea, escape, pheatmap requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 - r-patchwork + - r-purrr - r-reshape2 - r-rlang run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 - r-patchwork + - r-purrr - r-reshape2 - r-rlang + +source: + md5: 3af4bf60206bb2421a63d68009a361e0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Cepo for the identification of differentially stable genes' - description: 'Defining the identity of a cell is fundamental to understand the heterogeneity of cells to various environmental signals and perturbations. We present Cepo, a new method to explore cell identities from single-cell RNA-sequencing data using differential stability as a new metric to define cell identity genes. Cepo computes cell-type specific gene statistics pertaining to differential stable gene expression.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cernanetsim/meta.yaml b/recipes/bioconductor-cernanetsim/meta.yaml index 06a85239a44fc..6640b321fd8be 100644 --- a/recipes/bioconductor-cernanetsim/meta.yaml +++ b/recipes/bioconductor-cernanetsim/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "ceRNAnetsim" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package simulates regulations of ceRNA (Competing Endogenous) expression levels after a expression level change in one or more miRNA/mRNAs. The methodolgy adopted by the package has potential to incorparate any ceRNA (circRNA, lincRNA, etc.) into miRNA:target interaction network. The package basically distributes miRNA expression over available ceRNAs where each ceRNA attracks miRNAs proportional to its amount. But, the package can utilize multiple parameters that modify miRNA effect on its target (seed type, binding energy, binding location, etc.). The functions handle the given dataset as graph object and the processes progress via edge and node variables. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3.0) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a406a65a3e7bad478149f1587317a79 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cernanetsim", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, png, rmarkdown, testthat, covr requirements: host: @@ -47,13 +49,16 @@ requirements: - r-tibble - r-tidygraph - r-tidyr + +source: + md5: ca27a5d80639c67a55e91f91e49087b7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3.0)' - summary: 'Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)' - description: 'This package simulates regulations of ceRNA (Competing Endogenous) expression levels after a expression level change in one or more miRNA/mRNAs. The methodolgy adopted by the package has potential to incorparate any ceRNA (circRNA, lincRNA, etc.) into miRNA:target interaction network. The package basically distributes miRNA expression over available ceRNAs where each ceRNA attracks miRNAs proportional to its amount. But, the package can utilize multiple parameters that modify miRNA effect on its target (seed type, binding energy, binding location, etc.). The functions handle the given dataset as graph object and the processes progress via edge and node variables.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cetf/build_failure.osx-64.yaml b/recipes/bioconductor-cetf/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..532ce1f4daf6a --- /dev/null +++ b/recipes/bioconductor-cetf/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: baae5f5d924f179afafa7eea12a2ae8c1d3f8b5afea4d3ffddc9b7ffc03f6cbf # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cetf-1.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cetf-1.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cetf-1.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cetf-1.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cetf-1.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cetf-1.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cetf-1.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cetf-1.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cetf-1.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c PCIT.cpp -o PCIT.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L$PREFIX/lib/R/lib -Wl,-dead_strip_dylibs -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o CeTF.so PCIT.o RcppExports.o -L$PREFIX/lib/R/lib -lR -Wl,-framework -Wl,CoreFoundation + + Resource usage statistics from building bioconductor-cetf: + Process count: 6 + CPU time: Sys=0:00:02.9, User=0:00:33.9 + Memory: 1017.8M + Disk usage: 19.6K + Time elapsed: 0:00:51.3 + + + Packaging bioconductor-cetf + number of files: 31 + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2765, in build + newly_built_packages = bundlers[pkg_type]( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1874, in bundle_conda + files = post_process_files(metadata, initial_files) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1653, in post_process_files + post_build(m, new_files, build_python=python) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1759, in post_build + post_process_shared_lib(m, f, prefix_files, host_prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1635, in post_process_shared_lib + mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 477, in mk_relative_osx + names = macho.otool(path, prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 221, in otool + lines = check_output([otool, "-l", path], stderr=STDOUT).decode("utf-8") + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 421, in check_output + return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 526, in run + raise CalledProcessError(retcode, process.args, + subprocess.CalledProcessError: Command '['/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-cetf_1735946198160/_build_env/bin/llvm-otool', '-l', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-cetf_1735946198160/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/R/library/CeTF/libs/CeTF.so']' died with . +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-cetf/meta.yaml b/recipes/bioconductor-cetf/meta.yaml index a5a4a5da234e4..ce790eb69f999 100644 --- a/recipes/bioconductor-cetf/meta.yaml +++ b/recipes/bioconductor-cetf/meta.yaml @@ -1,33 +1,41 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "CeTF" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides the necessary functions for performing the Partial Correlation coefficient with Information Theory (PCIT) (Reverter and Chan 2008) and Regulatory Impact Factors (RIF) (Reverter et al. 2010) algorithm. The PCIT algorithm identifies meaningful correlations to define edges in a weighted network and can be applied to any correlation-based network including but not limited to gene co-expression networks, while the RIF algorithm identify critical Transcription Factors (TF) from gene expression data. These two algorithms when combined provide a very relevant layer of information for gene expression studies (Microarray, RNA-seq and single-cell RNA-seq data). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b79bf3680b81b7b6945eef89f6babfc1 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cetf", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat # SystemRequirements: libcurl4-openssl-dev, libxml2-dev, libssl-dev, gfortran, build-essential, libz-dev, zlib1g-dev requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-dplyr @@ -44,13 +52,14 @@ requirements: - r-rcpparmadillo - libblas - liblapack + run: - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-dplyr @@ -65,17 +74,16 @@ requirements: - r-network - r-rcpp - r-rcpparmadillo - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 665614295c8801ce022f8c75db2490dd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis' - description: 'This package provides the necessary functions for performing the Partial Correlation coefficient with Information Theory (PCIT) (Reverter and Chan 2008) and Regulatory Impact Factors (RIF) (Reverter et al. 2010) algorithm. The PCIT algorithm identifies meaningful correlations to define edges in a weighted network and can be applied to any correlation-based network including but not limited to gene co-expression networks, while the RIF algorithm identify critical Transcription Factors (TF) from gene expression data. These two algorithms when combined provide a very relevant layer of information for gene expression studies (Microarray, RNA-seq and single-cell RNA-seq data).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cexor/meta.yaml b/recipes/bioconductor-cexor/meta.yaml index 50afffdcd92be..583b34a487d37 100644 --- a/recipes/bioconductor-cexor/meta.yaml +++ b/recipes/bioconductor-cexor/meta.yaml @@ -1,63 +1,69 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "CexoR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Then, irreproducible discovery rate for overlapping peak-pairs across biological replicates is computed. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 | GPL-2 + file LICENSE + license_file: LICENSE + summary: An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 53f7febbb51a7f925322329e89a8d619 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cexor", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:cexor + - doi:10.14806/ej.21.0.837 + parent_recipe: + name: bioconductor-cexor + path: recipes/bioconductor-cexor + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-genomation >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomation >=1.38.0,<1.39.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-idr - r-rcolorbrewer run: - - 'bioconductor-genomation >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomation >=1.38.0,<1.39.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-idr - r-rcolorbrewer + +source: + md5: 9a65c1a3f37f4ce6e337db9f9f778cd2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Artistic-2.0 | GPL-2 + file LICENSE' - summary: 'An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates' - description: 'Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Then, irreproducible discovery rate for overlapping peak-pairs across biological replicates is computed.' - license_file: LICENSE -extra: - identifiers: - - biotools:cexor - - doi:10.14806/ej.21.0.837 - parent_recipe: - name: bioconductor-cexor - path: recipes/bioconductor-cexor - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cfassay/meta.yaml b/recipes/bioconductor-cfassay/meta.yaml index 96259a3f1aed1..b57a1b50a1e9d 100644 --- a/recipes/bioconductor-cfassay/meta.yaml +++ b/recipes/bioconductor-cfassay/meta.yaml @@ -1,38 +1,20 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "CFAssay" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 122c969248ffd92330d93a266db6cb3c +about: + description: The package provides functions for calculation of linear-quadratic cell survival curves and for ANOVA of experimental 2-way designs along with the colony formation assay. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Statistical analysis for the Colony Formation Assay build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cfassay", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Statistical analysis for the Colony Formation Assay' - description: 'The package provides functions for calculation of linear-quadratic cell survival curves and for ANOVA of experimental 2-way designs along with the colony formation assay.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' extra: identifiers: - biotools:cfassay @@ -41,4 +23,22 @@ extra: name: bioconductor-cfassay path: recipes/bioconductor-cfassay version: 1.16.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +requirements: + host: + - r-base + run: + - r-base +source: + md5: c001af8be528138722ca47779f942cab + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cfdnakit/meta.yaml b/recipes/bioconductor-cfdnakit/meta.yaml index b7735232ce60f..5695c4994aa37 100644 --- a/recipes/bioconductor-cfdnakit/meta.yaml +++ b/recipes/bioconductor-cfdnakit/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "cfdnakit" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides basic functions for analyzing shallow whole-genome sequencing (~0.3X or more) of cell-free DNA (cfDNA). The package basically extracts the length of cfDNA fragments and aids the vistualization of fragment-length information. The package also extract fragment-length information per non-overlapping fixed-sized bins and used it for calculating ctDNA estimation score (CES). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 967a84e96d20af4a0256e117afe272b7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cfdnakit", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, roxygen2, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-qdnaseq >=1.42.0,<1.43.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-ggplot2 @@ -36,26 +38,29 @@ requirements: - r-pscbs - r-rlang run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-qdnaseq >=1.42.0,<1.43.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-ggplot2 - r-magrittr - r-pscbs - r-rlang + +source: + md5: 5c2b321346a514f4aa3043afc450fd63 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)' - description: 'This package provides basic functions for analyzing shallow whole-genome sequencing (~0.3X or more) of cell-free DNA (cfDNA). The package basically extracts the length of cfDNA fragments and aids the vistualization of fragment-length information. The package also extract fragment-length information per non-overlapping fixed-sized bins and used it for calculating ctDNA estimation score (CES).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cfdnapro/meta.yaml b/recipes/bioconductor-cfdnapro/meta.yaml index 1b8813dc37295..0cdaef5c82c8e 100644 --- a/recipes/bioconductor-cfdnapro/meta.yaml +++ b/recipes/bioconductor-cfdnapro/meta.yaml @@ -1,71 +1,76 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "cfDNAPro" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: cfDNA fragments carry important features for building cancer sample classification ML models, such as fragment size, and fragment end motif etc. Analyzing and visualizing fragment size metrics, as well as other biological features in a curated, standardized, scalable, well-documented, and reproducible way might be time intensive. This package intends to resolve these problems and simplify the process. It offers two sets of functions for cfDNA feature characterization and visualization. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 377fb633e850fcef49fbe86f3c4d1505 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cfdnapro", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14), devtools (>= 2.3.0), BiocStyle, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome.hsapiens.ncbi.grch38 >=1.3.0,<1.4.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome.hsapiens.ncbi.grch38 >=1.3.0,<1.4.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - - 'r-dplyr >=0.8.3' - - 'r-ggplot2 >=3.2.1' - - 'r-magrittr >=1.5.0' - - 'r-quantmod >=0.4' - - 'r-rlang >=0.4.0' - - 'r-stringr >=1.4.0' + - r-dplyr >=0.8.3 + - r-ggplot2 >=3.2.1 + - r-magrittr >=1.5.0 + - r-quantmod >=0.4 + - r-rlang >=0.4.0 + - r-stringr >=1.4.0 - r-tibble run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome.hsapiens.ncbi.grch38 >=1.3.0,<1.4.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome.hsapiens.ncbi.grch38 >=1.3.0,<1.4.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - - 'r-dplyr >=0.8.3' - - 'r-ggplot2 >=3.2.1' - - 'r-magrittr >=1.5.0' - - 'r-quantmod >=0.4' - - 'r-rlang >=0.4.0' - - 'r-stringr >=1.4.0' + - r-dplyr >=0.8.3 + - r-ggplot2 >=3.2.1 + - r-magrittr >=1.5.0 + - r-quantmod >=0.4 + - r-rlang >=0.4.0 + - r-stringr >=1.4.0 - r-tibble + +source: + md5: ce0a562baef06d6c90bb8ef52872a7c1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA' - description: 'cfDNA fragments carry important features for building cancer sample classification ML models, such as fragment size, and fragment end motif etc. Analyzing and visualizing fragment size metrics, as well as other biological features in a curated, standardized, scalable, well-documented, and reproducible way might be time intensive. This package intends to resolve these problems and simplify the process. It offers two sets of functions for cfDNA feature characterization and visualization.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cftools/build_failure.osx-64.yaml b/recipes/bioconductor-cftools/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..2e64f4f24ac4d --- /dev/null +++ b/recipes/bioconductor-cftools/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a5421a61dedf4f346f8adf92b4c60cac4f704dbaabcc744666902738217c9a61 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-genomeinfodbdata [1.2.1|1.2.2] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-genomeinfodbdata [1.2.10|1.2.11] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.3|1.2.4] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.6|1.2.7] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-genomeinfodbdata 1.2.9 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-ucsc.utils >=1.2.0,<1.3.0 is not installable because it requires + r-base >=4.4,<4.5.0a0 , which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("clang==4.0.1=1"), MatchSpec("4.0.1==hcfea43d_1")} + Encountered problems while solving: + - nothing provides compiler-rt 4.0.1 hcfea43d_1 needed by clang-4.0.1-1 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-genomeinfodbdata >=1.2.0,<1.3.0 is installable with the potential options + bioconductor-genomeinfodbdata [1.2.0|1.2.1] would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-genomeinfodbdata [1.2.1|1.2.2] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-genomeinfodbdata [1.2.10|1.2.11] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.3|1.2.4] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.6|1.2.7] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-genomeinfodbdata 1.2.9 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-ucsc.utils >=1.2.0,<1.3.0 is not installable because it requires + r-base >=4.4,<4.5.0a0 , which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-cftools/meta.yaml b/recipes/bioconductor-cftools/meta.yaml index 7ad4099a140e5..3c048a125d085 100644 --- a/recipes/bioconductor-cftools/meta.yaml +++ b/recipes/bioconductor-cftools/meta.yaml @@ -1,29 +1,36 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "cfTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The cfTools R package provides methods for cell-free DNA (cfDNA) methylation data analysis to facilitate cfDNA-based studies. Given the methylation sequencing data of a cfDNA sample, for each cancer marker or tissue marker, we deconvolve the tumor-derived or tissue-specific reads from all reads falling in the marker region. Our read-based deconvolution algorithm exploits the pervasiveness of DNA methylation for signal enhancement, therefore can sensitively identify a trace amount of tumor-specific or tissue-specific cfDNA in plasma. cfTools provides functions for (1) cancer detection: sensitively detect tumor-derived cfDNA and estimate the tumor-derived cfDNA fraction (tumor burden); (2) tissue deconvolution: infer the tissue type composition and the cfDNA fraction of multiple tissue types for a plasma cfDNA sample. These functions can serve as foundations for more advanced cfDNA-based studies, including cancer diagnosis and disease monitoring.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Informatics Tools for Cell-Free DNA Study -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf0f03a9654984b3214bcadac889fc28 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cftools", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-cftoolsdata >=1.0.0,<1.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-cftoolsdata >=1.4.0,<1.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-bh - r-r.utils @@ -31,25 +38,23 @@ requirements: - libblas - liblapack run: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-cftoolsdata >=1.0.0,<1.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-cftoolsdata >=1.4.0,<1.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-bh - r-r.utils - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 26e50f626b640e5ce6d2b46d7646a520 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Informatics Tools for Cell-Free DNA Study' - description: 'The cfTools R package provides methods for cell-free DNA (cfDNA) methylation data analysis to facilitate cfDNA-based studies. Given the methylation sequencing data of a cfDNA sample, for each cancer marker or tissue marker, we deconvolve the tumor-derived or tissue-specific reads from all reads falling in the marker region. Our read-based deconvolution algorithm exploits the pervasiveness of DNA methylation for signal enhancement, therefore can sensitively identify a trace amount of tumor-specific or tissue-specific cfDNA in plasma. cfTools provides functions for (1) cancer detection: sensitively detect tumor-derived cfDNA and estimate the tumor-derived cfDNA fraction (tumor burden); (2) tissue deconvolution: infer the tissue type composition and the cfDNA fraction of multiple tissue types for a plasma cfDNA sample. These functions can serve as foundations for more advanced cfDNA-based studies, including cancer diagnosis and disease monitoring.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cftoolsdata/meta.yaml b/recipes/bioconductor-cftoolsdata/meta.yaml index 4150a2a029bdb..7ca2accd3e2ee 100644 --- a/recipes/bioconductor-cftoolsdata/meta.yaml +++ b/recipes/bioconductor-cftoolsdata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "cfToolsData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 00bbf328a45fb8731b3c7262b3521e0b +about: + description: The cfToolsData package supplies the data for the cfTools package. It contains two pre-trained deep neural network (DNN) models for the cfSort function. Additionally, it includes the shape parameters of beta distribution characterizing methylation markers associated with four tumor types for the CancerDetector function, as well as the parameters characterizing methylation markers specific to 29 primary human tissue types for the cfDeconvolve function. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: ExperimentHub data for the cfTools package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cftoolsdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b5b055a577c96c820f47fbfd28d25b35 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'ExperimentHub data for the cfTools package' - description: 'The cfToolsData package supplies the data for the cfTools package. It contains two pre-trained deep neural network (DNN) models for the cfSort function. Additionally, it includes the shape parameters of beta distribution characterizing methylation markers associated with four tumor types for the CancerDetector function, as well as the parameters characterizing methylation markers specific to 29 primary human tissue types for the cfDeconvolve function.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cftoolsdata/post-link.sh b/recipes/bioconductor-cftoolsdata/post-link.sh index 76ff4ad0b782b..576e3207f085b 100644 --- a/recipes/bioconductor-cftoolsdata/post-link.sh +++ b/recipes/bioconductor-cftoolsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cftoolsdata-1.0.0" +installBiocDataPackage.sh "cftoolsdata-1.4.0" diff --git a/recipes/bioconductor-cgen/meta.yaml b/recipes/bioconductor-cgen/meta.yaml index cc332a3a96b16..650d38bc46326 100644 --- a/recipes/bioconductor-cgen/meta.yaml +++ b/recipes/bioconductor-cgen/meta.yaml @@ -1,25 +1,31 @@ -{% set version = "3.38.0" %} +{% set version = "3.42.0" %} {% set name = "CGEN" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This is a package for analysis of case-control data in genetic epidemiology. It provides a set of statistical methods for evaluating gene-environment (or gene-genes) interactions under multiplicative and additive risk models, with or without assuming gene-environment (or gene-gene) independence in the underlying population. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + file LICENSE + license_file: LICENSE + summary: An R package for analysis of case-control studies in genetic epidemiology -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e62dd5874cfcaab65414fff648106633 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cgen", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: cluster requirements: + build: + - {{ compiler('c') }} + - {{ compiler('fortran') }} + - make host: - r-base - r-mvtnorm @@ -30,17 +36,16 @@ requirements: - r-base - r-mvtnorm - r-survival - build: - - {{ compiler('c') }} - - {{ compiler('fortran') }} - - make + +source: + md5: 2123e174ef8bc31e4d07896c434e5ae5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-2 + file LICENSE' - summary: 'An R package for analysis of case-control studies in genetic epidemiology' - description: 'This is a package for analysis of case-control data in genetic epidemiology. It provides a set of statistical methods for evaluating gene-environment (or gene-genes) interactions under multiplicative and additive risk models, with or without assuming gene-environment (or gene-gene) independence in the underlying population.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cghbase/meta.yaml b/recipes/bioconductor-cghbase/meta.yaml index 6a9c029f439be..c40712b027ff6 100644 --- a/recipes/bioconductor-cghbase/meta.yaml +++ b/recipes/bioconductor-cghbase/meta.yaml @@ -1,42 +1,22 @@ -{% set version = "1.62.0" %} +{% set version = "1.66.0" %} {% set name = "CGHbase" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Contains functions and classes that are needed by arrayCGH packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'CGHbase: Base functions and classes for arrayCGH data analysis.' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 806f73dc042c0bf46989606a4aa4dbe8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cghbase", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL - summary: 'CGHbase: Base functions and classes for arrayCGH data analysis.' - description: 'Contains functions and classes that are needed by arrayCGH packages.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:cghbase @@ -46,3 +26,29 @@ extra: path: recipes/bioconductor-cghbase version: 1.40.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-marray >=1.84.0,<1.85.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-marray >=1.84.0,<1.85.0 + - r-base + +source: + md5: 43e15239c0a4491b228ad2adb213426c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-cghcall/meta.yaml b/recipes/bioconductor-cghcall/meta.yaml index 0177f0dccb3bc..12c25f68bafc0 100644 --- a/recipes/bioconductor-cghcall/meta.yaml +++ b/recipes/bioconductor-cghcall/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "2.64.0" %} +{% set version = "2.68.0" %} {% set name = "CGHcall" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (http://www.gnu.org/copyleft/gpl.html) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Calling aberrations for array CGH tumor profiles. -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a43fd6ae1e6c288b98abd2b8824fed4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cghcall", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:cghcall + - doi:10.1093/bioinformatics/btm030 + parent_recipe: + name: bioconductor-cghcall + path: recipes/bioconductor-cghcall + version: 2.42.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-cghbase >=1.62.0,<1.63.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-cghbase >=1.66.0,<1.67.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-impute >=1.80.0,<1.81.0 - r-base - r-snowfall run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-cghbase >=1.62.0,<1.63.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-cghbase >=1.66.0,<1.67.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-impute >=1.80.0,<1.81.0 - r-base - r-snowfall + +source: + md5: ee70642467f3d4ce2b28679c6d6cb023 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (http://www.gnu.org/copyleft/gpl.html)' - summary: 'Calling aberrations for array CGH tumor profiles.' - description: 'Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:cghcall - - doi:10.1093/bioinformatics/btm030 - parent_recipe: - name: bioconductor-cghcall - path: recipes/bioconductor-cghcall - version: 2.42.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cghmcr/meta.yaml b/recipes/bioconductor-cghmcr/meta.yaml index ed85eb3edecc1..d4dee54445aed 100644 --- a/recipes/bioconductor-cghmcr/meta.yaml +++ b/recipes/bioconductor-cghmcr/meta.yaml @@ -1,46 +1,22 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "cghMCR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functions to identify genomic regions of interests based on segmented copy number data from multiple samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Find chromosome regions showing common gains/losses -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b3db4bfc3f23e690592a37414db360c9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cghmcr", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-cntools >=1.58.0,<1.59.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - r-base - run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-cntools >=1.58.0,<1.59.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Find chromosome regions showing common gains/losses' - description: 'This package provides functions to identify genomic regions of interests based on segmented copy number data from multiple samples.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + extra: identifiers: - biotools:cghmcr @@ -50,3 +26,33 @@ extra: path: recipes/bioconductor-cghmcr version: 1.38.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-cntools >=1.62.0,<1.63.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - r-base + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-cntools >=1.62.0,<1.63.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - r-base + +source: + md5: 99a36c5d74dba0d4b5118bd5da6c5ac2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-cghnormaliter/meta.yaml b/recipes/bioconductor-cghnormaliter/meta.yaml index b09f4d2b885e1..aabbd951ab6f4 100644 --- a/recipes/bioconductor-cghnormaliter/meta.yaml +++ b/recipes/bioconductor-cghnormaliter/meta.yaml @@ -1,44 +1,22 @@ -{% set version = "1.56.0" %} +{% set version = "1.60.0" %} {% set name = "CGHnormaliter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Normalization and centralization of array comparative genomic hybridization (aCGH) data. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Normalization of array CGH data with imbalanced aberrations. -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 948d3af66840226e7095e46d281df177 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cghnormaliter", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-cghbase >=1.62.0,<1.63.0' - - 'bioconductor-cghcall >=2.64.0,<2.65.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-cghbase >=1.62.0,<1.63.0' - - 'bioconductor-cghcall >=2.64.0,<2.65.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Normalization of array CGH data with imbalanced aberrations.' - description: 'Normalization and centralization of array comparative genomic hybridization (aCGH) data. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:cghnormaliter @@ -48,3 +26,31 @@ extra: path: recipes/bioconductor-cghnormaliter version: 1.34.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-cghbase >=1.66.0,<1.67.0 + - bioconductor-cghcall >=2.68.0,<2.69.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-cghbase >=1.66.0,<1.67.0 + - bioconductor-cghcall >=2.68.0,<2.69.0 + - r-base + +source: + md5: e648daccf420d2d4dfffb59525c5c52e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-cghregions/meta.yaml b/recipes/bioconductor-cghregions/meta.yaml index d10ed89bd1358..fafe4c79cd812 100644 --- a/recipes/bioconductor-cghregions/meta.yaml +++ b/recipes/bioconductor-cghregions/meta.yaml @@ -1,42 +1,22 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "CGHregions" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Dimension Reduction for Array CGH Data with Minimal Information Loss + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (http://www.gnu.org/copyleft/gpl.html) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Dimension Reduction for Array CGH Data with Minimal Information Loss. -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ec8f1bb5db1987f92932d29a31d74fe build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cghregions", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-cghbase >=1.62.0,<1.63.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-cghbase >=1.62.0,<1.63.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (http://www.gnu.org/copyleft/gpl.html)' - summary: 'Dimension Reduction for Array CGH Data with Minimal Information Loss.' - description: 'Dimension Reduction for Array CGH Data with Minimal Information Loss' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:cghregions @@ -46,3 +26,29 @@ extra: path: recipes/bioconductor-cghregions version: 1.38.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-cghbase >=1.66.0,<1.67.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-cghbase >=1.66.0,<1.67.0 + - r-base + +source: + md5: 319ffa72cf2aafb67b017b4478e77a1f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-champ/meta.yaml b/recipes/bioconductor-champ/meta.yaml index 554bc66264b07..9198818230fe3 100644 --- a/recipes/bioconductor-champ/meta.yaml +++ b/recipes/bioconductor-champ/meta.yaml @@ -1,47 +1,51 @@ -{% set version = "2.30.0" %} +{% set version = "2.36.0" %} {% set name = "ChAMP" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1ded54905a34c20745f367a5931683e0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic + run_exports: '{{ pin_subpackage("bioconductor-champ", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr,rmarkdown requirements: + host: - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-champdata >=2.32.0,<2.33.0' - - 'bioconductor-dmrcate >=2.14.0,<2.15.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-globaltest >=5.54.0,<5.55.0' - - 'bioconductor-goseq >=1.52.0,<1.53.0' - - 'bioconductor-illumina450probevariants.db >=1.36.0,<1.37.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-missmethyl >=1.34.0,<1.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' - - 'bioconductor-watermelon >=2.6.0,<2.7.0' + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-champdata >=2.38.0,<2.39.0 + - bioconductor-dmrcate >=3.2.0,<3.3.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-globaltest >=5.60.0,<5.61.0 + - bioconductor-goseq >=1.58.0,<1.59.0 + - bioconductor-illumina450probevariants.db >=1.42.0,<1.43.0 + - bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0 + - bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-marray >=1.84.0,<1.85.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-missmethyl >=1.40.0,<1.41.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-sva >=3.54.0,<3.55.0 + - bioconductor-watermelon >=2.12.0,<2.13.0 - r-base - r-combinat - r-dendextend @@ -52,7 +56,7 @@ requirements: - r-isva - r-kpmt - r-matrixstats - - 'r-plotly >=4.5.6' + - r-plotly >=4.5.6 - r-plyr - r-prettydoc - r-quadprog @@ -61,28 +65,29 @@ requirements: - r-rpmm - r-shiny - r-shinythemes + run: - - 'bioconductor-bumphunter >=1.42.0,<1.43.0' - - 'bioconductor-champdata >=2.32.0,<2.33.0' - - 'bioconductor-dmrcate >=2.14.0,<2.15.0' - - 'bioconductor-dnacopy >=1.74.0,<1.75.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-globaltest >=5.54.0,<5.55.0' - - 'bioconductor-goseq >=1.52.0,<1.53.0' - - 'bioconductor-illumina450probevariants.db >=1.36.0,<1.37.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-illuminaio >=0.42.0,<0.43.0' - - 'bioconductor-impute >=1.74.0,<1.75.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-missmethyl >=1.34.0,<1.35.0' - - 'bioconductor-preprocesscore >=1.62.0,<1.63.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' - - 'bioconductor-sva >=3.48.0,<3.49.0' - - 'bioconductor-watermelon >=2.6.0,<2.7.0' + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-champdata >=2.38.0,<2.39.0 + - bioconductor-dmrcate >=3.2.0,<3.3.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-globaltest >=5.60.0,<5.61.0 + - bioconductor-goseq >=1.58.0,<1.59.0 + - bioconductor-illumina450probevariants.db >=1.42.0,<1.43.0 + - bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0 + - bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-marray >=1.84.0,<1.85.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-missmethyl >=1.40.0,<1.41.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-sva >=3.54.0,<3.55.0 + - bioconductor-watermelon >=2.12.0,<2.13.0 - r-base - r-combinat - r-dendextend @@ -93,7 +98,7 @@ requirements: - r-isva - r-kpmt - r-matrixstats - - 'r-plotly >=4.5.6' + - r-plotly >=4.5.6 - r-plyr - r-prettydoc - r-quadprog @@ -102,13 +107,16 @@ requirements: - r-rpmm - r-shiny - r-shinythemes + +source: + md5: 238c0588da58c84d7c21ccb95de692b1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC' - description: 'The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-champdata/meta.yaml b/recipes/bioconductor-champdata/meta.yaml index 7e32b96919117..5992ef2fc2ccf 100644 --- a/recipes/bioconductor-champdata/meta.yaml +++ b/recipes/bioconductor-champdata/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "2.34.0" %} +{% set version = "2.38.0" %} {% set name = "ChAMPdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b12bfec01a1cfdd103bc0cb9bd44d4aa +about: + description: Provides datasets needed for ChAMP including a test dataset and blood controls for CNA analysis. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Data Packages for ChAMP package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-champdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 58ff4c4f195a082fcc386188d2c5dc81 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Data Packages for ChAMP package' - description: 'Provides datasets needed for ChAMP including a test dataset and blood controls for CNA analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-champdata/post-link.sh b/recipes/bioconductor-champdata/post-link.sh index af3862f5f24b1..b9a24e544b27e 100644 --- a/recipes/bioconductor-champdata/post-link.sh +++ b/recipes/bioconductor-champdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "champdata-2.34.0" +installBiocDataPackage.sh "champdata-2.38.0" diff --git a/recipes/bioconductor-chemminedrugs/meta.yaml b/recipes/bioconductor-chemminedrugs/meta.yaml index 97651c57e2bbe..4a97060b1763b 100644 --- a/recipes/bioconductor-chemminedrugs/meta.yaml +++ b/recipes/bioconductor-chemminedrugs/meta.yaml @@ -1,44 +1,44 @@ {% set version = "1.0.2" %} {% set name = "ChemmineDrugs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2a3646e5173e93080fb5b49564f5d545 +about: + description: An annotation package for use with ChemmineR. This package includes data from DrugBank. DUD data can be downloaded using the "DUD()" function in ChemmineR. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: DrugBank data set build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chemminedrugs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle,knitcitations,knitr requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-chemminer >=3.58.0,<3.59.0 - r-base - r-rsqlite run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-chemminer >=3.58.0,<3.59.0 - r-base - r-rsqlite - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2a3646e5173e93080fb5b49564f5d545 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'DrugBank data set' - description: 'An annotation package for use with ChemmineR. This package includes data from DrugBank. DUD data can be downloaded using the "DUD()" function in ChemmineR.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chemmineob/build.sh b/recipes/bioconductor-chemmineob/build.sh index ee892d72037fc..c1d13421f5f1e 100644 --- a/recipes/bioconductor-chemmineob/build.sh +++ b/recipes/bioconductor-chemmineob/build.sh @@ -4,8 +4,8 @@ grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION mkdir -p ~/.R echo -e "CC=$CC FC=$FC -CXX=$CXX -I$PREFIX/include/openbabel3 -I$PREFIX/include/eigen3 -L$PREFIX/lib +CXX=$CXX CXX98=$CXX CXX11=$CXX -CXX14=$CXX -I$PREFIX/include/openbabel3 -I$PREFIX/include/eigen3 -L$PREFIX/lib" > ~/.R/Makevars +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chemmineob/build_failure.linux-64.yaml b/recipes/bioconductor-chemmineob/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..395ac366a1f14 --- /dev/null +++ b/recipes/bioconductor-chemmineob/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: fd3c6e692f2e2f4c29c661cfbffe74f8cbd597984d34cfdd1d7c9d3e18d781d9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-chemmineob-1.44.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-chemmineob-1.44.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -std=c17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-chemmineob-1.44.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -std=c17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-chemmineob-1.44.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-chemmineob_1734317341151/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/R/library + * installing *source* package ChemmineOB ... + ** package ChemmineOB successfully unpacked and MD5 sums checked + ** using staged installation + checking for x86_64-conda-linux-gnu-pkg-config... no + checking for pkg-config... /usr/bin/pkg-config + checking pkg-config is at least version 0.9.0... yes + checking for OPENBABEL... no + checking for OPENBABEL... no + checking for x86_64-conda-linux-gnu-gcc... $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + checking whether the C compiler works... yes + checking for C compiler default output file name... a.out + checking for suffix of executables... + checking whether we are cross compiling... no + checking for suffix of object files... o + checking whether we are using the GNU C compiler... yes + checking whether $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc accepts -g... yes + checking for $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc option to accept ISO C89... none needed + checking how to run the C preprocessor... $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + configure: creating ./config.status + config.status: creating src/Makevars + ** libs + using C compiler: x86_64-conda-linux-gnu-c (conda-forge gcc 10.4.0-19) 10.4.0 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I"$PREFIX/lib/R/include" -DNDEBUG -I/usr/include/openbabel3 -I/usr/include/eigen3 -DUSE_BOOST -DHAVE_EIGEN -D_LIBCPP_ENABLE_CXX17_REMOVED_UNARY_BINARY_FUNCTION -I/usr/local/include/eigen3 -I/usr/local/include/openbabel3 -I'$PREFIX/lib/R/library/BH/include' -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/zlibbioc/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1732138515749/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ChemmineOB.cpp -o ChemmineOB.o + ChemmineOB.cpp:1569:10: fatal error: openbabel/obutil.h: No such file or directory + 1569 | #include + | ^~~~~~~~~~~~~~~~~~~~ + compilation terminated. + make: *** [/opt/conda/conda-bld/bioconductor-chemmineob_1734317341151/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/R/etc/Makeconf:204: ChemmineOB.o] Error 1 + ERROR: compilation failed for package ChemmineOB + * removing /opt/conda/conda-bld/bioconductor-chemmineob_1734317341151/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/R/library/ChemmineOB + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-chemmineob_1734317341151/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-chemmineob_1734317341151/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-netpathminer/build_failure.osx-64.yaml b/recipes/bioconductor-chemmineob/build_failure.osx-64.yaml similarity index 64% rename from recipes/bioconductor-netpathminer/build_failure.osx-64.yaml rename to recipes/bioconductor-chemmineob/build_failure.osx-64.yaml index 43131ce3691f9..19993b504ab35 100644 --- a/recipes/bioconductor-netpathminer/build_failure.osx-64.yaml +++ b/recipes/bioconductor-chemmineob/build_failure.osx-64.yaml @@ -1,43 +1,42 @@ -recipe_sha: 23cae448d4f716cd6f687090322e2d4d4738a88f5e747b922362e4635aa141fb # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: fd3c6e692f2e2f4c29c661cfbffe74f8cbd597984d34cfdd1d7c9d3e18d781d9 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-netpathminer_1717508392210/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-netpathminer_1717508392210/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-netpathminer_1717508392210/work +log: |- + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-chemmineob_1734406823378/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-chemmineob_1734406823378/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-chemmineob_1734406823378/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-chemmineob_1734406823378/work INFO: activate-gfortran_osx-64.sh made the following environmental changes: - DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-netpathminer-1.38.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments - DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-netpathminer-1.38.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-chemmineob-1.44.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-chemmineob-1.44.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-netpathminer-1.38.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-netpathminer-1.38.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-chemmineob-1.44.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-chemmineob-1.44.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as CC=x86_64-apple-darwin13.4.0-clang CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-netpathminer-1.38.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-chemmineob-1.44.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-netpathminer_1717508392210/work/conda_build.sh']' returned non-zero exit status 1. - CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-netpathminer-1.38.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-chemmineob-1.44.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool LD=x86_64-apple-darwin13.4.0-ld @@ -45,7 +44,7 @@ log: |2- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -54,7 +53,7 @@ log: |2- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -69,19 +68,26 @@ log: |2- INFO: activate_clangxx_osx-64.sh made the following environmental changes: CLANGXX=x86_64-apple-darwin13.4.0-clang CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-netpathminer-1.38.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-chemmineob-1.44.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-netpathminer-1.38.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-chemmineob-1.44.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix INFO: activate_clang_osx-64.sh made the following environmental changes: CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang INFO: activate_clangxx_osx-64.sh made the following environmental changes: CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + checking for x86_64-apple-darwin13.4.0-pkg-config... no + checking for pkg-config... /usr/local/bin/pkg-config + checking pkg-config is at least version 0.9.0... yes + checking for OPENBABEL... no + checking for OPENBABEL... no checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang checking whether the C compiler works... yes checking for C compiler default output file name... a.out @@ -91,14 +97,8 @@ log: |2- checking whether we are using the GNU C compiler... yes checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes checking for x86_64-apple-darwin13.4.0-clang option to accept ISO C89... none needed - checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang -E - checking for xmlParseFile in -lxml2... yes - checking for readSBML in -lsbml... no - untarring boost include tree... - SBML not found. - libXML2 found - checking for xml2-config... $BUILD_PREFIX/bin/xml2-config + checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang-cpp configure: creating ./config.status config.status: creating src/Makevars - x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -DHAVE_XML -I$BUILD_PREFIX/include/libxml2 -I$BUILD_PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1714471796105/work=/usr/local/src/conda/r-base-4.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c PathRanker.cpp -o PathRanker.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I/usr/include/openbabel3 -I/usr/include/eigen3 -DUSE_BOOST -DHAVE_EIGEN -D_LIBCPP_ENABLE_CXX17_REMOVED_UNARY_BINARY_FUNCTION -I/usr/local/include/eigen3 -I/usr/local/include/openbabel3 -I'$PREFIX/lib/R/library/BH/include' -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/zlibbioc/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734381577890/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ChemmineOB.cpp -o ChemmineOB.o # Last 100 lines of the build log. diff --git a/recipes/bioconductor-chemmineob/meta.yaml b/recipes/bioconductor-chemmineob/meta.yaml index e143fc83685a4..9e44ea2ecb051 100644 --- a/recipes/bioconductor-chemmineob/meta.yaml +++ b/recipes/bioconductor-chemmineob/meta.yaml @@ -1,58 +1,56 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "ChemmineOB" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ChemmineOB provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and more. ChemineOB aims to make a subset of these utilities available from within R. For non-developers, ChemineOB is primarily intended to be used from ChemmineR as an add-on package rather than used directly. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: R interface to a subset of OpenBabel functionalities -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5bd759ca398ffb70214a8076028bf0b2 - patches: - - patch build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chemmineob", max_pin="x.x") }}' -# Suggests: ChemmineR, BiocStyle, knitr, knitrBootstrap, BiocManager, rmarkdown,RUnit + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: ChemmineR, BiocStyle, knitr, knitrBootstrap, BiocManager, rmarkdown,RUnit,codetools # SystemRequirements: OpenBabel (>= 3.0.0) with headers (http://openbabel.org). Eigen3 with headers. requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-bh - - 'r-rcpp >=0.11.0' + - r-rcpp >=0.11.0 - libblas - liblapack - - openbabel >=3 - - eigen run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-bh - - 'r-rcpp >=0.11.0' - - openbabel >=3 - - eigen - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + - r-rcpp >=0.11.0 + +source: + md5: 4e3f20d57c46d1ff27d1ed273ef4d4c4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'R interface to a subset of OpenBabel functionalities' - description: 'ChemmineOB provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and more. ChemineOB aims to make a subset of these utilities available from within R. For non-developers, ChemineOB is primarily intended to be used from ChemmineR as an add-on package rather than used directly.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chemminer/meta.yaml b/recipes/bioconductor-chemminer/meta.yaml index bd56196b89d1a..d00db77f9ed15 100644 --- a/recipes/bioconductor-chemminer/meta.yaml +++ b/recipes/bioconductor-chemminer/meta.yaml @@ -1,28 +1,43 @@ -{% set version = "3.54.0" %} +{% set version = "3.58.0" %} {% set name = "ChemmineR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Cheminformatics Toolkit for R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8dd1886811bdc4ac23c24fad60a9b238 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chemminer", max_pin="x.x") }}' -# Suggests: RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs, png,rmarkdown, BiocManager,bibtex + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:chemminer + parent_recipe: + name: bioconductor-chemminer + path: recipes/bioconductor-chemminer + version: 3.32.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs, png,rmarkdown, BiocManager,bibtex,codetools # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-base64enc - r-bh @@ -33,7 +48,7 @@ requirements: - r-gridextra - r-jsonlite - r-png - - 'r-rcpp >=0.11.0' + - r-rcpp >=0.11.0 - r-rcurl - r-rjson - r-rsvg @@ -41,7 +56,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-base64enc - r-bh @@ -52,30 +67,21 @@ requirements: - r-gridextra - r-jsonlite - r-png - - 'r-rcpp >=0.11.0' + - r-rcpp >=0.11.0 - r-rcurl - r-rjson - r-rsvg - r-stringi - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 292f291e6708988f5f104a88e50d5260 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Cheminformatics Toolkit for R' - description: 'ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:chemminer - parent_recipe: - name: bioconductor-chemminer - path: recipes/bioconductor-chemminer - version: 3.32.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chetah/meta.yaml b/recipes/bioconductor-chetah/meta.yaml index 2dca0e66b8dbe..47a5d00f3ef31 100644 --- a/recipes/bioconductor-chetah/meta.yaml +++ b/recipes/bioconductor-chetah/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "CHETAH" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'CHETAH (CHaracterization of cEll Types Aided by Hierarchical classification) is an accurate, selective and fast scRNA-seq classifier. Classification is guided by a reference dataset, preferentially also a scRNA-seq dataset. By hierarchical clustering of the reference data, CHETAH creates a classification tree that enables a step-wise, top-to-bottom classification. Using a novel stopping rule, CHETAH classifies the input cells to the cell types of the references and to "intermediate types": more general classifications that ended in an intermediate node of the tree.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Fast and accurate scRNA-seq cell type identification -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a6b920a4a3f3f931acb3cd950c7a74c3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chetah", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, Matrix, testthat, vdiffr requirements: host: - - 'bioconductor-biodist >=1.74.0,<1.75.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biodist >=1.78.0,<1.79.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-corrplot - r-cowplot @@ -36,10 +38,10 @@ requirements: - r-reshape2 - r-shiny run: - - 'bioconductor-biodist >=1.74.0,<1.75.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biodist >=1.78.0,<1.79.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-corrplot - r-cowplot @@ -49,13 +51,16 @@ requirements: - r-plotly - r-reshape2 - r-shiny + +source: + md5: 963cda83ff567a407a28b5106b955d8d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Fast and accurate scRNA-seq cell type identification' - description: 'CHETAH (CHaracterization of cEll Types Aided by Hierarchical classification) is an accurate, selective and fast scRNA-seq classifier. Classification is guided by a reference dataset, preferentially also a scRNA-seq dataset. By hierarchical clustering of the reference data, CHETAH creates a classification tree that enables a step-wise, top-to-bottom classification. Using a novel stopping rule, CHETAH classifies the input cells to the cell types of the references and to "intermediate types": more general classifications that ended in an intermediate node of the tree.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chicago/meta.yaml b/recipes/bioconductor-chicago/meta.yaml index c5b8124eaea7d..ab7eb6a0a3c0a 100644 --- a/recipes/bioconductor-chicago/meta.yaml +++ b/recipes/bioconductor-chicago/meta.yaml @@ -1,24 +1,33 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "Chicago" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A pipeline for analysing Capture Hi-C data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'CHiCAGO: Capture Hi-C Analysis of Genomic Organization' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 854dccdecc3b0fc55c9146908bdeec27 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chicago", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:chicago + parent_recipe: + name: bioconductor-chicago + path: recipes/bioconductor-chicago + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub requirements: host: @@ -35,19 +44,16 @@ requirements: - r-hmisc - r-mass - r-matrixstats + +source: + md5: 02766cae10fde3a8843b053fb1612715 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'CHiCAGO: Capture Hi-C Analysis of Genomic Organization' - description: 'A pipeline for analysing Capture Hi-C data.' -extra: - identifiers: - - biotools:chicago - parent_recipe: - name: bioconductor-chicago - path: recipes/bioconductor-chicago - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chicken.db/meta.yaml b/recipes/bioconductor-chicken.db/meta.yaml index 3269f8ebba784..cdf75b9a8d6a3 100644 --- a/recipes/bioconductor-chicken.db/meta.yaml +++ b/recipes/bioconductor-chicken.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "chicken.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 512f887df339529d4883aad3f3eb6fb8 +about: + description: Affymetrix Affymetrix Chicken Array annotation data (chip chicken) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Chicken Array annotation data (chip chicken) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chicken.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.gg.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.gg.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.gg.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.gg.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 512f887df339529d4883aad3f3eb6fb8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Chicken Array annotation data (chip chicken)' - description: 'Affymetrix Affymetrix Chicken Array annotation data (chip chicken) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chicken.db0/meta.yaml b/recipes/bioconductor-chicken.db0/meta.yaml index f807a281abb07..865b1836c531c 100644 --- a/recipes/bioconductor-chicken.db0/meta.yaml +++ b/recipes/bioconductor-chicken.db0/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "chicken.db0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0f0c20a519a9490c0909b68ec67c206d +about: + description: Base annotation databases for chicken, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Level Annotation databases for chicken build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chicken.db0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 932b29dd4dc58ce6fc5ad5b48ff3ebe6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Level Annotation databases for chicken' - description: 'Base annotation databases for chicken, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chicken.db0/post-link.sh b/recipes/bioconductor-chicken.db0/post-link.sh index 23df0c7fd0516..7be920251cdee 100644 --- a/recipes/bioconductor-chicken.db0/post-link.sh +++ b/recipes/bioconductor-chicken.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chicken.db0-3.18.0" +installBiocDataPackage.sh "chicken.db0-3.20.0" diff --git a/recipes/bioconductor-chickencdf/meta.yaml b/recipes/bioconductor-chickencdf/meta.yaml index 3aa18b57b0fe8..a654b5366498b 100644 --- a/recipes/bioconductor-chickencdf/meta.yaml +++ b/recipes/bioconductor-chickencdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "chickencdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ab0097b4b7b6c4d94360feb84ab69972 +about: + description: A package containing an environment representing the Chicken.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: chickencdf build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chickencdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ab0097b4b7b6c4d94360feb84ab69972 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: chickencdf - description: 'A package containing an environment representing the Chicken.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chickenprobe/meta.yaml b/recipes/bioconductor-chickenprobe/meta.yaml index 21e051513a182..571904cfed792 100644 --- a/recipes/bioconductor-chickenprobe/meta.yaml +++ b/recipes/bioconductor-chickenprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "chickenprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b33599081ce1ba768ff7992e143c01d0 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Chicken\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type chicken build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chickenprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b33599081ce1ba768ff7992e143c01d0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type chicken' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Chicken\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chihaya/build_failure.linux-64.yaml b/recipes/bioconductor-chihaya/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..f69ad46583386 --- /dev/null +++ b/recipes/bioconductor-chihaya/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 24c61992c00ff869c0c3b9761a247995d24862c064be47dd6499a0d47db416f8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + export PREFIX=/opt/conda/conda-bld/bioconductor-chihaya_1734894680106/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-chihaya_1734894680106/_build_env + export SRC_DIR=/opt/conda/conda-bld/bioconductor-chihaya_1734894680106/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-chihaya-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-chihaya-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-chihaya-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-chihaya-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-chihaya_1734894680106/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library + * installing *source* package chihaya ... + ** package chihaya successfully unpacked and MD5 sums checked + ** using staged installation + ** libs + using C compiler: x86_64-conda-linux-gnu-c (conda-forge gcc 13.3.0-1) 13.3.0 + using C17 + x86_64-conda-linux-gnu-c -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I../inst/include -D USE_HDF5=1 -D USE_ZLIB=1 -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o + x86_64-conda-linux-gnu-c -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I../inst/include -D USE_HDF5=1 -D USE_ZLIB=1 -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c get_best_type.cpp -o get_best_type.o + x86_64-conda-linux-gnu-c -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I../inst/include -D USE_HDF5=1 -D USE_ZLIB=1 -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c h5exists.cpp -o h5exists.o + x86_64-conda-linux-gnu-c -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I../inst/include -D USE_HDF5=1 -D USE_ZLIB=1 -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c validate.cpp -o validate.o + x86_64-conda-linux-gnu-c -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I../inst/include -D USE_HDF5=1 -D USE_ZLIB=1 -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c write_scalar.cpp -o write_scalar.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + During startup - Warning message: + Setting LC_TIME failed, using "C" + x86_64-conda-linux-gnu-c -std=gnu17 -shared -L$PREFIX/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -o chihaya.so RcppExports.o get_best_type.o h5exists.o validate.o write_scalar.o $PREFIX/lib/R/library/Rhdf5lib/lib/libhdf5_cpp.a $PREFIX/lib/R/library/Rhdf5lib/lib/libhdf5.a -L$PREFIX/lib/R/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L$PREFIX/lib/R/lib -lR + /opt/conda/conda-bld/bioconductor-chihaya_1734894680106/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lz: No such file or directory + collect2: error: ld returned 1 exit status + make: *** [/opt/conda/conda-bld/bioconductor-chihaya_1734894680106/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/share/make/shlib.mk:10: chihaya.so] Error 1 + ERROR: compilation failed for package chihaya + * removing /opt/conda/conda-bld/bioconductor-chihaya_1734894680106/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/chihaya + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-chihaya_1734894680106/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-chihaya_1734894680106/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-chihaya/meta.yaml b/recipes/bioconductor-chihaya/meta.yaml index 48ed2f9721a59..b3fa47fd43b4f 100644 --- a/recipes/bioconductor-chihaya/meta.yaml +++ b/recipes/bioconductor-chihaya/meta.yaml @@ -1,55 +1,60 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "chihaya" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Saves the delayed operations of a DelayedArray to a HDF5 file. This enables efficient recovery of the DelayedArray's contents in other languages and analysis frameworks. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Save Delayed Operations to a HDF5 File -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fc8e24fa8ec373d01c938fbfe12c3b9a build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chihaya", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, S4Vectors, BiocSingular, ResidualMatrix, BiocStyle, testthat, rmarkdown, knitr # SystemRequirements: C++17, GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 - r-base - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 - r-base - r-matrix - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 4fbd85c67770e714a40d4632ed7b8938 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Save Delayed Operations to a HDF5 File' - description: 'Saves the delayed operations of a DelayedArray to a HDF5 file. This enables efficient recovery of the DelayedArray''s contents in other languages and analysis frameworks.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chimeraviz/meta.yaml b/recipes/bioconductor-chimeraviz/meta.yaml index e05583b96cc73..94e035ddb712f 100644 --- a/recipes/bioconductor-chimeraviz/meta.yaml +++ b/recipes/bioconductor-chimeraviz/meta.yaml @@ -1,44 +1,52 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "chimeraviz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: chimeraviz manages data from fusion gene finders and provides useful visualization tools. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Visualization tools for gene fusions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 30227635634cb01d8196626c86dabc26 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chimeraviz", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-chimeraviz + path: recipes/bioconductor-chimeraviz + version: 1.6.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, roxygen2, devtools, knitr, lintr # SystemRequirements: bowtie, samtools, and egrep are required for some functionalities requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-checkmate - r-data.table @@ -51,23 +59,24 @@ requirements: - r-rcolorbrewer - r-rmarkdown - bowtie2 + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-checkmate - r-data.table @@ -80,17 +89,16 @@ requirements: - r-rcolorbrewer - r-rmarkdown - bowtie2 + +source: + md5: 492ee5d90460b1ba46f1a1549fdf4527 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Visualization tools for gene fusions' - description: 'chimeraviz manages data from fusion gene finders and provides useful visualization tools.' -extra: - parent_recipe: - name: bioconductor-chimeraviz - path: recipes/bioconductor-chimeraviz - version: 1.6.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chimp.db0/meta.yaml b/recipes/bioconductor-chimp.db0/meta.yaml index ef4f45937f147..6c5bc87f019c8 100644 --- a/recipes/bioconductor-chimp.db0/meta.yaml +++ b/recipes/bioconductor-chimp.db0/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "chimp.db0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: afb020cefb808101626234257bf71f69 +about: + description: Base annotation databases for chimp, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Level Annotation databases for chimp build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chimp.db0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: da8f9a3b3ffa3ac728f373419ddd7775 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Level Annotation databases for chimp' - description: 'Base annotation databases for chimp, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chimp.db0/post-link.sh b/recipes/bioconductor-chimp.db0/post-link.sh index 1298c3be4a0f5..ce712f3d2c1a9 100644 --- a/recipes/bioconductor-chimp.db0/post-link.sh +++ b/recipes/bioconductor-chimp.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chimp.db0-3.18.0" +installBiocDataPackage.sh "chimp.db0-3.20.0" diff --git a/recipes/bioconductor-chimphumanbraindata/meta.yaml b/recipes/bioconductor-chimphumanbraindata/meta.yaml index 36d967d68a6ee..7438aa06472c1 100644 --- a/recipes/bioconductor-chimphumanbraindata/meta.yaml +++ b/recipes/bioconductor-chimphumanbraindata/meta.yaml @@ -1,46 +1,53 @@ -{% set version = "1.38.0" %} +{% set version = "1.44.0" %} {% set name = "ChimpHumanBrainData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: This data package contains chimp and human brain data extracted from the ArrayExpress accession E-AFMX-2. Both human and chimp RNAs were run on human hgu95av2 Affymetrix arrays. It is a useful dataset for tutorials. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + summary: Chimp and human brain data package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4c8b24136adf4492905f31e148674a5e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic + run_exports: '{{ pin_subpackage("bioconductor-chimphumanbraindata", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: hgu95av2cdf requirements: host: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - r-hexbin - r-statmod run: - - 'bioconductor-affy >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-qvalue >=2.32.0,<2.33.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - r-hexbin - r-statmod - curl - - bioconductor-data-packages >=20230706 + - bioconductor-data-packages >=20241103 + +source: + md5: a948b1af0f5549131860985eb9617116 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: MIT - summary: 'Chimp and human brain data package' - description: 'This data package contains chimp and human brain data extracted from the ArrayExpress accession E-AFMX-2. Both human and chimp RNAs were run on human hgu95av2 Affymetrix arrays. It is a useful dataset for tutorials.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chimphumanbraindata/post-link.sh b/recipes/bioconductor-chimphumanbraindata/post-link.sh index 5421c92870e80..a497fd9382e7c 100644 --- a/recipes/bioconductor-chimphumanbraindata/post-link.sh +++ b/recipes/bioconductor-chimphumanbraindata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chimphumanbraindata-1.38.0" +installBiocDataPackage.sh "chimphumanbraindata-1.44.0" diff --git a/recipes/bioconductor-chipanalyser/meta.yaml b/recipes/bioconductor-chipanalyser/meta.yaml index 252bfb7c4953c..748099cc726ff 100644 --- a/recipes/bioconductor-chipanalyser/meta.yaml +++ b/recipes/bioconductor-chipanalyser/meta.yaml @@ -1,59 +1,64 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "ChIPanalyser" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'ChIPanalyser is a package to predict and understand TF binding by utilizing a statistical thermodynamic model. The model incorporates 4 main factors thought to drive TF binding: Chromatin State, Binding energy, Number of bound molecules and a scaling factor modulating TF binding affinity. Taken together, ChIPanalyser produces ChIP-like profiles that closely mimic the patterns seens in real ChIP-seq data.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'ChIPanalyser: Predicting Transcription Factor Binding Sites' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 21d3f8fe9fc90548452dab5a3a8e5c0d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chipanalyser", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Dmelanogaster.UCSC.dm6,knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-biocmanager - r-rcolorbrewer - r-rcpproll - r-rocr run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-biocmanager - r-rcolorbrewer - r-rcpproll - r-rocr + +source: + md5: b2a33513fdb9d21f0397d5d99e16f4fc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'ChIPanalyser: Predicting Transcription Factor Binding Sites' - description: 'ChIPanalyser is a package to predict and understand TF binding by utilizing a statistical thermodynamic model. The model incorporates 4 main factors thought to drive TF binding: Chromatin State, Binding energy, Number of bound molecules and a scaling factor modulating TF binding affinity. Taken together, ChIPanalyser produces ChIP-like profiles that closely mimic the patterns seens in real ChIP-seq data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chipcomp/build_failure.linux-aarch64.yaml b/recipes/bioconductor-chipcomp/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..460bf47779e68 --- /dev/null +++ b/recipes/bioconductor-chipcomp/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 15637a57eced2c71733409e3d99f1723c021c0041b08528e10f807f6477a5358 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [31mbioconductor-bsgenome >=1.60.0,<1.61.0 [0m, which requires + [31mbioconductor-biostrings >=2.60.0,<2.61.0 [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.62.0,<1.63.0 [0m, which requires + [31mbioconductor-biostrings >=2.62.0,<2.63.0 [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.66.0,<1.67.0 [0m, which requires + [31mbioconductor-biostrings >=2.66.0,<2.67.0 [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.68.0,<1.69.0 [0m, which requires + [31mbioconductor-biostrings >=2.68.0,<2.69.0 [0m, which does not exist (perhaps a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec("bioconductor-bsgenome==1.52.0=r36_0"), MatchSpec(">=2.52.0,<2.53.0")} + Encountered problems while solving: + - nothing provides bioconductor-biostrings >=2.52.0,<2.53.0 needed by bioconductor-bsgenome-1.52.0-r36_0 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-biocgenerics >=0.52.0,<0.53.0 [0m is requested and can be installed; + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 [0m is not installable because there are no viable options + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.70.0,<1.71.0 [0m, which requires + [31mbioconductor-biocgenerics >=0.48.0,<0.49.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [31mr-base >=3.5.1,<3.5.2.0a0 [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.52.0,<1.53.0 [0m, which requires + [31mbioconductor-biostrings >=2.52.0,<2.53.0 [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.54.0,<1.55.0 [0m, which requires + [31mbioconductor-biostrings >=2.54.0,<2.55.0 [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.56.0,<1.57.0 [0m, which requires + [31mbioconductor-biostrings >=2.56.0,<2.57.0 [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.58.0,<1.59.0 [0m, which requires + [31mbioconductor-biostrings >=2.58.0,<2.59.0 [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.60.0,<1.61.0 [0m, which requires + [31mbioconductor-biostrings >=2.60.0,<2.61.0 [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.62.0,<1.63.0 [0m, which requires + [31mbioconductor-biostrings >=2.62.0,<2.63.0 [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.66.0,<1.67.0 [0m, which requires + [31mbioconductor-biostrings >=2.66.0,<2.67.0 [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.68.0,<1.69.0 [0m, which requires + [31mbioconductor-biostrings >=2.68.0,<2.69.0 [0m, which does not exist (perhaps a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-chipcomp/build_failure.osx-64.yaml b/recipes/bioconductor-chipcomp/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..ab59107aaa680 --- /dev/null +++ b/recipes/bioconductor-chipcomp/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 15637a57eced2c71733409e3d99f1723c021c0041b08528e10f807f6477a5358 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + bioconductor-biocgenerics >=0.28.0,<0.29.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.52.0 would require + bioconductor-biocgenerics >=0.30.0,<0.31.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.54.0 would require + bioconductor-biocgenerics >=0.32.0,<0.33.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.56.0 would require + bioconductor-biocgenerics >=0.34.0,<0.35.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.58.0 would require + bioconductor-biocgenerics >=0.36.0,<0.37.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.60.0 would require + bioconductor-biocgenerics >=0.38.0,<0.39.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.62.0 would require + bioconductor-biocgenerics >=0.40.0,<0.41.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome [1.66.1|1.66.3] would require + bioconductor-biocgenerics >=0.44.0,<0.45.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.68.0 would require + bioconductor-biocgenerics >=0.46.0,<0.47.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.70.1 would require + bioconductor-biocgenerics >=0.48.0,<0.49.0 , which conflicts with any installable versions previously reported; + r-base 3.3.2* , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0 would require + r 3.2.2* , which does not exist (perhaps a missing channel); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0 would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0 would require + bioconductor-bsgenome >=1.33.5 with the potential options + bioconductor-bsgenome 1.74.0, which can be installed (as previously explained); + bioconductor-bsgenome [1.38.0|1.42.0|1.44.2|1.46.0] conflicts with any installable versions previously reported; + bioconductor-bsgenome [1.40.1|1.42.0], which cannot be installed (as previously explained); + bioconductor-bsgenome 1.48.0, which cannot be installed (as previously explained); + bioconductor-bsgenome 1.50.0, which cannot be installed (as previously explained); + bioconductor-bsgenome 1.52.0, which cannot be installed (as previously explained); + bioconductor-bsgenome 1.54.0, which cannot be installed (as previously explained); + bioconductor-bsgenome 1.56.0, which cannot be installed (as previously explained); + bioconductor-bsgenome 1.58.0, which cannot be installed (as previously explained); + bioconductor-bsgenome 1.60.0, which cannot be installed (as previously explained); + bioconductor-bsgenome 1.62.0, which cannot be installed (as previously explained); + bioconductor-bsgenome [1.66.1|1.66.3], which cannot be installed (as previously explained); + bioconductor-bsgenome 1.68.0, which cannot be installed (as previously explained); + bioconductor-bsgenome 1.70.1, which cannot be installed (as previously explained); + r-base 3.4.1* , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0 would require + bioconductor-bsgenome >=1.48.0,<1.50.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0 would require + bioconductor-bsgenome >=1.50.0,<1.51.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0 would require + bioconductor-bsgenome >=1.52.0,<1.53.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0 would require + bioconductor-bsgenome >=1.54.0,<1.55.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3 would require + bioconductor-bsgenome >=1.56.0,<1.57.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3 would require + bioconductor-bsgenome >=1.58.0,<1.59.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3 would require + bioconductor-bsgenome >=1.60.0,<1.61.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3 would require + bioconductor-bsgenome >=1.62.0,<1.63.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3 would require + bioconductor-bsgenome >=1.66.0,<1.67.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3 would require + bioconductor-bsgenome >=1.68.0,<1.69.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3 would require + bioconductor-bsgenome >=1.70.0,<1.71.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0 is not installable because there are no viable options + bioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0 would require + r-base 3.3.2* , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0 would require + r 3.2.2* , which does not exist (perhaps a missing channel); + bioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0 would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0 would require + r-base 3.4.1* , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0 would require + bioconductor-bsgenome >=1.48.0,<1.50.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0 would require + bioconductor-bsgenome >=1.50.0,<1.51.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0 would require + bioconductor-bsgenome >=1.52.0,<1.53.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0 would require + bioconductor-bsgenome >=1.54.0,<1.55.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0 would require + bioconductor-bsgenome >=1.58.0,<1.59.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0 would require + bioconductor-bsgenome >=1.56.0,<1.57.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0 would require + bioconductor-bsgenome >=1.60.0,<1.61.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0 would require + bioconductor-bsgenome >=1.62.0,<1.63.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0 would require + bioconductor-bsgenome >=1.66.0,<1.67.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0 would require + bioconductor-bsgenome >=1.68.0,<1.69.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0 would require + bioconductor-bsgenome >=1.70.0,<1.71.0 , which cannot be installed (as previously explained); + bioconductor-rtracklayer >=1.66.0,<1.67.0 is installable and it requires + bioconductor-genomicalignments >=1.42.0,<1.43.0 , which requires + bioconductor-summarizedexperiment >=1.36.0,<1.37.0 , which requires + bioconductor-delayedarray >=0.32.0,<0.33.0 , which requires + bioconductor-sparsearray >=1.6.0,<1.7.0 , which requires + r-base >=4.4,<4.5.0a0 , which can be installed. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-chipcomp/meta.yaml b/recipes/bioconductor-chipcomp/meta.yaml index 8224feac33b41..912022d9933cf 100644 --- a/recipes/bioconductor-chipcomp/meta.yaml +++ b/recipes/bioconductor-chipcomp/meta.yaml @@ -1,70 +1,76 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "ChIPComp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Quantitative comparison of multiple ChIP-seq datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5294eab6ada6b66e52935843dd9acc6b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chipcomp", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:chipcomp + parent_recipe: + name: bioconductor-chipcomp + path: recipes/bioconductor-chipcomp + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle,RUnit requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: 0e6a6a35372ccce4c09783afd9e2b327 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'Quantitative comparison of multiple ChIP-seq datasets' - description: 'ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:chipcomp - parent_recipe: - name: bioconductor-chipcomp - path: recipes/bioconductor-chipcomp - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chipenrich.data/meta.yaml b/recipes/bioconductor-chipenrich.data/meta.yaml index d82da5fbc76ab..46522133c98f1 100644 --- a/recipes/bioconductor-chipenrich.data/meta.yaml +++ b/recipes/bioconductor-chipenrich.data/meta.yaml @@ -1,55 +1,60 @@ -{% set version = "2.26.0" %} +{% set version = "2.30.0" %} {% set name = "chipenrich.data" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Supporting data for the chipenrich package. Includes pre-defined gene sets, gene locus definitions, and mappability estimates. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Companion package to chipenrich -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4918da98125fee82afaeee84930051a8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chipenrich.data", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat, GO.db, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-readr run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-readr - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: a6575fd0dccbe1285e969003f25cbaea + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Companion package to chipenrich' - description: 'Supporting data for the chipenrich package. Includes pre-defined gene sets, gene locus definitions, and mappability estimates.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chipenrich.data/post-link.sh b/recipes/bioconductor-chipenrich.data/post-link.sh index 90df321032f62..2272e74eb71ee 100644 --- a/recipes/bioconductor-chipenrich.data/post-link.sh +++ b/recipes/bioconductor-chipenrich.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chipenrich.data-2.26.0" +installBiocDataPackage.sh "chipenrich.data-2.30.0" diff --git a/recipes/bioconductor-chipenrich/meta.yaml b/recipes/bioconductor-chipenrich/meta.yaml index 9f53939b6e86e..35cda907efbbd 100644 --- a/recipes/bioconductor-chipenrich/meta.yaml +++ b/recipes/bioconductor-chipenrich/meta.yaml @@ -1,40 +1,43 @@ -{% set version = "2.26.0" %} +{% set version = "2.30.0" %} {% set name = "chipenrich" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ChIP-Enrich and Poly-Enrich perform gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for confounding factors such as the length of genes, and the mappability of the sequence surrounding genes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Gene Set Enrichment For ChIP-seq Peak Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bb047e41aba2de216b8384322bb6a7aa build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chipenrich", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-chipenrich.data >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.dr.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-chipenrich.data >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.dm.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.dr.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-lattice - r-latticeextra @@ -43,20 +46,21 @@ requirements: - r-plyr - r-rms - r-stringr + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-chipenrich.data >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.dr.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-chipenrich.data >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.dm.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.dr.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-lattice - r-latticeextra @@ -65,13 +69,16 @@ requirements: - r-plyr - r-rms - r-stringr + +source: + md5: d052dc8804511f009ad18f135fec8466 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Gene Set Enrichment For ChIP-seq Peak Data' - description: 'ChIP-Enrich and Poly-Enrich perform gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for confounding factors such as the length of genes, and the mappability of the sequence surrounding genes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chipexoqual/meta.yaml b/recipes/bioconductor-chipexoqual/meta.yaml index eaacba6ed4f3c..9d651228274c1 100644 --- a/recipes/bioconductor-chipexoqual/meta.yaml +++ b/recipes/bioconductor-chipexoqual/meta.yaml @@ -1,71 +1,76 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "ChIPexoQual" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package with a quality control pipeline for ChIP-exo/nexus data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: ChIPexoQual -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c5fc56e308fbcfdf0630f2559c3556a3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chipexoqual", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biovizbase >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biovizbase >=1.54.0,<1.55.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-broom >=0.4' - - 'r-data.table >=1.9.6' - - 'r-dplyr >=0.5' - - 'r-ggplot2 >=1.0' - - 'r-hexbin >=1.27' - - 'r-rcolorbrewer >=1.1' + - r-broom >=0.4 + - r-data.table >=1.9.6 + - r-dplyr >=0.5 + - r-ggplot2 >=1.0 + - r-hexbin >=1.27 + - r-rcolorbrewer >=1.1 - r-rmarkdown - - 'r-scales >=0.4.0' - - 'r-viridis >=0.3' + - r-scales >=0.4.0 + - r-viridis >=0.3 run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biovizbase >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biovizbase >=1.54.0,<1.55.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-broom >=0.4' - - 'r-data.table >=1.9.6' - - 'r-dplyr >=0.5' - - 'r-ggplot2 >=1.0' - - 'r-hexbin >=1.27' - - 'r-rcolorbrewer >=1.1' + - r-broom >=0.4 + - r-data.table >=1.9.6 + - r-dplyr >=0.5 + - r-ggplot2 >=1.0 + - r-hexbin >=1.27 + - r-rcolorbrewer >=1.1 - r-rmarkdown - - 'r-scales >=0.4.0' - - 'r-viridis >=0.3' + - r-scales >=0.4.0 + - r-viridis >=0.3 + +source: + md5: d7331918c4816022cdb79723ff7a452a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: ChIPexoQual - description: 'Package with a quality control pipeline for ChIP-exo/nexus data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chipexoqualexample/meta.yaml b/recipes/bioconductor-chipexoqualexample/meta.yaml index b98adbff5998f..addc746bde315 100644 --- a/recipes/bioconductor-chipexoqualexample/meta.yaml +++ b/recipes/bioconductor-chipexoqualexample/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "ChIPexoQualExample" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ebb67a1848aa0e69557e795d236e24b +about: + description: Data for the ChIPexoQual package, consisting of (3) chromosome 1 aligned reads from a ChIP-exo experiment for FoxA1 in mouse liver cell lines aligned to the mm9 genome. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Example data for the ChIPexoQual package, which implements a quality control pipeline for ChIP-exo data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chipexoqualexample", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 25cceaa30a8a7a8fa3208c0357cab4db + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Example data for the ChIPexoQual package, which implements a quality control pipeline for ChIP-exo data' - description: 'Data for the ChIPexoQual package, consisting of (3) chromosome 1 aligned reads from a ChIP-exo experiment for FoxA1 in mouse liver cell lines aligned to the mm9 genome.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chipexoqualexample/post-link.sh b/recipes/bioconductor-chipexoqualexample/post-link.sh index 4cb76a02b9673..a9ed56eeb4416 100644 --- a/recipes/bioconductor-chipexoqualexample/post-link.sh +++ b/recipes/bioconductor-chipexoqualexample/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chipexoqualexample-1.26.0" +installBiocDataPackage.sh "chipexoqualexample-1.30.0" diff --git a/recipes/bioconductor-chippeakanno/meta.yaml b/recipes/bioconductor-chippeakanno/meta.yaml index 67ad871c9926b..001b403e05fb9 100644 --- a/recipes/bioconductor-chippeakanno/meta.yaml +++ b/recipes/bioconductor-chippeakanno/meta.yaml @@ -1,94 +1,116 @@ -{% set version = "3.36.0" %} +{% set version = "3.40.0" %} {% set name = "ChIPpeakAnno" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package encompasses a range of functions for identifying the closest gene, exon, miRNA, or custom features—such as highly conserved elements and user-supplied transcription factor binding sites. Additionally, users can retrieve sequences around the peaks and obtain enriched Gene Ontology (GO) or Pathway terms. In version 2.0.5 and beyond, new functionalities have been introduced. These include features for identifying peaks associated with bi-directional promoters along with summary statistics (peaksNearBDP), summarizing motif occurrences in peaks (summarizePatternInPeaks), and associating additional identifiers with annotated peaks or enrichedGO (addGeneIDs). The package integrates with various other packages such as biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest, and stat to enhance its analytical capabilities. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d9773752fca7bd32e512d3a5b72236e1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chippeakanno", max_pin="x.x") }}' - noarch: generic -# Suggests: AnnotationHub, BSgenome, limma, reactome.db, BiocManager, BiocStyle, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg38, DelayedArray, idr, seqinr, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR, knitr, rmarkdown, testthat, trackViewer, motifStack, OrganismDbi + +extra: + identifiers: + - biotools:chippeakanno + parent_recipe: + name: bioconductor-chippeakanno + path: recipes/bioconductor-chippeakanno + version: 3.14.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: AnnotationHub, BSgenome, limma, reactome.db, BiocManager, BiocStyle, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg38, DelayedArray, idr, seqinr, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, EnsDb.Hsapiens.v86, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR, knitr, rmarkdown, reshape2, testthat, trackViewer, motifStack, OrganismDbi, BiocFileCache requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-regioner >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-regioner >=1.38.0,<1.39.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-universalmotif >=1.24.0,<1.25.0 - r-base + - r-data.table - r-dbi - r-dplyr - r-ggplot2 - r-matrixstats + - r-scales + - r-stringr + - r-tibble + - r-tidyr - r-venndiagram + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-regioner >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-regioner >=1.38.0,<1.39.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-universalmotif >=1.24.0,<1.25.0 - r-base + - r-data.table - r-dbi - r-dplyr - r-ggplot2 - r-matrixstats + - r-scales + - r-stringr + - r-tibble + - r-tidyr - r-venndiagram + +source: + md5: 013df0ad1ca32d1c0f26de985a4d13e7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges' - description: 'The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting 2.0.5, new functions have been added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing the occurrence of motifs in peaks (summarizePatternInPeaks) and for adding other IDs to annotated peaks or enrichedGO (addGeneIDs). This package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:chippeakanno - parent_recipe: - name: bioconductor-chippeakanno - path: recipes/bioconductor-chippeakanno - version: 3.14.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chipqc/meta.yaml b/recipes/bioconductor-chipqc/meta.yaml index 2eb975a8384db..42d79c9facf5a 100644 --- a/recipes/bioconductor-chipqc/meta.yaml +++ b/recipes/bioconductor-chipqc/meta.yaml @@ -1,88 +1,96 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "ChIPQC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Quality metrics for ChIPseq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Quality metrics for ChIPseq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7437c357c5ba27db1f2721a50c15f13 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chipqc", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:chipqc + parent_recipe: + name: bioconductor-chipqc + path: recipes/bioconductor-chipqc + version: 1.16.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-chipseq >=1.52.0,<1.53.0' - - 'bioconductor-diffbind >=3.12.0,<3.13.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.celegans.ucsc.ce6.ensgene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene >=3.2.0,<3.3.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-chipseq >=1.56.0,<1.57.0 + - bioconductor-diffbind >=3.16.0,<3.17.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.celegans.ucsc.ce6.ensgene >=3.2.0,<3.3.0 + - bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0 + - bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene >=3.2.0,<3.3.0 - r-base - r-ggplot2 - r-gtools - r-nozzle.r1 - r-reshape2 + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-chipseq >=1.52.0,<1.53.0' - - 'bioconductor-diffbind >=3.12.0,<3.13.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.celegans.ucsc.ce6.ensgene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene >=3.2.0,<3.3.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-chipseq >=1.56.0,<1.57.0 + - bioconductor-diffbind >=3.16.0,<3.17.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.celegans.ucsc.ce6.ensgene >=3.2.0,<3.3.0 + - bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0 + - bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene >=3.2.0,<3.3.0 - r-base - r-ggplot2 - r-gtools - r-nozzle.r1 - r-reshape2 + +source: + md5: a312266b6573e840b379a867597fcc87 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Quality metrics for ChIPseq data' - description: 'Quality metrics for ChIPseq data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:chipqc - parent_recipe: - name: bioconductor-chipqc - path: recipes/bioconductor-chipqc - version: 1.16.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chipseeker/meta.yaml b/recipes/bioconductor-chipseeker/meta.yaml index fe501701d99dd..594f9c498efc9 100644 --- a/recipes/bioconductor-chipseeker/meta.yaml +++ b/recipes/bioconductor-chipseeker/meta.yaml @@ -1,37 +1,47 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "ChIPseeker" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: ChIPseeker for ChIP peak Annotation, Comparison, and Visualization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4e7b7622d7d9d1b3de7b8f9bf49eb8c4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chipseeker", max_pin="x.x") }}' - noarch: generic -# Suggests: clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram, ReactomePA, org.Hs.eg.db, knitr, rmarkdown, testthat, prettydoc + +extra: + identifiers: + - biotools:chipseeker + parent_recipe: + name: bioconductor-chipseeker + path: recipes/bioconductor-chipseeker + version: 1.16.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram, knitr, org.Hs.eg.db, prettydoc, ReactomePA, rmarkdown, testthat requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 - r-aplot - r-base - r-boot @@ -41,19 +51,23 @@ requirements: - r-gtools - r-magrittr - r-plotrix + - r-rcolorbrewer + - r-rlang + - r-scales - r-tibble - - r-yulab.utils + - r-yulab.utils >=0.1.5 + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 - r-aplot - r-base - r-boot @@ -63,21 +77,21 @@ requirements: - r-gtools - r-magrittr - r-plotrix + - r-rcolorbrewer + - r-rlang + - r-scales - r-tibble - - r-yulab.utils + - r-yulab.utils >=0.1.5 + +source: + md5: 08a999eb21b3ac5472a298493a5fd5c9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'ChIPseeker for ChIP peak Annotation, Comparison, and Visualization' - description: 'This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.' -extra: - identifiers: - - biotools:chipseeker - parent_recipe: - name: bioconductor-chipseeker - path: recipes/bioconductor-chipseeker - version: 1.16.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chipseq/meta.yaml b/recipes/bioconductor-chipseq/meta.yaml index 1ffd42a2f9cbc..07815c1e33f85 100644 --- a/recipes/bioconductor-chipseq/meta.yaml +++ b/recipes/bioconductor-chipseq/meta.yaml @@ -1,62 +1,68 @@ -{% set version = "1.52.0" %} +{% set version = "1.56.0" %} {% set name = "chipseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for helping process short read data for chipseq experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'chipseq: A package for analyzing chipseq data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5cf8ab297fc95d0a36b4359488c50358 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chipseq", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:chipseq + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-chipseq + path: recipes/bioconductor-chipseq + version: 1.30.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-lattice - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-lattice - build: - - {{ compiler('c') }} - - make + +source: + md5: 6888fd84f74773eed6b17375e94da8f0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'chipseq: A package for analyzing chipseq data' - description: 'Tools for helping process short read data for chipseq experiments.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:chipseq - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-chipseq - path: recipes/bioconductor-chipseq - version: 1.30.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chipseqdbdata/meta.yaml b/recipes/bioconductor-chipseqdbdata/meta.yaml index 51ec45e800c2a..482f718ec7a92 100644 --- a/recipes/bioconductor-chipseqdbdata/meta.yaml +++ b/recipes/bioconductor-chipseqdbdata/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "chipseqDBData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Sorted and indexed BAM files for ChIP-seq libraries, for use in the chipseqDB workflow. BAM indices are also included. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: CC BY 4.0 + summary: Data for the chipseqDB Workflow -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a6e50016d2d7c0cb085df2c4254b5f84 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chipseqdbdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 5ed0016ad2bd769e4959a755f78d9ed0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'CC BY 4.0' - summary: 'Data for the chipseqDB Workflow' - description: 'Sorted and indexed BAM files for ChIP-seq libraries, for use in the chipseqDB workflow. BAM indices are also included.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chipseqdbdata/post-link.sh b/recipes/bioconductor-chipseqdbdata/post-link.sh index 3d5e5956052e4..b37299ca9c5c1 100644 --- a/recipes/bioconductor-chipseqdbdata/post-link.sh +++ b/recipes/bioconductor-chipseqdbdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chipseqdbdata-1.18.0" +installBiocDataPackage.sh "chipseqdbdata-1.22.0" diff --git a/recipes/bioconductor-chipseqr/meta.yaml b/recipes/bioconductor-chipseqr/meta.yaml index 659339f6dc305..28f22f999f7f6 100644 --- a/recipes/bioconductor-chipseqr/meta.yaml +++ b/recipes/bioconductor-chipseqr/meta.yaml @@ -1,63 +1,69 @@ -{% set version = "1.56.0" %} +{% set version = "1.60.0" %} {% set name = "ChIPseqR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identifying Protein Binding Sites in High-Throughput Sequencing Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8696d6a783d26d8c6225ec4e3f294110 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chipseqr", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:chipseqr + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hilbertvis >=1.60.0,<1.61.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hilbertvis >=1.64.0,<1.65.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-fbasics - r-timsac - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hilbertvis >=1.60.0,<1.61.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hilbertvis >=1.64.0,<1.65.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-fbasics - r-timsac - build: - - {{ compiler('c') }} - - make + +source: + md5: beec6d66d14fb4359cf27bec202305f4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'Identifying Protein Binding Sites in High-Throughput Sequencing Data' - description: 'ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-chipsim/meta.yaml b/recipes/bioconductor-chipsim/meta.yaml index f81fdb6e13dc2..8ae7fee54fa2d 100644 --- a/recipes/bioconductor-chipsim/meta.yaml +++ b/recipes/bioconductor-chipsim/meta.yaml @@ -1,47 +1,22 @@ -{% set version = "1.56.0" %} +{% set version = "1.60.0" %} {% set name = "ChIPsim" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Simulation of ChIP-seq experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e6f1bd9d18f542abace1039c37ada326 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chipsim", max_pin="x.x") }}' - noarch: generic -# Suggests: actuar, zoo -requirements: - host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' - - r-base - run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Simulation of ChIP-seq experiments' - description: 'A general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:chipsim @@ -51,3 +26,34 @@ extra: path: recipes/bioconductor-chipsim version: 1.34.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: actuar, zoo +requirements: + host: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-xvector >=0.46.0,<0.47.0 + - r-base + run: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-xvector >=0.46.0,<0.47.0 + - r-base + +source: + md5: e01bef84f83bd67f61e93aa371af09be + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-chipxpress/meta.yaml b/recipes/bioconductor-chipxpress/meta.yaml index 3d91446325661..51588cfd6adcf 100644 --- a/recipes/bioconductor-chipxpress/meta.yaml +++ b/recipes/bioconductor-chipxpress/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "ChIPXpress" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ChIPXpress takes as input predicted TF bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL(>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bed7bbe60d0a51fb667cee9b01e4c407 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chipxpress", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:chipxpress + - doi:10.1186/1471-2105-14-188 + parent_recipe: + name: bioconductor-chipxpress + path: recipes/bioconductor-chipxpress + version: 1.24.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-chipxpressdata >=1.40.0,<1.41.0' - - 'bioconductor-frma >=1.54.0,<1.55.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-chipxpressdata >=1.44.0,<1.45.0 + - bioconductor-frma >=1.58.0,<1.59.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 - r-base - r-biganalytics - r-bigmemory run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-chipxpressdata >=1.40.0,<1.41.0' - - 'bioconductor-frma >=1.54.0,<1.55.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-chipxpressdata >=1.44.0,<1.45.0 + - bioconductor-frma >=1.58.0,<1.59.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 - r-base - r-biganalytics - r-bigmemory + +source: + md5: 51f755ef36fb5e7efc94527eed6d7c22 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL(>=2) - summary: 'ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles' - description: 'ChIPXpress takes as input predicted TF bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:chipxpress - - doi:10.1186/1471-2105-14-188 - parent_recipe: - name: bioconductor-chipxpress - path: recipes/bioconductor-chipxpress - version: 1.24.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chipxpressdata/meta.yaml b/recipes/bioconductor-chipxpressdata/meta.yaml index 5651a2b0910c0..eb291bb99d637 100644 --- a/recipes/bioconductor-chipxpressdata/meta.yaml +++ b/recipes/bioconductor-chipxpressdata/meta.yaml @@ -1,24 +1,32 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "ChIPXpressData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Contains pre-built mouse (GPL1261) and human (GPL570) database of gene expression profiles to be used for ChIPXpress ranking. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: ChIPXpress Pre-built Databases -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 029086a630df9533dedea4babd28f0d7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chipxpressdata", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-chipxpressdata + path: recipes/bioconductor-chipxpressdata + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -27,19 +35,17 @@ requirements: - r-base - r-bigmemory - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 2131b2a237b86063947c3526cfe53b6c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'ChIPXpress Pre-built Databases' - description: 'Contains pre-built mouse (GPL1261) and human (GPL570) database of gene expression profiles to be used for ChIPXpress ranking.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-chipxpressdata - path: recipes/bioconductor-chipxpressdata - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chipxpressdata/post-link.sh b/recipes/bioconductor-chipxpressdata/post-link.sh index 82a974e07cf07..7d5b14bac179f 100644 --- a/recipes/bioconductor-chipxpressdata/post-link.sh +++ b/recipes/bioconductor-chipxpressdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chipxpressdata-1.40.0" +installBiocDataPackage.sh "chipxpressdata-1.44.0" diff --git a/recipes/bioconductor-chopsticks/meta.yaml b/recipes/bioconductor-chopsticks/meta.yaml index 17c378b1395b0..94f1fca04d74a 100644 --- a/recipes/bioconductor-chopsticks/meta.yaml +++ b/recipes/bioconductor-chopsticks/meta.yaml @@ -1,25 +1,39 @@ -{% set version = "1.68.0" %} +{% set version = "1.72.0" %} {% set name = "chopsticks" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implements classes and methods for large-scale SNP association studies + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: The 'snp.matrix' and 'X.snp.matrix' Classes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b63b111068a6d42f7812010d1dc31047 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chopsticks", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:chopsticks + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-chopsticks + path: recipes/bioconductor-chopsticks + version: 1.46.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: hexbin requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - r-survival @@ -28,24 +42,16 @@ requirements: run: - r-base - r-survival - build: - - {{ compiler('c') }} - - make + +source: + md5: 7b4d334f96e86d4b6e90f5177710fe3e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'The ''snp.matrix'' and ''X.snp.matrix'' Classes' - description: 'Implements classes and methods for large-scale SNP association studies' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:chopsticks - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-chopsticks - path: recipes/bioconductor-chopsticks - version: 1.46.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chromdraw/meta.yaml b/recipes/bioconductor-chromdraw/meta.yaml index 8a7c74b6822e0..f45a094aac861 100644 --- a/recipes/bioconductor-chromdraw/meta.yaml +++ b/recipes/bioconductor-chromdraw/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "2.32.0" %} +{% set version = "2.36.0" %} {% set name = "chromDraw" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ChromDraw is a R package for drawing the schemes of karyotype(s) in the linear and circular fashion. It is possible to visualized cytogenetic marsk on the chromosomes. This tool has own input data format. Input data can be imported from the GenomicRanges data structure. This package can visualized the data in the BED file format. Here is requirement on to the first nine fields of the BED format. Output files format are *.eps and *.svg. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion. -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a2cb0f03cdde9853f68662b1783a2edb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chromdraw", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:chromdraw + parent_recipe: + name: bioconductor-chromdraw + path: recipes/bioconductor-chromdraw + version: 2.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # SystemRequirements: Rtools (>= 3.1) requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - - 'r-rcpp >=0.11.1' + - r-rcpp >=0.11.1 - libblas - liblapack run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - - 'r-rcpp >=0.11.1' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=0.11.1 + +source: + md5: 48a273a12b03d082dad3bdbeb300b01a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion.' - description: 'ChromDraw is a R package for drawing the schemes of karyotype(s) in the linear and circular fashion. It is possible to visualized cytogenetic marsk on the chromosomes. This tool has own input data format. Input data can be imported from the GenomicRanges data structure. This package can visualized the data in the BED file format. Here is requirement on to the first nine fields of the BED format. Output files format are *.eps and *.svg.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:chromdraw - parent_recipe: - name: bioconductor-chromdraw - path: recipes/bioconductor-chromdraw - version: 2.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chromheatmap/meta.yaml b/recipes/bioconductor-chromheatmap/meta.yaml index b777bfe8ed021..00f2a222b19f1 100644 --- a/recipes/bioconductor-chromheatmap/meta.yaml +++ b/recipes/bioconductor-chromheatmap/meta.yaml @@ -1,52 +1,21 @@ -{% set version = "1.56.0" %} +{% set version = "1.60.0" %} {% set name = "ChromHeatMap" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The ChromHeatMap package can be used to plot genome-wide data (e.g. expression, CGH, SNP) along each strand of a given chromosome as a heat map. The generated heat map can be used to interactively identify probes and genes of interest. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Heat map plotting by genome coordinate -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee08133257bb6da21d100e03fd720323 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chromheatmap", max_pin="x.x") }}' - noarch: generic -# Suggests: ALL, hgu95av2.db -requirements: - host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - r-base - run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Heat map plotting by genome coordinate' - description: 'The ChromHeatMap package can be used to plot genome-wide data (e.g. expression, CGH, SNP) along each strand of a given chromosome as a heat map. The generated heat map can be used to interactively identify probes and genes of interest.' + extra: identifiers: - biotools:chromheatmap @@ -56,3 +25,40 @@ extra: path: recipes/bioconductor-chromheatmap version: 1.34.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: ALL, hgu95av2.db +requirements: + host: + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - r-base + run: + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - r-base + +source: + md5: 37ff6e2451cb656481aa2f6fe75e5d98 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-chromhmmdata/meta.yaml b/recipes/bioconductor-chromhmmdata/meta.yaml index 0dabce226994f..21a4de2783a15 100644 --- a/recipes/bioconductor-chromhmmdata/meta.yaml +++ b/recipes/bioconductor-chromhmmdata/meta.yaml @@ -1,24 +1,23 @@ {% set version = "0.99.2" %} {% set name = "chromhmmData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eec85c20139b3d826f00264c7b28207c +about: + description: Annotation files of the formatted genomic annotation for ChromHMM. Three types of text files are included the chromosome sizes, region coordinates and anchors specifying the transcription start and end sites. The package includes data for two versions of the genome of humans and mice. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Chromosome Size, Coordinates and Anchor Files build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chromhmmdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: rmarkdown, knitr requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: eec85c20139b3d826f00264c7b28207c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: GPL-3 - summary: 'Chromosome Size, Coordinates and Anchor Files' - description: 'Annotation files of the formatted genomic annotation for ChromHMM. Three types of text files are included the chromosome sizes, region coordinates and anchors specifying the transcription start and end sites. The package includes data for two versions of the genome of humans and mice.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chromplot/meta.yaml b/recipes/bioconductor-chromplot/meta.yaml index 38a0a8e56bf16..964e1cf9b920f 100644 --- a/recipes/bioconductor-chromplot/meta.yaml +++ b/recipes/bioconductor-chromplot/meta.yaml @@ -1,43 +1,22 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "chromPlot" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package designed to visualize genomic data along the chromosomes, where the vertical chromosomes are sorted by number, with sex chromosomes at the end. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Global visualization tool of genomic data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a9a3e6d499f082698be0bf88f6432103 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chromplot", max_pin="x.x") }}' - noarch: generic -# Suggests: qtl, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene -requirements: - host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - r-base - run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Global visualization tool of genomic data' - description: 'Package designed to visualize genomic data along the chromosomes, where the vertical chromosomes are sorted by number, with sex chromosomes at the end.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:chromplot @@ -47,3 +26,30 @@ extra: path: recipes/bioconductor-chromplot version: 1.8.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: qtl, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene +requirements: + host: + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - r-base + run: + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - r-base + +source: + md5: fe85ead7e4f016176f9e7cd4ae47b58d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-chromscape/meta.yaml b/recipes/bioconductor-chromscape/meta.yaml index 06a80351408c4..2a039f2b8efb6 100644 --- a/recipes/bioconductor-chromscape/meta.yaml +++ b/recipes/bioconductor-chromscape/meta.yaml @@ -1,144 +1,258 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "ChromSCape" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'ChromSCape - Chromatin landscape profiling for Single Cells - is a ready-to-launch user-friendly Shiny Application for the analysis of single-cell epigenomics datasets (scChIP-seq, scATAC-seq, scCUT&Tag, ...) from aligned data to differential analysis & gene set enrichment analysis. It is highly interactive, enables users to save their analysis and covers a wide range of analytical steps: QC, preprocessing, filtering, batch correction, dimensionality reduction, vizualisation, clustering, differential analysis and gene set analysis.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Analysis of single-cell epigenomics datasets with a Shiny App -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a95b9c5be176f95c178ac7d3a1c26496 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chromscape", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, Signac, future, igraph, bluster, httr requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-batchelor >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + + - bioconductor-batchelor >=1.22.0,<1.23.0 + + - bioconductor-biocparallel >=1.40.0,<1.41.0 + + - bioconductor-consensusclusterplus >=1.70.0,<1.71.0 + + - bioconductor-delayedarray >=0.32.0,<0.33.0 + + - bioconductor-edger >=4.4.0,<4.5.0 + + - bioconductor-genomicranges >=1.58.0,<1.59.0 + + - bioconductor-iranges >=2.40.0,<2.41.0 + + - bioconductor-rsamtools >=2.22.0,<2.23.0 + + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + + - bioconductor-s4vectors >=0.44.0,<0.45.0 + + - bioconductor-scater >=1.34.0,<1.35.0 + + - bioconductor-scran >=1.34.0,<1.35.0 + + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-colorramps + - r-colourpicker + - r-coop + - r-dplyr + - r-dt + - r-forcats + - r-fs + - r-gggenes + - r-ggplot2 + - r-ggrepel + - r-gridextra + - r-irlba + - r-jsonlite + - r-kableextra + - r-matrix + - r-matrixtests + - r-msigdbr + - r-plotly + - r-qs + - r-qualv + - r-rcpp + - r-rlist + - r-rtsne + - r-shiny + - r-shinycssloaders + - r-shinydashboard + - r-shinydashboardplus + - r-shinyfiles + - r-shinyhelper + - r-shinyjs + - r-shinywidgets + - r-stringdist + - r-stringr + - r-tibble + - r-tidyr + - r-umap + - r-viridis + - libblas + - liblapack + run: - - 'bioconductor-batchelor >=1.18.0,<1.19.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + + - bioconductor-batchelor >=1.22.0,<1.23.0 + + - bioconductor-biocparallel >=1.40.0,<1.41.0 + + - bioconductor-consensusclusterplus >=1.70.0,<1.71.0 + + - bioconductor-delayedarray >=0.32.0,<0.33.0 + + - bioconductor-edger >=4.4.0,<4.5.0 + + - bioconductor-genomicranges >=1.58.0,<1.59.0 + + - bioconductor-iranges >=2.40.0,<2.41.0 + + - bioconductor-rsamtools >=2.22.0,<2.23.0 + + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + + - bioconductor-s4vectors >=0.44.0,<0.45.0 + + - bioconductor-scater >=1.34.0,<1.35.0 + + - bioconductor-scran >=1.34.0,<1.35.0 + + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-colorramps + - r-colourpicker + - r-coop + - r-dplyr + - r-dt + - r-forcats + - r-fs + - r-gggenes + - r-ggplot2 + - r-ggrepel + - r-gridextra + - r-irlba + - r-jsonlite + - r-kableextra + - r-matrix + - r-matrixtests + - r-msigdbr + - r-plotly + - r-qs + - r-qualv + - r-rcpp + - r-rlist + - r-rtsne + - r-shiny + - r-shinycssloaders + - r-shinydashboard + - r-shinydashboardplus + - r-shinyfiles + - r-shinyhelper + - r-shinyjs + - r-shinywidgets + - r-stringdist + - r-stringr + - r-tibble + - r-tidyr + - r-umap + - r-viridis - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 021eeaa20ddab5bc839d4344a8f9bd76 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Analysis of single-cell epigenomics datasets with a Shiny App' - description: 'ChromSCape - Chromatin landscape profiling for Single Cells - is a ready-to-launch user-friendly Shiny Application for the analysis of single-cell epigenomics datasets (scChIP-seq, scATAC-seq, scCUT&Tag, ...) from aligned data to differential analysis & gene set enrichment analysis. It is highly interactive, enables users to save their analysis and covers a wide range of analytical steps: QC, preprocessing, filtering, batch correction, dimensionality reduction, vizualisation, clustering, differential analysis and gene set analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chromstar/build_failure.osx-64.yaml b/recipes/bioconductor-chromstar/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..268d2997dbdce --- /dev/null +++ b/recipes/bioconductor-chromstar/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: a6c89c2c091aa7c041ede0e3d2d7b68d634b5472f11212878ec4d0e3217144f8 # The commit at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + 13:49:15 BIOCONDA INFO (ERR) /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-chromstar_1701870247148/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/include/omp.h:491:39: error: expected 'match' clause on 'omp declare variant' directive 13:49:15 BIOCONDA INFO (ERR) #pragma omp begin declare variant match(device={kind(nohost)}) +category: |- + compiler error diff --git a/recipes/bioconductor-chromstar/meta.yaml b/recipes/bioconductor-chromstar/meta.yaml index c2f40c3c66293..7d278be33b2ca 100644 --- a/recipes/bioconductor-chromstar/meta.yaml +++ b/recipes/bioconductor-chromstar/meta.yaml @@ -13,7 +13,6 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4288983863e4523b5c7e7750691e8987 build: - skip: True # [osx] number: 0 rpaths: - lib/R/lib/ diff --git a/recipes/bioconductor-chromstardata/meta.yaml b/recipes/bioconductor-chromstardata/meta.yaml index 1a844f8b5b766..583c95fed5de1 100644 --- a/recipes/bioconductor-chromstardata/meta.yaml +++ b/recipes/bioconductor-chromstardata/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "chromstaRData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7f4a965a6b5aa71874a5cca39046cabf +about: + description: ChIP-seq data for demonstration purposes in the chromstaR package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: ChIP-seq data for Demonstration Purposes build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chromstardata", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-chromstardata + path: recipes/bioconductor-chromstardata + version: 1.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6c16bfa6c7ff1f38da0154bd65f43d5a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'ChIP-seq data for Demonstration Purposes' - description: 'ChIP-seq data for demonstration purposes in the chromstaR package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-chromstardata - path: recipes/bioconductor-chromstardata - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chromstardata/post-link.sh b/recipes/bioconductor-chromstardata/post-link.sh index 3707fe3b3448a..c37f1d9c0a7d0 100644 --- a/recipes/bioconductor-chromstardata/post-link.sh +++ b/recipes/bioconductor-chromstardata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "chromstardata-1.28.0" +installBiocDataPackage.sh "chromstardata-1.32.0" diff --git a/recipes/bioconductor-chromvar/build_failure.osx-64.yaml b/recipes/bioconductor-chromvar/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..3dd80b2dfafa6 --- /dev/null +++ b/recipes/bioconductor-chromvar/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 82f6bf8d728b75703995077bc0bf222cf5ea33672b4a940795320b83a07e1f9b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: false # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Encountered problems while solving: + - nothing provides bioconductor-annotate >=1.84.0,<1.85.0 needed by bioconductor-cner-1.42.0-r44h2f393c0_0 + + Could not solve for environment specs + The following package could not be installed + bioconductor-tfbstools >=1.44.0,<1.45.0 is not installable because it requires + bioconductor-cner >=1.42.0,<1.43.0 , which requires + bioconductor-annotate >=1.84.0,<1.85.0 , which does not exist (perhaps a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-cner==1.42.0=r44h2f393c0_0"), MatchSpec(">=1.84.0,<1.85.0")} + Encountered problems while solving: + - nothing provides bioconductor-annotate >=1.84.0,<1.85.0 needed by bioconductor-cner-1.42.0-r44h2f393c0_0 + + Could not solve for environment specs + The following package could not be installed + bioconductor-tfbstools >=1.44.0,<1.45.0 is not installable because it requires + bioconductor-cner >=1.42.0,<1.43.0 , which requires + bioconductor-annotate >=1.84.0,<1.85.0 , which does not exist (perhaps a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-cner==1.42.0=r44h2f393c0_0"), MatchSpec(">=1.84.0,<1.85.0")} + Encountered problems while solving: + - nothing provides bioconductor-annotate >=1.84.0,<1.85.0 needed by bioconductor-cner-1.42.0-r44h2f393c0_0 + + Could not solve for environment specs + The following package could not be installed + bioconductor-tfbstools >=1.44.0,<1.45.0 is not installable because it requires + bioconductor-cner >=1.42.0,<1.43.0 , which requires + bioconductor-annotate >=1.84.0,<1.85.0 , which does not exist (perhaps a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-chromvar/meta.yaml b/recipes/bioconductor-chromvar/meta.yaml index dc83da4dba182..e1a50543171b8 100644 --- a/recipes/bioconductor-chromvar/meta.yaml +++ b/recipes/bioconductor-chromvar/meta.yaml @@ -1,38 +1,54 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "chromVAR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Determine variation in chromatin accessibility across sets of annotations or peaks. Designed primarily for single-cell or sparse chromatin accessibility data, e.g. from scATAC-seq or sparse bulk ATAC or DNAse-seq experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Chromatin Variation Across Regions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e42f2454ce39606fae40e85e437b47b build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chromvar", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:chromvar + parent_recipe: + name: bioconductor-chromvar + path: recipes/bioconductor-chromvar + version: 1.2.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr # SystemRequirements: C++11 requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tfbstools >=1.44.0,<1.45.0 - r-base - r-dt - r-ggplot2 @@ -47,18 +63,19 @@ requirements: - r-shiny - libblas - liblapack + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tfbstools >=1.44.0,<1.45.0 - r-base - r-dt - r-ggplot2 @@ -71,24 +88,16 @@ requirements: - r-rcpparmadillo - r-rtsne - r-shiny - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: aee29f3a8176335fd69099d868a7e461 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Chromatin Variation Across Regions' - description: 'Determine variation in chromatin accessibility across sets of annotations or peaks. Designed primarily for single-cell or sparse chromatin accessibility data, e.g. from scATAC-seq or sparse bulk ATAC or DNAse-seq experiments.' - license_file: LICENSE -extra: - identifiers: - - biotools:chromvar - parent_recipe: - name: bioconductor-chromvar - path: recipes/bioconductor-chromvar - version: 1.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-chronos/meta.yaml b/recipes/bioconductor-chronos/meta.yaml index d599b7baf0635..7ed882ddc58c2 100644 --- a/recipes/bioconductor-chronos/meta.yaml +++ b/recipes/bioconductor-chronos/meta.yaml @@ -1,31 +1,41 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "CHRONOS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package used for efficient unraveling of the inherent dynamic properties of pathways. MicroRNA-mediated subpathway topologies are extracted and evaluated by exploiting the temporal transition and the fold change activity of the linked genes/microRNAs. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7d2e5d9c89ea0163868d7b51bfd1c952 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-chronos", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:CHRONOS + parent_recipe: + name: bioconductor-chronos + path: recipes/bioconductor-chronos + version: 1.8.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, knitr, rmarkdown # SystemRequirements: Java version >= 1.7, Pandoc requirements: host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 - r-base - r-circlize - r-doparallel @@ -37,9 +47,9 @@ requirements: - r-xml - openjdk run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 - r-base - r-circlize - r-doparallel @@ -50,20 +60,16 @@ requirements: - r-rjava - r-xml - openjdk + +source: + md5: 8c5b64740c528b778512a95f1a87fb26 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis' - description: 'A package used for efficient unraveling of the inherent dynamic properties of pathways. MicroRNA-mediated subpathway topologies are extracted and evaluated by exploiting the temporal transition and the fold change activity of the linked genes/microRNAs.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:CHRONOS - parent_recipe: - name: bioconductor-chronos - path: recipes/bioconductor-chronos - version: 1.8.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cicero/meta.yaml b/recipes/bioconductor-cicero/meta.yaml index 3eccb1e945ea0..60e23f3f14f76 100644 --- a/recipes/bioconductor-cicero/meta.yaml +++ b/recipes/bioconductor-cicero/meta.yaml @@ -1,81 +1,88 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "cicero" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends monocle 2 for use in chromatin accessibility data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Predict cis-co-accessibility from single-cell chromatin accessibility data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 642264199171ac5b31a4f296c855dbb7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cicero", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationDbi (>= 1.38.2), knitr, markdown, rmarkdown, rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-monocle >=2.30.0,<2.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'r-assertthat >=0.2.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-monocle >=2.34.0,<2.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-assertthat >=0.2.0 - r-base - - 'r-data.table >=1.10.4' - - 'r-dplyr >=0.7.4' - - 'r-fnn >=1.1' - - 'r-ggplot2 >=2.2.1' - - 'r-glasso >=1.8' - - 'r-igraph >=1.1.0' - - 'r-matrix >=1.2-12' - - 'r-plyr >=1.8.4' - - 'r-reshape2 >=1.4.3' + - r-data.table >=1.10.4 + - r-dplyr >=0.7.4 + - r-fnn >=1.1 + - r-ggplot2 >=2.2.1 + - r-glasso >=1.8 + - r-igraph >=1.1.0 + - r-matrix >=1.2-12 + - r-plyr >=1.8.4 + - r-reshape2 >=1.4.3 - r-stringi - - 'r-stringr >=1.2.0' - - 'r-tibble >=1.4.2' + - r-stringr >=1.2.0 + - r-tibble >=1.4.2 - r-tidyr - - 'r-vgam >=1.0-5' + - r-vgam >=1.0-5 + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-monocle >=2.30.0,<2.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'r-assertthat >=0.2.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-monocle >=2.34.0,<2.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-assertthat >=0.2.0 - r-base - - 'r-data.table >=1.10.4' - - 'r-dplyr >=0.7.4' - - 'r-fnn >=1.1' - - 'r-ggplot2 >=2.2.1' - - 'r-glasso >=1.8' - - 'r-igraph >=1.1.0' - - 'r-matrix >=1.2-12' - - 'r-plyr >=1.8.4' - - 'r-reshape2 >=1.4.3' + - r-data.table >=1.10.4 + - r-dplyr >=0.7.4 + - r-fnn >=1.1 + - r-ggplot2 >=2.2.1 + - r-glasso >=1.8 + - r-igraph >=1.1.0 + - r-matrix >=1.2-12 + - r-plyr >=1.8.4 + - r-reshape2 >=1.4.3 - r-stringi - - 'r-stringr >=1.2.0' - - 'r-tibble >=1.4.2' + - r-stringr >=1.2.0 + - r-tibble >=1.4.2 - r-tidyr - - 'r-vgam >=1.0-5' + - r-vgam >=1.0-5 + +source: + md5: 672ea98f1fa212617161d78be0c3b72a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Predict cis-co-accessibility from single-cell chromatin accessibility data' - description: 'Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends monocle 2 for use in chromatin accessibility data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cimice/meta.yaml b/recipes/bioconductor-cimice/meta.yaml index fdd7c4e3115bd..b1ae60fbb2f9d 100644 --- a/recipes/bioconductor-cimice/meta.yaml +++ b/recipes/bioconductor-cimice/meta.yaml @@ -1,28 +1,29 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "CIMICE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CIMICE is a tool in the field of tumor phylogenetics and its goal is to build a Markov Chain (called Cancer Progression Markov Chain, CPMC) in order to model tumor subtypes evolution. The input of CIMICE is a Mutational Matrix, so a boolean matrix representing altered genes in a collection of samples. These samples are assumed to be obtained with single-cell DNA analysis techniques and the tool is specifically written to use the peculiarities of this data for the CMPC construction. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 510ab010752cd50654467583c6159ba1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cimice", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, webshot requirements: host: - - 'bioconductor-maftools >=2.18.0,<2.19.0' + - bioconductor-maftools >=2.22.0,<2.23.0 - r-assertthat - r-base - r-dplyr @@ -39,7 +40,7 @@ requirements: - r-tidyr - r-visnetwork run: - - 'bioconductor-maftools >=2.18.0,<2.19.0' + - bioconductor-maftools >=2.22.0,<2.23.0 - r-assertthat - r-base - r-dplyr @@ -55,12 +56,16 @@ requirements: - r-tidygraph - r-tidyr - r-visnetwork + +source: + md5: 1deec105e219fbd01d3a65d98e35be4d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution' - description: 'CIMICE is a tool in the field of tumor phylogenetics and its goal is to build a Markov Chain (called Cancer Progression Markov Chain, CPMC) in order to model tumor subtypes evolution. The input of CIMICE is a Mutational Matrix, so a boolean matrix representing altered genes in a collection of samples. These samples are assumed to be obtained with single-cell DNA analysis techniques and the tool is specifically written to use the peculiarities of this data for the CMPC construction.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cindex/meta.yaml b/recipes/bioconductor-cindex/meta.yaml index b76d809749c35..e1b11c56b90d7 100644 --- a/recipes/bioconductor-cindex/meta.yaml +++ b/recipes/bioconductor-cindex/meta.yaml @@ -1,31 +1,42 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "CINdex" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The CINdex package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar high throughput technologies. It calculates the chromosome instability (CIN) index that allows to quantitatively characterize genome-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Chromosome Instability Index -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2616a2a02791d966dbf54a54f2ad5f42 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cindex", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:cindex + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-cindex + path: recipes/bioconductor-cindex + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, ReactomePA, RUnit, BiocGenerics, AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db, biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods, Biostrings,Homo.sapiens, R.utils requirements: host: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-bitops - r-dplyr @@ -35,10 +46,10 @@ requirements: - r-som - r-stringr run: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-bitops - r-dplyr @@ -47,21 +58,16 @@ requirements: - r-png - r-som - r-stringr + +source: + md5: 926e80fe183c3a1ded29e9edd11462e3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Chromosome Instability Index' - description: 'The CINdex package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar high throughput technologies. It calculates the chromosome instability (CIN) index that allows to quantitatively characterize genome-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:cindex - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-cindex - path: recipes/bioconductor-cindex - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-circrnaprofiler/build_failure.linux-64.yaml b/recipes/bioconductor-circrnaprofiler/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..4382c384011cf --- /dev/null +++ b/recipes/bioconductor-circrnaprofiler/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 53804917aa18bf45f263617c38d7b1b7ac0b7bb6bad6605fc4f04ea8ed229bbc # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [31mbioconductor-delayedarray >=0.32.0,<0.33.0 [0m, which requires + [31mbioconductor-sparsearray >=1.6.0,<1.7.0 [0m, which requires + [31mr-base >=4.4,<4.5.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("3.2.2*"), MatchSpec("bioconductor-bsgenome.hsapiens.ucsc.hg19==1.4.0=r3.2.2_0")} + Encountered problems while solving: + - nothing provides r 3.2.2* needed by bioconductor-bsgenome.hsapiens.ucsc.hg19-1.4.0-r3.2.2_0 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 [0m is installable with the potential options + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [32mr-base 3.3.2* [0m, which can be installed; + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [31mr 3.2.2* [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [32mr-base 3.4.1* [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [32mbioconductor-bsgenome >=1.48.0,<1.50.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [32mbioconductor-bsgenome >=1.50.0,<1.51.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [32mbioconductor-bsgenome >=1.52.0,<1.53.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [32mbioconductor-bsgenome >=1.54.0,<1.55.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [32mbioconductor-bsgenome >=1.56.0,<1.57.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [32mbioconductor-bsgenome >=1.58.0,<1.59.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [32mbioconductor-bsgenome >=1.60.0,<1.61.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [32mbioconductor-bsgenome >=1.62.0,<1.63.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [32mbioconductor-bsgenome >=1.66.0,<1.67.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [32mbioconductor-bsgenome >=1.68.0,<1.69.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [32mbioconductor-bsgenome >=1.70.0,<1.71.0 [0m, which can be installed; + [31mbioconductor-bsgenome >=1.74.0,<1.75.0 [0m is not installable because it conflicts with any installable versions previously reported; + [31mbioconductor-deseq2 >=1.46.0,<1.47.0 [0m is not installable because it requires + [31mbioconductor-summarizedexperiment >=1.36.0,<1.37.0 [0m, which requires + [31mbioconductor-delayedarray >=0.32.0,<0.33.0 [0m, which requires + [31mbioconductor-sparsearray >=1.6.0,<1.7.0 [0m, which requires + [31mr-base >=4.4,<4.5.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-circrnaprofiler/meta.yaml b/recipes/bioconductor-circrnaprofiler/meta.yaml index 169e8226f8928..706c70120e4c8 100644 --- a/recipes/bioconductor-circrnaprofiler/meta.yaml +++ b/recipes/bioconductor-circrnaprofiler/meta.yaml @@ -1,40 +1,43 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "circRNAprofiler" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: R-based computational framework for a comprehensive in silico analysis of circRNAs. This computational framework allows to combine and analyze circRNAs previously detected by multiple publicly available annotation-based circRNA detection tools. It covers different aspects of circRNAs analysis from differential expression analysis, evolutionary conservation, biogenesis to functional analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5cd7f621f355f9d816938675dd550e2f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-circrnaprofiler", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, roxygen2, rmarkdown, devtools, gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocManager, requirements: + host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gwascat >=2.34.0,<2.35.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-universalmotif >=1.20.0,<1.21.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gwascat >=2.38.0,<2.39.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-universalmotif >=1.24.0,<1.25.0 - r-base - r-dplyr - r-ggplot2 @@ -46,20 +49,21 @@ requirements: - r-seqinr - r-stringi - r-stringr + run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gwascat >=2.34.0,<2.35.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-universalmotif >=1.20.0,<1.21.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gwascat >=2.38.0,<2.39.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-universalmotif >=1.24.0,<1.25.0 - r-base - r-dplyr - r-ggplot2 @@ -71,13 +75,16 @@ requirements: - r-seqinr - r-stringi - r-stringr + +source: + md5: 9471f99814829513ad417f85798f08ff + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs' - description: 'R-based computational framework for a comprehensive in silico analysis of circRNAs. This computational framework allows to combine and analyze circRNAs previously detected by multiple publicly available annotation-based circRNA detection tools. It covers different aspects of circRNAs analysis from differential expression analysis, evolutionary conservation, biogenesis to functional analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-circseqaligntk/build_failure.linux-64.yaml b/recipes/bioconductor-circseqaligntk/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..13e2c92942842 --- /dev/null +++ b/recipes/bioconductor-circseqaligntk/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 228ef1fbc80dfe9d51471c428d1147a08a2ea82961eab8980a1f95ae2b0a6d65 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rbowtie2[version='>=2.12.0,<2.13.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rbowtie2 >=2.12.0,<2.13.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rbowtie2 >=2.12.0,<2.13.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rbowtie2[version='>=2.12.0,<2.13.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rbowtie2 >=2.12.0,<2.13.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rbowtie2 >=2.12.0,<2.13.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rbowtie2[version='>=2.12.0,<2.13.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rbowtie2 >=2.12.0,<2.13.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rbowtie2 >=2.12.0,<2.13.0 [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-circseqaligntk/meta.yaml b/recipes/bioconductor-circseqaligntk/meta.yaml index 1552ea1595ddc..31bb49ecd9989 100644 --- a/recipes/bioconductor-circseqaligntk/meta.yaml +++ b/recipes/bioconductor-circseqaligntk/meta.yaml @@ -1,63 +1,82 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "CircSeqAlignTk" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CircSeqAlignTk is designed for end-to-end RNA-Seq data analysis of circular genome sequences, from alignment to visualization. It mainly targets viroids which are composed of 246-401 nt circular RNAs. In addition, CircSeqAlignTk implements a tidy interface to generate synthetic sequencing data that mimic real RNA-Seq data, allowing developers to evaluate the performance of alignment tools and workflows. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: A toolkit for end-to-end analysis of RNA-seq data for circular genomes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2c3b93fca2c2974a45af093edf7d9558 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-circseqaligntk", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, testthat, R.utils, BiocStyle + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' - - 'bioconductor-rhisat2 >=1.18.0,<1.19.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rbowtie2 >=2.12.0,<2.13.0 + - bioconductor-rhisat2 >=1.22.0,<1.23.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-dplyr - r-ggplot2 + - r-htmltools - r-magrittr + - r-plotly + - r-r.utils - r-rlang + - r-shiny + - r-shinyfiles + - r-shinyjs - r-tidyr + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' - - 'bioconductor-rhisat2 >=1.18.0,<1.19.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rbowtie2 >=2.12.0,<2.13.0 + - bioconductor-rhisat2 >=1.22.0,<1.23.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-dplyr - r-ggplot2 + - r-htmltools - r-magrittr + - r-plotly + - r-r.utils - r-rlang + - r-shiny + - r-shinyfiles + - r-shinyjs - r-tidyr + +source: + md5: b005b0ba95eb5f7eeddb32b35aae2101 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'A toolkit for end-to-end analysis of RNA-seq data for circular genomes' - description: 'CircSeqAlignTk is designed for end-to-end RNA-Seq data analysis of circular genome sequences, from alignment to visualization. It mainly targets viroids which are composed of 246-401 nt circular RNAs. In addition, CircSeqAlignTk implements a tidy interface to generate synthetic sequencing data that mimic real RNA-Seq data, allowing developers to evaluate the performance of alignment tools and workflows.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cispath/meta.yaml b/recipes/bioconductor-cispath/meta.yaml index cc4f2f6708169..9566b2520bcb5 100644 --- a/recipes/bioconductor-cispath/meta.yaml +++ b/recipes/bioconductor-cispath/meta.yaml @@ -1,49 +1,55 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "cisPath" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: cisPath is an R package that uses web browsers to visualize and manage protein-protein interaction networks. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Visualization and management of the protein-protein interaction networks. -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 958a35281b9aa98b2d5c3a5c4e9c8824 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cispath", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:cispath + - doi:10.1186/1752-0509-9-s1-s1 + parent_recipe: + name: bioconductor-cispath + path: recipes/bioconductor-cispath + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 85e7b9da3b42679a1b3b3cb45956e5d0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Visualization and management of the protein-protein interaction networks.' - description: 'cisPath is an R package that uses web browsers to visualize and manage protein-protein interaction networks.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:cispath - - doi:10.1186/1752-0509-9-s1-s1 - parent_recipe: - name: bioconductor-cispath - path: recipes/bioconductor-cispath - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-citefuse/meta.yaml b/recipes/bioconductor-citefuse/meta.yaml index c46d7faacc243..2cea2576540dc 100644 --- a/recipes/bioconductor-citefuse/meta.yaml +++ b/recipes/bioconductor-citefuse/meta.yaml @@ -1,31 +1,45 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "CiteFuse" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CiteFuse pacakage implements a suite of methods and tools for CITE-seq data from pre-processing to integrative analytics, including doublet detection, network-based modality integration, cell type clustering, differential RNA and protein expression analysis, ADT evaluation, ligand-receptor interaction analysis, and interactive web-based visualisation of the analyses. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'CiteFuse: multi-modal analysis of CITE-seq data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d612b20352aa6e753d90baa4f24b058f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-citefuse", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:citefuse + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle, pkgdown requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-compositions - r-cowplot @@ -47,12 +61,13 @@ requirements: - r-uwot - libblas - liblapack + run: - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-compositions - r-cowplot @@ -72,22 +87,16 @@ requirements: - r-rtsne - r-scales - r-uwot - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 8c6f27fdda8b6d29ad294d101213a00d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'CiteFuse: multi-modal analysis of CITE-seq data' - description: 'CiteFuse pacakage implements a suite of methods and tools for CITE-seq data from pre-processing to integrative analytics, including doublet detection, network-based modality integration, cell type clustering, differential RNA and protein expression analysis, ADT evaluation, ligand-receptor interaction analysis, and interactive web-based visualisation of the analyses.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-citruscdf/meta.yaml b/recipes/bioconductor-citruscdf/meta.yaml index 650b3066528a8..87172751c6f69 100644 --- a/recipes/bioconductor-citruscdf/meta.yaml +++ b/recipes/bioconductor-citruscdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "citruscdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4af821a0c1ae1adf42b7dc5ce7458593 +about: + description: A package containing an environment representing the Citrus.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: citruscdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-citruscdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4af821a0c1ae1adf42b7dc5ce7458593 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: citruscdf - description: 'A package containing an environment representing the Citrus.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-citrusprobe/meta.yaml b/recipes/bioconductor-citrusprobe/meta.yaml index 2c386ee4e5874..68848b39459de 100644 --- a/recipes/bioconductor-citrusprobe/meta.yaml +++ b/recipes/bioconductor-citrusprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "citrusprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 259b114f96d5307c447d000bd27a7d15 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Citrus\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type citrus build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-citrusprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 259b114f96d5307c447d000bd27a7d15 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type citrus' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Citrus\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clariomdhumanprobeset.db/meta.yaml b/recipes/bioconductor-clariomdhumanprobeset.db/meta.yaml index 85c5b7c172edf..00eea01fcb67d 100644 --- a/recipes/bioconductor-clariomdhumanprobeset.db/meta.yaml +++ b/recipes/bioconductor-clariomdhumanprobeset.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "clariomdhumanprobeset.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 01cb1a5cc4674750b6ce5988cd62fad3 +about: + description: Affymetrix clariomdhuman annotation data (chip clariomdhumanprobeset) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix clariomdhuman annotation data (chip clariomdhumanprobeset) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clariomdhumanprobeset.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 01cb1a5cc4674750b6ce5988cd62fad3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix clariomdhuman annotation data (chip clariomdhumanprobeset)' - description: 'Affymetrix clariomdhuman annotation data (chip clariomdhumanprobeset) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clariomdhumantranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomdhumantranscriptcluster.db/meta.yaml index a76e5a52dc2cb..13529e84091bc 100644 --- a/recipes/bioconductor-clariomdhumantranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomdhumantranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "clariomdhumantranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 80739a70d77ab785231a9367938035a8 +about: + description: Affymetrix clariomdhuman annotation data (chip clariomdhumantranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix clariomdhuman annotation data (chip clariomdhumantranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clariomdhumantranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 80739a70d77ab785231a9367938035a8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix clariomdhuman annotation data (chip clariomdhumantranscriptcluster)' - description: 'Affymetrix clariomdhuman annotation data (chip clariomdhumantranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clariomshumanhttranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomshumanhttranscriptcluster.db/meta.yaml index d70ad9cdca7f4..593445f6182f1 100644 --- a/recipes/bioconductor-clariomshumanhttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomshumanhttranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "clariomshumanhttranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6a5e8e1f9768694be99277aafcc0a69a +about: + description: Affymetrix clariomshumanht annotation data (chip clariomshumanhttranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix clariomshumanht annotation data (chip clariomshumanhttranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clariomshumanhttranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6a5e8e1f9768694be99277aafcc0a69a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix clariomshumanht annotation data (chip clariomshumanhttranscriptcluster)' - description: 'Affymetrix clariomshumanht annotation data (chip clariomshumanhttranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clariomshumantranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomshumantranscriptcluster.db/meta.yaml index 794a3936044f0..0734b5a36f872 100644 --- a/recipes/bioconductor-clariomshumantranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomshumantranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "clariomshumantranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 309b29e044e1227da6d4825bbdf04b76 +about: + description: Affymetrix clariomshuman annotation data (chip clariomshumantranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix clariomshuman annotation data (chip clariomshumantranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clariomshumantranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 309b29e044e1227da6d4825bbdf04b76 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix clariomshuman annotation data (chip clariomshumantranscriptcluster)' - description: 'Affymetrix clariomshuman annotation data (chip clariomshumantranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clariomsmousehttranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsmousehttranscriptcluster.db/meta.yaml index 1074e66c5774d..ff958663da648 100644 --- a/recipes/bioconductor-clariomsmousehttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomsmousehttranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "clariomsmousehttranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c0aa96cbd5ee7e19296dde5a72232d17 +about: + description: Affymetrix clariomsmouseht annotation data (chip clariomsmousehttranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix clariomsmouseht annotation data (chip clariomsmousehttranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clariomsmousehttranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c0aa96cbd5ee7e19296dde5a72232d17 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix clariomsmouseht annotation data (chip clariomsmousehttranscriptcluster)' - description: 'Affymetrix clariomsmouseht annotation data (chip clariomsmousehttranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clariomsmousetranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsmousetranscriptcluster.db/meta.yaml index 271042584f0fd..9caaec94d9b9e 100644 --- a/recipes/bioconductor-clariomsmousetranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomsmousetranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "clariomsmousetranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 76d0e2204dcbd5d85d8e53d43710aac5 +about: + description: Affymetrix clariomsmouse annotation data (chip clariomsmousetranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix clariomsmouse annotation data (chip clariomsmousetranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clariomsmousetranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 76d0e2204dcbd5d85d8e53d43710aac5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix clariomsmouse annotation data (chip clariomsmousetranscriptcluster)' - description: 'Affymetrix clariomsmouse annotation data (chip clariomsmousetranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clariomsrathttranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsrathttranscriptcluster.db/meta.yaml index 326e026ab0521..8ad408637455b 100644 --- a/recipes/bioconductor-clariomsrathttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomsrathttranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "clariomsrathttranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e7c71721f8201bfd1553a98cfbf47458 +about: + description: Affymetrix clariomsratht annotation data (chip clariomsrathttranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix clariomsratht annotation data (chip clariomsrathttranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clariomsrathttranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e7c71721f8201bfd1553a98cfbf47458 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix clariomsratht annotation data (chip clariomsrathttranscriptcluster)' - description: 'Affymetrix clariomsratht annotation data (chip clariomsrathttranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clariomsrattranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsrattranscriptcluster.db/meta.yaml index 15edbc0937e97..56a95abb43f88 100644 --- a/recipes/bioconductor-clariomsrattranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-clariomsrattranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "clariomsrattranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 72923a3a90f2df27a361b1730cfc0d00 +about: + description: Affymetrix clariomsrat annotation data (chip clariomsrattranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix clariomsrat annotation data (chip clariomsrattranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clariomsrattranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 72923a3a90f2df27a361b1730cfc0d00 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix clariomsrat annotation data (chip clariomsrattranscriptcluster)' - description: 'Affymetrix clariomsrat annotation data (chip clariomsrattranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-classifyr/meta.yaml b/recipes/bioconductor-classifyr/meta.yaml index 704f02bfee8e5..878f77effc1ab 100644 --- a/recipes/bioconductor-classifyr/meta.yaml +++ b/recipes/bioconductor-classifyr/meta.yaml @@ -1,34 +1,48 @@ -{% set version = "3.6.2" %} +{% set version = "3.10.0" %} {% set name = "ClassifyR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The software formalises a framework for classification and survival model evaluation in R. There are four stages; Data transformation, feature selection, model training, and prediction. The requirements of variable types and variable order are fixed, but specialised variables for functions can also be provided. The framework is wrapped in a driver loop that reproducibly carries out a number of cross-validation schemes. Functions for differential mean, differential variability, and differential distribution are included. Additional functions may be developed by the user, by creating an interface to the framework. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 002678b6aeace9d7967b87654547a4f3 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-classifyr", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:classifyr + parent_recipe: + name: bioconductor-classifyr + path: recipes/bioconductor-classifyr + version: 2.2.4 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: limma, edgeR, car, Rmixmod, gridExtra (>= 2.0.0), cowplot, BiocStyle, pamr, PoiClaClu, parathyroidSE, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, robustbase, glmnet, class, randomForestSRC, MatrixModels, xgboost, data.tree, ggnewscale requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-generics - - 'r-ggplot2 >=3.0.0' + - r-ggplot2 >=3.0.0 - r-ggpubr - r-ggupset - r-ranger @@ -39,14 +53,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-generics - - 'r-ggplot2 >=3.0.0' + - r-ggplot2 >=3.0.0 - r-ggpubr - r-ggupset - r-ranger @@ -54,24 +68,16 @@ requirements: - r-rlang - r-survival - r-tidyr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: a1a4fdbf38ce6f5b9a0d138b8d9943a5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing' - description: 'The software formalises a framework for classification and survival model evaluation in R. There are four stages; Data transformation, feature selection, model training, and prediction. The requirements of variable types and variable order are fixed, but specialised variables for functions can also be provided. The framework is wrapped in a driver loop that reproducibly carries out a number of cross-validation schemes. Functions for differential mean, differential variability, and differential distribution are included. Additional functions may be developed by the user, by creating an interface to the framework.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:classifyr - parent_recipe: - name: bioconductor-classifyr - path: recipes/bioconductor-classifyr - version: 2.2.4 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cleanupdtseq/meta.yaml b/recipes/bioconductor-cleanupdtseq/meta.yaml index 722708178c451..cc3ad3ecfaaa4 100644 --- a/recipes/bioconductor-cleanupdtseq/meta.yaml +++ b/recipes/bioconductor-cleanupdtseq/meta.yaml @@ -1,64 +1,70 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "cleanUpdTSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements a Naive Bayes classifier for accurately differentiating true polyadenylation sites (pA sites) from oligo(dT)-mediated 3' end sequencing such as PAS-Seq, PolyA-Seq and RNA-Seq by filtering out false polyadenylation sites, mainly due to oligo(dT)-mediated internal priming during reverse transcription. The classifer is highly accurate and outperforms other heuristic methods. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 52f27e948758be1db9d6b003d69a84b9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cleanupdtseq", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:cleanupdtseq + parent_recipe: + name: bioconductor-cleanupdtseq + path: recipes/bioconductor-cleanupdtseq + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics (>= 0.1.0) requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-e1071 - r-seqinr - r-stringr run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-e1071 - r-seqinr - r-stringr + +source: + md5: 0bc83ad524caf1515e16fd62735730d6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3'' end RNA sequending data' - description: 'This package implements a Naive Bayes classifier for accurately differentiating true polyadenylation sites (pA sites) from oligo(dT)-mediated 3'' end sequencing such as PAS-Seq, PolyA-Seq and RNA-Seq by filtering out false polyadenylation sites, mainly due to oligo(dT)-mediated internal priming during reverse transcription. The classifer is highly accurate and outperforms other heuristic methods.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:cleanupdtseq - parent_recipe: - name: bioconductor-cleanupdtseq - path: recipes/bioconductor-cleanupdtseq - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cleanuprnaseq/build.sh b/recipes/bioconductor-cleanuprnaseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cleanuprnaseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cleanuprnaseq/meta.yaml b/recipes/bioconductor-cleanuprnaseq/meta.yaml new file mode 100644 index 0000000000000..462d6cb87dbd2 --- /dev/null +++ b/recipes/bioconductor-cleanuprnaseq/meta.yaml @@ -0,0 +1,88 @@ +{% set version = "1.0.0" %} +{% set name = "CleanUpRNAseq" %} +{% set bioc = "3.20" %} + +about: + description: RNA-seq data generated by some library preparation methods, such as rRNA-depletion-based method and the SMART-seq method, might be contaminated by genomic DNA (gDNA), if DNase I disgestion is not performed properly during RNA preparation. CleanUpRNAseq is developed to check if RNA-seq data is suffered from gDNA contamination. If so, it can perform correction for gDNA contamination and reduce false discovery rate of differentially expressed genes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Detect and Correct Genomic DNA Contamination in RNA-seq Data + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cleanuprnaseq", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86, ggplotify, knitr, patchwork, R.utils, rmarkdown, testthat (>= 3.0.0) +requirements: + + host: + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-qsmooth >=1.22.0,<1.23.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rsubread >=2.20.0,<2.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tximport >=1.34.0,<1.35.0 + - r-base + - r-ggplot2 + - r-ggrepel + - r-kernsmooth + - r-pheatmap + - r-r6 + - r-rcolorbrewer + - r-reshape2 + + run: + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-qsmooth >=1.22.0,<1.23.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rsubread >=2.20.0,<2.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tximport >=1.34.0,<1.35.0 + - r-base + - r-ggplot2 + - r-ggrepel + - r-kernsmooth + - r-pheatmap + - r-r6 + - r-rcolorbrewer + - r-reshape2 + +source: + md5: 3fff7d3325a4839106824d215c6f1876 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-cleaver/meta.yaml b/recipes/bioconductor-cleaver/meta.yaml index e69fedb991a3b..f66be3c87b702 100644 --- a/recipes/bioconductor-cleaver/meta.yaml +++ b/recipes/bioconductor-cleaver/meta.yaml @@ -1,45 +1,22 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "cleaver" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'In-silico cleavage of polypeptide sequences. The cleavage rules are taken from: http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Cleavage of Polypeptide Sequences -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 978f7bba3eb0dae3a3edee5c5721de7b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cleaver", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown, BRAIN, UniProt.ws (>= 2.36.5) -requirements: - host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - r-base - run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Cleavage of Polypeptide Sequences' - description: 'In-silico cleavage of polypeptide sequences. The cleavage rules are taken from: http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:cleaver @@ -49,3 +26,32 @@ extra: path: recipes/bioconductor-cleaver version: 1.18.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown, BRAIN, UniProt.ws (>= 2.36.5) +requirements: + host: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + run: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + +source: + md5: 77d0ea8131956c1c3bde9d5e7d8e4dab + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-clevrvis/meta.yaml b/recipes/bioconductor-clevrvis/meta.yaml index 4cbdb433898df..f50254e77f3fc 100644 --- a/recipes/bioconductor-clevrvis/meta.yaml +++ b/recipes/bioconductor-clevrvis/meta.yaml @@ -1,26 +1,29 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "clevRvis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: clevRvis provides a set of visualization techniques for clonal evolution. These include shark plots, dolphin plots and plaice plots. Algorithms for time point interpolation as well as therapy effect estimation are provided. Phylogeny-aware color coding is implemented. A shiny-app for generating plots interactively is additionally provided. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Visualization Techniques for Clonal Evolution -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96fde7a442a2cdb69754ebf1e68ccc65 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clevrvis", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle requirements: + host: - r-base - r-colorspace @@ -46,6 +49,7 @@ requirements: - r-shinyhelper - r-shinywidgets - r-tibble + run: - r-base - r-colorspace @@ -71,13 +75,16 @@ requirements: - r-shinyhelper - r-shinywidgets - r-tibble + +source: + md5: e9ed8135aece62b029a3a7876ce68f95 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'Visualization Techniques for Clonal Evolution' - description: 'clevRvis provides a set of visualization techniques for clonal evolution. These include shark plots, dolphin plots and plaice plots. Algorithms for time point interpolation as well as therapy effect estimation are provided. Phylogeny-aware color coding is implemented. A shiny-app for generating plots interactively is additionally provided.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clippda/meta.yaml b/recipes/bioconductor-clippda/meta.yaml index 4aea5febf6e97..2eef6393d0b40 100644 --- a/recipes/bioconductor-clippda/meta.yaml +++ b/recipes/bioconductor-clippda/meta.yaml @@ -1,58 +1,64 @@ -{% set version = "1.52.0" %} +{% set version = "1.56.0" %} {% set name = "clippda" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Methods for the nalysis of data from clinical proteomic profiling studies. The focus is on the studies of human subjects, which are often observational case-control by design and have technical replicates. A method for sample size determination for planning these studies is proposed. It incorporates routines for adjusting for the expected heterogeneities and imbalances in the data and the within-sample replicate correlations. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A package for the clinical proteomic profiling data analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d416c567cfb3615472045bc57c2bce72 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clippda", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-lattice - r-rgl - r-scatterplot3d - r-statmod run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-lattice - r-rgl - r-scatterplot3d - r-statmod - build: - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - xorg-libxfixes # [linux] + +source: + md5: c8f925497e531dc0c1666957a52f1844 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'A package for the clinical proteomic profiling data analysis' - description: 'Methods for the nalysis of data from clinical proteomic profiling studies. The focus is on the studies of human subjects, which are often observational case-control by design and have technical replicates. A method for sample size determination for planning these studies is proposed. It incorporates routines for adjusting for the expected heterogeneities and imbalances in the data and the within-sample replicate correlations.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clipper/meta.yaml b/recipes/bioconductor-clipper/meta.yaml index acc5b59f261e9..3930b8002dac2 100644 --- a/recipes/bioconductor-clipper/meta.yaml +++ b/recipes/bioconductor-clipper/meta.yaml @@ -1,64 +1,70 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "clipper" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implements topological gene set analysis using a two-step empirical approach. It exploits graph decomposition theory to create a junction tree and reconstruct the most relevant signal path. In the first step clipper selects significant pathways according to statistical tests on the means and the concentration matrices of the graphs derived from pathway topologies. Then, it "clips" the whole pathway identifying the signal paths having the greatest association with a specific phenotype. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + summary: Gene Set Analysis Exploiting Pathway Topology -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 551f3c6ad3a56f2a70439f48a4aef431 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clipper", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:clipper + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS, BiocStyle requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - 'bioconductor-qpgraph >=2.36.0,<2.37.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - bioconductor-qpgraph >=2.40.0,<2.41.0 - r-base - r-corpcor - - 'r-grbase >=1.6.6' + - r-grbase >=1.6.6 - r-igraph - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - 'bioconductor-qpgraph >=2.36.0,<2.37.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - bioconductor-qpgraph >=2.40.0,<2.41.0 - r-base - r-corpcor - - 'r-grbase >=1.6.6' + - r-grbase >=1.6.6 - r-igraph - r-matrix - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} + +source: + md5: 5ffd8585e213573da25b5118f1d69e26 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3.0-only - summary: 'Gene Set Analysis Exploiting Pathway Topology' - description: 'Implements topological gene set analysis using a two-step empirical approach. It exploits graph decomposition theory to create a junction tree and reconstruct the most relevant signal path. In the first step clipper selects significant pathways according to statistical tests on the means and the concentration matrices of the graphs derived from pathway topologies. Then, it "clips" the whole pathway identifying the signal paths having the greatest association with a specific phenotype.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-cliprofiler/meta.yaml b/recipes/bioconductor-cliprofiler/meta.yaml index c0910f32ab09f..da951bbb854fa 100644 --- a/recipes/bioconductor-cliprofiler/meta.yaml +++ b/recipes/bioconductor-cliprofiler/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "cliProfiler" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An easy and fast way to visualize and profile the high-throughput IP data. This package generates the meta gene profile and other profiles. These profiles could provide valuable information for understanding the IP experiment results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: A package for the CLIP data visualization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 10a33ec5af89503fcb12a8142ec966f8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cliprofiler", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-ggplot2 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-ggplot2 + +source: + md5: 65c54643619d8f59e77564ab9ea2bb9d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A package for the CLIP data visualization' - description: 'An easy and fast way to visualize and profile the high-throughput IP data. This package generates the meta gene profile and other profiles. These profiles could provide valuable information for understanding the IP experiment results.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cliquems/meta.yaml b/recipes/bioconductor-cliquems/meta.yaml index 0c96850839c51..8597646dde952 100644 --- a/recipes/bioconductor-cliquems/meta.yaml +++ b/recipes/bioconductor-cliquems/meta.yaml @@ -1,59 +1,66 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "cliqueMS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Annotates data from liquid chromatography coupled to mass spectrometry (LC/MS) metabolomics experiments. Based on a network algorithm (O.Senan, A. Aguilar- Mogas, M. Navarro, O. Yanes, R.Guimerà and M. Sales-Pardo, Bioinformatics, 35(20), 2019), 'CliqueMS' builds a weighted similarity network where nodes are features and edges are weighted according to the similarity of this features. Then it searches for the most plausible division of the similarity network into cliques (fully connected components). Finally it annotates metabolites within each clique, obtaining for each annotated metabolite the neutral mass and their features, corresponding to isotopes, ionization adducts and fragmentation adducts of that metabolite. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f423e41dd4ca04cefe4bd5be77ceec3a build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cliquems", max_pin="x.x") }}' -# Suggests: knitr, rmarkdown, testthat, CAMERA + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocParallel, knitr, rmarkdown, testthat, CAMERA # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base - r-bh + - r-coop - r-igraph - r-matrixstats - - r-qlcmatrix - - 'r-rcpp >=0.12.15' + - r-rcpp >=0.12.15 - r-rcpparmadillo + - r-slam - libblas - liblapack run: - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base - r-bh + - r-coop - r-igraph - r-matrixstats - - r-qlcmatrix - - 'r-rcpp >=0.12.15' + - r-rcpp >=0.12.15 - r-rcpparmadillo - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-slam + +source: + md5: 4161bbb24c1fa3fdf7bc9b558f8c435f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data' - description: 'Annotates data from liquid chromatography coupled to mass spectrometry (LC/MS) metabolomics experiments. Based on a network algorithm (O.Senan, A. Aguilar- Mogas, M. Navarro, O. Yanes, R.Guimerà and M. Sales-Pardo, Bioinformatics, 35(20), 2019), ''CliqueMS'' builds a weighted similarity network where nodes are features and edges are weighted according to the similarity of this features. Then it searches for the most plausible division of the similarity network into cliques (fully connected components). Finally it annotates metabolites within each clique, obtaining for each annotated metabolite the neutral mass and their features, corresponding to isotopes, ionization adducts and fragmentation adducts of that metabolite.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cll/meta.yaml b/recipes/bioconductor-cll/meta.yaml index dfeb4ff22d3ea..ea8615773abd4 100644 --- a/recipes/bioconductor-cll/meta.yaml +++ b/recipes/bioconductor-cll/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "CLL" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4f71fa48ba2205b80c098275c866ac1f +about: + description: The CLL package contains the chronic lymphocytic leukemia (CLL) gene expression data. The CLL data had 24 samples that were either classified as progressive or stable in regards to disease progression. The data came from Dr. Sabina Chiaretti at Division of Hematology, Department of Cellular Biotechnologies and Hematology, University La Sapienza, Rome, Italy and Dr. Jerome Ritz at Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: A Package for CLL Gene Expression Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cll", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c8071d9e39beb9e79f8f81188299b7db + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'A Package for CLL Gene Expression Data' - description: 'The CLL package contains the chronic lymphocytic leukemia (CLL) gene expression data. The CLL data had 24 samples that were either classified as progressive or stable in regards to disease progression. The data came from Dr. Sabina Chiaretti at Division of Hematology, Department of Cellular Biotechnologies and Hematology, University La Sapienza, Rome, Italy and Dr. Jerome Ritz at Department of Medicine, Brigham and Women''s Hospital, Harvard Medical School, Boston, Massachusetts.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cll/post-link.sh b/recipes/bioconductor-cll/post-link.sh index bfc51d8a40c4f..9a601a659d03e 100644 --- a/recipes/bioconductor-cll/post-link.sh +++ b/recipes/bioconductor-cll/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cll-1.42.0" +installBiocDataPackage.sh "cll-1.46.0" diff --git a/recipes/bioconductor-cllmethylation/meta.yaml b/recipes/bioconductor-cllmethylation/meta.yaml index 1ed25ff3378d0..c1ae2b786f35b 100644 --- a/recipes/bioconductor-cllmethylation/meta.yaml +++ b/recipes/bioconductor-cllmethylation/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "CLLmethylation" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8c3768dca1df5bb9e911878b68ad4c4 +about: + description: The package includes DNA methylation data for the primary Chronic Lymphocytic Leukemia samples included in the Primary Blood Cancer Encyclopedia (PACE) project. Raw data from the 450k DNA methylation arrays is stored in the European Genome-Phenome Archive (EGA) under accession number EGAS0000100174. For more information concerning the project please refer to the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) and R/Bioconductor package BloodCancerMultiOmics2017. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Methylation data of primary CLL samples in PACE project build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cllmethylation", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, ggplot2, knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5ffc204c8259540a8cb73c7bf4549249 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Methylation data of primary CLL samples in PACE project' - description: 'The package includes DNA methylation data for the primary Chronic Lymphocytic Leukemia samples included in the Primary Blood Cancer Encyclopedia (PACE) project. Raw data from the 450k DNA methylation arrays is stored in the European Genome-Phenome Archive (EGA) under accession number EGAS0000100174. For more information concerning the project please refer to the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) and R/Bioconductor package BloodCancerMultiOmics2017.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cllmethylation/post-link.sh b/recipes/bioconductor-cllmethylation/post-link.sh index 24af32275232b..c7ab5ae4c9117 100644 --- a/recipes/bioconductor-cllmethylation/post-link.sh +++ b/recipes/bioconductor-cllmethylation/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cllmethylation-1.22.0" +installBiocDataPackage.sh "cllmethylation-1.26.0" diff --git a/recipes/bioconductor-clomial/meta.yaml b/recipes/bioconductor-clomial/meta.yaml index 280429af62f00..9c937fc360860 100644 --- a/recipes/bioconductor-clomial/meta.yaml +++ b/recipes/bioconductor-clomial/meta.yaml @@ -1,24 +1,34 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "Clomial" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained parameters can be interpreted to infer the clonal structure of the tumor. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Infers clonal composition of a tumor -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71e609b1bef40cdadcd812f99a5956e8 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clomial", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:clomial + parent_recipe: + name: bioconductor-clomial + path: recipes/bioconductor-clomial + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -28,20 +38,16 @@ requirements: - r-base - r-matrixstats - r-permute + +source: + md5: 02d9267198f2e0518f8e4d3209176cdd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Infers clonal composition of a tumor' - description: 'Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained parameters can be interpreted to infer the clonal structure of the tumor.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:clomial - parent_recipe: - name: bioconductor-clomial - path: recipes/bioconductor-clomial - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clst/meta.yaml b/recipes/bioconductor-clst/meta.yaml index 40c671b879c52..5fa35ba92ead0 100644 --- a/recipes/bioconductor-clst/meta.yaml +++ b/recipes/bioconductor-clst/meta.yaml @@ -1,49 +1,55 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "clst" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package for modified nearest-neighbor classification based on calculation of a similarity threshold distinguishing within-group from between-group comparisons. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Classification by local similarity threshold -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5988cf1c0b5207d2f78f75dbe6f2b467 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clst", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:clst + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-clst + path: recipes/bioconductor-clst + version: 1.28.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit requirements: host: - - 'bioconductor-roc >=1.78.0,<1.79.0' + - bioconductor-roc >=1.82.0,<1.83.0 - r-base - r-lattice run: - - 'bioconductor-roc >=1.78.0,<1.79.0' + - bioconductor-roc >=1.82.0,<1.83.0 - r-base - r-lattice + +source: + md5: 37d2fa0a70d7ba8774dc25b72981d860 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Classification by local similarity threshold' - description: 'Package for modified nearest-neighbor classification based on calculation of a similarity threshold distinguishing within-group from between-group comparisons.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:clst - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-clst - path: recipes/bioconductor-clst - version: 1.28.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clstutils/meta.yaml b/recipes/bioconductor-clstutils/meta.yaml index fbd9437560808..911980306a385 100644 --- a/recipes/bioconductor-clstutils/meta.yaml +++ b/recipes/bioconductor-clstutils/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "clstutils" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for performing taxonomic assignment based on phylogeny using pplacer and clst. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Tools for performing taxonomic assignment -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4343490b2b05bf2e4429f2081b3a82c5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clstutils", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:clstutils + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-clstutils + path: recipes/bioconductor-clstutils + version: 1.28.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit requirements: host: - - 'bioconductor-clst >=1.50.0,<1.51.0' + - bioconductor-clst >=1.54.0,<1.55.0 - r-ape - r-base - r-lattice - r-rjson - r-rsqlite run: - - 'bioconductor-clst >=1.50.0,<1.51.0' + - bioconductor-clst >=1.54.0,<1.55.0 - r-ape - r-base - r-lattice - r-rjson - r-rsqlite + +source: + md5: d2c9c35acd886699560233004b0ded61 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Tools for performing taxonomic assignment' - description: 'Tools for performing taxonomic assignment based on phylogeny using pplacer and clst.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:clstutils - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-clstutils - path: recipes/bioconductor-clstutils - version: 1.28.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clumsid/meta.yaml b/recipes/bioconductor-clumsid/meta.yaml index f845097e08a5c..b512d58c818a6 100644 --- a/recipes/bioconductor-clumsid/meta.yaml +++ b/recipes/bioconductor-clumsid/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "CluMSID" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CluMSID is a tool that aids the identification of features in untargeted LC-MS/MS analysis by the use of MS2 spectra similarity and unsupervised statistical methods. It offers functions for a complete and customisable workflow from raw data to visualisations and is interfaceable with the xmcs family of preprocessing packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Clustering of MS2 Spectra for Metabolite Identification -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0f441929cf30f7ab6c9a035023ef3a20 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clumsid", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr, CluMSIDdata, metaMS, metaMSdata, xcms requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-mzr >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-ape - r-base - r-dbscan @@ -37,10 +39,10 @@ requirements: - r-rcolorbrewer - r-sna run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-mzr >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-ape - r-base - r-dbscan @@ -51,13 +53,16 @@ requirements: - r-plotly - r-rcolorbrewer - r-sna + +source: + md5: aa9cea9b6146139325eed469d41e8551 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Clustering of MS2 Spectra for Metabolite Identification' - description: 'CluMSID is a tool that aids the identification of features in untargeted LC-MS/MS analysis by the use of MS2 spectra similarity and unsupervised statistical methods. It offers functions for a complete and customisable workflow from raw data to visualisations and is interfaceable with the xmcs family of preprocessing packages.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clumsiddata/meta.yaml b/recipes/bioconductor-clumsiddata/meta.yaml index ea06ae2fe5f88..3ba64ef9240f0 100644 --- a/recipes/bioconductor-clumsiddata/meta.yaml +++ b/recipes/bioconductor-clumsiddata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "CluMSIDdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 315da29d9f052e0abfbad59be9606f34 +about: + description: This package contains various LC-MS/MS and GC-MS data that is used in vignettes and examples in the CluMSID package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Data for the CluMSID package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clumsiddata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 11dcdada1eca12589c47e4d2bccdbe4d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Data for the CluMSID package' - description: 'This package contains various LC-MS/MS and GC-MS data that is used in vignettes and examples in the CluMSID package.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clumsiddata/post-link.sh b/recipes/bioconductor-clumsiddata/post-link.sh index 2e82be8661106..4fd97e7a5cdda 100644 --- a/recipes/bioconductor-clumsiddata/post-link.sh +++ b/recipes/bioconductor-clumsiddata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "clumsiddata-1.18.0" +installBiocDataPackage.sh "clumsiddata-1.22.0" diff --git a/recipes/bioconductor-clustall/build.sh b/recipes/bioconductor-clustall/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-clustall/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clustall/meta.yaml b/recipes/bioconductor-clustall/meta.yaml new file mode 100644 index 0000000000000..0451cb607b01f --- /dev/null +++ b/recipes/bioconductor-clustall/meta.yaml @@ -0,0 +1,76 @@ +{% set version = "1.2.0" %} +{% set name = "ClustAll" %} +{% set bioc = "3.20" %} + +about: + description: Data driven strategy to find hidden groups of patients with complex diseases using clinical data. ClustAll facilitates the unsupervised identification of multiple robust stratifications. ClustAll, is able to overcome the most common limitations found when dealing with clinical data (missing values, correlated data, mixed data types). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'ClustAll: Data driven strategy to robustly identify stratification of patients within complex diseases' + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clustall", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RUnit, knitr, BiocGenerics, rmarkdown, BiocStyle, roxygen2 +requirements: + host: + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - r-base + - r-bigstatsr + - r-circlize + - r-cluster + - r-clvalid + - r-dosnow + - r-dplyr + - r-factominer + - r-flock + - r-foreach + - r-fpc + - r-ggplot2 + - r-mice + - r-modeest + - r-networkd3 + - r-pbapply + - r-rcolorbrewer + run: + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - r-base + - r-bigstatsr + - r-circlize + - r-cluster + - r-clvalid + - r-dosnow + - r-dplyr + - r-factominer + - r-flock + - r-foreach + - r-fpc + - r-ggplot2 + - r-mice + - r-modeest + - r-networkd3 + - r-pbapply + - r-rcolorbrewer + +source: + md5: c04353f070372d31c3b70f51fb94f55d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-clustcomp/meta.yaml b/recipes/bioconductor-clustcomp/meta.yaml index b3fc8f1f502a3..a8c0e5e99af66 100644 --- a/recipes/bioconductor-clustcomp/meta.yaml +++ b/recipes/bioconductor-clustcomp/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "clustComp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: clustComp is a package that implements several techniques for the comparison and visualisation of relationships between different clustering results, either flat versus flat or hierarchical versus flat. These relationships among clusters are displayed using a weighted bi-graph, in which the nodes represent the clusters and the edges connect pairs of nodes with non-empty intersection; the weight of each edge is the number of elements in that intersection and is displayed through the edge thickness. The best layout of the bi-graph is provided by the barycentre algorithm, which minimises the weighted number of crossings. In the case of comparing a hierarchical and a non-hierarchical clustering, the dendrogram is pruned at different heights, selected by exploring the tree by depth-first search, starting at the root. Branches are decided to be split according to the value of a scoring function, that can be based either on the aesthetics of the bi-graph or on the mutual information between the hierarchical and the flat clusterings. A mapping between groups of clusters from each side is constructed with a greedy algorithm, and can be additionally visualised. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Clustering Comparison Package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c1783d91366b98b4afbe0b0acc49c452 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clustcomp", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:clustcomp + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-clustcomp + path: recipes/bioconductor-clustcomp + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biobase, colonCA, RUnit, BiocGenerics requirements: host: @@ -27,21 +38,16 @@ requirements: run: - r-base - r-sm + +source: + md5: ddc62c06e3b7f2e0ac92ec344b209ea7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Clustering Comparison Package' - description: 'clustComp is a package that implements several techniques for the comparison and visualisation of relationships between different clustering results, either flat versus flat or hierarchical versus flat. These relationships among clusters are displayed using a weighted bi-graph, in which the nodes represent the clusters and the edges connect pairs of nodes with non-empty intersection; the weight of each edge is the number of elements in that intersection and is displayed through the edge thickness. The best layout of the bi-graph is provided by the barycentre algorithm, which minimises the weighted number of crossings. In the case of comparing a hierarchical and a non-hierarchical clustering, the dendrogram is pruned at different heights, selected by exploring the tree by depth-first search, starting at the root. Branches are decided to be split according to the value of a scoring function, that can be based either on the aesthetics of the bi-graph or on the mutual information between the hierarchical and the flat clusterings. A mapping between groups of clusters from each side is constructed with a greedy algorithm, and can be additionally visualised.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:clustcomp - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-clustcomp - path: recipes/bioconductor-clustcomp - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clusterexperiment/meta.yaml b/recipes/bioconductor-clusterexperiment/meta.yaml index 3df5693d3099b..db3c3e06590ed 100644 --- a/recipes/bioconductor-clusterexperiment/meta.yaml +++ b/recipes/bioconductor-clusterexperiment/meta.yaml @@ -1,41 +1,53 @@ -{% set version = "2.22.0" %} +{% set version = "2.26.0" %} {% set name = "clusterExperiment" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA Expression data sets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Compare Clusterings for Single-Cell Sequencing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0a4bac02f2b310d941afe62b329e7eee build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clusterexperiment", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:clusterexperiment + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph, rmarkdown requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-mbkmeans >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zinbwave >=1.24.0,<1.25.0' - - 'r-ape >=5.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-mbkmeans >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zinbwave >=1.28.0,<1.29.0 + - r-ape >=5.0 - r-base - r-cluster - - r-howmany - r-kernlab - r-locfdr - r-matrix @@ -49,22 +61,22 @@ requirements: - r-stringr - libblas - liblapack + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-mbkmeans >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zinbwave >=1.24.0,<1.25.0' - - 'r-ape >=5.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-mbkmeans >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zinbwave >=1.28.0,<1.29.0 + - r-ape >=5.0 - r-base - r-cluster - - r-howmany - r-kernlab - r-locfdr - r-matrix @@ -76,21 +88,16 @@ requirements: - r-rcpp - r-scales - r-stringr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 5b62fb1a5cf835fdb7b463628d835691 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Compare Clusterings for Single-Cell Sequencing' - description: 'Provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA Expression data sets.' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} \ No newline at end of file diff --git a/recipes/bioconductor-clusterfoldsimilarity/build.sh b/recipes/bioconductor-clusterfoldsimilarity/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-clusterfoldsimilarity/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clusterfoldsimilarity/meta.yaml b/recipes/bioconductor-clusterfoldsimilarity/meta.yaml new file mode 100644 index 0000000000000..b673477ce5c22 --- /dev/null +++ b/recipes/bioconductor-clusterfoldsimilarity/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.2.0" %} +{% set name = "ClusterFoldSimilarity" %} +{% set bioc = "3.20" %} + +about: + description: This package calculates a similarity coefficient using the fold changes of shared features (e.g. genes) among clusters of different samples/batches/datasets. The similarity coefficient is calculated using the dot-product (Hadamard product) of every pairwise combination of Fold Changes between a source cluster i of sample/dataset n and all the target clusters j in sample/dataset m + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Calculate similarity of clusters from different single cell samples using foldchanges + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-clusterfoldsimilarity", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, kableExtra, scRNAseq, BiocStyle +requirements: + host: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - r-base + - r-cowplot + - r-dplyr + - r-ggdendro + - r-ggplot2 + - r-igraph + - r-matrix + - r-reshape2 + - r-scales + - r-seurat + - r-seuratobject + run: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - r-base + - r-cowplot + - r-dplyr + - r-ggdendro + - r-ggplot2 + - r-igraph + - r-matrix + - r-reshape2 + - r-scales + - r-seurat + - r-seuratobject + +source: + md5: 3c0b4aa95db88e8ccb61bef1d552df7a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-clusterjudge/meta.yaml b/recipes/bioconductor-clusterjudge/meta.yaml index 6b919674df414..a89a31fb56d93 100644 --- a/recipes/bioconductor-clusterjudge/meta.yaml +++ b/recipes/bioconductor-clusterjudge/meta.yaml @@ -1,24 +1,25 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "ClusterJudge" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ClusterJudge implements the functions, examples and other software published as an algorithm by Gibbons, FD and Roth FP. The article is called "Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation" and it appeared in Genome Research, vol. 12, pp1574-1581 (2002). See package?ClusterJudge for an overview. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Judging Quality of Clustering Methods using Mutual Information -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f1db5b57d83f67f60de690e6f224bde build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clusterjudge", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt requirements: host: @@ -35,12 +36,16 @@ requirements: - r-jsonlite - r-lattice - r-latticeextra + +source: + md5: 6d42b8ae4c9c4f1fc45de148a1daa440 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Judging Quality of Clustering Methods using Mutual Information' - description: 'ClusterJudge implements the functions, examples and other software published as an algorithm by Gibbons, FD and Roth FP. The article is called "Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation" and it appeared in Genome Research, vol. 12, pp1574-1581 (2002). See package?ClusterJudge for an overview.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clusterprofiler/meta.yaml b/recipes/bioconductor-clusterprofiler/meta.yaml index f55cd8017a8be..b85633dcbb77a 100644 --- a/recipes/bioconductor-clusterprofiler/meta.yaml +++ b/recipes/bioconductor-clusterprofiler/meta.yaml @@ -1,75 +1,79 @@ -{% set version = "4.10.0" %} +{% set version = "4.14.0" %} {% set name = "clusterProfiler" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. It provides a univeral interface for gene functional annotation from a variety of sources and thus can be applied in diverse scenarios. It provides a tidy interface to access, manipulate, and visualize enrichment results to help users achieve efficient data interpretation. Datasets obtained from multiple treatments and time points can be analyzed and compared in a single run, easily revealing functional consensus and differences among distinct conditions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: A universal enrichment tool for interpreting omics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6eb1c0888849211e04896b3431460048 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clusterprofiler", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:clusterprofiler + parent_recipe: + name: bioconductor-clusterprofiler + path: recipes/bioconductor-clusterprofiler + version: 3.8.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationHub, knitr, jsonlite, readr, rmarkdown, org.Hs.eg.db, prettydoc, BiocManager, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-gosemsim >=2.32.0,<2.33.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - - r-downloader - r-dplyr - - 'r-gson >=0.0.7' + - r-gson >=0.0.7 - r-httr - r-igraph - r-magrittr - r-plyr - r-rlang - r-tidyr - - 'r-yulab.utils >=0.0.7' + - r-yulab.utils >=0.1.6 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-gosemsim >=2.32.0,<2.33.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - - r-downloader - r-dplyr - - 'r-gson >=0.0.7' + - r-gson >=0.0.7 - r-httr - r-igraph - r-magrittr - r-plyr - r-rlang - r-tidyr - - 'r-yulab.utils >=0.0.7' + - r-yulab.utils >=0.1.6 + +source: + md5: 51c0ed29b4e3fdae1edd17722ac79880 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A universal enrichment tool for interpreting omics data' - description: 'This package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. It provides a univeral interface for gene functional annotation from a variety of sources and thus can be applied in diverse scenarios. It provides a tidy interface to access, manipulate, and visualize enrichment results to help users achieve efficient data interpretation. Datasets obtained from multiple treatments and time points can be analyzed and compared in a single run, easily revealing functional consensus and differences among distinct conditions.' -extra: - identifiers: - - biotools:clusterprofiler - parent_recipe: - name: bioconductor-clusterprofiler - path: recipes/bioconductor-clusterprofiler - version: 3.8.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clusterseq/meta.yaml b/recipes/bioconductor-clusterseq/meta.yaml index 89f709b6c7c02..5897a26944b7e 100644 --- a/recipes/bioconductor-clusterseq/meta.yaml +++ b/recipes/bioconductor-clusterseq/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "clusterSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c0f51fc6b851b707de4f53107c6179f5 +about: + description: Identification of clusters of co-expressed genes based on their expression across multiple (replicated) biological samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Clustering of high-throughput sequencing data by identifying co-expression patterns build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clusterseq", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle requirements: host: - - 'bioconductor-bayseq >=2.36.0,<2.37.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-bayseq >=2.40.0,<2.41.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base run: - - 'bioconductor-bayseq >=2.36.0,<2.37.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-bayseq >=2.40.0,<2.41.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base +source: + md5: 29ba984cbabf6bae7805a3d540d9a61e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Clustering of high-throughput sequencing data by identifying co-expression patterns' - description: 'Identification of clusters of co-expressed genes based on their expression across multiple (replicated) biological samples.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clustersignificance/meta.yaml b/recipes/bioconductor-clustersignificance/meta.yaml index 452ee4190c486..1ad3cd0bf3037 100644 --- a/recipes/bioconductor-clustersignificance/meta.yaml +++ b/recipes/bioconductor-clustersignificance/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "ClusterSignificance" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data. The term class clusters here refers to, clusters of points representing known classes in the data. This is particularly useful to determine if a subset of the variables, e.g. genes in a specific pathway, alone can separate samples into these established classes. ClusterSignificance accomplishes this by, projecting all points onto a one dimensional line. Cluster separations are then scored and the probability of the seen separation being due to chance is evaluated using a permutation method. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46f8a23ba4910712f2c65ebbb151ad4f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clustersignificance", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:clustersignificance + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-clustersignificance + path: recipes/bioconductor-clustersignificance + version: 1.8.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr requirements: host: - r-base - r-pracma - - 'r-princurve >=2.0.5' + - r-princurve >=2.0.5 - r-rcolorbrewer - r-scatterplot3d run: - r-base - r-pracma - - 'r-princurve >=2.0.5' + - r-princurve >=2.0.5 - r-rcolorbrewer - r-scatterplot3d + +source: + md5: 53bbdbb66e276ecc631b68fa03311736 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data' - description: 'The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data. The term class clusters here refers to, clusters of points representing known classes in the data. This is particularly useful to determine if a subset of the variables, e.g. genes in a specific pathway, alone can separate samples into these established classes. ClusterSignificance accomplishes this by, projecting all points onto a one dimensional line. Cluster separations are then scored and the probability of the seen separation being due to chance is evaluated using a permutation method.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:clustersignificance - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-clustersignificance - path: recipes/bioconductor-clustersignificance - version: 1.8.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clusterstab/meta.yaml b/recipes/bioconductor-clusterstab/meta.yaml index 0f20cc38a7835..c52789dd1d02a 100644 --- a/recipes/bioconductor-clusterstab/meta.yaml +++ b/recipes/bioconductor-clusterstab/meta.yaml @@ -1,40 +1,21 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "clusterStab" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Compute cluster stability scores for microarray data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 87f3941fd121e6a60acdefd9a682ba9a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clusterstab", max_pin="x.x") }}' - noarch: generic -# Suggests: fibroEset, genefilter -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Compute cluster stability scores for microarray data' - description: 'This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters.' + extra: identifiers: - biotools:clusterstab @@ -44,3 +25,28 @@ extra: path: recipes/bioconductor-clusterstab version: 1.52.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: fibroEset, genefilter +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + +source: + md5: f29f89a3b89fd713ff41e7adb8f18af2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-clustifyr/meta.yaml b/recipes/bioconductor-clustifyr/meta.yaml index 2cb67cd3a2219..4127fcc972821 100644 --- a/recipes/bioconductor-clustifyr/meta.yaml +++ b/recipes/bioconductor-clustifyr/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "clustifyr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package designed to aid in classifying cells from single-cell RNA sequencing data using external reference data (e.g., bulk RNA-seq, scRNA-seq, microarray, gene lists). A variety of correlation based methods and gene list enrichment methods are provided to assist cell type assignment. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Classifier for Single-cell RNA-seq Using Cell Clusters -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5fc803262c7a3b4d11d464f30a110802 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clustifyr", max_pin="x.x") }}' - noarch: generic -# Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, Seurat, gprofiler2, purrr, data.table, R.utils + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, gprofiler2, purrr, data.table, R.utils requirements: host: - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cowplot - r-dplyr @@ -37,14 +39,15 @@ requirements: - r-proxy - r-rlang - r-scales + - r-seuratobject - r-stringr - r-tibble - r-tidyr run: - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cowplot - r-dplyr @@ -56,16 +59,20 @@ requirements: - r-proxy - r-rlang - r-scales + - r-seuratobject - r-stringr - r-tibble - r-tidyr + +source: + md5: d77ecc21f83dc756601f836e80765342 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Classifier for Single-cell RNA-seq Using Cell Clusters' - description: 'Package designed to aid in classifying cells from single-cell RNA sequencing data using external reference data (e.g., bulk RNA-seq, scRNA-seq, microarray, gene lists). A variety of correlation based methods and gene list enrichment methods are provided to assist cell type assignment.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clustifyrdatahub/meta.yaml b/recipes/bioconductor-clustifyrdatahub/meta.yaml index c910400fc78c8..1433d9697ce12 100644 --- a/recipes/bioconductor-clustifyrdatahub/meta.yaml +++ b/recipes/bioconductor-clustifyrdatahub/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "clustifyrdatahub" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aac4529e5c0d71fdc49bda51c3915f61 +about: + description: References made from external single-cell mRNA sequencing data sets, stored as average gene expression matrices. For use with clustifyr to assign cell type identities. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: External data sets for clustifyr in ExperimentHub build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clustifyrdatahub", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: clustifyr, Seurat, usethis, rmarkdown, knitr, tidyr, BiocStyle requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 33c4f3c64aa6b75787aa6435a74f6416 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'External data sets for clustifyr in ExperimentHub' - description: 'References made from external single-cell mRNA sequencing data sets, stored as average gene expression matrices. For use with clustifyr to assign cell type identities.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-clustifyrdatahub/post-link.sh b/recipes/bioconductor-clustifyrdatahub/post-link.sh index 312ed6f9276d2..af8e924a1ff5b 100644 --- a/recipes/bioconductor-clustifyrdatahub/post-link.sh +++ b/recipes/bioconductor-clustifyrdatahub/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "clustifyrdatahub-1.12.0" +installBiocDataPackage.sh "clustifyrdatahub-1.16.0" diff --git a/recipes/bioconductor-clustirr/meta.yaml b/recipes/bioconductor-clustirr/meta.yaml index 58ca1182b4301..672b3c0ae61df 100644 --- a/recipes/bioconductor-clustirr/meta.yaml +++ b/recipes/bioconductor-clustirr/meta.yaml @@ -1,47 +1,82 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "ClustIRR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ClustIRR analyzes repertoires of B- and T-cell receptors. It starts by identifying communities of immune receptors with similar specificities, based on the sequences of their complementarity-determining regions (CDRs). Next, it employs a Bayesian probabilistic models to quantify differential community occupancy (DCO) between repertoires, allowing the identification of expanding or contracting communities in response to e.g. infection or cancer treatment. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Clustering of immune receptor repertoires -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ffd1884844b297c2e593e465a776fb6d build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-clustirr", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, knitr, testthat, ggplot2, patchwork, ggrepel + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, testthat, ggplot2, ggrepel, patchwork +# SystemRequirements: GNU make requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make + host: + - bioconductor-pwalign >=1.2.0,<1.3.0 - r-base + - r-bh >=1.66.0 + - r-blaster - r-future - r-future.apply - r-igraph + - r-rcpp >=0.12.0 + - r-rcppeigen >=0.3.3.3.0 + - r-rcppparallel >=5.0.1 + - r-reshape2 + - r-rstan >=2.18.1 + - r-rstantools >=2.4.0 + - r-stanheaders >=2.18.0 - r-stringdist - r-visnetwork + - libblas + - liblapack + run: + - bioconductor-pwalign >=1.2.0,<1.3.0 - r-base + - r-bh >=1.66.0 + - r-blaster - r-future - r-future.apply - r-igraph + - r-rcpp >=0.12.0 + - r-rcppeigen >=0.3.3.3.0 + - r-rcppparallel >=5.0.1 + - r-reshape2 + - r-rstan >=2.18.1 + - r-rstantools >=2.4.0 + - r-stanheaders >=2.18.0 - r-stringdist - r-visnetwork + +source: + md5: e40a8e88696411329f36d9b313fc7111 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Clustering of immune receptor repertoires' - description: 'ClustIRR is a quantitative method for clustering of immune receptor repertoires (IRRs). The algorithm identifies groups of T or B cell receptors (TCRs or BCRs) with similar specificity by comparing their sequences. ClustIRR uses graphs to visualize the specificity structures of IRRs.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cma/meta.yaml b/recipes/bioconductor-cma/meta.yaml index 7dcc40d917ad9..2d2dbe3163494 100644 --- a/recipes/bioconductor-cma/meta.yaml +++ b/recipes/bioconductor-cma/meta.yaml @@ -1,41 +1,22 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "CMA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Synthesis of microarray-based classification -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6654a3ef8f06edc618b81b8a059b2139 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cma", max_pin="x.x") }}' - noarch: generic -# Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st, mvtnorm -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Synthesis of microarray-based classification' - description: 'This package provides a comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:cma @@ -45,3 +26,28 @@ extra: path: recipes/bioconductor-cma version: 1.38.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st, mvtnorm +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + +source: + md5: 36009a31f66d88fc7e5f1136ce46880b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-cmap/meta.yaml b/recipes/bioconductor-cmap/meta.yaml index d9037cbfaab0a..cc5810be9d4a8 100644 --- a/recipes/bioconductor-cmap/meta.yaml +++ b/recipes/bioconductor-cmap/meta.yaml @@ -1,43 +1,43 @@ {% set version = "1.15.1" %} {% set name = "cMAP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dbf8df4d4540151936884e1c5d747bcf +about: + description: Annotation data file for cMAP assembled using data from public data repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: A data package containing annotation data for cMAP build: - number: 15 + noarch: generic + number: 16 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cmap", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-cmap + path: recipes/bioconductor-cmap + version: 1.15.1 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: dbf8df4d4540151936884e1c5d747bcf + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'A data package containing annotation data for cMAP' - description: 'Annotation data file for cMAP assembled using data from public data repositories' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - parent_recipe: - name: bioconductor-cmap - path: recipes/bioconductor-cmap - version: 1.15.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cmap2data/meta.yaml b/recipes/bioconductor-cmap2data/meta.yaml index 7b58d905ef119..95be49057492b 100644 --- a/recipes/bioconductor-cmap2data/meta.yaml +++ b/recipes/bioconductor-cmap2data/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "cMap2data" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c5ecbc59a690426c6def7feb720e1a7d +about: + description: Data package which provides default drug profiles for the DrugVsDisease package as well as associated gene lists and data clusters used by the DrugVsDisease package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Connectivity Map (version 2) Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cmap2data", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-cmap2data + path: recipes/bioconductor-cmap2data + version: 1.16.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9d53c236a9c4759d420576e0795f8813 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Connectivity Map (version 2) Data' - description: 'Data package which provides default drug profiles for the DrugVsDisease package as well as associated gene lists and data clusters used by the DrugVsDisease package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-cmap2data - path: recipes/bioconductor-cmap2data - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cmap2data/post-link.sh b/recipes/bioconductor-cmap2data/post-link.sh index ca70907c04096..287a6bc3a0117 100644 --- a/recipes/bioconductor-cmap2data/post-link.sh +++ b/recipes/bioconductor-cmap2data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cmap2data-1.38.0" +installBiocDataPackage.sh "cmap2data-1.42.0" diff --git a/recipes/bioconductor-cmapr/meta.yaml b/recipes/bioconductor-cmapr/meta.yaml index 03a057ffbe9ef..87533bd33b535 100644 --- a/recipes/bioconductor-cmapr/meta.yaml +++ b/recipes/bioconductor-cmapr/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "cmapR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The Connectivity Map (CMap) is a massive resource of perturbational gene expression profiles built by researchers at the Broad Institute and funded by the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) program. Please visit https://clue.io for more information. The cmapR package implements methods to parse, manipulate, and write common CMap data objects, such as annotated matrices and collections of gene sets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: CMap Tools in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 257c275c11341cac65aae8f0d8cd4e2f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cmapr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-matrixstats run: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-matrixstats + +source: + md5: 270cc4e8c96925b30015eefb5870fd63 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'CMap Tools in R' - description: 'The Connectivity Map (CMap) is a massive resource of perturbational gene expression profiles built by researchers at the Broad Institute and funded by the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) program. Please visit https://clue.io for more information. The cmapR package implements methods to parse, manipulate, and write common CMap data objects, such as annotated matrices and collections of gene sets.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cn.farms/meta.yaml b/recipes/bioconductor-cn.farms/meta.yaml index 43f61d3317be2..9f514ed475d0c 100644 --- a/recipes/bioconductor-cn.farms/meta.yaml +++ b/recipes/bioconductor-cn.farms/meta.yaml @@ -1,32 +1,47 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "cn.farms" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements the cn.FARMS algorithm for copy number variation (CNV) analysis. cn.FARMS allows to analyze the most common Affymetrix (250K-SNP6.0) array types, supports high-performance computing using snow and ff. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2.0) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: cn.FARMS - factor analysis for copy number estimation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8a991cf7fb9deb2d6ed855617dcfb853 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cn.farms", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:cn.farms + - doi:10.1093/nar/gkr197 + parent_recipe: + name: bioconductor-cn.farms + path: recipes/bioconductor-cn.farms + version: 1.28.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5, pd.genomewidesnp.6 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-affxparser >=1.74.0,<1.75.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-affxparser >=1.78.0,<1.79.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-dbi - r-ff @@ -35,36 +50,27 @@ requirements: - libblas - liblapack run: - - 'bioconductor-affxparser >=1.74.0,<1.75.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-affxparser >=1.78.0,<1.79.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-dbi - r-ff - r-lattice - r-snow - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 19b06587ff4179b8c96a74795ecac02e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2.0)' - summary: 'cn.FARMS - factor analysis for copy number estimation' - description: 'This package implements the cn.FARMS algorithm for copy number variation (CNV) analysis. cn.FARMS allows to analyze the most common Affymetrix (250K-SNP6.0) array types, supports high-performance computing using snow and ff.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:cn.farms - - doi:10.1093/nar/gkr197 - parent_recipe: - name: bioconductor-cn.farms - path: recipes/bioconductor-cn.farms - version: 1.28.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cn.mops/meta.yaml b/recipes/bioconductor-cn.mops/meta.yaml index d923f5f26fc2d..800349351ac52 100644 --- a/recipes/bioconductor-cn.mops/meta.yaml +++ b/recipes/bioconductor-cn.mops/meta.yaml @@ -1,65 +1,69 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "cn.mops" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: cn.mops (Copy Number estimation by a Mixture Of PoissonS) is a data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. The package supplies functions to convert BAM files into read count matrices or genomic ranges objects, which are the input objects for cn.mops. cn.mops models the depths of coverage across samples at each genomic position. Therefore, it does not suffer from read count biases along chromosomes. Using a Bayesian approach, cn.mops decomposes read variations across samples into integer copy numbers and noise by its mixture components and Poisson distributions, respectively. cn.mops guarantees a low FDR because wrong detections are indicated by high noise and filtered out. cn.mops is very fast and written in C++. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2.0) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: cn.mops - Mixture of Poissons for CNV detection in NGS data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e4e51a7ecd3810464be443ba9a6b6919 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cn.mops", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:cn.mops + parent_recipe: + name: bioconductor-cn.mops + path: recipes/bioconductor-cn.mops + version: 1.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: DNAcopy requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-exomecopy >=1.48.0,<1.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-exomecopy >=1.48.0,<1.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: a2b8d2bd8e4252b83429eae677e0b6e8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2.0)' - summary: 'cn.mops - Mixture of Poissons for CNV detection in NGS data' - description: 'cn.mops (Copy Number estimation by a Mixture Of PoissonS) is a data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. The package supplies functions to convert BAM files into read count matrices or genomic ranges objects, which are the input objects for cn.mops. cn.mops models the depths of coverage across samples at each genomic position. Therefore, it does not suffer from read count biases along chromosomes. Using a Bayesian approach, cn.mops decomposes read variations across samples into integer copy numbers and noise by its mixture components and Poisson distributions, respectively. cn.mops guarantees a low FDR because wrong detections are indicated by high noise and filtered out. cn.mops is very fast and written in C++.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:cn.mops - parent_recipe: - name: bioconductor-cn.mops - path: recipes/bioconductor-cn.mops - version: 1.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cnanorm/meta.yaml b/recipes/bioconductor-cnanorm/meta.yaml index 8a3abf24ba8c5..74a03badb92ce 100644 --- a/recipes/bioconductor-cnanorm/meta.yaml +++ b/recipes/bioconductor-cnanorm/meta.yaml @@ -1,45 +1,21 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "CNAnorm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Performs ratio, GC content correction and normalization of data obtained using low coverage (one read every 100-10,000 bp) high troughput sequencing. It performs a "discrete" normalization looking for the ploidy of the genome. It will also provide tumour content if at least two ploidy states can be found. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A normalization method for Copy Number Aberration in cancer samples -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b9d0f995f3466875285a152415863842 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cnanorm", max_pin="x.x") }}' -requirements: - host: - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - r-base - - libblas - - liblapack - run: - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - r-base - build: - - {{ compiler('c') }} - - {{ compiler('fortran') }} - - make -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-2-only' - summary: 'A normalization method for Copy Number Aberration in cancer samples' - description: 'Performs ratio, GC content correction and normalization of data obtained using low coverage (one read every 100-10,000 bp) high troughput sequencing. It performs a "discrete" normalization looking for the ploidy of the genome. It will also provide tumour content if at least two ploidy states can be found.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + extra: additional-platforms: - linux-aarch64 @@ -50,3 +26,33 @@ extra: path: recipes/bioconductor-cnanorm version: 1.26.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('fortran') }} + - make + host: + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - r-base + - libblas + - liblapack + run: + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - r-base + +source: + md5: ad9b870a77b07945bcd7c867c08fa04c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-cner/meta.yaml b/recipes/bioconductor-cner/meta.yaml index 902b5e1f637a4..1087a7628f691 100644 --- a/recipes/bioconductor-cner/meta.yaml +++ b/recipes/bioconductor-cner/meta.yaml @@ -1,81 +1,21 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "CNEr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Large-scale identification and advanced visualization of sets of conserved noncoding elements. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 | file LICENSE + license_file: LICENSE + summary: CNE Detection and Visualization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 56fdc5f3323b1f3efbb8d85584ff75d2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cner", max_pin="x.x") }}' -# Suggests: Gviz (>= 1.7.4), BiocStyle, knitr, rmarkdown, testthat, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, TxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Ggallus.UCSC.galGal3 -requirements: - host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' - - r-base - - 'r-dbi >=0.7' - - 'r-ggplot2 >=2.1.0' - - 'r-powerlaw >=0.60.3' - - 'r-r.utils >=2.3.0' - - 'r-readr >=0.2.2' - - 'r-reshape2 >=1.4.1' - - 'r-rsqlite >=0.11.4' - - libblas - - liblapack - run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' - - r-base - - 'r-dbi >=0.7' - - 'r-ggplot2 >=2.1.0' - - 'r-powerlaw >=0.60.3' - - 'r-r.utils >=2.3.0' - - 'r-readr >=0.2.2' - - 'r-reshape2 >=1.4.1' - - 'r-rsqlite >=0.11.4' - build: - - {{ compiler('c') }} - - make -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-2.0-only | file LICENSE' - summary: 'CNE Detection and Visualization' - description: 'Large-scale identification and advanced visualization of sets of conserved noncoding elements.' - license_file: LICENSE + extra: additional-platforms: - linux-aarch64 @@ -87,3 +27,75 @@ extra: path: recipes/bioconductor-cner version: 1.16.1 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: Gviz (>= 1.7.4), BiocStyle, knitr, rmarkdown, testthat, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, TxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Ggallus.UCSC.galGal3 +requirements: + + build: + - {{ compiler('c') }} + - make + + host: + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 + - r-base + - r-dbi >=0.7 + - r-ggplot2 >=2.1.0 + - r-powerlaw >=0.60.3 + - r-r.utils >=2.3.0 + - r-readr >=0.2.2 + - r-reshape2 >=1.4.1 + - r-rsqlite >=0.11.4 + - libblas + - liblapack + - zlib + + run: + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 + - r-base + - r-dbi >=0.7 + - r-ggplot2 >=2.1.0 + - r-powerlaw >=0.60.3 + - r-r.utils >=2.3.0 + - r-readr >=0.2.2 + - r-reshape2 >=1.4.1 + - r-rsqlite >=0.11.4 + +source: + md5: 9eeb740891291deab2ec013e894d6cdc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-cnordt/meta.yaml b/recipes/bioconductor-cnordt/meta.yaml index b6ac951b76ba2..7655a670a1555 100644 --- a/recipes/bioconductor-cnordt/meta.yaml +++ b/recipes/bioconductor-cnordt/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "CNORdt" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 74b0c2783638f7d5ce872577eb305ad3 +about: + description: This add-on to the package CellNOptR handles time-course data, as opposed to steady state data in CellNOptR. It scales the simulation step to allow comparison and model fitting for time-course data. Future versions will optimize delays and strengths for each edge. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'Add-on to CellNOptR: Discretized time treatments' build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cnordt", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' + - bioconductor-cellnoptr >=1.52.0,<1.53.0 - r-abind - r-base - libblas - liblapack run: - - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' + - bioconductor-cellnoptr >=1.52.0,<1.53.0 - r-abind - r-base - build: - - {{ compiler('c') }} - - make +source: + md5: 284c4e9d72b04ee2a6aea6b9f05dff5c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Add-on to CellNOptR: Discretized time treatments' - description: 'This add-on to the package CellNOptR handles time-course data, as opposed to steady state data in CellNOptR. It scales the simulation step to allow comparison and model fitting for time-course data. Future versions will optimize delays and strengths for each edge.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cnorfeeder/meta.yaml b/recipes/bioconductor-cnorfeeder/meta.yaml index 5e8b159d1d8a6..d27186e92a8ea 100644 --- a/recipes/bioconductor-cnorfeeder/meta.yaml +++ b/recipes/bioconductor-cnorfeeder/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "CNORfeeder" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4dd8271e71505e41edc9509155cb4f9f +about: + description: This package integrates literature-constrained and data-driven methods to infer signalling networks from perturbation experiments. It permits to extends a given network with links derived from the data via various inference methods and uses information on physical interactions of proteins to guide and validate the integration of links. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Integration of CellNOptR to add missing links build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cnorfeeder", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: minet, Rgraphviz, RUnit, BiocGenerics, igraph requirements: host: - - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-cellnoptr >=1.52.0,<1.53.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base run: - - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-cellnoptr >=1.52.0,<1.53.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base +source: + md5: d3605757ae1d4c8fe6cfff19fc9680c9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Integration of CellNOptR to add missing links' - description: 'This package integrates literature-constrained and data-driven methods to infer signalling networks from perturbation experiments. It permits to extends a given network with links derived from the data via various inference methods and uses information on physical interactions of proteins to guide and validate the integration of links.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cnorfuzzy/meta.yaml b/recipes/bioconductor-cnorfuzzy/meta.yaml index 7343bc5ed0dea..4492ebb89c0bb 100644 --- a/recipes/bioconductor-cnorfuzzy/meta.yaml +++ b/recipes/bioconductor-cnorfuzzy/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "CNORfuzzy" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is an extension to CellNOptR. It contains additional functionality needed to simulate and train a prior knowledge network to experimental data using constrained fuzzy logic (cFL, rather than Boolean logic as is the case in CellNOptR). Additionally, this package will contain functions to use for the compilation of multiple optimization results (either Boolean or cFL). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'Addon to CellNOptR: Fuzzy Logic' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c7d388f25498f45c39d8af83c5e14a89 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cnorfuzzy", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:cnorfuzzy + - doi:10.1186/1752-0509-6-133 + parent_recipe: + name: bioconductor-cnorfuzzy + path: recipes/bioconductor-cnorfuzzy + version: 1.22.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: xtable, Rgraphviz, RUnit, BiocGenerics requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' + - bioconductor-cellnoptr >=1.52.0,<1.53.0 - r-base - - 'r-nloptr >=0.8.5' + - r-nloptr >=0.8.5 - libblas - liblapack run: - - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' + - bioconductor-cellnoptr >=1.52.0,<1.53.0 - r-base - - 'r-nloptr >=0.8.5' - build: - - {{ compiler('c') }} - - make + - r-nloptr >=0.8.5 + +source: + md5: a8cde52abc735953fe73186424e16414 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Addon to CellNOptR: Fuzzy Logic' - description: 'This package is an extension to CellNOptR. It contains additional functionality needed to simulate and train a prior knowledge network to experimental data using constrained fuzzy logic (cFL, rather than Boolean logic as is the case in CellNOptR). Additionally, this package will contain functions to use for the compilation of multiple optimization results (either Boolean or cFL).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:cnorfuzzy - - doi:10.1186/1752-0509-6-133 - parent_recipe: - name: bioconductor-cnorfuzzy - path: recipes/bioconductor-cnorfuzzy - version: 1.22.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cnorode/meta.yaml b/recipes/bioconductor-cnorode/meta.yaml index 7e2f238c23ba1..2c2ea75a276dd 100644 --- a/recipes/bioconductor-cnorode/meta.yaml +++ b/recipes/bioconductor-cnorode/meta.yaml @@ -1,54 +1,59 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "CNORode" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Logic based ordinary differential equation (ODE) add-on to CellNOptR. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: ODE add-on to CellNOptR -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e93b3e3437c26f6cfab6690f78c6a6cc build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cnorode", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:cnorode + - doi:10.1186/1752-0509-6-133 + parent_recipe: + name: bioconductor-cnorode + path: recipes/bioconductor-cnorode + version: 1.22.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' + - bioconductor-cellnoptr >=1.52.0,<1.53.0 - r-base - r-genalg - - r-knitr - libblas - liblapack run: - - 'bioconductor-cellnoptr >=1.48.0,<1.49.0' + - bioconductor-cellnoptr >=1.52.0,<1.53.0 - r-base - r-genalg - - r-knitr - build: - - {{ compiler('c') }} - - make + +source: + md5: 2f2c282b6842b0648fb0571bf07d6860 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'ODE add-on to CellNOptR' - description: 'Logic based ordinary differential equation (ODE) add-on to CellNOptR.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:cnorode - - doi:10.1186/1752-0509-6-133 - parent_recipe: - name: bioconductor-cnorode - path: recipes/bioconductor-cnorode - version: 1.22.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cntools/meta.yaml b/recipes/bioconductor-cntools/meta.yaml index 45b503ee4cf32..d5895d108218a 100644 --- a/recipes/bioconductor-cntools/meta.yaml +++ b/recipes/bioconductor-cntools/meta.yaml @@ -1,44 +1,21 @@ -{% set version = "1.58.0" %} +{% set version = "1.62.0" %} {% set name = "CNTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Convert segment data into a region by sample matrix to allow for other high level computational analyses. -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e3ce148937711a84dadf67b5f09c5373 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cntools", max_pin="x.x") }}' -requirements: - host: - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - r-base - - libblas - - liblapack - run: - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - r-base - build: - - {{ compiler('c') }} - - make -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3.0-only - summary: 'Convert segment data into a region by sample matrix to allow for other high level computational analyses.' - description: 'This package provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + extra: additional-platforms: - linux-aarch64 @@ -50,3 +27,32 @@ extra: path: recipes/bioconductor-cntools version: 1.36.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + build: + - {{ compiler('c') }} + - make + host: + - bioconductor-genefilter >=1.88.0,<1.89.0 + - r-base + - libblas + - liblapack + run: + - bioconductor-genefilter >=1.88.0,<1.89.0 + - r-base + +source: + md5: 9b6334e87040b016f3f4359d07dd7a25 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-cnvfilter/meta.yaml b/recipes/bioconductor-cnvfilter/meta.yaml index 3908bc6abda4c..acd0a21ade689 100644 --- a/recipes/bioconductor-cnvfilter/meta.yaml +++ b/recipes/bioconductor-cnvfilter/meta.yaml @@ -1,60 +1,65 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "CNVfilteR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CNVfilteR identifies those CNVs that can be discarded by using the single nucleotide variant (SNV) calls that are usually obtained in common NGS pipelines. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Identifies false positives of CNV calling tools by using SNV calls -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dda71463a83db8c7aaf1bbfa79424ba3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cnvfilter", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-copynumberplots >=1.18.0,<1.19.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-karyoploter >=1.28.0,<1.29.0' - - 'bioconductor-regioner >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-copynumberplots >=1.22.0,<1.23.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-karyoploter >=1.32.0,<1.33.0 + - bioconductor-regioner >=1.38.0,<1.39.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-assertthat - r-base - r-pracma run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-copynumberplots >=1.18.0,<1.19.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-karyoploter >=1.28.0,<1.29.0' - - 'bioconductor-regioner >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-copynumberplots >=1.22.0,<1.23.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-karyoploter >=1.32.0,<1.33.0 + - bioconductor-regioner >=1.38.0,<1.39.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-assertthat - r-base - r-pracma + +source: + md5: 33255e124a5d0a8c0ce90b959defa31e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Identifies false positives of CNV calling tools by using SNV calls' - description: 'CNVfilteR identifies those CNVs that can be discarded by using the single nucleotide variant (SNV) calls that are usually obtained in common NGS pipelines.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cnvgsa/meta.yaml b/recipes/bioconductor-cnvgsa/meta.yaml index b0cf597118eb0..e80c986ca89c4 100644 --- a/recipes/bioconductor-cnvgsa/meta.yaml +++ b/recipes/bioconductor-cnvgsa/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "cnvGSA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is intended to facilitate gene-set association with rare CNVs in case-control studies. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Gene Set Analysis of (Rare) Copy Number Variants -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b3216442e27ff2c602e908aeb6a6f6e7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cnvgsa", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:cnvgsa + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-cnvgsa + path: recipes/bioconductor-cnvgsa + version: 1.24.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: cnvGSAdata, org.Hs.eg.db requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-brglm - r-doparallel - r-foreach - r-splitstackshape run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-brglm - r-doparallel - r-foreach - r-splitstackshape + +source: + md5: a4f8d41ba1f4940cc03cd262ef2a6743 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Gene Set Analysis of (Rare) Copy Number Variants' - description: 'This package is intended to facilitate gene-set association with rare CNVs in case-control studies.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:cnvgsa - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-cnvgsa - path: recipes/bioconductor-cnvgsa - version: 1.24.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cnvgsadata/meta.yaml b/recipes/bioconductor-cnvgsadata/meta.yaml index cea79ff073286..de72b3a61dd45 100644 --- a/recipes/bioconductor-cnvgsadata/meta.yaml +++ b/recipes/bioconductor-cnvgsadata/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "cnvGSAdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1cc86a2066cae55493d710c475cc7112 +about: + description: This package contains the data used in the vignette of the cnvGSA package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Data used in the vignette of the cnvGSA package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cnvgsadata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-cnvgsa >=1.46.0,<1.47.0' + - bioconductor-cnvgsa >=1.50.0,<1.51.0 - r-base run: - - 'bioconductor-cnvgsa >=1.46.0,<1.47.0' + - bioconductor-cnvgsa >=1.50.0,<1.51.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fe2b4f6e04f12f795b1b6fff123446ce + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Data used in the vignette of the cnvGSA package' - description: 'This package contains the data used in the vignette of the cnvGSA package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cnvgsadata/post-link.sh b/recipes/bioconductor-cnvgsadata/post-link.sh index 068b0cb6fee2b..249f432cef9ba 100644 --- a/recipes/bioconductor-cnvgsadata/post-link.sh +++ b/recipes/bioconductor-cnvgsadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cnvgsadata-1.38.0" +installBiocDataPackage.sh "cnvgsadata-1.42.0" diff --git a/recipes/bioconductor-cnviz/meta.yaml b/recipes/bioconductor-cnviz/meta.yaml index 000ef56911ecf..ed59df6b593e9 100644 --- a/recipes/bioconductor-cnviz/meta.yaml +++ b/recipes/bioconductor-cnviz/meta.yaml @@ -1,54 +1,59 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "CNViz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CNViz takes probe, gene, and segment-level log2 copy number ratios and launches a Shiny app to visualize your sample's copy number profile. You can also integrate loss of heterozygosity (LOH) and single nucleotide variant (SNV) data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Copy Number Visualization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e0499b53c29869a1f661e40f4e1f76ca build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cnviz", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr requirements: host: - - 'bioconductor-copynumberplots >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-karyoploter >=1.28.0,<1.29.0' + - bioconductor-copynumberplots >=1.22.0,<1.23.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-karyoploter >=1.32.0,<1.33.0 - r-base - r-dplyr - r-dt - r-magrittr - r-plotly - r-scales - - 'r-shiny >=1.5.0' + - r-shiny >=1.5.0 run: - - 'bioconductor-copynumberplots >=1.18.0,<1.19.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-karyoploter >=1.28.0,<1.29.0' + - bioconductor-copynumberplots >=1.22.0,<1.23.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-karyoploter >=1.32.0,<1.33.0 - r-base - r-dplyr - r-dt - r-magrittr - r-plotly - r-scales - - 'r-shiny >=1.5.0' + - r-shiny >=1.5.0 + +source: + md5: 7e459d52fa8d539173d08c277f26709e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Copy Number Visualization' - description: 'CNViz takes probe, gene, and segment-level log2 copy number ratios and launches a Shiny app to visualize your sample''s copy number profile. You can also integrate loss of heterozygosity (LOH) and single nucleotide variant (SNV) data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cnvmetrics/meta.yaml b/recipes/bioconductor-cnvmetrics/meta.yaml index 5a6a3e47ff376..16d9bdbad14cd 100644 --- a/recipes/bioconductor-cnvmetrics/meta.yaml +++ b/recipes/bioconductor-cnvmetrics/meta.yaml @@ -1,52 +1,57 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "CNVMetrics" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The CNVMetrics package calculates similarity metrics to facilitate copy number variant comparison among samples and/or methods. Similarity metrics can be employed to compare CNV profiles of genetically unrelated samples as well as those with a common genetic background. Some metrics are based on the shared amplified/deleted regions while other metrics rely on the level of amplification/deletion. The data type used as input is a plain text file containing the genomic position of the copy number variations, as well as the status and/or the log2 ratio values. Finally, a visualization tool is provided to explore resulting metrics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Copy Number Variant Metrics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ebb4f847744aaddcc125d870b1a67154 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cnvmetrics", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-gridextra - r-magrittr - r-pheatmap - r-rbeta2009 run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-gridextra - r-magrittr - r-pheatmap - r-rbeta2009 + +source: + md5: beeeff979554622def43fe96588bdf28 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Copy Number Variant Metrics' - description: 'The CNVMetrics package calculates similarity metrics to facilitate copy number variant comparison among samples and/or methods. Similarity metrics can be employed to compare CNV profiles of genetically unrelated samples as well as those with a common genetic background. Some metrics are based on the shared amplified/deleted regions while other metrics rely on the level of amplification/deletion. The data type used as input is a plain text file containing the genomic position of the copy number variations, as well as the status and/or the log2 ratio values. Finally, a visualization tool is provided to explore resulting metrics.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cnvpanelizer/meta.yaml b/recipes/bioconductor-cnvpanelizer/meta.yaml index 3af7fd5235897..a326a2326efd2 100644 --- a/recipes/bioconductor-cnvpanelizer/meta.yaml +++ b/recipes/bioconductor-cnvpanelizer/meta.yaml @@ -1,35 +1,45 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "CNVPanelizer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A method that allows for the use of a collection of non-matched normal tissue samples. Our approach uses a non-parametric bootstrap subsampling of the available reference samples to estimate the distribution of read counts from targeted sequencing. As inspired by random forest, this is combined with a procedure that subsamples the amplicons associated with each of the targeted genes. The obtained information allows us to reliably classify the copy number aberrations on the gene level. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Reliable CNV detection in targeted sequencing applications -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d984f2fa3f3db99f3ccf72b5c9a0890 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cnvpanelizer", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:cnvpanelizer + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-cnvpanelizer + path: recipes/bioconductor-cnvpanelizer + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-exomecopy >=1.48.0,<1.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-noiseq >=2.46.0,<2.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-noiseq >=2.50.0,<2.51.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-foreach - r-ggplot2 @@ -43,14 +53,13 @@ requirements: - r-stringr - r-testthat run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-exomecopy >=1.48.0,<1.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-noiseq >=2.46.0,<2.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-noiseq >=2.50.0,<2.51.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-foreach - r-ggplot2 @@ -63,21 +72,16 @@ requirements: - r-shinyjs - r-stringr - r-testthat + +source: + md5: 64d3644a559a62bc6712c36dfaf1275f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Reliable CNV detection in targeted sequencing applications' - description: 'A method that allows for the use of a collection of non-matched normal tissue samples. Our approach uses a non-parametric bootstrap subsampling of the available reference samples to estimate the distribution of read counts from targeted sequencing. As inspired by random forest, this is combined with a procedure that subsamples the amplicons associated with each of the targeted genes. The obtained information allows us to reliably classify the copy number aberrations on the gene level.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:cnvpanelizer - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-cnvpanelizer - path: recipes/bioconductor-cnvpanelizer - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cnvranger/meta.yaml b/recipes/bioconductor-cnvranger/meta.yaml index cba6dd7a6a6ec..6051ab27e2982 100644 --- a/recipes/bioconductor-cnvranger/meta.yaml +++ b/recipes/bioconductor-cnvranger/meta.yaml @@ -1,40 +1,42 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "CNVRanger" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The CNVRanger package implements a comprehensive tool suite for CNV analysis. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and association analysis with gene expression and quantitative phenotypes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Summarization and expression/phenotype association of CNV ranges -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3e68952c47447dfad311d1adf7b971d1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cnvranger", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked, BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment, TCGAutils, TxDb.Hsapiens.UCSC.hg19.knownGene, curatedTCGAData, ensembldb, grid, knitr, org.Hs.eg.db, regioneR, rmarkdown, statmod requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-gdsarray >=1.22.0,<1.23.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-snprelate >=1.36.0,<1.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-gdsarray >=1.26.0,<1.27.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-raggedexperiment >=1.30.0,<1.31.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-snprelate >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-lattice @@ -42,20 +44,21 @@ requirements: - r-qqman - r-rappdirs - r-reshape2 + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-gdsarray >=1.22.0,<1.23.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-snprelate >=1.36.0,<1.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-gdsarray >=1.26.0,<1.27.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-raggedexperiment >=1.30.0,<1.31.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-snprelate >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-lattice @@ -63,12 +66,16 @@ requirements: - r-qqman - r-rappdirs - r-reshape2 + +source: + md5: 557c616eefc094232f701cb1fd8babd3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Summarization and expression/phenotype association of CNV ranges' - description: 'The CNVRanger package implements a comprehensive tool suite for CNV analysis. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and association analysis with gene expression and quantitative phenotypes.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cnvrd2/meta.yaml b/recipes/bioconductor-cnvrd2/meta.yaml index 85d6f7fae13aa..c4a368bd9c2a6 100644 --- a/recipes/bioconductor-cnvrd2/meta.yaml +++ b/recipes/bioconductor-cnvrd2/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "CNVrd2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CNVrd2 uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9cc2c933a0a521472b5eb6f1382cefd5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cnvrd2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: host: - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-ggplot2 - r-gridextra - r-rjags run: - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-ggplot2 - r-gridextra - r-rjags + +source: + md5: 5a85b6adfb7f327bfad3278351807508 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.' - description: 'CNVrd2 uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cocitestats/meta.yaml b/recipes/bioconductor-cocitestats/meta.yaml index 5c72102058add..961d5d7fd9c2e 100644 --- a/recipes/bioconductor-cocitestats/meta.yaml +++ b/recipes/bioconductor-cocitestats/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "CoCiteStats" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de358f1bd9429dbedc2e7bc91037373a +about: + description: A collection of software tools for dealing with co-citation data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: CPL + summary: Different test statistics based on co-citation. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cocitestats", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base +source: + md5: 6a91c1816f1303cbaebd69f9bf7497f0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: CPL - summary: 'Different test statistics based on co-citation.' - description: 'A collection of software tools for dealing with co-citation data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cocoa/meta.yaml b/recipes/bioconductor-cocoa/meta.yaml index f61f932994f3b..8b5a9ca1f4054 100644 --- a/recipes/bioconductor-cocoa/meta.yaml +++ b/recipes/bioconductor-cocoa/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "2.16.0" %} +{% set version = "2.20.0" %} {% set name = "COCOA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: COCOA is a method for understanding epigenetic variation among samples. COCOA can be used with epigenetic data that includes genomic coordinates and an epigenetic signal, such as DNA methylation and chromatin accessibility data. To describe the method on a high level, COCOA quantifies inter-sample variation with either a supervised or unsupervised technique then uses a database of "region sets" to annotate the variation among samples. A region set is a set of genomic regions that share a biological annotation, for instance transcription factor (TF) binding regions, histone modification regions, or open chromatin regions. COCOA can identify region sets that are associated with epigenetic variation between samples and increase understanding of variation in your data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Coordinate Covariation Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6525a033b4b6ab78aa4ecb8e3f35b6e3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cocoa", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mira >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mira >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-fitdistrplus @@ -36,25 +38,29 @@ requirements: - r-simplecache - r-tidyr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mira >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mira >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-fitdistrplus - r-ggplot2 - r-simplecache - r-tidyr + +source: + md5: 954b277e8bb4ca0dc135f019f3d48849 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Coordinate Covariation Analysis' - description: 'COCOA is a method for understanding epigenetic variation among samples. COCOA can be used with epigenetic data that includes genomic coordinates and an epigenetic signal, such as DNA methylation and chromatin accessibility data. To describe the method on a high level, COCOA quantifies inter-sample variation with either a supervised or unsupervised technique then uses a database of "region sets" to annotate the variation among samples. A region set is a set of genomic regions that share a biological annotation, for instance transcription factor (TF) binding regions, histone modification regions, or open chromatin regions. COCOA can identify region sets that are associated with epigenetic variation between samples and increase understanding of variation in your data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-codelink/meta.yaml b/recipes/bioconductor-codelink/meta.yaml index 5aa4146f8d961..71311056c4b22 100644 --- a/recipes/bioconductor-codelink/meta.yaml +++ b/recipes/bioconductor-codelink/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.70.0" %} +{% set version = "1.74.0" %} {% set name = "codelink" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package facilitates reading, preprocessing and manipulating Codelink microarray data. The raw data must be exported as text file using the Codelink software. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Manipulation of Codelink microarray data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7988c997146174710b5faacc70c10328 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-codelink", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:codelink + parent_recipe: + name: bioconductor-codelink + path: recipes/bioconductor-codelink + version: 1.48.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: genefilter, parallel, knitr requirements: host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base + +source: + md5: 387c8424b0f557fb62bd72dd48ca34c2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Manipulation of Codelink microarray data' - description: 'This package facilitates reading, preprocessing and manipulating Codelink microarray data. The raw data must be exported as text file using the Codelink software.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:codelink - parent_recipe: - name: bioconductor-codelink - path: recipes/bioconductor-codelink - version: 1.48.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-codex/meta.yaml b/recipes/bioconductor-codex/meta.yaml index 0b4bb41c7a4db..b3fd9c501c1a9 100644 --- a/recipes/bioconductor-codex/meta.yaml +++ b/recipes/bioconductor-codex/meta.yaml @@ -1,51 +1,22 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "CODEX" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A normalization and copy number variation calling procedure for whole exome DNA sequencing data. CODEX relies on the availability of multiple samples processed using the same sequencing pipeline for normalization, and does not require matched controls. The normalization model in CODEX includes terms that specifically remove biases due to GC content, exon length and targeting and amplification efficiency, and latent systemic artifacts. CODEX also includes a Poisson likelihood-based recursive segmentation procedure that explicitly models the count-based exome sequencing data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b1f67c5fbf4bbe4a3ee4f6da956a886 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-codex", max_pin="x.x") }}' - noarch: generic -# Suggests: WES.1KG.WUGSC -requirements: - host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - r-base - run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing' - description: 'A normalization and copy number variation calling procedure for whole exome DNA sequencing data. CODEX relies on the availability of multiple samples processed using the same sequencing pipeline for normalization, and does not require matched controls. The normalization model in CODEX includes terms that specifically remove biases due to GC content, exon length and targeting and amplification efficiency, and latent systemic artifacts. CODEX also includes a Poisson likelihood-based recursive segmentation procedure that explicitly models the count-based exome sequencing data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + extra: identifiers: - biotools:codex @@ -55,3 +26,38 @@ extra: path: recipes/bioconductor-codex version: 1.12.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: WES.1KG.WUGSC +requirements: + host: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + run: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + +source: + md5: 55a9e6c438b1215103475aac74e9c49e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-cogaps/meta.yaml b/recipes/bioconductor-cogaps/meta.yaml index c891b02938f1c..478f08545c03c 100644 --- a/recipes/bioconductor-cogaps/meta.yaml +++ b/recipes/bioconductor-cogaps/meta.yaml @@ -1,33 +1,39 @@ -{% set version = "3.22.0" %} +{% set version = "3.26.0" %} {% set name = "CoGAPS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_3_clause + file LICENSE + license_file: LICENSE + summary: Coordinated Gene Activity in Pattern Sets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d4c9ec9b2be6c77fbb47c632b62c84b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cogaps", max_pin="x.x") }}' -# Suggests: testthat, knitr, rmarkdown, BiocStyle, SeuratObject + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, knitr, rmarkdown, BiocStyle, SeuratObject, BiocFileCache requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bh - r-cluster @@ -35,19 +41,17 @@ requirements: - r-forcats - r-ggplot2 - r-gplots - - r-msigdbr - r-rcolorbrewer - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bh - r-cluster @@ -55,21 +59,18 @@ requirements: - r-forcats - r-ggplot2 - r-gplots - - r-msigdbr - r-rcolorbrewer - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 599bdb86d2235555ce1540335932f4db + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_3_clause + file LICENSE' - summary: 'Coordinated Gene Activity in Pattern Sets' - description: 'Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cogena/meta.yaml b/recipes/bioconductor-cogena/meta.yaml index ea4472b90f122..849fa67a871f5 100644 --- a/recipes/bioconductor-cogena/meta.yaml +++ b/recipes/bioconductor-cogena/meta.yaml @@ -1,28 +1,40 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "cogena" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: cogena is a workflow for co-expressed gene-set enrichment analysis. It aims to discovery smaller scale, but highly correlated cellular events that may be of great biological relevance. A novel pipeline for drug discovery and drug repositioning based on the cogena workflow is proposed. Particularly, candidate drugs can be predicted based on the gene expression of disease-related data, or other similar drugs can be identified based on the gene expression of drug-related data. Moreover, the drug mode of action can be disclosed by the associated pathway analysis. In summary, cogena is a flexible workflow for various gene set enrichment analysis for co-expressed genes, with a focus on pathway/GO analysis and drug repositioning. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: co-expressed gene-set enrichment analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 47a50e5f5d62a9b2f6fcd7bf3f5b9cc6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cogena", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:cogena + - doi:10.1186/s12864-016-2737-8 + parent_recipe: + name: bioconductor-cogena + path: recipes/bioconductor-cogena + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown (>= 2.1) requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-amap - r-apcluster - r-base @@ -43,8 +55,9 @@ requirements: - r-stringr - r-tibble - r-tidyr + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-amap - r-apcluster - r-base @@ -65,21 +78,16 @@ requirements: - r-stringr - r-tibble - r-tidyr + +source: + md5: e323f5351be6fba8d4a0069f7f7fc609 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'co-expressed gene-set enrichment analysis' - description: 'cogena is a workflow for co-expressed gene-set enrichment analysis. It aims to discovery smaller scale, but highly correlated cellular events that may be of great biological relevance. A novel pipeline for drug discovery and drug repositioning based on the cogena workflow is proposed. Particularly, candidate drugs can be predicted based on the gene expression of disease-related data, or other similar drugs can be identified based on the gene expression of drug-related data. Moreover, the drug mode of action can be disclosed by the associated pathway analysis. In summary, cogena is a flexible workflow for various gene set enrichment analysis for co-expressed genes, with a focus on pathway/GO analysis and drug repositioning.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:cogena - - doi:10.1186/s12864-016-2737-8 - parent_recipe: - name: bioconductor-cogena - path: recipes/bioconductor-cogena - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cogeqc/meta.yaml b/recipes/bioconductor-cogeqc/meta.yaml index 49d2616f6027b..cd5897ab8b0bb 100644 --- a/recipes/bioconductor-cogeqc/meta.yaml +++ b/recipes/bioconductor-cogeqc/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "cogeqc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly and annotation quality with BUSCOs and comparisons of statistics with publicly available genomes on the NCBI; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualization functions to explore QC summary statistics.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Systematic quality checks on comparative genomics analyses -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 751833fc95e416546193b021e0cbfc69 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cogeqc", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle, rmarkdown, covr # SystemRequirements: BUSCO (>= 5.1.3) requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 - r-base - r-ggbeeswarm - r-ggplot2 @@ -35,8 +37,8 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 - r-base - r-ggbeeswarm - r-ggplot2 @@ -46,13 +48,16 @@ requirements: - r-reshape2 - r-rlang - r-scales + +source: + md5: fcade09d62bdf4581ae0b470ad66ea5d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Systematic quality checks on comparative genomics analyses' - description: 'cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly and annotation quality with BUSCOs and comparisons of statistics with publicly available genomes on the NCBI; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualization functions to explore QC summary statistics.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cogito/meta.yaml b/recipes/bioconductor-cogito/meta.yaml index 85a806043f509..7f53734de8c88 100644 --- a/recipes/bioconductor-cogito/meta.yaml +++ b/recipes/bioconductor-cogito/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "Cogito" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Biological studies often consist of multiple conditions which are examined with different laboratory set ups like RNA-sequencing or ChIP-sequencing. To get an overview about the whole resulting data set, Cogito provides an automated, complete, reproducible and clear report about all samples and basic comparisons between all different samples. This report can be used as documentation about the data set or as starting point for further custom analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 934ceee8a56ab742bbf3c09af96cb2ba build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cogito", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, markdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0 - r-base - r-biocmanager - r-entropy @@ -36,12 +38,12 @@ requirements: - r-magrittr - r-rmarkdown run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0 - r-base - r-biocmanager - r-entropy @@ -49,13 +51,16 @@ requirements: - r-jsonlite - r-magrittr - r-rmarkdown + +source: + md5: 8854881ef6815a33908f11ebd03c81ab + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets' - description: 'Biological studies often consist of multiple conditions which are examined with different laboratory set ups like RNA-sequencing or ChIP-sequencing. To get an overview about the whole resulting data set, Cogito provides an automated, complete, reproducible and clear report about all samples and basic comparisons between all different samples. This report can be used as documentation about the data set or as starting point for further custom analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cogps/meta.yaml b/recipes/bioconductor-cogps/meta.yaml index 558d1ed731974..d6fffb964527f 100644 --- a/recipes/bioconductor-cogps/meta.yaml +++ b/recipes/bioconductor-cogps/meta.yaml @@ -1,39 +1,20 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "coGPS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a824d8a41fee47628eb7f369adef4a2c +about: + description: Gene Set Enrichment Analysis of P-value based statistics for outlier gene detection in dataset merged from multiple studies + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: cancer outlier Gene Profile Sets build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cogps", max_pin="x.x") }}' - noarch: generic -# Suggests: limma -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'cancer outlier Gene Profile Sets' - description: 'Gene Set Enrichment Analysis of P-value based statistics for outlier gene detection in dataset merged from multiple studies' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' extra: identifiers: - biotools:cogps @@ -42,4 +23,23 @@ extra: name: bioconductor-cogps path: recipes/bioconductor-cogps version: 1.24.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: limma +requirements: + host: + - r-base + run: + - r-base +source: + md5: 24c06b97648ec7877c93dc5c8a98240f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cohcapanno/meta.yaml b/recipes/bioconductor-cohcapanno/meta.yaml index 4c64d0e2c842f..5c2e31afd9c8c 100644 --- a/recipes/bioconductor-cohcapanno/meta.yaml +++ b/recipes/bioconductor-cohcapanno/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "COHCAPanno" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 78fd4891651a8a62779fe402a13ba6b1 +about: + description: Provides genomic location, nearby CpG island and nearby gene information for common Illumina methylation array platforms + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Annotations for City of Hope CpG Island Analysis Pipeline build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cohcapanno", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-cohcapanno + path: recipes/bioconductor-cohcapanno + version: 1.16.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4e0bffabf3c275f5d2a17c52e478d02d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Annotations for City of Hope CpG Island Analysis Pipeline' - description: 'Provides genomic location, nearby CpG island and nearby gene information for common Illumina methylation array platforms' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-cohcapanno - path: recipes/bioconductor-cohcapanno - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cohcapanno/post-link.sh b/recipes/bioconductor-cohcapanno/post-link.sh index 4b2b9b6c06bfa..a2743a9ede433 100644 --- a/recipes/bioconductor-cohcapanno/post-link.sh +++ b/recipes/bioconductor-cohcapanno/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cohcapanno-1.38.0" +installBiocDataPackage.sh "cohcapanno-1.42.0" diff --git a/recipes/bioconductor-cola/meta.yaml b/recipes/bioconductor-cola/meta.yaml index f5913bc74f273..1d8e5f53dfc14 100644 --- a/recipes/bioconductor-cola/meta.yaml +++ b/recipes/bioconductor-cola/meta.yaml @@ -1,32 +1,40 @@ -{% set version = "2.8.0" %} +{% set version = "2.12.0" %} {% set name = "cola" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Subgroup classification is a basic task in genomic data analysis, especially for gene expression and DNA methylation data analysis. It can also be used to test the agreement to known clinical annotations, or to test whether there exist significant batch effects. The cola package provides a general framework for subgroup classification by consensus partitioning. It has the following features: 1. It modularizes the consensus partitioning processes that various methods can be easily integrated. 2. It provides rich visualizations for interpreting the results. 3. It allows running multiple methods at the same time and provides functionalities to straightforward compare results. 4. It provides a new method to extract features which are more efficient to separate subgroups. 5. It automatically generates detailed reports for the complete analysis. 6. It allows applying consensus partitioning in a hierarchical manner.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: A Framework for Consensus Partitioning -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 57e054e12610fb8d62de83c22f6ed1de build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cola", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE, AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree, dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot, flexclust, randomForest, e1071 requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-impute >=1.80.0,<1.81.0 - r-base - r-brew - - 'r-circlize >=0.4.7' + - r-circlize >=0.4.7 - r-clue - r-cluster - r-crayon @@ -36,28 +44,29 @@ requirements: - r-eulerr - r-foreach - r-getoptlong - - 'r-globaloptions >=0.1.0' + - r-globaloptions >=0.1.0 - r-httr - r-irlba - - 'r-knitr >=1.4.0' - - 'r-markdown >=1.6' + - r-knitr >=1.4.0 + - r-markdown >=1.6 - r-matrixstats - r-mclust - r-microbenchmark - r-png - r-rcolorbrewer - - 'r-rcpp >=0.11.0' + - r-rcpp >=0.11.0 - r-skmeans - r-xml2 - libblas - liblapack + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-impute >=1.80.0,<1.81.0 - r-base - r-brew - - 'r-circlize >=0.4.7' + - r-circlize >=0.4.7 - r-clue - r-cluster - r-crayon @@ -67,30 +76,29 @@ requirements: - r-eulerr - r-foreach - r-getoptlong - - 'r-globaloptions >=0.1.0' + - r-globaloptions >=0.1.0 - r-httr - r-irlba - - 'r-knitr >=1.4.0' - - 'r-markdown >=1.6' + - r-knitr >=1.4.0 + - r-markdown >=1.6 - r-matrixstats - r-mclust - r-microbenchmark - r-png - r-rcolorbrewer - - 'r-rcpp >=0.11.0' + - r-rcpp >=0.11.0 - r-skmeans - r-xml2 - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: b63066e926108c9466fe3aefad8c655f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'A Framework for Consensus Partitioning' - description: 'Subgroup classification is a basic task in genomic data analysis, especially for gene expression and DNA methylation data analysis. It can also be used to test the agreement to known clinical annotations, or to test whether there exist significant batch effects. The cola package provides a general framework for subgroup classification by consensus partitioning. It has the following features: 1. It modularizes the consensus partitioning processes that various methods can be easily integrated. 2. It provides rich visualizations for interpreting the results. 3. It allows running multiple methods at the same time and provides functionalities to straightforward compare results. 4. It provides a new method to extract features which are more efficient to separate subgroups. 5. It automatically generates detailed reports for the complete analysis. 6. It allows applying consensus partitioning in a hierarchical manner.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-colonca/meta.yaml b/recipes/bioconductor-colonca/meta.yaml index 642bf020f6e11..bad187882335a 100644 --- a/recipes/bioconductor-colonca/meta.yaml +++ b/recipes/bioconductor-colonca/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "colonCA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d12f03a7ded676f392dbbb26bbbef174 +about: + description: exprSet for Alon et al. (1999) colon cancer data + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: exprSet for Alon et al. (1999) colon cancer data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-colonca", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 06c2d5c6e9853feb34e80befab9356f7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'exprSet for Alon et al. (1999) colon cancer data' - description: 'exprSet for Alon et al. (1999) colon cancer data' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-colonca/post-link.sh b/recipes/bioconductor-colonca/post-link.sh index 63e3e55b7a7a0..8a1ce933aff6b 100644 --- a/recipes/bioconductor-colonca/post-link.sh +++ b/recipes/bioconductor-colonca/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "colonca-1.44.0" +installBiocDataPackage.sh "colonca-1.48.0" diff --git a/recipes/bioconductor-comapr/meta.yaml b/recipes/bioconductor-comapr/meta.yaml index 130fa29cd2cd1..0520eb38f2942 100644 --- a/recipes/bioconductor-comapr/meta.yaml +++ b/recipes/bioconductor-comapr/meta.yaml @@ -1,34 +1,37 @@ -{% set version = "1.6.1" %} +{% set version = "1.10.0" %} {% set name = "comapr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: comapr detects crossover intervals for single gametes from their haplotype states sequences and stores the crossovers in GRanges object. The genetic distances can then be calculated via the mapping functions using estimated crossover rates for maker intervals. Visualisation functions for plotting interval-based genetic map or cumulative genetic distances are implemented, which help reveal the variation of crossovers landscapes across the genome and across individuals. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Crossover analysis and genetic map construction -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 64dbcfb7f563dc874dc327988ebf8c07 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-comapr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), statmod requirements: + host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-dplyr @@ -43,14 +46,15 @@ requirements: - r-rlang - r-scales - r-tidyr + run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-dplyr @@ -65,13 +69,16 @@ requirements: - r-rlang - r-scales - r-tidyr + +source: + md5: 066b98a23a1f2031231e2b58f5cd3f18 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Crossover analysis and genetic map construction' - description: 'comapr detects crossover intervals for single gametes from their haplotype states sequences and stores the crossovers in GRanges object. The genetic distances can then be calculated via the mapping functions using estimated crossover rates for maker intervals. Visualisation functions for plotting interval-based genetic map or cumulative genetic distances are implemented, which help reveal the variation of crossovers landscapes across the genome and across individuals.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-combi/meta.yaml b/recipes/bioconductor-combi/meta.yaml index 9998659a07a49..ae70506f9252e 100644 --- a/recipes/bioconductor-combi/meta.yaml +++ b/recipes/bioconductor-combi/meta.yaml @@ -1,65 +1,70 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "combi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This explorative ordination method combines quasi-likelihood estimation, compositional regression models and latent variable models for integrative visualization of several omics datasets. Both unconstrained and constrained integration are available. The results are shown as interpretable, compositional multiplots. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Compositional omics model based visual integration -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6fe16559db40b31126eb543abf6819fa build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-combi", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-alabama - r-base - r-bb - r-cobs - r-dbi - r-ggplot2 - - 'r-matrix >=1.6.0' + - r-matrix >=1.6.0 - r-nleqslv - r-reshape2 - r-tensor - r-vegan run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-alabama - r-base - r-bb - r-cobs - r-dbi - r-ggplot2 - - 'r-matrix >=1.6.0' + - r-matrix >=1.6.0 - r-nleqslv - r-reshape2 - r-tensor - r-vegan + +source: + md5: f5df09ca854e0077d792b7cebc0f7d12 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Compositional omics model based visual integration' - description: 'This explorative ordination method combines quasi-likelihood estimation, compositional regression models and latent variable models for integrative visualization of several omics datasets. Both unconstrained and constrained integration are available. The results are shown as interpretable, compositional multiplots.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-comethdmr/meta.yaml b/recipes/bioconductor-comethdmr/meta.yaml index 710278af6f46a..da04da110191c 100644 --- a/recipes/bioconductor-comethdmr/meta.yaml +++ b/recipes/bioconductor-comethdmr/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "coMethDMR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: coMethDMR identifies genomic regions associated with continuous phenotypes by optimally leverages covariations among CpGs within predefined genomic regions. Instead of testing all CpGs within a genomic region, coMethDMR carries out an additional step that selects co-methylated sub-regions first without using any outcome information. Next, coMethDMR tests association between methylation within the sub-region and continuous phenotype using a random coefficient mixed effects model, which models both variations between CpG sites within the region and differential methylation simultaneously. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0a6229d90868a4a60eb0f72c4499d1fc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-comethdmr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, corrplot, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-lmertest run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-lmertest + +source: + md5: 10576754f41e3ca13eb173a258fb380c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies' - description: 'coMethDMR identifies genomic regions associated with continuous phenotypes by optimally leverages covariations among CpGs within predefined genomic regions. Instead of testing all CpGs within a genomic region, coMethDMR carries out an additional step that selects co-methylated sub-regions first without using any outcome information. Next, coMethDMR tests association between methylation within the sub-region and continuous phenotype using a random coefficient mixed effects model, which models both variations between CpG sites within the region and differential methylation simultaneously.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-compass/meta.yaml b/recipes/bioconductor-compass/meta.yaml index 7b4d01bdbc668..1e58f755b565b 100644 --- a/recipes/bioconductor-compass/meta.yaml +++ b/recipes/bioconductor-compass/meta.yaml @@ -1,27 +1,45 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "COMPASS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: COMPASS is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. COMPASS uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Combinatorial Polyfunctionality Analysis of Single Cells -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ab4a9ce40637244377f77b7baaecc38 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-compass", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:compass + - doi:10.1038/nbt.3187 + parent_recipe: + name: bioconductor-compass + path: recipes/bioconductor-compass + version: 1.18.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2, progress requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 - r-abind - r-base - r-clue @@ -34,7 +52,7 @@ requirements: - r-pdist - r-plyr - r-rcolorbrewer - - 'r-rcpp >=0.11.0' + - r-rcpp >=0.11.0 - r-reshape2 - r-rlang - r-rmarkdown @@ -42,8 +60,9 @@ requirements: - r-tidyr - libblas - liblapack + run: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 - r-abind - r-base - r-clue @@ -56,32 +75,22 @@ requirements: - r-pdist - r-plyr - r-rcolorbrewer - - 'r-rcpp >=0.11.0' + - r-rcpp >=0.11.0 - r-reshape2 - r-rlang - r-rmarkdown - r-scales - r-tidyr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 66b61eaa89a7de69465c9d5d98d8f7a6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Combinatorial Polyfunctionality Analysis of Single Cells' - description: 'COMPASS is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. COMPASS uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject''s immune response to external stimuli such as infection or vaccination.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:compass - - doi:10.1038/nbt.3187 - parent_recipe: - name: bioconductor-compass - path: recipes/bioconductor-compass - version: 1.18.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-compcoder/meta.yaml b/recipes/bioconductor-compcoder/meta.yaml index 5cc77115da02b..4ff6fff909d3f 100644 --- a/recipes/bioconductor-compcoder/meta.yaml +++ b/recipes/bioconductor-compcoder/meta.yaml @@ -1,29 +1,32 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "compcodeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides extensive functionality for comparing results obtained by different methods for differential expression analysis of RNAseq data. It also contains functions for simulating count data. Finally, it provides convenient interfaces to several packages for performing the differential expression analysis. These can also be used as templates for setting up and running a user-defined differential analysis workflow within the framework of the package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b1ec77496e614cf3399843b8c34e6ab2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-compcoder", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, EBSeq, DESeq2 (>= 1.1.31), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree, tidytree, statmod, covr, sva, tcltk requirements: + host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-ape - r-base - r-catools @@ -31,8 +34,8 @@ requirements: - r-gplots - r-gtools - r-kernsmooth - - 'r-knitr >=1.2' - - 'r-lattice >=0.16' + - r-knitr >=1.2 + - r-lattice >=0.16 - r-markdown - r-mass - r-matrixstats @@ -45,9 +48,10 @@ requirements: - r-sm - r-stringr - r-vioplot + run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-ape - r-base - r-catools @@ -55,8 +59,8 @@ requirements: - r-gplots - r-gtools - r-kernsmooth - - 'r-knitr >=1.2' - - 'r-lattice >=0.16' + - r-knitr >=1.2 + - r-lattice >=0.16 - r-markdown - r-mass - r-matrixstats @@ -69,13 +73,16 @@ requirements: - r-sm - r-stringr - r-vioplot + +source: + md5: ecec021bb3b146653a2ccd867faaa0b7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods' - description: 'This package provides extensive functionality for comparing results obtained by different methods for differential expression analysis of RNAseq data. It also contains functions for simulating count data. Finally, it provides convenient interfaces to several packages for performing the differential expression analysis. These can also be used as templates for setting up and running a user-defined differential analysis workflow within the framework of the package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-compepitools/meta.yaml b/recipes/bioconductor-compepitools/meta.yaml index df49a8380538b..abb9f3022b01b 100644 --- a/recipes/bioconductor-compepitools/meta.yaml +++ b/recipes/bioconductor-compepitools/meta.yaml @@ -1,72 +1,78 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "compEpiTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for computational epigenomics developed for the analysis, integration and simultaneous visualization of various (epi)genomics data types across multiple genomic regions in multiple samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Tools for computational epigenomics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ccd28b8de6020ae19f303fc7009ce19 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-compepitools", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:compepitools + parent_recipe: + name: bioconductor-compepitools + path: recipes/bioconductor-compepitools + version: 1.14.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-methylpipe >=1.36.0,<1.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-methylpipe >=1.40.0,<1.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-topgo >=2.58.0,<2.59.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-gplots run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-methylpipe >=1.36.0,<1.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-methylpipe >=1.40.0,<1.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-topgo >=2.58.0,<2.59.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-gplots + +source: + md5: daeea1cf6db4512a521be9dd55946c95 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL - summary: 'Tools for computational epigenomics' - description: 'Tools for computational epigenomics developed for the analysis, integration and simultaneous visualization of various (epi)genomics data types across multiple genomic regions in multiple samples.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:compepitools - parent_recipe: - name: bioconductor-compepitools - path: recipes/bioconductor-compepitools - version: 1.14.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-complexheatmap/meta.yaml b/recipes/bioconductor-complexheatmap/meta.yaml index e97a5929f5d7d..d21a72eb70f4c 100644 --- a/recipes/bioconductor-complexheatmap/meta.yaml +++ b/recipes/bioconductor-complexheatmap/meta.yaml @@ -1,30 +1,40 @@ -{% set version = "2.18.0" %} +{% set version = "2.22.0" %} {% set name = "ComplexHeatmap" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Make Complex Heatmaps -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4f19a1339c99471cb23ffc4a7272881 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-complexheatmap", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:complexheatmap + parent_recipe: + name: bioconductor-complexheatmap + path: recipes/bioconductor-complexheatmap + version: 1.18.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff, fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12), gridGraphics, gplots, rmarkdown, Cairo, magick requirements: host: - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - - 'r-circlize >=0.4.14' + - r-circlize >=0.4.14 - r-clue - r-codetools - r-colorspace @@ -32,14 +42,14 @@ requirements: - r-doparallel - r-foreach - r-getoptlong - - 'r-globaloptions >=0.1.0' + - r-globaloptions >=0.1.0 - r-matrixstats - r-png - r-rcolorbrewer run: - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - - 'r-circlize >=0.4.14' + - r-circlize >=0.4.14 - r-clue - r-codetools - r-colorspace @@ -47,24 +57,20 @@ requirements: - r-doparallel - r-foreach - r-getoptlong - - 'r-globaloptions >=0.1.0' + - r-globaloptions >=0.1.0 - r-matrixstats - r-png - r-rcolorbrewer + +source: + md5: fe0371ce669fb3ae8d4caccf27833463 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Make Complex Heatmaps' - description: 'Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.' - license_file: LICENSE -extra: - identifiers: - - biotools:complexheatmap - parent_recipe: - name: bioconductor-complexheatmap - path: recipes/bioconductor-complexheatmap - version: 1.18.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-compounddb/meta.yaml b/recipes/bioconductor-compounddb/meta.yaml index 6c581d53b553f..5e2841ab8c855 100644 --- a/recipes/bioconductor-compounddb/meta.yaml +++ b/recipes/bioconductor-compounddb/meta.yaml @@ -1,38 +1,39 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "CompoundDb" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CompoundDb provides functionality to create and use (chemical) compound annotation databases from a variety of different sources such as LipidMaps, HMDB, ChEBI or MassBank. The database format allows to store in addition MS/MS spectra along with compound information. The package provides also a backend for Bioconductor's Spectra package and allows thus to match experimetal MS/MS spectra against MS/MS spectra in the database. Databases can be stored in SQLite format and are thus portable. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Creating and Using (Chemical) Compound Annotation Databases -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7863bdbb64d2068c22225ece8ed5844c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-compounddb", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19), MsBackendMgf requirements: host: - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-chemminer >=3.54.0,<3.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-chemminer >=3.58.0,<3.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-metabocoreutils >=1.14.0,<1.15.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 - r-base - r-dbi - r-dbplyr @@ -42,17 +43,17 @@ requirements: - r-tibble - r-xml2 run: - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-chemminer >=3.54.0,<3.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-chemminer >=3.58.0,<3.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-metabocoreutils >=1.14.0,<1.15.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 - r-base - r-dbi - r-dbplyr @@ -61,12 +62,16 @@ requirements: - r-rsqlite - r-tibble - r-xml2 + +source: + md5: c79d6a2cc057e9505a1016d679642870 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Creating and Using (Chemical) Compound Annotation Databases' - description: 'CompoundDb provides functionality to create and use (chemical) compound annotation databases from a variety of different sources such as LipidMaps, HMDB, ChEBI or MassBank. The database format allows to store in addition MS/MS spectra along with compound information. The package provides also a backend for Bioconductor''s Spectra package and allows thus to match experimetal MS/MS spectra against MS/MS spectra in the database. Databases can be stored in SQLite format and are thus portable.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-compran/meta.yaml b/recipes/bioconductor-compran/meta.yaml index 487b8ff516290..c4cd50f8112a6 100644 --- a/recipes/bioconductor-compran/meta.yaml +++ b/recipes/bioconductor-compran/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "ComPrAn" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is for analysis of SILAC labeled complexome profiling data. It uses peptide table in tab-delimited format as an input and produces ready-to-use tables and plots. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Complexome Profiling Analysis package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 24011dcffe9f6c7b22be8e2de0e855b4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-compran", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 2.1.0), knitr, rmarkdown requirements: host: @@ -61,13 +63,16 @@ requirements: - r-tibble - r-tidyr - r-venndiagram + +source: + md5: 1732308f7c82b3bd731de7b5b8143fbf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Complexome Profiling Analysis package' - description: 'This package is for analysis of SILAC labeled complexome profiling data. It uses peptide table in tab-delimited format as an input and produces ready-to-use tables and plots.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-compspot/meta.yaml b/recipes/bioconductor-compspot/meta.yaml index c735ad00891b4..66b8ad101a2d8 100644 --- a/recipes/bioconductor-compspot/meta.yaml +++ b/recipes/bioconductor-compspot/meta.yaml @@ -1,24 +1,25 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "compSPOT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Clonal cell groups share common mutations within cancer, precancer, and even clinically normal appearing tissues. The frequency and location of these mutations may predict prognosis and cancer risk. It has also been well established that certain genomic regions have increased sensitivity to acquiring mutations. Mutation-sensitive genomic regions may therefore serve as markers for predicting cancer risk. This package contains multiple functions to establish significantly mutated hotspots, compare hotspot mutation burden between samples, and perform exploratory data analysis of the correlation between hotspot mutation burden and personal risk factors for cancer, such as age, gender, and history of carcinogen exposure. This package allows users to identify robust genomic markers to help establish cancer risk. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7aa69c9c3ec0c008ad0fdfb4dbbcac57 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-compspot", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: @@ -37,12 +38,16 @@ requirements: - r-gridextra - r-magrittr - r-plotly + +source: + md5: 6bd776b81a032021b7b90cb2d4582c7e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots' - description: 'Clonal cell groups share common mutations within cancer, precancer, and even clinically normal appearing tissues. The frequency and location of these mutations may predict prognosis and cancer risk. It has also been well established that certain genomic regions have increased sensitivity to acquiring mutations. Mutation-sensitive genomic regions may therefore serve as markers for predicting cancer risk. This package contains multiple functions to establish significantly mutated hotspots, compare hotspot mutation burden between samples, and perform exploratory data analysis of the correlation between hotspot mutation burden and personal risk factors for cancer, such as age, gender, and history of carcinogen exposure. This package allows users to identify robust genomic markers to help establish cancer risk.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-concordexr/meta.yaml b/recipes/bioconductor-concordexr/meta.yaml index 16a7d13375823..0dec8d674f2fa 100644 --- a/recipes/bioconductor-concordexr/meta.yaml +++ b/recipes/bioconductor-concordexr/meta.yaml @@ -1,52 +1,67 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "concordexR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Spatial homogeneous regions (SHRs) in tissues are domains that are homogenous with respect to cell type composition. We present a method for identifying SHRs using spatial transcriptomics data, and demonstrate that it is efficient and effective at finding SHRs for a wide variety of tissue types. concordex relies on analysis of k-nearest-neighbor (kNN) graphs. The tool is also useful for analysis of non-spatial transcriptomics data, and can elucidate the extent of concordance between partitions of cells derived from clustering algorithms, and transcriptomic similarity as represented in kNN graphs. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Identify Spatial Homogeneous Regions with concordex -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ffab81582264ccb300c9f937c698adf build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-concordexr", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocNeighbors, BiocStyle, bluster, covr, knitr, patchwork, rmarkdown, scater, TENxPBMCData, testthat (>= 3.0.0), vdiffr + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocManager, BiocStyle, ggplot2, glue, knitr, mbkmeans, patchwork, rmarkdown, scater, SFEData, SpatialFeatureExperiment, TENxPBMCData, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bluster >=1.16.0,<1.17.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cli - - r-ggplot2 - r-matrix - - r-pheatmap + - r-purrr - r-rlang - - r-scales run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bluster >=1.16.0,<1.17.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cli - - r-ggplot2 - r-matrix - - r-pheatmap + - r-purrr - r-rlang - - r-scales + +source: + md5: 8fb2be578b2e5a9b744cbec0db41bc2b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Calculate the concordex coefficient' - description: 'Many analysis workflows include approximation of a nearest neighbors graph followed by clustering of the graph structure. The concordex coefficient estimates the concordance between the graph and clustering results. The package ''concordexR'' is an R implementation of the original concordex Python-based command line tool.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-condiments/build_failure.linux-64.yaml b/recipes/bioconductor-condiments/build_failure.linux-64.yaml deleted file mode 100644 index 64bb7869e9bff..0000000000000 --- a/recipes/bioconductor-condiments/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: d70ad20d6aa8d5ec24cc58bdae0002e9ce657a5241a612189057a31a9a2b5902 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - - bioconductor-distinct >=1.14.0,<1.15.0 - - r-ecume >=0.9.1 - - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 - - r-mgcv - - bioconductor-slingshot >=2.10.0,<2.11.0 - - bioconductor-biocparallel >=1.36.0,<1.37.0 - - r-matrixstats - - r-base 4.3.* - - r-rann - - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested bioconductor-distinct >=1.14.0,<1.15.0 - - - - Leaving build/test directories: - Work: - /opt/conda/conda-bld/work - Test: - /opt/conda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl - Build: - source activate /opt/conda/conda-bld/_build_env - - - Traceback (most recent call last): - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action - t = self.solve(specs) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - r-pbapply - - r-igraph - - r-magrittr - - r-dplyr >=1.0 - - bioconductor-trajectoryutils >=1.10.0,<1.11.0 - - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 - - bioconductor-distinct >=1.14.0,<1.15.0 - - r-ecume >=0.9.1 - - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 - - r-mgcv - - bioconductor-slingshot >=2.10.0,<2.11.0 - - bioconductor-biocparallel >=1.36.0,<1.37.0 - - r-matrixstats - - r-base 4.3.* - - r-rann - - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested bioconductor-distinct >=1.14.0,<1.15.0 - - - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build - output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs - for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set - conda_packages = finalize_outputs_pass( - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass - fm = finalize_metadata( - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata - build_unsat, host_unsat = add_upstream_pins(m, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins - host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files - deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies - actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-distinct[version='>=1.14.0,<1.15.0']")} -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-condiments/meta.yaml b/recipes/bioconductor-condiments/meta.yaml index c6cceadc411f7..60eb1f685bfed 100644 --- a/recipes/bioconductor-condiments/meta.yaml +++ b/recipes/bioconductor-condiments/meta.yaml @@ -1,36 +1,38 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "condiments" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package encapsulate many functions to conduct a differential topology analysis. It focuses on analyzing an 'omic dataset with multiple conditions. While the package is mostly geared toward scRNASeq, it does not place any restriction on the actual input format. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Differential Topology, Progression and Differentiation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 63b9756275a532e7d38c67402cef7efd build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-condiments", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, testthat, rmarkdown, covr, viridis, ggplot2, RColorBrewer, randomForest, tidyr, TSCAN + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, testthat, rmarkdown, covr, viridis, ggplot2, RColorBrewer, randomForest, tidyr, TSCAN, DelayedMatrixStats requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-distinct >=1.14.0,<1.15.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-slingshot >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-distinct >=1.18.0,<1.19.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-slingshot >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-trajectoryutils >=1.14.0,<1.15.0 - r-base - - 'r-dplyr >=1.0' - - 'r-ecume >=0.9.1' + - r-dplyr >=1.0 + - r-ecume >=0.9.1 - r-igraph - r-magrittr - r-matrixstats @@ -38,28 +40,31 @@ requirements: - r-pbapply - r-rann run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-distinct >=1.14.0,<1.15.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-slingshot >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-distinct >=1.18.0,<1.19.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-slingshot >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-trajectoryutils >=1.14.0,<1.15.0 - r-base - - 'r-dplyr >=1.0' - - 'r-ecume >=0.9.1' + - r-dplyr >=1.0 + - r-ecume >=0.9.1 - r-igraph - r-magrittr - r-matrixstats - r-mgcv - r-pbapply - r-rann + +source: + md5: 01c6255f95b9277867ff063750b8f622 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Differential Topology, Progression and Differentiation' - description: 'This package encapsulate many functions to conduct a differential topology analysis. It focuses on analyzing an ''omic dataset with multiple conditions. While the package is mostly geared toward scRNASeq, it does not place any restriction on the actual input format.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-confess/meta.yaml b/recipes/bioconductor-confess/meta.yaml index 6e7de11118b8b..e81c9ad476973 100644 --- a/recipes/bioconductor-confess/meta.yaml +++ b/recipes/bioconductor-confess/meta.yaml @@ -1,40 +1,55 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "CONFESS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Single Cell Fluidigm Spot Detector. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Cell OrderiNg by FluorEScence Signal -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67bd1d40551528aab55620fc0a619713 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-confess", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, CONFESSdata requirements: + + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] + host: - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-flowclust >=3.40.0,<3.41.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowmeans >=1.62.0,<1.63.0' - - 'bioconductor-flowmerge >=2.50.0,<2.51.0' - - 'bioconductor-flowpeaks >=1.48.0,<1.49.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-samspectral >=1.56.0,<1.57.0' + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-flowclust >=3.44.0,<3.45.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowmeans >=1.66.0,<1.67.0 + - bioconductor-flowmerge >=2.54.0,<2.55.0 + - bioconductor-flowpeaks >=1.52.0,<1.53.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-samspectral >=1.60.0,<1.61.0 - r-base - r-changepoint - r-cluster - r-contrast - - 'r-data.table >=1.9.7' + - r-data.table >=1.9.7 - r-ecp - r-flexmix - r-foreach @@ -49,20 +64,21 @@ requirements: - r-waveslim - r-wavethresh - r-zoo + run: - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-flowclust >=3.40.0,<3.41.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowmeans >=1.62.0,<1.63.0' - - 'bioconductor-flowmerge >=2.50.0,<2.51.0' - - 'bioconductor-flowpeaks >=1.48.0,<1.49.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-samspectral >=1.56.0,<1.57.0' + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-flowclust >=3.44.0,<3.45.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowmeans >=1.66.0,<1.67.0 + - bioconductor-flowmerge >=2.54.0,<2.55.0 + - bioconductor-flowpeaks >=1.52.0,<1.53.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-samspectral >=1.60.0,<1.61.0 - r-base - r-changepoint - r-cluster - r-contrast - - 'r-data.table >=1.9.7' + - r-data.table >=1.9.7 - r-ecp - r-flexmix - r-foreach @@ -77,23 +93,16 @@ requirements: - r-waveslim - r-wavethresh - r-zoo - build: - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - xorg-libxfixes # [linux] + +source: + md5: d79b3ac5470a2deba9a1bd20a9761d38 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Cell OrderiNg by FluorEScence Signal' - description: 'Single Cell Fluidigm Spot Detector.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-confessdata/meta.yaml b/recipes/bioconductor-confessdata/meta.yaml index 68d94dd254c3a..70038b326172f 100644 --- a/recipes/bioconductor-confessdata/meta.yaml +++ b/recipes/bioconductor-confessdata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "CONFESSdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 07df3f8f783b3e734c4032b3f6ed61bd +about: + description: Example text-converted C01 image files for use in the CONFESS Bioconductor package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Example dataset for CONFESS package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-confessdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0a7503b919b1c5aab67f16b48391d0ac + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Example dataset for CONFESS package' - description: 'Example text-converted C01 image files for use in the CONFESS Bioconductor package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-confessdata/post-link.sh b/recipes/bioconductor-confessdata/post-link.sh index bd491dd59a8f3..3d475c23a7669 100644 --- a/recipes/bioconductor-confessdata/post-link.sh +++ b/recipes/bioconductor-confessdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "confessdata-1.30.0" +installBiocDataPackage.sh "confessdata-1.34.0" diff --git a/recipes/bioconductor-connectivitymap/meta.yaml b/recipes/bioconductor-connectivitymap/meta.yaml index ce2ee8169dab4..82dbcdee1dcdd 100644 --- a/recipes/bioconductor-connectivitymap/meta.yaml +++ b/recipes/bioconductor-connectivitymap/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "ConnectivityMap" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bac29780256afebfd49b90f268114eaf +about: + description: The Broad Institute's Connectivity Map (cmap02) is a "large reference catalogue of gene-expression data from cultured human cells perturbed with many chemicals and genetic reagents", containing more than 7000 gene expression profiles and 1300 small molecules. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Functional connections between drugs, genes and diseases as revealed by common gene-expression changes build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-connectivitymap", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: RUnit, BiocGenerics requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2dac511c451dee045d1ccfc8d9f418b4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Functional connections between drugs, genes and diseases as revealed by common gene-expression changes' - description: 'The Broad Institute''s Connectivity Map (cmap02) is a "large reference catalogue of gene-expression data from cultured human cells perturbed with many chemicals and genetic reagents", containing more than 7000 gene expression profiles and 1300 small molecules.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-connectivitymap/post-link.sh b/recipes/bioconductor-connectivitymap/post-link.sh index 6840e2570ebd7..2edf93e708aa5 100644 --- a/recipes/bioconductor-connectivitymap/post-link.sh +++ b/recipes/bioconductor-connectivitymap/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "connectivitymap-1.38.0" +installBiocDataPackage.sh "connectivitymap-1.42.0" diff --git a/recipes/bioconductor-consensus/meta.yaml b/recipes/bioconductor-consensus/meta.yaml index 3cfdf91faedfc..efaa8bccfe9de 100644 --- a/recipes/bioconductor-consensus/meta.yaml +++ b/recipes/bioconductor-consensus/meta.yaml @@ -1,24 +1,32 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "consensus" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An implementation of the American Society for Testing and Materials (ASTM) Standard E691 for interlaboratory testing procedures, designed for cross-platform genomic measurements. Given three (3) or more genomic platforms or laboratory protocols, this package provides interlaboratory testing procedures giving per-locus comparisons for sensitivity and precision between platforms. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_3_clause + file LICENSE + license_file: LICENSE + summary: Cross-platform consensus analysis of genomic measurements via interlaboratory testing method -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f930fc9b058bce80ccbb112082cf3dc7 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-consensus", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-consensus + path: recipes/bioconductor-consensus + version: 1.0.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, RUnit, rmarkdown, BiocGenerics requirements: host: @@ -31,18 +39,16 @@ requirements: - r-gplots - r-matrixstats - r-rcolorbrewer + +source: + md5: 9b886f8dba96b422e00f269a0b34b6e4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_3_clause + file LICENSE' - summary: 'Cross-platform consensus analysis of genomic measurements via interlaboratory testing method' - description: 'An implementation of the American Society for Testing and Materials (ASTM) Standard E691 for interlaboratory testing procedures, designed for cross-platform genomic measurements. Given three (3) or more genomic platforms or laboratory protocols, this package provides interlaboratory testing procedures giving per-locus comparisons for sensitivity and precision between platforms.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-consensus - path: recipes/bioconductor-consensus - version: 1.0.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-consensusclusterplus/meta.yaml b/recipes/bioconductor-consensusclusterplus/meta.yaml index 03b92e32b0a1c..ee46853b5e7f3 100644 --- a/recipes/bioconductor-consensusclusterplus/meta.yaml +++ b/recipes/bioconductor-consensusclusterplus/meta.yaml @@ -1,49 +1,55 @@ -{% set version = "1.66.0" %} +{% set version = "1.70.0" %} {% set name = "ConsensusClusterPlus" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: algorithm for determining cluster count and membership by stability evidence in unsupervised analysis + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL version 2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: ConsensusClusterPlus -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0943cc2a0d1dff314f384e65b8d71897 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-consensusclusterplus", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:consensusclusterplus + parent_recipe: + name: bioconductor-consensusclusterplus + path: recipes/bioconductor-consensusclusterplus + version: 1.44.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-all >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-all >=1.48.0,<1.49.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-cluster run: - - 'bioconductor-all >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-all >=1.48.0,<1.49.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-cluster + +source: + md5: 262afe9b8f479d8a98f655ef64d133b3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL version 2' - summary: ConsensusClusterPlus - description: 'algorithm for determining cluster count and membership by stability evidence in unsupervised analysis' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:consensusclusterplus - parent_recipe: - name: bioconductor-consensusclusterplus - path: recipes/bioconductor-consensusclusterplus - version: 1.44.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-consensusde/meta.yaml b/recipes/bioconductor-consensusde/meta.yaml index 303d9bae79e62..c0f7d78356faf 100644 --- a/recipes/bioconductor-consensusde/meta.yaml +++ b/recipes/bioconductor-consensusde/meta.yaml @@ -1,85 +1,92 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "consensusDE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package allows users to perform DE analysis using multiple algorithms. It seeks consensus from multiple methods. Currently it supports "Voom", "EdgeR" and "DESeq". It uses RUV-seq (optional) to remove unwanted sources of variation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: RNA-seq analysis using multiple algorithms -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4aedcdf9823551d0ea0cc2ae64ac475 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-consensusde", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: + host: - - 'bioconductor-airway >=1.22.0,<1.23.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edaseq >=2.36.0,<2.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-ruvseq >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' + - bioconductor-airway >=1.26.0,<1.27.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edaseq >=2.40.0,<2.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-ruvseq >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0 - r-base - r-data.table - r-dendextend - r-rcolorbrewer + run: - - 'bioconductor-airway >=1.22.0,<1.23.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edaseq >=2.36.0,<2.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-ruvseq >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' + - bioconductor-airway >=1.26.0,<1.27.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edaseq >=2.40.0,<2.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-ruvseq >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0 - r-base - r-data.table - r-dendextend - r-rcolorbrewer + +source: + md5: 0dc9df37ea716d2b05d9f1c299f18bb4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'RNA-seq analysis using multiple algorithms' - description: 'This package allows users to perform DE analysis using multiple algorithms. It seeks consensus from multiple methods. Currently it supports "Voom", "EdgeR" and "DESeq". It uses RUV-seq (optional) to remove unwanted sources of variation.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-consensusseeker/meta.yaml b/recipes/bioconductor-consensusseeker/meta.yaml index 55d0281d77d27..582f9aa7e263c 100644 --- a/recipes/bioconductor-consensusseeker/meta.yaml +++ b/recipes/bioconductor-consensusseeker/meta.yaml @@ -1,60 +1,66 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "consensusSeekeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package compares genomic positions and genomic ranges from multiple experiments to extract common regions. The size of the analyzed region is adjustable as well as the number of experiences in which a feature must be present in a potential region to tag this region as a consensus region. In genomic analysis where feature identification generates a position value surrounded by a genomic range, such as ChIP-Seq peaks and nucleosome positions, the replication of an experiment may result in slight differences between predicted values. This package enables the conciliation of the results into consensus regions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e752cec43fa487cd071a27a1f955b17e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-consensusseeker", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:consensusseeker + - doi:10.1515/sagmb-2014-0098 + parent_recipe: + name: bioconductor-consensusseeker + path: recipes/bioconductor-consensusseeker + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, ggplot2, knitr, rmarkdown, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-stringr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-stringr + +source: + md5: 56a13d57d00010129ed5eaec06377193 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges' - description: 'This package compares genomic positions and genomic ranges from multiple experiments to extract common regions. The size of the analyzed region is adjustable as well as the number of experiences in which a feature must be present in a potential region to tag this region as a consensus region.' -extra: - identifiers: - - biotools:consensusseeker - - doi:10.1515/sagmb-2014-0098 - parent_recipe: - name: bioconductor-consensusseeker - path: recipes/bioconductor-consensusseeker - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-consica/meta.yaml b/recipes/bioconductor-consica/meta.yaml index cfe5f1bd4e8c0..312be3cf80a38 100644 --- a/recipes/bioconductor-consica/meta.yaml +++ b/recipes/bioconductor-consica/meta.yaml @@ -1,61 +1,66 @@ -{% set version = "2.0.0" %} +{% set version = "2.4.0" %} {% set name = "consICA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: consICA implements a data-driven deconvolution method – consensus independent component analysis (ICA) to decompose heterogeneous omics data and extract features suitable for patient diagnostics and prognostics. The method separates biologically relevant transcriptional signals from technical effects and provides information about the cellular composition and biological processes. The implementation of parallel computing in the package ensures efficient analysis of modern multicore systems. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: consensus Independent Component Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b64f871ca062dc65d6a883b000c761d8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-consica", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, rmarkdown, testthat, Seurat requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-base - - 'r-fastica >=1.2.1' + - r-fastica >=1.2.1 - r-ggplot2 - r-pheatmap - r-rfast - r-sm - r-survival run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-base - - 'r-fastica >=1.2.1' + - r-fastica >=1.2.1 - r-ggplot2 - r-pheatmap - r-rfast - r-sm - r-survival + +source: + md5: 929848b8c5a45ff0ea43c42e500e6599 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'consensus Independent Component Analysis' - description: 'consICA implements a data-driven deconvolution method – consensus independent component analysis (ICA) to decompose heterogeneous omics data and extract features suitable for patient diagnostics and prognostics. The method separates biologically relevant transcriptional signals from technical effects and provides information about the cellular composition and biological processes. The implementation of parallel computing in the package ensures efficient analysis of modern multicore systems.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-constand/meta.yaml b/recipes/bioconductor-constand/meta.yaml index f4242d0e9f6d5..afe031cd5935b 100644 --- a/recipes/bioconductor-constand/meta.yaml +++ b/recipes/bioconductor-constand/meta.yaml @@ -1,37 +1,37 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "CONSTANd" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6337f6a248f820600a99fa9ef9fc1571 +about: + description: Normalizes a data matrix `data` by raking (using the RAS method by Bacharach, see references) the Nrows by Ncols matrix such that the row means and column means equal 1. The result is a normalized data matrix `K=RAS`, a product of row mulipliers `R` and column multipliers `S` with the original matrix `A`. Missing information needs to be presented as `NA` values and not as zero values, because CONSTANd is able to ignore missing values when calculating the mean. Using CONSTANd normalization allows for the direct comparison of values between samples within the same and even across different CONSTANd-normalized data matrices. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Data normalization by matrix raking build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-constand", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra, magick, Cairo, limma requirements: host: - r-base run: - r-base +source: + md5: 86711e287452f21bc57def13d529a624 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Data normalization by matrix raking' - description: 'Normalizes a data matrix `data` by raking (using the RAS method by Bacharach, see references) the Nrows by Ncols matrix such that the row means and column means equal 1. The result is a normalized data matrix `K=RAS`, a product of row mulipliers `R` and column multipliers `S` with the original matrix `A`. Missing information needs to be presented as `NA` values and not as zero values, because CONSTANd is able to ignore missing values when calculating the mean. Using CONSTANd normalization allows for the direct comparison of values between samples within the same and even across different CONSTANd-normalized data matrices.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-conumee/meta.yaml b/recipes/bioconductor-conumee/meta.yaml index e3dde4f6aeff4..18073bacb94e5 100644 --- a/recipes/bioconductor-conumee/meta.yaml +++ b/recipes/bioconductor-conumee/meta.yaml @@ -1,57 +1,62 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "conumee" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains a set of processing and plotting methods for performing copy-number variation (CNV) analysis using Illumina 450k or EPIC methylation arrays. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Enhanced copy-number variation analysis using Illumina DNA methylation arrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f7eab6e95ed82f050ef52895ef178ba0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-conumee", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, minfiData, RCurl requirements: host: - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0 + - bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base run: - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0 + - bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base + +source: + md5: b0df51d7b03f3b8c021d1b1c00d83fce + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Enhanced copy-number variation analysis using Illumina DNA methylation arrays' - description: 'This package contains a set of processing and plotting methods for performing copy-number variation (CNV) analysis using Illumina 450k or EPIC methylation arrays.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-convert/meta.yaml b/recipes/bioconductor-convert/meta.yaml index 82edc223b9c80..f96e8a3488cf1 100644 --- a/recipes/bioconductor-convert/meta.yaml +++ b/recipes/bioconductor-convert/meta.yaml @@ -1,44 +1,22 @@ -{% set version = "1.78.0" %} +{% set version = "1.82.0" %} {% set name = "convert" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Define coerce methods for microarray data objects. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Convert Microarray Data Objects -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 828a21b5a554d63faeb6cc2af0784394 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-convert", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Convert Microarray Data Objects' - description: 'Define coerce methods for microarray data objects.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + extra: identifiers: - biotools:convert @@ -48,3 +26,31 @@ extra: path: recipes/bioconductor-convert version: 1.56.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-marray >=1.84.0,<1.85.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-marray >=1.84.0,<1.85.0 + - r-base + +source: + md5: 39d558aaa3d460533b19b96b3d0426a9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-copa/meta.yaml b/recipes/bioconductor-copa/meta.yaml index 4c51fca6b7687..748b098a470b0 100644 --- a/recipes/bioconductor-copa/meta.yaml +++ b/recipes/bioconductor-copa/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "1.70.0" %} +{% set version = "1.74.0" %} {% set name = "copa" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Functions to perform cancer outlier profile analysis. -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bd372714a4dd7e70b90d9232fcba322d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-copa", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:copa + - usegalaxy-eu:copa + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: colonCA requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: 4a01631dd274c80e9005beb1021e1684 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Functions to perform cancer outlier profile analysis.' - description: 'COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles.' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} - - usegalaxy-eu:{{ name|lower }} diff --git a/recipes/bioconductor-copdsexualdimorphism.data/meta.yaml b/recipes/bioconductor-copdsexualdimorphism.data/meta.yaml index 2239bacb44612..dce8e3a009117 100644 --- a/recipes/bioconductor-copdsexualdimorphism.data/meta.yaml +++ b/recipes/bioconductor-copdsexualdimorphism.data/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "COPDSexualDimorphism.data" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d7cf1990679c90cbaf5250c4761effec +about: + description: Datasets to support COPDSexaulDimorphism Package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL-2.1 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2.1' + summary: Data to support sexually dimorphic and COPD differential analysis for gene expression and methylation. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-copdsexualdimorphism.data", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8b7f51a5af7e245e2bcc9e15aff15bf3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL-2.1 - summary: 'Data to support sexually dimorphic and COPD differential analysis for gene expression and methylation.' - description: 'Datasets to support COPDSexaulDimorphism Package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2.1' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-copdsexualdimorphism.data/post-link.sh b/recipes/bioconductor-copdsexualdimorphism.data/post-link.sh index 646f2cfcfb63e..0fda5e351b8bc 100644 --- a/recipes/bioconductor-copdsexualdimorphism.data/post-link.sh +++ b/recipes/bioconductor-copdsexualdimorphism.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "copdsexualdimorphism.data-1.38.0" +installBiocDataPackage.sh "copdsexualdimorphism.data-1.42.0" diff --git a/recipes/bioconductor-copyhelper/meta.yaml b/recipes/bioconductor-copyhelper/meta.yaml index 7b020ea9f183e..ae7cb17295577 100644 --- a/recipes/bioconductor-copyhelper/meta.yaml +++ b/recipes/bioconductor-copyhelper/meta.yaml @@ -1,24 +1,28 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "CopyhelpeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bb8d3e8cba0c27898e43cbdcfcac6c62 +about: + description: This package contains the helper files that are required to run the Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content and mappability files for the reference genomes hg18, hg19, hg38, mm9 and mm10. In addition, it contains a blacklist filter to remove regions that display CNV. Files are stored as GRanges objects from the GenomicRanges Bioconductor package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Helper files for CopywriteR build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-copyhelper", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-copyhelper + path: recipes/bioconductor-copyhelper + version: 1.12.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle requirements: host: @@ -26,19 +30,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 706b5d208852ce6b037f74e2e988f38a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Helper files for CopywriteR' - description: 'This package contains the helper files that are required to run the Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content and mappability files for the reference genomes hg18, hg19, hg38, mm9 and mm10. In addition, it contains a blacklist filter to remove regions that display CNV. Files are stored as GRanges objects from the GenomicRanges Bioconductor package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - parent_recipe: - name: bioconductor-copyhelper - path: recipes/bioconductor-copyhelper - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-copyhelper/post-link.sh b/recipes/bioconductor-copyhelper/post-link.sh index e5749ce2fa85f..26127243b3600 100644 --- a/recipes/bioconductor-copyhelper/post-link.sh +++ b/recipes/bioconductor-copyhelper/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "copyhelper-1.34.0" +installBiocDataPackage.sh "copyhelper-1.38.0" diff --git a/recipes/bioconductor-copyneutralima/meta.yaml b/recipes/bioconductor-copyneutralima/meta.yaml index ded511225ae06..f04385bebdaff 100644 --- a/recipes/bioconductor-copyneutralima/meta.yaml +++ b/recipes/bioconductor-copyneutralima/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "CopyNeutralIMA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f1921b0aff4c3f39b662cc1ae70bf28 +about: + description: Provides a set of genomic copy neutral samples hybridized using Illumina Methylation arrays (450k and EPIC). + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Copy Neutral Illumina Methylation Arrays build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-copyneutralima", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle,knitr,rmarkdown,minfi,conumee,minfiData requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - - 'r-rdpack >=0.8' + - r-rdpack >=0.8 run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - - 'r-rdpack >=0.8' + - r-rdpack >=0.8 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3e54ad70dd8271f19765fedb5ee849cc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Copy Neutral Illumina Methylation Arrays' - description: 'Provides a set of genomic copy neutral samples hybridized using Illumina Methylation arrays (450k and EPIC).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-copyneutralima/post-link.sh b/recipes/bioconductor-copyneutralima/post-link.sh index 4ee3bca445581..4025466d8a1c7 100644 --- a/recipes/bioconductor-copyneutralima/post-link.sh +++ b/recipes/bioconductor-copyneutralima/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "copyneutralima-1.20.0" +installBiocDataPackage.sh "copyneutralima-1.24.0" diff --git a/recipes/bioconductor-copynumberplots/meta.yaml b/recipes/bioconductor-copynumberplots/meta.yaml index cd504f81494c7..da9c4bfdff0a8 100644 --- a/recipes/bioconductor-copynumberplots/meta.yaml +++ b/recipes/bioconductor-copynumberplots/meta.yaml @@ -1,56 +1,61 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "CopyNumberPlots" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CopyNumberPlots have a set of functions extending karyoploteRs functionality to create beautiful, customizable and flexible plots of copy-number related data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Create Copy-Number Plots using karyoploteR functionality -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d35c96c521087a1183dd2ae465b3d2a7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-copynumberplots", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, panelcn.mops, BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy, testthat requirements: host: - - 'bioconductor-cn.mops >=1.48.0,<1.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-karyoploter >=1.28.0,<1.29.0' - - 'bioconductor-regioner >=1.34.0,<1.35.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-cn.mops >=1.52.0,<1.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-karyoploter >=1.32.0,<1.33.0 + - bioconductor-regioner >=1.38.0,<1.39.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-cn.mops >=1.48.0,<1.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-karyoploter >=1.28.0,<1.29.0' - - 'bioconductor-regioner >=1.34.0,<1.35.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-cn.mops >=1.52.0,<1.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-karyoploter >=1.32.0,<1.33.0 + - bioconductor-regioner >=1.38.0,<1.39.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base + +source: + md5: 1f5f855d127df42b2e54ead876d620a6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Create Copy-Number Plots using karyoploteR functionality' - description: 'CopyNumberPlots have a set of functions extending karyoploteRs functionality to create beautiful, customizable and flexible plots of copy-number related data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cordon/meta.yaml b/recipes/bioconductor-cordon/meta.yaml index 5733faeb89818..87fb4d66c9ce4 100644 --- a/recipes/bioconductor-cordon/meta.yaml +++ b/recipes/bioconductor-cordon/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "coRdon" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tool for analysis of codon usage in various unannotated or KEGG/COG annotated DNA sequences. Calculates different measures of CU bias and CU-based predictors of gene expressivity, and performs gene set enrichment analysis for annotated sequences. Implements several methods for visualization of CU and enrichment analysis results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Codon Usage Analysis and Prediction of Gene Expressivity -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 19e0e0e91d3cccd4c277710c9273275e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cordon", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - r-data.table - r-dplyr @@ -31,20 +32,24 @@ requirements: - r-purrr - r-stringr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - r-data.table - r-dplyr - r-ggplot2 - r-purrr - r-stringr + +source: + md5: a850cdc6396b75983df5e35341be85b9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Codon Usage Analysis and Prediction of Gene Expressivity' - description: 'Tool for analysis of codon usage in various unannotated or KEGG/COG annotated DNA sequences. Calculates different measures of CU bias and CU-based predictors of gene expressivity, and performs gene set enrichment analysis for annotated sequences. Implements several methods for visualization of CU and enrichment analysis results.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-coregx/meta.yaml b/recipes/bioconductor-coregx/meta.yaml index 42ac17580c6ed..07c2ca0b83c82 100644 --- a/recipes/bioconductor-coregx/meta.yaml +++ b/recipes/bioconductor-coregx/meta.yaml @@ -1,36 +1,38 @@ -{% set version = "2.6.0" %} +{% set version = "2.10.0" %} {% set name = "CoreGx" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'A collection of functions and classes which serve as the foundation for our lab''s suite of R packages, such as ''PharmacoGx'' and ''RadioGx''. This package was created to abstract shared functionality from other lab package releases to increase ease of maintainability and reduce code repetition in current and future ''Gx'' suite programs. Major features include a ''CoreSet'' class, from which ''RadioSet'' and ''PharmacoSet'' are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, as well as: Smirnov, P., Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., Freeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A., Aerts, H., Lupien, M., Goldenberg, A. (2015) . Manem, V., Labie, M., Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed, M., Haibe-Kains, B., Bratman, S. (2018) .' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Classes and Functions to Serve as the Basis for Other 'Gx' Packages -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3556f412bd014d5294b15feb8342d78e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-coregx", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: pander, markdown, BiocStyle, rmarkdown, knitr, formatR, testthat requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-piano >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bumpymatrix >=1.14.0,<1.15.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-piano >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bench - r-checkmate @@ -40,15 +42,15 @@ requirements: - r-lsa - r-rlang run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-piano >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bumpymatrix >=1.14.0,<1.15.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-piano >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bench - r-checkmate @@ -57,12 +59,16 @@ requirements: - r-glue - r-lsa - r-rlang + +source: + md5: 357826ed902da51ac7859c681bfaaf4d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Classes and Functions to Serve as the Basis for Other ''Gx'' Packages' - description: 'A collection of functions and classes which serve as the foundation for our lab''s suite of R packages, such as ''PharmacoGx'' and ''RadioGx''. This package was created to abstract shared functionality from other lab package releases to increase ease of maintainability and reduce code repetition in current and future ''Gx'' suite programs. Major features include a ''CoreSet'' class, from which ''RadioSet'' and ''PharmacoSet'' are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, as well as: Smirnov, P., Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., Freeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A., Aerts, H., Lupien, M., Goldenberg, A. (2015) . Manem, V., Labie, M., Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed, M., Haibe-Kains, B., Bratman, S. (2018) .' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-cormotif/meta.yaml b/recipes/bioconductor-cormotif/meta.yaml index 55b5aa549ab64..5dcda20a71b67 100644 --- a/recipes/bioconductor-cormotif/meta.yaml +++ b/recipes/bioconductor-cormotif/meta.yaml @@ -1,42 +1,22 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "Cormotif" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: It fits correlation motif model to multiple studies to detect study specific differential expression patterns. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Correlation Motif Fit -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6e65ec2460aecf6004e416d7c61c4c1d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cormotif", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - r-base - run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Correlation Motif Fit' - description: 'It fits correlation motif model to multiple studies to detect study specific differential expression patterns.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + extra: identifiers: - biotools:cormotif @@ -45,3 +25,29 @@ extra: path: recipes/bioconductor-cormotif version: 1.26.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - r-base + run: + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - r-base + +source: + md5: 512c9958c6ebc81e3b727c1dd0d4303f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-corral/meta.yaml b/recipes/bioconductor-corral/meta.yaml index 9086ae8658de5..1c4eb238f9d64 100644 --- a/recipes/bioconductor-corral/meta.yaml +++ b/recipes/bioconductor-corral/meta.yaml @@ -1,30 +1,43 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "corral" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Correspondence analysis (CA) is a matrix factorization method, and is similar to principal components analysis (PCA). Whereas PCA is designed for application to continuous, approximately normally distributed data, CA is appropriate for non-negative, count-based data that are in the same additive scale. The corral package implements CA for dimensionality reduction of a single matrix of single-cell data, as well as a multi-table adaptation of CA that leverages data-optimized scaling to align data generated from different sequencing platforms by projecting into a shared latent space. corral utilizes sparse matrices and a fast implementation of SVD, and can be called directly on Bioconductor objects (e.g., SingleCellExperiment) for easy pipeline integration. The package also includes additional options, including variations of CA to address overdispersion in count data (e.g., Freeman-Tukey chi-squared residual), as well as the option to apply CA-style processing to continuous data (e.g., proteomic TOF intensities) with the Hellinger distance adaptation of CA. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Correspondence Analysis for Single Cell Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7f1ebb217a695452605bd8aa94f8a5a1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-corral", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ade4, BiocStyle, CellBench, DuoClustering2018, knitr, rmarkdown, scater, testthat requirements: + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] host: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-ggthemes @@ -35,9 +48,9 @@ requirements: - r-reshape2 - r-transport run: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-ggthemes @@ -47,23 +60,16 @@ requirements: - r-pals - r-reshape2 - r-transport - build: - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - xorg-libxfixes # [linux] + +source: + md5: f000c9f03270e0695ed07cfa4c9c2a50 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Correspondence Analysis for Single Cell Data' - description: 'Correspondence analysis (CA) is a matrix factorization method, and is similar to principal components analysis (PCA). Whereas PCA is designed for application to continuous, approximately normally distributed data, CA is appropriate for non-negative, count-based data that are in the same additive scale. The corral package implements CA for dimensionality reduction of a single matrix of single-cell data, as well as a multi-table adaptation of CA that leverages data-optimized scaling to align data generated from different sequencing platforms by projecting into a shared latent space. corral utilizes sparse matrices and a fast implementation of SVD, and can be called directly on Bioconductor objects (e.g., SingleCellExperiment) for easy pipeline integration. The package also includes additional options, including variations of CA to address overdispersion in count data (e.g., Freeman-Tukey chi-squared residual), as well as the option to apply CA-style processing to continuous data (e.g., proteomic TOF intensities) with the Hellinger distance adaptation of CA.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-coseq/meta.yaml b/recipes/bioconductor-coseq/meta.yaml index 6d453975c5710..33ac195d1e5e5 100644 --- a/recipes/bioconductor-coseq/meta.yaml +++ b/recipes/bioconductor-coseq/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "coseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Co-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Co-Expression Analysis of Sequencing Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1e4bea8d520a2554f8f1095d6912074b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-coseq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biobase, knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-htsfilter >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-htsfilter >=1.46.0,<1.47.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-capushe - r-compositions @@ -39,12 +41,12 @@ requirements: - r-rmixmod - r-scales run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-htsfilter >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-htsfilter >=1.46.0,<1.47.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-capushe - r-compositions @@ -55,13 +57,16 @@ requirements: - r-mvtnorm - r-rmixmod - r-scales + +source: + md5: ec3576fa4743364edcd27c00e2443aaf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Co-Expression Analysis of Sequencing Data' - description: 'Co-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cosia/meta.yaml b/recipes/bioconductor-cosia/meta.yaml index 9db22300f331c..75c638bc03ecf 100644 --- a/recipes/bioconductor-cosia/meta.yaml +++ b/recipes/bioconductor-cosia/meta.yaml @@ -1,79 +1,86 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "CoSIA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Cross-Species Investigation and Analysis (CoSIA) is a package that provides researchers with an alternative methodology for comparing across species and tissues using normal wild-type RNA-Seq Gene Expression data from Bgee. Using RNA-Seq Gene Expression data, CoSIA provides multiple visualization tools to explore the transcriptome diversity and variation across genes, tissues, and species. CoSIA uses the Coefficient of Variation and Shannon Entropy and Specificity to calculate transcriptome diversity and variation. CoSIA also provides additional conversion tools and utilities to provide a streamlined methodology for cross-species comparison. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: An Investigation Across Different Species and Tissues -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 217ff53ed0aac2ca3c2d91ce5237c111 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cosia", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle (>= 2.22.0), tidyverse (>= 1.3.1), knitr (>= 1.42), rmarkdown (>= 2.20), testthat (>= 3.1.6), qpdf (>= 1.3.0) requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationtools >=1.76.0,<1.77.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-org.ce.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.dr.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationtools >=1.80.0,<1.81.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-org.ce.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.dm.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.dr.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - - 'r-dplyr >=1.0.7' - - 'r-ggplot2 >=3.3.5' - - 'r-homologene >=1.4.68.19' - - 'r-magrittr >=2.0.1' - - 'r-plotly >=4.10.0' - - 'r-rcolorbrewer >=1.1-2' - - 'r-readr >=2.1.1' - - 'r-stringr >=1.4.0' - - 'r-tibble >=3.1.7' - - 'r-tidyr >=1.2.0' - - 'r-tidyselect >=1.1.2' + - r-dplyr >=1.0.7 + - r-ggplot2 >=3.3.5 + - r-homologene >=1.4.68.19 + - r-magrittr >=2.0.1 + - r-plotly >=4.10.0 + - r-rcolorbrewer >=1.1-2 + - r-readr >=2.1.1 + - r-stringr >=1.4.0 + - r-tibble >=3.1.7 + - r-tidyr >=1.2.0 + - r-tidyselect >=1.1.2 + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationtools >=1.76.0,<1.77.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-org.ce.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.dr.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationtools >=1.80.0,<1.81.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-org.ce.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.dm.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.dr.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - - 'r-dplyr >=1.0.7' - - 'r-ggplot2 >=3.3.5' - - 'r-homologene >=1.4.68.19' - - 'r-magrittr >=2.0.1' - - 'r-plotly >=4.10.0' - - 'r-rcolorbrewer >=1.1-2' - - 'r-readr >=2.1.1' - - 'r-stringr >=1.4.0' - - 'r-tibble >=3.1.7' - - 'r-tidyr >=1.2.0' - - 'r-tidyselect >=1.1.2' + - r-dplyr >=1.0.7 + - r-ggplot2 >=3.3.5 + - r-homologene >=1.4.68.19 + - r-magrittr >=2.0.1 + - r-plotly >=4.10.0 + - r-rcolorbrewer >=1.1-2 + - r-readr >=2.1.1 + - r-stringr >=1.4.0 + - r-tibble >=3.1.7 + - r-tidyr >=1.2.0 + - r-tidyselect >=1.1.2 + +source: + md5: 5c3d04805fd84a3b63480d1a47df2c97 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'An Investigation Across Different Species and Tissues' - description: 'Cross-Species Investigation and Analysis (CoSIA) is a package that provides researchers with an alternative methodology for comparing across species and tissues using normal wild-type RNA-Seq Gene Expression data from Bgee. Using RNA-Seq Gene Expression data, CoSIA provides multiple visualization tools to explore the transcriptome diversity and variation across genes, tissues, and species. CoSIA uses the Coefficient of Variation and Shannon Entropy and Specificity to calculate transcriptome diversity and variation. CoSIA also provides additional conversion tools and utilities to provide a streamlined methodology for cross-species comparison.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cosiadata/meta.yaml b/recipes/bioconductor-cosiadata/meta.yaml index 22efff4627359..0bc8756449941 100644 --- a/recipes/bioconductor-cosiadata/meta.yaml +++ b/recipes/bioconductor-cosiadata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "CoSIAdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f0ec9d5ca01647ec3d52e264c0828273 +about: + description: Variance Stabilized Transformation of Read Counts derived from Bgee RNA-Seq Expression Data. Expression Data includes annotations and is across 6 species (Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Drosophila melanogaster, and Caenorhabditis elegans) and across more than 132 tissues. The data is represented as a RData files and is available in ExperimentHub. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: VST normalized RNA-Sequencing data with annotations for multiple species samples from Bgee build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cosiadata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle (>= 2.26.0), utils (>= 4.3.0), AnnotationHub (>= 3.7.3), knitr (>= 1.42) requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6527ebc803b5f2e34ca3c434e9e19b53 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'VST normalized RNA-Sequencing data with annotations for multiple species samples from Bgee' - description: 'Variance Stabilized Transformation of Read Counts derived from Bgee RNA-Seq Expression Data. Expression Data includes annotations and is across 6 species (Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Drosophila melanogaster, and Caenorhabditis elegans) and across more than 132 tissues. The data is represented as a RData files and is available in ExperimentHub.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cosiadata/post-link.sh b/recipes/bioconductor-cosiadata/post-link.sh index 1ec63202a4c96..0971b2ed27f4d 100644 --- a/recipes/bioconductor-cosiadata/post-link.sh +++ b/recipes/bioconductor-cosiadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cosiadata-1.2.0" +installBiocDataPackage.sh "cosiadata-1.6.0" diff --git a/recipes/bioconductor-cosmic.67/meta.yaml b/recipes/bioconductor-cosmic.67/meta.yaml index 4782b2a7ffb93..5b99ad3640f62 100644 --- a/recipes/bioconductor-cosmic.67/meta.yaml +++ b/recipes/bioconductor-cosmic.67/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "COSMIC.67" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 392f31ffd7e95a7558d248d36dcc37fe +about: + description: 'COSMIC: Catalogue Of Somatic Mutations In Cancer, version 67 (2013-10-24)' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: COSMIC.67 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cosmic.67", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat, BiocStyle, knitr requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 39f8a708222453da072d3b208afa15e3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: COSMIC.67 - description: 'COSMIC: Catalogue Of Somatic Mutations In Cancer, version 67 (2013-10-24)' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cosmic.67/post-link.sh b/recipes/bioconductor-cosmic.67/post-link.sh index fe6c437614e15..024c4a4969782 100644 --- a/recipes/bioconductor-cosmic.67/post-link.sh +++ b/recipes/bioconductor-cosmic.67/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "cosmic.67-1.38.0" +installBiocDataPackage.sh "cosmic.67-1.42.0" diff --git a/recipes/bioconductor-cosmiq/meta.yaml b/recipes/bioconductor-cosmiq/meta.yaml index 9b3100477fa33..d70ccc5fbde30 100644 --- a/recipes/bioconductor-cosmiq/meta.yaml +++ b/recipes/bioconductor-cosmiq/meta.yaml @@ -1,60 +1,66 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "cosmiq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: cosmiq is a tool for the preprocessing of liquid- or gas - chromatography mass spectrometry (LCMS/GCMS) data with a focus on metabolomics or lipidomics applications. To improve the detection of low abundant signals, cosmiq generates master maps of the mZ/RT space from all acquired runs before a peak detection algorithm is applied. The result is a more robust identification and quantification of low-intensity MS signals compared to conventional approaches where peak picking is performed in each LCMS/GCMS file separately. The cosmiq package builds on the xcmsSet object structure and can be therefore integrated well with the package xcms as an alternative preprocessing step. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: cosmiq - COmbining Single Masses Into Quantities -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ae02870f3759e09bb2c8f86d38306f01 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cosmiq", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:cosmiq + - doi:10.5167/uzh-107947 + parent_recipe: + name: bioconductor-cosmiq + path: recipes/bioconductor-cosmiq + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, BiocStyle requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-faahko >=1.42.0,<1.43.0' - - 'bioconductor-massspecwavelet >=1.68.0,<1.69.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-faahko >=1.46.0,<1.47.0 + - bioconductor-massspecwavelet >=1.72.0,<1.73.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base - r-pracma - r-rcpp - libblas - liblapack run: - - 'bioconductor-faahko >=1.42.0,<1.43.0' - - 'bioconductor-massspecwavelet >=1.68.0,<1.69.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-faahko >=1.46.0,<1.47.0 + - bioconductor-massspecwavelet >=1.72.0,<1.73.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base - r-pracma - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 226979d34620eb9e4a410f940bfd2384 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'cosmiq - COmbining Single Masses Into Quantities' - description: 'cosmiq is a tool for the preprocessing of liquid- or gas - chromatography mass spectrometry (LCMS/GCMS) data with a focus on metabolomics or lipidomics applications. To improve the detection of low abundant signals, cosmiq generates master maps of the mZ/RT space from all acquired runs before a peak detection algorithm is applied. The result is a more robust identification and quantification of low-intensity MS signals compared to conventional approaches where peak picking is performed in each LCMS/GCMS file separately. The cosmiq package builds on the xcmsSet object structure and can be therefore integrated well with the package xcms as an alternative preprocessing step.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:cosmiq - - doi:10.5167/uzh-107947 - parent_recipe: - name: bioconductor-cosmiq - path: recipes/bioconductor-cosmiq - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cosmosr/meta.yaml b/recipes/bioconductor-cosmosr/meta.yaml index 3e3679704e138..8fa64ddf3c235 100644 --- a/recipes/bioconductor-cosmosr/meta.yaml +++ b/recipes/bioconductor-cosmosr/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "cosmosR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets based on prior knowledge of signaling, metabolic, and gene regulatory networks. It estimated the activities of transcrption factors and kinases and finds a network-level causal reasoning. Thereby, COSMOS provides mechanistic hypotheses for experimental observations across mulit-omics datasets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: COSMOS (Causal Oriented Search of Multi-Omic Space) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f1e0ed65fc63cbdf3a7936bf45e73f3e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cosmosr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, piano, ggplot2 requirements: host: - - 'bioconductor-carnival >=2.12.0,<2.13.0' - - 'bioconductor-decoupler >=2.8.0,<2.9.0' - - 'bioconductor-dorothea >=1.14.0,<1.15.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - bioconductor-carnival >=2.16.0,<2.17.0 + - bioconductor-decoupler >=2.12.0,<2.13.0 + - bioconductor-dorothea >=1.18.0,<1.19.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 - r-base - r-dplyr - r-igraph @@ -35,10 +37,10 @@ requirements: - r-stringr - r-visnetwork run: - - 'bioconductor-carnival >=2.12.0,<2.13.0' - - 'bioconductor-decoupler >=2.8.0,<2.9.0' - - 'bioconductor-dorothea >=1.14.0,<1.15.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - bioconductor-carnival >=2.16.0,<2.17.0 + - bioconductor-decoupler >=2.12.0,<2.13.0 + - bioconductor-dorothea >=1.18.0,<1.19.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 - r-base - r-dplyr - r-igraph @@ -47,13 +49,16 @@ requirements: - r-rlang - r-stringr - r-visnetwork + +source: + md5: 8eec04fe8b6b4d900404ce51afa24088 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'COSMOS (Causal Oriented Search of Multi-Omic Space)' - description: 'COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets based on prior knowledge of signaling, metabolic, and gene regulatory networks. It estimated the activities of transcrption factors and kinases and finds a network-level causal reasoning. Thereby, COSMOS provides mechanistic hypotheses for experimental observations across mulit-omics datasets.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cosnet/meta.yaml b/recipes/bioconductor-cosnet/meta.yaml index 83ab3129d7fd1..41324a7bd3a1c 100644 --- a/recipes/bioconductor-cosnet/meta.yaml +++ b/recipes/bioconductor-cosnet/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "COSNet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6648998ac68e41642f1a7bad77e0bb7f +about: + description: Package that implements the COSNet classification algorithm. The algorithm predicts node labels in partially labeled graphs where few positives are available for the class being predicted. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cosnet", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: bionetdata, PerfMeas, RUnit, BiocGenerics requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - make +source: + md5: fefba7ec494488bdddf41fec06e21024 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings' - description: 'Package that implements the COSNet classification algorithm. The algorithm predicts node labels in partially labeled graphs where few positives are available for the class being predicted.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cotan/meta.yaml b/recipes/bioconductor-cotan/meta.yaml index 7b8cee0e472ab..45772097b8c77 100644 --- a/recipes/bioconductor-cotan/meta.yaml +++ b/recipes/bioconductor-cotan/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "2.2.1" %} +{% set version = "2.6.0" %} {% set name = "COTAN" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Statistical and computational method to analyze the co-expression of gene pairs at single cell level. It provides the foundation for single-cell gene interactome analysis. The basic idea is studying the zero UMI counts' distribution instead of focusing on positive counts; this is done with a generalized contingency tables framework. COTAN can effectively assess the correlated or anti-correlated expression of gene pairs. It provides a numerical index related to the correlation and an approximate p-value for the associated independence test. COTAN can also evaluate whether single genes are differentially expressed, scoring them with a newly defined global differentiation index. Moreover, this approach provides ways to plot and cluster genes according to their co-expression pattern with other genes, effectively helping the study of gene interactions and becoming a new tool to identify cell-identity marker genes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: COexpression Tables ANalysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec3bbfe10c1ede4ae12398534ab5395b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cotan", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat (>= 3.0.0), proto, spelling, knitr, data.table, gsubfn, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS, Rtsne, plotly, BiocStyle, cowplot, qpdf, GEOquery, sf + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat (>= 3.2.0), proto, spelling, knitr, data.table, gsubfn, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS, Rtsne, plotly, BiocStyle, cowplot, qpdf, GEOquery, sf, torch requirements: + host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-pcatools >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-circlize - r-dendextend - r-dplyr - - r-factoextra - r-ggplot2 - r-ggrepel - r-ggthemes - - r-irlba - r-matrix - r-paralleldist - r-parallelly @@ -48,18 +54,22 @@ requirements: - r-umap - r-withr - r-zeallot + run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-pcatools >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-circlize - r-dendextend - r-dplyr - - r-factoextra - r-ggplot2 - r-ggrepel - r-ggthemes - - r-irlba - r-matrix - r-paralleldist - r-parallelly @@ -75,13 +85,16 @@ requirements: - r-umap - r-withr - r-zeallot + +source: + md5: 3793761f685365e4c421eba140208990 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'COexpression Tables ANalysis' - description: 'Statistical and computational method to analyze the co-expression of gene pairs at single cell level. It provides the foundation for single-cell gene interactome analysis. The basic idea is studying the zero UMI counts'' distribution instead of focusing on positive counts; this is done with a generalized contingency tables framework. COTAN can effectively assess the correlated or anti-correlated expression of gene pairs. It provides a numerical index related to the correlation and an approximate p-value for the associated independence test. COTAN can also evaluate whether single genes are differentially expressed, scoring them with a newly defined global differentiation index. Moreover, this approach provides ways to plot and cluster genes according to their co-expression pattern with other genes, effectively helping the study of gene interactions and becoming a new tool to identify cell-identity marker genes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cottoncdf/meta.yaml b/recipes/bioconductor-cottoncdf/meta.yaml index c8d58aec1b26b..33c34e867967c 100644 --- a/recipes/bioconductor-cottoncdf/meta.yaml +++ b/recipes/bioconductor-cottoncdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "cottoncdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b9d2a4b43235c6e531b78cca006e84b2 +about: + description: A package containing an environment representing the Cotton.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: cottoncdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cottoncdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b9d2a4b43235c6e531b78cca006e84b2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: cottoncdf - description: 'A package containing an environment representing the Cotton.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cottonprobe/meta.yaml b/recipes/bioconductor-cottonprobe/meta.yaml index 6b4cc385024ae..e4f2ecf23e04b 100644 --- a/recipes/bioconductor-cottonprobe/meta.yaml +++ b/recipes/bioconductor-cottonprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "cottonprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 032fa94876685820d94526fd56dd0b65 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Cotton\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type cotton build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cottonprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 032fa94876685820d94526fd56dd0b65 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type cotton' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Cotton\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-countsimqc/meta.yaml b/recipes/bioconductor-countsimqc/meta.yaml index 718397f70710d..ec502a407a56f 100644 --- a/recipes/bioconductor-countsimqc/meta.yaml +++ b/recipes/bioconductor-countsimqc/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "countsimQC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: countsimQC provides functionality to create a comprehensive report comparing a broad range of characteristics across a collection of count matrices. One important use case is the comparison of one or more synthetic count matrices to a real count matrix, possibly the one underlying the simulations. However, any collection of count matrices can be compared. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Compare Characteristic Features of Count Data Sets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a44b69f7c0a9b3f5f822df61a6fcef73 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-countsimqc", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat requirements: host: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-genomeinfodbdata >=1.2.0,<1.3.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-catools - r-dplyr @@ -34,14 +36,14 @@ requirements: - r-ggplot2 - r-ragg - r-randtests - - 'r-rmarkdown >=2.5' + - r-rmarkdown >=2.5 - r-tidyr run: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-genomeinfodbdata >=1.2.0,<1.3.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-catools - r-dplyr @@ -49,15 +51,18 @@ requirements: - r-ggplot2 - r-ragg - r-randtests - - 'r-rmarkdown >=2.5' + - r-rmarkdown >=2.5 - r-tidyr + +source: + md5: 38853042acaa7a00388a06bc39ddf46e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Compare Characteristic Features of Count Data Sets' - description: 'countsimQC provides functionality to create a comprehensive report comparing a broad range of characteristics across a collection of count matrices. One important use case is the comparison of one or more synthetic count matrices to a real count matrix, possibly the one underlying the simulations. However, any collection of count matrices can be compared.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-coveb/meta.yaml b/recipes/bioconductor-coveb/meta.yaml index df6fb540d4b0b..de44aa754fb74 100644 --- a/recipes/bioconductor-coveb/meta.yaml +++ b/recipes/bioconductor-coveb/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "covEB" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Using bayesian methods to estimate correlation matrices assuming that they can be written and estimated as block diagonal matrices. These block diagonal matrices are determined using shrinkage parameters that values below this parameter to zero. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Empirical Bayes estimate of block diagonal covariance matrices -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5469ab09a3d502902dc4d698abd1cbae build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-coveb", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: curatedBladderData requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-gsl - r-igraph @@ -30,20 +32,23 @@ requirements: - r-matrix - r-mvtnorm run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-gsl - r-igraph - r-laplacesdemon - r-matrix - r-mvtnorm + +source: + md5: ba7e5e73c1cc164af05012a489f67c1d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Empirical Bayes estimate of block diagonal covariance matrices' - description: 'Using bayesian methods to estimate correlation matrices assuming that they can be written and estimated as block diagonal matrices. These block diagonal matrices are determined using shrinkage parameters that values below this parameter to zero.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-coverageview/meta.yaml b/recipes/bioconductor-coverageview/meta.yaml index c5783d123cbb9..f198c5b932090 100644 --- a/recipes/bioconductor-coverageview/meta.yaml +++ b/recipes/bioconductor-coverageview/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "CoverageView" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a framework for the visualization of genome coverage profiles. It can be used for ChIP-seq experiments, but it can be also used for genome-wide nucleosome positioning experiments or other experiment types where it is important to have a framework in order to inspect how the coverage distributed across the genome + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Coverage visualization package for R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 27821acd2787d95d95532f71d22378df build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-coverageview", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base + +source: + md5: 34b54696a30b3e5dc9addde643fcd0de + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Coverage visualization package for R' - description: 'This package provides a framework for the visualization of genome coverage profiles. It can be used for ChIP-seq experiments, but it can be also used for genome-wide nucleosome positioning experiments or other experiment types where it is important to have a framework in order to inspect how the coverage distributed across the genome' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-covrna/meta.yaml b/recipes/bioconductor-covrna/meta.yaml index 43b8f2d3c5e2f..a7f0ed26dfecd 100644 --- a/recipes/bioconductor-covrna/meta.yaml +++ b/recipes/bioconductor-covrna/meta.yaml @@ -1,51 +1,57 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "covRNA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides the analysis methods fourthcorner and RLQ analysis for large-scale transcriptomic data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Multivariate Analysis of Transcriptomic Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dd8405538f8c54345579ee7d0d5dc63f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-covrna", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:covrna + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-covrna + path: recipes/bioconductor-covrna + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 - r-ade4 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 - r-ade4 - r-base + +source: + md5: 95b8d91ef9583ec9d34edd3aca93847c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Multivariate Analysis of Transcriptomic Data' - description: 'This package provides the analysis methods fourthcorner and RLQ analysis for large-scale transcriptomic data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:covrna - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-covrna - path: recipes/bioconductor-covrna - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cpvsnp/meta.yaml b/recipes/bioconductor-cpvsnp/meta.yaml index c4c3bdc69a5f3..52e360e34ea77 100644 --- a/recipes/bioconductor-cpvsnp/meta.yaml +++ b/recipes/bioconductor-cpvsnp/meta.yaml @@ -1,56 +1,62 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "cpvSNP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Gene set analysis methods exist to combine SNP-level association p-values into gene sets, calculating a single association p-value for each gene set. This package implements two such methods that require only the calculated SNP p-values, the gene set(s) of interest, and a correlation matrix (if desired). One method (GLOSSI) requires independent SNPs and the other (VEGAS) can take into account correlation (LD) among the SNPs. Built-in plotting functions are available to help users visualize results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Gene set analysis methods for SNP association p-values that lie in genes in given gene sets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2edb50570eb609c9962e57d36d70ceba build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cpvsnp", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:cpvsnp + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-cpvsnp + path: recipes/bioconductor-cpvsnp + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 - r-base - r-corpcor - r-ggplot2 - r-plyr run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 - r-base - r-corpcor - r-ggplot2 - r-plyr + +source: + md5: b0920d0e350c81690d3287679df77285 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Gene set analysis methods for SNP association p-values that lie in genes in given gene sets' - description: 'Gene set analysis methods exist to combine SNP-level association p-values into gene sets, calculating a single association p-value for each gene set. This package implements two such methods that require only the calculated SNP p-values, the gene set(s) of interest, and a correlation matrix (if desired). One method (GLOSSI) requires independent SNPs and the other (VEGAS) can take into account correlation (LD) among the SNPs. Built-in plotting functions are available to help users visualize results.' -extra: - identifiers: - - biotools:cpvsnp - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-cpvsnp - path: recipes/bioconductor-cpvsnp - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cqn/meta.yaml b/recipes/bioconductor-cqn/meta.yaml index 267b7af6d65ba..5268ace860212 100644 --- a/recipes/bioconductor-cqn/meta.yaml +++ b/recipes/bioconductor-cqn/meta.yaml @@ -1,51 +1,55 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "cqn" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Conditional quantile normalization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a72eb9ae5c393dec7ecc4f992d11328f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cqn", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:cqn + parent_recipe: + name: bioconductor-cqn + path: recipes/bioconductor-cqn + version: 1.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: scales, edgeR requirements: host: - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-mclust - r-nor1mix - r-quantreg run: - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - r-base - r-mclust - r-nor1mix - r-quantreg + +source: + md5: f75885ab51fd672d84d12fd909ba8432 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Conditional quantile normalization' - description: 'A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.' -extra: - identifiers: - - biotools:cqn - parent_recipe: - name: bioconductor-cqn - path: recipes/bioconductor-cqn - version: 1.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-crcl18/meta.yaml b/recipes/bioconductor-crcl18/meta.yaml index 7a7776d0bfc5d..89d90de1ba61d 100644 --- a/recipes/bioconductor-crcl18/meta.yaml +++ b/recipes/bioconductor-crcl18/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "CRCL18" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 176bd921f08e717ec49e4e3eb4a5e5e5 +about: + description: colorectal cancer mRNA and miRNA on 18 cell lines + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: CRC cell line dataset build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-crcl18", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8e65ec467f42c7419a0f0a5d986c99f2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'CRC cell line dataset' - description: 'colorectal cancer mRNA and miRNA on 18 cell lines' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-crcl18/post-link.sh b/recipes/bioconductor-crcl18/post-link.sh index 841a4c62b2bb7..d425df97930c9 100644 --- a/recipes/bioconductor-crcl18/post-link.sh +++ b/recipes/bioconductor-crcl18/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "crcl18-1.22.0" +installBiocDataPackage.sh "crcl18-1.26.0" diff --git a/recipes/bioconductor-crimage/meta.yaml b/recipes/bioconductor-crimage/meta.yaml index 42e7d5fc48fd8..cb4553ffab6bf 100644 --- a/recipes/bioconductor-crimage/meta.yaml +++ b/recipes/bioconductor-crimage/meta.yaml @@ -1,57 +1,63 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "CRImage" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: CRImage a package to classify cells and calculate tumour cellularity -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84d9bedefc25b08b7e6d86c47bf233f9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-crimage", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:crimage + - doi:10.1126/scitranslmed.3004330 + parent_recipe: + name: bioconductor-crimage + path: recipes/bioconductor-crimage + version: 1.28.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-acgh >=1.80.0,<1.81.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - bioconductor-acgh >=1.84.0,<1.85.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 - r-base - r-e1071 - r-foreach - r-mass - r-sgeostat run: - - 'bioconductor-acgh >=1.80.0,<1.81.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - bioconductor-acgh >=1.84.0,<1.85.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 - r-base - r-e1071 - r-foreach - r-mass - r-sgeostat + +source: + md5: b7295efd23bc396a973fa89999ee342f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'CRImage a package to classify cells and calculate tumour cellularity' - description: 'CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity.' -extra: - identifiers: - - biotools:crimage - - doi:10.1126/scitranslmed.3004330 - parent_recipe: - name: bioconductor-crimage - path: recipes/bioconductor-crimage - version: 1.28.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-crisprbase/meta.yaml b/recipes/bioconductor-crisprbase/meta.yaml index 92d843a59a6cf..b58e6b9f3d835 100644 --- a/recipes/bioconductor-crisprbase/meta.yaml +++ b/recipes/bioconductor-crisprbase/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "crisprBase" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to help extract genomic coordinates of spacer and protospacer sequences. Commonly-used CRISPR nuclease objects are provided that can be readily used in other packages. Both DNA- and RNA-targeting nucleases are supported. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Base functions and classes for CRISPR gRNA design -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20cc1254ee7d33a966bb795f09f8be44 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-crisprbase", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-stringr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-stringr + +source: + md5: 0e88d059c03ecf11df89c18bc3811bba + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Base functions and classes for CRISPR gRNA design' - description: 'Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to help extract genomic coordinates of spacer and protospacer sequences. Commonly-used CRISPR nuclease objects are provided that can be readily used in other packages. Both DNA- and RNA-targeting nucleases are supported.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-crisprbowtie/meta.yaml b/recipes/bioconductor-crisprbowtie/meta.yaml index c2923cdfff081..72e292423a2ac 100644 --- a/recipes/bioconductor-crisprbowtie/meta.yaml +++ b/recipes/bioconductor-crisprbowtie/meta.yaml @@ -1,57 +1,62 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "crisprBowtie" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides a user-friendly interface to map on-targets and off-targets of CRISPR gRNA spacer sequences using bowtie. The alignment is fast, and can be performed using either commonly-used or custom CRISPR nucleases. The alignment can work with any reference or custom genomes. Both DNA- and RNA-targeting nucleases are supported. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Bowtie-based alignment of CRISPR gRNA spacer sequences -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eabea0206c16b87d8acaa65245390d30 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-crisprbowtie", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-crisprbase >=1.6.0,<1.7.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rbowtie >=1.42.0,<1.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-crisprbase >=1.10.0,<1.11.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rbowtie >=1.46.0,<1.47.0 - r-base - r-readr - r-stringr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-crisprbase >=1.6.0,<1.7.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rbowtie >=1.42.0,<1.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-crisprbase >=1.10.0,<1.11.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rbowtie >=1.46.0,<1.47.0 - r-base - r-readr - r-stringr + +source: + md5: ed35798ccf69c3888016b83f6f2eec49 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Bowtie-based alignment of CRISPR gRNA spacer sequences' - description: 'Provides a user-friendly interface to map on-targets and off-targets of CRISPR gRNA spacer sequences using bowtie. The alignment is fast, and can be performed using either commonly-used or custom CRISPR nucleases. The alignment can work with any reference or custom genomes. Both DNA- and RNA-targeting nucleases are supported.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-crisprbwa/build_failure.linux-64.yaml b/recipes/bioconductor-crisprbwa/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..3f21094477205 --- /dev/null +++ b/recipes/bioconductor-crisprbwa/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 2ac2ed55f5c2108b90cba76896450d02a78bcd57f96e872682e340095209daf1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rbwa[version='>=1.10.0,<1.11.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rbwa >=1.10.0,<1.11.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rbwa >=1.10.0,<1.11.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rbwa[version='>=1.10.0,<1.11.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rbwa >=1.10.0,<1.11.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rbwa >=1.10.0,<1.11.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rbwa[version='>=1.10.0,<1.11.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rbwa >=1.10.0,<1.11.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rbwa >=1.10.0,<1.11.0 [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-crisprbwa/meta.yaml b/recipes/bioconductor-crisprbwa/meta.yaml index 58f4eece924b8..fa07432773e47 100644 --- a/recipes/bioconductor-crisprbwa/meta.yaml +++ b/recipes/bioconductor-crisprbwa/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "crisprBwa" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides a user-friendly interface to map on-targets and off-targets of CRISPR gRNA spacer sequences using bwa. The alignment is fast, and can be performed using either commonly-used or custom CRISPR nucleases. The alignment can work with any reference or custom genomes. Currently not supported on Windows machines. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: BWA-based alignment of CRISPR gRNA spacer sequences -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d77734ef6cfa03fb7b08c21c59155518 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-crisprbwa", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-crisprbase >=1.6.0,<1.7.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-rbwa >=1.6.0,<1.7.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-crisprbase >=1.10.0,<1.11.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-rbwa >=1.10.0,<1.11.0 - r-base - r-readr - r-stringr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-crisprbase >=1.6.0,<1.7.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-rbwa >=1.6.0,<1.7.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-crisprbase >=1.10.0,<1.11.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-rbwa >=1.10.0,<1.11.0 - r-base - r-readr - r-stringr + +source: + md5: ac3055e06623fdbd23f05744a0fcfdba + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'BWA-based alignment of CRISPR gRNA spacer sequences' - description: 'Provides a user-friendly interface to map on-targets and off-targets of CRISPR gRNA spacer sequences using bwa. The alignment is fast, and can be performed using either commonly-used or custom CRISPR nucleases. The alignment can work with any reference or custom genomes. Currently not supported on Windows machines.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-crisprdesign/meta.yaml b/recipes/bioconductor-crisprdesign/meta.yaml index ead19116d4702..5408ca94b3b84 100644 --- a/recipes/bioconductor-crisprdesign/meta.yaml +++ b/recipes/bioconductor-crisprdesign/meta.yaml @@ -1,69 +1,76 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "crisprDesign" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including DNA- and RNA-target nucleases such as Cas9, Cas12a, and Cas13d. All types of base editors are also supported. gRNA design can be performed on reference genomes, transcriptomes, and custom DNA and RNA sequences. Both unpaired and paired gRNA designs are enabled.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Comprehensive design of CRISPR gRNAs for nucleases and base editors -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4efe77ba4d8f440af21a1e80f0e1f5d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-crisprdesign", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: biomaRt, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocStyle, crisprBwa (>= 0.99.7), knitr, rmarkdown, Rbowtie, Rbwa, RCurl, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-crisprbase >=1.6.0,<1.7.0' - - 'bioconductor-crisprbowtie >=1.6.0,<1.7.0' - - 'bioconductor-crisprscore >=1.6.0,<1.7.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-crisprbase >=1.10.0,<1.11.0 + - bioconductor-crisprbowtie >=1.10.0,<1.11.0 + - bioconductor-crisprscore >=1.10.0,<1.11.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-matrix run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-crisprbase >=1.6.0,<1.7.0' - - 'bioconductor-crisprbowtie >=1.6.0,<1.7.0' - - 'bioconductor-crisprscore >=1.6.0,<1.7.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-crisprbase >=1.10.0,<1.11.0 + - bioconductor-crisprbowtie >=1.10.0,<1.11.0 + - bioconductor-crisprscore >=1.10.0,<1.11.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-matrix + +source: + md5: f599d5ae19ba81fe8fad9eec73927f40 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Comprehensive design of CRISPR gRNAs for nucleases and base editors' - description: 'Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including DNA- and RNA-target nucleases such as Cas9, Cas12a, and Cas13d. All types of base editors are also supported. gRNA design can be performed on reference genomes, transcriptomes, and custom DNA and RNA sequences. Both unpaired and paired gRNA designs are enabled.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-crisprscore/meta.yaml b/recipes/bioconductor-crisprscore/meta.yaml index 2ac786f7e1988..64c952c274426 100644 --- a/recipes/bioconductor-crisprscore/meta.yaml +++ b/recipes/bioconductor-crisprscore/meta.yaml @@ -1,57 +1,62 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "crisprScore" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Provides R wrappers of several on-target and off-target scoring methods for CRISPR guide RNAs (gRNAs). The following nucleases are supported: SpCas9, AsCas12a, enAsCas12a, and RfxCas13d (CasRx). The available on-target cutting efficiency scoring methods are RuleSet1, Azimuth, DeepHF, DeepCpf1, enPAM+GB, and CRISPRscan. Both the CFD and MIT scoring methods are available for off-target specificity prediction. The package also provides a Lindel-derived score to predict the probability of a gRNA to produce indels inducing a frameshift for the Cas9 nuclease. Note that DeepHF, DeepCpf1 and enPAM+GB are not available on Windows machines.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c83f7928b03ce0308175835556dfcb54 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-crisprscore", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-basilisk.utils >=1.14.0,<1.15.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-crisprscoredata >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-basilisk.utils >=1.18.0,<1.19.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-crisprscoredata >=1.10.0,<1.11.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-randomforest - r-reticulate - r-stringr run: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-basilisk.utils >=1.14.0,<1.15.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-crisprscoredata >=1.6.0,<1.7.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-basilisk.utils >=1.18.0,<1.19.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-crisprscoredata >=1.10.0,<1.11.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-randomforest - r-reticulate - r-stringr + +source: + md5: 4dfe683c4ce70e62c4d5a0b6eadbcd19 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs' - description: 'Provides R wrappers of several on-target and off-target scoring methods for CRISPR guide RNAs (gRNAs). The following nucleases are supported: SpCas9, AsCas12a, enAsCas12a, and RfxCas13d (CasRx). The available on-target cutting efficiency scoring methods are RuleSet1, Azimuth, DeepHF, DeepCpf1, enPAM+GB, and CRISPRscan. Both the CFD and MIT scoring methods are available for off-target specificity prediction. The package also provides a Lindel-derived score to predict the probability of a gRNA to produce indels inducing a frameshift for the Cas9 nuclease. Note that DeepHF, DeepCpf1 and enPAM+GB are not available on Windows machines.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-crisprscoredata/meta.yaml b/recipes/bioconductor-crisprscoredata/meta.yaml index 56963b7b20d4a..675b3a6831e40 100644 --- a/recipes/bioconductor-crisprscoredata/meta.yaml +++ b/recipes/bioconductor-crisprscoredata/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "crisprScoreData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f4d86404f045ec36cf7d1b1c64373fe +about: + description: Provides an interface to access pre-trained models for on-target and off-target gRNA activity prediction algorithms implemented in the crisprScore package. Pre-trained model data are stored in the ExperimentHub database. Users should consider using the crisprScore package directly to use and load the pre-trained models. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Pre-trained models for the crisprScore package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-crisprscoredata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9e599deca608e23b7ec35db0579bff1b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Pre-trained models for the crisprScore package' - description: 'Provides an interface to access pre-trained models for on-target and off-target gRNA activity prediction algorithms implemented in the crisprScore package. Pre-trained model data are stored in the ExperimentHub database. Users should consider using the crisprScore package directly to use and load the pre-trained models.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-crisprscoredata/post-link.sh b/recipes/bioconductor-crisprscoredata/post-link.sh index 4fd2ecb7ae14e..df9f3021a2848 100644 --- a/recipes/bioconductor-crisprscoredata/post-link.sh +++ b/recipes/bioconductor-crisprscoredata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "crisprscoredata-1.6.0" +installBiocDataPackage.sh "crisprscoredata-1.10.0" diff --git a/recipes/bioconductor-crisprseek/meta.yaml b/recipes/bioconductor-crisprseek/meta.yaml index 56325695ce330..8186a81a22f14 100644 --- a/recipes/bioconductor-crisprseek/meta.yaml +++ b/recipes/bioconductor-crisprseek/meta.yaml @@ -1,37 +1,47 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "CRISPRseek" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package includes functions to find potential guide RNAs for the CRISPR editing system including Base Editors and the Prime Editor for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not. Potential guide RNAs are annotated with total score of the top5 and topN off-targets, detailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. The package also output indels and their frequencies for Cas9 targeted sites. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b14c3c52470140b9c7bc85b9ca4044a5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-crisprseek", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:crisprseek + parent_recipe: + name: bioconductor-crisprseek + path: recipes/bioconductor-crisprseek + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, lattice, MASS, tensorflow, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-data.table - r-dplyr @@ -41,16 +51,16 @@ requirements: - r-reticulate - r-seqinr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-data.table - r-dplyr @@ -59,20 +69,16 @@ requirements: - r-mltools - r-reticulate - r-seqinr + +source: + md5: 3bde56994f0385dbdf55ef70a04525f2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems' - description: 'The package includes functions to find potential guide RNAs for the CRISPR editing system including Base Editors and the Prime Editor for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not. Potential guide RNAs are annotated with total score of the top5 and topN off-targets, detailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. The package also output indels and their frequencies for Cas9 targeted sites.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:crisprseek - parent_recipe: - name: bioconductor-crisprseek - path: recipes/bioconductor-crisprseek - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-crisprshiny/build.sh b/recipes/bioconductor-crisprshiny/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-crisprshiny/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-crisprshiny/meta.yaml b/recipes/bioconductor-crisprshiny/meta.yaml new file mode 100644 index 0000000000000..07f92f72293dd --- /dev/null +++ b/recipes/bioconductor-crisprshiny/meta.yaml @@ -0,0 +1,74 @@ +{% set version = "1.2.0" %} +{% set name = "crisprShiny" %} +{% set bioc = "3.20" %} + +about: + description: Provides means to interactively visualize guide RNAs (gRNAs) in GuideSet objects via Shiny application. This GUI can be self-contained or as a module within a larger Shiny app. The content of the app reflects the annotations present in the passed GuideSet object, and includes intuitive tools to examine, filter, and export gRNAs, thereby making gRNA design more user-friendly. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Exploring curated CRISPR gRNAs via Shiny + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-crisprshiny", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, shinyFeedback, testthat (>= 3.0.0), BSgenome.Hsapiens.UCSC.hg38 +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-crisprbase >=1.10.0,<1.11.0 + - bioconductor-crisprdesign >=1.8.0,<1.9.0 + - bioconductor-crisprscore >=1.10.0,<1.11.0 + - bioconductor-crisprviz >=1.8.0,<1.9.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-dt + - r-htmlwidgets + - r-shiny + - r-shinybs + - r-shinyjs + - r-waiter + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-crisprbase >=1.10.0,<1.11.0 + - bioconductor-crisprdesign >=1.8.0,<1.9.0 + - bioconductor-crisprscore >=1.10.0,<1.11.0 + - bioconductor-crisprviz >=1.8.0,<1.9.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-dt + - r-htmlwidgets + - r-shiny + - r-shinybs + - r-shinyjs + - r-waiter + +source: + md5: f995905519c491f4cabe9d94743fe65f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-crisprvariants/meta.yaml b/recipes/bioconductor-crisprvariants/meta.yaml index a820551578ab1..4be5780fb0976 100644 --- a/recipes/bioconductor-crisprvariants/meta.yaml +++ b/recipes/bioconductor-crisprvariants/meta.yaml @@ -1,68 +1,74 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "CrispRVariants" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CrispRVariants provides tools for analysing the results of a CRISPR-Cas9 mutagenesis sequencing experiment, or other sequencing experiments where variants within a given region are of interest. These tools allow users to localize variant allele combinations with respect to any genomic location (e.g. the Cas9 cut site), plot allele combinations and calculate mutation rates with flexible filtering of unrelated variants. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Tools for counting and visualising mutations in a target location -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ede7cabcf986e2494f2e7b489621dd09 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-crisprvariants", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:crisprvariants + parent_recipe: + name: bioconductor-crisprvariants + path: recipes/bioconductor-crisprvariants + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, GenomicFeatures, knitr, rmarkdown, readxl, rtracklayer, sangerseqR, testthat, VariantAnnotation requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-ggplot2 >=2.2.0' + - r-ggplot2 >=2.2.0 - r-gridextra - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-ggplot2 >=2.2.0' + - r-ggplot2 >=2.2.0 - r-gridextra - r-reshape2 + +source: + md5: 47b2e6c902a7e79321ec14f4ee80bed8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Tools for counting and visualising mutations in a target location' - description: 'CrispRVariants provides tools for analysing the results of a CRISPR-Cas9 mutagenesis sequencing experiment, or other sequencing experiments where variants within a given region are of interest. These tools allow users to localize variant allele combinations with respect to any genomic location (e.g. the Cas9 cut site), plot allele combinations and calculate mutation rates with flexible filtering of unrelated variants.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:crisprvariants - parent_recipe: - name: bioconductor-crisprvariants - path: recipes/bioconductor-crisprvariants - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-crisprverse/meta.yaml b/recipes/bioconductor-crisprverse/meta.yaml index 112545aadf561..87e91af21bc6e 100644 --- a/recipes/bioconductor-crisprverse/meta.yaml +++ b/recipes/bioconductor-crisprverse/meta.yaml @@ -1,55 +1,60 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "crisprVerse" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The crisprVerse is a modular ecosystem of R packages developed for the design and manipulation of CRISPR guide RNAs (gRNAs). All packages share a common language and design principles. This package is designed to make it easy to install and load the crisprVerse packages in a single step. To learn more about the crisprVerse, visit . + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Easily install and load the crisprVerse ecosystem for CRISPR gRNA design -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dff359d1f63b8a58289ef0914c9260c5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-crisprverse", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-crisprbase >=1.6.0,<1.7.0' - - 'bioconductor-crisprbowtie >=1.6.0,<1.7.0' - - 'bioconductor-crisprdesign >=1.4.0,<1.5.0' - - 'bioconductor-crisprscore >=1.6.0,<1.7.0' - - 'bioconductor-crisprscoredata >=1.6.0,<1.7.0' - - 'bioconductor-crisprviz >=1.4.0,<1.5.0' + - bioconductor-crisprbase >=1.10.0,<1.11.0 + - bioconductor-crisprbowtie >=1.10.0,<1.11.0 + - bioconductor-crisprdesign >=1.8.0,<1.9.0 + - bioconductor-crisprscore >=1.10.0,<1.11.0 + - bioconductor-crisprscoredata >=1.10.0,<1.11.0 + - bioconductor-crisprviz >=1.8.0,<1.9.0 - r-base - r-biocmanager - r-cli - r-rlang run: - - 'bioconductor-crisprbase >=1.6.0,<1.7.0' - - 'bioconductor-crisprbowtie >=1.6.0,<1.7.0' - - 'bioconductor-crisprdesign >=1.4.0,<1.5.0' - - 'bioconductor-crisprscore >=1.6.0,<1.7.0' - - 'bioconductor-crisprscoredata >=1.6.0,<1.7.0' - - 'bioconductor-crisprviz >=1.4.0,<1.5.0' + - bioconductor-crisprbase >=1.10.0,<1.11.0 + - bioconductor-crisprbowtie >=1.10.0,<1.11.0 + - bioconductor-crisprdesign >=1.8.0,<1.9.0 + - bioconductor-crisprscore >=1.10.0,<1.11.0 + - bioconductor-crisprscoredata >=1.10.0,<1.11.0 + - bioconductor-crisprviz >=1.8.0,<1.9.0 - r-base - r-biocmanager - r-cli - r-rlang + +source: + md5: e20f861cf3be6fa077c631aa7f5d911b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Easily install and load the crisprVerse ecosystem for CRISPR gRNA design' - description: 'The crisprVerse is a modular ecosystem of R packages developed for the design and manipulation of CRISPR guide RNAs (gRNAs). All packages share a common language and design principles. This package is designed to make it easy to install and load the crisprVerse packages in a single step. To learn more about the crisprVerse, visit .' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-crisprviz/meta.yaml b/recipes/bioconductor-crisprviz/meta.yaml index 1c835bd954fd8..34854b30ecdda 100644 --- a/recipes/bioconductor-crisprviz/meta.yaml +++ b/recipes/bioconductor-crisprviz/meta.yaml @@ -1,59 +1,66 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "crisprViz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications. Works in conjunction with the crisprBase and crisprDesign Bioconductor packages. Plots are produced using the Gviz framework. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Visualization Functions for CRISPR gRNAs -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a95c0cc87c7934da1e9bbfeb1e27bd3a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-crisprviz", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, rtracklayer, testthat, utils requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-crisprbase >=1.6.0,<1.7.0' - - 'bioconductor-crisprdesign >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-crisprbase >=1.10.0,<1.11.0 + - bioconductor-crisprdesign >=1.8.0,<1.9.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-crisprbase >=1.6.0,<1.7.0' - - 'bioconductor-crisprdesign >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-crisprbase >=1.10.0,<1.11.0 + - bioconductor-crisprdesign >=1.8.0,<1.9.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base + +source: + md5: 7073ae848310d1e9dbf1aa45ab7c6538 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Visualization Functions for CRISPR gRNAs' - description: 'Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications. Works in conjunction with the crisprBase and crisprDesign Bioconductor packages. Plots are produced using the Gviz framework.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-crlmm/meta.yaml b/recipes/bioconductor-crlmm/meta.yaml index 6e0ee3be271f6..636bff7d4c597 100644 --- a/recipes/bioconductor-crlmm/meta.yaml +++ b/recipes/bioconductor-crlmm/meta.yaml @@ -1,33 +1,47 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "crlmm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d047359287ee832d97e95c0945dff8cc build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-crlmm", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:crlmm + parent_recipe: + name: bioconductor-crlmm + path: recipes/bioconductor-crlmm + version: 1.38.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats, RUnit requirements: + + build: + - {{ compiler('c') }} + - make + host: - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-beanplot - r-ellipse @@ -36,18 +50,19 @@ requirements: - r-lattice - r-matrixstats - r-mvtnorm - - 'r-rcppeigen >=0.3.1.2.1' + - r-rcppeigen >=0.3.1.2.1 - r-vgam - libblas - liblapack + run: - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-beanplot - r-ellipse @@ -56,24 +71,18 @@ requirements: - r-lattice - r-matrixstats - r-mvtnorm - - 'r-rcppeigen >=0.3.1.2.1' + - r-rcppeigen >=0.3.1.2.1 - r-vgam - build: - - {{ compiler('c') }} - - make + +source: + md5: 1f4e6f2c08d05240cb5ccb9165247de5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays' - description: 'Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms.' -extra: - identifiers: - - biotools:crlmm - parent_recipe: - name: bioconductor-crlmm - path: recipes/bioconductor-crlmm - version: 1.38.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-csar/meta.yaml b/recipes/bioconductor-csar/meta.yaml index 8a7ab11fb87da..23f8e7dce5915 100644 --- a/recipes/bioconductor-csar/meta.yaml +++ b/recipes/bioconductor-csar/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "1.54.0" %} +{% set version = "1.58.0" %} {% set name = "CSAR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Statistical tools for ChIP-seq data analysis. The package includes the statistical method described in Kaufmann et al. (2009) PLoS Biology: 7(4):e1000090. Briefly, Taking the average DNA fragment size subjected to sequencing into account, the software calculates genomic single-nucleotide read-enrichment values. After normalization, sample and control are compared using a test based on the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutation.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Statistical tools for the analysis of ChIP-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf22689abca527406f9f2b333739d7bc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-csar", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:csar + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ShortRead, Biostrings requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - libblas - liblapack run: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: 5d41177ffb070156de6f1e72406895dc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Statistical tools for the analysis of ChIP-seq data' - description: 'Statistical tools for ChIP-seq data analysis. The package includes the statistical method described in Kaufmann et al. (2009) PLoS Biology: 7(4):e1000090. Briefly, Taking the average DNA fragment size subjected to sequencing into account, the software calculates genomic single-nucleotide read-enrichment values. After normalization, sample and control are compared using a test based on the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutation.' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-csaw/meta.yaml b/recipes/bioconductor-csaw/meta.yaml index 444eb55b8a0ec..c5ee46b55de06 100644 --- a/recipes/bioconductor-csaw/meta.yaml +++ b/recipes/bioconductor-csaw/meta.yaml @@ -1,82 +1,90 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "csaw" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: ChIP-Seq Analysis with Windows -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 07ad4af3be8e5e799b06826cc97a449e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-csaw", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:csaw + parent_recipe: + name: bioconductor-csaw + path: recipes/bioconductor-csaw + version: 1.14.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationDbi, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager # SystemRequirements: C++11, GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-metapod >=1.10.0,<1.11.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-metapod >=1.14.0,<1.15.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-matrix - r-rcpp - libblas - liblapack + - zlib + - liblzma-devel run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-metapod >=1.10.0,<1.11.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-metapod >=1.14.0,<1.15.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-matrix - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 6601f4dfee57393d098727ea875d3d06 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'ChIP-Seq Analysis with Windows' - description: 'Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:csaw - parent_recipe: - name: bioconductor-csaw - path: recipes/bioconductor-csaw - version: 1.14.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-csdr/meta.yaml b/recipes/bioconductor-csdr/meta.yaml index 8f28df3937931..dce979e2b95a8 100644 --- a/recipes/bioconductor-csdr/meta.yaml +++ b/recipes/bioconductor-csdr/meta.yaml @@ -1,25 +1,31 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "csdR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains functionality to run differential gene co-expression across two different conditions. The algorithm is inspired by Voigt et al. 2017 and finds Conserved, Specific and Differentiated genes (hence the name CSD). This package include efficient and variance calculation by bootstrapping and Welford's algorithm. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Differential gene co-expression -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02132c2d953434d0bb7de9b58e8b5769 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-csdr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle, magrittr, igraph, dplyr requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-glue @@ -36,17 +42,16 @@ requirements: - r-rcpp - r-rhpcblasctl - r-wgcna - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 2849182bb98a5e009612dea807a4b677 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Differential gene co-expression' - description: 'This package contains functionality to run differential gene co-expression across two different conditions. The algorithm is inspired by Voigt et al. 2017 and finds Conserved, Specific and Differentiated genes (hence the name CSD). This package include efficient and variance calculation by bootstrapping and Welford''s algorithm.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cssq/meta.yaml b/recipes/bioconductor-cssq/meta.yaml index 52270a9d7e002..da4ac2af71e9a 100644 --- a/recipes/bioconductor-cssq/meta.yaml +++ b/recipes/bioconductor-cssq/meta.yaml @@ -1,54 +1,59 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "CSSQ" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is desgined to perform statistical analysis to identify statistically significant differentially bound regions between multiple groups of ChIP-seq dataset. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Chip-seq Signal Quantifier Pipeline -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d9a6f6200f67cc06173c30dcd6775e5a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cssq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, markdown requirements: host: - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 run: - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 + +source: + md5: 147adca7f99d5844d42f1613dec985d9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Chip-seq Signal Quantifier Pipeline' - description: 'This package is desgined to perform statistical analysis to identify statistically significant differentially bound regions between multiple groups of ChIP-seq dataset.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ctc/meta.yaml b/recipes/bioconductor-ctc/meta.yaml index 67bcc2e93f176..cf0baf84d889b 100644 --- a/recipes/bioconductor-ctc/meta.yaml +++ b/recipes/bioconductor-ctc/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.76.0" %} +{% set version = "1.80.0" %} {% set name = "ctc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for export and import classification trees and clusters to other programs + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Cluster and Tree Conversion. -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ea94b8b636b26d4f827ecd4569804d1e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ctc", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:ctc + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ctc + path: recipes/bioconductor-ctc + version: 1.54.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-amap @@ -26,21 +37,16 @@ requirements: run: - r-amap - r-base + +source: + md5: ee57a72b79ced1b575c9fe4f4b55ed6e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Cluster and Tree Conversion.' - description: 'Tools for export and import classification trees and clusters to other programs' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:ctc - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-ctc - path: recipes/bioconductor-ctc - version: 1.54.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ctcf/meta.yaml b/recipes/bioconductor-ctcf/meta.yaml index 1c4437ce61d37..1a36405f2b660 100644 --- a/recipes/bioconductor-ctcf/meta.yaml +++ b/recipes/bioconductor-ctcf/meta.yaml @@ -1,24 +1,23 @@ {% set version = "0.99.11" %} {% set name = "CTCF" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ec44245864395de390e68fa56e465af +about: + description: Genomic coordinates of CTCF binding sites, with strand orientation (directionality of binding). Position weight matrices (PWMs) from JASPAR, HOCOMOCO, CIS-BP, CTCFBSDB, SwissRegulon, Jolma 2013, were used to uniformly predict CTCF binding sites using FIMO (default settings) on human (hg18, hg19, hg38, T2T) and mouse (mm9, mm10, mm39) genome assemblies. Extra columns include motif/PWM name (e.g., MA0139.1), score, p-value, q-value, and the motif sequence. It is recommended to filter FIMO-predicted sites by 1e-6 p-value threshold instead of using the default 1e-4 threshold. Experimentally obtained CTCF-bound cis-regulatory elements from ENCODE SCREEN and predicted CTCF sites from CTCFBSDB are also included. Selected data are lifted over from a different genome assembly as we demonstrated liftOver is a viable option to obtain CTCF coordinates in different genome assemblies. CTCF sites obtained using JASPAR's MA0139.1 PWM and filtered at 1e-6 p-value threshold are recommended. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Genomic coordinates of CTCF binding sites, with orientation build: - number: 1 + noarch: generic + number: 2 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ctcf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, rmarkdown, knitr, AnnotationHub, GenomicRanges, plyranges, sessioninfo requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5ec44245864395de390e68fa56e465af + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Genomic coordinates of CTCF binding sites, with orientation' - description: 'Genomic coordinates of CTCF binding sites, with strand orientation (directionality of binding). Position weight matrices (PWMs) from JASPAR, HOCOMOCO, CIS-BP, CTCFBSDB, SwissRegulon, Jolma 2013, were used to uniformly predict CTCF binding sites using FIMO (default settings) on human (hg18, hg19, hg38, T2T) and mouse (mm9, mm10, mm39) genome assemblies. Extra columns include motif/PWM name (e.g., MA0139.1), score, p-value, q-value, and the motif sequence. It is recommended to filter FIMO-predicted sites by 1e-6 p-value threshold instead of using the default 1e-4 threshold. Experimentally obtained CTCF-bound cis-regulatory elements from ENCODE SCREEN and predicted CTCF sites from CTCFBSDB are also included. Selected data are lifted over from a different genome assembly as we demonstrated liftOver is a viable option to obtain CTCF coordinates in different genome assemblies. CTCF sites obtained using JASPAR''s MA0139.1 PWM and filtered at 1e-6 p-value threshold are recommended.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ctdata/meta.yaml b/recipes/bioconductor-ctdata/meta.yaml index 051c707054ba5..a659548e672ae 100644 --- a/recipes/bioconductor-ctdata/meta.yaml +++ b/recipes/bioconductor-ctdata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "CTdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d130308cf078329f4cc6a1cc8055475d +about: + description: Data from publicly available databases (GTEx, CCLE, TCGA and ENCODE) that go with CTexploreR in order to re-define a comprehensive and thoroughly curated list of CT genes and their main characteristics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Data companion to CTexploreR build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ctdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat (>= 3.0.0), DT, BiocStyle, knitr, rmarkdown, SummarizedExperiment, SingleCellExperiment requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base +source: + md5: d50ff1f52dd316752d8a277deb2b7f02 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Data companion to CTexploreR' - description: 'Data from publicly available databases (GTEx, CCLE, TCGA and ENCODE) that go with CTexploreR in order to re-define a comprehensive and thoroughly curated list of CT genes and their main characteristics.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ctdquerier/meta.yaml b/recipes/bioconductor-ctdquerier/meta.yaml index 9cfc17e349b4e..e8247114ef002 100644 --- a/recipes/bioconductor-ctdquerier/meta.yaml +++ b/recipes/bioconductor-ctdquerier/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "2.10.0" %} +{% set version = "2.14.0" %} {% set name = "CTDquerier" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package to retrieve and visualize data from the Comparative Toxicogenomics Database (http://ctdbase.org/). The downloaded data is formated as DataFrames for further downstream analyses. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Package for CTDbase data query, visualization and downstream analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 42c5654d014714b22e5c1c2c2e7a2118 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ctdquerier", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-gridextra @@ -32,8 +34,8 @@ requirements: - r-stringdist - r-stringr run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-gridextra @@ -41,13 +43,16 @@ requirements: - r-rcurl - r-stringdist - r-stringr + +source: + md5: 92236221356925cb6b7aa0800dcef65e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Package for CTDbase data query, visualization and downstream analysis' - description: 'Package to retrieve and visualize data from the Comparative Toxicogenomics Database (http://ctdbase.org/). The downloaded data is formated as DataFrames for further downstream analyses.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ctexplorer/build.sh b/recipes/bioconductor-ctexplorer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ctexplorer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ctexplorer/meta.yaml b/recipes/bioconductor-ctexplorer/meta.yaml new file mode 100644 index 0000000000000..94c4e965bfd72 --- /dev/null +++ b/recipes/bioconductor-ctexplorer/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.2.0" %} +{% set name = "CTexploreR" %} +{% set bioc = "3.20" %} + +about: + description: The CTexploreR package re-defines the list of Cancer Testis/Germline (CT) genes. It is based on publicly available RNAseq databases (GTEx, CCLE and TCGA) and summarises CT genes' main characteristics. Several visualisation functions allow to explore their expression in different types of tissues and cancer cells, or to inspect the methylation status of their promoters in normal tissues. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Explores Cancer Testis Genes + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ctexplorer", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), InteractiveComplexHeatmap +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-ctdata >=1.6.0,<1.7.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-circlize + - r-dplyr + - r-ggplot2 + - r-ggrepel + - r-rlang + - r-tibble + - r-tidyr + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-ctdata >=1.6.0,<1.7.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-circlize + - r-dplyr + - r-ggplot2 + - r-ggrepel + - r-rlang + - r-tibble + - r-tidyr + +source: + md5: c88af5a5f9a8391e3a201b5a46f42d74 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-ctrap/meta.yaml b/recipes/bioconductor-ctrap/meta.yaml index 07edfeb916d8a..93cc3542dcaca 100644 --- a/recipes/bioconductor-ctrap/meta.yaml +++ b/recipes/bioconductor-ctrap/meta.yaml @@ -1,32 +1,35 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "cTRAP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Compare differential gene expression results with those from known cellular perturbations (such as gene knock-down, overexpression or small molecules) derived from the Connectivity Map. Such analyses allow not only to infer the molecular causes of the observed difference in gene expression but also to identify small molecules that could drive or revert specific transcriptomic alterations. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Identification of candidate causal perturbations from differential gene expression data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 049de878508ce8d8031d7d93f6a1fd01 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ctrap", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 - r-base - r-binr - r-cowplot @@ -47,15 +50,16 @@ requirements: - r-reshape2 - r-rlang - r-scales - - 'r-shiny >=1.7.0' + - r-shiny >=1.7.0 - r-shinycssloaders - r-tibble + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 - r-base - r-binr - r-cowplot @@ -76,16 +80,19 @@ requirements: - r-reshape2 - r-rlang - r-scales - - 'r-shiny >=1.7.0' + - r-shiny >=1.7.0 - r-shinycssloaders - r-tibble + +source: + md5: 743e07fd5c56854aec06b87ac00cd371 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Identification of candidate causal perturbations from differential gene expression data' - description: 'Compare differential gene expression results with those from known cellular perturbations (such as gene knock-down, overexpression or small molecules) derived from the Connectivity Map. Such analyses allow not only to infer the molecular causes of the observed difference in gene expression but also to identify small molecules that could drive or revert specific transcriptomic alterations.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ctsge/meta.yaml b/recipes/bioconductor-ctsge/meta.yaml index 44c7878302301..6a8921999b0a8 100644 --- a/recipes/bioconductor-ctsge/meta.yaml +++ b/recipes/bioconductor-ctsge/meta.yaml @@ -1,28 +1,39 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "ctsGE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Methodology for supervised clustering of potentially many predictor variables, such as genes etc., in time series datasets Provides functions that help the user assigning genes to predefined set of model profiles. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Clustering of Time Series Gene Expression data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 31cfbfb8002cbb54747b9a4a41fb17d2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ctsge", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:ctsge + - doi:10.1093/bioinformatics/btx116 + parent_recipe: + name: bioconductor-ctsge + path: recipes/bioconductor-ctsge + version: 1.6.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown, testthat requirements: host: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-ccapp - r-ggplot2 @@ -30,28 +41,23 @@ requirements: - r-shiny - r-stringr run: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-ccapp - r-ggplot2 - r-reshape2 - r-shiny - r-stringr + +source: + md5: be8ca2572db018bdac423cbfff0682fd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Clustering of Time Series Gene Expression data' - description: 'Methodology for supervised clustering of potentially many predictor variables, such as genes etc., in time series datasets Provides functions that help the user assigning genes to predefined set of model profiles.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:ctsge - - doi:10.1093/bioinformatics/btx116 - parent_recipe: - name: bioconductor-ctsge - path: recipes/bioconductor-ctsge - version: 1.6.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ctsv/meta.yaml b/recipes/bioconductor-ctsv/meta.yaml index 209549d623061..ee6cc9b25d942 100644 --- a/recipes/bioconductor-ctsv/meta.yaml +++ b/recipes/bioconductor-ctsv/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "CTSV" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The R package CTSV implements the CTSV approach developed by Jinge Yu and Xiangyu Luo that detects cell-type-specific spatially variable genes accounting for excess zeros. CTSV directly models sparse raw count data through a zero-inflated negative binomial regression model, incorporates cell-type proportions, and performs hypothesis testing based on R package pscl. The package outputs p-values and q-values for genes in each cell type, and CTSV is scalable to datasets with tens of thousands of genes measured on hundreds of spots. CTSV can be installed in Windows, Linux, and Mac OS. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identification of cell-type-specific spatially variable genes accounting for excess zeros -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a3f8c7b5398449ea01b312ed7da1f43 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ctsv", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-knitr - r-pscl run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-knitr - r-pscl + +source: + md5: d83d4f38dedef85ddf27d656795c72b2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Identification of cell-type-specific spatially variable genes accounting for excess zeros' - description: 'The R package CTSV implements the CTSV approach developed by Jinge Yu and Xiangyu Luo that detects cell-type-specific spatially variable genes accounting for excess zeros. CTSV directly models sparse raw count data through a zero-inflated negative binomial regression model, incorporates cell-type proportions, and performs hypothesis testing based on R package pscl. The package outputs p-values and q-values for genes in each cell type, and CTSV is scalable to datasets with tens of thousands of genes measured on hundreds of spots. CTSV can be installed in Windows, Linux, and Mac OS.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cummerbund/meta.yaml b/recipes/bioconductor-cummerbund/meta.yaml index b02fb64575016..6fed767c7e7e7 100644 --- a/recipes/bioconductor-cummerbund/meta.yaml +++ b/recipes/bioconductor-cummerbund/meta.yaml @@ -1,32 +1,42 @@ -{% set version = "2.44.0" %} +{% set version = "2.48.0" %} {% set name = "cummeRbund" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data. -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 367d124a098eca55a6da149e35621c65 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cummerbund", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:cummerbund + - doi:10.1038/nprot.2012.016 + parent_recipe: + name: bioconductor-cummerbund + path: recipes/bioconductor-cummerbund + version: 2.22.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-fastcluster - r-ggplot2 @@ -34,31 +44,27 @@ requirements: - r-reshape2 - r-rsqlite run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-fastcluster - r-ggplot2 - r-plyr - r-reshape2 - r-rsqlite + +source: + md5: 165f719d08fff1b4b4b165a0762dfca3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.' - description: 'Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.' -extra: - identifiers: - - biotools:cummerbund - - doi:10.1038/nprot.2012.016 - parent_recipe: - name: bioconductor-cummerbund - path: recipes/bioconductor-cummerbund - version: 2.22.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-curatedadipoarray/meta.yaml b/recipes/bioconductor-curatedadipoarray/meta.yaml index 771e50a148b5c..6f3788be4f878 100644 --- a/recipes/bioconductor-curatedadipoarray/meta.yaml +++ b/recipes/bioconductor-curatedadipoarray/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "curatedAdipoArray" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 109be77c099e9d7b6da437577f619a54 +about: + description: A curated dataset of Microarrays samples. The samples are MDI- induced pre-adipocytes (3T3-L1) at different time points/stage of differentiation under different types of genetic (knockdown/overexpression) and pharmacological (drug treatment) perturbations. The package documents the data collection and processing. In addition to the documentation, the package contains the scripts that was used to generated the data. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: A Curated Microarrays Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Under Genetic and Pharmacological Perturbations build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-curatedadipoarray", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, ExperimentHub, SummarizedExperiment requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f61b7c6abf04088146901d2afc5698b0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'A Curated Microarrays Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Under Genetic and Pharmacological Perturbations' - description: 'A curated dataset of Microarrays samples. The samples are MDI- induced pre-adipocytes (3T3-L1) at different time points/stage of differentiation under different types of genetic (knockdown/overexpression) and pharmacological (drug treatment) perturbations. The package documents the data collection and processing. In addition to the documentation, the package contains the scripts that was used to generated the data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-curatedadipoarray/post-link.sh b/recipes/bioconductor-curatedadipoarray/post-link.sh index 7471a605b14e7..18069a504ae88 100644 --- a/recipes/bioconductor-curatedadipoarray/post-link.sh +++ b/recipes/bioconductor-curatedadipoarray/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedadipoarray-1.14.0" +installBiocDataPackage.sh "curatedadipoarray-1.18.0" diff --git a/recipes/bioconductor-curatedadipochip/meta.yaml b/recipes/bioconductor-curatedadipochip/meta.yaml index 5c312a510e921..0618975440ede 100644 --- a/recipes/bioconductor-curatedadipochip/meta.yaml +++ b/recipes/bioconductor-curatedadipochip/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "curatedAdipoChIP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0074cb63250ac197dad12e4138d47463 +about: + description: A curated dataset of publicly available ChIP-sequencing of transcription factors, chromatin remodelers and histone modifications in the 3T3-L1 pre-adipocyte cell line. The package document the data collection, pre-processing and processing of the data. In addition to the documentation, the package contains the scripts that was used to generated the data. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A Curated ChIP-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-curatedadipochip", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, GenomicFeatures, ChIPseeker, AnnotationDbi, S4Vectors, DESeq2, fastqcr, devtools, testthat, readr, dplyr, tidyr, ggplot2 requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 576a410fb96440ce887b3afa3e140339 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'A Curated ChIP-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1)' - description: 'A curated dataset of publicly available ChIP-sequencing of transcription factors, chromatin remodelers and histone modifications in the 3T3-L1 pre-adipocyte cell line. The package document the data collection, pre-processing and processing of the data. In addition to the documentation, the package contains the scripts that was used to generated the data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-curatedadipochip/post-link.sh b/recipes/bioconductor-curatedadipochip/post-link.sh index 452dbadac0268..3d3de2fee30ca 100644 --- a/recipes/bioconductor-curatedadipochip/post-link.sh +++ b/recipes/bioconductor-curatedadipochip/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedadipochip-1.18.0" +installBiocDataPackage.sh "curatedadipochip-1.22.0" diff --git a/recipes/bioconductor-curatedadiporna/meta.yaml b/recipes/bioconductor-curatedadiporna/meta.yaml index b7c5d9884fddc..91548ab11a5f9 100644 --- a/recipes/bioconductor-curatedadiporna/meta.yaml +++ b/recipes/bioconductor-curatedadiporna/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "curatedAdipoRNA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61c2e750fc2cf09a6bde6c0bf46e6b8b +about: + description: A curated dataset of RNA-Seq samples. The samples are MDI-induced pre-phagocytes (3T3-L1) at different time points/stage of differentiation. The package document the data collection, pre-processing and processing. In addition to the documentation, the package contains the scripts that was used to generated the data. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A Curated RNA-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-curatedadiporna", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, DESeq2, fastqcr, devtools, testthat, readr, dplyr, tidyr, ggplot2, S4Vectors requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: eb2fb76b4e65349c0f81211df911722e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'A Curated RNA-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1)' - description: 'A curated dataset of RNA-Seq samples. The samples are MDI-induced pre-phagocytes (3T3-L1) at different time points/stage of differentiation. The package document the data collection, pre-processing and processing. In addition to the documentation, the package contains the scripts that was used to generated the data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-curatedadiporna/post-link.sh b/recipes/bioconductor-curatedadiporna/post-link.sh index 71d70dbe2607b..1e0be3bb92685 100644 --- a/recipes/bioconductor-curatedadiporna/post-link.sh +++ b/recipes/bioconductor-curatedadiporna/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedadiporna-1.18.0" +installBiocDataPackage.sh "curatedadiporna-1.22.0" diff --git a/recipes/bioconductor-curatedatlasqueryr/meta.yaml b/recipes/bioconductor-curatedatlasqueryr/meta.yaml index 4599ae6b3e273..b28b12100a056 100644 --- a/recipes/bioconductor-curatedatlasqueryr/meta.yaml +++ b/recipes/bioconductor-curatedatlasqueryr/meta.yaml @@ -1,75 +1,82 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "CuratedAtlasQueryR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides access to a copy of the Human Cell Atlas, but with harmonised metadata. This allows for uniform querying across numerous datasets within the Atlas using common fields such as cell type, tissue type, and patient ethnicity. Usage involves first querying the metadata table for cells of interest, and then downloading the corresponding cells into a SingleCellExperiment object. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Queries the Human Cell Atlas -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 21e5bf1d5aa58d59098176dca867c42c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-curatedatlasqueryr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: zellkonverter, rmarkdown, knitr, testthat, basilisk, arrow, reticulate, spelling, forcats, ggplot2, tidySingleCellExperiment, rprojroot requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-cli - r-dbi - - 'r-dbplyr >=2.3.0' + - r-dbplyr >=2.3.0 - r-dplyr - r-duckdb - r-glue - r-httr - - 'r-purrr >=1.0.0' + - r-purrr >=1.0.0 - r-rlang - r-seurat - r-seuratobject - r-stringr - r-tibble + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-cli - r-dbi - - 'r-dbplyr >=2.3.0' + - r-dbplyr >=2.3.0 - r-dplyr - r-duckdb - r-glue - r-httr - - 'r-purrr >=1.0.0' + - r-purrr >=1.0.0 - r-rlang - r-seurat - r-seuratobject - r-stringr - r-tibble + +source: + md5: 00aa7d03efbbd85a4316c8f0733291b2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Queries the Human Cell Atlas' - description: 'Provides access to a copy of the Human Cell Atlas, but with harmonised metadata. This allows for uniform querying across numerous datasets within the Atlas using common fields such as cell type, tissue type, and patient ethnicity. Usage involves first querying the metadata table for cells of interest, and then downloading the corresponding cells into a SingleCellExperiment object.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-curatedbladderdata/meta.yaml b/recipes/bioconductor-curatedbladderdata/meta.yaml index a19912b009d71..4e6d6e6d136d1 100644 --- a/recipes/bioconductor-curatedbladderdata/meta.yaml +++ b/recipes/bioconductor-curatedbladderdata/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "curatedBladderData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bd8965c4ad49840b4985f90f3dc5a441 +about: + description: The curatedBladderData package provides relevant functions and data for gene expression analysis in patients with bladder cancer. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Bladder Cancer Gene Expression Analysis build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-curatedbladderdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, survival, xtable, sva, genefilter, logging requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' + - bioconductor-affy >=1.84.0,<1.85.0 - r-base run: - - 'bioconductor-affy >=1.80.0,<1.81.0' + - bioconductor-affy >=1.84.0,<1.85.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 83bfc27c8454339626527a592867303e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Bladder Cancer Gene Expression Analysis' - description: 'The curatedBladderData package provides relevant functions and data for gene expression analysis in patients with bladder cancer.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-curatedbladderdata/post-link.sh b/recipes/bioconductor-curatedbladderdata/post-link.sh index a5a74357ee58b..1cb1f56181757 100644 --- a/recipes/bioconductor-curatedbladderdata/post-link.sh +++ b/recipes/bioconductor-curatedbladderdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedbladderdata-1.38.0" +installBiocDataPackage.sh "curatedbladderdata-1.42.0" diff --git a/recipes/bioconductor-curatedbreastdata/meta.yaml b/recipes/bioconductor-curatedbreastdata/meta.yaml index 147d8dbd24191..0128da8bf5b4d 100644 --- a/recipes/bioconductor-curatedbreastdata/meta.yaml +++ b/recipes/bioconductor-curatedbreastdata/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "2.30.0" %} +{% set version = "2.34.0" %} {% set name = "curatedBreastData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Curated human breast cancer tissue S4 ExpresionSet datasets from over 16 clinical trials comprising over 2,000 patients. All datasets contain at least one type of outcomes variable and treatment information (minimum level: whether they had chemotherapy and whether they had hormonal therapy). Includes code to post-process these datasets.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Curated breast cancer gene expression data with survival and treatment information -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 41383ff9e1295448ec0e8004789ab9d5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-curatedbreastdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-impute >=1.80.0,<1.81.0 - r-base - r-ggplot2 - r-xml run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-impute >=1.80.0,<1.81.0 - r-base - r-ggplot2 - r-xml - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: cc543a530d62b3ad9eedc25abc953332 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Curated breast cancer gene expression data with survival and treatment information' - description: 'Curated human breast cancer tissue S4 ExpresionSet datasets from over 16 clinical trials comprising over 2,000 patients. All datasets contain at least one type of outcomes variable and treatment information (minimum level: whether they had chemotherapy and whether they had hormonal therapy). Includes code to post-process these datasets.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-curatedbreastdata/post-link.sh b/recipes/bioconductor-curatedbreastdata/post-link.sh index 58788177cdca3..5e105a0a3c5f8 100644 --- a/recipes/bioconductor-curatedbreastdata/post-link.sh +++ b/recipes/bioconductor-curatedbreastdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedbreastdata-2.30.0" +installBiocDataPackage.sh "curatedbreastdata-2.34.0" diff --git a/recipes/bioconductor-curatedmetagenomicdata/meta.yaml b/recipes/bioconductor-curatedmetagenomicdata/meta.yaml index 8f7bf4f49af2c..6cd7955dc98bd 100644 --- a/recipes/bioconductor-curatedmetagenomicdata/meta.yaml +++ b/recipes/bioconductor-curatedmetagenomicdata/meta.yaml @@ -1,33 +1,40 @@ -{% set version = "3.10.0" %} +{% set version = "3.14.0" %} {% set name = "curatedMetagenomicData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The curatedMetagenomicData package provides standardized, curated human microbiome data for novel analyses. It includes gene families, marker abundance, marker presence, pathway abundance, pathway coverage, and relative abundance for samples collected from different body sites. The bacterial, fungal, and archaeal taxonomic abundances for each sample were calculated with MetaPhlAn3, and metabolic functional potential was calculated with HUMAnN3. The manually curated sample metadata and standardized metagenomic data are available as (Tree)SummarizedExperiment objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Curated Metagenomic Data of the Human Microbiome -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 39c08149fe4261d4961ff1235825ae97 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-curatedmetagenomicdata", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-curatedmetagenomicdata + path: recipes/bioconductor-curatedmetagenomicdata + version: 3.2.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, DT, knitr, readr, rmarkdown, scater, testthat, utils, uwot, vegan requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-mia >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-mia >=1.14.0,<1.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 - r-base - r-dplyr - r-magrittr @@ -38,12 +45,12 @@ requirements: - r-tidyr - r-tidyselect run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-mia >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-mia >=1.14.0,<1.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 - r-base - r-dplyr - r-magrittr @@ -54,18 +61,17 @@ requirements: - r-tidyr - r-tidyselect - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: efb481b40f689c417e9dbab4a98f71f1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Curated Metagenomic Data of the Human Microbiome' - description: 'The curatedMetagenomicData package provides standardized, curated human microbiome data for novel analyses. It includes gene families, marker abundance, marker presence, pathway abundance, pathway coverage, and relative abundance for samples collected from different body sites. The bacterial, fungal, and archaeal taxonomic abundances for each sample were calculated with MetaPhlAn3, and metabolic functional potential was calculated with HUMAnN3. The manually curated sample metadata and standardized metagenomic data are available as (Tree)SummarizedExperiment objects.' -extra: - parent_recipe: - name: bioconductor-curatedmetagenomicdata - path: recipes/bioconductor-curatedmetagenomicdata - version: 3.2.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-curatedmetagenomicdata/post-link.sh b/recipes/bioconductor-curatedmetagenomicdata/post-link.sh index 1766abe724ad8..f28fc9500a6be 100644 --- a/recipes/bioconductor-curatedmetagenomicdata/post-link.sh +++ b/recipes/bioconductor-curatedmetagenomicdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedmetagenomicdata-3.10.0" +installBiocDataPackage.sh "curatedmetagenomicdata-3.14.0" diff --git a/recipes/bioconductor-curatedovariandata/meta.yaml b/recipes/bioconductor-curatedovariandata/meta.yaml index ae3f6134fef68..f1a8be2d016cc 100644 --- a/recipes/bioconductor-curatedovariandata/meta.yaml +++ b/recipes/bioconductor-curatedovariandata/meta.yaml @@ -1,47 +1,53 @@ -{% set version = "1.40.1" %} +{% set version = "1.44.0" %} {% set name = "curatedOvarianData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The curatedOvarianData package provides data for gene expression analysis in patients with ovarian cancer. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Clinically Annotated Data for the Ovarian Cancer Transcriptome -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7651ff7abb11057b3ceec8f869e259d6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-curatedovariandata", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-curatedovariandata + path: recipes/bioconductor-curatedovariandata + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 8e490181b4476a15c64aa78f6347defb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Clinically Annotated Data for the Ovarian Cancer Transcriptome' - description: 'The curatedOvarianData package provides data for gene expression analysis in patients with ovarian cancer.' -extra: - parent_recipe: - name: bioconductor-curatedovariandata - path: recipes/bioconductor-curatedovariandata - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-curatedovariandata/post-link.sh b/recipes/bioconductor-curatedovariandata/post-link.sh index 2dca151523690..9eda263490d62 100644 --- a/recipes/bioconductor-curatedovariandata/post-link.sh +++ b/recipes/bioconductor-curatedovariandata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedovariandata-1.40.1" +installBiocDataPackage.sh "curatedovariandata-1.44.0" diff --git a/recipes/bioconductor-curatedtbdata/meta.yaml b/recipes/bioconductor-curatedtbdata/meta.yaml index 86218926bfa5d..4401562200d3b 100644 --- a/recipes/bioconductor-curatedtbdata/meta.yaml +++ b/recipes/bioconductor-curatedtbdata/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.8.0" %} +{% set version = "2.2.0" %} {% set name = "curatedTBData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The curatedTBData is an R package that provides standardized, curated tuberculosis(TB) transcriptomic studies. The initial release of the package contains 49 studies. The curatedTBData package allows users to access tuberculosis trancriptomic efficiently and to make efficient comparison for different TB gene signatures across multiple datasets. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Curation of existing tuberculosis transcriptomic studies -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 190a770c4f5df45cf722b7ee287a2384 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-curatedtbdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, DT, dplyr, HGNChelper, knitr, methods, rmarkdown, SummarizedExperiment, sva, testthat requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 - r-base - r-rlang run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 - r-base - r-rlang - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: efdabbcb7fef2e04ae9a472637a7caeb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Curation of existing 49 tuberculosis transcriptomic studies' - description: 'The curatedTBData is an R package that provides standardized, curated tuberculosis(TB) transcriptomic studies. The initial release of the package contains 49 studies. The curatedTBData package allows users to access tuberculosis trancriptomic efficiently and to make efficient comparison for different TB gene signatures across multiple datasets.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-curatedtbdata/post-link.sh b/recipes/bioconductor-curatedtbdata/post-link.sh index 460b16dba5ca4..4d3f4c173bd64 100644 --- a/recipes/bioconductor-curatedtbdata/post-link.sh +++ b/recipes/bioconductor-curatedtbdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedtbdata-1.8.0" +installBiocDataPackage.sh "curatedtbdata-2.2.0" diff --git a/recipes/bioconductor-curatedtcgadata/meta.yaml b/recipes/bioconductor-curatedtcgadata/meta.yaml index a2dfc71c781c2..1dbe2c83e43aa 100644 --- a/recipes/bioconductor-curatedtcgadata/meta.yaml +++ b/recipes/bioconductor-curatedtcgadata/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.1" %} {% set name = "curatedTCGAData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. MultiAssayExperiment integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-'omics experiment. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de450b3bbb137b63a1ca46ae81a96909 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-curatedtcgadata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, RaggedExperiment, readr, rmarkdown, TCGAutils, testthat requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241231 + +source: + md5: 21b4e364a9d056d7010c96fc6fae28ed + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects' - description: 'This package provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. MultiAssayExperiment integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-''omics experiment.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-curatedtcgadata/post-link.sh b/recipes/bioconductor-curatedtcgadata/post-link.sh index 151fe01e10b62..a50658b61214e 100644 --- a/recipes/bioconductor-curatedtcgadata/post-link.sh +++ b/recipes/bioconductor-curatedtcgadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "curatedtcgadata-1.24.0" +installBiocDataPackage.sh "curatedtcgadata-1.28.1" diff --git a/recipes/bioconductor-customcmpdb/meta.yaml b/recipes/bioconductor-customcmpdb/meta.yaml index b6f9d4baff3ab..b40dcde6df16d 100644 --- a/recipes/bioconductor-customcmpdb/meta.yaml +++ b/recipes/bioconductor-customcmpdb/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "customCMPdb" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package serves as a query interface for important community collections of small molecules, while also allowing users to include custom compound collections. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Customize and Query Compound Annotation Database -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1aa1425d87c45ac42f2c7ed808a7a583 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-customcmpdb", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-chemminer >=3.58.0,<3.59.0 - r-base - r-rappdirs - r-rsqlite - r-xml run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-chemminer >=3.58.0,<3.59.0 - r-base - r-rappdirs - r-rsqlite - r-xml + +source: + md5: ab3e10a76d37ffae89e0f7eac786deae + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Customize and Query Compound Annotation Database' - description: 'This package serves as a query interface for important community collections of small molecules, while also allowing users to include custom compound collections.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-customprodb/meta.yaml b/recipes/bioconductor-customprodb/meta.yaml index a90f2ffde8365..f5649731016e7 100644 --- a/recipes/bioconductor-customprodb/meta.yaml +++ b/recipes/bioconductor-customprodb/meta.yaml @@ -1,39 +1,42 @@ -{% set version = "1.41.0" %} +{% set version = "1.46.0" %} {% set name = "customProDB" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Database search is the most widely used approach for peptide and protein identification in mass spectrometry-based proteomics studies. Our previous study showed that sample-specific protein databases derived from RNA-Seq data can better approximate the real protein pools in the samples and thus improve protein identification. More importantly, single nucleotide variations, short insertion and deletions and novel junctions identified from RNA-Seq data make protein database more complete and sample-specific. Here, we report an R package customProDB that enables the easy generation of customized databases from RNA-Seq data for proteomics search. This work bridges genomics and proteomics studies and facilitates cross-omics data integration. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 08f0eb20ac48a7b8f1e27b45522dd029 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-customprodb", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19 requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-ahocorasicktrie - r-base - r-dbi @@ -41,19 +44,21 @@ requirements: - r-rcurl - r-rsqlite - r-stringr + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-ahocorasicktrie - r-base - r-dbi @@ -61,12 +66,16 @@ requirements: - r-rcurl - r-rsqlite - r-stringr + +source: + md5: 546d4b85686b7f4786e4d765ee96eb44 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search' - description: 'Database search is the most widely used approach for peptide and protein identification in mass spectrometry-based proteomics studies. Our previous study showed that sample-specific protein databases derived from RNA-Seq data can better approximate the real protein pools in the samples and thus improve protein identification. More importantly, single nucleotide variations, short insertion and deletions and novel junctions identified from RNA-Seq data make protein database more complete and sample-specific. Here, we report an R package customProDB that enables the easy generation of customized databases from RNA-Seq data for proteomics search. This work bridges genomics and proteomics studies and facilitates cross-omics data integration.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cyanofilter/meta.yaml b/recipes/bioconductor-cyanofilter/meta.yaml index 35f0db1c71cb4..098864d2c2991 100644 --- a/recipes/bioconductor-cyanofilter/meta.yaml +++ b/recipes/bioconductor-cyanofilter/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "cyanoFilter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An approach to filter out and/or identify phytoplankton cells from all particles measured via flow cytometry pigment and cell complexity information. It does this using a sequence of one-dimensional gates on pre-defined channels measuring certain pigmentation and complexity. The package is especially tuned for cyanobacteria, but will work fine for phytoplankton communities where there is at least one cell characteristic that differentiates every phytoplankton in the community. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Phytoplankton Population Identification using Cell Pigmentation and/or Complexity -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a562257b012ddcf28b78c5cee7e85fa3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cyanofilter", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-flowclust >=3.40.0,<3.41.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowdensity >=1.36.0,<1.37.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-flowclust >=3.44.0,<3.45.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowdensity >=1.40.0,<1.41.0 - r-base - r-cytometree - r-ggally - r-ggplot2 - r-mrfdepth run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-flowclust >=3.40.0,<3.41.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowdensity >=1.36.0,<1.37.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-flowclust >=3.44.0,<3.45.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowdensity >=1.40.0,<1.41.0 - r-base - r-cytometree - r-ggally - r-ggplot2 - r-mrfdepth + +source: + md5: 8f17dd7bcafffce3fea12da112328b52 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Phytoplankton Population Identification using Cell Pigmentation and/or Complexity' - description: 'An approach to filter out and/or identify phytoplankton cells from all particles measured via flow cytometry pigment and cell complexity information. It does this using a sequence of one-dimensional gates on pre-defined channels measuring certain pigmentation and complexity. The package is especially tuned for cyanobacteria, but will work fine for phytoplankton communities where there is at least one cell characteristic that differentiates every phytoplankton in the community.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cycle/meta.yaml b/recipes/bioconductor-cycle/meta.yaml index f9388f490a65e..d867f9ed4a9eb 100644 --- a/recipes/bioconductor-cycle/meta.yaml +++ b/recipes/bioconductor-cycle/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.56.0" %} +{% set version = "1.60.0" %} {% set name = "cycle" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8c659d2ae2fb2b31f4b6dd07d68873be +about: + description: Package for assessing the statistical significance of periodic expression based on Fourier analysis and comparison with data generated by different background models + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Significance of periodic expression pattern in time-series data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cycle", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-mfuzz >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-mfuzz >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-mfuzz >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-mfuzz >=2.66.0,<2.67.0 - r-base +source: + md5: 24680be77d98031eadfd4c9365f7f5fc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Significance of periodic expression pattern in time-series data' - description: 'Package for assessing the statistical significance of periodic expression based on Fourier analysis and comparison with data generated by different background models' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cydar/meta.yaml b/recipes/bioconductor-cydar/meta.yaml index 4f5ab55d02786..ccbcefeb8048a 100644 --- a/recipes/bioconductor-cydar/meta.yaml +++ b/recipes/bioconductor-cydar/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "cydar" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Identifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Using Mass Cytometry for Differential Abundance Analyses -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b804632cc0742b1e2f9910353a6ed75d build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cydar", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ncdfFlow, testthat, rmarkdown, knitr, edgeR, limma, glmnet, BiocStyle, flowStats # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-rcpp - r-shiny @@ -37,29 +43,28 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-rcpp - r-shiny - r-viridis - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 12f6ab38d5cbb15a89a6cca546f9c27c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Using Mass Cytometry for Differential Abundance Analyses' - description: 'Identifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cyp450cdf/meta.yaml b/recipes/bioconductor-cyp450cdf/meta.yaml index 278e2ac3086d0..75dd0e352689c 100644 --- a/recipes/bioconductor-cyp450cdf/meta.yaml +++ b/recipes/bioconductor-cyp450cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "cyp450cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7923c4d24b7b654d0f59d52ed2258eb9 +about: + description: A package containing an environment representing the CYP450.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: cyp450cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cyp450cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7923c4d24b7b654d0f59d52ed2258eb9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: cyp450cdf - description: 'A package containing an environment representing the CYP450.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cypress/build.sh b/recipes/bioconductor-cypress/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cypress/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cypress/build_failure.linux-64.yaml b/recipes/bioconductor-cypress/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..7b68aa0a8aa40 --- /dev/null +++ b/recipes/bioconductor-cypress/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: 5164b9ffb36bf72e96cf31f765753afdbd1e696ba4103c85449f91db6385e8bc # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-sirt")} + Encountered problems while solving: + - nothing provides requested r-sirt + + Could not solve for environment specs + The following package could not be installed + [31mr-sirt[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-sirt")} + Encountered problems while solving: + - nothing provides requested r-sirt + + Could not solve for environment specs + The following package could not be installed + [31mr-sirt[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-sirt")} + Encountered problems while solving: + - nothing provides requested r-sirt + + Could not solve for environment specs + The following package could not be installed + [31mr-sirt[0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. +reason: |- + needs r-sirt to be in conda-forge +category: |- + dependency issue diff --git a/recipes/bioconductor-cypress/build_failure.osx-64.yaml b/recipes/bioconductor-cypress/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..7e9c28f208a02 --- /dev/null +++ b/recipes/bioconductor-cypress/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 5164b9ffb36bf72e96cf31f765753afdbd1e696ba4103c85449f91db6385e8bc # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + needs r-sirt to be in conda-forge +category: |- + dependency issue diff --git a/recipes/bioconductor-cypress/meta.yaml b/recipes/bioconductor-cypress/meta.yaml new file mode 100644 index 0000000000000..1fb221bdaaa68 --- /dev/null +++ b/recipes/bioconductor-cypress/meta.yaml @@ -0,0 +1,78 @@ +{% set version = "1.2.0" %} +{% set name = "cypress" %} +{% set bioc = "3.20" %} + +about: + description: CYPRESS is a cell-type-specific power tool. This package aims to perform power analysis for the cell-type-specific data. It calculates FDR, FDC, and power, under various study design parameters, including but not limited to sample size, and effect size. It takes the input of a SummarizeExperimental(SE) object with observed mixture data (feature by sample matrix), and the cell-type mixture proportions (sample by cell-type matrix). It can solve the cell-type mixture proportions from the reference free panel from TOAST and conduct tests to identify cell-type-specific differential expression (csDE) genes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 | GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Cell-Type-Specific Power Assessment + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cypress", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, MatrixGenerics, htmltools, RUnit, BiocGenerics, BiocManager, BiocStyle, Biobase +requirements: + host: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-proper >=1.38.0,<1.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-toast >=1.20.0,<1.21.0 + - r-abind + - r-base + - r-checkmate + - r-dplyr + - r-e1071 + - r-mass + - r-mvtnorm + - r-rcolorbrewer + - r-rlang + - r-sirt + - r-tca + - r-tibble + run: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-proper >=1.38.0,<1.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-toast >=1.20.0,<1.21.0 + - r-abind + - r-base + - r-checkmate + - r-dplyr + - r-e1071 + - r-mass + - r-mvtnorm + - r-rcolorbrewer + - r-rlang + - r-sirt + - r-tca + - r-tibble + +source: + md5: ba833b2876c4dc75fe75c208489025a7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-cytodx/meta.yaml b/recipes/bioconductor-cytodx/meta.yaml index fa2f5ec95a63d..53097e0d0497b 100644 --- a/recipes/bioconductor-cytodx/meta.yaml +++ b/recipes/bioconductor-cytodx/meta.yaml @@ -1,28 +1,36 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "CytoDx" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functions that predict clinical outcomes using single cell data (such as flow cytometry data, RNA single cell sequencing data) without the requirement of cell gating or clustering. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Robust prediction of clinical outcomes using cytometry data without cell gating -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 86d2f225be6ebdaecd3aa4960e443796 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cytodx", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-cytodx + path: recipes/bioconductor-cytodx + version: 1.2.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-doparallel - r-dplyr @@ -30,25 +38,23 @@ requirements: - r-rpart - r-rpart.plot run: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-doparallel - r-dplyr - r-glmnet - r-rpart - r-rpart.plot + +source: + md5: b3ba91bd8c9fcf8579fd8694d4b178d0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Robust prediction of clinical outcomes using cytometry data without cell gating' - description: 'This package provides functions that predict clinical outcomes using single cell data (such as flow cytometry data, RNA single cell sequencing data) without the requirement of cell gating or clustering.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - parent_recipe: - name: bioconductor-cytodx - path: recipes/bioconductor-cytodx - version: 1.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cytofqc/meta.yaml b/recipes/bioconductor-cytofqc/meta.yaml index 47f974c4c82e4..1d0806bda00e6 100644 --- a/recipes/bioconductor-cytofqc/meta.yaml +++ b/recipes/bioconductor-cytofqc/meta.yaml @@ -1,32 +1,33 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "cytofQC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: cytofQC is a package for initial cleaning of CyTOF data. It uses a semi-supervised approach for labeling cells with their most likely data type (bead, doublet, debris, dead) and the probability that they belong to each label type. This package does not remove data from the dataset, but provides labels and information to aid the data user in cleaning their data. Our algorithm is able to distinguish between doublets and large cells. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Labels normalized cells for CyTOF data and assigns probabilities for each label -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a4e866c0e57f639b41828c211aff31f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cytofqc", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: gridExtra, knitr, RColorBrewer, testthat, uwot requirements: host: - - 'bioconductor-catalyst >=1.26.0,<1.27.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-catalyst >=1.30.0,<1.31.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-e1071 - r-eztune @@ -38,11 +39,11 @@ requirements: - r-rmarkdown - r-ssc run: - - 'bioconductor-catalyst >=1.26.0,<1.27.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-catalyst >=1.30.0,<1.31.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-e1071 - r-eztune @@ -53,12 +54,16 @@ requirements: - r-randomforest - r-rmarkdown - r-ssc + +source: + md5: 3884c0b74e8168170174b23717c1f6fe + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Labels normalized cells for CyTOF data and assigns probabilities for each label' - description: 'cytofQC is a package for initial cleaning of CyTOF data. It uses a semi-supervised approach for labeling cells with their most likely data type (bead, doublet, debris, dead) and the probability that they belong to each label type. This package does not remove data from the dataset, but provides labels and information to aid the data user in cleaning their data. Our algorithm is able to distinguish between doublets and large cells.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cytoglmm/meta.yaml b/recipes/bioconductor-cytoglmm/meta.yaml index 7c2e9656c33dc..e262b0ccb8905 100644 --- a/recipes/bioconductor-cytoglmm/meta.yaml +++ b/recipes/bioconductor-cytoglmm/meta.yaml @@ -1,28 +1,31 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "CytoGLMM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The CytoGLMM R package implements two multiple regression strategies: A bootstrapped generalized linear model (GLM) and a generalized linear mixed model (GLMM). Most current data analysis tools compare expressions across many computationally discovered cell types. CytoGLMM focuses on just one cell type. Our narrower field of application allows us to define a more specific statistical model with easier to control statistical guarantees. As a result, CytoGLMM finds differential proteins in flow and mass cytometry data while reducing biases arising from marker correlations and safeguarding against false discoveries induced by patient heterogeneity.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Conditional Differential Analysis for Flow and Mass Cytometry Experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3a4b95062a82da6afe217f20ef905460 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cytoglmm", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: + host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-caret - r-cowplot @@ -44,8 +47,9 @@ requirements: - r-strucchange - r-tibble - r-tidyr + run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-caret - r-cowplot @@ -67,13 +71,16 @@ requirements: - r-strucchange - r-tibble - r-tidyr + +source: + md5: 95864d621bd37ead1e3a53672a4a022c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'Conditional Differential Analysis for Flow and Mass Cytometry Experiments' - description: 'The CytoGLMM R package implements two multiple regression strategies: A bootstrapped generalized linear model (GLM) and a generalized linear mixed model (GLMM). Most current data analysis tools compare expressions across many computationally discovered cell types. CytoGLMM focuses on just one cell type. Our narrower field of application allows us to define a more specific statistical model with easier to control statistical guarantees. As a result, CytoGLMM finds differential proteins in flow and mass cytometry data while reducing biases arising from marker correlations and safeguarding against false discoveries induced by patient heterogeneity.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cytokernel/meta.yaml b/recipes/bioconductor-cytokernel/meta.yaml index e78587f65500f..4e2ec863e98c2 100644 --- a/recipes/bioconductor-cytokernel/meta.yaml +++ b/recipes/bioconductor-cytokernel/meta.yaml @@ -1,30 +1,36 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "cytoKernel" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: cytoKernel implements a kernel-based score test to identify differentially expressed features in high-dimensional biological experiments. This approach can be applied across many different high-dimensional biological data including gene expression data and dimensionally reduced cytometry-based marker expression data. In this R package, we implement functions that compute the feature-wise p values and their corresponding adjusted p values. Additionally, it also computes the feature-wise shrunk effect sizes and their corresponding shrunken effect size. Further, it calculates the percent of differentially expressed features and plots user-friendly heatmap of the top differentially expressed features on the rows and samples on the columns. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Differential expression using kernel-based score test -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2e1e2b8d2c545a69a0cec180964f2fd9 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cytokernel", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-ashr - r-base - r-circlize @@ -36,10 +42,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-ashr - r-base - r-circlize @@ -48,17 +54,16 @@ requirements: - r-magrittr - r-rcpp - r-rlang - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 56436d895525b0b047346eba62a92171 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Differential expression using kernel-based score test' - description: 'cytoKernel implements a kernel-based score test to identify differentially expressed features in high-dimensional biological experiments. This approach can be applied across many different high-dimensional biological data including gene expression data and dimensionally reduced cytometry-based marker expression data. In this R package, we implement functions that compute the feature-wise p values and their corresponding adjusted p values. Additionally, it also computes the feature-wise shrunk effect sizes and their corresponding shrunken effect size. Further, it calculates the percent of differentially expressed features and plots user-friendly heatmap of the top differentially expressed features on the rows and samples on the columns.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cytolib/meta.yaml b/recipes/bioconductor-cytolib/meta.yaml index d3c88990f4372..3f03b4286d1a2 100644 --- a/recipes/bioconductor-cytolib/meta.yaml +++ b/recipes/bioconductor-cytolib/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "2.14.1" %} +{% set version = "2.18.0" %} {% set name = "cytolib" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides the core data structure and API to represent and interact with the gated cytometry data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3.0-only + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: C++ infrastructure for representing and interacting with the gated cytometry data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 32b6560c381660e2ed9aa1e7b6ab84f9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cytolib", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:cytolib + parent_recipe: + name: bioconductor-cytolib + path: recipes/bioconductor-cytolib + version: 1.4.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown # SystemRequirements: GNU make, C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-rprotobuflib >=2.18.0,<2.19.0 - r-base - - 'r-bh >=1.81.0.0' + - r-bh >=1.84.0.0 - libblas - liblapack run: - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-rprotobuflib >=2.18.0,<2.19.0 - r-base - - 'r-bh >=1.81.0.0' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + - r-bh >=1.84.0.0 + +source: + md5: 315a10e5ab4beca630554a17eaf56853 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'C++ infrastructure for representing and interacting with the gated cytometry data' - description: 'This package provides the core data structure and API to represent and interact with the gated cytometry data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} - parent_recipe: - name: bioconductor-cytolib - path: recipes/bioconductor-cytolib - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cytomapper/meta.yaml b/recipes/bioconductor-cytomapper/meta.yaml index cd40bb5f75e8b..ea6645e357e9f 100644 --- a/recipes/bioconductor-cytomapper/meta.yaml +++ b/recipes/bioconductor-cytomapper/meta.yaml @@ -1,36 +1,39 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "cytomapper" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Highly multiplexed imaging acquires the single-cell expression of selected proteins in a spatially-resolved fashion. These measurements can be visualised across multiple length-scales. First, pixel-level intensities represent the spatial distributions of feature expression with highest resolution. Second, after segmentation, expression values or cell-level metadata (e.g. cell-type information) can be visualised on segmented cell areas. This package contains functions for the visualisation of multiplexed read-outs and cell-level information obtained by multiplexed imaging technologies. The main functions of this package allow 1. the visualisation of pixel-level information across multiple channels, 2. the display of cell-level information (expression and/or metadata) on segmentation masks and 3. gating and visualisation of single cells. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Visualization of highly multiplexed imaging data in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 140e57707c43aeb7bd3b2e48b634464a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cytomapper", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat, shinytest requirements: + host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggbeeswarm - r-ggplot2 @@ -43,16 +46,17 @@ requirements: - r-svglite - r-svgpanzoom - r-viridis + run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggbeeswarm - r-ggplot2 @@ -65,13 +69,16 @@ requirements: - r-svglite - r-svgpanzoom - r-viridis + +source: + md5: 55961cd1bf5fbeb4cfaccf7974b56a10 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Visualization of highly multiplexed imaging data in R' - description: 'Highly multiplexed imaging acquires the single-cell expression of selected proteins in a spatially-resolved fashion. These measurements can be visualised across multiple length-scales. First, pixel-level intensities represent the spatial distributions of feature expression with highest resolution. Second, after segmentation, expression values or cell-level metadata (e.g. cell-type information) can be visualised on segmented cell areas. This package contains functions for the visualisation of multiplexed read-outs and cell-level information obtained by multiplexed imaging technologies. The main functions of this package allow 1. the visualisation of pixel-level information across multiple channels, 2. the display of cell-level information (expression and/or metadata) on segmentation masks and 3. gating and visualisation of single cells.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cytomds/build.sh b/recipes/bioconductor-cytomds/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cytomds/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cytomds/meta.yaml b/recipes/bioconductor-cytomds/meta.yaml new file mode 100644 index 0000000000000..c310447a90e18 --- /dev/null +++ b/recipes/bioconductor-cytomds/meta.yaml @@ -0,0 +1,68 @@ +{% set version = "1.2.0" %} +{% set name = "CytoMDS" %} +{% set bioc = "3.20" %} + +about: + description: This package implements a low dimensional visualization of a set of cytometry samples, in order to visually assess the 'distances' between them. This, in turn, can greatly help the user to identify quality issues like batch effects or outlier samples, and/or check the presence of potential sample clusters that might align with the exeprimental design. The CytoMDS algorithm combines, on the one hand, the concept of Earth Mover's Distance (EMD), a.k.a. Wasserstein metric and, on the other hand, the Multi Dimensional Scaling (MDS) algorithm for the low dimensional projection. Also, the package provides some diagnostic tools for both checking the quality of the MDS projection, as well as tools to help with the interpretation of the axes of the projection. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Low Dimensions projection of cytometry samples + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytomds", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, HDCytoData +requirements: + host: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-cytopipeline >=1.6.0,<1.7.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - r-base + - r-ggforce + - r-ggplot2 + - r-ggrepel + - r-patchwork + - r-pracma + - r-reshape2 + - r-rlang + - r-smacof + - r-transport + - r-withr + run: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-cytopipeline >=1.6.0,<1.7.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - r-base + - r-ggforce + - r-ggplot2 + - r-ggrepel + - r-patchwork + - r-pracma + - r-reshape2 + - r-rlang + - r-smacof + - r-transport + - r-withr + +source: + md5: ffe29cb8a8079ecd2fa20da75d196d7b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-cytomem/meta.yaml b/recipes/bioconductor-cytomem/meta.yaml index 5c3bb8333f7b3..28c34b8093b4e 100644 --- a/recipes/bioconductor-cytomem/meta.yaml +++ b/recipes/bioconductor-cytomem/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "cytoMEM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a407b89f327c4c88301e81f982598f9 +about: + description: MEM, Marker Enrichment Modeling, automatically generates and displays quantitative labels for cell populations that have been identified from single-cell data. The input for MEM is a dataset that has pre-clustered or pre-gated populations with cells in rows and features in columns. Labels convey a list of measured features and the features' levels of relative enrichment on each population. MEM can be applied to a wide variety of data types and can compare between MEM labels from flow cytometry, mass cytometry, single cell RNA-seq, and spectral flow cytometry using RMSD. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Marker Enrichment Modeling (MEM) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cytomem", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-gplots - r-matrixstats run: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-gplots - r-matrixstats +source: + md5: 81a1fd3e6e1a8cb0e08ef0868dff5820 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Marker Enrichment Modeling (MEM)' - description: 'MEM, Marker Enrichment Modeling, automatically generates and displays quantitative labels for cell populations that have been identified from single-cell data. The input for MEM is a dataset that has pre-clustered or pre-gated populations with cells in rows and features in columns. Labels convey a list of measured features and the features'' levels of relative enrichment on each population. MEM can be applied to a wide variety of data types and can compare between MEM labels from flow cytometry, mass cytometry, single cell RNA-seq, and spectral flow cytometry using RMSD.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cytomethic/meta.yaml b/recipes/bioconductor-cytomethic/meta.yaml new file mode 100644 index 0000000000000..06388327930f4 --- /dev/null +++ b/recipes/bioconductor-cytomethic/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.2.0" %} +{% set name = "CytoMethIC" %} +{% set bioc = "3.20" %} + +about: + description: This package provides DNA methylation-based prediction of cancer type, molecular signature and clinical outcomes. It provides convenience functions for missing value imputation, probe ID conversion, model interpretation and visualization. The package links to our models on ExperimentHub. The package currently supports HM450, EPIC and EPICv2. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: DNA methylation-based classification and regression + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-cytomethic", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, randomForest, testthat, knitr, rmarkdown, e1071, xgboost, keras, tensorflow +requirements: + host: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-sesame >=1.24.0,<1.25.0 + - bioconductor-sesamedata >=1.24.0,<1.25.0 + - r-base + - r-biocmanager + - r-tibble + run: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-sesame >=1.24.0,<1.25.0 + - bioconductor-sesamedata >=1.24.0,<1.25.0 + - r-base + - r-biocmanager + - r-tibble + - curl + - bioconductor-data-packages >=20241103 + +source: + md5: fec5611f2f4d02c220e277b66cea9439 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-cytomethic/post-link.sh b/recipes/bioconductor-cytomethic/post-link.sh new file mode 100644 index 0000000000000..8449c38ee6980 --- /dev/null +++ b/recipes/bioconductor-cytomethic/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "cytomethic-1.2.0" diff --git a/recipes/bioconductor-cytomethic/pre-unlink.sh b/recipes/bioconductor-cytomethic/pre-unlink.sh new file mode 100644 index 0000000000000..523345a38ed32 --- /dev/null +++ b/recipes/bioconductor-cytomethic/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ CytoMethIC diff --git a/recipes/bioconductor-cytoml/build.sh b/recipes/bioconductor-cytoml/build.sh index c1d13421f5f1e..b221c533ab59e 100644 --- a/recipes/bioconductor-cytoml/build.sh +++ b/recipes/bioconductor-cytoml/build.sh @@ -7,5 +7,9 @@ FC=$FC CXX=$CXX CXX98=$CXX CXX11=$CXX -CXX14=$CXX" > ~/.R/Makevars +CXX14=$CXX +PKG_CPPFLAGS =-DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors \ + -D_LIBCPP_ENABLE_CXX17_REMOVED_UNARY_BINARY_FUNCTION +" > ~/.R/Makevars +export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_ENABLE_CXX17_REMOVED_UNARY_BINARY_FUNCTION" $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cytoml/build_failure.linux-64.yaml b/recipes/bioconductor-cytoml/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..a095d79b2c7c7 --- /dev/null +++ b/recipes/bioconductor-cytoml/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: aa08212fc3ef7d546ab56ac9772a9221071fbf4e0341bb964f64857a5d7526b5 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-cytoml_1735917983111/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library + * installing *source* package CytoML ... + ** package CytoML successfully unpacked and MD5 sums checked + ** using staged installation + checking whether the C compiler works... yes + checking for C compiler default output file name... a.out + checking for suffix of executables... + checking whether we are cross compiling... no + checking for suffix of object files... o + checking whether we are using the GNU C compiler... yes + checking whether $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 accepts -g... yes + checking for x86_64-conda-linux-gnu-gcc... $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + checking whether we are using the GNU C compiler... yes + checking whether $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc accepts -g... yes + checking for $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc option to accept ISO C89... none needed + configure: setting xml2 flags... + configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods. + checking for xml2-config... $PREFIX/bin/xml2-config + configure: setting cytolib-ml commandline tool path... + configure: Using the following compilation and linking flags + configure: PKG_CPPFLAGS=-I$PREFIX/include/libxml2 -I$PREFIX/include + configure: PKG_LIBS=-L$PREFIX/lib -lxml2 -L$PREFIX/lib -lz -L$PREFIX/lib -llzma -L$PREFIX/lib -licui18n -licuuc -licudata -L$PREFIX/lib -liconv -lm -ldl + configure: CYTOLIBML_BIN=/usr/local/bin + configure: creating ./config.status + config.status: creating src/Makevars + config.status: creating R/cytolibml_bin_path.R + ** libs + using C compiler: x86_64-conda-linux-gnu-c (conda-forge gcc 13.3.0-1) 13.3.0 + using C11 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors -D_LIBCPP_ENABLE_CXX17_REMOVED_UNARY_BINARY_FUNCTION -I'$PREFIX/lib/R/library/cpp11/include' -I'$PREFIX/lib/R/library/BH/include' -I'$PREFIX/lib/R/library/RProtoBufLib/include' -I'$PREFIX/lib/R/library/cytolib/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -I'$PREFIX/lib/R/library/flowWorkspace/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c cpp11.cpp -o cpp11.o + In file included from ../inst/include/CytoML/workspace_type.hpp:4, + from ../inst/include/CytoML/workspace.hpp:10, + from ../inst/include/CytoML/flowJoWorkspace.hpp:11, + from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10, + from ../inst/include/CytoML/openWorkspace.hpp:11, + from CytoML_types.h:5, + from cpp11.cpp:4: + ../inst/include/CytoML/wsNode.hpp:10:10: fatal error: libxml/tree.h: No such file or directory + 10 | #include + | ^~~~~~~~~~~~~~~ + compilation terminated. + make: *** [/opt/conda/conda-bld/bioconductor-cytoml_1735917983111/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/etc/Makeconf:204: cpp11.o] Error 1 + ERROR: compilation failed for package CytoML + * removing /opt/conda/conda-bld/bioconductor-cytoml_1735917983111/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/CytoML + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-cytoml_1735917983111/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-cytoml_1735917983111/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/bioconductor-cytoml/build_failure.osx-64.yaml b/recipes/bioconductor-cytoml/build_failure.osx-64.yaml index 1c647ed38192b..b11c134a45b61 100644 --- a/recipes/bioconductor-cytoml/build_failure.osx-64.yaml +++ b/recipes/bioconductor-cytoml/build_failure.osx-64.yaml @@ -1,48 +1,36 @@ -recipe_sha: 1c91989f56fc78860ff6ec88f6e1816c3dd98bc98659434b3e9a5b02792c0fbb # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: aa08212fc3ef7d546ab56ac9772a9221071fbf4e0341bb964f64857a5d7526b5 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments - F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-cytoml_1717700284559/work/conda_build.sh']' returned non-zero exit status 1. - CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin +log: |2- + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool LD=x86_64-apple-darwin13.4.0-ld LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool + packages_from_this = build( LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-cytoml_1735920472313/work/conda_build.sh']' returned non-zero exit status 1. NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang @@ -50,7 +38,7 @@ log: |- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -65,15 +53,27 @@ log: |- INFO: activate_clangxx_osx-64.sh made the following environmental changes: CLANGXX=x86_64-apple-darwin13.4.0-clang CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix INFO: activate_clang_osx-64.sh made the following environmental changes: CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-cytoml-2.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang INFO: activate_clangxx_osx-64.sh made the following environmental changes: CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang @@ -95,10 +95,12 @@ log: |- configure: setting cytolib-ml commandline tool path... configure: Using the following compilation and linking flags configure: PKG_CPPFLAGS=-I$BUILD_PREFIX/include/libxml2 -I$BUILD_PREFIX/include - configure: PKG_LIBS=-L$BUILD_PREFIX/lib -lxml2 -L$BUILD_PREFIX/lib -lz -L$BUILD_PREFIX/lib -llzma -L$BUILD_PREFIX/lib -licui18n -licuuc -licudata -L$BUILD_PREFIX/lib -liconv + configure: PKG_LIBS=-L$BUILD_PREFIX/lib -lxml2 -L$BUILD_PREFIX/lib -lz -L$BUILD_PREFIX/lib -llzma -L$BUILD_PREFIX/lib -liconv configure: CYTOLIBML_BIN=/usr/local/bin configure: creating ./config.status config.status: creating src/Makevars config.status: creating R/cytolibml_bin_path.R - x86_64-apple-darwin13.4.0-clang -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -DROUT -I../inst/include/ -I$BUILD_PREFIX/include/libxml2 -I$BUILD_PREFIX/include -DBOOST_NO_AUTO_PTR -I'$PREFIX/lib/R/library/cpp11/include' -I'$PREFIX/lib/R/library/BH/include' -I'$PREFIX/lib/R/library/RProtoBufLib/include' -I'$PREFIX/lib/R/library/cytolib/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -I'$PREFIX/lib/R/library/flowWorkspace/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1714471796105/work=/usr/local/src/conda/r-base-4.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c cpp11.cpp -o cpp11.o + x86_64-apple-darwin13.4.0-clang -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -DROUT -I../inst/include/ -I$BUILD_PREFIX/include/libxml2 -I$BUILD_PREFIX/include -DBOOST_NO_AUTO_PTR -I'$PREFIX/lib/R/library/cpp11/include' -I'$PREFIX/lib/R/library/BH/include' -I'$PREFIX/lib/R/library/RProtoBufLib/include' -I'$PREFIX/lib/R/library/cytolib/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -I'$PREFIX/lib/R/library/flowWorkspace/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c cpp11.cpp -o cpp11.o # Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/bioconductor-cytoml/meta.yaml b/recipes/bioconductor-cytoml/meta.yaml index 61a0d13b69b74..486270e4a0fe0 100644 --- a/recipes/bioconductor-cytoml/meta.yaml +++ b/recipes/bioconductor-cytoml/meta.yaml @@ -1,40 +1,55 @@ -{% set version = "2.14.0" %} +{% set version = "2.18.0" %} {% set name = "CytoML" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Uses platform-specific implemenations of the GatingML2.0 standard to exchange gated cytometry data with other software platforms. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3.0-only + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A GatingML Interface for Cross Platform Cytometry Data Sharing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4b0060416cdeef7876cb9aaeb81dbaf7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cytoml", max_pin="x.x") }}' + +extra: + parent_recipe: + name: bioconductor-cytoml + path: recipes/bioconductor-cytoml + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, flowWorkspaceData , knitr, rmarkdown, parallel # SystemRequirements: xml2, GNU make, C++11 requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-cytolib >=2.14.0,<2.15.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' - - 'bioconductor-ggcyto >=1.30.0,<1.31.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-opencyto >=2.14.0,<2.15.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-cytolib >=2.18.0,<2.19.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowworkspace >=4.18.0,<4.19.0 + - bioconductor-ggcyto >=1.34.0,<1.35.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-opencyto >=2.18.0,<2.19.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-rprotobuflib >=2.18.0,<2.19.0 - r-base - - 'r-bh >=1.62.0-1' + - r-bh >=1.62.0-1 - r-cpp11 - r-data.table - r-dplyr @@ -45,20 +60,21 @@ requirements: - libblas - liblapack - libxml2 + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-cytolib >=2.14.0,<2.15.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' - - 'bioconductor-ggcyto >=1.30.0,<1.31.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-opencyto >=2.14.0,<2.15.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-cytolib >=2.18.0,<2.19.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowworkspace >=4.18.0,<4.19.0 + - bioconductor-ggcyto >=1.34.0,<1.35.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-opencyto >=2.18.0,<2.19.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-rprotobuflib >=2.18.0,<2.19.0 - r-base - - 'r-bh >=1.62.0-1' + - r-bh >=1.62.0-1 - r-cpp11 - r-data.table - r-dplyr @@ -67,23 +83,16 @@ requirements: - r-xml - r-yaml - libxml2 - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: baea277ec3848082a076df6b120fab03 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3.0-only - summary: 'A GatingML Interface for Cross Platform Cytometry Data Sharing' - description: 'Uses platform-specific implemenations of the GatingML2.0 standard to exchange gated cytometry data with other software platforms.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-cytoml - path: recipes/bioconductor-cytoml - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cytopipeline/meta.yaml b/recipes/bioconductor-cytopipeline/meta.yaml index 7e23057f3914e..63cc21f646b1e 100644 --- a/recipes/bioconductor-cytopipeline/meta.yaml +++ b/recipes/bioconductor-cytopipeline/meta.yaml @@ -1,61 +1,66 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "CytoPipeline" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides support for automation and visualization of flow cytometry data analysis pipelines. In the current state, the package focuses on the preprocessing and quality control part. The framework is based on two main S4 classes, i.e. CytoPipeline and CytoProcessingStep. The pipeline steps are linked to corresponding R functions - that are either provided in the CytoPipeline package itself, or exported from a third party package, or coded by the user her/himself. The processing steps need to be specified centrally and explicitly using either a json input file or through step by step creation of a CytoPipeline object with dedicated methods. After having run the pipeline, obtained results at all steps can be retrieved and visualized thanks to file caching (the running facility uses a BiocFileCache implementation). The package provides also specific visualization tools like pipeline workflow summary display, and 1D/2D comparison plots of obtained flowFrames at various steps of the pipeline. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Automation and visualization of flow cytometry data analysis pipelines -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a4ed3b88553c7115d7dce368a0fda5a5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cytopipeline", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, reshape2, dplyr, CytoPipelineGUI requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-flowai >=1.32.0,<1.33.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-ggcyto >=1.30.0,<1.31.0' - - 'bioconductor-peacoqc >=1.12.0,<1.13.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-flowai >=1.36.0,<1.37.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-ggcyto >=1.34.0,<1.35.0 + - bioconductor-peacoqc >=1.16.0,<1.17.0 - r-base - r-diagram - - 'r-ggplot2 >=3.4.1' + - r-ggplot2 >=3.4.1 - r-jsonlite - r-rlang - r-scales - r-withr run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-flowai >=1.32.0,<1.33.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-ggcyto >=1.30.0,<1.31.0' - - 'bioconductor-peacoqc >=1.12.0,<1.13.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-flowai >=1.36.0,<1.37.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-ggcyto >=1.34.0,<1.35.0 + - bioconductor-peacoqc >=1.16.0,<1.17.0 - r-base - r-diagram - - 'r-ggplot2 >=3.4.1' + - r-ggplot2 >=3.4.1 - r-jsonlite - r-rlang - r-scales - r-withr + +source: + md5: 6166a108d4604b10a9563dfc7641b35b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Automation and visualization of flow cytometry data analysis pipelines' - description: 'This package provides support for automation and visualization of flow cytometry data analysis pipelines. In the current state, the package focuses on the preprocessing and quality control part. The framework is based on two main S4 classes, i.e. CytoPipeline and CytoProcessingStep. The pipeline steps are linked to corresponding R functions - that are either provided in the CytoPipeline package itself, or exported from a third party package, or coded by the user her/himself. The processing steps need to be specified centrally and explicitly using either a json input file or through step by step creation of a CytoPipeline object with dedicated methods. After having run the pipeline, obtained results at all steps can be retrieved and visualized thanks to file caching (the running facility uses a BiocFileCache implementation). The package provides also specific visualization tools like pipeline workflow summary display, and 1D/2D comparison plots of obtained flowFrames at various steps of the pipeline.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cytopipelinegui/meta.yaml b/recipes/bioconductor-cytopipelinegui/meta.yaml index de5a7ec5baba2..837683593d48d 100644 --- a/recipes/bioconductor-cytopipelinegui/meta.yaml +++ b/recipes/bioconductor-cytopipelinegui/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "CytoPipelineGUI" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is the companion of the `CytoPipeline` package. It provides GUI's (shiny apps) for the visualization of flow cytometry data analysis pipelines that are run with `CytoPipeline`. Two shiny applications are provided, i.e. an interactive flow frame assessment and comparison tool and an interactive scale transformations visualization and adjustment tool. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: GUI's for visualization of flow cytometry data analysis pipelines -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fb6a6a7aad638be11919a144f3d9907a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cytopipelinegui", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, patchwork requirements: host: - - 'bioconductor-cytopipeline >=1.2.0,<1.3.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-cytopipeline >=1.6.0,<1.7.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-ggplot2 - r-plotly - r-shiny run: - - 'bioconductor-cytopipeline >=1.2.0,<1.3.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-cytopipeline >=1.6.0,<1.7.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-ggplot2 - r-plotly - r-shiny + +source: + md5: 2cd6a8f5eb5b986c2a2935c5b7c294a9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=3) | file LICENSE' - summary: 'GUI''s for visualization of flow cytometry data analysis pipelines' - description: 'This package is the companion of the `CytoPipeline` package. It provides GUI''s (shiny apps) for the visualization of flow cytometry data analysis pipelines that are run with `CytoPipeline`. Two shiny applications are provided, i.e. an interactive flow frame assessment and comparison tool and an interactive scale transformations visualization and adjustment tool.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-cytoviewer/meta.yaml b/recipes/bioconductor-cytoviewer/meta.yaml index dbf9da026b8dd..c43f8247ebcb2 100644 --- a/recipes/bioconductor-cytoviewer/meta.yaml +++ b/recipes/bioconductor-cytoviewer/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "cytoviewer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This R package supports interactive visualization of multi-channel images and segmentation masks generated by imaging mass cytometry and other highly multiplexed imaging techniques using shiny. The cytoviewer interface is divided into image-level (Composite and Channels) and cell-level visualization (Masks). It allows users to overlay individual images with segmentation masks, integrates well with SingleCellExperiment and SpatialExperiment objects for metadata visualization and supports image downloads. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: An interactive multi-channel image viewer for R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dc34f69f53490911e6f621d76db69f4c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-cytoviewer", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat requirements: host: - - 'bioconductor-cytomapper >=1.14.0,<1.15.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-cytomapper >=1.18.0,<1.19.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-archive - r-base - r-colourpicker @@ -38,11 +40,11 @@ requirements: - r-svgpanzoom - r-viridis run: - - 'bioconductor-cytomapper >=1.14.0,<1.15.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-cytomapper >=1.18.0,<1.19.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-archive - r-base - r-colourpicker @@ -53,13 +55,16 @@ requirements: - r-svglite - r-svgpanzoom - r-viridis + +source: + md5: bd28f195b0b83b1d2a8d5f44012385b7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'An interactive multi-channel image viewer for R' - description: 'This R package supports interactive visualization of multi-channel images and segmentation masks generated by imaging mass cytometry and other highly multiplexed imaging techniques using shiny. The cytoviewer interface is divided into image-level (Composite and Channels) and cell-level visualization (Masks). It allows users to overlay individual images with segmentation masks, integrates well with SingleCellExperiment and SpatialExperiment objects for metadata visualization and supports image downloads.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dada2/meta.yaml b/recipes/bioconductor-dada2/meta.yaml index 6e500493c1345..c76c7b86f11aa 100644 --- a/recipes/bioconductor-dada2/meta.yaml +++ b/recipes/bioconductor-dada2/meta.yaml @@ -1,68 +1,74 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "dada2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2' + summary: Accurate, high-resolution sample inference from amplicon sequencing data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 096baf34b4618af27b1b430945d3a189 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dada2", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:dada2 + parent_recipe: + name: bioconductor-dada2 + path: recipes/bioconductor-dada2 + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - - 'r-ggplot2 >=2.1.0' - - 'r-rcpp >=0.12.0' - - 'r-rcppparallel >=4.3.0' - - 'r-reshape2 >=1.4.1' + - r-ggplot2 >=2.1.0 + - r-rcpp >=0.12.0 + - r-rcppparallel >=4.3.0 + - r-reshape2 >=1.4.1 - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - - 'r-ggplot2 >=2.1.0' - - 'r-rcpp >=0.12.0' - - 'r-rcppparallel >=4.3.0' - - 'r-reshape2 >=1.4.1' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-ggplot2 >=2.1.0 + - r-rcpp >=0.12.0 + - r-rcppparallel >=4.3.0 + - r-reshape2 >=1.4.1 + +source: + md5: 5dff89c66a530ab9a0a52554943e8419 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-2 - summary: 'Accurate, high-resolution sample inference from amplicon sequencing data' - description: 'The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2' -extra: - identifiers: - - biotools:dada2 - parent_recipe: - name: bioconductor-dada2 - path: recipes/bioconductor-dada2 - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-daglogo/meta.yaml b/recipes/bioconductor-daglogo/meta.yaml index 0e97dccda1777..b68313ab2669b 100644 --- a/recipes/bioconductor-daglogo/meta.yaml +++ b/recipes/bioconductor-daglogo/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "dagLogo" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Visualize significant conserved amino acid sequence pattern in groups based on probability theory. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cb8662ee04599fa0076e344d2bf933d1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-daglogo", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: XML, grImport, grImport2, BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-motifstack >=1.46.0,<1.47.0' - - 'bioconductor-uniprot.ws >=2.42.0,<2.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-motifstack >=1.50.0,<1.51.0 + - bioconductor-uniprot.ws >=2.46.0,<2.47.0 - r-base - r-httr - r-pheatmap run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-motifstack >=1.46.0,<1.47.0' - - 'bioconductor-uniprot.ws >=2.42.0,<2.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-motifstack >=1.50.0,<1.51.0 + - bioconductor-uniprot.ws >=2.46.0,<2.47.0 - r-base - r-httr - r-pheatmap + +source: + md5: a68ad6ee07b435310316af11119dbcbd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory' - description: 'Visualize significant conserved amino acid sequence pattern in groups based on probability theory.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dama/meta.yaml b/recipes/bioconductor-dama/meta.yaml index 6f827bb23d349..40dfc0a3eed06 100644 --- a/recipes/bioconductor-dama/meta.yaml +++ b/recipes/bioconductor-dama/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "daMA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data. Statistical details are described in Bretz et al. (2003, submitted) + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Efficient design and analysis of factorial two-colour microarray data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec7e80e81b9d6eb5a76ce06c761bb7da build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dama", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:dama + - doi:10.1016/j.csda.2004.08.014 + parent_recipe: + name: bioconductor-dama + path: recipes/bioconductor-dama + version: 1.52.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -26,21 +37,16 @@ requirements: run: - r-base - r-mass + +source: + md5: 604d8b327a5ff84e4dfb0a73f18d7abb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Efficient design and analysis of factorial two-colour microarray data' - description: 'This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data. Statistical details are described in Bretz et al. (2003, submitted)' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:dama - - doi:10.1016/j.csda.2004.08.014 - parent_recipe: - name: bioconductor-dama - path: recipes/bioconductor-dama - version: 1.52.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-damefinder/meta.yaml b/recipes/bioconductor-damefinder/meta.yaml index 070f5d8dc6e1a..0de4a331e2e33 100644 --- a/recipes/bioconductor-damefinder/meta.yaml +++ b/recipes/bioconductor-damefinder/meta.yaml @@ -1,39 +1,41 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "DAMEfinder" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: '''DAMEfinder'' offers functionality for taking methtuple or bismark outputs to calculate ASM scores and compute DAMEs. It also offers nice visualization of methyl-circle plots.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Finds DAMEs - Differential Allelicly MEthylated regions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0f99003a20995ebd0c15fce1a407765f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-damefinder", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-cowplot - r-ggplot2 @@ -42,18 +44,18 @@ requirements: - r-reshape2 - r-stringr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-cowplot - r-ggplot2 @@ -61,13 +63,16 @@ requirements: - r-readr - r-reshape2 - r-stringr + +source: + md5: 3b4591363f6637491fd9899266c81ba9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Finds DAMEs - Differential Allelicly MEthylated regions' - description: '''DAMEfinder'' offers functionality for taking methtuple or bismark outputs to calculate ASM scores and compute DAMEs. It also offers nice visualization of methyl-circle plots.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-damirseq/meta.yaml b/recipes/bioconductor-damirseq/meta.yaml index 8f31010215ab8..6bd16627e5c97 100644 --- a/recipes/bioconductor-damirseq/meta.yaml +++ b/recipes/bioconductor-damirseq/meta.yaml @@ -1,33 +1,40 @@ -{% set version = "2.14.0" %} +{% set version = "2.18.0" %} {% set name = "DaMiRseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them for both binary and multi-class classification purposes. The package accepts any kind of data presented as a table of raw counts and allows including both continous and factorial variables that occur with the experimental setting. A series of functions enable the user to clean up the data by filtering genomic features and samples, to adjust data by identifying and removing the unwanted source of variation (i.e. batches and confounding factors) and to select the best predictors for modeling. Finally, a "stacking" ensemble learning technique is applied to build a robust classification model. Every step includes a checkpoint that the user may exploit to assess the effects of data management by looking at diagnostic plots, such as clustering and heatmaps, RLE boxplots, MDS or correlation plot. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'Data Mining for RNA-seq data: normalization, feature selection and classification' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 64986e7db314ddba69d156b35f974680 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-damirseq", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, testthat requirements: + host: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edaseq >=2.36.0,<2.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edaseq >=2.40.0,<2.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-arm - r-base - r-caret @@ -49,13 +56,14 @@ requirements: - r-rcolorbrewer - r-reshape2 - r-rsnns + run: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edaseq >=2.36.0,<2.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edaseq >=2.40.0,<2.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-arm - r-base - r-caret @@ -77,16 +85,16 @@ requirements: - r-rcolorbrewer - r-reshape2 - r-rsnns + +source: + md5: d63b5836ac8983c573f41cac1ed82fc7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Data Mining for RNA-seq data: normalization, feature selection and classification' - description: 'The DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them for both binary and multi-class classification purposes. The package accepts any kind of data presented as a table of raw counts and allows including both continous and factorial variables that occur with the experimental setting. A series of functions enable the user to clean up the data by filtering genomic features and samples, to adjust data by identifying and removing the unwanted source of variation (i.e. batches and confounding factors) and to select the best predictors for modeling. Finally, a "stacking" ensemble learning technique is applied to build a robust classification model. Every step includes a checkpoint that the user may exploit to assess the effects of data management by looking at diagnostic plots, such as clustering and heatmaps, RLE boxplots, MDS or correlation plot.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - container: - extended-base: true + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-damsel/build.sh b/recipes/bioconductor-damsel/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-damsel/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-damsel/meta.yaml b/recipes/bioconductor-damsel/meta.yaml new file mode 100644 index 0000000000000..a0b6f713fc3b8 --- /dev/null +++ b/recipes/bioconductor-damsel/meta.yaml @@ -0,0 +1,84 @@ +{% set version = "1.2.0" %} +{% set name = "Damsel" %} +{% set bioc = "3.20" %} + +about: + description: Damsel provides an end to end analysis of DamID data. Damsel takes bam files from Dam-only control and fusion samples and counts the reads matching to each GATC region. edgeR is utilised to identify regions of enrichment in the fusion relative to the control. Enriched regions are combined into peaks, and are associated with nearby genes. Damsel allows for IGV style plots to be built as the results build, inspired by ggcoverage, and using the functionality and layering ability of ggplot2. Damsel also conducts gene ontology testing with bias correction through goseq, and future versions of Damsel will also incorporate motif enrichment analysis. Overall, Damsel is the first package allowing for an end to end analysis with visual capabilities. The goal of Damsel was to bring all the analysis into one place, and allow for exploratory analysis within R. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 'Damsel: an end to end analysis of DamID' + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-damsel", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, biomaRt, biovizBase, BSgenome.Dmelanogaster.UCSC.dm6, knitr, limma, org.Dm.eg.db, rmarkdown, testthat (>= 3.0.0), TxDb.Dmelanogaster.UCSC.dm6.ensGene +requirements: + + host: + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-goseq >=1.58.0,<1.59.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rsubread >=2.20.0,<2.21.0 + - r-base + - r-dplyr + - r-ggplot2 + - r-magrittr + - r-patchwork + - r-reshape2 + - r-rlang + - r-stringr + - r-tidyr + + run: + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-goseq >=1.58.0,<1.59.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rsubread >=2.20.0,<2.21.0 + - r-base + - r-dplyr + - r-ggplot2 + - r-magrittr + - r-patchwork + - r-reshape2 + - r-rlang + - r-stringr + - r-tidyr + +source: + md5: 092df2b885b7fc10b382249f5a37c4bb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-dapar/meta.yaml b/recipes/bioconductor-dapar/meta.yaml index 3e5c822b5adaa..66815c37fe935 100644 --- a/recipes/bioconductor-dapar/meta.yaml +++ b/recipes/bioconductor-dapar/meta.yaml @@ -1,131 +1,57 @@ -{% set version = "1.34.2" %} +{% set version = "1.38.0" %} {% set name = "DAPAR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package DAPAR is a Bioconductor distributed R package which provides all the necessary functions to analyze quantitative data from label-free proteomics experiments. Contrarily to most other similar R packages, it is endowed with rich and user-friendly graphical interfaces, so that no programming skill is required (see `Prostar` package). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Tools for the Differential Analysis of Proteins Abundance with R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98c2672a3b694f6d1989cdd4f00cd8e0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dapar", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, BiocStyle + +extra: + parent_recipe: + name: bioconductor-dapar + path: recipes/bioconductor-dapar + version: 1.14.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, BiocStyle, AnnotationDbi, clusterProfiler, graph, diptest, cluster, vioplot, visNetwork, vsn, igraph, FactoMineR, factoextra, dendextend, parallel, doParallel, Mfuzz, apcluster, forcats, readxl, openxlsx, multcomp, purrr, tibble, knitr, norm, scales, tidyverse, cp4p, imp4p (>= 1.1),lme4, dplyr, limma, preprocessCore, stringr, tidyr, impute, gplots, grDevices, reshape2, graphics, stats, methods, ggplot2, RColorBrewer, Matrix, org.Sc.sgd.db requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-dapardata >=1.32.0,<1.33.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-mfuzz >=2.62.0,<2.63.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' - - r-apcluster + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-dapardata >=1.36.0,<1.37.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 - r-base - - r-cluster - - r-cp4p - - r-dendextend - - r-diptest - - r-doparallel - - r-dplyr - - r-factoextra - - r-factominer - - r-forcats - r-foreach - - r-ggplot2 - - r-gplots - r-highcharter - - r-igraph - - r-imp4p - - r-knitr - - r-lme4 - - r-matrix - - r-multcomp - - r-norm - - r-openxlsx - - r-purrr - - r-rcolorbrewer - - r-readxl - - r-reshape2 - - r-scales - - r-stringr - - r-tibble - - r-tidyr - - r-tidyverse - - r-vioplot - - r-visnetwork run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-dapardata >=1.32.0,<1.33.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-mfuzz >=2.62.0,<2.63.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' - - r-apcluster + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-dapardata >=1.36.0,<1.37.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 - r-base - - r-cluster - - r-cp4p - - r-dendextend - - r-diptest - - r-doparallel - - r-dplyr - - r-factoextra - - r-factominer - - r-forcats - r-foreach - - r-ggplot2 - - r-gplots - r-highcharter - - r-igraph - - r-imp4p - - r-knitr - - r-lme4 - - r-matrix - - r-multcomp - - r-norm - - r-openxlsx - - r-purrr - - r-rcolorbrewer - - r-readxl - - r-reshape2 - - r-scales - - r-stringr - - r-tibble - - r-tidyr - - r-tidyverse - - r-vioplot - - r-visnetwork + +source: + md5: dd51e0de294beab7baec943e13109940 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Tools for the Differential Analysis of Proteins Abundance with R' - description: 'The package DAPAR is a Bioconductor distributed R package which provides all the necessary functions to analyze quantitative data from label-free proteomics experiments. Contrarily to most other similar R packages, it is endowed with rich and user-friendly graphical interfaces, so that no programming skill is required (see `Prostar` package).' -extra: - parent_recipe: - name: bioconductor-dapar - path: recipes/bioconductor-dapar - version: 1.14.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dapardata/meta.yaml b/recipes/bioconductor-dapardata/meta.yaml index a88aae6c229f6..c4b717acf343f 100644 --- a/recipes/bioconductor-dapardata/meta.yaml +++ b/recipes/bioconductor-dapardata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "DAPARdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5906f180d2e824affe9f2850424c7612 +about: + description: 'Mass-spectrometry based UPS proteomics data sets from Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssie D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianferani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O, Schaeffer C, Coute Y, Gonzalez de Peredo A. Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods. Data Brief. 2015 Dec 17;6:286-94 and Giai Gianetto, Q., Combes, F., Ramus, C., Bruley, C., Coute, Y., Burger, T. (2016). Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments. Proteomics, 16(1), 29-32.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Data accompanying the DAPAR and Prostar packages build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dapardata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, DAPAR, BiocStyle requirements: host: - - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - bioconductor-msnbase >=2.32.0,<2.33.0 - r-base run: - - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - bioconductor-msnbase >=2.32.0,<2.33.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: dd1a03112ed37c1b800badd879a70bcf + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Data accompanying the DAPAR and Prostar packages' - description: 'Mass-spectrometry based UPS proteomics data sets from Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssie D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianferani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O, Schaeffer C, Coute Y, Gonzalez de Peredo A. Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods. Data Brief. 2015 Dec 17;6:286-94 and Giai Gianetto, Q., Combes, F., Ramus, C., Bruley, C., Coute, Y., Burger, T. (2016). Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments. Proteomics, 16(1), 29-32.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dapardata/post-link.sh b/recipes/bioconductor-dapardata/post-link.sh index 3788427c5fce2..2fce3ae9820b8 100644 --- a/recipes/bioconductor-dapardata/post-link.sh +++ b/recipes/bioconductor-dapardata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dapardata-1.32.0" +installBiocDataPackage.sh "dapardata-1.36.0" diff --git a/recipes/bioconductor-dar/build.sh b/recipes/bioconductor-dar/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dar/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dar/meta.yaml b/recipes/bioconductor-dar/meta.yaml new file mode 100644 index 0000000000000..6cc0aee5cd09a --- /dev/null +++ b/recipes/bioconductor-dar/meta.yaml @@ -0,0 +1,86 @@ +{% set version = "1.2.0" %} +{% set name = "dar" %} +{% set bioc = "3.20" %} + +about: + description: Differential abundance testing in microbiome data challenges both parametric and non-parametric statistical methods, due to its sparsity, high variability and compositional nature. Microbiome-specific statistical methods often assume classical distribution models or take into account compositional specifics. These produce results that range within the specificity vs sensitivity space in such a way that type I and type II error that are difficult to ascertain in real microbiome data when a single method is used. Recently, a consensus approach based on multiple differential abundance (DA) methods was recently suggested in order to increase robustness. With dar, you can use dplyr-like pipeable sequences of DA methods and then apply different consensus strategies. In this way we can obtain more reliable results in a fast, consistent and reproducible way. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Differential Abundance Analysis by Consensus + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dar", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: ALDEx2, ANCOMBC, apeglm, ashr, Biobase, corncob, covr, DESeq2, devtools, furrr, future, knitr, lefser, limma, Maaslin2, metagenomeSeq, microbiome, rmarkdown, roxygen2, roxyglobals, roxytest, rstatix, SummarizedExperiment, TreeSummarizedExperiment, testthat (>= 3.0.0) +requirements: + + host: + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-mia >=1.14.0,<1.15.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 + - r-base + - r-cli + - r-crayon + - r-dplyr + - r-generics + - r-ggplot2 + - r-glue + - r-gplots + - r-heatmaply + - r-magrittr + - r-purrr + - r-readr + - r-rlang >=0.4.11 + - r-scales + - r-stringr + - r-tibble + - r-tidyr + - r-upsetr + - r-waldo + + run: + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-mia >=1.14.0,<1.15.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 + - r-base + - r-cli + - r-crayon + - r-dplyr + - r-generics + - r-ggplot2 + - r-glue + - r-gplots + - r-heatmaply + - r-magrittr + - r-purrr + - r-readr + - r-rlang >=0.4.11 + - r-scales + - r-stringr + - r-tibble + - r-tidyr + - r-upsetr + - r-waldo + +source: + md5: 890a3fe2eec770fe82d3a41b5551d91c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-dart/meta.yaml b/recipes/bioconductor-dart/meta.yaml index a29f5a06cb466..15be2d46f4590 100644 --- a/recipes/bioconductor-dart/meta.yaml +++ b/recipes/bioconductor-dart/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "DART" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cc7bd6015b08890ec53f8004091c3bb5 +about: + description: Denoising Algorithm based on Relevance network Topology (DART) is an algorithm designed to evaluate the consistency of prior information molecular signatures (e.g in-vitro perturbation expression signatures) in independent molecular data (e.g gene expression data sets). If consistent, a pruning network strategy is then used to infer the activation status of the molecular signature in individual samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Denoising Algorithm based on Relevance network Topology build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dart", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: breastCancerVDX, breastCancerMAINZ, Biobase requirements: host: - r-base - - 'r-igraph >=0.6.0' + - r-igraph >=0.6.0 run: - r-base - - 'r-igraph >=0.6.0' + - r-igraph >=0.6.0 +source: + md5: 46ef1797530f165410506e282c9d9109 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Denoising Algorithm based on Relevance network Topology' - description: 'Denoising Algorithm based on Relevance network Topology (DART) is an algorithm designed to evaluate the consistency of prior information molecular signatures (e.g in-vitro perturbation expression signatures) in independent molecular data (e.g gene expression data sets). If consistent, a pruning network strategy is then used to infer the activation status of the molecular signature in individual samples.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-data-packages/dataURLs.json b/recipes/bioconductor-data-packages/dataURLs.json index 2b5d690d1d314..08dd11b65dc7e 100644 --- a/recipes/bioconductor-data-packages/dataURLs.json +++ b/recipes/bioconductor-data-packages/dataURLs.json @@ -1 +1 @@ -{"ritandata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.15/data/experiment/src/contrib/RITANdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/RITANdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ritandata/bioconductor-ritandata_1.20.0_src_all.tar.gz"], "md5": "4a9a65c5312893ef3bf279efd32d53f8", "fn": "RITANdata_1.20.0.tar.gz"}, "bioplex-1.3.4": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BioPlex_1.3.4.tar.gz", "https://bioarchive.galaxyproject.org/BioPlex_1.3.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bioplex/bioconductor-bioplex_1.3.4_src_all.tar.gz"], "md5": "1062ae3102262b55efd51cb48fb37d0c", "fn": "BioPlex_1.3.4.tar.gz"}, "adme16cod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/adme16cod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/adme16cod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-adme16cod.db/bioconductor-adme16cod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-adme16cod.db/bioconductor-adme16cod.db_3.4.0_src_all.tar.gz"], "md5": "3902516a40a503302ef732143b2394b9", "fn": "adme16cod.db_3.4.0.tar.gz"}, "ag.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ag.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/ag.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ag.db/bioconductor-ag.db_3.13.0_src_all.tar.gz"], "md5": "925e808d2c9b21a11ed131d483e75ab6", "fn": "ag.db_3.13.0.tar.gz"}, "agcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/agcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/agcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-agcdf/bioconductor-agcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-agcdf/bioconductor-agcdf_2.18.0_src_all.tar.gz"], "md5": "5dd14bc6a6d2729f5e7b170105c78e48", "fn": "agcdf_2.18.0.tar.gz"}, "agprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/agprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/agprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-agprobe/bioconductor-agprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-agprobe/bioconductor-agprobe_2.18.0_src_all.tar.gz"], "md5": "08f7527d4c8a30d8b2f86016a53f075a", "fn": "agprobe_2.18.0.tar.gz"}, "ahcytobands-0.99.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/AHCytoBands_0.99.1.tar.gz", "https://bioarchive.galaxyproject.org/AHCytoBands_0.99.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahcytobands/bioconductor-ahcytobands_0.99.1_src_all.tar.gz"], "md5": "3dd85d02e7ed3fca4c7898b5e395edeb", "fn": "AHCytoBands_0.99.1.tar.gz"}, "ahensdbs-1.1.8": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/AHEnsDbs_1.1.8.tar.gz", "https://bioarchive.galaxyproject.org/AHEnsDbs_1.1.8.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahensdbs/bioconductor-ahensdbs_1.1.8_src_all.tar.gz"], "md5": "f2c8c9338f09f480a46e1155d985d08f", "fn": "AHEnsDbs_1.1.8.tar.gz"}, "ahlrbasedbs-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/AHLRBaseDbs_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/AHLRBaseDbs_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahlrbasedbs/bioconductor-ahlrbasedbs_1.5.0_src_all.tar.gz"], "md5": "b1266d2bab652542d6f7289898c3e781", "fn": "AHLRBaseDbs_1.5.0.tar.gz"}, "ahmeshdbs-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/AHMeSHDbs_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/AHMeSHDbs_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahmeshdbs/bioconductor-ahmeshdbs_1.5.0_src_all.tar.gz"], "md5": "87c396d15191843ec3cdced73bf504f8", "fn": "AHMeSHDbs_1.5.0.tar.gz"}, "ahpathbankdbs-0.99.5": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/AHPathbankDbs_0.99.5.tar.gz", "https://bioarchive.galaxyproject.org/AHPathbankDbs_0.99.5.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahpathbankdbs/bioconductor-ahpathbankdbs_0.99.5_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahpathbankdbs/bioconductor-ahpathbankdbs_0.99.5_src_all.tar.gz"], "md5": "70339eae8c03c47248b612b365bda4ff", "fn": "AHPathbankDbs_0.99.5.tar.gz"}, "ahpubmeddbs-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/AHPubMedDbs_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/AHPubMedDbs_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahpubmeddbs/bioconductor-ahpubmeddbs_1.5.0_src_all.tar.gz"], "md5": "0fa89f6189085931f1245c31ddced2d4", "fn": "AHPubMedDbs_1.5.0.tar.gz"}, "ahwikipathwaysdbs-0.99.4": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/AHWikipathwaysDbs_0.99.4.tar.gz", "https://bioarchive.galaxyproject.org/AHWikipathwaysDbs_0.99.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahwikipathwaysdbs/bioconductor-ahwikipathwaysdbs_0.99.4_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahwikipathwaysdbs/bioconductor-ahwikipathwaysdbs_0.99.4_src_all.tar.gz"], "md5": "ffa90f6d6e8832ae6f4b5bf8b151cd46", "fn": "AHWikipathwaysDbs_0.99.4.tar.gz"}, "alternativesplicingevents.hg19-1.1.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/alternativeSplicingEvents.hg19_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/alternativeSplicingEvents.hg19_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-alternativesplicingevents.hg19/bioconductor-alternativesplicingevents.hg19_1.1.0_src_all.tar.gz"], "md5": "b1acae776c9e9c5d961cf4884cadc58f", "fn": "alternativeSplicingEvents.hg19_1.1.0.tar.gz"}, "alternativesplicingevents.hg38-1.1.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/alternativeSplicingEvents.hg38_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/alternativeSplicingEvents.hg38_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-alternativesplicingevents.hg38/bioconductor-alternativesplicingevents.hg38_1.1.0_src_all.tar.gz"], "md5": "8d49710eebd62fb15a48cab252ff3eca", "fn": "alternativeSplicingEvents.hg38_1.1.0.tar.gz"}, "anopheles.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/anopheles.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/anopheles.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-anopheles.db0/bioconductor-anopheles.db0_3.16.0_src_all.tar.gz"], "md5": "17c685b359943a1ef3b21e78f27dc469", "fn": "anopheles.db0_3.16.0.tar.gz"}, "arabidopsis.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/arabidopsis.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/arabidopsis.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-arabidopsis.db0/bioconductor-arabidopsis.db0_3.16.0_src_all.tar.gz"], "md5": "c72b535bf366b91986fa42ffbb2c6d41", "fn": "arabidopsis.db0_3.16.0.tar.gz"}, "ath1121501.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ath1121501.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/ath1121501.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ath1121501.db/bioconductor-ath1121501.db_3.13.0_src_all.tar.gz"], "md5": "c5d937ca9c6bcbb4385fb37a3b14ad15", "fn": "ath1121501.db_3.13.0.tar.gz"}, "ath1121501cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ath1121501cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ath1121501cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ath1121501cdf/bioconductor-ath1121501cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ath1121501cdf/bioconductor-ath1121501cdf_2.18.0_src_all.tar.gz"], "md5": "8b63798143219b7c1c2666a91a1a2440", "fn": "ath1121501cdf_2.18.0.tar.gz"}, "ath1121501probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ath1121501probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ath1121501probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ath1121501probe/bioconductor-ath1121501probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ath1121501probe/bioconductor-ath1121501probe_2.18.0_src_all.tar.gz"], "md5": "eeeae5e6550bb472ba3419d71bbd7dfb", "fn": "ath1121501probe_2.18.0.tar.gz"}, "barley1cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/barley1cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/barley1cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-barley1cdf/bioconductor-barley1cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-barley1cdf/bioconductor-barley1cdf_2.18.0_src_all.tar.gz"], "md5": "16a2ca83f550518756d9fa3273672157", "fn": "barley1cdf_2.18.0.tar.gz"}, "barley1probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/barley1probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/barley1probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-barley1probe/bioconductor-barley1probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-barley1probe/bioconductor-barley1probe_2.18.0_src_all.tar.gz"], "md5": "80595d8ecf83ba83ea84a722a24ab474", "fn": "barley1probe_2.18.0.tar.gz"}, "bovine.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/bovine.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/bovine.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bovine.db/bioconductor-bovine.db_3.13.0_src_all.tar.gz"], "md5": "dcc1180e8ac11247f9899f140082647e", "fn": "bovine.db_3.13.0.tar.gz"}, "bovine.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/bovine.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/bovine.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bovine.db0/bioconductor-bovine.db0_3.16.0_src_all.tar.gz"], "md5": "edf5e741183f2d47d76649bdbaa7dcf6", "fn": "bovine.db0_3.16.0.tar.gz"}, "bovinecdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/bovinecdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/bovinecdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bovinecdf/bioconductor-bovinecdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bovinecdf/bioconductor-bovinecdf_2.18.0_src_all.tar.gz"], "md5": "e155fc7d5f84ee420d9b250a639af305", "fn": "bovinecdf_2.18.0.tar.gz"}, "bovineprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/bovineprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/bovineprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bovineprobe/bioconductor-bovineprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bovineprobe/bioconductor-bovineprobe_2.18.0_src_all.tar.gz"], "md5": "9f9e25fc8c7a76acf541745b7c09748b", "fn": "bovineprobe_2.18.0.tar.gz"}, "bsgenome.alyrata.jgi.v1-1.0.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Alyrata.JGI.v1_1.0.1.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Alyrata.JGI.v1_1.0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.alyrata.jgi.v1/bioconductor-bsgenome.alyrata.jgi.v1_1.0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.alyrata.jgi.v1/bioconductor-bsgenome.alyrata.jgi.v1_1.0.1_src_all.tar.gz"], "md5": "64878499c633de66ccf4c5abc32c0aeb", "fn": "BSgenome.Alyrata.JGI.v1_1.0.1.tar.gz"}, "bsgenome.amellifera.beebase.assembly4-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Amellifera.BeeBase.assembly4_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Amellifera.BeeBase.assembly4_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.beebase.assembly4/bioconductor-bsgenome.amellifera.beebase.assembly4_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.beebase.assembly4/bioconductor-bsgenome.amellifera.beebase.assembly4_1.4.0_src_all.tar.gz"], "md5": "77495ee5eba48fe52902c9cc4f9ba7cc", "fn": "BSgenome.Amellifera.BeeBase.assembly4_1.4.0.tar.gz"}, "bsgenome.amellifera.ncbi.amelhav3.1-1.5.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Amellifera.NCBI.AmelHAv3.1_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Amellifera.NCBI.AmelHAv3.1_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1_1.5.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1_1.5.0_src_all.tar.gz"], "md5": "b119087dfe54805c90cb6bf901e8237e", "fn": "BSgenome.Amellifera.NCBI.AmelHAv3.1_1.5.0.tar.gz"}, "bsgenome.amellifera.ucsc.apimel2-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Amellifera.UCSC.apiMel2_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Amellifera.UCSC.apiMel2_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.ucsc.apimel2/bioconductor-bsgenome.amellifera.ucsc.apimel2_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.ucsc.apimel2/bioconductor-bsgenome.amellifera.ucsc.apimel2_1.4.0_src_all.tar.gz"], "md5": "436ddf54868906e7d1135369d41a2ffe", "fn": "BSgenome.Amellifera.UCSC.apiMel2_1.4.0.tar.gz"}, "bsgenome.amellifera.ucsc.apimel2.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Amellifera.UCSC.apiMel2.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Amellifera.UCSC.apiMel2.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked_1.3.99_src_all.tar.gz"], "md5": "e7a7ff8cfce8e239b22116855456f23d", "fn": "BSgenome.Amellifera.UCSC.apiMel2.masked_1.3.99.tar.gz"}, "bsgenome.aofficinalis.ncbi.v1-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Aofficinalis.NCBI.V1_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Aofficinalis.NCBI.V1_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.aofficinalis.ncbi.v1/bioconductor-bsgenome.aofficinalis.ncbi.v1_1.0.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.aofficinalis.ncbi.v1/bioconductor-bsgenome.aofficinalis.ncbi.v1_1.0.0_src_all.tar.gz"], "md5": "3f8fd13e74eee63895a5ef528004b60b", "fn": "BSgenome.Aofficinalis.NCBI.V1_1.0.0.tar.gz"}, "bsgenome.athaliana.tair.04232008-1.3.1000": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Athaliana.TAIR.04232008_1.3.1000.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Athaliana.TAIR.04232008_1.3.1000.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.athaliana.tair.04232008/bioconductor-bsgenome.athaliana.tair.04232008_1.3.1000_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.athaliana.tair.04232008/bioconductor-bsgenome.athaliana.tair.04232008_1.3.1000_src_all.tar.gz"], "md5": "6b8a31a228dbcf4468974f5ec1d98467", "fn": "BSgenome.Athaliana.TAIR.04232008_1.3.1000.tar.gz"}, "bsgenome.athaliana.tair.tair9-1.3.1000": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Athaliana.TAIR.TAIR9_1.3.1000.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Athaliana.TAIR.TAIR9_1.3.1000.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.athaliana.tair.tair9/bioconductor-bsgenome.athaliana.tair.tair9_1.3.1000_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.athaliana.tair.tair9/bioconductor-bsgenome.athaliana.tair.tair9_1.3.1000_src_all.tar.gz"], "md5": "8c6709a5f544616d59f4d39aac5787a7", "fn": "BSgenome.Athaliana.TAIR.TAIR9_1.3.1000.tar.gz"}, "bsgenome.btaurus.ucsc.bostau3-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau3_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau3_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau3/bioconductor-bsgenome.btaurus.ucsc.bostau3_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau3/bioconductor-bsgenome.btaurus.ucsc.bostau3_1.4.0_src_all.tar.gz"], "md5": "fe6c4d5853f91c3db3e716ddbc773580", "fn": "BSgenome.Btaurus.UCSC.bosTau3_1.4.0.tar.gz"}, "bsgenome.btaurus.ucsc.bostau3.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau3.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau3.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked_1.3.99_src_all.tar.gz"], "md5": "50f7da5907cbe0d08183dc7161a8ca56", "fn": "BSgenome.Btaurus.UCSC.bosTau3.masked_1.3.99.tar.gz"}, "bsgenome.btaurus.ucsc.bostau4-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau4_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau4_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau4/bioconductor-bsgenome.btaurus.ucsc.bostau4_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau4/bioconductor-bsgenome.btaurus.ucsc.bostau4_1.4.0_src_all.tar.gz"], "md5": "162cd253c719e347df5748ebb407a191", "fn": "BSgenome.Btaurus.UCSC.bosTau4_1.4.0.tar.gz"}, "bsgenome.btaurus.ucsc.bostau4.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau4.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau4.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked_1.3.99_src_all.tar.gz"], "md5": "7c5294349c7061adfb3948bc5659afeb", "fn": "BSgenome.Btaurus.UCSC.bosTau4.masked_1.3.99.tar.gz"}, "bsgenome.btaurus.ucsc.bostau6-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau6_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau6_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau6/bioconductor-bsgenome.btaurus.ucsc.bostau6_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau6/bioconductor-bsgenome.btaurus.ucsc.bostau6_1.4.0_src_all.tar.gz"], "md5": "b22391e0678fc3743daa4b77ecc55f66", "fn": "BSgenome.Btaurus.UCSC.bosTau6_1.4.0.tar.gz"}, "bsgenome.btaurus.ucsc.bostau6.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau6.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau6.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked_1.3.99_src_all.tar.gz"], "md5": "a176de6b1b91854d47e783b8249dbf58", "fn": "BSgenome.Btaurus.UCSC.bosTau6.masked_1.3.99.tar.gz"}, "bsgenome.btaurus.ucsc.bostau8-1.4.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau8_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau8_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau8/bioconductor-bsgenome.btaurus.ucsc.bostau8_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau8/bioconductor-bsgenome.btaurus.ucsc.bostau8_1.4.2_src_all.tar.gz"], "md5": "61ababa7b2b5360fceeb06f0bf49b208", "fn": "BSgenome.Btaurus.UCSC.bosTau8_1.4.2.tar.gz"}, "bsgenome.btaurus.ucsc.bostau9-1.4.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau9_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau9_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau9/bioconductor-bsgenome.btaurus.ucsc.bostau9_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau9/bioconductor-bsgenome.btaurus.ucsc.bostau9_1.4.2_src_all.tar.gz"], "md5": "9b3343725d85c093999413d91218079d", "fn": "BSgenome.Btaurus.UCSC.bosTau9_1.4.2.tar.gz"}, "bsgenome.btaurus.ucsc.bostau9.masked-1.4.4": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau9.masked_1.4.4.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau9.masked_1.4.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau9.masked/bioconductor-bsgenome.btaurus.ucsc.bostau9.masked_1.4.4_src_all.tar.gz"], "md5": "c96bd95c3b791d712aa5cb8c96f9c937", "fn": "BSgenome.Btaurus.UCSC.bosTau9.masked_1.4.4.tar.gz"}, "bsgenome.carietinum.ncbi.v1-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Carietinum.NCBI.v1_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Carietinum.NCBI.v1_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.carietinum.ncbi.v1/bioconductor-bsgenome.carietinum.ncbi.v1_1.0.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.carietinum.ncbi.v1/bioconductor-bsgenome.carietinum.ncbi.v1_1.0.0_src_all.tar.gz"], "md5": "eef018ecce6d32852aa18ac39cf377c6", "fn": "BSgenome.Carietinum.NCBI.v1_1.0.0.tar.gz"}, "bsgenome.celegans.ucsc.ce10-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce10/bioconductor-bsgenome.celegans.ucsc.ce10_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce10/bioconductor-bsgenome.celegans.ucsc.ce10_1.4.0_src_all.tar.gz"], "md5": "98a8ca836d6db23e46674552669d7942", "fn": "BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz"}, "bsgenome.celegans.ucsc.ce11-1.4.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce11_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Celegans.UCSC.ce11_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce11/bioconductor-bsgenome.celegans.ucsc.ce11_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce11/bioconductor-bsgenome.celegans.ucsc.ce11_1.4.2_src_all.tar.gz"], "md5": "b80e24149a0c6ed323d0c9a6d112ef52", "fn": "BSgenome.Celegans.UCSC.ce11_1.4.2.tar.gz"}, "bsgenome.celegans.ucsc.ce2-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce2_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Celegans.UCSC.ce2_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce2/bioconductor-bsgenome.celegans.ucsc.ce2_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce2/bioconductor-bsgenome.celegans.ucsc.ce2_1.4.0_src_all.tar.gz"], "md5": "b2bf7eec2b07685cf9dcdf42840db208", "fn": "BSgenome.Celegans.UCSC.ce2_1.4.0.tar.gz"}, "bsgenome.celegans.ucsc.ce6-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce6/bioconductor-bsgenome.celegans.ucsc.ce6_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce6/bioconductor-bsgenome.celegans.ucsc.ce6_1.4.0_src_all.tar.gz"], "md5": "cb86ff861d8f660c2abd8fc1907d84a6", "fn": "BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz"}, "bsgenome.cfamiliaris.ucsc.canfam2-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam2_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Cfamiliaris.UCSC.canFam2_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2_1.4.0_src_all.tar.gz"], "md5": "b98f5289ed5d362cd815db9352598634", "fn": "BSgenome.Cfamiliaris.UCSC.canFam2_1.4.0.tar.gz"}, "bsgenome.cfamiliaris.ucsc.canfam2.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam2.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Cfamiliaris.UCSC.canFam2.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked_1.3.99_src_all.tar.gz"], "md5": "6f921533bb83f83f43b8d227b00a48cb", "fn": "BSgenome.Cfamiliaris.UCSC.canFam2.masked_1.3.99.tar.gz"}, "bsgenome.cfamiliaris.ucsc.canfam3-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam3_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Cfamiliaris.UCSC.canFam3_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3_1.4.0_src_all.tar.gz"], "md5": "efcdc531042be86f99a734cd69c0688c", "fn": "BSgenome.Cfamiliaris.UCSC.canFam3_1.4.0.tar.gz"}, "bsgenome.cfamiliaris.ucsc.canfam3.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam3.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Cfamiliaris.UCSC.canFam3.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked_1.3.99_src_all.tar.gz"], "md5": "8e2246f51fc967dc2ed748cf967a7649", "fn": "BSgenome.Cfamiliaris.UCSC.canFam3.masked_1.3.99.tar.gz"}, "bsgenome.cjacchus.ucsc.caljac3-1.4.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Cjacchus.UCSC.calJac3_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Cjacchus.UCSC.calJac3_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cjacchus.ucsc.caljac3/bioconductor-bsgenome.cjacchus.ucsc.caljac3_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cjacchus.ucsc.caljac3/bioconductor-bsgenome.cjacchus.ucsc.caljac3_1.4.2_src_all.tar.gz"], "md5": "41f927aa0d6ffbdaa6ad93c9135409e6", "fn": "BSgenome.Cjacchus.UCSC.calJac3_1.4.2.tar.gz"}, "bsgenome.cjacchus.ucsc.caljac4-1.5.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Cjacchus.UCSC.calJac4_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Cjacchus.UCSC.calJac4_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cjacchus.ucsc.caljac4/bioconductor-bsgenome.cjacchus.ucsc.caljac4_1.5.0_src_all.tar.gz"], "md5": "b11d16ac2cfa81e04af74e2049e52670", "fn": "BSgenome.Cjacchus.UCSC.calJac4_1.5.0.tar.gz"}, "bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.CneoformansVarGrubiiKN99.NCBI.ASM221672v1_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.CneoformansVarGrubiiKN99.NCBI.ASM221672v1_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1/bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1_1.0.0_src_all.tar.gz"], "md5": "ea536a15bd932af794f672d9b204c141", "fn": "BSgenome.CneoformansVarGrubiiKN99.NCBI.ASM221672v1_1.0.0.tar.gz"}, "bsgenome.creinhardtii.jgi.v5.6-1.5.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Creinhardtii.JGI.v5.6_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Creinhardtii.JGI.v5.6_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.creinhardtii.jgi.v5.6/bioconductor-bsgenome.creinhardtii.jgi.v5.6_1.5.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.creinhardtii.jgi.v5.6/bioconductor-bsgenome.creinhardtii.jgi.v5.6_1.5.0_src_all.tar.gz"], "md5": "2bd1be53d19249ac14ad7f39dc00af0e", "fn": "BSgenome.Creinhardtii.JGI.v5.6_1.5.0.tar.gz"}, "bsgenome.dmelanogaster.ucsc.dm2-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm2_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm2_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/bioconductor-bsgenome.dmelanogaster.ucsc.dm2_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/bioconductor-bsgenome.dmelanogaster.ucsc.dm2_1.4.0_src_all.tar.gz"], "md5": "ebc88df5595fc7aad588b8f3f7de4784", "fn": "BSgenome.Dmelanogaster.UCSC.dm2_1.4.0.tar.gz"}, "bsgenome.dmelanogaster.ucsc.dm2.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm2.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm2.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked_1.3.99_src_all.tar.gz"], "md5": "ae7ca3053e97a0d6bd20bc2b9635ecce", "fn": "BSgenome.Dmelanogaster.UCSC.dm2.masked_1.3.99.tar.gz"}, "bsgenome.dmelanogaster.ucsc.dm3-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/bioconductor-bsgenome.dmelanogaster.ucsc.dm3_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/bioconductor-bsgenome.dmelanogaster.ucsc.dm3_1.4.0_src_all.tar.gz"], "md5": "b7ceebf7bfee766596f602f9e808d069", "fn": "BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz"}, "bsgenome.dmelanogaster.ucsc.dm3.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm3.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm3.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked_1.3.99_src_all.tar.gz"], "md5": "592e7ec451d126b2d314ab6c75d86830", "fn": "BSgenome.Dmelanogaster.UCSC.dm3.masked_1.3.99.tar.gz"}, "bsgenome.dmelanogaster.ucsc.dm6-1.4.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm6_1.4.1.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm6_1.4.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/bioconductor-bsgenome.dmelanogaster.ucsc.dm6_1.4.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/bioconductor-bsgenome.dmelanogaster.ucsc.dm6_1.4.1_src_all.tar.gz"], "md5": "f9d6e406b7893a17c08edd4521c2802f", "fn": "BSgenome.Dmelanogaster.UCSC.dm6_1.4.1.tar.gz"}, "bsgenome.drerio.ucsc.danrer10-1.4.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer10_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer10_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer10/bioconductor-bsgenome.drerio.ucsc.danrer10_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer10/bioconductor-bsgenome.drerio.ucsc.danrer10_1.4.2_src_all.tar.gz"], "md5": "b8dbcc8a338a021ed35656b27b3dd4c0", "fn": "BSgenome.Drerio.UCSC.danRer10_1.4.2.tar.gz"}, "bsgenome.drerio.ucsc.danrer11-1.4.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer11_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer11_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer11/bioconductor-bsgenome.drerio.ucsc.danrer11_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer11/bioconductor-bsgenome.drerio.ucsc.danrer11_1.4.2_src_all.tar.gz"], "md5": "cd586da56ca88ccebb85804f992ba204", "fn": "BSgenome.Drerio.UCSC.danRer11_1.4.2.tar.gz"}, "bsgenome.drerio.ucsc.danrer5-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer5_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer5_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer5/bioconductor-bsgenome.drerio.ucsc.danrer5_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer5/bioconductor-bsgenome.drerio.ucsc.danrer5_1.4.0_src_all.tar.gz"], "md5": "b1fee4bcc0d9cebb2bbdec5cb851f00d", "fn": "BSgenome.Drerio.UCSC.danRer5_1.4.0.tar.gz"}, "bsgenome.drerio.ucsc.danrer5.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer5.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer5.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/bioconductor-bsgenome.drerio.ucsc.danrer5.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/bioconductor-bsgenome.drerio.ucsc.danrer5.masked_1.3.99_src_all.tar.gz"], "md5": "8f0623bcbe1743754a56c55599b535f3", "fn": "BSgenome.Drerio.UCSC.danRer5.masked_1.3.99.tar.gz"}, "bsgenome.drerio.ucsc.danrer6-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer6_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer6_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer6/bioconductor-bsgenome.drerio.ucsc.danrer6_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer6/bioconductor-bsgenome.drerio.ucsc.danrer6_1.4.0_src_all.tar.gz"], "md5": "537d37d29d97ae0c31d77decc67b25b0", "fn": "BSgenome.Drerio.UCSC.danRer6_1.4.0.tar.gz"}, "bsgenome.drerio.ucsc.danrer6.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer6.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer6.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/bioconductor-bsgenome.drerio.ucsc.danrer6.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/bioconductor-bsgenome.drerio.ucsc.danrer6.masked_1.3.99_src_all.tar.gz"], "md5": "71c9b05c27b8d2e05735e6494a8f17ba", "fn": "BSgenome.Drerio.UCSC.danRer6.masked_1.3.99.tar.gz"}, "bsgenome.drerio.ucsc.danrer7-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer7/bioconductor-bsgenome.drerio.ucsc.danrer7_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer7/bioconductor-bsgenome.drerio.ucsc.danrer7_1.4.0_src_all.tar.gz"], "md5": "766b407a46f20d69a143eab0809eb10a", "fn": "BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz"}, "bsgenome.drerio.ucsc.danrer7.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer7.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer7.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/bioconductor-bsgenome.drerio.ucsc.danrer7.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/bioconductor-bsgenome.drerio.ucsc.danrer7.masked_1.3.99_src_all.tar.gz"], "md5": "5d68af24477d006ed22e7342ff97ac16", "fn": "BSgenome.Drerio.UCSC.danRer7.masked_1.3.99.tar.gz"}, "bsgenome.dvirilis.ensembl.dvircaf1-1.4.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Dvirilis.Ensembl.dvircaf1_1.4.3.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Dvirilis.Ensembl.dvircaf1_1.4.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1_1.4.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1_1.4.3_src_all.tar.gz"], "md5": "6a6a6dc7b2d68a741c85525045a67890", "fn": "BSgenome.Dvirilis.Ensembl.dvircaf1_1.4.3.tar.gz"}, "bsgenome.ecoli.ncbi.20080805-1.3.1000": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ecoli.ncbi.20080805/bioconductor-bsgenome.ecoli.ncbi.20080805_1.3.1000_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ecoli.ncbi.20080805/bioconductor-bsgenome.ecoli.ncbi.20080805_1.3.1000_src_all.tar.gz"], "md5": "c653e9cbee3faeb6fd5759b7575f234d", "fn": "BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz"}, "bsgenome.gaculeatus.ucsc.gasacu1-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Gaculeatus.UCSC.gasAcu1_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Gaculeatus.UCSC.gasAcu1_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1_1.4.0_src_all.tar.gz"], "md5": "412aa0570d9c556861b7bb9a5bbc2007", "fn": "BSgenome.Gaculeatus.UCSC.gasAcu1_1.4.0.tar.gz"}, "bsgenome.gaculeatus.ucsc.gasacu1.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Gaculeatus.UCSC.gasAcu1.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Gaculeatus.UCSC.gasAcu1.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked_1.3.99_src_all.tar.gz"], "md5": "9d9b9e70f4f4624ee4a2b09a59d44510", "fn": "BSgenome.Gaculeatus.UCSC.gasAcu1.masked_1.3.99.tar.gz"}, "bsgenome.ggallus.ucsc.galgal3-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal3_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal3_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal3/bioconductor-bsgenome.ggallus.ucsc.galgal3_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal3/bioconductor-bsgenome.ggallus.ucsc.galgal3_1.4.0_src_all.tar.gz"], "md5": "a463e5ccfc8c6d2c62a6ade0da65dbc4", "fn": "BSgenome.Ggallus.UCSC.galGal3_1.4.0.tar.gz"}, "bsgenome.ggallus.ucsc.galgal3.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal3.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal3.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked_1.3.99_src_all.tar.gz"], "md5": "b3224e3a2b15de379c068e61cedfefa6", "fn": "BSgenome.Ggallus.UCSC.galGal3.masked_1.3.99.tar.gz"}, "bsgenome.ggallus.ucsc.galgal4-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal4_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal4_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal4/bioconductor-bsgenome.ggallus.ucsc.galgal4_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal4/bioconductor-bsgenome.ggallus.ucsc.galgal4_1.4.0_src_all.tar.gz"], "md5": "c2cb4bfc39db93c060e78d8d12542c11", "fn": "BSgenome.Ggallus.UCSC.galGal4_1.4.0.tar.gz"}, "bsgenome.ggallus.ucsc.galgal4.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal4.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal4.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked_1.3.99_src_all.tar.gz"], "md5": "0166121ebd8d0b6a4d24d67e175cfe81", "fn": "BSgenome.Ggallus.UCSC.galGal4.masked_1.3.99.tar.gz"}, "bsgenome.ggallus.ucsc.galgal5-1.4.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal5_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal5_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal5/bioconductor-bsgenome.ggallus.ucsc.galgal5_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal5/bioconductor-bsgenome.ggallus.ucsc.galgal5_1.4.2_src_all.tar.gz"], "md5": "93b42354404edd848b21ea6781ca135c", "fn": "BSgenome.Ggallus.UCSC.galGal5_1.4.2.tar.gz"}, "bsgenome.ggallus.ucsc.galgal6-1.4.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal6_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal6_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal6/bioconductor-bsgenome.ggallus.ucsc.galgal6_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal6/bioconductor-bsgenome.ggallus.ucsc.galgal6_1.4.2_src_all.tar.gz"], "md5": "25ef08a5430fb337dbf752ca3378ea3e", "fn": "BSgenome.Ggallus.UCSC.galGal6_1.4.2.tar.gz"}, "bsgenome.gmax.ncbi.gmv40-4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Gmax.NCBI.Gmv40_4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Gmax.NCBI.Gmv40_4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.gmax.ncbi.gmv40/bioconductor-bsgenome.gmax.ncbi.gmv40_4.0_src_all.tar.gz"], "md5": "421c045b993b2cfbc2b08c8103835c56", "fn": "BSgenome.Gmax.NCBI.Gmv40_4.0.tar.gz"}, "bsgenome.hsapiens.1000genomes.hs37d5-0.99.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5_0.99.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5_0.99.1_src_all.tar.gz"], "md5": "164e1692d38fefa499c2c8ac5fc22793", "fn": "BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1.tar.gz"}, "bsgenome.hsapiens.ncbi.grch38-1.3.1000": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ncbi.grch38/bioconductor-bsgenome.hsapiens.ncbi.grch38_1.3.1000_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ncbi.grch38/bioconductor-bsgenome.hsapiens.ncbi.grch38_1.3.1000_src_all.tar.gz"], "md5": "733d324b34d34d7da8c4bf38459f4fae", "fn": "BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000.tar.gz"}, "bsgenome.hsapiens.ncbi.t2t.chm13v2.0-1.5.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0/bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0_1.5.0_src_all.tar.gz"], "md5": "22a99174e1e17718e0b4f8b66f32fd9b", "fn": "BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0_1.5.0.tar.gz"}, "bsgenome.hsapiens.ucsc.hg17-1.3.1000": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg17_1.3.1000.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg17_1.3.1000.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg17/bioconductor-bsgenome.hsapiens.ucsc.hg17_1.3.1000_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg17/bioconductor-bsgenome.hsapiens.ucsc.hg17_1.3.1000_src_all.tar.gz"], "md5": "cbea3029c3d3125a88e6c061c3d3abde", "fn": "BSgenome.Hsapiens.UCSC.hg17_1.3.1000.tar.gz"}, "bsgenome.hsapiens.ucsc.hg17.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg17.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg17.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked_1.3.99_src_all.tar.gz"], "md5": "ff6ee5196f234c5a2a3bcdd052c3c08e", "fn": "BSgenome.Hsapiens.UCSC.hg17.masked_1.3.99.tar.gz"}, "bsgenome.hsapiens.ucsc.hg18-1.3.1000": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg18_1.3.1000.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg18_1.3.1000.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg18/bioconductor-bsgenome.hsapiens.ucsc.hg18_1.3.1000_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg18/bioconductor-bsgenome.hsapiens.ucsc.hg18_1.3.1000_src_all.tar.gz"], "md5": "51bb2e1ed4009860bb21aaac32fffd9c", "fn": "BSgenome.Hsapiens.UCSC.hg18_1.3.1000.tar.gz"}, "bsgenome.hsapiens.ucsc.hg18.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg18.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg18.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked_1.3.99_src_all.tar.gz"], "md5": "e6a31e3cba34ce5e0eb6f76d2c19870c", "fn": "BSgenome.Hsapiens.UCSC.hg18.masked_1.3.99.tar.gz"}, "bsgenome.hsapiens.ucsc.hg19-1.4.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg19/bioconductor-bsgenome.hsapiens.ucsc.hg19_1.4.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg19/bioconductor-bsgenome.hsapiens.ucsc.hg19_1.4.3_src_all.tar.gz"], "md5": "bb3f864ab32450d895816b45f6105f4f", "fn": "BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz"}, "bsgenome.hsapiens.ucsc.hg19.masked-1.3.993": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19.masked_1.3.993.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg19.masked_1.3.993.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked_1.3.993_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked_1.3.993_src_all.tar.gz"], "md5": "4424e1bda9cc005d75f5f05ba4a50c77", "fn": "BSgenome.Hsapiens.UCSC.hg19.masked_1.3.993.tar.gz"}, "bsgenome.hsapiens.ucsc.hg38-1.4.4": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.4.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg38_1.4.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38/bioconductor-bsgenome.hsapiens.ucsc.hg38_1.4.4_src_all.tar.gz"], "md5": "360474907caa1c1ed31030f68f80f0a5", "fn": "BSgenome.Hsapiens.UCSC.hg38_1.4.4.tar.gz"}, "bsgenome.hsapiens.ucsc.hg38.dbsnp151.major-0.0.9999": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major_0.0.9999.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major_0.0.9999.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major_0.0.9999_src_all.tar.gz"], "md5": "c59f66e52d4982942bea2254223d58df", "fn": "BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major_0.0.9999.tar.gz"}, "bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor-0.0.9999": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor_0.0.9999.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor_0.0.9999.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor_0.0.9999_src_all.tar.gz"], "md5": "2cc3a612a2064624735d6a92910be7f3", "fn": "BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor_0.0.9999.tar.gz"}, "bsgenome.hsapiens.ucsc.hg38.masked-1.4.4": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38.masked_1.4.4.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg38.masked_1.4.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked_1.4.4_src_all.tar.gz"], "md5": "95b4e782a3e5970b929ff957befc2659", "fn": "BSgenome.Hsapiens.UCSC.hg38.masked_1.4.4.tar.gz"}, "bsgenome.mdomestica.ucsc.mondom5-1.4.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Mdomestica.UCSC.monDom5_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mdomestica.UCSC.monDom5_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mdomestica.ucsc.mondom5/bioconductor-bsgenome.mdomestica.ucsc.mondom5_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mdomestica.ucsc.mondom5/bioconductor-bsgenome.mdomestica.ucsc.mondom5_1.4.2_src_all.tar.gz"], "md5": "ff940f7446a275962f69a6f4cb84724c", "fn": "BSgenome.Mdomestica.UCSC.monDom5_1.4.2.tar.gz"}, "bsgenome.mfascicularis.ncbi.5.0-1.4.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Mfascicularis.NCBI.5.0_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mfascicularis.NCBI.5.0_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mfascicularis.ncbi.5.0/bioconductor-bsgenome.mfascicularis.ncbi.5.0_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mfascicularis.ncbi.5.0/bioconductor-bsgenome.mfascicularis.ncbi.5.0_1.4.2_src_all.tar.gz"], "md5": "dba6ade39dc6b4f6d06f488141b5550b", "fn": "BSgenome.Mfascicularis.NCBI.5.0_1.4.2.tar.gz"}, "bsgenome.mfascicularis.ncbi.6.0-1.5.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Mfascicularis.NCBI.6.0_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mfascicularis.NCBI.6.0_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mfascicularis.ncbi.6.0/bioconductor-bsgenome.mfascicularis.ncbi.6.0_1.5.0_src_all.tar.gz"], "md5": "67272a96950f485d3c0770265f59c85c", "fn": "BSgenome.Mfascicularis.NCBI.6.0_1.5.0.tar.gz"}, "bsgenome.mfuro.ucsc.musfur1-1.4.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Mfuro.UCSC.musFur1_1.4.1.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mfuro.UCSC.musFur1_1.4.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mfuro.ucsc.musfur1/bioconductor-bsgenome.mfuro.ucsc.musfur1_1.4.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mfuro.ucsc.musfur1/bioconductor-bsgenome.mfuro.ucsc.musfur1_1.4.1_src_all.tar.gz"], "md5": "c33e71746ce551bcbcd22be1979aee63", "fn": "BSgenome.Mfuro.UCSC.musFur1_1.4.1.tar.gz"}, "bsgenome.mmulatta.ucsc.rhemac10-1.4.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac10_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac10_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac10/bioconductor-bsgenome.mmulatta.ucsc.rhemac10_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac10/bioconductor-bsgenome.mmulatta.ucsc.rhemac10_1.4.2_src_all.tar.gz"], "md5": "2f2afe40d5dcf8d8620aa5e12e311fbc", "fn": "BSgenome.Mmulatta.UCSC.rheMac10_1.4.2.tar.gz"}, "bsgenome.mmulatta.ucsc.rhemac2-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac2_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac2_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/bioconductor-bsgenome.mmulatta.ucsc.rhemac2_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/bioconductor-bsgenome.mmulatta.ucsc.rhemac2_1.4.0_src_all.tar.gz"], "md5": "90c43e127e76dfd7cea90de9e1af9a50", "fn": "BSgenome.Mmulatta.UCSC.rheMac2_1.4.0.tar.gz"}, "bsgenome.mmulatta.ucsc.rhemac2.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac2.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac2.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked_1.3.99_src_all.tar.gz"], "md5": "7602d86b68df7e4c8d336fede4090a62", "fn": "BSgenome.Mmulatta.UCSC.rheMac2.masked_1.3.99.tar.gz"}, "bsgenome.mmulatta.ucsc.rhemac3-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac3_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac3_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/bioconductor-bsgenome.mmulatta.ucsc.rhemac3_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/bioconductor-bsgenome.mmulatta.ucsc.rhemac3_1.4.0_src_all.tar.gz"], "md5": "dfa1ecb9d0bb7a5d9fa628092fb1c354", "fn": "BSgenome.Mmulatta.UCSC.rheMac3_1.4.0.tar.gz"}, "bsgenome.mmulatta.ucsc.rhemac3.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac3.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac3.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked_1.3.99_src_all.tar.gz"], "md5": "94f8714865655d3144e14f6fc5c24e76", "fn": "BSgenome.Mmulatta.UCSC.rheMac3.masked_1.3.99.tar.gz"}, "bsgenome.mmulatta.ucsc.rhemac8-1.4.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac8_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac8_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/bioconductor-bsgenome.mmulatta.ucsc.rhemac8_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/bioconductor-bsgenome.mmulatta.ucsc.rhemac8_1.4.2_src_all.tar.gz"], "md5": "e9ad1f70f652c62554e2c5af7638c015", "fn": "BSgenome.Mmulatta.UCSC.rheMac8_1.4.2.tar.gz"}, "bsgenome.mmusculus.ucsc.mm10-1.4.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm10_1.4.3.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm10_1.4.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm10/bioconductor-bsgenome.mmusculus.ucsc.mm10_1.4.3_src_all.tar.gz"], "md5": "ffddc2e035527ed1a1e201ac4cc0b1f3", "fn": "BSgenome.Mmusculus.UCSC.mm10_1.4.3.tar.gz"}, "bsgenome.mmusculus.ucsc.mm10.masked-1.4.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm10.masked_1.4.3.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm10.masked_1.4.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked_1.4.3_src_all.tar.gz"], "md5": "40d51fb428a5fda8c05101a3dddb8957", "fn": "BSgenome.Mmusculus.UCSC.mm10.masked_1.4.3.tar.gz"}, "bsgenome.mmusculus.ucsc.mm39-1.4.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm39_1.4.3.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm39_1.4.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm39/bioconductor-bsgenome.mmusculus.ucsc.mm39_1.4.3_src_all.tar.gz"], "md5": "a130ef50dd55da9fd341e6c90b22637b", "fn": "BSgenome.Mmusculus.UCSC.mm39_1.4.3.tar.gz"}, "bsgenome.mmusculus.ucsc.mm8-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm8_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm8_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm8/bioconductor-bsgenome.mmusculus.ucsc.mm8_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm8/bioconductor-bsgenome.mmusculus.ucsc.mm8_1.4.0_src_all.tar.gz"], "md5": "f6aa91cdce2607f30a34f6dd0d678aff", "fn": "BSgenome.Mmusculus.UCSC.mm8_1.4.0.tar.gz"}, "bsgenome.mmusculus.ucsc.mm8.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm8.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm8.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked_1.3.99_src_all.tar.gz"], "md5": "5809f925e0fe7c4b73b78a90c9a36fdd", "fn": "BSgenome.Mmusculus.UCSC.mm8.masked_1.3.99.tar.gz"}, "bsgenome.mmusculus.ucsc.mm9-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm9/bioconductor-bsgenome.mmusculus.ucsc.mm9_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm9/bioconductor-bsgenome.mmusculus.ucsc.mm9_1.4.0_src_all.tar.gz"], "md5": "5a30ba2b4481a17e8e6979eb69eabf78", "fn": "BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz"}, "bsgenome.mmusculus.ucsc.mm9.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm9.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm9.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked_1.3.99_src_all.tar.gz"], "md5": "a5dadab14e55cdfc39649ede7a8483d5", "fn": "BSgenome.Mmusculus.UCSC.mm9.masked_1.3.99.tar.gz"}, "bsgenome.osativa.msu.msu7-0.99.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Osativa.MSU.MSU7_0.99.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Osativa.MSU.MSU7_0.99.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.osativa.msu.msu7/bioconductor-bsgenome.osativa.msu.msu7_0.99.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.osativa.msu.msu7/bioconductor-bsgenome.osativa.msu.msu7_0.99.2_src_all.tar.gz"], "md5": "80648058756a2f74aa5a246d38ecf576", "fn": "BSgenome.Osativa.MSU.MSU7_0.99.2.tar.gz"}, "bsgenome.ppaniscus.ucsc.panpan1-1.4.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Ppaniscus.UCSC.panPan1_1.4.3.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ppaniscus.UCSC.panPan1_1.4.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ppaniscus.ucsc.panpan1/bioconductor-bsgenome.ppaniscus.ucsc.panpan1_1.4.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ppaniscus.ucsc.panpan1/bioconductor-bsgenome.ppaniscus.ucsc.panpan1_1.4.3_src_all.tar.gz"], "md5": "186adb59264d468d17c0f6374e2eb1f6", "fn": "BSgenome.Ppaniscus.UCSC.panPan1_1.4.3.tar.gz"}, "bsgenome.ppaniscus.ucsc.panpan2-1.4.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Ppaniscus.UCSC.panPan2_1.4.3.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ppaniscus.UCSC.panPan2_1.4.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ppaniscus.ucsc.panpan2/bioconductor-bsgenome.ppaniscus.ucsc.panpan2_1.4.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ppaniscus.ucsc.panpan2/bioconductor-bsgenome.ppaniscus.ucsc.panpan2_1.4.3_src_all.tar.gz"], "md5": "74973376a6377d6820d6cd7fb3655a19", "fn": "BSgenome.Ppaniscus.UCSC.panPan2_1.4.3.tar.gz"}, "bsgenome.ptroglodytes.ucsc.pantro2-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro2_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro2_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2_1.4.0_src_all.tar.gz"], "md5": "780200c315779ac75fcf0bdeb9a2eb8c", "fn": "BSgenome.Ptroglodytes.UCSC.panTro2_1.4.0.tar.gz"}, "bsgenome.ptroglodytes.ucsc.pantro2.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro2.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro2.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked_1.3.99_src_all.tar.gz"], "md5": "e6d069be23712b483b4e4c71554594cf", "fn": "BSgenome.Ptroglodytes.UCSC.panTro2.masked_1.3.99.tar.gz"}, "bsgenome.ptroglodytes.ucsc.pantro3-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro3_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro3_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3_1.4.0_src_all.tar.gz"], "md5": "4677c75befd60742f3fc2a54c7f60666", "fn": "BSgenome.Ptroglodytes.UCSC.panTro3_1.4.0.tar.gz"}, "bsgenome.ptroglodytes.ucsc.pantro3.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro3.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro3.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked_1.3.99_src_all.tar.gz"], "md5": "89e96b3796d3b8e8793146597506e3f5", "fn": "BSgenome.Ptroglodytes.UCSC.panTro3.masked_1.3.99.tar.gz"}, "bsgenome.ptroglodytes.ucsc.pantro5-1.4.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro5_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro5_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5_1.4.2_src_all.tar.gz"], "md5": "5b88573dd9c3ef838699b65934f8abe3", "fn": "BSgenome.Ptroglodytes.UCSC.panTro5_1.4.2.tar.gz"}, "bsgenome.ptroglodytes.ucsc.pantro6-1.4.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro6_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro6_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6_1.4.2_src_all.tar.gz"], "md5": "1df05d985374e9edc1dd7c3df5118338", "fn": "BSgenome.Ptroglodytes.UCSC.panTro6_1.4.2.tar.gz"}, "bsgenome.rnorvegicus.ucsc.rn4-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn4_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn4_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/bioconductor-bsgenome.rnorvegicus.ucsc.rn4_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/bioconductor-bsgenome.rnorvegicus.ucsc.rn4_1.4.0_src_all.tar.gz"], "md5": "3afe6729237781445d99ec38228ee1a8", "fn": "BSgenome.Rnorvegicus.UCSC.rn4_1.4.0.tar.gz"}, "bsgenome.rnorvegicus.ucsc.rn4.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn4.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn4.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked_1.3.99_src_all.tar.gz"], "md5": "7e2ea7df588b6b10515e07ea3868c568", "fn": "BSgenome.Rnorvegicus.UCSC.rn4.masked_1.3.99.tar.gz"}, "bsgenome.rnorvegicus.ucsc.rn5-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn5_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn5_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/bioconductor-bsgenome.rnorvegicus.ucsc.rn5_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/bioconductor-bsgenome.rnorvegicus.ucsc.rn5_1.4.0_src_all.tar.gz"], "md5": "723b1f3ced395ef638b2d68053b05c86", "fn": "BSgenome.Rnorvegicus.UCSC.rn5_1.4.0.tar.gz"}, "bsgenome.rnorvegicus.ucsc.rn5.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn5.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn5.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked_1.3.99_src_all.tar.gz"], "md5": "663233774b79012cb2cc08224ac275ed", "fn": "BSgenome.Rnorvegicus.UCSC.rn5.masked_1.3.99.tar.gz"}, "bsgenome.rnorvegicus.ucsc.rn6-1.4.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn6_1.4.1.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn6_1.4.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/bioconductor-bsgenome.rnorvegicus.ucsc.rn6_1.4.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/bioconductor-bsgenome.rnorvegicus.ucsc.rn6_1.4.1_src_all.tar.gz"], "md5": "60d3fb201e0b1475912aaf681927096d", "fn": "BSgenome.Rnorvegicus.UCSC.rn6_1.4.1.tar.gz"}, "bsgenome.rnorvegicus.ucsc.rn7-1.4.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn7_1.4.3.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn7_1.4.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn7/bioconductor-bsgenome.rnorvegicus.ucsc.rn7_1.4.3_src_all.tar.gz"], "md5": "c64f7dd9e30ff88ce02ecd3712e4c454", "fn": "BSgenome.Rnorvegicus.UCSC.rn7_1.4.3.tar.gz"}, "bsgenome.scerevisiae.ucsc.saccer1-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer1_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Scerevisiae.UCSC.sacCer1_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/bioconductor-bsgenome.scerevisiae.ucsc.saccer1_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/bioconductor-bsgenome.scerevisiae.ucsc.saccer1_1.4.0_src_all.tar.gz"], "md5": "ad4c29c16a9635088bf13872b4a02ed4", "fn": "BSgenome.Scerevisiae.UCSC.sacCer1_1.4.0.tar.gz"}, "bsgenome.scerevisiae.ucsc.saccer2-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer2_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Scerevisiae.UCSC.sacCer2_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/bioconductor-bsgenome.scerevisiae.ucsc.saccer2_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/bioconductor-bsgenome.scerevisiae.ucsc.saccer2_1.4.0_src_all.tar.gz"], "md5": "f1025b4d0fa7891dc46301550163753e", "fn": "BSgenome.Scerevisiae.UCSC.sacCer2_1.4.0.tar.gz"}, "bsgenome.scerevisiae.ucsc.saccer3-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer3_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Scerevisiae.UCSC.sacCer3_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/bioconductor-bsgenome.scerevisiae.ucsc.saccer3_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/bioconductor-bsgenome.scerevisiae.ucsc.saccer3_1.4.0_src_all.tar.gz"], "md5": "7f2d8bba69c3dcebf426d9b19a6bed30", "fn": "BSgenome.Scerevisiae.UCSC.sacCer3_1.4.0.tar.gz"}, "bsgenome.sscrofa.ucsc.susscr11-1.4.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Sscrofa.UCSC.susScr11_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Sscrofa.UCSC.susScr11_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr11/bioconductor-bsgenome.sscrofa.ucsc.susscr11_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr11/bioconductor-bsgenome.sscrofa.ucsc.susscr11_1.4.2_src_all.tar.gz"], "md5": "db22832229e31e1a629d107df522dff9", "fn": "BSgenome.Sscrofa.UCSC.susScr11_1.4.2.tar.gz"}, "bsgenome.sscrofa.ucsc.susscr3-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Sscrofa.UCSC.susScr3_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Sscrofa.UCSC.susScr3_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr3/bioconductor-bsgenome.sscrofa.ucsc.susscr3_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr3/bioconductor-bsgenome.sscrofa.ucsc.susscr3_1.4.0_src_all.tar.gz"], "md5": "0457ca52a81c9d7ceadad5830169e6cf", "fn": "BSgenome.Sscrofa.UCSC.susScr3_1.4.0.tar.gz"}, "bsgenome.sscrofa.ucsc.susscr3.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Sscrofa.UCSC.susScr3.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Sscrofa.UCSC.susScr3.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked_1.3.99_src_all.tar.gz"], "md5": "fd240651d22d169fd1e27a2b66e40dd7", "fn": "BSgenome.Sscrofa.UCSC.susScr3.masked_1.3.99.tar.gz"}, "bsgenome.tgondii.toxodb.7.0-0.99.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Tgondii.ToxoDB.7.0_0.99.1.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Tgondii.ToxoDB.7.0_0.99.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tgondii.toxodb.7.0/bioconductor-bsgenome.tgondii.toxodb.7.0_0.99.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tgondii.toxodb.7.0/bioconductor-bsgenome.tgondii.toxodb.7.0_0.99.1_src_all.tar.gz"], "md5": "f67644d1a897fe2ff4139832d4ceaf80", "fn": "BSgenome.Tgondii.ToxoDB.7.0_0.99.1.tar.gz"}, "bsgenome.tguttata.ucsc.taegut1-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Tguttata.UCSC.taeGut1_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Tguttata.UCSC.taeGut1_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut1/bioconductor-bsgenome.tguttata.ucsc.taegut1_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut1/bioconductor-bsgenome.tguttata.ucsc.taegut1_1.4.0_src_all.tar.gz"], "md5": "9753d9568d2a866a627673a518a1dd8a", "fn": "BSgenome.Tguttata.UCSC.taeGut1_1.4.0.tar.gz"}, "bsgenome.tguttata.ucsc.taegut1.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Tguttata.UCSC.taeGut1.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Tguttata.UCSC.taeGut1.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked_1.3.99_src_all.tar.gz"], "md5": "63684abb5b330bb54ff89fe78f2e6444", "fn": "BSgenome.Tguttata.UCSC.taeGut1.masked_1.3.99.tar.gz"}, "bsgenome.tguttata.ucsc.taegut2-1.4.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Tguttata.UCSC.taeGut2_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Tguttata.UCSC.taeGut2_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut2/bioconductor-bsgenome.tguttata.ucsc.taegut2_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut2/bioconductor-bsgenome.tguttata.ucsc.taegut2_1.4.2_src_all.tar.gz"], "md5": "1d39678fb060e643f7e9c4ec25e828c0", "fn": "BSgenome.Tguttata.UCSC.taeGut2_1.4.2.tar.gz"}, "bsgenome.vvinifera.urgi.iggp12xv0-0.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Vvinifera.URGI.IGGP12Xv0_0.1.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Vvinifera.URGI.IGGP12Xv0_0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0_0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0_0.1_src_all.tar.gz"], "md5": "3f791de6d699325a97080cd98be86d89", "fn": "BSgenome.Vvinifera.URGI.IGGP12Xv0_0.1.tar.gz"}, "bsgenome.vvinifera.urgi.iggp12xv2-0.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Vvinifera.URGI.IGGP12Xv2_0.1.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Vvinifera.URGI.IGGP12Xv2_0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2_0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2_0.1_src_all.tar.gz"], "md5": "95472e574ab46327c19e241c381b26a2", "fn": "BSgenome.Vvinifera.URGI.IGGP12Xv2_0.1.tar.gz"}, "bsgenome.vvinifera.urgi.iggp8x-0.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Vvinifera.URGI.IGGP8X_0.1.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Vvinifera.URGI.IGGP8X_0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp8x/bioconductor-bsgenome.vvinifera.urgi.iggp8x_0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp8x/bioconductor-bsgenome.vvinifera.urgi.iggp8x_0.1_src_all.tar.gz"], "md5": "fccaf60e5c9352b9c454f7a8ecac2a20", "fn": "BSgenome.Vvinifera.URGI.IGGP8X_0.1.tar.gz"}, "bsubtiliscdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/bsubtiliscdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/bsubtiliscdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsubtiliscdf/bioconductor-bsubtiliscdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsubtiliscdf/bioconductor-bsubtiliscdf_2.18.0_src_all.tar.gz"], "md5": "7d7893d28c601206805819ae0e49b31b", "fn": "bsubtiliscdf_2.18.0.tar.gz"}, "bsubtilisprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/bsubtilisprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/bsubtilisprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsubtilisprobe/bioconductor-bsubtilisprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsubtilisprobe/bioconductor-bsubtilisprobe_2.18.0_src_all.tar.gz"], "md5": "83568fcea2122350b7ce982e79b7ec53", "fn": "bsubtilisprobe_2.18.0.tar.gz"}, "canine.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/canine.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/canine.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canine.db/bioconductor-canine.db_3.13.0_src_all.tar.gz"], "md5": "a876bb01eda62604a32a96b46e34162b", "fn": "canine.db_3.13.0.tar.gz"}, "canine.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/canine.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/canine.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canine.db0/bioconductor-canine.db0_3.16.0_src_all.tar.gz"], "md5": "99dd5f98cd9934998d081429f2b7cd36", "fn": "canine.db0_3.16.0.tar.gz"}, "canine2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/canine2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/canine2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canine2.db/bioconductor-canine2.db_3.13.0_src_all.tar.gz"], "md5": "24727f27cdf1e324f097a76db81dfc1d", "fn": "canine2.db_3.13.0.tar.gz"}, "canine2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/canine2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/canine2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canine2cdf/bioconductor-canine2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canine2cdf/bioconductor-canine2cdf_2.18.0_src_all.tar.gz"], "md5": "78740cde98c75e6680470564a4df74c3", "fn": "canine2cdf_2.18.0.tar.gz"}, "canine2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/canine2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/canine2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canine2probe/bioconductor-canine2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canine2probe/bioconductor-canine2probe_2.18.0_src_all.tar.gz"], "md5": "7de0f4ea616e8662dc2eaa9ab78d1f13", "fn": "canine2probe_2.18.0.tar.gz"}, "caninecdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/caninecdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/caninecdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-caninecdf/bioconductor-caninecdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-caninecdf/bioconductor-caninecdf_2.18.0_src_all.tar.gz"], "md5": "656f845cc66890015a4e13c5304ec262", "fn": "caninecdf_2.18.0.tar.gz"}, "canineprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/canineprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/canineprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canineprobe/bioconductor-canineprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canineprobe/bioconductor-canineprobe_2.18.0_src_all.tar.gz"], "md5": "e5467bc9b7e54c5adce6b409ba7df767", "fn": "canineprobe_2.18.0.tar.gz"}, "celegans.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/celegans.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/celegans.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celegans.db/bioconductor-celegans.db_3.13.0_src_all.tar.gz"], "md5": "3cfa9df5a81ef538a890ed8c5d5a98ad", "fn": "celegans.db_3.13.0.tar.gz"}, "celeganscdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/celeganscdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/celeganscdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celeganscdf/bioconductor-celeganscdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celeganscdf/bioconductor-celeganscdf_2.18.0_src_all.tar.gz"], "md5": "1098cd99bfc5000bf9858e4a3acaf452", "fn": "celeganscdf_2.18.0.tar.gz"}, "celegansprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/celegansprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/celegansprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celegansprobe/bioconductor-celegansprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celegansprobe/bioconductor-celegansprobe_2.18.0_src_all.tar.gz"], "md5": "7454bba10ff2dd7c03bfe0f9d450f148", "fn": "celegansprobe_2.18.0.tar.gz"}, "chemminedrugs-1.0.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ChemmineDrugs_1.0.2.tar.gz", "https://bioarchive.galaxyproject.org/ChemmineDrugs_1.0.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chemminedrugs/bioconductor-chemminedrugs_1.0.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chemminedrugs/bioconductor-chemminedrugs_1.0.2_src_all.tar.gz"], "md5": "2a3646e5173e93080fb5b49564f5d545", "fn": "ChemmineDrugs_1.0.2.tar.gz"}, "chicken.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/chicken.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/chicken.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chicken.db/bioconductor-chicken.db_3.13.0_src_all.tar.gz"], "md5": "512f887df339529d4883aad3f3eb6fb8", "fn": "chicken.db_3.13.0.tar.gz"}, "chicken.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/chicken.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/chicken.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chicken.db0/bioconductor-chicken.db0_3.16.0_src_all.tar.gz"], "md5": "63bc178c74709f98b0ba049f9a04b64c", "fn": "chicken.db0_3.16.0.tar.gz"}, "chickencdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/chickencdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/chickencdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chickencdf/bioconductor-chickencdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chickencdf/bioconductor-chickencdf_2.18.0_src_all.tar.gz"], "md5": "ab0097b4b7b6c4d94360feb84ab69972", "fn": "chickencdf_2.18.0.tar.gz"}, "chickenprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/chickenprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/chickenprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chickenprobe/bioconductor-chickenprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chickenprobe/bioconductor-chickenprobe_2.18.0_src_all.tar.gz"], "md5": "b33599081ce1ba768ff7992e143c01d0", "fn": "chickenprobe_2.18.0.tar.gz"}, "chimp.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/chimp.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/chimp.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chimp.db0/bioconductor-chimp.db0_3.16.0_src_all.tar.gz"], "md5": "6a221371b811f791fe332a194b47cfac", "fn": "chimp.db0_3.16.0.tar.gz"}, "chromhmmdata-0.99.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/chromhmmData_0.99.2.tar.gz", "https://bioarchive.galaxyproject.org/chromhmmData_0.99.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chromhmmdata/bioconductor-chromhmmdata_0.99.2_src_all.tar.gz"], "md5": "eec85c20139b3d826f00264c7b28207c", "fn": "chromhmmData_0.99.2.tar.gz"}, "citruscdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/citruscdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/citruscdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-citruscdf/bioconductor-citruscdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-citruscdf/bioconductor-citruscdf_2.18.0_src_all.tar.gz"], "md5": "4af821a0c1ae1adf42b7dc5ce7458593", "fn": "citruscdf_2.18.0.tar.gz"}, "citrusprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/citrusprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/citrusprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-citrusprobe/bioconductor-citrusprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-citrusprobe/bioconductor-citrusprobe_2.18.0_src_all.tar.gz"], "md5": "259b114f96d5307c447d000bd27a7d15", "fn": "citrusprobe_2.18.0.tar.gz"}, "clariomdhumanprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/clariomdhumanprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/clariomdhumanprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clariomdhumanprobeset.db/bioconductor-clariomdhumanprobeset.db_8.8.0_src_all.tar.gz"], "md5": "01cb1a5cc4674750b6ce5988cd62fad3", "fn": "clariomdhumanprobeset.db_8.8.0.tar.gz"}, "clariomdhumantranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/clariomdhumantranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/clariomdhumantranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clariomdhumantranscriptcluster.db/bioconductor-clariomdhumantranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "80739a70d77ab785231a9367938035a8", "fn": "clariomdhumantranscriptcluster.db_8.8.0.tar.gz"}, "clariomshumanhttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/clariomshumanhttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/clariomshumanhttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clariomshumanhttranscriptcluster.db/bioconductor-clariomshumanhttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "6a5e8e1f9768694be99277aafcc0a69a", "fn": "clariomshumanhttranscriptcluster.db_8.8.0.tar.gz"}, "clariomshumantranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/clariomshumantranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/clariomshumantranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clariomshumantranscriptcluster.db/bioconductor-clariomshumantranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "309b29e044e1227da6d4825bbdf04b76", "fn": "clariomshumantranscriptcluster.db_8.8.0.tar.gz"}, "clariomsmousehttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/clariomsmousehttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/clariomsmousehttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clariomsmousehttranscriptcluster.db/bioconductor-clariomsmousehttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "c0aa96cbd5ee7e19296dde5a72232d17", "fn": "clariomsmousehttranscriptcluster.db_8.8.0.tar.gz"}, "clariomsmousetranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/clariomsmousetranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/clariomsmousetranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clariomsmousetranscriptcluster.db/bioconductor-clariomsmousetranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "76d0e2204dcbd5d85d8e53d43710aac5", "fn": "clariomsmousetranscriptcluster.db_8.8.0.tar.gz"}, "clariomsrathttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/clariomsrathttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/clariomsrathttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clariomsrathttranscriptcluster.db/bioconductor-clariomsrathttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "e7c71721f8201bfd1553a98cfbf47458", "fn": "clariomsrathttranscriptcluster.db_8.8.0.tar.gz"}, "clariomsrattranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/clariomsrattranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/clariomsrattranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clariomsrattranscriptcluster.db/bioconductor-clariomsrattranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "72923a3a90f2df27a361b1730cfc0d00", "fn": "clariomsrattranscriptcluster.db_8.8.0.tar.gz"}, "cmap-1.15.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/cMAP_1.15.1.tar.gz", "https://bioarchive.galaxyproject.org/cMAP_1.15.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cmap/bioconductor-cmap_1.15.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cmap/bioconductor-cmap_1.15.1_src_all.tar.gz"], "md5": "dbf8df4d4540151936884e1c5d747bcf", "fn": "cMAP_1.15.1.tar.gz"}, "cottoncdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/cottoncdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/cottoncdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cottoncdf/bioconductor-cottoncdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cottoncdf/bioconductor-cottoncdf_2.18.0_src_all.tar.gz"], "md5": "b9d2a4b43235c6e531b78cca006e84b2", "fn": "cottoncdf_2.18.0.tar.gz"}, "cottonprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/cottonprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/cottonprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cottonprobe/bioconductor-cottonprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cottonprobe/bioconductor-cottonprobe_2.18.0_src_all.tar.gz"], "md5": "032fa94876685820d94526fd56dd0b65", "fn": "cottonprobe_2.18.0.tar.gz"}, "ctcf-0.99.9": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/CTCF_0.99.9.tar.gz", "https://bioarchive.galaxyproject.org/CTCF_0.99.9.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ctcf/bioconductor-ctcf_0.99.9_src_all.tar.gz"], "md5": "c5449543be4c56393d737bbe07c6255c", "fn": "CTCF_0.99.9.tar.gz"}, "cyp450cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/cyp450cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/cyp450cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cyp450cdf/bioconductor-cyp450cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cyp450cdf/bioconductor-cyp450cdf_2.18.0_src_all.tar.gz"], "md5": "7923c4d24b7b654d0f59d52ed2258eb9", "fn": "cyp450cdf_2.18.0.tar.gz"}, "do.db-2.9": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/DO.db_2.9.tar.gz", "https://bioarchive.galaxyproject.org/DO.db_2.9.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-do.db/bioconductor-do.db_2.9_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-do.db/bioconductor-do.db_2.9_src_all.tar.gz"], "md5": "63dda6d46d2fe40c52a2e79260a7fb9d", "fn": "DO.db_2.9.tar.gz"}, "drosgenome1.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/drosgenome1.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/drosgenome1.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosgenome1.db/bioconductor-drosgenome1.db_3.13.0_src_all.tar.gz"], "md5": "6432e2ae22cf58524278a559097bdf3a", "fn": "drosgenome1.db_3.13.0.tar.gz"}, "drosgenome1cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/drosgenome1cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/drosgenome1cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosgenome1cdf/bioconductor-drosgenome1cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosgenome1cdf/bioconductor-drosgenome1cdf_2.18.0_src_all.tar.gz"], "md5": "e12983f2148c10ef1faa50f810b6eee3", "fn": "drosgenome1cdf_2.18.0.tar.gz"}, "drosgenome1probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/drosgenome1probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/drosgenome1probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosgenome1probe/bioconductor-drosgenome1probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosgenome1probe/bioconductor-drosgenome1probe_2.18.0_src_all.tar.gz"], "md5": "1f12abdfeee65e8a6554f57507d86fb3", "fn": "drosgenome1probe_2.18.0.tar.gz"}, "drosophila2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/drosophila2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/drosophila2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosophila2.db/bioconductor-drosophila2.db_3.13.0_src_all.tar.gz"], "md5": "c01d0d1b5e17c3b36ad801b44da72b96", "fn": "drosophila2.db_3.13.0.tar.gz"}, "drosophila2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/drosophila2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/drosophila2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosophila2cdf/bioconductor-drosophila2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosophila2cdf/bioconductor-drosophila2cdf_2.18.0_src_all.tar.gz"], "md5": "3323e723c133ff2b6188e22bebf3e20a", "fn": "drosophila2cdf_2.18.0.tar.gz"}, "drosophila2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/drosophila2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/drosophila2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosophila2probe/bioconductor-drosophila2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosophila2probe/bioconductor-drosophila2probe_2.18.0_src_all.tar.gz"], "md5": "ba0251902ea0a5f0db61105bdcdc3530", "fn": "drosophila2probe_2.18.0.tar.gz"}, "ecoli2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ecoli2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoli2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoli2.db/bioconductor-ecoli2.db_3.13.0_src_all.tar.gz"], "md5": "110d6549b1d105fdff31ab8f45b08d65", "fn": "ecoli2.db_3.13.0.tar.gz"}, "ecoli2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ecoli2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoli2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoli2cdf/bioconductor-ecoli2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoli2cdf/bioconductor-ecoli2cdf_2.18.0_src_all.tar.gz"], "md5": "b5cd1f05322ce494132ff649de9806c6", "fn": "ecoli2cdf_2.18.0.tar.gz"}, "ecoli2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ecoli2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoli2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoli2probe/bioconductor-ecoli2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoli2probe/bioconductor-ecoli2probe_2.18.0_src_all.tar.gz"], "md5": "061fcb782ee9da3aa5108881677a4531", "fn": "ecoli2probe_2.18.0.tar.gz"}, "ecoliasv2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ecoliasv2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliasv2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoliasv2cdf/bioconductor-ecoliasv2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoliasv2cdf/bioconductor-ecoliasv2cdf_2.18.0_src_all.tar.gz"], "md5": "d7771ca1648b26a6af5bfb7582c6c778", "fn": "ecoliasv2cdf_2.18.0.tar.gz"}, "ecoliasv2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ecoliasv2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliasv2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoliasv2probe/bioconductor-ecoliasv2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoliasv2probe/bioconductor-ecoliasv2probe_2.18.0_src_all.tar.gz"], "md5": "b3e4332266184576279c3a478f286dc9", "fn": "ecoliasv2probe_2.18.0.tar.gz"}, "ecolicdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ecolicdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ecolicdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolicdf/bioconductor-ecolicdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolicdf/bioconductor-ecolicdf_2.18.0_src_all.tar.gz"], "md5": "4e664c1ac41a8ab68ef22f8a889b916c", "fn": "ecolicdf_2.18.0.tar.gz"}, "ecolik12.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/ecoliK12.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliK12.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolik12.db0/bioconductor-ecolik12.db0_3.16.0_src_all.tar.gz"], "md5": "b1fe10d0e57b1deaba86a553dd064583", "fn": "ecoliK12.db0_3.16.0.tar.gz"}, "ecoliprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ecoliprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoliprobe/bioconductor-ecoliprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoliprobe/bioconductor-ecoliprobe_2.18.0_src_all.tar.gz"], "md5": "09586f9907bdbc43ba5ea4ce07c1f756", "fn": "ecoliprobe_2.18.0.tar.gz"}, "ecolisakai.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/ecoliSakai.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliSakai.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolisakai.db0/bioconductor-ecolisakai.db0_3.16.0_src_all.tar.gz"], "md5": "5bb85fbeb56ce79f0cb62a2e89d5bff7", "fn": "ecoliSakai.db0_3.16.0.tar.gz"}, "encodexplorerdata-0.99.5": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ENCODExplorerData_0.99.5.tar.gz", "https://bioarchive.galaxyproject.org/ENCODExplorerData_0.99.5.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-encodexplorerdata/bioconductor-encodexplorerdata_0.99.5_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-encodexplorerdata/bioconductor-encodexplorerdata_0.99.5_src_all.tar.gz"], "md5": "c6d9b491548529db0739b79c98adacd7", "fn": "ENCODExplorerData_0.99.5.tar.gz"}, "ensdb.hsapiens.v75-2.99.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/EnsDb.Hsapiens.v75_2.99.0.tar.gz", "https://bioarchive.galaxyproject.org/EnsDb.Hsapiens.v75_2.99.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v75/bioconductor-ensdb.hsapiens.v75_2.99.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v75/bioconductor-ensdb.hsapiens.v75_2.99.0_src_all.tar.gz"], "md5": "6c896475252903972bfc6c0eb0d8f334", "fn": "EnsDb.Hsapiens.v75_2.99.0.tar.gz"}, "ensdb.hsapiens.v79-2.99.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/EnsDb.Hsapiens.v79_2.99.0.tar.gz", "https://bioarchive.galaxyproject.org/EnsDb.Hsapiens.v79_2.99.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v79/bioconductor-ensdb.hsapiens.v79_2.99.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v79/bioconductor-ensdb.hsapiens.v79_2.99.0_src_all.tar.gz"], "md5": "16b5629805c07649b2aa501d34fcc588", "fn": "EnsDb.Hsapiens.v79_2.99.0.tar.gz"}, "ensdb.hsapiens.v86-2.99.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/EnsDb.Hsapiens.v86_2.99.0.tar.gz", "https://bioarchive.galaxyproject.org/EnsDb.Hsapiens.v86_2.99.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v86/bioconductor-ensdb.hsapiens.v86_2.99.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v86/bioconductor-ensdb.hsapiens.v86_2.99.0_src_all.tar.gz"], "md5": "0c9e52512ff6dbbbdb754c4d41149939", "fn": "EnsDb.Hsapiens.v86_2.99.0.tar.gz"}, "ensdb.mmusculus.v75-2.99.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/EnsDb.Mmusculus.v75_2.99.0.tar.gz", "https://bioarchive.galaxyproject.org/EnsDb.Mmusculus.v75_2.99.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.mmusculus.v75/bioconductor-ensdb.mmusculus.v75_2.99.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.mmusculus.v75/bioconductor-ensdb.mmusculus.v75_2.99.0_src_all.tar.gz"], "md5": "081bf6f90ff77031b634b4fe32e00be8", "fn": "EnsDb.Mmusculus.v75_2.99.0.tar.gz"}, "ensdb.mmusculus.v79-2.99.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/EnsDb.Mmusculus.v79_2.99.0.tar.gz", "https://bioarchive.galaxyproject.org/EnsDb.Mmusculus.v79_2.99.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.mmusculus.v79/bioconductor-ensdb.mmusculus.v79_2.99.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.mmusculus.v79/bioconductor-ensdb.mmusculus.v79_2.99.0_src_all.tar.gz"], "md5": "28bbab743b0d2d550dbfa0bcd3274fad", "fn": "EnsDb.Mmusculus.v79_2.99.0.tar.gz"}, "ensdb.rnorvegicus.v75-2.99.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/EnsDb.Rnorvegicus.v75_2.99.0.tar.gz", "https://bioarchive.galaxyproject.org/EnsDb.Rnorvegicus.v75_2.99.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.rnorvegicus.v75/bioconductor-ensdb.rnorvegicus.v75_2.99.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.rnorvegicus.v75/bioconductor-ensdb.rnorvegicus.v75_2.99.0_src_all.tar.gz"], "md5": "40ff53b41aa6fad0d5bd15f9c6f3bad8", "fn": "EnsDb.Rnorvegicus.v75_2.99.0.tar.gz"}, "ensdb.rnorvegicus.v79-2.99.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/EnsDb.Rnorvegicus.v79_2.99.0.tar.gz", "https://bioarchive.galaxyproject.org/EnsDb.Rnorvegicus.v79_2.99.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.rnorvegicus.v79/bioconductor-ensdb.rnorvegicus.v79_2.99.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.rnorvegicus.v79/bioconductor-ensdb.rnorvegicus.v79_2.99.0_src_all.tar.gz"], "md5": "7d305bd0d1a073bd8c60063ae210a7a9", "fn": "EnsDb.Rnorvegicus.v79_2.99.0.tar.gz"}, "epitxdb.hs.hg38-0.99.7": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/EpiTxDb.Hs.hg38_0.99.7.tar.gz", "https://bioarchive.galaxyproject.org/EpiTxDb.Hs.hg38_0.99.7.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epitxdb.hs.hg38/bioconductor-epitxdb.hs.hg38_0.99.7_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epitxdb.hs.hg38/bioconductor-epitxdb.hs.hg38_0.99.7_src_all.tar.gz"], "md5": "e30af95f285788a9777a8207a8ef73a9", "fn": "EpiTxDb.Hs.hg38_0.99.7.tar.gz"}, "epitxdb.mm.mm10-0.99.6": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/EpiTxDb.Mm.mm10_0.99.6.tar.gz", "https://bioarchive.galaxyproject.org/EpiTxDb.Mm.mm10_0.99.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epitxdb.mm.mm10/bioconductor-epitxdb.mm.mm10_0.99.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epitxdb.mm.mm10/bioconductor-epitxdb.mm.mm10_0.99.6_src_all.tar.gz"], "md5": "518e4967f7f038e3cbf2865b74dc4f1b", "fn": "EpiTxDb.Mm.mm10_0.99.6.tar.gz"}, "epitxdb.sc.saccer3-0.99.5": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/EpiTxDb.Sc.sacCer3_0.99.5.tar.gz", "https://bioarchive.galaxyproject.org/EpiTxDb.Sc.sacCer3_0.99.5.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epitxdb.sc.saccer3/bioconductor-epitxdb.sc.saccer3_0.99.5_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epitxdb.sc.saccer3/bioconductor-epitxdb.sc.saccer3_0.99.5_src_all.tar.gz"], "md5": "6d9e5f37e5dcb60e890d99d80fddda00", "fn": "EpiTxDb.Sc.sacCer3_0.99.5.tar.gz"}, "eupathdb-1.0.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/EuPathDB_1.0.1.tar.gz", "https://bioarchive.galaxyproject.org/EuPathDB_1.0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-eupathdb/bioconductor-eupathdb_1.0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-eupathdb/bioconductor-eupathdb_1.0.1_src_all.tar.gz"], "md5": "1451c3ab6c224d9a4cfbdf27dc5c2680", "fn": "EuPathDB_1.0.1.tar.gz"}, "excluderanges-0.99.6": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/excluderanges_0.99.6.tar.gz", "https://bioarchive.galaxyproject.org/excluderanges_0.99.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-excluderanges/bioconductor-excluderanges_0.99.6_src_all.tar.gz"], "md5": "6bb7d6e24d6f2c231bb5cb676fc24e32", "fn": "excluderanges_0.99.6.tar.gz"}, "fdb.fantom4.promoters.hg19-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/FDb.FANTOM4.promoters.hg19_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/FDb.FANTOM4.promoters.hg19_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.fantom4.promoters.hg19/bioconductor-fdb.fantom4.promoters.hg19_1.0.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.fantom4.promoters.hg19/bioconductor-fdb.fantom4.promoters.hg19_1.0.0_src_all.tar.gz"], "md5": "99a610eb895470e3d945acc5cfb3ebe6", "fn": "FDb.FANTOM4.promoters.hg19_1.0.0.tar.gz"}, "fdb.infiniummethylation.hg18-2.2.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/FDb.InfiniumMethylation.hg18_2.2.0.tar.gz", "https://bioarchive.galaxyproject.org/FDb.InfiniumMethylation.hg18_2.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.infiniummethylation.hg18/bioconductor-fdb.infiniummethylation.hg18_2.2.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.infiniummethylation.hg18/bioconductor-fdb.infiniummethylation.hg18_2.2.0_src_all.tar.gz"], "md5": "95ceab50d0a7c3d417cee12fbe3defb3", "fn": "FDb.InfiniumMethylation.hg18_2.2.0.tar.gz"}, "fdb.infiniummethylation.hg19-2.2.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz", "https://bioarchive.galaxyproject.org/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.infiniummethylation.hg19/bioconductor-fdb.infiniummethylation.hg19_2.2.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.infiniummethylation.hg19/bioconductor-fdb.infiniummethylation.hg19_2.2.0_src_all.tar.gz"], "md5": "b8b1abc599b9556b9fe9c6e824cb2697", "fn": "FDb.InfiniumMethylation.hg19_2.2.0.tar.gz"}, "fdb.ucsc.snp135common.hg19-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/FDb.UCSC.snp135common.hg19_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/FDb.UCSC.snp135common.hg19_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.snp135common.hg19/bioconductor-fdb.ucsc.snp135common.hg19_1.0.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.snp135common.hg19/bioconductor-fdb.ucsc.snp135common.hg19_1.0.0_src_all.tar.gz"], "md5": "0cdca5fa595bb69464016ceb97635f78", "fn": "FDb.UCSC.snp135common.hg19_1.0.0.tar.gz"}, "fdb.ucsc.snp137common.hg19-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/FDb.UCSC.snp137common.hg19_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/FDb.UCSC.snp137common.hg19_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.snp137common.hg19/bioconductor-fdb.ucsc.snp137common.hg19_1.0.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.snp137common.hg19/bioconductor-fdb.ucsc.snp137common.hg19_1.0.0_src_all.tar.gz"], "md5": "dac83f2d2f9ea9f033e50beac5c44838", "fn": "FDb.UCSC.snp137common.hg19_1.0.0.tar.gz"}, "fdb.ucsc.trnas-1.0.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/FDb.UCSC.tRNAs_1.0.1.tar.gz", "https://bioarchive.galaxyproject.org/FDb.UCSC.tRNAs_1.0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.trnas/bioconductor-fdb.ucsc.trnas_1.0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.trnas/bioconductor-fdb.ucsc.trnas_1.0.1_src_all.tar.gz"], "md5": "77bfdadd4d9f995a72b001e4e41792fa", "fn": "FDb.UCSC.tRNAs_1.0.1.tar.gz"}, "fitcons.ucsc.hg19-3.7.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/fitCons.UCSC.hg19_3.7.1.tar.gz", "https://bioarchive.galaxyproject.org/fitCons.UCSC.hg19_3.7.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fitcons.ucsc.hg19/bioconductor-fitcons.ucsc.hg19_3.7.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fitcons.ucsc.hg19/bioconductor-fitcons.ucsc.hg19_3.7.1_src_all.tar.gz"], "md5": "53d954890ec9b91084664a10161ce391", "fn": "fitCons.UCSC.hg19_3.7.1.tar.gz"}, "fly.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/fly.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/fly.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fly.db0/bioconductor-fly.db0_3.16.0_src_all.tar.gz"], "md5": "7f4041d95bfefb33ebb6319274c5a766", "fn": "fly.db0_3.16.0.tar.gz"}, "geneplast.data-0.99.6": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/geneplast.data_0.99.6.tar.gz", "https://bioarchive.galaxyproject.org/geneplast.data_0.99.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-geneplast.data/bioconductor-geneplast.data_0.99.6_src_all.tar.gz"], "md5": "08ddcdb9b1cf56dab5fe358c85fe1526", "fn": "geneplast.data_0.99.6.tar.gz"}, "geneplast.data.string.v91-0.99.6": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/geneplast.data.string.v91_0.99.6.tar.gz", "https://bioarchive.galaxyproject.org/geneplast.data.string.v91_0.99.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-geneplast.data.string.v91/bioconductor-geneplast.data.string.v91_0.99.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-geneplast.data.string.v91/bioconductor-geneplast.data.string.v91_0.99.6_src_all.tar.gz"], "md5": "86433f8489d9228c5ed73e2b75a55398", "fn": "geneplast.data.string.v91_0.99.6.tar.gz"}, "genesummary-0.99.4": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/GeneSummary_0.99.4.tar.gz", "https://bioarchive.galaxyproject.org/GeneSummary_0.99.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genesummary/bioconductor-genesummary_0.99.4_src_all.tar.gz"], "md5": "39ee728e42c42ccf200568c9c736b15c", "fn": "GeneSummary_0.99.4.tar.gz"}, "genomeinfodbdata-1.2.9": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz", "https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.9.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.9_src_all.tar.gz"], "md5": "7cc138cfb74665fdfa8d1c244eac4879", "fn": "GenomeInfoDbData_1.2.9.tar.gz"}, "genomewidesnp5crlmm-1.0.6": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/genomewidesnp5Crlmm_1.0.6.tar.gz", "https://bioarchive.galaxyproject.org/genomewidesnp5Crlmm_1.0.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomewidesnp5crlmm/bioconductor-genomewidesnp5crlmm_1.0.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomewidesnp5crlmm/bioconductor-genomewidesnp5crlmm_1.0.6_src_all.tar.gz"], "md5": "cc24140cd17758b8e09f4fe6c931526a", "fn": "genomewidesnp5Crlmm_1.0.6.tar.gz"}, "genomewidesnp6crlmm-1.0.7": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/genomewidesnp6Crlmm_1.0.7.tar.gz", "https://bioarchive.galaxyproject.org/genomewidesnp6Crlmm_1.0.7.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomewidesnp6crlmm/bioconductor-genomewidesnp6crlmm_1.0.7_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomewidesnp6crlmm/bioconductor-genomewidesnp6crlmm_1.0.7_src_all.tar.gz"], "md5": "13dd5aef3d814524896f2f3013beb78b", "fn": "genomewidesnp6Crlmm_1.0.7.tar.gz"}, "genomicstate-0.99.15": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomicState_0.99.15.tar.gz", "https://bioarchive.galaxyproject.org/GenomicState_0.99.15.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomicstate/bioconductor-genomicstate_0.99.15_src_all.tar.gz"], "md5": "59c2d85a72f62cb12bad697fcbce5edc", "fn": "GenomicState_0.99.15.tar.gz"}, "gghumanmethcancerpanelv1.db-1.4.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GGHumanMethCancerPanelv1.db_1.4.1.tar.gz", "https://bioarchive.galaxyproject.org/GGHumanMethCancerPanelv1.db_1.4.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gghumanmethcancerpanelv1.db/bioconductor-gghumanmethcancerpanelv1.db_1.4.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gghumanmethcancerpanelv1.db/bioconductor-gghumanmethcancerpanelv1.db_1.4.1_src_all.tar.gz"], "md5": "e8f4a37182b175fb33dd54f8093e6f52", "fn": "GGHumanMethCancerPanelv1.db_1.4.1.tar.gz"}, "go.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GO.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/GO.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-go.db/bioconductor-go.db_3.16.0_src_all.tar.gz"], "md5": "291f5c8ce883d03243ca3a522afd81ce", "fn": "GO.db_3.16.0.tar.gz"}, "gp53cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/gp53cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/gp53cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gp53cdf/bioconductor-gp53cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gp53cdf/bioconductor-gp53cdf_2.18.0_src_all.tar.gz"], "md5": "2887dd15d3fa29b5c13b068c8d641f61", "fn": "gp53cdf_2.18.0.tar.gz"}, "grasp2db-1.1.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/grasp2db_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/grasp2db_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-grasp2db/bioconductor-grasp2db_1.1.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-grasp2db/bioconductor-grasp2db_1.1.0_src_all.tar.gz"], "md5": "3fc90fc7c99e7da51dcbb687fd2d5515", "fn": "grasp2db_1.1.0.tar.gz"}, "gwascatdata-0.99.6": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/gwascatData_0.99.6.tar.gz", "https://bioarchive.galaxyproject.org/gwascatData_0.99.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gwascatdata/bioconductor-gwascatdata_0.99.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gwascatdata/bioconductor-gwascatdata_0.99.6_src_all.tar.gz"], "md5": "fa09db539ac0a16ba136e810a5b9970a", "fn": "gwascatData_0.99.6.tar.gz"}, "h10kcod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/h10kcod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/h10kcod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-h10kcod.db/bioconductor-h10kcod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-h10kcod.db/bioconductor-h10kcod.db_3.4.0_src_all.tar.gz"], "md5": "a555739cea229f286953c3297c145e9c", "fn": "h10kcod.db_3.4.0.tar.gz"}, "h20kcod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/h20kcod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/h20kcod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-h20kcod.db/bioconductor-h20kcod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-h20kcod.db/bioconductor-h20kcod.db_3.4.0_src_all.tar.gz"], "md5": "3647facb272f58424f4c94ef92e8ee45", "fn": "h20kcod.db_3.4.0.tar.gz"}, "hapmap370k-1.0.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hapmap370k_1.0.1.tar.gz", "https://bioarchive.galaxyproject.org/hapmap370k_1.0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap370k/bioconductor-hapmap370k_1.0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap370k/bioconductor-hapmap370k_1.0.1_src_all.tar.gz"], "md5": "569556341a45da799372aaf1012be72e", "fn": "hapmap370k_1.0.1.tar.gz"}, "hcg110.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hcg110.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hcg110.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcg110.db/bioconductor-hcg110.db_3.13.0_src_all.tar.gz"], "md5": "4c536c3539a61d7f1f67dac149f10b11", "fn": "hcg110.db_3.13.0.tar.gz"}, "hcg110cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hcg110cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hcg110cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcg110cdf/bioconductor-hcg110cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcg110cdf/bioconductor-hcg110cdf_2.18.0_src_all.tar.gz"], "md5": "b53167876217ddb301204719da23eafc", "fn": "hcg110cdf_2.18.0.tar.gz"}, "hcg110probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hcg110probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hcg110probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcg110probe/bioconductor-hcg110probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcg110probe/bioconductor-hcg110probe_2.18.0_src_all.tar.gz"], "md5": "51af8d6a7090ea7c5fe630dcea68bfb3", "fn": "hcg110probe_2.18.0.tar.gz"}, "hdo.db-0.99.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/HDO.db_0.99.1.tar.gz", "https://bioarchive.galaxyproject.org/HDO.db_0.99.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hdo.db/bioconductor-hdo.db_0.99.1_src_all.tar.gz"], "md5": "007a50523f1de27048dfc97f4d458f59", "fn": "HDO.db_0.99.1.tar.gz"}, "hgfocus.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgfocus.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgfocus.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgfocus.db/bioconductor-hgfocus.db_3.13.0_src_all.tar.gz"], "md5": "a6bee48c0aa947d3c7d25ef2c5a4d485", "fn": "hgfocus.db_3.13.0.tar.gz"}, "hgfocuscdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgfocuscdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgfocuscdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgfocuscdf/bioconductor-hgfocuscdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgfocuscdf/bioconductor-hgfocuscdf_2.18.0_src_all.tar.gz"], "md5": "9883e53bfd9ddb9ad5f3a9c2e47bbd2c", "fn": "hgfocuscdf_2.18.0.tar.gz"}, "hgfocusprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgfocusprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgfocusprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgfocusprobe/bioconductor-hgfocusprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgfocusprobe/bioconductor-hgfocusprobe_2.18.0_src_all.tar.gz"], "md5": "0a399ed276b89e3d80946b6cbbf167b4", "fn": "hgfocusprobe_2.18.0.tar.gz"}, "hgu133a.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu133a.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133a.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133a.db/bioconductor-hgu133a.db_3.13.0_src_all.tar.gz"], "md5": "97675c27b13624bdfd760460dbca6bf0", "fn": "hgu133a.db_3.13.0.tar.gz"}, "hgu133a2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu133a2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133a2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133a2.db/bioconductor-hgu133a2.db_3.13.0_src_all.tar.gz"], "md5": "e3bf9c5c9941f5f378cbc3dbeb9919ee", "fn": "hgu133a2.db_3.13.0.tar.gz"}, "hgu133a2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu133a2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133a2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133a2cdf/bioconductor-hgu133a2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133a2cdf/bioconductor-hgu133a2cdf_2.18.0_src_all.tar.gz"], "md5": "566bc70f0bb94a376bf88f191a2f067e", "fn": "hgu133a2cdf_2.18.0.tar.gz"}, "hgu133a2frmavecs-1.2.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu133a2frmavecs_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133a2frmavecs_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133a2frmavecs/bioconductor-hgu133a2frmavecs_1.2.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133a2frmavecs/bioconductor-hgu133a2frmavecs_1.2.0_src_all.tar.gz"], "md5": "4bf8cf5cbaf288ce0a9618d764c87044", "fn": "hgu133a2frmavecs_1.2.0.tar.gz"}, "hgu133a2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu133a2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133a2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133a2probe/bioconductor-hgu133a2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133a2probe/bioconductor-hgu133a2probe_2.18.0_src_all.tar.gz"], "md5": "736b43cfc37a297ccc0d30cb75fcc95a", "fn": "hgu133a2probe_2.18.0.tar.gz"}, "hgu133acdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu133acdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133acdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133acdf/bioconductor-hgu133acdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133acdf/bioconductor-hgu133acdf_2.18.0_src_all.tar.gz"], "md5": "d3e0e22b2d3943d26c94e7c01b91035c", "fn": "hgu133acdf_2.18.0.tar.gz"}, "hgu133afrmavecs-1.5.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu133afrmavecs_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133afrmavecs_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133afrmavecs/bioconductor-hgu133afrmavecs_1.5.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133afrmavecs/bioconductor-hgu133afrmavecs_1.5.0_src_all.tar.gz"], "md5": "85034ab02491f5b3699d210cef50812d", "fn": "hgu133afrmavecs_1.5.0.tar.gz"}, "hgu133aprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu133aprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133aprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133aprobe/bioconductor-hgu133aprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133aprobe/bioconductor-hgu133aprobe_2.18.0_src_all.tar.gz"], "md5": "76cd9c54b0a8a0240dbb0fc758959d62", "fn": "hgu133aprobe_2.18.0.tar.gz"}, "hgu133atagcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu133atagcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133atagcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133atagcdf/bioconductor-hgu133atagcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133atagcdf/bioconductor-hgu133atagcdf_2.18.0_src_all.tar.gz"], "md5": "01f8809e0deb5b83f3f0decec881a1d8", "fn": "hgu133atagcdf_2.18.0.tar.gz"}, "hgu133atagprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu133atagprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133atagprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133atagprobe/bioconductor-hgu133atagprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133atagprobe/bioconductor-hgu133atagprobe_2.18.0_src_all.tar.gz"], "md5": "97aeaf9ac9450369cf030581b8ec5a53", "fn": "hgu133atagprobe_2.18.0.tar.gz"}, "hgu133b.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu133b.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133b.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133b.db/bioconductor-hgu133b.db_3.13.0_src_all.tar.gz"], "md5": "ff7930c99300c1022fde06ebe5c4a8cc", "fn": "hgu133b.db_3.13.0.tar.gz"}, "hgu133bcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu133bcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133bcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133bcdf/bioconductor-hgu133bcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133bcdf/bioconductor-hgu133bcdf_2.18.0_src_all.tar.gz"], "md5": "649aaa5e6275be6ee4d24d80ca390ea5", "fn": "hgu133bcdf_2.18.0.tar.gz"}, "hgu133bprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu133bprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133bprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133bprobe/bioconductor-hgu133bprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133bprobe/bioconductor-hgu133bprobe_2.18.0_src_all.tar.gz"], "md5": "203750510e51450e1267e08c241151c4", "fn": "hgu133bprobe_2.18.0.tar.gz"}, "hgu133plus2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu133plus2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2.db/bioconductor-hgu133plus2.db_3.13.0_src_all.tar.gz"], "md5": "459fcf4880a9eaa25b373c5635fede3d", "fn": "hgu133plus2.db_3.13.0.tar.gz"}, "hgu133plus2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu133plus2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2cdf/bioconductor-hgu133plus2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2cdf/bioconductor-hgu133plus2cdf_2.18.0_src_all.tar.gz"], "md5": "284fef2f0b777d7b53451538ddd53de3", "fn": "hgu133plus2cdf_2.18.0.tar.gz"}, "hgu133plus2frmavecs-1.5.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu133plus2frmavecs_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2frmavecs_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2frmavecs/bioconductor-hgu133plus2frmavecs_1.5.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2frmavecs/bioconductor-hgu133plus2frmavecs_1.5.0_src_all.tar.gz"], "md5": "a4781cbcccc1ee17dfd16259f1c7bebc", "fn": "hgu133plus2frmavecs_1.5.0.tar.gz"}, "hgu133plus2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu133plus2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2probe/bioconductor-hgu133plus2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2probe/bioconductor-hgu133plus2probe_2.18.0_src_all.tar.gz"], "md5": "7a244787a0269bc72732ac3d830f34dd", "fn": "hgu133plus2probe_2.18.0.tar.gz"}, "hgu219.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu219.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hgu219.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu219.db/bioconductor-hgu219.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu219.db/bioconductor-hgu219.db_3.2.3_src_all.tar.gz"], "md5": "a4a0fd2ac170a75d8b17618615fcd7a0", "fn": "hgu219.db_3.2.3.tar.gz"}, "hgu219cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu219cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu219cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu219cdf/bioconductor-hgu219cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu219cdf/bioconductor-hgu219cdf_2.18.0_src_all.tar.gz"], "md5": "157a4280a9de960902260ab18f678949", "fn": "hgu219cdf_2.18.0.tar.gz"}, "hgu219probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu219probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu219probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu219probe/bioconductor-hgu219probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu219probe/bioconductor-hgu219probe_2.18.0_src_all.tar.gz"], "md5": "c5bb2f7b2e0f8fa89e6a30befaee6497", "fn": "hgu219probe_2.18.0.tar.gz"}, "hgu95a.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95a.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95a.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95a.db/bioconductor-hgu95a.db_3.13.0_src_all.tar.gz"], "md5": "b228ec0eded3ba9bccf033c2fff8f7b8", "fn": "hgu95a.db_3.13.0.tar.gz"}, "hgu95acdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95acdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95acdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95acdf/bioconductor-hgu95acdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95acdf/bioconductor-hgu95acdf_2.18.0_src_all.tar.gz"], "md5": "afc999d77b1532154d45911ad15a5897", "fn": "hgu95acdf_2.18.0.tar.gz"}, "hgu95aprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95aprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95aprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95aprobe/bioconductor-hgu95aprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95aprobe/bioconductor-hgu95aprobe_2.18.0_src_all.tar.gz"], "md5": "67d94ecdc1889acc19dafd19d26700a2", "fn": "hgu95aprobe_2.18.0.tar.gz"}, "hgu95av2-2.2.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95av2_2.2.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95av2_2.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95av2/bioconductor-hgu95av2_2.2.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95av2/bioconductor-hgu95av2_2.2.0_src_all.tar.gz"], "md5": "b92585c0f43e91bd1abd234b9465a6a7", "fn": "hgu95av2_2.2.0.tar.gz"}, "hgu95av2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95av2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95av2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95av2.db/bioconductor-hgu95av2.db_3.13.0_src_all.tar.gz"], "md5": "0ada3f3c2507992b94d2daa7de8b7fbf", "fn": "hgu95av2.db_3.13.0.tar.gz"}, "hgu95av2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95av2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95av2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95av2cdf/bioconductor-hgu95av2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95av2cdf/bioconductor-hgu95av2cdf_2.18.0_src_all.tar.gz"], "md5": "026bae2f76433593f75ca6c79bc9a9d0", "fn": "hgu95av2cdf_2.18.0.tar.gz"}, "hgu95av2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95av2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95av2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95av2probe/bioconductor-hgu95av2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95av2probe/bioconductor-hgu95av2probe_2.18.0_src_all.tar.gz"], "md5": "d3efb56f7e7a264b633fac787a5a2b95", "fn": "hgu95av2probe_2.18.0.tar.gz"}, "hgu95b.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95b.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95b.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95b.db/bioconductor-hgu95b.db_3.13.0_src_all.tar.gz"], "md5": "12334c263cfd9f7dc835762b4661edc1", "fn": "hgu95b.db_3.13.0.tar.gz"}, "hgu95bcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95bcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95bcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95bcdf/bioconductor-hgu95bcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95bcdf/bioconductor-hgu95bcdf_2.18.0_src_all.tar.gz"], "md5": "e6e56b7a107bb2df25b3c25a8191385d", "fn": "hgu95bcdf_2.18.0.tar.gz"}, "hgu95bprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95bprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95bprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95bprobe/bioconductor-hgu95bprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95bprobe/bioconductor-hgu95bprobe_2.18.0_src_all.tar.gz"], "md5": "60dcb57fd402dc24d53ef9390c893cfc", "fn": "hgu95bprobe_2.18.0.tar.gz"}, "hgu95c.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95c.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95c.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95c.db/bioconductor-hgu95c.db_3.13.0_src_all.tar.gz"], "md5": "680cdfc3e63853ace2ec47caa00ded36", "fn": "hgu95c.db_3.13.0.tar.gz"}, "hgu95ccdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95ccdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95ccdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95ccdf/bioconductor-hgu95ccdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95ccdf/bioconductor-hgu95ccdf_2.18.0_src_all.tar.gz"], "md5": "976151eac05c320aec7a24397a6b5806", "fn": "hgu95ccdf_2.18.0.tar.gz"}, "hgu95cprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95cprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95cprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95cprobe/bioconductor-hgu95cprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95cprobe/bioconductor-hgu95cprobe_2.18.0_src_all.tar.gz"], "md5": "3fe935a52c70105dc7a214174c946455", "fn": "hgu95cprobe_2.18.0.tar.gz"}, "hgu95d.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95d.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95d.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95d.db/bioconductor-hgu95d.db_3.13.0_src_all.tar.gz"], "md5": "90ecf383640f6ab7314fa1babcdd5a0b", "fn": "hgu95d.db_3.13.0.tar.gz"}, "hgu95dcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95dcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95dcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95dcdf/bioconductor-hgu95dcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95dcdf/bioconductor-hgu95dcdf_2.18.0_src_all.tar.gz"], "md5": "36e11ff001b1bec3f34ba7c93132ad6f", "fn": "hgu95dcdf_2.18.0.tar.gz"}, "hgu95dprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95dprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95dprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95dprobe/bioconductor-hgu95dprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95dprobe/bioconductor-hgu95dprobe_2.18.0_src_all.tar.gz"], "md5": "165ce5029f49fc515b9ee0e6a6a29cb5", "fn": "hgu95dprobe_2.18.0.tar.gz"}, "hgu95e.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95e.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95e.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95e.db/bioconductor-hgu95e.db_3.13.0_src_all.tar.gz"], "md5": "116bd146279d19d50a7233bc61c22104", "fn": "hgu95e.db_3.13.0.tar.gz"}, "hgu95ecdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95ecdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95ecdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95ecdf/bioconductor-hgu95ecdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95ecdf/bioconductor-hgu95ecdf_2.18.0_src_all.tar.gz"], "md5": "fa27cfff62a38fc51640d797bd628105", "fn": "hgu95ecdf_2.18.0.tar.gz"}, "hgu95eprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95eprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95eprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95eprobe/bioconductor-hgu95eprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95eprobe/bioconductor-hgu95eprobe_2.18.0_src_all.tar.gz"], "md5": "9e5407ab80c5bbb4065484be0b9c6191", "fn": "hgu95eprobe_2.18.0.tar.gz"}, "hguatlas13k.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hguatlas13k.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hguatlas13k.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hguatlas13k.db/bioconductor-hguatlas13k.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hguatlas13k.db/bioconductor-hguatlas13k.db_3.2.3_src_all.tar.gz"], "md5": "ab9ffe1a1de44c0f938129f193e7fb63", "fn": "hguatlas13k.db_3.2.3.tar.gz"}, "hgubeta7.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgubeta7.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hgubeta7.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgubeta7.db/bioconductor-hgubeta7.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgubeta7.db/bioconductor-hgubeta7.db_3.2.3_src_all.tar.gz"], "md5": "1b8b065f95d2089985f59f22dcabc824", "fn": "hgubeta7.db_3.2.3.tar.gz"}, "hgudkfz31.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hguDKFZ31.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hguDKFZ31.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgudkfz31.db/bioconductor-hgudkfz31.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgudkfz31.db/bioconductor-hgudkfz31.db_3.2.3_src_all.tar.gz"], "md5": "fa3ba493cebdac4253dea8fe5d58452b", "fn": "hguDKFZ31.db_3.2.3.tar.gz"}, "hgug4100a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgug4100a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hgug4100a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4100a.db/bioconductor-hgug4100a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4100a.db/bioconductor-hgug4100a.db_3.2.3_src_all.tar.gz"], "md5": "b7856928278a77d71f963410ea4f2376", "fn": "hgug4100a.db_3.2.3.tar.gz"}, "hgug4101a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgug4101a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hgug4101a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4101a.db/bioconductor-hgug4101a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4101a.db/bioconductor-hgug4101a.db_3.2.3_src_all.tar.gz"], "md5": "e4731217efbffd05d3ee7eec68ce0aa0", "fn": "hgug4101a.db_3.2.3.tar.gz"}, "hgug4110b.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgug4110b.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hgug4110b.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4110b.db/bioconductor-hgug4110b.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4110b.db/bioconductor-hgug4110b.db_3.2.3_src_all.tar.gz"], "md5": "a9edcdbc121f22d4dec335a64598ff0e", "fn": "hgug4110b.db_3.2.3.tar.gz"}, "hgug4111a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgug4111a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hgug4111a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4111a.db/bioconductor-hgug4111a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4111a.db/bioconductor-hgug4111a.db_3.2.3_src_all.tar.gz"], "md5": "a5f2c3b463915fa1ab0ca21e6b0f5840", "fn": "hgug4111a.db_3.2.3.tar.gz"}, "hgug4112a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgug4112a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hgug4112a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4112a.db/bioconductor-hgug4112a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4112a.db/bioconductor-hgug4112a.db_3.2.3_src_all.tar.gz"], "md5": "67ecf8c887e2ebe1941cc51d0f5fb468", "fn": "hgug4112a.db_3.2.3.tar.gz"}, "hgug4845a.db-0.0.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgug4845a.db_0.0.3.tar.gz", "https://bioarchive.galaxyproject.org/hgug4845a.db_0.0.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4845a.db/bioconductor-hgug4845a.db_0.0.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4845a.db/bioconductor-hgug4845a.db_0.0.3_src_all.tar.gz"], "md5": "46133d7bcb6d8c24c026304e8ddd150d", "fn": "hgug4845a.db_0.0.3.tar.gz"}, "hguqiagenv3.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hguqiagenv3.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hguqiagenv3.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hguqiagenv3.db/bioconductor-hguqiagenv3.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hguqiagenv3.db/bioconductor-hguqiagenv3.db_3.2.3_src_all.tar.gz"], "md5": "91ebb82e773ff799befdb8921b38e90e", "fn": "hguqiagenv3.db_3.2.3.tar.gz"}, "hi16cod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hi16cod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/hi16cod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hi16cod.db/bioconductor-hi16cod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hi16cod.db/bioconductor-hi16cod.db_3.4.0_src_all.tar.gz"], "md5": "abdc77937e8d37fa5468691376ceb6a5", "fn": "hi16cod.db_3.4.0.tar.gz"}, "hivprtplus2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hivprtplus2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hivprtplus2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hivprtplus2cdf/bioconductor-hivprtplus2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hivprtplus2cdf/bioconductor-hivprtplus2cdf_2.18.0_src_all.tar.gz"], "md5": "143d9c2f5f328786bae7bb8dc4daf261", "fn": "hivprtplus2cdf_2.18.0.tar.gz"}, "homo.sapiens-1.3.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/Homo.sapiens_1.3.1.tar.gz", "https://bioarchive.galaxyproject.org/Homo.sapiens_1.3.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-homo.sapiens/bioconductor-homo.sapiens_1.3.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-homo.sapiens/bioconductor-homo.sapiens_1.3.1_src_all.tar.gz"], "md5": "653b60cfcdaefd171729115cd629b585", "fn": "Homo.sapiens_1.3.1.tar.gz"}, "hpannot-1.1.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hpAnnot_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/hpAnnot_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hpannot/bioconductor-hpannot_1.1.0_src_all.tar.gz"], "md5": "fbc94a00b0f33b41bc5ff53fbe060663", "fn": "hpAnnot_1.1.0.tar.gz"}, "hs25kresogen.db-2.5.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hs25kresogen.db_2.5.0.tar.gz", "https://bioarchive.galaxyproject.org/hs25kresogen.db_2.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hs25kresogen.db/bioconductor-hs25kresogen.db_2.5.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hs25kresogen.db/bioconductor-hs25kresogen.db_2.5.0_src_all.tar.gz"], "md5": "a3800d072ce0e5f6f5d8299538b99cca", "fn": "hs25kresogen.db_2.5.0.tar.gz"}, "hs6ug171.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/Hs6UG171.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/Hs6UG171.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hs6ug171.db/bioconductor-hs6ug171.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hs6ug171.db/bioconductor-hs6ug171.db_3.2.3_src_all.tar.gz"], "md5": "7aaf8a2441941f70247275c93735ed3b", "fn": "Hs6UG171.db_3.2.3.tar.gz"}, "hsagilentdesign026652.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/HsAgilentDesign026652.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/HsAgilentDesign026652.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hsagilentdesign026652.db/bioconductor-hsagilentdesign026652.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hsagilentdesign026652.db/bioconductor-hsagilentdesign026652.db_3.2.3_src_all.tar.gz"], "md5": "dcd2c748bf9d7c002611cd5cf2ff38c0", "fn": "HsAgilentDesign026652.db_3.2.3.tar.gz"}, "hspec-0.99.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/Hspec_0.99.1.tar.gz", "https://bioarchive.galaxyproject.org/Hspec_0.99.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hspec/bioconductor-hspec_0.99.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hspec/bioconductor-hspec_0.99.1_src_all.tar.gz"], "md5": "0ade3e3147c8f0086e9be2312cccdfeb", "fn": "Hspec_0.99.1.tar.gz"}, "hspeccdf-0.99.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hspeccdf_0.99.1.tar.gz", "https://bioarchive.galaxyproject.org/hspeccdf_0.99.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hspeccdf/bioconductor-hspeccdf_0.99.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hspeccdf/bioconductor-hspeccdf_0.99.1_src_all.tar.gz"], "md5": "89f81adf91094710558ce6aec79fc7fd", "fn": "hspeccdf_0.99.1.tar.gz"}, "hta20probeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hta20probeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hta20probeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hta20probeset.db/bioconductor-hta20probeset.db_8.8.0_src_all.tar.gz"], "md5": "8cc15bb71f3c2776015e55a2d7df2c2f", "fn": "hta20probeset.db_8.8.0.tar.gz"}, "hta20transcriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hta20transcriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hta20transcriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hta20transcriptcluster.db/bioconductor-hta20transcriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "9debbc190cc5f9f0ad97fbc452fe7025", "fn": "hta20transcriptcluster.db_8.8.0.tar.gz"}, "hthgu133a.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hthgu133a.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133a.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133a.db/bioconductor-hthgu133a.db_3.13.0_src_all.tar.gz"], "md5": "769ed088760102b61edfb73454d4c642", "fn": "hthgu133a.db_3.13.0.tar.gz"}, "hthgu133acdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hthgu133acdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133acdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133acdf/bioconductor-hthgu133acdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133acdf/bioconductor-hthgu133acdf_2.18.0_src_all.tar.gz"], "md5": "b92e543867f1f0c08bfa9299e123d608", "fn": "hthgu133acdf_2.18.0.tar.gz"}, "hthgu133afrmavecs-1.3.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hthgu133afrmavecs_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133afrmavecs_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133afrmavecs/bioconductor-hthgu133afrmavecs_1.3.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133afrmavecs/bioconductor-hthgu133afrmavecs_1.3.0_src_all.tar.gz"], "md5": "be3f3d67a94dca3b080c184fba5ff6d8", "fn": "hthgu133afrmavecs_1.3.0.tar.gz"}, "hthgu133aprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hthgu133aprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133aprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133aprobe/bioconductor-hthgu133aprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133aprobe/bioconductor-hthgu133aprobe_2.18.0_src_all.tar.gz"], "md5": "cdc17ea670719f055ee75bea1415c754", "fn": "hthgu133aprobe_2.18.0.tar.gz"}, "hthgu133b.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hthgu133b.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133b.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133b.db/bioconductor-hthgu133b.db_3.13.0_src_all.tar.gz"], "md5": "8501401a7385e28173ea7b60aa3bf3d2", "fn": "hthgu133b.db_3.13.0.tar.gz"}, "hthgu133bcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hthgu133bcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133bcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133bcdf/bioconductor-hthgu133bcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133bcdf/bioconductor-hthgu133bcdf_2.18.0_src_all.tar.gz"], "md5": "935ae53fb168d9c7890d71020ef4c366", "fn": "hthgu133bcdf_2.18.0.tar.gz"}, "hthgu133bprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hthgu133bprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133bprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133bprobe/bioconductor-hthgu133bprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133bprobe/bioconductor-hthgu133bprobe_2.18.0_src_all.tar.gz"], "md5": "8a2e306638a81fdec3b10a014c04c6b9", "fn": "hthgu133bprobe_2.18.0.tar.gz"}, "hthgu133plusa.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hthgu133plusa.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133plusa.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133plusa.db/bioconductor-hthgu133plusa.db_3.13.0_src_all.tar.gz"], "md5": "477cb32e1d8eb6da894486ad810b4232", "fn": "hthgu133plusa.db_3.13.0.tar.gz"}, "hthgu133plusb.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hthgu133plusb.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133plusb.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133plusb.db/bioconductor-hthgu133plusb.db_3.13.0_src_all.tar.gz"], "md5": "f3214792ba174598b0559937f46de937", "fn": "hthgu133plusb.db_3.13.0.tar.gz"}, "hthgu133pluspm.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hthgu133pluspm.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133pluspm.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133pluspm.db/bioconductor-hthgu133pluspm.db_3.13.0_src_all.tar.gz"], "md5": "b0b3cb0174608d5705ae6c80dac02e3c", "fn": "hthgu133pluspm.db_3.13.0.tar.gz"}, "hthgu133pluspmcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hthgu133pluspmcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133pluspmcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133pluspmcdf/bioconductor-hthgu133pluspmcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133pluspmcdf/bioconductor-hthgu133pluspmcdf_2.18.0_src_all.tar.gz"], "md5": "56d15101d59decac7811caa15b349a9c", "fn": "hthgu133pluspmcdf_2.18.0.tar.gz"}, "hthgu133pluspmprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hthgu133pluspmprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133pluspmprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133pluspmprobe/bioconductor-hthgu133pluspmprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133pluspmprobe/bioconductor-hthgu133pluspmprobe_2.18.0_src_all.tar.gz"], "md5": "74713e822a689007892d0eb92dbd456b", "fn": "hthgu133pluspmprobe_2.18.0.tar.gz"}, "htmg430a.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/htmg430a.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/htmg430a.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430a.db/bioconductor-htmg430a.db_3.13.0_src_all.tar.gz"], "md5": "171e457946a6b485b2ebd928b233abb3", "fn": "htmg430a.db_3.13.0.tar.gz"}, "htmg430acdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/htmg430acdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htmg430acdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430acdf/bioconductor-htmg430acdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430acdf/bioconductor-htmg430acdf_2.18.0_src_all.tar.gz"], "md5": "aef7a3c3af7d2624ee6fc6f2d22472e2", "fn": "htmg430acdf_2.18.0.tar.gz"}, "htmg430aprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/htmg430aprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htmg430aprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430aprobe/bioconductor-htmg430aprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430aprobe/bioconductor-htmg430aprobe_2.18.0_src_all.tar.gz"], "md5": "e50cc49b8887b6ef8ee1152ec12d5010", "fn": "htmg430aprobe_2.18.0.tar.gz"}, "htmg430b.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/htmg430b.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/htmg430b.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430b.db/bioconductor-htmg430b.db_3.13.0_src_all.tar.gz"], "md5": "70849a636e972a9be604a3320d3bd814", "fn": "htmg430b.db_3.13.0.tar.gz"}, "htmg430bcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/htmg430bcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htmg430bcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430bcdf/bioconductor-htmg430bcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430bcdf/bioconductor-htmg430bcdf_2.18.0_src_all.tar.gz"], "md5": "53cc1408504a5f07b5655aa46b969157", "fn": "htmg430bcdf_2.18.0.tar.gz"}, "htmg430bprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/htmg430bprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htmg430bprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430bprobe/bioconductor-htmg430bprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430bprobe/bioconductor-htmg430bprobe_2.18.0_src_all.tar.gz"], "md5": "f0e3eb56925d786762dee0c2dc82b530", "fn": "htmg430bprobe_2.18.0.tar.gz"}, "htmg430pm.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/htmg430pm.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/htmg430pm.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430pm.db/bioconductor-htmg430pm.db_3.13.0_src_all.tar.gz"], "md5": "f89738ce2e33d1c626aa2d15cd28a49b", "fn": "htmg430pm.db_3.13.0.tar.gz"}, "htmg430pmcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/htmg430pmcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htmg430pmcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430pmcdf/bioconductor-htmg430pmcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430pmcdf/bioconductor-htmg430pmcdf_2.18.0_src_all.tar.gz"], "md5": "016a54b47adbbed7db989787646a0084", "fn": "htmg430pmcdf_2.18.0.tar.gz"}, "htmg430pmprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/htmg430pmprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htmg430pmprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430pmprobe/bioconductor-htmg430pmprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430pmprobe/bioconductor-htmg430pmprobe_2.18.0_src_all.tar.gz"], "md5": "f0e053fcc0ca4b5f8c539fc0a3fcb076", "fn": "htmg430pmprobe_2.18.0.tar.gz"}, "htrat230pm.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/htrat230pm.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/htrat230pm.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htrat230pm.db/bioconductor-htrat230pm.db_3.13.0_src_all.tar.gz"], "md5": "46ed50806c568bf269fe4c51d3df3955", "fn": "htrat230pm.db_3.13.0.tar.gz"}, "htrat230pmcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/htrat230pmcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htrat230pmcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htrat230pmcdf/bioconductor-htrat230pmcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htrat230pmcdf/bioconductor-htrat230pmcdf_2.18.0_src_all.tar.gz"], "md5": "c6683d16e8aacccd326f7a7eebb79b98", "fn": "htrat230pmcdf_2.18.0.tar.gz"}, "htrat230pmprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/htrat230pmprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htrat230pmprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htrat230pmprobe/bioconductor-htrat230pmprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htrat230pmprobe/bioconductor-htrat230pmprobe_2.18.0_src_all.tar.gz"], "md5": "e4deeca2dc406367ac4a347e370267cf", "fn": "htrat230pmprobe_2.18.0.tar.gz"}, "htratfocus.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/htratfocus.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/htratfocus.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htratfocus.db/bioconductor-htratfocus.db_3.13.0_src_all.tar.gz"], "md5": "88be90edb1acb31faedde0b66b27a150", "fn": "htratfocus.db_3.13.0.tar.gz"}, "htratfocuscdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/htratfocuscdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htratfocuscdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htratfocuscdf/bioconductor-htratfocuscdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htratfocuscdf/bioconductor-htratfocuscdf_2.18.0_src_all.tar.gz"], "md5": "04b4952f7d8b607a7eb0f779c08c57dc", "fn": "htratfocuscdf_2.18.0.tar.gz"}, "htratfocusprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/htratfocusprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htratfocusprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htratfocusprobe/bioconductor-htratfocusprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htratfocusprobe/bioconductor-htratfocusprobe_2.18.0_src_all.tar.gz"], "md5": "26a0963d8aff314a4a1f2c47e9147a8a", "fn": "htratfocusprobe_2.18.0.tar.gz"}, "hu35ksuba.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hu35ksuba.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksuba.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksuba.db/bioconductor-hu35ksuba.db_3.13.0_src_all.tar.gz"], "md5": "4c2306a80f26bacb6172e84c896ef911", "fn": "hu35ksuba.db_3.13.0.tar.gz"}, "hu35ksubacdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hu35ksubacdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubacdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubacdf/bioconductor-hu35ksubacdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubacdf/bioconductor-hu35ksubacdf_2.18.0_src_all.tar.gz"], "md5": "c8b82c4755eb62818ca0dbf22de5d25e", "fn": "hu35ksubacdf_2.18.0.tar.gz"}, "hu35ksubaprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hu35ksubaprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubaprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubaprobe/bioconductor-hu35ksubaprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubaprobe/bioconductor-hu35ksubaprobe_2.18.0_src_all.tar.gz"], "md5": "49bd19ec3b6404211f2e410e473fa644", "fn": "hu35ksubaprobe_2.18.0.tar.gz"}, "hu35ksubb.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hu35ksubb.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubb.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubb.db/bioconductor-hu35ksubb.db_3.13.0_src_all.tar.gz"], "md5": "b82ece4860eddff8010faecaae802312", "fn": "hu35ksubb.db_3.13.0.tar.gz"}, "hu35ksubbcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hu35ksubbcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubbcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubbcdf/bioconductor-hu35ksubbcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubbcdf/bioconductor-hu35ksubbcdf_2.18.0_src_all.tar.gz"], "md5": "d873b6c521e926b331f799baf10a4e13", "fn": "hu35ksubbcdf_2.18.0.tar.gz"}, "hu35ksubbprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hu35ksubbprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubbprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubbprobe/bioconductor-hu35ksubbprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubbprobe/bioconductor-hu35ksubbprobe_2.18.0_src_all.tar.gz"], "md5": "0a63051d0faf38a56f17d5865cbed9b1", "fn": "hu35ksubbprobe_2.18.0.tar.gz"}, "hu35ksubc.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hu35ksubc.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubc.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubc.db/bioconductor-hu35ksubc.db_3.13.0_src_all.tar.gz"], "md5": "57e60b8d025e0e8cf7ac2b355111cf2d", "fn": "hu35ksubc.db_3.13.0.tar.gz"}, "hu35ksubccdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hu35ksubccdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubccdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubccdf/bioconductor-hu35ksubccdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubccdf/bioconductor-hu35ksubccdf_2.18.0_src_all.tar.gz"], "md5": "de96e69680c5f8747c99d170272d7c3c", "fn": "hu35ksubccdf_2.18.0.tar.gz"}, "hu35ksubcprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hu35ksubcprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubcprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubcprobe/bioconductor-hu35ksubcprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubcprobe/bioconductor-hu35ksubcprobe_2.18.0_src_all.tar.gz"], "md5": "b10453ea061b09172192bd21baa9083d", "fn": "hu35ksubcprobe_2.18.0.tar.gz"}, "hu35ksubd.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hu35ksubd.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubd.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubd.db/bioconductor-hu35ksubd.db_3.13.0_src_all.tar.gz"], "md5": "5ce6b6ede0f9733fd4dc527a28114327", "fn": "hu35ksubd.db_3.13.0.tar.gz"}, "hu35ksubdcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hu35ksubdcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubdcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubdcdf/bioconductor-hu35ksubdcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubdcdf/bioconductor-hu35ksubdcdf_2.18.0_src_all.tar.gz"], "md5": "6f6423426969f306fb0d5171e75b5380", "fn": "hu35ksubdcdf_2.18.0.tar.gz"}, "hu35ksubdprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hu35ksubdprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubdprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubdprobe/bioconductor-hu35ksubdprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubdprobe/bioconductor-hu35ksubdprobe_2.18.0_src_all.tar.gz"], "md5": "430a9b8ccd646d8cb06e6c1d750eec23", "fn": "hu35ksubdprobe_2.18.0.tar.gz"}, "hu6800.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hu6800.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hu6800.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800.db/bioconductor-hu6800.db_3.13.0_src_all.tar.gz"], "md5": "aa1cb6c107dee6d2ed1929b48aa831e9", "fn": "hu6800.db_3.13.0.tar.gz"}, "hu6800cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hu6800cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu6800cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800cdf/bioconductor-hu6800cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800cdf/bioconductor-hu6800cdf_2.18.0_src_all.tar.gz"], "md5": "fa2b2ab8f3aba517c63ad2e65873d2f0", "fn": "hu6800cdf_2.18.0.tar.gz"}, "hu6800probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hu6800probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu6800probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800probe/bioconductor-hu6800probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800probe/bioconductor-hu6800probe_2.18.0_src_all.tar.gz"], "md5": "7a2383bd870cbc0628c210174e911250", "fn": "hu6800probe_2.18.0.tar.gz"}, "hu6800subacdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hu6800subacdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu6800subacdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800subacdf/bioconductor-hu6800subacdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800subacdf/bioconductor-hu6800subacdf_2.18.0_src_all.tar.gz"], "md5": "9e8ec301e066e400564976cd9750297e", "fn": "hu6800subacdf_2.18.0.tar.gz"}, "hu6800subbcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hu6800subbcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu6800subbcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800subbcdf/bioconductor-hu6800subbcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800subbcdf/bioconductor-hu6800subbcdf_2.18.0_src_all.tar.gz"], "md5": "529aad5e4e73594c8cb66274d7e4adc5", "fn": "hu6800subbcdf_2.18.0.tar.gz"}, "hu6800subccdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hu6800subccdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu6800subccdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800subccdf/bioconductor-hu6800subccdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800subccdf/bioconductor-hu6800subccdf_2.18.0_src_all.tar.gz"], "md5": "020fe3a6bdf44efbde15432b968433e8", "fn": "hu6800subccdf_2.18.0.tar.gz"}, "hu6800subdcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hu6800subdcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu6800subdcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800subdcdf/bioconductor-hu6800subdcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800subdcdf/bioconductor-hu6800subdcdf_2.18.0_src_all.tar.gz"], "md5": "7966c21babb23e18cca4faafc8720f0a", "fn": "hu6800subdcdf_2.18.0.tar.gz"}, "huex.1.0.st.v2frmavecs-1.1.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/huex.1.0.st.v2frmavecs_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/huex.1.0.st.v2frmavecs_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huex.1.0.st.v2frmavecs/bioconductor-huex.1.0.st.v2frmavecs_1.1.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huex.1.0.st.v2frmavecs/bioconductor-huex.1.0.st.v2frmavecs_1.1.0_src_all.tar.gz"], "md5": "982935d07b526ff555790e309fe4147e", "fn": "huex.1.0.st.v2frmavecs_1.1.0.tar.gz"}, "huex10stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/huex10stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/huex10stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huex10stprobeset.db/bioconductor-huex10stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "fda9fc7340aeda2564a76756d2b8d4d3", "fn": "huex10stprobeset.db_8.8.0.tar.gz"}, "huex10sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/huex10sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/huex10sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huex10sttranscriptcluster.db/bioconductor-huex10sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "0789a1e8ee4474bd64c2772eab0db247", "fn": "huex10sttranscriptcluster.db_8.8.0.tar.gz"}, "huexexonprobesetlocation-1.15.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/HuExExonProbesetLocation_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/HuExExonProbesetLocation_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocation/bioconductor-huexexonprobesetlocation_1.15.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocation/bioconductor-huexexonprobesetlocation_1.15.0_src_all.tar.gz"], "md5": "11bf1b88d9e90711b4064497f611da4f", "fn": "HuExExonProbesetLocation_1.15.0.tar.gz"}, "huexexonprobesetlocationhg18-0.0.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/HuExExonProbesetLocationHg18_0.0.2.tar.gz", "https://bioarchive.galaxyproject.org/HuExExonProbesetLocationHg18_0.0.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocationhg18/bioconductor-huexexonprobesetlocationhg18_0.0.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocationhg18/bioconductor-huexexonprobesetlocationhg18_0.0.2_src_all.tar.gz"], "md5": "bb00b7f5e4db2b04dca5951aa6bd073e", "fn": "HuExExonProbesetLocationHg18_0.0.2.tar.gz"}, "huexexonprobesetlocationhg19-0.0.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/HuExExonProbesetLocationHg19_0.0.3.tar.gz", "https://bioarchive.galaxyproject.org/HuExExonProbesetLocationHg19_0.0.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocationhg19/bioconductor-huexexonprobesetlocationhg19_0.0.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocationhg19/bioconductor-huexexonprobesetlocationhg19_0.0.3_src_all.tar.gz"], "md5": "1a3843c95c82dc71a043d902961ba33a", "fn": "HuExExonProbesetLocationHg19_0.0.3.tar.gz"}, "hugene.1.0.st.v1frmavecs-1.1.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hugene.1.0.st.v1frmavecs_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene.1.0.st.v1frmavecs_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene.1.0.st.v1frmavecs/bioconductor-hugene.1.0.st.v1frmavecs_1.1.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene.1.0.st.v1frmavecs/bioconductor-hugene.1.0.st.v1frmavecs_1.1.0_src_all.tar.gz"], "md5": "711a69e6fa6dd3737a90615222416dfc", "fn": "hugene.1.0.st.v1frmavecs_1.1.0.tar.gz"}, "hugene10stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hugene10stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene10stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene10stprobeset.db/bioconductor-hugene10stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "0a4a87d64564cbec1e4bb1f9e5a67add", "fn": "hugene10stprobeset.db_8.8.0.tar.gz"}, "hugene10sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hugene10sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene10sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene10sttranscriptcluster.db/bioconductor-hugene10sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "a32fb5729d37e96f157b0a1085dff43e", "fn": "hugene10sttranscriptcluster.db_8.8.0.tar.gz"}, "hugene10stv1cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hugene10stv1cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene10stv1cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene10stv1cdf/bioconductor-hugene10stv1cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene10stv1cdf/bioconductor-hugene10stv1cdf_2.18.0_src_all.tar.gz"], "md5": "f1fb1c7076ac40b9e709f18e645d6181", "fn": "hugene10stv1cdf_2.18.0.tar.gz"}, "hugene10stv1probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hugene10stv1probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene10stv1probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene10stv1probe/bioconductor-hugene10stv1probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene10stv1probe/bioconductor-hugene10stv1probe_2.18.0_src_all.tar.gz"], "md5": "6ed3c17dd026acf008658a5994044c62", "fn": "hugene10stv1probe_2.18.0.tar.gz"}, "hugene11stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hugene11stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene11stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene11stprobeset.db/bioconductor-hugene11stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "4d22ec32dedd6c8603d5f545faeb4ba4", "fn": "hugene11stprobeset.db_8.8.0.tar.gz"}, "hugene11sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hugene11sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene11sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene11sttranscriptcluster.db/bioconductor-hugene11sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "7fed70c4bd904655459a41b5667f7c23", "fn": "hugene11sttranscriptcluster.db_8.8.0.tar.gz"}, "hugene20stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hugene20stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene20stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene20stprobeset.db/bioconductor-hugene20stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "bf7909fc41a80da59099327a6d9abb57", "fn": "hugene20stprobeset.db_8.8.0.tar.gz"}, "hugene20sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hugene20sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene20sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene20sttranscriptcluster.db/bioconductor-hugene20sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "0b929a3a959662e8a7265f58b81b4e35", "fn": "hugene20sttranscriptcluster.db_8.8.0.tar.gz"}, "hugene21stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hugene21stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene21stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene21stprobeset.db/bioconductor-hugene21stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "2b816dca48d0b2e1a946469b8d85d257", "fn": "hugene21stprobeset.db_8.8.0.tar.gz"}, "hugene21sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hugene21sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene21sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene21sttranscriptcluster.db/bioconductor-hugene21sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "ca90de6093bbad760abfcf0cfeada830", "fn": "hugene21sttranscriptcluster.db_8.8.0.tar.gz"}, "human.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/human.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/human.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human.db0/bioconductor-human.db0_3.16.0_src_all.tar.gz"], "md5": "19286619cd24ff1e3f9ac85debd5106f", "fn": "human.db0_3.16.0.tar.gz"}, "human1mduov3bcrlmm-1.0.4": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/human1mduov3bCrlmm_1.0.4.tar.gz", "https://bioarchive.galaxyproject.org/human1mduov3bCrlmm_1.0.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human1mduov3bcrlmm/bioconductor-human1mduov3bcrlmm_1.0.4_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human1mduov3bcrlmm/bioconductor-human1mduov3bcrlmm_1.0.4_src_all.tar.gz"], "md5": "0ff9f1e8bcc6348d6777bbb982ae0325", "fn": "human1mduov3bCrlmm_1.0.4.tar.gz"}, "human1mv1ccrlmm-1.0.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/human1mv1cCrlmm_1.0.3.tar.gz", "https://bioarchive.galaxyproject.org/human1mv1cCrlmm_1.0.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human1mv1ccrlmm/bioconductor-human1mv1ccrlmm_1.0.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human1mv1ccrlmm/bioconductor-human1mv1ccrlmm_1.0.3_src_all.tar.gz"], "md5": "b9f638c7b0ede50cb070f1bae85eb4dc", "fn": "human1mv1cCrlmm_1.0.3.tar.gz"}, "human370quadv3ccrlmm-1.0.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/human370quadv3cCrlmm_1.0.3.tar.gz", "https://bioarchive.galaxyproject.org/human370quadv3cCrlmm_1.0.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human370quadv3ccrlmm/bioconductor-human370quadv3ccrlmm_1.0.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human370quadv3ccrlmm/bioconductor-human370quadv3ccrlmm_1.0.3_src_all.tar.gz"], "md5": "33c3ccc3793ed95647418b746a5177f9", "fn": "human370quadv3cCrlmm_1.0.3.tar.gz"}, "human370v1ccrlmm-1.0.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/human370v1cCrlmm_1.0.2.tar.gz", "https://bioarchive.galaxyproject.org/human370v1cCrlmm_1.0.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human370v1ccrlmm/bioconductor-human370v1ccrlmm_1.0.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human370v1ccrlmm/bioconductor-human370v1ccrlmm_1.0.2_src_all.tar.gz"], "md5": "9ec4192f533faee2b14484de02548075", "fn": "human370v1cCrlmm_1.0.2.tar.gz"}, "human550v3bcrlmm-1.0.4": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/human550v3bCrlmm_1.0.4.tar.gz", "https://bioarchive.galaxyproject.org/human550v3bCrlmm_1.0.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human550v3bcrlmm/bioconductor-human550v3bcrlmm_1.0.4_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human550v3bcrlmm/bioconductor-human550v3bcrlmm_1.0.4_src_all.tar.gz"], "md5": "20e6b008fab5e1084354c87ad50d18a8", "fn": "human550v3bCrlmm_1.0.4.tar.gz"}, "human610quadv1bcrlmm-1.0.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/human610quadv1bCrlmm_1.0.3.tar.gz", "https://bioarchive.galaxyproject.org/human610quadv1bCrlmm_1.0.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human610quadv1bcrlmm/bioconductor-human610quadv1bcrlmm_1.0.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human610quadv1bcrlmm/bioconductor-human610quadv1bcrlmm_1.0.3_src_all.tar.gz"], "md5": "609cf09410774e084ee6a3286652bb1a", "fn": "human610quadv1bCrlmm_1.0.3.tar.gz"}, "human650v3acrlmm-1.0.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/human650v3aCrlmm_1.0.3.tar.gz", "https://bioarchive.galaxyproject.org/human650v3aCrlmm_1.0.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human650v3acrlmm/bioconductor-human650v3acrlmm_1.0.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human650v3acrlmm/bioconductor-human650v3acrlmm_1.0.3_src_all.tar.gz"], "md5": "4b0de367ccc0f7499dcffe21ef1893c2", "fn": "human650v3aCrlmm_1.0.3.tar.gz"}, "human660quadv1acrlmm-1.0.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/human660quadv1aCrlmm_1.0.3.tar.gz", "https://bioarchive.galaxyproject.org/human660quadv1aCrlmm_1.0.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human660quadv1acrlmm/bioconductor-human660quadv1acrlmm_1.0.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human660quadv1acrlmm/bioconductor-human660quadv1acrlmm_1.0.3_src_all.tar.gz"], "md5": "5fd2d94a462e150c888f13c5c0975c36", "fn": "human660quadv1aCrlmm_1.0.3.tar.gz"}, "humanchrloc-2.1.6": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/humanCHRLOC_2.1.6.tar.gz", "https://bioarchive.galaxyproject.org/humanCHRLOC_2.1.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanchrloc/bioconductor-humanchrloc_2.1.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanchrloc/bioconductor-humanchrloc_2.1.6_src_all.tar.gz"], "md5": "113450c0822000c9b4e8a0141cf4b819", "fn": "humanCHRLOC_2.1.6.tar.gz"}, "humancytosnp12v2p1hcrlmm-1.0.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/humancytosnp12v2p1hCrlmm_1.0.1.tar.gz", "https://bioarchive.galaxyproject.org/humancytosnp12v2p1hCrlmm_1.0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humancytosnp12v2p1hcrlmm/bioconductor-humancytosnp12v2p1hcrlmm_1.0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humancytosnp12v2p1hcrlmm/bioconductor-humancytosnp12v2p1hcrlmm_1.0.1_src_all.tar.gz"], "md5": "edf80245ddb28afb9fbaa6668187bf3a", "fn": "humancytosnp12v2p1hCrlmm_1.0.1.tar.gz"}, "humanomni1quadv1bcrlmm-1.0.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/humanomni1quadv1bCrlmm_1.0.3.tar.gz", "https://bioarchive.galaxyproject.org/humanomni1quadv1bCrlmm_1.0.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanomni1quadv1bcrlmm/bioconductor-humanomni1quadv1bcrlmm_1.0.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanomni1quadv1bcrlmm/bioconductor-humanomni1quadv1bcrlmm_1.0.3_src_all.tar.gz"], "md5": "e81b2603f37d4cda3f28cd69a7296a23", "fn": "humanomni1quadv1bCrlmm_1.0.3.tar.gz"}, "humanomni25quadv1bcrlmm-1.0.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/humanomni25quadv1bCrlmm_1.0.2.tar.gz", "https://bioarchive.galaxyproject.org/humanomni25quadv1bCrlmm_1.0.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanomni25quadv1bcrlmm/bioconductor-humanomni25quadv1bcrlmm_1.0.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanomni25quadv1bcrlmm/bioconductor-humanomni25quadv1bcrlmm_1.0.2_src_all.tar.gz"], "md5": "2ee1fa7bf712d7f81a167079c975d49f", "fn": "humanomni25quadv1bCrlmm_1.0.2.tar.gz"}, "humanomni5quadv1bcrlmm-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/humanomni5quadv1bCrlmm_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/humanomni5quadv1bCrlmm_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanomni5quadv1bcrlmm/bioconductor-humanomni5quadv1bcrlmm_1.0.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanomni5quadv1bcrlmm/bioconductor-humanomni5quadv1bcrlmm_1.0.0_src_all.tar.gz"], "md5": "3ac4d6867c3d5590a6308d6edff0912b", "fn": "humanomni5quadv1bCrlmm_1.0.0.tar.gz"}, "humanomniexpress12v1bcrlmm-1.0.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/humanomniexpress12v1bCrlmm_1.0.1.tar.gz", "https://bioarchive.galaxyproject.org/humanomniexpress12v1bCrlmm_1.0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanomniexpress12v1bcrlmm/bioconductor-humanomniexpress12v1bcrlmm_1.0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanomniexpress12v1bcrlmm/bioconductor-humanomniexpress12v1bcrlmm_1.0.1_src_all.tar.gz"], "md5": "abdb730fc230db669e588e024ee7624b", "fn": "humanomniexpress12v1bCrlmm_1.0.1.tar.gz"}, "huo22.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/HuO22.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/HuO22.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huo22.db/bioconductor-huo22.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huo22.db/bioconductor-huo22.db_3.2.3_src_all.tar.gz"], "md5": "ddabf6c01f94c1dfd6ab35b40852828a", "fn": "HuO22.db_3.2.3.tar.gz"}, "hwgcod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hwgcod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/hwgcod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hwgcod.db/bioconductor-hwgcod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hwgcod.db/bioconductor-hwgcod.db_3.4.0_src_all.tar.gz"], "md5": "a46bf1a242853bbab26351a11b18030a", "fn": "hwgcod.db_3.4.0.tar.gz"}, "illuminahumanmethylation27k.db-1.4.8": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/IlluminaHumanMethylation27k.db_1.4.8.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation27k.db_1.4.8.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27k.db/bioconductor-illuminahumanmethylation27k.db_1.4.8_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27k.db/bioconductor-illuminahumanmethylation27k.db_1.4.8_src_all.tar.gz"], "md5": "70586bda9db01d598723bb439c315367", "fn": "IlluminaHumanMethylation27k.db_1.4.8.tar.gz"}, "illuminahumanmethylation27kanno.ilmn12.hg19-0.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/IlluminaHumanMethylation27kanno.ilmn12.hg19_0.6.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation27kanno.ilmn12.hg19_0.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19_0.6.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19_0.6.0_src_all.tar.gz"], "md5": "765851336506120467c2e3cc6beef7ed", "fn": "IlluminaHumanMethylation27kanno.ilmn12.hg19_0.6.0.tar.gz"}, "illuminahumanmethylation27kmanifest-0.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/IlluminaHumanMethylation27kmanifest_0.4.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation27kmanifest_0.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27kmanifest/bioconductor-illuminahumanmethylation27kmanifest_0.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27kmanifest/bioconductor-illuminahumanmethylation27kmanifest_0.4.0_src_all.tar.gz"], "md5": "c4cdda637dccf85f193342c7262b02a6", "fn": "IlluminaHumanMethylation27kmanifest_0.4.0.tar.gz"}, "illuminahumanmethylation450kanno.ilmn12.hg19-0.6.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19_0.6.1_src_all.tar.gz"], "md5": "aeafc54d887b128ed265fa704a3efa42", "fn": "IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1.tar.gz"}, "illuminahumanmethylation450kmanifest-0.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kmanifest/bioconductor-illuminahumanmethylation450kmanifest_0.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kmanifest/bioconductor-illuminahumanmethylation450kmanifest_0.4.0_src_all.tar.gz"], "md5": "664d1f5a3892974334faa26757269509", "fn": "IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz"}, "illuminahumanmethylation450kprobe-2.0.6": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/IlluminaHumanMethylation450kprobe_2.0.6.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation450kprobe_2.0.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kprobe/bioconductor-illuminahumanmethylation450kprobe_2.0.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kprobe/bioconductor-illuminahumanmethylation450kprobe_2.0.6_src_all.tar.gz"], "md5": "84c31861fcbaddbf2a9c500b8d8d767d", "fn": "IlluminaHumanMethylation450kprobe_2.0.6.tar.gz"}, "illuminahumanmethylationepicanno.ilm10b2.hg19-0.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19_0.6.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19_0.6.0_src_all.tar.gz"], "md5": "6a8e2398a0f930aa7828a1412fb21e88", "fn": "IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz"}, "illuminahumanmethylationepicanno.ilm10b3.hg19-0.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19_0.6.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19_0.6.0_src_all.tar.gz"], "md5": "2dac8e889486386eaea1bb7ce1beea2e", "fn": "IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz"}, "illuminahumanmethylationepicanno.ilm10b4.hg19-0.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19_0.6.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19_0.6.0_src_all.tar.gz"], "md5": "2d0c05917bcbf9ba1e354380d4e17a77", "fn": "IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz"}, "illuminahumanmethylationepicmanifest-0.3.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicmanifest/bioconductor-illuminahumanmethylationepicmanifest_0.3.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicmanifest/bioconductor-illuminahumanmethylationepicmanifest_0.3.0_src_all.tar.gz"], "md5": "c6b0268de177badfe0b8184002da7e16", "fn": "IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz"}, "illuminahumanv1.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/illuminaHumanv1.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaHumanv1.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv1.db/bioconductor-illuminahumanv1.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv1.db/bioconductor-illuminahumanv1.db_1.26.0_src_all.tar.gz"], "md5": "2c362256b7be2861b8bf6e0d1fe46786", "fn": "illuminaHumanv1.db_1.26.0.tar.gz"}, "illuminahumanv2.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/illuminaHumanv2.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaHumanv2.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv2.db/bioconductor-illuminahumanv2.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv2.db/bioconductor-illuminahumanv2.db_1.26.0_src_all.tar.gz"], "md5": "006de5f671a9a68fb27a6b6bce39c555", "fn": "illuminaHumanv2.db_1.26.0.tar.gz"}, "illuminahumanv2beadid.db-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/illuminaHumanv2BeadID.db_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaHumanv2BeadID.db_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv2beadid.db/bioconductor-illuminahumanv2beadid.db_1.8.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv2beadid.db/bioconductor-illuminahumanv2beadid.db_1.8.0_src_all.tar.gz"], "md5": "b5a2b2deaa9a9b245a141043e7bc5270", "fn": "illuminaHumanv2BeadID.db_1.8.0.tar.gz"}, "illuminahumanv3.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/illuminaHumanv3.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaHumanv3.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv3.db/bioconductor-illuminahumanv3.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv3.db/bioconductor-illuminahumanv3.db_1.26.0_src_all.tar.gz"], "md5": "7d9e7534f0b60f0e3e7473e545ef373d", "fn": "illuminaHumanv3.db_1.26.0.tar.gz"}, "illuminahumanv4.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/illuminaHumanv4.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaHumanv4.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv4.db/bioconductor-illuminahumanv4.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv4.db/bioconductor-illuminahumanv4.db_1.26.0_src_all.tar.gz"], "md5": "42d554559ac0106dc71317ffaf466421", "fn": "illuminaHumanv4.db_1.26.0.tar.gz"}, "illuminahumanwgdaslv3.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/illuminaHumanWGDASLv3.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaHumanWGDASLv3.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanwgdaslv3.db/bioconductor-illuminahumanwgdaslv3.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanwgdaslv3.db/bioconductor-illuminahumanwgdaslv3.db_1.26.0_src_all.tar.gz"], "md5": "32e8e24555c16f6d0148438d4a841ab8", "fn": "illuminaHumanWGDASLv3.db_1.26.0.tar.gz"}, "illuminahumanwgdaslv4.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/illuminaHumanWGDASLv4.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaHumanWGDASLv4.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanwgdaslv4.db/bioconductor-illuminahumanwgdaslv4.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanwgdaslv4.db/bioconductor-illuminahumanwgdaslv4.db_1.26.0_src_all.tar.gz"], "md5": "4cc1f192de838f2b6c1b148706d354ca", "fn": "illuminaHumanWGDASLv4.db_1.26.0.tar.gz"}, "illuminamousev1.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/illuminaMousev1.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaMousev1.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminamousev1.db/bioconductor-illuminamousev1.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminamousev1.db/bioconductor-illuminamousev1.db_1.26.0_src_all.tar.gz"], "md5": "13818c3b9acabe75550492bbe638fc05", "fn": "illuminaMousev1.db_1.26.0.tar.gz"}, "illuminamousev1p1.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/illuminaMousev1p1.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaMousev1p1.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminamousev1p1.db/bioconductor-illuminamousev1p1.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminamousev1p1.db/bioconductor-illuminamousev1p1.db_1.26.0_src_all.tar.gz"], "md5": "f6a4af01480a6f8d1d2d9b9b64a2b073", "fn": "illuminaMousev1p1.db_1.26.0.tar.gz"}, "illuminamousev2.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/illuminaMousev2.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaMousev2.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminamousev2.db/bioconductor-illuminamousev2.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminamousev2.db/bioconductor-illuminamousev2.db_1.26.0_src_all.tar.gz"], "md5": "fba228a71f264f976d8cdb035861974d", "fn": "illuminaMousev2.db_1.26.0.tar.gz"}, "illuminaratv1.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/illuminaRatv1.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaRatv1.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminaratv1.db/bioconductor-illuminaratv1.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminaratv1.db/bioconductor-illuminaratv1.db_1.26.0_src_all.tar.gz"], "md5": "5de2324d7b96c0cdb3301ef269341aa8", "fn": "illuminaRatv1.db_1.26.0.tar.gz"}, "indac.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/indac.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/indac.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-indac.db/bioconductor-indac.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-indac.db/bioconductor-indac.db_3.2.3_src_all.tar.gz"], "md5": "cba72edcf7278033151e0eac077d8ff8", "fn": "indac.db_3.2.3.tar.gz"}, "jaspar2018-1.1.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/JASPAR2018_1.1.1.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2018_1.1.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2018/bioconductor-jaspar2018_1.1.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2018/bioconductor-jaspar2018_1.1.1_src_all.tar.gz"], "md5": "d91fce6ea0dc9fa6a3be6ebc05c1af5d", "fn": "JASPAR2018_1.1.1.tar.gz"}, "jaspar2020-0.99.10": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/JASPAR2020_0.99.10.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2020_0.99.10.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2020/bioconductor-jaspar2020_0.99.10_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2020/bioconductor-jaspar2020_0.99.10_src_all.tar.gz"], "md5": "bfcaf41ebf0935b8d146afd37719de2d", "fn": "JASPAR2020_0.99.10.tar.gz"}, "jaspar2022-0.99.7": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/JASPAR2022_0.99.7.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2022_0.99.7.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2022/bioconductor-jaspar2022_0.99.7_src_all.tar.gz"], "md5": "282af23228198a377fa9bd76c94dd5eb", "fn": "JASPAR2022_0.99.7.tar.gz"}, "jazaerimetadata.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/JazaeriMetaData.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/JazaeriMetaData.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jazaerimetadata.db/bioconductor-jazaerimetadata.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jazaerimetadata.db/bioconductor-jazaerimetadata.db_3.2.3_src_all.tar.gz"], "md5": "3a154a74ac2acebe3471b039c9d9a4dc", "fn": "JazaeriMetaData.db_3.2.3.tar.gz"}, "lapointe.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/LAPOINTE.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/LAPOINTE.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lapointe.db/bioconductor-lapointe.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lapointe.db/bioconductor-lapointe.db_3.2.3_src_all.tar.gz"], "md5": "434b25ad7411201d8be6bb1a0463b387", "fn": "LAPOINTE.db_3.2.3.tar.gz"}, "lowmacaannotation-0.99.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/LowMACAAnnotation_0.99.3.tar.gz", "https://bioarchive.galaxyproject.org/LowMACAAnnotation_0.99.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lowmacaannotation/bioconductor-lowmacaannotation_0.99.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lowmacaannotation/bioconductor-lowmacaannotation_0.99.3_src_all.tar.gz"], "md5": "9e0d3fe7f30fe48aef9c4387eb5bacfa", "fn": "LowMACAAnnotation_0.99.3.tar.gz"}, "lumihumanall.db-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/lumiHumanAll.db_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/lumiHumanAll.db_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumihumanall.db/bioconductor-lumihumanall.db_1.22.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumihumanall.db/bioconductor-lumihumanall.db_1.22.0_src_all.tar.gz"], "md5": "ce7e219b50833ceab203f0bbfb11d917", "fn": "lumiHumanAll.db_1.22.0.tar.gz"}, "lumihumanidmapping-1.10.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/lumiHumanIDMapping_1.10.1.tar.gz", "https://bioarchive.galaxyproject.org/lumiHumanIDMapping_1.10.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumihumanidmapping/bioconductor-lumihumanidmapping_1.10.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumihumanidmapping/bioconductor-lumihumanidmapping_1.10.1_src_all.tar.gz"], "md5": "007e5aa2f1596cc08d888ba6dce7148a", "fn": "lumiHumanIDMapping_1.10.1.tar.gz"}, "lumimouseall.db-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/lumiMouseAll.db_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/lumiMouseAll.db_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumimouseall.db/bioconductor-lumimouseall.db_1.22.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumimouseall.db/bioconductor-lumimouseall.db_1.22.0_src_all.tar.gz"], "md5": "6f12330377aaddc83bfa9c37477b999e", "fn": "lumiMouseAll.db_1.22.0.tar.gz"}, "lumimouseidmapping-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/lumiMouseIDMapping_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/lumiMouseIDMapping_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumimouseidmapping/bioconductor-lumimouseidmapping_1.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumimouseidmapping/bioconductor-lumimouseidmapping_1.10.0_src_all.tar.gz"], "md5": "305aba80ebf6ef4c26899302ea9e50e8", "fn": "lumiMouseIDMapping_1.10.0.tar.gz"}, "lumiratall.db-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/lumiRatAll.db_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/lumiRatAll.db_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumiratall.db/bioconductor-lumiratall.db_1.22.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumiratall.db/bioconductor-lumiratall.db_1.22.0_src_all.tar.gz"], "md5": "65027624574d5e33f18b0a54a54f4be9", "fn": "lumiRatAll.db_1.22.0.tar.gz"}, "lumiratidmapping-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/lumiRatIDMapping_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/lumiRatIDMapping_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumiratidmapping/bioconductor-lumiratidmapping_1.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumiratidmapping/bioconductor-lumiratidmapping_1.10.0_src_all.tar.gz"], "md5": "1122fc25e3fff62678bed36f9d7b5709", "fn": "lumiRatIDMapping_1.10.0.tar.gz"}, "lymphoseqdb-0.99.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/LymphoSeqDB_0.99.2.tar.gz", "https://bioarchive.galaxyproject.org/LymphoSeqDB_0.99.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lymphoseqdb/bioconductor-lymphoseqdb_0.99.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lymphoseqdb/bioconductor-lymphoseqdb_0.99.2_src_all.tar.gz"], "md5": "22fc0dc2439ef497982a5ffddda1e418", "fn": "LymphoSeqDB_0.99.2.tar.gz"}, "m10kcod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/m10kcod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/m10kcod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-m10kcod.db/bioconductor-m10kcod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-m10kcod.db/bioconductor-m10kcod.db_3.4.0_src_all.tar.gz"], "md5": "04811628e4b37cd6d24e0b2a17d79ab8", "fn": "m10kcod.db_3.4.0.tar.gz"}, "m20kcod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/m20kcod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/m20kcod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-m20kcod.db/bioconductor-m20kcod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-m20kcod.db/bioconductor-m20kcod.db_3.4.0_src_all.tar.gz"], "md5": "f2f734fb41e1ae4e949abf09687733bf", "fn": "m20kcod.db_3.4.0.tar.gz"}, "mafdb.1kgenomes.phase1.grch38-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MafDb.1Kgenomes.phase1.GRCh38_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.1Kgenomes.phase1.GRCh38_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase1.grch38/bioconductor-mafdb.1kgenomes.phase1.grch38_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase1.grch38/bioconductor-mafdb.1kgenomes.phase1.grch38_3.10.0_src_all.tar.gz"], "md5": "a20471906a41678ce710879e92d2a9dc", "fn": "MafDb.1Kgenomes.phase1.GRCh38_3.10.0.tar.gz"}, "mafdb.1kgenomes.phase1.hs37d5-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MafDb.1Kgenomes.phase1.hs37d5_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.1Kgenomes.phase1.hs37d5_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase1.hs37d5/bioconductor-mafdb.1kgenomes.phase1.hs37d5_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase1.hs37d5/bioconductor-mafdb.1kgenomes.phase1.hs37d5_3.10.0_src_all.tar.gz"], "md5": "ece6b758ca0e1a8a307b5cd5829671f4", "fn": "MafDb.1Kgenomes.phase1.hs37d5_3.10.0.tar.gz"}, "mafdb.1kgenomes.phase3.grch38-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.GRCh38_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.1Kgenomes.phase3.GRCh38_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase3.grch38/bioconductor-mafdb.1kgenomes.phase3.grch38_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase3.grch38/bioconductor-mafdb.1kgenomes.phase3.grch38_3.10.0_src_all.tar.gz"], "md5": "ee57d9cb6a1748932407d20b9bffd8a2", "fn": "MafDb.1Kgenomes.phase3.GRCh38_3.10.0.tar.gz"}, "mafdb.1kgenomes.phase3.hs37d5-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.hs37d5_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.1Kgenomes.phase3.hs37d5_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase3.hs37d5/bioconductor-mafdb.1kgenomes.phase3.hs37d5_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase3.hs37d5/bioconductor-mafdb.1kgenomes.phase3.hs37d5_3.10.0_src_all.tar.gz"], "md5": "ac3cbbf52eb2026f067a4f42c6654555", "fn": "MafDb.1Kgenomes.phase3.hs37d5_3.10.0.tar.gz"}, "mafdb.exac.r1.0.grch38-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MafDb.ExAC.r1.0.GRCh38_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.ExAC.r1.0.GRCh38_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.grch38/bioconductor-mafdb.exac.r1.0.grch38_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.grch38/bioconductor-mafdb.exac.r1.0.grch38_3.10.0_src_all.tar.gz"], "md5": "303332c918996d8cb3e7b7c74d694dd1", "fn": "MafDb.ExAC.r1.0.GRCh38_3.10.0.tar.gz"}, "mafdb.exac.r1.0.hs37d5-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MafDb.ExAC.r1.0.hs37d5_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.ExAC.r1.0.hs37d5_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.hs37d5/bioconductor-mafdb.exac.r1.0.hs37d5_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.hs37d5/bioconductor-mafdb.exac.r1.0.hs37d5_3.10.0_src_all.tar.gz"], "md5": "4d523554a2b0eb296bada9d33a78eefc", "fn": "MafDb.ExAC.r1.0.hs37d5_3.10.0.tar.gz"}, "mafdb.exac.r1.0.nontcga.grch38-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MafDb.ExAC.r1.0.nonTCGA.GRCh38_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.ExAC.r1.0.nonTCGA.GRCh38_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.nontcga.grch38/bioconductor-mafdb.exac.r1.0.nontcga.grch38_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.nontcga.grch38/bioconductor-mafdb.exac.r1.0.nontcga.grch38_3.10.0_src_all.tar.gz"], "md5": "cf447f59cc8b1cd7ca395fd3fe6e4730", "fn": "MafDb.ExAC.r1.0.nonTCGA.GRCh38_3.10.0.tar.gz"}, "mafdb.exac.r1.0.nontcga.hs37d5-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MafDb.ExAC.r1.0.nonTCGA.hs37d5_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.ExAC.r1.0.nonTCGA.hs37d5_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5_3.10.0_src_all.tar.gz"], "md5": "da3a699e9776b0b769b3bc1e9fb742f0", "fn": "MafDb.ExAC.r1.0.nonTCGA.hs37d5_3.10.0.tar.gz"}, "mafdb.gnomad.r2.1.grch38-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MafDb.gnomAD.r2.1.GRCh38_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.gnomAD.r2.1.GRCh38_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomad.r2.1.grch38/bioconductor-mafdb.gnomad.r2.1.grch38_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomad.r2.1.grch38/bioconductor-mafdb.gnomad.r2.1.grch38_3.10.0_src_all.tar.gz"], "md5": "0e842b24476aeb834f57f9302a36ea18", "fn": "MafDb.gnomAD.r2.1.GRCh38_3.10.0.tar.gz"}, "mafdb.gnomad.r2.1.hs37d5-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MafDb.gnomAD.r2.1.hs37d5_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.gnomAD.r2.1.hs37d5_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomad.r2.1.hs37d5/bioconductor-mafdb.gnomad.r2.1.hs37d5_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomad.r2.1.hs37d5/bioconductor-mafdb.gnomad.r2.1.hs37d5_3.10.0_src_all.tar.gz"], "md5": "12221c461930ae1ecfe925943a619d56", "fn": "MafDb.gnomAD.r2.1.hs37d5_3.10.0.tar.gz"}, "mafdb.gnomadex.r2.1.grch38-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MafDb.gnomADex.r2.1.GRCh38_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.gnomADex.r2.1.GRCh38_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomadex.r2.1.grch38/bioconductor-mafdb.gnomadex.r2.1.grch38_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomadex.r2.1.grch38/bioconductor-mafdb.gnomadex.r2.1.grch38_3.10.0_src_all.tar.gz"], "md5": "a0ab5b74997669fabb8aecfd9ef7f767", "fn": "MafDb.gnomADex.r2.1.GRCh38_3.10.0.tar.gz"}, "mafdb.gnomadex.r2.1.hs37d5-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MafDb.gnomADex.r2.1.hs37d5_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.gnomADex.r2.1.hs37d5_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomadex.r2.1.hs37d5/bioconductor-mafdb.gnomadex.r2.1.hs37d5_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomadex.r2.1.hs37d5/bioconductor-mafdb.gnomadex.r2.1.hs37d5_3.10.0_src_all.tar.gz"], "md5": "6ca4d742571687a13906d99cea2dbf1f", "fn": "MafDb.gnomADex.r2.1.hs37d5_3.10.0.tar.gz"}, "mafdb.topmed.freeze5.hg19-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MafDb.TOPMed.freeze5.hg19_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.TOPMed.freeze5.hg19_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.topmed.freeze5.hg19/bioconductor-mafdb.topmed.freeze5.hg19_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.topmed.freeze5.hg19/bioconductor-mafdb.topmed.freeze5.hg19_3.10.0_src_all.tar.gz"], "md5": "7fdb58eb69187ade189689da58ca6266", "fn": "MafDb.TOPMed.freeze5.hg19_3.10.0.tar.gz"}, "mafdb.topmed.freeze5.hg38-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MafDb.TOPMed.freeze5.hg38_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.TOPMed.freeze5.hg38_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.topmed.freeze5.hg38/bioconductor-mafdb.topmed.freeze5.hg38_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.topmed.freeze5.hg38/bioconductor-mafdb.topmed.freeze5.hg38_3.10.0_src_all.tar.gz"], "md5": "a3355623fde26b83dfd346a32829f073", "fn": "MafDb.TOPMed.freeze5.hg38_3.10.0.tar.gz"}, "mafh5.gnomad.v3.1.1.grch38-3.13.1": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/MafH5.gnomAD.v3.1.1.GRCh38_3.13.1.tar.gz", "https://bioarchive.galaxyproject.org/MafH5.gnomAD.v3.1.1.GRCh38_3.13.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafh5.gnomad.v3.1.1.grch38/bioconductor-mafh5.gnomad.v3.1.1.grch38_3.13.1_src_all.tar.gz"], "md5": "8944d686ba1ac335f6e76594b7c92ebe", "fn": "MafH5.gnomAD.v3.1.1.GRCh38_3.13.1.tar.gz"}, "mafh5.gnomad.v3.1.2.grch38-3.15.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MafH5.gnomAD.v3.1.2.GRCh38_3.15.0.tar.gz", "https://bioarchive.galaxyproject.org/MafH5.gnomAD.v3.1.2.GRCh38_3.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafh5.gnomad.v3.1.2.grch38/bioconductor-mafh5.gnomad.v3.1.2.grch38_3.15.0_src_all.tar.gz"], "md5": "e9c85173866caf998cf1af7dd35aac0b", "fn": "MafH5.gnomAD.v3.1.2.GRCh38_3.15.0.tar.gz"}, "maizecdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/maizecdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/maizecdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maizecdf/bioconductor-maizecdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maizecdf/bioconductor-maizecdf_2.18.0_src_all.tar.gz"], "md5": "f9dec9e46688d96daf1e07d4e815afb4", "fn": "maizecdf_2.18.0.tar.gz"}, "maizeprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/maizeprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/maizeprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maizeprobe/bioconductor-maizeprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maizeprobe/bioconductor-maizeprobe_2.18.0_src_all.tar.gz"], "md5": "ef7ba47de2346b3552621263399c05d1", "fn": "maizeprobe_2.18.0.tar.gz"}, "malaria.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/malaria.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/malaria.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-malaria.db0/bioconductor-malaria.db0_3.16.0_src_all.tar.gz"], "md5": "8cd45b5614ebfab6530cf9eefc57cfdb", "fn": "malaria.db0_3.16.0.tar.gz"}, "medicagocdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/medicagocdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/medicagocdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-medicagocdf/bioconductor-medicagocdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-medicagocdf/bioconductor-medicagocdf_2.18.0_src_all.tar.gz"], "md5": "1fbb2e4c070344d18e65f1b3993867db", "fn": "medicagocdf_2.18.0.tar.gz"}, "medicagoprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/medicagoprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/medicagoprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-medicagoprobe/bioconductor-medicagoprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-medicagoprobe/bioconductor-medicagoprobe_2.18.0_src_all.tar.gz"], "md5": "83b9887ad2ed26c704b0ca7115e5838d", "fn": "medicagoprobe_2.18.0.tar.gz"}, "metaboliteidmapping-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/metaboliteIDmapping_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/metaboliteIDmapping_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metaboliteidmapping/bioconductor-metaboliteidmapping_1.0.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metaboliteidmapping/bioconductor-metaboliteidmapping_1.0.0_src_all.tar.gz"], "md5": "bd78ec373ce90fac1a10d2c64c462e77", "fn": "metaboliteIDmapping_1.0.0.tar.gz"}, "mgu74a.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgu74a.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74a.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74a.db/bioconductor-mgu74a.db_3.13.0_src_all.tar.gz"], "md5": "9fb75c159c50e2ae316ee5a8abe1a48c", "fn": "mgu74a.db_3.13.0.tar.gz"}, "mgu74acdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgu74acdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74acdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74acdf/bioconductor-mgu74acdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74acdf/bioconductor-mgu74acdf_2.18.0_src_all.tar.gz"], "md5": "ed6e86398e51c7b0ddca4431797ecbc0", "fn": "mgu74acdf_2.18.0.tar.gz"}, "mgu74aprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgu74aprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74aprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74aprobe/bioconductor-mgu74aprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74aprobe/bioconductor-mgu74aprobe_2.18.0_src_all.tar.gz"], "md5": "7fea6d44856203e6293e0cd9fe1ad066", "fn": "mgu74aprobe_2.18.0.tar.gz"}, "mgu74av2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgu74av2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74av2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74av2.db/bioconductor-mgu74av2.db_3.13.0_src_all.tar.gz"], "md5": "3205856d0c7725acded5238415e907bc", "fn": "mgu74av2.db_3.13.0.tar.gz"}, "mgu74av2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgu74av2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74av2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74av2cdf/bioconductor-mgu74av2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74av2cdf/bioconductor-mgu74av2cdf_2.18.0_src_all.tar.gz"], "md5": "35e2abb9fbfd68d90dc32a2faae00c95", "fn": "mgu74av2cdf_2.18.0.tar.gz"}, "mgu74av2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgu74av2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74av2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74av2probe/bioconductor-mgu74av2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74av2probe/bioconductor-mgu74av2probe_2.18.0_src_all.tar.gz"], "md5": "ac540b0e26b14a411740233b02d3e11c", "fn": "mgu74av2probe_2.18.0.tar.gz"}, "mgu74b.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgu74b.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74b.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74b.db/bioconductor-mgu74b.db_3.13.0_src_all.tar.gz"], "md5": "205577a6e41d56910f221ffb940ee25b", "fn": "mgu74b.db_3.13.0.tar.gz"}, "mgu74bcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgu74bcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74bcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74bcdf/bioconductor-mgu74bcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74bcdf/bioconductor-mgu74bcdf_2.18.0_src_all.tar.gz"], "md5": "a1f0f98f29d34a421622447252113e1e", "fn": "mgu74bcdf_2.18.0.tar.gz"}, "mgu74bprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgu74bprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74bprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74bprobe/bioconductor-mgu74bprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74bprobe/bioconductor-mgu74bprobe_2.18.0_src_all.tar.gz"], "md5": "224d606e6fc87592d387dbaabe5cd353", "fn": "mgu74bprobe_2.18.0.tar.gz"}, "mgu74bv2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgu74bv2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74bv2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74bv2.db/bioconductor-mgu74bv2.db_3.13.0_src_all.tar.gz"], "md5": "4ec0fbed7343f0578ef11e2330d0d12a", "fn": "mgu74bv2.db_3.13.0.tar.gz"}, "mgu74bv2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgu74bv2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74bv2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74bv2cdf/bioconductor-mgu74bv2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74bv2cdf/bioconductor-mgu74bv2cdf_2.18.0_src_all.tar.gz"], "md5": "45c48d11af03633dc10f8682b7ad74c5", "fn": "mgu74bv2cdf_2.18.0.tar.gz"}, "mgu74bv2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgu74bv2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74bv2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74bv2probe/bioconductor-mgu74bv2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74bv2probe/bioconductor-mgu74bv2probe_2.18.0_src_all.tar.gz"], "md5": "f6a12f88ea3c43a3e885c7e9b3fd03d2", "fn": "mgu74bv2probe_2.18.0.tar.gz"}, "mgu74c.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgu74c.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74c.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74c.db/bioconductor-mgu74c.db_3.13.0_src_all.tar.gz"], "md5": "6c4f183e6ed5f0b5735596e7544746ae", "fn": "mgu74c.db_3.13.0.tar.gz"}, "mgu74ccdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgu74ccdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74ccdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74ccdf/bioconductor-mgu74ccdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74ccdf/bioconductor-mgu74ccdf_2.18.0_src_all.tar.gz"], "md5": "172e626b0e3072edc65c4efff35fe998", "fn": "mgu74ccdf_2.18.0.tar.gz"}, "mgu74cprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgu74cprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74cprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74cprobe/bioconductor-mgu74cprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74cprobe/bioconductor-mgu74cprobe_2.18.0_src_all.tar.gz"], "md5": "186992992708f0071fd552ef92b9e25c", "fn": "mgu74cprobe_2.18.0.tar.gz"}, "mgu74cv2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgu74cv2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74cv2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74cv2.db/bioconductor-mgu74cv2.db_3.13.0_src_all.tar.gz"], "md5": "1f860dfbf4400ede54eb30d9a70ec131", "fn": "mgu74cv2.db_3.13.0.tar.gz"}, "mgu74cv2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgu74cv2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74cv2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74cv2cdf/bioconductor-mgu74cv2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74cv2cdf/bioconductor-mgu74cv2cdf_2.18.0_src_all.tar.gz"], "md5": "9ef62b4b28f97770859db24393a07ed5", "fn": "mgu74cv2cdf_2.18.0.tar.gz"}, "mgu74cv2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgu74cv2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74cv2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74cv2probe/bioconductor-mgu74cv2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74cv2probe/bioconductor-mgu74cv2probe_2.18.0_src_all.tar.gz"], "md5": "0373496c817a1c1a153114047cfa7c5b", "fn": "mgu74cv2probe_2.18.0.tar.gz"}, "mguatlas5k.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mguatlas5k.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/mguatlas5k.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mguatlas5k.db/bioconductor-mguatlas5k.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mguatlas5k.db/bioconductor-mguatlas5k.db_3.2.3_src_all.tar.gz"], "md5": "826093fe7228c08962aff36ad89af28e", "fn": "mguatlas5k.db_3.2.3.tar.gz"}, "mgug4104a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgug4104a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/mgug4104a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgug4104a.db/bioconductor-mgug4104a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgug4104a.db/bioconductor-mgug4104a.db_3.2.3_src_all.tar.gz"], "md5": "7b1cef094a226257cd657ed8d61e9ef1", "fn": "mgug4104a.db_3.2.3.tar.gz"}, "mgug4120a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgug4120a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/mgug4120a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgug4120a.db/bioconductor-mgug4120a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgug4120a.db/bioconductor-mgug4120a.db_3.2.3_src_all.tar.gz"], "md5": "bb57e8b2efe3d038ec2a0ace0313a4e7", "fn": "mgug4120a.db_3.2.3.tar.gz"}, "mgug4121a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgug4121a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/mgug4121a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgug4121a.db/bioconductor-mgug4121a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgug4121a.db/bioconductor-mgug4121a.db_3.2.3_src_all.tar.gz"], "md5": "6b5cc321d5175356c383b91e30e120b7", "fn": "mgug4121a.db_3.2.3.tar.gz"}, "mgug4122a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mgug4122a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/mgug4122a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgug4122a.db/bioconductor-mgug4122a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgug4122a.db/bioconductor-mgug4122a.db_3.2.3_src_all.tar.gz"], "md5": "5fcdce909ac1c0ccbf06bf6411f6fe52", "fn": "mgug4122a.db_3.2.3.tar.gz"}, "mi16cod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mi16cod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/mi16cod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mi16cod.db/bioconductor-mi16cod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mi16cod.db/bioconductor-mi16cod.db_3.4.0_src_all.tar.gz"], "md5": "f3a8e6f45ce5c298c1b1c5b32bf2630c", "fn": "mi16cod.db_3.4.0.tar.gz"}, "mirbase.db-1.2.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mirbase.db_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/mirbase.db_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirbase.db/bioconductor-mirbase.db_1.2.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirbase.db/bioconductor-mirbase.db_1.2.0_src_all.tar.gz"], "md5": "316bc12cee8c2dd9240b7fc30cd1619e", "fn": "mirbase.db_1.2.0.tar.gz"}, "mirbaseversions.db-1.1.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/miRBaseVersions.db_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/miRBaseVersions.db_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirbaseversions.db/bioconductor-mirbaseversions.db_1.1.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirbaseversions.db/bioconductor-mirbaseversions.db_1.1.0_src_all.tar.gz"], "md5": "9944ab7a474f84a40100c56298f9cb77", "fn": "miRBaseVersions.db_1.1.0.tar.gz"}, "mirna102xgaincdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mirna102xgaincdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mirna102xgaincdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirna102xgaincdf/bioconductor-mirna102xgaincdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirna102xgaincdf/bioconductor-mirna102xgaincdf_2.18.0_src_all.tar.gz"], "md5": "9091a45c2ac15c2de0263743ab334f97", "fn": "mirna102xgaincdf_2.18.0.tar.gz"}, "mirna10cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mirna10cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mirna10cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirna10cdf/bioconductor-mirna10cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirna10cdf/bioconductor-mirna10cdf_2.18.0_src_all.tar.gz"], "md5": "814da2a2e298e132f4db0b2e8ab814be", "fn": "mirna10cdf_2.18.0.tar.gz"}, "mirna10probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mirna10probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mirna10probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirna10probe/bioconductor-mirna10probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirna10probe/bioconductor-mirna10probe_2.18.0_src_all.tar.gz"], "md5": "8bfa6cdfeee1c563b4881214bd5d4ce1", "fn": "mirna10probe_2.18.0.tar.gz"}, "mirna20cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mirna20cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mirna20cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirna20cdf/bioconductor-mirna20cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirna20cdf/bioconductor-mirna20cdf_2.18.0_src_all.tar.gz"], "md5": "56f7807673ff108427ae7f6bdf85ae1c", "fn": "mirna20cdf_2.18.0.tar.gz"}, "mirnatap.db-0.99.10": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/miRNAtap.db_0.99.10.tar.gz", "https://bioarchive.galaxyproject.org/miRNAtap.db_0.99.10.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirnatap.db/bioconductor-mirnatap.db_0.99.10_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirnatap.db/bioconductor-mirnatap.db_0.99.10_src_all.tar.gz"], "md5": "48010280b68d6f1ddbff3b374132ce0a", "fn": "miRNAtap.db_0.99.10.tar.gz"}, "mm24kresogen.db-2.5.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mm24kresogen.db_2.5.0.tar.gz", "https://bioarchive.galaxyproject.org/mm24kresogen.db_2.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mm24kresogen.db/bioconductor-mm24kresogen.db_2.5.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mm24kresogen.db/bioconductor-mm24kresogen.db_2.5.0_src_all.tar.gz"], "md5": "437f5d4bc225ee500af1ecc2d4da472b", "fn": "mm24kresogen.db_2.5.0.tar.gz"}, "mmagilentdesign026655.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MmAgilentDesign026655.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/MmAgilentDesign026655.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mmagilentdesign026655.db/bioconductor-mmagilentdesign026655.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mmagilentdesign026655.db/bioconductor-mmagilentdesign026655.db_3.2.3_src_all.tar.gz"], "md5": "7ef619bd2c74f22ea4f3c2b2c4131fe9", "fn": "MmAgilentDesign026655.db_3.2.3.tar.gz"}, "moe430a.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/moe430a.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/moe430a.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430a.db/bioconductor-moe430a.db_3.13.0_src_all.tar.gz"], "md5": "2bcdace3c55437bc8428b99064e486b1", "fn": "moe430a.db_3.13.0.tar.gz"}, "moe430acdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/moe430acdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/moe430acdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430acdf/bioconductor-moe430acdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430acdf/bioconductor-moe430acdf_2.18.0_src_all.tar.gz"], "md5": "b03f1295fc483f0d782a4615e8ca0137", "fn": "moe430acdf_2.18.0.tar.gz"}, "moe430aprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/moe430aprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/moe430aprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430aprobe/bioconductor-moe430aprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430aprobe/bioconductor-moe430aprobe_2.18.0_src_all.tar.gz"], "md5": "0aa83189d04599a65211d1a2f0a51c8f", "fn": "moe430aprobe_2.18.0.tar.gz"}, "moe430b.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/moe430b.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/moe430b.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430b.db/bioconductor-moe430b.db_3.13.0_src_all.tar.gz"], "md5": "2d8a80b9d3342fb943087cc327c824e7", "fn": "moe430b.db_3.13.0.tar.gz"}, "moe430bcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/moe430bcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/moe430bcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430bcdf/bioconductor-moe430bcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430bcdf/bioconductor-moe430bcdf_2.18.0_src_all.tar.gz"], "md5": "b7112dcf8ccfe4e079ca67ff62046f2e", "fn": "moe430bcdf_2.18.0.tar.gz"}, "moe430bprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/moe430bprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/moe430bprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430bprobe/bioconductor-moe430bprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430bprobe/bioconductor-moe430bprobe_2.18.0_src_all.tar.gz"], "md5": "1368e6f4225babe7a693ccd39a3a436a", "fn": "moe430bprobe_2.18.0.tar.gz"}, "moex10stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/moex10stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/moex10stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moex10stprobeset.db/bioconductor-moex10stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "b1c12c80a4424e2854beab9dc796cb00", "fn": "moex10stprobeset.db_8.8.0.tar.gz"}, "moex10sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/moex10sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/moex10sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moex10sttranscriptcluster.db/bioconductor-moex10sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "bc3357b3c77ab7bf1dfb66f5f7da36ec", "fn": "moex10sttranscriptcluster.db_8.8.0.tar.gz"}, "moexexonprobesetlocation-1.15.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MoExExonProbesetLocation_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/MoExExonProbesetLocation_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moexexonprobesetlocation/bioconductor-moexexonprobesetlocation_1.15.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moexexonprobesetlocation/bioconductor-moexexonprobesetlocation_1.15.0_src_all.tar.gz"], "md5": "07eea205fce2a8cf4585fa7e71fb0057", "fn": "MoExExonProbesetLocation_1.15.0.tar.gz"}, "mogene.1.0.st.v1frmavecs-1.1.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mogene.1.0.st.v1frmavecs_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene.1.0.st.v1frmavecs_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene.1.0.st.v1frmavecs/bioconductor-mogene.1.0.st.v1frmavecs_1.1.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene.1.0.st.v1frmavecs/bioconductor-mogene.1.0.st.v1frmavecs_1.1.0_src_all.tar.gz"], "md5": "b46f76903d0f19b85e8fa30347813ff5", "fn": "mogene.1.0.st.v1frmavecs_1.1.0.tar.gz"}, "mogene10stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mogene10stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene10stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene10stprobeset.db/bioconductor-mogene10stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "570d4cf3fcc42d1e9b54237b9e4eb5f7", "fn": "mogene10stprobeset.db_8.8.0.tar.gz"}, "mogene10sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mogene10sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene10sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene10sttranscriptcluster.db/bioconductor-mogene10sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "9553a8ecefad2baa7241c6b6bb8013f5", "fn": "mogene10sttranscriptcluster.db_8.8.0.tar.gz"}, "mogene10stv1cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mogene10stv1cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene10stv1cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene10stv1cdf/bioconductor-mogene10stv1cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene10stv1cdf/bioconductor-mogene10stv1cdf_2.18.0_src_all.tar.gz"], "md5": "9c0271f5d6493290fc47f041a8c3f925", "fn": "mogene10stv1cdf_2.18.0.tar.gz"}, "mogene10stv1probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mogene10stv1probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene10stv1probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene10stv1probe/bioconductor-mogene10stv1probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene10stv1probe/bioconductor-mogene10stv1probe_2.18.0_src_all.tar.gz"], "md5": "63cba1e2a0edee9f201267057fddb0fa", "fn": "mogene10stv1probe_2.18.0.tar.gz"}, "mogene11stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mogene11stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene11stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene11stprobeset.db/bioconductor-mogene11stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "1fba63da3f550e814a58c09d24d61cc0", "fn": "mogene11stprobeset.db_8.8.0.tar.gz"}, "mogene11sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mogene11sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene11sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene11sttranscriptcluster.db/bioconductor-mogene11sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "2a3bf07a4794e2349b7d09368dcb7d18", "fn": "mogene11sttranscriptcluster.db_8.8.0.tar.gz"}, "mogene20stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mogene20stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene20stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene20stprobeset.db/bioconductor-mogene20stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "a64ddbf33e4f2b96301452e808d0e81a", "fn": "mogene20stprobeset.db_8.8.0.tar.gz"}, "mogene20sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mogene20sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene20sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene20sttranscriptcluster.db/bioconductor-mogene20sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "e00e56d47bd19169875690e8e2129156", "fn": "mogene20sttranscriptcluster.db_8.8.0.tar.gz"}, "mogene21stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mogene21stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene21stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene21stprobeset.db/bioconductor-mogene21stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "d6b3c352329b46493a20f6c27db05d43", "fn": "mogene21stprobeset.db_8.8.0.tar.gz"}, "mogene21sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mogene21sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene21sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene21sttranscriptcluster.db/bioconductor-mogene21sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "10aaecc97bf06bfe770496b99612837a", "fn": "mogene21sttranscriptcluster.db_8.8.0.tar.gz"}, "mouse.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/mouse.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse.db0/bioconductor-mouse.db0_3.16.0_src_all.tar.gz"], "md5": "aac1d127bbce6e9a574a573335113db4", "fn": "mouse.db0_3.16.0.tar.gz"}, "mouse4302.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mouse4302.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse4302.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302.db/bioconductor-mouse4302.db_3.13.0_src_all.tar.gz"], "md5": "4ecaa53d32faca4199ba712c0e8ee570", "fn": "mouse4302.db_3.13.0.tar.gz"}, "mouse4302cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mouse4302cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse4302cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302cdf/bioconductor-mouse4302cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302cdf/bioconductor-mouse4302cdf_2.18.0_src_all.tar.gz"], "md5": "bda3463613f958de35c58777db05cec2", "fn": "mouse4302cdf_2.18.0.tar.gz"}, "mouse4302frmavecs-1.5.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mouse4302frmavecs_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse4302frmavecs_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302frmavecs/bioconductor-mouse4302frmavecs_1.5.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302frmavecs/bioconductor-mouse4302frmavecs_1.5.0_src_all.tar.gz"], "md5": "ec144b381abbe54d696356c1c124e372", "fn": "mouse4302frmavecs_1.5.0.tar.gz"}, "mouse4302probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mouse4302probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse4302probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302probe/bioconductor-mouse4302probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302probe/bioconductor-mouse4302probe_2.18.0_src_all.tar.gz"], "md5": "7116787a7db241a545e79e419a8cfa0d", "fn": "mouse4302probe_2.18.0.tar.gz"}, "mouse430a2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mouse430a2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse430a2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse430a2.db/bioconductor-mouse430a2.db_3.13.0_src_all.tar.gz"], "md5": "0f1d053517af5f973f3cc49289cca1e5", "fn": "mouse430a2.db_3.13.0.tar.gz"}, "mouse430a2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mouse430a2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse430a2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse430a2cdf/bioconductor-mouse430a2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse430a2cdf/bioconductor-mouse430a2cdf_2.18.0_src_all.tar.gz"], "md5": "1114c0415d1200bc21ad205e0830b075", "fn": "mouse430a2cdf_2.18.0.tar.gz"}, "mouse430a2frmavecs-1.3.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mouse430a2frmavecs_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse430a2frmavecs_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse430a2frmavecs/bioconductor-mouse430a2frmavecs_1.3.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse430a2frmavecs/bioconductor-mouse430a2frmavecs_1.3.0_src_all.tar.gz"], "md5": "3bcb8de9182bbb8de5d560748eafa0cc", "fn": "mouse430a2frmavecs_1.3.0.tar.gz"}, "mouse430a2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mouse430a2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse430a2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse430a2probe/bioconductor-mouse430a2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse430a2probe/bioconductor-mouse430a2probe_2.18.0_src_all.tar.gz"], "md5": "bb3c34477d4fcf03a539772011118795", "fn": "mouse430a2probe_2.18.0.tar.gz"}, "mousechrloc-2.1.6": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mouseCHRLOC_2.1.6.tar.gz", "https://bioarchive.galaxyproject.org/mouseCHRLOC_2.1.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousechrloc/bioconductor-mousechrloc_2.1.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousechrloc/bioconductor-mousechrloc_2.1.6_src_all.tar.gz"], "md5": "0b81d7391e628cc355af4de3c5585a5f", "fn": "mouseCHRLOC_2.1.6.tar.gz"}, "mpedbarray.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mpedbarray.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/mpedbarray.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mpedbarray.db/bioconductor-mpedbarray.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mpedbarray.db/bioconductor-mpedbarray.db_3.2.3_src_all.tar.gz"], "md5": "7bcd1fee1554b6f8844c9bf30b7db4ef", "fn": "mpedbarray.db_3.2.3.tar.gz"}, "mta10probeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mta10probeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mta10probeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mta10probeset.db/bioconductor-mta10probeset.db_8.8.0_src_all.tar.gz"], "md5": "84517c6b354690cd72ccefbe3b39d8e1", "fn": "mta10probeset.db_8.8.0.tar.gz"}, "mta10transcriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mta10transcriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mta10transcriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mta10transcriptcluster.db/bioconductor-mta10transcriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "bfd13b16b71ac2cfc82f40f2d102892b", "fn": "mta10transcriptcluster.db_8.8.0.tar.gz"}, "mu11ksuba.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mu11ksuba.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mu11ksuba.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksuba.db/bioconductor-mu11ksuba.db_3.13.0_src_all.tar.gz"], "md5": "73d80611d1eaf8ee1eb37ebc469d97e9", "fn": "mu11ksuba.db_3.13.0.tar.gz"}, "mu11ksubacdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mu11ksubacdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu11ksubacdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksubacdf/bioconductor-mu11ksubacdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksubacdf/bioconductor-mu11ksubacdf_2.18.0_src_all.tar.gz"], "md5": "52fb8ac56435775022fb62f40efafd22", "fn": "mu11ksubacdf_2.18.0.tar.gz"}, "mu11ksubaprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mu11ksubaprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu11ksubaprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksubaprobe/bioconductor-mu11ksubaprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksubaprobe/bioconductor-mu11ksubaprobe_2.18.0_src_all.tar.gz"], "md5": "813cd0750cca6ff0cfb696b83286177e", "fn": "mu11ksubaprobe_2.18.0.tar.gz"}, "mu11ksubb.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mu11ksubb.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mu11ksubb.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksubb.db/bioconductor-mu11ksubb.db_3.13.0_src_all.tar.gz"], "md5": "2b61d911c3595843e80041949cb79b41", "fn": "mu11ksubb.db_3.13.0.tar.gz"}, "mu11ksubbcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mu11ksubbcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu11ksubbcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksubbcdf/bioconductor-mu11ksubbcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksubbcdf/bioconductor-mu11ksubbcdf_2.18.0_src_all.tar.gz"], "md5": "f9691ea74e19dfe57bf6cca6ed396947", "fn": "mu11ksubbcdf_2.18.0.tar.gz"}, "mu11ksubbprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mu11ksubbprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu11ksubbprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksubbprobe/bioconductor-mu11ksubbprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksubbprobe/bioconductor-mu11ksubbprobe_2.18.0_src_all.tar.gz"], "md5": "28d162e18e4e16e3c6db47195d2ea0ac", "fn": "mu11ksubbprobe_2.18.0.tar.gz"}, "mu15v1.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/Mu15v1.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/Mu15v1.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu15v1.db/bioconductor-mu15v1.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu15v1.db/bioconductor-mu15v1.db_3.2.3_src_all.tar.gz"], "md5": "e9297b5fe223b046bc65dc6ea0b4376d", "fn": "Mu15v1.db_3.2.3.tar.gz"}, "mu19ksuba.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mu19ksuba.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mu19ksuba.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu19ksuba.db/bioconductor-mu19ksuba.db_3.13.0_src_all.tar.gz"], "md5": "c057d8793f2db914a93d2e1f5a3af178", "fn": "mu19ksuba.db_3.13.0.tar.gz"}, "mu19ksubacdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mu19ksubacdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu19ksubacdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu19ksubacdf/bioconductor-mu19ksubacdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu19ksubacdf/bioconductor-mu19ksubacdf_2.18.0_src_all.tar.gz"], "md5": "83a9e7a3bac665b655786e66dbd77848", "fn": "mu19ksubacdf_2.18.0.tar.gz"}, "mu19ksubb.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mu19ksubb.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mu19ksubb.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu19ksubb.db/bioconductor-mu19ksubb.db_3.13.0_src_all.tar.gz"], "md5": "1b177a3b5626c825c91e7c25e0acd897", "fn": "mu19ksubb.db_3.13.0.tar.gz"}, "mu19ksubbcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mu19ksubbcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu19ksubbcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu19ksubbcdf/bioconductor-mu19ksubbcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu19ksubbcdf/bioconductor-mu19ksubbcdf_2.18.0_src_all.tar.gz"], "md5": "35e5ebcb4cb51950a85c1e3622bb39f0", "fn": "mu19ksubbcdf_2.18.0.tar.gz"}, "mu19ksubc.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mu19ksubc.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mu19ksubc.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu19ksubc.db/bioconductor-mu19ksubc.db_3.13.0_src_all.tar.gz"], "md5": "bef37c9cd01032e9f1fb177a1af8cba4", "fn": "mu19ksubc.db_3.13.0.tar.gz"}, "mu19ksubccdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mu19ksubccdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu19ksubccdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu19ksubccdf/bioconductor-mu19ksubccdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu19ksubccdf/bioconductor-mu19ksubccdf_2.18.0_src_all.tar.gz"], "md5": "e53ef2716f88022e5e41e2cd857fc2a3", "fn": "mu19ksubccdf_2.18.0.tar.gz"}, "mu22v3.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/Mu22v3.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/Mu22v3.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu22v3.db/bioconductor-mu22v3.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu22v3.db/bioconductor-mu22v3.db_3.2.3_src_all.tar.gz"], "md5": "44aaebe909be9b0108256194c55cf6fb", "fn": "Mu22v3.db_3.2.3.tar.gz"}, "mu6500subacdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mu6500subacdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu6500subacdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu6500subacdf/bioconductor-mu6500subacdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu6500subacdf/bioconductor-mu6500subacdf_2.18.0_src_all.tar.gz"], "md5": "e72152fc4bae307e3858160e018b7f92", "fn": "mu6500subacdf_2.18.0.tar.gz"}, "mu6500subbcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mu6500subbcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu6500subbcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu6500subbcdf/bioconductor-mu6500subbcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu6500subbcdf/bioconductor-mu6500subbcdf_2.18.0_src_all.tar.gz"], "md5": "5000bea2a018b4b6ec05cda111438bc1", "fn": "mu6500subbcdf_2.18.0.tar.gz"}, "mu6500subccdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mu6500subccdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu6500subccdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu6500subccdf/bioconductor-mu6500subccdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu6500subccdf/bioconductor-mu6500subccdf_2.18.0_src_all.tar.gz"], "md5": "c7cbbe6c70a0a3ae11600ad6c0e540c1", "fn": "mu6500subccdf_2.18.0.tar.gz"}, "mu6500subdcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mu6500subdcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu6500subdcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu6500subdcdf/bioconductor-mu6500subdcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu6500subdcdf/bioconductor-mu6500subdcdf_2.18.0_src_all.tar.gz"], "md5": "a614674e8bc60fefd8520dd25d45f8d0", "fn": "mu6500subdcdf_2.18.0.tar.gz"}, "mus.musculus-1.3.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/Mus.musculus_1.3.1.tar.gz", "https://bioarchive.galaxyproject.org/Mus.musculus_1.3.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mus.musculus/bioconductor-mus.musculus_1.3.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mus.musculus/bioconductor-mus.musculus_1.3.1_src_all.tar.gz"], "md5": "1b8defe64c2dd308a88d1ac7a4ce04b9", "fn": "Mus.musculus_1.3.1.tar.gz"}, "mwgcod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mwgcod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/mwgcod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mwgcod.db/bioconductor-mwgcod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mwgcod.db/bioconductor-mwgcod.db_3.4.0_src_all.tar.gz"], "md5": "3d6e2af6b05d6e07a212c043dc9d37c4", "fn": "mwgcod.db_3.4.0.tar.gz"}, "norway981.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/Norway981.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/Norway981.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-norway981.db/bioconductor-norway981.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-norway981.db/bioconductor-norway981.db_3.2.3_src_all.tar.gz"], "md5": "85367390919bba9018438585e59fbb87", "fn": "Norway981.db_3.2.3.tar.gz"}, "nugohs1a520180.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/nugohs1a520180.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/nugohs1a520180.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180.db/bioconductor-nugohs1a520180.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180.db/bioconductor-nugohs1a520180.db_3.4.0_src_all.tar.gz"], "md5": "f83701b35b07e69e1ad503b546bb5eaf", "fn": "nugohs1a520180.db_3.4.0.tar.gz"}, "nugohs1a520180cdf-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/nugohs1a520180cdf_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/nugohs1a520180cdf_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180cdf/bioconductor-nugohs1a520180cdf_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180cdf/bioconductor-nugohs1a520180cdf_3.4.0_src_all.tar.gz"], "md5": "aa152658a4a801cc0edb552a98aee841", "fn": "nugohs1a520180cdf_3.4.0.tar.gz"}, "nugohs1a520180probe-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/nugohs1a520180probe_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/nugohs1a520180probe_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180probe/bioconductor-nugohs1a520180probe_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180probe/bioconductor-nugohs1a520180probe_3.4.0_src_all.tar.gz"], "md5": "6acf20ac4a799eaae97d0a64426d6ac3", "fn": "nugohs1a520180probe_3.4.0.tar.gz"}, "nugomm1a520177.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/nugomm1a520177.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/nugomm1a520177.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177.db/bioconductor-nugomm1a520177.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177.db/bioconductor-nugomm1a520177.db_3.4.0_src_all.tar.gz"], "md5": "99f69ea2cbb80a79bedee99e3d726e50", "fn": "nugomm1a520177.db_3.4.0.tar.gz"}, "nugomm1a520177cdf-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/nugomm1a520177cdf_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/nugomm1a520177cdf_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177cdf/bioconductor-nugomm1a520177cdf_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177cdf/bioconductor-nugomm1a520177cdf_3.4.0_src_all.tar.gz"], "md5": "fc60c2018580decaea30f09de55142fb", "fn": "nugomm1a520177cdf_3.4.0.tar.gz"}, "nugomm1a520177probe-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/nugomm1a520177probe_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/nugomm1a520177probe_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177probe/bioconductor-nugomm1a520177probe_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177probe/bioconductor-nugomm1a520177probe_3.4.0_src_all.tar.gz"], "md5": "7fa974389ad2be6ebda8810496221a9b", "fn": "nugomm1a520177probe_3.4.0.tar.gz"}, "oligodata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/oligoData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/oligoData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-oligodata/bioconductor-oligodata_1.8.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-oligodata/bioconductor-oligodata_1.8.0_src_all.tar.gz"], "md5": "9625cfd4b31bb575c4029a0632a7ee12", "fn": "oligoData_1.8.0.tar.gz"}, "ontoprocdata-0.99.9901": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ontoProcData_0.99.9901.tar.gz", "https://bioarchive.galaxyproject.org/ontoProcData_0.99.9901.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ontoprocdata/bioconductor-ontoprocdata_0.99.9901_src_all.tar.gz"], "md5": "d4160c1fc853db468ce73c7fe62ca00f", "fn": "ontoProcData_0.99.9901.tar.gz"}, "operonhumanv3.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/OperonHumanV3.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/OperonHumanV3.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-operonhumanv3.db/bioconductor-operonhumanv3.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-operonhumanv3.db/bioconductor-operonhumanv3.db_3.2.3_src_all.tar.gz"], "md5": "648da5d4d63c6c8327f6035ee09f2b65", "fn": "OperonHumanV3.db_3.2.3.tar.gz"}, "org.ag.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Ag.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ag.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ag.eg.db/bioconductor-org.ag.eg.db_3.16.0_src_all.tar.gz"], "md5": "93f7b3f4daff9242d79600e0de6794e2", "fn": "org.Ag.eg.db_3.16.0.tar.gz"}, "org.at.tair.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.At.tair.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.At.tair.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.at.tair.db/bioconductor-org.at.tair.db_3.16.0_src_all.tar.gz"], "md5": "7caa9f7667fb06ad359d752dee6ebcd2", "fn": "org.At.tair.db_3.16.0.tar.gz"}, "org.bt.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Bt.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Bt.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.bt.eg.db/bioconductor-org.bt.eg.db_3.16.0_src_all.tar.gz"], "md5": "d48424ecbe51745f86c8cfeea20a92d3", "fn": "org.Bt.eg.db_3.16.0.tar.gz"}, "org.ce.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Ce.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ce.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ce.eg.db/bioconductor-org.ce.eg.db_3.16.0_src_all.tar.gz"], "md5": "f72ee64f0cb5ff05d229feee3314dcd6", "fn": "org.Ce.eg.db_3.16.0.tar.gz"}, "org.cf.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Cf.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Cf.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.cf.eg.db/bioconductor-org.cf.eg.db_3.16.0_src_all.tar.gz"], "md5": "c50ad298c773c322e5131b5785ed66f2", "fn": "org.Cf.eg.db_3.16.0.tar.gz"}, "org.dm.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Dm.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Dm.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.dm.eg.db/bioconductor-org.dm.eg.db_3.16.0_src_all.tar.gz"], "md5": "797e55b8475e3429c8d25fe567e72c89", "fn": "org.Dm.eg.db_3.16.0.tar.gz"}, "org.dr.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Dr.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Dr.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.dr.eg.db/bioconductor-org.dr.eg.db_3.16.0_src_all.tar.gz"], "md5": "fd4fc1c4ac109140cdc5464f8d528c14", "fn": "org.Dr.eg.db_3.16.0.tar.gz"}, "org.eck12.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.EcK12.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.EcK12.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.eck12.eg.db/bioconductor-org.eck12.eg.db_3.16.0_src_all.tar.gz"], "md5": "5316dce945864ef99d72e9142d9564a6", "fn": "org.EcK12.eg.db_3.16.0.tar.gz"}, "org.ecsakai.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.EcSakai.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.EcSakai.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ecsakai.eg.db/bioconductor-org.ecsakai.eg.db_3.16.0_src_all.tar.gz"], "md5": "8393978e486f24d3274e564116a7b832", "fn": "org.EcSakai.eg.db_3.16.0.tar.gz"}, "org.gg.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Gg.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Gg.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.gg.eg.db/bioconductor-org.gg.eg.db_3.16.0_src_all.tar.gz"], "md5": "5e6701c610a8c90a2a5fd25f5a8ead0b", "fn": "org.Gg.eg.db_3.16.0.tar.gz"}, "org.hs.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Hs.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Hs.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.hs.eg.db/bioconductor-org.hs.eg.db_3.16.0_src_all.tar.gz"], "md5": "1d73f40088c6bc6c46fd1d805d165cc2", "fn": "org.Hs.eg.db_3.16.0.tar.gz"}, "org.mm.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Mm.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Mm.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.mm.eg.db/bioconductor-org.mm.eg.db_3.16.0_src_all.tar.gz"], "md5": "18c83b93687c5a618d5220cf5b0666c2", "fn": "org.Mm.eg.db_3.16.0.tar.gz"}, "org.mmu.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Mmu.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Mmu.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.mmu.eg.db/bioconductor-org.mmu.eg.db_3.16.0_src_all.tar.gz"], "md5": "2acd2c91068222d570510d4b41729ecb", "fn": "org.Mmu.eg.db_3.16.0.tar.gz"}, "org.mxanthus.db-1.0.27": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Mxanthus.db_1.0.27.tar.gz", "https://bioarchive.galaxyproject.org/org.Mxanthus.db_1.0.27.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.mxanthus.db/bioconductor-org.mxanthus.db_1.0.27_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.mxanthus.db/bioconductor-org.mxanthus.db_1.0.27_src_all.tar.gz"], "md5": "e493814c41401de383b4f6e0f3d39619", "fn": "org.Mxanthus.db_1.0.27.tar.gz"}, "org.pt.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Pt.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Pt.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.pt.eg.db/bioconductor-org.pt.eg.db_3.16.0_src_all.tar.gz"], "md5": "c8636440d961f2c46bc24afe784bea5f", "fn": "org.Pt.eg.db_3.16.0.tar.gz"}, "org.rn.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Rn.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Rn.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.rn.eg.db/bioconductor-org.rn.eg.db_3.16.0_src_all.tar.gz"], "md5": "307cfbfd11055ffa16aa41fddf7d47fe", "fn": "org.Rn.eg.db_3.16.0.tar.gz"}, "org.sc.sgd.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Sc.sgd.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Sc.sgd.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.sc.sgd.db/bioconductor-org.sc.sgd.db_3.16.0_src_all.tar.gz"], "md5": "207e829a62e588b5f8a3149accefabdc", "fn": "org.Sc.sgd.db_3.16.0.tar.gz"}, "org.ss.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Ss.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ss.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ss.eg.db/bioconductor-org.ss.eg.db_3.16.0_src_all.tar.gz"], "md5": "91cb8de8b50e586a3c327835afc77a23", "fn": "org.Ss.eg.db_3.16.0.tar.gz"}, "org.xl.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Xl.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Xl.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.xl.eg.db/bioconductor-org.xl.eg.db_3.16.0_src_all.tar.gz"], "md5": "8fe571e4d82fbe3f3886022fa68e92d3", "fn": "org.Xl.eg.db_3.16.0.tar.gz"}, "orthology.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/Orthology.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/Orthology.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-orthology.eg.db/bioconductor-orthology.eg.db_3.16.0_src_all.tar.gz"], "md5": "43e43cd1ca14213378047fc95e83b88c", "fn": "Orthology.eg.db_3.16.0.tar.gz"}, "paeg1acdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/paeg1acdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/paeg1acdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-paeg1acdf/bioconductor-paeg1acdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-paeg1acdf/bioconductor-paeg1acdf_2.18.0_src_all.tar.gz"], "md5": "73af974112051db0f715518393e84726", "fn": "paeg1acdf_2.18.0.tar.gz"}, "paeg1aprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/paeg1aprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/paeg1aprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-paeg1aprobe/bioconductor-paeg1aprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-paeg1aprobe/bioconductor-paeg1aprobe_2.18.0_src_all.tar.gz"], "md5": "493fa1fc7b92a78c8114b65038113c42", "fn": "paeg1aprobe_2.18.0.tar.gz"}, "panther.db-1.0.11": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PANTHER.db_1.0.11.tar.gz", "https://bioarchive.galaxyproject.org/PANTHER.db_1.0.11.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-panther.db/bioconductor-panther.db_1.0.11_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-panther.db/bioconductor-panther.db_1.0.11_src_all.tar.gz"], "md5": "561f6b164b27f6dc4287f0d7fd6bb8b3", "fn": "PANTHER.db_1.0.11.tar.gz"}, "partheenmetadata.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/PartheenMetaData.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/PartheenMetaData.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-partheenmetadata.db/bioconductor-partheenmetadata.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-partheenmetadata.db/bioconductor-partheenmetadata.db_3.2.3_src_all.tar.gz"], "md5": "1c9fd27e13a341b9aba9a235a67ce978", "fn": "PartheenMetaData.db_3.2.3.tar.gz"}, "pd.081229.hg18.promoter.medip.hx1-0.99.4": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.081229.hg18.promoter.medip.hx1_0.99.4.tar.gz", "https://bioarchive.galaxyproject.org/pd.081229.hg18.promoter.medip.hx1_0.99.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.081229.hg18.promoter.medip.hx1/bioconductor-pd.081229.hg18.promoter.medip.hx1_0.99.4_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.081229.hg18.promoter.medip.hx1/bioconductor-pd.081229.hg18.promoter.medip.hx1_0.99.4_src_all.tar.gz"], "md5": "f3c240fa0d4503e94047be5ee323856b", "fn": "pd.081229.hg18.promoter.medip.hx1_0.99.4.tar.gz"}, "pd.2006.07.18.hg18.refseq.promoter-1.8.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.2006.07.18.hg18.refseq.promoter_1.8.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.2006.07.18.hg18.refseq.promoter_1.8.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.2006.07.18.hg18.refseq.promoter/bioconductor-pd.2006.07.18.hg18.refseq.promoter_1.8.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.2006.07.18.hg18.refseq.promoter/bioconductor-pd.2006.07.18.hg18.refseq.promoter_1.8.1_src_all.tar.gz"], "md5": "00838332d75b82d212078a9957f495df", "fn": "pd.2006.07.18.hg18.refseq.promoter_1.8.1.tar.gz"}, "pd.2006.07.18.mm8.refseq.promoter-0.99.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.2006.07.18.mm8.refseq.promoter_0.99.3.tar.gz", "https://bioarchive.galaxyproject.org/pd.2006.07.18.mm8.refseq.promoter_0.99.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.2006.07.18.mm8.refseq.promoter/bioconductor-pd.2006.07.18.mm8.refseq.promoter_0.99.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.2006.07.18.mm8.refseq.promoter/bioconductor-pd.2006.07.18.mm8.refseq.promoter_0.99.3_src_all.tar.gz"], "md5": "084b0a6759fd96d1bc775dd4c66c42b0", "fn": "pd.2006.07.18.mm8.refseq.promoter_0.99.3.tar.gz"}, "pd.2006.10.31.rn34.refseq.promoter-0.99.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.2006.10.31.rn34.refseq.promoter_0.99.3.tar.gz", "https://bioarchive.galaxyproject.org/pd.2006.10.31.rn34.refseq.promoter_0.99.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.2006.10.31.rn34.refseq.promoter/bioconductor-pd.2006.10.31.rn34.refseq.promoter_0.99.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.2006.10.31.rn34.refseq.promoter/bioconductor-pd.2006.10.31.rn34.refseq.promoter_0.99.3_src_all.tar.gz"], "md5": "ab5bb767ad29b213e5a969a5fc51ee7d", "fn": "pd.2006.10.31.rn34.refseq.promoter_0.99.3.tar.gz"}, "pd.ag-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.ag_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.ag_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ag/bioconductor-pd.ag_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ag/bioconductor-pd.ag_3.12.0_src_all.tar.gz"], "md5": "21fb288536568ff010ad4847b671f9d6", "fn": "pd.ag_3.12.0.tar.gz"}, "pd.aragene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.aragene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.aragene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.aragene.1.0.st/bioconductor-pd.aragene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.aragene.1.0.st/bioconductor-pd.aragene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "ff87a0793fd4b713c4a45b6c1d4a4977", "fn": "pd.aragene.1.0.st_3.12.0.tar.gz"}, "pd.aragene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.aragene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.aragene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.aragene.1.1.st/bioconductor-pd.aragene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.aragene.1.1.st/bioconductor-pd.aragene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "828ad790eb2495e396d7fcd9bcbf9133", "fn": "pd.aragene.1.1.st_3.12.0.tar.gz"}, "pd.ath1.121501-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.ath1.121501_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.ath1.121501_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ath1.121501/bioconductor-pd.ath1.121501_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ath1.121501/bioconductor-pd.ath1.121501_3.12.0_src_all.tar.gz"], "md5": "d7ed8640f0deac552e0083a091e72a72", "fn": "pd.ath1.121501_3.12.0.tar.gz"}, "pd.barley1-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.barley1_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.barley1_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.barley1/bioconductor-pd.barley1_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.barley1/bioconductor-pd.barley1_3.12.0_src_all.tar.gz"], "md5": "b8d11f5ad42e75f7a91931b46d449c1a", "fn": "pd.barley1_3.12.0.tar.gz"}, "pd.bovgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.bovgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.bovgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.bovgene.1.0.st/bioconductor-pd.bovgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.bovgene.1.0.st/bioconductor-pd.bovgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "6e9747d13aee7825722562ccc49ad35f", "fn": "pd.bovgene.1.0.st_3.12.0.tar.gz"}, "pd.bovgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.bovgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.bovgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.bovgene.1.1.st/bioconductor-pd.bovgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.bovgene.1.1.st/bioconductor-pd.bovgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "342246c0a76755fcca458cd723b3e98e", "fn": "pd.bovgene.1.1.st_3.12.0.tar.gz"}, "pd.bovine-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.bovine_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.bovine_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.bovine/bioconductor-pd.bovine_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.bovine/bioconductor-pd.bovine_3.12.0_src_all.tar.gz"], "md5": "6c7026dba53b54b547b1f1e135d043b3", "fn": "pd.bovine_3.12.0.tar.gz"}, "pd.bsubtilis-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.bsubtilis_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.bsubtilis_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.bsubtilis/bioconductor-pd.bsubtilis_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.bsubtilis/bioconductor-pd.bsubtilis_3.12.0_src_all.tar.gz"], "md5": "2261d8b0ec178beb432d71eafd90ec9a", "fn": "pd.bsubtilis_3.12.0.tar.gz"}, "pd.cangene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.cangene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.cangene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cangene.1.0.st/bioconductor-pd.cangene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cangene.1.0.st/bioconductor-pd.cangene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "0a39d6378193e3f7d31a7210f6766eaf", "fn": "pd.cangene.1.0.st_3.12.0.tar.gz"}, "pd.cangene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.cangene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.cangene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cangene.1.1.st/bioconductor-pd.cangene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cangene.1.1.st/bioconductor-pd.cangene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "946074601e7bee72f3b3dd6ae6b3bc33", "fn": "pd.cangene.1.1.st_3.12.0.tar.gz"}, "pd.canine-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.canine_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.canine_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.canine/bioconductor-pd.canine_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.canine/bioconductor-pd.canine_3.12.0_src_all.tar.gz"], "md5": "5b40fe9e40d0b7f36d338e413d121ba7", "fn": "pd.canine_3.12.0.tar.gz"}, "pd.canine.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.canine.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.canine.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.canine.2/bioconductor-pd.canine.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.canine.2/bioconductor-pd.canine.2_3.12.0_src_all.tar.gz"], "md5": "bc918d1953a3c7ac7168b60a53405a93", "fn": "pd.canine.2_3.12.0.tar.gz"}, "pd.celegans-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.celegans_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.celegans_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.celegans/bioconductor-pd.celegans_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.celegans/bioconductor-pd.celegans_3.12.0_src_all.tar.gz"], "md5": "b90ea2e071522bb340c103a1c8270205", "fn": "pd.celegans_3.12.0.tar.gz"}, "pd.charm.hg18.example-0.99.4": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.charm.hg18.example_0.99.4.tar.gz", "https://bioarchive.galaxyproject.org/pd.charm.hg18.example_0.99.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.charm.hg18.example/bioconductor-pd.charm.hg18.example_0.99.4_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.charm.hg18.example/bioconductor-pd.charm.hg18.example_0.99.4_src_all.tar.gz"], "md5": "e201d4281a23c202f57bae1135e226b4", "fn": "pd.charm.hg18.example_0.99.4.tar.gz"}, "pd.chicken-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.chicken_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.chicken_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chicken/bioconductor-pd.chicken_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chicken/bioconductor-pd.chicken_3.12.0_src_all.tar.gz"], "md5": "af79b6d0910621910e72ea374499e5eb", "fn": "pd.chicken_3.12.0.tar.gz"}, "pd.chigene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.chigene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.chigene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chigene.1.0.st/bioconductor-pd.chigene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chigene.1.0.st/bioconductor-pd.chigene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "e37cb047678fabb1801109d4efd16773", "fn": "pd.chigene.1.0.st_3.12.0.tar.gz"}, "pd.chigene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.chigene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.chigene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chigene.1.1.st/bioconductor-pd.chigene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chigene.1.1.st/bioconductor-pd.chigene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "bec602b45961607f5a4571977d54e015", "fn": "pd.chigene.1.1.st_3.12.0.tar.gz"}, "pd.chogene.2.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.chogene.2.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.chogene.2.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chogene.2.0.st/bioconductor-pd.chogene.2.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chogene.2.0.st/bioconductor-pd.chogene.2.0.st_3.12.0_src_all.tar.gz"], "md5": "641718e3d172838185a200bac3d32433", "fn": "pd.chogene.2.0.st_3.12.0.tar.gz"}, "pd.chogene.2.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.chogene.2.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.chogene.2.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chogene.2.1.st/bioconductor-pd.chogene.2.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chogene.2.1.st/bioconductor-pd.chogene.2.1.st_3.12.0_src_all.tar.gz"], "md5": "ed25825e58a514cdde70b961bce9b4d7", "fn": "pd.chogene.2.1.st_3.12.0.tar.gz"}, "pd.citrus-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.citrus_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.citrus_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.citrus/bioconductor-pd.citrus_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.citrus/bioconductor-pd.citrus_3.12.0_src_all.tar.gz"], "md5": "dee9b3298b84e7dd5152f48ad449b15a", "fn": "pd.citrus_3.12.0.tar.gz"}, "pd.clariom.d.human-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.clariom.d.human_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.clariom.d.human_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.d.human/bioconductor-pd.clariom.d.human_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.d.human/bioconductor-pd.clariom.d.human_3.14.1_src_all.tar.gz"], "md5": "9d3505af53cc7c99980f29c527f0f37d", "fn": "pd.clariom.d.human_3.14.1.tar.gz"}, "pd.clariom.s.human-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.clariom.s.human_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.clariom.s.human_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.human/bioconductor-pd.clariom.s.human_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.human/bioconductor-pd.clariom.s.human_3.14.1_src_all.tar.gz"], "md5": "797afe8a6a8041453a34ced3cce34884", "fn": "pd.clariom.s.human_3.14.1.tar.gz"}, "pd.clariom.s.human.ht-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.clariom.s.human.ht_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.clariom.s.human.ht_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.human.ht/bioconductor-pd.clariom.s.human.ht_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.human.ht/bioconductor-pd.clariom.s.human.ht_3.14.1_src_all.tar.gz"], "md5": "90f910bea1b1aeb550a3f1bdd91d1a06", "fn": "pd.clariom.s.human.ht_3.14.1.tar.gz"}, "pd.clariom.s.mouse-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.clariom.s.mouse_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.clariom.s.mouse_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.mouse/bioconductor-pd.clariom.s.mouse_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.mouse/bioconductor-pd.clariom.s.mouse_3.14.1_src_all.tar.gz"], "md5": "e3e4ce2b22a78faf525dd6c0c0b2a42d", "fn": "pd.clariom.s.mouse_3.14.1.tar.gz"}, "pd.clariom.s.mouse.ht-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.clariom.s.mouse.ht_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.clariom.s.mouse.ht_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.mouse.ht/bioconductor-pd.clariom.s.mouse.ht_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.mouse.ht/bioconductor-pd.clariom.s.mouse.ht_3.14.1_src_all.tar.gz"], "md5": "9cb6f77cf9666a0d54e1eacb904fd57c", "fn": "pd.clariom.s.mouse.ht_3.14.1.tar.gz"}, "pd.clariom.s.rat-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.clariom.s.rat_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.clariom.s.rat_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.rat/bioconductor-pd.clariom.s.rat_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.rat/bioconductor-pd.clariom.s.rat_3.14.1_src_all.tar.gz"], "md5": "be464b3eaea8eb8bdbcca6047fce4dea", "fn": "pd.clariom.s.rat_3.14.1.tar.gz"}, "pd.clariom.s.rat.ht-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.clariom.s.rat.ht_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.clariom.s.rat.ht_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.rat.ht/bioconductor-pd.clariom.s.rat.ht_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.rat.ht/bioconductor-pd.clariom.s.rat.ht_3.14.1_src_all.tar.gz"], "md5": "be901eb9e8830f3e5bedf154189a3743", "fn": "pd.clariom.s.rat.ht_3.14.1.tar.gz"}, "pd.cotton-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.cotton_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.cotton_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cotton/bioconductor-pd.cotton_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cotton/bioconductor-pd.cotton_3.12.0_src_all.tar.gz"], "md5": "78c408902bcefb8c695119767534b393", "fn": "pd.cotton_3.12.0.tar.gz"}, "pd.cyngene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.cyngene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.cyngene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cyngene.1.0.st/bioconductor-pd.cyngene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cyngene.1.0.st/bioconductor-pd.cyngene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "784fac6cc92a0fe46dae32c9b737812a", "fn": "pd.cyngene.1.0.st_3.12.0.tar.gz"}, "pd.cyngene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.cyngene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.cyngene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cyngene.1.1.st/bioconductor-pd.cyngene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cyngene.1.1.st/bioconductor-pd.cyngene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "a6217267e3e08a15f70c600918c7d4f6", "fn": "pd.cyngene.1.1.st_3.12.0.tar.gz"}, "pd.cyrgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.cyrgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.cyrgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cyrgene.1.0.st/bioconductor-pd.cyrgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cyrgene.1.0.st/bioconductor-pd.cyrgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "63228c07d3d16d6c62e9c0e83f10a855", "fn": "pd.cyrgene.1.0.st_3.12.0.tar.gz"}, "pd.cyrgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.cyrgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.cyrgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cyrgene.1.1.st/bioconductor-pd.cyrgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cyrgene.1.1.st/bioconductor-pd.cyrgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "dbe3bb580b96aaddcc597de45159320d", "fn": "pd.cyrgene.1.1.st_3.12.0.tar.gz"}, "pd.cytogenetics.array-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.cytogenetics.array_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.cytogenetics.array_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cytogenetics.array/bioconductor-pd.cytogenetics.array_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cytogenetics.array/bioconductor-pd.cytogenetics.array_3.12.0_src_all.tar.gz"], "md5": "8c359ff56a9a558d370dc9a6a54218e0", "fn": "pd.cytogenetics.array_3.12.0.tar.gz"}, "pd.drogene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.drogene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.drogene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.drogene.1.0.st/bioconductor-pd.drogene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.drogene.1.0.st/bioconductor-pd.drogene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "67f92a97a5b78a95693edfdd32b67e93", "fn": "pd.drogene.1.0.st_3.12.0.tar.gz"}, "pd.drogene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.drogene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.drogene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.drogene.1.1.st/bioconductor-pd.drogene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.drogene.1.1.st/bioconductor-pd.drogene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "5c63236ea91390d49dbabea63a48f0a2", "fn": "pd.drogene.1.1.st_3.12.0.tar.gz"}, "pd.drosgenome1-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.drosgenome1_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.drosgenome1_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.drosgenome1/bioconductor-pd.drosgenome1_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.drosgenome1/bioconductor-pd.drosgenome1_3.12.0_src_all.tar.gz"], "md5": "59c1a37a7d6a43fc70ff8756bf1195ef", "fn": "pd.drosgenome1_3.12.0.tar.gz"}, "pd.drosophila.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.drosophila.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.drosophila.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.drosophila.2/bioconductor-pd.drosophila.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.drosophila.2/bioconductor-pd.drosophila.2_3.12.0_src_all.tar.gz"], "md5": "ddb821e35e722af8dcf0807c6da4fac1", "fn": "pd.drosophila.2_3.12.0.tar.gz"}, "pd.e.coli.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.e.coli.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.e.coli.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.e.coli.2/bioconductor-pd.e.coli.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.e.coli.2/bioconductor-pd.e.coli.2_3.12.0_src_all.tar.gz"], "md5": "9176faa60a0c252a815b2a74d2f63dd4", "fn": "pd.e.coli.2_3.12.0.tar.gz"}, "pd.ecoli-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.ecoli_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.ecoli_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ecoli/bioconductor-pd.ecoli_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ecoli/bioconductor-pd.ecoli_3.12.0_src_all.tar.gz"], "md5": "077e91b2567a32780305f0fb6b126fe9", "fn": "pd.ecoli_3.12.0.tar.gz"}, "pd.ecoli.asv2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.ecoli.asv2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.ecoli.asv2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ecoli.asv2/bioconductor-pd.ecoli.asv2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ecoli.asv2/bioconductor-pd.ecoli.asv2_3.12.0_src_all.tar.gz"], "md5": "d789ddf5a178a9a50c5587ee3ab294a4", "fn": "pd.ecoli.asv2_3.12.0.tar.gz"}, "pd.elegene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.elegene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.elegene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.elegene.1.0.st/bioconductor-pd.elegene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.elegene.1.0.st/bioconductor-pd.elegene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "b6110c58d5964703c7117e5e0668c901", "fn": "pd.elegene.1.0.st_3.12.0.tar.gz"}, "pd.elegene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.elegene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.elegene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.elegene.1.1.st/bioconductor-pd.elegene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.elegene.1.1.st/bioconductor-pd.elegene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "1dbe166ea347a5a7e240db925d2081c7", "fn": "pd.elegene.1.1.st_3.12.0.tar.gz"}, "pd.equgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.equgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.equgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.equgene.1.0.st/bioconductor-pd.equgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.equgene.1.0.st/bioconductor-pd.equgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "3448f36fdb899f04702be37ffab4c4c7", "fn": "pd.equgene.1.0.st_3.12.0.tar.gz"}, "pd.equgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.equgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.equgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.equgene.1.1.st/bioconductor-pd.equgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.equgene.1.1.st/bioconductor-pd.equgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "bed32525513ce25f14d433ce805e7d6c", "fn": "pd.equgene.1.1.st_3.12.0.tar.gz"}, "pd.feinberg.hg18.me.hx1-0.99.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.feinberg.hg18.me.hx1_0.99.3.tar.gz", "https://bioarchive.galaxyproject.org/pd.feinberg.hg18.me.hx1_0.99.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.feinberg.hg18.me.hx1/bioconductor-pd.feinberg.hg18.me.hx1_0.99.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.feinberg.hg18.me.hx1/bioconductor-pd.feinberg.hg18.me.hx1_0.99.3_src_all.tar.gz"], "md5": "b6eeaf79671bab6f597965009516ce57", "fn": "pd.feinberg.hg18.me.hx1_0.99.3.tar.gz"}, "pd.feinberg.mm8.me.hx1-0.99.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.feinberg.mm8.me.hx1_0.99.3.tar.gz", "https://bioarchive.galaxyproject.org/pd.feinberg.mm8.me.hx1_0.99.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.feinberg.mm8.me.hx1/bioconductor-pd.feinberg.mm8.me.hx1_0.99.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.feinberg.mm8.me.hx1/bioconductor-pd.feinberg.mm8.me.hx1_0.99.3_src_all.tar.gz"], "md5": "7332102b69fc9ee087f52d3cdc311d00", "fn": "pd.feinberg.mm8.me.hx1_0.99.3.tar.gz"}, "pd.felgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.felgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.felgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.felgene.1.0.st/bioconductor-pd.felgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.felgene.1.0.st/bioconductor-pd.felgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "b7ac0a5cbde5f248aac5d0a7422bd88d", "fn": "pd.felgene.1.0.st_3.12.0.tar.gz"}, "pd.felgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.felgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.felgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.felgene.1.1.st/bioconductor-pd.felgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.felgene.1.1.st/bioconductor-pd.felgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "734807a7f3608f6c44c76df7eee04c99", "fn": "pd.felgene.1.1.st_3.12.0.tar.gz"}, "pd.fingene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.fingene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.fingene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.fingene.1.0.st/bioconductor-pd.fingene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.fingene.1.0.st/bioconductor-pd.fingene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "b79e4f8a52cad3b62e32401bbe74603d", "fn": "pd.fingene.1.0.st_3.12.0.tar.gz"}, "pd.fingene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.fingene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.fingene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.fingene.1.1.st/bioconductor-pd.fingene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.fingene.1.1.st/bioconductor-pd.fingene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "29030b14a0e8f8073874fb694a8c0c09", "fn": "pd.fingene.1.1.st_3.12.0.tar.gz"}, "pd.genomewidesnp.5-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.genomewidesnp.5_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.genomewidesnp.5_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.genomewidesnp.5/bioconductor-pd.genomewidesnp.5_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.genomewidesnp.5/bioconductor-pd.genomewidesnp.5_3.14.1_src_all.tar.gz"], "md5": "d02255c861e82fca6a7445ada0c69e5d", "fn": "pd.genomewidesnp.5_3.14.1.tar.gz"}, "pd.genomewidesnp.6-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.genomewidesnp.6_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.genomewidesnp.6_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.genomewidesnp.6/bioconductor-pd.genomewidesnp.6_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.genomewidesnp.6/bioconductor-pd.genomewidesnp.6_3.14.1_src_all.tar.gz"], "md5": "6e5369234e251c763f4f6c0220fbcb0c", "fn": "pd.genomewidesnp.6_3.14.1.tar.gz"}, "pd.guigene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.guigene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.guigene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.guigene.1.0.st/bioconductor-pd.guigene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.guigene.1.0.st/bioconductor-pd.guigene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "29fe31499931836af72ddd0c7d06acfa", "fn": "pd.guigene.1.0.st_3.12.0.tar.gz"}, "pd.guigene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.guigene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.guigene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.guigene.1.1.st/bioconductor-pd.guigene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.guigene.1.1.st/bioconductor-pd.guigene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "aa3e0389c596a3676322104de5ad2358", "fn": "pd.guigene.1.1.st_3.12.0.tar.gz"}, "pd.hc.g110-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hc.g110_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hc.g110_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hc.g110/bioconductor-pd.hc.g110_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hc.g110/bioconductor-pd.hc.g110_3.12.0_src_all.tar.gz"], "md5": "5c5418c588ed28e2fa088c7952c48b91", "fn": "pd.hc.g110_3.12.0.tar.gz"}, "pd.hg.focus-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hg.focus_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.focus_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.focus/bioconductor-pd.hg.focus_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.focus/bioconductor-pd.hg.focus_3.12.0_src_all.tar.gz"], "md5": "a89f344ae7ff8061a8e7968f155f4bcf", "fn": "pd.hg.focus_3.12.0.tar.gz"}, "pd.hg.u133.plus.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hg.u133.plus.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u133.plus.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133.plus.2/bioconductor-pd.hg.u133.plus.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133.plus.2/bioconductor-pd.hg.u133.plus.2_3.12.0_src_all.tar.gz"], "md5": "8a87aa63c04e84266962bdde5226c06c", "fn": "pd.hg.u133.plus.2_3.12.0.tar.gz"}, "pd.hg.u133a-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hg.u133a_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u133a_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a/bioconductor-pd.hg.u133a_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a/bioconductor-pd.hg.u133a_3.12.0_src_all.tar.gz"], "md5": "05b4521f65ab294a5040a0c60198d22c", "fn": "pd.hg.u133a_3.12.0.tar.gz"}, "pd.hg.u133a.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hg.u133a.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u133a.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a.2/bioconductor-pd.hg.u133a.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a.2/bioconductor-pd.hg.u133a.2_3.12.0_src_all.tar.gz"], "md5": "a7941473bf081831fad4f4412023d9ee", "fn": "pd.hg.u133a.2_3.12.0.tar.gz"}, "pd.hg.u133a.tag-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hg.u133a.tag_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u133a.tag_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a.tag/bioconductor-pd.hg.u133a.tag_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a.tag/bioconductor-pd.hg.u133a.tag_3.12.0_src_all.tar.gz"], "md5": "e090383098d6e1062b290889fba065d5", "fn": "pd.hg.u133a.tag_3.12.0.tar.gz"}, "pd.hg.u133b-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hg.u133b_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u133b_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133b/bioconductor-pd.hg.u133b_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133b/bioconductor-pd.hg.u133b_3.12.0_src_all.tar.gz"], "md5": "c5eac82ad7480571b9f2b442b4a8faa6", "fn": "pd.hg.u133b_3.12.0.tar.gz"}, "pd.hg.u219-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hg.u219_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u219_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u219/bioconductor-pd.hg.u219_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u219/bioconductor-pd.hg.u219_3.12.0_src_all.tar.gz"], "md5": "dab073d315af47ff3001c72a6d1e7972", "fn": "pd.hg.u219_3.12.0.tar.gz"}, "pd.hg.u95a-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hg.u95a_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u95a_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95a/bioconductor-pd.hg.u95a_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95a/bioconductor-pd.hg.u95a_3.12.0_src_all.tar.gz"], "md5": "a9ad7d6a085e0e3ed7623902e7810da0", "fn": "pd.hg.u95a_3.12.0.tar.gz"}, "pd.hg.u95av2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hg.u95av2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u95av2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95av2/bioconductor-pd.hg.u95av2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95av2/bioconductor-pd.hg.u95av2_3.12.0_src_all.tar.gz"], "md5": "3a4182b529bc07ec91277a95b1462468", "fn": "pd.hg.u95av2_3.12.0.tar.gz"}, "pd.hg.u95b-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hg.u95b_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u95b_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95b/bioconductor-pd.hg.u95b_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95b/bioconductor-pd.hg.u95b_3.12.0_src_all.tar.gz"], "md5": "a7f10f91e920e191c5009fac8ca79c24", "fn": "pd.hg.u95b_3.12.0.tar.gz"}, "pd.hg.u95c-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hg.u95c_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u95c_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95c/bioconductor-pd.hg.u95c_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95c/bioconductor-pd.hg.u95c_3.12.0_src_all.tar.gz"], "md5": "85655bf7a9ecd7aaa867e05899c5e3e4", "fn": "pd.hg.u95c_3.12.0.tar.gz"}, "pd.hg.u95d-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hg.u95d_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u95d_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95d/bioconductor-pd.hg.u95d_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95d/bioconductor-pd.hg.u95d_3.12.0_src_all.tar.gz"], "md5": "946701ecfc9cccb46aaeb57a4d6fe1c5", "fn": "pd.hg.u95d_3.12.0.tar.gz"}, "pd.hg.u95e-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hg.u95e_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u95e_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95e/bioconductor-pd.hg.u95e_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95e/bioconductor-pd.hg.u95e_3.12.0_src_all.tar.gz"], "md5": "9295e2fd1b4be6ff58477ea5a5de45ee", "fn": "pd.hg.u95e_3.12.0.tar.gz"}, "pd.hg18.60mer.expr-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hg18.60mer.expr_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg18.60mer.expr_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg18.60mer.expr/bioconductor-pd.hg18.60mer.expr_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg18.60mer.expr/bioconductor-pd.hg18.60mer.expr_3.12.0_src_all.tar.gz"], "md5": "ee8d3813f74edce4e796933aa63999fb", "fn": "pd.hg18.60mer.expr_3.12.0.tar.gz"}, "pd.ht.hg.u133.plus.pm-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.ht.hg.u133.plus.pm_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.ht.hg.u133.plus.pm_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ht.hg.u133.plus.pm/bioconductor-pd.ht.hg.u133.plus.pm_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ht.hg.u133.plus.pm/bioconductor-pd.ht.hg.u133.plus.pm_3.12.0_src_all.tar.gz"], "md5": "5b1c3dd0ab3f8b21154982c197512a7c", "fn": "pd.ht.hg.u133.plus.pm_3.12.0.tar.gz"}, "pd.ht.hg.u133a-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.ht.hg.u133a_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.ht.hg.u133a_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ht.hg.u133a/bioconductor-pd.ht.hg.u133a_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ht.hg.u133a/bioconductor-pd.ht.hg.u133a_3.12.0_src_all.tar.gz"], "md5": "80a82f43083f95e1e9f5e2e2da2e288e", "fn": "pd.ht.hg.u133a_3.12.0.tar.gz"}, "pd.ht.mg.430a-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.ht.mg.430a_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.ht.mg.430a_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ht.mg.430a/bioconductor-pd.ht.mg.430a_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ht.mg.430a/bioconductor-pd.ht.mg.430a_3.12.0_src_all.tar.gz"], "md5": "65ea4fae22d21ad70998ba3ea034dcc0", "fn": "pd.ht.mg.430a_3.12.0.tar.gz"}, "pd.hta.2.0-3.12.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hta.2.0_3.12.2.tar.gz", "https://bioarchive.galaxyproject.org/pd.hta.2.0_3.12.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hta.2.0/bioconductor-pd.hta.2.0_3.12.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hta.2.0/bioconductor-pd.hta.2.0_3.12.2_src_all.tar.gz"], "md5": "8e13f85ece49c38da73eaf7b2247f5f0", "fn": "pd.hta.2.0_3.12.2.tar.gz"}, "pd.hu6800-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hu6800_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hu6800_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hu6800/bioconductor-pd.hu6800_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hu6800/bioconductor-pd.hu6800_3.12.0_src_all.tar.gz"], "md5": "9a3a3edde6d6f31b9e90dc32aa68875d", "fn": "pd.hu6800_3.12.0.tar.gz"}, "pd.huex.1.0.st.v2-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.huex.1.0.st.v2_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.huex.1.0.st.v2_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.huex.1.0.st.v2/bioconductor-pd.huex.1.0.st.v2_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.huex.1.0.st.v2/bioconductor-pd.huex.1.0.st.v2_3.14.1_src_all.tar.gz"], "md5": "f4c4836c53447890b75b012efbdef3e9", "fn": "pd.huex.1.0.st.v2_3.14.1.tar.gz"}, "pd.hugene.1.0.st.v1-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hugene.1.0.st.v1_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.hugene.1.0.st.v1_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.1.0.st.v1/bioconductor-pd.hugene.1.0.st.v1_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.1.0.st.v1/bioconductor-pd.hugene.1.0.st.v1_3.14.1_src_all.tar.gz"], "md5": "8cb24c351aee5bf216180e4b19742506", "fn": "pd.hugene.1.0.st.v1_3.14.1.tar.gz"}, "pd.hugene.1.1.st.v1-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hugene.1.1.st.v1_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.hugene.1.1.st.v1_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.1.1.st.v1/bioconductor-pd.hugene.1.1.st.v1_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.1.1.st.v1/bioconductor-pd.hugene.1.1.st.v1_3.14.1_src_all.tar.gz"], "md5": "7a17ee4f7d258792be1d21be7d03deb0", "fn": "pd.hugene.1.1.st.v1_3.14.1.tar.gz"}, "pd.hugene.2.0.st-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hugene.2.0.st_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.hugene.2.0.st_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.2.0.st/bioconductor-pd.hugene.2.0.st_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.2.0.st/bioconductor-pd.hugene.2.0.st_3.14.1_src_all.tar.gz"], "md5": "e484209aa0c2a839c3445d91c1a799ce", "fn": "pd.hugene.2.0.st_3.14.1.tar.gz"}, "pd.hugene.2.1.st-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.hugene.2.1.st_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.hugene.2.1.st_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.2.1.st/bioconductor-pd.hugene.2.1.st_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.2.1.st/bioconductor-pd.hugene.2.1.st_3.14.1_src_all.tar.gz"], "md5": "164227f10b87f87059e4ae27b40f5238", "fn": "pd.hugene.2.1.st_3.14.1.tar.gz"}, "pd.maize-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.maize_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.maize_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.maize/bioconductor-pd.maize_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.maize/bioconductor-pd.maize_3.12.0_src_all.tar.gz"], "md5": "a1689518c8525d3dfa97e870f90b7a7b", "fn": "pd.maize_3.12.0.tar.gz"}, "pd.mapping250k.nsp-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mapping250k.nsp_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mapping250k.nsp_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mapping250k.nsp/bioconductor-pd.mapping250k.nsp_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mapping250k.nsp/bioconductor-pd.mapping250k.nsp_3.12.0_src_all.tar.gz"], "md5": "2786d00e1d621a9c415a599b4afe838b", "fn": "pd.mapping250k.nsp_3.12.0.tar.gz"}, "pd.mapping250k.sty-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mapping250k.sty_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mapping250k.sty_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mapping250k.sty/bioconductor-pd.mapping250k.sty_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mapping250k.sty/bioconductor-pd.mapping250k.sty_3.12.0_src_all.tar.gz"], "md5": "0db5992855eaf9b8f61f8bc2e57ef347", "fn": "pd.mapping250k.sty_3.12.0.tar.gz"}, "pd.mapping50k.hind240-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mapping50k.hind240_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mapping50k.hind240_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mapping50k.hind240/bioconductor-pd.mapping50k.hind240_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mapping50k.hind240/bioconductor-pd.mapping50k.hind240_3.12.0_src_all.tar.gz"], "md5": "83615dcb01eb381f0c69e07504809094", "fn": "pd.mapping50k.hind240_3.12.0.tar.gz"}, "pd.mapping50k.xba240-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mapping50k.xba240_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mapping50k.xba240_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mapping50k.xba240/bioconductor-pd.mapping50k.xba240_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mapping50k.xba240/bioconductor-pd.mapping50k.xba240_3.12.0_src_all.tar.gz"], "md5": "eb0f9250fe0d7b590ca9938fee88f2e7", "fn": "pd.mapping50k.xba240_3.12.0.tar.gz"}, "pd.margene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.margene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.margene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.margene.1.0.st/bioconductor-pd.margene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.margene.1.0.st/bioconductor-pd.margene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "f670b192e4b453f13bb7cae154b5de42", "fn": "pd.margene.1.0.st_3.12.0.tar.gz"}, "pd.margene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.margene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.margene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.margene.1.1.st/bioconductor-pd.margene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.margene.1.1.st/bioconductor-pd.margene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "efd71aeb9c5ab36c2ddeccf9cb66ddec", "fn": "pd.margene.1.1.st_3.12.0.tar.gz"}, "pd.medgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.medgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.medgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.medgene.1.0.st/bioconductor-pd.medgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.medgene.1.0.st/bioconductor-pd.medgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "2a0048ccd5310ec5c45bb691f3c25885", "fn": "pd.medgene.1.0.st_3.12.0.tar.gz"}, "pd.medgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.medgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.medgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.medgene.1.1.st/bioconductor-pd.medgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.medgene.1.1.st/bioconductor-pd.medgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "d96894cfea509734af62110311100142", "fn": "pd.medgene.1.1.st_3.12.0.tar.gz"}, "pd.medicago-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.medicago_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.medicago_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.medicago/bioconductor-pd.medicago_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.medicago/bioconductor-pd.medicago_3.12.0_src_all.tar.gz"], "md5": "0e3f00777919374619a9dc8244167068", "fn": "pd.medicago_3.12.0.tar.gz"}, "pd.mg.u74a-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mg.u74a_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mg.u74a_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74a/bioconductor-pd.mg.u74a_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74a/bioconductor-pd.mg.u74a_3.12.0_src_all.tar.gz"], "md5": "a855c7d2b80e9b8f9bbc1a3f83aca799", "fn": "pd.mg.u74a_3.12.0.tar.gz"}, "pd.mg.u74av2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mg.u74av2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mg.u74av2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74av2/bioconductor-pd.mg.u74av2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74av2/bioconductor-pd.mg.u74av2_3.12.0_src_all.tar.gz"], "md5": "01c6e4da9c2ad0f1939482284dd5b421", "fn": "pd.mg.u74av2_3.12.0.tar.gz"}, "pd.mg.u74b-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mg.u74b_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mg.u74b_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74b/bioconductor-pd.mg.u74b_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74b/bioconductor-pd.mg.u74b_3.12.0_src_all.tar.gz"], "md5": "47bb81abaceba6dfaab3e0987f28706c", "fn": "pd.mg.u74b_3.12.0.tar.gz"}, "pd.mg.u74bv2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mg.u74bv2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mg.u74bv2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74bv2/bioconductor-pd.mg.u74bv2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74bv2/bioconductor-pd.mg.u74bv2_3.12.0_src_all.tar.gz"], "md5": "dbb6cd5b16bd5cafbf654744bc2d5c5c", "fn": "pd.mg.u74bv2_3.12.0.tar.gz"}, "pd.mg.u74c-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mg.u74c_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mg.u74c_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74c/bioconductor-pd.mg.u74c_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74c/bioconductor-pd.mg.u74c_3.12.0_src_all.tar.gz"], "md5": "01f10eae99481f03d1d5a6a2c2f01733", "fn": "pd.mg.u74c_3.12.0.tar.gz"}, "pd.mg.u74cv2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mg.u74cv2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mg.u74cv2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74cv2/bioconductor-pd.mg.u74cv2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74cv2/bioconductor-pd.mg.u74cv2_3.12.0_src_all.tar.gz"], "md5": "b60943b90b95a24fcf93f8c245fd88be", "fn": "pd.mg.u74cv2_3.12.0.tar.gz"}, "pd.mirna.1.0-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mirna.1.0_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mirna.1.0_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.1.0/bioconductor-pd.mirna.1.0_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.1.0/bioconductor-pd.mirna.1.0_3.12.0_src_all.tar.gz"], "md5": "8dfeb82a9da6d6f73e5fb716a2867a34", "fn": "pd.mirna.1.0_3.12.0.tar.gz"}, "pd.mirna.2.0-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mirna.2.0_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mirna.2.0_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.2.0/bioconductor-pd.mirna.2.0_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.2.0/bioconductor-pd.mirna.2.0_3.12.0_src_all.tar.gz"], "md5": "aab53cbc62fbd7727ca0303aeb1dca13", "fn": "pd.mirna.2.0_3.12.0.tar.gz"}, "pd.mirna.3.0-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mirna.3.0_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mirna.3.0_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.3.0/bioconductor-pd.mirna.3.0_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.3.0/bioconductor-pd.mirna.3.0_3.12.0_src_all.tar.gz"], "md5": "1265f1969c618b3b5121e6a77ba57009", "fn": "pd.mirna.3.0_3.12.0.tar.gz"}, "pd.mirna.3.1-3.8.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mirna.3.1_3.8.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.mirna.3.1_3.8.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.3.1/bioconductor-pd.mirna.3.1_3.8.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.3.1/bioconductor-pd.mirna.3.1_3.8.1_src_all.tar.gz"], "md5": "296b3584ee5e9416c9018353d3e29c6c", "fn": "pd.mirna.3.1_3.8.1.tar.gz"}, "pd.mirna.4.0-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mirna.4.0_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mirna.4.0_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.4.0/bioconductor-pd.mirna.4.0_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.4.0/bioconductor-pd.mirna.4.0_3.12.0_src_all.tar.gz"], "md5": "cae1a18c02aaa20a2f05172103e9d938", "fn": "pd.mirna.4.0_3.12.0.tar.gz"}, "pd.moe430a-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.moe430a_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.moe430a_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.moe430a/bioconductor-pd.moe430a_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.moe430a/bioconductor-pd.moe430a_3.12.0_src_all.tar.gz"], "md5": "f9a7cb62140e42c2a82177548a1c73fb", "fn": "pd.moe430a_3.12.0.tar.gz"}, "pd.moe430b-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.moe430b_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.moe430b_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.moe430b/bioconductor-pd.moe430b_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.moe430b/bioconductor-pd.moe430b_3.12.0_src_all.tar.gz"], "md5": "c19d2ee5e7e87703cf73afa33a5f3156", "fn": "pd.moe430b_3.12.0.tar.gz"}, "pd.moex.1.0.st.v1-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.moex.1.0.st.v1_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.moex.1.0.st.v1_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.moex.1.0.st.v1/bioconductor-pd.moex.1.0.st.v1_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.moex.1.0.st.v1/bioconductor-pd.moex.1.0.st.v1_3.14.1_src_all.tar.gz"], "md5": "57427e63b2d44258c12d796eada1897b", "fn": "pd.moex.1.0.st.v1_3.14.1.tar.gz"}, "pd.mogene.1.0.st.v1-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mogene.1.0.st.v1_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.mogene.1.0.st.v1_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.1.0.st.v1/bioconductor-pd.mogene.1.0.st.v1_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.1.0.st.v1/bioconductor-pd.mogene.1.0.st.v1_3.14.1_src_all.tar.gz"], "md5": "c3767385af3b9a120c777adb6d6e3364", "fn": "pd.mogene.1.0.st.v1_3.14.1.tar.gz"}, "pd.mogene.1.1.st.v1-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mogene.1.1.st.v1_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.mogene.1.1.st.v1_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.1.1.st.v1/bioconductor-pd.mogene.1.1.st.v1_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.1.1.st.v1/bioconductor-pd.mogene.1.1.st.v1_3.14.1_src_all.tar.gz"], "md5": "3d6c5d29e4d8a0b0152e109b68f82c37", "fn": "pd.mogene.1.1.st.v1_3.14.1.tar.gz"}, "pd.mogene.2.0.st-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mogene.2.0.st_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.mogene.2.0.st_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.2.0.st/bioconductor-pd.mogene.2.0.st_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.2.0.st/bioconductor-pd.mogene.2.0.st_3.14.1_src_all.tar.gz"], "md5": "71326d6bd85de02490171696f923d053", "fn": "pd.mogene.2.0.st_3.14.1.tar.gz"}, "pd.mogene.2.1.st-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mogene.2.1.st_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.mogene.2.1.st_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.2.1.st/bioconductor-pd.mogene.2.1.st_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.2.1.st/bioconductor-pd.mogene.2.1.st_3.14.1_src_all.tar.gz"], "md5": "2c7fc5644eae98359cb945ff16d072a2", "fn": "pd.mogene.2.1.st_3.14.1.tar.gz"}, "pd.mouse430.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mouse430.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mouse430.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mouse430.2/bioconductor-pd.mouse430.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mouse430.2/bioconductor-pd.mouse430.2_3.12.0_src_all.tar.gz"], "md5": "7f37397a57b06d15101ef86fa6242ca4", "fn": "pd.mouse430.2_3.12.0.tar.gz"}, "pd.mouse430a.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mouse430a.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mouse430a.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mouse430a.2/bioconductor-pd.mouse430a.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mouse430a.2/bioconductor-pd.mouse430a.2_3.12.0_src_all.tar.gz"], "md5": "0c28f564a1fa23f59c936d42c156796d", "fn": "pd.mouse430a.2_3.12.0.tar.gz"}, "pd.mta.1.0-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mta.1.0_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mta.1.0_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mta.1.0/bioconductor-pd.mta.1.0_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mta.1.0/bioconductor-pd.mta.1.0_3.12.0_src_all.tar.gz"], "md5": "0f737b4f1f1353733e56e2df637f554b", "fn": "pd.mta.1.0_3.12.0.tar.gz"}, "pd.mu11ksuba-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mu11ksuba_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mu11ksuba_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mu11ksuba/bioconductor-pd.mu11ksuba_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mu11ksuba/bioconductor-pd.mu11ksuba_3.12.0_src_all.tar.gz"], "md5": "56be58b3f444ccb9572dc4c3882964b2", "fn": "pd.mu11ksuba_3.12.0.tar.gz"}, "pd.mu11ksubb-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.mu11ksubb_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mu11ksubb_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mu11ksubb/bioconductor-pd.mu11ksubb_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mu11ksubb/bioconductor-pd.mu11ksubb_3.12.0_src_all.tar.gz"], "md5": "c45b0ebe777b99cec38499826cc1b457", "fn": "pd.mu11ksubb_3.12.0.tar.gz"}, "pd.nugo.hs1a520180-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.nugo.hs1a520180_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.nugo.hs1a520180_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.nugo.hs1a520180/bioconductor-pd.nugo.hs1a520180_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.nugo.hs1a520180/bioconductor-pd.nugo.hs1a520180_3.4.0_src_all.tar.gz"], "md5": "88a836472f0f9aab2e1d54e4bad7d6af", "fn": "pd.nugo.hs1a520180_3.4.0.tar.gz"}, "pd.nugo.mm1a520177-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.nugo.mm1a520177_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.nugo.mm1a520177_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.nugo.mm1a520177/bioconductor-pd.nugo.mm1a520177_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.nugo.mm1a520177/bioconductor-pd.nugo.mm1a520177_3.4.0_src_all.tar.gz"], "md5": "5cd64895eaddaf4cae1c48db9468c079", "fn": "pd.nugo.mm1a520177_3.4.0.tar.gz"}, "pd.ovigene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.ovigene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.ovigene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ovigene.1.0.st/bioconductor-pd.ovigene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ovigene.1.0.st/bioconductor-pd.ovigene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "88cfedfe10dd357539305051a69d31a1", "fn": "pd.ovigene.1.0.st_3.12.0.tar.gz"}, "pd.ovigene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.ovigene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.ovigene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ovigene.1.1.st/bioconductor-pd.ovigene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ovigene.1.1.st/bioconductor-pd.ovigene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "d6158cacd32a1892975fddd8dc8bb3f2", "fn": "pd.ovigene.1.1.st_3.12.0.tar.gz"}, "pd.pae.g1a-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.pae.g1a_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.pae.g1a_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.pae.g1a/bioconductor-pd.pae.g1a_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.pae.g1a/bioconductor-pd.pae.g1a_3.12.0_src_all.tar.gz"], "md5": "d96462eb35c63b30772bccae2a27a8cd", "fn": "pd.pae.g1a_3.12.0.tar.gz"}, "pd.plasmodium.anopheles-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.plasmodium.anopheles_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.plasmodium.anopheles_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.plasmodium.anopheles/bioconductor-pd.plasmodium.anopheles_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.plasmodium.anopheles/bioconductor-pd.plasmodium.anopheles_3.12.0_src_all.tar.gz"], "md5": "ae55b1451ceaed951f68213c0433f3d0", "fn": "pd.plasmodium.anopheles_3.12.0.tar.gz"}, "pd.poplar-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.poplar_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.poplar_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.poplar/bioconductor-pd.poplar_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.poplar/bioconductor-pd.poplar_3.12.0_src_all.tar.gz"], "md5": "9c33b7528e5a47654aeacf61b71058a8", "fn": "pd.poplar_3.12.0.tar.gz"}, "pd.porcine-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.porcine_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.porcine_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.porcine/bioconductor-pd.porcine_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.porcine/bioconductor-pd.porcine_3.12.0_src_all.tar.gz"], "md5": "5df404babadb1d6faef73e249c819a72", "fn": "pd.porcine_3.12.0.tar.gz"}, "pd.porgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.porgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.porgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.porgene.1.0.st/bioconductor-pd.porgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.porgene.1.0.st/bioconductor-pd.porgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "203fc56b0e2904fa7063c4a325e038f1", "fn": "pd.porgene.1.0.st_3.12.0.tar.gz"}, "pd.porgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.porgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.porgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.porgene.1.1.st/bioconductor-pd.porgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.porgene.1.1.st/bioconductor-pd.porgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "3a31d325861925a7428241207c461a1d", "fn": "pd.porgene.1.1.st_3.12.0.tar.gz"}, "pd.rabgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rabgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rabgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rabgene.1.0.st/bioconductor-pd.rabgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rabgene.1.0.st/bioconductor-pd.rabgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "7f1e33f4767a4c4653bdaff2b79989a0", "fn": "pd.rabgene.1.0.st_3.12.0.tar.gz"}, "pd.rabgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rabgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rabgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rabgene.1.1.st/bioconductor-pd.rabgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rabgene.1.1.st/bioconductor-pd.rabgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "2492695661309f5e6628612685460ee5", "fn": "pd.rabgene.1.1.st_3.12.0.tar.gz"}, "pd.rae230a-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rae230a_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rae230a_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rae230a/bioconductor-pd.rae230a_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rae230a/bioconductor-pd.rae230a_3.12.0_src_all.tar.gz"], "md5": "fa4a1c29d3457b1db82b1010c5f72412", "fn": "pd.rae230a_3.12.0.tar.gz"}, "pd.rae230b-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rae230b_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rae230b_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rae230b/bioconductor-pd.rae230b_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rae230b/bioconductor-pd.rae230b_3.12.0_src_all.tar.gz"], "md5": "10e2e70bb7538119127cd65f636f93b6", "fn": "pd.rae230b_3.12.0.tar.gz"}, "pd.raex.1.0.st.v1-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.raex.1.0.st.v1_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.raex.1.0.st.v1_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.raex.1.0.st.v1/bioconductor-pd.raex.1.0.st.v1_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.raex.1.0.st.v1/bioconductor-pd.raex.1.0.st.v1_3.14.1_src_all.tar.gz"], "md5": "e2160b549f63ffcc9222d88d82d4d393", "fn": "pd.raex.1.0.st.v1_3.14.1.tar.gz"}, "pd.ragene.1.0.st.v1-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.ragene.1.0.st.v1_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.ragene.1.0.st.v1_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.1.0.st.v1/bioconductor-pd.ragene.1.0.st.v1_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.1.0.st.v1/bioconductor-pd.ragene.1.0.st.v1_3.14.1_src_all.tar.gz"], "md5": "122cb69603e705218d01d70f48e90cad", "fn": "pd.ragene.1.0.st.v1_3.14.1.tar.gz"}, "pd.ragene.1.1.st.v1-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.ragene.1.1.st.v1_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.ragene.1.1.st.v1_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.1.1.st.v1/bioconductor-pd.ragene.1.1.st.v1_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.1.1.st.v1/bioconductor-pd.ragene.1.1.st.v1_3.14.1_src_all.tar.gz"], "md5": "7301ab6472849395ccb800c39807e969", "fn": "pd.ragene.1.1.st.v1_3.14.1.tar.gz"}, "pd.ragene.2.0.st-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.ragene.2.0.st_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.ragene.2.0.st_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.2.0.st/bioconductor-pd.ragene.2.0.st_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.2.0.st/bioconductor-pd.ragene.2.0.st_3.14.1_src_all.tar.gz"], "md5": "37157b09f009fef368b54e47711c313b", "fn": "pd.ragene.2.0.st_3.14.1.tar.gz"}, "pd.ragene.2.1.st-3.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.ragene.2.1.st_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.ragene.2.1.st_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.2.1.st/bioconductor-pd.ragene.2.1.st_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.2.1.st/bioconductor-pd.ragene.2.1.st_3.14.1_src_all.tar.gz"], "md5": "53adfa5ff2c7e466da83b807dbc7b237", "fn": "pd.ragene.2.1.st_3.14.1.tar.gz"}, "pd.rat230.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rat230.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rat230.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rat230.2/bioconductor-pd.rat230.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rat230.2/bioconductor-pd.rat230.2_3.12.0_src_all.tar.gz"], "md5": "286b1a7868ef6c795ebeb6dd8a5d5920", "fn": "pd.rat230.2_3.12.0.tar.gz"}, "pd.rcngene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rcngene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rcngene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rcngene.1.0.st/bioconductor-pd.rcngene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rcngene.1.0.st/bioconductor-pd.rcngene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "9c7c5ef4d4f5ed92d9130d77a99a0685", "fn": "pd.rcngene.1.0.st_3.12.0.tar.gz"}, "pd.rcngene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rcngene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rcngene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rcngene.1.1.st/bioconductor-pd.rcngene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rcngene.1.1.st/bioconductor-pd.rcngene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "9781549447d90b5423e820fff5cc6273", "fn": "pd.rcngene.1.1.st_3.12.0.tar.gz"}, "pd.rg.u34a-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rg.u34a_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rg.u34a_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34a/bioconductor-pd.rg.u34a_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34a/bioconductor-pd.rg.u34a_3.12.0_src_all.tar.gz"], "md5": "ac3a6cc203dabb8faab85b97f1a7ae3c", "fn": "pd.rg.u34a_3.12.0.tar.gz"}, "pd.rg.u34b-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rg.u34b_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rg.u34b_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34b/bioconductor-pd.rg.u34b_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34b/bioconductor-pd.rg.u34b_3.12.0_src_all.tar.gz"], "md5": "757966b66795d388c7169816d31977ad", "fn": "pd.rg.u34b_3.12.0.tar.gz"}, "pd.rg.u34c-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rg.u34c_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rg.u34c_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34c/bioconductor-pd.rg.u34c_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34c/bioconductor-pd.rg.u34c_3.12.0_src_all.tar.gz"], "md5": "bc9cb7b208972ac2901235bdabdee5b2", "fn": "pd.rg.u34c_3.12.0.tar.gz"}, "pd.rhegene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rhegene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rhegene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rhegene.1.0.st/bioconductor-pd.rhegene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rhegene.1.0.st/bioconductor-pd.rhegene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "6469add6928e663529df4df98fcdd7a8", "fn": "pd.rhegene.1.0.st_3.12.0.tar.gz"}, "pd.rhegene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rhegene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rhegene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rhegene.1.1.st/bioconductor-pd.rhegene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rhegene.1.1.st/bioconductor-pd.rhegene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "4f63424ab52283a95731767dce6623cd", "fn": "pd.rhegene.1.1.st_3.12.0.tar.gz"}, "pd.rhesus-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rhesus_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rhesus_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rhesus/bioconductor-pd.rhesus_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rhesus/bioconductor-pd.rhesus_3.12.0_src_all.tar.gz"], "md5": "51efcfe1384ac956ff93bf0530965054", "fn": "pd.rhesus_3.12.0.tar.gz"}, "pd.rice-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rice_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rice_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rice/bioconductor-pd.rice_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rice/bioconductor-pd.rice_3.12.0_src_all.tar.gz"], "md5": "9c456981b3d0b99a96ac6c71e3eb7c8a", "fn": "pd.rice_3.12.0.tar.gz"}, "pd.rjpgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rjpgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rjpgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rjpgene.1.0.st/bioconductor-pd.rjpgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rjpgene.1.0.st/bioconductor-pd.rjpgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "066f5dbacc1110e42ce4d457ad3b9306", "fn": "pd.rjpgene.1.0.st_3.12.0.tar.gz"}, "pd.rjpgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rjpgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rjpgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rjpgene.1.1.st/bioconductor-pd.rjpgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rjpgene.1.1.st/bioconductor-pd.rjpgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "265503774b15e0f4e71ac53a276a80f2", "fn": "pd.rjpgene.1.1.st_3.12.0.tar.gz"}, "pd.rn.u34-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rn.u34_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rn.u34_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rn.u34/bioconductor-pd.rn.u34_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rn.u34/bioconductor-pd.rn.u34_3.12.0_src_all.tar.gz"], "md5": "1728c547f1383bffab330796505119ec", "fn": "pd.rn.u34_3.12.0.tar.gz"}, "pd.rta.1.0-3.12.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rta.1.0_3.12.2.tar.gz", "https://bioarchive.galaxyproject.org/pd.rta.1.0_3.12.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rta.1.0/bioconductor-pd.rta.1.0_3.12.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rta.1.0/bioconductor-pd.rta.1.0_3.12.2_src_all.tar.gz"], "md5": "90752a892a103c7fe4cd6c86e61a61db", "fn": "pd.rta.1.0_3.12.2.tar.gz"}, "pd.rusgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rusgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rusgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rusgene.1.0.st/bioconductor-pd.rusgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rusgene.1.0.st/bioconductor-pd.rusgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "0b9b00fee58ef211e041395052344483", "fn": "pd.rusgene.1.0.st_3.12.0.tar.gz"}, "pd.rusgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.rusgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rusgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rusgene.1.1.st/bioconductor-pd.rusgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rusgene.1.1.st/bioconductor-pd.rusgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "228837c2de4a4b106806cb7f384564fa", "fn": "pd.rusgene.1.1.st_3.12.0.tar.gz"}, "pd.s.aureus-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.s.aureus_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.s.aureus_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.s.aureus/bioconductor-pd.s.aureus_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.s.aureus/bioconductor-pd.s.aureus_3.12.0_src_all.tar.gz"], "md5": "f173ae6e4316aaa2eafbde92d5868a5a", "fn": "pd.s.aureus_3.12.0.tar.gz"}, "pd.soybean-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.soybean_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.soybean_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.soybean/bioconductor-pd.soybean_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.soybean/bioconductor-pd.soybean_3.12.0_src_all.tar.gz"], "md5": "6dbe167be9d40c1d9096485afb4525f0", "fn": "pd.soybean_3.12.0.tar.gz"}, "pd.soygene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.soygene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.soygene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.soygene.1.0.st/bioconductor-pd.soygene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.soygene.1.0.st/bioconductor-pd.soygene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "b264df0648ec35d04f91e0ef8e26ac95", "fn": "pd.soygene.1.0.st_3.12.0.tar.gz"}, "pd.soygene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.soygene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.soygene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.soygene.1.1.st/bioconductor-pd.soygene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.soygene.1.1.st/bioconductor-pd.soygene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "4a911a4a4b5de927fe6239e500a2993f", "fn": "pd.soygene.1.1.st_3.12.0.tar.gz"}, "pd.sugar.cane-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.sugar.cane_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.sugar.cane_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.sugar.cane/bioconductor-pd.sugar.cane_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.sugar.cane/bioconductor-pd.sugar.cane_3.12.0_src_all.tar.gz"], "md5": "bd7eb8b1a1c9ac77359358a5347330fb", "fn": "pd.sugar.cane_3.12.0.tar.gz"}, "pd.tomato-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.tomato_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.tomato_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.tomato/bioconductor-pd.tomato_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.tomato/bioconductor-pd.tomato_3.12.0_src_all.tar.gz"], "md5": "ce78f6ee43d72e017608413dd4d50580", "fn": "pd.tomato_3.12.0.tar.gz"}, "pd.u133.x3p-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.u133.x3p_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.u133.x3p_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.u133.x3p/bioconductor-pd.u133.x3p_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.u133.x3p/bioconductor-pd.u133.x3p_3.12.0_src_all.tar.gz"], "md5": "e3f343e32273667f851e26d7b8a7a5db", "fn": "pd.u133.x3p_3.12.0.tar.gz"}, "pd.vitis.vinifera-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.vitis.vinifera_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.vitis.vinifera_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.vitis.vinifera/bioconductor-pd.vitis.vinifera_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.vitis.vinifera/bioconductor-pd.vitis.vinifera_3.12.0_src_all.tar.gz"], "md5": "104a8ac33a9baa25a61f953679795696", "fn": "pd.vitis.vinifera_3.12.0.tar.gz"}, "pd.wheat-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.wheat_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.wheat_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.wheat/bioconductor-pd.wheat_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.wheat/bioconductor-pd.wheat_3.12.0_src_all.tar.gz"], "md5": "38a7183c8d3b874cf62391a9e9169bb9", "fn": "pd.wheat_3.12.0.tar.gz"}, "pd.x.laevis.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.x.laevis.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.x.laevis.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.x.laevis.2/bioconductor-pd.x.laevis.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.x.laevis.2/bioconductor-pd.x.laevis.2_3.12.0_src_all.tar.gz"], "md5": "32416957e3cdc11ad4dbfcd9141ff113", "fn": "pd.x.laevis.2_3.12.0.tar.gz"}, "pd.x.tropicalis-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.x.tropicalis_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.x.tropicalis_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.x.tropicalis/bioconductor-pd.x.tropicalis_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.x.tropicalis/bioconductor-pd.x.tropicalis_3.12.0_src_all.tar.gz"], "md5": "79a4de91831e4b0153495e12b9c6e8d3", "fn": "pd.x.tropicalis_3.12.0.tar.gz"}, "pd.xenopus.laevis-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.xenopus.laevis_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.xenopus.laevis_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.xenopus.laevis/bioconductor-pd.xenopus.laevis_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.xenopus.laevis/bioconductor-pd.xenopus.laevis_3.12.0_src_all.tar.gz"], "md5": "6d5c2c9e8e3891770b1c6e9dcd823c0d", "fn": "pd.xenopus.laevis_3.12.0.tar.gz"}, "pd.yeast.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.yeast.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.yeast.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.yeast.2/bioconductor-pd.yeast.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.yeast.2/bioconductor-pd.yeast.2_3.12.0_src_all.tar.gz"], "md5": "780f5139ee9cda46c9e38122538ce129", "fn": "pd.yeast.2_3.12.0.tar.gz"}, "pd.yg.s98-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.yg.s98_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.yg.s98_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.yg.s98/bioconductor-pd.yg.s98_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.yg.s98/bioconductor-pd.yg.s98_3.12.0_src_all.tar.gz"], "md5": "caec3e8f29918f078b2dc7c76f4a74e2", "fn": "pd.yg.s98_3.12.0.tar.gz"}, "pd.zebgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.zebgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.zebgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.zebgene.1.0.st/bioconductor-pd.zebgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.zebgene.1.0.st/bioconductor-pd.zebgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "54fcf757b8069e95dd7e2f3ff74ae050", "fn": "pd.zebgene.1.0.st_3.12.0.tar.gz"}, "pd.zebgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.zebgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.zebgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.zebgene.1.1.st/bioconductor-pd.zebgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.zebgene.1.1.st/bioconductor-pd.zebgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "d87028cd9024bc33be518635cf2f48fc", "fn": "pd.zebgene.1.1.st_3.12.0.tar.gz"}, "pd.zebrafish-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pd.zebrafish_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.zebrafish_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.zebrafish/bioconductor-pd.zebrafish_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.zebrafish/bioconductor-pd.zebrafish_3.12.0_src_all.tar.gz"], "md5": "101f09a9d9304d1d8fbcc7f4812897b1", "fn": "pd.zebrafish_3.12.0.tar.gz"}, "pedbarrayv10.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pedbarrayv10.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/pedbarrayv10.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pedbarrayv10.db/bioconductor-pedbarrayv10.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pedbarrayv10.db/bioconductor-pedbarrayv10.db_3.2.3_src_all.tar.gz"], "md5": "25acc3bfee229015ecca1c7d688e5168", "fn": "pedbarrayv10.db_3.2.3.tar.gz"}, "pedbarrayv9.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pedbarrayv9.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/pedbarrayv9.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pedbarrayv9.db/bioconductor-pedbarrayv9.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pedbarrayv9.db/bioconductor-pedbarrayv9.db_3.2.3_src_all.tar.gz"], "md5": "da4b2f9c0a672e0c9ee53f017bacaff7", "fn": "pedbarrayv9.db_3.2.3.tar.gz"}, "pfam.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/PFAM.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/PFAM.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pfam.db/bioconductor-pfam.db_3.16.0_src_all.tar.gz"], "md5": "6fec4f9e7916ebcffee313775c774e09", "fn": "PFAM.db_3.16.0.tar.gz"}, "phastcons100way.ucsc.hg19-3.7.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/phastCons100way.UCSC.hg19_3.7.2.tar.gz", "https://bioarchive.galaxyproject.org/phastCons100way.UCSC.hg19_3.7.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phastcons100way.ucsc.hg19/bioconductor-phastcons100way.ucsc.hg19_3.7.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phastcons100way.ucsc.hg19/bioconductor-phastcons100way.ucsc.hg19_3.7.2_src_all.tar.gz"], "md5": "65aa706a567f7e328dbba0095f995cf1", "fn": "phastCons100way.UCSC.hg19_3.7.2.tar.gz"}, "phastcons100way.ucsc.hg38-3.7.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/phastCons100way.UCSC.hg38_3.7.1.tar.gz", "https://bioarchive.galaxyproject.org/phastCons100way.UCSC.hg38_3.7.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phastcons100way.ucsc.hg38/bioconductor-phastcons100way.ucsc.hg38_3.7.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phastcons100way.ucsc.hg38/bioconductor-phastcons100way.ucsc.hg38_3.7.1_src_all.tar.gz"], "md5": "878c757f9270b3410d11e4e4a4213c8e", "fn": "phastCons100way.UCSC.hg38_3.7.1.tar.gz"}, "phastcons30way.ucsc.hg38-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/phastCons30way.UCSC.hg38_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/phastCons30way.UCSC.hg38_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phastcons30way.ucsc.hg38/bioconductor-phastcons30way.ucsc.hg38_3.13.0_src_all.tar.gz"], "md5": "754faee8463bc494c502540cb8f6ea8d", "fn": "phastCons30way.UCSC.hg38_3.13.0.tar.gz"}, "phastcons35way.ucsc.mm39-3.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/phastCons35way.UCSC.mm39_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/phastCons35way.UCSC.mm39_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phastcons35way.ucsc.mm39/bioconductor-phastcons35way.ucsc.mm39_3.16.0_src_all.tar.gz"], "md5": "83fc2a2265bc341b6a00064a1286b5bc", "fn": "phastCons35way.UCSC.mm39_3.16.0.tar.gz"}, "phastcons7way.ucsc.hg38-3.7.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/phastCons7way.UCSC.hg38_3.7.1.tar.gz", "https://bioarchive.galaxyproject.org/phastCons7way.UCSC.hg38_3.7.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phastcons7way.ucsc.hg38/bioconductor-phastcons7way.ucsc.hg38_3.7.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phastcons7way.ucsc.hg38/bioconductor-phastcons7way.ucsc.hg38_3.7.1_src_all.tar.gz"], "md5": "c2d87446b022c166c1c325ea2aef521d", "fn": "phastCons7way.UCSC.hg38_3.7.1.tar.gz"}, "phylop35way.ucsc.mm39-3.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/phyloP35way.UCSC.mm39_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/phyloP35way.UCSC.mm39_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phylop35way.ucsc.mm39/bioconductor-phylop35way.ucsc.mm39_3.16.0_src_all.tar.gz"], "md5": "2c34eef5f20eace04efd47673cdf1062", "fn": "phyloP35way.UCSC.mm39_3.16.0.tar.gz"}, "pig.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/pig.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/pig.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pig.db0/bioconductor-pig.db0_3.16.0_src_all.tar.gz"], "md5": "3822cffa9665794639acfe1c59e35df5", "fn": "pig.db0_3.16.0.tar.gz"}, "plasmodiumanophelescdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/plasmodiumanophelescdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/plasmodiumanophelescdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-plasmodiumanophelescdf/bioconductor-plasmodiumanophelescdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-plasmodiumanophelescdf/bioconductor-plasmodiumanophelescdf_2.18.0_src_all.tar.gz"], "md5": "54c5c326977d6358c40cacf34cb2aca2", "fn": "plasmodiumanophelescdf_2.18.0.tar.gz"}, "plasmodiumanophelesprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/plasmodiumanophelesprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/plasmodiumanophelesprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-plasmodiumanophelesprobe/bioconductor-plasmodiumanophelesprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-plasmodiumanophelesprobe/bioconductor-plasmodiumanophelesprobe_2.18.0_src_all.tar.gz"], "md5": "281683dab923168c2eedb7b08c528935", "fn": "plasmodiumanophelesprobe_2.18.0.tar.gz"}, "pocrcannotation.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/POCRCannotation.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/POCRCannotation.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pocrcannotation.db/bioconductor-pocrcannotation.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pocrcannotation.db/bioconductor-pocrcannotation.db_3.2.3_src_all.tar.gz"], "md5": "da1d4dacc5fffb9c5dfea55649974aa5", "fn": "POCRCannotation.db_3.2.3.tar.gz"}, "polyphen.hsapiens.dbsnp131-1.0.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/PolyPhen.Hsapiens.dbSNP131_1.0.2.tar.gz", "https://bioarchive.galaxyproject.org/PolyPhen.Hsapiens.dbSNP131_1.0.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-polyphen.hsapiens.dbsnp131/bioconductor-polyphen.hsapiens.dbsnp131_1.0.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-polyphen.hsapiens.dbsnp131/bioconductor-polyphen.hsapiens.dbsnp131_1.0.2_src_all.tar.gz"], "md5": "763e9cd4afd97b36f7e659f5454ef61f", "fn": "PolyPhen.Hsapiens.dbSNP131_1.0.2.tar.gz"}, "poplarcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/poplarcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/poplarcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-poplarcdf/bioconductor-poplarcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-poplarcdf/bioconductor-poplarcdf_2.18.0_src_all.tar.gz"], "md5": "556e7f8f6f76436552d8044ef29279cb", "fn": "poplarcdf_2.18.0.tar.gz"}, "poplarprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/poplarprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/poplarprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-poplarprobe/bioconductor-poplarprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-poplarprobe/bioconductor-poplarprobe_2.18.0_src_all.tar.gz"], "md5": "87a608cd86084a06973a88e9b51f799a", "fn": "poplarprobe_2.18.0.tar.gz"}, "porcine.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/porcine.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/porcine.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-porcine.db/bioconductor-porcine.db_3.13.0_src_all.tar.gz"], "md5": "4a86b3e696d267dca673b4e9276d6368", "fn": "porcine.db_3.13.0.tar.gz"}, "porcinecdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/porcinecdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/porcinecdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-porcinecdf/bioconductor-porcinecdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-porcinecdf/bioconductor-porcinecdf_2.18.0_src_all.tar.gz"], "md5": "32a60b93829c06a935895fab0a469228", "fn": "porcinecdf_2.18.0.tar.gz"}, "porcineprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/porcineprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/porcineprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-porcineprobe/bioconductor-porcineprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-porcineprobe/bioconductor-porcineprobe_2.18.0_src_all.tar.gz"], "md5": "5ac483b6329a012d4c9954e3dee8869e", "fn": "porcineprobe_2.18.0.tar.gz"}, "primeviewcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/primeviewcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/primeviewcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-primeviewcdf/bioconductor-primeviewcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-primeviewcdf/bioconductor-primeviewcdf_2.18.0_src_all.tar.gz"], "md5": "71e39a59a5907e9b8a8dba58d36eee50", "fn": "primeviewcdf_2.18.0.tar.gz"}, "primeviewprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/primeviewprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/primeviewprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-primeviewprobe/bioconductor-primeviewprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-primeviewprobe/bioconductor-primeviewprobe_2.18.0_src_all.tar.gz"], "md5": "87cc56a8da4fb742ab1558ce1d3d26cc", "fn": "primeviewprobe_2.18.0.tar.gz"}, "r10kcod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/r10kcod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/r10kcod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-r10kcod.db/bioconductor-r10kcod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-r10kcod.db/bioconductor-r10kcod.db_3.4.0_src_all.tar.gz"], "md5": "4a7a25fee64294cfb5adccaa6cf28772", "fn": "r10kcod.db_3.4.0.tar.gz"}, "rae230a.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rae230a.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/rae230a.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230a.db/bioconductor-rae230a.db_3.13.0_src_all.tar.gz"], "md5": "a2a80af1669fc038a64effbf5a4b246d", "fn": "rae230a.db_3.13.0.tar.gz"}, "rae230acdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rae230acdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rae230acdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230acdf/bioconductor-rae230acdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230acdf/bioconductor-rae230acdf_2.18.0_src_all.tar.gz"], "md5": "6f2281124e1be164d5fd599e84f6adbc", "fn": "rae230acdf_2.18.0.tar.gz"}, "rae230aprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rae230aprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rae230aprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230aprobe/bioconductor-rae230aprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230aprobe/bioconductor-rae230aprobe_2.18.0_src_all.tar.gz"], "md5": "6f2d77e1d9c1e3afb96ef78b3202bb0b", "fn": "rae230aprobe_2.18.0.tar.gz"}, "rae230b.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rae230b.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/rae230b.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230b.db/bioconductor-rae230b.db_3.13.0_src_all.tar.gz"], "md5": "4f0474ed22bf5ebd932dd6a4d9573551", "fn": "rae230b.db_3.13.0.tar.gz"}, "rae230bcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rae230bcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rae230bcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230bcdf/bioconductor-rae230bcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230bcdf/bioconductor-rae230bcdf_2.18.0_src_all.tar.gz"], "md5": "bd61c17402e9c04be1000c16e0356618", "fn": "rae230bcdf_2.18.0.tar.gz"}, "rae230bprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rae230bprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rae230bprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230bprobe/bioconductor-rae230bprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230bprobe/bioconductor-rae230bprobe_2.18.0_src_all.tar.gz"], "md5": "7bdb3a07e1f00de8ff510a69bdac4c53", "fn": "rae230bprobe_2.18.0.tar.gz"}, "raex10stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/raex10stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/raex10stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-raex10stprobeset.db/bioconductor-raex10stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "a386809ea8da340f315e378fa329b3ac", "fn": "raex10stprobeset.db_8.8.0.tar.gz"}, "raex10sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/raex10sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/raex10sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-raex10sttranscriptcluster.db/bioconductor-raex10sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "3a0c511a1073c67172770bc3e4b842b5", "fn": "raex10sttranscriptcluster.db_8.8.0.tar.gz"}, "raexexonprobesetlocation-1.15.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/RaExExonProbesetLocation_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/RaExExonProbesetLocation_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-raexexonprobesetlocation/bioconductor-raexexonprobesetlocation_1.15.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-raexexonprobesetlocation/bioconductor-raexexonprobesetlocation_1.15.0_src_all.tar.gz"], "md5": "d547bcd30685495283b32f0f86ecc79b", "fn": "RaExExonProbesetLocation_1.15.0.tar.gz"}, "ragene10stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ragene10stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene10stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene10stprobeset.db/bioconductor-ragene10stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "358685c380b37027a064924069b9ee40", "fn": "ragene10stprobeset.db_8.8.0.tar.gz"}, "ragene10sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ragene10sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene10sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene10sttranscriptcluster.db/bioconductor-ragene10sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "5ff95454493a72bfa2546d82d32fbec1", "fn": "ragene10sttranscriptcluster.db_8.8.0.tar.gz"}, "ragene10stv1cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ragene10stv1cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene10stv1cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene10stv1cdf/bioconductor-ragene10stv1cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene10stv1cdf/bioconductor-ragene10stv1cdf_2.18.0_src_all.tar.gz"], "md5": "df696e9dbf5b3f2761b6a0a5914be058", "fn": "ragene10stv1cdf_2.18.0.tar.gz"}, "ragene10stv1probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ragene10stv1probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene10stv1probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene10stv1probe/bioconductor-ragene10stv1probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene10stv1probe/bioconductor-ragene10stv1probe_2.18.0_src_all.tar.gz"], "md5": "94978b6efb075aacf31ccdc8000e40fa", "fn": "ragene10stv1probe_2.18.0.tar.gz"}, "ragene11stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ragene11stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene11stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene11stprobeset.db/bioconductor-ragene11stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "86f7704c4852c514b3bc3221f7692ba3", "fn": "ragene11stprobeset.db_8.8.0.tar.gz"}, "ragene11sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ragene11sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene11sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene11sttranscriptcluster.db/bioconductor-ragene11sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "f7fbe318547f911b520415a90b3440e9", "fn": "ragene11sttranscriptcluster.db_8.8.0.tar.gz"}, "ragene20stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ragene20stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene20stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene20stprobeset.db/bioconductor-ragene20stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "23a43899a22078f4c13b7b1d45176319", "fn": "ragene20stprobeset.db_8.8.0.tar.gz"}, "ragene20sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ragene20sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene20sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene20sttranscriptcluster.db/bioconductor-ragene20sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "b44c5f6ac2b2e3eb4d820d08f7a38644", "fn": "ragene20sttranscriptcluster.db_8.8.0.tar.gz"}, "ragene21stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ragene21stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene21stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene21stprobeset.db/bioconductor-ragene21stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "6451885f99ce3873d5d4dbacdf968181", "fn": "ragene21stprobeset.db_8.8.0.tar.gz"}, "ragene21sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ragene21sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene21sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene21sttranscriptcluster.db/bioconductor-ragene21sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "6ffe13e1594add0a5169b2083b608336", "fn": "ragene21sttranscriptcluster.db_8.8.0.tar.gz"}, "rat.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/rat.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/rat.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat.db0/bioconductor-rat.db0_3.16.0_src_all.tar.gz"], "md5": "a244e0fa21d1ffa71b46694a7ddafb58", "fn": "rat.db0_3.16.0.tar.gz"}, "rat2302.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rat2302.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/rat2302.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat2302.db/bioconductor-rat2302.db_3.13.0_src_all.tar.gz"], "md5": "b1404d8a16fec681f0fd682589a685ea", "fn": "rat2302.db_3.13.0.tar.gz"}, "rat2302cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rat2302cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rat2302cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat2302cdf/bioconductor-rat2302cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat2302cdf/bioconductor-rat2302cdf_2.18.0_src_all.tar.gz"], "md5": "a033730f79a11d45b4cd7e7c520f8052", "fn": "rat2302cdf_2.18.0.tar.gz"}, "rat2302frmavecs-0.99.11": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rat2302frmavecs_0.99.11.tar.gz", "https://bioarchive.galaxyproject.org/rat2302frmavecs_0.99.11.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat2302frmavecs/bioconductor-rat2302frmavecs_0.99.11_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat2302frmavecs/bioconductor-rat2302frmavecs_0.99.11_src_all.tar.gz"], "md5": "44d9f00c2f3806899c6605d1ba274066", "fn": "rat2302frmavecs_0.99.11.tar.gz"}, "rat2302probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rat2302probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rat2302probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat2302probe/bioconductor-rat2302probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat2302probe/bioconductor-rat2302probe_2.18.0_src_all.tar.gz"], "md5": "d1d9215e52b9e845cc4d7c902536e0d6", "fn": "rat2302probe_2.18.0.tar.gz"}, "ratchrloc-2.1.6": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ratCHRLOC_2.1.6.tar.gz", "https://bioarchive.galaxyproject.org/ratCHRLOC_2.1.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ratchrloc/bioconductor-ratchrloc_2.1.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ratchrloc/bioconductor-ratchrloc_2.1.6_src_all.tar.gz"], "md5": "6fecff4821a5a47e3bd38a2ff78173d5", "fn": "ratCHRLOC_2.1.6.tar.gz"}, "rattoxfxcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rattoxfxcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rattoxfxcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rattoxfxcdf/bioconductor-rattoxfxcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rattoxfxcdf/bioconductor-rattoxfxcdf_2.18.0_src_all.tar.gz"], "md5": "912d0fa424615fcd92773ed174d5efdd", "fn": "rattoxfxcdf_2.18.0.tar.gz"}, "rattoxfxprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rattoxfxprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rattoxfxprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rattoxfxprobe/bioconductor-rattoxfxprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rattoxfxprobe/bioconductor-rattoxfxprobe_2.18.0_src_all.tar.gz"], "md5": "202791c72e8c956b9854fa4d9ba67a24", "fn": "rattoxfxprobe_2.18.0.tar.gz"}, "rattus.norvegicus-1.3.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/Rattus.norvegicus_1.3.1.tar.gz", "https://bioarchive.galaxyproject.org/Rattus.norvegicus_1.3.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rattus.norvegicus/bioconductor-rattus.norvegicus_1.3.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rattus.norvegicus/bioconductor-rattus.norvegicus_1.3.1_src_all.tar.gz"], "md5": "5692fdeb0bc7f94e1db35f097cad99a9", "fn": "Rattus.norvegicus_1.3.1.tar.gz"}, "reactome.db-1.82.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/reactome.db_1.82.0.tar.gz", "https://bioarchive.galaxyproject.org/reactome.db_1.82.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-reactome.db/bioconductor-reactome.db_1.82.0_src_all.tar.gz"], "md5": "54cf27d67bc854603f6ef2c5b6d2d633", "fn": "reactome.db_1.82.0.tar.gz"}, "rgenometracksdata-0.99.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rGenomeTracksData_0.99.0.tar.gz", "https://bioarchive.galaxyproject.org/rGenomeTracksData_0.99.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgenometracksdata/bioconductor-rgenometracksdata_0.99.0_src_all.tar.gz"], "md5": "713103a8b4b4e48fa762ef589a43ffb8", "fn": "rGenomeTracksData_0.99.0.tar.gz"}, "rgu34a.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rgu34a.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/rgu34a.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34a.db/bioconductor-rgu34a.db_3.13.0_src_all.tar.gz"], "md5": "e99dc4c05360b49a2249cb5de0b1dd4e", "fn": "rgu34a.db_3.13.0.tar.gz"}, "rgu34acdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rgu34acdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rgu34acdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34acdf/bioconductor-rgu34acdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34acdf/bioconductor-rgu34acdf_2.18.0_src_all.tar.gz"], "md5": "dcfa7ecce00e529f93809759ed837b8d", "fn": "rgu34acdf_2.18.0.tar.gz"}, "rgu34aprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rgu34aprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rgu34aprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34aprobe/bioconductor-rgu34aprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34aprobe/bioconductor-rgu34aprobe_2.18.0_src_all.tar.gz"], "md5": "902aee259a2894fa8713c4bf9266c0e2", "fn": "rgu34aprobe_2.18.0.tar.gz"}, "rgu34b.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rgu34b.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/rgu34b.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34b.db/bioconductor-rgu34b.db_3.13.0_src_all.tar.gz"], "md5": "5aeb80d5190bf2dcffa6b9264d3db33f", "fn": "rgu34b.db_3.13.0.tar.gz"}, "rgu34bcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rgu34bcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rgu34bcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34bcdf/bioconductor-rgu34bcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34bcdf/bioconductor-rgu34bcdf_2.18.0_src_all.tar.gz"], "md5": "428b3a39f0d8addd7d863539b8cda6ea", "fn": "rgu34bcdf_2.18.0.tar.gz"}, "rgu34bprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rgu34bprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rgu34bprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34bprobe/bioconductor-rgu34bprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34bprobe/bioconductor-rgu34bprobe_2.18.0_src_all.tar.gz"], "md5": "2d6488309c5e54231a18e2ecf5608bb1", "fn": "rgu34bprobe_2.18.0.tar.gz"}, "rgu34c.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rgu34c.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/rgu34c.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34c.db/bioconductor-rgu34c.db_3.13.0_src_all.tar.gz"], "md5": "e19f250869a9894bc9d069a4baf39a3c", "fn": "rgu34c.db_3.13.0.tar.gz"}, "rgu34ccdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rgu34ccdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rgu34ccdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34ccdf/bioconductor-rgu34ccdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34ccdf/bioconductor-rgu34ccdf_2.18.0_src_all.tar.gz"], "md5": "556a7130086004d26095594da31c6410", "fn": "rgu34ccdf_2.18.0.tar.gz"}, "rgu34cprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rgu34cprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rgu34cprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34cprobe/bioconductor-rgu34cprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34cprobe/bioconductor-rgu34cprobe_2.18.0_src_all.tar.gz"], "md5": "d1a6c433acd30b95fa7be89147105b74", "fn": "rgu34cprobe_2.18.0.tar.gz"}, "rguatlas4k.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rguatlas4k.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/rguatlas4k.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rguatlas4k.db/bioconductor-rguatlas4k.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rguatlas4k.db/bioconductor-rguatlas4k.db_3.2.3_src_all.tar.gz"], "md5": "6a360676e08319ec5465c47c758110bd", "fn": "rguatlas4k.db_3.2.3.tar.gz"}, "rgug4105a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rgug4105a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/rgug4105a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgug4105a.db/bioconductor-rgug4105a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgug4105a.db/bioconductor-rgug4105a.db_3.2.3_src_all.tar.gz"], "md5": "3ccf354083ae36a7ae687fb8209c4e5b", "fn": "rgug4105a.db_3.2.3.tar.gz"}, "rgug4130a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rgug4130a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/rgug4130a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgug4130a.db/bioconductor-rgug4130a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgug4130a.db/bioconductor-rgug4130a.db_3.2.3_src_all.tar.gz"], "md5": "13643ac109aaf12590a5b6e379609b79", "fn": "rgug4130a.db_3.2.3.tar.gz"}, "rgug4131a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rgug4131a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/rgug4131a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgug4131a.db/bioconductor-rgug4131a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgug4131a.db/bioconductor-rgug4131a.db_3.2.3_src_all.tar.gz"], "md5": "1168d4906fb8ce60cbc0fa6cfa3b8ec6", "fn": "rgug4131a.db_3.2.3.tar.gz"}, "rhesus.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/rhesus.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/rhesus.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rhesus.db0/bioconductor-rhesus.db0_3.16.0_src_all.tar.gz"], "md5": "7b57d4cd1362d889869c6f6e9a4062c5", "fn": "rhesus.db0_3.16.0.tar.gz"}, "rhesuscdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rhesuscdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rhesuscdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rhesuscdf/bioconductor-rhesuscdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rhesuscdf/bioconductor-rhesuscdf_2.18.0_src_all.tar.gz"], "md5": "994e16da5dd31bc2796d0da40aa2634f", "fn": "rhesuscdf_2.18.0.tar.gz"}, "rhesusprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rhesusprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rhesusprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rhesusprobe/bioconductor-rhesusprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rhesusprobe/bioconductor-rhesusprobe_2.18.0_src_all.tar.gz"], "md5": "4169c1c997c4c08b027bc7489533e11e", "fn": "rhesusprobe_2.18.0.tar.gz"}, "ri16cod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ri16cod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/ri16cod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ri16cod.db/bioconductor-ri16cod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ri16cod.db/bioconductor-ri16cod.db_3.4.0_src_all.tar.gz"], "md5": "cd01b429295fdbba21dbe566effacbdd", "fn": "ri16cod.db_3.4.0.tar.gz"}, "ricecdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ricecdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ricecdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ricecdf/bioconductor-ricecdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ricecdf/bioconductor-ricecdf_2.18.0_src_all.tar.gz"], "md5": "51db6f51f4adcfb7f4940d07668db8b8", "fn": "ricecdf_2.18.0.tar.gz"}, "riceprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/riceprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/riceprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-riceprobe/bioconductor-riceprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-riceprobe/bioconductor-riceprobe_2.18.0_src_all.tar.gz"], "md5": "2fac7746c343546cf30e6d54bc1e2019", "fn": "riceprobe_2.18.0.tar.gz"}, "rmir.hs.mirna-1.0.7": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/RmiR.Hs.miRNA_1.0.7.tar.gz", "https://bioarchive.galaxyproject.org/RmiR.Hs.miRNA_1.0.7.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rmir.hs.mirna/bioconductor-rmir.hs.mirna_1.0.7_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rmir.hs.mirna/bioconductor-rmir.hs.mirna_1.0.7_src_all.tar.gz"], "md5": "4aedac188382447d9907d2617aa2e8e6", "fn": "RmiR.Hs.miRNA_1.0.7.tar.gz"}, "rmir.hsa-1.0.5": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/RmiR.hsa_1.0.5.tar.gz", "https://bioarchive.galaxyproject.org/RmiR.hsa_1.0.5.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rmir.hsa/bioconductor-rmir.hsa_1.0.5_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rmir.hsa/bioconductor-rmir.hsa_1.0.5_src_all.tar.gz"], "md5": "f22a18d1a34d12f8fc4ba3daaf1379fd", "fn": "RmiR.hsa_1.0.5.tar.gz"}, "rnagilentdesign028282.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/RnAgilentDesign028282.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/RnAgilentDesign028282.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnagilentdesign028282.db/bioconductor-rnagilentdesign028282.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnagilentdesign028282.db/bioconductor-rnagilentdesign028282.db_3.2.3_src_all.tar.gz"], "md5": "72cafb0f7514a81f462acb3248e21aa9", "fn": "RnAgilentDesign028282.db_3.2.3.tar.gz"}, "rnu34.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rnu34.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/rnu34.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnu34.db/bioconductor-rnu34.db_3.13.0_src_all.tar.gz"], "md5": "7345817f2f26270779d2409b8a17a5bd", "fn": "rnu34.db_3.13.0.tar.gz"}, "rnu34cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rnu34cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rnu34cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnu34cdf/bioconductor-rnu34cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnu34cdf/bioconductor-rnu34cdf_2.18.0_src_all.tar.gz"], "md5": "0f2564fc6ac89de4d779faf253f23ce3", "fn": "rnu34cdf_2.18.0.tar.gz"}, "rnu34probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rnu34probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rnu34probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnu34probe/bioconductor-rnu34probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnu34probe/bioconductor-rnu34probe_2.18.0_src_all.tar.gz"], "md5": "c5ef9793a437f2bf990f6e84d31da0de", "fn": "rnu34probe_2.18.0.tar.gz"}, "roberts2005annotation.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/Roberts2005Annotation.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/Roberts2005Annotation.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-roberts2005annotation.db/bioconductor-roberts2005annotation.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-roberts2005annotation.db/bioconductor-roberts2005annotation.db_3.2.3_src_all.tar.gz"], "md5": "fb28aaf1a1e0c81cf936badc674b754a", "fn": "Roberts2005Annotation.db_3.2.3.tar.gz"}, "rta10probeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rta10probeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/rta10probeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rta10probeset.db/bioconductor-rta10probeset.db_8.8.0_src_all.tar.gz"], "md5": "ce002623471eef89fb841f0bf3e7c9f8", "fn": "rta10probeset.db_8.8.0.tar.gz"}, "rta10transcriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rta10transcriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/rta10transcriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rta10transcriptcluster.db/bioconductor-rta10transcriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "14ade3f4fca2d1091ccb28e7a777f3e5", "fn": "rta10transcriptcluster.db_8.8.0.tar.gz"}, "rtu34.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rtu34.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/rtu34.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtu34.db/bioconductor-rtu34.db_3.13.0_src_all.tar.gz"], "md5": "f46c4763627f1a9e00cdc9d0af8c5f2e", "fn": "rtu34.db_3.13.0.tar.gz"}, "rtu34cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rtu34cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rtu34cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtu34cdf/bioconductor-rtu34cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtu34cdf/bioconductor-rtu34cdf_2.18.0_src_all.tar.gz"], "md5": "317abfcca319d01eb14f16efa6d91da1", "fn": "rtu34cdf_2.18.0.tar.gz"}, "rtu34probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rtu34probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rtu34probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtu34probe/bioconductor-rtu34probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtu34probe/bioconductor-rtu34probe_2.18.0_src_all.tar.gz"], "md5": "1778d857a61bf181b80b9fcf46ebd2c3", "fn": "rtu34probe_2.18.0.tar.gz"}, "rwgcod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rwgcod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/rwgcod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rwgcod.db/bioconductor-rwgcod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rwgcod.db/bioconductor-rwgcod.db_3.4.0_src_all.tar.gz"], "md5": "c8d2fa81b6f03c4ee629a0883431e5fd", "fn": "rwgcod.db_3.4.0.tar.gz"}, "saureuscdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/saureuscdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/saureuscdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-saureuscdf/bioconductor-saureuscdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-saureuscdf/bioconductor-saureuscdf_2.18.0_src_all.tar.gz"], "md5": "d01883e4c3dd99f32012e6dbab8cdb8b", "fn": "saureuscdf_2.18.0.tar.gz"}, "saureusprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/saureusprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/saureusprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-saureusprobe/bioconductor-saureusprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-saureusprobe/bioconductor-saureusprobe_2.18.0_src_all.tar.gz"], "md5": "eb4e91b10a536cbde4ecc08951ddf4d3", "fn": "saureusprobe_2.18.0.tar.gz"}, "scannotatr.models-0.99.10": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/scAnnotatR.models_0.99.10.tar.gz", "https://bioarchive.galaxyproject.org/scAnnotatR.models_0.99.10.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scannotatr.models/bioconductor-scannotatr.models_0.99.10_src_all.tar.gz"], "md5": "77c6e16382645164d6413356c5ab52c5", "fn": "scAnnotatR.models_0.99.10.tar.gz"}, "shdz.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/SHDZ.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/SHDZ.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-shdz.db/bioconductor-shdz.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-shdz.db/bioconductor-shdz.db_3.2.3_src_all.tar.gz"], "md5": "63c4439a272a5cd0c4746e9e53a7bdc7", "fn": "SHDZ.db_3.2.3.tar.gz"}, "sift.hsapiens.dbsnp132-1.0.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/SIFT.Hsapiens.dbSNP132_1.0.2.tar.gz", "https://bioarchive.galaxyproject.org/SIFT.Hsapiens.dbSNP132_1.0.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sift.hsapiens.dbsnp132/bioconductor-sift.hsapiens.dbsnp132_1.0.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sift.hsapiens.dbsnp132/bioconductor-sift.hsapiens.dbsnp132_1.0.2_src_all.tar.gz"], "md5": "c374f0bf4c99357cfe99e0b192c00d75", "fn": "SIFT.Hsapiens.dbSNP132_1.0.2.tar.gz"}, "sift.hsapiens.dbsnp137-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/SIFT.Hsapiens.dbSNP137_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/SIFT.Hsapiens.dbSNP137_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sift.hsapiens.dbsnp137/bioconductor-sift.hsapiens.dbsnp137_1.0.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sift.hsapiens.dbsnp137/bioconductor-sift.hsapiens.dbsnp137_1.0.0_src_all.tar.gz"], "md5": "3c3e73f826399af5ff368d1aab12cfd1", "fn": "SIFT.Hsapiens.dbSNP137_1.0.0.tar.gz"}, "snplocs.hsapiens.dbsnp144.grch37-0.99.20": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20.tar.gz", "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp144.grch37/bioconductor-snplocs.hsapiens.dbsnp144.grch37_0.99.20_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp144.grch37/bioconductor-snplocs.hsapiens.dbsnp144.grch37_0.99.20_src_all.tar.gz"], "md5": "bd338bb583cacc18f210e871dac79ebf", "fn": "SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20.tar.gz"}, "snplocs.hsapiens.dbsnp144.grch38-0.99.20": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20.tar.gz", "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp144.grch38/bioconductor-snplocs.hsapiens.dbsnp144.grch38_0.99.20_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp144.grch38/bioconductor-snplocs.hsapiens.dbsnp144.grch38_0.99.20_src_all.tar.gz"], "md5": "128c95e327adf72ae137fb5ae58270fc", "fn": "SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20.tar.gz"}, "snplocs.hsapiens.dbsnp149.grch38-0.99.20": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP149.GRCh38_0.99.20.tar.gz", "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP149.GRCh38_0.99.20.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp149.grch38/bioconductor-snplocs.hsapiens.dbsnp149.grch38_0.99.20_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp149.grch38/bioconductor-snplocs.hsapiens.dbsnp149.grch38_0.99.20_src_all.tar.gz"], "md5": "8cf749a8649a53449066b54160a3745c", "fn": "SNPlocs.Hsapiens.dbSNP149.GRCh38_0.99.20.tar.gz"}, "snplocs.hsapiens.dbsnp150.grch38-0.99.20": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP150.GRCh38_0.99.20.tar.gz", "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP150.GRCh38_0.99.20.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp150.grch38/bioconductor-snplocs.hsapiens.dbsnp150.grch38_0.99.20_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp150.grch38/bioconductor-snplocs.hsapiens.dbsnp150.grch38_0.99.20_src_all.tar.gz"], "md5": "575a7aaa9125d52ca0634b3ac586c9a7", "fn": "SNPlocs.Hsapiens.dbSNP150.GRCh38_0.99.20.tar.gz"}, "snplocs.hsapiens.dbsnp155.grch37-0.99.22": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.22.tar.gz", "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.22.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp155.grch37/bioconductor-snplocs.hsapiens.dbsnp155.grch37_0.99.22_src_all.tar.gz"], "md5": "044601b86a60d140dc0819525d372cc7", "fn": "SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.22.tar.gz"}, "snplocs.hsapiens.dbsnp155.grch38-0.99.22": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP155.GRCh38_0.99.22.tar.gz", "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP155.GRCh38_0.99.22.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp155.grch38/bioconductor-snplocs.hsapiens.dbsnp155.grch38_0.99.22_src_all.tar.gz"], "md5": "da89eef4346ad1c3a6de82c7670ba24e", "fn": "SNPlocs.Hsapiens.dbSNP155.GRCh38_0.99.22.tar.gz"}, "soybeancdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/soybeancdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/soybeancdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-soybeancdf/bioconductor-soybeancdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-soybeancdf/bioconductor-soybeancdf_2.18.0_src_all.tar.gz"], "md5": "a18e0ba5dbcf2291bdec91091dc528e6", "fn": "soybeancdf_2.18.0.tar.gz"}, "soybeanprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/soybeanprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/soybeanprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-soybeanprobe/bioconductor-soybeanprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-soybeanprobe/bioconductor-soybeanprobe_2.18.0_src_all.tar.gz"], "md5": "3057a5c387ff35b6c647c4db27041a13", "fn": "soybeanprobe_2.18.0.tar.gz"}, "sugarcanecdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/sugarcanecdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/sugarcanecdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sugarcanecdf/bioconductor-sugarcanecdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sugarcanecdf/bioconductor-sugarcanecdf_2.18.0_src_all.tar.gz"], "md5": "f66d51868068f83d3693d3cb05be418a", "fn": "sugarcanecdf_2.18.0.tar.gz"}, "sugarcaneprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/sugarcaneprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/sugarcaneprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sugarcaneprobe/bioconductor-sugarcaneprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sugarcaneprobe/bioconductor-sugarcaneprobe_2.18.0_src_all.tar.gz"], "md5": "66c101ac73e9235d258b9f996c42778e", "fn": "sugarcaneprobe_2.18.0.tar.gz"}, "synaptome.data-0.99.6": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/synaptome.data_0.99.6.tar.gz", "https://bioarchive.galaxyproject.org/synaptome.data_0.99.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-synaptome.data/bioconductor-synaptome.data_0.99.6_src_all.tar.gz"], "md5": "4388c63219782a9aa3e384fcdb51ed47", "fn": "synaptome.data_0.99.6.tar.gz"}, "synaptome.db-0.99.12": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/synaptome.db_0.99.12.tar.gz", "https://bioarchive.galaxyproject.org/synaptome.db_0.99.12.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-synaptome.db/bioconductor-synaptome.db_0.99.12_src_all.tar.gz"], "md5": "383e2a16688e13d40d1f8e2efd3168ef", "fn": "synaptome.db_0.99.12.tar.gz"}, "targetscan.hs.eg.db-0.6.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/targetscan.Hs.eg.db_0.6.1.tar.gz", "https://bioarchive.galaxyproject.org/targetscan.Hs.eg.db_0.6.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetscan.hs.eg.db/bioconductor-targetscan.hs.eg.db_0.6.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetscan.hs.eg.db/bioconductor-targetscan.hs.eg.db_0.6.1_src_all.tar.gz"], "md5": "d10569315400f6c1b95ad2688632b6de", "fn": "targetscan.Hs.eg.db_0.6.1.tar.gz"}, "targetscan.mm.eg.db-0.6.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/targetscan.Mm.eg.db_0.6.1.tar.gz", "https://bioarchive.galaxyproject.org/targetscan.Mm.eg.db_0.6.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetscan.mm.eg.db/bioconductor-targetscan.mm.eg.db_0.6.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetscan.mm.eg.db/bioconductor-targetscan.mm.eg.db_0.6.1_src_all.tar.gz"], "md5": "1830815c9d1383739f1ff152da0508c5", "fn": "targetscan.Mm.eg.db_0.6.1.tar.gz"}, "test1cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/test1cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/test1cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-test1cdf/bioconductor-test1cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-test1cdf/bioconductor-test1cdf_2.18.0_src_all.tar.gz"], "md5": "8c94708b49ccc7bbf127485155970b9b", "fn": "test1cdf_2.18.0.tar.gz"}, "test2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/test2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/test2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-test2cdf/bioconductor-test2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-test2cdf/bioconductor-test2cdf_2.18.0_src_all.tar.gz"], "md5": "0d1c20d6450dfc83d62214be9dc46b5f", "fn": "test2cdf_2.18.0.tar.gz"}, "test3cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/test3cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/test3cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-test3cdf/bioconductor-test3cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-test3cdf/bioconductor-test3cdf_2.18.0_src_all.tar.gz"], "md5": "9904e7fa6599f68400a9b77d0caa159a", "fn": "test3cdf_2.18.0.tar.gz"}, "test3probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/test3probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/test3probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-test3probe/bioconductor-test3probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-test3probe/bioconductor-test3probe_2.18.0_src_all.tar.gz"], "md5": "ffcbfee4e5c486fd03b2b9b64820340c", "fn": "test3probe_2.18.0.tar.gz"}, "tomatocdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/tomatocdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/tomatocdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tomatocdf/bioconductor-tomatocdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tomatocdf/bioconductor-tomatocdf_2.18.0_src_all.tar.gz"], "md5": "200efc0637788d4bd3263fc9183c1aa6", "fn": "tomatocdf_2.18.0.tar.gz"}, "tomatoprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/tomatoprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/tomatoprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tomatoprobe/bioconductor-tomatoprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tomatoprobe/bioconductor-tomatoprobe_2.18.0_src_all.tar.gz"], "md5": "72020469f35c19399fd0be9eaffd8e77", "fn": "tomatoprobe_2.18.0.tar.gz"}, "txdb.athaliana.biomart.plantsmart22-3.0.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Athaliana.BioMart.plantsmart22_3.0.1.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Athaliana.BioMart.plantsmart22_3.0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart22/bioconductor-txdb.athaliana.biomart.plantsmart22_3.0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart22/bioconductor-txdb.athaliana.biomart.plantsmart22_3.0.1_src_all.tar.gz"], "md5": "3bab54295e300fedba99eef521220e50", "fn": "TxDb.Athaliana.BioMart.plantsmart22_3.0.1.tar.gz"}, "txdb.athaliana.biomart.plantsmart25-3.1.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Athaliana.BioMart.plantsmart25_3.1.3.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Athaliana.BioMart.plantsmart25_3.1.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart25/bioconductor-txdb.athaliana.biomart.plantsmart25_3.1.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart25/bioconductor-txdb.athaliana.biomart.plantsmart25_3.1.3_src_all.tar.gz"], "md5": "eb007c07317b9717c76949e5ed999978", "fn": "TxDb.Athaliana.BioMart.plantsmart25_3.1.3.tar.gz"}, "txdb.athaliana.biomart.plantsmart28-3.2.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Athaliana.BioMart.plantsmart28_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Athaliana.BioMart.plantsmart28_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart28/bioconductor-txdb.athaliana.biomart.plantsmart28_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart28/bioconductor-txdb.athaliana.biomart.plantsmart28_3.2.2_src_all.tar.gz"], "md5": "9ed52284f01e08fc382db179b544bb17", "fn": "TxDb.Athaliana.BioMart.plantsmart28_3.2.2.tar.gz"}, "txdb.athaliana.biomart.plantsmart51-0.99.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Athaliana.BioMart.plantsmart51_0.99.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Athaliana.BioMart.plantsmart51_0.99.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart51/bioconductor-txdb.athaliana.biomart.plantsmart51_0.99.0_src_all.tar.gz"], "md5": "c623af555537bfd9958f8f9573308103", "fn": "TxDb.Athaliana.BioMart.plantsmart51_0.99.0.tar.gz"}, "txdb.btaurus.ucsc.bostau8.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Btaurus.UCSC.bosTau8.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Btaurus.UCSC.bosTau8.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/bioconductor-txdb.btaurus.ucsc.bostau8.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/bioconductor-txdb.btaurus.ucsc.bostau8.refgene_3.12.0_src_all.tar.gz"], "md5": "2112b91fbecabf9c89d1b0a48d88ce03", "fn": "TxDb.Btaurus.UCSC.bosTau8.refGene_3.12.0.tar.gz"}, "txdb.btaurus.ucsc.bostau9.refgene-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Btaurus.UCSC.bosTau9.refGene_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Btaurus.UCSC.bosTau9.refGene_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.btaurus.ucsc.bostau9.refgene/bioconductor-txdb.btaurus.ucsc.bostau9.refgene_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.btaurus.ucsc.bostau9.refgene/bioconductor-txdb.btaurus.ucsc.bostau9.refgene_3.10.0_src_all.tar.gz"], "md5": "fe443d123b0b788e1e450f4e60036788", "fn": "TxDb.Btaurus.UCSC.bosTau9.refGene_3.10.0.tar.gz"}, "txdb.celegans.ucsc.ce11.ensgene-3.15.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce11.ensGene_3.15.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Celegans.UCSC.ce11.ensGene_3.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce11.ensgene/bioconductor-txdb.celegans.ucsc.ce11.ensgene_3.15.0_src_all.tar.gz"], "md5": "1b4d61d06ac8acb27e57d1fafc5b79ce", "fn": "TxDb.Celegans.UCSC.ce11.ensGene_3.15.0.tar.gz"}, "txdb.celegans.ucsc.ce11.refgene-3.4.6": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce11.refGene_3.4.6.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Celegans.UCSC.ce11.refGene_3.4.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce11.refgene/bioconductor-txdb.celegans.ucsc.ce11.refgene_3.4.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce11.refgene/bioconductor-txdb.celegans.ucsc.ce11.refgene_3.4.6_src_all.tar.gz"], "md5": "3765169432e745aff5e85afd239066ca", "fn": "TxDb.Celegans.UCSC.ce11.refGene_3.4.6.tar.gz"}, "txdb.celegans.ucsc.ce6.ensgene-3.2.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce6.ensgene/bioconductor-txdb.celegans.ucsc.ce6.ensgene_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce6.ensgene/bioconductor-txdb.celegans.ucsc.ce6.ensgene_3.2.2_src_all.tar.gz"], "md5": "215c2edd440a3df8229fe6a75b431aa8", "fn": "TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz"}, "txdb.cfamiliaris.ucsc.canfam3.refgene-3.11.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Cfamiliaris.UCSC.canFam3.refGene_3.11.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Cfamiliaris.UCSC.canFam3.refGene_3.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene_3.11.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene_3.11.0_src_all.tar.gz"], "md5": "bf6af84c14a30ad5d01f3678246b1180", "fn": "TxDb.Cfamiliaris.UCSC.canFam3.refGene_3.11.0.tar.gz"}, "txdb.cfamiliaris.ucsc.canfam4.refgene-3.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Cfamiliaris.UCSC.canFam4.refGene_3.14.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Cfamiliaris.UCSC.canFam4.refGene_3.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene/bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene_3.14.0_src_all.tar.gz"], "md5": "0b47072fa79cf8e99f8563002a0998cb", "fn": "TxDb.Cfamiliaris.UCSC.canFam4.refGene_3.14.0.tar.gz"}, "txdb.cfamiliaris.ucsc.canfam5.refgene-3.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Cfamiliaris.UCSC.canFam5.refGene_3.14.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Cfamiliaris.UCSC.canFam5.refGene_3.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene/bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene_3.14.0_src_all.tar.gz"], "md5": "fc3d84569c092b74e5e0bccb785db8b6", "fn": "TxDb.Cfamiliaris.UCSC.canFam5.refGene_3.14.0.tar.gz"}, "txdb.dmelanogaster.ucsc.dm3.ensgene-3.2.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene_3.2.2_src_all.tar.gz"], "md5": "46b7ffe0c516edf8a2a3b5d78e0d8b67", "fn": "TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz"}, "txdb.dmelanogaster.ucsc.dm6.ensgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene_3.12.0_src_all.tar.gz"], "md5": "bec18a1fb2768347e907e3171d5332ca", "fn": "TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.12.0.tar.gz"}, "txdb.drerio.ucsc.danrer10.refgene-3.4.6": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Drerio.UCSC.danRer10.refGene_3.4.6.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Drerio.UCSC.danRer10.refGene_3.4.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.drerio.ucsc.danrer10.refgene/bioconductor-txdb.drerio.ucsc.danrer10.refgene_3.4.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.drerio.ucsc.danrer10.refgene/bioconductor-txdb.drerio.ucsc.danrer10.refgene_3.4.6_src_all.tar.gz"], "md5": "fef9bbec3809e1b69991516988f146fb", "fn": "TxDb.Drerio.UCSC.danRer10.refGene_3.4.6.tar.gz"}, "txdb.drerio.ucsc.danrer11.refgene-3.4.6": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Drerio.UCSC.danRer11.refGene_3.4.6.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Drerio.UCSC.danRer11.refGene_3.4.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.drerio.ucsc.danrer11.refgene/bioconductor-txdb.drerio.ucsc.danrer11.refgene_3.4.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.drerio.ucsc.danrer11.refgene/bioconductor-txdb.drerio.ucsc.danrer11.refgene_3.4.6_src_all.tar.gz"], "md5": "3d4ded4cec068a807b8b86b31389b677", "fn": "TxDb.Drerio.UCSC.danRer11.refGene_3.4.6.tar.gz"}, "txdb.ggallus.ucsc.galgal4.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Ggallus.UCSC.galGal4.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Ggallus.UCSC.galGal4.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/bioconductor-txdb.ggallus.ucsc.galgal4.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/bioconductor-txdb.ggallus.ucsc.galgal4.refgene_3.12.0_src_all.tar.gz"], "md5": "d50eb467227cd9077a7a690ae6934d11", "fn": "TxDb.Ggallus.UCSC.galGal4.refGene_3.12.0.tar.gz"}, "txdb.ggallus.ucsc.galgal5.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Ggallus.UCSC.galGal5.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Ggallus.UCSC.galGal5.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/bioconductor-txdb.ggallus.ucsc.galgal5.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/bioconductor-txdb.ggallus.ucsc.galgal5.refgene_3.12.0_src_all.tar.gz"], "md5": "0df53cd4f8e29705df75867a427de56e", "fn": "TxDb.Ggallus.UCSC.galGal5.refGene_3.12.0.tar.gz"}, "txdb.ggallus.ucsc.galgal6.refgene-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Ggallus.UCSC.galGal6.refGene_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Ggallus.UCSC.galGal6.refGene_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ggallus.ucsc.galgal6.refgene/bioconductor-txdb.ggallus.ucsc.galgal6.refgene_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ggallus.ucsc.galgal6.refgene/bioconductor-txdb.ggallus.ucsc.galgal6.refgene_3.10.0_src_all.tar.gz"], "md5": "4d81026ecb786abf1fe0cb548238214c", "fn": "TxDb.Ggallus.UCSC.galGal6.refGene_3.10.0.tar.gz"}, "txdb.hsapiens.biomart.igis-2.3.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Hsapiens.BioMart.igis_2.3.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.BioMart.igis_2.3.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.biomart.igis/bioconductor-txdb.hsapiens.biomart.igis_2.3.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.biomart.igis/bioconductor-txdb.hsapiens.biomart.igis_2.3.2_src_all.tar.gz"], "md5": "75b793928d29bcd3f069b5986bc2cfae", "fn": "TxDb.Hsapiens.BioMart.igis_2.3.2.tar.gz"}, "txdb.hsapiens.ucsc.hg18.knowngene-3.2.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene_3.2.2_src_all.tar.gz"], "md5": "e8b32a672e87345c72bb30be73d1e2d6", "fn": "TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz"}, "txdb.hsapiens.ucsc.hg19.knowngene-3.2.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_3.2.2_src_all.tar.gz"], "md5": "61be88a81433958571b57d0952be48a0", "fn": "TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz"}, "txdb.hsapiens.ucsc.hg19.lincrnastranscripts-3.2.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts_3.2.2_src_all.tar.gz"], "md5": "a0d61cd90639c40b3d0bb6bdb043cf12", "fn": "TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz"}, "txdb.hsapiens.ucsc.hg38.knowngene-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_3.16.0_src_all.tar.gz"], "md5": "d2a6f04b1d1ec78ae3ccbfed3fa1e9cc", "fn": "TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0.tar.gz"}, "txdb.hsapiens.ucsc.hg38.refgene-3.15.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.refGene_3.15.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg38.refGene_3.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/bioconductor-txdb.hsapiens.ucsc.hg38.refgene_3.15.0_src_all.tar.gz"], "md5": "50e7c4ce068c4ca2d77a3c0b46a3ab45", "fn": "TxDb.Hsapiens.UCSC.hg38.refGene_3.15.0.tar.gz"}, "txdb.mmulatta.ucsc.rhemac10.refgene-3.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Mmulatta.UCSC.rheMac10.refGene_3.14.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmulatta.UCSC.rheMac10.refGene_3.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene/bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene_3.14.0_src_all.tar.gz"], "md5": "81b01b07d87ae91b4d9a269a2baf616e", "fn": "TxDb.Mmulatta.UCSC.rheMac10.refGene_3.14.0.tar.gz"}, "txdb.mmulatta.ucsc.rhemac3.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Mmulatta.UCSC.rheMac3.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmulatta.UCSC.rheMac3.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene_3.12.0_src_all.tar.gz"], "md5": "db84a9e85d613635d74002f11df41e1f", "fn": "TxDb.Mmulatta.UCSC.rheMac3.refGene_3.12.0.tar.gz"}, "txdb.mmulatta.ucsc.rhemac8.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Mmulatta.UCSC.rheMac8.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmulatta.UCSC.rheMac8.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene_3.12.0_src_all.tar.gz"], "md5": "8437e0a05ffd28b667c7b740e0db68a7", "fn": "TxDb.Mmulatta.UCSC.rheMac8.refGene_3.12.0.tar.gz"}, "txdb.mmusculus.ucsc.mm10.ensgene-3.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene_3.4.0_src_all.tar.gz"], "md5": "88d65b714d1f86b456aee2b8524e9d84", "fn": "TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz"}, "txdb.mmusculus.ucsc.mm10.knowngene-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene_3.10.0_src_all.tar.gz"], "md5": "129b610bf05ec77451731196baa55bcc", "fn": "TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0.tar.gz"}, "txdb.mmusculus.ucsc.mm39.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm39.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm39.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/bioconductor-txdb.mmusculus.ucsc.mm39.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/bioconductor-txdb.mmusculus.ucsc.mm39.refgene_3.12.0_src_all.tar.gz"], "md5": "2525799b85e0a52bf274ab5eed51cd84", "fn": "TxDb.Mmusculus.UCSC.mm39.refGene_3.12.0.tar.gz"}, "txdb.mmusculus.ucsc.mm9.knowngene-3.2.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene_3.2.2_src_all.tar.gz"], "md5": "cb72af039b011033477363bda8ed9104", "fn": "TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz"}, "txdb.ptroglodytes.ucsc.pantro4.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Ptroglodytes.UCSC.panTro4.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Ptroglodytes.UCSC.panTro4.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene_3.12.0_src_all.tar.gz"], "md5": "9bdd3ba81561550f50250368d7d52eaa", "fn": "TxDb.Ptroglodytes.UCSC.panTro4.refGene_3.12.0.tar.gz"}, "txdb.ptroglodytes.ucsc.pantro5.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Ptroglodytes.UCSC.panTro5.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Ptroglodytes.UCSC.panTro5.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene_3.12.0_src_all.tar.gz"], "md5": "76ee1d253d1c8e54c12e8d5b9db93303", "fn": "TxDb.Ptroglodytes.UCSC.panTro5.refGene_3.12.0.tar.gz"}, "txdb.ptroglodytes.ucsc.pantro6.refgene-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Ptroglodytes.UCSC.panTro6.refGene_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Ptroglodytes.UCSC.panTro6.refGene_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene_3.10.0_src_all.tar.gz"], "md5": "48a88973fe0e5117cadd5c816a46e6e9", "fn": "TxDb.Ptroglodytes.UCSC.panTro6.refGene_3.10.0.tar.gz"}, "txdb.rnorvegicus.biomart.igis-2.3.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Rnorvegicus.BioMart.igis_2.3.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.BioMart.igis_2.3.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.biomart.igis/bioconductor-txdb.rnorvegicus.biomart.igis_2.3.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.biomart.igis/bioconductor-txdb.rnorvegicus.biomart.igis_2.3.2_src_all.tar.gz"], "md5": "eaf695f63cd021074d68c76d148cdfb7", "fn": "TxDb.Rnorvegicus.BioMart.igis_2.3.2.tar.gz"}, "txdb.rnorvegicus.ucsc.rn4.ensgene-3.2.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene_3.2.2_src_all.tar.gz"], "md5": "6bf2ebc522c2828c036e52b2028792c1", "fn": "TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz"}, "txdb.rnorvegicus.ucsc.rn5.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn5.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn5.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene_3.12.0_src_all.tar.gz"], "md5": "8a93a15b37bf73e5c529c976c4561537", "fn": "TxDb.Rnorvegicus.UCSC.rn5.refGene_3.12.0.tar.gz"}, "txdb.rnorvegicus.ucsc.rn6.ncbirefseq-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn6.ncbiRefSeq_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn6.ncbiRefSeq_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq_3.12.0_src_all.tar.gz"], "md5": "6660ee000fbc956541728c6dadf1fca7", "fn": "TxDb.Rnorvegicus.UCSC.rn6.ncbiRefSeq_3.12.0.tar.gz"}, "txdb.rnorvegicus.ucsc.rn6.refgene-3.4.6": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.6.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene_3.4.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene_3.4.6_src_all.tar.gz"], "md5": "ea525daa75bcf165eb24f6e93f4dbf6c", "fn": "TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.6.tar.gz"}, "txdb.rnorvegicus.ucsc.rn7.refgene-3.15.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn7.refGene_3.15.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn7.refGene_3.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene_3.15.0_src_all.tar.gz"], "md5": "589dc0f8f4c6ee8f5ed11aeb95a74a7d", "fn": "TxDb.Rnorvegicus.UCSC.rn7.refGene_3.15.0.tar.gz"}, "txdb.scerevisiae.ucsc.saccer2.sgdgene-3.2.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene_3.2.2_src_all.tar.gz"], "md5": "8ce83ef2ba6cfc69f9b4435a0a047819", "fn": "TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz"}, "txdb.scerevisiae.ucsc.saccer3.sgdgene-3.2.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene_3.2.2_src_all.tar.gz"], "md5": "afb23b3265730b9e59c2f07ab37cc3a0", "fn": "TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz"}, "txdb.sscrofa.ucsc.susscr11.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Sscrofa.UCSC.susScr11.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Sscrofa.UCSC.susScr11.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene_3.12.0_src_all.tar.gz"], "md5": "a6c5a2c402ad904a2f55099e391d18de", "fn": "TxDb.Sscrofa.UCSC.susScr11.refGene_3.12.0.tar.gz"}, "txdb.sscrofa.ucsc.susscr3.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Sscrofa.UCSC.susScr3.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Sscrofa.UCSC.susScr3.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene_3.12.0_src_all.tar.gz"], "md5": "981602dc706e545d5acdf7590e222ca7", "fn": "TxDb.Sscrofa.UCSC.susScr3.refGene_3.12.0.tar.gz"}, "u133aaofav2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/u133aaofav2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/u133aaofav2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-u133aaofav2cdf/bioconductor-u133aaofav2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-u133aaofav2cdf/bioconductor-u133aaofav2cdf_2.18.0_src_all.tar.gz"], "md5": "716483ddb6664b8b7f0c58cd21136e8b", "fn": "u133aaofav2cdf_2.18.0.tar.gz"}, "u133x3p.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/u133x3p.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/u133x3p.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-u133x3p.db/bioconductor-u133x3p.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-u133x3p.db/bioconductor-u133x3p.db_3.2.3_src_all.tar.gz"], "md5": "1a36a09dc64b94728bf6ac75600b40c6", "fn": "u133x3p.db_3.2.3.tar.gz"}, "u133x3pcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/u133x3pcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/u133x3pcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-u133x3pcdf/bioconductor-u133x3pcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-u133x3pcdf/bioconductor-u133x3pcdf_2.18.0_src_all.tar.gz"], "md5": "ee4e62041bc8c63813e8cf8400ece2f3", "fn": "u133x3pcdf_2.18.0.tar.gz"}, "u133x3pprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/u133x3pprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/u133x3pprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-u133x3pprobe/bioconductor-u133x3pprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-u133x3pprobe/bioconductor-u133x3pprobe_2.18.0_src_all.tar.gz"], "md5": "81e2b00985688160805147bef0c638be", "fn": "u133x3pprobe_2.18.0.tar.gz"}, "ucscrepeatmasker-3.15.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/UCSCRepeatMasker_3.15.2.tar.gz", "https://bioarchive.galaxyproject.org/UCSCRepeatMasker_3.15.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ucscrepeatmasker/bioconductor-ucscrepeatmasker_3.15.2_src_all.tar.gz"], "md5": "ad19a6fbd936e478af88fa21bc918a29", "fn": "UCSCRepeatMasker_3.15.2.tar.gz"}, "uniprotkeywords-0.99.4": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/UniProtKeywords_0.99.4.tar.gz", "https://bioarchive.galaxyproject.org/UniProtKeywords_0.99.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-uniprotkeywords/bioconductor-uniprotkeywords_0.99.4_src_all.tar.gz"], "md5": "f3f91ac1b8eca20fabcf46cae4348ea5", "fn": "UniProtKeywords_0.99.4.tar.gz"}, "vitisviniferacdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/vitisviniferacdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/vitisviniferacdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vitisviniferacdf/bioconductor-vitisviniferacdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vitisviniferacdf/bioconductor-vitisviniferacdf_2.18.0_src_all.tar.gz"], "md5": "8eb491f3ffa3ff0814f5c155787ae160", "fn": "vitisviniferacdf_2.18.0.tar.gz"}, "vitisviniferaprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/vitisviniferaprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/vitisviniferaprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vitisviniferaprobe/bioconductor-vitisviniferaprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vitisviniferaprobe/bioconductor-vitisviniferaprobe_2.18.0_src_all.tar.gz"], "md5": "386c0d5e37896d073ac20970e88b3160", "fn": "vitisviniferaprobe_2.18.0.tar.gz"}, "wheatcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/wheatcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/wheatcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wheatcdf/bioconductor-wheatcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wheatcdf/bioconductor-wheatcdf_2.18.0_src_all.tar.gz"], "md5": "0abeeeb9700b8d93a1a83769bdd8480f", "fn": "wheatcdf_2.18.0.tar.gz"}, "wheatprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/wheatprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/wheatprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wheatprobe/bioconductor-wheatprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wheatprobe/bioconductor-wheatprobe_2.18.0_src_all.tar.gz"], "md5": "b602d5050239850515be9dce12286360", "fn": "wheatprobe_2.18.0.tar.gz"}, "worm.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/worm.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/worm.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-worm.db0/bioconductor-worm.db0_3.16.0_src_all.tar.gz"], "md5": "8c69f4127645a5c2c9c345a4f92d26d8", "fn": "worm.db0_3.16.0.tar.gz"}, "xenopus.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/xenopus.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/xenopus.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xenopus.db0/bioconductor-xenopus.db0_3.16.0_src_all.tar.gz"], "md5": "007bfcf52abad16cb04f1e95cdbee49a", "fn": "xenopus.db0_3.16.0.tar.gz"}, "xenopuslaeviscdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/xenopuslaeviscdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/xenopuslaeviscdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xenopuslaeviscdf/bioconductor-xenopuslaeviscdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xenopuslaeviscdf/bioconductor-xenopuslaeviscdf_2.18.0_src_all.tar.gz"], "md5": "9d09ff76471ae60faf71090e0638f240", "fn": "xenopuslaeviscdf_2.18.0.tar.gz"}, "xenopuslaevisprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/xenopuslaevisprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/xenopuslaevisprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xenopuslaevisprobe/bioconductor-xenopuslaevisprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xenopuslaevisprobe/bioconductor-xenopuslaevisprobe_2.18.0_src_all.tar.gz"], "md5": "06a25268a5ab57bddf28bbb364ea977b", "fn": "xenopuslaevisprobe_2.18.0.tar.gz"}, "xlaevis.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/xlaevis.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/xlaevis.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xlaevis.db/bioconductor-xlaevis.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xlaevis.db/bioconductor-xlaevis.db_3.2.3_src_all.tar.gz"], "md5": "deaffe47b4ee48a7edb159d8104dc241", "fn": "xlaevis.db_3.2.3.tar.gz"}, "xlaevis2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/xlaevis2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/xlaevis2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xlaevis2cdf/bioconductor-xlaevis2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xlaevis2cdf/bioconductor-xlaevis2cdf_2.18.0_src_all.tar.gz"], "md5": "9e4a80d66397299b4e66a8d6715ca4aa", "fn": "xlaevis2cdf_2.18.0.tar.gz"}, "xlaevis2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/xlaevis2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/xlaevis2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xlaevis2probe/bioconductor-xlaevis2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xlaevis2probe/bioconductor-xlaevis2probe_2.18.0_src_all.tar.gz"], "md5": "d86f8a05e106eb3123435da233ff851d", "fn": "xlaevis2probe_2.18.0.tar.gz"}, "xtrasnplocs.hsapiens.dbsnp144.grch37-0.99.12": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/XtraSNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.12.tar.gz", "https://bioarchive.galaxyproject.org/XtraSNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.12.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37_0.99.12_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37_0.99.12_src_all.tar.gz"], "md5": "758d024c50d2349036dc27cc689b4e5a", "fn": "XtraSNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.12.tar.gz"}, "xtrasnplocs.hsapiens.dbsnp144.grch38-0.99.12": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/XtraSNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.12.tar.gz", "https://bioarchive.galaxyproject.org/XtraSNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.12.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38_0.99.12_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38_0.99.12_src_all.tar.gz"], "md5": "c617aa805c7ecf60ee9283eb3c51b1c7", "fn": "XtraSNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.12.tar.gz"}, "xtropicaliscdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/xtropicaliscdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/xtropicaliscdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xtropicaliscdf/bioconductor-xtropicaliscdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xtropicaliscdf/bioconductor-xtropicaliscdf_2.18.0_src_all.tar.gz"], "md5": "253e3cde76a393789e124f395820e947", "fn": "xtropicaliscdf_2.18.0.tar.gz"}, "xtropicalisprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/xtropicalisprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/xtropicalisprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xtropicalisprobe/bioconductor-xtropicalisprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xtropicalisprobe/bioconductor-xtropicalisprobe_2.18.0_src_all.tar.gz"], "md5": "43d15a7e12edaec1bb5f24b87498b599", "fn": "xtropicalisprobe_2.18.0.tar.gz"}, "ye6100subacdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ye6100subacdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ye6100subacdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ye6100subacdf/bioconductor-ye6100subacdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ye6100subacdf/bioconductor-ye6100subacdf_2.18.0_src_all.tar.gz"], "md5": "27bd71410956bfe8bffc8de14b85bdb0", "fn": "ye6100subacdf_2.18.0.tar.gz"}, "ye6100subbcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ye6100subbcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ye6100subbcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ye6100subbcdf/bioconductor-ye6100subbcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ye6100subbcdf/bioconductor-ye6100subbcdf_2.18.0_src_all.tar.gz"], "md5": "ee9ec4bd941940745bad538d79bfeab4", "fn": "ye6100subbcdf_2.18.0.tar.gz"}, "ye6100subccdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ye6100subccdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ye6100subccdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ye6100subccdf/bioconductor-ye6100subccdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ye6100subccdf/bioconductor-ye6100subccdf_2.18.0_src_all.tar.gz"], "md5": "fcdfed29a695fe53b62bacfe13dfe0c1", "fn": "ye6100subccdf_2.18.0.tar.gz"}, "ye6100subdcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ye6100subdcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ye6100subdcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ye6100subdcdf/bioconductor-ye6100subdcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ye6100subdcdf/bioconductor-ye6100subdcdf_2.18.0_src_all.tar.gz"], "md5": "521b501ddbcdc680c3d27b5b201029b1", "fn": "ye6100subdcdf_2.18.0.tar.gz"}, "yeast.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/yeast.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/yeast.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeast.db0/bioconductor-yeast.db0_3.16.0_src_all.tar.gz"], "md5": "e69fc47d1c29e4b43d7f1b673460965e", "fn": "yeast.db0_3.16.0.tar.gz"}, "yeast2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/yeast2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/yeast2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeast2.db/bioconductor-yeast2.db_3.13.0_src_all.tar.gz"], "md5": "add5784349cde4d01b75ea4472d25597", "fn": "yeast2.db_3.13.0.tar.gz"}, "yeast2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/yeast2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/yeast2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeast2cdf/bioconductor-yeast2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeast2cdf/bioconductor-yeast2cdf_2.18.0_src_all.tar.gz"], "md5": "0a718d78ae56bef9bad8168123038ac8", "fn": "yeast2cdf_2.18.0.tar.gz"}, "yeast2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/yeast2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/yeast2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeast2probe/bioconductor-yeast2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeast2probe/bioconductor-yeast2probe_2.18.0_src_all.tar.gz"], "md5": "3f52a2b7bd379624bc2966ca28c9ddf9", "fn": "yeast2probe_2.18.0.tar.gz"}, "ygs98.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ygs98.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/ygs98.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ygs98.db/bioconductor-ygs98.db_3.13.0_src_all.tar.gz"], "md5": "d21c0dc1ee0f7512ae921a501b425fd3", "fn": "ygs98.db_3.13.0.tar.gz"}, "ygs98cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ygs98cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ygs98cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ygs98cdf/bioconductor-ygs98cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ygs98cdf/bioconductor-ygs98cdf_2.18.0_src_all.tar.gz"], "md5": "ec7df7564cf28e093646325ec55baf1e", "fn": "ygs98cdf_2.18.0.tar.gz"}, "ygs98frmavecs-1.3.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ygs98frmavecs_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/ygs98frmavecs_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ygs98frmavecs/bioconductor-ygs98frmavecs_1.3.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ygs98frmavecs/bioconductor-ygs98frmavecs_1.3.0_src_all.tar.gz"], "md5": "e78c8447eb381b91dafb2f9688da39dc", "fn": "ygs98frmavecs_1.3.0.tar.gz"}, "ygs98probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ygs98probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ygs98probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ygs98probe/bioconductor-ygs98probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ygs98probe/bioconductor-ygs98probe_2.18.0_src_all.tar.gz"], "md5": "f40f21d7074818a4ee74a45b5533e89d", "fn": "ygs98probe_2.18.0.tar.gz"}, "zebrafish.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/zebrafish.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafish.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafish.db/bioconductor-zebrafish.db_3.13.0_src_all.tar.gz"], "md5": "64e40a61e81ac9397affb09880846559", "fn": "zebrafish.db_3.13.0.tar.gz"}, "zebrafish.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/zebrafish.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafish.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafish.db0/bioconductor-zebrafish.db0_3.16.0_src_all.tar.gz"], "md5": "dacc0a32ee7a43a5efdc3282b2184504", "fn": "zebrafish.db0_3.16.0.tar.gz"}, "zebrafishcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/zebrafishcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafishcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafishcdf/bioconductor-zebrafishcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafishcdf/bioconductor-zebrafishcdf_2.18.0_src_all.tar.gz"], "md5": "04edbb632600c97610b86423c2d850e7", "fn": "zebrafishcdf_2.18.0.tar.gz"}, "zebrafishprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/zebrafishprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafishprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafishprobe/bioconductor-zebrafishprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafishprobe/bioconductor-zebrafishprobe_2.18.0_src_all.tar.gz"], "md5": "eea2747859afa763addc7313ab0a2452", "fn": "zebrafishprobe_2.18.0.tar.gz"}, "adductdata-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/adductData_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/adductData_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-adductdata/bioconductor-adductdata_1.13.0_src_all.tar.gz"], "md5": "f7bdef108829e66360d9980a094c076c", "fn": "adductData_1.13.0.tar.gz"}, "affycompdata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/affycompData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/affycompData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affycompdata/bioconductor-affycompdata_1.35.0_src_all.tar.gz"], "md5": "7f7289cfb331be5e649447a654cc99e5", "fn": "affycompData_1.35.0.tar.gz"}, "affydata-1.45.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/affydata_1.45.0.tar.gz", "https://bioarchive.galaxyproject.org/affydata_1.45.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affydata/bioconductor-affydata_1.45.0_src_all.tar.gz"], "md5": "eb7248342c402f03431386e385238c12", "fn": "affydata_1.45.0.tar.gz"}, "affyhgu133a2expr-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Affyhgu133A2Expr_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133A2Expr_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133a2expr/bioconductor-affyhgu133a2expr_1.33.0_src_all.tar.gz"], "md5": "3dc83464e541bcb8b4aad2e3d9918bea", "fn": "Affyhgu133A2Expr_1.33.0.tar.gz"}, "affyhgu133aexpr-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Affyhgu133aExpr_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133aExpr_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133aexpr/bioconductor-affyhgu133aexpr_1.35.0_src_all.tar.gz"], "md5": "cca6b5b450c8cf773653dee57727dd06", "fn": "Affyhgu133aExpr_1.35.0.tar.gz"}, "affyhgu133plus2expr-1.31.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Affyhgu133Plus2Expr_1.31.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133Plus2Expr_1.31.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133plus2expr/bioconductor-affyhgu133plus2expr_1.31.0_src_all.tar.gz"], "md5": "19ae44401f171e5db4a7dc0d99b5244a", "fn": "Affyhgu133Plus2Expr_1.31.0.tar.gz"}, "affymetrixdatatestfiles-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/AffymetrixDataTestFiles_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/AffymetrixDataTestFiles_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affymetrixdatatestfiles/bioconductor-affymetrixdatatestfiles_0.35.0_src_all.tar.gz"], "md5": "7e66d2018e02bb58c5eea8b5042a9392", "fn": "AffymetrixDataTestFiles_0.35.0.tar.gz"}, "affymoe4302expr-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Affymoe4302Expr_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/Affymoe4302Expr_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affymoe4302expr/bioconductor-affymoe4302expr_1.35.0_src_all.tar.gz"], "md5": "0b5eb08bf23fe69858041d13a0701d7a", "fn": "Affymoe4302Expr_1.35.0.tar.gz"}, "airway-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/airway_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/airway_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-airway/bioconductor-airway_1.17.0_src_all.tar.gz"], "md5": "b511a987d192a74f13c66b388ac2c8aa", "fn": "airway_1.17.0.tar.gz"}, "all-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ALL_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/ALL_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-all/bioconductor-all_1.39.0_src_all.tar.gz"], "md5": "2e8639047180f647b08ec054a631c528", "fn": "ALL_1.39.0.tar.gz"}, "allmll-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ALLMLL_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/ALLMLL_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-allmll/bioconductor-allmll_1.37.0_src_all.tar.gz"], "md5": "3cb133d5b6a10a1748894906a515855c", "fn": "ALLMLL_1.37.0.tar.gz"}, "alpinedata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/alpineData_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/alpineData_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-alpinedata/bioconductor-alpinedata_1.23.0_src_all.tar.gz"], "md5": "ab1bdaa198a27eb35e2d1dc067962af6", "fn": "alpineData_1.23.0.tar.gz"}, "ampaffyexample-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/AmpAffyExample_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/AmpAffyExample_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ampaffyexample/bioconductor-ampaffyexample_1.37.0_src_all.tar.gz"], "md5": "f7d456a2f49271ab1b521f83fe46d3a3", "fn": "AmpAffyExample_1.37.0.tar.gz"}, "aneufinderdata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/AneuFinderData_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/AneuFinderData_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-aneufinderdata/bioconductor-aneufinderdata_1.25.0_src_all.tar.gz"], "md5": "70bfddfd056387ad8e061abbbbd43f15", "fn": "AneuFinderData_1.25.0.tar.gz"}, "antiprofilesdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/antiProfilesData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/antiProfilesData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-antiprofilesdata/bioconductor-antiprofilesdata_1.33.0_src_all.tar.gz"], "md5": "8eeef0998371557a0e02df8f0a01cdc9", "fn": "antiProfilesData_1.33.0.tar.gz"}, "aracne.networks-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/aracne.networks_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/aracne.networks_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-aracne.networks/bioconductor-aracne.networks_1.23.0_src_all.tar.gz"], "md5": "5834e9955b8bf65823b890b78a100230", "fn": "aracne.networks_1.23.0.tar.gz"}, "arrmdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ARRmData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/ARRmData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-arrmdata/bioconductor-arrmdata_1.33.0_src_all.tar.gz"], "md5": "34aed24b7ef52e068f5620e7232fa205", "fn": "ARRmData_1.33.0.tar.gz"}, "ashkenazimsonchr21-1.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/AshkenazimSonChr21_1.27.0.tar.gz", "https://bioarchive.galaxyproject.org/AshkenazimSonChr21_1.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ashkenazimsonchr21/bioconductor-ashkenazimsonchr21_1.27.0_src_all.tar.gz"], "md5": "2d2eefb52dcfeeb340bc080d6d56d5ab", "fn": "AshkenazimSonChr21_1.27.0.tar.gz"}, "asicsdata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ASICSdata_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/ASICSdata_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-asicsdata/bioconductor-asicsdata_1.17.0_src_all.tar.gz"], "md5": "917b33b8529f1afb89f3e8e5f5ec09d6", "fn": "ASICSdata_1.17.0.tar.gz"}, "assessorfdata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/AssessORFData_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/AssessORFData_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-assessorfdata/bioconductor-assessorfdata_1.15.0_src_all.tar.gz"], "md5": "0da3442ef5aa5e70f658ff76b399231f", "fn": "AssessORFData_1.15.0.tar.gz"}, "bcellviper-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bcellViper_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/bcellViper_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bcellviper/bioconductor-bcellviper_1.33.0_src_all.tar.gz"], "md5": "02ea741280b78f5d11594a91f6bd891b", "fn": "bcellViper_1.33.0.tar.gz"}, "beadarrayexampledata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/beadarrayExampleData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/beadarrayExampleData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadarrayexampledata/bioconductor-beadarrayexampledata_1.35.0_src_all.tar.gz"], "md5": "bf8c7a219051a3c11576a647c45a84a0", "fn": "beadarrayExampleData_1.35.0.tar.gz"}, "beadarrayusecases-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BeadArrayUseCases_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/BeadArrayUseCases_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadarrayusecases/bioconductor-beadarrayusecases_1.35.0_src_all.tar.gz"], "md5": "cb6810c1e95d356e4c7e901039d6727d", "fn": "BeadArrayUseCases_1.35.0.tar.gz"}, "beadsorted.saliva.epic-1.5.3": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BeadSorted.Saliva.EPIC_1.5.3.tar.gz", "https://bioarchive.galaxyproject.org/BeadSorted.Saliva.EPIC_1.5.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadsorted.saliva.epic/bioconductor-beadsorted.saliva.epic_1.5.3_src_all.tar.gz"], "md5": "55e6a2682d45d3d804ed9b9e63b3f630", "fn": "BeadSorted.Saliva.EPIC_1.5.3.tar.gz"}, "benchmarkfdrdata2019-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/benchmarkfdrData2019_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/benchmarkfdrData2019_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-benchmarkfdrdata2019/bioconductor-benchmarkfdrdata2019_1.11.0_src_all.tar.gz"], "md5": "853f4f310575f873f9ef10fb0aa1b3a9", "fn": "benchmarkfdrData2019_1.11.0.tar.gz"}, "beta7-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/beta7_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/beta7_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beta7/bioconductor-beta7_1.35.0_src_all.tar.gz"], "md5": "e1d98c49f9862f483efe8461c5584b2a", "fn": "beta7_1.35.0.tar.gz"}, "bioimagedbs-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BioImageDbs_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/BioImageDbs_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bioimagedbs/bioconductor-bioimagedbs_1.5.0_src_all.tar.gz"], "md5": "dcbbbe1c7406a487cae2c60a1ff5d67c", "fn": "BioImageDbs_1.5.0.tar.gz"}, "biotmledata-1.21.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/biotmleData_1.21.0.tar.gz", "https://bioarchive.galaxyproject.org/biotmleData_1.21.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biotmledata/bioconductor-biotmledata_1.21.0_src_all.tar.gz"], "md5": "e65f071b28d3dec143a8eac73def1960", "fn": "biotmleData_1.21.0.tar.gz"}, "biscuiteerdata-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/biscuiteerData_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/biscuiteerData_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biscuiteerdata/bioconductor-biscuiteerdata_1.11.0_src_all.tar.gz"], "md5": "acefcab6344943c841e6b7acb3302e0e", "fn": "biscuiteerData_1.11.0.tar.gz"}, "bladderbatch-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bladderbatch_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/bladderbatch_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bladderbatch/bioconductor-bladderbatch_1.35.0_src_all.tar.gz"], "md5": "4a22b6770f01e6ba2e5a9cd8acf5e03d", "fn": "bladderbatch_1.35.0.tar.gz"}, "blimatestingdata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/blimaTestingData_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/blimaTestingData_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-blimatestingdata/bioconductor-blimatestingdata_1.17.0_src_all.tar.gz"], "md5": "7dfee1136a8cd4ec2ceadca17f41b8e7", "fn": "blimaTestingData_1.17.0.tar.gz"}, "bloodcancermultiomics2017-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BloodCancerMultiOmics2017_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/BloodCancerMultiOmics2017_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bloodcancermultiomics2017/bioconductor-bloodcancermultiomics2017_1.17.0_src_all.tar.gz"], "md5": "aa2fa7d4fd7e0dd3a6d837b1e25f00fc", "fn": "BloodCancerMultiOmics2017_1.17.0.tar.gz"}, "bodymaprat-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bodymapRat_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/bodymapRat_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bodymaprat/bioconductor-bodymaprat_1.13.0_src_all.tar.gz"], "md5": "9af11e23233d6adf602a93c664464a20", "fn": "bodymapRat_1.13.0.tar.gz"}, "breakpointrdata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breakpointRdata_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/breakpointRdata_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breakpointrdata/bioconductor-breakpointrdata_1.15.0_src_all.tar.gz"], "md5": "46852ceea4c6bceab7e03988b9323456", "fn": "breakpointRdata_1.15.0.tar.gz"}, "breastcancermainz-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breastCancerMAINZ_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerMAINZ_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancermainz/bioconductor-breastcancermainz_1.35.0_src_all.tar.gz"], "md5": "035be150382cf0c3e4c0fbd36266b94d", "fn": "breastCancerMAINZ_1.35.0.tar.gz"}, "breastcancernki-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breastCancerNKI_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerNKI_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancernki/bioconductor-breastcancernki_1.35.0_src_all.tar.gz"], "md5": "865b32139e93955b3260c4e6c3f9c5b0", "fn": "breastCancerNKI_1.35.0.tar.gz"}, "breastcancertransbig-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breastCancerTRANSBIG_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerTRANSBIG_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancertransbig/bioconductor-breastcancertransbig_1.35.0_src_all.tar.gz"], "md5": "8b5ce45ac2e0fd9985311fcbbf40b0a0", "fn": "breastCancerTRANSBIG_1.35.0.tar.gz"}, "breastcancerunt-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breastCancerUNT_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerUNT_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancerunt/bioconductor-breastcancerunt_1.35.0_src_all.tar.gz"], "md5": "35a5e3b9d90fd0eca80b2e41861f72e0", "fn": "breastCancerUNT_1.35.0.tar.gz"}, "breastcancerupp-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breastCancerUPP_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerUPP_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancerupp/bioconductor-breastcancerupp_1.35.0_src_all.tar.gz"], "md5": "641b81d2297680424e171446ef3932f0", "fn": "breastCancerUPP_1.35.0.tar.gz"}, "breastcancervdx-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breastCancerVDX_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerVDX_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancervdx/bioconductor-breastcancervdx_1.35.0_src_all.tar.gz"], "md5": "c03948851a026690cc126b1dbccfc437", "fn": "breastCancerVDX_1.35.0.tar.gz"}, "brgedata-1.19.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/brgedata_1.19.0.tar.gz", "https://bioarchive.galaxyproject.org/brgedata_1.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-brgedata/bioconductor-brgedata_1.19.0_src_all.tar.gz"], "md5": "8f208a0c31fc3f213a2e98664fb76f6f", "fn": "brgedata_1.19.0.tar.gz"}, "bronchialil13-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bronchialIL13_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/bronchialIL13_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bronchialil13/bioconductor-bronchialil13_1.35.0_src_all.tar.gz"], "md5": "49c4c7883c35ad7f5ad2bb9fd653dbaf", "fn": "bronchialIL13_1.35.0.tar.gz"}, "bsseqdata-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bsseqData_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/bsseqData_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsseqdata/bioconductor-bsseqdata_0.35.0_src_all.tar.gz"], "md5": "d28b6df2057f7446596e324349c3b6e3", "fn": "bsseqData_0.35.0.tar.gz"}, "cancerdata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/cancerdata_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/cancerdata_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cancerdata/bioconductor-cancerdata_1.35.0_src_all.tar.gz"], "md5": "ae810e3851f437e7e8fed62c3847654a", "fn": "cancerdata_1.35.0.tar.gz"}, "cardinalworkflows-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CardinalWorkflows_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/CardinalWorkflows_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cardinalworkflows/bioconductor-cardinalworkflows_1.29.0_src_all.tar.gz"], "md5": "c45b20fee59776be3f8b3d72044fc0df", "fn": "CardinalWorkflows_1.29.0.tar.gz"}, "ccdata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ccdata_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/ccdata_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ccdata/bioconductor-ccdata_1.23.0_src_all.tar.gz"], "md5": "60a8e955f832f304a6efb064fc7b745d", "fn": "ccdata_1.23.0.tar.gz"}, "ccl4-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CCl4_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/CCl4_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ccl4/bioconductor-ccl4_1.35.0_src_all.tar.gz"], "md5": "e93aff764de9700c7ec35004adcf9e58", "fn": "CCl4_1.35.0.tar.gz"}, "cctutorial-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ccTutorial_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/ccTutorial_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cctutorial/bioconductor-cctutorial_1.35.0_src_all.tar.gz"], "md5": "bff2ed77e233015b1c9d68b554b15d54", "fn": "ccTutorial_1.35.0.tar.gz"}, "celarefdata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/celarefData_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/celarefData_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celarefdata/bioconductor-celarefdata_1.15.0_src_all.tar.gz"], "md5": "e8a6ed55b993243f44e59128164408f6", "fn": "celarefData_1.15.0.tar.gz"}, "celldex-1.7.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/celldex_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/celldex_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celldex/bioconductor-celldex_1.7.0_src_all.tar.gz"], "md5": "0aeb9f9a2706022e7e176f85b5b3cf2c", "fn": "celldex_1.7.0.tar.gz"}, "cellmapperdata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CellMapperData_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/CellMapperData_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cellmapperdata/bioconductor-cellmapperdata_1.23.0_src_all.tar.gz"], "md5": "f5d3a8da2952ad4370c076b7d4eeaf87", "fn": "CellMapperData_1.23.0.tar.gz"}, "champdata-2.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ChAMPdata_2.29.0.tar.gz", "https://bioarchive.galaxyproject.org/ChAMPdata_2.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-champdata/bioconductor-champdata_2.29.0_src_all.tar.gz"], "md5": "2f1532eaaf56be4fc29c5440c573b780", "fn": "ChAMPdata_2.29.0.tar.gz"}, "chic.data-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ChIC.data_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIC.data_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chic.data/bioconductor-chic.data_1.17.0_src_all.tar.gz"], "md5": "bb4837e672e71ea19f267efb7c73e628", "fn": "ChIC.data_1.17.0.tar.gz"}, "chimphumanbraindata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ChimpHumanBrainData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/ChimpHumanBrainData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chimphumanbraindata/bioconductor-chimphumanbraindata_1.35.0_src_all.tar.gz"], "md5": "563b8a3cc9493f495231abd05186dc84", "fn": "ChimpHumanBrainData_1.35.0.tar.gz"}, "chipenrich.data-2.21.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/chipenrich.data_2.21.0.tar.gz", "https://bioarchive.galaxyproject.org/chipenrich.data_2.21.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipenrich.data/bioconductor-chipenrich.data_2.21.0_src_all.tar.gz"], "md5": "abac22075b37333ed5f75812bdf14c8b", "fn": "chipenrich.data_2.21.0.tar.gz"}, "chipexoqualexample-1.21.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ChIPexoQualExample_1.21.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIPexoQualExample_1.21.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipexoqualexample/bioconductor-chipexoqualexample_1.21.0_src_all.tar.gz"], "md5": "3eb292504d16ae828529dc19773ff386", "fn": "ChIPexoQualExample_1.21.0.tar.gz"}, "chipseqdbdata-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/chipseqDBData_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/chipseqDBData_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipseqdbdata/bioconductor-chipseqdbdata_1.13.0_src_all.tar.gz"], "md5": "1f161da550dcf468c611c4e749609252", "fn": "chipseqDBData_1.13.0.tar.gz"}, "chipxpressdata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ChIPXpressData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIPXpressData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipxpressdata/bioconductor-chipxpressdata_1.35.0_src_all.tar.gz"], "md5": "d9ec5e7450965cdb1852c6665258baae", "fn": "ChIPXpressData_1.35.0.tar.gz"}, "chromstardata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/chromstaRData_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/chromstaRData_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chromstardata/bioconductor-chromstardata_1.23.0_src_all.tar.gz"], "md5": "316d8ebd62a38259a97249f3155169c3", "fn": "chromstaRData_1.23.0.tar.gz"}, "cll-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CLL_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/CLL_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cll/bioconductor-cll_1.37.0_src_all.tar.gz"], "md5": "78dc93ad95f5c8e0cdf74d770ee107c3", "fn": "CLL_1.37.0.tar.gz"}, "cllmethylation-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CLLmethylation_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/CLLmethylation_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cllmethylation/bioconductor-cllmethylation_1.17.0_src_all.tar.gz"], "md5": "6b53bdfc9b8fcd807c8b21d577724603", "fn": "CLLmethylation_1.17.0.tar.gz"}, "clumsiddata-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CluMSIDdata_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/CluMSIDdata_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clumsiddata/bioconductor-clumsiddata_1.13.0_src_all.tar.gz"], "md5": "91ea4550cba4a816ac33416dd927c204", "fn": "CluMSIDdata_1.13.0.tar.gz"}, "clustifyrdatahub-1.7.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/clustifyrdatahub_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/clustifyrdatahub_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clustifyrdatahub/bioconductor-clustifyrdatahub_1.7.0_src_all.tar.gz"], "md5": "e21443c515d13ffad9583051de6eb7f9", "fn": "clustifyrdatahub_1.7.0.tar.gz"}, "cmap2data-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/cMap2data_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/cMap2data_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cmap2data/bioconductor-cmap2data_1.33.0_src_all.tar.gz"], "md5": "cb332a4a2cc9e6ac33d707343e7d9a50", "fn": "cMap2data_1.33.0.tar.gz"}, "cnvgsadata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/cnvGSAdata_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/cnvGSAdata_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cnvgsadata/bioconductor-cnvgsadata_1.33.0_src_all.tar.gz"], "md5": "69791ec6259062ccb7d6878d693b2a93", "fn": "cnvGSAdata_1.33.0.tar.gz"}, "cohcapanno-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/COHCAPanno_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/COHCAPanno_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cohcapanno/bioconductor-cohcapanno_1.33.0_src_all.tar.gz"], "md5": "a752e8bf0a3a8a2055875473128af8e4", "fn": "COHCAPanno_1.33.0.tar.gz"}, "colonca-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/colonCA_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/colonCA_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-colonca/bioconductor-colonca_1.39.0_src_all.tar.gz"], "md5": "b2c547250495b0f07f7be6d6b2d8d9ee", "fn": "colonCA_1.39.0.tar.gz"}, "confessdata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CONFESSdata_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/CONFESSdata_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-confessdata/bioconductor-confessdata_1.25.0_src_all.tar.gz"], "md5": "1183ab67900e96c15b99094ccf9682a8", "fn": "CONFESSdata_1.25.0.tar.gz"}, "connectivitymap-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ConnectivityMap_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/ConnectivityMap_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-connectivitymap/bioconductor-connectivitymap_1.33.0_src_all.tar.gz"], "md5": "092ead10d2076e80304552f15a798a6b", "fn": "ConnectivityMap_1.33.0.tar.gz"}, "copdsexualdimorphism.data-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/COPDSexualDimorphism.data_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/COPDSexualDimorphism.data_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copdsexualdimorphism.data/bioconductor-copdsexualdimorphism.data_1.33.0_src_all.tar.gz"], "md5": "31f19076ead578c5935f91fb9c94ecd1", "fn": "COPDSexualDimorphism.data_1.33.0.tar.gz"}, "copyhelper-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CopyhelpeR_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/CopyhelpeR_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copyhelper/bioconductor-copyhelper_1.29.0_src_all.tar.gz"], "md5": "fbe6ed1ae63caf241aeb6b3a45d92df1", "fn": "CopyhelpeR_1.29.0.tar.gz"}, "copyneutralima-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CopyNeutralIMA_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/CopyNeutralIMA_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copyneutralima/bioconductor-copyneutralima_1.15.0_src_all.tar.gz"], "md5": "5fdee9e6051aebcb432b3a39190ce577", "fn": "CopyNeutralIMA_1.15.0.tar.gz"}, "cosmic.67-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/COSMIC.67_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/COSMIC.67_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cosmic.67/bioconductor-cosmic.67_1.34.0_src_all.tar.gz"], "md5": "d877dcb6f30a3cb7ce86a984d5106843", "fn": "COSMIC.67_1.34.0.tar.gz"}, "crcl18-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CRCL18_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/CRCL18_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-crcl18/bioconductor-crcl18_1.17.0_src_all.tar.gz"], "md5": "7cda2fdb7a0c0371b1ed9647c7933861", "fn": "CRCL18_1.17.0.tar.gz"}, "crisprscoredata-1.1.4": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/crisprScoreData_1.1.4.tar.gz", "https://bioarchive.galaxyproject.org/crisprScoreData_1.1.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-crisprscoredata/bioconductor-crisprscoredata_1.1.4_src_all.tar.gz"], "md5": "a019dcfbfe4d3e7ef0248c04abe79991", "fn": "crisprScoreData_1.1.4.tar.gz"}, "curatedadipoarray-1.9.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedAdipoArray_1.9.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoArray_1.9.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadipoarray/bioconductor-curatedadipoarray_1.9.0_src_all.tar.gz"], "md5": "a42d5e328d173c9871b1360de440b974", "fn": "curatedAdipoArray_1.9.0.tar.gz"}, "curatedadipochip-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedAdipoChIP_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoChIP_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadipochip/bioconductor-curatedadipochip_1.13.0_src_all.tar.gz"], "md5": "2e7308eafaded3ac0a0f97bc74d1a020", "fn": "curatedAdipoChIP_1.13.0.tar.gz"}, "curatedadiporna-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedAdipoRNA_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoRNA_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadiporna/bioconductor-curatedadiporna_1.13.0_src_all.tar.gz"], "md5": "ab1250a2fdf3815509eb7fe45fd21813", "fn": "curatedAdipoRNA_1.13.0.tar.gz"}, "curatedbladderdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedBladderData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedBladderData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedbladderdata/bioconductor-curatedbladderdata_1.33.0_src_all.tar.gz"], "md5": "8b69b718e8e8de452affe947cd418b25", "fn": "curatedBladderData_1.33.0.tar.gz"}, "curatedbreastdata-2.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedBreastData_2.25.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedBreastData_2.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedbreastdata/bioconductor-curatedbreastdata_2.25.0_src_all.tar.gz"], "md5": "ffe0dc08d4c30b7c01a518a6e0978413", "fn": "curatedBreastData_2.25.0.tar.gz"}, "curatedcrcdata-2.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedCRCData_2.29.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedCRCData_2.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedcrcdata/bioconductor-curatedcrcdata_2.29.0_src_all.tar.gz"], "md5": "d1756e19a6aa3dd9bef2da4068575d73", "fn": "curatedCRCData_2.29.0.tar.gz"}, "curatedmetagenomicdata-3.5.3": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedMetagenomicData_3.5.3.tar.gz", "https://bioarchive.galaxyproject.org/curatedMetagenomicData_3.5.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedmetagenomicdata/bioconductor-curatedmetagenomicdata_3.5.3_src_all.tar.gz"], "md5": "f0fdcbea91c0e96231af934adb7abeb6", "fn": "curatedMetagenomicData_3.5.3.tar.gz"}, "curatedovariandata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedOvarianData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedOvarianData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedovariandata/bioconductor-curatedovariandata_1.35.0_src_all.tar.gz"], "md5": "2d40967e621ba9cfa668208104104b38", "fn": "curatedOvarianData_1.35.0.tar.gz"}, "curatedtbdata-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedTBData_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedTBData_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedtbdata/bioconductor-curatedtbdata_1.3.0_src_all.tar.gz"], "md5": "56f1be51f41d3880559e69099d95d892", "fn": "curatedTBData_1.3.0.tar.gz"}, "curatedtcgadata-1.19.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedTCGAData_1.19.2.tar.gz", "https://bioarchive.galaxyproject.org/curatedTCGAData_1.19.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedtcgadata/bioconductor-curatedtcgadata_1.19.2_src_all.tar.gz"], "md5": "41531a34565c73f2e283d54c23d6a9e1", "fn": "curatedTCGAData_1.19.2.tar.gz"}, "dapardata-1.27.3": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DAPARdata_1.27.3.tar.gz", "https://bioarchive.galaxyproject.org/DAPARdata_1.27.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dapardata/bioconductor-dapardata_1.27.3_src_all.tar.gz"], "md5": "bf958cfd896d6594f2f373f79a3112dd", "fn": "DAPARdata_1.27.3.tar.gz"}, "davidtiling-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/davidTiling_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/davidTiling_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-davidtiling/bioconductor-davidtiling_1.37.0_src_all.tar.gz"], "md5": "5fa3cbda64eb9e316ac95a60c8accaff", "fn": "davidTiling_1.37.0.tar.gz"}, "depmap-1.11.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/depmap_1.11.2.tar.gz", "https://bioarchive.galaxyproject.org/depmap_1.11.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-depmap/bioconductor-depmap_1.11.2_src_all.tar.gz"], "md5": "9941cd0aa923d6490b9626f8f0910522", "fn": "depmap_1.11.2.tar.gz"}, "derfinderdata-2.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/derfinderData_2.15.0.tar.gz", "https://bioarchive.galaxyproject.org/derfinderData_2.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-derfinderdata/bioconductor-derfinderdata_2.15.0_src_all.tar.gz"], "md5": "48fd28bb742d7c2c6a2dfe21ddf70e6c", "fn": "derfinderData_2.15.0.tar.gz"}, "desousa2013-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DeSousa2013_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/DeSousa2013_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-desousa2013/bioconductor-desousa2013_1.33.0_src_all.tar.gz"], "md5": "2f4b23c47cca2fd9decc870bbe6fd7c4", "fn": "DeSousa2013_1.33.0.tar.gz"}, "dexmadata-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DExMAdata_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/DExMAdata_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dexmadata/bioconductor-dexmadata_1.5.0_src_all.tar.gz"], "md5": "b8087b44f7e890b4132565f89e6f0a01", "fn": "DExMAdata_1.5.0.tar.gz"}, "diffloopdata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/diffloopdata_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/diffloopdata_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-diffloopdata/bioconductor-diffloopdata_1.25.0_src_all.tar.gz"], "md5": "3030cfcc5aff94e110fddc60354353e1", "fn": "diffloopdata_1.25.0.tar.gz"}, "diggitdata-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/diggitdata_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/diggitdata_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-diggitdata/bioconductor-diggitdata_1.29.0_src_all.tar.gz"], "md5": "bf2502604a31578d57df2e1dded0d236", "fn": "diggitdata_1.29.0.tar.gz"}, "dlbcl-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DLBCL_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/DLBCL_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dlbcl/bioconductor-dlbcl_1.37.0_src_all.tar.gz"], "md5": "b0ce5033e4bb2337c229dc71a2a1a346", "fn": "DLBCL_1.37.0.tar.gz"}, "dmelsgi-1.29.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DmelSGI_1.29.1.tar.gz", "https://bioarchive.galaxyproject.org/DmelSGI_1.29.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dmelsgi/bioconductor-dmelsgi_1.29.1_src_all.tar.gz"], "md5": "2a426748e03fdb05c2fc71f105222ce5", "fn": "DmelSGI_1.29.1.tar.gz"}, "dmrcatedata-2.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DMRcatedata_2.15.0.tar.gz", "https://bioarchive.galaxyproject.org/DMRcatedata_2.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dmrcatedata/bioconductor-dmrcatedata_2.15.0_src_all.tar.gz"], "md5": "33cd820499c1fb6488cdef2b2ef7e95a", "fn": "DMRcatedata_2.15.0.tar.gz"}, "donapllp2013-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DonaPLLP2013_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/DonaPLLP2013_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-donapllp2013/bioconductor-donapllp2013_1.35.0_src_all.tar.gz"], "md5": "69237e3c870ff29f281332a32624562a", "fn": "DonaPLLP2013_1.35.0.tar.gz"}, "dorothea-1.9.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/dorothea_1.9.0.tar.gz", "https://bioarchive.galaxyproject.org/dorothea_1.9.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dorothea/bioconductor-dorothea_1.9.0_src_all.tar.gz"], "md5": "d84571e5e954215fd5a1a56186754b69", "fn": "dorothea_1.9.0.tar.gz"}, "dresscheck-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/dressCheck_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/dressCheck_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dresscheck/bioconductor-dresscheck_0.35.0_src_all.tar.gz"], "md5": "782d9a2c8501061a9e236af3f279687c", "fn": "dressCheck_0.35.0.tar.gz"}, "droplettestfiles-1.7.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DropletTestFiles_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/DropletTestFiles_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-droplettestfiles/bioconductor-droplettestfiles_1.7.0_src_all.tar.gz"], "md5": "05e9b3f6b0c67715b1056ca74a32a433", "fn": "DropletTestFiles_1.7.0.tar.gz"}, "drugvsdiseasedata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DrugVsDiseasedata_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/DrugVsDiseasedata_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drugvsdiseasedata/bioconductor-drugvsdiseasedata_1.33.0_src_all.tar.gz"], "md5": "5cf59b0f5d6ac32d90d17f7d68f2daf7", "fn": "DrugVsDiseasedata_1.33.0.tar.gz"}, "duoclustering2018-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DuoClustering2018_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/DuoClustering2018_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-duoclustering2018/bioconductor-duoclustering2018_1.15.0_src_all.tar.gz"], "md5": "24f191e908b3b02322dd89508c784dc0", "fn": "DuoClustering2018_1.15.0.tar.gz"}, "dvddata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DvDdata_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/DvDdata_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dvddata/bioconductor-dvddata_1.33.0_src_all.tar.gz"], "md5": "ba8583f5689b5205dfb6d1adf70ae173", "fn": "DvDdata_1.33.0.tar.gz"}, "dyebiasexamples-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/dyebiasexamples_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/dyebiasexamples_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dyebiasexamples/bioconductor-dyebiasexamples_1.37.0_src_all.tar.gz"], "md5": "9875c284f5e3b185f712ffac9b5f885d", "fn": "dyebiasexamples_1.37.0.tar.gz"}, "easierdata-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/easierData_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/easierData_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-easierdata/bioconductor-easierdata_1.3.0_src_all.tar.gz"], "md5": "5ad8e103c1923dfe666922ec1650eb01", "fn": "easierData_1.3.0.tar.gz"}, "eatonetalchipseq-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/EatonEtAlChIPseq_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/EatonEtAlChIPseq_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-eatonetalchipseq/bioconductor-eatonetalchipseq_0.35.0_src_all.tar.gz"], "md5": "074f8622a6a55925f806206afc9d9453", "fn": "EatonEtAlChIPseq_0.35.0.tar.gz"}, "ecolileucine-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ecoliLeucine_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliLeucine_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolileucine/bioconductor-ecolileucine_1.37.0_src_all.tar.gz"], "md5": "6439893bbc79683e340532f46a938794", "fn": "ecoliLeucine_1.37.0.tar.gz"}, "egseadata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/EGSEAdata_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/EGSEAdata_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-egseadata/bioconductor-egseadata_1.25.0_src_all.tar.gz"], "md5": "de4580a90bd10aec4474965ed38969fc", "fn": "EGSEAdata_1.25.0.tar.gz"}, "elmer.data-2.21.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ELMER.data_2.21.0.tar.gz", "https://bioarchive.galaxyproject.org/ELMER.data_2.21.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-elmer.data/bioconductor-elmer.data_2.21.0_src_all.tar.gz"], "md5": "7f2d82a3f1a676f1d61af0348e2d0433", "fn": "ELMER.data_2.21.0.tar.gz"}, "emtdata-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/emtdata_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/emtdata_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-emtdata/bioconductor-emtdata_1.5.0_src_all.tar.gz"], "md5": "55ff8734578ed3523625c2a0fc437218", "fn": "emtdata_1.5.0.tar.gz"}, "epimix.data-0.99.5": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/EpiMix.data_0.99.5.tar.gz", "https://bioarchive.galaxyproject.org/EpiMix.data_0.99.5.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epimix.data/bioconductor-epimix.data_0.99.5_src_all.tar.gz"], "md5": "ac81f60fc4712a692fcb75b0fbafdaa8", "fn": "EpiMix.data_0.99.5.tar.gz"}, "epimutacionsdata-1.1.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/epimutacionsData_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/epimutacionsData_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epimutacionsdata/bioconductor-epimutacionsdata_1.1.0_src_all.tar.gz"], "md5": "377137aa2cb358c0f4ecffad7797a6d5", "fn": "epimutacionsData_1.1.0.tar.gz"}, "estrogen-1.43.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/estrogen_1.43.0.tar.gz", "https://bioarchive.galaxyproject.org/estrogen_1.43.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-estrogen/bioconductor-estrogen_1.43.0_src_all.tar.gz"], "md5": "57639fc79be1962b0f5e61e5d73f467d", "fn": "estrogen_1.43.0.tar.gz"}, "etec16s-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/etec16s_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/etec16s_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-etec16s/bioconductor-etec16s_1.25.0_src_all.tar.gz"], "md5": "f264cbe341d5c492b493fbedf6169ab6", "fn": "etec16s_1.25.0.tar.gz"}, "ewcedata-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ewceData_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/ewceData_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ewcedata/bioconductor-ewcedata_1.5.0_src_all.tar.gz"], "md5": "26a398a1f17ac1f456a94336cf01c91b", "fn": "ewceData_1.5.0.tar.gz"}, "faahko-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/faahKO_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/faahKO_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-faahko/bioconductor-faahko_1.37.0_src_all.tar.gz"], "md5": "29689a0406096b7f2350296bb28cab0c", "fn": "faahKO_1.37.0.tar.gz"}, "fabiadata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/fabiaData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/fabiaData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fabiadata/bioconductor-fabiadata_1.35.0_src_all.tar.gz"], "md5": "a97042ed4bd7333d6d03765e7d18e41f", "fn": "fabiaData_1.35.0.tar.gz"}, "fantom3and4cage-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FANTOM3and4CAGE_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/FANTOM3and4CAGE_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fantom3and4cage/bioconductor-fantom3and4cage_1.33.0_src_all.tar.gz"], "md5": "ef58ff673fa9e87360c1b2597ed630cd", "fn": "FANTOM3and4CAGE_1.33.0.tar.gz"}, "ffpeexampledata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ffpeExampleData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/ffpeExampleData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ffpeexampledata/bioconductor-ffpeexampledata_1.35.0_src_all.tar.gz"], "md5": "1f5b07dd83b975d47c0ee8ae853f4461", "fn": "ffpeExampleData_1.35.0.tar.gz"}, "fibroeset-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/fibroEset_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/fibroEset_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fibroeset/bioconductor-fibroeset_1.39.0_src_all.tar.gz"], "md5": "397b83d144aceabad6100ce9a40788b2", "fn": "fibroEset_1.39.0.tar.gz"}, "fieldeffectcrc-1.7.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FieldEffectCrc_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/FieldEffectCrc_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fieldeffectcrc/bioconductor-fieldeffectcrc_1.7.0_src_all.tar.gz"], "md5": "4bcdd34f91c52fe0fdd458071943bf18", "fn": "FieldEffectCrc_1.7.0.tar.gz"}, "fis-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FIs_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/FIs_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fis/bioconductor-fis_1.25.0_src_all.tar.gz"], "md5": "cf38942e76299391b806e84abf7bcc5a", "fn": "FIs_1.25.0.tar.gz"}, "fission-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/fission_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/fission_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fission/bioconductor-fission_1.17.0_src_all.tar.gz"], "md5": "265844b4e10ca44a77abb0e6fa675069", "fn": "fission_1.17.0.tar.gz"}, "fletcher2013a-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Fletcher2013a_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/Fletcher2013a_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fletcher2013a/bioconductor-fletcher2013a_1.33.0_src_all.tar.gz"], "md5": "1526efee133c6717a040c336a2681c4b", "fn": "Fletcher2013a_1.33.0.tar.gz"}, "fletcher2013b-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Fletcher2013b_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/Fletcher2013b_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fletcher2013b/bioconductor-fletcher2013b_1.33.0_src_all.tar.gz"], "md5": "56f703ab885e7783c8108d941b4afaae", "fn": "Fletcher2013b_1.33.0.tar.gz"}, "flowploidydata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/flowPloidyData_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/flowPloidyData_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowploidydata/bioconductor-flowploidydata_1.23.0_src_all.tar.gz"], "md5": "df67ab50329625f3706d7be198ace3e6", "fn": "flowPloidyData_1.23.0.tar.gz"}, "flowsorted.blood.450k-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.Blood.450k_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.Blood.450k_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.450k/bioconductor-flowsorted.blood.450k_1.35.0_src_all.tar.gz"], "md5": "0240c9344fe261672e179baf8e27476f", "fn": "FlowSorted.Blood.450k_1.35.0.tar.gz"}, "flowsorted.blood.epic-2.1.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.Blood.EPIC_2.1.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.Blood.EPIC_2.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.epic/bioconductor-flowsorted.blood.epic_2.1.0_src_all.tar.gz"], "md5": "39c91a9469f0873f01a9d1feeab94a1c", "fn": "FlowSorted.Blood.EPIC_2.1.0.tar.gz"}, "flowsorted.cordblood.450k-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.CordBlood.450k_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBlood.450k_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordblood.450k/bioconductor-flowsorted.cordblood.450k_1.25.0_src_all.tar.gz"], "md5": "d54d8a9a5158312f9762c93622b2ff05", "fn": "FlowSorted.CordBlood.450k_1.25.0.tar.gz"}, "flowsorted.cordbloodcombined.450k-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.CordBloodCombined.450k_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodCombined.450k_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodcombined.450k/bioconductor-flowsorted.cordbloodcombined.450k_1.13.0_src_all.tar.gz"], "md5": "c5da0cb1e09b0bfe2c18dae0a1b94022", "fn": "FlowSorted.CordBloodCombined.450k_1.13.0.tar.gz"}, "flowsorted.cordbloodnorway.450k-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.CordBloodNorway.450k_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodNorway.450k_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodnorway.450k/bioconductor-flowsorted.cordbloodnorway.450k_1.23.0_src_all.tar.gz"], "md5": "bc8f53c7897b85ea67bd7f55bd74032b", "fn": "FlowSorted.CordBloodNorway.450k_1.23.0.tar.gz"}, "flowsorted.dlpfc.450k-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.DLPFC.450k_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.DLPFC.450k_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.dlpfc.450k/bioconductor-flowsorted.dlpfc.450k_1.33.0_src_all.tar.gz"], "md5": "997330230a4946701ab2ed93e7c610e2", "fn": "FlowSorted.DLPFC.450k_1.33.0.tar.gz"}, "flowworkspacedata-3.9.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/flowWorkspaceData_3.9.0.tar.gz", "https://bioarchive.galaxyproject.org/flowWorkspaceData_3.9.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowworkspacedata/bioconductor-flowworkspacedata_3.9.0_src_all.tar.gz"], "md5": "0a6dc8c644c8d94c0bb156f877166141", "fn": "flowWorkspaceData_3.9.0.tar.gz"}, "frmaexampledata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/frmaExampleData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/frmaExampleData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-frmaexampledata/bioconductor-frmaexampledata_1.33.0_src_all.tar.gz"], "md5": "d87115fc10cdd6d7e318558a3e662a54", "fn": "frmaExampleData_1.33.0.tar.gz"}, "furrowseg-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/furrowSeg_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/furrowSeg_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-furrowseg/bioconductor-furrowseg_1.25.0_src_all.tar.gz"], "md5": "02f736dd1a28f20c54871e5074300c56", "fn": "furrowSeg_1.25.0.tar.gz"}, "gagedata-2.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/gageData_2.35.0.tar.gz", "https://bioarchive.galaxyproject.org/gageData_2.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gagedata/bioconductor-gagedata_2.35.0_src_all.tar.gz"], "md5": "66ef788823140ec9e961eaf4f9c6d216", "fn": "gageData_2.35.0.tar.gz"}, "gaschyhs-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/gaschYHS_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/gaschYHS_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gaschyhs/bioconductor-gaschyhs_1.35.0_src_all.tar.gz"], "md5": "ed4baf5f544937c9b55079757897c348", "fn": "gaschYHS_1.35.0.tar.gz"}, "gatingmldata-2.37.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/gatingMLData_2.37.1.tar.gz", "https://bioarchive.galaxyproject.org/gatingMLData_2.37.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gatingmldata/bioconductor-gatingmldata_2.37.1_src_all.tar.gz"], "md5": "6a23be1ca00989254f81814ea01f4b05", "fn": "gatingMLData_2.37.1.tar.gz"}, "gcspikelite-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/gcspikelite_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/gcspikelite_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gcspikelite/bioconductor-gcspikelite_1.35.0_src_all.tar.gz"], "md5": "1e5fc959af925b306f17c9d7acbfd5dc", "fn": "gcspikelite_1.35.0.tar.gz"}, "genelendatabase-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/geneLenDataBase_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/geneLenDataBase_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genelendatabase/bioconductor-genelendatabase_1.33.0_src_all.tar.gz"], "md5": "a01f46c6edbddfe6a18bd8fafae289aa", "fn": "geneLenDataBase_1.33.0.tar.gz"}, "genomationdata-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/genomationData_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/genomationData_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomationdata/bioconductor-genomationdata_1.29.0_src_all.tar.gz"], "md5": "5bf1b38f89fa6a815dcb7f054fa4595f", "fn": "genomationData_1.29.0.tar.gz"}, "genomicdistributionsdata-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GenomicDistributionsData_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/GenomicDistributionsData_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomicdistributionsdata/bioconductor-genomicdistributionsdata_1.5.0_src_all.tar.gz"], "md5": "6db02c21a1b63c743ddbf2f97a85a8c7", "fn": "GenomicDistributionsData_1.5.0.tar.gz"}, "geuvadistranscriptexpr-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GeuvadisTranscriptExpr_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/GeuvadisTranscriptExpr_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-geuvadistranscriptexpr/bioconductor-geuvadistranscriptexpr_1.25.0_src_all.tar.gz"], "md5": "6c4d64730e8436e2d60fabbcc277a19d", "fn": "GeuvadisTranscriptExpr_1.25.0.tar.gz"}, "gigseadata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GIGSEAdata_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/GIGSEAdata_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gigseadata/bioconductor-gigseadata_1.15.0_src_all.tar.gz"], "md5": "59d0c5010ede867111544cb60aaeb743", "fn": "GIGSEAdata_1.15.0.tar.gz"}, "golubesets-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/golubEsets_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/golubEsets_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-golubesets/bioconductor-golubesets_1.39.0_src_all.tar.gz"], "md5": "5f35a5bfaa6c9f9ee982b0b389ae8dca", "fn": "golubEsets_1.39.0.tar.gz"}, "gpaexample-1.9.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/gpaExample_1.9.0.tar.gz", "https://bioarchive.galaxyproject.org/gpaExample_1.9.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gpaexample/bioconductor-gpaexample_1.9.0_src_all.tar.gz"], "md5": "7f4ca4d7db53abbd193a9d6049d07e0b", "fn": "gpaExample_1.9.0.tar.gz"}, "grndata-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/grndata_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/grndata_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-grndata/bioconductor-grndata_1.29.0_src_all.tar.gz"], "md5": "e595ed5d5a0b319e0f30d7dc7cb3a654", "fn": "grndata_1.29.0.tar.gz"}, "gsbenchmark-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSBenchMark_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/GSBenchMark_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gsbenchmark/bioconductor-gsbenchmark_1.17.0_src_all.tar.gz"], "md5": "572f6442afd5bdc38e170a151f3f1608", "fn": "GSBenchMark_1.17.0.tar.gz"}, "gse103322-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSE103322_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE103322_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse103322/bioconductor-gse103322_1.3.0_src_all.tar.gz"], "md5": "a3bc32c0e159b1eda56c91b8dea1d390", "fn": "GSE103322_1.3.0.tar.gz"}, "gse13015-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSE13015_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE13015_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse13015/bioconductor-gse13015_1.5.0_src_all.tar.gz"], "md5": "a8e0a7247f465a86e87d0b133f0222c4", "fn": "GSE13015_1.5.0.tar.gz"}, "gse159526-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSE159526_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE159526_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse159526/bioconductor-gse159526_1.3.0_src_all.tar.gz"], "md5": "7ff762d8bd42d33c402e5cae076d6847", "fn": "GSE159526_1.3.0.tar.gz"}, "gse62944-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSE62944_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE62944_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse62944/bioconductor-gse62944_1.25.0_src_all.tar.gz"], "md5": "fb108ec00235f1acd928d6817390e621", "fn": "GSE62944_1.25.0.tar.gz"}, "gsvadata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSVAdata_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/GSVAdata_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gsvadata/bioconductor-gsvadata_1.33.0_src_all.tar.gz"], "md5": "56ab3cd5d08d6142f443f2e331f6135f", "fn": "GSVAdata_1.33.0.tar.gz"}, "gwasdata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GWASdata_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/GWASdata_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gwasdata/bioconductor-gwasdata_1.35.0_src_all.tar.gz"], "md5": "32d75b2498c3102a05956b81cfa32fa3", "fn": "GWASdata_1.35.0.tar.gz"}, "h5vcdata-2.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/h5vcData_2.17.0.tar.gz", "https://bioarchive.galaxyproject.org/h5vcData_2.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-h5vcdata/bioconductor-h5vcdata_2.17.0_src_all.tar.gz"], "md5": "613259aca1b067623da84294502dd7d3", "fn": "h5vcData_2.17.0.tar.gz"}, "hapmap100khind-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hapmap100khind_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap100khind_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap100khind/bioconductor-hapmap100khind_1.39.0_src_all.tar.gz"], "md5": "c208c35ed429b2e446977923d3f33efe", "fn": "hapmap100khind_1.39.0.tar.gz"}, "hapmap100kxba-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hapmap100kxba_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap100kxba_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap100kxba/bioconductor-hapmap100kxba_1.39.0_src_all.tar.gz"], "md5": "87d6c086cabd5f6e4931cd727ae3fd7a", "fn": "hapmap100kxba_1.39.0.tar.gz"}, "hapmap500knsp-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hapmap500knsp_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap500knsp_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap500knsp/bioconductor-hapmap500knsp_1.39.0_src_all.tar.gz"], "md5": "620b713d03cca3b91c38dc5da559aa45", "fn": "hapmap500knsp_1.39.0.tar.gz"}, "hapmap500ksty-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hapmap500ksty_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap500ksty_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap500ksty/bioconductor-hapmap500ksty_1.39.0_src_all.tar.gz"], "md5": "8168db3048b75243646fe074744f4a20", "fn": "hapmap500ksty_1.39.0.tar.gz"}, "hapmapsnp5-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hapmapsnp5_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmapsnp5_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp5/bioconductor-hapmapsnp5_1.39.0_src_all.tar.gz"], "md5": "8efb06dd875ccc70de2dd1cb363ea769", "fn": "hapmapsnp5_1.39.0.tar.gz"}, "hapmapsnp6-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hapmapsnp6_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmapsnp6_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp6/bioconductor-hapmapsnp6_1.39.0_src_all.tar.gz"], "md5": "f6ac77c3a1386f2e6bbfb41d88879973", "fn": "hapmapsnp6_1.39.0.tar.gz"}, "harbchip-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/harbChIP_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/harbChIP_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harbchip/bioconductor-harbchip_1.35.0_src_all.tar.gz"], "md5": "43c3c6e6949560bc7c3b233616a66c5e", "fn": "harbChIP_1.35.0.tar.gz"}, "harmandata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HarmanData_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/HarmanData_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harmandata/bioconductor-harmandata_1.25.0_src_all.tar.gz"], "md5": "a305dd9f4be567bde7c6e5f31bad3b49", "fn": "HarmanData_1.25.0.tar.gz"}, "harmonizedtcgadata-1.19.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HarmonizedTCGAData_1.19.0.tar.gz", "https://bioarchive.galaxyproject.org/HarmonizedTCGAData_1.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harmonizedtcgadata/bioconductor-harmonizedtcgadata_1.19.0_src_all.tar.gz"], "md5": "46546ba436bfa9457789fb3b1362597e", "fn": "HarmonizedTCGAData_1.19.0.tar.gz"}, "hcadata-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HCAData_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/HCAData_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcadata/bioconductor-hcadata_1.13.0_src_all.tar.gz"], "md5": "11d0f4f244f9e91ca08e8ca2f0deeae8", "fn": "HCAData_1.13.0.tar.gz"}, "hd2013sgi-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HD2013SGI_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/HD2013SGI_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hd2013sgi/bioconductor-hd2013sgi_1.37.0_src_all.tar.gz"], "md5": "f6ec4532136afecc8a49df728ae2148b", "fn": "HD2013SGI_1.37.0.tar.gz"}, "hdcytodata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HDCytoData_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/HDCytoData_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hdcytodata/bioconductor-hdcytodata_1.17.0_src_all.tar.gz"], "md5": "0264c9e4a88d12dc0588893ea2a990e6", "fn": "HDCytoData_1.17.0.tar.gz"}, "healthycontrolspresencechecker-1.1.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/healthyControlsPresenceChecker_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/healthyControlsPresenceChecker_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-healthycontrolspresencechecker/bioconductor-healthycontrolspresencechecker_1.1.0_src_all.tar.gz"], "md5": "bae0bae9c15427f8715df87076cc13fe", "fn": "healthyControlsPresenceChecker_1.1.0.tar.gz"}, "healthyflowdata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/healthyFlowData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/healthyFlowData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-healthyflowdata/bioconductor-healthyflowdata_1.35.0_src_all.tar.gz"], "md5": "84fdfd72c6a1f7588aef67364aef6ad3", "fn": "healthyFlowData_1.35.0.tar.gz"}, "heebodata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HEEBOdata_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/HEEBOdata_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-heebodata/bioconductor-heebodata_1.35.0_src_all.tar.gz"], "md5": "aedee799a5570c99f1ad23b467b041f1", "fn": "HEEBOdata_1.35.0.tar.gz"}, "hellorangesdata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HelloRangesData_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/HelloRangesData_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hellorangesdata/bioconductor-hellorangesdata_1.23.0_src_all.tar.gz"], "md5": "09e396c37aac16ed7ca93671cf2aebda", "fn": "HelloRangesData_1.23.0.tar.gz"}, "hgu133abarcodevecs-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hgu133abarcodevecs_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133abarcodevecs_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133abarcodevecs/bioconductor-hgu133abarcodevecs_1.35.0_src_all.tar.gz"], "md5": "65245450c48f91270cb69d1193c436c8", "fn": "hgu133abarcodevecs_1.35.0.tar.gz"}, "hgu133plus2barcodevecs-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hgu133plus2barcodevecs_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2barcodevecs_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2barcodevecs/bioconductor-hgu133plus2barcodevecs_1.35.0_src_all.tar.gz"], "md5": "28251d040bce6ef6b25aef07695574b1", "fn": "hgu133plus2barcodevecs_1.35.0.tar.gz"}, "hgu133plus2cellscore-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hgu133plus2CellScore_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2CellScore_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2cellscore/bioconductor-hgu133plus2cellscore_1.17.0_src_all.tar.gz"], "md5": "69f8d0c2c62ff1ee7ab09bd58c291f9c", "fn": "hgu133plus2CellScore_1.17.0.tar.gz"}, "hgu2beta7-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hgu2beta7_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu2beta7_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu2beta7/bioconductor-hgu2beta7_1.37.0_src_all.tar.gz"], "md5": "4229481dd34e813801659783600d66c0", "fn": "hgu2beta7_1.37.0.tar.gz"}, "hicdatahumanimr90-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HiCDataHumanIMR90_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/HiCDataHumanIMR90_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicdatahumanimr90/bioconductor-hicdatahumanimr90_1.17.0_src_all.tar.gz"], "md5": "b515d4670a93ce8ed2a0745e2da4513c", "fn": "HiCDataHumanIMR90_1.17.0.tar.gz"}, "hicdatalymphoblast-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HiCDataLymphoblast_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/HiCDataLymphoblast_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicdatalymphoblast/bioconductor-hicdatalymphoblast_1.33.0_src_all.tar.gz"], "md5": "0ca1dfbb9649eb697721fa8c9d4c4724", "fn": "HiCDataLymphoblast_1.33.0.tar.gz"}, "hicontactsdata-0.99.5": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HiContactsData_0.99.5.tar.gz", "https://bioarchive.galaxyproject.org/HiContactsData_0.99.5.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicontactsdata/bioconductor-hicontactsdata_0.99.5_src_all.tar.gz"], "md5": "fe7e5eaa27ef177427359184b31412b1", "fn": "HiContactsData_0.99.5.tar.gz"}, "highlyreplicatedrnaseq-1.9.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HighlyReplicatedRNASeq_1.9.0.tar.gz", "https://bioarchive.galaxyproject.org/HighlyReplicatedRNASeq_1.9.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-highlyreplicatedrnaseq/bioconductor-highlyreplicatedrnaseq_1.9.0_src_all.tar.gz"], "md5": "dfc27dcca211c331141b6f8d23cb5091", "fn": "HighlyReplicatedRNASeq_1.9.0.tar.gz"}, "hiiragi2013-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Hiiragi2013_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/Hiiragi2013_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hiiragi2013/bioconductor-hiiragi2013_1.33.0_src_all.tar.gz"], "md5": "b497df372201fb3871ad465960d15a92", "fn": "Hiiragi2013_1.33.0.tar.gz"}, "hivcdnavantwout03-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HIVcDNAvantWout03_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/HIVcDNAvantWout03_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hivcdnavantwout03/bioconductor-hivcdnavantwout03_1.37.0_src_all.tar.gz"], "md5": "12dcd1fc184daba1f8cc2f53aa5c7a94", "fn": "HIVcDNAvantWout03_1.37.0.tar.gz"}, "hmp16sdata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HMP16SData_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/HMP16SData_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hmp16sdata/bioconductor-hmp16sdata_1.17.0_src_all.tar.gz"], "md5": "02c02686d9bce0f69b97fb5f9a48a93c", "fn": "HMP16SData_1.17.0.tar.gz"}, "hmp2data-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HMP2Data_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/HMP2Data_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hmp2data/bioconductor-hmp2data_1.11.0_src_all.tar.gz"], "md5": "90fc108b530a866dab5e6def696b42d7", "fn": "HMP2Data_1.11.0.tar.gz"}, "hsmmsinglecell-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HSMMSingleCell_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/HSMMSingleCell_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hsmmsinglecell/bioconductor-hsmmsinglecell_1.17.0_src_all.tar.gz"], "md5": "111ae2345843dcfa88b21cc778a974c2", "fn": "HSMMSingleCell_1.17.0.tar.gz"}, "humanaffydata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HumanAffyData_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/HumanAffyData_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanaffydata/bioconductor-humanaffydata_1.23.0_src_all.tar.gz"], "md5": "217f2d6a33a6699ec5e971e6aa3518d5", "fn": "HumanAffyData_1.23.0.tar.gz"}, "humanstemcell-0.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/humanStemCell_0.37.0.tar.gz", "https://bioarchive.galaxyproject.org/humanStemCell_0.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanstemcell/bioconductor-humanstemcell_0.37.0_src_all.tar.gz"], "md5": "cd8d9c4ee5d7a58ea924b537b52331d5", "fn": "humanStemCell_0.37.0.tar.gz"}, "ihwpaper-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/IHWpaper_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/IHWpaper_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ihwpaper/bioconductor-ihwpaper_1.25.0_src_all.tar.gz"], "md5": "0fee0e7f9783b96109f7df5d70ce0825", "fn": "IHWpaper_1.25.0.tar.gz"}, "illumina450probevariants.db-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Illumina450ProbeVariants.db_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/Illumina450ProbeVariants.db_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illumina450probevariants.db/bioconductor-illumina450probevariants.db_1.33.0_src_all.tar.gz"], "md5": "0c7c67fb75b0ff43ed2d92e71a67264a", "fn": "Illumina450ProbeVariants.db_1.33.0.tar.gz"}, "illuminadatatestfiles-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/IlluminaDataTestFiles_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaDataTestFiles_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminadatatestfiles/bioconductor-illuminadatatestfiles_1.35.0_src_all.tar.gz"], "md5": "1c68249fe7576377a7ee11b301944c6e", "fn": "IlluminaDataTestFiles_1.35.0.tar.gz"}, "imcdatasets-1.5.4": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/imcdatasets_1.5.4.tar.gz", "https://bioarchive.galaxyproject.org/imcdatasets_1.5.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-imcdatasets/bioconductor-imcdatasets_1.5.4_src_all.tar.gz"], "md5": "8c5ab7a76c8be62231631162ef079ff4", "fn": "imcdatasets_1.5.4.tar.gz"}, "italicsdata-2.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ITALICSData_2.35.0.tar.gz", "https://bioarchive.galaxyproject.org/ITALICSData_2.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-italicsdata/bioconductor-italicsdata_2.35.0_src_all.tar.gz"], "md5": "d7d5506602842647b6355fabc12f7cd2", "fn": "ITALICSData_2.35.0.tar.gz"}, "iyer517-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Iyer517_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/Iyer517_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-iyer517/bioconductor-iyer517_1.39.0_src_all.tar.gz"], "md5": "07eecc5887ad248b990d18ecfbcbc4ae", "fn": "Iyer517_1.39.0.tar.gz"}, "jaspar2014-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/JASPAR2014_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2014_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2014/bioconductor-jaspar2014_1.33.0_src_all.tar.gz"], "md5": "9a7d6e0c267507e8308407cc3ebf4c42", "fn": "JASPAR2014_1.33.0.tar.gz"}, "jaspar2016-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/JASPAR2016_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2016_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2016/bioconductor-jaspar2016_1.25.0_src_all.tar.gz"], "md5": "f8e2bbf13cc8e3c84df1697d0b876580", "fn": "JASPAR2016_1.25.0.tar.gz"}, "keggandmetacoredzpathwaysgeo-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/KEGGandMetacoreDzPathwaysGEO_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/KEGGandMetacoreDzPathwaysGEO_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-keggandmetacoredzpathwaysgeo/bioconductor-keggandmetacoredzpathwaysgeo_1.17.0_src_all.tar.gz"], "md5": "c86429242308d77103832d055a72f648", "fn": "KEGGandMetacoreDzPathwaysGEO_1.17.0.tar.gz"}, "keggdzpathwaysgeo-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/KEGGdzPathwaysGEO_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/KEGGdzPathwaysGEO_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-keggdzpathwaysgeo/bioconductor-keggdzpathwaysgeo_1.35.0_src_all.tar.gz"], "md5": "f96019ab54d05fb8a39b6cae2305c714", "fn": "KEGGdzPathwaysGEO_1.35.0.tar.gz"}, "kidpack-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/kidpack_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/kidpack_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-kidpack/bioconductor-kidpack_1.39.0_src_all.tar.gz"], "md5": "d9143bf024de2fd61d9e70cd674c3dd9", "fn": "kidpack_1.39.0.tar.gz"}, "kodata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/KOdata_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/KOdata_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-kodata/bioconductor-kodata_1.23.0_src_all.tar.gz"], "md5": "799f98740b05254649fb8de864c9b9ea", "fn": "KOdata_1.23.0.tar.gz"}, "leebamviews-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/leeBamViews_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/leeBamViews_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-leebamviews/bioconductor-leebamviews_1.33.0_src_all.tar.gz"], "md5": "e20c1281821b5e34d639312437ca4dde", "fn": "leeBamViews_1.33.0.tar.gz"}, "leukemiaseset-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/leukemiasEset_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/leukemiasEset_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-leukemiaseset/bioconductor-leukemiaseset_1.33.0_src_all.tar.gz"], "md5": "09a0c9da3055a5d726cd5ae7de21888e", "fn": "leukemiasEset_1.33.0.tar.gz"}, "liebermanaidenhic2009-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/LiebermanAidenHiC2009_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/LiebermanAidenHiC2009_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-liebermanaidenhic2009/bioconductor-liebermanaidenhic2009_0.35.0_src_all.tar.gz"], "md5": "9db04114ddcc8937ac832837a7a82315", "fn": "LiebermanAidenHiC2009_0.35.0.tar.gz"}, "listeretalbsseq-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ListerEtAlBSseq_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/ListerEtAlBSseq_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-listeretalbsseq/bioconductor-listeretalbsseq_1.29.0_src_all.tar.gz"], "md5": "86bee8785a38e3ce483dd2749124bcc0", "fn": "ListerEtAlBSseq_1.29.0.tar.gz"}, "lrcelltypemarkers-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/LRcellTypeMarkers_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/LRcellTypeMarkers_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lrcelltypemarkers/bioconductor-lrcelltypemarkers_1.5.0_src_all.tar.gz"], "md5": "cde21ce4c254a41c9e17b4ef51a01521", "fn": "LRcellTypeMarkers_1.5.0.tar.gz"}, "lumibarnes-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/lumiBarnes_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/lumiBarnes_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumibarnes/bioconductor-lumibarnes_1.37.0_src_all.tar.gz"], "md5": "2700119944fcbd6595a1da40d11d4460", "fn": "lumiBarnes_1.37.0.tar.gz"}, "lungcanceracvssccgeo-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/LungCancerACvsSCCGEO_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/LungCancerACvsSCCGEO_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungcanceracvssccgeo/bioconductor-lungcanceracvssccgeo_1.33.0_src_all.tar.gz"], "md5": "450494d6d3dbeb03fa24331a13f7e87e", "fn": "LungCancerACvsSCCGEO_1.33.0.tar.gz"}, "lungcancerlines-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/LungCancerLines_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/LungCancerLines_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungcancerlines/bioconductor-lungcancerlines_0.35.0_src_all.tar.gz"], "md5": "71f67ae38f6f1df089256aa6fa5d8249", "fn": "LungCancerLines_0.35.0.tar.gz"}, "lungexpression-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/lungExpression_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/lungExpression_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungexpression/bioconductor-lungexpression_0.35.0_src_all.tar.gz"], "md5": "49cd2379de1eaa83e01fd979be94ee79", "fn": "lungExpression_0.35.0.tar.gz"}, "lydata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/lydata_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/lydata_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lydata/bioconductor-lydata_1.23.0_src_all.tar.gz"], "md5": "052166b4f3851b44ffc881c74b9c5821", "fn": "lydata_1.23.0.tar.gz"}, "m3dexampledata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/M3DExampleData_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/M3DExampleData_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-m3dexampledata/bioconductor-m3dexampledata_1.23.0_src_all.tar.gz"], "md5": "f7b2229f75874e9c97625e4642107c3f", "fn": "M3DExampleData_1.23.0.tar.gz"}, "macrophage-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/macrophage_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/macrophage_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-macrophage/bioconductor-macrophage_1.13.0_src_all.tar.gz"], "md5": "f75d462f270ebd4f9d7d65f35723ffe4", "fn": "macrophage_1.13.0.tar.gz"}, "macsdata-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MACSdata_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/MACSdata_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-macsdata/bioconductor-macsdata_1.5.0_src_all.tar.gz"], "md5": "12a2b57e87a7e7bf1af063951fbc23bd", "fn": "MACSdata_1.5.0.tar.gz"}, "mammaprintdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mammaPrintData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/mammaPrintData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mammaprintdata/bioconductor-mammaprintdata_1.33.0_src_all.tar.gz"], "md5": "59b4367e79119553450b73c13b8e2ab4", "fn": "mammaPrintData_1.33.0.tar.gz"}, "mapkldata-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mAPKLData_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/mAPKLData_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mapkldata/bioconductor-mapkldata_1.29.0_src_all.tar.gz"], "md5": "8062e0241ac2f340ffa73ccbd2c89cb5", "fn": "mAPKLData_1.29.0.tar.gz"}, "maqcexpression4plex-1.41.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/maqcExpression4plex_1.41.0.tar.gz", "https://bioarchive.galaxyproject.org/maqcExpression4plex_1.41.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcexpression4plex/bioconductor-maqcexpression4plex_1.41.0_src_all.tar.gz"], "md5": "54bab503992e2907b47e8a3dfe2d80f0", "fn": "maqcExpression4plex_1.41.0.tar.gz"}, "maqcsubset-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MAQCsubset_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/MAQCsubset_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcsubset/bioconductor-maqcsubset_1.35.0_src_all.tar.gz"], "md5": "182a8cb6b638164e3f83848c96d5b4d4", "fn": "MAQCsubset_1.35.0.tar.gz"}, "maqcsubsetilm-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MAQCsubsetILM_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/MAQCsubsetILM_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcsubsetilm/bioconductor-maqcsubsetilm_1.35.0_src_all.tar.gz"], "md5": "41a6ad9c3dfb6007756cc5a52077e226", "fn": "MAQCsubsetILM_1.35.0.tar.gz"}, "mcseadata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mCSEAdata_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/mCSEAdata_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcseadata/bioconductor-mcseadata_1.17.0_src_all.tar.gz"], "md5": "f41dfacd838689e29a41e7346899f671", "fn": "mCSEAdata_1.17.0.tar.gz"}, "mcsurvdata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mcsurvdata_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/mcsurvdata_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcsurvdata/bioconductor-mcsurvdata_1.15.0_src_all.tar.gz"], "md5": "ec0ca1c2609f7cd5d3081578bd186dd6", "fn": "mcsurvdata_1.15.0.tar.gz"}, "medipsdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MEDIPSData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/MEDIPSData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-medipsdata/bioconductor-medipsdata_1.33.0_src_all.tar.gz"], "md5": "cb3e1d5345ac273bb52647910a5088f6", "fn": "MEDIPSData_1.33.0.tar.gz"}, "meebodata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MEEBOdata_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/MEEBOdata_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-meebodata/bioconductor-meebodata_1.35.0_src_all.tar.gz"], "md5": "1c0b167cc3f2e53a3ce12b45820ca586", "fn": "MEEBOdata_1.35.0.tar.gz"}, "merfishdata-0.99.4": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MerfishData_0.99.4.tar.gz", "https://bioarchive.galaxyproject.org/MerfishData_0.99.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-merfishdata/bioconductor-merfishdata_0.99.4_src_all.tar.gz"], "md5": "eec70aea71ddd2d4fd9c35f759ac2f00", "fn": "MerfishData_0.99.4.tar.gz"}, "metagxbreast-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MetaGxBreast_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxBreast_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxbreast/bioconductor-metagxbreast_1.17.0_src_all.tar.gz"], "md5": "5a1cdda3d73df40f05d39840706a179a", "fn": "MetaGxBreast_1.17.0.tar.gz"}, "metagxovarian-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MetaGxOvarian_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxOvarian_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxovarian/bioconductor-metagxovarian_1.17.0_src_all.tar.gz"], "md5": "4515cf0e1cfe2cb6c83831c2530d6b67", "fn": "MetaGxOvarian_1.17.0.tar.gz"}, "metagxpancreas-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MetaGxPancreas_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxPancreas_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxpancreas/bioconductor-metagxpancreas_1.17.0_src_all.tar.gz"], "md5": "e0dfc63561474961fbc243efe77beb29", "fn": "MetaGxPancreas_1.17.0.tar.gz"}, "metamsdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/metaMSdata_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/metaMSdata_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metamsdata/bioconductor-metamsdata_1.33.0_src_all.tar.gz"], "md5": "c7f91a612bf189b5856f45eeaa22d75a", "fn": "metaMSdata_1.33.0.tar.gz"}, "methylaiddata-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MethylAidData_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/MethylAidData_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylaiddata/bioconductor-methylaiddata_1.29.0_src_all.tar.gz"], "md5": "e6cfbcf2f22b093617be964ba6f38a55", "fn": "MethylAidData_1.29.0.tar.gz"}, "methylclockdata-1.5.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/methylclockData_1.5.1.tar.gz", "https://bioarchive.galaxyproject.org/methylclockData_1.5.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylclockdata/bioconductor-methylclockdata_1.5.1_src_all.tar.gz"], "md5": "6d4b0b16c56e2f72763e4c4a7f9511a9", "fn": "methylclockData_1.5.1.tar.gz"}, "methylseqdata-1.7.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MethylSeqData_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/MethylSeqData_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylseqdata/bioconductor-methylseqdata_1.7.0_src_all.tar.gz"], "md5": "352df1846d59a3e3d8f170e484936899", "fn": "MethylSeqData_1.7.0.tar.gz"}, "microbiomebenchmarkdata-0.99.3": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MicrobiomeBenchmarkData_0.99.3.tar.gz", "https://bioarchive.galaxyproject.org/MicrobiomeBenchmarkData_0.99.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-microbiomebenchmarkdata/bioconductor-microbiomebenchmarkdata_0.99.3_src_all.tar.gz"], "md5": "d18fe5f84d2bc6fe3198ca8a2d96e93b", "fn": "MicrobiomeBenchmarkData_0.99.3.tar.gz"}, "microbiomedatasets-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/microbiomeDataSets_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/microbiomeDataSets_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-microbiomedatasets/bioconductor-microbiomedatasets_1.5.0_src_all.tar.gz"], "md5": "c5e76e08c3aa52155bd423c1fa39a935", "fn": "microbiomeDataSets_1.5.0.tar.gz"}, "micrornaome-1.19.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/microRNAome_1.19.0.tar.gz", "https://bioarchive.galaxyproject.org/microRNAome_1.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-micrornaome/bioconductor-micrornaome_1.19.0_src_all.tar.gz"], "md5": "a96e61bc3ce4ce30cb587018da5c3684", "fn": "microRNAome_1.19.0.tar.gz"}, "migsadata-1.21.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MIGSAdata_1.21.0.tar.gz", "https://bioarchive.galaxyproject.org/MIGSAdata_1.21.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-migsadata/bioconductor-migsadata_1.21.0_src_all.tar.gz"], "md5": "643e3a5b5f46302b7ae88edfb084dd12", "fn": "MIGSAdata_1.21.0.tar.gz"}, "minfidata-0.43.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/minfiData_0.43.0.tar.gz", "https://bioarchive.galaxyproject.org/minfiData_0.43.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minfidata/bioconductor-minfidata_0.43.0_src_all.tar.gz"], "md5": "80e4e542754fd9a48cf384aa2cfafe43", "fn": "minfiData_0.43.0.tar.gz"}, "minfidataepic-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/minfiDataEPIC_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/minfiDataEPIC_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minfidataepic/bioconductor-minfidataepic_1.23.0_src_all.tar.gz"], "md5": "dfe3432c455031f4e9da7194b024c8de", "fn": "minfiDataEPIC_1.23.0.tar.gz"}, "minionsummarydata-1.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/minionSummaryData_1.27.0.tar.gz", "https://bioarchive.galaxyproject.org/minionSummaryData_1.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minionsummarydata/bioconductor-minionsummarydata_1.27.0_src_all.tar.gz"], "md5": "85e222cdb24e11cdb22e2cbbf1e4320e", "fn": "minionSummaryData_1.27.0.tar.gz"}, "mircompdata-1.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/miRcompData_1.27.0.tar.gz", "https://bioarchive.galaxyproject.org/miRcompData_1.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mircompdata/bioconductor-mircompdata_1.27.0_src_all.tar.gz"], "md5": "3eb8338c98fa4b54a4ae71222b1c2ce0", "fn": "miRcompData_1.27.0.tar.gz"}, "mirnatarget-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/miRNATarget_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/miRNATarget_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirnatarget/bioconductor-mirnatarget_1.35.0_src_all.tar.gz"], "md5": "d88b2142f8df71518f24322e76ace811", "fn": "miRNATarget_1.35.0.tar.gz"}, "mmappr2data-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MMAPPR2data_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/MMAPPR2data_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mmappr2data/bioconductor-mmappr2data_1.11.0_src_all.tar.gz"], "md5": "caa2f5c69e9ac2d7ec2828345ddd32f3", "fn": "MMAPPR2data_1.11.0.tar.gz"}, "mmdiffbamsubset-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MMDiffBamSubset_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/MMDiffBamSubset_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mmdiffbamsubset/bioconductor-mmdiffbamsubset_1.33.0_src_all.tar.gz"], "md5": "dc953ce58ecdd627ba28713bd3c312f6", "fn": "MMDiffBamSubset_1.33.0.tar.gz"}, "mofadata-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MOFAdata_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/MOFAdata_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mofadata/bioconductor-mofadata_1.13.0_src_all.tar.gz"], "md5": "c2d0168b4072a4c585c74f54cfafcb57", "fn": "MOFAdata_1.13.0.tar.gz"}, "mosaicsexample-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mosaicsExample_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/mosaicsExample_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mosaicsexample/bioconductor-mosaicsexample_1.35.0_src_all.tar.gz"], "md5": "e9cd467badb82b605153c6c4320af466", "fn": "mosaicsExample_1.35.0.tar.gz"}, "mouse4302barcodevecs-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mouse4302barcodevecs_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse4302barcodevecs_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302barcodevecs/bioconductor-mouse4302barcodevecs_1.35.0_src_all.tar.gz"], "md5": "e7d4e9d76390dfe57d7a74ca94e7ca79", "fn": "mouse4302barcodevecs_1.35.0.tar.gz"}, "mousegastrulationdata-1.11.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MouseGastrulationData_1.11.1.tar.gz", "https://bioarchive.galaxyproject.org/MouseGastrulationData_1.11.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousegastrulationdata/bioconductor-mousegastrulationdata_1.11.1_src_all.tar.gz"], "md5": "3a73f3d193a842a530da88ec8280ee5d", "fn": "MouseGastrulationData_1.11.1.tar.gz"}, "mousethymusageing-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MouseThymusAgeing_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/MouseThymusAgeing_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousethymusageing/bioconductor-mousethymusageing_1.5.0_src_all.tar.gz"], "md5": "e396dade7dd782971468829efae0a869", "fn": "MouseThymusAgeing_1.5.0.tar.gz"}, "msd16s-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/msd16s_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/msd16s_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msd16s/bioconductor-msd16s_1.17.0_src_all.tar.gz"], "md5": "9fb66efe981c048b5b6719a2b3e4a05e", "fn": "msd16s_1.17.0.tar.gz"}, "msdata-0.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/msdata_0.37.0.tar.gz", "https://bioarchive.galaxyproject.org/msdata_0.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msdata/bioconductor-msdata_0.37.0_src_all.tar.gz"], "md5": "1642c062b0adf18cc4fbe4325b2da013", "fn": "msdata_0.37.0.tar.gz"}, "msigdb-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/msigdb_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/msigdb_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msigdb/bioconductor-msigdb_1.5.0_src_all.tar.gz"], "md5": "aacc6196dd1f49dacb6de609e759d85b", "fn": "msigdb_1.5.0.tar.gz"}, "msmb-1.15.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MSMB_1.15.2.tar.gz", "https://bioarchive.galaxyproject.org/MSMB_1.15.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msmb/bioconductor-msmb_1.15.2_src_all.tar.gz"], "md5": "6257a078ea4aedb9c85c9048f865d9c5", "fn": "MSMB_1.15.2.tar.gz"}, "mspuritydata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/msPurityData_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/msPurityData_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mspuritydata/bioconductor-mspuritydata_1.25.0_src_all.tar.gz"], "md5": "df95b6a4f33068cc8335aaa1425816bf", "fn": "msPurityData_1.25.0.tar.gz"}, "msqc1-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/msqc1_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/msqc1_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msqc1/bioconductor-msqc1_1.25.0_src_all.tar.gz"], "md5": "a3c33ff03b6609e9186def83fb6193c3", "fn": "msqc1_1.25.0.tar.gz"}, "mtbls2-1.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mtbls2_1.27.0.tar.gz", "https://bioarchive.galaxyproject.org/mtbls2_1.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mtbls2/bioconductor-mtbls2_1.27.0_src_all.tar.gz"], "md5": "20b309b57b8e6b480be5ffe1955faa15", "fn": "mtbls2_1.27.0.tar.gz"}, "mugaexampledata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MUGAExampleData_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/MUGAExampleData_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mugaexampledata/bioconductor-mugaexampledata_1.17.0_src_all.tar.gz"], "md5": "d6ccf772c75a8d68fe78aac36b4b042d", "fn": "MUGAExampleData_1.17.0.tar.gz"}, "muscdata-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/muscData_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/muscData_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-muscdata/bioconductor-muscdata_1.11.0_src_all.tar.gz"], "md5": "b0df5994604e48867035cfb2eb541e65", "fn": "muscData_1.11.0.tar.gz"}, "mvoutdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mvoutData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/mvoutData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mvoutdata/bioconductor-mvoutdata_1.33.0_src_all.tar.gz"], "md5": "86825abfe2d999710c77e56d2b4b8371", "fn": "mvoutData_1.33.0.tar.gz"}, "nanoporernaseq-1.7.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NanoporeRNASeq_1.7.1.tar.gz", "https://bioarchive.galaxyproject.org/NanoporeRNASeq_1.7.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nanoporernaseq/bioconductor-nanoporernaseq_1.7.1_src_all.tar.gz"], "md5": "85892a31a2c5e8dfaffcdc5492d2bce2", "fn": "NanoporeRNASeq_1.7.1.tar.gz"}, "nanotubes-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/nanotubes_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/nanotubes_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nanotubes/bioconductor-nanotubes_1.13.0_src_all.tar.gz"], "md5": "0853171cb24f37bcc3783c628cfcf408", "fn": "nanotubes_1.13.0.tar.gz"}, "ncigraphdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NCIgraphData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/NCIgraphData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ncigraphdata/bioconductor-ncigraphdata_1.33.0_src_all.tar.gz"], "md5": "defa41254bf294770846b80ec857df25", "fn": "NCIgraphData_1.33.0.tar.gz"}, "nestlink-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NestLink_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/NestLink_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nestlink/bioconductor-nestlink_1.13.0_src_all.tar.gz"], "md5": "1a5c4511b2116a70b04a9490542823a2", "fn": "NestLink_1.13.0.tar.gz"}, "netactivitydata-0.99.8": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NetActivityData_0.99.8.tar.gz", "https://bioarchive.galaxyproject.org/NetActivityData_0.99.8.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-netactivitydata/bioconductor-netactivitydata_0.99.8_src_all.tar.gz"], "md5": "cf1b94ebe0dcfb31ab7d1f2b5b09ce8f", "fn": "NetActivityData_0.99.8.tar.gz"}, "neve2006-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Neve2006_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/Neve2006_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-neve2006/bioconductor-neve2006_0.35.0_src_all.tar.gz"], "md5": "ba5066a6e72e829c1308c25cea7d24d1", "fn": "Neve2006_0.35.0.tar.gz"}, "ngscopydata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NGScopyData_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/NGScopyData_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ngscopydata/bioconductor-ngscopydata_1.17.0_src_all.tar.gz"], "md5": "61704ed687fa28933fc29bf733137438", "fn": "NGScopyData_1.17.0.tar.gz"}, "nullrangesdata-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/nullrangesData_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/nullrangesData_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nullrangesdata/bioconductor-nullrangesdata_1.3.0_src_all.tar.gz"], "md5": "fae6acf0dd112c87283416a889f59eae", "fn": "nullrangesData_1.3.0.tar.gz"}, "nxtirfdata-1.3.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NxtIRFdata_1.3.2.tar.gz", "https://bioarchive.galaxyproject.org/NxtIRFdata_1.3.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nxtirfdata/bioconductor-nxtirfdata_1.3.2_src_all.tar.gz"], "md5": "13f644045ca18190869a6e1d69fdc37a", "fn": "NxtIRFdata_1.3.2.tar.gz"}, "obmiti-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ObMiTi_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/ObMiTi_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-obmiti/bioconductor-obmiti_1.5.0_src_all.tar.gz"], "md5": "87d3aa74100f85b5643ee96bdfd5413d", "fn": "ObMiTi_1.5.0.tar.gz"}, "oct4-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/oct4_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/oct4_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-oct4/bioconductor-oct4_1.13.0_src_all.tar.gz"], "md5": "d1d65d9f1f6ff35d2df6713c51a684c2", "fn": "oct4_1.13.0.tar.gz"}, "octad.db-0.99.43": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/octad.db_0.99.43.tar.gz", "https://bioarchive.galaxyproject.org/octad.db_0.99.43.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-octad.db/bioconductor-octad.db_0.99.43_src_all.tar.gz"], "md5": "3815a8a295a5162ea585b57f00a1925e", "fn": "octad.db_0.99.43.tar.gz"}, "omicspcadata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/OMICsPCAdata_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/OMICsPCAdata_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-omicspcadata/bioconductor-omicspcadata_1.15.0_src_all.tar.gz"], "md5": "a2431a35117a8762f8bf86b81ee442b6", "fn": "OMICsPCAdata_1.15.0.tar.gz"}, "onassisjavalibs-1.19.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/OnassisJavaLibs_1.19.0.tar.gz", "https://bioarchive.galaxyproject.org/OnassisJavaLibs_1.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-onassisjavalibs/bioconductor-onassisjavalibs_1.19.0_src_all.tar.gz"], "md5": "3b5a9c4b77f33296aa9eec6c617e8a41", "fn": "OnassisJavaLibs_1.19.0.tar.gz"}, "optimalflowdata-1.9.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/optimalFlowData_1.9.0.tar.gz", "https://bioarchive.galaxyproject.org/optimalFlowData_1.9.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-optimalflowdata/bioconductor-optimalflowdata_1.9.0_src_all.tar.gz"], "md5": "951af94d3a9bfebc7d9be2e0ca6209dd", "fn": "optimalFlowData_1.9.0.tar.gz"}, "parathyroidse-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/parathyroidSE_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/parathyroidSE_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-parathyroidse/bioconductor-parathyroidse_1.35.0_src_all.tar.gz"], "md5": "c65fe2c82bac9730e22867a74aa6f2ba", "fn": "parathyroidSE_1.35.0.tar.gz"}, "pasilla-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pasilla_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/pasilla_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasilla/bioconductor-pasilla_1.25.0_src_all.tar.gz"], "md5": "0edb3fe08516d8d3c8ee2f7f45c156f0", "fn": "pasilla_1.25.0.tar.gz"}, "pasillabamsubset-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pasillaBamSubset_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/pasillaBamSubset_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasillabamsubset/bioconductor-pasillabamsubset_0.35.0_src_all.tar.gz"], "md5": "28f54b10b5a08f74dd07f0dd9dcf3dab", "fn": "pasillaBamSubset_0.35.0.tar.gz"}, "pasillatranscriptexpr-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PasillaTranscriptExpr_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/PasillaTranscriptExpr_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasillatranscriptexpr/bioconductor-pasillatranscriptexpr_1.25.0_src_all.tar.gz"], "md5": "1147d77b1b8cfb0963e99f241852ffbc", "fn": "PasillaTranscriptExpr_1.25.0.tar.gz"}, "pathnetdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PathNetData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/PathNetData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pathnetdata/bioconductor-pathnetdata_1.33.0_src_all.tar.gz"], "md5": "c150e591bddd66fcdc55a0ae1e17dc06", "fn": "PathNetData_1.33.0.tar.gz"}, "pchicdata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PCHiCdata_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/PCHiCdata_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pchicdata/bioconductor-pchicdata_1.25.0_src_all.tar.gz"], "md5": "59faa7d68d8c7e305c550846b3b639bc", "fn": "PCHiCdata_1.25.0.tar.gz"}, "pcxndata-2.19.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pcxnData_2.19.0.tar.gz", "https://bioarchive.galaxyproject.org/pcxnData_2.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pcxndata/bioconductor-pcxndata_2.19.0_src_all.tar.gz"], "md5": "a844676129f82b3a81719ec243a21252", "fn": "pcxnData_2.19.0.tar.gz"}, "pd.atdschip.tiling-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pd.atdschip.tiling_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.atdschip.tiling_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.atdschip.tiling/bioconductor-pd.atdschip.tiling_0.35.0_src_all.tar.gz"], "md5": "efd361b41cf9e3df5d629748707fede4", "fn": "pd.atdschip.tiling_0.35.0.tar.gz"}, "pepdat-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pepDat_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/pepDat_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pepdat/bioconductor-pepdat_1.17.0_src_all.tar.gz"], "md5": "2974e747656b1ea1987b1004b00a71e4", "fn": "pepDat_1.17.0.tar.gz"}, "pepsnmrdata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PepsNMRData_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/PepsNMRData_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pepsnmrdata/bioconductor-pepsnmrdata_1.15.0_src_all.tar.gz"], "md5": "339c9c0455823be6ec972a2ae69e6000", "fn": "PepsNMRData_1.15.0.tar.gz"}, "phyloprofiledata-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PhyloProfileData_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/PhyloProfileData_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phyloprofiledata/bioconductor-phyloprofiledata_1.11.0_src_all.tar.gz"], "md5": "d5dba91d23204c92146968d824753114", "fn": "PhyloProfileData_1.11.0.tar.gz"}, "plasfia-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/plasFIA_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/plasFIA_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-plasfia/bioconductor-plasfia_1.25.0_src_all.tar.gz"], "md5": "a97af6479ac842dc3e928b871ba61878", "fn": "plasFIA_1.25.0.tar.gz"}, "plotgardenerdata-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/plotgardenerData_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/plotgardenerData_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-plotgardenerdata/bioconductor-plotgardenerdata_1.3.0_src_all.tar.gz"], "md5": "9c6c3cc2b2d4b0450d21af1e3c888248", "fn": "plotgardenerData_1.3.0.tar.gz"}, "prebsdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prebsdata_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/prebsdata_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prebsdata/bioconductor-prebsdata_1.33.0_src_all.tar.gz"], "md5": "6574a4424628d14621fd7e81160e91d3", "fn": "prebsdata_1.33.0.tar.gz"}, "precisetadhub-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/preciseTADhub_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/preciseTADhub_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-precisetadhub/bioconductor-precisetadhub_1.5.0_src_all.tar.gz"], "md5": "3c395f5fa911600e628ad2d2528b01af", "fn": "preciseTADhub_1.5.0.tar.gz"}, "predasampledata-0.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PREDAsampledata_0.37.0.tar.gz", "https://bioarchive.galaxyproject.org/PREDAsampledata_0.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-predasampledata/bioconductor-predasampledata_0.37.0_src_all.tar.gz"], "md5": "55491dfcc26f2b86f32bc0f6d24ae70e", "fn": "PREDAsampledata_0.37.0.tar.gz"}, "prodata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ProData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/ProData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prodata/bioconductor-prodata_1.35.0_src_all.tar.gz"], "md5": "1f4cbc866bff251c9d9da84d248d573c", "fn": "ProData_1.35.0.tar.gz"}, "prolocdata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pRolocdata_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/pRolocdata_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prolocdata/bioconductor-prolocdata_1.35.0_src_all.tar.gz"], "md5": "022bb2ecedef6645c789c77cf81df02f", "fn": "pRolocdata_1.35.0.tar.gz"}, "prostatecancercamcap-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerCamcap_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerCamcap_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancercamcap/bioconductor-prostatecancercamcap_1.25.0_src_all.tar.gz"], "md5": "ebc9c45d833ffc639ea617615120a266", "fn": "prostateCancerCamcap_1.25.0.tar.gz"}, "prostatecancergrasso-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerGrasso_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerGrasso_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancergrasso/bioconductor-prostatecancergrasso_1.25.0_src_all.tar.gz"], "md5": "603e0a603a2be0a74aa134751f4d8bd4", "fn": "prostateCancerGrasso_1.25.0.tar.gz"}, "prostatecancerstockholm-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerStockholm_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerStockholm_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancerstockholm/bioconductor-prostatecancerstockholm_1.25.0_src_all.tar.gz"], "md5": "e95bb37704614ac74857659dab3fbcb0", "fn": "prostateCancerStockholm_1.25.0.tar.gz"}, "prostatecancertaylor-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerTaylor_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerTaylor_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancertaylor/bioconductor-prostatecancertaylor_1.25.0_src_all.tar.gz"], "md5": "66f146c541ed0d31c1b8c135c3d96264", "fn": "prostateCancerTaylor_1.25.0.tar.gz"}, "prostatecancervarambally-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerVarambally_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerVarambally_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancervarambally/bioconductor-prostatecancervarambally_1.25.0_src_all.tar.gz"], "md5": "5932c3c12140f4d28ac5a2e0a80e7a6f", "fn": "prostateCancerVarambally_1.25.0.tar.gz"}, "ptairdata-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ptairData_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/ptairData_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ptairdata/bioconductor-ptairdata_1.5.0_src_all.tar.gz"], "md5": "2d7b56e13204f1b91268abb8dff92363", "fn": "ptairData_1.5.0.tar.gz"}, "pth2o2lipids-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PtH2O2lipids_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/PtH2O2lipids_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pth2o2lipids/bioconductor-pth2o2lipids_1.23.0_src_all.tar.gz"], "md5": "c28311979e8a0eb57c2071b730e0a333", "fn": "PtH2O2lipids_1.23.0.tar.gz"}, "pumadata-2.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pumadata_2.33.0.tar.gz", "https://bioarchive.galaxyproject.org/pumadata_2.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pumadata/bioconductor-pumadata_2.33.0_src_all.tar.gz"], "md5": "d2ab4b9502b32fe38ee511381992afe9", "fn": "pumadata_2.33.0.tar.gz"}, "pwmenrich.dmelanogaster.background-4.31.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PWMEnrich.Dmelanogaster.background_4.31.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Dmelanogaster.background_4.31.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.dmelanogaster.background/bioconductor-pwmenrich.dmelanogaster.background_4.31.0_src_all.tar.gz"], "md5": "cd0675f1765e474fff6cf1f024f1724c", "fn": "PWMEnrich.Dmelanogaster.background_4.31.0.tar.gz"}, "pwmenrich.hsapiens.background-4.31.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PWMEnrich.Hsapiens.background_4.31.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Hsapiens.background_4.31.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.hsapiens.background/bioconductor-pwmenrich.hsapiens.background_4.31.0_src_all.tar.gz"], "md5": "8efdc209ce7f934d8cfbcb3ef42bfa4a", "fn": "PWMEnrich.Hsapiens.background_4.31.0.tar.gz"}, "pwmenrich.mmusculus.background-4.31.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PWMEnrich.Mmusculus.background_4.31.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Mmusculus.background_4.31.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.mmusculus.background/bioconductor-pwmenrich.mmusculus.background_4.31.0_src_all.tar.gz"], "md5": "3bff15a5eb02b34142880dab0092875e", "fn": "PWMEnrich.Mmusculus.background_4.31.0.tar.gz"}, "pwrewas.data-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pwrEWAS.data_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/pwrEWAS.data_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwrewas.data/bioconductor-pwrewas.data_1.11.0_src_all.tar.gz"], "md5": "173596e2dd38d12b4d32fad1bc6c9452", "fn": "pwrEWAS.data_1.11.0.tar.gz"}, "qdnaseq.hg19-1.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/QDNAseq.hg19_1.27.0.tar.gz", "https://bioarchive.galaxyproject.org/QDNAseq.hg19_1.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.hg19/bioconductor-qdnaseq.hg19_1.27.0_src_all.tar.gz"], "md5": "518d77883a6b46e2f874be69d84d4f68", "fn": "QDNAseq.hg19_1.27.0.tar.gz"}, "qdnaseq.mm10-1.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/QDNAseq.mm10_1.27.0.tar.gz", "https://bioarchive.galaxyproject.org/QDNAseq.mm10_1.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.mm10/bioconductor-qdnaseq.mm10_1.27.0_src_all.tar.gz"], "md5": "c53a875e47d38a8b21a47abacdbcda71", "fn": "QDNAseq.mm10_1.27.0.tar.gz"}, "qplexdata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/qPLEXdata_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/qPLEXdata_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qplexdata/bioconductor-qplexdata_1.15.0_src_all.tar.gz"], "md5": "bb2fa241c178b29f9282965a11a124ef", "fn": "qPLEXdata_1.15.0.tar.gz"}, "qubicdata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/QUBICdata_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/QUBICdata_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qubicdata/bioconductor-qubicdata_1.25.0_src_all.tar.gz"], "md5": "3c29904ce0171ebf2003ead6230e0810", "fn": "QUBICdata_1.25.0.tar.gz"}, "rcellminerdata-2.19.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/rcellminerData_2.19.1.tar.gz", "https://bioarchive.galaxyproject.org/rcellminerData_2.19.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rcellminerdata/bioconductor-rcellminerdata_2.19.1_src_all.tar.gz"], "md5": "db4a9f7371903f4c42c4465c48a6133e", "fn": "rcellminerData_2.19.1.tar.gz"}, "rcistarget.hg19.motifdbs.cisbponly.500bp-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp_1.17.0_src_all.tar.gz"], "md5": "856d7c1e8d71925b4f2b89bc72dab2e9", "fn": "RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.17.0.tar.gz"}, "reactomegsa.data-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ReactomeGSA.data_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/ReactomeGSA.data_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-reactomegsa.data/bioconductor-reactomegsa.data_1.11.0_src_all.tar.gz"], "md5": "f598a9890069ab14cce69b0c1488c47e", "fn": "ReactomeGSA.data_1.11.0.tar.gz"}, "regparallel-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RegParallel_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/RegParallel_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-regparallel/bioconductor-regparallel_1.15.0_src_all.tar.gz"], "md5": "0b1630990f1980bc6466867df598f207", "fn": "RegParallel_1.15.0.tar.gz"}, "restfulsedata-1.19.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/restfulSEData_1.19.0.tar.gz", "https://bioarchive.galaxyproject.org/restfulSEData_1.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-restfulsedata/bioconductor-restfulsedata_1.19.0_src_all.tar.gz"], "md5": "df09d45e9947259f318be8f81f73a0e6", "fn": "restfulSEData_1.19.0.tar.gz"}, "rforproteomics-1.35.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RforProteomics_1.35.1.tar.gz", "https://bioarchive.galaxyproject.org/RforProteomics_1.35.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rforproteomics/bioconductor-rforproteomics_1.35.1_src_all.tar.gz"], "md5": "3ffd6e19093de0c9db70a0b2460a0f4e", "fn": "RforProteomics_1.35.1.tar.gz"}, "rgmqllib-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RGMQLlib_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/RGMQLlib_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgmqllib/bioconductor-rgmqllib_1.17.0_src_all.tar.gz"], "md5": "fcbab98d1d444959fce27cf72575f78a", "fn": "RGMQLlib_1.17.0.tar.gz"}, "rheumaticconditionwollbold-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/rheumaticConditionWOLLBOLD_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/rheumaticConditionWOLLBOLD_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rheumaticconditionwollbold/bioconductor-rheumaticconditionwollbold_1.35.0_src_all.tar.gz"], "md5": "d2a9508ad9667781fea8e7b9cb841809", "fn": "rheumaticConditionWOLLBOLD_1.35.0.tar.gz"}, "ritandata-1.21.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RITANdata_1.21.0.tar.gz", "https://bioarchive.galaxyproject.org/RITANdata_1.21.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ritandata/bioconductor-ritandata_1.21.0_src_all.tar.gz"], "md5": "0b7b1ee673125332fdc786b1305a3071", "fn": "RITANdata_1.21.0.tar.gz"}, "rlhub-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RLHub_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/RLHub_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rlhub/bioconductor-rlhub_1.3.0_src_all.tar.gz"], "md5": "993a8252373fbe49176ad288bb18130d", "fn": "RLHub_1.3.0.tar.gz"}, "rmassbankdata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RMassBankData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/RMassBankData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rmassbankdata/bioconductor-rmassbankdata_1.35.0_src_all.tar.gz"], "md5": "796f21868672494e4e077820dface333", "fn": "RMassBankData_1.35.0.tar.gz"}, "rnainteractmapk-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RNAinteractMAPK_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAinteractMAPK_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnainteractmapk/bioconductor-rnainteractmapk_1.35.0_src_all.tar.gz"], "md5": "80f15d7f3d3238da524d1a14d71b1ef7", "fn": "RNAinteractMAPK_1.35.0.tar.gz"}, "rnamodr.data-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RNAmodR.Data_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAmodR.Data_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnamodr.data/bioconductor-rnamodr.data_1.11.0_src_all.tar.gz"], "md5": "ff9ff0deccfdec4c95548bbba9c3b1f7", "fn": "RNAmodR.Data_1.11.0.tar.gz"}, "rnaseqdata.hnrnpc.bam.chr14-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RNAseqData.HNRNPC.bam.chr14_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAseqData.HNRNPC.bam.chr14_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqdata.hnrnpc.bam.chr14/bioconductor-rnaseqdata.hnrnpc.bam.chr14_0.35.0_src_all.tar.gz"], "md5": "401b79849c78d01100e08e34d7a25292", "fn": "RNAseqData.HNRNPC.bam.chr14_0.35.0.tar.gz"}, "rnaseqrdata-1.15.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RNASeqRData_1.15.1.tar.gz", "https://bioarchive.galaxyproject.org/RNASeqRData_1.15.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqrdata/bioconductor-rnaseqrdata_1.15.1_src_all.tar.gz"], "md5": "478f32fc1d6a3580d101652ef2015546", "fn": "RNASeqRData_1.15.1.tar.gz"}, "rnaseqsamplesizedata-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnaSeqSampleSizeData_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/RnaSeqSampleSizeData_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqsamplesizedata/bioconductor-rnaseqsamplesizedata_1.29.0_src_all.tar.gz"], "md5": "bc2df4e881a94985ceb2b6bf0998de6a", "fn": "RnaSeqSampleSizeData_1.29.0.tar.gz"}, "rnbeads.hg19-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.hg19_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.hg19_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg19/bioconductor-rnbeads.hg19_1.29.0_src_all.tar.gz"], "md5": "c725e7435a196137ba885a8cca8f1991", "fn": "RnBeads.hg19_1.29.0.tar.gz"}, "rnbeads.hg38-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.hg38_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.hg38_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg38/bioconductor-rnbeads.hg38_1.29.0_src_all.tar.gz"], "md5": "055e1c7a0e00f53e53b07b7560865703", "fn": "RnBeads.hg38_1.29.0.tar.gz"}, "rnbeads.mm10-2.5.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.mm10_2.5.1.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.mm10_2.5.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm10/bioconductor-rnbeads.mm10_2.5.1_src_all.tar.gz"], "md5": "5c57fb0869667a8bda50c90f8028e8e1", "fn": "RnBeads.mm10_2.5.1.tar.gz"}, "rnbeads.mm9-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.mm9_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.mm9_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm9/bioconductor-rnbeads.mm9_1.29.0_src_all.tar.gz"], "md5": "d0c5a9b71d99cbcb21d4192b78774352", "fn": "RnBeads.mm9_1.29.0.tar.gz"}, "rnbeads.rn5-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.rn5_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.rn5_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.rn5/bioconductor-rnbeads.rn5_1.29.0_src_all.tar.gz"], "md5": "ca6bc3e9fe0a8a9f5e876cb9f1b76cae", "fn": "RnBeads.rn5_1.29.0.tar.gz"}, "rrbsdata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RRBSdata_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/RRBSdata_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rrbsdata/bioconductor-rrbsdata_1.17.0_src_all.tar.gz"], "md5": "5dd5415736896e85943d4330c091e694", "fn": "RRBSdata_1.17.0.tar.gz"}, "rrdpdata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/rRDPData_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/rRDPData_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rrdpdata/bioconductor-rrdpdata_1.17.0_src_all.tar.gz"], "md5": "4c364082e1cedd9ffab9d5275ec297d5", "fn": "rRDPData_1.17.0.tar.gz"}, "rtcga.clinical-20151101.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RTCGA.clinical_20151101.27.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.clinical_20151101.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.clinical/bioconductor-rtcga.clinical_20151101.27.0_src_all.tar.gz"], "md5": "35e8c14f6a582746b995c5c57224dc45", "fn": "RTCGA.clinical_20151101.27.0.tar.gz"}, "rtcga.cnv-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RTCGA.CNV_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.CNV_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.cnv/bioconductor-rtcga.cnv_1.25.0_src_all.tar.gz"], "md5": "7fc6cc257e7ee37df80002e8ab1335a4", "fn": "RTCGA.CNV_1.25.0.tar.gz"}, "rtcga.methylation-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RTCGA.methylation_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.methylation_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.methylation/bioconductor-rtcga.methylation_1.25.0_src_all.tar.gz"], "md5": "d87ab750ff3ccdd424dfae6442f4b5ad", "fn": "RTCGA.methylation_1.25.0.tar.gz"}, "rtcga.mirnaseq-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RTCGA.miRNASeq_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.miRNASeq_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mirnaseq/bioconductor-rtcga.mirnaseq_1.25.0_src_all.tar.gz"], "md5": "471abf3d4d571d7e36f564e3717d511e", "fn": "RTCGA.miRNASeq_1.25.0.tar.gz"}, "rtcga.mrna-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RTCGA.mRNA_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.mRNA_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mrna/bioconductor-rtcga.mrna_1.25.0_src_all.tar.gz"], "md5": "354a9449d7e97238fccec1c0b6f909ca", "fn": "RTCGA.mRNA_1.25.0.tar.gz"}, "rtcga.mutations-20151101.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RTCGA.mutations_20151101.27.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.mutations_20151101.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mutations/bioconductor-rtcga.mutations_20151101.27.0_src_all.tar.gz"], "md5": "d048b3ecd23a074d3fb83edbb97ef9f3", "fn": "RTCGA.mutations_20151101.27.0.tar.gz"}, "rtcga.pancan12-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RTCGA.PANCAN12_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.PANCAN12_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.pancan12/bioconductor-rtcga.pancan12_1.25.0_src_all.tar.gz"], "md5": "fec760cdd49da6ba627f54ff48cc1b93", "fn": "RTCGA.PANCAN12_1.25.0.tar.gz"}, "rtcga.rnaseq-20151101.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RTCGA.rnaseq_20151101.27.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.rnaseq_20151101.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.rnaseq/bioconductor-rtcga.rnaseq_20151101.27.0_src_all.tar.gz"], "md5": "e2d2bf42422003ace5ad96bef58ea405", "fn": "RTCGA.rnaseq_20151101.27.0.tar.gz"}, "rtcga.rppa-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RTCGA.RPPA_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.RPPA_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.rppa/bioconductor-rtcga.rppa_1.25.0_src_all.tar.gz"], "md5": "f9f2a9881310faad9361f7fdd026f128", "fn": "RTCGA.RPPA_1.25.0.tar.gz"}, "ruvnormalizedata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RUVnormalizeData_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/RUVnormalizeData_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ruvnormalizedata/bioconductor-ruvnormalizedata_1.17.0_src_all.tar.gz"], "md5": "306697e9fc77724556f118f23bf26485", "fn": "RUVnormalizeData_1.17.0.tar.gz"}, "sampleclassifierdata-1.21.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/sampleClassifierData_1.21.0.tar.gz", "https://bioarchive.galaxyproject.org/sampleClassifierData_1.21.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sampleclassifierdata/bioconductor-sampleclassifierdata_1.21.0_src_all.tar.gz"], "md5": "c12c28d1c72e9cf498ed86163d7ed783", "fn": "sampleClassifierData_1.21.0.tar.gz"}, "sbgnview.data-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SBGNview.data_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/SBGNview.data_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sbgnview.data/bioconductor-sbgnview.data_1.11.0_src_all.tar.gz"], "md5": "e6c7eb719b1d37cfa714406dfbdcc0a1", "fn": "SBGNview.data_1.11.0.tar.gz"}, "scanmirdata-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/scanMiRData_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/scanMiRData_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scanmirdata/bioconductor-scanmirdata_1.3.0_src_all.tar.gz"], "md5": "a43695113a97f647b5d126ed6a25e916", "fn": "scanMiRData_1.3.0.tar.gz"}, "scatac.explorer-1.3.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/scATAC.Explorer_1.3.1.tar.gz", "https://bioarchive.galaxyproject.org/scATAC.Explorer_1.3.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scatac.explorer/bioconductor-scatac.explorer_1.3.1_src_all.tar.gz"], "md5": "85b3806b74f97621c9060287ad23364b", "fn": "scATAC.Explorer_1.3.1.tar.gz"}, "scatedata-1.7.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SCATEData_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/SCATEData_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scatedata/bioconductor-scatedata_1.7.0_src_all.tar.gz"], "md5": "411679e006f3d67c0397047166899a19", "fn": "SCATEData_1.7.0.tar.gz"}, "sclcbam-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SCLCBam_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/SCLCBam_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sclcbam/bioconductor-sclcbam_1.29.0_src_all.tar.gz"], "md5": "16a8806e945c1102bf251522a3bb4245", "fn": "SCLCBam_1.29.0.tar.gz"}, "scpdata-1.5.6": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/scpdata_1.5.6.tar.gz", "https://bioarchive.galaxyproject.org/scpdata_1.5.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scpdata/bioconductor-scpdata_1.5.6_src_all.tar.gz"], "md5": "26b3cc33198ebf3866ab92cd6982503f", "fn": "scpdata_1.5.6.tar.gz"}, "scrnaseq-2.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/scRNAseq_2.11.0.tar.gz", "https://bioarchive.galaxyproject.org/scRNAseq_2.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scrnaseq/bioconductor-scrnaseq_2.11.0_src_all.tar.gz"], "md5": "70776b195a73f25a1bc4556f617aa6be", "fn": "scRNAseq_2.11.0.tar.gz"}, "scthi.data-1.9.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/scTHI.data_1.9.0.tar.gz", "https://bioarchive.galaxyproject.org/scTHI.data_1.9.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scthi.data/bioconductor-scthi.data_1.9.0_src_all.tar.gz"], "md5": "a698f50dd82951cb71f4cf478cc38333", "fn": "scTHI.data_1.9.0.tar.gz"}, "seq2pathway.data-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/seq2pathway.data_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/seq2pathway.data_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seq2pathway.data/bioconductor-seq2pathway.data_1.29.0_src_all.tar.gz"], "md5": "2ee5d460d650aaef586d7000881a0849", "fn": "seq2pathway.data_1.29.0.tar.gz"}, "seqc-1.31.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/seqc_1.31.0.tar.gz", "https://bioarchive.galaxyproject.org/seqc_1.31.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seqc/bioconductor-seqc_1.31.0_src_all.tar.gz"], "md5": "48815472de95968a75d74e674e431c26", "fn": "seqc_1.31.0.tar.gz"}, "seqcna.annot-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/seqCNA.annot_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/seqCNA.annot_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seqcna.annot/bioconductor-seqcna.annot_1.33.0_src_all.tar.gz"], "md5": "51b9a1bf62f20ba710dd42d6656e5aaa", "fn": "seqCNA.annot_1.33.0.tar.gz"}, "serumstimulation-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/serumStimulation_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/serumStimulation_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-serumstimulation/bioconductor-serumstimulation_1.33.0_src_all.tar.gz"], "md5": "9a8d66ab8dd4e884f8cbd570979710d4", "fn": "serumStimulation_1.33.0.tar.gz"}, "sesamedata-1.15.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/sesameData_1.15.2.tar.gz", "https://bioarchive.galaxyproject.org/sesameData_1.15.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sesamedata/bioconductor-sesamedata_1.15.2_src_all.tar.gz"], "md5": "5a0f67d044802b947e6b60a0b995b1ed", "fn": "sesameData_1.15.2.tar.gz"}, "seventygenedata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/seventyGeneData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/seventyGeneData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seventygenedata/bioconductor-seventygenedata_1.33.0_src_all.tar.gz"], "md5": "54f2663a062f96ce8e9accc6f6ca4ffc", "fn": "seventyGeneData_1.33.0.tar.gz"}, "sfedata-0.99.7": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SFEData_0.99.7.tar.gz", "https://bioarchive.galaxyproject.org/SFEData_0.99.7.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sfedata/bioconductor-sfedata_0.99.7_src_all.tar.gz"], "md5": "340d06a5b66dd38d058d0e0731c38c2a", "fn": "SFEData_0.99.7.tar.gz"}, "shinymethyldata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/shinyMethylData_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/shinyMethylData_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-shinymethyldata/bioconductor-shinymethyldata_1.17.0_src_all.tar.gz"], "md5": "6b95b7efb75a39bcd8e786f8f0719eef", "fn": "shinyMethylData_1.17.0.tar.gz"}, "signaturesearchdata-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/signatureSearchData_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/signatureSearchData_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-signaturesearchdata/bioconductor-signaturesearchdata_1.11.0_src_all.tar.gz"], "md5": "20cd61a7297ba49c4ede5ef2469e6c49", "fn": "signatureSearchData_1.11.0.tar.gz"}, "simbenchdata-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SimBenchData_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/SimBenchData_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-simbenchdata/bioconductor-simbenchdata_1.5.0_src_all.tar.gz"], "md5": "cd45939fd175a2bb4b55ff889628634a", "fn": "SimBenchData_1.5.0.tar.gz"}, "simpintlists-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/simpIntLists_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/simpIntLists_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-simpintlists/bioconductor-simpintlists_1.33.0_src_all.tar.gz"], "md5": "5a75c92aee4a1cbc367ec5a3477cfdd7", "fn": "simpIntLists_1.33.0.tar.gz"}, "single.mtec.transcriptomes-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Single.mTEC.Transcriptomes_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/Single.mTEC.Transcriptomes_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-single.mtec.transcriptomes/bioconductor-single.mtec.transcriptomes_1.25.0_src_all.tar.gz"], "md5": "560313eceb9231c01b678e08edb55a2e", "fn": "Single.mTEC.Transcriptomes_1.25.0.tar.gz"}, "singlecellmultimodal-1.9.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SingleCellMultiModal_1.9.1.tar.gz", "https://bioarchive.galaxyproject.org/SingleCellMultiModal_1.9.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-singlecellmultimodal/bioconductor-singlecellmultimodal_1.9.1_src_all.tar.gz"], "md5": "0c59bc44aaac749033e80fe0fcf1e857", "fn": "SingleCellMultiModal_1.9.1.tar.gz"}, "singlemoleculefootprintingdata-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SingleMoleculeFootprintingData_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/SingleMoleculeFootprintingData_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-singlemoleculefootprintingdata/bioconductor-singlemoleculefootprintingdata_1.5.0_src_all.tar.gz"], "md5": "ddcc1ca02d843daf3cc75ca9ce086316", "fn": "SingleMoleculeFootprintingData_1.5.0.tar.gz"}, "snadata-1.43.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SNAData_1.43.0.tar.gz", "https://bioarchive.galaxyproject.org/SNAData_1.43.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snadata/bioconductor-snadata_1.43.0_src_all.tar.gz"], "md5": "24320fe022729f78f187851b14b441e7", "fn": "SNAData_1.43.0.tar.gz"}, "snageedata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SNAGEEdata_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/SNAGEEdata_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snageedata/bioconductor-snageedata_1.33.0_src_all.tar.gz"], "md5": "8cb9091d5082ee082b0ec7139d28667d", "fn": "SNAGEEdata_1.33.0.tar.gz"}, "snphooddata-1.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SNPhoodData_1.27.0.tar.gz", "https://bioarchive.galaxyproject.org/SNPhoodData_1.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snphooddata/bioconductor-snphooddata_1.27.0_src_all.tar.gz"], "md5": "418848af2c57a34599486445325114de", "fn": "SNPhoodData_1.27.0.tar.gz"}, "somaticadata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SomatiCAData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/SomatiCAData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-somaticadata/bioconductor-somaticadata_1.35.0_src_all.tar.gz"], "md5": "9429c73a8a4b28926a8ea3f61233e8d1", "fn": "SomatiCAData_1.35.0.tar.gz"}, "somaticcanceralterations-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SomaticCancerAlterations_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/SomaticCancerAlterations_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-somaticcanceralterations/bioconductor-somaticcanceralterations_1.33.0_src_all.tar.gz"], "md5": "1974e96d47df6f7fde09f8e0eb069ac5", "fn": "SomaticCancerAlterations_1.33.0.tar.gz"}, "spatialdmelxsim-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/spatialDmelxsim_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/spatialDmelxsim_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatialdmelxsim/bioconductor-spatialdmelxsim_1.3.0_src_all.tar.gz"], "md5": "862af3f63791a570ea892fe39efe6e12", "fn": "spatialDmelxsim_1.3.0.tar.gz"}, "spatiallibd-1.9.19": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/spatialLIBD_1.9.19.tar.gz", "https://bioarchive.galaxyproject.org/spatialLIBD_1.9.19.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatiallibd/bioconductor-spatiallibd_1.9.19_src_all.tar.gz"], "md5": "f1e78d740cbb533190708bf59b1c8b3e", "fn": "spatialLIBD_1.9.19.tar.gz"}, "spikein-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SpikeIn_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/SpikeIn_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spikein/bioconductor-spikein_1.39.0_src_all.tar.gz"], "md5": "9effe497b629d75622cb90b15d6b0407", "fn": "SpikeIn_1.39.0.tar.gz"}, "spikeinsubset-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SpikeInSubset_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/SpikeInSubset_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spikeinsubset/bioconductor-spikeinsubset_1.37.0_src_all.tar.gz"], "md5": "acfc16b524f4a8862281006722f3f32a", "fn": "SpikeInSubset_1.37.0.tar.gz"}, "spqndata-1.9.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/spqnData_1.9.0.tar.gz", "https://bioarchive.galaxyproject.org/spqnData_1.9.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spqndata/bioconductor-spqndata_1.9.0_src_all.tar.gz"], "md5": "24599f986a8f2e4f06af4996fe1c2f3f", "fn": "spqnData_1.9.0.tar.gz"}, "stemhypoxia-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/stemHypoxia_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/stemHypoxia_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stemhypoxia/bioconductor-stemhypoxia_1.33.0_src_all.tar.gz"], "md5": "fe757bfe1c1876fb96ce163f45e3df58", "fn": "stemHypoxia_1.33.0.tar.gz"}, "stexampledata-1.5.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/STexampleData_1.5.2.tar.gz", "https://bioarchive.galaxyproject.org/STexampleData_1.5.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stexampledata/bioconductor-stexampledata_1.5.2_src_all.tar.gz"], "md5": "c1e37cafb1f6da572942e1eeec1241b4", "fn": "STexampleData_1.5.2.tar.gz"}, "stjudem-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/stjudem_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/stjudem_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stjudem/bioconductor-stjudem_1.37.0_src_all.tar.gz"], "md5": "6f2e08c7e679d02bac1b908aa7ad775e", "fn": "stjudem_1.37.0.tar.gz"}, "svm2crmdata-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SVM2CRMdata_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/SVM2CRMdata_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-svm2crmdata/bioconductor-svm2crmdata_1.29.0_src_all.tar.gz"], "md5": "3e07fd96096e1c15a05cd1e45b5173bc", "fn": "SVM2CRMdata_1.29.0.tar.gz"}, "synapterdata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/synapterdata_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/synapterdata_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-synapterdata/bioconductor-synapterdata_1.35.0_src_all.tar.gz"], "md5": "603dc62bd3d1b2e7daa8d1ab66285d2e", "fn": "synapterdata_1.35.0.tar.gz"}, "systempiperdata-2.1.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/systemPipeRdata_2.1.2.tar.gz", "https://bioarchive.galaxyproject.org/systemPipeRdata_2.1.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-systempiperdata/bioconductor-systempiperdata_2.1.2_src_all.tar.gz"], "md5": "6d2bd003dbdb72a83de0fb0026cfb7fe", "fn": "systemPipeRdata_2.1.2.tar.gz"}, "tabulamurisdata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TabulaMurisData_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/TabulaMurisData_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tabulamurisdata/bioconductor-tabulamurisdata_1.15.0_src_all.tar.gz"], "md5": "7f57c27412eca366c33144a428e9ead6", "fn": "TabulaMurisData_1.15.0.tar.gz"}, "tabulamurissenisdata-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TabulaMurisSenisData_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/TabulaMurisSenisData_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tabulamurissenisdata/bioconductor-tabulamurissenisdata_1.3.0_src_all.tar.gz"], "md5": "27d801ac7d3f9069160767e1fb0e5ecd", "fn": "TabulaMurisSenisData_1.3.0.tar.gz"}, "targetscoredata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TargetScoreData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/TargetScoreData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetscoredata/bioconductor-targetscoredata_1.33.0_src_all.tar.gz"], "md5": "ca583f136c849f6bf93ca1514abd5ff3", "fn": "TargetScoreData_1.33.0.tar.gz"}, "targetsearchdata-1.35.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TargetSearchData_1.35.2.tar.gz", "https://bioarchive.galaxyproject.org/TargetSearchData_1.35.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetsearchdata/bioconductor-targetsearchdata_1.35.2_src_all.tar.gz"], "md5": "43fb25187b147b819b0e23af4e335cdd", "fn": "TargetSearchData_1.35.2.tar.gz"}, "tartare-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tartare_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/tartare_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tartare/bioconductor-tartare_1.11.0_src_all.tar.gz"], "md5": "8c4138bab0fb88cde1506b336f55b879", "fn": "tartare_1.11.0.tar.gz"}, "tbx20bamsubset-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TBX20BamSubset_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/TBX20BamSubset_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tbx20bamsubset/bioconductor-tbx20bamsubset_1.33.0_src_all.tar.gz"], "md5": "87c505f0958e19fcdf8f7bed9ab92fbf", "fn": "TBX20BamSubset_1.33.0.tar.gz"}, "tcgabiolinksgui.data-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TCGAbiolinksGUI.data_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAbiolinksGUI.data_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgabiolinksgui.data/bioconductor-tcgabiolinksgui.data_1.17.0_src_all.tar.gz"], "md5": "5d6415ec86aaeb44f84b7a6481eb48b4", "fn": "TCGAbiolinksGUI.data_1.17.0.tar.gz"}, "tcgacrcmirna-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TCGAcrcmiRNA_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAcrcmiRNA_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmirna/bioconductor-tcgacrcmirna_1.17.0_src_all.tar.gz"], "md5": "82abd790e1b6bff2123696c614fef240", "fn": "TCGAcrcmiRNA_1.17.0.tar.gz"}, "tcgacrcmrna-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TCGAcrcmRNA_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAcrcmRNA_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmrna/bioconductor-tcgacrcmrna_1.17.0_src_all.tar.gz"], "md5": "7da254036ad12e64c49d47cf352b2c73", "fn": "TCGAcrcmRNA_1.17.0.tar.gz"}, "tcgamethylation450k-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TCGAMethylation450k_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAMethylation450k_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgamethylation450k/bioconductor-tcgamethylation450k_1.33.0_src_all.tar.gz"], "md5": "fe77cf245bce1750ce61e1a6b235829d", "fn": "TCGAMethylation450k_1.33.0.tar.gz"}, "tcgaworkflowdata-1.21.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TCGAWorkflowData_1.21.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAWorkflowData_1.21.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgaworkflowdata/bioconductor-tcgaworkflowdata_1.21.0_src_all.tar.gz"], "md5": "69dae77a3b3916f3cf884ad05c96cc7c", "fn": "TCGAWorkflowData_1.21.0.tar.gz"}, "tenxbraindata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TENxBrainData_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxBrainData_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxbraindata/bioconductor-tenxbraindata_1.17.0_src_all.tar.gz"], "md5": "45978a0b489aafe4edab0e1534f07978", "fn": "TENxBrainData_1.17.0.tar.gz"}, "tenxbusdata-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TENxBUSData_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxBUSData_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxbusdata/bioconductor-tenxbusdata_1.11.0_src_all.tar.gz"], "md5": "ffd6839b94b6fdd8ba41af3a455b0b92", "fn": "TENxBUSData_1.11.0.tar.gz"}, "tenxpbmcdata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TENxPBMCData_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxPBMCData_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxpbmcdata/bioconductor-tenxpbmcdata_1.15.0_src_all.tar.gz"], "md5": "a12628733b5ea103b62f449aaf0b10d7", "fn": "TENxPBMCData_1.15.0.tar.gz"}, "tenxvisiumdata-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TENxVisiumData_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxVisiumData_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxvisiumdata/bioconductor-tenxvisiumdata_1.5.0_src_all.tar.gz"], "md5": "9fe57094f0c7e344a01a80277736c84b", "fn": "TENxVisiumData_1.5.0.tar.gz"}, "timecoursedata-1.7.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/timecoursedata_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/timecoursedata_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-timecoursedata/bioconductor-timecoursedata_1.7.0_src_all.tar.gz"], "md5": "2cbd0fa6b4e66daa39a2bd1244309a97", "fn": "timecoursedata_1.7.0.tar.gz"}, "timerquant-1.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TimerQuant_1.27.0.tar.gz", "https://bioarchive.galaxyproject.org/TimerQuant_1.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-timerquant/bioconductor-timerquant_1.27.0_src_all.tar.gz"], "md5": "2456c8d6d3755eb65bd6cafa0f621a66", "fn": "TimerQuant_1.27.0.tar.gz"}, "tinesath1cdf-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tinesath1cdf_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/tinesath1cdf_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tinesath1cdf/bioconductor-tinesath1cdf_1.35.0_src_all.tar.gz"], "md5": "3b5ddb90839f9fb31cf91a9726a934a0", "fn": "tinesath1cdf_1.35.0.tar.gz"}, "tinesath1probe-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tinesath1probe_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/tinesath1probe_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tinesath1probe/bioconductor-tinesath1probe_1.35.0_src_all.tar.gz"], "md5": "72478cd47ca289c0214d7745f75291b3", "fn": "tinesath1probe_1.35.0.tar.gz"}, "tissuetreg-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tissueTreg_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/tissueTreg_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tissuetreg/bioconductor-tissuetreg_1.17.0_src_all.tar.gz"], "md5": "2dd7fc2211e8ae3d240fc82d7aef3d99", "fn": "tissueTreg_1.17.0.tar.gz"}, "tmexplorer-1.7.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TMExplorer_1.7.2.tar.gz", "https://bioarchive.galaxyproject.org/TMExplorer_1.7.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tmexplorer/bioconductor-tmexplorer_1.7.2_src_all.tar.gz"], "md5": "1271bcae8d7a46153441e3000f1dc307", "fn": "TMExplorer_1.7.2.tar.gz"}, "tofsimsdata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tofsimsData_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/tofsimsData_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tofsimsdata/bioconductor-tofsimsdata_1.25.0_src_all.tar.gz"], "md5": "b5faa9733183ff1d2aadd97c2b6f7a2a", "fn": "tofsimsData_1.25.0.tar.gz"}, "topdownrdata-1.19.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/topdownrdata_1.19.0.tar.gz", "https://bioarchive.galaxyproject.org/topdownrdata_1.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-topdownrdata/bioconductor-topdownrdata_1.19.0_src_all.tar.gz"], "md5": "e86dbcc5dfe0b8539d5dbac3492ffddf", "fn": "topdownrdata_1.19.0.tar.gz"}, "tuberculosis-1.3.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tuberculosis_1.3.1.tar.gz", "https://bioarchive.galaxyproject.org/tuberculosis_1.3.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tuberculosis/bioconductor-tuberculosis_1.3.1_src_all.tar.gz"], "md5": "14f353861c61befd1911a3dbd369a5ec", "fn": "tuberculosis_1.3.1.tar.gz"}, "tweedeseqcountdata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tweeDEseqCountData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/tweeDEseqCountData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tweedeseqcountdata/bioconductor-tweedeseqcountdata_1.35.0_src_all.tar.gz"], "md5": "a5ed31ba1cbf1170ee42df7c406bcd2d", "fn": "tweeDEseqCountData_1.35.0.tar.gz"}, "tximportdata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tximportData_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/tximportData_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tximportdata/bioconductor-tximportdata_1.25.0_src_all.tar.gz"], "md5": "3ba5ba44ef1eba13a0d2a6d801c4d0f2", "fn": "tximportData_1.25.0.tar.gz"}, "varianttoolsdata-1.21.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/VariantToolsData_1.21.0.tar.gz", "https://bioarchive.galaxyproject.org/VariantToolsData_1.21.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-varianttoolsdata/bioconductor-varianttoolsdata_1.21.0_src_all.tar.gz"], "md5": "929b183276d2619fe003924aa94087d8", "fn": "VariantToolsData_1.21.0.tar.gz"}, "vectrapolarisdata-1.1.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/VectraPolarisData_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/VectraPolarisData_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vectrapolarisdata/bioconductor-vectrapolarisdata_1.1.0_src_all.tar.gz"], "md5": "2d2adee263147ec6f77b64f6cf79f9ee", "fn": "VectraPolarisData_1.1.0.tar.gz"}, "vulcandata-1.19.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/vulcandata_1.19.0.tar.gz", "https://bioarchive.galaxyproject.org/vulcandata_1.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vulcandata/bioconductor-vulcandata_1.19.0_src_all.tar.gz"], "md5": "9c0222aaae9653366ad080b32e467e67", "fn": "vulcandata_1.19.0.tar.gz"}, "weberdivechalcdata-0.99.4": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/WeberDivechaLCdata_0.99.4.tar.gz", "https://bioarchive.galaxyproject.org/WeberDivechaLCdata_0.99.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-weberdivechalcdata/bioconductor-weberdivechalcdata_0.99.4_src_all.tar.gz"], "md5": "ac2cdb9ca4d0921e58cf36762ed552f2", "fn": "WeberDivechaLCdata_0.99.4.tar.gz"}, "wes.1kg.wugsc-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/WES.1KG.WUGSC_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/WES.1KG.WUGSC_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wes.1kg.wugsc/bioconductor-wes.1kg.wugsc_1.29.0_src_all.tar.gz"], "md5": "bda054ad4efc2754d2acbdab1ad7ee16", "fn": "WES.1KG.WUGSC_1.29.0.tar.gz"}, "wgsmapp-1.9.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/WGSmapp_1.9.0.tar.gz", "https://bioarchive.galaxyproject.org/WGSmapp_1.9.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wgsmapp/bioconductor-wgsmapp_1.9.0_src_all.tar.gz"], "md5": "0df4f6810324ffae4407ba030cd69a4b", "fn": "WGSmapp_1.9.0.tar.gz"}, "xcoredata-1.1.4": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/xcoredata_1.1.4.tar.gz", "https://bioarchive.galaxyproject.org/xcoredata_1.1.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xcoredata/bioconductor-xcoredata_1.1.4_src_all.tar.gz"], "md5": "556f844f7e54dd197196b938d44e6163", "fn": "xcoredata_1.1.4.tar.gz"}, "xhybcasneuf-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/XhybCasneuf_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/XhybCasneuf_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xhybcasneuf/bioconductor-xhybcasneuf_1.35.0_src_all.tar.gz"], "md5": "149bd49ac717ef10ad2765f41d465106", "fn": "XhybCasneuf_1.35.0.tar.gz"}, "yeastcc-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/yeastCC_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastCC_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastcc/bioconductor-yeastcc_1.37.0_src_all.tar.gz"], "md5": "13ca41f2737ac8daa603c99f973f3a47", "fn": "yeastCC_1.37.0.tar.gz"}, "yeastexpdata-0.43.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/yeastExpData_0.43.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastExpData_0.43.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastexpdata/bioconductor-yeastexpdata_0.43.0_src_all.tar.gz"], "md5": "83706c49ab5d73657adb5927b2514eed", "fn": "yeastExpData_0.43.0.tar.gz"}, "yeastgsdata-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/yeastGSData_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastGSData_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastgsdata/bioconductor-yeastgsdata_0.35.0_src_all.tar.gz"], "md5": "e8e80c40923d5f9a13d7cc336e715566", "fn": "yeastGSData_0.35.0.tar.gz"}, "yeastnagalakshmi-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/yeastNagalakshmi_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastNagalakshmi_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastnagalakshmi/bioconductor-yeastnagalakshmi_1.33.0_src_all.tar.gz"], "md5": "c44d92115c879fe8250df7add73731b2", "fn": "yeastNagalakshmi_1.33.0.tar.gz"}, "yeastrnaseq-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/yeastRNASeq_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastRNASeq_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastrnaseq/bioconductor-yeastrnaseq_0.35.0_src_all.tar.gz"], "md5": "679c8db4a43dc2ac394e33942418e050", "fn": "yeastRNASeq_0.35.0.tar.gz"}, "zebrafishrnaseq-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/zebrafishRNASeq_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafishRNASeq_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafishrnaseq/bioconductor-zebrafishrnaseq_1.17.0_src_all.tar.gz"], "md5": "241e5db9cba13ee69bfdea6bd3dd797e", "fn": "zebrafishRNASeq_1.17.0.tar.gz"}, "ashkenazimsonchr21-1.28.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/AshkenazimSonChr21_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/AshkenazimSonChr21_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ashkenazimsonchr21/bioconductor-ashkenazimsonchr21_1.28.0_src_all.tar.gz"], "md5": "ee16a1f96afbdf1a4c48af6b306e9c34", "fn": "AshkenazimSonChr21_1.28.0.tar.gz"}, "prodata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ProData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/ProData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prodata/bioconductor-prodata_1.36.0_src_all.tar.gz"], "md5": "5d8ebe9020f1d291d0d1b0925dec4071", "fn": "ProData_1.36.0.tar.gz"}, "bcellviper-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bcellViper_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/bcellViper_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bcellviper/bioconductor-bcellviper_1.34.0_src_all.tar.gz"], "md5": "74d0f84db2df6f2bbbb5a16cd9061049", "fn": "bcellViper_1.34.0.tar.gz"}, "dexmadata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DExMAdata_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/DExMAdata_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dexmadata/bioconductor-dexmadata_1.6.0_src_all.tar.gz"], "md5": "f8dd918540d6f8b88e0e7f51bd910d43", "fn": "DExMAdata_1.6.0.tar.gz"}, "prostatecancervarambally-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerVarambally_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerVarambally_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancervarambally/bioconductor-prostatecancervarambally_1.26.0_src_all.tar.gz"], "md5": "fadc3efac8e793c4064082806e55c625", "fn": "prostateCancerVarambally_1.26.0.tar.gz"}, "leukemiaseset-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/leukemiasEset_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/leukemiasEset_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-leukemiaseset/bioconductor-leukemiaseset_1.34.0_src_all.tar.gz"], "md5": "0e10f12c15965946d76301d679fc183b", "fn": "leukemiasEset_1.34.0.tar.gz"}, "etec16s-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/etec16s_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/etec16s_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-etec16s/bioconductor-etec16s_1.26.0_src_all.tar.gz"], "md5": "c7ef06ca5897b3db7ed8b743b53a1613", "fn": "etec16s_1.26.0.tar.gz"}, "msd16s-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/msd16s_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/msd16s_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msd16s/bioconductor-msd16s_1.18.0_src_all.tar.gz"], "md5": "e8b256082028528dd6a35fc3c6036504", "fn": "msd16s_1.18.0.tar.gz"}, "crcl18-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CRCL18_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/CRCL18_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-crcl18/bioconductor-crcl18_1.18.0_src_all.tar.gz"], "md5": "c208b19693ac14dd5c0fc1bb7c795ebb", "fn": "CRCL18_1.18.0.tar.gz"}, "seqc-1.32.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/seqc_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/seqc_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seqc/bioconductor-seqc_1.32.0_src_all.tar.gz"], "md5": "e8a94a9cc8f335206faa617e4176436a", "fn": "seqc_1.32.0.tar.gz"}, "tweedeseqcountdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tweeDEseqCountData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/tweeDEseqCountData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tweedeseqcountdata/bioconductor-tweedeseqcountdata_1.36.0_src_all.tar.gz"], "md5": "7cea3549465861a3a20ca8bf1edfaa55", "fn": "tweeDEseqCountData_1.36.0.tar.gz"}, "nanotubes-1.14.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/nanotubes_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/nanotubes_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nanotubes/bioconductor-nanotubes_1.14.0_src_all.tar.gz"], "md5": "679ba9b18a0a9e94e59b4906e413f64a", "fn": "nanotubes_1.14.0.tar.gz"}, "spikein-1.40.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SpikeIn_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/SpikeIn_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spikein/bioconductor-spikein_1.40.0_src_all.tar.gz"], "md5": "0e06e055a0cfe9e65d47e16aef933da5", "fn": "SpikeIn_1.40.0.tar.gz"}, "ampaffyexample-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/AmpAffyExample_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/AmpAffyExample_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ampaffyexample/bioconductor-ampaffyexample_1.38.0_src_all.tar.gz"], "md5": "5065f84a743080500b5e277e39057589", "fn": "AmpAffyExample_1.38.0.tar.gz"}, "spikeinsubset-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SpikeInSubset_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/SpikeInSubset_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spikeinsubset/bioconductor-spikeinsubset_1.38.0_src_all.tar.gz"], "md5": "94d2a5b8e9b8de425be147b5d808c347", "fn": "SpikeInSubset_1.38.0.tar.gz"}, "chimphumanbraindata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ChimpHumanBrainData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/ChimpHumanBrainData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chimphumanbraindata/bioconductor-chimphumanbraindata_1.36.0_src_all.tar.gz"], "md5": "3ab20ab0915bb24937cb076ab3080bf1", "fn": "ChimpHumanBrainData_1.36.0.tar.gz"}, "rnaseqrdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RNASeqRData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/RNASeqRData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqrdata/bioconductor-rnaseqrdata_1.16.0_src_all.tar.gz"], "md5": "4e697b6df3ba50597ad22199b6e605a1", "fn": "RNASeqRData_1.16.0.tar.gz"}, "tofsimsdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tofsimsData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/tofsimsData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tofsimsdata/bioconductor-tofsimsdata_1.26.0_src_all.tar.gz"], "md5": "1fdfc2ba981f909a86b14bcc493cf72d", "fn": "tofsimsData_1.26.0.tar.gz"}, "confessdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CONFESSdata_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/CONFESSdata_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-confessdata/bioconductor-confessdata_1.26.0_src_all.tar.gz"], "md5": "a85678e18baf274aa1d65283ad8b466b", "fn": "CONFESSdata_1.26.0.tar.gz"}, "yeastexpdata-0.44.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/yeastExpData_0.44.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastExpData_0.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastexpdata/bioconductor-yeastexpdata_0.44.0_src_all.tar.gz"], "md5": "d78dff0ef4e93825abaf4facd0dab782", "fn": "yeastExpData_0.44.0.tar.gz"}, "snadata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SNAData_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/SNAData_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snadata/bioconductor-snadata_1.44.0_src_all.tar.gz"], "md5": "185268ec941d950ba443ad1eb8e3b79a", "fn": "SNAData_1.44.0.tar.gz"}, "dresscheck-0.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/dressCheck_0.36.0.tar.gz", "https://bioarchive.galaxyproject.org/dressCheck_0.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dresscheck/bioconductor-dresscheck_0.36.0_src_all.tar.gz"], "md5": "35bc43d9f5b50f73f5912d9ed690d4dc", "fn": "dressCheck_0.36.0.tar.gz"}, "bronchialil13-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bronchialIL13_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/bronchialIL13_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bronchialil13/bioconductor-bronchialil13_1.36.0_src_all.tar.gz"], "md5": "f4ba15910e2cd95375fb234719f0c934", "fn": "bronchialIL13_1.36.0.tar.gz"}, "aracne.networks-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/aracne.networks_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/aracne.networks_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-aracne.networks/bioconductor-aracne.networks_1.24.0_src_all.tar.gz"], "md5": "b2e24fdcf142f295008018f3dfb83671", "fn": "aracne.networks_1.24.0.tar.gz"}, "diggitdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/diggitdata_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/diggitdata_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-diggitdata/bioconductor-diggitdata_1.30.0_src_all.tar.gz"], "md5": "c26bf6e890e506ef06eb50d120206be4", "fn": "diggitdata_1.30.0.tar.gz"}, "fibroeset-1.40.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/fibroEset_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/fibroEset_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fibroeset/bioconductor-fibroeset_1.40.0_src_all.tar.gz"], "md5": "d22fcc8ca8c62393a36b1a2a32c3efc5", "fn": "fibroEset_1.40.0.tar.gz"}, "golubesets-1.40.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/golubEsets_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/golubEsets_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-golubesets/bioconductor-golubesets_1.40.0_src_all.tar.gz"], "md5": "7c73ba0df7a265861312be51106e4887", "fn": "golubEsets_1.40.0.tar.gz"}, "dyebiasexamples-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/dyebiasexamples_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/dyebiasexamples_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dyebiasexamples/bioconductor-dyebiasexamples_1.38.0_src_all.tar.gz"], "md5": "0fbb623580c0c5d2ec99edded90815d8", "fn": "dyebiasexamples_1.38.0.tar.gz"}, "gse62944-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSE62944_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE62944_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse62944/bioconductor-gse62944_1.26.0_src_all.tar.gz"], "md5": "940bca93dee5fe79b30078c3c56a70b1", "fn": "GSE62944_1.26.0.tar.gz"}, "gse103322-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSE103322_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE103322_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse103322/bioconductor-gse103322_1.4.0_src_all.tar.gz"], "md5": "c82c8a5416a388e02b5210e0ed07d714", "fn": "GSE103322_1.4.0.tar.gz"}, "affydata-1.46.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/affydata_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/affydata_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affydata/bioconductor-affydata_1.46.0_src_all.tar.gz"], "md5": "99b85f3a09dcc5219ce0575d29146e62", "fn": "affydata_1.46.0.tar.gz"}, "cll-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CLL_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/CLL_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cll/bioconductor-cll_1.38.0_src_all.tar.gz"], "md5": "6c0918e73bb883e4ed4ed2127d1b85d1", "fn": "CLL_1.38.0.tar.gz"}, "rcellminerdata-2.20.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/rcellminerData_2.20.0.tar.gz", "https://bioarchive.galaxyproject.org/rcellminerData_2.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rcellminerdata/bioconductor-rcellminerdata_2.20.0_src_all.tar.gz"], "md5": "631229ce32f7135d171858051326f585", "fn": "rcellminerData_2.20.0.tar.gz"}, "prostatecancertaylor-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerTaylor_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerTaylor_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancertaylor/bioconductor-prostatecancertaylor_1.26.0_src_all.tar.gz"], "md5": "dcdc31e127be410f341977446705400a", "fn": "prostateCancerTaylor_1.26.0.tar.gz"}, "iyer517-1.40.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Iyer517_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/Iyer517_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-iyer517/bioconductor-iyer517_1.40.0_src_all.tar.gz"], "md5": "6ecddbc0bdf2af4e67dd8797717bdd85", "fn": "Iyer517_1.40.0.tar.gz"}, "affycompdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/affycompData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/affycompData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affycompdata/bioconductor-affycompdata_1.36.0_src_all.tar.gz"], "md5": "212b33c1fff0a98e1a661c1047878414", "fn": "affycompData_1.36.0.tar.gz"}, "breastcancervdx-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breastCancerVDX_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerVDX_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancervdx/bioconductor-breastcancervdx_1.36.0_src_all.tar.gz"], "md5": "10700a3df43cfd233db74763f032b1c4", "fn": "breastCancerVDX_1.36.0.tar.gz"}, "yeastcc-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/yeastCC_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastCC_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastcc/bioconductor-yeastcc_1.38.0_src_all.tar.gz"], "md5": "5037b9364754099a0dc6889ac2ef4a71", "fn": "yeastCC_1.38.0.tar.gz"}, "tcgacrcmrna-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TCGAcrcmRNA_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAcrcmRNA_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmrna/bioconductor-tcgacrcmrna_1.18.0_src_all.tar.gz"], "md5": "593226dac7e784f82515e5bb9b97abc4", "fn": "TCGAcrcmRNA_1.18.0.tar.gz"}, "dlbcl-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DLBCL_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/DLBCL_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dlbcl/bioconductor-dlbcl_1.38.0_src_all.tar.gz"], "md5": "e305d0cd25dedefdceb6a93030d5ac1b", "fn": "DLBCL_1.38.0.tar.gz"}, "fletcher2013a-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Fletcher2013a_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/Fletcher2013a_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fletcher2013a/bioconductor-fletcher2013a_1.34.0_src_all.tar.gz"], "md5": "01222416b0fa4fc2cc4900e0470a55e7", "fn": "Fletcher2013a_1.34.0.tar.gz"}, "hapmapsnp6-1.40.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hapmapsnp6_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmapsnp6_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp6/bioconductor-hapmapsnp6_1.40.0_src_all.tar.gz"], "md5": "9027b12aaeecaad3af7cb2481ab743aa", "fn": "hapmapsnp6_1.40.0.tar.gz"}, "curatedovariandata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedOvarianData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedOvarianData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedovariandata/bioconductor-curatedovariandata_1.36.0_src_all.tar.gz"], "md5": "c652f6015514846aba9f70ab668dde4e", "fn": "curatedOvarianData_1.36.0.tar.gz"}, "fabiadata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/fabiaData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/fabiaData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fabiadata/bioconductor-fabiadata_1.36.0_src_all.tar.gz"], "md5": "063160c25a97654ba5788619287688f3", "fn": "fabiaData_1.36.0.tar.gz"}, "keggandmetacoredzpathwaysgeo-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/KEGGandMetacoreDzPathwaysGEO_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/KEGGandMetacoreDzPathwaysGEO_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-keggandmetacoredzpathwaysgeo/bioconductor-keggandmetacoredzpathwaysgeo_1.18.0_src_all.tar.gz"], "md5": "f8216537fcfc6a5325bd19a0f0565683", "fn": "KEGGandMetacoreDzPathwaysGEO_1.18.0.tar.gz"}, "lungexpression-0.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/lungExpression_0.36.0.tar.gz", "https://bioarchive.galaxyproject.org/lungExpression_0.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungexpression/bioconductor-lungexpression_0.36.0_src_all.tar.gz"], "md5": "f29b02561dd243247057c3e08e72bd61", "fn": "lungExpression_0.36.0.tar.gz"}, "curatedbladderdata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedBladderData_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedBladderData_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedbladderdata/bioconductor-curatedbladderdata_1.34.0_src_all.tar.gz"], "md5": "9134e331ab9ae88367f7d00c1fb9197e", "fn": "curatedBladderData_1.34.0.tar.gz"}, "gsbenchmark-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSBenchMark_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/GSBenchMark_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gsbenchmark/bioconductor-gsbenchmark_1.18.0_src_all.tar.gz"], "md5": "19d53c30ea84ba516c229aabbd017cf8", "fn": "GSBenchMark_1.18.0.tar.gz"}, "breastcancerunt-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breastCancerUNT_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerUNT_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancerunt/bioconductor-breastcancerunt_1.36.0_src_all.tar.gz"], "md5": "f826792fb58b77b54d354dfb1b65e8b6", "fn": "breastCancerUNT_1.36.0.tar.gz"}, "all-1.40.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ALL_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/ALL_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-all/bioconductor-all_1.40.0_src_all.tar.gz"], "md5": "be645648c96684d12d2b4c98414ea9f4", "fn": "ALL_1.40.0.tar.gz"}, "prostatecancercamcap-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerCamcap_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerCamcap_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancercamcap/bioconductor-prostatecancercamcap_1.26.0_src_all.tar.gz"], "md5": "d013ac0e533925df356a4f787adad19d", "fn": "prostateCancerCamcap_1.26.0.tar.gz"}, "cancerdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/cancerdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/cancerdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cancerdata/bioconductor-cancerdata_1.36.0_src_all.tar.gz"], "md5": "b36e604efdfb085c1224186d7613ab23", "fn": "cancerdata_1.36.0.tar.gz"}, "curatedbreastdata-2.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedBreastData_2.26.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedBreastData_2.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedbreastdata/bioconductor-curatedbreastdata_2.26.0_src_all.tar.gz"], "md5": "b6da1604aabe30fc9967e6c1f4fbb70c", "fn": "curatedBreastData_2.26.0.tar.gz"}, "kidpack-1.40.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/kidpack_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/kidpack_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-kidpack/bioconductor-kidpack_1.40.0_src_all.tar.gz"], "md5": "1daaab1926c04577373fd35c82a9fc3d", "fn": "kidpack_1.40.0.tar.gz"}, "antiprofilesdata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/antiProfilesData_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/antiProfilesData_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-antiprofilesdata/bioconductor-antiprofilesdata_1.34.0_src_all.tar.gz"], "md5": "85ea52e2db6bedb5435591ef6767688f", "fn": "antiProfilesData_1.34.0.tar.gz"}, "mircompdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/miRcompData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/miRcompData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mircompdata/bioconductor-mircompdata_1.28.0_src_all.tar.gz"], "md5": "709f0e5b4554054e0fd62ddf12dd36c8", "fn": "miRcompData_1.28.0.tar.gz"}, "keggdzpathwaysgeo-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/KEGGdzPathwaysGEO_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/KEGGdzPathwaysGEO_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-keggdzpathwaysgeo/bioconductor-keggdzpathwaysgeo_1.36.0_src_all.tar.gz"], "md5": "6e2cd9431413ef100802fd01510c37b1", "fn": "KEGGdzPathwaysGEO_1.36.0.tar.gz"}, "optimalflowdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/optimalFlowData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/optimalFlowData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-optimalflowdata/bioconductor-optimalflowdata_1.10.0_src_all.tar.gz"], "md5": "77b8d80f1869cb76d2a8a1e67dcad833", "fn": "optimalFlowData_1.10.0.tar.gz"}, "healthyflowdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/healthyFlowData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/healthyFlowData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-healthyflowdata/bioconductor-healthyflowdata_1.36.0_src_all.tar.gz"], "md5": "ec9097c2d66f5350c9a9b1a00c1a43bb", "fn": "healthyFlowData_1.36.0.tar.gz"}, "ruvnormalizedata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RUVnormalizeData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/RUVnormalizeData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ruvnormalizedata/bioconductor-ruvnormalizedata_1.18.0_src_all.tar.gz"], "md5": "e61afc462760972da9575dae8bd5e4b3", "fn": "RUVnormalizeData_1.18.0.tar.gz"}, "allmll-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ALLMLL_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ALLMLL_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-allmll/bioconductor-allmll_1.38.0_src_all.tar.gz"], "md5": "87f063db352317fbf932da06915713ce", "fn": "ALLMLL_1.38.0.tar.gz"}, "prostatecancergrasso-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerGrasso_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerGrasso_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancergrasso/bioconductor-prostatecancergrasso_1.26.0_src_all.tar.gz"], "md5": "74d9204eca94b1372cafce7257693fa0", "fn": "prostateCancerGrasso_1.26.0.tar.gz"}, "bladderbatch-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bladderbatch_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/bladderbatch_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bladderbatch/bioconductor-bladderbatch_1.36.0_src_all.tar.gz"], "md5": "c2ac3760859c2440c12b946bd56efd57", "fn": "bladderbatch_1.36.0.tar.gz"}, "hgu133plus2cellscore-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hgu133plus2CellScore_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2CellScore_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2cellscore/bioconductor-hgu133plus2cellscore_1.18.0_src_all.tar.gz"], "md5": "e3a02cfbd1737fbc1e5b16d1d9d80a0c", "fn": "hgu133plus2CellScore_1.18.0.tar.gz"}, "tcgacrcmirna-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TCGAcrcmiRNA_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAcrcmiRNA_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmirna/bioconductor-tcgacrcmirna_1.18.0_src_all.tar.gz"], "md5": "c3c5b823cbbe0190072c6df6f06cb48c", "fn": "TCGAcrcmiRNA_1.18.0.tar.gz"}, "gwasdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GWASdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/GWASdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gwasdata/bioconductor-gwasdata_1.36.0_src_all.tar.gz"], "md5": "d28dee85eeec53c8956d091cfab9bbe2", "fn": "GWASdata_1.36.0.tar.gz"}, "italicsdata-2.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ITALICSData_2.36.0.tar.gz", "https://bioarchive.galaxyproject.org/ITALICSData_2.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-italicsdata/bioconductor-italicsdata_2.36.0_src_all.tar.gz"], "md5": "b2c8e222e18f28e6864213d45f92d7dd", "fn": "ITALICSData_2.36.0.tar.gz"}, "colonca-1.40.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/colonCA_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/colonCA_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-colonca/bioconductor-colonca_1.40.0_src_all.tar.gz"], "md5": "945aaff5b3d9fd9acf23da95b63e3b8d", "fn": "colonCA_1.40.0.tar.gz"}, "diffloopdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/diffloopdata_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/diffloopdata_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-diffloopdata/bioconductor-diffloopdata_1.26.0_src_all.tar.gz"], "md5": "3fd01ba7a1156002aa91ba8a0e747ecd", "fn": "diffloopdata_1.26.0.tar.gz"}, "dapardata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DAPARdata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/DAPARdata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dapardata/bioconductor-dapardata_1.28.0_src_all.tar.gz"], "md5": "fd105b01cb3fa99df2fddfa77bcad220", "fn": "DAPARdata_1.28.0.tar.gz"}, "prolocdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pRolocdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/pRolocdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prolocdata/bioconductor-prolocdata_1.36.0_src_all.tar.gz"], "md5": "6ca8bc71627048afb1d53821ed862128", "fn": "pRolocdata_1.36.0.tar.gz"}, "prostatecancerstockholm-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerStockholm_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerStockholm_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancerstockholm/bioconductor-prostatecancerstockholm_1.26.0_src_all.tar.gz"], "md5": "b54919a22b169df14275783c9b3775dc", "fn": "prostateCancerStockholm_1.26.0.tar.gz"}, "gaschyhs-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/gaschYHS_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/gaschYHS_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gaschyhs/bioconductor-gaschyhs_1.36.0_src_all.tar.gz"], "md5": "2907cf19d0cde8e8a7ee78b6de7c918b", "fn": "gaschYHS_1.36.0.tar.gz"}, "dorothea-1.10.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/dorothea_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/dorothea_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dorothea/bioconductor-dorothea_1.10.0_src_all.tar.gz"], "md5": "4afa62297950e5c0c896e46b1a8bfc0c", "fn": "dorothea_1.10.0.tar.gz"}, "tbx20bamsubset-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TBX20BamSubset_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/TBX20BamSubset_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tbx20bamsubset/bioconductor-tbx20bamsubset_1.34.0_src_all.tar.gz"], "md5": "beec14bdc62fd30f6831f33995a07a0f", "fn": "TBX20BamSubset_1.34.0.tar.gz"}, "champdata-2.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ChAMPdata_2.30.0.tar.gz", "https://bioarchive.galaxyproject.org/ChAMPdata_2.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-champdata/bioconductor-champdata_2.30.0_src_all.tar.gz"], "md5": "6f08e2b95484bd4053d4041f9538a3c3", "fn": "ChAMPdata_2.30.0.tar.gz"}, "rnbeads.rn5-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.rn5_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.rn5_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.rn5/bioconductor-rnbeads.rn5_1.30.0_src_all.tar.gz"], "md5": "10e73b8362f2f61efd36f469c0b96307", "fn": "RnBeads.rn5_1.30.0.tar.gz"}, "rnbeads.hg38-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.hg38_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.hg38_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg38/bioconductor-rnbeads.hg38_1.30.0_src_all.tar.gz"], "md5": "fa0b5109400fe09174ae2ee83d7ffef5", "fn": "RnBeads.hg38_1.30.0.tar.gz"}, "elmer.data-2.22.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ELMER.data_2.22.0.tar.gz", "https://bioarchive.galaxyproject.org/ELMER.data_2.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-elmer.data/bioconductor-elmer.data_2.22.0_src_all.tar.gz"], "md5": "ee1a00414e8c68d3bae34732f7fb35d7", "fn": "ELMER.data_2.22.0.tar.gz"}, "cnvgsadata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/cnvGSAdata_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/cnvGSAdata_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cnvgsadata/bioconductor-cnvgsadata_1.34.0_src_all.tar.gz"], "md5": "191d2a67eeeb2ded97f7fb93c1bfebb3", "fn": "cnvGSAdata_1.34.0.tar.gz"}, "rnbeads.mm9-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.mm9_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.mm9_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm9/bioconductor-rnbeads.mm9_1.30.0_src_all.tar.gz"], "md5": "5700a0b7acd3dbb0cf1412209efd0748", "fn": "RnBeads.mm9_1.30.0.tar.gz"}, "wgsmapp-1.10.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/WGSmapp_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/WGSmapp_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wgsmapp/bioconductor-wgsmapp_1.10.0_src_all.tar.gz"], "md5": "ca0e7c51fcea48bd610fe7da33356358", "fn": "WGSmapp_1.10.0.tar.gz"}, "chic.data-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ChIC.data_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIC.data_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chic.data/bioconductor-chic.data_1.18.0_src_all.tar.gz"], "md5": "035e4ff664badd19dd6bdf7e3b06a7ee", "fn": "ChIC.data_1.18.0.tar.gz"}, "rrdpdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/rRDPData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rRDPData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rrdpdata/bioconductor-rrdpdata_1.18.0_src_all.tar.gz"], "md5": "8aee1a2c5cf2f30553b3365034464991", "fn": "rRDPData_1.18.0.tar.gz"}, "micrornaome-1.20.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/microRNAome_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/microRNAome_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-micrornaome/bioconductor-micrornaome_1.20.0_src_all.tar.gz"], "md5": "bee29d4d77292ca4e696e9eca2ad8b71", "fn": "microRNAome_1.20.0.tar.gz"}, "brgedata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/brgedata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/brgedata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-brgedata/bioconductor-brgedata_1.20.0_src_all.tar.gz"], "md5": "8469d2963cd1052846deafd0ef88d563", "fn": "brgedata_1.20.0.tar.gz"}, "tcgaworkflowdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TCGAWorkflowData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAWorkflowData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgaworkflowdata/bioconductor-tcgaworkflowdata_1.22.0_src_all.tar.gz"], "md5": "b1e8bedba993bd452a501024e45a781c", "fn": "TCGAWorkflowData_1.22.0.tar.gz"}, "gse13015-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSE13015_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE13015_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse13015/bioconductor-gse13015_1.6.0_src_all.tar.gz"], "md5": "5e2ac694eb8b344f8dbdc97813634da9", "fn": "GSE13015_1.6.0.tar.gz"}, "bioplex-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BioPlex_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BioPlex_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bioplex/bioconductor-bioplex_1.4.0_src_all.tar.gz"], "md5": "e5d585d15a7f5fad7aee1e383f7bd7f2", "fn": "BioPlex_1.4.0.tar.gz"}, "spqndata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/spqnData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/spqnData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spqndata/bioconductor-spqndata_1.10.0_src_all.tar.gz"], "md5": "4c711fc002eaedfab147d140eeb73a35", "fn": "spqnData_1.10.0.tar.gz"}, "chipxpressdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ChIPXpressData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIPXpressData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipxpressdata/bioconductor-chipxpressdata_1.36.0_src_all.tar.gz"], "md5": "996fa1dfb5d101324b2cf318390624e3", "fn": "ChIPXpressData_1.36.0.tar.gz"}, "fission-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/fission_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/fission_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fission/bioconductor-fission_1.18.0_src_all.tar.gz"], "md5": "713c9407157bb015952a5e93ae60a448", "fn": "fission_1.18.0.tar.gz"}, "airway-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/airway_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/airway_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-airway/bioconductor-airway_1.18.0_src_all.tar.gz"], "md5": "e59c875751a9b5c44735e15b9a608aa6", "fn": "airway_1.18.0.tar.gz"}, "rnbeads.mm10-2.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.mm10_2.6.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.mm10_2.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm10/bioconductor-rnbeads.mm10_2.6.0_src_all.tar.gz"], "md5": "1d4c16df423b733b817129aaf26b27e2", "fn": "RnBeads.mm10_2.6.0.tar.gz"}, "somaticcanceralterations-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SomaticCancerAlterations_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/SomaticCancerAlterations_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-somaticcanceralterations/bioconductor-somaticcanceralterations_1.34.0_src_all.tar.gz"], "md5": "71f9fe3f0f1336444d3fbdfca35a1a07", "fn": "SomaticCancerAlterations_1.34.0.tar.gz"}, "omicspcadata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/OMICsPCAdata_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/OMICsPCAdata_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-omicspcadata/bioconductor-omicspcadata_1.16.0_src_all.tar.gz"], "md5": "878ae360fd0161bc300191971e7d5719", "fn": "OMICsPCAdata_1.16.0.tar.gz"}, "curatedadiporna-1.14.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedAdipoRNA_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoRNA_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadiporna/bioconductor-curatedadiporna_1.14.0_src_all.tar.gz"], "md5": "6c0bba7a02d359a10da87484257b4c7d", "fn": "curatedAdipoRNA_1.14.0.tar.gz"}, "fletcher2013b-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Fletcher2013b_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/Fletcher2013b_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fletcher2013b/bioconductor-fletcher2013b_1.34.0_src_all.tar.gz"], "md5": "74a84a932937b9fcce493feb691027d9", "fn": "Fletcher2013b_1.34.0.tar.gz"}, "timecoursedata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/timecoursedata_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/timecoursedata_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-timecoursedata/bioconductor-timecoursedata_1.8.0_src_all.tar.gz"], "md5": "3fd49ff1e819a2b749570221ea53be2c", "fn": "timecoursedata_1.8.0.tar.gz"}, "parathyroidse-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/parathyroidSE_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/parathyroidSE_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-parathyroidse/bioconductor-parathyroidse_1.36.0_src_all.tar.gz"], "md5": "233d66f21aebbc76d7d59cb65611eded", "fn": "parathyroidSE_1.36.0.tar.gz"}, "faahko-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/faahKO_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/faahKO_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-faahko/bioconductor-faahko_1.38.0_src_all.tar.gz"], "md5": "284437fc4e501ec253af2c22ed3d78fd", "fn": "faahKO_1.38.0.tar.gz"}, "rnbeads.hg19-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.hg19_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.hg19_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg19/bioconductor-rnbeads.hg19_1.30.0_src_all.tar.gz"], "md5": "b99797bffecd852e17ec1222edafd119", "fn": "RnBeads.hg19_1.30.0.tar.gz"}, "easierdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/easierData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/easierData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-easierdata/bioconductor-easierdata_1.4.0_src_all.tar.gz"], "md5": "639d40a2ce48bb59f6cdfd216a1416c5", "fn": "easierData_1.4.0.tar.gz"}, "sampleclassifierdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/sampleClassifierData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/sampleClassifierData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sampleclassifierdata/bioconductor-sampleclassifierdata_1.22.0_src_all.tar.gz"], "md5": "72ef1fbd73285e12de97276a88da7054", "fn": "sampleClassifierData_1.22.0.tar.gz"}, "pepdat-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pepDat_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/pepDat_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pepdat/bioconductor-pepdat_1.18.0_src_all.tar.gz"], "md5": "06ee7d37dc24921207eb8875436e43b9", "fn": "pepDat_1.18.0.tar.gz"}, "plasfia-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/plasFIA_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/plasFIA_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-plasfia/bioconductor-plasfia_1.26.0_src_all.tar.gz"], "md5": "91d91048fbe49907f5f7f246dae14f76", "fn": "plasFIA_1.26.0.tar.gz"}, "pth2o2lipids-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PtH2O2lipids_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/PtH2O2lipids_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pth2o2lipids/bioconductor-pth2o2lipids_1.24.0_src_all.tar.gz"], "md5": "1954409b3f9a4bf1251d9dd2bc93ca10", "fn": "PtH2O2lipids_1.24.0.tar.gz"}, "tmexplorer-1.8.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TMExplorer_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/TMExplorer_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tmexplorer/bioconductor-tmexplorer_1.8.0_src_all.tar.gz"], "md5": "5783b4ef82629743d898b1ff4c979c7d", "fn": "TMExplorer_1.8.0.tar.gz"}, "cohcapanno-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/COHCAPanno_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/COHCAPanno_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cohcapanno/bioconductor-cohcapanno_1.34.0_src_all.tar.gz"], "md5": "649c6a3c7a5727bfeae51aa75ad77f41", "fn": "COHCAPanno_1.34.0.tar.gz"}, "seqcna.annot-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/seqCNA.annot_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/seqCNA.annot_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seqcna.annot/bioconductor-seqcna.annot_1.34.0_src_all.tar.gz"], "md5": "6e54a0ade57c4581d5114fedf8dd3396", "fn": "seqCNA.annot_1.34.0.tar.gz"}, "scatac.explorer-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/scATAC.Explorer_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/scATAC.Explorer_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scatac.explorer/bioconductor-scatac.explorer_1.4.0_src_all.tar.gz"], "md5": "5348b5d62c7488c3049f412bfbb50d77", "fn": "scATAC.Explorer_1.4.0.tar.gz"}, "qplexdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/qPLEXdata_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/qPLEXdata_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qplexdata/bioconductor-qplexdata_1.16.0_src_all.tar.gz"], "md5": "92a7193ff160f6dee4c782f2bb81ca28", "fn": "qPLEXdata_1.16.0.tar.gz"}, "topdownrdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/topdownrdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/topdownrdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-topdownrdata/bioconductor-topdownrdata_1.20.0_src_all.tar.gz"], "md5": "9eddeb9f975a402ecae76e095fafd8da", "fn": "topdownrdata_1.20.0.tar.gz"}, "systempiperdata-2.2.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/systemPipeRdata_2.2.0.tar.gz", "https://bioarchive.galaxyproject.org/systemPipeRdata_2.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-systempiperdata/bioconductor-systempiperdata_2.2.0_src_all.tar.gz"], "md5": "340237544f57849ccb438a3fd5364a44", "fn": "systemPipeRdata_2.2.0.tar.gz"}, "curatedtcgadata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedTCGAData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedTCGAData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedtcgadata/bioconductor-curatedtcgadata_1.20.0_src_all.tar.gz"], "md5": "636d48084b1ee6f77cd1711813ae0dd5", "fn": "curatedTCGAData_1.20.0.tar.gz"}, "scanmirdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/scanMiRData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/scanMiRData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scanmirdata/bioconductor-scanmirdata_1.4.0_src_all.tar.gz"], "md5": "d7db4456d1805894b1de51215348486a", "fn": "scanMiRData_1.4.0.tar.gz"}, "qdnaseq.mm10-1.28.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/QDNAseq.mm10_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/QDNAseq.mm10_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.mm10/bioconductor-qdnaseq.mm10_1.28.0_src_all.tar.gz"], "md5": "1b0602ec8a5b3288a467873f2c1ac7a4", "fn": "QDNAseq.mm10_1.28.0.tar.gz"}, "qdnaseq.hg19-1.28.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/QDNAseq.hg19_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/QDNAseq.hg19_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.hg19/bioconductor-qdnaseq.hg19_1.28.0_src_all.tar.gz"], "md5": "df5304204233e1516330f9a664c0104c", "fn": "QDNAseq.hg19_1.28.0.tar.gz"}, "tinesath1cdf-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tinesath1cdf_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/tinesath1cdf_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tinesath1cdf/bioconductor-tinesath1cdf_1.36.0_src_all.tar.gz"], "md5": "a8d2c187507c669f46b8be19d678eb67", "fn": "tinesath1cdf_1.36.0.tar.gz"}, "breakpointrdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breakpointRdata_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/breakpointRdata_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breakpointrdata/bioconductor-breakpointrdata_1.16.0_src_all.tar.gz"], "md5": "137555d6fa04dffd1eebf87e036b4af7", "fn": "breakpointRdata_1.16.0.tar.gz"}, "gcspikelite-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/gcspikelite_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/gcspikelite_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gcspikelite/bioconductor-gcspikelite_1.36.0_src_all.tar.gz"], "md5": "0de3fbbe9db74d87ded035be2d1f8228", "fn": "gcspikelite_1.36.0.tar.gz"}, "jaspar2014-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/JASPAR2014_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2014_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2014/bioconductor-jaspar2014_1.34.0_src_all.tar.gz"], "md5": "5f7f767133d76a93a61eb2912489ae3a", "fn": "JASPAR2014_1.34.0.tar.gz"}, "h5vcdata-2.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/h5vcData_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/h5vcData_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-h5vcdata/bioconductor-h5vcdata_2.18.0_src_all.tar.gz"], "md5": "75b05adbd56ac87bf65201a9884970bc", "fn": "h5vcData_2.18.0.tar.gz"}, "beadarrayusecases-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BeadArrayUseCases_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/BeadArrayUseCases_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadarrayusecases/bioconductor-beadarrayusecases_1.36.0_src_all.tar.gz"], "md5": "ac177e655ff3ae365bf609e87a89bfbf", "fn": "BeadArrayUseCases_1.36.0.tar.gz"}, "beadarrayexampledata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/beadarrayExampleData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/beadarrayExampleData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadarrayexampledata/bioconductor-beadarrayexampledata_1.36.0_src_all.tar.gz"], "md5": "916245ad90b7aeabbd906130a568f7e3", "fn": "beadarrayExampleData_1.36.0.tar.gz"}, "tinesath1probe-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tinesath1probe_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/tinesath1probe_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tinesath1probe/bioconductor-tinesath1probe_1.36.0_src_all.tar.gz"], "md5": "3960a52d4e105837ab0d1347f5e7f336", "fn": "tinesath1probe_1.36.0.tar.gz"}, "chromstardata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/chromstaRData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/chromstaRData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chromstardata/bioconductor-chromstardata_1.24.0_src_all.tar.gz"], "md5": "218e270508f4c9eba2b4d7aa86131bcd", "fn": "chromstaRData_1.24.0.tar.gz"}, "mmappr2data-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MMAPPR2data_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/MMAPPR2data_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mmappr2data/bioconductor-mmappr2data_1.12.0_src_all.tar.gz"], "md5": "ad6b9b86c75df44c183e780fa7595ed3", "fn": "MMAPPR2data_1.12.0.tar.gz"}, "lungcancerlines-0.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/LungCancerLines_0.36.0.tar.gz", "https://bioarchive.galaxyproject.org/LungCancerLines_0.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungcancerlines/bioconductor-lungcancerlines_0.36.0_src_all.tar.gz"], "md5": "554cc1a603908ab361042250e6ae3868", "fn": "LungCancerLines_0.36.0.tar.gz"}, "chipenrich.data-2.22.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/chipenrich.data_2.22.0.tar.gz", "https://bioarchive.galaxyproject.org/chipenrich.data_2.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipenrich.data/bioconductor-chipenrich.data_2.22.0_src_all.tar.gz"], "md5": "b91128ffbc4be5a65c2caaf4f19882b1", "fn": "chipenrich.data_2.22.0.tar.gz"}, "synapterdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/synapterdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/synapterdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-synapterdata/bioconductor-synapterdata_1.36.0_src_all.tar.gz"], "md5": "969a10ed0c07a03fe46c38cc2c956fc2", "fn": "synapterdata_1.36.0.tar.gz"}, "microbiomebenchmarkdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MicrobiomeBenchmarkData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/MicrobiomeBenchmarkData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-microbiomebenchmarkdata/bioconductor-microbiomebenchmarkdata_1.0.0_src_all.tar.gz"], "md5": "bc455e7cd9f3cb056814f2a753f65b94", "fn": "MicrobiomeBenchmarkData_1.0.0.tar.gz"}, "aneufinderdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/AneuFinderData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/AneuFinderData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-aneufinderdata/bioconductor-aneufinderdata_1.26.0_src_all.tar.gz"], "md5": "65b87d69f2a2ccbb5457fd0a27b09822", "fn": "AneuFinderData_1.26.0.tar.gz"}, "assessorfdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/AssessORFData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/AssessORFData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-assessorfdata/bioconductor-assessorfdata_1.16.0_src_all.tar.gz"], "md5": "a199c70bca649017ca435f4d36258fdf", "fn": "AssessORFData_1.16.0.tar.gz"}, "ccdata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ccdata_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/ccdata_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ccdata/bioconductor-ccdata_1.24.0_src_all.tar.gz"], "md5": "e57244249f51a54162f5348ba0efe9e0", "fn": "ccdata_1.24.0.tar.gz"}, "pwmenrich.mmusculus.background-4.32.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PWMEnrich.Mmusculus.background_4.32.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Mmusculus.background_4.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.mmusculus.background/bioconductor-pwmenrich.mmusculus.background_4.32.0_src_all.tar.gz"], "md5": "1d6ac0083eb2378cabf63fc538dfe21f", "fn": "PWMEnrich.Mmusculus.background_4.32.0.tar.gz"}, "pwmenrich.dmelanogaster.background-4.32.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PWMEnrich.Dmelanogaster.background_4.32.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Dmelanogaster.background_4.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.dmelanogaster.background/bioconductor-pwmenrich.dmelanogaster.background_4.32.0_src_all.tar.gz"], "md5": "9935dc953969ff87c508415da52da35d", "fn": "PWMEnrich.Dmelanogaster.background_4.32.0.tar.gz"}, "pwmenrich.hsapiens.background-4.32.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PWMEnrich.Hsapiens.background_4.32.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Hsapiens.background_4.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.hsapiens.background/bioconductor-pwmenrich.hsapiens.background_4.32.0_src_all.tar.gz"], "md5": "23c1d431adf2add64dd129e917fbc5d5", "fn": "PWMEnrich.Hsapiens.background_4.32.0.tar.gz"}, "harbchip-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/harbChIP_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/harbChIP_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harbchip/bioconductor-harbchip_1.36.0_src_all.tar.gz"], "md5": "31cfe29898d79222e934f537337ecf76", "fn": "harbChIP_1.36.0.tar.gz"}, "sbgnview.data-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SBGNview.data_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/SBGNview.data_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sbgnview.data/bioconductor-sbgnview.data_1.12.0_src_all.tar.gz"], "md5": "226d4bdd8b8a2997daefbab058f6f092", "fn": "SBGNview.data_1.12.0.tar.gz"}, "ecolileucine-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ecoliLeucine_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliLeucine_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolileucine/bioconductor-ecolileucine_1.38.0_src_all.tar.gz"], "md5": "6e4b82b2dacef5cd368225d1c107d284", "fn": "ecoliLeucine_1.38.0.tar.gz"}, "seq2pathway.data-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/seq2pathway.data_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/seq2pathway.data_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seq2pathway.data/bioconductor-seq2pathway.data_1.30.0_src_all.tar.gz"], "md5": "ba746fb92617526bc8a994e098f66a7a", "fn": "seq2pathway.data_1.30.0.tar.gz"}, "humanstemcell-0.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/humanStemCell_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/humanStemCell_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanstemcell/bioconductor-humanstemcell_0.38.0_src_all.tar.gz"], "md5": "a2d31e0d51d4a7ddcd83a9e082600e88", "fn": "humanStemCell_0.38.0.tar.gz"}, "rgmqllib-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RGMQLlib_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/RGMQLlib_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgmqllib/bioconductor-rgmqllib_1.18.0_src_all.tar.gz"], "md5": "35bbaa5548539a87d12762b8c1c09787", "fn": "RGMQLlib_1.18.0.tar.gz"}, "leebamviews-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/leeBamViews_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/leeBamViews_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-leebamviews/bioconductor-leebamviews_1.34.0_src_all.tar.gz"], "md5": "fc82a41bfe18f54301c3cc187a565791", "fn": "leeBamViews_1.34.0.tar.gz"}, "pd.atdschip.tiling-0.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pd.atdschip.tiling_0.36.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.atdschip.tiling_0.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.atdschip.tiling/bioconductor-pd.atdschip.tiling_0.36.0_src_all.tar.gz"], "md5": "33888a53bc08d7e87849b19e19666470", "fn": "pd.atdschip.tiling_0.36.0.tar.gz"}, "bsseqdata-0.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bsseqData_0.36.0.tar.gz", "https://bioarchive.galaxyproject.org/bsseqData_0.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsseqdata/bioconductor-bsseqdata_0.36.0_src_all.tar.gz"], "md5": "7a286e716d70a12e296366fa8b07e20a", "fn": "bsseqData_0.36.0.tar.gz"}, "genelendatabase-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/geneLenDataBase_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/geneLenDataBase_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genelendatabase/bioconductor-genelendatabase_1.34.0_src_all.tar.gz"], "md5": "120f51fec9f71e6235cf2ef93b3a72d0", "fn": "geneLenDataBase_1.34.0.tar.gz"}, "tartare-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tartare_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/tartare_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tartare/bioconductor-tartare_1.12.0_src_all.tar.gz"], "md5": "ec5808dde140133fd510bd6831db8a2c", "fn": "tartare_1.12.0.tar.gz"}, "metagxpancreas-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MetaGxPancreas_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxPancreas_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxpancreas/bioconductor-metagxpancreas_1.18.0_src_all.tar.gz"], "md5": "0bacc282e7bf79ae23f5ba32ecab3363", "fn": "MetaGxPancreas_1.18.0.tar.gz"}, "spatiallibd-1.10.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/spatialLIBD_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/spatialLIBD_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatiallibd/bioconductor-spatiallibd_1.10.0_src_all.tar.gz"], "md5": "f827024e685180a16db92e610ee0d363", "fn": "spatialLIBD_1.10.0.tar.gz"}, "obmiti-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ObMiTi_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/ObMiTi_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-obmiti/bioconductor-obmiti_1.6.0_src_all.tar.gz"], "md5": "5a4f4fe10d1de1c94b48fffa16628a1b", "fn": "ObMiTi_1.6.0.tar.gz"}, "benchmarkfdrdata2019-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/benchmarkfdrData2019_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/benchmarkfdrData2019_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-benchmarkfdrdata2019/bioconductor-benchmarkfdrdata2019_1.12.0_src_all.tar.gz"], "md5": "5ffdc59009556304b8400fe84b874502", "fn": "benchmarkfdrData2019_1.12.0.tar.gz"}, "depmap-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/depmap_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/depmap_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-depmap/bioconductor-depmap_1.12.0_src_all.tar.gz"], "md5": "24fcff71d7af3a08bf179f7c7d016024", "fn": "depmap_1.12.0.tar.gz"}, "hcadata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HCAData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/HCAData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcadata/bioconductor-hcadata_1.14.0_src_all.tar.gz"], "md5": "24545ef0089951b6b0e5676efac72769", "fn": "HCAData_1.14.0.tar.gz"}, "sesamedata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/sesameData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/sesameData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sesamedata/bioconductor-sesamedata_1.16.0_src_all.tar.gz"], "md5": "b9bac97226943d8d82d17bc1553906c0", "fn": "sesameData_1.16.0.tar.gz"}, "singlecellmultimodal-1.10.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SingleCellMultiModal_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/SingleCellMultiModal_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-singlecellmultimodal/bioconductor-singlecellmultimodal_1.10.0_src_all.tar.gz"], "md5": "899a93365e9bc4521ccb71e5d45cccf3", "fn": "SingleCellMultiModal_1.10.0.tar.gz"}, "weberdivechalcdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/WeberDivechaLCdata_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/WeberDivechaLCdata_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-weberdivechalcdata/bioconductor-weberdivechalcdata_1.0.0_src_all.tar.gz"], "md5": "7a07e9403d7fb8383eb515027adead4e", "fn": "WeberDivechaLCdata_1.0.0.tar.gz"}, "tenxpbmcdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TENxPBMCData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxPBMCData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxpbmcdata/bioconductor-tenxpbmcdata_1.16.0_src_all.tar.gz"], "md5": "bba27db0cbddf5e1f58af0dc5feeb620", "fn": "TENxPBMCData_1.16.0.tar.gz"}, "epimix.data-1.0.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/EpiMix.data_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/EpiMix.data_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epimix.data/bioconductor-epimix.data_1.0.0_src_all.tar.gz"], "md5": "60ad87849d55d75238373a37ce14b4c8", "fn": "EpiMix.data_1.0.0.tar.gz"}, "rlhub-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RLHub_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/RLHub_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rlhub/bioconductor-rlhub_1.4.0_src_all.tar.gz"], "md5": "27339bc3533469566a34d579b616c015", "fn": "RLHub_1.4.0.tar.gz"}, "clustifyrdatahub-1.8.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/clustifyrdatahub_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/clustifyrdatahub_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clustifyrdatahub/bioconductor-clustifyrdatahub_1.8.0_src_all.tar.gz"], "md5": "9aa7df7c9f7fe8af844e4107f99e33ba", "fn": "clustifyrdatahub_1.8.0.tar.gz"}, "metagxbreast-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MetaGxBreast_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxBreast_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxbreast/bioconductor-metagxbreast_1.18.0_src_all.tar.gz"], "md5": "6fabfc375d149b23ee17fdaa339af511", "fn": "MetaGxBreast_1.18.0.tar.gz"}, "stexampledata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/STexampleData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/STexampleData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stexampledata/bioconductor-stexampledata_1.6.0_src_all.tar.gz"], "md5": "ff9053a3878f326298e4eefb76bdc44f", "fn": "STexampleData_1.6.0.tar.gz"}, "xcoredata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/xcoredata_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/xcoredata_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xcoredata/bioconductor-xcoredata_1.2.0_src_all.tar.gz"], "md5": "39bcc78922bb568d8156fda441537da7", "fn": "xcoredata_1.2.0.tar.gz"}, "curatedadipochip-1.14.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedAdipoChIP_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoChIP_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadipochip/bioconductor-curatedadipochip_1.14.0_src_all.tar.gz"], "md5": "125847ddd3e81270c50e0671e8fd4486", "fn": "curatedAdipoChIP_1.14.0.tar.gz"}, "nxtirfdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NxtIRFdata_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/NxtIRFdata_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nxtirfdata/bioconductor-nxtirfdata_1.4.0_src_all.tar.gz"], "md5": "d56460a1a65820925d274a7823c41abc", "fn": "NxtIRFdata_1.4.0.tar.gz"}, "chipseqdbdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/chipseqDBData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/chipseqDBData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipseqdbdata/bioconductor-chipseqdbdata_1.14.0_src_all.tar.gz"], "md5": "f28cb4de67134b4e80eb66b89fe7a44f", "fn": "chipseqDBData_1.14.0.tar.gz"}, "cllmethylation-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CLLmethylation_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/CLLmethylation_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cllmethylation/bioconductor-cllmethylation_1.18.0_src_all.tar.gz"], "md5": "cae7673674386c34c755bb17c3162ba4", "fn": "CLLmethylation_1.18.0.tar.gz"}, "tabulamurissenisdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TabulaMurisSenisData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/TabulaMurisSenisData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tabulamurissenisdata/bioconductor-tabulamurissenisdata_1.4.0_src_all.tar.gz"], "md5": "41978233013567a8d648353435087d1c", "fn": "TabulaMurisSenisData_1.4.0.tar.gz"}, "bodymaprat-1.14.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bodymapRat_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/bodymapRat_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bodymaprat/bioconductor-bodymaprat_1.14.0_src_all.tar.gz"], "md5": "f162978264a598bc463fed6a7611f4b0", "fn": "bodymapRat_1.14.0.tar.gz"}, "tenxbusdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TENxBUSData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxBUSData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxbusdata/bioconductor-tenxbusdata_1.12.0_src_all.tar.gz"], "md5": "8c7b4e3fe4c5f01ef71474d68d5b838b", "fn": "TENxBUSData_1.12.0.tar.gz"}, "hicontactsdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HiContactsData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/HiContactsData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicontactsdata/bioconductor-hicontactsdata_1.0.0_src_all.tar.gz"], "md5": "b146c39234a88d86183b4ea618cec5a2", "fn": "HiContactsData_1.0.0.tar.gz"}, "hdcytodata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HDCytoData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/HDCytoData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hdcytodata/bioconductor-hdcytodata_1.18.0_src_all.tar.gz"], "md5": "5f84f520dc1b7e6a684191812fcda70d", "fn": "HDCytoData_1.18.0.tar.gz"}, "metagxovarian-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MetaGxOvarian_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxOvarian_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxovarian/bioconductor-metagxovarian_1.18.0_src_all.tar.gz"], "md5": "a3cb093003dc2fd2f26773ae40d8d042", "fn": "MetaGxOvarian_1.18.0.tar.gz"}, "tenxvisiumdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TENxVisiumData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxVisiumData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxvisiumdata/bioconductor-tenxvisiumdata_1.6.0_src_all.tar.gz"], "md5": "b5b1e60d7f71343347cb9eadbe03a2c7", "fn": "TENxVisiumData_1.6.0.tar.gz"}, "methylseqdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MethylSeqData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/MethylSeqData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylseqdata/bioconductor-methylseqdata_1.8.0_src_all.tar.gz"], "md5": "6da1465b035fb5a4bf9512ae63b8b010", "fn": "MethylSeqData_1.8.0.tar.gz"}, "duoclustering2018-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DuoClustering2018_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/DuoClustering2018_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-duoclustering2018/bioconductor-duoclustering2018_1.16.0_src_all.tar.gz"], "md5": "f9d216a1ad3bfb201a2e390be6607958", "fn": "DuoClustering2018_1.16.0.tar.gz"}, "vectrapolarisdata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/VectraPolarisData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/VectraPolarisData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vectrapolarisdata/bioconductor-vectrapolarisdata_1.2.0_src_all.tar.gz"], "md5": "bdf56c0103a2d0679d2bdad1458d6e9f", "fn": "VectraPolarisData_1.2.0.tar.gz"}, "muscdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/muscData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/muscData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-muscdata/bioconductor-muscdata_1.12.0_src_all.tar.gz"], "md5": "2797b6ad19757b5ba961c937b7ef81c2", "fn": "muscData_1.12.0.tar.gz"}, "biscuiteerdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/biscuiteerData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/biscuiteerData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biscuiteerdata/bioconductor-biscuiteerdata_1.12.0_src_all.tar.gz"], "md5": "471091bf8b2ea2ed0a5704099cdb917c", "fn": "biscuiteerData_1.12.0.tar.gz"}, "alpinedata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/alpineData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/alpineData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-alpinedata/bioconductor-alpinedata_1.24.0_src_all.tar.gz"], "md5": "9aa0c7d41dfac337b05643d1ecd240ac", "fn": "alpineData_1.24.0.tar.gz"}, "spatialdmelxsim-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/spatialDmelxsim_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/spatialDmelxsim_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatialdmelxsim/bioconductor-spatialdmelxsim_1.4.0_src_all.tar.gz"], "md5": "254b60e8277dd31c29a710df639c6735", "fn": "spatialDmelxsim_1.4.0.tar.gz"}, "microbiomedatasets-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/microbiomeDataSets_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/microbiomeDataSets_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-microbiomedatasets/bioconductor-microbiomedatasets_1.6.0_src_all.tar.gz"], "md5": "c8e86f82bc8021289697c4887cabf453", "fn": "microbiomeDataSets_1.6.0.tar.gz"}, "octad.db-1.0.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/octad.db_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/octad.db_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-octad.db/bioconductor-octad.db_1.0.0_src_all.tar.gz"], "md5": "0fcec8c696d79556a7f2842f9b4558c3", "fn": "octad.db_1.0.0.tar.gz"}, "simbenchdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SimBenchData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/SimBenchData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-simbenchdata/bioconductor-simbenchdata_1.6.0_src_all.tar.gz"], "md5": "e5e51bcdd298437970b25e7dc0a0248c", "fn": "SimBenchData_1.6.0.tar.gz"}, "mcsurvdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mcsurvdata_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/mcsurvdata_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcsurvdata/bioconductor-mcsurvdata_1.16.0_src_all.tar.gz"], "md5": "eca9c8d18ae70e750db5f0a75817c8b8", "fn": "mcsurvdata_1.16.0.tar.gz"}, "tabulamurisdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TabulaMurisData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/TabulaMurisData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tabulamurisdata/bioconductor-tabulamurisdata_1.16.0_src_all.tar.gz"], "md5": "1d058a947e31a9f0f512688fc5509123", "fn": "TabulaMurisData_1.16.0.tar.gz"}, "eatonetalchipseq-0.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/EatonEtAlChIPseq_0.36.0.tar.gz", "https://bioarchive.galaxyproject.org/EatonEtAlChIPseq_0.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-eatonetalchipseq/bioconductor-eatonetalchipseq_0.36.0_src_all.tar.gz"], "md5": "102627bebf2744cc6df1d2327dd5ea2b", "fn": "EatonEtAlChIPseq_0.36.0.tar.gz"}, "nanoporernaseq-1.8.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NanoporeRNASeq_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/NanoporeRNASeq_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nanoporernaseq/bioconductor-nanoporernaseq_1.8.0_src_all.tar.gz"], "md5": "15a5b4b0117895a16185138fb591bba1", "fn": "NanoporeRNASeq_1.8.0.tar.gz"}, "signaturesearchdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/signatureSearchData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/signatureSearchData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-signaturesearchdata/bioconductor-signaturesearchdata_1.12.0_src_all.tar.gz"], "md5": "2dc242150755289df7553bd18155ed2d", "fn": "signatureSearchData_1.12.0.tar.gz"}, "lrcelltypemarkers-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/LRcellTypeMarkers_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/LRcellTypeMarkers_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lrcelltypemarkers/bioconductor-lrcelltypemarkers_1.6.0_src_all.tar.gz"], "md5": "b1082f830487f6aea1ad61ca04439941", "fn": "LRcellTypeMarkers_1.6.0.tar.gz"}, "hd2013sgi-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HD2013SGI_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/HD2013SGI_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hd2013sgi/bioconductor-hd2013sgi_1.38.0_src_all.tar.gz"], "md5": "b830f54da9280d3265cb70439bf5509b", "fn": "HD2013SGI_1.38.0.tar.gz"}, "imcdatasets-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/imcdatasets_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/imcdatasets_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-imcdatasets/bioconductor-imcdatasets_1.6.0_src_all.tar.gz"], "md5": "d8f916015bd3a1cc73a032cea58c335b", "fn": "imcdatasets_1.6.0.tar.gz"}, "bioimagedbs-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BioImageDbs_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/BioImageDbs_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bioimagedbs/bioconductor-bioimagedbs_1.6.0_src_all.tar.gz"], "md5": "33b92f3c68fb5aea2be89bca3ccf96a0", "fn": "BioImageDbs_1.6.0.tar.gz"}, "cellmapperdata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CellMapperData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/CellMapperData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cellmapperdata/bioconductor-cellmapperdata_1.24.0_src_all.tar.gz"], "md5": "865be918d3840063b609c1dea125eff5", "fn": "CellMapperData_1.24.0.tar.gz"}, "nestlink-1.14.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NestLink_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/NestLink_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nestlink/bioconductor-nestlink_1.14.0_src_all.tar.gz"], "md5": "5708030d17d01f5425a3fcb11fe600ba", "fn": "NestLink_1.14.0.tar.gz"}, "mousethymusageing-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MouseThymusAgeing_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/MouseThymusAgeing_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousethymusageing/bioconductor-mousethymusageing_1.6.0_src_all.tar.gz"], "md5": "ac4f2dfcc69421a51efec159c9427be9", "fn": "MouseThymusAgeing_1.6.0.tar.gz"}, "curatedmetagenomicdata-3.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedMetagenomicData_3.6.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedMetagenomicData_3.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedmetagenomicdata/bioconductor-curatedmetagenomicdata_3.6.0_src_all.tar.gz"], "md5": "02a7793d82cb65070e5b584a5dd03ff5", "fn": "curatedMetagenomicData_3.6.0.tar.gz"}, "mousegastrulationdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MouseGastrulationData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/MouseGastrulationData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousegastrulationdata/bioconductor-mousegastrulationdata_1.12.0_src_all.tar.gz"], "md5": "1f765b74acf4bfbee594883bd83377f2", "fn": "MouseGastrulationData_1.12.0.tar.gz"}, "merfishdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MerfishData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/MerfishData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-merfishdata/bioconductor-merfishdata_1.0.0_src_all.tar.gz"], "md5": "c8ac8b1fd9929c51402fb96a71bf4575", "fn": "MerfishData_1.0.0.tar.gz"}, "tenxbraindata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TENxBrainData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxBrainData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxbraindata/bioconductor-tenxbraindata_1.18.0_src_all.tar.gz"], "md5": "ddbd8f75cedd811eb4b83ec7f546b030", "fn": "TENxBrainData_1.18.0.tar.gz"}, "precisetadhub-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/preciseTADhub_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/preciseTADhub_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-precisetadhub/bioconductor-precisetadhub_1.6.0_src_all.tar.gz"], "md5": "5015e2d8bf3f51cb3d5bf2cfaba6dafc", "fn": "preciseTADhub_1.6.0.tar.gz"}, "copyneutralima-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CopyNeutralIMA_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/CopyNeutralIMA_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copyneutralima/bioconductor-copyneutralima_1.16.0_src_all.tar.gz"], "md5": "617773122d70885b29ccb6653966b30f", "fn": "CopyNeutralIMA_1.16.0.tar.gz"}, "droplettestfiles-1.8.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DropletTestFiles_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/DropletTestFiles_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-droplettestfiles/bioconductor-droplettestfiles_1.8.0_src_all.tar.gz"], "md5": "79168f83ce62f2185f71ba18ab5a7964", "fn": "DropletTestFiles_1.8.0.tar.gz"}, "harmonizedtcgadata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HarmonizedTCGAData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/HarmonizedTCGAData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harmonizedtcgadata/bioconductor-harmonizedtcgadata_1.20.0_src_all.tar.gz"], "md5": "920ab9b499b3dc57ca8c0cb8bd467bfd", "fn": "HarmonizedTCGAData_1.20.0.tar.gz"}, "rnaseqsamplesizedata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnaSeqSampleSizeData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RnaSeqSampleSizeData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqsamplesizedata/bioconductor-rnaseqsamplesizedata_1.30.0_src_all.tar.gz"], "md5": "69c1fec1894e56123a22a7d7ea10d9f1", "fn": "RnaSeqSampleSizeData_1.30.0.tar.gz"}, "fis-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FIs_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/FIs_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fis/bioconductor-fis_1.26.0_src_all.tar.gz"], "md5": "a49a375be44f4204bacc4546ef96b7a4", "fn": "FIs_1.26.0.tar.gz"}, "curatedtbdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedTBData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedTBData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedtbdata/bioconductor-curatedtbdata_1.4.0_src_all.tar.gz"], "md5": "309ada4a3d184dea658e44e06e8701bb", "fn": "curatedTBData_1.4.0.tar.gz"}, "neve2006-0.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Neve2006_0.36.0.tar.gz", "https://bioarchive.galaxyproject.org/Neve2006_0.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-neve2006/bioconductor-neve2006_0.36.0_src_all.tar.gz"], "md5": "e2c9f599cc81edf29b57abca8d32b6df", "fn": "Neve2006_0.36.0.tar.gz"}, "sfedata-1.0.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SFEData_1.0.2.tar.gz", "https://bioarchive.galaxyproject.org/SFEData_1.0.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sfedata/bioconductor-sfedata_1.0.2_src_all.tar.gz"], "md5": "90d276f09864634d9f2a24c66502422f", "fn": "SFEData_1.0.2.tar.gz"}, "phyloprofiledata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PhyloProfileData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/PhyloProfileData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phyloprofiledata/bioconductor-phyloprofiledata_1.12.0_src_all.tar.gz"], "md5": "40f15a8b8cf7bdf63362ecb46e24a58e", "fn": "PhyloProfileData_1.12.0.tar.gz"}, "pumadata-2.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pumadata_2.34.0.tar.gz", "https://bioarchive.galaxyproject.org/pumadata_2.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pumadata/bioconductor-pumadata_2.34.0_src_all.tar.gz"], "md5": "8f235c83d650b417f51f04ee4b3ca8ff", "fn": "pumadata_2.34.0.tar.gz"}, "varianttoolsdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/VariantToolsData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/VariantToolsData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-varianttoolsdata/bioconductor-varianttoolsdata_1.22.0_src_all.tar.gz"], "md5": "90196a5cd2ee5495beefcd96f4a231f2", "fn": "VariantToolsData_1.22.0.tar.gz"}, "msigdb-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/msigdb_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/msigdb_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msigdb/bioconductor-msigdb_1.6.0_src_all.tar.gz"], "md5": "ec3e80d41507001ce38796c1bb259c67", "fn": "msigdb_1.6.0.tar.gz"}, "highlyreplicatedrnaseq-1.10.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HighlyReplicatedRNASeq_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/HighlyReplicatedRNASeq_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-highlyreplicatedrnaseq/bioconductor-highlyreplicatedrnaseq_1.10.0_src_all.tar.gz"], "md5": "1386bf86842d87e343a4986e29dc9238", "fn": "HighlyReplicatedRNASeq_1.10.0.tar.gz"}, "scpdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/scpdata_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/scpdata_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scpdata/bioconductor-scpdata_1.6.0_src_all.tar.gz"], "md5": "4405ffd758f7cf5ef1671491d9cb514c", "fn": "scpdata_1.6.0.tar.gz"}, "hmp16sdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HMP16SData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/HMP16SData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hmp16sdata/bioconductor-hmp16sdata_1.18.0_src_all.tar.gz"], "md5": "11ec6263ac5f902a6a977bed215a030d", "fn": "HMP16SData_1.18.0.tar.gz"}, "celldex-1.8.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/celldex_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/celldex_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celldex/bioconductor-celldex_1.8.0_src_all.tar.gz"], "md5": "1321a36f50ddcc03ebe4f35fadfac5a7", "fn": "celldex_1.8.0.tar.gz"}, "predasampledata-0.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PREDAsampledata_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/PREDAsampledata_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-predasampledata/bioconductor-predasampledata_0.38.0_src_all.tar.gz"], "md5": "03314ac823a61b73125499b5cf584fa4", "fn": "PREDAsampledata_0.38.0.tar.gz"}, "tuberculosis-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tuberculosis_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/tuberculosis_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tuberculosis/bioconductor-tuberculosis_1.4.0_src_all.tar.gz"], "md5": "cbd44f869e33ec7bfc2e21f514bd4023", "fn": "tuberculosis_1.4.0.tar.gz"}, "tcgabiolinksgui.data-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TCGAbiolinksGUI.data_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAbiolinksGUI.data_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgabiolinksgui.data/bioconductor-tcgabiolinksgui.data_1.18.0_src_all.tar.gz"], "md5": "97227503c90be6fcdd5a8ca243847846", "fn": "TCGAbiolinksGUI.data_1.18.0.tar.gz"}, "xhybcasneuf-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/XhybCasneuf_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/XhybCasneuf_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xhybcasneuf/bioconductor-xhybcasneuf_1.36.0_src_all.tar.gz"], "md5": "21e37d41f64496c8cef99d60c3d7f2d3", "fn": "XhybCasneuf_1.36.0.tar.gz"}, "gsvadata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSVAdata_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/GSVAdata_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gsvadata/bioconductor-gsvadata_1.34.0_src_all.tar.gz"], "md5": "022262252cfef2c2a5b7924c720d4d1b", "fn": "GSVAdata_1.34.0.tar.gz"}, "ritandata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RITANdata_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/RITANdata_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ritandata/bioconductor-ritandata_1.22.0_src_all.tar.gz"], "md5": "4c7706977f26087281e7b0956d7d19d5", "fn": "RITANdata_1.22.0.tar.gz"}, "listeretalbsseq-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ListerEtAlBSseq_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/ListerEtAlBSseq_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-listeretalbsseq/bioconductor-listeretalbsseq_1.30.0_src_all.tar.gz"], "md5": "34e0e425d704f29b62840aeb318043a3", "fn": "ListerEtAlBSseq_1.30.0.tar.gz"}, "nullrangesdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/nullrangesData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/nullrangesData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nullrangesdata/bioconductor-nullrangesdata_1.4.0_src_all.tar.gz"], "md5": "39ebab6ebac4b73162925f2c6f5c654a", "fn": "nullrangesData_1.4.0.tar.gz"}, "rnamodr.data-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RNAmodR.Data_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAmodR.Data_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnamodr.data/bioconductor-rnamodr.data_1.12.0_src_all.tar.gz"], "md5": "f15f9939776393d3dfc6ea30d47590c0", "fn": "RNAmodR.Data_1.12.0.tar.gz"}, "methylclockdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/methylclockData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/methylclockData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylclockdata/bioconductor-methylclockdata_1.6.0_src_all.tar.gz"], "md5": "ab12ee063e08bd1109ee9400f63cf57a", "fn": "methylclockData_1.6.0.tar.gz"}, "genomicdistributionsdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GenomicDistributionsData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/GenomicDistributionsData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomicdistributionsdata/bioconductor-genomicdistributionsdata_1.6.0_src_all.tar.gz"], "md5": "b66482cc3c1cfddbb10922a1e8b38d3e", "fn": "GenomicDistributionsData_1.6.0.tar.gz"}, "singlemoleculefootprintingdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SingleMoleculeFootprintingData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/SingleMoleculeFootprintingData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-singlemoleculefootprintingdata/bioconductor-singlemoleculefootprintingdata_1.6.0_src_all.tar.gz"], "md5": "f7a07857cb19ab6f0e2eee8ff913b479", "fn": "SingleMoleculeFootprintingData_1.6.0.tar.gz"}, "scrnaseq-2.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/scRNAseq_2.12.0.tar.gz", "https://bioarchive.galaxyproject.org/scRNAseq_2.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scrnaseq/bioconductor-scrnaseq_2.12.0_src_all.tar.gz"], "md5": "54ced014f88eda70982b052a505fb864", "fn": "scRNAseq_2.12.0.tar.gz"}, "copyhelper-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CopyhelpeR_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/CopyhelpeR_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copyhelper/bioconductor-copyhelper_1.30.0_src_all.tar.gz"], "md5": "2be26e5fb90270541b426a5b2baf1824", "fn": "CopyhelpeR_1.30.0.tar.gz"}, "healthycontrolspresencechecker-1.2.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/healthyControlsPresenceChecker_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/healthyControlsPresenceChecker_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-healthycontrolspresencechecker/bioconductor-healthycontrolspresencechecker_1.2.0_src_all.tar.gz"], "md5": "8789ca7539d9cf83ce2db9fe89a6fb3e", "fn": "healthyControlsPresenceChecker_1.2.0.tar.gz"}, "emtdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/emtdata_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/emtdata_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-emtdata/bioconductor-emtdata_1.6.0_src_all.tar.gz"], "md5": "eb00c34c239c9909c2e09733600c092d", "fn": "emtdata_1.6.0.tar.gz"}, "ewcedata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ewceData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/ewceData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ewcedata/bioconductor-ewcedata_1.6.0_src_all.tar.gz"], "md5": "4c11a9afee7da412aab59546108b3dfb", "fn": "ewceData_1.6.0.tar.gz"}, "humanaffydata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HumanAffyData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/HumanAffyData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanaffydata/bioconductor-humanaffydata_1.24.0_src_all.tar.gz"], "md5": "93c6073e8e2bcce485f656e42c646fc3", "fn": "HumanAffyData_1.24.0.tar.gz"}, "restfulsedata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/restfulSEData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/restfulSEData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-restfulsedata/bioconductor-restfulsedata_1.20.0_src_all.tar.gz"], "md5": "184981fb35aab130042a69a96cd3b21c", "fn": "restfulSEData_1.20.0.tar.gz"}, "crisprscoredata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/crisprScoreData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/crisprScoreData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-crisprscoredata/bioconductor-crisprscoredata_1.2.0_src_all.tar.gz"], "md5": "3c91f9e9e2a330c08519fa5880cb28dd", "fn": "crisprScoreData_1.2.0.tar.gz"}, "cctutorial-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ccTutorial_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/ccTutorial_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cctutorial/bioconductor-cctutorial_1.36.0_src_all.tar.gz"], "md5": "08916c2f651fcf53b63590aa5dbc0db2", "fn": "ccTutorial_1.36.0.tar.gz"}, "hiiragi2013-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Hiiragi2013_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/Hiiragi2013_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hiiragi2013/bioconductor-hiiragi2013_1.34.0_src_all.tar.gz"], "md5": "739f5caa57eac27fdab269de30eccb33", "fn": "Hiiragi2013_1.34.0.tar.gz"}, "davidtiling-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/davidTiling_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/davidTiling_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-davidtiling/bioconductor-davidtiling_1.38.0_src_all.tar.gz"], "md5": "62cb2d1c5d877a095f6c25962b165262", "fn": "davidTiling_1.38.0.tar.gz"}, "mcseadata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mCSEAdata_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mCSEAdata_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcseadata/bioconductor-mcseadata_1.18.0_src_all.tar.gz"], "md5": "545b303774337c2286a8226dc2147677", "fn": "mCSEAdata_1.18.0.tar.gz"}, "adductdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/adductData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/adductData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-adductdata/bioconductor-adductdata_1.14.0_src_all.tar.gz"], "md5": "7a983571463b4566782cbfe478ea93a9", "fn": "adductData_1.14.0.tar.gz"}, "scatedata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SCATEData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/SCATEData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scatedata/bioconductor-scatedata_1.8.0_src_all.tar.gz"], "md5": "f6f4b950d1639c5ae565a71f3d7491fb", "fn": "SCATEData_1.8.0.tar.gz"}, "hmp2data-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HMP2Data_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/HMP2Data_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hmp2data/bioconductor-hmp2data_1.12.0_src_all.tar.gz"], "md5": "2945af451892098684b5fb0bdace152d", "fn": "HMP2Data_1.12.0.tar.gz"}, "rrbsdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RRBSdata_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/RRBSdata_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rrbsdata/bioconductor-rrbsdata_1.18.0_src_all.tar.gz"], "md5": "c4f7461c8314422810b456ff26ed0ff9", "fn": "RRBSdata_1.18.0.tar.gz"}, "pwrewas.data-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pwrEWAS.data_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pwrEWAS.data_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwrewas.data/bioconductor-pwrewas.data_1.12.0_src_all.tar.gz"], "md5": "2e60d579c30b55eb5357b59233b391a2", "fn": "pwrEWAS.data_1.12.0.tar.gz"}, "fieldeffectcrc-1.8.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FieldEffectCrc_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/FieldEffectCrc_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fieldeffectcrc/bioconductor-fieldeffectcrc_1.8.0_src_all.tar.gz"], "md5": "0be77552ce25ac628446391b1292decd", "fn": "FieldEffectCrc_1.8.0.tar.gz"}, "jaspar2016-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/JASPAR2016_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2016_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2016/bioconductor-jaspar2016_1.26.0_src_all.tar.gz"], "md5": "28e8034505a668913cf0bf50ae8f3331", "fn": "JASPAR2016_1.26.0.tar.gz"}, "bloodcancermultiomics2017-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BloodCancerMultiOmics2017_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/BloodCancerMultiOmics2017_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bloodcancermultiomics2017/bioconductor-bloodcancermultiomics2017_1.18.0_src_all.tar.gz"], "md5": "09621b2d3d7fec1f4f10d8227b0ec6ba", "fn": "BloodCancerMultiOmics2017_1.18.0.tar.gz"}, "netactivitydata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NetActivityData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/NetActivityData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-netactivitydata/bioconductor-netactivitydata_1.0.0_src_all.tar.gz"], "md5": "bcbd4a5622e1029caeb110195f72cc7d", "fn": "NetActivityData_1.0.0.tar.gz"}, "rnainteractmapk-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RNAinteractMAPK_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAinteractMAPK_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnainteractmapk/bioconductor-rnainteractmapk_1.36.0_src_all.tar.gz"], "md5": "7d626f19929cda149d56b340d3249942", "fn": "RNAinteractMAPK_1.36.0.tar.gz"}, "pasilla-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pasilla_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/pasilla_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasilla/bioconductor-pasilla_1.26.0_src_all.tar.gz"], "md5": "8a54d964fa80a98285d26d9f39e92159", "fn": "pasilla_1.26.0.tar.gz"}, "beadsorted.saliva.epic-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BeadSorted.Saliva.EPIC_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/BeadSorted.Saliva.EPIC_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadsorted.saliva.epic/bioconductor-beadsorted.saliva.epic_1.6.0_src_all.tar.gz"], "md5": "0b80c17ee21a3d2b7c7113ea1bde020c", "fn": "BeadSorted.Saliva.EPIC_1.6.0.tar.gz"}, "minfidataepic-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/minfiDataEPIC_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/minfiDataEPIC_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minfidataepic/bioconductor-minfidataepic_1.24.0_src_all.tar.gz"], "md5": "0af85d8d67f8d12264f944a27e868659", "fn": "minfiDataEPIC_1.24.0.tar.gz"}, "flowsorted.cordbloodnorway.450k-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.CordBloodNorway.450k_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodNorway.450k_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodnorway.450k/bioconductor-flowsorted.cordbloodnorway.450k_1.24.0_src_all.tar.gz"], "md5": "eaedd2ac35dfbf5363b198fbd89340ac", "fn": "FlowSorted.CordBloodNorway.450k_1.24.0.tar.gz"}, "flowsorted.cordblood.450k-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.CordBlood.450k_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBlood.450k_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordblood.450k/bioconductor-flowsorted.cordblood.450k_1.26.0_src_all.tar.gz"], "md5": "3634ebac8c3ea0ea40eaf413c015ce51", "fn": "FlowSorted.CordBlood.450k_1.26.0.tar.gz"}, "dmrcatedata-2.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DMRcatedata_2.16.0.tar.gz", "https://bioarchive.galaxyproject.org/DMRcatedata_2.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dmrcatedata/bioconductor-dmrcatedata_2.16.0_src_all.tar.gz"], "md5": "f3a23f5f3f4a10829006493ecfab3fa4", "fn": "DMRcatedata_2.16.0.tar.gz"}, "flowsorted.cordbloodcombined.450k-1.14.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.CordBloodCombined.450k_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodCombined.450k_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodcombined.450k/bioconductor-flowsorted.cordbloodcombined.450k_1.14.0_src_all.tar.gz"], "md5": "449c6036f08827fa2c72481bcb5b8974", "fn": "FlowSorted.CordBloodCombined.450k_1.14.0.tar.gz"}, "lungcanceracvssccgeo-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/LungCancerACvsSCCGEO_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/LungCancerACvsSCCGEO_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungcanceracvssccgeo/bioconductor-lungcanceracvssccgeo_1.34.0_src_all.tar.gz"], "md5": "1d7786eec9ef4a8c41ab26aaf7280241", "fn": "LungCancerACvsSCCGEO_1.34.0.tar.gz"}, "cmap2data-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/cMap2data_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/cMap2data_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cmap2data/bioconductor-cmap2data_1.34.0_src_all.tar.gz"], "md5": "c04b32c3d36cf3ff94dd074b9cee35b4", "fn": "cMap2data_1.34.0.tar.gz"}, "kodata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/KOdata_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/KOdata_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-kodata/bioconductor-kodata_1.24.0_src_all.tar.gz"], "md5": "56dcc1dbb530d00179ddc5494dbd92a3", "fn": "KOdata_1.24.0.tar.gz"}, "flowsorted.dlpfc.450k-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.DLPFC.450k_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.DLPFC.450k_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.dlpfc.450k/bioconductor-flowsorted.dlpfc.450k_1.34.0_src_all.tar.gz"], "md5": "fbf4414d97fcc8f2a67fd7900aecd4ca", "fn": "FlowSorted.DLPFC.450k_1.34.0.tar.gz"}, "flowsorted.blood.epic-2.2.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.Blood.EPIC_2.2.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.Blood.EPIC_2.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.epic/bioconductor-flowsorted.blood.epic_2.2.0_src_all.tar.gz"], "md5": "e386c74c9b0168a5891bec4445799438", "fn": "FlowSorted.Blood.EPIC_2.2.0.tar.gz"}, "flowsorted.blood.450k-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.Blood.450k_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.Blood.450k_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.450k/bioconductor-flowsorted.blood.450k_1.36.0_src_all.tar.gz"], "md5": "49bce6f7d31d9a37fef658108eefd5a4", "fn": "FlowSorted.Blood.450k_1.36.0.tar.gz"}, "desousa2013-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DeSousa2013_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/DeSousa2013_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-desousa2013/bioconductor-desousa2013_1.34.0_src_all.tar.gz"], "md5": "8fbba6b634001af0bcce09be50b3c457", "fn": "DeSousa2013_1.34.0.tar.gz"}, "methylaiddata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MethylAidData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/MethylAidData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylaiddata/bioconductor-methylaiddata_1.30.0_src_all.tar.gz"], "md5": "15f494b47ba64df59d4cb88eff250424", "fn": "MethylAidData_1.30.0.tar.gz"}, "minfidata-0.44.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/minfiData_0.44.0.tar.gz", "https://bioarchive.galaxyproject.org/minfiData_0.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minfidata/bioconductor-minfidata_0.44.0_src_all.tar.gz"], "md5": "988f1ac63c897662192cee4909fc5d70", "fn": "minfiData_0.44.0.tar.gz"}, "ihwpaper-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/IHWpaper_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/IHWpaper_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ihwpaper/bioconductor-ihwpaper_1.26.0_src_all.tar.gz"], "md5": "6eabaa4575f0c53258cf49caf497d708", "fn": "IHWpaper_1.26.0.tar.gz"}, "ffpeexampledata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ffpeExampleData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/ffpeExampleData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ffpeexampledata/bioconductor-ffpeexampledata_1.36.0_src_all.tar.gz"], "md5": "531c091065f07e82304bc9468cdd20cd", "fn": "ffpeExampleData_1.36.0.tar.gz"}, "lumibarnes-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/lumiBarnes_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/lumiBarnes_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumibarnes/bioconductor-lumibarnes_1.38.0_src_all.tar.gz"], "md5": "a46084b74e3fff1b80b4ce3f10f76ef7", "fn": "lumiBarnes_1.38.0.tar.gz"}, "maqcsubset-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MAQCsubset_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/MAQCsubset_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcsubset/bioconductor-maqcsubset_1.36.0_src_all.tar.gz"], "md5": "1fe763b7722d1cfaa2fecd08dae9f36e", "fn": "MAQCsubset_1.36.0.tar.gz"}, "egseadata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/EGSEAdata_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/EGSEAdata_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-egseadata/bioconductor-egseadata_1.26.0_src_all.tar.gz"], "md5": "f76bea52e1029aa018475868d499df0b", "fn": "EGSEAdata_1.26.0.tar.gz"}, "drugvsdiseasedata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DrugVsDiseasedata_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/DrugVsDiseasedata_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drugvsdiseasedata/bioconductor-drugvsdiseasedata_1.34.0_src_all.tar.gz"], "md5": "6e318b03d2fbe45a7b0a9247b23f0eb0", "fn": "DrugVsDiseasedata_1.34.0.tar.gz"}, "epimutacionsdata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/epimutacionsData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/epimutacionsData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epimutacionsdata/bioconductor-epimutacionsdata_1.2.0_src_all.tar.gz"], "md5": "02cd283b2fe78a29cdf1fc96f7c20a6c", "fn": "epimutacionsData_1.2.0.tar.gz"}, "mvoutdata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mvoutData_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/mvoutData_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mvoutdata/bioconductor-mvoutdata_1.34.0_src_all.tar.gz"], "md5": "3199373f2a97a6765f10198b3d9db7d5", "fn": "mvoutData_1.34.0.tar.gz"}, "maqcsubsetilm-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MAQCsubsetILM_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/MAQCsubsetILM_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcsubsetilm/bioconductor-maqcsubsetilm_1.36.0_src_all.tar.gz"], "md5": "c1e92632336069ac9764b52dbbd87e2a", "fn": "MAQCsubsetILM_1.36.0.tar.gz"}, "illumina450probevariants.db-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Illumina450ProbeVariants.db_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/Illumina450ProbeVariants.db_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illumina450probevariants.db/bioconductor-illumina450probevariants.db_1.34.0_src_all.tar.gz"], "md5": "228c2e089c604bd2c615c0ecb676ccd3", "fn": "Illumina450ProbeVariants.db_1.34.0.tar.gz"}, "hsmmsinglecell-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HSMMSingleCell_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/HSMMSingleCell_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hsmmsinglecell/bioconductor-hsmmsinglecell_1.18.0_src_all.tar.gz"], "md5": "030d50f78cca5810f70ab930e091ed87", "fn": "HSMMSingleCell_1.18.0.tar.gz"}, "mspuritydata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/msPurityData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/msPurityData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mspuritydata/bioconductor-mspuritydata_1.26.0_src_all.tar.gz"], "md5": "729d4691c7db6cb9fc7b880591b9d6e9", "fn": "msPurityData_1.26.0.tar.gz"}, "bsgenome.hsapiens.ucsc.hg38-1.4.5": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.5.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg38_1.4.5.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38/bioconductor-bsgenome.hsapiens.ucsc.hg38_1.4.5_src_all.tar.gz"], "md5": "b2e670c27944eed77fbe9a9b55be40d2", "fn": "BSgenome.Hsapiens.UCSC.hg38_1.4.5.tar.gz"}, "ahlrbasedbs-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/AHLRBaseDbs_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/AHLRBaseDbs_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahlrbasedbs/bioconductor-ahlrbasedbs_1.6.0_src_all.tar.gz"], "md5": "1427836afe85a5b580f7277e7d2c08ca", "fn": "AHLRBaseDbs_1.6.0.tar.gz"}, "ahmeshdbs-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/AHMeSHDbs_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/AHMeSHDbs_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahmeshdbs/bioconductor-ahmeshdbs_1.6.0_src_all.tar.gz"], "md5": "7fe9c77aaff9175d842cb4f4b9313360", "fn": "AHMeSHDbs_1.6.0.tar.gz"}, "ahpubmeddbs-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/AHPubMedDbs_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/AHPubMedDbs_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahpubmeddbs/bioconductor-ahpubmeddbs_1.6.0_src_all.tar.gz"], "md5": "91815a0aa91e19d171fad3b116d02eed", "fn": "AHPubMedDbs_1.6.0.tar.gz"}, "anopheles.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/anopheles.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/anopheles.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-anopheles.db0/bioconductor-anopheles.db0_3.17.0_src_all.tar.gz"], "md5": "d26110289d806c4d1bd6e039c5873100", "fn": "anopheles.db0_3.17.0.tar.gz"}, "arabidopsis.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/arabidopsis.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/arabidopsis.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-arabidopsis.db0/bioconductor-arabidopsis.db0_3.17.0_src_all.tar.gz"], "md5": "773844428cd90716c8e32f942328618d", "fn": "arabidopsis.db0_3.17.0.tar.gz"}, "bovine.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/bovine.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/bovine.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bovine.db0/bioconductor-bovine.db0_3.17.0_src_all.tar.gz"], "md5": "1e268d93f6206875bd73ad2caae53f27", "fn": "bovine.db0_3.17.0.tar.gz"}, "bsgenome.hsapiens.ucsc.hg38.masked-1.4.5": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38.masked_1.4.5.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg38.masked_1.4.5.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked_1.4.5_src_all.tar.gz"], "md5": "7570dd1b4f013b3c6acecd68602180b4", "fn": "BSgenome.Hsapiens.UCSC.hg38.masked_1.4.5.tar.gz"}, "bsgenome.hsapiens.ucsc.hs1-1.4.4": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hs1_1.4.4.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hs1_1.4.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hs1/bioconductor-bsgenome.hsapiens.ucsc.hs1_1.4.4_src_all.tar.gz"], "md5": "5812c5670f51a5c58a9da9e042e7e440", "fn": "BSgenome.Hsapiens.UCSC.hs1_1.4.4.tar.gz"}, "canine.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/canine.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/canine.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canine.db0/bioconductor-canine.db0_3.17.0_src_all.tar.gz"], "md5": "da4af1b026fe2775a020addd13920f71", "fn": "canine.db0_3.17.0.tar.gz"}, "chicken.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/chicken.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/chicken.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chicken.db0/bioconductor-chicken.db0_3.17.0_src_all.tar.gz"], "md5": "bfacdb3f67e914c4d364a512620ec50d", "fn": "chicken.db0_3.17.0.tar.gz"}, "chimp.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/chimp.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/chimp.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chimp.db0/bioconductor-chimp.db0_3.17.0_src_all.tar.gz"], "md5": "0a1382e14c2ace3a9cdc3daf7d7e4013", "fn": "chimp.db0_3.17.0.tar.gz"}, "ctcf-0.99.11": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/CTCF_0.99.11.tar.gz", "https://bioarchive.galaxyproject.org/CTCF_0.99.11.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ctcf/bioconductor-ctcf_0.99.11_src_all.tar.gz"], "md5": "5ec44245864395de390e68fa56e465af", "fn": "CTCF_0.99.11.tar.gz"}, "ecolik12.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/ecoliK12.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliK12.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolik12.db0/bioconductor-ecolik12.db0_3.17.0_src_all.tar.gz"], "md5": "acf1faa22de4e8b535baf0d7403acbe0", "fn": "ecoliK12.db0_3.17.0.tar.gz"}, "ecolisakai.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/ecoliSakai.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliSakai.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolisakai.db0/bioconductor-ecolisakai.db0_3.17.0_src_all.tar.gz"], "md5": "2f49e4fe2806f14f78db0de22d37a7e7", "fn": "ecoliSakai.db0_3.17.0.tar.gz"}, "excluderanges-0.99.8": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/excluderanges_0.99.8.tar.gz", "https://bioarchive.galaxyproject.org/excluderanges_0.99.8.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-excluderanges/bioconductor-excluderanges_0.99.8_src_all.tar.gz"], "md5": "2ec19df8a51df1900a339f7f505cd5fa", "fn": "excluderanges_0.99.8.tar.gz"}, "fly.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/fly.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/fly.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fly.db0/bioconductor-fly.db0_3.17.0_src_all.tar.gz"], "md5": "04b3d22c5825c9a31f5253746df5c4e0", "fn": "fly.db0_3.17.0.tar.gz"}, "genomeinfodbdata-1.2.10": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/GenomeInfoDbData_1.2.10.tar.gz", "https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.10.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.10_src_all.tar.gz"], "md5": "ebd78c10d672c0eb6c893d6135bdeca9", "fn": "GenomeInfoDbData_1.2.10.tar.gz"}, "go.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/GO.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/GO.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-go.db/bioconductor-go.db_3.17.0_src_all.tar.gz"], "md5": "f278f3cb015e04ead1cc3d982a3fd1b3", "fn": "GO.db_3.17.0.tar.gz"}, "human.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/human.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/human.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human.db0/bioconductor-human.db0_3.17.0_src_all.tar.gz"], "md5": "4597ee42fd14b0e83754027205d4ca17", "fn": "human.db0_3.17.0.tar.gz"}, "malaria.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/malaria.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/malaria.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-malaria.db0/bioconductor-malaria.db0_3.17.0_src_all.tar.gz"], "md5": "b8064752fa55d249e89e1c94db04b434", "fn": "malaria.db0_3.17.0.tar.gz"}, "mouse.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/mouse.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse.db0/bioconductor-mouse.db0_3.17.0_src_all.tar.gz"], "md5": "132244baa13685fdb259ecaecd9535af", "fn": "mouse.db0_3.17.0.tar.gz"}, "org.ag.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Ag.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ag.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ag.eg.db/bioconductor-org.ag.eg.db_3.17.0_src_all.tar.gz"], "md5": "fb3e06ad1afc3c386367a239e559f342", "fn": "org.Ag.eg.db_3.17.0.tar.gz"}, "org.at.tair.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.At.tair.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.At.tair.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.at.tair.db/bioconductor-org.at.tair.db_3.17.0_src_all.tar.gz"], "md5": "568e09bfbf9b86a9120b52ca6eb47879", "fn": "org.At.tair.db_3.17.0.tar.gz"}, "org.bt.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Bt.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Bt.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.bt.eg.db/bioconductor-org.bt.eg.db_3.17.0_src_all.tar.gz"], "md5": "13b2350bb7e6219a25caea3a4038f104", "fn": "org.Bt.eg.db_3.17.0.tar.gz"}, "org.ce.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Ce.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ce.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ce.eg.db/bioconductor-org.ce.eg.db_3.17.0_src_all.tar.gz"], "md5": "8884864a691574d7640b2059a8d6613b", "fn": "org.Ce.eg.db_3.17.0.tar.gz"}, "org.cf.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Cf.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Cf.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.cf.eg.db/bioconductor-org.cf.eg.db_3.17.0_src_all.tar.gz"], "md5": "594a306e7ac757df56e9563163168713", "fn": "org.Cf.eg.db_3.17.0.tar.gz"}, "org.dm.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Dm.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Dm.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.dm.eg.db/bioconductor-org.dm.eg.db_3.17.0_src_all.tar.gz"], "md5": "3a680c3ea7320013c7ab1181d11e2177", "fn": "org.Dm.eg.db_3.17.0.tar.gz"}, "org.dr.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Dr.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Dr.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.dr.eg.db/bioconductor-org.dr.eg.db_3.17.0_src_all.tar.gz"], "md5": "03edb42214f27a93743dfc57200cddbb", "fn": "org.Dr.eg.db_3.17.0.tar.gz"}, "org.eck12.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.EcK12.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.EcK12.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.eck12.eg.db/bioconductor-org.eck12.eg.db_3.17.0_src_all.tar.gz"], "md5": "676642eb784017bf9f82711274f8987e", "fn": "org.EcK12.eg.db_3.17.0.tar.gz"}, "org.ecsakai.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.EcSakai.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.EcSakai.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ecsakai.eg.db/bioconductor-org.ecsakai.eg.db_3.17.0_src_all.tar.gz"], "md5": "135a50e2604715a7c5f1c2a36bddf691", "fn": "org.EcSakai.eg.db_3.17.0.tar.gz"}, "org.gg.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Gg.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Gg.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.gg.eg.db/bioconductor-org.gg.eg.db_3.17.0_src_all.tar.gz"], "md5": "292b22ea846c6c184528e92ab4a53247", "fn": "org.Gg.eg.db_3.17.0.tar.gz"}, "org.hs.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Hs.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Hs.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.hs.eg.db/bioconductor-org.hs.eg.db_3.17.0_src_all.tar.gz"], "md5": "a1015fd071ab69055865940ef6e205f4", "fn": "org.Hs.eg.db_3.17.0.tar.gz"}, "org.mm.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Mm.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Mm.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.mm.eg.db/bioconductor-org.mm.eg.db_3.17.0_src_all.tar.gz"], "md5": "7b2124d1ef7c0936bb4ecfcbd2a979b8", "fn": "org.Mm.eg.db_3.17.0.tar.gz"}, "org.mmu.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Mmu.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Mmu.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.mmu.eg.db/bioconductor-org.mmu.eg.db_3.17.0_src_all.tar.gz"], "md5": "d59c3d744ec7def892edacf12c99b869", "fn": "org.Mmu.eg.db_3.17.0.tar.gz"}, "org.pt.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Pt.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Pt.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.pt.eg.db/bioconductor-org.pt.eg.db_3.17.0_src_all.tar.gz"], "md5": "b3c4135532486951e94ed5d182030217", "fn": "org.Pt.eg.db_3.17.0.tar.gz"}, "org.rn.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Rn.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Rn.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.rn.eg.db/bioconductor-org.rn.eg.db_3.17.0_src_all.tar.gz"], "md5": "bf40322d9b95075d75777ec63a797198", "fn": "org.Rn.eg.db_3.17.0.tar.gz"}, "org.sc.sgd.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Sc.sgd.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Sc.sgd.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.sc.sgd.db/bioconductor-org.sc.sgd.db_3.17.0_src_all.tar.gz"], "md5": "b0fd2fcd421007a5b9bd7bc2f5874ae3", "fn": "org.Sc.sgd.db_3.17.0.tar.gz"}, "org.ss.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Ss.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ss.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ss.eg.db/bioconductor-org.ss.eg.db_3.17.0_src_all.tar.gz"], "md5": "a9f8354c9869e86a610ad30f51eb533b", "fn": "org.Ss.eg.db_3.17.0.tar.gz"}, "org.xl.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Xl.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Xl.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.xl.eg.db/bioconductor-org.xl.eg.db_3.17.0_src_all.tar.gz"], "md5": "6ce9e0dc3566a220f5c12b70ffb2538c", "fn": "org.Xl.eg.db_3.17.0.tar.gz"}, "orthology.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/Orthology.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/Orthology.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-orthology.eg.db/bioconductor-orthology.eg.db_3.17.0_src_all.tar.gz"], "md5": "90c181057a638413afc54bb11071a42e", "fn": "Orthology.eg.db_3.17.0.tar.gz"}, "pfam.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PFAM.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/PFAM.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pfam.db/bioconductor-pfam.db_3.17.0_src_all.tar.gz"], "md5": "729496d021868b74cbecfd156066d0e9", "fn": "PFAM.db_3.17.0.tar.gz"}, "pig.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/pig.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/pig.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pig.db0/bioconductor-pig.db0_3.17.0_src_all.tar.gz"], "md5": "d4ea227fc9495dc815bb3ad2387a7e26", "fn": "pig.db0_3.17.0.tar.gz"}, "rat.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/rat.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/rat.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat.db0/bioconductor-rat.db0_3.17.0_src_all.tar.gz"], "md5": "86993da680822a050e85f1208713f3c8", "fn": "rat.db0_3.17.0.tar.gz"}, "reactome.db-1.84.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/reactome.db_1.84.0.tar.gz", "https://bioarchive.galaxyproject.org/reactome.db_1.84.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-reactome.db/bioconductor-reactome.db_1.84.0_src_all.tar.gz"], "md5": "ce62dbac370a30e260d8e45891939693", "fn": "reactome.db_1.84.0.tar.gz"}, "rhesus.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/rhesus.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/rhesus.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rhesus.db0/bioconductor-rhesus.db0_3.17.0_src_all.tar.gz"], "md5": "16b4999171a6b36e72c19b3f15b46354", "fn": "rhesus.db0_3.17.0.tar.gz"}, "snplocs.hsapiens.dbsnp155.grch37-0.99.24": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.24.tar.gz", "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.24.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp155.grch37/bioconductor-snplocs.hsapiens.dbsnp155.grch37_0.99.24_src_all.tar.gz"], "md5": "9473e23ffc7ae76e630a78324b245da8", "fn": "SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.24.tar.gz"}, "snplocs.hsapiens.dbsnp155.grch38-0.99.24": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP155.GRCh38_0.99.24.tar.gz", "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP155.GRCh38_0.99.24.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp155.grch38/bioconductor-snplocs.hsapiens.dbsnp155.grch38_0.99.24_src_all.tar.gz"], "md5": "a16b7b1f940c3fcc8fd2d78f438fd25c", "fn": "SNPlocs.Hsapiens.dbSNP155.GRCh38_0.99.24.tar.gz"}, "txdb.cfamiliaris.ucsc.canfam6.refgene-3.17.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Cfamiliaris.UCSC.canFam6.refGene_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Cfamiliaris.UCSC.canFam6.refGene_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene/bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene_3.17.0_src_all.tar.gz"], "md5": "9279204329323191fbb72717a57b13aa", "fn": "TxDb.Cfamiliaris.UCSC.canFam6.refGene_3.17.0.tar.gz"}, "txdb.hsapiens.ucsc.hg38.knowngene-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg38.knownGene_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_3.17.0_src_all.tar.gz"], "md5": "a9b7cfbf5ed7d9ef129c84abdd7858dc", "fn": "TxDb.Hsapiens.UCSC.hg38.knownGene_3.17.0.tar.gz"}, "txdb.mmusculus.ucsc.mm39.knowngene-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm39.knownGene_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm39.knownGene_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene_3.17.0_src_all.tar.gz"], "md5": "ca2e9ed7dc7fe96ef98b18e3c7e3245a", "fn": "TxDb.Mmusculus.UCSC.mm39.knownGene_3.17.0.tar.gz"}, "worm.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/worm.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/worm.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-worm.db0/bioconductor-worm.db0_3.17.0_src_all.tar.gz"], "md5": "5ab9b7c14dafa60945e528fe7b940d42", "fn": "worm.db0_3.17.0.tar.gz"}, "xenopus.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/xenopus.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/xenopus.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xenopus.db0/bioconductor-xenopus.db0_3.17.0_src_all.tar.gz"], "md5": "cbdcc91045acef0ea9998f965b24dc2e", "fn": "xenopus.db0_3.17.0.tar.gz"}, "yeast.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/yeast.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/yeast.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeast.db0/bioconductor-yeast.db0_3.17.0_src_all.tar.gz"], "md5": "ce5a6e6febb6565c3a382d188d7652c0", "fn": "yeast.db0_3.17.0.tar.gz"}, "zebrafish.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/zebrafish.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafish.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafish.db0/bioconductor-zebrafish.db0_3.17.0_src_all.tar.gz"], "md5": "bf2c5c9a8aaee76228e865cab2901cd2", "fn": "zebrafish.db0_3.17.0.tar.gz"}, "adductdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/adductData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/adductData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-adductdata/bioconductor-adductdata_1.16.0_src_all.tar.gz"], "md5": "abd834104d02465a0f32a64be9974c64", "fn": "adductData_1.16.0.tar.gz"}, "affycompdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/affycompData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/affycompData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affycompdata/bioconductor-affycompdata_1.38.0_src_all.tar.gz"], "md5": "adf2ee1552f1ee380e5ccbcf8246955d", "fn": "affycompData_1.38.0.tar.gz"}, "affydata-1.48.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/affydata_1.48.0.tar.gz", "https://bioarchive.galaxyproject.org/affydata_1.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affydata/bioconductor-affydata_1.48.0_src_all.tar.gz"], "md5": "ec63683a91e086cf51b0ff7b21dcc00b", "fn": "affydata_1.48.0.tar.gz"}, "affyhgu133a2expr-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Affyhgu133A2Expr_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133A2Expr_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133a2expr/bioconductor-affyhgu133a2expr_1.36.0_src_all.tar.gz"], "md5": "09a1e306ad46f08b9508343050ffa756", "fn": "Affyhgu133A2Expr_1.36.0.tar.gz"}, "affyhgu133aexpr-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Affyhgu133aExpr_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133aExpr_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133aexpr/bioconductor-affyhgu133aexpr_1.38.0_src_all.tar.gz"], "md5": "e745cf07453b1f7151f28ddddced6be1", "fn": "Affyhgu133aExpr_1.38.0.tar.gz"}, "affyhgu133plus2expr-1.34.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Affyhgu133Plus2Expr_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133Plus2Expr_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133plus2expr/bioconductor-affyhgu133plus2expr_1.34.0_src_all.tar.gz"], "md5": "210b20595daf5314b8d5b90b5497eab4", "fn": "Affyhgu133Plus2Expr_1.34.0.tar.gz"}, "affymetrixdatatestfiles-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/AffymetrixDataTestFiles_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/AffymetrixDataTestFiles_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affymetrixdatatestfiles/bioconductor-affymetrixdatatestfiles_0.38.0_src_all.tar.gz"], "md5": "3aa3891584be3bcdab25e2b72b092edc", "fn": "AffymetrixDataTestFiles_0.38.0.tar.gz"}, "affymoe4302expr-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Affymoe4302Expr_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/Affymoe4302Expr_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affymoe4302expr/bioconductor-affymoe4302expr_1.38.0_src_all.tar.gz"], "md5": "277537172df894a0e7384d3e48d059b1", "fn": "Affymoe4302Expr_1.38.0.tar.gz"}, "airway-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/airway_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/airway_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-airway/bioconductor-airway_1.20.0_src_all.tar.gz"], "md5": "9c79ded2f4d44b3a865a1e489c6d151d", "fn": "airway_1.20.0.tar.gz"}, "all-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ALL_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/ALL_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-all/bioconductor-all_1.42.0_src_all.tar.gz"], "md5": "11b7809ea96d31a9f1bc3eb56a2650c1", "fn": "ALL_1.42.0.tar.gz"}, "allmll-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ALLMLL_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/ALLMLL_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-allmll/bioconductor-allmll_1.40.0_src_all.tar.gz"], "md5": "f4c0642007ed854280b06339d989d94f", "fn": "ALLMLL_1.40.0.tar.gz"}, "alpinedata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/alpineData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/alpineData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-alpinedata/bioconductor-alpinedata_1.26.0_src_all.tar.gz"], "md5": "6883ade3b0bcab36b3d23f2bfa7ddc03", "fn": "alpineData_1.26.0.tar.gz"}, "ampaffyexample-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/AmpAffyExample_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/AmpAffyExample_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ampaffyexample/bioconductor-ampaffyexample_1.40.0_src_all.tar.gz"], "md5": "a8863d31491bb756d0f630d09c012904", "fn": "AmpAffyExample_1.40.0.tar.gz"}, "aneufinderdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/AneuFinderData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/AneuFinderData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-aneufinderdata/bioconductor-aneufinderdata_1.28.0_src_all.tar.gz"], "md5": "703ac91ee510ae00274632026f14a065", "fn": "AneuFinderData_1.28.0.tar.gz"}, "antiprofilesdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/antiProfilesData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/antiProfilesData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-antiprofilesdata/bioconductor-antiprofilesdata_1.36.0_src_all.tar.gz"], "md5": "d5eab300113940ec702cdd00de617761", "fn": "antiProfilesData_1.36.0.tar.gz"}, "aracne.networks-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/aracne.networks_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/aracne.networks_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-aracne.networks/bioconductor-aracne.networks_1.26.0_src_all.tar.gz"], "md5": "766b50311db15b7c36dffbb945277382", "fn": "aracne.networks_1.26.0.tar.gz"}, "arrmdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ARRmData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/ARRmData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-arrmdata/bioconductor-arrmdata_1.36.0_src_all.tar.gz"], "md5": "d1a4ecc042b17945f8a02625fbfa97b5", "fn": "ARRmData_1.36.0.tar.gz"}, "ashkenazimsonchr21-1.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/AshkenazimSonChr21_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/AshkenazimSonChr21_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ashkenazimsonchr21/bioconductor-ashkenazimsonchr21_1.30.0_src_all.tar.gz"], "md5": "6180e43108e29d9194ed93bc0f208124", "fn": "AshkenazimSonChr21_1.30.0.tar.gz"}, "asicsdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ASICSdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/ASICSdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-asicsdata/bioconductor-asicsdata_1.20.0_src_all.tar.gz"], "md5": "46a4e15b37bd49b3cd5693c1a900b581", "fn": "ASICSdata_1.20.0.tar.gz"}, "assessorfdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/AssessORFData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/AssessORFData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-assessorfdata/bioconductor-assessorfdata_1.18.0_src_all.tar.gz"], "md5": "d7c0f6953391e3f1f610467f14384774", "fn": "AssessORFData_1.18.0.tar.gz"}, "bcellviper-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/bcellViper_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/bcellViper_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bcellviper/bioconductor-bcellviper_1.36.0_src_all.tar.gz"], "md5": "c35a1f30610cc929acc8bfdc79af1d13", "fn": "bcellViper_1.36.0.tar.gz"}, "beadarrayexampledata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/beadarrayExampleData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/beadarrayExampleData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadarrayexampledata/bioconductor-beadarrayexampledata_1.38.0_src_all.tar.gz"], "md5": "c8607365b2ef3e8a20b33eac9ae52c51", "fn": "beadarrayExampleData_1.38.0.tar.gz"}, "beadarrayusecases-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/BeadArrayUseCases_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/BeadArrayUseCases_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadarrayusecases/bioconductor-beadarrayusecases_1.38.0_src_all.tar.gz"], "md5": "f02d0ef2902c1223d8e240b55bf77b91", "fn": "BeadArrayUseCases_1.38.0.tar.gz"}, "beadsorted.saliva.epic-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/BeadSorted.Saliva.EPIC_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/BeadSorted.Saliva.EPIC_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadsorted.saliva.epic/bioconductor-beadsorted.saliva.epic_1.8.0_src_all.tar.gz"], "md5": "c521cbcd30e56de9e00a659d9e349320", "fn": "BeadSorted.Saliva.EPIC_1.8.0.tar.gz"}, "benchmarkfdrdata2019-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/benchmarkfdrData2019_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/benchmarkfdrData2019_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-benchmarkfdrdata2019/bioconductor-benchmarkfdrdata2019_1.14.0_src_all.tar.gz"], "md5": "b50a599a3c8ca8b276400e6dc523b894", "fn": "benchmarkfdrData2019_1.14.0.tar.gz"}, "beta7-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/beta7_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/beta7_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beta7/bioconductor-beta7_1.38.0_src_all.tar.gz"], "md5": "0049331687b2d8ce06153507e09a4a03", "fn": "beta7_1.38.0.tar.gz"}, "bioimagedbs-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/BioImageDbs_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/BioImageDbs_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bioimagedbs/bioconductor-bioimagedbs_1.8.0_src_all.tar.gz"], "md5": "b8af4040411218fcfd81ab927747eb48", "fn": "BioImageDbs_1.8.0.tar.gz"}, "bioplex-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/BioPlex_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/BioPlex_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bioplex/bioconductor-bioplex_1.6.0_src_all.tar.gz"], "md5": "7a387711025f30513f09cf397c759e81", "fn": "BioPlex_1.6.0.tar.gz"}, "biotmledata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/biotmleData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/biotmleData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biotmledata/bioconductor-biotmledata_1.24.0_src_all.tar.gz"], "md5": "e21b4d8009abb77c03a67a9115c289dc", "fn": "biotmleData_1.24.0.tar.gz"}, "biscuiteerdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/biscuiteerData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/biscuiteerData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biscuiteerdata/bioconductor-biscuiteerdata_1.14.0_src_all.tar.gz"], "md5": "fc7a9731d1d9863636d0084602d8b22f", "fn": "biscuiteerData_1.14.0.tar.gz"}, "bladderbatch-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/bladderbatch_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/bladderbatch_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bladderbatch/bioconductor-bladderbatch_1.38.0_src_all.tar.gz"], "md5": "ab4457a6eebb75202730d4433d4aa245", "fn": "bladderbatch_1.38.0.tar.gz"}, "blimatestingdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/blimaTestingData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/blimaTestingData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-blimatestingdata/bioconductor-blimatestingdata_1.20.0_src_all.tar.gz"], "md5": "17e9a4119b1beaf61f30fbe192b9a20a", "fn": "blimaTestingData_1.20.0.tar.gz"}, "bloodcancermultiomics2017-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/BloodCancerMultiOmics2017_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/BloodCancerMultiOmics2017_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bloodcancermultiomics2017/bioconductor-bloodcancermultiomics2017_1.20.0_src_all.tar.gz"], "md5": "5d7ccf32b2249044c2b86aa4cf933372", "fn": "BloodCancerMultiOmics2017_1.20.0.tar.gz"}, "bodymaprat-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/bodymapRat_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/bodymapRat_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bodymaprat/bioconductor-bodymaprat_1.16.0_src_all.tar.gz"], "md5": "d15dd35c8ce1db80954afb9e4663fe29", "fn": "bodymapRat_1.16.0.tar.gz"}, "breakpointrdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/breakpointRdata_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/breakpointRdata_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breakpointrdata/bioconductor-breakpointrdata_1.18.0_src_all.tar.gz"], "md5": "59535154a02ede7347b6114c11292173", "fn": "breakpointRdata_1.18.0.tar.gz"}, "breastcancermainz-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/breastCancerMAINZ_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerMAINZ_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancermainz/bioconductor-breastcancermainz_1.38.0_src_all.tar.gz"], "md5": "4d906d493af2aa3a2fbf00029aa6f843", "fn": "breastCancerMAINZ_1.38.0.tar.gz"}, "breastcancernki-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/breastCancerNKI_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerNKI_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancernki/bioconductor-breastcancernki_1.38.0_src_all.tar.gz"], "md5": "61d8e072228b6bbb224793b35625d507", "fn": "breastCancerNKI_1.38.0.tar.gz"}, "breastcancertransbig-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/breastCancerTRANSBIG_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerTRANSBIG_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancertransbig/bioconductor-breastcancertransbig_1.38.0_src_all.tar.gz"], "md5": "7117b6426a4cf52736db5835ccdc4ccc", "fn": "breastCancerTRANSBIG_1.38.0.tar.gz"}, "breastcancerunt-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/breastCancerUNT_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerUNT_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancerunt/bioconductor-breastcancerunt_1.38.0_src_all.tar.gz"], "md5": "fab6de14673763f649a3cfd14fc62579", "fn": "breastCancerUNT_1.38.0.tar.gz"}, "breastcancerupp-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/breastCancerUPP_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerUPP_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancerupp/bioconductor-breastcancerupp_1.38.0_src_all.tar.gz"], "md5": "37f0587a0149e1abe5525dd7bbc76a7f", "fn": "breastCancerUPP_1.38.0.tar.gz"}, "breastcancervdx-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/breastCancerVDX_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerVDX_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancervdx/bioconductor-breastcancervdx_1.38.0_src_all.tar.gz"], "md5": "a20c1e1a3060af883ced8843600a1614", "fn": "breastCancerVDX_1.38.0.tar.gz"}, "brgedata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/brgedata_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/brgedata_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-brgedata/bioconductor-brgedata_1.22.0_src_all.tar.gz"], "md5": "5b448f1cfae2bb44babb2b1720d12234", "fn": "brgedata_1.22.0.tar.gz"}, "bronchialil13-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/bronchialIL13_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/bronchialIL13_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bronchialil13/bioconductor-bronchialil13_1.38.0_src_all.tar.gz"], "md5": "71116894de06b0faf014ae3be0f54b36", "fn": "bronchialIL13_1.38.0.tar.gz"}, "bsseqdata-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/bsseqData_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/bsseqData_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsseqdata/bioconductor-bsseqdata_0.38.0_src_all.tar.gz"], "md5": "aeca7a29ea03b49344cf7cc223389537", "fn": "bsseqData_0.38.0.tar.gz"}, "cancerdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/cancerdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/cancerdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cancerdata/bioconductor-cancerdata_1.38.0_src_all.tar.gz"], "md5": "23d4242144544786e0327a3144d8a6c6", "fn": "cancerdata_1.38.0.tar.gz"}, "cardinalworkflows-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CardinalWorkflows_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/CardinalWorkflows_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cardinalworkflows/bioconductor-cardinalworkflows_1.32.0_src_all.tar.gz"], "md5": "8a8b9945c7f7b5287510917c6bc1e1a4", "fn": "CardinalWorkflows_1.32.0.tar.gz"}, "ccdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ccdata_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/ccdata_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ccdata/bioconductor-ccdata_1.26.0_src_all.tar.gz"], "md5": "d21508b620d5328d66111ed0250bcaa8", "fn": "ccdata_1.26.0.tar.gz"}, "ccl4-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CCl4_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/CCl4_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ccl4/bioconductor-ccl4_1.38.0_src_all.tar.gz"], "md5": "a0bfca2abdda039b9376e9cc8ec71333", "fn": "CCl4_1.38.0.tar.gz"}, "cctutorial-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ccTutorial_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ccTutorial_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cctutorial/bioconductor-cctutorial_1.38.0_src_all.tar.gz"], "md5": "6515deef368eb06b2f0aabaa069b3f63", "fn": "ccTutorial_1.38.0.tar.gz"}, "celarefdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/celarefData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/celarefData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celarefdata/bioconductor-celarefdata_1.18.0_src_all.tar.gz"], "md5": "eb23383ea6cb3e84ef6c66f0617cc69e", "fn": "celarefData_1.18.0.tar.gz"}, "celldex-1.10.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/celldex_1.10.1.tar.gz", "https://bioarchive.galaxyproject.org/celldex_1.10.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celldex/bioconductor-celldex_1.10.1_src_all.tar.gz"], "md5": "fef4f15bc2e0a7427627cf1cd7d505dc", "fn": "celldex_1.10.1.tar.gz"}, "cellmapperdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CellMapperData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/CellMapperData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cellmapperdata/bioconductor-cellmapperdata_1.26.0_src_all.tar.gz"], "md5": "b9d311ad83cec787788c967e93cb290b", "fn": "CellMapperData_1.26.0.tar.gz"}, "champdata-2.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ChAMPdata_2.32.0.tar.gz", "https://bioarchive.galaxyproject.org/ChAMPdata_2.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-champdata/bioconductor-champdata_2.32.0_src_all.tar.gz"], "md5": "cf36209a25e3dbc4c8098a3fcb3327df", "fn": "ChAMPdata_2.32.0.tar.gz"}, "chic.data-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ChIC.data_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIC.data_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chic.data/bioconductor-chic.data_1.20.0_src_all.tar.gz"], "md5": "c846395a170d9e1601f20f2250b5b3e2", "fn": "ChIC.data_1.20.0.tar.gz"}, "chimphumanbraindata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ChimpHumanBrainData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ChimpHumanBrainData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chimphumanbraindata/bioconductor-chimphumanbraindata_1.38.0_src_all.tar.gz"], "md5": "4c8b24136adf4492905f31e148674a5e", "fn": "ChimpHumanBrainData_1.38.0.tar.gz"}, "chipenrich.data-2.24.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/chipenrich.data_2.24.0.tar.gz", "https://bioarchive.galaxyproject.org/chipenrich.data_2.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipenrich.data/bioconductor-chipenrich.data_2.24.0_src_all.tar.gz"], "md5": "4d9f38a90b43fad02b6448ecfbd36f2d", "fn": "chipenrich.data_2.24.0.tar.gz"}, "chipexoqualexample-1.24.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ChIPexoQualExample_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIPexoQualExample_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipexoqualexample/bioconductor-chipexoqualexample_1.24.0_src_all.tar.gz"], "md5": "b8a88d767a542955c8dfa93a67c843de", "fn": "ChIPexoQualExample_1.24.0.tar.gz"}, "chipseqdbdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/chipseqDBData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/chipseqDBData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipseqdbdata/bioconductor-chipseqdbdata_1.16.0_src_all.tar.gz"], "md5": "9417adbf6ebe305a0caf0d0eba440cac", "fn": "chipseqDBData_1.16.0.tar.gz"}, "chipxpressdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ChIPXpressData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIPXpressData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipxpressdata/bioconductor-chipxpressdata_1.38.0_src_all.tar.gz"], "md5": "d764e5abb6fadab9aa4184222665fd25", "fn": "ChIPXpressData_1.38.0.tar.gz"}, "chromstardata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/chromstaRData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/chromstaRData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chromstardata/bioconductor-chromstardata_1.26.0_src_all.tar.gz"], "md5": "316680e584e9e31c3000a87e666fda3b", "fn": "chromstaRData_1.26.0.tar.gz"}, "cll-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CLL_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/CLL_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cll/bioconductor-cll_1.40.0_src_all.tar.gz"], "md5": "af6541d53d8bb71eb10e661c0a6efde0", "fn": "CLL_1.40.0.tar.gz"}, "cllmethylation-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CLLmethylation_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/CLLmethylation_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cllmethylation/bioconductor-cllmethylation_1.20.0_src_all.tar.gz"], "md5": "e3304bdcdaa207660d51a29e1ad2a4c6", "fn": "CLLmethylation_1.20.0.tar.gz"}, "clumsiddata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CluMSIDdata_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/CluMSIDdata_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clumsiddata/bioconductor-clumsiddata_1.16.0_src_all.tar.gz"], "md5": "8f97c24b60d106fe1285496ace8fad79", "fn": "CluMSIDdata_1.16.0.tar.gz"}, "clustifyrdatahub-1.10.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/clustifyrdatahub_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/clustifyrdatahub_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clustifyrdatahub/bioconductor-clustifyrdatahub_1.10.0_src_all.tar.gz"], "md5": "d1345a885c1b770cd461cf3c69451b39", "fn": "clustifyrdatahub_1.10.0.tar.gz"}, "cmap2data-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/cMap2data_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/cMap2data_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cmap2data/bioconductor-cmap2data_1.36.0_src_all.tar.gz"], "md5": "dd007c68b5fd75539c62081497ab1ee5", "fn": "cMap2data_1.36.0.tar.gz"}, "cnvgsadata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/cnvGSAdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/cnvGSAdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cnvgsadata/bioconductor-cnvgsadata_1.36.0_src_all.tar.gz"], "md5": "706bef72dd4c818adc1295a3f93bd2cf", "fn": "cnvGSAdata_1.36.0.tar.gz"}, "cohcapanno-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/COHCAPanno_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/COHCAPanno_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cohcapanno/bioconductor-cohcapanno_1.36.0_src_all.tar.gz"], "md5": "d95f164282852d44cc982e461157b622", "fn": "COHCAPanno_1.36.0.tar.gz"}, "colonca-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/colonCA_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/colonCA_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-colonca/bioconductor-colonca_1.42.0_src_all.tar.gz"], "md5": "88a73e6339cf99f42858ddcb073c4e61", "fn": "colonCA_1.42.0.tar.gz"}, "confessdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CONFESSdata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/CONFESSdata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-confessdata/bioconductor-confessdata_1.28.0_src_all.tar.gz"], "md5": "dde8faa711c55ae0abd4a0b9f8132233", "fn": "CONFESSdata_1.28.0.tar.gz"}, "connectivitymap-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ConnectivityMap_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/ConnectivityMap_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-connectivitymap/bioconductor-connectivitymap_1.36.0_src_all.tar.gz"], "md5": "0c98c66f64c50f8ae262bccdd4cd0bae", "fn": "ConnectivityMap_1.36.0.tar.gz"}, "copdsexualdimorphism.data-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/COPDSexualDimorphism.data_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/COPDSexualDimorphism.data_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copdsexualdimorphism.data/bioconductor-copdsexualdimorphism.data_1.36.0_src_all.tar.gz"], "md5": "9ae2601608f8b3f711b73d24734e7d7c", "fn": "COPDSexualDimorphism.data_1.36.0.tar.gz"}, "copyhelper-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CopyhelpeR_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/CopyhelpeR_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copyhelper/bioconductor-copyhelper_1.32.0_src_all.tar.gz"], "md5": "c38e2379228446d4d94e5ced48633a54", "fn": "CopyhelpeR_1.32.0.tar.gz"}, "copyneutralima-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CopyNeutralIMA_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/CopyNeutralIMA_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copyneutralima/bioconductor-copyneutralima_1.18.0_src_all.tar.gz"], "md5": "8707f36701c11a45e25e92a63cb81f20", "fn": "CopyNeutralIMA_1.18.0.tar.gz"}, "cosiadata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CoSIAdata_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/CoSIAdata_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cosiadata/bioconductor-cosiadata_1.0.0_src_all.tar.gz"], "md5": "5a1d517d2c097ad8abf9c8298f4ab46d", "fn": "CoSIAdata_1.0.0.tar.gz"}, "cosmic.67-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/COSMIC.67_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/COSMIC.67_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cosmic.67/bioconductor-cosmic.67_1.36.0_src_all.tar.gz"], "md5": "f5242999a8b93e384ab8c05a2950ccde", "fn": "COSMIC.67_1.36.0.tar.gz"}, "crcl18-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CRCL18_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/CRCL18_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-crcl18/bioconductor-crcl18_1.20.0_src_all.tar.gz"], "md5": "df8b3bf91d7c7ac39d0fee78b65c1da0", "fn": "CRCL18_1.20.0.tar.gz"}, "crisprscoredata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/crisprScoreData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/crisprScoreData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-crisprscoredata/bioconductor-crisprscoredata_1.4.0_src_all.tar.gz"], "md5": "feb17485db66f6e86d92b42af3731f4a", "fn": "crisprScoreData_1.4.0.tar.gz"}, "curatedadipoarray-1.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedAdipoArray_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoArray_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadipoarray/bioconductor-curatedadipoarray_1.12.0_src_all.tar.gz"], "md5": "84600c36847d6fff69d646f1ff65dcbd", "fn": "curatedAdipoArray_1.12.0.tar.gz"}, "curatedadipochip-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedAdipoChIP_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoChIP_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadipochip/bioconductor-curatedadipochip_1.16.0_src_all.tar.gz"], "md5": "9c5ffe38c97500d4fadfdd2c6af165b4", "fn": "curatedAdipoChIP_1.16.0.tar.gz"}, "curatedadiporna-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedAdipoRNA_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoRNA_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadiporna/bioconductor-curatedadiporna_1.16.0_src_all.tar.gz"], "md5": "81535f56828fc6043a8461b0f9e09ca7", "fn": "curatedAdipoRNA_1.16.0.tar.gz"}, "curatedbladderdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedBladderData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedBladderData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedbladderdata/bioconductor-curatedbladderdata_1.36.0_src_all.tar.gz"], "md5": "7db958b1758a3b7bc3f2b552962ed51a", "fn": "curatedBladderData_1.36.0.tar.gz"}, "curatedbreastdata-2.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedBreastData_2.28.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedBreastData_2.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedbreastdata/bioconductor-curatedbreastdata_2.28.0_src_all.tar.gz"], "md5": "8e53cc4c883e3b3c94842727f34ad6a6", "fn": "curatedBreastData_2.28.0.tar.gz"}, "curatedcrcdata-2.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedCRCData_2.32.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedCRCData_2.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedcrcdata/bioconductor-curatedcrcdata_2.32.0_src_all.tar.gz"], "md5": "c88686b133a9f30f4904dc4e706ef5c8", "fn": "curatedCRCData_2.32.0.tar.gz"}, "curatedmetagenomicdata-3.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedMetagenomicData_3.8.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedMetagenomicData_3.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedmetagenomicdata/bioconductor-curatedmetagenomicdata_3.8.0_src_all.tar.gz"], "md5": "f24faacda7b263f1bcde098dbffa5f8f", "fn": "curatedMetagenomicData_3.8.0.tar.gz"}, "curatedovariandata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedOvarianData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedOvarianData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedovariandata/bioconductor-curatedovariandata_1.38.0_src_all.tar.gz"], "md5": "0cbda3a714637304ffcc38aa91588c86", "fn": "curatedOvarianData_1.38.0.tar.gz"}, "curatedtbdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedTBData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedTBData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedtbdata/bioconductor-curatedtbdata_1.6.0_src_all.tar.gz"], "md5": "d09277f807e04495c582052e25930d02", "fn": "curatedTBData_1.6.0.tar.gz"}, "curatedtcgadata-1.22.2": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedTCGAData_1.22.2.tar.gz", "https://bioarchive.galaxyproject.org/curatedTCGAData_1.22.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedtcgadata/bioconductor-curatedtcgadata_1.22.2_src_all.tar.gz"], "md5": "066107da416bfad28b75ee3488dbdad0", "fn": "curatedTCGAData_1.22.2.tar.gz"}, "dapardata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DAPARdata_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/DAPARdata_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dapardata/bioconductor-dapardata_1.30.0_src_all.tar.gz"], "md5": "4d730f1b7ef4aab628882f7b9355c7b5", "fn": "DAPARdata_1.30.0.tar.gz"}, "davidtiling-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/davidTiling_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/davidTiling_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-davidtiling/bioconductor-davidtiling_1.40.0_src_all.tar.gz"], "md5": "aa55aaed3cb0a0e29db8c538c636b447", "fn": "davidTiling_1.40.0.tar.gz"}, "depmap-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/depmap_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/depmap_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-depmap/bioconductor-depmap_1.14.0_src_all.tar.gz"], "md5": "d4405c4714a46efd721be9905eddc21f", "fn": "depmap_1.14.0.tar.gz"}, "derfinderdata-2.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/derfinderData_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/derfinderData_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-derfinderdata/bioconductor-derfinderdata_2.18.0_src_all.tar.gz"], "md5": "a7787e049bcee25cb354773f1fd2cf27", "fn": "derfinderData_2.18.0.tar.gz"}, "desousa2013-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DeSousa2013_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/DeSousa2013_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-desousa2013/bioconductor-desousa2013_1.36.0_src_all.tar.gz"], "md5": "1a12b8cbbcf6b3ccc758dacd1ef01852", "fn": "DeSousa2013_1.36.0.tar.gz"}, "dexmadata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DExMAdata_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/DExMAdata_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dexmadata/bioconductor-dexmadata_1.8.0_src_all.tar.gz"], "md5": "bc2fd62dd24eeaee294a624610b75918", "fn": "DExMAdata_1.8.0.tar.gz"}, "diffloopdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/diffloopdata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/diffloopdata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-diffloopdata/bioconductor-diffloopdata_1.28.0_src_all.tar.gz"], "md5": "8e004a82f024eb82c188415e8ca65563", "fn": "diffloopdata_1.28.0.tar.gz"}, "diggitdata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/diggitdata_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/diggitdata_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-diggitdata/bioconductor-diggitdata_1.32.0_src_all.tar.gz"], "md5": "d68dbde08e8d4b936a15a73a23a48830", "fn": "diggitdata_1.32.0.tar.gz"}, "dlbcl-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DLBCL_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/DLBCL_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dlbcl/bioconductor-dlbcl_1.40.0_src_all.tar.gz"], "md5": "f22495affaad1066fbe54791486ebd53", "fn": "DLBCL_1.40.0.tar.gz"}, "dmelsgi-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DmelSGI_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/DmelSGI_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dmelsgi/bioconductor-dmelsgi_1.32.0_src_all.tar.gz"], "md5": "611e89ab1359a4e0283b61e75205878f", "fn": "DmelSGI_1.32.0.tar.gz"}, "dmrcatedata-2.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DMRcatedata_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/DMRcatedata_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dmrcatedata/bioconductor-dmrcatedata_2.18.0_src_all.tar.gz"], "md5": "c2d0addb7984dadb9a3c0012dcd8c719", "fn": "DMRcatedata_2.18.0.tar.gz"}, "dnazoodata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DNAZooData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/DNAZooData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dnazoodata/bioconductor-dnazoodata_1.0.0_src_all.tar.gz"], "md5": "76d7687720d175ca13a1057c22b68b1e", "fn": "DNAZooData_1.0.0.tar.gz"}, "donapllp2013-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DonaPLLP2013_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/DonaPLLP2013_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-donapllp2013/bioconductor-donapllp2013_1.38.0_src_all.tar.gz"], "md5": "1ef96235e9049d31e27f5e5fff17d1ec", "fn": "DonaPLLP2013_1.38.0.tar.gz"}, "dorothea-1.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/dorothea_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/dorothea_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dorothea/bioconductor-dorothea_1.12.0_src_all.tar.gz"], "md5": "068a6de9744d9d5c7085dfe910968e17", "fn": "dorothea_1.12.0.tar.gz"}, "dresscheck-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/dressCheck_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/dressCheck_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dresscheck/bioconductor-dresscheck_0.38.0_src_all.tar.gz"], "md5": "27fc1d1485335601b86ab54b8380f1dc", "fn": "dressCheck_0.38.0.tar.gz"}, "droplettestfiles-1.10.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DropletTestFiles_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/DropletTestFiles_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-droplettestfiles/bioconductor-droplettestfiles_1.10.0_src_all.tar.gz"], "md5": "addd41a9a235a4216b4c7067879203d6", "fn": "DropletTestFiles_1.10.0.tar.gz"}, "drugvsdiseasedata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DrugVsDiseasedata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/DrugVsDiseasedata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drugvsdiseasedata/bioconductor-drugvsdiseasedata_1.36.0_src_all.tar.gz"], "md5": "64c011debe7f2f876d073b7383502db0", "fn": "DrugVsDiseasedata_1.36.0.tar.gz"}, "duoclustering2018-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DuoClustering2018_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/DuoClustering2018_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-duoclustering2018/bioconductor-duoclustering2018_1.18.0_src_all.tar.gz"], "md5": "697a0b8aecfb07cb6034d7626001f262", "fn": "DuoClustering2018_1.18.0.tar.gz"}, "dvddata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DvDdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/DvDdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dvddata/bioconductor-dvddata_1.36.0_src_all.tar.gz"], "md5": "c21d1ca3b1808272b1d90004201512b2", "fn": "DvDdata_1.36.0.tar.gz"}, "dyebiasexamples-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/dyebiasexamples_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/dyebiasexamples_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dyebiasexamples/bioconductor-dyebiasexamples_1.40.0_src_all.tar.gz"], "md5": "8ba42215153001f0334b098938eacf9c", "fn": "dyebiasexamples_1.40.0.tar.gz"}, "easierdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/easierData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/easierData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-easierdata/bioconductor-easierdata_1.6.0_src_all.tar.gz"], "md5": "c8cdf9119aa80107e2d8d6853c2a6fde", "fn": "easierData_1.6.0.tar.gz"}, "eatonetalchipseq-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/EatonEtAlChIPseq_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/EatonEtAlChIPseq_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-eatonetalchipseq/bioconductor-eatonetalchipseq_0.38.0_src_all.tar.gz"], "md5": "fa5225647fa5b852a38635bb2ba759ef", "fn": "EatonEtAlChIPseq_0.38.0.tar.gz"}, "ecolileucine-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ecoliLeucine_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliLeucine_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolileucine/bioconductor-ecolileucine_1.40.0_src_all.tar.gz"], "md5": "8f29571bdbf113fe17eb2a91638acf1a", "fn": "ecoliLeucine_1.40.0.tar.gz"}, "egseadata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/EGSEAdata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/EGSEAdata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-egseadata/bioconductor-egseadata_1.28.0_src_all.tar.gz"], "md5": "1ccaaafd4866fa1cf07e06b6370739a3", "fn": "EGSEAdata_1.28.0.tar.gz"}, "elmer.data-2.24.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ELMER.data_2.24.0.tar.gz", "https://bioarchive.galaxyproject.org/ELMER.data_2.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-elmer.data/bioconductor-elmer.data_2.24.0_src_all.tar.gz"], "md5": "4bb614a1bd1fd96f91af883bad29c914", "fn": "ELMER.data_2.24.0.tar.gz"}, "emtdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/emtdata_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/emtdata_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-emtdata/bioconductor-emtdata_1.8.0_src_all.tar.gz"], "md5": "e4c17e43c1d50287179f7fb2f594d6c3", "fn": "emtdata_1.8.0.tar.gz"}, "epimix.data-1.2.2": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/EpiMix.data_1.2.2.tar.gz", "https://bioarchive.galaxyproject.org/EpiMix.data_1.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epimix.data/bioconductor-epimix.data_1.2.2_src_all.tar.gz"], "md5": "3234766b0bc549ab200604206a9ba5b8", "fn": "EpiMix.data_1.2.2.tar.gz"}, "epimutacionsdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/epimutacionsData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/epimutacionsData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epimutacionsdata/bioconductor-epimutacionsdata_1.4.0_src_all.tar.gz"], "md5": "162b5aaa6a5f6df2528dce4285efdea4", "fn": "epimutacionsData_1.4.0.tar.gz"}, "estrogen-1.46.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/estrogen_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/estrogen_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-estrogen/bioconductor-estrogen_1.46.0_src_all.tar.gz"], "md5": "c7f687b7e46c1e224e9008143926f12e", "fn": "estrogen_1.46.0.tar.gz"}, "etec16s-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/etec16s_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/etec16s_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-etec16s/bioconductor-etec16s_1.28.0_src_all.tar.gz"], "md5": "b2540d5e5287458a7fbec76b5656d3c6", "fn": "etec16s_1.28.0.tar.gz"}, "ewcedata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ewceData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ewceData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ewcedata/bioconductor-ewcedata_1.8.0_src_all.tar.gz"], "md5": "3107bac6cd0fb07a4cba3ad59cabb665", "fn": "ewceData_1.8.0.tar.gz"}, "faahko-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/faahKO_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/faahKO_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-faahko/bioconductor-faahko_1.40.0_src_all.tar.gz"], "md5": "29697c16b4e90b21fd8515dfdfea7fde", "fn": "faahKO_1.40.0.tar.gz"}, "fabiadata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/fabiaData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/fabiaData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fabiadata/bioconductor-fabiadata_1.38.0_src_all.tar.gz"], "md5": "970fc1894222fe7eac67b8c94d9a2eab", "fn": "fabiaData_1.38.0.tar.gz"}, "fantom3and4cage-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/FANTOM3and4CAGE_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/FANTOM3and4CAGE_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fantom3and4cage/bioconductor-fantom3and4cage_1.36.0_src_all.tar.gz"], "md5": "049d0b3978f16771bd7e48aa80e8fb93", "fn": "FANTOM3and4CAGE_1.36.0.tar.gz"}, "ffpeexampledata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ffpeExampleData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ffpeExampleData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ffpeexampledata/bioconductor-ffpeexampledata_1.38.0_src_all.tar.gz"], "md5": "f5b4c1bcd2467b0b82973b2e70243ef0", "fn": "ffpeExampleData_1.38.0.tar.gz"}, "fibroeset-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/fibroEset_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/fibroEset_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fibroeset/bioconductor-fibroeset_1.42.0_src_all.tar.gz"], "md5": "42efffdc75032b3305ebdceb55f3754f", "fn": "fibroEset_1.42.0.tar.gz"}, "fieldeffectcrc-1.10.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/FieldEffectCrc_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/FieldEffectCrc_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fieldeffectcrc/bioconductor-fieldeffectcrc_1.10.0_src_all.tar.gz"], "md5": "b20c0c45eec814e077d124b45d6589a6", "fn": "FieldEffectCrc_1.10.0.tar.gz"}, "fis-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/FIs_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/FIs_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fis/bioconductor-fis_1.28.0_src_all.tar.gz"], "md5": "6a79abe38c53faa7176cd1dc4189351b", "fn": "FIs_1.28.0.tar.gz"}, "fission-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/fission_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/fission_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fission/bioconductor-fission_1.20.0_src_all.tar.gz"], "md5": "bf744d1be1f95417b4379e55aadfcef3", "fn": "fission_1.20.0.tar.gz"}, "fletcher2013a-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Fletcher2013a_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/Fletcher2013a_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fletcher2013a/bioconductor-fletcher2013a_1.36.0_src_all.tar.gz"], "md5": "69ea86d2f1e6aa8e8716c4db65f81cf0", "fn": "Fletcher2013a_1.36.0.tar.gz"}, "fletcher2013b-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Fletcher2013b_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/Fletcher2013b_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fletcher2013b/bioconductor-fletcher2013b_1.36.0_src_all.tar.gz"], "md5": "fd7177b33cc525534e80c197f4a14b0b", "fn": "Fletcher2013b_1.36.0.tar.gz"}, "flowploidydata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/flowPloidyData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/flowPloidyData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowploidydata/bioconductor-flowploidydata_1.26.0_src_all.tar.gz"], "md5": "10d8e5d5d636d7a78c7dd5aa79ba41a4", "fn": "flowPloidyData_1.26.0.tar.gz"}, "flowsorted.blood.450k-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/FlowSorted.Blood.450k_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.Blood.450k_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.450k/bioconductor-flowsorted.blood.450k_1.38.0_src_all.tar.gz"], "md5": "68977c1bf508dda29bc067929aecc006", "fn": "FlowSorted.Blood.450k_1.38.0.tar.gz"}, "flowsorted.blood.epic-2.4.2": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/FlowSorted.Blood.EPIC_2.4.2.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.Blood.EPIC_2.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.epic/bioconductor-flowsorted.blood.epic_2.4.2_src_all.tar.gz"], "md5": "4d9d98db39792aac4fe1ec1db0b0366b", "fn": "FlowSorted.Blood.EPIC_2.4.2.tar.gz"}, "flowsorted.cordblood.450k-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/FlowSorted.CordBlood.450k_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBlood.450k_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordblood.450k/bioconductor-flowsorted.cordblood.450k_1.28.0_src_all.tar.gz"], "md5": "dbef432e31c78c82fe4498a341d3a5a8", "fn": "FlowSorted.CordBlood.450k_1.28.0.tar.gz"}, "flowsorted.cordbloodcombined.450k-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/FlowSorted.CordBloodCombined.450k_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodCombined.450k_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodcombined.450k/bioconductor-flowsorted.cordbloodcombined.450k_1.16.0_src_all.tar.gz"], "md5": "0579c0d8bcb50c77d579b082a7bf4158", "fn": "FlowSorted.CordBloodCombined.450k_1.16.0.tar.gz"}, "flowsorted.cordbloodnorway.450k-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/FlowSorted.CordBloodNorway.450k_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodNorway.450k_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodnorway.450k/bioconductor-flowsorted.cordbloodnorway.450k_1.26.0_src_all.tar.gz"], "md5": "5a399952bf229258fe47964a8d3db910", "fn": "FlowSorted.CordBloodNorway.450k_1.26.0.tar.gz"}, "flowsorted.dlpfc.450k-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/FlowSorted.DLPFC.450k_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.DLPFC.450k_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.dlpfc.450k/bioconductor-flowsorted.dlpfc.450k_1.36.0_src_all.tar.gz"], "md5": "fb70a712a95eaa879d62d7751567aed5", "fn": "FlowSorted.DLPFC.450k_1.36.0.tar.gz"}, "flowworkspacedata-3.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/flowWorkspaceData_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/flowWorkspaceData_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowworkspacedata/bioconductor-flowworkspacedata_3.12.0_src_all.tar.gz"], "md5": "8d91993dd5a5c5b561a8063ec91046d3", "fn": "flowWorkspaceData_3.12.0.tar.gz"}, "fourdndata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/fourDNData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/fourDNData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fourdndata/bioconductor-fourdndata_1.0.0_src_all.tar.gz"], "md5": "2bea3be8c2abed679fc99cf6bdaee98f", "fn": "fourDNData_1.0.0.tar.gz"}, "frmaexampledata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/frmaExampleData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/frmaExampleData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-frmaexampledata/bioconductor-frmaexampledata_1.36.0_src_all.tar.gz"], "md5": "057a53ead8fde2bab4ee0cb71a4faaf6", "fn": "frmaExampleData_1.36.0.tar.gz"}, "furrowseg-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/furrowSeg_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/furrowSeg_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-furrowseg/bioconductor-furrowseg_1.28.0_src_all.tar.gz"], "md5": "6ee1d6bc3d7fe7c1855a6b96b429190b", "fn": "furrowSeg_1.28.0.tar.gz"}, "gagedata-2.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/gageData_2.38.0.tar.gz", "https://bioarchive.galaxyproject.org/gageData_2.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gagedata/bioconductor-gagedata_2.38.0_src_all.tar.gz"], "md5": "04f7869c72f70f6726372af0a4688d5d", "fn": "gageData_2.38.0.tar.gz"}, "gaschyhs-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/gaschYHS_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/gaschYHS_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gaschyhs/bioconductor-gaschyhs_1.38.0_src_all.tar.gz"], "md5": "adb36d86b4890c4f4c714d99aa3b3f93", "fn": "gaschYHS_1.38.0.tar.gz"}, "gcspikelite-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/gcspikelite_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/gcspikelite_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gcspikelite/bioconductor-gcspikelite_1.38.0_src_all.tar.gz"], "md5": "721566ac21590bc7f1e56dd1c716d30c", "fn": "gcspikelite_1.38.0.tar.gz"}, "gdnainrnaseqdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/gDNAinRNAseqData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/gDNAinRNAseqData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gdnainrnaseqdata/bioconductor-gdnainrnaseqdata_1.0.0_src_all.tar.gz"], "md5": "de757712c6890eb225ad26790e2a23f6", "fn": "gDNAinRNAseqData_1.0.0.tar.gz"}, "genelendatabase-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/geneLenDataBase_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/geneLenDataBase_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genelendatabase/bioconductor-genelendatabase_1.36.0_src_all.tar.gz"], "md5": "3063a75a94ecd65185c3490a1baba601", "fn": "geneLenDataBase_1.36.0.tar.gz"}, "genomationdata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/genomationData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/genomationData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomationdata/bioconductor-genomationdata_1.32.0_src_all.tar.gz"], "md5": "4954915523744efa6d6b3be3feb376eb", "fn": "genomationData_1.32.0.tar.gz"}, "genomicdistributionsdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GenomicDistributionsData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/GenomicDistributionsData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomicdistributionsdata/bioconductor-genomicdistributionsdata_1.8.0_src_all.tar.gz"], "md5": "55e98f9b1fe5ee9ab222a5aa3866943a", "fn": "GenomicDistributionsData_1.8.0.tar.gz"}, "geuvadistranscriptexpr-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GeuvadisTranscriptExpr_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/GeuvadisTranscriptExpr_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-geuvadistranscriptexpr/bioconductor-geuvadistranscriptexpr_1.28.0_src_all.tar.gz"], "md5": "5a37aba63d441f86e2b9eb68f34b92f0", "fn": "GeuvadisTranscriptExpr_1.28.0.tar.gz"}, "gigseadata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GIGSEAdata_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/GIGSEAdata_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gigseadata/bioconductor-gigseadata_1.18.0_src_all.tar.gz"], "md5": "ad905645333890eafd314cdac44f793a", "fn": "GIGSEAdata_1.18.0.tar.gz"}, "golubesets-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/golubEsets_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/golubEsets_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-golubesets/bioconductor-golubesets_1.42.0_src_all.tar.gz"], "md5": "ec7f4855c5a77d3ea3503a1102910a0c", "fn": "golubEsets_1.42.0.tar.gz"}, "gpaexample-1.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/gpaExample_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/gpaExample_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gpaexample/bioconductor-gpaexample_1.12.0_src_all.tar.gz"], "md5": "e5cd543667831a4996249fcc3dee8224", "fn": "gpaExample_1.12.0.tar.gz"}, "grndata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/grndata_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/grndata_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-grndata/bioconductor-grndata_1.32.0_src_all.tar.gz"], "md5": "e105a77f883593cbe67ddbdbe5ad91e3", "fn": "grndata_1.32.0.tar.gz"}, "gsbenchmark-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GSBenchMark_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/GSBenchMark_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gsbenchmark/bioconductor-gsbenchmark_1.20.0_src_all.tar.gz"], "md5": "67ad80e0d9aca2b2403031b8f5d79f57", "fn": "GSBenchMark_1.20.0.tar.gz"}, "gse103322-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GSE103322_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE103322_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse103322/bioconductor-gse103322_1.6.0_src_all.tar.gz"], "md5": "5f0ae42096e6851fc40f3c45831d38c7", "fn": "GSE103322_1.6.0.tar.gz"}, "gse13015-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GSE13015_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE13015_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse13015/bioconductor-gse13015_1.8.0_src_all.tar.gz"], "md5": "749148d0e8ddb719e43d6513e340e8b6", "fn": "GSE13015_1.8.0.tar.gz"}, "gse159526-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GSE159526_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE159526_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse159526/bioconductor-gse159526_1.6.0_src_all.tar.gz"], "md5": "930aac8c4e8b481b62e489d6e5d94487", "fn": "GSE159526_1.6.0.tar.gz"}, "gse62944-1.28.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GSE62944_1.28.1.tar.gz", "https://bioarchive.galaxyproject.org/GSE62944_1.28.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse62944/bioconductor-gse62944_1.28.1_src_all.tar.gz"], "md5": "8759202f2247d2a60d0bb17acfffad6a", "fn": "GSE62944_1.28.1.tar.gz"}, "gsvadata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GSVAdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/GSVAdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gsvadata/bioconductor-gsvadata_1.36.0_src_all.tar.gz"], "md5": "745225b064d2d82499906b03543ee0ac", "fn": "GSVAdata_1.36.0.tar.gz"}, "gwasdata-1.38.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GWASdata_1.38.1.tar.gz", "https://bioarchive.galaxyproject.org/GWASdata_1.38.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gwasdata/bioconductor-gwasdata_1.38.1_src_all.tar.gz"], "md5": "f613097e6cc22f457d1de41f8e677aa6", "fn": "GWASdata_1.38.1.tar.gz"}, "h5vcdata-2.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/h5vcData_2.20.0.tar.gz", "https://bioarchive.galaxyproject.org/h5vcData_2.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-h5vcdata/bioconductor-h5vcdata_2.20.0_src_all.tar.gz"], "md5": "e233ff9873648c459591fda6942a8790", "fn": "h5vcData_2.20.0.tar.gz"}, "hapmap100khind-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hapmap100khind_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap100khind_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap100khind/bioconductor-hapmap100khind_1.42.0_src_all.tar.gz"], "md5": "ec3213b4ced09f678386a981176e3410", "fn": "hapmap100khind_1.42.0.tar.gz"}, "hapmap100kxba-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hapmap100kxba_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap100kxba_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap100kxba/bioconductor-hapmap100kxba_1.42.0_src_all.tar.gz"], "md5": "46a995b0ad38d46aebdf89c52678c587", "fn": "hapmap100kxba_1.42.0.tar.gz"}, "hapmap500knsp-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hapmap500knsp_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap500knsp_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap500knsp/bioconductor-hapmap500knsp_1.42.0_src_all.tar.gz"], "md5": "c54725a8ec3607d9db051ef7dfb8b16f", "fn": "hapmap500knsp_1.42.0.tar.gz"}, "hapmap500ksty-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hapmap500ksty_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap500ksty_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap500ksty/bioconductor-hapmap500ksty_1.42.0_src_all.tar.gz"], "md5": "b283985ebfd5c8eace1e5f436fb1d07c", "fn": "hapmap500ksty_1.42.0.tar.gz"}, "hapmapsnp5-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hapmapsnp5_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmapsnp5_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp5/bioconductor-hapmapsnp5_1.42.0_src_all.tar.gz"], "md5": "ccc4fe2a3fcb840365fb2b3bdec3cfd8", "fn": "hapmapsnp5_1.42.0.tar.gz"}, "hapmapsnp6-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hapmapsnp6_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmapsnp6_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp6/bioconductor-hapmapsnp6_1.42.0_src_all.tar.gz"], "md5": "a6ca8fb7d228e64ba1567d4cb7bcd81e", "fn": "hapmapsnp6_1.42.0.tar.gz"}, "harbchip-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/harbChIP_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/harbChIP_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harbchip/bioconductor-harbchip_1.38.0_src_all.tar.gz"], "md5": "5713ddec61a7771a7c8be36ced779ef1", "fn": "harbChIP_1.38.0.tar.gz"}, "harmandata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HarmanData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/HarmanData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harmandata/bioconductor-harmandata_1.28.0_src_all.tar.gz"], "md5": "43bca3e57aee5603fda4b7be1cb9c738", "fn": "HarmanData_1.28.0.tar.gz"}, "harmonizedtcgadata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HarmonizedTCGAData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/HarmonizedTCGAData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harmonizedtcgadata/bioconductor-harmonizedtcgadata_1.22.0_src_all.tar.gz"], "md5": "c615eb02dbda3204fb5f3d9308a0115c", "fn": "HarmonizedTCGAData_1.22.0.tar.gz"}, "hcadata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HCAData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/HCAData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcadata/bioconductor-hcadata_1.16.0_src_all.tar.gz"], "md5": "c8a2e18f3a29f80ba013759f6c87619e", "fn": "HCAData_1.16.0.tar.gz"}, "hd2013sgi-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HD2013SGI_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/HD2013SGI_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hd2013sgi/bioconductor-hd2013sgi_1.40.0_src_all.tar.gz"], "md5": "4cc03451c32df17e2a946ab45d32659e", "fn": "HD2013SGI_1.40.0.tar.gz"}, "hdcytodata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HDCytoData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/HDCytoData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hdcytodata/bioconductor-hdcytodata_1.20.0_src_all.tar.gz"], "md5": "0ab01564970b77ca4d62db12c07a1ed4", "fn": "HDCytoData_1.20.0.tar.gz"}, "healthycontrolspresencechecker-1.4.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/healthyControlsPresenceChecker_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/healthyControlsPresenceChecker_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-healthycontrolspresencechecker/bioconductor-healthycontrolspresencechecker_1.4.0_src_all.tar.gz"], "md5": "cc422930fe0cf3237bc707d107517381", "fn": "healthyControlsPresenceChecker_1.4.0.tar.gz"}, "healthyflowdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/healthyFlowData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/healthyFlowData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-healthyflowdata/bioconductor-healthyflowdata_1.38.0_src_all.tar.gz"], "md5": "478453f16b73527c4f1a9c5697d0b576", "fn": "healthyFlowData_1.38.0.tar.gz"}, "heebodata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HEEBOdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/HEEBOdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-heebodata/bioconductor-heebodata_1.38.0_src_all.tar.gz"], "md5": "cf931bc3409e110143d9090c8cb37c9a", "fn": "HEEBOdata_1.38.0.tar.gz"}, "hellorangesdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HelloRangesData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/HelloRangesData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hellorangesdata/bioconductor-hellorangesdata_1.26.0_src_all.tar.gz"], "md5": "34dbe70ca5ea008e5a17803388bed705", "fn": "HelloRangesData_1.26.0.tar.gz"}, "hgu133abarcodevecs-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hgu133abarcodevecs_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133abarcodevecs_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133abarcodevecs/bioconductor-hgu133abarcodevecs_1.38.0_src_all.tar.gz"], "md5": "af366465c10e3dbc799cdedab97d179d", "fn": "hgu133abarcodevecs_1.38.0.tar.gz"}, "hgu133plus2barcodevecs-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hgu133plus2barcodevecs_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2barcodevecs_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2barcodevecs/bioconductor-hgu133plus2barcodevecs_1.38.0_src_all.tar.gz"], "md5": "a30a110289e8dff08599c97adb71adb0", "fn": "hgu133plus2barcodevecs_1.38.0.tar.gz"}, "hgu133plus2cellscore-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hgu133plus2CellScore_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2CellScore_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2cellscore/bioconductor-hgu133plus2cellscore_1.20.0_src_all.tar.gz"], "md5": "348bb596918ca6f6a51d72d20003545c", "fn": "hgu133plus2CellScore_1.20.0.tar.gz"}, "hgu2beta7-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hgu2beta7_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu2beta7_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu2beta7/bioconductor-hgu2beta7_1.40.0_src_all.tar.gz"], "md5": "2f1a9cc48f2608678e7349d6671a4949", "fn": "hgu2beta7_1.40.0.tar.gz"}, "hicdatahumanimr90-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HiCDataHumanIMR90_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/HiCDataHumanIMR90_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicdatahumanimr90/bioconductor-hicdatahumanimr90_1.20.0_src_all.tar.gz"], "md5": "8b6b0a8e4ccf7bd132a94748c2678be4", "fn": "HiCDataHumanIMR90_1.20.0.tar.gz"}, "hicdatalymphoblast-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HiCDataLymphoblast_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/HiCDataLymphoblast_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicdatalymphoblast/bioconductor-hicdatalymphoblast_1.36.0_src_all.tar.gz"], "md5": "f43877109c87896da3954f156798d19f", "fn": "HiCDataLymphoblast_1.36.0.tar.gz"}, "hicontactsdata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HiContactsData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/HiContactsData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicontactsdata/bioconductor-hicontactsdata_1.2.0_src_all.tar.gz"], "md5": "8d406482f89b932de475c12470bc8ef2", "fn": "HiContactsData_1.2.0.tar.gz"}, "highlyreplicatedrnaseq-1.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HighlyReplicatedRNASeq_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/HighlyReplicatedRNASeq_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-highlyreplicatedrnaseq/bioconductor-highlyreplicatedrnaseq_1.12.0_src_all.tar.gz"], "md5": "b5773c61f0e87d562b2c18aec8992689", "fn": "HighlyReplicatedRNASeq_1.12.0.tar.gz"}, "hiiragi2013-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Hiiragi2013_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/Hiiragi2013_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hiiragi2013/bioconductor-hiiragi2013_1.36.0_src_all.tar.gz"], "md5": "5e1b258226d9b83620113705d7328537", "fn": "Hiiragi2013_1.36.0.tar.gz"}, "hivcdnavantwout03-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HIVcDNAvantWout03_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/HIVcDNAvantWout03_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hivcdnavantwout03/bioconductor-hivcdnavantwout03_1.40.0_src_all.tar.gz"], "md5": "349ef6469ce73790078ba4b5d5206856", "fn": "HIVcDNAvantWout03_1.40.0.tar.gz"}, "hmp16sdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HMP16SData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/HMP16SData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hmp16sdata/bioconductor-hmp16sdata_1.20.0_src_all.tar.gz"], "md5": "a62c1eec817f876e015ee98ab937dfc6", "fn": "HMP16SData_1.20.0.tar.gz"}, "hmp2data-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HMP2Data_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/HMP2Data_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hmp2data/bioconductor-hmp2data_1.14.0_src_all.tar.gz"], "md5": "ff1bf8c6b78ebe9c09578c775c35a54a", "fn": "HMP2Data_1.14.0.tar.gz"}, "hsmmsinglecell-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HSMMSingleCell_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/HSMMSingleCell_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hsmmsinglecell/bioconductor-hsmmsinglecell_1.20.0_src_all.tar.gz"], "md5": "52c7427453286b6ba0f069bdf32457ac", "fn": "HSMMSingleCell_1.20.0.tar.gz"}, "humanaffydata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HumanAffyData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/HumanAffyData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanaffydata/bioconductor-humanaffydata_1.26.0_src_all.tar.gz"], "md5": "bbb55417c9bdc12d387677c47cb8fc19", "fn": "HumanAffyData_1.26.0.tar.gz"}, "humanstemcell-0.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/humanStemCell_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/humanStemCell_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanstemcell/bioconductor-humanstemcell_0.40.0_src_all.tar.gz"], "md5": "8388d74f0e892de07e04e2e200041e6d", "fn": "humanStemCell_0.40.0.tar.gz"}, "ihwpaper-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/IHWpaper_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/IHWpaper_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ihwpaper/bioconductor-ihwpaper_1.28.0_src_all.tar.gz"], "md5": "282cb3abcd7ee2a5d1c34c468ce806c2", "fn": "IHWpaper_1.28.0.tar.gz"}, "illumina450probevariants.db-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Illumina450ProbeVariants.db_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/Illumina450ProbeVariants.db_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illumina450probevariants.db/bioconductor-illumina450probevariants.db_1.36.0_src_all.tar.gz"], "md5": "362d8731f6c9067d58742be0d772a7ac", "fn": "Illumina450ProbeVariants.db_1.36.0.tar.gz"}, "illuminadatatestfiles-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/IlluminaDataTestFiles_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaDataTestFiles_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminadatatestfiles/bioconductor-illuminadatatestfiles_1.38.0_src_all.tar.gz"], "md5": "e11e060ddd803add7efac25b34ab2ff5", "fn": "IlluminaDataTestFiles_1.38.0.tar.gz"}, "imcdatasets-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/imcdatasets_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/imcdatasets_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-imcdatasets/bioconductor-imcdatasets_1.8.0_src_all.tar.gz"], "md5": "1e0e9d5ecc4a826887de1abc773d86b3", "fn": "imcdatasets_1.8.0.tar.gz"}, "italicsdata-2.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ITALICSData_2.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ITALICSData_2.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-italicsdata/bioconductor-italicsdata_2.38.0_src_all.tar.gz"], "md5": "390829582a6ace43fc47218d8f11e3c0", "fn": "ITALICSData_2.38.0.tar.gz"}, "iyer517-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Iyer517_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/Iyer517_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-iyer517/bioconductor-iyer517_1.42.0_src_all.tar.gz"], "md5": "962d1b3895541924544fd080008a5bc9", "fn": "Iyer517_1.42.0.tar.gz"}, "jaspar2014-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/JASPAR2014_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2014_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2014/bioconductor-jaspar2014_1.36.0_src_all.tar.gz"], "md5": "63249cf2e663d3823da3359b8e584ede", "fn": "JASPAR2014_1.36.0.tar.gz"}, "jaspar2016-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/JASPAR2016_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2016_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2016/bioconductor-jaspar2016_1.28.0_src_all.tar.gz"], "md5": "9022c6f9720312b9da10800535edec62", "fn": "JASPAR2016_1.28.0.tar.gz"}, "keggandmetacoredzpathwaysgeo-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/KEGGandMetacoreDzPathwaysGEO_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/KEGGandMetacoreDzPathwaysGEO_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-keggandmetacoredzpathwaysgeo/bioconductor-keggandmetacoredzpathwaysgeo_1.20.0_src_all.tar.gz"], "md5": "7a4483556f83ea2f860efe15052eebe9", "fn": "KEGGandMetacoreDzPathwaysGEO_1.20.0.tar.gz"}, "keggdzpathwaysgeo-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/KEGGdzPathwaysGEO_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/KEGGdzPathwaysGEO_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-keggdzpathwaysgeo/bioconductor-keggdzpathwaysgeo_1.38.0_src_all.tar.gz"], "md5": "cfdb271eede41d51e01844f8c7b06b70", "fn": "KEGGdzPathwaysGEO_1.38.0.tar.gz"}, "kidpack-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/kidpack_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/kidpack_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-kidpack/bioconductor-kidpack_1.42.0_src_all.tar.gz"], "md5": "4b8ee4f61037cd1b55cee61efe7101e9", "fn": "kidpack_1.42.0.tar.gz"}, "kodata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/KOdata_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/KOdata_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-kodata/bioconductor-kodata_1.26.0_src_all.tar.gz"], "md5": "11d0727f1c7e40be104b3d24168f2ae7", "fn": "KOdata_1.26.0.tar.gz"}, "leebamviews-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/leeBamViews_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/leeBamViews_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-leebamviews/bioconductor-leebamviews_1.36.0_src_all.tar.gz"], "md5": "8364b9ac80fcc1cbdd4eca1501d6651b", "fn": "leeBamViews_1.36.0.tar.gz"}, "leukemiaseset-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/leukemiasEset_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/leukemiasEset_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-leukemiaseset/bioconductor-leukemiaseset_1.36.0_src_all.tar.gz"], "md5": "6f2498f78d93dc35ed04c9e2e8abfad7", "fn": "leukemiasEset_1.36.0.tar.gz"}, "liebermanaidenhic2009-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/LiebermanAidenHiC2009_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/LiebermanAidenHiC2009_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-liebermanaidenhic2009/bioconductor-liebermanaidenhic2009_0.38.0_src_all.tar.gz"], "md5": "43f7f158c73c12d62e6cf471cd690667", "fn": "LiebermanAidenHiC2009_0.38.0.tar.gz"}, "listeretalbsseq-1.32.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ListerEtAlBSseq_1.32.1.tar.gz", "https://bioarchive.galaxyproject.org/ListerEtAlBSseq_1.32.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-listeretalbsseq/bioconductor-listeretalbsseq_1.32.1_src_all.tar.gz"], "md5": "8b0138cce25976d0d9180442505679d2", "fn": "ListerEtAlBSseq_1.32.1.tar.gz"}, "lrcelltypemarkers-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/LRcellTypeMarkers_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/LRcellTypeMarkers_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lrcelltypemarkers/bioconductor-lrcelltypemarkers_1.8.0_src_all.tar.gz"], "md5": "342747afa842b8009a5e2a6183c1bd83", "fn": "LRcellTypeMarkers_1.8.0.tar.gz"}, "lumibarnes-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/lumiBarnes_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/lumiBarnes_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumibarnes/bioconductor-lumibarnes_1.40.0_src_all.tar.gz"], "md5": "971e2cf62606ab98813418f8032b20dc", "fn": "lumiBarnes_1.40.0.tar.gz"}, "lungcanceracvssccgeo-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/LungCancerACvsSCCGEO_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/LungCancerACvsSCCGEO_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungcanceracvssccgeo/bioconductor-lungcanceracvssccgeo_1.36.0_src_all.tar.gz"], "md5": "4313ab0bff32de6945d2b4e159979b4f", "fn": "LungCancerACvsSCCGEO_1.36.0.tar.gz"}, "lungcancerlines-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/LungCancerLines_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/LungCancerLines_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungcancerlines/bioconductor-lungcancerlines_0.38.0_src_all.tar.gz"], "md5": "be24350e8e8312e9421f0f4dd1ffbf85", "fn": "LungCancerLines_0.38.0.tar.gz"}, "lungexpression-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/lungExpression_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/lungExpression_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungexpression/bioconductor-lungexpression_0.38.0_src_all.tar.gz"], "md5": "56e3a841d35e5167328f7a3cc3f04349", "fn": "lungExpression_0.38.0.tar.gz"}, "lydata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/lydata_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/lydata_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lydata/bioconductor-lydata_1.26.0_src_all.tar.gz"], "md5": "caffcda965c0d055e69f6f0eb2fe9d67", "fn": "lydata_1.26.0.tar.gz"}, "m3dexampledata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/M3DExampleData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/M3DExampleData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-m3dexampledata/bioconductor-m3dexampledata_1.26.0_src_all.tar.gz"], "md5": "1181ab509a8a85961ef586709f3eaba3", "fn": "M3DExampleData_1.26.0.tar.gz"}, "macrophage-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/macrophage_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/macrophage_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-macrophage/bioconductor-macrophage_1.16.0_src_all.tar.gz"], "md5": "94a66e9f410a44d2aa240ebc4cf5c106", "fn": "macrophage_1.16.0.tar.gz"}, "macsdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MACSdata_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/MACSdata_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-macsdata/bioconductor-macsdata_1.8.0_src_all.tar.gz"], "md5": "b5f6edbf074b1f0f5cb5d0d546cdbd0a", "fn": "MACSdata_1.8.0.tar.gz"}, "mammaprintdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/mammaPrintData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/mammaPrintData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mammaprintdata/bioconductor-mammaprintdata_1.36.0_src_all.tar.gz"], "md5": "cfd6915395a6a2adeebac6854f3359c9", "fn": "mammaPrintData_1.36.0.tar.gz"}, "mapkldata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/mAPKLData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/mAPKLData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mapkldata/bioconductor-mapkldata_1.32.0_src_all.tar.gz"], "md5": "6d1b511c7be1a423450a153fc118e7cb", "fn": "mAPKLData_1.32.0.tar.gz"}, "maqcexpression4plex-1.44.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/maqcExpression4plex_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/maqcExpression4plex_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcexpression4plex/bioconductor-maqcexpression4plex_1.44.0_src_all.tar.gz"], "md5": "761e3e1f398262f4c0cac3cd31979fc7", "fn": "maqcExpression4plex_1.44.0.tar.gz"}, "maqcsubset-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MAQCsubset_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/MAQCsubset_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcsubset/bioconductor-maqcsubset_1.38.0_src_all.tar.gz"], "md5": "eb3ea654ce6aa3db50c7a39c6d8cab28", "fn": "MAQCsubset_1.38.0.tar.gz"}, "maqcsubsetilm-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MAQCsubsetILM_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/MAQCsubsetILM_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcsubsetilm/bioconductor-maqcsubsetilm_1.38.0_src_all.tar.gz"], "md5": "4aaeddbd20f73e3f84dc630e9c02e219", "fn": "MAQCsubsetILM_1.38.0.tar.gz"}, "marinerdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/marinerData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/marinerData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-marinerdata/bioconductor-marinerdata_1.0.0_src_all.tar.gz"], "md5": "88417144bbc4ae0164445918ce73376d", "fn": "marinerData_1.0.0.tar.gz"}, "mcseadata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/mCSEAdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/mCSEAdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcseadata/bioconductor-mcseadata_1.20.0_src_all.tar.gz"], "md5": "44b91c410f01438e2d0d3946689207bd", "fn": "mCSEAdata_1.20.0.tar.gz"}, "mcsurvdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/mcsurvdata_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mcsurvdata_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcsurvdata/bioconductor-mcsurvdata_1.18.0_src_all.tar.gz"], "md5": "4e4b6fa4d49cfa4588d65cb3a22ab121", "fn": "mcsurvdata_1.18.0.tar.gz"}, "medipsdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MEDIPSData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/MEDIPSData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-medipsdata/bioconductor-medipsdata_1.36.0_src_all.tar.gz"], "md5": "d6d822abd5a2acc639cad1a270f03a2d", "fn": "MEDIPSData_1.36.0.tar.gz"}, "meebodata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MEEBOdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/MEEBOdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-meebodata/bioconductor-meebodata_1.38.0_src_all.tar.gz"], "md5": "0eb2ee76322ae64e44bb926769bd1f77", "fn": "MEEBOdata_1.38.0.tar.gz"}, "merfishdata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MerfishData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/MerfishData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-merfishdata/bioconductor-merfishdata_1.2.0_src_all.tar.gz"], "md5": "d4e86b95520641c0d3f1b5c938d5a3b7", "fn": "MerfishData_1.2.0.tar.gz"}, "metagxbreast-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MetaGxBreast_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxBreast_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxbreast/bioconductor-metagxbreast_1.20.0_src_all.tar.gz"], "md5": "38b605d1c36990f9ae722ed9391afb75", "fn": "MetaGxBreast_1.20.0.tar.gz"}, "metagxovarian-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MetaGxOvarian_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxOvarian_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxovarian/bioconductor-metagxovarian_1.20.0_src_all.tar.gz"], "md5": "180366821492879a0fc25f4b4117b20f", "fn": "MetaGxOvarian_1.20.0.tar.gz"}, "metagxpancreas-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MetaGxPancreas_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxPancreas_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxpancreas/bioconductor-metagxpancreas_1.20.0_src_all.tar.gz"], "md5": "837617be22e87ee2716a5bd6888bb204", "fn": "MetaGxPancreas_1.20.0.tar.gz"}, "metamsdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/metaMSdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/metaMSdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metamsdata/bioconductor-metamsdata_1.36.0_src_all.tar.gz"], "md5": "7c4408ceda2098402daaa6c94bbd3768", "fn": "metaMSdata_1.36.0.tar.gz"}, "metascope-1.0.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MetaScope_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaScope_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metascope/bioconductor-metascope_1.0.0_src_all.tar.gz"], "md5": "aef272f5f78bc787f42bd9c47b923cfb", "fn": "MetaScope_1.0.0.tar.gz"}, "methylaiddata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MethylAidData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/MethylAidData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylaiddata/bioconductor-methylaiddata_1.32.0_src_all.tar.gz"], "md5": "43ab55538e535cab63f2594898cfbda4", "fn": "MethylAidData_1.32.0.tar.gz"}, "methylclockdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/methylclockData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/methylclockData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylclockdata/bioconductor-methylclockdata_1.8.0_src_all.tar.gz"], "md5": "52774d13964d22556fdceb4458caaa27", "fn": "methylclockData_1.8.0.tar.gz"}, "methylseqdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MethylSeqData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MethylSeqData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylseqdata/bioconductor-methylseqdata_1.10.0_src_all.tar.gz"], "md5": "d1a6bd69401032cbdba32519c02fdf4c", "fn": "MethylSeqData_1.10.0.tar.gz"}, "microbiomebenchmarkdata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MicrobiomeBenchmarkData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/MicrobiomeBenchmarkData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-microbiomebenchmarkdata/bioconductor-microbiomebenchmarkdata_1.2.0_src_all.tar.gz"], "md5": "1116445da1265ebf3e4bf29678bd6cc3", "fn": "MicrobiomeBenchmarkData_1.2.0.tar.gz"}, "microbiomedatasets-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/microbiomeDataSets_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/microbiomeDataSets_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-microbiomedatasets/bioconductor-microbiomedatasets_1.8.0_src_all.tar.gz"], "md5": "084634f8885e50e157bbaef972b7ad8f", "fn": "microbiomeDataSets_1.8.0.tar.gz"}, "micrornaome-1.22.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/microRNAome_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/microRNAome_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-micrornaome/bioconductor-micrornaome_1.22.0_src_all.tar.gz"], "md5": "04f1271bdd22d4cc2dabd9e8db57e006", "fn": "microRNAome_1.22.0.tar.gz"}, "migsadata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MIGSAdata_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/MIGSAdata_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-migsadata/bioconductor-migsadata_1.24.0_src_all.tar.gz"], "md5": "baf8af22bafeaed754c45ce660a92420", "fn": "MIGSAdata_1.24.0.tar.gz"}, "minfidata-0.46.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/minfiData_0.46.0.tar.gz", "https://bioarchive.galaxyproject.org/minfiData_0.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minfidata/bioconductor-minfidata_0.46.0_src_all.tar.gz"], "md5": "a5edb94dae6adb108bd94fdf4e0e8c3d", "fn": "minfiData_0.46.0.tar.gz"}, "minfidataepic-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/minfiDataEPIC_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/minfiDataEPIC_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minfidataepic/bioconductor-minfidataepic_1.26.0_src_all.tar.gz"], "md5": "f61984902e4c4c2d0c01f375a3533935", "fn": "minfiDataEPIC_1.26.0.tar.gz"}, "minionsummarydata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/minionSummaryData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/minionSummaryData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minionsummarydata/bioconductor-minionsummarydata_1.30.0_src_all.tar.gz"], "md5": "cab7c2dd789ebe23e1c9410bdbc259c6", "fn": "minionSummaryData_1.30.0.tar.gz"}, "mircompdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/miRcompData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/miRcompData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mircompdata/bioconductor-mircompdata_1.30.0_src_all.tar.gz"], "md5": "df2f1f8eb6489db9c0e242224b47be36", "fn": "miRcompData_1.30.0.tar.gz"}, "mirnatarget-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/miRNATarget_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/miRNATarget_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirnatarget/bioconductor-mirnatarget_1.38.0_src_all.tar.gz"], "md5": "a7418be6b97608cabc13f0812caf9301", "fn": "miRNATarget_1.38.0.tar.gz"}, "mmappr2data-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MMAPPR2data_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/MMAPPR2data_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mmappr2data/bioconductor-mmappr2data_1.14.0_src_all.tar.gz"], "md5": "5ea459c418711fc37e694b10789d03ae", "fn": "MMAPPR2data_1.14.0.tar.gz"}, "mmdiffbamsubset-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MMDiffBamSubset_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/MMDiffBamSubset_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mmdiffbamsubset/bioconductor-mmdiffbamsubset_1.36.0_src_all.tar.gz"], "md5": "b9a590f3dc54a5b5b4e36232ca7e2538", "fn": "MMDiffBamSubset_1.36.0.tar.gz"}, "mofadata-1.16.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MOFAdata_1.16.1.tar.gz", "https://bioarchive.galaxyproject.org/MOFAdata_1.16.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mofadata/bioconductor-mofadata_1.16.1_src_all.tar.gz"], "md5": "7c3605011c45bfe05471c35727cf9896", "fn": "MOFAdata_1.16.1.tar.gz"}, "mosaicsexample-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/mosaicsExample_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/mosaicsExample_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mosaicsexample/bioconductor-mosaicsexample_1.38.0_src_all.tar.gz"], "md5": "dbbc0ae50f0d93a64a45efe4bb848a71", "fn": "mosaicsExample_1.38.0.tar.gz"}, "mouse4302barcodevecs-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/mouse4302barcodevecs_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse4302barcodevecs_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302barcodevecs/bioconductor-mouse4302barcodevecs_1.38.0_src_all.tar.gz"], "md5": "bb60f755fb3fc86b8dbb769bbe6f06c4", "fn": "mouse4302barcodevecs_1.38.0.tar.gz"}, "mousegastrulationdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MouseGastrulationData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/MouseGastrulationData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousegastrulationdata/bioconductor-mousegastrulationdata_1.14.0_src_all.tar.gz"], "md5": "671b5016215ff92409c4aba1f4a59c16", "fn": "MouseGastrulationData_1.14.0.tar.gz"}, "mousethymusageing-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MouseThymusAgeing_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/MouseThymusAgeing_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousethymusageing/bioconductor-mousethymusageing_1.8.0_src_all.tar.gz"], "md5": "e5453bec0eab9aa18f7f438bbfd63c27", "fn": "MouseThymusAgeing_1.8.0.tar.gz"}, "msd16s-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/msd16s_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/msd16s_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msd16s/bioconductor-msd16s_1.20.0_src_all.tar.gz"], "md5": "48cc66a74ec0aeff91a4c5217f69c57d", "fn": "msd16s_1.20.0.tar.gz"}, "msdata-0.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/msdata_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/msdata_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msdata/bioconductor-msdata_0.40.0_src_all.tar.gz"], "md5": "dc6c949e6d593b4220d08511155b9316", "fn": "msdata_0.40.0.tar.gz"}, "msigdb-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/msigdb_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/msigdb_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msigdb/bioconductor-msigdb_1.8.0_src_all.tar.gz"], "md5": "1468865f501a46ee6410f5fac54d9441", "fn": "msigdb_1.8.0.tar.gz"}, "msmb-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MSMB_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/MSMB_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msmb/bioconductor-msmb_1.18.0_src_all.tar.gz"], "md5": "6d9b11ea89215a562d46146b97e3208e", "fn": "MSMB_1.18.0.tar.gz"}, "mspuritydata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/msPurityData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/msPurityData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mspuritydata/bioconductor-mspuritydata_1.28.0_src_all.tar.gz"], "md5": "758e960ac371d347930ab01398f27127", "fn": "msPurityData_1.28.0.tar.gz"}, "msqc1-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/msqc1_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/msqc1_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msqc1/bioconductor-msqc1_1.28.0_src_all.tar.gz"], "md5": "eec753dc0f640e28b06685127ac3794e", "fn": "msqc1_1.28.0.tar.gz"}, "mtbls2-1.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/mtbls2_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/mtbls2_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mtbls2/bioconductor-mtbls2_1.30.0_src_all.tar.gz"], "md5": "9f3494d399dd599b5e462dba8bd126bb", "fn": "mtbls2_1.30.0.tar.gz"}, "mugaexampledata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MUGAExampleData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/MUGAExampleData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mugaexampledata/bioconductor-mugaexampledata_1.20.0_src_all.tar.gz"], "md5": "0e9d37ebfc20b7c46c5e0d98528dc188", "fn": "MUGAExampleData_1.20.0.tar.gz"}, "muscdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/muscData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/muscData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-muscdata/bioconductor-muscdata_1.14.0_src_all.tar.gz"], "md5": "d39accb42da56f5ca951a6f735f1586a", "fn": "muscData_1.14.0.tar.gz"}, "mvoutdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/mvoutData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/mvoutData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mvoutdata/bioconductor-mvoutdata_1.36.0_src_all.tar.gz"], "md5": "c4a2c65e797ec8403b7657afc81c2714", "fn": "mvoutData_1.36.0.tar.gz"}, "nanoporernaseq-1.10.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/NanoporeRNASeq_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/NanoporeRNASeq_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nanoporernaseq/bioconductor-nanoporernaseq_1.10.0_src_all.tar.gz"], "md5": "4efdad7f3e17485998405b6d05612ac2", "fn": "NanoporeRNASeq_1.10.0.tar.gz"}, "nanotubes-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/nanotubes_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/nanotubes_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nanotubes/bioconductor-nanotubes_1.16.0_src_all.tar.gz"], "md5": "7d068f3a955216378fe66463811e4adf", "fn": "nanotubes_1.16.0.tar.gz"}, "ncigraphdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/NCIgraphData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/NCIgraphData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ncigraphdata/bioconductor-ncigraphdata_1.36.0_src_all.tar.gz"], "md5": "beb23450c51a8f3bcac07438a25d6f9b", "fn": "NCIgraphData_1.36.0.tar.gz"}, "nestlink-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/NestLink_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/NestLink_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nestlink/bioconductor-nestlink_1.16.0_src_all.tar.gz"], "md5": "ae3c598105a6b4fc40e3ce4ad0bf1e99", "fn": "NestLink_1.16.0.tar.gz"}, "netactivitydata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/NetActivityData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/NetActivityData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-netactivitydata/bioconductor-netactivitydata_1.2.0_src_all.tar.gz"], "md5": "43f1651effd619c45926094b7f6df44b", "fn": "NetActivityData_1.2.0.tar.gz"}, "neve2006-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Neve2006_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/Neve2006_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-neve2006/bioconductor-neve2006_0.38.0_src_all.tar.gz"], "md5": "77132d53a223319770a7abcf21d8e202", "fn": "Neve2006_0.38.0.tar.gz"}, "ngscopydata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/NGScopyData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/NGScopyData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ngscopydata/bioconductor-ngscopydata_1.20.0_src_all.tar.gz"], "md5": "e2d29d8d5f08328e350974da855da611", "fn": "NGScopyData_1.20.0.tar.gz"}, "nullrangesdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/nullrangesData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/nullrangesData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nullrangesdata/bioconductor-nullrangesdata_1.6.0_src_all.tar.gz"], "md5": "54631ad9bc1a63e3c981cb9df919a1a4", "fn": "nullrangesData_1.6.0.tar.gz"}, "nxtirfdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/NxtIRFdata_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/NxtIRFdata_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nxtirfdata/bioconductor-nxtirfdata_1.6.0_src_all.tar.gz"], "md5": "49c677044a8e671562fec6f64533b284", "fn": "NxtIRFdata_1.6.0.tar.gz"}, "obmiti-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ObMiTi_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ObMiTi_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-obmiti/bioconductor-obmiti_1.8.0_src_all.tar.gz"], "md5": "679880ec1082c72dc04b91c7c43b86d1", "fn": "ObMiTi_1.8.0.tar.gz"}, "oct4-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/oct4_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/oct4_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-oct4/bioconductor-oct4_1.16.0_src_all.tar.gz"], "md5": "733c8377b6b7065265506a938f1c7c09", "fn": "oct4_1.16.0.tar.gz"}, "octad.db-1.2.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/octad.db_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/octad.db_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-octad.db/bioconductor-octad.db_1.2.0_src_all.tar.gz"], "md5": "242e1f3e5df68b1ccbc324eaf3924797", "fn": "octad.db_1.2.0.tar.gz"}, "omicspcadata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/OMICsPCAdata_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/OMICsPCAdata_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-omicspcadata/bioconductor-omicspcadata_1.18.0_src_all.tar.gz"], "md5": "058c8440badd8afe17e693d3055fbf23", "fn": "OMICsPCAdata_1.18.0.tar.gz"}, "onassisjavalibs-1.22.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/OnassisJavaLibs_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/OnassisJavaLibs_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-onassisjavalibs/bioconductor-onassisjavalibs_1.22.0_src_all.tar.gz"], "md5": "32a85e21248ac13de54dfee722eee3f1", "fn": "OnassisJavaLibs_1.22.0.tar.gz"}, "optimalflowdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/optimalFlowData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/optimalFlowData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-optimalflowdata/bioconductor-optimalflowdata_1.12.0_src_all.tar.gz"], "md5": "daba5d6a8b8fdde9d58fed555c569ad5", "fn": "optimalFlowData_1.12.0.tar.gz"}, "parathyroidse-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/parathyroidSE_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/parathyroidSE_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-parathyroidse/bioconductor-parathyroidse_1.38.0_src_all.tar.gz"], "md5": "055bda4d4376fcdec3bce484ec634117", "fn": "parathyroidSE_1.38.0.tar.gz"}, "pasilla-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/pasilla_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/pasilla_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasilla/bioconductor-pasilla_1.28.0_src_all.tar.gz"], "md5": "a6abc62e6e4ddde42ee0269256ac8342", "fn": "pasilla_1.28.0.tar.gz"}, "pasillabamsubset-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/pasillaBamSubset_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/pasillaBamSubset_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasillabamsubset/bioconductor-pasillabamsubset_0.38.0_src_all.tar.gz"], "md5": "6c80a6afcfb87c88e88e8c3c69e66e71", "fn": "pasillaBamSubset_0.38.0.tar.gz"}, "pasillatranscriptexpr-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PasillaTranscriptExpr_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/PasillaTranscriptExpr_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasillatranscriptexpr/bioconductor-pasillatranscriptexpr_1.28.0_src_all.tar.gz"], "md5": "8d5e8ec6f9ba14ca8da1565b8a2b0bac", "fn": "PasillaTranscriptExpr_1.28.0.tar.gz"}, "pathnetdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PathNetData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/PathNetData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pathnetdata/bioconductor-pathnetdata_1.36.0_src_all.tar.gz"], "md5": "20449e0dcf262e4f6c1f7e2521a00370", "fn": "PathNetData_1.36.0.tar.gz"}, "pchicdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PCHiCdata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/PCHiCdata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pchicdata/bioconductor-pchicdata_1.28.0_src_all.tar.gz"], "md5": "7048c278620231f478014314a1a16e74", "fn": "PCHiCdata_1.28.0.tar.gz"}, "pcxndata-2.22.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/pcxnData_2.22.0.tar.gz", "https://bioarchive.galaxyproject.org/pcxnData_2.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pcxndata/bioconductor-pcxndata_2.22.0_src_all.tar.gz"], "md5": "0d340cd964638e91faf2181216c06159", "fn": "pcxnData_2.22.0.tar.gz"}, "pd.atdschip.tiling-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/pd.atdschip.tiling_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.atdschip.tiling_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.atdschip.tiling/bioconductor-pd.atdschip.tiling_0.38.0_src_all.tar.gz"], "md5": "a38ac90ece38e2e9f980966194865fe0", "fn": "pd.atdschip.tiling_0.38.0.tar.gz"}, "pepdat-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/pepDat_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/pepDat_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pepdat/bioconductor-pepdat_1.20.0_src_all.tar.gz"], "md5": "6c0f8c749db61b37d83728109a2e08df", "fn": "pepDat_1.20.0.tar.gz"}, "pepsnmrdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PepsNMRData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/PepsNMRData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pepsnmrdata/bioconductor-pepsnmrdata_1.18.0_src_all.tar.gz"], "md5": "98f84b07316d8ec6aab7c64862c695d2", "fn": "PepsNMRData_1.18.0.tar.gz"}, "phyloprofiledata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PhyloProfileData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/PhyloProfileData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phyloprofiledata/bioconductor-phyloprofiledata_1.14.0_src_all.tar.gz"], "md5": "3be065a86910a062e9b63540157ff949", "fn": "PhyloProfileData_1.14.0.tar.gz"}, "plotgardenerdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/plotgardenerData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/plotgardenerData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-plotgardenerdata/bioconductor-plotgardenerdata_1.6.0_src_all.tar.gz"], "md5": "82519e095b0f464cd59388d4146d21db", "fn": "plotgardenerData_1.6.0.tar.gz"}, "prebsdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/prebsdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/prebsdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prebsdata/bioconductor-prebsdata_1.36.0_src_all.tar.gz"], "md5": "96c0666ea91a4bd5b5c8dbc584f873b3", "fn": "prebsdata_1.36.0.tar.gz"}, "precisetadhub-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/preciseTADhub_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/preciseTADhub_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-precisetadhub/bioconductor-precisetadhub_1.8.0_src_all.tar.gz"], "md5": "9e0da7747a2ae263545ef3e426701fd6", "fn": "preciseTADhub_1.8.0.tar.gz"}, "predasampledata-0.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PREDAsampledata_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/PREDAsampledata_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-predasampledata/bioconductor-predasampledata_0.40.0_src_all.tar.gz"], "md5": "478b0cd1f601998cfefcca0fdf60eb3d", "fn": "PREDAsampledata_0.40.0.tar.gz"}, "prodata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ProData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ProData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prodata/bioconductor-prodata_1.38.0_src_all.tar.gz"], "md5": "6a4c17dd4a55240fdeab52f3301e19f6", "fn": "ProData_1.38.0.tar.gz"}, "prolocdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/pRolocdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/pRolocdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prolocdata/bioconductor-prolocdata_1.38.0_src_all.tar.gz"], "md5": "3cf7b5644c6af5a158d0291d9b597cd2", "fn": "pRolocdata_1.38.0.tar.gz"}, "prostatecancercamcap-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/prostateCancerCamcap_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerCamcap_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancercamcap/bioconductor-prostatecancercamcap_1.28.0_src_all.tar.gz"], "md5": "ff2a0d04db22bce6d2d1722e718edeb5", "fn": "prostateCancerCamcap_1.28.0.tar.gz"}, "prostatecancergrasso-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/prostateCancerGrasso_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerGrasso_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancergrasso/bioconductor-prostatecancergrasso_1.28.0_src_all.tar.gz"], "md5": "cc2f4713d5950c0fcd99dd320adbdb2d", "fn": "prostateCancerGrasso_1.28.0.tar.gz"}, "prostatecancerstockholm-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/prostateCancerStockholm_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerStockholm_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancerstockholm/bioconductor-prostatecancerstockholm_1.28.0_src_all.tar.gz"], "md5": "f2ec2d712681d173c561a57451acae94", "fn": "prostateCancerStockholm_1.28.0.tar.gz"}, "prostatecancertaylor-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/prostateCancerTaylor_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerTaylor_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancertaylor/bioconductor-prostatecancertaylor_1.28.0_src_all.tar.gz"], "md5": "d41f91c630547581ccabf8159a79d889", "fn": "prostateCancerTaylor_1.28.0.tar.gz"}, "prostatecancervarambally-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/prostateCancerVarambally_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerVarambally_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancervarambally/bioconductor-prostatecancervarambally_1.28.0_src_all.tar.gz"], "md5": "8008e839c2e72aee55433f2361efb0cb", "fn": "prostateCancerVarambally_1.28.0.tar.gz"}, "ptairdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ptairData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ptairData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ptairdata/bioconductor-ptairdata_1.8.0_src_all.tar.gz"], "md5": "ede739875473864ed372a4fb877b1852", "fn": "ptairData_1.8.0.tar.gz"}, "pth2o2lipids-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PtH2O2lipids_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/PtH2O2lipids_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pth2o2lipids/bioconductor-pth2o2lipids_1.26.0_src_all.tar.gz"], "md5": "7555134e1714c1d20f25a30f2c74d33c", "fn": "PtH2O2lipids_1.26.0.tar.gz"}, "pumadata-2.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/pumadata_2.36.0.tar.gz", "https://bioarchive.galaxyproject.org/pumadata_2.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pumadata/bioconductor-pumadata_2.36.0_src_all.tar.gz"], "md5": "8201e94e0c66444c72b8f45bd3ca7020", "fn": "pumadata_2.36.0.tar.gz"}, "pwmenrich.dmelanogaster.background-4.34.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PWMEnrich.Dmelanogaster.background_4.34.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Dmelanogaster.background_4.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.dmelanogaster.background/bioconductor-pwmenrich.dmelanogaster.background_4.34.0_src_all.tar.gz"], "md5": "907d3ff8c0fb527c01dbf099a075f732", "fn": "PWMEnrich.Dmelanogaster.background_4.34.0.tar.gz"}, "pwmenrich.hsapiens.background-4.34.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PWMEnrich.Hsapiens.background_4.34.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Hsapiens.background_4.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.hsapiens.background/bioconductor-pwmenrich.hsapiens.background_4.34.0_src_all.tar.gz"], "md5": "02021cd798df13ad0f124fdc481ebe33", "fn": "PWMEnrich.Hsapiens.background_4.34.0.tar.gz"}, "pwmenrich.mmusculus.background-4.34.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PWMEnrich.Mmusculus.background_4.34.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Mmusculus.background_4.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.mmusculus.background/bioconductor-pwmenrich.mmusculus.background_4.34.0_src_all.tar.gz"], "md5": "e81cb70d4a4850829fa5a83003c75404", "fn": "PWMEnrich.Mmusculus.background_4.34.0.tar.gz"}, "pwrewas.data-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/pwrEWAS.data_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/pwrEWAS.data_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwrewas.data/bioconductor-pwrewas.data_1.14.0_src_all.tar.gz"], "md5": "4bc800d4a20edec551cbbcbbffd3d107", "fn": "pwrEWAS.data_1.14.0.tar.gz"}, "qdnaseq.hg19-1.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/QDNAseq.hg19_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/QDNAseq.hg19_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.hg19/bioconductor-qdnaseq.hg19_1.30.0_src_all.tar.gz"], "md5": "6b81f056006151fd4a2f55935ee57f67", "fn": "QDNAseq.hg19_1.30.0.tar.gz"}, "qdnaseq.mm10-1.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/QDNAseq.mm10_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/QDNAseq.mm10_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.mm10/bioconductor-qdnaseq.mm10_1.30.0_src_all.tar.gz"], "md5": "d7c1a5cec6ee30213a4389b40979b9ef", "fn": "QDNAseq.mm10_1.30.0.tar.gz"}, "qplexdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/qPLEXdata_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/qPLEXdata_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qplexdata/bioconductor-qplexdata_1.18.0_src_all.tar.gz"], "md5": "2ea69c2e1a071fd94fcb169af5c61422", "fn": "qPLEXdata_1.18.0.tar.gz"}, "qubicdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/QUBICdata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/QUBICdata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qubicdata/bioconductor-qubicdata_1.28.0_src_all.tar.gz"], "md5": "47be84c681eabf3ba1851a935762e23a", "fn": "QUBICdata_1.28.0.tar.gz"}, "rcellminerdata-2.22.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/rcellminerData_2.22.0.tar.gz", "https://bioarchive.galaxyproject.org/rcellminerData_2.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rcellminerdata/bioconductor-rcellminerdata_2.22.0_src_all.tar.gz"], "md5": "45f581dfcac9cd66a5cb2ca6f0706d7a", "fn": "rcellminerData_2.22.0.tar.gz"}, "rcistarget.hg19.motifdbs.cisbponly.500bp-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp_1.20.0_src_all.tar.gz"], "md5": "74b4a09e41b8af5f638848ca86f3ec53", "fn": "RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.20.0.tar.gz"}, "reactomegsa.data-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ReactomeGSA.data_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/ReactomeGSA.data_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-reactomegsa.data/bioconductor-reactomegsa.data_1.14.0_src_all.tar.gz"], "md5": "1c6b8b4eeacfc2f316c8c0aa021938f1", "fn": "ReactomeGSA.data_1.14.0.tar.gz"}, "regparallel-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RegParallel_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/RegParallel_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-regparallel/bioconductor-regparallel_1.18.0_src_all.tar.gz"], "md5": "ac6ed5e19a8dcfe359e97ccf89949dd1", "fn": "RegParallel_1.18.0.tar.gz"}, "restfulsedata-1.22.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/restfulSEData_1.22.1.tar.gz", "https://bioarchive.galaxyproject.org/restfulSEData_1.22.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-restfulsedata/bioconductor-restfulsedata_1.22.1_src_all.tar.gz"], "md5": "e92deb8a55a329887e87c9d4520e4b9e", "fn": "restfulSEData_1.22.1.tar.gz"}, "rforproteomics-1.38.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RforProteomics_1.38.1.tar.gz", "https://bioarchive.galaxyproject.org/RforProteomics_1.38.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rforproteomics/bioconductor-rforproteomics_1.38.1_src_all.tar.gz"], "md5": "2dbad7c535bf6a39299cad51ede9aafd", "fn": "RforProteomics_1.38.1.tar.gz"}, "rgmqllib-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RGMQLlib_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/RGMQLlib_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgmqllib/bioconductor-rgmqllib_1.20.0_src_all.tar.gz"], "md5": "a9153c4ade0f2149a136bdaefb123f6d", "fn": "RGMQLlib_1.20.0.tar.gz"}, "rheumaticconditionwollbold-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/rheumaticConditionWOLLBOLD_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/rheumaticConditionWOLLBOLD_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rheumaticconditionwollbold/bioconductor-rheumaticconditionwollbold_1.38.0_src_all.tar.gz"], "md5": "58d7b58e54ba5cbd75fafa85aa09f476", "fn": "rheumaticConditionWOLLBOLD_1.38.0.tar.gz"}, "ritandata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RITANdata_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/RITANdata_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ritandata/bioconductor-ritandata_1.24.0_src_all.tar.gz"], "md5": "ee9657a5c821eb892c79ef6a1ee4c5e5", "fn": "RITANdata_1.24.0.tar.gz"}, "rlhub-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RLHub_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/RLHub_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rlhub/bioconductor-rlhub_1.6.0_src_all.tar.gz"], "md5": "9072a588ef09512493ea389c50984153", "fn": "RLHub_1.6.0.tar.gz"}, "rmassbankdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RMassBankData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/RMassBankData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rmassbankdata/bioconductor-rmassbankdata_1.38.0_src_all.tar.gz"], "md5": "ea11a54b5f2465431c43bb8edde6a112", "fn": "RMassBankData_1.38.0.tar.gz"}, "rnainteractmapk-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RNAinteractMAPK_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAinteractMAPK_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnainteractmapk/bioconductor-rnainteractmapk_1.38.0_src_all.tar.gz"], "md5": "ed5fd6239416fbacc80a8995c6e13fb7", "fn": "RNAinteractMAPK_1.38.0.tar.gz"}, "rnamodr.data-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RNAmodR.Data_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAmodR.Data_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnamodr.data/bioconductor-rnamodr.data_1.14.0_src_all.tar.gz"], "md5": "1299a93be9ed1090e5890741cebde152", "fn": "RNAmodR.Data_1.14.0.tar.gz"}, "rnaseqdata.hnrnpc.bam.chr14-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RNAseqData.HNRNPC.bam.chr14_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAseqData.HNRNPC.bam.chr14_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqdata.hnrnpc.bam.chr14/bioconductor-rnaseqdata.hnrnpc.bam.chr14_0.38.0_src_all.tar.gz"], "md5": "7c39f3f2306bb10cb47a97b1d2c893ad", "fn": "RNAseqData.HNRNPC.bam.chr14_0.38.0.tar.gz"}, "rnaseqsamplesizedata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RnaSeqSampleSizeData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/RnaSeqSampleSizeData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqsamplesizedata/bioconductor-rnaseqsamplesizedata_1.32.0_src_all.tar.gz"], "md5": "415e0dc4f463089c632c9106f6df7d89", "fn": "RnaSeqSampleSizeData_1.32.0.tar.gz"}, "rnbeads.hg19-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RnBeads.hg19_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.hg19_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg19/bioconductor-rnbeads.hg19_1.32.0_src_all.tar.gz"], "md5": "83a4f81f4c411d8139ba8673687a6a49", "fn": "RnBeads.hg19_1.32.0.tar.gz"}, "rnbeads.hg38-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RnBeads.hg38_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.hg38_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg38/bioconductor-rnbeads.hg38_1.32.0_src_all.tar.gz"], "md5": "87b5a33c515443e05b5ab7cfeb7afa7a", "fn": "RnBeads.hg38_1.32.0.tar.gz"}, "rnbeads.mm10-2.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RnBeads.mm10_2.8.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.mm10_2.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm10/bioconductor-rnbeads.mm10_2.8.0_src_all.tar.gz"], "md5": "4b25dd4978d2d430192ae93b45945506", "fn": "RnBeads.mm10_2.8.0.tar.gz"}, "rnbeads.mm9-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RnBeads.mm9_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.mm9_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm9/bioconductor-rnbeads.mm9_1.32.0_src_all.tar.gz"], "md5": "83951bafa8f84863f5cdd3e0128c1e0d", "fn": "RnBeads.mm9_1.32.0.tar.gz"}, "rnbeads.rn5-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RnBeads.rn5_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.rn5_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.rn5/bioconductor-rnbeads.rn5_1.32.0_src_all.tar.gz"], "md5": "704db9c010242b63f68e02de58b77ee0", "fn": "RnBeads.rn5_1.32.0.tar.gz"}, "rrbsdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RRBSdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/RRBSdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rrbsdata/bioconductor-rrbsdata_1.20.0_src_all.tar.gz"], "md5": "a418c0df3db7d2285a1629bd473129ce", "fn": "RRBSdata_1.20.0.tar.gz"}, "rrdpdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/rRDPData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/rRDPData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rrdpdata/bioconductor-rrdpdata_1.20.0_src_all.tar.gz"], "md5": "81a8cf3a83812318bbacb9cc2503f8d1", "fn": "rRDPData_1.20.0.tar.gz"}, "rtcga.clinical-20151101.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RTCGA.clinical_20151101.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.clinical_20151101.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.clinical/bioconductor-rtcga.clinical_20151101.30.0_src_all.tar.gz"], "md5": "772ed6b2aafe700536b01d9b4c55dfef", "fn": "RTCGA.clinical_20151101.30.0.tar.gz"}, "rtcga.cnv-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RTCGA.CNV_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.CNV_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.cnv/bioconductor-rtcga.cnv_1.28.0_src_all.tar.gz"], "md5": "4c2f73f6edefa0ca82b7c6f9add37156", "fn": "RTCGA.CNV_1.28.0.tar.gz"}, "rtcga.methylation-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RTCGA.methylation_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.methylation_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.methylation/bioconductor-rtcga.methylation_1.28.0_src_all.tar.gz"], "md5": "1aff8900c676eb32d9655b0d4fbf834e", "fn": "RTCGA.methylation_1.28.0.tar.gz"}, "rtcga.mirnaseq-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RTCGA.miRNASeq_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.miRNASeq_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mirnaseq/bioconductor-rtcga.mirnaseq_1.28.0_src_all.tar.gz"], "md5": "61a11184082b390c05d74b660d06635d", "fn": "RTCGA.miRNASeq_1.28.0.tar.gz"}, "rtcga.mrna-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RTCGA.mRNA_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.mRNA_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mrna/bioconductor-rtcga.mrna_1.28.0_src_all.tar.gz"], "md5": "63adca06a76cfc761b88b853a34580d1", "fn": "RTCGA.mRNA_1.28.0.tar.gz"}, "rtcga.mutations-20151101.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RTCGA.mutations_20151101.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.mutations_20151101.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mutations/bioconductor-rtcga.mutations_20151101.30.0_src_all.tar.gz"], "md5": "d1f7686f0203ccdffd3c0d903947ffbb", "fn": "RTCGA.mutations_20151101.30.0.tar.gz"}, "rtcga.pancan12-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RTCGA.PANCAN12_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.PANCAN12_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.pancan12/bioconductor-rtcga.pancan12_1.28.0_src_all.tar.gz"], "md5": "3c4fcdde44501b93a022b8b1fe3abf96", "fn": "RTCGA.PANCAN12_1.28.0.tar.gz"}, "rtcga.rnaseq-20151101.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RTCGA.rnaseq_20151101.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.rnaseq_20151101.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.rnaseq/bioconductor-rtcga.rnaseq_20151101.30.0_src_all.tar.gz"], "md5": "df65c9add93e3fa3f2f321442057c807", "fn": "RTCGA.rnaseq_20151101.30.0.tar.gz"}, "rtcga.rppa-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RTCGA.RPPA_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.RPPA_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.rppa/bioconductor-rtcga.rppa_1.28.0_src_all.tar.gz"], "md5": "caff1ad6b62dbd868be8cf6452cc4312", "fn": "RTCGA.RPPA_1.28.0.tar.gz"}, "ruvnormalizedata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RUVnormalizeData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/RUVnormalizeData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ruvnormalizedata/bioconductor-ruvnormalizedata_1.20.0_src_all.tar.gz"], "md5": "138ed1f796a9967fce840e1f751769a2", "fn": "RUVnormalizeData_1.20.0.tar.gz"}, "sampleclassifierdata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/sampleClassifierData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/sampleClassifierData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sampleclassifierdata/bioconductor-sampleclassifierdata_1.24.0_src_all.tar.gz"], "md5": "f4b0d64737358fad818a4a1cc71a27c8", "fn": "sampleClassifierData_1.24.0.tar.gz"}, "sbgnview.data-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SBGNview.data_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/SBGNview.data_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sbgnview.data/bioconductor-sbgnview.data_1.14.0_src_all.tar.gz"], "md5": "ab6acd3a8b3411fcba1cf7ab1bbbd370", "fn": "SBGNview.data_1.14.0.tar.gz"}, "scanmirdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/scanMiRData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/scanMiRData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scanmirdata/bioconductor-scanmirdata_1.6.0_src_all.tar.gz"], "md5": "163f0250a82df0c4fb402b756a3010d7", "fn": "scanMiRData_1.6.0.tar.gz"}, "scatac.explorer-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/scATAC.Explorer_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/scATAC.Explorer_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scatac.explorer/bioconductor-scatac.explorer_1.6.0_src_all.tar.gz"], "md5": "74c840082c522937d200169fcb963f71", "fn": "scATAC.Explorer_1.6.0.tar.gz"}, "scatedata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SCATEData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/SCATEData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scatedata/bioconductor-scatedata_1.10.0_src_all.tar.gz"], "md5": "dd2241d946202b696c0a706b906425f4", "fn": "SCATEData_1.10.0.tar.gz"}, "sclcbam-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SCLCBam_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/SCLCBam_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sclcbam/bioconductor-sclcbam_1.32.0_src_all.tar.gz"], "md5": "ca48c42a5e16460f72eb8bfbc697258f", "fn": "SCLCBam_1.32.0.tar.gz"}, "scmultiome-1.0.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/scMultiome_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/scMultiome_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scmultiome/bioconductor-scmultiome_1.0.0_src_all.tar.gz"], "md5": "22aceaa129afbecd400b2d16b6333d43", "fn": "scMultiome_1.0.0.tar.gz"}, "scpdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/scpdata_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/scpdata_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scpdata/bioconductor-scpdata_1.8.0_src_all.tar.gz"], "md5": "0a00beb40a6ae72de0364698c7a0129b", "fn": "scpdata_1.8.0.tar.gz"}, "scrnaseq-2.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/scRNAseq_2.14.0.tar.gz", "https://bioarchive.galaxyproject.org/scRNAseq_2.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scrnaseq/bioconductor-scrnaseq_2.14.0_src_all.tar.gz"], "md5": "3adccc738839605191c0eda859e3d7c7", "fn": "scRNAseq_2.14.0.tar.gz"}, "scthi.data-1.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/scTHI.data_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/scTHI.data_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scthi.data/bioconductor-scthi.data_1.12.0_src_all.tar.gz"], "md5": "28e55c6ba60cb8527c376ca87993c95c", "fn": "scTHI.data_1.12.0.tar.gz"}, "seq2pathway.data-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/seq2pathway.data_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/seq2pathway.data_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seq2pathway.data/bioconductor-seq2pathway.data_1.32.0_src_all.tar.gz"], "md5": "f5b47c139925e607c100f2e3e0292db0", "fn": "seq2pathway.data_1.32.0.tar.gz"}, "seqc-1.34.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/seqc_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/seqc_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seqc/bioconductor-seqc_1.34.0_src_all.tar.gz"], "md5": "834e2a378860f1f6aea76581e87c876f", "fn": "seqc_1.34.0.tar.gz"}, "seqcna.annot-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/seqCNA.annot_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/seqCNA.annot_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seqcna.annot/bioconductor-seqcna.annot_1.36.0_src_all.tar.gz"], "md5": "feee6a27f305149bdfec8a823e2134ec", "fn": "seqCNA.annot_1.36.0.tar.gz"}, "serumstimulation-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/serumStimulation_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/serumStimulation_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-serumstimulation/bioconductor-serumstimulation_1.36.0_src_all.tar.gz"], "md5": "642cc4d3939f4a05e331ef5d1f965835", "fn": "serumStimulation_1.36.0.tar.gz"}, "sesamedata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/sesameData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/sesameData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sesamedata/bioconductor-sesamedata_1.18.0_src_all.tar.gz"], "md5": "4af907a4ed795d2493573b88d55fd4de", "fn": "sesameData_1.18.0.tar.gz"}, "seventygenedata-1.36.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/seventyGeneData_1.36.1.tar.gz", "https://bioarchive.galaxyproject.org/seventyGeneData_1.36.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seventygenedata/bioconductor-seventygenedata_1.36.1_src_all.tar.gz"], "md5": "f7c9703c12b845c5c2eb6cf583fb0f02", "fn": "seventyGeneData_1.36.1.tar.gz"}, "sfedata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SFEData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/SFEData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sfedata/bioconductor-sfedata_1.2.0_src_all.tar.gz"], "md5": "405e15fbe6e99736481e40164abf3b04", "fn": "SFEData_1.2.0.tar.gz"}, "shinymethyldata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/shinyMethylData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/shinyMethylData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-shinymethyldata/bioconductor-shinymethyldata_1.20.0_src_all.tar.gz"], "md5": "f633d8b104a4f61c393b15f59671039b", "fn": "shinyMethylData_1.20.0.tar.gz"}, "signaturesearchdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/signatureSearchData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/signatureSearchData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-signaturesearchdata/bioconductor-signaturesearchdata_1.14.0_src_all.tar.gz"], "md5": "5b3174e0e3af77fea49a107ef423adb3", "fn": "signatureSearchData_1.14.0.tar.gz"}, "simbenchdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SimBenchData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/SimBenchData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-simbenchdata/bioconductor-simbenchdata_1.8.0_src_all.tar.gz"], "md5": "5b2d78e96922a7935cbe5ba91a129b0f", "fn": "SimBenchData_1.8.0.tar.gz"}, "simpintlists-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/simpIntLists_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/simpIntLists_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-simpintlists/bioconductor-simpintlists_1.36.0_src_all.tar.gz"], "md5": "eb06f66a10c4e02738fdfaff769c2dfd", "fn": "simpIntLists_1.36.0.tar.gz"}, "single.mtec.transcriptomes-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Single.mTEC.Transcriptomes_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/Single.mTEC.Transcriptomes_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-single.mtec.transcriptomes/bioconductor-single.mtec.transcriptomes_1.28.0_src_all.tar.gz"], "md5": "11ebbf5ecaf89f0433719a71a8df67b2", "fn": "Single.mTEC.Transcriptomes_1.28.0.tar.gz"}, "singlecellmultimodal-1.12.2": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SingleCellMultiModal_1.12.2.tar.gz", "https://bioarchive.galaxyproject.org/SingleCellMultiModal_1.12.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-singlecellmultimodal/bioconductor-singlecellmultimodal_1.12.2_src_all.tar.gz"], "md5": "599f48321756805173d2069623a0319d", "fn": "SingleCellMultiModal_1.12.2.tar.gz"}, "singlemoleculefootprintingdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SingleMoleculeFootprintingData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/SingleMoleculeFootprintingData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-singlemoleculefootprintingdata/bioconductor-singlemoleculefootprintingdata_1.8.0_src_all.tar.gz"], "md5": "fc061d235ffc26615634a650aedd4ac0", "fn": "SingleMoleculeFootprintingData_1.8.0.tar.gz"}, "snadata-1.46.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SNAData_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/SNAData_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snadata/bioconductor-snadata_1.46.0_src_all.tar.gz"], "md5": "3d83f5e312b308aacb8c9c83d3226115", "fn": "SNAData_1.46.0.tar.gz"}, "snageedata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SNAGEEdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/SNAGEEdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snageedata/bioconductor-snageedata_1.36.0_src_all.tar.gz"], "md5": "e7786160ad882aea9132d3fb2ba77789", "fn": "SNAGEEdata_1.36.0.tar.gz"}, "snphooddata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SNPhoodData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/SNPhoodData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snphooddata/bioconductor-snphooddata_1.30.0_src_all.tar.gz"], "md5": "fbc9419fda8d78b06f76e62df5639ae9", "fn": "SNPhoodData_1.30.0.tar.gz"}, "somaticadata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SomatiCAData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/SomatiCAData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-somaticadata/bioconductor-somaticadata_1.38.0_src_all.tar.gz"], "md5": "1ec746e24a46ea58a782f2d7e18b9c29", "fn": "SomatiCAData_1.38.0.tar.gz"}, "somaticcanceralterations-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SomaticCancerAlterations_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/SomaticCancerAlterations_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-somaticcanceralterations/bioconductor-somaticcanceralterations_1.36.0_src_all.tar.gz"], "md5": "09b8e014009801826dde224175c1f774", "fn": "SomaticCancerAlterations_1.36.0.tar.gz"}, "spatialdmelxsim-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/spatialDmelxsim_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/spatialDmelxsim_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatialdmelxsim/bioconductor-spatialdmelxsim_1.6.0_src_all.tar.gz"], "md5": "22f1c5de1fd6bcbee102e17bbf0323eb", "fn": "spatialDmelxsim_1.6.0.tar.gz"}, "spatiallibd-1.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/spatialLIBD_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/spatialLIBD_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatiallibd/bioconductor-spatiallibd_1.12.0_src_all.tar.gz"], "md5": "1c14166eb3d988b152448d770f491507", "fn": "spatialLIBD_1.12.0.tar.gz"}, "spikein-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SpikeIn_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/SpikeIn_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spikein/bioconductor-spikein_1.42.0_src_all.tar.gz"], "md5": "e738872c55386dae6334ee399c4674a3", "fn": "SpikeIn_1.42.0.tar.gz"}, "spikeinsubset-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SpikeInSubset_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/SpikeInSubset_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spikeinsubset/bioconductor-spikeinsubset_1.40.0_src_all.tar.gz"], "md5": "25b553c357880acdabf962253d55d69b", "fn": "SpikeInSubset_1.40.0.tar.gz"}, "spqndata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/spqnData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/spqnData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spqndata/bioconductor-spqndata_1.12.0_src_all.tar.gz"], "md5": "1588ea6c755eb468f60af1a67712cac0", "fn": "spqnData_1.12.0.tar.gz"}, "stemhypoxia-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/stemHypoxia_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/stemHypoxia_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stemhypoxia/bioconductor-stemhypoxia_1.36.0_src_all.tar.gz"], "md5": "53b049bafffb969dea77f35479720221", "fn": "stemHypoxia_1.36.0.tar.gz"}, "stexampledata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/STexampleData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/STexampleData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stexampledata/bioconductor-stexampledata_1.8.0_src_all.tar.gz"], "md5": "21ccea26e0677e8ff1ec5ddfe7da0a32", "fn": "STexampleData_1.8.0.tar.gz"}, "stjudem-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/stjudem_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/stjudem_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stjudem/bioconductor-stjudem_1.40.0_src_all.tar.gz"], "md5": "d793d5b3f5abf684f188723111097faf", "fn": "stjudem_1.40.0.tar.gz"}, "svm2crmdata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SVM2CRMdata_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/SVM2CRMdata_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-svm2crmdata/bioconductor-svm2crmdata_1.32.0_src_all.tar.gz"], "md5": "e1d44ea0446ba41c2f9264ab088461e2", "fn": "SVM2CRMdata_1.32.0.tar.gz"}, "synapterdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/synapterdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/synapterdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-synapterdata/bioconductor-synapterdata_1.38.0_src_all.tar.gz"], "md5": "cfc22e448bd4d28d06535acfc93cea7b", "fn": "synapterdata_1.38.0.tar.gz"}, "systempiperdata-2.4.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/systemPipeRdata_2.4.0.tar.gz", "https://bioarchive.galaxyproject.org/systemPipeRdata_2.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-systempiperdata/bioconductor-systempiperdata_2.4.0_src_all.tar.gz"], "md5": "afa259f7cd53e2252902a48dd32df1b9", "fn": "systemPipeRdata_2.4.0.tar.gz"}, "tabulamurisdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TabulaMurisData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TabulaMurisData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tabulamurisdata/bioconductor-tabulamurisdata_1.18.0_src_all.tar.gz"], "md5": "c198946ebcce0c1e6c79c65f52a11642", "fn": "TabulaMurisData_1.18.0.tar.gz"}, "tabulamurissenisdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TabulaMurisSenisData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/TabulaMurisSenisData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tabulamurissenisdata/bioconductor-tabulamurissenisdata_1.6.0_src_all.tar.gz"], "md5": "c6a42dc2dc0bbabe7cfd25c91e11f050", "fn": "TabulaMurisSenisData_1.6.0.tar.gz"}, "targetscoredata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TargetScoreData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/TargetScoreData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetscoredata/bioconductor-targetscoredata_1.36.0_src_all.tar.gz"], "md5": "63ccf68833f45d1a853a719046cf9def", "fn": "TargetScoreData_1.36.0.tar.gz"}, "targetsearchdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TargetSearchData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/TargetSearchData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetsearchdata/bioconductor-targetsearchdata_1.38.0_src_all.tar.gz"], "md5": "6dd9996121d44e6f753ce68434de7aad", "fn": "TargetSearchData_1.38.0.tar.gz"}, "tartare-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/tartare_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/tartare_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tartare/bioconductor-tartare_1.14.0_src_all.tar.gz"], "md5": "10b4601e60890e48d47840d2a4f03a22", "fn": "tartare_1.14.0.tar.gz"}, "tbx20bamsubset-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TBX20BamSubset_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/TBX20BamSubset_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tbx20bamsubset/bioconductor-tbx20bamsubset_1.36.0_src_all.tar.gz"], "md5": "5b8761f75b20b32450d6cae46dc063a9", "fn": "TBX20BamSubset_1.36.0.tar.gz"}, "tcgabiolinksgui.data-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TCGAbiolinksGUI.data_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAbiolinksGUI.data_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgabiolinksgui.data/bioconductor-tcgabiolinksgui.data_1.20.0_src_all.tar.gz"], "md5": "d0764549e842b85e9ed17bb0e27b1c54", "fn": "TCGAbiolinksGUI.data_1.20.0.tar.gz"}, "tcgacrcmirna-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TCGAcrcmiRNA_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAcrcmiRNA_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmirna/bioconductor-tcgacrcmirna_1.20.0_src_all.tar.gz"], "md5": "a286cf4adf594bccf4910c3445e2901c", "fn": "TCGAcrcmiRNA_1.20.0.tar.gz"}, "tcgacrcmrna-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TCGAcrcmRNA_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAcrcmRNA_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmrna/bioconductor-tcgacrcmrna_1.20.0_src_all.tar.gz"], "md5": "d3f199714f9dba5ed0838af4e6646c7e", "fn": "TCGAcrcmRNA_1.20.0.tar.gz"}, "tcgamethylation450k-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TCGAMethylation450k_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAMethylation450k_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgamethylation450k/bioconductor-tcgamethylation450k_1.36.0_src_all.tar.gz"], "md5": "5d230a3e839f3ac33e404453c46dfa4f", "fn": "TCGAMethylation450k_1.36.0.tar.gz"}, "tcgaworkflowdata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TCGAWorkflowData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAWorkflowData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgaworkflowdata/bioconductor-tcgaworkflowdata_1.24.0_src_all.tar.gz"], "md5": "12be13d34d28928864db32c639257777", "fn": "TCGAWorkflowData_1.24.0.tar.gz"}, "tenxbraindata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TENxBrainData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxBrainData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxbraindata/bioconductor-tenxbraindata_1.20.0_src_all.tar.gz"], "md5": "74f64ec6654482787dcdc4d6edf085c0", "fn": "TENxBrainData_1.20.0.tar.gz"}, "tenxbusdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TENxBUSData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxBUSData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxbusdata/bioconductor-tenxbusdata_1.14.0_src_all.tar.gz"], "md5": "0ef9324a12e6e70e28a16def5f6e8f8f", "fn": "TENxBUSData_1.14.0.tar.gz"}, "tenxpbmcdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TENxPBMCData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxPBMCData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxpbmcdata/bioconductor-tenxpbmcdata_1.18.0_src_all.tar.gz"], "md5": "6902ddadd45f76cce7e73228ed4bdcaf", "fn": "TENxPBMCData_1.18.0.tar.gz"}, "tenxvisiumdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TENxVisiumData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxVisiumData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxvisiumdata/bioconductor-tenxvisiumdata_1.8.0_src_all.tar.gz"], "md5": "cd391f3b1849f658578a44cfe2aec13b", "fn": "TENxVisiumData_1.8.0.tar.gz"}, "timecoursedata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/timecoursedata_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/timecoursedata_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-timecoursedata/bioconductor-timecoursedata_1.10.0_src_all.tar.gz"], "md5": "7f2ad9b14757098a934109a0597a630b", "fn": "timecoursedata_1.10.0.tar.gz"}, "timerquant-1.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TimerQuant_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/TimerQuant_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-timerquant/bioconductor-timerquant_1.30.0_src_all.tar.gz"], "md5": "8cbdff0672ae0d06372f36e5de1dc86c", "fn": "TimerQuant_1.30.0.tar.gz"}, "tinesath1cdf-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/tinesath1cdf_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/tinesath1cdf_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tinesath1cdf/bioconductor-tinesath1cdf_1.38.0_src_all.tar.gz"], "md5": "9e3235aa047fc3dc7d77437a0afa5b71", "fn": "tinesath1cdf_1.38.0.tar.gz"}, "tinesath1probe-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/tinesath1probe_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/tinesath1probe_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tinesath1probe/bioconductor-tinesath1probe_1.38.0_src_all.tar.gz"], "md5": "d3dc0686f2651dff52a201923e73a751", "fn": "tinesath1probe_1.38.0.tar.gz"}, "tissuetreg-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/tissueTreg_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/tissueTreg_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tissuetreg/bioconductor-tissuetreg_1.20.0_src_all.tar.gz"], "md5": "9755c73b171a371afea8927b7d229a78", "fn": "tissueTreg_1.20.0.tar.gz"}, "tmexplorer-1.10.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TMExplorer_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/TMExplorer_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tmexplorer/bioconductor-tmexplorer_1.10.0_src_all.tar.gz"], "md5": "14411a5488789b44b63a2bc2b88cf33e", "fn": "TMExplorer_1.10.0.tar.gz"}, "tofsimsdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/tofsimsData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/tofsimsData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tofsimsdata/bioconductor-tofsimsdata_1.28.0_src_all.tar.gz"], "md5": "5eccad99f9e3cdfb3813eb1243926142", "fn": "tofsimsData_1.28.0.tar.gz"}, "topdownrdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/topdownrdata_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/topdownrdata_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-topdownrdata/bioconductor-topdownrdata_1.22.0_src_all.tar.gz"], "md5": "c105c5a497f0270c574b757c55eea433", "fn": "topdownrdata_1.22.0.tar.gz"}, "tuberculosis-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/tuberculosis_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/tuberculosis_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tuberculosis/bioconductor-tuberculosis_1.6.0_src_all.tar.gz"], "md5": "9f3fd16d5debb8705f56bf714fc3e860", "fn": "tuberculosis_1.6.0.tar.gz"}, "tweedeseqcountdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/tweeDEseqCountData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/tweeDEseqCountData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tweedeseqcountdata/bioconductor-tweedeseqcountdata_1.38.0_src_all.tar.gz"], "md5": "b48baebaa2abe35419bad4110d7523ec", "fn": "tweeDEseqCountData_1.38.0.tar.gz"}, "tximportdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/tximportData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/tximportData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tximportdata/bioconductor-tximportdata_1.28.0_src_all.tar.gz"], "md5": "8b5ef0f4b63bcd11c21a8389af32fa1f", "fn": "tximportData_1.28.0.tar.gz"}, "varianttoolsdata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/VariantToolsData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/VariantToolsData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-varianttoolsdata/bioconductor-varianttoolsdata_1.24.0_src_all.tar.gz"], "md5": "abaad839d98a3c855cac80bd443fa9b6", "fn": "VariantToolsData_1.24.0.tar.gz"}, "vectrapolarisdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/VectraPolarisData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/VectraPolarisData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vectrapolarisdata/bioconductor-vectrapolarisdata_1.4.0_src_all.tar.gz"], "md5": "f427b5860f7e3498064deabff0328263", "fn": "VectraPolarisData_1.4.0.tar.gz"}, "vulcandata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/vulcandata_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/vulcandata_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vulcandata/bioconductor-vulcandata_1.22.0_src_all.tar.gz"], "md5": "e51d04a9825be5fdb9591377095a0da9", "fn": "vulcandata_1.22.0.tar.gz"}, "weberdivechalcdata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/WeberDivechaLCdata_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/WeberDivechaLCdata_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-weberdivechalcdata/bioconductor-weberdivechalcdata_1.2.0_src_all.tar.gz"], "md5": "f7b4867dc3ce8463050bd897209d00c4", "fn": "WeberDivechaLCdata_1.2.0.tar.gz"}, "wes.1kg.wugsc-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/WES.1KG.WUGSC_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/WES.1KG.WUGSC_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wes.1kg.wugsc/bioconductor-wes.1kg.wugsc_1.32.0_src_all.tar.gz"], "md5": "4037de5e802a16f5aae76eca264b0be7", "fn": "WES.1KG.WUGSC_1.32.0.tar.gz"}, "wgsmapp-1.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/WGSmapp_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/WGSmapp_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wgsmapp/bioconductor-wgsmapp_1.12.0_src_all.tar.gz"], "md5": "7e4b497bab5e73445e19a84f86e40888", "fn": "WGSmapp_1.12.0.tar.gz"}, "xcoredata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/xcoredata_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/xcoredata_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xcoredata/bioconductor-xcoredata_1.4.0_src_all.tar.gz"], "md5": "172e8208ccf23b03ead836908e84522a", "fn": "xcoredata_1.4.0.tar.gz"}, "xhybcasneuf-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/XhybCasneuf_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/XhybCasneuf_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xhybcasneuf/bioconductor-xhybcasneuf_1.38.0_src_all.tar.gz"], "md5": "9522270bba562cca4c2e5e2438294eca", "fn": "XhybCasneuf_1.38.0.tar.gz"}, "yeastcc-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/yeastCC_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastCC_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastcc/bioconductor-yeastcc_1.40.0_src_all.tar.gz"], "md5": "bf769fb99f3c5b763cc44fb25947231a", "fn": "yeastCC_1.40.0.tar.gz"}, "yeastexpdata-0.46.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/yeastExpData_0.46.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastExpData_0.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastexpdata/bioconductor-yeastexpdata_0.46.0_src_all.tar.gz"], "md5": "57c3359351ed64d39e2d8d82abe2d852", "fn": "yeastExpData_0.46.0.tar.gz"}, "yeastgsdata-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/yeastGSData_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastGSData_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastgsdata/bioconductor-yeastgsdata_0.38.0_src_all.tar.gz"], "md5": "09f1e0c194efae4d807ab0b3b14629a5", "fn": "yeastGSData_0.38.0.tar.gz"}, "yeastnagalakshmi-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/yeastNagalakshmi_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastNagalakshmi_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastnagalakshmi/bioconductor-yeastnagalakshmi_1.36.0_src_all.tar.gz"], "md5": "e9c196bfda6e0909a324d88a616dc992", "fn": "yeastNagalakshmi_1.36.0.tar.gz"}, "yeastrnaseq-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/yeastRNASeq_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastRNASeq_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastrnaseq/bioconductor-yeastrnaseq_0.38.0_src_all.tar.gz"], "md5": "f8a8b1a80312aeac4d1676bc8adcb0ee", "fn": "yeastRNASeq_0.38.0.tar.gz"}, "zebrafishrnaseq-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/zebrafishRNASeq_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafishRNASeq_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafishrnaseq/bioconductor-zebrafishrnaseq_1.20.0_src_all.tar.gz"], "md5": "06390452c93fde30918ee5c5a3f6e5f2", "fn": "zebrafishRNASeq_1.20.0.tar.gz"}, "biscuiteerdata-1.14.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/biscuiteerData_1.14.1.tar.gz", "https://bioarchive.galaxyproject.org/biscuiteerData_1.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biscuiteerdata/bioconductor-biscuiteerdata_1.14.1_src_all.tar.gz"], "md5": "143bedc239cf56a25dc8bf6c1e98d392", "fn": "biscuiteerData_1.14.1.tar.gz"}, "spatialdmelxsim-1.6.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/spatialDmelxsim_1.6.1.tar.gz", "https://bioarchive.galaxyproject.org/spatialDmelxsim_1.6.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatialdmelxsim/bioconductor-spatialdmelxsim_1.6.1_src_all.tar.gz"], "md5": "8f999976552a56f39d49fd9ee186b017", "fn": "spatialDmelxsim_1.6.1.tar.gz"}, "mcseadata-1.20.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/mCSEAdata_1.20.1.tar.gz", "https://bioarchive.galaxyproject.org/mCSEAdata_1.20.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcseadata/bioconductor-mcseadata_1.20.1_src_all.tar.gz"], "md5": "43b69165fffc6652fc2df2395bd0b8e6", "fn": "mCSEAdata_1.20.1.tar.gz"}, "methylclockdata-1.8.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/methylclockData_1.8.1.tar.gz", "https://bioarchive.galaxyproject.org/methylclockData_1.8.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylclockdata/bioconductor-methylclockdata_1.8.1_src_all.tar.gz"], "md5": "c211da6ed8d39ba8cee6d4d630691bad", "fn": "methylclockData_1.8.1.tar.gz"}, "affydata-1.48.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/affydata_1.48.1.tar.gz", "https://bioarchive.galaxyproject.org/affydata_1.48.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affydata/bioconductor-affydata_1.48.1_src_all.tar.gz"], "md5": "1c03aa529e4854f6680fcf4702d2bea7", "fn": "affydata_1.48.1.tar.gz"}, "ahensdbs-1.1.10": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/AHEnsDbs_1.1.10.tar.gz", "https://bioarchive.galaxyproject.org/AHEnsDbs_1.1.10.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahensdbs/bioconductor-ahensdbs_1.1.10_src_all.tar.gz"], "md5": "63aa3efc1c85d5a26e4d69d50f781a2a", "fn": "AHEnsDbs_1.1.10.tar.gz"}, "ahlrbasedbs-1.7.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/AHLRBaseDbs_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/AHLRBaseDbs_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahlrbasedbs/bioconductor-ahlrbasedbs_1.7.0_src_all.tar.gz"], "md5": "5df6ef84988477d6262e54abd07c82da", "fn": "AHLRBaseDbs_1.7.0.tar.gz"}, "ahmeshdbs-1.7.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/AHMeSHDbs_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/AHMeSHDbs_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahmeshdbs/bioconductor-ahmeshdbs_1.7.0_src_all.tar.gz"], "md5": "9bbcae25794d2f854a122ba36a4e4c5c", "fn": "AHMeSHDbs_1.7.0.tar.gz"}, "ahpubmeddbs-1.7.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/AHPubMedDbs_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/AHPubMedDbs_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahpubmeddbs/bioconductor-ahpubmeddbs_1.7.0_src_all.tar.gz"], "md5": "b2db2eda6009bc9cdec579c4ab579f25", "fn": "AHPubMedDbs_1.7.0.tar.gz"}, "alphamissense.v2023.hg19-3.18.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/AlphaMissense.v2023.hg19_3.18.2.tar.gz", "https://bioarchive.galaxyproject.org/AlphaMissense.v2023.hg19_3.18.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-alphamissense.v2023.hg19/bioconductor-alphamissense.v2023.hg19_3.18.2_src_all.tar.gz"], "md5": "e8784ad000be637321f432188a5a3f45", "fn": "AlphaMissense.v2023.hg19_3.18.2.tar.gz"}, "alphamissense.v2023.hg38-3.18.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/AlphaMissense.v2023.hg38_3.18.2.tar.gz", "https://bioarchive.galaxyproject.org/AlphaMissense.v2023.hg38_3.18.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-alphamissense.v2023.hg38/bioconductor-alphamissense.v2023.hg38_3.18.2_src_all.tar.gz"], "md5": "bedac9523e18829c5067dec1ebf801d4", "fn": "AlphaMissense.v2023.hg38_3.18.2.tar.gz"}, "anopheles.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/anopheles.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/anopheles.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-anopheles.db0/bioconductor-anopheles.db0_3.18.0_src_all.tar.gz"], "md5": "cd7b03fffb4ffd0cf0877a55a3636d93", "fn": "anopheles.db0_3.18.0.tar.gz"}, "arabidopsis.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/arabidopsis.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/arabidopsis.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-arabidopsis.db0/bioconductor-arabidopsis.db0_3.18.0_src_all.tar.gz"], "md5": "5896dbae0f9f8fdc87712dba0bb6cbd1", "fn": "arabidopsis.db0_3.18.0.tar.gz"}, "biomartgogenesets-0.99.11": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BioMartGOGeneSets_0.99.11.tar.gz", "https://bioarchive.galaxyproject.org/BioMartGOGeneSets_0.99.11.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biomartgogenesets/bioconductor-biomartgogenesets_0.99.11_src_all.tar.gz"], "md5": "f96a12703fd2f9c357442a60e5f2c764", "fn": "BioMartGOGeneSets_0.99.11.tar.gz"}, "bovine.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/bovine.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/bovine.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bovine.db0/bioconductor-bovine.db0_3.18.0_src_all.tar.gz"], "md5": "658829797db74aec87af1914483d1af7", "fn": "bovine.db0_3.18.0.tar.gz"}, "cadd.v1.6.hg19-3.18.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/cadd.v1.6.hg19_3.18.1.tar.gz", "https://bioarchive.galaxyproject.org/cadd.v1.6.hg19_3.18.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cadd.v1.6.hg19/bioconductor-cadd.v1.6.hg19_3.18.1_src_all.tar.gz"], "md5": "10cc50d17dbca89406a2290f37d5203c", "fn": "cadd.v1.6.hg19_3.18.1.tar.gz"}, "cadd.v1.6.hg38-3.18.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/cadd.v1.6.hg38_3.18.1.tar.gz", "https://bioarchive.galaxyproject.org/cadd.v1.6.hg38_3.18.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cadd.v1.6.hg38/bioconductor-cadd.v1.6.hg38_3.18.1_src_all.tar.gz"], "md5": "620a889ea8bc55f98811a80a3aec814d", "fn": "cadd.v1.6.hg38_3.18.1.tar.gz"}, "canine.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/canine.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/canine.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canine.db0/bioconductor-canine.db0_3.18.0_src_all.tar.gz"], "md5": "dc4fff8ed0a758ddff3f52aa0e8652c6", "fn": "canine.db0_3.18.0.tar.gz"}, "chicken.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/chicken.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/chicken.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chicken.db0/bioconductor-chicken.db0_3.18.0_src_all.tar.gz"], "md5": "0f0c20a519a9490c0909b68ec67c206d", "fn": "chicken.db0_3.18.0.tar.gz"}, "chimp.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/chimp.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/chimp.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chimp.db0/bioconductor-chimp.db0_3.18.0_src_all.tar.gz"], "md5": "afb020cefb808101626234257bf71f69", "fn": "chimp.db0_3.18.0.tar.gz"}, "ecolik12.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ecoliK12.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliK12.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolik12.db0/bioconductor-ecolik12.db0_3.18.0_src_all.tar.gz"], "md5": "dd303204595a25bc730695462e930247", "fn": "ecoliK12.db0_3.18.0.tar.gz"}, "ecolisakai.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ecoliSakai.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliSakai.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolisakai.db0/bioconductor-ecolisakai.db0_3.18.0_src_all.tar.gz"], "md5": "2afd28e9062d869d37e3d65dbe410bcb", "fn": "ecoliSakai.db0_3.18.0.tar.gz"}, "fly.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/fly.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/fly.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fly.db0/bioconductor-fly.db0_3.18.0_src_all.tar.gz"], "md5": "49722b8a538d02f71631a418b92c44d7", "fn": "fly.db0_3.18.0.tar.gz"}, "geneplast.data-0.99.7": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/geneplast.data_0.99.7.tar.gz", "https://bioarchive.galaxyproject.org/geneplast.data_0.99.7.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-geneplast.data/bioconductor-geneplast.data_0.99.7_src_all.tar.gz"], "md5": "ef658e131138d87033fcd985c38cf45f", "fn": "geneplast.data_0.99.7.tar.gz"}, "genesummary-0.99.6": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GeneSummary_0.99.6.tar.gz", "https://bioarchive.galaxyproject.org/GeneSummary_0.99.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genesummary/bioconductor-genesummary_0.99.6_src_all.tar.gz"], "md5": "9df029a96bf0fa5bb76ee8b8923c458c", "fn": "GeneSummary_0.99.6.tar.gz"}, "genomeinfodbdata-1.2.11": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz", "https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.11.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.11_src_all.tar.gz"], "md5": "2a4cbfc2031992fed3c9445f450890a2", "fn": "GenomeInfoDbData_1.2.11.tar.gz"}, "go.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GO.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/GO.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-go.db/bioconductor-go.db_3.18.0_src_all.tar.gz"], "md5": "b23522167263afc45a9b115d01632cb1", "fn": "GO.db_3.18.0.tar.gz"}, "hpo.db-0.99.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/HPO.db_0.99.2.tar.gz", "https://bioarchive.galaxyproject.org/HPO.db_0.99.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hpo.db/bioconductor-hpo.db_0.99.2_src_all.tar.gz"], "md5": "977cfb31ff344c58fd2dd0a2c6b765ab", "fn": "HPO.db_0.99.2.tar.gz"}, "human.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/human.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/human.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human.db0/bioconductor-human.db0_3.18.0_src_all.tar.gz"], "md5": "e3b04d46f0618785b37fb84bb899295e", "fn": "human.db0_3.18.0.tar.gz"}, "jaspar2024-0.99.6": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/JASPAR2024_0.99.6.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2024_0.99.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2024/bioconductor-jaspar2024_0.99.6_src_all.tar.gz"], "md5": "9c8144547873a36473a5f9cad793f578", "fn": "JASPAR2024_0.99.6.tar.gz"}, "malaria.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/malaria.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/malaria.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-malaria.db0/bioconductor-malaria.db0_3.18.0_src_all.tar.gz"], "md5": "6f71b4ac69ae5237f3f5e1337d5073d7", "fn": "malaria.db0_3.18.0.tar.gz"}, "mouse.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mouse.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse.db0/bioconductor-mouse.db0_3.18.0_src_all.tar.gz"], "md5": "1ef6bb1d25e53443871e0e8c975b36c0", "fn": "mouse.db0_3.18.0.tar.gz"}, "mpo.db-0.99.7": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MPO.db_0.99.7.tar.gz", "https://bioarchive.galaxyproject.org/MPO.db_0.99.7.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mpo.db/bioconductor-mpo.db_0.99.7_src_all.tar.gz"], "md5": "1f1b83d5d03d69a82ca2b9e7179b537f", "fn": "MPO.db_0.99.7.tar.gz"}, "org.ag.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Ag.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ag.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ag.eg.db/bioconductor-org.ag.eg.db_3.18.0_src_all.tar.gz"], "md5": "a67c309f5472338fd47fe43ff20ce2e5", "fn": "org.Ag.eg.db_3.18.0.tar.gz"}, "org.at.tair.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.At.tair.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.At.tair.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.at.tair.db/bioconductor-org.at.tair.db_3.18.0_src_all.tar.gz"], "md5": "5d6161b859de99eaeadebc0e03ae9c68", "fn": "org.At.tair.db_3.18.0.tar.gz"}, "org.bt.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Bt.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Bt.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.bt.eg.db/bioconductor-org.bt.eg.db_3.18.0_src_all.tar.gz"], "md5": "23fd8017323c86930c50d596204bad54", "fn": "org.Bt.eg.db_3.18.0.tar.gz"}, "org.ce.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Ce.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ce.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ce.eg.db/bioconductor-org.ce.eg.db_3.18.0_src_all.tar.gz"], "md5": "441a5efb4649a1201b5552b14c1f1cef", "fn": "org.Ce.eg.db_3.18.0.tar.gz"}, "org.cf.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Cf.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Cf.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.cf.eg.db/bioconductor-org.cf.eg.db_3.18.0_src_all.tar.gz"], "md5": "038d08c046a81218a31ff8db0877dd15", "fn": "org.Cf.eg.db_3.18.0.tar.gz"}, "org.dm.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Dm.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Dm.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.dm.eg.db/bioconductor-org.dm.eg.db_3.18.0_src_all.tar.gz"], "md5": "92577ed3bc5d76b78905169eebfebe7d", "fn": "org.Dm.eg.db_3.18.0.tar.gz"}, "org.dr.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Dr.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Dr.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.dr.eg.db/bioconductor-org.dr.eg.db_3.18.0_src_all.tar.gz"], "md5": "cfea28c45f2f34c675975eacbe861a5f", "fn": "org.Dr.eg.db_3.18.0.tar.gz"}, "org.eck12.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.EcK12.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.EcK12.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.eck12.eg.db/bioconductor-org.eck12.eg.db_3.18.0_src_all.tar.gz"], "md5": "50d3d3ca9efec212eae3a920b00750a3", "fn": "org.EcK12.eg.db_3.18.0.tar.gz"}, "org.ecsakai.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.EcSakai.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.EcSakai.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ecsakai.eg.db/bioconductor-org.ecsakai.eg.db_3.18.0_src_all.tar.gz"], "md5": "3f26ffa55ce30fc8caa64f826207ac61", "fn": "org.EcSakai.eg.db_3.18.0.tar.gz"}, "org.gg.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Gg.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Gg.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.gg.eg.db/bioconductor-org.gg.eg.db_3.18.0_src_all.tar.gz"], "md5": "4ebcbfb0baeee3332a2a07aeae2402a9", "fn": "org.Gg.eg.db_3.18.0.tar.gz"}, "org.hs.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Hs.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Hs.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.hs.eg.db/bioconductor-org.hs.eg.db_3.18.0_src_all.tar.gz"], "md5": "e1f74b9d0c541b5678a0d88f6a8ec847", "fn": "org.Hs.eg.db_3.18.0.tar.gz"}, "org.mm.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Mm.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Mm.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.mm.eg.db/bioconductor-org.mm.eg.db_3.18.0_src_all.tar.gz"], "md5": "bd95e1ff46f764fff51acc60b249fe95", "fn": "org.Mm.eg.db_3.18.0.tar.gz"}, "org.mmu.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Mmu.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Mmu.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.mmu.eg.db/bioconductor-org.mmu.eg.db_3.18.0_src_all.tar.gz"], "md5": "45a35940d0d1ab91b2b262a8666afa53", "fn": "org.Mmu.eg.db_3.18.0.tar.gz"}, "org.pt.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Pt.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Pt.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.pt.eg.db/bioconductor-org.pt.eg.db_3.18.0_src_all.tar.gz"], "md5": "d6672365e68ece6415e2736f40bf096c", "fn": "org.Pt.eg.db_3.18.0.tar.gz"}, "org.rn.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Rn.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Rn.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.rn.eg.db/bioconductor-org.rn.eg.db_3.18.0_src_all.tar.gz"], "md5": "1ff92cec0fc2cbd5b3055d1153526ce3", "fn": "org.Rn.eg.db_3.18.0.tar.gz"}, "org.sc.sgd.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Sc.sgd.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Sc.sgd.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.sc.sgd.db/bioconductor-org.sc.sgd.db_3.18.0_src_all.tar.gz"], "md5": "cd83de7109be623e7a294a47ca65f160", "fn": "org.Sc.sgd.db_3.18.0.tar.gz"}, "org.ss.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Ss.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ss.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ss.eg.db/bioconductor-org.ss.eg.db_3.18.0_src_all.tar.gz"], "md5": "f9b32c76d23f9195df7a7eb6529f3340", "fn": "org.Ss.eg.db_3.18.0.tar.gz"}, "org.xl.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Xl.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Xl.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.xl.eg.db/bioconductor-org.xl.eg.db_3.18.0_src_all.tar.gz"], "md5": "bbea76a4373d8b51048029b83c591aca", "fn": "org.Xl.eg.db_3.18.0.tar.gz"}, "orthology.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/Orthology.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/Orthology.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-orthology.eg.db/bioconductor-orthology.eg.db_3.18.0_src_all.tar.gz"], "md5": "1e53a6a144a5074544cbe166ad241012", "fn": "Orthology.eg.db_3.18.0.tar.gz"}, "panther.db-1.0.12": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/PANTHER.db_1.0.12.tar.gz", "https://bioarchive.galaxyproject.org/PANTHER.db_1.0.12.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-panther.db/bioconductor-panther.db_1.0.12_src_all.tar.gz"], "md5": "edafd1c94f2f1cf3975f525fae7a9b83", "fn": "PANTHER.db_1.0.12.tar.gz"}, "pfam.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/PFAM.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/PFAM.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pfam.db/bioconductor-pfam.db_3.18.0_src_all.tar.gz"], "md5": "f98f5d1e5d335e6bbf1ea6426cde67bb", "fn": "PFAM.db_3.18.0.tar.gz"}, "pig.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pig.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/pig.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pig.db0/bioconductor-pig.db0_3.18.0_src_all.tar.gz"], "md5": "85aaccdbdb969825957db45db3fb7801", "fn": "pig.db0_3.18.0.tar.gz"}, "rat.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rat.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rat.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat.db0/bioconductor-rat.db0_3.18.0_src_all.tar.gz"], "md5": "cde666f86ec7b61beb8cf1037511f977", "fn": "rat.db0_3.18.0.tar.gz"}, "reactome.db-1.86.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/reactome.db_1.86.2.tar.gz", "https://bioarchive.galaxyproject.org/reactome.db_1.86.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-reactome.db/bioconductor-reactome.db_1.86.2_src_all.tar.gz"], "md5": "ff56f3908b347cb18e3e4ccedf7f584e", "fn": "reactome.db_1.86.2.tar.gz"}, "rhesus.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rhesus.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rhesus.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rhesus.db0/bioconductor-rhesus.db0_3.18.0_src_all.tar.gz"], "md5": "26d7aa426d23f0c64cb0918f90c32314", "fn": "rhesus.db0_3.18.0.tar.gz"}, "somascan.db-0.99.7": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/SomaScan.db_0.99.7.tar.gz", "https://bioarchive.galaxyproject.org/SomaScan.db_0.99.7.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-somascan.db/bioconductor-somascan.db_0.99.7_src_all.tar.gz"], "md5": "aa52f4f12dfb2f0aa4c7fe3633de4646", "fn": "SomaScan.db_0.99.7.tar.gz"}, "synaptome.db-0.99.15": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/synaptome.db_0.99.15.tar.gz", "https://bioarchive.galaxyproject.org/synaptome.db_0.99.15.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-synaptome.db/bioconductor-synaptome.db_0.99.15_src_all.tar.gz"], "md5": "7ed11d61ac8dca86372eeec59b5ab03b", "fn": "synaptome.db_0.99.15.tar.gz"}, "txdb.hsapiens.ucsc.hg38.knowngene-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg38.knownGene_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_3.18.0_src_all.tar.gz"], "md5": "2344dbd2878c82c6c860ed6529a700b2", "fn": "TxDb.Hsapiens.UCSC.hg38.knownGene_3.18.0.tar.gz"}, "txdb.hsapiens.ucsc.hg38.refgene-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.refGene_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg38.refGene_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/bioconductor-txdb.hsapiens.ucsc.hg38.refgene_3.18.0_src_all.tar.gz"], "md5": "7ec982095ea795b99d53b6549d7ba4d4", "fn": "TxDb.Hsapiens.UCSC.hg38.refGene_3.18.0.tar.gz"}, "txdb.mmusculus.ucsc.mm39.knowngene-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm39.knownGene_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm39.knownGene_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene_3.18.0_src_all.tar.gz"], "md5": "5ceb110ce3327d44f45bf5118ec7f3af", "fn": "TxDb.Mmusculus.UCSC.mm39.knownGene_3.18.0.tar.gz"}, "txdb.mmusculus.ucsc.mm39.refgene-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm39.refGene_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm39.refGene_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/bioconductor-txdb.mmusculus.ucsc.mm39.refgene_3.18.0_src_all.tar.gz"], "md5": "2fd64557d5f1bade11432b666c63f33a", "fn": "TxDb.Mmusculus.UCSC.mm39.refGene_3.18.0.tar.gz"}, "uniprotkeywords-0.99.7": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/UniProtKeywords_0.99.7.tar.gz", "https://bioarchive.galaxyproject.org/UniProtKeywords_0.99.7.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-uniprotkeywords/bioconductor-uniprotkeywords_0.99.7_src_all.tar.gz"], "md5": "b2cda32dda256fb0d110192e194af838", "fn": "UniProtKeywords_0.99.7.tar.gz"}, "worm.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/worm.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/worm.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-worm.db0/bioconductor-worm.db0_3.18.0_src_all.tar.gz"], "md5": "67be1277b5ae184558259ac720a5741e", "fn": "worm.db0_3.18.0.tar.gz"}, "xenopus.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/xenopus.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/xenopus.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xenopus.db0/bioconductor-xenopus.db0_3.18.0_src_all.tar.gz"], "md5": "67b245b456f21672e70fa0690d7e8410", "fn": "xenopus.db0_3.18.0.tar.gz"}, "yeast.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/yeast.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/yeast.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeast.db0/bioconductor-yeast.db0_3.18.0_src_all.tar.gz"], "md5": "483043596daee94866843e6a43dcf538", "fn": "yeast.db0_3.18.0.tar.gz"}, "zebrafish.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/zebrafish.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafish.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafish.db0/bioconductor-zebrafish.db0_3.18.0_src_all.tar.gz"], "md5": "5da71e369e2b538fe276cd58b511ebab", "fn": "zebrafish.db0_3.18.0.tar.gz"}, "adductdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/adductData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/adductData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-adductdata/bioconductor-adductdata_1.18.0_src_all.tar.gz"], "md5": "bf0e3549ee672a31f32759f0535f360a", "fn": "adductData_1.18.0.tar.gz"}, "affycompdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/affycompData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/affycompData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affycompdata/bioconductor-affycompdata_1.40.0_src_all.tar.gz"], "md5": "205391e19fb160dcff1531892f28b006", "fn": "affycompData_1.40.0.tar.gz"}, "affydata-1.50.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/affydata_1.50.0.tar.gz", "https://bioarchive.galaxyproject.org/affydata_1.50.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affydata/bioconductor-affydata_1.50.0_src_all.tar.gz"], "md5": "29caf389ca94d4c0c0b27d993f33354c", "fn": "affydata_1.50.0.tar.gz"}, "affyhgu133a2expr-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Affyhgu133A2Expr_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133A2Expr_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133a2expr/bioconductor-affyhgu133a2expr_1.38.0_src_all.tar.gz"], "md5": "56296960e5539a4fd84724344f30aaaa", "fn": "Affyhgu133A2Expr_1.38.0.tar.gz"}, "affyhgu133aexpr-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Affyhgu133aExpr_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133aExpr_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133aexpr/bioconductor-affyhgu133aexpr_1.40.0_src_all.tar.gz"], "md5": "2cf458278c574450a3a5ffe64a2aa72b", "fn": "Affyhgu133aExpr_1.40.0.tar.gz"}, "affyhgu133plus2expr-1.36.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Affyhgu133Plus2Expr_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133Plus2Expr_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133plus2expr/bioconductor-affyhgu133plus2expr_1.36.0_src_all.tar.gz"], "md5": "f8baac83db4de07f941552d7b62c8d62", "fn": "Affyhgu133Plus2Expr_1.36.0.tar.gz"}, "affymetrixdatatestfiles-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/AffymetrixDataTestFiles_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/AffymetrixDataTestFiles_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affymetrixdatatestfiles/bioconductor-affymetrixdatatestfiles_0.40.0_src_all.tar.gz"], "md5": "57ecb8e4d3f0d7a9cdcedb2a9648dd1e", "fn": "AffymetrixDataTestFiles_0.40.0.tar.gz"}, "affymoe4302expr-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Affymoe4302Expr_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/Affymoe4302Expr_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affymoe4302expr/bioconductor-affymoe4302expr_1.40.0_src_all.tar.gz"], "md5": "4dcd432d350cf2f8000f67774d95481c", "fn": "Affymoe4302Expr_1.40.0.tar.gz"}, "airway-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/airway_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/airway_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-airway/bioconductor-airway_1.22.0_src_all.tar.gz"], "md5": "ffed4ae3349ebeeeabff9f1456b8ba1d", "fn": "airway_1.22.0.tar.gz"}, "all-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ALL_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/ALL_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-all/bioconductor-all_1.44.0_src_all.tar.gz"], "md5": "b80eb482b4937ef4eac01027ac95a61a", "fn": "ALL_1.44.0.tar.gz"}, "allmll-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ALLMLL_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/ALLMLL_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-allmll/bioconductor-allmll_1.42.0_src_all.tar.gz"], "md5": "669e7ff030b6fea51c8013816bd6fae7", "fn": "ALLMLL_1.42.0.tar.gz"}, "ampaffyexample-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/AmpAffyExample_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/AmpAffyExample_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ampaffyexample/bioconductor-ampaffyexample_1.42.0_src_all.tar.gz"], "md5": "3277d6d26f145ddbb45c3808273cd150", "fn": "AmpAffyExample_1.42.0.tar.gz"}, "aneufinderdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/AneuFinderData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/AneuFinderData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-aneufinderdata/bioconductor-aneufinderdata_1.30.0_src_all.tar.gz"], "md5": "895230cd9b780dbb286a012f3c8777eb", "fn": "AneuFinderData_1.30.0.tar.gz"}, "antiprofilesdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/antiProfilesData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/antiProfilesData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-antiprofilesdata/bioconductor-antiprofilesdata_1.38.0_src_all.tar.gz"], "md5": "dc40c00fb296b31cf65369e801d6f2f8", "fn": "antiProfilesData_1.38.0.tar.gz"}, "aracne.networks-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/aracne.networks_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/aracne.networks_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-aracne.networks/bioconductor-aracne.networks_1.28.0_src_all.tar.gz"], "md5": "42657d0acf4c1ba54aa2057fa4525d51", "fn": "aracne.networks_1.28.0.tar.gz"}, "arrmdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ARRmData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ARRmData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-arrmdata/bioconductor-arrmdata_1.38.0_src_all.tar.gz"], "md5": "95475f869b8ff3d6344c0f45f2e616c9", "fn": "ARRmData_1.38.0.tar.gz"}, "ashkenazimsonchr21-1.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/AshkenazimSonChr21_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/AshkenazimSonChr21_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ashkenazimsonchr21/bioconductor-ashkenazimsonchr21_1.32.0_src_all.tar.gz"], "md5": "a4455fab1d47dcf8dc2411fec1066a2c", "fn": "AshkenazimSonChr21_1.32.0.tar.gz"}, "asicsdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ASICSdata_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/ASICSdata_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-asicsdata/bioconductor-asicsdata_1.22.0_src_all.tar.gz"], "md5": "afb117c0db733e23239bf2cf4e18d364", "fn": "ASICSdata_1.22.0.tar.gz"}, "assessorfdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/AssessORFData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/AssessORFData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-assessorfdata/bioconductor-assessorfdata_1.20.0_src_all.tar.gz"], "md5": "0dd44e672021a9179762efe4959e8608", "fn": "AssessORFData_1.20.0.tar.gz"}, "bcellviper-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/bcellViper_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/bcellViper_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bcellviper/bioconductor-bcellviper_1.38.0_src_all.tar.gz"], "md5": "7e93bbaa204826358c77282e2a370074", "fn": "bcellViper_1.38.0.tar.gz"}, "beadarrayexampledata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/beadarrayExampleData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/beadarrayExampleData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadarrayexampledata/bioconductor-beadarrayexampledata_1.40.0_src_all.tar.gz"], "md5": "d327e659adc868f1e3c7ae457c60087b", "fn": "beadarrayExampleData_1.40.0.tar.gz"}, "beadarrayusecases-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/BeadArrayUseCases_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/BeadArrayUseCases_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadarrayusecases/bioconductor-beadarrayusecases_1.40.0_src_all.tar.gz"], "md5": "a939c03744773755b9a80de63a925c3e", "fn": "BeadArrayUseCases_1.40.0.tar.gz"}, "beadsorted.saliva.epic-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/BeadSorted.Saliva.EPIC_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/BeadSorted.Saliva.EPIC_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadsorted.saliva.epic/bioconductor-beadsorted.saliva.epic_1.10.0_src_all.tar.gz"], "md5": "ca080a144452fad8ce1bdf8e86d88c74", "fn": "BeadSorted.Saliva.EPIC_1.10.0.tar.gz"}, "benchmarkfdrdata2019-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/benchmarkfdrData2019_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/benchmarkfdrData2019_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-benchmarkfdrdata2019/bioconductor-benchmarkfdrdata2019_1.16.0_src_all.tar.gz"], "md5": "50ce7eb4100da1909ddd6c71c31e7e0c", "fn": "benchmarkfdrData2019_1.16.0.tar.gz"}, "beta7-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/beta7_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/beta7_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beta7/bioconductor-beta7_1.40.0_src_all.tar.gz"], "md5": "7beee3699282a97c765cf418036fc0ed", "fn": "beta7_1.40.0.tar.gz"}, "bioimagedbs-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/BioImageDbs_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/BioImageDbs_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bioimagedbs/bioconductor-bioimagedbs_1.10.0_src_all.tar.gz"], "md5": "785e9ea81ef5699d70af969fd8d4703d", "fn": "BioImageDbs_1.10.0.tar.gz"}, "bioplex-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/BioPlex_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/BioPlex_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bioplex/bioconductor-bioplex_1.8.0_src_all.tar.gz"], "md5": "77e38da3b194e7776fa7007a2cef42bf", "fn": "BioPlex_1.8.0.tar.gz"}, "biotmledata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/biotmleData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/biotmleData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biotmledata/bioconductor-biotmledata_1.26.0_src_all.tar.gz"], "md5": "8c725d5c496f9bfe7ed4b5d5c538244a", "fn": "biotmleData_1.26.0.tar.gz"}, "biscuiteerdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/biscuiteerData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/biscuiteerData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biscuiteerdata/bioconductor-biscuiteerdata_1.16.0_src_all.tar.gz"], "md5": "9610f1ea2c2e8303acbb0b52204f8d3e", "fn": "biscuiteerData_1.16.0.tar.gz"}, "bladderbatch-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/bladderbatch_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/bladderbatch_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bladderbatch/bioconductor-bladderbatch_1.40.0_src_all.tar.gz"], "md5": "d59d10a87e8d62c6ba10f7e9c0160a44", "fn": "bladderbatch_1.40.0.tar.gz"}, "blimatestingdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/blimaTestingData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/blimaTestingData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-blimatestingdata/bioconductor-blimatestingdata_1.22.0_src_all.tar.gz"], "md5": "3ae3da97d0d020e16feee29b93c24825", "fn": "blimaTestingData_1.22.0.tar.gz"}, "bloodcancermultiomics2017-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/BloodCancerMultiOmics2017_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/BloodCancerMultiOmics2017_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bloodcancermultiomics2017/bioconductor-bloodcancermultiomics2017_1.22.0_src_all.tar.gz"], "md5": "d2b2dcb147bf904df505fedca2d1ea9e", "fn": "BloodCancerMultiOmics2017_1.22.0.tar.gz"}, "bodymaprat-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/bodymapRat_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/bodymapRat_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bodymaprat/bioconductor-bodymaprat_1.18.0_src_all.tar.gz"], "md5": "fc575d7f33dd1ee73f1860fb076a840b", "fn": "bodymapRat_1.18.0.tar.gz"}, "breakpointrdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/breakpointRdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/breakpointRdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breakpointrdata/bioconductor-breakpointrdata_1.20.0_src_all.tar.gz"], "md5": "e3f74132513d150cb5d5cc62bfd49586", "fn": "breakpointRdata_1.20.0.tar.gz"}, "breastcancermainz-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/breastCancerMAINZ_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerMAINZ_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancermainz/bioconductor-breastcancermainz_1.40.0_src_all.tar.gz"], "md5": "2b8df5af87b71c6706f909129212b504", "fn": "breastCancerMAINZ_1.40.0.tar.gz"}, "breastcancernki-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/breastCancerNKI_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerNKI_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancernki/bioconductor-breastcancernki_1.40.0_src_all.tar.gz"], "md5": "0a0940593d75deaed0aa6f01954cf61c", "fn": "breastCancerNKI_1.40.0.tar.gz"}, "breastcancertransbig-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/breastCancerTRANSBIG_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerTRANSBIG_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancertransbig/bioconductor-breastcancertransbig_1.40.0_src_all.tar.gz"], "md5": "170d89ddd3e554da50a0b2b5d040a96e", "fn": "breastCancerTRANSBIG_1.40.0.tar.gz"}, "breastcancerunt-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/breastCancerUNT_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerUNT_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancerunt/bioconductor-breastcancerunt_1.40.0_src_all.tar.gz"], "md5": "31e1b6d7e34b4acb9207e3e152539166", "fn": "breastCancerUNT_1.40.0.tar.gz"}, "breastcancerupp-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/breastCancerUPP_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerUPP_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancerupp/bioconductor-breastcancerupp_1.40.0_src_all.tar.gz"], "md5": "c5c10989a8a2dbfd20c228522474fac1", "fn": "breastCancerUPP_1.40.0.tar.gz"}, "breastcancervdx-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/breastCancerVDX_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerVDX_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancervdx/bioconductor-breastcancervdx_1.40.0_src_all.tar.gz"], "md5": "446ef46e0bdd1480e12de21ded7b58f0", "fn": "breastCancerVDX_1.40.0.tar.gz"}, "brgedata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/brgedata_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/brgedata_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-brgedata/bioconductor-brgedata_1.24.0_src_all.tar.gz"], "md5": "b8d26c8dfa756e9eb556e4662e3b3302", "fn": "brgedata_1.24.0.tar.gz"}, "bronchialil13-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/bronchialIL13_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/bronchialIL13_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bronchialil13/bioconductor-bronchialil13_1.40.0_src_all.tar.gz"], "md5": "be303e29450fb15b03a10f6caaf30159", "fn": "bronchialIL13_1.40.0.tar.gz"}, "bsseqdata-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/bsseqData_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/bsseqData_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsseqdata/bioconductor-bsseqdata_0.40.0_src_all.tar.gz"], "md5": "514171e8133c8d38e6b1ad31eff722a8", "fn": "bsseqData_0.40.0.tar.gz"}, "cancerdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/cancerdata_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/cancerdata_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cancerdata/bioconductor-cancerdata_1.40.0_src_all.tar.gz"], "md5": "7baa088ef320a0222a897987ea8c3e8b", "fn": "cancerdata_1.40.0.tar.gz"}, "cardinalworkflows-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CardinalWorkflows_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/CardinalWorkflows_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cardinalworkflows/bioconductor-cardinalworkflows_1.34.0_src_all.tar.gz"], "md5": "54c51a2ec2f20f96ad9e60c16eeb2ccb", "fn": "CardinalWorkflows_1.34.0.tar.gz"}, "ccdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ccdata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/ccdata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ccdata/bioconductor-ccdata_1.28.0_src_all.tar.gz"], "md5": "60cbd595e53467fd61e1edc4f8ea47e7", "fn": "ccdata_1.28.0.tar.gz"}, "ccl4-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CCl4_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/CCl4_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ccl4/bioconductor-ccl4_1.40.0_src_all.tar.gz"], "md5": "3247cf1db347f959d908e88b5e8febb5", "fn": "CCl4_1.40.0.tar.gz"}, "cctutorial-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ccTutorial_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/ccTutorial_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cctutorial/bioconductor-cctutorial_1.40.0_src_all.tar.gz"], "md5": "20af731ec83a03f12ec5d87060f5d168", "fn": "ccTutorial_1.40.0.tar.gz"}, "celarefdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/celarefData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/celarefData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celarefdata/bioconductor-celarefdata_1.20.0_src_all.tar.gz"], "md5": "6864c27f1d574314fe10612b37f6c433", "fn": "celarefData_1.20.0.tar.gz"}, "celldex-1.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/celldex_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/celldex_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celldex/bioconductor-celldex_1.12.0_src_all.tar.gz"], "md5": "62419c915beb91f7c228e1a125df68f8", "fn": "celldex_1.12.0.tar.gz"}, "cellmapperdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CellMapperData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/CellMapperData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cellmapperdata/bioconductor-cellmapperdata_1.28.0_src_all.tar.gz"], "md5": "5db37729dd49f26b6cba9ff4aff80b1d", "fn": "CellMapperData_1.28.0.tar.gz"}, "cftoolsdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/cfToolsData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/cfToolsData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cftoolsdata/bioconductor-cftoolsdata_1.0.0_src_all.tar.gz"], "md5": "00bbf328a45fb8731b3c7262b3521e0b", "fn": "cfToolsData_1.0.0.tar.gz"}, "champdata-2.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ChAMPdata_2.34.0.tar.gz", "https://bioarchive.galaxyproject.org/ChAMPdata_2.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-champdata/bioconductor-champdata_2.34.0_src_all.tar.gz"], "md5": "b12bfec01a1cfdd103bc0cb9bd44d4aa", "fn": "ChAMPdata_2.34.0.tar.gz"}, "chic.data-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ChIC.data_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIC.data_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chic.data/bioconductor-chic.data_1.22.0_src_all.tar.gz"], "md5": "34b50ea53e6b5c982dc044addc68c33b", "fn": "ChIC.data_1.22.0.tar.gz"}, "chipenrich.data-2.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/chipenrich.data_2.26.0.tar.gz", "https://bioarchive.galaxyproject.org/chipenrich.data_2.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipenrich.data/bioconductor-chipenrich.data_2.26.0_src_all.tar.gz"], "md5": "4918da98125fee82afaeee84930051a8", "fn": "chipenrich.data_2.26.0.tar.gz"}, "chipexoqualexample-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ChIPexoQualExample_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIPexoQualExample_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipexoqualexample/bioconductor-chipexoqualexample_1.26.0_src_all.tar.gz"], "md5": "5ebb67a1848aa0e69557e795d236e24b", "fn": "ChIPexoQualExample_1.26.0.tar.gz"}, "chipseqdbdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/chipseqDBData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/chipseqDBData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipseqdbdata/bioconductor-chipseqdbdata_1.18.0_src_all.tar.gz"], "md5": "a6e50016d2d7c0cb085df2c4254b5f84", "fn": "chipseqDBData_1.18.0.tar.gz"}, "chipxpressdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ChIPXpressData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIPXpressData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipxpressdata/bioconductor-chipxpressdata_1.40.0_src_all.tar.gz"], "md5": "029086a630df9533dedea4babd28f0d7", "fn": "ChIPXpressData_1.40.0.tar.gz"}, "chromstardata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/chromstaRData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/chromstaRData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chromstardata/bioconductor-chromstardata_1.28.0_src_all.tar.gz"], "md5": "7f4a965a6b5aa71874a5cca39046cabf", "fn": "chromstaRData_1.28.0.tar.gz"}, "cll-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CLL_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/CLL_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cll/bioconductor-cll_1.42.0_src_all.tar.gz"], "md5": "4f71fa48ba2205b80c098275c866ac1f", "fn": "CLL_1.42.0.tar.gz"}, "cllmethylation-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CLLmethylation_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/CLLmethylation_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cllmethylation/bioconductor-cllmethylation_1.22.0_src_all.tar.gz"], "md5": "a8c3768dca1df5bb9e911878b68ad4c4", "fn": "CLLmethylation_1.22.0.tar.gz"}, "clumsiddata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CluMSIDdata_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/CluMSIDdata_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clumsiddata/bioconductor-clumsiddata_1.18.0_src_all.tar.gz"], "md5": "315da29d9f052e0abfbad59be9606f34", "fn": "CluMSIDdata_1.18.0.tar.gz"}, "clustifyrdatahub-1.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/clustifyrdatahub_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/clustifyrdatahub_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clustifyrdatahub/bioconductor-clustifyrdatahub_1.12.0_src_all.tar.gz"], "md5": "aac4529e5c0d71fdc49bda51c3915f61", "fn": "clustifyrdatahub_1.12.0.tar.gz"}, "cmap2data-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/cMap2data_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/cMap2data_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cmap2data/bioconductor-cmap2data_1.38.0_src_all.tar.gz"], "md5": "c5ecbc59a690426c6def7feb720e1a7d", "fn": "cMap2data_1.38.0.tar.gz"}, "cnvgsadata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/cnvGSAdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/cnvGSAdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cnvgsadata/bioconductor-cnvgsadata_1.38.0_src_all.tar.gz"], "md5": "1cc86a2066cae55493d710c475cc7112", "fn": "cnvGSAdata_1.38.0.tar.gz"}, "cohcapanno-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/COHCAPanno_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/COHCAPanno_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cohcapanno/bioconductor-cohcapanno_1.38.0_src_all.tar.gz"], "md5": "78fd4891651a8a62779fe402a13ba6b1", "fn": "COHCAPanno_1.38.0.tar.gz"}, "colonca-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/colonCA_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/colonCA_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-colonca/bioconductor-colonca_1.44.0_src_all.tar.gz"], "md5": "d12f03a7ded676f392dbbb26bbbef174", "fn": "colonCA_1.44.0.tar.gz"}, "confessdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CONFESSdata_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/CONFESSdata_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-confessdata/bioconductor-confessdata_1.30.0_src_all.tar.gz"], "md5": "07df3f8f783b3e734c4032b3f6ed61bd", "fn": "CONFESSdata_1.30.0.tar.gz"}, "connectivitymap-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ConnectivityMap_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ConnectivityMap_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-connectivitymap/bioconductor-connectivitymap_1.38.0_src_all.tar.gz"], "md5": "bac29780256afebfd49b90f268114eaf", "fn": "ConnectivityMap_1.38.0.tar.gz"}, "copdsexualdimorphism.data-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/COPDSexualDimorphism.data_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/COPDSexualDimorphism.data_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copdsexualdimorphism.data/bioconductor-copdsexualdimorphism.data_1.38.0_src_all.tar.gz"], "md5": "d7cf1990679c90cbaf5250c4761effec", "fn": "COPDSexualDimorphism.data_1.38.0.tar.gz"}, "copyhelper-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CopyhelpeR_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/CopyhelpeR_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copyhelper/bioconductor-copyhelper_1.34.0_src_all.tar.gz"], "md5": "bb8d3e8cba0c27898e43cbdcfcac6c62", "fn": "CopyhelpeR_1.34.0.tar.gz"}, "copyneutralima-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CopyNeutralIMA_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/CopyNeutralIMA_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copyneutralima/bioconductor-copyneutralima_1.20.0_src_all.tar.gz"], "md5": "5f1921b0aff4c3f39b662cc1ae70bf28", "fn": "CopyNeutralIMA_1.20.0.tar.gz"}, "cosiadata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CoSIAdata_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/CoSIAdata_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cosiadata/bioconductor-cosiadata_1.2.0_src_all.tar.gz"], "md5": "f0ec9d5ca01647ec3d52e264c0828273", "fn": "CoSIAdata_1.2.0.tar.gz"}, "cosmic.67-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/COSMIC.67_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/COSMIC.67_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cosmic.67/bioconductor-cosmic.67_1.38.0_src_all.tar.gz"], "md5": "392f31ffd7e95a7558d248d36dcc37fe", "fn": "COSMIC.67_1.38.0.tar.gz"}, "crcl18-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CRCL18_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/CRCL18_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-crcl18/bioconductor-crcl18_1.22.0_src_all.tar.gz"], "md5": "176bd921f08e717ec49e4e3eb4a5e5e5", "fn": "CRCL18_1.22.0.tar.gz"}, "crisprscoredata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/crisprScoreData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/crisprScoreData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-crisprscoredata/bioconductor-crisprscoredata_1.6.0_src_all.tar.gz"], "md5": "1f4d86404f045ec36cf7d1b1c64373fe", "fn": "crisprScoreData_1.6.0.tar.gz"}, "curatedadipoarray-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedAdipoArray_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoArray_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadipoarray/bioconductor-curatedadipoarray_1.14.0_src_all.tar.gz"], "md5": "109be77c099e9d7b6da437577f619a54", "fn": "curatedAdipoArray_1.14.0.tar.gz"}, "curatedadipochip-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedAdipoChIP_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoChIP_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadipochip/bioconductor-curatedadipochip_1.18.0_src_all.tar.gz"], "md5": "0074cb63250ac197dad12e4138d47463", "fn": "curatedAdipoChIP_1.18.0.tar.gz"}, "curatedadiporna-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedAdipoRNA_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoRNA_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadiporna/bioconductor-curatedadiporna_1.18.0_src_all.tar.gz"], "md5": "61c2e750fc2cf09a6bde6c0bf46e6b8b", "fn": "curatedAdipoRNA_1.18.0.tar.gz"}, "curatedbladderdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedBladderData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedBladderData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedbladderdata/bioconductor-curatedbladderdata_1.38.0_src_all.tar.gz"], "md5": "bd8965c4ad49840b4985f90f3dc5a441", "fn": "curatedBladderData_1.38.0.tar.gz"}, "curatedbreastdata-2.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedBreastData_2.30.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedBreastData_2.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedbreastdata/bioconductor-curatedbreastdata_2.30.0_src_all.tar.gz"], "md5": "41383ff9e1295448ec0e8004789ab9d5", "fn": "curatedBreastData_2.30.0.tar.gz"}, "curatedcrcdata-2.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedCRCData_2.34.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedCRCData_2.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedcrcdata/bioconductor-curatedcrcdata_2.34.0_src_all.tar.gz"], "md5": "c36bf5dbc0970503f4137b55e8c65534", "fn": "curatedCRCData_2.34.0.tar.gz"}, "curatedmetagenomicdata-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedMetagenomicData_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedMetagenomicData_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedmetagenomicdata/bioconductor-curatedmetagenomicdata_3.10.0_src_all.tar.gz"], "md5": "39c08149fe4261d4961ff1235825ae97", "fn": "curatedMetagenomicData_3.10.0.tar.gz"}, "curatedovariandata-1.40.1": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedOvarianData_1.40.1.tar.gz", "https://bioarchive.galaxyproject.org/curatedOvarianData_1.40.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedovariandata/bioconductor-curatedovariandata_1.40.1_src_all.tar.gz"], "md5": "7651ff7abb11057b3ceec8f869e259d6", "fn": "curatedOvarianData_1.40.1.tar.gz"}, "curatedtbdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedTBData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedTBData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedtbdata/bioconductor-curatedtbdata_1.8.0_src_all.tar.gz"], "md5": "190a770c4f5df45cf722b7ee287a2384", "fn": "curatedTBData_1.8.0.tar.gz"}, "curatedtcgadata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedTCGAData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedTCGAData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedtcgadata/bioconductor-curatedtcgadata_1.24.0_src_all.tar.gz"], "md5": "de450b3bbb137b63a1ca46ae81a96909", "fn": "curatedTCGAData_1.24.0.tar.gz"}, "dapardata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DAPARdata_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/DAPARdata_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dapardata/bioconductor-dapardata_1.32.0_src_all.tar.gz"], "md5": "5906f180d2e824affe9f2850424c7612", "fn": "DAPARdata_1.32.0.tar.gz"}, "davidtiling-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/davidTiling_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/davidTiling_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-davidtiling/bioconductor-davidtiling_1.42.0_src_all.tar.gz"], "md5": "dace46d6f640014aff544e0faf355b5e", "fn": "davidTiling_1.42.0.tar.gz"}, "depmap-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/depmap_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/depmap_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-depmap/bioconductor-depmap_1.16.0_src_all.tar.gz"], "md5": "7f00d05c7f899e622293767baa04e120", "fn": "depmap_1.16.0.tar.gz"}, "derfinderdata-2.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/derfinderData_2.20.0.tar.gz", "https://bioarchive.galaxyproject.org/derfinderData_2.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-derfinderdata/bioconductor-derfinderdata_2.20.0_src_all.tar.gz"], "md5": "032efff51d29eae3fc1a5e032c0f3c40", "fn": "derfinderData_2.20.0.tar.gz"}, "desousa2013-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DeSousa2013_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/DeSousa2013_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-desousa2013/bioconductor-desousa2013_1.38.0_src_all.tar.gz"], "md5": "41a3ca5cba40653eb4be04203aaf60ac", "fn": "DeSousa2013_1.38.0.tar.gz"}, "dexmadata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DExMAdata_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/DExMAdata_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dexmadata/bioconductor-dexmadata_1.10.0_src_all.tar.gz"], "md5": "3d2a9cc7d0044ffc23e572f4c5cc4426", "fn": "DExMAdata_1.10.0.tar.gz"}, "diffloopdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/diffloopdata_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/diffloopdata_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-diffloopdata/bioconductor-diffloopdata_1.30.0_src_all.tar.gz"], "md5": "748ee71ae44999ca2c568619ad5a47eb", "fn": "diffloopdata_1.30.0.tar.gz"}, "diggitdata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/diggitdata_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/diggitdata_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-diggitdata/bioconductor-diggitdata_1.34.0_src_all.tar.gz"], "md5": "48dc6a1a35dae2169279a2766e3b56de", "fn": "diggitdata_1.34.0.tar.gz"}, "dlbcl-1.42.1": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DLBCL_1.42.1.tar.gz", "https://bioarchive.galaxyproject.org/DLBCL_1.42.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dlbcl/bioconductor-dlbcl_1.42.1_src_all.tar.gz"], "md5": "a2906f8e35b0457c1cd8052d2457d40b", "fn": "DLBCL_1.42.1.tar.gz"}, "dmelsgi-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DmelSGI_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/DmelSGI_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dmelsgi/bioconductor-dmelsgi_1.34.0_src_all.tar.gz"], "md5": "c13b3a8f881ca54d5e8ddf52ebe8b86a", "fn": "DmelSGI_1.34.0.tar.gz"}, "dmrcatedata-2.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DMRcatedata_2.20.0.tar.gz", "https://bioarchive.galaxyproject.org/DMRcatedata_2.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dmrcatedata/bioconductor-dmrcatedata_2.20.0_src_all.tar.gz"], "md5": "ac938c6259121c4a60ca3c8c5bfdf724", "fn": "DMRcatedata_2.20.0.tar.gz"}, "dnazoodata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DNAZooData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/DNAZooData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dnazoodata/bioconductor-dnazoodata_1.2.0_src_all.tar.gz"], "md5": "06c4b9dbbaddc3dd4dcdc51e34150aa7", "fn": "DNAZooData_1.2.0.tar.gz"}, "donapllp2013-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DonaPLLP2013_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/DonaPLLP2013_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-donapllp2013/bioconductor-donapllp2013_1.40.0_src_all.tar.gz"], "md5": "d8dc37afefc52856d520540b07faf545", "fn": "DonaPLLP2013_1.40.0.tar.gz"}, "dorothea-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/dorothea_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/dorothea_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dorothea/bioconductor-dorothea_1.14.0_src_all.tar.gz"], "md5": "d1ad1213db5d54f1fc6ef8d195b9bbc0", "fn": "dorothea_1.14.0.tar.gz"}, "dresscheck-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/dressCheck_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/dressCheck_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dresscheck/bioconductor-dresscheck_0.40.0_src_all.tar.gz"], "md5": "d6fb25eaad39c714024ed855c8c9c87d", "fn": "dressCheck_0.40.0.tar.gz"}, "droplettestfiles-1.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DropletTestFiles_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/DropletTestFiles_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-droplettestfiles/bioconductor-droplettestfiles_1.12.0_src_all.tar.gz"], "md5": "5a3a3f0d0901c90c6a2b173b976c4868", "fn": "DropletTestFiles_1.12.0.tar.gz"}, "drugvsdiseasedata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DrugVsDiseasedata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/DrugVsDiseasedata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drugvsdiseasedata/bioconductor-drugvsdiseasedata_1.38.0_src_all.tar.gz"], "md5": "40b800653aab57e822a18afe5bd1a2e7", "fn": "DrugVsDiseasedata_1.38.0.tar.gz"}, "duoclustering2018-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DuoClustering2018_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/DuoClustering2018_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-duoclustering2018/bioconductor-duoclustering2018_1.20.0_src_all.tar.gz"], "md5": "a2761f4db56025af2eaf8240392d01a0", "fn": "DuoClustering2018_1.20.0.tar.gz"}, "dvddata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DvDdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/DvDdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dvddata/bioconductor-dvddata_1.38.0_src_all.tar.gz"], "md5": "d07387219229c006ba96b9ab43ddf4ff", "fn": "DvDdata_1.38.0.tar.gz"}, "dyebiasexamples-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/dyebiasexamples_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/dyebiasexamples_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dyebiasexamples/bioconductor-dyebiasexamples_1.42.0_src_all.tar.gz"], "md5": "b73aa6c0c98150b2bccba7802dda8c86", "fn": "dyebiasexamples_1.42.0.tar.gz"}, "easierdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/easierData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/easierData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-easierdata/bioconductor-easierdata_1.8.0_src_all.tar.gz"], "md5": "5092649863b833021ff8593731571183", "fn": "easierData_1.8.0.tar.gz"}, "eatonetalchipseq-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/EatonEtAlChIPseq_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/EatonEtAlChIPseq_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-eatonetalchipseq/bioconductor-eatonetalchipseq_0.40.0_src_all.tar.gz"], "md5": "e7695c3761d5f3d41dec21b0c8b50947", "fn": "EatonEtAlChIPseq_0.40.0.tar.gz"}, "ecolileucine-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ecoliLeucine_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliLeucine_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolileucine/bioconductor-ecolileucine_1.42.0_src_all.tar.gz"], "md5": "30af71114480d851f4dad806e7f8e0d1", "fn": "ecoliLeucine_1.42.0.tar.gz"}, "egseadata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/EGSEAdata_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/EGSEAdata_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-egseadata/bioconductor-egseadata_1.30.0_src_all.tar.gz"], "md5": "838b30ae6caf7c3cbb854e0404b52cda", "fn": "EGSEAdata_1.30.0.tar.gz"}, "elmer.data-2.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ELMER.data_2.26.0.tar.gz", "https://bioarchive.galaxyproject.org/ELMER.data_2.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-elmer.data/bioconductor-elmer.data_2.26.0_src_all.tar.gz"], "md5": "565ea1aa52f3f61d16b7560859ed7a3a", "fn": "ELMER.data_2.26.0.tar.gz"}, "emtdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/emtdata_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/emtdata_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-emtdata/bioconductor-emtdata_1.10.0_src_all.tar.gz"], "md5": "4f861584cce979edd6d7bdce3624e916", "fn": "emtdata_1.10.0.tar.gz"}, "epimix.data-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/EpiMix.data_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/EpiMix.data_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epimix.data/bioconductor-epimix.data_1.4.0_src_all.tar.gz"], "md5": "52c386f6828945121acfca44eabb7827", "fn": "EpiMix.data_1.4.0.tar.gz"}, "epimutacionsdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/epimutacionsData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/epimutacionsData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epimutacionsdata/bioconductor-epimutacionsdata_1.6.0_src_all.tar.gz"], "md5": "e2681ab8096fd0f2b7e5d8ed68928280", "fn": "epimutacionsData_1.6.0.tar.gz"}, "estrogen-1.48.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/estrogen_1.48.0.tar.gz", "https://bioarchive.galaxyproject.org/estrogen_1.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-estrogen/bioconductor-estrogen_1.48.0_src_all.tar.gz"], "md5": "41a3321678d1a9cb057e979d675f0cee", "fn": "estrogen_1.48.0.tar.gz"}, "etec16s-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/etec16s_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/etec16s_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-etec16s/bioconductor-etec16s_1.30.0_src_all.tar.gz"], "md5": "86353b5f2f77274b883120dc043f8ce5", "fn": "etec16s_1.30.0.tar.gz"}, "ewcedata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ewceData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/ewceData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ewcedata/bioconductor-ewcedata_1.10.0_src_all.tar.gz"], "md5": "d2ee91be35e2c5433ce16e94717c50e7", "fn": "ewceData_1.10.0.tar.gz"}, "faahko-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/faahKO_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/faahKO_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-faahko/bioconductor-faahko_1.42.0_src_all.tar.gz"], "md5": "3525f525973323d33955a68ca38b5cd7", "fn": "faahKO_1.42.0.tar.gz"}, "fabiadata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/fabiaData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/fabiaData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fabiadata/bioconductor-fabiadata_1.40.0_src_all.tar.gz"], "md5": "7fd64db4d15610a66c609e60624bbff9", "fn": "fabiaData_1.40.0.tar.gz"}, "fantom3and4cage-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/FANTOM3and4CAGE_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/FANTOM3and4CAGE_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fantom3and4cage/bioconductor-fantom3and4cage_1.38.0_src_all.tar.gz"], "md5": "5d964e7a085d6a7b00e2b2215b765861", "fn": "FANTOM3and4CAGE_1.38.0.tar.gz"}, "ffpeexampledata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ffpeExampleData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/ffpeExampleData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ffpeexampledata/bioconductor-ffpeexampledata_1.40.0_src_all.tar.gz"], "md5": "6ea474bdf448ff6026ec4f1f376b7d69", "fn": "ffpeExampleData_1.40.0.tar.gz"}, "fibroeset-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/fibroEset_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/fibroEset_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fibroeset/bioconductor-fibroeset_1.44.0_src_all.tar.gz"], "md5": "cbc13cc5c4ac4f6445dc69383ad183ff", "fn": "fibroEset_1.44.0.tar.gz"}, "fieldeffectcrc-1.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/FieldEffectCrc_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/FieldEffectCrc_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fieldeffectcrc/bioconductor-fieldeffectcrc_1.12.0_src_all.tar.gz"], "md5": "73fa4e8649f3c4a523764d35afd421f2", "fn": "FieldEffectCrc_1.12.0.tar.gz"}, "fis-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/FIs_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/FIs_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fis/bioconductor-fis_1.30.0_src_all.tar.gz"], "md5": "ef807b75136742a1dcb5ea70993d5c38", "fn": "FIs_1.30.0.tar.gz"}, "fission-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/fission_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/fission_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fission/bioconductor-fission_1.22.0_src_all.tar.gz"], "md5": "7d404509808bfc439270093b647ccd80", "fn": "fission_1.22.0.tar.gz"}, "fletcher2013a-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Fletcher2013a_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/Fletcher2013a_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fletcher2013a/bioconductor-fletcher2013a_1.38.0_src_all.tar.gz"], "md5": "e4c4f9a4e8b24a7a72f9c63337a0eef9", "fn": "Fletcher2013a_1.38.0.tar.gz"}, "fletcher2013b-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Fletcher2013b_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/Fletcher2013b_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fletcher2013b/bioconductor-fletcher2013b_1.38.0_src_all.tar.gz"], "md5": "cf656c92425c8a63ef584be08e8b742e", "fn": "Fletcher2013b_1.38.0.tar.gz"}, "flowploidydata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/flowPloidyData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/flowPloidyData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowploidydata/bioconductor-flowploidydata_1.28.0_src_all.tar.gz"], "md5": "993a663f6d1cdc791c3f4e88d5b3b047", "fn": "flowPloidyData_1.28.0.tar.gz"}, "flowsorted.blood.450k-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/FlowSorted.Blood.450k_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.Blood.450k_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.450k/bioconductor-flowsorted.blood.450k_1.40.0_src_all.tar.gz"], "md5": "f88422c2d8a2f7ce4ca968292adfc8ab", "fn": "FlowSorted.Blood.450k_1.40.0.tar.gz"}, "flowsorted.blood.epic-2.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/FlowSorted.Blood.EPIC_2.6.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.Blood.EPIC_2.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.epic/bioconductor-flowsorted.blood.epic_2.6.0_src_all.tar.gz"], "md5": "e94cbb0480a032595cdb5d9714065bed", "fn": "FlowSorted.Blood.EPIC_2.6.0.tar.gz"}, "flowsorted.cordblood.450k-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/FlowSorted.CordBlood.450k_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBlood.450k_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordblood.450k/bioconductor-flowsorted.cordblood.450k_1.30.0_src_all.tar.gz"], "md5": "fca81b7412af68100d7aed4d57d5fc59", "fn": "FlowSorted.CordBlood.450k_1.30.0.tar.gz"}, "flowsorted.cordbloodcombined.450k-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/FlowSorted.CordBloodCombined.450k_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodCombined.450k_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodcombined.450k/bioconductor-flowsorted.cordbloodcombined.450k_1.18.0_src_all.tar.gz"], "md5": "769113b80606820ab2918dcacf1076b2", "fn": "FlowSorted.CordBloodCombined.450k_1.18.0.tar.gz"}, "flowsorted.cordbloodnorway.450k-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/FlowSorted.CordBloodNorway.450k_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodNorway.450k_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodnorway.450k/bioconductor-flowsorted.cordbloodnorway.450k_1.28.0_src_all.tar.gz"], "md5": "40016224becf643102bc3054f4e2508d", "fn": "FlowSorted.CordBloodNorway.450k_1.28.0.tar.gz"}, "flowsorted.dlpfc.450k-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/FlowSorted.DLPFC.450k_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.DLPFC.450k_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.dlpfc.450k/bioconductor-flowsorted.dlpfc.450k_1.38.0_src_all.tar.gz"], "md5": "ad95a51f7e8bcf7c0bec6dda80eb0a92", "fn": "FlowSorted.DLPFC.450k_1.38.0.tar.gz"}, "flowworkspacedata-3.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/flowWorkspaceData_3.14.0.tar.gz", "https://bioarchive.galaxyproject.org/flowWorkspaceData_3.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowworkspacedata/bioconductor-flowworkspacedata_3.14.0_src_all.tar.gz"], "md5": "96655cef2a21f1b9d303ec775597a2dc", "fn": "flowWorkspaceData_3.14.0.tar.gz"}, "fourdndata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/fourDNData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/fourDNData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fourdndata/bioconductor-fourdndata_1.2.0_src_all.tar.gz"], "md5": "bca623e919f7c17a40ffb4eae27cfe59", "fn": "fourDNData_1.2.0.tar.gz"}, "frmaexampledata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/frmaExampleData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/frmaExampleData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-frmaexampledata/bioconductor-frmaexampledata_1.38.0_src_all.tar.gz"], "md5": "9713801ffd08145323ca4d31a3631995", "fn": "frmaExampleData_1.38.0.tar.gz"}, "furrowseg-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/furrowSeg_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/furrowSeg_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-furrowseg/bioconductor-furrowseg_1.30.0_src_all.tar.gz"], "md5": "f41e88a4d47949b3b8b126b0fc7852eb", "fn": "furrowSeg_1.30.0.tar.gz"}, "gagedata-2.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/gageData_2.40.0.tar.gz", "https://bioarchive.galaxyproject.org/gageData_2.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gagedata/bioconductor-gagedata_2.40.0_src_all.tar.gz"], "md5": "889e4b6ceda6c2a80f61ad4e867c3b59", "fn": "gageData_2.40.0.tar.gz"}, "gaschyhs-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/gaschYHS_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/gaschYHS_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gaschyhs/bioconductor-gaschyhs_1.40.0_src_all.tar.gz"], "md5": "29983eadb2a2a20f7c5475206367d641", "fn": "gaschYHS_1.40.0.tar.gz"}, "gcspikelite-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/gcspikelite_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/gcspikelite_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gcspikelite/bioconductor-gcspikelite_1.40.0_src_all.tar.gz"], "md5": "91b995753732f0d5508fdc2d7dcb998f", "fn": "gcspikelite_1.40.0.tar.gz"}, "gdnainrnaseqdata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/gDNAinRNAseqData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/gDNAinRNAseqData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gdnainrnaseqdata/bioconductor-gdnainrnaseqdata_1.2.0_src_all.tar.gz"], "md5": "52e275ca255493684657a091667f987f", "fn": "gDNAinRNAseqData_1.2.0.tar.gz"}, "gdrtestdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/gDRtestData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/gDRtestData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gdrtestdata/bioconductor-gdrtestdata_1.0.0_src_all.tar.gz"], "md5": "8de3dea2673f0e7dc9412e36da2c4f9d", "fn": "gDRtestData_1.0.0.tar.gz"}, "genelendatabase-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/geneLenDataBase_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/geneLenDataBase_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genelendatabase/bioconductor-genelendatabase_1.38.0_src_all.tar.gz"], "md5": "c29099d3142aad07590e22ce37c6acf3", "fn": "geneLenDataBase_1.38.0.tar.gz"}, "genomationdata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/genomationData_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/genomationData_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomationdata/bioconductor-genomationdata_1.34.0_src_all.tar.gz"], "md5": "dc03eef7730719f7c66f72ca5e9915db", "fn": "genomationData_1.34.0.tar.gz"}, "genomicdistributionsdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GenomicDistributionsData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/GenomicDistributionsData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomicdistributionsdata/bioconductor-genomicdistributionsdata_1.10.0_src_all.tar.gz"], "md5": "84067e85ccbf3605bc1f5a1b7d8508ad", "fn": "GenomicDistributionsData_1.10.0.tar.gz"}, "geuvadistranscriptexpr-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GeuvadisTranscriptExpr_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/GeuvadisTranscriptExpr_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-geuvadistranscriptexpr/bioconductor-geuvadistranscriptexpr_1.30.0_src_all.tar.gz"], "md5": "806de22bef0659a3b6f9db122d87a1d6", "fn": "GeuvadisTranscriptExpr_1.30.0.tar.gz"}, "gigseadata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GIGSEAdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/GIGSEAdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gigseadata/bioconductor-gigseadata_1.20.0_src_all.tar.gz"], "md5": "470cdb6073d9af3d23056b55e6b8c98d", "fn": "GIGSEAdata_1.20.0.tar.gz"}, "golubesets-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/golubEsets_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/golubEsets_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-golubesets/bioconductor-golubesets_1.44.0_src_all.tar.gz"], "md5": "49e3527c00f06c189a048a6b871f3d54", "fn": "golubEsets_1.44.0.tar.gz"}, "gpaexample-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/gpaExample_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/gpaExample_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gpaexample/bioconductor-gpaexample_1.14.0_src_all.tar.gz"], "md5": "e989af58ed5bbc10573f7438b3ee7836", "fn": "gpaExample_1.14.0.tar.gz"}, "grndata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/grndata_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/grndata_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-grndata/bioconductor-grndata_1.34.0_src_all.tar.gz"], "md5": "0ebac67277a5ca915f9a971d3659af5e", "fn": "grndata_1.34.0.tar.gz"}, "gsbenchmark-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GSBenchMark_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/GSBenchMark_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gsbenchmark/bioconductor-gsbenchmark_1.22.0_src_all.tar.gz"], "md5": "bedfa52de1b414ae5fe9d5fc376380ba", "fn": "GSBenchMark_1.22.0.tar.gz"}, "gse103322-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GSE103322_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE103322_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse103322/bioconductor-gse103322_1.8.0_src_all.tar.gz"], "md5": "3816b430b716edaaa0ef22dba38cf58e", "fn": "GSE103322_1.8.0.tar.gz"}, "gse13015-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GSE13015_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE13015_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse13015/bioconductor-gse13015_1.10.0_src_all.tar.gz"], "md5": "99fae6872abf6820842a1340f7fd6b4e", "fn": "GSE13015_1.10.0.tar.gz"}, "gse159526-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GSE159526_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE159526_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse159526/bioconductor-gse159526_1.8.0_src_all.tar.gz"], "md5": "d89442c94cb87f0760a9f0f85426a8fa", "fn": "GSE159526_1.8.0.tar.gz"}, "gse62944-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GSE62944_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE62944_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse62944/bioconductor-gse62944_1.30.0_src_all.tar.gz"], "md5": "5b6c58aaee948c9cd0e0d52b5adcf264", "fn": "GSE62944_1.30.0.tar.gz"}, "gsvadata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GSVAdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/GSVAdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gsvadata/bioconductor-gsvadata_1.38.0_src_all.tar.gz"], "md5": "3c2d6a66967ab8c3c2545fc3323282b3", "fn": "GSVAdata_1.38.0.tar.gz"}, "gwasdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GWASdata_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/GWASdata_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gwasdata/bioconductor-gwasdata_1.40.0_src_all.tar.gz"], "md5": "57fec70f980b9e476f0c59d397797815", "fn": "GWASdata_1.40.0.tar.gz"}, "h5vcdata-2.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/h5vcData_2.22.0.tar.gz", "https://bioarchive.galaxyproject.org/h5vcData_2.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-h5vcdata/bioconductor-h5vcdata_2.22.0_src_all.tar.gz"], "md5": "c251316e2d6dc6cb90e8faad0015103b", "fn": "h5vcData_2.22.0.tar.gz"}, "hapmap100khind-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hapmap100khind_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap100khind_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap100khind/bioconductor-hapmap100khind_1.44.0_src_all.tar.gz"], "md5": "0168028295626d811e305d4008ce9996", "fn": "hapmap100khind_1.44.0.tar.gz"}, "hapmap100kxba-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hapmap100kxba_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap100kxba_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap100kxba/bioconductor-hapmap100kxba_1.44.0_src_all.tar.gz"], "md5": "b4a619fb108a36920109307fbf63985b", "fn": "hapmap100kxba_1.44.0.tar.gz"}, "hapmap500knsp-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hapmap500knsp_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap500knsp_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap500knsp/bioconductor-hapmap500knsp_1.44.0_src_all.tar.gz"], "md5": "15b799bba4a395ccf715acfc7bbdae04", "fn": "hapmap500knsp_1.44.0.tar.gz"}, "hapmap500ksty-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hapmap500ksty_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap500ksty_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap500ksty/bioconductor-hapmap500ksty_1.44.0_src_all.tar.gz"], "md5": "7a1d4983ac3e411dadedc130d85c2557", "fn": "hapmap500ksty_1.44.0.tar.gz"}, "hapmapsnp5-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hapmapsnp5_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmapsnp5_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp5/bioconductor-hapmapsnp5_1.44.0_src_all.tar.gz"], "md5": "2f14e60f39cf94c43f2dd0e5aa5a48e2", "fn": "hapmapsnp5_1.44.0.tar.gz"}, "hapmapsnp6-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hapmapsnp6_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmapsnp6_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp6/bioconductor-hapmapsnp6_1.44.0_src_all.tar.gz"], "md5": "2635c012a513343484177db2070209e9", "fn": "hapmapsnp6_1.44.0.tar.gz"}, "harbchip-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/harbChIP_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/harbChIP_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harbchip/bioconductor-harbchip_1.40.0_src_all.tar.gz"], "md5": "f5948fc0f4c1ced0a43e85c1885f5d9e", "fn": "harbChIP_1.40.0.tar.gz"}, "harmandata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HarmanData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/HarmanData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harmandata/bioconductor-harmandata_1.30.0_src_all.tar.gz"], "md5": "7df1447aff75abdf025678b51a0ee8fb", "fn": "HarmanData_1.30.0.tar.gz"}, "harmonizedtcgadata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HarmonizedTCGAData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/HarmonizedTCGAData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harmonizedtcgadata/bioconductor-harmonizedtcgadata_1.24.0_src_all.tar.gz"], "md5": "f6e8f685a67152c6f382089c0e6aae01", "fn": "HarmonizedTCGAData_1.24.0.tar.gz"}, "hcadata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HCAData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/HCAData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcadata/bioconductor-hcadata_1.18.0_src_all.tar.gz"], "md5": "4f16bf5904ca21c0fb0bd6515d7ab4d3", "fn": "HCAData_1.18.0.tar.gz"}, "hcatonsildata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HCATonsilData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/HCATonsilData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcatonsildata/bioconductor-hcatonsildata_1.0.0_src_all.tar.gz"], "md5": "dda9d216f608690d05bd5ffbcb73bb05", "fn": "HCATonsilData_1.0.0.tar.gz"}, "hd2013sgi-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HD2013SGI_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/HD2013SGI_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hd2013sgi/bioconductor-hd2013sgi_1.42.0_src_all.tar.gz"], "md5": "f8c7020a4fbfcb5c4026cea93e5a5bc6", "fn": "HD2013SGI_1.42.0.tar.gz"}, "hdcytodata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HDCytoData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/HDCytoData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hdcytodata/bioconductor-hdcytodata_1.22.0_src_all.tar.gz"], "md5": "8f962c6124539fea7a4a02a30e776de8", "fn": "HDCytoData_1.22.0.tar.gz"}, "healthycontrolspresencechecker-1.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/healthyControlsPresenceChecker_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/healthyControlsPresenceChecker_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-healthycontrolspresencechecker/bioconductor-healthycontrolspresencechecker_1.6.0_src_all.tar.gz"], "md5": "50ba7cea9e361d43c78d64ce1c89ba1a", "fn": "healthyControlsPresenceChecker_1.6.0.tar.gz"}, "healthyflowdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/healthyFlowData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/healthyFlowData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-healthyflowdata/bioconductor-healthyflowdata_1.40.0_src_all.tar.gz"], "md5": "ed0a9c99295e278a8445368a2cb226df", "fn": "healthyFlowData_1.40.0.tar.gz"}, "heebodata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HEEBOdata_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/HEEBOdata_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-heebodata/bioconductor-heebodata_1.40.0_src_all.tar.gz"], "md5": "885df0689d6663e079e952ea297ee777", "fn": "HEEBOdata_1.40.0.tar.gz"}, "hellorangesdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HelloRangesData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/HelloRangesData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hellorangesdata/bioconductor-hellorangesdata_1.28.0_src_all.tar.gz"], "md5": "6ae6ac65f3af7f41136eb6fb3558eb2a", "fn": "HelloRangesData_1.28.0.tar.gz"}, "hgu133abarcodevecs-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hgu133abarcodevecs_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133abarcodevecs_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133abarcodevecs/bioconductor-hgu133abarcodevecs_1.40.0_src_all.tar.gz"], "md5": "4a6ec67e649f7ca004242fd860f79521", "fn": "hgu133abarcodevecs_1.40.0.tar.gz"}, "hgu133plus2barcodevecs-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hgu133plus2barcodevecs_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2barcodevecs_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2barcodevecs/bioconductor-hgu133plus2barcodevecs_1.40.0_src_all.tar.gz"], "md5": "624bad8617d806474bc9406dc3c22384", "fn": "hgu133plus2barcodevecs_1.40.0.tar.gz"}, "hgu133plus2cellscore-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hgu133plus2CellScore_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2CellScore_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2cellscore/bioconductor-hgu133plus2cellscore_1.22.0_src_all.tar.gz"], "md5": "486b7084ad0056c1031545af9c6dd515", "fn": "hgu133plus2CellScore_1.22.0.tar.gz"}, "hgu2beta7-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hgu2beta7_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu2beta7_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu2beta7/bioconductor-hgu2beta7_1.42.0_src_all.tar.gz"], "md5": "0643f49d27bf1dd6b73fb9192b23ebaa", "fn": "hgu2beta7_1.42.0.tar.gz"}, "hibed-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HiBED_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/HiBED_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hibed/bioconductor-hibed_1.0.0_src_all.tar.gz"], "md5": "282aec6967013cdaa790ff191e4139b4", "fn": "HiBED_1.0.0.tar.gz"}, "hicdatahumanimr90-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HiCDataHumanIMR90_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/HiCDataHumanIMR90_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicdatahumanimr90/bioconductor-hicdatahumanimr90_1.22.0_src_all.tar.gz"], "md5": "02854f68384130b0bcd3d0f84d94b856", "fn": "HiCDataHumanIMR90_1.22.0.tar.gz"}, "hicdatalymphoblast-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HiCDataLymphoblast_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/HiCDataLymphoblast_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicdatalymphoblast/bioconductor-hicdatalymphoblast_1.38.0_src_all.tar.gz"], "md5": "4e51d696b30a37414375e6987c7ab59c", "fn": "HiCDataLymphoblast_1.38.0.tar.gz"}, "hicontactsdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HiContactsData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/HiContactsData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicontactsdata/bioconductor-hicontactsdata_1.4.0_src_all.tar.gz"], "md5": "bcd518f48342168f7a814a442cf9564c", "fn": "HiContactsData_1.4.0.tar.gz"}, "highlyreplicatedrnaseq-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HighlyReplicatedRNASeq_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/HighlyReplicatedRNASeq_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-highlyreplicatedrnaseq/bioconductor-highlyreplicatedrnaseq_1.14.0_src_all.tar.gz"], "md5": "a397cddffb2dfea70943930b992ea7c0", "fn": "HighlyReplicatedRNASeq_1.14.0.tar.gz"}, "hiiragi2013-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Hiiragi2013_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/Hiiragi2013_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hiiragi2013/bioconductor-hiiragi2013_1.38.0_src_all.tar.gz"], "md5": "dde13f333fe218976f71b626ed5eefa4", "fn": "Hiiragi2013_1.38.0.tar.gz"}, "hivcdnavantwout03-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HIVcDNAvantWout03_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/HIVcDNAvantWout03_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hivcdnavantwout03/bioconductor-hivcdnavantwout03_1.42.0_src_all.tar.gz"], "md5": "4936f53bb66cdf1983a8bcbcd667a188", "fn": "HIVcDNAvantWout03_1.42.0.tar.gz"}, "hmp16sdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HMP16SData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/HMP16SData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hmp16sdata/bioconductor-hmp16sdata_1.22.0_src_all.tar.gz"], "md5": "a137f917000e15acffca9bb0baac8fbb", "fn": "HMP16SData_1.22.0.tar.gz"}, "hmp2data-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HMP2Data_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/HMP2Data_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hmp2data/bioconductor-hmp2data_1.16.0_src_all.tar.gz"], "md5": "f334416386d2c1af677494e1fd5743d6", "fn": "HMP2Data_1.16.0.tar.gz"}, "hsmmsinglecell-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HSMMSingleCell_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/HSMMSingleCell_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hsmmsinglecell/bioconductor-hsmmsinglecell_1.22.0_src_all.tar.gz"], "md5": "dae440cd20110d25cd699a9a792ac4b8", "fn": "HSMMSingleCell_1.22.0.tar.gz"}, "humanaffydata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HumanAffyData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/HumanAffyData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanaffydata/bioconductor-humanaffydata_1.28.0_src_all.tar.gz"], "md5": "11341e772169b7141b9bd22161e14417", "fn": "HumanAffyData_1.28.0.tar.gz"}, "humanstemcell-0.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/humanStemCell_0.42.0.tar.gz", "https://bioarchive.galaxyproject.org/humanStemCell_0.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanstemcell/bioconductor-humanstemcell_0.42.0_src_all.tar.gz"], "md5": "be6367d8fa19187d644247ed8795eb0e", "fn": "humanStemCell_0.42.0.tar.gz"}, "ihwpaper-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/IHWpaper_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/IHWpaper_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ihwpaper/bioconductor-ihwpaper_1.30.0_src_all.tar.gz"], "md5": "21e65d900bf8e6015fd006fbf01237d5", "fn": "IHWpaper_1.30.0.tar.gz"}, "illumina450probevariants.db-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Illumina450ProbeVariants.db_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/Illumina450ProbeVariants.db_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illumina450probevariants.db/bioconductor-illumina450probevariants.db_1.38.0_src_all.tar.gz"], "md5": "ca34eec73a57e5f226b70a20ef706ee3", "fn": "Illumina450ProbeVariants.db_1.38.0.tar.gz"}, "illuminadatatestfiles-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/IlluminaDataTestFiles_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaDataTestFiles_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminadatatestfiles/bioconductor-illuminadatatestfiles_1.40.0_src_all.tar.gz"], "md5": "3afa4b143fbb1dd18b3a7acd8f2984b1", "fn": "IlluminaDataTestFiles_1.40.0.tar.gz"}, "imcdatasets-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/imcdatasets_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/imcdatasets_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-imcdatasets/bioconductor-imcdatasets_1.10.0_src_all.tar.gz"], "md5": "6e687f10502d7d9d369c384e99977953", "fn": "imcdatasets_1.10.0.tar.gz"}, "italicsdata-2.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ITALICSData_2.40.0.tar.gz", "https://bioarchive.galaxyproject.org/ITALICSData_2.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-italicsdata/bioconductor-italicsdata_2.40.0_src_all.tar.gz"], "md5": "e154526c43e11840acfd4c92ff1cee8f", "fn": "ITALICSData_2.40.0.tar.gz"}, "iyer517-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Iyer517_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/Iyer517_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-iyer517/bioconductor-iyer517_1.44.0_src_all.tar.gz"], "md5": "81226f1ad5acd16cff4c7371f37d1881", "fn": "Iyer517_1.44.0.tar.gz"}, "jaspar2014-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/JASPAR2014_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2014_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2014/bioconductor-jaspar2014_1.38.0_src_all.tar.gz"], "md5": "6ef536411db46944f6d5b9a23ee13be6", "fn": "JASPAR2014_1.38.0.tar.gz"}, "jaspar2016-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/JASPAR2016_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2016_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2016/bioconductor-jaspar2016_1.30.0_src_all.tar.gz"], "md5": "2976e4678291944f664396385049180b", "fn": "JASPAR2016_1.30.0.tar.gz"}, "keggandmetacoredzpathwaysgeo-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/KEGGandMetacoreDzPathwaysGEO_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/KEGGandMetacoreDzPathwaysGEO_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-keggandmetacoredzpathwaysgeo/bioconductor-keggandmetacoredzpathwaysgeo_1.22.0_src_all.tar.gz"], "md5": "3a5180de47f1c28949b77db9f79b44ed", "fn": "KEGGandMetacoreDzPathwaysGEO_1.22.0.tar.gz"}, "keggdzpathwaysgeo-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/KEGGdzPathwaysGEO_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/KEGGdzPathwaysGEO_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-keggdzpathwaysgeo/bioconductor-keggdzpathwaysgeo_1.40.0_src_all.tar.gz"], "md5": "2f30f9ac05c04214d25a9d49fb4ce8bd", "fn": "KEGGdzPathwaysGEO_1.40.0.tar.gz"}, "kidpack-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/kidpack_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/kidpack_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-kidpack/bioconductor-kidpack_1.44.0_src_all.tar.gz"], "md5": "26f5ad5fba1c63156e282d8eac7ac385", "fn": "kidpack_1.44.0.tar.gz"}, "kodata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/KOdata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/KOdata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-kodata/bioconductor-kodata_1.28.0_src_all.tar.gz"], "md5": "40e099053eae889ad66256a94427ac54", "fn": "KOdata_1.28.0.tar.gz"}, "leebamviews-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/leeBamViews_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/leeBamViews_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-leebamviews/bioconductor-leebamviews_1.38.0_src_all.tar.gz"], "md5": "58f7c7fdbb1f949f48924ac79d31b580", "fn": "leeBamViews_1.38.0.tar.gz"}, "leukemiaseset-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/leukemiasEset_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/leukemiasEset_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-leukemiaseset/bioconductor-leukemiaseset_1.38.0_src_all.tar.gz"], "md5": "f9e8274856b0d78de6da7ec0bce171f5", "fn": "leukemiasEset_1.38.0.tar.gz"}, "liebermanaidenhic2009-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/LiebermanAidenHiC2009_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/LiebermanAidenHiC2009_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-liebermanaidenhic2009/bioconductor-liebermanaidenhic2009_0.40.0_src_all.tar.gz"], "md5": "34818101f902d251b339864716cd2d1a", "fn": "LiebermanAidenHiC2009_0.40.0.tar.gz"}, "listeretalbsseq-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ListerEtAlBSseq_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/ListerEtAlBSseq_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-listeretalbsseq/bioconductor-listeretalbsseq_1.34.0_src_all.tar.gz"], "md5": "302e026ae021a5f26c149b5086569db1", "fn": "ListerEtAlBSseq_1.34.0.tar.gz"}, "lrcelltypemarkers-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/LRcellTypeMarkers_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/LRcellTypeMarkers_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lrcelltypemarkers/bioconductor-lrcelltypemarkers_1.10.0_src_all.tar.gz"], "md5": "f5731667b56b631291d22a830d212f04", "fn": "LRcellTypeMarkers_1.10.0.tar.gz"}, "lumibarnes-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/lumiBarnes_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/lumiBarnes_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumibarnes/bioconductor-lumibarnes_1.42.0_src_all.tar.gz"], "md5": "2be75f5470fd60f9919045fc8147b613", "fn": "lumiBarnes_1.42.0.tar.gz"}, "lungcanceracvssccgeo-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/LungCancerACvsSCCGEO_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/LungCancerACvsSCCGEO_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungcanceracvssccgeo/bioconductor-lungcanceracvssccgeo_1.38.0_src_all.tar.gz"], "md5": "f353aa0cc36dc25e67cdf1ba0738985e", "fn": "LungCancerACvsSCCGEO_1.38.0.tar.gz"}, "lungcancerlines-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/LungCancerLines_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/LungCancerLines_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungcancerlines/bioconductor-lungcancerlines_0.40.0_src_all.tar.gz"], "md5": "17b67ca0eac14ef832832b949972b277", "fn": "LungCancerLines_0.40.0.tar.gz"}, "lungexpression-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/lungExpression_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/lungExpression_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungexpression/bioconductor-lungexpression_0.40.0_src_all.tar.gz"], "md5": "35eab717cb2e24c92faf417ad7fb9cb8", "fn": "lungExpression_0.40.0.tar.gz"}, "lydata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/lydata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/lydata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lydata/bioconductor-lydata_1.28.0_src_all.tar.gz"], "md5": "4541ec0aad2bbee135b19b0bed4ea0af", "fn": "lydata_1.28.0.tar.gz"}, "m3dexampledata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/M3DExampleData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/M3DExampleData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-m3dexampledata/bioconductor-m3dexampledata_1.28.0_src_all.tar.gz"], "md5": "6988767aab7572ae3e701fd6854c061f", "fn": "M3DExampleData_1.28.0.tar.gz"}, "macrophage-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/macrophage_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/macrophage_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-macrophage/bioconductor-macrophage_1.18.0_src_all.tar.gz"], "md5": "5f83cf12d699a285cd228119b1d95cf0", "fn": "macrophage_1.18.0.tar.gz"}, "macsdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MACSdata_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MACSdata_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-macsdata/bioconductor-macsdata_1.10.0_src_all.tar.gz"], "md5": "1d10f4fe6b20d5c09148b8011fb3183f", "fn": "MACSdata_1.10.0.tar.gz"}, "mammaprintdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/mammaPrintData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/mammaPrintData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mammaprintdata/bioconductor-mammaprintdata_1.38.0_src_all.tar.gz"], "md5": "08b3249a36d5f165a933bfab5eb05a2a", "fn": "mammaPrintData_1.38.0.tar.gz"}, "mapkldata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/mAPKLData_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/mAPKLData_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mapkldata/bioconductor-mapkldata_1.34.0_src_all.tar.gz"], "md5": "ce6399a1c853cb4e78de226347c3dc5d", "fn": "mAPKLData_1.34.0.tar.gz"}, "maqcexpression4plex-1.46.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/maqcExpression4plex_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/maqcExpression4plex_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcexpression4plex/bioconductor-maqcexpression4plex_1.46.0_src_all.tar.gz"], "md5": "8312b7fbcba763a33630effb8c3b5f10", "fn": "maqcExpression4plex_1.46.0.tar.gz"}, "maqcsubset-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MAQCsubset_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/MAQCsubset_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcsubset/bioconductor-maqcsubset_1.40.0_src_all.tar.gz"], "md5": "5757c11a1af2150b8fd17c3a8b8b0c0c", "fn": "MAQCsubset_1.40.0.tar.gz"}, "maqcsubsetilm-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MAQCsubsetILM_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/MAQCsubsetILM_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcsubsetilm/bioconductor-maqcsubsetilm_1.40.0_src_all.tar.gz"], "md5": "1c975db69a86cc80e99c5245998ee255", "fn": "MAQCsubsetILM_1.40.0.tar.gz"}, "marinerdata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/marinerData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/marinerData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-marinerdata/bioconductor-marinerdata_1.2.0_src_all.tar.gz"], "md5": "7875113ebb6baaaed6eb6fc762ba92ca", "fn": "marinerData_1.2.0.tar.gz"}, "mcseadata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/mCSEAdata_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/mCSEAdata_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcseadata/bioconductor-mcseadata_1.22.0_src_all.tar.gz"], "md5": "11f8150e223a0e8d8fa5b9b8dedaa374", "fn": "mCSEAdata_1.22.0.tar.gz"}, "mcsurvdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/mcsurvdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/mcsurvdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcsurvdata/bioconductor-mcsurvdata_1.20.0_src_all.tar.gz"], "md5": "0299258c7610f3675dc0b9f8e333eefa", "fn": "mcsurvdata_1.20.0.tar.gz"}, "medipsdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MEDIPSData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/MEDIPSData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-medipsdata/bioconductor-medipsdata_1.38.0_src_all.tar.gz"], "md5": "7b329ecedb2e9911b92ad669856abf2b", "fn": "MEDIPSData_1.38.0.tar.gz"}, "meebodata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MEEBOdata_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/MEEBOdata_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-meebodata/bioconductor-meebodata_1.40.0_src_all.tar.gz"], "md5": "cd3b9bb8a918c9497903f6274f323904", "fn": "MEEBOdata_1.40.0.tar.gz"}, "merfishdata-1.4.1": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MerfishData_1.4.1.tar.gz", "https://bioarchive.galaxyproject.org/MerfishData_1.4.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-merfishdata/bioconductor-merfishdata_1.4.1_src_all.tar.gz"], "md5": "05369f89c4e1a15bdab1ce5174facbe4", "fn": "MerfishData_1.4.1.tar.gz"}, "metagxbreast-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MetaGxBreast_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxBreast_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxbreast/bioconductor-metagxbreast_1.22.0_src_all.tar.gz"], "md5": "e711302482bca1429de5fe2e5276c788", "fn": "MetaGxBreast_1.22.0.tar.gz"}, "metagxovarian-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MetaGxOvarian_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxOvarian_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxovarian/bioconductor-metagxovarian_1.22.0_src_all.tar.gz"], "md5": "f76dc6c912d3a8936f81509ba6559286", "fn": "MetaGxOvarian_1.22.0.tar.gz"}, "metagxpancreas-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MetaGxPancreas_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxPancreas_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxpancreas/bioconductor-metagxpancreas_1.22.0_src_all.tar.gz"], "md5": "0c1764dc18a9a180b2121649c98a26a1", "fn": "MetaGxPancreas_1.22.0.tar.gz"}, "metamsdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/metaMSdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/metaMSdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metamsdata/bioconductor-metamsdata_1.38.0_src_all.tar.gz"], "md5": "aa7ca09c8f43104cb85f69fda0a1fc1a", "fn": "metaMSdata_1.38.0.tar.gz"}, "metascope-1.2.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MetaScope_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaScope_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metascope/bioconductor-metascope_1.2.0_src_all.tar.gz"], "md5": "3e9dbacc12fa3bd332773ffa95325f0b", "fn": "MetaScope_1.2.0.tar.gz"}, "methylaiddata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MethylAidData_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/MethylAidData_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylaiddata/bioconductor-methylaiddata_1.34.0_src_all.tar.gz"], "md5": "95cc72b436067e4a8046564381101e04", "fn": "MethylAidData_1.34.0.tar.gz"}, "methylclockdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/methylclockData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/methylclockData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylclockdata/bioconductor-methylclockdata_1.10.0_src_all.tar.gz"], "md5": "633d9cc6c028025090e12004484fada1", "fn": "methylclockData_1.10.0.tar.gz"}, "methylseqdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MethylSeqData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/MethylSeqData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylseqdata/bioconductor-methylseqdata_1.12.0_src_all.tar.gz"], "md5": "ded280784f55a6ebec42069160de26ad", "fn": "MethylSeqData_1.12.0.tar.gz"}, "microbiomebenchmarkdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MicrobiomeBenchmarkData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/MicrobiomeBenchmarkData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-microbiomebenchmarkdata/bioconductor-microbiomebenchmarkdata_1.4.0_src_all.tar.gz"], "md5": "c6c791669de95bf2dc108798770ea5be", "fn": "MicrobiomeBenchmarkData_1.4.0.tar.gz"}, "microbiomedatasets-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/microbiomeDataSets_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/microbiomeDataSets_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-microbiomedatasets/bioconductor-microbiomedatasets_1.10.0_src_all.tar.gz"], "md5": "90cd4bb36dafcef8f6eb0e0232afdcd0", "fn": "microbiomeDataSets_1.10.0.tar.gz"}, "micrornaome-1.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/microRNAome_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/microRNAome_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-micrornaome/bioconductor-micrornaome_1.24.0_src_all.tar.gz"], "md5": "12d3baf395e82975bbcacfb9ff61a715", "fn": "microRNAome_1.24.0.tar.gz"}, "minfidata-0.48.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/minfiData_0.48.0.tar.gz", "https://bioarchive.galaxyproject.org/minfiData_0.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minfidata/bioconductor-minfidata_0.48.0_src_all.tar.gz"], "md5": "1ca7578aeab1a54db146c443870be6e7", "fn": "minfiData_0.48.0.tar.gz"}, "minfidataepic-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/minfiDataEPIC_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/minfiDataEPIC_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minfidataepic/bioconductor-minfidataepic_1.28.0_src_all.tar.gz"], "md5": "bcb0b01d571c5308e02db4c6b5c0d1ce", "fn": "minfiDataEPIC_1.28.0.tar.gz"}, "minionsummarydata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/minionSummaryData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/minionSummaryData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minionsummarydata/bioconductor-minionsummarydata_1.32.0_src_all.tar.gz"], "md5": "1679c45541b2d76094c3894abe9c011d", "fn": "minionSummaryData_1.32.0.tar.gz"}, "mircompdata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/miRcompData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/miRcompData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mircompdata/bioconductor-mircompdata_1.32.0_src_all.tar.gz"], "md5": "0b091222ebe8ac1a3a2c59384931393b", "fn": "miRcompData_1.32.0.tar.gz"}, "mirnatarget-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/miRNATarget_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/miRNATarget_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirnatarget/bioconductor-mirnatarget_1.40.0_src_all.tar.gz"], "md5": "f1988a96af5f0232abfbe507854d49bb", "fn": "miRNATarget_1.40.0.tar.gz"}, "mmappr2data-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MMAPPR2data_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/MMAPPR2data_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mmappr2data/bioconductor-mmappr2data_1.16.0_src_all.tar.gz"], "md5": "5b4772746766de5c40448c865fa2d60d", "fn": "MMAPPR2data_1.16.0.tar.gz"}, "mmdiffbamsubset-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MMDiffBamSubset_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/MMDiffBamSubset_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mmdiffbamsubset/bioconductor-mmdiffbamsubset_1.38.0_src_all.tar.gz"], "md5": "0becc66301b49b58a99efa19577ee27c", "fn": "MMDiffBamSubset_1.38.0.tar.gz"}, "mofadata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MOFAdata_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/MOFAdata_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mofadata/bioconductor-mofadata_1.18.0_src_all.tar.gz"], "md5": "23e46e209a43d7e62cfd6accc6a6fb44", "fn": "MOFAdata_1.18.0.tar.gz"}, "mosaicsexample-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/mosaicsExample_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/mosaicsExample_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mosaicsexample/bioconductor-mosaicsexample_1.40.0_src_all.tar.gz"], "md5": "8852ad56f152a138367e7630b6b21efb", "fn": "mosaicsExample_1.40.0.tar.gz"}, "mouse4302barcodevecs-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/mouse4302barcodevecs_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse4302barcodevecs_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302barcodevecs/bioconductor-mouse4302barcodevecs_1.40.0_src_all.tar.gz"], "md5": "365757fba17dae1ed483e184d2c9fcdb", "fn": "mouse4302barcodevecs_1.40.0.tar.gz"}, "mousegastrulationdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MouseGastrulationData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/MouseGastrulationData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousegastrulationdata/bioconductor-mousegastrulationdata_1.16.0_src_all.tar.gz"], "md5": "4af06fb157942c6cfd9f24494bd7ae1f", "fn": "MouseGastrulationData_1.16.0.tar.gz"}, "mousethymusageing-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MouseThymusAgeing_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MouseThymusAgeing_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousethymusageing/bioconductor-mousethymusageing_1.10.0_src_all.tar.gz"], "md5": "cf1889c22fa9e5ac5899a4d911907a90", "fn": "MouseThymusAgeing_1.10.0.tar.gz"}, "msd16s-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/msd16s_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/msd16s_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msd16s/bioconductor-msd16s_1.22.0_src_all.tar.gz"], "md5": "fddb80467192bbe28bb92599941be5d3", "fn": "msd16s_1.22.0.tar.gz"}, "msdata-0.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/msdata_0.42.0.tar.gz", "https://bioarchive.galaxyproject.org/msdata_0.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msdata/bioconductor-msdata_0.42.0_src_all.tar.gz"], "md5": "3ef7fea0866799a767fb8ac2d1da0a16", "fn": "msdata_0.42.0.tar.gz"}, "msigdb-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/msigdb_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/msigdb_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msigdb/bioconductor-msigdb_1.10.0_src_all.tar.gz"], "md5": "eb5822dab5f9ad68cc5a46beaf626de0", "fn": "msigdb_1.10.0.tar.gz"}, "msmb-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MSMB_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/MSMB_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msmb/bioconductor-msmb_1.20.0_src_all.tar.gz"], "md5": "bc2942708f54a40d59ce7e41daff7df0", "fn": "MSMB_1.20.0.tar.gz"}, "mspuritydata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/msPurityData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/msPurityData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mspuritydata/bioconductor-mspuritydata_1.30.0_src_all.tar.gz"], "md5": "6c86343515cbb9f81131baa3f25659f0", "fn": "msPurityData_1.30.0.tar.gz"}, "msqc1-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/msqc1_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/msqc1_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msqc1/bioconductor-msqc1_1.30.0_src_all.tar.gz"], "md5": "a95a760a0c0ef5e8053acee1d59170a4", "fn": "msqc1_1.30.0.tar.gz"}, "mtbls2-1.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/mtbls2_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/mtbls2_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mtbls2/bioconductor-mtbls2_1.32.0_src_all.tar.gz"], "md5": "820109836c79f398ea5b82f5887b7fea", "fn": "mtbls2_1.32.0.tar.gz"}, "mugaexampledata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MUGAExampleData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/MUGAExampleData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mugaexampledata/bioconductor-mugaexampledata_1.22.0_src_all.tar.gz"], "md5": "b7fe2c7ad41486695fb78263a8c9a854", "fn": "MUGAExampleData_1.22.0.tar.gz"}, "muscdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/muscData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/muscData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-muscdata/bioconductor-muscdata_1.16.0_src_all.tar.gz"], "md5": "f34c376f88f97c98d4aac5490b45bc24", "fn": "muscData_1.16.0.tar.gz"}, "mvoutdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/mvoutData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/mvoutData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mvoutdata/bioconductor-mvoutdata_1.38.0_src_all.tar.gz"], "md5": "abca7ca8ae7729ed8f146d0083aa9757", "fn": "mvoutData_1.38.0.tar.gz"}, "nanoporernaseq-1.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/NanoporeRNASeq_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/NanoporeRNASeq_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nanoporernaseq/bioconductor-nanoporernaseq_1.12.0_src_all.tar.gz"], "md5": "eca12ebcd403efd53e1b38d5f03f2027", "fn": "NanoporeRNASeq_1.12.0.tar.gz"}, "nanotubes-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/nanotubes_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/nanotubes_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nanotubes/bioconductor-nanotubes_1.18.0_src_all.tar.gz"], "md5": "ff283cb49c319a357c22e17d2df22715", "fn": "nanotubes_1.18.0.tar.gz"}, "ncigraphdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/NCIgraphData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/NCIgraphData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ncigraphdata/bioconductor-ncigraphdata_1.38.0_src_all.tar.gz"], "md5": "f144169473d42fafb1966986dcf15628", "fn": "NCIgraphData_1.38.0.tar.gz"}, "nestlink-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/NestLink_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/NestLink_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nestlink/bioconductor-nestlink_1.18.0_src_all.tar.gz"], "md5": "11cd94f5bd8b38cf261ae3346a283e81", "fn": "NestLink_1.18.0.tar.gz"}, "netactivitydata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/NetActivityData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/NetActivityData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-netactivitydata/bioconductor-netactivitydata_1.4.0_src_all.tar.gz"], "md5": "a3805046d14d13afc30a0f082952f200", "fn": "NetActivityData_1.4.0.tar.gz"}, "neve2006-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Neve2006_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/Neve2006_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-neve2006/bioconductor-neve2006_0.40.0_src_all.tar.gz"], "md5": "1feec2f09bac8c69ba9df5ea29e7e08c", "fn": "Neve2006_0.40.0.tar.gz"}, "ngscopydata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/NGScopyData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/NGScopyData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ngscopydata/bioconductor-ngscopydata_1.22.0_src_all.tar.gz"], "md5": "0ba77cf672a331e4c9dd90b26f41b5c6", "fn": "NGScopyData_1.22.0.tar.gz"}, "nullrangesdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/nullrangesData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/nullrangesData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nullrangesdata/bioconductor-nullrangesdata_1.8.0_src_all.tar.gz"], "md5": "c8b4cf63d70a2577251c03c093c014b1", "fn": "nullrangesData_1.8.0.tar.gz"}, "nxtirfdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/NxtIRFdata_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/NxtIRFdata_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nxtirfdata/bioconductor-nxtirfdata_1.8.0_src_all.tar.gz"], "md5": "3d9c35f12650fe6e2eb413224b3590dc", "fn": "NxtIRFdata_1.8.0.tar.gz"}, "obmiti-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ObMiTi_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/ObMiTi_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-obmiti/bioconductor-obmiti_1.10.0_src_all.tar.gz"], "md5": "0510665a5231cd3109d19478e4aadbd9", "fn": "ObMiTi_1.10.0.tar.gz"}, "oct4-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/oct4_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/oct4_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-oct4/bioconductor-oct4_1.18.0_src_all.tar.gz"], "md5": "1b6bbc6300c74c038689c7fb5b7d5eb2", "fn": "oct4_1.18.0.tar.gz"}, "octad.db-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/octad.db_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/octad.db_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-octad.db/bioconductor-octad.db_1.4.0_src_all.tar.gz"], "md5": "ef8723031fea32015ee26dbf30d2c8ba", "fn": "octad.db_1.4.0.tar.gz"}, "omicspcadata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/OMICsPCAdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/OMICsPCAdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-omicspcadata/bioconductor-omicspcadata_1.20.0_src_all.tar.gz"], "md5": "ba3167fdf846cb80aea07162b88c9b73", "fn": "OMICsPCAdata_1.20.0.tar.gz"}, "onassisjavalibs-1.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/OnassisJavaLibs_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/OnassisJavaLibs_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-onassisjavalibs/bioconductor-onassisjavalibs_1.24.0_src_all.tar.gz"], "md5": "88d86bc7e7d339146ba7ea689c2d8080", "fn": "OnassisJavaLibs_1.24.0.tar.gz"}, "optimalflowdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/optimalFlowData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/optimalFlowData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-optimalflowdata/bioconductor-optimalflowdata_1.14.0_src_all.tar.gz"], "md5": "790ea8af88ecf90abafdef9a7c4abb08", "fn": "optimalFlowData_1.14.0.tar.gz"}, "orthosdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/orthosData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/orthosData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-orthosdata/bioconductor-orthosdata_1.0.0_src_all.tar.gz"], "md5": "7970587455fa5197daf1f6b640b7f688", "fn": "orthosData_1.0.0.tar.gz"}, "parathyroidse-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/parathyroidSE_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/parathyroidSE_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-parathyroidse/bioconductor-parathyroidse_1.40.0_src_all.tar.gz"], "md5": "e4d06f888feb4015273e20b14f8ee37a", "fn": "parathyroidSE_1.40.0.tar.gz"}, "pasilla-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/pasilla_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/pasilla_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasilla/bioconductor-pasilla_1.30.0_src_all.tar.gz"], "md5": "e1fbdd57136d8a29edd1e0164dc2412e", "fn": "pasilla_1.30.0.tar.gz"}, "pasillabamsubset-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/pasillaBamSubset_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/pasillaBamSubset_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasillabamsubset/bioconductor-pasillabamsubset_0.40.0_src_all.tar.gz"], "md5": "8fd05eac2d37650e157871908cbaf306", "fn": "pasillaBamSubset_0.40.0.tar.gz"}, "pasillatranscriptexpr-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PasillaTranscriptExpr_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/PasillaTranscriptExpr_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasillatranscriptexpr/bioconductor-pasillatranscriptexpr_1.30.0_src_all.tar.gz"], "md5": "7d1d8c852fff7d80c11e8ab79dae7487", "fn": "PasillaTranscriptExpr_1.30.0.tar.gz"}, "pathnetdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PathNetData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/PathNetData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pathnetdata/bioconductor-pathnetdata_1.38.0_src_all.tar.gz"], "md5": "d72e955b33c92f1703ae072ec788c1d9", "fn": "PathNetData_1.38.0.tar.gz"}, "pchicdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PCHiCdata_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/PCHiCdata_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pchicdata/bioconductor-pchicdata_1.30.0_src_all.tar.gz"], "md5": "8791902075a44ae03c0366150aa3f61e", "fn": "PCHiCdata_1.30.0.tar.gz"}, "pcxndata-2.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/pcxnData_2.24.0.tar.gz", "https://bioarchive.galaxyproject.org/pcxnData_2.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pcxndata/bioconductor-pcxndata_2.24.0_src_all.tar.gz"], "md5": "7814b1a6f5dbd08e71df1e92ea4328f6", "fn": "pcxnData_2.24.0.tar.gz"}, "pd.atdschip.tiling-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/pd.atdschip.tiling_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.atdschip.tiling_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.atdschip.tiling/bioconductor-pd.atdschip.tiling_0.40.0_src_all.tar.gz"], "md5": "a81ffdc7dfb8eb04e09ec133db77d0d4", "fn": "pd.atdschip.tiling_0.40.0.tar.gz"}, "pepdat-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/pepDat_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/pepDat_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pepdat/bioconductor-pepdat_1.22.0_src_all.tar.gz"], "md5": "4ce373369604b54b15e5992ebe9355b9", "fn": "pepDat_1.22.0.tar.gz"}, "pepsnmrdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PepsNMRData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/PepsNMRData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pepsnmrdata/bioconductor-pepsnmrdata_1.20.0_src_all.tar.gz"], "md5": "96fc9090499b4460f72fb85a0428b357", "fn": "PepsNMRData_1.20.0.tar.gz"}, "phyloprofiledata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PhyloProfileData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/PhyloProfileData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phyloprofiledata/bioconductor-phyloprofiledata_1.16.0_src_all.tar.gz"], "md5": "68dda32e9151c0aba4eb5b29c0313f83", "fn": "PhyloProfileData_1.16.0.tar.gz"}, "plotgardenerdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/plotgardenerData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/plotgardenerData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-plotgardenerdata/bioconductor-plotgardenerdata_1.8.0_src_all.tar.gz"], "md5": "96055b11818bd59c0c91977b34973608", "fn": "plotgardenerData_1.8.0.tar.gz"}, "prebsdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/prebsdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/prebsdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prebsdata/bioconductor-prebsdata_1.38.0_src_all.tar.gz"], "md5": "a1c6aee2732035357adc3e2cb99d6bcc", "fn": "prebsdata_1.38.0.tar.gz"}, "precisetadhub-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/preciseTADhub_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/preciseTADhub_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-precisetadhub/bioconductor-precisetadhub_1.10.0_src_all.tar.gz"], "md5": "bff4bbf0a4ac1abf21ff72ad4346795c", "fn": "preciseTADhub_1.10.0.tar.gz"}, "predasampledata-0.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PREDAsampledata_0.42.0.tar.gz", "https://bioarchive.galaxyproject.org/PREDAsampledata_0.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-predasampledata/bioconductor-predasampledata_0.42.0_src_all.tar.gz"], "md5": "5acce57384c00a56d658281ba4fa57e5", "fn": "PREDAsampledata_0.42.0.tar.gz"}, "prodata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ProData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/ProData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prodata/bioconductor-prodata_1.40.0_src_all.tar.gz"], "md5": "73f3449db86899c83d61173f6bd02a79", "fn": "ProData_1.40.0.tar.gz"}, "prolocdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/pRolocdata_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/pRolocdata_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prolocdata/bioconductor-prolocdata_1.40.0_src_all.tar.gz"], "md5": "8aafd04221b21588077788ec79272e1a", "fn": "pRolocdata_1.40.0.tar.gz"}, "prostatecancercamcap-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/prostateCancerCamcap_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerCamcap_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancercamcap/bioconductor-prostatecancercamcap_1.30.0_src_all.tar.gz"], "md5": "5a27ee47f07162569e5e1e06ffd69886", "fn": "prostateCancerCamcap_1.30.0.tar.gz"}, "prostatecancergrasso-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/prostateCancerGrasso_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerGrasso_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancergrasso/bioconductor-prostatecancergrasso_1.30.0_src_all.tar.gz"], "md5": "c331c996d943a14687439dfdf37b8029", "fn": "prostateCancerGrasso_1.30.0.tar.gz"}, "prostatecancerstockholm-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/prostateCancerStockholm_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerStockholm_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancerstockholm/bioconductor-prostatecancerstockholm_1.30.0_src_all.tar.gz"], "md5": "49326bf3b6f66be78fa1e6d6768b5538", "fn": "prostateCancerStockholm_1.30.0.tar.gz"}, "prostatecancertaylor-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/prostateCancerTaylor_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerTaylor_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancertaylor/bioconductor-prostatecancertaylor_1.30.0_src_all.tar.gz"], "md5": "c90ff79776e9a658d4cf05e9a29706a8", "fn": "prostateCancerTaylor_1.30.0.tar.gz"}, "prostatecancervarambally-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/prostateCancerVarambally_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerVarambally_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancervarambally/bioconductor-prostatecancervarambally_1.30.0_src_all.tar.gz"], "md5": "cf8fc1872af8c5c2b47372ce94ed4c5c", "fn": "prostateCancerVarambally_1.30.0.tar.gz"}, "ptairdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ptairData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/ptairData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ptairdata/bioconductor-ptairdata_1.10.0_src_all.tar.gz"], "md5": "eea0fcfdd0047d72092a3b6beb326129", "fn": "ptairData_1.10.0.tar.gz"}, "pth2o2lipids-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PtH2O2lipids_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/PtH2O2lipids_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pth2o2lipids/bioconductor-pth2o2lipids_1.28.0_src_all.tar.gz"], "md5": "498d573bc33e7566708c38be5098bb2e", "fn": "PtH2O2lipids_1.28.0.tar.gz"}, "pumadata-2.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/pumadata_2.38.0.tar.gz", "https://bioarchive.galaxyproject.org/pumadata_2.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pumadata/bioconductor-pumadata_2.38.0_src_all.tar.gz"], "md5": "811d6234d1d4e310beb7111601b157b7", "fn": "pumadata_2.38.0.tar.gz"}, "pwmenrich.dmelanogaster.background-4.36.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PWMEnrich.Dmelanogaster.background_4.36.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Dmelanogaster.background_4.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.dmelanogaster.background/bioconductor-pwmenrich.dmelanogaster.background_4.36.0_src_all.tar.gz"], "md5": "b671ba0cff5c0c6017fd3f72d0afc547", "fn": "PWMEnrich.Dmelanogaster.background_4.36.0.tar.gz"}, "pwmenrich.hsapiens.background-4.36.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PWMEnrich.Hsapiens.background_4.36.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Hsapiens.background_4.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.hsapiens.background/bioconductor-pwmenrich.hsapiens.background_4.36.0_src_all.tar.gz"], "md5": "7c7b177c29fc31c7546d4e7160a9b977", "fn": "PWMEnrich.Hsapiens.background_4.36.0.tar.gz"}, "pwmenrich.mmusculus.background-4.36.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PWMEnrich.Mmusculus.background_4.36.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Mmusculus.background_4.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.mmusculus.background/bioconductor-pwmenrich.mmusculus.background_4.36.0_src_all.tar.gz"], "md5": "5d54401a941d1efe7148da2ddc714d65", "fn": "PWMEnrich.Mmusculus.background_4.36.0.tar.gz"}, "qdnaseq.hg19-1.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/QDNAseq.hg19_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/QDNAseq.hg19_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.hg19/bioconductor-qdnaseq.hg19_1.32.0_src_all.tar.gz"], "md5": "2b663d8771f16d55db88ec3321942ead", "fn": "QDNAseq.hg19_1.32.0.tar.gz"}, "qdnaseq.mm10-1.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/QDNAseq.mm10_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/QDNAseq.mm10_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.mm10/bioconductor-qdnaseq.mm10_1.32.0_src_all.tar.gz"], "md5": "2d7b80c2bec7146aec28384b7875acca", "fn": "QDNAseq.mm10_1.32.0.tar.gz"}, "qplexdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/qPLEXdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/qPLEXdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qplexdata/bioconductor-qplexdata_1.20.0_src_all.tar.gz"], "md5": "af947f54391fc79c81308890b1e95d96", "fn": "qPLEXdata_1.20.0.tar.gz"}, "qubicdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/QUBICdata_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/QUBICdata_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qubicdata/bioconductor-qubicdata_1.30.0_src_all.tar.gz"], "md5": "0670dfaee6f8d532cf3506428a5932c1", "fn": "QUBICdata_1.30.0.tar.gz"}, "raerdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/raerdata_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/raerdata_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-raerdata/bioconductor-raerdata_1.0.0_src_all.tar.gz"], "md5": "8f250d12f89396f8d4351da5045cf22c", "fn": "raerdata_1.0.0.tar.gz"}, "rcellminerdata-2.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/rcellminerData_2.24.0.tar.gz", "https://bioarchive.galaxyproject.org/rcellminerData_2.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rcellminerdata/bioconductor-rcellminerdata_2.24.0_src_all.tar.gz"], "md5": "2f45852d4eeb438b6a1feb156200b2bc", "fn": "rcellminerData_2.24.0.tar.gz"}, "rcistarget.hg19.motifdbs.cisbponly.500bp-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp_1.22.0_src_all.tar.gz"], "md5": "b8cdbfafeb9966332876fdf9be8dbb5a", "fn": "RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.22.0.tar.gz"}, "reactomegsa.data-1.16.1": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ReactomeGSA.data_1.16.1.tar.gz", "https://bioarchive.galaxyproject.org/ReactomeGSA.data_1.16.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-reactomegsa.data/bioconductor-reactomegsa.data_1.16.1_src_all.tar.gz"], "md5": "bd236d4d4078f99ea5d473fde1ff065f", "fn": "ReactomeGSA.data_1.16.1.tar.gz"}, "regparallel-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RegParallel_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/RegParallel_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-regparallel/bioconductor-regparallel_1.20.0_src_all.tar.gz"], "md5": "68533561edc82ac22088ffdd6e988aad", "fn": "RegParallel_1.20.0.tar.gz"}, "restfulsedata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/restfulSEData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/restfulSEData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-restfulsedata/bioconductor-restfulsedata_1.24.0_src_all.tar.gz"], "md5": "c69fe04b8675edd0faa593fb5ffc72c8", "fn": "restfulSEData_1.24.0.tar.gz"}, "rforproteomics-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RforProteomics_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/RforProteomics_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rforproteomics/bioconductor-rforproteomics_1.40.0_src_all.tar.gz"], "md5": "6d75aedb5902ea26a18e39da6848db4c", "fn": "RforProteomics_1.40.0.tar.gz"}, "rgmqllib-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RGMQLlib_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/RGMQLlib_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgmqllib/bioconductor-rgmqllib_1.22.0_src_all.tar.gz"], "md5": "d8ad27b1fe0c5eff6135285db972cab2", "fn": "RGMQLlib_1.22.0.tar.gz"}, "rheumaticconditionwollbold-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/rheumaticConditionWOLLBOLD_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/rheumaticConditionWOLLBOLD_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rheumaticconditionwollbold/bioconductor-rheumaticconditionwollbold_1.40.0_src_all.tar.gz"], "md5": "8c8a5f56b923fe79c4a4902028d6fc5c", "fn": "rheumaticConditionWOLLBOLD_1.40.0.tar.gz"}, "ritandata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RITANdata_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/RITANdata_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ritandata/bioconductor-ritandata_1.26.0_src_all.tar.gz"], "md5": "12987879ef374ad399dd440a058b9a47", "fn": "RITANdata_1.26.0.tar.gz"}, "rmassbankdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RMassBankData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/RMassBankData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rmassbankdata/bioconductor-rmassbankdata_1.40.0_src_all.tar.gz"], "md5": "ac6f883e962890eebb03c2368be8bcdc", "fn": "RMassBankData_1.40.0.tar.gz"}, "rnainteractmapk-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RNAinteractMAPK_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAinteractMAPK_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnainteractmapk/bioconductor-rnainteractmapk_1.40.0_src_all.tar.gz"], "md5": "c60bb748ed7dc37d409f5dde69354074", "fn": "RNAinteractMAPK_1.40.0.tar.gz"}, "rnamodr.data-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RNAmodR.Data_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAmodR.Data_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnamodr.data/bioconductor-rnamodr.data_1.16.0_src_all.tar.gz"], "md5": "cd4851e2f0c0a93c6d5a9163f542b07f", "fn": "RNAmodR.Data_1.16.0.tar.gz"}, "rnaseqdata.hnrnpc.bam.chr14-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RNAseqData.HNRNPC.bam.chr14_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAseqData.HNRNPC.bam.chr14_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqdata.hnrnpc.bam.chr14/bioconductor-rnaseqdata.hnrnpc.bam.chr14_0.40.0_src_all.tar.gz"], "md5": "9bfb7faf3c8770b15f3cf15bb670162d", "fn": "RNAseqData.HNRNPC.bam.chr14_0.40.0.tar.gz"}, "rnaseqsamplesizedata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RnaSeqSampleSizeData_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/RnaSeqSampleSizeData_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqsamplesizedata/bioconductor-rnaseqsamplesizedata_1.34.0_src_all.tar.gz"], "md5": "a4edc47422b0be1d83521282c0599440", "fn": "RnaSeqSampleSizeData_1.34.0.tar.gz"}, "rnbeads.hg19-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RnBeads.hg19_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.hg19_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg19/bioconductor-rnbeads.hg19_1.34.0_src_all.tar.gz"], "md5": "92612251679ba9c6d2b88b90838edf1c", "fn": "RnBeads.hg19_1.34.0.tar.gz"}, "rnbeads.hg38-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RnBeads.hg38_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.hg38_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg38/bioconductor-rnbeads.hg38_1.34.0_src_all.tar.gz"], "md5": "44dd2d3ae3703e045016a34060a14b0a", "fn": "RnBeads.hg38_1.34.0.tar.gz"}, "rnbeads.mm10-2.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RnBeads.mm10_2.10.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.mm10_2.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm10/bioconductor-rnbeads.mm10_2.10.0_src_all.tar.gz"], "md5": "0c935572ce46183bc5a7aaea31ea2519", "fn": "RnBeads.mm10_2.10.0.tar.gz"}, "rnbeads.mm9-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RnBeads.mm9_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.mm9_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm9/bioconductor-rnbeads.mm9_1.34.0_src_all.tar.gz"], "md5": "76f271051b1c542e5ac0da492777f933", "fn": "RnBeads.mm9_1.34.0.tar.gz"}, "rnbeads.rn5-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RnBeads.rn5_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.rn5_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.rn5/bioconductor-rnbeads.rn5_1.34.0_src_all.tar.gz"], "md5": "ed075717da62b68e7a9b47a14ac09a35", "fn": "RnBeads.rn5_1.34.0.tar.gz"}, "rrbsdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RRBSdata_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/RRBSdata_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rrbsdata/bioconductor-rrbsdata_1.22.0_src_all.tar.gz"], "md5": "04bcf0f0348dc54984ca9506773820ec", "fn": "RRBSdata_1.22.0.tar.gz"}, "rrdpdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/rRDPData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/rRDPData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rrdpdata/bioconductor-rrdpdata_1.22.0_src_all.tar.gz"], "md5": "9ca56f1bf00bfaefb27c351ccc7346ae", "fn": "rRDPData_1.22.0.tar.gz"}, "rtcga.clinical-20151101.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RTCGA.clinical_20151101.32.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.clinical_20151101.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.clinical/bioconductor-rtcga.clinical_20151101.32.0_src_all.tar.gz"], "md5": "9c32b8aef86c9ad34ea8c3672575d724", "fn": "RTCGA.clinical_20151101.32.0.tar.gz"}, "rtcga.cnv-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RTCGA.CNV_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.CNV_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.cnv/bioconductor-rtcga.cnv_1.30.0_src_all.tar.gz"], "md5": "15267c2322da59ccd344657a28d2ba6a", "fn": "RTCGA.CNV_1.30.0.tar.gz"}, "rtcga.methylation-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RTCGA.methylation_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.methylation_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.methylation/bioconductor-rtcga.methylation_1.30.0_src_all.tar.gz"], "md5": "9d90704cb34a57878ef719348489c702", "fn": "RTCGA.methylation_1.30.0.tar.gz"}, "rtcga.mirnaseq-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RTCGA.miRNASeq_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.miRNASeq_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mirnaseq/bioconductor-rtcga.mirnaseq_1.30.0_src_all.tar.gz"], "md5": "744062c2f0db68a88e27db9d61929a79", "fn": "RTCGA.miRNASeq_1.30.0.tar.gz"}, "rtcga.mrna-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RTCGA.mRNA_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.mRNA_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mrna/bioconductor-rtcga.mrna_1.30.0_src_all.tar.gz"], "md5": "c9774207df355ef5945677d36e915103", "fn": "RTCGA.mRNA_1.30.0.tar.gz"}, "rtcga.mutations-20151101.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RTCGA.mutations_20151101.32.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.mutations_20151101.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mutations/bioconductor-rtcga.mutations_20151101.32.0_src_all.tar.gz"], "md5": "0740acb5a6a47fd9d1281ccaf80bafed", "fn": "RTCGA.mutations_20151101.32.0.tar.gz"}, "rtcga.pancan12-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RTCGA.PANCAN12_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.PANCAN12_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.pancan12/bioconductor-rtcga.pancan12_1.30.0_src_all.tar.gz"], "md5": "8b0742d189afe05f47a2656556d85d0b", "fn": "RTCGA.PANCAN12_1.30.0.tar.gz"}, "rtcga.rnaseq-20151101.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RTCGA.rnaseq_20151101.32.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.rnaseq_20151101.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.rnaseq/bioconductor-rtcga.rnaseq_20151101.32.0_src_all.tar.gz"], "md5": "47bee14c68ff4d1014677eca0ed969a9", "fn": "RTCGA.rnaseq_20151101.32.0.tar.gz"}, "rtcga.rppa-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RTCGA.RPPA_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.RPPA_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.rppa/bioconductor-rtcga.rppa_1.30.0_src_all.tar.gz"], "md5": "5eccece412039d43cdf74aec284fa0d9", "fn": "RTCGA.RPPA_1.30.0.tar.gz"}, "ruvnormalizedata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RUVnormalizeData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/RUVnormalizeData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ruvnormalizedata/bioconductor-ruvnormalizedata_1.22.0_src_all.tar.gz"], "md5": "5d7104746a5cac16500870312dd769a6", "fn": "RUVnormalizeData_1.22.0.tar.gz"}, "sampleclassifierdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/sampleClassifierData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/sampleClassifierData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sampleclassifierdata/bioconductor-sampleclassifierdata_1.26.0_src_all.tar.gz"], "md5": "941790a92cde9051601206ed162f4151", "fn": "sampleClassifierData_1.26.0.tar.gz"}, "sbgnview.data-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SBGNview.data_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/SBGNview.data_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sbgnview.data/bioconductor-sbgnview.data_1.16.0_src_all.tar.gz"], "md5": "7e1bce0dfbc48b3cdc023d88e2ea7d9a", "fn": "SBGNview.data_1.16.0.tar.gz"}, "scanmirdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/scanMiRData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/scanMiRData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scanmirdata/bioconductor-scanmirdata_1.8.0_src_all.tar.gz"], "md5": "4c717492a3c85bbcf199873e35190219", "fn": "scanMiRData_1.8.0.tar.gz"}, "scatac.explorer-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/scATAC.Explorer_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/scATAC.Explorer_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scatac.explorer/bioconductor-scatac.explorer_1.8.0_src_all.tar.gz"], "md5": "80927899a83bb06d19b0f9800c183b36", "fn": "scATAC.Explorer_1.8.0.tar.gz"}, "sclcbam-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SCLCBam_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/SCLCBam_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sclcbam/bioconductor-sclcbam_1.34.0_src_all.tar.gz"], "md5": "660f11c1751b54cc942e91045884bfe6", "fn": "SCLCBam_1.34.0.tar.gz"}, "scmultiome-1.2.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/scMultiome_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/scMultiome_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scmultiome/bioconductor-scmultiome_1.2.0_src_all.tar.gz"], "md5": "db13145ffc5eb5430eee8ac7212e1b7d", "fn": "scMultiome_1.2.0.tar.gz"}, "scpdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/scpdata_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/scpdata_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scpdata/bioconductor-scpdata_1.10.0_src_all.tar.gz"], "md5": "eac9eae58fe9297359188c45a3dabd1f", "fn": "scpdata_1.10.0.tar.gz"}, "scrnaseq-2.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/scRNAseq_2.16.0.tar.gz", "https://bioarchive.galaxyproject.org/scRNAseq_2.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scrnaseq/bioconductor-scrnaseq_2.16.0_src_all.tar.gz"], "md5": "55196cb10876aa15733c6a29ffc38100", "fn": "scRNAseq_2.16.0.tar.gz"}, "scthi.data-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/scTHI.data_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/scTHI.data_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scthi.data/bioconductor-scthi.data_1.14.0_src_all.tar.gz"], "md5": "1fd101f8dc30262c323bdfa79810f6f5", "fn": "scTHI.data_1.14.0.tar.gz"}, "seq2pathway.data-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/seq2pathway.data_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/seq2pathway.data_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seq2pathway.data/bioconductor-seq2pathway.data_1.34.0_src_all.tar.gz"], "md5": "b0035ff986391159c1329eac9fb96661", "fn": "seq2pathway.data_1.34.0.tar.gz"}, "seqc-1.36.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/seqc_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/seqc_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seqc/bioconductor-seqc_1.36.0_src_all.tar.gz"], "md5": "105a278c97aca90968641aec403c1219", "fn": "seqc_1.36.0.tar.gz"}, "seqcna.annot-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/seqCNA.annot_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/seqCNA.annot_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seqcna.annot/bioconductor-seqcna.annot_1.38.0_src_all.tar.gz"], "md5": "a61df6e0824d7c3c3f4c697b5bd73e30", "fn": "seqCNA.annot_1.38.0.tar.gz"}, "serumstimulation-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/serumStimulation_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/serumStimulation_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-serumstimulation/bioconductor-serumstimulation_1.38.0_src_all.tar.gz"], "md5": "4d3f1a4e58f500d7e424eef0b22c05ad", "fn": "serumStimulation_1.38.0.tar.gz"}, "sesamedata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/sesameData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/sesameData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sesamedata/bioconductor-sesamedata_1.20.0_src_all.tar.gz"], "md5": "4cd44c4f5307d2775d94f2051b9a7f46", "fn": "sesameData_1.20.0.tar.gz"}, "sfedata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SFEData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/SFEData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sfedata/bioconductor-sfedata_1.4.0_src_all.tar.gz"], "md5": "7f3376870c972cba309b26d52d24fcbb", "fn": "SFEData_1.4.0.tar.gz"}, "shinymethyldata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/shinyMethylData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/shinyMethylData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-shinymethyldata/bioconductor-shinymethyldata_1.22.0_src_all.tar.gz"], "md5": "46f32db849aaa1467d09b0a371769374", "fn": "shinyMethylData_1.22.0.tar.gz"}, "signaturesearchdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/signatureSearchData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/signatureSearchData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-signaturesearchdata/bioconductor-signaturesearchdata_1.16.0_src_all.tar.gz"], "md5": "b30a7f1715a7525279c47db6df5ad995", "fn": "signatureSearchData_1.16.0.tar.gz"}, "simbenchdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SimBenchData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/SimBenchData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-simbenchdata/bioconductor-simbenchdata_1.10.0_src_all.tar.gz"], "md5": "c801056ea68c668cd98230e8956d551b", "fn": "SimBenchData_1.10.0.tar.gz"}, "simpintlists-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/simpIntLists_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/simpIntLists_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-simpintlists/bioconductor-simpintlists_1.38.0_src_all.tar.gz"], "md5": "9dbe0a1f390843a49bb11d05ac5f2e28", "fn": "simpIntLists_1.38.0.tar.gz"}, "single.mtec.transcriptomes-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Single.mTEC.Transcriptomes_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/Single.mTEC.Transcriptomes_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-single.mtec.transcriptomes/bioconductor-single.mtec.transcriptomes_1.30.0_src_all.tar.gz"], "md5": "574ee45ff1177688d68e6ae8295e67a2", "fn": "Single.mTEC.Transcriptomes_1.30.0.tar.gz"}, "singlecellmultimodal-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SingleCellMultiModal_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/SingleCellMultiModal_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-singlecellmultimodal/bioconductor-singlecellmultimodal_1.14.0_src_all.tar.gz"], "md5": "e397bc4fbd9ea63f6660758f01d01d38", "fn": "SingleCellMultiModal_1.14.0.tar.gz"}, "singlemoleculefootprintingdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SingleMoleculeFootprintingData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/SingleMoleculeFootprintingData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-singlemoleculefootprintingdata/bioconductor-singlemoleculefootprintingdata_1.10.0_src_all.tar.gz"], "md5": "451ecbdbb964607afbbe3b778b290246", "fn": "SingleMoleculeFootprintingData_1.10.0.tar.gz"}, "smokingmouse-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/smokingMouse_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/smokingMouse_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-smokingmouse/bioconductor-smokingmouse_1.0.0_src_all.tar.gz"], "md5": "0c2fad6bf0e911ae8c140c02bc29150e", "fn": "smokingMouse_1.0.0.tar.gz"}, "snadata-1.48.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SNAData_1.48.0.tar.gz", "https://bioarchive.galaxyproject.org/SNAData_1.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snadata/bioconductor-snadata_1.48.0_src_all.tar.gz"], "md5": "bfbd447afa550db44aa1db55e227cc10", "fn": "SNAData_1.48.0.tar.gz"}, "snageedata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SNAGEEdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/SNAGEEdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snageedata/bioconductor-snageedata_1.38.0_src_all.tar.gz"], "md5": "bfd0a2689cb9ac612cb2f8995c3a03d5", "fn": "SNAGEEdata_1.38.0.tar.gz"}, "snphooddata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SNPhoodData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/SNPhoodData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snphooddata/bioconductor-snphooddata_1.32.0_src_all.tar.gz"], "md5": "72ac86008c225c71df946cc8a7de1fa1", "fn": "SNPhoodData_1.32.0.tar.gz"}, "somaticadata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SomatiCAData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/SomatiCAData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-somaticadata/bioconductor-somaticadata_1.40.0_src_all.tar.gz"], "md5": "31d9100d6b5fa5f95c59eda9995f2684", "fn": "SomatiCAData_1.40.0.tar.gz"}, "somaticcanceralterations-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SomaticCancerAlterations_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/SomaticCancerAlterations_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-somaticcanceralterations/bioconductor-somaticcanceralterations_1.38.0_src_all.tar.gz"], "md5": "77b2b0312705c2a9581cdf7aab591db8", "fn": "SomaticCancerAlterations_1.38.0.tar.gz"}, "spatialdatasets-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SpatialDatasets_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/SpatialDatasets_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatialdatasets/bioconductor-spatialdatasets_1.0.0_src_all.tar.gz"], "md5": "36fd913ef0d7109d0be40afbc1255548", "fn": "SpatialDatasets_1.0.0.tar.gz"}, "spatialdmelxsim-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/spatialDmelxsim_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/spatialDmelxsim_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatialdmelxsim/bioconductor-spatialdmelxsim_1.8.0_src_all.tar.gz"], "md5": "2fec38c7672022e76f2b7a7ba7b9a677", "fn": "spatialDmelxsim_1.8.0.tar.gz"}, "spatiallibd-1.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/spatialLIBD_1.14.1.tar.gz", "https://bioarchive.galaxyproject.org/spatialLIBD_1.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatiallibd/bioconductor-spatiallibd_1.14.1_src_all.tar.gz"], "md5": "cd8c85a03e555f2dfdeb1627f7087002", "fn": "spatialLIBD_1.14.1.tar.gz"}, "spikein-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SpikeIn_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/SpikeIn_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spikein/bioconductor-spikein_1.44.0_src_all.tar.gz"], "md5": "439f9d2eda54024edb7c1c81862d74c8", "fn": "SpikeIn_1.44.0.tar.gz"}, "spikeinsubset-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SpikeInSubset_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/SpikeInSubset_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spikeinsubset/bioconductor-spikeinsubset_1.42.0_src_all.tar.gz"], "md5": "0c9b5af679c89a1468c9a6f581202e2b", "fn": "SpikeInSubset_1.42.0.tar.gz"}, "spqndata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/spqnData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/spqnData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spqndata/bioconductor-spqndata_1.14.0_src_all.tar.gz"], "md5": "453bf944ea40956afef2bd868f92d747", "fn": "spqnData_1.14.0.tar.gz"}, "stemhypoxia-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/stemHypoxia_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/stemHypoxia_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stemhypoxia/bioconductor-stemhypoxia_1.38.0_src_all.tar.gz"], "md5": "22ec9d76cac05ac7118873f7815225ba", "fn": "stemHypoxia_1.38.0.tar.gz"}, "stexampledata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/STexampleData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/STexampleData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stexampledata/bioconductor-stexampledata_1.10.0_src_all.tar.gz"], "md5": "5fa4bfb2e58e7f6bbcd957aa1aa7e938", "fn": "STexampleData_1.10.0.tar.gz"}, "stjudem-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/stjudem_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/stjudem_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stjudem/bioconductor-stjudem_1.42.0_src_all.tar.gz"], "md5": "4c6868a60726df51408834a227e551bf", "fn": "stjudem_1.42.0.tar.gz"}, "svm2crmdata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SVM2CRMdata_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/SVM2CRMdata_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-svm2crmdata/bioconductor-svm2crmdata_1.34.0_src_all.tar.gz"], "md5": "ce0c6615bfbb9a5a7cf4eeab0bd6199d", "fn": "SVM2CRMdata_1.34.0.tar.gz"}, "synapterdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/synapterdata_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/synapterdata_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-synapterdata/bioconductor-synapterdata_1.40.0_src_all.tar.gz"], "md5": "255aa756f0b6c0c1d95cdfbc889a67a2", "fn": "synapterdata_1.40.0.tar.gz"}, "systempiperdata-2.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/systemPipeRdata_2.6.0.tar.gz", "https://bioarchive.galaxyproject.org/systemPipeRdata_2.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-systempiperdata/bioconductor-systempiperdata_2.6.0_src_all.tar.gz"], "md5": "1af59929fb95c3a017b88fce32a4c833", "fn": "systemPipeRdata_2.6.0.tar.gz"}, "tabulamurisdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TabulaMurisData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/TabulaMurisData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tabulamurisdata/bioconductor-tabulamurisdata_1.20.0_src_all.tar.gz"], "md5": "39c27cc6646ea3bcdb4637a226b219b8", "fn": "TabulaMurisData_1.20.0.tar.gz"}, "tabulamurissenisdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TabulaMurisSenisData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/TabulaMurisSenisData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tabulamurissenisdata/bioconductor-tabulamurissenisdata_1.8.0_src_all.tar.gz"], "md5": "6d6120b18adce70e943a3da8e0e577b2", "fn": "TabulaMurisSenisData_1.8.0.tar.gz"}, "targetscoredata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TargetScoreData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/TargetScoreData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetscoredata/bioconductor-targetscoredata_1.38.0_src_all.tar.gz"], "md5": "61084f230f2c3dedb27988867f07f50f", "fn": "TargetScoreData_1.38.0.tar.gz"}, "targetsearchdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TargetSearchData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/TargetSearchData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetsearchdata/bioconductor-targetsearchdata_1.40.0_src_all.tar.gz"], "md5": "96bbec70706d8adcf4ee321261620d79", "fn": "TargetSearchData_1.40.0.tar.gz"}, "tartare-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tartare_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/tartare_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tartare/bioconductor-tartare_1.16.0_src_all.tar.gz"], "md5": "869743e16f05bc962de518ca925750d8", "fn": "tartare_1.16.0.tar.gz"}, "tbx20bamsubset-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TBX20BamSubset_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/TBX20BamSubset_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tbx20bamsubset/bioconductor-tbx20bamsubset_1.38.0_src_all.tar.gz"], "md5": "c158901ec6203e85569c600efb335ccf", "fn": "TBX20BamSubset_1.38.0.tar.gz"}, "tcgabiolinksgui.data-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TCGAbiolinksGUI.data_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAbiolinksGUI.data_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgabiolinksgui.data/bioconductor-tcgabiolinksgui.data_1.22.0_src_all.tar.gz"], "md5": "bd2042c0064583d666364a52ce3be17e", "fn": "TCGAbiolinksGUI.data_1.22.0.tar.gz"}, "tcgacrcmirna-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TCGAcrcmiRNA_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAcrcmiRNA_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmirna/bioconductor-tcgacrcmirna_1.22.0_src_all.tar.gz"], "md5": "451d09b5ec341d7e92211a1d42c35947", "fn": "TCGAcrcmiRNA_1.22.0.tar.gz"}, "tcgacrcmrna-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TCGAcrcmRNA_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAcrcmRNA_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmrna/bioconductor-tcgacrcmrna_1.22.0_src_all.tar.gz"], "md5": "bb9300e6ad6e4e5435a31487fdc22ed6", "fn": "TCGAcrcmRNA_1.22.0.tar.gz"}, "tcgamethylation450k-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TCGAMethylation450k_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAMethylation450k_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgamethylation450k/bioconductor-tcgamethylation450k_1.38.0_src_all.tar.gz"], "md5": "e913aa3b85d5cd1d0b27a346daf8c9ee", "fn": "TCGAMethylation450k_1.38.0.tar.gz"}, "tcgaworkflowdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TCGAWorkflowData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAWorkflowData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgaworkflowdata/bioconductor-tcgaworkflowdata_1.26.0_src_all.tar.gz"], "md5": "cbba498f1922aeedadf96a1911a81751", "fn": "TCGAWorkflowData_1.26.0.tar.gz"}, "tenxbraindata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TENxBrainData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxBrainData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxbraindata/bioconductor-tenxbraindata_1.22.0_src_all.tar.gz"], "md5": "1fa1b93ab8d144b860c83dc5741490a0", "fn": "TENxBrainData_1.22.0.tar.gz"}, "tenxbusdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TENxBUSData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxBUSData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxbusdata/bioconductor-tenxbusdata_1.16.0_src_all.tar.gz"], "md5": "35be2bd3c806b055fc9463e8f135dd32", "fn": "TENxBUSData_1.16.0.tar.gz"}, "tenxpbmcdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TENxPBMCData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxPBMCData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxpbmcdata/bioconductor-tenxpbmcdata_1.20.0_src_all.tar.gz"], "md5": "3e6c961a01998667f37de542858dbc09", "fn": "TENxPBMCData_1.20.0.tar.gz"}, "tenxvisiumdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TENxVisiumData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxVisiumData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxvisiumdata/bioconductor-tenxvisiumdata_1.10.0_src_all.tar.gz"], "md5": "f578add429847efff027a61b1749b9b4", "fn": "TENxVisiumData_1.10.0.tar.gz"}, "timecoursedata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/timecoursedata_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/timecoursedata_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-timecoursedata/bioconductor-timecoursedata_1.12.0_src_all.tar.gz"], "md5": "a5b9f962c12d69003eff9b6949d2b0af", "fn": "timecoursedata_1.12.0.tar.gz"}, "timerquant-1.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TimerQuant_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/TimerQuant_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-timerquant/bioconductor-timerquant_1.32.0_src_all.tar.gz"], "md5": "7033d0ae9a0731af8bafecbbfa5398c8", "fn": "TimerQuant_1.32.0.tar.gz"}, "tinesath1cdf-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tinesath1cdf_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/tinesath1cdf_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tinesath1cdf/bioconductor-tinesath1cdf_1.40.0_src_all.tar.gz"], "md5": "a58177f0ed4976f52370b35e13818ce3", "fn": "tinesath1cdf_1.40.0.tar.gz"}, "tinesath1probe-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tinesath1probe_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/tinesath1probe_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tinesath1probe/bioconductor-tinesath1probe_1.40.0_src_all.tar.gz"], "md5": "abd9396a4f17a0044018702394b62933", "fn": "tinesath1probe_1.40.0.tar.gz"}, "tissuetreg-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tissueTreg_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/tissueTreg_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tissuetreg/bioconductor-tissuetreg_1.22.0_src_all.tar.gz"], "md5": "5d975c08b7a19af832c4468ecb04c58b", "fn": "tissueTreg_1.22.0.tar.gz"}, "tmexplorer-1.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TMExplorer_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TMExplorer_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tmexplorer/bioconductor-tmexplorer_1.12.0_src_all.tar.gz"], "md5": "48b11be99739e61f54d9b442af739d49", "fn": "TMExplorer_1.12.0.tar.gz"}, "tofsimsdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tofsimsData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/tofsimsData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tofsimsdata/bioconductor-tofsimsdata_1.30.0_src_all.tar.gz"], "md5": "57fe35de7b03ee4f3ca07540949a6b5e", "fn": "tofsimsData_1.30.0.tar.gz"}, "topdownrdata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/topdownrdata_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/topdownrdata_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-topdownrdata/bioconductor-topdownrdata_1.24.0_src_all.tar.gz"], "md5": "28e746b858956bea0967344bfe363e7d", "fn": "topdownrdata_1.24.0.tar.gz"}, "tuberculosis-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tuberculosis_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/tuberculosis_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tuberculosis/bioconductor-tuberculosis_1.8.0_src_all.tar.gz"], "md5": "154cd343b8fba727ecf80a671a6a112d", "fn": "tuberculosis_1.8.0.tar.gz"}, "tumourmethdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TumourMethData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/TumourMethData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tumourmethdata/bioconductor-tumourmethdata_1.0.0_src_all.tar.gz"], "md5": "7b4ba6a8a59379a3b7f368e6c26fa0a6", "fn": "TumourMethData_1.0.0.tar.gz"}, "tweedeseqcountdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tweeDEseqCountData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/tweeDEseqCountData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tweedeseqcountdata/bioconductor-tweedeseqcountdata_1.40.0_src_all.tar.gz"], "md5": "d63e819cedf93ffbe115ed518bc9feaf", "fn": "tweeDEseqCountData_1.40.0.tar.gz"}, "tximportdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tximportData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/tximportData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tximportdata/bioconductor-tximportdata_1.30.0_src_all.tar.gz"], "md5": "4494d764fc087333e5c04ee7977c85c8", "fn": "tximportData_1.30.0.tar.gz"}, "varianttoolsdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/VariantToolsData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/VariantToolsData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-varianttoolsdata/bioconductor-varianttoolsdata_1.26.0_src_all.tar.gz"], "md5": "a85757ce237b03b0480f01488a78879b", "fn": "VariantToolsData_1.26.0.tar.gz"}, "vectrapolarisdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/VectraPolarisData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/VectraPolarisData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vectrapolarisdata/bioconductor-vectrapolarisdata_1.6.0_src_all.tar.gz"], "md5": "ea2006b85e374e76fbd70ca8b0819072", "fn": "VectraPolarisData_1.6.0.tar.gz"}, "vulcandata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/vulcandata_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/vulcandata_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vulcandata/bioconductor-vulcandata_1.24.0_src_all.tar.gz"], "md5": "cd95ea7ac7f2b9edfd46c1ffccb7c3c1", "fn": "vulcandata_1.24.0.tar.gz"}, "weberdivechalcdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/WeberDivechaLCdata_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/WeberDivechaLCdata_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-weberdivechalcdata/bioconductor-weberdivechalcdata_1.4.0_src_all.tar.gz"], "md5": "3b75c693f86ed228e2b7816872cfe4b7", "fn": "WeberDivechaLCdata_1.4.0.tar.gz"}, "wes.1kg.wugsc-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/WES.1KG.WUGSC_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/WES.1KG.WUGSC_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wes.1kg.wugsc/bioconductor-wes.1kg.wugsc_1.34.0_src_all.tar.gz"], "md5": "a0a3d230e27342090638ec4868756e5a", "fn": "WES.1KG.WUGSC_1.34.0.tar.gz"}, "wgsmapp-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/WGSmapp_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/WGSmapp_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wgsmapp/bioconductor-wgsmapp_1.14.0_src_all.tar.gz"], "md5": "dfc3f5a82d532551e2d6c21b11c99566", "fn": "WGSmapp_1.14.0.tar.gz"}, "xcoredata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/xcoredata_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/xcoredata_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xcoredata/bioconductor-xcoredata_1.6.0_src_all.tar.gz"], "md5": "214626bfcbb5d66445324f6e367142c7", "fn": "xcoredata_1.6.0.tar.gz"}, "xhybcasneuf-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/XhybCasneuf_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/XhybCasneuf_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xhybcasneuf/bioconductor-xhybcasneuf_1.40.0_src_all.tar.gz"], "md5": "f3e6306b5c05fb026e36e4c60656e25a", "fn": "XhybCasneuf_1.40.0.tar.gz"}, "yeastcc-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastCC_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastCC_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastcc/bioconductor-yeastcc_1.42.0_src_all.tar.gz"], "md5": "847d9bba73cb25f458f608c2cd6bf0e8", "fn": "yeastCC_1.42.0.tar.gz"}, "yeastexpdata-0.48.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastExpData_0.48.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastExpData_0.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastexpdata/bioconductor-yeastexpdata_0.48.0_src_all.tar.gz"], "md5": "7cd63808a957defe831bf3e9d3ef4789", "fn": "yeastExpData_0.48.0.tar.gz"}, "yeastgsdata-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastGSData_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastGSData_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastgsdata/bioconductor-yeastgsdata_0.40.0_src_all.tar.gz"], "md5": "bc455a9ecd3eb2652f887026841b3c69", "fn": "yeastGSData_0.40.0.tar.gz"}, "yeastnagalakshmi-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastNagalakshmi_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastNagalakshmi_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastnagalakshmi/bioconductor-yeastnagalakshmi_1.38.0_src_all.tar.gz"], "md5": "ea5068bf2b4053452f416c56ab32736a", "fn": "yeastNagalakshmi_1.38.0.tar.gz"}, "yeastrnaseq-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastRNASeq_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastRNASeq_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastrnaseq/bioconductor-yeastrnaseq_0.40.0_src_all.tar.gz"], "md5": "2344deacf993b96e1709ad96b710471f", "fn": "yeastRNASeq_0.40.0.tar.gz"}, "zebrafishrnaseq-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/zebrafishRNASeq_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafishRNASeq_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafishrnaseq/bioconductor-zebrafishrnaseq_1.22.0_src_all.tar.gz"], "md5": "c1fcbadec1b25e4b28483c015f7ab35c", "fn": "zebrafishRNASeq_1.22.0.tar.gz"}} \ No newline at end of file +{"ritandata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.15/data/experiment/src/contrib/RITANdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/RITANdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ritandata/bioconductor-ritandata_1.20.0_src_all.tar.gz"], "md5": "4a9a65c5312893ef3bf279efd32d53f8", "fn": "RITANdata_1.20.0.tar.gz"}, "bioplex-1.3.4": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BioPlex_1.3.4.tar.gz", "https://bioarchive.galaxyproject.org/BioPlex_1.3.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bioplex/bioconductor-bioplex_1.3.4_src_all.tar.gz"], "md5": "1062ae3102262b55efd51cb48fb37d0c", "fn": "BioPlex_1.3.4.tar.gz"}, "adme16cod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/adme16cod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/adme16cod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-adme16cod.db/bioconductor-adme16cod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-adme16cod.db/bioconductor-adme16cod.db_3.4.0_src_all.tar.gz"], "md5": "3902516a40a503302ef732143b2394b9", "fn": "adme16cod.db_3.4.0.tar.gz"}, "ag.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ag.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/ag.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ag.db/bioconductor-ag.db_3.13.0_src_all.tar.gz"], "md5": "925e808d2c9b21a11ed131d483e75ab6", "fn": "ag.db_3.13.0.tar.gz"}, "agcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/agcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/agcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-agcdf/bioconductor-agcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-agcdf/bioconductor-agcdf_2.18.0_src_all.tar.gz"], "md5": "5dd14bc6a6d2729f5e7b170105c78e48", "fn": "agcdf_2.18.0.tar.gz"}, "agprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/agprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/agprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-agprobe/bioconductor-agprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-agprobe/bioconductor-agprobe_2.18.0_src_all.tar.gz"], "md5": "08f7527d4c8a30d8b2f86016a53f075a", "fn": "agprobe_2.18.0.tar.gz"}, "ahcytobands-0.99.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/AHCytoBands_0.99.1.tar.gz", "https://bioarchive.galaxyproject.org/AHCytoBands_0.99.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahcytobands/bioconductor-ahcytobands_0.99.1_src_all.tar.gz"], "md5": "3dd85d02e7ed3fca4c7898b5e395edeb", "fn": "AHCytoBands_0.99.1.tar.gz"}, "ahensdbs-1.1.8": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/AHEnsDbs_1.1.8.tar.gz", "https://bioarchive.galaxyproject.org/AHEnsDbs_1.1.8.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahensdbs/bioconductor-ahensdbs_1.1.8_src_all.tar.gz"], "md5": "f2c8c9338f09f480a46e1155d985d08f", "fn": "AHEnsDbs_1.1.8.tar.gz"}, "ahlrbasedbs-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/AHLRBaseDbs_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/AHLRBaseDbs_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahlrbasedbs/bioconductor-ahlrbasedbs_1.5.0_src_all.tar.gz"], "md5": "b1266d2bab652542d6f7289898c3e781", "fn": "AHLRBaseDbs_1.5.0.tar.gz"}, "ahmeshdbs-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/AHMeSHDbs_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/AHMeSHDbs_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahmeshdbs/bioconductor-ahmeshdbs_1.5.0_src_all.tar.gz"], "md5": "87c396d15191843ec3cdced73bf504f8", "fn": "AHMeSHDbs_1.5.0.tar.gz"}, "ahpathbankdbs-0.99.5": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/AHPathbankDbs_0.99.5.tar.gz", "https://bioarchive.galaxyproject.org/AHPathbankDbs_0.99.5.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahpathbankdbs/bioconductor-ahpathbankdbs_0.99.5_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahpathbankdbs/bioconductor-ahpathbankdbs_0.99.5_src_all.tar.gz"], "md5": "70339eae8c03c47248b612b365bda4ff", "fn": "AHPathbankDbs_0.99.5.tar.gz"}, "ahpubmeddbs-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/AHPubMedDbs_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/AHPubMedDbs_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahpubmeddbs/bioconductor-ahpubmeddbs_1.5.0_src_all.tar.gz"], "md5": "0fa89f6189085931f1245c31ddced2d4", "fn": "AHPubMedDbs_1.5.0.tar.gz"}, "ahwikipathwaysdbs-0.99.4": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/AHWikipathwaysDbs_0.99.4.tar.gz", "https://bioarchive.galaxyproject.org/AHWikipathwaysDbs_0.99.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahwikipathwaysdbs/bioconductor-ahwikipathwaysdbs_0.99.4_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahwikipathwaysdbs/bioconductor-ahwikipathwaysdbs_0.99.4_src_all.tar.gz"], "md5": "ffa90f6d6e8832ae6f4b5bf8b151cd46", "fn": "AHWikipathwaysDbs_0.99.4.tar.gz"}, "alternativesplicingevents.hg19-1.1.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/alternativeSplicingEvents.hg19_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/alternativeSplicingEvents.hg19_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-alternativesplicingevents.hg19/bioconductor-alternativesplicingevents.hg19_1.1.0_src_all.tar.gz"], "md5": "b1acae776c9e9c5d961cf4884cadc58f", "fn": "alternativeSplicingEvents.hg19_1.1.0.tar.gz"}, "alternativesplicingevents.hg38-1.1.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/alternativeSplicingEvents.hg38_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/alternativeSplicingEvents.hg38_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-alternativesplicingevents.hg38/bioconductor-alternativesplicingevents.hg38_1.1.0_src_all.tar.gz"], "md5": "8d49710eebd62fb15a48cab252ff3eca", "fn": "alternativeSplicingEvents.hg38_1.1.0.tar.gz"}, "anopheles.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/anopheles.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/anopheles.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-anopheles.db0/bioconductor-anopheles.db0_3.16.0_src_all.tar.gz"], "md5": "17c685b359943a1ef3b21e78f27dc469", "fn": "anopheles.db0_3.16.0.tar.gz"}, "arabidopsis.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/arabidopsis.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/arabidopsis.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-arabidopsis.db0/bioconductor-arabidopsis.db0_3.16.0_src_all.tar.gz"], "md5": "c72b535bf366b91986fa42ffbb2c6d41", "fn": "arabidopsis.db0_3.16.0.tar.gz"}, "ath1121501.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ath1121501.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/ath1121501.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ath1121501.db/bioconductor-ath1121501.db_3.13.0_src_all.tar.gz"], "md5": "c5d937ca9c6bcbb4385fb37a3b14ad15", "fn": "ath1121501.db_3.13.0.tar.gz"}, "ath1121501cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ath1121501cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ath1121501cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ath1121501cdf/bioconductor-ath1121501cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ath1121501cdf/bioconductor-ath1121501cdf_2.18.0_src_all.tar.gz"], "md5": "8b63798143219b7c1c2666a91a1a2440", "fn": "ath1121501cdf_2.18.0.tar.gz"}, "ath1121501probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ath1121501probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ath1121501probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ath1121501probe/bioconductor-ath1121501probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ath1121501probe/bioconductor-ath1121501probe_2.18.0_src_all.tar.gz"], "md5": "eeeae5e6550bb472ba3419d71bbd7dfb", "fn": "ath1121501probe_2.18.0.tar.gz"}, "barley1cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/barley1cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/barley1cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-barley1cdf/bioconductor-barley1cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-barley1cdf/bioconductor-barley1cdf_2.18.0_src_all.tar.gz"], "md5": "16a2ca83f550518756d9fa3273672157", "fn": "barley1cdf_2.18.0.tar.gz"}, "barley1probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/barley1probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/barley1probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-barley1probe/bioconductor-barley1probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-barley1probe/bioconductor-barley1probe_2.18.0_src_all.tar.gz"], "md5": "80595d8ecf83ba83ea84a722a24ab474", "fn": "barley1probe_2.18.0.tar.gz"}, "bovine.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/bovine.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/bovine.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bovine.db/bioconductor-bovine.db_3.13.0_src_all.tar.gz"], "md5": "dcc1180e8ac11247f9899f140082647e", "fn": "bovine.db_3.13.0.tar.gz"}, "bovine.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/bovine.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/bovine.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bovine.db0/bioconductor-bovine.db0_3.16.0_src_all.tar.gz"], "md5": "edf5e741183f2d47d76649bdbaa7dcf6", "fn": "bovine.db0_3.16.0.tar.gz"}, "bovinecdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/bovinecdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/bovinecdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bovinecdf/bioconductor-bovinecdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bovinecdf/bioconductor-bovinecdf_2.18.0_src_all.tar.gz"], "md5": "e155fc7d5f84ee420d9b250a639af305", "fn": "bovinecdf_2.18.0.tar.gz"}, "bovineprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/bovineprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/bovineprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bovineprobe/bioconductor-bovineprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bovineprobe/bioconductor-bovineprobe_2.18.0_src_all.tar.gz"], "md5": "9f9e25fc8c7a76acf541745b7c09748b", "fn": "bovineprobe_2.18.0.tar.gz"}, "bsgenome.alyrata.jgi.v1-1.0.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Alyrata.JGI.v1_1.0.1.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Alyrata.JGI.v1_1.0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.alyrata.jgi.v1/bioconductor-bsgenome.alyrata.jgi.v1_1.0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.alyrata.jgi.v1/bioconductor-bsgenome.alyrata.jgi.v1_1.0.1_src_all.tar.gz"], "md5": "64878499c633de66ccf4c5abc32c0aeb", "fn": "BSgenome.Alyrata.JGI.v1_1.0.1.tar.gz"}, "bsgenome.amellifera.beebase.assembly4-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Amellifera.BeeBase.assembly4_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Amellifera.BeeBase.assembly4_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.beebase.assembly4/bioconductor-bsgenome.amellifera.beebase.assembly4_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.beebase.assembly4/bioconductor-bsgenome.amellifera.beebase.assembly4_1.4.0_src_all.tar.gz"], "md5": "77495ee5eba48fe52902c9cc4f9ba7cc", "fn": "BSgenome.Amellifera.BeeBase.assembly4_1.4.0.tar.gz"}, "bsgenome.amellifera.ncbi.amelhav3.1-1.5.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Amellifera.NCBI.AmelHAv3.1_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Amellifera.NCBI.AmelHAv3.1_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1_1.5.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1/bioconductor-bsgenome.amellifera.ncbi.amelhav3.1_1.5.0_src_all.tar.gz"], "md5": "b119087dfe54805c90cb6bf901e8237e", "fn": "BSgenome.Amellifera.NCBI.AmelHAv3.1_1.5.0.tar.gz"}, "bsgenome.amellifera.ucsc.apimel2-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Amellifera.UCSC.apiMel2_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Amellifera.UCSC.apiMel2_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.ucsc.apimel2/bioconductor-bsgenome.amellifera.ucsc.apimel2_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.ucsc.apimel2/bioconductor-bsgenome.amellifera.ucsc.apimel2_1.4.0_src_all.tar.gz"], "md5": "436ddf54868906e7d1135369d41a2ffe", "fn": "BSgenome.Amellifera.UCSC.apiMel2_1.4.0.tar.gz"}, "bsgenome.amellifera.ucsc.apimel2.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Amellifera.UCSC.apiMel2.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Amellifera.UCSC.apiMel2.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked_1.3.99_src_all.tar.gz"], "md5": "e7a7ff8cfce8e239b22116855456f23d", "fn": "BSgenome.Amellifera.UCSC.apiMel2.masked_1.3.99.tar.gz"}, "bsgenome.aofficinalis.ncbi.v1-1.0.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Aofficinalis.NCBI.V1_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Aofficinalis.NCBI.V1_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.aofficinalis.ncbi.v1/bioconductor-bsgenome.aofficinalis.ncbi.v1_1.0.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.aofficinalis.ncbi.v1/bioconductor-bsgenome.aofficinalis.ncbi.v1_1.0.0_src_all.tar.gz"], "md5": "3f8fd13e74eee63895a5ef528004b60b", "fn": "BSgenome.Aofficinalis.NCBI.V1_1.0.0.tar.gz"}, "bsgenome.athaliana.tair.04232008-1.3.1000": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Athaliana.TAIR.04232008_1.3.1000.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Athaliana.TAIR.04232008_1.3.1000.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.athaliana.tair.04232008/bioconductor-bsgenome.athaliana.tair.04232008_1.3.1000_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.athaliana.tair.04232008/bioconductor-bsgenome.athaliana.tair.04232008_1.3.1000_src_all.tar.gz"], "md5": "6b8a31a228dbcf4468974f5ec1d98467", "fn": "BSgenome.Athaliana.TAIR.04232008_1.3.1000.tar.gz"}, "bsgenome.athaliana.tair.tair9-1.3.1000": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Athaliana.TAIR.TAIR9_1.3.1000.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Athaliana.TAIR.TAIR9_1.3.1000.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.athaliana.tair.tair9/bioconductor-bsgenome.athaliana.tair.tair9_1.3.1000_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.athaliana.tair.tair9/bioconductor-bsgenome.athaliana.tair.tair9_1.3.1000_src_all.tar.gz"], "md5": "8c6709a5f544616d59f4d39aac5787a7", "fn": "BSgenome.Athaliana.TAIR.TAIR9_1.3.1000.tar.gz"}, "bsgenome.btaurus.ucsc.bostau3-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau3_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau3_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau3/bioconductor-bsgenome.btaurus.ucsc.bostau3_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau3/bioconductor-bsgenome.btaurus.ucsc.bostau3_1.4.0_src_all.tar.gz"], "md5": "fe6c4d5853f91c3db3e716ddbc773580", "fn": "BSgenome.Btaurus.UCSC.bosTau3_1.4.0.tar.gz"}, "bsgenome.btaurus.ucsc.bostau3.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau3.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau3.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked_1.3.99_src_all.tar.gz"], "md5": "50f7da5907cbe0d08183dc7161a8ca56", "fn": "BSgenome.Btaurus.UCSC.bosTau3.masked_1.3.99.tar.gz"}, "bsgenome.btaurus.ucsc.bostau4-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau4_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau4_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau4/bioconductor-bsgenome.btaurus.ucsc.bostau4_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau4/bioconductor-bsgenome.btaurus.ucsc.bostau4_1.4.0_src_all.tar.gz"], "md5": "162cd253c719e347df5748ebb407a191", "fn": "BSgenome.Btaurus.UCSC.bosTau4_1.4.0.tar.gz"}, "bsgenome.btaurus.ucsc.bostau4.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau4.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau4.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked_1.3.99_src_all.tar.gz"], "md5": "7c5294349c7061adfb3948bc5659afeb", "fn": "BSgenome.Btaurus.UCSC.bosTau4.masked_1.3.99.tar.gz"}, "bsgenome.btaurus.ucsc.bostau6-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau6_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau6_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau6/bioconductor-bsgenome.btaurus.ucsc.bostau6_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau6/bioconductor-bsgenome.btaurus.ucsc.bostau6_1.4.0_src_all.tar.gz"], "md5": "b22391e0678fc3743daa4b77ecc55f66", "fn": "BSgenome.Btaurus.UCSC.bosTau6_1.4.0.tar.gz"}, "bsgenome.btaurus.ucsc.bostau6.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau6.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau6.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked_1.3.99_src_all.tar.gz"], "md5": "a176de6b1b91854d47e783b8249dbf58", "fn": "BSgenome.Btaurus.UCSC.bosTau6.masked_1.3.99.tar.gz"}, "bsgenome.btaurus.ucsc.bostau8-1.4.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau8_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau8_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau8/bioconductor-bsgenome.btaurus.ucsc.bostau8_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau8/bioconductor-bsgenome.btaurus.ucsc.bostau8_1.4.2_src_all.tar.gz"], "md5": "61ababa7b2b5360fceeb06f0bf49b208", "fn": "BSgenome.Btaurus.UCSC.bosTau8_1.4.2.tar.gz"}, "bsgenome.btaurus.ucsc.bostau9-1.4.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau9_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau9_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau9/bioconductor-bsgenome.btaurus.ucsc.bostau9_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau9/bioconductor-bsgenome.btaurus.ucsc.bostau9_1.4.2_src_all.tar.gz"], "md5": "9b3343725d85c093999413d91218079d", "fn": "BSgenome.Btaurus.UCSC.bosTau9_1.4.2.tar.gz"}, "bsgenome.btaurus.ucsc.bostau9.masked-1.4.4": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau9.masked_1.4.4.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau9.masked_1.4.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau9.masked/bioconductor-bsgenome.btaurus.ucsc.bostau9.masked_1.4.4_src_all.tar.gz"], "md5": "c96bd95c3b791d712aa5cb8c96f9c937", "fn": "BSgenome.Btaurus.UCSC.bosTau9.masked_1.4.4.tar.gz"}, "bsgenome.carietinum.ncbi.v1-1.0.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Carietinum.NCBI.v1_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Carietinum.NCBI.v1_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.carietinum.ncbi.v1/bioconductor-bsgenome.carietinum.ncbi.v1_1.0.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.carietinum.ncbi.v1/bioconductor-bsgenome.carietinum.ncbi.v1_1.0.0_src_all.tar.gz"], "md5": "eef018ecce6d32852aa18ac39cf377c6", "fn": "BSgenome.Carietinum.NCBI.v1_1.0.0.tar.gz"}, "bsgenome.celegans.ucsc.ce10-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce10/bioconductor-bsgenome.celegans.ucsc.ce10_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce10/bioconductor-bsgenome.celegans.ucsc.ce10_1.4.0_src_all.tar.gz"], "md5": "98a8ca836d6db23e46674552669d7942", "fn": "BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz"}, "bsgenome.celegans.ucsc.ce11-1.4.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce11_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Celegans.UCSC.ce11_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce11/bioconductor-bsgenome.celegans.ucsc.ce11_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce11/bioconductor-bsgenome.celegans.ucsc.ce11_1.4.2_src_all.tar.gz"], "md5": "b80e24149a0c6ed323d0c9a6d112ef52", "fn": "BSgenome.Celegans.UCSC.ce11_1.4.2.tar.gz"}, "bsgenome.celegans.ucsc.ce2-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce2_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Celegans.UCSC.ce2_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce2/bioconductor-bsgenome.celegans.ucsc.ce2_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce2/bioconductor-bsgenome.celegans.ucsc.ce2_1.4.0_src_all.tar.gz"], "md5": "b2bf7eec2b07685cf9dcdf42840db208", "fn": "BSgenome.Celegans.UCSC.ce2_1.4.0.tar.gz"}, "bsgenome.celegans.ucsc.ce6-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce6/bioconductor-bsgenome.celegans.ucsc.ce6_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce6/bioconductor-bsgenome.celegans.ucsc.ce6_1.4.0_src_all.tar.gz"], "md5": "cb86ff861d8f660c2abd8fc1907d84a6", "fn": "BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz"}, "bsgenome.cfamiliaris.ucsc.canfam2-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam2_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Cfamiliaris.UCSC.canFam2_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2_1.4.0_src_all.tar.gz"], "md5": "b98f5289ed5d362cd815db9352598634", "fn": "BSgenome.Cfamiliaris.UCSC.canFam2_1.4.0.tar.gz"}, "bsgenome.cfamiliaris.ucsc.canfam2.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam2.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Cfamiliaris.UCSC.canFam2.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked_1.3.99_src_all.tar.gz"], "md5": "6f921533bb83f83f43b8d227b00a48cb", "fn": "BSgenome.Cfamiliaris.UCSC.canFam2.masked_1.3.99.tar.gz"}, "bsgenome.cfamiliaris.ucsc.canfam3-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam3_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Cfamiliaris.UCSC.canFam3_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3_1.4.0_src_all.tar.gz"], "md5": "efcdc531042be86f99a734cd69c0688c", "fn": "BSgenome.Cfamiliaris.UCSC.canFam3_1.4.0.tar.gz"}, "bsgenome.cfamiliaris.ucsc.canfam3.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam3.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Cfamiliaris.UCSC.canFam3.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked_1.3.99_src_all.tar.gz"], "md5": "8e2246f51fc967dc2ed748cf967a7649", "fn": "BSgenome.Cfamiliaris.UCSC.canFam3.masked_1.3.99.tar.gz"}, "bsgenome.cjacchus.ucsc.caljac3-1.4.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Cjacchus.UCSC.calJac3_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Cjacchus.UCSC.calJac3_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cjacchus.ucsc.caljac3/bioconductor-bsgenome.cjacchus.ucsc.caljac3_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cjacchus.ucsc.caljac3/bioconductor-bsgenome.cjacchus.ucsc.caljac3_1.4.2_src_all.tar.gz"], "md5": "41f927aa0d6ffbdaa6ad93c9135409e6", "fn": "BSgenome.Cjacchus.UCSC.calJac3_1.4.2.tar.gz"}, "bsgenome.cjacchus.ucsc.caljac4-1.5.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Cjacchus.UCSC.calJac4_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Cjacchus.UCSC.calJac4_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cjacchus.ucsc.caljac4/bioconductor-bsgenome.cjacchus.ucsc.caljac4_1.5.0_src_all.tar.gz"], "md5": "b11d16ac2cfa81e04af74e2049e52670", "fn": "BSgenome.Cjacchus.UCSC.calJac4_1.5.0.tar.gz"}, "bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1-1.0.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.CneoformansVarGrubiiKN99.NCBI.ASM221672v1_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.CneoformansVarGrubiiKN99.NCBI.ASM221672v1_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1/bioconductor-bsgenome.cneoformansvargrubiikn99.ncbi.asm221672v1_1.0.0_src_all.tar.gz"], "md5": "ea536a15bd932af794f672d9b204c141", "fn": "BSgenome.CneoformansVarGrubiiKN99.NCBI.ASM221672v1_1.0.0.tar.gz"}, "bsgenome.creinhardtii.jgi.v5.6-1.5.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Creinhardtii.JGI.v5.6_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Creinhardtii.JGI.v5.6_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.creinhardtii.jgi.v5.6/bioconductor-bsgenome.creinhardtii.jgi.v5.6_1.5.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.creinhardtii.jgi.v5.6/bioconductor-bsgenome.creinhardtii.jgi.v5.6_1.5.0_src_all.tar.gz"], "md5": "2bd1be53d19249ac14ad7f39dc00af0e", "fn": "BSgenome.Creinhardtii.JGI.v5.6_1.5.0.tar.gz"}, "bsgenome.dmelanogaster.ucsc.dm2-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm2_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm2_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/bioconductor-bsgenome.dmelanogaster.ucsc.dm2_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/bioconductor-bsgenome.dmelanogaster.ucsc.dm2_1.4.0_src_all.tar.gz"], "md5": "ebc88df5595fc7aad588b8f3f7de4784", "fn": "BSgenome.Dmelanogaster.UCSC.dm2_1.4.0.tar.gz"}, "bsgenome.dmelanogaster.ucsc.dm2.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm2.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm2.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked_1.3.99_src_all.tar.gz"], "md5": "ae7ca3053e97a0d6bd20bc2b9635ecce", "fn": "BSgenome.Dmelanogaster.UCSC.dm2.masked_1.3.99.tar.gz"}, "bsgenome.dmelanogaster.ucsc.dm3-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/bioconductor-bsgenome.dmelanogaster.ucsc.dm3_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/bioconductor-bsgenome.dmelanogaster.ucsc.dm3_1.4.0_src_all.tar.gz"], "md5": "b7ceebf7bfee766596f602f9e808d069", "fn": "BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz"}, "bsgenome.dmelanogaster.ucsc.dm3.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm3.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm3.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked_1.3.99_src_all.tar.gz"], "md5": "592e7ec451d126b2d314ab6c75d86830", "fn": "BSgenome.Dmelanogaster.UCSC.dm3.masked_1.3.99.tar.gz"}, "bsgenome.dmelanogaster.ucsc.dm6-1.4.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm6_1.4.1.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm6_1.4.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/bioconductor-bsgenome.dmelanogaster.ucsc.dm6_1.4.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/bioconductor-bsgenome.dmelanogaster.ucsc.dm6_1.4.1_src_all.tar.gz"], "md5": "f9d6e406b7893a17c08edd4521c2802f", "fn": "BSgenome.Dmelanogaster.UCSC.dm6_1.4.1.tar.gz"}, "bsgenome.drerio.ucsc.danrer10-1.4.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer10_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer10_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer10/bioconductor-bsgenome.drerio.ucsc.danrer10_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer10/bioconductor-bsgenome.drerio.ucsc.danrer10_1.4.2_src_all.tar.gz"], "md5": "b8dbcc8a338a021ed35656b27b3dd4c0", "fn": "BSgenome.Drerio.UCSC.danRer10_1.4.2.tar.gz"}, "bsgenome.drerio.ucsc.danrer11-1.4.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer11_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer11_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer11/bioconductor-bsgenome.drerio.ucsc.danrer11_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer11/bioconductor-bsgenome.drerio.ucsc.danrer11_1.4.2_src_all.tar.gz"], "md5": "cd586da56ca88ccebb85804f992ba204", "fn": "BSgenome.Drerio.UCSC.danRer11_1.4.2.tar.gz"}, "bsgenome.drerio.ucsc.danrer5-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer5_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer5_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer5/bioconductor-bsgenome.drerio.ucsc.danrer5_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer5/bioconductor-bsgenome.drerio.ucsc.danrer5_1.4.0_src_all.tar.gz"], "md5": "b1fee4bcc0d9cebb2bbdec5cb851f00d", "fn": "BSgenome.Drerio.UCSC.danRer5_1.4.0.tar.gz"}, "bsgenome.drerio.ucsc.danrer5.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer5.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer5.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/bioconductor-bsgenome.drerio.ucsc.danrer5.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/bioconductor-bsgenome.drerio.ucsc.danrer5.masked_1.3.99_src_all.tar.gz"], "md5": "8f0623bcbe1743754a56c55599b535f3", "fn": "BSgenome.Drerio.UCSC.danRer5.masked_1.3.99.tar.gz"}, "bsgenome.drerio.ucsc.danrer6-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer6_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer6_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer6/bioconductor-bsgenome.drerio.ucsc.danrer6_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer6/bioconductor-bsgenome.drerio.ucsc.danrer6_1.4.0_src_all.tar.gz"], "md5": "537d37d29d97ae0c31d77decc67b25b0", "fn": "BSgenome.Drerio.UCSC.danRer6_1.4.0.tar.gz"}, "bsgenome.drerio.ucsc.danrer6.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer6.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer6.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/bioconductor-bsgenome.drerio.ucsc.danrer6.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/bioconductor-bsgenome.drerio.ucsc.danrer6.masked_1.3.99_src_all.tar.gz"], "md5": "71c9b05c27b8d2e05735e6494a8f17ba", "fn": "BSgenome.Drerio.UCSC.danRer6.masked_1.3.99.tar.gz"}, "bsgenome.drerio.ucsc.danrer7-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer7/bioconductor-bsgenome.drerio.ucsc.danrer7_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer7/bioconductor-bsgenome.drerio.ucsc.danrer7_1.4.0_src_all.tar.gz"], "md5": "766b407a46f20d69a143eab0809eb10a", "fn": "BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz"}, "bsgenome.drerio.ucsc.danrer7.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer7.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer7.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/bioconductor-bsgenome.drerio.ucsc.danrer7.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/bioconductor-bsgenome.drerio.ucsc.danrer7.masked_1.3.99_src_all.tar.gz"], "md5": "5d68af24477d006ed22e7342ff97ac16", "fn": "BSgenome.Drerio.UCSC.danRer7.masked_1.3.99.tar.gz"}, "bsgenome.dvirilis.ensembl.dvircaf1-1.4.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Dvirilis.Ensembl.dvircaf1_1.4.3.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Dvirilis.Ensembl.dvircaf1_1.4.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1_1.4.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1/bioconductor-bsgenome.dvirilis.ensembl.dvircaf1_1.4.3_src_all.tar.gz"], "md5": "6a6a6dc7b2d68a741c85525045a67890", "fn": "BSgenome.Dvirilis.Ensembl.dvircaf1_1.4.3.tar.gz"}, "bsgenome.ecoli.ncbi.20080805-1.3.1000": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ecoli.ncbi.20080805/bioconductor-bsgenome.ecoli.ncbi.20080805_1.3.1000_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ecoli.ncbi.20080805/bioconductor-bsgenome.ecoli.ncbi.20080805_1.3.1000_src_all.tar.gz"], "md5": "c653e9cbee3faeb6fd5759b7575f234d", "fn": "BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz"}, "bsgenome.gaculeatus.ucsc.gasacu1-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Gaculeatus.UCSC.gasAcu1_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Gaculeatus.UCSC.gasAcu1_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1_1.4.0_src_all.tar.gz"], "md5": "412aa0570d9c556861b7bb9a5bbc2007", "fn": "BSgenome.Gaculeatus.UCSC.gasAcu1_1.4.0.tar.gz"}, "bsgenome.gaculeatus.ucsc.gasacu1.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Gaculeatus.UCSC.gasAcu1.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Gaculeatus.UCSC.gasAcu1.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked_1.3.99_src_all.tar.gz"], "md5": "9d9b9e70f4f4624ee4a2b09a59d44510", "fn": "BSgenome.Gaculeatus.UCSC.gasAcu1.masked_1.3.99.tar.gz"}, "bsgenome.ggallus.ucsc.galgal3-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal3_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal3_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal3/bioconductor-bsgenome.ggallus.ucsc.galgal3_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal3/bioconductor-bsgenome.ggallus.ucsc.galgal3_1.4.0_src_all.tar.gz"], "md5": "a463e5ccfc8c6d2c62a6ade0da65dbc4", "fn": "BSgenome.Ggallus.UCSC.galGal3_1.4.0.tar.gz"}, "bsgenome.ggallus.ucsc.galgal3.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal3.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal3.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked_1.3.99_src_all.tar.gz"], "md5": "b3224e3a2b15de379c068e61cedfefa6", "fn": "BSgenome.Ggallus.UCSC.galGal3.masked_1.3.99.tar.gz"}, "bsgenome.ggallus.ucsc.galgal4-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal4_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal4_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal4/bioconductor-bsgenome.ggallus.ucsc.galgal4_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal4/bioconductor-bsgenome.ggallus.ucsc.galgal4_1.4.0_src_all.tar.gz"], "md5": "c2cb4bfc39db93c060e78d8d12542c11", "fn": "BSgenome.Ggallus.UCSC.galGal4_1.4.0.tar.gz"}, "bsgenome.ggallus.ucsc.galgal4.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal4.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal4.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked_1.3.99_src_all.tar.gz"], "md5": "0166121ebd8d0b6a4d24d67e175cfe81", "fn": "BSgenome.Ggallus.UCSC.galGal4.masked_1.3.99.tar.gz"}, "bsgenome.ggallus.ucsc.galgal5-1.4.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal5_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal5_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal5/bioconductor-bsgenome.ggallus.ucsc.galgal5_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal5/bioconductor-bsgenome.ggallus.ucsc.galgal5_1.4.2_src_all.tar.gz"], "md5": "93b42354404edd848b21ea6781ca135c", "fn": "BSgenome.Ggallus.UCSC.galGal5_1.4.2.tar.gz"}, "bsgenome.ggallus.ucsc.galgal6-1.4.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal6_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal6_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal6/bioconductor-bsgenome.ggallus.ucsc.galgal6_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal6/bioconductor-bsgenome.ggallus.ucsc.galgal6_1.4.2_src_all.tar.gz"], "md5": "25ef08a5430fb337dbf752ca3378ea3e", "fn": "BSgenome.Ggallus.UCSC.galGal6_1.4.2.tar.gz"}, "bsgenome.gmax.ncbi.gmv40-4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Gmax.NCBI.Gmv40_4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Gmax.NCBI.Gmv40_4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.gmax.ncbi.gmv40/bioconductor-bsgenome.gmax.ncbi.gmv40_4.0_src_all.tar.gz"], "md5": "421c045b993b2cfbc2b08c8103835c56", "fn": "BSgenome.Gmax.NCBI.Gmv40_4.0.tar.gz"}, "bsgenome.hsapiens.1000genomes.hs37d5-0.99.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5_0.99.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5_0.99.1_src_all.tar.gz"], "md5": "164e1692d38fefa499c2c8ac5fc22793", "fn": "BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1.tar.gz"}, "bsgenome.hsapiens.ncbi.grch38-1.3.1000": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ncbi.grch38/bioconductor-bsgenome.hsapiens.ncbi.grch38_1.3.1000_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ncbi.grch38/bioconductor-bsgenome.hsapiens.ncbi.grch38_1.3.1000_src_all.tar.gz"], "md5": "733d324b34d34d7da8c4bf38459f4fae", "fn": "BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000.tar.gz"}, "bsgenome.hsapiens.ncbi.t2t.chm13v2.0-1.5.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0/bioconductor-bsgenome.hsapiens.ncbi.t2t.chm13v2.0_1.5.0_src_all.tar.gz"], "md5": "22a99174e1e17718e0b4f8b66f32fd9b", "fn": "BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0_1.5.0.tar.gz"}, "bsgenome.hsapiens.ucsc.hg17-1.3.1000": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg17_1.3.1000.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg17_1.3.1000.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg17/bioconductor-bsgenome.hsapiens.ucsc.hg17_1.3.1000_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg17/bioconductor-bsgenome.hsapiens.ucsc.hg17_1.3.1000_src_all.tar.gz"], "md5": "cbea3029c3d3125a88e6c061c3d3abde", "fn": "BSgenome.Hsapiens.UCSC.hg17_1.3.1000.tar.gz"}, "bsgenome.hsapiens.ucsc.hg17.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg17.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg17.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked_1.3.99_src_all.tar.gz"], "md5": "ff6ee5196f234c5a2a3bcdd052c3c08e", "fn": "BSgenome.Hsapiens.UCSC.hg17.masked_1.3.99.tar.gz"}, "bsgenome.hsapiens.ucsc.hg18-1.3.1000": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg18_1.3.1000.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg18_1.3.1000.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg18/bioconductor-bsgenome.hsapiens.ucsc.hg18_1.3.1000_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg18/bioconductor-bsgenome.hsapiens.ucsc.hg18_1.3.1000_src_all.tar.gz"], "md5": "51bb2e1ed4009860bb21aaac32fffd9c", "fn": "BSgenome.Hsapiens.UCSC.hg18_1.3.1000.tar.gz"}, "bsgenome.hsapiens.ucsc.hg18.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg18.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg18.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked_1.3.99_src_all.tar.gz"], "md5": "e6a31e3cba34ce5e0eb6f76d2c19870c", "fn": "BSgenome.Hsapiens.UCSC.hg18.masked_1.3.99.tar.gz"}, "bsgenome.hsapiens.ucsc.hg19-1.4.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg19/bioconductor-bsgenome.hsapiens.ucsc.hg19_1.4.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg19/bioconductor-bsgenome.hsapiens.ucsc.hg19_1.4.3_src_all.tar.gz"], "md5": "bb3f864ab32450d895816b45f6105f4f", "fn": "BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz"}, "bsgenome.hsapiens.ucsc.hg19.masked-1.3.993": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19.masked_1.3.993.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg19.masked_1.3.993.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked_1.3.993_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked_1.3.993_src_all.tar.gz"], "md5": "4424e1bda9cc005d75f5f05ba4a50c77", "fn": "BSgenome.Hsapiens.UCSC.hg19.masked_1.3.993.tar.gz"}, "bsgenome.hsapiens.ucsc.hg38-1.4.4": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.4.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg38_1.4.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38/bioconductor-bsgenome.hsapiens.ucsc.hg38_1.4.4_src_all.tar.gz"], "md5": "360474907caa1c1ed31030f68f80f0a5", "fn": "BSgenome.Hsapiens.UCSC.hg38_1.4.4.tar.gz"}, "bsgenome.hsapiens.ucsc.hg38.dbsnp151.major-0.0.9999": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major_0.0.9999.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major_0.0.9999.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.major_0.0.9999_src_all.tar.gz"], "md5": "c59f66e52d4982942bea2254223d58df", "fn": "BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major_0.0.9999.tar.gz"}, "bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor-0.0.9999": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor_0.0.9999.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor_0.0.9999.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor/bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor_0.0.9999_src_all.tar.gz"], "md5": "2cc3a612a2064624735d6a92910be7f3", "fn": "BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor_0.0.9999.tar.gz"}, "bsgenome.hsapiens.ucsc.hg38.masked-1.4.4": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38.masked_1.4.4.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg38.masked_1.4.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked_1.4.4_src_all.tar.gz"], "md5": "95b4e782a3e5970b929ff957befc2659", "fn": "BSgenome.Hsapiens.UCSC.hg38.masked_1.4.4.tar.gz"}, "bsgenome.mdomestica.ucsc.mondom5-1.4.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Mdomestica.UCSC.monDom5_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mdomestica.UCSC.monDom5_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mdomestica.ucsc.mondom5/bioconductor-bsgenome.mdomestica.ucsc.mondom5_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mdomestica.ucsc.mondom5/bioconductor-bsgenome.mdomestica.ucsc.mondom5_1.4.2_src_all.tar.gz"], "md5": "ff940f7446a275962f69a6f4cb84724c", "fn": "BSgenome.Mdomestica.UCSC.monDom5_1.4.2.tar.gz"}, "bsgenome.mfascicularis.ncbi.5.0-1.4.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Mfascicularis.NCBI.5.0_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mfascicularis.NCBI.5.0_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mfascicularis.ncbi.5.0/bioconductor-bsgenome.mfascicularis.ncbi.5.0_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mfascicularis.ncbi.5.0/bioconductor-bsgenome.mfascicularis.ncbi.5.0_1.4.2_src_all.tar.gz"], "md5": "dba6ade39dc6b4f6d06f488141b5550b", "fn": "BSgenome.Mfascicularis.NCBI.5.0_1.4.2.tar.gz"}, "bsgenome.mfascicularis.ncbi.6.0-1.5.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Mfascicularis.NCBI.6.0_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mfascicularis.NCBI.6.0_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mfascicularis.ncbi.6.0/bioconductor-bsgenome.mfascicularis.ncbi.6.0_1.5.0_src_all.tar.gz"], "md5": "67272a96950f485d3c0770265f59c85c", "fn": "BSgenome.Mfascicularis.NCBI.6.0_1.5.0.tar.gz"}, "bsgenome.mfuro.ucsc.musfur1-1.4.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Mfuro.UCSC.musFur1_1.4.1.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mfuro.UCSC.musFur1_1.4.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mfuro.ucsc.musfur1/bioconductor-bsgenome.mfuro.ucsc.musfur1_1.4.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mfuro.ucsc.musfur1/bioconductor-bsgenome.mfuro.ucsc.musfur1_1.4.1_src_all.tar.gz"], "md5": "c33e71746ce551bcbcd22be1979aee63", "fn": "BSgenome.Mfuro.UCSC.musFur1_1.4.1.tar.gz"}, "bsgenome.mmulatta.ucsc.rhemac10-1.4.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac10_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac10_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac10/bioconductor-bsgenome.mmulatta.ucsc.rhemac10_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac10/bioconductor-bsgenome.mmulatta.ucsc.rhemac10_1.4.2_src_all.tar.gz"], "md5": "2f2afe40d5dcf8d8620aa5e12e311fbc", "fn": "BSgenome.Mmulatta.UCSC.rheMac10_1.4.2.tar.gz"}, "bsgenome.mmulatta.ucsc.rhemac2-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac2_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac2_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/bioconductor-bsgenome.mmulatta.ucsc.rhemac2_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/bioconductor-bsgenome.mmulatta.ucsc.rhemac2_1.4.0_src_all.tar.gz"], "md5": "90c43e127e76dfd7cea90de9e1af9a50", "fn": "BSgenome.Mmulatta.UCSC.rheMac2_1.4.0.tar.gz"}, "bsgenome.mmulatta.ucsc.rhemac2.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac2.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac2.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked_1.3.99_src_all.tar.gz"], "md5": "7602d86b68df7e4c8d336fede4090a62", "fn": "BSgenome.Mmulatta.UCSC.rheMac2.masked_1.3.99.tar.gz"}, "bsgenome.mmulatta.ucsc.rhemac3-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac3_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac3_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/bioconductor-bsgenome.mmulatta.ucsc.rhemac3_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/bioconductor-bsgenome.mmulatta.ucsc.rhemac3_1.4.0_src_all.tar.gz"], "md5": "dfa1ecb9d0bb7a5d9fa628092fb1c354", "fn": "BSgenome.Mmulatta.UCSC.rheMac3_1.4.0.tar.gz"}, "bsgenome.mmulatta.ucsc.rhemac3.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac3.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac3.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked_1.3.99_src_all.tar.gz"], "md5": "94f8714865655d3144e14f6fc5c24e76", "fn": "BSgenome.Mmulatta.UCSC.rheMac3.masked_1.3.99.tar.gz"}, "bsgenome.mmulatta.ucsc.rhemac8-1.4.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac8_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac8_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/bioconductor-bsgenome.mmulatta.ucsc.rhemac8_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/bioconductor-bsgenome.mmulatta.ucsc.rhemac8_1.4.2_src_all.tar.gz"], "md5": "e9ad1f70f652c62554e2c5af7638c015", "fn": "BSgenome.Mmulatta.UCSC.rheMac8_1.4.2.tar.gz"}, "bsgenome.mmusculus.ucsc.mm10-1.4.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm10_1.4.3.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm10_1.4.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm10/bioconductor-bsgenome.mmusculus.ucsc.mm10_1.4.3_src_all.tar.gz"], "md5": "ffddc2e035527ed1a1e201ac4cc0b1f3", "fn": "BSgenome.Mmusculus.UCSC.mm10_1.4.3.tar.gz"}, "bsgenome.mmusculus.ucsc.mm10.masked-1.4.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm10.masked_1.4.3.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm10.masked_1.4.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked_1.4.3_src_all.tar.gz"], "md5": "40d51fb428a5fda8c05101a3dddb8957", "fn": "BSgenome.Mmusculus.UCSC.mm10.masked_1.4.3.tar.gz"}, "bsgenome.mmusculus.ucsc.mm39-1.4.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm39_1.4.3.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm39_1.4.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm39/bioconductor-bsgenome.mmusculus.ucsc.mm39_1.4.3_src_all.tar.gz"], "md5": "a130ef50dd55da9fd341e6c90b22637b", "fn": "BSgenome.Mmusculus.UCSC.mm39_1.4.3.tar.gz"}, "bsgenome.mmusculus.ucsc.mm8-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm8_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm8_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm8/bioconductor-bsgenome.mmusculus.ucsc.mm8_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm8/bioconductor-bsgenome.mmusculus.ucsc.mm8_1.4.0_src_all.tar.gz"], "md5": "f6aa91cdce2607f30a34f6dd0d678aff", "fn": "BSgenome.Mmusculus.UCSC.mm8_1.4.0.tar.gz"}, "bsgenome.mmusculus.ucsc.mm8.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm8.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm8.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked_1.3.99_src_all.tar.gz"], "md5": "5809f925e0fe7c4b73b78a90c9a36fdd", "fn": "BSgenome.Mmusculus.UCSC.mm8.masked_1.3.99.tar.gz"}, "bsgenome.mmusculus.ucsc.mm9-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm9/bioconductor-bsgenome.mmusculus.ucsc.mm9_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm9/bioconductor-bsgenome.mmusculus.ucsc.mm9_1.4.0_src_all.tar.gz"], "md5": "5a30ba2b4481a17e8e6979eb69eabf78", "fn": "BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz"}, "bsgenome.mmusculus.ucsc.mm9.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm9.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm9.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked_1.3.99_src_all.tar.gz"], "md5": "a5dadab14e55cdfc39649ede7a8483d5", "fn": "BSgenome.Mmusculus.UCSC.mm9.masked_1.3.99.tar.gz"}, "bsgenome.osativa.msu.msu7-0.99.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Osativa.MSU.MSU7_0.99.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Osativa.MSU.MSU7_0.99.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.osativa.msu.msu7/bioconductor-bsgenome.osativa.msu.msu7_0.99.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.osativa.msu.msu7/bioconductor-bsgenome.osativa.msu.msu7_0.99.2_src_all.tar.gz"], "md5": "80648058756a2f74aa5a246d38ecf576", "fn": "BSgenome.Osativa.MSU.MSU7_0.99.2.tar.gz"}, "bsgenome.ppaniscus.ucsc.panpan1-1.4.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Ppaniscus.UCSC.panPan1_1.4.3.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ppaniscus.UCSC.panPan1_1.4.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ppaniscus.ucsc.panpan1/bioconductor-bsgenome.ppaniscus.ucsc.panpan1_1.4.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ppaniscus.ucsc.panpan1/bioconductor-bsgenome.ppaniscus.ucsc.panpan1_1.4.3_src_all.tar.gz"], "md5": "186adb59264d468d17c0f6374e2eb1f6", "fn": "BSgenome.Ppaniscus.UCSC.panPan1_1.4.3.tar.gz"}, "bsgenome.ppaniscus.ucsc.panpan2-1.4.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Ppaniscus.UCSC.panPan2_1.4.3.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ppaniscus.UCSC.panPan2_1.4.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ppaniscus.ucsc.panpan2/bioconductor-bsgenome.ppaniscus.ucsc.panpan2_1.4.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ppaniscus.ucsc.panpan2/bioconductor-bsgenome.ppaniscus.ucsc.panpan2_1.4.3_src_all.tar.gz"], "md5": "74973376a6377d6820d6cd7fb3655a19", "fn": "BSgenome.Ppaniscus.UCSC.panPan2_1.4.3.tar.gz"}, "bsgenome.ptroglodytes.ucsc.pantro2-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro2_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro2_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2_1.4.0_src_all.tar.gz"], "md5": "780200c315779ac75fcf0bdeb9a2eb8c", "fn": "BSgenome.Ptroglodytes.UCSC.panTro2_1.4.0.tar.gz"}, "bsgenome.ptroglodytes.ucsc.pantro2.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro2.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro2.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked_1.3.99_src_all.tar.gz"], "md5": "e6d069be23712b483b4e4c71554594cf", "fn": "BSgenome.Ptroglodytes.UCSC.panTro2.masked_1.3.99.tar.gz"}, "bsgenome.ptroglodytes.ucsc.pantro3-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro3_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro3_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3_1.4.0_src_all.tar.gz"], "md5": "4677c75befd60742f3fc2a54c7f60666", "fn": "BSgenome.Ptroglodytes.UCSC.panTro3_1.4.0.tar.gz"}, "bsgenome.ptroglodytes.ucsc.pantro3.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro3.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro3.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked_1.3.99_src_all.tar.gz"], "md5": "89e96b3796d3b8e8793146597506e3f5", "fn": "BSgenome.Ptroglodytes.UCSC.panTro3.masked_1.3.99.tar.gz"}, "bsgenome.ptroglodytes.ucsc.pantro5-1.4.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro5_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro5_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5_1.4.2_src_all.tar.gz"], "md5": "5b88573dd9c3ef838699b65934f8abe3", "fn": "BSgenome.Ptroglodytes.UCSC.panTro5_1.4.2.tar.gz"}, "bsgenome.ptroglodytes.ucsc.pantro6-1.4.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro6_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro6_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6_1.4.2_src_all.tar.gz"], "md5": "1df05d985374e9edc1dd7c3df5118338", "fn": "BSgenome.Ptroglodytes.UCSC.panTro6_1.4.2.tar.gz"}, "bsgenome.rnorvegicus.ucsc.rn4-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn4_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn4_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/bioconductor-bsgenome.rnorvegicus.ucsc.rn4_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/bioconductor-bsgenome.rnorvegicus.ucsc.rn4_1.4.0_src_all.tar.gz"], "md5": "3afe6729237781445d99ec38228ee1a8", "fn": "BSgenome.Rnorvegicus.UCSC.rn4_1.4.0.tar.gz"}, "bsgenome.rnorvegicus.ucsc.rn4.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn4.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn4.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked_1.3.99_src_all.tar.gz"], "md5": "7e2ea7df588b6b10515e07ea3868c568", "fn": "BSgenome.Rnorvegicus.UCSC.rn4.masked_1.3.99.tar.gz"}, "bsgenome.rnorvegicus.ucsc.rn5-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn5_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn5_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/bioconductor-bsgenome.rnorvegicus.ucsc.rn5_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/bioconductor-bsgenome.rnorvegicus.ucsc.rn5_1.4.0_src_all.tar.gz"], "md5": "723b1f3ced395ef638b2d68053b05c86", "fn": "BSgenome.Rnorvegicus.UCSC.rn5_1.4.0.tar.gz"}, "bsgenome.rnorvegicus.ucsc.rn5.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn5.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn5.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked_1.3.99_src_all.tar.gz"], "md5": "663233774b79012cb2cc08224ac275ed", "fn": "BSgenome.Rnorvegicus.UCSC.rn5.masked_1.3.99.tar.gz"}, "bsgenome.rnorvegicus.ucsc.rn6-1.4.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn6_1.4.1.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn6_1.4.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/bioconductor-bsgenome.rnorvegicus.ucsc.rn6_1.4.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/bioconductor-bsgenome.rnorvegicus.ucsc.rn6_1.4.1_src_all.tar.gz"], "md5": "60d3fb201e0b1475912aaf681927096d", "fn": "BSgenome.Rnorvegicus.UCSC.rn6_1.4.1.tar.gz"}, "bsgenome.rnorvegicus.ucsc.rn7-1.4.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn7_1.4.3.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn7_1.4.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn7/bioconductor-bsgenome.rnorvegicus.ucsc.rn7_1.4.3_src_all.tar.gz"], "md5": "c64f7dd9e30ff88ce02ecd3712e4c454", "fn": "BSgenome.Rnorvegicus.UCSC.rn7_1.4.3.tar.gz"}, "bsgenome.scerevisiae.ucsc.saccer1-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer1_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Scerevisiae.UCSC.sacCer1_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/bioconductor-bsgenome.scerevisiae.ucsc.saccer1_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/bioconductor-bsgenome.scerevisiae.ucsc.saccer1_1.4.0_src_all.tar.gz"], "md5": "ad4c29c16a9635088bf13872b4a02ed4", "fn": "BSgenome.Scerevisiae.UCSC.sacCer1_1.4.0.tar.gz"}, "bsgenome.scerevisiae.ucsc.saccer2-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer2_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Scerevisiae.UCSC.sacCer2_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/bioconductor-bsgenome.scerevisiae.ucsc.saccer2_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/bioconductor-bsgenome.scerevisiae.ucsc.saccer2_1.4.0_src_all.tar.gz"], "md5": "f1025b4d0fa7891dc46301550163753e", "fn": "BSgenome.Scerevisiae.UCSC.sacCer2_1.4.0.tar.gz"}, "bsgenome.scerevisiae.ucsc.saccer3-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer3_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Scerevisiae.UCSC.sacCer3_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/bioconductor-bsgenome.scerevisiae.ucsc.saccer3_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/bioconductor-bsgenome.scerevisiae.ucsc.saccer3_1.4.0_src_all.tar.gz"], "md5": "7f2d8bba69c3dcebf426d9b19a6bed30", "fn": "BSgenome.Scerevisiae.UCSC.sacCer3_1.4.0.tar.gz"}, "bsgenome.sscrofa.ucsc.susscr11-1.4.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Sscrofa.UCSC.susScr11_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Sscrofa.UCSC.susScr11_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr11/bioconductor-bsgenome.sscrofa.ucsc.susscr11_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr11/bioconductor-bsgenome.sscrofa.ucsc.susscr11_1.4.2_src_all.tar.gz"], "md5": "db22832229e31e1a629d107df522dff9", "fn": "BSgenome.Sscrofa.UCSC.susScr11_1.4.2.tar.gz"}, "bsgenome.sscrofa.ucsc.susscr3-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Sscrofa.UCSC.susScr3_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Sscrofa.UCSC.susScr3_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr3/bioconductor-bsgenome.sscrofa.ucsc.susscr3_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr3/bioconductor-bsgenome.sscrofa.ucsc.susscr3_1.4.0_src_all.tar.gz"], "md5": "0457ca52a81c9d7ceadad5830169e6cf", "fn": "BSgenome.Sscrofa.UCSC.susScr3_1.4.0.tar.gz"}, "bsgenome.sscrofa.ucsc.susscr3.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Sscrofa.UCSC.susScr3.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Sscrofa.UCSC.susScr3.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked_1.3.99_src_all.tar.gz"], "md5": "fd240651d22d169fd1e27a2b66e40dd7", "fn": "BSgenome.Sscrofa.UCSC.susScr3.masked_1.3.99.tar.gz"}, "bsgenome.tgondii.toxodb.7.0-0.99.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Tgondii.ToxoDB.7.0_0.99.1.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Tgondii.ToxoDB.7.0_0.99.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tgondii.toxodb.7.0/bioconductor-bsgenome.tgondii.toxodb.7.0_0.99.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tgondii.toxodb.7.0/bioconductor-bsgenome.tgondii.toxodb.7.0_0.99.1_src_all.tar.gz"], "md5": "f67644d1a897fe2ff4139832d4ceaf80", "fn": "BSgenome.Tgondii.ToxoDB.7.0_0.99.1.tar.gz"}, "bsgenome.tguttata.ucsc.taegut1-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Tguttata.UCSC.taeGut1_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Tguttata.UCSC.taeGut1_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut1/bioconductor-bsgenome.tguttata.ucsc.taegut1_1.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut1/bioconductor-bsgenome.tguttata.ucsc.taegut1_1.4.0_src_all.tar.gz"], "md5": "9753d9568d2a866a627673a518a1dd8a", "fn": "BSgenome.Tguttata.UCSC.taeGut1_1.4.0.tar.gz"}, "bsgenome.tguttata.ucsc.taegut1.masked-1.3.99": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Tguttata.UCSC.taeGut1.masked_1.3.99.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Tguttata.UCSC.taeGut1.masked_1.3.99.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked_1.3.99_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked_1.3.99_src_all.tar.gz"], "md5": "63684abb5b330bb54ff89fe78f2e6444", "fn": "BSgenome.Tguttata.UCSC.taeGut1.masked_1.3.99.tar.gz"}, "bsgenome.tguttata.ucsc.taegut2-1.4.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Tguttata.UCSC.taeGut2_1.4.2.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Tguttata.UCSC.taeGut2_1.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut2/bioconductor-bsgenome.tguttata.ucsc.taegut2_1.4.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut2/bioconductor-bsgenome.tguttata.ucsc.taegut2_1.4.2_src_all.tar.gz"], "md5": "1d39678fb060e643f7e9c4ec25e828c0", "fn": "BSgenome.Tguttata.UCSC.taeGut2_1.4.2.tar.gz"}, "bsgenome.vvinifera.urgi.iggp12xv0-0.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Vvinifera.URGI.IGGP12Xv0_0.1.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Vvinifera.URGI.IGGP12Xv0_0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0_0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0_0.1_src_all.tar.gz"], "md5": "3f791de6d699325a97080cd98be86d89", "fn": "BSgenome.Vvinifera.URGI.IGGP12Xv0_0.1.tar.gz"}, "bsgenome.vvinifera.urgi.iggp12xv2-0.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Vvinifera.URGI.IGGP12Xv2_0.1.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Vvinifera.URGI.IGGP12Xv2_0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2_0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2_0.1_src_all.tar.gz"], "md5": "95472e574ab46327c19e241c381b26a2", "fn": "BSgenome.Vvinifera.URGI.IGGP12Xv2_0.1.tar.gz"}, "bsgenome.vvinifera.urgi.iggp8x-0.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Vvinifera.URGI.IGGP8X_0.1.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Vvinifera.URGI.IGGP8X_0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp8x/bioconductor-bsgenome.vvinifera.urgi.iggp8x_0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp8x/bioconductor-bsgenome.vvinifera.urgi.iggp8x_0.1_src_all.tar.gz"], "md5": "fccaf60e5c9352b9c454f7a8ecac2a20", "fn": "BSgenome.Vvinifera.URGI.IGGP8X_0.1.tar.gz"}, "bsubtiliscdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/bsubtiliscdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/bsubtiliscdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsubtiliscdf/bioconductor-bsubtiliscdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsubtiliscdf/bioconductor-bsubtiliscdf_2.18.0_src_all.tar.gz"], "md5": "7d7893d28c601206805819ae0e49b31b", "fn": "bsubtiliscdf_2.18.0.tar.gz"}, "bsubtilisprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/bsubtilisprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/bsubtilisprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsubtilisprobe/bioconductor-bsubtilisprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsubtilisprobe/bioconductor-bsubtilisprobe_2.18.0_src_all.tar.gz"], "md5": "83568fcea2122350b7ce982e79b7ec53", "fn": "bsubtilisprobe_2.18.0.tar.gz"}, "canine.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/canine.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/canine.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canine.db/bioconductor-canine.db_3.13.0_src_all.tar.gz"], "md5": "a876bb01eda62604a32a96b46e34162b", "fn": "canine.db_3.13.0.tar.gz"}, "canine.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/canine.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/canine.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canine.db0/bioconductor-canine.db0_3.16.0_src_all.tar.gz"], "md5": "99dd5f98cd9934998d081429f2b7cd36", "fn": "canine.db0_3.16.0.tar.gz"}, "canine2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/canine2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/canine2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canine2.db/bioconductor-canine2.db_3.13.0_src_all.tar.gz"], "md5": "24727f27cdf1e324f097a76db81dfc1d", "fn": "canine2.db_3.13.0.tar.gz"}, "canine2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/canine2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/canine2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canine2cdf/bioconductor-canine2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canine2cdf/bioconductor-canine2cdf_2.18.0_src_all.tar.gz"], "md5": "78740cde98c75e6680470564a4df74c3", "fn": "canine2cdf_2.18.0.tar.gz"}, "canine2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/canine2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/canine2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canine2probe/bioconductor-canine2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canine2probe/bioconductor-canine2probe_2.18.0_src_all.tar.gz"], "md5": "7de0f4ea616e8662dc2eaa9ab78d1f13", "fn": "canine2probe_2.18.0.tar.gz"}, "caninecdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/caninecdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/caninecdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-caninecdf/bioconductor-caninecdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-caninecdf/bioconductor-caninecdf_2.18.0_src_all.tar.gz"], "md5": "656f845cc66890015a4e13c5304ec262", "fn": "caninecdf_2.18.0.tar.gz"}, "canineprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/canineprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/canineprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canineprobe/bioconductor-canineprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canineprobe/bioconductor-canineprobe_2.18.0_src_all.tar.gz"], "md5": "e5467bc9b7e54c5adce6b409ba7df767", "fn": "canineprobe_2.18.0.tar.gz"}, "celegans.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/celegans.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/celegans.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celegans.db/bioconductor-celegans.db_3.13.0_src_all.tar.gz"], "md5": "3cfa9df5a81ef538a890ed8c5d5a98ad", "fn": "celegans.db_3.13.0.tar.gz"}, "celeganscdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/celeganscdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/celeganscdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celeganscdf/bioconductor-celeganscdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celeganscdf/bioconductor-celeganscdf_2.18.0_src_all.tar.gz"], "md5": "1098cd99bfc5000bf9858e4a3acaf452", "fn": "celeganscdf_2.18.0.tar.gz"}, "celegansprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/celegansprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/celegansprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celegansprobe/bioconductor-celegansprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celegansprobe/bioconductor-celegansprobe_2.18.0_src_all.tar.gz"], "md5": "7454bba10ff2dd7c03bfe0f9d450f148", "fn": "celegansprobe_2.18.0.tar.gz"}, "chemminedrugs-1.0.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ChemmineDrugs_1.0.2.tar.gz", "https://bioarchive.galaxyproject.org/ChemmineDrugs_1.0.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chemminedrugs/bioconductor-chemminedrugs_1.0.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chemminedrugs/bioconductor-chemminedrugs_1.0.2_src_all.tar.gz"], "md5": "2a3646e5173e93080fb5b49564f5d545", "fn": "ChemmineDrugs_1.0.2.tar.gz"}, "chicken.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/chicken.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/chicken.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chicken.db/bioconductor-chicken.db_3.13.0_src_all.tar.gz"], "md5": "512f887df339529d4883aad3f3eb6fb8", "fn": "chicken.db_3.13.0.tar.gz"}, "chicken.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/chicken.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/chicken.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chicken.db0/bioconductor-chicken.db0_3.16.0_src_all.tar.gz"], "md5": "63bc178c74709f98b0ba049f9a04b64c", "fn": "chicken.db0_3.16.0.tar.gz"}, "chickencdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/chickencdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/chickencdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chickencdf/bioconductor-chickencdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chickencdf/bioconductor-chickencdf_2.18.0_src_all.tar.gz"], "md5": "ab0097b4b7b6c4d94360feb84ab69972", "fn": "chickencdf_2.18.0.tar.gz"}, "chickenprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/chickenprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/chickenprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chickenprobe/bioconductor-chickenprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chickenprobe/bioconductor-chickenprobe_2.18.0_src_all.tar.gz"], "md5": "b33599081ce1ba768ff7992e143c01d0", "fn": "chickenprobe_2.18.0.tar.gz"}, "chimp.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/chimp.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/chimp.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chimp.db0/bioconductor-chimp.db0_3.16.0_src_all.tar.gz"], "md5": "6a221371b811f791fe332a194b47cfac", "fn": "chimp.db0_3.16.0.tar.gz"}, "chromhmmdata-0.99.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/chromhmmData_0.99.2.tar.gz", "https://bioarchive.galaxyproject.org/chromhmmData_0.99.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chromhmmdata/bioconductor-chromhmmdata_0.99.2_src_all.tar.gz"], "md5": "eec85c20139b3d826f00264c7b28207c", "fn": "chromhmmData_0.99.2.tar.gz"}, "citruscdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/citruscdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/citruscdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-citruscdf/bioconductor-citruscdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-citruscdf/bioconductor-citruscdf_2.18.0_src_all.tar.gz"], "md5": "4af821a0c1ae1adf42b7dc5ce7458593", "fn": "citruscdf_2.18.0.tar.gz"}, "citrusprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/citrusprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/citrusprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-citrusprobe/bioconductor-citrusprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-citrusprobe/bioconductor-citrusprobe_2.18.0_src_all.tar.gz"], "md5": "259b114f96d5307c447d000bd27a7d15", "fn": "citrusprobe_2.18.0.tar.gz"}, "clariomdhumanprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/clariomdhumanprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/clariomdhumanprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clariomdhumanprobeset.db/bioconductor-clariomdhumanprobeset.db_8.8.0_src_all.tar.gz"], "md5": "01cb1a5cc4674750b6ce5988cd62fad3", "fn": "clariomdhumanprobeset.db_8.8.0.tar.gz"}, "clariomdhumantranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/clariomdhumantranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/clariomdhumantranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clariomdhumantranscriptcluster.db/bioconductor-clariomdhumantranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "80739a70d77ab785231a9367938035a8", "fn": "clariomdhumantranscriptcluster.db_8.8.0.tar.gz"}, "clariomshumanhttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/clariomshumanhttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/clariomshumanhttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clariomshumanhttranscriptcluster.db/bioconductor-clariomshumanhttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "6a5e8e1f9768694be99277aafcc0a69a", "fn": "clariomshumanhttranscriptcluster.db_8.8.0.tar.gz"}, "clariomshumantranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/clariomshumantranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/clariomshumantranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clariomshumantranscriptcluster.db/bioconductor-clariomshumantranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "309b29e044e1227da6d4825bbdf04b76", "fn": "clariomshumantranscriptcluster.db_8.8.0.tar.gz"}, "clariomsmousehttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/clariomsmousehttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/clariomsmousehttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clariomsmousehttranscriptcluster.db/bioconductor-clariomsmousehttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "c0aa96cbd5ee7e19296dde5a72232d17", "fn": "clariomsmousehttranscriptcluster.db_8.8.0.tar.gz"}, "clariomsmousetranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/clariomsmousetranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/clariomsmousetranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clariomsmousetranscriptcluster.db/bioconductor-clariomsmousetranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "76d0e2204dcbd5d85d8e53d43710aac5", "fn": "clariomsmousetranscriptcluster.db_8.8.0.tar.gz"}, "clariomsrathttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/clariomsrathttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/clariomsrathttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clariomsrathttranscriptcluster.db/bioconductor-clariomsrathttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "e7c71721f8201bfd1553a98cfbf47458", "fn": "clariomsrathttranscriptcluster.db_8.8.0.tar.gz"}, "clariomsrattranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/clariomsrattranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/clariomsrattranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clariomsrattranscriptcluster.db/bioconductor-clariomsrattranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "72923a3a90f2df27a361b1730cfc0d00", "fn": "clariomsrattranscriptcluster.db_8.8.0.tar.gz"}, "cmap-1.15.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/cMAP_1.15.1.tar.gz", "https://bioarchive.galaxyproject.org/cMAP_1.15.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cmap/bioconductor-cmap_1.15.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cmap/bioconductor-cmap_1.15.1_src_all.tar.gz"], "md5": "dbf8df4d4540151936884e1c5d747bcf", "fn": "cMAP_1.15.1.tar.gz"}, "cottoncdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/cottoncdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/cottoncdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cottoncdf/bioconductor-cottoncdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cottoncdf/bioconductor-cottoncdf_2.18.0_src_all.tar.gz"], "md5": "b9d2a4b43235c6e531b78cca006e84b2", "fn": "cottoncdf_2.18.0.tar.gz"}, "cottonprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/cottonprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/cottonprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cottonprobe/bioconductor-cottonprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cottonprobe/bioconductor-cottonprobe_2.18.0_src_all.tar.gz"], "md5": "032fa94876685820d94526fd56dd0b65", "fn": "cottonprobe_2.18.0.tar.gz"}, "ctcf-0.99.9": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/CTCF_0.99.9.tar.gz", "https://bioarchive.galaxyproject.org/CTCF_0.99.9.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ctcf/bioconductor-ctcf_0.99.9_src_all.tar.gz"], "md5": "c5449543be4c56393d737bbe07c6255c", "fn": "CTCF_0.99.9.tar.gz"}, "cyp450cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/cyp450cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/cyp450cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cyp450cdf/bioconductor-cyp450cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cyp450cdf/bioconductor-cyp450cdf_2.18.0_src_all.tar.gz"], "md5": "7923c4d24b7b654d0f59d52ed2258eb9", "fn": "cyp450cdf_2.18.0.tar.gz"}, "do.db-2.9": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/DO.db_2.9.tar.gz", "https://bioarchive.galaxyproject.org/DO.db_2.9.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-do.db/bioconductor-do.db_2.9_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-do.db/bioconductor-do.db_2.9_src_all.tar.gz"], "md5": "63dda6d46d2fe40c52a2e79260a7fb9d", "fn": "DO.db_2.9.tar.gz"}, "drosgenome1.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/drosgenome1.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/drosgenome1.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosgenome1.db/bioconductor-drosgenome1.db_3.13.0_src_all.tar.gz"], "md5": "6432e2ae22cf58524278a559097bdf3a", "fn": "drosgenome1.db_3.13.0.tar.gz"}, "drosgenome1cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/drosgenome1cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/drosgenome1cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosgenome1cdf/bioconductor-drosgenome1cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosgenome1cdf/bioconductor-drosgenome1cdf_2.18.0_src_all.tar.gz"], "md5": "e12983f2148c10ef1faa50f810b6eee3", "fn": "drosgenome1cdf_2.18.0.tar.gz"}, "drosgenome1probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/drosgenome1probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/drosgenome1probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosgenome1probe/bioconductor-drosgenome1probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosgenome1probe/bioconductor-drosgenome1probe_2.18.0_src_all.tar.gz"], "md5": "1f12abdfeee65e8a6554f57507d86fb3", "fn": "drosgenome1probe_2.18.0.tar.gz"}, "drosophila2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/drosophila2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/drosophila2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosophila2.db/bioconductor-drosophila2.db_3.13.0_src_all.tar.gz"], "md5": "c01d0d1b5e17c3b36ad801b44da72b96", "fn": "drosophila2.db_3.13.0.tar.gz"}, "drosophila2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/drosophila2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/drosophila2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosophila2cdf/bioconductor-drosophila2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosophila2cdf/bioconductor-drosophila2cdf_2.18.0_src_all.tar.gz"], "md5": "3323e723c133ff2b6188e22bebf3e20a", "fn": "drosophila2cdf_2.18.0.tar.gz"}, "drosophila2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/drosophila2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/drosophila2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosophila2probe/bioconductor-drosophila2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drosophila2probe/bioconductor-drosophila2probe_2.18.0_src_all.tar.gz"], "md5": "ba0251902ea0a5f0db61105bdcdc3530", "fn": "drosophila2probe_2.18.0.tar.gz"}, "ecoli2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ecoli2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoli2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoli2.db/bioconductor-ecoli2.db_3.13.0_src_all.tar.gz"], "md5": "110d6549b1d105fdff31ab8f45b08d65", "fn": "ecoli2.db_3.13.0.tar.gz"}, "ecoli2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ecoli2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoli2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoli2cdf/bioconductor-ecoli2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoli2cdf/bioconductor-ecoli2cdf_2.18.0_src_all.tar.gz"], "md5": "b5cd1f05322ce494132ff649de9806c6", "fn": "ecoli2cdf_2.18.0.tar.gz"}, "ecoli2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ecoli2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoli2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoli2probe/bioconductor-ecoli2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoli2probe/bioconductor-ecoli2probe_2.18.0_src_all.tar.gz"], "md5": "061fcb782ee9da3aa5108881677a4531", "fn": "ecoli2probe_2.18.0.tar.gz"}, "ecoliasv2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ecoliasv2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliasv2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoliasv2cdf/bioconductor-ecoliasv2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoliasv2cdf/bioconductor-ecoliasv2cdf_2.18.0_src_all.tar.gz"], "md5": "d7771ca1648b26a6af5bfb7582c6c778", "fn": "ecoliasv2cdf_2.18.0.tar.gz"}, "ecoliasv2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ecoliasv2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliasv2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoliasv2probe/bioconductor-ecoliasv2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoliasv2probe/bioconductor-ecoliasv2probe_2.18.0_src_all.tar.gz"], "md5": "b3e4332266184576279c3a478f286dc9", "fn": "ecoliasv2probe_2.18.0.tar.gz"}, "ecolicdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ecolicdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ecolicdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolicdf/bioconductor-ecolicdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolicdf/bioconductor-ecolicdf_2.18.0_src_all.tar.gz"], "md5": "4e664c1ac41a8ab68ef22f8a889b916c", "fn": "ecolicdf_2.18.0.tar.gz"}, "ecolik12.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/ecoliK12.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliK12.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolik12.db0/bioconductor-ecolik12.db0_3.16.0_src_all.tar.gz"], "md5": "b1fe10d0e57b1deaba86a553dd064583", "fn": "ecoliK12.db0_3.16.0.tar.gz"}, "ecoliprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ecoliprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoliprobe/bioconductor-ecoliprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecoliprobe/bioconductor-ecoliprobe_2.18.0_src_all.tar.gz"], "md5": "09586f9907bdbc43ba5ea4ce07c1f756", "fn": "ecoliprobe_2.18.0.tar.gz"}, "ecolisakai.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/ecoliSakai.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliSakai.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolisakai.db0/bioconductor-ecolisakai.db0_3.16.0_src_all.tar.gz"], "md5": "5bb85fbeb56ce79f0cb62a2e89d5bff7", "fn": "ecoliSakai.db0_3.16.0.tar.gz"}, "encodexplorerdata-0.99.5": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ENCODExplorerData_0.99.5.tar.gz", "https://bioarchive.galaxyproject.org/ENCODExplorerData_0.99.5.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-encodexplorerdata/bioconductor-encodexplorerdata_0.99.5_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-encodexplorerdata/bioconductor-encodexplorerdata_0.99.5_src_all.tar.gz"], "md5": "c6d9b491548529db0739b79c98adacd7", "fn": "ENCODExplorerData_0.99.5.tar.gz"}, "ensdb.hsapiens.v75-2.99.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/EnsDb.Hsapiens.v75_2.99.0.tar.gz", "https://bioarchive.galaxyproject.org/EnsDb.Hsapiens.v75_2.99.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v75/bioconductor-ensdb.hsapiens.v75_2.99.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v75/bioconductor-ensdb.hsapiens.v75_2.99.0_src_all.tar.gz"], "md5": "6c896475252903972bfc6c0eb0d8f334", "fn": "EnsDb.Hsapiens.v75_2.99.0.tar.gz"}, "ensdb.hsapiens.v79-2.99.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/EnsDb.Hsapiens.v79_2.99.0.tar.gz", "https://bioarchive.galaxyproject.org/EnsDb.Hsapiens.v79_2.99.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v79/bioconductor-ensdb.hsapiens.v79_2.99.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v79/bioconductor-ensdb.hsapiens.v79_2.99.0_src_all.tar.gz"], "md5": "16b5629805c07649b2aa501d34fcc588", "fn": "EnsDb.Hsapiens.v79_2.99.0.tar.gz"}, "ensdb.hsapiens.v86-2.99.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/EnsDb.Hsapiens.v86_2.99.0.tar.gz", "https://bioarchive.galaxyproject.org/EnsDb.Hsapiens.v86_2.99.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v86/bioconductor-ensdb.hsapiens.v86_2.99.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v86/bioconductor-ensdb.hsapiens.v86_2.99.0_src_all.tar.gz"], "md5": "0c9e52512ff6dbbbdb754c4d41149939", "fn": "EnsDb.Hsapiens.v86_2.99.0.tar.gz"}, "ensdb.mmusculus.v75-2.99.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/EnsDb.Mmusculus.v75_2.99.0.tar.gz", "https://bioarchive.galaxyproject.org/EnsDb.Mmusculus.v75_2.99.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.mmusculus.v75/bioconductor-ensdb.mmusculus.v75_2.99.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.mmusculus.v75/bioconductor-ensdb.mmusculus.v75_2.99.0_src_all.tar.gz"], "md5": "081bf6f90ff77031b634b4fe32e00be8", "fn": "EnsDb.Mmusculus.v75_2.99.0.tar.gz"}, "ensdb.mmusculus.v79-2.99.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/EnsDb.Mmusculus.v79_2.99.0.tar.gz", "https://bioarchive.galaxyproject.org/EnsDb.Mmusculus.v79_2.99.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.mmusculus.v79/bioconductor-ensdb.mmusculus.v79_2.99.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.mmusculus.v79/bioconductor-ensdb.mmusculus.v79_2.99.0_src_all.tar.gz"], "md5": "28bbab743b0d2d550dbfa0bcd3274fad", "fn": "EnsDb.Mmusculus.v79_2.99.0.tar.gz"}, "ensdb.rnorvegicus.v75-2.99.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/EnsDb.Rnorvegicus.v75_2.99.0.tar.gz", "https://bioarchive.galaxyproject.org/EnsDb.Rnorvegicus.v75_2.99.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.rnorvegicus.v75/bioconductor-ensdb.rnorvegicus.v75_2.99.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.rnorvegicus.v75/bioconductor-ensdb.rnorvegicus.v75_2.99.0_src_all.tar.gz"], "md5": "40ff53b41aa6fad0d5bd15f9c6f3bad8", "fn": "EnsDb.Rnorvegicus.v75_2.99.0.tar.gz"}, "ensdb.rnorvegicus.v79-2.99.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/EnsDb.Rnorvegicus.v79_2.99.0.tar.gz", "https://bioarchive.galaxyproject.org/EnsDb.Rnorvegicus.v79_2.99.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.rnorvegicus.v79/bioconductor-ensdb.rnorvegicus.v79_2.99.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ensdb.rnorvegicus.v79/bioconductor-ensdb.rnorvegicus.v79_2.99.0_src_all.tar.gz"], "md5": "7d305bd0d1a073bd8c60063ae210a7a9", "fn": "EnsDb.Rnorvegicus.v79_2.99.0.tar.gz"}, "epitxdb.hs.hg38-0.99.7": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/EpiTxDb.Hs.hg38_0.99.7.tar.gz", "https://bioarchive.galaxyproject.org/EpiTxDb.Hs.hg38_0.99.7.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epitxdb.hs.hg38/bioconductor-epitxdb.hs.hg38_0.99.7_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epitxdb.hs.hg38/bioconductor-epitxdb.hs.hg38_0.99.7_src_all.tar.gz"], "md5": "e30af95f285788a9777a8207a8ef73a9", "fn": "EpiTxDb.Hs.hg38_0.99.7.tar.gz"}, "epitxdb.mm.mm10-0.99.6": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/EpiTxDb.Mm.mm10_0.99.6.tar.gz", "https://bioarchive.galaxyproject.org/EpiTxDb.Mm.mm10_0.99.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epitxdb.mm.mm10/bioconductor-epitxdb.mm.mm10_0.99.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epitxdb.mm.mm10/bioconductor-epitxdb.mm.mm10_0.99.6_src_all.tar.gz"], "md5": "518e4967f7f038e3cbf2865b74dc4f1b", "fn": "EpiTxDb.Mm.mm10_0.99.6.tar.gz"}, "epitxdb.sc.saccer3-0.99.5": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/EpiTxDb.Sc.sacCer3_0.99.5.tar.gz", "https://bioarchive.galaxyproject.org/EpiTxDb.Sc.sacCer3_0.99.5.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epitxdb.sc.saccer3/bioconductor-epitxdb.sc.saccer3_0.99.5_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epitxdb.sc.saccer3/bioconductor-epitxdb.sc.saccer3_0.99.5_src_all.tar.gz"], "md5": "6d9e5f37e5dcb60e890d99d80fddda00", "fn": "EpiTxDb.Sc.sacCer3_0.99.5.tar.gz"}, "eupathdb-1.0.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/EuPathDB_1.0.1.tar.gz", "https://bioarchive.galaxyproject.org/EuPathDB_1.0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-eupathdb/bioconductor-eupathdb_1.0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-eupathdb/bioconductor-eupathdb_1.0.1_src_all.tar.gz"], "md5": "1451c3ab6c224d9a4cfbdf27dc5c2680", "fn": "EuPathDB_1.0.1.tar.gz"}, "excluderanges-0.99.6": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/excluderanges_0.99.6.tar.gz", "https://bioarchive.galaxyproject.org/excluderanges_0.99.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-excluderanges/bioconductor-excluderanges_0.99.6_src_all.tar.gz"], "md5": "6bb7d6e24d6f2c231bb5cb676fc24e32", "fn": "excluderanges_0.99.6.tar.gz"}, "fdb.fantom4.promoters.hg19-1.0.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/FDb.FANTOM4.promoters.hg19_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/FDb.FANTOM4.promoters.hg19_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.fantom4.promoters.hg19/bioconductor-fdb.fantom4.promoters.hg19_1.0.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.fantom4.promoters.hg19/bioconductor-fdb.fantom4.promoters.hg19_1.0.0_src_all.tar.gz"], "md5": "99a610eb895470e3d945acc5cfb3ebe6", "fn": "FDb.FANTOM4.promoters.hg19_1.0.0.tar.gz"}, "fdb.infiniummethylation.hg18-2.2.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/FDb.InfiniumMethylation.hg18_2.2.0.tar.gz", "https://bioarchive.galaxyproject.org/FDb.InfiniumMethylation.hg18_2.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.infiniummethylation.hg18/bioconductor-fdb.infiniummethylation.hg18_2.2.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.infiniummethylation.hg18/bioconductor-fdb.infiniummethylation.hg18_2.2.0_src_all.tar.gz"], "md5": "95ceab50d0a7c3d417cee12fbe3defb3", "fn": "FDb.InfiniumMethylation.hg18_2.2.0.tar.gz"}, "fdb.infiniummethylation.hg19-2.2.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz", "https://bioarchive.galaxyproject.org/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.infiniummethylation.hg19/bioconductor-fdb.infiniummethylation.hg19_2.2.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.infiniummethylation.hg19/bioconductor-fdb.infiniummethylation.hg19_2.2.0_src_all.tar.gz"], "md5": "b8b1abc599b9556b9fe9c6e824cb2697", "fn": "FDb.InfiniumMethylation.hg19_2.2.0.tar.gz"}, "fdb.ucsc.snp135common.hg19-1.0.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/FDb.UCSC.snp135common.hg19_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/FDb.UCSC.snp135common.hg19_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.snp135common.hg19/bioconductor-fdb.ucsc.snp135common.hg19_1.0.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.snp135common.hg19/bioconductor-fdb.ucsc.snp135common.hg19_1.0.0_src_all.tar.gz"], "md5": "0cdca5fa595bb69464016ceb97635f78", "fn": "FDb.UCSC.snp135common.hg19_1.0.0.tar.gz"}, "fdb.ucsc.snp137common.hg19-1.0.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/FDb.UCSC.snp137common.hg19_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/FDb.UCSC.snp137common.hg19_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.snp137common.hg19/bioconductor-fdb.ucsc.snp137common.hg19_1.0.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.snp137common.hg19/bioconductor-fdb.ucsc.snp137common.hg19_1.0.0_src_all.tar.gz"], "md5": "dac83f2d2f9ea9f033e50beac5c44838", "fn": "FDb.UCSC.snp137common.hg19_1.0.0.tar.gz"}, "fdb.ucsc.trnas-1.0.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/FDb.UCSC.tRNAs_1.0.1.tar.gz", "https://bioarchive.galaxyproject.org/FDb.UCSC.tRNAs_1.0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.trnas/bioconductor-fdb.ucsc.trnas_1.0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.trnas/bioconductor-fdb.ucsc.trnas_1.0.1_src_all.tar.gz"], "md5": "77bfdadd4d9f995a72b001e4e41792fa", "fn": "FDb.UCSC.tRNAs_1.0.1.tar.gz"}, "fitcons.ucsc.hg19-3.7.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/fitCons.UCSC.hg19_3.7.1.tar.gz", "https://bioarchive.galaxyproject.org/fitCons.UCSC.hg19_3.7.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fitcons.ucsc.hg19/bioconductor-fitcons.ucsc.hg19_3.7.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fitcons.ucsc.hg19/bioconductor-fitcons.ucsc.hg19_3.7.1_src_all.tar.gz"], "md5": "53d954890ec9b91084664a10161ce391", "fn": "fitCons.UCSC.hg19_3.7.1.tar.gz"}, "fly.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/fly.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/fly.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fly.db0/bioconductor-fly.db0_3.16.0_src_all.tar.gz"], "md5": "7f4041d95bfefb33ebb6319274c5a766", "fn": "fly.db0_3.16.0.tar.gz"}, "geneplast.data-0.99.6": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/geneplast.data_0.99.6.tar.gz", "https://bioarchive.galaxyproject.org/geneplast.data_0.99.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-geneplast.data/bioconductor-geneplast.data_0.99.6_src_all.tar.gz"], "md5": "08ddcdb9b1cf56dab5fe358c85fe1526", "fn": "geneplast.data_0.99.6.tar.gz"}, "geneplast.data.string.v91-0.99.6": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/geneplast.data.string.v91_0.99.6.tar.gz", "https://bioarchive.galaxyproject.org/geneplast.data.string.v91_0.99.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-geneplast.data.string.v91/bioconductor-geneplast.data.string.v91_0.99.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-geneplast.data.string.v91/bioconductor-geneplast.data.string.v91_0.99.6_src_all.tar.gz"], "md5": "86433f8489d9228c5ed73e2b75a55398", "fn": "geneplast.data.string.v91_0.99.6.tar.gz"}, "genesummary-0.99.4": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/GeneSummary_0.99.4.tar.gz", "https://bioarchive.galaxyproject.org/GeneSummary_0.99.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genesummary/bioconductor-genesummary_0.99.4_src_all.tar.gz"], "md5": "39ee728e42c42ccf200568c9c736b15c", "fn": "GeneSummary_0.99.4.tar.gz"}, "genomeinfodbdata-1.2.9": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz", "https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.9.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.9_src_all.tar.gz"], "md5": "7cc138cfb74665fdfa8d1c244eac4879", "fn": "GenomeInfoDbData_1.2.9.tar.gz"}, "genomewidesnp5crlmm-1.0.6": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/genomewidesnp5Crlmm_1.0.6.tar.gz", "https://bioarchive.galaxyproject.org/genomewidesnp5Crlmm_1.0.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomewidesnp5crlmm/bioconductor-genomewidesnp5crlmm_1.0.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomewidesnp5crlmm/bioconductor-genomewidesnp5crlmm_1.0.6_src_all.tar.gz"], "md5": "cc24140cd17758b8e09f4fe6c931526a", "fn": "genomewidesnp5Crlmm_1.0.6.tar.gz"}, "genomewidesnp6crlmm-1.0.7": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/genomewidesnp6Crlmm_1.0.7.tar.gz", "https://bioarchive.galaxyproject.org/genomewidesnp6Crlmm_1.0.7.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomewidesnp6crlmm/bioconductor-genomewidesnp6crlmm_1.0.7_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomewidesnp6crlmm/bioconductor-genomewidesnp6crlmm_1.0.7_src_all.tar.gz"], "md5": "13dd5aef3d814524896f2f3013beb78b", "fn": "genomewidesnp6Crlmm_1.0.7.tar.gz"}, "genomicstate-0.99.15": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/GenomicState_0.99.15.tar.gz", "https://bioarchive.galaxyproject.org/GenomicState_0.99.15.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomicstate/bioconductor-genomicstate_0.99.15_src_all.tar.gz"], "md5": "59c2d85a72f62cb12bad697fcbce5edc", "fn": "GenomicState_0.99.15.tar.gz"}, "gghumanmethcancerpanelv1.db-1.4.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/GGHumanMethCancerPanelv1.db_1.4.1.tar.gz", "https://bioarchive.galaxyproject.org/GGHumanMethCancerPanelv1.db_1.4.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gghumanmethcancerpanelv1.db/bioconductor-gghumanmethcancerpanelv1.db_1.4.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gghumanmethcancerpanelv1.db/bioconductor-gghumanmethcancerpanelv1.db_1.4.1_src_all.tar.gz"], "md5": "e8f4a37182b175fb33dd54f8093e6f52", "fn": "GGHumanMethCancerPanelv1.db_1.4.1.tar.gz"}, "go.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GO.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/GO.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-go.db/bioconductor-go.db_3.16.0_src_all.tar.gz"], "md5": "291f5c8ce883d03243ca3a522afd81ce", "fn": "GO.db_3.16.0.tar.gz"}, "gp53cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/gp53cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/gp53cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gp53cdf/bioconductor-gp53cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gp53cdf/bioconductor-gp53cdf_2.18.0_src_all.tar.gz"], "md5": "2887dd15d3fa29b5c13b068c8d641f61", "fn": "gp53cdf_2.18.0.tar.gz"}, "grasp2db-1.1.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/grasp2db_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/grasp2db_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-grasp2db/bioconductor-grasp2db_1.1.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-grasp2db/bioconductor-grasp2db_1.1.0_src_all.tar.gz"], "md5": "3fc90fc7c99e7da51dcbb687fd2d5515", "fn": "grasp2db_1.1.0.tar.gz"}, "gwascatdata-0.99.6": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/gwascatData_0.99.6.tar.gz", "https://bioarchive.galaxyproject.org/gwascatData_0.99.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gwascatdata/bioconductor-gwascatdata_0.99.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gwascatdata/bioconductor-gwascatdata_0.99.6_src_all.tar.gz"], "md5": "fa09db539ac0a16ba136e810a5b9970a", "fn": "gwascatData_0.99.6.tar.gz"}, "h10kcod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/h10kcod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/h10kcod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-h10kcod.db/bioconductor-h10kcod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-h10kcod.db/bioconductor-h10kcod.db_3.4.0_src_all.tar.gz"], "md5": "a555739cea229f286953c3297c145e9c", "fn": "h10kcod.db_3.4.0.tar.gz"}, "h20kcod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/h20kcod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/h20kcod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-h20kcod.db/bioconductor-h20kcod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-h20kcod.db/bioconductor-h20kcod.db_3.4.0_src_all.tar.gz"], "md5": "3647facb272f58424f4c94ef92e8ee45", "fn": "h20kcod.db_3.4.0.tar.gz"}, "hapmap370k-1.0.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hapmap370k_1.0.1.tar.gz", "https://bioarchive.galaxyproject.org/hapmap370k_1.0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap370k/bioconductor-hapmap370k_1.0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap370k/bioconductor-hapmap370k_1.0.1_src_all.tar.gz"], "md5": "569556341a45da799372aaf1012be72e", "fn": "hapmap370k_1.0.1.tar.gz"}, "hcg110.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hcg110.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hcg110.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcg110.db/bioconductor-hcg110.db_3.13.0_src_all.tar.gz"], "md5": "4c536c3539a61d7f1f67dac149f10b11", "fn": "hcg110.db_3.13.0.tar.gz"}, "hcg110cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hcg110cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hcg110cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcg110cdf/bioconductor-hcg110cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcg110cdf/bioconductor-hcg110cdf_2.18.0_src_all.tar.gz"], "md5": "b53167876217ddb301204719da23eafc", "fn": "hcg110cdf_2.18.0.tar.gz"}, "hcg110probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hcg110probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hcg110probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcg110probe/bioconductor-hcg110probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcg110probe/bioconductor-hcg110probe_2.18.0_src_all.tar.gz"], "md5": "51af8d6a7090ea7c5fe630dcea68bfb3", "fn": "hcg110probe_2.18.0.tar.gz"}, "hdo.db-0.99.1": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/HDO.db_0.99.1.tar.gz", "https://bioarchive.galaxyproject.org/HDO.db_0.99.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hdo.db/bioconductor-hdo.db_0.99.1_src_all.tar.gz"], "md5": "007a50523f1de27048dfc97f4d458f59", "fn": "HDO.db_0.99.1.tar.gz"}, "hgfocus.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgfocus.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgfocus.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgfocus.db/bioconductor-hgfocus.db_3.13.0_src_all.tar.gz"], "md5": "a6bee48c0aa947d3c7d25ef2c5a4d485", "fn": "hgfocus.db_3.13.0.tar.gz"}, "hgfocuscdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgfocuscdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgfocuscdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgfocuscdf/bioconductor-hgfocuscdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgfocuscdf/bioconductor-hgfocuscdf_2.18.0_src_all.tar.gz"], "md5": "9883e53bfd9ddb9ad5f3a9c2e47bbd2c", "fn": "hgfocuscdf_2.18.0.tar.gz"}, "hgfocusprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgfocusprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgfocusprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgfocusprobe/bioconductor-hgfocusprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgfocusprobe/bioconductor-hgfocusprobe_2.18.0_src_all.tar.gz"], "md5": "0a399ed276b89e3d80946b6cbbf167b4", "fn": "hgfocusprobe_2.18.0.tar.gz"}, "hgu133a.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu133a.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133a.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133a.db/bioconductor-hgu133a.db_3.13.0_src_all.tar.gz"], "md5": "97675c27b13624bdfd760460dbca6bf0", "fn": "hgu133a.db_3.13.0.tar.gz"}, "hgu133a2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu133a2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133a2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133a2.db/bioconductor-hgu133a2.db_3.13.0_src_all.tar.gz"], "md5": "e3bf9c5c9941f5f378cbc3dbeb9919ee", "fn": "hgu133a2.db_3.13.0.tar.gz"}, "hgu133a2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu133a2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133a2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133a2cdf/bioconductor-hgu133a2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133a2cdf/bioconductor-hgu133a2cdf_2.18.0_src_all.tar.gz"], "md5": "566bc70f0bb94a376bf88f191a2f067e", "fn": "hgu133a2cdf_2.18.0.tar.gz"}, "hgu133a2frmavecs-1.2.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu133a2frmavecs_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133a2frmavecs_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133a2frmavecs/bioconductor-hgu133a2frmavecs_1.2.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133a2frmavecs/bioconductor-hgu133a2frmavecs_1.2.0_src_all.tar.gz"], "md5": "4bf8cf5cbaf288ce0a9618d764c87044", "fn": "hgu133a2frmavecs_1.2.0.tar.gz"}, "hgu133a2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu133a2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133a2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133a2probe/bioconductor-hgu133a2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133a2probe/bioconductor-hgu133a2probe_2.18.0_src_all.tar.gz"], "md5": "736b43cfc37a297ccc0d30cb75fcc95a", "fn": "hgu133a2probe_2.18.0.tar.gz"}, "hgu133acdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu133acdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133acdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133acdf/bioconductor-hgu133acdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133acdf/bioconductor-hgu133acdf_2.18.0_src_all.tar.gz"], "md5": "d3e0e22b2d3943d26c94e7c01b91035c", "fn": "hgu133acdf_2.18.0.tar.gz"}, "hgu133afrmavecs-1.5.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu133afrmavecs_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133afrmavecs_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133afrmavecs/bioconductor-hgu133afrmavecs_1.5.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133afrmavecs/bioconductor-hgu133afrmavecs_1.5.0_src_all.tar.gz"], "md5": "85034ab02491f5b3699d210cef50812d", "fn": "hgu133afrmavecs_1.5.0.tar.gz"}, "hgu133aprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu133aprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133aprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133aprobe/bioconductor-hgu133aprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133aprobe/bioconductor-hgu133aprobe_2.18.0_src_all.tar.gz"], "md5": "76cd9c54b0a8a0240dbb0fc758959d62", "fn": "hgu133aprobe_2.18.0.tar.gz"}, "hgu133atagcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu133atagcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133atagcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133atagcdf/bioconductor-hgu133atagcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133atagcdf/bioconductor-hgu133atagcdf_2.18.0_src_all.tar.gz"], "md5": "01f8809e0deb5b83f3f0decec881a1d8", "fn": "hgu133atagcdf_2.18.0.tar.gz"}, "hgu133atagprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu133atagprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133atagprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133atagprobe/bioconductor-hgu133atagprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133atagprobe/bioconductor-hgu133atagprobe_2.18.0_src_all.tar.gz"], "md5": "97aeaf9ac9450369cf030581b8ec5a53", "fn": "hgu133atagprobe_2.18.0.tar.gz"}, "hgu133b.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu133b.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133b.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133b.db/bioconductor-hgu133b.db_3.13.0_src_all.tar.gz"], "md5": "ff7930c99300c1022fde06ebe5c4a8cc", "fn": "hgu133b.db_3.13.0.tar.gz"}, "hgu133bcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu133bcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133bcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133bcdf/bioconductor-hgu133bcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133bcdf/bioconductor-hgu133bcdf_2.18.0_src_all.tar.gz"], "md5": "649aaa5e6275be6ee4d24d80ca390ea5", "fn": "hgu133bcdf_2.18.0.tar.gz"}, "hgu133bprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu133bprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133bprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133bprobe/bioconductor-hgu133bprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133bprobe/bioconductor-hgu133bprobe_2.18.0_src_all.tar.gz"], "md5": "203750510e51450e1267e08c241151c4", "fn": "hgu133bprobe_2.18.0.tar.gz"}, "hgu133plus2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu133plus2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2.db/bioconductor-hgu133plus2.db_3.13.0_src_all.tar.gz"], "md5": "459fcf4880a9eaa25b373c5635fede3d", "fn": "hgu133plus2.db_3.13.0.tar.gz"}, "hgu133plus2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu133plus2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2cdf/bioconductor-hgu133plus2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2cdf/bioconductor-hgu133plus2cdf_2.18.0_src_all.tar.gz"], "md5": "284fef2f0b777d7b53451538ddd53de3", "fn": "hgu133plus2cdf_2.18.0.tar.gz"}, "hgu133plus2frmavecs-1.5.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu133plus2frmavecs_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2frmavecs_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2frmavecs/bioconductor-hgu133plus2frmavecs_1.5.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2frmavecs/bioconductor-hgu133plus2frmavecs_1.5.0_src_all.tar.gz"], "md5": "a4781cbcccc1ee17dfd16259f1c7bebc", "fn": "hgu133plus2frmavecs_1.5.0.tar.gz"}, "hgu133plus2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu133plus2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2probe/bioconductor-hgu133plus2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2probe/bioconductor-hgu133plus2probe_2.18.0_src_all.tar.gz"], "md5": "7a244787a0269bc72732ac3d830f34dd", "fn": "hgu133plus2probe_2.18.0.tar.gz"}, "hgu219.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu219.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hgu219.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu219.db/bioconductor-hgu219.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu219.db/bioconductor-hgu219.db_3.2.3_src_all.tar.gz"], "md5": "a4a0fd2ac170a75d8b17618615fcd7a0", "fn": "hgu219.db_3.2.3.tar.gz"}, "hgu219cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu219cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu219cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu219cdf/bioconductor-hgu219cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu219cdf/bioconductor-hgu219cdf_2.18.0_src_all.tar.gz"], "md5": "157a4280a9de960902260ab18f678949", "fn": "hgu219cdf_2.18.0.tar.gz"}, "hgu219probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu219probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu219probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu219probe/bioconductor-hgu219probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu219probe/bioconductor-hgu219probe_2.18.0_src_all.tar.gz"], "md5": "c5bb2f7b2e0f8fa89e6a30befaee6497", "fn": "hgu219probe_2.18.0.tar.gz"}, "hgu95a.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu95a.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95a.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95a.db/bioconductor-hgu95a.db_3.13.0_src_all.tar.gz"], "md5": "b228ec0eded3ba9bccf033c2fff8f7b8", "fn": "hgu95a.db_3.13.0.tar.gz"}, "hgu95acdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu95acdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95acdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95acdf/bioconductor-hgu95acdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95acdf/bioconductor-hgu95acdf_2.18.0_src_all.tar.gz"], "md5": "afc999d77b1532154d45911ad15a5897", "fn": "hgu95acdf_2.18.0.tar.gz"}, "hgu95aprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu95aprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95aprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95aprobe/bioconductor-hgu95aprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95aprobe/bioconductor-hgu95aprobe_2.18.0_src_all.tar.gz"], "md5": "67d94ecdc1889acc19dafd19d26700a2", "fn": "hgu95aprobe_2.18.0.tar.gz"}, "hgu95av2-2.2.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu95av2_2.2.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95av2_2.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95av2/bioconductor-hgu95av2_2.2.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95av2/bioconductor-hgu95av2_2.2.0_src_all.tar.gz"], "md5": "b92585c0f43e91bd1abd234b9465a6a7", "fn": "hgu95av2_2.2.0.tar.gz"}, "hgu95av2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu95av2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95av2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95av2.db/bioconductor-hgu95av2.db_3.13.0_src_all.tar.gz"], "md5": "0ada3f3c2507992b94d2daa7de8b7fbf", "fn": "hgu95av2.db_3.13.0.tar.gz"}, "hgu95av2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu95av2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95av2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95av2cdf/bioconductor-hgu95av2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95av2cdf/bioconductor-hgu95av2cdf_2.18.0_src_all.tar.gz"], "md5": "026bae2f76433593f75ca6c79bc9a9d0", "fn": "hgu95av2cdf_2.18.0.tar.gz"}, "hgu95av2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu95av2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95av2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95av2probe/bioconductor-hgu95av2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95av2probe/bioconductor-hgu95av2probe_2.18.0_src_all.tar.gz"], "md5": "d3efb56f7e7a264b633fac787a5a2b95", "fn": "hgu95av2probe_2.18.0.tar.gz"}, "hgu95b.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu95b.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95b.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95b.db/bioconductor-hgu95b.db_3.13.0_src_all.tar.gz"], "md5": "12334c263cfd9f7dc835762b4661edc1", "fn": "hgu95b.db_3.13.0.tar.gz"}, "hgu95bcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu95bcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95bcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95bcdf/bioconductor-hgu95bcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95bcdf/bioconductor-hgu95bcdf_2.18.0_src_all.tar.gz"], "md5": "e6e56b7a107bb2df25b3c25a8191385d", "fn": "hgu95bcdf_2.18.0.tar.gz"}, "hgu95bprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu95bprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95bprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95bprobe/bioconductor-hgu95bprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95bprobe/bioconductor-hgu95bprobe_2.18.0_src_all.tar.gz"], "md5": "60dcb57fd402dc24d53ef9390c893cfc", "fn": "hgu95bprobe_2.18.0.tar.gz"}, "hgu95c.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu95c.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95c.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95c.db/bioconductor-hgu95c.db_3.13.0_src_all.tar.gz"], "md5": "680cdfc3e63853ace2ec47caa00ded36", "fn": "hgu95c.db_3.13.0.tar.gz"}, "hgu95ccdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu95ccdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95ccdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95ccdf/bioconductor-hgu95ccdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95ccdf/bioconductor-hgu95ccdf_2.18.0_src_all.tar.gz"], "md5": "976151eac05c320aec7a24397a6b5806", "fn": "hgu95ccdf_2.18.0.tar.gz"}, "hgu95cprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu95cprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95cprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95cprobe/bioconductor-hgu95cprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95cprobe/bioconductor-hgu95cprobe_2.18.0_src_all.tar.gz"], "md5": "3fe935a52c70105dc7a214174c946455", "fn": "hgu95cprobe_2.18.0.tar.gz"}, "hgu95d.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu95d.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95d.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95d.db/bioconductor-hgu95d.db_3.13.0_src_all.tar.gz"], "md5": "90ecf383640f6ab7314fa1babcdd5a0b", "fn": "hgu95d.db_3.13.0.tar.gz"}, "hgu95dcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu95dcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95dcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95dcdf/bioconductor-hgu95dcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95dcdf/bioconductor-hgu95dcdf_2.18.0_src_all.tar.gz"], "md5": "36e11ff001b1bec3f34ba7c93132ad6f", "fn": "hgu95dcdf_2.18.0.tar.gz"}, "hgu95dprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu95dprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95dprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95dprobe/bioconductor-hgu95dprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95dprobe/bioconductor-hgu95dprobe_2.18.0_src_all.tar.gz"], "md5": "165ce5029f49fc515b9ee0e6a6a29cb5", "fn": "hgu95dprobe_2.18.0.tar.gz"}, "hgu95e.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu95e.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95e.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95e.db/bioconductor-hgu95e.db_3.13.0_src_all.tar.gz"], "md5": "116bd146279d19d50a7233bc61c22104", "fn": "hgu95e.db_3.13.0.tar.gz"}, "hgu95ecdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu95ecdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95ecdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95ecdf/bioconductor-hgu95ecdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95ecdf/bioconductor-hgu95ecdf_2.18.0_src_all.tar.gz"], "md5": "fa27cfff62a38fc51640d797bd628105", "fn": "hgu95ecdf_2.18.0.tar.gz"}, "hgu95eprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgu95eprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu95eprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95eprobe/bioconductor-hgu95eprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu95eprobe/bioconductor-hgu95eprobe_2.18.0_src_all.tar.gz"], "md5": "9e5407ab80c5bbb4065484be0b9c6191", "fn": "hgu95eprobe_2.18.0.tar.gz"}, "hguatlas13k.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hguatlas13k.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hguatlas13k.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hguatlas13k.db/bioconductor-hguatlas13k.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hguatlas13k.db/bioconductor-hguatlas13k.db_3.2.3_src_all.tar.gz"], "md5": "ab9ffe1a1de44c0f938129f193e7fb63", "fn": "hguatlas13k.db_3.2.3.tar.gz"}, "hgubeta7.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgubeta7.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hgubeta7.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgubeta7.db/bioconductor-hgubeta7.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgubeta7.db/bioconductor-hgubeta7.db_3.2.3_src_all.tar.gz"], "md5": "1b8b065f95d2089985f59f22dcabc824", "fn": "hgubeta7.db_3.2.3.tar.gz"}, "hgudkfz31.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hguDKFZ31.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hguDKFZ31.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgudkfz31.db/bioconductor-hgudkfz31.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgudkfz31.db/bioconductor-hgudkfz31.db_3.2.3_src_all.tar.gz"], "md5": "fa3ba493cebdac4253dea8fe5d58452b", "fn": "hguDKFZ31.db_3.2.3.tar.gz"}, "hgug4100a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgug4100a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hgug4100a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4100a.db/bioconductor-hgug4100a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4100a.db/bioconductor-hgug4100a.db_3.2.3_src_all.tar.gz"], "md5": "b7856928278a77d71f963410ea4f2376", "fn": "hgug4100a.db_3.2.3.tar.gz"}, "hgug4101a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgug4101a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hgug4101a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4101a.db/bioconductor-hgug4101a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4101a.db/bioconductor-hgug4101a.db_3.2.3_src_all.tar.gz"], "md5": "e4731217efbffd05d3ee7eec68ce0aa0", "fn": "hgug4101a.db_3.2.3.tar.gz"}, "hgug4110b.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgug4110b.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hgug4110b.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4110b.db/bioconductor-hgug4110b.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4110b.db/bioconductor-hgug4110b.db_3.2.3_src_all.tar.gz"], "md5": "a9edcdbc121f22d4dec335a64598ff0e", "fn": "hgug4110b.db_3.2.3.tar.gz"}, "hgug4111a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgug4111a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hgug4111a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4111a.db/bioconductor-hgug4111a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4111a.db/bioconductor-hgug4111a.db_3.2.3_src_all.tar.gz"], "md5": "a5f2c3b463915fa1ab0ca21e6b0f5840", "fn": "hgug4111a.db_3.2.3.tar.gz"}, "hgug4112a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgug4112a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hgug4112a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4112a.db/bioconductor-hgug4112a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4112a.db/bioconductor-hgug4112a.db_3.2.3_src_all.tar.gz"], "md5": "67ecf8c887e2ebe1941cc51d0f5fb468", "fn": "hgug4112a.db_3.2.3.tar.gz"}, "hgug4845a.db-0.0.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hgug4845a.db_0.0.3.tar.gz", "https://bioarchive.galaxyproject.org/hgug4845a.db_0.0.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4845a.db/bioconductor-hgug4845a.db_0.0.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgug4845a.db/bioconductor-hgug4845a.db_0.0.3_src_all.tar.gz"], "md5": "46133d7bcb6d8c24c026304e8ddd150d", "fn": "hgug4845a.db_0.0.3.tar.gz"}, "hguqiagenv3.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hguqiagenv3.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/hguqiagenv3.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hguqiagenv3.db/bioconductor-hguqiagenv3.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hguqiagenv3.db/bioconductor-hguqiagenv3.db_3.2.3_src_all.tar.gz"], "md5": "91ebb82e773ff799befdb8921b38e90e", "fn": "hguqiagenv3.db_3.2.3.tar.gz"}, "hi16cod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hi16cod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/hi16cod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hi16cod.db/bioconductor-hi16cod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hi16cod.db/bioconductor-hi16cod.db_3.4.0_src_all.tar.gz"], "md5": "abdc77937e8d37fa5468691376ceb6a5", "fn": "hi16cod.db_3.4.0.tar.gz"}, "hivprtplus2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hivprtplus2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hivprtplus2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hivprtplus2cdf/bioconductor-hivprtplus2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hivprtplus2cdf/bioconductor-hivprtplus2cdf_2.18.0_src_all.tar.gz"], "md5": "143d9c2f5f328786bae7bb8dc4daf261", "fn": "hivprtplus2cdf_2.18.0.tar.gz"}, "homo.sapiens-1.3.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/Homo.sapiens_1.3.1.tar.gz", "https://bioarchive.galaxyproject.org/Homo.sapiens_1.3.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-homo.sapiens/bioconductor-homo.sapiens_1.3.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-homo.sapiens/bioconductor-homo.sapiens_1.3.1_src_all.tar.gz"], "md5": "653b60cfcdaefd171729115cd629b585", "fn": "Homo.sapiens_1.3.1.tar.gz"}, "hpannot-1.1.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hpAnnot_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/hpAnnot_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hpannot/bioconductor-hpannot_1.1.0_src_all.tar.gz"], "md5": "fbc94a00b0f33b41bc5ff53fbe060663", "fn": "hpAnnot_1.1.0.tar.gz"}, "hs25kresogen.db-2.5.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hs25kresogen.db_2.5.0.tar.gz", "https://bioarchive.galaxyproject.org/hs25kresogen.db_2.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hs25kresogen.db/bioconductor-hs25kresogen.db_2.5.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hs25kresogen.db/bioconductor-hs25kresogen.db_2.5.0_src_all.tar.gz"], "md5": "a3800d072ce0e5f6f5d8299538b99cca", "fn": "hs25kresogen.db_2.5.0.tar.gz"}, "hs6ug171.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/Hs6UG171.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/Hs6UG171.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hs6ug171.db/bioconductor-hs6ug171.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hs6ug171.db/bioconductor-hs6ug171.db_3.2.3_src_all.tar.gz"], "md5": "7aaf8a2441941f70247275c93735ed3b", "fn": "Hs6UG171.db_3.2.3.tar.gz"}, "hsagilentdesign026652.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/HsAgilentDesign026652.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/HsAgilentDesign026652.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hsagilentdesign026652.db/bioconductor-hsagilentdesign026652.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hsagilentdesign026652.db/bioconductor-hsagilentdesign026652.db_3.2.3_src_all.tar.gz"], "md5": "dcd2c748bf9d7c002611cd5cf2ff38c0", "fn": "HsAgilentDesign026652.db_3.2.3.tar.gz"}, "hspec-0.99.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/Hspec_0.99.1.tar.gz", "https://bioarchive.galaxyproject.org/Hspec_0.99.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hspec/bioconductor-hspec_0.99.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hspec/bioconductor-hspec_0.99.1_src_all.tar.gz"], "md5": "0ade3e3147c8f0086e9be2312cccdfeb", "fn": "Hspec_0.99.1.tar.gz"}, "hspeccdf-0.99.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hspeccdf_0.99.1.tar.gz", "https://bioarchive.galaxyproject.org/hspeccdf_0.99.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hspeccdf/bioconductor-hspeccdf_0.99.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hspeccdf/bioconductor-hspeccdf_0.99.1_src_all.tar.gz"], "md5": "89f81adf91094710558ce6aec79fc7fd", "fn": "hspeccdf_0.99.1.tar.gz"}, "hta20probeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hta20probeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hta20probeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hta20probeset.db/bioconductor-hta20probeset.db_8.8.0_src_all.tar.gz"], "md5": "8cc15bb71f3c2776015e55a2d7df2c2f", "fn": "hta20probeset.db_8.8.0.tar.gz"}, "hta20transcriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hta20transcriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hta20transcriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hta20transcriptcluster.db/bioconductor-hta20transcriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "9debbc190cc5f9f0ad97fbc452fe7025", "fn": "hta20transcriptcluster.db_8.8.0.tar.gz"}, "hthgu133a.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hthgu133a.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133a.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133a.db/bioconductor-hthgu133a.db_3.13.0_src_all.tar.gz"], "md5": "769ed088760102b61edfb73454d4c642", "fn": "hthgu133a.db_3.13.0.tar.gz"}, "hthgu133acdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hthgu133acdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133acdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133acdf/bioconductor-hthgu133acdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133acdf/bioconductor-hthgu133acdf_2.18.0_src_all.tar.gz"], "md5": "b92e543867f1f0c08bfa9299e123d608", "fn": "hthgu133acdf_2.18.0.tar.gz"}, "hthgu133afrmavecs-1.3.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hthgu133afrmavecs_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133afrmavecs_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133afrmavecs/bioconductor-hthgu133afrmavecs_1.3.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133afrmavecs/bioconductor-hthgu133afrmavecs_1.3.0_src_all.tar.gz"], "md5": "be3f3d67a94dca3b080c184fba5ff6d8", "fn": "hthgu133afrmavecs_1.3.0.tar.gz"}, "hthgu133aprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hthgu133aprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133aprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133aprobe/bioconductor-hthgu133aprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133aprobe/bioconductor-hthgu133aprobe_2.18.0_src_all.tar.gz"], "md5": "cdc17ea670719f055ee75bea1415c754", "fn": "hthgu133aprobe_2.18.0.tar.gz"}, "hthgu133b.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hthgu133b.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133b.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133b.db/bioconductor-hthgu133b.db_3.13.0_src_all.tar.gz"], "md5": "8501401a7385e28173ea7b60aa3bf3d2", "fn": "hthgu133b.db_3.13.0.tar.gz"}, "hthgu133bcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hthgu133bcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133bcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133bcdf/bioconductor-hthgu133bcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133bcdf/bioconductor-hthgu133bcdf_2.18.0_src_all.tar.gz"], "md5": "935ae53fb168d9c7890d71020ef4c366", "fn": "hthgu133bcdf_2.18.0.tar.gz"}, "hthgu133bprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hthgu133bprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133bprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133bprobe/bioconductor-hthgu133bprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133bprobe/bioconductor-hthgu133bprobe_2.18.0_src_all.tar.gz"], "md5": "8a2e306638a81fdec3b10a014c04c6b9", "fn": "hthgu133bprobe_2.18.0.tar.gz"}, "hthgu133plusa.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hthgu133plusa.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133plusa.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133plusa.db/bioconductor-hthgu133plusa.db_3.13.0_src_all.tar.gz"], "md5": "477cb32e1d8eb6da894486ad810b4232", "fn": "hthgu133plusa.db_3.13.0.tar.gz"}, "hthgu133plusb.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hthgu133plusb.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133plusb.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133plusb.db/bioconductor-hthgu133plusb.db_3.13.0_src_all.tar.gz"], "md5": "f3214792ba174598b0559937f46de937", "fn": "hthgu133plusb.db_3.13.0.tar.gz"}, "hthgu133pluspm.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hthgu133pluspm.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133pluspm.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133pluspm.db/bioconductor-hthgu133pluspm.db_3.13.0_src_all.tar.gz"], "md5": "b0b3cb0174608d5705ae6c80dac02e3c", "fn": "hthgu133pluspm.db_3.13.0.tar.gz"}, "hthgu133pluspmcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hthgu133pluspmcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133pluspmcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133pluspmcdf/bioconductor-hthgu133pluspmcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133pluspmcdf/bioconductor-hthgu133pluspmcdf_2.18.0_src_all.tar.gz"], "md5": "56d15101d59decac7811caa15b349a9c", "fn": "hthgu133pluspmcdf_2.18.0.tar.gz"}, "hthgu133pluspmprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hthgu133pluspmprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hthgu133pluspmprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133pluspmprobe/bioconductor-hthgu133pluspmprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hthgu133pluspmprobe/bioconductor-hthgu133pluspmprobe_2.18.0_src_all.tar.gz"], "md5": "74713e822a689007892d0eb92dbd456b", "fn": "hthgu133pluspmprobe_2.18.0.tar.gz"}, "htmg430a.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/htmg430a.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/htmg430a.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430a.db/bioconductor-htmg430a.db_3.13.0_src_all.tar.gz"], "md5": "171e457946a6b485b2ebd928b233abb3", "fn": "htmg430a.db_3.13.0.tar.gz"}, "htmg430acdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/htmg430acdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htmg430acdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430acdf/bioconductor-htmg430acdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430acdf/bioconductor-htmg430acdf_2.18.0_src_all.tar.gz"], "md5": "aef7a3c3af7d2624ee6fc6f2d22472e2", "fn": "htmg430acdf_2.18.0.tar.gz"}, "htmg430aprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/htmg430aprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htmg430aprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430aprobe/bioconductor-htmg430aprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430aprobe/bioconductor-htmg430aprobe_2.18.0_src_all.tar.gz"], "md5": "e50cc49b8887b6ef8ee1152ec12d5010", "fn": "htmg430aprobe_2.18.0.tar.gz"}, "htmg430b.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/htmg430b.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/htmg430b.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430b.db/bioconductor-htmg430b.db_3.13.0_src_all.tar.gz"], "md5": "70849a636e972a9be604a3320d3bd814", "fn": "htmg430b.db_3.13.0.tar.gz"}, "htmg430bcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/htmg430bcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htmg430bcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430bcdf/bioconductor-htmg430bcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430bcdf/bioconductor-htmg430bcdf_2.18.0_src_all.tar.gz"], "md5": "53cc1408504a5f07b5655aa46b969157", "fn": "htmg430bcdf_2.18.0.tar.gz"}, "htmg430bprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/htmg430bprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htmg430bprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430bprobe/bioconductor-htmg430bprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430bprobe/bioconductor-htmg430bprobe_2.18.0_src_all.tar.gz"], "md5": "f0e3eb56925d786762dee0c2dc82b530", "fn": "htmg430bprobe_2.18.0.tar.gz"}, "htmg430pm.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/htmg430pm.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/htmg430pm.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430pm.db/bioconductor-htmg430pm.db_3.13.0_src_all.tar.gz"], "md5": "f89738ce2e33d1c626aa2d15cd28a49b", "fn": "htmg430pm.db_3.13.0.tar.gz"}, "htmg430pmcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/htmg430pmcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htmg430pmcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430pmcdf/bioconductor-htmg430pmcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430pmcdf/bioconductor-htmg430pmcdf_2.18.0_src_all.tar.gz"], "md5": "016a54b47adbbed7db989787646a0084", "fn": "htmg430pmcdf_2.18.0.tar.gz"}, "htmg430pmprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/htmg430pmprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htmg430pmprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430pmprobe/bioconductor-htmg430pmprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htmg430pmprobe/bioconductor-htmg430pmprobe_2.18.0_src_all.tar.gz"], "md5": "f0e053fcc0ca4b5f8c539fc0a3fcb076", "fn": "htmg430pmprobe_2.18.0.tar.gz"}, "htrat230pm.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/htrat230pm.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/htrat230pm.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htrat230pm.db/bioconductor-htrat230pm.db_3.13.0_src_all.tar.gz"], "md5": "46ed50806c568bf269fe4c51d3df3955", "fn": "htrat230pm.db_3.13.0.tar.gz"}, "htrat230pmcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/htrat230pmcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htrat230pmcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htrat230pmcdf/bioconductor-htrat230pmcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htrat230pmcdf/bioconductor-htrat230pmcdf_2.18.0_src_all.tar.gz"], "md5": "c6683d16e8aacccd326f7a7eebb79b98", "fn": "htrat230pmcdf_2.18.0.tar.gz"}, "htrat230pmprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/htrat230pmprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htrat230pmprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htrat230pmprobe/bioconductor-htrat230pmprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htrat230pmprobe/bioconductor-htrat230pmprobe_2.18.0_src_all.tar.gz"], "md5": "e4deeca2dc406367ac4a347e370267cf", "fn": "htrat230pmprobe_2.18.0.tar.gz"}, "htratfocus.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/htratfocus.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/htratfocus.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htratfocus.db/bioconductor-htratfocus.db_3.13.0_src_all.tar.gz"], "md5": "88be90edb1acb31faedde0b66b27a150", "fn": "htratfocus.db_3.13.0.tar.gz"}, "htratfocuscdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/htratfocuscdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htratfocuscdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htratfocuscdf/bioconductor-htratfocuscdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htratfocuscdf/bioconductor-htratfocuscdf_2.18.0_src_all.tar.gz"], "md5": "04b4952f7d8b607a7eb0f779c08c57dc", "fn": "htratfocuscdf_2.18.0.tar.gz"}, "htratfocusprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/htratfocusprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/htratfocusprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htratfocusprobe/bioconductor-htratfocusprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-htratfocusprobe/bioconductor-htratfocusprobe_2.18.0_src_all.tar.gz"], "md5": "26a0963d8aff314a4a1f2c47e9147a8a", "fn": "htratfocusprobe_2.18.0.tar.gz"}, "hu35ksuba.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hu35ksuba.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksuba.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksuba.db/bioconductor-hu35ksuba.db_3.13.0_src_all.tar.gz"], "md5": "4c2306a80f26bacb6172e84c896ef911", "fn": "hu35ksuba.db_3.13.0.tar.gz"}, "hu35ksubacdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hu35ksubacdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubacdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubacdf/bioconductor-hu35ksubacdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubacdf/bioconductor-hu35ksubacdf_2.18.0_src_all.tar.gz"], "md5": "c8b82c4755eb62818ca0dbf22de5d25e", "fn": "hu35ksubacdf_2.18.0.tar.gz"}, "hu35ksubaprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hu35ksubaprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubaprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubaprobe/bioconductor-hu35ksubaprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubaprobe/bioconductor-hu35ksubaprobe_2.18.0_src_all.tar.gz"], "md5": "49bd19ec3b6404211f2e410e473fa644", "fn": "hu35ksubaprobe_2.18.0.tar.gz"}, "hu35ksubb.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hu35ksubb.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubb.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubb.db/bioconductor-hu35ksubb.db_3.13.0_src_all.tar.gz"], "md5": "b82ece4860eddff8010faecaae802312", "fn": "hu35ksubb.db_3.13.0.tar.gz"}, "hu35ksubbcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hu35ksubbcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubbcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubbcdf/bioconductor-hu35ksubbcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubbcdf/bioconductor-hu35ksubbcdf_2.18.0_src_all.tar.gz"], "md5": "d873b6c521e926b331f799baf10a4e13", "fn": "hu35ksubbcdf_2.18.0.tar.gz"}, "hu35ksubbprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hu35ksubbprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubbprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubbprobe/bioconductor-hu35ksubbprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubbprobe/bioconductor-hu35ksubbprobe_2.18.0_src_all.tar.gz"], "md5": "0a63051d0faf38a56f17d5865cbed9b1", "fn": "hu35ksubbprobe_2.18.0.tar.gz"}, "hu35ksubc.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hu35ksubc.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubc.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubc.db/bioconductor-hu35ksubc.db_3.13.0_src_all.tar.gz"], "md5": "57e60b8d025e0e8cf7ac2b355111cf2d", "fn": "hu35ksubc.db_3.13.0.tar.gz"}, "hu35ksubccdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hu35ksubccdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubccdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubccdf/bioconductor-hu35ksubccdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubccdf/bioconductor-hu35ksubccdf_2.18.0_src_all.tar.gz"], "md5": "de96e69680c5f8747c99d170272d7c3c", "fn": "hu35ksubccdf_2.18.0.tar.gz"}, "hu35ksubcprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hu35ksubcprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubcprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubcprobe/bioconductor-hu35ksubcprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubcprobe/bioconductor-hu35ksubcprobe_2.18.0_src_all.tar.gz"], "md5": "b10453ea061b09172192bd21baa9083d", "fn": "hu35ksubcprobe_2.18.0.tar.gz"}, "hu35ksubd.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hu35ksubd.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubd.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubd.db/bioconductor-hu35ksubd.db_3.13.0_src_all.tar.gz"], "md5": "5ce6b6ede0f9733fd4dc527a28114327", "fn": "hu35ksubd.db_3.13.0.tar.gz"}, "hu35ksubdcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hu35ksubdcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubdcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubdcdf/bioconductor-hu35ksubdcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubdcdf/bioconductor-hu35ksubdcdf_2.18.0_src_all.tar.gz"], "md5": "6f6423426969f306fb0d5171e75b5380", "fn": "hu35ksubdcdf_2.18.0.tar.gz"}, "hu35ksubdprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hu35ksubdprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu35ksubdprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubdprobe/bioconductor-hu35ksubdprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu35ksubdprobe/bioconductor-hu35ksubdprobe_2.18.0_src_all.tar.gz"], "md5": "430a9b8ccd646d8cb06e6c1d750eec23", "fn": "hu35ksubdprobe_2.18.0.tar.gz"}, "hu6800.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hu6800.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/hu6800.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800.db/bioconductor-hu6800.db_3.13.0_src_all.tar.gz"], "md5": "aa1cb6c107dee6d2ed1929b48aa831e9", "fn": "hu6800.db_3.13.0.tar.gz"}, "hu6800cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hu6800cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu6800cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800cdf/bioconductor-hu6800cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800cdf/bioconductor-hu6800cdf_2.18.0_src_all.tar.gz"], "md5": "fa2b2ab8f3aba517c63ad2e65873d2f0", "fn": "hu6800cdf_2.18.0.tar.gz"}, "hu6800probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hu6800probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu6800probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800probe/bioconductor-hu6800probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800probe/bioconductor-hu6800probe_2.18.0_src_all.tar.gz"], "md5": "7a2383bd870cbc0628c210174e911250", "fn": "hu6800probe_2.18.0.tar.gz"}, "hu6800subacdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hu6800subacdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu6800subacdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800subacdf/bioconductor-hu6800subacdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800subacdf/bioconductor-hu6800subacdf_2.18.0_src_all.tar.gz"], "md5": "9e8ec301e066e400564976cd9750297e", "fn": "hu6800subacdf_2.18.0.tar.gz"}, "hu6800subbcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hu6800subbcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu6800subbcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800subbcdf/bioconductor-hu6800subbcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800subbcdf/bioconductor-hu6800subbcdf_2.18.0_src_all.tar.gz"], "md5": "529aad5e4e73594c8cb66274d7e4adc5", "fn": "hu6800subbcdf_2.18.0.tar.gz"}, "hu6800subccdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hu6800subccdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu6800subccdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800subccdf/bioconductor-hu6800subccdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800subccdf/bioconductor-hu6800subccdf_2.18.0_src_all.tar.gz"], "md5": "020fe3a6bdf44efbde15432b968433e8", "fn": "hu6800subccdf_2.18.0.tar.gz"}, "hu6800subdcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hu6800subdcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hu6800subdcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800subdcdf/bioconductor-hu6800subdcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hu6800subdcdf/bioconductor-hu6800subdcdf_2.18.0_src_all.tar.gz"], "md5": "7966c21babb23e18cca4faafc8720f0a", "fn": "hu6800subdcdf_2.18.0.tar.gz"}, "huex.1.0.st.v2frmavecs-1.1.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/huex.1.0.st.v2frmavecs_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/huex.1.0.st.v2frmavecs_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huex.1.0.st.v2frmavecs/bioconductor-huex.1.0.st.v2frmavecs_1.1.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huex.1.0.st.v2frmavecs/bioconductor-huex.1.0.st.v2frmavecs_1.1.0_src_all.tar.gz"], "md5": "982935d07b526ff555790e309fe4147e", "fn": "huex.1.0.st.v2frmavecs_1.1.0.tar.gz"}, "huex10stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/huex10stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/huex10stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huex10stprobeset.db/bioconductor-huex10stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "fda9fc7340aeda2564a76756d2b8d4d3", "fn": "huex10stprobeset.db_8.8.0.tar.gz"}, "huex10sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/huex10sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/huex10sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huex10sttranscriptcluster.db/bioconductor-huex10sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "0789a1e8ee4474bd64c2772eab0db247", "fn": "huex10sttranscriptcluster.db_8.8.0.tar.gz"}, "huexexonprobesetlocation-1.15.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/HuExExonProbesetLocation_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/HuExExonProbesetLocation_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocation/bioconductor-huexexonprobesetlocation_1.15.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocation/bioconductor-huexexonprobesetlocation_1.15.0_src_all.tar.gz"], "md5": "11bf1b88d9e90711b4064497f611da4f", "fn": "HuExExonProbesetLocation_1.15.0.tar.gz"}, "huexexonprobesetlocationhg18-0.0.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/HuExExonProbesetLocationHg18_0.0.2.tar.gz", "https://bioarchive.galaxyproject.org/HuExExonProbesetLocationHg18_0.0.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocationhg18/bioconductor-huexexonprobesetlocationhg18_0.0.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocationhg18/bioconductor-huexexonprobesetlocationhg18_0.0.2_src_all.tar.gz"], "md5": "bb00b7f5e4db2b04dca5951aa6bd073e", "fn": "HuExExonProbesetLocationHg18_0.0.2.tar.gz"}, "huexexonprobesetlocationhg19-0.0.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/HuExExonProbesetLocationHg19_0.0.3.tar.gz", "https://bioarchive.galaxyproject.org/HuExExonProbesetLocationHg19_0.0.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocationhg19/bioconductor-huexexonprobesetlocationhg19_0.0.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocationhg19/bioconductor-huexexonprobesetlocationhg19_0.0.3_src_all.tar.gz"], "md5": "1a3843c95c82dc71a043d902961ba33a", "fn": "HuExExonProbesetLocationHg19_0.0.3.tar.gz"}, "hugene.1.0.st.v1frmavecs-1.1.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hugene.1.0.st.v1frmavecs_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene.1.0.st.v1frmavecs_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene.1.0.st.v1frmavecs/bioconductor-hugene.1.0.st.v1frmavecs_1.1.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene.1.0.st.v1frmavecs/bioconductor-hugene.1.0.st.v1frmavecs_1.1.0_src_all.tar.gz"], "md5": "711a69e6fa6dd3737a90615222416dfc", "fn": "hugene.1.0.st.v1frmavecs_1.1.0.tar.gz"}, "hugene10stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hugene10stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene10stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene10stprobeset.db/bioconductor-hugene10stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "0a4a87d64564cbec1e4bb1f9e5a67add", "fn": "hugene10stprobeset.db_8.8.0.tar.gz"}, "hugene10sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hugene10sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene10sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene10sttranscriptcluster.db/bioconductor-hugene10sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "a32fb5729d37e96f157b0a1085dff43e", "fn": "hugene10sttranscriptcluster.db_8.8.0.tar.gz"}, "hugene10stv1cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hugene10stv1cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene10stv1cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene10stv1cdf/bioconductor-hugene10stv1cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene10stv1cdf/bioconductor-hugene10stv1cdf_2.18.0_src_all.tar.gz"], "md5": "f1fb1c7076ac40b9e709f18e645d6181", "fn": "hugene10stv1cdf_2.18.0.tar.gz"}, "hugene10stv1probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hugene10stv1probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene10stv1probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene10stv1probe/bioconductor-hugene10stv1probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene10stv1probe/bioconductor-hugene10stv1probe_2.18.0_src_all.tar.gz"], "md5": "6ed3c17dd026acf008658a5994044c62", "fn": "hugene10stv1probe_2.18.0.tar.gz"}, "hugene11stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hugene11stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene11stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene11stprobeset.db/bioconductor-hugene11stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "4d22ec32dedd6c8603d5f545faeb4ba4", "fn": "hugene11stprobeset.db_8.8.0.tar.gz"}, "hugene11sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hugene11sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene11sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene11sttranscriptcluster.db/bioconductor-hugene11sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "7fed70c4bd904655459a41b5667f7c23", "fn": "hugene11sttranscriptcluster.db_8.8.0.tar.gz"}, "hugene20stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hugene20stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene20stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene20stprobeset.db/bioconductor-hugene20stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "bf7909fc41a80da59099327a6d9abb57", "fn": "hugene20stprobeset.db_8.8.0.tar.gz"}, "hugene20sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hugene20sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene20sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene20sttranscriptcluster.db/bioconductor-hugene20sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "0b929a3a959662e8a7265f58b81b4e35", "fn": "hugene20sttranscriptcluster.db_8.8.0.tar.gz"}, "hugene21stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hugene21stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene21stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene21stprobeset.db/bioconductor-hugene21stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "2b816dca48d0b2e1a946469b8d85d257", "fn": "hugene21stprobeset.db_8.8.0.tar.gz"}, "hugene21sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hugene21sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/hugene21sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hugene21sttranscriptcluster.db/bioconductor-hugene21sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "ca90de6093bbad760abfcf0cfeada830", "fn": "hugene21sttranscriptcluster.db_8.8.0.tar.gz"}, "human.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/human.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/human.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human.db0/bioconductor-human.db0_3.16.0_src_all.tar.gz"], "md5": "19286619cd24ff1e3f9ac85debd5106f", "fn": "human.db0_3.16.0.tar.gz"}, "human1mduov3bcrlmm-1.0.4": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/human1mduov3bCrlmm_1.0.4.tar.gz", "https://bioarchive.galaxyproject.org/human1mduov3bCrlmm_1.0.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human1mduov3bcrlmm/bioconductor-human1mduov3bcrlmm_1.0.4_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human1mduov3bcrlmm/bioconductor-human1mduov3bcrlmm_1.0.4_src_all.tar.gz"], "md5": "0ff9f1e8bcc6348d6777bbb982ae0325", "fn": "human1mduov3bCrlmm_1.0.4.tar.gz"}, "human1mv1ccrlmm-1.0.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/human1mv1cCrlmm_1.0.3.tar.gz", "https://bioarchive.galaxyproject.org/human1mv1cCrlmm_1.0.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human1mv1ccrlmm/bioconductor-human1mv1ccrlmm_1.0.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human1mv1ccrlmm/bioconductor-human1mv1ccrlmm_1.0.3_src_all.tar.gz"], "md5": "b9f638c7b0ede50cb070f1bae85eb4dc", "fn": "human1mv1cCrlmm_1.0.3.tar.gz"}, "human370quadv3ccrlmm-1.0.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/human370quadv3cCrlmm_1.0.3.tar.gz", "https://bioarchive.galaxyproject.org/human370quadv3cCrlmm_1.0.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human370quadv3ccrlmm/bioconductor-human370quadv3ccrlmm_1.0.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human370quadv3ccrlmm/bioconductor-human370quadv3ccrlmm_1.0.3_src_all.tar.gz"], "md5": "33c3ccc3793ed95647418b746a5177f9", "fn": "human370quadv3cCrlmm_1.0.3.tar.gz"}, "human370v1ccrlmm-1.0.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/human370v1cCrlmm_1.0.2.tar.gz", "https://bioarchive.galaxyproject.org/human370v1cCrlmm_1.0.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human370v1ccrlmm/bioconductor-human370v1ccrlmm_1.0.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human370v1ccrlmm/bioconductor-human370v1ccrlmm_1.0.2_src_all.tar.gz"], "md5": "9ec4192f533faee2b14484de02548075", "fn": "human370v1cCrlmm_1.0.2.tar.gz"}, "human550v3bcrlmm-1.0.4": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/human550v3bCrlmm_1.0.4.tar.gz", "https://bioarchive.galaxyproject.org/human550v3bCrlmm_1.0.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human550v3bcrlmm/bioconductor-human550v3bcrlmm_1.0.4_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human550v3bcrlmm/bioconductor-human550v3bcrlmm_1.0.4_src_all.tar.gz"], "md5": "20e6b008fab5e1084354c87ad50d18a8", "fn": "human550v3bCrlmm_1.0.4.tar.gz"}, "human610quadv1bcrlmm-1.0.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/human610quadv1bCrlmm_1.0.3.tar.gz", "https://bioarchive.galaxyproject.org/human610quadv1bCrlmm_1.0.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human610quadv1bcrlmm/bioconductor-human610quadv1bcrlmm_1.0.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human610quadv1bcrlmm/bioconductor-human610quadv1bcrlmm_1.0.3_src_all.tar.gz"], "md5": "609cf09410774e084ee6a3286652bb1a", "fn": "human610quadv1bCrlmm_1.0.3.tar.gz"}, "human650v3acrlmm-1.0.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/human650v3aCrlmm_1.0.3.tar.gz", "https://bioarchive.galaxyproject.org/human650v3aCrlmm_1.0.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human650v3acrlmm/bioconductor-human650v3acrlmm_1.0.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human650v3acrlmm/bioconductor-human650v3acrlmm_1.0.3_src_all.tar.gz"], "md5": "4b0de367ccc0f7499dcffe21ef1893c2", "fn": "human650v3aCrlmm_1.0.3.tar.gz"}, "human660quadv1acrlmm-1.0.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/human660quadv1aCrlmm_1.0.3.tar.gz", "https://bioarchive.galaxyproject.org/human660quadv1aCrlmm_1.0.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human660quadv1acrlmm/bioconductor-human660quadv1acrlmm_1.0.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human660quadv1acrlmm/bioconductor-human660quadv1acrlmm_1.0.3_src_all.tar.gz"], "md5": "5fd2d94a462e150c888f13c5c0975c36", "fn": "human660quadv1aCrlmm_1.0.3.tar.gz"}, "humanchrloc-2.1.6": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/humanCHRLOC_2.1.6.tar.gz", "https://bioarchive.galaxyproject.org/humanCHRLOC_2.1.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanchrloc/bioconductor-humanchrloc_2.1.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanchrloc/bioconductor-humanchrloc_2.1.6_src_all.tar.gz"], "md5": "113450c0822000c9b4e8a0141cf4b819", "fn": "humanCHRLOC_2.1.6.tar.gz"}, "humancytosnp12v2p1hcrlmm-1.0.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/humancytosnp12v2p1hCrlmm_1.0.1.tar.gz", "https://bioarchive.galaxyproject.org/humancytosnp12v2p1hCrlmm_1.0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humancytosnp12v2p1hcrlmm/bioconductor-humancytosnp12v2p1hcrlmm_1.0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humancytosnp12v2p1hcrlmm/bioconductor-humancytosnp12v2p1hcrlmm_1.0.1_src_all.tar.gz"], "md5": "edf80245ddb28afb9fbaa6668187bf3a", "fn": "humancytosnp12v2p1hCrlmm_1.0.1.tar.gz"}, "humanomni1quadv1bcrlmm-1.0.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/humanomni1quadv1bCrlmm_1.0.3.tar.gz", "https://bioarchive.galaxyproject.org/humanomni1quadv1bCrlmm_1.0.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanomni1quadv1bcrlmm/bioconductor-humanomni1quadv1bcrlmm_1.0.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanomni1quadv1bcrlmm/bioconductor-humanomni1quadv1bcrlmm_1.0.3_src_all.tar.gz"], "md5": "e81b2603f37d4cda3f28cd69a7296a23", "fn": "humanomni1quadv1bCrlmm_1.0.3.tar.gz"}, "humanomni25quadv1bcrlmm-1.0.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/humanomni25quadv1bCrlmm_1.0.2.tar.gz", "https://bioarchive.galaxyproject.org/humanomni25quadv1bCrlmm_1.0.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanomni25quadv1bcrlmm/bioconductor-humanomni25quadv1bcrlmm_1.0.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanomni25quadv1bcrlmm/bioconductor-humanomni25quadv1bcrlmm_1.0.2_src_all.tar.gz"], "md5": "2ee1fa7bf712d7f81a167079c975d49f", "fn": "humanomni25quadv1bCrlmm_1.0.2.tar.gz"}, "humanomni5quadv1bcrlmm-1.0.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/humanomni5quadv1bCrlmm_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/humanomni5quadv1bCrlmm_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanomni5quadv1bcrlmm/bioconductor-humanomni5quadv1bcrlmm_1.0.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanomni5quadv1bcrlmm/bioconductor-humanomni5quadv1bcrlmm_1.0.0_src_all.tar.gz"], "md5": "3ac4d6867c3d5590a6308d6edff0912b", "fn": "humanomni5quadv1bCrlmm_1.0.0.tar.gz"}, "humanomniexpress12v1bcrlmm-1.0.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/humanomniexpress12v1bCrlmm_1.0.1.tar.gz", "https://bioarchive.galaxyproject.org/humanomniexpress12v1bCrlmm_1.0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanomniexpress12v1bcrlmm/bioconductor-humanomniexpress12v1bcrlmm_1.0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanomniexpress12v1bcrlmm/bioconductor-humanomniexpress12v1bcrlmm_1.0.1_src_all.tar.gz"], "md5": "abdb730fc230db669e588e024ee7624b", "fn": "humanomniexpress12v1bCrlmm_1.0.1.tar.gz"}, "huo22.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/HuO22.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/HuO22.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huo22.db/bioconductor-huo22.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-huo22.db/bioconductor-huo22.db_3.2.3_src_all.tar.gz"], "md5": "ddabf6c01f94c1dfd6ab35b40852828a", "fn": "HuO22.db_3.2.3.tar.gz"}, "hwgcod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/hwgcod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/hwgcod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hwgcod.db/bioconductor-hwgcod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hwgcod.db/bioconductor-hwgcod.db_3.4.0_src_all.tar.gz"], "md5": "a46bf1a242853bbab26351a11b18030a", "fn": "hwgcod.db_3.4.0.tar.gz"}, "illuminahumanmethylation27k.db-1.4.8": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/IlluminaHumanMethylation27k.db_1.4.8.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation27k.db_1.4.8.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27k.db/bioconductor-illuminahumanmethylation27k.db_1.4.8_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27k.db/bioconductor-illuminahumanmethylation27k.db_1.4.8_src_all.tar.gz"], "md5": "70586bda9db01d598723bb439c315367", "fn": "IlluminaHumanMethylation27k.db_1.4.8.tar.gz"}, "illuminahumanmethylation27kanno.ilmn12.hg19-0.6.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/IlluminaHumanMethylation27kanno.ilmn12.hg19_0.6.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation27kanno.ilmn12.hg19_0.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19_0.6.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19_0.6.0_src_all.tar.gz"], "md5": "765851336506120467c2e3cc6beef7ed", "fn": "IlluminaHumanMethylation27kanno.ilmn12.hg19_0.6.0.tar.gz"}, "illuminahumanmethylation27kmanifest-0.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/IlluminaHumanMethylation27kmanifest_0.4.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation27kmanifest_0.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27kmanifest/bioconductor-illuminahumanmethylation27kmanifest_0.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27kmanifest/bioconductor-illuminahumanmethylation27kmanifest_0.4.0_src_all.tar.gz"], "md5": "c4cdda637dccf85f193342c7262b02a6", "fn": "IlluminaHumanMethylation27kmanifest_0.4.0.tar.gz"}, "illuminahumanmethylation450kanno.ilmn12.hg19-0.6.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19_0.6.1_src_all.tar.gz"], "md5": "aeafc54d887b128ed265fa704a3efa42", "fn": "IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1.tar.gz"}, "illuminahumanmethylation450kmanifest-0.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kmanifest/bioconductor-illuminahumanmethylation450kmanifest_0.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kmanifest/bioconductor-illuminahumanmethylation450kmanifest_0.4.0_src_all.tar.gz"], "md5": "664d1f5a3892974334faa26757269509", "fn": "IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz"}, "illuminahumanmethylation450kprobe-2.0.6": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/IlluminaHumanMethylation450kprobe_2.0.6.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation450kprobe_2.0.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kprobe/bioconductor-illuminahumanmethylation450kprobe_2.0.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kprobe/bioconductor-illuminahumanmethylation450kprobe_2.0.6_src_all.tar.gz"], "md5": "84c31861fcbaddbf2a9c500b8d8d767d", "fn": "IlluminaHumanMethylation450kprobe_2.0.6.tar.gz"}, "illuminahumanmethylationepicanno.ilm10b2.hg19-0.6.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19_0.6.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19_0.6.0_src_all.tar.gz"], "md5": "6a8e2398a0f930aa7828a1412fb21e88", "fn": "IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz"}, "illuminahumanmethylationepicanno.ilm10b3.hg19-0.6.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19_0.6.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19_0.6.0_src_all.tar.gz"], "md5": "2dac8e889486386eaea1bb7ce1beea2e", "fn": "IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz"}, "illuminahumanmethylationepicanno.ilm10b4.hg19-0.6.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19_0.6.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19_0.6.0_src_all.tar.gz"], "md5": "2d0c05917bcbf9ba1e354380d4e17a77", "fn": "IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz"}, "illuminahumanmethylationepicmanifest-0.3.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicmanifest/bioconductor-illuminahumanmethylationepicmanifest_0.3.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicmanifest/bioconductor-illuminahumanmethylationepicmanifest_0.3.0_src_all.tar.gz"], "md5": "c6b0268de177badfe0b8184002da7e16", "fn": "IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz"}, "illuminahumanv1.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/illuminaHumanv1.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaHumanv1.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv1.db/bioconductor-illuminahumanv1.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv1.db/bioconductor-illuminahumanv1.db_1.26.0_src_all.tar.gz"], "md5": "2c362256b7be2861b8bf6e0d1fe46786", "fn": "illuminaHumanv1.db_1.26.0.tar.gz"}, "illuminahumanv2.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/illuminaHumanv2.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaHumanv2.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv2.db/bioconductor-illuminahumanv2.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv2.db/bioconductor-illuminahumanv2.db_1.26.0_src_all.tar.gz"], "md5": "006de5f671a9a68fb27a6b6bce39c555", "fn": "illuminaHumanv2.db_1.26.0.tar.gz"}, "illuminahumanv2beadid.db-1.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/illuminaHumanv2BeadID.db_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaHumanv2BeadID.db_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv2beadid.db/bioconductor-illuminahumanv2beadid.db_1.8.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv2beadid.db/bioconductor-illuminahumanv2beadid.db_1.8.0_src_all.tar.gz"], "md5": "b5a2b2deaa9a9b245a141043e7bc5270", "fn": "illuminaHumanv2BeadID.db_1.8.0.tar.gz"}, "illuminahumanv3.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/illuminaHumanv3.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaHumanv3.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv3.db/bioconductor-illuminahumanv3.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv3.db/bioconductor-illuminahumanv3.db_1.26.0_src_all.tar.gz"], "md5": "7d9e7534f0b60f0e3e7473e545ef373d", "fn": "illuminaHumanv3.db_1.26.0.tar.gz"}, "illuminahumanv4.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/illuminaHumanv4.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaHumanv4.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv4.db/bioconductor-illuminahumanv4.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv4.db/bioconductor-illuminahumanv4.db_1.26.0_src_all.tar.gz"], "md5": "42d554559ac0106dc71317ffaf466421", "fn": "illuminaHumanv4.db_1.26.0.tar.gz"}, "illuminahumanwgdaslv3.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/illuminaHumanWGDASLv3.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaHumanWGDASLv3.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanwgdaslv3.db/bioconductor-illuminahumanwgdaslv3.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanwgdaslv3.db/bioconductor-illuminahumanwgdaslv3.db_1.26.0_src_all.tar.gz"], "md5": "32e8e24555c16f6d0148438d4a841ab8", "fn": "illuminaHumanWGDASLv3.db_1.26.0.tar.gz"}, "illuminahumanwgdaslv4.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/illuminaHumanWGDASLv4.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaHumanWGDASLv4.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanwgdaslv4.db/bioconductor-illuminahumanwgdaslv4.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminahumanwgdaslv4.db/bioconductor-illuminahumanwgdaslv4.db_1.26.0_src_all.tar.gz"], "md5": "4cc1f192de838f2b6c1b148706d354ca", "fn": "illuminaHumanWGDASLv4.db_1.26.0.tar.gz"}, "illuminamousev1.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/illuminaMousev1.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaMousev1.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminamousev1.db/bioconductor-illuminamousev1.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminamousev1.db/bioconductor-illuminamousev1.db_1.26.0_src_all.tar.gz"], "md5": "13818c3b9acabe75550492bbe638fc05", "fn": "illuminaMousev1.db_1.26.0.tar.gz"}, "illuminamousev1p1.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/illuminaMousev1p1.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaMousev1p1.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminamousev1p1.db/bioconductor-illuminamousev1p1.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminamousev1p1.db/bioconductor-illuminamousev1p1.db_1.26.0_src_all.tar.gz"], "md5": "f6a4af01480a6f8d1d2d9b9b64a2b073", "fn": "illuminaMousev1p1.db_1.26.0.tar.gz"}, "illuminamousev2.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/illuminaMousev2.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaMousev2.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminamousev2.db/bioconductor-illuminamousev2.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminamousev2.db/bioconductor-illuminamousev2.db_1.26.0_src_all.tar.gz"], "md5": "fba228a71f264f976d8cdb035861974d", "fn": "illuminaMousev2.db_1.26.0.tar.gz"}, "illuminaratv1.db-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/illuminaRatv1.db_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/illuminaRatv1.db_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminaratv1.db/bioconductor-illuminaratv1.db_1.26.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminaratv1.db/bioconductor-illuminaratv1.db_1.26.0_src_all.tar.gz"], "md5": "5de2324d7b96c0cdb3301ef269341aa8", "fn": "illuminaRatv1.db_1.26.0.tar.gz"}, "indac.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/indac.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/indac.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-indac.db/bioconductor-indac.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-indac.db/bioconductor-indac.db_3.2.3_src_all.tar.gz"], "md5": "cba72edcf7278033151e0eac077d8ff8", "fn": "indac.db_3.2.3.tar.gz"}, "jaspar2018-1.1.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/JASPAR2018_1.1.1.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2018_1.1.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2018/bioconductor-jaspar2018_1.1.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2018/bioconductor-jaspar2018_1.1.1_src_all.tar.gz"], "md5": "d91fce6ea0dc9fa6a3be6ebc05c1af5d", "fn": "JASPAR2018_1.1.1.tar.gz"}, "jaspar2020-0.99.10": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/JASPAR2020_0.99.10.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2020_0.99.10.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2020/bioconductor-jaspar2020_0.99.10_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2020/bioconductor-jaspar2020_0.99.10_src_all.tar.gz"], "md5": "bfcaf41ebf0935b8d146afd37719de2d", "fn": "JASPAR2020_0.99.10.tar.gz"}, "jaspar2022-0.99.7": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/JASPAR2022_0.99.7.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2022_0.99.7.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2022/bioconductor-jaspar2022_0.99.7_src_all.tar.gz"], "md5": "282af23228198a377fa9bd76c94dd5eb", "fn": "JASPAR2022_0.99.7.tar.gz"}, "jazaerimetadata.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/JazaeriMetaData.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/JazaeriMetaData.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jazaerimetadata.db/bioconductor-jazaerimetadata.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jazaerimetadata.db/bioconductor-jazaerimetadata.db_3.2.3_src_all.tar.gz"], "md5": "3a154a74ac2acebe3471b039c9d9a4dc", "fn": "JazaeriMetaData.db_3.2.3.tar.gz"}, "lapointe.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/LAPOINTE.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/LAPOINTE.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lapointe.db/bioconductor-lapointe.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lapointe.db/bioconductor-lapointe.db_3.2.3_src_all.tar.gz"], "md5": "434b25ad7411201d8be6bb1a0463b387", "fn": "LAPOINTE.db_3.2.3.tar.gz"}, "lowmacaannotation-0.99.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/LowMACAAnnotation_0.99.3.tar.gz", "https://bioarchive.galaxyproject.org/LowMACAAnnotation_0.99.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lowmacaannotation/bioconductor-lowmacaannotation_0.99.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lowmacaannotation/bioconductor-lowmacaannotation_0.99.3_src_all.tar.gz"], "md5": "9e0d3fe7f30fe48aef9c4387eb5bacfa", "fn": "LowMACAAnnotation_0.99.3.tar.gz"}, "lumihumanall.db-1.22.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/lumiHumanAll.db_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/lumiHumanAll.db_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumihumanall.db/bioconductor-lumihumanall.db_1.22.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumihumanall.db/bioconductor-lumihumanall.db_1.22.0_src_all.tar.gz"], "md5": "ce7e219b50833ceab203f0bbfb11d917", "fn": "lumiHumanAll.db_1.22.0.tar.gz"}, "lumihumanidmapping-1.10.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/lumiHumanIDMapping_1.10.1.tar.gz", "https://bioarchive.galaxyproject.org/lumiHumanIDMapping_1.10.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumihumanidmapping/bioconductor-lumihumanidmapping_1.10.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumihumanidmapping/bioconductor-lumihumanidmapping_1.10.1_src_all.tar.gz"], "md5": "007e5aa2f1596cc08d888ba6dce7148a", "fn": "lumiHumanIDMapping_1.10.1.tar.gz"}, "lumimouseall.db-1.22.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/lumiMouseAll.db_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/lumiMouseAll.db_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumimouseall.db/bioconductor-lumimouseall.db_1.22.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumimouseall.db/bioconductor-lumimouseall.db_1.22.0_src_all.tar.gz"], "md5": "6f12330377aaddc83bfa9c37477b999e", "fn": "lumiMouseAll.db_1.22.0.tar.gz"}, "lumimouseidmapping-1.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/lumiMouseIDMapping_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/lumiMouseIDMapping_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumimouseidmapping/bioconductor-lumimouseidmapping_1.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumimouseidmapping/bioconductor-lumimouseidmapping_1.10.0_src_all.tar.gz"], "md5": "305aba80ebf6ef4c26899302ea9e50e8", "fn": "lumiMouseIDMapping_1.10.0.tar.gz"}, "lumiratall.db-1.22.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/lumiRatAll.db_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/lumiRatAll.db_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumiratall.db/bioconductor-lumiratall.db_1.22.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumiratall.db/bioconductor-lumiratall.db_1.22.0_src_all.tar.gz"], "md5": "65027624574d5e33f18b0a54a54f4be9", "fn": "lumiRatAll.db_1.22.0.tar.gz"}, "lumiratidmapping-1.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/lumiRatIDMapping_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/lumiRatIDMapping_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumiratidmapping/bioconductor-lumiratidmapping_1.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumiratidmapping/bioconductor-lumiratidmapping_1.10.0_src_all.tar.gz"], "md5": "1122fc25e3fff62678bed36f9d7b5709", "fn": "lumiRatIDMapping_1.10.0.tar.gz"}, "lymphoseqdb-0.99.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/LymphoSeqDB_0.99.2.tar.gz", "https://bioarchive.galaxyproject.org/LymphoSeqDB_0.99.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lymphoseqdb/bioconductor-lymphoseqdb_0.99.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lymphoseqdb/bioconductor-lymphoseqdb_0.99.2_src_all.tar.gz"], "md5": "22fc0dc2439ef497982a5ffddda1e418", "fn": "LymphoSeqDB_0.99.2.tar.gz"}, "m10kcod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/m10kcod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/m10kcod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-m10kcod.db/bioconductor-m10kcod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-m10kcod.db/bioconductor-m10kcod.db_3.4.0_src_all.tar.gz"], "md5": "04811628e4b37cd6d24e0b2a17d79ab8", "fn": "m10kcod.db_3.4.0.tar.gz"}, "m20kcod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/m20kcod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/m20kcod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-m20kcod.db/bioconductor-m20kcod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-m20kcod.db/bioconductor-m20kcod.db_3.4.0_src_all.tar.gz"], "md5": "f2f734fb41e1ae4e949abf09687733bf", "fn": "m20kcod.db_3.4.0.tar.gz"}, "mafdb.1kgenomes.phase1.grch38-3.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/MafDb.1Kgenomes.phase1.GRCh38_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.1Kgenomes.phase1.GRCh38_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase1.grch38/bioconductor-mafdb.1kgenomes.phase1.grch38_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase1.grch38/bioconductor-mafdb.1kgenomes.phase1.grch38_3.10.0_src_all.tar.gz"], "md5": "a20471906a41678ce710879e92d2a9dc", "fn": "MafDb.1Kgenomes.phase1.GRCh38_3.10.0.tar.gz"}, "mafdb.1kgenomes.phase1.hs37d5-3.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/MafDb.1Kgenomes.phase1.hs37d5_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.1Kgenomes.phase1.hs37d5_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase1.hs37d5/bioconductor-mafdb.1kgenomes.phase1.hs37d5_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase1.hs37d5/bioconductor-mafdb.1kgenomes.phase1.hs37d5_3.10.0_src_all.tar.gz"], "md5": "ece6b758ca0e1a8a307b5cd5829671f4", "fn": "MafDb.1Kgenomes.phase1.hs37d5_3.10.0.tar.gz"}, "mafdb.1kgenomes.phase3.grch38-3.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.GRCh38_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.1Kgenomes.phase3.GRCh38_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase3.grch38/bioconductor-mafdb.1kgenomes.phase3.grch38_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase3.grch38/bioconductor-mafdb.1kgenomes.phase3.grch38_3.10.0_src_all.tar.gz"], "md5": "ee57d9cb6a1748932407d20b9bffd8a2", "fn": "MafDb.1Kgenomes.phase3.GRCh38_3.10.0.tar.gz"}, "mafdb.1kgenomes.phase3.hs37d5-3.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.hs37d5_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.1Kgenomes.phase3.hs37d5_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase3.hs37d5/bioconductor-mafdb.1kgenomes.phase3.hs37d5_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase3.hs37d5/bioconductor-mafdb.1kgenomes.phase3.hs37d5_3.10.0_src_all.tar.gz"], "md5": "ac3cbbf52eb2026f067a4f42c6654555", "fn": "MafDb.1Kgenomes.phase3.hs37d5_3.10.0.tar.gz"}, "mafdb.exac.r1.0.grch38-3.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/MafDb.ExAC.r1.0.GRCh38_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.ExAC.r1.0.GRCh38_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.grch38/bioconductor-mafdb.exac.r1.0.grch38_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.grch38/bioconductor-mafdb.exac.r1.0.grch38_3.10.0_src_all.tar.gz"], "md5": "303332c918996d8cb3e7b7c74d694dd1", "fn": "MafDb.ExAC.r1.0.GRCh38_3.10.0.tar.gz"}, "mafdb.exac.r1.0.hs37d5-3.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/MafDb.ExAC.r1.0.hs37d5_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.ExAC.r1.0.hs37d5_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.hs37d5/bioconductor-mafdb.exac.r1.0.hs37d5_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.hs37d5/bioconductor-mafdb.exac.r1.0.hs37d5_3.10.0_src_all.tar.gz"], "md5": "4d523554a2b0eb296bada9d33a78eefc", "fn": "MafDb.ExAC.r1.0.hs37d5_3.10.0.tar.gz"}, "mafdb.exac.r1.0.nontcga.grch38-3.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/MafDb.ExAC.r1.0.nonTCGA.GRCh38_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.ExAC.r1.0.nonTCGA.GRCh38_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.nontcga.grch38/bioconductor-mafdb.exac.r1.0.nontcga.grch38_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.nontcga.grch38/bioconductor-mafdb.exac.r1.0.nontcga.grch38_3.10.0_src_all.tar.gz"], "md5": "cf447f59cc8b1cd7ca395fd3fe6e4730", "fn": "MafDb.ExAC.r1.0.nonTCGA.GRCh38_3.10.0.tar.gz"}, "mafdb.exac.r1.0.nontcga.hs37d5-3.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/MafDb.ExAC.r1.0.nonTCGA.hs37d5_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.ExAC.r1.0.nonTCGA.hs37d5_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5_3.10.0_src_all.tar.gz"], "md5": "da3a699e9776b0b769b3bc1e9fb742f0", "fn": "MafDb.ExAC.r1.0.nonTCGA.hs37d5_3.10.0.tar.gz"}, "mafdb.gnomad.r2.1.grch38-3.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/MafDb.gnomAD.r2.1.GRCh38_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.gnomAD.r2.1.GRCh38_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomad.r2.1.grch38/bioconductor-mafdb.gnomad.r2.1.grch38_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomad.r2.1.grch38/bioconductor-mafdb.gnomad.r2.1.grch38_3.10.0_src_all.tar.gz"], "md5": "0e842b24476aeb834f57f9302a36ea18", "fn": "MafDb.gnomAD.r2.1.GRCh38_3.10.0.tar.gz"}, "mafdb.gnomad.r2.1.hs37d5-3.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/MafDb.gnomAD.r2.1.hs37d5_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.gnomAD.r2.1.hs37d5_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomad.r2.1.hs37d5/bioconductor-mafdb.gnomad.r2.1.hs37d5_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomad.r2.1.hs37d5/bioconductor-mafdb.gnomad.r2.1.hs37d5_3.10.0_src_all.tar.gz"], "md5": "12221c461930ae1ecfe925943a619d56", "fn": "MafDb.gnomAD.r2.1.hs37d5_3.10.0.tar.gz"}, "mafdb.gnomadex.r2.1.grch38-3.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/MafDb.gnomADex.r2.1.GRCh38_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.gnomADex.r2.1.GRCh38_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomadex.r2.1.grch38/bioconductor-mafdb.gnomadex.r2.1.grch38_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomadex.r2.1.grch38/bioconductor-mafdb.gnomadex.r2.1.grch38_3.10.0_src_all.tar.gz"], "md5": "a0ab5b74997669fabb8aecfd9ef7f767", "fn": "MafDb.gnomADex.r2.1.GRCh38_3.10.0.tar.gz"}, "mafdb.gnomadex.r2.1.hs37d5-3.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/MafDb.gnomADex.r2.1.hs37d5_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.gnomADex.r2.1.hs37d5_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomadex.r2.1.hs37d5/bioconductor-mafdb.gnomadex.r2.1.hs37d5_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomadex.r2.1.hs37d5/bioconductor-mafdb.gnomadex.r2.1.hs37d5_3.10.0_src_all.tar.gz"], "md5": "6ca4d742571687a13906d99cea2dbf1f", "fn": "MafDb.gnomADex.r2.1.hs37d5_3.10.0.tar.gz"}, "mafdb.topmed.freeze5.hg19-3.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/MafDb.TOPMed.freeze5.hg19_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.TOPMed.freeze5.hg19_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.topmed.freeze5.hg19/bioconductor-mafdb.topmed.freeze5.hg19_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.topmed.freeze5.hg19/bioconductor-mafdb.topmed.freeze5.hg19_3.10.0_src_all.tar.gz"], "md5": "7fdb58eb69187ade189689da58ca6266", "fn": "MafDb.TOPMed.freeze5.hg19_3.10.0.tar.gz"}, "mafdb.topmed.freeze5.hg38-3.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/MafDb.TOPMed.freeze5.hg38_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MafDb.TOPMed.freeze5.hg38_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.topmed.freeze5.hg38/bioconductor-mafdb.topmed.freeze5.hg38_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafdb.topmed.freeze5.hg38/bioconductor-mafdb.topmed.freeze5.hg38_3.10.0_src_all.tar.gz"], "md5": "a3355623fde26b83dfd346a32829f073", "fn": "MafDb.TOPMed.freeze5.hg38_3.10.0.tar.gz"}, "mafh5.gnomad.v3.1.1.grch38-3.13.1": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/MafH5.gnomAD.v3.1.1.GRCh38_3.13.1.tar.gz", "https://bioarchive.galaxyproject.org/MafH5.gnomAD.v3.1.1.GRCh38_3.13.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafh5.gnomad.v3.1.1.grch38/bioconductor-mafh5.gnomad.v3.1.1.grch38_3.13.1_src_all.tar.gz"], "md5": "8944d686ba1ac335f6e76594b7c92ebe", "fn": "MafH5.gnomAD.v3.1.1.GRCh38_3.13.1.tar.gz"}, "mafh5.gnomad.v3.1.2.grch38-3.15.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MafH5.gnomAD.v3.1.2.GRCh38_3.15.0.tar.gz", "https://bioarchive.galaxyproject.org/MafH5.gnomAD.v3.1.2.GRCh38_3.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mafh5.gnomad.v3.1.2.grch38/bioconductor-mafh5.gnomad.v3.1.2.grch38_3.15.0_src_all.tar.gz"], "md5": "e9c85173866caf998cf1af7dd35aac0b", "fn": "MafH5.gnomAD.v3.1.2.GRCh38_3.15.0.tar.gz"}, "maizecdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/maizecdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/maizecdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maizecdf/bioconductor-maizecdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maizecdf/bioconductor-maizecdf_2.18.0_src_all.tar.gz"], "md5": "f9dec9e46688d96daf1e07d4e815afb4", "fn": "maizecdf_2.18.0.tar.gz"}, "maizeprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/maizeprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/maizeprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maizeprobe/bioconductor-maizeprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maizeprobe/bioconductor-maizeprobe_2.18.0_src_all.tar.gz"], "md5": "ef7ba47de2346b3552621263399c05d1", "fn": "maizeprobe_2.18.0.tar.gz"}, "malaria.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/malaria.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/malaria.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-malaria.db0/bioconductor-malaria.db0_3.16.0_src_all.tar.gz"], "md5": "8cd45b5614ebfab6530cf9eefc57cfdb", "fn": "malaria.db0_3.16.0.tar.gz"}, "medicagocdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/medicagocdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/medicagocdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-medicagocdf/bioconductor-medicagocdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-medicagocdf/bioconductor-medicagocdf_2.18.0_src_all.tar.gz"], "md5": "1fbb2e4c070344d18e65f1b3993867db", "fn": "medicagocdf_2.18.0.tar.gz"}, "medicagoprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/medicagoprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/medicagoprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-medicagoprobe/bioconductor-medicagoprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-medicagoprobe/bioconductor-medicagoprobe_2.18.0_src_all.tar.gz"], "md5": "83b9887ad2ed26c704b0ca7115e5838d", "fn": "medicagoprobe_2.18.0.tar.gz"}, "metaboliteidmapping-1.0.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/metaboliteIDmapping_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/metaboliteIDmapping_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metaboliteidmapping/bioconductor-metaboliteidmapping_1.0.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metaboliteidmapping/bioconductor-metaboliteidmapping_1.0.0_src_all.tar.gz"], "md5": "bd78ec373ce90fac1a10d2c64c462e77", "fn": "metaboliteIDmapping_1.0.0.tar.gz"}, "mgu74a.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgu74a.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74a.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74a.db/bioconductor-mgu74a.db_3.13.0_src_all.tar.gz"], "md5": "9fb75c159c50e2ae316ee5a8abe1a48c", "fn": "mgu74a.db_3.13.0.tar.gz"}, "mgu74acdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgu74acdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74acdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74acdf/bioconductor-mgu74acdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74acdf/bioconductor-mgu74acdf_2.18.0_src_all.tar.gz"], "md5": "ed6e86398e51c7b0ddca4431797ecbc0", "fn": "mgu74acdf_2.18.0.tar.gz"}, "mgu74aprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgu74aprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74aprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74aprobe/bioconductor-mgu74aprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74aprobe/bioconductor-mgu74aprobe_2.18.0_src_all.tar.gz"], "md5": "7fea6d44856203e6293e0cd9fe1ad066", "fn": "mgu74aprobe_2.18.0.tar.gz"}, "mgu74av2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgu74av2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74av2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74av2.db/bioconductor-mgu74av2.db_3.13.0_src_all.tar.gz"], "md5": "3205856d0c7725acded5238415e907bc", "fn": "mgu74av2.db_3.13.0.tar.gz"}, "mgu74av2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgu74av2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74av2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74av2cdf/bioconductor-mgu74av2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74av2cdf/bioconductor-mgu74av2cdf_2.18.0_src_all.tar.gz"], "md5": "35e2abb9fbfd68d90dc32a2faae00c95", "fn": "mgu74av2cdf_2.18.0.tar.gz"}, "mgu74av2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgu74av2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74av2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74av2probe/bioconductor-mgu74av2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74av2probe/bioconductor-mgu74av2probe_2.18.0_src_all.tar.gz"], "md5": "ac540b0e26b14a411740233b02d3e11c", "fn": "mgu74av2probe_2.18.0.tar.gz"}, "mgu74b.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgu74b.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74b.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74b.db/bioconductor-mgu74b.db_3.13.0_src_all.tar.gz"], "md5": "205577a6e41d56910f221ffb940ee25b", "fn": "mgu74b.db_3.13.0.tar.gz"}, "mgu74bcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgu74bcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74bcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74bcdf/bioconductor-mgu74bcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74bcdf/bioconductor-mgu74bcdf_2.18.0_src_all.tar.gz"], "md5": "a1f0f98f29d34a421622447252113e1e", "fn": "mgu74bcdf_2.18.0.tar.gz"}, "mgu74bprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgu74bprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74bprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74bprobe/bioconductor-mgu74bprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74bprobe/bioconductor-mgu74bprobe_2.18.0_src_all.tar.gz"], "md5": "224d606e6fc87592d387dbaabe5cd353", "fn": "mgu74bprobe_2.18.0.tar.gz"}, "mgu74bv2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgu74bv2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74bv2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74bv2.db/bioconductor-mgu74bv2.db_3.13.0_src_all.tar.gz"], "md5": "4ec0fbed7343f0578ef11e2330d0d12a", "fn": "mgu74bv2.db_3.13.0.tar.gz"}, "mgu74bv2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgu74bv2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74bv2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74bv2cdf/bioconductor-mgu74bv2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74bv2cdf/bioconductor-mgu74bv2cdf_2.18.0_src_all.tar.gz"], "md5": "45c48d11af03633dc10f8682b7ad74c5", "fn": "mgu74bv2cdf_2.18.0.tar.gz"}, "mgu74bv2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgu74bv2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74bv2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74bv2probe/bioconductor-mgu74bv2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74bv2probe/bioconductor-mgu74bv2probe_2.18.0_src_all.tar.gz"], "md5": "f6a12f88ea3c43a3e885c7e9b3fd03d2", "fn": "mgu74bv2probe_2.18.0.tar.gz"}, "mgu74c.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgu74c.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74c.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74c.db/bioconductor-mgu74c.db_3.13.0_src_all.tar.gz"], "md5": "6c4f183e6ed5f0b5735596e7544746ae", "fn": "mgu74c.db_3.13.0.tar.gz"}, "mgu74ccdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgu74ccdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74ccdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74ccdf/bioconductor-mgu74ccdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74ccdf/bioconductor-mgu74ccdf_2.18.0_src_all.tar.gz"], "md5": "172e626b0e3072edc65c4efff35fe998", "fn": "mgu74ccdf_2.18.0.tar.gz"}, "mgu74cprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgu74cprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74cprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74cprobe/bioconductor-mgu74cprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74cprobe/bioconductor-mgu74cprobe_2.18.0_src_all.tar.gz"], "md5": "186992992708f0071fd552ef92b9e25c", "fn": "mgu74cprobe_2.18.0.tar.gz"}, "mgu74cv2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgu74cv2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74cv2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74cv2.db/bioconductor-mgu74cv2.db_3.13.0_src_all.tar.gz"], "md5": "1f860dfbf4400ede54eb30d9a70ec131", "fn": "mgu74cv2.db_3.13.0.tar.gz"}, "mgu74cv2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgu74cv2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74cv2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74cv2cdf/bioconductor-mgu74cv2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74cv2cdf/bioconductor-mgu74cv2cdf_2.18.0_src_all.tar.gz"], "md5": "9ef62b4b28f97770859db24393a07ed5", "fn": "mgu74cv2cdf_2.18.0.tar.gz"}, "mgu74cv2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgu74cv2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mgu74cv2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74cv2probe/bioconductor-mgu74cv2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgu74cv2probe/bioconductor-mgu74cv2probe_2.18.0_src_all.tar.gz"], "md5": "0373496c817a1c1a153114047cfa7c5b", "fn": "mgu74cv2probe_2.18.0.tar.gz"}, "mguatlas5k.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mguatlas5k.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/mguatlas5k.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mguatlas5k.db/bioconductor-mguatlas5k.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mguatlas5k.db/bioconductor-mguatlas5k.db_3.2.3_src_all.tar.gz"], "md5": "826093fe7228c08962aff36ad89af28e", "fn": "mguatlas5k.db_3.2.3.tar.gz"}, "mgug4104a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgug4104a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/mgug4104a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgug4104a.db/bioconductor-mgug4104a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgug4104a.db/bioconductor-mgug4104a.db_3.2.3_src_all.tar.gz"], "md5": "7b1cef094a226257cd657ed8d61e9ef1", "fn": "mgug4104a.db_3.2.3.tar.gz"}, "mgug4120a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgug4120a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/mgug4120a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgug4120a.db/bioconductor-mgug4120a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgug4120a.db/bioconductor-mgug4120a.db_3.2.3_src_all.tar.gz"], "md5": "bb57e8b2efe3d038ec2a0ace0313a4e7", "fn": "mgug4120a.db_3.2.3.tar.gz"}, "mgug4121a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgug4121a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/mgug4121a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgug4121a.db/bioconductor-mgug4121a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgug4121a.db/bioconductor-mgug4121a.db_3.2.3_src_all.tar.gz"], "md5": "6b5cc321d5175356c383b91e30e120b7", "fn": "mgug4121a.db_3.2.3.tar.gz"}, "mgug4122a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mgug4122a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/mgug4122a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgug4122a.db/bioconductor-mgug4122a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mgug4122a.db/bioconductor-mgug4122a.db_3.2.3_src_all.tar.gz"], "md5": "5fcdce909ac1c0ccbf06bf6411f6fe52", "fn": "mgug4122a.db_3.2.3.tar.gz"}, "mi16cod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mi16cod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/mi16cod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mi16cod.db/bioconductor-mi16cod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mi16cod.db/bioconductor-mi16cod.db_3.4.0_src_all.tar.gz"], "md5": "f3a8e6f45ce5c298c1b1c5b32bf2630c", "fn": "mi16cod.db_3.4.0.tar.gz"}, "mirbase.db-1.2.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mirbase.db_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/mirbase.db_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirbase.db/bioconductor-mirbase.db_1.2.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirbase.db/bioconductor-mirbase.db_1.2.0_src_all.tar.gz"], "md5": "316bc12cee8c2dd9240b7fc30cd1619e", "fn": "mirbase.db_1.2.0.tar.gz"}, "mirbaseversions.db-1.1.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/miRBaseVersions.db_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/miRBaseVersions.db_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirbaseversions.db/bioconductor-mirbaseversions.db_1.1.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirbaseversions.db/bioconductor-mirbaseversions.db_1.1.0_src_all.tar.gz"], "md5": "9944ab7a474f84a40100c56298f9cb77", "fn": "miRBaseVersions.db_1.1.0.tar.gz"}, "mirna102xgaincdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mirna102xgaincdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mirna102xgaincdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirna102xgaincdf/bioconductor-mirna102xgaincdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirna102xgaincdf/bioconductor-mirna102xgaincdf_2.18.0_src_all.tar.gz"], "md5": "9091a45c2ac15c2de0263743ab334f97", "fn": "mirna102xgaincdf_2.18.0.tar.gz"}, "mirna10cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mirna10cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mirna10cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirna10cdf/bioconductor-mirna10cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirna10cdf/bioconductor-mirna10cdf_2.18.0_src_all.tar.gz"], "md5": "814da2a2e298e132f4db0b2e8ab814be", "fn": "mirna10cdf_2.18.0.tar.gz"}, "mirna10probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mirna10probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mirna10probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirna10probe/bioconductor-mirna10probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirna10probe/bioconductor-mirna10probe_2.18.0_src_all.tar.gz"], "md5": "8bfa6cdfeee1c563b4881214bd5d4ce1", "fn": "mirna10probe_2.18.0.tar.gz"}, "mirna20cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mirna20cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mirna20cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirna20cdf/bioconductor-mirna20cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirna20cdf/bioconductor-mirna20cdf_2.18.0_src_all.tar.gz"], "md5": "56f7807673ff108427ae7f6bdf85ae1c", "fn": "mirna20cdf_2.18.0.tar.gz"}, "mirnatap.db-0.99.10": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/miRNAtap.db_0.99.10.tar.gz", "https://bioarchive.galaxyproject.org/miRNAtap.db_0.99.10.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirnatap.db/bioconductor-mirnatap.db_0.99.10_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirnatap.db/bioconductor-mirnatap.db_0.99.10_src_all.tar.gz"], "md5": "48010280b68d6f1ddbff3b374132ce0a", "fn": "miRNAtap.db_0.99.10.tar.gz"}, "mm24kresogen.db-2.5.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mm24kresogen.db_2.5.0.tar.gz", "https://bioarchive.galaxyproject.org/mm24kresogen.db_2.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mm24kresogen.db/bioconductor-mm24kresogen.db_2.5.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mm24kresogen.db/bioconductor-mm24kresogen.db_2.5.0_src_all.tar.gz"], "md5": "437f5d4bc225ee500af1ecc2d4da472b", "fn": "mm24kresogen.db_2.5.0.tar.gz"}, "mmagilentdesign026655.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/MmAgilentDesign026655.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/MmAgilentDesign026655.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mmagilentdesign026655.db/bioconductor-mmagilentdesign026655.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mmagilentdesign026655.db/bioconductor-mmagilentdesign026655.db_3.2.3_src_all.tar.gz"], "md5": "7ef619bd2c74f22ea4f3c2b2c4131fe9", "fn": "MmAgilentDesign026655.db_3.2.3.tar.gz"}, "moe430a.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/moe430a.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/moe430a.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430a.db/bioconductor-moe430a.db_3.13.0_src_all.tar.gz"], "md5": "2bcdace3c55437bc8428b99064e486b1", "fn": "moe430a.db_3.13.0.tar.gz"}, "moe430acdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/moe430acdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/moe430acdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430acdf/bioconductor-moe430acdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430acdf/bioconductor-moe430acdf_2.18.0_src_all.tar.gz"], "md5": "b03f1295fc483f0d782a4615e8ca0137", "fn": "moe430acdf_2.18.0.tar.gz"}, "moe430aprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/moe430aprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/moe430aprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430aprobe/bioconductor-moe430aprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430aprobe/bioconductor-moe430aprobe_2.18.0_src_all.tar.gz"], "md5": "0aa83189d04599a65211d1a2f0a51c8f", "fn": "moe430aprobe_2.18.0.tar.gz"}, "moe430b.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/moe430b.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/moe430b.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430b.db/bioconductor-moe430b.db_3.13.0_src_all.tar.gz"], "md5": "2d8a80b9d3342fb943087cc327c824e7", "fn": "moe430b.db_3.13.0.tar.gz"}, "moe430bcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/moe430bcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/moe430bcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430bcdf/bioconductor-moe430bcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430bcdf/bioconductor-moe430bcdf_2.18.0_src_all.tar.gz"], "md5": "b7112dcf8ccfe4e079ca67ff62046f2e", "fn": "moe430bcdf_2.18.0.tar.gz"}, "moe430bprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/moe430bprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/moe430bprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430bprobe/bioconductor-moe430bprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moe430bprobe/bioconductor-moe430bprobe_2.18.0_src_all.tar.gz"], "md5": "1368e6f4225babe7a693ccd39a3a436a", "fn": "moe430bprobe_2.18.0.tar.gz"}, "moex10stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/moex10stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/moex10stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moex10stprobeset.db/bioconductor-moex10stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "b1c12c80a4424e2854beab9dc796cb00", "fn": "moex10stprobeset.db_8.8.0.tar.gz"}, "moex10sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/moex10sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/moex10sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moex10sttranscriptcluster.db/bioconductor-moex10sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "bc3357b3c77ab7bf1dfb66f5f7da36ec", "fn": "moex10sttranscriptcluster.db_8.8.0.tar.gz"}, "moexexonprobesetlocation-1.15.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/MoExExonProbesetLocation_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/MoExExonProbesetLocation_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moexexonprobesetlocation/bioconductor-moexexonprobesetlocation_1.15.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-moexexonprobesetlocation/bioconductor-moexexonprobesetlocation_1.15.0_src_all.tar.gz"], "md5": "07eea205fce2a8cf4585fa7e71fb0057", "fn": "MoExExonProbesetLocation_1.15.0.tar.gz"}, "mogene.1.0.st.v1frmavecs-1.1.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mogene.1.0.st.v1frmavecs_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene.1.0.st.v1frmavecs_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene.1.0.st.v1frmavecs/bioconductor-mogene.1.0.st.v1frmavecs_1.1.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene.1.0.st.v1frmavecs/bioconductor-mogene.1.0.st.v1frmavecs_1.1.0_src_all.tar.gz"], "md5": "b46f76903d0f19b85e8fa30347813ff5", "fn": "mogene.1.0.st.v1frmavecs_1.1.0.tar.gz"}, "mogene10stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mogene10stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene10stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene10stprobeset.db/bioconductor-mogene10stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "570d4cf3fcc42d1e9b54237b9e4eb5f7", "fn": "mogene10stprobeset.db_8.8.0.tar.gz"}, "mogene10sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mogene10sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene10sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene10sttranscriptcluster.db/bioconductor-mogene10sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "9553a8ecefad2baa7241c6b6bb8013f5", "fn": "mogene10sttranscriptcluster.db_8.8.0.tar.gz"}, "mogene10stv1cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mogene10stv1cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene10stv1cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene10stv1cdf/bioconductor-mogene10stv1cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene10stv1cdf/bioconductor-mogene10stv1cdf_2.18.0_src_all.tar.gz"], "md5": "9c0271f5d6493290fc47f041a8c3f925", "fn": "mogene10stv1cdf_2.18.0.tar.gz"}, "mogene10stv1probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mogene10stv1probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene10stv1probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene10stv1probe/bioconductor-mogene10stv1probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene10stv1probe/bioconductor-mogene10stv1probe_2.18.0_src_all.tar.gz"], "md5": "63cba1e2a0edee9f201267057fddb0fa", "fn": "mogene10stv1probe_2.18.0.tar.gz"}, "mogene11stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mogene11stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene11stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene11stprobeset.db/bioconductor-mogene11stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "1fba63da3f550e814a58c09d24d61cc0", "fn": "mogene11stprobeset.db_8.8.0.tar.gz"}, "mogene11sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mogene11sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene11sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene11sttranscriptcluster.db/bioconductor-mogene11sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "2a3bf07a4794e2349b7d09368dcb7d18", "fn": "mogene11sttranscriptcluster.db_8.8.0.tar.gz"}, "mogene20stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mogene20stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene20stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene20stprobeset.db/bioconductor-mogene20stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "a64ddbf33e4f2b96301452e808d0e81a", "fn": "mogene20stprobeset.db_8.8.0.tar.gz"}, "mogene20sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mogene20sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene20sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene20sttranscriptcluster.db/bioconductor-mogene20sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "e00e56d47bd19169875690e8e2129156", "fn": "mogene20sttranscriptcluster.db_8.8.0.tar.gz"}, "mogene21stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mogene21stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene21stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene21stprobeset.db/bioconductor-mogene21stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "d6b3c352329b46493a20f6c27db05d43", "fn": "mogene21stprobeset.db_8.8.0.tar.gz"}, "mogene21sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mogene21sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mogene21sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mogene21sttranscriptcluster.db/bioconductor-mogene21sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "10aaecc97bf06bfe770496b99612837a", "fn": "mogene21sttranscriptcluster.db_8.8.0.tar.gz"}, "mouse.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/mouse.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse.db0/bioconductor-mouse.db0_3.16.0_src_all.tar.gz"], "md5": "aac1d127bbce6e9a574a573335113db4", "fn": "mouse.db0_3.16.0.tar.gz"}, "mouse4302.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mouse4302.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse4302.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302.db/bioconductor-mouse4302.db_3.13.0_src_all.tar.gz"], "md5": "4ecaa53d32faca4199ba712c0e8ee570", "fn": "mouse4302.db_3.13.0.tar.gz"}, "mouse4302cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mouse4302cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse4302cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302cdf/bioconductor-mouse4302cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302cdf/bioconductor-mouse4302cdf_2.18.0_src_all.tar.gz"], "md5": "bda3463613f958de35c58777db05cec2", "fn": "mouse4302cdf_2.18.0.tar.gz"}, "mouse4302frmavecs-1.5.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mouse4302frmavecs_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse4302frmavecs_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302frmavecs/bioconductor-mouse4302frmavecs_1.5.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302frmavecs/bioconductor-mouse4302frmavecs_1.5.0_src_all.tar.gz"], "md5": "ec144b381abbe54d696356c1c124e372", "fn": "mouse4302frmavecs_1.5.0.tar.gz"}, "mouse4302probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mouse4302probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse4302probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302probe/bioconductor-mouse4302probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302probe/bioconductor-mouse4302probe_2.18.0_src_all.tar.gz"], "md5": "7116787a7db241a545e79e419a8cfa0d", "fn": "mouse4302probe_2.18.0.tar.gz"}, "mouse430a2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mouse430a2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse430a2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse430a2.db/bioconductor-mouse430a2.db_3.13.0_src_all.tar.gz"], "md5": "0f1d053517af5f973f3cc49289cca1e5", "fn": "mouse430a2.db_3.13.0.tar.gz"}, "mouse430a2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mouse430a2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse430a2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse430a2cdf/bioconductor-mouse430a2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse430a2cdf/bioconductor-mouse430a2cdf_2.18.0_src_all.tar.gz"], "md5": "1114c0415d1200bc21ad205e0830b075", "fn": "mouse430a2cdf_2.18.0.tar.gz"}, "mouse430a2frmavecs-1.3.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mouse430a2frmavecs_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse430a2frmavecs_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse430a2frmavecs/bioconductor-mouse430a2frmavecs_1.3.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse430a2frmavecs/bioconductor-mouse430a2frmavecs_1.3.0_src_all.tar.gz"], "md5": "3bcb8de9182bbb8de5d560748eafa0cc", "fn": "mouse430a2frmavecs_1.3.0.tar.gz"}, "mouse430a2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mouse430a2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse430a2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse430a2probe/bioconductor-mouse430a2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse430a2probe/bioconductor-mouse430a2probe_2.18.0_src_all.tar.gz"], "md5": "bb3c34477d4fcf03a539772011118795", "fn": "mouse430a2probe_2.18.0.tar.gz"}, "mousechrloc-2.1.6": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mouseCHRLOC_2.1.6.tar.gz", "https://bioarchive.galaxyproject.org/mouseCHRLOC_2.1.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousechrloc/bioconductor-mousechrloc_2.1.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousechrloc/bioconductor-mousechrloc_2.1.6_src_all.tar.gz"], "md5": "0b81d7391e628cc355af4de3c5585a5f", "fn": "mouseCHRLOC_2.1.6.tar.gz"}, "mpedbarray.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mpedbarray.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/mpedbarray.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mpedbarray.db/bioconductor-mpedbarray.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mpedbarray.db/bioconductor-mpedbarray.db_3.2.3_src_all.tar.gz"], "md5": "7bcd1fee1554b6f8844c9bf30b7db4ef", "fn": "mpedbarray.db_3.2.3.tar.gz"}, "mta10probeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mta10probeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mta10probeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mta10probeset.db/bioconductor-mta10probeset.db_8.8.0_src_all.tar.gz"], "md5": "84517c6b354690cd72ccefbe3b39d8e1", "fn": "mta10probeset.db_8.8.0.tar.gz"}, "mta10transcriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mta10transcriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/mta10transcriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mta10transcriptcluster.db/bioconductor-mta10transcriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "bfd13b16b71ac2cfc82f40f2d102892b", "fn": "mta10transcriptcluster.db_8.8.0.tar.gz"}, "mu11ksuba.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mu11ksuba.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mu11ksuba.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksuba.db/bioconductor-mu11ksuba.db_3.13.0_src_all.tar.gz"], "md5": "73d80611d1eaf8ee1eb37ebc469d97e9", "fn": "mu11ksuba.db_3.13.0.tar.gz"}, "mu11ksubacdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mu11ksubacdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu11ksubacdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksubacdf/bioconductor-mu11ksubacdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksubacdf/bioconductor-mu11ksubacdf_2.18.0_src_all.tar.gz"], "md5": "52fb8ac56435775022fb62f40efafd22", "fn": "mu11ksubacdf_2.18.0.tar.gz"}, "mu11ksubaprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mu11ksubaprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu11ksubaprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksubaprobe/bioconductor-mu11ksubaprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksubaprobe/bioconductor-mu11ksubaprobe_2.18.0_src_all.tar.gz"], "md5": "813cd0750cca6ff0cfb696b83286177e", "fn": "mu11ksubaprobe_2.18.0.tar.gz"}, "mu11ksubb.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mu11ksubb.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mu11ksubb.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksubb.db/bioconductor-mu11ksubb.db_3.13.0_src_all.tar.gz"], "md5": "2b61d911c3595843e80041949cb79b41", "fn": "mu11ksubb.db_3.13.0.tar.gz"}, "mu11ksubbcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mu11ksubbcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu11ksubbcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksubbcdf/bioconductor-mu11ksubbcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksubbcdf/bioconductor-mu11ksubbcdf_2.18.0_src_all.tar.gz"], "md5": "f9691ea74e19dfe57bf6cca6ed396947", "fn": "mu11ksubbcdf_2.18.0.tar.gz"}, "mu11ksubbprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mu11ksubbprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu11ksubbprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksubbprobe/bioconductor-mu11ksubbprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu11ksubbprobe/bioconductor-mu11ksubbprobe_2.18.0_src_all.tar.gz"], "md5": "28d162e18e4e16e3c6db47195d2ea0ac", "fn": "mu11ksubbprobe_2.18.0.tar.gz"}, "mu15v1.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/Mu15v1.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/Mu15v1.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu15v1.db/bioconductor-mu15v1.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu15v1.db/bioconductor-mu15v1.db_3.2.3_src_all.tar.gz"], "md5": "e9297b5fe223b046bc65dc6ea0b4376d", "fn": "Mu15v1.db_3.2.3.tar.gz"}, "mu19ksuba.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mu19ksuba.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mu19ksuba.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu19ksuba.db/bioconductor-mu19ksuba.db_3.13.0_src_all.tar.gz"], "md5": "c057d8793f2db914a93d2e1f5a3af178", "fn": "mu19ksuba.db_3.13.0.tar.gz"}, "mu19ksubacdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mu19ksubacdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu19ksubacdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu19ksubacdf/bioconductor-mu19ksubacdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu19ksubacdf/bioconductor-mu19ksubacdf_2.18.0_src_all.tar.gz"], "md5": "83a9e7a3bac665b655786e66dbd77848", "fn": "mu19ksubacdf_2.18.0.tar.gz"}, "mu19ksubb.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mu19ksubb.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mu19ksubb.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu19ksubb.db/bioconductor-mu19ksubb.db_3.13.0_src_all.tar.gz"], "md5": "1b177a3b5626c825c91e7c25e0acd897", "fn": "mu19ksubb.db_3.13.0.tar.gz"}, "mu19ksubbcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mu19ksubbcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu19ksubbcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu19ksubbcdf/bioconductor-mu19ksubbcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu19ksubbcdf/bioconductor-mu19ksubbcdf_2.18.0_src_all.tar.gz"], "md5": "35e5ebcb4cb51950a85c1e3622bb39f0", "fn": "mu19ksubbcdf_2.18.0.tar.gz"}, "mu19ksubc.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mu19ksubc.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/mu19ksubc.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu19ksubc.db/bioconductor-mu19ksubc.db_3.13.0_src_all.tar.gz"], "md5": "bef37c9cd01032e9f1fb177a1af8cba4", "fn": "mu19ksubc.db_3.13.0.tar.gz"}, "mu19ksubccdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mu19ksubccdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu19ksubccdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu19ksubccdf/bioconductor-mu19ksubccdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu19ksubccdf/bioconductor-mu19ksubccdf_2.18.0_src_all.tar.gz"], "md5": "e53ef2716f88022e5e41e2cd857fc2a3", "fn": "mu19ksubccdf_2.18.0.tar.gz"}, "mu22v3.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/Mu22v3.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/Mu22v3.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu22v3.db/bioconductor-mu22v3.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu22v3.db/bioconductor-mu22v3.db_3.2.3_src_all.tar.gz"], "md5": "44aaebe909be9b0108256194c55cf6fb", "fn": "Mu22v3.db_3.2.3.tar.gz"}, "mu6500subacdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mu6500subacdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu6500subacdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu6500subacdf/bioconductor-mu6500subacdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu6500subacdf/bioconductor-mu6500subacdf_2.18.0_src_all.tar.gz"], "md5": "e72152fc4bae307e3858160e018b7f92", "fn": "mu6500subacdf_2.18.0.tar.gz"}, "mu6500subbcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mu6500subbcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu6500subbcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu6500subbcdf/bioconductor-mu6500subbcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu6500subbcdf/bioconductor-mu6500subbcdf_2.18.0_src_all.tar.gz"], "md5": "5000bea2a018b4b6ec05cda111438bc1", "fn": "mu6500subbcdf_2.18.0.tar.gz"}, "mu6500subccdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mu6500subccdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu6500subccdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu6500subccdf/bioconductor-mu6500subccdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu6500subccdf/bioconductor-mu6500subccdf_2.18.0_src_all.tar.gz"], "md5": "c7cbbe6c70a0a3ae11600ad6c0e540c1", "fn": "mu6500subccdf_2.18.0.tar.gz"}, "mu6500subdcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mu6500subdcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mu6500subdcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu6500subdcdf/bioconductor-mu6500subdcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mu6500subdcdf/bioconductor-mu6500subdcdf_2.18.0_src_all.tar.gz"], "md5": "a614674e8bc60fefd8520dd25d45f8d0", "fn": "mu6500subdcdf_2.18.0.tar.gz"}, "mus.musculus-1.3.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/Mus.musculus_1.3.1.tar.gz", "https://bioarchive.galaxyproject.org/Mus.musculus_1.3.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mus.musculus/bioconductor-mus.musculus_1.3.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mus.musculus/bioconductor-mus.musculus_1.3.1_src_all.tar.gz"], "md5": "1b8defe64c2dd308a88d1ac7a4ce04b9", "fn": "Mus.musculus_1.3.1.tar.gz"}, "mwgcod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mwgcod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/mwgcod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mwgcod.db/bioconductor-mwgcod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mwgcod.db/bioconductor-mwgcod.db_3.4.0_src_all.tar.gz"], "md5": "3d6e2af6b05d6e07a212c043dc9d37c4", "fn": "mwgcod.db_3.4.0.tar.gz"}, "norway981.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/Norway981.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/Norway981.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-norway981.db/bioconductor-norway981.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-norway981.db/bioconductor-norway981.db_3.2.3_src_all.tar.gz"], "md5": "85367390919bba9018438585e59fbb87", "fn": "Norway981.db_3.2.3.tar.gz"}, "nugohs1a520180.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/nugohs1a520180.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/nugohs1a520180.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180.db/bioconductor-nugohs1a520180.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180.db/bioconductor-nugohs1a520180.db_3.4.0_src_all.tar.gz"], "md5": "f83701b35b07e69e1ad503b546bb5eaf", "fn": "nugohs1a520180.db_3.4.0.tar.gz"}, "nugohs1a520180cdf-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/nugohs1a520180cdf_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/nugohs1a520180cdf_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180cdf/bioconductor-nugohs1a520180cdf_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180cdf/bioconductor-nugohs1a520180cdf_3.4.0_src_all.tar.gz"], "md5": "aa152658a4a801cc0edb552a98aee841", "fn": "nugohs1a520180cdf_3.4.0.tar.gz"}, "nugohs1a520180probe-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/nugohs1a520180probe_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/nugohs1a520180probe_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180probe/bioconductor-nugohs1a520180probe_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180probe/bioconductor-nugohs1a520180probe_3.4.0_src_all.tar.gz"], "md5": "6acf20ac4a799eaae97d0a64426d6ac3", "fn": "nugohs1a520180probe_3.4.0.tar.gz"}, "nugomm1a520177.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/nugomm1a520177.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/nugomm1a520177.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177.db/bioconductor-nugomm1a520177.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177.db/bioconductor-nugomm1a520177.db_3.4.0_src_all.tar.gz"], "md5": "99f69ea2cbb80a79bedee99e3d726e50", "fn": "nugomm1a520177.db_3.4.0.tar.gz"}, "nugomm1a520177cdf-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/nugomm1a520177cdf_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/nugomm1a520177cdf_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177cdf/bioconductor-nugomm1a520177cdf_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177cdf/bioconductor-nugomm1a520177cdf_3.4.0_src_all.tar.gz"], "md5": "fc60c2018580decaea30f09de55142fb", "fn": "nugomm1a520177cdf_3.4.0.tar.gz"}, "nugomm1a520177probe-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/nugomm1a520177probe_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/nugomm1a520177probe_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177probe/bioconductor-nugomm1a520177probe_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177probe/bioconductor-nugomm1a520177probe_3.4.0_src_all.tar.gz"], "md5": "7fa974389ad2be6ebda8810496221a9b", "fn": "nugomm1a520177probe_3.4.0.tar.gz"}, "oligodata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/oligoData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/oligoData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-oligodata/bioconductor-oligodata_1.8.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-oligodata/bioconductor-oligodata_1.8.0_src_all.tar.gz"], "md5": "9625cfd4b31bb575c4029a0632a7ee12", "fn": "oligoData_1.8.0.tar.gz"}, "ontoprocdata-0.99.9901": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ontoProcData_0.99.9901.tar.gz", "https://bioarchive.galaxyproject.org/ontoProcData_0.99.9901.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ontoprocdata/bioconductor-ontoprocdata_0.99.9901_src_all.tar.gz"], "md5": "d4160c1fc853db468ce73c7fe62ca00f", "fn": "ontoProcData_0.99.9901.tar.gz"}, "operonhumanv3.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/OperonHumanV3.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/OperonHumanV3.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-operonhumanv3.db/bioconductor-operonhumanv3.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-operonhumanv3.db/bioconductor-operonhumanv3.db_3.2.3_src_all.tar.gz"], "md5": "648da5d4d63c6c8327f6035ee09f2b65", "fn": "OperonHumanV3.db_3.2.3.tar.gz"}, "org.ag.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Ag.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ag.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ag.eg.db/bioconductor-org.ag.eg.db_3.16.0_src_all.tar.gz"], "md5": "93f7b3f4daff9242d79600e0de6794e2", "fn": "org.Ag.eg.db_3.16.0.tar.gz"}, "org.at.tair.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.At.tair.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.At.tair.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.at.tair.db/bioconductor-org.at.tair.db_3.16.0_src_all.tar.gz"], "md5": "7caa9f7667fb06ad359d752dee6ebcd2", "fn": "org.At.tair.db_3.16.0.tar.gz"}, "org.bt.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Bt.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Bt.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.bt.eg.db/bioconductor-org.bt.eg.db_3.16.0_src_all.tar.gz"], "md5": "d48424ecbe51745f86c8cfeea20a92d3", "fn": "org.Bt.eg.db_3.16.0.tar.gz"}, "org.ce.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Ce.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ce.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ce.eg.db/bioconductor-org.ce.eg.db_3.16.0_src_all.tar.gz"], "md5": "f72ee64f0cb5ff05d229feee3314dcd6", "fn": "org.Ce.eg.db_3.16.0.tar.gz"}, "org.cf.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Cf.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Cf.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.cf.eg.db/bioconductor-org.cf.eg.db_3.16.0_src_all.tar.gz"], "md5": "c50ad298c773c322e5131b5785ed66f2", "fn": "org.Cf.eg.db_3.16.0.tar.gz"}, "org.dm.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Dm.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Dm.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.dm.eg.db/bioconductor-org.dm.eg.db_3.16.0_src_all.tar.gz"], "md5": "797e55b8475e3429c8d25fe567e72c89", "fn": "org.Dm.eg.db_3.16.0.tar.gz"}, "org.dr.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Dr.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Dr.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.dr.eg.db/bioconductor-org.dr.eg.db_3.16.0_src_all.tar.gz"], "md5": "fd4fc1c4ac109140cdc5464f8d528c14", "fn": "org.Dr.eg.db_3.16.0.tar.gz"}, "org.eck12.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.EcK12.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.EcK12.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.eck12.eg.db/bioconductor-org.eck12.eg.db_3.16.0_src_all.tar.gz"], "md5": "5316dce945864ef99d72e9142d9564a6", "fn": "org.EcK12.eg.db_3.16.0.tar.gz"}, "org.ecsakai.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.EcSakai.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.EcSakai.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ecsakai.eg.db/bioconductor-org.ecsakai.eg.db_3.16.0_src_all.tar.gz"], "md5": "8393978e486f24d3274e564116a7b832", "fn": "org.EcSakai.eg.db_3.16.0.tar.gz"}, "org.gg.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Gg.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Gg.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.gg.eg.db/bioconductor-org.gg.eg.db_3.16.0_src_all.tar.gz"], "md5": "5e6701c610a8c90a2a5fd25f5a8ead0b", "fn": "org.Gg.eg.db_3.16.0.tar.gz"}, "org.hs.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Hs.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Hs.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.hs.eg.db/bioconductor-org.hs.eg.db_3.16.0_src_all.tar.gz"], "md5": "1d73f40088c6bc6c46fd1d805d165cc2", "fn": "org.Hs.eg.db_3.16.0.tar.gz"}, "org.mm.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Mm.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Mm.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.mm.eg.db/bioconductor-org.mm.eg.db_3.16.0_src_all.tar.gz"], "md5": "18c83b93687c5a618d5220cf5b0666c2", "fn": "org.Mm.eg.db_3.16.0.tar.gz"}, "org.mmu.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Mmu.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Mmu.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.mmu.eg.db/bioconductor-org.mmu.eg.db_3.16.0_src_all.tar.gz"], "md5": "2acd2c91068222d570510d4b41729ecb", "fn": "org.Mmu.eg.db_3.16.0.tar.gz"}, "org.mxanthus.db-1.0.27": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Mxanthus.db_1.0.27.tar.gz", "https://bioarchive.galaxyproject.org/org.Mxanthus.db_1.0.27.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.mxanthus.db/bioconductor-org.mxanthus.db_1.0.27_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.mxanthus.db/bioconductor-org.mxanthus.db_1.0.27_src_all.tar.gz"], "md5": "929fa3dd8c5e1fdbcdbcbcd468845798", "fn": "org.Mxanthus.db_1.0.27.tar.gz"}, "org.pt.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Pt.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Pt.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.pt.eg.db/bioconductor-org.pt.eg.db_3.16.0_src_all.tar.gz"], "md5": "c8636440d961f2c46bc24afe784bea5f", "fn": "org.Pt.eg.db_3.16.0.tar.gz"}, "org.rn.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Rn.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Rn.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.rn.eg.db/bioconductor-org.rn.eg.db_3.16.0_src_all.tar.gz"], "md5": "307cfbfd11055ffa16aa41fddf7d47fe", "fn": "org.Rn.eg.db_3.16.0.tar.gz"}, "org.sc.sgd.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Sc.sgd.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Sc.sgd.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.sc.sgd.db/bioconductor-org.sc.sgd.db_3.16.0_src_all.tar.gz"], "md5": "207e829a62e588b5f8a3149accefabdc", "fn": "org.Sc.sgd.db_3.16.0.tar.gz"}, "org.ss.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Ss.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ss.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ss.eg.db/bioconductor-org.ss.eg.db_3.16.0_src_all.tar.gz"], "md5": "91cb8de8b50e586a3c327835afc77a23", "fn": "org.Ss.eg.db_3.16.0.tar.gz"}, "org.xl.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/org.Xl.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Xl.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.xl.eg.db/bioconductor-org.xl.eg.db_3.16.0_src_all.tar.gz"], "md5": "8fe571e4d82fbe3f3886022fa68e92d3", "fn": "org.Xl.eg.db_3.16.0.tar.gz"}, "orthology.eg.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/Orthology.eg.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/Orthology.eg.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-orthology.eg.db/bioconductor-orthology.eg.db_3.16.0_src_all.tar.gz"], "md5": "43e43cd1ca14213378047fc95e83b88c", "fn": "Orthology.eg.db_3.16.0.tar.gz"}, "paeg1acdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/paeg1acdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/paeg1acdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-paeg1acdf/bioconductor-paeg1acdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-paeg1acdf/bioconductor-paeg1acdf_2.18.0_src_all.tar.gz"], "md5": "73af974112051db0f715518393e84726", "fn": "paeg1acdf_2.18.0.tar.gz"}, "paeg1aprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/paeg1aprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/paeg1aprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-paeg1aprobe/bioconductor-paeg1aprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-paeg1aprobe/bioconductor-paeg1aprobe_2.18.0_src_all.tar.gz"], "md5": "493fa1fc7b92a78c8114b65038113c42", "fn": "paeg1aprobe_2.18.0.tar.gz"}, "panther.db-1.0.11": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PANTHER.db_1.0.11.tar.gz", "https://bioarchive.galaxyproject.org/PANTHER.db_1.0.11.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-panther.db/bioconductor-panther.db_1.0.11_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-panther.db/bioconductor-panther.db_1.0.11_src_all.tar.gz"], "md5": "561f6b164b27f6dc4287f0d7fd6bb8b3", "fn": "PANTHER.db_1.0.11.tar.gz"}, "partheenmetadata.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/PartheenMetaData.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/PartheenMetaData.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-partheenmetadata.db/bioconductor-partheenmetadata.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-partheenmetadata.db/bioconductor-partheenmetadata.db_3.2.3_src_all.tar.gz"], "md5": "1c9fd27e13a341b9aba9a235a67ce978", "fn": "PartheenMetaData.db_3.2.3.tar.gz"}, "pd.081229.hg18.promoter.medip.hx1-0.99.4": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.081229.hg18.promoter.medip.hx1_0.99.4.tar.gz", "https://bioarchive.galaxyproject.org/pd.081229.hg18.promoter.medip.hx1_0.99.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.081229.hg18.promoter.medip.hx1/bioconductor-pd.081229.hg18.promoter.medip.hx1_0.99.4_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.081229.hg18.promoter.medip.hx1/bioconductor-pd.081229.hg18.promoter.medip.hx1_0.99.4_src_all.tar.gz"], "md5": "f3c240fa0d4503e94047be5ee323856b", "fn": "pd.081229.hg18.promoter.medip.hx1_0.99.4.tar.gz"}, "pd.2006.07.18.hg18.refseq.promoter-1.8.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.2006.07.18.hg18.refseq.promoter_1.8.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.2006.07.18.hg18.refseq.promoter_1.8.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.2006.07.18.hg18.refseq.promoter/bioconductor-pd.2006.07.18.hg18.refseq.promoter_1.8.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.2006.07.18.hg18.refseq.promoter/bioconductor-pd.2006.07.18.hg18.refseq.promoter_1.8.1_src_all.tar.gz"], "md5": "00838332d75b82d212078a9957f495df", "fn": "pd.2006.07.18.hg18.refseq.promoter_1.8.1.tar.gz"}, "pd.2006.07.18.mm8.refseq.promoter-0.99.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.2006.07.18.mm8.refseq.promoter_0.99.3.tar.gz", "https://bioarchive.galaxyproject.org/pd.2006.07.18.mm8.refseq.promoter_0.99.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.2006.07.18.mm8.refseq.promoter/bioconductor-pd.2006.07.18.mm8.refseq.promoter_0.99.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.2006.07.18.mm8.refseq.promoter/bioconductor-pd.2006.07.18.mm8.refseq.promoter_0.99.3_src_all.tar.gz"], "md5": "084b0a6759fd96d1bc775dd4c66c42b0", "fn": "pd.2006.07.18.mm8.refseq.promoter_0.99.3.tar.gz"}, "pd.2006.10.31.rn34.refseq.promoter-0.99.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.2006.10.31.rn34.refseq.promoter_0.99.3.tar.gz", "https://bioarchive.galaxyproject.org/pd.2006.10.31.rn34.refseq.promoter_0.99.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.2006.10.31.rn34.refseq.promoter/bioconductor-pd.2006.10.31.rn34.refseq.promoter_0.99.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.2006.10.31.rn34.refseq.promoter/bioconductor-pd.2006.10.31.rn34.refseq.promoter_0.99.3_src_all.tar.gz"], "md5": "ab5bb767ad29b213e5a969a5fc51ee7d", "fn": "pd.2006.10.31.rn34.refseq.promoter_0.99.3.tar.gz"}, "pd.ag-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.ag_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.ag_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ag/bioconductor-pd.ag_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ag/bioconductor-pd.ag_3.12.0_src_all.tar.gz"], "md5": "21fb288536568ff010ad4847b671f9d6", "fn": "pd.ag_3.12.0.tar.gz"}, "pd.aragene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.aragene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.aragene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.aragene.1.0.st/bioconductor-pd.aragene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.aragene.1.0.st/bioconductor-pd.aragene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "ff87a0793fd4b713c4a45b6c1d4a4977", "fn": "pd.aragene.1.0.st_3.12.0.tar.gz"}, "pd.aragene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.aragene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.aragene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.aragene.1.1.st/bioconductor-pd.aragene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.aragene.1.1.st/bioconductor-pd.aragene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "828ad790eb2495e396d7fcd9bcbf9133", "fn": "pd.aragene.1.1.st_3.12.0.tar.gz"}, "pd.ath1.121501-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.ath1.121501_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.ath1.121501_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ath1.121501/bioconductor-pd.ath1.121501_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ath1.121501/bioconductor-pd.ath1.121501_3.12.0_src_all.tar.gz"], "md5": "d7ed8640f0deac552e0083a091e72a72", "fn": "pd.ath1.121501_3.12.0.tar.gz"}, "pd.barley1-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.barley1_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.barley1_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.barley1/bioconductor-pd.barley1_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.barley1/bioconductor-pd.barley1_3.12.0_src_all.tar.gz"], "md5": "b8d11f5ad42e75f7a91931b46d449c1a", "fn": "pd.barley1_3.12.0.tar.gz"}, "pd.bovgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.bovgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.bovgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.bovgene.1.0.st/bioconductor-pd.bovgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.bovgene.1.0.st/bioconductor-pd.bovgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "6e9747d13aee7825722562ccc49ad35f", "fn": "pd.bovgene.1.0.st_3.12.0.tar.gz"}, "pd.bovgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.bovgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.bovgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.bovgene.1.1.st/bioconductor-pd.bovgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.bovgene.1.1.st/bioconductor-pd.bovgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "342246c0a76755fcca458cd723b3e98e", "fn": "pd.bovgene.1.1.st_3.12.0.tar.gz"}, "pd.bovine-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.bovine_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.bovine_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.bovine/bioconductor-pd.bovine_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.bovine/bioconductor-pd.bovine_3.12.0_src_all.tar.gz"], "md5": "6c7026dba53b54b547b1f1e135d043b3", "fn": "pd.bovine_3.12.0.tar.gz"}, "pd.bsubtilis-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.bsubtilis_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.bsubtilis_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.bsubtilis/bioconductor-pd.bsubtilis_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.bsubtilis/bioconductor-pd.bsubtilis_3.12.0_src_all.tar.gz"], "md5": "2261d8b0ec178beb432d71eafd90ec9a", "fn": "pd.bsubtilis_3.12.0.tar.gz"}, "pd.cangene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.cangene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.cangene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cangene.1.0.st/bioconductor-pd.cangene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cangene.1.0.st/bioconductor-pd.cangene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "0a39d6378193e3f7d31a7210f6766eaf", "fn": "pd.cangene.1.0.st_3.12.0.tar.gz"}, "pd.cangene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.cangene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.cangene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cangene.1.1.st/bioconductor-pd.cangene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cangene.1.1.st/bioconductor-pd.cangene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "946074601e7bee72f3b3dd6ae6b3bc33", "fn": "pd.cangene.1.1.st_3.12.0.tar.gz"}, "pd.canine-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.canine_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.canine_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.canine/bioconductor-pd.canine_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.canine/bioconductor-pd.canine_3.12.0_src_all.tar.gz"], "md5": "5b40fe9e40d0b7f36d338e413d121ba7", "fn": "pd.canine_3.12.0.tar.gz"}, "pd.canine.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.canine.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.canine.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.canine.2/bioconductor-pd.canine.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.canine.2/bioconductor-pd.canine.2_3.12.0_src_all.tar.gz"], "md5": "bc918d1953a3c7ac7168b60a53405a93", "fn": "pd.canine.2_3.12.0.tar.gz"}, "pd.celegans-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.celegans_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.celegans_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.celegans/bioconductor-pd.celegans_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.celegans/bioconductor-pd.celegans_3.12.0_src_all.tar.gz"], "md5": "b90ea2e071522bb340c103a1c8270205", "fn": "pd.celegans_3.12.0.tar.gz"}, "pd.charm.hg18.example-0.99.4": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.charm.hg18.example_0.99.4.tar.gz", "https://bioarchive.galaxyproject.org/pd.charm.hg18.example_0.99.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.charm.hg18.example/bioconductor-pd.charm.hg18.example_0.99.4_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.charm.hg18.example/bioconductor-pd.charm.hg18.example_0.99.4_src_all.tar.gz"], "md5": "e201d4281a23c202f57bae1135e226b4", "fn": "pd.charm.hg18.example_0.99.4.tar.gz"}, "pd.chicken-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.chicken_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.chicken_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chicken/bioconductor-pd.chicken_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chicken/bioconductor-pd.chicken_3.12.0_src_all.tar.gz"], "md5": "af79b6d0910621910e72ea374499e5eb", "fn": "pd.chicken_3.12.0.tar.gz"}, "pd.chigene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.chigene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.chigene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chigene.1.0.st/bioconductor-pd.chigene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chigene.1.0.st/bioconductor-pd.chigene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "e37cb047678fabb1801109d4efd16773", "fn": "pd.chigene.1.0.st_3.12.0.tar.gz"}, "pd.chigene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.chigene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.chigene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chigene.1.1.st/bioconductor-pd.chigene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chigene.1.1.st/bioconductor-pd.chigene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "bec602b45961607f5a4571977d54e015", "fn": "pd.chigene.1.1.st_3.12.0.tar.gz"}, "pd.chogene.2.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.chogene.2.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.chogene.2.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chogene.2.0.st/bioconductor-pd.chogene.2.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chogene.2.0.st/bioconductor-pd.chogene.2.0.st_3.12.0_src_all.tar.gz"], "md5": "641718e3d172838185a200bac3d32433", "fn": "pd.chogene.2.0.st_3.12.0.tar.gz"}, "pd.chogene.2.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.chogene.2.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.chogene.2.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chogene.2.1.st/bioconductor-pd.chogene.2.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.chogene.2.1.st/bioconductor-pd.chogene.2.1.st_3.12.0_src_all.tar.gz"], "md5": "ed25825e58a514cdde70b961bce9b4d7", "fn": "pd.chogene.2.1.st_3.12.0.tar.gz"}, "pd.citrus-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.citrus_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.citrus_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.citrus/bioconductor-pd.citrus_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.citrus/bioconductor-pd.citrus_3.12.0_src_all.tar.gz"], "md5": "dee9b3298b84e7dd5152f48ad449b15a", "fn": "pd.citrus_3.12.0.tar.gz"}, "pd.clariom.d.human-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.clariom.d.human_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.clariom.d.human_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.d.human/bioconductor-pd.clariom.d.human_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.d.human/bioconductor-pd.clariom.d.human_3.14.1_src_all.tar.gz"], "md5": "9d3505af53cc7c99980f29c527f0f37d", "fn": "pd.clariom.d.human_3.14.1.tar.gz"}, "pd.clariom.s.human-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.clariom.s.human_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.clariom.s.human_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.human/bioconductor-pd.clariom.s.human_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.human/bioconductor-pd.clariom.s.human_3.14.1_src_all.tar.gz"], "md5": "797afe8a6a8041453a34ced3cce34884", "fn": "pd.clariom.s.human_3.14.1.tar.gz"}, "pd.clariom.s.human.ht-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.clariom.s.human.ht_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.clariom.s.human.ht_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.human.ht/bioconductor-pd.clariom.s.human.ht_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.human.ht/bioconductor-pd.clariom.s.human.ht_3.14.1_src_all.tar.gz"], "md5": "90f910bea1b1aeb550a3f1bdd91d1a06", "fn": "pd.clariom.s.human.ht_3.14.1.tar.gz"}, "pd.clariom.s.mouse-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.clariom.s.mouse_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.clariom.s.mouse_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.mouse/bioconductor-pd.clariom.s.mouse_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.mouse/bioconductor-pd.clariom.s.mouse_3.14.1_src_all.tar.gz"], "md5": "e3e4ce2b22a78faf525dd6c0c0b2a42d", "fn": "pd.clariom.s.mouse_3.14.1.tar.gz"}, "pd.clariom.s.mouse.ht-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.clariom.s.mouse.ht_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.clariom.s.mouse.ht_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.mouse.ht/bioconductor-pd.clariom.s.mouse.ht_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.mouse.ht/bioconductor-pd.clariom.s.mouse.ht_3.14.1_src_all.tar.gz"], "md5": "9cb6f77cf9666a0d54e1eacb904fd57c", "fn": "pd.clariom.s.mouse.ht_3.14.1.tar.gz"}, "pd.clariom.s.rat-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.clariom.s.rat_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.clariom.s.rat_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.rat/bioconductor-pd.clariom.s.rat_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.rat/bioconductor-pd.clariom.s.rat_3.14.1_src_all.tar.gz"], "md5": "be464b3eaea8eb8bdbcca6047fce4dea", "fn": "pd.clariom.s.rat_3.14.1.tar.gz"}, "pd.clariom.s.rat.ht-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.clariom.s.rat.ht_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.clariom.s.rat.ht_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.rat.ht/bioconductor-pd.clariom.s.rat.ht_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.rat.ht/bioconductor-pd.clariom.s.rat.ht_3.14.1_src_all.tar.gz"], "md5": "be901eb9e8830f3e5bedf154189a3743", "fn": "pd.clariom.s.rat.ht_3.14.1.tar.gz"}, "pd.cotton-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.cotton_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.cotton_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cotton/bioconductor-pd.cotton_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cotton/bioconductor-pd.cotton_3.12.0_src_all.tar.gz"], "md5": "78c408902bcefb8c695119767534b393", "fn": "pd.cotton_3.12.0.tar.gz"}, "pd.cyngene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.cyngene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.cyngene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cyngene.1.0.st/bioconductor-pd.cyngene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cyngene.1.0.st/bioconductor-pd.cyngene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "784fac6cc92a0fe46dae32c9b737812a", "fn": "pd.cyngene.1.0.st_3.12.0.tar.gz"}, "pd.cyngene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.cyngene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.cyngene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cyngene.1.1.st/bioconductor-pd.cyngene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cyngene.1.1.st/bioconductor-pd.cyngene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "a6217267e3e08a15f70c600918c7d4f6", "fn": "pd.cyngene.1.1.st_3.12.0.tar.gz"}, "pd.cyrgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.cyrgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.cyrgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cyrgene.1.0.st/bioconductor-pd.cyrgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cyrgene.1.0.st/bioconductor-pd.cyrgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "63228c07d3d16d6c62e9c0e83f10a855", "fn": "pd.cyrgene.1.0.st_3.12.0.tar.gz"}, "pd.cyrgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.cyrgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.cyrgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cyrgene.1.1.st/bioconductor-pd.cyrgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cyrgene.1.1.st/bioconductor-pd.cyrgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "dbe3bb580b96aaddcc597de45159320d", "fn": "pd.cyrgene.1.1.st_3.12.0.tar.gz"}, "pd.cytogenetics.array-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.cytogenetics.array_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.cytogenetics.array_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cytogenetics.array/bioconductor-pd.cytogenetics.array_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.cytogenetics.array/bioconductor-pd.cytogenetics.array_3.12.0_src_all.tar.gz"], "md5": "8c359ff56a9a558d370dc9a6a54218e0", "fn": "pd.cytogenetics.array_3.12.0.tar.gz"}, "pd.drogene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.drogene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.drogene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.drogene.1.0.st/bioconductor-pd.drogene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.drogene.1.0.st/bioconductor-pd.drogene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "67f92a97a5b78a95693edfdd32b67e93", "fn": "pd.drogene.1.0.st_3.12.0.tar.gz"}, "pd.drogene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.drogene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.drogene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.drogene.1.1.st/bioconductor-pd.drogene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.drogene.1.1.st/bioconductor-pd.drogene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "5c63236ea91390d49dbabea63a48f0a2", "fn": "pd.drogene.1.1.st_3.12.0.tar.gz"}, "pd.drosgenome1-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.drosgenome1_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.drosgenome1_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.drosgenome1/bioconductor-pd.drosgenome1_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.drosgenome1/bioconductor-pd.drosgenome1_3.12.0_src_all.tar.gz"], "md5": "59c1a37a7d6a43fc70ff8756bf1195ef", "fn": "pd.drosgenome1_3.12.0.tar.gz"}, "pd.drosophila.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.drosophila.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.drosophila.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.drosophila.2/bioconductor-pd.drosophila.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.drosophila.2/bioconductor-pd.drosophila.2_3.12.0_src_all.tar.gz"], "md5": "ddb821e35e722af8dcf0807c6da4fac1", "fn": "pd.drosophila.2_3.12.0.tar.gz"}, "pd.e.coli.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.e.coli.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.e.coli.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.e.coli.2/bioconductor-pd.e.coli.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.e.coli.2/bioconductor-pd.e.coli.2_3.12.0_src_all.tar.gz"], "md5": "9176faa60a0c252a815b2a74d2f63dd4", "fn": "pd.e.coli.2_3.12.0.tar.gz"}, "pd.ecoli-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.ecoli_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.ecoli_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ecoli/bioconductor-pd.ecoli_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ecoli/bioconductor-pd.ecoli_3.12.0_src_all.tar.gz"], "md5": "077e91b2567a32780305f0fb6b126fe9", "fn": "pd.ecoli_3.12.0.tar.gz"}, "pd.ecoli.asv2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.ecoli.asv2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.ecoli.asv2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ecoli.asv2/bioconductor-pd.ecoli.asv2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ecoli.asv2/bioconductor-pd.ecoli.asv2_3.12.0_src_all.tar.gz"], "md5": "d789ddf5a178a9a50c5587ee3ab294a4", "fn": "pd.ecoli.asv2_3.12.0.tar.gz"}, "pd.elegene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.elegene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.elegene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.elegene.1.0.st/bioconductor-pd.elegene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.elegene.1.0.st/bioconductor-pd.elegene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "b6110c58d5964703c7117e5e0668c901", "fn": "pd.elegene.1.0.st_3.12.0.tar.gz"}, "pd.elegene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.elegene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.elegene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.elegene.1.1.st/bioconductor-pd.elegene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.elegene.1.1.st/bioconductor-pd.elegene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "1dbe166ea347a5a7e240db925d2081c7", "fn": "pd.elegene.1.1.st_3.12.0.tar.gz"}, "pd.equgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.equgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.equgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.equgene.1.0.st/bioconductor-pd.equgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.equgene.1.0.st/bioconductor-pd.equgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "3448f36fdb899f04702be37ffab4c4c7", "fn": "pd.equgene.1.0.st_3.12.0.tar.gz"}, "pd.equgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.equgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.equgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.equgene.1.1.st/bioconductor-pd.equgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.equgene.1.1.st/bioconductor-pd.equgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "bed32525513ce25f14d433ce805e7d6c", "fn": "pd.equgene.1.1.st_3.12.0.tar.gz"}, "pd.feinberg.hg18.me.hx1-0.99.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.feinberg.hg18.me.hx1_0.99.3.tar.gz", "https://bioarchive.galaxyproject.org/pd.feinberg.hg18.me.hx1_0.99.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.feinberg.hg18.me.hx1/bioconductor-pd.feinberg.hg18.me.hx1_0.99.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.feinberg.hg18.me.hx1/bioconductor-pd.feinberg.hg18.me.hx1_0.99.3_src_all.tar.gz"], "md5": "b6eeaf79671bab6f597965009516ce57", "fn": "pd.feinberg.hg18.me.hx1_0.99.3.tar.gz"}, "pd.feinberg.mm8.me.hx1-0.99.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.feinberg.mm8.me.hx1_0.99.3.tar.gz", "https://bioarchive.galaxyproject.org/pd.feinberg.mm8.me.hx1_0.99.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.feinberg.mm8.me.hx1/bioconductor-pd.feinberg.mm8.me.hx1_0.99.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.feinberg.mm8.me.hx1/bioconductor-pd.feinberg.mm8.me.hx1_0.99.3_src_all.tar.gz"], "md5": "7332102b69fc9ee087f52d3cdc311d00", "fn": "pd.feinberg.mm8.me.hx1_0.99.3.tar.gz"}, "pd.felgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.felgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.felgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.felgene.1.0.st/bioconductor-pd.felgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.felgene.1.0.st/bioconductor-pd.felgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "b7ac0a5cbde5f248aac5d0a7422bd88d", "fn": "pd.felgene.1.0.st_3.12.0.tar.gz"}, "pd.felgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.felgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.felgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.felgene.1.1.st/bioconductor-pd.felgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.felgene.1.1.st/bioconductor-pd.felgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "734807a7f3608f6c44c76df7eee04c99", "fn": "pd.felgene.1.1.st_3.12.0.tar.gz"}, "pd.fingene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.fingene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.fingene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.fingene.1.0.st/bioconductor-pd.fingene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.fingene.1.0.st/bioconductor-pd.fingene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "b79e4f8a52cad3b62e32401bbe74603d", "fn": "pd.fingene.1.0.st_3.12.0.tar.gz"}, "pd.fingene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.fingene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.fingene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.fingene.1.1.st/bioconductor-pd.fingene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.fingene.1.1.st/bioconductor-pd.fingene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "29030b14a0e8f8073874fb694a8c0c09", "fn": "pd.fingene.1.1.st_3.12.0.tar.gz"}, "pd.genomewidesnp.5-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.genomewidesnp.5_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.genomewidesnp.5_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.genomewidesnp.5/bioconductor-pd.genomewidesnp.5_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.genomewidesnp.5/bioconductor-pd.genomewidesnp.5_3.14.1_src_all.tar.gz"], "md5": "d02255c861e82fca6a7445ada0c69e5d", "fn": "pd.genomewidesnp.5_3.14.1.tar.gz"}, "pd.genomewidesnp.6-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.genomewidesnp.6_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.genomewidesnp.6_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.genomewidesnp.6/bioconductor-pd.genomewidesnp.6_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.genomewidesnp.6/bioconductor-pd.genomewidesnp.6_3.14.1_src_all.tar.gz"], "md5": "6e5369234e251c763f4f6c0220fbcb0c", "fn": "pd.genomewidesnp.6_3.14.1.tar.gz"}, "pd.guigene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.guigene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.guigene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.guigene.1.0.st/bioconductor-pd.guigene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.guigene.1.0.st/bioconductor-pd.guigene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "29fe31499931836af72ddd0c7d06acfa", "fn": "pd.guigene.1.0.st_3.12.0.tar.gz"}, "pd.guigene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.guigene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.guigene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.guigene.1.1.st/bioconductor-pd.guigene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.guigene.1.1.st/bioconductor-pd.guigene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "aa3e0389c596a3676322104de5ad2358", "fn": "pd.guigene.1.1.st_3.12.0.tar.gz"}, "pd.hc.g110-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hc.g110_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hc.g110_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hc.g110/bioconductor-pd.hc.g110_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hc.g110/bioconductor-pd.hc.g110_3.12.0_src_all.tar.gz"], "md5": "5c5418c588ed28e2fa088c7952c48b91", "fn": "pd.hc.g110_3.12.0.tar.gz"}, "pd.hg.focus-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hg.focus_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.focus_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.focus/bioconductor-pd.hg.focus_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.focus/bioconductor-pd.hg.focus_3.12.0_src_all.tar.gz"], "md5": "a89f344ae7ff8061a8e7968f155f4bcf", "fn": "pd.hg.focus_3.12.0.tar.gz"}, "pd.hg.u133.plus.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hg.u133.plus.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u133.plus.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133.plus.2/bioconductor-pd.hg.u133.plus.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133.plus.2/bioconductor-pd.hg.u133.plus.2_3.12.0_src_all.tar.gz"], "md5": "8a87aa63c04e84266962bdde5226c06c", "fn": "pd.hg.u133.plus.2_3.12.0.tar.gz"}, "pd.hg.u133a-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hg.u133a_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u133a_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a/bioconductor-pd.hg.u133a_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a/bioconductor-pd.hg.u133a_3.12.0_src_all.tar.gz"], "md5": "05b4521f65ab294a5040a0c60198d22c", "fn": "pd.hg.u133a_3.12.0.tar.gz"}, "pd.hg.u133a.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hg.u133a.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u133a.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a.2/bioconductor-pd.hg.u133a.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a.2/bioconductor-pd.hg.u133a.2_3.12.0_src_all.tar.gz"], "md5": "a7941473bf081831fad4f4412023d9ee", "fn": "pd.hg.u133a.2_3.12.0.tar.gz"}, "pd.hg.u133a.tag-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hg.u133a.tag_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u133a.tag_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a.tag/bioconductor-pd.hg.u133a.tag_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a.tag/bioconductor-pd.hg.u133a.tag_3.12.0_src_all.tar.gz"], "md5": "e090383098d6e1062b290889fba065d5", "fn": "pd.hg.u133a.tag_3.12.0.tar.gz"}, "pd.hg.u133b-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hg.u133b_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u133b_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133b/bioconductor-pd.hg.u133b_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133b/bioconductor-pd.hg.u133b_3.12.0_src_all.tar.gz"], "md5": "c5eac82ad7480571b9f2b442b4a8faa6", "fn": "pd.hg.u133b_3.12.0.tar.gz"}, "pd.hg.u219-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hg.u219_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u219_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u219/bioconductor-pd.hg.u219_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u219/bioconductor-pd.hg.u219_3.12.0_src_all.tar.gz"], "md5": "dab073d315af47ff3001c72a6d1e7972", "fn": "pd.hg.u219_3.12.0.tar.gz"}, "pd.hg.u95a-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hg.u95a_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u95a_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95a/bioconductor-pd.hg.u95a_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95a/bioconductor-pd.hg.u95a_3.12.0_src_all.tar.gz"], "md5": "a9ad7d6a085e0e3ed7623902e7810da0", "fn": "pd.hg.u95a_3.12.0.tar.gz"}, "pd.hg.u95av2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hg.u95av2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u95av2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95av2/bioconductor-pd.hg.u95av2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95av2/bioconductor-pd.hg.u95av2_3.12.0_src_all.tar.gz"], "md5": "3a4182b529bc07ec91277a95b1462468", "fn": "pd.hg.u95av2_3.12.0.tar.gz"}, "pd.hg.u95b-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hg.u95b_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u95b_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95b/bioconductor-pd.hg.u95b_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95b/bioconductor-pd.hg.u95b_3.12.0_src_all.tar.gz"], "md5": "a7f10f91e920e191c5009fac8ca79c24", "fn": "pd.hg.u95b_3.12.0.tar.gz"}, "pd.hg.u95c-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hg.u95c_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u95c_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95c/bioconductor-pd.hg.u95c_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95c/bioconductor-pd.hg.u95c_3.12.0_src_all.tar.gz"], "md5": "85655bf7a9ecd7aaa867e05899c5e3e4", "fn": "pd.hg.u95c_3.12.0.tar.gz"}, "pd.hg.u95d-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hg.u95d_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u95d_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95d/bioconductor-pd.hg.u95d_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95d/bioconductor-pd.hg.u95d_3.12.0_src_all.tar.gz"], "md5": "946701ecfc9cccb46aaeb57a4d6fe1c5", "fn": "pd.hg.u95d_3.12.0.tar.gz"}, "pd.hg.u95e-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hg.u95e_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg.u95e_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95e/bioconductor-pd.hg.u95e_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95e/bioconductor-pd.hg.u95e_3.12.0_src_all.tar.gz"], "md5": "9295e2fd1b4be6ff58477ea5a5de45ee", "fn": "pd.hg.u95e_3.12.0.tar.gz"}, "pd.hg18.60mer.expr-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hg18.60mer.expr_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hg18.60mer.expr_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg18.60mer.expr/bioconductor-pd.hg18.60mer.expr_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hg18.60mer.expr/bioconductor-pd.hg18.60mer.expr_3.12.0_src_all.tar.gz"], "md5": "ee8d3813f74edce4e796933aa63999fb", "fn": "pd.hg18.60mer.expr_3.12.0.tar.gz"}, "pd.ht.hg.u133.plus.pm-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.ht.hg.u133.plus.pm_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.ht.hg.u133.plus.pm_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ht.hg.u133.plus.pm/bioconductor-pd.ht.hg.u133.plus.pm_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ht.hg.u133.plus.pm/bioconductor-pd.ht.hg.u133.plus.pm_3.12.0_src_all.tar.gz"], "md5": "5b1c3dd0ab3f8b21154982c197512a7c", "fn": "pd.ht.hg.u133.plus.pm_3.12.0.tar.gz"}, "pd.ht.hg.u133a-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.ht.hg.u133a_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.ht.hg.u133a_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ht.hg.u133a/bioconductor-pd.ht.hg.u133a_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ht.hg.u133a/bioconductor-pd.ht.hg.u133a_3.12.0_src_all.tar.gz"], "md5": "80a82f43083f95e1e9f5e2e2da2e288e", "fn": "pd.ht.hg.u133a_3.12.0.tar.gz"}, "pd.ht.mg.430a-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.ht.mg.430a_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.ht.mg.430a_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ht.mg.430a/bioconductor-pd.ht.mg.430a_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ht.mg.430a/bioconductor-pd.ht.mg.430a_3.12.0_src_all.tar.gz"], "md5": "65ea4fae22d21ad70998ba3ea034dcc0", "fn": "pd.ht.mg.430a_3.12.0.tar.gz"}, "pd.hta.2.0-3.12.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hta.2.0_3.12.2.tar.gz", "https://bioarchive.galaxyproject.org/pd.hta.2.0_3.12.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hta.2.0/bioconductor-pd.hta.2.0_3.12.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hta.2.0/bioconductor-pd.hta.2.0_3.12.2_src_all.tar.gz"], "md5": "8e13f85ece49c38da73eaf7b2247f5f0", "fn": "pd.hta.2.0_3.12.2.tar.gz"}, "pd.hu6800-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hu6800_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.hu6800_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hu6800/bioconductor-pd.hu6800_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hu6800/bioconductor-pd.hu6800_3.12.0_src_all.tar.gz"], "md5": "9a3a3edde6d6f31b9e90dc32aa68875d", "fn": "pd.hu6800_3.12.0.tar.gz"}, "pd.huex.1.0.st.v2-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.huex.1.0.st.v2_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.huex.1.0.st.v2_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.huex.1.0.st.v2/bioconductor-pd.huex.1.0.st.v2_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.huex.1.0.st.v2/bioconductor-pd.huex.1.0.st.v2_3.14.1_src_all.tar.gz"], "md5": "f4c4836c53447890b75b012efbdef3e9", "fn": "pd.huex.1.0.st.v2_3.14.1.tar.gz"}, "pd.hugene.1.0.st.v1-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hugene.1.0.st.v1_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.hugene.1.0.st.v1_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.1.0.st.v1/bioconductor-pd.hugene.1.0.st.v1_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.1.0.st.v1/bioconductor-pd.hugene.1.0.st.v1_3.14.1_src_all.tar.gz"], "md5": "8cb24c351aee5bf216180e4b19742506", "fn": "pd.hugene.1.0.st.v1_3.14.1.tar.gz"}, "pd.hugene.1.1.st.v1-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hugene.1.1.st.v1_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.hugene.1.1.st.v1_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.1.1.st.v1/bioconductor-pd.hugene.1.1.st.v1_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.1.1.st.v1/bioconductor-pd.hugene.1.1.st.v1_3.14.1_src_all.tar.gz"], "md5": "7a17ee4f7d258792be1d21be7d03deb0", "fn": "pd.hugene.1.1.st.v1_3.14.1.tar.gz"}, "pd.hugene.2.0.st-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hugene.2.0.st_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.hugene.2.0.st_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.2.0.st/bioconductor-pd.hugene.2.0.st_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.2.0.st/bioconductor-pd.hugene.2.0.st_3.14.1_src_all.tar.gz"], "md5": "e484209aa0c2a839c3445d91c1a799ce", "fn": "pd.hugene.2.0.st_3.14.1.tar.gz"}, "pd.hugene.2.1.st-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.hugene.2.1.st_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.hugene.2.1.st_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.2.1.st/bioconductor-pd.hugene.2.1.st_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.2.1.st/bioconductor-pd.hugene.2.1.st_3.14.1_src_all.tar.gz"], "md5": "164227f10b87f87059e4ae27b40f5238", "fn": "pd.hugene.2.1.st_3.14.1.tar.gz"}, "pd.maize-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.maize_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.maize_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.maize/bioconductor-pd.maize_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.maize/bioconductor-pd.maize_3.12.0_src_all.tar.gz"], "md5": "a1689518c8525d3dfa97e870f90b7a7b", "fn": "pd.maize_3.12.0.tar.gz"}, "pd.mapping250k.nsp-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mapping250k.nsp_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mapping250k.nsp_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mapping250k.nsp/bioconductor-pd.mapping250k.nsp_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mapping250k.nsp/bioconductor-pd.mapping250k.nsp_3.12.0_src_all.tar.gz"], "md5": "2786d00e1d621a9c415a599b4afe838b", "fn": "pd.mapping250k.nsp_3.12.0.tar.gz"}, "pd.mapping250k.sty-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mapping250k.sty_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mapping250k.sty_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mapping250k.sty/bioconductor-pd.mapping250k.sty_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mapping250k.sty/bioconductor-pd.mapping250k.sty_3.12.0_src_all.tar.gz"], "md5": "0db5992855eaf9b8f61f8bc2e57ef347", "fn": "pd.mapping250k.sty_3.12.0.tar.gz"}, "pd.mapping50k.hind240-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mapping50k.hind240_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mapping50k.hind240_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mapping50k.hind240/bioconductor-pd.mapping50k.hind240_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mapping50k.hind240/bioconductor-pd.mapping50k.hind240_3.12.0_src_all.tar.gz"], "md5": "83615dcb01eb381f0c69e07504809094", "fn": "pd.mapping50k.hind240_3.12.0.tar.gz"}, "pd.mapping50k.xba240-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mapping50k.xba240_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mapping50k.xba240_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mapping50k.xba240/bioconductor-pd.mapping50k.xba240_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mapping50k.xba240/bioconductor-pd.mapping50k.xba240_3.12.0_src_all.tar.gz"], "md5": "eb0f9250fe0d7b590ca9938fee88f2e7", "fn": "pd.mapping50k.xba240_3.12.0.tar.gz"}, "pd.margene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.margene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.margene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.margene.1.0.st/bioconductor-pd.margene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.margene.1.0.st/bioconductor-pd.margene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "f670b192e4b453f13bb7cae154b5de42", "fn": "pd.margene.1.0.st_3.12.0.tar.gz"}, "pd.margene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.margene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.margene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.margene.1.1.st/bioconductor-pd.margene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.margene.1.1.st/bioconductor-pd.margene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "efd71aeb9c5ab36c2ddeccf9cb66ddec", "fn": "pd.margene.1.1.st_3.12.0.tar.gz"}, "pd.medgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.medgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.medgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.medgene.1.0.st/bioconductor-pd.medgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.medgene.1.0.st/bioconductor-pd.medgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "2a0048ccd5310ec5c45bb691f3c25885", "fn": "pd.medgene.1.0.st_3.12.0.tar.gz"}, "pd.medgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.medgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.medgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.medgene.1.1.st/bioconductor-pd.medgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.medgene.1.1.st/bioconductor-pd.medgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "d96894cfea509734af62110311100142", "fn": "pd.medgene.1.1.st_3.12.0.tar.gz"}, "pd.medicago-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.medicago_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.medicago_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.medicago/bioconductor-pd.medicago_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.medicago/bioconductor-pd.medicago_3.12.0_src_all.tar.gz"], "md5": "0e3f00777919374619a9dc8244167068", "fn": "pd.medicago_3.12.0.tar.gz"}, "pd.mg.u74a-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mg.u74a_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mg.u74a_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74a/bioconductor-pd.mg.u74a_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74a/bioconductor-pd.mg.u74a_3.12.0_src_all.tar.gz"], "md5": "a855c7d2b80e9b8f9bbc1a3f83aca799", "fn": "pd.mg.u74a_3.12.0.tar.gz"}, "pd.mg.u74av2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mg.u74av2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mg.u74av2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74av2/bioconductor-pd.mg.u74av2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74av2/bioconductor-pd.mg.u74av2_3.12.0_src_all.tar.gz"], "md5": "01c6e4da9c2ad0f1939482284dd5b421", "fn": "pd.mg.u74av2_3.12.0.tar.gz"}, "pd.mg.u74b-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mg.u74b_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mg.u74b_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74b/bioconductor-pd.mg.u74b_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74b/bioconductor-pd.mg.u74b_3.12.0_src_all.tar.gz"], "md5": "47bb81abaceba6dfaab3e0987f28706c", "fn": "pd.mg.u74b_3.12.0.tar.gz"}, "pd.mg.u74bv2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mg.u74bv2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mg.u74bv2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74bv2/bioconductor-pd.mg.u74bv2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74bv2/bioconductor-pd.mg.u74bv2_3.12.0_src_all.tar.gz"], "md5": "dbb6cd5b16bd5cafbf654744bc2d5c5c", "fn": "pd.mg.u74bv2_3.12.0.tar.gz"}, "pd.mg.u74c-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mg.u74c_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mg.u74c_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74c/bioconductor-pd.mg.u74c_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74c/bioconductor-pd.mg.u74c_3.12.0_src_all.tar.gz"], "md5": "01f10eae99481f03d1d5a6a2c2f01733", "fn": "pd.mg.u74c_3.12.0.tar.gz"}, "pd.mg.u74cv2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mg.u74cv2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mg.u74cv2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74cv2/bioconductor-pd.mg.u74cv2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74cv2/bioconductor-pd.mg.u74cv2_3.12.0_src_all.tar.gz"], "md5": "b60943b90b95a24fcf93f8c245fd88be", "fn": "pd.mg.u74cv2_3.12.0.tar.gz"}, "pd.mirna.1.0-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mirna.1.0_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mirna.1.0_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.1.0/bioconductor-pd.mirna.1.0_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.1.0/bioconductor-pd.mirna.1.0_3.12.0_src_all.tar.gz"], "md5": "8dfeb82a9da6d6f73e5fb716a2867a34", "fn": "pd.mirna.1.0_3.12.0.tar.gz"}, "pd.mirna.2.0-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mirna.2.0_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mirna.2.0_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.2.0/bioconductor-pd.mirna.2.0_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.2.0/bioconductor-pd.mirna.2.0_3.12.0_src_all.tar.gz"], "md5": "aab53cbc62fbd7727ca0303aeb1dca13", "fn": "pd.mirna.2.0_3.12.0.tar.gz"}, "pd.mirna.3.0-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mirna.3.0_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mirna.3.0_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.3.0/bioconductor-pd.mirna.3.0_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.3.0/bioconductor-pd.mirna.3.0_3.12.0_src_all.tar.gz"], "md5": "1265f1969c618b3b5121e6a77ba57009", "fn": "pd.mirna.3.0_3.12.0.tar.gz"}, "pd.mirna.3.1-3.8.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mirna.3.1_3.8.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.mirna.3.1_3.8.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.3.1/bioconductor-pd.mirna.3.1_3.8.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.3.1/bioconductor-pd.mirna.3.1_3.8.1_src_all.tar.gz"], "md5": "296b3584ee5e9416c9018353d3e29c6c", "fn": "pd.mirna.3.1_3.8.1.tar.gz"}, "pd.mirna.4.0-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mirna.4.0_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mirna.4.0_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.4.0/bioconductor-pd.mirna.4.0_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.4.0/bioconductor-pd.mirna.4.0_3.12.0_src_all.tar.gz"], "md5": "cae1a18c02aaa20a2f05172103e9d938", "fn": "pd.mirna.4.0_3.12.0.tar.gz"}, "pd.moe430a-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.moe430a_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.moe430a_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.moe430a/bioconductor-pd.moe430a_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.moe430a/bioconductor-pd.moe430a_3.12.0_src_all.tar.gz"], "md5": "f9a7cb62140e42c2a82177548a1c73fb", "fn": "pd.moe430a_3.12.0.tar.gz"}, "pd.moe430b-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.moe430b_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.moe430b_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.moe430b/bioconductor-pd.moe430b_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.moe430b/bioconductor-pd.moe430b_3.12.0_src_all.tar.gz"], "md5": "c19d2ee5e7e87703cf73afa33a5f3156", "fn": "pd.moe430b_3.12.0.tar.gz"}, "pd.moex.1.0.st.v1-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.moex.1.0.st.v1_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.moex.1.0.st.v1_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.moex.1.0.st.v1/bioconductor-pd.moex.1.0.st.v1_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.moex.1.0.st.v1/bioconductor-pd.moex.1.0.st.v1_3.14.1_src_all.tar.gz"], "md5": "57427e63b2d44258c12d796eada1897b", "fn": "pd.moex.1.0.st.v1_3.14.1.tar.gz"}, "pd.mogene.1.0.st.v1-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mogene.1.0.st.v1_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.mogene.1.0.st.v1_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.1.0.st.v1/bioconductor-pd.mogene.1.0.st.v1_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.1.0.st.v1/bioconductor-pd.mogene.1.0.st.v1_3.14.1_src_all.tar.gz"], "md5": "c3767385af3b9a120c777adb6d6e3364", "fn": "pd.mogene.1.0.st.v1_3.14.1.tar.gz"}, "pd.mogene.1.1.st.v1-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mogene.1.1.st.v1_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.mogene.1.1.st.v1_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.1.1.st.v1/bioconductor-pd.mogene.1.1.st.v1_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.1.1.st.v1/bioconductor-pd.mogene.1.1.st.v1_3.14.1_src_all.tar.gz"], "md5": "3d6c5d29e4d8a0b0152e109b68f82c37", "fn": "pd.mogene.1.1.st.v1_3.14.1.tar.gz"}, "pd.mogene.2.0.st-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mogene.2.0.st_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.mogene.2.0.st_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.2.0.st/bioconductor-pd.mogene.2.0.st_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.2.0.st/bioconductor-pd.mogene.2.0.st_3.14.1_src_all.tar.gz"], "md5": "71326d6bd85de02490171696f923d053", "fn": "pd.mogene.2.0.st_3.14.1.tar.gz"}, "pd.mogene.2.1.st-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mogene.2.1.st_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.mogene.2.1.st_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.2.1.st/bioconductor-pd.mogene.2.1.st_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.2.1.st/bioconductor-pd.mogene.2.1.st_3.14.1_src_all.tar.gz"], "md5": "2c7fc5644eae98359cb945ff16d072a2", "fn": "pd.mogene.2.1.st_3.14.1.tar.gz"}, "pd.mouse430.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mouse430.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mouse430.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mouse430.2/bioconductor-pd.mouse430.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mouse430.2/bioconductor-pd.mouse430.2_3.12.0_src_all.tar.gz"], "md5": "7f37397a57b06d15101ef86fa6242ca4", "fn": "pd.mouse430.2_3.12.0.tar.gz"}, "pd.mouse430a.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mouse430a.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mouse430a.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mouse430a.2/bioconductor-pd.mouse430a.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mouse430a.2/bioconductor-pd.mouse430a.2_3.12.0_src_all.tar.gz"], "md5": "0c28f564a1fa23f59c936d42c156796d", "fn": "pd.mouse430a.2_3.12.0.tar.gz"}, "pd.mta.1.0-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mta.1.0_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mta.1.0_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mta.1.0/bioconductor-pd.mta.1.0_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mta.1.0/bioconductor-pd.mta.1.0_3.12.0_src_all.tar.gz"], "md5": "0f737b4f1f1353733e56e2df637f554b", "fn": "pd.mta.1.0_3.12.0.tar.gz"}, "pd.mu11ksuba-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mu11ksuba_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mu11ksuba_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mu11ksuba/bioconductor-pd.mu11ksuba_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mu11ksuba/bioconductor-pd.mu11ksuba_3.12.0_src_all.tar.gz"], "md5": "56be58b3f444ccb9572dc4c3882964b2", "fn": "pd.mu11ksuba_3.12.0.tar.gz"}, "pd.mu11ksubb-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.mu11ksubb_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.mu11ksubb_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mu11ksubb/bioconductor-pd.mu11ksubb_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.mu11ksubb/bioconductor-pd.mu11ksubb_3.12.0_src_all.tar.gz"], "md5": "c45b0ebe777b99cec38499826cc1b457", "fn": "pd.mu11ksubb_3.12.0.tar.gz"}, "pd.nugo.hs1a520180-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.nugo.hs1a520180_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.nugo.hs1a520180_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.nugo.hs1a520180/bioconductor-pd.nugo.hs1a520180_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.nugo.hs1a520180/bioconductor-pd.nugo.hs1a520180_3.4.0_src_all.tar.gz"], "md5": "88a836472f0f9aab2e1d54e4bad7d6af", "fn": "pd.nugo.hs1a520180_3.4.0.tar.gz"}, "pd.nugo.mm1a520177-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.nugo.mm1a520177_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.nugo.mm1a520177_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.nugo.mm1a520177/bioconductor-pd.nugo.mm1a520177_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.nugo.mm1a520177/bioconductor-pd.nugo.mm1a520177_3.4.0_src_all.tar.gz"], "md5": "5cd64895eaddaf4cae1c48db9468c079", "fn": "pd.nugo.mm1a520177_3.4.0.tar.gz"}, "pd.ovigene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.ovigene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.ovigene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ovigene.1.0.st/bioconductor-pd.ovigene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ovigene.1.0.st/bioconductor-pd.ovigene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "88cfedfe10dd357539305051a69d31a1", "fn": "pd.ovigene.1.0.st_3.12.0.tar.gz"}, "pd.ovigene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.ovigene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.ovigene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ovigene.1.1.st/bioconductor-pd.ovigene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ovigene.1.1.st/bioconductor-pd.ovigene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "d6158cacd32a1892975fddd8dc8bb3f2", "fn": "pd.ovigene.1.1.st_3.12.0.tar.gz"}, "pd.pae.g1a-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.pae.g1a_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.pae.g1a_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.pae.g1a/bioconductor-pd.pae.g1a_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.pae.g1a/bioconductor-pd.pae.g1a_3.12.0_src_all.tar.gz"], "md5": "d96462eb35c63b30772bccae2a27a8cd", "fn": "pd.pae.g1a_3.12.0.tar.gz"}, "pd.plasmodium.anopheles-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.plasmodium.anopheles_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.plasmodium.anopheles_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.plasmodium.anopheles/bioconductor-pd.plasmodium.anopheles_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.plasmodium.anopheles/bioconductor-pd.plasmodium.anopheles_3.12.0_src_all.tar.gz"], "md5": "ae55b1451ceaed951f68213c0433f3d0", "fn": "pd.plasmodium.anopheles_3.12.0.tar.gz"}, "pd.poplar-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.poplar_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.poplar_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.poplar/bioconductor-pd.poplar_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.poplar/bioconductor-pd.poplar_3.12.0_src_all.tar.gz"], "md5": "9c33b7528e5a47654aeacf61b71058a8", "fn": "pd.poplar_3.12.0.tar.gz"}, "pd.porcine-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.porcine_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.porcine_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.porcine/bioconductor-pd.porcine_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.porcine/bioconductor-pd.porcine_3.12.0_src_all.tar.gz"], "md5": "5df404babadb1d6faef73e249c819a72", "fn": "pd.porcine_3.12.0.tar.gz"}, "pd.porgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.porgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.porgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.porgene.1.0.st/bioconductor-pd.porgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.porgene.1.0.st/bioconductor-pd.porgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "203fc56b0e2904fa7063c4a325e038f1", "fn": "pd.porgene.1.0.st_3.12.0.tar.gz"}, "pd.porgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.porgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.porgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.porgene.1.1.st/bioconductor-pd.porgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.porgene.1.1.st/bioconductor-pd.porgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "3a31d325861925a7428241207c461a1d", "fn": "pd.porgene.1.1.st_3.12.0.tar.gz"}, "pd.rabgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rabgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rabgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rabgene.1.0.st/bioconductor-pd.rabgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rabgene.1.0.st/bioconductor-pd.rabgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "7f1e33f4767a4c4653bdaff2b79989a0", "fn": "pd.rabgene.1.0.st_3.12.0.tar.gz"}, "pd.rabgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rabgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rabgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rabgene.1.1.st/bioconductor-pd.rabgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rabgene.1.1.st/bioconductor-pd.rabgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "2492695661309f5e6628612685460ee5", "fn": "pd.rabgene.1.1.st_3.12.0.tar.gz"}, "pd.rae230a-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rae230a_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rae230a_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rae230a/bioconductor-pd.rae230a_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rae230a/bioconductor-pd.rae230a_3.12.0_src_all.tar.gz"], "md5": "fa4a1c29d3457b1db82b1010c5f72412", "fn": "pd.rae230a_3.12.0.tar.gz"}, "pd.rae230b-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rae230b_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rae230b_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rae230b/bioconductor-pd.rae230b_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rae230b/bioconductor-pd.rae230b_3.12.0_src_all.tar.gz"], "md5": "10e2e70bb7538119127cd65f636f93b6", "fn": "pd.rae230b_3.12.0.tar.gz"}, "pd.raex.1.0.st.v1-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.raex.1.0.st.v1_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.raex.1.0.st.v1_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.raex.1.0.st.v1/bioconductor-pd.raex.1.0.st.v1_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.raex.1.0.st.v1/bioconductor-pd.raex.1.0.st.v1_3.14.1_src_all.tar.gz"], "md5": "e2160b549f63ffcc9222d88d82d4d393", "fn": "pd.raex.1.0.st.v1_3.14.1.tar.gz"}, "pd.ragene.1.0.st.v1-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.ragene.1.0.st.v1_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.ragene.1.0.st.v1_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.1.0.st.v1/bioconductor-pd.ragene.1.0.st.v1_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.1.0.st.v1/bioconductor-pd.ragene.1.0.st.v1_3.14.1_src_all.tar.gz"], "md5": "122cb69603e705218d01d70f48e90cad", "fn": "pd.ragene.1.0.st.v1_3.14.1.tar.gz"}, "pd.ragene.1.1.st.v1-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.ragene.1.1.st.v1_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.ragene.1.1.st.v1_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.1.1.st.v1/bioconductor-pd.ragene.1.1.st.v1_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.1.1.st.v1/bioconductor-pd.ragene.1.1.st.v1_3.14.1_src_all.tar.gz"], "md5": "7301ab6472849395ccb800c39807e969", "fn": "pd.ragene.1.1.st.v1_3.14.1.tar.gz"}, "pd.ragene.2.0.st-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.ragene.2.0.st_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.ragene.2.0.st_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.2.0.st/bioconductor-pd.ragene.2.0.st_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.2.0.st/bioconductor-pd.ragene.2.0.st_3.14.1_src_all.tar.gz"], "md5": "37157b09f009fef368b54e47711c313b", "fn": "pd.ragene.2.0.st_3.14.1.tar.gz"}, "pd.ragene.2.1.st-3.14.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.ragene.2.1.st_3.14.1.tar.gz", "https://bioarchive.galaxyproject.org/pd.ragene.2.1.st_3.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.2.1.st/bioconductor-pd.ragene.2.1.st_3.14.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.2.1.st/bioconductor-pd.ragene.2.1.st_3.14.1_src_all.tar.gz"], "md5": "53adfa5ff2c7e466da83b807dbc7b237", "fn": "pd.ragene.2.1.st_3.14.1.tar.gz"}, "pd.rat230.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rat230.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rat230.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rat230.2/bioconductor-pd.rat230.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rat230.2/bioconductor-pd.rat230.2_3.12.0_src_all.tar.gz"], "md5": "286b1a7868ef6c795ebeb6dd8a5d5920", "fn": "pd.rat230.2_3.12.0.tar.gz"}, "pd.rcngene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rcngene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rcngene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rcngene.1.0.st/bioconductor-pd.rcngene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rcngene.1.0.st/bioconductor-pd.rcngene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "9c7c5ef4d4f5ed92d9130d77a99a0685", "fn": "pd.rcngene.1.0.st_3.12.0.tar.gz"}, "pd.rcngene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rcngene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rcngene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rcngene.1.1.st/bioconductor-pd.rcngene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rcngene.1.1.st/bioconductor-pd.rcngene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "9781549447d90b5423e820fff5cc6273", "fn": "pd.rcngene.1.1.st_3.12.0.tar.gz"}, "pd.rg.u34a-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rg.u34a_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rg.u34a_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34a/bioconductor-pd.rg.u34a_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34a/bioconductor-pd.rg.u34a_3.12.0_src_all.tar.gz"], "md5": "ac3a6cc203dabb8faab85b97f1a7ae3c", "fn": "pd.rg.u34a_3.12.0.tar.gz"}, "pd.rg.u34b-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rg.u34b_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rg.u34b_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34b/bioconductor-pd.rg.u34b_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34b/bioconductor-pd.rg.u34b_3.12.0_src_all.tar.gz"], "md5": "757966b66795d388c7169816d31977ad", "fn": "pd.rg.u34b_3.12.0.tar.gz"}, "pd.rg.u34c-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rg.u34c_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rg.u34c_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34c/bioconductor-pd.rg.u34c_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34c/bioconductor-pd.rg.u34c_3.12.0_src_all.tar.gz"], "md5": "bc9cb7b208972ac2901235bdabdee5b2", "fn": "pd.rg.u34c_3.12.0.tar.gz"}, "pd.rhegene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rhegene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rhegene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rhegene.1.0.st/bioconductor-pd.rhegene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rhegene.1.0.st/bioconductor-pd.rhegene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "6469add6928e663529df4df98fcdd7a8", "fn": "pd.rhegene.1.0.st_3.12.0.tar.gz"}, "pd.rhegene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rhegene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rhegene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rhegene.1.1.st/bioconductor-pd.rhegene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rhegene.1.1.st/bioconductor-pd.rhegene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "4f63424ab52283a95731767dce6623cd", "fn": "pd.rhegene.1.1.st_3.12.0.tar.gz"}, "pd.rhesus-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rhesus_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rhesus_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rhesus/bioconductor-pd.rhesus_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rhesus/bioconductor-pd.rhesus_3.12.0_src_all.tar.gz"], "md5": "51efcfe1384ac956ff93bf0530965054", "fn": "pd.rhesus_3.12.0.tar.gz"}, "pd.rice-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rice_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rice_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rice/bioconductor-pd.rice_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rice/bioconductor-pd.rice_3.12.0_src_all.tar.gz"], "md5": "9c456981b3d0b99a96ac6c71e3eb7c8a", "fn": "pd.rice_3.12.0.tar.gz"}, "pd.rjpgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rjpgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rjpgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rjpgene.1.0.st/bioconductor-pd.rjpgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rjpgene.1.0.st/bioconductor-pd.rjpgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "066f5dbacc1110e42ce4d457ad3b9306", "fn": "pd.rjpgene.1.0.st_3.12.0.tar.gz"}, "pd.rjpgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rjpgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rjpgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rjpgene.1.1.st/bioconductor-pd.rjpgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rjpgene.1.1.st/bioconductor-pd.rjpgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "265503774b15e0f4e71ac53a276a80f2", "fn": "pd.rjpgene.1.1.st_3.12.0.tar.gz"}, "pd.rn.u34-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rn.u34_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rn.u34_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rn.u34/bioconductor-pd.rn.u34_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rn.u34/bioconductor-pd.rn.u34_3.12.0_src_all.tar.gz"], "md5": "1728c547f1383bffab330796505119ec", "fn": "pd.rn.u34_3.12.0.tar.gz"}, "pd.rta.1.0-3.12.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rta.1.0_3.12.2.tar.gz", "https://bioarchive.galaxyproject.org/pd.rta.1.0_3.12.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rta.1.0/bioconductor-pd.rta.1.0_3.12.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rta.1.0/bioconductor-pd.rta.1.0_3.12.2_src_all.tar.gz"], "md5": "90752a892a103c7fe4cd6c86e61a61db", "fn": "pd.rta.1.0_3.12.2.tar.gz"}, "pd.rusgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rusgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rusgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rusgene.1.0.st/bioconductor-pd.rusgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rusgene.1.0.st/bioconductor-pd.rusgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "0b9b00fee58ef211e041395052344483", "fn": "pd.rusgene.1.0.st_3.12.0.tar.gz"}, "pd.rusgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.rusgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.rusgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rusgene.1.1.st/bioconductor-pd.rusgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.rusgene.1.1.st/bioconductor-pd.rusgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "228837c2de4a4b106806cb7f384564fa", "fn": "pd.rusgene.1.1.st_3.12.0.tar.gz"}, "pd.s.aureus-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.s.aureus_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.s.aureus_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.s.aureus/bioconductor-pd.s.aureus_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.s.aureus/bioconductor-pd.s.aureus_3.12.0_src_all.tar.gz"], "md5": "f173ae6e4316aaa2eafbde92d5868a5a", "fn": "pd.s.aureus_3.12.0.tar.gz"}, "pd.soybean-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.soybean_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.soybean_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.soybean/bioconductor-pd.soybean_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.soybean/bioconductor-pd.soybean_3.12.0_src_all.tar.gz"], "md5": "6dbe167be9d40c1d9096485afb4525f0", "fn": "pd.soybean_3.12.0.tar.gz"}, "pd.soygene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.soygene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.soygene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.soygene.1.0.st/bioconductor-pd.soygene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.soygene.1.0.st/bioconductor-pd.soygene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "b264df0648ec35d04f91e0ef8e26ac95", "fn": "pd.soygene.1.0.st_3.12.0.tar.gz"}, "pd.soygene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.soygene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.soygene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.soygene.1.1.st/bioconductor-pd.soygene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.soygene.1.1.st/bioconductor-pd.soygene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "4a911a4a4b5de927fe6239e500a2993f", "fn": "pd.soygene.1.1.st_3.12.0.tar.gz"}, "pd.sugar.cane-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.sugar.cane_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.sugar.cane_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.sugar.cane/bioconductor-pd.sugar.cane_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.sugar.cane/bioconductor-pd.sugar.cane_3.12.0_src_all.tar.gz"], "md5": "bd7eb8b1a1c9ac77359358a5347330fb", "fn": "pd.sugar.cane_3.12.0.tar.gz"}, "pd.tomato-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.tomato_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.tomato_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.tomato/bioconductor-pd.tomato_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.tomato/bioconductor-pd.tomato_3.12.0_src_all.tar.gz"], "md5": "ce78f6ee43d72e017608413dd4d50580", "fn": "pd.tomato_3.12.0.tar.gz"}, "pd.u133.x3p-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.u133.x3p_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.u133.x3p_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.u133.x3p/bioconductor-pd.u133.x3p_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.u133.x3p/bioconductor-pd.u133.x3p_3.12.0_src_all.tar.gz"], "md5": "e3f343e32273667f851e26d7b8a7a5db", "fn": "pd.u133.x3p_3.12.0.tar.gz"}, "pd.vitis.vinifera-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.vitis.vinifera_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.vitis.vinifera_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.vitis.vinifera/bioconductor-pd.vitis.vinifera_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.vitis.vinifera/bioconductor-pd.vitis.vinifera_3.12.0_src_all.tar.gz"], "md5": "104a8ac33a9baa25a61f953679795696", "fn": "pd.vitis.vinifera_3.12.0.tar.gz"}, "pd.wheat-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.wheat_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.wheat_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.wheat/bioconductor-pd.wheat_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.wheat/bioconductor-pd.wheat_3.12.0_src_all.tar.gz"], "md5": "38a7183c8d3b874cf62391a9e9169bb9", "fn": "pd.wheat_3.12.0.tar.gz"}, "pd.x.laevis.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.x.laevis.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.x.laevis.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.x.laevis.2/bioconductor-pd.x.laevis.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.x.laevis.2/bioconductor-pd.x.laevis.2_3.12.0_src_all.tar.gz"], "md5": "32416957e3cdc11ad4dbfcd9141ff113", "fn": "pd.x.laevis.2_3.12.0.tar.gz"}, "pd.x.tropicalis-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.x.tropicalis_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.x.tropicalis_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.x.tropicalis/bioconductor-pd.x.tropicalis_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.x.tropicalis/bioconductor-pd.x.tropicalis_3.12.0_src_all.tar.gz"], "md5": "79a4de91831e4b0153495e12b9c6e8d3", "fn": "pd.x.tropicalis_3.12.0.tar.gz"}, "pd.xenopus.laevis-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.xenopus.laevis_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.xenopus.laevis_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.xenopus.laevis/bioconductor-pd.xenopus.laevis_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.xenopus.laevis/bioconductor-pd.xenopus.laevis_3.12.0_src_all.tar.gz"], "md5": "6d5c2c9e8e3891770b1c6e9dcd823c0d", "fn": "pd.xenopus.laevis_3.12.0.tar.gz"}, "pd.yeast.2-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.yeast.2_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.yeast.2_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.yeast.2/bioconductor-pd.yeast.2_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.yeast.2/bioconductor-pd.yeast.2_3.12.0_src_all.tar.gz"], "md5": "780f5139ee9cda46c9e38122538ce129", "fn": "pd.yeast.2_3.12.0.tar.gz"}, "pd.yg.s98-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.yg.s98_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.yg.s98_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.yg.s98/bioconductor-pd.yg.s98_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.yg.s98/bioconductor-pd.yg.s98_3.12.0_src_all.tar.gz"], "md5": "caec3e8f29918f078b2dc7c76f4a74e2", "fn": "pd.yg.s98_3.12.0.tar.gz"}, "pd.zebgene.1.0.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.zebgene.1.0.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.zebgene.1.0.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.zebgene.1.0.st/bioconductor-pd.zebgene.1.0.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.zebgene.1.0.st/bioconductor-pd.zebgene.1.0.st_3.12.0_src_all.tar.gz"], "md5": "54fcf757b8069e95dd7e2f3ff74ae050", "fn": "pd.zebgene.1.0.st_3.12.0.tar.gz"}, "pd.zebgene.1.1.st-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.zebgene.1.1.st_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.zebgene.1.1.st_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.zebgene.1.1.st/bioconductor-pd.zebgene.1.1.st_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.zebgene.1.1.st/bioconductor-pd.zebgene.1.1.st_3.12.0_src_all.tar.gz"], "md5": "d87028cd9024bc33be518635cf2f48fc", "fn": "pd.zebgene.1.1.st_3.12.0.tar.gz"}, "pd.zebrafish-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pd.zebrafish_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.zebrafish_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.zebrafish/bioconductor-pd.zebrafish_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.zebrafish/bioconductor-pd.zebrafish_3.12.0_src_all.tar.gz"], "md5": "101f09a9d9304d1d8fbcc7f4812897b1", "fn": "pd.zebrafish_3.12.0.tar.gz"}, "pedbarrayv10.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pedbarrayv10.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/pedbarrayv10.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pedbarrayv10.db/bioconductor-pedbarrayv10.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pedbarrayv10.db/bioconductor-pedbarrayv10.db_3.2.3_src_all.tar.gz"], "md5": "25acc3bfee229015ecca1c7d688e5168", "fn": "pedbarrayv10.db_3.2.3.tar.gz"}, "pedbarrayv9.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pedbarrayv9.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/pedbarrayv9.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pedbarrayv9.db/bioconductor-pedbarrayv9.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pedbarrayv9.db/bioconductor-pedbarrayv9.db_3.2.3_src_all.tar.gz"], "md5": "da4b2f9c0a672e0c9ee53f017bacaff7", "fn": "pedbarrayv9.db_3.2.3.tar.gz"}, "pfam.db-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/PFAM.db_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/PFAM.db_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pfam.db/bioconductor-pfam.db_3.16.0_src_all.tar.gz"], "md5": "6fec4f9e7916ebcffee313775c774e09", "fn": "PFAM.db_3.16.0.tar.gz"}, "phastcons100way.ucsc.hg19-3.7.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/phastCons100way.UCSC.hg19_3.7.2.tar.gz", "https://bioarchive.galaxyproject.org/phastCons100way.UCSC.hg19_3.7.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phastcons100way.ucsc.hg19/bioconductor-phastcons100way.ucsc.hg19_3.7.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phastcons100way.ucsc.hg19/bioconductor-phastcons100way.ucsc.hg19_3.7.2_src_all.tar.gz"], "md5": "65aa706a567f7e328dbba0095f995cf1", "fn": "phastCons100way.UCSC.hg19_3.7.2.tar.gz"}, "phastcons100way.ucsc.hg38-3.7.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/phastCons100way.UCSC.hg38_3.7.1.tar.gz", "https://bioarchive.galaxyproject.org/phastCons100way.UCSC.hg38_3.7.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phastcons100way.ucsc.hg38/bioconductor-phastcons100way.ucsc.hg38_3.7.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phastcons100way.ucsc.hg38/bioconductor-phastcons100way.ucsc.hg38_3.7.1_src_all.tar.gz"], "md5": "878c757f9270b3410d11e4e4a4213c8e", "fn": "phastCons100way.UCSC.hg38_3.7.1.tar.gz"}, "phastcons30way.ucsc.hg38-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/phastCons30way.UCSC.hg38_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/phastCons30way.UCSC.hg38_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phastcons30way.ucsc.hg38/bioconductor-phastcons30way.ucsc.hg38_3.13.0_src_all.tar.gz"], "md5": "754faee8463bc494c502540cb8f6ea8d", "fn": "phastCons30way.UCSC.hg38_3.13.0.tar.gz"}, "phastcons35way.ucsc.mm39-3.16.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/phastCons35way.UCSC.mm39_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/phastCons35way.UCSC.mm39_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phastcons35way.ucsc.mm39/bioconductor-phastcons35way.ucsc.mm39_3.16.0_src_all.tar.gz"], "md5": "83fc2a2265bc341b6a00064a1286b5bc", "fn": "phastCons35way.UCSC.mm39_3.16.0.tar.gz"}, "phastcons7way.ucsc.hg38-3.7.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/phastCons7way.UCSC.hg38_3.7.1.tar.gz", "https://bioarchive.galaxyproject.org/phastCons7way.UCSC.hg38_3.7.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phastcons7way.ucsc.hg38/bioconductor-phastcons7way.ucsc.hg38_3.7.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phastcons7way.ucsc.hg38/bioconductor-phastcons7way.ucsc.hg38_3.7.1_src_all.tar.gz"], "md5": "c2d87446b022c166c1c325ea2aef521d", "fn": "phastCons7way.UCSC.hg38_3.7.1.tar.gz"}, "phylop35way.ucsc.mm39-3.16.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/phyloP35way.UCSC.mm39_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/phyloP35way.UCSC.mm39_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phylop35way.ucsc.mm39/bioconductor-phylop35way.ucsc.mm39_3.16.0_src_all.tar.gz"], "md5": "2c34eef5f20eace04efd47673cdf1062", "fn": "phyloP35way.UCSC.mm39_3.16.0.tar.gz"}, "pig.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/pig.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/pig.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pig.db0/bioconductor-pig.db0_3.16.0_src_all.tar.gz"], "md5": "3822cffa9665794639acfe1c59e35df5", "fn": "pig.db0_3.16.0.tar.gz"}, "plasmodiumanophelescdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/plasmodiumanophelescdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/plasmodiumanophelescdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-plasmodiumanophelescdf/bioconductor-plasmodiumanophelescdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-plasmodiumanophelescdf/bioconductor-plasmodiumanophelescdf_2.18.0_src_all.tar.gz"], "md5": "54c5c326977d6358c40cacf34cb2aca2", "fn": "plasmodiumanophelescdf_2.18.0.tar.gz"}, "plasmodiumanophelesprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/plasmodiumanophelesprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/plasmodiumanophelesprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-plasmodiumanophelesprobe/bioconductor-plasmodiumanophelesprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-plasmodiumanophelesprobe/bioconductor-plasmodiumanophelesprobe_2.18.0_src_all.tar.gz"], "md5": "281683dab923168c2eedb7b08c528935", "fn": "plasmodiumanophelesprobe_2.18.0.tar.gz"}, "pocrcannotation.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/POCRCannotation.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/POCRCannotation.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pocrcannotation.db/bioconductor-pocrcannotation.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pocrcannotation.db/bioconductor-pocrcannotation.db_3.2.3_src_all.tar.gz"], "md5": "da1d4dacc5fffb9c5dfea55649974aa5", "fn": "POCRCannotation.db_3.2.3.tar.gz"}, "polyphen.hsapiens.dbsnp131-1.0.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/PolyPhen.Hsapiens.dbSNP131_1.0.2.tar.gz", "https://bioarchive.galaxyproject.org/PolyPhen.Hsapiens.dbSNP131_1.0.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-polyphen.hsapiens.dbsnp131/bioconductor-polyphen.hsapiens.dbsnp131_1.0.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-polyphen.hsapiens.dbsnp131/bioconductor-polyphen.hsapiens.dbsnp131_1.0.2_src_all.tar.gz"], "md5": "763e9cd4afd97b36f7e659f5454ef61f", "fn": "PolyPhen.Hsapiens.dbSNP131_1.0.2.tar.gz"}, "poplarcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/poplarcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/poplarcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-poplarcdf/bioconductor-poplarcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-poplarcdf/bioconductor-poplarcdf_2.18.0_src_all.tar.gz"], "md5": "556e7f8f6f76436552d8044ef29279cb", "fn": "poplarcdf_2.18.0.tar.gz"}, "poplarprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/poplarprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/poplarprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-poplarprobe/bioconductor-poplarprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-poplarprobe/bioconductor-poplarprobe_2.18.0_src_all.tar.gz"], "md5": "87a608cd86084a06973a88e9b51f799a", "fn": "poplarprobe_2.18.0.tar.gz"}, "porcine.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/porcine.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/porcine.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-porcine.db/bioconductor-porcine.db_3.13.0_src_all.tar.gz"], "md5": "4a86b3e696d267dca673b4e9276d6368", "fn": "porcine.db_3.13.0.tar.gz"}, "porcinecdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/porcinecdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/porcinecdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-porcinecdf/bioconductor-porcinecdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-porcinecdf/bioconductor-porcinecdf_2.18.0_src_all.tar.gz"], "md5": "32a60b93829c06a935895fab0a469228", "fn": "porcinecdf_2.18.0.tar.gz"}, "porcineprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/porcineprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/porcineprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-porcineprobe/bioconductor-porcineprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-porcineprobe/bioconductor-porcineprobe_2.18.0_src_all.tar.gz"], "md5": "5ac483b6329a012d4c9954e3dee8869e", "fn": "porcineprobe_2.18.0.tar.gz"}, "primeviewcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/primeviewcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/primeviewcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-primeviewcdf/bioconductor-primeviewcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-primeviewcdf/bioconductor-primeviewcdf_2.18.0_src_all.tar.gz"], "md5": "71e39a59a5907e9b8a8dba58d36eee50", "fn": "primeviewcdf_2.18.0.tar.gz"}, "primeviewprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/primeviewprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/primeviewprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-primeviewprobe/bioconductor-primeviewprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-primeviewprobe/bioconductor-primeviewprobe_2.18.0_src_all.tar.gz"], "md5": "87cc56a8da4fb742ab1558ce1d3d26cc", "fn": "primeviewprobe_2.18.0.tar.gz"}, "r10kcod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/r10kcod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/r10kcod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-r10kcod.db/bioconductor-r10kcod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-r10kcod.db/bioconductor-r10kcod.db_3.4.0_src_all.tar.gz"], "md5": "4a7a25fee64294cfb5adccaa6cf28772", "fn": "r10kcod.db_3.4.0.tar.gz"}, "rae230a.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rae230a.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/rae230a.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230a.db/bioconductor-rae230a.db_3.13.0_src_all.tar.gz"], "md5": "a2a80af1669fc038a64effbf5a4b246d", "fn": "rae230a.db_3.13.0.tar.gz"}, "rae230acdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rae230acdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rae230acdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230acdf/bioconductor-rae230acdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230acdf/bioconductor-rae230acdf_2.18.0_src_all.tar.gz"], "md5": "6f2281124e1be164d5fd599e84f6adbc", "fn": "rae230acdf_2.18.0.tar.gz"}, "rae230aprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rae230aprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rae230aprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230aprobe/bioconductor-rae230aprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230aprobe/bioconductor-rae230aprobe_2.18.0_src_all.tar.gz"], "md5": "6f2d77e1d9c1e3afb96ef78b3202bb0b", "fn": "rae230aprobe_2.18.0.tar.gz"}, "rae230b.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rae230b.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/rae230b.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230b.db/bioconductor-rae230b.db_3.13.0_src_all.tar.gz"], "md5": "4f0474ed22bf5ebd932dd6a4d9573551", "fn": "rae230b.db_3.13.0.tar.gz"}, "rae230bcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rae230bcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rae230bcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230bcdf/bioconductor-rae230bcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230bcdf/bioconductor-rae230bcdf_2.18.0_src_all.tar.gz"], "md5": "bd61c17402e9c04be1000c16e0356618", "fn": "rae230bcdf_2.18.0.tar.gz"}, "rae230bprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rae230bprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rae230bprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230bprobe/bioconductor-rae230bprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rae230bprobe/bioconductor-rae230bprobe_2.18.0_src_all.tar.gz"], "md5": "7bdb3a07e1f00de8ff510a69bdac4c53", "fn": "rae230bprobe_2.18.0.tar.gz"}, "raex10stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/raex10stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/raex10stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-raex10stprobeset.db/bioconductor-raex10stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "a386809ea8da340f315e378fa329b3ac", "fn": "raex10stprobeset.db_8.8.0.tar.gz"}, "raex10sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/raex10sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/raex10sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-raex10sttranscriptcluster.db/bioconductor-raex10sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "3a0c511a1073c67172770bc3e4b842b5", "fn": "raex10sttranscriptcluster.db_8.8.0.tar.gz"}, "raexexonprobesetlocation-1.15.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/RaExExonProbesetLocation_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/RaExExonProbesetLocation_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-raexexonprobesetlocation/bioconductor-raexexonprobesetlocation_1.15.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-raexexonprobesetlocation/bioconductor-raexexonprobesetlocation_1.15.0_src_all.tar.gz"], "md5": "d547bcd30685495283b32f0f86ecc79b", "fn": "RaExExonProbesetLocation_1.15.0.tar.gz"}, "ragene10stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ragene10stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene10stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene10stprobeset.db/bioconductor-ragene10stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "358685c380b37027a064924069b9ee40", "fn": "ragene10stprobeset.db_8.8.0.tar.gz"}, "ragene10sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ragene10sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene10sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene10sttranscriptcluster.db/bioconductor-ragene10sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "5ff95454493a72bfa2546d82d32fbec1", "fn": "ragene10sttranscriptcluster.db_8.8.0.tar.gz"}, "ragene10stv1cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ragene10stv1cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene10stv1cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene10stv1cdf/bioconductor-ragene10stv1cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene10stv1cdf/bioconductor-ragene10stv1cdf_2.18.0_src_all.tar.gz"], "md5": "df696e9dbf5b3f2761b6a0a5914be058", "fn": "ragene10stv1cdf_2.18.0.tar.gz"}, "ragene10stv1probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ragene10stv1probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene10stv1probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene10stv1probe/bioconductor-ragene10stv1probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene10stv1probe/bioconductor-ragene10stv1probe_2.18.0_src_all.tar.gz"], "md5": "94978b6efb075aacf31ccdc8000e40fa", "fn": "ragene10stv1probe_2.18.0.tar.gz"}, "ragene11stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ragene11stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene11stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene11stprobeset.db/bioconductor-ragene11stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "86f7704c4852c514b3bc3221f7692ba3", "fn": "ragene11stprobeset.db_8.8.0.tar.gz"}, "ragene11sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ragene11sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene11sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene11sttranscriptcluster.db/bioconductor-ragene11sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "f7fbe318547f911b520415a90b3440e9", "fn": "ragene11sttranscriptcluster.db_8.8.0.tar.gz"}, "ragene20stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ragene20stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene20stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene20stprobeset.db/bioconductor-ragene20stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "23a43899a22078f4c13b7b1d45176319", "fn": "ragene20stprobeset.db_8.8.0.tar.gz"}, "ragene20sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ragene20sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene20sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene20sttranscriptcluster.db/bioconductor-ragene20sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "b44c5f6ac2b2e3eb4d820d08f7a38644", "fn": "ragene20sttranscriptcluster.db_8.8.0.tar.gz"}, "ragene21stprobeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ragene21stprobeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene21stprobeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene21stprobeset.db/bioconductor-ragene21stprobeset.db_8.8.0_src_all.tar.gz"], "md5": "6451885f99ce3873d5d4dbacdf968181", "fn": "ragene21stprobeset.db_8.8.0.tar.gz"}, "ragene21sttranscriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ragene21sttranscriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ragene21sttranscriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ragene21sttranscriptcluster.db/bioconductor-ragene21sttranscriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "6ffe13e1594add0a5169b2083b608336", "fn": "ragene21sttranscriptcluster.db_8.8.0.tar.gz"}, "rat.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/rat.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/rat.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat.db0/bioconductor-rat.db0_3.16.0_src_all.tar.gz"], "md5": "a244e0fa21d1ffa71b46694a7ddafb58", "fn": "rat.db0_3.16.0.tar.gz"}, "rat2302.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rat2302.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/rat2302.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat2302.db/bioconductor-rat2302.db_3.13.0_src_all.tar.gz"], "md5": "b1404d8a16fec681f0fd682589a685ea", "fn": "rat2302.db_3.13.0.tar.gz"}, "rat2302cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rat2302cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rat2302cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat2302cdf/bioconductor-rat2302cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat2302cdf/bioconductor-rat2302cdf_2.18.0_src_all.tar.gz"], "md5": "a033730f79a11d45b4cd7e7c520f8052", "fn": "rat2302cdf_2.18.0.tar.gz"}, "rat2302frmavecs-0.99.11": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rat2302frmavecs_0.99.11.tar.gz", "https://bioarchive.galaxyproject.org/rat2302frmavecs_0.99.11.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat2302frmavecs/bioconductor-rat2302frmavecs_0.99.11_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat2302frmavecs/bioconductor-rat2302frmavecs_0.99.11_src_all.tar.gz"], "md5": "44d9f00c2f3806899c6605d1ba274066", "fn": "rat2302frmavecs_0.99.11.tar.gz"}, "rat2302probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rat2302probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rat2302probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat2302probe/bioconductor-rat2302probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat2302probe/bioconductor-rat2302probe_2.18.0_src_all.tar.gz"], "md5": "d1d9215e52b9e845cc4d7c902536e0d6", "fn": "rat2302probe_2.18.0.tar.gz"}, "ratchrloc-2.1.6": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ratCHRLOC_2.1.6.tar.gz", "https://bioarchive.galaxyproject.org/ratCHRLOC_2.1.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ratchrloc/bioconductor-ratchrloc_2.1.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ratchrloc/bioconductor-ratchrloc_2.1.6_src_all.tar.gz"], "md5": "6fecff4821a5a47e3bd38a2ff78173d5", "fn": "ratCHRLOC_2.1.6.tar.gz"}, "rattoxfxcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rattoxfxcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rattoxfxcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rattoxfxcdf/bioconductor-rattoxfxcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rattoxfxcdf/bioconductor-rattoxfxcdf_2.18.0_src_all.tar.gz"], "md5": "912d0fa424615fcd92773ed174d5efdd", "fn": "rattoxfxcdf_2.18.0.tar.gz"}, "rattoxfxprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rattoxfxprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rattoxfxprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rattoxfxprobe/bioconductor-rattoxfxprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rattoxfxprobe/bioconductor-rattoxfxprobe_2.18.0_src_all.tar.gz"], "md5": "202791c72e8c956b9854fa4d9ba67a24", "fn": "rattoxfxprobe_2.18.0.tar.gz"}, "rattus.norvegicus-1.3.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/Rattus.norvegicus_1.3.1.tar.gz", "https://bioarchive.galaxyproject.org/Rattus.norvegicus_1.3.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rattus.norvegicus/bioconductor-rattus.norvegicus_1.3.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rattus.norvegicus/bioconductor-rattus.norvegicus_1.3.1_src_all.tar.gz"], "md5": "5692fdeb0bc7f94e1db35f097cad99a9", "fn": "Rattus.norvegicus_1.3.1.tar.gz"}, "reactome.db-1.82.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/reactome.db_1.82.0.tar.gz", "https://bioarchive.galaxyproject.org/reactome.db_1.82.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-reactome.db/bioconductor-reactome.db_1.82.0_src_all.tar.gz"], "md5": "54cf27d67bc854603f6ef2c5b6d2d633", "fn": "reactome.db_1.82.0.tar.gz"}, "rgenometracksdata-0.99.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rGenomeTracksData_0.99.0.tar.gz", "https://bioarchive.galaxyproject.org/rGenomeTracksData_0.99.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgenometracksdata/bioconductor-rgenometracksdata_0.99.0_src_all.tar.gz"], "md5": "713103a8b4b4e48fa762ef589a43ffb8", "fn": "rGenomeTracksData_0.99.0.tar.gz"}, "rgu34a.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rgu34a.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/rgu34a.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34a.db/bioconductor-rgu34a.db_3.13.0_src_all.tar.gz"], "md5": "e99dc4c05360b49a2249cb5de0b1dd4e", "fn": "rgu34a.db_3.13.0.tar.gz"}, "rgu34acdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rgu34acdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rgu34acdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34acdf/bioconductor-rgu34acdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34acdf/bioconductor-rgu34acdf_2.18.0_src_all.tar.gz"], "md5": "dcfa7ecce00e529f93809759ed837b8d", "fn": "rgu34acdf_2.18.0.tar.gz"}, "rgu34aprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rgu34aprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rgu34aprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34aprobe/bioconductor-rgu34aprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34aprobe/bioconductor-rgu34aprobe_2.18.0_src_all.tar.gz"], "md5": "902aee259a2894fa8713c4bf9266c0e2", "fn": "rgu34aprobe_2.18.0.tar.gz"}, "rgu34b.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rgu34b.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/rgu34b.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34b.db/bioconductor-rgu34b.db_3.13.0_src_all.tar.gz"], "md5": "5aeb80d5190bf2dcffa6b9264d3db33f", "fn": "rgu34b.db_3.13.0.tar.gz"}, "rgu34bcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rgu34bcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rgu34bcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34bcdf/bioconductor-rgu34bcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34bcdf/bioconductor-rgu34bcdf_2.18.0_src_all.tar.gz"], "md5": "428b3a39f0d8addd7d863539b8cda6ea", "fn": "rgu34bcdf_2.18.0.tar.gz"}, "rgu34bprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rgu34bprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rgu34bprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34bprobe/bioconductor-rgu34bprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34bprobe/bioconductor-rgu34bprobe_2.18.0_src_all.tar.gz"], "md5": "2d6488309c5e54231a18e2ecf5608bb1", "fn": "rgu34bprobe_2.18.0.tar.gz"}, "rgu34c.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rgu34c.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/rgu34c.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34c.db/bioconductor-rgu34c.db_3.13.0_src_all.tar.gz"], "md5": "e19f250869a9894bc9d069a4baf39a3c", "fn": "rgu34c.db_3.13.0.tar.gz"}, "rgu34ccdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rgu34ccdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rgu34ccdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34ccdf/bioconductor-rgu34ccdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34ccdf/bioconductor-rgu34ccdf_2.18.0_src_all.tar.gz"], "md5": "556a7130086004d26095594da31c6410", "fn": "rgu34ccdf_2.18.0.tar.gz"}, "rgu34cprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rgu34cprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rgu34cprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34cprobe/bioconductor-rgu34cprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgu34cprobe/bioconductor-rgu34cprobe_2.18.0_src_all.tar.gz"], "md5": "d1a6c433acd30b95fa7be89147105b74", "fn": "rgu34cprobe_2.18.0.tar.gz"}, "rguatlas4k.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rguatlas4k.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/rguatlas4k.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rguatlas4k.db/bioconductor-rguatlas4k.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rguatlas4k.db/bioconductor-rguatlas4k.db_3.2.3_src_all.tar.gz"], "md5": "6a360676e08319ec5465c47c758110bd", "fn": "rguatlas4k.db_3.2.3.tar.gz"}, "rgug4105a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rgug4105a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/rgug4105a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgug4105a.db/bioconductor-rgug4105a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgug4105a.db/bioconductor-rgug4105a.db_3.2.3_src_all.tar.gz"], "md5": "3ccf354083ae36a7ae687fb8209c4e5b", "fn": "rgug4105a.db_3.2.3.tar.gz"}, "rgug4130a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rgug4130a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/rgug4130a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgug4130a.db/bioconductor-rgug4130a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgug4130a.db/bioconductor-rgug4130a.db_3.2.3_src_all.tar.gz"], "md5": "13643ac109aaf12590a5b6e379609b79", "fn": "rgug4130a.db_3.2.3.tar.gz"}, "rgug4131a.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rgug4131a.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/rgug4131a.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgug4131a.db/bioconductor-rgug4131a.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgug4131a.db/bioconductor-rgug4131a.db_3.2.3_src_all.tar.gz"], "md5": "1168d4906fb8ce60cbc0fa6cfa3b8ec6", "fn": "rgug4131a.db_3.2.3.tar.gz"}, "rhesus.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/rhesus.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/rhesus.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rhesus.db0/bioconductor-rhesus.db0_3.16.0_src_all.tar.gz"], "md5": "7b57d4cd1362d889869c6f6e9a4062c5", "fn": "rhesus.db0_3.16.0.tar.gz"}, "rhesuscdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rhesuscdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rhesuscdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rhesuscdf/bioconductor-rhesuscdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rhesuscdf/bioconductor-rhesuscdf_2.18.0_src_all.tar.gz"], "md5": "994e16da5dd31bc2796d0da40aa2634f", "fn": "rhesuscdf_2.18.0.tar.gz"}, "rhesusprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rhesusprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rhesusprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rhesusprobe/bioconductor-rhesusprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rhesusprobe/bioconductor-rhesusprobe_2.18.0_src_all.tar.gz"], "md5": "4169c1c997c4c08b027bc7489533e11e", "fn": "rhesusprobe_2.18.0.tar.gz"}, "ri16cod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ri16cod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/ri16cod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ri16cod.db/bioconductor-ri16cod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ri16cod.db/bioconductor-ri16cod.db_3.4.0_src_all.tar.gz"], "md5": "cd01b429295fdbba21dbe566effacbdd", "fn": "ri16cod.db_3.4.0.tar.gz"}, "ricecdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ricecdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ricecdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ricecdf/bioconductor-ricecdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ricecdf/bioconductor-ricecdf_2.18.0_src_all.tar.gz"], "md5": "51db6f51f4adcfb7f4940d07668db8b8", "fn": "ricecdf_2.18.0.tar.gz"}, "riceprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/riceprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/riceprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-riceprobe/bioconductor-riceprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-riceprobe/bioconductor-riceprobe_2.18.0_src_all.tar.gz"], "md5": "2fac7746c343546cf30e6d54bc1e2019", "fn": "riceprobe_2.18.0.tar.gz"}, "rmir.hs.mirna-1.0.7": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/RmiR.Hs.miRNA_1.0.7.tar.gz", "https://bioarchive.galaxyproject.org/RmiR.Hs.miRNA_1.0.7.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rmir.hs.mirna/bioconductor-rmir.hs.mirna_1.0.7_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rmir.hs.mirna/bioconductor-rmir.hs.mirna_1.0.7_src_all.tar.gz"], "md5": "4aedac188382447d9907d2617aa2e8e6", "fn": "RmiR.Hs.miRNA_1.0.7.tar.gz"}, "rmir.hsa-1.0.5": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/RmiR.hsa_1.0.5.tar.gz", "https://bioarchive.galaxyproject.org/RmiR.hsa_1.0.5.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rmir.hsa/bioconductor-rmir.hsa_1.0.5_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rmir.hsa/bioconductor-rmir.hsa_1.0.5_src_all.tar.gz"], "md5": "f22a18d1a34d12f8fc4ba3daaf1379fd", "fn": "RmiR.hsa_1.0.5.tar.gz"}, "rnagilentdesign028282.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/RnAgilentDesign028282.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/RnAgilentDesign028282.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnagilentdesign028282.db/bioconductor-rnagilentdesign028282.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnagilentdesign028282.db/bioconductor-rnagilentdesign028282.db_3.2.3_src_all.tar.gz"], "md5": "72cafb0f7514a81f462acb3248e21aa9", "fn": "RnAgilentDesign028282.db_3.2.3.tar.gz"}, "rnu34.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rnu34.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/rnu34.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnu34.db/bioconductor-rnu34.db_3.13.0_src_all.tar.gz"], "md5": "7345817f2f26270779d2409b8a17a5bd", "fn": "rnu34.db_3.13.0.tar.gz"}, "rnu34cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rnu34cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rnu34cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnu34cdf/bioconductor-rnu34cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnu34cdf/bioconductor-rnu34cdf_2.18.0_src_all.tar.gz"], "md5": "0f2564fc6ac89de4d779faf253f23ce3", "fn": "rnu34cdf_2.18.0.tar.gz"}, "rnu34probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rnu34probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rnu34probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnu34probe/bioconductor-rnu34probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnu34probe/bioconductor-rnu34probe_2.18.0_src_all.tar.gz"], "md5": "c5ef9793a437f2bf990f6e84d31da0de", "fn": "rnu34probe_2.18.0.tar.gz"}, "roberts2005annotation.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/Roberts2005Annotation.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/Roberts2005Annotation.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-roberts2005annotation.db/bioconductor-roberts2005annotation.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-roberts2005annotation.db/bioconductor-roberts2005annotation.db_3.2.3_src_all.tar.gz"], "md5": "fb28aaf1a1e0c81cf936badc674b754a", "fn": "Roberts2005Annotation.db_3.2.3.tar.gz"}, "rta10probeset.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rta10probeset.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/rta10probeset.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rta10probeset.db/bioconductor-rta10probeset.db_8.8.0_src_all.tar.gz"], "md5": "ce002623471eef89fb841f0bf3e7c9f8", "fn": "rta10probeset.db_8.8.0.tar.gz"}, "rta10transcriptcluster.db-8.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rta10transcriptcluster.db_8.8.0.tar.gz", "https://bioarchive.galaxyproject.org/rta10transcriptcluster.db_8.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rta10transcriptcluster.db/bioconductor-rta10transcriptcluster.db_8.8.0_src_all.tar.gz"], "md5": "14ade3f4fca2d1091ccb28e7a777f3e5", "fn": "rta10transcriptcluster.db_8.8.0.tar.gz"}, "rtu34.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rtu34.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/rtu34.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtu34.db/bioconductor-rtu34.db_3.13.0_src_all.tar.gz"], "md5": "f46c4763627f1a9e00cdc9d0af8c5f2e", "fn": "rtu34.db_3.13.0.tar.gz"}, "rtu34cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rtu34cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rtu34cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtu34cdf/bioconductor-rtu34cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtu34cdf/bioconductor-rtu34cdf_2.18.0_src_all.tar.gz"], "md5": "317abfcca319d01eb14f16efa6d91da1", "fn": "rtu34cdf_2.18.0.tar.gz"}, "rtu34probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rtu34probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rtu34probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtu34probe/bioconductor-rtu34probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtu34probe/bioconductor-rtu34probe_2.18.0_src_all.tar.gz"], "md5": "1778d857a61bf181b80b9fcf46ebd2c3", "fn": "rtu34probe_2.18.0.tar.gz"}, "rwgcod.db-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rwgcod.db_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/rwgcod.db_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rwgcod.db/bioconductor-rwgcod.db_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rwgcod.db/bioconductor-rwgcod.db_3.4.0_src_all.tar.gz"], "md5": "c8d2fa81b6f03c4ee629a0883431e5fd", "fn": "rwgcod.db_3.4.0.tar.gz"}, "saureuscdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/saureuscdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/saureuscdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-saureuscdf/bioconductor-saureuscdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-saureuscdf/bioconductor-saureuscdf_2.18.0_src_all.tar.gz"], "md5": "d01883e4c3dd99f32012e6dbab8cdb8b", "fn": "saureuscdf_2.18.0.tar.gz"}, "saureusprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/saureusprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/saureusprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-saureusprobe/bioconductor-saureusprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-saureusprobe/bioconductor-saureusprobe_2.18.0_src_all.tar.gz"], "md5": "eb4e91b10a536cbde4ecc08951ddf4d3", "fn": "saureusprobe_2.18.0.tar.gz"}, "scannotatr.models-0.99.10": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/scAnnotatR.models_0.99.10.tar.gz", "https://bioarchive.galaxyproject.org/scAnnotatR.models_0.99.10.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scannotatr.models/bioconductor-scannotatr.models_0.99.10_src_all.tar.gz"], "md5": "77c6e16382645164d6413356c5ab52c5", "fn": "scAnnotatR.models_0.99.10.tar.gz"}, "shdz.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/SHDZ.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/SHDZ.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-shdz.db/bioconductor-shdz.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-shdz.db/bioconductor-shdz.db_3.2.3_src_all.tar.gz"], "md5": "63c4439a272a5cd0c4746e9e53a7bdc7", "fn": "SHDZ.db_3.2.3.tar.gz"}, "sift.hsapiens.dbsnp132-1.0.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/SIFT.Hsapiens.dbSNP132_1.0.2.tar.gz", "https://bioarchive.galaxyproject.org/SIFT.Hsapiens.dbSNP132_1.0.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sift.hsapiens.dbsnp132/bioconductor-sift.hsapiens.dbsnp132_1.0.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sift.hsapiens.dbsnp132/bioconductor-sift.hsapiens.dbsnp132_1.0.2_src_all.tar.gz"], "md5": "c374f0bf4c99357cfe99e0b192c00d75", "fn": "SIFT.Hsapiens.dbSNP132_1.0.2.tar.gz"}, "sift.hsapiens.dbsnp137-1.0.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/SIFT.Hsapiens.dbSNP137_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/SIFT.Hsapiens.dbSNP137_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sift.hsapiens.dbsnp137/bioconductor-sift.hsapiens.dbsnp137_1.0.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sift.hsapiens.dbsnp137/bioconductor-sift.hsapiens.dbsnp137_1.0.0_src_all.tar.gz"], "md5": "3c3e73f826399af5ff368d1aab12cfd1", "fn": "SIFT.Hsapiens.dbSNP137_1.0.0.tar.gz"}, "snplocs.hsapiens.dbsnp144.grch37-0.99.20": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20.tar.gz", "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp144.grch37/bioconductor-snplocs.hsapiens.dbsnp144.grch37_0.99.20_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp144.grch37/bioconductor-snplocs.hsapiens.dbsnp144.grch37_0.99.20_src_all.tar.gz"], "md5": "bd338bb583cacc18f210e871dac79ebf", "fn": "SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20.tar.gz"}, "snplocs.hsapiens.dbsnp144.grch38-0.99.20": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20.tar.gz", "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp144.grch38/bioconductor-snplocs.hsapiens.dbsnp144.grch38_0.99.20_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp144.grch38/bioconductor-snplocs.hsapiens.dbsnp144.grch38_0.99.20_src_all.tar.gz"], "md5": "128c95e327adf72ae137fb5ae58270fc", "fn": "SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20.tar.gz"}, "snplocs.hsapiens.dbsnp149.grch38-0.99.20": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP149.GRCh38_0.99.20.tar.gz", "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP149.GRCh38_0.99.20.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp149.grch38/bioconductor-snplocs.hsapiens.dbsnp149.grch38_0.99.20_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp149.grch38/bioconductor-snplocs.hsapiens.dbsnp149.grch38_0.99.20_src_all.tar.gz"], "md5": "8cf749a8649a53449066b54160a3745c", "fn": "SNPlocs.Hsapiens.dbSNP149.GRCh38_0.99.20.tar.gz"}, "snplocs.hsapiens.dbsnp150.grch38-0.99.20": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP150.GRCh38_0.99.20.tar.gz", "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP150.GRCh38_0.99.20.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp150.grch38/bioconductor-snplocs.hsapiens.dbsnp150.grch38_0.99.20_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp150.grch38/bioconductor-snplocs.hsapiens.dbsnp150.grch38_0.99.20_src_all.tar.gz"], "md5": "575a7aaa9125d52ca0634b3ac586c9a7", "fn": "SNPlocs.Hsapiens.dbSNP150.GRCh38_0.99.20.tar.gz"}, "snplocs.hsapiens.dbsnp155.grch37-0.99.22": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.22.tar.gz", "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.22.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp155.grch37/bioconductor-snplocs.hsapiens.dbsnp155.grch37_0.99.22_src_all.tar.gz"], "md5": "044601b86a60d140dc0819525d372cc7", "fn": "SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.22.tar.gz"}, "snplocs.hsapiens.dbsnp155.grch38-0.99.22": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP155.GRCh38_0.99.22.tar.gz", "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP155.GRCh38_0.99.22.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp155.grch38/bioconductor-snplocs.hsapiens.dbsnp155.grch38_0.99.22_src_all.tar.gz"], "md5": "da89eef4346ad1c3a6de82c7670ba24e", "fn": "SNPlocs.Hsapiens.dbSNP155.GRCh38_0.99.22.tar.gz"}, "soybeancdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/soybeancdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/soybeancdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-soybeancdf/bioconductor-soybeancdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-soybeancdf/bioconductor-soybeancdf_2.18.0_src_all.tar.gz"], "md5": "a18e0ba5dbcf2291bdec91091dc528e6", "fn": "soybeancdf_2.18.0.tar.gz"}, "soybeanprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/soybeanprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/soybeanprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-soybeanprobe/bioconductor-soybeanprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-soybeanprobe/bioconductor-soybeanprobe_2.18.0_src_all.tar.gz"], "md5": "3057a5c387ff35b6c647c4db27041a13", "fn": "soybeanprobe_2.18.0.tar.gz"}, "sugarcanecdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/sugarcanecdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/sugarcanecdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sugarcanecdf/bioconductor-sugarcanecdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sugarcanecdf/bioconductor-sugarcanecdf_2.18.0_src_all.tar.gz"], "md5": "f66d51868068f83d3693d3cb05be418a", "fn": "sugarcanecdf_2.18.0.tar.gz"}, "sugarcaneprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/sugarcaneprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/sugarcaneprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sugarcaneprobe/bioconductor-sugarcaneprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sugarcaneprobe/bioconductor-sugarcaneprobe_2.18.0_src_all.tar.gz"], "md5": "66c101ac73e9235d258b9f996c42778e", "fn": "sugarcaneprobe_2.18.0.tar.gz"}, "synaptome.data-0.99.6": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/synaptome.data_0.99.6.tar.gz", "https://bioarchive.galaxyproject.org/synaptome.data_0.99.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-synaptome.data/bioconductor-synaptome.data_0.99.6_src_all.tar.gz"], "md5": "4388c63219782a9aa3e384fcdb51ed47", "fn": "synaptome.data_0.99.6.tar.gz"}, "synaptome.db-0.99.12": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/synaptome.db_0.99.12.tar.gz", "https://bioarchive.galaxyproject.org/synaptome.db_0.99.12.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-synaptome.db/bioconductor-synaptome.db_0.99.12_src_all.tar.gz"], "md5": "383e2a16688e13d40d1f8e2efd3168ef", "fn": "synaptome.db_0.99.12.tar.gz"}, "targetscan.hs.eg.db-0.6.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/targetscan.Hs.eg.db_0.6.1.tar.gz", "https://bioarchive.galaxyproject.org/targetscan.Hs.eg.db_0.6.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetscan.hs.eg.db/bioconductor-targetscan.hs.eg.db_0.6.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetscan.hs.eg.db/bioconductor-targetscan.hs.eg.db_0.6.1_src_all.tar.gz"], "md5": "d10569315400f6c1b95ad2688632b6de", "fn": "targetscan.Hs.eg.db_0.6.1.tar.gz"}, "targetscan.mm.eg.db-0.6.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/targetscan.Mm.eg.db_0.6.1.tar.gz", "https://bioarchive.galaxyproject.org/targetscan.Mm.eg.db_0.6.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetscan.mm.eg.db/bioconductor-targetscan.mm.eg.db_0.6.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetscan.mm.eg.db/bioconductor-targetscan.mm.eg.db_0.6.1_src_all.tar.gz"], "md5": "1830815c9d1383739f1ff152da0508c5", "fn": "targetscan.Mm.eg.db_0.6.1.tar.gz"}, "test1cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/test1cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/test1cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-test1cdf/bioconductor-test1cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-test1cdf/bioconductor-test1cdf_2.18.0_src_all.tar.gz"], "md5": "8c94708b49ccc7bbf127485155970b9b", "fn": "test1cdf_2.18.0.tar.gz"}, "test2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/test2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/test2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-test2cdf/bioconductor-test2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-test2cdf/bioconductor-test2cdf_2.18.0_src_all.tar.gz"], "md5": "0d1c20d6450dfc83d62214be9dc46b5f", "fn": "test2cdf_2.18.0.tar.gz"}, "test3cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/test3cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/test3cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-test3cdf/bioconductor-test3cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-test3cdf/bioconductor-test3cdf_2.18.0_src_all.tar.gz"], "md5": "9904e7fa6599f68400a9b77d0caa159a", "fn": "test3cdf_2.18.0.tar.gz"}, "test3probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/test3probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/test3probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-test3probe/bioconductor-test3probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-test3probe/bioconductor-test3probe_2.18.0_src_all.tar.gz"], "md5": "ffcbfee4e5c486fd03b2b9b64820340c", "fn": "test3probe_2.18.0.tar.gz"}, "tomatocdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/tomatocdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/tomatocdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tomatocdf/bioconductor-tomatocdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tomatocdf/bioconductor-tomatocdf_2.18.0_src_all.tar.gz"], "md5": "200efc0637788d4bd3263fc9183c1aa6", "fn": "tomatocdf_2.18.0.tar.gz"}, "tomatoprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/tomatoprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/tomatoprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tomatoprobe/bioconductor-tomatoprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tomatoprobe/bioconductor-tomatoprobe_2.18.0_src_all.tar.gz"], "md5": "72020469f35c19399fd0be9eaffd8e77", "fn": "tomatoprobe_2.18.0.tar.gz"}, "txdb.athaliana.biomart.plantsmart22-3.0.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Athaliana.BioMart.plantsmart22_3.0.1.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Athaliana.BioMart.plantsmart22_3.0.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart22/bioconductor-txdb.athaliana.biomart.plantsmart22_3.0.1_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart22/bioconductor-txdb.athaliana.biomart.plantsmart22_3.0.1_src_all.tar.gz"], "md5": "3bab54295e300fedba99eef521220e50", "fn": "TxDb.Athaliana.BioMart.plantsmart22_3.0.1.tar.gz"}, "txdb.athaliana.biomart.plantsmart25-3.1.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Athaliana.BioMart.plantsmart25_3.1.3.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Athaliana.BioMart.plantsmart25_3.1.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart25/bioconductor-txdb.athaliana.biomart.plantsmart25_3.1.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart25/bioconductor-txdb.athaliana.biomart.plantsmart25_3.1.3_src_all.tar.gz"], "md5": "eb007c07317b9717c76949e5ed999978", "fn": "TxDb.Athaliana.BioMart.plantsmart25_3.1.3.tar.gz"}, "txdb.athaliana.biomart.plantsmart28-3.2.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Athaliana.BioMart.plantsmart28_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Athaliana.BioMart.plantsmart28_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart28/bioconductor-txdb.athaliana.biomart.plantsmart28_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart28/bioconductor-txdb.athaliana.biomart.plantsmart28_3.2.2_src_all.tar.gz"], "md5": "9ed52284f01e08fc382db179b544bb17", "fn": "TxDb.Athaliana.BioMart.plantsmart28_3.2.2.tar.gz"}, "txdb.athaliana.biomart.plantsmart51-0.99.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Athaliana.BioMart.plantsmart51_0.99.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Athaliana.BioMart.plantsmart51_0.99.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart51/bioconductor-txdb.athaliana.biomart.plantsmart51_0.99.0_src_all.tar.gz"], "md5": "c623af555537bfd9958f8f9573308103", "fn": "TxDb.Athaliana.BioMart.plantsmart51_0.99.0.tar.gz"}, "txdb.btaurus.ucsc.bostau8.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Btaurus.UCSC.bosTau8.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Btaurus.UCSC.bosTau8.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/bioconductor-txdb.btaurus.ucsc.bostau8.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/bioconductor-txdb.btaurus.ucsc.bostau8.refgene_3.12.0_src_all.tar.gz"], "md5": "2112b91fbecabf9c89d1b0a48d88ce03", "fn": "TxDb.Btaurus.UCSC.bosTau8.refGene_3.12.0.tar.gz"}, "txdb.btaurus.ucsc.bostau9.refgene-3.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Btaurus.UCSC.bosTau9.refGene_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Btaurus.UCSC.bosTau9.refGene_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.btaurus.ucsc.bostau9.refgene/bioconductor-txdb.btaurus.ucsc.bostau9.refgene_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.btaurus.ucsc.bostau9.refgene/bioconductor-txdb.btaurus.ucsc.bostau9.refgene_3.10.0_src_all.tar.gz"], "md5": "fe443d123b0b788e1e450f4e60036788", "fn": "TxDb.Btaurus.UCSC.bosTau9.refGene_3.10.0.tar.gz"}, "txdb.celegans.ucsc.ce11.ensgene-3.15.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce11.ensGene_3.15.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Celegans.UCSC.ce11.ensGene_3.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce11.ensgene/bioconductor-txdb.celegans.ucsc.ce11.ensgene_3.15.0_src_all.tar.gz"], "md5": "1b4d61d06ac8acb27e57d1fafc5b79ce", "fn": "TxDb.Celegans.UCSC.ce11.ensGene_3.15.0.tar.gz"}, "txdb.celegans.ucsc.ce11.refgene-3.4.6": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce11.refGene_3.4.6.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Celegans.UCSC.ce11.refGene_3.4.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce11.refgene/bioconductor-txdb.celegans.ucsc.ce11.refgene_3.4.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce11.refgene/bioconductor-txdb.celegans.ucsc.ce11.refgene_3.4.6_src_all.tar.gz"], "md5": "3765169432e745aff5e85afd239066ca", "fn": "TxDb.Celegans.UCSC.ce11.refGene_3.4.6.tar.gz"}, "txdb.celegans.ucsc.ce6.ensgene-3.2.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce6.ensgene/bioconductor-txdb.celegans.ucsc.ce6.ensgene_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce6.ensgene/bioconductor-txdb.celegans.ucsc.ce6.ensgene_3.2.2_src_all.tar.gz"], "md5": "215c2edd440a3df8229fe6a75b431aa8", "fn": "TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz"}, "txdb.cfamiliaris.ucsc.canfam3.refgene-3.11.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Cfamiliaris.UCSC.canFam3.refGene_3.11.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Cfamiliaris.UCSC.canFam3.refGene_3.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene_3.11.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene_3.11.0_src_all.tar.gz"], "md5": "bf6af84c14a30ad5d01f3678246b1180", "fn": "TxDb.Cfamiliaris.UCSC.canFam3.refGene_3.11.0.tar.gz"}, "txdb.cfamiliaris.ucsc.canfam4.refgene-3.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Cfamiliaris.UCSC.canFam4.refGene_3.14.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Cfamiliaris.UCSC.canFam4.refGene_3.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene/bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene_3.14.0_src_all.tar.gz"], "md5": "0b47072fa79cf8e99f8563002a0998cb", "fn": "TxDb.Cfamiliaris.UCSC.canFam4.refGene_3.14.0.tar.gz"}, "txdb.cfamiliaris.ucsc.canfam5.refgene-3.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Cfamiliaris.UCSC.canFam5.refGene_3.14.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Cfamiliaris.UCSC.canFam5.refGene_3.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene/bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene_3.14.0_src_all.tar.gz"], "md5": "fc3d84569c092b74e5e0bccb785db8b6", "fn": "TxDb.Cfamiliaris.UCSC.canFam5.refGene_3.14.0.tar.gz"}, "txdb.dmelanogaster.ucsc.dm3.ensgene-3.2.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene_3.2.2_src_all.tar.gz"], "md5": "46b7ffe0c516edf8a2a3b5d78e0d8b67", "fn": "TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz"}, "txdb.dmelanogaster.ucsc.dm6.ensgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene_3.12.0_src_all.tar.gz"], "md5": "bec18a1fb2768347e907e3171d5332ca", "fn": "TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.12.0.tar.gz"}, "txdb.drerio.ucsc.danrer10.refgene-3.4.6": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Drerio.UCSC.danRer10.refGene_3.4.6.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Drerio.UCSC.danRer10.refGene_3.4.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.drerio.ucsc.danrer10.refgene/bioconductor-txdb.drerio.ucsc.danrer10.refgene_3.4.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.drerio.ucsc.danrer10.refgene/bioconductor-txdb.drerio.ucsc.danrer10.refgene_3.4.6_src_all.tar.gz"], "md5": "fef9bbec3809e1b69991516988f146fb", "fn": "TxDb.Drerio.UCSC.danRer10.refGene_3.4.6.tar.gz"}, "txdb.drerio.ucsc.danrer11.refgene-3.4.6": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Drerio.UCSC.danRer11.refGene_3.4.6.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Drerio.UCSC.danRer11.refGene_3.4.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.drerio.ucsc.danrer11.refgene/bioconductor-txdb.drerio.ucsc.danrer11.refgene_3.4.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.drerio.ucsc.danrer11.refgene/bioconductor-txdb.drerio.ucsc.danrer11.refgene_3.4.6_src_all.tar.gz"], "md5": "3d4ded4cec068a807b8b86b31389b677", "fn": "TxDb.Drerio.UCSC.danRer11.refGene_3.4.6.tar.gz"}, "txdb.ggallus.ucsc.galgal4.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Ggallus.UCSC.galGal4.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Ggallus.UCSC.galGal4.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/bioconductor-txdb.ggallus.ucsc.galgal4.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/bioconductor-txdb.ggallus.ucsc.galgal4.refgene_3.12.0_src_all.tar.gz"], "md5": "d50eb467227cd9077a7a690ae6934d11", "fn": "TxDb.Ggallus.UCSC.galGal4.refGene_3.12.0.tar.gz"}, "txdb.ggallus.ucsc.galgal5.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Ggallus.UCSC.galGal5.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Ggallus.UCSC.galGal5.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/bioconductor-txdb.ggallus.ucsc.galgal5.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/bioconductor-txdb.ggallus.ucsc.galgal5.refgene_3.12.0_src_all.tar.gz"], "md5": "0df53cd4f8e29705df75867a427de56e", "fn": "TxDb.Ggallus.UCSC.galGal5.refGene_3.12.0.tar.gz"}, "txdb.ggallus.ucsc.galgal6.refgene-3.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Ggallus.UCSC.galGal6.refGene_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Ggallus.UCSC.galGal6.refGene_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ggallus.ucsc.galgal6.refgene/bioconductor-txdb.ggallus.ucsc.galgal6.refgene_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ggallus.ucsc.galgal6.refgene/bioconductor-txdb.ggallus.ucsc.galgal6.refgene_3.10.0_src_all.tar.gz"], "md5": "4d81026ecb786abf1fe0cb548238214c", "fn": "TxDb.Ggallus.UCSC.galGal6.refGene_3.10.0.tar.gz"}, "txdb.hsapiens.biomart.igis-2.3.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Hsapiens.BioMart.igis_2.3.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.BioMart.igis_2.3.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.biomart.igis/bioconductor-txdb.hsapiens.biomart.igis_2.3.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.biomart.igis/bioconductor-txdb.hsapiens.biomart.igis_2.3.2_src_all.tar.gz"], "md5": "75b793928d29bcd3f069b5986bc2cfae", "fn": "TxDb.Hsapiens.BioMart.igis_2.3.2.tar.gz"}, "txdb.hsapiens.ucsc.hg18.knowngene-3.2.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene_3.2.2_src_all.tar.gz"], "md5": "e8b32a672e87345c72bb30be73d1e2d6", "fn": "TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz"}, "txdb.hsapiens.ucsc.hg19.knowngene-3.2.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_3.2.2_src_all.tar.gz"], "md5": "61be88a81433958571b57d0952be48a0", "fn": "TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz"}, "txdb.hsapiens.ucsc.hg19.lincrnastranscripts-3.2.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts_3.2.2_src_all.tar.gz"], "md5": "a0d61cd90639c40b3d0bb6bdb043cf12", "fn": "TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz"}, "txdb.hsapiens.ucsc.hg38.knowngene-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_3.16.0_src_all.tar.gz"], "md5": "d2a6f04b1d1ec78ae3ccbfed3fa1e9cc", "fn": "TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0.tar.gz"}, "txdb.hsapiens.ucsc.hg38.refgene-3.15.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.refGene_3.15.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg38.refGene_3.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/bioconductor-txdb.hsapiens.ucsc.hg38.refgene_3.15.0_src_all.tar.gz"], "md5": "50e7c4ce068c4ca2d77a3c0b46a3ab45", "fn": "TxDb.Hsapiens.UCSC.hg38.refGene_3.15.0.tar.gz"}, "txdb.mmulatta.ucsc.rhemac10.refgene-3.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Mmulatta.UCSC.rheMac10.refGene_3.14.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmulatta.UCSC.rheMac10.refGene_3.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene/bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene_3.14.0_src_all.tar.gz"], "md5": "81b01b07d87ae91b4d9a269a2baf616e", "fn": "TxDb.Mmulatta.UCSC.rheMac10.refGene_3.14.0.tar.gz"}, "txdb.mmulatta.ucsc.rhemac3.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Mmulatta.UCSC.rheMac3.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmulatta.UCSC.rheMac3.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene_3.12.0_src_all.tar.gz"], "md5": "db84a9e85d613635d74002f11df41e1f", "fn": "TxDb.Mmulatta.UCSC.rheMac3.refGene_3.12.0.tar.gz"}, "txdb.mmulatta.ucsc.rhemac8.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Mmulatta.UCSC.rheMac8.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmulatta.UCSC.rheMac8.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene_3.12.0_src_all.tar.gz"], "md5": "8437e0a05ffd28b667c7b740e0db68a7", "fn": "TxDb.Mmulatta.UCSC.rheMac8.refGene_3.12.0.tar.gz"}, "txdb.mmusculus.ucsc.mm10.ensgene-3.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene_3.4.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene_3.4.0_src_all.tar.gz"], "md5": "88d65b714d1f86b456aee2b8524e9d84", "fn": "TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz"}, "txdb.mmusculus.ucsc.mm10.knowngene-3.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene_3.10.0_src_all.tar.gz"], "md5": "129b610bf05ec77451731196baa55bcc", "fn": "TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0.tar.gz"}, "txdb.mmusculus.ucsc.mm39.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm39.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm39.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/bioconductor-txdb.mmusculus.ucsc.mm39.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/bioconductor-txdb.mmusculus.ucsc.mm39.refgene_3.12.0_src_all.tar.gz"], "md5": "2525799b85e0a52bf274ab5eed51cd84", "fn": "TxDb.Mmusculus.UCSC.mm39.refGene_3.12.0.tar.gz"}, "txdb.mmusculus.ucsc.mm9.knowngene-3.2.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene_3.2.2_src_all.tar.gz"], "md5": "cb72af039b011033477363bda8ed9104", "fn": "TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz"}, "txdb.ptroglodytes.ucsc.pantro4.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Ptroglodytes.UCSC.panTro4.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Ptroglodytes.UCSC.panTro4.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene_3.12.0_src_all.tar.gz"], "md5": "9bdd3ba81561550f50250368d7d52eaa", "fn": "TxDb.Ptroglodytes.UCSC.panTro4.refGene_3.12.0.tar.gz"}, "txdb.ptroglodytes.ucsc.pantro5.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Ptroglodytes.UCSC.panTro5.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Ptroglodytes.UCSC.panTro5.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene_3.12.0_src_all.tar.gz"], "md5": "76ee1d253d1c8e54c12e8d5b9db93303", "fn": "TxDb.Ptroglodytes.UCSC.panTro5.refGene_3.12.0.tar.gz"}, "txdb.ptroglodytes.ucsc.pantro6.refgene-3.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Ptroglodytes.UCSC.panTro6.refGene_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Ptroglodytes.UCSC.panTro6.refGene_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene_3.10.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene_3.10.0_src_all.tar.gz"], "md5": "48a88973fe0e5117cadd5c816a46e6e9", "fn": "TxDb.Ptroglodytes.UCSC.panTro6.refGene_3.10.0.tar.gz"}, "txdb.rnorvegicus.biomart.igis-2.3.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Rnorvegicus.BioMart.igis_2.3.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.BioMart.igis_2.3.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.biomart.igis/bioconductor-txdb.rnorvegicus.biomart.igis_2.3.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.biomart.igis/bioconductor-txdb.rnorvegicus.biomart.igis_2.3.2_src_all.tar.gz"], "md5": "eaf695f63cd021074d68c76d148cdfb7", "fn": "TxDb.Rnorvegicus.BioMart.igis_2.3.2.tar.gz"}, "txdb.rnorvegicus.ucsc.rn4.ensgene-3.2.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene_3.2.2_src_all.tar.gz"], "md5": "6bf2ebc522c2828c036e52b2028792c1", "fn": "TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz"}, "txdb.rnorvegicus.ucsc.rn5.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn5.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn5.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene_3.12.0_src_all.tar.gz"], "md5": "8a93a15b37bf73e5c529c976c4561537", "fn": "TxDb.Rnorvegicus.UCSC.rn5.refGene_3.12.0.tar.gz"}, "txdb.rnorvegicus.ucsc.rn6.ncbirefseq-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn6.ncbiRefSeq_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn6.ncbiRefSeq_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq_3.12.0_src_all.tar.gz"], "md5": "6660ee000fbc956541728c6dadf1fca7", "fn": "TxDb.Rnorvegicus.UCSC.rn6.ncbiRefSeq_3.12.0.tar.gz"}, "txdb.rnorvegicus.ucsc.rn6.refgene-3.4.6": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.6.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene_3.4.6_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene_3.4.6_src_all.tar.gz"], "md5": "ea525daa75bcf165eb24f6e93f4dbf6c", "fn": "TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.6.tar.gz"}, "txdb.rnorvegicus.ucsc.rn7.refgene-3.15.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn7.refGene_3.15.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn7.refGene_3.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene_3.15.0_src_all.tar.gz"], "md5": "589dc0f8f4c6ee8f5ed11aeb95a74a7d", "fn": "TxDb.Rnorvegicus.UCSC.rn7.refGene_3.15.0.tar.gz"}, "txdb.scerevisiae.ucsc.saccer2.sgdgene-3.2.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene_3.2.2_src_all.tar.gz"], "md5": "8ce83ef2ba6cfc69f9b4435a0a047819", "fn": "TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz"}, "txdb.scerevisiae.ucsc.saccer3.sgdgene-3.2.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene_3.2.2_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene_3.2.2_src_all.tar.gz"], "md5": "afb23b3265730b9e59c2f07ab37cc3a0", "fn": "TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz"}, "txdb.sscrofa.ucsc.susscr11.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Sscrofa.UCSC.susScr11.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Sscrofa.UCSC.susScr11.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene_3.12.0_src_all.tar.gz"], "md5": "a6c5a2c402ad904a2f55099e391d18de", "fn": "TxDb.Sscrofa.UCSC.susScr11.refGene_3.12.0.tar.gz"}, "txdb.sscrofa.ucsc.susscr3.refgene-3.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Sscrofa.UCSC.susScr3.refGene_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Sscrofa.UCSC.susScr3.refGene_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene_3.12.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene_3.12.0_src_all.tar.gz"], "md5": "981602dc706e545d5acdf7590e222ca7", "fn": "TxDb.Sscrofa.UCSC.susScr3.refGene_3.12.0.tar.gz"}, "u133aaofav2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/u133aaofav2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/u133aaofav2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-u133aaofav2cdf/bioconductor-u133aaofav2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-u133aaofav2cdf/bioconductor-u133aaofav2cdf_2.18.0_src_all.tar.gz"], "md5": "716483ddb6664b8b7f0c58cd21136e8b", "fn": "u133aaofav2cdf_2.18.0.tar.gz"}, "u133x3p.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/u133x3p.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/u133x3p.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-u133x3p.db/bioconductor-u133x3p.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-u133x3p.db/bioconductor-u133x3p.db_3.2.3_src_all.tar.gz"], "md5": "1a36a09dc64b94728bf6ac75600b40c6", "fn": "u133x3p.db_3.2.3.tar.gz"}, "u133x3pcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/u133x3pcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/u133x3pcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-u133x3pcdf/bioconductor-u133x3pcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-u133x3pcdf/bioconductor-u133x3pcdf_2.18.0_src_all.tar.gz"], "md5": "ee4e62041bc8c63813e8cf8400ece2f3", "fn": "u133x3pcdf_2.18.0.tar.gz"}, "u133x3pprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/u133x3pprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/u133x3pprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-u133x3pprobe/bioconductor-u133x3pprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-u133x3pprobe/bioconductor-u133x3pprobe_2.18.0_src_all.tar.gz"], "md5": "81e2b00985688160805147bef0c638be", "fn": "u133x3pprobe_2.18.0.tar.gz"}, "ucscrepeatmasker-3.15.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/UCSCRepeatMasker_3.15.2.tar.gz", "https://bioarchive.galaxyproject.org/UCSCRepeatMasker_3.15.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ucscrepeatmasker/bioconductor-ucscrepeatmasker_3.15.2_src_all.tar.gz"], "md5": "ad19a6fbd936e478af88fa21bc918a29", "fn": "UCSCRepeatMasker_3.15.2.tar.gz"}, "uniprotkeywords-0.99.4": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/UniProtKeywords_0.99.4.tar.gz", "https://bioarchive.galaxyproject.org/UniProtKeywords_0.99.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-uniprotkeywords/bioconductor-uniprotkeywords_0.99.4_src_all.tar.gz"], "md5": "f3f91ac1b8eca20fabcf46cae4348ea5", "fn": "UniProtKeywords_0.99.4.tar.gz"}, "vitisviniferacdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/vitisviniferacdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/vitisviniferacdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vitisviniferacdf/bioconductor-vitisviniferacdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vitisviniferacdf/bioconductor-vitisviniferacdf_2.18.0_src_all.tar.gz"], "md5": "8eb491f3ffa3ff0814f5c155787ae160", "fn": "vitisviniferacdf_2.18.0.tar.gz"}, "vitisviniferaprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/vitisviniferaprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/vitisviniferaprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vitisviniferaprobe/bioconductor-vitisviniferaprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vitisviniferaprobe/bioconductor-vitisviniferaprobe_2.18.0_src_all.tar.gz"], "md5": "386c0d5e37896d073ac20970e88b3160", "fn": "vitisviniferaprobe_2.18.0.tar.gz"}, "wheatcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/wheatcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/wheatcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wheatcdf/bioconductor-wheatcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wheatcdf/bioconductor-wheatcdf_2.18.0_src_all.tar.gz"], "md5": "0abeeeb9700b8d93a1a83769bdd8480f", "fn": "wheatcdf_2.18.0.tar.gz"}, "wheatprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/wheatprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/wheatprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wheatprobe/bioconductor-wheatprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wheatprobe/bioconductor-wheatprobe_2.18.0_src_all.tar.gz"], "md5": "b602d5050239850515be9dce12286360", "fn": "wheatprobe_2.18.0.tar.gz"}, "worm.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/worm.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/worm.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-worm.db0/bioconductor-worm.db0_3.16.0_src_all.tar.gz"], "md5": "8c69f4127645a5c2c9c345a4f92d26d8", "fn": "worm.db0_3.16.0.tar.gz"}, "xenopus.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/xenopus.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/xenopus.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xenopus.db0/bioconductor-xenopus.db0_3.16.0_src_all.tar.gz"], "md5": "007bfcf52abad16cb04f1e95cdbee49a", "fn": "xenopus.db0_3.16.0.tar.gz"}, "xenopuslaeviscdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/xenopuslaeviscdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/xenopuslaeviscdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xenopuslaeviscdf/bioconductor-xenopuslaeviscdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xenopuslaeviscdf/bioconductor-xenopuslaeviscdf_2.18.0_src_all.tar.gz"], "md5": "9d09ff76471ae60faf71090e0638f240", "fn": "xenopuslaeviscdf_2.18.0.tar.gz"}, "xenopuslaevisprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/xenopuslaevisprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/xenopuslaevisprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xenopuslaevisprobe/bioconductor-xenopuslaevisprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xenopuslaevisprobe/bioconductor-xenopuslaevisprobe_2.18.0_src_all.tar.gz"], "md5": "06a25268a5ab57bddf28bbb364ea977b", "fn": "xenopuslaevisprobe_2.18.0.tar.gz"}, "xlaevis.db-3.2.3": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/xlaevis.db_3.2.3.tar.gz", "https://bioarchive.galaxyproject.org/xlaevis.db_3.2.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xlaevis.db/bioconductor-xlaevis.db_3.2.3_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xlaevis.db/bioconductor-xlaevis.db_3.2.3_src_all.tar.gz"], "md5": "deaffe47b4ee48a7edb159d8104dc241", "fn": "xlaevis.db_3.2.3.tar.gz"}, "xlaevis2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/xlaevis2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/xlaevis2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xlaevis2cdf/bioconductor-xlaevis2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xlaevis2cdf/bioconductor-xlaevis2cdf_2.18.0_src_all.tar.gz"], "md5": "9e4a80d66397299b4e66a8d6715ca4aa", "fn": "xlaevis2cdf_2.18.0.tar.gz"}, "xlaevis2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/xlaevis2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/xlaevis2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xlaevis2probe/bioconductor-xlaevis2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xlaevis2probe/bioconductor-xlaevis2probe_2.18.0_src_all.tar.gz"], "md5": "d86f8a05e106eb3123435da233ff851d", "fn": "xlaevis2probe_2.18.0.tar.gz"}, "xtrasnplocs.hsapiens.dbsnp144.grch37-0.99.12": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/XtraSNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.12.tar.gz", "https://bioarchive.galaxyproject.org/XtraSNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.12.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37_0.99.12_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37_0.99.12_src_all.tar.gz"], "md5": "758d024c50d2349036dc27cc689b4e5a", "fn": "XtraSNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.12.tar.gz"}, "xtrasnplocs.hsapiens.dbsnp144.grch38-0.99.12": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/XtraSNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.12.tar.gz", "https://bioarchive.galaxyproject.org/XtraSNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.12.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38_0.99.12_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38_0.99.12_src_all.tar.gz"], "md5": "c617aa805c7ecf60ee9283eb3c51b1c7", "fn": "XtraSNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.12.tar.gz"}, "xtropicaliscdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/xtropicaliscdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/xtropicaliscdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xtropicaliscdf/bioconductor-xtropicaliscdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xtropicaliscdf/bioconductor-xtropicaliscdf_2.18.0_src_all.tar.gz"], "md5": "253e3cde76a393789e124f395820e947", "fn": "xtropicaliscdf_2.18.0.tar.gz"}, "xtropicalisprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/xtropicalisprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/xtropicalisprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xtropicalisprobe/bioconductor-xtropicalisprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xtropicalisprobe/bioconductor-xtropicalisprobe_2.18.0_src_all.tar.gz"], "md5": "43d15a7e12edaec1bb5f24b87498b599", "fn": "xtropicalisprobe_2.18.0.tar.gz"}, "ye6100subacdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ye6100subacdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ye6100subacdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ye6100subacdf/bioconductor-ye6100subacdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ye6100subacdf/bioconductor-ye6100subacdf_2.18.0_src_all.tar.gz"], "md5": "27bd71410956bfe8bffc8de14b85bdb0", "fn": "ye6100subacdf_2.18.0.tar.gz"}, "ye6100subbcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ye6100subbcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ye6100subbcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ye6100subbcdf/bioconductor-ye6100subbcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ye6100subbcdf/bioconductor-ye6100subbcdf_2.18.0_src_all.tar.gz"], "md5": "ee9ec4bd941940745bad538d79bfeab4", "fn": "ye6100subbcdf_2.18.0.tar.gz"}, "ye6100subccdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ye6100subccdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ye6100subccdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ye6100subccdf/bioconductor-ye6100subccdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ye6100subccdf/bioconductor-ye6100subccdf_2.18.0_src_all.tar.gz"], "md5": "fcdfed29a695fe53b62bacfe13dfe0c1", "fn": "ye6100subccdf_2.18.0.tar.gz"}, "ye6100subdcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ye6100subdcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ye6100subdcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ye6100subdcdf/bioconductor-ye6100subdcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ye6100subdcdf/bioconductor-ye6100subdcdf_2.18.0_src_all.tar.gz"], "md5": "521b501ddbcdc680c3d27b5b201029b1", "fn": "ye6100subdcdf_2.18.0.tar.gz"}, "yeast.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/yeast.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/yeast.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeast.db0/bioconductor-yeast.db0_3.16.0_src_all.tar.gz"], "md5": "e69fc47d1c29e4b43d7f1b673460965e", "fn": "yeast.db0_3.16.0.tar.gz"}, "yeast2.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/yeast2.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/yeast2.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeast2.db/bioconductor-yeast2.db_3.13.0_src_all.tar.gz"], "md5": "add5784349cde4d01b75ea4472d25597", "fn": "yeast2.db_3.13.0.tar.gz"}, "yeast2cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/yeast2cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/yeast2cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeast2cdf/bioconductor-yeast2cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeast2cdf/bioconductor-yeast2cdf_2.18.0_src_all.tar.gz"], "md5": "0a718d78ae56bef9bad8168123038ac8", "fn": "yeast2cdf_2.18.0.tar.gz"}, "yeast2probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/yeast2probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/yeast2probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeast2probe/bioconductor-yeast2probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeast2probe/bioconductor-yeast2probe_2.18.0_src_all.tar.gz"], "md5": "3f52a2b7bd379624bc2966ca28c9ddf9", "fn": "yeast2probe_2.18.0.tar.gz"}, "ygs98.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ygs98.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/ygs98.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ygs98.db/bioconductor-ygs98.db_3.13.0_src_all.tar.gz"], "md5": "d21c0dc1ee0f7512ae921a501b425fd3", "fn": "ygs98.db_3.13.0.tar.gz"}, "ygs98cdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ygs98cdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ygs98cdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ygs98cdf/bioconductor-ygs98cdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ygs98cdf/bioconductor-ygs98cdf_2.18.0_src_all.tar.gz"], "md5": "ec7df7564cf28e093646325ec55baf1e", "fn": "ygs98cdf_2.18.0.tar.gz"}, "ygs98frmavecs-1.3.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ygs98frmavecs_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/ygs98frmavecs_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ygs98frmavecs/bioconductor-ygs98frmavecs_1.3.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ygs98frmavecs/bioconductor-ygs98frmavecs_1.3.0_src_all.tar.gz"], "md5": "e78c8447eb381b91dafb2f9688da39dc", "fn": "ygs98frmavecs_1.3.0.tar.gz"}, "ygs98probe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ygs98probe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ygs98probe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ygs98probe/bioconductor-ygs98probe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ygs98probe/bioconductor-ygs98probe_2.18.0_src_all.tar.gz"], "md5": "f40f21d7074818a4ee74a45b5533e89d", "fn": "ygs98probe_2.18.0.tar.gz"}, "zebrafish.db-3.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/zebrafish.db_3.13.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafish.db_3.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafish.db/bioconductor-zebrafish.db_3.13.0_src_all.tar.gz"], "md5": "64e40a61e81ac9397affb09880846559", "fn": "zebrafish.db_3.13.0.tar.gz"}, "zebrafish.db0-3.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/annotation/src/contrib/zebrafish.db0_3.16.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafish.db0_3.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafish.db0/bioconductor-zebrafish.db0_3.16.0_src_all.tar.gz"], "md5": "dacc0a32ee7a43a5efdc3282b2184504", "fn": "zebrafish.db0_3.16.0.tar.gz"}, "zebrafishcdf-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/zebrafishcdf_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafishcdf_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafishcdf/bioconductor-zebrafishcdf_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafishcdf/bioconductor-zebrafishcdf_2.18.0_src_all.tar.gz"], "md5": "04edbb632600c97610b86423c2d850e7", "fn": "zebrafishcdf_2.18.0.tar.gz"}, "zebrafishprobe-2.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/zebrafishprobe_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafishprobe_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafishprobe/bioconductor-zebrafishprobe_2.18.0_src_all.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafishprobe/bioconductor-zebrafishprobe_2.18.0_src_all.tar.gz"], "md5": "eea2747859afa763addc7313ab0a2452", "fn": "zebrafishprobe_2.18.0.tar.gz"}, "adductdata-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/adductData_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/adductData_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-adductdata/bioconductor-adductdata_1.13.0_src_all.tar.gz"], "md5": "f7bdef108829e66360d9980a094c076c", "fn": "adductData_1.13.0.tar.gz"}, "affycompdata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/affycompData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/affycompData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affycompdata/bioconductor-affycompdata_1.35.0_src_all.tar.gz"], "md5": "7f7289cfb331be5e649447a654cc99e5", "fn": "affycompData_1.35.0.tar.gz"}, "affydata-1.45.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/affydata_1.45.0.tar.gz", "https://bioarchive.galaxyproject.org/affydata_1.45.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affydata/bioconductor-affydata_1.45.0_src_all.tar.gz"], "md5": "eb7248342c402f03431386e385238c12", "fn": "affydata_1.45.0.tar.gz"}, "affyhgu133a2expr-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Affyhgu133A2Expr_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133A2Expr_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133a2expr/bioconductor-affyhgu133a2expr_1.33.0_src_all.tar.gz"], "md5": "3dc83464e541bcb8b4aad2e3d9918bea", "fn": "Affyhgu133A2Expr_1.33.0.tar.gz"}, "affyhgu133aexpr-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Affyhgu133aExpr_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133aExpr_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133aexpr/bioconductor-affyhgu133aexpr_1.35.0_src_all.tar.gz"], "md5": "cca6b5b450c8cf773653dee57727dd06", "fn": "Affyhgu133aExpr_1.35.0.tar.gz"}, "affyhgu133plus2expr-1.31.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Affyhgu133Plus2Expr_1.31.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133Plus2Expr_1.31.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133plus2expr/bioconductor-affyhgu133plus2expr_1.31.0_src_all.tar.gz"], "md5": "19ae44401f171e5db4a7dc0d99b5244a", "fn": "Affyhgu133Plus2Expr_1.31.0.tar.gz"}, "affymetrixdatatestfiles-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/AffymetrixDataTestFiles_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/AffymetrixDataTestFiles_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affymetrixdatatestfiles/bioconductor-affymetrixdatatestfiles_0.35.0_src_all.tar.gz"], "md5": "7e66d2018e02bb58c5eea8b5042a9392", "fn": "AffymetrixDataTestFiles_0.35.0.tar.gz"}, "affymoe4302expr-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Affymoe4302Expr_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/Affymoe4302Expr_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affymoe4302expr/bioconductor-affymoe4302expr_1.35.0_src_all.tar.gz"], "md5": "0b5eb08bf23fe69858041d13a0701d7a", "fn": "Affymoe4302Expr_1.35.0.tar.gz"}, "airway-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/airway_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/airway_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-airway/bioconductor-airway_1.17.0_src_all.tar.gz"], "md5": "b511a987d192a74f13c66b388ac2c8aa", "fn": "airway_1.17.0.tar.gz"}, "all-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ALL_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/ALL_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-all/bioconductor-all_1.39.0_src_all.tar.gz"], "md5": "2e8639047180f647b08ec054a631c528", "fn": "ALL_1.39.0.tar.gz"}, "allmll-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ALLMLL_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/ALLMLL_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-allmll/bioconductor-allmll_1.37.0_src_all.tar.gz"], "md5": "3cb133d5b6a10a1748894906a515855c", "fn": "ALLMLL_1.37.0.tar.gz"}, "alpinedata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/alpineData_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/alpineData_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-alpinedata/bioconductor-alpinedata_1.23.0_src_all.tar.gz"], "md5": "ab1bdaa198a27eb35e2d1dc067962af6", "fn": "alpineData_1.23.0.tar.gz"}, "ampaffyexample-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/AmpAffyExample_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/AmpAffyExample_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ampaffyexample/bioconductor-ampaffyexample_1.37.0_src_all.tar.gz"], "md5": "f7d456a2f49271ab1b521f83fe46d3a3", "fn": "AmpAffyExample_1.37.0.tar.gz"}, "aneufinderdata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/AneuFinderData_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/AneuFinderData_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-aneufinderdata/bioconductor-aneufinderdata_1.25.0_src_all.tar.gz"], "md5": "70bfddfd056387ad8e061abbbbd43f15", "fn": "AneuFinderData_1.25.0.tar.gz"}, "antiprofilesdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/antiProfilesData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/antiProfilesData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-antiprofilesdata/bioconductor-antiprofilesdata_1.33.0_src_all.tar.gz"], "md5": "8eeef0998371557a0e02df8f0a01cdc9", "fn": "antiProfilesData_1.33.0.tar.gz"}, "aracne.networks-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/aracne.networks_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/aracne.networks_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-aracne.networks/bioconductor-aracne.networks_1.23.0_src_all.tar.gz"], "md5": "5834e9955b8bf65823b890b78a100230", "fn": "aracne.networks_1.23.0.tar.gz"}, "arrmdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ARRmData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/ARRmData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-arrmdata/bioconductor-arrmdata_1.33.0_src_all.tar.gz"], "md5": "34aed24b7ef52e068f5620e7232fa205", "fn": "ARRmData_1.33.0.tar.gz"}, "ashkenazimsonchr21-1.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/AshkenazimSonChr21_1.27.0.tar.gz", "https://bioarchive.galaxyproject.org/AshkenazimSonChr21_1.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ashkenazimsonchr21/bioconductor-ashkenazimsonchr21_1.27.0_src_all.tar.gz"], "md5": "2d2eefb52dcfeeb340bc080d6d56d5ab", "fn": "AshkenazimSonChr21_1.27.0.tar.gz"}, "asicsdata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ASICSdata_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/ASICSdata_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-asicsdata/bioconductor-asicsdata_1.17.0_src_all.tar.gz"], "md5": "917b33b8529f1afb89f3e8e5f5ec09d6", "fn": "ASICSdata_1.17.0.tar.gz"}, "assessorfdata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/AssessORFData_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/AssessORFData_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-assessorfdata/bioconductor-assessorfdata_1.15.0_src_all.tar.gz"], "md5": "0da3442ef5aa5e70f658ff76b399231f", "fn": "AssessORFData_1.15.0.tar.gz"}, "bcellviper-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bcellViper_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/bcellViper_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bcellviper/bioconductor-bcellviper_1.33.0_src_all.tar.gz"], "md5": "02ea741280b78f5d11594a91f6bd891b", "fn": "bcellViper_1.33.0.tar.gz"}, "beadarrayexampledata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/beadarrayExampleData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/beadarrayExampleData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadarrayexampledata/bioconductor-beadarrayexampledata_1.35.0_src_all.tar.gz"], "md5": "bf8c7a219051a3c11576a647c45a84a0", "fn": "beadarrayExampleData_1.35.0.tar.gz"}, "beadarrayusecases-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BeadArrayUseCases_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/BeadArrayUseCases_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadarrayusecases/bioconductor-beadarrayusecases_1.35.0_src_all.tar.gz"], "md5": "cb6810c1e95d356e4c7e901039d6727d", "fn": "BeadArrayUseCases_1.35.0.tar.gz"}, "beadsorted.saliva.epic-1.5.3": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BeadSorted.Saliva.EPIC_1.5.3.tar.gz", "https://bioarchive.galaxyproject.org/BeadSorted.Saliva.EPIC_1.5.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadsorted.saliva.epic/bioconductor-beadsorted.saliva.epic_1.5.3_src_all.tar.gz"], "md5": "55e6a2682d45d3d804ed9b9e63b3f630", "fn": "BeadSorted.Saliva.EPIC_1.5.3.tar.gz"}, "benchmarkfdrdata2019-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/benchmarkfdrData2019_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/benchmarkfdrData2019_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-benchmarkfdrdata2019/bioconductor-benchmarkfdrdata2019_1.11.0_src_all.tar.gz"], "md5": "853f4f310575f873f9ef10fb0aa1b3a9", "fn": "benchmarkfdrData2019_1.11.0.tar.gz"}, "beta7-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/beta7_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/beta7_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beta7/bioconductor-beta7_1.35.0_src_all.tar.gz"], "md5": "e1d98c49f9862f483efe8461c5584b2a", "fn": "beta7_1.35.0.tar.gz"}, "bioimagedbs-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BioImageDbs_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/BioImageDbs_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bioimagedbs/bioconductor-bioimagedbs_1.5.0_src_all.tar.gz"], "md5": "dcbbbe1c7406a487cae2c60a1ff5d67c", "fn": "BioImageDbs_1.5.0.tar.gz"}, "biotmledata-1.21.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/biotmleData_1.21.0.tar.gz", "https://bioarchive.galaxyproject.org/biotmleData_1.21.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biotmledata/bioconductor-biotmledata_1.21.0_src_all.tar.gz"], "md5": "e65f071b28d3dec143a8eac73def1960", "fn": "biotmleData_1.21.0.tar.gz"}, "biscuiteerdata-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/biscuiteerData_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/biscuiteerData_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biscuiteerdata/bioconductor-biscuiteerdata_1.11.0_src_all.tar.gz"], "md5": "acefcab6344943c841e6b7acb3302e0e", "fn": "biscuiteerData_1.11.0.tar.gz"}, "bladderbatch-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bladderbatch_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/bladderbatch_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bladderbatch/bioconductor-bladderbatch_1.35.0_src_all.tar.gz"], "md5": "4a22b6770f01e6ba2e5a9cd8acf5e03d", "fn": "bladderbatch_1.35.0.tar.gz"}, "blimatestingdata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/blimaTestingData_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/blimaTestingData_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-blimatestingdata/bioconductor-blimatestingdata_1.17.0_src_all.tar.gz"], "md5": "7dfee1136a8cd4ec2ceadca17f41b8e7", "fn": "blimaTestingData_1.17.0.tar.gz"}, "bloodcancermultiomics2017-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BloodCancerMultiOmics2017_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/BloodCancerMultiOmics2017_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bloodcancermultiomics2017/bioconductor-bloodcancermultiomics2017_1.17.0_src_all.tar.gz"], "md5": "aa2fa7d4fd7e0dd3a6d837b1e25f00fc", "fn": "BloodCancerMultiOmics2017_1.17.0.tar.gz"}, "bodymaprat-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bodymapRat_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/bodymapRat_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bodymaprat/bioconductor-bodymaprat_1.13.0_src_all.tar.gz"], "md5": "9af11e23233d6adf602a93c664464a20", "fn": "bodymapRat_1.13.0.tar.gz"}, "breakpointrdata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breakpointRdata_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/breakpointRdata_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breakpointrdata/bioconductor-breakpointrdata_1.15.0_src_all.tar.gz"], "md5": "46852ceea4c6bceab7e03988b9323456", "fn": "breakpointRdata_1.15.0.tar.gz"}, "breastcancermainz-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breastCancerMAINZ_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerMAINZ_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancermainz/bioconductor-breastcancermainz_1.35.0_src_all.tar.gz"], "md5": "035be150382cf0c3e4c0fbd36266b94d", "fn": "breastCancerMAINZ_1.35.0.tar.gz"}, "breastcancernki-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breastCancerNKI_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerNKI_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancernki/bioconductor-breastcancernki_1.35.0_src_all.tar.gz"], "md5": "865b32139e93955b3260c4e6c3f9c5b0", "fn": "breastCancerNKI_1.35.0.tar.gz"}, "breastcancertransbig-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breastCancerTRANSBIG_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerTRANSBIG_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancertransbig/bioconductor-breastcancertransbig_1.35.0_src_all.tar.gz"], "md5": "8b5ce45ac2e0fd9985311fcbbf40b0a0", "fn": "breastCancerTRANSBIG_1.35.0.tar.gz"}, "breastcancerunt-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breastCancerUNT_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerUNT_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancerunt/bioconductor-breastcancerunt_1.35.0_src_all.tar.gz"], "md5": "35a5e3b9d90fd0eca80b2e41861f72e0", "fn": "breastCancerUNT_1.35.0.tar.gz"}, "breastcancerupp-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breastCancerUPP_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerUPP_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancerupp/bioconductor-breastcancerupp_1.35.0_src_all.tar.gz"], "md5": "641b81d2297680424e171446ef3932f0", "fn": "breastCancerUPP_1.35.0.tar.gz"}, "breastcancervdx-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breastCancerVDX_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerVDX_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancervdx/bioconductor-breastcancervdx_1.35.0_src_all.tar.gz"], "md5": "c03948851a026690cc126b1dbccfc437", "fn": "breastCancerVDX_1.35.0.tar.gz"}, "brgedata-1.19.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/brgedata_1.19.0.tar.gz", "https://bioarchive.galaxyproject.org/brgedata_1.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-brgedata/bioconductor-brgedata_1.19.0_src_all.tar.gz"], "md5": "8f208a0c31fc3f213a2e98664fb76f6f", "fn": "brgedata_1.19.0.tar.gz"}, "bronchialil13-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bronchialIL13_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/bronchialIL13_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bronchialil13/bioconductor-bronchialil13_1.35.0_src_all.tar.gz"], "md5": "49c4c7883c35ad7f5ad2bb9fd653dbaf", "fn": "bronchialIL13_1.35.0.tar.gz"}, "bsseqdata-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bsseqData_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/bsseqData_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsseqdata/bioconductor-bsseqdata_0.35.0_src_all.tar.gz"], "md5": "d28b6df2057f7446596e324349c3b6e3", "fn": "bsseqData_0.35.0.tar.gz"}, "cancerdata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/cancerdata_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/cancerdata_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cancerdata/bioconductor-cancerdata_1.35.0_src_all.tar.gz"], "md5": "ae810e3851f437e7e8fed62c3847654a", "fn": "cancerdata_1.35.0.tar.gz"}, "cardinalworkflows-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CardinalWorkflows_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/CardinalWorkflows_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cardinalworkflows/bioconductor-cardinalworkflows_1.29.0_src_all.tar.gz"], "md5": "c45b20fee59776be3f8b3d72044fc0df", "fn": "CardinalWorkflows_1.29.0.tar.gz"}, "ccdata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ccdata_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/ccdata_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ccdata/bioconductor-ccdata_1.23.0_src_all.tar.gz"], "md5": "60a8e955f832f304a6efb064fc7b745d", "fn": "ccdata_1.23.0.tar.gz"}, "ccl4-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CCl4_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/CCl4_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ccl4/bioconductor-ccl4_1.35.0_src_all.tar.gz"], "md5": "e93aff764de9700c7ec35004adcf9e58", "fn": "CCl4_1.35.0.tar.gz"}, "cctutorial-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ccTutorial_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/ccTutorial_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cctutorial/bioconductor-cctutorial_1.35.0_src_all.tar.gz"], "md5": "bff2ed77e233015b1c9d68b554b15d54", "fn": "ccTutorial_1.35.0.tar.gz"}, "celarefdata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/celarefData_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/celarefData_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celarefdata/bioconductor-celarefdata_1.15.0_src_all.tar.gz"], "md5": "e8a6ed55b993243f44e59128164408f6", "fn": "celarefData_1.15.0.tar.gz"}, "celldex-1.7.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/celldex_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/celldex_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celldex/bioconductor-celldex_1.7.0_src_all.tar.gz"], "md5": "0aeb9f9a2706022e7e176f85b5b3cf2c", "fn": "celldex_1.7.0.tar.gz"}, "cellmapperdata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CellMapperData_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/CellMapperData_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cellmapperdata/bioconductor-cellmapperdata_1.23.0_src_all.tar.gz"], "md5": "f5d3a8da2952ad4370c076b7d4eeaf87", "fn": "CellMapperData_1.23.0.tar.gz"}, "champdata-2.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ChAMPdata_2.29.0.tar.gz", "https://bioarchive.galaxyproject.org/ChAMPdata_2.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-champdata/bioconductor-champdata_2.29.0_src_all.tar.gz"], "md5": "2f1532eaaf56be4fc29c5440c573b780", "fn": "ChAMPdata_2.29.0.tar.gz"}, "chic.data-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ChIC.data_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIC.data_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chic.data/bioconductor-chic.data_1.17.0_src_all.tar.gz"], "md5": "bb4837e672e71ea19f267efb7c73e628", "fn": "ChIC.data_1.17.0.tar.gz"}, "chimphumanbraindata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ChimpHumanBrainData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/ChimpHumanBrainData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chimphumanbraindata/bioconductor-chimphumanbraindata_1.35.0_src_all.tar.gz"], "md5": "563b8a3cc9493f495231abd05186dc84", "fn": "ChimpHumanBrainData_1.35.0.tar.gz"}, "chipenrich.data-2.21.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/chipenrich.data_2.21.0.tar.gz", "https://bioarchive.galaxyproject.org/chipenrich.data_2.21.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipenrich.data/bioconductor-chipenrich.data_2.21.0_src_all.tar.gz"], "md5": "abac22075b37333ed5f75812bdf14c8b", "fn": "chipenrich.data_2.21.0.tar.gz"}, "chipexoqualexample-1.21.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ChIPexoQualExample_1.21.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIPexoQualExample_1.21.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipexoqualexample/bioconductor-chipexoqualexample_1.21.0_src_all.tar.gz"], "md5": "3eb292504d16ae828529dc19773ff386", "fn": "ChIPexoQualExample_1.21.0.tar.gz"}, "chipseqdbdata-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/chipseqDBData_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/chipseqDBData_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipseqdbdata/bioconductor-chipseqdbdata_1.13.0_src_all.tar.gz"], "md5": "1f161da550dcf468c611c4e749609252", "fn": "chipseqDBData_1.13.0.tar.gz"}, "chipxpressdata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ChIPXpressData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIPXpressData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipxpressdata/bioconductor-chipxpressdata_1.35.0_src_all.tar.gz"], "md5": "d9ec5e7450965cdb1852c6665258baae", "fn": "ChIPXpressData_1.35.0.tar.gz"}, "chromstardata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/chromstaRData_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/chromstaRData_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chromstardata/bioconductor-chromstardata_1.23.0_src_all.tar.gz"], "md5": "316d8ebd62a38259a97249f3155169c3", "fn": "chromstaRData_1.23.0.tar.gz"}, "cll-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CLL_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/CLL_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cll/bioconductor-cll_1.37.0_src_all.tar.gz"], "md5": "78dc93ad95f5c8e0cdf74d770ee107c3", "fn": "CLL_1.37.0.tar.gz"}, "cllmethylation-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CLLmethylation_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/CLLmethylation_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cllmethylation/bioconductor-cllmethylation_1.17.0_src_all.tar.gz"], "md5": "6b53bdfc9b8fcd807c8b21d577724603", "fn": "CLLmethylation_1.17.0.tar.gz"}, "clumsiddata-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CluMSIDdata_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/CluMSIDdata_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clumsiddata/bioconductor-clumsiddata_1.13.0_src_all.tar.gz"], "md5": "91ea4550cba4a816ac33416dd927c204", "fn": "CluMSIDdata_1.13.0.tar.gz"}, "clustifyrdatahub-1.7.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/clustifyrdatahub_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/clustifyrdatahub_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clustifyrdatahub/bioconductor-clustifyrdatahub_1.7.0_src_all.tar.gz"], "md5": "e21443c515d13ffad9583051de6eb7f9", "fn": "clustifyrdatahub_1.7.0.tar.gz"}, "cmap2data-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/cMap2data_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/cMap2data_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cmap2data/bioconductor-cmap2data_1.33.0_src_all.tar.gz"], "md5": "cb332a4a2cc9e6ac33d707343e7d9a50", "fn": "cMap2data_1.33.0.tar.gz"}, "cnvgsadata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/cnvGSAdata_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/cnvGSAdata_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cnvgsadata/bioconductor-cnvgsadata_1.33.0_src_all.tar.gz"], "md5": "69791ec6259062ccb7d6878d693b2a93", "fn": "cnvGSAdata_1.33.0.tar.gz"}, "cohcapanno-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/COHCAPanno_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/COHCAPanno_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cohcapanno/bioconductor-cohcapanno_1.33.0_src_all.tar.gz"], "md5": "a752e8bf0a3a8a2055875473128af8e4", "fn": "COHCAPanno_1.33.0.tar.gz"}, "colonca-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/colonCA_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/colonCA_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-colonca/bioconductor-colonca_1.39.0_src_all.tar.gz"], "md5": "b2c547250495b0f07f7be6d6b2d8d9ee", "fn": "colonCA_1.39.0.tar.gz"}, "confessdata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CONFESSdata_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/CONFESSdata_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-confessdata/bioconductor-confessdata_1.25.0_src_all.tar.gz"], "md5": "1183ab67900e96c15b99094ccf9682a8", "fn": "CONFESSdata_1.25.0.tar.gz"}, "connectivitymap-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ConnectivityMap_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/ConnectivityMap_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-connectivitymap/bioconductor-connectivitymap_1.33.0_src_all.tar.gz"], "md5": "092ead10d2076e80304552f15a798a6b", "fn": "ConnectivityMap_1.33.0.tar.gz"}, "copdsexualdimorphism.data-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/COPDSexualDimorphism.data_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/COPDSexualDimorphism.data_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copdsexualdimorphism.data/bioconductor-copdsexualdimorphism.data_1.33.0_src_all.tar.gz"], "md5": "31f19076ead578c5935f91fb9c94ecd1", "fn": "COPDSexualDimorphism.data_1.33.0.tar.gz"}, "copyhelper-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CopyhelpeR_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/CopyhelpeR_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copyhelper/bioconductor-copyhelper_1.29.0_src_all.tar.gz"], "md5": "fbe6ed1ae63caf241aeb6b3a45d92df1", "fn": "CopyhelpeR_1.29.0.tar.gz"}, "copyneutralima-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CopyNeutralIMA_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/CopyNeutralIMA_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copyneutralima/bioconductor-copyneutralima_1.15.0_src_all.tar.gz"], "md5": "5fdee9e6051aebcb432b3a39190ce577", "fn": "CopyNeutralIMA_1.15.0.tar.gz"}, "cosmic.67-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/COSMIC.67_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/COSMIC.67_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cosmic.67/bioconductor-cosmic.67_1.34.0_src_all.tar.gz"], "md5": "d877dcb6f30a3cb7ce86a984d5106843", "fn": "COSMIC.67_1.34.0.tar.gz"}, "crcl18-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CRCL18_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/CRCL18_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-crcl18/bioconductor-crcl18_1.17.0_src_all.tar.gz"], "md5": "7cda2fdb7a0c0371b1ed9647c7933861", "fn": "CRCL18_1.17.0.tar.gz"}, "crisprscoredata-1.1.4": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/crisprScoreData_1.1.4.tar.gz", "https://bioarchive.galaxyproject.org/crisprScoreData_1.1.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-crisprscoredata/bioconductor-crisprscoredata_1.1.4_src_all.tar.gz"], "md5": "a019dcfbfe4d3e7ef0248c04abe79991", "fn": "crisprScoreData_1.1.4.tar.gz"}, "curatedadipoarray-1.9.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedAdipoArray_1.9.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoArray_1.9.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadipoarray/bioconductor-curatedadipoarray_1.9.0_src_all.tar.gz"], "md5": "a42d5e328d173c9871b1360de440b974", "fn": "curatedAdipoArray_1.9.0.tar.gz"}, "curatedadipochip-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedAdipoChIP_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoChIP_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadipochip/bioconductor-curatedadipochip_1.13.0_src_all.tar.gz"], "md5": "2e7308eafaded3ac0a0f97bc74d1a020", "fn": "curatedAdipoChIP_1.13.0.tar.gz"}, "curatedadiporna-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedAdipoRNA_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoRNA_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadiporna/bioconductor-curatedadiporna_1.13.0_src_all.tar.gz"], "md5": "ab1250a2fdf3815509eb7fe45fd21813", "fn": "curatedAdipoRNA_1.13.0.tar.gz"}, "curatedbladderdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedBladderData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedBladderData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedbladderdata/bioconductor-curatedbladderdata_1.33.0_src_all.tar.gz"], "md5": "8b69b718e8e8de452affe947cd418b25", "fn": "curatedBladderData_1.33.0.tar.gz"}, "curatedbreastdata-2.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedBreastData_2.25.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedBreastData_2.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedbreastdata/bioconductor-curatedbreastdata_2.25.0_src_all.tar.gz"], "md5": "ffe0dc08d4c30b7c01a518a6e0978413", "fn": "curatedBreastData_2.25.0.tar.gz"}, "curatedcrcdata-2.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedCRCData_2.29.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedCRCData_2.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedcrcdata/bioconductor-curatedcrcdata_2.29.0_src_all.tar.gz"], "md5": "d1756e19a6aa3dd9bef2da4068575d73", "fn": "curatedCRCData_2.29.0.tar.gz"}, "curatedmetagenomicdata-3.5.3": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedMetagenomicData_3.5.3.tar.gz", "https://bioarchive.galaxyproject.org/curatedMetagenomicData_3.5.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedmetagenomicdata/bioconductor-curatedmetagenomicdata_3.5.3_src_all.tar.gz"], "md5": "f0fdcbea91c0e96231af934adb7abeb6", "fn": "curatedMetagenomicData_3.5.3.tar.gz"}, "curatedovariandata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedOvarianData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedOvarianData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedovariandata/bioconductor-curatedovariandata_1.35.0_src_all.tar.gz"], "md5": "2d40967e621ba9cfa668208104104b38", "fn": "curatedOvarianData_1.35.0.tar.gz"}, "curatedtbdata-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedTBData_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedTBData_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedtbdata/bioconductor-curatedtbdata_1.3.0_src_all.tar.gz"], "md5": "56f1be51f41d3880559e69099d95d892", "fn": "curatedTBData_1.3.0.tar.gz"}, "curatedtcgadata-1.19.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedTCGAData_1.19.2.tar.gz", "https://bioarchive.galaxyproject.org/curatedTCGAData_1.19.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedtcgadata/bioconductor-curatedtcgadata_1.19.2_src_all.tar.gz"], "md5": "41531a34565c73f2e283d54c23d6a9e1", "fn": "curatedTCGAData_1.19.2.tar.gz"}, "dapardata-1.27.3": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DAPARdata_1.27.3.tar.gz", "https://bioarchive.galaxyproject.org/DAPARdata_1.27.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dapardata/bioconductor-dapardata_1.27.3_src_all.tar.gz"], "md5": "bf958cfd896d6594f2f373f79a3112dd", "fn": "DAPARdata_1.27.3.tar.gz"}, "davidtiling-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/davidTiling_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/davidTiling_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-davidtiling/bioconductor-davidtiling_1.37.0_src_all.tar.gz"], "md5": "5fa3cbda64eb9e316ac95a60c8accaff", "fn": "davidTiling_1.37.0.tar.gz"}, "depmap-1.11.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/depmap_1.11.2.tar.gz", "https://bioarchive.galaxyproject.org/depmap_1.11.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-depmap/bioconductor-depmap_1.11.2_src_all.tar.gz"], "md5": "9941cd0aa923d6490b9626f8f0910522", "fn": "depmap_1.11.2.tar.gz"}, "derfinderdata-2.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/derfinderData_2.15.0.tar.gz", "https://bioarchive.galaxyproject.org/derfinderData_2.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-derfinderdata/bioconductor-derfinderdata_2.15.0_src_all.tar.gz"], "md5": "48fd28bb742d7c2c6a2dfe21ddf70e6c", "fn": "derfinderData_2.15.0.tar.gz"}, "desousa2013-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DeSousa2013_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/DeSousa2013_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-desousa2013/bioconductor-desousa2013_1.33.0_src_all.tar.gz"], "md5": "2f4b23c47cca2fd9decc870bbe6fd7c4", "fn": "DeSousa2013_1.33.0.tar.gz"}, "dexmadata-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DExMAdata_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/DExMAdata_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dexmadata/bioconductor-dexmadata_1.5.0_src_all.tar.gz"], "md5": "b8087b44f7e890b4132565f89e6f0a01", "fn": "DExMAdata_1.5.0.tar.gz"}, "diffloopdata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/diffloopdata_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/diffloopdata_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-diffloopdata/bioconductor-diffloopdata_1.25.0_src_all.tar.gz"], "md5": "3030cfcc5aff94e110fddc60354353e1", "fn": "diffloopdata_1.25.0.tar.gz"}, "diggitdata-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/diggitdata_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/diggitdata_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-diggitdata/bioconductor-diggitdata_1.29.0_src_all.tar.gz"], "md5": "bf2502604a31578d57df2e1dded0d236", "fn": "diggitdata_1.29.0.tar.gz"}, "dlbcl-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DLBCL_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/DLBCL_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dlbcl/bioconductor-dlbcl_1.37.0_src_all.tar.gz"], "md5": "b0ce5033e4bb2337c229dc71a2a1a346", "fn": "DLBCL_1.37.0.tar.gz"}, "dmelsgi-1.29.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DmelSGI_1.29.1.tar.gz", "https://bioarchive.galaxyproject.org/DmelSGI_1.29.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dmelsgi/bioconductor-dmelsgi_1.29.1_src_all.tar.gz"], "md5": "2a426748e03fdb05c2fc71f105222ce5", "fn": "DmelSGI_1.29.1.tar.gz"}, "dmrcatedata-2.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DMRcatedata_2.15.0.tar.gz", "https://bioarchive.galaxyproject.org/DMRcatedata_2.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dmrcatedata/bioconductor-dmrcatedata_2.15.0_src_all.tar.gz"], "md5": "33cd820499c1fb6488cdef2b2ef7e95a", "fn": "DMRcatedata_2.15.0.tar.gz"}, "donapllp2013-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DonaPLLP2013_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/DonaPLLP2013_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-donapllp2013/bioconductor-donapllp2013_1.35.0_src_all.tar.gz"], "md5": "69237e3c870ff29f281332a32624562a", "fn": "DonaPLLP2013_1.35.0.tar.gz"}, "dorothea-1.9.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/dorothea_1.9.0.tar.gz", "https://bioarchive.galaxyproject.org/dorothea_1.9.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dorothea/bioconductor-dorothea_1.9.0_src_all.tar.gz"], "md5": "d84571e5e954215fd5a1a56186754b69", "fn": "dorothea_1.9.0.tar.gz"}, "dresscheck-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/dressCheck_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/dressCheck_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dresscheck/bioconductor-dresscheck_0.35.0_src_all.tar.gz"], "md5": "782d9a2c8501061a9e236af3f279687c", "fn": "dressCheck_0.35.0.tar.gz"}, "droplettestfiles-1.7.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DropletTestFiles_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/DropletTestFiles_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-droplettestfiles/bioconductor-droplettestfiles_1.7.0_src_all.tar.gz"], "md5": "05e9b3f6b0c67715b1056ca74a32a433", "fn": "DropletTestFiles_1.7.0.tar.gz"}, "drugvsdiseasedata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DrugVsDiseasedata_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/DrugVsDiseasedata_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drugvsdiseasedata/bioconductor-drugvsdiseasedata_1.33.0_src_all.tar.gz"], "md5": "5cf59b0f5d6ac32d90d17f7d68f2daf7", "fn": "DrugVsDiseasedata_1.33.0.tar.gz"}, "duoclustering2018-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DuoClustering2018_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/DuoClustering2018_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-duoclustering2018/bioconductor-duoclustering2018_1.15.0_src_all.tar.gz"], "md5": "24f191e908b3b02322dd89508c784dc0", "fn": "DuoClustering2018_1.15.0.tar.gz"}, "dvddata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DvDdata_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/DvDdata_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dvddata/bioconductor-dvddata_1.33.0_src_all.tar.gz"], "md5": "ba8583f5689b5205dfb6d1adf70ae173", "fn": "DvDdata_1.33.0.tar.gz"}, "dyebiasexamples-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/dyebiasexamples_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/dyebiasexamples_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dyebiasexamples/bioconductor-dyebiasexamples_1.37.0_src_all.tar.gz"], "md5": "9875c284f5e3b185f712ffac9b5f885d", "fn": "dyebiasexamples_1.37.0.tar.gz"}, "easierdata-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/easierData_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/easierData_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-easierdata/bioconductor-easierdata_1.3.0_src_all.tar.gz"], "md5": "5ad8e103c1923dfe666922ec1650eb01", "fn": "easierData_1.3.0.tar.gz"}, "eatonetalchipseq-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/EatonEtAlChIPseq_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/EatonEtAlChIPseq_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-eatonetalchipseq/bioconductor-eatonetalchipseq_0.35.0_src_all.tar.gz"], "md5": "074f8622a6a55925f806206afc9d9453", "fn": "EatonEtAlChIPseq_0.35.0.tar.gz"}, "ecolileucine-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ecoliLeucine_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliLeucine_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolileucine/bioconductor-ecolileucine_1.37.0_src_all.tar.gz"], "md5": "6439893bbc79683e340532f46a938794", "fn": "ecoliLeucine_1.37.0.tar.gz"}, "egseadata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/EGSEAdata_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/EGSEAdata_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-egseadata/bioconductor-egseadata_1.25.0_src_all.tar.gz"], "md5": "de4580a90bd10aec4474965ed38969fc", "fn": "EGSEAdata_1.25.0.tar.gz"}, "elmer.data-2.21.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ELMER.data_2.21.0.tar.gz", "https://bioarchive.galaxyproject.org/ELMER.data_2.21.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-elmer.data/bioconductor-elmer.data_2.21.0_src_all.tar.gz"], "md5": "7f2d82a3f1a676f1d61af0348e2d0433", "fn": "ELMER.data_2.21.0.tar.gz"}, "emtdata-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/emtdata_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/emtdata_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-emtdata/bioconductor-emtdata_1.5.0_src_all.tar.gz"], "md5": "55ff8734578ed3523625c2a0fc437218", "fn": "emtdata_1.5.0.tar.gz"}, "epimix.data-0.99.5": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/EpiMix.data_0.99.5.tar.gz", "https://bioarchive.galaxyproject.org/EpiMix.data_0.99.5.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epimix.data/bioconductor-epimix.data_0.99.5_src_all.tar.gz"], "md5": "ac81f60fc4712a692fcb75b0fbafdaa8", "fn": "EpiMix.data_0.99.5.tar.gz"}, "epimutacionsdata-1.1.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/epimutacionsData_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/epimutacionsData_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epimutacionsdata/bioconductor-epimutacionsdata_1.1.0_src_all.tar.gz"], "md5": "377137aa2cb358c0f4ecffad7797a6d5", "fn": "epimutacionsData_1.1.0.tar.gz"}, "estrogen-1.43.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/estrogen_1.43.0.tar.gz", "https://bioarchive.galaxyproject.org/estrogen_1.43.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-estrogen/bioconductor-estrogen_1.43.0_src_all.tar.gz"], "md5": "57639fc79be1962b0f5e61e5d73f467d", "fn": "estrogen_1.43.0.tar.gz"}, "etec16s-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/etec16s_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/etec16s_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-etec16s/bioconductor-etec16s_1.25.0_src_all.tar.gz"], "md5": "f264cbe341d5c492b493fbedf6169ab6", "fn": "etec16s_1.25.0.tar.gz"}, "ewcedata-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ewceData_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/ewceData_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ewcedata/bioconductor-ewcedata_1.5.0_src_all.tar.gz"], "md5": "26a398a1f17ac1f456a94336cf01c91b", "fn": "ewceData_1.5.0.tar.gz"}, "faahko-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/faahKO_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/faahKO_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-faahko/bioconductor-faahko_1.37.0_src_all.tar.gz"], "md5": "29689a0406096b7f2350296bb28cab0c", "fn": "faahKO_1.37.0.tar.gz"}, "fabiadata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/fabiaData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/fabiaData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fabiadata/bioconductor-fabiadata_1.35.0_src_all.tar.gz"], "md5": "a97042ed4bd7333d6d03765e7d18e41f", "fn": "fabiaData_1.35.0.tar.gz"}, "fantom3and4cage-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FANTOM3and4CAGE_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/FANTOM3and4CAGE_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fantom3and4cage/bioconductor-fantom3and4cage_1.33.0_src_all.tar.gz"], "md5": "ef58ff673fa9e87360c1b2597ed630cd", "fn": "FANTOM3and4CAGE_1.33.0.tar.gz"}, "ffpeexampledata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ffpeExampleData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/ffpeExampleData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ffpeexampledata/bioconductor-ffpeexampledata_1.35.0_src_all.tar.gz"], "md5": "1f5b07dd83b975d47c0ee8ae853f4461", "fn": "ffpeExampleData_1.35.0.tar.gz"}, "fibroeset-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/fibroEset_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/fibroEset_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fibroeset/bioconductor-fibroeset_1.39.0_src_all.tar.gz"], "md5": "397b83d144aceabad6100ce9a40788b2", "fn": "fibroEset_1.39.0.tar.gz"}, "fieldeffectcrc-1.7.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FieldEffectCrc_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/FieldEffectCrc_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fieldeffectcrc/bioconductor-fieldeffectcrc_1.7.0_src_all.tar.gz"], "md5": "4bcdd34f91c52fe0fdd458071943bf18", "fn": "FieldEffectCrc_1.7.0.tar.gz"}, "fis-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FIs_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/FIs_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fis/bioconductor-fis_1.25.0_src_all.tar.gz"], "md5": "cf38942e76299391b806e84abf7bcc5a", "fn": "FIs_1.25.0.tar.gz"}, "fission-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/fission_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/fission_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fission/bioconductor-fission_1.17.0_src_all.tar.gz"], "md5": "265844b4e10ca44a77abb0e6fa675069", "fn": "fission_1.17.0.tar.gz"}, "fletcher2013a-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Fletcher2013a_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/Fletcher2013a_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fletcher2013a/bioconductor-fletcher2013a_1.33.0_src_all.tar.gz"], "md5": "1526efee133c6717a040c336a2681c4b", "fn": "Fletcher2013a_1.33.0.tar.gz"}, "fletcher2013b-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Fletcher2013b_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/Fletcher2013b_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fletcher2013b/bioconductor-fletcher2013b_1.33.0_src_all.tar.gz"], "md5": "56f703ab885e7783c8108d941b4afaae", "fn": "Fletcher2013b_1.33.0.tar.gz"}, "flowploidydata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/flowPloidyData_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/flowPloidyData_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowploidydata/bioconductor-flowploidydata_1.23.0_src_all.tar.gz"], "md5": "df67ab50329625f3706d7be198ace3e6", "fn": "flowPloidyData_1.23.0.tar.gz"}, "flowsorted.blood.450k-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.Blood.450k_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.Blood.450k_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.450k/bioconductor-flowsorted.blood.450k_1.35.0_src_all.tar.gz"], "md5": "0240c9344fe261672e179baf8e27476f", "fn": "FlowSorted.Blood.450k_1.35.0.tar.gz"}, "flowsorted.blood.epic-2.1.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.Blood.EPIC_2.1.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.Blood.EPIC_2.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.epic/bioconductor-flowsorted.blood.epic_2.1.0_src_all.tar.gz"], "md5": "39c91a9469f0873f01a9d1feeab94a1c", "fn": "FlowSorted.Blood.EPIC_2.1.0.tar.gz"}, "flowsorted.cordblood.450k-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.CordBlood.450k_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBlood.450k_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordblood.450k/bioconductor-flowsorted.cordblood.450k_1.25.0_src_all.tar.gz"], "md5": "d54d8a9a5158312f9762c93622b2ff05", "fn": "FlowSorted.CordBlood.450k_1.25.0.tar.gz"}, "flowsorted.cordbloodcombined.450k-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.CordBloodCombined.450k_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodCombined.450k_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodcombined.450k/bioconductor-flowsorted.cordbloodcombined.450k_1.13.0_src_all.tar.gz"], "md5": "c5da0cb1e09b0bfe2c18dae0a1b94022", "fn": "FlowSorted.CordBloodCombined.450k_1.13.0.tar.gz"}, "flowsorted.cordbloodnorway.450k-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.CordBloodNorway.450k_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodNorway.450k_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodnorway.450k/bioconductor-flowsorted.cordbloodnorway.450k_1.23.0_src_all.tar.gz"], "md5": "bc8f53c7897b85ea67bd7f55bd74032b", "fn": "FlowSorted.CordBloodNorway.450k_1.23.0.tar.gz"}, "flowsorted.dlpfc.450k-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.DLPFC.450k_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.DLPFC.450k_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.dlpfc.450k/bioconductor-flowsorted.dlpfc.450k_1.33.0_src_all.tar.gz"], "md5": "997330230a4946701ab2ed93e7c610e2", "fn": "FlowSorted.DLPFC.450k_1.33.0.tar.gz"}, "flowworkspacedata-3.9.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/flowWorkspaceData_3.9.0.tar.gz", "https://bioarchive.galaxyproject.org/flowWorkspaceData_3.9.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowworkspacedata/bioconductor-flowworkspacedata_3.9.0_src_all.tar.gz"], "md5": "0a6dc8c644c8d94c0bb156f877166141", "fn": "flowWorkspaceData_3.9.0.tar.gz"}, "frmaexampledata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/frmaExampleData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/frmaExampleData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-frmaexampledata/bioconductor-frmaexampledata_1.33.0_src_all.tar.gz"], "md5": "d87115fc10cdd6d7e318558a3e662a54", "fn": "frmaExampleData_1.33.0.tar.gz"}, "furrowseg-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/furrowSeg_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/furrowSeg_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-furrowseg/bioconductor-furrowseg_1.25.0_src_all.tar.gz"], "md5": "02f736dd1a28f20c54871e5074300c56", "fn": "furrowSeg_1.25.0.tar.gz"}, "gagedata-2.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/gageData_2.35.0.tar.gz", "https://bioarchive.galaxyproject.org/gageData_2.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gagedata/bioconductor-gagedata_2.35.0_src_all.tar.gz"], "md5": "66ef788823140ec9e961eaf4f9c6d216", "fn": "gageData_2.35.0.tar.gz"}, "gaschyhs-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/gaschYHS_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/gaschYHS_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gaschyhs/bioconductor-gaschyhs_1.35.0_src_all.tar.gz"], "md5": "ed4baf5f544937c9b55079757897c348", "fn": "gaschYHS_1.35.0.tar.gz"}, "gatingmldata-2.37.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/gatingMLData_2.37.1.tar.gz", "https://bioarchive.galaxyproject.org/gatingMLData_2.37.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gatingmldata/bioconductor-gatingmldata_2.37.1_src_all.tar.gz"], "md5": "6a23be1ca00989254f81814ea01f4b05", "fn": "gatingMLData_2.37.1.tar.gz"}, "gcspikelite-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/gcspikelite_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/gcspikelite_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gcspikelite/bioconductor-gcspikelite_1.35.0_src_all.tar.gz"], "md5": "1e5fc959af925b306f17c9d7acbfd5dc", "fn": "gcspikelite_1.35.0.tar.gz"}, "genelendatabase-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/geneLenDataBase_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/geneLenDataBase_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genelendatabase/bioconductor-genelendatabase_1.33.0_src_all.tar.gz"], "md5": "a01f46c6edbddfe6a18bd8fafae289aa", "fn": "geneLenDataBase_1.33.0.tar.gz"}, "genomationdata-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/genomationData_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/genomationData_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomationdata/bioconductor-genomationdata_1.29.0_src_all.tar.gz"], "md5": "5bf1b38f89fa6a815dcb7f054fa4595f", "fn": "genomationData_1.29.0.tar.gz"}, "genomicdistributionsdata-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GenomicDistributionsData_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/GenomicDistributionsData_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomicdistributionsdata/bioconductor-genomicdistributionsdata_1.5.0_src_all.tar.gz"], "md5": "6db02c21a1b63c743ddbf2f97a85a8c7", "fn": "GenomicDistributionsData_1.5.0.tar.gz"}, "geuvadistranscriptexpr-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GeuvadisTranscriptExpr_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/GeuvadisTranscriptExpr_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-geuvadistranscriptexpr/bioconductor-geuvadistranscriptexpr_1.25.0_src_all.tar.gz"], "md5": "6c4d64730e8436e2d60fabbcc277a19d", "fn": "GeuvadisTranscriptExpr_1.25.0.tar.gz"}, "gigseadata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GIGSEAdata_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/GIGSEAdata_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gigseadata/bioconductor-gigseadata_1.15.0_src_all.tar.gz"], "md5": "59d0c5010ede867111544cb60aaeb743", "fn": "GIGSEAdata_1.15.0.tar.gz"}, "golubesets-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/golubEsets_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/golubEsets_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-golubesets/bioconductor-golubesets_1.39.0_src_all.tar.gz"], "md5": "5f35a5bfaa6c9f9ee982b0b389ae8dca", "fn": "golubEsets_1.39.0.tar.gz"}, "gpaexample-1.9.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/gpaExample_1.9.0.tar.gz", "https://bioarchive.galaxyproject.org/gpaExample_1.9.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gpaexample/bioconductor-gpaexample_1.9.0_src_all.tar.gz"], "md5": "7f4ca4d7db53abbd193a9d6049d07e0b", "fn": "gpaExample_1.9.0.tar.gz"}, "grndata-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/grndata_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/grndata_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-grndata/bioconductor-grndata_1.29.0_src_all.tar.gz"], "md5": "e595ed5d5a0b319e0f30d7dc7cb3a654", "fn": "grndata_1.29.0.tar.gz"}, "gsbenchmark-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSBenchMark_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/GSBenchMark_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gsbenchmark/bioconductor-gsbenchmark_1.17.0_src_all.tar.gz"], "md5": "572f6442afd5bdc38e170a151f3f1608", "fn": "GSBenchMark_1.17.0.tar.gz"}, "gse103322-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSE103322_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE103322_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse103322/bioconductor-gse103322_1.3.0_src_all.tar.gz"], "md5": "a3bc32c0e159b1eda56c91b8dea1d390", "fn": "GSE103322_1.3.0.tar.gz"}, "gse13015-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSE13015_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE13015_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse13015/bioconductor-gse13015_1.5.0_src_all.tar.gz"], "md5": "a8e0a7247f465a86e87d0b133f0222c4", "fn": "GSE13015_1.5.0.tar.gz"}, "gse159526-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSE159526_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE159526_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse159526/bioconductor-gse159526_1.3.0_src_all.tar.gz"], "md5": "7ff762d8bd42d33c402e5cae076d6847", "fn": "GSE159526_1.3.0.tar.gz"}, "gse62944-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSE62944_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE62944_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse62944/bioconductor-gse62944_1.25.0_src_all.tar.gz"], "md5": "fb108ec00235f1acd928d6817390e621", "fn": "GSE62944_1.25.0.tar.gz"}, "gsvadata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSVAdata_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/GSVAdata_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gsvadata/bioconductor-gsvadata_1.33.0_src_all.tar.gz"], "md5": "56ab3cd5d08d6142f443f2e331f6135f", "fn": "GSVAdata_1.33.0.tar.gz"}, "gwasdata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GWASdata_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/GWASdata_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gwasdata/bioconductor-gwasdata_1.35.0_src_all.tar.gz"], "md5": "32d75b2498c3102a05956b81cfa32fa3", "fn": "GWASdata_1.35.0.tar.gz"}, "h5vcdata-2.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/h5vcData_2.17.0.tar.gz", "https://bioarchive.galaxyproject.org/h5vcData_2.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-h5vcdata/bioconductor-h5vcdata_2.17.0_src_all.tar.gz"], "md5": "613259aca1b067623da84294502dd7d3", "fn": "h5vcData_2.17.0.tar.gz"}, "hapmap100khind-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hapmap100khind_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap100khind_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap100khind/bioconductor-hapmap100khind_1.39.0_src_all.tar.gz"], "md5": "c208c35ed429b2e446977923d3f33efe", "fn": "hapmap100khind_1.39.0.tar.gz"}, "hapmap100kxba-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hapmap100kxba_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap100kxba_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap100kxba/bioconductor-hapmap100kxba_1.39.0_src_all.tar.gz"], "md5": "87d6c086cabd5f6e4931cd727ae3fd7a", "fn": "hapmap100kxba_1.39.0.tar.gz"}, "hapmap500knsp-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hapmap500knsp_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap500knsp_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap500knsp/bioconductor-hapmap500knsp_1.39.0_src_all.tar.gz"], "md5": "620b713d03cca3b91c38dc5da559aa45", "fn": "hapmap500knsp_1.39.0.tar.gz"}, "hapmap500ksty-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hapmap500ksty_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap500ksty_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap500ksty/bioconductor-hapmap500ksty_1.39.0_src_all.tar.gz"], "md5": "8168db3048b75243646fe074744f4a20", "fn": "hapmap500ksty_1.39.0.tar.gz"}, "hapmapsnp5-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hapmapsnp5_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmapsnp5_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp5/bioconductor-hapmapsnp5_1.39.0_src_all.tar.gz"], "md5": "8efb06dd875ccc70de2dd1cb363ea769", "fn": "hapmapsnp5_1.39.0.tar.gz"}, "hapmapsnp6-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hapmapsnp6_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmapsnp6_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp6/bioconductor-hapmapsnp6_1.39.0_src_all.tar.gz"], "md5": "f6ac77c3a1386f2e6bbfb41d88879973", "fn": "hapmapsnp6_1.39.0.tar.gz"}, "harbchip-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/harbChIP_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/harbChIP_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harbchip/bioconductor-harbchip_1.35.0_src_all.tar.gz"], "md5": "43c3c6e6949560bc7c3b233616a66c5e", "fn": "harbChIP_1.35.0.tar.gz"}, "harmandata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HarmanData_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/HarmanData_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harmandata/bioconductor-harmandata_1.25.0_src_all.tar.gz"], "md5": "a305dd9f4be567bde7c6e5f31bad3b49", "fn": "HarmanData_1.25.0.tar.gz"}, "harmonizedtcgadata-1.19.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HarmonizedTCGAData_1.19.0.tar.gz", "https://bioarchive.galaxyproject.org/HarmonizedTCGAData_1.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harmonizedtcgadata/bioconductor-harmonizedtcgadata_1.19.0_src_all.tar.gz"], "md5": "46546ba436bfa9457789fb3b1362597e", "fn": "HarmonizedTCGAData_1.19.0.tar.gz"}, "hcadata-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HCAData_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/HCAData_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcadata/bioconductor-hcadata_1.13.0_src_all.tar.gz"], "md5": "11d0f4f244f9e91ca08e8ca2f0deeae8", "fn": "HCAData_1.13.0.tar.gz"}, "hd2013sgi-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HD2013SGI_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/HD2013SGI_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hd2013sgi/bioconductor-hd2013sgi_1.37.0_src_all.tar.gz"], "md5": "f6ec4532136afecc8a49df728ae2148b", "fn": "HD2013SGI_1.37.0.tar.gz"}, "hdcytodata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HDCytoData_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/HDCytoData_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hdcytodata/bioconductor-hdcytodata_1.17.0_src_all.tar.gz"], "md5": "0264c9e4a88d12dc0588893ea2a990e6", "fn": "HDCytoData_1.17.0.tar.gz"}, "healthycontrolspresencechecker-1.1.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/healthyControlsPresenceChecker_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/healthyControlsPresenceChecker_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-healthycontrolspresencechecker/bioconductor-healthycontrolspresencechecker_1.1.0_src_all.tar.gz"], "md5": "bae0bae9c15427f8715df87076cc13fe", "fn": "healthyControlsPresenceChecker_1.1.0.tar.gz"}, "healthyflowdata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/healthyFlowData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/healthyFlowData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-healthyflowdata/bioconductor-healthyflowdata_1.35.0_src_all.tar.gz"], "md5": "84fdfd72c6a1f7588aef67364aef6ad3", "fn": "healthyFlowData_1.35.0.tar.gz"}, "heebodata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HEEBOdata_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/HEEBOdata_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-heebodata/bioconductor-heebodata_1.35.0_src_all.tar.gz"], "md5": "aedee799a5570c99f1ad23b467b041f1", "fn": "HEEBOdata_1.35.0.tar.gz"}, "hellorangesdata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HelloRangesData_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/HelloRangesData_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hellorangesdata/bioconductor-hellorangesdata_1.23.0_src_all.tar.gz"], "md5": "09e396c37aac16ed7ca93671cf2aebda", "fn": "HelloRangesData_1.23.0.tar.gz"}, "hgu133abarcodevecs-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hgu133abarcodevecs_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133abarcodevecs_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133abarcodevecs/bioconductor-hgu133abarcodevecs_1.35.0_src_all.tar.gz"], "md5": "65245450c48f91270cb69d1193c436c8", "fn": "hgu133abarcodevecs_1.35.0.tar.gz"}, "hgu133plus2barcodevecs-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hgu133plus2barcodevecs_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2barcodevecs_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2barcodevecs/bioconductor-hgu133plus2barcodevecs_1.35.0_src_all.tar.gz"], "md5": "28251d040bce6ef6b25aef07695574b1", "fn": "hgu133plus2barcodevecs_1.35.0.tar.gz"}, "hgu133plus2cellscore-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hgu133plus2CellScore_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2CellScore_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2cellscore/bioconductor-hgu133plus2cellscore_1.17.0_src_all.tar.gz"], "md5": "69f8d0c2c62ff1ee7ab09bd58c291f9c", "fn": "hgu133plus2CellScore_1.17.0.tar.gz"}, "hgu2beta7-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hgu2beta7_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu2beta7_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu2beta7/bioconductor-hgu2beta7_1.37.0_src_all.tar.gz"], "md5": "4229481dd34e813801659783600d66c0", "fn": "hgu2beta7_1.37.0.tar.gz"}, "hicdatahumanimr90-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HiCDataHumanIMR90_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/HiCDataHumanIMR90_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicdatahumanimr90/bioconductor-hicdatahumanimr90_1.17.0_src_all.tar.gz"], "md5": "b515d4670a93ce8ed2a0745e2da4513c", "fn": "HiCDataHumanIMR90_1.17.0.tar.gz"}, "hicdatalymphoblast-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HiCDataLymphoblast_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/HiCDataLymphoblast_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicdatalymphoblast/bioconductor-hicdatalymphoblast_1.33.0_src_all.tar.gz"], "md5": "0ca1dfbb9649eb697721fa8c9d4c4724", "fn": "HiCDataLymphoblast_1.33.0.tar.gz"}, "hicontactsdata-0.99.5": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HiContactsData_0.99.5.tar.gz", "https://bioarchive.galaxyproject.org/HiContactsData_0.99.5.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicontactsdata/bioconductor-hicontactsdata_0.99.5_src_all.tar.gz"], "md5": "fe7e5eaa27ef177427359184b31412b1", "fn": "HiContactsData_0.99.5.tar.gz"}, "highlyreplicatedrnaseq-1.9.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HighlyReplicatedRNASeq_1.9.0.tar.gz", "https://bioarchive.galaxyproject.org/HighlyReplicatedRNASeq_1.9.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-highlyreplicatedrnaseq/bioconductor-highlyreplicatedrnaseq_1.9.0_src_all.tar.gz"], "md5": "dfc27dcca211c331141b6f8d23cb5091", "fn": "HighlyReplicatedRNASeq_1.9.0.tar.gz"}, "hiiragi2013-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Hiiragi2013_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/Hiiragi2013_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hiiragi2013/bioconductor-hiiragi2013_1.33.0_src_all.tar.gz"], "md5": "b497df372201fb3871ad465960d15a92", "fn": "Hiiragi2013_1.33.0.tar.gz"}, "hivcdnavantwout03-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HIVcDNAvantWout03_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/HIVcDNAvantWout03_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hivcdnavantwout03/bioconductor-hivcdnavantwout03_1.37.0_src_all.tar.gz"], "md5": "12dcd1fc184daba1f8cc2f53aa5c7a94", "fn": "HIVcDNAvantWout03_1.37.0.tar.gz"}, "hmp16sdata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HMP16SData_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/HMP16SData_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hmp16sdata/bioconductor-hmp16sdata_1.17.0_src_all.tar.gz"], "md5": "02c02686d9bce0f69b97fb5f9a48a93c", "fn": "HMP16SData_1.17.0.tar.gz"}, "hmp2data-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HMP2Data_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/HMP2Data_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hmp2data/bioconductor-hmp2data_1.11.0_src_all.tar.gz"], "md5": "90fc108b530a866dab5e6def696b42d7", "fn": "HMP2Data_1.11.0.tar.gz"}, "hsmmsinglecell-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HSMMSingleCell_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/HSMMSingleCell_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hsmmsinglecell/bioconductor-hsmmsinglecell_1.17.0_src_all.tar.gz"], "md5": "111ae2345843dcfa88b21cc778a974c2", "fn": "HSMMSingleCell_1.17.0.tar.gz"}, "humanaffydata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HumanAffyData_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/HumanAffyData_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanaffydata/bioconductor-humanaffydata_1.23.0_src_all.tar.gz"], "md5": "217f2d6a33a6699ec5e971e6aa3518d5", "fn": "HumanAffyData_1.23.0.tar.gz"}, "humanstemcell-0.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/humanStemCell_0.37.0.tar.gz", "https://bioarchive.galaxyproject.org/humanStemCell_0.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanstemcell/bioconductor-humanstemcell_0.37.0_src_all.tar.gz"], "md5": "cd8d9c4ee5d7a58ea924b537b52331d5", "fn": "humanStemCell_0.37.0.tar.gz"}, "ihwpaper-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/IHWpaper_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/IHWpaper_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ihwpaper/bioconductor-ihwpaper_1.25.0_src_all.tar.gz"], "md5": "0fee0e7f9783b96109f7df5d70ce0825", "fn": "IHWpaper_1.25.0.tar.gz"}, "illumina450probevariants.db-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Illumina450ProbeVariants.db_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/Illumina450ProbeVariants.db_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illumina450probevariants.db/bioconductor-illumina450probevariants.db_1.33.0_src_all.tar.gz"], "md5": "0c7c67fb75b0ff43ed2d92e71a67264a", "fn": "Illumina450ProbeVariants.db_1.33.0.tar.gz"}, "illuminadatatestfiles-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/IlluminaDataTestFiles_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaDataTestFiles_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminadatatestfiles/bioconductor-illuminadatatestfiles_1.35.0_src_all.tar.gz"], "md5": "1c68249fe7576377a7ee11b301944c6e", "fn": "IlluminaDataTestFiles_1.35.0.tar.gz"}, "imcdatasets-1.5.4": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/imcdatasets_1.5.4.tar.gz", "https://bioarchive.galaxyproject.org/imcdatasets_1.5.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-imcdatasets/bioconductor-imcdatasets_1.5.4_src_all.tar.gz"], "md5": "8c5ab7a76c8be62231631162ef079ff4", "fn": "imcdatasets_1.5.4.tar.gz"}, "italicsdata-2.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ITALICSData_2.35.0.tar.gz", "https://bioarchive.galaxyproject.org/ITALICSData_2.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-italicsdata/bioconductor-italicsdata_2.35.0_src_all.tar.gz"], "md5": "d7d5506602842647b6355fabc12f7cd2", "fn": "ITALICSData_2.35.0.tar.gz"}, "iyer517-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Iyer517_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/Iyer517_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-iyer517/bioconductor-iyer517_1.39.0_src_all.tar.gz"], "md5": "07eecc5887ad248b990d18ecfbcbc4ae", "fn": "Iyer517_1.39.0.tar.gz"}, "jaspar2014-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/JASPAR2014_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2014_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2014/bioconductor-jaspar2014_1.33.0_src_all.tar.gz"], "md5": "9a7d6e0c267507e8308407cc3ebf4c42", "fn": "JASPAR2014_1.33.0.tar.gz"}, "jaspar2016-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/JASPAR2016_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2016_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2016/bioconductor-jaspar2016_1.25.0_src_all.tar.gz"], "md5": "f8e2bbf13cc8e3c84df1697d0b876580", "fn": "JASPAR2016_1.25.0.tar.gz"}, "keggandmetacoredzpathwaysgeo-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/KEGGandMetacoreDzPathwaysGEO_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/KEGGandMetacoreDzPathwaysGEO_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-keggandmetacoredzpathwaysgeo/bioconductor-keggandmetacoredzpathwaysgeo_1.17.0_src_all.tar.gz"], "md5": "c86429242308d77103832d055a72f648", "fn": "KEGGandMetacoreDzPathwaysGEO_1.17.0.tar.gz"}, "keggdzpathwaysgeo-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/KEGGdzPathwaysGEO_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/KEGGdzPathwaysGEO_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-keggdzpathwaysgeo/bioconductor-keggdzpathwaysgeo_1.35.0_src_all.tar.gz"], "md5": "f96019ab54d05fb8a39b6cae2305c714", "fn": "KEGGdzPathwaysGEO_1.35.0.tar.gz"}, "kidpack-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/kidpack_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/kidpack_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-kidpack/bioconductor-kidpack_1.39.0_src_all.tar.gz"], "md5": "d9143bf024de2fd61d9e70cd674c3dd9", "fn": "kidpack_1.39.0.tar.gz"}, "kodata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/KOdata_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/KOdata_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-kodata/bioconductor-kodata_1.23.0_src_all.tar.gz"], "md5": "799f98740b05254649fb8de864c9b9ea", "fn": "KOdata_1.23.0.tar.gz"}, "leebamviews-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/leeBamViews_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/leeBamViews_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-leebamviews/bioconductor-leebamviews_1.33.0_src_all.tar.gz"], "md5": "e20c1281821b5e34d639312437ca4dde", "fn": "leeBamViews_1.33.0.tar.gz"}, "leukemiaseset-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/leukemiasEset_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/leukemiasEset_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-leukemiaseset/bioconductor-leukemiaseset_1.33.0_src_all.tar.gz"], "md5": "09a0c9da3055a5d726cd5ae7de21888e", "fn": "leukemiasEset_1.33.0.tar.gz"}, "liebermanaidenhic2009-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/LiebermanAidenHiC2009_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/LiebermanAidenHiC2009_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-liebermanaidenhic2009/bioconductor-liebermanaidenhic2009_0.35.0_src_all.tar.gz"], "md5": "9db04114ddcc8937ac832837a7a82315", "fn": "LiebermanAidenHiC2009_0.35.0.tar.gz"}, "listeretalbsseq-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ListerEtAlBSseq_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/ListerEtAlBSseq_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-listeretalbsseq/bioconductor-listeretalbsseq_1.29.0_src_all.tar.gz"], "md5": "86bee8785a38e3ce483dd2749124bcc0", "fn": "ListerEtAlBSseq_1.29.0.tar.gz"}, "lrcelltypemarkers-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/LRcellTypeMarkers_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/LRcellTypeMarkers_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lrcelltypemarkers/bioconductor-lrcelltypemarkers_1.5.0_src_all.tar.gz"], "md5": "cde21ce4c254a41c9e17b4ef51a01521", "fn": "LRcellTypeMarkers_1.5.0.tar.gz"}, "lumibarnes-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/lumiBarnes_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/lumiBarnes_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumibarnes/bioconductor-lumibarnes_1.37.0_src_all.tar.gz"], "md5": "2700119944fcbd6595a1da40d11d4460", "fn": "lumiBarnes_1.37.0.tar.gz"}, "lungcanceracvssccgeo-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/LungCancerACvsSCCGEO_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/LungCancerACvsSCCGEO_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungcanceracvssccgeo/bioconductor-lungcanceracvssccgeo_1.33.0_src_all.tar.gz"], "md5": "450494d6d3dbeb03fa24331a13f7e87e", "fn": "LungCancerACvsSCCGEO_1.33.0.tar.gz"}, "lungcancerlines-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/LungCancerLines_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/LungCancerLines_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungcancerlines/bioconductor-lungcancerlines_0.35.0_src_all.tar.gz"], "md5": "71f67ae38f6f1df089256aa6fa5d8249", "fn": "LungCancerLines_0.35.0.tar.gz"}, "lungexpression-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/lungExpression_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/lungExpression_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungexpression/bioconductor-lungexpression_0.35.0_src_all.tar.gz"], "md5": "49cd2379de1eaa83e01fd979be94ee79", "fn": "lungExpression_0.35.0.tar.gz"}, "lydata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/lydata_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/lydata_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lydata/bioconductor-lydata_1.23.0_src_all.tar.gz"], "md5": "052166b4f3851b44ffc881c74b9c5821", "fn": "lydata_1.23.0.tar.gz"}, "m3dexampledata-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/M3DExampleData_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/M3DExampleData_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-m3dexampledata/bioconductor-m3dexampledata_1.23.0_src_all.tar.gz"], "md5": "f7b2229f75874e9c97625e4642107c3f", "fn": "M3DExampleData_1.23.0.tar.gz"}, "macrophage-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/macrophage_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/macrophage_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-macrophage/bioconductor-macrophage_1.13.0_src_all.tar.gz"], "md5": "f75d462f270ebd4f9d7d65f35723ffe4", "fn": "macrophage_1.13.0.tar.gz"}, "macsdata-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MACSdata_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/MACSdata_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-macsdata/bioconductor-macsdata_1.5.0_src_all.tar.gz"], "md5": "12a2b57e87a7e7bf1af063951fbc23bd", "fn": "MACSdata_1.5.0.tar.gz"}, "mammaprintdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mammaPrintData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/mammaPrintData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mammaprintdata/bioconductor-mammaprintdata_1.33.0_src_all.tar.gz"], "md5": "59b4367e79119553450b73c13b8e2ab4", "fn": "mammaPrintData_1.33.0.tar.gz"}, "mapkldata-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mAPKLData_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/mAPKLData_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mapkldata/bioconductor-mapkldata_1.29.0_src_all.tar.gz"], "md5": "8062e0241ac2f340ffa73ccbd2c89cb5", "fn": "mAPKLData_1.29.0.tar.gz"}, "maqcexpression4plex-1.41.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/maqcExpression4plex_1.41.0.tar.gz", "https://bioarchive.galaxyproject.org/maqcExpression4plex_1.41.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcexpression4plex/bioconductor-maqcexpression4plex_1.41.0_src_all.tar.gz"], "md5": "54bab503992e2907b47e8a3dfe2d80f0", "fn": "maqcExpression4plex_1.41.0.tar.gz"}, "maqcsubset-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MAQCsubset_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/MAQCsubset_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcsubset/bioconductor-maqcsubset_1.35.0_src_all.tar.gz"], "md5": "182a8cb6b638164e3f83848c96d5b4d4", "fn": "MAQCsubset_1.35.0.tar.gz"}, "maqcsubsetilm-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MAQCsubsetILM_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/MAQCsubsetILM_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcsubsetilm/bioconductor-maqcsubsetilm_1.35.0_src_all.tar.gz"], "md5": "41a6ad9c3dfb6007756cc5a52077e226", "fn": "MAQCsubsetILM_1.35.0.tar.gz"}, "mcseadata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mCSEAdata_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/mCSEAdata_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcseadata/bioconductor-mcseadata_1.17.0_src_all.tar.gz"], "md5": "f41dfacd838689e29a41e7346899f671", "fn": "mCSEAdata_1.17.0.tar.gz"}, "mcsurvdata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mcsurvdata_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/mcsurvdata_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcsurvdata/bioconductor-mcsurvdata_1.15.0_src_all.tar.gz"], "md5": "ec0ca1c2609f7cd5d3081578bd186dd6", "fn": "mcsurvdata_1.15.0.tar.gz"}, "medipsdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MEDIPSData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/MEDIPSData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-medipsdata/bioconductor-medipsdata_1.33.0_src_all.tar.gz"], "md5": "cb3e1d5345ac273bb52647910a5088f6", "fn": "MEDIPSData_1.33.0.tar.gz"}, "meebodata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MEEBOdata_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/MEEBOdata_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-meebodata/bioconductor-meebodata_1.35.0_src_all.tar.gz"], "md5": "1c0b167cc3f2e53a3ce12b45820ca586", "fn": "MEEBOdata_1.35.0.tar.gz"}, "merfishdata-0.99.4": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MerfishData_0.99.4.tar.gz", "https://bioarchive.galaxyproject.org/MerfishData_0.99.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-merfishdata/bioconductor-merfishdata_0.99.4_src_all.tar.gz"], "md5": "eec70aea71ddd2d4fd9c35f759ac2f00", "fn": "MerfishData_0.99.4.tar.gz"}, "metagxbreast-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MetaGxBreast_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxBreast_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxbreast/bioconductor-metagxbreast_1.17.0_src_all.tar.gz"], "md5": "5a1cdda3d73df40f05d39840706a179a", "fn": "MetaGxBreast_1.17.0.tar.gz"}, "metagxovarian-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MetaGxOvarian_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxOvarian_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxovarian/bioconductor-metagxovarian_1.17.0_src_all.tar.gz"], "md5": "4515cf0e1cfe2cb6c83831c2530d6b67", "fn": "MetaGxOvarian_1.17.0.tar.gz"}, "metagxpancreas-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MetaGxPancreas_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxPancreas_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxpancreas/bioconductor-metagxpancreas_1.17.0_src_all.tar.gz"], "md5": "e0dfc63561474961fbc243efe77beb29", "fn": "MetaGxPancreas_1.17.0.tar.gz"}, "metamsdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/metaMSdata_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/metaMSdata_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metamsdata/bioconductor-metamsdata_1.33.0_src_all.tar.gz"], "md5": "c7f91a612bf189b5856f45eeaa22d75a", "fn": "metaMSdata_1.33.0.tar.gz"}, "methylaiddata-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MethylAidData_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/MethylAidData_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylaiddata/bioconductor-methylaiddata_1.29.0_src_all.tar.gz"], "md5": "e6cfbcf2f22b093617be964ba6f38a55", "fn": "MethylAidData_1.29.0.tar.gz"}, "methylclockdata-1.5.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/methylclockData_1.5.1.tar.gz", "https://bioarchive.galaxyproject.org/methylclockData_1.5.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylclockdata/bioconductor-methylclockdata_1.5.1_src_all.tar.gz"], "md5": "6d4b0b16c56e2f72763e4c4a7f9511a9", "fn": "methylclockData_1.5.1.tar.gz"}, "methylseqdata-1.7.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MethylSeqData_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/MethylSeqData_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylseqdata/bioconductor-methylseqdata_1.7.0_src_all.tar.gz"], "md5": "352df1846d59a3e3d8f170e484936899", "fn": "MethylSeqData_1.7.0.tar.gz"}, "microbiomebenchmarkdata-0.99.3": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MicrobiomeBenchmarkData_0.99.3.tar.gz", "https://bioarchive.galaxyproject.org/MicrobiomeBenchmarkData_0.99.3.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-microbiomebenchmarkdata/bioconductor-microbiomebenchmarkdata_0.99.3_src_all.tar.gz"], "md5": "d18fe5f84d2bc6fe3198ca8a2d96e93b", "fn": "MicrobiomeBenchmarkData_0.99.3.tar.gz"}, "microbiomedatasets-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/microbiomeDataSets_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/microbiomeDataSets_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-microbiomedatasets/bioconductor-microbiomedatasets_1.5.0_src_all.tar.gz"], "md5": "c5e76e08c3aa52155bd423c1fa39a935", "fn": "microbiomeDataSets_1.5.0.tar.gz"}, "micrornaome-1.19.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/microRNAome_1.19.0.tar.gz", "https://bioarchive.galaxyproject.org/microRNAome_1.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-micrornaome/bioconductor-micrornaome_1.19.0_src_all.tar.gz"], "md5": "a96e61bc3ce4ce30cb587018da5c3684", "fn": "microRNAome_1.19.0.tar.gz"}, "migsadata-1.21.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MIGSAdata_1.21.0.tar.gz", "https://bioarchive.galaxyproject.org/MIGSAdata_1.21.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-migsadata/bioconductor-migsadata_1.21.0_src_all.tar.gz"], "md5": "643e3a5b5f46302b7ae88edfb084dd12", "fn": "MIGSAdata_1.21.0.tar.gz"}, "minfidata-0.43.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/minfiData_0.43.0.tar.gz", "https://bioarchive.galaxyproject.org/minfiData_0.43.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minfidata/bioconductor-minfidata_0.43.0_src_all.tar.gz"], "md5": "80e4e542754fd9a48cf384aa2cfafe43", "fn": "minfiData_0.43.0.tar.gz"}, "minfidataepic-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/minfiDataEPIC_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/minfiDataEPIC_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minfidataepic/bioconductor-minfidataepic_1.23.0_src_all.tar.gz"], "md5": "dfe3432c455031f4e9da7194b024c8de", "fn": "minfiDataEPIC_1.23.0.tar.gz"}, "minionsummarydata-1.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/minionSummaryData_1.27.0.tar.gz", "https://bioarchive.galaxyproject.org/minionSummaryData_1.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minionsummarydata/bioconductor-minionsummarydata_1.27.0_src_all.tar.gz"], "md5": "85e222cdb24e11cdb22e2cbbf1e4320e", "fn": "minionSummaryData_1.27.0.tar.gz"}, "mircompdata-1.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/miRcompData_1.27.0.tar.gz", "https://bioarchive.galaxyproject.org/miRcompData_1.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mircompdata/bioconductor-mircompdata_1.27.0_src_all.tar.gz"], "md5": "3eb8338c98fa4b54a4ae71222b1c2ce0", "fn": "miRcompData_1.27.0.tar.gz"}, "mirnatarget-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/miRNATarget_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/miRNATarget_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirnatarget/bioconductor-mirnatarget_1.35.0_src_all.tar.gz"], "md5": "d88b2142f8df71518f24322e76ace811", "fn": "miRNATarget_1.35.0.tar.gz"}, "mmappr2data-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MMAPPR2data_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/MMAPPR2data_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mmappr2data/bioconductor-mmappr2data_1.11.0_src_all.tar.gz"], "md5": "caa2f5c69e9ac2d7ec2828345ddd32f3", "fn": "MMAPPR2data_1.11.0.tar.gz"}, "mmdiffbamsubset-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MMDiffBamSubset_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/MMDiffBamSubset_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mmdiffbamsubset/bioconductor-mmdiffbamsubset_1.33.0_src_all.tar.gz"], "md5": "dc953ce58ecdd627ba28713bd3c312f6", "fn": "MMDiffBamSubset_1.33.0.tar.gz"}, "mofadata-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MOFAdata_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/MOFAdata_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mofadata/bioconductor-mofadata_1.13.0_src_all.tar.gz"], "md5": "c2d0168b4072a4c585c74f54cfafcb57", "fn": "MOFAdata_1.13.0.tar.gz"}, "mosaicsexample-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mosaicsExample_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/mosaicsExample_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mosaicsexample/bioconductor-mosaicsexample_1.35.0_src_all.tar.gz"], "md5": "e9cd467badb82b605153c6c4320af466", "fn": "mosaicsExample_1.35.0.tar.gz"}, "mouse4302barcodevecs-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mouse4302barcodevecs_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse4302barcodevecs_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302barcodevecs/bioconductor-mouse4302barcodevecs_1.35.0_src_all.tar.gz"], "md5": "e7d4e9d76390dfe57d7a74ca94e7ca79", "fn": "mouse4302barcodevecs_1.35.0.tar.gz"}, "mousegastrulationdata-1.11.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MouseGastrulationData_1.11.1.tar.gz", "https://bioarchive.galaxyproject.org/MouseGastrulationData_1.11.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousegastrulationdata/bioconductor-mousegastrulationdata_1.11.1_src_all.tar.gz"], "md5": "3a73f3d193a842a530da88ec8280ee5d", "fn": "MouseGastrulationData_1.11.1.tar.gz"}, "mousethymusageing-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MouseThymusAgeing_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/MouseThymusAgeing_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousethymusageing/bioconductor-mousethymusageing_1.5.0_src_all.tar.gz"], "md5": "e396dade7dd782971468829efae0a869", "fn": "MouseThymusAgeing_1.5.0.tar.gz"}, "msd16s-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/msd16s_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/msd16s_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msd16s/bioconductor-msd16s_1.17.0_src_all.tar.gz"], "md5": "9fb66efe981c048b5b6719a2b3e4a05e", "fn": "msd16s_1.17.0.tar.gz"}, "msdata-0.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/msdata_0.37.0.tar.gz", "https://bioarchive.galaxyproject.org/msdata_0.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msdata/bioconductor-msdata_0.37.0_src_all.tar.gz"], "md5": "1642c062b0adf18cc4fbe4325b2da013", "fn": "msdata_0.37.0.tar.gz"}, "msigdb-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/msigdb_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/msigdb_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msigdb/bioconductor-msigdb_1.5.0_src_all.tar.gz"], "md5": "aacc6196dd1f49dacb6de609e759d85b", "fn": "msigdb_1.5.0.tar.gz"}, "msmb-1.15.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MSMB_1.15.2.tar.gz", "https://bioarchive.galaxyproject.org/MSMB_1.15.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msmb/bioconductor-msmb_1.15.2_src_all.tar.gz"], "md5": "6257a078ea4aedb9c85c9048f865d9c5", "fn": "MSMB_1.15.2.tar.gz"}, "mspuritydata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/msPurityData_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/msPurityData_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mspuritydata/bioconductor-mspuritydata_1.25.0_src_all.tar.gz"], "md5": "df95b6a4f33068cc8335aaa1425816bf", "fn": "msPurityData_1.25.0.tar.gz"}, "msqc1-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/msqc1_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/msqc1_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msqc1/bioconductor-msqc1_1.25.0_src_all.tar.gz"], "md5": "a3c33ff03b6609e9186def83fb6193c3", "fn": "msqc1_1.25.0.tar.gz"}, "mtbls2-1.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mtbls2_1.27.0.tar.gz", "https://bioarchive.galaxyproject.org/mtbls2_1.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mtbls2/bioconductor-mtbls2_1.27.0_src_all.tar.gz"], "md5": "20b309b57b8e6b480be5ffe1955faa15", "fn": "mtbls2_1.27.0.tar.gz"}, "mugaexampledata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MUGAExampleData_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/MUGAExampleData_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mugaexampledata/bioconductor-mugaexampledata_1.17.0_src_all.tar.gz"], "md5": "d6ccf772c75a8d68fe78aac36b4b042d", "fn": "MUGAExampleData_1.17.0.tar.gz"}, "muscdata-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/muscData_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/muscData_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-muscdata/bioconductor-muscdata_1.11.0_src_all.tar.gz"], "md5": "b0df5994604e48867035cfb2eb541e65", "fn": "muscData_1.11.0.tar.gz"}, "mvoutdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mvoutData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/mvoutData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mvoutdata/bioconductor-mvoutdata_1.33.0_src_all.tar.gz"], "md5": "86825abfe2d999710c77e56d2b4b8371", "fn": "mvoutData_1.33.0.tar.gz"}, "nanoporernaseq-1.7.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NanoporeRNASeq_1.7.1.tar.gz", "https://bioarchive.galaxyproject.org/NanoporeRNASeq_1.7.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nanoporernaseq/bioconductor-nanoporernaseq_1.7.1_src_all.tar.gz"], "md5": "85892a31a2c5e8dfaffcdc5492d2bce2", "fn": "NanoporeRNASeq_1.7.1.tar.gz"}, "nanotubes-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/nanotubes_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/nanotubes_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nanotubes/bioconductor-nanotubes_1.13.0_src_all.tar.gz"], "md5": "0853171cb24f37bcc3783c628cfcf408", "fn": "nanotubes_1.13.0.tar.gz"}, "ncigraphdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NCIgraphData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/NCIgraphData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ncigraphdata/bioconductor-ncigraphdata_1.33.0_src_all.tar.gz"], "md5": "defa41254bf294770846b80ec857df25", "fn": "NCIgraphData_1.33.0.tar.gz"}, "nestlink-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NestLink_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/NestLink_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nestlink/bioconductor-nestlink_1.13.0_src_all.tar.gz"], "md5": "1a5c4511b2116a70b04a9490542823a2", "fn": "NestLink_1.13.0.tar.gz"}, "netactivitydata-0.99.8": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NetActivityData_0.99.8.tar.gz", "https://bioarchive.galaxyproject.org/NetActivityData_0.99.8.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-netactivitydata/bioconductor-netactivitydata_0.99.8_src_all.tar.gz"], "md5": "cf1b94ebe0dcfb31ab7d1f2b5b09ce8f", "fn": "NetActivityData_0.99.8.tar.gz"}, "neve2006-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Neve2006_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/Neve2006_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-neve2006/bioconductor-neve2006_0.35.0_src_all.tar.gz"], "md5": "ba5066a6e72e829c1308c25cea7d24d1", "fn": "Neve2006_0.35.0.tar.gz"}, "ngscopydata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NGScopyData_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/NGScopyData_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ngscopydata/bioconductor-ngscopydata_1.17.0_src_all.tar.gz"], "md5": "61704ed687fa28933fc29bf733137438", "fn": "NGScopyData_1.17.0.tar.gz"}, "nullrangesdata-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/nullrangesData_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/nullrangesData_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nullrangesdata/bioconductor-nullrangesdata_1.3.0_src_all.tar.gz"], "md5": "fae6acf0dd112c87283416a889f59eae", "fn": "nullrangesData_1.3.0.tar.gz"}, "nxtirfdata-1.3.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NxtIRFdata_1.3.2.tar.gz", "https://bioarchive.galaxyproject.org/NxtIRFdata_1.3.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nxtirfdata/bioconductor-nxtirfdata_1.3.2_src_all.tar.gz"], "md5": "13f644045ca18190869a6e1d69fdc37a", "fn": "NxtIRFdata_1.3.2.tar.gz"}, "obmiti-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ObMiTi_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/ObMiTi_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-obmiti/bioconductor-obmiti_1.5.0_src_all.tar.gz"], "md5": "87d3aa74100f85b5643ee96bdfd5413d", "fn": "ObMiTi_1.5.0.tar.gz"}, "oct4-1.13.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/oct4_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/oct4_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-oct4/bioconductor-oct4_1.13.0_src_all.tar.gz"], "md5": "d1d65d9f1f6ff35d2df6713c51a684c2", "fn": "oct4_1.13.0.tar.gz"}, "octad.db-0.99.43": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/octad.db_0.99.43.tar.gz", "https://bioarchive.galaxyproject.org/octad.db_0.99.43.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-octad.db/bioconductor-octad.db_0.99.43_src_all.tar.gz"], "md5": "3815a8a295a5162ea585b57f00a1925e", "fn": "octad.db_0.99.43.tar.gz"}, "omicspcadata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/OMICsPCAdata_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/OMICsPCAdata_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-omicspcadata/bioconductor-omicspcadata_1.15.0_src_all.tar.gz"], "md5": "a2431a35117a8762f8bf86b81ee442b6", "fn": "OMICsPCAdata_1.15.0.tar.gz"}, "onassisjavalibs-1.19.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/OnassisJavaLibs_1.19.0.tar.gz", "https://bioarchive.galaxyproject.org/OnassisJavaLibs_1.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-onassisjavalibs/bioconductor-onassisjavalibs_1.19.0_src_all.tar.gz"], "md5": "3b5a9c4b77f33296aa9eec6c617e8a41", "fn": "OnassisJavaLibs_1.19.0.tar.gz"}, "optimalflowdata-1.9.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/optimalFlowData_1.9.0.tar.gz", "https://bioarchive.galaxyproject.org/optimalFlowData_1.9.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-optimalflowdata/bioconductor-optimalflowdata_1.9.0_src_all.tar.gz"], "md5": "951af94d3a9bfebc7d9be2e0ca6209dd", "fn": "optimalFlowData_1.9.0.tar.gz"}, "parathyroidse-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/parathyroidSE_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/parathyroidSE_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-parathyroidse/bioconductor-parathyroidse_1.35.0_src_all.tar.gz"], "md5": "c65fe2c82bac9730e22867a74aa6f2ba", "fn": "parathyroidSE_1.35.0.tar.gz"}, "pasilla-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pasilla_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/pasilla_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasilla/bioconductor-pasilla_1.25.0_src_all.tar.gz"], "md5": "0edb3fe08516d8d3c8ee2f7f45c156f0", "fn": "pasilla_1.25.0.tar.gz"}, "pasillabamsubset-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pasillaBamSubset_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/pasillaBamSubset_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasillabamsubset/bioconductor-pasillabamsubset_0.35.0_src_all.tar.gz"], "md5": "28f54b10b5a08f74dd07f0dd9dcf3dab", "fn": "pasillaBamSubset_0.35.0.tar.gz"}, "pasillatranscriptexpr-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PasillaTranscriptExpr_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/PasillaTranscriptExpr_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasillatranscriptexpr/bioconductor-pasillatranscriptexpr_1.25.0_src_all.tar.gz"], "md5": "1147d77b1b8cfb0963e99f241852ffbc", "fn": "PasillaTranscriptExpr_1.25.0.tar.gz"}, "pathnetdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PathNetData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/PathNetData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pathnetdata/bioconductor-pathnetdata_1.33.0_src_all.tar.gz"], "md5": "c150e591bddd66fcdc55a0ae1e17dc06", "fn": "PathNetData_1.33.0.tar.gz"}, "pchicdata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PCHiCdata_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/PCHiCdata_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pchicdata/bioconductor-pchicdata_1.25.0_src_all.tar.gz"], "md5": "59faa7d68d8c7e305c550846b3b639bc", "fn": "PCHiCdata_1.25.0.tar.gz"}, "pcxndata-2.19.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pcxnData_2.19.0.tar.gz", "https://bioarchive.galaxyproject.org/pcxnData_2.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pcxndata/bioconductor-pcxndata_2.19.0_src_all.tar.gz"], "md5": "a844676129f82b3a81719ec243a21252", "fn": "pcxnData_2.19.0.tar.gz"}, "pd.atdschip.tiling-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pd.atdschip.tiling_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.atdschip.tiling_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.atdschip.tiling/bioconductor-pd.atdschip.tiling_0.35.0_src_all.tar.gz"], "md5": "efd361b41cf9e3df5d629748707fede4", "fn": "pd.atdschip.tiling_0.35.0.tar.gz"}, "pepdat-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pepDat_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/pepDat_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pepdat/bioconductor-pepdat_1.17.0_src_all.tar.gz"], "md5": "2974e747656b1ea1987b1004b00a71e4", "fn": "pepDat_1.17.0.tar.gz"}, "pepsnmrdata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PepsNMRData_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/PepsNMRData_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pepsnmrdata/bioconductor-pepsnmrdata_1.15.0_src_all.tar.gz"], "md5": "339c9c0455823be6ec972a2ae69e6000", "fn": "PepsNMRData_1.15.0.tar.gz"}, "phyloprofiledata-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PhyloProfileData_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/PhyloProfileData_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phyloprofiledata/bioconductor-phyloprofiledata_1.11.0_src_all.tar.gz"], "md5": "d5dba91d23204c92146968d824753114", "fn": "PhyloProfileData_1.11.0.tar.gz"}, "plasfia-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/plasFIA_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/plasFIA_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-plasfia/bioconductor-plasfia_1.25.0_src_all.tar.gz"], "md5": "a97af6479ac842dc3e928b871ba61878", "fn": "plasFIA_1.25.0.tar.gz"}, "plotgardenerdata-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/plotgardenerData_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/plotgardenerData_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-plotgardenerdata/bioconductor-plotgardenerdata_1.3.0_src_all.tar.gz"], "md5": "9c6c3cc2b2d4b0450d21af1e3c888248", "fn": "plotgardenerData_1.3.0.tar.gz"}, "prebsdata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prebsdata_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/prebsdata_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prebsdata/bioconductor-prebsdata_1.33.0_src_all.tar.gz"], "md5": "6574a4424628d14621fd7e81160e91d3", "fn": "prebsdata_1.33.0.tar.gz"}, "precisetadhub-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/preciseTADhub_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/preciseTADhub_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-precisetadhub/bioconductor-precisetadhub_1.5.0_src_all.tar.gz"], "md5": "3c395f5fa911600e628ad2d2528b01af", "fn": "preciseTADhub_1.5.0.tar.gz"}, "predasampledata-0.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PREDAsampledata_0.37.0.tar.gz", "https://bioarchive.galaxyproject.org/PREDAsampledata_0.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-predasampledata/bioconductor-predasampledata_0.37.0_src_all.tar.gz"], "md5": "55491dfcc26f2b86f32bc0f6d24ae70e", "fn": "PREDAsampledata_0.37.0.tar.gz"}, "prodata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ProData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/ProData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prodata/bioconductor-prodata_1.35.0_src_all.tar.gz"], "md5": "1f4cbc866bff251c9d9da84d248d573c", "fn": "ProData_1.35.0.tar.gz"}, "prolocdata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pRolocdata_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/pRolocdata_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prolocdata/bioconductor-prolocdata_1.35.0_src_all.tar.gz"], "md5": "022bb2ecedef6645c789c77cf81df02f", "fn": "pRolocdata_1.35.0.tar.gz"}, "prostatecancercamcap-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerCamcap_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerCamcap_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancercamcap/bioconductor-prostatecancercamcap_1.25.0_src_all.tar.gz"], "md5": "ebc9c45d833ffc639ea617615120a266", "fn": "prostateCancerCamcap_1.25.0.tar.gz"}, "prostatecancergrasso-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerGrasso_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerGrasso_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancergrasso/bioconductor-prostatecancergrasso_1.25.0_src_all.tar.gz"], "md5": "603e0a603a2be0a74aa134751f4d8bd4", "fn": "prostateCancerGrasso_1.25.0.tar.gz"}, "prostatecancerstockholm-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerStockholm_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerStockholm_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancerstockholm/bioconductor-prostatecancerstockholm_1.25.0_src_all.tar.gz"], "md5": "e95bb37704614ac74857659dab3fbcb0", "fn": "prostateCancerStockholm_1.25.0.tar.gz"}, "prostatecancertaylor-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerTaylor_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerTaylor_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancertaylor/bioconductor-prostatecancertaylor_1.25.0_src_all.tar.gz"], "md5": "66f146c541ed0d31c1b8c135c3d96264", "fn": "prostateCancerTaylor_1.25.0.tar.gz"}, "prostatecancervarambally-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerVarambally_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerVarambally_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancervarambally/bioconductor-prostatecancervarambally_1.25.0_src_all.tar.gz"], "md5": "5932c3c12140f4d28ac5a2e0a80e7a6f", "fn": "prostateCancerVarambally_1.25.0.tar.gz"}, "ptairdata-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ptairData_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/ptairData_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ptairdata/bioconductor-ptairdata_1.5.0_src_all.tar.gz"], "md5": "2d7b56e13204f1b91268abb8dff92363", "fn": "ptairData_1.5.0.tar.gz"}, "pth2o2lipids-1.23.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PtH2O2lipids_1.23.0.tar.gz", "https://bioarchive.galaxyproject.org/PtH2O2lipids_1.23.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pth2o2lipids/bioconductor-pth2o2lipids_1.23.0_src_all.tar.gz"], "md5": "c28311979e8a0eb57c2071b730e0a333", "fn": "PtH2O2lipids_1.23.0.tar.gz"}, "pumadata-2.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pumadata_2.33.0.tar.gz", "https://bioarchive.galaxyproject.org/pumadata_2.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pumadata/bioconductor-pumadata_2.33.0_src_all.tar.gz"], "md5": "d2ab4b9502b32fe38ee511381992afe9", "fn": "pumadata_2.33.0.tar.gz"}, "pwmenrich.dmelanogaster.background-4.31.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PWMEnrich.Dmelanogaster.background_4.31.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Dmelanogaster.background_4.31.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.dmelanogaster.background/bioconductor-pwmenrich.dmelanogaster.background_4.31.0_src_all.tar.gz"], "md5": "cd0675f1765e474fff6cf1f024f1724c", "fn": "PWMEnrich.Dmelanogaster.background_4.31.0.tar.gz"}, "pwmenrich.hsapiens.background-4.31.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PWMEnrich.Hsapiens.background_4.31.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Hsapiens.background_4.31.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.hsapiens.background/bioconductor-pwmenrich.hsapiens.background_4.31.0_src_all.tar.gz"], "md5": "8efdc209ce7f934d8cfbcb3ef42bfa4a", "fn": "PWMEnrich.Hsapiens.background_4.31.0.tar.gz"}, "pwmenrich.mmusculus.background-4.31.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PWMEnrich.Mmusculus.background_4.31.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Mmusculus.background_4.31.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.mmusculus.background/bioconductor-pwmenrich.mmusculus.background_4.31.0_src_all.tar.gz"], "md5": "3bff15a5eb02b34142880dab0092875e", "fn": "PWMEnrich.Mmusculus.background_4.31.0.tar.gz"}, "pwrewas.data-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pwrEWAS.data_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/pwrEWAS.data_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwrewas.data/bioconductor-pwrewas.data_1.11.0_src_all.tar.gz"], "md5": "173596e2dd38d12b4d32fad1bc6c9452", "fn": "pwrEWAS.data_1.11.0.tar.gz"}, "qdnaseq.hg19-1.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/QDNAseq.hg19_1.27.0.tar.gz", "https://bioarchive.galaxyproject.org/QDNAseq.hg19_1.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.hg19/bioconductor-qdnaseq.hg19_1.27.0_src_all.tar.gz"], "md5": "518d77883a6b46e2f874be69d84d4f68", "fn": "QDNAseq.hg19_1.27.0.tar.gz"}, "qdnaseq.mm10-1.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/QDNAseq.mm10_1.27.0.tar.gz", "https://bioarchive.galaxyproject.org/QDNAseq.mm10_1.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.mm10/bioconductor-qdnaseq.mm10_1.27.0_src_all.tar.gz"], "md5": "c53a875e47d38a8b21a47abacdbcda71", "fn": "QDNAseq.mm10_1.27.0.tar.gz"}, "qplexdata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/qPLEXdata_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/qPLEXdata_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qplexdata/bioconductor-qplexdata_1.15.0_src_all.tar.gz"], "md5": "bb2fa241c178b29f9282965a11a124ef", "fn": "qPLEXdata_1.15.0.tar.gz"}, "qubicdata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/QUBICdata_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/QUBICdata_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qubicdata/bioconductor-qubicdata_1.25.0_src_all.tar.gz"], "md5": "3c29904ce0171ebf2003ead6230e0810", "fn": "QUBICdata_1.25.0.tar.gz"}, "rcellminerdata-2.19.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/rcellminerData_2.19.1.tar.gz", "https://bioarchive.galaxyproject.org/rcellminerData_2.19.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rcellminerdata/bioconductor-rcellminerdata_2.19.1_src_all.tar.gz"], "md5": "db4a9f7371903f4c42c4465c48a6133e", "fn": "rcellminerData_2.19.1.tar.gz"}, "rcistarget.hg19.motifdbs.cisbponly.500bp-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp_1.17.0_src_all.tar.gz"], "md5": "856d7c1e8d71925b4f2b89bc72dab2e9", "fn": "RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.17.0.tar.gz"}, "reactomegsa.data-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ReactomeGSA.data_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/ReactomeGSA.data_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-reactomegsa.data/bioconductor-reactomegsa.data_1.11.0_src_all.tar.gz"], "md5": "f598a9890069ab14cce69b0c1488c47e", "fn": "ReactomeGSA.data_1.11.0.tar.gz"}, "regparallel-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RegParallel_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/RegParallel_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-regparallel/bioconductor-regparallel_1.15.0_src_all.tar.gz"], "md5": "0b1630990f1980bc6466867df598f207", "fn": "RegParallel_1.15.0.tar.gz"}, "restfulsedata-1.19.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/restfulSEData_1.19.0.tar.gz", "https://bioarchive.galaxyproject.org/restfulSEData_1.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-restfulsedata/bioconductor-restfulsedata_1.19.0_src_all.tar.gz"], "md5": "df09d45e9947259f318be8f81f73a0e6", "fn": "restfulSEData_1.19.0.tar.gz"}, "rforproteomics-1.35.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RforProteomics_1.35.1.tar.gz", "https://bioarchive.galaxyproject.org/RforProteomics_1.35.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rforproteomics/bioconductor-rforproteomics_1.35.1_src_all.tar.gz"], "md5": "3ffd6e19093de0c9db70a0b2460a0f4e", "fn": "RforProteomics_1.35.1.tar.gz"}, "rgmqllib-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RGMQLlib_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/RGMQLlib_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgmqllib/bioconductor-rgmqllib_1.17.0_src_all.tar.gz"], "md5": "fcbab98d1d444959fce27cf72575f78a", "fn": "RGMQLlib_1.17.0.tar.gz"}, "rheumaticconditionwollbold-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/rheumaticConditionWOLLBOLD_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/rheumaticConditionWOLLBOLD_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rheumaticconditionwollbold/bioconductor-rheumaticconditionwollbold_1.35.0_src_all.tar.gz"], "md5": "d2a9508ad9667781fea8e7b9cb841809", "fn": "rheumaticConditionWOLLBOLD_1.35.0.tar.gz"}, "ritandata-1.21.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RITANdata_1.21.0.tar.gz", "https://bioarchive.galaxyproject.org/RITANdata_1.21.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ritandata/bioconductor-ritandata_1.21.0_src_all.tar.gz"], "md5": "0b7b1ee673125332fdc786b1305a3071", "fn": "RITANdata_1.21.0.tar.gz"}, "rlhub-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RLHub_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/RLHub_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rlhub/bioconductor-rlhub_1.3.0_src_all.tar.gz"], "md5": "993a8252373fbe49176ad288bb18130d", "fn": "RLHub_1.3.0.tar.gz"}, "rmassbankdata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RMassBankData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/RMassBankData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rmassbankdata/bioconductor-rmassbankdata_1.35.0_src_all.tar.gz"], "md5": "796f21868672494e4e077820dface333", "fn": "RMassBankData_1.35.0.tar.gz"}, "rnainteractmapk-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RNAinteractMAPK_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAinteractMAPK_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnainteractmapk/bioconductor-rnainteractmapk_1.35.0_src_all.tar.gz"], "md5": "80f15d7f3d3238da524d1a14d71b1ef7", "fn": "RNAinteractMAPK_1.35.0.tar.gz"}, "rnamodr.data-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RNAmodR.Data_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAmodR.Data_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnamodr.data/bioconductor-rnamodr.data_1.11.0_src_all.tar.gz"], "md5": "ff9ff0deccfdec4c95548bbba9c3b1f7", "fn": "RNAmodR.Data_1.11.0.tar.gz"}, "rnaseqdata.hnrnpc.bam.chr14-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RNAseqData.HNRNPC.bam.chr14_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAseqData.HNRNPC.bam.chr14_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqdata.hnrnpc.bam.chr14/bioconductor-rnaseqdata.hnrnpc.bam.chr14_0.35.0_src_all.tar.gz"], "md5": "401b79849c78d01100e08e34d7a25292", "fn": "RNAseqData.HNRNPC.bam.chr14_0.35.0.tar.gz"}, "rnaseqrdata-1.15.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RNASeqRData_1.15.1.tar.gz", "https://bioarchive.galaxyproject.org/RNASeqRData_1.15.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqrdata/bioconductor-rnaseqrdata_1.15.1_src_all.tar.gz"], "md5": "478f32fc1d6a3580d101652ef2015546", "fn": "RNASeqRData_1.15.1.tar.gz"}, "rnaseqsamplesizedata-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnaSeqSampleSizeData_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/RnaSeqSampleSizeData_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqsamplesizedata/bioconductor-rnaseqsamplesizedata_1.29.0_src_all.tar.gz"], "md5": "bc2df4e881a94985ceb2b6bf0998de6a", "fn": "RnaSeqSampleSizeData_1.29.0.tar.gz"}, "rnbeads.hg19-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.hg19_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.hg19_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg19/bioconductor-rnbeads.hg19_1.29.0_src_all.tar.gz"], "md5": "c725e7435a196137ba885a8cca8f1991", "fn": "RnBeads.hg19_1.29.0.tar.gz"}, "rnbeads.hg38-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.hg38_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.hg38_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg38/bioconductor-rnbeads.hg38_1.29.0_src_all.tar.gz"], "md5": "055e1c7a0e00f53e53b07b7560865703", "fn": "RnBeads.hg38_1.29.0.tar.gz"}, "rnbeads.mm10-2.5.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.mm10_2.5.1.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.mm10_2.5.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm10/bioconductor-rnbeads.mm10_2.5.1_src_all.tar.gz"], "md5": "5c57fb0869667a8bda50c90f8028e8e1", "fn": "RnBeads.mm10_2.5.1.tar.gz"}, "rnbeads.mm9-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.mm9_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.mm9_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm9/bioconductor-rnbeads.mm9_1.29.0_src_all.tar.gz"], "md5": "d0c5a9b71d99cbcb21d4192b78774352", "fn": "RnBeads.mm9_1.29.0.tar.gz"}, "rnbeads.rn5-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.rn5_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.rn5_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.rn5/bioconductor-rnbeads.rn5_1.29.0_src_all.tar.gz"], "md5": "ca6bc3e9fe0a8a9f5e876cb9f1b76cae", "fn": "RnBeads.rn5_1.29.0.tar.gz"}, "rrbsdata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RRBSdata_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/RRBSdata_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rrbsdata/bioconductor-rrbsdata_1.17.0_src_all.tar.gz"], "md5": "5dd5415736896e85943d4330c091e694", "fn": "RRBSdata_1.17.0.tar.gz"}, "rrdpdata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/rRDPData_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/rRDPData_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rrdpdata/bioconductor-rrdpdata_1.17.0_src_all.tar.gz"], "md5": "4c364082e1cedd9ffab9d5275ec297d5", "fn": "rRDPData_1.17.0.tar.gz"}, "rtcga.clinical-20151101.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RTCGA.clinical_20151101.27.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.clinical_20151101.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.clinical/bioconductor-rtcga.clinical_20151101.27.0_src_all.tar.gz"], "md5": "35e8c14f6a582746b995c5c57224dc45", "fn": "RTCGA.clinical_20151101.27.0.tar.gz"}, "rtcga.cnv-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RTCGA.CNV_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.CNV_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.cnv/bioconductor-rtcga.cnv_1.25.0_src_all.tar.gz"], "md5": "7fc6cc257e7ee37df80002e8ab1335a4", "fn": "RTCGA.CNV_1.25.0.tar.gz"}, "rtcga.methylation-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RTCGA.methylation_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.methylation_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.methylation/bioconductor-rtcga.methylation_1.25.0_src_all.tar.gz"], "md5": "d87ab750ff3ccdd424dfae6442f4b5ad", "fn": "RTCGA.methylation_1.25.0.tar.gz"}, "rtcga.mirnaseq-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RTCGA.miRNASeq_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.miRNASeq_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mirnaseq/bioconductor-rtcga.mirnaseq_1.25.0_src_all.tar.gz"], "md5": "471abf3d4d571d7e36f564e3717d511e", "fn": "RTCGA.miRNASeq_1.25.0.tar.gz"}, "rtcga.mrna-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RTCGA.mRNA_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.mRNA_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mrna/bioconductor-rtcga.mrna_1.25.0_src_all.tar.gz"], "md5": "354a9449d7e97238fccec1c0b6f909ca", "fn": "RTCGA.mRNA_1.25.0.tar.gz"}, "rtcga.mutations-20151101.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RTCGA.mutations_20151101.27.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.mutations_20151101.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mutations/bioconductor-rtcga.mutations_20151101.27.0_src_all.tar.gz"], "md5": "d048b3ecd23a074d3fb83edbb97ef9f3", "fn": "RTCGA.mutations_20151101.27.0.tar.gz"}, "rtcga.pancan12-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RTCGA.PANCAN12_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.PANCAN12_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.pancan12/bioconductor-rtcga.pancan12_1.25.0_src_all.tar.gz"], "md5": "fec760cdd49da6ba627f54ff48cc1b93", "fn": "RTCGA.PANCAN12_1.25.0.tar.gz"}, "rtcga.rnaseq-20151101.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RTCGA.rnaseq_20151101.27.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.rnaseq_20151101.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.rnaseq/bioconductor-rtcga.rnaseq_20151101.27.0_src_all.tar.gz"], "md5": "e2d2bf42422003ace5ad96bef58ea405", "fn": "RTCGA.rnaseq_20151101.27.0.tar.gz"}, "rtcga.rppa-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RTCGA.RPPA_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.RPPA_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.rppa/bioconductor-rtcga.rppa_1.25.0_src_all.tar.gz"], "md5": "f9f2a9881310faad9361f7fdd026f128", "fn": "RTCGA.RPPA_1.25.0.tar.gz"}, "ruvnormalizedata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RUVnormalizeData_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/RUVnormalizeData_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ruvnormalizedata/bioconductor-ruvnormalizedata_1.17.0_src_all.tar.gz"], "md5": "306697e9fc77724556f118f23bf26485", "fn": "RUVnormalizeData_1.17.0.tar.gz"}, "sampleclassifierdata-1.21.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/sampleClassifierData_1.21.0.tar.gz", "https://bioarchive.galaxyproject.org/sampleClassifierData_1.21.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sampleclassifierdata/bioconductor-sampleclassifierdata_1.21.0_src_all.tar.gz"], "md5": "c12c28d1c72e9cf498ed86163d7ed783", "fn": "sampleClassifierData_1.21.0.tar.gz"}, "sbgnview.data-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SBGNview.data_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/SBGNview.data_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sbgnview.data/bioconductor-sbgnview.data_1.11.0_src_all.tar.gz"], "md5": "e6c7eb719b1d37cfa714406dfbdcc0a1", "fn": "SBGNview.data_1.11.0.tar.gz"}, "scanmirdata-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/scanMiRData_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/scanMiRData_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scanmirdata/bioconductor-scanmirdata_1.3.0_src_all.tar.gz"], "md5": "a43695113a97f647b5d126ed6a25e916", "fn": "scanMiRData_1.3.0.tar.gz"}, "scatac.explorer-1.3.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/scATAC.Explorer_1.3.1.tar.gz", "https://bioarchive.galaxyproject.org/scATAC.Explorer_1.3.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scatac.explorer/bioconductor-scatac.explorer_1.3.1_src_all.tar.gz"], "md5": "85b3806b74f97621c9060287ad23364b", "fn": "scATAC.Explorer_1.3.1.tar.gz"}, "scatedata-1.7.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SCATEData_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/SCATEData_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scatedata/bioconductor-scatedata_1.7.0_src_all.tar.gz"], "md5": "411679e006f3d67c0397047166899a19", "fn": "SCATEData_1.7.0.tar.gz"}, "sclcbam-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SCLCBam_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/SCLCBam_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sclcbam/bioconductor-sclcbam_1.29.0_src_all.tar.gz"], "md5": "16a8806e945c1102bf251522a3bb4245", "fn": "SCLCBam_1.29.0.tar.gz"}, "scpdata-1.5.6": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/scpdata_1.5.6.tar.gz", "https://bioarchive.galaxyproject.org/scpdata_1.5.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scpdata/bioconductor-scpdata_1.5.6_src_all.tar.gz"], "md5": "26b3cc33198ebf3866ab92cd6982503f", "fn": "scpdata_1.5.6.tar.gz"}, "scrnaseq-2.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/scRNAseq_2.11.0.tar.gz", "https://bioarchive.galaxyproject.org/scRNAseq_2.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scrnaseq/bioconductor-scrnaseq_2.11.0_src_all.tar.gz"], "md5": "70776b195a73f25a1bc4556f617aa6be", "fn": "scRNAseq_2.11.0.tar.gz"}, "scthi.data-1.9.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/scTHI.data_1.9.0.tar.gz", "https://bioarchive.galaxyproject.org/scTHI.data_1.9.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scthi.data/bioconductor-scthi.data_1.9.0_src_all.tar.gz"], "md5": "a698f50dd82951cb71f4cf478cc38333", "fn": "scTHI.data_1.9.0.tar.gz"}, "seq2pathway.data-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/seq2pathway.data_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/seq2pathway.data_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seq2pathway.data/bioconductor-seq2pathway.data_1.29.0_src_all.tar.gz"], "md5": "2ee5d460d650aaef586d7000881a0849", "fn": "seq2pathway.data_1.29.0.tar.gz"}, "seqc-1.31.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/seqc_1.31.0.tar.gz", "https://bioarchive.galaxyproject.org/seqc_1.31.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seqc/bioconductor-seqc_1.31.0_src_all.tar.gz"], "md5": "48815472de95968a75d74e674e431c26", "fn": "seqc_1.31.0.tar.gz"}, "seqcna.annot-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/seqCNA.annot_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/seqCNA.annot_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seqcna.annot/bioconductor-seqcna.annot_1.33.0_src_all.tar.gz"], "md5": "51b9a1bf62f20ba710dd42d6656e5aaa", "fn": "seqCNA.annot_1.33.0.tar.gz"}, "serumstimulation-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/serumStimulation_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/serumStimulation_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-serumstimulation/bioconductor-serumstimulation_1.33.0_src_all.tar.gz"], "md5": "9a8d66ab8dd4e884f8cbd570979710d4", "fn": "serumStimulation_1.33.0.tar.gz"}, "sesamedata-1.15.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/sesameData_1.15.2.tar.gz", "https://bioarchive.galaxyproject.org/sesameData_1.15.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sesamedata/bioconductor-sesamedata_1.15.2_src_all.tar.gz"], "md5": "5a0f67d044802b947e6b60a0b995b1ed", "fn": "sesameData_1.15.2.tar.gz"}, "seventygenedata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/seventyGeneData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/seventyGeneData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seventygenedata/bioconductor-seventygenedata_1.33.0_src_all.tar.gz"], "md5": "54f2663a062f96ce8e9accc6f6ca4ffc", "fn": "seventyGeneData_1.33.0.tar.gz"}, "sfedata-0.99.7": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SFEData_0.99.7.tar.gz", "https://bioarchive.galaxyproject.org/SFEData_0.99.7.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sfedata/bioconductor-sfedata_0.99.7_src_all.tar.gz"], "md5": "340d06a5b66dd38d058d0e0731c38c2a", "fn": "SFEData_0.99.7.tar.gz"}, "shinymethyldata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/shinyMethylData_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/shinyMethylData_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-shinymethyldata/bioconductor-shinymethyldata_1.17.0_src_all.tar.gz"], "md5": "6b95b7efb75a39bcd8e786f8f0719eef", "fn": "shinyMethylData_1.17.0.tar.gz"}, "signaturesearchdata-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/signatureSearchData_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/signatureSearchData_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-signaturesearchdata/bioconductor-signaturesearchdata_1.11.0_src_all.tar.gz"], "md5": "20cd61a7297ba49c4ede5ef2469e6c49", "fn": "signatureSearchData_1.11.0.tar.gz"}, "simbenchdata-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SimBenchData_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/SimBenchData_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-simbenchdata/bioconductor-simbenchdata_1.5.0_src_all.tar.gz"], "md5": "cd45939fd175a2bb4b55ff889628634a", "fn": "SimBenchData_1.5.0.tar.gz"}, "simpintlists-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/simpIntLists_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/simpIntLists_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-simpintlists/bioconductor-simpintlists_1.33.0_src_all.tar.gz"], "md5": "5a75c92aee4a1cbc367ec5a3477cfdd7", "fn": "simpIntLists_1.33.0.tar.gz"}, "single.mtec.transcriptomes-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Single.mTEC.Transcriptomes_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/Single.mTEC.Transcriptomes_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-single.mtec.transcriptomes/bioconductor-single.mtec.transcriptomes_1.25.0_src_all.tar.gz"], "md5": "560313eceb9231c01b678e08edb55a2e", "fn": "Single.mTEC.Transcriptomes_1.25.0.tar.gz"}, "singlecellmultimodal-1.9.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SingleCellMultiModal_1.9.1.tar.gz", "https://bioarchive.galaxyproject.org/SingleCellMultiModal_1.9.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-singlecellmultimodal/bioconductor-singlecellmultimodal_1.9.1_src_all.tar.gz"], "md5": "0c59bc44aaac749033e80fe0fcf1e857", "fn": "SingleCellMultiModal_1.9.1.tar.gz"}, "singlemoleculefootprintingdata-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SingleMoleculeFootprintingData_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/SingleMoleculeFootprintingData_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-singlemoleculefootprintingdata/bioconductor-singlemoleculefootprintingdata_1.5.0_src_all.tar.gz"], "md5": "ddcc1ca02d843daf3cc75ca9ce086316", "fn": "SingleMoleculeFootprintingData_1.5.0.tar.gz"}, "snadata-1.43.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SNAData_1.43.0.tar.gz", "https://bioarchive.galaxyproject.org/SNAData_1.43.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snadata/bioconductor-snadata_1.43.0_src_all.tar.gz"], "md5": "24320fe022729f78f187851b14b441e7", "fn": "SNAData_1.43.0.tar.gz"}, "snageedata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SNAGEEdata_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/SNAGEEdata_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snageedata/bioconductor-snageedata_1.33.0_src_all.tar.gz"], "md5": "8cb9091d5082ee082b0ec7139d28667d", "fn": "SNAGEEdata_1.33.0.tar.gz"}, "snphooddata-1.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SNPhoodData_1.27.0.tar.gz", "https://bioarchive.galaxyproject.org/SNPhoodData_1.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snphooddata/bioconductor-snphooddata_1.27.0_src_all.tar.gz"], "md5": "418848af2c57a34599486445325114de", "fn": "SNPhoodData_1.27.0.tar.gz"}, "somaticadata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SomatiCAData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/SomatiCAData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-somaticadata/bioconductor-somaticadata_1.35.0_src_all.tar.gz"], "md5": "9429c73a8a4b28926a8ea3f61233e8d1", "fn": "SomatiCAData_1.35.0.tar.gz"}, "somaticcanceralterations-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SomaticCancerAlterations_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/SomaticCancerAlterations_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-somaticcanceralterations/bioconductor-somaticcanceralterations_1.33.0_src_all.tar.gz"], "md5": "1974e96d47df6f7fde09f8e0eb069ac5", "fn": "SomaticCancerAlterations_1.33.0.tar.gz"}, "spatialdmelxsim-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/spatialDmelxsim_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/spatialDmelxsim_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatialdmelxsim/bioconductor-spatialdmelxsim_1.3.0_src_all.tar.gz"], "md5": "862af3f63791a570ea892fe39efe6e12", "fn": "spatialDmelxsim_1.3.0.tar.gz"}, "spatiallibd-1.9.19": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/spatialLIBD_1.9.19.tar.gz", "https://bioarchive.galaxyproject.org/spatialLIBD_1.9.19.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatiallibd/bioconductor-spatiallibd_1.9.19_src_all.tar.gz"], "md5": "f1e78d740cbb533190708bf59b1c8b3e", "fn": "spatialLIBD_1.9.19.tar.gz"}, "spikein-1.39.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SpikeIn_1.39.0.tar.gz", "https://bioarchive.galaxyproject.org/SpikeIn_1.39.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spikein/bioconductor-spikein_1.39.0_src_all.tar.gz"], "md5": "9effe497b629d75622cb90b15d6b0407", "fn": "SpikeIn_1.39.0.tar.gz"}, "spikeinsubset-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SpikeInSubset_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/SpikeInSubset_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spikeinsubset/bioconductor-spikeinsubset_1.37.0_src_all.tar.gz"], "md5": "acfc16b524f4a8862281006722f3f32a", "fn": "SpikeInSubset_1.37.0.tar.gz"}, "spqndata-1.9.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/spqnData_1.9.0.tar.gz", "https://bioarchive.galaxyproject.org/spqnData_1.9.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spqndata/bioconductor-spqndata_1.9.0_src_all.tar.gz"], "md5": "24599f986a8f2e4f06af4996fe1c2f3f", "fn": "spqnData_1.9.0.tar.gz"}, "stemhypoxia-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/stemHypoxia_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/stemHypoxia_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stemhypoxia/bioconductor-stemhypoxia_1.33.0_src_all.tar.gz"], "md5": "fe757bfe1c1876fb96ce163f45e3df58", "fn": "stemHypoxia_1.33.0.tar.gz"}, "stexampledata-1.5.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/STexampleData_1.5.2.tar.gz", "https://bioarchive.galaxyproject.org/STexampleData_1.5.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stexampledata/bioconductor-stexampledata_1.5.2_src_all.tar.gz"], "md5": "c1e37cafb1f6da572942e1eeec1241b4", "fn": "STexampleData_1.5.2.tar.gz"}, "stjudem-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/stjudem_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/stjudem_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stjudem/bioconductor-stjudem_1.37.0_src_all.tar.gz"], "md5": "6f2e08c7e679d02bac1b908aa7ad775e", "fn": "stjudem_1.37.0.tar.gz"}, "svm2crmdata-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SVM2CRMdata_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/SVM2CRMdata_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-svm2crmdata/bioconductor-svm2crmdata_1.29.0_src_all.tar.gz"], "md5": "3e07fd96096e1c15a05cd1e45b5173bc", "fn": "SVM2CRMdata_1.29.0.tar.gz"}, "synapterdata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/synapterdata_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/synapterdata_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-synapterdata/bioconductor-synapterdata_1.35.0_src_all.tar.gz"], "md5": "603dc62bd3d1b2e7daa8d1ab66285d2e", "fn": "synapterdata_1.35.0.tar.gz"}, "systempiperdata-2.1.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/systemPipeRdata_2.1.2.tar.gz", "https://bioarchive.galaxyproject.org/systemPipeRdata_2.1.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-systempiperdata/bioconductor-systempiperdata_2.1.2_src_all.tar.gz"], "md5": "6d2bd003dbdb72a83de0fb0026cfb7fe", "fn": "systemPipeRdata_2.1.2.tar.gz"}, "tabulamurisdata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TabulaMurisData_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/TabulaMurisData_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tabulamurisdata/bioconductor-tabulamurisdata_1.15.0_src_all.tar.gz"], "md5": "7f57c27412eca366c33144a428e9ead6", "fn": "TabulaMurisData_1.15.0.tar.gz"}, "tabulamurissenisdata-1.3.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TabulaMurisSenisData_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/TabulaMurisSenisData_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tabulamurissenisdata/bioconductor-tabulamurissenisdata_1.3.0_src_all.tar.gz"], "md5": "27d801ac7d3f9069160767e1fb0e5ecd", "fn": "TabulaMurisSenisData_1.3.0.tar.gz"}, "targetscoredata-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TargetScoreData_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/TargetScoreData_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetscoredata/bioconductor-targetscoredata_1.33.0_src_all.tar.gz"], "md5": "ca583f136c849f6bf93ca1514abd5ff3", "fn": "TargetScoreData_1.33.0.tar.gz"}, "targetsearchdata-1.35.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TargetSearchData_1.35.2.tar.gz", "https://bioarchive.galaxyproject.org/TargetSearchData_1.35.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetsearchdata/bioconductor-targetsearchdata_1.35.2_src_all.tar.gz"], "md5": "43fb25187b147b819b0e23af4e335cdd", "fn": "TargetSearchData_1.35.2.tar.gz"}, "tartare-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tartare_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/tartare_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tartare/bioconductor-tartare_1.11.0_src_all.tar.gz"], "md5": "8c4138bab0fb88cde1506b336f55b879", "fn": "tartare_1.11.0.tar.gz"}, "tbx20bamsubset-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TBX20BamSubset_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/TBX20BamSubset_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tbx20bamsubset/bioconductor-tbx20bamsubset_1.33.0_src_all.tar.gz"], "md5": "87c505f0958e19fcdf8f7bed9ab92fbf", "fn": "TBX20BamSubset_1.33.0.tar.gz"}, "tcgabiolinksgui.data-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TCGAbiolinksGUI.data_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAbiolinksGUI.data_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgabiolinksgui.data/bioconductor-tcgabiolinksgui.data_1.17.0_src_all.tar.gz"], "md5": "5d6415ec86aaeb44f84b7a6481eb48b4", "fn": "TCGAbiolinksGUI.data_1.17.0.tar.gz"}, "tcgacrcmirna-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TCGAcrcmiRNA_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAcrcmiRNA_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmirna/bioconductor-tcgacrcmirna_1.17.0_src_all.tar.gz"], "md5": "82abd790e1b6bff2123696c614fef240", "fn": "TCGAcrcmiRNA_1.17.0.tar.gz"}, "tcgacrcmrna-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TCGAcrcmRNA_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAcrcmRNA_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmrna/bioconductor-tcgacrcmrna_1.17.0_src_all.tar.gz"], "md5": "7da254036ad12e64c49d47cf352b2c73", "fn": "TCGAcrcmRNA_1.17.0.tar.gz"}, "tcgamethylation450k-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TCGAMethylation450k_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAMethylation450k_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgamethylation450k/bioconductor-tcgamethylation450k_1.33.0_src_all.tar.gz"], "md5": "fe77cf245bce1750ce61e1a6b235829d", "fn": "TCGAMethylation450k_1.33.0.tar.gz"}, "tcgaworkflowdata-1.21.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TCGAWorkflowData_1.21.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAWorkflowData_1.21.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgaworkflowdata/bioconductor-tcgaworkflowdata_1.21.0_src_all.tar.gz"], "md5": "69dae77a3b3916f3cf884ad05c96cc7c", "fn": "TCGAWorkflowData_1.21.0.tar.gz"}, "tenxbraindata-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TENxBrainData_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxBrainData_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxbraindata/bioconductor-tenxbraindata_1.17.0_src_all.tar.gz"], "md5": "45978a0b489aafe4edab0e1534f07978", "fn": "TENxBrainData_1.17.0.tar.gz"}, "tenxbusdata-1.11.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TENxBUSData_1.11.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxBUSData_1.11.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxbusdata/bioconductor-tenxbusdata_1.11.0_src_all.tar.gz"], "md5": "ffd6839b94b6fdd8ba41af3a455b0b92", "fn": "TENxBUSData_1.11.0.tar.gz"}, "tenxpbmcdata-1.15.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TENxPBMCData_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxPBMCData_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxpbmcdata/bioconductor-tenxpbmcdata_1.15.0_src_all.tar.gz"], "md5": "a12628733b5ea103b62f449aaf0b10d7", "fn": "TENxPBMCData_1.15.0.tar.gz"}, "tenxvisiumdata-1.5.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TENxVisiumData_1.5.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxVisiumData_1.5.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxvisiumdata/bioconductor-tenxvisiumdata_1.5.0_src_all.tar.gz"], "md5": "9fe57094f0c7e344a01a80277736c84b", "fn": "TENxVisiumData_1.5.0.tar.gz"}, "timecoursedata-1.7.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/timecoursedata_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/timecoursedata_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-timecoursedata/bioconductor-timecoursedata_1.7.0_src_all.tar.gz"], "md5": "2cbd0fa6b4e66daa39a2bd1244309a97", "fn": "timecoursedata_1.7.0.tar.gz"}, "timerquant-1.27.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TimerQuant_1.27.0.tar.gz", "https://bioarchive.galaxyproject.org/TimerQuant_1.27.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-timerquant/bioconductor-timerquant_1.27.0_src_all.tar.gz"], "md5": "2456c8d6d3755eb65bd6cafa0f621a66", "fn": "TimerQuant_1.27.0.tar.gz"}, "tinesath1cdf-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tinesath1cdf_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/tinesath1cdf_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tinesath1cdf/bioconductor-tinesath1cdf_1.35.0_src_all.tar.gz"], "md5": "3b5ddb90839f9fb31cf91a9726a934a0", "fn": "tinesath1cdf_1.35.0.tar.gz"}, "tinesath1probe-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tinesath1probe_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/tinesath1probe_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tinesath1probe/bioconductor-tinesath1probe_1.35.0_src_all.tar.gz"], "md5": "72478cd47ca289c0214d7745f75291b3", "fn": "tinesath1probe_1.35.0.tar.gz"}, "tissuetreg-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tissueTreg_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/tissueTreg_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tissuetreg/bioconductor-tissuetreg_1.17.0_src_all.tar.gz"], "md5": "2dd7fc2211e8ae3d240fc82d7aef3d99", "fn": "tissueTreg_1.17.0.tar.gz"}, "tmexplorer-1.7.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TMExplorer_1.7.2.tar.gz", "https://bioarchive.galaxyproject.org/TMExplorer_1.7.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tmexplorer/bioconductor-tmexplorer_1.7.2_src_all.tar.gz"], "md5": "1271bcae8d7a46153441e3000f1dc307", "fn": "TMExplorer_1.7.2.tar.gz"}, "tofsimsdata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tofsimsData_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/tofsimsData_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tofsimsdata/bioconductor-tofsimsdata_1.25.0_src_all.tar.gz"], "md5": "b5faa9733183ff1d2aadd97c2b6f7a2a", "fn": "tofsimsData_1.25.0.tar.gz"}, "topdownrdata-1.19.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/topdownrdata_1.19.0.tar.gz", "https://bioarchive.galaxyproject.org/topdownrdata_1.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-topdownrdata/bioconductor-topdownrdata_1.19.0_src_all.tar.gz"], "md5": "e86dbcc5dfe0b8539d5dbac3492ffddf", "fn": "topdownrdata_1.19.0.tar.gz"}, "tuberculosis-1.3.1": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tuberculosis_1.3.1.tar.gz", "https://bioarchive.galaxyproject.org/tuberculosis_1.3.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tuberculosis/bioconductor-tuberculosis_1.3.1_src_all.tar.gz"], "md5": "14f353861c61befd1911a3dbd369a5ec", "fn": "tuberculosis_1.3.1.tar.gz"}, "tweedeseqcountdata-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tweeDEseqCountData_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/tweeDEseqCountData_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tweedeseqcountdata/bioconductor-tweedeseqcountdata_1.35.0_src_all.tar.gz"], "md5": "a5ed31ba1cbf1170ee42df7c406bcd2d", "fn": "tweeDEseqCountData_1.35.0.tar.gz"}, "tximportdata-1.25.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tximportData_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/tximportData_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tximportdata/bioconductor-tximportdata_1.25.0_src_all.tar.gz"], "md5": "3ba5ba44ef1eba13a0d2a6d801c4d0f2", "fn": "tximportData_1.25.0.tar.gz"}, "varianttoolsdata-1.21.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/VariantToolsData_1.21.0.tar.gz", "https://bioarchive.galaxyproject.org/VariantToolsData_1.21.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-varianttoolsdata/bioconductor-varianttoolsdata_1.21.0_src_all.tar.gz"], "md5": "929b183276d2619fe003924aa94087d8", "fn": "VariantToolsData_1.21.0.tar.gz"}, "vectrapolarisdata-1.1.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/VectraPolarisData_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/VectraPolarisData_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vectrapolarisdata/bioconductor-vectrapolarisdata_1.1.0_src_all.tar.gz"], "md5": "2d2adee263147ec6f77b64f6cf79f9ee", "fn": "VectraPolarisData_1.1.0.tar.gz"}, "vulcandata-1.19.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/vulcandata_1.19.0.tar.gz", "https://bioarchive.galaxyproject.org/vulcandata_1.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vulcandata/bioconductor-vulcandata_1.19.0_src_all.tar.gz"], "md5": "9c0222aaae9653366ad080b32e467e67", "fn": "vulcandata_1.19.0.tar.gz"}, "weberdivechalcdata-0.99.4": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/WeberDivechaLCdata_0.99.4.tar.gz", "https://bioarchive.galaxyproject.org/WeberDivechaLCdata_0.99.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-weberdivechalcdata/bioconductor-weberdivechalcdata_0.99.4_src_all.tar.gz"], "md5": "ac2cdb9ca4d0921e58cf36762ed552f2", "fn": "WeberDivechaLCdata_0.99.4.tar.gz"}, "wes.1kg.wugsc-1.29.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/WES.1KG.WUGSC_1.29.0.tar.gz", "https://bioarchive.galaxyproject.org/WES.1KG.WUGSC_1.29.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wes.1kg.wugsc/bioconductor-wes.1kg.wugsc_1.29.0_src_all.tar.gz"], "md5": "bda054ad4efc2754d2acbdab1ad7ee16", "fn": "WES.1KG.WUGSC_1.29.0.tar.gz"}, "wgsmapp-1.9.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/WGSmapp_1.9.0.tar.gz", "https://bioarchive.galaxyproject.org/WGSmapp_1.9.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wgsmapp/bioconductor-wgsmapp_1.9.0_src_all.tar.gz"], "md5": "0df4f6810324ffae4407ba030cd69a4b", "fn": "WGSmapp_1.9.0.tar.gz"}, "xcoredata-1.1.4": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/xcoredata_1.1.4.tar.gz", "https://bioarchive.galaxyproject.org/xcoredata_1.1.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xcoredata/bioconductor-xcoredata_1.1.4_src_all.tar.gz"], "md5": "556f844f7e54dd197196b938d44e6163", "fn": "xcoredata_1.1.4.tar.gz"}, "xhybcasneuf-1.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/XhybCasneuf_1.35.0.tar.gz", "https://bioarchive.galaxyproject.org/XhybCasneuf_1.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xhybcasneuf/bioconductor-xhybcasneuf_1.35.0_src_all.tar.gz"], "md5": "149bd49ac717ef10ad2765f41d465106", "fn": "XhybCasneuf_1.35.0.tar.gz"}, "yeastcc-1.37.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/yeastCC_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastCC_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastcc/bioconductor-yeastcc_1.37.0_src_all.tar.gz"], "md5": "13ca41f2737ac8daa603c99f973f3a47", "fn": "yeastCC_1.37.0.tar.gz"}, "yeastexpdata-0.43.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/yeastExpData_0.43.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastExpData_0.43.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastexpdata/bioconductor-yeastexpdata_0.43.0_src_all.tar.gz"], "md5": "83706c49ab5d73657adb5927b2514eed", "fn": "yeastExpData_0.43.0.tar.gz"}, "yeastgsdata-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/yeastGSData_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastGSData_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastgsdata/bioconductor-yeastgsdata_0.35.0_src_all.tar.gz"], "md5": "e8e80c40923d5f9a13d7cc336e715566", "fn": "yeastGSData_0.35.0.tar.gz"}, "yeastnagalakshmi-1.33.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/yeastNagalakshmi_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastNagalakshmi_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastnagalakshmi/bioconductor-yeastnagalakshmi_1.33.0_src_all.tar.gz"], "md5": "c44d92115c879fe8250df7add73731b2", "fn": "yeastNagalakshmi_1.33.0.tar.gz"}, "yeastrnaseq-0.35.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/yeastRNASeq_0.35.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastRNASeq_0.35.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastrnaseq/bioconductor-yeastrnaseq_0.35.0_src_all.tar.gz"], "md5": "679c8db4a43dc2ac394e33942418e050", "fn": "yeastRNASeq_0.35.0.tar.gz"}, "zebrafishrnaseq-1.17.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/zebrafishRNASeq_1.17.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafishRNASeq_1.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafishrnaseq/bioconductor-zebrafishrnaseq_1.17.0_src_all.tar.gz"], "md5": "241e5db9cba13ee69bfdea6bd3dd797e", "fn": "zebrafishRNASeq_1.17.0.tar.gz"}, "ashkenazimsonchr21-1.28.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/AshkenazimSonChr21_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/AshkenazimSonChr21_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ashkenazimsonchr21/bioconductor-ashkenazimsonchr21_1.28.0_src_all.tar.gz"], "md5": "ee16a1f96afbdf1a4c48af6b306e9c34", "fn": "AshkenazimSonChr21_1.28.0.tar.gz"}, "prodata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ProData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/ProData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prodata/bioconductor-prodata_1.36.0_src_all.tar.gz"], "md5": "5d8ebe9020f1d291d0d1b0925dec4071", "fn": "ProData_1.36.0.tar.gz"}, "bcellviper-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bcellViper_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/bcellViper_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bcellviper/bioconductor-bcellviper_1.34.0_src_all.tar.gz"], "md5": "74d0f84db2df6f2bbbb5a16cd9061049", "fn": "bcellViper_1.34.0.tar.gz"}, "dexmadata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DExMAdata_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/DExMAdata_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dexmadata/bioconductor-dexmadata_1.6.0_src_all.tar.gz"], "md5": "f8dd918540d6f8b88e0e7f51bd910d43", "fn": "DExMAdata_1.6.0.tar.gz"}, "prostatecancervarambally-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerVarambally_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerVarambally_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancervarambally/bioconductor-prostatecancervarambally_1.26.0_src_all.tar.gz"], "md5": "fadc3efac8e793c4064082806e55c625", "fn": "prostateCancerVarambally_1.26.0.tar.gz"}, "leukemiaseset-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/leukemiasEset_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/leukemiasEset_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-leukemiaseset/bioconductor-leukemiaseset_1.34.0_src_all.tar.gz"], "md5": "0e10f12c15965946d76301d679fc183b", "fn": "leukemiasEset_1.34.0.tar.gz"}, "etec16s-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/etec16s_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/etec16s_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-etec16s/bioconductor-etec16s_1.26.0_src_all.tar.gz"], "md5": "c7ef06ca5897b3db7ed8b743b53a1613", "fn": "etec16s_1.26.0.tar.gz"}, "msd16s-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/msd16s_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/msd16s_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msd16s/bioconductor-msd16s_1.18.0_src_all.tar.gz"], "md5": "e8b256082028528dd6a35fc3c6036504", "fn": "msd16s_1.18.0.tar.gz"}, "crcl18-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CRCL18_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/CRCL18_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-crcl18/bioconductor-crcl18_1.18.0_src_all.tar.gz"], "md5": "c208b19693ac14dd5c0fc1bb7c795ebb", "fn": "CRCL18_1.18.0.tar.gz"}, "seqc-1.32.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/seqc_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/seqc_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seqc/bioconductor-seqc_1.32.0_src_all.tar.gz"], "md5": "e8a94a9cc8f335206faa617e4176436a", "fn": "seqc_1.32.0.tar.gz"}, "tweedeseqcountdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tweeDEseqCountData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/tweeDEseqCountData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tweedeseqcountdata/bioconductor-tweedeseqcountdata_1.36.0_src_all.tar.gz"], "md5": "7cea3549465861a3a20ca8bf1edfaa55", "fn": "tweeDEseqCountData_1.36.0.tar.gz"}, "nanotubes-1.14.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/nanotubes_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/nanotubes_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nanotubes/bioconductor-nanotubes_1.14.0_src_all.tar.gz"], "md5": "679ba9b18a0a9e94e59b4906e413f64a", "fn": "nanotubes_1.14.0.tar.gz"}, "spikein-1.40.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SpikeIn_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/SpikeIn_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spikein/bioconductor-spikein_1.40.0_src_all.tar.gz"], "md5": "0e06e055a0cfe9e65d47e16aef933da5", "fn": "SpikeIn_1.40.0.tar.gz"}, "ampaffyexample-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/AmpAffyExample_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/AmpAffyExample_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ampaffyexample/bioconductor-ampaffyexample_1.38.0_src_all.tar.gz"], "md5": "5065f84a743080500b5e277e39057589", "fn": "AmpAffyExample_1.38.0.tar.gz"}, "spikeinsubset-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SpikeInSubset_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/SpikeInSubset_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spikeinsubset/bioconductor-spikeinsubset_1.38.0_src_all.tar.gz"], "md5": "94d2a5b8e9b8de425be147b5d808c347", "fn": "SpikeInSubset_1.38.0.tar.gz"}, "chimphumanbraindata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ChimpHumanBrainData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/ChimpHumanBrainData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chimphumanbraindata/bioconductor-chimphumanbraindata_1.36.0_src_all.tar.gz"], "md5": "3ab20ab0915bb24937cb076ab3080bf1", "fn": "ChimpHumanBrainData_1.36.0.tar.gz"}, "rnaseqrdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RNASeqRData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/RNASeqRData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqrdata/bioconductor-rnaseqrdata_1.16.0_src_all.tar.gz"], "md5": "4e697b6df3ba50597ad22199b6e605a1", "fn": "RNASeqRData_1.16.0.tar.gz"}, "tofsimsdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tofsimsData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/tofsimsData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tofsimsdata/bioconductor-tofsimsdata_1.26.0_src_all.tar.gz"], "md5": "1fdfc2ba981f909a86b14bcc493cf72d", "fn": "tofsimsData_1.26.0.tar.gz"}, "confessdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CONFESSdata_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/CONFESSdata_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-confessdata/bioconductor-confessdata_1.26.0_src_all.tar.gz"], "md5": "a85678e18baf274aa1d65283ad8b466b", "fn": "CONFESSdata_1.26.0.tar.gz"}, "yeastexpdata-0.44.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/yeastExpData_0.44.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastExpData_0.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastexpdata/bioconductor-yeastexpdata_0.44.0_src_all.tar.gz"], "md5": "d78dff0ef4e93825abaf4facd0dab782", "fn": "yeastExpData_0.44.0.tar.gz"}, "snadata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SNAData_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/SNAData_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snadata/bioconductor-snadata_1.44.0_src_all.tar.gz"], "md5": "185268ec941d950ba443ad1eb8e3b79a", "fn": "SNAData_1.44.0.tar.gz"}, "dresscheck-0.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/dressCheck_0.36.0.tar.gz", "https://bioarchive.galaxyproject.org/dressCheck_0.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dresscheck/bioconductor-dresscheck_0.36.0_src_all.tar.gz"], "md5": "35bc43d9f5b50f73f5912d9ed690d4dc", "fn": "dressCheck_0.36.0.tar.gz"}, "bronchialil13-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bronchialIL13_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/bronchialIL13_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bronchialil13/bioconductor-bronchialil13_1.36.0_src_all.tar.gz"], "md5": "f4ba15910e2cd95375fb234719f0c934", "fn": "bronchialIL13_1.36.0.tar.gz"}, "aracne.networks-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/aracne.networks_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/aracne.networks_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-aracne.networks/bioconductor-aracne.networks_1.24.0_src_all.tar.gz"], "md5": "b2e24fdcf142f295008018f3dfb83671", "fn": "aracne.networks_1.24.0.tar.gz"}, "diggitdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/diggitdata_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/diggitdata_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-diggitdata/bioconductor-diggitdata_1.30.0_src_all.tar.gz"], "md5": "c26bf6e890e506ef06eb50d120206be4", "fn": "diggitdata_1.30.0.tar.gz"}, "fibroeset-1.40.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/fibroEset_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/fibroEset_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fibroeset/bioconductor-fibroeset_1.40.0_src_all.tar.gz"], "md5": "d22fcc8ca8c62393a36b1a2a32c3efc5", "fn": "fibroEset_1.40.0.tar.gz"}, "golubesets-1.40.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/golubEsets_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/golubEsets_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-golubesets/bioconductor-golubesets_1.40.0_src_all.tar.gz"], "md5": "7c73ba0df7a265861312be51106e4887", "fn": "golubEsets_1.40.0.tar.gz"}, "dyebiasexamples-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/dyebiasexamples_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/dyebiasexamples_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dyebiasexamples/bioconductor-dyebiasexamples_1.38.0_src_all.tar.gz"], "md5": "0fbb623580c0c5d2ec99edded90815d8", "fn": "dyebiasexamples_1.38.0.tar.gz"}, "gse62944-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSE62944_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE62944_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse62944/bioconductor-gse62944_1.26.0_src_all.tar.gz"], "md5": "940bca93dee5fe79b30078c3c56a70b1", "fn": "GSE62944_1.26.0.tar.gz"}, "gse103322-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSE103322_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE103322_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse103322/bioconductor-gse103322_1.4.0_src_all.tar.gz"], "md5": "c82c8a5416a388e02b5210e0ed07d714", "fn": "GSE103322_1.4.0.tar.gz"}, "affydata-1.46.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/affydata_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/affydata_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affydata/bioconductor-affydata_1.46.0_src_all.tar.gz"], "md5": "99b85f3a09dcc5219ce0575d29146e62", "fn": "affydata_1.46.0.tar.gz"}, "cll-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CLL_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/CLL_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cll/bioconductor-cll_1.38.0_src_all.tar.gz"], "md5": "6c0918e73bb883e4ed4ed2127d1b85d1", "fn": "CLL_1.38.0.tar.gz"}, "rcellminerdata-2.20.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/rcellminerData_2.20.0.tar.gz", "https://bioarchive.galaxyproject.org/rcellminerData_2.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rcellminerdata/bioconductor-rcellminerdata_2.20.0_src_all.tar.gz"], "md5": "631229ce32f7135d171858051326f585", "fn": "rcellminerData_2.20.0.tar.gz"}, "prostatecancertaylor-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerTaylor_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerTaylor_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancertaylor/bioconductor-prostatecancertaylor_1.26.0_src_all.tar.gz"], "md5": "dcdc31e127be410f341977446705400a", "fn": "prostateCancerTaylor_1.26.0.tar.gz"}, "iyer517-1.40.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Iyer517_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/Iyer517_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-iyer517/bioconductor-iyer517_1.40.0_src_all.tar.gz"], "md5": "6ecddbc0bdf2af4e67dd8797717bdd85", "fn": "Iyer517_1.40.0.tar.gz"}, "affycompdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/affycompData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/affycompData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affycompdata/bioconductor-affycompdata_1.36.0_src_all.tar.gz"], "md5": "212b33c1fff0a98e1a661c1047878414", "fn": "affycompData_1.36.0.tar.gz"}, "breastcancervdx-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breastCancerVDX_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerVDX_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancervdx/bioconductor-breastcancervdx_1.36.0_src_all.tar.gz"], "md5": "10700a3df43cfd233db74763f032b1c4", "fn": "breastCancerVDX_1.36.0.tar.gz"}, "yeastcc-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/yeastCC_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastCC_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastcc/bioconductor-yeastcc_1.38.0_src_all.tar.gz"], "md5": "5037b9364754099a0dc6889ac2ef4a71", "fn": "yeastCC_1.38.0.tar.gz"}, "tcgacrcmrna-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TCGAcrcmRNA_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAcrcmRNA_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmrna/bioconductor-tcgacrcmrna_1.18.0_src_all.tar.gz"], "md5": "593226dac7e784f82515e5bb9b97abc4", "fn": "TCGAcrcmRNA_1.18.0.tar.gz"}, "dlbcl-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DLBCL_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/DLBCL_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dlbcl/bioconductor-dlbcl_1.38.0_src_all.tar.gz"], "md5": "e305d0cd25dedefdceb6a93030d5ac1b", "fn": "DLBCL_1.38.0.tar.gz"}, "fletcher2013a-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Fletcher2013a_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/Fletcher2013a_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fletcher2013a/bioconductor-fletcher2013a_1.34.0_src_all.tar.gz"], "md5": "01222416b0fa4fc2cc4900e0470a55e7", "fn": "Fletcher2013a_1.34.0.tar.gz"}, "hapmapsnp6-1.40.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hapmapsnp6_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmapsnp6_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp6/bioconductor-hapmapsnp6_1.40.0_src_all.tar.gz"], "md5": "9027b12aaeecaad3af7cb2481ab743aa", "fn": "hapmapsnp6_1.40.0.tar.gz"}, "curatedovariandata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedOvarianData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedOvarianData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedovariandata/bioconductor-curatedovariandata_1.36.0_src_all.tar.gz"], "md5": "c652f6015514846aba9f70ab668dde4e", "fn": "curatedOvarianData_1.36.0.tar.gz"}, "fabiadata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/fabiaData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/fabiaData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fabiadata/bioconductor-fabiadata_1.36.0_src_all.tar.gz"], "md5": "063160c25a97654ba5788619287688f3", "fn": "fabiaData_1.36.0.tar.gz"}, "keggandmetacoredzpathwaysgeo-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/KEGGandMetacoreDzPathwaysGEO_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/KEGGandMetacoreDzPathwaysGEO_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-keggandmetacoredzpathwaysgeo/bioconductor-keggandmetacoredzpathwaysgeo_1.18.0_src_all.tar.gz"], "md5": "f8216537fcfc6a5325bd19a0f0565683", "fn": "KEGGandMetacoreDzPathwaysGEO_1.18.0.tar.gz"}, "lungexpression-0.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/lungExpression_0.36.0.tar.gz", "https://bioarchive.galaxyproject.org/lungExpression_0.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungexpression/bioconductor-lungexpression_0.36.0_src_all.tar.gz"], "md5": "f29b02561dd243247057c3e08e72bd61", "fn": "lungExpression_0.36.0.tar.gz"}, "curatedbladderdata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedBladderData_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedBladderData_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedbladderdata/bioconductor-curatedbladderdata_1.34.0_src_all.tar.gz"], "md5": "9134e331ab9ae88367f7d00c1fb9197e", "fn": "curatedBladderData_1.34.0.tar.gz"}, "gsbenchmark-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSBenchMark_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/GSBenchMark_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gsbenchmark/bioconductor-gsbenchmark_1.18.0_src_all.tar.gz"], "md5": "19d53c30ea84ba516c229aabbd017cf8", "fn": "GSBenchMark_1.18.0.tar.gz"}, "breastcancerunt-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breastCancerUNT_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerUNT_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancerunt/bioconductor-breastcancerunt_1.36.0_src_all.tar.gz"], "md5": "f826792fb58b77b54d354dfb1b65e8b6", "fn": "breastCancerUNT_1.36.0.tar.gz"}, "all-1.40.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ALL_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/ALL_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-all/bioconductor-all_1.40.0_src_all.tar.gz"], "md5": "be645648c96684d12d2b4c98414ea9f4", "fn": "ALL_1.40.0.tar.gz"}, "prostatecancercamcap-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerCamcap_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerCamcap_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancercamcap/bioconductor-prostatecancercamcap_1.26.0_src_all.tar.gz"], "md5": "d013ac0e533925df356a4f787adad19d", "fn": "prostateCancerCamcap_1.26.0.tar.gz"}, "cancerdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/cancerdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/cancerdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cancerdata/bioconductor-cancerdata_1.36.0_src_all.tar.gz"], "md5": "b36e604efdfb085c1224186d7613ab23", "fn": "cancerdata_1.36.0.tar.gz"}, "curatedbreastdata-2.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedBreastData_2.26.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedBreastData_2.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedbreastdata/bioconductor-curatedbreastdata_2.26.0_src_all.tar.gz"], "md5": "b6da1604aabe30fc9967e6c1f4fbb70c", "fn": "curatedBreastData_2.26.0.tar.gz"}, "kidpack-1.40.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/kidpack_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/kidpack_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-kidpack/bioconductor-kidpack_1.40.0_src_all.tar.gz"], "md5": "1daaab1926c04577373fd35c82a9fc3d", "fn": "kidpack_1.40.0.tar.gz"}, "antiprofilesdata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/antiProfilesData_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/antiProfilesData_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-antiprofilesdata/bioconductor-antiprofilesdata_1.34.0_src_all.tar.gz"], "md5": "85ea52e2db6bedb5435591ef6767688f", "fn": "antiProfilesData_1.34.0.tar.gz"}, "mircompdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/miRcompData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/miRcompData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mircompdata/bioconductor-mircompdata_1.28.0_src_all.tar.gz"], "md5": "709f0e5b4554054e0fd62ddf12dd36c8", "fn": "miRcompData_1.28.0.tar.gz"}, "keggdzpathwaysgeo-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/KEGGdzPathwaysGEO_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/KEGGdzPathwaysGEO_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-keggdzpathwaysgeo/bioconductor-keggdzpathwaysgeo_1.36.0_src_all.tar.gz"], "md5": "6e2cd9431413ef100802fd01510c37b1", "fn": "KEGGdzPathwaysGEO_1.36.0.tar.gz"}, "optimalflowdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/optimalFlowData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/optimalFlowData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-optimalflowdata/bioconductor-optimalflowdata_1.10.0_src_all.tar.gz"], "md5": "77b8d80f1869cb76d2a8a1e67dcad833", "fn": "optimalFlowData_1.10.0.tar.gz"}, "healthyflowdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/healthyFlowData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/healthyFlowData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-healthyflowdata/bioconductor-healthyflowdata_1.36.0_src_all.tar.gz"], "md5": "ec9097c2d66f5350c9a9b1a00c1a43bb", "fn": "healthyFlowData_1.36.0.tar.gz"}, "ruvnormalizedata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RUVnormalizeData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/RUVnormalizeData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ruvnormalizedata/bioconductor-ruvnormalizedata_1.18.0_src_all.tar.gz"], "md5": "e61afc462760972da9575dae8bd5e4b3", "fn": "RUVnormalizeData_1.18.0.tar.gz"}, "allmll-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ALLMLL_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ALLMLL_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-allmll/bioconductor-allmll_1.38.0_src_all.tar.gz"], "md5": "87f063db352317fbf932da06915713ce", "fn": "ALLMLL_1.38.0.tar.gz"}, "prostatecancergrasso-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerGrasso_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerGrasso_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancergrasso/bioconductor-prostatecancergrasso_1.26.0_src_all.tar.gz"], "md5": "74d9204eca94b1372cafce7257693fa0", "fn": "prostateCancerGrasso_1.26.0.tar.gz"}, "bladderbatch-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bladderbatch_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/bladderbatch_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bladderbatch/bioconductor-bladderbatch_1.36.0_src_all.tar.gz"], "md5": "c2ac3760859c2440c12b946bd56efd57", "fn": "bladderbatch_1.36.0.tar.gz"}, "hgu133plus2cellscore-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/hgu133plus2CellScore_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2CellScore_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2cellscore/bioconductor-hgu133plus2cellscore_1.18.0_src_all.tar.gz"], "md5": "e3a02cfbd1737fbc1e5b16d1d9d80a0c", "fn": "hgu133plus2CellScore_1.18.0.tar.gz"}, "tcgacrcmirna-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TCGAcrcmiRNA_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAcrcmiRNA_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmirna/bioconductor-tcgacrcmirna_1.18.0_src_all.tar.gz"], "md5": "c3c5b823cbbe0190072c6df6f06cb48c", "fn": "TCGAcrcmiRNA_1.18.0.tar.gz"}, "gwasdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GWASdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/GWASdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gwasdata/bioconductor-gwasdata_1.36.0_src_all.tar.gz"], "md5": "d28dee85eeec53c8956d091cfab9bbe2", "fn": "GWASdata_1.36.0.tar.gz"}, "italicsdata-2.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ITALICSData_2.36.0.tar.gz", "https://bioarchive.galaxyproject.org/ITALICSData_2.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-italicsdata/bioconductor-italicsdata_2.36.0_src_all.tar.gz"], "md5": "b2c8e222e18f28e6864213d45f92d7dd", "fn": "ITALICSData_2.36.0.tar.gz"}, "colonca-1.40.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/colonCA_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/colonCA_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-colonca/bioconductor-colonca_1.40.0_src_all.tar.gz"], "md5": "945aaff5b3d9fd9acf23da95b63e3b8d", "fn": "colonCA_1.40.0.tar.gz"}, "diffloopdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/diffloopdata_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/diffloopdata_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-diffloopdata/bioconductor-diffloopdata_1.26.0_src_all.tar.gz"], "md5": "3fd01ba7a1156002aa91ba8a0e747ecd", "fn": "diffloopdata_1.26.0.tar.gz"}, "dapardata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DAPARdata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/DAPARdata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dapardata/bioconductor-dapardata_1.28.0_src_all.tar.gz"], "md5": "fd105b01cb3fa99df2fddfa77bcad220", "fn": "DAPARdata_1.28.0.tar.gz"}, "prolocdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pRolocdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/pRolocdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prolocdata/bioconductor-prolocdata_1.36.0_src_all.tar.gz"], "md5": "6ca8bc71627048afb1d53821ed862128", "fn": "pRolocdata_1.36.0.tar.gz"}, "prostatecancerstockholm-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/prostateCancerStockholm_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerStockholm_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancerstockholm/bioconductor-prostatecancerstockholm_1.26.0_src_all.tar.gz"], "md5": "b54919a22b169df14275783c9b3775dc", "fn": "prostateCancerStockholm_1.26.0.tar.gz"}, "gaschyhs-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/gaschYHS_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/gaschYHS_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gaschyhs/bioconductor-gaschyhs_1.36.0_src_all.tar.gz"], "md5": "2907cf19d0cde8e8a7ee78b6de7c918b", "fn": "gaschYHS_1.36.0.tar.gz"}, "dorothea-1.10.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/dorothea_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/dorothea_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dorothea/bioconductor-dorothea_1.10.0_src_all.tar.gz"], "md5": "4afa62297950e5c0c896e46b1a8bfc0c", "fn": "dorothea_1.10.0.tar.gz"}, "tbx20bamsubset-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TBX20BamSubset_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/TBX20BamSubset_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tbx20bamsubset/bioconductor-tbx20bamsubset_1.34.0_src_all.tar.gz"], "md5": "beec14bdc62fd30f6831f33995a07a0f", "fn": "TBX20BamSubset_1.34.0.tar.gz"}, "champdata-2.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ChAMPdata_2.30.0.tar.gz", "https://bioarchive.galaxyproject.org/ChAMPdata_2.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-champdata/bioconductor-champdata_2.30.0_src_all.tar.gz"], "md5": "6f08e2b95484bd4053d4041f9538a3c3", "fn": "ChAMPdata_2.30.0.tar.gz"}, "rnbeads.rn5-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.rn5_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.rn5_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.rn5/bioconductor-rnbeads.rn5_1.30.0_src_all.tar.gz"], "md5": "10e73b8362f2f61efd36f469c0b96307", "fn": "RnBeads.rn5_1.30.0.tar.gz"}, "rnbeads.hg38-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.hg38_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.hg38_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg38/bioconductor-rnbeads.hg38_1.30.0_src_all.tar.gz"], "md5": "fa0b5109400fe09174ae2ee83d7ffef5", "fn": "RnBeads.hg38_1.30.0.tar.gz"}, "elmer.data-2.22.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ELMER.data_2.22.0.tar.gz", "https://bioarchive.galaxyproject.org/ELMER.data_2.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-elmer.data/bioconductor-elmer.data_2.22.0_src_all.tar.gz"], "md5": "ee1a00414e8c68d3bae34732f7fb35d7", "fn": "ELMER.data_2.22.0.tar.gz"}, "cnvgsadata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/cnvGSAdata_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/cnvGSAdata_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cnvgsadata/bioconductor-cnvgsadata_1.34.0_src_all.tar.gz"], "md5": "191d2a67eeeb2ded97f7fb93c1bfebb3", "fn": "cnvGSAdata_1.34.0.tar.gz"}, "rnbeads.mm9-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.mm9_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.mm9_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm9/bioconductor-rnbeads.mm9_1.30.0_src_all.tar.gz"], "md5": "5700a0b7acd3dbb0cf1412209efd0748", "fn": "RnBeads.mm9_1.30.0.tar.gz"}, "wgsmapp-1.10.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/WGSmapp_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/WGSmapp_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wgsmapp/bioconductor-wgsmapp_1.10.0_src_all.tar.gz"], "md5": "ca0e7c51fcea48bd610fe7da33356358", "fn": "WGSmapp_1.10.0.tar.gz"}, "chic.data-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ChIC.data_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIC.data_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chic.data/bioconductor-chic.data_1.18.0_src_all.tar.gz"], "md5": "035e4ff664badd19dd6bdf7e3b06a7ee", "fn": "ChIC.data_1.18.0.tar.gz"}, "rrdpdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/rRDPData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rRDPData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rrdpdata/bioconductor-rrdpdata_1.18.0_src_all.tar.gz"], "md5": "8aee1a2c5cf2f30553b3365034464991", "fn": "rRDPData_1.18.0.tar.gz"}, "micrornaome-1.20.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/microRNAome_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/microRNAome_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-micrornaome/bioconductor-micrornaome_1.20.0_src_all.tar.gz"], "md5": "bee29d4d77292ca4e696e9eca2ad8b71", "fn": "microRNAome_1.20.0.tar.gz"}, "brgedata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/brgedata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/brgedata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-brgedata/bioconductor-brgedata_1.20.0_src_all.tar.gz"], "md5": "8469d2963cd1052846deafd0ef88d563", "fn": "brgedata_1.20.0.tar.gz"}, "tcgaworkflowdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TCGAWorkflowData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAWorkflowData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgaworkflowdata/bioconductor-tcgaworkflowdata_1.22.0_src_all.tar.gz"], "md5": "b1e8bedba993bd452a501024e45a781c", "fn": "TCGAWorkflowData_1.22.0.tar.gz"}, "gse13015-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSE13015_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE13015_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse13015/bioconductor-gse13015_1.6.0_src_all.tar.gz"], "md5": "5e2ac694eb8b344f8dbdc97813634da9", "fn": "GSE13015_1.6.0.tar.gz"}, "bioplex-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BioPlex_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/BioPlex_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bioplex/bioconductor-bioplex_1.4.0_src_all.tar.gz"], "md5": "e5d585d15a7f5fad7aee1e383f7bd7f2", "fn": "BioPlex_1.4.0.tar.gz"}, "spqndata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/spqnData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/spqnData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spqndata/bioconductor-spqndata_1.10.0_src_all.tar.gz"], "md5": "4c711fc002eaedfab147d140eeb73a35", "fn": "spqnData_1.10.0.tar.gz"}, "chipxpressdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ChIPXpressData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIPXpressData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipxpressdata/bioconductor-chipxpressdata_1.36.0_src_all.tar.gz"], "md5": "996fa1dfb5d101324b2cf318390624e3", "fn": "ChIPXpressData_1.36.0.tar.gz"}, "fission-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/fission_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/fission_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fission/bioconductor-fission_1.18.0_src_all.tar.gz"], "md5": "713c9407157bb015952a5e93ae60a448", "fn": "fission_1.18.0.tar.gz"}, "airway-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/airway_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/airway_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-airway/bioconductor-airway_1.18.0_src_all.tar.gz"], "md5": "e59c875751a9b5c44735e15b9a608aa6", "fn": "airway_1.18.0.tar.gz"}, "rnbeads.mm10-2.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.mm10_2.6.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.mm10_2.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm10/bioconductor-rnbeads.mm10_2.6.0_src_all.tar.gz"], "md5": "1d4c16df423b733b817129aaf26b27e2", "fn": "RnBeads.mm10_2.6.0.tar.gz"}, "somaticcanceralterations-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SomaticCancerAlterations_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/SomaticCancerAlterations_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-somaticcanceralterations/bioconductor-somaticcanceralterations_1.34.0_src_all.tar.gz"], "md5": "71f9fe3f0f1336444d3fbdfca35a1a07", "fn": "SomaticCancerAlterations_1.34.0.tar.gz"}, "omicspcadata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/OMICsPCAdata_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/OMICsPCAdata_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-omicspcadata/bioconductor-omicspcadata_1.16.0_src_all.tar.gz"], "md5": "878ae360fd0161bc300191971e7d5719", "fn": "OMICsPCAdata_1.16.0.tar.gz"}, "curatedadiporna-1.14.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedAdipoRNA_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoRNA_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadiporna/bioconductor-curatedadiporna_1.14.0_src_all.tar.gz"], "md5": "6c0bba7a02d359a10da87484257b4c7d", "fn": "curatedAdipoRNA_1.14.0.tar.gz"}, "fletcher2013b-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Fletcher2013b_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/Fletcher2013b_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fletcher2013b/bioconductor-fletcher2013b_1.34.0_src_all.tar.gz"], "md5": "74a84a932937b9fcce493feb691027d9", "fn": "Fletcher2013b_1.34.0.tar.gz"}, "timecoursedata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/timecoursedata_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/timecoursedata_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-timecoursedata/bioconductor-timecoursedata_1.8.0_src_all.tar.gz"], "md5": "3fd49ff1e819a2b749570221ea53be2c", "fn": "timecoursedata_1.8.0.tar.gz"}, "parathyroidse-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/parathyroidSE_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/parathyroidSE_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-parathyroidse/bioconductor-parathyroidse_1.36.0_src_all.tar.gz"], "md5": "233d66f21aebbc76d7d59cb65611eded", "fn": "parathyroidSE_1.36.0.tar.gz"}, "faahko-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/faahKO_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/faahKO_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-faahko/bioconductor-faahko_1.38.0_src_all.tar.gz"], "md5": "284437fc4e501ec253af2c22ed3d78fd", "fn": "faahKO_1.38.0.tar.gz"}, "rnbeads.hg19-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnBeads.hg19_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.hg19_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg19/bioconductor-rnbeads.hg19_1.30.0_src_all.tar.gz"], "md5": "b99797bffecd852e17ec1222edafd119", "fn": "RnBeads.hg19_1.30.0.tar.gz"}, "easierdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/easierData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/easierData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-easierdata/bioconductor-easierdata_1.4.0_src_all.tar.gz"], "md5": "639d40a2ce48bb59f6cdfd216a1416c5", "fn": "easierData_1.4.0.tar.gz"}, "sampleclassifierdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/sampleClassifierData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/sampleClassifierData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sampleclassifierdata/bioconductor-sampleclassifierdata_1.22.0_src_all.tar.gz"], "md5": "72ef1fbd73285e12de97276a88da7054", "fn": "sampleClassifierData_1.22.0.tar.gz"}, "pepdat-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pepDat_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/pepDat_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pepdat/bioconductor-pepdat_1.18.0_src_all.tar.gz"], "md5": "06ee7d37dc24921207eb8875436e43b9", "fn": "pepDat_1.18.0.tar.gz"}, "plasfia-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/plasFIA_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/plasFIA_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-plasfia/bioconductor-plasfia_1.26.0_src_all.tar.gz"], "md5": "91d91048fbe49907f5f7f246dae14f76", "fn": "plasFIA_1.26.0.tar.gz"}, "pth2o2lipids-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PtH2O2lipids_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/PtH2O2lipids_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pth2o2lipids/bioconductor-pth2o2lipids_1.24.0_src_all.tar.gz"], "md5": "1954409b3f9a4bf1251d9dd2bc93ca10", "fn": "PtH2O2lipids_1.24.0.tar.gz"}, "tmexplorer-1.8.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TMExplorer_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/TMExplorer_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tmexplorer/bioconductor-tmexplorer_1.8.0_src_all.tar.gz"], "md5": "5783b4ef82629743d898b1ff4c979c7d", "fn": "TMExplorer_1.8.0.tar.gz"}, "cohcapanno-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/COHCAPanno_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/COHCAPanno_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cohcapanno/bioconductor-cohcapanno_1.34.0_src_all.tar.gz"], "md5": "649c6a3c7a5727bfeae51aa75ad77f41", "fn": "COHCAPanno_1.34.0.tar.gz"}, "seqcna.annot-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/seqCNA.annot_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/seqCNA.annot_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seqcna.annot/bioconductor-seqcna.annot_1.34.0_src_all.tar.gz"], "md5": "6e54a0ade57c4581d5114fedf8dd3396", "fn": "seqCNA.annot_1.34.0.tar.gz"}, "scatac.explorer-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/scATAC.Explorer_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/scATAC.Explorer_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scatac.explorer/bioconductor-scatac.explorer_1.4.0_src_all.tar.gz"], "md5": "5348b5d62c7488c3049f412bfbb50d77", "fn": "scATAC.Explorer_1.4.0.tar.gz"}, "qplexdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/qPLEXdata_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/qPLEXdata_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qplexdata/bioconductor-qplexdata_1.16.0_src_all.tar.gz"], "md5": "92a7193ff160f6dee4c782f2bb81ca28", "fn": "qPLEXdata_1.16.0.tar.gz"}, "topdownrdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/topdownrdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/topdownrdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-topdownrdata/bioconductor-topdownrdata_1.20.0_src_all.tar.gz"], "md5": "9eddeb9f975a402ecae76e095fafd8da", "fn": "topdownrdata_1.20.0.tar.gz"}, "systempiperdata-2.2.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/systemPipeRdata_2.2.0.tar.gz", "https://bioarchive.galaxyproject.org/systemPipeRdata_2.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-systempiperdata/bioconductor-systempiperdata_2.2.0_src_all.tar.gz"], "md5": "340237544f57849ccb438a3fd5364a44", "fn": "systemPipeRdata_2.2.0.tar.gz"}, "curatedtcgadata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedTCGAData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedTCGAData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedtcgadata/bioconductor-curatedtcgadata_1.20.0_src_all.tar.gz"], "md5": "636d48084b1ee6f77cd1711813ae0dd5", "fn": "curatedTCGAData_1.20.0.tar.gz"}, "scanmirdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/scanMiRData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/scanMiRData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scanmirdata/bioconductor-scanmirdata_1.4.0_src_all.tar.gz"], "md5": "d7db4456d1805894b1de51215348486a", "fn": "scanMiRData_1.4.0.tar.gz"}, "qdnaseq.mm10-1.28.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/QDNAseq.mm10_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/QDNAseq.mm10_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.mm10/bioconductor-qdnaseq.mm10_1.28.0_src_all.tar.gz"], "md5": "1b0602ec8a5b3288a467873f2c1ac7a4", "fn": "QDNAseq.mm10_1.28.0.tar.gz"}, "qdnaseq.hg19-1.28.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/QDNAseq.hg19_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/QDNAseq.hg19_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.hg19/bioconductor-qdnaseq.hg19_1.28.0_src_all.tar.gz"], "md5": "df5304204233e1516330f9a664c0104c", "fn": "QDNAseq.hg19_1.28.0.tar.gz"}, "tinesath1cdf-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tinesath1cdf_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/tinesath1cdf_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tinesath1cdf/bioconductor-tinesath1cdf_1.36.0_src_all.tar.gz"], "md5": "a8d2c187507c669f46b8be19d678eb67", "fn": "tinesath1cdf_1.36.0.tar.gz"}, "breakpointrdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/breakpointRdata_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/breakpointRdata_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breakpointrdata/bioconductor-breakpointrdata_1.16.0_src_all.tar.gz"], "md5": "137555d6fa04dffd1eebf87e036b4af7", "fn": "breakpointRdata_1.16.0.tar.gz"}, "gcspikelite-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/gcspikelite_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/gcspikelite_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gcspikelite/bioconductor-gcspikelite_1.36.0_src_all.tar.gz"], "md5": "0de3fbbe9db74d87ded035be2d1f8228", "fn": "gcspikelite_1.36.0.tar.gz"}, "jaspar2014-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/JASPAR2014_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2014_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2014/bioconductor-jaspar2014_1.34.0_src_all.tar.gz"], "md5": "5f7f767133d76a93a61eb2912489ae3a", "fn": "JASPAR2014_1.34.0.tar.gz"}, "h5vcdata-2.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/h5vcData_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/h5vcData_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-h5vcdata/bioconductor-h5vcdata_2.18.0_src_all.tar.gz"], "md5": "75b05adbd56ac87bf65201a9884970bc", "fn": "h5vcData_2.18.0.tar.gz"}, "beadarrayusecases-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BeadArrayUseCases_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/BeadArrayUseCases_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadarrayusecases/bioconductor-beadarrayusecases_1.36.0_src_all.tar.gz"], "md5": "ac177e655ff3ae365bf609e87a89bfbf", "fn": "BeadArrayUseCases_1.36.0.tar.gz"}, "beadarrayexampledata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/beadarrayExampleData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/beadarrayExampleData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadarrayexampledata/bioconductor-beadarrayexampledata_1.36.0_src_all.tar.gz"], "md5": "916245ad90b7aeabbd906130a568f7e3", "fn": "beadarrayExampleData_1.36.0.tar.gz"}, "tinesath1probe-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tinesath1probe_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/tinesath1probe_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tinesath1probe/bioconductor-tinesath1probe_1.36.0_src_all.tar.gz"], "md5": "3960a52d4e105837ab0d1347f5e7f336", "fn": "tinesath1probe_1.36.0.tar.gz"}, "chromstardata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/chromstaRData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/chromstaRData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chromstardata/bioconductor-chromstardata_1.24.0_src_all.tar.gz"], "md5": "218e270508f4c9eba2b4d7aa86131bcd", "fn": "chromstaRData_1.24.0.tar.gz"}, "mmappr2data-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MMAPPR2data_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/MMAPPR2data_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mmappr2data/bioconductor-mmappr2data_1.12.0_src_all.tar.gz"], "md5": "ad6b9b86c75df44c183e780fa7595ed3", "fn": "MMAPPR2data_1.12.0.tar.gz"}, "lungcancerlines-0.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/LungCancerLines_0.36.0.tar.gz", "https://bioarchive.galaxyproject.org/LungCancerLines_0.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungcancerlines/bioconductor-lungcancerlines_0.36.0_src_all.tar.gz"], "md5": "554cc1a603908ab361042250e6ae3868", "fn": "LungCancerLines_0.36.0.tar.gz"}, "chipenrich.data-2.22.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/chipenrich.data_2.22.0.tar.gz", "https://bioarchive.galaxyproject.org/chipenrich.data_2.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipenrich.data/bioconductor-chipenrich.data_2.22.0_src_all.tar.gz"], "md5": "b91128ffbc4be5a65c2caaf4f19882b1", "fn": "chipenrich.data_2.22.0.tar.gz"}, "synapterdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/synapterdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/synapterdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-synapterdata/bioconductor-synapterdata_1.36.0_src_all.tar.gz"], "md5": "969a10ed0c07a03fe46c38cc2c956fc2", "fn": "synapterdata_1.36.0.tar.gz"}, "microbiomebenchmarkdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MicrobiomeBenchmarkData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/MicrobiomeBenchmarkData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-microbiomebenchmarkdata/bioconductor-microbiomebenchmarkdata_1.0.0_src_all.tar.gz"], "md5": "bc455e7cd9f3cb056814f2a753f65b94", "fn": "MicrobiomeBenchmarkData_1.0.0.tar.gz"}, "aneufinderdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/AneuFinderData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/AneuFinderData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-aneufinderdata/bioconductor-aneufinderdata_1.26.0_src_all.tar.gz"], "md5": "65b87d69f2a2ccbb5457fd0a27b09822", "fn": "AneuFinderData_1.26.0.tar.gz"}, "assessorfdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/AssessORFData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/AssessORFData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-assessorfdata/bioconductor-assessorfdata_1.16.0_src_all.tar.gz"], "md5": "a199c70bca649017ca435f4d36258fdf", "fn": "AssessORFData_1.16.0.tar.gz"}, "ccdata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ccdata_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/ccdata_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ccdata/bioconductor-ccdata_1.24.0_src_all.tar.gz"], "md5": "e57244249f51a54162f5348ba0efe9e0", "fn": "ccdata_1.24.0.tar.gz"}, "pwmenrich.mmusculus.background-4.32.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PWMEnrich.Mmusculus.background_4.32.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Mmusculus.background_4.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.mmusculus.background/bioconductor-pwmenrich.mmusculus.background_4.32.0_src_all.tar.gz"], "md5": "1d6ac0083eb2378cabf63fc538dfe21f", "fn": "PWMEnrich.Mmusculus.background_4.32.0.tar.gz"}, "pwmenrich.dmelanogaster.background-4.32.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PWMEnrich.Dmelanogaster.background_4.32.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Dmelanogaster.background_4.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.dmelanogaster.background/bioconductor-pwmenrich.dmelanogaster.background_4.32.0_src_all.tar.gz"], "md5": "9935dc953969ff87c508415da52da35d", "fn": "PWMEnrich.Dmelanogaster.background_4.32.0.tar.gz"}, "pwmenrich.hsapiens.background-4.32.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PWMEnrich.Hsapiens.background_4.32.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Hsapiens.background_4.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.hsapiens.background/bioconductor-pwmenrich.hsapiens.background_4.32.0_src_all.tar.gz"], "md5": "23c1d431adf2add64dd129e917fbc5d5", "fn": "PWMEnrich.Hsapiens.background_4.32.0.tar.gz"}, "harbchip-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/harbChIP_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/harbChIP_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harbchip/bioconductor-harbchip_1.36.0_src_all.tar.gz"], "md5": "31cfe29898d79222e934f537337ecf76", "fn": "harbChIP_1.36.0.tar.gz"}, "sbgnview.data-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SBGNview.data_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/SBGNview.data_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sbgnview.data/bioconductor-sbgnview.data_1.12.0_src_all.tar.gz"], "md5": "226d4bdd8b8a2997daefbab058f6f092", "fn": "SBGNview.data_1.12.0.tar.gz"}, "ecolileucine-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ecoliLeucine_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliLeucine_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolileucine/bioconductor-ecolileucine_1.38.0_src_all.tar.gz"], "md5": "6e4b82b2dacef5cd368225d1c107d284", "fn": "ecoliLeucine_1.38.0.tar.gz"}, "seq2pathway.data-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/seq2pathway.data_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/seq2pathway.data_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seq2pathway.data/bioconductor-seq2pathway.data_1.30.0_src_all.tar.gz"], "md5": "ba746fb92617526bc8a994e098f66a7a", "fn": "seq2pathway.data_1.30.0.tar.gz"}, "humanstemcell-0.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/humanStemCell_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/humanStemCell_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanstemcell/bioconductor-humanstemcell_0.38.0_src_all.tar.gz"], "md5": "a2d31e0d51d4a7ddcd83a9e082600e88", "fn": "humanStemCell_0.38.0.tar.gz"}, "rgmqllib-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RGMQLlib_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/RGMQLlib_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgmqllib/bioconductor-rgmqllib_1.18.0_src_all.tar.gz"], "md5": "35bbaa5548539a87d12762b8c1c09787", "fn": "RGMQLlib_1.18.0.tar.gz"}, "leebamviews-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/leeBamViews_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/leeBamViews_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-leebamviews/bioconductor-leebamviews_1.34.0_src_all.tar.gz"], "md5": "fc82a41bfe18f54301c3cc187a565791", "fn": "leeBamViews_1.34.0.tar.gz"}, "pd.atdschip.tiling-0.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pd.atdschip.tiling_0.36.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.atdschip.tiling_0.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.atdschip.tiling/bioconductor-pd.atdschip.tiling_0.36.0_src_all.tar.gz"], "md5": "33888a53bc08d7e87849b19e19666470", "fn": "pd.atdschip.tiling_0.36.0.tar.gz"}, "bsseqdata-0.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bsseqData_0.36.0.tar.gz", "https://bioarchive.galaxyproject.org/bsseqData_0.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsseqdata/bioconductor-bsseqdata_0.36.0_src_all.tar.gz"], "md5": "7a286e716d70a12e296366fa8b07e20a", "fn": "bsseqData_0.36.0.tar.gz"}, "genelendatabase-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/geneLenDataBase_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/geneLenDataBase_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genelendatabase/bioconductor-genelendatabase_1.34.0_src_all.tar.gz"], "md5": "120f51fec9f71e6235cf2ef93b3a72d0", "fn": "geneLenDataBase_1.34.0.tar.gz"}, "tartare-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tartare_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/tartare_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tartare/bioconductor-tartare_1.12.0_src_all.tar.gz"], "md5": "ec5808dde140133fd510bd6831db8a2c", "fn": "tartare_1.12.0.tar.gz"}, "metagxpancreas-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MetaGxPancreas_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxPancreas_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxpancreas/bioconductor-metagxpancreas_1.18.0_src_all.tar.gz"], "md5": "0bacc282e7bf79ae23f5ba32ecab3363", "fn": "MetaGxPancreas_1.18.0.tar.gz"}, "spatiallibd-1.10.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/spatialLIBD_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/spatialLIBD_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatiallibd/bioconductor-spatiallibd_1.10.0_src_all.tar.gz"], "md5": "f827024e685180a16db92e610ee0d363", "fn": "spatialLIBD_1.10.0.tar.gz"}, "obmiti-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ObMiTi_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/ObMiTi_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-obmiti/bioconductor-obmiti_1.6.0_src_all.tar.gz"], "md5": "5a4f4fe10d1de1c94b48fffa16628a1b", "fn": "ObMiTi_1.6.0.tar.gz"}, "benchmarkfdrdata2019-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/benchmarkfdrData2019_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/benchmarkfdrData2019_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-benchmarkfdrdata2019/bioconductor-benchmarkfdrdata2019_1.12.0_src_all.tar.gz"], "md5": "5ffdc59009556304b8400fe84b874502", "fn": "benchmarkfdrData2019_1.12.0.tar.gz"}, "depmap-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/depmap_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/depmap_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-depmap/bioconductor-depmap_1.12.0_src_all.tar.gz"], "md5": "24fcff71d7af3a08bf179f7c7d016024", "fn": "depmap_1.12.0.tar.gz"}, "hcadata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HCAData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/HCAData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcadata/bioconductor-hcadata_1.14.0_src_all.tar.gz"], "md5": "24545ef0089951b6b0e5676efac72769", "fn": "HCAData_1.14.0.tar.gz"}, "sesamedata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/sesameData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/sesameData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sesamedata/bioconductor-sesamedata_1.16.0_src_all.tar.gz"], "md5": "b9bac97226943d8d82d17bc1553906c0", "fn": "sesameData_1.16.0.tar.gz"}, "singlecellmultimodal-1.10.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SingleCellMultiModal_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/SingleCellMultiModal_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-singlecellmultimodal/bioconductor-singlecellmultimodal_1.10.0_src_all.tar.gz"], "md5": "899a93365e9bc4521ccb71e5d45cccf3", "fn": "SingleCellMultiModal_1.10.0.tar.gz"}, "weberdivechalcdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/WeberDivechaLCdata_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/WeberDivechaLCdata_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-weberdivechalcdata/bioconductor-weberdivechalcdata_1.0.0_src_all.tar.gz"], "md5": "7a07e9403d7fb8383eb515027adead4e", "fn": "WeberDivechaLCdata_1.0.0.tar.gz"}, "tenxpbmcdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TENxPBMCData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxPBMCData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxpbmcdata/bioconductor-tenxpbmcdata_1.16.0_src_all.tar.gz"], "md5": "bba27db0cbddf5e1f58af0dc5feeb620", "fn": "TENxPBMCData_1.16.0.tar.gz"}, "epimix.data-1.0.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/EpiMix.data_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/EpiMix.data_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epimix.data/bioconductor-epimix.data_1.0.0_src_all.tar.gz"], "md5": "60ad87849d55d75238373a37ce14b4c8", "fn": "EpiMix.data_1.0.0.tar.gz"}, "rlhub-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RLHub_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/RLHub_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rlhub/bioconductor-rlhub_1.4.0_src_all.tar.gz"], "md5": "27339bc3533469566a34d579b616c015", "fn": "RLHub_1.4.0.tar.gz"}, "clustifyrdatahub-1.8.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/clustifyrdatahub_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/clustifyrdatahub_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clustifyrdatahub/bioconductor-clustifyrdatahub_1.8.0_src_all.tar.gz"], "md5": "9aa7df7c9f7fe8af844e4107f99e33ba", "fn": "clustifyrdatahub_1.8.0.tar.gz"}, "metagxbreast-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MetaGxBreast_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxBreast_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxbreast/bioconductor-metagxbreast_1.18.0_src_all.tar.gz"], "md5": "6fabfc375d149b23ee17fdaa339af511", "fn": "MetaGxBreast_1.18.0.tar.gz"}, "stexampledata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/STexampleData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/STexampleData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stexampledata/bioconductor-stexampledata_1.6.0_src_all.tar.gz"], "md5": "ff9053a3878f326298e4eefb76bdc44f", "fn": "STexampleData_1.6.0.tar.gz"}, "xcoredata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/xcoredata_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/xcoredata_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xcoredata/bioconductor-xcoredata_1.2.0_src_all.tar.gz"], "md5": "39bcc78922bb568d8156fda441537da7", "fn": "xcoredata_1.2.0.tar.gz"}, "curatedadipochip-1.14.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedAdipoChIP_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoChIP_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadipochip/bioconductor-curatedadipochip_1.14.0_src_all.tar.gz"], "md5": "125847ddd3e81270c50e0671e8fd4486", "fn": "curatedAdipoChIP_1.14.0.tar.gz"}, "nxtirfdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NxtIRFdata_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/NxtIRFdata_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nxtirfdata/bioconductor-nxtirfdata_1.4.0_src_all.tar.gz"], "md5": "d56460a1a65820925d274a7823c41abc", "fn": "NxtIRFdata_1.4.0.tar.gz"}, "chipseqdbdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/chipseqDBData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/chipseqDBData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipseqdbdata/bioconductor-chipseqdbdata_1.14.0_src_all.tar.gz"], "md5": "f28cb4de67134b4e80eb66b89fe7a44f", "fn": "chipseqDBData_1.14.0.tar.gz"}, "cllmethylation-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CLLmethylation_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/CLLmethylation_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cllmethylation/bioconductor-cllmethylation_1.18.0_src_all.tar.gz"], "md5": "cae7673674386c34c755bb17c3162ba4", "fn": "CLLmethylation_1.18.0.tar.gz"}, "tabulamurissenisdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TabulaMurisSenisData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/TabulaMurisSenisData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tabulamurissenisdata/bioconductor-tabulamurissenisdata_1.4.0_src_all.tar.gz"], "md5": "41978233013567a8d648353435087d1c", "fn": "TabulaMurisSenisData_1.4.0.tar.gz"}, "bodymaprat-1.14.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/bodymapRat_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/bodymapRat_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bodymaprat/bioconductor-bodymaprat_1.14.0_src_all.tar.gz"], "md5": "f162978264a598bc463fed6a7611f4b0", "fn": "bodymapRat_1.14.0.tar.gz"}, "tenxbusdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TENxBUSData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxBUSData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxbusdata/bioconductor-tenxbusdata_1.12.0_src_all.tar.gz"], "md5": "8c7b4e3fe4c5f01ef71474d68d5b838b", "fn": "TENxBUSData_1.12.0.tar.gz"}, "hicontactsdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HiContactsData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/HiContactsData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicontactsdata/bioconductor-hicontactsdata_1.0.0_src_all.tar.gz"], "md5": "b146c39234a88d86183b4ea618cec5a2", "fn": "HiContactsData_1.0.0.tar.gz"}, "hdcytodata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HDCytoData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/HDCytoData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hdcytodata/bioconductor-hdcytodata_1.18.0_src_all.tar.gz"], "md5": "5f84f520dc1b7e6a684191812fcda70d", "fn": "HDCytoData_1.18.0.tar.gz"}, "metagxovarian-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MetaGxOvarian_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxOvarian_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxovarian/bioconductor-metagxovarian_1.18.0_src_all.tar.gz"], "md5": "a3cb093003dc2fd2f26773ae40d8d042", "fn": "MetaGxOvarian_1.18.0.tar.gz"}, "tenxvisiumdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TENxVisiumData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxVisiumData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxvisiumdata/bioconductor-tenxvisiumdata_1.6.0_src_all.tar.gz"], "md5": "b5b1e60d7f71343347cb9eadbe03a2c7", "fn": "TENxVisiumData_1.6.0.tar.gz"}, "methylseqdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MethylSeqData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/MethylSeqData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylseqdata/bioconductor-methylseqdata_1.8.0_src_all.tar.gz"], "md5": "6da1465b035fb5a4bf9512ae63b8b010", "fn": "MethylSeqData_1.8.0.tar.gz"}, "duoclustering2018-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DuoClustering2018_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/DuoClustering2018_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-duoclustering2018/bioconductor-duoclustering2018_1.16.0_src_all.tar.gz"], "md5": "f9d216a1ad3bfb201a2e390be6607958", "fn": "DuoClustering2018_1.16.0.tar.gz"}, "vectrapolarisdata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/VectraPolarisData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/VectraPolarisData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vectrapolarisdata/bioconductor-vectrapolarisdata_1.2.0_src_all.tar.gz"], "md5": "bdf56c0103a2d0679d2bdad1458d6e9f", "fn": "VectraPolarisData_1.2.0.tar.gz"}, "muscdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/muscData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/muscData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-muscdata/bioconductor-muscdata_1.12.0_src_all.tar.gz"], "md5": "2797b6ad19757b5ba961c937b7ef81c2", "fn": "muscData_1.12.0.tar.gz"}, "biscuiteerdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/biscuiteerData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/biscuiteerData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biscuiteerdata/bioconductor-biscuiteerdata_1.12.0_src_all.tar.gz"], "md5": "471091bf8b2ea2ed0a5704099cdb917c", "fn": "biscuiteerData_1.12.0.tar.gz"}, "alpinedata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/alpineData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/alpineData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-alpinedata/bioconductor-alpinedata_1.24.0_src_all.tar.gz"], "md5": "9aa0c7d41dfac337b05643d1ecd240ac", "fn": "alpineData_1.24.0.tar.gz"}, "spatialdmelxsim-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/spatialDmelxsim_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/spatialDmelxsim_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatialdmelxsim/bioconductor-spatialdmelxsim_1.4.0_src_all.tar.gz"], "md5": "254b60e8277dd31c29a710df639c6735", "fn": "spatialDmelxsim_1.4.0.tar.gz"}, "microbiomedatasets-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/microbiomeDataSets_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/microbiomeDataSets_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-microbiomedatasets/bioconductor-microbiomedatasets_1.6.0_src_all.tar.gz"], "md5": "c8e86f82bc8021289697c4887cabf453", "fn": "microbiomeDataSets_1.6.0.tar.gz"}, "octad.db-1.0.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/octad.db_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/octad.db_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-octad.db/bioconductor-octad.db_1.0.0_src_all.tar.gz"], "md5": "0fcec8c696d79556a7f2842f9b4558c3", "fn": "octad.db_1.0.0.tar.gz"}, "simbenchdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SimBenchData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/SimBenchData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-simbenchdata/bioconductor-simbenchdata_1.6.0_src_all.tar.gz"], "md5": "e5e51bcdd298437970b25e7dc0a0248c", "fn": "SimBenchData_1.6.0.tar.gz"}, "mcsurvdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mcsurvdata_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/mcsurvdata_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcsurvdata/bioconductor-mcsurvdata_1.16.0_src_all.tar.gz"], "md5": "eca9c8d18ae70e750db5f0a75817c8b8", "fn": "mcsurvdata_1.16.0.tar.gz"}, "tabulamurisdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TabulaMurisData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/TabulaMurisData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tabulamurisdata/bioconductor-tabulamurisdata_1.16.0_src_all.tar.gz"], "md5": "1d058a947e31a9f0f512688fc5509123", "fn": "TabulaMurisData_1.16.0.tar.gz"}, "eatonetalchipseq-0.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/EatonEtAlChIPseq_0.36.0.tar.gz", "https://bioarchive.galaxyproject.org/EatonEtAlChIPseq_0.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-eatonetalchipseq/bioconductor-eatonetalchipseq_0.36.0_src_all.tar.gz"], "md5": "102627bebf2744cc6df1d2327dd5ea2b", "fn": "EatonEtAlChIPseq_0.36.0.tar.gz"}, "nanoporernaseq-1.8.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NanoporeRNASeq_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/NanoporeRNASeq_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nanoporernaseq/bioconductor-nanoporernaseq_1.8.0_src_all.tar.gz"], "md5": "15a5b4b0117895a16185138fb591bba1", "fn": "NanoporeRNASeq_1.8.0.tar.gz"}, "signaturesearchdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/signatureSearchData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/signatureSearchData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-signaturesearchdata/bioconductor-signaturesearchdata_1.12.0_src_all.tar.gz"], "md5": "2dc242150755289df7553bd18155ed2d", "fn": "signatureSearchData_1.12.0.tar.gz"}, "lrcelltypemarkers-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/LRcellTypeMarkers_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/LRcellTypeMarkers_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lrcelltypemarkers/bioconductor-lrcelltypemarkers_1.6.0_src_all.tar.gz"], "md5": "b1082f830487f6aea1ad61ca04439941", "fn": "LRcellTypeMarkers_1.6.0.tar.gz"}, "hd2013sgi-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HD2013SGI_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/HD2013SGI_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hd2013sgi/bioconductor-hd2013sgi_1.38.0_src_all.tar.gz"], "md5": "b830f54da9280d3265cb70439bf5509b", "fn": "HD2013SGI_1.38.0.tar.gz"}, "imcdatasets-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/imcdatasets_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/imcdatasets_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-imcdatasets/bioconductor-imcdatasets_1.6.0_src_all.tar.gz"], "md5": "d8f916015bd3a1cc73a032cea58c335b", "fn": "imcdatasets_1.6.0.tar.gz"}, "bioimagedbs-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BioImageDbs_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/BioImageDbs_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bioimagedbs/bioconductor-bioimagedbs_1.6.0_src_all.tar.gz"], "md5": "33b92f3c68fb5aea2be89bca3ccf96a0", "fn": "BioImageDbs_1.6.0.tar.gz"}, "cellmapperdata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CellMapperData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/CellMapperData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cellmapperdata/bioconductor-cellmapperdata_1.24.0_src_all.tar.gz"], "md5": "865be918d3840063b609c1dea125eff5", "fn": "CellMapperData_1.24.0.tar.gz"}, "nestlink-1.14.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NestLink_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/NestLink_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nestlink/bioconductor-nestlink_1.14.0_src_all.tar.gz"], "md5": "5708030d17d01f5425a3fcb11fe600ba", "fn": "NestLink_1.14.0.tar.gz"}, "mousethymusageing-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MouseThymusAgeing_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/MouseThymusAgeing_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousethymusageing/bioconductor-mousethymusageing_1.6.0_src_all.tar.gz"], "md5": "ac4f2dfcc69421a51efec159c9427be9", "fn": "MouseThymusAgeing_1.6.0.tar.gz"}, "curatedmetagenomicdata-3.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedMetagenomicData_3.6.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedMetagenomicData_3.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedmetagenomicdata/bioconductor-curatedmetagenomicdata_3.6.0_src_all.tar.gz"], "md5": "02a7793d82cb65070e5b584a5dd03ff5", "fn": "curatedMetagenomicData_3.6.0.tar.gz"}, "mousegastrulationdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MouseGastrulationData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/MouseGastrulationData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousegastrulationdata/bioconductor-mousegastrulationdata_1.12.0_src_all.tar.gz"], "md5": "1f765b74acf4bfbee594883bd83377f2", "fn": "MouseGastrulationData_1.12.0.tar.gz"}, "merfishdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MerfishData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/MerfishData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-merfishdata/bioconductor-merfishdata_1.0.0_src_all.tar.gz"], "md5": "c8ac8b1fd9929c51402fb96a71bf4575", "fn": "MerfishData_1.0.0.tar.gz"}, "tenxbraindata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TENxBrainData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxBrainData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxbraindata/bioconductor-tenxbraindata_1.18.0_src_all.tar.gz"], "md5": "ddbd8f75cedd811eb4b83ec7f546b030", "fn": "TENxBrainData_1.18.0.tar.gz"}, "precisetadhub-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/preciseTADhub_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/preciseTADhub_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-precisetadhub/bioconductor-precisetadhub_1.6.0_src_all.tar.gz"], "md5": "5015e2d8bf3f51cb3d5bf2cfaba6dafc", "fn": "preciseTADhub_1.6.0.tar.gz"}, "copyneutralima-1.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CopyNeutralIMA_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/CopyNeutralIMA_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copyneutralima/bioconductor-copyneutralima_1.16.0_src_all.tar.gz"], "md5": "617773122d70885b29ccb6653966b30f", "fn": "CopyNeutralIMA_1.16.0.tar.gz"}, "droplettestfiles-1.8.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DropletTestFiles_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/DropletTestFiles_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-droplettestfiles/bioconductor-droplettestfiles_1.8.0_src_all.tar.gz"], "md5": "79168f83ce62f2185f71ba18ab5a7964", "fn": "DropletTestFiles_1.8.0.tar.gz"}, "harmonizedtcgadata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HarmonizedTCGAData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/HarmonizedTCGAData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harmonizedtcgadata/bioconductor-harmonizedtcgadata_1.20.0_src_all.tar.gz"], "md5": "920ab9b499b3dc57ca8c0cb8bd467bfd", "fn": "HarmonizedTCGAData_1.20.0.tar.gz"}, "rnaseqsamplesizedata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RnaSeqSampleSizeData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RnaSeqSampleSizeData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqsamplesizedata/bioconductor-rnaseqsamplesizedata_1.30.0_src_all.tar.gz"], "md5": "69c1fec1894e56123a22a7d7ea10d9f1", "fn": "RnaSeqSampleSizeData_1.30.0.tar.gz"}, "fis-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FIs_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/FIs_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fis/bioconductor-fis_1.26.0_src_all.tar.gz"], "md5": "a49a375be44f4204bacc4546ef96b7a4", "fn": "FIs_1.26.0.tar.gz"}, "curatedtbdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/curatedTBData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedTBData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedtbdata/bioconductor-curatedtbdata_1.4.0_src_all.tar.gz"], "md5": "309ada4a3d184dea658e44e06e8701bb", "fn": "curatedTBData_1.4.0.tar.gz"}, "neve2006-0.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Neve2006_0.36.0.tar.gz", "https://bioarchive.galaxyproject.org/Neve2006_0.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-neve2006/bioconductor-neve2006_0.36.0_src_all.tar.gz"], "md5": "e2c9f599cc81edf29b57abca8d32b6df", "fn": "Neve2006_0.36.0.tar.gz"}, "sfedata-1.0.2": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SFEData_1.0.2.tar.gz", "https://bioarchive.galaxyproject.org/SFEData_1.0.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sfedata/bioconductor-sfedata_1.0.2_src_all.tar.gz"], "md5": "90d276f09864634d9f2a24c66502422f", "fn": "SFEData_1.0.2.tar.gz"}, "phyloprofiledata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PhyloProfileData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/PhyloProfileData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phyloprofiledata/bioconductor-phyloprofiledata_1.12.0_src_all.tar.gz"], "md5": "40f15a8b8cf7bdf63362ecb46e24a58e", "fn": "PhyloProfileData_1.12.0.tar.gz"}, "pumadata-2.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pumadata_2.34.0.tar.gz", "https://bioarchive.galaxyproject.org/pumadata_2.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pumadata/bioconductor-pumadata_2.34.0_src_all.tar.gz"], "md5": "8f235c83d650b417f51f04ee4b3ca8ff", "fn": "pumadata_2.34.0.tar.gz"}, "varianttoolsdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/VariantToolsData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/VariantToolsData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-varianttoolsdata/bioconductor-varianttoolsdata_1.22.0_src_all.tar.gz"], "md5": "90196a5cd2ee5495beefcd96f4a231f2", "fn": "VariantToolsData_1.22.0.tar.gz"}, "msigdb-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/msigdb_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/msigdb_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msigdb/bioconductor-msigdb_1.6.0_src_all.tar.gz"], "md5": "ec3e80d41507001ce38796c1bb259c67", "fn": "msigdb_1.6.0.tar.gz"}, "highlyreplicatedrnaseq-1.10.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HighlyReplicatedRNASeq_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/HighlyReplicatedRNASeq_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-highlyreplicatedrnaseq/bioconductor-highlyreplicatedrnaseq_1.10.0_src_all.tar.gz"], "md5": "1386bf86842d87e343a4986e29dc9238", "fn": "HighlyReplicatedRNASeq_1.10.0.tar.gz"}, "scpdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/scpdata_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/scpdata_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scpdata/bioconductor-scpdata_1.6.0_src_all.tar.gz"], "md5": "4405ffd758f7cf5ef1671491d9cb514c", "fn": "scpdata_1.6.0.tar.gz"}, "hmp16sdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HMP16SData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/HMP16SData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hmp16sdata/bioconductor-hmp16sdata_1.18.0_src_all.tar.gz"], "md5": "11ec6263ac5f902a6a977bed215a030d", "fn": "HMP16SData_1.18.0.tar.gz"}, "celldex-1.8.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/celldex_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/celldex_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celldex/bioconductor-celldex_1.8.0_src_all.tar.gz"], "md5": "1321a36f50ddcc03ebe4f35fadfac5a7", "fn": "celldex_1.8.0.tar.gz"}, "predasampledata-0.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PREDAsampledata_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/PREDAsampledata_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-predasampledata/bioconductor-predasampledata_0.38.0_src_all.tar.gz"], "md5": "03314ac823a61b73125499b5cf584fa4", "fn": "PREDAsampledata_0.38.0.tar.gz"}, "tuberculosis-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/tuberculosis_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/tuberculosis_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tuberculosis/bioconductor-tuberculosis_1.4.0_src_all.tar.gz"], "md5": "cbd44f869e33ec7bfc2e21f514bd4023", "fn": "tuberculosis_1.4.0.tar.gz"}, "tcgabiolinksgui.data-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/TCGAbiolinksGUI.data_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAbiolinksGUI.data_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgabiolinksgui.data/bioconductor-tcgabiolinksgui.data_1.18.0_src_all.tar.gz"], "md5": "97227503c90be6fcdd5a8ca243847846", "fn": "TCGAbiolinksGUI.data_1.18.0.tar.gz"}, "xhybcasneuf-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/XhybCasneuf_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/XhybCasneuf_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xhybcasneuf/bioconductor-xhybcasneuf_1.36.0_src_all.tar.gz"], "md5": "21e37d41f64496c8cef99d60c3d7f2d3", "fn": "XhybCasneuf_1.36.0.tar.gz"}, "gsvadata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GSVAdata_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/GSVAdata_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gsvadata/bioconductor-gsvadata_1.34.0_src_all.tar.gz"], "md5": "022262252cfef2c2a5b7924c720d4d1b", "fn": "GSVAdata_1.34.0.tar.gz"}, "ritandata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RITANdata_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/RITANdata_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ritandata/bioconductor-ritandata_1.22.0_src_all.tar.gz"], "md5": "4c7706977f26087281e7b0956d7d19d5", "fn": "RITANdata_1.22.0.tar.gz"}, "listeretalbsseq-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ListerEtAlBSseq_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/ListerEtAlBSseq_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-listeretalbsseq/bioconductor-listeretalbsseq_1.30.0_src_all.tar.gz"], "md5": "34e0e425d704f29b62840aeb318043a3", "fn": "ListerEtAlBSseq_1.30.0.tar.gz"}, "nullrangesdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/nullrangesData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/nullrangesData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nullrangesdata/bioconductor-nullrangesdata_1.4.0_src_all.tar.gz"], "md5": "39ebab6ebac4b73162925f2c6f5c654a", "fn": "nullrangesData_1.4.0.tar.gz"}, "rnamodr.data-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RNAmodR.Data_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAmodR.Data_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnamodr.data/bioconductor-rnamodr.data_1.12.0_src_all.tar.gz"], "md5": "f15f9939776393d3dfc6ea30d47590c0", "fn": "RNAmodR.Data_1.12.0.tar.gz"}, "methylclockdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/methylclockData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/methylclockData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylclockdata/bioconductor-methylclockdata_1.6.0_src_all.tar.gz"], "md5": "ab12ee063e08bd1109ee9400f63cf57a", "fn": "methylclockData_1.6.0.tar.gz"}, "genomicdistributionsdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/GenomicDistributionsData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/GenomicDistributionsData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomicdistributionsdata/bioconductor-genomicdistributionsdata_1.6.0_src_all.tar.gz"], "md5": "b66482cc3c1cfddbb10922a1e8b38d3e", "fn": "GenomicDistributionsData_1.6.0.tar.gz"}, "singlemoleculefootprintingdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SingleMoleculeFootprintingData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/SingleMoleculeFootprintingData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-singlemoleculefootprintingdata/bioconductor-singlemoleculefootprintingdata_1.6.0_src_all.tar.gz"], "md5": "f7a07857cb19ab6f0e2eee8ff913b479", "fn": "SingleMoleculeFootprintingData_1.6.0.tar.gz"}, "scrnaseq-2.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/scRNAseq_2.12.0.tar.gz", "https://bioarchive.galaxyproject.org/scRNAseq_2.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scrnaseq/bioconductor-scrnaseq_2.12.0_src_all.tar.gz"], "md5": "54ced014f88eda70982b052a505fb864", "fn": "scRNAseq_2.12.0.tar.gz"}, "copyhelper-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/CopyhelpeR_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/CopyhelpeR_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copyhelper/bioconductor-copyhelper_1.30.0_src_all.tar.gz"], "md5": "2be26e5fb90270541b426a5b2baf1824", "fn": "CopyhelpeR_1.30.0.tar.gz"}, "healthycontrolspresencechecker-1.2.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/healthyControlsPresenceChecker_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/healthyControlsPresenceChecker_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-healthycontrolspresencechecker/bioconductor-healthycontrolspresencechecker_1.2.0_src_all.tar.gz"], "md5": "8789ca7539d9cf83ce2db9fe89a6fb3e", "fn": "healthyControlsPresenceChecker_1.2.0.tar.gz"}, "emtdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/emtdata_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/emtdata_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-emtdata/bioconductor-emtdata_1.6.0_src_all.tar.gz"], "md5": "eb00c34c239c9909c2e09733600c092d", "fn": "emtdata_1.6.0.tar.gz"}, "ewcedata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ewceData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/ewceData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ewcedata/bioconductor-ewcedata_1.6.0_src_all.tar.gz"], "md5": "4c11a9afee7da412aab59546108b3dfb", "fn": "ewceData_1.6.0.tar.gz"}, "humanaffydata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HumanAffyData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/HumanAffyData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanaffydata/bioconductor-humanaffydata_1.24.0_src_all.tar.gz"], "md5": "93c6073e8e2bcce485f656e42c646fc3", "fn": "HumanAffyData_1.24.0.tar.gz"}, "restfulsedata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/restfulSEData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/restfulSEData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-restfulsedata/bioconductor-restfulsedata_1.20.0_src_all.tar.gz"], "md5": "184981fb35aab130042a69a96cd3b21c", "fn": "restfulSEData_1.20.0.tar.gz"}, "crisprscoredata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/crisprScoreData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/crisprScoreData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-crisprscoredata/bioconductor-crisprscoredata_1.2.0_src_all.tar.gz"], "md5": "3c91f9e9e2a330c08519fa5880cb28dd", "fn": "crisprScoreData_1.2.0.tar.gz"}, "cctutorial-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ccTutorial_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/ccTutorial_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cctutorial/bioconductor-cctutorial_1.36.0_src_all.tar.gz"], "md5": "08916c2f651fcf53b63590aa5dbc0db2", "fn": "ccTutorial_1.36.0.tar.gz"}, "hiiragi2013-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Hiiragi2013_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/Hiiragi2013_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hiiragi2013/bioconductor-hiiragi2013_1.34.0_src_all.tar.gz"], "md5": "739f5caa57eac27fdab269de30eccb33", "fn": "Hiiragi2013_1.34.0.tar.gz"}, "davidtiling-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/davidTiling_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/davidTiling_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-davidtiling/bioconductor-davidtiling_1.38.0_src_all.tar.gz"], "md5": "62cb2d1c5d877a095f6c25962b165262", "fn": "davidTiling_1.38.0.tar.gz"}, "mcseadata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mCSEAdata_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mCSEAdata_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcseadata/bioconductor-mcseadata_1.18.0_src_all.tar.gz"], "md5": "545b303774337c2286a8226dc2147677", "fn": "mCSEAdata_1.18.0.tar.gz"}, "adductdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/adductData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/adductData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-adductdata/bioconductor-adductdata_1.14.0_src_all.tar.gz"], "md5": "7a983571463b4566782cbfe478ea93a9", "fn": "adductData_1.14.0.tar.gz"}, "scatedata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/SCATEData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/SCATEData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scatedata/bioconductor-scatedata_1.8.0_src_all.tar.gz"], "md5": "f6f4b950d1639c5ae565a71f3d7491fb", "fn": "SCATEData_1.8.0.tar.gz"}, "hmp2data-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HMP2Data_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/HMP2Data_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hmp2data/bioconductor-hmp2data_1.12.0_src_all.tar.gz"], "md5": "2945af451892098684b5fb0bdace152d", "fn": "HMP2Data_1.12.0.tar.gz"}, "rrbsdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RRBSdata_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/RRBSdata_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rrbsdata/bioconductor-rrbsdata_1.18.0_src_all.tar.gz"], "md5": "c4f7461c8314422810b456ff26ed0ff9", "fn": "RRBSdata_1.18.0.tar.gz"}, "pwrewas.data-1.12.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pwrEWAS.data_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/pwrEWAS.data_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwrewas.data/bioconductor-pwrewas.data_1.12.0_src_all.tar.gz"], "md5": "2e60d579c30b55eb5357b59233b391a2", "fn": "pwrEWAS.data_1.12.0.tar.gz"}, "fieldeffectcrc-1.8.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FieldEffectCrc_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/FieldEffectCrc_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fieldeffectcrc/bioconductor-fieldeffectcrc_1.8.0_src_all.tar.gz"], "md5": "0be77552ce25ac628446391b1292decd", "fn": "FieldEffectCrc_1.8.0.tar.gz"}, "jaspar2016-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/JASPAR2016_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2016_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2016/bioconductor-jaspar2016_1.26.0_src_all.tar.gz"], "md5": "28e8034505a668913cf0bf50ae8f3331", "fn": "JASPAR2016_1.26.0.tar.gz"}, "bloodcancermultiomics2017-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BloodCancerMultiOmics2017_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/BloodCancerMultiOmics2017_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bloodcancermultiomics2017/bioconductor-bloodcancermultiomics2017_1.18.0_src_all.tar.gz"], "md5": "09621b2d3d7fec1f4f10d8227b0ec6ba", "fn": "BloodCancerMultiOmics2017_1.18.0.tar.gz"}, "netactivitydata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/NetActivityData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/NetActivityData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-netactivitydata/bioconductor-netactivitydata_1.0.0_src_all.tar.gz"], "md5": "bcbd4a5622e1029caeb110195f72cc7d", "fn": "NetActivityData_1.0.0.tar.gz"}, "rnainteractmapk-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/RNAinteractMAPK_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAinteractMAPK_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnainteractmapk/bioconductor-rnainteractmapk_1.36.0_src_all.tar.gz"], "md5": "7d626f19929cda149d56b340d3249942", "fn": "RNAinteractMAPK_1.36.0.tar.gz"}, "pasilla-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/pasilla_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/pasilla_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasilla/bioconductor-pasilla_1.26.0_src_all.tar.gz"], "md5": "8a54d964fa80a98285d26d9f39e92159", "fn": "pasilla_1.26.0.tar.gz"}, "beadsorted.saliva.epic-1.6.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/BeadSorted.Saliva.EPIC_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/BeadSorted.Saliva.EPIC_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadsorted.saliva.epic/bioconductor-beadsorted.saliva.epic_1.6.0_src_all.tar.gz"], "md5": "0b80c17ee21a3d2b7c7113ea1bde020c", "fn": "BeadSorted.Saliva.EPIC_1.6.0.tar.gz"}, "minfidataepic-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/minfiDataEPIC_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/minfiDataEPIC_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minfidataepic/bioconductor-minfidataepic_1.24.0_src_all.tar.gz"], "md5": "0af85d8d67f8d12264f944a27e868659", "fn": "minfiDataEPIC_1.24.0.tar.gz"}, "flowsorted.cordbloodnorway.450k-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.CordBloodNorway.450k_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodNorway.450k_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodnorway.450k/bioconductor-flowsorted.cordbloodnorway.450k_1.24.0_src_all.tar.gz"], "md5": "eaedd2ac35dfbf5363b198fbd89340ac", "fn": "FlowSorted.CordBloodNorway.450k_1.24.0.tar.gz"}, "flowsorted.cordblood.450k-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.CordBlood.450k_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBlood.450k_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordblood.450k/bioconductor-flowsorted.cordblood.450k_1.26.0_src_all.tar.gz"], "md5": "3634ebac8c3ea0ea40eaf413c015ce51", "fn": "FlowSorted.CordBlood.450k_1.26.0.tar.gz"}, "dmrcatedata-2.16.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DMRcatedata_2.16.0.tar.gz", "https://bioarchive.galaxyproject.org/DMRcatedata_2.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dmrcatedata/bioconductor-dmrcatedata_2.16.0_src_all.tar.gz"], "md5": "f3a23f5f3f4a10829006493ecfab3fa4", "fn": "DMRcatedata_2.16.0.tar.gz"}, "flowsorted.cordbloodcombined.450k-1.14.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.CordBloodCombined.450k_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodCombined.450k_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodcombined.450k/bioconductor-flowsorted.cordbloodcombined.450k_1.14.0_src_all.tar.gz"], "md5": "449c6036f08827fa2c72481bcb5b8974", "fn": "FlowSorted.CordBloodCombined.450k_1.14.0.tar.gz"}, "lungcanceracvssccgeo-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/LungCancerACvsSCCGEO_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/LungCancerACvsSCCGEO_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungcanceracvssccgeo/bioconductor-lungcanceracvssccgeo_1.34.0_src_all.tar.gz"], "md5": "1d7786eec9ef4a8c41ab26aaf7280241", "fn": "LungCancerACvsSCCGEO_1.34.0.tar.gz"}, "cmap2data-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/cMap2data_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/cMap2data_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cmap2data/bioconductor-cmap2data_1.34.0_src_all.tar.gz"], "md5": "c04b32c3d36cf3ff94dd074b9cee35b4", "fn": "cMap2data_1.34.0.tar.gz"}, "kodata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/KOdata_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/KOdata_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-kodata/bioconductor-kodata_1.24.0_src_all.tar.gz"], "md5": "56dcc1dbb530d00179ddc5494dbd92a3", "fn": "KOdata_1.24.0.tar.gz"}, "flowsorted.dlpfc.450k-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.DLPFC.450k_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.DLPFC.450k_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.dlpfc.450k/bioconductor-flowsorted.dlpfc.450k_1.34.0_src_all.tar.gz"], "md5": "fbf4414d97fcc8f2a67fd7900aecd4ca", "fn": "FlowSorted.DLPFC.450k_1.34.0.tar.gz"}, "flowsorted.blood.epic-2.2.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.Blood.EPIC_2.2.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.Blood.EPIC_2.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.epic/bioconductor-flowsorted.blood.epic_2.2.0_src_all.tar.gz"], "md5": "e386c74c9b0168a5891bec4445799438", "fn": "FlowSorted.Blood.EPIC_2.2.0.tar.gz"}, "flowsorted.blood.450k-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/FlowSorted.Blood.450k_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.Blood.450k_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.450k/bioconductor-flowsorted.blood.450k_1.36.0_src_all.tar.gz"], "md5": "49bce6f7d31d9a37fef658108eefd5a4", "fn": "FlowSorted.Blood.450k_1.36.0.tar.gz"}, "desousa2013-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DeSousa2013_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/DeSousa2013_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-desousa2013/bioconductor-desousa2013_1.34.0_src_all.tar.gz"], "md5": "8fbba6b634001af0bcce09be50b3c457", "fn": "DeSousa2013_1.34.0.tar.gz"}, "methylaiddata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MethylAidData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/MethylAidData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylaiddata/bioconductor-methylaiddata_1.30.0_src_all.tar.gz"], "md5": "15f494b47ba64df59d4cb88eff250424", "fn": "MethylAidData_1.30.0.tar.gz"}, "minfidata-0.44.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/minfiData_0.44.0.tar.gz", "https://bioarchive.galaxyproject.org/minfiData_0.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minfidata/bioconductor-minfidata_0.44.0_src_all.tar.gz"], "md5": "988f1ac63c897662192cee4909fc5d70", "fn": "minfiData_0.44.0.tar.gz"}, "ihwpaper-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/IHWpaper_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/IHWpaper_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ihwpaper/bioconductor-ihwpaper_1.26.0_src_all.tar.gz"], "md5": "6eabaa4575f0c53258cf49caf497d708", "fn": "IHWpaper_1.26.0.tar.gz"}, "ffpeexampledata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/ffpeExampleData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/ffpeExampleData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ffpeexampledata/bioconductor-ffpeexampledata_1.36.0_src_all.tar.gz"], "md5": "531c091065f07e82304bc9468cdd20cd", "fn": "ffpeExampleData_1.36.0.tar.gz"}, "lumibarnes-1.38.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/lumiBarnes_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/lumiBarnes_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumibarnes/bioconductor-lumibarnes_1.38.0_src_all.tar.gz"], "md5": "a46084b74e3fff1b80b4ce3f10f76ef7", "fn": "lumiBarnes_1.38.0.tar.gz"}, "maqcsubset-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MAQCsubset_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/MAQCsubset_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcsubset/bioconductor-maqcsubset_1.36.0_src_all.tar.gz"], "md5": "1fe763b7722d1cfaa2fecd08dae9f36e", "fn": "MAQCsubset_1.36.0.tar.gz"}, "egseadata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/EGSEAdata_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/EGSEAdata_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-egseadata/bioconductor-egseadata_1.26.0_src_all.tar.gz"], "md5": "f76bea52e1029aa018475868d499df0b", "fn": "EGSEAdata_1.26.0.tar.gz"}, "drugvsdiseasedata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/DrugVsDiseasedata_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/DrugVsDiseasedata_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drugvsdiseasedata/bioconductor-drugvsdiseasedata_1.34.0_src_all.tar.gz"], "md5": "6e318b03d2fbe45a7b0a9247b23f0eb0", "fn": "DrugVsDiseasedata_1.34.0.tar.gz"}, "epimutacionsdata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/epimutacionsData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/epimutacionsData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epimutacionsdata/bioconductor-epimutacionsdata_1.2.0_src_all.tar.gz"], "md5": "02cd283b2fe78a29cdf1fc96f7c20a6c", "fn": "epimutacionsData_1.2.0.tar.gz"}, "mvoutdata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/mvoutData_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/mvoutData_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mvoutdata/bioconductor-mvoutdata_1.34.0_src_all.tar.gz"], "md5": "3199373f2a97a6765f10198b3d9db7d5", "fn": "mvoutData_1.34.0.tar.gz"}, "maqcsubsetilm-1.36.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/MAQCsubsetILM_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/MAQCsubsetILM_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcsubsetilm/bioconductor-maqcsubsetilm_1.36.0_src_all.tar.gz"], "md5": "c1e92632336069ac9764b52dbbd87e2a", "fn": "MAQCsubsetILM_1.36.0.tar.gz"}, "illumina450probevariants.db-1.34.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/Illumina450ProbeVariants.db_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/Illumina450ProbeVariants.db_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illumina450probevariants.db/bioconductor-illumina450probevariants.db_1.34.0_src_all.tar.gz"], "md5": "228c2e089c604bd2c615c0ecb676ccd3", "fn": "Illumina450ProbeVariants.db_1.34.0.tar.gz"}, "hsmmsinglecell-1.18.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/HSMMSingleCell_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/HSMMSingleCell_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hsmmsinglecell/bioconductor-hsmmsinglecell_1.18.0_src_all.tar.gz"], "md5": "030d50f78cca5810f70ab930e091ed87", "fn": "HSMMSingleCell_1.18.0.tar.gz"}, "mspuritydata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.16/data/experiment/src/contrib/msPurityData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/msPurityData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mspuritydata/bioconductor-mspuritydata_1.26.0_src_all.tar.gz"], "md5": "729d4691c7db6cb9fc7b880591b9d6e9", "fn": "msPurityData_1.26.0.tar.gz"}, "bsgenome.hsapiens.ucsc.hg38-1.4.5": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.5.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg38_1.4.5.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38/bioconductor-bsgenome.hsapiens.ucsc.hg38_1.4.5_src_all.tar.gz"], "md5": "b2e670c27944eed77fbe9a9b55be40d2", "fn": "BSgenome.Hsapiens.UCSC.hg38_1.4.5.tar.gz"}, "ahlrbasedbs-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/AHLRBaseDbs_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/AHLRBaseDbs_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahlrbasedbs/bioconductor-ahlrbasedbs_1.6.0_src_all.tar.gz"], "md5": "1427836afe85a5b580f7277e7d2c08ca", "fn": "AHLRBaseDbs_1.6.0.tar.gz"}, "ahmeshdbs-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/AHMeSHDbs_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/AHMeSHDbs_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahmeshdbs/bioconductor-ahmeshdbs_1.6.0_src_all.tar.gz"], "md5": "7fe9c77aaff9175d842cb4f4b9313360", "fn": "AHMeSHDbs_1.6.0.tar.gz"}, "ahpubmeddbs-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/AHPubMedDbs_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/AHPubMedDbs_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahpubmeddbs/bioconductor-ahpubmeddbs_1.6.0_src_all.tar.gz"], "md5": "91815a0aa91e19d171fad3b116d02eed", "fn": "AHPubMedDbs_1.6.0.tar.gz"}, "anopheles.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/anopheles.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/anopheles.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-anopheles.db0/bioconductor-anopheles.db0_3.17.0_src_all.tar.gz"], "md5": "d26110289d806c4d1bd6e039c5873100", "fn": "anopheles.db0_3.17.0.tar.gz"}, "arabidopsis.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/arabidopsis.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/arabidopsis.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-arabidopsis.db0/bioconductor-arabidopsis.db0_3.17.0_src_all.tar.gz"], "md5": "773844428cd90716c8e32f942328618d", "fn": "arabidopsis.db0_3.17.0.tar.gz"}, "bovine.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/bovine.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/bovine.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bovine.db0/bioconductor-bovine.db0_3.17.0_src_all.tar.gz"], "md5": "1e268d93f6206875bd73ad2caae53f27", "fn": "bovine.db0_3.17.0.tar.gz"}, "bsgenome.hsapiens.ucsc.hg38.masked-1.4.5": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38.masked_1.4.5.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg38.masked_1.4.5.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked_1.4.5_src_all.tar.gz"], "md5": "7570dd1b4f013b3c6acecd68602180b4", "fn": "BSgenome.Hsapiens.UCSC.hg38.masked_1.4.5.tar.gz"}, "bsgenome.hsapiens.ucsc.hs1-1.4.4": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hs1_1.4.4.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hs1_1.4.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hs1/bioconductor-bsgenome.hsapiens.ucsc.hs1_1.4.4_src_all.tar.gz"], "md5": "5812c5670f51a5c58a9da9e042e7e440", "fn": "BSgenome.Hsapiens.UCSC.hs1_1.4.4.tar.gz"}, "canine.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/canine.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/canine.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canine.db0/bioconductor-canine.db0_3.17.0_src_all.tar.gz"], "md5": "da4af1b026fe2775a020addd13920f71", "fn": "canine.db0_3.17.0.tar.gz"}, "chicken.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/chicken.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/chicken.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chicken.db0/bioconductor-chicken.db0_3.17.0_src_all.tar.gz"], "md5": "bfacdb3f67e914c4d364a512620ec50d", "fn": "chicken.db0_3.17.0.tar.gz"}, "chimp.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/chimp.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/chimp.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chimp.db0/bioconductor-chimp.db0_3.17.0_src_all.tar.gz"], "md5": "0a1382e14c2ace3a9cdc3daf7d7e4013", "fn": "chimp.db0_3.17.0.tar.gz"}, "ctcf-0.99.11": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/CTCF_0.99.11.tar.gz", "https://bioarchive.galaxyproject.org/CTCF_0.99.11.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ctcf/bioconductor-ctcf_0.99.11_src_all.tar.gz"], "md5": "5ec44245864395de390e68fa56e465af", "fn": "CTCF_0.99.11.tar.gz"}, "ecolik12.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/ecoliK12.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliK12.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolik12.db0/bioconductor-ecolik12.db0_3.17.0_src_all.tar.gz"], "md5": "acf1faa22de4e8b535baf0d7403acbe0", "fn": "ecoliK12.db0_3.17.0.tar.gz"}, "ecolisakai.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/ecoliSakai.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliSakai.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolisakai.db0/bioconductor-ecolisakai.db0_3.17.0_src_all.tar.gz"], "md5": "2f49e4fe2806f14f78db0de22d37a7e7", "fn": "ecoliSakai.db0_3.17.0.tar.gz"}, "excluderanges-0.99.8": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/excluderanges_0.99.8.tar.gz", "https://bioarchive.galaxyproject.org/excluderanges_0.99.8.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-excluderanges/bioconductor-excluderanges_0.99.8_src_all.tar.gz"], "md5": "2ec19df8a51df1900a339f7f505cd5fa", "fn": "excluderanges_0.99.8.tar.gz"}, "fly.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/fly.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/fly.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fly.db0/bioconductor-fly.db0_3.17.0_src_all.tar.gz"], "md5": "04b3d22c5825c9a31f5253746df5c4e0", "fn": "fly.db0_3.17.0.tar.gz"}, "genomeinfodbdata-1.2.10": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/GenomeInfoDbData_1.2.10.tar.gz", "https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.10.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.10_src_all.tar.gz"], "md5": "ebd78c10d672c0eb6c893d6135bdeca9", "fn": "GenomeInfoDbData_1.2.10.tar.gz"}, "go.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/GO.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/GO.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-go.db/bioconductor-go.db_3.17.0_src_all.tar.gz"], "md5": "f278f3cb015e04ead1cc3d982a3fd1b3", "fn": "GO.db_3.17.0.tar.gz"}, "human.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/human.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/human.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human.db0/bioconductor-human.db0_3.17.0_src_all.tar.gz"], "md5": "4597ee42fd14b0e83754027205d4ca17", "fn": "human.db0_3.17.0.tar.gz"}, "malaria.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/malaria.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/malaria.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-malaria.db0/bioconductor-malaria.db0_3.17.0_src_all.tar.gz"], "md5": "b8064752fa55d249e89e1c94db04b434", "fn": "malaria.db0_3.17.0.tar.gz"}, "mouse.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/mouse.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse.db0/bioconductor-mouse.db0_3.17.0_src_all.tar.gz"], "md5": "132244baa13685fdb259ecaecd9535af", "fn": "mouse.db0_3.17.0.tar.gz"}, "org.ag.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Ag.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ag.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ag.eg.db/bioconductor-org.ag.eg.db_3.17.0_src_all.tar.gz"], "md5": "fb3e06ad1afc3c386367a239e559f342", "fn": "org.Ag.eg.db_3.17.0.tar.gz"}, "org.at.tair.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.At.tair.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.At.tair.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.at.tair.db/bioconductor-org.at.tair.db_3.17.0_src_all.tar.gz"], "md5": "568e09bfbf9b86a9120b52ca6eb47879", "fn": "org.At.tair.db_3.17.0.tar.gz"}, "org.bt.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Bt.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Bt.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.bt.eg.db/bioconductor-org.bt.eg.db_3.17.0_src_all.tar.gz"], "md5": "13b2350bb7e6219a25caea3a4038f104", "fn": "org.Bt.eg.db_3.17.0.tar.gz"}, "org.ce.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Ce.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ce.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ce.eg.db/bioconductor-org.ce.eg.db_3.17.0_src_all.tar.gz"], "md5": "8884864a691574d7640b2059a8d6613b", "fn": "org.Ce.eg.db_3.17.0.tar.gz"}, "org.cf.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Cf.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Cf.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.cf.eg.db/bioconductor-org.cf.eg.db_3.17.0_src_all.tar.gz"], "md5": "594a306e7ac757df56e9563163168713", "fn": "org.Cf.eg.db_3.17.0.tar.gz"}, "org.dm.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Dm.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Dm.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.dm.eg.db/bioconductor-org.dm.eg.db_3.17.0_src_all.tar.gz"], "md5": "3a680c3ea7320013c7ab1181d11e2177", "fn": "org.Dm.eg.db_3.17.0.tar.gz"}, "org.dr.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Dr.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Dr.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.dr.eg.db/bioconductor-org.dr.eg.db_3.17.0_src_all.tar.gz"], "md5": "03edb42214f27a93743dfc57200cddbb", "fn": "org.Dr.eg.db_3.17.0.tar.gz"}, "org.eck12.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.EcK12.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.EcK12.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.eck12.eg.db/bioconductor-org.eck12.eg.db_3.17.0_src_all.tar.gz"], "md5": "676642eb784017bf9f82711274f8987e", "fn": "org.EcK12.eg.db_3.17.0.tar.gz"}, "org.ecsakai.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.EcSakai.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.EcSakai.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ecsakai.eg.db/bioconductor-org.ecsakai.eg.db_3.17.0_src_all.tar.gz"], "md5": "135a50e2604715a7c5f1c2a36bddf691", "fn": "org.EcSakai.eg.db_3.17.0.tar.gz"}, "org.gg.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Gg.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Gg.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.gg.eg.db/bioconductor-org.gg.eg.db_3.17.0_src_all.tar.gz"], "md5": "292b22ea846c6c184528e92ab4a53247", "fn": "org.Gg.eg.db_3.17.0.tar.gz"}, "org.hs.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Hs.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Hs.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.hs.eg.db/bioconductor-org.hs.eg.db_3.17.0_src_all.tar.gz"], "md5": "a1015fd071ab69055865940ef6e205f4", "fn": "org.Hs.eg.db_3.17.0.tar.gz"}, "org.mm.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Mm.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Mm.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.mm.eg.db/bioconductor-org.mm.eg.db_3.17.0_src_all.tar.gz"], "md5": "7b2124d1ef7c0936bb4ecfcbd2a979b8", "fn": "org.Mm.eg.db_3.17.0.tar.gz"}, "org.mmu.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Mmu.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Mmu.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.mmu.eg.db/bioconductor-org.mmu.eg.db_3.17.0_src_all.tar.gz"], "md5": "d59c3d744ec7def892edacf12c99b869", "fn": "org.Mmu.eg.db_3.17.0.tar.gz"}, "org.pt.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Pt.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Pt.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.pt.eg.db/bioconductor-org.pt.eg.db_3.17.0_src_all.tar.gz"], "md5": "b3c4135532486951e94ed5d182030217", "fn": "org.Pt.eg.db_3.17.0.tar.gz"}, "org.rn.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Rn.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Rn.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.rn.eg.db/bioconductor-org.rn.eg.db_3.17.0_src_all.tar.gz"], "md5": "bf40322d9b95075d75777ec63a797198", "fn": "org.Rn.eg.db_3.17.0.tar.gz"}, "org.sc.sgd.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Sc.sgd.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Sc.sgd.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.sc.sgd.db/bioconductor-org.sc.sgd.db_3.17.0_src_all.tar.gz"], "md5": "b0fd2fcd421007a5b9bd7bc2f5874ae3", "fn": "org.Sc.sgd.db_3.17.0.tar.gz"}, "org.ss.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Ss.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ss.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ss.eg.db/bioconductor-org.ss.eg.db_3.17.0_src_all.tar.gz"], "md5": "a9f8354c9869e86a610ad30f51eb533b", "fn": "org.Ss.eg.db_3.17.0.tar.gz"}, "org.xl.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Xl.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Xl.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.xl.eg.db/bioconductor-org.xl.eg.db_3.17.0_src_all.tar.gz"], "md5": "6ce9e0dc3566a220f5c12b70ffb2538c", "fn": "org.Xl.eg.db_3.17.0.tar.gz"}, "orthology.eg.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/Orthology.eg.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/Orthology.eg.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-orthology.eg.db/bioconductor-orthology.eg.db_3.17.0_src_all.tar.gz"], "md5": "90c181057a638413afc54bb11071a42e", "fn": "Orthology.eg.db_3.17.0.tar.gz"}, "pfam.db-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PFAM.db_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/PFAM.db_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pfam.db/bioconductor-pfam.db_3.17.0_src_all.tar.gz"], "md5": "729496d021868b74cbecfd156066d0e9", "fn": "PFAM.db_3.17.0.tar.gz"}, "pig.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/pig.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/pig.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pig.db0/bioconductor-pig.db0_3.17.0_src_all.tar.gz"], "md5": "d4ea227fc9495dc815bb3ad2387a7e26", "fn": "pig.db0_3.17.0.tar.gz"}, "rat.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/rat.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/rat.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat.db0/bioconductor-rat.db0_3.17.0_src_all.tar.gz"], "md5": "86993da680822a050e85f1208713f3c8", "fn": "rat.db0_3.17.0.tar.gz"}, "reactome.db-1.84.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/reactome.db_1.84.0.tar.gz", "https://bioarchive.galaxyproject.org/reactome.db_1.84.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-reactome.db/bioconductor-reactome.db_1.84.0_src_all.tar.gz"], "md5": "ce62dbac370a30e260d8e45891939693", "fn": "reactome.db_1.84.0.tar.gz"}, "rhesus.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/rhesus.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/rhesus.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rhesus.db0/bioconductor-rhesus.db0_3.17.0_src_all.tar.gz"], "md5": "16b4999171a6b36e72c19b3f15b46354", "fn": "rhesus.db0_3.17.0.tar.gz"}, "snplocs.hsapiens.dbsnp155.grch37-0.99.24": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.24.tar.gz", "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.24.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp155.grch37/bioconductor-snplocs.hsapiens.dbsnp155.grch37_0.99.24_src_all.tar.gz"], "md5": "9473e23ffc7ae76e630a78324b245da8", "fn": "SNPlocs.Hsapiens.dbSNP155.GRCh37_0.99.24.tar.gz"}, "snplocs.hsapiens.dbsnp155.grch38-0.99.24": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP155.GRCh38_0.99.24.tar.gz", "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP155.GRCh38_0.99.24.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp155.grch38/bioconductor-snplocs.hsapiens.dbsnp155.grch38_0.99.24_src_all.tar.gz"], "md5": "a16b7b1f940c3fcc8fd2d78f438fd25c", "fn": "SNPlocs.Hsapiens.dbSNP155.GRCh38_0.99.24.tar.gz"}, "txdb.cfamiliaris.ucsc.canfam6.refgene-3.17.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Cfamiliaris.UCSC.canFam6.refGene_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Cfamiliaris.UCSC.canFam6.refGene_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene/bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene_3.17.0_src_all.tar.gz"], "md5": "9279204329323191fbb72717a57b13aa", "fn": "TxDb.Cfamiliaris.UCSC.canFam6.refGene_3.17.0.tar.gz"}, "txdb.hsapiens.ucsc.hg38.knowngene-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg38.knownGene_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_3.17.0_src_all.tar.gz"], "md5": "a9b7cfbf5ed7d9ef129c84abdd7858dc", "fn": "TxDb.Hsapiens.UCSC.hg38.knownGene_3.17.0.tar.gz"}, "txdb.mmusculus.ucsc.mm39.knowngene-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm39.knownGene_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm39.knownGene_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene_3.17.0_src_all.tar.gz"], "md5": "ca2e9ed7dc7fe96ef98b18e3c7e3245a", "fn": "TxDb.Mmusculus.UCSC.mm39.knownGene_3.17.0.tar.gz"}, "worm.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/worm.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/worm.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-worm.db0/bioconductor-worm.db0_3.17.0_src_all.tar.gz"], "md5": "5ab9b7c14dafa60945e528fe7b940d42", "fn": "worm.db0_3.17.0.tar.gz"}, "xenopus.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/xenopus.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/xenopus.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xenopus.db0/bioconductor-xenopus.db0_3.17.0_src_all.tar.gz"], "md5": "cbdcc91045acef0ea9998f965b24dc2e", "fn": "xenopus.db0_3.17.0.tar.gz"}, "yeast.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/yeast.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/yeast.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeast.db0/bioconductor-yeast.db0_3.17.0_src_all.tar.gz"], "md5": "ce5a6e6febb6565c3a382d188d7652c0", "fn": "yeast.db0_3.17.0.tar.gz"}, "zebrafish.db0-3.17.0": {"urls": ["https://bioconductor.org/packages/3.17/data/annotation/src/contrib/zebrafish.db0_3.17.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafish.db0_3.17.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafish.db0/bioconductor-zebrafish.db0_3.17.0_src_all.tar.gz"], "md5": "bf2c5c9a8aaee76228e865cab2901cd2", "fn": "zebrafish.db0_3.17.0.tar.gz"}, "adductdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/adductData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/adductData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-adductdata/bioconductor-adductdata_1.16.0_src_all.tar.gz"], "md5": "abd834104d02465a0f32a64be9974c64", "fn": "adductData_1.16.0.tar.gz"}, "affycompdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/affycompData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/affycompData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affycompdata/bioconductor-affycompdata_1.38.0_src_all.tar.gz"], "md5": "adf2ee1552f1ee380e5ccbcf8246955d", "fn": "affycompData_1.38.0.tar.gz"}, "affydata-1.48.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/affydata_1.48.0.tar.gz", "https://bioarchive.galaxyproject.org/affydata_1.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affydata/bioconductor-affydata_1.48.0_src_all.tar.gz"], "md5": "ec63683a91e086cf51b0ff7b21dcc00b", "fn": "affydata_1.48.0.tar.gz"}, "affyhgu133a2expr-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Affyhgu133A2Expr_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133A2Expr_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133a2expr/bioconductor-affyhgu133a2expr_1.36.0_src_all.tar.gz"], "md5": "09a1e306ad46f08b9508343050ffa756", "fn": "Affyhgu133A2Expr_1.36.0.tar.gz"}, "affyhgu133aexpr-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Affyhgu133aExpr_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133aExpr_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133aexpr/bioconductor-affyhgu133aexpr_1.38.0_src_all.tar.gz"], "md5": "e745cf07453b1f7151f28ddddced6be1", "fn": "Affyhgu133aExpr_1.38.0.tar.gz"}, "affyhgu133plus2expr-1.34.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Affyhgu133Plus2Expr_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133Plus2Expr_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133plus2expr/bioconductor-affyhgu133plus2expr_1.34.0_src_all.tar.gz"], "md5": "210b20595daf5314b8d5b90b5497eab4", "fn": "Affyhgu133Plus2Expr_1.34.0.tar.gz"}, "affymetrixdatatestfiles-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/AffymetrixDataTestFiles_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/AffymetrixDataTestFiles_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affymetrixdatatestfiles/bioconductor-affymetrixdatatestfiles_0.38.0_src_all.tar.gz"], "md5": "3aa3891584be3bcdab25e2b72b092edc", "fn": "AffymetrixDataTestFiles_0.38.0.tar.gz"}, "affymoe4302expr-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Affymoe4302Expr_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/Affymoe4302Expr_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affymoe4302expr/bioconductor-affymoe4302expr_1.38.0_src_all.tar.gz"], "md5": "277537172df894a0e7384d3e48d059b1", "fn": "Affymoe4302Expr_1.38.0.tar.gz"}, "airway-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/airway_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/airway_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-airway/bioconductor-airway_1.20.0_src_all.tar.gz"], "md5": "9c79ded2f4d44b3a865a1e489c6d151d", "fn": "airway_1.20.0.tar.gz"}, "all-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ALL_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/ALL_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-all/bioconductor-all_1.42.0_src_all.tar.gz"], "md5": "11b7809ea96d31a9f1bc3eb56a2650c1", "fn": "ALL_1.42.0.tar.gz"}, "allmll-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ALLMLL_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/ALLMLL_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-allmll/bioconductor-allmll_1.40.0_src_all.tar.gz"], "md5": "f4c0642007ed854280b06339d989d94f", "fn": "ALLMLL_1.40.0.tar.gz"}, "alpinedata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/alpineData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/alpineData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-alpinedata/bioconductor-alpinedata_1.26.0_src_all.tar.gz"], "md5": "6883ade3b0bcab36b3d23f2bfa7ddc03", "fn": "alpineData_1.26.0.tar.gz"}, "ampaffyexample-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/AmpAffyExample_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/AmpAffyExample_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ampaffyexample/bioconductor-ampaffyexample_1.40.0_src_all.tar.gz"], "md5": "a8863d31491bb756d0f630d09c012904", "fn": "AmpAffyExample_1.40.0.tar.gz"}, "aneufinderdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/AneuFinderData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/AneuFinderData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-aneufinderdata/bioconductor-aneufinderdata_1.28.0_src_all.tar.gz"], "md5": "703ac91ee510ae00274632026f14a065", "fn": "AneuFinderData_1.28.0.tar.gz"}, "antiprofilesdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/antiProfilesData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/antiProfilesData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-antiprofilesdata/bioconductor-antiprofilesdata_1.36.0_src_all.tar.gz"], "md5": "d5eab300113940ec702cdd00de617761", "fn": "antiProfilesData_1.36.0.tar.gz"}, "aracne.networks-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/aracne.networks_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/aracne.networks_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-aracne.networks/bioconductor-aracne.networks_1.26.0_src_all.tar.gz"], "md5": "766b50311db15b7c36dffbb945277382", "fn": "aracne.networks_1.26.0.tar.gz"}, "arrmdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ARRmData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/ARRmData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-arrmdata/bioconductor-arrmdata_1.36.0_src_all.tar.gz"], "md5": "d1a4ecc042b17945f8a02625fbfa97b5", "fn": "ARRmData_1.36.0.tar.gz"}, "ashkenazimsonchr21-1.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/AshkenazimSonChr21_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/AshkenazimSonChr21_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ashkenazimsonchr21/bioconductor-ashkenazimsonchr21_1.30.0_src_all.tar.gz"], "md5": "6180e43108e29d9194ed93bc0f208124", "fn": "AshkenazimSonChr21_1.30.0.tar.gz"}, "asicsdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ASICSdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/ASICSdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-asicsdata/bioconductor-asicsdata_1.20.0_src_all.tar.gz"], "md5": "46a4e15b37bd49b3cd5693c1a900b581", "fn": "ASICSdata_1.20.0.tar.gz"}, "assessorfdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/AssessORFData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/AssessORFData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-assessorfdata/bioconductor-assessorfdata_1.18.0_src_all.tar.gz"], "md5": "d7c0f6953391e3f1f610467f14384774", "fn": "AssessORFData_1.18.0.tar.gz"}, "bcellviper-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/bcellViper_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/bcellViper_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bcellviper/bioconductor-bcellviper_1.36.0_src_all.tar.gz"], "md5": "c35a1f30610cc929acc8bfdc79af1d13", "fn": "bcellViper_1.36.0.tar.gz"}, "beadarrayexampledata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/beadarrayExampleData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/beadarrayExampleData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadarrayexampledata/bioconductor-beadarrayexampledata_1.38.0_src_all.tar.gz"], "md5": "c8607365b2ef3e8a20b33eac9ae52c51", "fn": "beadarrayExampleData_1.38.0.tar.gz"}, "beadarrayusecases-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/BeadArrayUseCases_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/BeadArrayUseCases_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadarrayusecases/bioconductor-beadarrayusecases_1.38.0_src_all.tar.gz"], "md5": "f02d0ef2902c1223d8e240b55bf77b91", "fn": "BeadArrayUseCases_1.38.0.tar.gz"}, "beadsorted.saliva.epic-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/BeadSorted.Saliva.EPIC_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/BeadSorted.Saliva.EPIC_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadsorted.saliva.epic/bioconductor-beadsorted.saliva.epic_1.8.0_src_all.tar.gz"], "md5": "c521cbcd30e56de9e00a659d9e349320", "fn": "BeadSorted.Saliva.EPIC_1.8.0.tar.gz"}, "benchmarkfdrdata2019-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/benchmarkfdrData2019_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/benchmarkfdrData2019_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-benchmarkfdrdata2019/bioconductor-benchmarkfdrdata2019_1.14.0_src_all.tar.gz"], "md5": "b50a599a3c8ca8b276400e6dc523b894", "fn": "benchmarkfdrData2019_1.14.0.tar.gz"}, "beta7-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/beta7_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/beta7_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beta7/bioconductor-beta7_1.38.0_src_all.tar.gz"], "md5": "0049331687b2d8ce06153507e09a4a03", "fn": "beta7_1.38.0.tar.gz"}, "bioimagedbs-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/BioImageDbs_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/BioImageDbs_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bioimagedbs/bioconductor-bioimagedbs_1.8.0_src_all.tar.gz"], "md5": "b8af4040411218fcfd81ab927747eb48", "fn": "BioImageDbs_1.8.0.tar.gz"}, "bioplex-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/BioPlex_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/BioPlex_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bioplex/bioconductor-bioplex_1.6.0_src_all.tar.gz"], "md5": "7a387711025f30513f09cf397c759e81", "fn": "BioPlex_1.6.0.tar.gz"}, "biotmledata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/biotmleData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/biotmleData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biotmledata/bioconductor-biotmledata_1.24.0_src_all.tar.gz"], "md5": "e21b4d8009abb77c03a67a9115c289dc", "fn": "biotmleData_1.24.0.tar.gz"}, "biscuiteerdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/biscuiteerData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/biscuiteerData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biscuiteerdata/bioconductor-biscuiteerdata_1.14.0_src_all.tar.gz"], "md5": "fc7a9731d1d9863636d0084602d8b22f", "fn": "biscuiteerData_1.14.0.tar.gz"}, "bladderbatch-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/bladderbatch_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/bladderbatch_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bladderbatch/bioconductor-bladderbatch_1.38.0_src_all.tar.gz"], "md5": "ab4457a6eebb75202730d4433d4aa245", "fn": "bladderbatch_1.38.0.tar.gz"}, "blimatestingdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/blimaTestingData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/blimaTestingData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-blimatestingdata/bioconductor-blimatestingdata_1.20.0_src_all.tar.gz"], "md5": "17e9a4119b1beaf61f30fbe192b9a20a", "fn": "blimaTestingData_1.20.0.tar.gz"}, "bloodcancermultiomics2017-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/BloodCancerMultiOmics2017_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/BloodCancerMultiOmics2017_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bloodcancermultiomics2017/bioconductor-bloodcancermultiomics2017_1.20.0_src_all.tar.gz"], "md5": "5d7ccf32b2249044c2b86aa4cf933372", "fn": "BloodCancerMultiOmics2017_1.20.0.tar.gz"}, "bodymaprat-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/bodymapRat_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/bodymapRat_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bodymaprat/bioconductor-bodymaprat_1.16.0_src_all.tar.gz"], "md5": "d15dd35c8ce1db80954afb9e4663fe29", "fn": "bodymapRat_1.16.0.tar.gz"}, "breakpointrdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/breakpointRdata_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/breakpointRdata_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breakpointrdata/bioconductor-breakpointrdata_1.18.0_src_all.tar.gz"], "md5": "59535154a02ede7347b6114c11292173", "fn": "breakpointRdata_1.18.0.tar.gz"}, "breastcancermainz-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/breastCancerMAINZ_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerMAINZ_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancermainz/bioconductor-breastcancermainz_1.38.0_src_all.tar.gz"], "md5": "4d906d493af2aa3a2fbf00029aa6f843", "fn": "breastCancerMAINZ_1.38.0.tar.gz"}, "breastcancernki-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/breastCancerNKI_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerNKI_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancernki/bioconductor-breastcancernki_1.38.0_src_all.tar.gz"], "md5": "61d8e072228b6bbb224793b35625d507", "fn": "breastCancerNKI_1.38.0.tar.gz"}, "breastcancertransbig-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/breastCancerTRANSBIG_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerTRANSBIG_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancertransbig/bioconductor-breastcancertransbig_1.38.0_src_all.tar.gz"], "md5": "7117b6426a4cf52736db5835ccdc4ccc", "fn": "breastCancerTRANSBIG_1.38.0.tar.gz"}, "breastcancerunt-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/breastCancerUNT_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerUNT_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancerunt/bioconductor-breastcancerunt_1.38.0_src_all.tar.gz"], "md5": "fab6de14673763f649a3cfd14fc62579", "fn": "breastCancerUNT_1.38.0.tar.gz"}, "breastcancerupp-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/breastCancerUPP_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerUPP_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancerupp/bioconductor-breastcancerupp_1.38.0_src_all.tar.gz"], "md5": "37f0587a0149e1abe5525dd7bbc76a7f", "fn": "breastCancerUPP_1.38.0.tar.gz"}, "breastcancervdx-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/breastCancerVDX_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerVDX_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancervdx/bioconductor-breastcancervdx_1.38.0_src_all.tar.gz"], "md5": "a20c1e1a3060af883ced8843600a1614", "fn": "breastCancerVDX_1.38.0.tar.gz"}, "brgedata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/brgedata_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/brgedata_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-brgedata/bioconductor-brgedata_1.22.0_src_all.tar.gz"], "md5": "5b448f1cfae2bb44babb2b1720d12234", "fn": "brgedata_1.22.0.tar.gz"}, "bronchialil13-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/bronchialIL13_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/bronchialIL13_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bronchialil13/bioconductor-bronchialil13_1.38.0_src_all.tar.gz"], "md5": "71116894de06b0faf014ae3be0f54b36", "fn": "bronchialIL13_1.38.0.tar.gz"}, "bsseqdata-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/bsseqData_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/bsseqData_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsseqdata/bioconductor-bsseqdata_0.38.0_src_all.tar.gz"], "md5": "aeca7a29ea03b49344cf7cc223389537", "fn": "bsseqData_0.38.0.tar.gz"}, "cancerdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/cancerdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/cancerdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cancerdata/bioconductor-cancerdata_1.38.0_src_all.tar.gz"], "md5": "23d4242144544786e0327a3144d8a6c6", "fn": "cancerdata_1.38.0.tar.gz"}, "cardinalworkflows-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CardinalWorkflows_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/CardinalWorkflows_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cardinalworkflows/bioconductor-cardinalworkflows_1.32.0_src_all.tar.gz"], "md5": "8a8b9945c7f7b5287510917c6bc1e1a4", "fn": "CardinalWorkflows_1.32.0.tar.gz"}, "ccdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ccdata_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/ccdata_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ccdata/bioconductor-ccdata_1.26.0_src_all.tar.gz"], "md5": "d21508b620d5328d66111ed0250bcaa8", "fn": "ccdata_1.26.0.tar.gz"}, "ccl4-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CCl4_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/CCl4_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ccl4/bioconductor-ccl4_1.38.0_src_all.tar.gz"], "md5": "a0bfca2abdda039b9376e9cc8ec71333", "fn": "CCl4_1.38.0.tar.gz"}, "cctutorial-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ccTutorial_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ccTutorial_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cctutorial/bioconductor-cctutorial_1.38.0_src_all.tar.gz"], "md5": "6515deef368eb06b2f0aabaa069b3f63", "fn": "ccTutorial_1.38.0.tar.gz"}, "celarefdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/celarefData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/celarefData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celarefdata/bioconductor-celarefdata_1.18.0_src_all.tar.gz"], "md5": "eb23383ea6cb3e84ef6c66f0617cc69e", "fn": "celarefData_1.18.0.tar.gz"}, "celldex-1.10.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/celldex_1.10.1.tar.gz", "https://bioarchive.galaxyproject.org/celldex_1.10.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celldex/bioconductor-celldex_1.10.1_src_all.tar.gz"], "md5": "fef4f15bc2e0a7427627cf1cd7d505dc", "fn": "celldex_1.10.1.tar.gz"}, "cellmapperdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CellMapperData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/CellMapperData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cellmapperdata/bioconductor-cellmapperdata_1.26.0_src_all.tar.gz"], "md5": "b9d311ad83cec787788c967e93cb290b", "fn": "CellMapperData_1.26.0.tar.gz"}, "champdata-2.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ChAMPdata_2.32.0.tar.gz", "https://bioarchive.galaxyproject.org/ChAMPdata_2.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-champdata/bioconductor-champdata_2.32.0_src_all.tar.gz"], "md5": "cf36209a25e3dbc4c8098a3fcb3327df", "fn": "ChAMPdata_2.32.0.tar.gz"}, "chic.data-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ChIC.data_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIC.data_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chic.data/bioconductor-chic.data_1.20.0_src_all.tar.gz"], "md5": "c846395a170d9e1601f20f2250b5b3e2", "fn": "ChIC.data_1.20.0.tar.gz"}, "chimphumanbraindata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ChimpHumanBrainData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ChimpHumanBrainData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chimphumanbraindata/bioconductor-chimphumanbraindata_1.38.0_src_all.tar.gz"], "md5": "4c8b24136adf4492905f31e148674a5e", "fn": "ChimpHumanBrainData_1.38.0.tar.gz"}, "chipenrich.data-2.24.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/chipenrich.data_2.24.0.tar.gz", "https://bioarchive.galaxyproject.org/chipenrich.data_2.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipenrich.data/bioconductor-chipenrich.data_2.24.0_src_all.tar.gz"], "md5": "4d9f38a90b43fad02b6448ecfbd36f2d", "fn": "chipenrich.data_2.24.0.tar.gz"}, "chipexoqualexample-1.24.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ChIPexoQualExample_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIPexoQualExample_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipexoqualexample/bioconductor-chipexoqualexample_1.24.0_src_all.tar.gz"], "md5": "b8a88d767a542955c8dfa93a67c843de", "fn": "ChIPexoQualExample_1.24.0.tar.gz"}, "chipseqdbdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/chipseqDBData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/chipseqDBData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipseqdbdata/bioconductor-chipseqdbdata_1.16.0_src_all.tar.gz"], "md5": "9417adbf6ebe305a0caf0d0eba440cac", "fn": "chipseqDBData_1.16.0.tar.gz"}, "chipxpressdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ChIPXpressData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIPXpressData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipxpressdata/bioconductor-chipxpressdata_1.38.0_src_all.tar.gz"], "md5": "d764e5abb6fadab9aa4184222665fd25", "fn": "ChIPXpressData_1.38.0.tar.gz"}, "chromstardata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/chromstaRData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/chromstaRData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chromstardata/bioconductor-chromstardata_1.26.0_src_all.tar.gz"], "md5": "316680e584e9e31c3000a87e666fda3b", "fn": "chromstaRData_1.26.0.tar.gz"}, "cll-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CLL_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/CLL_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cll/bioconductor-cll_1.40.0_src_all.tar.gz"], "md5": "af6541d53d8bb71eb10e661c0a6efde0", "fn": "CLL_1.40.0.tar.gz"}, "cllmethylation-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CLLmethylation_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/CLLmethylation_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cllmethylation/bioconductor-cllmethylation_1.20.0_src_all.tar.gz"], "md5": "e3304bdcdaa207660d51a29e1ad2a4c6", "fn": "CLLmethylation_1.20.0.tar.gz"}, "clumsiddata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CluMSIDdata_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/CluMSIDdata_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clumsiddata/bioconductor-clumsiddata_1.16.0_src_all.tar.gz"], "md5": "8f97c24b60d106fe1285496ace8fad79", "fn": "CluMSIDdata_1.16.0.tar.gz"}, "clustifyrdatahub-1.10.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/clustifyrdatahub_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/clustifyrdatahub_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clustifyrdatahub/bioconductor-clustifyrdatahub_1.10.0_src_all.tar.gz"], "md5": "d1345a885c1b770cd461cf3c69451b39", "fn": "clustifyrdatahub_1.10.0.tar.gz"}, "cmap2data-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/cMap2data_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/cMap2data_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cmap2data/bioconductor-cmap2data_1.36.0_src_all.tar.gz"], "md5": "dd007c68b5fd75539c62081497ab1ee5", "fn": "cMap2data_1.36.0.tar.gz"}, "cnvgsadata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/cnvGSAdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/cnvGSAdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cnvgsadata/bioconductor-cnvgsadata_1.36.0_src_all.tar.gz"], "md5": "706bef72dd4c818adc1295a3f93bd2cf", "fn": "cnvGSAdata_1.36.0.tar.gz"}, "cohcapanno-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/COHCAPanno_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/COHCAPanno_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cohcapanno/bioconductor-cohcapanno_1.36.0_src_all.tar.gz"], "md5": "d95f164282852d44cc982e461157b622", "fn": "COHCAPanno_1.36.0.tar.gz"}, "colonca-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/colonCA_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/colonCA_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-colonca/bioconductor-colonca_1.42.0_src_all.tar.gz"], "md5": "88a73e6339cf99f42858ddcb073c4e61", "fn": "colonCA_1.42.0.tar.gz"}, "confessdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CONFESSdata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/CONFESSdata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-confessdata/bioconductor-confessdata_1.28.0_src_all.tar.gz"], "md5": "dde8faa711c55ae0abd4a0b9f8132233", "fn": "CONFESSdata_1.28.0.tar.gz"}, "connectivitymap-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ConnectivityMap_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/ConnectivityMap_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-connectivitymap/bioconductor-connectivitymap_1.36.0_src_all.tar.gz"], "md5": "0c98c66f64c50f8ae262bccdd4cd0bae", "fn": "ConnectivityMap_1.36.0.tar.gz"}, "copdsexualdimorphism.data-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/COPDSexualDimorphism.data_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/COPDSexualDimorphism.data_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copdsexualdimorphism.data/bioconductor-copdsexualdimorphism.data_1.36.0_src_all.tar.gz"], "md5": "9ae2601608f8b3f711b73d24734e7d7c", "fn": "COPDSexualDimorphism.data_1.36.0.tar.gz"}, "copyhelper-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CopyhelpeR_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/CopyhelpeR_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copyhelper/bioconductor-copyhelper_1.32.0_src_all.tar.gz"], "md5": "c38e2379228446d4d94e5ced48633a54", "fn": "CopyhelpeR_1.32.0.tar.gz"}, "copyneutralima-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CopyNeutralIMA_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/CopyNeutralIMA_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copyneutralima/bioconductor-copyneutralima_1.18.0_src_all.tar.gz"], "md5": "8707f36701c11a45e25e92a63cb81f20", "fn": "CopyNeutralIMA_1.18.0.tar.gz"}, "cosiadata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CoSIAdata_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/CoSIAdata_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cosiadata/bioconductor-cosiadata_1.0.0_src_all.tar.gz"], "md5": "5a1d517d2c097ad8abf9c8298f4ab46d", "fn": "CoSIAdata_1.0.0.tar.gz"}, "cosmic.67-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/COSMIC.67_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/COSMIC.67_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cosmic.67/bioconductor-cosmic.67_1.36.0_src_all.tar.gz"], "md5": "f5242999a8b93e384ab8c05a2950ccde", "fn": "COSMIC.67_1.36.0.tar.gz"}, "crcl18-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/CRCL18_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/CRCL18_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-crcl18/bioconductor-crcl18_1.20.0_src_all.tar.gz"], "md5": "df8b3bf91d7c7ac39d0fee78b65c1da0", "fn": "CRCL18_1.20.0.tar.gz"}, "crisprscoredata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/crisprScoreData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/crisprScoreData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-crisprscoredata/bioconductor-crisprscoredata_1.4.0_src_all.tar.gz"], "md5": "feb17485db66f6e86d92b42af3731f4a", "fn": "crisprScoreData_1.4.0.tar.gz"}, "curatedadipoarray-1.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedAdipoArray_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoArray_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadipoarray/bioconductor-curatedadipoarray_1.12.0_src_all.tar.gz"], "md5": "84600c36847d6fff69d646f1ff65dcbd", "fn": "curatedAdipoArray_1.12.0.tar.gz"}, "curatedadipochip-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedAdipoChIP_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoChIP_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadipochip/bioconductor-curatedadipochip_1.16.0_src_all.tar.gz"], "md5": "9c5ffe38c97500d4fadfdd2c6af165b4", "fn": "curatedAdipoChIP_1.16.0.tar.gz"}, "curatedadiporna-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedAdipoRNA_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoRNA_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadiporna/bioconductor-curatedadiporna_1.16.0_src_all.tar.gz"], "md5": "81535f56828fc6043a8461b0f9e09ca7", "fn": "curatedAdipoRNA_1.16.0.tar.gz"}, "curatedbladderdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedBladderData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedBladderData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedbladderdata/bioconductor-curatedbladderdata_1.36.0_src_all.tar.gz"], "md5": "7db958b1758a3b7bc3f2b552962ed51a", "fn": "curatedBladderData_1.36.0.tar.gz"}, "curatedbreastdata-2.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedBreastData_2.28.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedBreastData_2.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedbreastdata/bioconductor-curatedbreastdata_2.28.0_src_all.tar.gz"], "md5": "8e53cc4c883e3b3c94842727f34ad6a6", "fn": "curatedBreastData_2.28.0.tar.gz"}, "curatedcrcdata-2.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedCRCData_2.32.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedCRCData_2.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedcrcdata/bioconductor-curatedcrcdata_2.32.0_src_all.tar.gz"], "md5": "c88686b133a9f30f4904dc4e706ef5c8", "fn": "curatedCRCData_2.32.0.tar.gz"}, "curatedmetagenomicdata-3.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedMetagenomicData_3.8.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedMetagenomicData_3.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedmetagenomicdata/bioconductor-curatedmetagenomicdata_3.8.0_src_all.tar.gz"], "md5": "f24faacda7b263f1bcde098dbffa5f8f", "fn": "curatedMetagenomicData_3.8.0.tar.gz"}, "curatedovariandata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedOvarianData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedOvarianData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedovariandata/bioconductor-curatedovariandata_1.38.0_src_all.tar.gz"], "md5": "0cbda3a714637304ffcc38aa91588c86", "fn": "curatedOvarianData_1.38.0.tar.gz"}, "curatedtbdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedTBData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedTBData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedtbdata/bioconductor-curatedtbdata_1.6.0_src_all.tar.gz"], "md5": "d09277f807e04495c582052e25930d02", "fn": "curatedTBData_1.6.0.tar.gz"}, "curatedtcgadata-1.22.2": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/curatedTCGAData_1.22.2.tar.gz", "https://bioarchive.galaxyproject.org/curatedTCGAData_1.22.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedtcgadata/bioconductor-curatedtcgadata_1.22.2_src_all.tar.gz"], "md5": "066107da416bfad28b75ee3488dbdad0", "fn": "curatedTCGAData_1.22.2.tar.gz"}, "dapardata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DAPARdata_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/DAPARdata_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dapardata/bioconductor-dapardata_1.30.0_src_all.tar.gz"], "md5": "4d730f1b7ef4aab628882f7b9355c7b5", "fn": "DAPARdata_1.30.0.tar.gz"}, "davidtiling-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/davidTiling_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/davidTiling_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-davidtiling/bioconductor-davidtiling_1.40.0_src_all.tar.gz"], "md5": "aa55aaed3cb0a0e29db8c538c636b447", "fn": "davidTiling_1.40.0.tar.gz"}, "depmap-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/depmap_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/depmap_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-depmap/bioconductor-depmap_1.14.0_src_all.tar.gz"], "md5": "d4405c4714a46efd721be9905eddc21f", "fn": "depmap_1.14.0.tar.gz"}, "derfinderdata-2.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/derfinderData_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/derfinderData_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-derfinderdata/bioconductor-derfinderdata_2.18.0_src_all.tar.gz"], "md5": "a7787e049bcee25cb354773f1fd2cf27", "fn": "derfinderData_2.18.0.tar.gz"}, "desousa2013-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DeSousa2013_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/DeSousa2013_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-desousa2013/bioconductor-desousa2013_1.36.0_src_all.tar.gz"], "md5": "1a12b8cbbcf6b3ccc758dacd1ef01852", "fn": "DeSousa2013_1.36.0.tar.gz"}, "dexmadata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DExMAdata_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/DExMAdata_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dexmadata/bioconductor-dexmadata_1.8.0_src_all.tar.gz"], "md5": "bc2fd62dd24eeaee294a624610b75918", "fn": "DExMAdata_1.8.0.tar.gz"}, "diffloopdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/diffloopdata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/diffloopdata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-diffloopdata/bioconductor-diffloopdata_1.28.0_src_all.tar.gz"], "md5": "8e004a82f024eb82c188415e8ca65563", "fn": "diffloopdata_1.28.0.tar.gz"}, "diggitdata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/diggitdata_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/diggitdata_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-diggitdata/bioconductor-diggitdata_1.32.0_src_all.tar.gz"], "md5": "d68dbde08e8d4b936a15a73a23a48830", "fn": "diggitdata_1.32.0.tar.gz"}, "dlbcl-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DLBCL_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/DLBCL_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dlbcl/bioconductor-dlbcl_1.40.0_src_all.tar.gz"], "md5": "f22495affaad1066fbe54791486ebd53", "fn": "DLBCL_1.40.0.tar.gz"}, "dmelsgi-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DmelSGI_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/DmelSGI_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dmelsgi/bioconductor-dmelsgi_1.32.0_src_all.tar.gz"], "md5": "611e89ab1359a4e0283b61e75205878f", "fn": "DmelSGI_1.32.0.tar.gz"}, "dmrcatedata-2.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DMRcatedata_2.18.0.tar.gz", "https://bioarchive.galaxyproject.org/DMRcatedata_2.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dmrcatedata/bioconductor-dmrcatedata_2.18.0_src_all.tar.gz"], "md5": "c2d0addb7984dadb9a3c0012dcd8c719", "fn": "DMRcatedata_2.18.0.tar.gz"}, "dnazoodata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DNAZooData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/DNAZooData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dnazoodata/bioconductor-dnazoodata_1.0.0_src_all.tar.gz"], "md5": "76d7687720d175ca13a1057c22b68b1e", "fn": "DNAZooData_1.0.0.tar.gz"}, "donapllp2013-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DonaPLLP2013_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/DonaPLLP2013_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-donapllp2013/bioconductor-donapllp2013_1.38.0_src_all.tar.gz"], "md5": "1ef96235e9049d31e27f5e5fff17d1ec", "fn": "DonaPLLP2013_1.38.0.tar.gz"}, "dorothea-1.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/dorothea_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/dorothea_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dorothea/bioconductor-dorothea_1.12.0_src_all.tar.gz"], "md5": "068a6de9744d9d5c7085dfe910968e17", "fn": "dorothea_1.12.0.tar.gz"}, "dresscheck-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/dressCheck_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/dressCheck_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dresscheck/bioconductor-dresscheck_0.38.0_src_all.tar.gz"], "md5": "27fc1d1485335601b86ab54b8380f1dc", "fn": "dressCheck_0.38.0.tar.gz"}, "droplettestfiles-1.10.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DropletTestFiles_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/DropletTestFiles_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-droplettestfiles/bioconductor-droplettestfiles_1.10.0_src_all.tar.gz"], "md5": "addd41a9a235a4216b4c7067879203d6", "fn": "DropletTestFiles_1.10.0.tar.gz"}, "drugvsdiseasedata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DrugVsDiseasedata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/DrugVsDiseasedata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drugvsdiseasedata/bioconductor-drugvsdiseasedata_1.36.0_src_all.tar.gz"], "md5": "64c011debe7f2f876d073b7383502db0", "fn": "DrugVsDiseasedata_1.36.0.tar.gz"}, "duoclustering2018-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DuoClustering2018_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/DuoClustering2018_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-duoclustering2018/bioconductor-duoclustering2018_1.18.0_src_all.tar.gz"], "md5": "697a0b8aecfb07cb6034d7626001f262", "fn": "DuoClustering2018_1.18.0.tar.gz"}, "dvddata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/DvDdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/DvDdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dvddata/bioconductor-dvddata_1.36.0_src_all.tar.gz"], "md5": "c21d1ca3b1808272b1d90004201512b2", "fn": "DvDdata_1.36.0.tar.gz"}, "dyebiasexamples-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/dyebiasexamples_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/dyebiasexamples_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dyebiasexamples/bioconductor-dyebiasexamples_1.40.0_src_all.tar.gz"], "md5": "8ba42215153001f0334b098938eacf9c", "fn": "dyebiasexamples_1.40.0.tar.gz"}, "easierdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/easierData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/easierData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-easierdata/bioconductor-easierdata_1.6.0_src_all.tar.gz"], "md5": "c8cdf9119aa80107e2d8d6853c2a6fde", "fn": "easierData_1.6.0.tar.gz"}, "eatonetalchipseq-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/EatonEtAlChIPseq_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/EatonEtAlChIPseq_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-eatonetalchipseq/bioconductor-eatonetalchipseq_0.38.0_src_all.tar.gz"], "md5": "fa5225647fa5b852a38635bb2ba759ef", "fn": "EatonEtAlChIPseq_0.38.0.tar.gz"}, "ecolileucine-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ecoliLeucine_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliLeucine_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolileucine/bioconductor-ecolileucine_1.40.0_src_all.tar.gz"], "md5": "8f29571bdbf113fe17eb2a91638acf1a", "fn": "ecoliLeucine_1.40.0.tar.gz"}, "egseadata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/EGSEAdata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/EGSEAdata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-egseadata/bioconductor-egseadata_1.28.0_src_all.tar.gz"], "md5": "1ccaaafd4866fa1cf07e06b6370739a3", "fn": "EGSEAdata_1.28.0.tar.gz"}, "elmer.data-2.24.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ELMER.data_2.24.0.tar.gz", "https://bioarchive.galaxyproject.org/ELMER.data_2.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-elmer.data/bioconductor-elmer.data_2.24.0_src_all.tar.gz"], "md5": "4bb614a1bd1fd96f91af883bad29c914", "fn": "ELMER.data_2.24.0.tar.gz"}, "emtdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/emtdata_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/emtdata_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-emtdata/bioconductor-emtdata_1.8.0_src_all.tar.gz"], "md5": "e4c17e43c1d50287179f7fb2f594d6c3", "fn": "emtdata_1.8.0.tar.gz"}, "epimix.data-1.2.2": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/EpiMix.data_1.2.2.tar.gz", "https://bioarchive.galaxyproject.org/EpiMix.data_1.2.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epimix.data/bioconductor-epimix.data_1.2.2_src_all.tar.gz"], "md5": "3234766b0bc549ab200604206a9ba5b8", "fn": "EpiMix.data_1.2.2.tar.gz"}, "epimutacionsdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/epimutacionsData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/epimutacionsData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epimutacionsdata/bioconductor-epimutacionsdata_1.4.0_src_all.tar.gz"], "md5": "162b5aaa6a5f6df2528dce4285efdea4", "fn": "epimutacionsData_1.4.0.tar.gz"}, "estrogen-1.46.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/estrogen_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/estrogen_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-estrogen/bioconductor-estrogen_1.46.0_src_all.tar.gz"], "md5": "c7f687b7e46c1e224e9008143926f12e", "fn": "estrogen_1.46.0.tar.gz"}, "etec16s-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/etec16s_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/etec16s_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-etec16s/bioconductor-etec16s_1.28.0_src_all.tar.gz"], "md5": "b2540d5e5287458a7fbec76b5656d3c6", "fn": "etec16s_1.28.0.tar.gz"}, "ewcedata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ewceData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ewceData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ewcedata/bioconductor-ewcedata_1.8.0_src_all.tar.gz"], "md5": "3107bac6cd0fb07a4cba3ad59cabb665", "fn": "ewceData_1.8.0.tar.gz"}, "faahko-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/faahKO_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/faahKO_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-faahko/bioconductor-faahko_1.40.0_src_all.tar.gz"], "md5": "29697c16b4e90b21fd8515dfdfea7fde", "fn": "faahKO_1.40.0.tar.gz"}, "fabiadata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/fabiaData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/fabiaData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fabiadata/bioconductor-fabiadata_1.38.0_src_all.tar.gz"], "md5": "970fc1894222fe7eac67b8c94d9a2eab", "fn": "fabiaData_1.38.0.tar.gz"}, "fantom3and4cage-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/FANTOM3and4CAGE_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/FANTOM3and4CAGE_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fantom3and4cage/bioconductor-fantom3and4cage_1.36.0_src_all.tar.gz"], "md5": "049d0b3978f16771bd7e48aa80e8fb93", "fn": "FANTOM3and4CAGE_1.36.0.tar.gz"}, "ffpeexampledata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ffpeExampleData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ffpeExampleData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ffpeexampledata/bioconductor-ffpeexampledata_1.38.0_src_all.tar.gz"], "md5": "f5b4c1bcd2467b0b82973b2e70243ef0", "fn": "ffpeExampleData_1.38.0.tar.gz"}, "fibroeset-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/fibroEset_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/fibroEset_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fibroeset/bioconductor-fibroeset_1.42.0_src_all.tar.gz"], "md5": "42efffdc75032b3305ebdceb55f3754f", "fn": "fibroEset_1.42.0.tar.gz"}, "fieldeffectcrc-1.10.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/FieldEffectCrc_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/FieldEffectCrc_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fieldeffectcrc/bioconductor-fieldeffectcrc_1.10.0_src_all.tar.gz"], "md5": "b20c0c45eec814e077d124b45d6589a6", "fn": "FieldEffectCrc_1.10.0.tar.gz"}, "fis-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/FIs_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/FIs_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fis/bioconductor-fis_1.28.0_src_all.tar.gz"], "md5": "6a79abe38c53faa7176cd1dc4189351b", "fn": "FIs_1.28.0.tar.gz"}, "fission-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/fission_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/fission_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fission/bioconductor-fission_1.20.0_src_all.tar.gz"], "md5": "bf744d1be1f95417b4379e55aadfcef3", "fn": "fission_1.20.0.tar.gz"}, "fletcher2013a-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Fletcher2013a_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/Fletcher2013a_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fletcher2013a/bioconductor-fletcher2013a_1.36.0_src_all.tar.gz"], "md5": "69ea86d2f1e6aa8e8716c4db65f81cf0", "fn": "Fletcher2013a_1.36.0.tar.gz"}, "fletcher2013b-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Fletcher2013b_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/Fletcher2013b_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fletcher2013b/bioconductor-fletcher2013b_1.36.0_src_all.tar.gz"], "md5": "fd7177b33cc525534e80c197f4a14b0b", "fn": "Fletcher2013b_1.36.0.tar.gz"}, "flowploidydata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/flowPloidyData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/flowPloidyData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowploidydata/bioconductor-flowploidydata_1.26.0_src_all.tar.gz"], "md5": "10d8e5d5d636d7a78c7dd5aa79ba41a4", "fn": "flowPloidyData_1.26.0.tar.gz"}, "flowsorted.blood.450k-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/FlowSorted.Blood.450k_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.Blood.450k_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.450k/bioconductor-flowsorted.blood.450k_1.38.0_src_all.tar.gz"], "md5": "68977c1bf508dda29bc067929aecc006", "fn": "FlowSorted.Blood.450k_1.38.0.tar.gz"}, "flowsorted.blood.epic-2.4.2": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/FlowSorted.Blood.EPIC_2.4.2.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.Blood.EPIC_2.4.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.epic/bioconductor-flowsorted.blood.epic_2.4.2_src_all.tar.gz"], "md5": "4d9d98db39792aac4fe1ec1db0b0366b", "fn": "FlowSorted.Blood.EPIC_2.4.2.tar.gz"}, "flowsorted.cordblood.450k-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/FlowSorted.CordBlood.450k_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBlood.450k_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordblood.450k/bioconductor-flowsorted.cordblood.450k_1.28.0_src_all.tar.gz"], "md5": "dbef432e31c78c82fe4498a341d3a5a8", "fn": "FlowSorted.CordBlood.450k_1.28.0.tar.gz"}, "flowsorted.cordbloodcombined.450k-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/FlowSorted.CordBloodCombined.450k_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodCombined.450k_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodcombined.450k/bioconductor-flowsorted.cordbloodcombined.450k_1.16.0_src_all.tar.gz"], "md5": "0579c0d8bcb50c77d579b082a7bf4158", "fn": "FlowSorted.CordBloodCombined.450k_1.16.0.tar.gz"}, "flowsorted.cordbloodnorway.450k-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/FlowSorted.CordBloodNorway.450k_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodNorway.450k_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodnorway.450k/bioconductor-flowsorted.cordbloodnorway.450k_1.26.0_src_all.tar.gz"], "md5": "5a399952bf229258fe47964a8d3db910", "fn": "FlowSorted.CordBloodNorway.450k_1.26.0.tar.gz"}, "flowsorted.dlpfc.450k-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/FlowSorted.DLPFC.450k_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.DLPFC.450k_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.dlpfc.450k/bioconductor-flowsorted.dlpfc.450k_1.36.0_src_all.tar.gz"], "md5": "fb70a712a95eaa879d62d7751567aed5", "fn": "FlowSorted.DLPFC.450k_1.36.0.tar.gz"}, "flowworkspacedata-3.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/flowWorkspaceData_3.12.0.tar.gz", "https://bioarchive.galaxyproject.org/flowWorkspaceData_3.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowworkspacedata/bioconductor-flowworkspacedata_3.12.0_src_all.tar.gz"], "md5": "8d91993dd5a5c5b561a8063ec91046d3", "fn": "flowWorkspaceData_3.12.0.tar.gz"}, "fourdndata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/fourDNData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/fourDNData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fourdndata/bioconductor-fourdndata_1.0.0_src_all.tar.gz"], "md5": "2bea3be8c2abed679fc99cf6bdaee98f", "fn": "fourDNData_1.0.0.tar.gz"}, "frmaexampledata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/frmaExampleData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/frmaExampleData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-frmaexampledata/bioconductor-frmaexampledata_1.36.0_src_all.tar.gz"], "md5": "057a53ead8fde2bab4ee0cb71a4faaf6", "fn": "frmaExampleData_1.36.0.tar.gz"}, "furrowseg-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/furrowSeg_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/furrowSeg_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-furrowseg/bioconductor-furrowseg_1.28.0_src_all.tar.gz"], "md5": "6ee1d6bc3d7fe7c1855a6b96b429190b", "fn": "furrowSeg_1.28.0.tar.gz"}, "gagedata-2.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/gageData_2.38.0.tar.gz", "https://bioarchive.galaxyproject.org/gageData_2.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gagedata/bioconductor-gagedata_2.38.0_src_all.tar.gz"], "md5": "04f7869c72f70f6726372af0a4688d5d", "fn": "gageData_2.38.0.tar.gz"}, "gaschyhs-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/gaschYHS_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/gaschYHS_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gaschyhs/bioconductor-gaschyhs_1.38.0_src_all.tar.gz"], "md5": "adb36d86b4890c4f4c714d99aa3b3f93", "fn": "gaschYHS_1.38.0.tar.gz"}, "gcspikelite-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/gcspikelite_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/gcspikelite_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gcspikelite/bioconductor-gcspikelite_1.38.0_src_all.tar.gz"], "md5": "721566ac21590bc7f1e56dd1c716d30c", "fn": "gcspikelite_1.38.0.tar.gz"}, "gdnainrnaseqdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/gDNAinRNAseqData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/gDNAinRNAseqData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gdnainrnaseqdata/bioconductor-gdnainrnaseqdata_1.0.0_src_all.tar.gz"], "md5": "de757712c6890eb225ad26790e2a23f6", "fn": "gDNAinRNAseqData_1.0.0.tar.gz"}, "genelendatabase-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/geneLenDataBase_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/geneLenDataBase_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genelendatabase/bioconductor-genelendatabase_1.36.0_src_all.tar.gz"], "md5": "3063a75a94ecd65185c3490a1baba601", "fn": "geneLenDataBase_1.36.0.tar.gz"}, "genomationdata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/genomationData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/genomationData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomationdata/bioconductor-genomationdata_1.32.0_src_all.tar.gz"], "md5": "4954915523744efa6d6b3be3feb376eb", "fn": "genomationData_1.32.0.tar.gz"}, "genomicdistributionsdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GenomicDistributionsData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/GenomicDistributionsData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomicdistributionsdata/bioconductor-genomicdistributionsdata_1.8.0_src_all.tar.gz"], "md5": "55e98f9b1fe5ee9ab222a5aa3866943a", "fn": "GenomicDistributionsData_1.8.0.tar.gz"}, "geuvadistranscriptexpr-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GeuvadisTranscriptExpr_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/GeuvadisTranscriptExpr_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-geuvadistranscriptexpr/bioconductor-geuvadistranscriptexpr_1.28.0_src_all.tar.gz"], "md5": "5a37aba63d441f86e2b9eb68f34b92f0", "fn": "GeuvadisTranscriptExpr_1.28.0.tar.gz"}, "gigseadata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GIGSEAdata_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/GIGSEAdata_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gigseadata/bioconductor-gigseadata_1.18.0_src_all.tar.gz"], "md5": "ad905645333890eafd314cdac44f793a", "fn": "GIGSEAdata_1.18.0.tar.gz"}, "golubesets-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/golubEsets_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/golubEsets_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-golubesets/bioconductor-golubesets_1.42.0_src_all.tar.gz"], "md5": "ec7f4855c5a77d3ea3503a1102910a0c", "fn": "golubEsets_1.42.0.tar.gz"}, "gpaexample-1.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/gpaExample_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/gpaExample_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gpaexample/bioconductor-gpaexample_1.12.0_src_all.tar.gz"], "md5": "e5cd543667831a4996249fcc3dee8224", "fn": "gpaExample_1.12.0.tar.gz"}, "grndata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/grndata_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/grndata_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-grndata/bioconductor-grndata_1.32.0_src_all.tar.gz"], "md5": "e105a77f883593cbe67ddbdbe5ad91e3", "fn": "grndata_1.32.0.tar.gz"}, "gsbenchmark-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GSBenchMark_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/GSBenchMark_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gsbenchmark/bioconductor-gsbenchmark_1.20.0_src_all.tar.gz"], "md5": "67ad80e0d9aca2b2403031b8f5d79f57", "fn": "GSBenchMark_1.20.0.tar.gz"}, "gse103322-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GSE103322_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE103322_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse103322/bioconductor-gse103322_1.6.0_src_all.tar.gz"], "md5": "5f0ae42096e6851fc40f3c45831d38c7", "fn": "GSE103322_1.6.0.tar.gz"}, "gse13015-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GSE13015_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE13015_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse13015/bioconductor-gse13015_1.8.0_src_all.tar.gz"], "md5": "749148d0e8ddb719e43d6513e340e8b6", "fn": "GSE13015_1.8.0.tar.gz"}, "gse159526-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GSE159526_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE159526_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse159526/bioconductor-gse159526_1.6.0_src_all.tar.gz"], "md5": "930aac8c4e8b481b62e489d6e5d94487", "fn": "GSE159526_1.6.0.tar.gz"}, "gse62944-1.28.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GSE62944_1.28.1.tar.gz", "https://bioarchive.galaxyproject.org/GSE62944_1.28.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse62944/bioconductor-gse62944_1.28.1_src_all.tar.gz"], "md5": "8759202f2247d2a60d0bb17acfffad6a", "fn": "GSE62944_1.28.1.tar.gz"}, "gsvadata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GSVAdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/GSVAdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gsvadata/bioconductor-gsvadata_1.36.0_src_all.tar.gz"], "md5": "745225b064d2d82499906b03543ee0ac", "fn": "GSVAdata_1.36.0.tar.gz"}, "gwasdata-1.38.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/GWASdata_1.38.1.tar.gz", "https://bioarchive.galaxyproject.org/GWASdata_1.38.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gwasdata/bioconductor-gwasdata_1.38.1_src_all.tar.gz"], "md5": "f613097e6cc22f457d1de41f8e677aa6", "fn": "GWASdata_1.38.1.tar.gz"}, "h5vcdata-2.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/h5vcData_2.20.0.tar.gz", "https://bioarchive.galaxyproject.org/h5vcData_2.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-h5vcdata/bioconductor-h5vcdata_2.20.0_src_all.tar.gz"], "md5": "e233ff9873648c459591fda6942a8790", "fn": "h5vcData_2.20.0.tar.gz"}, "hapmap100khind-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hapmap100khind_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap100khind_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap100khind/bioconductor-hapmap100khind_1.42.0_src_all.tar.gz"], "md5": "ec3213b4ced09f678386a981176e3410", "fn": "hapmap100khind_1.42.0.tar.gz"}, "hapmap100kxba-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hapmap100kxba_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap100kxba_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap100kxba/bioconductor-hapmap100kxba_1.42.0_src_all.tar.gz"], "md5": "46a995b0ad38d46aebdf89c52678c587", "fn": "hapmap100kxba_1.42.0.tar.gz"}, "hapmap500knsp-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hapmap500knsp_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap500knsp_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap500knsp/bioconductor-hapmap500knsp_1.42.0_src_all.tar.gz"], "md5": "c54725a8ec3607d9db051ef7dfb8b16f", "fn": "hapmap500knsp_1.42.0.tar.gz"}, "hapmap500ksty-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hapmap500ksty_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap500ksty_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap500ksty/bioconductor-hapmap500ksty_1.42.0_src_all.tar.gz"], "md5": "b283985ebfd5c8eace1e5f436fb1d07c", "fn": "hapmap500ksty_1.42.0.tar.gz"}, "hapmapsnp5-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hapmapsnp5_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmapsnp5_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp5/bioconductor-hapmapsnp5_1.42.0_src_all.tar.gz"], "md5": "ccc4fe2a3fcb840365fb2b3bdec3cfd8", "fn": "hapmapsnp5_1.42.0.tar.gz"}, "hapmapsnp6-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hapmapsnp6_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmapsnp6_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp6/bioconductor-hapmapsnp6_1.42.0_src_all.tar.gz"], "md5": "a6ca8fb7d228e64ba1567d4cb7bcd81e", "fn": "hapmapsnp6_1.42.0.tar.gz"}, "harbchip-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/harbChIP_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/harbChIP_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harbchip/bioconductor-harbchip_1.38.0_src_all.tar.gz"], "md5": "5713ddec61a7771a7c8be36ced779ef1", "fn": "harbChIP_1.38.0.tar.gz"}, "harmandata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HarmanData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/HarmanData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harmandata/bioconductor-harmandata_1.28.0_src_all.tar.gz"], "md5": "43bca3e57aee5603fda4b7be1cb9c738", "fn": "HarmanData_1.28.0.tar.gz"}, "harmonizedtcgadata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HarmonizedTCGAData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/HarmonizedTCGAData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harmonizedtcgadata/bioconductor-harmonizedtcgadata_1.22.0_src_all.tar.gz"], "md5": "c615eb02dbda3204fb5f3d9308a0115c", "fn": "HarmonizedTCGAData_1.22.0.tar.gz"}, "hcadata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HCAData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/HCAData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcadata/bioconductor-hcadata_1.16.0_src_all.tar.gz"], "md5": "c8a2e18f3a29f80ba013759f6c87619e", "fn": "HCAData_1.16.0.tar.gz"}, "hd2013sgi-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HD2013SGI_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/HD2013SGI_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hd2013sgi/bioconductor-hd2013sgi_1.40.0_src_all.tar.gz"], "md5": "4cc03451c32df17e2a946ab45d32659e", "fn": "HD2013SGI_1.40.0.tar.gz"}, "hdcytodata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HDCytoData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/HDCytoData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hdcytodata/bioconductor-hdcytodata_1.20.0_src_all.tar.gz"], "md5": "0ab01564970b77ca4d62db12c07a1ed4", "fn": "HDCytoData_1.20.0.tar.gz"}, "healthycontrolspresencechecker-1.4.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/healthyControlsPresenceChecker_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/healthyControlsPresenceChecker_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-healthycontrolspresencechecker/bioconductor-healthycontrolspresencechecker_1.4.0_src_all.tar.gz"], "md5": "cc422930fe0cf3237bc707d107517381", "fn": "healthyControlsPresenceChecker_1.4.0.tar.gz"}, "healthyflowdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/healthyFlowData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/healthyFlowData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-healthyflowdata/bioconductor-healthyflowdata_1.38.0_src_all.tar.gz"], "md5": "478453f16b73527c4f1a9c5697d0b576", "fn": "healthyFlowData_1.38.0.tar.gz"}, "heebodata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HEEBOdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/HEEBOdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-heebodata/bioconductor-heebodata_1.38.0_src_all.tar.gz"], "md5": "cf931bc3409e110143d9090c8cb37c9a", "fn": "HEEBOdata_1.38.0.tar.gz"}, "hellorangesdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HelloRangesData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/HelloRangesData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hellorangesdata/bioconductor-hellorangesdata_1.26.0_src_all.tar.gz"], "md5": "34dbe70ca5ea008e5a17803388bed705", "fn": "HelloRangesData_1.26.0.tar.gz"}, "hgu133abarcodevecs-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hgu133abarcodevecs_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133abarcodevecs_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133abarcodevecs/bioconductor-hgu133abarcodevecs_1.38.0_src_all.tar.gz"], "md5": "af366465c10e3dbc799cdedab97d179d", "fn": "hgu133abarcodevecs_1.38.0.tar.gz"}, "hgu133plus2barcodevecs-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hgu133plus2barcodevecs_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2barcodevecs_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2barcodevecs/bioconductor-hgu133plus2barcodevecs_1.38.0_src_all.tar.gz"], "md5": "a30a110289e8dff08599c97adb71adb0", "fn": "hgu133plus2barcodevecs_1.38.0.tar.gz"}, "hgu133plus2cellscore-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hgu133plus2CellScore_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2CellScore_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2cellscore/bioconductor-hgu133plus2cellscore_1.20.0_src_all.tar.gz"], "md5": "348bb596918ca6f6a51d72d20003545c", "fn": "hgu133plus2CellScore_1.20.0.tar.gz"}, "hgu2beta7-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/hgu2beta7_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu2beta7_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu2beta7/bioconductor-hgu2beta7_1.40.0_src_all.tar.gz"], "md5": "2f1a9cc48f2608678e7349d6671a4949", "fn": "hgu2beta7_1.40.0.tar.gz"}, "hicdatahumanimr90-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HiCDataHumanIMR90_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/HiCDataHumanIMR90_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicdatahumanimr90/bioconductor-hicdatahumanimr90_1.20.0_src_all.tar.gz"], "md5": "8b6b0a8e4ccf7bd132a94748c2678be4", "fn": "HiCDataHumanIMR90_1.20.0.tar.gz"}, "hicdatalymphoblast-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HiCDataLymphoblast_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/HiCDataLymphoblast_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicdatalymphoblast/bioconductor-hicdatalymphoblast_1.36.0_src_all.tar.gz"], "md5": "f43877109c87896da3954f156798d19f", "fn": "HiCDataLymphoblast_1.36.0.tar.gz"}, "hicontactsdata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HiContactsData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/HiContactsData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicontactsdata/bioconductor-hicontactsdata_1.2.0_src_all.tar.gz"], "md5": "8d406482f89b932de475c12470bc8ef2", "fn": "HiContactsData_1.2.0.tar.gz"}, "highlyreplicatedrnaseq-1.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HighlyReplicatedRNASeq_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/HighlyReplicatedRNASeq_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-highlyreplicatedrnaseq/bioconductor-highlyreplicatedrnaseq_1.12.0_src_all.tar.gz"], "md5": "b5773c61f0e87d562b2c18aec8992689", "fn": "HighlyReplicatedRNASeq_1.12.0.tar.gz"}, "hiiragi2013-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Hiiragi2013_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/Hiiragi2013_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hiiragi2013/bioconductor-hiiragi2013_1.36.0_src_all.tar.gz"], "md5": "5e1b258226d9b83620113705d7328537", "fn": "Hiiragi2013_1.36.0.tar.gz"}, "hivcdnavantwout03-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HIVcDNAvantWout03_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/HIVcDNAvantWout03_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hivcdnavantwout03/bioconductor-hivcdnavantwout03_1.40.0_src_all.tar.gz"], "md5": "349ef6469ce73790078ba4b5d5206856", "fn": "HIVcDNAvantWout03_1.40.0.tar.gz"}, "hmp16sdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HMP16SData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/HMP16SData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hmp16sdata/bioconductor-hmp16sdata_1.20.0_src_all.tar.gz"], "md5": "a62c1eec817f876e015ee98ab937dfc6", "fn": "HMP16SData_1.20.0.tar.gz"}, "hmp2data-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HMP2Data_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/HMP2Data_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hmp2data/bioconductor-hmp2data_1.14.0_src_all.tar.gz"], "md5": "ff1bf8c6b78ebe9c09578c775c35a54a", "fn": "HMP2Data_1.14.0.tar.gz"}, "hsmmsinglecell-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HSMMSingleCell_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/HSMMSingleCell_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hsmmsinglecell/bioconductor-hsmmsinglecell_1.20.0_src_all.tar.gz"], "md5": "52c7427453286b6ba0f069bdf32457ac", "fn": "HSMMSingleCell_1.20.0.tar.gz"}, "humanaffydata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/HumanAffyData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/HumanAffyData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanaffydata/bioconductor-humanaffydata_1.26.0_src_all.tar.gz"], "md5": "bbb55417c9bdc12d387677c47cb8fc19", "fn": "HumanAffyData_1.26.0.tar.gz"}, "humanstemcell-0.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/humanStemCell_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/humanStemCell_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanstemcell/bioconductor-humanstemcell_0.40.0_src_all.tar.gz"], "md5": "8388d74f0e892de07e04e2e200041e6d", "fn": "humanStemCell_0.40.0.tar.gz"}, "ihwpaper-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/IHWpaper_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/IHWpaper_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ihwpaper/bioconductor-ihwpaper_1.28.0_src_all.tar.gz"], "md5": "282cb3abcd7ee2a5d1c34c468ce806c2", "fn": "IHWpaper_1.28.0.tar.gz"}, "illumina450probevariants.db-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Illumina450ProbeVariants.db_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/Illumina450ProbeVariants.db_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illumina450probevariants.db/bioconductor-illumina450probevariants.db_1.36.0_src_all.tar.gz"], "md5": "362d8731f6c9067d58742be0d772a7ac", "fn": "Illumina450ProbeVariants.db_1.36.0.tar.gz"}, "illuminadatatestfiles-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/IlluminaDataTestFiles_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaDataTestFiles_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminadatatestfiles/bioconductor-illuminadatatestfiles_1.38.0_src_all.tar.gz"], "md5": "e11e060ddd803add7efac25b34ab2ff5", "fn": "IlluminaDataTestFiles_1.38.0.tar.gz"}, "imcdatasets-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/imcdatasets_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/imcdatasets_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-imcdatasets/bioconductor-imcdatasets_1.8.0_src_all.tar.gz"], "md5": "1e0e9d5ecc4a826887de1abc773d86b3", "fn": "imcdatasets_1.8.0.tar.gz"}, "italicsdata-2.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ITALICSData_2.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ITALICSData_2.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-italicsdata/bioconductor-italicsdata_2.38.0_src_all.tar.gz"], "md5": "390829582a6ace43fc47218d8f11e3c0", "fn": "ITALICSData_2.38.0.tar.gz"}, "iyer517-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Iyer517_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/Iyer517_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-iyer517/bioconductor-iyer517_1.42.0_src_all.tar.gz"], "md5": "962d1b3895541924544fd080008a5bc9", "fn": "Iyer517_1.42.0.tar.gz"}, "jaspar2014-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/JASPAR2014_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2014_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2014/bioconductor-jaspar2014_1.36.0_src_all.tar.gz"], "md5": "63249cf2e663d3823da3359b8e584ede", "fn": "JASPAR2014_1.36.0.tar.gz"}, "jaspar2016-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/JASPAR2016_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2016_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2016/bioconductor-jaspar2016_1.28.0_src_all.tar.gz"], "md5": "9022c6f9720312b9da10800535edec62", "fn": "JASPAR2016_1.28.0.tar.gz"}, "keggandmetacoredzpathwaysgeo-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/KEGGandMetacoreDzPathwaysGEO_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/KEGGandMetacoreDzPathwaysGEO_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-keggandmetacoredzpathwaysgeo/bioconductor-keggandmetacoredzpathwaysgeo_1.20.0_src_all.tar.gz"], "md5": "7a4483556f83ea2f860efe15052eebe9", "fn": "KEGGandMetacoreDzPathwaysGEO_1.20.0.tar.gz"}, "keggdzpathwaysgeo-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/KEGGdzPathwaysGEO_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/KEGGdzPathwaysGEO_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-keggdzpathwaysgeo/bioconductor-keggdzpathwaysgeo_1.38.0_src_all.tar.gz"], "md5": "cfdb271eede41d51e01844f8c7b06b70", "fn": "KEGGdzPathwaysGEO_1.38.0.tar.gz"}, "kidpack-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/kidpack_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/kidpack_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-kidpack/bioconductor-kidpack_1.42.0_src_all.tar.gz"], "md5": "4b8ee4f61037cd1b55cee61efe7101e9", "fn": "kidpack_1.42.0.tar.gz"}, "kodata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/KOdata_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/KOdata_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-kodata/bioconductor-kodata_1.26.0_src_all.tar.gz"], "md5": "11d0727f1c7e40be104b3d24168f2ae7", "fn": "KOdata_1.26.0.tar.gz"}, "leebamviews-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/leeBamViews_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/leeBamViews_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-leebamviews/bioconductor-leebamviews_1.36.0_src_all.tar.gz"], "md5": "8364b9ac80fcc1cbdd4eca1501d6651b", "fn": "leeBamViews_1.36.0.tar.gz"}, "leukemiaseset-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/leukemiasEset_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/leukemiasEset_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-leukemiaseset/bioconductor-leukemiaseset_1.36.0_src_all.tar.gz"], "md5": "6f2498f78d93dc35ed04c9e2e8abfad7", "fn": "leukemiasEset_1.36.0.tar.gz"}, "liebermanaidenhic2009-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/LiebermanAidenHiC2009_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/LiebermanAidenHiC2009_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-liebermanaidenhic2009/bioconductor-liebermanaidenhic2009_0.38.0_src_all.tar.gz"], "md5": "43f7f158c73c12d62e6cf471cd690667", "fn": "LiebermanAidenHiC2009_0.38.0.tar.gz"}, "listeretalbsseq-1.32.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ListerEtAlBSseq_1.32.1.tar.gz", "https://bioarchive.galaxyproject.org/ListerEtAlBSseq_1.32.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-listeretalbsseq/bioconductor-listeretalbsseq_1.32.1_src_all.tar.gz"], "md5": "8b0138cce25976d0d9180442505679d2", "fn": "ListerEtAlBSseq_1.32.1.tar.gz"}, "lrcelltypemarkers-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/LRcellTypeMarkers_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/LRcellTypeMarkers_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lrcelltypemarkers/bioconductor-lrcelltypemarkers_1.8.0_src_all.tar.gz"], "md5": "342747afa842b8009a5e2a6183c1bd83", "fn": "LRcellTypeMarkers_1.8.0.tar.gz"}, "lumibarnes-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/lumiBarnes_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/lumiBarnes_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumibarnes/bioconductor-lumibarnes_1.40.0_src_all.tar.gz"], "md5": "971e2cf62606ab98813418f8032b20dc", "fn": "lumiBarnes_1.40.0.tar.gz"}, "lungcanceracvssccgeo-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/LungCancerACvsSCCGEO_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/LungCancerACvsSCCGEO_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungcanceracvssccgeo/bioconductor-lungcanceracvssccgeo_1.36.0_src_all.tar.gz"], "md5": "4313ab0bff32de6945d2b4e159979b4f", "fn": "LungCancerACvsSCCGEO_1.36.0.tar.gz"}, "lungcancerlines-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/LungCancerLines_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/LungCancerLines_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungcancerlines/bioconductor-lungcancerlines_0.38.0_src_all.tar.gz"], "md5": "be24350e8e8312e9421f0f4dd1ffbf85", "fn": "LungCancerLines_0.38.0.tar.gz"}, "lungexpression-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/lungExpression_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/lungExpression_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungexpression/bioconductor-lungexpression_0.38.0_src_all.tar.gz"], "md5": "56e3a841d35e5167328f7a3cc3f04349", "fn": "lungExpression_0.38.0.tar.gz"}, "lydata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/lydata_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/lydata_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lydata/bioconductor-lydata_1.26.0_src_all.tar.gz"], "md5": "caffcda965c0d055e69f6f0eb2fe9d67", "fn": "lydata_1.26.0.tar.gz"}, "m3dexampledata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/M3DExampleData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/M3DExampleData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-m3dexampledata/bioconductor-m3dexampledata_1.26.0_src_all.tar.gz"], "md5": "1181ab509a8a85961ef586709f3eaba3", "fn": "M3DExampleData_1.26.0.tar.gz"}, "macrophage-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/macrophage_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/macrophage_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-macrophage/bioconductor-macrophage_1.16.0_src_all.tar.gz"], "md5": "94a66e9f410a44d2aa240ebc4cf5c106", "fn": "macrophage_1.16.0.tar.gz"}, "macsdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MACSdata_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/MACSdata_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-macsdata/bioconductor-macsdata_1.8.0_src_all.tar.gz"], "md5": "b5f6edbf074b1f0f5cb5d0d546cdbd0a", "fn": "MACSdata_1.8.0.tar.gz"}, "mammaprintdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/mammaPrintData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/mammaPrintData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mammaprintdata/bioconductor-mammaprintdata_1.36.0_src_all.tar.gz"], "md5": "cfd6915395a6a2adeebac6854f3359c9", "fn": "mammaPrintData_1.36.0.tar.gz"}, "mapkldata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/mAPKLData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/mAPKLData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mapkldata/bioconductor-mapkldata_1.32.0_src_all.tar.gz"], "md5": "6d1b511c7be1a423450a153fc118e7cb", "fn": "mAPKLData_1.32.0.tar.gz"}, "maqcexpression4plex-1.44.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/maqcExpression4plex_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/maqcExpression4plex_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcexpression4plex/bioconductor-maqcexpression4plex_1.44.0_src_all.tar.gz"], "md5": "761e3e1f398262f4c0cac3cd31979fc7", "fn": "maqcExpression4plex_1.44.0.tar.gz"}, "maqcsubset-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MAQCsubset_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/MAQCsubset_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcsubset/bioconductor-maqcsubset_1.38.0_src_all.tar.gz"], "md5": "eb3ea654ce6aa3db50c7a39c6d8cab28", "fn": "MAQCsubset_1.38.0.tar.gz"}, "maqcsubsetilm-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MAQCsubsetILM_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/MAQCsubsetILM_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcsubsetilm/bioconductor-maqcsubsetilm_1.38.0_src_all.tar.gz"], "md5": "4aaeddbd20f73e3f84dc630e9c02e219", "fn": "MAQCsubsetILM_1.38.0.tar.gz"}, "marinerdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/marinerData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/marinerData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-marinerdata/bioconductor-marinerdata_1.0.0_src_all.tar.gz"], "md5": "88417144bbc4ae0164445918ce73376d", "fn": "marinerData_1.0.0.tar.gz"}, "mcseadata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/mCSEAdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/mCSEAdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcseadata/bioconductor-mcseadata_1.20.0_src_all.tar.gz"], "md5": "44b91c410f01438e2d0d3946689207bd", "fn": "mCSEAdata_1.20.0.tar.gz"}, "mcsurvdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/mcsurvdata_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mcsurvdata_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcsurvdata/bioconductor-mcsurvdata_1.18.0_src_all.tar.gz"], "md5": "4e4b6fa4d49cfa4588d65cb3a22ab121", "fn": "mcsurvdata_1.18.0.tar.gz"}, "medipsdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MEDIPSData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/MEDIPSData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-medipsdata/bioconductor-medipsdata_1.36.0_src_all.tar.gz"], "md5": "d6d822abd5a2acc639cad1a270f03a2d", "fn": "MEDIPSData_1.36.0.tar.gz"}, "meebodata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MEEBOdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/MEEBOdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-meebodata/bioconductor-meebodata_1.38.0_src_all.tar.gz"], "md5": "0eb2ee76322ae64e44bb926769bd1f77", "fn": "MEEBOdata_1.38.0.tar.gz"}, "merfishdata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MerfishData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/MerfishData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-merfishdata/bioconductor-merfishdata_1.2.0_src_all.tar.gz"], "md5": "d4e86b95520641c0d3f1b5c938d5a3b7", "fn": "MerfishData_1.2.0.tar.gz"}, "metagxbreast-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MetaGxBreast_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxBreast_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxbreast/bioconductor-metagxbreast_1.20.0_src_all.tar.gz"], "md5": "38b605d1c36990f9ae722ed9391afb75", "fn": "MetaGxBreast_1.20.0.tar.gz"}, "metagxovarian-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MetaGxOvarian_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxOvarian_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxovarian/bioconductor-metagxovarian_1.20.0_src_all.tar.gz"], "md5": "180366821492879a0fc25f4b4117b20f", "fn": "MetaGxOvarian_1.20.0.tar.gz"}, "metagxpancreas-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MetaGxPancreas_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxPancreas_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxpancreas/bioconductor-metagxpancreas_1.20.0_src_all.tar.gz"], "md5": "837617be22e87ee2716a5bd6888bb204", "fn": "MetaGxPancreas_1.20.0.tar.gz"}, "metamsdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/metaMSdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/metaMSdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metamsdata/bioconductor-metamsdata_1.36.0_src_all.tar.gz"], "md5": "7c4408ceda2098402daaa6c94bbd3768", "fn": "metaMSdata_1.36.0.tar.gz"}, "metascope-1.0.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MetaScope_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaScope_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metascope/bioconductor-metascope_1.0.0_src_all.tar.gz"], "md5": "aef272f5f78bc787f42bd9c47b923cfb", "fn": "MetaScope_1.0.0.tar.gz"}, "methylaiddata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MethylAidData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/MethylAidData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylaiddata/bioconductor-methylaiddata_1.32.0_src_all.tar.gz"], "md5": "43ab55538e535cab63f2594898cfbda4", "fn": "MethylAidData_1.32.0.tar.gz"}, "methylclockdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/methylclockData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/methylclockData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylclockdata/bioconductor-methylclockdata_1.8.0_src_all.tar.gz"], "md5": "52774d13964d22556fdceb4458caaa27", "fn": "methylclockData_1.8.0.tar.gz"}, "methylseqdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MethylSeqData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MethylSeqData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylseqdata/bioconductor-methylseqdata_1.10.0_src_all.tar.gz"], "md5": "d1a6bd69401032cbdba32519c02fdf4c", "fn": "MethylSeqData_1.10.0.tar.gz"}, "microbiomebenchmarkdata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MicrobiomeBenchmarkData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/MicrobiomeBenchmarkData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-microbiomebenchmarkdata/bioconductor-microbiomebenchmarkdata_1.2.0_src_all.tar.gz"], "md5": "1116445da1265ebf3e4bf29678bd6cc3", "fn": "MicrobiomeBenchmarkData_1.2.0.tar.gz"}, "microbiomedatasets-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/microbiomeDataSets_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/microbiomeDataSets_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-microbiomedatasets/bioconductor-microbiomedatasets_1.8.0_src_all.tar.gz"], "md5": "084634f8885e50e157bbaef972b7ad8f", "fn": "microbiomeDataSets_1.8.0.tar.gz"}, "micrornaome-1.22.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/microRNAome_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/microRNAome_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-micrornaome/bioconductor-micrornaome_1.22.0_src_all.tar.gz"], "md5": "04f1271bdd22d4cc2dabd9e8db57e006", "fn": "microRNAome_1.22.0.tar.gz"}, "migsadata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MIGSAdata_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/MIGSAdata_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-migsadata/bioconductor-migsadata_1.24.0_src_all.tar.gz"], "md5": "baf8af22bafeaed754c45ce660a92420", "fn": "MIGSAdata_1.24.0.tar.gz"}, "minfidata-0.46.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/minfiData_0.46.0.tar.gz", "https://bioarchive.galaxyproject.org/minfiData_0.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minfidata/bioconductor-minfidata_0.46.0_src_all.tar.gz"], "md5": "a5edb94dae6adb108bd94fdf4e0e8c3d", "fn": "minfiData_0.46.0.tar.gz"}, "minfidataepic-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/minfiDataEPIC_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/minfiDataEPIC_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minfidataepic/bioconductor-minfidataepic_1.26.0_src_all.tar.gz"], "md5": "f61984902e4c4c2d0c01f375a3533935", "fn": "minfiDataEPIC_1.26.0.tar.gz"}, "minionsummarydata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/minionSummaryData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/minionSummaryData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minionsummarydata/bioconductor-minionsummarydata_1.30.0_src_all.tar.gz"], "md5": "cab7c2dd789ebe23e1c9410bdbc259c6", "fn": "minionSummaryData_1.30.0.tar.gz"}, "mircompdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/miRcompData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/miRcompData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mircompdata/bioconductor-mircompdata_1.30.0_src_all.tar.gz"], "md5": "df2f1f8eb6489db9c0e242224b47be36", "fn": "miRcompData_1.30.0.tar.gz"}, "mirnatarget-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/miRNATarget_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/miRNATarget_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirnatarget/bioconductor-mirnatarget_1.38.0_src_all.tar.gz"], "md5": "a7418be6b97608cabc13f0812caf9301", "fn": "miRNATarget_1.38.0.tar.gz"}, "mmappr2data-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MMAPPR2data_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/MMAPPR2data_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mmappr2data/bioconductor-mmappr2data_1.14.0_src_all.tar.gz"], "md5": "5ea459c418711fc37e694b10789d03ae", "fn": "MMAPPR2data_1.14.0.tar.gz"}, "mmdiffbamsubset-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MMDiffBamSubset_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/MMDiffBamSubset_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mmdiffbamsubset/bioconductor-mmdiffbamsubset_1.36.0_src_all.tar.gz"], "md5": "b9a590f3dc54a5b5b4e36232ca7e2538", "fn": "MMDiffBamSubset_1.36.0.tar.gz"}, "mofadata-1.16.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MOFAdata_1.16.1.tar.gz", "https://bioarchive.galaxyproject.org/MOFAdata_1.16.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mofadata/bioconductor-mofadata_1.16.1_src_all.tar.gz"], "md5": "7c3605011c45bfe05471c35727cf9896", "fn": "MOFAdata_1.16.1.tar.gz"}, "mosaicsexample-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/mosaicsExample_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/mosaicsExample_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mosaicsexample/bioconductor-mosaicsexample_1.38.0_src_all.tar.gz"], "md5": "dbbc0ae50f0d93a64a45efe4bb848a71", "fn": "mosaicsExample_1.38.0.tar.gz"}, "mouse4302barcodevecs-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/mouse4302barcodevecs_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse4302barcodevecs_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302barcodevecs/bioconductor-mouse4302barcodevecs_1.38.0_src_all.tar.gz"], "md5": "bb60f755fb3fc86b8dbb769bbe6f06c4", "fn": "mouse4302barcodevecs_1.38.0.tar.gz"}, "mousegastrulationdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MouseGastrulationData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/MouseGastrulationData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousegastrulationdata/bioconductor-mousegastrulationdata_1.14.0_src_all.tar.gz"], "md5": "671b5016215ff92409c4aba1f4a59c16", "fn": "MouseGastrulationData_1.14.0.tar.gz"}, "mousethymusageing-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MouseThymusAgeing_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/MouseThymusAgeing_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousethymusageing/bioconductor-mousethymusageing_1.8.0_src_all.tar.gz"], "md5": "e5453bec0eab9aa18f7f438bbfd63c27", "fn": "MouseThymusAgeing_1.8.0.tar.gz"}, "msd16s-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/msd16s_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/msd16s_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msd16s/bioconductor-msd16s_1.20.0_src_all.tar.gz"], "md5": "48cc66a74ec0aeff91a4c5217f69c57d", "fn": "msd16s_1.20.0.tar.gz"}, "msdata-0.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/msdata_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/msdata_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msdata/bioconductor-msdata_0.40.0_src_all.tar.gz"], "md5": "dc6c949e6d593b4220d08511155b9316", "fn": "msdata_0.40.0.tar.gz"}, "msigdb-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/msigdb_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/msigdb_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msigdb/bioconductor-msigdb_1.8.0_src_all.tar.gz"], "md5": "1468865f501a46ee6410f5fac54d9441", "fn": "msigdb_1.8.0.tar.gz"}, "msmb-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MSMB_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/MSMB_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msmb/bioconductor-msmb_1.18.0_src_all.tar.gz"], "md5": "6d9b11ea89215a562d46146b97e3208e", "fn": "MSMB_1.18.0.tar.gz"}, "mspuritydata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/msPurityData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/msPurityData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mspuritydata/bioconductor-mspuritydata_1.28.0_src_all.tar.gz"], "md5": "758e960ac371d347930ab01398f27127", "fn": "msPurityData_1.28.0.tar.gz"}, "msqc1-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/msqc1_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/msqc1_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msqc1/bioconductor-msqc1_1.28.0_src_all.tar.gz"], "md5": "eec753dc0f640e28b06685127ac3794e", "fn": "msqc1_1.28.0.tar.gz"}, "mtbls2-1.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/mtbls2_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/mtbls2_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mtbls2/bioconductor-mtbls2_1.30.0_src_all.tar.gz"], "md5": "9f3494d399dd599b5e462dba8bd126bb", "fn": "mtbls2_1.30.0.tar.gz"}, "mugaexampledata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/MUGAExampleData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/MUGAExampleData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mugaexampledata/bioconductor-mugaexampledata_1.20.0_src_all.tar.gz"], "md5": "0e9d37ebfc20b7c46c5e0d98528dc188", "fn": "MUGAExampleData_1.20.0.tar.gz"}, "muscdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/muscData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/muscData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-muscdata/bioconductor-muscdata_1.14.0_src_all.tar.gz"], "md5": "d39accb42da56f5ca951a6f735f1586a", "fn": "muscData_1.14.0.tar.gz"}, "mvoutdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/mvoutData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/mvoutData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mvoutdata/bioconductor-mvoutdata_1.36.0_src_all.tar.gz"], "md5": "c4a2c65e797ec8403b7657afc81c2714", "fn": "mvoutData_1.36.0.tar.gz"}, "nanoporernaseq-1.10.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/NanoporeRNASeq_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/NanoporeRNASeq_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nanoporernaseq/bioconductor-nanoporernaseq_1.10.0_src_all.tar.gz"], "md5": "4efdad7f3e17485998405b6d05612ac2", "fn": "NanoporeRNASeq_1.10.0.tar.gz"}, "nanotubes-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/nanotubes_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/nanotubes_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nanotubes/bioconductor-nanotubes_1.16.0_src_all.tar.gz"], "md5": "7d068f3a955216378fe66463811e4adf", "fn": "nanotubes_1.16.0.tar.gz"}, "ncigraphdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/NCIgraphData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/NCIgraphData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ncigraphdata/bioconductor-ncigraphdata_1.36.0_src_all.tar.gz"], "md5": "beb23450c51a8f3bcac07438a25d6f9b", "fn": "NCIgraphData_1.36.0.tar.gz"}, "nestlink-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/NestLink_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/NestLink_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nestlink/bioconductor-nestlink_1.16.0_src_all.tar.gz"], "md5": "ae3c598105a6b4fc40e3ce4ad0bf1e99", "fn": "NestLink_1.16.0.tar.gz"}, "netactivitydata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/NetActivityData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/NetActivityData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-netactivitydata/bioconductor-netactivitydata_1.2.0_src_all.tar.gz"], "md5": "43f1651effd619c45926094b7f6df44b", "fn": "NetActivityData_1.2.0.tar.gz"}, "neve2006-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Neve2006_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/Neve2006_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-neve2006/bioconductor-neve2006_0.38.0_src_all.tar.gz"], "md5": "77132d53a223319770a7abcf21d8e202", "fn": "Neve2006_0.38.0.tar.gz"}, "ngscopydata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/NGScopyData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/NGScopyData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ngscopydata/bioconductor-ngscopydata_1.20.0_src_all.tar.gz"], "md5": "e2d29d8d5f08328e350974da855da611", "fn": "NGScopyData_1.20.0.tar.gz"}, "nullrangesdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/nullrangesData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/nullrangesData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nullrangesdata/bioconductor-nullrangesdata_1.6.0_src_all.tar.gz"], "md5": "54631ad9bc1a63e3c981cb9df919a1a4", "fn": "nullrangesData_1.6.0.tar.gz"}, "nxtirfdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/NxtIRFdata_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/NxtIRFdata_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nxtirfdata/bioconductor-nxtirfdata_1.6.0_src_all.tar.gz"], "md5": "49c677044a8e671562fec6f64533b284", "fn": "NxtIRFdata_1.6.0.tar.gz"}, "obmiti-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ObMiTi_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ObMiTi_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-obmiti/bioconductor-obmiti_1.8.0_src_all.tar.gz"], "md5": "679880ec1082c72dc04b91c7c43b86d1", "fn": "ObMiTi_1.8.0.tar.gz"}, "oct4-1.16.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/oct4_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/oct4_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-oct4/bioconductor-oct4_1.16.0_src_all.tar.gz"], "md5": "733c8377b6b7065265506a938f1c7c09", "fn": "oct4_1.16.0.tar.gz"}, "octad.db-1.2.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/octad.db_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/octad.db_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-octad.db/bioconductor-octad.db_1.2.0_src_all.tar.gz"], "md5": "242e1f3e5df68b1ccbc324eaf3924797", "fn": "octad.db_1.2.0.tar.gz"}, "omicspcadata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/OMICsPCAdata_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/OMICsPCAdata_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-omicspcadata/bioconductor-omicspcadata_1.18.0_src_all.tar.gz"], "md5": "058c8440badd8afe17e693d3055fbf23", "fn": "OMICsPCAdata_1.18.0.tar.gz"}, "onassisjavalibs-1.22.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/OnassisJavaLibs_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/OnassisJavaLibs_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-onassisjavalibs/bioconductor-onassisjavalibs_1.22.0_src_all.tar.gz"], "md5": "32a85e21248ac13de54dfee722eee3f1", "fn": "OnassisJavaLibs_1.22.0.tar.gz"}, "optimalflowdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/optimalFlowData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/optimalFlowData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-optimalflowdata/bioconductor-optimalflowdata_1.12.0_src_all.tar.gz"], "md5": "daba5d6a8b8fdde9d58fed555c569ad5", "fn": "optimalFlowData_1.12.0.tar.gz"}, "parathyroidse-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/parathyroidSE_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/parathyroidSE_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-parathyroidse/bioconductor-parathyroidse_1.38.0_src_all.tar.gz"], "md5": "055bda4d4376fcdec3bce484ec634117", "fn": "parathyroidSE_1.38.0.tar.gz"}, "pasilla-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/pasilla_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/pasilla_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasilla/bioconductor-pasilla_1.28.0_src_all.tar.gz"], "md5": "a6abc62e6e4ddde42ee0269256ac8342", "fn": "pasilla_1.28.0.tar.gz"}, "pasillabamsubset-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/pasillaBamSubset_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/pasillaBamSubset_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasillabamsubset/bioconductor-pasillabamsubset_0.38.0_src_all.tar.gz"], "md5": "6c80a6afcfb87c88e88e8c3c69e66e71", "fn": "pasillaBamSubset_0.38.0.tar.gz"}, "pasillatranscriptexpr-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PasillaTranscriptExpr_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/PasillaTranscriptExpr_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasillatranscriptexpr/bioconductor-pasillatranscriptexpr_1.28.0_src_all.tar.gz"], "md5": "8d5e8ec6f9ba14ca8da1565b8a2b0bac", "fn": "PasillaTranscriptExpr_1.28.0.tar.gz"}, "pathnetdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PathNetData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/PathNetData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pathnetdata/bioconductor-pathnetdata_1.36.0_src_all.tar.gz"], "md5": "20449e0dcf262e4f6c1f7e2521a00370", "fn": "PathNetData_1.36.0.tar.gz"}, "pchicdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PCHiCdata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/PCHiCdata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pchicdata/bioconductor-pchicdata_1.28.0_src_all.tar.gz"], "md5": "7048c278620231f478014314a1a16e74", "fn": "PCHiCdata_1.28.0.tar.gz"}, "pcxndata-2.22.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/pcxnData_2.22.0.tar.gz", "https://bioarchive.galaxyproject.org/pcxnData_2.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pcxndata/bioconductor-pcxndata_2.22.0_src_all.tar.gz"], "md5": "0d340cd964638e91faf2181216c06159", "fn": "pcxnData_2.22.0.tar.gz"}, "pd.atdschip.tiling-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/pd.atdschip.tiling_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.atdschip.tiling_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.atdschip.tiling/bioconductor-pd.atdschip.tiling_0.38.0_src_all.tar.gz"], "md5": "a38ac90ece38e2e9f980966194865fe0", "fn": "pd.atdschip.tiling_0.38.0.tar.gz"}, "pepdat-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/pepDat_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/pepDat_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pepdat/bioconductor-pepdat_1.20.0_src_all.tar.gz"], "md5": "6c0f8c749db61b37d83728109a2e08df", "fn": "pepDat_1.20.0.tar.gz"}, "pepsnmrdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PepsNMRData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/PepsNMRData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pepsnmrdata/bioconductor-pepsnmrdata_1.18.0_src_all.tar.gz"], "md5": "98f84b07316d8ec6aab7c64862c695d2", "fn": "PepsNMRData_1.18.0.tar.gz"}, "phyloprofiledata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PhyloProfileData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/PhyloProfileData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phyloprofiledata/bioconductor-phyloprofiledata_1.14.0_src_all.tar.gz"], "md5": "3be065a86910a062e9b63540157ff949", "fn": "PhyloProfileData_1.14.0.tar.gz"}, "plotgardenerdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/plotgardenerData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/plotgardenerData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-plotgardenerdata/bioconductor-plotgardenerdata_1.6.0_src_all.tar.gz"], "md5": "82519e095b0f464cd59388d4146d21db", "fn": "plotgardenerData_1.6.0.tar.gz"}, "prebsdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/prebsdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/prebsdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prebsdata/bioconductor-prebsdata_1.36.0_src_all.tar.gz"], "md5": "96c0666ea91a4bd5b5c8dbc584f873b3", "fn": "prebsdata_1.36.0.tar.gz"}, "precisetadhub-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/preciseTADhub_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/preciseTADhub_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-precisetadhub/bioconductor-precisetadhub_1.8.0_src_all.tar.gz"], "md5": "9e0da7747a2ae263545ef3e426701fd6", "fn": "preciseTADhub_1.8.0.tar.gz"}, "predasampledata-0.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PREDAsampledata_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/PREDAsampledata_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-predasampledata/bioconductor-predasampledata_0.40.0_src_all.tar.gz"], "md5": "478b0cd1f601998cfefcca0fdf60eb3d", "fn": "PREDAsampledata_0.40.0.tar.gz"}, "prodata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ProData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ProData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prodata/bioconductor-prodata_1.38.0_src_all.tar.gz"], "md5": "6a4c17dd4a55240fdeab52f3301e19f6", "fn": "ProData_1.38.0.tar.gz"}, "prolocdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/pRolocdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/pRolocdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prolocdata/bioconductor-prolocdata_1.38.0_src_all.tar.gz"], "md5": "3cf7b5644c6af5a158d0291d9b597cd2", "fn": "pRolocdata_1.38.0.tar.gz"}, "prostatecancercamcap-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/prostateCancerCamcap_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerCamcap_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancercamcap/bioconductor-prostatecancercamcap_1.28.0_src_all.tar.gz"], "md5": "ff2a0d04db22bce6d2d1722e718edeb5", "fn": "prostateCancerCamcap_1.28.0.tar.gz"}, "prostatecancergrasso-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/prostateCancerGrasso_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerGrasso_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancergrasso/bioconductor-prostatecancergrasso_1.28.0_src_all.tar.gz"], "md5": "cc2f4713d5950c0fcd99dd320adbdb2d", "fn": "prostateCancerGrasso_1.28.0.tar.gz"}, "prostatecancerstockholm-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/prostateCancerStockholm_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerStockholm_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancerstockholm/bioconductor-prostatecancerstockholm_1.28.0_src_all.tar.gz"], "md5": "f2ec2d712681d173c561a57451acae94", "fn": "prostateCancerStockholm_1.28.0.tar.gz"}, "prostatecancertaylor-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/prostateCancerTaylor_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerTaylor_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancertaylor/bioconductor-prostatecancertaylor_1.28.0_src_all.tar.gz"], "md5": "d41f91c630547581ccabf8159a79d889", "fn": "prostateCancerTaylor_1.28.0.tar.gz"}, "prostatecancervarambally-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/prostateCancerVarambally_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerVarambally_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancervarambally/bioconductor-prostatecancervarambally_1.28.0_src_all.tar.gz"], "md5": "8008e839c2e72aee55433f2361efb0cb", "fn": "prostateCancerVarambally_1.28.0.tar.gz"}, "ptairdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ptairData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/ptairData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ptairdata/bioconductor-ptairdata_1.8.0_src_all.tar.gz"], "md5": "ede739875473864ed372a4fb877b1852", "fn": "ptairData_1.8.0.tar.gz"}, "pth2o2lipids-1.26.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PtH2O2lipids_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/PtH2O2lipids_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pth2o2lipids/bioconductor-pth2o2lipids_1.26.0_src_all.tar.gz"], "md5": "7555134e1714c1d20f25a30f2c74d33c", "fn": "PtH2O2lipids_1.26.0.tar.gz"}, "pumadata-2.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/pumadata_2.36.0.tar.gz", "https://bioarchive.galaxyproject.org/pumadata_2.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pumadata/bioconductor-pumadata_2.36.0_src_all.tar.gz"], "md5": "8201e94e0c66444c72b8f45bd3ca7020", "fn": "pumadata_2.36.0.tar.gz"}, "pwmenrich.dmelanogaster.background-4.34.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PWMEnrich.Dmelanogaster.background_4.34.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Dmelanogaster.background_4.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.dmelanogaster.background/bioconductor-pwmenrich.dmelanogaster.background_4.34.0_src_all.tar.gz"], "md5": "907d3ff8c0fb527c01dbf099a075f732", "fn": "PWMEnrich.Dmelanogaster.background_4.34.0.tar.gz"}, "pwmenrich.hsapiens.background-4.34.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PWMEnrich.Hsapiens.background_4.34.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Hsapiens.background_4.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.hsapiens.background/bioconductor-pwmenrich.hsapiens.background_4.34.0_src_all.tar.gz"], "md5": "02021cd798df13ad0f124fdc481ebe33", "fn": "PWMEnrich.Hsapiens.background_4.34.0.tar.gz"}, "pwmenrich.mmusculus.background-4.34.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PWMEnrich.Mmusculus.background_4.34.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Mmusculus.background_4.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.mmusculus.background/bioconductor-pwmenrich.mmusculus.background_4.34.0_src_all.tar.gz"], "md5": "e81cb70d4a4850829fa5a83003c75404", "fn": "PWMEnrich.Mmusculus.background_4.34.0.tar.gz"}, "pwrewas.data-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/pwrEWAS.data_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/pwrEWAS.data_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwrewas.data/bioconductor-pwrewas.data_1.14.0_src_all.tar.gz"], "md5": "4bc800d4a20edec551cbbcbbffd3d107", "fn": "pwrEWAS.data_1.14.0.tar.gz"}, "qdnaseq.hg19-1.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/QDNAseq.hg19_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/QDNAseq.hg19_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.hg19/bioconductor-qdnaseq.hg19_1.30.0_src_all.tar.gz"], "md5": "6b81f056006151fd4a2f55935ee57f67", "fn": "QDNAseq.hg19_1.30.0.tar.gz"}, "qdnaseq.mm10-1.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/QDNAseq.mm10_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/QDNAseq.mm10_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.mm10/bioconductor-qdnaseq.mm10_1.30.0_src_all.tar.gz"], "md5": "d7c1a5cec6ee30213a4389b40979b9ef", "fn": "QDNAseq.mm10_1.30.0.tar.gz"}, "qplexdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/qPLEXdata_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/qPLEXdata_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qplexdata/bioconductor-qplexdata_1.18.0_src_all.tar.gz"], "md5": "2ea69c2e1a071fd94fcb169af5c61422", "fn": "qPLEXdata_1.18.0.tar.gz"}, "qubicdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/QUBICdata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/QUBICdata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qubicdata/bioconductor-qubicdata_1.28.0_src_all.tar.gz"], "md5": "47be84c681eabf3ba1851a935762e23a", "fn": "QUBICdata_1.28.0.tar.gz"}, "rcellminerdata-2.22.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/rcellminerData_2.22.0.tar.gz", "https://bioarchive.galaxyproject.org/rcellminerData_2.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rcellminerdata/bioconductor-rcellminerdata_2.22.0_src_all.tar.gz"], "md5": "45f581dfcac9cd66a5cb2ca6f0706d7a", "fn": "rcellminerData_2.22.0.tar.gz"}, "rcistarget.hg19.motifdbs.cisbponly.500bp-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp_1.20.0_src_all.tar.gz"], "md5": "74b4a09e41b8af5f638848ca86f3ec53", "fn": "RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.20.0.tar.gz"}, "reactomegsa.data-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/ReactomeGSA.data_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/ReactomeGSA.data_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-reactomegsa.data/bioconductor-reactomegsa.data_1.14.0_src_all.tar.gz"], "md5": "1c6b8b4eeacfc2f316c8c0aa021938f1", "fn": "ReactomeGSA.data_1.14.0.tar.gz"}, "regparallel-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RegParallel_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/RegParallel_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-regparallel/bioconductor-regparallel_1.18.0_src_all.tar.gz"], "md5": "ac6ed5e19a8dcfe359e97ccf89949dd1", "fn": "RegParallel_1.18.0.tar.gz"}, "restfulsedata-1.22.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/restfulSEData_1.22.1.tar.gz", "https://bioarchive.galaxyproject.org/restfulSEData_1.22.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-restfulsedata/bioconductor-restfulsedata_1.22.1_src_all.tar.gz"], "md5": "e92deb8a55a329887e87c9d4520e4b9e", "fn": "restfulSEData_1.22.1.tar.gz"}, "rforproteomics-1.38.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RforProteomics_1.38.1.tar.gz", "https://bioarchive.galaxyproject.org/RforProteomics_1.38.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rforproteomics/bioconductor-rforproteomics_1.38.1_src_all.tar.gz"], "md5": "2dbad7c535bf6a39299cad51ede9aafd", "fn": "RforProteomics_1.38.1.tar.gz"}, "rgmqllib-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RGMQLlib_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/RGMQLlib_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgmqllib/bioconductor-rgmqllib_1.20.0_src_all.tar.gz"], "md5": "a9153c4ade0f2149a136bdaefb123f6d", "fn": "RGMQLlib_1.20.0.tar.gz"}, "rheumaticconditionwollbold-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/rheumaticConditionWOLLBOLD_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/rheumaticConditionWOLLBOLD_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rheumaticconditionwollbold/bioconductor-rheumaticconditionwollbold_1.38.0_src_all.tar.gz"], "md5": "58d7b58e54ba5cbd75fafa85aa09f476", "fn": "rheumaticConditionWOLLBOLD_1.38.0.tar.gz"}, "ritandata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RITANdata_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/RITANdata_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ritandata/bioconductor-ritandata_1.24.0_src_all.tar.gz"], "md5": "ee9657a5c821eb892c79ef6a1ee4c5e5", "fn": "RITANdata_1.24.0.tar.gz"}, "rlhub-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RLHub_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/RLHub_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rlhub/bioconductor-rlhub_1.6.0_src_all.tar.gz"], "md5": "9072a588ef09512493ea389c50984153", "fn": "RLHub_1.6.0.tar.gz"}, "rmassbankdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RMassBankData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/RMassBankData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rmassbankdata/bioconductor-rmassbankdata_1.38.0_src_all.tar.gz"], "md5": "ea11a54b5f2465431c43bb8edde6a112", "fn": "RMassBankData_1.38.0.tar.gz"}, "rnainteractmapk-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RNAinteractMAPK_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAinteractMAPK_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnainteractmapk/bioconductor-rnainteractmapk_1.38.0_src_all.tar.gz"], "md5": "ed5fd6239416fbacc80a8995c6e13fb7", "fn": "RNAinteractMAPK_1.38.0.tar.gz"}, "rnamodr.data-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RNAmodR.Data_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAmodR.Data_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnamodr.data/bioconductor-rnamodr.data_1.14.0_src_all.tar.gz"], "md5": "1299a93be9ed1090e5890741cebde152", "fn": "RNAmodR.Data_1.14.0.tar.gz"}, "rnaseqdata.hnrnpc.bam.chr14-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RNAseqData.HNRNPC.bam.chr14_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAseqData.HNRNPC.bam.chr14_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqdata.hnrnpc.bam.chr14/bioconductor-rnaseqdata.hnrnpc.bam.chr14_0.38.0_src_all.tar.gz"], "md5": "7c39f3f2306bb10cb47a97b1d2c893ad", "fn": "RNAseqData.HNRNPC.bam.chr14_0.38.0.tar.gz"}, "rnaseqsamplesizedata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RnaSeqSampleSizeData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/RnaSeqSampleSizeData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqsamplesizedata/bioconductor-rnaseqsamplesizedata_1.32.0_src_all.tar.gz"], "md5": "415e0dc4f463089c632c9106f6df7d89", "fn": "RnaSeqSampleSizeData_1.32.0.tar.gz"}, "rnbeads.hg19-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RnBeads.hg19_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.hg19_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg19/bioconductor-rnbeads.hg19_1.32.0_src_all.tar.gz"], "md5": "83a4f81f4c411d8139ba8673687a6a49", "fn": "RnBeads.hg19_1.32.0.tar.gz"}, "rnbeads.hg38-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RnBeads.hg38_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.hg38_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg38/bioconductor-rnbeads.hg38_1.32.0_src_all.tar.gz"], "md5": "87b5a33c515443e05b5ab7cfeb7afa7a", "fn": "RnBeads.hg38_1.32.0.tar.gz"}, "rnbeads.mm10-2.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RnBeads.mm10_2.8.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.mm10_2.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm10/bioconductor-rnbeads.mm10_2.8.0_src_all.tar.gz"], "md5": "4b25dd4978d2d430192ae93b45945506", "fn": "RnBeads.mm10_2.8.0.tar.gz"}, "rnbeads.mm9-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RnBeads.mm9_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.mm9_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm9/bioconductor-rnbeads.mm9_1.32.0_src_all.tar.gz"], "md5": "83951bafa8f84863f5cdd3e0128c1e0d", "fn": "RnBeads.mm9_1.32.0.tar.gz"}, "rnbeads.rn5-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RnBeads.rn5_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.rn5_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.rn5/bioconductor-rnbeads.rn5_1.32.0_src_all.tar.gz"], "md5": "704db9c010242b63f68e02de58b77ee0", "fn": "RnBeads.rn5_1.32.0.tar.gz"}, "rrbsdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RRBSdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/RRBSdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rrbsdata/bioconductor-rrbsdata_1.20.0_src_all.tar.gz"], "md5": "a418c0df3db7d2285a1629bd473129ce", "fn": "RRBSdata_1.20.0.tar.gz"}, "rrdpdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/rRDPData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/rRDPData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rrdpdata/bioconductor-rrdpdata_1.20.0_src_all.tar.gz"], "md5": "81a8cf3a83812318bbacb9cc2503f8d1", "fn": "rRDPData_1.20.0.tar.gz"}, "rtcga.clinical-20151101.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RTCGA.clinical_20151101.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.clinical_20151101.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.clinical/bioconductor-rtcga.clinical_20151101.30.0_src_all.tar.gz"], "md5": "772ed6b2aafe700536b01d9b4c55dfef", "fn": "RTCGA.clinical_20151101.30.0.tar.gz"}, "rtcga.cnv-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RTCGA.CNV_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.CNV_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.cnv/bioconductor-rtcga.cnv_1.28.0_src_all.tar.gz"], "md5": "4c2f73f6edefa0ca82b7c6f9add37156", "fn": "RTCGA.CNV_1.28.0.tar.gz"}, "rtcga.methylation-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RTCGA.methylation_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.methylation_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.methylation/bioconductor-rtcga.methylation_1.28.0_src_all.tar.gz"], "md5": "1aff8900c676eb32d9655b0d4fbf834e", "fn": "RTCGA.methylation_1.28.0.tar.gz"}, "rtcga.mirnaseq-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RTCGA.miRNASeq_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.miRNASeq_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mirnaseq/bioconductor-rtcga.mirnaseq_1.28.0_src_all.tar.gz"], "md5": "61a11184082b390c05d74b660d06635d", "fn": "RTCGA.miRNASeq_1.28.0.tar.gz"}, "rtcga.mrna-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RTCGA.mRNA_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.mRNA_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mrna/bioconductor-rtcga.mrna_1.28.0_src_all.tar.gz"], "md5": "63adca06a76cfc761b88b853a34580d1", "fn": "RTCGA.mRNA_1.28.0.tar.gz"}, "rtcga.mutations-20151101.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RTCGA.mutations_20151101.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.mutations_20151101.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mutations/bioconductor-rtcga.mutations_20151101.30.0_src_all.tar.gz"], "md5": "d1f7686f0203ccdffd3c0d903947ffbb", "fn": "RTCGA.mutations_20151101.30.0.tar.gz"}, "rtcga.pancan12-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RTCGA.PANCAN12_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.PANCAN12_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.pancan12/bioconductor-rtcga.pancan12_1.28.0_src_all.tar.gz"], "md5": "3c4fcdde44501b93a022b8b1fe3abf96", "fn": "RTCGA.PANCAN12_1.28.0.tar.gz"}, "rtcga.rnaseq-20151101.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RTCGA.rnaseq_20151101.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.rnaseq_20151101.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.rnaseq/bioconductor-rtcga.rnaseq_20151101.30.0_src_all.tar.gz"], "md5": "df65c9add93e3fa3f2f321442057c807", "fn": "RTCGA.rnaseq_20151101.30.0.tar.gz"}, "rtcga.rppa-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RTCGA.RPPA_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.RPPA_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.rppa/bioconductor-rtcga.rppa_1.28.0_src_all.tar.gz"], "md5": "caff1ad6b62dbd868be8cf6452cc4312", "fn": "RTCGA.RPPA_1.28.0.tar.gz"}, "ruvnormalizedata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/RUVnormalizeData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/RUVnormalizeData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ruvnormalizedata/bioconductor-ruvnormalizedata_1.20.0_src_all.tar.gz"], "md5": "138ed1f796a9967fce840e1f751769a2", "fn": "RUVnormalizeData_1.20.0.tar.gz"}, "sampleclassifierdata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/sampleClassifierData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/sampleClassifierData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sampleclassifierdata/bioconductor-sampleclassifierdata_1.24.0_src_all.tar.gz"], "md5": "f4b0d64737358fad818a4a1cc71a27c8", "fn": "sampleClassifierData_1.24.0.tar.gz"}, "sbgnview.data-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SBGNview.data_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/SBGNview.data_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sbgnview.data/bioconductor-sbgnview.data_1.14.0_src_all.tar.gz"], "md5": "ab6acd3a8b3411fcba1cf7ab1bbbd370", "fn": "SBGNview.data_1.14.0.tar.gz"}, "scanmirdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/scanMiRData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/scanMiRData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scanmirdata/bioconductor-scanmirdata_1.6.0_src_all.tar.gz"], "md5": "163f0250a82df0c4fb402b756a3010d7", "fn": "scanMiRData_1.6.0.tar.gz"}, "scatac.explorer-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/scATAC.Explorer_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/scATAC.Explorer_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scatac.explorer/bioconductor-scatac.explorer_1.6.0_src_all.tar.gz"], "md5": "74c840082c522937d200169fcb963f71", "fn": "scATAC.Explorer_1.6.0.tar.gz"}, "scatedata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SCATEData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/SCATEData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scatedata/bioconductor-scatedata_1.10.0_src_all.tar.gz"], "md5": "dd2241d946202b696c0a706b906425f4", "fn": "SCATEData_1.10.0.tar.gz"}, "sclcbam-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SCLCBam_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/SCLCBam_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sclcbam/bioconductor-sclcbam_1.32.0_src_all.tar.gz"], "md5": "ca48c42a5e16460f72eb8bfbc697258f", "fn": "SCLCBam_1.32.0.tar.gz"}, "scmultiome-1.0.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/scMultiome_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/scMultiome_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scmultiome/bioconductor-scmultiome_1.0.0_src_all.tar.gz"], "md5": "22aceaa129afbecd400b2d16b6333d43", "fn": "scMultiome_1.0.0.tar.gz"}, "scpdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/scpdata_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/scpdata_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scpdata/bioconductor-scpdata_1.8.0_src_all.tar.gz"], "md5": "0a00beb40a6ae72de0364698c7a0129b", "fn": "scpdata_1.8.0.tar.gz"}, "scrnaseq-2.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/scRNAseq_2.14.0.tar.gz", "https://bioarchive.galaxyproject.org/scRNAseq_2.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scrnaseq/bioconductor-scrnaseq_2.14.0_src_all.tar.gz"], "md5": "3adccc738839605191c0eda859e3d7c7", "fn": "scRNAseq_2.14.0.tar.gz"}, "scthi.data-1.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/scTHI.data_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/scTHI.data_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scthi.data/bioconductor-scthi.data_1.12.0_src_all.tar.gz"], "md5": "28e55c6ba60cb8527c376ca87993c95c", "fn": "scTHI.data_1.12.0.tar.gz"}, "seq2pathway.data-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/seq2pathway.data_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/seq2pathway.data_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seq2pathway.data/bioconductor-seq2pathway.data_1.32.0_src_all.tar.gz"], "md5": "f5b47c139925e607c100f2e3e0292db0", "fn": "seq2pathway.data_1.32.0.tar.gz"}, "seqc-1.34.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/seqc_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/seqc_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seqc/bioconductor-seqc_1.34.0_src_all.tar.gz"], "md5": "834e2a378860f1f6aea76581e87c876f", "fn": "seqc_1.34.0.tar.gz"}, "seqcna.annot-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/seqCNA.annot_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/seqCNA.annot_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seqcna.annot/bioconductor-seqcna.annot_1.36.0_src_all.tar.gz"], "md5": "feee6a27f305149bdfec8a823e2134ec", "fn": "seqCNA.annot_1.36.0.tar.gz"}, "serumstimulation-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/serumStimulation_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/serumStimulation_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-serumstimulation/bioconductor-serumstimulation_1.36.0_src_all.tar.gz"], "md5": "642cc4d3939f4a05e331ef5d1f965835", "fn": "serumStimulation_1.36.0.tar.gz"}, "sesamedata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/sesameData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/sesameData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sesamedata/bioconductor-sesamedata_1.18.0_src_all.tar.gz"], "md5": "4af907a4ed795d2493573b88d55fd4de", "fn": "sesameData_1.18.0.tar.gz"}, "seventygenedata-1.36.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/seventyGeneData_1.36.1.tar.gz", "https://bioarchive.galaxyproject.org/seventyGeneData_1.36.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seventygenedata/bioconductor-seventygenedata_1.36.1_src_all.tar.gz"], "md5": "f7c9703c12b845c5c2eb6cf583fb0f02", "fn": "seventyGeneData_1.36.1.tar.gz"}, "sfedata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SFEData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/SFEData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sfedata/bioconductor-sfedata_1.2.0_src_all.tar.gz"], "md5": "405e15fbe6e99736481e40164abf3b04", "fn": "SFEData_1.2.0.tar.gz"}, "shinymethyldata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/shinyMethylData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/shinyMethylData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-shinymethyldata/bioconductor-shinymethyldata_1.20.0_src_all.tar.gz"], "md5": "f633d8b104a4f61c393b15f59671039b", "fn": "shinyMethylData_1.20.0.tar.gz"}, "signaturesearchdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/signatureSearchData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/signatureSearchData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-signaturesearchdata/bioconductor-signaturesearchdata_1.14.0_src_all.tar.gz"], "md5": "5b3174e0e3af77fea49a107ef423adb3", "fn": "signatureSearchData_1.14.0.tar.gz"}, "simbenchdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SimBenchData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/SimBenchData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-simbenchdata/bioconductor-simbenchdata_1.8.0_src_all.tar.gz"], "md5": "5b2d78e96922a7935cbe5ba91a129b0f", "fn": "SimBenchData_1.8.0.tar.gz"}, "simpintlists-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/simpIntLists_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/simpIntLists_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-simpintlists/bioconductor-simpintlists_1.36.0_src_all.tar.gz"], "md5": "eb06f66a10c4e02738fdfaff769c2dfd", "fn": "simpIntLists_1.36.0.tar.gz"}, "single.mtec.transcriptomes-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/Single.mTEC.Transcriptomes_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/Single.mTEC.Transcriptomes_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-single.mtec.transcriptomes/bioconductor-single.mtec.transcriptomes_1.28.0_src_all.tar.gz"], "md5": "11ebbf5ecaf89f0433719a71a8df67b2", "fn": "Single.mTEC.Transcriptomes_1.28.0.tar.gz"}, "singlecellmultimodal-1.12.2": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SingleCellMultiModal_1.12.2.tar.gz", "https://bioarchive.galaxyproject.org/SingleCellMultiModal_1.12.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-singlecellmultimodal/bioconductor-singlecellmultimodal_1.12.2_src_all.tar.gz"], "md5": "599f48321756805173d2069623a0319d", "fn": "SingleCellMultiModal_1.12.2.tar.gz"}, "singlemoleculefootprintingdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SingleMoleculeFootprintingData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/SingleMoleculeFootprintingData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-singlemoleculefootprintingdata/bioconductor-singlemoleculefootprintingdata_1.8.0_src_all.tar.gz"], "md5": "fc061d235ffc26615634a650aedd4ac0", "fn": "SingleMoleculeFootprintingData_1.8.0.tar.gz"}, "snadata-1.46.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SNAData_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/SNAData_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snadata/bioconductor-snadata_1.46.0_src_all.tar.gz"], "md5": "3d83f5e312b308aacb8c9c83d3226115", "fn": "SNAData_1.46.0.tar.gz"}, "snageedata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SNAGEEdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/SNAGEEdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snageedata/bioconductor-snageedata_1.36.0_src_all.tar.gz"], "md5": "e7786160ad882aea9132d3fb2ba77789", "fn": "SNAGEEdata_1.36.0.tar.gz"}, "snphooddata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SNPhoodData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/SNPhoodData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snphooddata/bioconductor-snphooddata_1.30.0_src_all.tar.gz"], "md5": "fbc9419fda8d78b06f76e62df5639ae9", "fn": "SNPhoodData_1.30.0.tar.gz"}, "somaticadata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SomatiCAData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/SomatiCAData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-somaticadata/bioconductor-somaticadata_1.38.0_src_all.tar.gz"], "md5": "1ec746e24a46ea58a782f2d7e18b9c29", "fn": "SomatiCAData_1.38.0.tar.gz"}, "somaticcanceralterations-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SomaticCancerAlterations_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/SomaticCancerAlterations_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-somaticcanceralterations/bioconductor-somaticcanceralterations_1.36.0_src_all.tar.gz"], "md5": "09b8e014009801826dde224175c1f774", "fn": "SomaticCancerAlterations_1.36.0.tar.gz"}, "spatialdmelxsim-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/spatialDmelxsim_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/spatialDmelxsim_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatialdmelxsim/bioconductor-spatialdmelxsim_1.6.0_src_all.tar.gz"], "md5": "22f1c5de1fd6bcbee102e17bbf0323eb", "fn": "spatialDmelxsim_1.6.0.tar.gz"}, "spatiallibd-1.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/spatialLIBD_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/spatialLIBD_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatiallibd/bioconductor-spatiallibd_1.12.0_src_all.tar.gz"], "md5": "1c14166eb3d988b152448d770f491507", "fn": "spatialLIBD_1.12.0.tar.gz"}, "spikein-1.42.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SpikeIn_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/SpikeIn_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spikein/bioconductor-spikein_1.42.0_src_all.tar.gz"], "md5": "e738872c55386dae6334ee399c4674a3", "fn": "SpikeIn_1.42.0.tar.gz"}, "spikeinsubset-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SpikeInSubset_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/SpikeInSubset_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spikeinsubset/bioconductor-spikeinsubset_1.40.0_src_all.tar.gz"], "md5": "25b553c357880acdabf962253d55d69b", "fn": "SpikeInSubset_1.40.0.tar.gz"}, "spqndata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/spqnData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/spqnData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spqndata/bioconductor-spqndata_1.12.0_src_all.tar.gz"], "md5": "1588ea6c755eb468f60af1a67712cac0", "fn": "spqnData_1.12.0.tar.gz"}, "stemhypoxia-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/stemHypoxia_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/stemHypoxia_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stemhypoxia/bioconductor-stemhypoxia_1.36.0_src_all.tar.gz"], "md5": "53b049bafffb969dea77f35479720221", "fn": "stemHypoxia_1.36.0.tar.gz"}, "stexampledata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/STexampleData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/STexampleData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stexampledata/bioconductor-stexampledata_1.8.0_src_all.tar.gz"], "md5": "21ccea26e0677e8ff1ec5ddfe7da0a32", "fn": "STexampleData_1.8.0.tar.gz"}, "stjudem-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/stjudem_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/stjudem_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stjudem/bioconductor-stjudem_1.40.0_src_all.tar.gz"], "md5": "d793d5b3f5abf684f188723111097faf", "fn": "stjudem_1.40.0.tar.gz"}, "svm2crmdata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/SVM2CRMdata_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/SVM2CRMdata_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-svm2crmdata/bioconductor-svm2crmdata_1.32.0_src_all.tar.gz"], "md5": "e1d44ea0446ba41c2f9264ab088461e2", "fn": "SVM2CRMdata_1.32.0.tar.gz"}, "synapterdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/synapterdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/synapterdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-synapterdata/bioconductor-synapterdata_1.38.0_src_all.tar.gz"], "md5": "cfc22e448bd4d28d06535acfc93cea7b", "fn": "synapterdata_1.38.0.tar.gz"}, "systempiperdata-2.4.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/systemPipeRdata_2.4.0.tar.gz", "https://bioarchive.galaxyproject.org/systemPipeRdata_2.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-systempiperdata/bioconductor-systempiperdata_2.4.0_src_all.tar.gz"], "md5": "afa259f7cd53e2252902a48dd32df1b9", "fn": "systemPipeRdata_2.4.0.tar.gz"}, "tabulamurisdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TabulaMurisData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TabulaMurisData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tabulamurisdata/bioconductor-tabulamurisdata_1.18.0_src_all.tar.gz"], "md5": "c198946ebcce0c1e6c79c65f52a11642", "fn": "TabulaMurisData_1.18.0.tar.gz"}, "tabulamurissenisdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TabulaMurisSenisData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/TabulaMurisSenisData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tabulamurissenisdata/bioconductor-tabulamurissenisdata_1.6.0_src_all.tar.gz"], "md5": "c6a42dc2dc0bbabe7cfd25c91e11f050", "fn": "TabulaMurisSenisData_1.6.0.tar.gz"}, "targetscoredata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TargetScoreData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/TargetScoreData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetscoredata/bioconductor-targetscoredata_1.36.0_src_all.tar.gz"], "md5": "63ccf68833f45d1a853a719046cf9def", "fn": "TargetScoreData_1.36.0.tar.gz"}, "targetsearchdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TargetSearchData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/TargetSearchData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetsearchdata/bioconductor-targetsearchdata_1.38.0_src_all.tar.gz"], "md5": "6dd9996121d44e6f753ce68434de7aad", "fn": "TargetSearchData_1.38.0.tar.gz"}, "tartare-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/tartare_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/tartare_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tartare/bioconductor-tartare_1.14.0_src_all.tar.gz"], "md5": "10b4601e60890e48d47840d2a4f03a22", "fn": "tartare_1.14.0.tar.gz"}, "tbx20bamsubset-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TBX20BamSubset_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/TBX20BamSubset_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tbx20bamsubset/bioconductor-tbx20bamsubset_1.36.0_src_all.tar.gz"], "md5": "5b8761f75b20b32450d6cae46dc063a9", "fn": "TBX20BamSubset_1.36.0.tar.gz"}, "tcgabiolinksgui.data-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TCGAbiolinksGUI.data_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAbiolinksGUI.data_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgabiolinksgui.data/bioconductor-tcgabiolinksgui.data_1.20.0_src_all.tar.gz"], "md5": "d0764549e842b85e9ed17bb0e27b1c54", "fn": "TCGAbiolinksGUI.data_1.20.0.tar.gz"}, "tcgacrcmirna-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TCGAcrcmiRNA_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAcrcmiRNA_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmirna/bioconductor-tcgacrcmirna_1.20.0_src_all.tar.gz"], "md5": "a286cf4adf594bccf4910c3445e2901c", "fn": "TCGAcrcmiRNA_1.20.0.tar.gz"}, "tcgacrcmrna-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TCGAcrcmRNA_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAcrcmRNA_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmrna/bioconductor-tcgacrcmrna_1.20.0_src_all.tar.gz"], "md5": "d3f199714f9dba5ed0838af4e6646c7e", "fn": "TCGAcrcmRNA_1.20.0.tar.gz"}, "tcgamethylation450k-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TCGAMethylation450k_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAMethylation450k_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgamethylation450k/bioconductor-tcgamethylation450k_1.36.0_src_all.tar.gz"], "md5": "5d230a3e839f3ac33e404453c46dfa4f", "fn": "TCGAMethylation450k_1.36.0.tar.gz"}, "tcgaworkflowdata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TCGAWorkflowData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAWorkflowData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgaworkflowdata/bioconductor-tcgaworkflowdata_1.24.0_src_all.tar.gz"], "md5": "12be13d34d28928864db32c639257777", "fn": "TCGAWorkflowData_1.24.0.tar.gz"}, "tenxbraindata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TENxBrainData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxBrainData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxbraindata/bioconductor-tenxbraindata_1.20.0_src_all.tar.gz"], "md5": "74f64ec6654482787dcdc4d6edf085c0", "fn": "TENxBrainData_1.20.0.tar.gz"}, "tenxbusdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TENxBUSData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxBUSData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxbusdata/bioconductor-tenxbusdata_1.14.0_src_all.tar.gz"], "md5": "0ef9324a12e6e70e28a16def5f6e8f8f", "fn": "TENxBUSData_1.14.0.tar.gz"}, "tenxpbmcdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TENxPBMCData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxPBMCData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxpbmcdata/bioconductor-tenxpbmcdata_1.18.0_src_all.tar.gz"], "md5": "6902ddadd45f76cce7e73228ed4bdcaf", "fn": "TENxPBMCData_1.18.0.tar.gz"}, "tenxvisiumdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TENxVisiumData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxVisiumData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxvisiumdata/bioconductor-tenxvisiumdata_1.8.0_src_all.tar.gz"], "md5": "cd391f3b1849f658578a44cfe2aec13b", "fn": "TENxVisiumData_1.8.0.tar.gz"}, "timecoursedata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/timecoursedata_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/timecoursedata_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-timecoursedata/bioconductor-timecoursedata_1.10.0_src_all.tar.gz"], "md5": "7f2ad9b14757098a934109a0597a630b", "fn": "timecoursedata_1.10.0.tar.gz"}, "timerquant-1.30.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TimerQuant_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/TimerQuant_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-timerquant/bioconductor-timerquant_1.30.0_src_all.tar.gz"], "md5": "8cbdff0672ae0d06372f36e5de1dc86c", "fn": "TimerQuant_1.30.0.tar.gz"}, "tinesath1cdf-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/tinesath1cdf_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/tinesath1cdf_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tinesath1cdf/bioconductor-tinesath1cdf_1.38.0_src_all.tar.gz"], "md5": "9e3235aa047fc3dc7d77437a0afa5b71", "fn": "tinesath1cdf_1.38.0.tar.gz"}, "tinesath1probe-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/tinesath1probe_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/tinesath1probe_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tinesath1probe/bioconductor-tinesath1probe_1.38.0_src_all.tar.gz"], "md5": "d3dc0686f2651dff52a201923e73a751", "fn": "tinesath1probe_1.38.0.tar.gz"}, "tissuetreg-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/tissueTreg_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/tissueTreg_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tissuetreg/bioconductor-tissuetreg_1.20.0_src_all.tar.gz"], "md5": "9755c73b171a371afea8927b7d229a78", "fn": "tissueTreg_1.20.0.tar.gz"}, "tmexplorer-1.10.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/TMExplorer_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/TMExplorer_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tmexplorer/bioconductor-tmexplorer_1.10.0_src_all.tar.gz"], "md5": "14411a5488789b44b63a2bc2b88cf33e", "fn": "TMExplorer_1.10.0.tar.gz"}, "tofsimsdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/tofsimsData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/tofsimsData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tofsimsdata/bioconductor-tofsimsdata_1.28.0_src_all.tar.gz"], "md5": "5eccad99f9e3cdfb3813eb1243926142", "fn": "tofsimsData_1.28.0.tar.gz"}, "topdownrdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/topdownrdata_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/topdownrdata_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-topdownrdata/bioconductor-topdownrdata_1.22.0_src_all.tar.gz"], "md5": "c105c5a497f0270c574b757c55eea433", "fn": "topdownrdata_1.22.0.tar.gz"}, "tuberculosis-1.6.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/tuberculosis_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/tuberculosis_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tuberculosis/bioconductor-tuberculosis_1.6.0_src_all.tar.gz"], "md5": "9f3fd16d5debb8705f56bf714fc3e860", "fn": "tuberculosis_1.6.0.tar.gz"}, "tweedeseqcountdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/tweeDEseqCountData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/tweeDEseqCountData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tweedeseqcountdata/bioconductor-tweedeseqcountdata_1.38.0_src_all.tar.gz"], "md5": "b48baebaa2abe35419bad4110d7523ec", "fn": "tweeDEseqCountData_1.38.0.tar.gz"}, "tximportdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/tximportData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/tximportData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tximportdata/bioconductor-tximportdata_1.28.0_src_all.tar.gz"], "md5": "8b5ef0f4b63bcd11c21a8389af32fa1f", "fn": "tximportData_1.28.0.tar.gz"}, "varianttoolsdata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/VariantToolsData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/VariantToolsData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-varianttoolsdata/bioconductor-varianttoolsdata_1.24.0_src_all.tar.gz"], "md5": "abaad839d98a3c855cac80bd443fa9b6", "fn": "VariantToolsData_1.24.0.tar.gz"}, "vectrapolarisdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/VectraPolarisData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/VectraPolarisData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vectrapolarisdata/bioconductor-vectrapolarisdata_1.4.0_src_all.tar.gz"], "md5": "f427b5860f7e3498064deabff0328263", "fn": "VectraPolarisData_1.4.0.tar.gz"}, "vulcandata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/vulcandata_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/vulcandata_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vulcandata/bioconductor-vulcandata_1.22.0_src_all.tar.gz"], "md5": "e51d04a9825be5fdb9591377095a0da9", "fn": "vulcandata_1.22.0.tar.gz"}, "weberdivechalcdata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/WeberDivechaLCdata_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/WeberDivechaLCdata_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-weberdivechalcdata/bioconductor-weberdivechalcdata_1.2.0_src_all.tar.gz"], "md5": "f7b4867dc3ce8463050bd897209d00c4", "fn": "WeberDivechaLCdata_1.2.0.tar.gz"}, "wes.1kg.wugsc-1.32.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/WES.1KG.WUGSC_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/WES.1KG.WUGSC_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wes.1kg.wugsc/bioconductor-wes.1kg.wugsc_1.32.0_src_all.tar.gz"], "md5": "4037de5e802a16f5aae76eca264b0be7", "fn": "WES.1KG.WUGSC_1.32.0.tar.gz"}, "wgsmapp-1.12.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/WGSmapp_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/WGSmapp_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wgsmapp/bioconductor-wgsmapp_1.12.0_src_all.tar.gz"], "md5": "7e4b497bab5e73445e19a84f86e40888", "fn": "WGSmapp_1.12.0.tar.gz"}, "xcoredata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/xcoredata_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/xcoredata_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xcoredata/bioconductor-xcoredata_1.4.0_src_all.tar.gz"], "md5": "172e8208ccf23b03ead836908e84522a", "fn": "xcoredata_1.4.0.tar.gz"}, "xhybcasneuf-1.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/XhybCasneuf_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/XhybCasneuf_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xhybcasneuf/bioconductor-xhybcasneuf_1.38.0_src_all.tar.gz"], "md5": "9522270bba562cca4c2e5e2438294eca", "fn": "XhybCasneuf_1.38.0.tar.gz"}, "yeastcc-1.40.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/yeastCC_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastCC_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastcc/bioconductor-yeastcc_1.40.0_src_all.tar.gz"], "md5": "bf769fb99f3c5b763cc44fb25947231a", "fn": "yeastCC_1.40.0.tar.gz"}, "yeastexpdata-0.46.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/yeastExpData_0.46.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastExpData_0.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastexpdata/bioconductor-yeastexpdata_0.46.0_src_all.tar.gz"], "md5": "57c3359351ed64d39e2d8d82abe2d852", "fn": "yeastExpData_0.46.0.tar.gz"}, "yeastgsdata-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/yeastGSData_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastGSData_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastgsdata/bioconductor-yeastgsdata_0.38.0_src_all.tar.gz"], "md5": "09f1e0c194efae4d807ab0b3b14629a5", "fn": "yeastGSData_0.38.0.tar.gz"}, "yeastnagalakshmi-1.36.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/yeastNagalakshmi_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastNagalakshmi_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastnagalakshmi/bioconductor-yeastnagalakshmi_1.36.0_src_all.tar.gz"], "md5": "e9c196bfda6e0909a324d88a616dc992", "fn": "yeastNagalakshmi_1.36.0.tar.gz"}, "yeastrnaseq-0.38.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/yeastRNASeq_0.38.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastRNASeq_0.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastrnaseq/bioconductor-yeastrnaseq_0.38.0_src_all.tar.gz"], "md5": "f8a8b1a80312aeac4d1676bc8adcb0ee", "fn": "yeastRNASeq_0.38.0.tar.gz"}, "zebrafishrnaseq-1.20.0": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/zebrafishRNASeq_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafishRNASeq_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafishrnaseq/bioconductor-zebrafishrnaseq_1.20.0_src_all.tar.gz"], "md5": "06390452c93fde30918ee5c5a3f6e5f2", "fn": "zebrafishRNASeq_1.20.0.tar.gz"}, "biscuiteerdata-1.14.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/biscuiteerData_1.14.1.tar.gz", "https://bioarchive.galaxyproject.org/biscuiteerData_1.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biscuiteerdata/bioconductor-biscuiteerdata_1.14.1_src_all.tar.gz"], "md5": "143bedc239cf56a25dc8bf6c1e98d392", "fn": "biscuiteerData_1.14.1.tar.gz"}, "spatialdmelxsim-1.6.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/spatialDmelxsim_1.6.1.tar.gz", "https://bioarchive.galaxyproject.org/spatialDmelxsim_1.6.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatialdmelxsim/bioconductor-spatialdmelxsim_1.6.1_src_all.tar.gz"], "md5": "8f999976552a56f39d49fd9ee186b017", "fn": "spatialDmelxsim_1.6.1.tar.gz"}, "mcseadata-1.20.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/mCSEAdata_1.20.1.tar.gz", "https://bioarchive.galaxyproject.org/mCSEAdata_1.20.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcseadata/bioconductor-mcseadata_1.20.1_src_all.tar.gz"], "md5": "43b69165fffc6652fc2df2395bd0b8e6", "fn": "mCSEAdata_1.20.1.tar.gz"}, "methylclockdata-1.8.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/methylclockData_1.8.1.tar.gz", "https://bioarchive.galaxyproject.org/methylclockData_1.8.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylclockdata/bioconductor-methylclockdata_1.8.1_src_all.tar.gz"], "md5": "c211da6ed8d39ba8cee6d4d630691bad", "fn": "methylclockData_1.8.1.tar.gz"}, "affydata-1.48.1": {"urls": ["https://bioconductor.org/packages/3.17/data/experiment/src/contrib/affydata_1.48.1.tar.gz", "https://bioarchive.galaxyproject.org/affydata_1.48.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affydata/bioconductor-affydata_1.48.1_src_all.tar.gz"], "md5": "1c03aa529e4854f6680fcf4702d2bea7", "fn": "affydata_1.48.1.tar.gz"}, "ahensdbs-1.1.10": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/AHEnsDbs_1.1.10.tar.gz", "https://bioarchive.galaxyproject.org/AHEnsDbs_1.1.10.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahensdbs/bioconductor-ahensdbs_1.1.10_src_all.tar.gz"], "md5": "63aa3efc1c85d5a26e4d69d50f781a2a", "fn": "AHEnsDbs_1.1.10.tar.gz"}, "ahlrbasedbs-1.7.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/AHLRBaseDbs_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/AHLRBaseDbs_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahlrbasedbs/bioconductor-ahlrbasedbs_1.7.0_src_all.tar.gz"], "md5": "5df6ef84988477d6262e54abd07c82da", "fn": "AHLRBaseDbs_1.7.0.tar.gz"}, "ahmeshdbs-1.7.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/AHMeSHDbs_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/AHMeSHDbs_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahmeshdbs/bioconductor-ahmeshdbs_1.7.0_src_all.tar.gz"], "md5": "9bbcae25794d2f854a122ba36a4e4c5c", "fn": "AHMeSHDbs_1.7.0.tar.gz"}, "ahpubmeddbs-1.7.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/AHPubMedDbs_1.7.0.tar.gz", "https://bioarchive.galaxyproject.org/AHPubMedDbs_1.7.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahpubmeddbs/bioconductor-ahpubmeddbs_1.7.0_src_all.tar.gz"], "md5": "b2db2eda6009bc9cdec579c4ab579f25", "fn": "AHPubMedDbs_1.7.0.tar.gz"}, "alphamissense.v2023.hg19-3.18.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/AlphaMissense.v2023.hg19_3.18.2.tar.gz", "https://bioarchive.galaxyproject.org/AlphaMissense.v2023.hg19_3.18.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-alphamissense.v2023.hg19/bioconductor-alphamissense.v2023.hg19_3.18.2_src_all.tar.gz"], "md5": "e8784ad000be637321f432188a5a3f45", "fn": "AlphaMissense.v2023.hg19_3.18.2.tar.gz"}, "alphamissense.v2023.hg38-3.18.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/AlphaMissense.v2023.hg38_3.18.2.tar.gz", "https://bioarchive.galaxyproject.org/AlphaMissense.v2023.hg38_3.18.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-alphamissense.v2023.hg38/bioconductor-alphamissense.v2023.hg38_3.18.2_src_all.tar.gz"], "md5": "bedac9523e18829c5067dec1ebf801d4", "fn": "AlphaMissense.v2023.hg38_3.18.2.tar.gz"}, "anopheles.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/anopheles.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/anopheles.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-anopheles.db0/bioconductor-anopheles.db0_3.18.0_src_all.tar.gz"], "md5": "cd7b03fffb4ffd0cf0877a55a3636d93", "fn": "anopheles.db0_3.18.0.tar.gz"}, "arabidopsis.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/arabidopsis.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/arabidopsis.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-arabidopsis.db0/bioconductor-arabidopsis.db0_3.18.0_src_all.tar.gz"], "md5": "5896dbae0f9f8fdc87712dba0bb6cbd1", "fn": "arabidopsis.db0_3.18.0.tar.gz"}, "biomartgogenesets-0.99.11": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BioMartGOGeneSets_0.99.11.tar.gz", "https://bioarchive.galaxyproject.org/BioMartGOGeneSets_0.99.11.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biomartgogenesets/bioconductor-biomartgogenesets_0.99.11_src_all.tar.gz"], "md5": "f96a12703fd2f9c357442a60e5f2c764", "fn": "BioMartGOGeneSets_0.99.11.tar.gz"}, "bovine.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/bovine.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/bovine.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bovine.db0/bioconductor-bovine.db0_3.18.0_src_all.tar.gz"], "md5": "658829797db74aec87af1914483d1af7", "fn": "bovine.db0_3.18.0.tar.gz"}, "cadd.v1.6.hg19-3.18.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/cadd.v1.6.hg19_3.18.1.tar.gz", "https://bioarchive.galaxyproject.org/cadd.v1.6.hg19_3.18.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cadd.v1.6.hg19/bioconductor-cadd.v1.6.hg19_3.18.1_src_all.tar.gz"], "md5": "10cc50d17dbca89406a2290f37d5203c", "fn": "cadd.v1.6.hg19_3.18.1.tar.gz"}, "cadd.v1.6.hg38-3.18.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/cadd.v1.6.hg38_3.18.1.tar.gz", "https://bioarchive.galaxyproject.org/cadd.v1.6.hg38_3.18.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cadd.v1.6.hg38/bioconductor-cadd.v1.6.hg38_3.18.1_src_all.tar.gz"], "md5": "620a889ea8bc55f98811a80a3aec814d", "fn": "cadd.v1.6.hg38_3.18.1.tar.gz"}, "canine.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/canine.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/canine.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canine.db0/bioconductor-canine.db0_3.18.0_src_all.tar.gz"], "md5": "dc4fff8ed0a758ddff3f52aa0e8652c6", "fn": "canine.db0_3.18.0.tar.gz"}, "chicken.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/chicken.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/chicken.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chicken.db0/bioconductor-chicken.db0_3.18.0_src_all.tar.gz"], "md5": "0f0c20a519a9490c0909b68ec67c206d", "fn": "chicken.db0_3.18.0.tar.gz"}, "chimp.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/chimp.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/chimp.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chimp.db0/bioconductor-chimp.db0_3.18.0_src_all.tar.gz"], "md5": "afb020cefb808101626234257bf71f69", "fn": "chimp.db0_3.18.0.tar.gz"}, "ecolik12.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ecoliK12.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliK12.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolik12.db0/bioconductor-ecolik12.db0_3.18.0_src_all.tar.gz"], "md5": "dd303204595a25bc730695462e930247", "fn": "ecoliK12.db0_3.18.0.tar.gz"}, "ecolisakai.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/ecoliSakai.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliSakai.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolisakai.db0/bioconductor-ecolisakai.db0_3.18.0_src_all.tar.gz"], "md5": "2afd28e9062d869d37e3d65dbe410bcb", "fn": "ecoliSakai.db0_3.18.0.tar.gz"}, "fly.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/fly.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/fly.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fly.db0/bioconductor-fly.db0_3.18.0_src_all.tar.gz"], "md5": "49722b8a538d02f71631a418b92c44d7", "fn": "fly.db0_3.18.0.tar.gz"}, "geneplast.data-0.99.7": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/geneplast.data_0.99.7.tar.gz", "https://bioarchive.galaxyproject.org/geneplast.data_0.99.7.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-geneplast.data/bioconductor-geneplast.data_0.99.7_src_all.tar.gz"], "md5": "ef658e131138d87033fcd985c38cf45f", "fn": "geneplast.data_0.99.7.tar.gz"}, "genesummary-0.99.6": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/GeneSummary_0.99.6.tar.gz", "https://bioarchive.galaxyproject.org/GeneSummary_0.99.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genesummary/bioconductor-genesummary_0.99.6_src_all.tar.gz"], "md5": "9df029a96bf0fa5bb76ee8b8923c458c", "fn": "GeneSummary_0.99.6.tar.gz"}, "genomeinfodbdata-1.2.11": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz", "https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.11.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.11_src_all.tar.gz"], "md5": "2a4cbfc2031992fed3c9445f450890a2", "fn": "GenomeInfoDbData_1.2.11.tar.gz"}, "go.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GO.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/GO.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-go.db/bioconductor-go.db_3.18.0_src_all.tar.gz"], "md5": "b23522167263afc45a9b115d01632cb1", "fn": "GO.db_3.18.0.tar.gz"}, "hpo.db-0.99.2": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/HPO.db_0.99.2.tar.gz", "https://bioarchive.galaxyproject.org/HPO.db_0.99.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hpo.db/bioconductor-hpo.db_0.99.2_src_all.tar.gz"], "md5": "977cfb31ff344c58fd2dd0a2c6b765ab", "fn": "HPO.db_0.99.2.tar.gz"}, "human.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/human.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/human.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human.db0/bioconductor-human.db0_3.18.0_src_all.tar.gz"], "md5": "e3b04d46f0618785b37fb84bb899295e", "fn": "human.db0_3.18.0.tar.gz"}, "jaspar2024-0.99.6": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/JASPAR2024_0.99.6.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2024_0.99.6.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2024/bioconductor-jaspar2024_0.99.6_src_all.tar.gz"], "md5": "9c8144547873a36473a5f9cad793f578", "fn": "JASPAR2024_0.99.6.tar.gz"}, "malaria.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/malaria.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/malaria.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-malaria.db0/bioconductor-malaria.db0_3.18.0_src_all.tar.gz"], "md5": "6f71b4ac69ae5237f3f5e1337d5073d7", "fn": "malaria.db0_3.18.0.tar.gz"}, "mouse.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/mouse.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse.db0/bioconductor-mouse.db0_3.18.0_src_all.tar.gz"], "md5": "1ef6bb1d25e53443871e0e8c975b36c0", "fn": "mouse.db0_3.18.0.tar.gz"}, "mpo.db-0.99.7": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/MPO.db_0.99.7.tar.gz", "https://bioarchive.galaxyproject.org/MPO.db_0.99.7.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mpo.db/bioconductor-mpo.db_0.99.7_src_all.tar.gz"], "md5": "1f1b83d5d03d69a82ca2b9e7179b537f", "fn": "MPO.db_0.99.7.tar.gz"}, "org.ag.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Ag.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ag.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ag.eg.db/bioconductor-org.ag.eg.db_3.18.0_src_all.tar.gz"], "md5": "a67c309f5472338fd47fe43ff20ce2e5", "fn": "org.Ag.eg.db_3.18.0.tar.gz"}, "org.at.tair.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.At.tair.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.At.tair.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.at.tair.db/bioconductor-org.at.tair.db_3.18.0_src_all.tar.gz"], "md5": "5d6161b859de99eaeadebc0e03ae9c68", "fn": "org.At.tair.db_3.18.0.tar.gz"}, "org.bt.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Bt.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Bt.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.bt.eg.db/bioconductor-org.bt.eg.db_3.18.0_src_all.tar.gz"], "md5": "23fd8017323c86930c50d596204bad54", "fn": "org.Bt.eg.db_3.18.0.tar.gz"}, "org.ce.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Ce.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ce.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ce.eg.db/bioconductor-org.ce.eg.db_3.18.0_src_all.tar.gz"], "md5": "441a5efb4649a1201b5552b14c1f1cef", "fn": "org.Ce.eg.db_3.18.0.tar.gz"}, "org.cf.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Cf.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Cf.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.cf.eg.db/bioconductor-org.cf.eg.db_3.18.0_src_all.tar.gz"], "md5": "038d08c046a81218a31ff8db0877dd15", "fn": "org.Cf.eg.db_3.18.0.tar.gz"}, "org.dm.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Dm.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Dm.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.dm.eg.db/bioconductor-org.dm.eg.db_3.18.0_src_all.tar.gz"], "md5": "92577ed3bc5d76b78905169eebfebe7d", "fn": "org.Dm.eg.db_3.18.0.tar.gz"}, "org.dr.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Dr.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Dr.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.dr.eg.db/bioconductor-org.dr.eg.db_3.18.0_src_all.tar.gz"], "md5": "cfea28c45f2f34c675975eacbe861a5f", "fn": "org.Dr.eg.db_3.18.0.tar.gz"}, "org.eck12.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.EcK12.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.EcK12.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.eck12.eg.db/bioconductor-org.eck12.eg.db_3.18.0_src_all.tar.gz"], "md5": "50d3d3ca9efec212eae3a920b00750a3", "fn": "org.EcK12.eg.db_3.18.0.tar.gz"}, "org.ecsakai.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.EcSakai.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.EcSakai.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ecsakai.eg.db/bioconductor-org.ecsakai.eg.db_3.18.0_src_all.tar.gz"], "md5": "3f26ffa55ce30fc8caa64f826207ac61", "fn": "org.EcSakai.eg.db_3.18.0.tar.gz"}, "org.gg.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Gg.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Gg.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.gg.eg.db/bioconductor-org.gg.eg.db_3.18.0_src_all.tar.gz"], "md5": "4ebcbfb0baeee3332a2a07aeae2402a9", "fn": "org.Gg.eg.db_3.18.0.tar.gz"}, "org.hs.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Hs.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Hs.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.hs.eg.db/bioconductor-org.hs.eg.db_3.18.0_src_all.tar.gz"], "md5": "e1f74b9d0c541b5678a0d88f6a8ec847", "fn": "org.Hs.eg.db_3.18.0.tar.gz"}, "org.mm.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Mm.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Mm.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.mm.eg.db/bioconductor-org.mm.eg.db_3.18.0_src_all.tar.gz"], "md5": "bd95e1ff46f764fff51acc60b249fe95", "fn": "org.Mm.eg.db_3.18.0.tar.gz"}, "org.mmu.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Mmu.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Mmu.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.mmu.eg.db/bioconductor-org.mmu.eg.db_3.18.0_src_all.tar.gz"], "md5": "45a35940d0d1ab91b2b262a8666afa53", "fn": "org.Mmu.eg.db_3.18.0.tar.gz"}, "org.pt.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Pt.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Pt.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.pt.eg.db/bioconductor-org.pt.eg.db_3.18.0_src_all.tar.gz"], "md5": "d6672365e68ece6415e2736f40bf096c", "fn": "org.Pt.eg.db_3.18.0.tar.gz"}, "org.rn.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Rn.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Rn.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.rn.eg.db/bioconductor-org.rn.eg.db_3.18.0_src_all.tar.gz"], "md5": "1ff92cec0fc2cbd5b3055d1153526ce3", "fn": "org.Rn.eg.db_3.18.0.tar.gz"}, "org.sc.sgd.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Sc.sgd.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Sc.sgd.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.sc.sgd.db/bioconductor-org.sc.sgd.db_3.18.0_src_all.tar.gz"], "md5": "cd83de7109be623e7a294a47ca65f160", "fn": "org.Sc.sgd.db_3.18.0.tar.gz"}, "org.ss.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Ss.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ss.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ss.eg.db/bioconductor-org.ss.eg.db_3.18.0_src_all.tar.gz"], "md5": "f9b32c76d23f9195df7a7eb6529f3340", "fn": "org.Ss.eg.db_3.18.0.tar.gz"}, "org.xl.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Xl.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Xl.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.xl.eg.db/bioconductor-org.xl.eg.db_3.18.0_src_all.tar.gz"], "md5": "bbea76a4373d8b51048029b83c591aca", "fn": "org.Xl.eg.db_3.18.0.tar.gz"}, "orthology.eg.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/Orthology.eg.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/Orthology.eg.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-orthology.eg.db/bioconductor-orthology.eg.db_3.18.0_src_all.tar.gz"], "md5": "1e53a6a144a5074544cbe166ad241012", "fn": "Orthology.eg.db_3.18.0.tar.gz"}, "panther.db-1.0.12": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/PANTHER.db_1.0.12.tar.gz", "https://bioarchive.galaxyproject.org/PANTHER.db_1.0.12.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-panther.db/bioconductor-panther.db_1.0.12_src_all.tar.gz"], "md5": "edafd1c94f2f1cf3975f525fae7a9b83", "fn": "PANTHER.db_1.0.12.tar.gz"}, "pfam.db-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/PFAM.db_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/PFAM.db_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pfam.db/bioconductor-pfam.db_3.18.0_src_all.tar.gz"], "md5": "f98f5d1e5d335e6bbf1ea6426cde67bb", "fn": "PFAM.db_3.18.0.tar.gz"}, "pig.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/pig.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/pig.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pig.db0/bioconductor-pig.db0_3.18.0_src_all.tar.gz"], "md5": "85aaccdbdb969825957db45db3fb7801", "fn": "pig.db0_3.18.0.tar.gz"}, "rat.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rat.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rat.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat.db0/bioconductor-rat.db0_3.18.0_src_all.tar.gz"], "md5": "cde666f86ec7b61beb8cf1037511f977", "fn": "rat.db0_3.18.0.tar.gz"}, "reactome.db-1.86.2": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/reactome.db_1.86.2.tar.gz", "https://bioarchive.galaxyproject.org/reactome.db_1.86.2.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-reactome.db/bioconductor-reactome.db_1.86.2_src_all.tar.gz"], "md5": "ff56f3908b347cb18e3e4ccedf7f584e", "fn": "reactome.db_1.86.2.tar.gz"}, "rhesus.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/rhesus.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/rhesus.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rhesus.db0/bioconductor-rhesus.db0_3.18.0_src_all.tar.gz"], "md5": "26d7aa426d23f0c64cb0918f90c32314", "fn": "rhesus.db0_3.18.0.tar.gz"}, "somascan.db-0.99.7": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/SomaScan.db_0.99.7.tar.gz", "https://bioarchive.galaxyproject.org/SomaScan.db_0.99.7.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-somascan.db/bioconductor-somascan.db_0.99.7_src_all.tar.gz"], "md5": "aa52f4f12dfb2f0aa4c7fe3633de4646", "fn": "SomaScan.db_0.99.7.tar.gz"}, "synaptome.db-0.99.15": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/synaptome.db_0.99.15.tar.gz", "https://bioarchive.galaxyproject.org/synaptome.db_0.99.15.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-synaptome.db/bioconductor-synaptome.db_0.99.15_src_all.tar.gz"], "md5": "7ed11d61ac8dca86372eeec59b5ab03b", "fn": "synaptome.db_0.99.15.tar.gz"}, "txdb.hsapiens.ucsc.hg38.knowngene-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg38.knownGene_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_3.18.0_src_all.tar.gz"], "md5": "2344dbd2878c82c6c860ed6529a700b2", "fn": "TxDb.Hsapiens.UCSC.hg38.knownGene_3.18.0.tar.gz"}, "txdb.hsapiens.ucsc.hg38.refgene-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.refGene_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg38.refGene_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/bioconductor-txdb.hsapiens.ucsc.hg38.refgene_3.18.0_src_all.tar.gz"], "md5": "7ec982095ea795b99d53b6549d7ba4d4", "fn": "TxDb.Hsapiens.UCSC.hg38.refGene_3.18.0.tar.gz"}, "txdb.mmusculus.ucsc.mm39.knowngene-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm39.knownGene_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm39.knownGene_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene_3.18.0_src_all.tar.gz"], "md5": "5ceb110ce3327d44f45bf5118ec7f3af", "fn": "TxDb.Mmusculus.UCSC.mm39.knownGene_3.18.0.tar.gz"}, "txdb.mmusculus.ucsc.mm39.refgene-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm39.refGene_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm39.refGene_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/bioconductor-txdb.mmusculus.ucsc.mm39.refgene_3.18.0_src_all.tar.gz"], "md5": "2fd64557d5f1bade11432b666c63f33a", "fn": "TxDb.Mmusculus.UCSC.mm39.refGene_3.18.0.tar.gz"}, "uniprotkeywords-0.99.7": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/UniProtKeywords_0.99.7.tar.gz", "https://bioarchive.galaxyproject.org/UniProtKeywords_0.99.7.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-uniprotkeywords/bioconductor-uniprotkeywords_0.99.7_src_all.tar.gz"], "md5": "b2cda32dda256fb0d110192e194af838", "fn": "UniProtKeywords_0.99.7.tar.gz"}, "worm.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/worm.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/worm.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-worm.db0/bioconductor-worm.db0_3.18.0_src_all.tar.gz"], "md5": "67be1277b5ae184558259ac720a5741e", "fn": "worm.db0_3.18.0.tar.gz"}, "xenopus.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/xenopus.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/xenopus.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xenopus.db0/bioconductor-xenopus.db0_3.18.0_src_all.tar.gz"], "md5": "67b245b456f21672e70fa0690d7e8410", "fn": "xenopus.db0_3.18.0.tar.gz"}, "yeast.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/yeast.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/yeast.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeast.db0/bioconductor-yeast.db0_3.18.0_src_all.tar.gz"], "md5": "483043596daee94866843e6a43dcf538", "fn": "yeast.db0_3.18.0.tar.gz"}, "zebrafish.db0-3.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/annotation/src/contrib/zebrafish.db0_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafish.db0_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafish.db0/bioconductor-zebrafish.db0_3.18.0_src_all.tar.gz"], "md5": "5da71e369e2b538fe276cd58b511ebab", "fn": "zebrafish.db0_3.18.0.tar.gz"}, "adductdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/adductData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/adductData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-adductdata/bioconductor-adductdata_1.18.0_src_all.tar.gz"], "md5": "bf0e3549ee672a31f32759f0535f360a", "fn": "adductData_1.18.0.tar.gz"}, "affycompdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/affycompData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/affycompData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affycompdata/bioconductor-affycompdata_1.40.0_src_all.tar.gz"], "md5": "205391e19fb160dcff1531892f28b006", "fn": "affycompData_1.40.0.tar.gz"}, "affydata-1.50.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/affydata_1.50.0.tar.gz", "https://bioarchive.galaxyproject.org/affydata_1.50.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affydata/bioconductor-affydata_1.50.0_src_all.tar.gz"], "md5": "29caf389ca94d4c0c0b27d993f33354c", "fn": "affydata_1.50.0.tar.gz"}, "affyhgu133a2expr-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Affyhgu133A2Expr_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133A2Expr_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133a2expr/bioconductor-affyhgu133a2expr_1.38.0_src_all.tar.gz"], "md5": "56296960e5539a4fd84724344f30aaaa", "fn": "Affyhgu133A2Expr_1.38.0.tar.gz"}, "affyhgu133aexpr-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Affyhgu133aExpr_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133aExpr_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133aexpr/bioconductor-affyhgu133aexpr_1.40.0_src_all.tar.gz"], "md5": "2cf458278c574450a3a5ffe64a2aa72b", "fn": "Affyhgu133aExpr_1.40.0.tar.gz"}, "affyhgu133plus2expr-1.36.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Affyhgu133Plus2Expr_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133Plus2Expr_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133plus2expr/bioconductor-affyhgu133plus2expr_1.36.0_src_all.tar.gz"], "md5": "f8baac83db4de07f941552d7b62c8d62", "fn": "Affyhgu133Plus2Expr_1.36.0.tar.gz"}, "affymetrixdatatestfiles-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/AffymetrixDataTestFiles_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/AffymetrixDataTestFiles_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affymetrixdatatestfiles/bioconductor-affymetrixdatatestfiles_0.40.0_src_all.tar.gz"], "md5": "57ecb8e4d3f0d7a9cdcedb2a9648dd1e", "fn": "AffymetrixDataTestFiles_0.40.0.tar.gz"}, "affymoe4302expr-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Affymoe4302Expr_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/Affymoe4302Expr_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affymoe4302expr/bioconductor-affymoe4302expr_1.40.0_src_all.tar.gz"], "md5": "4dcd432d350cf2f8000f67774d95481c", "fn": "Affymoe4302Expr_1.40.0.tar.gz"}, "airway-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/airway_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/airway_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-airway/bioconductor-airway_1.22.0_src_all.tar.gz"], "md5": "ffed4ae3349ebeeeabff9f1456b8ba1d", "fn": "airway_1.22.0.tar.gz"}, "all-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ALL_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/ALL_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-all/bioconductor-all_1.44.0_src_all.tar.gz"], "md5": "b80eb482b4937ef4eac01027ac95a61a", "fn": "ALL_1.44.0.tar.gz"}, "allmll-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ALLMLL_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/ALLMLL_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-allmll/bioconductor-allmll_1.42.0_src_all.tar.gz"], "md5": "669e7ff030b6fea51c8013816bd6fae7", "fn": "ALLMLL_1.42.0.tar.gz"}, "ampaffyexample-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/AmpAffyExample_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/AmpAffyExample_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ampaffyexample/bioconductor-ampaffyexample_1.42.0_src_all.tar.gz"], "md5": "3277d6d26f145ddbb45c3808273cd150", "fn": "AmpAffyExample_1.42.0.tar.gz"}, "aneufinderdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/AneuFinderData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/AneuFinderData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-aneufinderdata/bioconductor-aneufinderdata_1.30.0_src_all.tar.gz"], "md5": "895230cd9b780dbb286a012f3c8777eb", "fn": "AneuFinderData_1.30.0.tar.gz"}, "antiprofilesdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/antiProfilesData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/antiProfilesData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-antiprofilesdata/bioconductor-antiprofilesdata_1.38.0_src_all.tar.gz"], "md5": "dc40c00fb296b31cf65369e801d6f2f8", "fn": "antiProfilesData_1.38.0.tar.gz"}, "aracne.networks-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/aracne.networks_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/aracne.networks_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-aracne.networks/bioconductor-aracne.networks_1.28.0_src_all.tar.gz"], "md5": "42657d0acf4c1ba54aa2057fa4525d51", "fn": "aracne.networks_1.28.0.tar.gz"}, "arrmdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ARRmData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ARRmData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-arrmdata/bioconductor-arrmdata_1.38.0_src_all.tar.gz"], "md5": "95475f869b8ff3d6344c0f45f2e616c9", "fn": "ARRmData_1.38.0.tar.gz"}, "ashkenazimsonchr21-1.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/AshkenazimSonChr21_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/AshkenazimSonChr21_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ashkenazimsonchr21/bioconductor-ashkenazimsonchr21_1.32.0_src_all.tar.gz"], "md5": "a4455fab1d47dcf8dc2411fec1066a2c", "fn": "AshkenazimSonChr21_1.32.0.tar.gz"}, "asicsdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ASICSdata_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/ASICSdata_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-asicsdata/bioconductor-asicsdata_1.22.0_src_all.tar.gz"], "md5": "afb117c0db733e23239bf2cf4e18d364", "fn": "ASICSdata_1.22.0.tar.gz"}, "assessorfdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/AssessORFData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/AssessORFData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-assessorfdata/bioconductor-assessorfdata_1.20.0_src_all.tar.gz"], "md5": "0dd44e672021a9179762efe4959e8608", "fn": "AssessORFData_1.20.0.tar.gz"}, "bcellviper-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/bcellViper_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/bcellViper_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bcellviper/bioconductor-bcellviper_1.38.0_src_all.tar.gz"], "md5": "7e93bbaa204826358c77282e2a370074", "fn": "bcellViper_1.38.0.tar.gz"}, "beadarrayexampledata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/beadarrayExampleData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/beadarrayExampleData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadarrayexampledata/bioconductor-beadarrayexampledata_1.40.0_src_all.tar.gz"], "md5": "d327e659adc868f1e3c7ae457c60087b", "fn": "beadarrayExampleData_1.40.0.tar.gz"}, "beadarrayusecases-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/BeadArrayUseCases_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/BeadArrayUseCases_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadarrayusecases/bioconductor-beadarrayusecases_1.40.0_src_all.tar.gz"], "md5": "a939c03744773755b9a80de63a925c3e", "fn": "BeadArrayUseCases_1.40.0.tar.gz"}, "beadsorted.saliva.epic-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/BeadSorted.Saliva.EPIC_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/BeadSorted.Saliva.EPIC_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadsorted.saliva.epic/bioconductor-beadsorted.saliva.epic_1.10.0_src_all.tar.gz"], "md5": "ca080a144452fad8ce1bdf8e86d88c74", "fn": "BeadSorted.Saliva.EPIC_1.10.0.tar.gz"}, "benchmarkfdrdata2019-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/benchmarkfdrData2019_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/benchmarkfdrData2019_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-benchmarkfdrdata2019/bioconductor-benchmarkfdrdata2019_1.16.0_src_all.tar.gz"], "md5": "50ce7eb4100da1909ddd6c71c31e7e0c", "fn": "benchmarkfdrData2019_1.16.0.tar.gz"}, "beta7-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/beta7_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/beta7_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beta7/bioconductor-beta7_1.40.0_src_all.tar.gz"], "md5": "7beee3699282a97c765cf418036fc0ed", "fn": "beta7_1.40.0.tar.gz"}, "bioimagedbs-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/BioImageDbs_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/BioImageDbs_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bioimagedbs/bioconductor-bioimagedbs_1.10.0_src_all.tar.gz"], "md5": "785e9ea81ef5699d70af969fd8d4703d", "fn": "BioImageDbs_1.10.0.tar.gz"}, "bioplex-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/BioPlex_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/BioPlex_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bioplex/bioconductor-bioplex_1.8.0_src_all.tar.gz"], "md5": "77e38da3b194e7776fa7007a2cef42bf", "fn": "BioPlex_1.8.0.tar.gz"}, "biotmledata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/biotmleData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/biotmleData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biotmledata/bioconductor-biotmledata_1.26.0_src_all.tar.gz"], "md5": "8c725d5c496f9bfe7ed4b5d5c538244a", "fn": "biotmleData_1.26.0.tar.gz"}, "biscuiteerdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/biscuiteerData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/biscuiteerData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biscuiteerdata/bioconductor-biscuiteerdata_1.16.0_src_all.tar.gz"], "md5": "9610f1ea2c2e8303acbb0b52204f8d3e", "fn": "biscuiteerData_1.16.0.tar.gz"}, "bladderbatch-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/bladderbatch_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/bladderbatch_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bladderbatch/bioconductor-bladderbatch_1.40.0_src_all.tar.gz"], "md5": "d59d10a87e8d62c6ba10f7e9c0160a44", "fn": "bladderbatch_1.40.0.tar.gz"}, "blimatestingdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/blimaTestingData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/blimaTestingData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-blimatestingdata/bioconductor-blimatestingdata_1.22.0_src_all.tar.gz"], "md5": "3ae3da97d0d020e16feee29b93c24825", "fn": "blimaTestingData_1.22.0.tar.gz"}, "bloodcancermultiomics2017-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/BloodCancerMultiOmics2017_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/BloodCancerMultiOmics2017_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bloodcancermultiomics2017/bioconductor-bloodcancermultiomics2017_1.22.0_src_all.tar.gz"], "md5": "d2b2dcb147bf904df505fedca2d1ea9e", "fn": "BloodCancerMultiOmics2017_1.22.0.tar.gz"}, "bodymaprat-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/bodymapRat_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/bodymapRat_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bodymaprat/bioconductor-bodymaprat_1.18.0_src_all.tar.gz"], "md5": "fc575d7f33dd1ee73f1860fb076a840b", "fn": "bodymapRat_1.18.0.tar.gz"}, "breakpointrdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/breakpointRdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/breakpointRdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breakpointrdata/bioconductor-breakpointrdata_1.20.0_src_all.tar.gz"], "md5": "e3f74132513d150cb5d5cc62bfd49586", "fn": "breakpointRdata_1.20.0.tar.gz"}, "breastcancermainz-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/breastCancerMAINZ_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerMAINZ_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancermainz/bioconductor-breastcancermainz_1.40.0_src_all.tar.gz"], "md5": "2b8df5af87b71c6706f909129212b504", "fn": "breastCancerMAINZ_1.40.0.tar.gz"}, "breastcancernki-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/breastCancerNKI_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerNKI_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancernki/bioconductor-breastcancernki_1.40.0_src_all.tar.gz"], "md5": "0a0940593d75deaed0aa6f01954cf61c", "fn": "breastCancerNKI_1.40.0.tar.gz"}, "breastcancertransbig-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/breastCancerTRANSBIG_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerTRANSBIG_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancertransbig/bioconductor-breastcancertransbig_1.40.0_src_all.tar.gz"], "md5": "170d89ddd3e554da50a0b2b5d040a96e", "fn": "breastCancerTRANSBIG_1.40.0.tar.gz"}, "breastcancerunt-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/breastCancerUNT_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerUNT_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancerunt/bioconductor-breastcancerunt_1.40.0_src_all.tar.gz"], "md5": "31e1b6d7e34b4acb9207e3e152539166", "fn": "breastCancerUNT_1.40.0.tar.gz"}, "breastcancerupp-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/breastCancerUPP_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerUPP_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancerupp/bioconductor-breastcancerupp_1.40.0_src_all.tar.gz"], "md5": "c5c10989a8a2dbfd20c228522474fac1", "fn": "breastCancerUPP_1.40.0.tar.gz"}, "breastcancervdx-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/breastCancerVDX_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerVDX_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancervdx/bioconductor-breastcancervdx_1.40.0_src_all.tar.gz"], "md5": "446ef46e0bdd1480e12de21ded7b58f0", "fn": "breastCancerVDX_1.40.0.tar.gz"}, "brgedata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/brgedata_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/brgedata_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-brgedata/bioconductor-brgedata_1.24.0_src_all.tar.gz"], "md5": "b8d26c8dfa756e9eb556e4662e3b3302", "fn": "brgedata_1.24.0.tar.gz"}, "bronchialil13-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/bronchialIL13_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/bronchialIL13_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bronchialil13/bioconductor-bronchialil13_1.40.0_src_all.tar.gz"], "md5": "be303e29450fb15b03a10f6caaf30159", "fn": "bronchialIL13_1.40.0.tar.gz"}, "bsseqdata-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/bsseqData_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/bsseqData_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsseqdata/bioconductor-bsseqdata_0.40.0_src_all.tar.gz"], "md5": "514171e8133c8d38e6b1ad31eff722a8", "fn": "bsseqData_0.40.0.tar.gz"}, "cancerdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/cancerdata_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/cancerdata_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cancerdata/bioconductor-cancerdata_1.40.0_src_all.tar.gz"], "md5": "7baa088ef320a0222a897987ea8c3e8b", "fn": "cancerdata_1.40.0.tar.gz"}, "cardinalworkflows-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CardinalWorkflows_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/CardinalWorkflows_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cardinalworkflows/bioconductor-cardinalworkflows_1.34.0_src_all.tar.gz"], "md5": "54c51a2ec2f20f96ad9e60c16eeb2ccb", "fn": "CardinalWorkflows_1.34.0.tar.gz"}, "ccdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ccdata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/ccdata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ccdata/bioconductor-ccdata_1.28.0_src_all.tar.gz"], "md5": "60cbd595e53467fd61e1edc4f8ea47e7", "fn": "ccdata_1.28.0.tar.gz"}, "ccl4-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CCl4_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/CCl4_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ccl4/bioconductor-ccl4_1.40.0_src_all.tar.gz"], "md5": "3247cf1db347f959d908e88b5e8febb5", "fn": "CCl4_1.40.0.tar.gz"}, "cctutorial-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ccTutorial_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/ccTutorial_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cctutorial/bioconductor-cctutorial_1.40.0_src_all.tar.gz"], "md5": "20af731ec83a03f12ec5d87060f5d168", "fn": "ccTutorial_1.40.0.tar.gz"}, "celarefdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/celarefData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/celarefData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celarefdata/bioconductor-celarefdata_1.20.0_src_all.tar.gz"], "md5": "6864c27f1d574314fe10612b37f6c433", "fn": "celarefData_1.20.0.tar.gz"}, "celldex-1.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/celldex_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/celldex_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celldex/bioconductor-celldex_1.12.0_src_all.tar.gz"], "md5": "62419c915beb91f7c228e1a125df68f8", "fn": "celldex_1.12.0.tar.gz"}, "cellmapperdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CellMapperData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/CellMapperData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cellmapperdata/bioconductor-cellmapperdata_1.28.0_src_all.tar.gz"], "md5": "5db37729dd49f26b6cba9ff4aff80b1d", "fn": "CellMapperData_1.28.0.tar.gz"}, "cftoolsdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/cfToolsData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/cfToolsData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cftoolsdata/bioconductor-cftoolsdata_1.0.0_src_all.tar.gz"], "md5": "00bbf328a45fb8731b3c7262b3521e0b", "fn": "cfToolsData_1.0.0.tar.gz"}, "champdata-2.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ChAMPdata_2.34.0.tar.gz", "https://bioarchive.galaxyproject.org/ChAMPdata_2.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-champdata/bioconductor-champdata_2.34.0_src_all.tar.gz"], "md5": "b12bfec01a1cfdd103bc0cb9bd44d4aa", "fn": "ChAMPdata_2.34.0.tar.gz"}, "chic.data-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ChIC.data_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIC.data_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chic.data/bioconductor-chic.data_1.22.0_src_all.tar.gz"], "md5": "34b50ea53e6b5c982dc044addc68c33b", "fn": "ChIC.data_1.22.0.tar.gz"}, "chipenrich.data-2.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/chipenrich.data_2.26.0.tar.gz", "https://bioarchive.galaxyproject.org/chipenrich.data_2.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipenrich.data/bioconductor-chipenrich.data_2.26.0_src_all.tar.gz"], "md5": "4918da98125fee82afaeee84930051a8", "fn": "chipenrich.data_2.26.0.tar.gz"}, "chipexoqualexample-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ChIPexoQualExample_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIPexoQualExample_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipexoqualexample/bioconductor-chipexoqualexample_1.26.0_src_all.tar.gz"], "md5": "5ebb67a1848aa0e69557e795d236e24b", "fn": "ChIPexoQualExample_1.26.0.tar.gz"}, "chipseqdbdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/chipseqDBData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/chipseqDBData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipseqdbdata/bioconductor-chipseqdbdata_1.18.0_src_all.tar.gz"], "md5": "a6e50016d2d7c0cb085df2c4254b5f84", "fn": "chipseqDBData_1.18.0.tar.gz"}, "chipxpressdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ChIPXpressData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIPXpressData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipxpressdata/bioconductor-chipxpressdata_1.40.0_src_all.tar.gz"], "md5": "029086a630df9533dedea4babd28f0d7", "fn": "ChIPXpressData_1.40.0.tar.gz"}, "chromstardata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/chromstaRData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/chromstaRData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chromstardata/bioconductor-chromstardata_1.28.0_src_all.tar.gz"], "md5": "7f4a965a6b5aa71874a5cca39046cabf", "fn": "chromstaRData_1.28.0.tar.gz"}, "cll-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CLL_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/CLL_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cll/bioconductor-cll_1.42.0_src_all.tar.gz"], "md5": "4f71fa48ba2205b80c098275c866ac1f", "fn": "CLL_1.42.0.tar.gz"}, "cllmethylation-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CLLmethylation_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/CLLmethylation_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cllmethylation/bioconductor-cllmethylation_1.22.0_src_all.tar.gz"], "md5": "a8c3768dca1df5bb9e911878b68ad4c4", "fn": "CLLmethylation_1.22.0.tar.gz"}, "clumsiddata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CluMSIDdata_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/CluMSIDdata_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clumsiddata/bioconductor-clumsiddata_1.18.0_src_all.tar.gz"], "md5": "315da29d9f052e0abfbad59be9606f34", "fn": "CluMSIDdata_1.18.0.tar.gz"}, "clustifyrdatahub-1.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/clustifyrdatahub_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/clustifyrdatahub_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clustifyrdatahub/bioconductor-clustifyrdatahub_1.12.0_src_all.tar.gz"], "md5": "aac4529e5c0d71fdc49bda51c3915f61", "fn": "clustifyrdatahub_1.12.0.tar.gz"}, "cmap2data-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/cMap2data_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/cMap2data_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cmap2data/bioconductor-cmap2data_1.38.0_src_all.tar.gz"], "md5": "c5ecbc59a690426c6def7feb720e1a7d", "fn": "cMap2data_1.38.0.tar.gz"}, "cnvgsadata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/cnvGSAdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/cnvGSAdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cnvgsadata/bioconductor-cnvgsadata_1.38.0_src_all.tar.gz"], "md5": "1cc86a2066cae55493d710c475cc7112", "fn": "cnvGSAdata_1.38.0.tar.gz"}, "cohcapanno-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/COHCAPanno_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/COHCAPanno_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cohcapanno/bioconductor-cohcapanno_1.38.0_src_all.tar.gz"], "md5": "78fd4891651a8a62779fe402a13ba6b1", "fn": "COHCAPanno_1.38.0.tar.gz"}, "colonca-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/colonCA_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/colonCA_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-colonca/bioconductor-colonca_1.44.0_src_all.tar.gz"], "md5": "d12f03a7ded676f392dbbb26bbbef174", "fn": "colonCA_1.44.0.tar.gz"}, "confessdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CONFESSdata_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/CONFESSdata_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-confessdata/bioconductor-confessdata_1.30.0_src_all.tar.gz"], "md5": "07df3f8f783b3e734c4032b3f6ed61bd", "fn": "CONFESSdata_1.30.0.tar.gz"}, "connectivitymap-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ConnectivityMap_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ConnectivityMap_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-connectivitymap/bioconductor-connectivitymap_1.38.0_src_all.tar.gz"], "md5": "bac29780256afebfd49b90f268114eaf", "fn": "ConnectivityMap_1.38.0.tar.gz"}, "copdsexualdimorphism.data-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/COPDSexualDimorphism.data_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/COPDSexualDimorphism.data_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copdsexualdimorphism.data/bioconductor-copdsexualdimorphism.data_1.38.0_src_all.tar.gz"], "md5": "d7cf1990679c90cbaf5250c4761effec", "fn": "COPDSexualDimorphism.data_1.38.0.tar.gz"}, "copyhelper-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CopyhelpeR_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/CopyhelpeR_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copyhelper/bioconductor-copyhelper_1.34.0_src_all.tar.gz"], "md5": "bb8d3e8cba0c27898e43cbdcfcac6c62", "fn": "CopyhelpeR_1.34.0.tar.gz"}, "copyneutralima-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CopyNeutralIMA_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/CopyNeutralIMA_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copyneutralima/bioconductor-copyneutralima_1.20.0_src_all.tar.gz"], "md5": "5f1921b0aff4c3f39b662cc1ae70bf28", "fn": "CopyNeutralIMA_1.20.0.tar.gz"}, "cosiadata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CoSIAdata_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/CoSIAdata_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cosiadata/bioconductor-cosiadata_1.2.0_src_all.tar.gz"], "md5": "f0ec9d5ca01647ec3d52e264c0828273", "fn": "CoSIAdata_1.2.0.tar.gz"}, "cosmic.67-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/COSMIC.67_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/COSMIC.67_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cosmic.67/bioconductor-cosmic.67_1.38.0_src_all.tar.gz"], "md5": "392f31ffd7e95a7558d248d36dcc37fe", "fn": "COSMIC.67_1.38.0.tar.gz"}, "crcl18-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/CRCL18_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/CRCL18_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-crcl18/bioconductor-crcl18_1.22.0_src_all.tar.gz"], "md5": "176bd921f08e717ec49e4e3eb4a5e5e5", "fn": "CRCL18_1.22.0.tar.gz"}, "crisprscoredata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/crisprScoreData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/crisprScoreData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-crisprscoredata/bioconductor-crisprscoredata_1.6.0_src_all.tar.gz"], "md5": "1f4d86404f045ec36cf7d1b1c64373fe", "fn": "crisprScoreData_1.6.0.tar.gz"}, "curatedadipoarray-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedAdipoArray_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoArray_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadipoarray/bioconductor-curatedadipoarray_1.14.0_src_all.tar.gz"], "md5": "109be77c099e9d7b6da437577f619a54", "fn": "curatedAdipoArray_1.14.0.tar.gz"}, "curatedadipochip-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedAdipoChIP_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoChIP_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadipochip/bioconductor-curatedadipochip_1.18.0_src_all.tar.gz"], "md5": "0074cb63250ac197dad12e4138d47463", "fn": "curatedAdipoChIP_1.18.0.tar.gz"}, "curatedadiporna-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedAdipoRNA_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoRNA_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadiporna/bioconductor-curatedadiporna_1.18.0_src_all.tar.gz"], "md5": "61c2e750fc2cf09a6bde6c0bf46e6b8b", "fn": "curatedAdipoRNA_1.18.0.tar.gz"}, "curatedbladderdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedBladderData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedBladderData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedbladderdata/bioconductor-curatedbladderdata_1.38.0_src_all.tar.gz"], "md5": "bd8965c4ad49840b4985f90f3dc5a441", "fn": "curatedBladderData_1.38.0.tar.gz"}, "curatedbreastdata-2.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedBreastData_2.30.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedBreastData_2.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedbreastdata/bioconductor-curatedbreastdata_2.30.0_src_all.tar.gz"], "md5": "41383ff9e1295448ec0e8004789ab9d5", "fn": "curatedBreastData_2.30.0.tar.gz"}, "curatedcrcdata-2.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedCRCData_2.34.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedCRCData_2.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedcrcdata/bioconductor-curatedcrcdata_2.34.0_src_all.tar.gz"], "md5": "c36bf5dbc0970503f4137b55e8c65534", "fn": "curatedCRCData_2.34.0.tar.gz"}, "curatedmetagenomicdata-3.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedMetagenomicData_3.10.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedMetagenomicData_3.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedmetagenomicdata/bioconductor-curatedmetagenomicdata_3.10.0_src_all.tar.gz"], "md5": "39c08149fe4261d4961ff1235825ae97", "fn": "curatedMetagenomicData_3.10.0.tar.gz"}, "curatedovariandata-1.40.1": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedOvarianData_1.40.1.tar.gz", "https://bioarchive.galaxyproject.org/curatedOvarianData_1.40.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedovariandata/bioconductor-curatedovariandata_1.40.1_src_all.tar.gz"], "md5": "7651ff7abb11057b3ceec8f869e259d6", "fn": "curatedOvarianData_1.40.1.tar.gz"}, "curatedtbdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedTBData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedTBData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedtbdata/bioconductor-curatedtbdata_1.8.0_src_all.tar.gz"], "md5": "190a770c4f5df45cf722b7ee287a2384", "fn": "curatedTBData_1.8.0.tar.gz"}, "curatedtcgadata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/curatedTCGAData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedTCGAData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedtcgadata/bioconductor-curatedtcgadata_1.24.0_src_all.tar.gz"], "md5": "de450b3bbb137b63a1ca46ae81a96909", "fn": "curatedTCGAData_1.24.0.tar.gz"}, "dapardata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DAPARdata_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/DAPARdata_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dapardata/bioconductor-dapardata_1.32.0_src_all.tar.gz"], "md5": "5906f180d2e824affe9f2850424c7612", "fn": "DAPARdata_1.32.0.tar.gz"}, "davidtiling-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/davidTiling_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/davidTiling_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-davidtiling/bioconductor-davidtiling_1.42.0_src_all.tar.gz"], "md5": "dace46d6f640014aff544e0faf355b5e", "fn": "davidTiling_1.42.0.tar.gz"}, "depmap-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/depmap_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/depmap_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-depmap/bioconductor-depmap_1.16.0_src_all.tar.gz"], "md5": "7f00d05c7f899e622293767baa04e120", "fn": "depmap_1.16.0.tar.gz"}, "derfinderdata-2.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/derfinderData_2.20.0.tar.gz", "https://bioarchive.galaxyproject.org/derfinderData_2.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-derfinderdata/bioconductor-derfinderdata_2.20.0_src_all.tar.gz"], "md5": "032efff51d29eae3fc1a5e032c0f3c40", "fn": "derfinderData_2.20.0.tar.gz"}, "desousa2013-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DeSousa2013_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/DeSousa2013_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-desousa2013/bioconductor-desousa2013_1.38.0_src_all.tar.gz"], "md5": "41a3ca5cba40653eb4be04203aaf60ac", "fn": "DeSousa2013_1.38.0.tar.gz"}, "dexmadata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DExMAdata_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/DExMAdata_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dexmadata/bioconductor-dexmadata_1.10.0_src_all.tar.gz"], "md5": "3d2a9cc7d0044ffc23e572f4c5cc4426", "fn": "DExMAdata_1.10.0.tar.gz"}, "diffloopdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/diffloopdata_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/diffloopdata_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-diffloopdata/bioconductor-diffloopdata_1.30.0_src_all.tar.gz"], "md5": "748ee71ae44999ca2c568619ad5a47eb", "fn": "diffloopdata_1.30.0.tar.gz"}, "diggitdata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/diggitdata_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/diggitdata_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-diggitdata/bioconductor-diggitdata_1.34.0_src_all.tar.gz"], "md5": "48dc6a1a35dae2169279a2766e3b56de", "fn": "diggitdata_1.34.0.tar.gz"}, "dlbcl-1.42.1": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DLBCL_1.42.1.tar.gz", "https://bioarchive.galaxyproject.org/DLBCL_1.42.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dlbcl/bioconductor-dlbcl_1.42.1_src_all.tar.gz"], "md5": "a2906f8e35b0457c1cd8052d2457d40b", "fn": "DLBCL_1.42.1.tar.gz"}, "dmelsgi-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DmelSGI_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/DmelSGI_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dmelsgi/bioconductor-dmelsgi_1.34.0_src_all.tar.gz"], "md5": "c13b3a8f881ca54d5e8ddf52ebe8b86a", "fn": "DmelSGI_1.34.0.tar.gz"}, "dmrcatedata-2.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DMRcatedata_2.20.0.tar.gz", "https://bioarchive.galaxyproject.org/DMRcatedata_2.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dmrcatedata/bioconductor-dmrcatedata_2.20.0_src_all.tar.gz"], "md5": "ac938c6259121c4a60ca3c8c5bfdf724", "fn": "DMRcatedata_2.20.0.tar.gz"}, "dnazoodata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DNAZooData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/DNAZooData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dnazoodata/bioconductor-dnazoodata_1.2.0_src_all.tar.gz"], "md5": "06c4b9dbbaddc3dd4dcdc51e34150aa7", "fn": "DNAZooData_1.2.0.tar.gz"}, "donapllp2013-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DonaPLLP2013_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/DonaPLLP2013_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-donapllp2013/bioconductor-donapllp2013_1.40.0_src_all.tar.gz"], "md5": "d8dc37afefc52856d520540b07faf545", "fn": "DonaPLLP2013_1.40.0.tar.gz"}, "dorothea-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/dorothea_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/dorothea_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dorothea/bioconductor-dorothea_1.14.0_src_all.tar.gz"], "md5": "d1ad1213db5d54f1fc6ef8d195b9bbc0", "fn": "dorothea_1.14.0.tar.gz"}, "dresscheck-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/dressCheck_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/dressCheck_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dresscheck/bioconductor-dresscheck_0.40.0_src_all.tar.gz"], "md5": "d6fb25eaad39c714024ed855c8c9c87d", "fn": "dressCheck_0.40.0.tar.gz"}, "droplettestfiles-1.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DropletTestFiles_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/DropletTestFiles_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-droplettestfiles/bioconductor-droplettestfiles_1.12.0_src_all.tar.gz"], "md5": "5a3a3f0d0901c90c6a2b173b976c4868", "fn": "DropletTestFiles_1.12.0.tar.gz"}, "drugvsdiseasedata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DrugVsDiseasedata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/DrugVsDiseasedata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drugvsdiseasedata/bioconductor-drugvsdiseasedata_1.38.0_src_all.tar.gz"], "md5": "40b800653aab57e822a18afe5bd1a2e7", "fn": "DrugVsDiseasedata_1.38.0.tar.gz"}, "duoclustering2018-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DuoClustering2018_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/DuoClustering2018_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-duoclustering2018/bioconductor-duoclustering2018_1.20.0_src_all.tar.gz"], "md5": "a2761f4db56025af2eaf8240392d01a0", "fn": "DuoClustering2018_1.20.0.tar.gz"}, "dvddata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/DvDdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/DvDdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dvddata/bioconductor-dvddata_1.38.0_src_all.tar.gz"], "md5": "d07387219229c006ba96b9ab43ddf4ff", "fn": "DvDdata_1.38.0.tar.gz"}, "dyebiasexamples-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/dyebiasexamples_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/dyebiasexamples_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dyebiasexamples/bioconductor-dyebiasexamples_1.42.0_src_all.tar.gz"], "md5": "b73aa6c0c98150b2bccba7802dda8c86", "fn": "dyebiasexamples_1.42.0.tar.gz"}, "easierdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/easierData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/easierData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-easierdata/bioconductor-easierdata_1.8.0_src_all.tar.gz"], "md5": "5092649863b833021ff8593731571183", "fn": "easierData_1.8.0.tar.gz"}, "eatonetalchipseq-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/EatonEtAlChIPseq_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/EatonEtAlChIPseq_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-eatonetalchipseq/bioconductor-eatonetalchipseq_0.40.0_src_all.tar.gz"], "md5": "e7695c3761d5f3d41dec21b0c8b50947", "fn": "EatonEtAlChIPseq_0.40.0.tar.gz"}, "ecolileucine-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ecoliLeucine_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliLeucine_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolileucine/bioconductor-ecolileucine_1.42.0_src_all.tar.gz"], "md5": "30af71114480d851f4dad806e7f8e0d1", "fn": "ecoliLeucine_1.42.0.tar.gz"}, "egseadata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/EGSEAdata_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/EGSEAdata_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-egseadata/bioconductor-egseadata_1.30.0_src_all.tar.gz"], "md5": "838b30ae6caf7c3cbb854e0404b52cda", "fn": "EGSEAdata_1.30.0.tar.gz"}, "elmer.data-2.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ELMER.data_2.26.0.tar.gz", "https://bioarchive.galaxyproject.org/ELMER.data_2.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-elmer.data/bioconductor-elmer.data_2.26.0_src_all.tar.gz"], "md5": "565ea1aa52f3f61d16b7560859ed7a3a", "fn": "ELMER.data_2.26.0.tar.gz"}, "emtdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/emtdata_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/emtdata_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-emtdata/bioconductor-emtdata_1.10.0_src_all.tar.gz"], "md5": "4f861584cce979edd6d7bdce3624e916", "fn": "emtdata_1.10.0.tar.gz"}, "epimix.data-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/EpiMix.data_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/EpiMix.data_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epimix.data/bioconductor-epimix.data_1.4.0_src_all.tar.gz"], "md5": "52c386f6828945121acfca44eabb7827", "fn": "EpiMix.data_1.4.0.tar.gz"}, "epimutacionsdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/epimutacionsData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/epimutacionsData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epimutacionsdata/bioconductor-epimutacionsdata_1.6.0_src_all.tar.gz"], "md5": "e2681ab8096fd0f2b7e5d8ed68928280", "fn": "epimutacionsData_1.6.0.tar.gz"}, "estrogen-1.48.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/estrogen_1.48.0.tar.gz", "https://bioarchive.galaxyproject.org/estrogen_1.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-estrogen/bioconductor-estrogen_1.48.0_src_all.tar.gz"], "md5": "41a3321678d1a9cb057e979d675f0cee", "fn": "estrogen_1.48.0.tar.gz"}, "etec16s-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/etec16s_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/etec16s_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-etec16s/bioconductor-etec16s_1.30.0_src_all.tar.gz"], "md5": "86353b5f2f77274b883120dc043f8ce5", "fn": "etec16s_1.30.0.tar.gz"}, "ewcedata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ewceData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/ewceData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ewcedata/bioconductor-ewcedata_1.10.0_src_all.tar.gz"], "md5": "d2ee91be35e2c5433ce16e94717c50e7", "fn": "ewceData_1.10.0.tar.gz"}, "faahko-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/faahKO_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/faahKO_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-faahko/bioconductor-faahko_1.42.0_src_all.tar.gz"], "md5": "3525f525973323d33955a68ca38b5cd7", "fn": "faahKO_1.42.0.tar.gz"}, "fabiadata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/fabiaData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/fabiaData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fabiadata/bioconductor-fabiadata_1.40.0_src_all.tar.gz"], "md5": "7fd64db4d15610a66c609e60624bbff9", "fn": "fabiaData_1.40.0.tar.gz"}, "fantom3and4cage-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/FANTOM3and4CAGE_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/FANTOM3and4CAGE_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fantom3and4cage/bioconductor-fantom3and4cage_1.38.0_src_all.tar.gz"], "md5": "5d964e7a085d6a7b00e2b2215b765861", "fn": "FANTOM3and4CAGE_1.38.0.tar.gz"}, "ffpeexampledata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ffpeExampleData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/ffpeExampleData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ffpeexampledata/bioconductor-ffpeexampledata_1.40.0_src_all.tar.gz"], "md5": "6ea474bdf448ff6026ec4f1f376b7d69", "fn": "ffpeExampleData_1.40.0.tar.gz"}, "fibroeset-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/fibroEset_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/fibroEset_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fibroeset/bioconductor-fibroeset_1.44.0_src_all.tar.gz"], "md5": "cbc13cc5c4ac4f6445dc69383ad183ff", "fn": "fibroEset_1.44.0.tar.gz"}, "fieldeffectcrc-1.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/FieldEffectCrc_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/FieldEffectCrc_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fieldeffectcrc/bioconductor-fieldeffectcrc_1.12.0_src_all.tar.gz"], "md5": "73fa4e8649f3c4a523764d35afd421f2", "fn": "FieldEffectCrc_1.12.0.tar.gz"}, "fis-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/FIs_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/FIs_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fis/bioconductor-fis_1.30.0_src_all.tar.gz"], "md5": "ef807b75136742a1dcb5ea70993d5c38", "fn": "FIs_1.30.0.tar.gz"}, "fission-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/fission_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/fission_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fission/bioconductor-fission_1.22.0_src_all.tar.gz"], "md5": "7d404509808bfc439270093b647ccd80", "fn": "fission_1.22.0.tar.gz"}, "fletcher2013a-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Fletcher2013a_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/Fletcher2013a_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fletcher2013a/bioconductor-fletcher2013a_1.38.0_src_all.tar.gz"], "md5": "e4c4f9a4e8b24a7a72f9c63337a0eef9", "fn": "Fletcher2013a_1.38.0.tar.gz"}, "fletcher2013b-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Fletcher2013b_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/Fletcher2013b_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fletcher2013b/bioconductor-fletcher2013b_1.38.0_src_all.tar.gz"], "md5": "cf656c92425c8a63ef584be08e8b742e", "fn": "Fletcher2013b_1.38.0.tar.gz"}, "flowploidydata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/flowPloidyData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/flowPloidyData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowploidydata/bioconductor-flowploidydata_1.28.0_src_all.tar.gz"], "md5": "993a663f6d1cdc791c3f4e88d5b3b047", "fn": "flowPloidyData_1.28.0.tar.gz"}, "flowsorted.blood.450k-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/FlowSorted.Blood.450k_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.Blood.450k_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.450k/bioconductor-flowsorted.blood.450k_1.40.0_src_all.tar.gz"], "md5": "f88422c2d8a2f7ce4ca968292adfc8ab", "fn": "FlowSorted.Blood.450k_1.40.0.tar.gz"}, "flowsorted.blood.epic-2.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/FlowSorted.Blood.EPIC_2.6.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.Blood.EPIC_2.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.epic/bioconductor-flowsorted.blood.epic_2.6.0_src_all.tar.gz"], "md5": "e94cbb0480a032595cdb5d9714065bed", "fn": "FlowSorted.Blood.EPIC_2.6.0.tar.gz"}, "flowsorted.cordblood.450k-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/FlowSorted.CordBlood.450k_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBlood.450k_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordblood.450k/bioconductor-flowsorted.cordblood.450k_1.30.0_src_all.tar.gz"], "md5": "fca81b7412af68100d7aed4d57d5fc59", "fn": "FlowSorted.CordBlood.450k_1.30.0.tar.gz"}, "flowsorted.cordbloodcombined.450k-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/FlowSorted.CordBloodCombined.450k_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodCombined.450k_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodcombined.450k/bioconductor-flowsorted.cordbloodcombined.450k_1.18.0_src_all.tar.gz"], "md5": "769113b80606820ab2918dcacf1076b2", "fn": "FlowSorted.CordBloodCombined.450k_1.18.0.tar.gz"}, "flowsorted.cordbloodnorway.450k-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/FlowSorted.CordBloodNorway.450k_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodNorway.450k_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodnorway.450k/bioconductor-flowsorted.cordbloodnorway.450k_1.28.0_src_all.tar.gz"], "md5": "40016224becf643102bc3054f4e2508d", "fn": "FlowSorted.CordBloodNorway.450k_1.28.0.tar.gz"}, "flowsorted.dlpfc.450k-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/FlowSorted.DLPFC.450k_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.DLPFC.450k_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.dlpfc.450k/bioconductor-flowsorted.dlpfc.450k_1.38.0_src_all.tar.gz"], "md5": "ad95a51f7e8bcf7c0bec6dda80eb0a92", "fn": "FlowSorted.DLPFC.450k_1.38.0.tar.gz"}, "flowworkspacedata-3.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/flowWorkspaceData_3.14.0.tar.gz", "https://bioarchive.galaxyproject.org/flowWorkspaceData_3.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowworkspacedata/bioconductor-flowworkspacedata_3.14.0_src_all.tar.gz"], "md5": "96655cef2a21f1b9d303ec775597a2dc", "fn": "flowWorkspaceData_3.14.0.tar.gz"}, "fourdndata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/fourDNData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/fourDNData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fourdndata/bioconductor-fourdndata_1.2.0_src_all.tar.gz"], "md5": "bca623e919f7c17a40ffb4eae27cfe59", "fn": "fourDNData_1.2.0.tar.gz"}, "frmaexampledata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/frmaExampleData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/frmaExampleData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-frmaexampledata/bioconductor-frmaexampledata_1.38.0_src_all.tar.gz"], "md5": "9713801ffd08145323ca4d31a3631995", "fn": "frmaExampleData_1.38.0.tar.gz"}, "furrowseg-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/furrowSeg_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/furrowSeg_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-furrowseg/bioconductor-furrowseg_1.30.0_src_all.tar.gz"], "md5": "f41e88a4d47949b3b8b126b0fc7852eb", "fn": "furrowSeg_1.30.0.tar.gz"}, "gagedata-2.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/gageData_2.40.0.tar.gz", "https://bioarchive.galaxyproject.org/gageData_2.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gagedata/bioconductor-gagedata_2.40.0_src_all.tar.gz"], "md5": "889e4b6ceda6c2a80f61ad4e867c3b59", "fn": "gageData_2.40.0.tar.gz"}, "gaschyhs-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/gaschYHS_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/gaschYHS_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gaschyhs/bioconductor-gaschyhs_1.40.0_src_all.tar.gz"], "md5": "29983eadb2a2a20f7c5475206367d641", "fn": "gaschYHS_1.40.0.tar.gz"}, "gcspikelite-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/gcspikelite_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/gcspikelite_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gcspikelite/bioconductor-gcspikelite_1.40.0_src_all.tar.gz"], "md5": "91b995753732f0d5508fdc2d7dcb998f", "fn": "gcspikelite_1.40.0.tar.gz"}, "gdnainrnaseqdata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/gDNAinRNAseqData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/gDNAinRNAseqData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gdnainrnaseqdata/bioconductor-gdnainrnaseqdata_1.2.0_src_all.tar.gz"], "md5": "52e275ca255493684657a091667f987f", "fn": "gDNAinRNAseqData_1.2.0.tar.gz"}, "gdrtestdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/gDRtestData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/gDRtestData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gdrtestdata/bioconductor-gdrtestdata_1.0.0_src_all.tar.gz"], "md5": "8de3dea2673f0e7dc9412e36da2c4f9d", "fn": "gDRtestData_1.0.0.tar.gz"}, "genelendatabase-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/geneLenDataBase_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/geneLenDataBase_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genelendatabase/bioconductor-genelendatabase_1.38.0_src_all.tar.gz"], "md5": "c29099d3142aad07590e22ce37c6acf3", "fn": "geneLenDataBase_1.38.0.tar.gz"}, "genomationdata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/genomationData_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/genomationData_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomationdata/bioconductor-genomationdata_1.34.0_src_all.tar.gz"], "md5": "dc03eef7730719f7c66f72ca5e9915db", "fn": "genomationData_1.34.0.tar.gz"}, "genomicdistributionsdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GenomicDistributionsData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/GenomicDistributionsData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomicdistributionsdata/bioconductor-genomicdistributionsdata_1.10.0_src_all.tar.gz"], "md5": "84067e85ccbf3605bc1f5a1b7d8508ad", "fn": "GenomicDistributionsData_1.10.0.tar.gz"}, "geuvadistranscriptexpr-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GeuvadisTranscriptExpr_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/GeuvadisTranscriptExpr_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-geuvadistranscriptexpr/bioconductor-geuvadistranscriptexpr_1.30.0_src_all.tar.gz"], "md5": "806de22bef0659a3b6f9db122d87a1d6", "fn": "GeuvadisTranscriptExpr_1.30.0.tar.gz"}, "gigseadata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GIGSEAdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/GIGSEAdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gigseadata/bioconductor-gigseadata_1.20.0_src_all.tar.gz"], "md5": "470cdb6073d9af3d23056b55e6b8c98d", "fn": "GIGSEAdata_1.20.0.tar.gz"}, "golubesets-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/golubEsets_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/golubEsets_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-golubesets/bioconductor-golubesets_1.44.0_src_all.tar.gz"], "md5": "49e3527c00f06c189a048a6b871f3d54", "fn": "golubEsets_1.44.0.tar.gz"}, "gpaexample-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/gpaExample_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/gpaExample_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gpaexample/bioconductor-gpaexample_1.14.0_src_all.tar.gz"], "md5": "e989af58ed5bbc10573f7438b3ee7836", "fn": "gpaExample_1.14.0.tar.gz"}, "grndata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/grndata_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/grndata_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-grndata/bioconductor-grndata_1.34.0_src_all.tar.gz"], "md5": "0ebac67277a5ca915f9a971d3659af5e", "fn": "grndata_1.34.0.tar.gz"}, "gsbenchmark-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GSBenchMark_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/GSBenchMark_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gsbenchmark/bioconductor-gsbenchmark_1.22.0_src_all.tar.gz"], "md5": "bedfa52de1b414ae5fe9d5fc376380ba", "fn": "GSBenchMark_1.22.0.tar.gz"}, "gse103322-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GSE103322_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE103322_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse103322/bioconductor-gse103322_1.8.0_src_all.tar.gz"], "md5": "3816b430b716edaaa0ef22dba38cf58e", "fn": "GSE103322_1.8.0.tar.gz"}, "gse13015-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GSE13015_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE13015_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse13015/bioconductor-gse13015_1.10.0_src_all.tar.gz"], "md5": "99fae6872abf6820842a1340f7fd6b4e", "fn": "GSE13015_1.10.0.tar.gz"}, "gse159526-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GSE159526_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE159526_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse159526/bioconductor-gse159526_1.8.0_src_all.tar.gz"], "md5": "d89442c94cb87f0760a9f0f85426a8fa", "fn": "GSE159526_1.8.0.tar.gz"}, "gse62944-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GSE62944_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE62944_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse62944/bioconductor-gse62944_1.30.0_src_all.tar.gz"], "md5": "5b6c58aaee948c9cd0e0d52b5adcf264", "fn": "GSE62944_1.30.0.tar.gz"}, "gsvadata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GSVAdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/GSVAdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gsvadata/bioconductor-gsvadata_1.38.0_src_all.tar.gz"], "md5": "3c2d6a66967ab8c3c2545fc3323282b3", "fn": "GSVAdata_1.38.0.tar.gz"}, "gwasdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/GWASdata_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/GWASdata_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gwasdata/bioconductor-gwasdata_1.40.0_src_all.tar.gz"], "md5": "57fec70f980b9e476f0c59d397797815", "fn": "GWASdata_1.40.0.tar.gz"}, "h5vcdata-2.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/h5vcData_2.22.0.tar.gz", "https://bioarchive.galaxyproject.org/h5vcData_2.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-h5vcdata/bioconductor-h5vcdata_2.22.0_src_all.tar.gz"], "md5": "c251316e2d6dc6cb90e8faad0015103b", "fn": "h5vcData_2.22.0.tar.gz"}, "hapmap100khind-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hapmap100khind_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap100khind_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap100khind/bioconductor-hapmap100khind_1.44.0_src_all.tar.gz"], "md5": "0168028295626d811e305d4008ce9996", "fn": "hapmap100khind_1.44.0.tar.gz"}, "hapmap100kxba-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hapmap100kxba_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap100kxba_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap100kxba/bioconductor-hapmap100kxba_1.44.0_src_all.tar.gz"], "md5": "b4a619fb108a36920109307fbf63985b", "fn": "hapmap100kxba_1.44.0.tar.gz"}, "hapmap500knsp-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hapmap500knsp_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap500knsp_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap500knsp/bioconductor-hapmap500knsp_1.44.0_src_all.tar.gz"], "md5": "15b799bba4a395ccf715acfc7bbdae04", "fn": "hapmap500knsp_1.44.0.tar.gz"}, "hapmap500ksty-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hapmap500ksty_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap500ksty_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap500ksty/bioconductor-hapmap500ksty_1.44.0_src_all.tar.gz"], "md5": "7a1d4983ac3e411dadedc130d85c2557", "fn": "hapmap500ksty_1.44.0.tar.gz"}, "hapmapsnp5-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hapmapsnp5_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmapsnp5_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp5/bioconductor-hapmapsnp5_1.44.0_src_all.tar.gz"], "md5": "2f14e60f39cf94c43f2dd0e5aa5a48e2", "fn": "hapmapsnp5_1.44.0.tar.gz"}, "hapmapsnp6-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hapmapsnp6_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmapsnp6_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp6/bioconductor-hapmapsnp6_1.44.0_src_all.tar.gz"], "md5": "2635c012a513343484177db2070209e9", "fn": "hapmapsnp6_1.44.0.tar.gz"}, "harbchip-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/harbChIP_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/harbChIP_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harbchip/bioconductor-harbchip_1.40.0_src_all.tar.gz"], "md5": "f5948fc0f4c1ced0a43e85c1885f5d9e", "fn": "harbChIP_1.40.0.tar.gz"}, "harmandata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HarmanData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/HarmanData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harmandata/bioconductor-harmandata_1.30.0_src_all.tar.gz"], "md5": "7df1447aff75abdf025678b51a0ee8fb", "fn": "HarmanData_1.30.0.tar.gz"}, "harmonizedtcgadata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HarmonizedTCGAData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/HarmonizedTCGAData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harmonizedtcgadata/bioconductor-harmonizedtcgadata_1.24.0_src_all.tar.gz"], "md5": "f6e8f685a67152c6f382089c0e6aae01", "fn": "HarmonizedTCGAData_1.24.0.tar.gz"}, "hcadata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HCAData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/HCAData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcadata/bioconductor-hcadata_1.18.0_src_all.tar.gz"], "md5": "4f16bf5904ca21c0fb0bd6515d7ab4d3", "fn": "HCAData_1.18.0.tar.gz"}, "hcatonsildata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HCATonsilData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/HCATonsilData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcatonsildata/bioconductor-hcatonsildata_1.0.0_src_all.tar.gz"], "md5": "dda9d216f608690d05bd5ffbcb73bb05", "fn": "HCATonsilData_1.0.0.tar.gz"}, "hd2013sgi-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HD2013SGI_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/HD2013SGI_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hd2013sgi/bioconductor-hd2013sgi_1.42.0_src_all.tar.gz"], "md5": "f8c7020a4fbfcb5c4026cea93e5a5bc6", "fn": "HD2013SGI_1.42.0.tar.gz"}, "hdcytodata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HDCytoData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/HDCytoData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hdcytodata/bioconductor-hdcytodata_1.22.0_src_all.tar.gz"], "md5": "8f962c6124539fea7a4a02a30e776de8", "fn": "HDCytoData_1.22.0.tar.gz"}, "healthycontrolspresencechecker-1.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/healthyControlsPresenceChecker_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/healthyControlsPresenceChecker_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-healthycontrolspresencechecker/bioconductor-healthycontrolspresencechecker_1.6.0_src_all.tar.gz"], "md5": "50ba7cea9e361d43c78d64ce1c89ba1a", "fn": "healthyControlsPresenceChecker_1.6.0.tar.gz"}, "healthyflowdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/healthyFlowData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/healthyFlowData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-healthyflowdata/bioconductor-healthyflowdata_1.40.0_src_all.tar.gz"], "md5": "ed0a9c99295e278a8445368a2cb226df", "fn": "healthyFlowData_1.40.0.tar.gz"}, "heebodata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HEEBOdata_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/HEEBOdata_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-heebodata/bioconductor-heebodata_1.40.0_src_all.tar.gz"], "md5": "885df0689d6663e079e952ea297ee777", "fn": "HEEBOdata_1.40.0.tar.gz"}, "hellorangesdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HelloRangesData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/HelloRangesData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hellorangesdata/bioconductor-hellorangesdata_1.28.0_src_all.tar.gz"], "md5": "6ae6ac65f3af7f41136eb6fb3558eb2a", "fn": "HelloRangesData_1.28.0.tar.gz"}, "hgu133abarcodevecs-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hgu133abarcodevecs_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133abarcodevecs_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133abarcodevecs/bioconductor-hgu133abarcodevecs_1.40.0_src_all.tar.gz"], "md5": "4a6ec67e649f7ca004242fd860f79521", "fn": "hgu133abarcodevecs_1.40.0.tar.gz"}, "hgu133plus2barcodevecs-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hgu133plus2barcodevecs_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2barcodevecs_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2barcodevecs/bioconductor-hgu133plus2barcodevecs_1.40.0_src_all.tar.gz"], "md5": "624bad8617d806474bc9406dc3c22384", "fn": "hgu133plus2barcodevecs_1.40.0.tar.gz"}, "hgu133plus2cellscore-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hgu133plus2CellScore_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2CellScore_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2cellscore/bioconductor-hgu133plus2cellscore_1.22.0_src_all.tar.gz"], "md5": "486b7084ad0056c1031545af9c6dd515", "fn": "hgu133plus2CellScore_1.22.0.tar.gz"}, "hgu2beta7-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/hgu2beta7_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu2beta7_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu2beta7/bioconductor-hgu2beta7_1.42.0_src_all.tar.gz"], "md5": "0643f49d27bf1dd6b73fb9192b23ebaa", "fn": "hgu2beta7_1.42.0.tar.gz"}, "hibed-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HiBED_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/HiBED_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hibed/bioconductor-hibed_1.0.0_src_all.tar.gz"], "md5": "282aec6967013cdaa790ff191e4139b4", "fn": "HiBED_1.0.0.tar.gz"}, "hicdatahumanimr90-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HiCDataHumanIMR90_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/HiCDataHumanIMR90_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicdatahumanimr90/bioconductor-hicdatahumanimr90_1.22.0_src_all.tar.gz"], "md5": "02854f68384130b0bcd3d0f84d94b856", "fn": "HiCDataHumanIMR90_1.22.0.tar.gz"}, "hicdatalymphoblast-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HiCDataLymphoblast_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/HiCDataLymphoblast_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicdatalymphoblast/bioconductor-hicdatalymphoblast_1.38.0_src_all.tar.gz"], "md5": "4e51d696b30a37414375e6987c7ab59c", "fn": "HiCDataLymphoblast_1.38.0.tar.gz"}, "hicontactsdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HiContactsData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/HiContactsData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicontactsdata/bioconductor-hicontactsdata_1.4.0_src_all.tar.gz"], "md5": "bcd518f48342168f7a814a442cf9564c", "fn": "HiContactsData_1.4.0.tar.gz"}, "highlyreplicatedrnaseq-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HighlyReplicatedRNASeq_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/HighlyReplicatedRNASeq_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-highlyreplicatedrnaseq/bioconductor-highlyreplicatedrnaseq_1.14.0_src_all.tar.gz"], "md5": "a397cddffb2dfea70943930b992ea7c0", "fn": "HighlyReplicatedRNASeq_1.14.0.tar.gz"}, "hiiragi2013-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Hiiragi2013_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/Hiiragi2013_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hiiragi2013/bioconductor-hiiragi2013_1.38.0_src_all.tar.gz"], "md5": "dde13f333fe218976f71b626ed5eefa4", "fn": "Hiiragi2013_1.38.0.tar.gz"}, "hivcdnavantwout03-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HIVcDNAvantWout03_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/HIVcDNAvantWout03_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hivcdnavantwout03/bioconductor-hivcdnavantwout03_1.42.0_src_all.tar.gz"], "md5": "4936f53bb66cdf1983a8bcbcd667a188", "fn": "HIVcDNAvantWout03_1.42.0.tar.gz"}, "hmp16sdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HMP16SData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/HMP16SData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hmp16sdata/bioconductor-hmp16sdata_1.22.0_src_all.tar.gz"], "md5": "a137f917000e15acffca9bb0baac8fbb", "fn": "HMP16SData_1.22.0.tar.gz"}, "hmp2data-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HMP2Data_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/HMP2Data_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hmp2data/bioconductor-hmp2data_1.16.0_src_all.tar.gz"], "md5": "f334416386d2c1af677494e1fd5743d6", "fn": "HMP2Data_1.16.0.tar.gz"}, "hsmmsinglecell-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HSMMSingleCell_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/HSMMSingleCell_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hsmmsinglecell/bioconductor-hsmmsinglecell_1.22.0_src_all.tar.gz"], "md5": "dae440cd20110d25cd699a9a792ac4b8", "fn": "HSMMSingleCell_1.22.0.tar.gz"}, "humanaffydata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HumanAffyData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/HumanAffyData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanaffydata/bioconductor-humanaffydata_1.28.0_src_all.tar.gz"], "md5": "11341e772169b7141b9bd22161e14417", "fn": "HumanAffyData_1.28.0.tar.gz"}, "humanstemcell-0.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/humanStemCell_0.42.0.tar.gz", "https://bioarchive.galaxyproject.org/humanStemCell_0.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanstemcell/bioconductor-humanstemcell_0.42.0_src_all.tar.gz"], "md5": "be6367d8fa19187d644247ed8795eb0e", "fn": "humanStemCell_0.42.0.tar.gz"}, "ihwpaper-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/IHWpaper_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/IHWpaper_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ihwpaper/bioconductor-ihwpaper_1.30.0_src_all.tar.gz"], "md5": "21e65d900bf8e6015fd006fbf01237d5", "fn": "IHWpaper_1.30.0.tar.gz"}, "illumina450probevariants.db-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Illumina450ProbeVariants.db_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/Illumina450ProbeVariants.db_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illumina450probevariants.db/bioconductor-illumina450probevariants.db_1.38.0_src_all.tar.gz"], "md5": "ca34eec73a57e5f226b70a20ef706ee3", "fn": "Illumina450ProbeVariants.db_1.38.0.tar.gz"}, "illuminadatatestfiles-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/IlluminaDataTestFiles_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaDataTestFiles_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminadatatestfiles/bioconductor-illuminadatatestfiles_1.40.0_src_all.tar.gz"], "md5": "3afa4b143fbb1dd18b3a7acd8f2984b1", "fn": "IlluminaDataTestFiles_1.40.0.tar.gz"}, "imcdatasets-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/imcdatasets_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/imcdatasets_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-imcdatasets/bioconductor-imcdatasets_1.10.0_src_all.tar.gz"], "md5": "6e687f10502d7d9d369c384e99977953", "fn": "imcdatasets_1.10.0.tar.gz"}, "italicsdata-2.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ITALICSData_2.40.0.tar.gz", "https://bioarchive.galaxyproject.org/ITALICSData_2.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-italicsdata/bioconductor-italicsdata_2.40.0_src_all.tar.gz"], "md5": "e154526c43e11840acfd4c92ff1cee8f", "fn": "ITALICSData_2.40.0.tar.gz"}, "iyer517-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Iyer517_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/Iyer517_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-iyer517/bioconductor-iyer517_1.44.0_src_all.tar.gz"], "md5": "81226f1ad5acd16cff4c7371f37d1881", "fn": "Iyer517_1.44.0.tar.gz"}, "jaspar2014-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/JASPAR2014_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2014_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2014/bioconductor-jaspar2014_1.38.0_src_all.tar.gz"], "md5": "6ef536411db46944f6d5b9a23ee13be6", "fn": "JASPAR2014_1.38.0.tar.gz"}, "jaspar2016-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/JASPAR2016_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2016_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2016/bioconductor-jaspar2016_1.30.0_src_all.tar.gz"], "md5": "2976e4678291944f664396385049180b", "fn": "JASPAR2016_1.30.0.tar.gz"}, "keggandmetacoredzpathwaysgeo-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/KEGGandMetacoreDzPathwaysGEO_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/KEGGandMetacoreDzPathwaysGEO_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-keggandmetacoredzpathwaysgeo/bioconductor-keggandmetacoredzpathwaysgeo_1.22.0_src_all.tar.gz"], "md5": "3a5180de47f1c28949b77db9f79b44ed", "fn": "KEGGandMetacoreDzPathwaysGEO_1.22.0.tar.gz"}, "keggdzpathwaysgeo-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/KEGGdzPathwaysGEO_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/KEGGdzPathwaysGEO_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-keggdzpathwaysgeo/bioconductor-keggdzpathwaysgeo_1.40.0_src_all.tar.gz"], "md5": "2f30f9ac05c04214d25a9d49fb4ce8bd", "fn": "KEGGdzPathwaysGEO_1.40.0.tar.gz"}, "kidpack-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/kidpack_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/kidpack_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-kidpack/bioconductor-kidpack_1.44.0_src_all.tar.gz"], "md5": "26f5ad5fba1c63156e282d8eac7ac385", "fn": "kidpack_1.44.0.tar.gz"}, "kodata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/KOdata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/KOdata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-kodata/bioconductor-kodata_1.28.0_src_all.tar.gz"], "md5": "40e099053eae889ad66256a94427ac54", "fn": "KOdata_1.28.0.tar.gz"}, "leebamviews-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/leeBamViews_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/leeBamViews_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-leebamviews/bioconductor-leebamviews_1.38.0_src_all.tar.gz"], "md5": "58f7c7fdbb1f949f48924ac79d31b580", "fn": "leeBamViews_1.38.0.tar.gz"}, "leukemiaseset-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/leukemiasEset_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/leukemiasEset_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-leukemiaseset/bioconductor-leukemiaseset_1.38.0_src_all.tar.gz"], "md5": "f9e8274856b0d78de6da7ec0bce171f5", "fn": "leukemiasEset_1.38.0.tar.gz"}, "liebermanaidenhic2009-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/LiebermanAidenHiC2009_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/LiebermanAidenHiC2009_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-liebermanaidenhic2009/bioconductor-liebermanaidenhic2009_0.40.0_src_all.tar.gz"], "md5": "34818101f902d251b339864716cd2d1a", "fn": "LiebermanAidenHiC2009_0.40.0.tar.gz"}, "listeretalbsseq-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ListerEtAlBSseq_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/ListerEtAlBSseq_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-listeretalbsseq/bioconductor-listeretalbsseq_1.34.0_src_all.tar.gz"], "md5": "302e026ae021a5f26c149b5086569db1", "fn": "ListerEtAlBSseq_1.34.0.tar.gz"}, "lrcelltypemarkers-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/LRcellTypeMarkers_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/LRcellTypeMarkers_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lrcelltypemarkers/bioconductor-lrcelltypemarkers_1.10.0_src_all.tar.gz"], "md5": "f5731667b56b631291d22a830d212f04", "fn": "LRcellTypeMarkers_1.10.0.tar.gz"}, "lumibarnes-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/lumiBarnes_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/lumiBarnes_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumibarnes/bioconductor-lumibarnes_1.42.0_src_all.tar.gz"], "md5": "2be75f5470fd60f9919045fc8147b613", "fn": "lumiBarnes_1.42.0.tar.gz"}, "lungcanceracvssccgeo-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/LungCancerACvsSCCGEO_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/LungCancerACvsSCCGEO_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungcanceracvssccgeo/bioconductor-lungcanceracvssccgeo_1.38.0_src_all.tar.gz"], "md5": "f353aa0cc36dc25e67cdf1ba0738985e", "fn": "LungCancerACvsSCCGEO_1.38.0.tar.gz"}, "lungcancerlines-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/LungCancerLines_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/LungCancerLines_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungcancerlines/bioconductor-lungcancerlines_0.40.0_src_all.tar.gz"], "md5": "17b67ca0eac14ef832832b949972b277", "fn": "LungCancerLines_0.40.0.tar.gz"}, "lungexpression-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/lungExpression_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/lungExpression_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungexpression/bioconductor-lungexpression_0.40.0_src_all.tar.gz"], "md5": "35eab717cb2e24c92faf417ad7fb9cb8", "fn": "lungExpression_0.40.0.tar.gz"}, "lydata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/lydata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/lydata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lydata/bioconductor-lydata_1.28.0_src_all.tar.gz"], "md5": "4541ec0aad2bbee135b19b0bed4ea0af", "fn": "lydata_1.28.0.tar.gz"}, "m3dexampledata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/M3DExampleData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/M3DExampleData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-m3dexampledata/bioconductor-m3dexampledata_1.28.0_src_all.tar.gz"], "md5": "6988767aab7572ae3e701fd6854c061f", "fn": "M3DExampleData_1.28.0.tar.gz"}, "macrophage-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/macrophage_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/macrophage_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-macrophage/bioconductor-macrophage_1.18.0_src_all.tar.gz"], "md5": "5f83cf12d699a285cd228119b1d95cf0", "fn": "macrophage_1.18.0.tar.gz"}, "macsdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MACSdata_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MACSdata_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-macsdata/bioconductor-macsdata_1.10.0_src_all.tar.gz"], "md5": "1d10f4fe6b20d5c09148b8011fb3183f", "fn": "MACSdata_1.10.0.tar.gz"}, "mammaprintdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/mammaPrintData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/mammaPrintData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mammaprintdata/bioconductor-mammaprintdata_1.38.0_src_all.tar.gz"], "md5": "08b3249a36d5f165a933bfab5eb05a2a", "fn": "mammaPrintData_1.38.0.tar.gz"}, "mapkldata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/mAPKLData_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/mAPKLData_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mapkldata/bioconductor-mapkldata_1.34.0_src_all.tar.gz"], "md5": "ce6399a1c853cb4e78de226347c3dc5d", "fn": "mAPKLData_1.34.0.tar.gz"}, "maqcexpression4plex-1.46.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/maqcExpression4plex_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/maqcExpression4plex_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcexpression4plex/bioconductor-maqcexpression4plex_1.46.0_src_all.tar.gz"], "md5": "8312b7fbcba763a33630effb8c3b5f10", "fn": "maqcExpression4plex_1.46.0.tar.gz"}, "maqcsubset-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MAQCsubset_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/MAQCsubset_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcsubset/bioconductor-maqcsubset_1.40.0_src_all.tar.gz"], "md5": "5757c11a1af2150b8fd17c3a8b8b0c0c", "fn": "MAQCsubset_1.40.0.tar.gz"}, "maqcsubsetilm-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MAQCsubsetILM_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/MAQCsubsetILM_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcsubsetilm/bioconductor-maqcsubsetilm_1.40.0_src_all.tar.gz"], "md5": "1c975db69a86cc80e99c5245998ee255", "fn": "MAQCsubsetILM_1.40.0.tar.gz"}, "marinerdata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/marinerData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/marinerData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-marinerdata/bioconductor-marinerdata_1.2.0_src_all.tar.gz"], "md5": "7875113ebb6baaaed6eb6fc762ba92ca", "fn": "marinerData_1.2.0.tar.gz"}, "mcseadata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/mCSEAdata_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/mCSEAdata_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcseadata/bioconductor-mcseadata_1.22.0_src_all.tar.gz"], "md5": "11f8150e223a0e8d8fa5b9b8dedaa374", "fn": "mCSEAdata_1.22.0.tar.gz"}, "mcsurvdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/mcsurvdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/mcsurvdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcsurvdata/bioconductor-mcsurvdata_1.20.0_src_all.tar.gz"], "md5": "0299258c7610f3675dc0b9f8e333eefa", "fn": "mcsurvdata_1.20.0.tar.gz"}, "medipsdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MEDIPSData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/MEDIPSData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-medipsdata/bioconductor-medipsdata_1.38.0_src_all.tar.gz"], "md5": "7b329ecedb2e9911b92ad669856abf2b", "fn": "MEDIPSData_1.38.0.tar.gz"}, "meebodata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MEEBOdata_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/MEEBOdata_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-meebodata/bioconductor-meebodata_1.40.0_src_all.tar.gz"], "md5": "cd3b9bb8a918c9497903f6274f323904", "fn": "MEEBOdata_1.40.0.tar.gz"}, "merfishdata-1.4.1": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MerfishData_1.4.1.tar.gz", "https://bioarchive.galaxyproject.org/MerfishData_1.4.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-merfishdata/bioconductor-merfishdata_1.4.1_src_all.tar.gz"], "md5": "05369f89c4e1a15bdab1ce5174facbe4", "fn": "MerfishData_1.4.1.tar.gz"}, "metagxbreast-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MetaGxBreast_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxBreast_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxbreast/bioconductor-metagxbreast_1.22.0_src_all.tar.gz"], "md5": "e711302482bca1429de5fe2e5276c788", "fn": "MetaGxBreast_1.22.0.tar.gz"}, "metagxovarian-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MetaGxOvarian_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxOvarian_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxovarian/bioconductor-metagxovarian_1.22.0_src_all.tar.gz"], "md5": "f76dc6c912d3a8936f81509ba6559286", "fn": "MetaGxOvarian_1.22.0.tar.gz"}, "metagxpancreas-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MetaGxPancreas_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxPancreas_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxpancreas/bioconductor-metagxpancreas_1.22.0_src_all.tar.gz"], "md5": "0c1764dc18a9a180b2121649c98a26a1", "fn": "MetaGxPancreas_1.22.0.tar.gz"}, "metamsdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/metaMSdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/metaMSdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metamsdata/bioconductor-metamsdata_1.38.0_src_all.tar.gz"], "md5": "aa7ca09c8f43104cb85f69fda0a1fc1a", "fn": "metaMSdata_1.38.0.tar.gz"}, "metascope-1.2.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MetaScope_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaScope_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metascope/bioconductor-metascope_1.2.0_src_all.tar.gz"], "md5": "3e9dbacc12fa3bd332773ffa95325f0b", "fn": "MetaScope_1.2.0.tar.gz"}, "methylaiddata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MethylAidData_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/MethylAidData_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylaiddata/bioconductor-methylaiddata_1.34.0_src_all.tar.gz"], "md5": "95cc72b436067e4a8046564381101e04", "fn": "MethylAidData_1.34.0.tar.gz"}, "methylclockdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/methylclockData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/methylclockData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylclockdata/bioconductor-methylclockdata_1.10.0_src_all.tar.gz"], "md5": "633d9cc6c028025090e12004484fada1", "fn": "methylclockData_1.10.0.tar.gz"}, "methylseqdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MethylSeqData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/MethylSeqData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylseqdata/bioconductor-methylseqdata_1.12.0_src_all.tar.gz"], "md5": "ded280784f55a6ebec42069160de26ad", "fn": "MethylSeqData_1.12.0.tar.gz"}, "microbiomebenchmarkdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MicrobiomeBenchmarkData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/MicrobiomeBenchmarkData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-microbiomebenchmarkdata/bioconductor-microbiomebenchmarkdata_1.4.0_src_all.tar.gz"], "md5": "c6c791669de95bf2dc108798770ea5be", "fn": "MicrobiomeBenchmarkData_1.4.0.tar.gz"}, "microbiomedatasets-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/microbiomeDataSets_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/microbiomeDataSets_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-microbiomedatasets/bioconductor-microbiomedatasets_1.10.0_src_all.tar.gz"], "md5": "90cd4bb36dafcef8f6eb0e0232afdcd0", "fn": "microbiomeDataSets_1.10.0.tar.gz"}, "micrornaome-1.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/microRNAome_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/microRNAome_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-micrornaome/bioconductor-micrornaome_1.24.0_src_all.tar.gz"], "md5": "12d3baf395e82975bbcacfb9ff61a715", "fn": "microRNAome_1.24.0.tar.gz"}, "minfidata-0.48.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/minfiData_0.48.0.tar.gz", "https://bioarchive.galaxyproject.org/minfiData_0.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minfidata/bioconductor-minfidata_0.48.0_src_all.tar.gz"], "md5": "1ca7578aeab1a54db146c443870be6e7", "fn": "minfiData_0.48.0.tar.gz"}, "minfidataepic-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/minfiDataEPIC_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/minfiDataEPIC_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minfidataepic/bioconductor-minfidataepic_1.28.0_src_all.tar.gz"], "md5": "bcb0b01d571c5308e02db4c6b5c0d1ce", "fn": "minfiDataEPIC_1.28.0.tar.gz"}, "minionsummarydata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/minionSummaryData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/minionSummaryData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minionsummarydata/bioconductor-minionsummarydata_1.32.0_src_all.tar.gz"], "md5": "1679c45541b2d76094c3894abe9c011d", "fn": "minionSummaryData_1.32.0.tar.gz"}, "mircompdata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/miRcompData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/miRcompData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mircompdata/bioconductor-mircompdata_1.32.0_src_all.tar.gz"], "md5": "0b091222ebe8ac1a3a2c59384931393b", "fn": "miRcompData_1.32.0.tar.gz"}, "mirnatarget-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/miRNATarget_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/miRNATarget_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirnatarget/bioconductor-mirnatarget_1.40.0_src_all.tar.gz"], "md5": "f1988a96af5f0232abfbe507854d49bb", "fn": "miRNATarget_1.40.0.tar.gz"}, "mmappr2data-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MMAPPR2data_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/MMAPPR2data_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mmappr2data/bioconductor-mmappr2data_1.16.0_src_all.tar.gz"], "md5": "5b4772746766de5c40448c865fa2d60d", "fn": "MMAPPR2data_1.16.0.tar.gz"}, "mmdiffbamsubset-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MMDiffBamSubset_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/MMDiffBamSubset_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mmdiffbamsubset/bioconductor-mmdiffbamsubset_1.38.0_src_all.tar.gz"], "md5": "0becc66301b49b58a99efa19577ee27c", "fn": "MMDiffBamSubset_1.38.0.tar.gz"}, "mofadata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MOFAdata_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/MOFAdata_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mofadata/bioconductor-mofadata_1.18.0_src_all.tar.gz"], "md5": "23e46e209a43d7e62cfd6accc6a6fb44", "fn": "MOFAdata_1.18.0.tar.gz"}, "mosaicsexample-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/mosaicsExample_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/mosaicsExample_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mosaicsexample/bioconductor-mosaicsexample_1.40.0_src_all.tar.gz"], "md5": "8852ad56f152a138367e7630b6b21efb", "fn": "mosaicsExample_1.40.0.tar.gz"}, "mouse4302barcodevecs-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/mouse4302barcodevecs_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse4302barcodevecs_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302barcodevecs/bioconductor-mouse4302barcodevecs_1.40.0_src_all.tar.gz"], "md5": "365757fba17dae1ed483e184d2c9fcdb", "fn": "mouse4302barcodevecs_1.40.0.tar.gz"}, "mousegastrulationdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MouseGastrulationData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/MouseGastrulationData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousegastrulationdata/bioconductor-mousegastrulationdata_1.16.0_src_all.tar.gz"], "md5": "4af06fb157942c6cfd9f24494bd7ae1f", "fn": "MouseGastrulationData_1.16.0.tar.gz"}, "mousethymusageing-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MouseThymusAgeing_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/MouseThymusAgeing_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousethymusageing/bioconductor-mousethymusageing_1.10.0_src_all.tar.gz"], "md5": "cf1889c22fa9e5ac5899a4d911907a90", "fn": "MouseThymusAgeing_1.10.0.tar.gz"}, "msd16s-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/msd16s_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/msd16s_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msd16s/bioconductor-msd16s_1.22.0_src_all.tar.gz"], "md5": "fddb80467192bbe28bb92599941be5d3", "fn": "msd16s_1.22.0.tar.gz"}, "msdata-0.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/msdata_0.42.0.tar.gz", "https://bioarchive.galaxyproject.org/msdata_0.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msdata/bioconductor-msdata_0.42.0_src_all.tar.gz"], "md5": "3ef7fea0866799a767fb8ac2d1da0a16", "fn": "msdata_0.42.0.tar.gz"}, "msigdb-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/msigdb_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/msigdb_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msigdb/bioconductor-msigdb_1.10.0_src_all.tar.gz"], "md5": "eb5822dab5f9ad68cc5a46beaf626de0", "fn": "msigdb_1.10.0.tar.gz"}, "msmb-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MSMB_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/MSMB_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msmb/bioconductor-msmb_1.20.0_src_all.tar.gz"], "md5": "bc2942708f54a40d59ce7e41daff7df0", "fn": "MSMB_1.20.0.tar.gz"}, "mspuritydata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/msPurityData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/msPurityData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mspuritydata/bioconductor-mspuritydata_1.30.0_src_all.tar.gz"], "md5": "6c86343515cbb9f81131baa3f25659f0", "fn": "msPurityData_1.30.0.tar.gz"}, "msqc1-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/msqc1_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/msqc1_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msqc1/bioconductor-msqc1_1.30.0_src_all.tar.gz"], "md5": "a95a760a0c0ef5e8053acee1d59170a4", "fn": "msqc1_1.30.0.tar.gz"}, "mtbls2-1.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/mtbls2_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/mtbls2_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mtbls2/bioconductor-mtbls2_1.32.0_src_all.tar.gz"], "md5": "820109836c79f398ea5b82f5887b7fea", "fn": "mtbls2_1.32.0.tar.gz"}, "mugaexampledata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/MUGAExampleData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/MUGAExampleData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mugaexampledata/bioconductor-mugaexampledata_1.22.0_src_all.tar.gz"], "md5": "b7fe2c7ad41486695fb78263a8c9a854", "fn": "MUGAExampleData_1.22.0.tar.gz"}, "muscdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/muscData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/muscData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-muscdata/bioconductor-muscdata_1.16.0_src_all.tar.gz"], "md5": "f34c376f88f97c98d4aac5490b45bc24", "fn": "muscData_1.16.0.tar.gz"}, "mvoutdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/mvoutData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/mvoutData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mvoutdata/bioconductor-mvoutdata_1.38.0_src_all.tar.gz"], "md5": "abca7ca8ae7729ed8f146d0083aa9757", "fn": "mvoutData_1.38.0.tar.gz"}, "nanoporernaseq-1.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/NanoporeRNASeq_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/NanoporeRNASeq_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nanoporernaseq/bioconductor-nanoporernaseq_1.12.0_src_all.tar.gz"], "md5": "eca12ebcd403efd53e1b38d5f03f2027", "fn": "NanoporeRNASeq_1.12.0.tar.gz"}, "nanotubes-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/nanotubes_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/nanotubes_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nanotubes/bioconductor-nanotubes_1.18.0_src_all.tar.gz"], "md5": "ff283cb49c319a357c22e17d2df22715", "fn": "nanotubes_1.18.0.tar.gz"}, "ncigraphdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/NCIgraphData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/NCIgraphData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ncigraphdata/bioconductor-ncigraphdata_1.38.0_src_all.tar.gz"], "md5": "f144169473d42fafb1966986dcf15628", "fn": "NCIgraphData_1.38.0.tar.gz"}, "nestlink-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/NestLink_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/NestLink_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nestlink/bioconductor-nestlink_1.18.0_src_all.tar.gz"], "md5": "11cd94f5bd8b38cf261ae3346a283e81", "fn": "NestLink_1.18.0.tar.gz"}, "netactivitydata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/NetActivityData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/NetActivityData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-netactivitydata/bioconductor-netactivitydata_1.4.0_src_all.tar.gz"], "md5": "a3805046d14d13afc30a0f082952f200", "fn": "NetActivityData_1.4.0.tar.gz"}, "neve2006-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Neve2006_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/Neve2006_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-neve2006/bioconductor-neve2006_0.40.0_src_all.tar.gz"], "md5": "1feec2f09bac8c69ba9df5ea29e7e08c", "fn": "Neve2006_0.40.0.tar.gz"}, "ngscopydata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/NGScopyData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/NGScopyData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ngscopydata/bioconductor-ngscopydata_1.22.0_src_all.tar.gz"], "md5": "0ba77cf672a331e4c9dd90b26f41b5c6", "fn": "NGScopyData_1.22.0.tar.gz"}, "nullrangesdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/nullrangesData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/nullrangesData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nullrangesdata/bioconductor-nullrangesdata_1.8.0_src_all.tar.gz"], "md5": "c8b4cf63d70a2577251c03c093c014b1", "fn": "nullrangesData_1.8.0.tar.gz"}, "nxtirfdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/NxtIRFdata_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/NxtIRFdata_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nxtirfdata/bioconductor-nxtirfdata_1.8.0_src_all.tar.gz"], "md5": "3d9c35f12650fe6e2eb413224b3590dc", "fn": "NxtIRFdata_1.8.0.tar.gz"}, "obmiti-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ObMiTi_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/ObMiTi_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-obmiti/bioconductor-obmiti_1.10.0_src_all.tar.gz"], "md5": "0510665a5231cd3109d19478e4aadbd9", "fn": "ObMiTi_1.10.0.tar.gz"}, "oct4-1.18.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/oct4_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/oct4_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-oct4/bioconductor-oct4_1.18.0_src_all.tar.gz"], "md5": "1b6bbc6300c74c038689c7fb5b7d5eb2", "fn": "oct4_1.18.0.tar.gz"}, "octad.db-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/octad.db_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/octad.db_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-octad.db/bioconductor-octad.db_1.4.0_src_all.tar.gz"], "md5": "ef8723031fea32015ee26dbf30d2c8ba", "fn": "octad.db_1.4.0.tar.gz"}, "omicspcadata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/OMICsPCAdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/OMICsPCAdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-omicspcadata/bioconductor-omicspcadata_1.20.0_src_all.tar.gz"], "md5": "ba3167fdf846cb80aea07162b88c9b73", "fn": "OMICsPCAdata_1.20.0.tar.gz"}, "onassisjavalibs-1.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/OnassisJavaLibs_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/OnassisJavaLibs_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-onassisjavalibs/bioconductor-onassisjavalibs_1.24.0_src_all.tar.gz"], "md5": "88d86bc7e7d339146ba7ea689c2d8080", "fn": "OnassisJavaLibs_1.24.0.tar.gz"}, "optimalflowdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/optimalFlowData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/optimalFlowData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-optimalflowdata/bioconductor-optimalflowdata_1.14.0_src_all.tar.gz"], "md5": "790ea8af88ecf90abafdef9a7c4abb08", "fn": "optimalFlowData_1.14.0.tar.gz"}, "orthosdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/orthosData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/orthosData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-orthosdata/bioconductor-orthosdata_1.0.0_src_all.tar.gz"], "md5": "7970587455fa5197daf1f6b640b7f688", "fn": "orthosData_1.0.0.tar.gz"}, "parathyroidse-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/parathyroidSE_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/parathyroidSE_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-parathyroidse/bioconductor-parathyroidse_1.40.0_src_all.tar.gz"], "md5": "e4d06f888feb4015273e20b14f8ee37a", "fn": "parathyroidSE_1.40.0.tar.gz"}, "pasilla-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/pasilla_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/pasilla_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasilla/bioconductor-pasilla_1.30.0_src_all.tar.gz"], "md5": "e1fbdd57136d8a29edd1e0164dc2412e", "fn": "pasilla_1.30.0.tar.gz"}, "pasillabamsubset-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/pasillaBamSubset_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/pasillaBamSubset_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasillabamsubset/bioconductor-pasillabamsubset_0.40.0_src_all.tar.gz"], "md5": "8fd05eac2d37650e157871908cbaf306", "fn": "pasillaBamSubset_0.40.0.tar.gz"}, "pasillatranscriptexpr-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PasillaTranscriptExpr_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/PasillaTranscriptExpr_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasillatranscriptexpr/bioconductor-pasillatranscriptexpr_1.30.0_src_all.tar.gz"], "md5": "7d1d8c852fff7d80c11e8ab79dae7487", "fn": "PasillaTranscriptExpr_1.30.0.tar.gz"}, "pathnetdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PathNetData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/PathNetData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pathnetdata/bioconductor-pathnetdata_1.38.0_src_all.tar.gz"], "md5": "d72e955b33c92f1703ae072ec788c1d9", "fn": "PathNetData_1.38.0.tar.gz"}, "pchicdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PCHiCdata_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/PCHiCdata_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pchicdata/bioconductor-pchicdata_1.30.0_src_all.tar.gz"], "md5": "8791902075a44ae03c0366150aa3f61e", "fn": "PCHiCdata_1.30.0.tar.gz"}, "pcxndata-2.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/pcxnData_2.24.0.tar.gz", "https://bioarchive.galaxyproject.org/pcxnData_2.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pcxndata/bioconductor-pcxndata_2.24.0_src_all.tar.gz"], "md5": "7814b1a6f5dbd08e71df1e92ea4328f6", "fn": "pcxnData_2.24.0.tar.gz"}, "pd.atdschip.tiling-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/pd.atdschip.tiling_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.atdschip.tiling_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.atdschip.tiling/bioconductor-pd.atdschip.tiling_0.40.0_src_all.tar.gz"], "md5": "a81ffdc7dfb8eb04e09ec133db77d0d4", "fn": "pd.atdschip.tiling_0.40.0.tar.gz"}, "pepdat-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/pepDat_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/pepDat_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pepdat/bioconductor-pepdat_1.22.0_src_all.tar.gz"], "md5": "4ce373369604b54b15e5992ebe9355b9", "fn": "pepDat_1.22.0.tar.gz"}, "pepsnmrdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PepsNMRData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/PepsNMRData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pepsnmrdata/bioconductor-pepsnmrdata_1.20.0_src_all.tar.gz"], "md5": "96fc9090499b4460f72fb85a0428b357", "fn": "PepsNMRData_1.20.0.tar.gz"}, "phyloprofiledata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PhyloProfileData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/PhyloProfileData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phyloprofiledata/bioconductor-phyloprofiledata_1.16.0_src_all.tar.gz"], "md5": "68dda32e9151c0aba4eb5b29c0313f83", "fn": "PhyloProfileData_1.16.0.tar.gz"}, "plotgardenerdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/plotgardenerData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/plotgardenerData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-plotgardenerdata/bioconductor-plotgardenerdata_1.8.0_src_all.tar.gz"], "md5": "96055b11818bd59c0c91977b34973608", "fn": "plotgardenerData_1.8.0.tar.gz"}, "prebsdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/prebsdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/prebsdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prebsdata/bioconductor-prebsdata_1.38.0_src_all.tar.gz"], "md5": "a1c6aee2732035357adc3e2cb99d6bcc", "fn": "prebsdata_1.38.0.tar.gz"}, "precisetadhub-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/preciseTADhub_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/preciseTADhub_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-precisetadhub/bioconductor-precisetadhub_1.10.0_src_all.tar.gz"], "md5": "bff4bbf0a4ac1abf21ff72ad4346795c", "fn": "preciseTADhub_1.10.0.tar.gz"}, "predasampledata-0.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PREDAsampledata_0.42.0.tar.gz", "https://bioarchive.galaxyproject.org/PREDAsampledata_0.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-predasampledata/bioconductor-predasampledata_0.42.0_src_all.tar.gz"], "md5": "5acce57384c00a56d658281ba4fa57e5", "fn": "PREDAsampledata_0.42.0.tar.gz"}, "prodata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ProData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/ProData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prodata/bioconductor-prodata_1.40.0_src_all.tar.gz"], "md5": "73f3449db86899c83d61173f6bd02a79", "fn": "ProData_1.40.0.tar.gz"}, "prolocdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/pRolocdata_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/pRolocdata_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prolocdata/bioconductor-prolocdata_1.40.0_src_all.tar.gz"], "md5": "8aafd04221b21588077788ec79272e1a", "fn": "pRolocdata_1.40.0.tar.gz"}, "prostatecancercamcap-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/prostateCancerCamcap_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerCamcap_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancercamcap/bioconductor-prostatecancercamcap_1.30.0_src_all.tar.gz"], "md5": "5a27ee47f07162569e5e1e06ffd69886", "fn": "prostateCancerCamcap_1.30.0.tar.gz"}, "prostatecancergrasso-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/prostateCancerGrasso_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerGrasso_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancergrasso/bioconductor-prostatecancergrasso_1.30.0_src_all.tar.gz"], "md5": "c331c996d943a14687439dfdf37b8029", "fn": "prostateCancerGrasso_1.30.0.tar.gz"}, "prostatecancerstockholm-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/prostateCancerStockholm_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerStockholm_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancerstockholm/bioconductor-prostatecancerstockholm_1.30.0_src_all.tar.gz"], "md5": "49326bf3b6f66be78fa1e6d6768b5538", "fn": "prostateCancerStockholm_1.30.0.tar.gz"}, "prostatecancertaylor-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/prostateCancerTaylor_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerTaylor_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancertaylor/bioconductor-prostatecancertaylor_1.30.0_src_all.tar.gz"], "md5": "c90ff79776e9a658d4cf05e9a29706a8", "fn": "prostateCancerTaylor_1.30.0.tar.gz"}, "prostatecancervarambally-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/prostateCancerVarambally_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerVarambally_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancervarambally/bioconductor-prostatecancervarambally_1.30.0_src_all.tar.gz"], "md5": "cf8fc1872af8c5c2b47372ce94ed4c5c", "fn": "prostateCancerVarambally_1.30.0.tar.gz"}, "ptairdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ptairData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/ptairData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ptairdata/bioconductor-ptairdata_1.10.0_src_all.tar.gz"], "md5": "eea0fcfdd0047d72092a3b6beb326129", "fn": "ptairData_1.10.0.tar.gz"}, "pth2o2lipids-1.28.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PtH2O2lipids_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/PtH2O2lipids_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pth2o2lipids/bioconductor-pth2o2lipids_1.28.0_src_all.tar.gz"], "md5": "498d573bc33e7566708c38be5098bb2e", "fn": "PtH2O2lipids_1.28.0.tar.gz"}, "pumadata-2.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/pumadata_2.38.0.tar.gz", "https://bioarchive.galaxyproject.org/pumadata_2.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pumadata/bioconductor-pumadata_2.38.0_src_all.tar.gz"], "md5": "811d6234d1d4e310beb7111601b157b7", "fn": "pumadata_2.38.0.tar.gz"}, "pwmenrich.dmelanogaster.background-4.36.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PWMEnrich.Dmelanogaster.background_4.36.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Dmelanogaster.background_4.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.dmelanogaster.background/bioconductor-pwmenrich.dmelanogaster.background_4.36.0_src_all.tar.gz"], "md5": "b671ba0cff5c0c6017fd3f72d0afc547", "fn": "PWMEnrich.Dmelanogaster.background_4.36.0.tar.gz"}, "pwmenrich.hsapiens.background-4.36.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PWMEnrich.Hsapiens.background_4.36.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Hsapiens.background_4.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.hsapiens.background/bioconductor-pwmenrich.hsapiens.background_4.36.0_src_all.tar.gz"], "md5": "7c7b177c29fc31c7546d4e7160a9b977", "fn": "PWMEnrich.Hsapiens.background_4.36.0.tar.gz"}, "pwmenrich.mmusculus.background-4.36.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PWMEnrich.Mmusculus.background_4.36.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Mmusculus.background_4.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.mmusculus.background/bioconductor-pwmenrich.mmusculus.background_4.36.0_src_all.tar.gz"], "md5": "5d54401a941d1efe7148da2ddc714d65", "fn": "PWMEnrich.Mmusculus.background_4.36.0.tar.gz"}, "qdnaseq.hg19-1.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/QDNAseq.hg19_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/QDNAseq.hg19_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.hg19/bioconductor-qdnaseq.hg19_1.32.0_src_all.tar.gz"], "md5": "2b663d8771f16d55db88ec3321942ead", "fn": "QDNAseq.hg19_1.32.0.tar.gz"}, "qdnaseq.mm10-1.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/QDNAseq.mm10_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/QDNAseq.mm10_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.mm10/bioconductor-qdnaseq.mm10_1.32.0_src_all.tar.gz"], "md5": "2d7b80c2bec7146aec28384b7875acca", "fn": "QDNAseq.mm10_1.32.0.tar.gz"}, "qplexdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/qPLEXdata_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/qPLEXdata_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qplexdata/bioconductor-qplexdata_1.20.0_src_all.tar.gz"], "md5": "af947f54391fc79c81308890b1e95d96", "fn": "qPLEXdata_1.20.0.tar.gz"}, "qubicdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/QUBICdata_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/QUBICdata_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qubicdata/bioconductor-qubicdata_1.30.0_src_all.tar.gz"], "md5": "0670dfaee6f8d532cf3506428a5932c1", "fn": "QUBICdata_1.30.0.tar.gz"}, "raerdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/raerdata_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/raerdata_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-raerdata/bioconductor-raerdata_1.0.0_src_all.tar.gz"], "md5": "8f250d12f89396f8d4351da5045cf22c", "fn": "raerdata_1.0.0.tar.gz"}, "rcellminerdata-2.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/rcellminerData_2.24.0.tar.gz", "https://bioarchive.galaxyproject.org/rcellminerData_2.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rcellminerdata/bioconductor-rcellminerdata_2.24.0_src_all.tar.gz"], "md5": "2f45852d4eeb438b6a1feb156200b2bc", "fn": "rcellminerData_2.24.0.tar.gz"}, "rcistarget.hg19.motifdbs.cisbponly.500bp-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp_1.22.0_src_all.tar.gz"], "md5": "b8cdbfafeb9966332876fdf9be8dbb5a", "fn": "RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.22.0.tar.gz"}, "reactomegsa.data-1.16.1": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/ReactomeGSA.data_1.16.1.tar.gz", "https://bioarchive.galaxyproject.org/ReactomeGSA.data_1.16.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-reactomegsa.data/bioconductor-reactomegsa.data_1.16.1_src_all.tar.gz"], "md5": "bd236d4d4078f99ea5d473fde1ff065f", "fn": "ReactomeGSA.data_1.16.1.tar.gz"}, "regparallel-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RegParallel_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/RegParallel_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-regparallel/bioconductor-regparallel_1.20.0_src_all.tar.gz"], "md5": "68533561edc82ac22088ffdd6e988aad", "fn": "RegParallel_1.20.0.tar.gz"}, "restfulsedata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/restfulSEData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/restfulSEData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-restfulsedata/bioconductor-restfulsedata_1.24.0_src_all.tar.gz"], "md5": "c69fe04b8675edd0faa593fb5ffc72c8", "fn": "restfulSEData_1.24.0.tar.gz"}, "rforproteomics-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RforProteomics_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/RforProteomics_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rforproteomics/bioconductor-rforproteomics_1.40.0_src_all.tar.gz"], "md5": "6d75aedb5902ea26a18e39da6848db4c", "fn": "RforProteomics_1.40.0.tar.gz"}, "rgmqllib-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RGMQLlib_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/RGMQLlib_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgmqllib/bioconductor-rgmqllib_1.22.0_src_all.tar.gz"], "md5": "d8ad27b1fe0c5eff6135285db972cab2", "fn": "RGMQLlib_1.22.0.tar.gz"}, "rheumaticconditionwollbold-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/rheumaticConditionWOLLBOLD_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/rheumaticConditionWOLLBOLD_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rheumaticconditionwollbold/bioconductor-rheumaticconditionwollbold_1.40.0_src_all.tar.gz"], "md5": "8c8a5f56b923fe79c4a4902028d6fc5c", "fn": "rheumaticConditionWOLLBOLD_1.40.0.tar.gz"}, "ritandata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RITANdata_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/RITANdata_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ritandata/bioconductor-ritandata_1.26.0_src_all.tar.gz"], "md5": "12987879ef374ad399dd440a058b9a47", "fn": "RITANdata_1.26.0.tar.gz"}, "rmassbankdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RMassBankData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/RMassBankData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rmassbankdata/bioconductor-rmassbankdata_1.40.0_src_all.tar.gz"], "md5": "ac6f883e962890eebb03c2368be8bcdc", "fn": "RMassBankData_1.40.0.tar.gz"}, "rnainteractmapk-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RNAinteractMAPK_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAinteractMAPK_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnainteractmapk/bioconductor-rnainteractmapk_1.40.0_src_all.tar.gz"], "md5": "c60bb748ed7dc37d409f5dde69354074", "fn": "RNAinteractMAPK_1.40.0.tar.gz"}, "rnamodr.data-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RNAmodR.Data_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAmodR.Data_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnamodr.data/bioconductor-rnamodr.data_1.16.0_src_all.tar.gz"], "md5": "cd4851e2f0c0a93c6d5a9163f542b07f", "fn": "RNAmodR.Data_1.16.0.tar.gz"}, "rnaseqdata.hnrnpc.bam.chr14-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RNAseqData.HNRNPC.bam.chr14_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAseqData.HNRNPC.bam.chr14_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqdata.hnrnpc.bam.chr14/bioconductor-rnaseqdata.hnrnpc.bam.chr14_0.40.0_src_all.tar.gz"], "md5": "9bfb7faf3c8770b15f3cf15bb670162d", "fn": "RNAseqData.HNRNPC.bam.chr14_0.40.0.tar.gz"}, "rnaseqsamplesizedata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RnaSeqSampleSizeData_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/RnaSeqSampleSizeData_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqsamplesizedata/bioconductor-rnaseqsamplesizedata_1.34.0_src_all.tar.gz"], "md5": "a4edc47422b0be1d83521282c0599440", "fn": "RnaSeqSampleSizeData_1.34.0.tar.gz"}, "rnbeads.hg19-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RnBeads.hg19_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.hg19_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg19/bioconductor-rnbeads.hg19_1.34.0_src_all.tar.gz"], "md5": "92612251679ba9c6d2b88b90838edf1c", "fn": "RnBeads.hg19_1.34.0.tar.gz"}, "rnbeads.hg38-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RnBeads.hg38_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.hg38_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg38/bioconductor-rnbeads.hg38_1.34.0_src_all.tar.gz"], "md5": "44dd2d3ae3703e045016a34060a14b0a", "fn": "RnBeads.hg38_1.34.0.tar.gz"}, "rnbeads.mm10-2.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RnBeads.mm10_2.10.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.mm10_2.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm10/bioconductor-rnbeads.mm10_2.10.0_src_all.tar.gz"], "md5": "0c935572ce46183bc5a7aaea31ea2519", "fn": "RnBeads.mm10_2.10.0.tar.gz"}, "rnbeads.mm9-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RnBeads.mm9_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.mm9_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm9/bioconductor-rnbeads.mm9_1.34.0_src_all.tar.gz"], "md5": "76f271051b1c542e5ac0da492777f933", "fn": "RnBeads.mm9_1.34.0.tar.gz"}, "rnbeads.rn5-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RnBeads.rn5_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.rn5_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.rn5/bioconductor-rnbeads.rn5_1.34.0_src_all.tar.gz"], "md5": "ed075717da62b68e7a9b47a14ac09a35", "fn": "RnBeads.rn5_1.34.0.tar.gz"}, "rrbsdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RRBSdata_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/RRBSdata_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rrbsdata/bioconductor-rrbsdata_1.22.0_src_all.tar.gz"], "md5": "04bcf0f0348dc54984ca9506773820ec", "fn": "RRBSdata_1.22.0.tar.gz"}, "rrdpdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/rRDPData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/rRDPData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rrdpdata/bioconductor-rrdpdata_1.22.0_src_all.tar.gz"], "md5": "9ca56f1bf00bfaefb27c351ccc7346ae", "fn": "rRDPData_1.22.0.tar.gz"}, "rtcga.clinical-20151101.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RTCGA.clinical_20151101.32.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.clinical_20151101.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.clinical/bioconductor-rtcga.clinical_20151101.32.0_src_all.tar.gz"], "md5": "9c32b8aef86c9ad34ea8c3672575d724", "fn": "RTCGA.clinical_20151101.32.0.tar.gz"}, "rtcga.cnv-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RTCGA.CNV_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.CNV_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.cnv/bioconductor-rtcga.cnv_1.30.0_src_all.tar.gz"], "md5": "15267c2322da59ccd344657a28d2ba6a", "fn": "RTCGA.CNV_1.30.0.tar.gz"}, "rtcga.methylation-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RTCGA.methylation_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.methylation_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.methylation/bioconductor-rtcga.methylation_1.30.0_src_all.tar.gz"], "md5": "9d90704cb34a57878ef719348489c702", "fn": "RTCGA.methylation_1.30.0.tar.gz"}, "rtcga.mirnaseq-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RTCGA.miRNASeq_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.miRNASeq_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mirnaseq/bioconductor-rtcga.mirnaseq_1.30.0_src_all.tar.gz"], "md5": "744062c2f0db68a88e27db9d61929a79", "fn": "RTCGA.miRNASeq_1.30.0.tar.gz"}, "rtcga.mrna-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RTCGA.mRNA_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.mRNA_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mrna/bioconductor-rtcga.mrna_1.30.0_src_all.tar.gz"], "md5": "c9774207df355ef5945677d36e915103", "fn": "RTCGA.mRNA_1.30.0.tar.gz"}, "rtcga.mutations-20151101.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RTCGA.mutations_20151101.32.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.mutations_20151101.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mutations/bioconductor-rtcga.mutations_20151101.32.0_src_all.tar.gz"], "md5": "0740acb5a6a47fd9d1281ccaf80bafed", "fn": "RTCGA.mutations_20151101.32.0.tar.gz"}, "rtcga.pancan12-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RTCGA.PANCAN12_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.PANCAN12_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.pancan12/bioconductor-rtcga.pancan12_1.30.0_src_all.tar.gz"], "md5": "8b0742d189afe05f47a2656556d85d0b", "fn": "RTCGA.PANCAN12_1.30.0.tar.gz"}, "rtcga.rnaseq-20151101.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RTCGA.rnaseq_20151101.32.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.rnaseq_20151101.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.rnaseq/bioconductor-rtcga.rnaseq_20151101.32.0_src_all.tar.gz"], "md5": "47bee14c68ff4d1014677eca0ed969a9", "fn": "RTCGA.rnaseq_20151101.32.0.tar.gz"}, "rtcga.rppa-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RTCGA.RPPA_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.RPPA_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.rppa/bioconductor-rtcga.rppa_1.30.0_src_all.tar.gz"], "md5": "5eccece412039d43cdf74aec284fa0d9", "fn": "RTCGA.RPPA_1.30.0.tar.gz"}, "ruvnormalizedata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/RUVnormalizeData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/RUVnormalizeData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ruvnormalizedata/bioconductor-ruvnormalizedata_1.22.0_src_all.tar.gz"], "md5": "5d7104746a5cac16500870312dd769a6", "fn": "RUVnormalizeData_1.22.0.tar.gz"}, "sampleclassifierdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/sampleClassifierData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/sampleClassifierData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sampleclassifierdata/bioconductor-sampleclassifierdata_1.26.0_src_all.tar.gz"], "md5": "941790a92cde9051601206ed162f4151", "fn": "sampleClassifierData_1.26.0.tar.gz"}, "sbgnview.data-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SBGNview.data_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/SBGNview.data_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sbgnview.data/bioconductor-sbgnview.data_1.16.0_src_all.tar.gz"], "md5": "7e1bce0dfbc48b3cdc023d88e2ea7d9a", "fn": "SBGNview.data_1.16.0.tar.gz"}, "scanmirdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/scanMiRData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/scanMiRData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scanmirdata/bioconductor-scanmirdata_1.8.0_src_all.tar.gz"], "md5": "4c717492a3c85bbcf199873e35190219", "fn": "scanMiRData_1.8.0.tar.gz"}, "scatac.explorer-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/scATAC.Explorer_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/scATAC.Explorer_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scatac.explorer/bioconductor-scatac.explorer_1.8.0_src_all.tar.gz"], "md5": "80927899a83bb06d19b0f9800c183b36", "fn": "scATAC.Explorer_1.8.0.tar.gz"}, "sclcbam-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SCLCBam_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/SCLCBam_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sclcbam/bioconductor-sclcbam_1.34.0_src_all.tar.gz"], "md5": "660f11c1751b54cc942e91045884bfe6", "fn": "SCLCBam_1.34.0.tar.gz"}, "scmultiome-1.2.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/scMultiome_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/scMultiome_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scmultiome/bioconductor-scmultiome_1.2.0_src_all.tar.gz"], "md5": "db13145ffc5eb5430eee8ac7212e1b7d", "fn": "scMultiome_1.2.0.tar.gz"}, "scpdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/scpdata_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/scpdata_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scpdata/bioconductor-scpdata_1.10.0_src_all.tar.gz"], "md5": "eac9eae58fe9297359188c45a3dabd1f", "fn": "scpdata_1.10.0.tar.gz"}, "scrnaseq-2.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/scRNAseq_2.16.0.tar.gz", "https://bioarchive.galaxyproject.org/scRNAseq_2.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scrnaseq/bioconductor-scrnaseq_2.16.0_src_all.tar.gz"], "md5": "55196cb10876aa15733c6a29ffc38100", "fn": "scRNAseq_2.16.0.tar.gz"}, "scthi.data-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/scTHI.data_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/scTHI.data_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scthi.data/bioconductor-scthi.data_1.14.0_src_all.tar.gz"], "md5": "1fd101f8dc30262c323bdfa79810f6f5", "fn": "scTHI.data_1.14.0.tar.gz"}, "seq2pathway.data-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/seq2pathway.data_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/seq2pathway.data_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seq2pathway.data/bioconductor-seq2pathway.data_1.34.0_src_all.tar.gz"], "md5": "b0035ff986391159c1329eac9fb96661", "fn": "seq2pathway.data_1.34.0.tar.gz"}, "seqc-1.36.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/seqc_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/seqc_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seqc/bioconductor-seqc_1.36.0_src_all.tar.gz"], "md5": "105a278c97aca90968641aec403c1219", "fn": "seqc_1.36.0.tar.gz"}, "seqcna.annot-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/seqCNA.annot_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/seqCNA.annot_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seqcna.annot/bioconductor-seqcna.annot_1.38.0_src_all.tar.gz"], "md5": "a61df6e0824d7c3c3f4c697b5bd73e30", "fn": "seqCNA.annot_1.38.0.tar.gz"}, "serumstimulation-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/serumStimulation_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/serumStimulation_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-serumstimulation/bioconductor-serumstimulation_1.38.0_src_all.tar.gz"], "md5": "4d3f1a4e58f500d7e424eef0b22c05ad", "fn": "serumStimulation_1.38.0.tar.gz"}, "sesamedata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/sesameData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/sesameData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sesamedata/bioconductor-sesamedata_1.20.0_src_all.tar.gz"], "md5": "4cd44c4f5307d2775d94f2051b9a7f46", "fn": "sesameData_1.20.0.tar.gz"}, "sfedata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SFEData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/SFEData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sfedata/bioconductor-sfedata_1.4.0_src_all.tar.gz"], "md5": "7f3376870c972cba309b26d52d24fcbb", "fn": "SFEData_1.4.0.tar.gz"}, "shinymethyldata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/shinyMethylData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/shinyMethylData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-shinymethyldata/bioconductor-shinymethyldata_1.22.0_src_all.tar.gz"], "md5": "46f32db849aaa1467d09b0a371769374", "fn": "shinyMethylData_1.22.0.tar.gz"}, "signaturesearchdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/signatureSearchData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/signatureSearchData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-signaturesearchdata/bioconductor-signaturesearchdata_1.16.0_src_all.tar.gz"], "md5": "b30a7f1715a7525279c47db6df5ad995", "fn": "signatureSearchData_1.16.0.tar.gz"}, "simbenchdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SimBenchData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/SimBenchData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-simbenchdata/bioconductor-simbenchdata_1.10.0_src_all.tar.gz"], "md5": "c801056ea68c668cd98230e8956d551b", "fn": "SimBenchData_1.10.0.tar.gz"}, "simpintlists-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/simpIntLists_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/simpIntLists_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-simpintlists/bioconductor-simpintlists_1.38.0_src_all.tar.gz"], "md5": "9dbe0a1f390843a49bb11d05ac5f2e28", "fn": "simpIntLists_1.38.0.tar.gz"}, "single.mtec.transcriptomes-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/Single.mTEC.Transcriptomes_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/Single.mTEC.Transcriptomes_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-single.mtec.transcriptomes/bioconductor-single.mtec.transcriptomes_1.30.0_src_all.tar.gz"], "md5": "574ee45ff1177688d68e6ae8295e67a2", "fn": "Single.mTEC.Transcriptomes_1.30.0.tar.gz"}, "singlecellmultimodal-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SingleCellMultiModal_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/SingleCellMultiModal_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-singlecellmultimodal/bioconductor-singlecellmultimodal_1.14.0_src_all.tar.gz"], "md5": "e397bc4fbd9ea63f6660758f01d01d38", "fn": "SingleCellMultiModal_1.14.0.tar.gz"}, "singlemoleculefootprintingdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SingleMoleculeFootprintingData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/SingleMoleculeFootprintingData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-singlemoleculefootprintingdata/bioconductor-singlemoleculefootprintingdata_1.10.0_src_all.tar.gz"], "md5": "451ecbdbb964607afbbe3b778b290246", "fn": "SingleMoleculeFootprintingData_1.10.0.tar.gz"}, "smokingmouse-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/smokingMouse_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/smokingMouse_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-smokingmouse/bioconductor-smokingmouse_1.0.0_src_all.tar.gz"], "md5": "0c2fad6bf0e911ae8c140c02bc29150e", "fn": "smokingMouse_1.0.0.tar.gz"}, "snadata-1.48.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SNAData_1.48.0.tar.gz", "https://bioarchive.galaxyproject.org/SNAData_1.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snadata/bioconductor-snadata_1.48.0_src_all.tar.gz"], "md5": "bfbd447afa550db44aa1db55e227cc10", "fn": "SNAData_1.48.0.tar.gz"}, "snageedata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SNAGEEdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/SNAGEEdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snageedata/bioconductor-snageedata_1.38.0_src_all.tar.gz"], "md5": "bfd0a2689cb9ac612cb2f8995c3a03d5", "fn": "SNAGEEdata_1.38.0.tar.gz"}, "snphooddata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SNPhoodData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/SNPhoodData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snphooddata/bioconductor-snphooddata_1.32.0_src_all.tar.gz"], "md5": "72ac86008c225c71df946cc8a7de1fa1", "fn": "SNPhoodData_1.32.0.tar.gz"}, "somaticadata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SomatiCAData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/SomatiCAData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-somaticadata/bioconductor-somaticadata_1.40.0_src_all.tar.gz"], "md5": "31d9100d6b5fa5f95c59eda9995f2684", "fn": "SomatiCAData_1.40.0.tar.gz"}, "somaticcanceralterations-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SomaticCancerAlterations_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/SomaticCancerAlterations_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-somaticcanceralterations/bioconductor-somaticcanceralterations_1.38.0_src_all.tar.gz"], "md5": "77b2b0312705c2a9581cdf7aab591db8", "fn": "SomaticCancerAlterations_1.38.0.tar.gz"}, "spatialdatasets-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SpatialDatasets_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/SpatialDatasets_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatialdatasets/bioconductor-spatialdatasets_1.0.0_src_all.tar.gz"], "md5": "36fd913ef0d7109d0be40afbc1255548", "fn": "SpatialDatasets_1.0.0.tar.gz"}, "spatialdmelxsim-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/spatialDmelxsim_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/spatialDmelxsim_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatialdmelxsim/bioconductor-spatialdmelxsim_1.8.0_src_all.tar.gz"], "md5": "2fec38c7672022e76f2b7a7ba7b9a677", "fn": "spatialDmelxsim_1.8.0.tar.gz"}, "spatiallibd-1.14.1": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/spatialLIBD_1.14.1.tar.gz", "https://bioarchive.galaxyproject.org/spatialLIBD_1.14.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatiallibd/bioconductor-spatiallibd_1.14.1_src_all.tar.gz"], "md5": "cd8c85a03e555f2dfdeb1627f7087002", "fn": "spatialLIBD_1.14.1.tar.gz"}, "spikein-1.44.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SpikeIn_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/SpikeIn_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spikein/bioconductor-spikein_1.44.0_src_all.tar.gz"], "md5": "439f9d2eda54024edb7c1c81862d74c8", "fn": "SpikeIn_1.44.0.tar.gz"}, "spikeinsubset-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SpikeInSubset_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/SpikeInSubset_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spikeinsubset/bioconductor-spikeinsubset_1.42.0_src_all.tar.gz"], "md5": "0c9b5af679c89a1468c9a6f581202e2b", "fn": "SpikeInSubset_1.42.0.tar.gz"}, "spqndata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/spqnData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/spqnData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spqndata/bioconductor-spqndata_1.14.0_src_all.tar.gz"], "md5": "453bf944ea40956afef2bd868f92d747", "fn": "spqnData_1.14.0.tar.gz"}, "stemhypoxia-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/stemHypoxia_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/stemHypoxia_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stemhypoxia/bioconductor-stemhypoxia_1.38.0_src_all.tar.gz"], "md5": "22ec9d76cac05ac7118873f7815225ba", "fn": "stemHypoxia_1.38.0.tar.gz"}, "stexampledata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/STexampleData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/STexampleData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stexampledata/bioconductor-stexampledata_1.10.0_src_all.tar.gz"], "md5": "5fa4bfb2e58e7f6bbcd957aa1aa7e938", "fn": "STexampleData_1.10.0.tar.gz"}, "stjudem-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/stjudem_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/stjudem_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stjudem/bioconductor-stjudem_1.42.0_src_all.tar.gz"], "md5": "4c6868a60726df51408834a227e551bf", "fn": "stjudem_1.42.0.tar.gz"}, "svm2crmdata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/SVM2CRMdata_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/SVM2CRMdata_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-svm2crmdata/bioconductor-svm2crmdata_1.34.0_src_all.tar.gz"], "md5": "ce0c6615bfbb9a5a7cf4eeab0bd6199d", "fn": "SVM2CRMdata_1.34.0.tar.gz"}, "synapterdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/synapterdata_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/synapterdata_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-synapterdata/bioconductor-synapterdata_1.40.0_src_all.tar.gz"], "md5": "255aa756f0b6c0c1d95cdfbc889a67a2", "fn": "synapterdata_1.40.0.tar.gz"}, "systempiperdata-2.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/systemPipeRdata_2.6.0.tar.gz", "https://bioarchive.galaxyproject.org/systemPipeRdata_2.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-systempiperdata/bioconductor-systempiperdata_2.6.0_src_all.tar.gz"], "md5": "1af59929fb95c3a017b88fce32a4c833", "fn": "systemPipeRdata_2.6.0.tar.gz"}, "tabulamurisdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TabulaMurisData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/TabulaMurisData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tabulamurisdata/bioconductor-tabulamurisdata_1.20.0_src_all.tar.gz"], "md5": "39c27cc6646ea3bcdb4637a226b219b8", "fn": "TabulaMurisData_1.20.0.tar.gz"}, "tabulamurissenisdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TabulaMurisSenisData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/TabulaMurisSenisData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tabulamurissenisdata/bioconductor-tabulamurissenisdata_1.8.0_src_all.tar.gz"], "md5": "6d6120b18adce70e943a3da8e0e577b2", "fn": "TabulaMurisSenisData_1.8.0.tar.gz"}, "targetscoredata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TargetScoreData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/TargetScoreData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetscoredata/bioconductor-targetscoredata_1.38.0_src_all.tar.gz"], "md5": "61084f230f2c3dedb27988867f07f50f", "fn": "TargetScoreData_1.38.0.tar.gz"}, "targetsearchdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TargetSearchData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/TargetSearchData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetsearchdata/bioconductor-targetsearchdata_1.40.0_src_all.tar.gz"], "md5": "96bbec70706d8adcf4ee321261620d79", "fn": "TargetSearchData_1.40.0.tar.gz"}, "tartare-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tartare_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/tartare_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tartare/bioconductor-tartare_1.16.0_src_all.tar.gz"], "md5": "869743e16f05bc962de518ca925750d8", "fn": "tartare_1.16.0.tar.gz"}, "tbx20bamsubset-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TBX20BamSubset_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/TBX20BamSubset_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tbx20bamsubset/bioconductor-tbx20bamsubset_1.38.0_src_all.tar.gz"], "md5": "c158901ec6203e85569c600efb335ccf", "fn": "TBX20BamSubset_1.38.0.tar.gz"}, "tcgabiolinksgui.data-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TCGAbiolinksGUI.data_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAbiolinksGUI.data_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgabiolinksgui.data/bioconductor-tcgabiolinksgui.data_1.22.0_src_all.tar.gz"], "md5": "bd2042c0064583d666364a52ce3be17e", "fn": "TCGAbiolinksGUI.data_1.22.0.tar.gz"}, "tcgacrcmirna-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TCGAcrcmiRNA_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAcrcmiRNA_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmirna/bioconductor-tcgacrcmirna_1.22.0_src_all.tar.gz"], "md5": "451d09b5ec341d7e92211a1d42c35947", "fn": "TCGAcrcmiRNA_1.22.0.tar.gz"}, "tcgacrcmrna-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TCGAcrcmRNA_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAcrcmRNA_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmrna/bioconductor-tcgacrcmrna_1.22.0_src_all.tar.gz"], "md5": "bb9300e6ad6e4e5435a31487fdc22ed6", "fn": "TCGAcrcmRNA_1.22.0.tar.gz"}, "tcgamethylation450k-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TCGAMethylation450k_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAMethylation450k_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgamethylation450k/bioconductor-tcgamethylation450k_1.38.0_src_all.tar.gz"], "md5": "e913aa3b85d5cd1d0b27a346daf8c9ee", "fn": "TCGAMethylation450k_1.38.0.tar.gz"}, "tcgaworkflowdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TCGAWorkflowData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAWorkflowData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgaworkflowdata/bioconductor-tcgaworkflowdata_1.26.0_src_all.tar.gz"], "md5": "cbba498f1922aeedadf96a1911a81751", "fn": "TCGAWorkflowData_1.26.0.tar.gz"}, "tenxbraindata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TENxBrainData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxBrainData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxbraindata/bioconductor-tenxbraindata_1.22.0_src_all.tar.gz"], "md5": "1fa1b93ab8d144b860c83dc5741490a0", "fn": "TENxBrainData_1.22.0.tar.gz"}, "tenxbusdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TENxBUSData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxBUSData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxbusdata/bioconductor-tenxbusdata_1.16.0_src_all.tar.gz"], "md5": "35be2bd3c806b055fc9463e8f135dd32", "fn": "TENxBUSData_1.16.0.tar.gz"}, "tenxpbmcdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TENxPBMCData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxPBMCData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxpbmcdata/bioconductor-tenxpbmcdata_1.20.0_src_all.tar.gz"], "md5": "3e6c961a01998667f37de542858dbc09", "fn": "TENxPBMCData_1.20.0.tar.gz"}, "tenxvisiumdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TENxVisiumData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxVisiumData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxvisiumdata/bioconductor-tenxvisiumdata_1.10.0_src_all.tar.gz"], "md5": "f578add429847efff027a61b1749b9b4", "fn": "TENxVisiumData_1.10.0.tar.gz"}, "timecoursedata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/timecoursedata_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/timecoursedata_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-timecoursedata/bioconductor-timecoursedata_1.12.0_src_all.tar.gz"], "md5": "a5b9f962c12d69003eff9b6949d2b0af", "fn": "timecoursedata_1.12.0.tar.gz"}, "timerquant-1.32.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TimerQuant_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/TimerQuant_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-timerquant/bioconductor-timerquant_1.32.0_src_all.tar.gz"], "md5": "7033d0ae9a0731af8bafecbbfa5398c8", "fn": "TimerQuant_1.32.0.tar.gz"}, "tinesath1cdf-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tinesath1cdf_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/tinesath1cdf_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tinesath1cdf/bioconductor-tinesath1cdf_1.40.0_src_all.tar.gz"], "md5": "a58177f0ed4976f52370b35e13818ce3", "fn": "tinesath1cdf_1.40.0.tar.gz"}, "tinesath1probe-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tinesath1probe_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/tinesath1probe_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tinesath1probe/bioconductor-tinesath1probe_1.40.0_src_all.tar.gz"], "md5": "abd9396a4f17a0044018702394b62933", "fn": "tinesath1probe_1.40.0.tar.gz"}, "tissuetreg-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tissueTreg_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/tissueTreg_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tissuetreg/bioconductor-tissuetreg_1.22.0_src_all.tar.gz"], "md5": "5d975c08b7a19af832c4468ecb04c58b", "fn": "tissueTreg_1.22.0.tar.gz"}, "tmexplorer-1.12.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TMExplorer_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TMExplorer_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tmexplorer/bioconductor-tmexplorer_1.12.0_src_all.tar.gz"], "md5": "48b11be99739e61f54d9b442af739d49", "fn": "TMExplorer_1.12.0.tar.gz"}, "tofsimsdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tofsimsData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/tofsimsData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tofsimsdata/bioconductor-tofsimsdata_1.30.0_src_all.tar.gz"], "md5": "57fe35de7b03ee4f3ca07540949a6b5e", "fn": "tofsimsData_1.30.0.tar.gz"}, "topdownrdata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/topdownrdata_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/topdownrdata_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-topdownrdata/bioconductor-topdownrdata_1.24.0_src_all.tar.gz"], "md5": "28e746b858956bea0967344bfe363e7d", "fn": "topdownrdata_1.24.0.tar.gz"}, "tuberculosis-1.8.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tuberculosis_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/tuberculosis_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tuberculosis/bioconductor-tuberculosis_1.8.0_src_all.tar.gz"], "md5": "154cd343b8fba727ecf80a671a6a112d", "fn": "tuberculosis_1.8.0.tar.gz"}, "tumourmethdata-1.0.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/TumourMethData_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/TumourMethData_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tumourmethdata/bioconductor-tumourmethdata_1.0.0_src_all.tar.gz"], "md5": "7b4ba6a8a59379a3b7f368e6c26fa0a6", "fn": "TumourMethData_1.0.0.tar.gz"}, "tweedeseqcountdata-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tweeDEseqCountData_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/tweeDEseqCountData_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tweedeseqcountdata/bioconductor-tweedeseqcountdata_1.40.0_src_all.tar.gz"], "md5": "d63e819cedf93ffbe115ed518bc9feaf", "fn": "tweeDEseqCountData_1.40.0.tar.gz"}, "tximportdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tximportData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/tximportData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tximportdata/bioconductor-tximportdata_1.30.0_src_all.tar.gz"], "md5": "4494d764fc087333e5c04ee7977c85c8", "fn": "tximportData_1.30.0.tar.gz"}, "varianttoolsdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/VariantToolsData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/VariantToolsData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-varianttoolsdata/bioconductor-varianttoolsdata_1.26.0_src_all.tar.gz"], "md5": "a85757ce237b03b0480f01488a78879b", "fn": "VariantToolsData_1.26.0.tar.gz"}, "vectrapolarisdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/VectraPolarisData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/VectraPolarisData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vectrapolarisdata/bioconductor-vectrapolarisdata_1.6.0_src_all.tar.gz"], "md5": "ea2006b85e374e76fbd70ca8b0819072", "fn": "VectraPolarisData_1.6.0.tar.gz"}, "vulcandata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/vulcandata_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/vulcandata_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vulcandata/bioconductor-vulcandata_1.24.0_src_all.tar.gz"], "md5": "cd95ea7ac7f2b9edfd46c1ffccb7c3c1", "fn": "vulcandata_1.24.0.tar.gz"}, "weberdivechalcdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/WeberDivechaLCdata_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/WeberDivechaLCdata_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-weberdivechalcdata/bioconductor-weberdivechalcdata_1.4.0_src_all.tar.gz"], "md5": "3b75c693f86ed228e2b7816872cfe4b7", "fn": "WeberDivechaLCdata_1.4.0.tar.gz"}, "wes.1kg.wugsc-1.34.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/WES.1KG.WUGSC_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/WES.1KG.WUGSC_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wes.1kg.wugsc/bioconductor-wes.1kg.wugsc_1.34.0_src_all.tar.gz"], "md5": "a0a3d230e27342090638ec4868756e5a", "fn": "WES.1KG.WUGSC_1.34.0.tar.gz"}, "wgsmapp-1.14.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/WGSmapp_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/WGSmapp_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wgsmapp/bioconductor-wgsmapp_1.14.0_src_all.tar.gz"], "md5": "dfc3f5a82d532551e2d6c21b11c99566", "fn": "WGSmapp_1.14.0.tar.gz"}, "xcoredata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/xcoredata_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/xcoredata_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xcoredata/bioconductor-xcoredata_1.6.0_src_all.tar.gz"], "md5": "214626bfcbb5d66445324f6e367142c7", "fn": "xcoredata_1.6.0.tar.gz"}, "xhybcasneuf-1.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/XhybCasneuf_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/XhybCasneuf_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xhybcasneuf/bioconductor-xhybcasneuf_1.40.0_src_all.tar.gz"], "md5": "f3e6306b5c05fb026e36e4c60656e25a", "fn": "XhybCasneuf_1.40.0.tar.gz"}, "yeastcc-1.42.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastCC_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastCC_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastcc/bioconductor-yeastcc_1.42.0_src_all.tar.gz"], "md5": "847d9bba73cb25f458f608c2cd6bf0e8", "fn": "yeastCC_1.42.0.tar.gz"}, "yeastexpdata-0.48.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastExpData_0.48.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastExpData_0.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastexpdata/bioconductor-yeastexpdata_0.48.0_src_all.tar.gz"], "md5": "7cd63808a957defe831bf3e9d3ef4789", "fn": "yeastExpData_0.48.0.tar.gz"}, "yeastgsdata-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastGSData_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastGSData_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastgsdata/bioconductor-yeastgsdata_0.40.0_src_all.tar.gz"], "md5": "bc455a9ecd3eb2652f887026841b3c69", "fn": "yeastGSData_0.40.0.tar.gz"}, "yeastnagalakshmi-1.38.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastNagalakshmi_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastNagalakshmi_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastnagalakshmi/bioconductor-yeastnagalakshmi_1.38.0_src_all.tar.gz"], "md5": "ea5068bf2b4053452f416c56ab32736a", "fn": "yeastNagalakshmi_1.38.0.tar.gz"}, "yeastrnaseq-0.40.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/yeastRNASeq_0.40.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastRNASeq_0.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastrnaseq/bioconductor-yeastrnaseq_0.40.0_src_all.tar.gz"], "md5": "2344deacf993b96e1709ad96b710471f", "fn": "yeastRNASeq_0.40.0.tar.gz"}, "zebrafishrnaseq-1.22.0": {"urls": ["https://bioconductor.org/packages/3.18/data/experiment/src/contrib/zebrafishRNASeq_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafishRNASeq_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafishrnaseq/bioconductor-zebrafishrnaseq_1.22.0_src_all.tar.gz"], "md5": "c1fcbadec1b25e4b28483c015f7ab35c", "fn": "zebrafishRNASeq_1.22.0.tar.gz"}, "mvoutdata-1.41.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/mvoutData_1.41.0.tar.gz", "https://bioarchive.galaxyproject.org/mvoutData_1.41.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mvoutdata/bioconductor-mvoutdata_1.41.0_src_all.tar.gz"], "md5": "f90c34ca89a251588ea39dfe27febe15", "fn": "mvoutData_1.41.0.tar.gz"}, "ahensdbs-1.5.1": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/AHEnsDbs_1.5.1.tar.gz", "https://bioarchive.galaxyproject.org/AHEnsDbs_1.5.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahensdbs/bioconductor-ahensdbs_1.5.1_src_all.tar.gz"], "md5": "be76ea879496d8b031f8996cff09c6c0", "fn": "AHEnsDbs_1.5.1.tar.gz"}, "ahlrbasedbs-1.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/AHLRBaseDbs_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/AHLRBaseDbs_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahlrbasedbs/bioconductor-ahlrbasedbs_1.8.0_src_all.tar.gz"], "md5": "a6628fab5cc4b0b8b129b20082e14380", "fn": "AHLRBaseDbs_1.8.0.tar.gz"}, "ahmeshdbs-1.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/AHMeSHDbs_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/AHMeSHDbs_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahmeshdbs/bioconductor-ahmeshdbs_1.8.0_src_all.tar.gz"], "md5": "4c370cd555a57e564b65d83106d7a7b0", "fn": "AHMeSHDbs_1.8.0.tar.gz"}, "ahpubmeddbs-1.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/AHPubMedDbs_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/AHPubMedDbs_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ahpubmeddbs/bioconductor-ahpubmeddbs_1.8.0_src_all.tar.gz"], "md5": "a5c32ec183a48fc624a5a09cf2472196", "fn": "AHPubMedDbs_1.8.0.tar.gz"}, "anopheles.db0-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/anopheles.db0_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/anopheles.db0_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-anopheles.db0/bioconductor-anopheles.db0_3.20.0_src_all.tar.gz"], "md5": "947db8d7057679f9f1340dc883cc7e1c", "fn": "anopheles.db0_3.20.0.tar.gz"}, "arabidopsis.db0-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/arabidopsis.db0_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/arabidopsis.db0_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-arabidopsis.db0/bioconductor-arabidopsis.db0_3.20.0_src_all.tar.gz"], "md5": "1c09bf13aaf74707cae7583fb4cef467", "fn": "arabidopsis.db0_3.20.0.tar.gz"}, "bovine.db0-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/bovine.db0_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/bovine.db0_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bovine.db0/bioconductor-bovine.db0_3.20.0_src_all.tar.gz"], "md5": "8a8cd59df5a98057def6c71806cd5f68", "fn": "bovine.db0_3.20.0.tar.gz"}, "bsgenome.hsapiens.ucsc.hg17-1.3.1001": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg17_1.3.1001.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg17_1.3.1001.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg17/bioconductor-bsgenome.hsapiens.ucsc.hg17_1.3.1001_src_all.tar.gz"], "md5": "9568b8979caae68531475136ed71316d", "fn": "BSgenome.Hsapiens.UCSC.hg17_1.3.1001.tar.gz"}, "bsgenome.hsapiens.ucsc.hg17.masked-1.3.999": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg17.masked_1.3.999.tar.gz", "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg17.masked_1.3.999.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked_1.3.999_src_all.tar.gz"], "md5": "e3257cb973663f54841fd62a643ecaa7", "fn": "BSgenome.Hsapiens.UCSC.hg17.masked_1.3.999.tar.gz"}, "canine.db0-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/canine.db0_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/canine.db0_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-canine.db0/bioconductor-canine.db0_3.20.0_src_all.tar.gz"], "md5": "26d30a229ee9309b9f473dba4d1a61eb", "fn": "canine.db0_3.20.0.tar.gz"}, "chicken.db0-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/chicken.db0_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/chicken.db0_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chicken.db0/bioconductor-chicken.db0_3.20.0_src_all.tar.gz"], "md5": "932b29dd4dc58ce6fc5ad5b48ff3ebe6", "fn": "chicken.db0_3.20.0.tar.gz"}, "chimp.db0-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/chimp.db0_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/chimp.db0_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chimp.db0/bioconductor-chimp.db0_3.20.0_src_all.tar.gz"], "md5": "da8f9a3b3ffa3ac728f373419ddd7775", "fn": "chimp.db0_3.20.0.tar.gz"}, "ecolik12.db0-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ecoliK12.db0_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliK12.db0_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolik12.db0/bioconductor-ecolik12.db0_3.20.0_src_all.tar.gz"], "md5": "0bb11ff1e532df7d2ad9af58d898f4d0", "fn": "ecoliK12.db0_3.20.0.tar.gz"}, "ecolisakai.db0-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ecoliSakai.db0_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliSakai.db0_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolisakai.db0/bioconductor-ecolisakai.db0_3.20.0_src_all.tar.gz"], "md5": "0975b5ae0a2318f8a266e35a86d2bcf1", "fn": "ecoliSakai.db0_3.20.0.tar.gz"}, "fly.db0-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/fly.db0_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/fly.db0_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fly.db0/bioconductor-fly.db0_3.20.0_src_all.tar.gz"], "md5": "faeba43dee9e5ff967b35501ca25294c", "fn": "fly.db0_3.20.0.tar.gz"}, "geneplast.data-0.99.9": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/geneplast.data_0.99.9.tar.gz", "https://bioarchive.galaxyproject.org/geneplast.data_0.99.9.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-geneplast.data/bioconductor-geneplast.data_0.99.9_src_all.tar.gz"], "md5": "c25d661b13014ce9abc6da7411a6e539", "fn": "geneplast.data_0.99.9.tar.gz"}, "genomeinfodbdata-1.2.13": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/GenomeInfoDbData_1.2.13.tar.gz", "https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.13.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.13_src_all.tar.gz"], "md5": "8798e58b89d84d9fa6a85f2191704668", "fn": "GenomeInfoDbData_1.2.13.tar.gz"}, "go.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/GO.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/GO.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-go.db/bioconductor-go.db_3.20.0_src_all.tar.gz"], "md5": "a41513069bb1ff4a2ecfa1a538110699", "fn": "GO.db_3.20.0.tar.gz"}, "hdo.db-1.0.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/HDO.db_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/HDO.db_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hdo.db/bioconductor-hdo.db_1.0.0_src_all.tar.gz"], "md5": "adb9df8c89fa3f2f877e7db1fbeb6b70", "fn": "HDO.db_1.0.0.tar.gz"}, "human.db0-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/human.db0_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/human.db0_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-human.db0/bioconductor-human.db0_3.20.0_src_all.tar.gz"], "md5": "1e484144eaebbc7b654640a105c8dea4", "fn": "human.db0_3.20.0.tar.gz"}, "jaspar2022-0.99.8": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/JASPAR2022_0.99.8.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2022_0.99.8.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2022/bioconductor-jaspar2022_0.99.8_src_all.tar.gz"], "md5": "f3ac6c35365f8d8f670adad6e30c3b2f", "fn": "JASPAR2022_0.99.8.tar.gz"}, "malaria.db0-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/malaria.db0_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/malaria.db0_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-malaria.db0/bioconductor-malaria.db0_3.20.0_src_all.tar.gz"], "md5": "fbcf1c6f5d5a6a2c33ab9a3200c51166", "fn": "malaria.db0_3.20.0.tar.gz"}, "mouse.db0-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/mouse.db0_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse.db0_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse.db0/bioconductor-mouse.db0_3.20.0_src_all.tar.gz"], "md5": "9790c803e9b9c2a74e2b711991a27009", "fn": "mouse.db0_3.20.0.tar.gz"}, "mpo.db-0.99.8": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/MPO.db_0.99.8.tar.gz", "https://bioarchive.galaxyproject.org/MPO.db_0.99.8.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mpo.db/bioconductor-mpo.db_0.99.8_src_all.tar.gz"], "md5": "fd9bff2a147bbef37b58cef85ec79488", "fn": "MPO.db_0.99.8.tar.gz"}, "org.ag.eg.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Ag.eg.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ag.eg.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ag.eg.db/bioconductor-org.ag.eg.db_3.20.0_src_all.tar.gz"], "md5": "b7bba2a1eee2f69084937f03d993d3ba", "fn": "org.Ag.eg.db_3.20.0.tar.gz"}, "org.at.tair.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.At.tair.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/org.At.tair.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.at.tair.db/bioconductor-org.at.tair.db_3.20.0_src_all.tar.gz"], "md5": "5f9cfc458b0af5cd4e6a2db04d304f13", "fn": "org.At.tair.db_3.20.0.tar.gz"}, "org.bt.eg.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Bt.eg.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Bt.eg.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.bt.eg.db/bioconductor-org.bt.eg.db_3.20.0_src_all.tar.gz"], "md5": "9eea3d6ba55f61524a04aafb1be83356", "fn": "org.Bt.eg.db_3.20.0.tar.gz"}, "org.ce.eg.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Ce.eg.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ce.eg.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ce.eg.db/bioconductor-org.ce.eg.db_3.20.0_src_all.tar.gz"], "md5": "3b3cbc21c9f362b436ba4a80d9824da4", "fn": "org.Ce.eg.db_3.20.0.tar.gz"}, "org.cf.eg.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Cf.eg.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Cf.eg.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.cf.eg.db/bioconductor-org.cf.eg.db_3.20.0_src_all.tar.gz"], "md5": "85da47fb3b35030884cf5b14940015d8", "fn": "org.Cf.eg.db_3.20.0.tar.gz"}, "org.dm.eg.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Dm.eg.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Dm.eg.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.dm.eg.db/bioconductor-org.dm.eg.db_3.20.0_src_all.tar.gz"], "md5": "29d33ed6c67a4562038f549dab8d536e", "fn": "org.Dm.eg.db_3.20.0.tar.gz"}, "org.dr.eg.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Dr.eg.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Dr.eg.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.dr.eg.db/bioconductor-org.dr.eg.db_3.20.0_src_all.tar.gz"], "md5": "e0c8b01442611df62c594b5552bd1a29", "fn": "org.Dr.eg.db_3.20.0.tar.gz"}, "org.eck12.eg.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.EcK12.eg.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/org.EcK12.eg.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.eck12.eg.db/bioconductor-org.eck12.eg.db_3.20.0_src_all.tar.gz"], "md5": "ee62df51636d67d2b3a29cd758c37251", "fn": "org.EcK12.eg.db_3.20.0.tar.gz"}, "org.ecsakai.eg.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.EcSakai.eg.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/org.EcSakai.eg.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ecsakai.eg.db/bioconductor-org.ecsakai.eg.db_3.20.0_src_all.tar.gz"], "md5": "85c37f3ed2ee6a80e54e1020c0895404", "fn": "org.EcSakai.eg.db_3.20.0.tar.gz"}, "org.gg.eg.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Gg.eg.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Gg.eg.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.gg.eg.db/bioconductor-org.gg.eg.db_3.20.0_src_all.tar.gz"], "md5": "c9a62fecb11dd4dc0b34392f354ffe5a", "fn": "org.Gg.eg.db_3.20.0.tar.gz"}, "org.hs.eg.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Hs.eg.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Hs.eg.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.hs.eg.db/bioconductor-org.hs.eg.db_3.20.0_src_all.tar.gz"], "md5": "191276f1fde82d731babe624c7a9063f", "fn": "org.Hs.eg.db_3.20.0.tar.gz"}, "org.mm.eg.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Mm.eg.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Mm.eg.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.mm.eg.db/bioconductor-org.mm.eg.db_3.20.0_src_all.tar.gz"], "md5": "63357791b48f3fc181edd8c772ee6f94", "fn": "org.Mm.eg.db_3.20.0.tar.gz"}, "org.mmu.eg.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Mmu.eg.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Mmu.eg.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.mmu.eg.db/bioconductor-org.mmu.eg.db_3.20.0_src_all.tar.gz"], "md5": "7c23ce0a276f52e0c34029b9094da1db", "fn": "org.Mmu.eg.db_3.20.0.tar.gz"}, "org.pt.eg.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Pt.eg.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Pt.eg.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.pt.eg.db/bioconductor-org.pt.eg.db_3.20.0_src_all.tar.gz"], "md5": "3385bff8e6ccc1693fa90b41e2d37826", "fn": "org.Pt.eg.db_3.20.0.tar.gz"}, "org.rn.eg.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Rn.eg.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Rn.eg.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.rn.eg.db/bioconductor-org.rn.eg.db_3.20.0_src_all.tar.gz"], "md5": "b3c38250a9c848390589cbecd663fc69", "fn": "org.Rn.eg.db_3.20.0.tar.gz"}, "org.sc.sgd.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Sc.sgd.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Sc.sgd.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.sc.sgd.db/bioconductor-org.sc.sgd.db_3.20.0_src_all.tar.gz"], "md5": "bbd0c3aa1aa0277c0a72d504042f9eea", "fn": "org.Sc.sgd.db_3.20.0.tar.gz"}, "org.ss.eg.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Ss.eg.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Ss.eg.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.ss.eg.db/bioconductor-org.ss.eg.db_3.20.0_src_all.tar.gz"], "md5": "bbcc19e949a008100b54f4d336a55be3", "fn": "org.Ss.eg.db_3.20.0.tar.gz"}, "org.xl.eg.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Xl.eg.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/org.Xl.eg.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-org.xl.eg.db/bioconductor-org.xl.eg.db_3.20.0_src_all.tar.gz"], "md5": "4fb37259b7169c9b62b605604f3fc0de", "fn": "org.Xl.eg.db_3.20.0.tar.gz"}, "orthology.eg.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/Orthology.eg.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/Orthology.eg.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-orthology.eg.db/bioconductor-orthology.eg.db_3.20.0_src_all.tar.gz"], "md5": "09c5048fda8f1df91892305c09f38227", "fn": "Orthology.eg.db_3.20.0.tar.gz"}, "pfam.db-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/PFAM.db_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/PFAM.db_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pfam.db/bioconductor-pfam.db_3.20.0_src_all.tar.gz"], "md5": "b5fd5c9c43685f2b45a3102b98673d36", "fn": "PFAM.db_3.20.0.tar.gz"}, "pig.db0-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/pig.db0_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/pig.db0_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pig.db0/bioconductor-pig.db0_3.20.0_src_all.tar.gz"], "md5": "a3941b9af7837e468df8f53546072c5f", "fn": "pig.db0_3.20.0.tar.gz"}, "rat.db0-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rat.db0_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/rat.db0_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rat.db0/bioconductor-rat.db0_3.20.0_src_all.tar.gz"], "md5": "b183489f8247adea901952a51faea48e", "fn": "rat.db0_3.20.0.tar.gz"}, "reactome.db-1.89.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/reactome.db_1.89.0.tar.gz", "https://bioarchive.galaxyproject.org/reactome.db_1.89.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-reactome.db/bioconductor-reactome.db_1.89.0_src_all.tar.gz"], "md5": "9cb7d59e83b3dfbe265d3264d880d5f2", "fn": "reactome.db_1.89.0.tar.gz"}, "rhesus.db0-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/rhesus.db0_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/rhesus.db0_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rhesus.db0/bioconductor-rhesus.db0_3.20.0_src_all.tar.gz"], "md5": "40063317ca33adad8023d1fe7c014970", "fn": "rhesus.db0_3.20.0.tar.gz"}, "somascan.db-0.99.10": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/SomaScan.db_0.99.10.tar.gz", "https://bioarchive.galaxyproject.org/SomaScan.db_0.99.10.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-somascan.db/bioconductor-somascan.db_0.99.10_src_all.tar.gz"], "md5": "4a5ba80cc1038c6adeb887147e691ca8", "fn": "SomaScan.db_0.99.10.tar.gz"}, "synaptome.db-0.99.16": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/synaptome.db_0.99.16.tar.gz", "https://bioarchive.galaxyproject.org/synaptome.db_0.99.16.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-synaptome.db/bioconductor-synaptome.db_0.99.16_src_all.tar.gz"], "md5": "f59812004d1b9b433203dab3b41d10f7", "fn": "synaptome.db_0.99.16.tar.gz"}, "txdb.hsapiens.ucsc.hg38.knowngene-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg38.knownGene_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_3.20.0_src_all.tar.gz"], "md5": "416c5b08453bcfa1687dc06c15af3fa7", "fn": "TxDb.Hsapiens.UCSC.hg38.knownGene_3.20.0.tar.gz"}, "txdb.hsapiens.ucsc.hg38.refgene-3.19.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.refGene_3.19.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg38.refGene_3.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/bioconductor-txdb.hsapiens.ucsc.hg38.refgene_3.19.0_src_all.tar.gz"], "md5": "b5b5034f8674fafd9bd5a352264fc0a5", "fn": "TxDb.Hsapiens.UCSC.hg38.refGene_3.19.0.tar.gz"}, "txdb.mmusculus.ucsc.mm39.knowngene-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm39.knownGene_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm39.knownGene_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene_3.20.0_src_all.tar.gz"], "md5": "59d302d11980ad599da45918d2891242", "fn": "TxDb.Mmusculus.UCSC.mm39.knownGene_3.20.0.tar.gz"}, "txdb.mmusculus.ucsc.mm39.refgene-3.19.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm39.refGene_3.19.0.tar.gz", "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm39.refGene_3.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/bioconductor-txdb.mmusculus.ucsc.mm39.refgene_3.19.0_src_all.tar.gz"], "md5": "2c2c41adc8b05f6353ee7ae744cdbd98", "fn": "TxDb.Mmusculus.UCSC.mm39.refGene_3.19.0.tar.gz"}, "worm.db0-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/worm.db0_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/worm.db0_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-worm.db0/bioconductor-worm.db0_3.20.0_src_all.tar.gz"], "md5": "4d526e85bb77f45595eaa31861a0ea3d", "fn": "worm.db0_3.20.0.tar.gz"}, "xenopus.db0-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/xenopus.db0_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/xenopus.db0_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xenopus.db0/bioconductor-xenopus.db0_3.20.0_src_all.tar.gz"], "md5": "aeaf9b5fddc97f1c79ef98ff452b4858", "fn": "xenopus.db0_3.20.0.tar.gz"}, "yeast.db0-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/yeast.db0_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/yeast.db0_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeast.db0/bioconductor-yeast.db0_3.20.0_src_all.tar.gz"], "md5": "579b93c0d1d3aa777f771cb25478d55f", "fn": "yeast.db0_3.20.0.tar.gz"}, "zebrafish.db0-3.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/zebrafish.db0_3.20.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafish.db0_3.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafish.db0/bioconductor-zebrafish.db0_3.20.0_src_all.tar.gz"], "md5": "a1d3664debe24db9c7c610717d2650b9", "fn": "zebrafish.db0_3.20.0.tar.gz"}, "adductdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/adductData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/adductData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-adductdata/bioconductor-adductdata_1.22.0_src_all.tar.gz"], "md5": "ed236e56217a786e98246e4db03eda1e", "fn": "adductData_1.22.0.tar.gz"}, "affycompdata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/affycompData_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/affycompData_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affycompdata/bioconductor-affycompdata_1.44.0_src_all.tar.gz"], "md5": "5c7cbe480087fc6f1fd20a85c954f9fc", "fn": "affycompData_1.44.0.tar.gz"}, "affydata-1.54.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/affydata_1.54.0.tar.gz", "https://bioarchive.galaxyproject.org/affydata_1.54.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affydata/bioconductor-affydata_1.54.0_src_all.tar.gz"], "md5": "dfb8275fc3bb96847e867ddcdced9c52", "fn": "affydata_1.54.0.tar.gz"}, "affyhgu133a2expr-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/Affyhgu133A2Expr_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133A2Expr_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133a2expr/bioconductor-affyhgu133a2expr_1.42.0_src_all.tar.gz"], "md5": "92f8f2e7fad2450606a57456cff8f5c1", "fn": "Affyhgu133A2Expr_1.42.0.tar.gz"}, "affyhgu133aexpr-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/Affyhgu133aExpr_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133aExpr_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133aexpr/bioconductor-affyhgu133aexpr_1.44.0_src_all.tar.gz"], "md5": "4127126e7740a9c964f667637c67e5c9", "fn": "Affyhgu133aExpr_1.44.0.tar.gz"}, "affyhgu133plus2expr-1.40.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/Affyhgu133Plus2Expr_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/Affyhgu133Plus2Expr_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affyhgu133plus2expr/bioconductor-affyhgu133plus2expr_1.40.0_src_all.tar.gz"], "md5": "026699f8f4eba1143c4ca44dc773a48d", "fn": "Affyhgu133Plus2Expr_1.40.0.tar.gz"}, "affymetrixdatatestfiles-0.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/AffymetrixDataTestFiles_0.44.0.tar.gz", "https://bioarchive.galaxyproject.org/AffymetrixDataTestFiles_0.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affymetrixdatatestfiles/bioconductor-affymetrixdatatestfiles_0.44.0_src_all.tar.gz"], "md5": "7a7a9f89c31c1628a0d1e7c34dca730a", "fn": "AffymetrixDataTestFiles_0.44.0.tar.gz"}, "affymoe4302expr-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/Affymoe4302Expr_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/Affymoe4302Expr_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-affymoe4302expr/bioconductor-affymoe4302expr_1.44.0_src_all.tar.gz"], "md5": "295950e1bd7dcc3617cd3de48e7187ec", "fn": "Affymoe4302Expr_1.44.0.tar.gz"}, "airway-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/airway_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/airway_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-airway/bioconductor-airway_1.26.0_src_all.tar.gz"], "md5": "46b3c23c9c6d6fcf5973d6dcee659f94", "fn": "airway_1.26.0.tar.gz"}, "all-1.48.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ALL_1.48.0.tar.gz", "https://bioarchive.galaxyproject.org/ALL_1.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-all/bioconductor-all_1.48.0_src_all.tar.gz"], "md5": "5580b83d2affbc83bfe4d3c7c090ceff", "fn": "ALL_1.48.0.tar.gz"}, "allmll-1.46.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ALLMLL_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/ALLMLL_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-allmll/bioconductor-allmll_1.46.0_src_all.tar.gz"], "md5": "b97903b1c1a6e0333549512656ede245", "fn": "ALLMLL_1.46.0.tar.gz"}, "ampaffyexample-1.46.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/AmpAffyExample_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/AmpAffyExample_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ampaffyexample/bioconductor-ampaffyexample_1.46.0_src_all.tar.gz"], "md5": "f4bcd408e003773b8dd09c6299c5a7c6", "fn": "AmpAffyExample_1.46.0.tar.gz"}, "aneufinderdata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/AneuFinderData_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/AneuFinderData_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-aneufinderdata/bioconductor-aneufinderdata_1.34.0_src_all.tar.gz"], "md5": "e003f8236f1f1b4e2c1049ca787bdab2", "fn": "AneuFinderData_1.34.0.tar.gz"}, "antiprofilesdata-1.41.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/antiProfilesData_1.41.0.tar.gz", "https://bioarchive.galaxyproject.org/antiProfilesData_1.41.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-antiprofilesdata/bioconductor-antiprofilesdata_1.41.0_src_all.tar.gz"], "md5": "78cdf58c935b2e6d2bbd053938d45092", "fn": "antiProfilesData_1.41.0.tar.gz"}, "aracne.networks-1.32.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/aracne.networks_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/aracne.networks_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-aracne.networks/bioconductor-aracne.networks_1.32.0_src_all.tar.gz"], "md5": "5f2866bb8b3db3bf6e87a9773d76da17", "fn": "aracne.networks_1.32.0.tar.gz"}, "arrmdata-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ARRmData_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/ARRmData_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-arrmdata/bioconductor-arrmdata_1.42.0_src_all.tar.gz"], "md5": "372caa2484b4a15568d1afd7574d16b1", "fn": "ARRmData_1.42.0.tar.gz"}, "ashkenazimsonchr21-1.36.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/AshkenazimSonChr21_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/AshkenazimSonChr21_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ashkenazimsonchr21/bioconductor-ashkenazimsonchr21_1.36.0_src_all.tar.gz"], "md5": "c7fe6ce4801ab4d0d7f3405b03a1b605", "fn": "AshkenazimSonChr21_1.36.0.tar.gz"}, "asicsdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ASICSdata_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/ASICSdata_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-asicsdata/bioconductor-asicsdata_1.26.0_src_all.tar.gz"], "md5": "d2a2fba95d9d2d4edf0fbeca46cc7bef", "fn": "ASICSdata_1.26.0.tar.gz"}, "bcellviper-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/bcellViper_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/bcellViper_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bcellviper/bioconductor-bcellviper_1.42.0_src_all.tar.gz"], "md5": "72732d35e21a870acb5095bf03b05128", "fn": "bcellViper_1.42.0.tar.gz"}, "beadarrayexampledata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/beadarrayExampleData_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/beadarrayExampleData_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadarrayexampledata/bioconductor-beadarrayexampledata_1.44.0_src_all.tar.gz"], "md5": "435c0cf9624aef923febb8c90a8bcc6a", "fn": "beadarrayExampleData_1.44.0.tar.gz"}, "beadarrayusecases-1.43.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/BeadArrayUseCases_1.43.0.tar.gz", "https://bioarchive.galaxyproject.org/BeadArrayUseCases_1.43.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadarrayusecases/bioconductor-beadarrayusecases_1.43.0_src_all.tar.gz"], "md5": "6540429ac7c52046a6bf1aa3c7eb2100", "fn": "BeadArrayUseCases_1.43.0.tar.gz"}, "beadsorted.saliva.epic-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/BeadSorted.Saliva.EPIC_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/BeadSorted.Saliva.EPIC_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beadsorted.saliva.epic/bioconductor-beadsorted.saliva.epic_1.14.0_src_all.tar.gz"], "md5": "10b9f6f46be07aa4e2b5fd5ff4dae4ff", "fn": "BeadSorted.Saliva.EPIC_1.14.0.tar.gz"}, "benchmarkfdrdata2019-1.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/benchmarkfdrData2019_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/benchmarkfdrData2019_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-benchmarkfdrdata2019/bioconductor-benchmarkfdrdata2019_1.20.0_src_all.tar.gz"], "md5": "93fd3ecc26e32fdc7f4086ddd4a06a02", "fn": "benchmarkfdrData2019_1.20.0.tar.gz"}, "beta7-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/beta7_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/beta7_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-beta7/bioconductor-beta7_1.44.0_src_all.tar.gz"], "md5": "b3f1aa522feccc463e3d7aca2da3c03f", "fn": "beta7_1.44.0.tar.gz"}, "bioimagedbs-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/BioImageDbs_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/BioImageDbs_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bioimagedbs/bioconductor-bioimagedbs_1.14.0_src_all.tar.gz"], "md5": "3cc77545922812f009e5c6444f20b985", "fn": "BioImageDbs_1.14.0.tar.gz"}, "bioplex-1.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/BioPlex_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/BioPlex_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bioplex/bioconductor-bioplex_1.12.0_src_all.tar.gz"], "md5": "6082010a89fc4adbb51185459ab189f5", "fn": "BioPlex_1.12.0.tar.gz"}, "biotmledata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/biotmleData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/biotmleData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biotmledata/bioconductor-biotmledata_1.30.0_src_all.tar.gz"], "md5": "ebc2c473d76e484b65b601f4be16190b", "fn": "biotmleData_1.30.0.tar.gz"}, "biscuiteerdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/biscuiteerData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/biscuiteerData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-biscuiteerdata/bioconductor-biscuiteerdata_1.20.0_src_all.tar.gz"], "md5": "71b2c48b7e095c2546f3ebfc8331b7a5", "fn": "biscuiteerData_1.20.0.tar.gz"}, "bladderbatch-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/bladderbatch_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/bladderbatch_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bladderbatch/bioconductor-bladderbatch_1.44.0_src_all.tar.gz"], "md5": "3447e61de0537a4b0541b25a3aadc0b4", "fn": "bladderbatch_1.44.0.tar.gz"}, "blimatestingdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/blimaTestingData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/blimaTestingData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-blimatestingdata/bioconductor-blimatestingdata_1.26.0_src_all.tar.gz"], "md5": "2e6d3952baeb1a16f51291872a56e932", "fn": "blimaTestingData_1.26.0.tar.gz"}, "bloodcancermultiomics2017-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/BloodCancerMultiOmics2017_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/BloodCancerMultiOmics2017_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bloodcancermultiomics2017/bioconductor-bloodcancermultiomics2017_1.26.0_src_all.tar.gz"], "md5": "b3f8ec1359432e60d43fd88217e07889", "fn": "BloodCancerMultiOmics2017_1.26.0.tar.gz"}, "bodymaprat-1.22.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/bodymapRat_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/bodymapRat_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bodymaprat/bioconductor-bodymaprat_1.22.0_src_all.tar.gz"], "md5": "bb02b15c5ef09829d18834e0f7e37440", "fn": "bodymapRat_1.22.0.tar.gz"}, "breakpointrdata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/breakpointRdata_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/breakpointRdata_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breakpointrdata/bioconductor-breakpointrdata_1.24.0_src_all.tar.gz"], "md5": "11f2cc0f64846cce27286f3cb0e3aea5", "fn": "breakpointRdata_1.24.0.tar.gz"}, "breastcancermainz-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/breastCancerMAINZ_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerMAINZ_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancermainz/bioconductor-breastcancermainz_1.44.0_src_all.tar.gz"], "md5": "22952cca74ba799453172c26a1b9e095", "fn": "breastCancerMAINZ_1.44.0.tar.gz"}, "breastcancernki-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/breastCancerNKI_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerNKI_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancernki/bioconductor-breastcancernki_1.44.0_src_all.tar.gz"], "md5": "d33d1f8a22c9a9c46a2d3d0979e73a43", "fn": "breastCancerNKI_1.44.0.tar.gz"}, "breastcancertransbig-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/breastCancerTRANSBIG_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerTRANSBIG_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancertransbig/bioconductor-breastcancertransbig_1.44.0_src_all.tar.gz"], "md5": "fc586508a997c8c11e7597e313af8656", "fn": "breastCancerTRANSBIG_1.44.0.tar.gz"}, "breastcancerunt-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/breastCancerUNT_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerUNT_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancerunt/bioconductor-breastcancerunt_1.44.0_src_all.tar.gz"], "md5": "59b7e8804b56e38b43e6fdbe27c7467d", "fn": "breastCancerUNT_1.44.0.tar.gz"}, "breastcancerupp-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/breastCancerUPP_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerUPP_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancerupp/bioconductor-breastcancerupp_1.44.0_src_all.tar.gz"], "md5": "164ea026b64aa6ed9c09feedd1b9b348", "fn": "breastCancerUPP_1.44.0.tar.gz"}, "breastcancervdx-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/breastCancerVDX_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/breastCancerVDX_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-breastcancervdx/bioconductor-breastcancervdx_1.44.0_src_all.tar.gz"], "md5": "b9c4ab9d76d527bef300fa0cfc0f7786", "fn": "breastCancerVDX_1.44.0.tar.gz"}, "brgedata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/brgedata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/brgedata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-brgedata/bioconductor-brgedata_1.28.0_src_all.tar.gz"], "md5": "576c30227addd3d7feda172a74c0b869", "fn": "brgedata_1.28.0.tar.gz"}, "bronchialil13-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/bronchialIL13_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/bronchialIL13_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bronchialil13/bioconductor-bronchialil13_1.44.0_src_all.tar.gz"], "md5": "00ffcfd4e6583e294b378101c011efd7", "fn": "bronchialIL13_1.44.0.tar.gz"}, "bsseqdata-0.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/bsseqData_0.44.0.tar.gz", "https://bioarchive.galaxyproject.org/bsseqData_0.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bsseqdata/bioconductor-bsseqdata_0.44.0_src_all.tar.gz"], "md5": "759f2d070264c33866572d991c5723af", "fn": "bsseqData_0.44.0.tar.gz"}, "cancerdata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/cancerdata_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/cancerdata_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cancerdata/bioconductor-cancerdata_1.44.0_src_all.tar.gz"], "md5": "0765bb89fc39828f03110a42851e1a02", "fn": "cancerdata_1.44.0.tar.gz"}, "cardinalworkflows-1.38.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/CardinalWorkflows_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/CardinalWorkflows_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cardinalworkflows/bioconductor-cardinalworkflows_1.38.0_src_all.tar.gz"], "md5": "d245d4c9f068e8618542e73c1ccb4973", "fn": "CardinalWorkflows_1.38.0.tar.gz"}, "ccdata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ccdata_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/ccdata_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ccdata/bioconductor-ccdata_1.32.0_src_all.tar.gz"], "md5": "310ec3465e4b2c78427eff60b91aeaae", "fn": "ccdata_1.32.0.tar.gz"}, "ccl4-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/CCl4_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/CCl4_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ccl4/bioconductor-ccl4_1.44.0_src_all.tar.gz"], "md5": "fb2ae341e4ce02f9252126a652638004", "fn": "CCl4_1.44.0.tar.gz"}, "celarefdata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/celarefData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/celarefData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celarefdata/bioconductor-celarefdata_1.24.0_src_all.tar.gz"], "md5": "53757d12a0a75e5220f8a1ceac494942", "fn": "celarefData_1.24.0.tar.gz"}, "celldex-1.16.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/celldex_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/celldex_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-celldex/bioconductor-celldex_1.16.0_src_all.tar.gz"], "md5": "ba3dc1f475b673ee0303293d6d997194", "fn": "celldex_1.16.0.tar.gz"}, "cellmapperdata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/CellMapperData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/CellMapperData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cellmapperdata/bioconductor-cellmapperdata_1.32.0_src_all.tar.gz"], "md5": "0ddd6a344cf219cebb22142890c1b2d3", "fn": "CellMapperData_1.32.0.tar.gz"}, "cftoolsdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/cfToolsData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/cfToolsData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cftoolsdata/bioconductor-cftoolsdata_1.4.0_src_all.tar.gz"], "md5": "b5b055a577c96c820f47fbfd28d25b35", "fn": "cfToolsData_1.4.0.tar.gz"}, "champdata-2.38.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ChAMPdata_2.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ChAMPdata_2.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-champdata/bioconductor-champdata_2.38.0_src_all.tar.gz"], "md5": "58ff4c4f195a082fcc386188d2c5dc81", "fn": "ChAMPdata_2.38.0.tar.gz"}, "chimphumanbraindata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ChimpHumanBrainData_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/ChimpHumanBrainData_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chimphumanbraindata/bioconductor-chimphumanbraindata_1.44.0_src_all.tar.gz"], "md5": "a948b1af0f5549131860985eb9617116", "fn": "ChimpHumanBrainData_1.44.0.tar.gz"}, "chipenrich.data-2.30.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/chipenrich.data_2.30.0.tar.gz", "https://bioarchive.galaxyproject.org/chipenrich.data_2.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipenrich.data/bioconductor-chipenrich.data_2.30.0_src_all.tar.gz"], "md5": "a6575fd0dccbe1285e969003f25cbaea", "fn": "chipenrich.data_2.30.0.tar.gz"}, "chipexoqualexample-1.30.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ChIPexoQualExample_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIPexoQualExample_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipexoqualexample/bioconductor-chipexoqualexample_1.30.0_src_all.tar.gz"], "md5": "25cceaa30a8a7a8fa3208c0357cab4db", "fn": "ChIPexoQualExample_1.30.0.tar.gz"}, "chipseqdbdata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/chipseqDBData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/chipseqDBData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipseqdbdata/bioconductor-chipseqdbdata_1.22.0_src_all.tar.gz"], "md5": "5ed0016ad2bd769e4959a755f78d9ed0", "fn": "chipseqDBData_1.22.0.tar.gz"}, "chipxpressdata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ChIPXpressData_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/ChIPXpressData_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chipxpressdata/bioconductor-chipxpressdata_1.44.0_src_all.tar.gz"], "md5": "2131b2a237b86063947c3526cfe53b6c", "fn": "ChIPXpressData_1.44.0.tar.gz"}, "chromstardata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/chromstaRData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/chromstaRData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-chromstardata/bioconductor-chromstardata_1.32.0_src_all.tar.gz"], "md5": "6c16bfa6c7ff1f38da0154bd65f43d5a", "fn": "chromstaRData_1.32.0.tar.gz"}, "cll-1.46.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/CLL_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/CLL_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cll/bioconductor-cll_1.46.0_src_all.tar.gz"], "md5": "c8071d9e39beb9e79f8f81188299b7db", "fn": "CLL_1.46.0.tar.gz"}, "cllmethylation-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/CLLmethylation_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/CLLmethylation_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cllmethylation/bioconductor-cllmethylation_1.26.0_src_all.tar.gz"], "md5": "5ffc204c8259540a8cb73c7bf4549249", "fn": "CLLmethylation_1.26.0.tar.gz"}, "clumsiddata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/CluMSIDdata_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/CluMSIDdata_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clumsiddata/bioconductor-clumsiddata_1.22.0_src_all.tar.gz"], "md5": "11dcdada1eca12589c47e4d2bccdbe4d", "fn": "CluMSIDdata_1.22.0.tar.gz"}, "clustifyrdatahub-1.16.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/clustifyrdatahub_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/clustifyrdatahub_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-clustifyrdatahub/bioconductor-clustifyrdatahub_1.16.0_src_all.tar.gz"], "md5": "33c4f3c64aa6b75787aa6435a74f6416", "fn": "clustifyrdatahub_1.16.0.tar.gz"}, "cmap2data-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/cMap2data_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/cMap2data_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cmap2data/bioconductor-cmap2data_1.42.0_src_all.tar.gz"], "md5": "9d53c236a9c4759d420576e0795f8813", "fn": "cMap2data_1.42.0.tar.gz"}, "cnvgsadata-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/cnvGSAdata_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/cnvGSAdata_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cnvgsadata/bioconductor-cnvgsadata_1.42.0_src_all.tar.gz"], "md5": "fe2b4f6e04f12f795b1b6fff123446ce", "fn": "cnvGSAdata_1.42.0.tar.gz"}, "cohcapanno-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/COHCAPanno_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/COHCAPanno_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cohcapanno/bioconductor-cohcapanno_1.42.0_src_all.tar.gz"], "md5": "4e0bffabf3c275f5d2a17c52e478d02d", "fn": "COHCAPanno_1.42.0.tar.gz"}, "colonca-1.48.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/colonCA_1.48.0.tar.gz", "https://bioarchive.galaxyproject.org/colonCA_1.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-colonca/bioconductor-colonca_1.48.0_src_all.tar.gz"], "md5": "06c2d5c6e9853feb34e80befab9356f7", "fn": "colonCA_1.48.0.tar.gz"}, "confessdata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/CONFESSdata_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/CONFESSdata_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-confessdata/bioconductor-confessdata_1.34.0_src_all.tar.gz"], "md5": "0a7503b919b1c5aab67f16b48391d0ac", "fn": "CONFESSdata_1.34.0.tar.gz"}, "connectivitymap-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ConnectivityMap_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/ConnectivityMap_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-connectivitymap/bioconductor-connectivitymap_1.42.0_src_all.tar.gz"], "md5": "2dac511c451dee045d1ccfc8d9f418b4", "fn": "ConnectivityMap_1.42.0.tar.gz"}, "copdsexualdimorphism.data-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/COPDSexualDimorphism.data_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/COPDSexualDimorphism.data_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copdsexualdimorphism.data/bioconductor-copdsexualdimorphism.data_1.42.0_src_all.tar.gz"], "md5": "8b7f51a5af7e245e2bcc9e15aff15bf3", "fn": "COPDSexualDimorphism.data_1.42.0.tar.gz"}, "copyhelper-1.38.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/CopyhelpeR_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/CopyhelpeR_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copyhelper/bioconductor-copyhelper_1.38.0_src_all.tar.gz"], "md5": "706b5d208852ce6b037f74e2e988f38a", "fn": "CopyhelpeR_1.38.0.tar.gz"}, "copyneutralima-1.24.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/CopyNeutralIMA_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/CopyNeutralIMA_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-copyneutralima/bioconductor-copyneutralima_1.24.0_src_all.tar.gz"], "md5": "3e54ad70dd8271f19765fedb5ee849cc", "fn": "CopyNeutralIMA_1.24.0.tar.gz"}, "cosiadata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/CoSIAdata_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/CoSIAdata_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cosiadata/bioconductor-cosiadata_1.6.0_src_all.tar.gz"], "md5": "6527ebc803b5f2e34ca3c434e9e19b53", "fn": "CoSIAdata_1.6.0.tar.gz"}, "cosmic.67-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/COSMIC.67_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/COSMIC.67_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cosmic.67/bioconductor-cosmic.67_1.42.0_src_all.tar.gz"], "md5": "39f8a708222453da072d3b208afa15e3", "fn": "COSMIC.67_1.42.0.tar.gz"}, "crcl18-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/CRCL18_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/CRCL18_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-crcl18/bioconductor-crcl18_1.26.0_src_all.tar.gz"], "md5": "8e65ec467f42c7419a0f0a5d986c99f2", "fn": "CRCL18_1.26.0.tar.gz"}, "crisprscoredata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/crisprScoreData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/crisprScoreData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-crisprscoredata/bioconductor-crisprscoredata_1.10.0_src_all.tar.gz"], "md5": "9e599deca608e23b7ec35db0579bff1b", "fn": "crisprScoreData_1.10.0.tar.gz"}, "curatedadipoarray-1.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/curatedAdipoArray_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoArray_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadipoarray/bioconductor-curatedadipoarray_1.18.0_src_all.tar.gz"], "md5": "f61b7c6abf04088146901d2afc5698b0", "fn": "curatedAdipoArray_1.18.0.tar.gz"}, "curatedadipochip-1.22.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/curatedAdipoChIP_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoChIP_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadipochip/bioconductor-curatedadipochip_1.22.0_src_all.tar.gz"], "md5": "576a410fb96440ce887b3afa3e140339", "fn": "curatedAdipoChIP_1.22.0.tar.gz"}, "curatedadiporna-1.22.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/curatedAdipoRNA_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedAdipoRNA_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedadiporna/bioconductor-curatedadiporna_1.22.0_src_all.tar.gz"], "md5": "eb2fb76b4e65349c0f81211df911722e", "fn": "curatedAdipoRNA_1.22.0.tar.gz"}, "curatedbladderdata-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/curatedBladderData_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedBladderData_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedbladderdata/bioconductor-curatedbladderdata_1.42.0_src_all.tar.gz"], "md5": "83bfc27c8454339626527a592867303e", "fn": "curatedBladderData_1.42.0.tar.gz"}, "curatedbreastdata-2.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/curatedBreastData_2.34.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedBreastData_2.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedbreastdata/bioconductor-curatedbreastdata_2.34.0_src_all.tar.gz"], "md5": "cc543a530d62b3ad9eedc25abc953332", "fn": "curatedBreastData_2.34.0.tar.gz"}, "curatedmetagenomicdata-3.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/curatedMetagenomicData_3.14.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedMetagenomicData_3.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedmetagenomicdata/bioconductor-curatedmetagenomicdata_3.14.0_src_all.tar.gz"], "md5": "efb481b40f689c417e9dbab4a98f71f1", "fn": "curatedMetagenomicData_3.14.0.tar.gz"}, "curatedovariandata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/curatedOvarianData_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedOvarianData_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedovariandata/bioconductor-curatedovariandata_1.44.0_src_all.tar.gz"], "md5": "8e490181b4476a15c64aa78f6347defb", "fn": "curatedOvarianData_1.44.0.tar.gz"}, "curatedtbdata-2.2.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/curatedTBData_2.2.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedTBData_2.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedtbdata/bioconductor-curatedtbdata_2.2.0_src_all.tar.gz"], "md5": "efdabbcb7fef2e04ae9a472637a7caeb", "fn": "curatedTBData_2.2.0.tar.gz"}, "curatedtcgadata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/curatedTCGAData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/curatedTCGAData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedtcgadata/bioconductor-curatedtcgadata_1.28.0_src_all.tar.gz"], "md5": "081d2bb84962bb75df2af33bd1ccd3a8", "fn": "curatedTCGAData_1.28.0.tar.gz"}, "dapardata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/DAPARdata_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/DAPARdata_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dapardata/bioconductor-dapardata_1.36.0_src_all.tar.gz"], "md5": "dd1a03112ed37c1b800badd879a70bcf", "fn": "DAPARdata_1.36.0.tar.gz"}, "davidtiling-1.46.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/davidTiling_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/davidTiling_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-davidtiling/bioconductor-davidtiling_1.46.0_src_all.tar.gz"], "md5": "4519817d00468376b430162bb2464c61", "fn": "davidTiling_1.46.0.tar.gz"}, "depmap-1.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/depmap_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/depmap_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-depmap/bioconductor-depmap_1.20.0_src_all.tar.gz"], "md5": "7570708bfa0edac82ad43e8f73600460", "fn": "depmap_1.20.0.tar.gz"}, "derfinderdata-2.24.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/derfinderData_2.24.0.tar.gz", "https://bioarchive.galaxyproject.org/derfinderData_2.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-derfinderdata/bioconductor-derfinderdata_2.24.0_src_all.tar.gz"], "md5": "29d921dc8f08b7699fdf23d90fbca0d1", "fn": "derfinderData_2.24.0.tar.gz"}, "desousa2013-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/DeSousa2013_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/DeSousa2013_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-desousa2013/bioconductor-desousa2013_1.42.0_src_all.tar.gz"], "md5": "62b95939db5cc4149c72f97a4dbd5ca6", "fn": "DeSousa2013_1.42.0.tar.gz"}, "dexmadata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/DExMAdata_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/DExMAdata_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dexmadata/bioconductor-dexmadata_1.14.0_src_all.tar.gz"], "md5": "6c03e9b7bdf0dd3c28a6aedbecf1de44", "fn": "DExMAdata_1.14.0.tar.gz"}, "diffloopdata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/diffloopdata_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/diffloopdata_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-diffloopdata/bioconductor-diffloopdata_1.34.0_src_all.tar.gz"], "md5": "f5906bd3830809ec05a36aaaaab6f8dc", "fn": "diffloopdata_1.34.0.tar.gz"}, "diggitdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/diggitdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/diggitdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-diggitdata/bioconductor-diggitdata_1.38.0_src_all.tar.gz"], "md5": "156206689cf62a4efdaed7eab550c59c", "fn": "diggitdata_1.38.0.tar.gz"}, "dlbcl-1.46.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/DLBCL_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/DLBCL_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dlbcl/bioconductor-dlbcl_1.46.0_src_all.tar.gz"], "md5": "e797d9de721064ed702845a0bd87b95e", "fn": "DLBCL_1.46.0.tar.gz"}, "dmelsgi-1.37.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/DmelSGI_1.37.0.tar.gz", "https://bioarchive.galaxyproject.org/DmelSGI_1.37.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dmelsgi/bioconductor-dmelsgi_1.37.0_src_all.tar.gz"], "md5": "a4f0d7af10a602b42c62e78a54785269", "fn": "DmelSGI_1.37.0.tar.gz"}, "dmrcatedata-2.24.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/DMRcatedata_2.24.0.tar.gz", "https://bioarchive.galaxyproject.org/DMRcatedata_2.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dmrcatedata/bioconductor-dmrcatedata_2.24.0_src_all.tar.gz"], "md5": "0f41fc4cf1bac6a239be095eab5139c0", "fn": "DMRcatedata_2.24.0.tar.gz"}, "dnazoodata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/DNAZooData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/DNAZooData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dnazoodata/bioconductor-dnazoodata_1.6.0_src_all.tar.gz"], "md5": "ebf660c8af5efe9626a5e9a80c8a897f", "fn": "DNAZooData_1.6.0.tar.gz"}, "donapllp2013-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/DonaPLLP2013_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/DonaPLLP2013_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-donapllp2013/bioconductor-donapllp2013_1.44.0_src_all.tar.gz"], "md5": "f8ac609e6018b26a1aec2d087a8f30f4", "fn": "DonaPLLP2013_1.44.0.tar.gz"}, "dorothea-1.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/dorothea_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/dorothea_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dorothea/bioconductor-dorothea_1.18.0_src_all.tar.gz"], "md5": "5787d956a54680963aff5ce33c12307c", "fn": "dorothea_1.18.0.tar.gz"}, "dresscheck-0.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/dressCheck_0.44.0.tar.gz", "https://bioarchive.galaxyproject.org/dressCheck_0.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dresscheck/bioconductor-dresscheck_0.44.0_src_all.tar.gz"], "md5": "64019291fc041eeb4821f83b27fb1681", "fn": "dressCheck_0.44.0.tar.gz"}, "droplettestfiles-1.16.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/DropletTestFiles_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/DropletTestFiles_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-droplettestfiles/bioconductor-droplettestfiles_1.16.0_src_all.tar.gz"], "md5": "a63075748b3844f580a535c87b92440c", "fn": "DropletTestFiles_1.16.0.tar.gz"}, "drugvsdiseasedata-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/DrugVsDiseasedata_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/DrugVsDiseasedata_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-drugvsdiseasedata/bioconductor-drugvsdiseasedata_1.42.0_src_all.tar.gz"], "md5": "c14a86c5d506d84420eb41edd7858d8c", "fn": "DrugVsDiseasedata_1.42.0.tar.gz"}, "duoclustering2018-1.24.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/DuoClustering2018_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/DuoClustering2018_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-duoclustering2018/bioconductor-duoclustering2018_1.24.0_src_all.tar.gz"], "md5": "6aec8bc9d4f6620e71312a5691168a7d", "fn": "DuoClustering2018_1.24.0.tar.gz"}, "dvddata-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/DvDdata_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/DvDdata_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dvddata/bioconductor-dvddata_1.42.0_src_all.tar.gz"], "md5": "f2eec0f8e77512e32112a66a592a9351", "fn": "DvDdata_1.42.0.tar.gz"}, "dyebiasexamples-1.46.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/dyebiasexamples_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/dyebiasexamples_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-dyebiasexamples/bioconductor-dyebiasexamples_1.46.0_src_all.tar.gz"], "md5": "3f52ef68b5944fbc0ceeec8632626d29", "fn": "dyebiasexamples_1.46.0.tar.gz"}, "easierdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/easierData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/easierData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-easierdata/bioconductor-easierdata_1.12.0_src_all.tar.gz"], "md5": "845c7b7a2d851903bbdaff40d0d4503b", "fn": "easierData_1.12.0.tar.gz"}, "eatonetalchipseq-0.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/EatonEtAlChIPseq_0.44.0.tar.gz", "https://bioarchive.galaxyproject.org/EatonEtAlChIPseq_0.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-eatonetalchipseq/bioconductor-eatonetalchipseq_0.44.0_src_all.tar.gz"], "md5": "89c7bd11b6d15aac7f373151e8d517f1", "fn": "EatonEtAlChIPseq_0.44.0.tar.gz"}, "ecolileucine-1.46.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ecoliLeucine_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/ecoliLeucine_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ecolileucine/bioconductor-ecolileucine_1.46.0_src_all.tar.gz"], "md5": "7596646155beb8c35bf2670f2c22788d", "fn": "ecoliLeucine_1.46.0.tar.gz"}, "egseadata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/EGSEAdata_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/EGSEAdata_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-egseadata/bioconductor-egseadata_1.34.0_src_all.tar.gz"], "md5": "422fcaa7f47c394358600cfb268d265b", "fn": "EGSEAdata_1.34.0.tar.gz"}, "elmer.data-2.30.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ELMER.data_2.30.0.tar.gz", "https://bioarchive.galaxyproject.org/ELMER.data_2.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-elmer.data/bioconductor-elmer.data_2.30.0_src_all.tar.gz"], "md5": "611a1275cc893a59759673a36dd5e272", "fn": "ELMER.data_2.30.0.tar.gz"}, "emtdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/emtdata_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/emtdata_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-emtdata/bioconductor-emtdata_1.14.0_src_all.tar.gz"], "md5": "8db81c389458586cc9c291f05cfcd7d1", "fn": "emtdata_1.14.0.tar.gz"}, "epimix.data-1.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/EpiMix.data_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/EpiMix.data_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epimix.data/bioconductor-epimix.data_1.8.0_src_all.tar.gz"], "md5": "64dd6bc27966ef5920f06823dcc4af94", "fn": "EpiMix.data_1.8.0.tar.gz"}, "epimutacionsdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/epimutacionsData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/epimutacionsData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-epimutacionsdata/bioconductor-epimutacionsdata_1.10.0_src_all.tar.gz"], "md5": "1bb081472a039407ea2bb74f109cf1ae", "fn": "epimutacionsData_1.10.0.tar.gz"}, "estrogen-1.52.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/estrogen_1.52.0.tar.gz", "https://bioarchive.galaxyproject.org/estrogen_1.52.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-estrogen/bioconductor-estrogen_1.52.0_src_all.tar.gz"], "md5": "a15821f8002bf76ac7261b6982c970a5", "fn": "estrogen_1.52.0.tar.gz"}, "etec16s-1.33.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/etec16s_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/etec16s_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-etec16s/bioconductor-etec16s_1.33.0_src_all.tar.gz"], "md5": "fcaa0b82c184de2e434fce35b0422c7e", "fn": "etec16s_1.33.0.tar.gz"}, "ewcedata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ewceData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/ewceData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ewcedata/bioconductor-ewcedata_1.14.0_src_all.tar.gz"], "md5": "24cd796cc090d45d4d6cda652a12d394", "fn": "ewceData_1.14.0.tar.gz"}, "faahko-1.46.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/faahKO_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/faahKO_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-faahko/bioconductor-faahko_1.46.0_src_all.tar.gz"], "md5": "6182750f76d8f196207b7ec0efaf06fc", "fn": "faahKO_1.46.0.tar.gz"}, "fabiadata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/fabiaData_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/fabiaData_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fabiadata/bioconductor-fabiadata_1.44.0_src_all.tar.gz"], "md5": "eda95b365fa1731facc3828ef343e176", "fn": "fabiaData_1.44.0.tar.gz"}, "fantom3and4cage-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/FANTOM3and4CAGE_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/FANTOM3and4CAGE_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fantom3and4cage/bioconductor-fantom3and4cage_1.42.0_src_all.tar.gz"], "md5": "a4c297c5de2e697b0aaddf7a5e1b1c91", "fn": "FANTOM3and4CAGE_1.42.0.tar.gz"}, "ffpeexampledata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ffpeExampleData_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/ffpeExampleData_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ffpeexampledata/bioconductor-ffpeexampledata_1.44.0_src_all.tar.gz"], "md5": "6f800c039d810e224c1ed7726fe18396", "fn": "ffpeExampleData_1.44.0.tar.gz"}, "fibroeset-1.48.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/fibroEset_1.48.0.tar.gz", "https://bioarchive.galaxyproject.org/fibroEset_1.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fibroeset/bioconductor-fibroeset_1.48.0_src_all.tar.gz"], "md5": "86edf1f76f8d9627b678835b13535e9c", "fn": "fibroEset_1.48.0.tar.gz"}, "fieldeffectcrc-1.16.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/FieldEffectCrc_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/FieldEffectCrc_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fieldeffectcrc/bioconductor-fieldeffectcrc_1.16.0_src_all.tar.gz"], "md5": "184e4ee06f9eba119f7aa0ec4dd9ec2e", "fn": "FieldEffectCrc_1.16.0.tar.gz"}, "fis-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/FIs_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/FIs_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fis/bioconductor-fis_1.34.0_src_all.tar.gz"], "md5": "76cdfe37dba524d956bfd1a0f27b1843", "fn": "FIs_1.34.0.tar.gz"}, "fission-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/fission_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/fission_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fission/bioconductor-fission_1.26.0_src_all.tar.gz"], "md5": "00d2bde8a4da959730467dc66fcaeef0", "fn": "fission_1.26.0.tar.gz"}, "fletcher2013a-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/Fletcher2013a_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/Fletcher2013a_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fletcher2013a/bioconductor-fletcher2013a_1.42.0_src_all.tar.gz"], "md5": "5641358237faed180be98f2794357119", "fn": "Fletcher2013a_1.42.0.tar.gz"}, "fletcher2013b-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/Fletcher2013b_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/Fletcher2013b_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fletcher2013b/bioconductor-fletcher2013b_1.42.0_src_all.tar.gz"], "md5": "3f9698b0e3c2785036a65560ac1e4141", "fn": "Fletcher2013b_1.42.0.tar.gz"}, "flowploidydata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/flowPloidyData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/flowPloidyData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowploidydata/bioconductor-flowploidydata_1.32.0_src_all.tar.gz"], "md5": "ed761a0cd77a9b186cfd6f09860d39a3", "fn": "flowPloidyData_1.32.0.tar.gz"}, "flowsorted.blood.450k-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/FlowSorted.Blood.450k_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.Blood.450k_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.450k/bioconductor-flowsorted.blood.450k_1.44.0_src_all.tar.gz"], "md5": "6df54186a88be5c6335467a86ec2e219", "fn": "FlowSorted.Blood.450k_1.44.0.tar.gz"}, "flowsorted.blood.epic-2.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/FlowSorted.Blood.EPIC_2.10.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.Blood.EPIC_2.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.epic/bioconductor-flowsorted.blood.epic_2.10.0_src_all.tar.gz"], "md5": "a51230659106aa6ba33a7bdd616d4ae6", "fn": "FlowSorted.Blood.EPIC_2.10.0.tar.gz"}, "flowsorted.cordblood.450k-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/FlowSorted.CordBlood.450k_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBlood.450k_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordblood.450k/bioconductor-flowsorted.cordblood.450k_1.34.0_src_all.tar.gz"], "md5": "3afca2babc77db996268a0b383c2a5f0", "fn": "FlowSorted.CordBlood.450k_1.34.0.tar.gz"}, "flowsorted.cordbloodcombined.450k-1.22.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/FlowSorted.CordBloodCombined.450k_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodCombined.450k_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodcombined.450k/bioconductor-flowsorted.cordbloodcombined.450k_1.22.0_src_all.tar.gz"], "md5": "edafe41e6489b95f1b3279e8bfd324a7", "fn": "FlowSorted.CordBloodCombined.450k_1.22.0.tar.gz"}, "flowsorted.cordbloodnorway.450k-1.32.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/FlowSorted.CordBloodNorway.450k_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodNorway.450k_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodnorway.450k/bioconductor-flowsorted.cordbloodnorway.450k_1.32.0_src_all.tar.gz"], "md5": "21a44f2a9ffb55f053f32c398f4689b7", "fn": "FlowSorted.CordBloodNorway.450k_1.32.0.tar.gz"}, "flowsorted.dlpfc.450k-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/FlowSorted.DLPFC.450k_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/FlowSorted.DLPFC.450k_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowsorted.dlpfc.450k/bioconductor-flowsorted.dlpfc.450k_1.42.0_src_all.tar.gz"], "md5": "f77547b8703af30a4f248b5f8a75cd92", "fn": "FlowSorted.DLPFC.450k_1.42.0.tar.gz"}, "flowworkspacedata-3.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/flowWorkspaceData_3.18.0.tar.gz", "https://bioarchive.galaxyproject.org/flowWorkspaceData_3.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-flowworkspacedata/bioconductor-flowworkspacedata_3.18.0_src_all.tar.gz"], "md5": "7133f0addd24a8713d2b57ffe7646bd8", "fn": "flowWorkspaceData_3.18.0.tar.gz"}, "fourdndata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/fourDNData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/fourDNData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-fourdndata/bioconductor-fourdndata_1.6.0_src_all.tar.gz"], "md5": "afe1fdf692cb248b2bd937b2bed37b03", "fn": "fourDNData_1.6.0.tar.gz"}, "frmaexampledata-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/frmaExampleData_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/frmaExampleData_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-frmaexampledata/bioconductor-frmaexampledata_1.42.0_src_all.tar.gz"], "md5": "4dd690a166195829ba5a45856448bf49", "fn": "frmaExampleData_1.42.0.tar.gz"}, "furrowseg-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/furrowSeg_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/furrowSeg_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-furrowseg/bioconductor-furrowseg_1.34.0_src_all.tar.gz"], "md5": "b6b176917d5ecdcdc8a6b9f91e06fe95", "fn": "furrowSeg_1.34.0.tar.gz"}, "gagedata-2.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/gageData_2.44.0.tar.gz", "https://bioarchive.galaxyproject.org/gageData_2.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gagedata/bioconductor-gagedata_2.44.0_src_all.tar.gz"], "md5": "340f02c98e843eddf50694a88ee3c18f", "fn": "gageData_2.44.0.tar.gz"}, "gaschyhs-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/gaschYHS_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/gaschYHS_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gaschyhs/bioconductor-gaschyhs_1.44.0_src_all.tar.gz"], "md5": "c6033103748cbec679796f36cd9d2bba", "fn": "gaschYHS_1.44.0.tar.gz"}, "gcspikelite-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/gcspikelite_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/gcspikelite_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gcspikelite/bioconductor-gcspikelite_1.44.0_src_all.tar.gz"], "md5": "3b8732b7eb8743bd3f92cb0eaa1308b3", "fn": "gcspikelite_1.44.0.tar.gz"}, "gdnainrnaseqdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/gDNAinRNAseqData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/gDNAinRNAseqData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gdnainrnaseqdata/bioconductor-gdnainrnaseqdata_1.6.0_src_all.tar.gz"], "md5": "1051ca9adac9bf173e6ae6db69c7d5f8", "fn": "gDNAinRNAseqData_1.6.0.tar.gz"}, "gdrtestdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/gDRtestData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/gDRtestData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gdrtestdata/bioconductor-gdrtestdata_1.4.0_src_all.tar.gz"], "md5": "edefc42aeca53a188b512659ae557f6d", "fn": "gDRtestData_1.4.0.tar.gz"}, "genelendatabase-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/geneLenDataBase_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/geneLenDataBase_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genelendatabase/bioconductor-genelendatabase_1.42.0_src_all.tar.gz"], "md5": "383f08d23aa5b28f812f4d353bc5dd6f", "fn": "geneLenDataBase_1.42.0.tar.gz"}, "genomationdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/genomationData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/genomationData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomationdata/bioconductor-genomationdata_1.38.0_src_all.tar.gz"], "md5": "c5c850508ccd391d1a16689bcbab0879", "fn": "genomationData_1.38.0.tar.gz"}, "genomicdistributionsdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/GenomicDistributionsData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/GenomicDistributionsData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-genomicdistributionsdata/bioconductor-genomicdistributionsdata_1.14.0_src_all.tar.gz"], "md5": "76d8227fa4c313fdc471bb14415d8962", "fn": "GenomicDistributionsData_1.14.0.tar.gz"}, "geuvadistranscriptexpr-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/GeuvadisTranscriptExpr_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/GeuvadisTranscriptExpr_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-geuvadistranscriptexpr/bioconductor-geuvadistranscriptexpr_1.34.0_src_all.tar.gz"], "md5": "6a7d1b4c1733a4bbff15b5e1863160c4", "fn": "GeuvadisTranscriptExpr_1.34.0.tar.gz"}, "gigseadata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/GIGSEAdata_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/GIGSEAdata_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gigseadata/bioconductor-gigseadata_1.24.0_src_all.tar.gz"], "md5": "d4b48ce5a328de15cf771451f9d89c51", "fn": "GIGSEAdata_1.24.0.tar.gz"}, "golubesets-1.48.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/golubEsets_1.48.0.tar.gz", "https://bioarchive.galaxyproject.org/golubEsets_1.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-golubesets/bioconductor-golubesets_1.48.0_src_all.tar.gz"], "md5": "b464be536b50df612af2caa81b4395ea", "fn": "golubEsets_1.48.0.tar.gz"}, "gpaexample-1.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/gpaExample_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/gpaExample_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gpaexample/bioconductor-gpaexample_1.18.0_src_all.tar.gz"], "md5": "96d55ecbe0c635ee1e296e371f213ef1", "fn": "gpaExample_1.18.0.tar.gz"}, "grndata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/grndata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/grndata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-grndata/bioconductor-grndata_1.38.0_src_all.tar.gz"], "md5": "267a7286c8e9207afa54c0e5b1fff229", "fn": "grndata_1.38.0.tar.gz"}, "gsbenchmark-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/GSBenchMark_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/GSBenchMark_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gsbenchmark/bioconductor-gsbenchmark_1.26.0_src_all.tar.gz"], "md5": "9225e7c0e665cac115205f804d932d00", "fn": "GSBenchMark_1.26.0.tar.gz"}, "gse103322-1.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/GSE103322_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE103322_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse103322/bioconductor-gse103322_1.12.0_src_all.tar.gz"], "md5": "ef8a6be2fbc94685daf9df2aa7b69085", "fn": "GSE103322_1.12.0.tar.gz"}, "gse13015-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/GSE13015_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE13015_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse13015/bioconductor-gse13015_1.14.0_src_all.tar.gz"], "md5": "016137663819811515c8a31ad8970e36", "fn": "GSE13015_1.14.0.tar.gz"}, "gse159526-1.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/GSE159526_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE159526_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse159526/bioconductor-gse159526_1.12.0_src_all.tar.gz"], "md5": "996ed6300106923241c4624b1fbd27bb", "fn": "GSE159526_1.12.0.tar.gz"}, "gse62944-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/GSE62944_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/GSE62944_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gse62944/bioconductor-gse62944_1.34.0_src_all.tar.gz"], "md5": "314ad5bf5a423531bc075f753658e28a", "fn": "GSE62944_1.34.0.tar.gz"}, "gsvadata-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/GSVAdata_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/GSVAdata_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gsvadata/bioconductor-gsvadata_1.42.0_src_all.tar.gz"], "md5": "19ce23485bb46391ee186ffc9558660e", "fn": "GSVAdata_1.42.0.tar.gz"}, "gwasdata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/GWASdata_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/GWASdata_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-gwasdata/bioconductor-gwasdata_1.44.0_src_all.tar.gz"], "md5": "b27980b5cacc933bf897da291ad17871", "fn": "GWASdata_1.44.0.tar.gz"}, "h5vcdata-2.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/h5vcData_2.26.0.tar.gz", "https://bioarchive.galaxyproject.org/h5vcData_2.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-h5vcdata/bioconductor-h5vcdata_2.26.0_src_all.tar.gz"], "md5": "da6264ea480859df1c681611088aeb89", "fn": "h5vcData_2.26.0.tar.gz"}, "hapmap100khind-1.48.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/hapmap100khind_1.48.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap100khind_1.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap100khind/bioconductor-hapmap100khind_1.48.0_src_all.tar.gz"], "md5": "164c26d681c90e1ddff583a7cf69e1d4", "fn": "hapmap100khind_1.48.0.tar.gz"}, "hapmap100kxba-1.48.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/hapmap100kxba_1.48.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap100kxba_1.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap100kxba/bioconductor-hapmap100kxba_1.48.0_src_all.tar.gz"], "md5": "512c4b503328303dd5171444eb3c1e64", "fn": "hapmap100kxba_1.48.0.tar.gz"}, "hapmap500knsp-1.48.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/hapmap500knsp_1.48.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap500knsp_1.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap500knsp/bioconductor-hapmap500knsp_1.48.0_src_all.tar.gz"], "md5": "37c94ad018546ed485cb9112c448aefe", "fn": "hapmap500knsp_1.48.0.tar.gz"}, "hapmap500ksty-1.48.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/hapmap500ksty_1.48.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmap500ksty_1.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmap500ksty/bioconductor-hapmap500ksty_1.48.0_src_all.tar.gz"], "md5": "f5f4aeccf821977db1f500d8f2c20717", "fn": "hapmap500ksty_1.48.0.tar.gz"}, "hapmapsnp5-1.48.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/hapmapsnp5_1.48.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmapsnp5_1.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp5/bioconductor-hapmapsnp5_1.48.0_src_all.tar.gz"], "md5": "eeecae8e0670dcd874224997a8925116", "fn": "hapmapsnp5_1.48.0.tar.gz"}, "hapmapsnp6-1.48.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/hapmapsnp6_1.48.0.tar.gz", "https://bioarchive.galaxyproject.org/hapmapsnp6_1.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp6/bioconductor-hapmapsnp6_1.48.0_src_all.tar.gz"], "md5": "be147d4601ac606b148642d5399c0f12", "fn": "hapmapsnp6_1.48.0.tar.gz"}, "harbchip-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/harbChIP_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/harbChIP_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harbchip/bioconductor-harbchip_1.44.0_src_all.tar.gz"], "md5": "f4cac0290c8ca0b869d065858e08ef1b", "fn": "harbChIP_1.44.0.tar.gz"}, "harmandata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/HarmanData_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/HarmanData_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harmandata/bioconductor-harmandata_1.34.0_src_all.tar.gz"], "md5": "f02d7d5fe9c935069af10076dade4bac", "fn": "HarmanData_1.34.0.tar.gz"}, "harmonizedtcgadata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/HarmonizedTCGAData_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/HarmonizedTCGAData_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-harmonizedtcgadata/bioconductor-harmonizedtcgadata_1.28.0_src_all.tar.gz"], "md5": "6c789331d5bae50ac2645b29768ef1b5", "fn": "HarmonizedTCGAData_1.28.0.tar.gz"}, "hcadata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/HCAData_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/HCAData_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcadata/bioconductor-hcadata_1.22.0_src_all.tar.gz"], "md5": "20709447d85048afded279c78fe2c531", "fn": "HCAData_1.22.0.tar.gz"}, "hcatonsildata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/HCATonsilData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/HCATonsilData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hcatonsildata/bioconductor-hcatonsildata_1.4.0_src_all.tar.gz"], "md5": "5b5ff3154f189e90ed13a40a0904d16c", "fn": "HCATonsilData_1.4.0.tar.gz"}, "hd2013sgi-1.46.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/HD2013SGI_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/HD2013SGI_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hd2013sgi/bioconductor-hd2013sgi_1.46.0_src_all.tar.gz"], "md5": "1cb210d619cf563fb29d05ba42f1cefa", "fn": "HD2013SGI_1.46.0.tar.gz"}, "hdcytodata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/HDCytoData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/HDCytoData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hdcytodata/bioconductor-hdcytodata_1.26.0_src_all.tar.gz"], "md5": "8a0dae06b9da48f201c3c1332c6d57d9", "fn": "HDCytoData_1.26.0.tar.gz"}, "healthycontrolspresencechecker-1.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/healthyControlsPresenceChecker_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/healthyControlsPresenceChecker_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-healthycontrolspresencechecker/bioconductor-healthycontrolspresencechecker_1.10.0_src_all.tar.gz"], "md5": "7834e53a3995caf74a55a7f4c63fb344", "fn": "healthyControlsPresenceChecker_1.10.0.tar.gz"}, "healthyflowdata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/healthyFlowData_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/healthyFlowData_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-healthyflowdata/bioconductor-healthyflowdata_1.44.0_src_all.tar.gz"], "md5": "a93dbeb707da467b9072d8926d5e79e6", "fn": "healthyFlowData_1.44.0.tar.gz"}, "heebodata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/HEEBOdata_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/HEEBOdata_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-heebodata/bioconductor-heebodata_1.44.0_src_all.tar.gz"], "md5": "521b9fe3601e422c49f5259ad67780ce", "fn": "HEEBOdata_1.44.0.tar.gz"}, "hellorangesdata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/HelloRangesData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/HelloRangesData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hellorangesdata/bioconductor-hellorangesdata_1.32.0_src_all.tar.gz"], "md5": "acda716ebef959e29b29129559d11134", "fn": "HelloRangesData_1.32.0.tar.gz"}, "hgu133abarcodevecs-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/hgu133abarcodevecs_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133abarcodevecs_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133abarcodevecs/bioconductor-hgu133abarcodevecs_1.44.0_src_all.tar.gz"], "md5": "86e728d6eabf7c2b2d0629e4489ba140", "fn": "hgu133abarcodevecs_1.44.0.tar.gz"}, "hgu133plus2barcodevecs-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/hgu133plus2barcodevecs_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2barcodevecs_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2barcodevecs/bioconductor-hgu133plus2barcodevecs_1.44.0_src_all.tar.gz"], "md5": "8e70491d7b0590fa84517fbb449ec2db", "fn": "hgu133plus2barcodevecs_1.44.0.tar.gz"}, "hgu133plus2cellscore-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/hgu133plus2CellScore_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu133plus2CellScore_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2cellscore/bioconductor-hgu133plus2cellscore_1.26.0_src_all.tar.gz"], "md5": "ece73161aa2c3ec43a558994e4a81dd1", "fn": "hgu133plus2CellScore_1.26.0.tar.gz"}, "hgu2beta7-1.46.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/hgu2beta7_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/hgu2beta7_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hgu2beta7/bioconductor-hgu2beta7_1.46.0_src_all.tar.gz"], "md5": "4b1f0eca6477f5475ebdccb2c06f6634", "fn": "hgu2beta7_1.46.0.tar.gz"}, "hibed-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/HiBED_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/HiBED_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hibed/bioconductor-hibed_1.4.0_src_all.tar.gz"], "md5": "2858803aaed3e0110711dfb4246789bc", "fn": "HiBED_1.4.0.tar.gz"}, "hicdatahumanimr90-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/HiCDataHumanIMR90_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/HiCDataHumanIMR90_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicdatahumanimr90/bioconductor-hicdatahumanimr90_1.26.0_src_all.tar.gz"], "md5": "6fa599b5b8d54523c6bb6dcd12d135a5", "fn": "HiCDataHumanIMR90_1.26.0.tar.gz"}, "hicdatalymphoblast-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/HiCDataLymphoblast_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/HiCDataLymphoblast_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicdatalymphoblast/bioconductor-hicdatalymphoblast_1.42.0_src_all.tar.gz"], "md5": "22efbfbd94821942a7e1c9e0e9df0db6", "fn": "HiCDataLymphoblast_1.42.0.tar.gz"}, "hicontactsdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/HiContactsData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/HiContactsData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hicontactsdata/bioconductor-hicontactsdata_1.8.0_src_all.tar.gz"], "md5": "0798e7ca7fd4015c2885161ce8db285a", "fn": "HiContactsData_1.8.0.tar.gz"}, "highlyreplicatedrnaseq-1.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/HighlyReplicatedRNASeq_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/HighlyReplicatedRNASeq_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-highlyreplicatedrnaseq/bioconductor-highlyreplicatedrnaseq_1.18.0_src_all.tar.gz"], "md5": "99ee0dea69d529c22e03384cc5a61941", "fn": "HighlyReplicatedRNASeq_1.18.0.tar.gz"}, "hiiragi2013-1.41.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/Hiiragi2013_1.41.0.tar.gz", "https://bioarchive.galaxyproject.org/Hiiragi2013_1.41.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hiiragi2013/bioconductor-hiiragi2013_1.41.0_src_all.tar.gz"], "md5": "71c665b10052ac72002701dd45990dc7", "fn": "Hiiragi2013_1.41.0.tar.gz"}, "hivcdnavantwout03-1.46.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/HIVcDNAvantWout03_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/HIVcDNAvantWout03_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hivcdnavantwout03/bioconductor-hivcdnavantwout03_1.46.0_src_all.tar.gz"], "md5": "d8a55d85bce20ea0197759f2da10a230", "fn": "HIVcDNAvantWout03_1.46.0.tar.gz"}, "hmp16sdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/HMP16SData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/HMP16SData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hmp16sdata/bioconductor-hmp16sdata_1.26.0_src_all.tar.gz"], "md5": "7dcdd859e777169f9dacff8369a65e15", "fn": "HMP16SData_1.26.0.tar.gz"}, "hmp2data-1.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/HMP2Data_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/HMP2Data_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hmp2data/bioconductor-hmp2data_1.20.0_src_all.tar.gz"], "md5": "6d8778e92c4375d4bc35c25ab174473d", "fn": "HMP2Data_1.20.0.tar.gz"}, "homosapiendee2cellscore-1.2.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/homosapienDEE2CellScore_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/homosapienDEE2CellScore_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-homosapiendee2cellscore/bioconductor-homosapiendee2cellscore_1.2.0_src_all.tar.gz"], "md5": "4894dd9b37b59acd890668da27325b53", "fn": "homosapienDEE2CellScore_1.2.0.tar.gz"}, "hsmmsinglecell-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/HSMMSingleCell_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/HSMMSingleCell_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-hsmmsinglecell/bioconductor-hsmmsinglecell_1.26.0_src_all.tar.gz"], "md5": "81add770e941f389d38651577056a14e", "fn": "HSMMSingleCell_1.26.0.tar.gz"}, "humanaffydata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/HumanAffyData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/HumanAffyData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanaffydata/bioconductor-humanaffydata_1.32.0_src_all.tar.gz"], "md5": "abaf3ed8ff9db09d86de2a6f5f364e54", "fn": "HumanAffyData_1.32.0.tar.gz"}, "humanstemcell-0.46.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/humanStemCell_0.46.0.tar.gz", "https://bioarchive.galaxyproject.org/humanStemCell_0.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-humanstemcell/bioconductor-humanstemcell_0.46.0_src_all.tar.gz"], "md5": "4531bfaff7e8e167ce039037db799cd6", "fn": "humanStemCell_0.46.0.tar.gz"}, "ihwpaper-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/IHWpaper_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/IHWpaper_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ihwpaper/bioconductor-ihwpaper_1.34.0_src_all.tar.gz"], "md5": "a934c0fe5745d5172c0bc40d7fe67166", "fn": "IHWpaper_1.34.0.tar.gz"}, "illumina450probevariants.db-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/Illumina450ProbeVariants.db_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/Illumina450ProbeVariants.db_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illumina450probevariants.db/bioconductor-illumina450probevariants.db_1.42.0_src_all.tar.gz"], "md5": "a439949b2c954d589bc6e56ba1d13b0a", "fn": "Illumina450ProbeVariants.db_1.42.0.tar.gz"}, "illuminadatatestfiles-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/IlluminaDataTestFiles_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/IlluminaDataTestFiles_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-illuminadatatestfiles/bioconductor-illuminadatatestfiles_1.44.0_src_all.tar.gz"], "md5": "b7ef98a177e46103b696291264e4238e", "fn": "IlluminaDataTestFiles_1.44.0.tar.gz"}, "imcdatasets-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/imcdatasets_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/imcdatasets_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-imcdatasets/bioconductor-imcdatasets_1.14.0_src_all.tar.gz"], "md5": "c93de5b533351ab9d7414616e1d45d08", "fn": "imcdatasets_1.14.0.tar.gz"}, "italicsdata-2.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ITALICSData_2.44.0.tar.gz", "https://bioarchive.galaxyproject.org/ITALICSData_2.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-italicsdata/bioconductor-italicsdata_2.44.0_src_all.tar.gz"], "md5": "90f027ec991724ac688d30ceb7a0b103", "fn": "ITALICSData_2.44.0.tar.gz"}, "iyer517-1.48.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/Iyer517_1.48.0.tar.gz", "https://bioarchive.galaxyproject.org/Iyer517_1.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-iyer517/bioconductor-iyer517_1.48.0_src_all.tar.gz"], "md5": "b9822faff0be8722db82a5e8340b9873", "fn": "Iyer517_1.48.0.tar.gz"}, "jaspar2014-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/JASPAR2014_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2014_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2014/bioconductor-jaspar2014_1.42.0_src_all.tar.gz"], "md5": "f69c9d61904b3a4279535d61c3ef9597", "fn": "JASPAR2014_1.42.0.tar.gz"}, "jaspar2016-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/JASPAR2016_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/JASPAR2016_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-jaspar2016/bioconductor-jaspar2016_1.34.0_src_all.tar.gz"], "md5": "15bad5cb473e295ea4c509c366f4568a", "fn": "JASPAR2016_1.34.0.tar.gz"}, "johnsonkinasedata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/JohnsonKinaseData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/JohnsonKinaseData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-johnsonkinasedata/bioconductor-johnsonkinasedata_1.2.0_src_all.tar.gz"], "md5": "3da2bcf23b00fe365074130338eb347c", "fn": "JohnsonKinaseData_1.2.0.tar.gz"}, "keggandmetacoredzpathwaysgeo-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/KEGGandMetacoreDzPathwaysGEO_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/KEGGandMetacoreDzPathwaysGEO_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-keggandmetacoredzpathwaysgeo/bioconductor-keggandmetacoredzpathwaysgeo_1.26.0_src_all.tar.gz"], "md5": "bc64484970f91516654ad091857f000b", "fn": "KEGGandMetacoreDzPathwaysGEO_1.26.0.tar.gz"}, "keggdzpathwaysgeo-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/KEGGdzPathwaysGEO_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/KEGGdzPathwaysGEO_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-keggdzpathwaysgeo/bioconductor-keggdzpathwaysgeo_1.44.0_src_all.tar.gz"], "md5": "2edbe2925b386b52a1fd7231d93d006b", "fn": "KEGGdzPathwaysGEO_1.44.0.tar.gz"}, "kidpack-1.48.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/kidpack_1.48.0.tar.gz", "https://bioarchive.galaxyproject.org/kidpack_1.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-kidpack/bioconductor-kidpack_1.48.0_src_all.tar.gz"], "md5": "52f60c471d09226cba0e0938924b4bda", "fn": "kidpack_1.48.0.tar.gz"}, "kodata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/KOdata_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/KOdata_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-kodata/bioconductor-kodata_1.32.0_src_all.tar.gz"], "md5": "b31e70b88fa60ec9a64d94fe6b2b487e", "fn": "KOdata_1.32.0.tar.gz"}, "leebamviews-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/leeBamViews_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/leeBamViews_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-leebamviews/bioconductor-leebamviews_1.42.0_src_all.tar.gz"], "md5": "80635485b599e011e632e0c9f82f6e88", "fn": "leeBamViews_1.42.0.tar.gz"}, "legato-1.0.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/LegATo_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/LegATo_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-legato/bioconductor-legato_1.0.0_src_all.tar.gz"], "md5": "aef951790167d23ba254573540b628bd", "fn": "LegATo_1.0.0.tar.gz"}, "leukemiaseset-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/leukemiasEset_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/leukemiasEset_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-leukemiaseset/bioconductor-leukemiaseset_1.42.0_src_all.tar.gz"], "md5": "5adc5dcc59cbe7e760ae276724f98fad", "fn": "leukemiasEset_1.42.0.tar.gz"}, "liebermanaidenhic2009-0.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/LiebermanAidenHiC2009_0.44.0.tar.gz", "https://bioarchive.galaxyproject.org/LiebermanAidenHiC2009_0.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-liebermanaidenhic2009/bioconductor-liebermanaidenhic2009_0.44.0_src_all.tar.gz"], "md5": "66667bb8dda5d64584a6fcb82c893d2d", "fn": "LiebermanAidenHiC2009_0.44.0.tar.gz"}, "listeretalbsseq-1.38.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ListerEtAlBSseq_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/ListerEtAlBSseq_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-listeretalbsseq/bioconductor-listeretalbsseq_1.38.0_src_all.tar.gz"], "md5": "c985f67b2cfdb549d614ae350ac50029", "fn": "ListerEtAlBSseq_1.38.0.tar.gz"}, "lrcelltypemarkers-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/LRcellTypeMarkers_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/LRcellTypeMarkers_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lrcelltypemarkers/bioconductor-lrcelltypemarkers_1.14.0_src_all.tar.gz"], "md5": "1acc45444ff327ed8d97526b019d5369", "fn": "LRcellTypeMarkers_1.14.0.tar.gz"}, "lumibarnes-1.46.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/lumiBarnes_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/lumiBarnes_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lumibarnes/bioconductor-lumibarnes_1.46.0_src_all.tar.gz"], "md5": "a91894c192736dabcdd81493fd693d6a", "fn": "lumiBarnes_1.46.0.tar.gz"}, "lungcanceracvssccgeo-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/LungCancerACvsSCCGEO_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/LungCancerACvsSCCGEO_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungcanceracvssccgeo/bioconductor-lungcanceracvssccgeo_1.42.0_src_all.tar.gz"], "md5": "e6408dab179c36800a5a9f501c20b6f5", "fn": "LungCancerACvsSCCGEO_1.42.0.tar.gz"}, "lungcancerlines-0.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/LungCancerLines_0.44.0.tar.gz", "https://bioarchive.galaxyproject.org/LungCancerLines_0.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungcancerlines/bioconductor-lungcancerlines_0.44.0_src_all.tar.gz"], "md5": "cbedb747be0dc1ed37072304b42e29cb", "fn": "LungCancerLines_0.44.0.tar.gz"}, "lungexpression-0.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/lungExpression_0.44.0.tar.gz", "https://bioarchive.galaxyproject.org/lungExpression_0.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lungexpression/bioconductor-lungexpression_0.44.0_src_all.tar.gz"], "md5": "51b928a75488636d40016a51e9fe0f40", "fn": "lungExpression_0.44.0.tar.gz"}, "lydata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/lydata_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/lydata_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-lydata/bioconductor-lydata_1.32.0_src_all.tar.gz"], "md5": "1f492ef0a9ea66a511aef7b9c0fc8ce8", "fn": "lydata_1.32.0.tar.gz"}, "m3dexampledata-1.32.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/M3DExampleData_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/M3DExampleData_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-m3dexampledata/bioconductor-m3dexampledata_1.32.0_src_all.tar.gz"], "md5": "b277ae479790377a52b91adb72f9f916", "fn": "M3DExampleData_1.32.0.tar.gz"}, "macrophage-1.22.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/macrophage_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/macrophage_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-macrophage/bioconductor-macrophage_1.22.0_src_all.tar.gz"], "md5": "0782d719de282a1fb033344185c2d3ff", "fn": "macrophage_1.22.0.tar.gz"}, "macsdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MACSdata_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/MACSdata_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-macsdata/bioconductor-macsdata_1.14.0_src_all.tar.gz"], "md5": "ad077b7b288ff5fec2b011453af70aad", "fn": "MACSdata_1.14.0.tar.gz"}, "mammaprintdata-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/mammaPrintData_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/mammaPrintData_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mammaprintdata/bioconductor-mammaprintdata_1.42.0_src_all.tar.gz"], "md5": "698b5dfa798c98b7d8478b23fbfeb560", "fn": "mammaPrintData_1.42.0.tar.gz"}, "maqcexpression4plex-1.50.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/maqcExpression4plex_1.50.0.tar.gz", "https://bioarchive.galaxyproject.org/maqcExpression4plex_1.50.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcexpression4plex/bioconductor-maqcexpression4plex_1.50.0_src_all.tar.gz"], "md5": "898e52d569cdc046e620e674ece0104f", "fn": "maqcExpression4plex_1.50.0.tar.gz"}, "maqcsubset-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MAQCsubset_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/MAQCsubset_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-maqcsubset/bioconductor-maqcsubset_1.44.0_src_all.tar.gz"], "md5": "c65a03cafbb8d0d6a644a491d0516f7a", "fn": "MAQCsubset_1.44.0.tar.gz"}, "marinerdata-1.6.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/marinerData_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/marinerData_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-marinerdata/bioconductor-marinerdata_1.6.0_src_all.tar.gz"], "md5": "a107161ab0d78f794f5088aa17e219bc", "fn": "marinerData_1.6.0.tar.gz"}, "mcseadata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/mCSEAdata_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/mCSEAdata_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcseadata/bioconductor-mcseadata_1.26.0_src_all.tar.gz"], "md5": "74984aaa639100dac5d0a4ddbc2fa08c", "fn": "mCSEAdata_1.26.0.tar.gz"}, "mcsurvdata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/mcsurvdata_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/mcsurvdata_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcsurvdata/bioconductor-mcsurvdata_1.24.0_src_all.tar.gz"], "md5": "9195686975c6647629ceed2276471756", "fn": "mcsurvdata_1.24.0.tar.gz"}, "medipsdata-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MEDIPSData_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/MEDIPSData_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-medipsdata/bioconductor-medipsdata_1.42.0_src_all.tar.gz"], "md5": "7c0968e7c9e258a93e85879626e3e08a", "fn": "MEDIPSData_1.42.0.tar.gz"}, "meebodata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MEEBOdata_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/MEEBOdata_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-meebodata/bioconductor-meebodata_1.44.0_src_all.tar.gz"], "md5": "85b931867f6b8761f474e911d7632f86", "fn": "MEEBOdata_1.44.0.tar.gz"}, "merfishdata-1.7.1": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MerfishData_1.7.1.tar.gz", "https://bioarchive.galaxyproject.org/MerfishData_1.7.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-merfishdata/bioconductor-merfishdata_1.7.1_src_all.tar.gz"], "md5": "ecfdf0daad174834c84f024ebc71129c", "fn": "MerfishData_1.7.1.tar.gz"}, "metagxbreast-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MetaGxBreast_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxBreast_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxbreast/bioconductor-metagxbreast_1.26.0_src_all.tar.gz"], "md5": "6022b5352915c1777c7c600ffc2cc86c", "fn": "MetaGxBreast_1.26.0.tar.gz"}, "metagxovarian-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MetaGxOvarian_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxOvarian_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxovarian/bioconductor-metagxovarian_1.26.0_src_all.tar.gz"], "md5": "aa02381feac47d0d6a29bfa33249caf1", "fn": "MetaGxOvarian_1.26.0.tar.gz"}, "metagxpancreas-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MetaGxPancreas_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/MetaGxPancreas_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metagxpancreas/bioconductor-metagxpancreas_1.26.0_src_all.tar.gz"], "md5": "a662c1634949436c2fe455a8d59abb07", "fn": "MetaGxPancreas_1.26.0.tar.gz"}, "metamsdata-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/metaMSdata_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/metaMSdata_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metamsdata/bioconductor-metamsdata_1.42.0_src_all.tar.gz"], "md5": "a7a51ec5456a74897baff56060a85fae", "fn": "metaMSdata_1.42.0.tar.gz"}, "metascope-1.5.4": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MetaScope_1.5.4.tar.gz", "https://bioarchive.galaxyproject.org/MetaScope_1.5.4.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-metascope/bioconductor-metascope_1.5.4_src_all.tar.gz"], "md5": "d3f60d78fb0987fa182b408d6a83fe8b", "fn": "MetaScope_1.5.4.tar.gz"}, "methylaiddata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MethylAidData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/MethylAidData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylaiddata/bioconductor-methylaiddata_1.38.0_src_all.tar.gz"], "md5": "8790cb85810d6013ce273669a726c75e", "fn": "MethylAidData_1.38.0.tar.gz"}, "methylclockdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/methylclockData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/methylclockData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylclockdata/bioconductor-methylclockdata_1.14.0_src_all.tar.gz"], "md5": "ad071093db338056dbd6cf1951640286", "fn": "methylclockData_1.14.0.tar.gz"}, "methylseqdata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MethylSeqData_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/MethylSeqData_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-methylseqdata/bioconductor-methylseqdata_1.16.0_src_all.tar.gz"], "md5": "16f7382e59811b9cead8c141c39d0b5f", "fn": "MethylSeqData_1.16.0.tar.gz"}, "microbiomebenchmarkdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MicrobiomeBenchmarkData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/MicrobiomeBenchmarkData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-microbiomebenchmarkdata/bioconductor-microbiomebenchmarkdata_1.8.0_src_all.tar.gz"], "md5": "f0c2276607641ceeab25744f8b83fad9", "fn": "MicrobiomeBenchmarkData_1.8.0.tar.gz"}, "microbiomedatasets-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/microbiomeDataSets_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/microbiomeDataSets_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-microbiomedatasets/bioconductor-microbiomedatasets_1.14.0_src_all.tar.gz"], "md5": "df3b92fa8bb2edd4cb6b98d4d6215542", "fn": "microbiomeDataSets_1.14.0.tar.gz"}, "micrornaome-1.28.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/microRNAome_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/microRNAome_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-micrornaome/bioconductor-micrornaome_1.28.0_src_all.tar.gz"], "md5": "e1eeee6effefa7c38c24ac14ccdbb9c1", "fn": "microRNAome_1.28.0.tar.gz"}, "minfidata-0.52.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/minfiData_0.52.0.tar.gz", "https://bioarchive.galaxyproject.org/minfiData_0.52.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minfidata/bioconductor-minfidata_0.52.0_src_all.tar.gz"], "md5": "8a4cef6c4c950cfa8c6484c289a084c1", "fn": "minfiData_0.52.0.tar.gz"}, "minfidataepic-1.32.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/minfiDataEPIC_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/minfiDataEPIC_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minfidataepic/bioconductor-minfidataepic_1.32.0_src_all.tar.gz"], "md5": "ee3086e570c8bb7a0283e30d3e9d06a6", "fn": "minfiDataEPIC_1.32.0.tar.gz"}, "minionsummarydata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/minionSummaryData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/minionSummaryData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-minionsummarydata/bioconductor-minionsummarydata_1.36.0_src_all.tar.gz"], "md5": "46fb1c1bc260bfa260fc0935ca887972", "fn": "minionSummaryData_1.36.0.tar.gz"}, "mircompdata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/miRcompData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/miRcompData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mircompdata/bioconductor-mircompdata_1.36.0_src_all.tar.gz"], "md5": "c4ca934e422f56d80d298f8f51a82aa8", "fn": "miRcompData_1.36.0.tar.gz"}, "mirnatarget-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/miRNATarget_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/miRNATarget_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mirnatarget/bioconductor-mirnatarget_1.44.0_src_all.tar.gz"], "md5": "c31b5caacb79947f7bc47db42c9931d0", "fn": "miRNATarget_1.44.0.tar.gz"}, "mmdiffbamsubset-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MMDiffBamSubset_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/MMDiffBamSubset_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mmdiffbamsubset/bioconductor-mmdiffbamsubset_1.42.0_src_all.tar.gz"], "md5": "d8195c879ffc8680c7eb2b3ca6dd690d", "fn": "MMDiffBamSubset_1.42.0.tar.gz"}, "mofadata-1.22.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MOFAdata_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/MOFAdata_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mofadata/bioconductor-mofadata_1.22.0_src_all.tar.gz"], "md5": "3f8a0f3d03b4fa72d75a782592539c5c", "fn": "MOFAdata_1.22.0.tar.gz"}, "mosaicsexample-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/mosaicsExample_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/mosaicsExample_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mosaicsexample/bioconductor-mosaicsexample_1.44.0_src_all.tar.gz"], "md5": "8e41d96ae8a0d1cc915db718a0dfd2a7", "fn": "mosaicsExample_1.44.0.tar.gz"}, "mouse4302barcodevecs-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/mouse4302barcodevecs_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/mouse4302barcodevecs_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouse4302barcodevecs/bioconductor-mouse4302barcodevecs_1.44.0_src_all.tar.gz"], "md5": "9f4d2c9dfa9224f36db3c05fa37d8a85", "fn": "mouse4302barcodevecs_1.44.0.tar.gz"}, "mouseagingdata-1.1.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MouseAgingData_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/MouseAgingData_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mouseagingdata/bioconductor-mouseagingdata_1.1.0_src_all.tar.gz"], "md5": "acd4c0fd89a012f414d50c8266a0ad43", "fn": "MouseAgingData_1.1.0.tar.gz"}, "mousegastrulationdata-1.19.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MouseGastrulationData_1.19.0.tar.gz", "https://bioarchive.galaxyproject.org/MouseGastrulationData_1.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousegastrulationdata/bioconductor-mousegastrulationdata_1.19.0_src_all.tar.gz"], "md5": "16126f4e927357245915ba465dcd34e3", "fn": "MouseGastrulationData_1.19.0.tar.gz"}, "mousethymusageing-1.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MouseThymusAgeing_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/MouseThymusAgeing_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mousethymusageing/bioconductor-mousethymusageing_1.13.0_src_all.tar.gz"], "md5": "99ea8978220d8b887a917005eb990533", "fn": "MouseThymusAgeing_1.13.0.tar.gz"}, "msd16s-1.25.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/msd16s_1.25.0.tar.gz", "https://bioarchive.galaxyproject.org/msd16s_1.25.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msd16s/bioconductor-msd16s_1.25.0_src_all.tar.gz"], "md5": "2f1e1f51527fd43615f898bc898357d1", "fn": "msd16s_1.25.0.tar.gz"}, "msdata-0.45.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/msdata_0.45.0.tar.gz", "https://bioarchive.galaxyproject.org/msdata_0.45.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msdata/bioconductor-msdata_0.45.0_src_all.tar.gz"], "md5": "857589a062cc24324f16c86b099639e4", "fn": "msdata_0.45.0.tar.gz"}, "msigdb-1.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/msigdb_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/msigdb_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msigdb/bioconductor-msigdb_1.13.0_src_all.tar.gz"], "md5": "54dadb02b9e61dad223aaa4f3e97d779", "fn": "msigdb_1.13.0.tar.gz"}, "msmb-1.24.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MSMB_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/MSMB_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msmb/bioconductor-msmb_1.24.0_src_all.tar.gz"], "md5": "5167cfe5c0b53d2cc730be93fb20218c", "fn": "MSMB_1.24.0.tar.gz"}, "mspuritydata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/msPurityData_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/msPurityData_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mspuritydata/bioconductor-mspuritydata_1.34.0_src_all.tar.gz"], "md5": "c167bd73ab7483ee04320b8a18824b03", "fn": "msPurityData_1.34.0.tar.gz"}, "msqc1-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/msqc1_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/msqc1_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msqc1/bioconductor-msqc1_1.34.0_src_all.tar.gz"], "md5": "db71d1e332bca83be8180f47fab9bd14", "fn": "msqc1_1.34.0.tar.gz"}, "mtbls2-1.36.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/mtbls2_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/mtbls2_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mtbls2/bioconductor-mtbls2_1.36.0_src_all.tar.gz"], "md5": "79a28f68b38f98d6ce03a37e9c345eca", "fn": "mtbls2_1.36.0.tar.gz"}, "mugaexampledata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MUGAExampleData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/MUGAExampleData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mugaexampledata/bioconductor-mugaexampledata_1.26.0_src_all.tar.gz"], "md5": "d5088f4c87dbb3d54790d75dd7402dcc", "fn": "MUGAExampleData_1.26.0.tar.gz"}, "muleadata-1.1.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/muleaData_1.1.0.tar.gz", "https://bioarchive.galaxyproject.org/muleaData_1.1.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-muleadata/bioconductor-muleadata_1.1.0_src_all.tar.gz"], "md5": "49e3a05d1cbf9531269ba6bd3f80c95c", "fn": "muleaData_1.1.0.tar.gz"}, "multiwgcnadata-1.3.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/multiWGCNAdata_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/multiWGCNAdata_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-multiwgcnadata/bioconductor-multiwgcnadata_1.3.0_src_all.tar.gz"], "md5": "ca203d46da5d8a9297856339c6453178", "fn": "multiWGCNAdata_1.3.0.tar.gz"}, "muscdata-1.19.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/muscData_1.19.0.tar.gz", "https://bioarchive.galaxyproject.org/muscData_1.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-muscdata/bioconductor-muscdata_1.19.0_src_all.tar.gz"], "md5": "b755e80dc18c3213b147a32c54fa0755", "fn": "muscData_1.19.0.tar.gz"}, "nanoporernaseq-1.15.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/NanoporeRNASeq_1.15.0.tar.gz", "https://bioarchive.galaxyproject.org/NanoporeRNASeq_1.15.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nanoporernaseq/bioconductor-nanoporernaseq_1.15.0_src_all.tar.gz"], "md5": "62af5121b9015934e82a2cafeae598a2", "fn": "NanoporeRNASeq_1.15.0.tar.gz"}, "nanotubes-1.22.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/nanotubes_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/nanotubes_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nanotubes/bioconductor-nanotubes_1.22.0_src_all.tar.gz"], "md5": "e12d5b3c6facf1c6aa320715282de427", "fn": "nanotubes_1.22.0.tar.gz"}, "ncigraphdata-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/NCIgraphData_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/NCIgraphData_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ncigraphdata/bioconductor-ncigraphdata_1.42.0_src_all.tar.gz"], "md5": "10459d011efb985487e297cbe4b9ffac", "fn": "NCIgraphData_1.42.0.tar.gz"}, "nestlink-1.21.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/NestLink_1.21.0.tar.gz", "https://bioarchive.galaxyproject.org/NestLink_1.21.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nestlink/bioconductor-nestlink_1.21.0_src_all.tar.gz"], "md5": "6f32e7d9eaf0f8cdee734d13421a9523", "fn": "NestLink_1.21.0.tar.gz"}, "netactivitydata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/NetActivityData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/NetActivityData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-netactivitydata/bioconductor-netactivitydata_1.8.0_src_all.tar.gz"], "md5": "48e57fff0a0666f0e03312f686825c25", "fn": "NetActivityData_1.8.0.tar.gz"}, "neve2006-0.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/Neve2006_0.44.0.tar.gz", "https://bioarchive.galaxyproject.org/Neve2006_0.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-neve2006/bioconductor-neve2006_0.44.0_src_all.tar.gz"], "md5": "2728c25e8357e4a82c70e4f6a82b492d", "fn": "Neve2006_0.44.0.tar.gz"}, "ngscopydata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/NGScopyData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/NGScopyData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ngscopydata/bioconductor-ngscopydata_1.26.0_src_all.tar.gz"], "md5": "765a3d0f4a4c7faae9cfae3d1275f233", "fn": "NGScopyData_1.26.0.tar.gz"}, "nullrangesdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/nullrangesData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/nullrangesData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nullrangesdata/bioconductor-nullrangesdata_1.12.0_src_all.tar.gz"], "md5": "5fc9168190de6f06922ed63027aba161", "fn": "nullrangesData_1.12.0.tar.gz"}, "nxtirfdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/NxtIRFdata_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/NxtIRFdata_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nxtirfdata/bioconductor-nxtirfdata_1.12.0_src_all.tar.gz"], "md5": "74ae8288457bfc954fecd85de9b16580", "fn": "NxtIRFdata_1.12.0.tar.gz"}, "obmiti-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ObMiTi_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/ObMiTi_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-obmiti/bioconductor-obmiti_1.14.0_src_all.tar.gz"], "md5": "c207988f479ca296dbc34cab5399e2d7", "fn": "ObMiTi_1.14.0.tar.gz"}, "oct4-1.22.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/oct4_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/oct4_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-oct4/bioconductor-oct4_1.22.0_src_all.tar.gz"], "md5": "9a2784c2fdbf88a19542be9870628f76", "fn": "oct4_1.22.0.tar.gz"}, "octad.db-1.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/octad.db_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/octad.db_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-octad.db/bioconductor-octad.db_1.8.0_src_all.tar.gz"], "md5": "0afebff9d9a140dbdb280de68a39cc0e", "fn": "octad.db_1.8.0.tar.gz"}, "omicspcadata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/OMICsPCAdata_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/OMICsPCAdata_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-omicspcadata/bioconductor-omicspcadata_1.24.0_src_all.tar.gz"], "md5": "0662aa06eb12503247db63f9eb7589b2", "fn": "OMICsPCAdata_1.24.0.tar.gz"}, "onassisjavalibs-1.28.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/OnassisJavaLibs_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/OnassisJavaLibs_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-onassisjavalibs/bioconductor-onassisjavalibs_1.28.0_src_all.tar.gz"], "md5": "835d47c58d358149eaf643a280345200", "fn": "OnassisJavaLibs_1.28.0.tar.gz"}, "optimalflowdata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/optimalFlowData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/optimalFlowData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-optimalflowdata/bioconductor-optimalflowdata_1.18.0_src_all.tar.gz"], "md5": "55a3488bbc6c8f1d9caac07a42a513fb", "fn": "optimalFlowData_1.18.0.tar.gz"}, "orthosdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/orthosData_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/orthosData_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-orthosdata/bioconductor-orthosdata_1.4.0_src_all.tar.gz"], "md5": "31ec483008cbe76b4ad674381133bb91", "fn": "orthosData_1.4.0.tar.gz"}, "parathyroidse-1.43.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/parathyroidSE_1.43.0.tar.gz", "https://bioarchive.galaxyproject.org/parathyroidSE_1.43.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-parathyroidse/bioconductor-parathyroidse_1.43.0_src_all.tar.gz"], "md5": "1e65ae1c86ad412e58b32b4d4c697486", "fn": "parathyroidSE_1.43.0.tar.gz"}, "pasilla-1.33.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/pasilla_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/pasilla_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasilla/bioconductor-pasilla_1.33.0_src_all.tar.gz"], "md5": "9ef958e79b65ef073d95024663f64140", "fn": "pasilla_1.33.0.tar.gz"}, "pasillabamsubset-0.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/pasillaBamSubset_0.44.0.tar.gz", "https://bioarchive.galaxyproject.org/pasillaBamSubset_0.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasillabamsubset/bioconductor-pasillabamsubset_0.44.0_src_all.tar.gz"], "md5": "6c11c77d7bfecf2e07d1de5153c6f36f", "fn": "pasillaBamSubset_0.44.0.tar.gz"}, "pasillatranscriptexpr-1.33.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/PasillaTranscriptExpr_1.33.0.tar.gz", "https://bioarchive.galaxyproject.org/PasillaTranscriptExpr_1.33.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasillatranscriptexpr/bioconductor-pasillatranscriptexpr_1.33.0_src_all.tar.gz"], "md5": "90e4ec9cc4a2e56e8d096d3d45b6f5b0", "fn": "PasillaTranscriptExpr_1.33.0.tar.gz"}, "pathnetdata-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/PathNetData_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/PathNetData_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pathnetdata/bioconductor-pathnetdata_1.42.0_src_all.tar.gz"], "md5": "a253ad75c30b3b91a5069d7f270d16da", "fn": "PathNetData_1.42.0.tar.gz"}, "pchicdata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/PCHiCdata_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/PCHiCdata_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pchicdata/bioconductor-pchicdata_1.34.0_src_all.tar.gz"], "md5": "77d9d2d9ac8fb77a6c4824c15a0cac64", "fn": "PCHiCdata_1.34.0.tar.gz"}, "pd.atdschip.tiling-0.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/pd.atdschip.tiling_0.44.0.tar.gz", "https://bioarchive.galaxyproject.org/pd.atdschip.tiling_0.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pd.atdschip.tiling/bioconductor-pd.atdschip.tiling_0.44.0_src_all.tar.gz"], "md5": "738e3686e09fe6833e550da18e79328a", "fn": "pd.atdschip.tiling_0.44.0.tar.gz"}, "pepdat-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/pepDat_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/pepDat_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pepdat/bioconductor-pepdat_1.26.0_src_all.tar.gz"], "md5": "36b1a23bdd2410788bba91e2c156e869", "fn": "pepDat_1.26.0.tar.gz"}, "pepsnmrdata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/PepsNMRData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/PepsNMRData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pepsnmrdata/bioconductor-pepsnmrdata_1.24.0_src_all.tar.gz"], "md5": "015d1ec6d08d8544d1d1c21de64d61ac", "fn": "PepsNMRData_1.24.0.tar.gz"}, "phyloprofiledata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/PhyloProfileData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/PhyloProfileData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-phyloprofiledata/bioconductor-phyloprofiledata_1.20.0_src_all.tar.gz"], "md5": "c90f4558af49b28657028abe5d402f4f", "fn": "PhyloProfileData_1.20.0.tar.gz"}, "plotgardenerdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/plotgardenerData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/plotgardenerData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-plotgardenerdata/bioconductor-plotgardenerdata_1.12.0_src_all.tar.gz"], "md5": "4404a379e2a65bf165af4d5e434341ca", "fn": "plotgardenerData_1.12.0.tar.gz"}, "prebsdata-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/prebsdata_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/prebsdata_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prebsdata/bioconductor-prebsdata_1.42.0_src_all.tar.gz"], "md5": "fbab2ecd59d9a1dc6f3e106f8ad9ffc4", "fn": "prebsdata_1.42.0.tar.gz"}, "precisetadhub-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/preciseTADhub_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/preciseTADhub_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-precisetadhub/bioconductor-precisetadhub_1.14.0_src_all.tar.gz"], "md5": "695ed7dbc12e20c3f6bd9484fdfb309b", "fn": "preciseTADhub_1.14.0.tar.gz"}, "predasampledata-0.46.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/PREDAsampledata_0.46.0.tar.gz", "https://bioarchive.galaxyproject.org/PREDAsampledata_0.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-predasampledata/bioconductor-predasampledata_0.46.0_src_all.tar.gz"], "md5": "05358c3ac8d86e34a872c1105f66fc33", "fn": "PREDAsampledata_0.46.0.tar.gz"}, "prodata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ProData_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/ProData_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prodata/bioconductor-prodata_1.44.0_src_all.tar.gz"], "md5": "6ada21309a6f88bf79e69a563a8b4c86", "fn": "ProData_1.44.0.tar.gz"}, "prolocdata-1.43.1": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/pRolocdata_1.43.1.tar.gz", "https://bioarchive.galaxyproject.org/pRolocdata_1.43.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prolocdata/bioconductor-prolocdata_1.43.1_src_all.tar.gz"], "md5": "4b8aade9f26846dd6103643dbb59d66d", "fn": "pRolocdata_1.43.1.tar.gz"}, "prostatecancercamcap-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/prostateCancerCamcap_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerCamcap_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancercamcap/bioconductor-prostatecancercamcap_1.34.0_src_all.tar.gz"], "md5": "5dfbd00d06352a039fbc0c1a91837731", "fn": "prostateCancerCamcap_1.34.0.tar.gz"}, "prostatecancergrasso-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/prostateCancerGrasso_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerGrasso_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancergrasso/bioconductor-prostatecancergrasso_1.34.0_src_all.tar.gz"], "md5": "7c020aa40d54f0633ed989b8de1126af", "fn": "prostateCancerGrasso_1.34.0.tar.gz"}, "prostatecancerstockholm-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/prostateCancerStockholm_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerStockholm_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancerstockholm/bioconductor-prostatecancerstockholm_1.34.0_src_all.tar.gz"], "md5": "dff545fcd888a091cdbce5b71aef45a9", "fn": "prostateCancerStockholm_1.34.0.tar.gz"}, "prostatecancertaylor-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/prostateCancerTaylor_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerTaylor_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancertaylor/bioconductor-prostatecancertaylor_1.34.0_src_all.tar.gz"], "md5": "4f8e97c1c1a342e44b183018b870b508", "fn": "prostateCancerTaylor_1.34.0.tar.gz"}, "prostatecancervarambally-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/prostateCancerVarambally_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/prostateCancerVarambally_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prostatecancervarambally/bioconductor-prostatecancervarambally_1.34.0_src_all.tar.gz"], "md5": "fb2f47a16abe1e3bba18ad518a17815f", "fn": "prostateCancerVarambally_1.34.0.tar.gz"}, "proteingymr-1.0.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ProteinGymR_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/ProteinGymR_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-proteingymr/bioconductor-proteingymr_1.0.0_src_all.tar.gz"], "md5": "d7be5eeec1cc0645e89670a68fcef3d3", "fn": "ProteinGymR_1.0.0.tar.gz"}, "ptairdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ptairData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/ptairData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ptairdata/bioconductor-ptairdata_1.14.0_src_all.tar.gz"], "md5": "0197eba91d104f6fad9cd91e98f7c03b", "fn": "ptairData_1.14.0.tar.gz"}, "pth2o2lipids-1.32.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/PtH2O2lipids_1.32.0.tar.gz", "https://bioarchive.galaxyproject.org/PtH2O2lipids_1.32.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pth2o2lipids/bioconductor-pth2o2lipids_1.32.0_src_all.tar.gz"], "md5": "2136bebfb44a436fdb84d3e40f8bf23a", "fn": "PtH2O2lipids_1.32.0.tar.gz"}, "pumadata-2.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/pumadata_2.42.0.tar.gz", "https://bioarchive.galaxyproject.org/pumadata_2.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pumadata/bioconductor-pumadata_2.42.0_src_all.tar.gz"], "md5": "1ea3a80569c46dd7c018c794284601f2", "fn": "pumadata_2.42.0.tar.gz"}, "pwmenrich.dmelanogaster.background-4.40.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/PWMEnrich.Dmelanogaster.background_4.40.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Dmelanogaster.background_4.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.dmelanogaster.background/bioconductor-pwmenrich.dmelanogaster.background_4.40.0_src_all.tar.gz"], "md5": "a8ce5a506cb9ccc09eb0e2825728b13d", "fn": "PWMEnrich.Dmelanogaster.background_4.40.0.tar.gz"}, "pwmenrich.hsapiens.background-4.40.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/PWMEnrich.Hsapiens.background_4.40.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Hsapiens.background_4.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.hsapiens.background/bioconductor-pwmenrich.hsapiens.background_4.40.0_src_all.tar.gz"], "md5": "53e1366ff04f7bb46e6e74958adabd0a", "fn": "PWMEnrich.Hsapiens.background_4.40.0.tar.gz"}, "pwmenrich.mmusculus.background-4.40.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/PWMEnrich.Mmusculus.background_4.40.0.tar.gz", "https://bioarchive.galaxyproject.org/PWMEnrich.Mmusculus.background_4.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.mmusculus.background/bioconductor-pwmenrich.mmusculus.background_4.40.0_src_all.tar.gz"], "md5": "b26f2429a164aa6030315248fc874210", "fn": "PWMEnrich.Mmusculus.background_4.40.0.tar.gz"}, "qdnaseq.hg19-1.36.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/QDNAseq.hg19_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/QDNAseq.hg19_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.hg19/bioconductor-qdnaseq.hg19_1.36.0_src_all.tar.gz"], "md5": "465422a4f1297d961ebd5ed5be39228d", "fn": "QDNAseq.hg19_1.36.0.tar.gz"}, "qdnaseq.mm10-1.36.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/QDNAseq.mm10_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/QDNAseq.mm10_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.mm10/bioconductor-qdnaseq.mm10_1.36.0_src_all.tar.gz"], "md5": "777629429e38d4c424de62579fa35b3b", "fn": "QDNAseq.mm10_1.36.0.tar.gz"}, "qplexdata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/qPLEXdata_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/qPLEXdata_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qplexdata/bioconductor-qplexdata_1.24.0_src_all.tar.gz"], "md5": "91470ae70dda6162161bd64ffb7cb9b2", "fn": "qPLEXdata_1.24.0.tar.gz"}, "qubicdata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/QUBICdata_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/QUBICdata_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-qubicdata/bioconductor-qubicdata_1.34.0_src_all.tar.gz"], "md5": "c69aac772f8adcd444c82b2fa37605e1", "fn": "QUBICdata_1.34.0.tar.gz"}, "raerdata-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/raerdata_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/raerdata_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-raerdata/bioconductor-raerdata_1.4.0_src_all.tar.gz"], "md5": "d23f3d1df443467be1f57d2e9c6f4deb", "fn": "raerdata_1.4.0.tar.gz"}, "rcellminerdata-2.28.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/rcellminerData_2.28.0.tar.gz", "https://bioarchive.galaxyproject.org/rcellminerData_2.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rcellminerdata/bioconductor-rcellminerdata_2.28.0_src_all.tar.gz"], "md5": "bd3a4c4313595d2fdff46bcbafd61eca", "fn": "rcellminerData_2.28.0.tar.gz"}, "rcistarget.hg19.motifdbs.cisbponly.500bp-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp_1.26.0_src_all.tar.gz"], "md5": "f95b8be5e180ae1207c328a9255145f4", "fn": "RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.26.0.tar.gz"}, "reactomegsa.data-1.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/ReactomeGSA.data_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/ReactomeGSA.data_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-reactomegsa.data/bioconductor-reactomegsa.data_1.20.0_src_all.tar.gz"], "md5": "f81cfbbd26d41eb728363bdc5b8d2f8c", "fn": "ReactomeGSA.data_1.20.0.tar.gz"}, "regparallel-1.24.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RegParallel_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/RegParallel_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-regparallel/bioconductor-regparallel_1.24.0_src_all.tar.gz"], "md5": "dc949c5ebd514bd0020a203585bba26b", "fn": "RegParallel_1.24.0.tar.gz"}, "rforproteomics-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RforProteomics_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/RforProteomics_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rforproteomics/bioconductor-rforproteomics_1.44.0_src_all.tar.gz"], "md5": "8c73b19d4642edded08e28a0c194d2e1", "fn": "RforProteomics_1.44.0.tar.gz"}, "rgmqllib-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RGMQLlib_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/RGMQLlib_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rgmqllib/bioconductor-rgmqllib_1.26.0_src_all.tar.gz"], "md5": "93c5a7fd1d93d309300ab5a679790507", "fn": "RGMQLlib_1.26.0.tar.gz"}, "rheumaticconditionwollbold-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/rheumaticConditionWOLLBOLD_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/rheumaticConditionWOLLBOLD_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rheumaticconditionwollbold/bioconductor-rheumaticconditionwollbold_1.44.0_src_all.tar.gz"], "md5": "c9b78e6ccf15509071a4c8b6167eb3eb", "fn": "rheumaticConditionWOLLBOLD_1.44.0.tar.gz"}, "ritandata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RITANdata_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/RITANdata_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ritandata/bioconductor-ritandata_1.30.0_src_all.tar.gz"], "md5": "5636c146679aece62409941126b1b162", "fn": "RITANdata_1.30.0.tar.gz"}, "rmassbankdata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RMassBankData_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/RMassBankData_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rmassbankdata/bioconductor-rmassbankdata_1.44.0_src_all.tar.gz"], "md5": "d1aa782369d4a3b48f49343eaf62fe48", "fn": "RMassBankData_1.44.0.tar.gz"}, "rnainteractmapk-1.41.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RNAinteractMAPK_1.41.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAinteractMAPK_1.41.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnainteractmapk/bioconductor-rnainteractmapk_1.41.0_src_all.tar.gz"], "md5": "41bafca51c673429835afbcf60b89454", "fn": "RNAinteractMAPK_1.41.0.tar.gz"}, "rnamodr.data-1.19.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RNAmodR.Data_1.19.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAmodR.Data_1.19.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnamodr.data/bioconductor-rnamodr.data_1.19.0_src_all.tar.gz"], "md5": "b8b56a5e310771c78f3076d338eaeb02", "fn": "RNAmodR.Data_1.19.0.tar.gz"}, "rnaseqdata.hnrnpc.bam.chr14-0.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RNAseqData.HNRNPC.bam.chr14_0.44.0.tar.gz", "https://bioarchive.galaxyproject.org/RNAseqData.HNRNPC.bam.chr14_0.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqdata.hnrnpc.bam.chr14/bioconductor-rnaseqdata.hnrnpc.bam.chr14_0.44.0_src_all.tar.gz"], "md5": "aa012879d391a2c536ccaa7fb16862f7", "fn": "RNAseqData.HNRNPC.bam.chr14_0.44.0.tar.gz"}, "rnaseqsamplesizedata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RnaSeqSampleSizeData_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/RnaSeqSampleSizeData_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnaseqsamplesizedata/bioconductor-rnaseqsamplesizedata_1.38.0_src_all.tar.gz"], "md5": "806d652a73359e09fe4c124dacb85507", "fn": "RnaSeqSampleSizeData_1.38.0.tar.gz"}, "rnbeads.hg19-1.38.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RnBeads.hg19_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.hg19_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg19/bioconductor-rnbeads.hg19_1.38.0_src_all.tar.gz"], "md5": "cb644f72ba6539bec603163702cd0162", "fn": "RnBeads.hg19_1.38.0.tar.gz"}, "rnbeads.hg38-1.38.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RnBeads.hg38_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.hg38_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg38/bioconductor-rnbeads.hg38_1.38.0_src_all.tar.gz"], "md5": "43ecf19a9513772a76d0470d1dae9366", "fn": "RnBeads.hg38_1.38.0.tar.gz"}, "rnbeads.mm10-2.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RnBeads.mm10_2.14.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.mm10_2.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm10/bioconductor-rnbeads.mm10_2.14.0_src_all.tar.gz"], "md5": "ccb483fc635f66ae10551ddb55bcbd3b", "fn": "RnBeads.mm10_2.14.0.tar.gz"}, "rnbeads.mm9-1.38.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RnBeads.mm9_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.mm9_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm9/bioconductor-rnbeads.mm9_1.38.0_src_all.tar.gz"], "md5": "caa3adcbf9caa032ac80937e9f93d1d3", "fn": "RnBeads.mm9_1.38.0.tar.gz"}, "rnbeads.rn5-1.38.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RnBeads.rn5_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/RnBeads.rn5_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rnbeads.rn5/bioconductor-rnbeads.rn5_1.38.0_src_all.tar.gz"], "md5": "e07ef02cf744ae07ef1fa429005280f5", "fn": "RnBeads.rn5_1.38.0.tar.gz"}, "rrbsdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RRBSdata_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/RRBSdata_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rrbsdata/bioconductor-rrbsdata_1.26.0_src_all.tar.gz"], "md5": "ac09dd08a5f708241944185cac584cae", "fn": "RRBSdata_1.26.0.tar.gz"}, "rrdpdata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/rRDPData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/rRDPData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rrdpdata/bioconductor-rrdpdata_1.26.0_src_all.tar.gz"], "md5": "fa19b2b3f0f17eca244b65480bce1ddd", "fn": "rRDPData_1.26.0.tar.gz"}, "rtcga.clinical-20151101.36.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RTCGA.clinical_20151101.36.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.clinical_20151101.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.clinical/bioconductor-rtcga.clinical_20151101.36.0_src_all.tar.gz"], "md5": "cccba079e0c1ad585e69e976dd71927b", "fn": "RTCGA.clinical_20151101.36.0.tar.gz"}, "rtcga.cnv-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RTCGA.CNV_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.CNV_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.cnv/bioconductor-rtcga.cnv_1.34.0_src_all.tar.gz"], "md5": "bb5c72be005d63b713116dca5c820eb2", "fn": "RTCGA.CNV_1.34.0.tar.gz"}, "rtcga.methylation-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RTCGA.methylation_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.methylation_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.methylation/bioconductor-rtcga.methylation_1.34.0_src_all.tar.gz"], "md5": "604a06aaf5996979357d6a255ef8a48e", "fn": "RTCGA.methylation_1.34.0.tar.gz"}, "rtcga.mirnaseq-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RTCGA.miRNASeq_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.miRNASeq_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mirnaseq/bioconductor-rtcga.mirnaseq_1.34.0_src_all.tar.gz"], "md5": "559ca4b4c3d24d5f545dbfc0649fdf84", "fn": "RTCGA.miRNASeq_1.34.0.tar.gz"}, "rtcga.mrna-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RTCGA.mRNA_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.mRNA_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mrna/bioconductor-rtcga.mrna_1.34.0_src_all.tar.gz"], "md5": "1adff9c1adfebeee25b3bd907467c3e5", "fn": "RTCGA.mRNA_1.34.0.tar.gz"}, "rtcga.mutations-20151101.36.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RTCGA.mutations_20151101.36.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.mutations_20151101.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.mutations/bioconductor-rtcga.mutations_20151101.36.0_src_all.tar.gz"], "md5": "b9efa7c97e496294c8867d9d6f615451", "fn": "RTCGA.mutations_20151101.36.0.tar.gz"}, "rtcga.pancan12-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RTCGA.PANCAN12_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.PANCAN12_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.pancan12/bioconductor-rtcga.pancan12_1.34.0_src_all.tar.gz"], "md5": "0efe506e10b90bfe638f397568f4ece9", "fn": "RTCGA.PANCAN12_1.34.0.tar.gz"}, "rtcga.rnaseq-20151101.36.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RTCGA.rnaseq_20151101.36.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.rnaseq_20151101.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.rnaseq/bioconductor-rtcga.rnaseq_20151101.36.0_src_all.tar.gz"], "md5": "83acecb23e87c7b053d904279ada3512", "fn": "RTCGA.rnaseq_20151101.36.0.tar.gz"}, "rtcga.rppa-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RTCGA.RPPA_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/RTCGA.RPPA_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-rtcga.rppa/bioconductor-rtcga.rppa_1.34.0_src_all.tar.gz"], "md5": "d1264823bcf1bb89103b73f31c00e376", "fn": "RTCGA.RPPA_1.34.0.tar.gz"}, "ruvnormalizedata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RUVnormalizeData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/RUVnormalizeData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ruvnormalizedata/bioconductor-ruvnormalizedata_1.26.0_src_all.tar.gz"], "md5": "01b2d1a2ab2ff4433e5b3f64abdf3f43", "fn": "RUVnormalizeData_1.26.0.tar.gz"}, "sampleclassifierdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/sampleClassifierData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/sampleClassifierData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sampleclassifierdata/bioconductor-sampleclassifierdata_1.30.0_src_all.tar.gz"], "md5": "dbda361a9401f68ae3935368e7555135", "fn": "sampleClassifierData_1.30.0.tar.gz"}, "sbgnview.data-1.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/SBGNview.data_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/SBGNview.data_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sbgnview.data/bioconductor-sbgnview.data_1.20.0_src_all.tar.gz"], "md5": "bccffd0ac4bad51dd8d5d2f78b4a84a0", "fn": "SBGNview.data_1.20.0.tar.gz"}, "scaedata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/scaeData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/scaeData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scaedata/bioconductor-scaedata_1.2.0_src_all.tar.gz"], "md5": "bd842cf1587a0264a124ee24ef5025cf", "fn": "scaeData_1.2.0.tar.gz"}, "scanmirdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/scanMiRData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/scanMiRData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scanmirdata/bioconductor-scanmirdata_1.12.0_src_all.tar.gz"], "md5": "b003e73d86828d212a916bba13912ca6", "fn": "scanMiRData_1.12.0.tar.gz"}, "scatac.explorer-1.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/scATAC.Explorer_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/scATAC.Explorer_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scatac.explorer/bioconductor-scatac.explorer_1.12.0_src_all.tar.gz"], "md5": "5a6a5b6b4e2bdc79e5b6352d36928ad3", "fn": "scATAC.Explorer_1.12.0.tar.gz"}, "sclcbam-1.38.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/SCLCBam_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/SCLCBam_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sclcbam/bioconductor-sclcbam_1.38.0_src_all.tar.gz"], "md5": "2e1013ff182c81e75551154d3849aa06", "fn": "SCLCBam_1.38.0.tar.gz"}, "scmultiome-1.6.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/scMultiome_1.6.0.tar.gz", "https://bioarchive.galaxyproject.org/scMultiome_1.6.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scmultiome/bioconductor-scmultiome_1.6.0_src_all.tar.gz"], "md5": "64a106794e0af59f4249dba3124aaed3", "fn": "scMultiome_1.6.0.tar.gz"}, "scpdata-1.13.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/scpdata_1.13.0.tar.gz", "https://bioarchive.galaxyproject.org/scpdata_1.13.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scpdata/bioconductor-scpdata_1.13.0_src_all.tar.gz"], "md5": "9a026357adcb402892f64764ad09a6a6", "fn": "scpdata_1.13.0.tar.gz"}, "scrnaseq-2.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/scRNAseq_2.20.0.tar.gz", "https://bioarchive.galaxyproject.org/scRNAseq_2.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scrnaseq/bioconductor-scrnaseq_2.20.0_src_all.tar.gz"], "md5": "9712b05cec1dd4c33c67fffa06e3257d", "fn": "scRNAseq_2.20.0.tar.gz"}, "scthi.data-1.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/scTHI.data_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/scTHI.data_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scthi.data/bioconductor-scthi.data_1.18.0_src_all.tar.gz"], "md5": "c4e56ab66669c550520df2fb0ad688b1", "fn": "scTHI.data_1.18.0.tar.gz"}, "seq2pathway.data-1.38.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/seq2pathway.data_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/seq2pathway.data_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seq2pathway.data/bioconductor-seq2pathway.data_1.38.0_src_all.tar.gz"], "md5": "56fcfc87bf877f64ff1283275f37ab73", "fn": "seq2pathway.data_1.38.0.tar.gz"}, "seqc-1.40.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/seqc_1.40.0.tar.gz", "https://bioarchive.galaxyproject.org/seqc_1.40.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seqc/bioconductor-seqc_1.40.0_src_all.tar.gz"], "md5": "36346eaad47ac3ef20ae0b8979145247", "fn": "seqc_1.40.0.tar.gz"}, "serumstimulation-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/serumStimulation_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/serumStimulation_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-serumstimulation/bioconductor-serumstimulation_1.42.0_src_all.tar.gz"], "md5": "9ae60ca2091b47da1d3d887067f89135", "fn": "serumStimulation_1.42.0.tar.gz"}, "sesamedata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/sesameData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/sesameData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sesamedata/bioconductor-sesamedata_1.24.0_src_all.tar.gz"], "md5": "0e78ee4d14094d812a39b12167c8d747", "fn": "sesameData_1.24.0.tar.gz"}, "seventygenedata-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/seventyGeneData_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/seventyGeneData_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-seventygenedata/bioconductor-seventygenedata_1.42.0_src_all.tar.gz"], "md5": "0f1a3ab072300477276d2dc9bc5e16e4", "fn": "seventyGeneData_1.42.0.tar.gz"}, "sfedata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/SFEData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/SFEData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-sfedata/bioconductor-sfedata_1.8.0_src_all.tar.gz"], "md5": "0e1005c4fc1b0ca2bef593cffedb87d3", "fn": "SFEData_1.8.0.tar.gz"}, "shinymethyldata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/shinyMethylData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/shinyMethylData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-shinymethyldata/bioconductor-shinymethyldata_1.26.0_src_all.tar.gz"], "md5": "e27eb788611027ac6995ce44df9076f3", "fn": "shinyMethylData_1.26.0.tar.gz"}, "signaturesearchdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/signatureSearchData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/signatureSearchData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-signaturesearchdata/bioconductor-signaturesearchdata_1.20.0_src_all.tar.gz"], "md5": "98c11cb295e59f4f3caae25cdc4d616e", "fn": "signatureSearchData_1.20.0.tar.gz"}, "simbenchdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/SimBenchData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/SimBenchData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-simbenchdata/bioconductor-simbenchdata_1.14.0_src_all.tar.gz"], "md5": "3a786d414a97f00b39d6ab12811996ff", "fn": "SimBenchData_1.14.0.tar.gz"}, "simpintlists-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/simpIntLists_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/simpIntLists_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-simpintlists/bioconductor-simpintlists_1.42.0_src_all.tar.gz"], "md5": "22e154a884965c1309c378abc80c602a", "fn": "simpIntLists_1.42.0.tar.gz"}, "single.mtec.transcriptomes-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/Single.mTEC.Transcriptomes_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/Single.mTEC.Transcriptomes_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-single.mtec.transcriptomes/bioconductor-single.mtec.transcriptomes_1.34.0_src_all.tar.gz"], "md5": "5b2e48b74d9d995d70016366038e5a9d", "fn": "Single.mTEC.Transcriptomes_1.34.0.tar.gz"}, "singlecellmultimodal-1.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/SingleCellMultiModal_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/SingleCellMultiModal_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-singlecellmultimodal/bioconductor-singlecellmultimodal_1.18.0_src_all.tar.gz"], "md5": "61f436e43d8121f6eef92a6e9445e96f", "fn": "SingleCellMultiModal_1.18.0.tar.gz"}, "singlemoleculefootprintingdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/SingleMoleculeFootprintingData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/SingleMoleculeFootprintingData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-singlemoleculefootprintingdata/bioconductor-singlemoleculefootprintingdata_1.14.0_src_all.tar.gz"], "md5": "202e6ff943df3b9150db62ee77671784", "fn": "SingleMoleculeFootprintingData_1.14.0.tar.gz"}, "smokingmouse-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/smokingMouse_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/smokingMouse_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-smokingmouse/bioconductor-smokingmouse_1.4.0_src_all.tar.gz"], "md5": "7a530bd77d1c17a739dd2e070ed1f4b8", "fn": "smokingMouse_1.4.0.tar.gz"}, "snadata-1.52.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/SNAData_1.52.0.tar.gz", "https://bioarchive.galaxyproject.org/SNAData_1.52.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snadata/bioconductor-snadata_1.52.0_src_all.tar.gz"], "md5": "37724640b8892123d6e4fd6f426a2461", "fn": "SNAData_1.52.0.tar.gz"}, "snageedata-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/SNAGEEdata_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/SNAGEEdata_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snageedata/bioconductor-snageedata_1.42.0_src_all.tar.gz"], "md5": "ad1629bee4e1cb85c3dfe006369b272e", "fn": "SNAGEEdata_1.42.0.tar.gz"}, "snphooddata-1.36.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/SNPhoodData_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/SNPhoodData_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-snphooddata/bioconductor-snphooddata_1.36.0_src_all.tar.gz"], "md5": "66d3827ba213bcbf04e5cde90529f975", "fn": "SNPhoodData_1.36.0.tar.gz"}, "somaticadata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/SomatiCAData_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/SomatiCAData_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-somaticadata/bioconductor-somaticadata_1.44.0_src_all.tar.gz"], "md5": "5376764d2b06ef447b96d362e80f5ad1", "fn": "SomatiCAData_1.44.0.tar.gz"}, "somaticcanceralterations-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/SomaticCancerAlterations_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/SomaticCancerAlterations_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-somaticcanceralterations/bioconductor-somaticcanceralterations_1.42.0_src_all.tar.gz"], "md5": "89c1936e44be3156ca5170d210806ad9", "fn": "SomaticCancerAlterations_1.42.0.tar.gz"}, "spatialdatasets-1.4.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/SpatialDatasets_1.4.0.tar.gz", "https://bioarchive.galaxyproject.org/SpatialDatasets_1.4.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatialdatasets/bioconductor-spatialdatasets_1.4.0_src_all.tar.gz"], "md5": "0d46aa02771cb1ca6428d46e88d89654", "fn": "SpatialDatasets_1.4.0.tar.gz"}, "spatialdmelxsim-1.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/spatialDmelxsim_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/spatialDmelxsim_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatialdmelxsim/bioconductor-spatialdmelxsim_1.12.0_src_all.tar.gz"], "md5": "3480463b7d6ea68d2755d643f65549be", "fn": "spatialDmelxsim_1.12.0.tar.gz"}, "spatiallibd-1.17.8": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/spatialLIBD_1.17.8.tar.gz", "https://bioarchive.galaxyproject.org/spatialLIBD_1.17.8.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatiallibd/bioconductor-spatiallibd_1.17.8_src_all.tar.gz"], "md5": "79dd91d330a1f0e646e464ddbb9f104d", "fn": "spatialLIBD_1.17.8.tar.gz"}, "spikein-1.48.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/SpikeIn_1.48.0.tar.gz", "https://bioarchive.galaxyproject.org/SpikeIn_1.48.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spikein/bioconductor-spikein_1.48.0_src_all.tar.gz"], "md5": "f3fe76424ae86180f43ef63bbeb06181", "fn": "SpikeIn_1.48.0.tar.gz"}, "spikeinsubset-1.46.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/SpikeInSubset_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/SpikeInSubset_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spikeinsubset/bioconductor-spikeinsubset_1.46.0_src_all.tar.gz"], "md5": "9f377e32d90cb3e23ae288363c767af7", "fn": "SpikeInSubset_1.46.0.tar.gz"}, "spqndata-1.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/spqnData_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/spqnData_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spqndata/bioconductor-spqndata_1.18.0_src_all.tar.gz"], "md5": "8366c866aac67ef93786d2f59a98d015", "fn": "spqnData_1.18.0.tar.gz"}, "stemhypoxia-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/stemHypoxia_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/stemHypoxia_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stemhypoxia/bioconductor-stemhypoxia_1.42.0_src_all.tar.gz"], "md5": "49bf6a9e4b05c1ae7841672ab7484457", "fn": "stemHypoxia_1.42.0.tar.gz"}, "stexampledata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/STexampleData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/STexampleData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-stexampledata/bioconductor-stexampledata_1.14.0_src_all.tar.gz"], "md5": "20e089ef88575b871a5e0edc17c520ca", "fn": "STexampleData_1.14.0.tar.gz"}, "subcellularspatialdata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/SubcellularSpatialData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/SubcellularSpatialData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-subcellularspatialdata/bioconductor-subcellularspatialdata_1.2.0_src_all.tar.gz"], "md5": "33c9b36b6b41c5ebeb5567b5c64aa5fb", "fn": "SubcellularSpatialData_1.2.0.tar.gz"}, "svm2crmdata-1.38.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/SVM2CRMdata_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/SVM2CRMdata_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-svm2crmdata/bioconductor-svm2crmdata_1.38.0_src_all.tar.gz"], "md5": "0a323250bb842533ddf675228e0ff0b7", "fn": "SVM2CRMdata_1.38.0.tar.gz"}, "synapterdata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/synapterdata_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/synapterdata_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-synapterdata/bioconductor-synapterdata_1.44.0_src_all.tar.gz"], "md5": "e13319e22eff32d961f703684f9a23dc", "fn": "synapterdata_1.44.0.tar.gz"}, "systempiperdata-2.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/systemPipeRdata_2.10.0.tar.gz", "https://bioarchive.galaxyproject.org/systemPipeRdata_2.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-systempiperdata/bioconductor-systempiperdata_2.10.0_src_all.tar.gz"], "md5": "73820a7b33a8d1df288467179c3d96cc", "fn": "systemPipeRdata_2.10.0.tar.gz"}, "tabulamurisdata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/TabulaMurisData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/TabulaMurisData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tabulamurisdata/bioconductor-tabulamurisdata_1.24.0_src_all.tar.gz"], "md5": "c1bd6839155817b5f01874ac53fe91cd", "fn": "TabulaMurisData_1.24.0.tar.gz"}, "tabulamurissenisdata-1.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/TabulaMurisSenisData_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/TabulaMurisSenisData_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tabulamurissenisdata/bioconductor-tabulamurissenisdata_1.12.0_src_all.tar.gz"], "md5": "3335145c932f9c89f2ba43b229209575", "fn": "TabulaMurisSenisData_1.12.0.tar.gz"}, "targetscoredata-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/TargetScoreData_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/TargetScoreData_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetscoredata/bioconductor-targetscoredata_1.42.0_src_all.tar.gz"], "md5": "3fac4abe234ab4439fd08e5a8d8c7035", "fn": "TargetScoreData_1.42.0.tar.gz"}, "targetsearchdata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/TargetSearchData_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/TargetSearchData_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-targetsearchdata/bioconductor-targetsearchdata_1.44.0_src_all.tar.gz"], "md5": "ed882cf4fe96e35cb9be14e429a9acfc", "fn": "TargetSearchData_1.44.0.tar.gz"}, "tartare-1.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/tartare_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/tartare_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tartare/bioconductor-tartare_1.20.0_src_all.tar.gz"], "md5": "6eeeb4d2495f54d9ea03ec88a99d6124", "fn": "tartare_1.20.0.tar.gz"}, "tbx20bamsubset-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/TBX20BamSubset_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/TBX20BamSubset_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tbx20bamsubset/bioconductor-tbx20bamsubset_1.42.0_src_all.tar.gz"], "md5": "c4621f88eceaa2b24655558964790f51", "fn": "TBX20BamSubset_1.42.0.tar.gz"}, "tcgabiolinksgui.data-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/TCGAbiolinksGUI.data_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAbiolinksGUI.data_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgabiolinksgui.data/bioconductor-tcgabiolinksgui.data_1.26.0_src_all.tar.gz"], "md5": "280de6c6b0ebc043613aa8fd5e79d2b5", "fn": "TCGAbiolinksGUI.data_1.26.0.tar.gz"}, "tcgacrcmirna-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/TCGAcrcmiRNA_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAcrcmiRNA_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmirna/bioconductor-tcgacrcmirna_1.26.0_src_all.tar.gz"], "md5": "987fb490cde2a7c1387a03ce1a38efe8", "fn": "TCGAcrcmiRNA_1.26.0.tar.gz"}, "tcgacrcmrna-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/TCGAcrcmRNA_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAcrcmRNA_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmrna/bioconductor-tcgacrcmrna_1.26.0_src_all.tar.gz"], "md5": "da22bfc5ef7e6cf3b67e3bd4b9ccdb03", "fn": "TCGAcrcmRNA_1.26.0.tar.gz"}, "tcgamethylation450k-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/TCGAMethylation450k_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAMethylation450k_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgamethylation450k/bioconductor-tcgamethylation450k_1.42.0_src_all.tar.gz"], "md5": "14bf9c5d9f61ad9f29b0e6fdf1a76506", "fn": "TCGAMethylation450k_1.42.0.tar.gz"}, "tcgaworkflowdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/TCGAWorkflowData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/TCGAWorkflowData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tcgaworkflowdata/bioconductor-tcgaworkflowdata_1.30.0_src_all.tar.gz"], "md5": "5d7066d5244562eb269a1c8bef037a30", "fn": "TCGAWorkflowData_1.30.0.tar.gz"}, "tenxbraindata-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/TENxBrainData_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxBrainData_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxbraindata/bioconductor-tenxbraindata_1.26.0_src_all.tar.gz"], "md5": "c75922e698f3cfea4aeceff12647f0c4", "fn": "TENxBrainData_1.26.0.tar.gz"}, "tenxbusdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/TENxBUSData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxBUSData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxbusdata/bioconductor-tenxbusdata_1.20.0_src_all.tar.gz"], "md5": "d06d50a0967cda65a36e27a32d2e6c6e", "fn": "TENxBUSData_1.20.0.tar.gz"}, "tenxpbmcdata-1.24.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/TENxPBMCData_1.24.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxPBMCData_1.24.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxpbmcdata/bioconductor-tenxpbmcdata_1.24.0_src_all.tar.gz"], "md5": "15f610613ce383ac323033ee5a8f42c5", "fn": "TENxPBMCData_1.24.0.tar.gz"}, "tenxvisiumdata-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/TENxVisiumData_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxVisiumData_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxvisiumdata/bioconductor-tenxvisiumdata_1.14.0_src_all.tar.gz"], "md5": "51c4de649c20eb710f34c5e6803f98ed", "fn": "TENxVisiumData_1.14.0.tar.gz"}, "tenxxeniumdata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/TENxXeniumData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/TENxXeniumData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tenxxeniumdata/bioconductor-tenxxeniumdata_1.2.0_src_all.tar.gz"], "md5": "1c7e013460ed287c5d666e0a488b24ef", "fn": "TENxXeniumData_1.2.0.tar.gz"}, "timecoursedata-1.16.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/timecoursedata_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/timecoursedata_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-timecoursedata/bioconductor-timecoursedata_1.16.0_src_all.tar.gz"], "md5": "28f66d8ccee52d67473922f1e417c78d", "fn": "timecoursedata_1.16.0.tar.gz"}, "timerquant-1.36.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/TimerQuant_1.36.0.tar.gz", "https://bioarchive.galaxyproject.org/TimerQuant_1.36.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-timerquant/bioconductor-timerquant_1.36.0_src_all.tar.gz"], "md5": "ba7baf3dc9562fe7c00adae7f5fe1ad2", "fn": "TimerQuant_1.36.0.tar.gz"}, "tinesath1cdf-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/tinesath1cdf_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/tinesath1cdf_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tinesath1cdf/bioconductor-tinesath1cdf_1.44.0_src_all.tar.gz"], "md5": "7876f5f8916518557139bfd5dab1f4f3", "fn": "tinesath1cdf_1.44.0.tar.gz"}, "tinesath1probe-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/tinesath1probe_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/tinesath1probe_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tinesath1probe/bioconductor-tinesath1probe_1.44.0_src_all.tar.gz"], "md5": "b62b0add44a447b6c38c051cf70aa87c", "fn": "tinesath1probe_1.44.0.tar.gz"}, "tissuetreg-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/tissueTreg_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/tissueTreg_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tissuetreg/bioconductor-tissuetreg_1.26.0_src_all.tar.gz"], "md5": "6d508115f45fe5ec1faf5349c9497e7d", "fn": "tissueTreg_1.26.0.tar.gz"}, "tmexplorer-1.16.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/TMExplorer_1.16.0.tar.gz", "https://bioarchive.galaxyproject.org/TMExplorer_1.16.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tmexplorer/bioconductor-tmexplorer_1.16.0_src_all.tar.gz"], "md5": "6554fe5db5049cfe19f9b9f7d3f662c2", "fn": "TMExplorer_1.16.0.tar.gz"}, "tofsimsdata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/tofsimsData_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/tofsimsData_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tofsimsdata/bioconductor-tofsimsdata_1.34.0_src_all.tar.gz"], "md5": "820073aaa32a9664721c1245015c78db", "fn": "tofsimsData_1.34.0.tar.gz"}, "topdownrdata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/topdownrdata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/topdownrdata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-topdownrdata/bioconductor-topdownrdata_1.28.0_src_all.tar.gz"], "md5": "c74335a0fdebf3646e25eac76164738b", "fn": "topdownrdata_1.28.0.tar.gz"}, "transomicsdata-1.2.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/TransOmicsData_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/TransOmicsData_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-transomicsdata/bioconductor-transomicsdata_1.2.0_src_all.tar.gz"], "md5": "49ad14256811563aac93e9cb8b87e2a0", "fn": "TransOmicsData_1.2.0.tar.gz"}, "tuberculosis-1.12.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/tuberculosis_1.12.0.tar.gz", "https://bioarchive.galaxyproject.org/tuberculosis_1.12.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tuberculosis/bioconductor-tuberculosis_1.12.0_src_all.tar.gz"], "md5": "232d8eebba6c53dead1fd5025f806613", "fn": "tuberculosis_1.12.0.tar.gz"}, "tumourmethdata-1.3.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/TumourMethData_1.3.0.tar.gz", "https://bioarchive.galaxyproject.org/TumourMethData_1.3.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tumourmethdata/bioconductor-tumourmethdata_1.3.0_src_all.tar.gz"], "md5": "33c0ff42d0fbc47bb824bd29b06c34f2", "fn": "TumourMethData_1.3.0.tar.gz"}, "tweedeseqcountdata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/tweeDEseqCountData_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/tweeDEseqCountData_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tweedeseqcountdata/bioconductor-tweedeseqcountdata_1.44.0_src_all.tar.gz"], "md5": "d948402ffc023b37cf2347865a1f1e2e", "fn": "tweeDEseqCountData_1.44.0.tar.gz"}, "tximportdata-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/tximportData_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/tximportData_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-tximportdata/bioconductor-tximportdata_1.34.0_src_all.tar.gz"], "md5": "fc6bbc67c32e7eac6e11b68af9343745", "fn": "tximportData_1.34.0.tar.gz"}, "varianttoolsdata-1.30.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/VariantToolsData_1.30.0.tar.gz", "https://bioarchive.galaxyproject.org/VariantToolsData_1.30.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-varianttoolsdata/bioconductor-varianttoolsdata_1.30.0_src_all.tar.gz"], "md5": "00072c40be7324743e9a1d9f7507a743", "fn": "VariantToolsData_1.30.0.tar.gz"}, "vectrapolarisdata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/VectraPolarisData_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/VectraPolarisData_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vectrapolarisdata/bioconductor-vectrapolarisdata_1.10.0_src_all.tar.gz"], "md5": "9a68d6def6946fea171b63621c349a0b", "fn": "VectraPolarisData_1.10.0.tar.gz"}, "vulcandata-1.28.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/vulcandata_1.28.0.tar.gz", "https://bioarchive.galaxyproject.org/vulcandata_1.28.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-vulcandata/bioconductor-vulcandata_1.28.0_src_all.tar.gz"], "md5": "967ff4f5f3eeef805d666b70f3659a5e", "fn": "vulcandata_1.28.0.tar.gz"}, "weberdivechalcdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/WeberDivechaLCdata_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/WeberDivechaLCdata_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-weberdivechalcdata/bioconductor-weberdivechalcdata_1.8.0_src_all.tar.gz"], "md5": "c8a89a9a75b7249249905d8f2e5dc775", "fn": "WeberDivechaLCdata_1.8.0.tar.gz"}, "wes.1kg.wugsc-1.38.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/WES.1KG.WUGSC_1.38.0.tar.gz", "https://bioarchive.galaxyproject.org/WES.1KG.WUGSC_1.38.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wes.1kg.wugsc/bioconductor-wes.1kg.wugsc_1.38.0_src_all.tar.gz"], "md5": "5fab1142aa178a13bf1f056d9db5d8bb", "fn": "WES.1KG.WUGSC_1.38.0.tar.gz"}, "wgsmapp-1.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/WGSmapp_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/WGSmapp_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-wgsmapp/bioconductor-wgsmapp_1.18.0_src_all.tar.gz"], "md5": "b6b076672a568d3e456f3a934d444c3f", "fn": "WGSmapp_1.18.0.tar.gz"}, "xcoredata-1.10.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/xcoredata_1.10.0.tar.gz", "https://bioarchive.galaxyproject.org/xcoredata_1.10.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xcoredata/bioconductor-xcoredata_1.10.0_src_all.tar.gz"], "md5": "7ef4acfdabec19615e077d46749c32be", "fn": "xcoredata_1.10.0.tar.gz"}, "xhybcasneuf-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/XhybCasneuf_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/XhybCasneuf_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-xhybcasneuf/bioconductor-xhybcasneuf_1.44.0_src_all.tar.gz"], "md5": "ef8eb72da053078342f2468969e41db2", "fn": "XhybCasneuf_1.44.0.tar.gz"}, "yeastcc-1.46.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/yeastCC_1.46.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastCC_1.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastcc/bioconductor-yeastcc_1.46.0_src_all.tar.gz"], "md5": "5748a2de9c433d4f49c28744fef17e67", "fn": "yeastCC_1.46.0.tar.gz"}, "yeastexpdata-0.52.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/yeastExpData_0.52.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastExpData_0.52.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastexpdata/bioconductor-yeastexpdata_0.52.0_src_all.tar.gz"], "md5": "2298a34217fed5055d1526e3d72c1231", "fn": "yeastExpData_0.52.0.tar.gz"}, "yeastgsdata-0.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/yeastGSData_0.44.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastGSData_0.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastgsdata/bioconductor-yeastgsdata_0.44.0_src_all.tar.gz"], "md5": "bc968a47f5247e09b8a88af9d8289cbb", "fn": "yeastGSData_0.44.0.tar.gz"}, "yeastnagalakshmi-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/yeastNagalakshmi_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastNagalakshmi_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastnagalakshmi/bioconductor-yeastnagalakshmi_1.42.0_src_all.tar.gz"], "md5": "ce6fc59baa125ba08237e40b8be636dc", "fn": "yeastNagalakshmi_1.42.0.tar.gz"}, "yeastrnaseq-0.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/yeastRNASeq_0.44.0.tar.gz", "https://bioarchive.galaxyproject.org/yeastRNASeq_0.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-yeastrnaseq/bioconductor-yeastrnaseq_0.44.0_src_all.tar.gz"], "md5": "9d6061c54c1265775e1dd58a26822cde", "fn": "yeastRNASeq_0.44.0.tar.gz"}, "zebrafishrnaseq-1.26.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/zebrafishRNASeq_1.26.0.tar.gz", "https://bioarchive.galaxyproject.org/zebrafishRNASeq_1.26.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-zebrafishrnaseq/bioconductor-zebrafishrnaseq_1.26.0_src_all.tar.gz"], "md5": "9efd43091fe0990c57a8fc8f5414885b", "fn": "zebrafishRNASeq_1.26.0.tar.gz"}, "ath1121501frmavecs-1.0.0": {"urls": ["https://bioconductor.org/packages/3.20/data/annotation/src/contrib/ath1121501frmavecs_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/ath1121501frmavecs_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-ath1121501frmavecs/bioconductor-ath1121501frmavecs_1.0.0_src_all.tar.gz"], "md5": "e77c631160730a18037caf3f656e82c5", "fn": "ath1121501frmavecs_1.0.0.tar.gz"}, "bugphyzz-1.0.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/bugphyzz_1.0.0.tar.gz", "https://bioarchive.galaxyproject.org/bugphyzz_1.0.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-bugphyzz/bioconductor-bugphyzz_1.0.0_src_all.tar.gz"], "md5": "b29c65abe5333278bea9cbd13db6dc77", "fn": "bugphyzz_1.0.0.tar.gz"}, "cytomethic-1.2.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/CytoMethIC_1.2.0.tar.gz", "https://bioarchive.galaxyproject.org/CytoMethIC_1.2.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-cytomethic/bioconductor-cytomethic_1.2.0_src_all.tar.gz"], "md5": "fec5611f2f4d02c220e277b66cea9439", "fn": "CytoMethIC_1.2.0.tar.gz"}, "msdata-0.46.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/msdata_0.46.0.tar.gz", "https://bioarchive.galaxyproject.org/msdata_0.46.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msdata/bioconductor-msdata_0.46.0_src_all.tar.gz"], "md5": "280e355d2ab77124dcf82cf8625e1c4f", "fn": "msdata_0.46.0.tar.gz"}, "pasilla-1.34.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/pasilla_1.34.0.tar.gz", "https://bioarchive.galaxyproject.org/pasilla_1.34.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-pasilla/bioconductor-pasilla_1.34.0_src_all.tar.gz"], "md5": "b1521054ce2e43ced5de491d1ea26e8b", "fn": "pasilla_1.34.0.tar.gz"}, "msigdb-1.14.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/msigdb_1.14.0.tar.gz", "https://bioarchive.galaxyproject.org/msigdb_1.14.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-msigdb/bioconductor-msigdb_1.14.0_src_all.tar.gz"], "md5": "1c8a6d642d596cc654fa254d9cef809e", "fn": "msigdb_1.14.0.tar.gz"}, "mcseadata-1.26.1": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/mCSEAdata_1.26.1.tar.gz", "https://bioarchive.galaxyproject.org/mCSEAdata_1.26.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mcseadata/bioconductor-mcseadata_1.26.1_src_all.tar.gz"], "md5": "1081e2c4a6e4e868c409a7ec19cb515a", "fn": "mCSEAdata_1.26.1.tar.gz"}, "curatedtcgadata-1.28.1": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/curatedTCGAData_1.28.1.tar.gz", "https://bioarchive.galaxyproject.org/curatedTCGAData_1.28.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-curatedtcgadata/bioconductor-curatedtcgadata_1.28.1_src_all.tar.gz"], "md5": "21b4e364a9d056d7010c96fc6fae28ed", "fn": "curatedTCGAData_1.28.1.tar.gz"}, "prolocdata-1.44.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/pRolocdata_1.44.0.tar.gz", "https://bioarchive.galaxyproject.org/pRolocdata_1.44.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-prolocdata/bioconductor-prolocdata_1.44.0_src_all.tar.gz"], "md5": "3a5b9d9bf4fe38873a4b16eeb7f73d29", "fn": "pRolocdata_1.44.0.tar.gz"}, "mvoutdata-1.42.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/mvoutData_1.42.0.tar.gz", "https://bioarchive.galaxyproject.org/mvoutData_1.42.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-mvoutdata/bioconductor-mvoutdata_1.42.0_src_all.tar.gz"], "md5": "313c7e57d9a26a53342aa415b0370cbd", "fn": "mvoutData_1.42.0.tar.gz"}, "scatac.explorer-1.12.1": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/scATAC.Explorer_1.12.1.tar.gz", "https://bioarchive.galaxyproject.org/scATAC.Explorer_1.12.1.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-scatac.explorer/bioconductor-scatac.explorer_1.12.1_src_all.tar.gz"], "md5": "e031fee987eb77af3299313b5a5f391b", "fn": "scATAC.Explorer_1.12.1.tar.gz"}, "nestlink-1.22.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/NestLink_1.22.0.tar.gz", "https://bioarchive.galaxyproject.org/NestLink_1.22.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-nestlink/bioconductor-nestlink_1.22.0_src_all.tar.gz"], "md5": "3fc4cdd3cb28a6f27b3be814b3e9334d", "fn": "NestLink_1.22.0.tar.gz"}, "muscdata-1.20.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/muscData_1.20.0.tar.gz", "https://bioarchive.galaxyproject.org/muscData_1.20.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-muscdata/bioconductor-muscdata_1.20.0_src_all.tar.gz"], "md5": "157c067dfb062ac305f9e79a6fb42bd1", "fn": "muscData_1.20.0.tar.gz"}, "merfishdata-1.8.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MerfishData_1.8.0.tar.gz", "https://bioarchive.galaxyproject.org/MerfishData_1.8.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-merfishdata/bioconductor-merfishdata_1.8.0_src_all.tar.gz"], "md5": "86f043a416a009f9fd1ebb30f8a83360", "fn": "MerfishData_1.8.0.tar.gz"}, "spatiallibd-1.18.0": {"urls": ["https://bioconductor.org/packages/3.20/data/experiment/src/contrib/spatialLIBD_1.18.0.tar.gz", "https://bioarchive.galaxyproject.org/spatialLIBD_1.18.0.tar.gz", "https://depot.galaxyproject.org/software/bioconductor-spatiallibd/bioconductor-spatiallibd_1.18.0_src_all.tar.gz"], "md5": "a261eafe19ca77ff46ca694974b64923", "fn": "spatialLIBD_1.18.0.tar.gz"}} \ No newline at end of file diff --git a/recipes/bioconductor-data-packages/meta.yaml b/recipes/bioconductor-data-packages/meta.yaml index 9a5e1a2092398..2f9dc2dc80086 100644 --- a/recipes/bioconductor-data-packages/meta.yaml +++ b/recipes/bioconductor-data-packages/meta.yaml @@ -1,6 +1,6 @@ package: name: 'bioconductor-data-packages' - version: '20231203' + version: '20250105.1' source: build: number: 0 diff --git a/recipes/bioconductor-davidtiling/meta.yaml b/recipes/bioconductor-davidtiling/meta.yaml index 35f0720944fec..17c3ef48d37f0 100644 --- a/recipes/bioconductor-davidtiling/meta.yaml +++ b/recipes/bioconductor-davidtiling/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "davidTiling" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dace46d6f640014aff544e0faf355b5e +about: + description: 'This package contains the data for the paper by L. David et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix genechips, an ExpressionSet object with the raw feature data, a probe annotation data structure for the chip and the yeast genome annotation (GFF file) that was used. In addition, some custom-written analysis functions are provided, as well as R scripts in the scripts directory.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Data and analysis scripts for David, Huber et al. yeast tiling array paper build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-davidtiling", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-tilingarray >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-tilingarray >=1.84.0,<1.85.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-tilingarray >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-tilingarray >=1.84.0,<1.85.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4519817d00468376b430162bb2464c61 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Data and analysis scripts for David, Huber et al. yeast tiling array paper' - description: 'This package contains the data for the paper by L. David et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix genechips, an ExpressionSet object with the raw feature data, a probe annotation data structure for the chip and the yeast genome annotation (GFF file) that was used. In addition, some custom-written analysis functions are provided, as well as R scripts in the scripts directory.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-davidtiling/post-link.sh b/recipes/bioconductor-davidtiling/post-link.sh index ebb07a26801fe..dda268983ba6e 100644 --- a/recipes/bioconductor-davidtiling/post-link.sh +++ b/recipes/bioconductor-davidtiling/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "davidtiling-1.42.0" +installBiocDataPackage.sh "davidtiling-1.46.0" diff --git a/recipes/bioconductor-dcanr/meta.yaml b/recipes/bioconductor-dcanr/meta.yaml index 839e3b308764b..06fb3e8544e84 100644 --- a/recipes/bioconductor-dcanr/meta.yaml +++ b/recipes/bioconductor-dcanr/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "dcanr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements methods and an evaluation framework to infer differential co-expression/association networks. Various methods are implemented and can be evaluated using simulated datasets. Inference of differential co-expression networks can allow identification of networks that are altered between two conditions (e.g., health and disease). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Differential co-expression/association network analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1a30832879c85ae9430a463d581ba978 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dcanr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: EBcoexpress, testthat, EBarrays, GeneNet, mclust, minqa, SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle, edgeR requirements: host: @@ -43,13 +45,16 @@ requirements: - r-rcolorbrewer - r-reshape2 - r-stringr + +source: + md5: 457aab9c14c63448f2341f970742ac16 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Differential co-expression/association network analysis' - description: 'This package implements methods and an evaluation framework to infer differential co-expression/association networks. Various methods are implemented and can be evaluated using simulated datasets. Inference of differential co-expression networks can allow identification of networks that are altered between two conditions (e.g., health and disease).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dcats/meta.yaml b/recipes/bioconductor-dcats/meta.yaml index 121d93a21050b..bb5aed1d2e0ce 100644 --- a/recipes/bioconductor-dcats/meta.yaml +++ b/recipes/bioconductor-dcats/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "DCATS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Methods to detect the differential composition abundances between conditions in singel-cell RNA-seq experiments, with or without replicates. It aims to correct bias introduced by missclaisification and enable controlling of confounding covariates. To avoid the influence of proportion change from big cell types, DCATS can use either total cell number or specific reference group as normalization term. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Differential Composition Analysis Transformed by a Similarity matrix -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a6002426027bd88d05a2b8759d5a12e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dcats", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.0.0), knitr, Seurat, SeuratObject, tidyverse, rmarkdown, BiocStyle requirements: host: @@ -35,13 +37,16 @@ requirements: - r-matrixstats - r-mcmcpack - r-robustbase + +source: + md5: de7f2ed5215d0945dcb3c77705cb7394 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Differential Composition Analysis Transformed by a Similarity matrix' - description: 'Methods to detect the differential composition abundances between conditions in singel-cell RNA-seq experiments, with or without replicates. It aims to correct bias introduced by missclaisification and enable controlling of confounding covariates. To avoid the influence of proportion change from big cell types, DCATS can use either total cell number or specific reference group as normalization term.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dce/build_failure.linux-64.yaml b/recipes/bioconductor-dce/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..4304d8fa298fa --- /dev/null +++ b/recipes/bioconductor-dce/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 0ea093005664848b828d1abc944733500331b3aaa80b90f3734ad62422ebadcc # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-epinem[version='>=1.30.0,<1.31.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-epinem >=1.30.0,<1.31.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-epinem >=1.30.0,<1.31.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-epinem[version='>=1.30.0,<1.31.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-epinem >=1.30.0,<1.31.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-epinem >=1.30.0,<1.31.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-epinem[version='>=1.30.0,<1.31.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-epinem >=1.30.0,<1.31.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-epinem >=1.30.0,<1.31.0 [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-dce/meta.yaml b/recipes/bioconductor-dce/meta.yaml index 82addc1e3b3ab..44d765e13035a 100644 --- a/recipes/bioconductor-dce/meta.yaml +++ b/recipes/bioconductor-dce/meta.yaml @@ -1,34 +1,37 @@ -{% set version = "1.10.0" %} +{% set version = "1.13.0" %} {% set name = "dce" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Compute differential causal effects (dce) on (biological) networks. Given observational samples from a control experiment and non-control (e.g., cancer) for two genes A and B, we can compute differential causal effects with a (generalized) linear regression. If the causal effect of gene A on gene B in the control samples is different from the causal effect in the non-control samples the dce will differ from zero. We regularize the dce computation by the inclusion of prior network information from pathway databases such as KEGG. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Pathway Enrichment Based on Differential Causal Effects -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dbebdd246ea193f92c1a466a84617876 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dce", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, cowplot, ggplotify, dagitty, lmtest, sandwich, devtools, curatedTCGAData, TCGAutils, SummarizedExperiment, RcppParallel, docopt, CARNIVAL requirements: + host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-epinem >=1.26.0,<1.27.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-graphite >=1.48.0,<1.49.0' - - 'bioconductor-mnem >=1.18.0,<1.19.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-epinem >=1.30.0,<1.31.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-graphite >=1.52.0,<1.53.0 + - bioconductor-mnem >=1.22.0,<1.23.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-assertthat - r-base - r-dplyr @@ -53,14 +56,15 @@ requirements: - r-shadowtext - r-tidygraph - r-tidyverse + run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-epinem >=1.26.0,<1.27.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-graphite >=1.48.0,<1.49.0' - - 'bioconductor-mnem >=1.18.0,<1.19.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-epinem >=1.30.0,<1.31.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-graphite >=1.52.0,<1.53.0 + - bioconductor-mnem >=1.22.0,<1.23.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-assertthat - r-base - r-dplyr @@ -85,13 +89,16 @@ requirements: - r-shadowtext - r-tidygraph - r-tidyverse + +source: + md5: 9079525e96b53b9b2d11fe7eed33f328 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Pathway Enrichment Based on Differential Causal Effects' - description: 'Compute differential causal effects (dce) on (biological) networks. Given observational samples from a control experiment and non-control (e.g., cancer) for two genes A and B, we can compute differential causal effects with a (generalized) linear regression. If the causal effect of gene A on gene B in the control samples is different from the causal effect in the non-control samples the dce will differ from zero. We regularize the dce computation by the inclusion of prior network information from pathway databases such as KEGG.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dcgsa/meta.yaml b/recipes/bioconductor-dcgsa/meta.yaml index 81d2701989b49..399a90829331c 100644 --- a/recipes/bioconductor-dcgsa/meta.yaml +++ b/recipes/bioconductor-dcgsa/meta.yaml @@ -1,49 +1,55 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "dcGSA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles. In longitudinal studies, the gene expression profiles were collected at each visit from each subject and hence there are multiple measurements of the gene expression profiles for each subject. The dcGSA package could be used to assess the associations between gene sets and clinical outcomes of interest by fully taking advantage of the longitudinal nature of both the gene expression profiles and clinical outcomes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f824cffdf3d7c4f41b44d2cc46b69998 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dcgsa", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:dcgsa + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-dcgsa + path: recipes/bioconductor-dcgsa + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-matrix run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-matrix + +source: + md5: fef80ac1e4eed95e64c0ae6f1d1f725e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles' - description: 'Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles. In longitudinal studies, the gene expression profiles were collected at each visit from each subject and hence there are multiple measurements of the gene expression profiles for each subject. The dcGSA package could be used to assess the associations between gene sets and clinical outcomes of interest by fully taking advantage of the longitudinal nature of both the gene expression profiles and clinical outcomes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:dcgsa - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-dcgsa - path: recipes/bioconductor-dcgsa - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ddct/meta.yaml b/recipes/bioconductor-ddct/meta.yaml index 88e86641ae0b3..e6051caa11070 100644 --- a/recipes/bioconductor-ddct/meta.yaml +++ b/recipes/bioconductor-ddct/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.58.0" %} +{% set version = "1.62.0" %} {% set name = "ddCt" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The ddCt package implements a pipeline to collect, analyse and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 560588380b356d55a4e11811ae9100e6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ddct", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:ddct + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ddct + path: recipes/bioconductor-ddct + version: 1.36.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.0.0), RUnit requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-lattice - - 'r-rcolorbrewer >=0.1-3' + - r-rcolorbrewer >=0.1-3 - r-xtable run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-lattice - - 'r-rcolorbrewer >=0.1-3' + - r-rcolorbrewer >=0.1-3 - r-xtable + +source: + md5: e85c726d144ee68358302cdcc536abc9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)' - description: 'The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The ddCt package implements a pipeline to collect, analyse and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:ddct - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-ddct - path: recipes/bioconductor-ddct - version: 1.36.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ddpcrclust/meta.yaml b/recipes/bioconductor-ddpcrclust/meta.yaml index 342aec460ad83..8828f90ce8154 100644 --- a/recipes/bioconductor-ddpcrclust/meta.yaml +++ b/recipes/bioconductor-ddpcrclust/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "ddPCRclust" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The ddPCRclust algorithm can automatically quantify the CPDs of non-orthogonal ddPCR reactions with up to four targets. In order to determine the correct droplet count for each target, it is crucial to both identify all clusters and label them correctly based on their position. For more information on what data can be analyzed and how a template needs to be formatted, please check the vignette. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Clustering algorithm for ddPCR data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 63c29b24786957fcb604e73a61066e47 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ddpcrclust", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle requirements: host: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowdensity >=1.36.0,<1.37.0' - - 'bioconductor-flowpeaks >=1.48.0,<1.49.0' - - 'bioconductor-samspectral >=1.56.0,<1.57.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowdensity >=1.40.0,<1.41.0 + - bioconductor-flowpeaks >=1.52.0,<1.53.0 + - bioconductor-samspectral >=1.60.0,<1.61.0 - r-base - r-clue - r-ggplot2 @@ -33,22 +34,26 @@ requirements: - r-plotrix - r-r.utils run: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowdensity >=1.36.0,<1.37.0' - - 'bioconductor-flowpeaks >=1.48.0,<1.49.0' - - 'bioconductor-samspectral >=1.56.0,<1.57.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowdensity >=1.40.0,<1.41.0 + - bioconductor-flowpeaks >=1.52.0,<1.53.0 + - bioconductor-samspectral >=1.60.0,<1.61.0 - r-base - r-clue - r-ggplot2 - r-openxlsx - r-plotrix - r-r.utils + +source: + md5: 49f1c9ea525a02b3f1951e2d3e6098b0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Clustering algorithm for ddPCR data' - description: 'The ddPCRclust algorithm can automatically quantify the CPDs of non-orthogonal ddPCR reactions with up to four targets. In order to determine the correct droplet count for each target, it is crucial to both identify all clusters and label them correctly based on their position. For more information on what data can be analyzed and how a template needs to be formatted, please check the vignette.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dearseq/meta.yaml b/recipes/bioconductor-dearseq/meta.yaml index d73ece4475cbb..7f3e18ce38d48 100644 --- a/recipes/bioconductor-dearseq/meta.yaml +++ b/recipes/bioconductor-dearseq/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "dearseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Differential Expression Analysis RNA-seq data with variance component score test accounting for data heteroscedasticity through precision weights. Perform both gene-wise and gene set analyses, and can deal with repeated or longitudinal data. Methods are detailed in: i) Agniel D & Hejblum BP (2017) Variance component score test for time-course gene set analysis of longitudinal RNA-seq data, Biostatistics, 18(4):589-604 ; and ii) Gauthier M, Agniel D, Thiébaut R & Hejblum BP (2020) dearseq: a variance component score test for RNA-Seq differential analysis that effectively controls the false discovery rate, NAR Genomics and Bioinformatics, 2(4):lqaa093.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 | file LICENSE + license_file: LICENSE + summary: Differential Expression Analysis for RNA-seq data through a robust variance component test -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 40f5669b310e7d2142836e3b1592bdd6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dearseq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA, knitr, limma, readxl, rmarkdown, S4Vectors, SummarizedExperiment, testthat, covr requirements: host: @@ -55,13 +57,16 @@ requirements: - r-survey - r-tibble - r-viridislite + +source: + md5: 6f4003b3e3321981299e5b5ab5bbf707 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-2 | file LICENSE' - summary: 'Differential Expression Analysis for RNA-seq data through a robust variance component test' - description: 'Differential Expression Analysis RNA-seq data with variance component score test accounting for data heteroscedasticity through precision weights. Perform both gene-wise and gene set analyses, and can deal with repeated or longitudinal data. Methods are detailed in: i) Agniel D & Hejblum BP (2017) Variance component score test for time-course gene set analysis of longitudinal RNA-seq data, Biostatistics, 18(4):589-604 ; and ii) Gauthier M, Agniel D, Thiébaut R & Hejblum BP (2020) dearseq: a variance component score test for RNA-Seq differential analysis that effectively controls the false discovery rate, NAR Genomics and Bioinformatics, 2(4):lqaa093.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-debcam/meta.yaml b/recipes/bioconductor-debcam/meta.yaml index 0af1f12365332..ef55f21c75125 100644 --- a/recipes/bioconductor-debcam/meta.yaml +++ b/recipes/bioconductor-debcam/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "debCAM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An R package for fully unsupervised deconvolution of complex tissues. It provides basic functions to perform unsupervised deconvolution on mixture expression profiles by Convex Analysis of Mixtures (CAM) and some auxiliary functions to help understand the subpopulation-specific results. It also implements functions to perform supervised deconvolution based on prior knowledge of molecular markers, S matrix or A matrix. Combining molecular markers from CAM and from prior knowledge can achieve semi-supervised deconvolution of mixtures. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Deconvolution by Convex Analysis of Mixtures -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 87d118edcaf90e70fd6aafc865ac5c6a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-debcam", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl # SystemRequirements: Java (>= 1.8) requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-apcluster - r-base - r-corpcor @@ -37,9 +39,9 @@ requirements: - r-rjava - openjdk run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-apcluster - r-base - r-corpcor @@ -50,13 +52,16 @@ requirements: - r-pcapp - r-rjava - openjdk + +source: + md5: 4193a1e2dd224d47d45808040b37fa89 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Deconvolution by Convex Analysis of Mixtures' - description: 'An R package for fully unsupervised deconvolution of complex tissues. It provides basic functions to perform unsupervised deconvolution on mixture expression profiles by Convex Analysis of Mixtures (CAM) and some auxiliary functions to help understand the subpopulation-specific results. It also implements functions to perform supervised deconvolution based on prior knowledge of molecular markers, S matrix or A matrix. Combining molecular markers from CAM and from prior knowledge can achieve semi-supervised deconvolution of mixtures.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-debrowser/meta.yaml b/recipes/bioconductor-debrowser/meta.yaml index ba6472bfcdadd..a1dc9fb986c03 100644 --- a/recipes/bioconductor-debrowser/meta.yaml +++ b/recipes/bioconductor-debrowser/meta.yaml @@ -1,45 +1,48 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "debrowser" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Bioinformatics platform containing interactive plots and tables for differential gene and region expression studies. Allows visualizing expression data much more deeply in an interactive and faster way. By changing the parameters, users can easily discover different parts of the data that like never have been done before. Manually creating and looking these plots takes time. With DEBrowser users can prepare plots without writing any code. Differential expression, PCA and clustering analysis are made on site and the results are shown in various plots such as scatter, bar, box, volcano, ma plots and Heatmaps. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Interactive Differential Expresion Analysis Browser -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dc51add531d95b1e7a924062aa773018 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-debrowser", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, rmarkdown, knitr requirements: + host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-apeglm >=1.24.0,<1.25.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-harman >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-pathview >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-apeglm >=1.28.0,<1.29.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-harman >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-pathview >=1.46.0,<1.47.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-ashr - r-base - r-colourpicker @@ -58,25 +61,26 @@ requirements: - r-shinydashboard - r-shinyjs - r-stringi + run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-apeglm >=1.24.0,<1.25.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-harman >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-pathview >=1.42.0,<1.43.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-apeglm >=1.28.0,<1.29.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-harman >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-pathview >=1.46.0,<1.47.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-ashr - r-base - r-colourpicker @@ -95,13 +99,16 @@ requirements: - r-shinydashboard - r-shinyjs - r-stringi + +source: + md5: 5b2bf81aad3691865f35d0342553832e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Interactive Differential Expresion Analysis Browser' - description: 'Bioinformatics platform containing interactive plots and tables for differential gene and region expression studies. Allows visualizing expression data much more deeply in an interactive and faster way. By changing the parameters, users can easily discover different parts of the data that like never have been done before. Manually creating and looking these plots takes time. With DEBrowser users can prepare plots without writing any code. Differential expression, PCA and clustering analysis are made on site and the results are shown in various plots such as scatter, bar, box, volcano, ma plots and Heatmaps.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-decipher/meta.yaml b/recipes/bioconductor-decipher/meta.yaml index 32250e45f3280..e7c75be7bd20d 100644 --- a/recipes/bioconductor-decipher/meta.yaml +++ b/recipes/bioconductor-decipher/meta.yaml @@ -1,61 +1,66 @@ -{% set version = "2.30.0" %} +{% set version = "3.2.0" %} {% set name = "DECIPHER" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A toolset for deciphering and managing biological sequences. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Tools for curating, analyzing, and manipulating biological sequences -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0a32c782d61a604dc3594c684daa8c75 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-decipher", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:DECIPHER + parent_recipe: + name: bioconductor-decipher + path: recipes/bioconductor-decipher + version: 2.8.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RSQLite (>= 1.1) requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-dbi - - 'r-rsqlite >=1.1' - libblas - liblapack run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-dbi - - 'r-rsqlite >=1.1' - build: - - {{ compiler('c') }} - - make + +source: + md5: 4c8df0ce5a47a0dd9cda5c3231fa35ab + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'Tools for curating, analyzing, and manipulating biological sequences' - description: 'A toolset for deciphering and managing biological sequences.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:DECIPHER - parent_recipe: - name: bioconductor-decipher - path: recipes/bioconductor-decipher - version: 2.8.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-decomptumor2sig/meta.yaml b/recipes/bioconductor-decomptumor2sig/meta.yaml index a220fbdc707c4..c66d9b6b08cee 100644 --- a/recipes/bioconductor-decomptumor2sig/meta.yaml +++ b/recipes/bioconductor-decomptumor2sig/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "2.18.0" %} +{% set version = "2.22.0" %} {% set name = "decompTumor2Sig" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Uses quadratic programming for signature refitting, i.e., to decompose the mutation catalog from an individual tumor sample into a set of given mutational signatures (either Alexandrov-model signatures or Shiraishi-model signatures), computing weights that reflect the contributions of the signatures to the mutation load of the tumor. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Decomposition of individual tumors into mutational signatures by signature refitting -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: efd7bdadb25752241823124b560e9214 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-decomptumor2sig", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-data.table - r-ggplot2 @@ -39,19 +41,19 @@ requirements: - r-gridextra - r-matrix - r-plyr - - 'r-quadprog >=1.5-5' + - r-quadprog >=1.5-5 - r-readxl run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-data.table - r-ggplot2 @@ -59,15 +61,18 @@ requirements: - r-gridextra - r-matrix - r-plyr - - 'r-quadprog >=1.5-5' + - r-quadprog >=1.5-5 - r-readxl + +source: + md5: 933a799a10eb6517f24f3aa6e70aae41 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Decomposition of individual tumors into mutational signatures by signature refitting' - description: 'Uses quadratic programming for signature refitting, i.e., to decompose the mutation catalog from an individual tumor sample into a set of given mutational signatures (either Alexandrov-model signatures or Shiraishi-model signatures), computing weights that reflect the contributions of the signatures to the mutation load of the tumor.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-deconrnaseq/meta.yaml b/recipes/bioconductor-deconrnaseq/meta.yaml index a32a24d5aab35..94577fb80f265 100644 --- a/recipes/bioconductor-deconrnaseq/meta.yaml +++ b/recipes/bioconductor-deconrnaseq/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "DeconRNASeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d38af67b8408b66b85fbb4061442b953 +about: + description: DeconSeq is an R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It modeled expression levels from heterogeneous cell populations in mRNA-Seq as the weighted average of expression from different constituting cell types and predicted cell type proportions of single expression profiles. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-deconrnaseq", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - bioconductor-pcamethods >=1.98.0,<1.99.0 - r-base - r-ggplot2 - r-limsolve run: - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - bioconductor-pcamethods >=1.98.0,<1.99.0 - r-base - r-ggplot2 - r-limsolve +source: + md5: 966402a781d69613923264344eca362a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data' - description: 'DeconSeq is an R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It modeled expression levels from heterogeneous cell populations in mRNA-Seq as the weighted average of expression from different constituting cell types and predicted cell type proportions of single expression profiles.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-decontam/meta.yaml b/recipes/bioconductor-decontam/meta.yaml index 92c3bba5ab045..79799f3885ab7 100644 --- a/recipes/bioconductor-decontam/meta.yaml +++ b/recipes/bioconductor-decontam/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "decontam" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0e6be1cbff9c4396692e39aadc0a5b9e +about: + description: Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data (e.g. ASVs, OTUs, taxonomic groups, MAGs,...). Requires DNA quantitation data or sequenced negative control samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Identify Contaminants in Marker-gene and Metagenomics Sequencing Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-decontam", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-decontam + path: recipes/bioconductor-decontam + version: 1.2.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, phyloseq requirements: host: - r-base - - 'r-ggplot2 >=2.1.0' - - 'r-reshape2 >=1.4.1' + - r-ggplot2 >=2.1.0 + - r-reshape2 >=1.4.1 run: - r-base - - 'r-ggplot2 >=2.1.0' - - 'r-reshape2 >=1.4.1' + - r-ggplot2 >=2.1.0 + - r-reshape2 >=1.4.1 +source: + md5: 8f7e6f21488cf6384358db33630651d6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Identify Contaminants in Marker-gene and Metagenomics Sequencing Data' - description: 'Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data (e.g. ASVs, OTUs, taxonomic groups, MAGs,...). Requires DNA quantitation data or sequenced negative control samples.' -extra: - parent_recipe: - name: bioconductor-decontam - path: recipes/bioconductor-decontam - version: 1.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-decontx/meta.yaml b/recipes/bioconductor-decontx/meta.yaml index 4a08a6867b10a..5aef6041cc3e5 100644 --- a/recipes/bioconductor-decontx/meta.yaml +++ b/recipes/bioconductor-decontx/meta.yaml @@ -1,88 +1,96 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "decontX" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains implementation of DecontX (Yang et al. 2020), a decontamination algorithm for single-cell RNA-seq, and DecontPro (Yin et al. 2023), a decontamination algorithm for single cell protein expression data. DecontX is a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. DecontPro is a Bayesian method that estimates the level of contamination from ambient and background sources in CITE-seq ADT dataset and decontaminate the dataset. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Decontamination of single cell genomics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1e2f4af9204397b8104543dd954bb390 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-decontx", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, dplyr, knitr, rmarkdown, scran, SingleCellMultiModal, TENxPBMCData, testthat (>= 3.0.0) # SystemRequirements: GNU make requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make + host: - - 'bioconductor-celda >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-celda >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-bh >=1.66.0' + - r-bh >=1.66.0 - r-dbscan - r-ggplot2 - - 'r-matrix >=1.5.3' + - r-matrix >=1.5.3 - r-mcmcprecision - r-patchwork - r-plyr - - 'r-rcpp >=0.12.0' - - 'r-rcppeigen >=0.3.3.3.0' - - 'r-rcppparallel >=5.0.1' + - r-rcpp >=0.12.0 + - r-rcppeigen >=0.3.3.3.0 + - r-rcppparallel >=5.0.1 - r-reshape2 - - 'r-rstan >=2.18.1' - - 'r-rstantools >=2.2.0' + - r-rstan >=2.18.1 + - r-rstantools >=2.2.0 - r-seurat - - 'r-stanheaders >=2.18.0' + - r-stanheaders >=2.18.0 - r-withr - libblas - liblapack + run: - - 'bioconductor-celda >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-celda >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-bh >=1.66.0' + - r-bh >=1.66.0 - r-dbscan - r-ggplot2 - - 'r-matrix >=1.5.3' + - r-matrix >=1.5.3 - r-mcmcprecision - r-patchwork - r-plyr - - 'r-rcpp >=0.12.0' - - 'r-rcppeigen >=0.3.3.3.0' - - 'r-rcppparallel >=5.0.1' + - r-rcpp >=0.12.0 + - r-rcppeigen >=0.3.3.3.0 + - r-rcppparallel >=5.0.1 - r-reshape2 - - 'r-rstan >=2.18.1' - - 'r-rstantools >=2.2.0' + - r-rstan >=2.18.1 + - r-rstantools >=2.2.0 - r-seurat - - 'r-stanheaders >=2.18.0' + - r-stanheaders >=2.18.0 - r-withr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 5c6db8fb24a68f239b36e8a8af5f93a8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Decontamination of single cell genomics data' - description: 'This package contains implementation of DecontX (Yang et al. 2020), a decontamination algorithm for single-cell RNA-seq, and DecontPro (Yin et al. 2023), a decontamination algorithm for single cell protein expression data. DecontX is a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. DecontPro is a Bayesian method that estimates the level of contamination from ambient and background sources in CITE-seq ADT dataset and decontaminate the dataset.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-deconvr/meta.yaml b/recipes/bioconductor-deconvr/meta.yaml index ea453fe8601db..64b889f77e8ef 100644 --- a/recipes/bioconductor-deconvr/meta.yaml +++ b/recipes/bioconductor-deconvr/meta.yaml @@ -1,72 +1,77 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "deconvR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types.The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally,we included BSmeth2Probe, to make mapping WGBS data to their probe IDs easier. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Simulation and Deconvolution of Omic Profiles -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 77963b41f8655665f3aac5e2cb1d529c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-deconvr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.0.0), roxygen2 (>= 7.1.2), doParallel (>= 1.0.16), parallel, knitr (>= 1.34), BiocStyle (>= 2.20.2), reshape2 (>= 1.4.4), ggplot2 (>= 3.3.5), rmarkdown, devtools (>= 2.4.2), sessioninfo (>= 1.1.1), covr, granulator, RefManageR requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-methylkit >=1.28.0,<1.29.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-methylkit >=1.32.0,<1.33.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-assertthat - r-base - - 'r-data.table >=1.14.0' - - 'r-dplyr >=1.0.7' - - 'r-e1071 >=1.7.9' - - 'r-foreach >=1.5.1' - - 'r-magrittr >=2.0.1' + - r-data.table >=1.14.0 + - r-dplyr >=1.0.7 + - r-e1071 >=1.7.9 + - r-foreach >=1.5.1 + - r-magrittr >=2.0.1 - r-mass - - 'r-matrixstats >=0.61.0' - - 'r-nnls >=1.4' - - 'r-quadprog >=1.5.8' - - 'r-rsq >=2.2' - - 'r-tidyr >=1.1.3' + - r-matrixstats >=0.61.0 + - r-nnls >=1.4 + - r-quadprog >=1.5.8 + - r-rsq >=2.2 + - r-tidyr >=1.1.3 run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-methylkit >=1.28.0,<1.29.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-methylkit >=1.32.0,<1.33.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-assertthat - r-base - - 'r-data.table >=1.14.0' - - 'r-dplyr >=1.0.7' - - 'r-e1071 >=1.7.9' - - 'r-foreach >=1.5.1' - - 'r-magrittr >=2.0.1' + - r-data.table >=1.14.0 + - r-dplyr >=1.0.7 + - r-e1071 >=1.7.9 + - r-foreach >=1.5.1 + - r-magrittr >=2.0.1 - r-mass - - 'r-matrixstats >=0.61.0' - - 'r-nnls >=1.4' - - 'r-quadprog >=1.5.8' - - 'r-rsq >=2.2' - - 'r-tidyr >=1.1.3' + - r-matrixstats >=0.61.0 + - r-nnls >=1.4 + - r-quadprog >=1.5.8 + - r-rsq >=2.2 + - r-tidyr >=1.1.3 + +source: + md5: 02af5fc0240d7bbec1932ea9f66e1512 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Simulation and Deconvolution of Omic Profiles' - description: 'This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types.The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally,we included BSmeth2Probe, to make mapping WGBS data to their probe IDs easier.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-decoupler/meta.yaml b/recipes/bioconductor-decoupler/meta.yaml index 5694c36e329e4..b9ab87f31a1e3 100644 --- a/recipes/bioconductor-decoupler/meta.yaml +++ b/recipes/bioconductor-decoupler/meta.yaml @@ -1,32 +1,36 @@ -{% set version = "2.8.0" %} +{% set version = "2.12.0" %} {% set name = "decoupleR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Many methods allow us to extract biological activities from omics data using information from prior knowledge resources, reducing the dimensionality for increased statistical power and better interpretability. Here, we present decoupleR, a Bioconductor package containing different statistical methods to extract these signatures within a unified framework. decoupleR allows the user to flexibly test any method with any resource. It incorporates methods that take into account the sign and weight of network interactions. decoupleR can be used with any omic, as long as its features can be linked to a biological process based on prior knowledge. For example, in transcriptomics gene sets regulated by a transcription factor, or in phospho-proteomics phosphosites that are targeted by a kinase. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: 'decoupleR: Ensemble of computational methods to infer biological activities from omics data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: de2a391693476223ec54521aa77ba121 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-decoupler", max_pin="x.x") }}' - noarch: generic -# Suggests: glmnet (>= 4.1.0), GSVA, viper, fgsea (>= 1.15.4), AUCell, SummarizedExperiment, rpart, ranger, BiocStyle, covr, knitr, pkgdown, RefManageR, rmarkdown, roxygen2, sessioninfo, pheatmap, testthat, OmnipathR, Seurat, ggplot2, ggrepel, patchwork + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: glmnet (>= 4.1-7), GSVA, viper, fgsea (>= 1.15.4), AUCell, SummarizedExperiment, rpart, ranger, BiocStyle, covr, knitr, pkgdown, RefManageR, rmarkdown, roxygen2, sessioninfo, pheatmap, testthat, OmnipathR, Seurat, ggplot2, ggrepel, patchwork, magick requirements: host: + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-broom - r-dplyr - r-magrittr - r-matrix + - r-parallelly - r-purrr - r-rlang - r-stringr @@ -35,11 +39,13 @@ requirements: - r-tidyselect - r-withr run: + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-broom - r-dplyr - r-magrittr - r-matrix + - r-parallelly - r-purrr - r-rlang - r-stringr @@ -47,13 +53,16 @@ requirements: - r-tidyr - r-tidyselect - r-withr + +source: + md5: d5e3f97892978162549b29bdd78b9f65 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'decoupleR: Ensemble of computational methods to infer biological activities from omics data' - description: 'Many methods allow us to extract biological activities from omics data using information from prior knowledge resources, reducing the dimensionality for increased statistical power and better interpretability. Here, we present decoupleR, a Bioconductor package containing different statistical methods to extract these signatures within a unified framework. decoupleR allows the user to flexibly test any method with any resource. It incorporates methods that take into account the sign and weight of network interactions. decoupleR can be used with any omic, as long as its features can be linked to a biological process based on prior knowledge. For example, in transcriptomics gene sets regulated by a transcription factor, or in phospho-proteomics phosphosites that are targeted by a kinase.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-deeppincs/meta.yaml b/recipes/bioconductor-deeppincs/meta.yaml index 9e15f3e125853..10ae112da3e1a 100644 --- a/recipes/bioconductor-deeppincs/meta.yaml +++ b/recipes/bioconductor-deeppincs/meta.yaml @@ -1,28 +1,29 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "DeepPINCS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The identification of novel compound-protein interaction (CPI) is important in drug discovery. Revealing unknown compound-protein interactions is useful to design a new drug for a target protein by screening candidate compounds. The accurate CPI prediction assists in effective drug discovery process. To identify potential CPI effectively, prediction methods based on machine learning and deep learning have been developed. Data for sequences are provided as discrete symbolic data. In the data, compounds are represented as SMILES (simplified molecular-input line-entry system) strings and proteins are sequences in which the characters are amino acids. The outcome is defined as a variable that indicates how strong two molecules interact with each other or whether there is an interaction between them. In this package, a deep-learning based model that takes only sequence information of both compounds and proteins as input and the outcome as output is used to predict CPI. The model is implemented by using compound and protein encoders with useful features. The CPI model also supports other modeling tasks, including protein-protein interaction (PPI), chemical-chemical interaction (CCI), or single compounds and proteins. Although the model is designed for proteins, DNA and RNA can be used if they are represented as sequences. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Protein Interactions and Networks with Compounds based on Sequences using Deep Learning -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cc5fbdd874a89f88ffed9c215f1e3d74 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-deeppincs", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-ttgsea >=1.10.0,<1.11.0' + - bioconductor-ttgsea >=1.14.0,<1.15.0 - r-base - r-catencoders - r-keras @@ -36,7 +37,7 @@ requirements: - r-tokenizers - r-webchem run: - - 'bioconductor-ttgsea >=1.10.0,<1.11.0' + - bioconductor-ttgsea >=1.14.0,<1.15.0 - r-base - r-catencoders - r-keras @@ -49,12 +50,16 @@ requirements: - r-tensorflow - r-tokenizers - r-webchem + +source: + md5: bccffa092f6a224af833650957782fe3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Protein Interactions and Networks with Compounds based on Sequences using Deep Learning' - description: 'The identification of novel compound-protein interaction (CPI) is important in drug discovery. Revealing unknown compound-protein interactions is useful to design a new drug for a target protein by screening candidate compounds. The accurate CPI prediction assists in effective drug discovery process. To identify potential CPI effectively, prediction methods based on machine learning and deep learning have been developed. Data for sequences are provided as discrete symbolic data. In the data, compounds are represented as SMILES (simplified molecular-input line-entry system) strings and proteins are sequences in which the characters are amino acids. The outcome is defined as a variable that indicates how strong two molecules interact with each other or whether there is an interaction between them. In this package, a deep-learning based model that takes only sequence information of both compounds and proteins as input and the outcome as output is used to predict CPI. The model is implemented by using compound and protein encoders with useful features. The CPI model also supports other modeling tasks, including protein-protein interaction (PPI), chemical-chemical interaction (CCI), or single compounds and proteins. Although the model is designed for proteins, DNA and RNA can be used if they are represented as sequences.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-deepsnv/meta.yaml b/recipes/bioconductor-deepsnv/meta.yaml index 66edfae750ac9..2d810e3d8fbba 100644 --- a/recipes/bioconductor-deepsnv/meta.yaml +++ b/recipes/bioconductor-deepsnv/meta.yaml @@ -1,64 +1,72 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "deepSNV" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The deepSNV algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs. The shearwater algorithm computes a Bayes classifier based on a beta-binomial model for variant calling with multiple samples for precisely estimating model parameters - such as local error rates and dispersion - and prior knowledge, e.g. from variation data bases such as COSMIC. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Detection of subclonal SNVs in deep sequencing data. -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4df42adbe4997ad401a7d2505ee2b227 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-deepsnv", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:deepsnv + parent_recipe: + name: bioconductor-deepsnv + path: recipes/bioconductor-deepsnv + version: 1.26.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RColorBrewer, knitr, rmarkdown # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-vgam - libblas - liblapack + - zlib + - liblzma-devel run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-vgam - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 23f4830f8b5ad3b1c38ef91ad6427a9a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Detection of subclonal SNVs in deep sequencing data.' - description: 'This package provides provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The deepSNV algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs. The shearwater algorithm computes a Bayes classifier based on a beta-binomial model for variant calling with multiple samples for precisely estimating model parameters - such as local error rates and dispersion - and prior knowledge, e.g. from variation data bases such as COSMIC.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:deepsnv - parent_recipe: - name: bioconductor-deepsnv - path: recipes/bioconductor-deepsnv - version: 1.26.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-deeptarget/build.sh b/recipes/bioconductor-deeptarget/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-deeptarget/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-deeptarget/meta.yaml b/recipes/bioconductor-deeptarget/meta.yaml new file mode 100644 index 0000000000000..372234013dcdb --- /dev/null +++ b/recipes/bioconductor-deeptarget/meta.yaml @@ -0,0 +1,60 @@ +{% set version = "1.0.0" %} +{% set name = "DeepTarget" %} +{% set bioc = "3.20" %} + +about: + description: This package predicts a drug’s primary target(s) or secondary target(s) by integrating large-scale genetic and drug screens from the Cancer Dependency Map project run by the Broad Institute. It further investigates whether the drug specifically targets the wild-type or mutated target forms. To show how to use this package in practice, we provided sample data along with step-by-step example. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Deep characterization of cancer drugs + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-deeptarget", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-depmap >=1.20.0,<1.21.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - r-base + - r-dplyr + - r-ggplot2 + - r-ggpubr + - r-proc + - r-readr + - r-stringr + run: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-depmap >=1.20.0,<1.21.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - r-base + - r-dplyr + - r-ggplot2 + - r-ggpubr + - r-proc + - r-readr + - r-stringr + +source: + md5: f915639c27146a68c56c4f495bb3da50 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-deformats/meta.yaml b/recipes/bioconductor-deformats/meta.yaml index e9aaba108780e..725ed80ce71d0 100644 --- a/recipes/bioconductor-deformats/meta.yaml +++ b/recipes/bioconductor-deformats/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "DEFormats" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Convert between different data formats used by differential gene expression analysis tools. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Differential gene expression data formats converter -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d4fd53366cc3ead5959b9af782ff6790 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-deformats", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:deformats + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-deformats + path: recipes/bioconductor-deformats + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-checkmate - r-data.table run: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-checkmate - r-data.table + +source: + md5: a0a1cd102dae3cf3e95e61067c3f8b80 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Differential gene expression data formats converter' - description: 'Convert between different data formats used by differential gene expression analysis tools.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:deformats - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-deformats - path: recipes/bioconductor-deformats - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-degcre/build.sh b/recipes/bioconductor-degcre/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-degcre/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-degcre/meta.yaml b/recipes/bioconductor-degcre/meta.yaml new file mode 100644 index 0000000000000..0454352590ef2 --- /dev/null +++ b/recipes/bioconductor-degcre/meta.yaml @@ -0,0 +1,64 @@ +{% set version = "1.2.0" %} +{% set name = "DegCre" %} +{% set bioc = "3.20" %} + +about: + description: DegCre generates associations between differentially expressed genes (DEGs) and cis-regulatory elements (CREs) based on non-parametric concordance between differential data. The user provides GRanges of DEG TSS and CRE regions with differential p-value and optionally log-fold changes and DegCre returns an annotated Hits object with associations and their calculated probabilities. Additionally, the package provides functionality for visualization and conversion to other formats. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Probabilistic association of DEGs to CREs from differential data + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-degcre", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BSgenome, BSgenome.Hsapiens.UCSC.hg38, BiocStyle, magick, knitr, rmarkdown, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-plotgardener >=1.12.0,<1.13.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 + - r-base + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-plotgardener >=1.12.0,<1.13.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 + - r-base + +source: + md5: e20e09465bcfbff03f342e8a4619639d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-degnorm/meta.yaml b/recipes/bioconductor-degnorm/meta.yaml index a0f2b8bb9bca8..30cba6e38e4cd 100644 --- a/recipes/bioconductor-degnorm/meta.yaml +++ b/recipes/bioconductor-degnorm/meta.yaml @@ -1,32 +1,41 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "DegNorm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package performs degradation normalization in bulk RNA-seq data to improve differential expression analysis accuracy. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: 'DegNorm: degradation normalization for RNA-seq data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45dbc8183e1e18f3027b7880d3b5ef5a build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-degnorm", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr,rmarkdown,formatR requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-data.table - r-doparallel @@ -35,18 +44,20 @@ requirements: - r-heatmaply - r-plotly - r-plyr - - 'r-rcpp >=1.0.2' + - r-rcpp >=1.0.2 - r-rcpparmadillo - r-viridis - libblas - liblapack + run: - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-data.table - r-doparallel @@ -55,20 +66,19 @@ requirements: - r-heatmaply - r-plotly - r-plyr - - 'r-rcpp >=1.0.2' + - r-rcpp >=1.0.2 - r-rcpparmadillo - r-viridis - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 8a748f1e380b01592e3ae7b67dab5db2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 3)' - summary: 'DegNorm: degradation normalization for RNA-seq data' - description: 'This package performs degradation normalization in bulk RNA-seq data to improve differential expression analysis accuracy.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-degraph/meta.yaml b/recipes/bioconductor-degraph/meta.yaml index d8a23d376a3ec..d63e04a9cae13 100644 --- a/recipes/bioconductor-degraph/meta.yaml +++ b/recipes/bioconductor-degraph/meta.yaml @@ -1,32 +1,43 @@ -{% set version = "1.54.0" %} +{% set version = "1.58.0" %} {% set name = "DEGraph" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: DEGraph implements recent hypothesis testing methods which directly assess whether a particular gene network is differentially expressed between two conditions. This is to be contrasted with the more classical two-step approaches which first test individual genes, then test gene sets for enrichment in differentially expressed genes. These recent methods take into account the topology of the network to yield more powerful detection procedures. DEGraph provides methods to easily test all KEGG pathways for differential expression on any gene expression data set and tools to visualize the results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Two-sample tests on a graph -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c61fb687376b321b9a52dfd15375e0b1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-degraph", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:degraph + - doi:10.1214/11-AOAS528 + parent_recipe: + name: bioconductor-degraph + path: recipes/bioconductor-degraph + version: 1.32.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph requirements: host: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - 'bioconductor-ncigraph >=1.50.0,<1.51.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - bioconductor-ncigraph >=1.54.0,<1.55.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-lattice - r-mvtnorm @@ -34,32 +45,27 @@ requirements: - r-r.utils - r-rrcov run: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - 'bioconductor-ncigraph >=1.50.0,<1.51.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - bioconductor-ncigraph >=1.54.0,<1.55.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-lattice - r-mvtnorm - r-r.methodss3 - r-r.utils - r-rrcov + +source: + md5: 34bf1f3fcf16cb6fa2ad9ea26595762e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Two-sample tests on a graph' - description: 'DEGraph implements recent hypothesis testing methods which directly assess whether a particular gene network is differentially expressed between two conditions. This is to be contrasted with the more classical two-step approaches which first test individual genes, then test gene sets for enrichment in differentially expressed genes. These recent methods take into account the topology of the network to yield more powerful detection procedures. DEGraph provides methods to easily test all KEGG pathways for differential expression on any gene expression data set and tools to visualize the results.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:degraph - - doi:10.1214/11-AOAS528 - parent_recipe: - name: bioconductor-degraph - path: recipes/bioconductor-degraph - version: 1.32.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-degreport/meta.yaml b/recipes/bioconductor-degreport/meta.yaml index 73f13f7830437..5297b9d26d488 100644 --- a/recipes/bioconductor-degreport/meta.yaml +++ b/recipes/bioconductor-degreport/meta.yaml @@ -1,35 +1,47 @@ -{% set version = "1.38.4" %} +{% set version = "1.42.0" %} {% set name = "DEGreport" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Creation of ready-to-share figures of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Report of DEG analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d7c43c419f87827c0a116e3ae905ead7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-degreport", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:degreport + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-degreport + path: recipes/bioconductor-degreport + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-consensusclusterplus >=1.70.0,<1.71.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-broom - r-circlize @@ -52,15 +64,16 @@ requirements: - r-stringr - r-tibble - r-tidyr + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-consensusclusterplus >=1.70.0,<1.71.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-broom - r-circlize @@ -83,21 +96,16 @@ requirements: - r-stringr - r-tibble - r-tidyr + +source: + md5: 6fb70abc2614171e46f5abab6d9aad2a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Report of DEG analysis' - description: 'Creation of a HTML report of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.' - license_file: LICENSE -extra: - identifiers: - - biotools:degreport - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-degreport - path: recipes/bioconductor-degreport - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-degseq/meta.yaml b/recipes/bioconductor-degseq/meta.yaml index 6d4d4a1ad423b..e827e87b45709 100644 --- a/recipes/bioconductor-degseq/meta.yaml +++ b/recipes/bioconductor-degseq/meta.yaml @@ -1,45 +1,21 @@ -{% set version = "1.56.1" %} +{% set version = "1.60.0" %} {% set name = "DEGseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: DEGseq is an R package to identify differentially expressed genes from RNA-Seq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Identify Differentially Expressed Genes from RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cc89e25cb7e9afc38b5fb2bba34722b5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-degseq", max_pin="x.x") }}' -requirements: - host: - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - r-base - - libblas - - liblapack - run: - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL-3-or-above' - summary: 'Identify Differentially Expressed Genes from RNA-seq data' - description: 'DEGseq is an R package to identify differentially expressed genes from RNA-Seq data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + extra: additional-platforms: - linux-aarch64 @@ -51,3 +27,33 @@ extra: path: recipes/bioconductor-degseq version: 1.34.1 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: + - bioconductor-qvalue >=2.38.0,<2.39.0 + - r-base + - libblas + - liblapack + run: + - bioconductor-qvalue >=2.38.0,<2.39.0 + - r-base + +source: + md5: 145b014bc5a5494fdc9d361b383c9017 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-delayedarray/meta.yaml b/recipes/bioconductor-delayedarray/meta.yaml index 2096ed4c080c8..73e67a1ba901f 100644 --- a/recipes/bioconductor-delayedarray/meta.yaml +++ b/recipes/bioconductor-delayedarray/meta.yaml @@ -1,61 +1,67 @@ -{% set version = "0.28.0" %} +{% set version = "0.32.0" %} {% set name = "DelayedArray" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, ordinary arrays and, data frames. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: A unified framework for working transparently with on-disk and in-memory array-like datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 812e7575d6eaa61f5b68364cdf1da3d9 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-delayedarray", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + parent_recipe: + name: bioconductor-delayedarray + path: recipes/bioconductor-delayedarray + version: 0.6.6 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocParallel, HDF5Array (>= 1.17.12), genefilter, SummarizedExperiment, airway, lobstr, DelayedMatrixStats, knitr, rmarkdown, BiocStyle, RUnit requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4arrays >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-sparsearray >=1.2.0,<1.3.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4arrays >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 - r-base - r-matrix - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4arrays >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-sparsearray >=1.2.0,<1.3.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4arrays >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 - r-base - r-matrix - build: - - {{ compiler('c') }} - - make + +source: + md5: 518800dac5483993eae24c728967cb7d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A unified framework for working transparently with on-disk and in-memory array-like datasets' - description: 'Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, ordinary arrays and, data frames.' -extra: - additional-platforms: - - linux-aarch64 - parent_recipe: - name: bioconductor-delayedarray - path: recipes/bioconductor-delayedarray - version: 0.6.6 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-delayeddataframe/meta.yaml b/recipes/bioconductor-delayeddataframe/meta.yaml index 986a848355d4e..32a7f1556d3ed 100644 --- a/recipes/bioconductor-delayeddataframe/meta.yaml +++ b/recipes/bioconductor-delayeddataframe/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "DelayedDataFrame" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dd12410d16a2e6cf7bb022d2aa334bf7 +about: + description: Based on the standard DataFrame metaphor, we are trying to implement the feature of delayed operation on the DelayedDataFrame, with a slot of lazyIndex, which saves the mapping indexes for each column of DelayedDataFrame. Methods like show, validity check, [/[[ subsetting, rbind/cbind are implemented for DelayedDataFrame to be operated around lazyIndex. The listData slot stays untouched until a realization call e.g., DataFrame constructor OR as.list() is invoked. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Delayed operation on DataFrame using standard DataFrame metaphor build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-delayeddataframe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat, knitr, rmarkdown, BiocStyle, SeqArray, GDSArray requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base +source: + md5: 9dbea588b6d677efbb0917b8a6674cd2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Delayed operation on DataFrame using standard DataFrame metaphor' - description: 'Based on the standard DataFrame metaphor, we are trying to implement the feature of delayed operation on the DelayedDataFrame, with a slot of lazyIndex, which saves the mapping indexes for each column of DelayedDataFrame. Methods like show, validity check, [/[[ subsetting, rbind/cbind are implemented for DelayedDataFrame to be operated around lazyIndex. The listData slot stays untouched until a realization call e.g., DataFrame constructor OR as.list() is invoked.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-delayedmatrixstats/meta.yaml b/recipes/bioconductor-delayedmatrixstats/meta.yaml index f3b73711617f5..f52bc0cd5fd48 100644 --- a/recipes/bioconductor-delayedmatrixstats/meta.yaml +++ b/recipes/bioconductor-delayedmatrixstats/meta.yaml @@ -1,54 +1,62 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "DelayedMatrixStats" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A port of the 'matrixStats' API for use with DelayedMatrix objects from the 'DelayedArray' package. High-performing functions operating on rows and columns of DelayedMatrix objects, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 890845d8c80a2b64cd02b3ff7f1e504d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-delayedmatrixstats", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-delayedmatrixstats + path: recipes/bioconductor-delayedmatrixstats + version: 1.2.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocStyle, microbenchmark, profmem, HDF5Array, matrixStats (>= 1.0.0) requirements: host: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 - r-base - - 'r-matrix >=1.5-0' + - r-matrix >=1.5-0 run: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 - r-base - - 'r-matrix >=1.5-0' + - r-matrix >=1.5-0 + +source: + md5: 1417e01b05f813b1955f3bd2cc62043c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Functions that Apply to Rows and Columns of ''DelayedMatrix'' Objects' - description: 'A port of the ''matrixStats'' API for use with DelayedMatrix objects from the ''DelayedArray'' package. High-performing functions operating on rows and columns of DelayedMatrix objects, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-delayedmatrixstats - path: recipes/bioconductor-delayedmatrixstats - version: 1.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-delayedrandomarray/meta.yaml b/recipes/bioconductor-delayedrandomarray/meta.yaml index 084a5e1dbc8b2..aef72b5b82951 100644 --- a/recipes/bioconductor-delayedrandomarray/meta.yaml +++ b/recipes/bioconductor-delayedrandomarray/meta.yaml @@ -1,28 +1,35 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "DelayedRandomArray" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implements a DelayedArray of random values where the realization of the sampled values is delayed until they are needed. Reproducible sampling within any subarray is achieved by chunking where each chunk is initialized with a different random seed and stream. The usual distributions in the stats package are supported, along with scalar, vector and arrays for the parameters. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Delayed Arrays of Random Values -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f583ab177fd333cf626827fc28a6faf build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-delayedrandomarray", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, BiocStyle, rmarkdown, Matrix # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 - r-base - r-bh - r-dqrng @@ -30,22 +37,22 @@ requirements: - libblas - liblapack run: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 - r-base - r-bh - r-dqrng - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 1f0a54dc7043aa1fb5ae32e44d1b5249 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Delayed Arrays of Random Values' - description: 'Implements a DelayedArray of random values where the realization of the sampled values is delayed until they are needed. Reproducible sampling within any subarray is achieved by chunking where each chunk is initialized with a different random seed and stream. The usual distributions in the stats package are supported, along with scalar, vector and arrays for the parameters.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-delayedtensor/meta.yaml b/recipes/bioconductor-delayedtensor/meta.yaml index be01c68df53e5..da72b22dbdd95 100644 --- a/recipes/bioconductor-delayedtensor/meta.yaml +++ b/recipes/bioconductor-delayedtensor/meta.yaml @@ -1,52 +1,61 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "DelayedTensor" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: DelayedTensor operates Tensor arithmetic directly on DelayedArray object. DelayedTensor provides some generic function related to Tensor arithmetic/decompotision and dispatches it on the DelayedArray class. DelayedTensor also suppors Tensor contraction by einsum function, which is inspired by numpy einsum. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: R package for sparse and out-of-core arithmetic and decomposition of Tensor -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee3e89ac7a0b9f3ca79f744edfdc69b8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-delayedtensor", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: markdown, rmarkdown, BiocStyle, knitr, testthat, magrittr, dplyr, reticulate requirements: host: - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedrandomarray >=1.10.0,<1.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedrandomarray >=1.14.0,<1.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-s4arrays >=1.6.0,<1.7.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 - r-base - r-einsum - r-irlba - r-matrix - r-rtensor run: - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedrandomarray >=1.10.0,<1.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedrandomarray >=1.14.0,<1.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-s4arrays >=1.6.0,<1.7.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 - r-base - r-einsum - r-irlba - r-matrix - r-rtensor + +source: + md5: a49d895a1b5c9a63ce9bd298119907fb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'R package for sparse and out-of-core arithmetic and decomposition of Tensor' - description: 'DelayedTensor operates Tensor arithmetic directly on DelayedArray object. DelayedTensor provides some generic function related to Tensor arithmetic/decompotision and dispatches it on the DelayedArray class. DelayedTensor also suppors Tensor contraction by einsum function, which is inspired by numpy einsum.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-delocal/meta.yaml b/recipes/bioconductor-delocal/meta.yaml index f9361e910db48..09d389a43b76d 100644 --- a/recipes/bioconductor-delocal/meta.yaml +++ b/recipes/bioconductor-delocal/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "DELocal" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The goal of DELocal is to identify DE genes compared to their neighboring genes from the same chromosomal location. It has been shown that genes of related functions are generally very far from each other in the chromosome. DELocal utilzes this information to identify DE genes comparing with their neighbouring genes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Identifies differentially expressed genes with respect to other local genes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 40f2eac89260ff4692fb02047990d048 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-delocal", max_pin="x.x") }}' - noarch: generic -# Suggests: biomaRt, knitr, PCRedux, rmarkdown, stringr, BiocStyle + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: biomaRt, knitr, rmarkdown, stringr, BiocStyle requirements: host: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 - r-matrixstats - r-reshape2 run: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 - r-matrixstats - r-reshape2 + +source: + md5: bf1f669d1cfeb5fc1b7e5b448a46ffac + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Identifies differentially expressed genes with respect to other local genes' - description: 'The goal of DELocal is to identify DE genes compared to their neighboring genes from the same chromosomal location. It has been shown that genes of related functions are generally very far from each other in the chromosome. DELocal utilzes this information to identify DE genes comparing with their neighbouring genes.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-deltacapturec/meta.yaml b/recipes/bioconductor-deltacapturec/meta.yaml index 16b711e2ce632..c5e9fbe227bf7 100644 --- a/recipes/bioconductor-deltacapturec/meta.yaml +++ b/recipes/bioconductor-deltacapturec/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "deltaCaptureC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package discovers meso-scale chromatin remodelling from 3C data. 3C data is local in nature. It givens interaction counts between restriction enzyme digestion fragments and a preferred 'viewpoint' region. By binning this data and using permutation testing, this package can test whether there are statistically significant changes in the interaction counts between the data from two cell types or two treatments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: This Package Discovers Meso-scale Chromatin Remodeling from 3C Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e70cf57b6d22164dd5712a3441b0a788 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-deltacapturec", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-tictoc run: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-tictoc + +source: + md5: 60553473556a2603e8b2e3ead74e6078 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'This Package Discovers Meso-scale Chromatin Remodeling from 3C Data' - description: 'This package discovers meso-scale chromatin remodelling from 3C data. 3C data is local in nature. It givens interaction counts between restriction enzyme digestion fragments and a preferred ''viewpoint'' region. By binning this data and using permutation testing, this package can test whether there are statistically significant changes in the interaction counts between the data from two cell types or two treatments.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-deltagseg/meta.yaml b/recipes/bioconductor-deltagseg/meta.yaml index a0a6ce76a69a8..370500e37ffac 100644 --- a/recipes/bioconductor-deltagseg/meta.yaml +++ b/recipes/bioconductor-deltagseg/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "deltaGseg" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Identifying distinct subpopulations through multiscale time series analysis + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: deltaGseg -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e92ca25a67a9250f26c6263043c60ee2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-deltagseg", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: host: @@ -41,13 +43,16 @@ requirements: - r-scales - r-tseries - r-wavethresh + +source: + md5: 0ca03a53234fb95dd82971bbd443d912 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: deltaGseg - description: 'Identifying distinct subpopulations through multiscale time series analysis' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-demand/meta.yaml b/recipes/bioconductor-demand/meta.yaml index b56d0286db48a..d2da8c5ad0216 100644 --- a/recipes/bioconductor-demand/meta.yaml +++ b/recipes/bioconductor-demand/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "DeMAND" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: DEMAND predicts Drug MoA by interrogating a cell context specific regulatory network with a small number (N >= 6) of compound-induced gene expression signatures, to elucidate specific proteins whose interactions in the network is dysregulated by the compound. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: DeMAND -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ccb354bddebbebda6c42453810f10e70 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-demand", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:demand + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-demand + path: recipes/bioconductor-demand + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -26,21 +37,16 @@ requirements: run: - r-base - r-kernsmooth + +source: + md5: 95e46f54af4ce19f9d6c81ad31d13aed + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: DeMAND - description: 'DEMAND predicts Drug MoA by interrogating a cell context specific regulatory network with a small number (N >= 6) of compound-induced gene expression signatures, to elucidate specific proteins whose interactions in the network is dysregulated by the compound.' - license_file: LICENSE -extra: - identifiers: - - biotools:demand - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-demand - path: recipes/bioconductor-demand - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-demixt/meta.yaml b/recipes/bioconductor-demixt/meta.yaml index ff2585eb72ffd..157528e22c9e3 100644 --- a/recipes/bioconductor-demixt/meta.yaml +++ b/recipes/bioconductor-demixt/meta.yaml @@ -1,27 +1,40 @@ -{% set version = "1.16.0" %} +{% set version = "1.22.0" %} {% set name = "DeMixT" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: DeMixT is a software package that performs deconvolution on transcriptome data from a mixture of two or three components. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4aca565a57e59b7b0849f3c3419727f2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-demixt", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:DeMixT + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-dss >=2.48.0,<2.49.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-dss >=2.54.0,<2.55.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-base64enc - r-dendextend @@ -31,15 +44,15 @@ requirements: - r-matrixcalc - r-matrixstats - r-psych - - 'r-rcpp >=1.0.0' + - r-rcpp >=1.0.0 - r-rmarkdown - r-truncdist - libblas - liblapack run: - - 'bioconductor-dss >=2.48.0,<2.49.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-dss >=2.54.0,<2.55.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-base64enc - r-dendextend @@ -49,25 +62,19 @@ requirements: - r-matrixcalc - r-matrixstats - r-psych - - 'r-rcpp >=1.0.0' + - r-rcpp >=1.0.0 - r-rmarkdown - r-truncdist - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: eb2787dc4a420364dc9af2b2f8262cc1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms' - description: 'DeMixT is a software package that performs deconvolution on transcriptome data from a mixture of two or three components.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name }} \ No newline at end of file diff --git a/recipes/bioconductor-demuxmix/meta.yaml b/recipes/bioconductor-demuxmix/meta.yaml index 252585cebc11f..64e21ad5f104b 100644 --- a/recipes/bioconductor-demuxmix/meta.yaml +++ b/recipes/bioconductor-demuxmix/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "demuxmix" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9bbdcc634e542fe151a50a2511206140 +about: + description: A package for demultiplexing single-cell sequencing experiments of pooled cells labeled with barcode oligonucleotides. The package implements methods to fit regression mixture models for a probabilistic classification of cells, including multiplet detection. Demultiplexing error rates can be estimated, and methods for quality control are provided. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-demuxmix", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, cowplot, DropletUtils, knitr, reshape2, rmarkdown, testthat (>= 3.0.0) requirements: host: @@ -33,12 +31,14 @@ requirements: - r-gridextra - r-mass - r-matrix +source: + md5: c0fd77abf91ae084a776a415876a3bea + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models' - description: 'A package for demultiplexing single-cell sequencing experiments of pooled cells labeled with barcode oligonucleotides. The package implements methods to fit regression mixture models for a probabilistic classification of cells, including multiplet detection. Demultiplexing error rates can be estimated, and methods for quality control are provided.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-demuxsnp/meta.yaml b/recipes/bioconductor-demuxsnp/meta.yaml index ad5982ba15810..1c4b6f96ccaec 100644 --- a/recipes/bioconductor-demuxsnp/meta.yaml +++ b/recipes/bioconductor-demuxsnp/meta.yaml @@ -1,61 +1,68 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "demuxSNP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package assists in demultiplexing scRNAseq data using both cell hashing and SNPs data. The SNP profile of each group os learned using high confidence assignments from the cell hashing data. Cells which cannot be assigned with high confidence from the cell hashing data are assigned to their most similar group based on their SNPs. We also provide some helper function to optimise SNP selection, create training data and merge SNP data into the SingleCellExperiment framework. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: scRNAseq demultiplexing using cell hashing and SNPs -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 66a0ed302acbc18c7a106d99bf645133 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-demuxsnp", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, Seurat, ComplexHeatmap, viridisLite, ggpubr, dittoSeq, EnsDb.Hsapiens.v86, BiocStyle, RefManageR, testthat (>= 3.0.0) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, ComplexHeatmap, viridisLite, ggpubr, dittoSeq, EnsDb.Hsapiens.v86, BiocStyle, RefManageR, testthat (>= 3.0.0), Seurat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-demuxmix >=1.4.0,<1.5.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-demuxmix >=1.8.0,<1.9.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-class - - r-combinat + - r-dplyr + - r-kernelknn - r-matrix run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-demuxmix >=1.4.0,<1.5.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-demuxmix >=1.8.0,<1.9.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-class - - r-combinat + - r-dplyr + - r-kernelknn - r-matrix + +source: + md5: 3b31e85995d4a7c5a2f43a26bc515cfe + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'scRNAseq demultiplexing using cell hashing and SNPs' - description: 'This package assists in demultiplexing scRNAseq data using both cell hashing and SNPs data. The SNP profile of each group os learned using high confidence assignments from the cell hashing data. Cells which cannot be assigned with high confidence from the cell hashing data are assigned to their most similar group based on their SNPs. We also provide some helper function to optimise SNP selection, create training data and merge SNP data into the SingleCellExperiment framework.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-densvis/meta.yaml b/recipes/bioconductor-densvis/meta.yaml index 936a9b9557490..03fc68ab17e74 100644 --- a/recipes/bioconductor-densvis/meta.yaml +++ b/recipes/bioconductor-densvis/meta.yaml @@ -1,27 +1,34 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "densvis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implements the density-preserving modification to t-SNE and UMAP described by Narayan et al. (2020) . The non-linear dimensionality reduction techniques t-SNE and UMAP enable users to summarise complex high-dimensional sequencing data such as single cell RNAseq using lower dimensional representations. These lower dimensional representations enable the visualisation of discrete transcriptional states, as well as continuous trajectory (for example, in early development). However, these methods focus on the local neighbourhood structure of the data. In some cases, this results in misleading visualisations, where the density of cells in the low-dimensional embedding does not represent the transcriptional heterogeneity of data in the original high-dimensional space. den-SNE and densMAP aim to enable more accurate visual interpretation of high-dimensional datasets by producing lower-dimensional embeddings that accurately represent the heterogeneity of the original high-dimensional space, enabling the identification of homogeneous and heterogeneous cell states. This accuracy is accomplished by including in the optimisation process a term which considers the local density of points in the original high-dimensional space. This can help to create visualisations that are more representative of heterogeneity in the original high-dimensional space. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cf3ee330c8c9f0b396feb398e342cf8d build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-densvis", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, ggplot2, uwot, testthat requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 - r-assertthat - r-base - r-irlba @@ -31,25 +38,23 @@ requirements: - libblas - liblapack run: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 - r-assertthat - r-base - r-irlba - r-rcpp - r-reticulate - r-rtsne - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 7a064a7b3f4051ea071e9704bfe8817e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction' - description: 'Implements the density-preserving modification to t-SNE and UMAP described by Narayan et al. (2020) . The non-linear dimensionality reduction techniques t-SNE and UMAP enable users to summarise complex high-dimensional sequencing data such as single cell RNAseq using lower dimensional representations. These lower dimensional representations enable the visualisation of discrete transcriptional states, as well as continuous trajectory (for example, in early development). However, these methods focus on the local neighbourhood structure of the data. In some cases, this results in misleading visualisations, where the density of cells in the low-dimensional embedding does not represent the transcriptional heterogeneity of data in the original high-dimensional space. den-SNE and densMAP aim to enable more accurate visual interpretation of high-dimensional datasets by producing lower-dimensional embeddings that accurately represent the heterogeneity of the original high-dimensional space, enabling the identification of homogeneous and heterogeneous cell states. This accuracy is accomplished by including in the optimisation process a term which considers the local density of points in the original high-dimensional space. This can help to create visualisations that are more representative of heterogeneity in the original high-dimensional space.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dep/meta.yaml b/recipes/bioconductor-dep/meta.yaml index 6f0664c7a0333..a124f8fb7ac76 100644 --- a/recipes/bioconductor-dep/meta.yaml +++ b/recipes/bioconductor-dep/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "DEP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides an integrated analysis workflow for robust and reproducible analysis of mass spectrometry proteomics data for differential protein expression or differential enrichment. It requires tabular input (e.g. txt files) as generated by quantitative analysis softwares of raw mass spectrometry data, such as MaxQuant or IsobarQuant. Functions are provided for data preparation, filtering, variance normalization and imputation of missing values, as well as statistical testing of differentially enriched / expressed proteins. It also includes tools to check intermediate steps in the workflow, such as normalization and missing values imputation. Finally, visualization tools are provided to explore the results, including heatmap, volcano plot and barplot representations. For scientists with limited experience in R, the package also contains wrapper functions that entail the complete analysis workflow and generate a report. Even easier to use are the interactive Shiny apps that are provided by the package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Differential Enrichment analysis of Proteomics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://{{ name|lower }}ot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2bfaf5d5bfd3f05c7a7a80742bd43f7c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dep", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, enrichR, knitr, BiocStyle requirements: + host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-assertthat - r-base - r-circlize @@ -46,12 +48,13 @@ requirements: - r-shinydashboard - r-tibble - r-tidyr + run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-assertthat - r-base - r-circlize @@ -71,12 +74,16 @@ requirements: - r-shinydashboard - r-tibble - r-tidyr + +source: + md5: e3c15ed03cc63a3d310192734f426cc7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://{{ name|lower }}ot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Differential Enrichment analysis of Proteomics data' - description: 'This package provides an integrated analysis workflow for robust and reproducible analysis of mass spectrometry proteomics data for differential protein expression or differential enrichment. It requires tabular input (e.g. txt files) as generated by quantitative analysis softwares of raw mass spectrometry data, such as MaxQuant or IsobarQuant. Functions are provided for data preparation, filtering, variance normalization and imputation of missing values, as well as statistical testing of differentially enriched / expressed proteins. It also includes tools to check intermediate steps in the workflow, such as normalization and missing values imputation. Finally, visualization tools are provided to explore the results, including heatmap, volcano plot and barplot representations. For scientists with limited experience in R, the package also contains wrapper functions that entail the complete analysis workflow and generate a report. Even easier to use are the interactive Shiny apps that are provided by the package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-depecher/meta.yaml b/recipes/bioconductor-depecher/meta.yaml index 74da60263ebdb..6b5dbb63699d8 100644 --- a/recipes/bioconductor-depecher/meta.yaml +++ b/recipes/bioconductor-depecher/meta.yaml @@ -1,67 +1,32 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "DepecheR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The purpose of this package is to identify traits in a dataset that can separate groups. This is done on two levels. First, clustering is performed, using an implementation of sparse K-means. Secondly, the generated clusters are used to predict outcomes of groups of individuals based on their distribution of observations in the different clusters. As certain clusters with separating information will be identified, and these clusters are defined by a sparse number of variables, this method can reduce the complexity of data, to only emphasize the data that actually matters. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Determination of essential phenotypic elements of clusters in high-dimensional entities -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 201fe937f16e843f49fbe35a4ae1ebb6 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-depecher", max_pin="x.x") }}' + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: uwot, testthat, knitr, rmarkdown, BiocStyle requirements: - host: - - 'bioconductor-mixomics >=6.26.0,<6.27.0' - - r-base - - 'r-beanplot >=1.2' - - 'r-collapse >=1.9.2' - - 'r-dosnow >=1.0.16' - - 'r-dplyr >=0.7.8' - - 'r-fnn >=1.1.3' - - 'r-foreach >=1.4.4' - - 'r-ggplot2 >=3.1.0' - - 'r-gmodels >=2.18.1' - - 'r-gplots >=3.0.1' - - 'r-mass >=7.3.51' - - 'r-matrixstats >=0.54.0' - - 'r-moments >=0.14' - - 'r-rcpp >=1.0.0' - - r-rcppeigen - - 'r-reshape2 >=1.4.3' - - 'r-robustbase >=0.93.5' - - 'r-viridis >=0.5.1' - - libblas - - liblapack - run: - - 'bioconductor-mixomics >=6.26.0,<6.27.0' - - r-base - - 'r-beanplot >=1.2' - - 'r-collapse >=1.9.2' - - 'r-dosnow >=1.0.16' - - 'r-dplyr >=0.7.8' - - 'r-fnn >=1.1.3' - - 'r-foreach >=1.4.4' - - 'r-ggplot2 >=3.1.0' - - 'r-gmodels >=2.18.1' - - 'r-gplots >=3.0.1' - - 'r-mass >=7.3.51' - - 'r-matrixstats >=0.54.0' - - 'r-moments >=0.14' - - 'r-rcpp >=1.0.0' - - r-rcppeigen - - 'r-reshape2 >=1.4.3' - - 'r-robustbase >=0.93.5' - - 'r-viridis >=0.5.1' + build: - {{ cdt('mesa-libgl-devel') }} # [linux] - {{ cdt('mesa-dri-drivers') }} # [linux] @@ -72,16 +37,62 @@ requirements: - {{ compiler('c') }} - {{ compiler('cxx') }} - make + + host: + - bioconductor-mixomics >=6.30.0,<6.31.0 + - r-base + - r-beanplot >=1.2 + - r-clusterr >=1.3.2 + - r-collapse >=1.9.2 + - r-dosnow >=1.0.16 + - r-dplyr >=0.7.8 + - r-fnn >=1.1.3 + - r-foreach >=1.4.4 + - r-ggplot2 >=3.1.0 + - r-gmodels >=2.18.1 + - r-gplots >=3.0.1 + - r-mass >=7.3.51 + - r-matrixstats >=0.54.0 + - r-moments >=0.14 + - r-rcpp >=1.0.0 + - r-rcppeigen + - r-reshape2 >=1.4.3 + - r-robustbase >=0.93.5 + - r-viridis >=0.5.1 + - libblas + - liblapack + + run: + - bioconductor-mixomics >=6.30.0,<6.31.0 + - r-base + - r-beanplot >=1.2 + - r-clusterr >=1.3.2 + - r-collapse >=1.9.2 + - r-dosnow >=1.0.16 + - r-dplyr >=0.7.8 + - r-fnn >=1.1.3 + - r-foreach >=1.4.4 + - r-ggplot2 >=3.1.0 + - r-gmodels >=2.18.1 + - r-gplots >=3.0.1 + - r-mass >=7.3.51 + - r-matrixstats >=0.54.0 + - r-moments >=0.14 + - r-rcpp >=1.0.0 + - r-rcppeigen + - r-reshape2 >=1.4.3 + - r-robustbase >=0.93.5 + - r-viridis >=0.5.1 + +source: + md5: 92e4d0d9bdaa1db09f4a2785693aa15e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Determination of essential phenotypic elements of clusters in high-dimensional entities' - description: 'The purpose of this package is to identify traits in a dataset that can separate groups. This is done on two levels. First, clustering is performed, using an implementation of sparse K-means. Secondly, the generated clusters are used to predict outcomes of groups of individuals based on their distribution of observations in the different clusters. As certain clusters with separating information will be identified, and these clusters are defined by a sparse number of variables, this method can reduce the complexity of data, to only emphasize the data that actually matters.' - license_file: LICENSE -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-depinfer/meta.yaml b/recipes/bioconductor-depinfer/meta.yaml index 94dc1dcdf83ca..a22cd360a5bdb 100644 --- a/recipes/bioconductor-depinfer/meta.yaml +++ b/recipes/bioconductor-depinfer/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "DepInfeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d673a7cc6ac21a4d899238878c09533f +about: + description: 'DepInfeR integrates two experimentally accessible input data matrices: the drug sensitivity profiles of cancer cell lines or primary tumors ex-vivo (X), and the drug affinities of a set of proteins (Y), to infer a matrix of molecular protein dependencies of the cancers (ß). DepInfeR deconvolutes the protein inhibition effect on the viability phenotype by using regularized multivariate linear regression. It assigns a “dependence coefficient” to each protein and each sample, and therefore could be used to gain a causal and accurate understanding of functional consequences of genomic aberrations in a heterogeneous disease, as well as to guide the choice of pharmacological intervention for a specific cancer type, sub-type, or an individual patient. For more information, please read out preprint on bioRxiv: https://doi.org/10.1101/2022.01.11.475864.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-depinfer", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat (>= 3.0.0), knitr, rmarkdown, dplyr, tidyr, tibble, ggplot2, missForest, pheatmap, RColorBrewer, ggrepel, BiocStyle, ggbeeswarm requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-glmnet - r-matrixstats run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-glmnet - r-matrixstats +source: + md5: 9b73ea2db7a9bf683124b5ba5d603c50 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling' - description: 'DepInfeR integrates two experimentally accessible input data matrices: the drug sensitivity profiles of cancer cell lines or primary tumors ex-vivo (X), and the drug affinities of a set of proteins (Y), to infer a matrix of molecular protein dependencies of the cancers (ß). DepInfeR deconvolutes the protein inhibition effect on the viability phenotype by using regularized multivariate linear regression. It assigns a “dependence coefficient” to each protein and each sample, and therefore could be used to gain a causal and accurate understanding of functional consequences of genomic aberrations in a heterogeneous disease, as well as to guide the choice of pharmacological intervention for a specific cancer type, sub-type, or an individual patient. For more information, please read out preprint on bioRxiv: https://doi.org/10.1101/2022.01.11.475864.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-depmap/meta.yaml b/recipes/bioconductor-depmap/meta.yaml index f38b98fd584e6..a5f3f1275e15d 100644 --- a/recipes/bioconductor-depmap/meta.yaml +++ b/recipes/bioconductor-depmap/meta.yaml @@ -1,44 +1,57 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "depmap" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The depmap package is a data package that accesses datsets from the Broad Institute DepMap cancer dependency study using ExperimentHub. Datasets from the most current release are available, including RNAI and CRISPR-Cas9 gene knockout screens quantifying the genetic dependency for select cancer cell lines. Additional datasets are also available pertaining to the log copy number of genes for select cell lines, protein expression of cell lines as measured by reverse phase protein lysate microarray (RPPA), 'Transcript Per Million' (TPM) data, as well as supplementary datasets which contain metadata and mutation calls for the other datasets found in the current release. The 19Q3 release adds the drug_dependency dataset, that contains cancer cell line dependency data with respect to drug and drug-candidate compounds. The 20Q2 release adds the proteomic dataset that contains quantitative profiling of proteins via mass spectrometry. This package will be updated on a quarterly basis to incorporate the latest Broad Institute DepMap Public cancer dependency datasets. All data made available in this package was generated by the Broad Institute DepMap for research purposes and not intended for clinical use. This data is distributed under the Creative Commons license (Attribution 4.0 International (CC BY 4.0)). + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Cancer Dependency Map Data Package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7f00d05c7f899e622293767baa04e120 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-depmap", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, BiocStyle, viridis, gridExtra, ggplot2, readr, tibble, stringr, tidyr + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, BiocStyle, viridis, gridExtra, ggplot2, readr, stringr, tidyverse, magick requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base + - r-curl - r-dplyr + - r-httr2 + - r-tibble run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base + - r-curl - r-dplyr + - r-httr2 + - r-tibble - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 7570708bfa0edac82ad43e8f73600460 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Cancer Dependency Map Data Package' - description: 'The depmap package is a data package that accesses datsets from the Broad Institute DepMap cancer dependency study using ExperimentHub. Datasets from the most current release are available, including RNAI and CRISPR-Cas9 gene knockout screens quantifying the genetic dependency for select cancer cell lines. Additional datasets are also available pertaining to the log copy number of genes for select cell lines, protein expression of cell lines as measured by reverse phase protein lysate microarray (RPPA), ''Transcript Per Million'' (TPM) data, as well as supplementary datasets which contain metadata and mutation calls for the other datasets found in the current release. The 19Q3 release adds the drug_dependency dataset, that contains cancer cell line dependency data with respect to drug and drug-candidate compounds. The 20Q2 release adds the proteomic dataset that contains quantitative profiling of proteins via mass spectrometry. This package will be updated on a quarterly basis to incorporate the latest Broad Institute DepMap Public cancer dependency datasets. All data made available in this package was generated by the Broad Institute DepMap for research purposes and not intended for clinical use. This data is distributed under the Creative Commons license (Attribution 4.0 International (CC BY 4.0)).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-depmap/post-link.sh b/recipes/bioconductor-depmap/post-link.sh index a1ee9c05ab0be..0167a35f5c8e1 100644 --- a/recipes/bioconductor-depmap/post-link.sh +++ b/recipes/bioconductor-depmap/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "depmap-1.16.0" +installBiocDataPackage.sh "depmap-1.20.0" diff --git a/recipes/bioconductor-deqms/meta.yaml b/recipes/bioconductor-deqms/meta.yaml index 7fee72622c3bd..59fdddbe84785 100644 --- a/recipes/bioconductor-deqms/meta.yaml +++ b/recipes/bioconductor-deqms/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "DEqMS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: DEqMS is developped on top of Limma. However, Limma assumes same prior variance for all genes. In proteomics, the accuracy of protein abundance estimates varies by the number of peptides/PSMs quantified in both label-free and labelled data. Proteins quantification by multiple peptides or PSMs are more accurate. DEqMS package is able to estimate different prior variances for proteins quantified by different number of PSMs/peptides, therefore acchieving better accuracy. The package can be applied to analyze both label-free and labelled proteomics data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: a tool to perform statistical analysis of differential protein expression for quantitative proteomics data. -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bc308e6f683ca1bf0dcdb703274575ac build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-deqms", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle,knitr,rmarkdown,markdown,plyr,reshape2,farms,utils,ggrepel,ExperimentHub,LSD + +extra: + parent_recipe: + name: bioconductor-deqms + path: recipes/bioconductor-deqms + version: 1.0.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle,knitr,rmarkdown,markdown,plyr,reshape2,utils,ggrepel,ExperimentHub,LSD requirements: host: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-ggplot2 - r-matrixstats run: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-ggplot2 - r-matrixstats + +source: + md5: 8eaf7116c761b1cb77ba33ff389536d9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.' - description: 'DEqMS is developped on top of Limma. However, Limma assumes same prior variance for all genes. In proteomics, the accuracy of protein abundance estimates varies by the number of peptides/PSMs quantified in both label-free and labelled data. Proteins quantification by multiple peptides or PSMs are more accurate. DEqMS package is able to estimate different prior variances for proteins quantified by different number of PSMs/peptides, therefore acchieving better accuracy. The package can be applied to analyze both label-free and labelled proteomics data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - parent_recipe: - name: bioconductor-deqms - path: recipes/bioconductor-deqms - version: 1.0.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-derfinder/meta.yaml b/recipes/bioconductor-derfinder/meta.yaml index 5f1ca01fd980f..5aa146fa4c76a 100644 --- a/recipes/bioconductor-derfinder/meta.yaml +++ b/recipes/bioconductor-derfinder/meta.yaml @@ -1,79 +1,81 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "derfinder" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a3ef629c180b64b0776c880164603c7b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-derfinder", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:derfinder + parent_recipe: + name: bioconductor-derfinder + path: recipes/bioconductor-derfinder + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle (>= 2.5.19), sessioninfo, derfinderData (>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitr (>= 1.6), limma, RefManageR, rmarkdown (>= 0.3.3), testthat (>= 2.1.0), TxDb.Hsapiens.UCSC.hg19.knownGene, covr requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-derfinderhelper >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-derfinderhelper >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicfiles >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-hmisc run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-derfinderhelper >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-derfinderhelper >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicfiles >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-hmisc + +source: + md5: ed63e8dd5060fbfc0dac93c18ada5876 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach' - description: | - This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. - Two implementations of the DER Finder approach are included in this package: (1) single base-level - F-statistics and (2) DER identification at the expressed regions-level. - The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks. -extra: - identifiers: - - biotools:derfinder - parent_recipe: - name: bioconductor-derfinder - path: recipes/bioconductor-derfinder - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-derfinderdata/meta.yaml b/recipes/bioconductor-derfinderdata/meta.yaml index ab731b2b7adf4..7e50f94874098 100644 --- a/recipes/bioconductor-derfinderdata/meta.yaml +++ b/recipes/bioconductor-derfinderdata/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "2.20.0" %} +{% set version = "2.24.0" %} {% set name = "derfinderData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 032efff51d29eae3fc1a5e032c0f3c40 +about: + description: Processed 22 samples from BrainSpan keeping only the information for chromosome 21. Data is stored in the BigWig format and is used for examples in other packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Processed BigWigs from BrainSpan for examples build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-derfinderdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: sessioninfo, knitr (>= 1.6), RefManageR, rmarkdown (>= 0.3.3), BiocStyle requirements: host: @@ -26,13 +24,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 29d921dc8f08b7699fdf23d90fbca0d1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Processed BigWigs from BrainSpan for examples' - description: 'Processed 22 samples from BrainSpan keeping only the information for chromosome 21. Data is stored in the BigWig format and is used for examples in other packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-derfinderdata/post-link.sh b/recipes/bioconductor-derfinderdata/post-link.sh index 07fd8f6c6666d..a22d08e13851e 100644 --- a/recipes/bioconductor-derfinderdata/post-link.sh +++ b/recipes/bioconductor-derfinderdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "derfinderdata-2.20.0" +installBiocDataPackage.sh "derfinderdata-2.24.0" diff --git a/recipes/bioconductor-derfinderhelper/meta.yaml b/recipes/bioconductor-derfinderhelper/meta.yaml index d23d5cb1f7b01..5c4807ebc6560 100644 --- a/recipes/bioconductor-derfinderhelper/meta.yaml +++ b/recipes/bioconductor-derfinderhelper/meta.yaml @@ -1,49 +1,55 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "derfinderHelper" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Helper package for speeding up the derfinder package when using multiple cores. This package is particularly useful when using BiocParallel and it helps reduce the time spent loading the full derfinder package when running the F-statistics calculation in parallel. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: derfinder helper package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2544077112525d7f25f34270ed365423 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-derfinderhelper", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:derfinderhelper + parent_recipe: + name: bioconductor-derfinderhelper + path: recipes/bioconductor-derfinderhelper + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19), RefManageR, rmarkdown (>= 0.3.3), testthat, covr requirements: host: - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-matrix run: - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-matrix + +source: + md5: 214937e15ae7769c646482c71ca7f02a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'derfinder helper package' - description: 'Helper package for speeding up the derfinder package when using multiple cores. This package is particularly useful when using BiocParallel and it helps reduce the time spent loading the full derfinder package when running the F-statistics calculation in parallel.' -extra: - identifiers: - - biotools:derfinderhelper - parent_recipe: - name: bioconductor-derfinderhelper - path: recipes/bioconductor-derfinderhelper - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-derfinderplot/meta.yaml b/recipes/bioconductor-derfinderplot/meta.yaml index 2890878efb489..a09572dd9279e 100644 --- a/recipes/bioconductor-derfinderplot/meta.yaml +++ b/recipes/bioconductor-derfinderplot/meta.yaml @@ -1,35 +1,44 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "derfinderPlot" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides plotting functions for results from the derfinder package. This helps separate the graphical dependencies required for making these plots from the core functionality of derfinder. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Plotting functions for derfinder -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c3dbd553554f3b043b8f03e4b05a964a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-derfinderplot", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:derfinderplot + parent_recipe: + name: bioconductor-derfinderplot + path: recipes/bioconductor-derfinderplot + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: biovizBase (>= 1.27.2), bumphunter (>= 1.7.6), derfinderData (>= 0.99.0), sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19), org.Hs.eg.db, RefManageR, rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, covr requirements: host: - - 'bioconductor-derfinder >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-derfinder >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-plyr @@ -37,33 +46,30 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-derfinder >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-derfinder >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-plyr - r-rcolorbrewer - r-reshape2 - r-scales + +source: + md5: 972812349ec65988ca88d2593f523574 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Plotting functions for derfinder' - description: 'This package provides plotting functions for results from the derfinder package. This helps separate the graphical dependencies required for making these plots from the core functionality of derfinder.' -extra: - identifiers: - - biotools:derfinderplot - parent_recipe: - name: bioconductor-derfinderplot - path: recipes/bioconductor-derfinderplot - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-descan2/build_failure.linux-aarch64.yaml b/recipes/bioconductor-descan2/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..075f94ff36c21 --- /dev/null +++ b/recipes/bioconductor-descan2/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 86810688d09de06470ed81906a6fadaece1457a94a0564632cde667da5a217e7 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec("bioconductor-chippeakanno==3.40.0=r44hdfd78af_0"), MatchSpec(">=1.24.0,<1.25.0")} + Encountered problems while solving: + - nothing provides bioconductor-universalmotif >=1.24.0,<1.25.0 needed by bioconductor-chippeakanno-3.40.0-r44hdfd78af_0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-chippeakanno >=3.40.0,<3.41.0 [0m is not installable because it requires + [31mbioconductor-universalmotif >=1.24.0,<1.25.0 [0m, which does not exist (perhaps a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec("bioconductor-chippeakanno==3.40.0=r44hdfd78af_0"), MatchSpec(">=1.24.0,<1.25.0")} + Encountered problems while solving: + - nothing provides bioconductor-universalmotif >=1.24.0,<1.25.0 needed by bioconductor-chippeakanno-3.40.0-r44hdfd78af_0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-chippeakanno >=3.40.0,<3.41.0 [0m is not installable because it requires + [31mbioconductor-universalmotif >=1.24.0,<1.25.0 [0m, which does not exist (perhaps a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec("bioconductor-chippeakanno==3.40.0=r44hdfd78af_0"), MatchSpec(">=1.24.0,<1.25.0")} + Encountered problems while solving: + - nothing provides bioconductor-universalmotif >=1.24.0,<1.25.0 needed by bioconductor-chippeakanno-3.40.0-r44hdfd78af_0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-chippeakanno >=3.40.0,<3.41.0 [0m is not installable because it requires + [31mbioconductor-universalmotif >=1.24.0,<1.25.0 [0m, which does not exist (perhaps a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-descan2/meta.yaml b/recipes/bioconductor-descan2/meta.yaml index 76ec1100b9233..b882cc674bb46 100644 --- a/recipes/bioconductor-descan2/meta.yaml +++ b/recipes/bioconductor-descan2/meta.yaml @@ -1,78 +1,87 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "DEScan2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Integrated peak and differential caller, specifically designed for broad epigenomic signals. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Differential Enrichment Scan 2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 476f052d4a86e27d332812852fd7e0c1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-descan2", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:descan2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq, RUVSeq, RColorBrewer, statmod requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-chippeakanno >=3.40.0,<3.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-glue - r-plyr - - 'r-rcpp >=0.12.13' + - r-rcpp >=0.12.13 - r-rcpparmadillo - libblas - liblapack + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-chippeakanno >=3.40.0,<3.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-glue - r-plyr - - 'r-rcpp >=0.12.13' + - r-rcpp >=0.12.13 - r-rcpparmadillo - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: e11dbe2954f8936d2d3a0df5f8239aac + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Differential Enrichment Scan 2' - description: 'Integrated peak and differential caller, specifically designed for broad epigenomic signals.' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-deseq2/meta.yaml b/recipes/bioconductor-deseq2/meta.yaml index b374f1aa2c05d..66a2cfe635f29 100644 --- a/recipes/bioconductor-deseq2/meta.yaml +++ b/recipes/bioconductor-deseq2/meta.yaml @@ -1,83 +1,85 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "DESeq2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Differential gene expression analysis based on the negative binomial distribution -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5eb89526ce9fd4da98b1a5e0b5ba0bf3 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-deseq2", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:deseq2 + - doi:10.1186/s13059-014-0550-8 + - usegalaxy-eu:deseq2 + parent_recipe: + name: bioconductor-deseq2 + path: recipes/bioconductor-deseq2 + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, pasilla (>= 0.2.10), glmGamPoi, BiocManager requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - bioconductor-apeglm - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - r-ashr + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-ggplot2 >=3.4.0' + - r-ggplot2 >=3.4.0 - r-locfit - r-matrixstats - - 'r-rcpp >=0.11.0' + - r-rcpp >=0.11.0 - r-rcpparmadillo - libblas - liblapack run: - - bioconductor-apeglm - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - r-ashr + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-ggplot2 >=3.4.0' + - r-ggplot2 >=3.4.0 - r-locfit - r-matrixstats - - 'r-rcpp >=0.11.0' + - r-rcpp >=0.11.0 - r-rcpparmadillo - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 211812c23e1a25da4396c82582cba27e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL-3.0-or-later' - summary: 'Differential gene expression analysis based on the negative binomial distribution' - description: 'Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:deseq2 - - doi:10.1186/s13059-014-0550-8 - - usegalaxy-eu:deseq2 - parent_recipe: - name: bioconductor-deseq2 - path: recipes/bioconductor-deseq2 - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-desingle/meta.yaml b/recipes/bioconductor-desingle/meta.yaml index 2f3cbbd1c30a4..9b07e7e833ab6 100644 --- a/recipes/bioconductor-desingle/meta.yaml +++ b/recipes/bioconductor-desingle/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "DEsingle" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: DEsingle is an R package for differential expression (DE) analysis of single-cell RNA-seq (scRNA-seq) data. It defines and detects 3 types of differentially expressed genes between two groups of single cells, with regard to different expression status (DEs), differential expression abundance (DEa), and general differential expression (DEg). DEsingle employs Zero-Inflated Negative Binomial model to estimate the proportion of real and dropout zeros and to define and detect the 3 types of DE genes. Results showed that DEsingle outperforms existing methods for scRNA-seq DE analysis, and can reveal different types of DE genes that are enriched in different biological functions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: DEsingle for detecting three types of differential expression in single-cell RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6969e960919434ccd6e5b9bdd926aece build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-desingle", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, SingleCellExperiment requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - - 'r-bbmle >=1.0.18' - - 'r-gamlss >=4.4-0' - - 'r-mass >=7.3-45' - - 'r-matrix >=1.2-14' - - 'r-maxlik >=1.3-4' - - 'r-pscl >=1.4.9' - - 'r-vgam >=1.0-2' + - r-bbmle >=1.0.18 + - r-gamlss >=4.4-0 + - r-mass >=7.3-45 + - r-matrix >=1.2-14 + - r-maxlik >=1.3-4 + - r-pscl >=1.4.9 + - r-vgam >=1.0-2 run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - - 'r-bbmle >=1.0.18' - - 'r-gamlss >=4.4-0' - - 'r-mass >=7.3-45' - - 'r-matrix >=1.2-14' - - 'r-maxlik >=1.3-4' - - 'r-pscl >=1.4.9' - - 'r-vgam >=1.0-2' + - r-bbmle >=1.0.18 + - r-gamlss >=4.4-0 + - r-mass >=7.3-45 + - r-matrix >=1.2-14 + - r-maxlik >=1.3-4 + - r-pscl >=1.4.9 + - r-vgam >=1.0-2 + +source: + md5: 6d854234a35297b998abc3086af9af28 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'DEsingle for detecting three types of differential expression in single-cell RNA-seq data' - description: 'DEsingle is an R package for differential expression (DE) analysis of single-cell RNA-seq (scRNA-seq) data. It defines and detects 3 types of differentially expressed genes between two groups of single cells, with regard to different expression status (DEs), differential expression abundance (DEa), and general differential expression (DEg). DEsingle employs Zero-Inflated Negative Binomial model to estimate the proportion of real and dropout zeros and to define and detect the 3 types of DE genes. Results showed that DEsingle outperforms existing methods for scRNA-seq DE analysis, and can reveal different types of DE genes that are enriched in different biological functions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-desousa2013/meta.yaml b/recipes/bioconductor-desousa2013/meta.yaml index ffb817248a4d9..98302e8c5a672 100644 --- a/recipes/bioconductor-desousa2013/meta.yaml +++ b/recipes/bioconductor-desousa2013/meta.yaml @@ -1,36 +1,48 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "DeSousa2013" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package reproduces the main pipeline to analyze the AMC-AJCCII-90 microarray data set in De Sousa et al. accepted by Nature Medicine in 2013. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Poor prognosis colon cancer is defined by a molecularly distinct subtype and precursor lesion -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 41a3ca5cba40653eb4be04203aaf60ac build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-desousa2013", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' - - 'bioconductor-frma >=1.54.0,<1.55.0' - - 'bioconductor-frmatools >=1.54.0,<1.55.0' - - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-hgu133plus2frmavecs >=1.5.0,<1.6.0' - - 'bioconductor-siggenes >=1.76.0,<1.77.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-consensusclusterplus >=1.70.0,<1.71.0 + - bioconductor-frma >=1.58.0,<1.59.0 + - bioconductor-frmatools >=1.58.0,<1.59.0 + - bioconductor-hgu133plus2.db >=3.13.0,<3.14.0 + - bioconductor-hgu133plus2frmavecs >=1.5.0,<1.6.0 + - bioconductor-siggenes >=1.80.0,<1.81.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-cluster - r-gplots @@ -39,16 +51,16 @@ requirements: - r-rocr - r-survival run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' - - 'bioconductor-frma >=1.54.0,<1.55.0' - - 'bioconductor-frmatools >=1.54.0,<1.55.0' - - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-hgu133plus2frmavecs >=1.5.0,<1.6.0' - - 'bioconductor-siggenes >=1.76.0,<1.77.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-consensusclusterplus >=1.70.0,<1.71.0 + - bioconductor-frma >=1.58.0,<1.59.0 + - bioconductor-frmatools >=1.58.0,<1.59.0 + - bioconductor-hgu133plus2.db >=3.13.0,<3.14.0 + - bioconductor-hgu133plus2frmavecs >=1.5.0,<1.6.0 + - bioconductor-siggenes >=1.80.0,<1.81.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-cluster - r-gplots @@ -57,23 +69,17 @@ requirements: - r-rocr - r-survival - curl - - 'bioconductor-data-packages >=20231203' - build: - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - xorg-libxfixes # [linux] + - bioconductor-data-packages >=20241103 + +source: + md5: 62b95939db5cc4149c72f97a4dbd5ca6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Poor prognosis colon cancer is defined by a molecularly distinct subtype and precursor lesion' - description: 'This package reproduces the main pipeline to analyze the AMC-AJCCII-90 microarray data set in De Sousa et al. accepted by Nature Medicine in 2013.' -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-desousa2013/post-link.sh b/recipes/bioconductor-desousa2013/post-link.sh index 4c31f29da3892..04669769c7370 100644 --- a/recipes/bioconductor-desousa2013/post-link.sh +++ b/recipes/bioconductor-desousa2013/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "desousa2013-1.38.0" +installBiocDataPackage.sh "desousa2013-1.42.0" diff --git a/recipes/bioconductor-despace/meta.yaml b/recipes/bioconductor-despace/meta.yaml index 6ad56c3815333..b7ba31d9f7463 100644 --- a/recipes/bioconductor-despace/meta.yaml +++ b/recipes/bioconductor-despace/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "DESpace" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Intuitive framework for identifying spatially variable genes (SVGs) via edgeR, a popular method for performing differential expression analyses. Based on pre-annotated spatial clusters as summarized spatial information, DESpace models gene expression using a negative binomial (NB), via edgeR, with spatial clusters as covariates. SVGs are then identified by testing the significance of spatial clusters. The method is flexible and robust, and is faster than the most SV methods. Furthermore, to the best of our knowledge, it is the only SV approach that allows: - performing a SV test on each individual spatial cluster, hence identifying the key regions of the tissue affected by spatial variability; - jointly fitting multiple samples, targeting genes with consistent spatial patterns across replicates.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'DESpace: a framework to discover spatially variable genes' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 436915bded5ec94da6e412ccdff80e8e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-despace", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, BiocStyle, ExperimentHub, concaveman, spatialLIBD, purrr, scuttle, utils requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-cowplot @@ -42,13 +44,13 @@ requirements: - r-patchwork - r-scales run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-cowplot @@ -61,13 +63,16 @@ requirements: - r-matrix - r-patchwork - r-scales + +source: + md5: dc34a1f5bdc23f3ab631228c10f1a4b6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'DESpace: a framework to discover spatially variable genes' - description: 'Intuitive framework for identifying spatially variable genes (SVGs) via edgeR, a popular method for performing differential expression analyses. Based on pre-annotated spatial clusters as summarized spatial information, DESpace models gene expression using a negative binomial (NB), via edgeR, with spatial clusters as covariates. SVGs are then identified by testing the significance of spatial clusters. The method is flexible and robust, and is faster than the most SV methods. Furthermore, to the best of our knowledge, it is the only SV approach that allows: - performing a SV test on each individual spatial cluster, hence identifying the key regions of the tissue affected by spatial variability; - jointly fitting multiple samples, targeting genes with consistent spatial patterns across replicates.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-desubs/meta.yaml b/recipes/bioconductor-desubs/meta.yaml index 98b6a9306f8b5..586dcf5f9ded7 100644 --- a/recipes/bioconductor-desubs/meta.yaml +++ b/recipes/bioconductor-desubs/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "DEsubs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: DEsubs is a network-based systems biology package that extracts disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments. It contains an extensive and customizable framework covering a broad range of operation modes at all stages of the subpathway analysis, enabling a case-specific approach. The operation modes refer to the pathway network construction and processing, the subpathway extraction, visualization and enrichment analysis with regard to various biological and pharmacological features. Its capabilities render it a tool-guide for both the modeler and experimentalist for the identification of more robust systems-level biomarkers for complex diseases. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1e2b74c85e35888eab89ac39a363c32c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-desubs", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, knitr, rmarkdown requirements: host: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-ebseq >=2.0.0,<2.1.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-ebseq >=2.4.0,<2.5.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 - r-base - r-circlize - r-ggplot2 @@ -38,12 +40,12 @@ requirements: - r-nbpseq - r-pheatmap run: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-ebseq >=2.0.0,<2.1.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-ebseq >=2.4.0,<2.5.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 - r-base - r-circlize - r-ggplot2 @@ -53,13 +55,16 @@ requirements: - r-matrix - r-nbpseq - r-pheatmap + +source: + md5: 7eeaa2d15bdfdfcbc3b957b3688e873d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments' - description: 'DEsubs is a network-based systems biology package that extracts disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments. It contains an extensive and customizable framework covering a broad range of operation modes at all stages of the subpathway analysis, enabling a case-specific approach. The operation modes refer to the pathway network construction and processing, the subpathway extraction, visualization and enrichment analysis with regard to various biological and pharmacological features. Its capabilities render it a tool-guide for both the modeler and experimentalist for the identification of more robust systems-level biomarkers for complex diseases.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dewseq/meta.yaml b/recipes/bioconductor-dewseq/meta.yaml index 035c2b2dbe9ed..2e6eabbf6e058 100644 --- a/recipes/bioconductor-dewseq/meta.yaml +++ b/recipes/bioconductor-dewseq/meta.yaml @@ -1,55 +1,60 @@ -{% set version = "1.16.2" %} +{% set version = "1.20.0" %} {% set name = "DEWSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: DEWSeq is a sliding window approach for the analysis of differentially enriched binding regions eCLIP or iCLIP next generation sequencing data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Differential Expressed Windows Based on Negative Binomial Distribution -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4164c3c7d4967586861e0c2d40815ec5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dewseq", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, tidyverse, testthat, BiocStyle, IHW + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, tidyverse, rmarkdown, testthat, BiocStyle, IHW requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-data.table >=1.11.8' + - r-data.table >=1.11.8 - r-r.utils run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-data.table >=1.11.8' + - r-data.table >=1.11.8 - r-r.utils + +source: + md5: 85f79fefdd2693dd19a371f5c1cd47e2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 3)' - summary: 'Differential Expressed Windows Based on Negative Binomial Distribution' - description: 'DEWSeq is a sliding window approach for the analysis of differentially enriched binding regions eCLIP or iCLIP next generation sequencing data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dexma/meta.yaml b/recipes/bioconductor-dexma/meta.yaml index f828df78731c2..50ae7162e1f60 100644 --- a/recipes/bioconductor-dexma/meta.yaml +++ b/recipes/bioconductor-dexma/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.10.6" %} +{% set version = "1.14.0" %} {% set name = "DExMA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: performing all the steps of gene expression meta-analysis considering the possible existence of missing genes. It provides the necessary functions to be able to perform the different methods of gene expression meta-analysis. In addition, it contains functions to apply quality controls, download GEO datasets and show graphical representations of the results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Differential Expression Meta-Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7397f231c7a241e6bfb258ca064ff8b7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dexma", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, qpdf, BiocGenerics, RUnit requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-dexmadata >=1.10.0,<1.11.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-snpstats >=1.52.0,<1.53.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-dexmadata >=1.14.0,<1.15.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-snpstats >=1.56.0,<1.57.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-bnstruct - r-pheatmap @@ -37,13 +39,13 @@ requirements: - r-scales - r-swamp run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-dexmadata >=1.10.0,<1.11.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-snpstats >=1.52.0,<1.53.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-dexmadata >=1.14.0,<1.15.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-snpstats >=1.56.0,<1.57.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-bnstruct - r-pheatmap @@ -51,13 +53,16 @@ requirements: - r-rcolorbrewer - r-scales - r-swamp + +source: + md5: 2db6cbb01b58ca63b9372cd70d698f1a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Differential Expression Meta-Analysis' - description: 'performing all the steps of gene expression meta-analysis considering the possible existence of missing genes. It provides the necessary functions to be able to perform the different methods of gene expression meta-analysis. In addition, it contains functions to apply quality controls, download GEO datasets and show graphical representations of the results.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dexmadata/meta.yaml b/recipes/bioconductor-dexmadata/meta.yaml index 418aaacbbfa95..263a2c149362c 100644 --- a/recipes/bioconductor-dexmadata/meta.yaml +++ b/recipes/bioconductor-dexmadata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "DExMAdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d2a9cc7d0044ffc23e572f4c5cc4426 +about: + description: Data objects needed to allSameID() function of DExMA package. There are also some objects that are necessary to be able to apply the examples of the DExMA package, which illustrate package functionality. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Data package for DExMA package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dexmadata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6c03e9b7bdf0dd3c28a6aedbecf1de44 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Data package for DExMA package' - description: 'Data objects needed to allSameID() function of DExMA package. There are also some objects that are necessary to be able to apply the examples of the DExMA package, which illustrate package functionality.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dexmadata/post-link.sh b/recipes/bioconductor-dexmadata/post-link.sh index deb9a0366746c..83836682645dd 100644 --- a/recipes/bioconductor-dexmadata/post-link.sh +++ b/recipes/bioconductor-dexmadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dexmadata-1.10.0" +installBiocDataPackage.sh "dexmadata-1.14.0" diff --git a/recipes/bioconductor-dexseq/build.sh b/recipes/bioconductor-dexseq/build.sh index a9c2ad544d4dc..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dexseq/build.sh +++ b/recipes/bioconductor-dexseq/build.sh @@ -8,11 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars - -$R CMD INSTALL --build . -python_path=$PREFIX/lib/R/library/DEXSeq/python_scripts -echo python3 ${python_path}/dexseq_prepare_annotation.py '"$@"' > $PREFIX/bin/dexseq_prepare_annotation.py -chmod +x $PREFIX/bin/dexseq_prepare_annotation.py - -echo python3 ${python_path}/dexseq_count.py '"$@"' > $PREFIX/bin/dexseq_count.py -chmod +x $PREFIX/bin/dexseq_count.py +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dexseq/meta.yaml b/recipes/bioconductor-dexseq/meta.yaml index c2dea7842a4e5..fa2a9a304b601 100644 --- a/recipes/bioconductor-dexseq/meta.yaml +++ b/recipes/bioconductor-dexseq/meta.yaml @@ -1,82 +1,85 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "DEXSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Inference of differential exon usage in RNA-Seq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e5876f927b0b0cdfc4a402bfb4fb3d6 build: - number: 2 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dexseq", max_pin="x.x") }}' - noarch: generic -# Suggests: GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22), parathyroidSE, BiocStyle, knitr, rmarkdown, testthat, pasillaBamSubset, GenomicAlignments, roxygen2, glmGamPoi + +extra: + identifiers: + - biotools:dexseq + - usegalaxy-eu:dexseq + parent_recipe: + name: bioconductor-dexseq + path: recipes/bioconductor-dexseq + version: 1.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: GenomicFeatures, txdbmaker, pasilla (>= 0.2.22), parathyroidSE, BiocStyle, knitr, rmarkdown, testthat, pasillaBamSubset, GenomicAlignments, roxygen2, glmGamPoi requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-geneplotter >=1.80.0,<1.81.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-geneplotter >=1.84.0,<1.85.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-hwriter - r-rcolorbrewer - r-statmod - r-stringr run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-geneplotter >=1.80.0,<1.81.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'htseq >=2.0.2,<2.1' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-geneplotter >=1.84.0,<1.85.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-hwriter - r-rcolorbrewer - r-statmod - r-stringr + +source: + md5: 065a8022b6c167143856252edcf4ff8e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' - - dexseq_prepare_annotation.py --help - - dexseq_count.py --help -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Inference of differential exon usage in RNA-Seq' - description: 'The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:dexseq - - usegalaxy-eu:dexseq - parent_recipe: - name: bioconductor-dexseq - path: recipes/bioconductor-dexseq - version: 1.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dfp/meta.yaml b/recipes/bioconductor-dfp/meta.yaml index 846c1dbfc78a7..024a796f4b68b 100644 --- a/recipes/bioconductor-dfp/meta.yaml +++ b/recipes/bioconductor-dfp/meta.yaml @@ -1,40 +1,22 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "DFP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a supervised technique able to identify differentially expressed genes, based on the construction of \emph{Fuzzy Patterns} (FPs). The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Gene Selection -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5eb14fe67a6dd0599cd24c3473eec349 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dfp", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Gene Selection' - description: 'This package provides a supervised technique able to identify differentially expressed genes, based on the construction of \emph{Fuzzy Patterns} (FPs). The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + extra: identifiers: - biotools:dfp @@ -44,3 +26,27 @@ extra: path: recipes/bioconductor-dfp version: 1.38.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + +source: + md5: 7da84966f3e54463d5c52c1d432b8d71 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-dfplyr/build.sh b/recipes/bioconductor-dfplyr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dfplyr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dfplyr/meta.yaml b/recipes/bioconductor-dfplyr/meta.yaml new file mode 100644 index 0000000000000..547db9f068d09 --- /dev/null +++ b/recipes/bioconductor-dfplyr/meta.yaml @@ -0,0 +1,52 @@ +{% set version = "1.0.0" %} +{% set name = "DFplyr" %} +{% set bioc = "3.20" %} + +about: + description: Provides `dplyr` verbs (`mutate`, `select`, `filter`, etc...) supporting `S4Vectors::DataFrame` objects. Importantly, this is achieved without conversion to an intermediate `tibble`. Adds grouping infrastructure to `DataFrame` which is respected by the transformation verbs. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A `DataFrame` (`S4Vectors`) backend for `dplyr` + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dfplyr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, GenomeInfoDb, GenomicRanges, IRanges, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), tibble +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-dplyr + - r-rlang + - r-tidyselect + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-dplyr + - r-rlang + - r-tidyselect + +source: + md5: 56bdadfe6079d09a0fe0457b20f519bb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-diffbind/build_failure.osx-64.yaml b/recipes/bioconductor-diffbind/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..aa0f68122520a --- /dev/null +++ b/recipes/bioconductor-diffbind/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 2dd0cf30db54f91167edb0fdaae039ff85134cad3b5d376eb83403ed5de98c35 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-diffbind-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-diffbind_1735858628220/work/conda_build.sh']' returned non-zero exit status 1. + + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-diffbind-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-diffbind-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-diffbind_1735858628220/work/conda_build.sh']' returned non-zero exit status 1. + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-diffbind-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-diffbind-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-diffbind-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-diffbind-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-diffbind-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-diffbind-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-diffbind-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-diffbind-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-diffbind-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rhtslib/include' -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rhtslib/include' -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c bamReader.cpp -o bamReader.o + x86_64-apple-darwin13.4.0-clang -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rhtslib/include' -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c bam_plbuf.c -o bam_plbuf.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rhtslib/include' -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c bedReader.cpp -o bedReader.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rhtslib/include' -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c bitBucket.cpp -o bitBucket.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rhtslib/include' -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c croi_func.cpp -o croi_func.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rhtslib/include' -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c croi_main.cpp -o croi_main.o +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/bioconductor-diffbind/meta.yaml b/recipes/bioconductor-diffbind/meta.yaml index 389a476e49efb..eb55d29c2e339 100644 --- a/recipes/bioconductor-diffbind/meta.yaml +++ b/recipes/bioconductor-diffbind/meta.yaml @@ -1,40 +1,58 @@ -{% set version = "3.12.0" %} +{% set version = "3.16.0" %} {% set name = "DiffBind" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Differential Binding Analysis of ChIP-Seq Peak Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa7c15e33713ad0ced01a5b6442e2d3d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-diffbind", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:diffbind + - usegalaxy-eu:diffbind + parent_recipe: + name: bioconductor-diffbind + path: recipes/bioconductor-diffbind + version: 2.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat, xtable, rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid # SystemRequirements: GNU make requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-apeglm >=1.24.0,<1.25.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-greylistchip >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-systempiper >=2.8.0,<2.9.0' + - bioconductor-apeglm >=1.28.0,<1.29.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-greylistchip >=1.38.0,<1.39.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-systempiper >=2.12.0,<2.13.0 - r-amap - r-ashr - r-base @@ -48,20 +66,23 @@ requirements: - r-rcpp - libblas - liblapack + - zlib + - liblzma-devel + run: - - 'bioconductor-apeglm >=1.24.0,<1.25.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-greylistchip >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-systempiper >=2.8.0,<2.9.0' + - bioconductor-apeglm >=1.28.0,<1.29.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-greylistchip >=1.38.0,<1.39.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-systempiper >=2.12.0,<2.13.0 - r-amap - r-ashr - r-base @@ -73,27 +94,16 @@ requirements: - r-locfit - r-rcolorbrewer - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make - - libcxx <17 # [osx] + +source: + md5: efe14379a227c57892f1e0a5985b728c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Differential Binding Analysis of ChIP-Seq Peak Data' - description: 'Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:diffbind - - usegalaxy-eu:diffbind - parent_recipe: - name: bioconductor-diffbind - path: recipes/bioconductor-diffbind - version: 2.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-diffcoexp/meta.yaml b/recipes/bioconductor-diffcoexp/meta.yaml index aa9d59c7e2550..5466be7f50760 100644 --- a/recipes/bioconductor-diffcoexp/meta.yaml +++ b/recipes/bioconductor-diffcoexp/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "diffcoexp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A tool for the identification of differentially coexpressed links (DCLs) and differentially coexpressed genes (DCGs). DCLs are gene pairs with significantly different correlation coefficients under two conditions. DCGs are genes with significantly more DCLs than by chance. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Differential Co-expression Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0985f656837da53f557041125f7583a0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-diffcoexp", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: GEOquery, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-diffcorr - r-igraph - r-psych - r-wgcna run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-diffcorr - r-igraph - r-psych - r-wgcna + +source: + md5: fc417bab57f77a79a0dd5ac9cced3569 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>2)' - summary: 'Differential Co-expression Analysis' - description: 'A tool for the identification of differentially coexpressed links (DCLs) and differentially coexpressed genes (DCGs). DCLs are gene pairs with significantly different correlation coefficients under two conditions. DCGs are genes with significantly more DCLs than by chance.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-diffcyt/meta.yaml b/recipes/bioconductor-diffcyt/meta.yaml index cd7e975c7fa60..5a9b78c6cf0c0 100644 --- a/recipes/bioconductor-diffcyt/meta.yaml +++ b/recipes/bioconductor-diffcyt/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "diffcyt" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Statistical methods for differential discovery analyses in high-dimensional cytometry data (including flow cytometry, mass cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a combination of high-resolution clustering and empirical Bayes moderated tests adapted from transcriptomics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Differential discovery in high-dimensional cytometry via high-resolution clustering -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8118267e493c2646533a9730a876d340 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-diffcyt", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST requirements: host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowsom >=2.10.0,<2.11.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowsom >=2.14.0,<2.15.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-dplyr @@ -38,13 +40,13 @@ requirements: - r-reshape2 - r-tidyr run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowsom >=2.10.0,<2.11.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowsom >=2.14.0,<2.15.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-dplyr @@ -53,13 +55,16 @@ requirements: - r-multcomp - r-reshape2 - r-tidyr + +source: + md5: 36746fa6a908f973272a264242b0b39a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Differential discovery in high-dimensional cytometry via high-resolution clustering' - description: 'Statistical methods for differential discovery analyses in high-dimensional cytometry data (including flow cytometry, mass cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a combination of high-resolution clustering and empirical Bayes moderated tests adapted from transcriptomics.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-differentialregulation/meta.yaml b/recipes/bioconductor-differentialregulation/meta.yaml index a4577cc53de1e..b848eb218c8c1 100644 --- a/recipes/bioconductor-differentialregulation/meta.yaml +++ b/recipes/bioconductor-differentialregulation/meta.yaml @@ -1,31 +1,37 @@ -{% set version = "2.0.2" %} +{% set version = "2.4.0" %} {% set name = "DifferentialRegulation" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'DifferentialRegulation is a method for detecting differentially regulated genes between two groups of samples (e.g., healthy vs. disease, or treated vs. untreated samples), by targeting differences in the balance of spliced and unspliced mRNA abundances, obtained from single-cell RNA-sequencing (scRNA-seq) data. From a mathematical point of view, DifferentialRegulation accounts for the sample-to-sample variability, and embeds multiple samples in a Bayesian hierarchical model. Furthermore, our method also deals with two major sources of mapping uncertainty: i) ''ambiguous'' reads, compatible with both spliced and unspliced versions of a gene, and ii) reads mapping to multiple genes. In particular, ambiguous reads are treated separately from spliced and unsplced reads, while reads that are compatible with multiple genes are allocated to the gene of origin. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques (Metropolis-within-Gibbs).' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Differentially regulated genes from scRNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 875793d502c3e521b4faa3eba0d1c2e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-differentialregulation", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, BiocStyle # SystemRequirements: C++17 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-bandits >=1.18.0,<1.19.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tximport >=1.30.0,<1.31.0' + - bioconductor-bandits >=1.22.0,<1.23.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tximport >=1.34.0,<1.35.0 - r-base - r-data.table - r-doparallel @@ -40,10 +46,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-bandits >=1.18.0,<1.19.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tximport >=1.30.0,<1.31.0' + - bioconductor-bandits >=1.22.0,<1.23.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tximport >=1.34.0,<1.35.0 - r-base - r-data.table - r-doparallel @@ -55,17 +61,16 @@ requirements: - r-matrix - r-rcpp - r-rcpparmadillo - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: a246cfd93fb21229ebb7ff130557a983 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Differentially regulated genes from scRNA-seq data' - description: 'DifferentialRegulation is a method for detecting differentially regulated genes between two groups of samples (e.g., healthy vs. disease, or treated vs. untreated samples), by targeting differences in the balance of spliced and unspliced mRNA abundances, obtained from single-cell RNA-sequencing (scRNA-seq) data. From a mathematical point of view, DifferentialRegulation accounts for the sample-to-sample variability, and embeds multiple samples in a Bayesian hierarchical model. Furthermore, our method also deals with two major sources of mapping uncertainty: i) ''ambiguous'' reads, compatible with both spliced and unspliced versions of a gene, and ii) reads mapping to multiple genes. In particular, ambiguous reads are treated separately from spliced and unsplced reads, while reads that are compatible with multiple genes are allocated to the gene of origin. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques (Metropolis-within-Gibbs).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-diffgeneanalysis/meta.yaml b/recipes/bioconductor-diffgeneanalysis/meta.yaml index 2ddba971b2d64..d6daf839d3dca 100644 --- a/recipes/bioconductor-diffgeneanalysis/meta.yaml +++ b/recipes/bioconductor-diffgeneanalysis/meta.yaml @@ -1,40 +1,22 @@ -{% set version = "1.84.0" %} +{% set version = "1.88.0" %} {% set name = "diffGeneAnalysis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Analyze microarray data + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Performs differential gene expression Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa3d8c4ce3b83b8a6f02e87384dd649f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-diffgeneanalysis", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - r-base - - 'r-minpack.lm >=1.0-4' - run: - - r-base - - 'r-minpack.lm >=1.0-4' -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL - summary: 'Performs differential gene expression Analysis' - description: 'Analyze microarray data' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:diffgeneanalysis @@ -44,3 +26,27 @@ extra: path: recipes/bioconductor-diffgeneanalysis version: 1.62.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - r-base + - r-minpack.lm >=1.0-4 + run: + - r-base + - r-minpack.lm >=1.0-4 + +source: + md5: f79e8f1c7aa51cabcccbc4ec0a2af842 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-diffhic/meta.yaml b/recipes/bioconductor-diffhic/meta.yaml index e60731e0d4def..d9236710aa0af 100644 --- a/recipes/bioconductor-diffhic/meta.yaml +++ b/recipes/bioconductor-diffhic/meta.yaml @@ -1,86 +1,97 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "diffHic" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Detects differential interactions across biological conditions in a Hi-C experiment. Methods are provided for read alignment and data pre-processing into interaction counts. Statistical analysis is based on edgeR and supports normalization and filtering. Several visualization options are also available. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Differential Analysis of Hi-C Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ba97084f7b4e4510514df43be6eb9bf8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-diffhic", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:diffhic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Ecoli.NCBI.20080805, Matrix, testthat -# SystemRequirements: C++11, GNU make +# SystemRequirements: C++, GNU make requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-csaw >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-csaw >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-locfit - r-rcpp - libblas - liblapack + - zlib + - liblzma-devel + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-csaw >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-csaw >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-locfit - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 9fc3ba56d7699aad6f36a0437a8753f4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'Differential Analyis of Hi-C Data' - description: 'Detects differential interactions across biological conditions in a Hi-C experiment. Methods are provided for read alignment and data pre-processing into interaction counts. Statistical analysis is based on edgeR and supports normalization and filtering. Several visualization options are also available.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-difflogo/meta.yaml b/recipes/bioconductor-difflogo/meta.yaml index 7021a22253322..382e90a81f11a 100644 --- a/recipes/bioconductor-difflogo/meta.yaml +++ b/recipes/bioconductor-difflogo/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "2.26.0" %} +{% set version = "2.30.0" %} {% set name = "DiffLogo" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f122cc5f6153c8dc4fabe92b33d1e608 +about: + description: DiffLogo is an easy-to-use tool to visualize motif differences. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'DiffLogo: A comparative visualisation of biooligomer motifs' build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-difflogo", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, testthat, seqLogo, MotifDb requirements: host: @@ -27,13 +26,14 @@ requirements: run: - r-base - r-cba +source: + md5: 74d723e9fde469a861d01ece063de837 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'DiffLogo: A comparative visualisation of biooligomer motifs' - description: 'DiffLogo is an easy-to-use tool to visualize motif differences.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-diffloopdata/meta.yaml b/recipes/bioconductor-diffloopdata/meta.yaml index 5578e9031bc30..834fa648b433c 100644 --- a/recipes/bioconductor-diffloopdata/meta.yaml +++ b/recipes/bioconductor-diffloopdata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "diffloopdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 748ee71ae44999ca2c568619ad5a47eb +about: + description: ChIA-PET example datasets and additional data for use with the diffloop package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Example ChIA-PET Datasets for the diffloop Package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-diffloopdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f5906bd3830809ec05a36aaaaab6f8dc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Example ChIA-PET Datasets for the diffloop Package' - description: 'ChIA-PET example datasets and additional data for use with the diffloop package.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-diffloopdata/post-link.sh b/recipes/bioconductor-diffloopdata/post-link.sh index 51e96d69fdede..bb3f7270edab1 100644 --- a/recipes/bioconductor-diffloopdata/post-link.sh +++ b/recipes/bioconductor-diffloopdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "diffloopdata-1.30.0" +installBiocDataPackage.sh "diffloopdata-1.34.0" diff --git a/recipes/bioconductor-diffustats/meta.yaml b/recipes/bioconductor-diffustats/meta.yaml index 0a7ea0001788f..a83833610a573 100644 --- a/recipes/bioconductor-diffustats/meta.yaml +++ b/recipes/bioconductor-diffustats/meta.yaml @@ -1,26 +1,41 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "diffuStats" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Label propagation approaches are a widely used procedure in computational biology for giving context to molecular entities using network data. Node labels, which can derive from gene expression, genome-wide association studies, protein domains or metabolomics profiling, are propagated to their neighbours in the network, effectively smoothing the scores through prior annotated knowledge and prioritising novel candidates. The R package diffuStats contains a collection of diffusion kernels and scoring approaches that facilitates their computation, characterisation and benchmarking. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Diffusion scores on biological networks -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c47ae0431034f3de807ad1fa3684530 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-diffustats", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:diffuStats + - doi:10.1093/bioinformatics/btx632 + parent_recipe: + name: bioconductor-diffustats + path: recipes/bioconductor-diffustats + version: 0.104.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata, BiocStyle, reshape2, utils # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-checkmate @@ -47,25 +62,16 @@ requirements: - r-rcpp - r-rcpparmadillo - r-rcppparallel - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 898b1d3d9490425dac135e1cc272f6f7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Diffusion scores on biological networks' - description: 'Label propagation approaches are a widely used procedure in computational biology for giving context to molecular entities using network data. Node labels, which can derive from gene expression, genome-wide association studies, protein domains or metabolomics profiling, are propagated to their neighbours in the network, effectively smoothing the scores through prior annotated knowledge and prioritising novel candidates. The R package diffuStats contains a collection of diffusion kernels and scoring approaches that facilitates their computation, characterisation and benchmarking.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:diffuStats - - doi:10.1093/bioinformatics/btx632 - parent_recipe: - name: bioconductor-diffustats - path: recipes/bioconductor-diffustats - version: 0.104.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-diffutr/meta.yaml b/recipes/bioconductor-diffutr/meta.yaml index e43e853baf8f8..6e1919a453015 100644 --- a/recipes/bioconductor-diffutr/meta.yaml +++ b/recipes/bioconductor-diffutr/meta.yaml @@ -1,39 +1,41 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "diffUTR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The diffUTR package provides a uniform interface and plotting functions for limma/edgeR/DEXSeq -powered differential bin/exon usage. It includes in addition an improved version of the limma::diffSplice method. Most importantly, diffUTR further extends the application of these frameworks to differential UTR usage analysis using poly-A site databases. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'diffUTR: Streamlining differential exon and 3'' UTR usage' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 10b4af48c1a3f5e823c67cf569dcf1c2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-diffutr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-dexseq >=1.48.0,<1.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsubread >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-dexseq >=1.52.0,<1.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsubread >=2.20.0,<2.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -42,18 +44,18 @@ requirements: - r-stringi - r-viridislite run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-dexseq >=1.48.0,<1.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsubread >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-dexseq >=1.52.0,<1.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsubread >=2.20.0,<2.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -61,13 +63,16 @@ requirements: - r-matrixstats - r-stringi - r-viridislite + +source: + md5: f091028afb4cf2572d5db0e04a87c17b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'diffUTR: Streamlining differential exon and 3'' UTR usage' - description: 'The diffUTR package provides a uniform interface and plotting functions for limma/edgeR/DEXSeq -powered differential bin/exon usage. It includes in addition an improved version of the limma::diffSplice method. Most importantly, diffUTR further extends the application of these frameworks to differential UTR usage analysis using poly-A site databases.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-diggit/meta.yaml b/recipes/bioconductor-diggit/meta.yaml index 43b921f1c6b65..7711f9112b5ae 100644 --- a/recipes/bioconductor-diggit/meta.yaml +++ b/recipes/bioconductor-diggit/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "diggit" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8685d9b55ebfad0b44d6ca96d6fb4ab0 +about: + description: Inference of Genetic Variants Driving Cellullar Phenotypes by the DIGGIT algorithm + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Inference of Genetic Variants Driving Cellular Phenotypes build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-diggit", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: diggitdata requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-viper >=1.36.0,<1.37.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-viper >=1.40.0,<1.41.0 - r-base - r-ks run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-viper >=1.36.0,<1.37.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-viper >=1.40.0,<1.41.0 - r-base - r-ks +source: + md5: 4e6dafcb2e7245fd3f1cb6020a94986e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Inference of Genetic Variants Driving Cellular Phenotypes' - description: 'Inference of Genetic Variants Driving Cellullar Phenotypes by the DIGGIT algorithm' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-diggitdata/meta.yaml b/recipes/bioconductor-diggitdata/meta.yaml index b4c6cdf57ec45..f856eacd7a292 100644 --- a/recipes/bioconductor-diggitdata/meta.yaml +++ b/recipes/bioconductor-diggitdata/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "diggitdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 48dc6a1a35dae2169279a2766e3b56de +about: + description: This package provides expression profile and CNV data for glioblastoma from TCGA, and transcriptional and post-translational regulatory networks assembled with the ARACNe and MINDy algorithms, respectively. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Example data for the diggit package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-diggitdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-viper >=1.36.0,<1.37.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-viper >=1.40.0,<1.41.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-viper >=1.36.0,<1.37.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-viper >=1.40.0,<1.41.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 156206689cf62a4efdaed7eab550c59c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Example data for the diggit package' - description: 'This package provides expression profile and CNV data for glioblastoma from TCGA, and transcriptional and post-translational regulatory networks assembled with the ARACNe and MINDy algorithms, respectively.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-diggitdata/post-link.sh b/recipes/bioconductor-diggitdata/post-link.sh index 3d3e3107cca47..bf70467c24447 100644 --- a/recipes/bioconductor-diggitdata/post-link.sh +++ b/recipes/bioconductor-diggitdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "diggitdata-1.34.0" +installBiocDataPackage.sh "diggitdata-1.38.0" diff --git a/recipes/bioconductor-dino/meta.yaml b/recipes/bioconductor-dino/meta.yaml index f3775ab4fc288..449a8c09d3de8 100644 --- a/recipes/bioconductor-dino/meta.yaml +++ b/recipes/bioconductor-dino/meta.yaml @@ -1,55 +1,60 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "Dino" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Dino normalizes single-cell, mRNA sequencing data to correct for technical variation, particularly sequencing depth, prior to downstream analysis. The approach produces a matrix of corrected expression for which the dependency between sequencing depth and the full distribution of normalized expression; many existing methods aim to remove only the dependency between sequencing depth and the mean of the normalized expression. This is particuarly useful in the context of highly sparse datasets such as those produced by 10X genomics and other uninque molecular identifier (UMI) based microfluidics protocols for which the depth-dependent proportion of zeros in the raw expression data can otherwise present a challenge. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Normalization of Single-Cell mRNA Sequencing Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf084f6d83c8245a5c4969849a7e3e82 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dino", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 2.1.0), knitr, rmarkdown, BiocStyle, devtools, ggplot2, gridExtra, ggpubr, grid, magick, hexbin requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-matrixstats - r-seurat run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-matrixstats - r-seurat + +source: + md5: c83c67fd5a0a83ab3ac6ea080fbfbc8b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Normalization of Single-Cell mRNA Sequencing Data' - description: 'Dino normalizes single-cell, mRNA sequencing data to correct for technical variation, particularly sequencing depth, prior to downstream analysis. The approach produces a matrix of corrected expression for which the dependency between sequencing depth and the full distribution of normalized expression; many existing methods aim to remove only the dependency between sequencing depth and the mean of the normalized expression. This is particuarly useful in the context of highly sparse datasets such as those produced by 10X genomics and other uninque molecular identifier (UMI) based microfluidics protocols for which the depth-dependent proportion of zeros in the raw expression data can otherwise present a challenge.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dinor/build.sh b/recipes/bioconductor-dinor/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dinor/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dinor/meta.yaml b/recipes/bioconductor-dinor/meta.yaml new file mode 100644 index 0000000000000..afc5ed101fbea --- /dev/null +++ b/recipes/bioconductor-dinor/meta.yaml @@ -0,0 +1,72 @@ +{% set version = "1.2.0" %} +{% set name = "dinoR" %} +{% set bioc = "3.20" %} + +about: + description: dinoR tests for significant differences in NOMe-seq footprints between two conditions, using genomic regions of interest (ROI) centered around a landmark, for example a transcription factor (TF) motif. This package takes NOMe-seq data (GCH methylation/protection) in the form of a Ranged Summarized Experiment as input. dinoR can be used to group sequencing fragments into 3 or 5 categories representing characteristic footprints (TF bound, nculeosome bound, open chromatin), plot the percentage of fragments in each category in a heatmap, or averaged across different ROI groups, for example, containing a common TF motif. It is designed to compare footprints between two sample groups, using edgeR's quasi-likelihood methods on the total fragment counts per ROI, sample, and footprint category. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Differential NOMe-seq analysis + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dinor", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-circlize + - r-cowplot + - r-dplyr + - r-ggplot2 + - r-matrix + - r-rlang + - r-stringr + - r-tibble + - r-tidyr + - r-tidyselect + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-circlize + - r-cowplot + - r-dplyr + - r-ggplot2 + - r-matrix + - r-rlang + - r-stringr + - r-tibble + - r-tidyr + - r-tidyselect + +source: + md5: 5c4fc734805779e90b1678bc575f104a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-dir.expiry/meta.yaml b/recipes/bioconductor-dir.expiry/meta.yaml index 77e5aabe1d30e..6ccf43f22cb02 100644 --- a/recipes/bioconductor-dir.expiry/meta.yaml +++ b/recipes/bioconductor-dir.expiry/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "dir.expiry" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ddefb728416ca4283805e19a898e9245 +about: + description: Implements an expiration system for access to versioned directories. Directories that have not been accessed by a registered function within a certain time frame are deleted. This aims to reduce disk usage by eliminating obsolete caches generated by old versions of packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Managing Expiration for Cache Directories build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dir.expiry", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: rmarkdown, knitr, testthat, BiocStyle requirements: host: @@ -27,13 +26,14 @@ requirements: run: - r-base - r-filelock +source: + md5: c34f1ba65eeb7ab02784f252fe20477b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Managing Expiration for Cache Directories' - description: 'Implements an expiration system for access to versioned directories. Directories that have not been accessed by a registered function within a certain time frame are deleted. This aims to reduce disk usage by eliminating obsolete caches generated by old versions of packages.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-director/meta.yaml b/recipes/bioconductor-director/meta.yaml index 8cd98393738e0..69191f947b694 100644 --- a/recipes/bioconductor-director/meta.yaml +++ b/recipes/bioconductor-director/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "Director" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Director is an R package designed to streamline the visualization of molecular effects in regulatory cascades. It utilizes the R package htmltools and a modified Sankey plugin of the JavaScript library D3 to provide a fast and easy, browser-enabled solution to discovering potentially interesting downstream effects of regulatory and/or co-expressed molecules. The diagrams are robust, interactive, and packaged as highly-portable HTML files that eliminate the need for third-party software to view. This enables a straightforward approach for scientists to interpret the data produced, and bioinformatics developers an alternative means to present relevant data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: A dynamic visualization tool of multi-level data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c6c9d1a4762ffbdf723111273ee0899 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-director", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:director + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-director + path: recipes/bioconductor-director + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -26,21 +37,16 @@ requirements: run: - r-base - r-htmltools + +source: + md5: 635f5ad07d7d794137c72fc43d06e122 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'A dynamic visualization tool of multi-level data' - description: 'Director is an R package designed to streamline the visualization of molecular effects in regulatory cascades. It utilizes the R package htmltools and a modified Sankey plugin of the JavaScript library D3 to provide a fast and easy, browser-enabled solution to discovering potentially interesting downstream effects of regulatory and/or co-expressed molecules. The diagrams are robust, interactive, and packaged as highly-portable HTML files that eliminate the need for third-party software to view. This enables a straightforward approach for scientists to interpret the data produced, and bioinformatics developers an alternative means to present relevant data.' - license_file: LICENSE -extra: - identifiers: - - biotools:director - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-director - path: recipes/bioconductor-director - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dirichletmultinomial/meta.yaml b/recipes/bioconductor-dirichletmultinomial/meta.yaml index 94f6743365b39..6026ceaf1ba30 100644 --- a/recipes/bioconductor-dirichletmultinomial/meta.yaml +++ b/recipes/bioconductor-dirichletmultinomial/meta.yaml @@ -1,60 +1,66 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "DirichletMultinomial" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8527c543b1ada9640d2f434fb516ff4e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dirichletmultinomial", max_pin="x.x") }}' -# Suggests: lattice, parallel, MASS, RColorBrewer, xtable + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:dirichletmultinomial + - doi:10.1371/journal.pone.0030126 + parent_recipe: + name: bioconductor-dirichletmultinomial + path: recipes/bioconductor-dirichletmultinomial + version: 1.22.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: lattice, parallel, MASS, RColorBrewer, DT, knitr, rmarkdown, BiocStyle # SystemRequirements: gsl requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - libblas - liblapack - gsl run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - gsl - build: - - {{ compiler('c') }} - - make + +source: + md5: ff5ee6c605c511ad6e8f2e3e6ad1165c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3.0-only - summary: 'Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data' - description: 'Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:dirichletmultinomial - - doi:10.1371/journal.pone.0030126 - parent_recipe: - name: bioconductor-dirichletmultinomial - path: recipes/bioconductor-dirichletmultinomial - version: 1.22.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-discordant/meta.yaml b/recipes/bioconductor-discordant/meta.yaml index 8a2f3fd4b1593..040c21d67dd43 100644 --- a/recipes/bioconductor-discordant/meta.yaml +++ b/recipes/bioconductor-discordant/meta.yaml @@ -1,27 +1,33 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "discordant" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Discordant is an R package that identifies pairs of features that correlate differently between phenotypic groups, with application to -omics data sets. Discordant uses a mixture model that “bins” molecular feature pairs based on their type of coexpression or coabbundance. Algorithm is explained further in "Differential Correlation for Sequencing Data"" (Siska et al. 2016). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'The Discordant Method: A Novel Approach for Differential Correlation' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 78ce10a5d9777c9db9b72fec29688bee build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-discordant", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, testthat (>= 3.0.0) requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-biwt - r-dplyr @@ -31,24 +37,23 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-biwt - r-dplyr - r-gtools - r-mass - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 7498dbbb0f00998da67fb537e1fe5ed0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'The Discordant Method: A Novel Approach for Differential Correlation' - description: 'Discordant is an R package that identifies pairs of features that correlate differently between phenotypic groups, with application to -omics data sets. Discordant uses a mixture model that “bins” molecular feature pairs based on their type of coexpression or coabbundance. Algorithm is explained further in "Differential Correlation for Sequencing Data"" (Siska et al. 2016).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-discorhythm/meta.yaml b/recipes/bioconductor-discorhythm/meta.yaml index f66f116d7b1fa..feaa42ef76a1b 100644 --- a/recipes/bioconductor-discorhythm/meta.yaml +++ b/recipes/bioconductor-discorhythm/meta.yaml @@ -1,32 +1,35 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "DiscoRhythm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Set of functions for estimation of cyclical characteristics, such as period, phase, amplitude, and statistical significance in large temporal datasets. Supporting functions are available for quality control, dimensionality reduction, spectral analysis, and analysis of experimental replicates. Contains a R Shiny web interface to execute all workflow steps. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Interactive Workflow for Discovering Rhythmicity in Biological Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c502bfa871cb7e3aa322684117a70b2f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-discorhythm", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat # SystemRequirements: To generate html reports pandoc (http://pandoc.org/installing.html) is required. requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-broom - r-data.table @@ -41,7 +44,7 @@ requirements: - r-magick - r-matrixstats - r-matrixtests - - 'r-metacycle >=1.2.0' + - r-metacycle >=1.2.0 - r-plotly - r-reshape2 - r-rmarkdown @@ -55,11 +58,12 @@ requirements: - r-viridis - r-zip - pandoc + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-broom - r-data.table @@ -74,7 +78,7 @@ requirements: - r-magick - r-matrixstats - r-matrixtests - - 'r-metacycle >=1.2.0' + - r-metacycle >=1.2.0 - r-plotly - r-reshape2 - r-rmarkdown @@ -88,13 +92,16 @@ requirements: - r-viridis - r-zip - pandoc + +source: + md5: 7e233ff69cf7337ec1e8115d4c8f6130 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Interactive Workflow for Discovering Rhythmicity in Biological Data' - description: 'Set of functions for estimation of cyclical characteristics, such as period, phase, amplitude, and statistical significance in large temporal datasets. Supporting functions are available for quality control, dimensionality reduction, spectral analysis, and analysis of experimental replicates. Contains a R Shiny web interface to execute all workflow steps.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-distinct/build_failure.linux-64.yaml b/recipes/bioconductor-distinct/build_failure.linux-64.yaml deleted file mode 100644 index b4346b41f3fe8..0000000000000 --- a/recipes/bioconductor-distinct/build_failure.linux-64.yaml +++ /dev/null @@ -1,106 +0,0 @@ -recipe_sha: 4cdee96b11c599d7d86852005b1fcdb8fc168a77b8c4cd0973697dbfc2af519f # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: |- - compiler error -log: |2- - - An HTTP error occurred when trying to retrieve this URL. - HTTP errors are often intermittent, and a simple retry will get you on your way. - Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/Archive/distinct/distinct_1.14.0.tar.gz - INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/Archive/distinct/distinct_1.14.0.tar.gz - Success - INFO:conda_build.source:Success - Extracting download - source tree in: /opt/conda/conda-bld/bioconductor-distinct_1703301470415/work - export PREFIX=/opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p - export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-distinct_1703301470415/_build_env - export SRC_DIR=/opt/conda/conda-bld/bioconductor-distinct_1703301470415/work - INFO: activate-binutils_linux-64.sh made the following environmental changes: - ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line - AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar - AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as - CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt - ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit - GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof - LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld - LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold - NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm - OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy - OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump - RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib - READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf - SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size - STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings - STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip - INFO: activate-gcc_linux-64.sh made the following environmental changes: - BUILD=x86_64-conda-linux-gnu - CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-distinct-1.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr - CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot - CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu - CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu - CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp - CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include - DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-distinct-1.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include - GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc - GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar - GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm - GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib - HOST=x86_64-conda-linux-gnu - LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu - build_alias=x86_64-conda-linux-gnu - host_alias=x86_64-conda-linux-gnu - -BUILD=x86_64-conda_cos6-linux-gnu - -CONDA_BUILD_SYSROOT= - INFO: activate-gxx_linux-64.sh made the following environmental changes: - CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-distinct-1.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-distinct-1.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g - During startup - Warning message: - Setting LC_TIME failed, using "C" - * installing to library /opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library - * installing *source* package distinct ... - ** using staged installation - ** libs - using C compiler: x86_64-conda-linux-gnu-c (conda-forge gcc 12.3.0-3) 12.3.0 - using C11 - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rfast/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1700316003380/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c Perm.cpp -o Perm.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rfast/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1700316003380/work=/usr/local/src/conda/r-base-4.3.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c Perm_covariates.cpp -o Perm_covariates.o - In file included from /opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/Rfast/include/Rfast/templates.h:10, - from /opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/Rfast/include/Rfast/matrix.hpp:14, - from /opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/Rfast/include/Rfast.h:5, - from Perm_covariates.cpp:2: - /opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/Rfast/include/Rfast/parallel.h:7:10: fatal error: RcppParallel.h: No such file or directory - 7 | #include - | ^~~~~~~~~~~~~~~~ - compilation terminated. - make: *** [/opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/etc/Makeconf:200: Perm_covariates.o] Error 1 - ERROR: compilation failed for package distinct - * removing /opt/conda/conda-bld/bioconductor-distinct_1703301470415/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/distinct - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-distinct_1703301470415/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-distinct/build_failure.osx-64.yaml b/recipes/bioconductor-distinct/build_failure.osx-64.yaml deleted file mode 100644 index be50a664177f3..0000000000000 --- a/recipes/bioconductor-distinct/build_failure.osx-64.yaml +++ /dev/null @@ -1,38 +0,0 @@ -recipe_sha: 4cdee96b11c599d7d86852005b1fcdb8fc168a77b8c4cd0973697dbfc2af519f # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -reason: |- - parallel.h:7:10: fatal error: 'RcppParallel.h' file not found -category: |- - compiler error -log: |- - 12:17:08 BIOCONDA INFO (ERR) In file included from Perm_covariates.cpp:2: - 12:17:08 BIOCONDA INFO (ERR) In file included from /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/Rfast/include/Rfast.h:5: - 12:17:08 BIOCONDA INFO (ERR) In file included from /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/Rfast/include/Rfast/matrix.hpp:14: - 12:17:08 BIOCONDA INFO (ERR) In file included from /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/Rfast/include/Rfast/templates.h:10: - 12:17:08 BIOCONDA INFO (ERR) /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/Rfast/include/Rfast/parallel.h:7:10: fatal error: 'RcppParallel.h' file not found - 12:17:08 BIOCONDA INFO (ERR) #include - 12:17:08 BIOCONDA INFO (ERR) ^~~~~~~~~~~~~~~~ - 12:17:08 BIOCONDA INFO (ERR) 1 error generated. - 12:17:08 BIOCONDA INFO (ERR) make: *** [/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/etc/Makeconf:200: Perm_covariates.o] Error 1 - 12:17:08 BIOCONDA INFO (ERR) ERROR: compilation failed for package ‘distinct’ - 12:17:08 BIOCONDA INFO (ERR) * removing ‘/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/distinct’ - 12:17:09 BIOCONDA INFO (ERR) Traceback (most recent call last): - 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - 12:17:09 BIOCONDA INFO (ERR) sys.exit(main()) - 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - 12:17:09 BIOCONDA INFO (ERR) call_conda_build(action, config) - 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - 12:17:09 BIOCONDA INFO (ERR) result = api.build( - 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - 12:17:09 BIOCONDA INFO (ERR) return build_tree( - 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - 12:17:09 BIOCONDA INFO (ERR) packages_from_this = build(metadata, stats, - 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - 12:17:09 BIOCONDA INFO (ERR) utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - 12:17:09 BIOCONDA INFO (ERR) return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - 12:17:09 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - 12:17:09 BIOCONDA INFO (ERR) raise subprocess.CalledProcessError(proc.returncode, _args) - 12:17:09 BIOCONDA INFO (ERR) subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-distinct_1702469402679/work/conda_build.sh']' returned non-zero exit status 1. - 12:17:18 BIOCONDA ERROR COMMAND FAILED (exited with 1): /opt/mambaforge/envs/bioconda/bin/conda mambabuild --override-channels --no-anaconda-upload -c conda-forge -c bioconda -c defaults -e /opt/mambaforge/envs/bioconda/conda_build_config.yaml -e /opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml recipes/bioconductor-distinct/meta.yaml - diff --git a/recipes/bioconductor-distinct/meta.yaml b/recipes/bioconductor-distinct/meta.yaml index 94fd0a58dc596..7d2985152e881 100644 --- a/recipes/bioconductor-distinct/meta.yaml +++ b/recipes/bioconductor-distinct/meta.yaml @@ -1,31 +1,37 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "distinct" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'distinct is a statistical method to perform differential testing between two or more groups of distributions; differential testing is performed via hierarchical non-parametric permutation tests on the cumulative distribution functions (cdfs) of each sample. While most methods for differential expression target differences in the mean abundance between conditions, distinct, by comparing full cdfs, identifies, both, differential patterns involving changes in the mean, as well as more subtle variations that do not involve the mean (e.g., unimodal vs. bi-modal distributions with the same mean). distinct is a general and flexible tool: due to its fully non-parametric nature, which makes no assumptions on how the data was generated, it can be applied to a variety of datasets. It is particularly suitable to perform differential state analyses on single cell data (i.e., differential analyses within sub-populations of cells), such as single cell RNA sequencing (scRNA-seq) and high-dimensional flow or mass cytometry (HDCyto) data. To use distinct one needs data from two or more groups of samples (i.e., experimental conditions), with at least 2 samples (i.e., biological replicates) per group.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'distinct: a method for differential analyses via hierarchical permutation tests' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b4817384f7f8fad6e30ee01270e31d10 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-distinct", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, UpSetR, BiocStyle -# SystemRequirements: C++11 +# SystemRequirements: C++17 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-doparallel - r-dorng @@ -34,14 +40,13 @@ requirements: - r-matrix - r-rcpp - r-rcpparmadillo - - r-rfast - libblas - liblapack run: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-doparallel - r-dorng @@ -50,18 +55,16 @@ requirements: - r-matrix - r-rcpp - r-rcpparmadillo - - r-rfast - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 468ef5d0f94a8ef22c78d0bfbb7be45e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'distinct: a method for differential analyses via hierarchical permutation tests' - description: 'distinct is a statistical method to perform differential testing between two or more groups of distributions; differential testing is performed via hierarchical non-parametric permutation tests on the cumulative distribution functions (cdfs) of each sample. While most methods for differential expression target differences in the mean abundance between conditions, distinct, by comparing full cdfs, identifies, both, differential patterns involving changes in the mean, as well as more subtle variations that do not involve the mean (e.g., unimodal vs. bi-modal distributions with the same mean). distinct is a general and flexible tool: due to its fully non-parametric nature, which makes no assumptions on how the data was generated, it can be applied to a variety of datasets. It is particularly suitable to perform differential state analyses on single cell data (i.e., differential analyses within sub-populations of cells), such as single cell RNA sequencing (scRNA-seq) and high-dimensional flow or mass cytometry (HDCyto) data. To use distinct one needs data from two or more groups of samples (i.e., experimental conditions), with at least 2 samples (i.e., biological replicates) per group.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dittoseq/meta.yaml b/recipes/bioconductor-dittoseq/meta.yaml index 2c331373afe40..9a6801698cda9 100644 --- a/recipes/bioconductor-dittoseq/meta.yaml +++ b/recipes/bioconductor-dittoseq/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "dittoSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A universal, user friendly, single-cell and bulk RNA sequencing visualization toolkit that allows highly customizable creation of color blindness friendly, publication-quality figures. dittoSeq accepts both SingleCellExperiment (SCE) and Seurat objects, as well as the import and usage, via conversion to an SCE, of SummarizedExperiment or DGEList bulk data. Visualizations include dimensionality reduction plots, heatmaps, scatterplots, percent composition or expression across groups, and more. Customizations range from size and title adjustments to automatic generation of annotations for heatmaps, overlay of trajectory analysis onto any dimensionality reduciton plot, hidden data overlay upon cursor hovering via ggplotly conversion, and many more. All with simple, discrete inputs. Color blindness friendliness is powered by legend adjustments (enlarged keys), and by allowing the use of shapes or letter-overlay in addition to the carefully selected dittoColors(). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: User Friendly Single-Cell and Bulk RNA Sequencing Visualization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d7e63c0018a57726033bb5862dccf7e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dittoseq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: plotly, testthat, Seurat (>= 2.2), DESeq2, edgeR, ggplot.multistats, knitr, rmarkdown, BiocStyle, scRNAseq, ggrastr (>= 0.2.0), ComplexHeatmap, bluster, scater, scran requirements: host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-colorspace >=1.4' + - r-colorspace >=1.4 - r-cowplot - r-ggplot2 - r-ggrepel @@ -35,11 +37,11 @@ requirements: - r-pheatmap - r-reshape2 run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-colorspace >=1.4' + - r-colorspace >=1.4 - r-cowplot - r-ggplot2 - r-ggrepel @@ -47,13 +49,16 @@ requirements: - r-gridextra - r-pheatmap - r-reshape2 + +source: + md5: 3cf2635611082328b10df0bd1a96960c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'User Friendly Single-Cell and Bulk RNA Sequencing Visualization' - description: 'A universal, user friendly, single-cell and bulk RNA sequencing visualization toolkit that allows highly customizable creation of color blindness friendly, publication-quality figures. dittoSeq accepts both SingleCellExperiment (SCE) and Seurat objects, as well as the import and usage, via conversion to an SCE, of SummarizedExperiment or DGEList bulk data. Visualizations include dimensionality reduction plots, heatmaps, scatterplots, percent composition or expression across groups, and more. Customizations range from size and title adjustments to automatic generation of annotations for heatmaps, overlay of trajectory analysis onto any dimensionality reduciton plot, hidden data overlay upon cursor hovering via ggplotly conversion, and many more. All with simple, discrete inputs. Color blindness friendliness is powered by legend adjustments (enlarged keys), and by allowing the use of shapes or letter-overlay in addition to the carefully selected dittoColors().' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-divergence/meta.yaml b/recipes/bioconductor-divergence/meta.yaml index a322557c552a1..7bff8bd7a9b05 100644 --- a/recipes/bioconductor-divergence/meta.yaml +++ b/recipes/bioconductor-divergence/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "divergence" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0ead0047c69549361f0f86d7207aee2b +about: + description: This package provides functionality for performing divergence analysis as presented in Dinalankara et al, "Digitizing omics profiles by divergence from a baseline", PANS 2018. This allows the user to simplify high dimensional omics data into a binary or ternary format which encapsulates how the data is divergent from a specified baseline group with the same univariate or multivariate features. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'Divergence: Functionality for assessing omics data by divergence with respect to a baseline' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-divergence", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base +source: + md5: 88ffd440264bcc970ecdb76ca53b8d2c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Divergence: Functionality for assessing omics data by divergence with respect to a baseline' - description: 'This package provides functionality for performing divergence analysis as presented in Dinalankara et al, "Digitizing omics profiles by divergence from a baseline", PANS 2018. This allows the user to simplify high dimensional omics data into a binary or ternary format which encapsulates how the data is divergent from a specified baseline group with the same univariate or multivariate features.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dks/meta.yaml b/recipes/bioconductor-dks/meta.yaml index ea476c6b5f0f4..7dcfbff2bfd52 100644 --- a/recipes/bioconductor-dks/meta.yaml +++ b/recipes/bioconductor-dks/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "dks" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f15cb2d88222e2936dc9460d69a924ad +about: + description: The dks package consists of a set of diagnostic functions for multiple testing methods. The functions can be used to determine if the p-values produced by a multiple testing procedure are correct. These functions are designed to be applied to simulated data. The functions require the entire set of p-values from multiple simulated studies, so that the joint distribution can be evaluated. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: The double Kolmogorov-Smirnov package for evaluating multiple testing procedures. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dks", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base @@ -26,13 +25,14 @@ requirements: run: - r-base - r-cubature +source: + md5: 63404c3bfc062f81249bdd219e229ef5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL - summary: 'The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.' - description: 'The dks package consists of a set of diagnostic functions for multiple testing methods. The functions can be used to determine if the p-values produced by a multiple testing procedure are correct. These functions are designed to be applied to simulated data. The functions require the entire set of p-values from multiple simulated studies, so that the joint distribution can be evaluated.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dlbcl/meta.yaml b/recipes/bioconductor-dlbcl/meta.yaml index 5324572ce48c0..242f27a893c41 100644 --- a/recipes/bioconductor-dlbcl/meta.yaml +++ b/recipes/bioconductor-dlbcl/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.42.1" %} +{% set version = "1.46.0" %} {% set name = "DLBCL" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a2906f8e35b0457c1cd8052d2457d40b +about: + description: This package provides additional expression data on diffuse large B-cell lymphomas for the BioNet package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Diffuse large B-cell lymphoma expression data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dlbcl", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e797d9de721064ed702845a0bd87b95e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Diffuse large B-cell lymphoma expression data' - description: 'This package provides additional expression data on diffuse large B-cell lymphomas for the BioNet package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dlbcl/post-link.sh b/recipes/bioconductor-dlbcl/post-link.sh index c17921df4bc39..513b23820452b 100644 --- a/recipes/bioconductor-dlbcl/post-link.sh +++ b/recipes/bioconductor-dlbcl/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dlbcl-1.42.1" +installBiocDataPackage.sh "dlbcl-1.46.0" diff --git a/recipes/bioconductor-dmcfb/meta.yaml b/recipes/bioconductor-dmcfb/meta.yaml index ae5ab6e964f0b..fbf8043b401b4 100644 --- a/recipes/bioconductor-dmcfb/meta.yaml +++ b/recipes/bioconductor-dmcfb/meta.yaml @@ -1,32 +1,35 @@ -{% set version = "1.14.0" %} +{% set version = "1.20.0" %} {% set name = "DMCFB" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: DMCFB is a pipeline for identifying differentially methylated cytosines using a Bayesian functional regression model in bisulfite sequencing data. By using a functional regression data model, it tries to capture position-specific, group-specific and other covariates-specific methylation patterns as well as spatial correlation patterns and unknown underlying models of methylation data. It is robust and flexible with respect to the true underlying models and inclusion of any covariates, and the missing values are imputed using spatial correlation between positions and samples. A Bayesian approach is adopted for estimation and inference in the proposed method. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Differentially Methylated Cytosines via a Bayesian Functional Approach -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3c58d3e03a24fc315eefcb8c8c987feb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic -# Suggests: testthat, knitr, rmarkdown + run_exports: '{{ pin_subpackage("bioconductor-dmcfb", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-arm - r-base - r-benchmarkme @@ -37,12 +40,12 @@ requirements: - r-speedglm - r-tibble run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-arm - r-base - r-benchmarkme @@ -52,13 +55,16 @@ requirements: - r-matrixstats - r-speedglm - r-tibble + +source: + md5: 454e7d7fc1d95d097ea4ed164531fe23 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Differentially Methylated Cytosines via a Bayesian Functional Approach' - description: 'DMCFB is a pipeline for identifying differentially methylated cytosines using a Bayesian functional regression model in bisulfite sequencing data. By using a functional regression data model, it tries to capture position-specific, group-specific and other covariates-specific methylation patterns as well as spatial correlation patterns and unknown underlying models of methylation data. It is robust and flexible with respect to the true underlying models and inclusion of any covariates, and the missing values are imputed using spatial correlation between positions and samples. A Bayesian approach is adopted for estimation and inference in the proposed method.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dmchmm/meta.yaml b/recipes/bioconductor-dmchmm/meta.yaml index 440303fd576f2..550ef4972d20b 100644 --- a/recipes/bioconductor-dmchmm/meta.yaml +++ b/recipes/bioconductor-dmchmm/meta.yaml @@ -1,55 +1,60 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "DMCHMM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'A pipeline for identifying differentially methylated CpG sites using Hidden Markov Model in bisulfite sequencing data. DNA methylation studies have enabled researchers to understand methylation patterns and their regulatory roles in biological processes and disease. However, only a limited number of statistical approaches have been developed to provide formal quantitative analysis. Specifically, a few available methods do identify differentially methylated CpG (DMC) sites or regions (DMR), but they suffer from limitations that arise mostly due to challenges inherent in bisulfite sequencing data. These challenges include: (1) that read-depths vary considerably among genomic positions and are often low; (2) both methylation and autocorrelation patterns change as regions change; and (3) CpG sites are distributed unevenly. Furthermore, there are several methodological limitations: almost none of these tools is capable of comparing multiple groups and/or working with missing values, and only a few allow continuous or multiple covariates. The last of these is of great interest among researchers, as the goal is often to find which regions of the genome are associated with several exposures and traits. To tackle these issues, we have developed an efficient DMC identification method based on Hidden Markov Models (HMMs) called “DMCHMM” which is a three-step approach (model selection, prediction, testing) aiming to address the aforementioned drawbacks.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Differentially Methylated CpG using Hidden Markov Model -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a4e52e12df4e699e0e20d13828f25f0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dmchmm", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-calibrate - r-fdrtool - r-multcomp run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-calibrate - r-fdrtool - r-multcomp + +source: + md5: 48059a3a3eccca8c9da8fb433be4d43b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Differentially Methylated CpG using Hidden Markov Model' - description: 'A pipeline for identifying differentially methylated CpG sites using Hidden Markov Model in bisulfite sequencing data. DNA methylation studies have enabled researchers to understand methylation patterns and their regulatory roles in biological processes and disease. However, only a limited number of statistical approaches have been developed to provide formal quantitative analysis. Specifically, a few available methods do identify differentially methylated CpG (DMC) sites or regions (DMR), but they suffer from limitations that arise mostly due to challenges inherent in bisulfite sequencing data. These challenges include: (1) that read-depths vary considerably among genomic positions and are often low; (2) both methylation and autocorrelation patterns change as regions change; and (3) CpG sites are distributed unevenly. Furthermore, there are several methodological limitations: almost none of these tools is capable of comparing multiple groups and/or working with missing values, and only a few allow continuous or multiple covariates. The last of these is of great interest among researchers, as the goal is often to find which regions of the genome are associated with several exposures and traits. To tackle these issues, we have developed an efficient DMC identification method based on Hidden Markov Models (HMMs) called “DMCHMM” which is a three-step approach (model selection, prediction, testing) aiming to address the aforementioned drawbacks.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dmelsgi/meta.yaml b/recipes/bioconductor-dmelsgi/meta.yaml index 6dabf001c9956..633e63c2a2f01 100644 --- a/recipes/bioconductor-dmelsgi/meta.yaml +++ b/recipes/bioconductor-dmelsgi/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.34.0" %} +{% set version = "1.37.0" %} {% set name = "DmelSGI" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package contains the experimental data and documented source code of the manuscript "Fischer et al., A Map of Directional Genetic Interactions in a Metazoan Cell, eLife, 2015, in Press.". The vignette code generates all figures in the paper. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Experimental data and documented source code for the paper "A Map of Directional Genetic Interactions in a Metazoan Cell" -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c13b3a8f881ca54d5e8ddf52ebe8b86a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dmelsgi", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, EBImage, RColorBrewer, RNAinteractMAPK, hwriter, xtable, beeswarm requirements: host: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 - r-abind - r-base - r-gplots @@ -31,8 +32,8 @@ requirements: - r-knitr - r-tsp run: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 - r-abind - r-base - r-gplots @@ -40,13 +41,17 @@ requirements: - r-knitr - r-tsp - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: a4f0d7af10a602b42c62e78a54785269 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Experimental data and documented source code for the paper "A Map of Directional Genetic Interactions in a Metazoan Cell"' - description: 'The package contains the experimental data and documented source code of the manuscript "Fischer et al., A Map of Directional Genetic Interactions in a Metazoan Cell, eLife, 2015, in Press.". The vignette code generates all figures in the paper.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dmelsgi/post-link.sh b/recipes/bioconductor-dmelsgi/post-link.sh index 9666ced12ef5f..1358749012510 100644 --- a/recipes/bioconductor-dmelsgi/post-link.sh +++ b/recipes/bioconductor-dmelsgi/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dmelsgi-1.34.0" +installBiocDataPackage.sh "dmelsgi-1.37.0" diff --git a/recipes/bioconductor-dmrcaller/build_failure.linux-aarch64.yaml b/recipes/bioconductor-dmrcaller/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..9fadef3153076 --- /dev/null +++ b/recipes/bioconductor-dmrcaller/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 45e125607b6f8d0b890b006f573288e5a518c6628c408cb710ce81c88015fa6d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - nothing provides r-base >=3.5.1,<3.5.2.0a0 needed by r-betareg-3.1_1-r351h6115d3f_1000 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-genomicranges >=1.58.0,<1.59.0 [0m is installable and it requires + [32mbioconductor-genomeinfodb >=1.42.0,<1.43.0 [0m, which requires + [32mbioconductor-ucsc.utils >=1.2.0,<1.3.0 [0m, which requires + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [31mr-betareg[0m is not installable because there are no viable options + [31mr-betareg [3.1_1|3.1_2][0m would require + [31mr-base >=3.5.1,<3.5.2.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-betareg [3.1_2|3.1_3][0m would require + [31mr-base >=3.5,<3.6.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-betareg [3.1_2|3.1_3|3.1_4][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-betareg [3.1_3|3.1_4][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-betareg 3.1_4[0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-betareg 3.1_4[0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-betareg 3.1_4[0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec(">=3.5.1,<3.5.2.0a0"), MatchSpec("r-betareg==3.1_1=r351h6115d3f_1000")} + Encountered problems while solving: + - nothing provides r-base >=3.5.1,<3.5.2.0a0 needed by r-betareg-3.1_1-r351h6115d3f_1000 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-genomicranges >=1.58.0,<1.59.0 [0m is installable and it requires + [32mbioconductor-genomeinfodb >=1.42.0,<1.43.0 [0m, which requires + [32mbioconductor-ucsc.utils >=1.2.0,<1.3.0 [0m, which requires + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [31mr-betareg[0m is not installable because there are no viable options + [31mr-betareg [3.1_1|3.1_2][0m would require + [31mr-base >=3.5.1,<3.5.2.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-betareg [3.1_2|3.1_3][0m would require + [31mr-base >=3.5,<3.6.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-betareg [3.1_2|3.1_3|3.1_4][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-betareg [3.1_3|3.1_4][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-betareg 3.1_4[0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-betareg 3.1_4[0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-betareg 3.1_4[0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-dmrcaller/meta.yaml b/recipes/bioconductor-dmrcaller/meta.yaml index a58fdd462be2d..0976c0931d2f6 100644 --- a/recipes/bioconductor-dmrcaller/meta.yaml +++ b/recipes/bioconductor-dmrcaller/meta.yaml @@ -1,29 +1,40 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "DMRcaller" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Uses Bisulfite sequencing data in two conditions and identifies differentially methylated regions between the conditions in CG and non-CG context. The input is the CX report files produced by Bismark and the output is a list of DMRs stored as GRanges objects. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Differentially Methylated Regions caller -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c5b37620b4950eb63e32c3063235e8e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dmrcaller", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:dmrcaller + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, RUnit, BiocGenerics requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-betareg - r-rcpp @@ -31,29 +42,23 @@ requirements: - libblas - liblapack run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-betareg - r-rcpp - r-rcpproll - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} + +source: + md5: f8f0246094a04c162577b779e291467f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'Differentially Methylated Regions caller' - description: 'Uses Bisulfite sequencing data in two conditions and identifies differentially methylated regions between the conditions in CG and non-CG context. The input is the CX report files produced by Bismark and the output is a list of DMRs stored as GRanges objects.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dmrcate/meta.yaml b/recipes/bioconductor-dmrcate/meta.yaml index 3afce1ec8160d..38c60c3c45952 100644 --- a/recipes/bioconductor-dmrcate/meta.yaml +++ b/recipes/bioconductor-dmrcate/meta.yaml @@ -1,71 +1,80 @@ -{% set version = "2.14.0" %} +{% set version = "3.2.0" %} {% set name = "DMRcate" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: De novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulfite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Methylation array and sequencing spatial analysis methods -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 05b84f7838613f6f7c4236c35858b5da build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic -# Suggests: knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata + run_exports: '{{ pin_subpackage("bioconductor-dmrcate", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:dmrcate + parent_recipe: + name: bioconductor-dmrcate + path: recipes/bioconductor-dmrcate + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38, FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata, EPICv2manifest requirements: host: - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-dss >=2.48.0,<2.49.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-missmethyl >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-bsseq >=1.42.0,<1.43.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-missmethyl >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-plyr run: - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-dss >=2.48.0,<2.49.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-experimenthub >=2.8.0,<2.9.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gviz >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-minfi >=1.46.0,<1.47.0' - - 'bioconductor-missmethyl >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-bsseq >=1.42.0,<1.43.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-missmethyl >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-plyr + +source: + md5: 756031baaead90f2b11124d082479f3d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Methylation array and sequencing spatial analysis methods' - description: 'De novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulfite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions.' - license_file: LICENSE -extra: - identifiers: - - biotools:dmrcate - parent_recipe: - name: bioconductor-dmrcate - path: recipes/bioconductor-dmrcate - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dmrcatedata/build_failure.linux-64.yaml b/recipes/bioconductor-dmrcatedata/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..5286bb1df2e5e --- /dev/null +++ b/recipes/bioconductor-dmrcatedata/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: f71d12109b5fab596d2e724bd810c2756d1436932dbe9e8f214bce3666b934ea # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - package bioconductor-gviz-1.50.0-r44hdfd78af_0 requires bioconductor-biovizbase >=1.54.0,<1.55.0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-experimenthub >=2.14.0,<2.15.0 [0m is installable and it requires + [32mbioconductor-s4vectors >=0.44.0,<0.45.0 [0m, which can be installed; + [32mbioconductor-genomicfeatures >=1.58.0,<1.59.0 [0m is installable and it requires + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [32mbioconductor-gviz >=1.50.0,<1.51.0 [0m is installable and it requires + [32mbioconductor-biovizbase >=1.54.0,<1.55.0 [0m, which requires + [32mbioconductor-summarizedexperiment >=1.36.0,<1.37.0 [0m, which requires + [32mbioconductor-delayedarray >=0.32.0,<0.33.0 [0m, which requires + [32mbioconductor-sparsearray >=1.6.0,<1.7.0 [0m, which requires + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [31mbioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 [0m is not installable because there are no viable options + [31mbioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 0.6.0[0m would require + [31mr-base [3.3.2* |>=3.3,<3.4 ][0m, which conflicts with any installable versions previously reported; + [31mbioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 0.6.0[0m would require + [31mr-base 3.4.1* [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 0.6.0[0m would require + [31mbioconductor-minfi >=1.26.2,<1.28.0 [0m, which requires + [31mbioconductor-bumphunter >=1.22.0,<1.24.0 [0m, which requires + [31mbioconductor-genomicfeatures >=1.32.2,<1.34.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-s4vectors >=0.18.3,<0.20.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 0.6.0[0m would require + [31mbioconductor-minfi >=1.28.0,<1.29.0 [0m, which requires + [31mbioconductor-bumphunter >=1.24.0,<1.25.0 [0m, which requires + [31mbioconductor-genomicfeatures >=1.34.0,<1.35.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-s4vectors >=0.20.0,<0.21.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 0.6.0[0m would require + [31mbioconductor-minfi >=1.30.0,<1.31.0 [0m, which requires + [31mbioconductor-bumphunter >=1.26.0,<1.27.0 [0m, which requires + [31mbioconductor-genomicfeatures >=1.36.0,<1.37.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-s4vectors >=0.22.0,<0.23.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 0.6.0[0m would require + [31mbioconductor-minfi >=1.32.0,<1.33.0 [0m, which requires + [31mbioconductor-bumphunter >=1.28.0,<1.29.0 [0m, which requires + [31mbioconductor-genomicfeatures >=1.38.0,<1.39.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-s4vectors >=0.24.0,<0.25.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 0.6.0[0m would require + [31mbioconductor-minfi >=1.36.0,<1.37.0 [0m, which requires + [31mbioconductor-bumphunter >=1.32.0,<1.33.0 [0m, which requires + [31mbioconductor-genomicfeatures >=1.42.0,<1.43.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-s4vectors >=0.28.0,<0.29.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 0.6.0[0m would require + [31mbioconductor-minfi >=1.34.0,<1.35.0 [0m, which requires + [31mbioconductor-bumphunter >=1.30.0,<1.31.0 [0m, which requires + [31mbioconductor-genomicfeatures >=1.40.0,<1.41.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-s4vectors >=0.26.0,<0.27.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 0.6.0[0m would require + [31mbioconductor-minfi >=1.38.0,<1.39.0 [0m, which requires + [31mbioconductor-bumphunter >=1.34.0,<1.35.0 [0m, which requires + [31mbioconductor-genomicfeatures >=1.44.0,<1.45.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-s4vectors >=0.30.0,<0.31.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 0.6.0[0m would require + [31mbioconductor-minfi >=1.40.0,<1.41.0 [0m, which requires + [31mbioconductor-bumphunter >=1.36.0,<1.37.0 [0m, which requires + [31mbioconductor-genomicfeatures >=1.46.0,<1.47.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-s4vectors >=0.32.0,<0.33.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 0.6.1[0m would require + [31mbioconductor-minfi >=1.44.0,<1.45.0 [0m, which requires + [31mbioconductor-bumphunter >=1.40.0,<1.41.0 [0m, which requires + [31mbioconductor-genomicfeatures >=1.50.0,<1.51.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-s4vectors >=0.36.0,<0.37.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 0.6.1[0m would require + [31mbioconductor-minfi >=1.46.0,<1.47.0 [0m, which requires + [31mbioconductor-bumphunter >=1.42.0,<1.43.0 [0m, which requires + [31mbioconductor-genomicfeatures >=1.52.0,<1.53.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-s4vectors >=0.38.0,<0.39.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 0.6.1[0m would require + [31mbioconductor-minfi >=1.48.0,<1.49.0 [0m, which requires + [31mbioconductor-bumphunter >=1.44.0,<1.45.0 [0m, which requires + [31mbioconductor-genomicfeatures >=1.54.0,<1.55.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-s4vectors >=0.40.0,<0.41.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0 [0m is not installable because there are no viable options + [31mbioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 0.6.0[0m would require + [31mr-base 3.4.1* [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 0.6.0[0m would require + [31mbioconductor-minfi >=1.26.2,<1.28.0 [0m, which cannot be installed (as previously explained); + [31mbioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 0.6.0[0m would require + [31mbioconductor-minfi >=1.28.0,<1.29.0 [0m, which cannot be installed (as previously explained); + [31mbioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 0.6.0[0m would require + [31mbioconductor-minfi >=1.30.0,<1.31.0 [0m, which cannot be installed (as previously explained); + [31mbioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 0.6.0[0m would require + [31mbioconductor-minfi >=1.32.0,<1.33.0 [0m, which cannot be installed (as previously explained); + [31mbioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 0.6.0[0m would require + [31mbioconductor-minfi >=1.34.0,<1.35.0 [0m, which cannot be installed (as previously explained); + [31mbioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 0.6.0[0m would require + [31mbioconductor-minfi >=1.36.0,<1.37.0 [0m, which cannot be installed (as previously explained); + [31mbioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 0.6.0[0m would require + [31mbioconductor-minfi >=1.38.0,<1.39.0 [0m, which cannot be installed (as previously explained); + [31mbioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 0.6.0[0m would require + [31mbioconductor-minfi >=1.40.0,<1.41.0 [0m, which cannot be installed (as previously explained); + [31mbioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 0.6.0[0m would require + [31mbioconductor-minfi >=1.44.0,<1.45.0 [0m, which cannot be installed (as previously explained); + [31mbioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 0.6.0[0m would require + [31mbioconductor-minfi >=1.46.0,<1.47.0 [0m, which cannot be installed (as previously explained); + [31mbioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 0.6.0[0m would require + [31mbioconductor-minfi >=1.48.0,<1.49.0 [0m, which cannot be installed (as previously explained); + [32mr-base 4.4.* [0m is requested and can be installed. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-dmrcatedata/meta.yaml b/recipes/bioconductor-dmrcatedata/meta.yaml index 06d80da935efd..f6d8487420c51 100644 --- a/recipes/bioconductor-dmrcatedata/meta.yaml +++ b/recipes/bioconductor-dmrcatedata/meta.yaml @@ -1,60 +1,66 @@ -{% set version = "2.20.0" %} +{% set version = "2.24.0" %} {% set name = "DMRcatedata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains 9 data objects supporting functionality and examples of the Bioconductor package DMRcate. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Data Package for DMRcate -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ac938c6259121c4a60ca3c8c5bfdf724 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dmrcatedata", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-dmrcatedata + path: recipes/bioconductor-dmrcatedata + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-plyr - r-readxl run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-plyr - r-readxl - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 0f41fc4cf1bac6a239be095eab5139c0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Data Package for DMRcate' - description: 'This package contains 9 data objects supporting functionality and examples of the Bioconductor package DMRcate.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-dmrcatedata - path: recipes/bioconductor-dmrcatedata - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dmrcatedata/post-link.sh b/recipes/bioconductor-dmrcatedata/post-link.sh index d4ad6b968cb0a..2db75e7aa977d 100644 --- a/recipes/bioconductor-dmrcatedata/post-link.sh +++ b/recipes/bioconductor-dmrcatedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dmrcatedata-2.20.0" +installBiocDataPackage.sh "dmrcatedata-2.24.0" diff --git a/recipes/bioconductor-dmrscan/meta.yaml b/recipes/bioconductor-dmrscan/meta.yaml index 0b03fd4a53375..d86a1bab371b1 100644 --- a/recipes/bioconductor-dmrscan/meta.yaml +++ b/recipes/bioconductor-dmrscan/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "DMRScan" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'This package detects significant differentially methylated regions (for both qualitative and quantitative traits), using a scan statistic with underlying Poisson heuristics. The scan statistic will depend on a sequence of window sizes (# of CpGs within each window) and on a threshold for each window size. This threshold can be calculated by three different means: i) analytically using Siegmund et.al (2012) solution (preferred), ii) an important sampling as suggested by Zhang (2008), and a iii) full MCMC modeling of the data, choosing between a number of different options for modeling the dependency between each CpG.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Detection of Differentially Methylated Regions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 698b81baf921ef394adedb8d8ff7ba7f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dmrscan", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, BiocManager requirements: host: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-mass - r-matrix - r-mvtnorm - r-rcpproll run: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-mass - r-matrix - r-mvtnorm - r-rcpproll + +source: + md5: 627081fa7eccd3d649e117ef14b351ec + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Detection of Differentially Methylated Regions' - description: 'This package detects significant differentially methylated regions (for both qualitative and quantitative traits), using a scan statistic with underlying Poisson heuristics. The scan statistic will depend on a sequence of window sizes (# of CpGs within each window) and on a threshold for each window size. This threshold can be calculated by three different means: i) analytically using Siegmund et.al (2012) solution (preferred), ii) an important sampling as suggested by Zhang (2008), and a iii) full MCMC modeling of the data, choosing between a number of different options for modeling the dependency between each CpG.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dmrseq/meta.yaml b/recipes/bioconductor-dmrseq/meta.yaml index 505c49b1d0fb8..5ef08911760f4 100644 --- a/recipes/bioconductor-dmrseq/meta.yaml +++ b/recipes/bioconductor-dmrseq/meta.yaml @@ -1,38 +1,40 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "dmrseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements an approach for scanning the genome to detect and perform accurate inference on differentially methylated regions from Whole Genome Bisulfite Sequencing data. The method is based on comparing detected regions to a pooled null distribution, that can be implemented even when as few as two samples per population are available. Region-level statistics are obtained by fitting a generalized least squares (GLS) regression model with a nested autoregressive correlated error structure for the effect of interest on transformed methylation proportions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a8181423ea50609ae16545b9f8bb1895 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dmrseq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-annotatr >=1.28.0,<1.29.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bsseq >=1.38.0,<1.39.0' - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-annotatr >=1.32.0,<1.33.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bsseq >=1.42.0,<1.43.0 + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-locfit @@ -41,17 +43,17 @@ requirements: - r-outliers - r-rcolorbrewer run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-annotatr >=1.28.0,<1.29.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bsseq >=1.38.0,<1.39.0' - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-annotatr >=1.32.0,<1.33.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bsseq >=1.42.0,<1.43.0 + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-locfit @@ -59,13 +61,16 @@ requirements: - r-nlme - r-outliers - r-rcolorbrewer + +source: + md5: 2d2587cf01f801f71925719e452948bd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing' - description: 'This package implements an approach for scanning the genome to detect and perform accurate inference on differentially methylated regions from Whole Genome Bisulfite Sequencing data. The method is based on comparing detected regions to a pooled null distribution, that can be implemented even when as few as two samples per population are available. Region-level statistics are obtained by fitting a generalized least squares (GLS) regression model with a nested autoregressive correlated error structure for the effect of interest on transformed methylation proportions.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dnabarcodecompatibility/meta.yaml b/recipes/bioconductor-dnabarcodecompatibility/meta.yaml index bc74f779dfa5a..e9680fafc2b10 100644 --- a/recipes/bioconductor-dnabarcodecompatibility/meta.yaml +++ b/recipes/bioconductor-dnabarcodecompatibility/meta.yaml @@ -1,49 +1,61 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "DNABarcodeCompatibility" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package allows one to obtain optimised combinations of DNA barcodes to be used for multiplex sequencing. In each barcode combination, barcodes are pooled with respect to Illumina chemistry constraints. Combinations can be filtered to keep those that are robust against substitution and insertion/deletion errors thereby facilitating the demultiplexing step. In addition, the package provides an optimiser function to further favor the selection of barcode combinations with least heterogeneity in barcode usage. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b1e2988c254cf089a2f887abf139b7bf build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dnabarcodecompatibility", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-dnabarcodes >=1.32.0,<1.33.0' - r-base + - r-bh - r-dplyr - r-numbers - r-purrr + - r-rcpp >=0.11.2 - r-stringr - r-tidyr + - libblas + - liblapack run: - - 'bioconductor-dnabarcodes >=1.32.0,<1.33.0' - r-base + - r-bh - r-dplyr - r-numbers - r-purrr + - r-rcpp >=0.11.2 - r-stringr - r-tidyr + +source: + md5: e57f1831f939739ea375d835f0447a5e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms' - description: 'The package allows one to obtain optimised combinations of DNA barcodes to be used for multiplex sequencing. In each barcode combination, barcodes are pooled with respect to Illumina chemistry constraints. Combinations can be filtered to keep those that are robust against substitution and insertion/deletion errors thereby facilitating the demultiplexing step. In addition, the package provides an optimiser function to further favor the selection of barcode combinations with least heterogeneity in barcode usage.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dnabarcodes/meta.yaml b/recipes/bioconductor-dnabarcodes/meta.yaml index 53c9caad94d27..b92b2ba9f20a5 100644 --- a/recipes/bioconductor-dnabarcodes/meta.yaml +++ b/recipes/bioconductor-dnabarcodes/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "DNABarcodes" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package offers a function to create DNA barcode sets capable of correcting insertion, deletion, and substitution errors. Existing barcodes can be analysed regarding their minimal, maximal and average distances between barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e., assigned to their original reference barcode. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6047e393e89e644fbf9aa4aa5a9faa64 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dnabarcodes", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:dnabarcodes + parent_recipe: + name: bioconductor-dnabarcodes + path: recipes/bioconductor-dnabarcodes + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, rmarkdown requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-bh - r-matrix - - 'r-rcpp >=0.11.2' + - r-rcpp >=0.11.2 - libblas - liblapack run: - r-base - r-bh - r-matrix - - 'r-rcpp >=0.11.2' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=0.11.2 + +source: + md5: a095e98696182153e9e2cd36bac1c728 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments' - description: 'The package offers a function to create DNA barcode sets capable of correcting insertion, deletion, and substitution errors. Existing barcodes can be analysed regarding their minimal, maximal and average distances between barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e., assigned to their original reference barcode.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:dnabarcodes - parent_recipe: - name: bioconductor-dnabarcodes - path: recipes/bioconductor-dnabarcodes - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dnacopy/meta.yaml b/recipes/bioconductor-dnacopy/meta.yaml index f189045b214b5..42a2e6a453b17 100644 --- a/recipes/bioconductor-dnacopy/meta.yaml +++ b/recipes/bioconductor-dnacopy/meta.yaml @@ -1,47 +1,53 @@ -{% set version = "1.76.0" %} +{% set version = "1.80.0" %} {% set name = "DNAcopy" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: DNA Copy Number Data Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b80859f79a39def302664f11b91a98f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dnacopy", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:dnacopy + - doi:10.1038/nmeth.3252 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - {{ compiler('fortran') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - {{ compiler('fortran') }} - - make + +source: + md5: be3239ff013047618e2b859e8c9c7209 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'DNA Copy Number Data Analysis' - description: 'Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:dnacopy - - doi:10.1038/nmeth.3252 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dnafusion/meta.yaml b/recipes/bioconductor-dnafusion/meta.yaml index 03be682d7e794..bb2e5a17d2d61 100644 --- a/recipes/bioconductor-dnafusion/meta.yaml +++ b/recipes/bioconductor-dnafusion/meta.yaml @@ -1,57 +1,62 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "DNAfusion" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: DNAfusion can identify gene fusions such as EML4-ALK based on paired-end sequencing results. This package was developed using position deduplicated BAM files generated with the AVENIO Oncology Analysis Software. These files are made using the AVENIO ctDNA surveillance kit and Illumina Nextseq 500 sequencing. This is a targeted hybridization NGS approach and includes ALK-specific but not EML4-specific probes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identification of gene fusions using paired-end sequencing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7ef2bb10bea5334d6d159208c284c16 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dnafusion", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, sessioninfo, BiocStyle requirements: host: - - 'bioconductor-bamsignals >=1.34.0,<1.35.0' - - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - bioconductor-bamsignals >=1.38.0,<1.39.0 + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-bamsignals >=1.34.0,<1.35.0' - - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - bioconductor-bamsignals >=1.38.0,<1.39.0 + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 - r-base + +source: + md5: 1cda8d4924a5b43b55cff5f17ec1ade3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Identification of gene fusions using paired-end sequencing' - description: 'DNAfusion can identify gene fusions such as EML4-ALK based on paired-end sequencing results. This package was developed using position deduplicated BAM files generated with the AVENIO Oncology Analysis Software. These files are made using the AVENIO ctDNA surveillance kit and Illumina Nextseq 500 sequencing. This is a targeted hybridization NGS approach and includes ALK-specific but not EML4-specific probes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dnashaper/meta.yaml b/recipes/bioconductor-dnashaper/meta.yaml index 06c57e6991e97..22aee00220612 100644 --- a/recipes/bioconductor-dnashaper/meta.yaml +++ b/recipes/bioconductor-dnashaper/meta.yaml @@ -1,57 +1,63 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "DNAshapeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: DNAhapeR is an R/BioConductor package for ultra-fast, high-throughput predictions of DNA shape features. The package allows to predict, visualize and encode DNA shape features for statistical learning. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: High-throughput prediction of DNA shape features -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f2b90849d52bce75d88a4970f08c2544 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dnashaper", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:dnashaper + parent_recipe: + name: bioconductor-dnashaper + path: recipes/bioconductor-dnashaper + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationHub, knitr, rmarkdown, testthat, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19, caret requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-fields - - 'r-rcpp >=0.12.1' + - r-rcpp >=0.12.1 - libblas - liblapack run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-fields - - 'r-rcpp >=0.12.1' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=0.12.1 + +source: + md5: f6735dc4a979507e5af6b7385bab61da + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'High-throughput prediction of DNA shape features' - description: 'DNAhapeR is an R/BioConductor package for ultra-fast, high-throughput predictions of DNA shape features. The package allows to predict, visualize and encode DNA shape features for statistical learning.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:dnashaper - parent_recipe: - name: bioconductor-dnashaper - path: recipes/bioconductor-dnashaper - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dnazoodata/meta.yaml b/recipes/bioconductor-dnazoodata/meta.yaml index 6ac0f55444cfb..25378660cff22 100644 --- a/recipes/bioconductor-dnazoodata/meta.yaml +++ b/recipes/bioconductor-dnazoodata/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "DNAZooData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: DNAZooData is a data package giving programmatic access to genome assemblies and Hi-C contact matrices uniformly processed by the [DNA Zoo Consortium](https://www.dnazoo.org/). The matrices are available in the multi-resolution `.hic` format. A URL to corrected genome assemblies in `.fastq` format is also provided to the end-user. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: DNA Zoo data package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 06c4b9dbbaddc3dd4dcdc51e34150aa7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dnazoodata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: dplyr, testthat, methods, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-hicexperiment >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-rjson run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-hicexperiment >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-rjson - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: ebf660c8af5efe9626a5e9a80c8a897f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'DNA Zoo data package' - description: 'DNAZooData is a data package giving programmatic access to genome assemblies and Hi-C contact matrices uniformly processed by the [DNA Zoo Consortium](https://www.dnazoo.org/). The matrices are available in the multi-resolution `.hic` format. A URL to corrected genome assemblies in `.fastq` format is also provided to the end-user.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dnazoodata/post-link.sh b/recipes/bioconductor-dnazoodata/post-link.sh index 34b10c2512e29..bb6b5630d99b7 100644 --- a/recipes/bioconductor-dnazoodata/post-link.sh +++ b/recipes/bioconductor-dnazoodata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dnazoodata-1.2.0" +installBiocDataPackage.sh "dnazoodata-1.6.0" diff --git a/recipes/bioconductor-do.db/meta.yaml b/recipes/bioconductor-do.db/meta.yaml index 5c3b17b44eba8..6c985a8c0f174 100644 --- a/recipes/bioconductor-do.db/meta.yaml +++ b/recipes/bioconductor-do.db/meta.yaml @@ -1,44 +1,44 @@ {% set version = "2.9" %} {% set name = "DO.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 63dda6d46d2fe40c52a2e79260a7fb9d +about: + description: A set of annotation maps describing the entire Disease Ontology assembled using data from DO + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: A set of annotation maps describing the entire Disease Ontology build: - number: 16 + noarch: generic + number: 17 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-do.db", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-do.db + path: recipes/bioconductor-do.db + version: '2.9' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 63dda6d46d2fe40c52a2e79260a7fb9d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A set of annotation maps describing the entire Disease Ontology' - description: 'A set of annotation maps describing the entire Disease Ontology assembled using data from DO' -extra: - parent_recipe: - name: bioconductor-do.db - path: recipes/bioconductor-do.db - version: 2.9 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dominoeffect/meta.yaml b/recipes/bioconductor-dominoeffect/meta.yaml index eb625150b9ecb..93f1d180fc1b3 100644 --- a/recipes/bioconductor-dominoeffect/meta.yaml +++ b/recipes/bioconductor-dominoeffect/meta.yaml @@ -1,55 +1,62 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "DominoEffect" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The functions support identification and annotation of hotspot residues in proteins. These are individual amino acids that accumulate mutations at a much higher rate than their surrounding regions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identification and Annotation of Protein Hotspot Residues -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2e92d099e31b5feaf035b8eb5ad92376 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dominoeffect", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-data.table run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-data.table + +source: + md5: fb13c8fd16dd9cd3426bc1c39b02447e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Identification and Annotation of Protein Hotspot Residues' - description: 'The functions support identification and annotation of hotspot residues in proteins. These are individual amino acids that accumulate mutations at a much higher rate than their surrounding regions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dominosignal/build.sh b/recipes/bioconductor-dominosignal/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dominosignal/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dominosignal/meta.yaml b/recipes/bioconductor-dominosignal/meta.yaml new file mode 100644 index 0000000000000..9d3d503cf51c8 --- /dev/null +++ b/recipes/bioconductor-dominosignal/meta.yaml @@ -0,0 +1,56 @@ +{% set version = "1.0.0" %} +{% set name = "dominoSignal" %} +{% set bioc = "3.20" %} + +about: + description: dominoSignal is a package developed to analyze cell signaling through ligand - receptor - transcription factor networks in scRNAseq data. It takes as input information transcriptomic data, requiring counts, z-scored counts, and cluster labels, as well as information on transcription factor activation (such as from SCENIC) and a database of ligand and receptor pairings (such as from CellPhoneDB). This package creates an object storing ligand - receptor - transcription factor linkages by cluster and provides several methods for exploring, summarizing, and visualizing the analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 | file LICENSE + license_file: LICENSE + summary: Cell Communication Analysis for Single Cell RNA Sequencing + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-dominosignal", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, patchwork, rmarkdown, Seurat, testthat, formatR, BiocFileCache, SingleCellExperiment +requirements: + host: + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - r-base + - r-circlize + - r-ggpubr + - r-igraph + - r-matrix + - r-plyr + run: + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - r-base + - r-circlize + - r-ggpubr + - r-igraph + - r-matrix + - r-plyr + +source: + md5: 8a23703b89f2fb779fbb0af24625120f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-donapllp2013/meta.yaml b/recipes/bioconductor-donapllp2013/meta.yaml index abdd5e739d806..bf8719a7c97e0 100644 --- a/recipes/bioconductor-donapllp2013/meta.yaml +++ b/recipes/bioconductor-donapllp2013/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "DonaPLLP2013" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d8dc37afefc52856d520540b07faf545 +about: + description: An experiment data package associated with the publication Dona et al. (2013). Package contains runnable vignettes showing an example image segmentation for one posterior lateral line primordium, and also the data table and code used to analyze tissue-scale lifetime-ratio statistics. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Supplementary data package for Dona et al. (2013) containing example images and tables build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-donapllp2013", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - bioconductor-ebimage >=4.48.0,<4.49.0 - r-base run: - - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - bioconductor-ebimage >=4.48.0,<4.49.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f8ac609e6018b26a1aec2d087a8f30f4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Supplementary data package for Dona et al. (2013) containing example images and tables' - description: 'An experiment data package associated with the publication Dona et al. (2013). Package contains runnable vignettes showing an example image segmentation for one posterior lateral line primordium, and also the data table and code used to analyze tissue-scale lifetime-ratio statistics.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-donapllp2013/post-link.sh b/recipes/bioconductor-donapllp2013/post-link.sh index 5921a0116e213..6f3498dc2fd11 100644 --- a/recipes/bioconductor-donapllp2013/post-link.sh +++ b/recipes/bioconductor-donapllp2013/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "donapllp2013-1.40.0" +installBiocDataPackage.sh "donapllp2013-1.44.0" diff --git a/recipes/bioconductor-doppelgangr/meta.yaml b/recipes/bioconductor-doppelgangr/meta.yaml index 8038472db593b..6d4e7b3fef178 100644 --- a/recipes/bioconductor-doppelgangr/meta.yaml +++ b/recipes/bioconductor-doppelgangr/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "doppelgangR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The main function is doppelgangR(), which takes as minimal input a list of ExpressionSet object, and searches all list pairs for duplicated samples. The search is based on the genomic data (exprs(eset)), phenotype/clinical data (pData(eset)), and "smoking guns" - supposedly unique identifiers found in pData(eset). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2.0) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identify likely duplicate samples from genomic or meta-data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c50eff7bb5871b545a8199a9b1c4667b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-doppelgangr", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:doppelgangr + - doi:10.1093/jnci/djw146 + parent_recipe: + name: bioconductor-doppelgangr + path: recipes/bioconductor-doppelgangr + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-digest - r-mnormt run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-digest - r-mnormt + +source: + md5: dc715e98732ecc99e88ce2418cbf2b45 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2.0)' - summary: 'Identify likely duplicate samples from genomic or meta-data' - description: 'The main function is doppelgangR(), which takes as minimal input a list of ExpressionSet object, and searches all list pairs for duplicated samples. The search is based on the genomic data (exprs(eset)), phenotype/clinical data (pData(eset)), and "smoking guns" - supposedly unique identifiers found in pData(eset).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:doppelgangr - - doi:10.1093/jnci/djw146 - parent_recipe: - name: bioconductor-doppelgangr - path: recipes/bioconductor-doppelgangr - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dorothea/meta.yaml b/recipes/bioconductor-dorothea/meta.yaml index e6eda607d7e68..2427b884cc0a5 100644 --- a/recipes/bioconductor-dorothea/meta.yaml +++ b/recipes/bioconductor-dorothea/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "dorothea" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: DoRothEA is a gene regulatory network containing signed transcription factor (TF) - target gene interactions. DoRothEA regulons, the collection of a TF and its transcriptional targets, were curated and collected from different types of evidence for both human and mouse. A confidence level was assigned to each TF-target interaction based on the number of supporting evidence. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Collection Of Human And Mouse TF Regulons -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d1ad1213db5d54f1fc6ef8d195b9bbc0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dorothea", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biobase, BiocStyle, OmnipathR, viper, knitr, pheatmap, pkgdown, rmarkdown, Seurat, SingleCellExperiment, SummarizedExperiment, testthat (>= 2.1.0), tibble, tidyr, utils requirements: host: - - 'bioconductor-bcellviper >=1.38.0,<1.39.0' - - 'bioconductor-decoupler >=2.8.0,<2.9.0' + - bioconductor-bcellviper >=1.42.0,<1.43.0 + - bioconductor-decoupler >=2.12.0,<2.13.0 - r-base - r-dplyr - r-magrittr run: - - 'bioconductor-bcellviper >=1.38.0,<1.39.0' - - 'bioconductor-decoupler >=2.8.0,<2.9.0' + - bioconductor-bcellviper >=1.42.0,<1.43.0 + - bioconductor-decoupler >=2.12.0,<2.13.0 - r-base - r-dplyr - r-magrittr - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 5787d956a54680963aff5ce33c12307c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Collection Of Human And Mouse TF Regulons' - description: 'DoRothEA is a gene regulatory network containing signed transcription factor (TF) - target gene interactions. DoRothEA regulons, the collection of a TF and its transcriptional targets, were curated and collected from different types of evidence for both human and mouse. A confidence level was assigned to each TF-target interaction based on the number of supporting evidence.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dorothea/post-link.sh b/recipes/bioconductor-dorothea/post-link.sh index b77af7c38dc2e..d7f673da4b078 100644 --- a/recipes/bioconductor-dorothea/post-link.sh +++ b/recipes/bioconductor-dorothea/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dorothea-1.14.0" +installBiocDataPackage.sh "dorothea-1.18.0" diff --git a/recipes/bioconductor-doscheda/meta.yaml b/recipes/bioconductor-doscheda/meta.yaml index 896c4140c8007..32cc50c0a7fc4 100644 --- a/recipes/bioconductor-doscheda/meta.yaml +++ b/recipes/bioconductor-doscheda/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "Doscheda" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Doscheda focuses on quantitative chemoproteomics used to determine protein interaction profiles of small molecules from whole cell or tissue lysates using Mass Spectrometry data. The package provides a shiny application to run the pipeline, several visualisations and a downloadable report of an experiment. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A DownStream Chemo-Proteomics Analysis Pipeline -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3eee0480f798b00860daaf2cb88325ca build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-doscheda", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-base - r-calibrate - r-corrgram @@ -42,9 +44,9 @@ requirements: - r-shinydashboard - r-stringr run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-base - r-calibrate - r-corrgram @@ -61,13 +63,16 @@ requirements: - r-shiny - r-shinydashboard - r-stringr + +source: + md5: 7384a205a6521c4073d181cf3c9d1645 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'A DownStream Chemo-Proteomics Analysis Pipeline' - description: 'Doscheda focuses on quantitative chemoproteomics used to determine protein interaction profiles of small molecules from whole cell or tissue lysates using Mass Spectrometry data. The package provides a shiny application to run the pipeline, several visualisations and a downloadable report of an experiment.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dose/meta.yaml b/recipes/bioconductor-dose/meta.yaml index 0d10dde0a81d3..3a9450cf0b311 100644 --- a/recipes/bioconductor-dose/meta.yaml +++ b/recipes/bioconductor-dose/meta.yaml @@ -1,61 +1,65 @@ -{% set version = "3.28.1" %} +{% set version = "4.0.0" %} {% set name = "DOSE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Disease Ontology Semantic and Enrichment analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11096edb2862c8a442f53435082e40b6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dose", max_pin="x.x") }}' - noarch: generic -# Suggests: prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, rmarkdown, org.Hs.eg.db, MPO.db, HPO.db, testthat + +extra: + identifiers: + - biotools:dose + parent_recipe: + name: bioconductor-dose + path: recipes/bioconductor-dose + version: 3.6.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, memoise, org.Hs.eg.db, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - - 'bioconductor-hdo.db >=0.99.0,<0.100.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-gosemsim >=2.32.0,<2.33.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - r-ggplot2 - r-reshape2 - - r-yulab.utils + - r-yulab.utils >=0.1.6 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - - 'bioconductor-hdo.db >=0.99.0,<0.100.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-gosemsim >=2.32.0,<2.33.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - r-ggplot2 - r-reshape2 - - r-yulab.utils + - r-yulab.utils >=0.1.6 + +source: + md5: 01b762c6bd25214fd4fa713df1da6e52 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Disease Ontology Semantic and Enrichment analysis' - description: 'This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.' -extra: - identifiers: - - biotools:dose - parent_recipe: - name: bioconductor-dose - path: recipes/bioconductor-dose - version: 3.6.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-doser/meta.yaml b/recipes/bioconductor-doser/meta.yaml index 7b6a6fdc3f312..597d65afa025e 100644 --- a/recipes/bioconductor-doser/meta.yaml +++ b/recipes/bioconductor-doser/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "doseR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: doseR package is a next generation sequencing package for sex chromosome dosage compensation which can be applied broadly to detect shifts in gene expression among an arbitrary number of pre-defined groups of loci. doseR is a differential gene expression package for count data, that detects directional shifts in expression for multiple, specific subsets of genes, broad utility in systems biology research. doseR has been prepared to manage the nature of the data and the desired set of inferences. doseR uses S4 classes to store count data from sequencing experiment. It contains functions to normalize and filter count data, as well as to plot and calculate statistics of count data. It contains a framework for linear modeling of count data. The package has been tested using real and simulated data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: doseR -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20251942acb7343859507c138bc2b902 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-doser", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-digest - r-lme4 @@ -32,22 +34,25 @@ requirements: - r-mclust - r-runit run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-digest - r-lme4 - r-matrixstats - r-mclust - r-runit + +source: + md5: 0cb977802d565342d2a516ee39f3a13c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL - summary: doseR - description: 'doseR package is a next generation sequencing package for sex chromosome dosage compensation which can be applied broadly to detect shifts in gene expression among an arbitrary number of pre-defined groups of loci. doseR is a differential gene expression package for count data, that detects directional shifts in expression for multiple, specific subsets of genes, broad utility in systems biology research. doseR has been prepared to manage the nature of the data and the desired set of inferences. doseR uses S4 classes to store count data from sequencing experiment. It contains functions to normalize and filter count data, as well as to plot and calculate statistics of count data. It contains a framework for linear modeling of count data. The package has been tested using real and simulated data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-doubletrouble/meta.yaml b/recipes/bioconductor-doubletrouble/meta.yaml index a6b8eb760d0b6..4d7c41842bef8 100644 --- a/recipes/bioconductor-doubletrouble/meta.yaml +++ b/recipes/bioconductor-doubletrouble/meta.yaml @@ -1,55 +1,60 @@ -{% set version = "1.2.1" %} +{% set version = "1.6.0" %} {% set name = "doubletrouble" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler classification scheme, duplicates can also be classified into SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identification and classification of duplicated genes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e494ee8650e6c8a13c7149c68683bea8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-doubletrouble", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat (>= 3.0.0), knitr, feature, BiocStyle, rmarkdown, covr, sessioninfo + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: txdbmaker, testthat (>= 3.0.0), knitr, feature, patchwork, BiocStyle, rmarkdown, covr, sessioninfo requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-msa2dist >=1.6.0,<1.7.0' - - 'bioconductor-syntenet >=1.4.0,<1.5.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-msa2dist >=1.10.0,<1.11.0 + - bioconductor-syntenet >=1.8.0,<1.9.0 - r-base - r-ggplot2 - r-mclust - r-rlang run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-msa2dist >=1.6.0,<1.7.0' - - 'bioconductor-syntenet >=1.4.0,<1.5.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-msa2dist >=1.10.0,<1.11.0 + - bioconductor-syntenet >=1.8.0,<1.9.0 - r-base - r-ggplot2 - r-mclust - r-rlang + +source: + md5: 75b4d3b74df39726954baba245e872ea + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Identification and classification of duplicated genes' - description: 'doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler classification scheme, duplicates can also be classified into SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-drawproteins/meta.yaml b/recipes/bioconductor-drawproteins/meta.yaml index 54bccf2331977..8f0de150ad40d 100644 --- a/recipes/bioconductor-drawproteins/meta.yaml +++ b/recipes/bioconductor-drawproteins/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "drawProteins" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package draws protein schematics from Uniprot API output. From the JSON returned by the GET command, it creates a dataframe from the Uniprot Features API. This dataframe can then be used by geoms based on ggplot2 and base R to draw protein schematics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Package to Draw Protein Schematics from Uniprot API output -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67cbf634b37851946e9cc3885cdda6c5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-drawproteins", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: covr, testthat, knitr, rmarkdown, BiocStyle requirements: host: @@ -35,13 +37,16 @@ requirements: - r-httr - r-readr - r-tidyr + +source: + md5: 86c0434b0dffac8f856ec5c3e2336808 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Package to Draw Protein Schematics from Uniprot API output' - description: 'This package draws protein schematics from Uniprot API output. From the JSON returned by the GET command, it creates a dataframe from the Uniprot Features API. This dataframe can then be used by geoms based on ggplot2 and base R to draw protein schematics.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dreamlet/build_failure.linux-64.yaml b/recipes/bioconductor-dreamlet/build_failure.linux-64.yaml index 0e452d24e3b59..63cd585a78f25 100644 --- a/recipes/bioconductor-dreamlet/build_failure.linux-64.yaml +++ b/recipes/bioconductor-dreamlet/build_failure.linux-64.yaml @@ -1,6 +1,104 @@ -recipe_sha: 9267c92fbfbee2b151933e110f05e516a8f84863f222f244128a2f63b327fcf7 # The commit at which this recipe failed to build. +recipe_sha: 9267c92fbfbee2b151933e110f05e516a8f84863f222f244128a2f63b327fcf7 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -reason: |- - nothing provides requested r-mashr >=0.2.52 -category: |- - dependency issue +log: |- + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-delayedmatrixstats >=1.24.0,<1.25.0 [0m is installable and it requires + [32mbioconductor-sparsematrixstats >=1.14.0,<1.15.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-sparsematrixstats[version='>=1.14.0,<1.15.0']"), MatchSpec("bioconductor-delayedmatrixstats==1.24.0=r43hdfd78af_0")} + Encountered problems while solving: + - package bioconductor-delayedmatrixstats-1.24.0-r43hdfd78af_0 requires bioconductor-sparsematrixstats >=1.14.0,<1.15.0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-delayedmatrixstats >=1.24.0,<1.25.0 [0m is installable and it requires + [32mbioconductor-sparsematrixstats >=1.14.0,<1.15.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-sparsematrixstats[version='>=1.14.0,<1.15.0']"), MatchSpec("bioconductor-delayedmatrixstats==1.24.0=r43hdfd78af_0")} + Encountered problems while solving: + - package bioconductor-delayedmatrixstats-1.24.0-r43hdfd78af_0 requires bioconductor-sparsematrixstats >=1.14.0,<1.15.0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-delayedmatrixstats >=1.24.0,<1.25.0 [0m is installable and it requires + [32mbioconductor-sparsematrixstats >=1.14.0,<1.15.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-dreamlet/build_failure.osx-64.yaml b/recipes/bioconductor-dreamlet/build_failure.osx-64.yaml index 0e452d24e3b59..c4f9defef3631 100644 --- a/recipes/bioconductor-dreamlet/build_failure.osx-64.yaml +++ b/recipes/bioconductor-dreamlet/build_failure.osx-64.yaml @@ -1,6 +1,104 @@ -recipe_sha: 9267c92fbfbee2b151933e110f05e516a8f84863f222f244128a2f63b327fcf7 # The commit at which this recipe failed to build. +recipe_sha: 9267c92fbfbee2b151933e110f05e516a8f84863f222f244128a2f63b327fcf7 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -reason: |- - nothing provides requested r-mashr >=0.2.52 -category: |- - dependency issue +log: |- + Could not solve for environment specs + The following packages are incompatible + bioconductor-delayedmatrixstats >=1.24.0,<1.25.0 is installable and it requires + bioconductor-sparsematrixstats >=1.14.0,<1.15.0 , which requires + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-sparsematrixstats[version='>=1.14.0,<1.15.0']"), MatchSpec("bioconductor-delayedmatrixstats==1.24.0=r43hdfd78af_0")} + Encountered problems while solving: + - package bioconductor-delayedmatrixstats-1.24.0-r43hdfd78af_0 requires bioconductor-sparsematrixstats >=1.14.0,<1.15.0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + bioconductor-delayedmatrixstats >=1.24.0,<1.25.0 is installable and it requires + bioconductor-sparsematrixstats >=1.14.0,<1.15.0 , which requires + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-sparsematrixstats[version='>=1.14.0,<1.15.0']"), MatchSpec("bioconductor-delayedmatrixstats==1.24.0=r43hdfd78af_0")} + Encountered problems while solving: + - package bioconductor-delayedmatrixstats-1.24.0-r43hdfd78af_0 requires bioconductor-sparsematrixstats >=1.14.0,<1.15.0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + bioconductor-delayedmatrixstats >=1.24.0,<1.25.0 is installable and it requires + bioconductor-sparsematrixstats >=1.14.0,<1.15.0 , which requires + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-dresscheck/meta.yaml b/recipes/bioconductor-dresscheck/meta.yaml index 5c21bedf99cda..533e43a818eb7 100644 --- a/recipes/bioconductor-dresscheck/meta.yaml +++ b/recipes/bioconductor-dresscheck/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "0.40.0" %} +{% set version = "0.44.0" %} {% set name = "dressCheck" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d6fb25eaad39c714024ed855c8c9c87d +about: + description: data and software for checking Dressman JCO 25(5) 2007 + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: data and software for checking Dressman JCO 25(5) 2007 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dresscheck", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: survival, chron requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 64019291fc041eeb4821f83b27fb1681 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'data and software for checking Dressman JCO 25(5) 2007' - description: 'data and software for checking Dressman JCO 25(5) 2007' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dresscheck/post-link.sh b/recipes/bioconductor-dresscheck/post-link.sh index 307a736efcaa5..e60b6dd9ea115 100644 --- a/recipes/bioconductor-dresscheck/post-link.sh +++ b/recipes/bioconductor-dresscheck/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dresscheck-0.40.0" +installBiocDataPackage.sh "dresscheck-0.44.0" diff --git a/recipes/bioconductor-drimseq/meta.yaml b/recipes/bioconductor-drimseq/meta.yaml index 0900c40f993b6..872b1821fdddd 100644 --- a/recipes/bioconductor-drimseq/meta.yaml +++ b/recipes/bioconductor-drimseq/meta.yaml @@ -1,64 +1,70 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "DRIMSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package provides two frameworks. One for the differential transcript usage analysis between different conditions and one for the tuQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts) with the Dirichlet-multinomial distribution. The package also makes available functions for visualization and exploration of the data and results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fae7a1b0945b2942ef3f633d68a74fd2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-drimseq", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:drimseq + parent_recipe: + name: bioconductor-drimseq + path: recipes/bioconductor-drimseq + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-mass - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-mass - r-reshape2 + +source: + md5: f952192f16a1d28d15d55a63bb693bb1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq' - description: 'The package provides two frameworks. One for the differential transcript usage analysis between different conditions and one for the tuQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts) with the Dirichlet-multinomial distribution. The package also makes available functions for visualization and exploration of the data and results.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:drimseq - parent_recipe: - name: bioconductor-drimseq - path: recipes/bioconductor-drimseq - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-drivernet/meta.yaml b/recipes/bioconductor-drivernet/meta.yaml index 6b233cd48cc6b..0ccb0c9175ca4 100644 --- a/recipes/bioconductor-drivernet/meta.yaml +++ b/recipes/bioconductor-drivernet/meta.yaml @@ -1,38 +1,20 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "DriverNet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 78b923b016f6bd8097c1edc43ca0cca4 +about: + description: DriverNet is a package to predict functional important driver genes in cancer by integrating genome data (mutation and copy number variation data) and transcriptome data (gene expression data). The different kinds of data are combined by an influence graph, which is a gene-gene interaction network deduced from pathway data. A greedy algorithm is used to find the possible driver genes, which may mutated in a larger number of patients and these mutations will push the gene expression values of the connected genes to some extreme values. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-drivernet", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer' - description: 'DriverNet is a package to predict functional important driver genes in cancer by integrating genome data (mutation and copy number variation data) and transcriptome data (gene expression data). The different kinds of data are combined by an influence graph, which is a gene-gene interaction network deduced from pathway data. A greedy algorithm is used to find the possible driver genes, which may mutated in a larger number of patients and these mutations will push the gene expression values of the connected genes to some extreme values.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: identifiers: - biotools:drivernet @@ -41,4 +23,22 @@ extra: name: bioconductor-drivernet path: recipes/bioconductor-drivernet version: 1.20.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +requirements: + host: + - r-base + run: + - r-base +source: + md5: b17a31108a784ec376ad3aa6e7f0da14 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-droplettestfiles/meta.yaml b/recipes/bioconductor-droplettestfiles/meta.yaml index 505870f109933..4301a8563525b 100644 --- a/recipes/bioconductor-droplettestfiles/meta.yaml +++ b/recipes/bioconductor-droplettestfiles/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "DropletTestFiles" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a3a3f0d0901c90c6a2b173b976c4868 +about: + description: Assorted files generated from droplet-based single-cell protocols, to be used for testing functions in DropletUtils. Primarily intended for storing files that directly come out of processing pipelines like 10X Genomics' CellRanger software, prior to the formation of a SingleCellExperiment object. Unlike other packages, this is not designed to provide objects that are immediately ready for analysis. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Test Files for Single-Cell Droplet Utilities build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-droplettestfiles", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat, DropletUtils requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a63075748b3844f580a535c87b92440c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Test Files for Single-Cell Droplet Utilities' - description: 'Assorted files generated from droplet-based single-cell protocols, to be used for testing functions in DropletUtils. Primarily intended for storing files that directly come out of processing pipelines like 10X Genomics'' CellRanger software, prior to the formation of a SingleCellExperiment object. Unlike other packages, this is not designed to provide objects that are immediately ready for analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-droplettestfiles/post-link.sh b/recipes/bioconductor-droplettestfiles/post-link.sh index 968fbe466a2dc..a07909caf899c 100644 --- a/recipes/bioconductor-droplettestfiles/post-link.sh +++ b/recipes/bioconductor-droplettestfiles/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "droplettestfiles-1.12.0" +installBiocDataPackage.sh "droplettestfiles-1.16.0" diff --git a/recipes/bioconductor-dropletutils/meta.yaml b/recipes/bioconductor-dropletutils/meta.yaml index 211af9c8e5c59..541639a75ffe1 100644 --- a/recipes/bioconductor-dropletutils/meta.yaml +++ b/recipes/bioconductor-dropletutils/meta.yaml @@ -1,42 +1,59 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "DropletUtils" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading from count matrices or molecule information files, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Utilities for Handling Single-Cell Droplet Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f1fe907e6269e652adc4607fdb335c41 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dropletutils", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:DropletUtils + parent_recipe: + name: bioconductor-dropletutils + path: recipes/bioconductor-dropletutils + version: 1.0.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles # SystemRequirements: C++11, GNU make requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bh - r-dqrng @@ -45,46 +62,41 @@ requirements: - r-rcpp - libblas - liblapack + - zlib + run: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bh - r-dqrng - r-matrix - r-r.utils - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 0137dbe60c919b23d861ff226a1b933b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Utilities for Handling Single-Cell Droplet Data' - description: 'Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading from count matrices or molecule information files, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:DropletUtils - parent_recipe: - name: bioconductor-dropletutils - path: recipes/bioconductor-dropletutils - version: 1.0.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-drosgenome1.db/meta.yaml b/recipes/bioconductor-drosgenome1.db/meta.yaml index 8fc4379c2d8c6..69012548cf48e 100644 --- a/recipes/bioconductor-drosgenome1.db/meta.yaml +++ b/recipes/bioconductor-drosgenome1.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "drosgenome1.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6432e2ae22cf58524278a559097bdf3a +about: + description: Affymetrix Affymetrix DrosGenome1 Array annotation data (chip drosgenome1) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix DrosGenome1 Array annotation data (chip drosgenome1) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-drosgenome1.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.dm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.dm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6432e2ae22cf58524278a559097bdf3a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix DrosGenome1 Array annotation data (chip drosgenome1)' - description: 'Affymetrix Affymetrix DrosGenome1 Array annotation data (chip drosgenome1) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-drosgenome1cdf/meta.yaml b/recipes/bioconductor-drosgenome1cdf/meta.yaml index a6ce8e5c2a650..e9b8401c96f1d 100644 --- a/recipes/bioconductor-drosgenome1cdf/meta.yaml +++ b/recipes/bioconductor-drosgenome1cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "drosgenome1cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e12983f2148c10ef1faa50f810b6eee3 +about: + description: A package containing an environment representing the DrosGenome1.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: drosgenome1cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-drosgenome1cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e12983f2148c10ef1faa50f810b6eee3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: drosgenome1cdf - description: 'A package containing an environment representing the DrosGenome1.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-drosgenome1probe/meta.yaml b/recipes/bioconductor-drosgenome1probe/meta.yaml index ec78a4874ba4f..305266d231838 100644 --- a/recipes/bioconductor-drosgenome1probe/meta.yaml +++ b/recipes/bioconductor-drosgenome1probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "drosgenome1probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1f12abdfeee65e8a6554f57507d86fb3 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was DrosGenome1\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type drosgenome1 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-drosgenome1probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1f12abdfeee65e8a6554f57507d86fb3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type drosgenome1' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was DrosGenome1\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-drosophila2.db/meta.yaml b/recipes/bioconductor-drosophila2.db/meta.yaml index 93fbb18884cc1..0bcb533d448c8 100644 --- a/recipes/bioconductor-drosophila2.db/meta.yaml +++ b/recipes/bioconductor-drosophila2.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "drosophila2.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c01d0d1b5e17c3b36ad801b44da72b96 +about: + description: Affymetrix Affymetrix Drosophila_2 Array annotation data (chip drosophila2) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Drosophila_2 Array annotation data (chip drosophila2) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-drosophila2.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.dm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.dm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c01d0d1b5e17c3b36ad801b44da72b96 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Drosophila_2 Array annotation data (chip drosophila2)' - description: 'Affymetrix Affymetrix Drosophila_2 Array annotation data (chip drosophila2) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-drosophila2cdf/meta.yaml b/recipes/bioconductor-drosophila2cdf/meta.yaml index 1b1e175abbed9..a89dbe9f1754a 100644 --- a/recipes/bioconductor-drosophila2cdf/meta.yaml +++ b/recipes/bioconductor-drosophila2cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "drosophila2cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3323e723c133ff2b6188e22bebf3e20a +about: + description: A package containing an environment representing the Drosophila_2.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: drosophila2cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-drosophila2cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3323e723c133ff2b6188e22bebf3e20a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: drosophila2cdf - description: 'A package containing an environment representing the Drosophila_2.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-drosophila2probe/meta.yaml b/recipes/bioconductor-drosophila2probe/meta.yaml index 15be4b2d9a764..174cd73662c1f 100644 --- a/recipes/bioconductor-drosophila2probe/meta.yaml +++ b/recipes/bioconductor-drosophila2probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "drosophila2probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ba0251902ea0a5f0db61105bdcdc3530 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Drosophila\_2\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type drosophila2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-drosophila2probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ba0251902ea0a5f0db61105bdcdc3530 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type drosophila2' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Drosophila\_2\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-drugtargetinteractions/meta.yaml b/recipes/bioconductor-drugtargetinteractions/meta.yaml index 27b696b08cd54..4e5e0279760fc 100644 --- a/recipes/bioconductor-drugtargetinteractions/meta.yaml +++ b/recipes/bioconductor-drugtargetinteractions/meta.yaml @@ -1,54 +1,59 @@ -{% set version = "1.10.1" %} +{% set version = "1.14.0" %} {% set name = "drugTargetInteractions" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides utilities for identifying drug-target interactions for sets of small molecule or gene/protein identifiers. The required drug-target interaction information is obained from a local SQLite instance of the ChEMBL database. ChEMBL has been chosen for this purpose, because it provides one of the most comprehensive and best annotatated knowledge resources for drug-target information available in the public domain. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Drug-Target Interactions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c1a702c085df262e0a697b6687ea3ee4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-drugtargetinteractions", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocStyle, knitr, rmarkdown, ggplot2, reshape2, DT, EnsDb.Hsapiens.v86 requirements: host: - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-uniprot.ws >=2.42.0,<2.43.0' + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-uniprot.ws >=2.46.0,<2.47.0 - r-base - r-dplyr - r-rappdirs - r-rsqlite run: - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-uniprot.ws >=2.42.0,<2.43.0' + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-uniprot.ws >=2.46.0,<2.47.0 - r-base - r-dplyr - r-rappdirs - r-rsqlite + +source: + md5: c3a5b2c3bfffb066cc015a2cdfbda44a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Drug-Target Interactions' - description: 'Provides utilities for identifying drug-target interactions for sets of small molecule or gene/protein identifiers. The required drug-target interaction information is obained from a local SQLite instance of the ChEMBL database. ChEMBL has been chosen for this purpose, because it provides one of the most comprehensive and best annotatated knowledge resources for drug-target information available in the public domain.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-drugvsdisease/meta.yaml b/recipes/bioconductor-drugvsdisease/meta.yaml index 1189be641777b..a8ea1410320d3 100644 --- a/recipes/bioconductor-drugvsdisease/meta.yaml +++ b/recipes/bioconductor-drugvsdisease/meta.yaml @@ -1,74 +1,80 @@ -{% set version = "2.44.0" %} +{% set version = "2.48.0" %} {% set name = "DrugVsDisease" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package generates ranked lists of differential gene expression for either disease or drug profiles. Input data can be downloaded from Array Express or GEO, or from local CEL files. Ranked lists of differential expression and associated p-values are calculated using Limma. Enrichment scores (Subramanian et al. PNAS 2005) are calculated to a reference set of default drug or disease profiles, or a set of custom data supplied by the user. Network visualisation of significant scores are output in Cytoscape format. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Comparison of disease and drug profiles using Gene set Enrichment Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cfb6f4111b0003213278308c1672e49c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-drugvsdisease", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:drugvsdisease + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-drugvsdisease + path: recipes/bioconductor-drugvsdisease + version: 2.24.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-arrayexpress >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-cmap2data >=1.38.0,<1.39.0' - - 'bioconductor-drugvsdiseasedata >=1.38.0,<1.39.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - - 'bioconductor-hgu133a2.db >=3.13.0,<3.14.0' - - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-arrayexpress >=1.66.0,<1.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-cmap2data >=1.42.0,<1.43.0 + - bioconductor-drugvsdiseasedata >=1.42.0,<1.43.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-hgu133a.db >=3.13.0,<3.14.0 + - bioconductor-hgu133a2.db >=3.13.0,<3.14.0 + - bioconductor-hgu133plus2.db >=3.13.0,<3.14.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - r-runit - r-xtable run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-arrayexpress >=1.62.0,<1.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-cmap2data >=1.38.0,<1.39.0' - - 'bioconductor-drugvsdiseasedata >=1.38.0,<1.39.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - - 'bioconductor-hgu133a2.db >=3.13.0,<3.14.0' - - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-arrayexpress >=1.66.0,<1.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-cmap2data >=1.42.0,<1.43.0 + - bioconductor-drugvsdiseasedata >=1.42.0,<1.43.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-hgu133a.db >=3.13.0,<3.14.0 + - bioconductor-hgu133a2.db >=3.13.0,<3.14.0 + - bioconductor-hgu133plus2.db >=3.13.0,<3.14.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - r-runit - r-xtable + +source: + md5: 5f8a0210c876582dc57b8fd1e5fdcde5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Comparison of disease and drug profiles using Gene set Enrichment Analysis' - description: 'This package generates ranked lists of differential gene expression for either disease or drug profiles. Input data can be downloaded from Array Express or GEO, or from local CEL files. Ranked lists of differential expression and associated p-values are calculated using Limma. Enrichment scores (Subramanian et al. PNAS 2005) are calculated to a reference set of default drug or disease profiles, or a set of custom data supplied by the user. Network visualisation of significant scores are output in Cytoscape format.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:drugvsdisease - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-drugvsdisease - path: recipes/bioconductor-drugvsdisease - version: 2.24.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-drugvsdiseasedata/meta.yaml b/recipes/bioconductor-drugvsdiseasedata/meta.yaml index ddef5ea5e9960..260bd6ea64813 100644 --- a/recipes/bioconductor-drugvsdiseasedata/meta.yaml +++ b/recipes/bioconductor-drugvsdiseasedata/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "DrugVsDiseasedata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 40b800653aab57e822a18afe5bd1a2e7 +about: + description: Data package which provides default disease expression profiles, clusters and annotation information for use with the DrugVsDisease package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Drug versus Disease Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-drugvsdiseasedata", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-drugvsdiseasedata + path: recipes/bioconductor-drugvsdiseasedata + version: 1.16.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c14a86c5d506d84420eb41edd7858d8c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Drug versus Disease Data' - description: 'Data package which provides default disease expression profiles, clusters and annotation information for use with the DrugVsDisease package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-drugvsdiseasedata - path: recipes/bioconductor-drugvsdiseasedata - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-drugvsdiseasedata/post-link.sh b/recipes/bioconductor-drugvsdiseasedata/post-link.sh index f2a69117547ff..d472f73511002 100644 --- a/recipes/bioconductor-drugvsdiseasedata/post-link.sh +++ b/recipes/bioconductor-drugvsdiseasedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "drugvsdiseasedata-1.38.0" +installBiocDataPackage.sh "drugvsdiseasedata-1.42.0" diff --git a/recipes/bioconductor-dss/meta.yaml b/recipes/bioconductor-dss/meta.yaml index 10ad525ab1f0d..d3d3ea04c4712 100644 --- a/recipes/bioconductor-dss/meta.yaml +++ b/recipes/bioconductor-dss/meta.yaml @@ -1,48 +1,21 @@ -{% set version = "2.48.0" %} +{% set version = "2.54.0" %} {% set name = "DSS" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: DSS is an R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Dispersion shrinkage for sequencing data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bbdc2e1dd734b2c002e9ae034b86f78e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ -# Suggests: BiocStyle, knitr, rmarkdown -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bsseq >=1.38.0,<1.39.0' - - r-base - - libblas - - liblapack - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bsseq >=1.38.0,<1.39.0' - - r-base - build: - - {{ compiler('c') }} - - make -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'Dispersion shrinkage for sequencing data' - description: 'DSS is an R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + run_exports: '{{ pin_subpackage("bioconductor-dss", max_pin="x.x") }}' + extra: additional-platforms: - linux-aarch64 @@ -53,3 +26,37 @@ extra: path: recipes/bioconductor-dss version: 2.28.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, edgeR +requirements: + build: + - {{ compiler('c') }} + - make + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bsseq >=1.42.0,<1.43.0 + - r-base + - libblas + - liblapack + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bsseq >=1.42.0,<1.43.0 + - r-base + +source: + md5: 3fd544ed0a03c9cef006ac13e158249a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-dstruct/meta.yaml b/recipes/bioconductor-dstruct/meta.yaml index 6324f6b91a238..e9822c7f3d6d0 100644 --- a/recipes/bioconductor-dstruct/meta.yaml +++ b/recipes/bioconductor-dstruct/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "dStruct" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: dStruct identifies differentially reactive regions from RNA structurome profiling data. dStruct is compatible with a broad range of structurome profiling technologies, e.g., SHAPE-MaP, DMS-MaPseq, Structure-Seq, SHAPE-Seq, etc. See Choudhary et al., Genome Biology, 2019 for the underlying method. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identifying differentially reactive regions from RNA structurome profiling data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 294cd694534f0d82a92aaabeea86836f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dstruct", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, tidyverse, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-purrr @@ -31,21 +33,24 @@ requirements: - r-rlang - r-zoo run: - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-purrr - r-reshape2 - r-rlang - r-zoo + +source: + md5: 2a08d655623318d111774316db4707c8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Identifying differentially reactive regions from RNA structurome profiling data' - description: 'dStruct identifies differentially reactive regions from RNA structurome profiling data. dStruct is compatible with a broad range of structurome profiling technologies, e.g., SHAPE-MaP, DMS-MaPseq, Structure-Seq, SHAPE-Seq, etc. See Choudhary et al., Genome Biology, 2019 for the underlying method.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dta/meta.yaml b/recipes/bioconductor-dta/meta.yaml index 8ce1f64afc9a8..079e13c298f89 100644 --- a/recipes/bioconductor-dta/meta.yaml +++ b/recipes/bioconductor-dta/meta.yaml @@ -1,24 +1,34 @@ -{% set version = "2.48.0" %} +{% set version = "2.52.0" %} {% set name = "DTA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Dynamic Transcriptome Analysis (DTA) can monitor the cellular response to perturbations with higher sensitivity and temporal resolution than standard transcriptomics. The package implements the underlying kinetic modeling approach capable of the precise determination of synthesis- and decay rates from individual microarray or RNAseq measurements. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Dynamic Transcriptome Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 58705aacdbf08c61d4713273dbd9bc6f build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dta", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:dta + - doi:10.1093/bioinformatics/bts052 + parent_recipe: + name: bioconductor-dta + path: recipes/bioconductor-dta + version: 2.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -28,20 +38,16 @@ requirements: - r-base - r-lsd - r-scatterplot3d + +source: + md5: 80978164209532213255a996f4b91b67 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Dynamic Transcriptome Analysis' - description: 'Dynamic Transcriptome Analysis (DTA) can monitor the cellular response to perturbations with higher sensitivity and temporal resolution than standard transcriptomics. The package implements the underlying kinetic modeling approach capable of the precise determination of synthesis- and decay rates from individual microarray or RNAseq measurements.' -extra: - identifiers: - - biotools:dta - - doi:10.1093/bioinformatics/bts052 - parent_recipe: - name: bioconductor-dta - path: recipes/bioconductor-dta - version: 2.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dune/meta.yaml b/recipes/bioconductor-dune/meta.yaml index 5b2e50d6b815b..8365ca9111947 100644 --- a/recipes/bioconductor-dune/meta.yaml +++ b/recipes/bioconductor-dune/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "Dune" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Given a set of clustering labels, Dune merges pairs of clusters to increase mean ARI between labels, improving replicability. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Improving replicability in single-cell RNA-Seq cell type discovery -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: afc7d133de0af7ccdc64a9a7a3722ccb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dune", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-aricode - r-base - r-dplyr @@ -34,8 +36,8 @@ requirements: - r-rcolorbrewer - r-tidyr run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-aricode - r-base - r-dplyr @@ -45,13 +47,16 @@ requirements: - r-purrr - r-rcolorbrewer - r-tidyr + +source: + md5: 2550b356019d43f1dd52fc997a55f115 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Improving replicability in single-cell RNA-Seq cell type discovery' - description: 'Given a set of clustering labels, Dune merges pairs of clusters to increase mean ARI between labels, improving replicability.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-duoclustering2018/meta.yaml b/recipes/bioconductor-duoclustering2018/meta.yaml index 4d5c22819da1a..5e1a031b4a68d 100644 --- a/recipes/bioconductor-duoclustering2018/meta.yaml +++ b/recipes/bioconductor-duoclustering2018/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "DuoClustering2018" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Preprocessed experimental and simulated scRNA-seq data sets used for evaluation of clustering methods for scRNA-seq data in Duò et al (2018). Also contains results from applying several clustering methods to each of the data sets, and functions for plotting method performance. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Data, Clustering Results and Visualization Functions From Duò et al (2018) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a2761f4db56025af2eaf8240392d01a0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-duoclustering2018", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, iSEE, scater, SingleCellExperiment, SummarizedExperiment, plyr requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - r-dplyr - r-ggplot2 @@ -34,7 +36,7 @@ requirements: - r-tidyr - r-viridis run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - r-dplyr - r-ggplot2 @@ -46,14 +48,17 @@ requirements: - r-tidyr - r-viridis - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 6aec8bc9d4f6620e71312a5691168a7d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Data, Clustering Results and Visualization Functions From Duò et al (2018)' - description: 'Preprocessed experimental and simulated scRNA-seq data sets used for evaluation of clustering methods for scRNA-seq data in Duò et al (2018). Also contains results from applying several clustering methods to each of the data sets, and functions for plotting method performance.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-duoclustering2018/post-link.sh b/recipes/bioconductor-duoclustering2018/post-link.sh index 25113c1241a25..fae5da6b8b78f 100644 --- a/recipes/bioconductor-duoclustering2018/post-link.sh +++ b/recipes/bioconductor-duoclustering2018/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "duoclustering2018-1.20.0" +installBiocDataPackage.sh "duoclustering2018-1.24.0" diff --git a/recipes/bioconductor-duplexdiscoverer/build.sh b/recipes/bioconductor-duplexdiscoverer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-duplexdiscoverer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-duplexdiscoverer/meta.yaml b/recipes/bioconductor-duplexdiscoverer/meta.yaml new file mode 100644 index 0000000000000..397b984372194 --- /dev/null +++ b/recipes/bioconductor-duplexdiscoverer/meta.yaml @@ -0,0 +1,72 @@ +{% set version = "1.0.0" %} +{% set name = "DuplexDiscovereR" %} +{% set bioc = "3.20" %} + +about: + description: DuplexDiscovereR is a package designed for analyzing data from RNA cross-linking and proximity ligation protocols such as SPLASH, PARIS, LIGR-seq, and others. DuplexDiscovereR accepts input in the form of chimerically or split-aligned reads. It includes procedures for alignment classification, filtering, and efficient clustering of individual chimeric reads into duplex groups (DGs). Once DGs are identified, the package predicts RNA duplex formation and their hybridization energies. Additional metrics, such as p-values for random ligation hypothesis or mean DG alignment scores, can be calculated to rank final set of RNA duplexes. Data from multiple experiments or replicates can be processed separately and further compared to check the reproducibility of the experimental method. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Analysis of the data from RNA duplex probing experiments + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-duplexdiscoverer", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, UpSetR, BiocStyle, rmarkdown, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - r-base + - r-dplyr + - r-ggsci + - r-igraph + - r-purrr + - r-rlang + - r-scales + - r-stringr + - r-tibble + - r-tidyr + run: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - r-base + - r-dplyr + - r-ggsci + - r-igraph + - r-purrr + - r-rlang + - r-scales + - r-stringr + - r-tibble + - r-tidyr + +source: + md5: ea563a8a0d98a2b3ac68c30d5c5909cd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-dupradar/meta.yaml b/recipes/bioconductor-dupradar/meta.yaml index c628243cfea17..7e63da3ccb0ce 100644 --- a/recipes/bioconductor-dupradar/meta.yaml +++ b/recipes/bioconductor-dupradar/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "dupRadar" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Duplication rate quality control for RNA-Seq datasets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Assessment of duplication rates in RNA-Seq datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 306ba6ddb1786eb7ec5e6cb4bc15562e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dupradar", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:dupradar + parent_recipe: + name: bioconductor-dupradar + path: recipes/bioconductor-dupradar + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, AnnotationHub requirements: host: - - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - bioconductor-rsubread >=2.20.0,<2.21.0 - r-base - r-kernsmooth run: - - 'bioconductor-rsubread >=2.16.0,<2.17.0' + - bioconductor-rsubread >=2.20.0,<2.21.0 - r-base - r-kernsmooth + +source: + md5: 879bcf1c2da3dd0fd29b22263fc05fb7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Assessment of duplication rates in RNA-Seq datasets' - description: 'Duplication rate quality control for RNA-Seq datasets.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:dupradar - parent_recipe: - name: bioconductor-dupradar - path: recipes/bioconductor-dupradar - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dvddata/meta.yaml b/recipes/bioconductor-dvddata/meta.yaml index 2ab2b9dc07a65..b2fba47e02f3e 100644 --- a/recipes/bioconductor-dvddata/meta.yaml +++ b/recipes/bioconductor-dvddata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "DvDdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d07387219229c006ba96b9ab43ddf4ff +about: + description: Data package which provides default drug and disease expression profiles for the DvD package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Drug versus Disease Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dvddata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f2eec0f8e77512e32112a66a592a9351 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Drug versus Disease Data' - description: 'Data package which provides default drug and disease expression profiles for the DvD package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dvddata/post-link.sh b/recipes/bioconductor-dvddata/post-link.sh index 650d586b47f90..05bd866419271 100644 --- a/recipes/bioconductor-dvddata/post-link.sh +++ b/recipes/bioconductor-dvddata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dvddata-1.38.0" +installBiocDataPackage.sh "dvddata-1.42.0" diff --git a/recipes/bioconductor-dyebias/meta.yaml b/recipes/bioconductor-dyebias/meta.yaml index fbbc05f23ec24..6e6905d91ed77 100644 --- a/recipes/bioconductor-dyebias/meta.yaml +++ b/recipes/bioconductor-dyebias/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "1.62.0" %} +{% set version = "1.66.0" %} {% set name = "dyebias" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Many two-colour hybridizations suffer from a dye bias that is both gene-specific and slide-specific. The former depends on the content of the nucleotide used for labeling; the latter depends on the labeling percentage. The slide-dependency was hitherto not recognized, and made addressing the artefact impossible. Given a reasonable number of dye-swapped pairs of hybridizations, or of same vs. same hybridizations, both the gene- and slide-biases can be estimated and corrected using the GASSCO method (Margaritis et al., Mol. Sys. Biol. 5:266 (2009), doi:10.1038/msb.2009.21) + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: The GASSCO method for correcting for slide-dependent gene-specific dye bias -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2b3e10379a29b0cb931514e06fe7259f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dyebias", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:dyebias + parent_recipe: + name: bioconductor-dyebias + path: recipes/bioconductor-dyebias + version: 1.40.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: limma, convert, GEOquery, dyebiasexamples, methods requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-marray >=1.84.0,<1.85.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-marray >=1.84.0,<1.85.0 - r-base + +source: + md5: ff4b8a165d42629cc2794925b2afb926 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'The GASSCO method for correcting for slide-dependent gene-specific dye bias' - description: 'Many two-colour hybridizations suffer from a dye bias that is both gene-specific and slide-specific. The former depends on the content of the nucleotide used for labeling; the latter depends on the labeling percentage. The slide-dependency was hitherto not recognized, and made addressing the artefact impossible. Given a reasonable number of dye-swapped pairs of hybridizations, or of same vs. same hybridizations, both the gene- and slide-biases can be estimated and corrected using the GASSCO method (Margaritis et al., Mol. Sys. Biol. 5:266 (2009), doi:10.1038/msb.2009.21)' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:dyebias - parent_recipe: - name: bioconductor-dyebias - path: recipes/bioconductor-dyebias - version: 1.40.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dyebiasexamples/meta.yaml b/recipes/bioconductor-dyebiasexamples/meta.yaml index 060513470d522..117f1776d65ad 100644 --- a/recipes/bioconductor-dyebiasexamples/meta.yaml +++ b/recipes/bioconductor-dyebiasexamples/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "dyebiasexamples" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b73aa6c0c98150b2bccba7802dda8c86 +about: + description: Data for the dyebias package, consisting of 4 self-self hybrizations of self-spotted yeast slides, as well as data from Array Express accession E-MTAB-32 + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Example data for the dyebias package, which implements the GASSCO method. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dyebiasexamples", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: dyebias, convert, Biobase requirements: host: - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-marray >=1.84.0,<1.85.0 - r-base run: - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-marray >=1.84.0,<1.85.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3f52ef68b5944fbc0ceeec8632626d29 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Example data for the dyebias package, which implements the GASSCO method.' - description: 'Data for the dyebias package, consisting of 4 self-self hybrizations of self-spotted yeast slides, as well as data from Array Express accession E-MTAB-32' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-dyebiasexamples/post-link.sh b/recipes/bioconductor-dyebiasexamples/post-link.sh index 15ba43db540e5..92d51a92b16b1 100644 --- a/recipes/bioconductor-dyebiasexamples/post-link.sh +++ b/recipes/bioconductor-dyebiasexamples/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "dyebiasexamples-1.42.0" +installBiocDataPackage.sh "dyebiasexamples-1.46.0" diff --git a/recipes/bioconductor-dyndoc/meta.yaml b/recipes/bioconductor-dyndoc/meta.yaml index e987221cef2d7..98ae60efb82f0 100644 --- a/recipes/bioconductor-dyndoc/meta.yaml +++ b/recipes/bioconductor-dyndoc/meta.yaml @@ -1,37 +1,19 @@ -{% set version = "1.80.0" %} +{% set version = "1.84.0" %} {% set name = "DynDoc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d5ea2c0b36289466bdb8095b39634fd +about: + description: A set of functions to create and interact with dynamic documents and vignettes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Dynamic document tools build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-dyndoc", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Dynamic document tools' - description: 'A set of functions to create and interact with dynamic documents and vignettes.' extra: identifiers: - biotools:dyndoc @@ -40,4 +22,22 @@ extra: name: bioconductor-dyndoc path: recipes/bioconductor-dyndoc version: 1.58.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +requirements: + host: + - r-base + run: + - r-base +source: + md5: c224a8b539655fa7ded03e4f0ec5b2f7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-easier/meta.yaml b/recipes/bioconductor-easier/meta.yaml index 340d682ef186c..a235b146aa499 100644 --- a/recipes/bioconductor-easier/meta.yaml +++ b/recipes/bioconductor-easier/meta.yaml @@ -1,34 +1,37 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "easier" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a workflow for the use of EaSIeR tool, developed to assess patients' likelihood to respond to ICB therapies providing just the patients' RNA-seq data as input. We integrate RNA-seq data with different types of prior knowledge to extract quantitative descriptors of the tumor microenvironment from several points of view, including composition of the immune repertoire, and activity of intra- and extra-cellular communications. Then, we use multi-task machine learning trained in TCGA data to identify how these descriptors can simultaneously predict several state-of-the-art hallmarks of anti-cancer immune response. In this way we derive cancer-specific models and identify cancer-specific systems biomarkers of immune response. These biomarkers have been experimentally validated in the literature and the performance of EaSIeR predictions has been validated using independent datasets form four different cancer types with patients treated with anti-PD1 or anti-PDL1 therapy. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Estimate Systems Immune Response from RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 65f72a669a157fdf57501fb32d1c0333 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-easier", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment, viper requirements: + host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-decoupler >=2.8.0,<2.9.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-dorothea >=1.14.0,<1.15.0' - - 'bioconductor-easierdata >=1.8.0,<1.9.0' - - 'bioconductor-progeny >=1.24.0,<1.25.0' - - 'bioconductor-quantiseqr >=1.10.0,<1.11.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-decoupler >=2.12.0,<2.13.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-dorothea >=1.18.0,<1.19.0 + - bioconductor-easierdata >=1.12.0,<1.13.0 + - bioconductor-progeny >=1.28.0,<1.29.0 + - bioconductor-quantiseqr >=1.14.0,<1.15.0 - r-base - r-coin - r-dplyr @@ -43,14 +46,15 @@ requirements: - r-rstatix - r-tibble - r-tidyr + run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-decoupler >=2.8.0,<2.9.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-dorothea >=1.14.0,<1.15.0' - - 'bioconductor-easierdata >=1.8.0,<1.9.0' - - 'bioconductor-progeny >=1.24.0,<1.25.0' - - 'bioconductor-quantiseqr >=1.10.0,<1.11.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-decoupler >=2.12.0,<2.13.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-dorothea >=1.18.0,<1.19.0 + - bioconductor-easierdata >=1.12.0,<1.13.0 + - bioconductor-progeny >=1.28.0,<1.29.0 + - bioconductor-quantiseqr >=1.14.0,<1.15.0 - r-base - r-coin - r-dplyr @@ -65,13 +69,16 @@ requirements: - r-rstatix - r-tibble - r-tidyr + +source: + md5: bd5033bb11657c5b0a89b7d633fddf09 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Estimate Systems Immune Response from RNA-seq data' - description: 'This package provides a workflow for the use of EaSIeR tool, developed to assess patients'' likelihood to respond to ICB therapies providing just the patients'' RNA-seq data as input. We integrate RNA-seq data with different types of prior knowledge to extract quantitative descriptors of the tumor microenvironment from several points of view, including composition of the immune repertoire, and activity of intra- and extra-cellular communications. Then, we use multi-task machine learning trained in TCGA data to identify how these descriptors can simultaneously predict several state-of-the-art hallmarks of anti-cancer immune response. In this way we derive cancer-specific models and identify cancer-specific systems biomarkers of immune response. These biomarkers have been experimentally validated in the literature and the performance of EaSIeR predictions has been validated using independent datasets form four different cancer types with patients treated with anti-PD1 or anti-PDL1 therapy.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-easierdata/meta.yaml b/recipes/bioconductor-easierdata/meta.yaml index b7b3eb87fc60f..4ad70596a7af5 100644 --- a/recipes/bioconductor-easierdata/meta.yaml +++ b/recipes/bioconductor-easierdata/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "easierData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5092649863b833021ff8593731571183 +about: + description: Access to internal data required for the functional performance of easier package and exemplary bladder cancer dataset with both processed RNA-seq data and information on response to ICB therapy generated by Mariathasan et al. "TGF-B attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells", published in Nature, 2018 [doi:10.1038/nature25501](https://doi.org/10.1038/nature25501). The data is made available via [`IMvigor210CoreBiologies`](http://research-pub.gene.com/IMvigor210CoreBiologies/) package under the CC-BY license. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: easier internal data and exemplary dataset from IMvigor210CoreBiologies package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-easierdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 845c7b7a2d851903bbdaff40d0d4503b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'easier internal data and exemplary dataset from IMvigor210CoreBiologies package' - description: 'Access to internal data required for the functional performance of easier package and exemplary bladder cancer dataset with both processed RNA-seq data and information on response to ICB therapy generated by Mariathasan et al. "TGF-B attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells", published in Nature, 2018 [doi:10.1038/nature25501](https://doi.org/10.1038/nature25501). The data is made available via [`IMvigor210CoreBiologies`](http://research-pub.gene.com/IMvigor210CoreBiologies/) package under the CC-BY license.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-easierdata/post-link.sh b/recipes/bioconductor-easierdata/post-link.sh index c4e73343e9661..cb3dcd2e3db0e 100644 --- a/recipes/bioconductor-easierdata/post-link.sh +++ b/recipes/bioconductor-easierdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "easierdata-1.8.0" +installBiocDataPackage.sh "easierdata-1.12.0" diff --git a/recipes/bioconductor-easycelltype/meta.yaml b/recipes/bioconductor-easycelltype/meta.yaml index 7a37cb99a3152..8d1491f0661b6 100644 --- a/recipes/bioconductor-easycelltype/meta.yaml +++ b/recipes/bioconductor-easycelltype/meta.yaml @@ -1,53 +1,63 @@ -{% set version = "1.2.0" %} +{% set version = "1.8.0" %} {% set name = "EasyCellType" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: 'We developed EasyCellType which can automatically examine the input marker lists obtained from existing software such as Seurat over the cell markerdatabases. Two quantification approaches to annotate cell types are provided: Gene set enrichment analysis (GSEA) and a modified versio of Fisher''s exact test. The function presents annotation recommendations in graphical outcomes: bar plots for each cluster showing candidate cell types, as well as a dot plot summarizing the top 5 significant annotations for each cluster.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotate cell types for scRNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d10603402aa8243504432071a2e60155 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic -# Suggests: knitr, rmarkdown, testthat (>= 3.0.0), Seurat, BiocManager, devtools + run_exports: '{{ pin_subpackage("bioconductor-easycelltype", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, testthat (>= 3.0.0), Seurat, BiocManager, devtools, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - r-dplyr - r-forcats - r-ggplot2 - r-magrittr - r-rlang + - r-vctrs >=0.6.4 run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - r-dplyr - r-forcats - r-ggplot2 - r-magrittr - r-rlang + - r-vctrs >=0.6.4 + +source: + md5: 0f729cb62a1682ad1e0d282612989734 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotate cell types for scRNA-seq data' - description: 'We developed EasyCellType which can automatically examine the input marker lists obtained from existing software such as Seurat over the cell markerdatabases. Two quantification approaches to annotate cell types are provided: Gene set enrichment analysis (GSEA) and a modified versio of Fisher''s exact test. The function presents annotation recommendations in graphical outcomes: bar plots for each cluster showing candidate cell types, as well as a dot plot summarizing the top 5 significant annotations for each cluster.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-easylift/meta.yaml b/recipes/bioconductor-easylift/meta.yaml index 61eabc651b5e0..ad52e5d2fa5bf 100644 --- a/recipes/bioconductor-easylift/meta.yaml +++ b/recipes/bioconductor-easylift/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "easylift" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The easylift package provides a convenient tool for genomic liftover operations between different genome assemblies. It seamlessly works with Bioconductor's GRanges objects and chain files from the UCSC Genome Browser, allowing for straightforward handling of genomic ranges across various genome versions. One noteworthy feature of easylift is its integration with the BiocFileCache package. This integration automates the management and caching of chain files necessary for liftover operations. Users no longer need to manually specify chain file paths in their function calls, reducing the complexity of the liftover process. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: An R package to perform genomic liftover -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 86d8c0188c35ab56732fd5cc55475e8c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-easylift", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.0.0), IRanges, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-r.utils run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-r.utils + +source: + md5: ffc5f970619f6de99418696f4534c2c6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'An R package to perform genomic liftover' - description: 'The easylift package provides a convenient tool for genomic liftover operations between different genome assemblies. It seamlessly works with Bioconductor''s GRanges objects and chain files from the UCSC Genome Browser, allowing for straightforward handling of genomic ranges across various genome versions. One noteworthy feature of easylift is its integration with the BiocFileCache package. This integration automates the management and caching of chain files necessary for liftover operations. Users no longer need to manually specify chain file paths in their function calls, reducing the complexity of the liftover process.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-easyreporting/meta.yaml b/recipes/bioconductor-easyreporting/meta.yaml index aa88366c1a868..e45c3d159f19a 100644 --- a/recipes/bioconductor-easyreporting/meta.yaml +++ b/recipes/bioconductor-easyreporting/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "easyreporting" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cffad8bbd7df1cd9ac54b4605a0c555e +about: + description: An S4 class for facilitating the automated creation of rmarkdown files inside other packages/software even without knowing rmarkdown language. Best if implemented in functions as "recursive" style programming. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Helps creating report for improving Reproducible Computational Research build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-easyreporting", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: distill, BiocStyle, knitr, readxl, edgeR, limma, EDASeq, statmod requirements: host: @@ -31,12 +29,14 @@ requirements: - r-rlang - r-rmarkdown - r-shiny +source: + md5: b512509c72239b8dbb0cb1f7ce63629a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Helps creating report for improving Reproducible Computational Research' - description: 'An S4 class for facilitating the automated creation of rmarkdown files inside other packages/software even without knowing rmarkdown language. Best if implemented in functions as "recursive" style programming.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-easyrnaseq/meta.yaml b/recipes/bioconductor-easyrnaseq/meta.yaml index 4f704725ab89e..42dd0858d0a0d 100644 --- a/recipes/bioconductor-easyrnaseq/meta.yaml +++ b/recipes/bioconductor-easyrnaseq/meta.yaml @@ -1,74 +1,77 @@ -{% set version = "2.38.0" %} +{% set version = "2.42.0" %} {% set name = "easyRNASeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq' or 'edgeR' package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Count summarization and normalization for RNA-Seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c763a083ce852695593a183ff7f9edcb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-easyrnaseq", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle (>= 2.18.0), BSgenome (>= 1.58.0), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.32) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle (>= 2.32.1), BSgenome (>= 1.72.0), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.33) requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomeintervals >=1.58.0,<1.59.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomeintervals >=1.62.0,<1.63.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - r-locfit - - 'r-lsd >=4.1-0' - - 'r-rappdirs >=0.3.1' + - r-lsd >=4.1-0 + - r-rappdirs >=0.3.3 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomeintervals >=1.58.0,<1.59.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomeintervals >=1.62.0,<1.63.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - r-locfit - - 'r-lsd >=4.1-0' - - 'r-rappdirs >=0.3.1' + - r-lsd >=4.1-0 + - r-rappdirs >=0.3.3 + +source: + md5: 30fc573f9978a1e3e1d4aa767074567f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Count summarization and normalization for RNA-Seq data' - description: 'Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as ''RPKM'' or by the ''DESeq'' or ''edgeR'' package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-eatonetalchipseq/meta.yaml b/recipes/bioconductor-eatonetalchipseq/meta.yaml index 54fe87b9b4f10..f51ddb9e21322 100644 --- a/recipes/bioconductor-eatonetalchipseq/meta.yaml +++ b/recipes/bioconductor-eatonetalchipseq/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "0.40.0" %} +{% set version = "0.44.0" %} {% set name = "EatonEtAlChIPseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e7695c3761d5f3d41dec21b0c8b50947 +about: + description: ChIP-seq analysis subset from "Conserved nucleosome positioning defines replication origins" (PMID 20351051) + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic 2.0 + summary: ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton et al. 2010 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-eatonetalchipseq", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 89c7bd11b6d15aac7f373151e8d517f1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'Artistic 2.0' - summary: 'ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton et al. 2010' - description: 'ChIP-seq analysis subset from "Conserved nucleosome positioning defines replication origins" (PMID 20351051)' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-eatonetalchipseq/post-link.sh b/recipes/bioconductor-eatonetalchipseq/post-link.sh index 346813c7b54e0..b98a40809d25a 100644 --- a/recipes/bioconductor-eatonetalchipseq/post-link.sh +++ b/recipes/bioconductor-eatonetalchipseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "eatonetalchipseq-0.40.0" +installBiocDataPackage.sh "eatonetalchipseq-0.44.0" diff --git a/recipes/bioconductor-ebarrays/meta.yaml b/recipes/bioconductor-ebarrays/meta.yaml index 54575ad557b04..2184413d66f9c 100644 --- a/recipes/bioconductor-ebarrays/meta.yaml +++ b/recipes/bioconductor-ebarrays/meta.yaml @@ -1,56 +1,62 @@ -{% set version = "2.66.0" %} +{% set version = "2.70.0" %} {% set name = "EBarrays" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: EBarrays provides tools for the analysis of replicated/unreplicated microarray data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d273e2e9411207653d4e079e14484026 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ebarrays", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:ebarrays + - doi:10.1111/j.1541-0420.2006.00611.x + parent_recipe: + name: bioconductor-ebarrays + path: recipes/bioconductor-ebarrays + version: 2.44.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-cluster - r-lattice - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-cluster - r-lattice - build: - - {{ compiler('c') }} - - make + +source: + md5: 42b160cbe3852901a1e5b964aff75c42 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification' - description: 'EBarrays provides tools for the analysis of replicated/unreplicated microarray data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:ebarrays - - doi:10.1111/j.1541-0420.2006.00611.x - parent_recipe: - name: bioconductor-ebarrays - path: recipes/bioconductor-ebarrays - version: 2.44.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ebcoexpress/meta.yaml b/recipes/bioconductor-ebcoexpress/meta.yaml index e9424815f0a43..3be646f55e2d5 100644 --- a/recipes/bioconductor-ebcoexpress/meta.yaml +++ b/recipes/bioconductor-ebcoexpress/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "EBcoexpress" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An Empirical Bayesian Approach to Differential Co-Expression Analysis at the Gene-Pair Level + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: EBcoexpress for Differential Co-Expression Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 66fa4257fbd0222064b30f6c15e74ab1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ebcoexpress", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:ebcoexpress + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: graph, igraph, colorspace requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-ebarrays >=2.66.0,<2.67.0' + - bioconductor-ebarrays >=2.70.0,<2.71.0 - r-base - r-mclust - r-minqa - libblas - liblapack run: - - 'bioconductor-ebarrays >=2.66.0,<2.67.0' + - bioconductor-ebarrays >=2.70.0,<2.71.0 - r-base - r-mclust - r-minqa - build: - - {{ compiler('c') }} - - make + +source: + md5: 131412269ffc5281f53b02f89df14d48 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'EBcoexpress for Differential Co-Expression Analysis' - description: 'An Empirical Bayesian Approach to Differential Co-Expression Analysis at the Gene-Pair Level' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ebimage/meta.yaml b/recipes/bioconductor-ebimage/meta.yaml index f946397d7761d..723a7087ccf72 100644 --- a/recipes/bioconductor-ebimage/meta.yaml +++ b/recipes/bioconductor-ebimage/meta.yaml @@ -1,30 +1,46 @@ -{% set version = "4.44.0" %} +{% set version = "4.48.0" %} {% set name = "EBImage" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Image processing and analysis toolbox for R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 22e920a81ab633cdbf753daf3e128d64 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ebimage", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:ebimage + parent_recipe: + name: bioconductor-ebimage + path: recipes/bioconductor-ebimage + version: 4.22.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, digest, knitr, rmarkdown, shiny requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-abind - r-base - - 'r-fftwtools >=0.9-7' + - r-fftwtools >=0.9-7 - r-htmltools - r-htmlwidgets - r-jpeg @@ -35,10 +51,10 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-abind - r-base - - 'r-fftwtools >=0.9-7' + - r-fftwtools >=0.9-7 - r-htmltools - r-htmlwidgets - r-jpeg @@ -46,27 +62,16 @@ requirements: - r-png - r-rcurl - r-tiff - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make - - libcxx <17 # [osx] + +source: + md5: e8bcb4c4a3c7c36005ad0c7992f836fd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3.0-only - summary: 'Image processing and analysis toolbox for R' - description: 'EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:ebimage - parent_recipe: - name: bioconductor-ebimage - path: recipes/bioconductor-ebimage - version: 4.22.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ebsea/meta.yaml b/recipes/bioconductor-ebsea/meta.yaml index d16b40144208f..5900d2367f668 100644 --- a/recipes/bioconductor-ebsea/meta.yaml +++ b/recipes/bioconductor-ebsea/meta.yaml @@ -1,43 +1,22 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "EBSEA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Calculates differential expression of genes based on exon counts of genes obtained from RNA-seq sequencing data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Exon Based Strategy for Expression Analysis of genes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d016b1e83c4b885565a573db1b134fbd build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ebsea", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown -requirements: - host: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-empiricalbrownsmethod >=1.30.0,<1.31.0' - - r-base - run: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-empiricalbrownsmethod >=1.30.0,<1.31.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Exon Based Strategy for Expression Analysis of genes' - description: 'Calculates differential expression of genes based on exon counts of genes obtained from RNA-seq sequencing data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + extra: identifiers: - biotools:ebsea @@ -47,3 +26,30 @@ extra: path: recipes/bioconductor-ebsea version: 1.8.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown +requirements: + host: + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-empiricalbrownsmethod >=1.34.0,<1.35.0 + - r-base + run: + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-empiricalbrownsmethod >=1.34.0,<1.35.0 + - r-base + +source: + md5: 210e0c09dc646a8a07edfa0c9f5a5b3d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-ebseq/meta.yaml b/recipes/bioconductor-ebseq/meta.yaml index d02c515a1c886..a7d22733d1194 100644 --- a/recipes/bioconductor-ebseq/meta.yaml +++ b/recipes/bioconductor-ebseq/meta.yaml @@ -1,32 +1,48 @@ -{% set version = "2.0.0" %} +{% set version = "2.4.0" %} {% set name = "EBSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Differential Expression analysis at both gene and isoform level using RNA-seq data + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: An R package for gene and isoform differential expression analysis of RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e64aabb38197aba0ee5985a1558cce60 build: - number: 3 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ebseq", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:ebseq + - doi:10.1093/bioinformatics/btt087 + parent_recipe: + name: bioconductor-ebseq + path: recipes/bioconductor-ebseq + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # SystemRequirements: c++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-bh - r-blockmodeling - r-gplots - - 'r-rcpp >=0.12.11' - - 'r-rcppeigen >=0.3.2.9.0' + - r-rcpp >=0.12.11 + - r-rcppeigen >=0.3.2.9.0 - r-testthat - libblas - liblapack @@ -35,29 +51,19 @@ requirements: - r-bh - r-blockmodeling - r-gplots - - 'r-rcpp >=0.12.11' - - 'r-rcppeigen >=0.3.2.9.0' + - r-rcpp >=0.12.11 + - r-rcppeigen >=0.3.2.9.0 - r-testthat - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 31e2325303d52aadc8a034eec7cab8cd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'An R package for gene and isoform differential expression analysis of RNA-seq data' - description: 'Differential Expression analysis at both gene and isoform level using RNA-seq data' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:ebseq - - doi:10.1093/bioinformatics/btt087 - parent_recipe: - name: bioconductor-ebseq - path: recipes/bioconductor-ebseq - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ecoli2.db/meta.yaml b/recipes/bioconductor-ecoli2.db/meta.yaml index 50e6af2815625..862476eab76b0 100644 --- a/recipes/bioconductor-ecoli2.db/meta.yaml +++ b/recipes/bioconductor-ecoli2.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "ecoli2.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 110d6549b1d105fdff31ab8f45b08d65 +about: + description: Affymetrix Affymetrix E_coli_2 Array annotation data (chip ecoli2) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix E_coli_2 Array annotation data (chip ecoli2) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ecoli2.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.eck12.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.eck12.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.eck12.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.eck12.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 110d6549b1d105fdff31ab8f45b08d65 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix E_coli_2 Array annotation data (chip ecoli2)' - description: 'Affymetrix Affymetrix E_coli_2 Array annotation data (chip ecoli2) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ecoli2cdf/meta.yaml b/recipes/bioconductor-ecoli2cdf/meta.yaml index 12b93a0ff9c58..6263b81ce1bf5 100644 --- a/recipes/bioconductor-ecoli2cdf/meta.yaml +++ b/recipes/bioconductor-ecoli2cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "ecoli2cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b5cd1f05322ce494132ff649de9806c6 +about: + description: A package containing an environment representing the E_coli_2.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: ecoli2cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ecoli2cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b5cd1f05322ce494132ff649de9806c6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: ecoli2cdf - description: 'A package containing an environment representing the E_coli_2.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ecoli2probe/meta.yaml b/recipes/bioconductor-ecoli2probe/meta.yaml index 1d0e8f7b2081f..9a7b2f05f133f 100644 --- a/recipes/bioconductor-ecoli2probe/meta.yaml +++ b/recipes/bioconductor-ecoli2probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "ecoli2probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 061fcb782ee9da3aa5108881677a4531 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was E\_coli\_2\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type ecoli2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ecoli2probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 061fcb782ee9da3aa5108881677a4531 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type ecoli2' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was E\_coli\_2\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ecoliasv2cdf/meta.yaml b/recipes/bioconductor-ecoliasv2cdf/meta.yaml index dda890ce3dddf..1367455e1998f 100644 --- a/recipes/bioconductor-ecoliasv2cdf/meta.yaml +++ b/recipes/bioconductor-ecoliasv2cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "ecoliasv2cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d7771ca1648b26a6af5bfb7582c6c778 +about: + description: A package containing an environment representing the Ecoli_ASv2.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: ecoliasv2cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ecoliasv2cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d7771ca1648b26a6af5bfb7582c6c778 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: ecoliasv2cdf - description: 'A package containing an environment representing the Ecoli_ASv2.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ecoliasv2probe/meta.yaml b/recipes/bioconductor-ecoliasv2probe/meta.yaml index 189c801a32b21..42e0da41010fd 100644 --- a/recipes/bioconductor-ecoliasv2probe/meta.yaml +++ b/recipes/bioconductor-ecoliasv2probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "ecoliasv2probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b3e4332266184576279c3a478f286dc9 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was E\_coli\_Asv2\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type ecoliasv2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ecoliasv2probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b3e4332266184576279c3a478f286dc9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type ecoliasv2' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was E\_coli\_Asv2\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ecolicdf/meta.yaml b/recipes/bioconductor-ecolicdf/meta.yaml index ae5dec1242d25..764d457395369 100644 --- a/recipes/bioconductor-ecolicdf/meta.yaml +++ b/recipes/bioconductor-ecolicdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "ecolicdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4e664c1ac41a8ab68ef22f8a889b916c +about: + description: A package containing an environment representing the Ecoli.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: ecolicdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ecolicdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4e664c1ac41a8ab68ef22f8a889b916c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: ecolicdf - description: 'A package containing an environment representing the Ecoli.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ecolik12.db0/meta.yaml b/recipes/bioconductor-ecolik12.db0/meta.yaml index 5fe013dc64149..4a07ae536517f 100644 --- a/recipes/bioconductor-ecolik12.db0/meta.yaml +++ b/recipes/bioconductor-ecolik12.db0/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "ecoliK12.db0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dd303204595a25bc730695462e930247 +about: + description: Base annotation databases for E coli K12 Strain, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Level Annotation databases for E coli K12 Strain build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ecolik12.db0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0bb11ff1e532df7d2ad9af58d898f4d0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Level Annotation databases for E coli K12 Strain' - description: 'Base annotation databases for E coli K12 Strain, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ecolik12.db0/post-link.sh b/recipes/bioconductor-ecolik12.db0/post-link.sh index 1ea1a96c05c6f..99501d772a2b3 100644 --- a/recipes/bioconductor-ecolik12.db0/post-link.sh +++ b/recipes/bioconductor-ecolik12.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ecolik12.db0-3.18.0" +installBiocDataPackage.sh "ecolik12.db0-3.20.0" diff --git a/recipes/bioconductor-ecolileucine/meta.yaml b/recipes/bioconductor-ecolileucine/meta.yaml index d735e051bbdef..ff990f4b38a63 100644 --- a/recipes/bioconductor-ecolileucine/meta.yaml +++ b/recipes/bioconductor-ecolileucine/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "ecoliLeucine" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 30af71114480d851f4dad806e7f8e0d1 +about: + description: Experimental data with Affymetrix E. coli chips, as reported in She-pin Hung, Pierre Baldi, and G. Wesley Hatfield, J. Biol. Chem., Vol. 277, Issue 43, 40309-40323, October 25, 2002 + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Experimental data with Affymetrix E. coli chips build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ecolileucine", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-ecolicdf >=2.18.0,<2.19.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-ecolicdf >=2.18.0,<2.19.0 - r-base run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-ecolicdf >=2.18.0,<2.19.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-ecolicdf >=2.18.0,<2.19.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7596646155beb8c35bf2670f2c22788d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Experimental data with Affymetrix E. coli chips' - description: 'Experimental data with Affymetrix E. coli chips, as reported in She-pin Hung, Pierre Baldi, and G. Wesley Hatfield, J. Biol. Chem., Vol. 277, Issue 43, 40309-40323, October 25, 2002' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ecolileucine/post-link.sh b/recipes/bioconductor-ecolileucine/post-link.sh index 069ee49494795..8398d609e4bf6 100644 --- a/recipes/bioconductor-ecolileucine/post-link.sh +++ b/recipes/bioconductor-ecolileucine/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ecolileucine-1.42.0" +installBiocDataPackage.sh "ecolileucine-1.46.0" diff --git a/recipes/bioconductor-ecoliprobe/meta.yaml b/recipes/bioconductor-ecoliprobe/meta.yaml index fc9b2941ec792..c8aed9dc37b9e 100644 --- a/recipes/bioconductor-ecoliprobe/meta.yaml +++ b/recipes/bioconductor-ecoliprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "ecoliprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 09586f9907bdbc43ba5ea4ce07c1f756 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was E\_coli\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type ecoli build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ecoliprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 09586f9907bdbc43ba5ea4ce07c1f756 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type ecoli' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was E\_coli\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ecolisakai.db0/meta.yaml b/recipes/bioconductor-ecolisakai.db0/meta.yaml index f4a33593ee350..a1a32f8468336 100644 --- a/recipes/bioconductor-ecolisakai.db0/meta.yaml +++ b/recipes/bioconductor-ecolisakai.db0/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "ecoliSakai.db0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2afd28e9062d869d37e3d65dbe410bcb +about: + description: Base annotation databases for E coli Sakai Strain, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Level Annotation databases for E coli Sakai Strain build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ecolisakai.db0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0975b5ae0a2318f8a266e35a86d2bcf1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Level Annotation databases for E coli Sakai Strain' - description: 'Base annotation databases for E coli Sakai Strain, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ecolisakai.db0/post-link.sh b/recipes/bioconductor-ecolisakai.db0/post-link.sh index 5a26a1ced0260..94ae88c3feacf 100644 --- a/recipes/bioconductor-ecolisakai.db0/post-link.sh +++ b/recipes/bioconductor-ecolisakai.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ecolisakai.db0-3.18.0" +installBiocDataPackage.sh "ecolisakai.db0-3.20.0" diff --git a/recipes/bioconductor-ecolitk/meta.yaml b/recipes/bioconductor-ecolitk/meta.yaml index eb82d060744b5..f567cbada17b4 100644 --- a/recipes/bioconductor-ecolitk/meta.yaml +++ b/recipes/bioconductor-ecolitk/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "ecolitk" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 58667dc1f403986935c98a97f2e0b9e2 +about: + description: Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Meta-data and tools for E. coli build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ecolitk", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: ecoliLeucine, ecolicdf, graph, multtest, affy requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base +source: + md5: 9382890863bad6e353aba9689cde885f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Meta-data and tools for E. coli' - description: 'Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-edaseq/meta.yaml b/recipes/bioconductor-edaseq/meta.yaml index 4e0352c7939f4..c6c23115d6c63 100644 --- a/recipes/bioconductor-edaseq/meta.yaml +++ b/recipes/bioconductor-edaseq/meta.yaml @@ -1,67 +1,73 @@ -{% set version = "2.36.0" %} +{% set version = "2.40.0" %} {% set name = "EDASeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Exploratory Data Analysis and Normalization for RNA-Seq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b2d28fdad31e8c56f68873b599ffc235 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-edaseq", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:edaseq + parent_recipe: + name: bioconductor-edaseq + path: recipes/bioconductor-edaseq + version: 2.14.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat, DESeq2, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-aroma.light >=3.32.0,<3.33.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-aroma.light >=3.36.0,<3.37.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-biocmanager run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-aroma.light >=3.32.0,<3.33.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-aroma.light >=3.36.0,<3.37.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-biocmanager + +source: + md5: 69a8fca452bc37e8e641366bce4357df + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Exploratory Data Analysis and Normalization for RNA-Seq' - description: 'Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).' -extra: - identifiers: - - biotools:edaseq - parent_recipe: - name: bioconductor-edaseq - path: recipes/bioconductor-edaseq - version: 2.14.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-edge/meta.yaml b/recipes/bioconductor-edge/meta.yaml index 9a280bb34b019..962495e93dcb7 100644 --- a/recipes/bioconductor-edge/meta.yaml +++ b/recipes/bioconductor-edge/meta.yaml @@ -1,56 +1,60 @@ -{% set version = "2.34.0" %} +{% set version = "2.38.0" %} {% set name = "edge" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The edge package implements methods for carrying out differential expression analyses of genome-wide gene expression studies. Significance testing using the optimal discovery procedure and generalized likelihood ratio tests (equivalent to F-tests and t-tests) are implemented for general study designs. Special functions are available to facilitate the analysis of common study designs, including time course experiments. Other packages such as sva and qvalue are integrated in edge to provide a wide range of tools for gene expression analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Extraction of Differential Gene Expression -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 89d1683b6b4f9723b4c4fcef6972d543 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-edge", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:edge + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, ggplot2, reshape2 requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-snm >=1.50.0,<1.51.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-mass - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-snm >=1.50.0,<1.51.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-mass - build: - - {{ compiler('c') }} - - make + +source: + md5: 99f1e4889963beb7376407c4dc92fd15 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Extraction of Differential Gene Expression' - description: 'The edge package implements methods for carrying out differential expression analyses of genome-wide gene expression studies. Significance testing using the optimal discovery procedure and generalized likelihood ratio tests (equivalent to F-tests and t-tests) are implemented for general study designs. Special functions are available to facilitate the analysis of common study designs, including time course experiments. Other packages such as snm, sva, and qvalue are integrated in edge to provide a wide range of tools for gene expression analysis.' - license_file: LICENSE + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} \ No newline at end of file diff --git a/recipes/bioconductor-edger/meta.yaml b/recipes/bioconductor-edger/meta.yaml index b8f25cddfaf0d..d7903215cdb61 100644 --- a/recipes/bioconductor-edger/meta.yaml +++ b/recipes/bioconductor-edger/meta.yaml @@ -1,58 +1,61 @@ -{% set version = "4.0.16" %} +{% set version = "4.4.0" %} {% set name = "edgeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce read counts, including ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE and CAGE. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Empirical Analysis of Digital Gene Expression Data in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8fb1c6c67e29d299c991d16d0f6c5f5b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-edger", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:edger + - usegalaxy-eu:edger + parent_recipe: + name: bioconductor-edger + path: recipes/bioconductor-edger + version: 3.22.5 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: jsonlite, readr, rhdf5, splines, knitr, AnnotationDbi, Biobase, BiocStyle, SummarizedExperiment, org.Hs.eg.db, Matrix, SeuratObject requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-locfit - - r-rcpp - libblas - liblapack run: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-locfit - - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: db45a60f88cb89ea135743c1eb39b99c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'Empirical Analysis of Digital Gene Expression Data in R' - description: 'Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce read counts, including ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE and CAGE.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:edger - - usegalaxy-eu:edger - parent_recipe: - name: bioconductor-edger - path: recipes/bioconductor-edger - version: 3.22.5 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-edirquery/meta.yaml b/recipes/bioconductor-edirquery/meta.yaml index 2adef6a882208..e82e0a819a8bb 100644 --- a/recipes/bioconductor-edirquery/meta.yaml +++ b/recipes/bioconductor-edirquery/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "EDIRquery" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: EDIRquery provides a tool to search for genes of interest within the Exome Database of Interspersed Repeats (EDIR). A gene name is a required input, and users can additionally specify repeat sequence lengths, minimum and maximum distance between sequences, and whether to allow a 1-bp mismatch. Outputs include a summary of results by repeat length, as well as a dataframe of query results. Example data provided includes a subset of the data for the gene GAA (ENSG00000171298). To query the full database requires providing a path to the downloaded database files as a parameter. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Query the EDIR Database For Specific Gene -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ff19937af17cf0a7a874b986192d6b1c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-edirquery", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 - r-base - - 'r-readr >=2.1.2' - - 'r-tibble >=3.1.6' - - 'r-tictoc >=1.0.1' + - r-readr >=2.1.2 + - r-tibble >=3.1.6 + - r-tictoc >=1.0.1 run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 - r-base - - 'r-readr >=2.1.2' - - 'r-tibble >=3.1.6' - - 'r-tictoc >=1.0.1' + - r-readr >=2.1.2 + - r-tibble >=3.1.6 + - r-tictoc >=1.0.1 + +source: + md5: db302d2df4cfbadc64b20c9d9c800cbf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Query the EDIR Database For Specific Gene' - description: 'EDIRquery provides a tool to search for genes of interest within the Exome Database of Interspersed Repeats (EDIR). A gene name is a required input, and users can additionally specify repeat sequence lengths, minimum and maximum distance between sequences, and whether to allow a 1-bp mismatch. Outputs include a summary of results by repeat length, as well as a dataframe of query results. Example data provided includes a subset of the data for the gene GAA (ENSG00000171298). To query the full database requires providing a path to the downloaded database files as a parameter.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-eds/meta.yaml b/recipes/bioconductor-eds/meta.yaml index de545d756c8e0..4809d41f7f02c 100644 --- a/recipes/bioconductor-eds/meta.yaml +++ b/recipes/bioconductor-eds/meta.yaml @@ -1,47 +1,53 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "eds" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This packages provides a single function, readEDS. This is a low-level utility for reading in Alevin EDS format into R. This function is not designed for end-users but instead the package is predominantly for simplifying package dependency graph for other Bioconductor packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'eds: Low-level reader for Alevin EDS format' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5992ff2692afb665a65bc9755175de5c build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-eds", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, tximportData, testthat (>= 3.0.0) # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-matrix - r-rcpp - libblas - liblapack + - zlib run: - r-base - r-matrix - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 82a00e0316df5d28613dcfedd4c7d488 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'eds: Low-level reader for Alevin EDS format' - description: 'This packages provides a single function, readEDS. This is a low-level utility for reading in Alevin EDS format into R. This function is not designed for end-users but instead the package is predominantly for simplifying package dependency graph for other Bioconductor packages.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-egad/meta.yaml b/recipes/bioconductor-egad/meta.yaml index d7cb742f73393..f8dec43d658e7 100644 --- a/recipes/bioconductor-egad/meta.yaml +++ b/recipes/bioconductor-egad/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "EGAD" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package implements a series of highly efficient tools to calculate functional properties of networks based on guilt by association methods. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Extending guilt by association by degree -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9a76ae26d942a1e8b8c8764b80c69927 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-egad", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, rmarkdown, markdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-gplots - r-igraph @@ -35,10 +37,10 @@ requirements: - r-rcurl - r-zoo run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-gplots - r-igraph @@ -47,13 +49,16 @@ requirements: - r-rcolorbrewer - r-rcurl - r-zoo + +source: + md5: 450678549ca33c6c8e9f15cf4dedcb41 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Extending guilt by association by degree' - description: 'The package implements a series of highly efficient tools to calculate functional properties of networks based on guilt by association methods.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-egsea/meta.yaml b/recipes/bioconductor-egsea/meta.yaml index 69bf582553dc2..c88763c44e16a 100644 --- a/recipes/bioconductor-egsea/meta.yaml +++ b/recipes/bioconductor-egsea/meta.yaml @@ -1,94 +1,103 @@ -{% set version = "1.28.0" %} +{% set version = "1.34.0" %} {% set name = "EGSEA" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. EGSEA algorithm utilizes the analysis results of twelve prominent GSE algorithms in the literature to calculate collective significance scores for each gene set. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Ensemble of Gene Set Enrichment Analyses -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9509dd4e4ea00e7a3ee4c237586d8dcc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic + run_exports: '{{ pin_subpackage("bioconductor-egsea", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:egsea + - usegalaxy-eu:egsea + parent_recipe: + name: bioconductor-egsea + path: recipes/bioconductor-egsea + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, testthat requirements: + host: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-egseadata >=1.28.0,<1.29.0' - - 'bioconductor-gage >=2.50.0,<2.51.0' - - 'bioconductor-globaltest >=5.54.0,<5.55.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-padog >=1.42.0,<1.43.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' - - 'bioconductor-safe >=3.40.0,<3.41.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-egseadata >=1.34.0,<1.35.0 + - bioconductor-gage >=2.56.0,<2.57.0 + - bioconductor-globaltest >=5.60.0,<5.61.0 + - bioconductor-gsva >=2.0.0,<2.1.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 + - bioconductor-padog >=1.48.0,<1.49.0 + - bioconductor-pathview >=1.46.0,<1.47.0 + - bioconductor-safe >=3.46.0,<3.47.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-base - r-dt - - 'r-ggplot2 >=1.0.0' - - 'r-gplots >=2.14.2' - - 'r-htmlutils >=0.1.5' + - r-ggplot2 >=1.0.0 + - r-gplots >=2.14.2 + - r-htmlutils >=0.1.5 - r-htmlwidgets - - 'r-hwriter >=1.2.2' + - r-hwriter >=1.2.2 - r-metap - r-plotly - r-rcolorbrewer - - 'r-stringi >=0.5.0' + - r-stringi >=0.5.0 + run: - - 'bioconductor-annotationdbi >=1.62.0,<1.63.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-edger >=3.42.0,<3.43.0' - - 'bioconductor-egseadata >=1.28.0,<1.29.0' - - 'bioconductor-gage >=2.50.0,<2.51.0' - - 'bioconductor-globaltest >=5.54.0,<5.55.0' - - 'bioconductor-gsva >=1.48.0,<1.49.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.mm.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-org.rn.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-padog >=1.42.0,<1.43.0' - - 'bioconductor-pathview >=1.40.0,<1.41.0' - - 'bioconductor-safe >=3.40.0,<3.41.0' - - 'bioconductor-topgo >=2.52.0,<2.53.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-egseadata >=1.34.0,<1.35.0 + - bioconductor-gage >=2.56.0,<2.57.0 + - bioconductor-globaltest >=5.60.0,<5.61.0 + - bioconductor-gsva >=2.0.0,<2.1.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 + - bioconductor-padog >=1.48.0,<1.49.0 + - bioconductor-pathview >=1.46.0,<1.47.0 + - bioconductor-safe >=3.46.0,<3.47.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-base - r-dt - - 'r-ggplot2 >=1.0.0' - - 'r-gplots >=2.14.2' - - 'r-htmlutils >=0.1.5' + - r-ggplot2 >=1.0.0 + - r-gplots >=2.14.2 + - r-htmlutils >=0.1.5 - r-htmlwidgets - - 'r-hwriter >=1.2.2' + - r-hwriter >=1.2.2 - r-metap - r-plotly - r-rcolorbrewer - - 'r-stringi >=0.5.0' + - r-stringi >=0.5.0 + +source: + md5: dd9dc90dceecdd45b7b37e62fbbbcdf8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Ensemble of Gene Set Enrichment Analyses' - description: 'This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:egsea - - usegalaxy-eu:egsea - parent_recipe: - name: bioconductor-egsea - path: recipes/bioconductor-egsea - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-egseadata/meta.yaml b/recipes/bioconductor-egseadata/meta.yaml index aab5bfb3fdc69..22192d6633ecc 100644 --- a/recipes/bioconductor-egseadata/meta.yaml +++ b/recipes/bioconductor-egseadata/meta.yaml @@ -1,24 +1,28 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "EGSEAdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 838b30ae6caf7c3cbb854e0404b52cda +about: + description: This package includes gene set collections that are used for the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. It includes Human and Mouse versions of the MSidDB (Subramanian, et al. (2005) PNAS, 102(43):15545-15550) and GeneSetDB (Araki, et al. (2012) FEBS Open Bio, 2:76-82) collections. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Gene set collections for the EGSEA package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-egseadata", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-egseadata + path: recipes/bioconductor-egseadata + version: 1.8.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: EGSEA requirements: host: @@ -26,19 +30,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 422fcaa7f47c394358600cfb268d265b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Gene set collections for the EGSEA package' - description: 'This package includes gene set collections that are used for the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. It includes Human and Mouse versions of the MSidDB (Subramanian, et al. (2005) PNAS, 102(43):15545-15550) and GeneSetDB (Araki, et al. (2012) FEBS Open Bio, 2:76-82) collections.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-egseadata - path: recipes/bioconductor-egseadata - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-egseadata/post-link.sh b/recipes/bioconductor-egseadata/post-link.sh index 4969b6b51c98a..cb2583ce0839e 100644 --- a/recipes/bioconductor-egseadata/post-link.sh +++ b/recipes/bioconductor-egseadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "egseadata-1.30.0" +installBiocDataPackage.sh "egseadata-1.34.0" diff --git a/recipes/bioconductor-eir/meta.yaml b/recipes/bioconductor-eir/meta.yaml index 882112a2aaeb1..3f3ac0ae48ca8 100644 --- a/recipes/bioconductor-eir/meta.yaml +++ b/recipes/bioconductor-eir/meta.yaml @@ -1,32 +1,37 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "eiR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Accelerated similarity searching of small molecules -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71e5c96821411e053b417fb15618e1cb build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-eir", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitcitations, knitr, knitrBootstrap,rmarkdown,RSQLite requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-chemminer >=3.58.0,<3.59.0 - r-base - r-dbi - r-digest - - 'r-rcppannoy >=0.0.9' + - r-rcppannoy >=0.0.9 - r-rcurl - r-runit - r-snow @@ -34,26 +39,26 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-chemminer >=3.58.0,<3.59.0 - r-base - r-dbi - r-digest - - 'r-rcppannoy >=0.0.9' + - r-rcppannoy >=0.0.9 - r-rcurl - r-runit - r-snow - r-snowfall - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 201d0aca2349715fe0295945ad1fe34a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Accelerated similarity searching of small molecules' - description: 'The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-eisar/meta.yaml b/recipes/bioconductor-eisar/meta.yaml index 5daa7b7fcd320..b4b9c4e493feb 100644 --- a/recipes/bioconductor-eisar/meta.yaml +++ b/recipes/bioconductor-eisar/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "eisaR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Exon-intron split analysis (EISA) uses ordinary RNA-seq data to measure changes in mature RNA and pre-mRNA reads across different experimental conditions to quantify transcriptional and post-transcriptional regulation of gene expression. For details see Gaidatzis et al., Nat Biotechnol 2015. doi: 10.1038/nbt.3269. eisaR implements the major steps of EISA in R.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Exon-Intron Split Analysis (EISA) in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0a81a6727f2514ce8e2836cc170bdb19 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-eisar", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie, Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38, ensembldb, AnnotationDbi, GenomicFeatures, rtracklayer + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie, Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38, ensembldb, AnnotationDbi, GenomicFeatures, txdbmaker, rtracklayer requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + +source: + md5: e105d18727c70098da1a0efbc9686c51 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Exon-Intron Split Analysis (EISA) in R' - description: 'Exon-intron split analysis (EISA) uses ordinary RNA-seq data to measure changes in mature RNA and pre-mRNA reads across different experimental conditions to quantify transcriptional and post-transcriptional regulation of gene expression. For details see Gaidatzis et al., Nat Biotechnol 2015. doi: 10.1038/nbt.3269. eisaR implements the major steps of EISA in R.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-elmer.data/meta.yaml b/recipes/bioconductor-elmer.data/meta.yaml index 46a704674c673..d476c72fd8629 100644 --- a/recipes/bioconductor-elmer.data/meta.yaml +++ b/recipes/bioconductor-elmer.data/meta.yaml @@ -1,46 +1,52 @@ -{% set version = "2.26.0" %} +{% set version = "2.30.0" %} {% set name = "ELMER.data" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Supporting data for the ELMER package. It includes: - elmer.data.example.promoter: mae.promoter - elmer.data.example: data - EPIC.hg38.manifest - EPIC.hg19.manifest - hm450.hg38.manifest - hm450.hg19.manifest - hocomoco.table - human.TF - LUSC_meth_refined: Meth - LUSC_RNA_refined: GeneExp - Probes.motif.hg19.450K - Probes.motif.hg19.EPIC - Probes.motif.hg38.450K - Probes.motif.hg38.EPIC - TF.family - TF.subfamily - Human_genes__GRCh37_p13 - Human_genes__GRCh38_p12 - Human_genes__GRCh37_p13__tss - Human_genes__GRCh38_p12__tss' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Data for the ELMER package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 565ea1aa52f3f61d16b7560859ed7a3a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-elmer.data", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-elmer.data + path: recipes/bioconductor-elmer.data + version: 2.4.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, dplyr, devtools, DT, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 611a1275cc893a59759673a36dd5e272 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Data for the ELMER package' - description: 'Supporting data for the ELMER package. It includes: - elmer.data.example.promoter: mae.promoter - elmer.data.example: data - EPIC.hg38.manifest - EPIC.hg19.manifest - hm450.hg38.manifest - hm450.hg19.manifest - hocomoco.table - human.TF - LUSC_meth_refined: Meth - LUSC_RNA_refined: GeneExp - Probes.motif.hg19.450K - Probes.motif.hg19.EPIC - Probes.motif.hg38.450K - Probes.motif.hg38.EPIC - TF.family - TF.subfamily - Human_genes__GRCh37_p13 - Human_genes__GRCh38_p12 - Human_genes__GRCh37_p13__tss - Human_genes__GRCh38_p12__tss' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-elmer.data - path: recipes/bioconductor-elmer.data - version: 2.4.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-elmer.data/post-link.sh b/recipes/bioconductor-elmer.data/post-link.sh index f070b978224f7..a4ce5e1905f06 100644 --- a/recipes/bioconductor-elmer.data/post-link.sh +++ b/recipes/bioconductor-elmer.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "elmer.data-2.26.0" +installBiocDataPackage.sh "elmer.data-2.30.0" diff --git a/recipes/bioconductor-elmer/build_failure.linux-64.yaml b/recipes/bioconductor-elmer/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..e1d3b1019d563 --- /dev/null +++ b/recipes/bioconductor-elmer/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: b3ae2bd9733e916ee96038c0c4101e9c1e41f4f705c319133244f309a4537893 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-progress: 1.2.3-r44hc72bb7e_1 conda-forge + r-progressr: 0.15.1-r44hc72bb7e_0 conda-forge + r-promises: 1.3.2-r44h93ab643_0 conda-forge + r-proxy: 0.4_27-r44hb1dbf0f_3 conda-forge + r-purrr: 1.0.2-r44hdb488b9_1 conda-forge + r-quantreg: 5.99.1-r44h9ad1c49_0 conda-forge + r-r.methodss3: 1.8.2-r44hc72bb7e_3 conda-forge + r-r.oo: 1.27.0-r44hc72bb7e_0 conda-forge + r-r.utils: 2.12.3-r44hc72bb7e_1 conda-forge + r-r6: 2.5.1-r44hc72bb7e_3 conda-forge + r-rappdirs: 0.3.3-r44hb1dbf0f_3 conda-forge + r-rcolorbrewer: 1.1_3-r44h785f33e_3 conda-forge + r-rcpp: 1.0.13_1-r44h93ab643_0 conda-forge + r-rcpparmadillo: 14.2.2_1-r44hb79369c_0 conda-forge + r-rcppeigen: 0.3.4.0.2-r44hb79369c_0 conda-forge + r-rcurl: 1.98_1.16-r44he8228da_1 conda-forge + r-readr: 2.1.5-r44h0d4f4ea_1 conda-forge + r-recipes: 1.1.0-r44hc72bb7e_1 conda-forge + r-reshape: 0.8.9-r44hc72bb7e_3 conda-forge + r-reshape2: 1.4.4-r44h0d4f4ea_4 conda-forge + r-restfulr: 0.0.15-r44h5ef9028_5 bioconda + r-rjson: 0.2.23-r44h93ab643_0 conda-forge + r-rlang: 1.1.4-r44ha18555a_1 conda-forge + r-rmarkdown: 2.29-r44hc72bb7e_0 conda-forge + r-rpart: 4.1.23-r44hb1dbf0f_1 conda-forge + r-rsqlite: 2.3.9-r44h93ab643_0 conda-forge + r-rstatix: 0.7.2-r44hc72bb7e_2 conda-forge + r-rstudioapi: 0.17.1-r44hc72bb7e_0 conda-forge + r-rvest: 1.0.4-r44hc72bb7e_1 conda-forge + r-sass: 0.4.9-r44ha18555a_1 conda-forge + r-scales: 1.3.0-r44hc72bb7e_1 conda-forge + r-selectr: 0.4_2-r44hc72bb7e_4 conda-forge + r-shape: 1.4.6.1-r44ha770c72_1 conda-forge + r-snow: 0.4_4-r44hc72bb7e_3 conda-forge + r-sparsem: 1.84_2-r44hc4980d5_0 conda-forge + r-squarem: 2021.1-r44hc72bb7e_3 conda-forge + r-stringi: 1.8.4-r44h33cde33_3 conda-forge + r-stringr: 1.5.1-r44h785f33e_1 conda-forge + r-survival: 3.8_3-r44h2b5f3a1_0 conda-forge + r-sys: 3.4.3-r44h2b5f3a1_0 conda-forge + r-tibble: 3.2.1-r44hdb488b9_3 conda-forge + r-tidyr: 1.3.1-r44h0d4f4ea_1 conda-forge + r-tidyselect: 1.2.1-r44hc72bb7e_1 conda-forge + r-timechange: 0.3.0-r44ha18555a_1 conda-forge + r-timedate: 4041.110-r44hc72bb7e_0 conda-forge + r-tinytex: 0.54-r44hc72bb7e_0 conda-forge + r-tzdb: 0.4.0-r44ha18555a_2 conda-forge + r-utf8: 1.2.4-r44hb1dbf0f_1 conda-forge + r-vctrs: 0.6.5-r44h0d4f4ea_1 conda-forge + r-viridis: 0.6.5-r44hc72bb7e_1 conda-forge + r-viridislite: 0.4.2-r44hc72bb7e_2 conda-forge + r-vroom: 1.6.5-r44h0d4f4ea_1 conda-forge + r-withr: 3.0.2-r44hc72bb7e_0 conda-forge + r-xfun: 0.49-r44h93ab643_0 conda-forge + r-xml: 3.99_0.17-r44h5bae778_2 conda-forge + r-xml2: 1.3.6-r44h8194278_2 conda-forge + r-yaml: 2.3.10-r44hdb488b9_0 conda-forge + readline: 8.2-h8228510_1 conda-forge + sed: 4.8-he412f7d_0 conda-forge + setuptools: 75.6.0-pyhff2d567_1 conda-forge + sysroot_linux-64: 2.17-h0157908_18 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tktable: 2.10-h8bc8fbc_6 conda-forge + toml: 0.10.2-pyhd8ed1ab_1 conda-forge + tomlkit: 0.13.2-pyha770c72_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + xmltodict: 0.14.2-pyhd8ed1ab_1 conda-forge + xorg-libice: 1.1.2-hb9d3cd8_0 conda-forge + xorg-libsm: 1.2.5-he73a12e_0 conda-forge + xorg-libx11: 1.8.10-h4f16b4b_1 conda-forge + xorg-libxau: 1.0.12-hb9d3cd8_0 conda-forge + xorg-libxdmcp: 1.1.5-hb9d3cd8_0 conda-forge + xorg-libxext: 1.3.6-hb9d3cd8_0 conda-forge + xorg-libxrender: 0.9.12-hb9d3cd8_0 conda-forge + xorg-libxt: 1.3.1-hb9d3cd8_0 conda-forge + yaml: 0.2.5-h7f98852_2 conda-forge + yq: 3.4.3-pyhd8ed1ab_1 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2213, in create_build_envs + environ.create_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1050, in create_env + _execute_actions(prefix, precs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1338, in _execute_actions + progressive_fetch_extract.execute() + File "/opt/conda/lib/python3.10/site-packages/conda/core/package_cache_data.py", line 900, in execute + raise CondaMultiError(not_cancelled) + conda.CondaMultiError: ('Connection broken: IncompleteRead(2357572 bytes read, 1850789 more expected)', IncompleteRead(2357572 bytes read, 1850789 more expected)) + ('Connection broken: IncompleteRead(2357572 bytes read, 1850789 more expected)', IncompleteRead(2357572 bytes read, 1850789 more expected)) +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-elmer/meta.yaml b/recipes/bioconductor-elmer/meta.yaml index 680af36125772..a49ed13ba1209 100644 --- a/recipes/bioconductor-elmer/meta.yaml +++ b/recipes/bioconductor-elmer/meta.yaml @@ -1,41 +1,50 @@ -{% set version = "2.26.0" %} +{% set version = "2.30.0" %} {% set name = "ELMER" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 528e6779b95faafbb8ff2e32e0b28ca5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-elmer", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-elmer + path: recipes/bioconductor-elmer + version: 2.4.4 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, AnnotationHub, ExperimentHub, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr, sesameData requirements: + host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-elmer.data >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tcgabiolinks >=2.30.0,<2.31.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-elmer.data >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tcgabiolinks >=2.34.0,<2.35.0 - r-base - r-circlize - r-doparallel @@ -62,21 +71,22 @@ requirements: - r-tibble - r-tidyr - r-xml2 + run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-elmer.data >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tcgabiolinks >=2.30.0,<2.31.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-elmer.data >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tcgabiolinks >=2.34.0,<2.35.0 - r-base - r-circlize - r-doparallel @@ -103,18 +113,16 @@ requirements: - r-tibble - r-tidyr - r-xml2 + +source: + md5: d21ee994d4b8293e2d097f38206b8fcd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes' - description: 'ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-elmer - path: recipes/bioconductor-elmer - version: 2.4.4 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-emdomics/meta.yaml b/recipes/bioconductor-emdomics/meta.yaml index f0657e63a91b6..773a518763a01 100644 --- a/recipes/bioconductor-emdomics/meta.yaml +++ b/recipes/bioconductor-emdomics/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "2.32.0" %} +{% set version = "2.36.0" %} {% set name = "EMDomics" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The EMDomics algorithm is used to perform a supervised multi-class analysis to measure the magnitude and statistical significance of observed continuous genomics data between groups. Usually the data will be gene expression values from array-based or sequence-based experiments, but data from other types of experiments can also be analyzed (e.g. copy number variation). Traditional methods like Significance Analysis of Microarrays (SAM) and Linear Models for Microarray Data (LIMMA) use significance tests based on summary statistics (mean and standard deviation) of the distributions. This approach lacks power to identify expression differences between groups that show high levels of intra-group heterogeneity. The Earth Mover's Distance (EMD) algorithm instead computes the "work" needed to transform one distribution into another, thus providing a metric of the overall difference in shape between two distributions. Permutation of sample labels is used to generate q-values for the observed EMD scores. This package also incorporates the Komolgorov-Smirnov (K-S) test and the Cramer von Mises test (CVM), which are both common distribution comparison tests. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Earth Mover's Distance for Differential Analysis of Genomics Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ac097828648747f0be1ed4d956ecfa7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-emdomics", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-cdft - r-emdist - r-ggplot2 - r-matrixstats run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-cdft - r-emdist - r-ggplot2 - r-matrixstats + +source: + md5: 0e828323561e9f1264bae1cb25717efe + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Earth Mover''s Distance for Differential Analysis of Genomics Data' - description: 'The EMDomics algorithm is used to perform a supervised multi-class analysis to measure the magnitude and statistical significance of observed continuous genomics data between groups. Usually the data will be gene expression values from array-based or sequence-based experiments, but data from other types of experiments can also be analyzed (e.g. copy number variation). Traditional methods like Significance Analysis of Microarrays (SAM) and Linear Models for Microarray Data (LIMMA) use significance tests based on summary statistics (mean and standard deviation) of the distributions. This approach lacks power to identify expression differences between groups that show high levels of intra-group heterogeneity. The Earth Mover''s Distance (EMD) algorithm instead computes the "work" needed to transform one distribution into another, thus providing a metric of the overall difference in shape between two distributions. Permutation of sample labels is used to generate q-values for the observed EMD scores. This package also incorporates the Komolgorov-Smirnov (K-S) test and the Cramer von Mises test (CVM), which are both common distribution comparison tests.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-empiricalbrownsmethod/meta.yaml b/recipes/bioconductor-empiricalbrownsmethod/meta.yaml index e73e26279321b..c000208f690a3 100644 --- a/recipes/bioconductor-empiricalbrownsmethod/meta.yaml +++ b/recipes/bioconductor-empiricalbrownsmethod/meta.yaml @@ -1,39 +1,20 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "EmpiricalBrownsMethod" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cde2165928019f9c13982d640a1303c5 +about: + description: Combining P-values from multiple statistical tests is common in bioinformatics. However, this procedure is non-trivial for dependent P-values. This package implements an empirical adaptation of Brown’s Method (an extension of Fisher’s Method) for combining dependent P-values which is appropriate for highly correlated data sets found in high-throughput biological experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Uses Brown's method to combine p-values from dependent tests build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-empiricalbrownsmethod", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, testthat, knitr, rmarkdown -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Uses Brown''s method to combine p-values from dependent tests' - description: 'Combining P-values from multiple statistical tests is common in bioinformatics. However, this procedure is non-trivial for dependent P-values. This package implements an empirical adaptation of Brown’s Method (an extension of Fisher’s Method) for combining dependent P-values which is appropriate for highly correlated data sets found in high-throughput biological experiments.' - license_file: LICENSE extra: identifiers: - biotools:empiricalbrownsmethod @@ -42,4 +23,23 @@ extra: name: bioconductor-empiricalbrownsmethod path: recipes/bioconductor-empiricalbrownsmethod version: 1.8.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: BiocStyle, testthat, knitr, rmarkdown +requirements: + host: + - r-base + run: + - r-base +source: + md5: d1aa72408cdb1d64b5527f9dd93a6abe + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-emtdata/meta.yaml b/recipes/bioconductor-emtdata/meta.yaml index 7dbe179742d90..9075a7ed26d31 100644 --- a/recipes/bioconductor-emtdata/meta.yaml +++ b/recipes/bioconductor-emtdata/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "emtdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4f861584cce979edd6d7bdce3624e916 +about: + description: This package provides pre-processed RNA-seq data where the epithelial to mesenchymal transition was induced on cell lines. These data come from three publications Cursons et al. (2015), Cursons etl al. (2018) and Foroutan et al. (2017). In each of these publications, EMT was induces across multiple cell lines following treatment by TGFb among other stimulants. This data will be useful in determining the regulatory programs modified in order to achieve an EMT. Data were processed by the Davis laboratory in the Bioinformatics division at WEHI. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: An ExperimentHub Package for data sets with an Epithelial to Mesenchymal Transition (EMT) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-emtdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat (>= 3.0.0), stringr, plyr, prettydoc, BiocStyle, Homo.sapiens, RColorBrewer, rmarkdown, BiocFileCache, knitr requirements: host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8db81c389458586cc9c291f05cfcd7d1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'An ExperimentHub Package for data sets with an Epithelial to Mesenchymal Transition (EMT)' - description: 'This package provides pre-processed RNA-seq data where the epithelial to mesenchymal transition was induced on cell lines. These data come from three publications Cursons et al. (2015), Cursons etl al. (2018) and Foroutan et al. (2017). In each of these publications, EMT was induces across multiple cell lines following treatment by TGFb among other stimulants. This data will be useful in determining the regulatory programs modified in order to achieve an EMT. Data were processed by the Davis laboratory in the Bioinformatics division at WEHI.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-emtdata/post-link.sh b/recipes/bioconductor-emtdata/post-link.sh index 93baa8560da53..bb48b845751d9 100644 --- a/recipes/bioconductor-emtdata/post-link.sh +++ b/recipes/bioconductor-emtdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "emtdata-1.10.0" +installBiocDataPackage.sh "emtdata-1.14.0" diff --git a/recipes/bioconductor-encodexplorerdata/meta.yaml b/recipes/bioconductor-encodexplorerdata/meta.yaml index 5eb72ebf61053..d9f04fd44d29a 100644 --- a/recipes/bioconductor-encodexplorerdata/meta.yaml +++ b/recipes/bioconductor-encodexplorerdata/meta.yaml @@ -1,24 +1,22 @@ {% set version = "0.99.5" %} {% set name = "ENCODExplorerData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c6d9b491548529db0739b79c98adacd7 +about: + description: This package allows user to quickly access ENCODE project files metadata and give access to helper functions to query the ENCODE rest api, download ENCODE datasets and save the database in SQLite format. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: A compilation of ENCODE metadata build: - number: 8 + noarch: generic + number: 9 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-encodexplorerdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: AnnotationHub, RUnit, BiocGenerics, knitr, curl, httr requirements: host: @@ -32,13 +30,15 @@ requirements: - r-jsonlite - r-rcurl - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c6d9b491548529db0739b79c98adacd7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A compilation of ENCODE metadata' - description: 'This package allows user to quickly access ENCODE project files metadata and give access to helper functions to query the ENCODE rest api, download ENCODE datasets and save the database in SQLite format.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-enhancedvolcano/meta.yaml b/recipes/bioconductor-enhancedvolcano/meta.yaml index 717cd7a75281d..39d627c80abdd 100644 --- a/recipes/bioconductor-enhancedvolcano/meta.yaml +++ b/recipes/bioconductor-enhancedvolcano/meta.yaml @@ -1,24 +1,32 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "EnhancedVolcano" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Volcano plots represent a useful way to visualise the results of differential expression analyses. Here, we present a highly-configurable function that produces publication-ready volcano plots. EnhancedVolcano will attempt to fit as many point labels in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise have been read. Other functionality allows the user to identify up to 4 different types of attributes in the same plot space via colour, shape, size, and shade parameter configurations. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Publication-ready volcano plots with enhanced colouring and labeling -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b8224be72afe86d3d951a6a8fdc6788e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-enhancedvolcano", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-enhancedvolcano + path: recipes/bioconductor-enhancedvolcano + version: 1.0.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ggalt, ggrastr, RUnit, BiocGenerics, knitr, DESeq2, pasilla, airway, org.Hs.eg.db, gridExtra, magrittr, rmarkdown requirements: host: @@ -29,18 +37,16 @@ requirements: - r-base - r-ggplot2 - r-ggrepel + +source: + md5: 6a01a421edeb41c12b7dbd150c511184 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Publication-ready volcano plots with enhanced colouring and labeling' - description: 'Volcano plots represent a useful way to visualise the results of differential expression analyses. Here, we present a highly-configurable function that produces publication-ready volcano plots. EnhancedVolcano will attempt to fit as many point labels in the plot window as possible, thus avoiding ''clogging'' up the plot with labels that could not otherwise have been read. Other functionality allows the user to identify up to 4 different types of attributes in the same plot space via colour, shape, size, and shade parameter configurations.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-enhancedvolcano - path: recipes/bioconductor-enhancedvolcano - version: 1.0.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-enhancerhomologsearch/meta.yaml b/recipes/bioconductor-enhancerhomologsearch/meta.yaml index 2d0d66cd9e7d2..69439609c0cc7 100644 --- a/recipes/bioconductor-enhancerhomologsearch/meta.yaml +++ b/recipes/bioconductor-enhancerhomologsearch/meta.yaml @@ -1,37 +1,46 @@ -{% set version = "1.8.2" %} +{% set version = "1.12.0" %} {% set name = "enhancerHomologSearch" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Get ENCODE data of enhancer region via H3K4me1 peaks and search homolog regions for given sequences. The candidates of enhancer homolog regions can be filtered by distance to target TSS. The top candidates from human and mouse will be aligned to each other and then exported as multiple alignments with given enhancer. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identification of putative mammalian orthologs to given enhancer -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ce4ad762be83b367c02fc926bf67c383 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-enhancerhomologsearch", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, MotifDb, testthat, TFBSTools requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-motifmatchr >=1.28.0,<1.29.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-httr - r-jsonlite @@ -39,34 +48,35 @@ requirements: - r-rcpp - libblas - liblapack + run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-motifmatchr >=1.28.0,<1.29.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-httr - r-jsonlite - r-matrix - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: c7826171752570183616e0d2063f50e0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Identification of putative mammalian orthologs to given enhancer' - description: 'Get ENCODE data of enhancer region via H3K4me1 peaks and search homolog regions for given sequences. The candidates of enhancer homolog regions can be filtered by distance to target TSS. The top candidates from human and mouse will be aligned to each other and then exported as multiple alignments with given enhancer.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-enmcb/meta.yaml b/recipes/bioconductor-enmcb/meta.yaml index 137714b151321..232953deb555e 100644 --- a/recipes/bioconductor-enmcb/meta.yaml +++ b/recipes/bioconductor-enmcb/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "EnMCB" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Creation of the correlated blocks using DNA methylation profiles. Machine learning models can be constructed to predict differentially methylated blocks and disease progression. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f9fee363d9285ffdf2895062fc0cf26b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-enmcb", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SummarizedExperiment, testthat, Biobase, survminer, affycoretools, knitr, plotROC, limma, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base - r-boot - r-e1071 @@ -36,7 +38,7 @@ requirements: - r-survivalroc - r-survivalsvm run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base - r-boot - r-e1071 @@ -49,13 +51,16 @@ requirements: - r-survival - r-survivalroc - r-survivalsvm + +source: + md5: 8ffa6ebe8f3a3038947a7a113cb601ca + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models' - description: 'Creation of the correlated blocks using DNA methylation profiles. Machine learning models can be constructed to predict differentially methylated blocks and disease progression.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-enmix/meta.yaml b/recipes/bioconductor-enmix/meta.yaml index d38d91df9f69a..e6c3268c9e165 100644 --- a/recipes/bioconductor-enmix/meta.yaml +++ b/recipes/bioconductor-enmix/meta.yaml @@ -1,38 +1,40 @@ -{% set version = "1.38.01" %} +{% set version = "1.42.0" %} {% set name = "ENmix" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for quanlity control, analysis and visulization of Illumina DNA methylation array data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Quality control and analysis tools for Illumina DNA methylation BeadChip -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ac8861e8c3ad067b1baa266958227cd build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-enmix", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: minfiData, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: + host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-geneplotter >=1.80.0,<1.81.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-geneplotter >=1.84.0,<1.85.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-doparallel - r-dynamictreecut @@ -43,18 +45,19 @@ requirements: - r-matrixstats - r-quadprog - r-rpmm + run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-geneplotter >=1.80.0,<1.81.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-geneplotter >=1.84.0,<1.85.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-doparallel - r-dynamictreecut @@ -65,12 +68,16 @@ requirements: - r-matrixstats - r-quadprog - r-rpmm + +source: + md5: 656f87e801362779b919ff4f8a81e6de + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Quality control and analysis tools for Illumina DNA methylation BeadChip' - description: 'Tools for quanlity control, analysis and visulization of Illumina DNA methylation array data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-enrichdo/build.sh b/recipes/bioconductor-enrichdo/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-enrichdo/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-enrichdo/meta.yaml b/recipes/bioconductor-enrichdo/meta.yaml new file mode 100644 index 0000000000000..190188b67f4a8 --- /dev/null +++ b/recipes/bioconductor-enrichdo/meta.yaml @@ -0,0 +1,72 @@ +{% set version = "1.0.0" %} +{% set name = "EnrichDO" %} +{% set bioc = "3.20" %} + +about: + description: To implement disease ontology (DO) enrichment analysis, this package is designed and presents a double weighted model based on the latest annotations of the human genome with DO terms, by integrating the DO graph topology on a global scale. This package exhibits high accuracy that it can identify more specific DO terms, which alleviates the over enriched problem. The package includes various statistical models and visualization schemes for discovering the associations between genes and diseases from biological big data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: a Global Weighted Model for Disease Ontology Enrichment Analysis + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-enrichdo", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, org.Hs.eg.db, testthat (>= 3.0.0), BiocStyle +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-dplyr + - r-ggplot2 + - r-hash + - r-magrittr + - r-pheatmap + - r-purrr + - r-rcolorbrewer + - r-readr + - r-stringr + - r-tidyr + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-dplyr + - r-ggplot2 + - r-hash + - r-magrittr + - r-pheatmap + - r-purrr + - r-rcolorbrewer + - r-readr + - r-stringr + - r-tidyr + +source: + md5: 76c2dbebc8d829a78054c6591f81266a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-enrichedheatmap/build_failure.osx-64.yaml b/recipes/bioconductor-enrichedheatmap/build_failure.osx-64.yaml deleted file mode 100644 index a339ea97f8532..0000000000000 --- a/recipes/bioconductor-enrichedheatmap/build_failure.osx-64.yaml +++ /dev/null @@ -1,6 +0,0 @@ -recipe_sha: 9a6c8d621c8da5f9299d5af966645abebfcfa7fd1cab2bbd703ca5e6f763fec7 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -reason: |- - 11:47:03 BIOCONDA INFO (ERR) dyld[20647]: Library not loaded: '@rpath/libtapi.dylib' 11:47:03 BIOCONDA INFO (ERR) Referenced from: '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-609-h0fd476b_15/bin/x86_64-apple-darwin13.4.0-ld' 11:47:03 BIOCONDA INFO (ERR) Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-609-h0fd476b_15/bin/../lib/libtapi.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-609-h0fd476b_15/bin/../lib/libtapi.dylib' (no such file), '/usr/local/lib/libtapi.dylib' (no such file), '/usr/lib/libtapi.dylib' (no such file) 11:47:03 BIOCONDA INFO (ERR) clang-15: error: unable to execute command: Abort trap: 6 11:47:03 BIOCONDA INFO (ERR) clang-15: error: linker command failed due to signal (use -v to see invocation) -category: |- - compiler error diff --git a/recipes/bioconductor-enrichedheatmap/meta.yaml b/recipes/bioconductor-enrichedheatmap/meta.yaml index 87efa37d244c1..cab9746b04dee 100644 --- a/recipes/bioconductor-enrichedheatmap/meta.yaml +++ b/recipes/bioconductor-enrichedheatmap/meta.yaml @@ -1,31 +1,37 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "EnrichedHeatmap" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. Here we implement enriched heatmap by ComplexHeatmap package. Since this type of heatmap is just a normal heatmap but with some special settings, with the functionality of ComplexHeatmap, it would be much easier to customize the heatmap as well as concatenating to a list of heatmaps to show correspondance between different data sources. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Making Enriched Heatmaps -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 269aeb6d749072508069805663216dc4 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-enrichedheatmap", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter, RColorBrewer requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - - 'r-circlize >=0.4.5' + - r-circlize >=0.4.5 - r-getoptlong - r-locfit - r-matrixstats @@ -33,26 +39,25 @@ requirements: - libblas - liblapack run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - - 'r-circlize >=0.4.5' + - r-circlize >=0.4.5 - r-getoptlong - r-locfit - r-matrixstats - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 13e7e9874c4f2dc40e48d2d8235d37b8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Making Enriched Heatmaps' - description: 'Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. Here we implement enriched heatmap by ComplexHeatmap package. Since this type of heatmap is just a normal heatmap but with some special settings, with the functionality of ComplexHeatmap, it would be much easier to customize the heatmap as well as concatenating to a list of heatmaps to show correspondance between different data sources.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-enrichmentbrowser/meta.yaml b/recipes/bioconductor-enrichmentbrowser/meta.yaml index b55ecad92a7c4..aa81201fc4c43 100644 --- a/recipes/bioconductor-enrichmentbrowser/meta.yaml +++ b/recipes/bioconductor-enrichmentbrowser/meta.yaml @@ -1,77 +1,83 @@ -{% set version = "2.32.0" %} +{% set version = "2.36.0" %} {% set name = "EnrichmentBrowser" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. The analysis combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Seamless navigation through combined results of set-based and network-based enrichment analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fa4ec5a19513178896d60057a26ec6ce build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-enrichmentbrowser", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-enrichmentbrowser + path: recipes/bioconductor-enrichmentbrowser + version: 2.10.11 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools, airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr, rmarkdown, statmod requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-graphite >=1.48.0,<1.49.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-pathview >=1.42.0,<1.43.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-safe >=3.42.0,<3.43.0' - - 'bioconductor-spia >=2.54.0,<2.55.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-graphite >=1.52.0,<1.53.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-pathview >=1.46.0,<1.47.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-safe >=3.46.0,<3.47.0 + - bioconductor-spia >=2.58.0,<2.59.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-biocmanager - r-hwriter run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-graphite >=1.48.0,<1.49.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-pathview >=1.42.0,<1.43.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-safe >=3.42.0,<3.43.0' - - 'bioconductor-spia >=2.54.0,<2.55.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-graphite >=1.52.0,<1.53.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-pathview >=1.46.0,<1.47.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-safe >=3.46.0,<3.47.0 + - bioconductor-spia >=2.58.0,<2.59.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-biocmanager - r-hwriter + +source: + md5: 7df62f32d727300cf5941fe822abaf2f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Seamless navigation through combined results of set-based and network-based enrichment analysis' - description: 'The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. The analysis combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.' -extra: - parent_recipe: - name: bioconductor-enrichmentbrowser - path: recipes/bioconductor-enrichmentbrowser - version: 2.10.11 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-enrichplot/meta.yaml b/recipes/bioconductor-enrichplot/meta.yaml index 60ac7b0cc9d3b..96e917d3d13cc 100644 --- a/recipes/bioconductor-enrichplot/meta.yaml +++ b/recipes/bioconductor-enrichplot/meta.yaml @@ -1,36 +1,44 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.1" %} {% set name = "enrichplot" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The 'enrichplot' package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis. It is mainly designed to work with the 'clusterProfiler' package suite. All the visualization methods are developed based on 'ggplot2' graphics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Visualization of Functional Enrichment Result -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4accfec43292c11ec0165092f3266ac2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-enrichplot", max_pin="x.x") }}' - noarch: generic -# Suggests: clusterProfiler, dplyr, europepmc, ggupset, knitr, rmarkdown, org.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, AnnotationDbi, ggplotify, ggridges, grDevices, gridExtra, ggrepel (>= 0.9.0), ggstar, scales, ggtreeExtra, tidydr + +extra: + parent_recipe: + name: bioconductor-enrichplot + path: recipes/bioconductor-enrichplot + version: 1.0.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: clusterProfiler, dplyr, europepmc, ggarchery, ggupset, knitr, rmarkdown, org.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, ggHoriPlot, AnnotationDbi, ggplotify, ggridges, grDevices, gridExtra, ggstar, scales, ggtreeExtra, tidydr requirements: host: - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - - 'r-aplot >=0.2.1' + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-gosemsim >=2.32.0,<2.33.0 + - r-aplot >=0.2.1 - r-base - - 'r-ggfun >=0.1.3' + - r-ggfun >=0.1.7 - r-ggnewscale - r-ggplot2 - - r-ggraph + - r-ggrepel >=0.9.0 + - r-ggtangle >=0.0.4 - r-igraph - r-magrittr - r-plyr @@ -39,18 +47,18 @@ requirements: - r-reshape2 - r-rlang - r-scatterpie - - r-shadowtext - - 'r-yulab.utils >=0.0.8' + - r-yulab.utils >=0.1.6 run: - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - - 'r-aplot >=0.2.1' + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-gosemsim >=2.32.0,<2.33.0 + - r-aplot >=0.2.1 - r-base - - 'r-ggfun >=0.1.3' + - r-ggfun >=0.1.7 - r-ggnewscale - r-ggplot2 - - r-ggraph + - r-ggrepel >=0.9.0 + - r-ggtangle >=0.0.4 - r-igraph - r-magrittr - r-plyr @@ -59,19 +67,17 @@ requirements: - r-reshape2 - r-rlang - r-scatterpie - - r-shadowtext - - 'r-yulab.utils >=0.0.8' + - r-yulab.utils >=0.1.6 + +source: + md5: b39875381ca4d8a349acc632e1c369ab + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Visualization of Functional Enrichment Result' - description: 'The ''enrichplot'' package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis. It is mainly designed to work with the ''clusterProfiler'' package suite. All the visualization methods are developed based on ''ggplot2'' graphics.' -extra: - parent_recipe: - name: bioconductor-enrichplot - path: recipes/bioconductor-enrichplot - version: 1.0.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-enrichviewnet/meta.yaml b/recipes/bioconductor-enrichviewnet/meta.yaml index 853b3336dc8e7..be31d3d32d88d 100644 --- a/recipes/bioconductor-enrichviewnet/meta.yaml +++ b/recipes/bioconductor-enrichviewnet/meta.yaml @@ -1,48 +1,55 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "enrichViewNet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package enables the visualization of functional enrichment results as network graphs. First the package enables the visualization of enrichment results, in a format corresponding to the one generated by gprofiler2, as a customizable Cytoscape network. In those networks, both gene datasets (GO terms/pathways/protein complexes) and genes associated to the datasets are represented as nodes. While the edges connect each gene to its dataset(s). The package also provides the option to create enrichment maps from functional enrichment results. Enrichment maps enable the visualization of enriched terms into a network with edges connecting overlapping genes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: From functional enrichment results to biological networks -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b2eb51ee4f57abd3b77da182e7e5d1a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-enrichviewnet", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, testthat + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, ggplot2, testthat, magick requirements: host: - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 - r-base - r-gprofiler2 - r-jsonlite - r-strex - r-stringr run: - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 - r-base - r-gprofiler2 - r-jsonlite - r-strex - r-stringr + +source: + md5: 24bfac4e66bb94854260dd6a535e7c6e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'From functional enrichment results to biological networks' - description: 'This package enables the visualization of functional enrichment results as network graphs. First the package enables the visualization of enrichment results, in a format corresponding to the one generated by gprofiler2, as a customizable Cytoscape network. In those networks, both gene datasets (GO terms/pathways/protein complexes) and genes associated to the datasets are represented as nodes. While the edges connect each gene to its dataset(s). The package also provides the option to create enrichment maps from functional enrichment results. Enrichment maps enable the visualization of enriched terms into a network with edges connecting overlapping genes.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml b/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml index e9d78eb695b76..b372e543ae675 100644 --- a/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml +++ b/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml @@ -1,44 +1,44 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Hsapiens.v75" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6c896475252903972bfc6c0eb0d8f334 +about: + description: Exposes an annotation databases generated from Ensembl. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Ensembl based annotation package build: - number: 15 + noarch: generic + number: 16 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ensdb.hsapiens.v75", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-ensdb.hsapiens.v75 + path: recipes/bioconductor-ensdb.hsapiens.v75 + version: 2.99.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - bioconductor-ensembldb >=2.30.0,<2.31.0 - r-base run: - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - bioconductor-ensembldb >=2.30.0,<2.31.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6c896475252903972bfc6c0eb0d8f334 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Ensembl based annotation package' - description: 'Exposes an annotation databases generated from Ensembl.' -extra: - parent_recipe: - name: bioconductor-ensdb.hsapiens.v75 - path: recipes/bioconductor-ensdb.hsapiens.v75 - version: 2.99.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ensdb.hsapiens.v79/meta.yaml b/recipes/bioconductor-ensdb.hsapiens.v79/meta.yaml index 1ba0892011aad..e49ac14bdd8c1 100644 --- a/recipes/bioconductor-ensdb.hsapiens.v79/meta.yaml +++ b/recipes/bioconductor-ensdb.hsapiens.v79/meta.yaml @@ -1,39 +1,39 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Hsapiens.v79" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 16b5629805c07649b2aa501d34fcc588 +about: + description: Exposes an annotation databases generated from Ensembl. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Ensembl based annotation package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ensdb.hsapiens.v79", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - bioconductor-ensembldb >=2.30.0,<2.31.0 - r-base run: - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - bioconductor-ensembldb >=2.30.0,<2.31.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 16b5629805c07649b2aa501d34fcc588 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Ensembl based annotation package' - description: 'Exposes an annotation databases generated from Ensembl.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ensdb.hsapiens.v86/meta.yaml b/recipes/bioconductor-ensdb.hsapiens.v86/meta.yaml index f91361ab9fb38..5745eabc044a4 100644 --- a/recipes/bioconductor-ensdb.hsapiens.v86/meta.yaml +++ b/recipes/bioconductor-ensdb.hsapiens.v86/meta.yaml @@ -1,39 +1,39 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Hsapiens.v86" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0c9e52512ff6dbbbdb754c4d41149939 +about: + description: Exposes an annotation databases generated from Ensembl. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Ensembl based annotation package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ensdb.hsapiens.v86", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - bioconductor-ensembldb >=2.30.0,<2.31.0 - r-base run: - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - bioconductor-ensembldb >=2.30.0,<2.31.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0c9e52512ff6dbbbdb754c4d41149939 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Ensembl based annotation package' - description: 'Exposes an annotation databases generated from Ensembl.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ensdb.mmusculus.v75/meta.yaml b/recipes/bioconductor-ensdb.mmusculus.v75/meta.yaml index 53552d68e3b42..e21ddf6502e63 100644 --- a/recipes/bioconductor-ensdb.mmusculus.v75/meta.yaml +++ b/recipes/bioconductor-ensdb.mmusculus.v75/meta.yaml @@ -1,39 +1,39 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Mmusculus.v75" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 081bf6f90ff77031b634b4fe32e00be8 +about: + description: Exposes an annotation databases generated from Ensembl. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Ensembl based annotation package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ensdb.mmusculus.v75", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - bioconductor-ensembldb >=2.30.0,<2.31.0 - r-base run: - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - bioconductor-ensembldb >=2.30.0,<2.31.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 081bf6f90ff77031b634b4fe32e00be8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Ensembl based annotation package' - description: 'Exposes an annotation databases generated from Ensembl.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ensdb.mmusculus.v79/meta.yaml b/recipes/bioconductor-ensdb.mmusculus.v79/meta.yaml index b07f2e2eb5bd1..8530ff257837f 100644 --- a/recipes/bioconductor-ensdb.mmusculus.v79/meta.yaml +++ b/recipes/bioconductor-ensdb.mmusculus.v79/meta.yaml @@ -1,39 +1,39 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Mmusculus.v79" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 28bbab743b0d2d550dbfa0bcd3274fad +about: + description: Exposes an annotation databases generated from Ensembl. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Ensembl based annotation package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ensdb.mmusculus.v79", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - bioconductor-ensembldb >=2.30.0,<2.31.0 - r-base run: - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - bioconductor-ensembldb >=2.30.0,<2.31.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 28bbab743b0d2d550dbfa0bcd3274fad + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Ensembl based annotation package' - description: 'Exposes an annotation databases generated from Ensembl.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ensdb.rnorvegicus.v75/meta.yaml b/recipes/bioconductor-ensdb.rnorvegicus.v75/meta.yaml index a89441fa23d47..98e4868deb4a2 100644 --- a/recipes/bioconductor-ensdb.rnorvegicus.v75/meta.yaml +++ b/recipes/bioconductor-ensdb.rnorvegicus.v75/meta.yaml @@ -1,39 +1,39 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Rnorvegicus.v75" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 40ff53b41aa6fad0d5bd15f9c6f3bad8 +about: + description: Exposes an annotation databases generated from Ensembl. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Ensembl based annotation package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ensdb.rnorvegicus.v75", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - bioconductor-ensembldb >=2.30.0,<2.31.0 - r-base run: - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - bioconductor-ensembldb >=2.30.0,<2.31.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 40ff53b41aa6fad0d5bd15f9c6f3bad8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Ensembl based annotation package' - description: 'Exposes an annotation databases generated from Ensembl.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ensdb.rnorvegicus.v79/meta.yaml b/recipes/bioconductor-ensdb.rnorvegicus.v79/meta.yaml index 5646d093a9d17..b0eede4b7e5f7 100644 --- a/recipes/bioconductor-ensdb.rnorvegicus.v79/meta.yaml +++ b/recipes/bioconductor-ensdb.rnorvegicus.v79/meta.yaml @@ -1,39 +1,39 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Rnorvegicus.v79" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7d305bd0d1a073bd8c60063ae210a7a9 +about: + description: Exposes an annotation databases generated from Ensembl. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Ensembl based annotation package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ensdb.rnorvegicus.v79", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - bioconductor-ensembldb >=2.30.0,<2.31.0 - r-base run: - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' + - bioconductor-ensembldb >=2.30.0,<2.31.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7d305bd0d1a073bd8c60063ae210a7a9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Ensembl based annotation package' - description: 'Exposes an annotation databases generated from Ensembl.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ensembldb/meta.yaml b/recipes/bioconductor-ensembldb/meta.yaml index c421d63cd8558..bea95d7a1f816 100644 --- a/recipes/bioconductor-ensembldb/meta.yaml +++ b/recipes/bioconductor-ensembldb/meta.yaml @@ -1,77 +1,83 @@ -{% set version = "2.26.0" %} +{% set version = "2.30.0" %} {% set name = "ensembldb" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Utilities to create and use Ensembl-based annotation databases -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0ad7a33ad9592f54e39d647195aa4c91 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ensembldb", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:ensembldb + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ensembldb + path: recipes/bioconductor-ensembldb + version: 2.4.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), rmarkdown, AnnotationHub requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-curl - r-dbi - - 'r-rsqlite >=1.1' + - r-rsqlite >=1.1 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-curl - r-dbi - - 'r-rsqlite >=1.1' + - r-rsqlite >=1.1 + +source: + md5: 4e6f2211c1cfbcf026fd4302a42d8912 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Utilities to create and use Ensembl-based annotation databases' - description: 'The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:ensembldb - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-ensembldb - path: recipes/bioconductor-ensembldb - version: 2.4.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epialleler/meta.yaml b/recipes/bioconductor-epialleler/meta.yaml index c3950d568d811..ebac587741605 100644 --- a/recipes/bioconductor-epialleler/meta.yaml +++ b/recipes/bioconductor-epialleler/meta.yaml @@ -1,62 +1,61 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "epialleleR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls and reports cytosine methylation as well as frequencies of hypermethylated epialleles at the level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map (BAM) files as an input. Among other things, this package can also extract and visualise methylation patterns and assess allele specificity of methylation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Fast, Epiallele-Aware Methylation Caller and Reporter -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cbe73c32dc61dac41266279db72e4bee build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epialleler", max_pin="x.x") }}' -# Suggests: RUnit, knitr, rmarkdown, ggplot2, ggstance, gridExtra + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: GenomeInfoDb, SummarizedExperiment, VariantAnnotation, RUnit, knitr, rmarkdown, ggplot2 # SystemRequirements: C++17, GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 - r-base - r-bh - r-data.table - r-rcpp - libblas - liblapack + - zlib + - liblzma-devel run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 - r-base - r-bh - r-data.table - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 4bfbef7adb6ed8da885b81a9b72335ca + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Fast, Epiallele-Aware Methylation Caller and Reporter' - description: 'Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls and reports cytosine methylation as well as frequencies of hypermethylated epialleles at the level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map (BAM) files as an input. Among other things, this package can also extract methylation patterns and assess allele specificity of methylation.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epicompare/meta.yaml b/recipes/bioconductor-epicompare/meta.yaml index e5f51032100d4..bad34d063a9db 100644 --- a/recipes/bioconductor-epicompare/meta.yaml +++ b/recipes/bioconductor-epicompare/meta.yaml @@ -1,70 +1,74 @@ -{% set version = "1.4.0" %} +{% set version = "1.10.0" %} {% set name = "EpiCompare" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: 'EpiCompare is used to compare and analyse epigenetic datasets for quality control and benchmarking purposes. The package outputs an HTML report consisting of three sections: (1. General metrics) Metrics on peaks (percentage of blacklisted and non-standard peaks, and peak widths) and fragments (duplication rate) of samples, (2. Peak overlap) Percentage and statistical significance of overlapping and non-overlapping peaks. Also includes upset plot and (3. Functional annotation) functional annotation (ChromHMM, ChIPseeker and enrichment analysis) of peaks. Also includes peak enrichment around TSS.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Comparison, Benchmarking & QC of Epigenomic Datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d3fe802aa6ce051dc5594ee151e574a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic -# Suggests: rworkflows, BiocFileCache, BiocParallel, BiocStyle, clusterProfiler, GenomicAlignments, grDevices, htmlwidgets, knitr, org.Hs.eg.db, testthat (>= 3.0.0), tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, ComplexUpset, plyranges, scales, Matrix, consensusSeekeR, heatmaply, viridis + run_exports: '{{ pin_subpackage("bioconductor-epicompare", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: rworkflows, BiocFileCache, BiocParallel, BiocStyle, clusterProfiler, GenomicAlignments, grDevices, knitr, org.Hs.eg.db, testthat (>= 3.0.0), tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, ComplexUpset, plyranges, scales, Matrix, consensusSeekeR, heatmaply, viridis requirements: host: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-brgenomics >=1.12.0,<1.13.0' - - 'bioconductor-chipseeker >=1.36.0,<1.37.0' - - 'bioconductor-genomation >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-chipseeker >=1.42.0,<1.43.0 + - bioconductor-genomation >=1.38.0,<1.39.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-data.table - r-downloadthis - - r-ggplot2 + - r-ggplot2 >=3.5.0 - r-htmltools - r-plotly - r-reshape2 - r-rmarkdown - r-stringr run: - - 'bioconductor-annotationhub >=3.8.0,<3.9.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-brgenomics >=1.12.0,<1.13.0' - - 'bioconductor-chipseeker >=1.36.0,<1.37.0' - - 'bioconductor-genomation >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.60.0,<1.61.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-chipseeker >=1.42.0,<1.43.0 + - bioconductor-genomation >=1.38.0,<1.39.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-data.table - r-downloadthis - - r-ggplot2 + - r-ggplot2 >=3.5.0 - r-htmltools - r-plotly - r-reshape2 - r-rmarkdown - r-stringr + +source: + md5: 43fa9bd01394be7668434ee655901dad + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Comparison, Benchmarking & QC of Epigenomic Datasets' - description: 'EpiCompare is used to compare and analyse epigenetic datasets for quality control and benchmarking purposes. The package outputs an HTML report consisting of three sections: (1. General metrics) Metrics on peaks (percentage of blacklisted and non-standard peaks, and peak widths) and fragments (duplication rate) of samples, (2. Peak overlap) Percentage and statistical significance of overlapping and non-overlapping peaks. Also includes upset plot and (3. Functional annotation) functional annotation (ChromHMM, ChIPseeker and enrichment analysis) of peaks. Also includes peak enrichment around TSS.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epidecoder/meta.yaml b/recipes/bioconductor-epidecoder/meta.yaml index c322d6f121c8b..438ce0843f768 100644 --- a/recipes/bioconductor-epidecoder/meta.yaml +++ b/recipes/bioconductor-epidecoder/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "epidecodeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: epidecodeR is a package capable of analysing impact of degree of DNA/RNA epigenetic chemical modifications on dysregulation of genes or proteins. This package integrates chemical modification data generated from a host of epigenomic or epitranscriptomic techniques such as ChIP-seq, ATAC-seq, m6A-seq, etc. and dysregulated gene lists in the form of differential gene expression, ribosome occupancy or differential protein translation and identify impact of dysregulation of genes caused due to varying degrees of chemical modifications associated with the genes. epidecodeR generates cumulative distribution function (CDF) plots showing shifts in trend of overall log2FC between genes divided into groups based on the degree of modification associated with the genes. The tool also tests for significance of difference in log2FC between groups of genes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 409ed7c959818b7400944e1d20653f68 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epidecoder", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-dplyr - r-envstats @@ -32,22 +34,25 @@ requirements: - r-ggpubr - r-rstatix run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-dplyr - r-envstats - r-ggplot2 - r-ggpubr - r-rstatix + +source: + md5: df73afdcff0bc97e8d155b692eecb61e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation' - description: 'epidecodeR is a package capable of analysing impact of degree of DNA/RNA epigenetic chemical modifications on dysregulation of genes or proteins. This package integrates chemical modification data generated from a host of epigenomic or epitranscriptomic techniques such as ChIP-seq, ATAC-seq, m6A-seq, etc. and dysregulated gene lists in the form of differential gene expression, ribosome occupancy or differential protein translation and identify impact of dysregulation of genes caused due to varying degrees of chemical modifications associated with the genes. epidecodeR generates cumulative distribution function (CDF) plots showing shifts in trend of overall log2FC between genes divided into groups based on the degree of modification associated with the genes. The tool also tests for significance of difference in log2FC between groups of genes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epidish/meta.yaml b/recipes/bioconductor-epidish/meta.yaml index 5ae9b8411ac2a..d8b41c29a9458 100644 --- a/recipes/bioconductor-epidish/meta.yaml +++ b/recipes/bioconductor-epidish/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "2.18.0" %} +{% set version = "2.22.0" %} {% set name = "EpiDISH" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: EpiDISH is a R package to infer the proportions of a priori known cell-types present in a sample representing a mixture of such cell-types. Right now, the package can be used on DNAm data of whole blood, generic epithelial tissue and breast tissue. Besides, the package provides a function that allows the identification of differentially methylated cell-types and their directionality of change in Epigenome-Wide Association Studies. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Epigenetic Dissection of Intra-Sample-Heterogeneity -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: db7b5d2165fad653dabc1bfd8faeab83 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epidish", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat requirements: host: @@ -39,13 +41,16 @@ requirements: - r-matrixstats - r-quadprog - r-stringr + +source: + md5: 0cdee5ee225c0101a6a65342b98d010c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Epigenetic Dissection of Intra-Sample-Heterogeneity' - description: 'EpiDISH is a R package to infer the proportions of a priori known cell-types present in a sample representing a mixture of such cell-types. Right now, the package can be used on DNAm data of whole blood, generic epithelial tissue and breast tissue. Besides, the package provides a function that allows the identification of differentially methylated cell-types and their directionality of change in Epigenome-Wide Association Studies.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epigenomix/meta.yaml b/recipes/bioconductor-epigenomix/meta.yaml index 44a46bcbbb2a0..1f82b4c9afdac 100644 --- a/recipes/bioconductor-epigenomix/meta.yaml +++ b/recipes/bioconductor-epigenomix/meta.yaml @@ -1,63 +1,69 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "epigenomix" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package for the integrative analysis of RNA-seq or microarray based gene transcription and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Epigenetic and gene transcription data normalization and integration with mixture models -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eef6318b8b342675c1fdd4c99ed541e8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epigenomix", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:epigenomix + parent_recipe: + name: bioconductor-epigenomix + path: recipes/bioconductor-epigenomix + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-beadarray >=2.52.0,<2.53.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-beadarray >=2.56.0,<2.57.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-mcmcpack run: - - 'bioconductor-beadarray >=2.52.0,<2.53.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-beadarray >=2.56.0,<2.57.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-mcmcpack + +source: + md5: a7046c9b26598dec36381afa98854f48 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'Epigenetic and gene transcription data normalization and integration with mixture models' - description: 'A package for the integrative analysis of RNA-seq or microarray based gene transcription and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:epigenomix - parent_recipe: - name: bioconductor-epigenomix - path: recipes/bioconductor-epigenomix - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epigrahmm/build_failure.linux-64.yaml b/recipes/bioconductor-epigrahmm/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..6bb651139a2cf --- /dev/null +++ b/recipes/bioconductor-epigrahmm/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: feea3fae87c1b361c276813022a8b4a05040eb2290bee5a5d73f13a9e6f9dc94 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-epigrahmm-1.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-epigrahmm-1.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-epigrahmm-1.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-epigrahmm-1.14.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-epigrahmm_1735620789774/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library + * installing *source* package epigraHMM ... + ** package epigraHMM successfully unpacked and MD5 sums checked + ** using staged installation + ** libs + using C compiler: x86_64-conda-linux-gnu-c (conda-forge gcc 13.3.0-1) 13.3.0 + using C11 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -DARMA_USE_HDF5 -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -DARMA_USE_HDF5 -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c aggregate.cpp -o aggregate.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -DARMA_USE_HDF5 -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c computeBIC.cpp -o computeBIC.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -DARMA_USE_HDF5 -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c computeQFunction.cpp -o computeQFunction.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -DARMA_USE_HDF5 -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c computeViterbiSequence.cpp -o computeViterbiSequence.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -DARMA_USE_HDF5 -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c consensusRejectionControlled.cpp -o consensusRejectionControlled.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -DARMA_USE_HDF5 -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c differentialRejectionControlled.cpp -o differentialRejectionControlled.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -DARMA_USE_HDF5 -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c expStep.cpp -o expStep.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -DARMA_USE_HDF5 -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c getMarginalProbability.cpp -o getMarginalProbability.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -DARMA_USE_HDF5 -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c innerMaxStepProb.cpp -o innerMaxStepProb.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -DARMA_USE_HDF5 -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c maxStepProb.cpp -o maxStepProb.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -DARMA_USE_HDF5 -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c rbinomVectorized.cpp -o rbinomVectorized.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -DARMA_USE_HDF5 -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c reweight.cpp -o reweight.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/Rhdf5lib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -DARMA_USE_HDF5 -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c simulateMarkovChain.cpp -o simulateMarkovChain.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -shared -L$PREFIX/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -o epigraHMM.so RcppExports.o aggregate.o computeBIC.o computeQFunction.o computeViterbiSequence.o consensusRejectionControlled.o differentialRejectionControlled.o expStep.o getMarginalProbability.o innerMaxStepProb.o maxStepProb.o rbinomVectorized.o reweight.o simulateMarkovChain.o $PREFIX/lib/R/library/Rhdf5lib/lib/libhdf5_cpp.a $PREFIX/lib/R/library/Rhdf5lib/lib/libhdf5.a -L$PREFIX/lib/R/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L$PREFIX/lib/R/lib -lR + /opt/conda/conda-bld/bioconductor-epigrahmm_1735620789774/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lz: No such file or directory + collect2: error: ld returned 1 exit status + make: *** [/opt/conda/conda-bld/bioconductor-epigrahmm_1735620789774/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/share/make/shlib.mk:10: epigraHMM.so] Error 1 + ERROR: compilation failed for package epigraHMM + * removing /opt/conda/conda-bld/bioconductor-epigrahmm_1735620789774/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/epigraHMM + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-epigrahmm_1735620789774/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-epigrahmm_1735620789774/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-epigrahmm/meta.yaml b/recipes/bioconductor-epigrahmm/meta.yaml index 6ac28075e8219..624eaa684945c 100644 --- a/recipes/bioconductor-epigrahmm/meta.yaml +++ b/recipes/bioconductor-epigrahmm/meta.yaml @@ -1,40 +1,48 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "epigraHMM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. It contains two separate peak callers, one for consensus peaks from biological or technical replicates, and one for differential peaks from multi-replicate multi-condition experiments. In differential peak calling, epigraHMM provides window-specific posterior probabilities associated with every possible combinatorial pattern of read enrichment across conditions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Epigenomic R-based analysis with hidden Markov models -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c86fa9edec93550acae520d84420b88 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epigrahmm", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocStyle, BSgenome.Rnorvegicus.UCSC.rn4, gcapc, chromstaRData # SystemRequirements: GNU make requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-bamsignals >=1.34.0,<1.35.0' - - 'bioconductor-csaw >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-greylistchip >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-bamsignals >=1.38.0,<1.39.0 + - bioconductor-csaw >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-greylistchip >=1.38.0,<1.39.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-ggplot2 @@ -48,20 +56,21 @@ requirements: - r-scales - libblas - liblapack + run: - - 'bioconductor-bamsignals >=1.34.0,<1.35.0' - - 'bioconductor-csaw >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-greylistchip >=1.34.0,<1.35.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-bamsignals >=1.38.0,<1.39.0 + - bioconductor-csaw >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-greylistchip >=1.38.0,<1.39.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-ggplot2 @@ -73,17 +82,16 @@ requirements: - r-rcpp - r-rcpparmadillo - r-scales - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 6d9e1195bcf7500a41b6de80b212b3d0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Epigenomic R-based analysis with hidden Markov models' - description: 'epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. It contains two separate peak callers, one for consensus peaks from biological or technical replicates, and one for differential peaks from multi-replicate multi-condition experiments. In differential peak calling, epigraHMM provides window-specific posterior probabilities associated with every possible combinatorial pattern of read enrichment across conditions.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epimix.data/meta.yaml b/recipes/bioconductor-epimix.data/meta.yaml index 38d41a4d5a840..e0674ff7e1c01 100644 --- a/recipes/bioconductor-epimix.data/meta.yaml +++ b/recipes/bioconductor-epimix.data/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "EpiMix.data" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 52c386f6828945121acfca44eabb7827 +about: + description: 'Supporting data for the EpiMix R package. It include: - HM450_lncRNA_probes.rda - HM450_miRNA_probes.rda - EPIC_lncRNA_probes.rda - EPIC_miRNA_probes.rda - EpigenomeMap.rda - LUAD.sample.annotation - TCGA_BatchData - MET.data - mRNA.data - microRNA.data - lncRNA.data - Sample_EpiMixResults_lncRNA - Sample_EpiMixResults_miRNA - Sample_EpiMixResults_Regular - Sample_EpiMixResults_Enhancer - lncRNA expression data of tumors from TCGA that are stored in the ExperimentHub.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Data for the EpiMix package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epimix.data", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: rmarkdown, knitr requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 64dd6bc27966ef5920f06823dcc4af94 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Data for the EpiMix package' - description: 'Supporting data for the EpiMix R package. It include: - HM450_lncRNA_probes.rda - HM450_miRNA_probes.rda - EPIC_lncRNA_probes.rda - EPIC_miRNA_probes.rda - EpigenomeMap.rda - LUAD.sample.annotation - TCGA_BatchData - MET.data - mRNA.data - microRNA.data - lncRNA.data - Sample_EpiMixResults_lncRNA - Sample_EpiMixResults_miRNA - Sample_EpiMixResults_Regular - Sample_EpiMixResults_Enhancer - lncRNA expression data of tumors from TCGA that are stored in the ExperimentHub.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epimix.data/post-link.sh b/recipes/bioconductor-epimix.data/post-link.sh index 62d257d916df8..05fd2cf64ca34 100644 --- a/recipes/bioconductor-epimix.data/post-link.sh +++ b/recipes/bioconductor-epimix.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "epimix.data-1.4.0" +installBiocDataPackage.sh "epimix.data-1.8.0" diff --git a/recipes/bioconductor-epimix/meta.yaml b/recipes/bioconductor-epimix/meta.yaml index 2f933593dc46b..4caeda6b88081 100644 --- a/recipes/bioconductor-epimix/meta.yaml +++ b/recipes/bioconductor-epimix/meta.yaml @@ -1,42 +1,45 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "EpiMix" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: EpiMix is a comprehensive tool for the integrative analysis of high-throughput DNA methylation data and gene expression data. EpiMix enables automated data downloading (from TCGA or GEO), preprocessing, methylation modeling, interactive visualization and functional annotation.To identify hypo- or hypermethylated CpG sites across physiological or pathological conditions, EpiMix uses a beta mixture modeling to identify the methylation states of each CpG probe and compares the methylation of the experimental group to the control group.The output from EpiMix is the functional DNA methylation that is predictive of gene expression. EpiMix incorporates specialized algorithms to identify functional DNA methylation at various genetic elements, including proximal cis-regulatory elements of protein-coding genes, distal enhancers, and genes encoding microRNAs and lncRNAs. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'EpiMix: an integrative tool for the population-level analysis of DNA methylation' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d86305c56618b7f327d0068e09ad6558 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epimix", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, clusterProfiler, GEOquery, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, multiMiR, miRBaseConverter + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, clusterProfiler, DT, GEOquery, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, multiMiR, miRBaseConverter requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-elmer.data >=2.26.0,<2.27.0' - - 'bioconductor-epimix.data >=1.4.0,<1.5.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-elmer.data >=2.30.0,<2.31.0 + - bioconductor-epimix.data >=1.8.0,<1.9.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-doparallel @@ -54,22 +57,23 @@ requirements: - r-rpmm - r-tibble - r-tidyr + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-elmer.data >=2.26.0,<2.27.0' - - 'bioconductor-epimix.data >=1.4.0,<1.5.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-elmer.data >=2.30.0,<2.31.0 + - bioconductor-epimix.data >=1.8.0,<1.9.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-doparallel @@ -87,13 +91,16 @@ requirements: - r-rpmm - r-tibble - r-tidyr + +source: + md5: 57f538e07e645b5c7599f157ef2716ad + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'EpiMix: an integrative tool for the population-level analysis of DNA methylation' - description: 'EpiMix is a comprehensive tool for the integrative analysis of high-throughput DNA methylation data and gene expression data. EpiMix enables automated data downloading (from TCGA or GEO), preprocessing, methylation modeling, interactive visualization and functional annotation.To identify hypo- or hypermethylated CpG sites across physiological or pathological conditions, EpiMix uses a beta mixture modeling to identify the methylation states of each CpG probe and compares the methylation of the experimental group to the control group.The output from EpiMix is the functional DNA methylation that is predictive of gene expression. EpiMix incorporates specialized algorithms to identify functional DNA methylation at various genetic elements, including proximal cis-regulatory elements of protein-coding genes, distal enhancers, and genes encoding microRNAs and lncRNAs.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epimutacions/meta.yaml b/recipes/bioconductor-epimutacions/meta.yaml index dec1d85892e1b..a1cfeab79408f 100644 --- a/recipes/bioconductor-epimutacions/meta.yaml +++ b/recipes/bioconductor-epimutacions/meta.yaml @@ -1,52 +1,60 @@ -{% set version = "1.6.1" %} +{% set version = "1.10.0" %} {% set name = "epimutacions" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package includes some statistical outlier detection methods for epimutations detection in DNA methylation data. The methods included in the package are MANOVA, Multivariate linear models, isolation forest, robust mahalanobis distance, quantile and beta. The methods compare a case sample with a suspected disease against a reference panel (composed of healthy individuals) to identify epimutations in the given case sample. It also contains functions to annotate and visualize the identified epimutations. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Robust outlier identification for DNA methylation data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 73fdaf9db5e5d035601282d6e5d832fd build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epimutacions", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra, methods, grDevices requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-epimutacionsdata >=1.6.0,<1.7.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-epimutacionsdata >=1.10.0,<1.11.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-homo.sapiens >=1.3.0,<1.4.0 + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0 + - bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 - r-base - r-ggplot2 - r-ggrepel @@ -59,33 +67,34 @@ requirements: - r-tibble - libblas - liblapack + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-epimutacionsdata >=1.6.0,<1.7.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-epimutacionsdata >=1.10.0,<1.11.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-homo.sapiens >=1.3.0,<1.4.0 + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0 + - bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 - r-base - r-ggplot2 - r-ggrepel @@ -96,17 +105,16 @@ requirements: - r-reshape2 - r-robustbase - r-tibble - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 30df10a44d353e8f963c72c0822682e3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Robust outlier identification for DNA methylation data' - description: 'The package includes some statistical outlier detection methods for epimutations detection in DNA methylation data. The methods included in the package are MANOVA, Multivariate linear models, isolation forest, robust mahalanobis distance, quantile and beta. The methods compare a case sample with a suspected disease against a reference panel (composed of healthy individuals) to identify epimutations in the given case sample. It also contains functions to annotate and visualize the identified epimutations.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epimutacionsdata/meta.yaml b/recipes/bioconductor-epimutacionsdata/meta.yaml index 761c0fbdf4067..0b4132a1c9259 100644 --- a/recipes/bioconductor-epimutacionsdata/meta.yaml +++ b/recipes/bioconductor-epimutacionsdata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "epimutacionsData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e2681ab8096fd0f2b7e5d8ed68928280 +about: + description: 'This package includes the data necessary to run functions and examples in epimutacions package. Collection of DNA methylation data. The package contains 2 datasets: (1) Control ( GEO: GSE104812), (GEO: GSE97362) case samples; and (2) reference panel (GEO: GSE127824). It also contains candidate regions to be epimutations in 450k methylation arrays.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Data for epimutacions package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epimutacionsdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: rmarkdown, BiocStyle, knitr, ExperimentHub, minfi requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1bb081472a039407ea2bb74f109cf1ae + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Data for epimutacions package' - description: 'This package includes the data necessary to run functions and examples in epimutacions package. Collection of DNA methylation data. The package contains 2 datasets: (1) Control ( GEO: GSE104812), (GEO: GSE97362) case samples; and (2) reference panel (GEO: GSE127824). It also contains candidate regions to be epimutations in 450k methylation arrays.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epimutacionsdata/post-link.sh b/recipes/bioconductor-epimutacionsdata/post-link.sh index 04b4600843e28..e3bfae076317c 100644 --- a/recipes/bioconductor-epimutacionsdata/post-link.sh +++ b/recipes/bioconductor-epimutacionsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "epimutacionsdata-1.6.0" +installBiocDataPackage.sh "epimutacionsdata-1.10.0" diff --git a/recipes/bioconductor-epinem/build_failure.linux-64.yaml b/recipes/bioconductor-epinem/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..5a3e79675ec8b --- /dev/null +++ b/recipes/bioconductor-epinem/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: 24cdf793e83053734bdf2a1c53006452cd683b25810aa84cced14bff5b11748a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-boutroslab.plotting.general")} + Encountered problems while solving: + - nothing provides requested r-boutroslab.plotting.general + + Could not solve for environment specs + The following package could not be installed + [31mr-boutroslab.plotting.general[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-boutroslab.plotting.general")} + Encountered problems while solving: + - nothing provides requested r-boutroslab.plotting.general + + Could not solve for environment specs + The following package could not be installed + [31mr-boutroslab.plotting.general[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-boutroslab.plotting.general")} + Encountered problems while solving: + - nothing provides requested r-boutroslab.plotting.general + + Could not solve for environment specs + The following package could not be installed + [31mr-boutroslab.plotting.general[0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. +reason: |- + needs r-bourtroslab.plotting.general added to conda-forge +category: |- + dependency issue diff --git a/recipes/bioconductor-epinem/build_failure.osx-64.yaml b/recipes/bioconductor-epinem/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..981c530061a79 --- /dev/null +++ b/recipes/bioconductor-epinem/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 24cdf793e83053734bdf2a1c53006452cd683b25810aa84cced14bff5b11748a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + needs r-bourtroslab.plotting.general added to conda-forge +category: |- + dependency issue diff --git a/recipes/bioconductor-epinem/meta.yaml b/recipes/bioconductor-epinem/meta.yaml index 704d6f0117daf..16cc483728d22 100644 --- a/recipes/bioconductor-epinem/meta.yaml +++ b/recipes/bioconductor-epinem/meta.yaml @@ -1,32 +1,35 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "epiNEM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: epiNEM is an extension of the original Nested Effects Models (NEM). EpiNEM is able to take into account double knockouts and infer more complex network signalling pathways. It is tailored towards large scale double knock-out screens. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: epiNEM -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 03702ef94f047496994ebaf19f750787 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epinem", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db, BiocStyle requirements: host: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-minet >=3.60.0,<3.61.0' - - 'bioconductor-mnem >=1.18.0,<1.19.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-minet >=3.64.0,<3.65.0 + - bioconductor-mnem >=1.22.0,<1.23.0 - r-base - r-boolnet + - r-boutroslab.plotting.general - r-e1071 - r-gtools - r-igraph @@ -36,11 +39,12 @@ requirements: - r-pcalg - r-rcolorbrewer run: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-minet >=3.60.0,<3.61.0' - - 'bioconductor-mnem >=1.18.0,<1.19.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-minet >=3.64.0,<3.65.0 + - bioconductor-mnem >=1.22.0,<1.23.0 - r-base - r-boolnet + - r-boutroslab.plotting.general - r-e1071 - r-gtools - r-igraph @@ -49,13 +53,16 @@ requirements: - r-latticeextra - r-pcalg - r-rcolorbrewer + +source: + md5: adaa278273f422c193ade7a17158f16f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: epiNEM - description: 'epiNEM is an extension of the original Nested Effects Models (NEM). EpiNEM is able to take into account double knockouts and infer more complex network signalling pathways. It is tailored towards large scale double knock-out screens.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epiregulon.extra/build.sh b/recipes/bioconductor-epiregulon.extra/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-epiregulon.extra/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-epiregulon.extra/meta.yaml b/recipes/bioconductor-epiregulon.extra/meta.yaml new file mode 100644 index 0000000000000..0868d06a6cd1a --- /dev/null +++ b/recipes/bioconductor-epiregulon.extra/meta.yaml @@ -0,0 +1,74 @@ +{% set version = "1.2.0" %} +{% set name = "epiregulon.extra" %} +{% set bioc = "3.20" %} + +about: + description: Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Companion package to epiregulon with additional plotting, differential and graph functions + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epiregulon.extra", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: epiregulon, knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), EnrichmentBrowser, msigdbr, dorothea, scMultiome, S4Vectors, scuttle, vdiffr, ggrastr, ggrepel +requirements: + host: + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-checkmate + - r-circlize + - r-ggplot2 + - r-ggraph + - r-igraph + - r-lifecycle + - r-matrix + - r-patchwork + - r-reshape2 + - r-scales + run: + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-checkmate + - r-circlize + - r-ggplot2 + - r-ggraph + - r-igraph + - r-lifecycle + - r-matrix + - r-patchwork + - r-reshape2 + - r-scales + +source: + md5: fb307e3793cb8874546e7767238ae58b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-epiregulon/build.sh b/recipes/bioconductor-epiregulon/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-epiregulon/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-epiregulon/build_failure.osx-64.yaml b/recipes/bioconductor-epiregulon/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..b7cf5baf7debf --- /dev/null +++ b/recipes/bioconductor-epiregulon/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 67991a2fd2f74c0147d38b79ebb31d85e03f14e4f0f62bbb116faef9f5b961e6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + bioconductor-bsgenome 1.58.0, which cannot be installed (as previously explained); + bioconductor-bsgenome 1.60.0, which cannot be installed (as previously explained); + bioconductor-bsgenome 1.62.0, which cannot be installed (as previously explained); + bioconductor-bsgenome [1.66.1|1.66.3], which cannot be installed (as previously explained); + bioconductor-bsgenome 1.68.0, which cannot be installed (as previously explained); + bioconductor-bsgenome 1.70.1, which cannot be installed (as previously explained); + r-base 3.4.1* , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0 would require + bioconductor-bsgenome >=1.48.0,<1.50.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0 would require + bioconductor-bsgenome >=1.50.0,<1.51.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0 would require + bioconductor-bsgenome >=1.52.0,<1.53.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0 would require + bioconductor-bsgenome >=1.54.0,<1.55.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3 would require + bioconductor-bsgenome >=1.56.0,<1.57.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3 would require + bioconductor-bsgenome >=1.58.0,<1.59.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3 would require + bioconductor-bsgenome >=1.60.0,<1.61.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3 would require + bioconductor-bsgenome >=1.62.0,<1.63.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3 would require + bioconductor-bsgenome >=1.66.0,<1.67.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3 would require + bioconductor-bsgenome >=1.68.0,<1.69.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3 would require + bioconductor-bsgenome >=1.70.0,<1.71.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0 is installable with the potential options + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.1 would require + r-base 3.3.2* , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.1 would require + r-base 3.4.1* , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.1 would require + bioconductor-bsgenome >=1.48.0,<1.50.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.1 would require + bioconductor-bsgenome >=1.50.0,<1.51.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.1 would require + bioconductor-bsgenome >=1.52.0,<1.53.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.1 would require + bioconductor-bsgenome >=1.54.0,<1.55.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.3 would require + bioconductor-bsgenome >=1.56.0,<1.57.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.3 would require + bioconductor-bsgenome >=1.58.0,<1.59.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.3 would require + bioconductor-bsgenome >=1.60.0,<1.61.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.4 would require + bioconductor-bsgenome >=1.62.0,<1.63.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.4 would require + bioconductor-bsgenome >=1.66.0,<1.67.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.5 would require + bioconductor-genomeinfodb >=1.34.9,<1.35.0 , which can be installed; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.5 would require + bioconductor-genomeinfodb >=1.36.0,<1.37.0 , which can be installed; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.5 would require + bioconductor-genomeinfodb >=1.38.0,<1.39.0 , which can be installed; + bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0 is not installable because there are no viable options + bioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0 would require + r-base 3.3.2* , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0 would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0 would require + r-base 3.4.1* , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0 would require + bioconductor-bsgenome >=1.48.0,<1.50.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0 would require + bioconductor-bsgenome >=1.50.0,<1.51.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0 would require + bioconductor-bsgenome >=1.52.0,<1.53.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0 would require + bioconductor-bsgenome >=1.54.0,<1.55.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0 would require + bioconductor-bsgenome >=1.58.0,<1.59.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0 would require + bioconductor-bsgenome >=1.56.0,<1.57.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0 would require + bioconductor-bsgenome >=1.60.0,<1.61.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.3 would require + bioconductor-bsgenome >=1.62.0,<1.63.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.3 would require + bioconductor-bsgenome >=1.66.0,<1.67.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.3 would require + bioconductor-bsgenome >=1.68.0,<1.69.0 , which cannot be installed (as previously explained); + bioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.3 would require + bioconductor-bsgenome >=1.70.0,<1.71.0 , which cannot be installed (as previously explained); + bioconductor-experimenthub >=2.14.0,<2.15.0 does not exist (perhaps a typo or a missing channel); + bioconductor-genomeinfodb >=1.42.0,<1.43.0 is not installable because it conflicts with any installable versions previously reported; + bioconductor-genomicranges >=1.58.0,<1.59.0 is not installable because it conflicts with any installable versions previously reported; + bioconductor-motifmatchr >=1.28.0,<1.29.0 does not exist (perhaps a typo or a missing channel); + bioconductor-scmultiome >=1.6.0,<1.7.0 does not exist (perhaps a typo or a missing channel); + bioconductor-scran >=1.34.0,<1.35.0 is installable with the potential options + bioconductor-scran 1.34.0 would require + bioconductor-biocsingular >=1.22.0,<1.23.0 with the potential options + bioconductor-biocsingular 1.22.0 would require + bioconductor-scaledmatrix >=1.14.0,<1.15.0 , which requires + r-base >=4.4,<4.5.0a0 , which can be installed; + bioconductor-biocsingular 1.22.0 conflicts with any installable versions previously reported; + bioconductor-scran 1.34.0 conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-epiregulon/meta.yaml b/recipes/bioconductor-epiregulon/meta.yaml new file mode 100644 index 0000000000000..f5c804d9955ea --- /dev/null +++ b/recipes/bioconductor-epiregulon/meta.yaml @@ -0,0 +1,100 @@ +{% set version = "1.2.0" %} +{% set name = "epiregulon" %} +{% set bioc = "3.20" %} + +about: + description: Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Gene regulatory network inference from single cell epigenomic data + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-epiregulon", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), coin, scater, beachmat.hdf5 +requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + + host: + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-assorthead >=1.0.0,<1.1.0 + - bioconductor-aucell >=1.28.0,<1.29.0 + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bluster >=1.16.0,<1.17.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0 + - bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-motifmatchr >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scmultiome >=1.6.0,<1.7.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-checkmate + - r-entropy + - r-lifecycle + - r-matrix + - r-rcpp + - libblas + - liblapack + + run: + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-assorthead >=1.0.0,<1.1.0 + - bioconductor-aucell >=1.28.0,<1.29.0 + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bluster >=1.16.0,<1.17.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0 + - bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-motifmatchr >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scmultiome >=1.6.0,<1.7.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-checkmate + - r-entropy + - r-lifecycle + - r-matrix + - r-rcpp + +source: + md5: 02404d676e884de53853503c0b8dc5a1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-epistack/meta.yaml b/recipes/bioconductor-epistack/meta.yaml index 3dab4be583771..977ad94ed35b5 100644 --- a/recipes/bioconductor-epistack/meta.yaml +++ b/recipes/bioconductor-epistack/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "epistack" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq, DNA methyation or genomic conservation data) centered at genomic regions of interest. epistack needs three different inputs: 1) a genomic score objects, such as ChIP-seq coverage or DNA methylation values, provided as a `GRanges` (easily obtained from `bigwig` or `bam` files). 2) a list of feature of interest, such as peaks or transcription start sites, provided as a `GRanges` (easily obtained from `gtf` or `bed` files). 3) a score to sort the features, such as peak height or gene expression value.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Heatmaps of Stack Profiles from Epigenetic Signals -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7d06dbae71f93e2c3cb91ba3d16fa916 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epistack", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-plotrix run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-plotrix + +source: + md5: cb4dbd8d61a6ed76a1c078fa0c3443e6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Heatmaps of Stack Profiles from Epigenetic Signals' - description: 'The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq, DNA methyation or genomic conservation data) centered at genomic regions of interest. epistack needs three different inputs: 1) a genomic score objects, such as ChIP-seq coverage or DNA methylation values, provided as a `GRanges` (easily obtained from `bigwig` or `bam` files). 2) a list of feature of interest, such as peaks or transcription start sites, provided as a `GRanges` (easily obtained from `gtf` or `bed` files). 3) a score to sort the features, such as peak height or gene expression value.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epistasisga/meta.yaml b/recipes/bioconductor-epistasisga/meta.yaml index f7bb792a8c68a..af41b5e19bdd2 100644 --- a/recipes/bioconductor-epistasisga/meta.yaml +++ b/recipes/bioconductor-epistasisga/meta.yaml @@ -1,27 +1,33 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "epistasisGA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package runs the GADGETS method to identify epistatic effects in nuclear family studies. It also provides functions for permutation-based inference and graphical visualization of the results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: An R package to identify multi-snp effects in nuclear family studies using the GADGETS method -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 79635d9683f002813e51fa3c17e49b39 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epistasisga", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat (>= 3.0.0) requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-batchtools - r-bh @@ -37,7 +43,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-batchtools - r-bh @@ -50,17 +56,16 @@ requirements: - r-rcpp - r-rcpparmadillo - r-survival - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: becb50c407ab48cee495562d867da943 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'An R package to identify multi-snp effects in nuclear family studies using the GADGETS method' - description: 'This package runs the GADGETS method to identify epistatic effects in nuclear family studies. It also provides functions for permutation-based inference and graphical visualization of the results.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epitxdb.hs.hg38/meta.yaml b/recipes/bioconductor-epitxdb.hs.hg38/meta.yaml index 9edb215bfcecc..c7340653cfcbf 100644 --- a/recipes/bioconductor-epitxdb.hs.hg38/meta.yaml +++ b/recipes/bioconductor-epitxdb.hs.hg38/meta.yaml @@ -1,42 +1,42 @@ {% set version = "0.99.7" %} {% set name = "EpiTxDb.Hs.hg38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e30af95f285788a9777a8207a8ef73a9 +about: + description: Exposes an annotation databases generated from several sources by exposing these as EpiTxDb object. Generated for Homo sapiens/hg38. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for EpiTxDb objects build: - number: 7 + noarch: generic + number: 8 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epitxdb.hs.hg38", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat, Modstrings, rtracklayer requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-epitxdb >=1.14.0,<1.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-epitxdb >=1.18.0,<1.19.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-epitxdb >=1.14.0,<1.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-epitxdb >=1.18.0,<1.19.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e30af95f285788a9777a8207a8ef73a9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for EpiTxDb objects' - description: 'Exposes an annotation databases generated from several sources by exposing these as EpiTxDb object. Generated for Homo sapiens/hg38.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epitxdb.mm.mm10/meta.yaml b/recipes/bioconductor-epitxdb.mm.mm10/meta.yaml index 526e3d97d4b4e..a12ebcabeae71 100644 --- a/recipes/bioconductor-epitxdb.mm.mm10/meta.yaml +++ b/recipes/bioconductor-epitxdb.mm.mm10/meta.yaml @@ -1,42 +1,42 @@ {% set version = "0.99.6" %} {% set name = "EpiTxDb.Mm.mm10" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 518e4967f7f038e3cbf2865b74dc4f1b +about: + description: Exposes an annotation databases generated from several sources by exposing these as EpiTxDb object. Generated for Mus musculus/mm10. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for EpiTxDb objects build: - number: 7 + noarch: generic + number: 8 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epitxdb.mm.mm10", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-epitxdb >=1.14.0,<1.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-epitxdb >=1.18.0,<1.19.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-epitxdb >=1.14.0,<1.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-epitxdb >=1.18.0,<1.19.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 518e4967f7f038e3cbf2865b74dc4f1b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for EpiTxDb objects' - description: 'Exposes an annotation databases generated from several sources by exposing these as EpiTxDb object. Generated for Mus musculus/mm10.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epitxdb.sc.saccer3/meta.yaml b/recipes/bioconductor-epitxdb.sc.saccer3/meta.yaml index 69da19dba72fc..a5e14d5b940b5 100644 --- a/recipes/bioconductor-epitxdb.sc.saccer3/meta.yaml +++ b/recipes/bioconductor-epitxdb.sc.saccer3/meta.yaml @@ -1,42 +1,42 @@ {% set version = "0.99.5" %} {% set name = "EpiTxDb.Sc.sacCer3" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d9e5f37e5dcb60e890d99d80fddda00 +about: + description: Exposes an annotation databases generated from several sources by exposing these as EpiTxDb object. Generated for Saccharomyces cerevisiae/sacCer3. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for EpiTxDb objects build: - number: 5 + noarch: generic + number: 6 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epitxdb.sc.saccer3", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat, Modstrings, rtracklayer requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-epitxdb >=1.14.0,<1.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-epitxdb >=1.18.0,<1.19.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-epitxdb >=1.14.0,<1.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-epitxdb >=1.18.0,<1.19.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6d9e5f37e5dcb60e890d99d80fddda00 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for EpiTxDb objects' - description: 'Exposes an annotation databases generated from several sources by exposing these as EpiTxDb object. Generated for Saccharomyces cerevisiae/sacCer3.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epitxdb/meta.yaml b/recipes/bioconductor-epitxdb/meta.yaml index 9120d238c9984..43cefd5ae5e09 100644 --- a/recipes/bioconductor-epitxdb/meta.yaml +++ b/recipes/bioconductor-epitxdb/meta.yaml @@ -1,68 +1,77 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "EpiTxDb" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: EpiTxDb facilitates the storage of epitranscriptomic information. More specifically, it can keep track of modification identity, position, the enzyme for introducing it on the RNA, a specifier which determines the position on the RNA to be modified and the literature references each modification is associated with. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Storing and accessing epitranscriptomic information using the AnnotationDbi interface -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a693697bcccd27be6e57c304438d94a6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epitxdb", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, httptest, AnnotationHub, ensembldb, ggplot2, EpiTxDb.Hs.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Scerevisiae.UCSC.sacCer3, TxDb.Hsapiens.UCSC.hg38.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-modstrings >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-trnadbimport >=1.20.0,<1.21.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-modstrings >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-trnadbimport >=1.24.0,<1.25.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-curl - r-dbi - r-httr + - r-rex - r-rsqlite - r-xml2 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-modstrings >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-trnadbimport >=1.20.0,<1.21.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-modstrings >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-trnadbimport >=1.24.0,<1.25.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-curl - r-dbi - r-httr + - r-rex - r-rsqlite - r-xml2 + +source: + md5: 9eaa3d39c3126909d669fd4e98b76ac7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Storing and accessing epitranscriptomic information using the AnnotationDbi interface' - description: 'EpiTxDb facilitates the storage of epitranscriptomic information. More specifically, it can keep track of modification identity, position, the enzyme for introducing it on the RNA, a specifier which determines the position on the RNA to be modified and the literature references each modification is associated with.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epivizr/meta.yaml b/recipes/bioconductor-epivizr/meta.yaml index 51bbf203d8997..2f3a4716f5ace 100644 --- a/recipes/bioconductor-epivizr/meta.yaml +++ b/recipes/bioconductor-epivizr/meta.yaml @@ -1,52 +1,21 @@ -{% set version = "2.32.0" %} +{% set version = "2.36.0" %} {% set name = "epivizr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides connections to the epiviz web app (http://epiviz.cbcb.umd.edu) for interactive visualization of genomic data. Objects in R/bioc interactive sessions can be displayed in genome browser tracks or plots to be explored by navigation through genomic regions. Fundamental Bioconductor data structures are supported (e.g., GenomicRanges and RangedSummarizedExperiment objects), while providing an easy mechanism to support other data structures (through package epivizrData). Visualizations (using d3.js) can be easily added to the web app as well. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: R Interface to epiviz web app -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aaf997f0c4eccf72d795d79a3ebd7bfe build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epivizr", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, minfi, rmarkdown -requirements: - host: - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-epivizrdata >=1.30.0,<1.31.0' - - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - r-base - run: - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-epivizrdata >=1.30.0,<1.31.0' - - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'R Interface to epiviz web app' - description: 'This package provides connections to the epiviz web app (http://epiviz.cbcb.umd.edu) for interactive visualization of genomic data. Objects in R/bioc interactive sessions can be displayed in genome browser tracks or plots to be explored by navigation through genomic regions. Fundamental Bioconductor data structures are supported (e.g., GenomicRanges and RangedSummarizedExperiment objects), while providing an easy mechanism to support other data structures (through package epivizrData). Visualizations (using d3.js) can be easily added to the web app as well.' + extra: identifiers: - biotools:epivizr @@ -56,3 +25,40 @@ extra: path: recipes/bioconductor-epivizr version: 2.10.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, minfi, rmarkdown +requirements: + host: + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-epivizrdata >=1.34.0,<1.35.0 + - bioconductor-epivizrserver >=1.34.0,<1.35.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + run: + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-epivizrdata >=1.34.0,<1.35.0 + - bioconductor-epivizrserver >=1.34.0,<1.35.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + +source: + md5: b10969252af0074ea50a17cab34b5cca + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-epivizrchart/meta.yaml b/recipes/bioconductor-epivizrchart/meta.yaml index f66a753816ffa..5fc01668bac34 100644 --- a/recipes/bioconductor-epivizrchart/meta.yaml +++ b/recipes/bioconductor-epivizrchart/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "epivizrChart" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides an API for interactive visualization of genomic data using epiviz web components. Objects in R/BioConductor can be used to generate interactive R markdown/notebook documents or can be visualized in the R Studio's default viewer. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: R interface to epiviz web components -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 076ebf7f9141cb71df0867f480ff960c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epivizrchart", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr, AnnotationHub requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-epivizrdata >=1.30.0,<1.31.0' - - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-epivizrdata >=1.34.0,<1.35.0 + - bioconductor-epivizrserver >=1.34.0,<1.35.0 - r-base - r-htmltools - r-rjson run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-epivizrdata >=1.30.0,<1.31.0' - - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-epivizrdata >=1.34.0,<1.35.0 + - bioconductor-epivizrserver >=1.34.0,<1.35.0 - r-base - r-htmltools - r-rjson + +source: + md5: 531a00665452b6e44af700a0f779d789 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'R interface to epiviz web components' - description: 'This package provides an API for interactive visualization of genomic data using epiviz web components. Objects in R/BioConductor can be used to generate interactive R markdown/notebook documents or can be visualized in the R Studio''s default viewer.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epivizrdata/meta.yaml b/recipes/bioconductor-epivizrdata/meta.yaml index 412409f2896f3..8f6509ab0d823 100644 --- a/recipes/bioconductor-epivizrdata/meta.yaml +++ b/recipes/bioconductor-epivizrdata/meta.yaml @@ -1,59 +1,22 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "epivizrData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Serve data from Bioconductor Objects through a WebSocket connection. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Data Management API for epiviz interactive visualization app -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa9cf42fdbb0ad293964de33fc62e27a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epivizrdata", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI, matrixStats -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Data Management API for epiviz interactive visualization app' - description: 'Serve data from Bioconductor Objects through a WebSocket connection.' - license_file: LICENSE + extra: identifiers: - biotools:epivizrdata @@ -63,3 +26,46 @@ extra: path: recipes/bioconductor-epivizrdata version: 1.8.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI, matrixStats +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-epivizrserver >=1.34.0,<1.35.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-organismdbi >=1.48.0,<1.49.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-epivizrserver >=1.34.0,<1.35.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-organismdbi >=1.48.0,<1.49.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + +source: + md5: 5b011ec28c3b00330f80c0f691457ef4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-epivizrserver/meta.yaml b/recipes/bioconductor-epivizrserver/meta.yaml index 7b384efc68bd6..991e251b2bd88 100644 --- a/recipes/bioconductor-epivizrserver/meta.yaml +++ b/recipes/bioconductor-epivizrserver/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "epivizrServer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides objects to manage WebSocket connections to epiviz apps. Other epivizr package use this infrastructure. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: WebSocket server infrastructure for epivizr apps and packages -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4bc67106aa169616232174c422fb6e2b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epivizrserver", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:epivizrserver + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-epivizrserver + path: recipes/bioconductor-epivizrserver + version: 1.8.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocStyle requirements: host: - r-base - - 'r-httpuv >=1.3.0' - - 'r-mime >=0.2' - - 'r-r6 >=2.0.0' + - r-httpuv >=1.3.0 + - r-mime >=0.2 + - r-r6 >=2.0.0 - r-rjson run: - r-base - - 'r-httpuv >=1.3.0' - - 'r-mime >=0.2' - - 'r-r6 >=2.0.0' + - r-httpuv >=1.3.0 + - r-mime >=0.2 + - r-r6 >=2.0.0 - r-rjson + +source: + md5: 6156ae07bce88bf1bc59d633186cc1b3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'WebSocket server infrastructure for epivizr apps and packages' - description: 'This package provides objects to manage WebSocket connections to epiviz apps. Other epivizr package use this infrastructure.' - license_file: LICENSE -extra: - identifiers: - - biotools:epivizrserver - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-epivizrserver - path: recipes/bioconductor-epivizrserver - version: 1.8.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-epivizrstandalone/meta.yaml b/recipes/bioconductor-epivizrstandalone/meta.yaml index fba6c056e868e..61d17419c0104 100644 --- a/recipes/bioconductor-epivizrstandalone/meta.yaml +++ b/recipes/bioconductor-epivizrstandalone/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "epivizrStandalone" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package imports the epiviz visualization JavaScript app for genomic data interactive visualization. The 'epivizrServer' package is used to provide a web server running completely within R. This standalone version allows to browse arbitrary genomes through genome annotations provided by Bioconductor packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Run Epiviz Interactive Genomic Data Visualization App within R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa34f18a7a4f4340f2e4a0ecc46af0a2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-epivizrstandalone", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:epivizrstandalone + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-epivizrstandalone + path: recipes/bioconductor-epivizrstandalone + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9), Mus.musculus, Biobase, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-epivizr >=2.32.0,<2.33.0' - - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-epivizr >=2.36.0,<2.37.0 + - bioconductor-epivizrserver >=1.34.0,<1.35.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-git2r run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-epivizr >=2.32.0,<2.33.0' - - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-epivizr >=2.36.0,<2.37.0 + - bioconductor-epivizrserver >=1.34.0,<1.35.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-git2r + +source: + md5: d28db86675c8d23e2d6c19c8e7f834d2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Run Epiviz Interactive Genomic Data Visualization App within R' - description: 'This package imports the epiviz visualization JavaScript app for genomic data interactive visualization. The ''epivizrServer'' package is used to provide a web server running completely within R. This standalone version allows to browse arbitrary genomes through genome annotations provided by Bioconductor packages.' - license_file: LICENSE -extra: - identifiers: - - biotools:epivizrstandalone - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-epivizrstandalone - path: recipes/bioconductor-epivizrstandalone - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-erccdashboard/meta.yaml b/recipes/bioconductor-erccdashboard/meta.yaml index f0d714a1af896..e433dc8a18a61 100644 --- a/recipes/bioconductor-erccdashboard/meta.yaml +++ b/recipes/bioconductor-erccdashboard/meta.yaml @@ -1,34 +1,38 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "erccdashboard" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Technical performance metrics for differential gene expression experiments using External RNA Controls Consortium (ERCC) spike-in ratio mixtures. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Assess Differential Gene Expression Experiments with ERCC Controls -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fa211269012a775dcdc114f3eb0282bb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-erccdashboard", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - - 'r-ggplot2 >=2.1.0' + - r-ggplot2 >=2.1.0 - r-gplots - - 'r-gridextra >=2.0.0' + - r-gridextra >=2.0.0 - r-gtools + - r-knitr - r-locfit - r-mass - r-plyr @@ -37,14 +41,15 @@ requirements: - r-scales - r-stringr run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - - 'r-ggplot2 >=2.1.0' + - r-ggplot2 >=2.1.0 - r-gplots - - 'r-gridextra >=2.0.0' + - r-gridextra >=2.0.0 - r-gtools + - r-knitr - r-locfit - r-mass - r-plyr @@ -52,13 +57,16 @@ requirements: - r-rocr - r-scales - r-stringr + +source: + md5: 937e15f505e42ce6d612dfb53423772c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Assess Differential Gene Expression Experiments with ERCC Controls' - description: 'Technical performance metrics for differential gene expression experiments using External RNA Controls Consortium (ERCC) spike-in ratio mixtures.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-erma/meta.yaml b/recipes/bioconductor-erma/meta.yaml index 18cea096ef670..1d8f6903e82d8 100644 --- a/recipes/bioconductor-erma/meta.yaml +++ b/recipes/bioconductor-erma/meta.yaml @@ -1,64 +1,69 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "erma" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Software and data to support epigenomic road map adventures. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: epigenomic road map adventures -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 38679c439fbeb31db81c90c90ba4f79d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-erma", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, BiocStyle, knitr, GO.db, png, DT, doParallel requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfiles >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-homo.sapiens >=1.3.0,<1.4.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-shiny run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfiles >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-homo.sapiens >=1.3.0,<1.4.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-shiny + +source: + md5: e14b464c4f13677f6bb28677bb121427 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'epigenomic road map adventures' - description: 'Software and data to support epigenomic road map adventures.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-erssa/meta.yaml b/recipes/bioconductor-erssa/meta.yaml index aa706e6ec05ae..d842db4c68b1f 100644 --- a/recipes/bioconductor-erssa/meta.yaml +++ b/recipes/bioconductor-erssa/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "ERSSA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The ERSSA package takes user supplied RNA-seq differential expression dataset and calculates the number of differentially expressed genes at varying biological replicate levels. This allows the user to determine, without relying on any a priori assumptions, whether sufficient differential detection has been acheived with their RNA-seq dataset. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 | file LICENSE + license_file: LICENSE + summary: Empirical RNA-seq Sample Size Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 160e82bdb1b7af9f6452d4767a7e8a1a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-erssa", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-apeglm >=1.24.0,<1.25.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' + - bioconductor-apeglm >=1.28.0,<1.29.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 - r-base - - 'r-ggplot2 >=3.0.0' - - 'r-plyr >=1.8.4' - - 'r-rcolorbrewer >=1.1-2' + - r-ggplot2 >=3.0.0 + - r-plyr >=1.8.4 + - r-rcolorbrewer >=1.1-2 run: - - 'bioconductor-apeglm >=1.24.0,<1.25.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' + - bioconductor-apeglm >=1.28.0,<1.29.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 - r-base - - 'r-ggplot2 >=3.0.0' - - 'r-plyr >=1.8.4' - - 'r-rcolorbrewer >=1.1-2' + - r-ggplot2 >=3.0.0 + - r-plyr >=1.8.4 + - r-rcolorbrewer >=1.1-2 + +source: + md5: 4e7fad04389212d758c60234001a521d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 | file LICENSE' - summary: 'Empirical RNA-seq Sample Size Analysis' - description: 'The ERSSA package takes user supplied RNA-seq differential expression dataset and calculates the number of differentially expressed genes at varying biological replicate levels. This allows the user to determine, without relying on any a priori assumptions, whether sufficient differential detection has been acheived with their RNA-seq dataset.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-esatac/build_failure.linux-64.yaml b/recipes/bioconductor-esatac/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..3b71a1cbbc427 --- /dev/null +++ b/recipes/bioconductor-esatac/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 28f06c056e813ddab661293b6a9c27375a8015248498e026ecb9967a4eee554a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + The following packages are incompatible + [31mbioconductor-chipseeker >=1.42.0,<1.43.0 [0m does not exist (perhaps a typo or a missing channel); + [31mbioconductor-clusterprofiler >=4.14.0,<4.15.0 [0m does not exist (perhaps a typo or a missing channel); + [31mbioconductor-rbowtie2 >=2.12.0,<2.13.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-clusterprofiler[version='>=4.14.0,<4.15.0']"), MatchSpec("bioconductor-chipseeker[version='>=1.42.0,<1.43.0']"), MatchSpec("bioconductor-rbowtie2[version='>=2.12.0,<2.13.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-chipseeker >=1.42.0,<1.43.0 + - nothing provides requested bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - nothing provides requested bioconductor-rbowtie2 >=2.12.0,<2.13.0 + + Could not solve for environment specs + The following packages are incompatible + [31mbioconductor-chipseeker >=1.42.0,<1.43.0 [0m does not exist (perhaps a typo or a missing channel); + [31mbioconductor-clusterprofiler >=4.14.0,<4.15.0 [0m does not exist (perhaps a typo or a missing channel); + [31mbioconductor-rbowtie2 >=2.12.0,<2.13.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-clusterprofiler[version='>=4.14.0,<4.15.0']"), MatchSpec("bioconductor-chipseeker[version='>=1.42.0,<1.43.0']"), MatchSpec("bioconductor-rbowtie2[version='>=2.12.0,<2.13.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-chipseeker >=1.42.0,<1.43.0 + - nothing provides requested bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - nothing provides requested bioconductor-rbowtie2 >=2.12.0,<2.13.0 + + Could not solve for environment specs + The following packages are incompatible + [31mbioconductor-chipseeker >=1.42.0,<1.43.0 [0m does not exist (perhaps a typo or a missing channel); + [31mbioconductor-clusterprofiler >=4.14.0,<4.15.0 [0m does not exist (perhaps a typo or a missing channel); + [31mbioconductor-rbowtie2 >=2.12.0,<2.13.0 [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-esatac/build_failure.linux-aarch64.yaml b/recipes/bioconductor-esatac/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..b086e488a0b86 --- /dev/null +++ b/recipes/bioconductor-esatac/build_failure.linux-aarch64.yaml @@ -0,0 +1,4 @@ +recipe_sha: 28f06c056e813ddab661293b6a9c27375a8015248498e026ecb9967a4eee554a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: dependency issue +reason: needs bioconductor-rbowtie2 \ No newline at end of file diff --git a/recipes/bioconductor-esatac/build_failure.osx-64.yaml b/recipes/bioconductor-esatac/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..7575163247404 --- /dev/null +++ b/recipes/bioconductor-esatac/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 28f06c056e813ddab661293b6a9c27375a8015248498e026ecb9967a4eee554a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + additional-platforms: + - linux-aarch64 + copy_test_source_files: true + final: true + identifiers: + - biotools:rbowtie2 + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rbowtie2_1735782661546/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rbowtie2_1735782661546/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rbowtie2_1735782661546/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rbowtie2_1735782661546/work + INFO: activate-gfortran_osx-64.sh made the following environmental changes: + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + mkdir -p ../inst + (cd adapterremoval && (make CXX="g -std=gnu11" -f Makefile)) + make[1]: Entering directory '$SRC_DIR/src/adapterremoval' + g -std=gnu11 -O3 -pthread -DNDEBUG -c adapterset.cc + make[1]: Leaving directory '$SRC_DIR/src/adapterremoval' +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-esatac/meta.yaml b/recipes/bioconductor-esatac/meta.yaml index 70ee8c371f47c..3d6206c4226d2 100644 --- a/recipes/bioconductor-esatac/meta.yaml +++ b/recipes/bioconductor-esatac/meta.yaml @@ -1,47 +1,61 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "esATAC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw sequencing reads preprocessing (FASTQ files), reads alignment (Rbowtie2), aligned reads file operations (SAM, BAM, and BED files), peak calling (F-seq), genome annotations (Motif, GO, SNP analysis) and quality control report. The package is managed by dataflow graph. It is easy for user to pass variables seamlessly between processes and understand the workflow. Users can process FASTQ files through end-to-end preset pipeline which produces a pretty HTML report for quality control and preliminary statistical results, or customize workflow starting from any intermediate stages with esATAC functions easily and flexibly. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 | file LICENSE + license_file: LICENSE + summary: An Easy-to-use Systematic pipeline for ATACseq data analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ea63da6e75365243df878d55d6b39f9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-esatac", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:esATAC + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat, webshot, prettydoc # SystemRequirements: C++11 requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-chipseeker >=1.38.0,<1.39.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' - - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' - - 'bioconductor-pipeframe >=1.18.0,<1.19.0' - - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-chipseeker >=1.42.0,<1.43.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-jaspar2018 >=1.1.0,<1.2.0 + - bioconductor-motifmatchr >=1.28.0,<1.29.0 + - bioconductor-pipeframe >=1.22.0,<1.23.0 + - bioconductor-rbowtie2 >=2.12.0,<2.13.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-tfbstools >=1.44.0,<1.45.0 - r-base - r-biocmanager - r-corrplot @@ -51,33 +65,34 @@ requirements: - r-knitr - r-magrittr - r-r.utils - - 'r-rcpp >=0.12.11' + - r-rcpp >=0.12.11 - r-rjava - r-rmarkdown - r-venndiagram - libblas - liblapack + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-chipseeker >=1.38.0,<1.39.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' - - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' - - 'bioconductor-pipeframe >=1.18.0,<1.19.0' - - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-chipseeker >=1.42.0,<1.43.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-jaspar2018 >=1.1.0,<1.2.0 + - bioconductor-motifmatchr >=1.28.0,<1.29.0 + - bioconductor-pipeframe >=1.22.0,<1.23.0 + - bioconductor-rbowtie2 >=2.12.0,<2.13.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-tfbstools >=1.44.0,<1.45.0 - r-base - r-biocmanager - r-corrplot @@ -87,26 +102,20 @@ requirements: - r-knitr - r-magrittr - r-r.utils - - 'r-rcpp >=0.12.11' + - r-rcpp >=0.12.11 - r-rjava - r-rmarkdown - r-venndiagram - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 9a8b1fef6ff14f18a9b532b60e1cdc5c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-only | file LICENSE' - summary: 'An Easy-to-use Systematic pipeline for ATACseq data analysis' - description: 'This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw sequencing reads preprocessing (FASTQ files), reads alignment (Rbowtie2), aligned reads file operations (SAM, BAM, and BED files), peak calling (F-seq), genome annotations (Motif, GO, SNP analysis) and quality control report. The package is managed by dataflow graph. It is easy for user to pass variables seamlessly between processes and understand the workflow. Users can process FASTQ files through end-to-end preset pipeline which produces a pretty HTML report for quality control and preliminary statistical results, or customize workflow starting from any intermediate stages with esATAC functions easily and flexibly.' - license_file: LICENSE + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name }} \ No newline at end of file diff --git a/recipes/bioconductor-escape/meta.yaml b/recipes/bioconductor-escape/meta.yaml index 86ec8bba522ff..c7639dea18ce7 100644 --- a/recipes/bioconductor-escape/meta.yaml +++ b/recipes/bioconductor-escape/meta.yaml @@ -1,73 +1,82 @@ -{% set version = "1.12.0" %} +{% set version = "2.2.0" %} {% set name = "escape" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A bridging R package to facilitate gene set enrichment analysis (GSEA) in the context of single-cell RNA sequencing. Using raw count information, Seurat objects, or SingleCellExperiment format, users can perform and visualize ssGSEA, GSVA, AUCell, and UCell-based enrichment calculations across individual cells. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Easy single cell analysis platform for enrichment -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e3dc22e072190e21938689fc0f3ab112 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-escape", max_pin="x.x") }}' - noarch: generic -# Suggests: Seurat, SeuratObject, knitr, rmarkdown, markdown, BiocStyle, testthat, dittoSeq (>= 1.1.2) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: Seurat, hexbin, scran, knitr, rmarkdown, markdown, BiocStyle, RColorBrewer, rlang, spelling, testthat (>= 3.0.0), vdiffr requirements: + host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-gsva >=1.50.0,<1.51.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-ucell >=2.6.0,<2.7.0' + - bioconductor-aucell >=1.28.0,<1.29.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-gsva >=2.0.0,<2.1.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-ucell >=2.10.0,<2.11.0 - r-base - - r-broom - - r-data.table - r-dplyr + - r-ggdist - r-ggplot2 + - r-ggpointdensity - r-ggridges - r-matrix - r-msigdbr - r-patchwork - r-reshape2 - - r-rlang + - r-seuratobject - r-stringr + run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-gsva >=1.50.0,<1.51.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-ucell >=2.6.0,<2.7.0' + - bioconductor-aucell >=1.28.0,<1.29.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-gsva >=2.0.0,<2.1.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-ucell >=2.10.0,<2.11.0 - r-base - - r-broom - - r-data.table - r-dplyr + - r-ggdist - r-ggplot2 + - r-ggpointdensity - r-ggridges - r-matrix - r-msigdbr - r-patchwork - r-reshape2 - - r-rlang + - r-seuratobject - r-stringr + +source: + md5: a860f542eac2f9cf59ea1dbb0f84fa11 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Easy single cell analysis platform for enrichment' - description: 'A bridging R package to facilitate gene set enrichment analysis (GSEA) in the context of single-cell RNA sequencing. Using raw count information, Seurat objects, or SingleCellExperiment format, users can perform and visualize GSEA across individual cells.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-escher/meta.yaml b/recipes/bioconductor-escher/meta.yaml index e8649e5391cf2..7f88178651865 100644 --- a/recipes/bioconductor-escher/meta.yaml +++ b/recipes/bioconductor-escher/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "escheR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables. The proposed visualization can be applied to spatially-resolved transcriptomics data, but also broadly to data visualized in 2D space, such as embedding visualizations. We provide this open source R package escheR, which is built off of the state-of-the-art ggplot2 visualization framework and can be seamlessly integrated into genomics toolboxes and workflows. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Unified multi-dimensional visualizations with Gestalt principles -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed2586d2e42f89db85790889863421b8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-escher", max_pin="x.x") }}' - noarch: generic -# Suggests: STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle, ggpubr, scran, scater, scuttle, Seurat + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle, ggpubr, scran, scater, scuttle, Seurat, hexbin requirements: host: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-rlang run: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-rlang + +source: + md5: 3980a08dda22b12c250f35ad9c738ce6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Unified multi-dimensional visualizations with Gestalt principles' - description: 'The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables. The proposed visualization can be applied to spatially-resolved transcriptomics data, but also broadly to data visualized in 2D space, such as embedding visualizations. We provide this open source R package escheR, which is built off of the state-of-the-art ggplot2 visualization framework and can be seamlessly integrated into genomics toolboxes and workflows.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-esetvis/meta.yaml b/recipes/bioconductor-esetvis/meta.yaml index 7ce7e35074dd0..141ad3adbb020 100644 --- a/recipes/bioconductor-esetvis/meta.yaml +++ b/recipes/bioconductor-esetvis/meta.yaml @@ -1,57 +1,63 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "esetVis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Utility functions for visualization of expressionSet (or SummarizedExperiment) Bioconductor object, including spectral map, tsne and linear discriminant analysis. Static plot via the ggplot2 package or interactive via the ggvis or rbokeh packages are available. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Visualizations of expressionSet Bioconductor object -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2edbf6b1764a5ebfdcefaf7a8b6c247d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-esetvis", max_pin="x.x") }}' - noarch: generic -# Suggests: ggplot2, ggvis, rbokeh, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment, GO.db + +extra: + identifiers: + - biotools:esetvis + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-esetvis + path: recipes/bioconductor-esetvis + version: 1.6.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: ggplot2, ggvis, plotly, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment, GO.db requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-mlp >=1.50.0,<1.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-mlp >=1.54.0,<1.55.0 - r-base - r-hexbin - r-mass - r-mpm - r-rtsne run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-mlp >=1.50.0,<1.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-mlp >=1.54.0,<1.55.0 - r-base - r-hexbin - r-mass - r-mpm - r-rtsne + +source: + md5: 34b45c706cd1ff67811d71c67cce0d98 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Visualizations of expressionSet Bioconductor object' - description: 'Utility functions for visualization of expressionSet (or SummarizedExperiment) Bioconductor object, including spectral map, tsne and linear discriminant analysis. Static plot via the ggplot2 package or interactive via the ggvis or rbokeh packages are available.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:esetvis - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-esetvis - path: recipes/bioconductor-esetvis - version: 1.6.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-estrogen/meta.yaml b/recipes/bioconductor-estrogen/meta.yaml index cd11513496376..21df985c01a5a 100644 --- a/recipes/bioconductor-estrogen/meta.yaml +++ b/recipes/bioconductor-estrogen/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "estrogen" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 41a3321678d1a9cb057e979d675f0cee +about: + description: Data from 8 Affymetrix genechips, looking at a 2x2 factorial design (with 2 repeats per level). + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Microarray dataset that can be used as example for 2x2 factorial designs build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-estrogen", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: affy, hgu95av2.db, hgu95av2cdf, vsn, knitr, genefilter requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a15821f8002bf76ac7261b6982c970a5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Microarray dataset that can be used as example for 2x2 factorial designs' - description: 'Data from 8 Affymetrix genechips, looking at a 2x2 factorial design (with 2 repeats per level).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-estrogen/post-link.sh b/recipes/bioconductor-estrogen/post-link.sh index 92a917b9ef078..4d61e2d1a952c 100644 --- a/recipes/bioconductor-estrogen/post-link.sh +++ b/recipes/bioconductor-estrogen/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "estrogen-1.48.0" +installBiocDataPackage.sh "estrogen-1.52.0" diff --git a/recipes/bioconductor-etec16s/build_failure.linux-64.yaml b/recipes/bioconductor-etec16s/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..d1a8b2b6e7f10 --- /dev/null +++ b/recipes/bioconductor-etec16s/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 39d46d7f4a8631437258365148b781b67f0f3542d31fa54b44e7a0a366a1c969 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: metagenomeseq 1.47 Not ready for BioC 3.20 +category: dependency issue +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-metagenomeseq[version='>=1.47.0,<1.48.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-metagenomeseq >=1.47.0,<1.48.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-metagenomeseq >=1.47.0,<1.48.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-metagenomeseq[version='>=1.47.0,<1.48.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-metagenomeseq >=1.47.0,<1.48.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-metagenomeseq >=1.47.0,<1.48.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-metagenomeseq[version='>=1.47.0,<1.48.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-metagenomeseq >=1.47.0,<1.48.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-metagenomeseq >=1.47.0,<1.48.0 [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-etec16s/meta.yaml b/recipes/bioconductor-etec16s/meta.yaml index e4180b711643d..3a1ca61f5b18c 100644 --- a/recipes/bioconductor-etec16s/meta.yaml +++ b/recipes/bioconductor-etec16s/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.30.0" %} +{% set version = "1.33.0" %} {% set name = "etec16s" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 86353b5f2f77274b883120dc043f8ce5 +about: + description: 16S rRNA gene sequencing data to study changes in the faecal microbiota of 12 volunteers during a human challenge study with ETEC (H10407) and subsequent treatment with ciprofloxacin. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-etec16s", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-metagenomeseq >=1.47.0,<1.48.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-metagenomeseq >=1.47.0,<1.48.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fcaa0b82c184de2e434fce35b0422c7e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment' - description: '16S rRNA gene sequencing data to study changes in the faecal microbiota of 12 volunteers during a human challenge study with ETEC (H10407) and subsequent treatment with ciprofloxacin.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-etec16s/post-link.sh b/recipes/bioconductor-etec16s/post-link.sh index 7ab2be62ab9c5..34ab01a1ee988 100644 --- a/recipes/bioconductor-etec16s/post-link.sh +++ b/recipes/bioconductor-etec16s/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "etec16s-1.30.0" +installBiocDataPackage.sh "etec16s-1.33.0" diff --git a/recipes/bioconductor-eudysbiome/meta.yaml b/recipes/bioconductor-eudysbiome/meta.yaml index c4d7c109e3260..1e1abe67ac964 100644 --- a/recipes/bioconductor-eudysbiome/meta.yaml +++ b/recipes/bioconductor-eudysbiome/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "eudysbiome" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: eudysbiome a package that permits to annotate the differential genera as harmful/harmless based on their ability to contribute to host diseases (as indicated in literature) or unknown based on their ambiguous genus classification. Further, the package statistically measures the eubiotic (harmless genera increase or harmful genera decrease) or dysbiotic(harmless genera decrease or harmful genera increase) impact of a given treatment or environmental change on the (gut-intestinal, GI) microbiome in comparison to the microbiome of the reference condition. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Cartesian plot and contingency test on 16S Microbial data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 76023a8328d58f7d5b783679a08c7ea8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-eudysbiome", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:eudysbiome + - doi:10.1186/s12918-016-0344-6 + parent_recipe: + name: bioconductor-eudysbiome + path: recipes/bioconductor-eudysbiome + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-plyr - r-r.utils run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-plyr - r-r.utils + +source: + md5: 72f91101f718f87703e7846bb596a02a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Cartesian plot and contingency test on 16S Microbial data' - description: 'eudysbiome a package that permits to annotate the differential genera as harmful/harmless based on their ability to contribute to host diseases (as indicated in literature) or unknown based on their ambiguous genus classification. Further, the package statistically measures the eubiotic (harmless genera increase or harmful genera decrease) or dysbiotic(harmless genera decrease or harmful genera increase) impact of a given treatment or environmental change on the (gut-intestinal, GI) microbiome in comparison to the microbiome of the reference condition.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:eudysbiome - - doi:10.1186/s12918-016-0344-6 - parent_recipe: - name: bioconductor-eudysbiome - path: recipes/bioconductor-eudysbiome - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-eupathdb/meta.yaml b/recipes/bioconductor-eupathdb/meta.yaml index c302fc335cb08..c63a18b60db9e 100644 --- a/recipes/bioconductor-eupathdb/meta.yaml +++ b/recipes/bioconductor-eupathdb/meta.yaml @@ -1,52 +1,57 @@ {% set version = "1.0.1" %} {% set name = "EuPathDB" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Brings together annotation resources from the various EuPathDB databases (PlasmoDB, ToxoDB, TriTrypDB, etc.) and makes them available in R using the AnnotationHub framework. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Provides access to pathogen annotation resources available on EuPathDB databases -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1451c3ab6c224d9a4cfbdf27dc5c2680 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-eupathdb", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: dplyr, knitr, BiocStyle, rmarkdown, jsonlite requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-annotationhubdata >=1.36.0,<1.37.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodbdata >=1.2.0,<1.3.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-biocmanager run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-annotationhubdata >=1.36.0,<1.37.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodbdata >=1.2.0,<1.3.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-biocmanager - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 1451c3ab6c224d9a4cfbdf27dc5c2680 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Provides access to pathogen annotation resources available on EuPathDB databases' - description: 'Brings together annotation resources from the various EuPathDB databases (PlasmoDB, ToxoDB, TriTrypDB, etc.) and makes them available in R using the AnnotationHub framework.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-evaluomer/build_failure.linux-64.yaml b/recipes/bioconductor-evaluomer/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..069149bec5b5b --- /dev/null +++ b/recipes/bioconductor-evaluomer/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 2b651d1a59d3076e0974c7da0ab9c6d9f9b2abf9ae0d49b348ff81cf36fa2c5a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Encountered problems while solving: + - nothing provides requested r-rskc >=2.4.2 + - nothing provides requested r-sparcl >=1.0.4 + + Could not solve for environment specs + The following packages are incompatible + [31mr-rskc >=2.4.2 [0m does not exist (perhaps a typo or a missing channel); + [31mr-sparcl >=1.0.4 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-sparcl[version='>=1.0.4']"), MatchSpec("r-rskc[version='>=2.4.2']")} + Encountered problems while solving: + - nothing provides requested r-rskc >=2.4.2 + - nothing provides requested r-sparcl >=1.0.4 + + Could not solve for environment specs + The following packages are incompatible + [31mr-rskc >=2.4.2 [0m does not exist (perhaps a typo or a missing channel); + [31mr-sparcl >=1.0.4 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-sparcl[version='>=1.0.4']"), MatchSpec("r-rskc[version='>=2.4.2']")} + Encountered problems while solving: + - nothing provides requested r-rskc >=2.4.2 + - nothing provides requested r-sparcl >=1.0.4 + + Could not solve for environment specs + The following packages are incompatible + [31mr-rskc >=2.4.2 [0m does not exist (perhaps a typo or a missing channel); + [31mr-sparcl >=1.0.4 [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-evaluomer/meta.yaml b/recipes/bioconductor-evaluomer/meta.yaml index d60206052a04d..43d0f0503dd75 100644 --- a/recipes/bioconductor-evaluomer/meta.yaml +++ b/recipes/bioconductor-evaluomer/meta.yaml @@ -1,35 +1,40 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "evaluomeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Evaluating the reliability of your own metrics and the measurements done on your own datasets by analysing the stability and goodness of the classifications of such metrics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Evaluation of Bioinformatics Metrics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2cee372b9bb28916d6ab543be8eca9b2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-evaluomer", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, magrittr requirements: + host: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-class - - 'r-cluster >=2.0.9' - - 'r-corrplot >=0.84' - - 'r-flexmix >=2.3.15' - - 'r-fpc >=2.2-3' + - r-cluster >=2.0.9 + - r-corrplot >=0.84 + - r-dendextend >=1.16.0 + - r-dplyr + - r-flexmix >=2.3.15 + - r-fpc >=2.2-3 - r-ggdendro - r-ggplot2 - r-kableextra @@ -38,18 +43,23 @@ requirements: - r-mclust - r-plotrix - r-prabclus - - 'r-randomforest >=4.6.14' + - r-randomforest >=4.6.14 - r-rdpack - r-reshape2 + - r-rskc >=2.4.2 + - r-sparcl >=1.0.4 + run: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-class - - 'r-cluster >=2.0.9' - - 'r-corrplot >=0.84' - - 'r-flexmix >=2.3.15' - - 'r-fpc >=2.2-3' + - r-cluster >=2.0.9 + - r-corrplot >=0.84 + - r-dendextend >=1.16.0 + - r-dplyr + - r-flexmix >=2.3.15 + - r-fpc >=2.2-3 - r-ggdendro - r-ggplot2 - r-kableextra @@ -58,16 +68,21 @@ requirements: - r-mclust - r-plotrix - r-prabclus - - 'r-randomforest >=4.6.14' + - r-randomforest >=4.6.14 - r-rdpack - r-reshape2 + - r-rskc >=2.4.2 + - r-sparcl >=1.0.4 + +source: + md5: 0e266ceb6584309cbed2a0e4c5808390 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Evaluation of Bioinformatics Metrics' - description: 'Evaluating the reliability of your own metrics and the measurements done on your own datasets by analysing the stability and goodness of the classifications of such metrics.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-eventpointer/meta.yaml b/recipes/bioconductor-eventpointer/meta.yaml index 5bf12d43a71a1..adac499a715ec 100644 --- a/recipes/bioconductor-eventpointer/meta.yaml +++ b/recipes/bioconductor-eventpointer/meta.yaml @@ -1,43 +1,49 @@ -{% set version = "3.10.0" %} +{% set version = "3.14.0" %} {% set name = "EventPointer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'EventPointer is an R package to identify alternative splicing events that involve either simple (case-control experiment) or complex experimental designs such as time course experiments and studies including paired-samples. The algorithm can be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq). The software returns a data.frame with the detected alternative splicing events: gene name, type of event (cassette, alternative 3'',...,etc), genomic position, statistical significance and increment of the percent spliced in (Delta PSI) for all the events. The algorithm can generate a series of files to visualize the detected alternative splicing events in IGV. This eases the interpretation of results and the design of primers for standard PCR validation.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: An effective identification of alternative splicing events using junction arrays and RNA-Seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d25561e0288a54ed43c823b371941972 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-eventpointer", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr, kableExtra requirements: + + build: + - {{ compiler('c') }} + - make + host: - - 'bioconductor-affxparser >=1.74.0,<1.75.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-sgseq >=1.36.0,<1.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tximport >=1.30.0,<1.31.0' + - bioconductor-affxparser >=1.78.0,<1.79.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sgseq >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tximport >=1.34.0,<1.35.0 - r-abind - r-base - r-cobs @@ -57,24 +63,25 @@ requirements: - r-stringr - libblas - liblapack + run: - - 'bioconductor-affxparser >=1.74.0,<1.75.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-sgseq >=1.36.0,<1.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tximport >=1.30.0,<1.31.0' + - bioconductor-affxparser >=1.78.0,<1.79.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sgseq >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tximport >=1.34.0,<1.35.0 - r-abind - r-base - r-cobs @@ -92,15 +99,16 @@ requirements: - r-prodlim - r-speedglm - r-stringr - build: - - {{ compiler('c') }} - - make + +source: + md5: 3a6367af008681a816461b940909bca8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'An effective identification of alternative splicing events using junction arrays and RNA-Seq data' - description: 'EventPointer is an R package to identify alternative splicing events that involve either simple (case-control experiment) or complex experimental designs such as time course experiments and studies including paired-samples. The algorithm can be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq). The software returns a data.frame with the detected alternative splicing events: gene name, type of event (cassette, alternative 3'',...,etc), genomic position, statistical significance and increment of the percent spliced in (Delta PSI) for all the events. The algorithm can generate a series of files to visualize the detected alternative splicing events in IGV. This eases the interpretation of results and the design of primers for standard PCR validation.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ewce/meta.yaml b/recipes/bioconductor-ewce/meta.yaml index f085f9b01d230..4d87968f2aed9 100644 --- a/recipes/bioconductor-ewce/meta.yaml +++ b/recipes/bioconductor-ewce/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.10.2" %} +{% set version = "1.14.0" %} {% set name = "EWCE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Used to determine which cell types are enriched within gene lists. The package provides tools for testing enrichments within simple gene lists (such as human disease associated genes) and those resulting from differential expression studies. The package does not depend upon any particular Single Cell Transcriptome dataset and user defined datasets can be loaded in and used in the analyses. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Expression Weighted Celltype Enrichment -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b00b3feb36956603c46e6de1f03e9c09 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ewce", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rworkflows, remotes, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2, MAST, DelayedMatrixStats, ggdendro, scales, patchwork requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-ewcedata >=1.10.0,<1.11.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-orthogene >=1.8.0,<1.9.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-ewcedata >=1.14.0,<1.15.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-orthogene >=1.12.0,<1.13.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-dplyr @@ -36,16 +38,16 @@ requirements: - r-hgnchelper - r-matrix - r-reshape2 - - 'r-rnomni >=1.0' + - r-rnomni >=1.0 - r-stringr run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-ewcedata >=1.10.0,<1.11.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-orthogene >=1.8.0,<1.9.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-ewcedata >=1.14.0,<1.15.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-orthogene >=1.12.0,<1.13.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-dplyr @@ -53,15 +55,18 @@ requirements: - r-hgnchelper - r-matrix - r-reshape2 - - 'r-rnomni >=1.0' + - r-rnomni >=1.0 - r-stringr + +source: + md5: e13b2171ed0942acfd68bc0fb37d8ee0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Expression Weighted Celltype Enrichment' - description: 'Used to determine which cell types are enriched within gene lists. The package provides tools for testing enrichments within simple gene lists (such as human disease associated genes) and those resulting from differential expression studies. The package does not depend upon any particular Single Cell Transcriptome dataset and user defined datasets can be loaded in and used in the analyses.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ewcedata/meta.yaml b/recipes/bioconductor-ewcedata/meta.yaml index e46f489867173..07a499f2ecd6d 100644 --- a/recipes/bioconductor-ewcedata/meta.yaml +++ b/recipes/bioconductor-ewcedata/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "ewceData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d2ee91be35e2c5433ce16e94717c50e7 +about: + description: This package provides reference data required for ewce. Expression Weighted Celltype Enrichment (EWCE) is used to determine which cell types are enriched within gene lists. The package provides tools for testing enrichments within simple gene lists (such as human disease associated genes) and those resulting from differential expression studies. The package does not depend upon any particular Single Cell Transcriptome dataset and user defined datasets can be loaded in and used in the analyses. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: The ewceData package provides reference data required for ewce build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ewcedata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, BiocStyle, ggplot2, cowplot, rmarkdown, markdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 24cd796cc090d45d4d6cda652a12d394 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'The ewceData package provides reference data required for ewce' - description: 'This package provides reference data required for ewce. Expression Weighted Celltype Enrichment (EWCE) is used to determine which cell types are enriched within gene lists. The package provides tools for testing enrichments within simple gene lists (such as human disease associated genes) and those resulting from differential expression studies. The package does not depend upon any particular Single Cell Transcriptome dataset and user defined datasets can be loaded in and used in the analyses.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ewcedata/post-link.sh b/recipes/bioconductor-ewcedata/post-link.sh index 16e7f83675a3c..fd12208341193 100644 --- a/recipes/bioconductor-ewcedata/post-link.sh +++ b/recipes/bioconductor-ewcedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ewcedata-1.10.0" +installBiocDataPackage.sh "ewcedata-1.14.0" diff --git a/recipes/bioconductor-excluderanges/meta.yaml b/recipes/bioconductor-excluderanges/meta.yaml index 01959646c16da..e41e682755992 100644 --- a/recipes/bioconductor-excluderanges/meta.yaml +++ b/recipes/bioconductor-excluderanges/meta.yaml @@ -1,41 +1,41 @@ {% set version = "0.99.8" %} {% set name = "excluderanges" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2ec19df8a51df1900a339f7f505cd5fa +about: + description: Genomic coordinates of problematic genomic regions that should be avoided when working with genomic data. GRanges of exclusion regions (formerly known as blacklisted), centromeres, telomeres, known heterochromatin regions, etc. (UCSC 'gap' table data). Primarily for human and mouse genomes, hg19/hg38 and mm9/mm10 genome assemblies. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Genomic coordinates of problematic genomic regions build: - number: 1 + noarch: generic + number: 2 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-excluderanges", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, RefManageR, rmarkdown, ggridges, httr, readr, pheatmap, rtracklayer, AnnotationHub requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2ec19df8a51df1900a339f7f505cd5fa + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Genomic coordinates of problematic genomic regions' - description: 'Genomic coordinates of problematic genomic regions that should be avoided when working with genomic data. GRanges of exclusion regions (formerly known as blacklisted), centromeres, telomeres, known heterochromatin regions, etc. (UCSC ''gap'' table data). Primarily for human and mouse genomes, hg19/hg38 and mm9/mm10 genome assemblies.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-excluster/meta.yaml b/recipes/bioconductor-excluster/meta.yaml index d71771d5759d4..d73be919cddd5 100644 --- a/recipes/bioconductor-excluster/meta.yaml +++ b/recipes/bioconductor-excluster/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "ExCluster" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ExCluster flattens Ensembl and GENCODE GTF files into GFF files, which are used to count reads per non-overlapping exon bin from BAM files. This read counting is done using the function featureCounts from the package Rsubread. Library sizes are normalized across all biological replicates, and ExCluster then compares two different conditions to detect signifcantly differentially spliced genes. This process requires at least two independent biological repliates per condition, and ExCluster accepts only exactly two conditions at a time. ExCluster ultimately produces false discovery rates (FDRs) per gene, which are used to detect significance. Exon log2 fold change (log2FC) means and variances may be plotted for each significantly differentially spliced gene, which helps scientists develop hypothesis and target differential splicing events for RT-qPCR validation in the wet lab. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f60d612945a7f431831ce690d01d042 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-excluster", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsubread >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsubread >=2.20.0,<2.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-matrixstats run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsubread >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsubread >=2.20.0,<2.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-matrixstats + +source: + md5: 6e63697c865c6a3e6870c64c9f445c5f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition' - description: 'ExCluster flattens Ensembl and GENCODE GTF files into GFF files, which are used to count reads per non-overlapping exon bin from BAM files. This read counting is done using the function featureCounts from the package Rsubread. Library sizes are normalized across all biological replicates, and ExCluster then compares two different conditions to detect signifcantly differentially spliced genes. This process requires at least two independent biological repliates per condition, and ExCluster accepts only exactly two conditions at a time. ExCluster ultimately produces false discovery rates (FDRs) per gene, which are used to detect significance. Exon log2 fold change (log2FC) means and variances may be plotted for each significantly differentially spliced gene, which helps scientists develop hypothesis and target differential splicing events for RT-qPCR validation in the wet lab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-eximir/meta.yaml b/recipes/bioconductor-eximir/meta.yaml index 5aea5abeb29f4..17abd91a30654 100644 --- a/recipes/bioconductor-eximir/meta.yaml +++ b/recipes/bioconductor-eximir/meta.yaml @@ -1,49 +1,22 @@ -{% set version = "2.44.0" %} +{% set version = "2.48.0" %} {% set name = "ExiMiR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains functions for reading raw data in ImaGene TXT format obtained from Exiqon miRCURY LNA arrays, annotating them with appropriate GAL files, and normalizing them using a spike-in probe-based method. Other platforms and data formats are also supported. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: R functions for the normalization of Exiqon miRNA array data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a68c067ab91567287317a760f9e4c738 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-eximir", max_pin="x.x") }}' - noarch: generic -# Suggests: mirna10cdf -requirements: - host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - r-base - run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'R functions for the normalization of Exiqon miRNA array data' - description: 'This package contains functions for reading raw data in ImaGene TXT format obtained from Exiqon miRCURY LNA arrays, annotating them with appropriate GAL files, and normalizing them using a spike-in probe-based method. Other platforms and data formats are also supported.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + extra: identifiers: - biotools:eximir @@ -53,3 +26,36 @@ extra: path: recipes/bioconductor-eximir version: 2.22.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: mirna10cdf +requirements: + host: + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - r-base + run: + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - r-base + +source: + md5: 1731710afbb17675530b4164c95fe599 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-experimenthub/meta.yaml b/recipes/bioconductor-experimenthub/meta.yaml index 931b307d36148..cb5a2a9b9483e 100644 --- a/recipes/bioconductor-experimenthub/meta.yaml +++ b/recipes/bioconductor-experimenthub/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "2.10.0" %} +{% set version = "2.14.0" %} {% set name = "ExperimentHub" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated metadata, tags and date of modification. The client creates and manages a local cache of files retrieved enabling quick and reproducible access. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Client to access ExperimentHub resources -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bea896eadb8eb999e48d1cf5974dfe9e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-experimenthub", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-experimenthub + path: recipes/bioconductor-experimenthub + version: 1.6.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, rmarkdown, HubPub, GenomicAlignments requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-biocmanager - r-rappdirs run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-biocmanager - r-rappdirs + +source: + md5: 3608b4b40bdde65c4ed1b960412c2d47 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Client to access ExperimentHub resources' - description: 'This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated metadata, tags and date of modification. The client creates and manages a local cache of files retrieved enabling quick and reproducible access.' -extra: - parent_recipe: - name: bioconductor-experimenthub - path: recipes/bioconductor-experimenthub - version: 1.6.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-experimenthubdata/meta.yaml b/recipes/bioconductor-experimenthubdata/meta.yaml index 67fe9eb4addd6..4b2223a17bd80 100644 --- a/recipes/bioconductor-experimenthubdata/meta.yaml +++ b/recipes/bioconductor-experimenthubdata/meta.yaml @@ -1,52 +1,57 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "ExperimentHubData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions to add metadata to ExperimentHub db and resource files to AWS S3 buckets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Add resources to ExperimentHub -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e36d1a7958213cce85feccfd46fd7d5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-experimenthubdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: GenomeInfoDb, RUnit, knitr, BiocStyle, rmarkdown, HubPub requirements: host: - - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhubdata >=1.36.0,<1.37.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-biocmanager - r-curl - r-dbi - r-httr run: - - 'bioconductor-annotationhubdata >=1.32.0,<1.33.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhubdata >=1.36.0,<1.37.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-biocmanager - r-curl - r-dbi - r-httr + +source: + md5: cd6859088d3aa6cbeca30efde006244e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Add resources to ExperimentHub' - description: 'Functions to add metadata to ExperimentHub db and resource files to AWS S3 buckets.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-experimentsubset/meta.yaml b/recipes/bioconductor-experimentsubset/meta.yaml index b3c0f29e6a81f..fb319d8554e94 100644 --- a/recipes/bioconductor-experimentsubset/meta.yaml +++ b/recipes/bioconductor-experimentsubset/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "ExperimentSubset" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Experiment objects such as the SummarizedExperiment or SingleCellExperiment are data containers for one or more matrix-like assays along with the associated row and column data. Often only a subset of the original data is needed for down-stream analysis. For example, filtering out poor quality samples will require excluding some columns before analysis. The ExperimentSubset object is a container to efficiently manage different subsets of the same data without having to make separate objects for each new subset. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Manages subsets of data with Bioconductor Experiment objects -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fc52b3d67f7f9641a3851f987af7cdee build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-experimentsubset", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, covr, stats, scran, scater, scds, TENxPBMCData, airway requirements: host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 - r-base - r-matrix run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 - r-base - r-matrix + +source: + md5: c44f4126bb15efbf7c758493862a1e48 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Manages subsets of data with Bioconductor Experiment objects' - description: 'Experiment objects such as the SummarizedExperiment or SingleCellExperiment are data containers for one or more matrix-like assays along with the associated row and column data. Often only a subset of the original data is needed for down-stream analysis. For example, filtering out poor quality samples will require excluding some columns before analysis. The ExperimentSubset object is a container to efficiently manage different subsets of the same data without having to make separate objects for each new subset.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-exploremodelmatrix/meta.yaml b/recipes/bioconductor-exploremodelmatrix/meta.yaml index 810de26338c61..e1586107b9cce 100644 --- a/recipes/bioconductor-exploremodelmatrix/meta.yaml +++ b/recipes/bioconductor-exploremodelmatrix/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "ExploreModelMatrix" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Given a sample data table and a design formula, ExploreModelMatrix generates an interactive application for exploration of the resulting design matrix. This can be helpful for interpreting model coefficients and constructing appropriate contrasts in (generalized) linear models. Static visualizations can also be generated. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Graphical Exploration of Design Matrices -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 86f96045b0ae6877428f28466b113097 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-exploremodelmatrix", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 2.1.0), knitr, rmarkdown, htmltools, BiocStyle requirements: host: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cowplot - r-dplyr @@ -33,14 +35,14 @@ requirements: - r-mass - r-rintrojs - r-scales - - 'r-shiny >=1.5.0' + - r-shiny >=1.5.0 - r-shinydashboard - r-shinyjs - r-tibble - r-tidyr run: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cowplot - r-dplyr @@ -50,18 +52,21 @@ requirements: - r-mass - r-rintrojs - r-scales - - 'r-shiny >=1.5.0' + - r-shiny >=1.5.0 - r-shinydashboard - r-shinyjs - r-tibble - r-tidyr + +source: + md5: 39297c72f297757b65253adc109a23a6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Graphical Exploration of Design Matrices' - description: 'Given a sample data table and a design formula, ExploreModelMatrix generates an interactive application for exploration of the resulting design matrix. This can be helpful for interpreting model coefficients and constructing appropriate contrasts in (generalized) linear models. Static visualizations can also be generated.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-expressionatlas/meta.yaml b/recipes/bioconductor-expressionatlas/meta.yaml index 07e7c2df9194b..7cffc1e5aacb9 100644 --- a/recipes/bioconductor-expressionatlas/meta.yaml +++ b/recipes/bioconductor-expressionatlas/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "ExpressionAtlas" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is for searching for datasets in EMBL-EBI Expression Atlas, and downloading them into R for further analysis. Each Expression Atlas dataset is represented as a SimpleList object with one element per platform. Sequencing data is contained in a SummarizedExperiment object, while microarray data is contained in an ExpressionSet or MAList object. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Download datasets from EMBL-EBI Expression Atlas -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eb11568a0a2a81e1bf636eaa24e45906 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-expressionatlas", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-httr - r-jsonlite @@ -34,24 +36,27 @@ requirements: - r-xml - r-xml2 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-httr - r-jsonlite - r-rcurl - r-xml - r-xml2 + +source: + md5: ec6bb311127f2fa788c3786cdd4f1ddb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Download datasets from EMBL-EBI Expression Atlas' - description: 'This package is for searching for datasets in EMBL-EBI Expression Atlas, and downloading them into R for further analysis. Each Expression Atlas dataset is represented as a SimpleList object with one element per platform. Sequencing data is contained in a SummarizedExperiment object, while microarray data is contained in an ExpressionSet or MAList object.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-extrachips/build_failure.osx-64.yaml b/recipes/bioconductor-extrachips/build_failure.osx-64.yaml index 4061ce0faf29f..e419dfdae1dc7 100644 --- a/recipes/bioconductor-extrachips/build_failure.osx-64.yaml +++ b/recipes/bioconductor-extrachips/build_failure.osx-64.yaml @@ -1,106 +1,104 @@ -recipe_sha: cd6c654642b58a1ae021676e3516975dbc01a6ba6e27b668bc181e21ad457739 # The commit at which this recipe failed to build. +recipe_sha: 46c5f9e74ae90aee525f13dedf6513c9970931a7f29f33b172a33ac71f2b0cc3 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: |- - dependency issue log: |2- - /opt/mambaforge/envs/bioconda/conda-bld/work - Test: - /opt/mambaforge/envs/bioconda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/mambaforge/envs/bioconda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla - Build: - source activate /opt/mambaforge/envs/bioconda/conda-bld/_build_env - - - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action - t = self.solve(specs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - r-ggside >=0.2.2 - - r-glue - - libblas 3.9.* *netlib - - r-ggplot2 >=3.4.0 - - bioconductor-interactionset >=1.30.0,<1.31.0 - - r-dplyr >=1.1.1 - - liblapack 3.9.* *netlib - - bioconductor-enrichedheatmap >=1.32.0,<1.33.0 - - bioconductor-limma >=3.58.0,<3.59.0 - - bioconductor-rtracklayer >=1.62.0,<1.63.0 - - r-tidyr - - r-ggforce - - bioconductor-genomicranges >=1.54.0,<1.55.0 - - bioconductor-genomicinteractions >=1.36.0,<1.37.0 - - r-stringr - - r-scales - - r-tidyselect - - r-ggrepel - - r-base 4.3.* - - r-rlang - - bioconductor-iranges >=2.36.0,<2.37.0 - - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 - - bioconductor-edger >=4.0.0,<4.1.0 - - r-vctrs - - r-broom - - r-complexupset - - bioconductor-s4vectors >=0.40.0,<0.41.0 - - bioconductor-genomeinfodb >=1.38.0,<1.39.0 - - r-matrixstats - - r-patchwork - - bioconductor-csaw >=1.36.0,<1.37.0 - - r-forcats - - r-venndiagram - - bioconductor-biocio >=1.12.0,<1.13.0 - - bioconductor-gviz >=1.46.0,<1.47.0 - - r-rcolorbrewer - - r-tibble - - bioconductor-rsamtools >=2.18.0,<2.19.0 - - bioconductor-biocparallel >=1.36.0,<1.37.0 - - with channels: - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested bioconductor-enrichedheatmap >=1.32.0,<1.33.0 - - + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-genomeinfodbdata [1.2.1|1.2.2] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-genomeinfodbdata [1.2.10|1.2.11] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.3|1.2.4] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.6|1.2.7] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-genomeinfodbdata 1.2.9 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-ucsc.utils >=1.2.0,<1.3.0 is not installable because it requires + r-base >=4.4,<4.5.0a0 , which conflicts with any installable versions previously reported. During handling of the above exception, another exception occurred: Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs - for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set conda_packages = finalize_outputs_pass( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass fm = finalize_metadata( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata - build_unsat, host_unsat = add_upstream_pins(m, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins - host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files - deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies - actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-enrichedheatmap[version='>=1.32.0,<1.33.0']")} + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("4.0.1==hcfea43d_1"), MatchSpec("clang==4.0.1=1")} + Encountered problems while solving: + - nothing provides compiler-rt 4.0.1 hcfea43d_1 needed by clang-4.0.1-1 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-genomeinfodbdata >=1.2.0,<1.3.0 is installable with the potential options + bioconductor-genomeinfodbdata [1.2.0|1.2.1] would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-genomeinfodbdata [1.2.1|1.2.2] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-genomeinfodbdata [1.2.10|1.2.11] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.3|1.2.4] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.6|1.2.7] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-genomeinfodbdata 1.2.9 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-ucsc.utils >=1.2.0,<1.3.0 is not installable because it requires + r-base >=4.4,<4.5.0a0 , which conflicts with any installable versions previously reported. # Last 100 lines of the build log. diff --git a/recipes/bioconductor-extrachips/meta.yaml b/recipes/bioconductor-extrachips/meta.yaml index 678c82cbb0c55..722b7f4627c33 100644 --- a/recipes/bioconductor-extrachips/meta.yaml +++ b/recipes/bioconductor-extrachips/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "extraChIPs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data. The focus is on detecting differential binding windows/regions. One set of functions focusses on set-operations retaining mcols for GRanges objects, whilst another group of functions are to aid visualisation of results. Coercion to tibble objects is also implemented. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Additional functions for working with ChIP-Seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 462672c12f16f912b7e3d4b30a07162f build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-extrachips", max_pin="x.x") }}' -# Suggests: BiocStyle, covr, cqn, harmonicmeanp, here, knitr, magrittr, plyranges, quantro, rmarkdown, testthat (>= 3.0.0), tidyverse + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: apeglm, BiocStyle, covr, DESeq2, EnrichedHeatmap, Gviz, harmonicmeanp, here, knitr, limma, magrittr, plyranges, quantro, rmarkdown, testthat (>= 3.0.0), tidyverse requirements: + + build: + - {{ compiler('c') }} + - make + host: - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-csaw >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-enrichedheatmap >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-csaw >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicinteractions >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-broom - r-complexupset - - 'r-dplyr >=1.1.1' + - r-dplyr >=1.1.1 - r-forcats - r-ggforce - - 'r-ggplot2 >=3.4.0' + - r-ggplot2 >=3.5.0 - r-ggrepel - - 'r-ggside >=0.2.2' + - r-ggside >=0.3.1 - r-glue - r-matrixstats - r-patchwork @@ -60,32 +65,31 @@ requirements: - r-venndiagram - libblas - liblapack + run: - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-csaw >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-enrichedheatmap >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-csaw >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicinteractions >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-broom - r-complexupset - - 'r-dplyr >=1.1.1' + - r-dplyr >=1.1.1 - r-forcats - r-ggforce - - 'r-ggplot2 >=3.4.0' + - r-ggplot2 >=3.5.0 - r-ggrepel - - 'r-ggside >=0.2.2' + - r-ggside >=0.3.1 - r-glue - r-matrixstats - r-patchwork @@ -98,16 +102,16 @@ requirements: - r-tidyselect - r-vctrs - r-venndiagram - build: - - {{ compiler('c') }} - - make + +source: + md5: 922d1c66195a54c8d0918f64196a3ab3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Additional functions for working with ChIP-Seq data' - description: 'This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data. The focus is on detecting differential binding windows/regions. One set of functions focusses on set-operations retaining mcols for GRanges objects, whilst another group of functions are to aid visualisation of results. Coercion to tibble objects is also included.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-faahko/meta.yaml b/recipes/bioconductor-faahko/meta.yaml index 16959e9059ddd..9da2c9236b610 100644 --- a/recipes/bioconductor-faahko/meta.yaml +++ b/recipes/bioconductor-faahko/meta.yaml @@ -1,45 +1,51 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "faahKO" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Positive ionization mode data in NetCDF file format. Centroided subset from 200-600 m/z and 2500-4500 seconds. Data originally reported in "Assignment of Endogenous Substrates to Enzymes by Global Metabolite Profiling" Biochemistry; 2004; 43(45). Also includes detected peaks in an xcmsSet. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Saghatelian et al. (2004) FAAH knockout LC/MS data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3525f525973323d33955a68ca38b5cd7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-faahko", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-faahko + path: recipes/bioconductor-faahko + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base run: - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 6182750f76d8f196207b7ec0efaf06fc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Saghatelian et al. (2004) FAAH knockout LC/MS data' - description: 'Positive ionization mode data in NetCDF file format. Centroided subset from 200-600 m/z and 2500-4500 seconds. Data originally reported in "Assignment of Endogenous Substrates to Enzymes by Global Metabolite Profiling" Biochemistry; 2004; 43(45). Also includes detected peaks in an xcmsSet.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - parent_recipe: - name: bioconductor-faahko - path: recipes/bioconductor-faahko - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-faahko/post-link.sh b/recipes/bioconductor-faahko/post-link.sh index 8d50d83771269..4a4786c689388 100644 --- a/recipes/bioconductor-faahko/post-link.sh +++ b/recipes/bioconductor-faahko/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "faahko-1.42.0" +installBiocDataPackage.sh "faahko-1.46.0" diff --git a/recipes/bioconductor-fabia/meta.yaml b/recipes/bioconductor-fabia/meta.yaml index aadcaa307b6c8..b568f8d6698e9 100644 --- a/recipes/bioconductor-fabia/meta.yaml +++ b/recipes/bioconductor-fabia/meta.yaml @@ -1,49 +1,55 @@ -{% set version = "2.48.0" %} +{% set version = "2.52.0" %} {% set name = "fabia" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Biclustering by "Factor Analysis for Bicluster Acquisition" (FABIA). FABIA is a model-based technique for biclustering, that is clustering rows and columns simultaneously. Biclusters are found by factor analysis where both the factors and the loading matrix are sparse. FABIA is a multiplicative model that extracts linear dependencies between samples and feature patterns. It captures realistic non-Gaussian data distributions with heavy tails as observed in gene expression measurements. FABIA utilizes well understood model selection techniques like the EM algorithm and variational approaches and is embedded into a Bayesian framework. FABIA ranks biclusters according to their information content and separates spurious biclusters from true biclusters. The code is written in C. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2.1) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: 'FABIA: Factor Analysis for Bicluster Acquisition' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9d336b3c9a97aca0a6b062ec137f5566 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fabia", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:fabia + parent_recipe: + name: bioconductor-fabia + path: recipes/bioconductor-fabia + version: 2.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: c723d86c1d22e511ae29ad03f922be6a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2.1)' - summary: 'FABIA: Factor Analysis for Bicluster Acquisition' - description: 'Biclustering by "Factor Analysis for Bicluster Acquisition" (FABIA). FABIA is a model-based technique for biclustering, that is clustering rows and columns simultaneously. Biclusters are found by factor analysis where both the factors and the loading matrix are sparse. FABIA is a multiplicative model that extracts linear dependencies between samples and feature patterns. It captures realistic non-Gaussian data distributions with heavy tails as observed in gene expression measurements. FABIA utilizes well understood model selection techniques like the EM algorithm and variational approaches and is embedded into a Bayesian framework. FABIA ranks biclusters according to their information content and separates spurious biclusters from true biclusters. The code is written in C.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:fabia - parent_recipe: - name: bioconductor-fabia - path: recipes/bioconductor-fabia - version: 2.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fabiadata/meta.yaml b/recipes/bioconductor-fabiadata/meta.yaml index 8de5e015973e7..5c956dbcfd19c 100644 --- a/recipes/bioconductor-fabiadata/meta.yaml +++ b/recipes/bioconductor-fabiadata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "fabiaData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7fd64db4d15610a66c609e60624bbff9 +about: + description: 'Supplying gene expression data sets for the demos of the biclustering method "Factor Analysis for Bicluster Acquisition" (FABIA). The following three data sets are provided: A) breast cancer (van''t Veer, Nature, 2002), B) multiple tissues (Su, PNAS, 2002), and C) diffuse large-B-cell lymphoma (Rosenwald, N Engl J Med, 2002).' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL (>= 2.1) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Data sets for FABIA (Factor Analysis for Bicluster Acquisition) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fabiadata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: fabia requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: eda95b365fa1731facc3828ef343e176 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'LGPL (>= 2.1)' - summary: 'Data sets for FABIA (Factor Analysis for Bicluster Acquisition)' - description: 'Supplying gene expression data sets for the demos of the biclustering method "Factor Analysis for Bicluster Acquisition" (FABIA). The following three data sets are provided: A) breast cancer (van''t Veer, Nature, 2002), B) multiple tissues (Su, PNAS, 2002), and C) diffuse large-B-cell lymphoma (Rosenwald, N Engl J Med, 2002).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fabiadata/post-link.sh b/recipes/bioconductor-fabiadata/post-link.sh index 561c4ec71758f..b7e617575186a 100644 --- a/recipes/bioconductor-fabiadata/post-link.sh +++ b/recipes/bioconductor-fabiadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fabiadata-1.40.0" +installBiocDataPackage.sh "fabiadata-1.44.0" diff --git a/recipes/bioconductor-factdesign/meta.yaml b/recipes/bioconductor-factdesign/meta.yaml index 695bb48686cab..42003cbee10b3 100644 --- a/recipes/bioconductor-factdesign/meta.yaml +++ b/recipes/bioconductor-factdesign/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.78.0" %} +{% set version = "1.82.0" %} {% set name = "factDesign" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 774d444f3227bbac6bc13e48d3974b20 +about: + description: This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Factorial designed microarray experiment analysis build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-factdesign", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: affy, genefilter, multtest requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base +source: + md5: e8df9ca9d1db52d2c8180e2447bdb8c5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Factorial designed microarray experiment analysis' - description: 'This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-factr/meta.yaml b/recipes/bioconductor-factr/meta.yaml index a9c19a5db30aa..e3d2141224ce1 100644 --- a/recipes/bioconductor-factr/meta.yaml +++ b/recipes/bioconductor-factr/meta.yaml @@ -1,83 +1,90 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "factR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: factR contain tools to process and interact with custom-assembled transcriptomes (GTF). At its core, factR constructs CDS information on custom transcripts and subsequently predicts its functional output. In addition, factR has tools capable of plotting transcripts, correcting chromosome and gene information and shortlisting new transcripts. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Functional Annotation of Custom Transcriptomes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 55b088d84e382a7068b40062151e4bec build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-factr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationHub (>= 2.22), BSgenome (>= 1.58), BSgenome.Mmusculus.UCSC.mm10, testthat, knitr, rmarkdown, markdown, zeallot, rmdformats, bio3d (>= 2.4), signalHsmm (>= 1.5), tidyverse (>= 1.3), covr, patchwork requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-drawproteins >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-wiggleplotr >=1.26.0,<1.27.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-drawproteins >=1.26.0,<1.27.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-wiggleplotr >=1.30.0,<1.31.0 - r-base - - 'r-crayon >=1.5' - - 'r-data.table >=1.14' - - 'r-dplyr >=1.1' - - 'r-ggplot2 >=3.4' - - 'r-pbapply >=1.7' - - 'r-purrr >=1.0' - - 'r-rcurl >=1.98' - - 'r-rlang >=1.1' - - 'r-stringr >=1.5' - - 'r-tibble >=3.2' - - 'r-tidyr >=1.3' - - 'r-xml >=3.99' + - r-crayon >=1.5 + - r-data.table >=1.14 + - r-dplyr >=1.1 + - r-ggplot2 >=3.4 + - r-pbapply >=1.7 + - r-purrr >=1.0 + - r-rcurl >=1.98 + - r-rlang >=1.1 + - r-stringr >=1.5 + - r-tibble >=3.2 + - r-tidyr >=1.3 + - r-xml >=3.99 + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-drawproteins >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-wiggleplotr >=1.26.0,<1.27.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-drawproteins >=1.26.0,<1.27.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-wiggleplotr >=1.30.0,<1.31.0 - r-base - - 'r-crayon >=1.5' - - 'r-data.table >=1.14' - - 'r-dplyr >=1.1' - - 'r-ggplot2 >=3.4' - - 'r-pbapply >=1.7' - - 'r-purrr >=1.0' - - 'r-rcurl >=1.98' - - 'r-rlang >=1.1' - - 'r-stringr >=1.5' - - 'r-tibble >=3.2' - - 'r-tidyr >=1.3' - - 'r-xml >=3.99' + - r-crayon >=1.5 + - r-data.table >=1.14 + - r-dplyr >=1.1 + - r-ggplot2 >=3.4 + - r-pbapply >=1.7 + - r-purrr >=1.0 + - r-rcurl >=1.98 + - r-rlang >=1.1 + - r-stringr >=1.5 + - r-tibble >=3.2 + - r-tidyr >=1.3 + - r-xml >=3.99 + +source: + md5: 7398ad1642ccd6524192c11bf748a93b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Functional Annotation of Custom Transcriptomes' - description: 'factR contain tools to process and interact with custom-assembled transcriptomes (GTF). At its core, factR constructs CDS information on custom transcripts and subsequently predicts its functional output. In addition, factR has tools capable of plotting transcripts, correcting chromosome and gene information and shortlisting new transcripts.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-faers/build.sh b/recipes/bioconductor-faers/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-faers/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-faers/build_failure.linux-64.yaml b/recipes/bioconductor-faers/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..b9ccf30760f2c --- /dev/null +++ b/recipes/bioconductor-faers/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 2e04b042853d6c495a623c5e5d5eb9c21c68b4f69e569ef896c1b8f23be2c58e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-openebgm")} + Encountered problems while solving: + - nothing provides requested r-openebgm + + Could not solve for environment specs + The following package could not be installed + [31mr-openebgm[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-openebgm")} + Encountered problems while solving: + - nothing provides requested r-openebgm + + Could not solve for environment specs + The following package could not be installed + [31mr-openebgm[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-openebgm")} + Encountered problems while solving: + - nothing provides requested r-openebgm + + Could not solve for environment specs + The following package could not be installed + [31mr-openebgm[0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-faers/meta.yaml b/recipes/bioconductor-faers/meta.yaml new file mode 100644 index 0000000000000..cfe4c42b8c8ad --- /dev/null +++ b/recipes/bioconductor-faers/meta.yaml @@ -0,0 +1,66 @@ +{% set version = "1.2.0" %} +{% set name = "faers" %} +{% set bioc = "3.20" %} + +about: + description: The FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and medication errors related to human drugs and therapeutic biological products. faers pacakge serves as the interface between the FAERS database and R. Furthermore, faers pacakge offers a standardized approach for performing pharmacovigilance analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: R interface for FDA Adverse Event Reporting System + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-faers", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, countrycode, knitr, rmarkdown, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - r-base + - r-brio + - r-cli + - r-curl >=5.0.0 + - r-data.table + - r-httr2 >=1.0.0 + - r-mcmcpack + - r-openebgm + - r-rlang >=1.1.0 + - r-rvest + - r-vroom + - r-xml2 + run: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - r-base + - r-brio + - r-cli + - r-curl >=5.0.0 + - r-data.table + - r-httr2 >=1.0.0 + - r-mcmcpack + - r-openebgm + - r-rlang >=1.1.0 + - r-rvest + - r-vroom + - r-xml2 + +source: + md5: 6f5b9f73f58794d713d58eb894d029cf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-famagg/meta.yaml b/recipes/bioconductor-famagg/meta.yaml index b68b0c8f34645..9f54f19feed52 100644 --- a/recipes/bioconductor-famagg/meta.yaml +++ b/recipes/bioconductor-famagg/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "FamAgg" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Framework providing basic pedigree analysis and plotting utilities as well as a variety of methods to evaluate familial aggregation of traits in large pedigrees. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Pedigree Analysis and Familial Aggregation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0169ebe9c05d0b540946e2d111fe6437 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-famagg", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, RUnit, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - - 'r-gap >=1.1-17' + - r-gap >=1.1-17 - r-igraph - r-kinship2 - r-matrix - r-survey run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - - 'r-gap >=1.1-17' + - r-gap >=1.1-17 - r-igraph - r-kinship2 - r-matrix - r-survey + +source: + md5: 1fb97ae7499d620a5b30effc29cd5fe9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Pedigree Analysis and Familial Aggregation' - description: 'Framework providing basic pedigree analysis and plotting utilities as well as a variety of methods to evaluate familial aggregation of traits in large pedigrees.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-famat/meta.yaml b/recipes/bioconductor-famat/meta.yaml index 425dee5ad0e88..144e2520cd016 100644 --- a/recipes/bioconductor-famat/meta.yaml +++ b/recipes/bioconductor-famat/meta.yaml @@ -1,33 +1,36 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "famat" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Famat is made to collect data about lists of genes and metabolites provided by user, and to visualize it through a Shiny app. Information collected is: - Pathways containing some of the user''s genes and metabolites (obtained using a pathway enrichment analysis). - Direct interactions between user''s elements inside pathways. - Information about elements (their identifiers and descriptions). - Go terms enrichment analysis performed on user''s genes. The Shiny app is composed of: - information about genes, metabolites, and direct interactions between them inside pathways. - an heatmap showing which elements from the list are in pathways (pathways are structured in hierarchies). - hierarchies of enriched go terms using Molecular Function and Biological Process.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Functional analysis of metabolic and transcriptomic data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 12883ce4989ed35758a8902493e2bb07 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-famat", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, BiocManager requirements: + host: - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - - 'bioconductor-rwikipathways >=1.22.0,<1.23.0' + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-reactome.db >=1.89.0,<1.90.0 + - bioconductor-rwikipathways >=1.26.0,<1.27.0 - r-base - r-biasedurn - r-dplyr @@ -42,13 +45,14 @@ requirements: - r-shinydashboard - r-stringr - r-tidyr + run: - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - - 'bioconductor-rwikipathways >=1.22.0,<1.23.0' + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-reactome.db >=1.89.0,<1.90.0 + - bioconductor-rwikipathways >=1.26.0,<1.27.0 - r-base - r-biasedurn - r-dplyr @@ -63,13 +67,16 @@ requirements: - r-shinydashboard - r-stringr - r-tidyr + +source: + md5: 986dd091cadc19b393396a41dfb898d3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Functional analysis of metabolic and transcriptomic data' - description: 'Famat is made to collect data about lists of genes and metabolites provided by user, and to visualize it through a Shiny app. Information collected is: - Pathways containing some of the user''s genes and metabolites (obtained using a pathway enrichment analysis). - Direct interactions between user''s elements inside pathways. - Information about elements (their identifiers and descriptions). - Go terms enrichment analysis performed on user''s genes. The Shiny app is composed of: - information about genes, metabolites, and direct interactions between them inside pathways. - an heatmap showing which elements from the list are in pathways (pathways are structured in hierarchies). - hierarchies of enriched go terms using Molecular Function and Biological Process.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fantom3and4cage/meta.yaml b/recipes/bioconductor-fantom3and4cage/meta.yaml index bffc9cb885992..1ecef6b9b06cd 100644 --- a/recipes/bioconductor-fantom3and4cage/meta.yaml +++ b/recipes/bioconductor-fantom3and4cage/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "FANTOM3and4CAGE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d964e7a085d6a7b00e2b2215b765861 +about: + description: CAGE (Cap Analysis Gene Expression) data from FANTOM3 and FANTOM4 projects produced by RIKEN Omics Science Center. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: CAGE data from FANTOM3 and FANTOM4 projects build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fantom3and4cage", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a4c297c5de2e697b0aaddf7a5e1b1c91 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'CAGE data from FANTOM3 and FANTOM4 projects' - description: 'CAGE (Cap Analysis Gene Expression) data from FANTOM3 and FANTOM4 projects produced by RIKEN Omics Science Center.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fantom3and4cage/post-link.sh b/recipes/bioconductor-fantom3and4cage/post-link.sh index 53f3c97e37d5f..b42cfd4fa5dec 100644 --- a/recipes/bioconductor-fantom3and4cage/post-link.sh +++ b/recipes/bioconductor-fantom3and4cage/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fantom3and4cage-1.38.0" +installBiocDataPackage.sh "fantom3and4cage-1.42.0" diff --git a/recipes/bioconductor-fastliquidassociation/meta.yaml b/recipes/bioconductor-fastliquidassociation/meta.yaml index c8a5f515cdf33..c021be9ff330a 100644 --- a/recipes/bioconductor-fastliquidassociation/meta.yaml +++ b/recipes/bioconductor-fastliquidassociation/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "fastLiquidAssociation" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package extends the function of the LiquidAssociation package for genome-wide application. It integrates a screening method into the LA analysis to reduce the number of triplets to be examined for a high LA value and provides code for use in subsequent significance analyses. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: functions for genome-wide application of Liquid Association -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b57e0af4700d6a6872d88ca0d2eda5d1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fastliquidassociation", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: GOstats, yeastCC, org.Sc.sgd.db requirements: host: - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-liquidassociation >=1.56.0,<1.57.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-liquidassociation >=1.60.0,<1.61.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-doparallel - r-hmisc - r-wgcna run: - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-liquidassociation >=1.56.0,<1.57.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-liquidassociation >=1.60.0,<1.61.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-doparallel - r-hmisc - r-wgcna + +source: + md5: 1d83122b0da29a445f44549a39efa3f4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'functions for genome-wide application of Liquid Association' - description: 'This package extends the function of the LiquidAssociation package for genome-wide application. It integrates a screening method into the LA analysis to reduce the number of triplets to be examined for a high LA value and provides code for use in subsequent significance analyses.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fastqcleaner/meta.yaml b/recipes/bioconductor-fastqcleaner/meta.yaml index 5b847ec2591fe..c970be0d19574 100644 --- a/recipes/bioconductor-fastqcleaner/meta.yaml +++ b/recipes/bioconductor-fastqcleaner/meta.yaml @@ -1,65 +1,71 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "FastqCleaner" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An interactive web application for quality control, filtering and trimming of FASTQ files. This user-friendly tool combines a pipeline for data processing based on Biostrings and ShortRead infrastructure, with a cutting-edge visual environment. Single-Read and Paired-End files can be locally processed. Diagnostic interactive plots (CG content, per-base sequence quality, etc.) are provided for both the input and output files. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bace77f4e33bd7fe58cbbadaefd896d8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fastqcleaner", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:fastqcleaner + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-dt - r-htmltools - - 'r-rcpp >=0.12.12' + - r-rcpp >=0.12.12 - r-shiny - r-shinybs - libblas - liblapack run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-dt - r-htmltools - - 'r-rcpp >=0.12.12' + - r-rcpp >=0.12.12 - r-shiny - r-shinybs - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: f47adc4ac67b674b457019978bbc1313 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files' - description: 'An interactive web application for quality control, filtering and trimming of FASTQ files. This user-friendly tool combines a pipeline for data processing based on Biostrings and ShortRead infrastructure, with a cutting-edge visual environment. Single-Read and Paired-End files can be locally processed. Diagnostic interactive plots (CG content, per-base sequence quality, etc.) are provided for both the input and output files.' - license_file: LICENSE + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-fastreer/meta.yaml b/recipes/bioconductor-fastreer/meta.yaml index cf391745726da..0bf3476295911 100644 --- a/recipes/bioconductor-fastreer/meta.yaml +++ b/recipes/bioconductor-fastreer/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "fastreeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Calculate distances, build phylogenetic trees or perform hierarchical clustering between the samples of a VCF or FASTA file. Functions are implemented in Java and called via rJava. Parallel implementation that operates directly on the VCF or FASTA file for fast execution. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Phylogenetic, Distance and Other Calculations on VCF and Fasta Files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e2b7164aeaa305f819536d9b85e4de12 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fastreer", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocFileCache, BiocStyle, graphics, knitr, memuse, rmarkdown, spelling, testthat (>= 3.0.0) # SystemRequirements: Java (>= 8) requirements: @@ -40,13 +42,16 @@ requirements: - r-rjava - r-stringr - openjdk + +source: + md5: a6a0b1b9179ba80a049c4f873f216154 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Phylogenetic, Distance and Other Calculations on VCF and Fasta Files' - description: 'Calculate distances, build phylogenetic trees or perform hierarchical clustering between the samples of a VCF or FASTA file. Functions are implemented in Java and called via rJava. Parallel implementation that operates directly on the VCF or FASTA file for fast execution.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fastseg/meta.yaml b/recipes/bioconductor-fastseg/meta.yaml index 5e6686b13d3d2..a634a1ab6e57d 100644 --- a/recipes/bioconductor-fastseg/meta.yaml +++ b/recipes/bioconductor-fastseg/meta.yaml @@ -1,61 +1,67 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "fastseg" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: fastseg implements a very fast and efficient segmentation algorithm. It has similar functionality as DNACopy (Olshen and Venkatraman 2004), but is considerably faster and more flexible. fastseg can segment data from DNA microarrays and data from next generation sequencing for example to detect copy number segments. Further it can segment data from RNA microarrays like tiling arrays to identify transcripts. Most generally, it can segment data given as a matrix or as a vector. Various data formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data. The segmentation criterion of fastseg is based on a statistical test in a Bayesian framework, namely the cyber t-test (Baldi 2001). The speed-up arises from the facts, that sampling is not necessary in for fastseg and that a dynamic programming approach is used for calculation of the segments' first and higher order moments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2.0) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: fastseg - a fast segmentation algorithm -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ca8ead071a9b881b19dea7b71e0e73b4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fastseg", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:fastseg + parent_recipe: + name: bioconductor-fastseg + path: recipes/bioconductor-fastseg + version: 1.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: DNAcopy, oligo, BiocStyle, knitr requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: ee2d82665f214b479c99618ff566a7eb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL-3.0-or-later' - summary: 'fastseg - a fast segmentation algorithm' - description: 'fastseg implements a very fast and efficient segmentation algorithm. It has similar functionality as DNACopy (Olshen and Venkatraman 2004), but is considerably faster and more flexible. fastseg can segment data from DNA microarrays and data from next generation sequencing for example to detect copy number segments. Further it can segment data from RNA microarrays like tiling arrays to identify transcripts. Most generally, it can segment data given as a matrix or as a vector. Various data formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data. The segmentation criterion of fastseg is based on a statistical test in a Bayesian framework, namely the cyber t-test (Baldi 2001). The speed-up arises from the facts, that sampling is not necessary in for fastseg and that a dynamic programming approach is used for calculation of the segments'' first and higher order moments.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:fastseg - parent_recipe: - name: bioconductor-fastseg - path: recipes/bioconductor-fastseg - version: 1.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fccac/meta.yaml b/recipes/bioconductor-fccac/meta.yaml index e2b8cff1c58c2..528fa0237980f 100644 --- a/recipes/bioconductor-fccac/meta.yaml +++ b/recipes/bioconductor-fccac/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "fCCAC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Computational evaluation of variability across DNA or RNA sequencing datasets is a crucial step in genomics, as it allows both to evaluate reproducibility of replicates, and to compare different datasets to identify potential correlations. fCCAC applies functional Canonical Correlation Analysis to allow the assessment of: (i) reproducibility of biological or technical replicates, analyzing their shared covariance in higher order components; and (ii) the associations between different datasets. fCCAC represents a more sophisticated approach that complements Pearson correlation of genomic coverage.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4152105666120b6529f55983c4e2aa3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fccac", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:fccac + parent_recipe: + name: bioconductor-fccac + path: recipes/bioconductor-fccac + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomation >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genomation >=1.38.0,<1.39.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-fda - r-ggplot2 - r-rcolorbrewer run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomation >=1.34.0,<1.35.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genomation >=1.38.0,<1.39.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-fda - r-ggplot2 - r-rcolorbrewer + +source: + md5: fdc39a1bc4364b4639d38de2066b50e9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets' - description: 'Computational evaluation of variability across DNA or RNA sequencing datasets is a crucial step in genomics, as it allows both to evaluate reproducibility of replicates, and to compare different datasets to identify potential correlations. fCCAC applies functional Canonical Correlation Analysis to allow the assessment of: (i) reproducibility of biological or technical replicates, analyzing their shared covariance in higher order components; and (ii) the associations between different datasets. fCCAC represents a more sophisticated approach that complements Pearson correlation of genomic coverage.' -extra: - identifiers: - - biotools:fccac - parent_recipe: - name: bioconductor-fccac - path: recipes/bioconductor-fccac - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fci/meta.yaml b/recipes/bioconductor-fci/meta.yaml index de6bb8839434c..e9d4a567b5e76 100644 --- a/recipes/bioconductor-fci/meta.yaml +++ b/recipes/bioconductor-fci/meta.yaml @@ -1,26 +1,39 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "fCI" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: (f-divergence Cutoff Index), is to find DEGs in the transcriptomic & proteomic data, and identify DEGs by computing the difference between the distribution of fold-changes for the control-control and remaining (non-differential) case-control gene expression ratio data. fCI provides several advantages compared to existing methods. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a6ec7dcf6303ef44018924283b87586 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fci", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle requirements: + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] host: - r-base - r-fnn @@ -37,23 +50,16 @@ requirements: - r-rgl - r-venndiagram - r-zoo - build: - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - xorg-libxfixes # [linux] + +source: + md5: 78b2c630b7bbfd7653b2ba78aa7bf84b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics' - description: '(f-divergence Cutoff Index), is to find DEGs in the transcriptomic & proteomic data, and identify DEGs by computing the difference between the distribution of fold-changes for the control-control and remaining (non-differential) case-control gene expression ratio data. fCI provides several advantages compared to existing methods.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fcscan/meta.yaml b/recipes/bioconductor-fcscan/meta.yaml index bcf4f078fb8c9..0ceee65ad4b05 100644 --- a/recipes/bioconductor-fcscan/meta.yaml +++ b/recipes/bioconductor-fcscan/meta.yaml @@ -1,52 +1,57 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "fcScan" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is used to detect combination of genomic coordinates falling within a user defined window size along with user defined overlap between identified neighboring clusters. It can be used for genomic data where the clusters are built on a specific chromosome or specific strand. Clustering can be performed with a "greedy" option allowing thus the presence of additional sites within the allowed window size. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: fcScan for detecting clusters of coordinates with user defined options -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a23eab38b0106852ecca920f1f1db0bb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fcscan", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-doparallel - r-foreach - r-plyr run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-doparallel - r-foreach - r-plyr + +source: + md5: f16e62a21e927d148ab2847ce804c2a6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'fcScan for detecting clusters of coordinates with user defined options' - description: 'This package is used to detect combination of genomic coordinates falling within a user defined window size along with user defined overlap between identified neighboring clusters. It can be used for genomic data where the clusters are built on a specific chromosome or specific strand. Clustering can be performed with a "greedy" option allowing thus the presence of additional sites within the allowed window size.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fdb.fantom4.promoters.hg19/meta.yaml b/recipes/bioconductor-fdb.fantom4.promoters.hg19/meta.yaml index 3a5d0aac46574..4d67077da9d45 100644 --- a/recipes/bioconductor-fdb.fantom4.promoters.hg19/meta.yaml +++ b/recipes/bioconductor-fdb.fantom4.promoters.hg19/meta.yaml @@ -1,44 +1,44 @@ {% set version = "1.0.0" %} {% set name = "FDb.FANTOM4.promoters.hg19" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 99a610eb895470e3d945acc5cfb3ebe6 +about: + description: FANTOM4 promoters, liftOver'ed from hg18 to hg19, CpGs quantified + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for FANTOM4 promoters identified from THP-1 cells build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fdb.fantom4.promoters.hg19", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BSgenome.Hsapiens.UCSC.hg19, rtracklayer, matrixStats requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 99a610eb895470e3d945acc5cfb3ebe6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for FANTOM4 promoters identified from THP-1 cells' - description: 'FANTOM4 promoters, liftOver''ed from hg18 to hg19, CpGs quantified' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg18/meta.yaml b/recipes/bioconductor-fdb.infiniummethylation.hg18/meta.yaml index 66990d70a99d3..55b7406d9eebd 100644 --- a/recipes/bioconductor-fdb.infiniummethylation.hg18/meta.yaml +++ b/recipes/bioconductor-fdb.infiniummethylation.hg18/meta.yaml @@ -1,47 +1,52 @@ {% set version = "2.2.0" %} {% set name = "FDb.InfiniumMethylation.hg18" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Compiled HumanMethylation27 and HumanMethylation450 annotations + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for Illumina Infinium DNA methylation probes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 95ceab50d0a7c3d417cee12fbe3defb3 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fdb.infiniummethylation.hg18", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 95ceab50d0a7c3d417cee12fbe3defb3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for Illumina Infinium DNA methylation probes' - description: 'Compiled HumanMethylation27 and HumanMethylation450 annotations' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml b/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml index 3f4a764d09a61..d40d08579d4f8 100644 --- a/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml +++ b/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml @@ -1,53 +1,59 @@ {% set version = "2.2.0" %} {% set name = "FDb.InfiniumMethylation.hg19" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Compiled HumanMethylation27 and HumanMethylation450 annotations + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for Illumina Infinium DNA methylation probes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b8b1abc599b9556b9fe9c6e824cb2697 build: - number: 16 + noarch: generic + number: 17 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fdb.infiniummethylation.hg19", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-fdb.infiniummethylation.hg19 + path: recipes/bioconductor-fdb.infiniummethylation.hg19 + version: 2.2.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: FDb.UCSC.snp135common.hg19 requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: b8b1abc599b9556b9fe9c6e824cb2697 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for Illumina Infinium DNA methylation probes' - description: 'Compiled HumanMethylation27 and HumanMethylation450 annotations' -extra: - parent_recipe: - name: bioconductor-fdb.infiniummethylation.hg19 - path: recipes/bioconductor-fdb.infiniummethylation.hg19 - version: 2.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fdb.ucsc.snp135common.hg19/meta.yaml b/recipes/bioconductor-fdb.ucsc.snp135common.hg19/meta.yaml index 76eab4357415e..9bdf5def8533c 100644 --- a/recipes/bioconductor-fdb.ucsc.snp135common.hg19/meta.yaml +++ b/recipes/bioconductor-fdb.ucsc.snp135common.hg19/meta.yaml @@ -1,42 +1,42 @@ {% set version = "1.0.0" %} {% set name = "FDb.UCSC.snp135common.hg19" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0cdca5fa595bb69464016ceb97635f78 +about: + description: makeFeatureDbFromUCSC cannot cope with this track, hence a package + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: UCSC common SNPs track for dbSNP build 135 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fdb.ucsc.snp135common.hg19", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP.20111119 requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0cdca5fa595bb69464016ceb97635f78 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'UCSC common SNPs track for dbSNP build 135' - description: 'makeFeatureDbFromUCSC cannot cope with this track, hence a package' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fdb.ucsc.snp137common.hg19/meta.yaml b/recipes/bioconductor-fdb.ucsc.snp137common.hg19/meta.yaml index 0fd1755b911dc..9a7d4c8665391 100644 --- a/recipes/bioconductor-fdb.ucsc.snp137common.hg19/meta.yaml +++ b/recipes/bioconductor-fdb.ucsc.snp137common.hg19/meta.yaml @@ -1,42 +1,42 @@ {% set version = "1.0.0" %} {% set name = "FDb.UCSC.snp137common.hg19" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dac83f2d2f9ea9f033e50beac5c44838 +about: + description: makeFeatureDbFromUCSC cannot cope with this track, hence a package + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: UCSC common SNPs track for dbSNP build 137 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fdb.ucsc.snp137common.hg19", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: dac83f2d2f9ea9f033e50beac5c44838 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'UCSC common SNPs track for dbSNP build 137' - description: 'makeFeatureDbFromUCSC cannot cope with this track, hence a package' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fdb.ucsc.trnas/meta.yaml b/recipes/bioconductor-fdb.ucsc.trnas/meta.yaml index c95a592d717ad..0f7373aa683b0 100644 --- a/recipes/bioconductor-fdb.ucsc.trnas/meta.yaml +++ b/recipes/bioconductor-fdb.ucsc.trnas/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.0.1" %} {% set name = "FDb.UCSC.tRNAs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 77bfdadd4d9f995a72b001e4e41792fa +about: + description: Exposes an annotation databases generated from UCSC by exposing these as FeatureDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for FeatureDb object(s) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fdb.ucsc.trnas", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 77bfdadd4d9f995a72b001e4e41792fa + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for FeatureDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as FeatureDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fdrame/meta.yaml b/recipes/bioconductor-fdrame/meta.yaml index 37166d2fd75f6..b7bb6977ba0eb 100644 --- a/recipes/bioconductor-fdrame/meta.yaml +++ b/recipes/bioconductor-fdrame/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "fdrame" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d7fafba89f784f421a43b4b4d9a10000 +about: + description: This package contains two main functions. The first is fdr.ma which takes normalized expression data array, experimental design and computes adjusted p-values It returns the fdr adjusted p-values and plots, according to the methods described in (Reiner, Yekutieli and Benjamini 2002). The second, is fdr.gui() which creates a simple graphic user interface to access fdr.ma + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: FDR adjustments of Microarray Experiments (FDR-AME) build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fdrame", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - make +source: + md5: 6de56b8d555e47e22016d7db11cfd809 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'FDR adjustments of Microarray Experiments (FDR-AME)' - description: 'This package contains two main functions. The first is fdr.ma which takes normalized expression data array, experimental design and computes adjusted p-values It returns the fdr adjusted p-values and plots, according to the methods described in (Reiner, Yekutieli and Benjamini 2002). The second, is fdr.gui() which creates a simple graphic user interface to access fdr.ma' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-feast/meta.yaml b/recipes/bioconductor-feast/meta.yaml index 1ba80d9f1fc73..902594355e9c4 100644 --- a/recipes/bioconductor-feast/meta.yaml +++ b/recipes/bioconductor-feast/meta.yaml @@ -1,31 +1,36 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "FEAST" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Cell clustering is one of the most important and commonly performed tasks in single-cell RNA sequencing (scRNA-seq) data analysis. An important step in cell clustering is to select a subset of genes (referred to as “features”), whose expression patterns will then be used for downstream clustering. A good set of features should include the ones that distinguish different cell types, and the quality of such set could have significant impact on the clustering accuracy. FEAST is an R library for selecting most representative features before performing the core of scRNA-seq clustering. It can be used as a plug-in for the etablished clustering algorithms such as SC3, TSCAN, SHARP, SIMLR, and Seurat. The core of FEAST algorithm includes three steps: 1. consensus clustering; 2. gene-level significance inference; 3. validation of an optimized feature set.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: FEAture SelcTion (FEAST) for Single-cell clustering -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b32fdf869bc97368c62f50ccd8fe9f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-feast", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, Seurat, ggpubr, knitr, testthat (>= 3.0.0), BiocStyle requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-sc3 >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tscan >=1.40.0,<1.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-sc3 >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tscan >=1.44.0,<1.45.0 - r-base - r-irlba - r-matrixstats @@ -33,25 +38,25 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-sc3 >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tscan >=1.40.0,<1.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-sc3 >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tscan >=1.44.0,<1.45.0 - r-base - r-irlba - r-matrixstats - r-mclust - build: - - {{ compiler('c') }} - - make + +source: + md5: d33e020a1f78f62b8d8a2a4372b4cd25 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'FEAture SelcTion (FEAST) for Single-cell clustering' - description: 'Cell clustering is one of the most important and commonly performed tasks in single-cell RNA sequencing (scRNA-seq) data analysis. An important step in cell clustering is to select a subset of genes (referred to as “features”), whose expression patterns will then be used for downstream clustering. A good set of features should include the ones that distinguish different cell types, and the quality of such set could have significant impact on the clustering accuracy. FEAST is an R library for selecting most representative features before performing the core of scRNA-seq clustering. It can be used as a plug-in for the etablished clustering algorithms such as SC3, TSCAN, SHARP, SIMLR, and Seurat. The core of FEAST algorithm includes three steps: 1. consensus clustering; 2. gene-level significance inference; 3. validation of an optimized feature set.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-featseekr/meta.yaml b/recipes/bioconductor-featseekr/meta.yaml index b13b10cada5f1..f372b919070ed 100644 --- a/recipes/bioconductor-featseekr/meta.yaml +++ b/recipes/bioconductor-featseekr/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "FeatSeekR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9792a703c1ec0b4a58c759274c2cb571 +about: + description: FeatSeekR performs unsupervised feature selection using replicated measurements. It iteratively selects features with the highest reproducibility across replicates, after projecting out those dimensions from the data that are spanned by the previously selected features. The selected a set of features has a high replicate reproducibility and a high degree of uniqueness. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: FeatSeekR an R package for unsupervised feature selection build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-featseekr", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: rmarkdown, knitr, BiocStyle, DmelSGI, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-mass - r-pheatmap - r-pracma run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-mass - r-pheatmap - r-pracma +source: + md5: 23c49ca8d640009f029e1d88ae812f0c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'FeatSeekR an R package for unsupervised feature selection' - description: 'FeatSeekR performs unsupervised feature selection using replicated measurements. It iteratively selects features with the highest reproducibility across replicates, after projecting out those dimensions from the data that are spanned by the previously selected features. The selected a set of features has a high replicate reproducibility and a high degree of uniqueness.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fedup/meta.yaml b/recipes/bioconductor-fedup/meta.yaml index ab157eb4d27ac..82a273a3c4647 100644 --- a/recipes/bioconductor-fedup/meta.yaml +++ b/recipes/bioconductor-fedup/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "fedup" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An R package that tests for enrichment and depletion of user-defined pathways using a Fisher's exact test. The method is designed for versatile pathway annotation formats (eg. gmt, txt, xlsx) to allow the user to run pathway analysis on custom annotations. This package is also integrated with Cytoscape to provide network-based pathway visualization that enhances the interpretability of the results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Fisher's Test for Enrichment and Depletion of User-Defined Pathways -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a5ac34da42c1a460ab50e307c73f8116 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fedup", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: biomaRt, tidyr, testthat, knitr, rmarkdown, devtools, covr requirements: host: - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - bioconductor-rcy3 >=2.26.0,<2.27.0 - r-base - r-data.table - r-dplyr @@ -33,7 +35,7 @@ requirements: - r-rcolorbrewer - r-tibble run: - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - bioconductor-rcy3 >=2.26.0,<2.27.0 - r-base - r-data.table - r-dplyr @@ -43,13 +45,16 @@ requirements: - r-openxlsx - r-rcolorbrewer - r-tibble + +source: + md5: 2fb7cdf5b4e1ff7c7db26097ff526ceb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Fisher''s Test for Enrichment and Depletion of User-Defined Pathways' - description: 'An R package that tests for enrichment and depletion of user-defined pathways using a Fisher''s exact test. The method is designed for versatile pathway annotation formats (eg. gmt, txt, xlsx) to allow the user to run pathway analysis on custom annotations. This package is also integrated with Cytoscape to provide network-based pathway visualization that enhances the interpretability of the results.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fella/meta.yaml b/recipes/bioconductor-fella/meta.yaml index 0b00c88027e81..be2683cd21f29 100644 --- a/recipes/bioconductor-fella/meta.yaml +++ b/recipes/bioconductor-fella/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "FELLA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 106f8558197df891cfb6e28e406363e1 +about: + description: Enrichment of metabolomics data using KEGG entries. Given a set of affected compounds, FELLA suggests affected reactions, enzymes, modules and pathways using label propagation in a knowledge model network. The resulting subnetwork can be visualised and exported. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Interpretation and enrichment for metabolomics data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fella", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown, testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, GOSemSim requirements: host: - - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - bioconductor-keggrest >=1.46.0,<1.47.0 - r-base - r-igraph - r-matrix - r-plyr run: - - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - bioconductor-keggrest >=1.46.0,<1.47.0 - r-base - r-igraph - r-matrix - r-plyr +source: + md5: d75553fa94f41f0c2076f9db1e28ca78 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Interpretation and enrichment for metabolomics data' - description: 'Enrichment of metabolomics data using KEGG entries. Given a set of affected compounds, FELLA suggests affected reactions, enzymes, modules and pathways using label propagation in a knowledge model network. The resulting subnetwork can be visualised and exported.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fenr/meta.yaml b/recipes/bioconductor-fenr/meta.yaml index 1c2c8d0c43996..363b16b16cf59 100644 --- a/recipes/bioconductor-fenr/meta.yaml +++ b/recipes/bioconductor-fenr/meta.yaml @@ -1,71 +1,72 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "fenr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Perform fast functional enrichment on feature lists (like genes or proteins) using the hypergeometric distribution. Tailored for speed, this package is ideal for interactive platforms such as Shiny. It supports the retrieval of functional data from sources like GO, KEGG, Reactome, Bioplanet and WikiPathways. By downloading and preparing data first, it allows for rapid successive tests on various feature selections without the need for repetitive, time-consuming preparatory steps typical of other packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Fast functional enrichment for interactive applications -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f908fa38bd91672d7d0567d6232d2214 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fenr", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, testthat, knitr, rmarkdown, topGO, org.Hs.eg.db + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, testthat, knitr, rmarkdown, topGO requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-assertthat - r-base - r-dplyr - r-ggplot2 - - r-httr - - r-jsonlite + - r-httr2 - r-progress - r-purrr - r-readr - r-rlang + - r-rvest - r-shiny - r-stringr - r-tibble - r-tidyr - r-tidyselect - - r-xml run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-assertthat - r-base - r-dplyr - r-ggplot2 - - r-httr - - r-jsonlite + - r-httr2 - r-progress - r-purrr - r-readr - r-rlang + - r-rvest - r-shiny - r-stringr - r-tibble - r-tidyr - r-tidyselect - - r-xml + +source: + md5: 8dabad11245207b7387522c33936103c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Fast functional enrichment for interactive applications' - description: 'Perform fast functional enrichment on feature lists (like genes or proteins) using the hypergeometric distribution. Tailored for speed, this package is ideal for interactive platforms such as Shiny. It supports the retrieval of functional data from sources like GO, KEGG, Reactome, and WikiPathways. By downloading and preparing data first, it allows for rapid successive tests on various feature selections without the need for repetitive, time-consuming preparatory steps typical of other packages.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ffpe/meta.yaml b/recipes/bioconductor-ffpe/meta.yaml index 0a41ce9b5dabf..acae4cbbce87f 100644 --- a/recipes/bioconductor-ffpe/meta.yaml +++ b/recipes/bioconductor-ffpe/meta.yaml @@ -1,58 +1,64 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "ffpe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Quality assessment and control for FFPE microarray expression data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c2a3dbd53e85caf82d7c8f91a8277454 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ffpe", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:ffpe + parent_recipe: + name: bioconductor-ffpe + path: recipes/bioconductor-ffpe + version: 1.24.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: genefilter, ffpeExampleData requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' - - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-lumi >=2.58.0,<2.59.0 + - bioconductor-methylumi >=2.52.0,<2.53.0 - r-base - r-sfsmisc - r-ttr run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' - - 'bioconductor-methylumi >=2.48.0,<2.49.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-lumi >=2.58.0,<2.59.0 + - bioconductor-methylumi >=2.52.0,<2.53.0 - r-base - r-sfsmisc - r-ttr + +source: + md5: 03c8fd5b65c89bd2ea1cbe61e45fda1f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>2)' - summary: 'Quality assessment and control for FFPE microarray expression data' - description: 'Identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:ffpe - parent_recipe: - name: bioconductor-ffpe - path: recipes/bioconductor-ffpe - version: 1.24.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ffpeexampledata/meta.yaml b/recipes/bioconductor-ffpeexampledata/meta.yaml index e47fc10975fe9..e440287d9a49b 100644 --- a/recipes/bioconductor-ffpeexampledata/meta.yaml +++ b/recipes/bioconductor-ffpeexampledata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "ffpeExampleData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ea474bdf448ff6026ec4f1f376b7d69 +about: + description: A subset of GSE17565 (April et al. 2009) containing 32 FFPE samples of Burkitts Lymphoma and Breast Adenocarcinoma, with a dilution series in technical duplicate. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Illumina DASL example microarray data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ffpeexampledata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: genefilter, affy requirements: host: - - 'bioconductor-lumi >=2.54.0,<2.55.0' + - bioconductor-lumi >=2.58.0,<2.59.0 - r-base run: - - 'bioconductor-lumi >=2.54.0,<2.55.0' + - bioconductor-lumi >=2.58.0,<2.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6f800c039d810e224c1ed7726fe18396 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>2)' - summary: 'Illumina DASL example microarray data' - description: 'A subset of GSE17565 (April et al. 2009) containing 32 FFPE samples of Burkitts Lymphoma and Breast Adenocarcinoma, with a dilution series in technical duplicate.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ffpeexampledata/post-link.sh b/recipes/bioconductor-ffpeexampledata/post-link.sh index 8070c5cbda31e..633eecc9a4d49 100644 --- a/recipes/bioconductor-ffpeexampledata/post-link.sh +++ b/recipes/bioconductor-ffpeexampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ffpeexampledata-1.40.0" +installBiocDataPackage.sh "ffpeexampledata-1.44.0" diff --git a/recipes/bioconductor-fgga/meta.yaml b/recipes/bioconductor-fgga/meta.yaml index 5988b466d1305..74fcb0a042901 100644 --- a/recipes/bioconductor-fgga/meta.yaml +++ b/recipes/bioconductor-fgga/meta.yaml @@ -1,51 +1,58 @@ -{% set version = "1.9.0" %} +{% set version = "1.14.0" %} {% set name = "fgga" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package that implements the FGGA algorithm. This package provides a hierarchical ensemble method based ob factor graphs for the consistent cross-ontology annotation of protein coding genes. FGGA embodies elements of predicate logic, communication theory, supervised learning and inference in graphical models. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Hierarchical ensemble method based on factor graph -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eaa84557f2fd00490bb5f9f12e8ca1d3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fgga", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, GOstats, GO.db, BiocGenerics, pROC, RUnit, BiocStyle requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 - r-base - r-curl - r-e1071 - r-grbase + - r-igraph - r-jsonlite run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 - r-base - r-curl - r-e1071 - r-grbase + - r-igraph - r-jsonlite + +source: + md5: 74238ec93d8563e6f4477a065b954889 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Hierarchical ensemble method based on factor graph' - description: 'Package that implements the FGGA algorithm. This package provides a hierarchical ensemble method based ob factor graphs for the consistent cross-ontology annotation of protein coding genes. FGGA embodies elements of predicate logic, communication theory, supervised learning and inference in graphical models.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fgnet/meta.yaml b/recipes/bioconductor-fgnet/meta.yaml index c90b268edfc43..c98245cc585b5 100644 --- a/recipes/bioconductor-fgnet/meta.yaml +++ b/recipes/bioconductor-fgnet/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "3.36.0" %} +{% set version = "3.40.0" %} {% set name = "FGNet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Build and visualize functional gene and term networks from clustering of enrichment analyses in multiple annotation spaces. The package includes a graphical user interface (GUI) and functions to perform the functional enrichment analysis through DAVID, GeneTerm Linker, gage (GSEA) and topGO. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Functional Gene Networks derived from biological enrichment analyses -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 00da241d84bdc16ec9a8b1e27a3db509 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fgnet", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RCurl, gage, topGO, GO.db, reactome.db, RUnit, BiocGenerics, org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, BiocManager requirements: host: - r-base - r-hwriter - - 'r-igraph >=0.6' + - r-igraph >=0.6 - r-plotrix - r-png - r-r.utils @@ -34,20 +36,23 @@ requirements: run: - r-base - r-hwriter - - 'r-igraph >=0.6' + - r-igraph >=0.6 - r-plotrix - r-png - r-r.utils - r-rcolorbrewer - r-reshape2 - r-xml + +source: + md5: 5f52e86b12e3148c9c3b571964b8b5da + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Functional Gene Networks derived from biological enrichment analyses' - description: 'Build and visualize functional gene and term networks from clustering of enrichment analyses in multiple annotation spaces. The package includes a graphical user interface (GUI) and functions to perform the functional enrichment analysis through DAVID, GeneTerm Linker, gage (GSEA) and topGO.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fgsea/meta.yaml b/recipes/bioconductor-fgsea/meta.yaml index 8463d4f6d6021..1ddb1be75991c 100644 --- a/recipes/bioconductor-fgsea/meta.yaml +++ b/recipes/bioconductor-fgsea/meta.yaml @@ -1,70 +1,76 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "fgsea" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENCE + summary: Fast Gene Set Enrichment Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 53b8ab8a13390a0920bc13eeba3aa1b8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fgsea", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:fgsea + - doi:10.1101/060012 + parent_recipe: + name: bioconductor-fgsea + path: recipes/bioconductor-fgsea + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel, org.Mm.eg.db, limma, GEOquery, msigdbr, aggregation, Seurat # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-bh - r-cowplot - r-data.table - r-fastmatch - - 'r-ggplot2 >=2.2.0' + - r-ggplot2 >=2.2.0 - r-matrix - r-rcpp - r-scales - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-bh - r-cowplot - r-data.table - r-fastmatch - - 'r-ggplot2 >=2.2.0' + - r-ggplot2 >=2.2.0 - r-matrix - r-rcpp - r-scales - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: e03160202b15071056b5205a036af9a8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENCE' - summary: 'Fast Gene Set Enrichment Analysis' - description: 'The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:fgsea - - doi:10.1101/060012 - parent_recipe: - name: bioconductor-fgsea - path: recipes/bioconductor-fgsea - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fibroeset/meta.yaml b/recipes/bioconductor-fibroeset/meta.yaml index 8f520b8b38f59..8af3ad4a48417 100644 --- a/recipes/bioconductor-fibroeset/meta.yaml +++ b/recipes/bioconductor-fibroeset/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "fibroEset" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cbc13cc5c4ac4f6445dc69383ad183ff +about: + description: exprSet for Karaman et al. (2003) human, bonobo and gorilla fibroblasts data + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: exprSet for Karaman et al. (2003) fibroblasts data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fibroeset", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 86edf1f76f8d9627b678835b13535e9c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'exprSet for Karaman et al. (2003) fibroblasts data' - description: 'exprSet for Karaman et al. (2003) human, bonobo and gorilla fibroblasts data' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fibroeset/post-link.sh b/recipes/bioconductor-fibroeset/post-link.sh index bee7497a33fcb..65f38606442b0 100644 --- a/recipes/bioconductor-fibroeset/post-link.sh +++ b/recipes/bioconductor-fibroeset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fibroeset-1.44.0" +installBiocDataPackage.sh "fibroeset-1.48.0" diff --git a/recipes/bioconductor-fieldeffectcrc/meta.yaml b/recipes/bioconductor-fieldeffectcrc/meta.yaml index a75f40d2d0445..97fd74feb8dd5 100644 --- a/recipes/bioconductor-fieldeffectcrc/meta.yaml +++ b/recipes/bioconductor-fieldeffectcrc/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "FieldEffectCrc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Processed RNA-seq data for 1,139 human primary colorectal tissue samples across three phenotypes, including tumor, normal adjacent-to-tumor, and healthy, available as Synapse ID syn22237139 on synapse.org. Data have been parsed into SummarizedExperiment objects available via ExperimentHub to facilitate reproducibility and extension of results from Dampier et al. (PMCID: PMC7386360, PMID: 32764205).' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Tumor, tumor-adjacent normal, and healthy colorectal transcriptomes as SummarizedExperiment objects -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73fa4e8649f3c4a523764d35afd421f2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fieldeffectcrc", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocGenerics, sva, BiocManager requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-runit run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-runit - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 184e4ee06f9eba119f7aa0ec4dd9ec2e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Tumor, tumor-adjacent normal, and healthy colorectal transcriptomes as SummarizedExperiment objects' - description: 'Processed RNA-seq data for 1,139 human primary colorectal tissue samples across three phenotypes, including tumor, normal adjacent-to-tumor, and healthy, available as Synapse ID syn22237139 on synapse.org. Data have been parsed into SummarizedExperiment objects available via ExperimentHub to facilitate reproducibility and extension of results from Dampier et al. (PMCID: PMC7386360, PMID: 32764205).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fieldeffectcrc/post-link.sh b/recipes/bioconductor-fieldeffectcrc/post-link.sh index dca22c34d2083..0d7f7abf32f0d 100644 --- a/recipes/bioconductor-fieldeffectcrc/post-link.sh +++ b/recipes/bioconductor-fieldeffectcrc/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fieldeffectcrc-1.12.0" +installBiocDataPackage.sh "fieldeffectcrc-1.16.0" diff --git a/recipes/bioconductor-filterffpe/meta.yaml b/recipes/bioconductor-filterffpe/meta.yaml index 94d1f62824669..7747c5cf9dae7 100644 --- a/recipes/bioconductor-filterffpe/meta.yaml +++ b/recipes/bioconductor-filterffpe/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "FilterFFPE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package finds and filters artificial chimeric reads specifically generated in next-generation sequencing (NGS) process of formalin-fixed paraffin-embedded (FFPE) tissues. These artificial chimeric reads can lead to a large number of false positive structural variation (SV) calls. The required input is an indexed BAM file of a FFPE sample. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: FFPE Artificial Chimeric Read Filter for NGS data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e2aabe533af9d2779d1ffc2f76017ecd build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-filterffpe", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-doparallel - r-foreach run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-doparallel - r-foreach + +source: + md5: 51160456b5a170058da3be7cf01c2a02 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'FFPE Artificial Chimeric Read Filter for NGS data' - description: 'This package finds and filters artificial chimeric reads specifically generated in next-generation sequencing (NGS) process of formalin-fixed paraffin-embedded (FFPE) tissues. These artificial chimeric reads can lead to a large number of false positive structural variation (SV) calls. The required input is an indexed BAM file of a FFPE sample.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-findit2/meta.yaml b/recipes/bioconductor-findit2/meta.yaml index 62b26bed34e95..6b05139e2e32c 100644 --- a/recipes/bioconductor-findit2/meta.yaml +++ b/recipes/bioconductor-findit2/meta.yaml @@ -1,38 +1,40 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "FindIT2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'This package implements functions to find influential TF and target based on different input type. It have five module: Multi-peak multi-gene annotaion(mmPeakAnno module), Calculate regulation potential(calcRP module), Find influential Target based on ChIP-Seq and RNA-Seq data(Find influential Target module), Find influential TF based on different input(Find influential TF module), Calculate peak-gene or peak-peak correlation(peakGeneCor module). And there are also some other useful function like integrate different source information, calculate jaccard similarity for your TF.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: find influential TF and Target based on multi-omics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d48fffebc5ff34ec3276d3f4675d6c71 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-findit2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), TxDb.Athaliana.BioMart.plantsmart28 requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -46,18 +48,19 @@ requirements: - r-tibble - r-tidyr - r-withr + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -71,12 +74,16 @@ requirements: - r-tibble - r-tidyr - r-withr + +source: + md5: 3aee2d54a0360824c1edc2be3a7c021e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'find influential TF and Target based on multi-omics data' - description: 'This package implements functions to find influential TF and target based on different input type. It have five module: Multi-peak multi-gene annotaion(mmPeakAnno module), Calculate regulation potential(calcRP module), Find influential Target based on ChIP-Seq and RNA-Seq data(Find influential Target module), Find influential TF based on different input(Find influential TF module), Calculate peak-gene or peak-peak correlation(peakGeneCor module). And there are also some other useful function like integrate different source information, calculate jaccard similarity for your TF.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fis/meta.yaml b/recipes/bioconductor-fis/meta.yaml index bc6ce25a237ce..9c0a2ac9f6cb5 100644 --- a/recipes/bioconductor-fis/meta.yaml +++ b/recipes/bioconductor-fis/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "FIs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef807b75136742a1dcb5ea70993d5c38 +about: + description: Data set containing two complete lists of identified functional interaction partners in Human. Data are derived from Reactome and BioGRID databases. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Human Functional Interactions (FIs) for splineTimeR package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fis", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-fis + path: recipes/bioconductor-fis + version: 1.8.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 76cdfe37dba524d956bfd1a0f27b1843 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Human Functional Interactions (FIs) for splineTimeR package' - description: 'Data set containing two complete lists of identified functional interaction partners in Human. Data are derived from Reactome and BioGRID databases.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-fis - path: recipes/bioconductor-fis - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fis/post-link.sh b/recipes/bioconductor-fis/post-link.sh index 081f3868dae51..343bdfb05d8b2 100644 --- a/recipes/bioconductor-fis/post-link.sh +++ b/recipes/bioconductor-fis/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fis-1.30.0" +installBiocDataPackage.sh "fis-1.34.0" diff --git a/recipes/bioconductor-fishalyser/meta.yaml b/recipes/bioconductor-fishalyser/meta.yaml index 54a8f41dc04b4..2e6724a784b9b 100644 --- a/recipes/bioconductor-fishalyser/meta.yaml +++ b/recipes/bioconductor-fishalyser/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "FISHalyseR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: FISHalyseR provides functionality to process and analyse digital cell culture images, in particular to quantify FISH probes within nuclei. Furthermore, it extract the spatial location of each nucleus as well as each probe enabling spatial co-localisation analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: FISHalyseR a package for automated FISH quantification -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fea17ba4629a7d53c62eef47a3cdfab2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fishalyser", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:fishalyser + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-fishalyser + path: recipes/bioconductor-fishalyser + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: host: - - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - bioconductor-ebimage >=4.48.0,<4.49.0 - r-abind - r-base run: - - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - bioconductor-ebimage >=4.48.0,<4.49.0 - r-abind - r-base + +source: + md5: b6fb1a67f22be6ffd631e1d69c2e5e3a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'FISHalyseR a package for automated FISH quantification' - description: 'FISHalyseR provides functionality to process and analyse digital cell culture images, in particular to quantify FISH probes within nuclei. Furthermore, it extract the spatial location of each nucleus as well as each probe enabling spatial co-localisation analysis.' -extra: - identifiers: - - biotools:fishalyser - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-fishalyser - path: recipes/bioconductor-fishalyser - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fishpond/meta.yaml b/recipes/bioconductor-fishpond/meta.yaml index 92bd84c80a051..e0b01817af155 100644 --- a/recipes/bioconductor-fishpond/meta.yaml +++ b/recipes/bioconductor-fishpond/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "2.8.0" %} +{% set version = "2.12.0" %} {% set name = "fishpond" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Fishpond contains methods for differential transcript and gene expression analysis of RNA-seq data using inferential replicates for uncertainty of abundance quantification, as generated by Gibbs sampling or bootstrap sampling. Also the package contains a number of utilities for working with Salmon and Alevin quantification files. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'Fishpond: downstream methods and tools for expression data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 407bd027d801c207371750eba2c9d735 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fishpond", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db, samr, DESeq2, apeglm, tximportData, limma, ensembldb, EnsDb.Hsapiens.v86, GenomicFeatures, AnnotationDbi, pheatmap, Gviz, GenomeInfoDb, data.table requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-abind - r-base - r-gtools @@ -36,12 +38,12 @@ requirements: - r-matrixstats - r-svmisc run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-abind - r-base - r-gtools @@ -49,13 +51,16 @@ requirements: - r-matrix - r-matrixstats - r-svmisc + +source: + md5: 2a80b5aebb1d25f196c64571dac63941 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Fishpond: downstream methods and tools for expression data' - description: 'Fishpond contains methods for differential transcript and gene expression analysis of RNA-seq data using inferential replicates for uncertainty of abundance quantification, as generated by Gibbs sampling or bootstrap sampling. Also the package contains a number of utilities for working with Salmon and Alevin quantification files.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fission/meta.yaml b/recipes/bioconductor-fission/meta.yaml index 113cdd94fae1d..b0bb9dc107d6d 100644 --- a/recipes/bioconductor-fission/meta.yaml +++ b/recipes/bioconductor-fission/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "fission" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7d404509808bfc439270093b647ccd80 +about: + description: 'This package provides a RangedSummarizedExperiment object of read counts in genes for a time course RNA-Seq experiment of fission yeast (Schizosaccharomyces pombe) in response to oxidative stress (1M sorbitol treatment) at 0, 15, 30, 60, 120 and 180 mins. The samples are further divided between a wild-type group and a group with deletion of atf21. The read count matrix was prepared and provided by the author of the study: Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL, Wilkinson CR, Miller CJ. "A global non-coding RNA system modulates fission yeast protein levels in response to stress". Nat Commun 2014 May 23;5:3947. PMID: 24853205. GEO: GSE56761.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: RangedSummarizedExperiment for time course RNA-Seq of fission yeast in response to stress, by Leong et al., Nat Commun 2014. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fission", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, markdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 00d2bde8a4da959730467dc66fcaeef0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'RangedSummarizedExperiment for time course RNA-Seq of fission yeast in response to stress, by Leong et al., Nat Commun 2014.' - description: 'This package provides a RangedSummarizedExperiment object of read counts in genes for a time course RNA-Seq experiment of fission yeast (Schizosaccharomyces pombe) in response to oxidative stress (1M sorbitol treatment) at 0, 15, 30, 60, 120 and 180 mins. The samples are further divided between a wild-type group and a group with deletion of atf21. The read count matrix was prepared and provided by the author of the study: Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL, Wilkinson CR, Miller CJ. "A global non-coding RNA system modulates fission yeast protein levels in response to stress". Nat Commun 2014 May 23;5:3947. PMID: 24853205. GEO: GSE56761.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fission/post-link.sh b/recipes/bioconductor-fission/post-link.sh index e0380f99e57cd..da1f39de141d6 100644 --- a/recipes/bioconductor-fission/post-link.sh +++ b/recipes/bioconductor-fission/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fission-1.22.0" +installBiocDataPackage.sh "fission-1.26.0" diff --git a/recipes/bioconductor-fitcons.ucsc.hg19/meta.yaml b/recipes/bioconductor-fitcons.ucsc.hg19/meta.yaml index 8d3045a648c6b..37370f0a07cdc 100644 --- a/recipes/bioconductor-fitcons.ucsc.hg19/meta.yaml +++ b/recipes/bioconductor-fitcons.ucsc.hg19/meta.yaml @@ -1,49 +1,54 @@ {% set version = "3.7.1" %} {% set name = "fitCons.UCSC.hg19" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Store UCSC fitCons fitness consequences scores version 1.01 for the human genome (hg19). + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: UCSC fitCons fitness consequences scores for hg19 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 53d954890ec9b91084664a10161ce391 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fitcons.ucsc.hg19", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 53d954890ec9b91084664a10161ce391 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'UCSC fitCons fitness consequences scores for hg19' - description: 'Store UCSC fitCons fitness consequences scores version 1.01 for the human genome (hg19).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fithic/meta.yaml b/recipes/bioconductor-fithic/meta.yaml index adf18559a5108..67ea2b32a2ebc 100644 --- a/recipes/bioconductor-fithic/meta.yaml +++ b/recipes/bioconductor-fithic/meta.yaml @@ -1,25 +1,40 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "FitHiC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Confidence estimation for intra-chromosomal contact maps -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee894d402d0c5567935ade4f8dc75c29 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fithic", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:fithic + - doi:10.1101/gr.160374 + parent_recipe: + name: bioconductor-fithic + path: recipes/bioconductor-fithic + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-data.table @@ -32,25 +47,16 @@ requirements: - r-data.table - r-fdrtool - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: f47acf05e3efbc1d9718fe0b050cbee4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Confidence estimation for intra-chromosomal contact maps' - description: 'Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:fithic - - doi:10.1101/gr.160374 - parent_recipe: - name: bioconductor-fithic - path: recipes/bioconductor-fithic - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flagme/meta.yaml b/recipes/bioconductor-flagme/meta.yaml index 03d2d8604976d..5f27537840f50 100644 --- a/recipes/bioconductor-flagme/meta.yaml +++ b/recipes/bioconductor-flagme/meta.yaml @@ -1,28 +1,44 @@ -{% set version = "1.58.0" %} +{% set version = "1.62.0" %} {% set name = "flagme" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Fragment-level analysis of gas chromatography-massspectrometry metabolomics data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Analysis of Metabolomics GC/MS Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ada68435478c0172b282919125008b1f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flagme", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:flagme + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-flagme + path: recipes/bioconductor-flagme + version: 1.38.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-camera >=1.58.0,<1.59.0' - - 'bioconductor-gcspikelite >=1.40.0,<1.41.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-camera >=1.62.0,<1.63.0 + - bioconductor-gcspikelite >=1.44.0,<1.45.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base - r-gplots - r-mass @@ -30,33 +46,23 @@ requirements: - libblas - liblapack run: - - 'bioconductor-camera >=1.58.0,<1.59.0' - - 'bioconductor-gcspikelite >=1.40.0,<1.41.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-camera >=1.62.0,<1.63.0 + - bioconductor-gcspikelite >=1.44.0,<1.45.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base - r-gplots - r-mass - r-sparsem - build: - - {{ compiler('c') }} - - make + +source: + md5: c6d9abc07580087cde4663471c082727 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'Analysis of Metabolomics GC/MS Data' - description: 'Fragment-level analysis of gas chromatography-massspectrometry metabolomics data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:flagme - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-flagme - path: recipes/bioconductor-flagme - version: 1.38.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flames/build_failure.linux-64.yaml b/recipes/bioconductor-flames/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..fb8744fc90115 --- /dev/null +++ b/recipes/bioconductor-flames/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 460e3c44bf03344b2cd7de0a49cf7900a2d6846b4b8d651bd781b2cdc13e8528 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-bambu[version='>=3.8.0,<3.9.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-bambu >=3.8.0,<3.9.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-bambu >=3.8.0,<3.9.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-bambu[version='>=3.8.0,<3.9.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-bambu >=3.8.0,<3.9.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-bambu >=3.8.0,<3.9.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-bambu[version='>=3.8.0,<3.9.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-bambu >=3.8.0,<3.9.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-bambu >=3.8.0,<3.9.0 [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-flames/build_failure.osx-64.yaml b/recipes/bioconductor-flames/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..3865ed8de2f87 --- /dev/null +++ b/recipes/bioconductor-flames/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 460e3c44bf03344b2cd7de0a49cf7900a2d6846b4b8d651bd781b2cdc13e8528 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1 conflicts with any installable versions previously reported; + r-xgboost [0.82|0.90|...|1.4.0] would require + r-base >=3.6,<3.7.0a0 but there are no viable options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3] conflicts with any installable versions previously reported; + r-xgboost [1.0.2|1.1.1|...|1.6.2] would require + r-base >=4.0,<4.1.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.4.0|1.4.1|...|1.7.4] would require + r-base >=4.1,<4.2.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.6.2|1.7.0|...|2.0.3] would require + r-base >=4.2,<4.3.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.7.4|1.7.6|...|2.1.3] would require + r-base >=4.3,<4.4.0a0 , which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("clang==4.0.1=1"), MatchSpec("4.0.1==hcfea43d_1")} + Encountered problems while solving: + - nothing provides compiler-rt 4.0.1 hcfea43d_1 needed by clang-4.0.1-1 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-summarizedexperiment >=1.36.0,<1.37.0 is installable and it requires + bioconductor-delayedarray >=0.32.0,<0.33.0 , which requires + bioconductor-sparsearray >=1.6.0,<1.7.0 , which requires + r-base >=4.4,<4.5.0a0 , which can be installed; + r-xgboost is not installable because there are no viable options + r-xgboost [0.80|0.81|0.82|0.90|1.0.2] would require + r-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ] but there are no viable options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1 conflicts with any installable versions previously reported; + r-xgboost [0.82|0.90|...|1.4.0] would require + r-base >=3.6,<3.7.0a0 but there are no viable options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3] conflicts with any installable versions previously reported; + r-xgboost [1.0.2|1.1.1|...|1.6.2] would require + r-base >=4.0,<4.1.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.4.0|1.4.1|...|1.7.4] would require + r-base >=4.1,<4.2.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.6.2|1.7.0|...|2.0.3] would require + r-base >=4.2,<4.3.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.7.4|1.7.6|...|2.1.3] would require + r-base >=4.3,<4.4.0a0 , which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-flames/meta.yaml b/recipes/bioconductor-flames/meta.yaml index 05cea2c22df0e..497d58024010f 100644 --- a/recipes/bioconductor-flames/meta.yaml +++ b/recipes/bioconductor-flames/meta.yaml @@ -1,121 +1,240 @@ -{% set version = "1.8.0" %} +{% set version = "2.0.1" %} {% set name = "FLAMES" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Semi-supervised isoform detection and annotation from both bulk and single-cell long read RNA-seq data. Flames provides automated pipelines for analysing isoforms, as well as intermediate functions for manual execution. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ecfe856c54464ffd2c27f8e10063d494 build: - skip: True # [osx] number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flames", max_pin="x.x") }}' -# Suggests: BiocStyle, GEOquery, knitr, rmarkdown, markdown, BiocFileCache, R.utils, ShortRead, uwot, testthat (>= 3.0.0) -# SystemRequirements: GNU make, C++17 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, GEOquery, knitr, rmarkdown, BiocFileCache, R.utils, ShortRead, uwot, testthat (>= 3.0.0), xml2 +# SystemRequirements: GNU make, C++17, samtools (>= 1.19), minimap2 (>= 2.17) requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make + host: - - 'bioconductor-bambu >=3.4.0,<3.5.0' - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-dropletutils >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + + - bioconductor-bambu >=3.8.0,<3.9.0 + + - bioconductor-basilisk >=1.18.0,<1.19.0 + + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + + - bioconductor-biocparallel >=1.40.0,<1.41.0 + + - bioconductor-biostrings >=2.74.0,<2.75.0 + + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + + - bioconductor-dropletutils >=1.26.0,<1.27.0 + + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + + - bioconductor-genomicranges >=1.58.0,<1.59.0 + + - bioconductor-ggbio >=1.54.0,<1.55.0 + + - bioconductor-iranges >=2.40.0,<2.41.0 + + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + + - bioconductor-rhtslib >=3.2.0,<3.3.0 + + - bioconductor-rsamtools >=2.22.0,<2.23.0 + + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + + - bioconductor-s4vectors >=0.44.0,<0.45.0 + + - bioconductor-scater >=1.34.0,<1.35.0 + + - bioconductor-scran >=1.34.0,<1.35.0 + + - bioconductor-scuttle >=1.16.0,<1.17.0 + + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + + - bioconductor-txdbmaker >=1.2.0,<1.3.0 + - r-base + - r-circlize + - r-cowplot + - r-dplyr + - r-future + - r-ggplot2 + - r-gridextra + - r-igraph + - r-jsonlite + - r-magrittr + - r-matrix + - r-rcolorbrewer + - r-rcpp + + - r-readr + - r-reticulate + + - r-scatterpie + - r-stringr + + - r-testthat + + - r-tibble + - r-tidyr + + - r-tidyselect + - r-withr + - libblas + - liblapack + run: - - 'bioconductor-bambu >=3.4.0,<3.5.0' - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-dropletutils >=1.22.0,<1.23.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + + - bioconductor-bambu >=3.8.0,<3.9.0 + + - bioconductor-basilisk >=1.18.0,<1.19.0 + + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + + - bioconductor-biocparallel >=1.40.0,<1.41.0 + + - bioconductor-biostrings >=2.74.0,<2.75.0 + + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + + - bioconductor-dropletutils >=1.26.0,<1.27.0 + + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + + - bioconductor-genomicranges >=1.58.0,<1.59.0 + + - bioconductor-ggbio >=1.54.0,<1.55.0 + + - bioconductor-iranges >=2.40.0,<2.41.0 + + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + + - bioconductor-rhtslib >=3.2.0,<3.3.0 + + - bioconductor-rsamtools >=2.22.0,<2.23.0 + + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + + - bioconductor-s4vectors >=0.44.0,<0.45.0 + + - bioconductor-scater >=1.34.0,<1.35.0 + + - bioconductor-scran >=1.34.0,<1.35.0 + + - bioconductor-scuttle >=1.16.0,<1.17.0 + + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + + - bioconductor-txdbmaker >=1.2.0,<1.3.0 + - r-base + - r-circlize + - r-cowplot + - r-dplyr + - r-future + - r-ggplot2 + - r-gridextra + - r-igraph + - r-jsonlite + - r-magrittr + - r-matrix + - r-rcolorbrewer + - r-rcpp + + - r-readr + - r-reticulate + + - r-scatterpie + - r-stringr + + - r-testthat + + - r-tibble + - r-tidyr + + - r-tidyselect + - r-withr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 91b575154510fee50b3a3edc7fb4c9fc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data' - description: 'Semi-supervised isoform detection and annotation from both bulk and single-cell long read RNA-seq data. Flames provides automated pipelines for analysing isoforms, as well as intermediate functions for manual execution.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fletcher2013a/meta.yaml b/recipes/bioconductor-fletcher2013a/meta.yaml index e4bd34e45937a..d8020f796028b 100644 --- a/recipes/bioconductor-fletcher2013a/meta.yaml +++ b/recipes/bioconductor-fletcher2013a/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "Fletcher2013a" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package Fletcher2013a contains time-course gene expression data from MCF-7 cells treated under different experimental systems in order to perturb FGFR2 signalling. The data comes from Fletcher et al. (Nature Comms 4:2464, 2013) where further details about the background and the experimental design of the study can be found. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Gene expression data from breast cancer cells under FGFR2 signalling perturbation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e4c4f9a4e8b24a7a72f9c63337a0eef9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fletcher2013a", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-gplots - r-venndiagram run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-gplots - r-venndiagram - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 5641358237faed180be98f2794357119 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Gene expression data from breast cancer cells under FGFR2 signalling perturbation' - description: 'The package Fletcher2013a contains time-course gene expression data from MCF-7 cells treated under different experimental systems in order to perturb FGFR2 signalling. The data comes from Fletcher et al. (Nature Comms 4:2464, 2013) where further details about the background and the experimental design of the study can be found.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fletcher2013a/post-link.sh b/recipes/bioconductor-fletcher2013a/post-link.sh index 36042cfbda031..937c22c521e07 100644 --- a/recipes/bioconductor-fletcher2013a/post-link.sh +++ b/recipes/bioconductor-fletcher2013a/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fletcher2013a-1.38.0" +installBiocDataPackage.sh "fletcher2013a-1.42.0" diff --git a/recipes/bioconductor-fletcher2013b/meta.yaml b/recipes/bioconductor-fletcher2013b/meta.yaml index 5c2e191438443..5d0fd1b646bd7 100644 --- a/recipes/bioconductor-fletcher2013b/meta.yaml +++ b/recipes/bioconductor-fletcher2013b/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "Fletcher2013b" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package reproduces the systems biology analysis for the data in package Fletcher2013a using RTN. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Master regulators of FGFR2 signalling and breast cancer risk -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf656c92425c8a63ef584be08e8b742e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fletcher2013b", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-fletcher2013a >=1.38.0,<1.39.0' - - 'bioconductor-reder >=2.6.0,<2.7.0' - - 'bioconductor-rtn >=2.26.0,<2.27.0' + - bioconductor-fletcher2013a >=1.42.0,<1.43.0 + - bioconductor-reder >=3.2.0,<3.3.0 + - bioconductor-rtn >=2.30.0,<2.31.0 - r-base - r-igraph - r-rcolorbrewer run: - - 'bioconductor-fletcher2013a >=1.38.0,<1.39.0' - - 'bioconductor-reder >=2.6.0,<2.7.0' - - 'bioconductor-rtn >=2.26.0,<2.27.0' + - bioconductor-fletcher2013a >=1.42.0,<1.43.0 + - bioconductor-reder >=3.2.0,<3.3.0 + - bioconductor-rtn >=2.30.0,<2.31.0 - r-base - r-igraph - r-rcolorbrewer - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 3f9698b0e3c2785036a65560ac1e4141 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Master regulators of FGFR2 signalling and breast cancer risk' - description: 'This package reproduces the systems biology analysis for the data in package Fletcher2013a using RTN.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fletcher2013b/post-link.sh b/recipes/bioconductor-fletcher2013b/post-link.sh index 94b06ce4f03df..24bc41776b89f 100644 --- a/recipes/bioconductor-fletcher2013b/post-link.sh +++ b/recipes/bioconductor-fletcher2013b/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fletcher2013b-1.38.0" +installBiocDataPackage.sh "fletcher2013b-1.42.0" diff --git a/recipes/bioconductor-flowai/meta.yaml b/recipes/bioconductor-flowai/meta.yaml index 2a294b9332201..e5174a8c36e7b 100644 --- a/recipes/bioconductor-flowai/meta.yaml +++ b/recipes/bioconductor-flowai/meta.yaml @@ -1,28 +1,39 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "flowAI" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The package is able to perform an automatic or interactive quality control on FCS data acquired using flow cytometry instruments. By evaluating three different properties: 1) flow rate, 2) signal acquisition, 3) dynamic range, the quality control enables the detection and removal of anomalies.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Automatic and interactive quality control for flow cytometry data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 714cb015ac01ee026e02fc24536770e5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowai", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:flowai + - doi:10.1093/bioinformatics/btw191 + parent_recipe: + name: bioconductor-flowai + path: recipes/bioconductor-flowai + version: 1.10.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, shiny, BiocStyle requirements: host: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-changepoint - r-ggplot2 @@ -33,7 +44,7 @@ requirements: - r-rmarkdown - r-scales run: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-changepoint - r-ggplot2 @@ -43,21 +54,16 @@ requirements: - r-reshape2 - r-rmarkdown - r-scales + +source: + md5: d91a44359ec49ba9c4639ea7881e48a0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Automatic and interactive quality control for flow cytometry data' - description: 'The package is able to perform an automatic or interactive quality control on FCS data acquired using flow cytometry instruments. By evaluating three different properties: 1) flow rate, 2) signal acquisition, 3) dynamic range, the quality control enables the detection and removal of anomalies.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:flowai - - doi:10.1093/bioinformatics/btw191 - parent_recipe: - name: bioconductor-flowai - path: recipes/bioconductor-flowai - version: 1.10.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowbeads/meta.yaml b/recipes/bioconductor-flowbeads/meta.yaml index 275b1e5c29f2b..4250dbcb6c477 100644 --- a/recipes/bioconductor-flowbeads/meta.yaml +++ b/recipes/bioconductor-flowbeads/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "flowBeads" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalisation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'flowBeads: Analysis of flow bead data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3c9aa4f78c8b1b2397d6004773311174 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowbeads", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:flowbeads + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-flowbeads + path: recipes/bioconductor-flowbeads + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: flowViz requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-knitr - r-rrcov - r-xtable run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-knitr - r-rrcov - r-xtable + +source: + md5: dc5401946ec5a96b9a8a8b73faa4baf9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'flowBeads: Analysis of flow bead data' - description: 'This package extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalisation.' -extra: - identifiers: - - biotools:flowbeads - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-flowbeads - path: recipes/bioconductor-flowbeads - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowbin/meta.yaml b/recipes/bioconductor-flowbin/meta.yaml index 50962c3a7aee2..3a4f51d07f711 100644 --- a/recipes/bioconductor-flowbin/meta.yaml +++ b/recipes/bioconductor-flowbin/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "flowBin" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Software to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them, by establishing common bins across tubes in terms of the common markers, then determining expression within each tube for each bin in terms of the tube-specific markers. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Combining multitube flow cytometry data by binning -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d761d597ff6b4f6929e9f68ea83b366 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowbin", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: parallel requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowfp >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowfp >=1.64.0,<1.65.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-class - r-snow run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowfp >=1.60.0,<1.61.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowfp >=1.64.0,<1.65.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-class - r-snow + +source: + md5: f05c3c067de2d922e69795ec37957999 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Combining multitube flow cytometry data by binning' - description: 'Software to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them, by establishing common bins across tubes in terms of the common markers, then determining expression within each tube for each bin in terms of the tube-specific markers.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowcatchr/meta.yaml b/recipes/bioconductor-flowcatchr/meta.yaml index 5f47ecd63335c..d41a8d7e8e443 100644 --- a/recipes/bioconductor-flowcatchr/meta.yaml +++ b/recipes/bioconductor-flowcatchr/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "flowcatchR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: flowcatchR is a set of tools to analyze in vivo microscopy imaging data, focused on tracking flowing blood cells. It guides the steps from segmentation to calculation of features, filtering out particles not of interest, providing also a set of utilities to help checking the quality of the performed operations (e.g. how good the segmentation was). It allows investigating the issue of tracking flowing cells such as in blood vessels, to categorize the particles in flowing, rolling and adherent. This classification is applied in the study of phenomena such as hemostasis and study of thrombosis development. Moreover, flowcatchR presents an integrated workflow solution, based on the integration with a Shiny App and Jupyter notebooks, which is delivered alongside the package, and can enable fully reproducible bioimage analysis in the R environment. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_3_clause + file LICENSE + license_file: LICENSE + summary: Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a823367e5e1e432980ca41c1516c97f2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowcatchr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown # SystemRequirements: ImageMagick requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 - r-abind - r-base - r-colorramps @@ -32,21 +34,24 @@ requirements: - r-shiny - imagemagick run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 - r-abind - r-base - r-colorramps - r-plotly - r-shiny - imagemagick + +source: + md5: e205cf7f16c865551d2ad270faacf51c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_3_clause + file LICENSE' - summary: 'Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells' - description: 'flowcatchR is a set of tools to analyze in vivo microscopy imaging data, focused on tracking flowing blood cells. It guides the steps from segmentation to calculation of features, filtering out particles not of interest, providing also a set of utilities to help checking the quality of the performed operations (e.g. how good the segmentation was). It allows investigating the issue of tracking flowing cells such as in blood vessels, to categorize the particles in flowing, rolling and adherent. This classification is applied in the study of phenomena such as hemostasis and study of thrombosis development. Moreover, flowcatchR presents an integrated workflow solution, based on the integration with a Shiny App and Jupyter notebooks, which is delivered alongside the package, and can enable fully reproducible bioimage analysis in the R environment.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowchic/meta.yaml b/recipes/bioconductor-flowchic/meta.yaml index 2aaf6235bb116..0adea25b3fb6b 100644 --- a/recipes/bioconductor-flowchic/meta.yaml +++ b/recipes/bioconductor-flowchic/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "flowCHIC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package to analyze flow cytometric data of complex microbial communities based on histogram images + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Analyze flow cytometric data using histogram information -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 72e50628c116c31eebd78d620514dca1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowchic", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-ggplot2 - r-hexbin - r-vegan run: - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-ggplot2 - r-hexbin - r-vegan + +source: + md5: 50b1faabdbe5df483bca814fc0a3968e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Analyze flow cytometric data using histogram information' - description: 'A package to analyze flow cytometric data of complex microbial communities based on histogram images' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowclean/meta.yaml b/recipes/bioconductor-flowclean/meta.yaml index 02be800eea903..e5502f2d3382c 100644 --- a/recipes/bioconductor-flowclean/meta.yaml +++ b/recipes/bioconductor-flowclean/meta.yaml @@ -1,51 +1,57 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "flowClean" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A quality control tool for flow cytometry data based on compositional data analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: flowClean -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 77f86a84c8ed6dbd2df24d9458765205 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowclean", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:flowclean + parent_recipe: + name: bioconductor-flowclean + path: recipes/bioconductor-flowclean + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: flowViz, grid, gridExtra requirements: host: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-bit - r-changepoint - r-sfsmisc run: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-bit - r-changepoint - r-sfsmisc + +source: + md5: eee02602a4a92cfc96c356f4b2551001 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: flowClean - description: 'A quality control tool for flow cytometry data based on compositional data analysis.' -extra: - identifiers: - - biotools:flowclean - parent_recipe: - name: bioconductor-flowclean - path: recipes/bioconductor-flowclean - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowclust/meta.yaml b/recipes/bioconductor-flowclust/meta.yaml index e23f51ab272d9..cd87e100ce033 100644 --- a/recipes/bioconductor-flowclust/meta.yaml +++ b/recipes/bioconductor-flowclust/meta.yaml @@ -1,56 +1,61 @@ -{% set version = "3.40.0" %} +{% set version = "3.44.0" %} {% set name = "flowClust" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed. Windows users: ''consult the README file available in the inst directory of the source distribution for necessary configuration instructions''.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + summary: Clustering for Flow Cytometry -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 50e5d774ae44b8aaca69069733c175e3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowclust", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:flowclust + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, flowWorkspace, flowWorkspaceData, knitr, rmarkdown, openCyto, flowStats(>= 4.7.1) # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - automake + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - build: - - {{ compiler('c') }} - - automake - - make + +source: + md5: b1190a9b07cbb7a05d2e88572a2b7523 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: MIT - summary: 'Clustering for Flow Cytometry' - description: 'Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed. Windows users: ''consult the README file available in the inst directory of the source distribution for necessary configuration instructions''.' - -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowcore/Makevars.osx.patch b/recipes/bioconductor-flowcore/Makevars.osx.patch new file mode 100644 index 0000000000000..019f6524a0cf4 --- /dev/null +++ b/recipes/bioconductor-flowcore/Makevars.osx.patch @@ -0,0 +1,12 @@ +diff --git a/src/Makevars b/src/Makevars +index 96f0804..f5313ff 100644 +--- a/src/Makevars ++++ b/src/Makevars +@@ -2,6 +2,7 @@ CXX_STD = CXX17 + + PKG_CPPFLAGS =-DBOOST_NO_AUTO_PTR -w -Wfatal-errors + PKG_LIBS = `${R_HOME}/bin/Rscript -e "cytolib:::cytolib_LdFlags()"` ++PKG_CXXFLAGS = -D_LIBCPP_ENABLE_CXX17_REMOVED_UNARY_BINARY_FUNCTION + + .PHONY: all clean + diff --git a/recipes/bioconductor-flowcore/build.sh b/recipes/bioconductor-flowcore/build.sh index c1d13421f5f1e..5ea71a1203cac 100644 --- a/recipes/bioconductor-flowcore/build.sh +++ b/recipes/bioconductor-flowcore/build.sh @@ -8,4 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . \ No newline at end of file +$R CMD INSTALL --build . diff --git a/recipes/bioconductor-flowcore/meta.yaml b/recipes/bioconductor-flowcore/meta.yaml index f5a254a4c935c..ff6bc5fdcb158 100644 --- a/recipes/bioconductor-flowcore/meta.yaml +++ b/recipes/bioconductor-flowcore/meta.yaml @@ -1,70 +1,78 @@ -{% set version = "2.14.0" %} +{% set version = "2.18.0" %} {% set name = "flowCore" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides S4 data structures and basic functions to deal with flow cytometry data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'flowCore: Basic structures for flow cytometry data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3b0696fd3fc45a87531ab3503be00277 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowcore", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:flowcore + - doi:10.1186/1471-2105-10-106 + parent_recipe: + name: bioconductor-flowcore + path: recipes/bioconductor-flowcore + version: 1.46.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Rgraphviz, flowViz, flowStats (>= 3.43.4), testthat, flowWorkspace, flowWorkspaceData, openCyto, knitr, ggcyto, gridExtra # SystemRequirements: GNU make, C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-cytolib >=2.14.0,<2.15.0' - - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-cytolib >=2.18.0,<2.19.0 + - bioconductor-rprotobuflib >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-bh >=1.81.0.0' + - r-bh >=1.81.0.0 - r-cpp11 - r-matrixstats - r-rcpp - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-cytolib >=2.14.0,<2.15.0' - - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-cytolib >=2.18.0,<2.19.0 + - bioconductor-rprotobuflib >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-bh >=1.81.0.0' + - r-bh >=1.81.0.0 - r-cpp11 - r-matrixstats - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: b411dca0e1a3795bfb137ff69c12be5c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + patches: + - Makevars.osx.patch # [osx] + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'flowCore: Basic structures for flow cytometry data' - description: 'Provides S4 data structures and basic functions to deal with flow cytometry data.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:flowcore - - doi:10.1186/1471-2105-10-106 - parent_recipe: - name: bioconductor-flowcore - path: recipes/bioconductor-flowcore - version: 1.46.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowcut/meta.yaml b/recipes/bioconductor-flowcut/meta.yaml index f60fa58a8ac7a..e4e7b5b0eadb5 100644 --- a/recipes/bioconductor-flowcut/meta.yaml +++ b/recipes/bioconductor-flowcut/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "flowCut" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b79bc38dd887cef19040c2d7178311d0 +about: + description: Common techinical complications such as clogging can result in spurious events and fluorescence intensity shifting, flowCut is designed to detect and remove technical artifacts from your data by removing segments that show statistical differences from other segments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence Analysis build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowcut", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: RUnit, BiocGenerics, knitr, markdown, rmarkdown requirements: host: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowdensity >=1.36.0,<1.37.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowdensity >=1.40.0,<1.41.0 - r-base - r-cairo - r-e1071 run: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowdensity >=1.36.0,<1.37.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowdensity >=1.40.0,<1.41.0 - r-base - r-cairo - r-e1071 +source: + md5: 6f7365a1629078183175226e937235df + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence Analysis' - description: 'Common techinical complications such as clogging can result in spurious events and fluorescence intensity shifting, flowCut is designed to detect and remove technical artifacts from your data by removing segments that show statistical differences from other segments.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowcybar/meta.yaml b/recipes/bioconductor-flowcybar/meta.yaml index cf71a394b6ac8..f1fd5eb4fce55 100644 --- a/recipes/bioconductor-flowcybar/meta.yaml +++ b/recipes/bioconductor-flowcybar/meta.yaml @@ -1,24 +1,32 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "flowCyBar" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package to analyze flow cytometric data using gate information to follow population/community dynamics + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Analyze flow cytometric data using gate information -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9236c02598960d4536906fb7449a7dd4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowcybar", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-flowcybar + path: recipes/bioconductor-flowcybar + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -28,18 +36,16 @@ requirements: - r-base - r-gplots - r-vegan + +source: + md5: 1a3b177d6f50d31ac264a2ae92be1088 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Analyze flow cytometric data using gate information' - description: 'A package to analyze flow cytometric data using gate information to follow population/community dynamics' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - parent_recipe: - name: bioconductor-flowcybar - path: recipes/bioconductor-flowcybar - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowdensity/meta.yaml b/recipes/bioconductor-flowdensity/meta.yaml index 4e52b04c18b7d..4f0b2c22a31b3 100644 --- a/recipes/bioconductor-flowdensity/meta.yaml +++ b/recipes/bioconductor-flowdensity/meta.yaml @@ -1,57 +1,63 @@ -{% set version = "1.36.1" %} +{% set version = "1.40.0" %} {% set name = "flowDensity" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides tools for automated sequential gating analogous to the manual gating strategy based on the density of the data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Sequential Flow Cytometry Data Gating -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 30c661d010484bff6c2eb427a7056aa1 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowdensity", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:flowdensity + - doi:10.1093/bioinformatics/btu677 + parent_recipe: + name: bioconductor-flowdensity + path: recipes/bioconductor-flowdensity + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr,rmarkdown # SystemRequirements: xml2, GNU make, C++11 requirements: host: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowviz >=1.66.0,<1.67.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowviz >=1.70.0,<1.71.0 - r-base - r-car - r-gplots - r-polyclip - libxml2 run: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowviz >=1.66.0,<1.67.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowviz >=1.70.0,<1.71.0 - r-base - r-car - r-gplots - r-polyclip - libxml2 + +source: + md5: f8a6179a1f1db37cd7145195943ea570 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Sequential Flow Cytometry Data Gating' - description: 'This package provides tools for automated sequential gating analogous to the manual gating strategy based on the density of the data.' -extra: - identifiers: - - biotools:flowdensity - - doi:10.1093/bioinformatics/btu677 - parent_recipe: - name: bioconductor-flowdensity - path: recipes/bioconductor-flowdensity - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowfp/meta.yaml b/recipes/bioconductor-flowfp/meta.yaml index 8d91ab91bc4af..5ba3b2c1bdc94 100644 --- a/recipes/bioconductor-flowfp/meta.yaml +++ b/recipes/bioconductor-flowfp/meta.yaml @@ -1,51 +1,20 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "flowFP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Fingerprinting for Flow Cytometry -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f0424d8a662d2d65bacbcff080d9c7a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowfp", max_pin="x.x") }}' -# Suggests: RUnit -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowviz >=1.66.0,<1.67.0' - - r-base - - libblas - - liblapack - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowviz >=1.66.0,<1.67.0' - - r-base - build: - - {{ compiler('c') }} - - automake - - make -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Fingerprinting for Flow Cytometry' - description: 'Fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry.' + extra: additional-platforms: - linux-aarch64 @@ -57,3 +26,40 @@ extra: path: recipes/bioconductor-flowfp version: 1.38.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RUnit +requirements: + build: + - {{ compiler('c') }} + - automake + - make + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowviz >=1.70.0,<1.71.0 + - r-base + - libblas + - liblapack + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowviz >=1.70.0,<1.71.0 + - r-base + +source: + md5: 4acdf7ed2e759488602cf4625b99f1f5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-flowgate/meta.yaml b/recipes/bioconductor-flowgate/meta.yaml index c565637710606..9749e1ed9982a 100644 --- a/recipes/bioconductor-flowgate/meta.yaml +++ b/recipes/bioconductor-flowgate/meta.yaml @@ -1,57 +1,62 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "flowGate" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: flowGate adds an interactive Shiny app to allow manual GUI-based gating of flow cytometry data in R. Using flowGate, you can draw 1D and 2D span/rectangle gates, quadrant gates, and polygon gates on flow cytometry data by interactively drawing the gates on a plot of your data, rather than by specifying gate coordinates. This package is especially geared toward wet-lab cytometerists looking to take advantage of R for cytometry analysis, without necessarily having a lot of R experience. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Interactive Cytometry Gating in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d5b19dee6139d26306d14563f445a64f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowgate", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, stringr, tidyverse, testthat requirements: host: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' - - 'bioconductor-ggcyto >=1.30.0,<1.31.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowworkspace >=4.18.0,<4.19.0 + - bioconductor-ggcyto >=1.34.0,<1.35.0 - r-base - - 'r-biocmanager >=1.30.10' - - 'r-dplyr >=1.0.0' - - 'r-ggplot2 >=3.3.2' + - r-biocmanager >=1.30.10 + - r-dplyr >=1.0.0 + - r-ggplot2 >=3.3.2 - r-purrr - - 'r-rlang >=0.4.7' - - 'r-shiny >=1.5.0' + - r-rlang >=0.4.7 + - r-shiny >=1.5.0 - r-tibble run: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' - - 'bioconductor-ggcyto >=1.30.0,<1.31.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowworkspace >=4.18.0,<4.19.0 + - bioconductor-ggcyto >=1.34.0,<1.35.0 - r-base - - 'r-biocmanager >=1.30.10' - - 'r-dplyr >=1.0.0' - - 'r-ggplot2 >=3.3.2' + - r-biocmanager >=1.30.10 + - r-dplyr >=1.0.0 + - r-ggplot2 >=3.3.2 - r-purrr - - 'r-rlang >=0.4.7' - - 'r-shiny >=1.5.0' + - r-rlang >=0.4.7 + - r-shiny >=1.5.0 - r-tibble + +source: + md5: 6839d6a9ee70a9095f5c78417d5e1c4a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Interactive Cytometry Gating in R' - description: 'flowGate adds an interactive Shiny app to allow manual GUI-based gating of flow cytometry data in R. Using flowGate, you can draw 1D and 2D span/rectangle gates, quadrant gates, and polygon gates on flow cytometry data by interactively drawing the gates on a plot of your data, rather than by specifying gate coordinates. This package is especially geared toward wet-lab cytometerists looking to take advantage of R for cytometry analysis, without necessarily having a lot of R experience.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowgraph/meta.yaml b/recipes/bioconductor-flowgraph/meta.yaml index a0e5db9f2c1f9..179d53e2fda36 100644 --- a/recipes/bioconductor-flowgraph/meta.yaml +++ b/recipes/bioconductor-flowgraph/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "flowGraph" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Identifies maximal differential cell populations in flow cytometry data taking into account dependencies between cell populations; flowGraph calculates and plots SpecEnr abundance scores given cell population cell counts. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Identifying differential cell populations in flow cytometry data accounting for marker frequency -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 68abd457f6a200f435ebbf41183c0e94 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowgraph", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, dplyr, knitr, rmarkdown, testthat (>= 2.1.0) requirements: host: - r-base - - 'r-data.table >=1.9.5' + - r-data.table >=1.9.5 - r-effsize - r-furrr - r-future @@ -42,7 +43,7 @@ requirements: - r-visnetwork run: - r-base - - 'r-data.table >=1.9.5' + - r-data.table >=1.9.5 - r-effsize - r-furrr - r-future @@ -59,12 +60,16 @@ requirements: - r-stringi - r-stringr - r-visnetwork + +source: + md5: 3e0352ed9503c0f07870b7cdb680e16e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Identifying differential cell populations in flow cytometry data accounting for marker frequency' - description: 'Identifies maximal differential cell populations in flow cytometry data taking into account dependencies between cell populations; flowGraph calculates and plots SpecEnr abundance scores given cell population cell counts.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowmatch/meta.yaml b/recipes/bioconductor-flowmatch/meta.yaml index c27636b543ddd..c9cb65aa7b92e 100644 --- a/recipes/bioconductor-flowmatch/meta.yaml +++ b/recipes/bioconductor-flowmatch/meta.yaml @@ -1,49 +1,20 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "flowMatch" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Matching cell populations and building meta-clusters and templates from a collection of FC samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Matching and meta-clustering in flow cytometry -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 78b2b9dc87eec35dbc65c59dadb1ffd9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowmatch", max_pin="x.x") }}' -# Suggests: healthyFlowData -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - r-base - - 'r-rcpp >=0.11.0' - - libblas - - liblapack - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - r-base - - 'r-rcpp >=0.11.0' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Matching and meta-clustering in flow cytometry' - description: 'Matching cell populations and building meta-clusters and templates from a collection of FC samples.' + extra: additional-platforms: - linux-aarch64 @@ -55,3 +26,38 @@ extra: path: recipes/bioconductor-flowmatch version: 1.16.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: healthyFlowData +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - r-base + - r-rcpp >=0.11.0 + - libblas + - liblapack + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - r-base + - r-rcpp >=0.11.0 + +source: + md5: 92ecb83b13231e14d0da52577b4d337d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-flowmeans/meta.yaml b/recipes/bioconductor-flowmeans/meta.yaml index 4830d38e0f6a9..9c649bb12463e 100644 --- a/recipes/bioconductor-flowmeans/meta.yaml +++ b/recipes/bioconductor-flowmeans/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "1.62.0" %} +{% set version = "1.66.0" %} {% set name = "flowMeans" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. Note: R 2.11.0 or newer is required.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Non-parametric Flow Cytometry Data Gating -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5cbb796502f09bf65cae60e4f0f53c1f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowmeans", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-feature - r-rrcov run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-feature - r-rrcov - build: - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - xorg-libxfixes # [linux] + +source: + md5: 8fb6fa14a8a5b2081c6c48cda14a45ff + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Non-parametric Flow Cytometry Data Gating' - description: 'Identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. Note: R 2.11.0 or newer is required.' -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowmerge/meta.yaml b/recipes/bioconductor-flowmerge/meta.yaml index cb220a14afbac..f1cdf757fc635 100644 --- a/recipes/bioconductor-flowmerge/meta.yaml +++ b/recipes/bioconductor-flowmerge/meta.yaml @@ -1,62 +1,68 @@ -{% set version = "2.50.0" %} +{% set version = "2.54.0" %} {% set name = "flowMerge" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. Note: users should have a working copy of flowClust 2.0 installed.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Cluster Merging for Flow Cytometry Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c0d4d124e3d94a0eab8fc138f9044d2c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowmerge", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] host: - - 'bioconductor-flowclust >=3.40.0,<3.41.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-flowclust >=3.44.0,<3.45.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-feature - r-foreach - r-rrcov - r-snow run: - - 'bioconductor-flowclust >=3.40.0,<3.41.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-flowclust >=3.44.0,<3.45.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-feature - r-foreach - r-rrcov - r-snow - build: - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - xorg-libxfixes # [linux] + +source: + md5: 19db512773324d4b85928cc44e5622ef + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Cluster Merging for Flow Cytometry Data' - description: 'Merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. Note: users should have a working copy of flowClust 2.0 installed.' -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowpeaks/meta.yaml b/recipes/bioconductor-flowpeaks/meta.yaml index dad0728d2ef7d..3b1ca669abe91 100644 --- a/recipes/bioconductor-flowpeaks/meta.yaml +++ b/recipes/bioconductor-flowpeaks/meta.yaml @@ -1,25 +1,41 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "flowPeaks" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-1.0 + summary: An R package for flow data clustering -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f68db373a0d053a7eabd112df80a25f1 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowpeaks", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:flowpeaks + parent_recipe: + name: bioconductor-flowpeaks + path: recipes/bioconductor-flowpeaks + version: 1.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: flowCore # SystemRequirements: gsl requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - libblas @@ -28,25 +44,16 @@ requirements: run: - r-base - gsl - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: c4329653202e60c9d1d73f5134e36f8e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-1.0 - summary: 'An R package for flow data clustering' - description: 'A fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:flowpeaks - parent_recipe: - name: bioconductor-flowpeaks - path: recipes/bioconductor-flowpeaks - version: 1.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowploidy/meta.yaml b/recipes/bioconductor-flowploidy/meta.yaml index c1569c3b88b46..4711ec643cf33 100644 --- a/recipes/bioconductor-flowploidy/meta.yaml +++ b/recipes/bioconductor-flowploidy/meta.yaml @@ -1,28 +1,39 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "flowPloidy" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Determine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Analyze flow cytometer data to determine sample ploidy -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1020981a0f645d2dcbf1a38a3e42b7e0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowploidy", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:flowploidy + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-flowploidy + path: recipes/bioconductor-flowploidy + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: flowPloidyData, testthat requirements: host: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-car - r-catools @@ -31,7 +42,7 @@ requirements: - r-rmarkdown - r-shiny run: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-car - r-catools @@ -39,21 +50,16 @@ requirements: - r-minpack.lm - r-rmarkdown - r-shiny + +source: + md5: ab6d11a779e6a9112cd52b81ccd5f7f3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Analyze flow cytometer data to determine sample ploidy' - description: 'Determine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:flowploidy - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-flowploidy - path: recipes/bioconductor-flowploidy - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowploidydata/meta.yaml b/recipes/bioconductor-flowploidydata/meta.yaml index 1df2c16869432..361e88f3f9de5 100644 --- a/recipes/bioconductor-flowploidydata/meta.yaml +++ b/recipes/bioconductor-flowploidydata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "flowPloidyData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 993a663f6d1cdc791c3f4e88d5b3b047 +about: + description: A collection of raw flow cytometry data for use in vignettes for the flowPloidy package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Example Flow Cytometry Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowploidydata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, flowCore requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ed761a0cd77a9b186cfd6f09860d39a3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Example Flow Cytometry Data' - description: 'A collection of raw flow cytometry data for use in vignettes for the flowPloidy package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowploidydata/post-link.sh b/recipes/bioconductor-flowploidydata/post-link.sh index dbb4d93fd487f..f43b80f2601e1 100644 --- a/recipes/bioconductor-flowploidydata/post-link.sh +++ b/recipes/bioconductor-flowploidydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowploidydata-1.28.0" +installBiocDataPackage.sh "flowploidydata-1.32.0" diff --git a/recipes/bioconductor-flowplots/meta.yaml b/recipes/bioconductor-flowplots/meta.yaml index e7893a2db7cac..7e6e64504845a 100644 --- a/recipes/bioconductor-flowplots/meta.yaml +++ b/recipes/bioconductor-flowplots/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "flowPlots" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 523b0d79646813f56d711d3e0f38a5e9 +about: + description: Graphical displays with embedded statistical tests for gated ICS flow cytometry data, and a data class which stores "stacked" data and has methods for computing summary measures on stacked data, such as marginal and polyfunctional degree data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'flowPlots: analysis plots and data class for gated flow cytometry data' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowplots", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-flowplots + path: recipes/bioconductor-flowplots + version: 1.30.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: vcd requirements: host: - r-base run: - r-base +source: + md5: 807698c9a81aec5ad37757a55f41eee9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'flowPlots: analysis plots and data class for gated flow cytometry data' - description: 'Graphical displays with embedded statistical tests for gated ICS flow cytometry data, and a data class which stores "stacked" data and has methods for computing summary measures on stacked data, such as marginal and polyfunctional degree data.' -extra: - parent_recipe: - name: bioconductor-flowplots - path: recipes/bioconductor-flowplots - version: 1.30.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowsom/meta.yaml b/recipes/bioconductor-flowsom/meta.yaml index b149ec1e272b1..ae24f69954b0d 100644 --- a/recipes/bioconductor-flowsom/meta.yaml +++ b/recipes/bioconductor-flowsom/meta.yaml @@ -1,29 +1,45 @@ -{% set version = "2.10.0" %} +{% set version = "2.14.0" %} {% set name = "FlowSOM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Using self-organizing maps for visualization and interpretation of cytometry data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9bc309cc9948473d101d91ba6f1a37f2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowsom", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:flowsom + - doi:10.1002/cyto.a.22625 + parent_recipe: + name: bioconductor-flowsom + path: recipes/bioconductor-flowsom + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat, CytoML, flowWorkspace, ggrepel, scattermore, pheatmap, ggpointdensity requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-consensusclusterplus >=1.70.0,<1.71.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-colorramps - r-dplyr @@ -40,9 +56,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-consensusclusterplus >=1.66.0,<1.67.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-consensusclusterplus >=1.70.0,<1.71.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-colorramps - r-dplyr @@ -56,26 +72,16 @@ requirements: - r-rtsne - r-tidyr - r-xml - build: - - {{ compiler('c') }} - - make + +source: + md5: 77f31b52207d411114cfa91650cee894 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'Using self-organizing maps for visualization and interpretation of cytometry data' - description: 'FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:flowsom - - doi:10.1002/cyto.a.22625 - parent_recipe: - name: bioconductor-flowsom - path: recipes/bioconductor-flowsom - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowsorted.blood.450k/meta.yaml b/recipes/bioconductor-flowsorted.blood.450k/meta.yaml index 9c9dcba953274..7c2cc825b7c79 100644 --- a/recipes/bioconductor-flowsorted.blood.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.blood.450k/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "FlowSorted.Blood.450k" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f88422c2d8a2f7ce4ca968292adfc8ab +about: + description: Raw data objects for the Illumina 450k DNA methylation microarrays, and an object depicting which CpGs on the array are associated with cell type. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina HumanMethylation data on sorted blood cell populations build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowsorted.blood.450k", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-flowsorted.blood.450k + path: recipes/bioconductor-flowsorted.blood.450k + version: 1.18.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6df54186a88be5c6335467a86ec2e219 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina HumanMethylation data on sorted blood cell populations' - description: 'Raw data objects for the Illumina 450k DNA methylation microarrays, and an object depicting which CpGs on the array are associated with cell type.' -extra: - parent_recipe: - name: bioconductor-flowsorted.blood.450k - path: recipes/bioconductor-flowsorted.blood.450k - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowsorted.blood.450k/post-link.sh b/recipes/bioconductor-flowsorted.blood.450k/post-link.sh index 291888eff33cc..4f904802af6fe 100644 --- a/recipes/bioconductor-flowsorted.blood.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.blood.450k/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowsorted.blood.450k-1.40.0" +installBiocDataPackage.sh "flowsorted.blood.450k-1.44.0" diff --git a/recipes/bioconductor-flowsorted.blood.epic/meta.yaml b/recipes/bioconductor-flowsorted.blood.epic/meta.yaml index 90ba4f67f6423..9f5396d3c9dd5 100644 --- a/recipes/bioconductor-flowsorted.blood.epic/meta.yaml +++ b/recipes/bioconductor-flowsorted.blood.epic/meta.yaml @@ -1,55 +1,60 @@ -{% set version = "2.6.0" %} +{% set version = "2.10.0" %} {% set name = "FlowSorted.Blood.EPIC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Raw data objects to be used for blood cell proportion estimation in minfi and similar packages. The FlowSorted.Blood.EPIC object is based in samples assayed by Brock Christensen and colleagues; for details see Salas et al. 2018. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e94cbb0480a032595cdb5d9714065bed build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowsorted.blood.epic", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr,rmarkdown, FlowSorted.CordBlood.450k, FlowSorted.Blood.450k(>= 1.0.1), EpiDISH,FlowSorted.CordBloodNorway.450k, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b4.hg19 requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-nlme - r-quadprog run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-nlme - r-quadprog - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: a51230659106aa6ba33a7bdd616d4ae6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells' - description: 'Raw data objects to be used for blood cell proportion estimation in minfi and similar packages. The FlowSorted.Blood.EPIC object is based in samples assayed by Brock Christensen and colleagues; for details see Salas et al. 2018. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowsorted.blood.epic/post-link.sh b/recipes/bioconductor-flowsorted.blood.epic/post-link.sh index 82feccd703411..b76fb585c8be6 100644 --- a/recipes/bioconductor-flowsorted.blood.epic/post-link.sh +++ b/recipes/bioconductor-flowsorted.blood.epic/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowsorted.blood.epic-2.6.0" +installBiocDataPackage.sh "flowsorted.blood.epic-2.10.0" diff --git a/recipes/bioconductor-flowsorted.cordblood.450k/meta.yaml b/recipes/bioconductor-flowsorted.cordblood.450k/meta.yaml index 20523ec1de672..9dd71b2323f79 100644 --- a/recipes/bioconductor-flowsorted.cordblood.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.cordblood.450k/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "FlowSorted.CordBlood.450k" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fca81b7412af68100d7aed4d57d5fc59 +about: + description: Raw data objects to be used for cord blood cell proportion estimation in minfi. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina 450k data on sorted cord blood cells build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowsorted.cordblood.450k", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3afca2babc77db996268a0b383c2a5f0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina 450k data on sorted cord blood cells' - description: 'Raw data objects to be used for cord blood cell proportion estimation in minfi.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowsorted.cordblood.450k/post-link.sh b/recipes/bioconductor-flowsorted.cordblood.450k/post-link.sh index 0b82dabf176d0..b6636151f91b5 100644 --- a/recipes/bioconductor-flowsorted.cordblood.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.cordblood.450k/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowsorted.cordblood.450k-1.30.0" +installBiocDataPackage.sh "flowsorted.cordblood.450k-1.34.0" diff --git a/recipes/bioconductor-flowsorted.cordbloodcombined.450k/meta.yaml b/recipes/bioconductor-flowsorted.cordbloodcombined.450k/meta.yaml index 6aef7e141a811..2b48080b12e80 100644 --- a/recipes/bioconductor-flowsorted.cordbloodcombined.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.cordbloodcombined.450k/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "FlowSorted.CordBloodCombined.450k" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Raw data objects to be used for umbilical cord blood cell proportion estimation in minfi and similar packages. The FlowSorted.CordBloodCombined.450k object is based in samples assayed by Bakulski et al, Gervin et al., de Goede et al., and Lin et al. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Illumina 450k/EPIC data on FACS and MACS umbilical blood cells -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 769113b80606820ab2918dcacf1076b2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowsorted.cordbloodcombined.450k", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: FlowSorted.Blood.EPIC, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylationEPICanno.ilm10b2.hg19 requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: edafe41e6489b95f1b3279e8bfd324a7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Illumina 450k/EPIC data on FACS and MACS umbilical blood cells' - description: 'Raw data objects to be used for umbilical cord blood cell proportion estimation in minfi and similar packages. The FlowSorted.CordBloodCombined.450k object is based in samples assayed by Bakulski et al, Gervin et al., de Goede et al., and Lin et al.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowsorted.cordbloodcombined.450k/post-link.sh b/recipes/bioconductor-flowsorted.cordbloodcombined.450k/post-link.sh index c540b53ecf269..1ceb91898c642 100644 --- a/recipes/bioconductor-flowsorted.cordbloodcombined.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.cordbloodcombined.450k/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowsorted.cordbloodcombined.450k-1.18.0" +installBiocDataPackage.sh "flowsorted.cordbloodcombined.450k-1.22.0" diff --git a/recipes/bioconductor-flowsorted.cordbloodnorway.450k/meta.yaml b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/meta.yaml index 13471afc01d9a..833e30286457c 100644 --- a/recipes/bioconductor-flowsorted.cordbloodnorway.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "FlowSorted.CordBloodNorway.450k" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 40016224becf643102bc3054f4e2508d +about: + description: Raw data objects for the Illumina 450k DNA methylation microarrays, for cell type composition estimation. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina HumanMethylation data on sorted cord blood cell populations build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowsorted.cordbloodnorway.450k", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 21a44f2a9ffb55f053f32c398f4689b7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina HumanMethylation data on sorted cord blood cell populations' - description: 'Raw data objects for the Illumina 450k DNA methylation microarrays, for cell type composition estimation.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowsorted.cordbloodnorway.450k/post-link.sh b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/post-link.sh index 142aa56ecf3a3..62862595b06e0 100644 --- a/recipes/bioconductor-flowsorted.cordbloodnorway.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowsorted.cordbloodnorway.450k-1.28.0" +installBiocDataPackage.sh "flowsorted.cordbloodnorway.450k-1.32.0" diff --git a/recipes/bioconductor-flowsorted.dlpfc.450k/meta.yaml b/recipes/bioconductor-flowsorted.dlpfc.450k/meta.yaml index b9bfdbe04b88e..1ac2323879263 100644 --- a/recipes/bioconductor-flowsorted.dlpfc.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.dlpfc.450k/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "FlowSorted.DLPFC.450k" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad95a51f7e8bcf7c0bec6dda80eb0a92 +about: + description: Raw data objects for the Illumina 450k DNA methylation microarrays. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina HumanMethylation data on sorted frontal cortex cell populations build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowsorted.dlpfc.450k", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f77547b8703af30a4f248b5f8a75cd92 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina HumanMethylation data on sorted frontal cortex cell populations' - description: 'Raw data objects for the Illumina 450k DNA methylation microarrays.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowsorted.dlpfc.450k/post-link.sh b/recipes/bioconductor-flowsorted.dlpfc.450k/post-link.sh index bdd7e31f4b074..ed4260d500ab2 100644 --- a/recipes/bioconductor-flowsorted.dlpfc.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.dlpfc.450k/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowsorted.dlpfc.450k-1.38.0" +installBiocDataPackage.sh "flowsorted.dlpfc.450k-1.42.0" diff --git a/recipes/bioconductor-flowspecs/meta.yaml b/recipes/bioconductor-flowspecs/meta.yaml index f3dea0389b41d..e5a8be0148752 100644 --- a/recipes/bioconductor-flowspecs/meta.yaml +++ b/recipes/bioconductor-flowspecs/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "flowSpecs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is intended to fill the role of conventional cytometry pre-processing software, for spectral decomposition, transformation, visualization and cleanup, and to aid further downstream analyses, such as with DepecheR, by enabling transformation of flowFrames and flowSets to dataframes. Functions for flowCore-compliant automatic 1D-gating/filtering are in the pipe line. The package name has been chosen both as it will deal with spectral cytometry and as it will hopefully give the user a nice pair of spectacles through which to view their data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Tools for processing of high-dimensional cytometry data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 502f1e04027fab8076745a5386401f2e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowspecs", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocStyle, DepecheR requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - - 'r-ggplot2 >=3.1.0' - - 'r-reshape2 >=1.4.3' - - 'r-zoo >=1.8.6' + - r-ggplot2 >=3.1.0 + - r-reshape2 >=1.4.3 + - r-zoo >=1.8.6 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - - 'r-ggplot2 >=3.1.0' - - 'r-reshape2 >=1.4.3' - - 'r-zoo >=1.8.6' + - r-ggplot2 >=3.1.0 + - r-reshape2 >=1.4.3 + - r-zoo >=1.8.6 + +source: + md5: 19ea4a763cdd2ad429f47472c348b87a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Tools for processing of high-dimensional cytometry data' - description: 'This package is intended to fill the role of conventional cytometry pre-processing software, for spectral decomposition, transformation, visualization and cleanup, and to aid further downstream analyses, such as with DepecheR, by enabling transformation of flowFrames and flowSets to dataframes. Functions for flowCore-compliant automatic 1D-gating/filtering are in the pipe line. The package name has been chosen both as it will deal with spectral cytometry and as it will hopefully give the user a nice pair of spectacles through which to view their data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowstats/meta.yaml b/recipes/bioconductor-flowstats/meta.yaml index 6ea2f22d7384f..d231f0a9a4448 100644 --- a/recipes/bioconductor-flowstats/meta.yaml +++ b/recipes/bioconductor-flowstats/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "4.14.0" %} +{% set version = "4.18.0" %} {% set name = "flowStats" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Statistical methods for the analysis of flow cytometry data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2817bb2cbd74b07bb948d0988be2a57e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowstats", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-flowstats + path: recipes/bioconductor-flowstats + version: 3.40.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: xtable, testthat, openCyto, ggcyto, ggridges requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowviz >=1.66.0,<1.67.0' - - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' - - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowviz >=1.70.0,<1.71.0 + - bioconductor-flowworkspace >=4.18.0,<4.19.0 + - bioconductor-ncdfflow >=2.52.0,<2.53.0 - r-base - r-clue - r-cluster - r-corpcor - - 'r-fda >=2.2.6' + - r-fda >=2.2.6 - r-kernsmooth - r-ks - r-lattice @@ -41,17 +48,17 @@ requirements: - r-rcolorbrewer - r-rrcov run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowviz >=1.66.0,<1.67.0' - - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' - - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowviz >=1.70.0,<1.71.0 + - bioconductor-flowworkspace >=4.18.0,<4.19.0 + - bioconductor-ncdfflow >=2.52.0,<2.53.0 - r-base - r-clue - r-cluster - r-corpcor - - 'r-fda >=2.2.6' + - r-fda >=2.2.6 - r-kernsmooth - r-ks - r-lattice @@ -59,17 +66,16 @@ requirements: - r-mnormt - r-rcolorbrewer - r-rrcov + +source: + md5: 40303230fdbecf52ebe00053c8509533 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Statistical methods for the analysis of flow cytometry data' - description: 'Methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package.' -extra: - parent_recipe: - name: bioconductor-flowstats - path: recipes/bioconductor-flowstats - version: 3.40.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowtime/meta.yaml b/recipes/bioconductor-flowtime/meta.yaml index eb87ab80635af..2fbc49609f0af 100644 --- a/recipes/bioconductor-flowtime/meta.yaml +++ b/recipes/bioconductor-flowtime/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "flowTime" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package facilitates analysis of both timecourse and steady state flow cytometry experiments. This package was originially developed for quantifying the function of gene regulatory networks in yeast (strain W303) expressing fluorescent reporter proteins using BD Accuri C6 and SORP cytometers. However, the functions are for the most part general and may be adapted for analysis of other organisms using other flow cytometers. Functions in this package facilitate the annotation of flow cytometry data with experimental metadata, as often required for publication and general ease-of-reuse. Functions for creating, saving and loading gate sets are also included. In the past, we have typically generated summary statistics for each flowset for each timepoint and then annotated and analyzed these summary statistics. This method loses a great deal of the power that comes from the large amounts of individual cell data generated in flow cytometry, by essentially collapsing this data into a bulk measurement after subsetting. In addition to these summary functions, this package also contains functions to facilitate annotation and analysis of steady-state or time-lapse data utilizing all of the data collected from the thousands of individual cells in each sample. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation and analysis of biological dynamical systems using flow cytometry -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 04ca452b54e7309493c814844fc1b772 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowtime", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, stats, flowClust, openCyto, flowStats, ggcyto requirements: host: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - - 'r-dplyr >=1.0.0' + - r-dplyr >=1.0.0 - r-magrittr - r-plyr - r-rlang - r-tibble run: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - - 'r-dplyr >=1.0.0' + - r-dplyr >=1.0.0 - r-magrittr - r-plyr - r-rlang - r-tibble + +source: + md5: 4cf8fa191c53e28f93497bda45dcfa88 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation and analysis of biological dynamical systems using flow cytometry' - description: 'This package facilitates analysis of both timecourse and steady state flow cytometry experiments. This package was originially developed for quantifying the function of gene regulatory networks in yeast (strain W303) expressing fluorescent reporter proteins using BD Accuri C6 and SORP cytometers. However, the functions are for the most part general and may be adapted for analysis of other organisms using other flow cytometers. Functions in this package facilitate the annotation of flow cytometry data with experimental metadata, as often required for publication and general ease-of-reuse. Functions for creating, saving and loading gate sets are also included. In the past, we have typically generated summary statistics for each flowset for each timepoint and then annotated and analyzed these summary statistics. This method loses a great deal of the power that comes from the large amounts of individual cell data generated in flow cytometry, by essentially collapsing this data into a bulk measurement after subsetting. In addition to these summary functions, this package also contains functions to facilitate annotation and analysis of steady-state or time-lapse data utilizing all of the data collected from the thousands of individual cells in each sample.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowtrans/meta.yaml b/recipes/bioconductor-flowtrans/meta.yaml index ebddba32b3bfd..ec2e5fe6fcf0e 100644 --- a/recipes/bioconductor-flowtrans/meta.yaml +++ b/recipes/bioconductor-flowtrans/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.54.0" %} +{% set version = "1.58.0" %} {% set name = "flowTrans" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d98daa4177e5f6b8cda8d8475e34c09a +about: + description: Profile maximum likelihood estimation of parameters for flow cytometry data transformations. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Parameter Optimization for Flow Cytometry Data Transformation build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowtrans", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-flowclust >=3.40.0,<3.41.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowviz >=1.66.0,<1.67.0' + - bioconductor-flowclust >=3.44.0,<3.45.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowviz >=1.70.0,<1.71.0 - r-base run: - - 'bioconductor-flowclust >=3.40.0,<3.41.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowviz >=1.66.0,<1.67.0' + - bioconductor-flowclust >=3.44.0,<3.45.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowviz >=1.70.0,<1.71.0 - r-base +source: + md5: 514414edb07e7be8c6528334b4742cda + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Parameter Optimization for Flow Cytometry Data Transformation' - description: 'Profile maximum likelihood estimation of parameters for flow cytometry data transformations.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowviz/meta.yaml b/recipes/bioconductor-flowviz/meta.yaml index 46eab38ac8366..7341a91d4be4a 100644 --- a/recipes/bioconductor-flowviz/meta.yaml +++ b/recipes/bioconductor-flowviz/meta.yaml @@ -1,29 +1,39 @@ -{% set version = "1.66.0" %} +{% set version = "1.70.0" %} {% set name = "flowViz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides visualization tools for flow cytometry data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Visualization for flow cytometry -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 320d8392618efe06e6c2a8923b3c6652 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowviz", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:flowviz + - doi:10.1093/bioinformatics/btn021 + parent_recipe: + name: bioconductor-flowviz + path: recipes/bioconductor-flowviz + version: 1.44.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: colorspace, flowStats, knitr, rmarkdown, markdown, testthat requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-hexbin - r-idpmisc @@ -33,8 +43,8 @@ requirements: - r-mass - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-hexbin - r-idpmisc @@ -43,20 +53,16 @@ requirements: - r-latticeextra - r-mass - r-rcolorbrewer + +source: + md5: 5a244ca03b2106555274d5dab9d19d41 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Visualization for flow cytometry' - description: 'Provides visualization tools for flow cytometry data.' -extra: - identifiers: - - biotools:flowviz - - doi:10.1093/bioinformatics/btn021 - parent_recipe: - name: bioconductor-flowviz - path: recipes/bioconductor-flowviz - version: 1.44.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowvs/meta.yaml b/recipes/bioconductor-flowvs/meta.yaml index 9469254038a37..b5d21b186b664 100644 --- a/recipes/bioconductor-flowvs/meta.yaml +++ b/recipes/bioconductor-flowvs/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "flowVS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43fc57f2be5ccbfcff9ac9b9bc0bb857 +about: + description: Per-channel variance stabilization from a collection of flow cytometry samples by Bertlett test for homogeneity of variances. The approach is applicable to microarrays data as well. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Variance stabilization in flow cytometry (and microarrays) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowvs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, vsn, requirements: host: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowstats >=4.14.0,<4.15.0' - - 'bioconductor-flowviz >=1.66.0,<1.67.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowstats >=4.18.0,<4.19.0 + - bioconductor-flowviz >=1.70.0,<1.71.0 - r-base run: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowstats >=4.14.0,<4.15.0' - - 'bioconductor-flowviz >=1.66.0,<1.67.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowstats >=4.18.0,<4.19.0 + - bioconductor-flowviz >=1.70.0,<1.71.0 - r-base +source: + md5: dcad670495d2a289eadf70ce8367f928 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Variance stabilization in flow cytometry (and microarrays)' - description: 'Per-channel variance stabilization from a collection of flow cytometry samples by Bertlett test for homogeneity of variances. The approach is applicable to microarrays data as well.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowworkspace/Makevars.osx.patch b/recipes/bioconductor-flowworkspace/Makevars.osx.patch new file mode 100644 index 0000000000000..6eb0f285acdaf --- /dev/null +++ b/recipes/bioconductor-flowworkspace/Makevars.osx.patch @@ -0,0 +1,17 @@ +diff --git a/src/Makevars b/src/Makevars +index 404ba20..d47b943 100644 +--- a/src/Makevars ++++ b/src/Makevars +@@ -7,7 +7,8 @@ This makefile requires GNU Make. + endif + + CXX_STD = CXX17 +-PKG_CPPFLAGS =-DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors ++PKG_CPPFLAGS =-DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -Wno-pedantic -w -Wfatal-errors \ ++ -D_LIBCPP_ENABLE_CXX17_REMOVED_UNARY_BINARY_FUNCTION + + + +-- +2.46.0 + diff --git a/recipes/bioconductor-flowworkspace/meta.yaml b/recipes/bioconductor-flowworkspace/meta.yaml index 5df796f644a70..6c10a653fce8b 100644 --- a/recipes/bioconductor-flowworkspace/meta.yaml +++ b/recipes/bioconductor-flowworkspace/meta.yaml @@ -1,91 +1,103 @@ -{% set version = "4.14.0" %} +{% set version = "4.18.0" %} {% set name = "flowWorkspace" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3.0-only + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Infrastructure for representing and interacting with gated and ungated cytometry data sets. -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e97cd561c6a61ae778261cb55f29af90 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowworkspace", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:flowworkspace + - doi:10.1186/1471-2105-13-252 + parent_recipe: + name: bioconductor-flowworkspace + path: recipes/bioconductor-flowworkspace + version: 3.28.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, flowWorkspaceData (>= 2.23.2), knitr, rmarkdown, ggcyto, parallel, CytoML, openCyto # SystemRequirements: GNU make, C++11 requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-cytolib >=2.14.0,<2.15.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-cytolib >=2.18.0,<2.19.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-ncdfflow >=2.52.0,<2.53.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-rprotobuflib >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-bh >=1.62.0-1' + - r-bh >=1.62.0-1 - r-cpp11 - r-data.table - r-dplyr - r-ggplot2 - r-matrixstats - - r-scales + - r-scales >=1.3.0 - r-xml - libblas - liblapack + - zlib + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-cytolib >=2.14.0,<2.15.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-rprotobuflib >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-cytolib >=2.18.0,<2.19.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-ncdfflow >=2.52.0,<2.53.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-rprotobuflib >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-bh >=1.62.0-1' + - r-bh >=1.62.0-1 - r-cpp11 - r-data.table - r-dplyr - r-ggplot2 - r-matrixstats - - r-scales + - r-scales >=1.3.0 - r-xml - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 6c2010307be1f1484a32a9d09a4752b3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + patches: + - Makevars.osx.patch # [osx] + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3.0-only - summary: 'Infrastructure for representing and interacting with gated and ungated cytometry data sets.' - description: 'This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:flowworkspace - - doi:10.1186/1471-2105-13-252 - parent_recipe: - name: bioconductor-flowworkspace - path: recipes/bioconductor-flowworkspace - version: 3.28.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowworkspacedata/meta.yaml b/recipes/bioconductor-flowworkspacedata/meta.yaml index ec95026f5f295..0de684541f3a4 100644 --- a/recipes/bioconductor-flowworkspacedata/meta.yaml +++ b/recipes/bioconductor-flowworkspacedata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "3.14.0" %} +{% set version = "3.18.0" %} {% set name = "flowWorkspaceData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96655cef2a21f1b9d303ec775597a2dc +about: + description: The necessary external data to run the flowWorkspace and openCyto vignette is found in this package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A data package containing two flowJo, one diva xml workspace and the associated fcs files as well as three GatingSets for testing the flowWorkspace, openCyto and CytoML packages. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-flowworkspacedata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7133f0addd24a8713d2b57ffe7646bd8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'A data package containing two flowJo, one diva xml workspace and the associated fcs files as well as three GatingSets for testing the flowWorkspace, openCyto and CytoML packages.' - description: 'The necessary external data to run the flowWorkspace and openCyto vignette is found in this package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-flowworkspacedata/post-link.sh b/recipes/bioconductor-flowworkspacedata/post-link.sh index f0331f23198c7..4b0733b4b70be 100644 --- a/recipes/bioconductor-flowworkspacedata/post-link.sh +++ b/recipes/bioconductor-flowworkspacedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "flowworkspacedata-3.14.0" +installBiocDataPackage.sh "flowworkspacedata-3.18.0" diff --git a/recipes/bioconductor-fly.db0/meta.yaml b/recipes/bioconductor-fly.db0/meta.yaml index 0ed06aa0d7e48..c5865cc13ced1 100644 --- a/recipes/bioconductor-fly.db0/meta.yaml +++ b/recipes/bioconductor-fly.db0/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "fly.db0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 49722b8a538d02f71631a418b92c44d7 +about: + description: Base annotation databases for fly, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Level Annotation databases for fly build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fly.db0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: faeba43dee9e5ff967b35501ca25294c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Level Annotation databases for fly' - description: 'Base annotation databases for fly, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fly.db0/post-link.sh b/recipes/bioconductor-fly.db0/post-link.sh index 3fab31db8f277..b6eb55d67a4c7 100644 --- a/recipes/bioconductor-fly.db0/post-link.sh +++ b/recipes/bioconductor-fly.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fly.db0-3.18.0" +installBiocDataPackage.sh "fly.db0-3.20.0" diff --git a/recipes/bioconductor-fmcsr/meta.yaml b/recipes/bioconductor-fmcsr/meta.yaml index d62cc7de82aea..36ec59206f73a 100644 --- a/recipes/bioconductor-fmcsr/meta.yaml +++ b/recipes/bioconductor-fmcsr/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "fmcsR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Mismatch Tolerant Maximum Common Substructure Searching -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 21a6242a61cba8dd537bf846af3260c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fmcsr", max_pin="x.x") }}' -# Suggests: BiocStyle, knitr, knitcitations, knitrBootstrap,rmarkdown + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, knitcitations, knitrBootstrap,rmarkdown, codetools requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-chemminer >=3.58.0,<3.59.0 - r-base - r-runit - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-chemminer >=3.58.0,<3.59.0 - r-base - r-runit - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 3f2343f3b7a3f5e98c2c46020dd4794b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Mismatch Tolerant Maximum Common Substructure Searching' - description: 'The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fmrs/meta.yaml b/recipes/bioconductor-fmrs/meta.yaml index 667e0c6c78dac..6fb09f5c727c9 100644 --- a/recipes/bioconductor-fmrs/meta.yaml +++ b/recipes/bioconductor-fmrs/meta.yaml @@ -1,25 +1,27 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "fmrs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ccf41504ab27d93464e555b363ef406a +about: + description: The package obtains parameter estimation, i.e., maximum likelihood estimators (MLE), via the Expectation-Maximization (EM) algorithm for the Finite Mixture of Regression (FMR) models with Normal distribution, and MLE for the Finite Mixture of Accelerated Failure Time Regression (FMAFTR) subject to right censoring with Log-Normal and Weibull distributions via the EM algorithm and the Newton-Raphson algorithm (for Weibull distribution). More importantly, the package obtains the maximum penalized likelihood (MPLE) for both FMR and FMAFTR models (collectively called FMRs). A component-wise tuning parameter selection based on a component-wise BIC is implemented in the package. Furthermore, this package provides Ridge Regression and Elastic Net. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Variable Selection in Finite Mixture of AFT Regression and FMR Models build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fmrs", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocGenerics, testthat, knitr, utils requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - r-survival @@ -28,16 +30,14 @@ requirements: run: - r-base - r-survival - build: - - {{ compiler('c') }} - - make +source: + md5: f0f16341a2b953039012da537bba3d6c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Variable Selection in Finite Mixture of AFT Regression and FMR Models' - description: 'The package obtains parameter estimation, i.e., maximum likelihood estimators (MLE), via the Expectation-Maximization (EM) algorithm for the Finite Mixture of Regression (FMR) models with Normal distribution, and MLE for the Finite Mixture of Accelerated Failure Time Regression (FMAFTR) subject to right censoring with Log-Normal and Weibull distributions via the EM algorithm and the Newton-Raphson algorithm (for Weibull distribution). More importantly, the package obtains the maximum penalized likelihood (MPLE) for both FMR and FMAFTR models (collectively called FMRs). A component-wise tuning parameter selection based on a component-wise BIC is implemented in the package. Furthermore, this package provides Ridge Regression and Elastic Net.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fobitools/meta.yaml b/recipes/bioconductor-fobitools/meta.yaml index d9b0d175e64b0..af78fee308937 100644 --- a/recipes/bioconductor-fobitools/meta.yaml +++ b/recipes/bioconductor-fobitools/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "fobitools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A set of tools for interacting with the Food-Biomarker Ontology (FOBI). A collection of basic manipulation tools for biological significance analysis, graphs, and text mining strategies for annotating nutritional data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Tools for Manipulating the FOBI Ontology -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 24ebda3aed06055ab55d7cdf88a7c2a0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fobitools", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, covr, ggrepel, kableExtra, knitr, metabolomicsWorkbenchR, POMA, rmarkdown, rvest, SummarizedExperiment, testthat (>= 2.3.2), tidyverse requirements: host: - - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - bioconductor-fgsea >=1.32.0,<1.33.0 - r-base - r-clisymbols - r-crayon @@ -40,7 +42,7 @@ requirements: - r-tidyr - r-vroom run: - - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - bioconductor-fgsea >=1.32.0,<1.33.0 - r-base - r-clisymbols - r-crayon @@ -57,13 +59,16 @@ requirements: - r-tidygraph - r-tidyr - r-vroom + +source: + md5: a1bfbea449a5e6fdfb29e5847eeb07f8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Tools For Manipulating FOBI Ontology' - description: 'A set of tools for interacting with Food-Biomarker Ontology (FOBI). A collection of basic manipulation tools for biological significance analysis, graphs, and text mining strategies for annotating nutritional data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fourdndata/meta.yaml b/recipes/bioconductor-fourdndata/meta.yaml index 4b1339af9b5b5..fa11989b064bd 100644 --- a/recipes/bioconductor-fourdndata/meta.yaml +++ b/recipes/bioconductor-fourdndata/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "fourDNData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: fourDNData is a data package giving programmatic access to Hi-C contact matrices uniformly processed by the [4DN consortium](https://www.4dnucleome.org/). The matrices are available in the multi-resolution `.mcool` format. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 4DN data package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bca623e919f7c17a40ffb4eae27cfe59 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fourdndata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rtracklayer, dplyr, testthat, methods, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hicexperiment >=1.6.0,<1.7.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hicexperiment >=1.6.0,<1.7.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: afe1fdf692cb248b2bd937b2bed37b03 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: '4DN data package' - description: 'fourDNData is a data package giving programmatic access to Hi-C contact matrices uniformly processed by the [4DN consortium](https://www.4dnucleome.org/). The matrices are available in the multi-resolution `.mcool` format.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-fourdndata/post-link.sh b/recipes/bioconductor-fourdndata/post-link.sh index f062b27931ef6..a180f57bf43b6 100644 --- a/recipes/bioconductor-fourdndata/post-link.sh +++ b/recipes/bioconductor-fourdndata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "fourdndata-1.2.0" +installBiocDataPackage.sh "fourdndata-1.6.0" diff --git a/recipes/bioconductor-fraser/meta.yaml b/recipes/bioconductor-fraser/meta.yaml index d6293dfb094db..7e9df7c1b4447 100644 --- a/recipes/bioconductor-fraser/meta.yaml +++ b/recipes/bioconductor-fraser/meta.yaml @@ -1,87 +1,145 @@ -{% set version = "1.99.4" %} +{% set version = "2.2.0" %} {% set name = "FRASER" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Detection of rare aberrant splicing events in transcriptome profiles. Read count ratio expectations are modeled by an autoencoder to control for confounding factors in the data. Given these expectations, the ratios are assumed to follow a beta-binomial distribution with a junction specific dispersion. Outlier events are then identified as read-count ratios that deviate significantly from this distribution. FRASER is able to detect alternative splicing, but also intron retention. The package aims to support diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Find RAre Splicing Events in RNA-Seq Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://github.com/gagneurlab/FRASER/archive/refs/tags/{{ version }}.tar.gz' - md5: 37b2d4b80b66f19d71eaf481e77b0eec build: - skip: True # [osx] number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fraser", max_pin="x.x") }}' -# Suggests: BiocStyle, knitr, rmarkdown, testthat, covr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, + +extra: + identifiers: + - https://doi.org/10.1038/s41467-020-20573-7 + recipe-maintainers: + - c-mertes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: magick, BiocStyle, knitr, rmarkdown, testthat, covr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, rtracklayer, SGSeq, ggbio, biovizBase requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-outrider >=1.20.0,<1.21.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rsubread >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + + - bioconductor-biobase >=2.66.0,<2.67.0 + + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + + - bioconductor-biocparallel >=1.40.0,<1.41.0 + + - bioconductor-biomart >=2.62.0,<2.63.0 + + - bioconductor-bsgenome >=1.74.0,<1.75.0 + + - bioconductor-delayedarray >=0.32.0,<0.33.0 + + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + + - bioconductor-genomicranges >=1.58.0,<1.59.0 + + - bioconductor-hdf5array >=1.34.0,<1.35.0 + + - bioconductor-iranges >=2.40.0,<2.41.0 + + - bioconductor-outrider >=1.24.0,<1.25.0 + + - bioconductor-pcamethods >=1.98.0,<1.99.0 + + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + + - bioconductor-rsamtools >=2.22.0,<2.23.0 + + - bioconductor-rsubread >=2.20.0,<2.21.0 + + - bioconductor-s4vectors >=0.44.0,<0.45.0 + + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-bbmisc + - r-cowplot + - r-data.table + - r-extradistr + - r-generics + - r-ggplot2 + - r-ggrepel + - r-matrixstats + - r-pheatmap + - r-plotly + - r-prroc + - r-r.utils + - r-rcolorbrewer + - r-rcpp + - r-rcpparmadillo + - r-tibble + - r-vgam + - libblas + - liblapack + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-outrider >=1.20.0,<1.21.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rsubread >=2.16.0,<2.17.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-outrider >=1.24.0,<1.25.0 + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rsubread >=2.20.0,<2.21.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bbmisc - r-cowplot @@ -100,21 +158,16 @@ requirements: - r-rcpparmadillo - r-tibble - r-vgam - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 4c5df0ae54e1b564d4c1b886a125ee58 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Find RAre Splicing Events in RNA-Seq Data' - description: 'Detection of rare aberrant splicing events in transcriptome profiles. Read count ratio expectations are modeled by an autoencoder to control for confounding factors in the data. Given these expectations, the ratios are assumed to follow a beta-binomial distribution with a junction specific dispersion. Outlier events are then identified as read-count ratios that deviate significantly from this distribution. FRASER is able to detect alternative splicing, but also intron retention. The package aims to support diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects.' - license_file: LICENSE -extra: - identifiers: - - https://doi.org/10.1038/s41467-020-20573-7 - recipe-maintainers: - - c-mertes + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-frenchfish/meta.yaml b/recipes/bioconductor-frenchfish/meta.yaml index 3b703c9f03fda..229883cbc91ca 100644 --- a/recipes/bioconductor-frenchfish/meta.yaml +++ b/recipes/bioconductor-frenchfish/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "frenchFISH" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 170f9e757e12e766a8a455d6d3ca9f81 +about: + description: 'FrenchFISH comprises a nuclear volume correction method coupled with two types of Poisson models: either a Poisson model for improved manual spot counting without the need for control probes; or a homogenous Poisson Point Process model for automated spot counting.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-frenchfish", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, testthat requirements: host: @@ -29,12 +27,14 @@ requirements: - r-base - r-mcmcpack - r-nhpoisson +source: + md5: 21e4686d1b7f0ed6819c9f862aec2c78 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections' - description: 'FrenchFISH comprises a nuclear volume correction method coupled with two types of Poisson models: either a Poisson model for improved manual spot counting without the need for control probes; or a homogenous Poisson Point Process model for automated spot counting.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-frgepistasis/meta.yaml b/recipes/bioconductor-frgepistasis/meta.yaml index 18dcf4c202ea4..74db42625c7fe 100644 --- a/recipes/bioconductor-frgepistasis/meta.yaml +++ b/recipes/bioconductor-frgepistasis/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "FRGEpistasis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a5804d62a4e375df7706ebc0573929f5 +about: + description: A Tool for Epistasis Analysis Based on Functional Regression Model + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Epistasis Analysis for Quantitative Traits by Functional Regression Model build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-frgepistasis", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base @@ -28,13 +27,14 @@ requirements: - r-base - r-fda - r-mass +source: + md5: 490532f8cee43117ff346a5cab8209cb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Epistasis Analysis for Quantitative Traits by Functional Regression Model' - description: 'A Tool for Epistasis Analysis Based on Functional Regression Model' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-frma/meta.yaml b/recipes/bioconductor-frma/meta.yaml index 6e27095a3ca5a..17da5757d857c 100644 --- a/recipes/bioconductor-frma/meta.yaml +++ b/recipes/bioconductor-frma/meta.yaml @@ -1,60 +1,66 @@ -{% set version = "1.54.0" %} +{% set version = "1.58.0" %} {% set name = "frma" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Preprocessing and analysis for single microarrays and microarray batches. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Frozen RMA and Barcode -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4892707c54a5698c48151bd630feb0e0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-frma", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:frma + parent_recipe: + name: bioconductor-frma + path: recipes/bioconductor-frma + version: 1.32.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: hgu133afrmavecs, frmaExampleData requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-dbi - r-mass run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-dbi - r-mass + +source: + md5: 102ea012249dc8c3bc37e6d37b4f5d2e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Frozen RMA and Barcode' - description: 'Preprocessing and analysis for single microarrays and microarray batches.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:frma - parent_recipe: - name: bioconductor-frma - path: recipes/bioconductor-frma - version: 1.32.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-frmaexampledata/meta.yaml b/recipes/bioconductor-frmaexampledata/meta.yaml index 9f29cd6e5963e..531125c34491b 100644 --- a/recipes/bioconductor-frmaexampledata/meta.yaml +++ b/recipes/bioconductor-frmaexampledata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "frmaExampleData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9713801ffd08145323ca4d31a3631995 +about: + description: Data files used by the examples in frma and frmaTools packages + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Frma Example Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-frmaexampledata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4dd690a166195829ba5a45856448bf49 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Frma Example Data' - description: 'Data files used by the examples in frma and frmaTools packages' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-frmaexampledata/post-link.sh b/recipes/bioconductor-frmaexampledata/post-link.sh index 11252f324dcf4..d0edd03fcf591 100644 --- a/recipes/bioconductor-frmaexampledata/post-link.sh +++ b/recipes/bioconductor-frmaexampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "frmaexampledata-1.38.0" +installBiocDataPackage.sh "frmaexampledata-1.42.0" diff --git a/recipes/bioconductor-frmatools/meta.yaml b/recipes/bioconductor-frmatools/meta.yaml index 113507f7441f4..69825e88833d2 100644 --- a/recipes/bioconductor-frmatools/meta.yaml +++ b/recipes/bioconductor-frmatools/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.54.0" %} +{% set version = "1.58.0" %} {% set name = "frmaTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for advanced use of the frma package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Frozen RMA Tools -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 270e71dc903bb77add1154782cf17342 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-frmatools", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:frmatools + parent_recipe: + name: bioconductor-frmatools + path: recipes/bioconductor-frmatools + version: 1.32.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM, hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf, hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-dbi run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-dbi + +source: + md5: e8d187a2f6dab22515c8c8e152ae1ff3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Frozen RMA Tools' - description: 'Tools for advanced use of the frma package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:frmatools - parent_recipe: - name: bioconductor-frmatools - path: recipes/bioconductor-frmatools - version: 1.32.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-funtoonorm/meta.yaml b/recipes/bioconductor-funtoonorm/meta.yaml index ecdc54d66593c..ad33ae3a2ac09 100644 --- a/recipes/bioconductor-funtoonorm/meta.yaml +++ b/recipes/bioconductor-funtoonorm/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "funtooNorm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides a function to normalize Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K), correcting for tissue and/or cell type. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 32208fd7734fe0fcfb1278b80a98c28e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-funtoonorm", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: prettydoc, minfiData, knitr, rmarkdown requirements: host: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0 + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - r-matrixstats - r-pls run: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0 + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - r-matrixstats - r-pls + +source: + md5: ff2b3bc8feb6504131ef20038bce3f22 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit' - description: 'Provides a function to normalize Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K), correcting for tissue and/or cell type.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-furrowseg/meta.yaml b/recipes/bioconductor-furrowseg/meta.yaml index 19e3d0d33ddfd..e9ab43c77e935 100644 --- a/recipes/bioconductor-furrowseg/meta.yaml +++ b/recipes/bioconductor-furrowseg/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "furrowSeg" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Image feature data and analysis codes for the Guglielmi, Barry et al. paper describing the application of an optogenetics tools to disrupt Drosophila embryo furrowing. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Furrow Segmentation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f41e88a4d47949b3b8b126b0fc7852eb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-furrowseg", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, ggplot2, knitr requirements: host: - - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - bioconductor-ebimage >=4.48.0,<4.49.0 - r-abind - r-base - r-dplyr - r-locfit - r-tiff run: - - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - bioconductor-ebimage >=4.48.0,<4.49.0 - r-abind - r-base - r-dplyr - r-locfit - r-tiff - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: b6b176917d5ecdcdc8a6b9f91e06fe95 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Furrow Segmentation' - description: 'Image feature data and analysis codes for the Guglielmi, Barry et al. paper describing the application of an optogenetics tools to disrupt Drosophila embryo furrowing.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-furrowseg/post-link.sh b/recipes/bioconductor-furrowseg/post-link.sh index 1cf285a2cc4fd..0fcb8f55a34b4 100644 --- a/recipes/bioconductor-furrowseg/post-link.sh +++ b/recipes/bioconductor-furrowseg/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "furrowseg-1.30.0" +installBiocDataPackage.sh "furrowseg-1.34.0" diff --git a/recipes/bioconductor-fusesom/meta.yaml b/recipes/bioconductor-fusesom/meta.yaml index 972591b6661df..e0d517ea2d3d8 100644 --- a/recipes/bioconductor-fusesom/meta.yaml +++ b/recipes/bioconductor-fusesom/meta.yaml @@ -1,28 +1,36 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "FuseSOM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A correlation-based multiview self-organizing map for the characterization of cell types in highly multiplexed in situ imaging cytometry assays (`FuseSOM`) is a tool for unsupervised clustering. `FuseSOM` is robust and achieves high accuracy by combining a `Self Organizing Map` architecture and a `Multiview` integration of correlation based metrics. This allows FuseSOM to cluster highly multiplexed in situ imaging cytometry assays. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f53b251d77ea648cb8e56bb5eb72b18 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-fusesom", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, rmarkdown, SingleCellExperiment requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-analogue - r-base - r-cluster @@ -41,9 +49,10 @@ requirements: - r-stringr - libblas - liblapack + run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-analogue - r-base - r-cluster @@ -60,17 +69,16 @@ requirements: - r-psych - r-rcpp - r-stringr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: c3ce10f4ae9e1beeb75462de27e8c7ae + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets' - description: 'A correlation-based multiview self-organizing map for the characterization of cell types in highly multiplexed in situ imaging cytometry assays (`FuseSOM`) is a tool for unsupervised clustering. `FuseSOM` is robust and achieves high accuracy by combining a `Self Organizing Map` architecture and a `Multiview` integration of correlation based metrics. This allows FuseSOM to cluster highly multiplexed in situ imaging cytometry assays.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ga4ghclient/meta.yaml b/recipes/bioconductor-ga4ghclient/meta.yaml index aef75f3842b74..5d85c1622e48e 100644 --- a/recipes/bioconductor-ga4ghclient/meta.yaml +++ b/recipes/bioconductor-ga4ghclient/meta.yaml @@ -1,57 +1,62 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "GA4GHclient" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: GA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A Bioconductor package for accessing GA4GH API data servers -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d0e8b9a21eda6320d15642c12fcb8392 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ga4ghclient", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-dplyr - r-httr - r-jsonlite run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-dplyr - r-httr - r-jsonlite + +source: + md5: 3de0274ec327a93066b76d5d9f2dc0e8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'A Bioconductor package for accessing GA4GH API data servers' - description: 'GA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ga4ghshiny/meta.yaml b/recipes/bioconductor-ga4ghshiny/meta.yaml index ae26ca82d7726..f0c4a2939e7f7 100644 --- a/recipes/bioconductor-ga4ghshiny/meta.yaml +++ b/recipes/bioconductor-ga4ghshiny/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "GA4GHshiny" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: GA4GHshiny package provides an easy way to interact with data servers based on Global Alliance for Genomics and Health (GA4GH) genomics API through a Shiny application. It also integrates with Beacon Network. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Shiny application for interacting with GA4GH-based data servers -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 629ca5d338b8435b238169892016d447 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ga4ghshiny", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-ga4ghclient >=1.26.0,<1.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-ga4ghclient >=1.30.0,<1.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-dt @@ -38,12 +40,12 @@ requirements: - r-shinythemes - r-tidyr run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-ga4ghclient >=1.26.0,<1.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-ga4ghclient >=1.30.0,<1.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-dt @@ -53,13 +55,16 @@ requirements: - r-shinyjs - r-shinythemes - r-tidyr + +source: + md5: 4b034c674d3a0c0ed0756bfb0f8b2829 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Shiny application for interacting with GA4GH-based data servers' - description: 'GA4GHshiny package provides an easy way to interact with data servers based on Global Alliance for Genomics and Health (GA4GH) genomics API through a Shiny application. It also integrates with Beacon Network.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gaga/meta.yaml b/recipes/bioconductor-gaga/meta.yaml index 929fa49e04c27..b496c92173a1f 100644 --- a/recipes/bioconductor-gaga/meta.yaml +++ b/recipes/bioconductor-gaga/meta.yaml @@ -1,58 +1,64 @@ -{% set version = "2.48.0" %} +{% set version = "2.52.0" %} {% set name = "gaga" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implements the GaGa model for high-throughput data analysis, including differential expression analysis, supervised gene clustering and classification. Additionally, it performs sequential sample size calculations using the GaGa and LNNGV models (the latter from EBarrays package). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: GaGa hierarchical model for high-throughput data analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d1b404912b9a23365c9085dc91e20a10 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gaga", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:gaga + - doi:10.1214/09-aoas244 + parent_recipe: + name: bioconductor-gaga + path: recipes/bioconductor-gaga + version: 2.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-ebarrays >=2.66.0,<2.67.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-ebarrays >=2.70.0,<2.71.0 - r-base - r-coda - r-mgcv - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-ebarrays >=2.66.0,<2.67.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-ebarrays >=2.70.0,<2.71.0 - r-base - r-coda - r-mgcv - build: - - {{ compiler('c') }} - - make + +source: + md5: 6daf11229cf54709ab828ea07e7a1874 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'GaGa hierarchical model for high-throughput data analysis' - description: 'Implements the GaGa model for high-throughput data analysis, including differential expression analysis, supervised gene clustering and classification. Additionally, it performs sequential sample size calculations using the GaGa and LNNGV models (the latter from EBarrays package).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:gaga - - doi:10.1214/09-aoas244 - parent_recipe: - name: bioconductor-gaga - path: recipes/bioconductor-gaga - version: 2.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gage/meta.yaml b/recipes/bioconductor-gage/meta.yaml index 4724a254b4280..1d7577221f603 100644 --- a/recipes/bioconductor-gage/meta.yaml +++ b/recipes/bioconductor-gage/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "2.52.0" %} +{% set version = "2.56.0" %} {% set name = "gage" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: GAGE is a published method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray or RNA-Seq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity, and consistently achieves superior performance over other frequently used methods. In gage package, we provide functions for basic GAGE analysis, result processing and presentation. We have also built pipeline routines for of multiple GAGE analyses in a batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources/studies. In addition, we provide demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These funtions and data are also useful for gene set analysis using other methods. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2.0) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Generally Applicable Gene-set Enrichment for Pathway Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ffb5ec419d5e08f9b31154202e0e04c8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gage", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:gage + parent_recipe: + name: bioconductor-gage + path: recipes/bioconductor-gage + version: 2.30.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: pathview, gageData, org.Hs.eg.db, hgu133a.db, GSEABase, Rsamtools, GenomicAlignments, TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq2, edgeR, limma requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 - r-base + +source: + md5: b911a6e61d639d7b20accdfd00600806 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2.0)' - summary: 'Generally Applicable Gene-set Enrichment for Pathway Analysis' - description: 'GAGE is a published method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray or RNA-Seq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity, and consistently achieves superior performance over other frequently used methods. In gage package, we provide functions for basic GAGE analysis, result processing and presentation. We have also built pipeline routines for of multiple GAGE analyses in a batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources/studies. In addition, we provide demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These funtions and data are also useful for gene set analysis using other methods.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:gage - parent_recipe: - name: bioconductor-gage - path: recipes/bioconductor-gage - version: 2.30.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gagedata/meta.yaml b/recipes/bioconductor-gagedata/meta.yaml index eeef14a1c426c..efbae8b5e9ca7 100644 --- a/recipes/bioconductor-gagedata/meta.yaml +++ b/recipes/bioconductor-gagedata/meta.yaml @@ -1,24 +1,28 @@ -{% set version = "2.40.0" %} +{% set version = "2.44.0" %} {% set name = "gageData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 889e4b6ceda6c2a80f61ad4e867c3b59 +about: + description: 'This is a supportive data package for the software package, gage. However, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general. In this package, we provide two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6 (originally published as an demo dataset for GAGE, also registered as GSE13604 in GEO). This package also includes commonly used gene set data based on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data between common gene IDs for budding yeast are also included.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>=2.0) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Auxillary data for gage package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gagedata", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-gagedata + path: recipes/bioconductor-gagedata + version: 2.18.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: gage, pathview, genefilter requirements: host: @@ -26,19 +30,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 340f02c98e843eddf50694a88ee3c18f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>=2.0)' - summary: 'Auxillary data for gage package' - description: 'This is a supportive data package for the software package, gage. However, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general. In this package, we provide two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6 (originally published as an demo dataset for GAGE, also registered as GSE13604 in GEO). This package also includes commonly used gene set data based on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data between common gene IDs for budding yeast are also included.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-gagedata - path: recipes/bioconductor-gagedata - version: 2.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gagedata/post-link.sh b/recipes/bioconductor-gagedata/post-link.sh index 1e6ddee3415bd..5935b6a281fac 100644 --- a/recipes/bioconductor-gagedata/post-link.sh +++ b/recipes/bioconductor-gagedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gagedata-2.40.0" +installBiocDataPackage.sh "gagedata-2.44.0" diff --git a/recipes/bioconductor-gaprediction/meta.yaml b/recipes/bioconductor-gaprediction/meta.yaml index 04d4db4123a5b..284c3bf1f2481 100644 --- a/recipes/bioconductor-gaprediction/meta.yaml +++ b/recipes/bioconductor-gaprediction/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "GAprediction" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: '[GAprediction] predicts gestational age using Illumina HumanMethylation450 CpG data.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Prediction of gestational age with Illumina HumanMethylation450 data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5aceb1005e134eeeb2fc6a77941d8348 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gaprediction", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:gaprediction + - doi:10.1186/s13059-016-1063-4 + parent_recipe: + name: bioconductor-gaprediction + path: recipes/bioconductor-gaprediction + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: @@ -29,21 +40,16 @@ requirements: - r-base - r-glmnet - r-matrix + +source: + md5: fdeeff05707a2548faf9b7059e96c076 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Prediction of gestational age with Illumina HumanMethylation450 data' - description: "[GAprediction] predicts gestational age using Illumina HumanMethylation450 CpG data." - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:gaprediction - - doi:10.1186/s13059-016-1063-4 - parent_recipe: - name: bioconductor-gaprediction - path: recipes/bioconductor-gaprediction - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-garfield/meta.yaml b/recipes/bioconductor-garfield/meta.yaml index 628d30c46a398..ee1e4c0f963bd 100644 --- a/recipes/bioconductor-garfield/meta.yaml +++ b/recipes/bioconductor-garfield/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "garfield" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bf1974925a6c10b95ada01ff6d46bf15 +about: + description: 'GARFIELD is a non-parametric functional enrichment analysis approach described in the paper GARFIELD: GWAS analysis of regulatory or functional information enrichment with LD correction. Briefly, it is a method that leverages GWAS findings with regulatory or functional annotations (primarily from ENCODE and Roadmap epigenomics data) to find features relevant to a phenotype of interest. It performs greedy pruning of GWAS SNPs (LD r2 > 0.1) and then annotates them based on functional information overlap. Next, it quantifies Fold Enrichment (FE) at various GWAS significance cutoffs and assesses them by permutation testing, while matching for minor allele frequency, distance to nearest transcription start site and number of LD proxies (r2 > 0.8).' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction build: - number: 3 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-garfield", max_pin="x.x") }}' +extra: + additional-platforms: + - linux-aarch64 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make +source: + md5: 5ed9866ae0522a9c2741de17f6f42da2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction' - description: 'GARFIELD is a non-parametric functional enrichment analysis approach described in the paper GARFIELD: GWAS analysis of regulatory or functional information enrichment with LD correction. Briefly, it is a method that leverages GWAS findings with regulatory or functional annotations (primarily from ENCODE and Roadmap epigenomics data) to find features relevant to a phenotype of interest. It performs greedy pruning of GWAS SNPs (LD r2 > 0.1) and then annotates them based on functional information overlap. Next, it quantifies Fold Enrichment (FE) at various GWAS significance cutoffs and assesses them by permutation testing, while matching for minor allele frequency, distance to nearest transcription start site and number of LD proxies (r2 > 0.8).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 diff --git a/recipes/bioconductor-gars/meta.yaml b/recipes/bioconductor-gars/meta.yaml index aadcd040d41db..8f652ecab7228 100644 --- a/recipes/bioconductor-gars/meta.yaml +++ b/recipes/bioconductor-gars/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "GARS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Feature selection aims to identify and remove redundant, irrelevant and noisy variables from high-dimensional datasets. Selecting informative features affects the subsequent classification and regression analyses by improving their overall performances. Several methods have been proposed to perform feature selection: most of them relies on univariate statistics, correlation, entropy measurements or the usage of backward/forward regressions. Herein, we propose an efficient, robust and fast method that adopts stochastic optimization approaches for high-dimensional. GARS is an innovative implementation of a genetic algorithm that selects robust features in high-dimensional and challenging datasets.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasets' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 205eceff8f152fa6ac308b7830ef2876 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gars", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-damirseq >=2.14.0,<2.15.0' - - 'bioconductor-mlseq >=2.20.0,<2.21.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-damirseq >=2.18.0,<2.19.0 + - bioconductor-mlseq >=2.24.0,<2.25.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-ggplot2 run: - - 'bioconductor-damirseq >=2.14.0,<2.15.0' - - 'bioconductor-mlseq >=2.20.0,<2.21.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-damirseq >=2.18.0,<2.19.0 + - bioconductor-mlseq >=2.24.0,<2.25.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-ggplot2 + +source: + md5: d0bc85304436facb815d3ee3cc5c3f0b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasets' - description: 'Feature selection aims to identify and remove redundant, irrelevant and noisy variables from high-dimensional datasets. Selecting informative features affects the subsequent classification and regression analyses by improving their overall performances. Several methods have been proposed to perform feature selection: most of them relies on univariate statistics, correlation, entropy measurements or the usage of backward/forward regressions. Herein, we propose an efficient, robust and fast method that adopts stochastic optimization approaches for high-dimensional. GARS is an innovative implementation of a genetic algorithm that selects robust features in high-dimensional and challenging datasets.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - container: - extended-base: true + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gaschyhs/meta.yaml b/recipes/bioconductor-gaschyhs/meta.yaml index 0bbd7d13201a1..45894281c3818 100644 --- a/recipes/bioconductor-gaschyhs/meta.yaml +++ b/recipes/bioconductor-gaschyhs/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "gaschYHS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 29983eadb2a2a20f7c5475206367d641 +about: + description: Data from PMID 11102521 + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: ExpressionSet for response of yeast to heat shock and other environmental stresses build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gaschyhs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c6033103748cbec679796f36cd9d2bba + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'ExpressionSet for response of yeast to heat shock and other environmental stresses' - description: 'Data from PMID 11102521' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gaschyhs/post-link.sh b/recipes/bioconductor-gaschyhs/post-link.sh index 51ff00a4819a6..6e613f92d3499 100644 --- a/recipes/bioconductor-gaschyhs/post-link.sh +++ b/recipes/bioconductor-gaschyhs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gaschyhs-1.40.0" +installBiocDataPackage.sh "gaschyhs-1.44.0" diff --git a/recipes/bioconductor-gatefinder/meta.yaml b/recipes/bioconductor-gatefinder/meta.yaml index ac9a8afe6eacc..80f8bdc330977 100644 --- a/recipes/bioconductor-gatefinder/meta.yaml +++ b/recipes/bioconductor-gatefinder/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "GateFinder" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Given a vector of cluster memberships for a cell population, identifies a sequence of gates (polygon filters on 2D scatter plots) for isolation of that cell type. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Projection-based Gating Strategy Optimization for Flow and Mass Cytometry -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4fcb13ba6ee293d3ffb30122b652df12 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gatefinder", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowfp >=1.60.0,<1.61.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowfp >=1.64.0,<1.65.0 - r-base - r-diptest - r-mvoutlier - r-splancs run: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowfp >=1.60.0,<1.61.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowfp >=1.64.0,<1.65.0 - r-base - r-diptest - r-mvoutlier - r-splancs + +source: + md5: 7ded8c08a5b2f23aae8bb9328c11668a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Projection-based Gating Strategy Optimization for Flow and Mass Cytometry' - description: 'Given a vector of cluster memberships for a cell population, identifies a sequence of gates (polygon filters on 2D scatter plots) for isolation of that cell type.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gatom/build_failure.linux-64.yaml b/recipes/bioconductor-gatom/build_failure.linux-64.yaml deleted file mode 100644 index 253ed0b0d61b5..0000000000000 --- a/recipes/bioconductor-gatom/build_failure.linux-64.yaml +++ /dev/null @@ -1,106 +0,0 @@ -recipe_sha: 7ebb01aa7b6769d098059934bddb98ded4a89c60a59b8400436d8a3a28fb92c1 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: |- - dependency issue -log: |2- - - r-mwcsr - - r-pryr - - r-data.table - - r-plyr - - r-shinycyjs >=1.0.0 - - r-base 4.3.* - - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested r-mwcsr - - - nothing provides requested r-shinycyjs >=1.0.0 - - - - Leaving build/test directories: - Work: - /opt/conda/conda-bld/work - Test: - /opt/conda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl - Build: - source activate /opt/conda/conda-bld/_build_env - - - Traceback (most recent call last): - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action - t = self.solve(specs) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - r-ggally - - r-xml - - r-sna - - r-htmltools - - r-htmlwidgets - - r-intergraph - - r-ggplot2 - - bioconductor-bionet >=1.62.0,<1.63.0 - - r-network - - r-igraph - - r-mwcsr - - r-pryr - - r-data.table - - r-plyr - - r-shinycyjs >=1.0.0 - - r-base 4.3.* - - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested r-mwcsr - - - nothing provides requested r-shinycyjs >=1.0.0 - - - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build - output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs - for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set - conda_packages = finalize_outputs_pass( - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass - fm = finalize_metadata( - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata - build_unsat, host_unsat = add_upstream_pins(m, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins - host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files - deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies - actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-mwcsr"), MatchSpec("r-shinycyjs[version='>=1.0.0']")} -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-gatom/meta.yaml b/recipes/bioconductor-gatom/meta.yaml index e51c528dd385d..0fc470a1d7ce2 100644 --- a/recipes/bioconductor-gatom/meta.yaml +++ b/recipes/bioconductor-gatom/meta.yaml @@ -1,28 +1,29 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "gatom" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module) most regulated between the two conditions of interest. The package further provides functions for module post-processing, annotation and visualization. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENCE + summary: Finding an Active Metabolic Module in Atom Transition Network -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0e86773c5bafed3a4c13b7db82015463 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gatom", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, KEGGREST, AnnotationDbi, org.Mm.eg.db, reactome.db, fgsea, readr, BiocStyle, R.utils requirements: host: - - 'bioconductor-bionet >=1.62.0,<1.63.0' + - bioconductor-bionet >=1.66.0,<1.67.0 - r-base - r-data.table - r-ggally @@ -35,11 +36,11 @@ requirements: - r-network - r-plyr - r-pryr - - 'r-shinycyjs >=1.0.0' + - r-shinycyjs >=1.0.0 - r-sna - r-xml run: - - 'bioconductor-bionet >=1.62.0,<1.63.0' + - bioconductor-bionet >=1.66.0,<1.67.0 - r-base - r-data.table - r-ggally @@ -52,15 +53,19 @@ requirements: - r-network - r-plyr - r-pryr - - 'r-shinycyjs >=1.0.0' + - r-shinycyjs >=1.0.0 - r-sna - r-xml + +source: + md5: 53c7f36266f15eca255e6c6ef3c83cc1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENCE' - summary: 'Finding an Active Metabolic Module in Atom Transition Network' - description: 'This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module) most regulated between the two conditions of interest. The package further provides functions for module post-processing, annotation and visualization.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gbscleanr/meta.yaml b/recipes/bioconductor-gbscleanr/meta.yaml index 7b565ff74bd52..b4c93dcba5941 100644 --- a/recipes/bioconductor-gbscleanr/meta.yaml +++ b/recipes/bioconductor-gbscleanr/meta.yaml @@ -1,29 +1,35 @@ -{% set version = "1.6.0" %} +{% set version = "2.0.2" %} {% set name = "GBScleanR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: GBScleanR is a package for quality check, filtering, and error correction of genotype data derived from next generation sequcener (NGS) based genotyping platforms. GBScleanR takes Variant Call Format (VCF) file as input. The main function of this package is `estGeno()` which estimates the true genotypes of samples from given read counts for genotype markers using a hidden Markov model with incorporating uneven observation ratio of allelic reads. This implementation gives robust genotype estimation even in noisy genotype data usually observed in Genotyping-By-Sequnencing (GBS) and similar methods, e.g. RADseq. The current implementation accepts genotype data of a diploid population at any generation of multi-parental cross, e.g. biparental F2 from inbred parents, biparental F2 from outbred parents, and 8-way recombinant inbred lines (8-way RILs) which can be refered to as MAGIC population. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Error correction tool for noisy genotyping by sequencing (GBS) data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f54a8356b8931c5c6dd6150a021c56cf build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gbscleanr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown # SystemRequirements: GNU make, C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-seqarray >=1.46.0,<1.47.0 - r-base - r-expm - r-ggplot2 @@ -33,25 +39,24 @@ requirements: - libblas - liblapack run: - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-seqarray >=1.46.0,<1.47.0 - r-base - r-expm - r-ggplot2 - r-rcpp - r-rcppparallel - r-tidyr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 5d2b0379d1feb8d5326fdd8de9041407 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Error correction tool for noisy genotyping by sequencing (GBS) data' - description: 'GBScleanR is a package for quality check, filtering, and error correction of genotype data derived from next generation sequcener (NGS) based genotyping platforms. GBScleanR takes Variant Call Format (VCF) file as input. The main function of this package is `estGeno()` which estimates the true genotypes of samples from given read counts for genotype markers using a hidden Markov model with incorporating uneven observation ratio of allelic reads. This implementation gives robust genotype estimation even in noisy genotype data usually observed in Genotyping-By-Sequnencing (GBS) and similar methods, e.g. RADseq. The current implementation accepts genotype data of a diploid population at any generation of multi-parental cross, e.g. biparental F2 from inbred parents, biparental F2 from outbred parents, and 8-way recombinant inbred lines (8-way RILs) which can be refered to as MAGIC population.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gcapc/meta.yaml b/recipes/bioconductor-gcapc/meta.yaml index 9270c58bf5303..95932468cce4c 100644 --- a/recipes/bioconductor-gcapc/meta.yaml +++ b/recipes/bioconductor-gcapc/meta.yaml @@ -1,59 +1,64 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "gcapc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: GC Aware Peak Caller -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 16c0a9ac78843641871680c0e0d48dfc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gcapc", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-mass - r-matrixstats run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-mass - r-matrixstats + +source: + md5: 0a44b8ff045c206665d0f3ee8355f717 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'GC Aware Peak Caller' - description: 'Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gcatest/meta.yaml b/recipes/bioconductor-gcatest/meta.yaml index 82f540b32e039..e24d6c614104d 100644 --- a/recipes/bioconductor-gcatest/meta.yaml +++ b/recipes/bioconductor-gcatest/meta.yaml @@ -1,41 +1,22 @@ -{% set version = "2.2.0" %} +{% set version = "2.6.0" %} {% set name = "gcatest" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: GCAT is an association test for genome wide association studies that controls for population structure under a general class of trait models. This test conditions on the trait, which makes it immune to confounding by unmodeled environmental factors. Population structure is modeled via logistic factors, which are estimated using the `lfa` package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Genotype Conditional Association TEST -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ddfda402a2332e9c16ecfaa035b689a9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gcatest", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, ggplot2, testthat, BEDMatrix, genio -requirements: - host: - - 'bioconductor-lfa >=2.2.0,<2.3.0' - - r-base - run: - - 'bioconductor-lfa >=2.2.0,<2.3.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Genotype Conditional Association TEST' - description: 'GCAT is an association test for genome wide association studies that controls for population structure under a general class of trait models. This test conditions on the trait, which makes it immune to confounding by unmodeled environmental factors. Population structure is modeled via logistic factors, which are estimated using the `lfa` package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:gcatest @@ -45,3 +26,28 @@ extra: path: recipes/bioconductor-gcatest version: 1.10.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, ggplot2, testthat, BEDMatrix, genio +requirements: + host: + - bioconductor-lfa >=2.6.0,<2.7.0 + - r-base + run: + - bioconductor-lfa >=2.6.0,<2.7.0 + - r-base + +source: + md5: 4b1cc9bf33fbed8d138db711a9fbd6cd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-gcrisprtools/meta.yaml b/recipes/bioconductor-gcrisprtools/meta.yaml index 421388b058ba2..21e756cfd25db 100644 --- a/recipes/bioconductor-gcrisprtools/meta.yaml +++ b/recipes/bioconductor-gcrisprtools/meta.yaml @@ -1,58 +1,64 @@ -{% set version = "2.8.0" %} +{% set version = "2.12.0" %} {% set name = "gCrisprTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Set of tools for evaluating pooled high-throughput screening experiments, typically employing CRISPR/Cas9 or shRNA expression cassettes. Contains methods for interrogating library and cassette behavior within an experiment, identifying differentially abundant cassettes, aggregating signals to identify candidate targets for empirical validation, hypothesis testing, and comprehensive reporting. Version 2.0 extends these applications to include a variety of tools for contextualizing and integrating signals across many experiments, incorporates extended signal enrichment methodologies via the "sparrow" package, and streamlines many formal requirements to aid in interpretablity. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Suite of Functions for Pooled Crispr Screen QC and Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 113ef693d51de0459865934e9a16d90a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gcrisprtools", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:gcrisprtools + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-gcrisprtools + path: recipes/bioconductor-gcrisprtools + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: edgeR, knitr, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, BiocGenerics, markdown, RUnit, sparrow, msigdbr, fgsea requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-rmarkdown - r-robustrankaggreg run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-rmarkdown - r-robustrankaggreg + +source: + md5: 523c4cdbf2b7285014df7a7f25ef5df1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Suite of Functions for Pooled Crispr Screen QC and Analysis' - description: 'Set of tools for evaluating pooled high-throughput screening experiments, typically employing CRISPR/Cas9 or shRNA expression cassettes. Contains methods for interrogating library and cassette behavior within an experiment, identifying differentially abundant cassettes, aggregating signals to identify candidate targets for empirical validation, hypothesis testing, and comprehensive reporting. Version 2.0 extends these applications to include a variety of tools for contextualizing and integrating signals across many experiments, incorporates extended signal enrichment methodologies via the "sparrow" package, and streamlines many formal requirements to aid in interpretablity.' -extra: - identifiers: - - biotools:gcrisprtools - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-gcrisprtools - path: recipes/bioconductor-gcrisprtools - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gcrma/meta.yaml b/recipes/bioconductor-gcrma/meta.yaml index c742e33709f8f..a5037a4fadd34 100644 --- a/recipes/bioconductor-gcrma/meta.yaml +++ b/recipes/bioconductor-gcrma/meta.yaml @@ -1,61 +1,67 @@ -{% set version = "2.74.0" %} +{% set version = "2.78.0" %} {% set name = "gcrma" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Background adjustment using sequence information + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Background Adjustment Using Sequence Information -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d28b6c225b2677e476da8d0348af4695 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gcrma", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:gcrma + - doi:10.1186/1471-2105-9-452 + parent_recipe: + name: bioconductor-gcrma + path: recipes/bioconductor-gcrma + version: 2.52.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-biocmanager - libblas - liblapack run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-biocmanager - build: - - {{ compiler('c') }} - - make + +source: + md5: aa2eac73f440177d1ad450a9faa09b27 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Background Adjustment Using Sequence Information' - description: 'Background adjustment using sequence information' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:gcrma - - doi:10.1186/1471-2105-9-452 - parent_recipe: - name: bioconductor-gcrma - path: recipes/bioconductor-gcrma - version: 2.52.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gcspikelite/meta.yaml b/recipes/bioconductor-gcspikelite/meta.yaml index c6c53cd0af3c6..299f42f735206 100644 --- a/recipes/bioconductor-gcspikelite/meta.yaml +++ b/recipes/bioconductor-gcspikelite/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "gcspikelite" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 91b995753732f0d5508fdc2d7dcb998f +about: + description: Spike-in data for GC/MS data and methods within flagme + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Spike-in data for GC/MS data and methods within flagme build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gcspikelite", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-gcspikelite + path: recipes/bioconductor-gcspikelite + version: 1.18.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3b8732b7eb8743bd3f92cb0eaa1308b3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Spike-in data for GC/MS data and methods within flagme' - description: 'Spike-in data for GC/MS data and methods within flagme' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - parent_recipe: - name: bioconductor-gcspikelite - path: recipes/bioconductor-gcspikelite - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gcspikelite/post-link.sh b/recipes/bioconductor-gcspikelite/post-link.sh index 56da58607707c..1d7bb8e252344 100644 --- a/recipes/bioconductor-gcspikelite/post-link.sh +++ b/recipes/bioconductor-gcspikelite/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gcspikelite-1.40.0" +installBiocDataPackage.sh "gcspikelite-1.44.0" diff --git a/recipes/bioconductor-gdcrnatools/meta.yaml b/recipes/bioconductor-gdcrnatools/meta.yaml index 4ce47ee1d8f08..cae170d06f3d8 100644 --- a/recipes/bioconductor-gdcrnatools/meta.yaml +++ b/recipes/bioconductor-gdcrnatools/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "GDCRNATools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This is an easy-to-use package for downloading, organizing, and integrative analyzing RNA expression data in GDC with an emphasis on deciphering the lncRNA-mRNA related ceRNA regulatory network in cancer. Three databases of lncRNA-miRNA interactions including spongeScan, starBase, and miRcode, as well as three databases of mRNA-miRNA interactions including miRTarBase, starBase, and miRcode are incorporated into the package for ceRNAs network construction. limma, edgeR, and DESeq2 can be used to identify differentially expressed genes/miRNAs. Functional enrichment analyses including GO, KEGG, and DO can be performed based on the clusterProfiler and DO packages. Both univariate CoxPH and KM survival analyses of multiple genes can be implemented in the package. Besides some routine visualization functions such as volcano plot, bar plot, and KM plot, a few simply shiny apps are developed to facilitate visualization of results on a local webpage. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bf97cefce864ca1443cb0b0d53601799 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gdcrnatools", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, prettydoc, rmarkdown requirements: + host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicdatacommons >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-pathview >=1.42.0,<1.43.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicdatacommons >=1.30.0,<1.31.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-pathview >=1.46.0,<1.47.0 - r-base - r-dt - r-ggplot2 @@ -42,17 +44,18 @@ requirements: - r-survival - r-survminer - r-xml + run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicdatacommons >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-pathview >=1.42.0,<1.43.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicdatacommons >=1.30.0,<1.31.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-pathview >=1.46.0,<1.47.0 - r-base - r-dt - r-ggplot2 @@ -63,12 +66,16 @@ requirements: - r-survival - r-survminer - r-xml + +source: + md5: dc35fc44cf7a39cda5f87e23adefbe2f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC' - description: 'This is an easy-to-use package for downloading, organizing, and integrative analyzing RNA expression data in GDC with an emphasis on deciphering the lncRNA-mRNA related ceRNA regulatory network in cancer. Three databases of lncRNA-miRNA interactions including spongeScan, starBase, and miRcode, as well as three databases of mRNA-miRNA interactions including miRTarBase, starBase, and miRcode are incorporated into the package for ceRNAs network construction. limma, edgeR, and DESeq2 can be used to identify differentially expressed genes/miRNAs. Functional enrichment analyses including GO, KEGG, and DO can be performed based on the clusterProfiler and DO packages. Both univariate CoxPH and KM survival analyses of multiple genes can be implemented in the package. Besides some routine visualization functions such as volcano plot, bar plot, and KM plot, a few simply shiny apps are developed to facilitate visualization of results on a local webpage.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gdnainrnaseqdata/meta.yaml b/recipes/bioconductor-gdnainrnaseqdata/meta.yaml index bb3142cbcf0d4..5f119efc5c04c 100644 --- a/recipes/bioconductor-gdnainrnaseqdata/meta.yaml +++ b/recipes/bioconductor-gdnainrnaseqdata/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "gDNAinRNAseqData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides access to BAM files generated from RNA-seq data produced with different levels of gDNA contamination. It currently allows one to download a subset of the data published by Li et al., BMC Genomics, 23:554, 2022. This subset of data is formed by BAM files with about 100,000 alignments with three different levels of gDNA contamination. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: RNA-seq data with different levels of gDNA contamination -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 52e275ca255493684657a091667f987f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gdnainrnaseqdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-rcurl - r-xml run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-rcurl - r-xml - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 1051ca9adac9bf173e6ae6db69c7d5f8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'RNA-seq data with different levels of gDNA contamination' - description: 'Provides access to BAM files generated from RNA-seq data produced with different levels of gDNA contamination. It currently allows one to download a subset of the data published by Li et al., BMC Genomics, 23:554, 2022. This subset of data is formed by BAM files with about 100,000 alignments with three different levels of gDNA contamination.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gdnainrnaseqdata/post-link.sh b/recipes/bioconductor-gdnainrnaseqdata/post-link.sh index 4daf109d60fca..e0d2f87e5aa2a 100644 --- a/recipes/bioconductor-gdnainrnaseqdata/post-link.sh +++ b/recipes/bioconductor-gdnainrnaseqdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gdnainrnaseqdata-1.2.0" +installBiocDataPackage.sh "gdnainrnaseqdata-1.6.0" diff --git a/recipes/bioconductor-gdnax/meta.yaml b/recipes/bioconductor-gdnax/meta.yaml index d582e28ee690b..fc7e855bc6d90 100644 --- a/recipes/bioconductor-gdnax/meta.yaml +++ b/recipes/bioconductor-gdnax/meta.yaml @@ -1,70 +1,81 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "gDNAx" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides diagnostics for assessing genomic DNA contamination in RNA-seq data, as well as plots representing these diagnostics. Moreover, the package can be used to get an insight into the strand library protocol used and, in case of strand-specific libraries, the strandedness of the data. Furthermore, it provides functionality to filter out reads of potential gDNA origin. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Diagnostics for assessing genomic DNA contamination in RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ca3a7370388bf64ba5ccae7161c64ebd build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gdnax", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, RUnit, TxDb.Hsapiens.UCSC.hg38.knownGene, gDNAinRNAseqData requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicfiles >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bitops + - r-cli + - r-matrixstats - r-plotrix - r-rcolorbrewer + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicfiles >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bitops + - r-cli + - r-matrixstats - r-plotrix - r-rcolorbrewer + +source: + md5: 6926dccba12870cb64efe08bdeff939a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Diagnostics for assessing genomic DNA contamination in RNA-seq data' - description: 'Provides diagnostics for assessing genomic DNA contamination in RNA-seq data, as well as plots representing these diagnostics. Moreover, the package can be used to get an insight into the strand library protocol used and, in case of strand-specific libraries, the strandedness of the data. Furthermore, it provides functionality to filter out reads of potential gDNA origin.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gdr/meta.yaml b/recipes/bioconductor-gdr/meta.yaml index 8b311b353ff7d..56673c698b1af 100644 --- a/recipes/bioconductor-gdr/meta.yaml +++ b/recipes/bioconductor-gdr/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "gDR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: abefb906e5c9ec014a443b0367844ac9 +about: + description: Package is a part of the gDR suite. It reexports functions from other packages in the gDR suite that contain critical processing functions and utilities. The vignette walks through the full processing pipeline for drug response analyses that the gDR suite offers. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Umbrella package for R packages in the gDR suite build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gdr", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, BumpyMatrix, futile.logger, gDRstyle (>= 0.99.11), gDRtestData (>= 0.99.11), kableExtra, knitr, markdown, purrr, rmarkdown, SummarizedExperiment, testthat, yaml +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: BiocStyle, BumpyMatrix, futile.logger, gDRstyle (>= 1.1.5), gDRtestData (>= 1.1.10), kableExtra, knitr, markdown, purrr, rmarkdown, SummarizedExperiment, testthat, yaml requirements: host: - - 'bioconductor-gdrcore >=1.0.0,<1.1.0' - - 'bioconductor-gdrimport >=1.0.0,<1.1.0' - - 'bioconductor-gdrutils >=1.0.0,<1.1.0' + - bioconductor-gdrcore >=1.4.0,<1.5.0 + - bioconductor-gdrimport >=1.4.0,<1.5.0 + - bioconductor-gdrutils >=1.4.0,<1.5.0 - r-base run: - - 'bioconductor-gdrcore >=1.0.0,<1.1.0' - - 'bioconductor-gdrimport >=1.0.0,<1.1.0' - - 'bioconductor-gdrutils >=1.0.0,<1.1.0' + - bioconductor-gdrcore >=1.4.0,<1.5.0 + - bioconductor-gdrimport >=1.4.0,<1.5.0 + - bioconductor-gdrutils >=1.4.0,<1.5.0 - r-base +source: + md5: b438eb9a45f17715858b15e4ba01e004 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Umbrella package for R packages in the gDR suite' - description: 'Package is a part of the gDR suite. It reexports functions from other packages in the gDR suite that contain critical processing functions and utilities. The vignette walks through the full processing pipeline for drug response analyses that the gDR suite offers.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gdrcore/meta.yaml b/recipes/bioconductor-gdrcore/meta.yaml index 91fd6a2760db8..0e37cc0bcccda 100644 --- a/recipes/bioconductor-gdrcore/meta.yaml +++ b/recipes/bioconductor-gdrcore/meta.yaml @@ -1,32 +1,37 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "gDRcore" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains core functions to process and analyze drug response data. The package provides tools for normalizing, averaging, and calculation of gDR metrics data. All core functions are wrapped into the pipeline function allowing analyzing the data in a straightforward way. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Processing functions and interface to process and analyze drug dose-response data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 76f729e9fce669107120d0ec73c32bfc build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gdrcore", max_pin="x.x") }}' -# Suggests: BiocStyle, gDRstyle (>= 0.99.15), gDRimport (>= 0.99.10), gDRtestData (>= 0.99.20), IRanges, knitr, pkgbuild, qs, testthat, yaml + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, gDRstyle (>= 1.1.5), gDRimport (>= 1.1.9), gDRtestData (>= 1.1.10), IRanges, knitr, pkgbuild, qs, testthat, yaml requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' - - 'bioconductor-gdrutils >=1.0.0,<1.1.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bumpymatrix >=1.14.0,<1.15.0 + - bioconductor-gdrutils >=1.4.0,<1.5.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-checkmate - r-data.table @@ -36,28 +41,28 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' - - 'bioconductor-gdrutils >=1.0.0,<1.1.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bumpymatrix >=1.14.0,<1.15.0 + - bioconductor-gdrutils >=1.4.0,<1.5.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-checkmate - r-data.table - r-futile.logger - r-purrr - r-stringr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: bb7ea3782d4eaa6fe7faf4ae08251bd6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Processing functions and interface to process and analyze drug dose-response data' - description: 'This package contains core functions to process and analyze drug response data. The package provides tools for normalizing, averaging, and calculation of gDR metrics data. All core functions are wrapped into the pipeline function allowing analyzing the data in a straightforward way.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gdrimport/meta.yaml b/recipes/bioconductor-gdrimport/meta.yaml index 2b32dd59962bc..f11fa323a7765 100644 --- a/recipes/bioconductor-gdrimport/meta.yaml +++ b/recipes/bioconductor-gdrimport/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "gDRimport" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package is a part of the gDR suite. It helps to prepare raw drug response data for downstream processing. It mainly contains helper functions for importing/loading/validating dose-response data provided in different file formats. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Package for handling the import of dose-response data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0390ee6a16f21624044bc509ebdbabd1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gdrimport", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, gDRtestData (>= 0.99.10), gDRstyle (>= 0.99.11), knitr, purrr, qs, testthat + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, gDRtestData (>= 1.1.10), gDRstyle (>= 1.1.5), knitr, purrr, qs, testthat requirements: + host: - - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' - - 'bioconductor-coregx >=2.6.0,<2.7.0' - - 'bioconductor-gdrutils >=1.0.0,<1.1.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-pharmacogx >=3.6.0,<3.7.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-bumpymatrix >=1.14.0,<1.15.0 + - bioconductor-coregx >=2.10.0,<2.11.0 + - bioconductor-gdrutils >=1.4.0,<1.5.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-pharmacogx >=3.10.0,<3.11.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-checkmate @@ -42,14 +44,15 @@ requirements: - r-tibble - r-xml - r-yaml + run: - - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' - - 'bioconductor-coregx >=2.6.0,<2.7.0' - - 'bioconductor-gdrutils >=1.0.0,<1.1.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-pharmacogx >=3.6.0,<3.7.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-bumpymatrix >=1.14.0,<1.15.0 + - bioconductor-coregx >=2.10.0,<2.11.0 + - bioconductor-gdrutils >=1.4.0,<1.5.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-pharmacogx >=3.10.0,<3.11.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-checkmate @@ -63,12 +66,16 @@ requirements: - r-tibble - r-xml - r-yaml + +source: + md5: 78229e1a4d3bca3bd0ab7b71deb53512 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Package for handling the import of dose-response data' - description: 'The package is a part of the gDR suite. It helps to prepare raw drug response data for downstream processing. It mainly contains helper functions for importing/loading/validating dose-response data provided in different file formats.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gdrstyle/meta.yaml b/recipes/bioconductor-gdrstyle/meta.yaml index e8ec2ff8fdf2a..699bdac546856 100644 --- a/recipes/bioconductor-gdrstyle/meta.yaml +++ b/recipes/bioconductor-gdrstyle/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "gDRstyle" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package fills a helper package role for whole gDR suite. It helps to support good development practices by keeping style requirements and style tests for other packages. It also contains build helpers to make all package requirements met. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: A package with style requirements for the gDR suite -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 473f3c2e73e05f50ec3af2b72bb18a55 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gdrstyle", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-bioccheck >=1.38.0,<1.39.0' + - bioconductor-bioccheck >=1.42.0,<1.43.0 - r-base - r-biocmanager + - r-checkmate - r-desc - r-git2r - - 'r-lintr >=3.0.0' + - r-lintr >=3.0.0 - r-pkgbuild - r-rcmdcheck - r-remotes @@ -35,24 +37,29 @@ requirements: - r-withr - r-yaml run: - - 'bioconductor-bioccheck >=1.38.0,<1.39.0' + - bioconductor-bioccheck >=1.42.0,<1.43.0 - r-base - r-biocmanager + - r-checkmate - r-desc - r-git2r - - 'r-lintr >=3.0.0' + - r-lintr >=3.0.0 - r-pkgbuild - r-rcmdcheck - r-remotes - r-rjson - r-withr - r-yaml + +source: + md5: 8c65fb73bd818d5a00adbc49fab2de0c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A package with style requirements for the gDR suite' - description: 'Package fills a helper package role for whole gDR suite. It helps to support good development practices by keeping style requirements and style tests for other packages. It also contains build helpers to make all package requirements met.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gdrtestdata/meta.yaml b/recipes/bioconductor-gdrtestdata/meta.yaml index 0118da30f9290..ae304e9bc5d1d 100644 --- a/recipes/bioconductor-gdrtestdata/meta.yaml +++ b/recipes/bioconductor-gdrtestdata/meta.yaml @@ -1,40 +1,42 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "gDRtestData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8de3dea2673f0e7dc9412e36da2c4f9d +about: + description: R package with internal dose-response test data. Package provides functions to generate input testing data that can be used as the input for gDR pipeline. It also contains qs files with MAE data processed by gDR. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: gDRtestData - R data package with testing dose response data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gdrtestdata", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, data.table, gDRstyle (>= 0.99.16), knitr, qs, reshape2, rmarkdown, SummarizedExperiment, testthat +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: BiocStyle, gDRstyle (>= 1.1.5), knitr, qs, reshape2, rmarkdown, SummarizedExperiment, testthat, yaml requirements: host: - r-base - r-checkmate + - r-data.table run: - r-base - r-checkmate + - r-data.table - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: edefc42aeca53a188b512659ae557f6d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'gDRtestData - R data package with testing dose reponse data' - description: 'R package with internal dose-response test data. Package provides functions to generate input testing data that can be used as the input for gDR pipeline. It also contains RDS files with MAE data processed by gDR.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gdrtestdata/post-link.sh b/recipes/bioconductor-gdrtestdata/post-link.sh index 1e1afaeb5de88..5ee11bfc2b5c8 100644 --- a/recipes/bioconductor-gdrtestdata/post-link.sh +++ b/recipes/bioconductor-gdrtestdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gdrtestdata-1.0.0" +installBiocDataPackage.sh "gdrtestdata-1.4.0" diff --git a/recipes/bioconductor-gdrutils/meta.yaml b/recipes/bioconductor-gdrutils/meta.yaml index ea940ee0ab23d..975f2e1e700d8 100644 --- a/recipes/bioconductor-gdrutils/meta.yaml +++ b/recipes/bioconductor-gdrutils/meta.yaml @@ -1,60 +1,63 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "gDRutils" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains utility functions used throughout the gDR platform to fit data, manipulate data, and convert and validate data structures. This package also has the necessary default constants for gDR platform. Many of the functions are utilized by the gDRcore package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: A package with helper functions for processing drug response data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fdf71802bbd5967b163447eda2fe37ef build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gdrutils", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocManager, BiocStyle, futile.logger, gDRstyle (>= 0.99.15), gDRtestData (>= 0.99.12), IRanges, knitr, lintr, purrr, qs, rcmdcheck, rmarkdown, testthat, tools, yaml + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocManager, BiocStyle, futile.logger, gDRstyle (>= 1.1.5), gDRtestData (>= 1.1.10), IRanges, knitr, lintr, purrr, qs, rcmdcheck, rmarkdown, scales, testthat, tools, yaml requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bumpymatrix >=1.14.0,<1.15.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-checkmate - r-data.table - r-drc - r-jsonlite - r-jsonvalidate - - r-magrittr - r-stringr run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bumpymatrix >=1.14.0,<1.15.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-checkmate - r-data.table - r-drc - r-jsonlite - r-jsonvalidate - - r-magrittr - r-stringr + +source: + md5: f357676625d090a95321b1b293bd3d45 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A package with helper functions for processing drug response data' - description: 'This package contains utility functions used throughout the gDR platform to fit data, manipulate data, and convert and validate data structures. This package also has the necessary default constants for gDR platform. Many of the functions are utilized by the gDRcore package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gdsarray/meta.yaml b/recipes/bioconductor-gdsarray/meta.yaml index 66ec184fb02c7..41d27a95edc7a 100644 --- a/recipes/bioconductor-gdsarray/meta.yaml +++ b/recipes/bioconductor-gdsarray/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "GDSArray" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: GDS files are widely used to represent genotyping or sequence data. The GDSArray package implements the `GDSArray` class to represent nodes in GDS files in a matrix-like representation that allows easy manipulation (e.g., subsetting, mathematical transformation) in _R_. The data remains on disk until needed, so that very large files can be processed. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Representing GDS files as array-like objects -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ae99d95017d67dd67e17f47436f0301 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gdsarray", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, BiocManager requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-seqarray >=1.42.0,<1.43.0' - - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqarray >=1.46.0,<1.47.0 + - bioconductor-snprelate >=1.40.0,<1.41.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-seqarray >=1.42.0,<1.43.0' - - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqarray >=1.46.0,<1.47.0 + - bioconductor-snprelate >=1.40.0,<1.41.0 - r-base + +source: + md5: a218ee5f76a8115b1126dfa077be9a3e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Representing GDS files as array-like objects' - description: 'GDS files are widely used to represent genotyping or sequence data. The GDSArray package implements the `GDSArray` class to represent nodes in GDS files in a matrix-like representation that allows easy manipulation (e.g., subsetting, mathematical transformation) in _R_. The data remains on disk until needed, so that very large files can be processed.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gdsfmt/meta.yaml b/recipes/bioconductor-gdsfmt/meta.yaml index 7569c70324307..7f17c88216737 100644 --- a/recipes/bioconductor-gdsfmt/meta.yaml +++ b/recipes/bioconductor-gdsfmt/meta.yaml @@ -1,49 +1,55 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "gdsfmt" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers the efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package parallel. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: R Interface to CoreArray Genomic Data Structure (GDS) Files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8851c188356c12f7e99488ceb4daeca8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gdsfmt", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + parent_recipe: + name: bioconductor-gdsfmt + path: recipes/bioconductor-gdsfmt + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: parallel, digest, Matrix, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 394bd408a3aa442689ffdcb7d1999f6b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'R Interface to CoreArray Genomic Data Structure (GDS) Files' - description: 'Provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers the efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package parallel.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - additional-platforms: - - linux-aarch64 - parent_recipe: - name: bioconductor-gdsfmt - path: recipes/bioconductor-gdsfmt - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gem/meta.yaml b/recipes/bioconductor-gem/meta.yaml index 3cb07be59e5e2..ac6124e948de9 100644 --- a/recipes/bioconductor-gem/meta.yaml +++ b/recipes/bioconductor-gem/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "GEM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2c2c8e79fda151dee0060411c9610ff4 +about: + description: Tools for analyzing EWAS, methQTL and GxE genome widely. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'GEM: fast association study for the interplay of Gene, Environment and Methylation' build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gem", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown requirements: host: @@ -27,12 +25,14 @@ requirements: run: - r-base - r-ggplot2 +source: + md5: 58de7f773c0abeb5b13dff866cf05f0a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'GEM: fast association study for the interplay of Gene, Environment and Methylation' - description: 'Tools for analyzing EWAS, methQTL and GxE genome widely.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gemini/meta.yaml b/recipes/bioconductor-gemini/meta.yaml index 974ee79f5a978..b760837f41584 100644 --- a/recipes/bioconductor-gemini/meta.yaml +++ b/recipes/bioconductor-gemini/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "gemini" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: GEMINI uses log-fold changes to model sample-dependent and independent effects, and uses a variational Bayes approach to infer these effects. The inferred effects are used to score and identify genetic interactions, such as lethality and recovery. More details can be found in Zamanighomi et al. 2019 (in press). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_3_clause + file LICENSE + license_file: LICENSE + summary: 'GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e8c26d0e8208f56017c8c83a17582f37 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gemini", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat requirements: host: @@ -37,13 +39,16 @@ requirements: - r-mixtools - r-pbmcapply - r-scales + +source: + md5: f51d601db3f201a97c98935260e12446 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_3_clause + file LICENSE' - summary: 'GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens' - description: 'GEMINI uses log-fold changes to model sample-dependent and independent effects, and uses a variational Bayes approach to infer these effects. The inferred effects are used to score and identify genetic interactions, such as lethality and recovery. More details can be found in Zamanighomi et al. 2019 (in press).' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gemma.r/meta.yaml b/recipes/bioconductor-gemma.r/meta.yaml index d15d66baff3ab..156c55c25b49a 100644 --- a/recipes/bioconductor-gemma.r/meta.yaml +++ b/recipes/bioconductor-gemma.r/meta.yaml @@ -1,32 +1,35 @@ -{% set version = "2.0.0" %} +{% set version = "3.2.0" %} {% set name = "gemma.R" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Low- and high-level wrappers for Gemma's RESTful API. They enable access to curated expression and differential expression data from over 10,000 published studies. Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Apache License (>= 2) + summary: A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 404ce4fa50032ebf727cfdccece32ba2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gemma.r", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis, poolr, digest + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis, poolr, kableExtra, listviewer, shiny requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base + - r-base64enc - r-bit64 - r-data.table - r-digest @@ -36,17 +39,20 @@ requirements: - r-lubridate - r-magrittr - r-memoise + - r-r.utils - r-rappdirs - r-rlang - r-stringr - r-tibble - r-tidyr + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base + - r-base64enc - r-bit64 - r-data.table - r-digest @@ -56,17 +62,22 @@ requirements: - r-lubridate - r-magrittr - r-memoise + - r-r.utils - r-rappdirs - r-rlang - r-stringr - r-tibble - r-tidyr + +source: + md5: 7a91640afaf517a51ef99db1851a5afd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Apache License (>= 2)' - summary: 'A wrapper for Gemma''s Restful API to access curated gene expression data and differential expression analyses' - description: 'Low- and high-level wrappers for Gemma''s RESTful API. They enable access to curated expression and differential expression data from over 10,000 published studies. Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genarise/meta.yaml b/recipes/bioconductor-genarise/meta.yaml index ade2b312fe4f8..288f906db10df 100644 --- a/recipes/bioconductor-genarise/meta.yaml +++ b/recipes/bioconductor-genarise/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.78.0" %} +{% set version = "1.82.0" %} {% set name = "genArise" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d81489147ccfe688c07c228b7fcfcf7d +about: + description: genArise is an easy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Microarray Analysis tool build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genarise", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base @@ -30,13 +29,14 @@ requirements: - r-locfit - r-tkrplot - r-xtable +source: + md5: 514f7c20dc7d1821f39817ad00c0af8e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Microarray Analysis tool' - description: 'genArise is an easy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-geneattribution/meta.yaml b/recipes/bioconductor-geneattribution/meta.yaml index e0e87d633ea5f..fbc4a27b07bc0 100644 --- a/recipes/bioconductor-geneattribution/meta.yaml +++ b/recipes/bioconductor-geneattribution/meta.yaml @@ -1,52 +1,21 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "geneAttribution" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Identification of the most likely gene or genes through which variation at a given genomic locus in the human genome acts. The most basic functionality assumes that the closer gene is to the input locus, the more likely the gene is to be causative. Additionally, any empirical data that links genomic regions to genes (e.g. eQTL or genome conformation data) can be used if it is supplied in the UCSC .BED file format. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Identification of candidate genes associated with genetic variation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 62d05af7aabb146fb41a5d91fa460dff build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-geneattribution", max_pin="x.x") }}' - noarch: generic -# Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat -requirements: - host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - r-base - run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Identification of candidate genes associated with genetic variation' - description: 'Identification of the most likely gene or genes through which variation at a given genomic locus in the human genome acts. The most basic functionality assumes that the closer gene is to the input locus, the more likely the gene is to be causative. Additionally, any empirical data that links genomic regions to genes (e.g. eQTL or genome conformation data) can be used if it is supplied in the UCSC .BED file format.' + extra: identifiers: - biotools:geneattribution @@ -56,3 +25,40 @@ extra: path: recipes/bioconductor-geneattribution version: 1.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - r-base + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - r-base + +source: + md5: 70b1dc253483bd498bbfb18412cabe08 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-genebreak/meta.yaml b/recipes/bioconductor-genebreak/meta.yaml index fded2e8fdf46a..f81d7787a52b5 100644 --- a/recipes/bioconductor-genebreak/meta.yaml +++ b/recipes/bioconductor-genebreak/meta.yaml @@ -1,46 +1,22 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "GeneBreak" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Recurrent breakpoint gene detection on copy number aberration profiles. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Gene Break Detection -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 32b69bf4150c25c908235217dc805ed3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genebreak", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-cghbase >=1.62.0,<1.63.0' - - 'bioconductor-cghcall >=2.64.0,<2.65.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - - r-base - run: - - 'bioconductor-cghbase >=1.62.0,<1.63.0' - - 'bioconductor-cghcall >=2.64.0,<2.65.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Gene Break Detection' - description: 'Recurrent breakpoint gene detection on copy number aberration profiles.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + extra: identifiers: - biotools:genebreak @@ -50,3 +26,33 @@ extra: path: recipes/bioconductor-genebreak version: 1.10.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-cghbase >=1.66.0,<1.67.0 + - bioconductor-cghcall >=2.68.0,<2.69.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-qdnaseq >=1.42.0,<1.43.0 + - r-base + run: + - bioconductor-cghbase >=1.66.0,<1.67.0 + - bioconductor-cghcall >=2.68.0,<2.69.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-qdnaseq >=1.42.0,<1.43.0 + - r-base + +source: + md5: fad78dcf860cd3a3c9a9960ddae99aa9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-geneclassifiers/meta.yaml b/recipes/bioconductor-geneclassifiers/meta.yaml index 1bbd879fd921b..444a42a296a05 100644 --- a/recipes/bioconductor-geneclassifiers/meta.yaml +++ b/recipes/bioconductor-geneclassifiers/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "geneClassifiers" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 79b7de2354913e5a91e6026f3f815a46 +about: + description: This packages aims for easy accessible application of classifiers which have been published in literature using an ExpressionSet as input. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Application of gene classifiers build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-geneclassifiers", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base +source: + md5: 237032d0dffde4694d5de463536ec1f5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Application of gene classifiers' - description: 'This packages aims for easy accessible application of classifiers which have been published in literature using an ExpressionSet as input.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-geneexpressionsignature/meta.yaml b/recipes/bioconductor-geneexpressionsignature/meta.yaml index 784b7d4b4cc8a..b051283e4aa10 100644 --- a/recipes/bioconductor-geneexpressionsignature/meta.yaml +++ b/recipes/bioconductor-geneexpressionsignature/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "GeneExpressionSignature" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee82254ee781e3cd6657c89d94e052b3 +about: + description: This package gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Gene Expression Signature based Similarity Metric build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-geneexpressionsignature", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: apcluster, GEOquery, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base +source: + md5: 4a1d31a2fe3f57f4429534a22317aee1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Gene Expression Signature based Similarity Metric' - description: 'This package gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genefilter/meta.yaml b/recipes/bioconductor-genefilter/meta.yaml index 0c9c1b258bc3d..b8d2453fc9c8e 100644 --- a/recipes/bioconductor-genefilter/meta.yaml +++ b/recipes/bioconductor-genefilter/meta.yaml @@ -1,62 +1,68 @@ -{% set version = "1.84.0" %} +{% set version = "1.88.0" %} {% set name = "genefilter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Some basic functions for filtering genes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'genefilter: methods for filtering genes from high-throughput experiments' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 15011d1662a58967aeb3e89f1f660e40 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genefilter", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:genefilter + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-genefilter + path: recipes/bioconductor-genefilter + version: 1.62.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - {{ compiler('fortran') }} + - make host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 - r-base - r-survival - libblas - liblapack run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 - r-base - r-survival - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - {{ compiler('fortran') }} - - make + +source: + md5: 95bc8cdec8e895d1f36507ace3dc0b3c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'genefilter: methods for filtering genes from high-throughput experiments' - description: 'Some basic functions for filtering genes.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:genefilter - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-genefilter - path: recipes/bioconductor-genefilter - version: 1.62.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genega/meta.yaml b/recipes/bioconductor-genega/meta.yaml index 296123222ca7a..95f90bdfa6250 100644 --- a/recipes/bioconductor-genega/meta.yaml +++ b/recipes/bioconductor-genega/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.52.0" %} +{% set version = "1.56.0" %} {% set name = "GeneGA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3047f864af1845ce91869fc2560733c4 +about: + description: R based Genetic algorithm for gene expression optimization by considering both mRNA secondary structure and codon usage bias, GeneGA includes the information of highly expressed genes of almost 200 genomes. Meanwhile, Vienna RNA Package is needed to ensure GeneGA to function properly. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL version 2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genega", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base @@ -28,13 +27,14 @@ requirements: - r-base - r-hash - r-seqinr +source: + md5: dc0258cfb1f0c223cba51aa35f738057 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL version 2' - summary: 'Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm' - description: 'R based Genetic algorithm for gene expression optimization by considering both mRNA secondary structure and codon usage bias, GeneGA includes the information of highly expressed genes of almost 200 genomes. Meanwhile, Vienna RNA Package is needed to ensure GeneGA to function properly.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genegeneinter/meta.yaml b/recipes/bioconductor-genegeneinter/meta.yaml index ea75dfc6378c3..8c8d8153de61c 100644 --- a/recipes/bioconductor-genegeneinter/meta.yaml +++ b/recipes/bioconductor-genegeneinter/meta.yaml @@ -1,29 +1,41 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "GeneGeneInteR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The aim of this package is to propose several methods for testing gene-gene interaction in case-control association studies. Such a test can be done by aggregating SNP-SNP interaction tests performed at the SNP level (SSI) or by using gene-gene multidimensionnal methods (GGI) methods. The package also proposes tools for a graphic display of the results. . + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Tools for Testing Gene-Gene Interaction at the Gene Level -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 119efde24626155c173e9b24b5f2c9e6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genegeneinter", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:genegeneinter + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-snpstats >=1.56.0,<1.57.0 - r-base - r-data.table - r-factominer @@ -33,32 +45,26 @@ requirements: - libblas - liblapack run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-snpstats >=1.56.0,<1.57.0 - r-base - r-data.table - r-factominer - r-igraph - r-kernlab - r-mvtnorm - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: f7913598aed390843211d46146aef0a9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0.-or-later' - summary: 'Tools for Testing Gene-Gene Interaction at the Gene Level' - description: 'The aim of this package is to propose several methods for testing gene-gene interaction in case-control association studies. Such a test can be done by aggregating SNP-SNP interaction tests performed at the SNP level (SSI) or by using gene-gene multidimensionnal methods (GGI) methods. The package also proposes tools for a graphic display of the results. .' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} \ No newline at end of file diff --git a/recipes/bioconductor-genelendatabase/meta.yaml b/recipes/bioconductor-genelendatabase/meta.yaml index 7619efdaf2175..61834cb8f55c8 100644 --- a/recipes/bioconductor-genelendatabase/meta.yaml +++ b/recipes/bioconductor-genelendatabase/meta.yaml @@ -1,47 +1,55 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "geneLenDataBase" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Length of mRNA transcripts for a number of genomes and gene ID formats, largely based on UCSC table browser. Data objects are provided as individual pieces of information to be retrieved and loaded. A variety of different gene identifiers and genomes is supported to ensure wide applicability. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Lengths of mRNA transcripts for a number of genomes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c29099d3142aad07590e22ce37c6acf3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genelendatabase", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-genelendatabase + path: recipes/bioconductor-genelendatabase + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base run: - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 383f08d23aa5b28f812f4d353bc5dd6f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'Lengths of mRNA transcripts for a number of genomes' - description: 'Length of mRNA transcripts for a number of genomes and gene ID formats, largely based on UCSC table browser' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - parent_recipe: - name: bioconductor-genelendatabase - path: recipes/bioconductor-genelendatabase - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genelendatabase/post-link.sh b/recipes/bioconductor-genelendatabase/post-link.sh index 5423b1add506e..2df95f73e1dd1 100644 --- a/recipes/bioconductor-genelendatabase/post-link.sh +++ b/recipes/bioconductor-genelendatabase/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "genelendatabase-1.38.0" +installBiocDataPackage.sh "genelendatabase-1.42.0" diff --git a/recipes/bioconductor-genemeta/meta.yaml b/recipes/bioconductor-genemeta/meta.yaml index 46829e4dab0d2..e1512f7f0e04e 100644 --- a/recipes/bioconductor-genemeta/meta.yaml +++ b/recipes/bioconductor-genemeta/meta.yaml @@ -1,42 +1,21 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "GeneMeta" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A collection of meta-analysis tools for analysing high throughput experimental data + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: MetaAnalysis for High Throughput Experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9d9d2d3dff0ee8a497ac86b5ef8ddac7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genemeta", max_pin="x.x") }}' - noarch: generic -# Suggests: RColorBrewer -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'MetaAnalysis for High Throughput Experiments' - description: 'A collection of meta-analysis tools for analysing high throughput experimental data' + extra: identifiers: - biotools:genemeta @@ -46,3 +25,30 @@ extra: path: recipes/bioconductor-genemeta version: 1.52.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RColorBrewer +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - r-base + +source: + md5: 485b54a222fe7a17466df0c1d85c9107 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-genenetworkbuilder/meta.yaml b/recipes/bioconductor-genenetworkbuilder/meta.yaml index 840e50663cdde..a93a941199134 100644 --- a/recipes/bioconductor-genenetworkbuilder/meta.yaml +++ b/recipes/bioconductor-genenetworkbuilder/meta.yaml @@ -1,61 +1,69 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "GeneNetworkBuilder" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Appliation for discovering direct or indirect targets of transcription factors using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, GeneNetworkBuilder generates a regulatory network of the TF. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aedb0b143d59865acfad5ce4d635ff77 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genenetworkbuilder", max_pin="x.x") }}' -# Suggests: RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:genenetworkbuilder + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RUnit, BiocGenerics, RBGL, knitr, shiny, STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-htmlwidgets - r-plyr - - 'r-rcpp >=0.9.13' + - r-rcpp >=0.9.13 - r-rjson - r-xml - libblas - liblapack run: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-htmlwidgets - r-plyr - - 'r-rcpp >=0.9.13' + - r-rcpp >=0.9.13 - r-rjson - r-xml - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 9c30af079b04a3731ce69403dbefb465 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data' - description: 'Appliation for discovering direct or indirect targets of transcription factors using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, GeneNetworkBuilder generates a regulatory network of the TF.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-geneoverlap/meta.yaml b/recipes/bioconductor-geneoverlap/meta.yaml index 3912599cb2a10..028d63d207c8e 100644 --- a/recipes/bioconductor-geneoverlap/meta.yaml +++ b/recipes/bioconductor-geneoverlap/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "GeneOverlap" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Test two sets of gene lists and visualize the results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Test and visualize gene overlaps -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0b5179a1183a82869935ca6c2c55aab3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-geneoverlap", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:geneoverlap + - doi:10.1167/iovs.16-20618 + parent_recipe: + name: bioconductor-geneoverlap + path: recipes/bioconductor-geneoverlap + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, BiocStyle requirements: host: @@ -29,21 +40,16 @@ requirements: - r-base - r-gplots - r-rcolorbrewer + +source: + md5: 4ae5390946a3e0a23aca20198e6474ab + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Test and visualize gene overlaps' - description: 'Test two sets of gene lists and visualize the results.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:geneoverlap - - doi:10.1167/iovs.16-20618 - parent_recipe: - name: bioconductor-geneoverlap - path: recipes/bioconductor-geneoverlap - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-geneplast.data.string.v91/build_failure.linux-64.yaml b/recipes/bioconductor-geneplast.data.string.v91/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..8e4a135579c34 --- /dev/null +++ b/recipes/bioconductor-geneplast.data.string.v91/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: dbececfc4dc1487aed6b5ef72c75f3a6c54650e6ec58b1721e6e155f9a38fef1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-base=4.4")} + Encountered problems while solving: + - nothing provides requested r-base 4.4.* + + Could not solve for environment specs + The following package could not be installed + [31mr-base 4.4.* [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-base=4.4")} + Encountered problems while solving: + - nothing provides requested r-base 4.4.* + + Could not solve for environment specs + The following package could not be installed + [31mr-base 4.4.* [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-base=4.4")} + Encountered problems while solving: + - nothing provides requested r-base 4.4.* + + Could not solve for environment specs + The following package could not be installed + [31mr-base 4.4.* [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-geneplast.data.string.v91/meta.yaml b/recipes/bioconductor-geneplast.data.string.v91/meta.yaml index db3e08458d885..8bf039149924a 100644 --- a/recipes/bioconductor-geneplast.data.string.v91/meta.yaml +++ b/recipes/bioconductor-geneplast.data.string.v91/meta.yaml @@ -1,37 +1,37 @@ {% set version = "0.99.6" %} {% set name = "geneplast.data.string.v91" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 86433f8489d9228c5ed73e2b75a55398 +about: + description: The package geneplast.data.string.v91 contains input data used in the analysis pipelines available in the geneplast package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Input data for the geneplast package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-geneplast.data.string.v91", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 86433f8489d9228c5ed73e2b75a55398 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Input data for the geneplast package' - description: 'The package geneplast.data.string.v91 contains input data used in the analysis pipelines available in the geneplast package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-geneplast.data/meta.yaml b/recipes/bioconductor-geneplast.data/meta.yaml index 20f45bdf6867b..d4369c46a9ba6 100644 --- a/recipes/bioconductor-geneplast.data/meta.yaml +++ b/recipes/bioconductor-geneplast.data/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "0.99.7" %} +{% set version = "0.99.9" %} {% set name = "geneplast.data" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package geneplast.data provides datasets from different sources via AnnotationHub to use in geneplast pipelines. The datasets have species, phylogenetic trees, and orthology relationships among eukaryotes from different orthologs databases. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Input data for the geneplast package via AnnotationHub -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ef658e131138d87033fcd985c38cf45f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-geneplast.data", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: geneplast, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-geneplast >=1.28.0,<1.29.0' - - 'bioconductor-treeio >=1.26.0,<1.27.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-geneplast >=1.32.0,<1.33.0 + - bioconductor-treeio >=1.30.0,<1.31.0 - r-ape - r-base - r-dplyr @@ -32,10 +33,11 @@ requirements: - r-purrr - r-readr - r-tibble + - r-tidyr run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-geneplast >=1.28.0,<1.29.0' - - 'bioconductor-treeio >=1.26.0,<1.27.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-geneplast >=1.32.0,<1.33.0 + - bioconductor-treeio >=1.30.0,<1.31.0 - r-ape - r-base - r-dplyr @@ -43,14 +45,19 @@ requirements: - r-purrr - r-readr - r-tibble + - r-tidyr - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: c25d661b13014ce9abc6da7411a6e539 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Input data for the geneplast package via AnnotationHub' - description: 'The package geneplast.data provides datasets from different sources via AnnotationHub to use in geneplast pipelines. The datasets have species, phylogenetic trees, and orthology relationships among eukaryotes from different orthologs databases.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-geneplast.data/post-link.sh b/recipes/bioconductor-geneplast.data/post-link.sh index 879df13431c7f..d32c2e1081e01 100644 --- a/recipes/bioconductor-geneplast.data/post-link.sh +++ b/recipes/bioconductor-geneplast.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "geneplast.data-0.99.7" +installBiocDataPackage.sh "geneplast.data-0.99.9" diff --git a/recipes/bioconductor-geneplast/meta.yaml b/recipes/bioconductor-geneplast/meta.yaml index c78eca2385118..61a867de252e7 100644 --- a/recipes/bioconductor-geneplast/meta.yaml +++ b/recipes/bioconductor-geneplast/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "geneplast" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Geneplast is designed for evolutionary and plasticity analysis based on orthologous groups distribution in a given species tree. It uses Shannon information theory and orthologs abundance to estimate the Evolutionary Plasticity Index. Additionally, it implements the Bridge algorithm to determine the evolutionary root of a given gene based on its orthologs distribution. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Evolutionary and plasticity analysis of orthologous groups -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2cb6b3ec6dbd0978146ea5139cc06e60 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-geneplast", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:geneplast + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-geneplast + path: recipes/bioconductor-geneplast + version: 1.6.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data, geneplast.data.string.v91, ggplot2, ggpubr, plyr requirements: host: @@ -33,21 +44,16 @@ requirements: - r-data.table - r-igraph - r-snow + +source: + md5: c2117a32bc2ff90ecf3890b5571dc730 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Evolutionary and plasticity analysis of orthologous groups' - description: 'Geneplast is designed for evolutionary and plasticity analysis based on orthologous groups distribution in a given species tree. It uses Shannon information theory and orthologs abundance to estimate the Evolutionary Plasticity Index. Additionally, it implements the Bridge algorithm to determine the evolutionary root of a given gene based on its orthologs distribution.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:geneplast - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-geneplast - path: recipes/bioconductor-geneplast - version: 1.6.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-geneplotter/meta.yaml b/recipes/bioconductor-geneplotter/meta.yaml index 67627719ca339..06a8bb3451bb5 100644 --- a/recipes/bioconductor-geneplotter/meta.yaml +++ b/recipes/bioconductor-geneplotter/meta.yaml @@ -1,56 +1,62 @@ -{% set version = "1.80.0" %} +{% set version = "1.84.0" %} {% set name = "geneplotter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions for plotting genomic data + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Graphics related functions for Bioconductor -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 29d4ec34db2e953fc9b7306f4d3b7733 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-geneplotter", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:geneplotter + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-geneplotter + path: recipes/bioconductor-geneplotter + version: 1.58.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db, BiocStyle, knitr requirements: host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-lattice - r-rcolorbrewer run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-lattice - r-rcolorbrewer + +source: + md5: e2c75ec7716edbbc43de5a768f2eac85 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Graphics related functions for Bioconductor' - description: 'Functions for plotting genomic data' -extra: - identifiers: - - biotools:geneplotter - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-geneplotter - path: recipes/bioconductor-geneplotter - version: 1.58.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-generecommender/meta.yaml b/recipes/bioconductor-generecommender/meta.yaml index 55b5c7e1ae759..dadd3526f965b 100644 --- a/recipes/bioconductor-generecommender/meta.yaml +++ b/recipes/bioconductor-generecommender/meta.yaml @@ -1,40 +1,22 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "geneRecommender" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A gene recommender algorithm to identify genes coexpressed with a query set of genes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd697c11912a8f48b5ceaf0abfbb206e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-generecommender", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'A gene recommender algorithm to identify genes coexpressed with a query set of genes' - description: 'This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:generecommender @@ -44,3 +26,27 @@ extra: path: recipes/bioconductor-generecommender version: 1.52.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + +source: + md5: 8e6c386e1aaa70a6b04cda30cc0cbf92 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-generegionscan/meta.yaml b/recipes/bioconductor-generegionscan/meta.yaml index c81ed957e93b0..1287fc45e2574 100644 --- a/recipes/bioconductor-generegionscan/meta.yaml +++ b/recipes/bioconductor-generegionscan/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "1.58.0" %} +{% set version = "1.62.0" %} {% set name = "GeneRegionScan" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: GeneRegionScan -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9b3e0cfd305d2db2aae5cfd4003e56a7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-generegionscan", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:generegionscan + parent_recipe: + name: bioconductor-generegionscan + path: recipes/bioconductor-generegionscan + version: 1.36.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome, affy, AnnotationDbi requirements: host: - - 'bioconductor-affxparser >=1.74.0,<1.75.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-affxparser >=1.78.0,<1.79.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-rcolorbrewer run: - - 'bioconductor-affxparser >=1.74.0,<1.75.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-affxparser >=1.78.0,<1.79.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-rcolorbrewer + +source: + md5: eda7a12b518083d821d7243e3a756749 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: GeneRegionScan - description: 'A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:generegionscan - parent_recipe: - name: bioconductor-generegionscan - path: recipes/bioconductor-generegionscan - version: 1.36.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-generxcluster/meta.yaml b/recipes/bioconductor-generxcluster/meta.yaml index 47294fc1e4560..2116d263c8504 100644 --- a/recipes/bioconductor-generxcluster/meta.yaml +++ b/recipes/bioconductor-generxcluster/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "geneRxCluster" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Detect Differential Clustering of Genomic Sites such as gene therapy integrations. The package provides some functions for exploring genomic insertion sites originating from two different sources. Possibly, the two sources are two different gene therapy vectors. Vectors are preferred that target sensitive regions less frequently, motivating the search for localized clusters of insertions and comparison of the clusters formed by integration of different vectors. Scan statistics allow the discovery of spatial differences in clustering and calculation of False Discovery Rates (FDRs) providing statistical methods for comparing retroviral vectors. A scan statistic for comparing two vectors using multiple window widths to detect clustering differentials and compute FDRs is implemented here. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: gRx Differential Clustering -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61f7d4c5cd314cf84f8648b3097f65b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-generxcluster", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:generxcluster + parent_recipe: + name: bioconductor-generxcluster + path: recipes/bioconductor-generxcluster + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - libblas - liblapack run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: b73e1f6855885ab29b6ccfbd19247bd4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'gRx Differential Clustering' - description: 'Detect Differential Clustering of Genomic Sites such as gene therapy integrations. The package provides some functions for exploring genomic insertion sites originating from two different sources. Possibly, the two sources are two different gene therapy vectors. Vectors are preferred that target sensitive regions less frequently, motivating the search for localized clusters of insertions and comparison of the clusters formed by integration of different vectors. Scan statistics allow the discovery of spatial differences in clustering and calculation of False Discovery Rates (FDRs) providing statistical methods for comparing retroviral vectors. A scan statistic for comparing two vectors using multiple window widths to detect clustering differentials and compute FDRs is implemented here.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:generxcluster - parent_recipe: - name: bioconductor-generxcluster - path: recipes/bioconductor-generxcluster - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-geneselectmmd/meta.yaml b/recipes/bioconductor-geneselectmmd/meta.yaml index f28cf53ec6c7b..ce53ccdb989de 100644 --- a/recipes/bioconductor-geneselectmmd/meta.yaml +++ b/recipes/bioconductor-geneselectmmd/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "2.46.0" %} +{% set version = "2.50.0" %} {% set name = "GeneSelectMMD" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Gene selection based on a mixture of marginal distributions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dd6cd07bbe095fca03ce4b134c1507b8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-geneselectmmd", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:geneselectmmd + - usegalaxy-eu:geneselectmmd + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ALL requirements: + build: + - {{ compiler('c') }} + - {{ compiler('fortran') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-mass - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-mass - build: - - {{ compiler('c') }} - - {{ compiler('fortran') }} - - make + +source: + md5: 92000e264119ad74cd9a7fcccbe73706 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions' - description: 'Gene selection based on a mixture of marginal distributions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} - - usegalaxy-eu:{{ name|lower }} diff --git a/recipes/bioconductor-genesis/meta.yaml b/recipes/bioconductor-genesis/meta.yaml index 49123fdd70790..8aa7d644dbfab 100644 --- a/recipes/bioconductor-genesis/meta.yaml +++ b/recipes/bioconductor-genesis/meta.yaml @@ -1,37 +1,42 @@ -{% set version = "2.32.0" %} +{% set version = "2.36.0" %} {% set name = "GENESIS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The GENESIS package provides methodology for estimating, inferring, and accounting for population and pedigree structure in genetic analyses. The current implementation provides functions to perform PC-AiR (Conomos et al., 2015, Gen Epi) and PC-Relate (Conomos et al., 2016, AJHG). PC-AiR performs a Principal Components Analysis on genome-wide SNP data for the detection of population structure in a sample that may contain known or cryptic relatedness. Unlike standard PCA, PC-AiR accounts for relatedness in the sample to provide accurate ancestry inference that is not confounded by family structure. PC-Relate uses ancestry representative principal components to adjust for population structure/ancestry and accurately estimate measures of recent genetic relatedness such as kinship coefficients, IBD sharing probabilities, and inbreeding coefficients. Additionally, functions are provided to perform efficient variance component estimation and mixed model association testing for both quantitative and binary phenotypes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 909c6b6ea17b2de1716f3a5102caa0df build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genesis", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: CompQuadForm, COMPoissonReg, poibin, SPAtest, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gwastools >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-seqarray >=1.42.0,<1.43.0' - - 'bioconductor-seqvartools >=1.40.0,<1.41.0' - - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gwastools >=1.52.0,<1.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqarray >=1.46.0,<1.47.0 + - bioconductor-seqvartools >=1.44.0,<1.45.0 + - bioconductor-snprelate >=1.40.0,<1.41.0 - r-base - r-data.table - r-igraph @@ -40,32 +45,32 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gwastools >=1.48.0,<1.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-seqarray >=1.42.0,<1.43.0' - - 'bioconductor-seqvartools >=1.40.0,<1.41.0' - - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gwastools >=1.52.0,<1.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqarray >=1.46.0,<1.47.0 + - bioconductor-seqvartools >=1.44.0,<1.45.0 + - bioconductor-snprelate >=1.40.0,<1.41.0 - r-base - r-data.table - r-igraph - r-matrix - r-reshape2 - build: - - {{ compiler('c') }} - - make + +source: + md5: 34c9fbd04570d82dc6d31539b9c958f9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness' - description: 'The GENESIS package provides methodology for estimating, inferring, and accounting for population and pedigree structure in genetic analyses. The current implementation provides functions to perform PC-AiR (Conomos et al., 2015, Gen Epi) and PC-Relate (Conomos et al., 2016, AJHG). PC-AiR performs a Principal Components Analysis on genome-wide SNP data for the detection of population structure in a sample that may contain known or cryptic relatedness. Unlike standard PCA, PC-AiR accounts for relatedness in the sample to provide accurate ancestry inference that is not confounded by family structure. PC-Relate uses ancestry representative principal components to adjust for population structure/ancestry and accurately estimate measures of recent genetic relatedness such as kinship coefficients, IBD sharing probabilities, and inbreeding coefficients. Additionally, functions are provided to perform efficient variance component estimation and mixed model association testing for both quantitative and binary phenotypes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genestructuretools/build_failure.linux-64.yaml b/recipes/bioconductor-genestructuretools/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..d850461fc0cb0 --- /dev/null +++ b/recipes/bioconductor-genestructuretools/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 51550799c6b6654131486b699075564ea1ac3867297aaeb0fa0ed1d2f35b1b35 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("3.3.1*"), MatchSpec("bioconductor-bsgenome.mmusculus.ucsc.mm10==1.4.0=r3.3.1_0")} + Encountered problems while solving: + - nothing provides r 3.3.1* needed by bioconductor-bsgenome.mmusculus.ucsc.mm10-1.4.0-r3.3.1_0 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-biostrings >=2.74.0,<2.75.0 [0m is requested and can be installed; + [32mbioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0 [0m is installable with the potential options + [32mbioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0[0m would require + [32mr-base 3.3.2* [0m, which can be installed; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0[0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [32mbioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0[0m would require + [32mr-base 3.4.1* [0m, which can be installed; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.48.0,<1.50.0 [0m, which requires + [31mbioconductor-biostrings >=2.48.0,<2.50.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.50.0,<1.51.0 [0m, which requires + [31mbioconductor-biostrings >=2.50.0,<2.51.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.52.0,<1.53.0 [0m, which requires + [31mbioconductor-biostrings >=2.52.0,<2.53.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.54.0,<1.55.0 [0m, which requires + [31mbioconductor-biostrings >=2.54.0,<2.55.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.58.0,<1.59.0 [0m, which requires + [31mbioconductor-biostrings >=2.58.0,<2.59.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.56.0,<1.57.0 [0m, which requires + [31mbioconductor-biostrings >=2.56.0,<2.57.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.60.0,<1.61.0 [0m, which requires + [31mbioconductor-biostrings >=2.60.0,<2.61.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.62.0,<1.63.0 [0m, which requires + [31mbioconductor-biostrings >=2.62.0,<2.63.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.66.0,<1.67.0 [0m, which requires + [31mbioconductor-biostrings >=2.66.0,<2.67.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.68.0,<1.69.0 [0m, which requires + [31mbioconductor-biostrings >=2.68.0,<2.69.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm10 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.70.0,<1.71.0 [0m, which requires + [31mbioconductor-biostrings >=2.70.0,<2.71.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-gviz >=1.50.0,<1.51.0 [0m is not installable because it requires + [31mbioconductor-biovizbase >=1.54.0,<1.55.0 [0m, which requires + [31mbioconductor-summarizedexperiment >=1.36.0,<1.37.0 [0m, which requires + [31mbioconductor-delayedarray >=0.32.0,<0.33.0 [0m, which requires + [31mbioconductor-sparsearray >=1.6.0,<1.7.0 [0m, which requires + [31mr-base >=4.4,<4.5.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-genestructuretools/meta.yaml b/recipes/bioconductor-genestructuretools/meta.yaml index b68d6a11f06d2..2e78c9b017c5a 100644 --- a/recipes/bioconductor-genestructuretools/meta.yaml +++ b/recipes/bioconductor-genestructuretools/meta.yaml @@ -1,59 +1,64 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "GeneStructureTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: GeneStructureTools can be used to create in silico alternative splicing events, and analyse potential effects this has on functional gene products. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_3_clause + file LICENSE + license_file: LICENSE + summary: Tools for spliced gene structure manipulation and analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 513385498b639ea6acc724bb3795de38 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genestructuretools", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-plyr - r-stringdist - r-stringr run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-plyr - r-stringdist - r-stringr + +source: + md5: 7134d4484dfd9541cb421473da018aa8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_3_clause + file LICENSE' - summary: 'Tools for spliced gene structure manipulation and analysis' - description: 'GeneStructureTools can be used to create in silico alternative splicing events, and analyse potential effects this has on functional gene products.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genesummary/meta.yaml b/recipes/bioconductor-genesummary/meta.yaml index 3f59623599845..9fe5245917ab3 100644 --- a/recipes/bioconductor-genesummary/meta.yaml +++ b/recipes/bioconductor-genesummary/meta.yaml @@ -1,24 +1,23 @@ {% set version = "0.99.6" %} {% set name = "GeneSummary" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9df029a96bf0fa5bb76ee8b8923c458c +about: + description: This package provides long description of genes collected from the RefSeq database. The text in "COMMENT" section started with "Summary" is extracted as the description of the gene. The long text descriptions can be used for analysis such as text mining. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: RefSeq Gene Summaries build: - number: 0 + noarch: generic + number: 1 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genesummary", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, markdown, testthat requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9df029a96bf0fa5bb76ee8b8923c458c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'RefSeq Gene Summaries' - description: 'This package provides long description of genes collected from the RefSeq database. The text in "COMMENT" section started with "Summary" is extracted as the description of the gene. The long text descriptions can be used for analysis such as text mining.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genetclassifier/meta.yaml b/recipes/bioconductor-genetclassifier/meta.yaml index d449d168bddc2..2cc1f04558f2e 100644 --- a/recipes/bioconductor-genetclassifier/meta.yaml +++ b/recipes/bioconductor-genetclassifier/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "geNetClassifier" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Comprehensive package to automatically train and validate a multi-class SVM classifier based on gene expression data. Provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Classify diseases and build associated gene networks using gene expression profiles -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7fed3e42e9ec93956b71960e271aa090 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genetclassifier", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:genetclassifier + parent_recipe: + name: bioconductor-genetclassifier + path: recipes/bioconductor-genetclassifier + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: leukemiasEset, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-ebarrays >=2.66.0,<2.67.0' - - 'bioconductor-minet >=3.60.0,<3.61.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-ebarrays >=2.70.0,<2.71.0 + - bioconductor-minet >=3.64.0,<3.65.0 - r-base - r-e1071 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-ebarrays >=2.66.0,<2.67.0' - - 'bioconductor-minet >=3.60.0,<3.61.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-ebarrays >=2.70.0,<2.71.0 + - bioconductor-minet >=3.64.0,<3.65.0 - r-base - r-e1071 + +source: + md5: bc29ee3feafccc630ed6268b887eca7a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Classify diseases and build associated gene networks using gene expression profiles' - description: 'Comprehensive package to automatically train and validate a multi-class SVM classifier based on gene expression data. Provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:genetclassifier - parent_recipe: - name: bioconductor-genetclassifier - path: recipes/bioconductor-genetclassifier - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-geneticsped/build_failure.osx-64.yaml b/recipes/bioconductor-geneticsped/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..4f61f1a34b774 --- /dev/null +++ b/recipes/bioconductor-geneticsped/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: d0d04302d4173444d27c5f13c432d03bf47d374e12ccd83bcdb612c6a5e67719 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-geneticsped_1734400645563/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-geneticsped_1734400645563/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-geneticsped_1734400645563/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-geneticsped_1734400645563/work + INFO: activate-gfortran_osx-64.sh made the following environmental changes: + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-geneticsped-1.68.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-geneticsped-1.68.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-geneticsped-1.68.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-geneticsped-1.68.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-geneticsped-1.68.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-geneticsped-1.68.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-geneticsped-1.68.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-geneticsped-1.68.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate-gfortran_osx-64.sh made the following environmental changes: + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-geneticsped-1.68.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-geneticsped-1.68.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + GFORTRAN=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + -DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-geneticsped-1.68.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + -DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-geneticsped-1.68.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + -FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + -GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-geneticsped-1.68.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-geneticsped-1.68.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-geneticsped-1.68.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-geneticsped-1.68.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-geneticsped-1.68.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-geneticsped-1.68.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734381577890/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ainverse.cc -o ainverse.o +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-geneticsped/meta.yaml b/recipes/bioconductor-geneticsped/meta.yaml index d2fc3bea27908..87799c46bce56 100644 --- a/recipes/bioconductor-geneticsped/meta.yaml +++ b/recipes/bioconductor-geneticsped/meta.yaml @@ -1,25 +1,36 @@ -{% set version = "1.64.0" %} +{% set version = "1.68.0" %} {% set name = "GeneticsPed" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities. Note that package is not yet stable. Use it with care! + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2.1) | file LICENSE + license_file: LICENSE + summary: Pedigree and genetic relationship functions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7d2a79c363e79459dd3edf3b4571f313 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-geneticsped", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, gtools requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - {{ compiler('fortran') }} + - make host: - r-base - r-gdata @@ -32,21 +43,16 @@ requirements: - r-gdata - r-genetics - r-mass - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - {{ compiler('fortran') }} - - make + +source: + md5: 39ef0bf3833462aaa66cef37ea4da4b9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2.1) | file LICENSE' - summary: 'Pedigree and genetic relationship functions' - description: 'Classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities. Note that package is not yet stable. Use it with care!' - license_file: LICENSE + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 diff --git a/recipes/bioconductor-genetonic/build_failure.linux-64.yaml b/recipes/bioconductor-genetonic/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..7b74f46d64e77 --- /dev/null +++ b/recipes/bioconductor-genetonic/build_failure.linux-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: af0e4a8d59c1ac40663b78be796c0970c691c5871e6f8bb16749857239bf0fa0 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bioconductor-mosdef needs to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-genetonic/build_failure.osx-64.yaml b/recipes/bioconductor-genetonic/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..7b74f46d64e77 --- /dev/null +++ b/recipes/bioconductor-genetonic/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: af0e4a8d59c1ac40663b78be796c0970c691c5871e6f8bb16749857239bf0fa0 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bioconductor-mosdef needs to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-genetonic/meta.yaml b/recipes/bioconductor-genetonic/meta.yaml index 4c8e329fd8f3d..54370c4e7b82a 100644 --- a/recipes/bioconductor-genetonic/meta.yaml +++ b/recipes/bioconductor-genetonic/meta.yaml @@ -1,36 +1,40 @@ -{% set version = "2.6.0" %} +{% set version = "3.0.0" %} {% set name = "GeneTonic" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functionality to combine the existing pieces of the transcriptome data and results, making it easier to generate insightful observations and hypothesis. Its usage is made easy with a Shiny application, combining the benefits of interactivity and reproducibility e.g. by capturing the features and gene sets of interest highlighted during the live session, and creating an HTML report as an artifact where text, code, and output coexist. Using the GeneTonicList as a standardized container for all the required components, it is possible to simplify the generation of multiple visualizations and summaries. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: efbbb39095cb7ff8af87ed47d058d8d8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genetonic", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0) requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-mosdef >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-backbone - r-base - - 'r-bs4dash >=2.0.0' + - r-bs4dash >=2.0.0 - r-circlize - r-colorspace - r-colourpicker @@ -41,7 +45,7 @@ requirements: - r-dynamictreecut - r-expm - r-ggforce - - r-ggplot2 + - r-ggplot2 >=3.5.0 - r-ggrepel - r-ggridges - r-igraph @@ -60,16 +64,18 @@ requirements: - r-tippy - r-viridis - r-visnetwork + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-mosdef >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-backbone - r-base - - 'r-bs4dash >=2.0.0' + - r-bs4dash >=2.0.0 - r-circlize - r-colorspace - r-colourpicker @@ -80,7 +86,7 @@ requirements: - r-dynamictreecut - r-expm - r-ggforce - - r-ggplot2 + - r-ggplot2 >=3.5.0 - r-ggrepel - r-ggridges - r-igraph @@ -99,13 +105,16 @@ requirements: - r-tippy - r-viridis - r-visnetwork + +source: + md5: df5cb9fd911fbad1896f64fa0b7c2089 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis' - description: 'This package provides functionality to combine the existing pieces of the transcriptome data and results, making it easier to generate insightful observations and hypothesis. Its usage is made easy with a Shiny application, combining the benefits of interactivity and reproducibility e.g. by capturing the features and gene sets of interest highlighted during the live session, and creating an HTML report as an artifact where text, code, and output coexist. Using the GeneTonicList as a standardized container for all the required components, it is possible to simplify the generation of multiple visualizations and summaries.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genextender/meta.yaml b/recipes/bioconductor-genextender/meta.yaml index cc7257f170ded..14fb0551d42e9 100644 --- a/recipes/bioconductor-genextender/meta.yaml +++ b/recipes/bioconductor-genextender/meta.yaml @@ -1,31 +1,42 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "geneXtendeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: geneXtendeR optimizes the functional annotation of ChIP-seq peaks by exploring relative differences in annotating ChIP-seq peak sets to variable-length gene bodies. In contrast to prior techniques, geneXtendeR considers peak annotations beyond just the closest gene, allowing users to see peak summary statistics for the first-closest gene, second-closest gene, ..., n-closest gene whilst ranking the output according to biologically relevant events and iteratively comparing the fidelity of peak-to-gene overlap across a user-defined range of upstream and downstream extensions on the original boundaries of each gene's coordinates. Since different ChIP-seq peak callers produce different differentially enriched peaks with a large variance in peak length distribution and total peak count, annotating peak lists with their nearest genes can often be a noisy process. As such, the goal of geneXtendeR is to robustly link differentially enriched peaks with their respective genes, thereby aiding experimental follow-up and validation in designing primers for a set of prospective gene candidates during qPCR. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Optimized Functional Annotation Of ChIP-seq Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 63ab36f83aa3d05bf932dc3c0e0c173a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genextender", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:genextender + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Pt.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, rtracklayer requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-data.table - r-dplyr @@ -37,11 +48,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-data.table - r-dplyr @@ -50,21 +61,16 @@ requirements: - r-snowballc - r-tm - r-wordcloud - build: - - {{ compiler('c') }} - - make + +source: + md5: 0d04eee225b9e1593e7aa54b4bbd359b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'Optimized Functional Annotation Of ChIP-seq Data' - description: 'geneXtendeR optimizes the functional annotation of ChIP-seq peaks by exploring relative differences in annotating ChIP-seq peak sets to variable-length gene bodies. In contrast to prior techniques, geneXtendeR considers peak annotations beyond just the closest gene, allowing users to see peak summary statistics for the first-closest gene, second-closest gene, ..., n-closest gene whilst ranking the output according to biologically relevant events and iteratively comparing the fidelity of peak-to-gene overlap across a user-defined range of upstream and downstream extensions on the original boundaries of each gene''s coordinates. Since different ChIP-seq peak callers produce different differentially enriched peaks with a large variance in peak length distribution and total peak count, annotating peak lists with their nearest genes can often be a noisy process. As such, the goal of geneXtendeR is to robustly link differentially enriched peaks with their respective genes, thereby aiding experimental follow-up and validation in designing primers for a set of prospective gene candidates during qPCR.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-genie3/meta.yaml b/recipes/bioconductor-genie3/meta.yaml index bfc164119e27e..5747ab42602cd 100644 --- a/recipes/bioconductor-genie3/meta.yaml +++ b/recipes/bioconductor-genie3/meta.yaml @@ -1,25 +1,27 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "GENIE3" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fb7d197e0e34175eba7dd31608aa67d6 +about: + description: This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: GEne Network Inference with Ensemble of trees build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genie3", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods, BiocStyle requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - r-dplyr @@ -30,16 +32,14 @@ requirements: - r-base - r-dplyr - r-reshape2 - build: - - {{ compiler('c') }} - - make +source: + md5: d6b04353b7e95c5e8cc60c6b7d701922 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'GEne Network Inference with Ensemble of trees' - description: 'This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genocn/meta.yaml b/recipes/bioconductor-genocn/meta.yaml index 12d3392a05b05..cb64e13008adb 100644 --- a/recipes/bioconductor-genocn/meta.yaml +++ b/recipes/bioconductor-genocn/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.54.0" %} +{% set version = "1.58.0" %} {% set name = "genoCN" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ebc7fc5cb3b5c2bcd98718a7bcd95d6a +about: + description: Simultaneous identification of copy number states and genotype calls for regions of either copy number variations or copy number aberrations + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: genotyping and copy number study tools build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genocn", max_pin="x.x") }}' +extra: + additional-platforms: + - linux-aarch64 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - make +source: + md5: f1d64e3799c3378276c6921f175ec367 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'genotyping and copy number study tools' - description: 'Simultaneous identification of copy number states and genotype calls for regions of either copy number variations or copy number aberrations' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 diff --git a/recipes/bioconductor-genomation/meta.yaml b/recipes/bioconductor-genomation/meta.yaml index 9f025c887b497..158411d3362f9 100644 --- a/recipes/bioconductor-genomation/meta.yaml +++ b/recipes/bioconductor-genomation/meta.yaml @@ -1,37 +1,54 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "genomation" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Summary, annotation and visualization of genomic data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5453f50009f3f7227025431d4d10f4bb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomation", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:genomation + parent_recipe: + name: bioconductor-genomation + path: recipes/bioconductor-genomation + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown, RUnit requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-seqpattern >=1.34.0,<1.35.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqpattern >=1.38.0,<1.39.0 - r-base - r-data.table - r-ggplot2 @@ -39,23 +56,24 @@ requirements: - r-matrixstats - r-plotrix - r-plyr - - 'r-rcpp >=0.12.14' + - r-rcpp >=0.12.14 - r-readr - r-reshape2 - libblas - liblapack + run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-seqpattern >=1.34.0,<1.35.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqpattern >=1.38.0,<1.39.0 - r-base - r-data.table - r-ggplot2 @@ -63,28 +81,19 @@ requirements: - r-matrixstats - r-plotrix - r-plyr - - 'r-rcpp >=0.12.14' + - r-rcpp >=0.12.14 - r-readr - r-reshape2 - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 42c83bf663d193ae51b9baaabc45f648 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Summary, annotation and visualization of genomic data' - description: 'A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:genomation - parent_recipe: - name: bioconductor-genomation - path: recipes/bioconductor-genomation - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genomationdata/meta.yaml b/recipes/bioconductor-genomationdata/meta.yaml index 8cb6a2198f75f..c9bb088b01478 100644 --- a/recipes/bioconductor-genomationdata/meta.yaml +++ b/recipes/bioconductor-genomationdata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "genomationData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dc03eef7730719f7c66f72ca5e9915db +about: + description: The package contains Chip Seq, Methylation and Cage data, downloaded from Encode + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Experimental data for showing functionalities of the genomation package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomationdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c5c850508ccd391d1a16689bcbab0879 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Experimental data for showing functionalities of the genomation package' - description: 'The package contains Chip Seq, Methylation and Cage data, downloaded from Encode' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genomationdata/post-link.sh b/recipes/bioconductor-genomationdata/post-link.sh index e092bd607d41b..4497a548f8be5 100644 --- a/recipes/bioconductor-genomationdata/post-link.sh +++ b/recipes/bioconductor-genomationdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "genomationdata-1.34.0" +installBiocDataPackage.sh "genomationdata-1.38.0" diff --git a/recipes/bioconductor-genomautomorphism/meta.yaml b/recipes/bioconductor-genomautomorphism/meta.yaml index e16df4a231b76..b053ca6b6f7b4 100644 --- a/recipes/bioconductor-genomautomorphism/meta.yaml +++ b/recipes/bioconductor-genomautomorphism/meta.yaml @@ -1,60 +1,69 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "GenomAutomorphism" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This is a R package to compute the automorphisms between pairwise aligned DNA sequences represented as elements from a Genomic Abelian group. In a general scenario, from genomic regions till the whole genomes from a given population (from any species or close related species) can be algebraically represented as a direct sum of cyclic groups or more specifically Abelian p-groups. Basically, we propose the representation of multiple sequence alignments of length N bp as element of a finite Abelian group created by the direct sum of homocyclic Abelian group of prime-power order. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Compute the automorphisms between DNA's Abelian group representations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 36ebcd90b454dc7450e875730537811b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomautomorphism", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-data.table - r-doparallel - r-dplyr - r-foreach + - r-matrixstats - r-numbers run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-data.table - r-doparallel - r-dplyr - r-foreach + - r-matrixstats - r-numbers + +source: + md5: cb2c2c82d65e36c8f2a95afd46b8dc03 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Compute the automorphisms between DNA''s Abelian group representations' - description: 'This is a R package to compute the automorphisms between pairwise aligned DNA sequences represented as elements from a Genomic Abelian group. In a general scenario, from genomic regions till the whole genomes from a given population (from any species or close related species) can be algebraically represented as a direct sum of cyclic groups or more specifically Abelian p-groups. Basically, we propose the representation of multiple sequence alignments of length N bp as element of a finite Abelian group created by the direct sum of homocyclic Abelian group of prime-power order.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genomeinfodb/meta.yaml b/recipes/bioconductor-genomeinfodb/meta.yaml index e033652eb641c..3efdcfabb7426 100644 --- a/recipes/bioconductor-genomeinfodb/meta.yaml +++ b/recipes/bioconductor-genomeinfodb/meta.yaml @@ -1,48 +1,21 @@ -{% set version = "1.38.1" %} +{% set version = "1.42.0" %} {% set name = "GenomeInfoDb" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Utilities for manipulating chromosome names, including modifying them to follow a particular naming style -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4bb1aef4ea2a6422141e3024e11b85e1 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomeinfodb", max_pin="x.x") }}' - noarch: generic -# Suggests: GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr -requirements: - host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - r-base - - r-rcurl - run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - r-base - - r-rcurl -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Utilities for manipulating chromosome names, including modifying them to follow a particular naming style' - description: 'Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.' + extra: identifiers: - biotools:genomeinfodb @@ -52,3 +25,36 @@ extra: path: recipes/bioconductor-genomeinfodb version: 1.16.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: R.utils, data.table, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodbdata >=1.2.0,<1.3.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-ucsc.utils >=1.2.0,<1.3.0 + - r-base + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodbdata >=1.2.0,<1.3.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-ucsc.utils >=1.2.0,<1.3.0 + - r-base + +source: + md5: 1ef0130131721e4679be168f42e1736e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-genomeinfodbdata/meta.yaml b/recipes/bioconductor-genomeinfodbdata/meta.yaml index f4d61f874b1f7..5aa4042c02c18 100644 --- a/recipes/bioconductor-genomeinfodbdata/meta.yaml +++ b/recipes/bioconductor-genomeinfodbdata/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.2.11" %} +{% set version = "1.2.13" %} {% set name = "GenomeInfoDbData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2a4cbfc2031992fed3c9445f450890a2 +about: + description: Files for mapping between NCBI taxonomy ID and species. Used by functions in the GenomeInfoDb package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Species and taxonomy ID look up tables used by GenomeInfoDb build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomeinfodbdata", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-genomeinfodbdata + path: recipes/bioconductor-genomeinfodbdata + version: 1.1.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8798e58b89d84d9fa6a85f2191704668 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Species and taxonomy ID look up tables used by GenomeInfoDb' - description: 'Files for mapping between NCBI taxonomy ID and species. Used by functions in the GenomeInfoDb package.' -extra: - parent_recipe: - name: bioconductor-genomeinfodbdata - path: recipes/bioconductor-genomeinfodbdata - version: 1.1.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genomeinfodbdata/post-link.sh b/recipes/bioconductor-genomeinfodbdata/post-link.sh index 42b37c9d4d1ca..cdeacb7f2ab69 100644 --- a/recipes/bioconductor-genomeinfodbdata/post-link.sh +++ b/recipes/bioconductor-genomeinfodbdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "genomeinfodbdata-1.2.11" +installBiocDataPackage.sh "genomeinfodbdata-1.2.13" diff --git a/recipes/bioconductor-genomeintervals/meta.yaml b/recipes/bioconductor-genomeintervals/meta.yaml index a0b7c1292199a..751132e21cfde 100644 --- a/recipes/bioconductor-genomeintervals/meta.yaml +++ b/recipes/bioconductor-genomeintervals/meta.yaml @@ -1,49 +1,21 @@ -{% set version = "1.58.0" %} +{% set version = "1.62.0" %} {% set name = "genomeIntervals" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'This package defines classes for representing genomic intervals and provides functions and methods for working with these. Note: The package provides the basic infrastructure for and is enhanced by the package ''girafe''.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Operations on genomic intervals -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c47b9bb1293b799a7ac75fef82f45589 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomeintervals", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - r-base - - 'r-intervals >=0.14.0' - run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - r-base - - 'r-intervals >=0.14.0' -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Operations on genomic intervals' - description: 'This package defines classes for representing genomic intervals and provides functions and methods for working with these. Note: The package provides the basic infrastructure for and is enhanced by the package ''girafe''.' + extra: identifiers: - biotools:genomeintervals @@ -53,3 +25,37 @@ extra: path: recipes/bioconductor-genomeintervals version: 1.36.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-intervals >=0.14.0 + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-intervals >=0.14.0 + +source: + md5: 0978b8fa7f7194aec99680f891662758 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-genomes/meta.yaml b/recipes/bioconductor-genomes/meta.yaml index 580bd6df948d1..f59e71a0d6f6d 100644 --- a/recipes/bioconductor-genomes/meta.yaml +++ b/recipes/bioconductor-genomes/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "3.32.0" %} +{% set version = "3.36.0" %} {% set name = "genomes" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4c11ca2b7b1d4dfd1ffc178b1d9e87e2 +about: + description: Download genome and assembly reports from NCBI + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Genome sequencing project metadata build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomes", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base @@ -28,13 +27,14 @@ requirements: - r-base - r-curl - r-readr +source: + md5: 8e7e01f2b21493fe25d60b78a8a3c051 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Genome sequencing project metadata' - description: 'Download genome and assembly reports from NCBI' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genomewidesnp5crlmm/meta.yaml b/recipes/bioconductor-genomewidesnp5crlmm/meta.yaml index 5c85ea0ef7f2e..f260da58dee28 100644 --- a/recipes/bioconductor-genomewidesnp5crlmm/meta.yaml +++ b/recipes/bioconductor-genomewidesnp5crlmm/meta.yaml @@ -1,37 +1,37 @@ {% set version = "1.0.6" %} {% set name = "genomewidesnp5Crlmm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cc24140cd17758b8e09f4fe6c931526a +about: + description: Package with metadata for fast genotyping Affymetrix GenomeWideSnp_5 arrays using the 'crlmm' package. Annotation build is hg19. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Metadata for fast genotyping with the 'crlmm' package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomewidesnp5crlmm", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: cc24140cd17758b8e09f4fe6c931526a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Metadata for fast genotyping with the ''crlmm'' package' - description: 'Package with metadata for fast genotyping Affymetrix GenomeWideSnp_5 arrays using the ''crlmm'' package. Annotation build is hg19.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genomewidesnp6crlmm/meta.yaml b/recipes/bioconductor-genomewidesnp6crlmm/meta.yaml index 097994bdee0b6..446b43f33e48c 100644 --- a/recipes/bioconductor-genomewidesnp6crlmm/meta.yaml +++ b/recipes/bioconductor-genomewidesnp6crlmm/meta.yaml @@ -1,37 +1,37 @@ {% set version = "1.0.7" %} {% set name = "genomewidesnp6Crlmm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 13dd5aef3d814524896f2f3013beb78b +about: + description: Package with metadata for fast genotyping Affymetrix GenomeWideSnp_6 arrays using the 'crlmm' package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Metadata for fast genotyping with the 'crlmm' package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomewidesnp6crlmm", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 13dd5aef3d814524896f2f3013beb78b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Metadata for fast genotyping with the ''crlmm'' package' - description: 'Package with metadata for fast genotyping Affymetrix GenomeWideSnp_6 arrays using the ''crlmm'' package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genomicalignments/meta.yaml b/recipes/bioconductor-genomicalignments/meta.yaml index a8dc964e444f8..198d914255b38 100644 --- a/recipes/bioconductor-genomicalignments/meta.yaml +++ b/recipes/bioconductor-genomicalignments/meta.yaml @@ -1,60 +1,20 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "GenomicAlignments" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Representation and manipulation of short genomic alignments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a5b7669b8ef7444527c2e43c49840014 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomicalignments", max_pin="x.x") }}' -# Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, BiocStyle -requirements: - host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - r-base - - libblas - - liblapack - run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - r-base - build: - - {{ compiler('c') }} - - make -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Representation and manipulation of short genomic alignments' - description: 'Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.' + extra: additional-platforms: - linux-aarch64 @@ -65,3 +25,49 @@ extra: path: recipes/bioconductor-genomicalignments version: 1.18.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, knitr, BiocStyle +requirements: + build: + - {{ compiler('c') }} + - make + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - libblas + - liblapack + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + +source: + md5: 70693f9d949390658a171ad2139860c8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-genomicdatacommons/meta.yaml b/recipes/bioconductor-genomicdatacommons/meta.yaml index fd0e442c7e4ad..11f77ba45dbc2 100644 --- a/recipes/bioconductor-genomicdatacommons/meta.yaml +++ b/recipes/bioconductor-genomicdatacommons/meta.yaml @@ -1,34 +1,40 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "GenomicDataCommons" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Programmatically access the NIH / NCI Genomic Data Commons RESTful service. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: NIH / NCI Genomic Data Commons Access -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6c945795f62ce3e0b470b07b892d3357 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomicdatacommons", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-genomicdatacommons + path: recipes/bioconductor-genomicdatacommons + version: 1.4.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools, BiocParallel, TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation, maftools, R.utils, data.table requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-dplyr - r-httr - r-jsonlite - - r-magrittr - r-rappdirs - r-readr - r-rlang @@ -36,30 +42,28 @@ requirements: - r-tidyr - r-xml2 run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-dplyr - r-httr - r-jsonlite - - r-magrittr - r-rappdirs - r-readr - r-rlang - r-tibble - r-tidyr - r-xml2 + +source: + md5: 94e0717882cfec78f9f0479a47886b59 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'NIH / NCI Genomic Data Commons Access' - description: 'Programmatically access the NIH / NCI Genomic Data Commons RESTful service.' -extra: - parent_recipe: - name: bioconductor-genomicdatacommons - path: recipes/bioconductor-genomicdatacommons - version: 1.4.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genomicdistributions/meta.yaml b/recipes/bioconductor-genomicdistributions/meta.yaml index fb182b1896bd6..07edfb906c7f1 100644 --- a/recipes/bioconductor-genomicdistributions/meta.yaml +++ b/recipes/bioconductor-genomicdistributions/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "GenomicDistributions" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'If you have a set of genomic ranges, this package can help you with visualization and comparison. It produces several kinds of plots, for example: Chromosome distribution plots, which visualize how your regions are distributed over chromosomes; feature distance distribution plots, which visualizes how your regions are distributed relative to a feature of interest, like Transcription Start Sites (TSSs); genomic partition plots, which visualize how your regions overlap given genomic features such as promoters, introns, exons, or intergenic regions. It also makes it easy to compare one set of ranges to another.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_2_clause + file LICENSE + license_file: LICENSE + summary: 'GenomicDistributions: fast analysis of genomic intervals with Bioconductor' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0b8c2d9df85f9884bb40e3fcd015c824 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomicdistributions", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle, rmarkdown, GenomicDistributionsData requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-broom - r-data.table @@ -35,10 +37,10 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-broom - r-data.table @@ -47,13 +49,16 @@ requirements: - r-plyr - r-reshape2 - r-scales + +source: + md5: 81bc808ceb76e2e9bd841a5de5f454f0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_2_clause + file LICENSE' - summary: 'GenomicDistributions: fast analysis of genomic intervals with Bioconductor' - description: 'If you have a set of genomic ranges, this package can help you with visualization and comparison. It produces several kinds of plots, for example: Chromosome distribution plots, which visualize how your regions are distributed over chromosomes; feature distance distribution plots, which visualizes how your regions are distributed relative to a feature of interest, like Transcription Start Sites (TSSs); genomic partition plots, which visualize how your regions overlap given genomic features such as promoters, introns, exons, or intergenic regions. It also makes it easy to compare one set of ranges to another.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genomicdistributionsdata/meta.yaml b/recipes/bioconductor-genomicdistributionsdata/meta.yaml index 2cb349acc7580..b6ababd33188d 100644 --- a/recipes/bioconductor-genomicdistributionsdata/meta.yaml +++ b/recipes/bioconductor-genomicdistributionsdata/meta.yaml @@ -1,57 +1,62 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "GenomicDistributionsData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'This package provides ready to use reference data for GenomicDistributions package. Raw data was obtained from ensembldb and processed with helper functions. Data files are available for the following genome assemblies: hg19, hg38, mm9 and mm10.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: BSD_2_clause + file LICENSE + license_file: LICENSE + summary: Reference data for GenomicDistributions package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84067e85ccbf3605bc1f5a1b7d8508ad build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomicdistributionsdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-data.table run: - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-data.table - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 76d8227fa4c313fdc471bb14415d8962 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'BSD_2_clause + file LICENSE' - summary: 'Reference data for GenomicDistributions package' - description: 'This package provides ready to use reference data for GenomicDistributions package. Raw data was obtained from ensembldb and processed with helper functions. Data files are available for the following genome assemblies: hg19, hg38, mm9 and mm10.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genomicdistributionsdata/post-link.sh b/recipes/bioconductor-genomicdistributionsdata/post-link.sh index 08f6cdb719a09..9891292c1bc87 100644 --- a/recipes/bioconductor-genomicdistributionsdata/post-link.sh +++ b/recipes/bioconductor-genomicdistributionsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "genomicdistributionsdata-1.10.0" +installBiocDataPackage.sh "genomicdistributionsdata-1.14.0" diff --git a/recipes/bioconductor-genomicfeatures/meta.yaml b/recipes/bioconductor-genomicfeatures/meta.yaml index 705fb92048fa5..3672dbe2efb92 100644 --- a/recipes/bioconductor-genomicfeatures/meta.yaml +++ b/recipes/bioconductor-genomicfeatures/meta.yaml @@ -1,73 +1,69 @@ -{% set version = "1.54.1" %} +{% set version = "1.58.0" %} {% set name = "GenomicFeatures" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a small collection of TxDb objects in the form of ready-to-install TxDb packages for the most commonly studied organisms. Additionally, the user can easily make a TxDb object (or package) for the organism/assembly of their choice by using the tools from the txdbmaker package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Query the gene models of a given organism/assembly -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 863085394fd911039eca1603e6393c1d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomicfeatures", max_pin="x.x") }}' - noarch: generic -# Suggests: RMariaDB, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, AnnotationFilter, RUnit, BiocStyle, knitr, markdown + +extra: + identifiers: + - biotools:genomicfeatures + parent_recipe: + name: bioconductor-genomicfeatures + path: recipes/bioconductor-genomicfeatures + version: 1.32.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: txdbmaker, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, AnnotationFilter, RUnit, BiocStyle, knitr, markdown requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-dbi - - r-rcurl - - 'r-rsqlite >=2.0' run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-dbi - - r-rcurl - - 'r-rsqlite >=2.0' + +source: + md5: 0a02cd9968d3de134153953d7320c44a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Conveniently import and query gene models' - description: 'A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.' -extra: - identifiers: - - biotools:genomicfeatures - parent_recipe: - name: bioconductor-genomicfeatures - path: recipes/bioconductor-genomicfeatures - version: 1.32.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genomicfiles/meta.yaml b/recipes/bioconductor-genomicfiles/meta.yaml index bb74043dc99a0..1c8da2cd715ce 100644 --- a/recipes/bioconductor-genomicfiles/meta.yaml +++ b/recipes/bioconductor-genomicfiles/meta.yaml @@ -1,62 +1,21 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "GenomicFiles" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides infrastructure for parallel computations distributed 'by file' or 'by range'. User defined MAPPER and REDUCER functions provide added flexibility for data combination and manipulation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Distributed computing by file or by range -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a58dc35c19ed34afe95d505d15db3f4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomicfiles", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, RUnit, genefilter, deepSNV, snpStats, knitr, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens -requirements: - host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - - r-base - run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Distributed computing by file or by range' - description: 'This package provides infrastructure for parallel computations distributed ''by file'' or ''by range''. User defined MAPPER and REDUCER functions provide added flexibility for data combination and manipulation.' + extra: identifiers: - biotools:genomicfiles @@ -66,3 +25,50 @@ extra: path: recipes/bioconductor-genomicfiles version: 1.16.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, RUnit, genefilter, deepSNV, snpStats, knitr, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - r-base + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - r-base + +source: + md5: c70e78283b0a1f90ddd4cbcddf71d7df + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-genomicinstability/meta.yaml b/recipes/bioconductor-genomicinstability/meta.yaml index 01dd64732ea05..cb8525d67e302 100644 --- a/recipes/bioconductor-genomicinstability/meta.yaml +++ b/recipes/bioconductor-genomicinstability/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "genomicInstability" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0d7c244a904ea9286d4e965cddeaf2d7 +about: + description: This package contain functions to run genomic instability analysis (GIA) from scRNA-Seq data. GIA estimates the association between gene expression and genomic location of the coding genes. It uses the aREA algorithm to quantify the enrichment of sets of contiguous genes (loci-blocks) on the gene expression profiles and estimates the Genomic Instability Score (GIS) for each analyzed cell. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Genomic Instability estimation for scRNA-Seq build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomicinstability", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: SingleCellExperiment, ExperimentHub, pROC requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-checkmate - r-mixtools run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-checkmate - r-mixtools +source: + md5: 6393fc6f34d3774e5be91fd04fe04b57 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Genomic Instability estimation for scRNA-Seq' - description: 'This package contain functions to run genomic instability analysis (GIA) from scRNA-Seq data. GIA estimates the association between gene expression and genomic location of the coding genes. It uses the aREA algorithm to quantify the enrichment of sets of contiguous genes (loci-blocks) on the gene expression profiles and estimates the Genomic Instability Score (GIS) for each analyzed cell.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genomicinteractionnodes/meta.yaml b/recipes/bioconductor-genomicinteractionnodes/meta.yaml index 322240c8d1118..275fac32b4b09 100644 --- a/recipes/bioconductor-genomicinteractionnodes/meta.yaml +++ b/recipes/bioconductor-genomicinteractionnodes/meta.yaml @@ -1,55 +1,60 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "GenomicInteractionNodes" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The GenomicInteractionNodes package can import interactions from bedpe file and define the interaction nodes, the genomic interaction sites with multiple interaction loops. The interaction nodes is a binding platform regulates one or multiple genes. The detected interaction nodes will be annotated for downstream validation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bacb75bdd25ea06d5102c1ef2648c588 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomicinteractionnodes", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base + +source: + md5: 5d250124934c9785b2c9b3c53727330f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data' - description: 'The GenomicInteractionNodes package can import interactions from bedpe file and define the interaction nodes, the genomic interaction sites with multiple interaction loops. The interaction nodes is a binding platform regulates one or multiple genes. The detected interaction nodes will be annotated for downstream validation.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genomicinteractions/meta.yaml b/recipes/bioconductor-genomicinteractions/meta.yaml index 64e03a3fa483f..66ae2807eb754 100644 --- a/recipes/bioconductor-genomicinteractions/meta.yaml +++ b/recipes/bioconductor-genomicinteractions/meta.yaml @@ -1,37 +1,48 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "GenomicInteractions" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Utilities for handling genomic interaction data such as ChIA-PET or Hi-C, annotating genomic features with interaction information, and producing plots and summary statistics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Utilities for handling genomic interaction data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4bccdd21d639ba8b9907ced202c0082 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomicinteractions", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:genomicinteractions + - doi:10.1186/s12864-015-2140-x + parent_recipe: + name: bioconductor-genomicinteractions + path: recipes/bioconductor-genomicinteractions + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-dplyr @@ -40,16 +51,16 @@ requirements: - r-igraph - r-stringr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-dplyr @@ -57,21 +68,16 @@ requirements: - r-gridextra - r-igraph - r-stringr + +source: + md5: 371e9bf3be8b30da67681dccba28c670 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Utilities for handling genomic interaction data' - description: 'Utilities for handling genomic interaction data such as ChIA-PET or Hi-C, annotating genomic features with interaction information, and producing plots and summary statistics.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:genomicinteractions - - doi:10.1186/s12864-015-2140-x - parent_recipe: - name: bioconductor-genomicinteractions - path: recipes/bioconductor-genomicinteractions - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genomicozone/meta.yaml b/recipes/bioconductor-genomicozone/meta.yaml index 6c9364066561c..d38eefdfe8dbd 100644 --- a/recipes/bioconductor-genomicozone/meta.yaml +++ b/recipes/bioconductor-genomicozone/meta.yaml @@ -1,61 +1,66 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "GenomicOZone" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package clusters gene activity along chromosome into zones, detects differential zones as outstanding, and visualizes maps of outstanding zones across the genome. It enables characterization of effects on multiple genes within adaptive genomic neighborhoods, which could arise from genome reorganization, structural variation, or epigenome alteration. It guarantees cluster optimality, linear runtime to sample size, and reproducibility. One can apply it on genome-wide activity measurements such as copy number, transcriptomic, proteomic, and methylation data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>=3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Delineate outstanding genomic zones of differential gene activity -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c975a4b1c29d471efe90a5bba68247bb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomicozone", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: readxl, GEOquery, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-ckmeans.1d.dp >=4.3.0' + - r-ckmeans.1d.dp >=4.3.0 - r-ggplot2 - r-gridextra - r-lsr - r-plyr - r-rdpack run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-ckmeans.1d.dp >=4.3.0' + - r-ckmeans.1d.dp >=4.3.0 - r-ggplot2 - r-gridextra - r-lsr - r-plyr - r-rdpack + +source: + md5: 463dff2c8d2d97d3df176d57b2a5a377 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>=3)' - summary: 'Delineate outstanding genomic zones of differential gene activity' - description: 'The package clusters gene activity along chromosome into zones, detects differential zones as outstanding, and visualizes maps of outstanding zones across the genome. It enables characterization of effects on multiple genes within adaptive genomic neighborhoods, which could arise from genome reorganization, structural variation, or epigenome alteration. It guarantees cluster optimality, linear runtime to sample size, and reproducibility. One can apply it on genome-wide activity measurements such as copy number, transcriptomic, proteomic, and methylation data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genomicplot/meta.yaml b/recipes/bioconductor-genomicplot/meta.yaml index de408ccbe32ff..a34de767a058f 100644 --- a/recipes/bioconductor-genomicplot/meta.yaml +++ b/recipes/bioconductor-genomicplot/meta.yaml @@ -1,87 +1,96 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "GenomicPlot" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Visualization of next generation sequencing (NGS) data is essential for interpreting high-throughput genomics experiment results. 'GenomicPlot' facilitates plotting of NGS data in various formats (bam, bed, wig and bigwig); both coverage and enrichment over input can be computed and displayed with respect to genomic features (such as UTR, CDS, enhancer), and user defined genomic loci or regions. Statistical tests on signal intensity within user defined regions of interest can be performed and represented as boxplots or bar graphs. Parallel processing is used to speed up computation on multicore platforms. In addition to genomic plots which is suitable for displaying of coverage of genomic DNA (such as ChIPseq data), metagenomic (without introns) plots can also be made for RNAseq or CLIPseq data as well. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Plot profiles of next generation sequencing data in genomic features -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ff0cee9d866f4cea69ee355bdac1f574 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomicplot", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, AnnotationHub, AnnotationDbi, R.utils, Biobase, BSgenome.Hsapiens.UCSC.hg19, BiocFileCache, TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), BiocStyle, testthat + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, R.utils, Biobase, BiocStyle, testthat, AnnotationDbi requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomation >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-rcas >=1.28.0,<1.29.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomation >=1.38.0,<1.39.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-rcas >=1.32.0,<1.33.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-circlize - - 'r-cowplot >=1.1.1' + - r-cowplot >=1.1.1 - r-dplyr - - 'r-ggplot2 >=3.3.5' + - r-ggplot2 >=3.3.5 - r-ggplotify - r-ggpubr - - 'r-ggsci >=2.9' - - 'r-ggsignif >=0.6.3' - - 'r-scales >=1.2.0' + - r-ggsci >=2.9 + - r-ggsignif >=0.6.3 + - r-scales >=1.2.0 - r-tidyr - r-venndiagram - r-viridis + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomation >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-rcas >=1.28.0,<1.29.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomation >=1.38.0,<1.39.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-rcas >=1.32.0,<1.33.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-circlize - - 'r-cowplot >=1.1.1' + - r-cowplot >=1.1.1 - r-dplyr - - 'r-ggplot2 >=3.3.5' + - r-ggplot2 >=3.3.5 - r-ggplotify - r-ggpubr - - 'r-ggsci >=2.9' - - 'r-ggsignif >=0.6.3' - - 'r-scales >=1.2.0' + - r-ggsci >=2.9 + - r-ggsignif >=0.6.3 + - r-scales >=1.2.0 - r-tidyr - r-venndiagram - r-viridis + +source: + md5: 6427ba00460ed3545974ecbfdf27fc41 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Plot profiles of next generation sequencing data in genomic features' - description: 'Visualization of next generation sequencing (NGS) data is essential for interpreting high-throughput genomics experiment results. ''GenomicPlot'' facilitates plotting of NGS data in various formats (bam, bed, wig and bigwig); both coverage and enrichment over input can be computed and displayed with respect to genomic features (such as UTR, CDS, enhancer), and user defined genomic loci or regions. Statistical tests on signal intensity within user defined regions of interest can be performed and represented as boxplots or bar graphs. Parallel processing is used to speed up computation on multicore platforms. In addition to genomic plots which is suitable for displaying of coverage of genomic DNA (such as ChIPseq data), metagenomic (without introns) plots can also be made for RNAseq or CLIPseq data as well.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genomicranges/meta.yaml b/recipes/bioconductor-genomicranges/meta.yaml index c097a42a81db0..9e8b8779a32f3 100644 --- a/recipes/bioconductor-genomicranges/meta.yaml +++ b/recipes/bioconductor-genomicranges/meta.yaml @@ -1,52 +1,20 @@ -{% set version = "1.54.1" %} +{% set version = "1.58.0" %} {% set name = "GenomicRanges" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Representation and manipulation of genomic intervals -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 19fe37133cae70c1c3a1a164e6c8eaed build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomicranges", max_pin="x.x") }}' -# Suggests: Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle -requirements: - host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' - - r-base - - libblas - - liblapack - run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' - - r-base - build: - - {{ compiler('c') }} - - make -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Representation and manipulation of genomic intervals' - description: 'The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.' + extra: additional-platforms: - linux-aarch64 @@ -57,3 +25,41 @@ extra: path: recipes/bioconductor-genomicranges version: 1.32.7 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, txdbmaker, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle +requirements: + build: + - {{ compiler('c') }} + - make + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 + - r-base + - libblas + - liblapack + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 + - r-base + +source: + md5: cca337e05cca2a77511c410397e8d415 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-genomicscores/meta.yaml b/recipes/bioconductor-genomicscores/meta.yaml index 905f77be5004e..260b64b592638 100644 --- a/recipes/bioconductor-genomicscores/meta.yaml +++ b/recipes/bioconductor-genomicscores/meta.yaml @@ -1,71 +1,77 @@ -{% set version = "2.14.1" %} +{% set version = "2.18.0" %} {% set name = "GenomicScores" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Infrastructure to work with genomewide position-specific scores -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f3be6b84303478d0d061081b2dcf261 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomicscores", max_pin="x.x") }}' - noarch: generic -# Suggests: RUnit, BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, phastCons100way.UCSC.hg19, MafDb.1Kgenomes.phase1.hs37d5, SNPlocs.Hsapiens.dbSNP144.GRCh37, VariantAnnotation, TxDb.Hsapiens.UCSC.hg19.knownGene, gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader, data.table, DT, magrittr, shinydashboard + +extra: + parent_recipe: + name: bioconductor-genomicscores + path: recipes/bioconductor-genomicscores + version: 1.4.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RUnit, BiocStyle, knitr, rmarkdown, VariantAnnotation, gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader, data.table, DT, magrittr, shinydashboard, BSgenome.Hsapiens.UCSC.hg38, phastCons100way.UCSC.hg38, MafDb.1Kgenomes.phase1.hs37d5, MafH5.gnomAD.v4.0.GRCh38, SNPlocs.Hsapiens.dbSNP144.GRCh37, TxDb.Hsapiens.UCSC.hg38.knownGene requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-biocmanager - r-httr - r-xml run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-biocmanager - r-httr - r-xml + +source: + md5: 9ca3e21913a73d4e1cacfff4e0e72fb8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Infrastructure to work with genomewide position-specific scores' - description: 'Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.' -extra: - parent_recipe: - name: bioconductor-genomicscores - path: recipes/bioconductor-genomicscores - version: 1.4.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genomicstate/meta.yaml b/recipes/bioconductor-genomicstate/meta.yaml index 641f4618a5d8d..64689a499af2b 100644 --- a/recipes/bioconductor-genomicstate/meta.yaml +++ b/recipes/bioconductor-genomicstate/meta.yaml @@ -1,56 +1,61 @@ {% set version = "0.99.15" %} {% set name = "GenomicState" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains functions for building GenomicState objects from different annotation sources such as Gencode. It also provides access to these files at JHPCE. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Build and access GenomicState objects for use with derfinder tools from sources like Gencode -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 59c2d85a72f62cb12bad697fcbce5edc build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomicstate", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, sessioninfo, testthat (>= 2.1.0), glue, derfinderPlot, AnnotationHubData, RefManageR, GenomicRanges, covr requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-derfinder >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-derfinder >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-derfinder >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-derfinder >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 59c2d85a72f62cb12bad697fcbce5edc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Build and access GenomicState objects for use with derfinder tools from sources like Gencode' - description: 'This package contains functions for building GenomicState objects from different annotation sources such as Gencode. It also provides access to these files at JHPCE.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genomicsupersignature/meta.yaml b/recipes/bioconductor-genomicsupersignature/meta.yaml index 231b42a102ceb..3db4ba54b87c1 100644 --- a/recipes/bioconductor-genomicsupersignature/meta.yaml +++ b/recipes/bioconductor-genomicsupersignature/meta.yaml @@ -1,32 +1,33 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "GenomicSuperSignature" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a novel method for interpreting new transcriptomic datasets through near-instantaneous comparison to public archives without high-performance computing requirements. Through the pre-computed index, users can identify public resources associated with their dataset such as gene sets, MeSH term, and publication. Functions to identify interpretable annotations and intuitive visualization options are implemented in this package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Interpretation of RNA-seq experiments through robust, efficient comparison to public databases -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ecb55ebec91620ff435715563d8ba304 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomicsupersignature", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis, BiocStyle, testthat, forcats, stats, wordcloud, circlize, EnrichmentBrowser, clusterProfiler, msigdbr, cluster, RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr, utils requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-flextable @@ -35,11 +36,11 @@ requirements: - r-irlba - r-plotly run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-flextable @@ -47,12 +48,16 @@ requirements: - r-ggpubr - r-irlba - r-plotly + +source: + md5: efa8078ab97b7a012aeed34e7e966e9e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Interpretation of RNA-seq experiments through robust, efficient comparison to public databases' - description: 'This package provides a novel method for interpreting new transcriptomic datasets through near-instantaneous comparison to public archives without high-performance computing requirements. Through the pre-computed index, users can identify public resources associated with their dataset such as gene sets, MeSH term, and publication. Functions to identify interpretable annotations and intuitive visualization options are implemented in this package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genomictuples/meta.yaml b/recipes/bioconductor-genomictuples/meta.yaml index f664c665aa978..a15f379b46826 100644 --- a/recipes/bioconductor-genomictuples/meta.yaml +++ b/recipes/bioconductor-genomictuples/meta.yaml @@ -1,63 +1,69 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "GenomicTuples" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges Bioconductor package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Representation and Manipulation of Genomic Tuples -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 69e0c80982690604f35d9878f6640f37 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genomictuples", max_pin="x.x") }}' -# Suggests: testthat, knitr, BiocStyle, rmarkdown, covr + +extra: + identifiers: + - biotools:genomictuples + - doi:10.21105/joss.00020 + parent_recipe: + name: bioconductor-genomictuples + path: recipes/bioconductor-genomictuples + version: 1.14.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, knitr, BiocStyle, rmarkdown, covr, GenomicAlignments, Biostrings requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - - 'r-rcpp >=0.11.2' + - r-rcpp >=0.11.2 - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - - 'r-rcpp >=0.11.2' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=0.11.2 + +source: + md5: 5169bf3e778f72a79c992445d8555b0c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Representation and Manipulation of Genomic Tuples' - description: 'GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges Bioconductor package.' -extra: - identifiers: - - biotools:genomictuples - - doi:10.21105/joss.00020 - parent_recipe: - name: bioconductor-genomictuples - path: recipes/bioconductor-genomictuples - version: 1.14.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genproseq/meta.yaml b/recipes/bioconductor-genproseq/meta.yaml index 0145607611a75..fb0ad372e5293 100644 --- a/recipes/bioconductor-genproseq/meta.yaml +++ b/recipes/bioconductor-genproseq/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "GenProSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Generative modeling for protein engineering is key to solving fundamental problems in synthetic biology, medicine, and material science. Machine learning has enabled us to generate useful protein sequences on a variety of scales. Generative models are machine learning methods which seek to model the distribution underlying the data, allowing for the generation of novel samples with similar properties to those on which the model was trained. Generative models of proteins can learn biologically meaningful representations helpful for a variety of downstream tasks. Furthermore, they can learn to generate protein sequences that have not been observed before and to assign higher probability to protein sequences that satisfy desired criteria. In this package, common deep generative models for protein sequences, such as variational autoencoder (VAE), generative adversarial networks (GAN), and autoregressive models are available. In the VAE and GAN, the Word2vec is used for embedding. The transformer encoder is applied to protein sequences for the autoregressive model. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Generating Protein Sequences with Deep Generative Models -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 15e772912f2019256df52d192edd5402 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genproseq", max_pin="x.x") }}' - noarch: generic -# Suggests: ggseqlogo, VAExprs, stringdist, knitr, testthat, rmarkdown + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: VAExprs, stringdist, knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-deeppincs >=1.10.0,<1.11.0' - - 'bioconductor-ttgsea >=1.10.0,<1.11.0' + - bioconductor-deeppincs >=1.14.0,<1.15.0 + - bioconductor-ttgsea >=1.14.0,<1.15.0 - r-base - r-catencoders - r-keras @@ -32,8 +33,8 @@ requirements: - r-tensorflow - r-word2vec run: - - 'bioconductor-deeppincs >=1.10.0,<1.11.0' - - 'bioconductor-ttgsea >=1.10.0,<1.11.0' + - bioconductor-deeppincs >=1.14.0,<1.15.0 + - bioconductor-ttgsea >=1.14.0,<1.15.0 - r-base - r-catencoders - r-keras @@ -41,12 +42,16 @@ requirements: - r-reticulate - r-tensorflow - r-word2vec + +source: + md5: a32d030b971c3014f578dd24c9ca4858 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Generating Protein Sequences with Deep Generative Models' - description: 'Generative modeling for protein engineering is key to solving fundamental problems in synthetic biology, medicine, and material science. Machine learning has enabled us to generate useful protein sequences on a variety of scales. Generative models are machine learning methods which seek to model the distribution underlying the data, allowing for the generation of novel samples with similar properties to those on which the model was trained. Generative models of proteins can learn biologically meaningful representations helpful for a variety of downstream tasks. Furthermore, they can learn to generate protein sequences that have not been observed before and to assign higher probability to protein sequences that satisfy desired criteria. In this package, common deep generative models for protein sequences, such as variational autoencoder (VAE), generative adversarial networks (GAN), and autoregressive models are available. In the VAE and GAN, the Word2vec is used for embedding. The transformer encoder is applied to protein sequences for the autoregressive model.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-genvisr/meta.yaml b/recipes/bioconductor-genvisr/meta.yaml index 1358bedd1c531..5a8d07a8c6814 100644 --- a/recipes/bioconductor-genvisr/meta.yaml +++ b/recipes/bioconductor-genvisr/meta.yaml @@ -1,86 +1,94 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "GenVisR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Produce highly customizable publication quality graphics for genomic data primarily at the cohort level. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Genomic Visualizations in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f05fdc7c5736ba49ccf4eebcc1bc28ec build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-genvisr", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:genvisr + parent_recipe: + name: bioconductor-genvisr + path: recipes/bioconductor-genvisr + version: 1.12.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL, roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38 requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-data.table - r-dbi - - 'r-ggplot2 >=2.1.0' - - 'r-gridextra >=2.0.0' + - r-ggplot2 >=2.1.0 + - r-gridextra >=2.0.0 - r-gtable - r-gtools - - 'r-plyr >=1.8.3' + - r-plyr >=1.8.3 - r-reshape2 - r-scales - r-viridis + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-data.table - r-dbi - - 'r-ggplot2 >=2.1.0' - - 'r-gridextra >=2.0.0' + - r-ggplot2 >=2.1.0 + - r-gridextra >=2.0.0 - r-gtable - r-gtools - - 'r-plyr >=1.8.3' + - r-plyr >=1.8.3 - r-reshape2 - r-scales - r-viridis + +source: + md5: 80e65c64b1130682ef831f38e4d9227a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Genomic Visualizations in R' - description: 'Produce highly customizable publication quality graphics for genomic data primarily at the cohort level.' - license_file: LICENSE -extra: - identifiers: - - biotools:genvisr - parent_recipe: - name: bioconductor-genvisr - path: recipes/bioconductor-genvisr - version: 1.12.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-geodiff/meta.yaml b/recipes/bioconductor-geodiff/meta.yaml index 71a1b028708ae..4b444a625dbb7 100644 --- a/recipes/bioconductor-geodiff/meta.yaml +++ b/recipes/bioconductor-geodiff/meta.yaml @@ -1,34 +1,40 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "GeoDiff" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A series of statistical models using count generating distributions for background modelling, feature and sample QC, normalization and differential expression analysis on GeoMx RNA data. The application of these methods are demonstrated by example data analysis vignette. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Count model based differential expression and normalization on GeoMx RNA data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f719fddf3486b6aad1f36ca439b55114 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-geodiff", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, dplyr requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-geomxtools >=3.5.0,<3.6.0' - - 'bioconductor-nanostringnctools >=1.10.0,<1.11.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-geomxtools >=3.10.0,<3.11.0 + - bioconductor-nanostringnctools >=1.14.0,<1.15.0 - r-base - r-lme4 - r-matrix - r-plyr - - 'r-rcpp >=1.0.4.6' + - r-rcpp >=1.0.4.6 - r-rcpparmadillo - r-robust - r-roptim @@ -37,30 +43,29 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-geomxtools >=3.5.0,<3.6.0' - - 'bioconductor-nanostringnctools >=1.10.0,<1.11.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-geomxtools >=3.10.0,<3.11.0 + - bioconductor-nanostringnctools >=1.14.0,<1.15.0 - r-base - r-lme4 - r-matrix - r-plyr - - 'r-rcpp >=1.0.4.6' + - r-rcpp >=1.0.4.6 - r-rcpparmadillo - r-robust - r-roptim - r-testthat - r-withr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: a3c5d6ea2abd61fa18c86ed57e6a5432 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Count model based differential expression and normalization on GeoMx RNA data' - description: 'A series of statistical models using count generating distributions for background modelling, feature and sample QC, normalization and differential expression analysis on GeoMx RNA data. The application of these methods are demonstrated by example data analysis vignette.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-geoexplorer/meta.yaml b/recipes/bioconductor-geoexplorer/meta.yaml index 5002ad1d02b93..b78e9fcb0fcc0 100644 --- a/recipes/bioconductor-geoexplorer/meta.yaml +++ b/recipes/bioconductor-geoexplorer/meta.yaml @@ -1,33 +1,36 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "GEOexplorer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'GEOexplorer is a webserver and R/Bioconductor package and web application that enables users to perform gene expression analysis. The development of GEOexplorer was made possible because of the excellent code provided by GEO2R (https: //www.ncbi.nlm.nih.gov/geo/geo2r/).' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'GEOexplorer: a webserver for gene expression analysis and visualisation' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 213a1b499ce1d0640b267c8fb41e3204 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-geoexplorer", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, usethis, testthat (>= 3.0.0) requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-car - r-dt @@ -53,13 +56,14 @@ requirements: - r-xfun - r-xml - r-xml2 + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-car - r-dt @@ -85,13 +89,16 @@ requirements: - r-xfun - r-xml - r-xml2 + +source: + md5: 4c551b3a32be33591646d06feae085b9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'GEOexplorer: a webserver for gene expression analysis and visualisation' - description: 'GEOexplorer is a webserver and R/Bioconductor package and web application that enables users to perform gene expression analysis. The development of GEOexplorer was made possible because of the excellent code provided by GEO2R (https: //www.ncbi.nlm.nih.gov/geo/geo2r/).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-geofastq/meta.yaml b/recipes/bioconductor-geofastq/meta.yaml index df5a172e6e81f..ba6adf9d55e30 100644 --- a/recipes/bioconductor-geofastq/meta.yaml +++ b/recipes/bioconductor-geofastq/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "GEOfastq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: GEOfastq is used to download fastq files from the European Nucleotide Archive (ENA) starting with an accession from the Gene Expression Omnibus (GEO). To do this, sample metadata is retrieved from GEO and the Sequence Read Archive (SRA). SRA run accessions are then used to construct FTP and aspera download links for fastq files generated by the ENA. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Downloads ENA Fastqs With GEO Accessions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 339bd0c2f6a3f505457fc436997965a6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-geofastq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocCheck, roxygen2, knitr, rmarkdown, testthat requirements: host: @@ -39,13 +41,16 @@ requirements: - r-rvest - r-stringr - r-xml2 + +source: + md5: a47fe421885d917b2bf5ad557778d5fb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Downloads ENA Fastqs With GEO Accessions' - description: 'GEOfastq is used to download fastq files from the European Nucleotide Archive (ENA) starting with an accession from the Gene Expression Omnibus (GEO). To do this, sample metadata is retrieved from GEO and the Sequence Read Archive (SRA). SRA run accessions are then used to construct FTP and aspera download links for fastq files generated by the ENA.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-geomxtools/meta.yaml b/recipes/bioconductor-geomxtools/meta.yaml index f8e4400a66844..7295a9cdaf30e 100644 --- a/recipes/bioconductor-geomxtools/meta.yaml +++ b/recipes/bioconductor-geomxtools/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "3.5.0" %} +{% set version = "3.10.0" %} {% set name = "GeomxTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for NanoString Technologies GeoMx Technology. Package provides functions for reading in DCC and PKC files based on an ExpressionSet derived object. Normalization and QC functions are also included. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + summary: NanoString GeoMx Tools -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ac9d92476a27e642927f906be2756db build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-geomxtools", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment (>= 1.4.0), SpatialDecon, patchwork requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-nanostringnctools >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-nanostringnctools >=1.14.0,<1.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-dplyr @@ -40,10 +41,10 @@ requirements: - r-seuratobject - r-stringr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-nanostringnctools >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-nanostringnctools >=1.14.0,<1.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-dplyr @@ -57,12 +58,16 @@ requirements: - r-rlang - r-seuratobject - r-stringr + +source: + md5: aa853eaa64a4d45a48c8c825136eae3d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: MIT - summary: 'NanoString GeoMx Tools' - description: 'Tools for NanoString Technologies GeoMx Technology. Package provides functions for reading in DCC and PKC files based on an ExpressionSet derived object. Normalization and QC functions are also included.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-geoquery/meta.yaml b/recipes/bioconductor-geoquery/meta.yaml index d4246ec8b5641..8029f2ce2729b 100644 --- a/recipes/bioconductor-geoquery/meta.yaml +++ b/recipes/bioconductor-geoquery/meta.yaml @@ -1,64 +1,84 @@ -{% set version = "2.70.0" %} +{% set version = "2.74.0" %} {% set name = "GEOquery" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Get data from NCBI Gene Expression Omnibus (GEO) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5e8f233065ccb97c7cbb231479c936a0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-geoquery", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + identifiers: + - biotools:geoquery + parent_recipe: + name: bioconductor-geoquery + path: recipes/bioconductor-geoquery + version: 2.48.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr, markdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-curl - r-data.table - r-dplyr + - r-httr2 - r-magrittr - r-r.utils - - 'r-readr >=1.3.1' + - r-readr >=1.3.1 + - r-rentrez + - r-rvest + - r-stringr - r-tidyr - r-xml2 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-curl - r-data.table - r-dplyr + - r-httr2 - r-magrittr - r-r.utils - - 'r-readr >=1.3.1' + - r-readr >=1.3.1 + - r-rentrez + - r-rvest + - r-stringr - r-tidyr - r-xml2 + +source: + md5: ce6364a7f5cc1085e48a8639e7afba50 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: MIT - summary: 'Get data from NCBI Gene Expression Omnibus (GEO)' - description: 'The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.' -extra: - container: - extended-base: true - identifiers: - - biotools:geoquery - parent_recipe: - name: bioconductor-geoquery - path: recipes/bioconductor-geoquery - version: 2.48.0 + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-geosubmission/meta.yaml b/recipes/bioconductor-geosubmission/meta.yaml index 171c6416978eb..d2c7da761bbab 100644 --- a/recipes/bioconductor-geosubmission/meta.yaml +++ b/recipes/bioconductor-geosubmission/meta.yaml @@ -1,42 +1,22 @@ -{% set version = "1.54.0" %} +{% set version = "1.58.0" %} {% set name = "GEOsubmission" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Helps to easily submit a microarray dataset and the associated sample information to GEO by preparing a single file for upload (direct deposit). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Prepares microarray data for submission to GEO -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 835a74433a1f0235676bf2d1012096af build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-geosubmission", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base - run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Prepares microarray data for submission to GEO' - description: 'Helps to easily submit a microarray dataset and the associated sample information to GEO by preparing a single file for upload (direct deposit).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:geosubmission @@ -46,3 +26,29 @@ extra: path: recipes/bioconductor-geosubmission version: 1.32.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + run: + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + +source: + md5: 3feade6905874636f47697d1a9f30595 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-geotcgadata/meta.yaml b/recipes/bioconductor-geotcgadata/meta.yaml index 4cba7f0dfdbe6..05f05d302e16d 100644 --- a/recipes/bioconductor-geotcgadata/meta.yaml +++ b/recipes/bioconductor-geotcgadata/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "2.2.0" %} +{% set version = "2.6.0" %} {% set name = "GeoTcgaData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. It's easy to download data from TCGA using the gdc tool, but processing these data into a format suitable for bioinformatics analysis requires more work. This R package was developed to handle these data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Processing Various Types of Data on GEO and TCGA -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 653a353d37b0bcfbd892dfe12d420100 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-geotcgadata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, DESeq2, S4Vectors, ChAMP, impute, tidyr, clusterProfiler, org.Hs.eg.db, edgeR, limma, quantreg, minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, dearseq, NOISeq, testthat (>= 3.0.0), CATT, TCGAbiolinks, enrichplot, GEOquery, BiocGenerics requirements: host: - - 'bioconductor-cqn >=1.48.0,<1.49.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-topconfects >=1.18.0,<1.19.0' + - bioconductor-cqn >=1.52.0,<1.53.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-topconfects >=1.22.0,<1.23.0 - r-base - r-data.table - r-plyr run: - - 'bioconductor-cqn >=1.48.0,<1.49.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-topconfects >=1.18.0,<1.19.0' + - bioconductor-cqn >=1.52.0,<1.53.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-topconfects >=1.22.0,<1.23.0 - r-base - r-data.table - r-plyr + +source: + md5: e666c601fc82d083681c9a74e6f43bd6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Processing Various Types of Data on GEO and TCGA' - description: 'Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. It''s easy to download data from TCGA using the gdc tool, but processing these data into a format suitable for bioinformatics analysis requires more work. This R package was developed to handle these data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gep2pep/meta.yaml b/recipes/bioconductor-gep2pep/meta.yaml index 8250b9d598084..3073fc2a6b95f 100644 --- a/recipes/bioconductor-gep2pep/meta.yaml +++ b/recipes/bioconductor-gep2pep/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "gep2pep" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Pathway Expression Profiles (PEPs) are based on the expression of pathways (defined as sets of genes) as opposed to individual genes. This package converts gene expression profiles to PEPs and performs enrichment analysis of both pathways and experimental conditions, such as "drug set enrichment analysis" and "gene2drug" drug discovery analysis respectively. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Creation and Analysis of Pathway Expression Profiles (PEPs) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0a8f1b44003eba297c44f8115f870df0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gep2pep", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: WriteXLS, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 - r-base - r-digest - r-foreach - r-iterators - - 'r-repo >=2.1.1' + - r-repo >=2.1.1 - r-xml run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 - r-base - r-digest - r-foreach - r-iterators - - 'r-repo >=2.1.1' + - r-repo >=2.1.1 - r-xml + +source: + md5: b8045fd5dedd9cd25f0266817795fb6d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Creation and Analysis of Pathway Expression Profiles (PEPs)' - description: 'Pathway Expression Profiles (PEPs) are based on the expression of pathways (defined as sets of genes) as opposed to individual genes. This package converts gene expression profiles to PEPs and performs enrichment analysis of both pathways and experimental conditions, such as "drug set enrichment analysis" and "gene2drug" drug discovery analysis respectively.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-getdee2/meta.yaml b/recipes/bioconductor-getdee2/meta.yaml index 1ff51ddaf967c..d4d0f1a2d36e6 100644 --- a/recipes/bioconductor-getdee2/meta.yaml +++ b/recipes/bioconductor-getdee2/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "getDEE2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5bae73105adbd3fba6517601379594c0 +about: + description: Digital Expression Explorer 2 (or DEE2 for short) is a repository of processed RNA-seq data in the form of counts. It was designed so that researchers could undertake re-analysis and meta-analysis of published RNA-seq studies quickly and easily. As of April 2020, over 1 million SRA datasets have been processed. This package provides an R interface to access these expression data. More information about the DEE2 project can be found at the project homepage (http://dee2.io) and main publication (https://doi.org/10.1093/gigascience/giz022). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Programmatic access to the DEE2 RNA expression dataset build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-getdee2", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-htm2txt run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-htm2txt +source: + md5: de5f9b90fe00b79fea973088dca042fe + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Programmatic access to the DEE2 RNA expression dataset' - description: 'Digital Expression Explorer 2 (or DEE2 for short) is a repository of processed RNA-seq data in the form of counts. It was designed so that researchers could undertake re-analysis and meta-analysis of published RNA-seq studies quickly and easily. As of April 2020, over 1 million SRA datasets have been processed. This package provides an R interface to access these expression data. More information about the DEE2 project can be found at the project homepage (http://dee2.io) and main publication (https://doi.org/10.1093/gigascience/giz022).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-geuvadistranscriptexpr/meta.yaml b/recipes/bioconductor-geuvadistranscriptexpr/meta.yaml index 6cda616d59429..c1a566c509d86 100644 --- a/recipes/bioconductor-geuvadistranscriptexpr/meta.yaml +++ b/recipes/bioconductor-geuvadistranscriptexpr/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "GeuvadisTranscriptExpr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 806de22bef0659a3b6f9db122d87a1d6 +about: + description: Provides transcript expression and bi-allelic genotypes corresponding to the chromosome 19 for CEU individuals from the GEUVADIS project, Lappalainen et al. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Data package with transcript expression and bi-allelic genotypes from the GEUVADIS project build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-geuvadistranscriptexpr", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: limma, rtracklayer, GenomicRanges, Rsamtools, VariantAnnotation, tools, BiocStyle, knitr, testthat requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6a7d1b4c1733a4bbff15b5e1863160c4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Data package with transcript expression and bi-allelic genotypes from the GEUVADIS project' - description: 'Provides transcript expression and bi-allelic genotypes corresponding to the chromosome 19 for CEU individuals from the GEUVADIS project, Lappalainen et al.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-geuvadistranscriptexpr/post-link.sh b/recipes/bioconductor-geuvadistranscriptexpr/post-link.sh index 4723d360c3b55..383b3ed4684d6 100644 --- a/recipes/bioconductor-geuvadistranscriptexpr/post-link.sh +++ b/recipes/bioconductor-geuvadistranscriptexpr/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "geuvadistranscriptexpr-1.30.0" +installBiocDataPackage.sh "geuvadistranscriptexpr-1.34.0" diff --git a/recipes/bioconductor-geva/meta.yaml b/recipes/bioconductor-geva/meta.yaml index 05f850b06b2ec..ddd9f4fdca263 100644 --- a/recipes/bioconductor-geva/meta.yaml +++ b/recipes/bioconductor-geva/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "geva" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ac06c7a9df29f5eb16fe102c81369ccb +about: + description: Statistic methods to evaluate variations of differential expression (DE) between multiple biological conditions. It takes into account the fold-changes and p-values from previous differential expression (DE) results that use large-scale data (*e.g.*, microarray and RNA-seq) and evaluates which genes would react in response to the distinct experiments. This evaluation involves an unique pipeline of statistical methods, including weighted summarization, quantile detection, cluster analysis, and ANOVA tests, in order to classify a subset of relevant genes whose DE is similar or dependent to certain biological factors. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Gene Expression Variation Analysis (GEVA) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-geva", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: devtools, knitr, rmarkdown, roxygen2, limma, topGO, testthat (>= 3.0.0) requirements: host: @@ -31,13 +30,14 @@ requirements: - r-dbscan - r-fastcluster - r-matrixstats +source: + md5: 4367f4a5c6e06d2241d403a920b73e18 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'Gene Expression Variation Analysis (GEVA)' - description: 'Statistic methods to evaluate variations of differential expression (DE) between multiple biological conditions. It takes into account the fold-changes and p-values from previous differential expression (DE) results that use large-scale data (*e.g.*, microarray and RNA-seq) and evaluates which genes would react in response to the distinct experiments. This evaluation involves an unique pipeline of statistical methods, including weighted summarization, quantile detection, cluster analysis, and ANOVA tests, in order to classify a subset of relevant genes whose DE is similar or dependent to certain biological factors.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gewist/meta.yaml b/recipes/bioconductor-gewist/meta.yaml index 5e0d3c2bb02e2..45b013601269c 100644 --- a/recipes/bioconductor-gewist/meta.yaml +++ b/recipes/bioconductor-gewist/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "GEWIST" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This 'GEWIST' package provides statistical tools to efficiently optimize SNP prioritization for gene-gene and gene-environment interactions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Gene Environment Wide Interaction Search Threshold -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3fe24d9c2f80cfc18dc41b37b118be6e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gewist", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:gewist + - doi:10.1002/gepi.20624 + parent_recipe: + name: bioconductor-gewist + path: recipes/bioconductor-gewist + version: 1.24.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -26,21 +37,16 @@ requirements: run: - r-base - r-car + +source: + md5: 930a8d333795fde8f0bd0299b6db5b7d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Gene Environment Wide Interaction Search Threshold' - description: 'This ''GEWIST'' package provides statistical tools to efficiently optimize SNP prioritization for gene-gene and gene-environment interactions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:gewist - - doi:10.1002/gepi.20624 - parent_recipe: - name: bioconductor-gewist - path: recipes/bioconductor-gewist - version: 1.24.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gg4way/meta.yaml b/recipes/bioconductor-gg4way/meta.yaml index 835f32f2578c0..4a743283a6abe 100644 --- a/recipes/bioconductor-gg4way/meta.yaml +++ b/recipes/bioconductor-gg4way/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "gg4way" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 4way plots enable a comparison of the logFC values from two contrasts of differential gene expression. The gg4way package creates 4way plots using the ggplot2 framework and supports popular Bioconductor objects. The package also provides information about the correlation between contrasts and significant genes of interest. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 4way Plots of Differential Expression -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 500552b8ab9c3fc5cc58fcf56378a928 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gg4way", max_pin="x.x") }}' - noarch: generic -# Suggests: airway, BiocStyle, knitr, org.Hs.eg.db, rmarkdown, testthat + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: airway, BiocStyle, knitr, org.Hs.eg.db, rmarkdown, testthat, vdiffr requirements: host: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-dplyr - r-ggplot2 @@ -39,9 +41,9 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-dplyr - r-ggplot2 @@ -55,13 +57,16 @@ requirements: - r-stringr - r-tibble - r-tidyr + +source: + md5: 707ade7d103b74d1c1d71f8e001ea561 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: '4way Plots of Differential Expression' - description: '4way plots enable a comparison of the logFC values from two contrasts of differential gene expression. The gg4way package creates 4way plots using the ggplot2 framework and supports popular Bioconductor objects. The package also provides information about the correlation between contrasts and significant genes of interest.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ggbio/meta.yaml b/recipes/bioconductor-ggbio/meta.yaml index 2ae0c837632c1..e9134e1b8e5e9 100644 --- a/recipes/bioconductor-ggbio/meta.yaml +++ b/recipes/bioconductor-ggbio/meta.yaml @@ -1,97 +1,105 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "ggbio" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Visualization tools for genomic data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: de7ec73480f41c35fca2a8a758fbc7d0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ggbio", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:ggbio + parent_recipe: + name: bioconductor-ggbio + path: recipes/bioconductor-ggbio + version: 1.28.5 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-biovizbase >=1.50.0,<1.51.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-biovizbase >=1.54.0,<1.55.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-organismdbi >=1.48.0,<1.49.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-ggally - - 'r-ggplot2 >=1.0.0' + - r-ggplot2 >=1.0.0 - r-gridextra - r-gtable - r-hmisc - r-reshape2 - r-rlang - r-scales + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-biovizbase >=1.50.0,<1.51.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-biovizbase >=1.54.0,<1.55.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-organismdbi >=1.48.0,<1.49.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-ggally - - 'r-ggplot2 >=1.0.0' + - r-ggplot2 >=1.0.0 - r-gridextra - r-gtable - r-hmisc - r-reshape2 - r-rlang - r-scales + +source: + md5: c5c9142454e8930f9837b82eefb2477e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Visualization tools for genomic data' - description: 'The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.' -extra: - identifiers: - - biotools:ggbio - parent_recipe: - name: bioconductor-ggbio - path: recipes/bioconductor-ggbio - version: 1.28.5 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ggcyto/meta.yaml b/recipes/bioconductor-ggcyto/meta.yaml index 996e3aeda5742..05d90d7c81e3b 100644 --- a/recipes/bioconductor-ggcyto/meta.yaml +++ b/recipes/bioconductor-ggcyto/meta.yaml @@ -1,33 +1,44 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "ggcyto" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: With the dedicated fortify method implemented for flowSet, ncdfFlowSet and GatingSet classes, both raw and gated flow cytometry data can be plotted directly with ggplot. ggcyto wrapper and some customed layers also make it easy to add gates and population statistics to the plot. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Visualize Cytometry data with ggplot -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f50828f54e40b73d30aa3ac0ef06de21 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ggcyto", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:ggcyto + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ggcyto + path: recipes/bioconductor-ggcyto + version: 1.8.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr requirements: host: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' - - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowworkspace >=4.18.0,<4.19.0 + - bioconductor-ncdfflow >=2.52.0,<2.53.0 - r-base - r-data.table - - 'r-ggplot2 >=3.4.2' + - r-ggplot2 >=3.5.0 - r-gridextra - r-hexbin - r-plyr @@ -35,33 +46,28 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' - - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowworkspace >=4.18.0,<4.19.0 + - bioconductor-ncdfflow >=2.52.0,<2.53.0 - r-base - r-data.table - - 'r-ggplot2 >=3.4.2' + - r-ggplot2 >=3.5.0 - r-gridextra - r-hexbin - r-plyr - r-rcolorbrewer - r-rlang - r-scales + +source: + md5: 21deb9ad12806e54f05b1e58aa75f99f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Visualize Cytometry data with ggplot' - description: 'With the dedicated fortify method implemented for flowSet, ncdfFlowSet and GatingSet classes, both raw and gated flow cytometry data can be plotted directly with ggplot. ggcyto wrapper and some customed layers also make it easy to add gates and population statistics to the plot.' - license_file: LICENSE -extra: - identifiers: - - biotools:ggcyto - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-ggcyto - path: recipes/bioconductor-ggcyto - version: 1.8.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gghumanmethcancerpanelv1.db/meta.yaml b/recipes/bioconductor-gghumanmethcancerpanelv1.db/meta.yaml index 4bb5bc685c883..e0fd123b2f51e 100644 --- a/recipes/bioconductor-gghumanmethcancerpanelv1.db/meta.yaml +++ b/recipes/bioconductor-gghumanmethcancerpanelv1.db/meta.yaml @@ -1,44 +1,44 @@ {% set version = "1.4.1" %} {% set name = "GGHumanMethCancerPanelv1.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e8f4a37182b175fb33dd54f8093e6f52 +about: + description: Illumina Golden Gate Human Methylation Cancer Panel Version 1 annotation data (chip GGHumanMethCancerPanelv1) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina Golden Gate Human Methylation Cancer Panel Version 1 annotation data (chip GGHumanMethCancerPanelv1) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gghumanmethcancerpanelv1.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationforge >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationforge >=1.48.0,<1.49.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationforge >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationforge >=1.48.0,<1.49.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e8f4a37182b175fb33dd54f8093e6f52 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina Golden Gate Human Methylation Cancer Panel Version 1 annotation data (chip GGHumanMethCancerPanelv1)' - description: 'Illumina Golden Gate Human Methylation Cancer Panel Version 1 annotation data (chip GGHumanMethCancerPanelv1) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ggkegg/meta.yaml b/recipes/bioconductor-ggkegg/meta.yaml index 613b9acdc3d6a..4f1ab0549977f 100644 --- a/recipes/bioconductor-ggkegg/meta.yaml +++ b/recipes/bioconductor-ggkegg/meta.yaml @@ -1,37 +1,37 @@ -{% set version = "1.0.2" %} +{% set version = "1.4.0" %} {% set name = "ggkegg" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package aims to import, parse, and analyze KEGG data such as KEGG PATHWAY and KEGG MODULE. The package supports visualizing KEGG information using ggplot2 and ggraph through using the grammar of graphics. The package enables the direct visualization of the results from various omics analysis packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Analyzing and visualizing KEGG information using the grammar of graphics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 747219ce420df145e10ee4b9243b17dc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ggkegg", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, clusterProfiler, bnlearn, rmarkdown, BiocStyle, testthat (>= 3.0.0) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, clusterProfiler, bnlearn, rmarkdown, BiocStyle, AnnotationDbi, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base - - r-cairo - r-data.table - r-dplyr - r-getoptlong - r-ggplot2 - r-ggraph + - r-gtable - r-igraph - r-magick - r-patchwork @@ -41,16 +41,14 @@ requirements: - r-tidygraph - r-xml run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base - - r-cairo - r-data.table - r-dplyr - r-getoptlong - r-ggplot2 - r-ggraph + - r-gtable - r-igraph - r-magick - r-patchwork @@ -59,13 +57,16 @@ requirements: - r-tibble - r-tidygraph - r-xml + +source: + md5: e67f320ba80e9456e60289f919285c14 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'KEGG pathway visualization by ggplot2' - description: 'This package aims to import, parse, and analyze KEGG data such as KEGG PATHWAY and KEGG MODULE. The package supports visualizing KEGG information using ggplot2 and ggraph through using the grammar of graphics. The package enables the direct visualization of the results from various omics analysis packages.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ggmanh/build.sh b/recipes/bioconductor-ggmanh/build.sh index c1d13421f5f1e..497f7b5bdb678 100644 --- a/recipes/bioconductor-ggmanh/build.sh +++ b/recipes/bioconductor-ggmanh/build.sh @@ -8,4 +8,5 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars +export LD_LIBRARY_PATH=${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ggmanh/meta.yaml b/recipes/bioconductor-ggmanh/meta.yaml index ab0bfd97963ec..6038826ea98e1 100644 --- a/recipes/bioconductor-ggmanh/meta.yaml +++ b/recipes/bioconductor-ggmanh/meta.yaml @@ -1,51 +1,77 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "ggmanh" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Manhattan plot and QQ Plot are commonly used to visualize the end result of Genome Wide Association Study. The "ggmanh" package aims to keep the generation of these plots simple while maintaining customizability. Main functions include manhattan_plot, qqunif, and thinPoints. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Visualization Tool for GWAS Result -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dbbd8130e9ef70cb69c7e305af0c37d7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ggmanh", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0), markdown, GenomicRanges + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0), GenomicRanges requirements: + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] host: - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-seqarray >=1.46.0,<1.47.0 - r-base + - r-dplyr - r-ggplot2 - r-ggrepel + - r-magrittr + - r-paletteer + - r-pals - r-rcolorbrewer - r-rlang - r-scales + - r-tidyr run: - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-seqarray >=1.46.0,<1.47.0 - r-base + - r-dplyr - r-ggplot2 - r-ggrepel + - r-magrittr + - r-paletteer + - r-pals - r-rcolorbrewer - r-rlang - r-scales + - r-tidyr + +source: + md5: d94150a3e04430c48f8fa76d3b0bf870 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Visualization Tool for GWAS Result' - description: 'Manhattan plot and QQ Plot are commonly used to visualize the end result of Genome Wide Association Study. The "ggmanh" package aims to keep the generation of these plots simple while maintaining customizability. Main functions include manhattan_plot, qqunif, and thinPoints.' - license_file: LICENSE + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ggmsa/meta.yaml b/recipes/bioconductor-ggmsa/meta.yaml index 1ca7bf62799d6..82e205d6e1466 100644 --- a/recipes/bioconductor-ggmsa/meta.yaml +++ b/recipes/bioconductor-ggmsa/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "ggmsa" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'A visual exploration tool for multiple sequence alignment and associated data. Supports MSA of DNA, RNA, and protein sequences using ''ggplot2''. Multiple sequence alignment can easily be combined with other ''ggplot2'' plots, such as phylogenetic tree Visualized by ''ggtree'', boxplot, genome map and so on. More features: visualization of sequence logos, sequence bundles, RNA secondary structures and detection of sequence recombinations.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Plot Multiple Sequence Alignment using 'ggplot2' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1faea3aedc093bb7e151208c9a11b60c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ggmsa", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ggtreeExtra, ape, cowplot, knitr, BiocStyle, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-r4rna >=1.30.0,<1.31.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-r4rna >=1.34.0,<1.35.0 - r-aplot - r-base - r-dplyr @@ -37,9 +38,9 @@ requirements: - r-statebins - r-tidyr run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-r4rna >=1.30.0,<1.31.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-r4rna >=1.34.0,<1.35.0 - r-aplot - r-base - r-dplyr @@ -51,12 +52,16 @@ requirements: - r-seqmagick - r-statebins - r-tidyr + +source: + md5: ed87adaaf651d7d5aafdd910d47395e8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Plot Multiple Sequence Alignment using ''ggplot2''' - description: 'A visual exploration tool for multiple sequence alignment and associated data. Supports MSA of DNA, RNA, and protein sequences using ''ggplot2''. Multiple sequence alignment can easily be combined with other ''ggplot2'' plots, such as phylogenetic tree Visualized by ''ggtree'', boxplot, genome map and so on. More features: visualization of sequence logos, sequence bundles, RNA secondary structures and detection of sequence recombinations.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ggpa/meta.yaml b/recipes/bioconductor-ggpa/meta.yaml index 5d4865bce21db..b9c511b6477f8 100644 --- a/recipes/bioconductor-ggpa/meta.yaml +++ b/recipes/bioconductor-ggpa/meta.yaml @@ -1,32 +1,38 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "GGPA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Genome-wide association studies (GWAS) is a widely used tool for identification of genetic variants associated with phenotypes and diseases, though complex diseases featuring many genetic variants with small effects present difficulties for traditional these studies. By leveraging pleiotropy, the statistical power of a single GWAS can be increased. This package provides functions for fitting graph-GPA, a statistical framework to prioritize GWAS results by integrating pleiotropy. 'GGPA' package provides user-friendly interface to fit graph-GPA models, implement association mapping, and generate a phenotype graph. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5c50ef4040a18ac94848d7c42484d28d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ggpa", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-ggally - r-matrixstats - r-network - - 'r-rcpp >=0.11.3' + - r-rcpp >=0.11.3 - r-rcpparmadillo - r-scales - r-sna @@ -37,21 +43,20 @@ requirements: - r-ggally - r-matrixstats - r-network - - 'r-rcpp >=0.11.3' + - r-rcpp >=0.11.3 - r-rcpparmadillo - r-scales - r-sna - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 41f5478a2aa44282a8e74e8a9ac5a334 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture' - description: 'Genome-wide association studies (GWAS) is a widely used tool for identification of genetic variants associated with phenotypes and diseases, though complex diseases featuring many genetic variants with small effects present difficulties for traditional these studies. By leveraging pleiotropy, the statistical power of a single GWAS can be increased. This package provides functions for fitting graph-GPA, a statistical framework to prioritize GWAS results by integrating pleiotropy. ''GGPA'' package provides user-friendly interface to fit graph-GPA models, implement association mapping, and generate a phenotype graph.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ggsc/meta.yaml b/recipes/bioconductor-ggsc/meta.yaml index 1441cbbb7e759..d2bc280ba8a55 100644 --- a/recipes/bioconductor-ggsc/meta.yaml +++ b/recipes/bioconductor-ggsc/meta.yaml @@ -1,36 +1,47 @@ -{% set version = "1.0.2" %} +{% set version = "1.4.0" %} {% set name = "ggsc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Useful functions to visualize single cell and spatial data. It supports visualizing 'Seurat', 'SingleCellExperiment' and 'SpatialExperiment' objects through grammar of graphics syntax implemented in 'ggplot2'. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Visualizing Single Cell and Spatial Transcriptomics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4c0a1656e9943cadf436244c65b18242 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ggsc", max_pin="x.x") }}' -# Suggests: aplot, BiocParallel, forcats, ggforce, ggnewscale, igraph, knitr, ks, Matrix, prettydoc, rmarkdown, scran, scater, scuttle, shadowtext, sf, SeuratObject, SpatialExperiment, STexampleData, testthat (>= 3.0.0) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: aplot, BiocParallel, forcats, ggforce, ggnewscale, igraph, knitr, ks, Matrix, prettydoc, rmarkdown, scran, scater, scatterpie (>= 0.2.4), scuttle, shadowtext, sf, SeuratObject, SpatialExperiment, STexampleData, testthat (>= 3.0.0), MASS +# SystemRequirements: GNU make requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cli - r-dplyr + - r-ggfun >=0.1.5 - r-ggplot2 + - r-rcolorbrewer - r-rcpp - r-rcpparmadillo - r-rcppparallel - r-rlang + - r-scales - r-scattermore - r-seurat - r-tibble @@ -39,33 +50,37 @@ requirements: - r-yulab.utils - libblas - liblapack + run: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cli - r-dplyr + - r-ggfun >=0.1.5 - r-ggplot2 + - r-rcolorbrewer - r-rcpp - r-rcpparmadillo - r-rcppparallel - r-rlang + - r-scales - r-scattermore - r-seurat - r-tibble - r-tidydr - r-tidyr - r-yulab.utils - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 1caafa93bcd57a5ba6fbf0725f899fa4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Visualizing Single Cell Data' - description: 'Useful functions to visualize single cell and spatial data. It supports both ''SingleCellExperiment'' and ''Seurat'' objects. It also supports visualizing the data using grammar of graphics implemented in ''ggplot2''.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ggseqalign/build.sh b/recipes/bioconductor-ggseqalign/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ggseqalign/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ggseqalign/meta.yaml b/recipes/bioconductor-ggseqalign/meta.yaml new file mode 100644 index 0000000000000..299d3b7da04fd --- /dev/null +++ b/recipes/bioconductor-ggseqalign/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.0.0" %} +{% set name = "ggseqalign" %} +{% set bioc = "3.20" %} + +about: + description: Simple visualizations of alignments of DNA or AA sequences as well as arbitrary strings. Compatible with Biostrings and ggplot2. The plots are fully customizable using ggplot2 modifiers such as theme(). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Minimal Visualization of Sequence Alignments +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ggseqalign", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: Biostrings, BiocStyle, knitr, rmarkdown +requirements: + host: + - bioconductor-pwalign >=1.2.0,<1.3.0 + - r-base + - r-dplyr + - r-ggplot2 + run: + - bioconductor-pwalign >=1.2.0,<1.3.0 + - r-base + - r-dplyr + - r-ggplot2 +source: + md5: b463e7352980ec3297edb2ba877a5a8c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-ggspavis/meta.yaml b/recipes/bioconductor-ggspavis/meta.yaml index eabd7d3e68766..e1ee6fbc3f2f1 100644 --- a/recipes/bioconductor-ggspavis/meta.yaml +++ b/recipes/bioconductor-ggspavis/meta.yaml @@ -1,47 +1,58 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "ggspavis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Visualization functions for spatial transcriptomics data. Includes functions to generate several types of plots, including spot plots, feature (molecule) plots, reduced dimension plots, spot-level quality control (QC) plots, and feature-level QC plots, for datasets from the 10x Genomics Visium and other technological platforms. Datasets are assumed to be in either SpatialExperiment or SingleCellExperiment format. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Visualization functions for spatial transcriptomics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c79337783dc059e449506a61c5579337 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ggspavis", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix, scater, scran, uwot, testthat (>= 3.0.0) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix, scater, scran, uwot, testthat, patchwork requirements: host: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 + - r-ggrepel - r-ggside + - r-rcolorbrewer + - r-scales run: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 + - r-ggrepel - r-ggside + - r-rcolorbrewer + - r-scales + +source: + md5: 625803fb55152e66fda4a8491a6edcbe + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Visualization functions for spatially resolved transcriptomics data' - description: 'Visualization functions for spatially resolved transcriptomics datasets stored in SpatialExperiment format. Includes functions to create several types of plots for data from from spot-based (e.g. 10x Genomics Visium) and molecule-based (e.g. seqFISH) technological platforms.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ggtree/meta.yaml b/recipes/bioconductor-ggtree/meta.yaml index 2a7d2de5144dc..97b21dc79936b 100644 --- a/recipes/bioconductor-ggtree/meta.yaml +++ b/recipes/bioconductor-ggtree/meta.yaml @@ -1,72 +1,78 @@ -{% set version = "3.10.0" %} +{% set version = "3.14.0" %} {% set name = "ggtree" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: '''ggtree'' extends the ''ggplot2'' plotting system which implemented the grammar of graphics. ''ggtree'' is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: an R package for visualization of tree and annotation data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7e1894ce01245d811286b0ce1fbe8266 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ggtree", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:ggtree + - doi:10.1111/2041-210X.12628 + parent_recipe: + name: bioconductor-ggtree + path: recipes/bioconductor-ggtree + version: 1.12.7 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, testthat, tibble, glue requirements: host: - - 'bioconductor-treeio >=1.26.0,<1.27.0' + - bioconductor-treeio >=1.30.0,<1.31.0 - r-ape - r-aplot - r-base - r-cli - r-dplyr - - 'r-ggfun >=0.0.9' - - 'r-ggplot2 >3.3.6' + - r-ggfun >=0.1.7 + - r-ggplot2 >3.3.6 - r-magrittr - r-purrr - r-rlang - r-scales - r-tidyr - - 'r-tidytree >=0.4.5' - - r-yulab.utils + - r-tidytree >=0.4.5 + - r-yulab.utils >=0.1.6 run: - - 'bioconductor-treeio >=1.26.0,<1.27.0' + - bioconductor-treeio >=1.30.0,<1.31.0 - r-ape - r-aplot - r-base - r-cli - r-dplyr - - 'r-ggfun >=0.0.9' - - 'r-ggplot2 >3.3.6' + - r-ggfun >=0.1.7 + - r-ggplot2 >3.3.6 - r-magrittr - r-purrr - r-rlang - r-scales - r-tidyr - - 'r-tidytree >=0.4.5' - - r-yulab.utils + - r-tidytree >=0.4.5 + - r-yulab.utils >=0.1.6 + +source: + md5: b11dc775fba54bfb7674c8cedffe8f5c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'an R package for visualization of tree and annotation data' - description: '''ggtree'' extends the ''ggplot2'' plotting system which implemented the grammar of graphics. ''ggtree'' is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.' -extra: - identifiers: - - biotools:ggtree - - doi:10.1111/2041-210X.12628 - parent_recipe: - name: bioconductor-ggtree - path: recipes/bioconductor-ggtree - version: 1.12.7 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ggtreedendro/meta.yaml b/recipes/bioconductor-ggtreedendro/meta.yaml index 262bc36ce9821..12cdff6488583 100644 --- a/recipes/bioconductor-ggtreedendro/meta.yaml +++ b/recipes/bioconductor-ggtreedendro/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "ggtreeDendro" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e5839d466e08665eb2475a99fb74e833 +about: + description: Offers a set of 'autoplot' methods to visualize tree-like structures (e.g., hierarchical clustering and classification/regression trees) using 'ggtree'. You can adjust graphical parameters using grammar of graphic syntax and integrate external data to the tree. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Drawing 'dendrogram' using 'ggtree' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ggtreedendro", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: aplot, cluster, knitr, MASS, mdendro, prettydoc, pvclust, rmarkdown, testthat (>= 3.0.0), treeio, yulab.utils requirements: host: - - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - bioconductor-ggtree >=3.14.0,<3.15.0 - r-base - r-ggplot2 - r-tidytree run: - - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - bioconductor-ggtree >=3.14.0,<3.15.0 - r-base - r-ggplot2 - r-tidytree +source: + md5: defc1f45bc699d6ef9d433146de0c62d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Drawing ''dendrogram'' using ''ggtree''' - description: 'Offers a set of ''autoplot'' methods to visualize tree-like structures (e.g., hierarchical clustering and classification/regression trees) using ''ggtree''. You can adjust graphical parameters using grammar of graphic syntax and integrate external data to the tree.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ggtreeextra/meta.yaml b/recipes/bioconductor-ggtreeextra/meta.yaml index 43bbe1f1f6038..c5907bce485a5 100644 --- a/recipes/bioconductor-ggtreeextra/meta.yaml +++ b/recipes/bioconductor-ggtreeextra/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "ggtreeExtra" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: '''ggtreeExtra'' extends the method for mapping and visualizing associated data on phylogenetic tree using ''ggtree''. These associated data can be presented on the external panels to circular layout, fan layout, or other rectangular layout tree built by ''ggtree'' with the grammar of ''ggplot2''.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree" -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0bfd8a30c6fbd323763722927d30296a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ggtreeextra", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc, markdown, testthat (>= 3.0.0), pillar requirements: host: - - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - bioconductor-ggtree >=3.14.0,<3.15.0 - r-base - r-cli - r-ggnewscale - r-ggplot2 - r-magrittr - r-rlang - - 'r-tidytree >=0.3.9' + - r-tidytree >=0.3.9 run: - - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - bioconductor-ggtree >=3.14.0,<3.15.0 - r-base - r-cli - r-ggnewscale - r-ggplot2 - r-magrittr - r-rlang - - 'r-tidytree >=0.3.9' + - r-tidytree >=0.3.9 + +source: + md5: 986a039ba11b2062a7b4fdb4945d308e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"' - description: '''ggtreeExtra'' extends the method for mapping and visualizing associated data on phylogenetic tree using ''ggtree''. These associated data can be presented on the external panels to circular layout, fan layout, or other rectangular layout tree built by ''ggtree'' with the grammar of ''ggplot2''.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gigsea/meta.yaml b/recipes/bioconductor-gigsea/meta.yaml index 0e0d6eec70f7b..750326d9f2c55 100644 --- a/recipes/bioconductor-gigsea/meta.yaml +++ b/recipes/bioconductor-gigsea/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "GIGSEA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1325b20f84be334e607b7ebec7db0d07 +about: + description: We presented the Genotype-imputed Gene Set Enrichment Analysis (GIGSEA), a novel method that uses GWAS-and-eQTL-imputed trait-associated differential gene expression to interrogate gene set enrichment for the trait-associated SNPs. By incorporating eQTL from large gene expression studies, e.g. GTEx, GIGSEA appropriately addresses such challenges for SNP enrichment as gene size, gene boundary, SNP distal regulation, and multiple-marker regulation. The weighted linear regression model, taking as weights both imputation accuracy and model completeness, was used to perform the enrichment test, properly adjusting the bias due to redundancy in different gene sets. The permutation test, furthermore, is used to evaluate the significance of enrichment, whose efficiency can be largely elevated by expressing the computational intensive part in terms of large matrix operation. We have shown the appropriate type I error rates for GIGSEA (<5%), and the preliminary results also demonstrate its good performance to uncover the real signal. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Genotype Imputed Gene Set Enrichment Analysis build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gigsea", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: @@ -31,13 +30,14 @@ requirements: - r-locfdr - r-mass - r-matrix +source: + md5: 6be6e775cb39122d45921cfdb767abe3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'Genotype Imputed Gene Set Enrichment Analysis' - description: 'We presented the Genotype-imputed Gene Set Enrichment Analysis (GIGSEA), a novel method that uses GWAS-and-eQTL-imputed trait-associated differential gene expression to interrogate gene set enrichment for the trait-associated SNPs. By incorporating eQTL from large gene expression studies, e.g. GTEx, GIGSEA appropriately addresses such challenges for SNP enrichment as gene size, gene boundary, SNP distal regulation, and multiple-marker regulation. The weighted linear regression model, taking as weights both imputation accuracy and model completeness, was used to perform the enrichment test, properly adjusting the bias due to redundancy in different gene sets. The permutation test, furthermore, is used to evaluate the significance of enrichment, whose efficiency can be largely elevated by expressing the computational intensive part in terms of large matrix operation. We have shown the appropriate type I error rates for GIGSEA (<5%), and the preliminary results also demonstrate its good performance to uncover the real signal.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gigseadata/meta.yaml b/recipes/bioconductor-gigseadata/meta.yaml index 6430624693d11..8885aa3891a3e 100644 --- a/recipes/bioconductor-gigseadata/meta.yaml +++ b/recipes/bioconductor-gigseadata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "GIGSEAdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 470cdb6073d9af3d23056b55e6b8c98d +about: + description: The gene set collection used for the GIGSEA package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Gene set collections for the GIGSEA package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gigseadata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GIGSEA, knitr, rmarkdown requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d4b48ce5a328de15cf771451f9d89c51 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL-3 - summary: 'Gene set collections for the GIGSEA package' - description: 'The gene set collection used for the GIGSEA package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gigseadata/post-link.sh b/recipes/bioconductor-gigseadata/post-link.sh index ee46d067c6e87..19393bb87b6ee 100644 --- a/recipes/bioconductor-gigseadata/post-link.sh +++ b/recipes/bioconductor-gigseadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gigseadata-1.20.0" +installBiocDataPackage.sh "gigseadata-1.24.0" diff --git a/recipes/bioconductor-girafe/meta.yaml b/recipes/bioconductor-girafe/meta.yaml index 4ce52be365f1b..af3314713c3e4 100644 --- a/recipes/bioconductor-girafe/meta.yaml +++ b/recipes/bioconductor-girafe/meta.yaml @@ -1,68 +1,76 @@ -{% set version = "1.54.0" %} +{% set version = "1.58.0" %} {% set name = "girafe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package 'girafe' deals with the genome-level representation of aligned reads from next-generation sequencing data. It contains an object class for enabling a detailed description of genome intervals with aligned reads and functions for comparing, visualising, exporting and working with such intervals and the aligned reads. As such, the package interacts with and provides a link between the packages ShortRead, IRanges and genomeIntervals. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome Intervals and Read Alignments for Functional Exploration -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4cf228e6d7f73cf97c923f1c349fb6c3 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-girafe", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:girafe + parent_recipe: + name: bioconductor-girafe + path: recipes/bioconductor-girafe + version: 1.32.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: MASS, org.Mm.eg.db, RColorBrewer requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeintervals >=1.58.0,<1.59.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeintervals >=1.62.0,<1.63.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - - 'r-intervals >=0.13.1' + - r-intervals >=0.13.1 - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeintervals >=1.58.0,<1.59.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeintervals >=1.62.0,<1.63.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - - 'r-intervals >=0.13.1' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-intervals >=0.13.1 + +source: + md5: 6f0e15954795e581f61d6f2ae3a04dc3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome Intervals and Read Alignments for Functional Exploration' - description: 'The package ''girafe'' deals with the genome-level representation of aligned reads from next-generation sequencing data. It contains an object class for enabling a detailed description of genome intervals with aligned reads and functions for comparing, visualising, exporting and working with such intervals and the aligned reads. As such, the package interacts with and provides a link between the packages ShortRead, IRanges and genomeIntervals.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:girafe - parent_recipe: - name: bioconductor-girafe - path: recipes/bioconductor-girafe - version: 1.32.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-glad/build.sh b/recipes/bioconductor-glad/build.sh index c74d5641a31dc..4ba3ceccbf2e6 100644 --- a/recipes/bioconductor-glad/build.sh +++ b/recipes/bioconductor-glad/build.sh @@ -9,4 +9,4 @@ CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars sed -i.bak 's/^ac_unique_file="GLAD"/ac_unique_file="NAMESPACE"/' configure -$R CMD INSTALL --build --configure-vars='GSL_LIBS="-L$PREFIX/lib -lgsl -lgslcblas -lm"' . \ No newline at end of file +$R CMD INSTALL --build --configure-vars='GSL_LIBS="-L$PREFIX/lib -lgsl -lgslcblas -lm"' . diff --git a/recipes/bioconductor-glad/meta.yaml b/recipes/bioconductor-glad/meta.yaml index 98a43342fbfd0..d7a606d38e4b2 100644 --- a/recipes/bioconductor-glad/meta.yaml +++ b/recipes/bioconductor-glad/meta.yaml @@ -1,25 +1,32 @@ -{% set version = "2.66.0" %} +{% set version = "2.70.0" %} {% set name = "GLAD" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Gain and Loss Analysis of DNA -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f222e07624fb8b1c4780a4960b0f2008 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-glad", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # SystemRequirements: gsl. Note: users should have GSL installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'. requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - r-aws - r-base @@ -30,18 +37,16 @@ requirements: - r-aws - r-base - gsl - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 913c405c4a653fa34c64f72750ed95b4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Gain and Loss Analysis of DNA' - description: 'Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gladiatox/meta.yaml b/recipes/bioconductor-gladiatox/meta.yaml index 75bf22493ac9e..6ce2b9bee460a 100644 --- a/recipes/bioconductor-gladiatox/meta.yaml +++ b/recipes/bioconductor-gladiatox/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "GladiaTOX" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'GladiaTOX R package is an open-source, flexible solution to high-content screening data processing and reporting in biomedical research. GladiaTOX takes advantage of the tcpl core functionalities and provides a number of extensions: it provides a web-service solution to fetch raw data; it computes severity scores and exports ToxPi formatted files; furthermore it contains a suite of functionalities to generate pdf reports for quality control and data processing.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: R Package for Processing High Content Screening data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8affcce15bf1f5e9d03220e0de3fbe9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gladiatox", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: roxygen2, knitr, rmarkdown, testthat, BiocStyle requirements: host: - r-base - r-brew - - 'r-data.table >=1.9.4' + - r-data.table >=1.9.4 - r-dbi - r-ggplot2 - r-ggrepel @@ -41,7 +43,7 @@ requirements: run: - r-base - r-brew - - 'r-data.table >=1.9.4' + - r-data.table >=1.9.4 - r-dbi - r-ggplot2 - r-ggrepel @@ -55,13 +57,16 @@ requirements: - r-tidyr - r-xml - r-xtable + +source: + md5: 9d9290cf476a663e129f6032813f8b94 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'R Package for Processing High Content Screening data' - description: 'GladiaTOX R package is an open-source, flexible solution to high-content screening data processing and reporting in biomedical research. GladiaTOX takes advantage of the tcpl core functionalities and provides a number of extensions: it provides a web-service solution to fetch raw data; it computes severity scores and exports ToxPi formatted files; furthermore it contains a suite of functionalities to generate pdf reports for quality control and data processing.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-glimma/meta.yaml b/recipes/bioconductor-glimma/meta.yaml index 32dc9bba1cbf7..9a3a15bde081a 100644 --- a/recipes/bioconductor-glimma/meta.yaml +++ b/recipes/bioconductor-glimma/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "2.12.0" %} +{% set version = "2.16.0" %} {% set name = "Glimma" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package produces interactive visualizations for RNA-seq data analysis, utilizing output from limma, edgeR, or DESeq2. It produces interactive htmlwidgets versions of popular RNA-seq analysis plots to enhance the exploration of analysis results by overlaying interactive features. The plots can be viewed in a web browser or embedded in notebook documents. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Interactive visualizations for gene expression analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bea9aeee00dca519586661d33ba8dc74 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-glimma", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:glimma + - doi:10.1101/096107 + parent_recipe: + name: bioconductor-glimma + path: recipes/bioconductor-glimma + version: 1.8.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocStyle, IRanges, GenomicRanges, pryr, AnnotationHub, scRNAseq, scater, scran requirements: host: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-htmlwidgets - r-jsonlite run: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-htmlwidgets - r-jsonlite + +source: + md5: da67376f1be85c53ee7e1063972246c0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Interactive visualizations for gene expression analysis' - description: 'This package produces interactive visualizations for RNA-seq data analysis, utilizing output from limma, edgeR, or DESeq2. It produces interactive htmlwidgets versions of popular RNA-seq analysis plots to enhance the exploration of analysis results by overlaying interactive features. The plots can be viewed in a web browser or embedded in notebook documents.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:glimma - - doi:10.1101/096107 - parent_recipe: - name: bioconductor-glimma - path: recipes/bioconductor-glimma - version: 1.8.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-glmgampoi/meta.yaml b/recipes/bioconductor-glmgampoi/meta.yaml index 68d5da5ce2f73..4d7ffa622ba70 100644 --- a/recipes/bioconductor-glmgampoi/meta.yaml +++ b/recipes/bioconductor-glmgampoi/meta.yaml @@ -1,35 +1,42 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "glmGamPoi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Fit linear models to overdispersed count data. The package can estimate the overdispersion and fit repeated models for matrix input. It is designed to handle large input datasets as they typically occur in single cell RNA-seq experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Fit a Gamma-Poisson Generalized Linear Model -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ff74c3d78a7edc7d0a5f4521f7c5b9b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-glmgampoi", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, beachmat, MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown, BiocStyle, TENxPBMCData, muscData, scran, Matrix, dplyr # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrixstats - r-rcpp @@ -39,31 +46,31 @@ requirements: - libblas - liblapack run: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrixstats - r-rcpp - r-rcpparmadillo - r-rlang - r-vctrs - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: f223a16caa055e19d88568b362065c24 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Fit a Gamma-Poisson Generalized Linear Model' - description: 'Fit linear models to overdispersed count data. The package can estimate the overdispersion and fit repeated models for matrix input. It is designed to handle large input datasets as they typically occur in single cell RNA-seq experiments.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-glmsparsenet/meta.yaml b/recipes/bioconductor-glmsparsenet/meta.yaml index b0bfedfe3022a..36977b6ae4133 100644 --- a/recipes/bioconductor-glmsparsenet/meta.yaml +++ b/recipes/bioconductor-glmsparsenet/meta.yaml @@ -1,71 +1,76 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "glmSparseNet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: glmSparseNet is an R-package that generalizes sparse regression models when the features (e.g. genes) have a graph structure (e.g. protein-protein interactions), by including network-based regularizers. glmSparseNet uses the glmnet R-package, by including centrality measures of the network as penalty weights in the regularization. The current version implements regularization based on node degree, i.e. the strength and/or number of its associated edges, either by promoting hubs in the solution or orphan genes in the solution. All the glmnet distribution families are supported, namely "gaussian", "poisson", "binomial", "multinomial", "cox", and "mgaussian". + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Network Centrality Metrics for Elastic-Net Regularized Models -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b029a96bf3a653a8a3c24d764c841512 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-glmsparsenet", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, knitr, rmarkdown, survival, survcomp, pROC, VennDiagram, BiocStyle, curatedTCGAData, TCGAutils + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, curatedTCGAData, knitr, magrittr, reshape2, pROC, rmarkdown, survival, testthat, VennDiagram, withr requirements: host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tcgautils >=1.26.0,<1.27.0 - r-base - - r-digest + - r-checkmate - r-dplyr - r-forcats - r-futile.logger - - r-futile.options - r-ggplot2 - r-glmnet - r-glue - r-httr + - r-lifecycle - r-matrix - r-readr - - r-reshape2 - - r-stringr + - r-rlang - r-survminer run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tcgautils >=1.26.0,<1.27.0 - r-base - - r-digest + - r-checkmate - r-dplyr - r-forcats - r-futile.logger - - r-futile.options - r-ggplot2 - r-glmnet - r-glue - r-httr + - r-lifecycle - r-matrix - r-readr - - r-reshape2 - - r-stringr + - r-rlang - r-survminer + +source: + md5: d853ca6bb133d5c7f64ed46a73712a76 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Network Centrality Metrics for Elastic-Net Regularized Models' - description: 'glmSparseNet is an R-package that generalizes sparse regression models when the features (e.g. genes) have a graph structure (e.g. protein-protein interactions), by including network-based regularizers. glmSparseNet uses the glmnet R-package, by including centrality measures of the network as penalty weights in the regularization. The current version implements regularization based on node degree, i.e. the strength and/or number of its associated edges, either by promoting hubs in the solution or orphan genes in the solution. All the glmnet distribution families are supported, namely "gaussian", "poisson", "binomial", "multinomial", "cox", and "mgaussian".' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-globalancova/meta.yaml b/recipes/bioconductor-globalancova/meta.yaml index 84aa7d322bd84..213d22552b541 100644 --- a/recipes/bioconductor-globalancova/meta.yaml +++ b/recipes/bioconductor-globalancova/meta.yaml @@ -1,31 +1,45 @@ -{% set version = "4.20.0" %} +{% set version = "4.24.0" %} {% set name = "GlobalAncova" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The association between a variable of interest (e.g. two groups) and the global pattern of a group of variables (e.g. a gene set) is tested via a global F-test. We give the following arguments in support of the GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. The framework is generalized to groups of categorical variables or even mixed data by a likelihood ratio approach. Closed and hierarchical testing procedures are supported. This work was supported by the NGFN grant 01 GR 0459, BMBF, Germany and BMBF grant 01ZX1309B, Germany.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Global test for groups of variables via model comparisons -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4fcc19ebc2bba1f610912cde1745b549 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-globalancova", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:globalancova + - doi:10.1093/bioinformatics/btm531 + parent_recipe: + name: bioconductor-globalancova + path: recipes/bioconductor-globalancova + version: 3.48.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: GO.db, golubEsets, hu6800.db, vsn, Rgraphviz requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-globaltest >=5.56.0,<5.57.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-globaltest >=5.60.0,<5.61.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 - r-base - r-corpcor - r-dendextend @@ -33,33 +47,25 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-globaltest >=5.56.0,<5.57.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-globaltest >=5.60.0,<5.61.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 - r-base - r-corpcor - r-dendextend - r-vgam - build: - - {{ compiler('c') }} - - make + +source: + md5: ae770156a4d068a5e444bcf05271d78c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Global test for groups of variables via model comparisons' - description: 'The association between a variable of interest (e.g. two groups) and the global pattern of a group of variables (e.g. a gene set) is tested via a global F-test. We give the following arguments in support of the GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. The framework is generalized to groups of categorical variables or even mixed data by a likelihood ratio approach. Closed and hierarchical testing procedures are supported. This work was supported by the NGFN grant 01 GR 0459, BMBF, Germany and BMBF grant 01ZX1309B, Germany.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:globalancova - - doi:10.1093/bioinformatics/btm531 - parent_recipe: - name: bioconductor-globalancova - path: recipes/bioconductor-globalancova - version: 3.48.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-globalseq/meta.yaml b/recipes/bioconductor-globalseq/meta.yaml index 0d5af193580c1..a50e15362e587 100644 --- a/recipes/bioconductor-globalseq/meta.yaml +++ b/recipes/bioconductor-globalseq/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "globalSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b427214cf1345b8d75ba69dc02adb77 +about: + description: The method may be conceptualised as a test of overall significance in regression analysis, where the response variable is overdispersed and the number of explanatory variables exceeds the sample size. Useful for testing for association between RNA-Seq and high-dimensional data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Global Test for Counts build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-globalseq", max_pin="x.x") }}' - noarch: generic +extra: + identifiers: + - biotools:globalseq + parent_recipe: + name: bioconductor-globalseq + path: recipes/bioconductor-globalseq + version: 1.10.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, testthat, SummarizedExperiment, S4Vectors requirements: host: - r-base run: - r-base +source: + md5: 65ec70596f293b700433848c14244e81 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Global Test for Counts' - description: 'The method may be conceptualised as a test of overall significance in regression analysis, where the response variable is overdispersed and the number of explanatory variables exceeds the sample size. Useful for testing for association between RNA-Seq and high-dimensional data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:globalseq - parent_recipe: - name: bioconductor-globalseq - path: recipes/bioconductor-globalseq - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-globaltest/meta.yaml b/recipes/bioconductor-globaltest/meta.yaml index 7cd5098ec0714..7340dad6ef1bf 100644 --- a/recipes/bioconductor-globaltest/meta.yaml +++ b/recipes/bioconductor-globaltest/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "5.56.0" %} +{% set version = "5.60.0" %} {% set name = "globaltest" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The global test tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ca389a7105fc08bc6172ce755d842a31 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-globaltest", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:globaltest + parent_recipe: + name: bioconductor-globaltest + path: recipes/bioconductor-globaltest + version: 5.34.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: vsn, golubEsets, KEGGREST, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS, boot, rpart, mstate requirements: host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-survival run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-survival + +source: + md5: 99e16f9e75e03abff0577483bf09feba + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing' - description: 'The global test tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:globaltest - parent_recipe: - name: bioconductor-globaltest - path: recipes/bioconductor-globaltest - version: 5.34.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gloscope/meta.yaml b/recipes/bioconductor-gloscope/meta.yaml index c2c78a32218ab..d7d0cc9ca6045 100644 --- a/recipes/bioconductor-gloscope/meta.yaml +++ b/recipes/bioconductor-gloscope/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "GloScope" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package aims at representing and summarizing the entire single-cell profile of a sample. It allows researchers to perform important bioinformatic analyses at the sample-level such as visualization and quality control. The main functions Estimate sample distribution and calculate statistical divergence among samples, and visualize the distance matrix through MDS plots. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Population-level Representation on scRNA-Seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 00ab18ecdd0a5768690b841f2f2448e5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gloscope", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown, zellkonverter requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-fnn - r-ggplot2 @@ -33,8 +34,8 @@ requirements: - r-rann - r-rlang run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-fnn - r-ggplot2 @@ -43,12 +44,16 @@ requirements: - r-mvnfast - r-rann - r-rlang + +source: + md5: b1936d66de98c5249f5d5b3fd02e9ec3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Population-level Representation on scRNA-Seq data' - description: 'This package aims at representing and summarizing the entire single-cell profile of a sample. It allows researchers to perform important bioinformatic analyses at the sample-level such as visualization and quality control. The main functions Estimate sample distribution and calculate statistical divergence among samples, and visualize the distance matrix through MDS plots.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gmapr/build.sh b/recipes/bioconductor-gmapr/build.sh index 3c9546c924fe5..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gmapr/build.sh +++ b/recipes/bioconductor-gmapr/build.sh @@ -8,6 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -# Remove object files (if present) that should not be in the source tarball -rm -f src/samtools/*.[oa] $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gmapr/build_failure.linux-aarch64.yaml b/recipes/bioconductor-gmapr/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..b865b708805bc --- /dev/null +++ b/recipes/bioconductor-gmapr/build_failure.linux-aarch64.yaml @@ -0,0 +1,107 @@ +recipe_sha: b2d5e4755a159055f9b727e022dfec5dd0019e3404a04a019e679afc9fca3cd4 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + /bin/sh ../libtool --tag=CC --mode=compile $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -DHAVE_CONFIG_H -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -pthread -I. -fPIC -DTARGET=\"aarch64-conda-linux-gnu\" -DGMAPDB=\"$SRC_DIR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tally.lo -MD -MP -MF .deps/libgstruct_1.0_la-tally.Tpo -c -o libgstruct_1.0_la-tally.lo test -f 'tally.c' || echo './'tally.c + libtool: compile: $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -DHAVE_CONFIG_H -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -pthread -I. -fPIC -DTARGET=\"aarch64-conda-linux-gnu\" -DGMAPDB=\"$SRC_DIR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tally.lo -MD -MP -MF .deps/libgstruct_1.0_la-tally.Tpo -c tally.c -o libgstruct_1.0_la-tally.o + mv -f .deps/libgstruct_1.0_la-tally.Tpo .deps/libgstruct_1.0_la-tally.Plo + /bin/sh ../libtool --tag=CC --mode=compile $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -DHAVE_CONFIG_H -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -pthread -I. -fPIC -DTARGET=\"aarch64-conda-linux-gnu\" -DGMAPDB=\"$SRC_DIR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c -o libgstruct_1.0_la-translation.lo test -f 'translation.c' || echo './'translation.c + libtool: compile: $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -DHAVE_CONFIG_H -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -pthread -I. -fPIC -DTARGET=\"aarch64-conda-linux-gnu\" -DGMAPDB=\"$SRC_DIR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c translation.c -o libgstruct_1.0_la-translation.o + mv -f .deps/libgstruct_1.0_la-translation.Tpo .deps/libgstruct_1.0_la-translation.Plo + /bin/sh ../libtool --tag=CC --mode=compile $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -DHAVE_CONFIG_H -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -pthread -I. -fPIC -DTARGET=\"aarch64-conda-linux-gnu\" -DGMAPDB=\"$SRC_DIR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-expr.lo -MD -MP -MF .deps/libgstruct_1.0_la-expr.Tpo -c -o libgstruct_1.0_la-expr.lo test -f 'expr.c' || echo './'expr.c + libtool: compile: $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -DHAVE_CONFIG_H -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -pthread -I. -fPIC -DTARGET=\"aarch64-conda-linux-gnu\" -DGMAPDB=\"$SRC_DIR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-expr.lo -MD -MP -MF .deps/libgstruct_1.0_la-expr.Tpo -c expr.c -o libgstruct_1.0_la-expr.o + mv -f .deps/libgstruct_1.0_la-expr.Tpo .deps/libgstruct_1.0_la-expr.Plo + /bin/sh ../libtool --tag=CC --mode=compile $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -DHAVE_CONFIG_H -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -pthread -I. -fPIC -DTARGET=\"aarch64-conda-linux-gnu\" -DGMAPDB=\"$SRC_DIR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c -o libgstruct_1.0_la-bamtally.lo test -f 'bamtally.c' || echo './'bamtally.c + libtool: compile: $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -DHAVE_CONFIG_H -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -pthread -I. -fPIC -DTARGET=\"aarch64-conda-linux-gnu\" -DGMAPDB=\"$SRC_DIR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c bamtally.c -o libgstruct_1.0_la-bamtally.o + mv -f .deps/libgstruct_1.0_la-bamtally.Tpo .deps/libgstruct_1.0_la-bamtally.Plo + /bin/sh ../libtool --tag=CC --mode=compile $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -DHAVE_CONFIG_H -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -pthread -I. -fPIC -DTARGET=\"aarch64-conda-linux-gnu\" -DGMAPDB=\"$SRC_DIR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-datadir.lo -MD -MP -MF .deps/libgstruct_1.0_la-datadir.Tpo -c -o libgstruct_1.0_la-datadir.lo test -f 'datadir.c' || echo './'datadir.c + libtool: compile: $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -DHAVE_CONFIG_H -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -pthread -I. -fPIC -DTARGET=\"aarch64-conda-linux-gnu\" -DGMAPDB=\"$SRC_DIR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-datadir.lo -MD -MP -MF .deps/libgstruct_1.0_la-datadir.Tpo -c datadir.c -o libgstruct_1.0_la-datadir.o + mv -f .deps/libgstruct_1.0_la-datadir.Tpo .deps/libgstruct_1.0_la-datadir.Plo + /bin/sh ../libtool --tag=CC --mode=link $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -pthread -I. -fPIC -DTARGET=\"aarch64-conda-linux-gnu\" -DGMAPDB=\"$SRC_DIR/src/../inst/usr/share\" -g -O3 -pthread -version-info 1:0:0 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -o libgstruct-1.0.la -rpath $SRC_DIR/src/../inst/usr/lib libgstruct_1.0_la-except.lo libgstruct_1.0_la-assert.lo libgstruct_1.0_la-mem.lo libgstruct_1.0_la-intlist.lo libgstruct_1.0_la-list.lo libgstruct_1.0_la-littleendian.lo libgstruct_1.0_la-bigendian.lo libgstruct_1.0_la-interval.lo libgstruct_1.0_la-uintlist.lo libgstruct_1.0_la-stopwatch.lo libgstruct_1.0_la-access.lo libgstruct_1.0_la-iit-read.lo libgstruct_1.0_la-chrom.lo libgstruct_1.0_la-genomicpos.lo libgstruct_1.0_la-md5.lo libgstruct_1.0_la-sequence.lo libgstruct_1.0_la-genome.lo libgstruct_1.0_la-uinttable.lo libgstruct_1.0_la-table.lo libgstruct_1.0_la-chrnum.lo libgstruct_1.0_la-bamread.lo libgstruct_1.0_la-samread.lo libgstruct_1.0_la-parserange.lo libgstruct_1.0_la-tableuint.lo libgstruct_1.0_la-iit-write.lo libgstruct_1.0_la-ucharlist.lo libgstruct_1.0_la-matchpool.lo libgstruct_1.0_la-mismatchpool.lo libgstruct_1.0_la-tally.lo libgstruct_1.0_la-translation.lo libgstruct_1.0_la-expr.lo libgstruct_1.0_la-bamtally.lo libgstruct_1.0_la-datadir.lo -lz -lm + libtool: link: aarch64-conda-linux-gnu-ar cru .libs/libgstruct-1.0.a libgstruct_1.0_la-except.o libgstruct_1.0_la-assert.o libgstruct_1.0_la-mem.o libgstruct_1.0_la-intlist.o libgstruct_1.0_la-list.o libgstruct_1.0_la-littleendian.o libgstruct_1.0_la-bigendian.o libgstruct_1.0_la-interval.o libgstruct_1.0_la-uintlist.o libgstruct_1.0_la-stopwatch.o libgstruct_1.0_la-access.o libgstruct_1.0_la-iit-read.o libgstruct_1.0_la-chrom.o libgstruct_1.0_la-genomicpos.o libgstruct_1.0_la-md5.o libgstruct_1.0_la-sequence.o libgstruct_1.0_la-genome.o libgstruct_1.0_la-uinttable.o libgstruct_1.0_la-table.o libgstruct_1.0_la-chrnum.o libgstruct_1.0_la-bamread.o libgstruct_1.0_la-samread.o libgstruct_1.0_la-parserange.o libgstruct_1.0_la-tableuint.o libgstruct_1.0_la-iit-write.o libgstruct_1.0_la-ucharlist.o libgstruct_1.0_la-matchpool.o libgstruct_1.0_la-mismatchpool.o libgstruct_1.0_la-tally.o libgstruct_1.0_la-translation.o libgstruct_1.0_la-expr.o libgstruct_1.0_la-bamtally.o libgstruct_1.0_la-datadir.o + libtool: link: aarch64-conda-linux-gnu-ranlib .libs/libgstruct-1.0.a + libtool: link: ( cd ".libs" && rm -f "libgstruct-1.0.la" && ln -s "../libgstruct-1.0.la" "libgstruct-1.0.la" ) + make[3]: Entering directory '$SRC_DIR/src/gstruct/src' + /usr/bin/mkdir -p '$SRC_DIR/src/../inst/usr/lib' + /bin/sh ../libtool --mode=install /usr/bin/install -c libgstruct-1.0.la '$SRC_DIR/src/../inst/usr/lib' + libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.lai $SRC_DIR/src/../inst/usr/lib/libgstruct-1.0.la + libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.a $SRC_DIR/src/../inst/usr/lib/libgstruct-1.0.a + libtool: install: chmod 644 $SRC_DIR/src/../inst/usr/lib/libgstruct-1.0.a + libtool: install: aarch64-conda-linux-gnu-ranlib $SRC_DIR/src/../inst/usr/lib/libgstruct-1.0.a + libtool: finish: PATH="$BUILD_PREFIX/bin:$PREFIX/bin:/opt/conda/condabin:$BUILD_PREFIX/bin:$PREFIX/bin:/opt/conda/bin:/opt/conda/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/conda/bin:/sbin" ldconfig -n $SRC_DIR/src/../inst/usr/lib + ---------------------------------------------------------------------- + Libraries have been installed in: + $SRC_DIR/src/../inst/usr/lib + + If you ever happen to want to link against installed libraries + in a given directory, LIBDIR, you must either use libtool, and + specify the full pathname of the library, or use the '-LLIBDIR' + flag during linking and do at least one of the following: + - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable + during execution + - add LIBDIR to the 'LD_RUN_PATH' environment variable + during linking + - use the '-Wl,-rpath -Wl,LIBDIR' linker flag + - have your system administrator add LIBDIR to '/etc/ld.so.conf' + + See any operating system documentation about shared libraries for + more information, such as the ld(1) and ld.so(8) manual pages. + ---------------------------------------------------------------------- + /usr/bin/mkdir -p '$SRC_DIR/src/../inst/usr/include/gstruct' + /usr/bin/install -c -m 644 config.h fopen.h bool.h types.h except.h assert.h mem.h intlistdef.h intlist.h listdef.h list.h littleendian.h bigendian.h interval.h uintlist.h stopwatch.h access.h iitdef.h iit-read.h chrom.h genomicpos.h md5.h complement.h sequence.h genome.h uinttable.h table.h chrnum.h bamread.h samread.h parserange.h dynprog.h dynprog_nogap.h dynprog_simd.h dynprog_cigar.h dynprog_single.h tableuint.h iit-write.h ucharlist.h matchdef.h '$SRC_DIR/src/../inst/usr/include/gstruct' + /usr/bin/install -c -m 644 matchpool.h mismatchdef.h mismatchpool.h tally.h translation.h bamtally.h datadir.h '$SRC_DIR/src/../inst/usr/include/gstruct' + /usr/bin/mkdir -p '$SRC_DIR/src/../inst/usr/lib/pkgconfig' + /usr/bin/install -c -m 644 ../lib/gstruct-1.0.pc '$SRC_DIR/src/../inst/usr/lib/pkgconfig' + make[3]: Leaving directory '$SRC_DIR/src/gstruct/src' + make[2]: Leaving directory '$SRC_DIR/src/gstruct/src' + make[2]: Entering directory '$SRC_DIR/src/gstruct' + make[3]: Entering directory '$SRC_DIR/src/gstruct' + make[3]: Nothing to be done for 'install-exec-am'. + make[3]: Nothing to be done for 'install-data-am'. + make[3]: Leaving directory '$SRC_DIR/src/gstruct' + make[2]: Leaving directory '$SRC_DIR/src/gstruct' + make[1]: Leaving directory '$SRC_DIR/src/gstruct' + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -I$SRC_DIR/src/../inst/usr/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fPIC -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433516836/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c bamreader.c -o bamreader.o + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -I$SRC_DIR/src/../inst/usr/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fPIC -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433516836/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c bamtally.c -o bamtally.o + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -I$SRC_DIR/src/../inst/usr/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fPIC -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433516836/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c iit.c -o iit.o + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -I$SRC_DIR/src/../inst/usr/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fPIC -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433516836/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c variantsummary.c -o variantsummary.o + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -I$SRC_DIR/src/../inst/usr/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fPIC -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433516836/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c genome.c -o genome.o + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -I$SRC_DIR/src/../inst/usr/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fPIC -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433516836/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c R_init_gmapR.c -o R_init_gmapR.o + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -shared -L"$PREFIX/lib/R/lib" -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -o gmapR.so bamreader.o bamtally.o iit.o variantsummary.o genome.o R_init_gmapR.o $SRC_DIR/src/../inst/usr/lib/libgstruct-1.0.a samtools/libbam.a -lz -L"$PREFIX/lib/R/lib" -lR + /opt/conda/conda-bld/bioconductor-gmapr_1736171878032/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: samtools/libbam.a(bgzf.o): Relocations in generic ELF (EM: 62) + /opt/conda/conda-bld/bioconductor-gmapr_1736171878032/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: samtools/libbam.a(bgzf.o): Relocations in generic ELF (EM: 62) + /opt/conda/conda-bld/bioconductor-gmapr_1736171878032/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: samtools/libbam.a(bgzf.o): Relocations in generic ELF (EM: 62) + /opt/conda/conda-bld/bioconductor-gmapr_1736171878032/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: samtools/libbam.a(bgzf.o): Relocations in generic ELF (EM: 62) + /opt/conda/conda-bld/bioconductor-gmapr_1736171878032/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: samtools/libbam.a(bgzf.o): Relocations in generic ELF (EM: 62) + /opt/conda/conda-bld/bioconductor-gmapr_1736171878032/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: samtools/libbam.a(bgzf.o): Relocations in generic ELF (EM: 62) + /opt/conda/conda-bld/bioconductor-gmapr_1736171878032/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: samtools/libbam.a: error adding symbols: file in wrong format + collect2: error: ld returned 1 exit status + make: *** [Makefile:37: gmapR.so] Error 1 + ERROR: compilation failed for package gmapR + * removing /opt/conda/conda-bld/bioconductor-gmapr_1736171878032/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/R/library/gmapR + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-gmapr_1736171878032/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-gmapr_1736171878032/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + compiler error +reason: samtools/libbam.a error adding symbols file in wrong format diff --git a/recipes/bioconductor-gmapr/build_failure.osx-64.yaml b/recipes/bioconductor-gmapr/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..683ca42b0871d --- /dev/null +++ b/recipes/bioconductor-gmapr/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: b2d5e4755a159055f9b727e022dfec5dd0019e3404a04a019e679afc9fca3cd4 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + make[3]: Entering directory '$SRC_DIR/src/gmap/src' + ../config/install-sh -c -d '$SRC_DIR/src/../inst/usr/bin' + /bin/sh ../libtool --mode=install /usr/bin/install -c gmap gmapl get-genome gmapindex iit_store iit_get iit_dump gsnap gsnapl uniqscan uniqscanl snpindex cmetindex atoiindex '$SRC_DIR/src/../inst/usr/bin' + libtool: install: /usr/bin/install -c gmap $SRC_DIR/src/../inst/usr/bin/gmap + libtool: install: /usr/bin/install -c gmapl $SRC_DIR/src/../inst/usr/bin/gmapl + libtool: install: /usr/bin/install -c get-genome $SRC_DIR/src/../inst/usr/bin/get-genome + libtool: install: /usr/bin/install -c gmapindex $SRC_DIR/src/../inst/usr/bin/gmapindex + libtool: install: /usr/bin/install -c iit_store $SRC_DIR/src/../inst/usr/bin/iit_store + sys.exit(execute()) + libtool: install: /usr/bin/install -c iit_get $SRC_DIR/src/../inst/usr/bin/iit_get + libtool: install: /usr/bin/install -c iit_dump $SRC_DIR/src/../inst/usr/bin/iit_dump + libtool: install: /usr/bin/install -c gsnap $SRC_DIR/src/../inst/usr/bin/gsnap + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + libtool: install: /usr/bin/install -c gsnapl $SRC_DIR/src/../inst/usr/bin/gsnapl + libtool: install: /usr/bin/install -c uniqscan $SRC_DIR/src/../inst/usr/bin/uniqscan + libtool: install: /usr/bin/install -c uniqscanl $SRC_DIR/src/../inst/usr/bin/uniqscanl + libtool: install: /usr/bin/install -c snpindex $SRC_DIR/src/../inst/usr/bin/snpindex + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + libtool: install: /usr/bin/install -c cmetindex $SRC_DIR/src/../inst/usr/bin/cmetindex + return build_tree( + libtool: install: /usr/bin/install -c atoiindex $SRC_DIR/src/../inst/usr/bin/atoiindex + make[3]: Nothing to be done for 'install-data-am'. + make[3]: Leaving directory '$SRC_DIR/src/gmap/src' + make[2]: Leaving directory '$SRC_DIR/src/gmap/src' + Making install in util + make[2]: Entering directory '$SRC_DIR/src/gmap/util' + cp gmap_compress.pl gmap_compress + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + chmod x gmap_compress + cp gmap_uncompress.pl gmap_uncompress + chmod x gmap_uncompress + cp gmap_process.pl gmap_process + chmod x gmap_process + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-gmapr_1735858995018/work/conda_build.sh']' returned non-zero exit status 1. + cp gmap_setup.pl gmap_setup + chmod x gmap_setup + cp gmap_build.pl gmap_build + chmod x gmap_build + cp gmap_reassemble.pl gmap_reassemble + chmod x gmap_reassemble + cp md_coords.pl md_coords + chmod x md_coords + cp fa_coords.pl fa_coords + chmod x fa_coords + cp psl_splicesites.pl psl_splicesites + chmod x psl_splicesites + cp psl_introns.pl psl_introns + chmod x psl_introns + cp psl_genes.pl psl_genes + chmod x psl_genes + cp gtf_splicesites.pl gtf_splicesites + chmod x gtf_splicesites + cp gtf_introns.pl gtf_introns + chmod x gtf_introns + cp gtf_genes.pl gtf_genes + chmod x gtf_genes + cp gff3_splicesites.pl gff3_splicesites + chmod x gff3_splicesites + cp gff3_introns.pl gff3_introns + chmod x gff3_introns + cp gff3_genes.pl gff3_genes + chmod x gff3_genes + cp dbsnp_iit.pl dbsnp_iit + chmod x dbsnp_iit + cp gvf_iit.pl gvf_iit + chmod x gvf_iit + cp vcf_iit.pl vcf_iit + chmod x vcf_iit + make[3]: Entering directory '$SRC_DIR/src/gmap/util' + ../config/install-sh -c -d '$SRC_DIR/src/../inst/usr/bin' + /usr/bin/install -c gmap_compress gmap_uncompress gmap_process gmap_setup gmap_build gmap_reassemble md_coords fa_coords psl_splicesites psl_introns psl_genes gtf_splicesites gtf_introns gtf_genes gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '$SRC_DIR/src/../inst/usr/bin' + make[3]: Nothing to be done for 'install-data-am'. + make[3]: Leaving directory '$SRC_DIR/src/gmap/util' + make[2]: Leaving directory '$SRC_DIR/src/gmap/util' + Making install in tests + make[2]: Entering directory '$SRC_DIR/src/gmap/tests' + make[3]: Entering directory '$SRC_DIR/src/gmap/tests' + make[3]: Nothing to be done for 'install-exec-am'. + make[3]: Nothing to be done for 'install-data-am'. + make[3]: Leaving directory '$SRC_DIR/src/gmap/tests' + make[2]: Leaving directory '$SRC_DIR/src/gmap/tests' + make[2]: Entering directory '$SRC_DIR/src/gmap' + make[3]: Entering directory '$SRC_DIR/src/gmap' + make[3]: Nothing to be done for 'install-exec-am'. + make[3]: Nothing to be done for 'install-data-am'. + make[3]: Leaving directory '$SRC_DIR/src/gmap' + make[2]: Leaving directory '$SRC_DIR/src/gmap' + make[1]: Leaving directory '$SRC_DIR/src/gmap' + Creating a generic function from function directory in package gmapR + Creating a generic function for bamPaths from package Rsamtools in package gmapR + Note: ... may be used in an incorrect context + Error: package or namespace load failed for gmapR in dyn.load(file, DLLpath = DLLpath, ...): + unable to load shared object '$PREFIX/lib/R/library/00LOCK-work/00new/gmapR/libs/gmapR.so': + dlopen($PREFIX/lib/R/library/00LOCK-work/00new/gmapR/libs/gmapR.so, 0x0006): symbol not found in flat namespace '_bam_aux2A' + Error: loading failed + Execution halted +# Last 100 lines of the build log. +category: |- + test failure diff --git a/recipes/bioconductor-gmapr/meta.yaml b/recipes/bioconductor-gmapr/meta.yaml index ce440aad1fe2b..69f0f387dd5b6 100644 --- a/recipes/bioconductor-gmapr/meta.yaml +++ b/recipes/bioconductor-gmapr/meta.yaml @@ -1,74 +1,81 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "gmapR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: GSNAP and GMAP are a pair of tools to align short-read data written by Tom Wu. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: An R interface to the GMAP/GSNAP/GSTRUCT suite -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3398b4dd3f0c05c2a748f9ecb0a28c41 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gmapr", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:gmapr + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines requirements: + build: + - {{ compiler('c') }} + - automake + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - libblas - liblapack + - zlib run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - build: - - {{ compiler('c') }} - - automake - - make + +source: + md5: bd60ae0c34ef6495f66df098245e19fe + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'An R interface to the GMAP/GSNAP/GSTRUCT suite' - description: 'GSNAP and GMAP are a pair of tools to align short-read data written by Tom Wu. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool.' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} \ No newline at end of file diff --git a/recipes/bioconductor-gmicr/meta.yaml b/recipes/bioconductor-gmicr/meta.yaml index 9e030aeb49653..ec9c524e03017 100644 --- a/recipes/bioconductor-gmicr/meta.yaml +++ b/recipes/bioconductor-gmicr/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "GmicR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package uses bayesian network learning to detect relationships between Gene Modules detected by WGCNA and immune cell signatures defined by xCell. It is a hypothesis generating tool. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + file LICENSE + license_file: LICENSE + summary: Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 13466f8e105c84116d73b39d38eed3cd build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gmicr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-category >=2.68.0,<2.69.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-category >=2.72.0,<2.73.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-ape - r-base - r-bnlearn @@ -41,12 +43,12 @@ requirements: - r-shiny - r-wgcna run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-category >=2.68.0,<2.69.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-category >=2.72.0,<2.73.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-ape - r-base - r-bnlearn @@ -59,13 +61,16 @@ requirements: - r-reshape2 - r-shiny - r-wgcna + +source: + md5: f655d057f072577b385fe8b265545a97 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-2 + file LICENSE' - summary: 'Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)' - description: 'This package uses bayesian network learning to detect relationships between Gene Modules detected by WGCNA and immune cell signatures defined by xCell. It is a hypothesis generating tool.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gmoviz/meta.yaml b/recipes/bioconductor-gmoviz/meta.yaml index 1a7e6dd17007e..904ab8a898bb1 100644 --- a/recipes/bioconductor-gmoviz/meta.yaml +++ b/recipes/bioconductor-gmoviz/meta.yaml @@ -1,67 +1,72 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "gmoviz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Genetically modified organisms (GMOs) and cell lines are widely used models in all kinds of biological research. As part of characterising these models, DNA sequencing technology and bioinformatics analyses are used systematically to study their genomes. Therefore, large volumes of data are generated and various algorithms are applied to analyse this data, which introduces a challenge on representing all findings in an informative and concise manner. `gmoviz` provides users with an easy way to visualise and facilitate the explanation of complex genomic editing events on a larger, biologically-relevant scale. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Seamless visualization of complex genomic variations in GMOs and edited cell lines -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 19164c63f0edf9ae927bef7bae0b1a12 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gmoviz", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle, BiocManager requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-circlize - r-colorspace - r-gridbase - r-pracma run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-circlize - r-colorspace - r-gridbase - r-pracma + +source: + md5: 4f04f72f9c7f5f66fdd7a46292cca616 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Seamless visualization of complex genomic variations in GMOs and edited cell lines' - description: 'Genetically modified organisms (GMOs) and cell lines are widely used models in all kinds of biological research. As part of characterising these models, DNA sequencing technology and bioinformatics analyses are used systematically to study their genomes. Therefore, large volumes of data are generated and various algorithms are applied to analyse this data, which introduces a challenge on representing all findings in an informative and concise manner. `gmoviz` provides users with an easy way to visualise and facilitate the explanation of complex genomic editing events on a larger, biologically-relevant scale.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gmrp/meta.yaml b/recipes/bioconductor-gmrp/meta.yaml index b548aa45a5dea..8284e9bb57174 100644 --- a/recipes/bioconductor-gmrp/meta.yaml +++ b/recipes/bioconductor-gmrp/meta.yaml @@ -1,51 +1,57 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "GMRP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Perform Mendelian randomization analysis of multiple SNPs to determine risk factors causing disease of study and to exclude confounding variabels and perform path analysis to construct path of risk factors to the disease. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: GWAS-based Mendelian Randomization and Path Analyses -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d33e226ce1134e0f16d4d531fadc7339 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gmrp", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:gmrp + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-gmrp + path: recipes/bioconductor-gmrp + version: 1.8.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, BiocGenerics requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-diagram - r-plotrix run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-diagram - r-plotrix + +source: + md5: 8357cef5fe7f17944b506228929f96c0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'GWAS-based Mendelian Randomization and Path Analyses' - description: 'Perform Mendelian randomization analysis of multiple SNPs to determine risk factors causing disease of study and to exclude confounding variabels and perform path analysis to construct path of risk factors to the disease.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:gmrp - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-gmrp - path: recipes/bioconductor-gmrp - version: 1.8.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gnet2/build_failure.linux-64.yaml b/recipes/bioconductor-gnet2/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..6536c67f6b1b8 --- /dev/null +++ b/recipes/bioconductor-gnet2/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: bdd099eff1421eb32e731c84de19f76e52586e1fab8a0b1e8c5a5d3324032dba # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [32mbioconductor-xvector >=0.46.0,<0.47.0 [0m, which requires + [32mbioconductor-zlibbioc >=1.52.0,<1.53.0 [0m, which requires + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [31mr-xgboost[0m is not installable because there are no viable options + [31mr-xgboost 0.80[0m would require + [31mmro-base >=3.5.0,<3.5.1.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-xgboost [0.80|0.81|0.82|0.90|1.0.2][0m would require + [31mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [0.82|0.90|...|1.4.0][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.0.2|1.1.1|...|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.4.0|1.4.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec(">=3.5.0,<3.5.1.0a0"), MatchSpec("r-xgboost==0.80=mro350h255eb88_1")} + Encountered problems while solving: + - nothing provides mro-base >=3.5.0,<3.5.1.0a0 needed by r-xgboost-0.80-mro350h255eb88_1 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-summarizedexperiment >=1.36.0,<1.37.0 [0m is installable and it requires + [32mbioconductor-genomicranges >=1.58.0,<1.59.0 [0m, which requires + [32mbioconductor-xvector >=0.46.0,<0.47.0 [0m, which requires + [32mbioconductor-zlibbioc >=1.52.0,<1.53.0 [0m, which requires + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [31mr-xgboost[0m is not installable because there are no viable options + [31mr-xgboost 0.80[0m would require + [31mmro-base >=3.5.0,<3.5.1.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-xgboost [0.80|0.81|0.82|0.90|1.0.2][0m would require + [31mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [0.82|0.90|...|1.4.0][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.0.2|1.1.1|...|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.4.0|1.4.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-gnet2/build_failure.linux-aarch64.yaml b/recipes/bioconductor-gnet2/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..dd308bb01d4b9 --- /dev/null +++ b/recipes/bioconductor-gnet2/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: bdd099eff1421eb32e731c84de19f76e52586e1fab8a0b1e8c5a5d3324032dba # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec("__cuda"), MatchSpec("r-xgboost==1.7.4=cuda112_r41hb1b98f1_1")} + Encountered problems while solving: + - nothing provides __cuda needed by r-xgboost-1.7.4-cuda112_r41hb1b98f1_1 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-summarizedexperiment >=1.36.0,<1.37.0 [0m is installable and it requires + [32mbioconductor-genomicranges >=1.58.0,<1.59.0 [0m, which requires + [32mbioconductor-xvector >=0.46.0,<0.47.0 [0m, which requires + [32mbioconductor-zlibbioc >=1.52.0,<1.53.0 [0m, which requires + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [31mr-xgboost[0m is not installable because there are no viable options + [31mr-xgboost [1.5.1|1.6.1|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec("__cuda"), MatchSpec("r-xgboost==1.7.4=cuda112_r41hb1b98f1_1")} + Encountered problems while solving: + - nothing provides __cuda needed by r-xgboost-1.7.4-cuda112_r41hb1b98f1_1 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-summarizedexperiment >=1.36.0,<1.37.0 [0m is installable and it requires + [32mbioconductor-genomicranges >=1.58.0,<1.59.0 [0m, which requires + [32mbioconductor-xvector >=0.46.0,<0.47.0 [0m, which requires + [32mbioconductor-zlibbioc >=1.52.0,<1.53.0 [0m, which requires + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [31mr-xgboost[0m is not installable because there are no viable options + [31mr-xgboost [1.5.1|1.6.1|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-gnet2/build_failure.osx-64.yaml b/recipes/bioconductor-gnet2/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..d0a4af1150380 --- /dev/null +++ b/recipes/bioconductor-gnet2/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: bdd099eff1421eb32e731c84de19f76e52586e1fab8a0b1e8c5a5d3324032dba # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1 conflicts with any installable versions previously reported; + r-xgboost [0.82|0.90|...|1.4.0] would require + r-base >=3.6,<3.7.0a0 but there are no viable options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3] conflicts with any installable versions previously reported; + r-xgboost [1.0.2|1.1.1|...|1.6.2] would require + r-base >=4.0,<4.1.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.4.0|1.4.1|...|1.7.4] would require + r-base >=4.1,<4.2.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.6.2|1.7.0|...|2.0.3] would require + r-base >=4.2,<4.3.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.7.4|1.7.6|...|2.1.3] would require + r-base >=4.3,<4.4.0a0 , which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("4.0.1==hcfea43d_1"), MatchSpec("clang==4.0.1=1")} + Encountered problems while solving: + - nothing provides compiler-rt 4.0.1 hcfea43d_1 needed by clang-4.0.1-1 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-summarizedexperiment >=1.36.0,<1.37.0 is installable and it requires + bioconductor-genomicranges >=1.58.0,<1.59.0 , which requires + bioconductor-xvector >=0.46.0,<0.47.0 , which requires + bioconductor-zlibbioc >=1.52.0,<1.53.0 , which requires + r-base >=4.4,<4.5.0a0 , which can be installed; + r-xgboost is not installable because there are no viable options + r-xgboost [0.80|0.81|0.82|0.90|1.0.2] would require + r-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ] but there are no viable options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1 conflicts with any installable versions previously reported; + r-xgboost [0.82|0.90|...|1.4.0] would require + r-base >=3.6,<3.7.0a0 but there are no viable options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3] conflicts with any installable versions previously reported; + r-xgboost [1.0.2|1.1.1|...|1.6.2] would require + r-base >=4.0,<4.1.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.4.0|1.4.1|...|1.7.4] would require + r-base >=4.1,<4.2.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.6.2|1.7.0|...|2.0.3] would require + r-base >=4.2,<4.3.0a0 , which conflicts with any installable versions previously reported; + r-xgboost [1.7.4|1.7.6|...|2.1.3] would require + r-base >=4.3,<4.4.0a0 , which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-gnet2/meta.yaml b/recipes/bioconductor-gnet2/meta.yaml index acf7bfe64973c..031575d8ad9c7 100644 --- a/recipes/bioconductor-gnet2/meta.yaml +++ b/recipes/bioconductor-gnet2/meta.yaml @@ -1,27 +1,38 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "GNET2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Cluster genes to functional groups with E-M process. Iteratively perform TF assigning and Gene assigning, until the assignment of genes did not change, or max number of iterations is reached. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Apache License 2.0 + summary: Constructing gene regulatory networks from expression data through functional module inference -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 06382e36858e9d55d44aabba748d49b8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gnet2", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:gnet2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-diagrammer - r-dplyr @@ -34,7 +45,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-diagrammer - r-dplyr @@ -44,21 +55,16 @@ requirements: - r-rcpp - r-reshape2 - r-xgboost - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: b9256f15935ad47d9827488af55187bc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Apache License 2.0' - summary: 'Constructing gene regulatory networks from expression data through functional module inference' - description: 'Cluster genes to functional groups with E-M process. Iteratively perform TF assigning and Gene assigning, until the assignment of genes did not change, or max number of iterations is reached.' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-gnosis/meta.yaml b/recipes/bioconductor-gnosis/meta.yaml index ed68757eb4d4d..11295f672bb46 100644 --- a/recipes/bioconductor-gnosis/meta.yaml +++ b/recipes/bioconductor-gnosis/meta.yaml @@ -1,29 +1,32 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "GNOSIS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: GNOSIS incorporates a range of R packages enabling users to efficiently explore and visualise clinical and genomic data obtained from cBioPortal. GNOSIS uses an intuitive GUI and multiple tab panels supporting a range of functionalities. These include data upload and initial exploration, data recoding and subsetting, multiple visualisations, survival analysis, statistical analysis and mutation analysis, in addition to facilitating reproducible research. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Genomics explorer using statistical and survival analysis in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e3cbf07a76da1ae0aa6e669bad2cb778 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gnosis", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: + host: - - 'bioconductor-cbioportaldata >=2.14.0,<2.15.0' - - 'bioconductor-maftools >=2.18.0,<2.19.0' + - bioconductor-cbioportaldata >=2.18.0,<2.19.0 + - bioconductor-maftools >=2.22.0,<2.23.0 - r-base - r-car - r-comparegroups @@ -50,9 +53,10 @@ requirements: - r-survival - r-survminer - r-tidyverse + run: - - 'bioconductor-cbioportaldata >=2.14.0,<2.15.0' - - 'bioconductor-maftools >=2.18.0,<2.19.0' + - bioconductor-cbioportaldata >=2.18.0,<2.19.0 + - bioconductor-maftools >=2.22.0,<2.23.0 - r-base - r-car - r-comparegroups @@ -79,13 +83,16 @@ requirements: - r-survival - r-survminer - r-tidyverse + +source: + md5: bc1d8518e1973a5b898f25970a194879 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Genomics explorer using statistical and survival analysis in R' - description: 'GNOSIS incorporates a range of R packages enabling users to efficiently explore and visualise clinical and genomic data obtained from cBioPortal. GNOSIS uses an intuitive GUI and multiple tab panels supporting a range of functionalities. These include data upload and initial exploration, data recoding and subsetting, multiple visualisations, survival analysis, statistical analysis and mutation analysis, in addition to facilitating reproducible research.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-go.db/meta.yaml b/recipes/bioconductor-go.db/meta.yaml index 9311de2ff1dc9..f63d626226d8b 100644 --- a/recipes/bioconductor-go.db/meta.yaml +++ b/recipes/bioconductor-go.db/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "GO.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b23522167263afc45a9b115d01632cb1 +about: + description: A set of annotation maps describing the entire Gene Ontology assembled using data from GO + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: A set of annotation maps describing the entire Gene Ontology build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-go.db", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-go.db + path: recipes/bioconductor-go.db + version: 3.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a41513069bb1ff4a2ecfa1a538110699 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A set of annotation maps describing the entire Gene Ontology' - description: 'A set of annotation maps describing the entire Gene Ontology assembled using data from GO' -extra: - parent_recipe: - name: bioconductor-go.db - path: recipes/bioconductor-go.db - version: 3.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-go.db/post-link.sh b/recipes/bioconductor-go.db/post-link.sh index f1547533d3cd4..ccce3a607bc6b 100644 --- a/recipes/bioconductor-go.db/post-link.sh +++ b/recipes/bioconductor-go.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "go.db-3.18.0" +installBiocDataPackage.sh "go.db-3.20.0" diff --git a/recipes/bioconductor-goexpress/meta.yaml b/recipes/bioconductor-goexpress/meta.yaml index 2ad3dd05dc553..5289fe750df4d 100644 --- a/recipes/bioconductor-goexpress/meta.yaml +++ b/recipes/bioconductor-goexpress/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "GOexpress" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package contains methods to visualise the expression profile of genes from a microarray or RNA-seq experiment, and offers a supervised clustering approach to identify GO terms containing genes with expression levels that best classify two or more predefined groups of samples. Annotations for the genes present in the expression dataset may be obtained from Ensembl through the biomaRt package, if not provided by the user. The default random forest framework is used to evaluate the capacity of each gene to cluster samples according to the factor of interest. Finally, GO terms are scored by averaging the rank (alternatively, score) of their respective gene sets to cluster the samples. P-values may be computed to assess the significance of GO term ranking. Visualisation function include gene expression profile, gene ontology-based heatmaps, and hierarchical clustering of experimental samples using gene expression data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Visualise microarray and RNAseq data using gene ontology annotations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b313b2555495c3d3fc5674120b7bb01b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-goexpress", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biomart >=2.62.0,<2.63.0 - r-base - - 'r-ggplot2 >=0.9.0' - - 'r-gplots >=2.13.0' - - 'r-randomforest >=4.6' - - 'r-rcolorbrewer >=1.0' - - 'r-rcurl >=1.95' - - 'r-stringr >=0.6.2' + - r-ggplot2 >=0.9.0 + - r-gplots >=2.13.0 + - r-randomforest >=4.6 + - r-rcolorbrewer >=1.0 + - r-rcurl >=1.95 + - r-stringr >=0.6.2 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biomart >=2.62.0,<2.63.0 - r-base - - 'r-ggplot2 >=0.9.0' - - 'r-gplots >=2.13.0' - - 'r-randomforest >=4.6' - - 'r-rcolorbrewer >=1.0' - - 'r-rcurl >=1.95' - - 'r-stringr >=0.6.2' + - r-ggplot2 >=0.9.0 + - r-gplots >=2.13.0 + - r-randomforest >=4.6 + - r-rcolorbrewer >=1.0 + - r-rcurl >=1.95 + - r-stringr >=0.6.2 + +source: + md5: 20975c857147c270e93591d4b3b0fe4c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Visualise microarray and RNAseq data using gene ontology annotations' - description: 'The package contains methods to visualise the expression profile of genes from a microarray or RNA-seq experiment, and offers a supervised clustering approach to identify GO terms containing genes with expression levels that best classify two or more predefined groups of samples. Annotations for the genes present in the expression dataset may be obtained from Ensembl through the biomaRt package, if not provided by the user. The default random forest framework is used to evaluate the capacity of each gene to cluster samples according to the factor of interest. Finally, GO terms are scored by averaging the rank (alternatively, score) of their respective gene sets to cluster the samples. P-values may be computed to assess the significance of GO term ranking. Visualisation function include gene expression profile, gene ontology-based heatmaps, and hierarchical clustering of experimental samples using gene expression data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gofuncr/meta.yaml b/recipes/bioconductor-gofuncr/meta.yaml index 71d2d0bf7bc4f..47b8e49087d2f 100644 --- a/recipes/bioconductor-gofuncr/meta.yaml +++ b/recipes/bioconductor-gofuncr/meta.yaml @@ -1,56 +1,61 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "GOfuncR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO-annotations are obtained from OrganismDb or OrgDb packages (''Homo.sapiens'' by default); the GO-graph is included in the package and updated regularly (01-May-2021). GOfuncR provides the standard candidate vs. background enrichment analysis using the hypergeometric test, as well as three additional tests: (i) the Wilcoxon rank-sum test that is used when genes are ranked, (ii) a binomial test that is used when genes are associated with two counts and (iii) a Chi-square or Fisher''s exact test that is used in cases when genes are associated with four counts. To correct for multiple testing and interdependency of the tests, family-wise error rates are computed based on random permutations of the gene-associated variables. GOfuncR also provides tools for exploring the ontology graph and the annotations, and options to take gene-length or spatial clustering of genes into account. It is also possible to provide custom gene coordinates, annotations and ontologies.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Gene ontology enrichment using FUNC -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d84c71ebda463871117ea00394d551ce build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gofuncr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - - 'r-gtools >=3.5.0' - - 'r-mapplots >=1.5' - - 'r-rcpp >=0.11.5' - - 'r-vioplot >=0.2' + - r-gtools >=3.5.0 + - r-mapplots >=1.5 + - r-rcpp >=0.11.5 + - r-vioplot >=0.2 - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - - 'r-gtools >=3.5.0' - - 'r-mapplots >=1.5' - - 'r-rcpp >=0.11.5' - - 'r-vioplot >=0.2' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-gtools >=3.5.0 + - r-mapplots >=1.5 + - r-rcpp >=0.11.5 + - r-vioplot >=0.2 + +source: + md5: c255f3412faded1dfadfc216992eca39 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Gene ontology enrichment using FUNC' - description: 'GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO-annotations are obtained from OrganismDb or OrgDb packages (''Homo.sapiens'' by default); the GO-graph is included in the package and updated regularly (01-May-2021). GOfuncR provides the standard candidate vs. background enrichment analysis using the hypergeometric test, as well as three additional tests: (i) the Wilcoxon rank-sum test that is used when genes are ranked, (ii) a binomial test that is used when genes are associated with two counts and (iii) a Chi-square or Fisher''s exact test that is used in cases when genes are associated with four counts. To correct for multiple testing and interdependency of the tests, family-wise error rates are computed based on random permutations of the gene-associated variables. GOfuncR also provides tools for exploring the ontology graph and the annotations, and options to take gene-length or spatial clustering of genes into account. It is also possible to provide custom gene coordinates, annotations and ontologies.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-golubesets/meta.yaml b/recipes/bioconductor-golubesets/meta.yaml index 07b2c538aa5a1..7fe0b0a1a4b99 100644 --- a/recipes/bioconductor-golubesets/meta.yaml +++ b/recipes/bioconductor-golubesets/meta.yaml @@ -1,45 +1,51 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "golubEsets" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: representation of public golub data with some covariate data of provenance unknown to the maintainer at present; now employs ExpressionSet format + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: exprSets for golub leukemia data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 49e3527c00f06c189a048a6b871f3d54 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-golubesets", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-golubesets + path: recipes/bioconductor-golubesets + version: 1.22.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: b464be536b50df612af2caa81b4395ea + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'exprSets for golub leukemia data' - description: 'representation of public golub data with some covariate data of provenance unknown to the maintainer at present; now employs ExpressionSet format' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - parent_recipe: - name: bioconductor-golubesets - path: recipes/bioconductor-golubesets - version: 1.22.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-golubesets/post-link.sh b/recipes/bioconductor-golubesets/post-link.sh index 2a6d36332ced8..a8dbf38689c90 100644 --- a/recipes/bioconductor-golubesets/post-link.sh +++ b/recipes/bioconductor-golubesets/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "golubesets-1.44.0" +installBiocDataPackage.sh "golubesets-1.48.0" diff --git a/recipes/bioconductor-gopro/meta.yaml b/recipes/bioconductor-gopro/meta.yaml index 28fc93fb2f3c8..ac464c491f38e 100644 --- a/recipes/bioconductor-gopro/meta.yaml +++ b/recipes/bioconductor-gopro/meta.yaml @@ -1,32 +1,38 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "GOpro" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Find the most characteristic gene ontology terms for groups of human genes. This package was created as a part of the thesis which was developed under the auspices of MI^2 Group (http://mi2.mini.pw.edu.pl/, https://github.com/geneticsMiNIng). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Find the most characteristic gene ontology terms for groups of human genes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c92dbcab08a7cdac3ee8ee6c28c6dc78 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gopro", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-bh - r-dendextend @@ -36,29 +42,28 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-bh - r-dendextend - r-doparallel - r-foreach - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 322bf28520208bfae9cbd508ebebd7e2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Find the most characteristic gene ontology terms for groups of human genes' - description: 'Find the most characteristic gene ontology terms for groups of human genes. This package was created as a part of the thesis which was developed under the auspices of MI^2 Group (http://mi2.mini.pw.edu.pl/, https://github.com/geneticsMiNIng).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-goprofiles/meta.yaml b/recipes/bioconductor-goprofiles/meta.yaml index f8cc90bc58c9f..79e7b8679aaf8 100644 --- a/recipes/bioconductor-goprofiles/meta.yaml +++ b/recipes/bioconductor-goprofiles/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.64.0" %} +{% set version = "1.68.0" %} {% set name = "goProfiles" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package implements methods to compare lists of genes based on comparing the corresponding 'functional profiles'. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'goProfiles: an R package for the statistical analysis of functional profiles' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ff2a664ff7284cf03e9caf932ad86d63 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-goprofiles", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: org.Hs.eg.db requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-go.db >=3.20.0,<3.21.0 - r-base - r-compquadform - r-stringr run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-go.db >=3.20.0,<3.21.0 - r-base - r-compquadform - r-stringr + +source: + md5: 27de9f94bca2c176f1e40558b8a513d3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'goProfiles: an R package for the statistical analysis of functional profiles' - description: 'The package implements methods to compare lists of genes based on comparing the corresponding ''functional profiles''.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gosemsim/meta.yaml b/recipes/bioconductor-gosemsim/meta.yaml index ae4cc675372b4..12752f06db26e 100644 --- a/recipes/bioconductor-gosemsim/meta.yaml +++ b/recipes/bioconductor-gosemsim/meta.yaml @@ -1,58 +1,72 @@ -{% set version = "2.28.0" %} +{% set version = "2.32.0" %} {% set name = "GOSemSim" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: GO-terms Semantic Similarity Measures -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea9c9c6e25cc507a2b5cff51f268d848 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gosemsim", max_pin="x.x") }}' -# Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat, tidyr, tidyselect, ROCR + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:gosemsim + parent_recipe: + name: bioconductor-gosemsim + path: recipes/bioconductor-gosemsim + version: 2.6.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, rappdirs, readr, rmarkdown, testthat, tidyr, tidyselect, ROCR requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-go.db >=3.20.0,<3.21.0 - r-base + - r-dbi + - r-digest + - r-r.utils - r-rcpp - r-rlang + - r-yulab.utils >=0.1.6 - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-go.db >=3.20.0,<3.21.0 - r-base + - r-dbi + - r-digest + - r-r.utils - r-rcpp - r-rlang - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-yulab.utils >=0.1.6 + +source: + md5: 91ac358b6d115c6f33062c7e57ca4484 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'GO-terms Semantic Similarity Measures' - description: 'The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:gosemsim - parent_recipe: - name: bioconductor-gosemsim - path: recipes/bioconductor-gosemsim - version: 2.6.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-goseq/meta.yaml b/recipes/bioconductor-goseq/meta.yaml index ee94c1535f052..42c772f583f9a 100644 --- a/recipes/bioconductor-goseq/meta.yaml +++ b/recipes/bioconductor-goseq/meta.yaml @@ -1,52 +1,64 @@ -{% set version = "1.54.0" %} +{% set version = "1.58.0" %} {% set name = "goseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Gene Ontology analyser for RNA-seq and other length biased data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4c39d7fbb51594a70dd3e54b1bc10375 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-goseq", max_pin="x.x") }}' - noarch: generic -# Suggests: edgeR, org.Hs.eg.db, rtracklayer + +extra: + identifiers: + - biotools:goseq + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: edgeR, org.Hs.eg.db requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genelendatabase >=1.38.0,<1.39.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genelendatabase >=1.42.0,<1.43.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-biasedurn - r-mgcv run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genelendatabase >=1.38.0,<1.39.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genelendatabase >=1.42.0,<1.43.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-biasedurn - r-mgcv + +source: + md5: 2f8e14aea3c76338ad18c7a1bfe8c502 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'Gene Ontology analyser for RNA-seq and other length biased data' - description: 'Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:goseq + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gosorensen/meta.yaml b/recipes/bioconductor-gosorensen/meta.yaml index a6ccadcbdd826..f576e306119ee 100644 --- a/recipes/bioconductor-gosorensen/meta.yaml +++ b/recipes/bioconductor-gosorensen/meta.yaml @@ -1,47 +1,45 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "goSorensen" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8fa5cc982341291dd857ab340abe4c73 +about: + description: This package implements inferential methods to compare gene lists in terms of their biological meaning as expressed in the GO. The compared gene lists are characterized by cross-tabulation frequency tables of enriched GO items. Dissimilarity between gene lists is evaluated using the Sorensen-Dice index. The fundamental guiding principle is that two gene lists are taken as similar if they share a great proportion of common enriched GO items. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gosorensen", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: BiocManager, BiocStyle, knitr, rmarkdown, org.At.tair.db, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcSakai.eg.db, org.EcK12.eg.db, org.Gg.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Pt.eg.db, org.Xl.eg.db requirements: host: - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-goprofiles >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-goprofiles >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - r-stringr run: - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-goprofiles >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-goprofiles >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - r-stringr +source: + md5: aba6bdd63cc6e5ee46dac40d3297caca + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)' - description: 'This package implements inferential methods to compare gene lists in terms of their biological meaning as expressed in the GO. The compared gene lists are characterized by cross-tabulation frequency tables of enriched GO items. Dissimilarity between gene lists is evaluated using the Sorensen-Dice index. The fundamental guiding principle is that two gene lists are taken as similar if they share a great proportion of common enriched GO items.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gostag/meta.yaml b/recipes/bioconductor-gostag/meta.yaml index 4ea3c9b583493..4400ce64b8ce1 100644 --- a/recipes/bioconductor-gostag/meta.yaml +++ b/recipes/bioconductor-gostag/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "goSTAG" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d3245abbcc5813366a9393dc7bf79c7 +about: + description: Gene lists derived from the results of genomic analyses are rich in biological information. For instance, differentially expressed genes (DEGs) from a microarray or RNA-Seq analysis are related functionally in terms of their response to a treatment or condition. Gene lists can vary in size, up to several thousand genes, depending on the robustness of the perturbations or how widely different the conditions are biologically. Having a way to associate biological relatedness between hundreds and thousands of genes systematically is impractical by manually curating the annotation and function of each gene. Over-representation analysis (ORA) of genes was developed to identify biological themes. Given a Gene Ontology (GO) and an annotation of genes that indicate the categories each one fits into, significance of the over-representation of the genes within the ontological categories is determined by a Fisher's exact test or modeling according to a hypergeometric distribution. Comparing a small number of enriched biological categories for a few samples is manageable using Venn diagrams or other means for assessing overlaps. However, with hundreds of enriched categories and many samples, the comparisons are laborious. Furthermore, if there are enriched categories that are shared between samples, trying to represent a common theme across them is highly subjective. goSTAG uses GO subtrees to tag and annotate genes within a set. goSTAG visualizes the similarities between the over-representation of DEGs by clustering the p-values from the enrichment statistical tests and labels clusters with the GO term that has the most paths to the root within the subtree generated from all the GO terms in the cluster. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A tool to use GO Subtrees to Tag and Annotate Genes within a set build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gostag", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-go.db >=3.20.0,<3.21.0 - r-base - r-memoise run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-go.db >=3.20.0,<3.21.0 - r-base - r-memoise +source: + md5: 3f60375f304188998dba89a635f4a6e2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'A tool to use GO Subtrees to Tag and Annotate Genes within a set' - description: 'Gene lists derived from the results of genomic analyses are rich in biological information. For instance, differentially expressed genes (DEGs) from a microarray or RNA-Seq analysis are related functionally in terms of their response to a treatment or condition. Gene lists can vary in size, up to several thousand genes, depending on the robustness of the perturbations or how widely different the conditions are biologically. Having a way to associate biological relatedness between hundreds and thousands of genes systematically is impractical by manually curating the annotation and function of each gene. Over-representation analysis (ORA) of genes was developed to identify biological themes. Given a Gene Ontology (GO) and an annotation of genes that indicate the categories each one fits into, significance of the over-representation of the genes within the ontological categories is determined by a Fisher''s exact test or modeling according to a hypergeometric distribution. Comparing a small number of enriched biological categories for a few samples is manageable using Venn diagrams or other means for assessing overlaps. However, with hundreds of enriched categories and many samples, the comparisons are laborious. Furthermore, if there are enriched categories that are shared between samples, trying to represent a common theme across them is highly subjective. goSTAG uses GO subtrees to tag and annotate genes within a set. goSTAG visualizes the similarities between the over-representation of DEGs by clustering the p-values from the enrichment statistical tests and labels clusters with the GO term that has the most paths to the root within the subtree generated from all the GO terms in the cluster.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gostats/meta.yaml b/recipes/bioconductor-gostats/meta.yaml index d2f24d9217bbd..9b8ff6aa5933e 100644 --- a/recipes/bioconductor-gostats/meta.yaml +++ b/recipes/bioconductor-gostats/meta.yaml @@ -1,61 +1,67 @@ -{% set version = "2.68.0" %} +{% set version = "2.72.0" %} {% set name = "GOstats" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Tools for manipulating GO and microarrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4489bff9142d2a3357ac2de0efc1b1b4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gostats", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:gostats + parent_recipe: + name: bioconductor-gostats + path: recipes/bioconductor-gostats + version: 2.46.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics, BiocStyle, knitr requirements: host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationforge >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-category >=2.68.0,<2.69.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationforge >=1.48.0,<1.49.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-category >=2.72.0,<2.73.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationforge >=1.44.0,<1.45.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-category >=2.68.0,<2.69.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationforge >=1.48.0,<1.49.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-category >=2.72.0,<2.73.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base + +source: + md5: 17647610e9758110420e9b7498978d54 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Tools for manipulating GO and microarrays' - description: 'A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.' -extra: - identifiers: - - biotools:gostats - parent_recipe: - name: bioconductor-gostats - path: recipes/bioconductor-gostats - version: 2.46.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gothic/meta.yaml b/recipes/bioconductor-gothic/meta.yaml index 7651748e307e3..32b435673c400 100644 --- a/recipes/bioconductor-gothic/meta.yaml +++ b/recipes/bioconductor-gothic/meta.yaml @@ -1,71 +1,77 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "GOTHiC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This is a Hi-C analysis package using a cumulative binomial test to detect interactions between distal genomic loci that have significantly more reads than expected by chance in Hi-C experiments. It takes mapped paired NGS reads as input and gives back the list of significant interactions for a given bin size in the genome. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Binomial test for Hi-C data analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4674978396dedfc730c8ad85662dac8c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gothic", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:gothic + - doi:10.1101/gr.185272.114 + parent_recipe: + name: bioconductor-gothic + path: recipes/bioconductor-gothic + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: HiCDataLymphoblast requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-biocmanager - r-data.table - r-ggplot2 run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-biocmanager - r-data.table - r-ggplot2 + +source: + md5: 4307142707add23652db5f3e9abef9f4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Binomial test for Hi-C data analysis' - description: 'This is a Hi-C analysis package using a cumulative binomial test to detect interactions between distal genomic loci that have significantly more reads than expected by chance in Hi-C experiments. It takes mapped paired NGS reads as input and gives back the list of significant interactions for a given bin size in the genome.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:gothic - - doi:10.1101/gr.185272.114 - parent_recipe: - name: bioconductor-gothic - path: recipes/bioconductor-gothic - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gotools/meta.yaml b/recipes/bioconductor-gotools/meta.yaml index 0da93c1095d5d..531b35ab56f5e 100644 --- a/recipes/bioconductor-gotools/meta.yaml +++ b/recipes/bioconductor-gotools/meta.yaml @@ -1,43 +1,22 @@ -{% set version = "1.76.0" %} +{% set version = "1.80.0" %} {% set name = "goTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Wraper functions for description/comparison of oligo ID list using Gene Ontology database + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Functions for Gene Ontology database -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a91344726dcce37779380a18f6e9bc1d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gotools", max_pin="x.x") }}' - noarch: generic -# Suggests: hgu133a.db -requirements: - host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - r-base - run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Functions for Gene Ontology database' - description: 'Wraper functions for description/comparison of oligo ID list using Gene Ontology database' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + extra: identifiers: - biotools:gotools @@ -47,3 +26,30 @@ extra: path: recipes/bioconductor-gotools version: 1.54.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: hgu133a.db +requirements: + host: + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - r-base + run: + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - r-base + +source: + md5: 64aabdeff248a4131615200e0d83a673 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-gp53cdf/meta.yaml b/recipes/bioconductor-gp53cdf/meta.yaml index 8bdbd9cb32bf1..6eb17cedce054 100644 --- a/recipes/bioconductor-gp53cdf/meta.yaml +++ b/recipes/bioconductor-gp53cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "gp53cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2887dd15d3fa29b5c13b068c8d641f61 +about: + description: A package containing an environment representing the GP53.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: gp53cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gp53cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2887dd15d3fa29b5c13b068c8d641f61 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: gp53cdf - description: 'A package containing an environment representing the GP53.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gpa/meta.yaml b/recipes/bioconductor-gpa/meta.yaml index aca43c441e96b..26ae0fcdff68a 100644 --- a/recipes/bioconductor-gpa/meta.yaml +++ b/recipes/bioconductor-gpa/meta.yaml @@ -1,26 +1,38 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "GPA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functions for fitting GPA, a statistical framework to prioritize GWAS results by integrating pleiotropy information and annotation data. In addition, it also includes ShinyGPA, an interactive visualization toolkit to investigate pleiotropic architecture. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: GPA (Genetic analysis incorporating Pleiotropy and Annotation) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2c1f0f3436c036a3e098d7780deb7282 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gpa", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:GPA + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: gpaExample # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-dt @@ -43,22 +55,16 @@ requirements: - r-shiny - r-shinybs - r-vegan - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 86ef048b32f842667b4f198e85533e3a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'GPA (Genetic analysis incorporating Pleiotropy and Annotation)' - description: 'This package provides functions for fitting GPA, a statistical framework to prioritize GWAS results by integrating pleiotropy information and annotation data. In addition, it also includes ShinyGPA, an interactive visualization toolkit to investigate pleiotropic architecture.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name }} diff --git a/recipes/bioconductor-gpaexample/meta.yaml b/recipes/bioconductor-gpaexample/meta.yaml index 66694127c605d..4e85cda7895cc 100644 --- a/recipes/bioconductor-gpaexample/meta.yaml +++ b/recipes/bioconductor-gpaexample/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "gpaExample" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e989af58ed5bbc10573f7438b3ee7836 +about: + description: Example data for the GPA package, consisting of the p-values of 1,219,805 SNPs for five psychiatric disorder GWAS from the psychiatric GWAS consortium (PGC), with the annotation data using genes preferentially expressed in the central nervous system (CNS). + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Example data for the GPA package (Genetic analysis incorporating Pleiotropy and Annotation) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gpaexample", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 96d55ecbe0c635ee1e296e371f213ef1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Example data for the GPA package (Genetic analysis incorporating Pleiotropy and Annotation)' - description: 'Example data for the GPA package, consisting of the p-values of 1,219,805 SNPs for five psychiatric disorder GWAS from the psychiatric GWAS consortium (PGC), with the annotation data using genes preferentially expressed in the central nervous system (CNS).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gpaexample/post-link.sh b/recipes/bioconductor-gpaexample/post-link.sh index b48e9f2168532..e23b64d077ec2 100644 --- a/recipes/bioconductor-gpaexample/post-link.sh +++ b/recipes/bioconductor-gpaexample/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gpaexample-1.14.0" +installBiocDataPackage.sh "gpaexample-1.18.0" diff --git a/recipes/bioconductor-gpls/meta.yaml b/recipes/bioconductor-gpls/meta.yaml index a685bbc90fd0d..a241376fe8dd2 100644 --- a/recipes/bioconductor-gpls/meta.yaml +++ b/recipes/bioconductor-gpls/meta.yaml @@ -1,38 +1,19 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "gpls" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: db6bc720156a5f7571a34e64b1189d3b +about: + description: Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Classification using generalized partial least squares build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gpls", max_pin="x.x") }}' - noarch: generic -# Suggests: MASS -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Classification using generalized partial least squares' - description: 'Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification.' extra: identifiers: - biotools:gpls @@ -41,4 +22,23 @@ extra: name: bioconductor-gpls path: recipes/bioconductor-gpls version: 1.52.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: MASS +requirements: + host: + - r-base + run: + - r-base +source: + md5: 00ede3e4a045b572128e573d7fbbf945 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gpumagic/build_failure.linux-64.yaml b/recipes/bioconductor-gpumagic/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..c94051a23391c --- /dev/null +++ b/recipes/bioconductor-gpumagic/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: e3b4de213437b2a6160a430fc1fa8c01f3c5ad57d6a9e9ab98261fdca47e5443 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + export PREFIX=/opt/conda/conda-bld/bioconductor-gpumagic_1734320199575/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-gpumagic_1734320199575/_build_env + export SRC_DIR=/opt/conda/conda-bld/bioconductor-gpumagic_1734320199575/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-gpumagic-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-gpumagic-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-gpumagic-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-gpumagic-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-gpumagic_1734320199575/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library + * installing *source* package gpuMagic ... + ** package gpuMagic successfully unpacked and MD5 sums checked + ** using staged installation + ** libs + using C compiler: x86_64-conda-linux-gnu-c (conda-forge gcc 13.3.0-1) 13.3.0 + using C11 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I$PREFIX/lib/R/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS -DCL_SILENCE_DEPRECATION -I'$PREFIX/lib/R/library/Rcpp/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1732138515749/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c C_Interface.cpp -o C_Interface.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I$PREFIX/lib/R/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS -DCL_SILENCE_DEPRECATION -I'$PREFIX/lib/R/library/Rcpp/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1732138515749/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c R_functionRegistration.cpp -o R_functionRegistration.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I$PREFIX/lib/R/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS -DCL_SILENCE_DEPRECATION -I'$PREFIX/lib/R/library/Rcpp/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1732138515749/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c Tools.cpp -o Tools.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I$PREFIX/lib/R/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS -DCL_SILENCE_DEPRECATION -I'$PREFIX/lib/R/library/Rcpp/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1732138515749/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c kernelManager.cpp -o kernelManager.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I$PREFIX/lib/R/include -I../inst/include/OpenCL_header -DCL_TARGET_OPENCL_VERSION=220 -DCL_USE_DEPRECATED_OPENCL_1_2_APIS -DCL_SILENCE_DEPRECATION -I'$PREFIX/lib/R/library/Rcpp/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1732138515749/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c openArray.cpp -o openArray.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -shared -L$PREFIX/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -o gpuMagic.so C_Interface.o R_functionRegistration.o Tools.o kernelManager.o openArray.o -lOpenCL -L$PREFIX/lib/R/lib -lR + During startup - Warning message: + Setting LC_TIME failed, using "C" + /opt/conda/conda-bld/bioconductor-gpumagic_1734320199575/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lOpenCL: No such file or directory + collect2: error: ld returned 1 exit status + make: *** [/opt/conda/conda-bld/bioconductor-gpumagic_1734320199575/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/share/make/shlib.mk:10: gpuMagic.so] Error 1 + ERROR: compilation failed for package gpuMagic + * removing /opt/conda/conda-bld/bioconductor-gpumagic_1734320199575/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/gpuMagic + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-gpumagic_1734320199575/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-gpumagic_1734320199575/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-gpumagic/meta.yaml b/recipes/bioconductor-gpumagic/meta.yaml index 4aaa1e52b559b..066e33f5c8d48 100644 --- a/recipes/bioconductor-gpumagic/meta.yaml +++ b/recipes/bioconductor-gpumagic/meta.yaml @@ -1,31 +1,34 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "gpuMagic" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package aims to help users write openCL code with little or no effort. It is able to compile an user-defined R function and run it on a device such as a CPU or a GPU. The user can also write and run their openCL code directly by calling .kernel function. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: An openCL compiler with the capacity to compile R functions and run the code on GPU -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b720e953b36ccc2db0c6b359f84b5c94 build: - skip: True # [osx] - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gpumagic", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocStyle # SystemRequirements: 1. C++11, 2. a graphic driver or a CPU SDK. 3. ICD loader For Windows user, an ICD loader is required at C:/windows/system32/OpenCL.dll (Usually it is installed by the graphic driver). For Linux user (Except mac): ocl-icd-opencl-dev package is required. For Mac user, no action is needed for the system has installed the dependency. 4. GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - ocl-icd # [linux] - - khronos-opencl-icd-loader # [osx] - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-deriv - r-desctools @@ -36,7 +39,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-deriv - r-desctools @@ -44,17 +47,16 @@ requirements: - r-pryr - r-rcpp - r-stringr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: cc537f655d58c0a240bb6905612a2ac3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'An openCL compiler with the capacity to compile R functions and run the code on GPU' - description: 'The package aims to help users write openCL code with little or no effort. It is able to compile an user-defined R function and run it on a device such as a CPU or a GPU. The user can also write and run their openCL code directly by calling .kernel function.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-granie/meta.yaml b/recipes/bioconductor-granie/meta.yaml index b29c58c558196..85ff9abd4999e 100644 --- a/recipes/bioconductor-granie/meta.yaml +++ b/recipes/bioconductor-granie/meta.yaml @@ -1,39 +1,41 @@ -{% set version = "1.6.1" %} +{% set version = "1.10.0" %} {% set name = "GRaNIE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Genetic variants associated with diseases often affect non-coding regions, thus likely having a regulatory role. To understand the effects of genetic variants in these regulatory regions, identifying genes that are modulated by specific regulatory elements (REs) is crucial. The effect of gene regulatory elements, such as enhancers, is often cell-type specific, likely because the combinations of transcription factors (TFs) that are regulating a given enhancer have cell-type specific activity. This TF activity can be quantified with existing tools such as diffTF and captures differences in binding of a TF in open chromatin regions. Collectively, this forms a gene regulatory network (GRN) with cell-type and data-specific TF-RE and RE-gene links. Here, we reconstruct such a GRN using single-cell or bulk RNAseq and open chromatin (e.g., using ATACseq or ChIPseq for open chromatin marks) and optionally (Capture) Hi-C data. Our network contains different types of links, connecting TFs to regulatory elements, the latter of which is connected to genes in the vicinity or within the same chromatin domain (TAD). We use a statistical framework to assign empirical FDRs and weights to all links using a permutation-based approach. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using single-cell or bulk chromatin accessibility and RNA-seq data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d9db703063398ccd263ce6b54def9266 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-granie", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Mmulatta.UCSC.rheMac10, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn6.refGene, TxDb.Rnorvegicus.UCSC.rn7.refGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Mmulatta.UCSC.rheMac10.refGene, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dm.eg.db, org.Mmu.eg.db, IHW, clusterProfiler, ReactomePA, DOSE, BiocFileCache, ChIPseeker, testthat (>= 3.0.0), BiocStyle, csaw, BiocParallel, WGCNA, variancePartition, purrr, EDASeq, JASPAR2022, TFBSTools, motifmatchr, rbioapi, LDlinkR + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Mmulatta.UCSC.rheMac10, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm39.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn6.refGene, TxDb.Rnorvegicus.UCSC.rn7.refGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Mmulatta.UCSC.rheMac10.refGene, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dm.eg.db, org.Mmu.eg.db, IHW, clusterProfiler, ReactomePA, DOSE, BiocFileCache, ChIPseeker, testthat (>= 3.0.0), BiocStyle, csaw, BiocParallel, WGCNA, variancePartition, purrr, EDASeq, JASPAR2022, JASPAR2024, RSQLite, TFBSTools, motifmatchr, rbioapi, LDlinkR requirements: + host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-base - r-checkmate - r-circlize @@ -48,7 +50,7 @@ requirements: - r-magrittr - r-matrix - r-matrixstats - - r-patchwork + - r-patchwork >=1.2.0 - r-progress - r-rcolorbrewer - r-readr @@ -57,22 +59,23 @@ requirements: - r-scales - r-stringr - r-tibble - - r-tidyr + - r-tidyr >=1.3.0 - r-tidyselect - r-viridis + run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-base - r-checkmate - r-circlize @@ -87,7 +90,7 @@ requirements: - r-magrittr - r-matrix - r-matrixstats - - r-patchwork + - r-patchwork >=1.2.0 - r-progress - r-rcolorbrewer - r-readr @@ -96,15 +99,19 @@ requirements: - r-scales - r-stringr - r-tibble - - r-tidyr + - r-tidyr >=1.3.0 - r-tidyselect - r-viridis + +source: + md5: b414946644b0a626067a257b8f00626b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data' - description: 'Genetic variants associated with diseases often affect non-coding regions, thus likely having a regulatory role. To understand the effects of genetic variants in these regulatory regions, identifying genes that are modulated by specific regulatory elements (REs) is crucial. The effect of gene regulatory elements, such as enhancers, is often cell-type specific, likely because the combinations of transcription factors (TFs) that are regulating a given enhancer have celltype specific activity. This TF activity can be quantified with existing tools such as diffTF and captures differences in binding of a TF in open chromatin regions. Collectively, this forms a gene regulatory network (GRN) with cell-type and data-specific TF-RE and RE-gene links. Here, we reconstruct such a GRN using bulk RNAseq and open chromatin (e.g., using ATACseq or ChIPseq for open chromatin marks) and optionally TF activity data. Our network contains different types of links, connecting TFs to regulatory elements, the latter of which is connected to genes in the vicinity or within the same chromatin domain (TAD). We use a statistical framework to assign empirical FDRs and weights to all links using a permutation-based approach.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-granulator/meta.yaml b/recipes/bioconductor-granulator/meta.yaml index 1a7ce94a61265..2cc214174d7a5 100644 --- a/recipes/bioconductor-granulator/meta.yaml +++ b/recipes/bioconductor-granulator/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "granulator" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: granulator is an R package for the cell type deconvolution of heterogeneous tissues based on bulk RNA-seq data or single cell RNA-seq expression profiles. The package provides a unified testing interface to rapidly run and benchmark multiple state-of-the-art deconvolution methods. Data for the deconvolution of peripheral blood mononuclear cells (PBMCs) into individual immune cell types is provided as well. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Rapid benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 05c4025460a33eb195280f676bd5695f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-granulator", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: @@ -57,13 +59,16 @@ requirements: - r-rlang - r-tibble - r-tidyr + +source: + md5: 24b4d506d8a9dbd7c3d6db64d8aa3257 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Rapid benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data' - description: 'granulator is an R package for the cell type deconvolution of heterogeneous tissues based on bulk RNA-seq data or single cell RNA-seq expression profiles. The package provides a unified testing interface to rapidly run and benchmark multiple state-of-the-art deconvolution methods. Data for the deconvolution of peripheral blood mononuclear cells (PBMCs) into individual immune cell types is provided as well.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-graper/meta.yaml b/recipes/bioconductor-graper/meta.yaml index 5f18d9093b48a..a149671d75e01 100644 --- a/recipes/bioconductor-graper/meta.yaml +++ b/recipes/bioconductor-graper/meta.yaml @@ -1,25 +1,31 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "graper" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package enables regression and classification on high-dimensional data with different relative strengths of penalization for different feature groups, such as different assays or omic types. The optimal relative strengths are chosen adaptively. Optimisation is performed using a variational Bayes approach. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e969608b591224df6c92d73194adea89 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-graper", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-bh @@ -40,17 +46,16 @@ requirements: - r-matrixstats - r-rcpp - r-rcpparmadillo - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 9359b64d5e98409d31c081cb4a93a086 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes' - description: 'This package enables regression and classification on high-dimensional data with different relative strengths of penalization for different feature groups, such as different assays or omic types. The optimal relative strengths are chosen adaptively. Optimisation is performed using a variational Bayes approach.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-graph/meta.yaml b/recipes/bioconductor-graph/meta.yaml index 3d9995b0183a9..75dbfc37e4d57 100644 --- a/recipes/bioconductor-graph/meta.yaml +++ b/recipes/bioconductor-graph/meta.yaml @@ -1,46 +1,20 @@ -{% set version = "1.80.0" %} +{% set version = "1.84.0" %} {% set name = "graph" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package that implements some simple graph handling capabilities. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'graph: A package to handle graph data structures' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 735b96df0f7c955806148170220b75b2 - patches: - - patch build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-graph", max_pin="x.x") }}' -# Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle, knitr -requirements: - host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - r-base - - libblas - - liblapack - run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - r-base - build: - - {{ compiler('c') }} - - make -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'graph: A package to handle graph data structures' - description: 'A package that implements some simple graph handling capabilities.' + extra: additional-platforms: - linux-aarch64 @@ -52,3 +26,35 @@ extra: path: recipes/bioconductor-graph version: 1.58.2 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle, knitr +requirements: + build: + - {{ compiler('c') }} + - make + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - r-base + - libblas + - liblapack + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - r-base + +source: + md5: a38351439991155e17115982b8f2e559 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + patches: + - Makevars.patch + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-graph/patch b/recipes/bioconductor-graph/patch deleted file mode 100644 index 1c45221f5ae62..0000000000000 --- a/recipes/bioconductor-graph/patch +++ /dev/null @@ -1,11 +0,0 @@ -diff --git a/src/Makevars b/src/Makevars -index 5ddfd10..77759f9 100644 ---- src/Makevars -+++ src/Makevars -@@ -1,5 +1,5 @@ - after: $(SHLIB) -- mv $(SHLIB) BioC_graph$(SHLIB_EXT) -+ cp $(SHLIB) BioC_graph$(SHLIB_EXT) - - # By default, 'R CMD build' won't remove that file so it will end up in the - # source tarball (observed with R 2.12.0). diff --git a/recipes/bioconductor-graphalignment/meta.yaml b/recipes/bioconductor-graphalignment/meta.yaml index 29442eaaf9529..acf835e3cbaac 100644 --- a/recipes/bioconductor-graphalignment/meta.yaml +++ b/recipes/bioconductor-graphalignment/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.66.0" %} +{% set version = "1.70.0" %} {% set name = "GraphAlignment" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0bc71a4722d0771d97671e81103bc8bb +about: + description: Graph alignment is an extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores. (J. Berg and M. Laessig, "Cross-species analysis of biological networks by Bayesian alignment", PNAS 103 (29), 10967-10972 (2006)) + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: GraphAlignment build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-graphalignment", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - make +source: + md5: 810f6b4520c38556ae64726d1873620d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: GraphAlignment - description: 'Graph alignment is an extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores. (J. Berg and M. Laessig, "Cross-species analysis of biological networks by Bayesian alignment", PNAS 103 (29), 10967-10972 (2006))' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-graphat/meta.yaml b/recipes/bioconductor-graphat/meta.yaml index 39efd6cd695cd..b359ce6b001fd 100644 --- a/recipes/bioconductor-graphat/meta.yaml +++ b/recipes/bioconductor-graphat/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "GraphAT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions and data used in Balasubramanian, et al. (2004) + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Graph Theoretic Association Tests -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 075a7ac1af3518ac6ef4b9087107b482 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-graphat", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:graphat + - doi:10.1093/bioinformatics/bth405 + parent_recipe: + name: bioconductor-graphat + path: recipes/bioconductor-graphat + version: 1.52.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-mcmcpack run: - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-mcmcpack + +source: + md5: 5509da5e60b7666f716c5363318e670a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Graph Theoretic Association Tests' - description: 'Functions and data used in Balasubramanian, et al. (2004)' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:graphat - - doi:10.1093/bioinformatics/bth405 - parent_recipe: - name: bioconductor-graphat - path: recipes/bioconductor-graphat - version: 1.52.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-graphite/meta.yaml b/recipes/bioconductor-graphite/meta.yaml index cbbc5f5590f62..4448d8625946e 100644 --- a/recipes/bioconductor-graphite/meta.yaml +++ b/recipes/bioconductor-graphite/meta.yaml @@ -1,56 +1,62 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "graphite" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Graph objects from pathway topology derived from KEGG, Panther, PathBank, PharmGKB, Reactome SMPDB and WikiPathways databases. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + summary: GRAPH Interaction from pathway Topological Environment -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 532e304cdb96a828c4b764bfd36cce85 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-graphite", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:graphite + parent_recipe: + name: bioconductor-graphite + path: recipes/bioconductor-graphite + version: 1.26.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: checkmate, a4Preproc, ALL, BiocStyle, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-httr - r-purrr - r-rappdirs - r-rlang run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-httr - r-purrr - r-rappdirs - r-rlang + +source: + md5: c18e901f2f944c9d1115237ad417ee35 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3 - summary: 'GRAPH Interaction from pathway Topological Environment' - description: 'Graph objects from pathway topology derived from KEGG, Panther, PathBank, PharmGKB, Reactome SMPDB and WikiPathways databases.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' -extra: - identifiers: - - biotools:graphite - parent_recipe: - name: bioconductor-graphite - path: recipes/bioconductor-graphite - version: 1.26.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-grasp2db/meta.yaml b/recipes/bioconductor-grasp2db/meta.yaml index d1c3907d36ee0..0cfcf038045d6 100644 --- a/recipes/bioconductor-grasp2db/meta.yaml +++ b/recipes/bioconductor-grasp2db/meta.yaml @@ -1,51 +1,56 @@ {% set version = "1.1.0" %} {% set name = "grasp2db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: grasp2db, sqlite wrap of NHLBI GRASP 2.0, an extended GWAS catalog. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + file LICENSE + license_file: LICENSE + summary: grasp2db, sqlite wrap of GRASP 2.0 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3fc90fc7c99e7da51dcbb687fd2d5515 build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-grasp2db", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: gwascat, knitr requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 - r-base - r-dbplyr - r-digest - r-dplyr - r-rsqlite run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 - r-base - r-dbplyr - r-digest - r-dplyr - r-rsqlite - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 3fc90fc7c99e7da51dcbb687fd2d5515 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'Artistic-2.0 + file LICENSE' - summary: 'grasp2db, sqlite wrap of GRASP 2.0' - description: 'grasp2db, sqlite wrap of NHLBI GRASP 2.0, an extended GWAS catalog.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-grenits/meta.yaml b/recipes/bioconductor-grenits/meta.yaml index 3625cf4b661d6..4ba740dd5fcbd 100644 --- a/recipes/bioconductor-grenits/meta.yaml +++ b/recipes/bioconductor-grenits/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.54.0" %} +{% set version = "1.58.0" %} {% set name = "GRENITS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The package offers four network inference statistical models using Dynamic Bayesian Networks and Gibbs Variable Selection: a linear interaction model, two linear interaction models with added experimental noise (Gaussian and Student distributed) for the case where replicates are available and a non-linear interaction model.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Gene Regulatory Network Inference Using Time Series -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fd00e191f8c57c6ef54146263d21a089 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-grenits", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: network requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - - 'r-ggplot2 >=0.9.0' - - 'r-rcpp >=0.8.6' - - 'r-rcpparmadillo >=0.2.8' + - r-ggplot2 >=0.9.0 + - r-rcpp >=0.8.6 + - r-rcpparmadillo >=0.2.8 - r-reshape2 - libblas - liblapack run: - r-base - - 'r-ggplot2 >=0.9.0' - - 'r-rcpp >=0.8.6' - - 'r-rcpparmadillo >=0.2.8' + - r-ggplot2 >=0.9.0 + - r-rcpp >=0.8.6 + - r-rcpparmadillo >=0.2.8 - r-reshape2 - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: c7cb716ed0a16b2af28309de7dac9a38 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Gene Regulatory Network Inference Using Time Series' - description: 'The package offers four network inference statistical models using Dynamic Bayesian Networks and Gibbs Variable Selection: a linear interaction model, two linear interaction models with added experimental noise (Gaussian and Student distributed) for the case where replicates are available and a non-linear interaction model.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-greylistchip/meta.yaml b/recipes/bioconductor-greylistchip/meta.yaml index 69807bd80c9c9..8ac7cc2336db2 100644 --- a/recipes/bioconductor-greylistchip/meta.yaml +++ b/recipes/bioconductor-greylistchip/meta.yaml @@ -1,52 +1,57 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "GreyListChIP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Identify regions of ChIP experiments with high signal in the input, that lead to spurious peaks during peak calling. Remove reads aligning to these regions prior to peak calling, for cleaner ChIP analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Grey Lists -- Mask Artefact Regions Based on ChIP Inputs -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 42fa9dbbc56cc2c4fdf511ce67ee234e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-greylistchip", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, BiocGenerics, RUnit, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-mass run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-mass + +source: + md5: f5a1217e86a8866af3bc6b2fd034418b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Grey Lists -- Mask Artefact Regions Based on ChIP Inputs' - description: 'Identify regions of ChIP experiments with high signal in the input, that lead to spurious peaks during peak calling. Remove reads aligning to these regions prior to peak calling, for cleaner ChIP analysis.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-grmetrics/meta.yaml b/recipes/bioconductor-grmetrics/meta.yaml index 138a1f01df8f1..732bb23397e2a 100644 --- a/recipes/bioconductor-grmetrics/meta.yaml +++ b/recipes/bioconductor-grmetrics/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "GRmetrics" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions for calculating and visualizing growth-rate inhibition (GR) metrics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Calculate growth-rate inhibition (GR) metrics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 16b27cb79eafe9dbdbb84f0626c5f8da build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-grmetrics", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:grmetrics + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-grmetrics + path: recipes/bioconductor-grmetrics + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, tinytex requirements: host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-drc - r-ggplot2 - r-plotly run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-drc - r-ggplot2 - r-plotly + +source: + md5: eeda95aa1c3d989869038bc56556bc03 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Calculate growth-rate inhibition (GR) metrics' - description: 'Functions for calculating and visualizing growth-rate inhibition (GR) metrics.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:grmetrics - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-grmetrics - path: recipes/bioconductor-grmetrics - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-grndata/meta.yaml b/recipes/bioconductor-grndata/meta.yaml index 19ec93513a47e..178b26de71e82 100644 --- a/recipes/bioconductor-grndata/meta.yaml +++ b/recipes/bioconductor-grndata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "grndata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0ebac67277a5ca915f9a971d3659af5e +about: + description: Simulated expression data for five large Gene Regulatory Networks from different simulators + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Synthetic Expression Data for Gene Regulatory Network Inference build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-grndata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: RUnit, BiocGenerics, knitr requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 267a7286c8e9207afa54c0e5b1fff229 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Synthetic Expression Data for Gene Regulatory Network Inference' - description: 'Simulated expression data for five large Gene Regulatory Networks from different simulators' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-grndata/post-link.sh b/recipes/bioconductor-grndata/post-link.sh index cc47b0a1e8a7f..92ce49c7bf87e 100644 --- a/recipes/bioconductor-grndata/post-link.sh +++ b/recipes/bioconductor-grndata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "grndata-1.34.0" +installBiocDataPackage.sh "grndata-1.38.0" diff --git a/recipes/bioconductor-gsalightning/meta.yaml b/recipes/bioconductor-gsalightning/meta.yaml index f343d529a8d02..148cd8400da74 100644 --- a/recipes/bioconductor-gsalightning/meta.yaml +++ b/recipes/bioconductor-gsalightning/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "GSALightning" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: GSALightning provides a fast implementation of permutation-based gene set analysis for two-sample problem. This package is particularly useful when testing simultaneously a large number of gene sets, or when a large number of permutations is necessary for more accurate p-values estimation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Fast Permutation-based Gene Set Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c6828603275d57045e613f1e7c0f143d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gsalightning", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:gsalightning + - doi:10.1093/bioinformatics/btw349 + parent_recipe: + name: bioconductor-gsalightning + path: recipes/bioconductor-gsalightning + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: @@ -29,21 +40,16 @@ requirements: - r-base - r-data.table - r-matrix + +source: + md5: f3f437dfffed696cc81cc9093210823e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Fast Permutation-based Gene Set Analysis' - description: 'GSALightning provides a fast implementation of permutation-based gene set analysis for two-sample problem. This package is particularly useful when testing simultaneously a large number of gene sets, or when a large number of permutations is necessary for more accurate p-values estimation.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:gsalightning - - doi:10.1093/bioinformatics/btw349 - parent_recipe: - name: bioconductor-gsalightning - path: recipes/bioconductor-gsalightning - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gsar/meta.yaml b/recipes/bioconductor-gsar/meta.yaml index 294a6678158ba..61b41193a3285 100644 --- a/recipes/bioconductor-gsar/meta.yaml +++ b/recipes/bioconductor-gsar/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "GSAR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9828682d8721bde17ea31c9ed807174d +about: + description: Gene set analysis using specific alternative hypotheses. Tests for differential expression, scale and net correlation structure. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Gene Set Analysis in R build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gsar", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate, org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR, BiocStyle requirements: host: - r-base - - 'r-igraph >=0.7.1' + - r-igraph >=0.7.1 run: - r-base - - 'r-igraph >=0.7.1' + - r-igraph >=0.7.1 +source: + md5: 1f1a274ccebaff6a0a2ee6ffbb01c8ea + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Gene Set Analysis in R' - description: 'Gene set analysis using specific alternative hypotheses. Tests for differential expression, scale and net correlation structure.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gsbenchmark/meta.yaml b/recipes/bioconductor-gsbenchmark/meta.yaml index 562dacde1d6fc..51d1146894b12 100644 --- a/recipes/bioconductor-gsbenchmark/meta.yaml +++ b/recipes/bioconductor-gsbenchmark/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "GSBenchMark" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bedfa52de1b414ae5fe9d5fc376380ba +about: + description: Benchmarks for Machine Learning Analysis of the Gene Sets. The package contains a list of pathways and gene expression data sets used in "Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)" (2010) by Eddy et al. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Gene Set Benchmark build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gsbenchmark", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9225e7c0e665cac115205f804d932d00 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Gene Set Benchmark' - description: 'Benchmarks for Machine Learning Analysis of the Gene Sets. The package contains a list of pathways and gene expression data sets used in "Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)" (2010) by Eddy et al.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gsbenchmark/post-link.sh b/recipes/bioconductor-gsbenchmark/post-link.sh index 7e75d49468c5e..c534cd40bf9aa 100644 --- a/recipes/bioconductor-gsbenchmark/post-link.sh +++ b/recipes/bioconductor-gsbenchmark/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gsbenchmark-1.22.0" +installBiocDataPackage.sh "gsbenchmark-1.26.0" diff --git a/recipes/bioconductor-gsca/meta.yaml b/recipes/bioconductor-gsca/meta.yaml index a02a1031371d3..cd4ce8c3db640 100644 --- a/recipes/bioconductor-gsca/meta.yaml +++ b/recipes/bioconductor-gsca/meta.yaml @@ -1,28 +1,38 @@ -{% set version = "2.32.0" %} +{% set version = "2.36.0" %} {% set name = "GSCA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: GSCA takes as input several lists of activated and repressed genes. GSCA then searches through a compendium of publicly available gene expression profiles for biological contexts that are enriched with a specified pattern of gene expression. GSCA provides both traditional R functions and interactive, user-friendly user interface. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL(>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'GSCA: Gene Set Context Analysis' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6cf569e7be20a330c190c8c3af6f0654 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gsca", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:gsca + parent_recipe: + name: bioconductor-gsca + path: recipes/bioconductor-gsca + version: 2.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr, Affyhgu133Plus2Expr requirements: host: - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - bioconductor-rhdf5 >=2.50.0,<2.51.0 - r-base - r-ggplot2 - r-gplots @@ -31,7 +41,7 @@ requirements: - r-shiny - r-sp run: - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - bioconductor-rhdf5 >=2.50.0,<2.51.0 - r-base - r-ggplot2 - r-gplots @@ -39,20 +49,16 @@ requirements: - r-reshape2 - r-shiny - r-sp + +source: + md5: ae96234baeb055b3cbf1f2995f7692cc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL(>=2) - summary: 'GSCA: Gene Set Context Analysis' - description: 'GSCA takes as input several lists of activated and repressed genes. GSCA then searches through a compendium of publicly available gene expression profiles for biological contexts that are enriched with a specified pattern of gene expression. GSCA provides both traditional R functions and interactive, user-friendly user interface.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:gsca - parent_recipe: - name: bioconductor-gsca - path: recipes/bioconductor-gsca - version: 2.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gscreend/meta.yaml b/recipes/bioconductor-gscreend/meta.yaml index 8e69d8eeb82c9..08a2191b806dd 100644 --- a/recipes/bioconductor-gscreend/meta.yaml +++ b/recipes/bioconductor-gscreend/meta.yaml @@ -1,44 +1,45 @@ -{% set version = "1.14.0" %} +{% set version = "1.20.0" %} {% set name = "gscreend" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6d79483ce0c766b1779a2dab5614e249 +about: + description: Package for the analysis of pooled genetic screens (e.g. CRISPR-KO). The analysis of such screens is based on the comparison of gRNA abundances before and after a cell proliferation phase. The gscreend packages takes gRNA counts as input and allows detection of genes whose knockout decreases or increases cell proliferation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Analysis of pooled genetic screens build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic -# Suggests: knitr, testthat, rmarkdown + run_exports: '{{ pin_subpackage("bioconductor-gscreend", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: knitr, testthat, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-fgarch - r-nloptr run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-fgarch - r-nloptr +source: + md5: d1ac4dce80355323745f3a10cd12d7ad + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Analysis of pooled genetic screens' - description: 'Package for the analysis of pooled genetic screens (e.g. CRISPR-KO). The analysis of such screens is based on the comparison of gRNA abundances before and after a cell proliferation phase. The gscreend packages takes gRNA counts as input and allows detection of genes whose knockout decreases or increases cell proliferation.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gse103322/meta.yaml b/recipes/bioconductor-gse103322/meta.yaml index 78cde2aa8566a..ce1000d44de82 100644 --- a/recipes/bioconductor-gse103322/meta.yaml +++ b/recipes/bioconductor-gse103322/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "GSE103322" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3816b430b716edaaa0ef22dba38cf58e +about: + description: Single cell RNA-Seq data for 5902 cells from 18 patients with oral cavity head and neck squamous cell carcinoma available as GEO accession [GSE103322] (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE103322). GSE103322 data have been parsed into a SincleCellExperiment object available in ExperimentHub. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: GEO accession data GSE103322 as a SingleCellExperiment build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gse103322", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown, SummarizedExperiment, SingleCellExperiment requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ef8a6be2fbc94685daf9df2aa7b69085 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'GEO accession data GSE103322 as a SingleCellExperiment' - description: 'Single cell RNA-Seq data for 5902 cells from 18 patients with oral cavity head and neck squamous cell carcinoma available as GEO accession [GSE103322] (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE103322). GSE103322 data have been parsed into a SincleCellExperiment object available in ExperimentHub.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gse103322/post-link.sh b/recipes/bioconductor-gse103322/post-link.sh index 719c9773297fe..eb95c2e29f926 100644 --- a/recipes/bioconductor-gse103322/post-link.sh +++ b/recipes/bioconductor-gse103322/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gse103322-1.8.0" +installBiocDataPackage.sh "gse103322-1.12.0" diff --git a/recipes/bioconductor-gse13015/meta.yaml b/recipes/bioconductor-gse13015/meta.yaml index f6b004027246e..91e0aa0df7a46 100644 --- a/recipes/bioconductor-gse13015/meta.yaml +++ b/recipes/bioconductor-gse13015/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "GSE13015" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Microarray expression matrix platform GPL6106 and clinical data for 67 septicemic patients and made them available as GEO accession [GSE13015](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13015). GSE13015 data have been parsed into a SummarizedExperiment object available in ExperimentHub. This data data could be used as an example supporting BloodGen3Module R package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT License + summary: GEO accession data GSE13015_GPL6106 as a SummarizedExperiment -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 99fae6872abf6820842a1340f7fd6b4e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gse13015", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 016137663819811515c8a31ad8970e36 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT License' - summary: 'GEO accession data GSE13015_GPL6106 as a SummarizedExperiment' - description: 'Microarray expression matrix platform GPL6106 and clinical data for 67 septicemic patients and made them available as GEO accession [GSE13015](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13015). GSE13015 data have been parsed into a SummarizedExperiment object available in ExperimentHub. This data data could be used as an example supporting BloodGen3Module R package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gse13015/post-link.sh b/recipes/bioconductor-gse13015/post-link.sh index 03e9a7afbddbe..678aa6346dcc1 100644 --- a/recipes/bioconductor-gse13015/post-link.sh +++ b/recipes/bioconductor-gse13015/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gse13015-1.10.0" +installBiocDataPackage.sh "gse13015-1.14.0" diff --git a/recipes/bioconductor-gse159526/meta.yaml b/recipes/bioconductor-gse159526/meta.yaml index abca80d825751..bbb5656bc3cd6 100644 --- a/recipes/bioconductor-gse159526/meta.yaml +++ b/recipes/bioconductor-gse159526/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "GSE159526" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d89442c94cb87f0760a9f0f85426a8fa +about: + description: 19 term and 9 first trimester placental chorionic villi and matched cell-sorted samples ran on Illumina HumanMethylationEPIC DNA methylation microarrays. This data was made available on GEO accession [GSE159526](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159526). Both the raw and processed data has been made available on \code{ExperimentHub}. Raw unprocessed data formatted as an RGChannelSet object for integration and normalization using minfi and other existing Bioconductor packages. Processed normalized data is also available as a DNA methylation \code{matrix}, with a corresponding phenotype information as a \code{data.frame} object. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Placental cell DNA methylation data from GEO accession GSE159526 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gse159526", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: ExperimentHub, BiocStyle, RefManageR, knitr, rmarkdown, testthat, minfi, tibble, sessioninfo requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 996ed6300106923241c4624b1fbd27bb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Placental cell DNA methylation data from GEO accession GSE159526' - description: '19 term and 9 first trimester placental chorionic villi and matched cell-sorted samples ran on Illumina HumanMethylationEPIC DNA methylation microarrays. This data was made available on GEO accession [GSE159526](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159526). Both the raw and processed data has been made available on \code{ExperimentHub}. Raw unprocessed data formatted as an RGChannelSet object for integration and normalization using minfi and other existing Bioconductor packages. Processed normalized data is also available as a DNA methylation \code{matrix}, with a corresponding phenotype information as a \code{data.frame} object.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gse159526/post-link.sh b/recipes/bioconductor-gse159526/post-link.sh index 70558b3f8c891..12815431f97c8 100644 --- a/recipes/bioconductor-gse159526/post-link.sh +++ b/recipes/bioconductor-gse159526/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gse159526-1.8.0" +installBiocDataPackage.sh "gse159526-1.12.0" diff --git a/recipes/bioconductor-gse62944/meta.yaml b/recipes/bioconductor-gse62944/meta.yaml index 925d457637f38..ba21f3f2683ff 100644 --- a/recipes/bioconductor-gse62944/meta.yaml +++ b/recipes/bioconductor-gse62944/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "GSE62944" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b6c58aaee948c9cd0e0d52b5adcf264 +about: + description: TCGA processed RNA-Seq data for 9264 tumor and 741 normal samples across 24 cancer types and made them available as GEO accession [GSE62944](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944). GSE62944 data have been parsed into a SummarizedExperiment object available in ExperimentHub. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: GEO accession data GSE62944 as a SummarizedExperiment build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gse62944", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown, DESeq2 requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 314ad5bf5a423531bc075f753658e28a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'GEO accession data GSE62944 as a SummarizedExperiment' - description: 'TCGA processed RNA-Seq data for 9264 tumor and 741 normal samples across 24 cancer types and made them available as GEO accession [GSE62944](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944). GSE62944 data have been parsed into a SummarizedExperiment object available in ExperimentHub.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gse62944/post-link.sh b/recipes/bioconductor-gse62944/post-link.sh index 35edd4d1cec52..73ffb235c9e85 100644 --- a/recipes/bioconductor-gse62944/post-link.sh +++ b/recipes/bioconductor-gse62944/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gse62944-1.30.0" +installBiocDataPackage.sh "gse62944-1.34.0" diff --git a/recipes/bioconductor-gseabase/meta.yaml b/recipes/bioconductor-gseabase/meta.yaml index 87db5ecfad250..fa01e2f0fbbda 100644 --- a/recipes/bioconductor-gseabase/meta.yaml +++ b/recipes/bioconductor-gseabase/meta.yaml @@ -1,56 +1,62 @@ -{% set version = "1.64.0" %} +{% set version = "1.68.0" %} {% set name = "GSEABase" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Gene set enrichment data structures and methods -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a9d4d48654c9a05cdec2f09f8f805c4e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gseabase", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:gseabase + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-gseabase + path: recipes/bioconductor-gseabase + version: 1.42.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools, testthat, BiocStyle, knitr, RUnit requirements: host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-xml run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-xml + +source: + md5: 161a7472eefd9f19ed422d52396e646c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Gene set enrichment data structures and methods' - description: 'This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).' -extra: - identifiers: - - biotools:gseabase - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-gseabase - path: recipes/bioconductor-gseabase - version: 1.42.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gseabenchmarker/meta.yaml b/recipes/bioconductor-gseabenchmarker/meta.yaml index d3a50bed81819..d0928f6930792 100644 --- a/recipes/bioconductor-gseabenchmarker/meta.yaml +++ b/recipes/bioconductor-gseabenchmarker/meta.yaml @@ -1,60 +1,65 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "GSEABenchmarkeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The GSEABenchmarkeR package implements an extendable framework for reproducible evaluation of set- and network-based methods for enrichment analysis of gene expression data. This includes support for the efficient execution of these methods on comprehensive real data compendia (microarray and RNA-seq) using parallel computation on standard workstations and institutional computer grids. Methods can then be assessed with respect to runtime, statistical significance, and relevance of the results for the phenotypes investigated. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Reproducible GSEA Benchmarking -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9f297d155b3c254f091eb70a180ea9fa build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gseabenchmarker", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, GSE62944, knitr, rappdirs, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-enrichmentbrowser >=2.32.0,<2.33.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-keggandmetacoredzpathwaysgeo >=1.22.0,<1.23.0' - - 'bioconductor-keggdzpathwaysgeo >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-enrichmentbrowser >=2.36.0,<2.37.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-keggandmetacoredzpathwaysgeo >=1.26.0,<1.27.0 + - bioconductor-keggdzpathwaysgeo >=1.44.0,<1.45.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-enrichmentbrowser >=2.32.0,<2.33.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-keggandmetacoredzpathwaysgeo >=1.22.0,<1.23.0' - - 'bioconductor-keggdzpathwaysgeo >=1.40.0,<1.41.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-enrichmentbrowser >=2.36.0,<2.37.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-keggandmetacoredzpathwaysgeo >=1.26.0,<1.27.0 + - bioconductor-keggdzpathwaysgeo >=1.44.0,<1.45.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + +source: + md5: f42af8cd3a0b50828a91a5c8b99d4be7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Reproducible GSEA Benchmarking' - description: 'The GSEABenchmarkeR package implements an extendable framework for reproducible evaluation of set- and network-based methods for enrichment analysis of gene expression data. This includes support for the efficient execution of these methods on comprehensive real data compendia (microarray and RNA-seq) using parallel computation on standard workstations and institutional computer grids. Methods can then be assessed with respect to runtime, statistical significance, and relevance of the results for the phenotypes investigated.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gsealm/meta.yaml b/recipes/bioconductor-gsealm/meta.yaml index 502e5017b9cf4..c15d1f5a9a00b 100644 --- a/recipes/bioconductor-gsealm/meta.yaml +++ b/recipes/bioconductor-gsealm/meta.yaml @@ -1,40 +1,21 @@ -{% set version = "1.62.0" %} +{% set version = "1.66.0" %} {% set name = "GSEAlm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Linear Model Toolset for Gene Set Enrichment Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b88623d080b75bb6775026e9e6c4dd9e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gsealm", max_pin="x.x") }}' - noarch: generic -# Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Linear Model Toolset for Gene Set Enrichment Analysis' - description: 'Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics.' + extra: identifiers: - biotools:gsealm @@ -44,3 +25,28 @@ extra: path: recipes/bioconductor-gsealm version: 1.40.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + +source: + md5: 2c7b3b95a50d2fcc962e5693be5142cb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-gseamining/meta.yaml b/recipes/bioconductor-gseamining/meta.yaml index bff37cad1e697..3e7e5dad24257 100644 --- a/recipes/bioconductor-gseamining/meta.yaml +++ b/recipes/bioconductor-gseamining/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "GSEAmining" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Gene Set Enrichment Analysis is a very powerful and interesting computational method that allows an easy correlation between differential expressed genes and biological processes. Unfortunately, although it was designed to help researchers to interpret gene expression data it can generate huge amounts of results whose biological meaning can be difficult to interpret. Many available tools rely on the hierarchically structured Gene Ontology (GO) classification to reduce reundandcy in the results. However, due to the popularity of GSEA many more gene set collections, such as those in the Molecular Signatures Database are emerging. Since these collections are not organized as those in GO, their usage for GSEA do not always give a straightforward answer or, in other words, getting all the meaninful information can be challenging with the currently available tools. For these reasons, GSEAmining was born to be an easy tool to create reproducible reports to help researchers make biological sense of GSEA outputs. Given the results of GSEA, GSEAmining clusters the different gene sets collections based on the presence of the same genes in the leadind edge (core) subset. Leading edge subsets are those genes that contribute most to the enrichment score of each collection of genes or gene sets. For this reason, gene sets that participate in similar biological processes should share genes in common and in turn cluster together. After that, GSEAmining is able to identify and represent for each cluster: - The most enriched terms in the names of gene sets (as wordclouds) - The most enriched genes in the leading edge subsets (as bar plots). In each case, positive and negative enrichments are shown in different colors so it is easy to distinguish biological processes or genes that may be of interest in that particular study.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 | file LICENSE + license_file: LICENSE + summary: Make Biological Sense of Gene Set Enrichment Analysis Outputs -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 703f12fed97e95761b2cd41894da0645 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gseamining", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, clusterProfiler, testthat, tm requirements: host: @@ -43,13 +45,16 @@ requirements: - r-stringr - r-tibble - r-tidytext + +source: + md5: 425b74e84fb163671dbc3e8dc28a4064 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 | file LICENSE' - summary: 'Make Biological Sense of Gene Set Enrichment Analysis Outputs' - description: 'Gene Set Enrichment Analysis is a very powerful and interesting computational method that allows an easy correlation between differential expressed genes and biological processes. Unfortunately, although it was designed to help researchers to interpret gene expression data it can generate huge amounts of results whose biological meaning can be difficult to interpret. Many available tools rely on the hierarchically structured Gene Ontology (GO) classification to reduce reundandcy in the results. However, due to the popularity of GSEA many more gene set collections, such as those in the Molecular Signatures Database are emerging. Since these collections are not organized as those in GO, their usage for GSEA do not always give a straightforward answer or, in other words, getting all the meaninful information can be challenging with the currently available tools. For these reasons, GSEAmining was born to be an easy tool to create reproducible reports to help researchers make biological sense of GSEA outputs. Given the results of GSEA, GSEAmining clusters the different gene sets collections based on the presence of the same genes in the leadind edge (core) subset. Leading edge subsets are those genes that contribute most to the enrichment score of each collection of genes or gene sets. For this reason, gene sets that participate in similar biological processes should share genes in common and in turn cluster together. After that, GSEAmining is able to identify and represent for each cluster: - The most enriched terms in the names of gene sets (as wordclouds) - The most enriched genes in the leading edge subsets (as bar plots). In each case, positive and negative enrichments are shown in different colors so it is easy to distinguish biological processes or genes that may be of interest in that particular study.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gsean/meta.yaml b/recipes/bioconductor-gsean/meta.yaml index 56e88aeaa6ee8..988c22bc8d33f 100644 --- a/recipes/bioconductor-gsean/meta.yaml +++ b/recipes/bioconductor-gsean/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "gsean" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 501dfe30896b53197345abe9d1600247 +about: + description: Biological molecules in a living organism seldom work individually. They usually interact each other in a cooperative way. Biological process is too complicated to understand without considering such interactions. Thus, network-based procedures can be seen as powerful methods for studying complex process. However, many methods are devised for analyzing individual genes. It is said that techniques based on biological networks such as gene co-expression are more precise ways to represent information than those using lists of genes only. This package is aimed to integrate the gene expression and biological network. A biological network is constructed from gene expression data and it is used for Gene Set Enrichment Analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Gene Set Enrichment Analysis with Networks build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gsean", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: SummarizedExperiment, pasilla, org.Dm.eg.db, AnnotationDbi, knitr, plotly, WGCNA, rmarkdown requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-ppinfer >=1.28.0,<1.29.0' + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-ppinfer >=1.32.0,<1.33.0 - r-base - libblas - liblapack run: - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-ppinfer >=1.28.0,<1.29.0' + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-ppinfer >=1.32.0,<1.33.0 - r-base - build: - - {{ compiler('c') }} - - make +source: + md5: a8d81fcf1bcae07319491d83059e6eb3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Gene Set Enrichment Analysis with Networks' - description: 'Biological molecules in a living organism seldom work individually. They usually interact each other in a cooperative way. Biological process is too complicated to understand without considering such interactions. Thus, network-based procedures can be seen as powerful methods for studying complex process. However, many methods are devised for analyzing individual genes. It is said that techniques based on biological networks such as gene co-expression are more precise ways to represent information than those using lists of genes only. This package is aimed to integrate the gene expression and biological network. A biological network is constructed from gene expression data and it is used for Gene Set Enrichment Analysis.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gsgalgor/meta.yaml b/recipes/bioconductor-gsgalgor/meta.yaml index cf311c036c026..b780668052ca7 100644 --- a/recipes/bioconductor-gsgalgor/meta.yaml +++ b/recipes/bioconductor-gsgalgor/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "GSgalgoR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A multi-objective optimization algorithm for disease sub-type discovery based on a non-dominated sorting genetic algorithm. The 'Galgo' framework combines the advantages of clustering algorithms for grouping heterogeneous 'omics' data and the searching properties of genetic algorithms for feature selection. The algorithm search for the optimal number of clusters determination considering the features that maximize the survival difference between sub-types while keeping cluster consistency high. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: An Evolutionary Framework for the Identification and Study of Prognostic Gene Expression Signatures in Cancer -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 09d5b90490f44ee7384c71762228244d build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gsgalgor", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, ggplot2, BiocStyle, genefu, survcomp, Biobase, survminer, breastCancerTRANSBIG, breastCancerUPP, iC10TrainingData, pamr, testthat requirements: host: @@ -39,13 +41,16 @@ requirements: - r-nsga2r - r-proxy - r-survival + +source: + md5: e8e7811793c9610d8981316c7043c129 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'An Evolutionary Framework for the Identification and Study of Prognostic Gene Expression Signatures in Cancer' - description: 'A multi-objective optimization algorithm for disease sub-type discovery based on a non-dominated sorting genetic algorithm. The ''Galgo'' framework combines the advantages of clustering algorithms for grouping heterogeneous ''omics'' data and the searching properties of genetic algorithms for feature selection. The algorithm search for the optimal number of clusters determination considering the features that maximize the survival difference between sub-types while keeping cluster consistency high.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gsreg/meta.yaml b/recipes/bioconductor-gsreg/meta.yaml index 42f7a252d92c8..cd52bd52667a7 100644 --- a/recipes/bioconductor-gsreg/meta.yaml +++ b/recipes/bioconductor-gsreg/meta.yaml @@ -1,58 +1,64 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "GSReg" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package for gene set analysis based on the variability of expressions as well as a method to detect Alternative Splicing Events . It implements DIfferential RAnk Conservation (DIRAC) and gene set Expression Variation Analysis (EVA) methods. For detecting Differentially Spliced genes, it provides an implementation of the Spliced-EVA (SEVA). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Gene Set Regulation (GS-Reg) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 631e2589b571bfcdf38b5673ba0693d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gsreg", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:gsreg + - doi:10.4137/CIN.S14066 + parent_recipe: + name: bioconductor-gsreg + path: recipes/bioconductor-gsreg + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: GenomicRanges, GSBenchMark requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-homo.sapiens >=1.3.0,<1.4.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - libblas - liblapack run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-homo.sapiens >=1.3.0,<1.4.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 66bab6fa85136de1d62091d22cc9e7ea + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Gene Set Regulation (GS-Reg)' - description: 'A package for gene set analysis based on the variability of expressions as well as a method to detect Alternative Splicing Events . It implements DIfferential RAnk Conservation (DIRAC) and gene set Expression Variation Analysis (EVA) methods. For detecting Differentially Spliced genes, it provides an implementation of the Spliced-EVA (SEVA).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:gsreg - - doi:10.4137/CIN.S14066 - parent_recipe: - name: bioconductor-gsreg - path: recipes/bioconductor-gsreg - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gsri/meta.yaml b/recipes/bioconductor-gsri/meta.yaml index 80acc691c0711..a4317f4e2700a 100644 --- a/recipes/bioconductor-gsri/meta.yaml +++ b/recipes/bioconductor-gsri/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "2.50.0" %} +{% set version = "2.54.0" %} {% set name = "GSRI" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The GSRI package estimates the number of differentially expressed genes in gene sets, utilizing the concept of the Gene Set Regulation Index (GSRI). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Gene Set Regulation Index -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 686ab91e4ee0adeb4828a5b2ac2f6943 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gsri", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:gsri + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-gsri + path: recipes/bioconductor-gsri + version: 2.28.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: limma, hgu95av2.db requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-les >=1.52.0,<1.53.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-les >=1.56.0,<1.57.0 - r-base - r-fdrtool run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-les >=1.52.0,<1.53.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-les >=1.56.0,<1.57.0 - r-base - r-fdrtool + +source: + md5: c49ff95b7bfa48c298c85425dc2ed22e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Gene Set Regulation Index' - description: 'The GSRI package estimates the number of differentially expressed genes in gene sets, utilizing the concept of the Gene Set Regulation Index (GSRI).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:gsri - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-gsri - path: recipes/bioconductor-gsri - version: 2.28.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gsva/build_failure.linux-aarch64.yaml b/recipes/bioconductor-gsva/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..5cc7cf520036e --- /dev/null +++ b/recipes/bioconductor-gsva/build_failure.linux-aarch64.yaml @@ -0,0 +1,108 @@ +recipe_sha: 870498c1a4ae98536717037a3f90be0d66d146ed8c1646fe200088b5e235b007 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec("r-magick"), MatchSpec("bioconductor-spatialexperiment==1.16.0=r44hdfd78af_0")} + Encountered problems while solving: + - nothing provides r-magick needed by bioconductor-spatialexperiment-1.16.0-r44hdfd78af_0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-spatialexperiment >=1.16.0,<1.17.0 [0m is not installable because it requires + [31mr-magick[0m, which does not exist (perhaps a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec("r-magick"), MatchSpec("bioconductor-spatialexperiment==1.16.0=r44hdfd78af_0")} + Encountered problems while solving: + - nothing provides r-magick needed by bioconductor-spatialexperiment-1.16.0-r44hdfd78af_0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-spatialexperiment >=1.16.0,<1.17.0 [0m is not installable because it requires + [31mr-magick[0m, which does not exist (perhaps a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec("r-magick"), MatchSpec("bioconductor-spatialexperiment==1.16.0=r44hdfd78af_0")} + Encountered problems while solving: + - nothing provides r-magick needed by bioconductor-spatialexperiment-1.16.0-r44hdfd78af_0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-spatialexperiment >=1.16.0,<1.17.0 [0m is not installable because it requires + [31mr-magick[0m, which does not exist (perhaps a missing channel). +# Last 100 lines of the build log. +reason: |- + r-magick is not built for aarch64 +category: |- + dependency issue diff --git a/recipes/bioconductor-gsva/meta.yaml b/recipes/bioconductor-gsva/meta.yaml index 9a5eb542d6fa0..b26ffe8046e84 100644 --- a/recipes/bioconductor-gsva/meta.yaml +++ b/recipes/bioconductor-gsva/meta.yaml @@ -1,76 +1,86 @@ -{% set version = "1.50.0" %} +{% set version = "2.0.0" %} {% set name = "GSVA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Gene Set Variation Analysis for Microarray and RNA-Seq Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e21af1ab9dabfa5801fb978b50f992e2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gsva", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:gsva + parent_recipe: + name: bioconductor-gsva + path: recipes/bioconductor-gsva + version: 1.28.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinydashboard, ggplot2, data.table, plotly, future, promises, shinybusy, shinyjs requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-matrix >=1.5-0' + - r-cli + - r-matrix >=1.5-0 - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-matrix >=1.5-0' - build: - - {{ compiler('c') }} - - make + - r-cli + - r-matrix >=1.5-0 + +source: + md5: be4d135cda723baf10c62f2f6357261e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'Gene Set Variation Analysis for Microarray and RNA-Seq Data' - description: 'Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:gsva - parent_recipe: - name: bioconductor-gsva - path: recipes/bioconductor-gsva - version: 1.28.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gsvadata/meta.yaml b/recipes/bioconductor-gsvadata/meta.yaml index b4a138b0bd959..4fd8237d0b6eb 100644 --- a/recipes/bioconductor-gsvadata/meta.yaml +++ b/recipes/bioconductor-gsvadata/meta.yaml @@ -1,43 +1,50 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "GSVAdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'This package stores the data employed in the vignette of the GSVA package. These data belong to the following publications: Armstrong et al. Nat Genet 30:41-47, 2002; Cahoy et al. J Neurosci 28:264-278, 2008; Carrel and Willard, Nature, 434:400-404, 2005; Huang et al. PNAS, 104:9758-9763, 2007; Pickrell et al. Nature, 464:768-722, 2010; Skaletsky et al. Nature, 423:825-837; Verhaak et al. Cancer Cell 17:98-110, 2010; Costa et al. FEBS J, 288:2311-2331, 2021.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Data employed in the vignette of the GSVA package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3c2d6a66967ab8c3c2545fc3323282b3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gsvadata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-hgu95a.db >=3.13.0,<3.14.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-hgu95a.db >=3.13.0,<3.14.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-hgu95a.db >=3.13.0,<3.14.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-hgu95a.db >=3.13.0,<3.14.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 19ce23485bb46391ee186ffc9558660e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Data employed in the vignette of the GSVA package' - description: 'This package stores the data employed in the vignette of the GSVA package. These data belong to the following publications: Armstrong et al. Nat Genet 30:41-47, 2002; Cahoy et al. J Neurosci 28:264-278, 2008; Carrel and Willard, Nature, 434:400-404, 2005; Huang et al. PNAS, 104:9758-9763, 2007; Pickrell et al. Nature, 464:768-722, 2010; Skaletsky et al. Nature, 423:825-837; Verhaak et al. Cancer Cell 17:98-110, 2010' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gsvadata/post-link.sh b/recipes/bioconductor-gsvadata/post-link.sh index 47efe8a70a147..13cf14fcfad3f 100644 --- a/recipes/bioconductor-gsvadata/post-link.sh +++ b/recipes/bioconductor-gsvadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gsvadata-1.38.0" +installBiocDataPackage.sh "gsvadata-1.42.0" diff --git a/recipes/bioconductor-gtrellis/meta.yaml b/recipes/bioconductor-gtrellis/meta.yaml index 161c476c7d085..ff3917a5fc2ad 100644 --- a/recipes/bioconductor-gtrellis/meta.yaml +++ b/recipes/bioconductor-gtrellis/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "gtrellis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Genome Level Trellis Layout -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 795b74d96310e3cd9a5771bd8695cf64 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gtrellis", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:gtrellis + parent_recipe: + name: bioconductor-gtrellis + path: recipes/bioconductor-gtrellis + version: 1.12.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 1.0.0), knitr, RColorBrewer, markdown, rmarkdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - - 'r-circlize >=0.4.8' + - r-circlize >=0.4.8 - r-getoptlong run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - - 'r-circlize >=0.4.8' + - r-circlize >=0.4.8 - r-getoptlong + +source: + md5: 6d86179be5d84e09062f5870ea6ce797 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Genome Level Trellis Layout' - description: 'Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.' - license_file: LICENSE -extra: - identifiers: - - biotools:gtrellis - parent_recipe: - name: bioconductor-gtrellis - path: recipes/bioconductor-gtrellis - version: 1.12.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-guideseq/meta.yaml b/recipes/bioconductor-guideseq/meta.yaml index b3a7b618ced7e..a935ccc369943 100644 --- a/recipes/bioconductor-guideseq/meta.yaml +++ b/recipes/bioconductor-guideseq/meta.yaml @@ -1,41 +1,54 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "GUIDEseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package implements GUIDE-seq and PEtag-seq analysis workflow including functions for filtering UMI and reads with low coverage, obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites with mismatches and indels. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: GUIDE-seq and PEtag-seq analysis pipeline -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fe01afa9546bc7bdc1fbeea8c8bda8db build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-guideseq", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:guideseq + - doi:10.1186/s12864-017-3746-y + parent_recipe: + name: bioconductor-guideseq + path: recipes/bioconductor-guideseq + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat (>= 3.0.0) requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' - - 'bioconductor-crisprseek >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-chippeakanno >=3.40.0,<3.41.0 + - bioconductor-crisprseek >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-dplyr @@ -49,21 +62,23 @@ requirements: - r-rlang - r-stringr - r-tidyr + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' - - 'bioconductor-crisprseek >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-chippeakanno >=3.40.0,<3.41.0 + - bioconductor-crisprseek >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-dplyr @@ -77,21 +92,16 @@ requirements: - r-rlang - r-stringr - r-tidyr + +source: + md5: c3904595d1e820e765cbd00e3fb6b9ae + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'GUIDE-seq and PEtag-seq analysis pipeline' - description: 'The package implements GUIDE-seq and PEtag-seq analysis workflow including functions for filtering UMI and reads with low coverage, obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites with mismatches and indels.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:guideseq - - doi:10.1186/s12864-017-3746-y - parent_recipe: - name: bioconductor-guideseq - path: recipes/bioconductor-guideseq - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-guitar/meta.yaml b/recipes/bioconductor-guitar/meta.yaml index 5ead73d849ee9..a20e7fda4e908 100644 --- a/recipes/bioconductor-guitar/meta.yaml +++ b/recipes/bioconductor-guitar/meta.yaml @@ -1,57 +1,63 @@ -{% set version = "2.18.0" %} +{% set version = "2.22.0" %} {% set name = "Guitar" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package is designed for visualization of RNA-related genomic features with respect to the landmarks of RNA transcripts, i.e., transcription starting site, start codon, stop codon and transcription ending site. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Guitar -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e62e4238e3e3b939a2195eb384079bb3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-guitar", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-guitar + path: recipes/bioconductor-guitar + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-dplyr - r-ggplot2 - r-knitr - r-magrittr run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-dplyr - r-ggplot2 - r-knitr - r-magrittr + +source: + md5: 1427674b03dd7a763df3aeaf2ec12ab1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: Guitar - description: 'The package is designed for visualization of RNA-related genomic features with respect to the landmarks of RNA transcripts, i.e., transcription starting site, start codon, stop codon and transcription ending site.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - parent_recipe: - name: bioconductor-guitar - path: recipes/bioconductor-guitar - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gviz/meta.yaml b/recipes/bioconductor-gviz/meta.yaml index e0c413f6a6708..170daf49f4372 100644 --- a/recipes/bioconductor-gviz/meta.yaml +++ b/recipes/bioconductor-gviz/meta.yaml @@ -1,87 +1,95 @@ -{% set version = "1.46.1" %} +{% set version = "1.50.0" %} {% set name = "Gviz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Plotting data and annotation information along genomic coordinates -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2e1eba2ac7cb0d1178f17bba471b0a62 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gviz", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:gviz + parent_recipe: + name: bioconductor-gviz + path: recipes/bioconductor-gviz + version: 1.24.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Hsapiens.UCSC.hg19, xml2, BiocStyle, knitr, rmarkdown, testthat requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-biovizbase >=1.50.0,<1.51.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-biovizbase >=1.54.0,<1.55.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - - 'r-digest >=0.6.8' + - r-digest >=0.6.8 - r-lattice - - 'r-latticeextra >=0.6-26' - - 'r-matrixstats >=0.8.14' + - r-latticeextra >=0.6-26 + - r-matrixstats >=0.8.14 - r-rcolorbrewer + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-biovizbase >=1.50.0,<1.51.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-biovizbase >=1.54.0,<1.55.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - - 'r-digest >=0.6.8' + - r-digest >=0.6.8 - r-lattice - - 'r-latticeextra >=0.6-26' - - 'r-matrixstats >=0.8.14' + - r-latticeextra >=0.6-26 + - r-matrixstats >=0.8.14 - r-rcolorbrewer + +source: + md5: 2f391f9a0a775012b4135996633d1412 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Plotting data and annotation information along genomic coordinates' - description: 'Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.' -extra: - identifiers: - - biotools:gviz - parent_recipe: - name: bioconductor-gviz - path: recipes/bioconductor-gviz - version: 1.24.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gwas.bayes/meta.yaml b/recipes/bioconductor-gwas.bayes/meta.yaml index e00fe8aad9e30..e21bd3eeb7933 100644 --- a/recipes/bioconductor-gwas.bayes/meta.yaml +++ b/recipes/bioconductor-gwas.bayes/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "GWAS.BAYES" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'This package is built to perform GWAS analysis using Bayesian techniques. Currently, GWAS.BAYES has functionality for the implementation of BICOSS (Williams, J., Ferreira, M. A., and Ji, T. (2022). BICOSS: Bayesian iterative conditional stochastic search for GWAS. BMC Bioinformatics), BGWAS (Williams, J., Xu, S., Ferreira, M. A.. (2023) "BGWAS: Bayesian variable selection in linear mixed models with nonlocal priors for genome-wide association studies." BMC Bioinformatics), and GINA. All methods currently are for the analysis of Gaussian phenotypes The research related to this package was supported in part by National Science Foundation awards DMS 1853549, DMS 1853556, and DMS 2054173.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Bayesian analysis of Gaussian GWAS data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf62f1d1c5f69ef4051bf659da548b1f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gwas.bayes", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP requirements: host: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - - 'r-caret >=6.0-86' - - 'r-ga >=3.2' - - 'r-mass >=7.3-58.1' - - 'r-matrix >=1.2-18' - - 'r-memoise >=1.1.0' + - r-caret >=6.0-86 + - r-ga >=3.2 + - r-mass >=7.3-58.1 + - r-matrix >=1.2-18 + - r-memoise >=1.1.0 run: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - - 'r-caret >=6.0-86' - - 'r-ga >=3.2' - - 'r-mass >=7.3-58.1' - - 'r-matrix >=1.2-18' - - 'r-memoise >=1.1.0' + - r-caret >=6.0-86 + - r-ga >=3.2 + - r-mass >=7.3-58.1 + - r-matrix >=1.2-18 + - r-memoise >=1.1.0 + +source: + md5: 4f113111d05801f70ffed9e580023f5f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Bayesian analysis of Gaussian GWAS data' - description: 'This package is built to perform GWAS analysis using Bayesian techniques. Currently, GWAS.BAYES has functionality for the implementation of BICOSS for Gaussian phenotypes (Williams, J., Ferreira, M. A., and Ji, T. (2022). BICOSS: Bayesian iterative conditional stochastic search for GWAS. BMC Bioinformatics 23, 475). The research related to this package was supported in part by National Science Foundation awards DMS 1853549, DMS 1853556, and DMS 2054173.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gwascat/meta.yaml b/recipes/bioconductor-gwascat/meta.yaml index fd05265aa675a..19d8aaa03ebfe 100644 --- a/recipes/bioconductor-gwascat/meta.yaml +++ b/recipes/bioconductor-gwascat/meta.yaml @@ -1,60 +1,65 @@ -{% set version = "2.34.0" %} +{% set version = "2.38.0" %} {% set name = "gwascat" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Represent and model data in the EMBL-EBI GWAS catalog. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: representing and modeling data in the EMBL-EBI GWAS catalog -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a7cbd1d5ac4b3d4fbb8d1fbd77269e44 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gwascat", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: DO.db, DT, knitr, RBGL, testthat, rmarkdown, dplyr, Gviz, Rsamtools, rtracklayer, graph, ggbio, DelayedArray, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-snpstats >=1.52.0,<1.53.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-snpstats >=1.56.0,<1.57.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-readr run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-snpstats >=1.52.0,<1.53.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-snpstats >=1.56.0,<1.57.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-readr + +source: + md5: 778367e9bf0f9f655dcb42a122ffcafe + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'representing and modeling data in the EMBL-EBI GWAS catalog' - description: 'Represent and model data in the EMBL-EBI GWAS catalog.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gwascatdata/meta.yaml b/recipes/bioconductor-gwascatdata/meta.yaml index 993381303c0d2..8128d0c2509ad 100644 --- a/recipes/bioconductor-gwascatdata/meta.yaml +++ b/recipes/bioconductor-gwascatdata/meta.yaml @@ -1,24 +1,22 @@ {% set version = "0.99.6" %} {% set name = "gwascatData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fa09db539ac0a16ba136e810a5b9970a +about: + description: This package manages a text file in cloud with March 30 2021 snapshot of EBI/EMBL GWAS catalog.This simplifies access to a snapshot of EBI GWASCAT. More current images can be obtained using the gwascat package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: A text file in cloud with March 30 2021 snapshot of EBI/EMBL GWAS catalog build: - number: 5 + noarch: generic + number: 6 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gwascatdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat, AnnotationHub, rmarkdown, knitr requirements: host: @@ -28,13 +26,15 @@ requirements: - r-base - r-data.table - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fa09db539ac0a16ba136e810a5b9970a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A text file in cloud with March 30 2021 snapshot of EBI/EMBL GWAS catalog' - description: 'This package manages a text file in cloud with March 30 2021 snapshot of EBI/EMBL GWAS catalog.This simplifies access to a snapshot of EBI GWASCAT. More current images can be obtained using the gwascat package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gwasdata/meta.yaml b/recipes/bioconductor-gwasdata/meta.yaml index f30c72237cf4e..702ed3a81e233 100644 --- a/recipes/bioconductor-gwasdata/meta.yaml +++ b/recipes/bioconductor-gwasdata/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "GWASdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 57fec70f980b9e476f0c59d397797815 +about: + description: Selected Affymetrix and Illlumina SNP data for HapMap subjects. Data provided by the Center for Inherited Disease Research at Johns Hopkins University and the Broad Institute of MIT and Harvard University. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Data used in the examples and vignettes of the GWASTools package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gwasdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: ncdf4 requirements: host: - - 'bioconductor-gwastools >=1.48.0,<1.49.0' + - bioconductor-gwastools >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-gwastools >=1.48.0,<1.49.0' + - bioconductor-gwastools >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b27980b5cacc933bf897da291ad17871 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Data used in the examples and vignettes of the GWASTools package' - description: 'Selected Affymetrix and Illlumina SNP data for HapMap subjects. Data provided by the Center for Inherited Disease Research at Johns Hopkins University and the Broad Institute of MIT and Harvard University.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gwasdata/post-link.sh b/recipes/bioconductor-gwasdata/post-link.sh index 11e8192ddace6..be052b127d750 100644 --- a/recipes/bioconductor-gwasdata/post-link.sh +++ b/recipes/bioconductor-gwasdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "gwasdata-1.40.0" +installBiocDataPackage.sh "gwasdata-1.44.0" diff --git a/recipes/bioconductor-gwastools/meta.yaml b/recipes/bioconductor-gwastools/meta.yaml index 1607a30635493..cc865cbd57034 100644 --- a/recipes/bioconductor-gwastools/meta.yaml +++ b/recipes/bioconductor-gwastools/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "GWASTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Tools for Genome Wide Association Studies -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af968b8e8a3e4a1981cae02cb2a781ec build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gwastools", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel, BiocStyle, knitr requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-quantsmooth >=1.68.0,<1.69.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-quantsmooth >=1.72.0,<1.73.0 - r-base - r-data.table - r-dbi @@ -36,10 +37,10 @@ requirements: - r-sandwich - r-survival run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-quantsmooth >=1.68.0,<1.69.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-quantsmooth >=1.72.0,<1.73.0 - r-base - r-data.table - r-dbi @@ -49,12 +50,16 @@ requirements: - r-rsqlite - r-sandwich - r-survival + +source: + md5: 9f03101b34ca747d379e633beed25cf0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Tools for Genome Wide Association Studies' - description: 'Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gwasurvivr/meta.yaml b/recipes/bioconductor-gwasurvivr/meta.yaml index c62748b8cba02..55e3762e6d392 100644 --- a/recipes/bioconductor-gwasurvivr/meta.yaml +++ b/recipes/bioconductor-gwasurvivr/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "gwasurvivr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: gwasurvivr is a package to perform survival analysis using Cox proportional hazard models on imputed genetic data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'gwasurvivr: an R package for genome wide survival analysis' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 699843eb7ff1528732a6a2e093600aef build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gwasurvivr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-gwastools >=1.48.0,<1.49.0' - - 'bioconductor-snprelate >=1.36.0,<1.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-gwastools >=1.52.0,<1.53.0 + - bioconductor-snprelate >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-matrixstats - r-survival run: - - 'bioconductor-gwastools >=1.48.0,<1.49.0' - - 'bioconductor-snprelate >=1.36.0,<1.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-gwastools >=1.52.0,<1.53.0 + - bioconductor-snprelate >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-matrixstats - r-survival + +source: + md5: 63649a8022aff721b2010c4cc9e0f641 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'gwasurvivr: an R package for genome wide survival analysis' - description: 'gwasurvivr is a package to perform survival analysis using Cox proportional hazard models on imputed genetic data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gwena/meta.yaml b/recipes/bioconductor-gwena/meta.yaml index 9ded48032ed13..d1c004db330c5 100644 --- a/recipes/bioconductor-gwena/meta.yaml +++ b/recipes/bioconductor-gwena/meta.yaml @@ -1,71 +1,76 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "GWENA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The development of high-throughput sequencing led to increased use of co-expression analysis to go beyong single feature (i.e. gene) focus. We propose GWENA (Gene Whole co-Expression Network Analysis) , a tool designed to perform gene co-expression network analysis and explore the results in a single pipeline. It includes functional enrichment of modules of co-expressed genes, phenotypcal association, topological analysis and comparison of networks configuration between conditions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Pipeline for augmented co-expression analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f1bd435deae9546d0ec3f8605a0b682 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-gwena", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 2.1.0), knitr (>= 1.25), rmarkdown (>= 1.16), prettydoc (>= 0.3.0), httr (>= 1.4.1), S4Vectors (>= 0.22.1), BiocStyle (>= 2.15.8) requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-cluster >=2.1.0' - - 'r-dplyr >=0.8.3' - - 'r-dynamictreecut >=1.63-1' - - 'r-ggplot2 >=3.1.1' - - 'r-gprofiler2 >=0.1.6' - - 'r-igraph >=1.2.4.1' - - 'r-magrittr >=1.5' - - 'r-matrixstats >=0.55.0' - - 'r-netrep >=1.2.1' - - 'r-purrr >=0.3.3' - - 'r-rcolorbrewer >=1.1-2' - - 'r-rlist >=0.4.6.1' - - 'r-stringr >=1.4.0' - - 'r-tibble >=2.1.1' - - 'r-tidyr >=1.0.0' - - 'r-wgcna >=1.67' + - r-cluster >=2.1.0 + - r-dplyr >=0.8.3 + - r-dynamictreecut >=1.63-1 + - r-ggplot2 >=3.1.1 + - r-gprofiler2 >=0.1.6 + - r-igraph >=1.2.4.1 + - r-magrittr >=1.5 + - r-matrixstats >=0.55.0 + - r-netrep >=1.2.1 + - r-purrr >=0.3.3 + - r-rcolorbrewer >=1.1-2 + - r-rlist >=0.4.6.1 + - r-stringr >=1.4.0 + - r-tibble >=2.1.1 + - r-tidyr >=1.0.0 + - r-wgcna >=1.67 run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-cluster >=2.1.0' - - 'r-dplyr >=0.8.3' - - 'r-dynamictreecut >=1.63-1' - - 'r-ggplot2 >=3.1.1' - - 'r-gprofiler2 >=0.1.6' - - 'r-igraph >=1.2.4.1' - - 'r-magrittr >=1.5' - - 'r-matrixstats >=0.55.0' - - 'r-netrep >=1.2.1' - - 'r-purrr >=0.3.3' - - 'r-rcolorbrewer >=1.1-2' - - 'r-rlist >=0.4.6.1' - - 'r-stringr >=1.4.0' - - 'r-tibble >=2.1.1' - - 'r-tidyr >=1.0.0' - - 'r-wgcna >=1.67' + - r-cluster >=2.1.0 + - r-dplyr >=0.8.3 + - r-dynamictreecut >=1.63-1 + - r-ggplot2 >=3.1.1 + - r-gprofiler2 >=0.1.6 + - r-igraph >=1.2.4.1 + - r-magrittr >=1.5 + - r-matrixstats >=0.55.0 + - r-netrep >=1.2.1 + - r-purrr >=0.3.3 + - r-rcolorbrewer >=1.1-2 + - r-rlist >=0.4.6.1 + - r-stringr >=1.4.0 + - r-tibble >=2.1.1 + - r-tidyr >=1.0.0 + - r-wgcna >=1.67 + +source: + md5: 1106c3d4f7d9b88505555faad509aa1b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Pipeline for augmented co-expression analysis' - description: 'The development of high-throughput sequencing led to increased use of co-expression analysis to go beyong single feature (i.e. gene) focus. We propose GWENA (Gene Whole co-Expression Network Analysis) , a tool designed to perform gene co-expression network analysis and explore the results in a single pipeline. It includes functional enrichment of modules of co-expressed genes, phenotypcal association, topological analysis and comparison of networks configuration between conditions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-gypsum/build.sh b/recipes/bioconductor-gypsum/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gypsum/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gypsum/meta.yaml b/recipes/bioconductor-gypsum/meta.yaml new file mode 100644 index 0000000000000..0b1aa6a1e3e9a --- /dev/null +++ b/recipes/bioconductor-gypsum/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.2.0" %} +{% set name = "gypsum" %} +{% set bioc = "3.20" %} + +about: + description: Client for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based file store in the ArtifactDB ecosystem. This package provides functions for uploads, downloads, and various adminstrative and management tasks. Check out the documentation at https://github.com/ArtifactDB/gypsum-worker for more details. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Interface to the gypsum REST API +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-gypsum", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: knitr, rmarkdown, testthat, BiocStyle, digest, jsonvalidate, DBI, RSQLite, S4Vectors, methods +requirements: + host: + - r-base + - r-filelock + - r-httr2 + - r-jsonlite + - r-rappdirs + run: + - r-base + - r-filelock + - r-httr2 + - r-jsonlite + - r-rappdirs +source: + md5: 9d2f3c483225865a0bf4639fee72cd03 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-h10kcod.db/meta.yaml b/recipes/bioconductor-h10kcod.db/meta.yaml index c4c1dfaeef710..662db3936fb64 100644 --- a/recipes/bioconductor-h10kcod.db/meta.yaml +++ b/recipes/bioconductor-h10kcod.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.4.0" %} {% set name = "h10kcod.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a555739cea229f286953c3297c145e9c +about: + description: Codelink UniSet Human I Bioarray (~10 000 human genes) annotation data (chip h10kcod) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Codelink UniSet Human I Bioarray (~10 000 human genes) annotation data (chip h10kcod) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-h10kcod.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a555739cea229f286953c3297c145e9c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Codelink UniSet Human I Bioarray (~10 000 human genes) annotation data (chip h10kcod)' - description: 'Codelink UniSet Human I Bioarray (~10 000 human genes) annotation data (chip h10kcod) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-h20kcod.db/meta.yaml b/recipes/bioconductor-h20kcod.db/meta.yaml index 8427bc3859258..1f9b11b52b705 100644 --- a/recipes/bioconductor-h20kcod.db/meta.yaml +++ b/recipes/bioconductor-h20kcod.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.4.0" %} {% set name = "h20kcod.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3647facb272f58424f4c94ef92e8ee45 +about: + description: Codelink UniSet Human 20k I Bioarray annotation data (chip h20kcod) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Codelink UniSet Human 20k I Bioarray annotation data (chip h20kcod) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-h20kcod.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3647facb272f58424f4c94ef92e8ee45 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Codelink UniSet Human 20k I Bioarray annotation data (chip h20kcod)' - description: 'Codelink UniSet Human 20k I Bioarray annotation data (chip h20kcod) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-h5vc/meta.yaml b/recipes/bioconductor-h5vc/meta.yaml index d5c396bb578ac..f53c0955fea20 100644 --- a/recipes/bioconductor-h5vc/meta.yaml +++ b/recipes/bioconductor-h5vc/meta.yaml @@ -1,37 +1,43 @@ -{% set version = "2.36.0" %} +{% set version = "2.40.0" %} {% set name = "h5vc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains functions to interact with tally data from NGS experiments that is stored in HDF5 files. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Managing alignment tallies using a hdf5 backend -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2d827ac4606ef723005e479de8540b7a build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-h5vc", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics, rmarkdown # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-h5vcdata >=2.22.0,<2.23.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-h5vcdata >=2.26.0,<2.27.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-abind - r-base - r-batchjobs @@ -40,34 +46,35 @@ requirements: - r-reshape - libblas - liblapack + - zlib + - liblzma-devel run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-h5vcdata >=2.22.0,<2.23.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-h5vcdata >=2.26.0,<2.27.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-abind - r-base - r-batchjobs - r-ggplot2 - r-gridextra - r-reshape - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 45544d9a82d2658418bcc6d376aa64e1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Managing alignment tallies using a hdf5 backend' - description: 'This package contains functions to interact with tally data from NGS experiments that is stored in HDF5 files.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-h5vcdata/meta.yaml b/recipes/bioconductor-h5vcdata/meta.yaml index 7edd272d4b3ef..7d3285aae6f4e 100644 --- a/recipes/bioconductor-h5vcdata/meta.yaml +++ b/recipes/bioconductor-h5vcdata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "2.22.0" %} +{% set version = "2.26.0" %} {% set name = "h5vcData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c251316e2d6dc6cb90e8faad0015103b +about: + description: This package contains the data used in the vignettes and examples of the 'h5vc' package + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Example data for the h5vc package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-h5vcdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: h5vc requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: da6264ea480859df1c681611088aeb89 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Example data for the h5vc package' - description: 'This package contains the data used in the vignettes and examples of the ''h5vc'' package' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-h5vcdata/post-link.sh b/recipes/bioconductor-h5vcdata/post-link.sh index 1962bfe15c1eb..07caa1b23b490 100644 --- a/recipes/bioconductor-h5vcdata/post-link.sh +++ b/recipes/bioconductor-h5vcdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "h5vcdata-2.22.0" +installBiocDataPackage.sh "h5vcdata-2.26.0" diff --git a/recipes/bioconductor-hapfabia/meta.yaml b/recipes/bioconductor-hapfabia/meta.yaml index ff56c6ea7dada..fa6978b892538 100644 --- a/recipes/bioconductor-hapfabia/meta.yaml +++ b/recipes/bioconductor-hapfabia/meta.yaml @@ -1,51 +1,57 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "hapFabia" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package to identify very short IBD segments in large sequencing data by FABIA biclustering. Two haplotypes are identical by descent (IBD) if they share a segment that both inherited from a common ancestor. Current IBD methods reliably detect long IBD segments because many minor alleles in the segment are concordant between the two haplotypes. However, many cohort studies contain unrelated individuals which share only short IBD segments. This package provides software to identify short IBD segments in sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2.1) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: 'hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a14370aec9e86245541aea68b90c3812 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hapfabia", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:hapfabia + parent_recipe: + name: bioconductor-hapfabia + path: recipes/bioconductor-hapfabia + version: 1.22.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-fabia >=2.48.0,<2.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-fabia >=2.52.0,<2.53.0 - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-fabia >=2.48.0,<2.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-fabia >=2.52.0,<2.53.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: e09b54d156c25cb911d247c29fb3c622 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2.1)' - summary: 'hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data' - description: 'A package to identify very short IBD segments in large sequencing data by FABIA biclustering. Two haplotypes are identical by descent (IBD) if they share a segment that both inherited from a common ancestor. Current IBD methods reliably detect long IBD segments because many minor alleles in the segment are concordant between the two haplotypes. However, many cohort studies contain unrelated individuals which share only short IBD segments. This package provides software to identify short IBD segments in sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:hapfabia - parent_recipe: - name: bioconductor-hapfabia - path: recipes/bioconductor-hapfabia - version: 1.22.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hapmap100khind/meta.yaml b/recipes/bioconductor-hapmap100khind/meta.yaml index 3b61d5d83e55f..9661570b65caa 100644 --- a/recipes/bioconductor-hapmap100khind/meta.yaml +++ b/recipes/bioconductor-hapmap100khind/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "hapmap100khind" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0168028295626d811e305d4008ce9996 +about: + description: Sample dataset obtained from http://www.hapmap.org + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Sample data - Hapmap 100K HIND Affymetrix build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hapmap100khind", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: oligo requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 164c26d681c90e1ddff583a7cf69e1d4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL - summary: 'Sample data - Hapmap 100K HIND Affymetrix' - description: 'Sample dataset obtained from http://www.hapmap.org' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hapmap100khind/post-link.sh b/recipes/bioconductor-hapmap100khind/post-link.sh index d9f5a26dbbc86..d69df38d018ee 100644 --- a/recipes/bioconductor-hapmap100khind/post-link.sh +++ b/recipes/bioconductor-hapmap100khind/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hapmap100khind-1.44.0" +installBiocDataPackage.sh "hapmap100khind-1.48.0" diff --git a/recipes/bioconductor-hapmap100kxba/meta.yaml b/recipes/bioconductor-hapmap100kxba/meta.yaml index 50530871601de..e4c74c55f5929 100644 --- a/recipes/bioconductor-hapmap100kxba/meta.yaml +++ b/recipes/bioconductor-hapmap100kxba/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "hapmap100kxba" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b4a619fb108a36920109307fbf63985b +about: + description: Sample dataset obtained from http://www.hapmap.org + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Sample data - Hapmap 100K XBA Affymetrix build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hapmap100kxba", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: oligo requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 512c4b503328303dd5171444eb3c1e64 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL - summary: 'Sample data - Hapmap 100K XBA Affymetrix' - description: 'Sample dataset obtained from http://www.hapmap.org' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hapmap100kxba/post-link.sh b/recipes/bioconductor-hapmap100kxba/post-link.sh index e71f400872e77..38dbc29f12e32 100644 --- a/recipes/bioconductor-hapmap100kxba/post-link.sh +++ b/recipes/bioconductor-hapmap100kxba/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hapmap100kxba-1.44.0" +installBiocDataPackage.sh "hapmap100kxba-1.48.0" diff --git a/recipes/bioconductor-hapmap370k/meta.yaml b/recipes/bioconductor-hapmap370k/meta.yaml index 4711fa3319d8d..66680f2896c5b 100644 --- a/recipes/bioconductor-hapmap370k/meta.yaml +++ b/recipes/bioconductor-hapmap370k/meta.yaml @@ -1,24 +1,23 @@ {% set version = "1.0.1" %} {% set name = "hapmap370k" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 569556341a45da799372aaf1012be72e +about: + description: Example HapMap data from Illumina 370k BeadChips + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Example Illumina 370k HapMap Data build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hapmap370k", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: crlmm requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 569556341a45da799372aaf1012be72e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: GPL - summary: 'Example Illumina 370k HapMap Data' - description: 'Example HapMap data from Illumina 370k BeadChips' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hapmap500knsp/meta.yaml b/recipes/bioconductor-hapmap500knsp/meta.yaml index 379eb3e96b54a..e30a0c37b957b 100644 --- a/recipes/bioconductor-hapmap500knsp/meta.yaml +++ b/recipes/bioconductor-hapmap500knsp/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "hapmap500knsp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 15b799bba4a395ccf715acfc7bbdae04 +about: + description: Sample dataset obtained from http://www.hapmap.org + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Sample data - Hapmap 500K NSP Affymetrix build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hapmap500knsp", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: oligo requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 37c94ad018546ed485cb9112c448aefe + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL - summary: 'Sample data - Hapmap 500K NSP Affymetrix' - description: 'Sample dataset obtained from http://www.hapmap.org' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hapmap500knsp/post-link.sh b/recipes/bioconductor-hapmap500knsp/post-link.sh index 1d91347c61c09..1e742c7be12b9 100644 --- a/recipes/bioconductor-hapmap500knsp/post-link.sh +++ b/recipes/bioconductor-hapmap500knsp/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hapmap500knsp-1.44.0" +installBiocDataPackage.sh "hapmap500knsp-1.48.0" diff --git a/recipes/bioconductor-hapmap500ksty/meta.yaml b/recipes/bioconductor-hapmap500ksty/meta.yaml index d4b94cf67c00c..c36a75bc96cf7 100644 --- a/recipes/bioconductor-hapmap500ksty/meta.yaml +++ b/recipes/bioconductor-hapmap500ksty/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "hapmap500ksty" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7a1d4983ac3e411dadedc130d85c2557 +about: + description: Sample dataset obtained from http://www.hapmap.org + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Sample data - Hapmap 500K STY Affymetrix build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hapmap500ksty", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: oligo requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f5f4aeccf821977db1f500d8f2c20717 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL - summary: 'Sample data - Hapmap 500K STY Affymetrix' - description: 'Sample dataset obtained from http://www.hapmap.org' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hapmap500ksty/post-link.sh b/recipes/bioconductor-hapmap500ksty/post-link.sh index fe55de17a68f4..6ff33c73c7530 100644 --- a/recipes/bioconductor-hapmap500ksty/post-link.sh +++ b/recipes/bioconductor-hapmap500ksty/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hapmap500ksty-1.44.0" +installBiocDataPackage.sh "hapmap500ksty-1.48.0" diff --git a/recipes/bioconductor-hapmapsnp5/meta.yaml b/recipes/bioconductor-hapmapsnp5/meta.yaml index d3d9f4de67114..b20e6b973c1a9 100644 --- a/recipes/bioconductor-hapmapsnp5/meta.yaml +++ b/recipes/bioconductor-hapmapsnp5/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "hapmapsnp5" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2f14e60f39cf94c43f2dd0e5aa5a48e2 +about: + description: Sample dataset obtained from http://www.hapmap.org + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Sample data - Hapmap SNP 5.0 Affymetrix build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hapmapsnp5", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: oligo requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: eeecae8e0670dcd874224997a8925116 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL - summary: 'Sample data - Hapmap SNP 5.0 Affymetrix' - description: 'Sample dataset obtained from http://www.hapmap.org' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hapmapsnp5/post-link.sh b/recipes/bioconductor-hapmapsnp5/post-link.sh index de833d94f68c6..c348d36be0462 100644 --- a/recipes/bioconductor-hapmapsnp5/post-link.sh +++ b/recipes/bioconductor-hapmapsnp5/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hapmapsnp5-1.44.0" +installBiocDataPackage.sh "hapmapsnp5-1.48.0" diff --git a/recipes/bioconductor-hapmapsnp6/meta.yaml b/recipes/bioconductor-hapmapsnp6/meta.yaml index 17aec4ff0bb9d..be059758df444 100644 --- a/recipes/bioconductor-hapmapsnp6/meta.yaml +++ b/recipes/bioconductor-hapmapsnp6/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "hapmapsnp6" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2635c012a513343484177db2070209e9 +about: + description: Sample dataset obtained from http://www.hapmap.org + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Sample data - Hapmap SNP 6.0 Affymetrix build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hapmapsnp6", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: oligo, oligoClasses requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: be147d4601ac606b148642d5399c0f12 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL - summary: 'Sample data - Hapmap SNP 6.0 Affymetrix' - description: 'Sample dataset obtained from http://www.hapmap.org' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hapmapsnp6/post-link.sh b/recipes/bioconductor-hapmapsnp6/post-link.sh index 44c99a5802936..cbef0c9c12bb3 100644 --- a/recipes/bioconductor-hapmapsnp6/post-link.sh +++ b/recipes/bioconductor-hapmapsnp6/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hapmapsnp6-1.44.0" +installBiocDataPackage.sh "hapmapsnp6-1.48.0" diff --git a/recipes/bioconductor-harbchip/meta.yaml b/recipes/bioconductor-harbchip/meta.yaml index ee6acbfff7d6f..7c13d21951092 100644 --- a/recipes/bioconductor-harbchip/meta.yaml +++ b/recipes/bioconductor-harbchip/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "harbChIP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5948fc0f4c1ced0a43e85c1885f5d9e +about: + description: data from a yeast ChIP-chip experiment + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: 'Experimental Data Package: harbChIP' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-harbchip", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f4cac0290c8ca0b869d065858e08ef1b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Experimental Data Package: harbChIP' - description: 'data from a yeast ChIP-chip experiment' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-harbchip/post-link.sh b/recipes/bioconductor-harbchip/post-link.sh index d2133dee6fc33..1f664a3691149 100644 --- a/recipes/bioconductor-harbchip/post-link.sh +++ b/recipes/bioconductor-harbchip/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "harbchip-1.40.0" +installBiocDataPackage.sh "harbchip-1.44.0" diff --git a/recipes/bioconductor-harman/meta.yaml b/recipes/bioconductor-harman/meta.yaml index aa06daaaff680..e1f4acd3895d1 100644 --- a/recipes/bioconductor-harman/meta.yaml +++ b/recipes/bioconductor-harman/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "Harman" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Harman is a PCA and constrained optimisation based technique that maximises the removal of batch effects from datasets, with the constraint that the probability of overcorrection (i.e. removing genuine biological signal along with batch noise) is kept to a fraction which is set by the end-user. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENCE + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: The removal of batch effects from datasets using a PCA and constrained optimisation based technique -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aaec4256c0cb2949d553ff81d94e48d2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-harman", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:harman + parent_recipe: + name: bioconductor-harman + path: recipes/bioconductor-harman + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-ckmeans.1d.dp - r-matrixstats - - 'r-rcpp >=0.11.2' + - r-rcpp >=0.11.2 - libblas - liblapack run: - r-base - r-ckmeans.1d.dp - r-matrixstats - - 'r-rcpp >=0.11.2' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=0.11.2 + +source: + md5: b0a5390448e4021a5337f1d8145c414b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENCE' - summary: 'The removal of batch effects from datasets using a PCA and constrained optimisation based technique' - description: 'Harman is a PCA and constrained optimisation based technique that maximises the removal of batch effects from datasets, with the constraint that the probability of overcorrection (i.e. removing genuine biological signal along with batch noise) is kept to a fraction which is set by the end-user.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:harman - parent_recipe: - name: bioconductor-harman - path: recipes/bioconductor-harman - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-harmandata/meta.yaml b/recipes/bioconductor-harmandata/meta.yaml index f0076f4ffdd6a..b78165825ff15 100644 --- a/recipes/bioconductor-harmandata/meta.yaml +++ b/recipes/bioconductor-harmandata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "HarmanData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7df1447aff75abdf025678b51a0ee8fb +about: + description: 'Datasets of accompany Harman, a PCA and constrained optimisation based technique. Contains three example datasets: IMR90, Human lung fibroblast cells exposed to nitric oxide; NPM, an experiment to test skin penetration of metal oxide nanoparticles following topical application of sunscreens in non-pregnant mice; OLF; an experiment to gauge the response of human olfactory neurosphere-derived (hONS) cells to ZnO nanoparticles. Since version 1.24, this package also contains the Infinium5 dataset, a set of batch correction adjustments across 5 Illumina Infinium Methylation BeadChip datasets. This file does not contain methylation data, but summary statistics of 5 datasets after correction. There is also an EpiSCOPE_sample file as exampling for the new methylation clustering functionality in Harman.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Data for the Harman package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-harmandata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocGenerics, BiocStyle, knitr, rmarkdown, Harman (>= 1.23.3) requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f02d7d5fe9c935069af10076dade4bac + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Data for the Harman package' - description: 'Datasets of accompany Harman, a PCA and constrained optimisation based technique. Contains three example datasets: IMR90, Human lung fibroblast cells exposed to nitric oxide; NPM, an experiment to test skin penetration of metal oxide nanoparticles following topical application of sunscreens in non-pregnant mice; OLF; an experiment to gauge the response of human olfactory neurosphere-derived (hONS) cells to ZnO nanoparticles. Since version 1.24, this package also contains the Infinium5 dataset, a set of batch correction adjustments across 5 Illumina Infinium Methylation BeadChip datasets. This file does not contain methylation data, but summary statistics of 5 datasets after correction. There is also an EpiSCOPE_sample file as exampling for the new methylation clustering functionality in Harman.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-harmandata/post-link.sh b/recipes/bioconductor-harmandata/post-link.sh index bfce705eabe09..b63e282d5b490 100644 --- a/recipes/bioconductor-harmandata/post-link.sh +++ b/recipes/bioconductor-harmandata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "harmandata-1.30.0" +installBiocDataPackage.sh "harmandata-1.34.0" diff --git a/recipes/bioconductor-harmonizedtcgadata/meta.yaml b/recipes/bioconductor-harmonizedtcgadata/meta.yaml index c421c5e1b4ec4..111079253146f 100644 --- a/recipes/bioconductor-harmonizedtcgadata/meta.yaml +++ b/recipes/bioconductor-harmonizedtcgadata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "HarmonizedTCGAData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f6e8f685a67152c6f382089c0e6aae01 +about: + description: This package contains the processed harmonized TCGA data of five cancer types used in "Tianle Ma and Aidong Zhang, Integrate Multi-omic Data Using Affinity Network Fusion (ANF) for Cancer Patient Clustering". + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Processed Harmonized TCGA Data of Five Selected Cancer Types build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-harmonizedtcgadata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: AnnotationHub, knitr, rmarkdown, igraph, survival, ANF, stats, testthat requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6c789331d5bae50ac2645b29768ef1b5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Processed Harmonized TCGA Data of Five Selected Cancer Types' - description: 'This package contains the processed harmonized TCGA data of five cancer types used in "Tianle Ma and Aidong Zhang, Integrate Multi-omic Data Using Affinity Network Fusion (ANF) for Cancer Patient Clustering".' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-harmonizedtcgadata/post-link.sh b/recipes/bioconductor-harmonizedtcgadata/post-link.sh index dbe5eabb855e7..c7bd0981a9869 100644 --- a/recipes/bioconductor-harmonizedtcgadata/post-link.sh +++ b/recipes/bioconductor-harmonizedtcgadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "harmonizedtcgadata-1.24.0" +installBiocDataPackage.sh "harmonizedtcgadata-1.28.0" diff --git a/recipes/bioconductor-harmonizr/meta.yaml b/recipes/bioconductor-harmonizr/meta.yaml index ee8a16ab953cf..b79ac893f77b1 100644 --- a/recipes/bioconductor-harmonizr/meta.yaml +++ b/recipes/bioconductor-harmonizr/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "HarmonizR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma. The implementation appropriately handles missing values by dissecting the input matrix into smaller matrices with sufficient data to feed the ComBat or limma algorithm. The adjusted data is returned to the user as a rebuild matrix. The implementation is meant to make as much data available as possible with minimal data loss. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Handles missing values and makes more data available -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6e81c009fe8678273d8091378ae2f8e3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-harmonizr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - - 'r-doparallel >=1.0.16' - - 'r-foreach >=1.5.1' - - 'r-janitor >=2.1.0' - - 'r-plyr >=1.8.6' - - 'r-seriation >=1.3.5' + - r-doparallel >=1.0.16 + - r-foreach >=1.5.1 + - r-janitor >=2.1.0 + - r-plyr >=1.8.6 + - r-seriation >=1.3.5 run: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - - 'r-doparallel >=1.0.16' - - 'r-foreach >=1.5.1' - - 'r-janitor >=2.1.0' - - 'r-plyr >=1.8.6' - - 'r-seriation >=1.3.5' + - r-doparallel >=1.0.16 + - r-foreach >=1.5.1 + - r-janitor >=2.1.0 + - r-plyr >=1.8.6 + - r-seriation >=1.3.5 + +source: + md5: c9b05bca57f63d6620a24fd199ab5425 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Handles missing values and makes more data available' - description: 'An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma. The implementation appropriately handles missing values by dissecting the input matrix into smaller matrices with sufficient data to feed the ComBat or limma algorithm. The adjusted data is returned to the user as a rebuild matrix. The implementation is meant to make as much data available as possible with minimal data loss.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-harshlight/build_failure.osx-64.yaml b/recipes/bioconductor-harshlight/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..e2555e6440f1e --- /dev/null +++ b/recipes/bioconductor-harshlight/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 4299a5c11300745cd220f51d10751f9d3ac48b73efb87f4c2a50de895310bece # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Encountered problems while solving: + - nothing provides bioconductor-graph >=1.84.0,<1.85.0 needed by bioconductor-hypergraph-1.78.0-r44hdfd78af_0 + + Could not solve for environment specs + The following package could not be installed + bioconductor-altcdfenvs >=2.68.0,<2.69.0 is not installable because it requires + bioconductor-hypergraph >=1.78.0,<1.79.0 , which requires + bioconductor-graph >=1.84.0,<1.85.0 , which does not exist (perhaps a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-hypergraph==1.78.0=r44hdfd78af_0"), MatchSpec(">=1.84.0,<1.85.0")} + Encountered problems while solving: + - nothing provides bioconductor-graph >=1.84.0,<1.85.0 needed by bioconductor-hypergraph-1.78.0-r44hdfd78af_0 + + Could not solve for environment specs + The following package could not be installed + bioconductor-altcdfenvs >=2.68.0,<2.69.0 is not installable because it requires + bioconductor-hypergraph >=1.78.0,<1.79.0 , which requires + bioconductor-graph >=1.84.0,<1.85.0 , which does not exist (perhaps a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-hypergraph==1.78.0=r44hdfd78af_0"), MatchSpec(">=1.84.0,<1.85.0")} + Encountered problems while solving: + - nothing provides bioconductor-graph >=1.84.0,<1.85.0 needed by bioconductor-hypergraph-1.78.0-r44hdfd78af_0 + + Could not solve for environment specs + The following package could not be installed + bioconductor-altcdfenvs >=2.68.0,<2.69.0 is not installable because it requires + bioconductor-hypergraph >=1.78.0,<1.79.0 , which requires + bioconductor-graph >=1.84.0,<1.85.0 , which does not exist (perhaps a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-harshlight/meta.yaml b/recipes/bioconductor-harshlight/meta.yaml index 2a5a3f49a1f5e..b9badb8e2107a 100644 --- a/recipes/bioconductor-harshlight/meta.yaml +++ b/recipes/bioconductor-harshlight/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "Harshlight" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitute value as whole matrix to solve the memory problem. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A "corrective make-up" program for microarray chips -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 36adabb3111ae035069431431dd9434a build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-harshlight", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:harshlight + - doi:10.1186/1471-2105-6-294 + parent_recipe: + name: bioconductor-harshlight + path: recipes/bioconductor-harshlight + version: 1.52.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-altcdfenvs >=2.64.0,<2.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-altcdfenvs >=2.68.0,<2.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - libblas - liblapack run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-altcdfenvs >=2.64.0,<2.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-altcdfenvs >=2.68.0,<2.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: 5162b3281dbfd34f228cb45996aab222 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'A "corrective make-up" program for microarray chips' - description: 'The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitute value as whole matrix to solve the memory problem.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:harshlight - - doi:10.1186/1471-2105-6-294 - parent_recipe: - name: bioconductor-harshlight - path: recipes/bioconductor-harshlight - version: 1.52.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hca/meta.yaml b/recipes/bioconductor-hca/meta.yaml index 0d284f48c3444..252638842be09 100644 --- a/recipes/bioconductor-hca/meta.yaml +++ b/recipes/bioconductor-hca/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "hca" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides users with the ability to query the Human Cell Atlas data repository for single-cell experiment data. The `projects()`, `files()`, `samples()` and `bundles()` functions retrieve summary information on each of these indexes; corresponding `*_details()` are available for individual entries of each index. File-based resources can be downloaded using `files_download()`. Advanced use of the package allows the user to page through large result sets, and to flexibly query the 'list-of-lists' structure representing query responses. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Exploring the Human Cell Atlas Data Coordinating Platform -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8a1c812efb51ab7e30a7d419bdf918a3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hca", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: LoomExperiment, SummarizedExperiment, SingleCellExperiment, S4Vectors, methods, testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base - r-digest - r-dplyr @@ -35,7 +37,7 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base - r-digest - r-dplyr @@ -47,13 +49,16 @@ requirements: - r-shiny - r-tibble - r-tidyr + +source: + md5: 0992e3bac4384a3c334382f2d43623df + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Exploring the Human Cell Atlas Data Coordinating Platform' - description: 'This package provides users with the ability to query the Human Cell Atlas data repository for single-cell experiment data. The `projects()`, `files()`, `samples()` and `bundles()` functions retrieve summary information on each of these indexes; corresponding `*_details()` are available for individual entries of each index. File-based resources can be downloaded using `files_download()`. Advanced use of the package allows the user to page through large result sets, and to flexibly query the ''list-of-lists'' structure representing query responses.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hcadata/meta.yaml b/recipes/bioconductor-hcadata/meta.yaml index de0348abe7497..fa272bf87f674 100644 --- a/recipes/bioconductor-hcadata/meta.yaml +++ b/recipes/bioconductor-hcadata/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "HCAData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'This package allows a direct access to the dataset generated by the Human Cell Atlas project for further processing in R and Bioconductor, in the comfortable format of SingleCellExperiment objects (available in other formats here: http://preview.data.humancellatlas.org/).' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Accessing The Datasets Of The Human Cell Atlas in R/Bioconductor -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4f16bf5904ca21c0fb0bd6515d7ab4d3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hcadata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, scran (>= 1.11.4), BiocSingular, scater, scuttle, Rtsne, igraph, iSEE, testthat requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 20709447d85048afded279c78fe2c531 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Accessing The Datasets Of The Human Cell Atlas in R/Bioconductor' - description: 'This package allows a direct access to the dataset generated by the Human Cell Atlas project for further processing in R and Bioconductor, in the comfortable format of SingleCellExperiment objects (available in other formats here: http://preview.data.humancellatlas.org/).' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hcadata/post-link.sh b/recipes/bioconductor-hcadata/post-link.sh index 66d5690d2efbb..dfbc93cb48d45 100644 --- a/recipes/bioconductor-hcadata/post-link.sh +++ b/recipes/bioconductor-hcadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hcadata-1.18.0" +installBiocDataPackage.sh "hcadata-1.22.0" diff --git a/recipes/bioconductor-hcatonsildata/meta.yaml b/recipes/bioconductor-hcatonsildata/meta.yaml index c329508ef650e..d7ccc6f0c45cf 100644 --- a/recipes/bioconductor-hcatonsildata/meta.yaml +++ b/recipes/bioconductor-hcatonsildata/meta.yaml @@ -1,57 +1,62 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "HCATonsilData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides access to the scRNA-seq, scATAC-seq, multiome, CITE-seq and spatial transcriptomics (Visium) data generated by the tonsil cell atlas in the context of the Human Cell Atlas (HCA). The data is provided via the Bioconductor project in the form of SingleCellExperiments. Additionally, information on the whole compendium of identified cell types is provided in form of a glossary. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Provide programmatic access to the tonsil cell atlas datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dda9d216f608690d05bd5ffbcb73bb05 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hcatonsildata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, ggplot2, testthat (>= 3.0.0), scater, Seurat, Signac, zellkonverter, iSEE, ggspavis, kableExtra, BiocStyle requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-base64enc - r-htmltools - r-rmarkdown run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-base64enc - r-htmltools - r-rmarkdown - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 5b5ff3154f189e90ed13a40a0904d16c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Provide programmatic access to the tonsil cell atlas datasets' - description: 'This package provides access to the scRNA-seq, scATAC-seq, multiome, CITE-seq and spatial transcriptomics (Visium) data generated by the tonsil cell atlas in the context of the Human Cell Atlas (HCA). The data is provided via the Bioconductor project in the form of SingleCellExperiments. Additionally, information on the whole compendium of identified cell types is provided in form of a glossary.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hcatonsildata/post-link.sh b/recipes/bioconductor-hcatonsildata/post-link.sh index 55f8721ee344a..d8eaa1448bf48 100644 --- a/recipes/bioconductor-hcatonsildata/post-link.sh +++ b/recipes/bioconductor-hcatonsildata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hcatonsildata-1.0.0" +installBiocDataPackage.sh "hcatonsildata-1.4.0" diff --git a/recipes/bioconductor-hcg110.db/meta.yaml b/recipes/bioconductor-hcg110.db/meta.yaml index c77a258d0c61b..af831ec4af187 100644 --- a/recipes/bioconductor-hcg110.db/meta.yaml +++ b/recipes/bioconductor-hcg110.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "hcg110.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4c536c3539a61d7f1f67dac149f10b11 +about: + description: Affymetrix Affymetrix HC_G110 Array annotation data (chip hcg110) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HC_G110 Array annotation data (chip hcg110) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hcg110.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4c536c3539a61d7f1f67dac149f10b11 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HC_G110 Array annotation data (chip hcg110)' - description: 'Affymetrix Affymetrix HC_G110 Array annotation data (chip hcg110) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hcg110cdf/meta.yaml b/recipes/bioconductor-hcg110cdf/meta.yaml index 6460e345d15fd..37c5272456c5e 100644 --- a/recipes/bioconductor-hcg110cdf/meta.yaml +++ b/recipes/bioconductor-hcg110cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hcg110cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b53167876217ddb301204719da23eafc +about: + description: A package containing an environment representing the HC_G110.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hcg110cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hcg110cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b53167876217ddb301204719da23eafc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hcg110cdf - description: 'A package containing an environment representing the HC_G110.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hcg110probe/meta.yaml b/recipes/bioconductor-hcg110probe/meta.yaml index 43ac0da0bf42d..444eaccab2b2b 100644 --- a/recipes/bioconductor-hcg110probe/meta.yaml +++ b/recipes/bioconductor-hcg110probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hcg110probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 51af8d6a7090ea7c5fe630dcea68bfb3 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HC-G110\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hcg110 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hcg110probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 51af8d6a7090ea7c5fe630dcea68bfb3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hcg110' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HC-G110\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hd2013sgi/meta.yaml b/recipes/bioconductor-hd2013sgi/meta.yaml index bfee69a492903..8f284cf656d3d 100644 --- a/recipes/bioconductor-hd2013sgi/meta.yaml +++ b/recipes/bioconductor-hd2013sgi/meta.yaml @@ -1,55 +1,60 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "HD2013SGI" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'This package contains the experimental data and a complete executable transcript (vignette) of the analysis of the HCT116 genetic interaction matrix presented in the paper "Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping" by C. Laufer, B. Fischer, M. Billmann, W. Huber, M. Boutros; Nature Methods (2013) 10:427-31. doi: 10.1038/nmeth.2436.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f8c7020a4fbfcb5c4026cea93e5a5bc6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hd2013sgi", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle # SystemRequirements: GNU make requirements: host: - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-geneplotter >=1.80.0,<1.81.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-splots >=1.68.0,<1.69.0' + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-geneplotter >=1.84.0,<1.85.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-splots >=1.72.0,<1.73.0 - r-base - r-gplots - r-lsd - r-rcolorbrewer - r-vcd run: - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-geneplotter >=1.80.0,<1.81.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-splots >=1.68.0,<1.69.0' + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-geneplotter >=1.84.0,<1.85.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-splots >=1.72.0,<1.73.0 - r-base - r-gplots - r-lsd - r-rcolorbrewer - r-vcd - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 1cb210d619cf563fb29d05ba42f1cefa + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping' - description: 'This package contains the experimental data and a complete executable transcript (vignette) of the analysis of the HCT116 genetic interaction matrix presented in the paper "Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping" by C. Laufer, B. Fischer, M. Billmann, W. Huber, M. Boutros; Nature Methods (2013) 10:427-31. doi: 10.1038/nmeth.2436.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hd2013sgi/post-link.sh b/recipes/bioconductor-hd2013sgi/post-link.sh index 498c6fc12a428..12ce555ef85f9 100644 --- a/recipes/bioconductor-hd2013sgi/post-link.sh +++ b/recipes/bioconductor-hd2013sgi/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hd2013sgi-1.42.0" +installBiocDataPackage.sh "hd2013sgi-1.46.0" diff --git a/recipes/bioconductor-hdcytodata/meta.yaml b/recipes/bioconductor-hdcytodata/meta.yaml index 45497fcf65184..5bca99e404dfc 100644 --- a/recipes/bioconductor-hdcytodata/meta.yaml +++ b/recipes/bioconductor-hdcytodata/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "HDCytoData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f962c6124539fea7a4a02a30e776de8 +about: + description: Data package containing a set of publicly available high-dimensional cytometry benchmark datasets, formatted into SummarizedExperiment and flowSet Bioconductor object formats, including all required metadata. Row metadata includes sample IDs, group IDs, patient IDs, reference cell population or cluster labels (where available), and labels identifying 'spiked in' cells (where available). Column metadata includes channel names, protein marker names, and protein marker classes (cell type or cell state). + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hdcytodata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM, mclust requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8a0dae06b9da48f201c3c1332c6d57d9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats' - description: 'Data package containing a set of publicly available high-dimensional cytometry benchmark datasets, formatted into SummarizedExperiment and flowSet Bioconductor object formats, including all required metadata. Row metadata includes sample IDs, group IDs, patient IDs, reference cell population or cluster labels (where available), and labels identifying ''spiked in'' cells (where available). Column metadata includes channel names, protein marker names, and protein marker classes (cell type or cell state).' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hdcytodata/post-link.sh b/recipes/bioconductor-hdcytodata/post-link.sh index d0ac96449fd70..532d3a0282727 100644 --- a/recipes/bioconductor-hdcytodata/post-link.sh +++ b/recipes/bioconductor-hdcytodata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hdcytodata-1.22.0" +installBiocDataPackage.sh "hdcytodata-1.26.0" diff --git a/recipes/bioconductor-hdf5array/meta.yaml b/recipes/bioconductor-hdf5array/meta.yaml index c3284e5d6eadf..fb348d3a1869d 100644 --- a/recipes/bioconductor-hdf5array/meta.yaml +++ b/recipes/bioconductor-hdf5array/meta.yaml @@ -1,69 +1,78 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "HDF5Array" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The HDF5Array package is an HDF5 backend for DelayedArray objects. It implements the HDF5Array, H5SparseMatrix, H5ADMatrix, and TENxMatrix classes, 4 convenient and memory-efficient array-like containers for representing and manipulating either: (1) a conventional (a.k.a. dense) HDF5 dataset, (2) an HDF5 sparse matrix (stored in CSR/CSC/Yale format), (3) the central matrix of an h5ad file (or any matrix in the /layers group), or (4) a 10x Genomics sparse matrix. All these containers are DelayedArray extensions and thus support all operations (delayed or block-processed) supported by DelayedArray objects.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: HDF5 datasets as array-like objects in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c59fcd283e0f9877f68457524b9d86bb build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hdf5array", max_pin="x.x") }}' -# Suggests: BiocParallel, GenomicRanges, SummarizedExperiment (>= 1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter, GenomicFeatures, RUnit, SingleCellExperiment + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:hdf5array + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-hdf5array + path: recipes/bioconductor-hdf5array + version: 1.8.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocParallel, GenomicRanges, SummarizedExperiment (>= 1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter, GenomicFeatures, RUnit, SingleCellExperiment, DelayedMatrixStats, genefilter # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rhdf5filters >=1.14.0,<1.15.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-s4arrays >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rhdf5filters >=1.18.0,<1.19.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-s4arrays >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 - r-base - r-matrix - libblas - liblapack + - zlib run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rhdf5filters >=1.14.0,<1.15.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-s4arrays >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rhdf5filters >=1.18.0,<1.19.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-s4arrays >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 - r-base - r-matrix - build: - - {{ compiler('c') }} - - make + +source: + md5: 82321c8a1bad0392f898462a6d8a1d60 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'HDF5 backend for DelayedArray objects' - description: 'Implement the HDF5Array, H5SparseMatrix, H5ADMatrix, and TENxMatrix classes, 4 convenient and memory-efficient array-like containers for representing and manipulating either: (1) a conventional (a.k.a. dense) HDF5 dataset, (2) an HDF5 sparse matrix (stored in CSR/CSC/Yale format), (3) the central matrix of an h5ad file (or any matrix in the /layers group), or (4) a 10x Genomics sparse matrix. All these containers are DelayedArray extensions and thus support all operations (delayed or block-processed) supported by DelayedArray objects.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:hdf5array - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-hdf5array - path: recipes/bioconductor-hdf5array - version: 1.8.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hdo.db/meta.yaml b/recipes/bioconductor-hdo.db/meta.yaml index 451b87e2c1add..398317d37dc60 100644 --- a/recipes/bioconductor-hdo.db/meta.yaml +++ b/recipes/bioconductor-hdo.db/meta.yaml @@ -1,40 +1,42 @@ -{% set version = "0.99.1" %} +{% set version = "1.0.0" %} {% set name = "HDO.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 007a50523f1de27048dfc97f4d458f59 +about: + description: A set of annotation maps describing the entire Human Disease Ontology assembled using data from DO. Its annotation data comes from https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: A set of annotation maps describing the entire Human Disease Ontology build: - number: 2 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hdo.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: rmarkdown, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base + - r-dbi run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base + - r-dbi - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: adb9df8c89fa3f2f877e7db1fbeb6b70 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A set of annotation maps describing the entire Human Disease Ontology' - description: 'A set of annotation maps describing the entire Human Disease Ontology assembled using data from DO. Its annotation data comes from https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hdo.db/post-link.sh b/recipes/bioconductor-hdo.db/post-link.sh index 9458063534034..ea02d451c73c6 100644 --- a/recipes/bioconductor-hdo.db/post-link.sh +++ b/recipes/bioconductor-hdo.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hdo.db-0.99.1" +installBiocDataPackage.sh "hdo.db-1.0.0" diff --git a/recipes/bioconductor-hdtd/meta.yaml b/recipes/bioconductor-hdtd/meta.yaml index f9eedc12bc226..d09705c82dbc1 100644 --- a/recipes/bioconductor-hdtd/meta.yaml +++ b/recipes/bioconductor-hdtd/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "HDTD" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Characterization of intra-individual variability using physiologically relevant measurements provides important insights into fundamental biological questions ranging from cell type identity to tumor development. For each individual, the data measurements can be written as a matrix with the different subsamples of the individual recorded in the columns and the different phenotypic units recorded in the rows. Datasets of this type are called high-dimensional transposable data. The HDTD package provides functions for conducting statistical inference for the mean relationship between the row and column variables and for the covariance structure within and between the row and column variables. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c990bac6152195272ae3aa3557f8b82b build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hdtd", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - - 'r-rcpp >=1.0.1' + - r-rcpp >=1.0.1 - r-rcpparmadillo - libblas - liblapack run: - r-base - - 'r-rcpp >=1.0.1' + - r-rcpp >=1.0.1 - r-rcpparmadillo - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 9eba270a4a162092391b4436491d053b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)' - description: 'Characterization of intra-individual variability using physiologically relevant measurements provides important insights into fundamental biological questions ranging from cell type identity to tumor development. For each individual, the data measurements can be written as a matrix with the different subsamples of the individual recorded in the columns and the different phenotypic units recorded in the rows. Datasets of this type are called high-dimensional transposable data. The HDTD package provides functions for conducting statistical inference for the mean relationship between the row and column variables and for the covariance structure within and between the row and column variables.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hdxmsqc/build.sh b/recipes/bioconductor-hdxmsqc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hdxmsqc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hdxmsqc/meta.yaml b/recipes/bioconductor-hdxmsqc/meta.yaml new file mode 100644 index 0000000000000..31ed8b557b009 --- /dev/null +++ b/recipes/bioconductor-hdxmsqc/meta.yaml @@ -0,0 +1,60 @@ +{% set version = "1.2.0" %} +{% set name = "hdxmsqc" %} +{% set bioc = "3.20" %} + +about: + description: The hdxmsqc package enables us to analyse and visualise the quality of HDX-MS experiments. Either as a final quality check before downstream analysis and publication or as part of a interative procedure to determine the quality of the data. The package builds on the QFeatures and Spectra packages to integrate with other mass-spectrometry data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: An R package for quality Control for hydrogen deuterium exchange mass spectrometry experiments + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hdxmsqc", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RColorBrewer, pheatmap, MASS, patchwork, testthat +requirements: + host: + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-qfeatures >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 + - r-base + - r-dplyr + - r-ggplot2 + - r-knitr + - r-tidyr + run: + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-qfeatures >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 + - r-base + - r-dplyr + - r-ggplot2 + - r-knitr + - r-tidyr + +source: + md5: 28a0051a468b7ca0db28cccde9eede14 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-healthycontrolspresencechecker/meta.yaml b/recipes/bioconductor-healthycontrolspresencechecker/meta.yaml index e9081da4b5fd8..61dcd784741f2 100644 --- a/recipes/bioconductor-healthycontrolspresencechecker/meta.yaml +++ b/recipes/bioconductor-healthycontrolspresencechecker/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "healthyControlsPresenceChecker" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'A function that reads in the GEO accession code of a gene expression dataset, retrieves its data from GEO, and checks if data of healthy controls are present in the dataset. It returns true if healthy controls data are found, and false otherwise. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL .' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Dowloads A Gene Expression Dataset From GEO And Checks If It Contains Data Of Healthy Controls Or Not -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 50ba7cea9e361d43c78d64ce1c89ba1a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-healthycontrolspresencechecker", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, markdown, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - bioconductor-geoquery >=2.74.0,<2.75.0 - r-base - r-geneexpressionfromgeo - r-magrittr - r-xml2 run: - - 'bioconductor-geoquery >=2.70.0,<2.71.0' + - bioconductor-geoquery >=2.74.0,<2.75.0 - r-base - r-geneexpressionfromgeo - r-magrittr - r-xml2 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 7834e53a3995caf74a55a7f4c63fb344 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Dowloads A Gene Expression Dataset From GEO And Checks If It Contains Data Of Healthy Controls Or Not' - description: 'A function that reads in the GEO accession code of a gene expression dataset, retrieves its data from GEO, and checks if data of healthy controls are present in the dataset. It returns true if healthy controls data are found, and false otherwise. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL .' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-healthycontrolspresencechecker/post-link.sh b/recipes/bioconductor-healthycontrolspresencechecker/post-link.sh index a259bb6b38c3a..c56f6548d9890 100644 --- a/recipes/bioconductor-healthycontrolspresencechecker/post-link.sh +++ b/recipes/bioconductor-healthycontrolspresencechecker/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "healthycontrolspresencechecker-1.6.0" +installBiocDataPackage.sh "healthycontrolspresencechecker-1.10.0" diff --git a/recipes/bioconductor-healthyflowdata/meta.yaml b/recipes/bioconductor-healthyflowdata/meta.yaml index 8797dd046a6e7..cf0ac21f48568 100644 --- a/recipes/bioconductor-healthyflowdata/meta.yaml +++ b/recipes/bioconductor-healthyflowdata/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "healthyFlowData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed0a9c99295e278a8445368a2cb226df +about: + description: A healthy dataset with 20 flow cytometry samples used by the flowMatch package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Healthy dataset used by the flowMatch package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-healthyflowdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base run: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a93dbeb707da467b9072d8926d5e79e6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Healthy dataset used by the flowMatch package' - description: 'A healthy dataset with 20 flow cytometry samples used by the flowMatch package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-healthyflowdata/post-link.sh b/recipes/bioconductor-healthyflowdata/post-link.sh index 0e206a9e263b2..8a91f978c04a7 100644 --- a/recipes/bioconductor-healthyflowdata/post-link.sh +++ b/recipes/bioconductor-healthyflowdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "healthyflowdata-1.40.0" +installBiocDataPackage.sh "healthyflowdata-1.44.0" diff --git a/recipes/bioconductor-heatmaps/meta.yaml b/recipes/bioconductor-heatmaps/meta.yaml index 5e3b7691db75b..02b30aed26406 100644 --- a/recipes/bioconductor-heatmaps/meta.yaml +++ b/recipes/bioconductor-heatmaps/meta.yaml @@ -1,61 +1,67 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "heatmaps" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functions for plotting heatmaps of genome-wide data across genomic intervals, such as ChIP-seq signals at peaks or across promoters. Many functions are also provided for investigating sequence features. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Flexible Heatmaps for Functional Genomics and Sequence Features -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 68b0a507dd5b2bcdfef2106195429dc2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-heatmaps", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-heatmaps + path: recipes/bioconductor-heatmaps + version: 1.4.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Drerio.UCSC.danRer7, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-kernsmooth - r-matrix - r-plotrix - r-rcolorbrewer run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-kernsmooth - r-matrix - r-plotrix - r-rcolorbrewer + +source: + md5: 13b9183ebc899d46076243552753b16b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Flexible Heatmaps for Functional Genomics and Sequence Features' - description: 'This package provides functions for plotting heatmaps of genome-wide data across genomic intervals, such as ChIP-seq signals at peaks or across promoters. Many functions are also provided for investigating sequence features.' -extra: - parent_recipe: - name: bioconductor-heatmaps - path: recipes/bioconductor-heatmaps - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-heatplus/meta.yaml b/recipes/bioconductor-heatplus/meta.yaml index 2e65c161b133c..123b92bb0feb6 100644 --- a/recipes/bioconductor-heatplus/meta.yaml +++ b/recipes/bioconductor-heatplus/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "3.10.0" %} +{% set version = "3.14.0" %} {% set name = "Heatplus" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is plotted. Optionally, panels with additional information about samples and features can be added to the plot. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Heatmaps with row and/or column covariates and colored clusters -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 459fb0dbd1242699e9f394f156a7e0c1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-heatplus", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:heatplus + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-heatplus + path: recipes/bioconductor-heatplus + version: 2.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biobase, hgu95av2.db, limma requirements: host: @@ -27,21 +38,16 @@ requirements: run: - r-base - r-rcolorbrewer + +source: + md5: 3794d207cd8b71b7b02a93ee56e7a07b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Heatmaps with row and/or column covariates and colored clusters' - description: 'Display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is plotted. Optionally, panels with additional information about samples and features can be added to the plot.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:heatplus - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-heatplus - path: recipes/bioconductor-heatplus - version: 2.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-heebodata/meta.yaml b/recipes/bioconductor-heebodata/meta.yaml index b2bccf7c7e017..35d85f5d159e7 100644 --- a/recipes/bioconductor-heebodata/meta.yaml +++ b/recipes/bioconductor-heebodata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "HEEBOdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 885df0689d6663e079e952ea297ee777 +about: + description: R objects describing the HEEBO oligo set. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: HEEBO set and HEEBO controls. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-heebodata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 521b9fe3601e422c49f5259ad67780ce + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'HEEBO set and HEEBO controls.' - description: 'R objects describing the HEEBO oligo set.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-heebodata/post-link.sh b/recipes/bioconductor-heebodata/post-link.sh index af9b31ef9b0a2..8891b93e157b9 100644 --- a/recipes/bioconductor-heebodata/post-link.sh +++ b/recipes/bioconductor-heebodata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "heebodata-1.40.0" +installBiocDataPackage.sh "heebodata-1.44.0" diff --git a/recipes/bioconductor-helloranges/meta.yaml b/recipes/bioconductor-helloranges/meta.yaml index 5e449934f1360..cd5a431bc5b57 100644 --- a/recipes/bioconductor-helloranges/meta.yaml +++ b/recipes/bioconductor-helloranges/meta.yaml @@ -1,75 +1,81 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "HelloRanges" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Translates bedtools command-line invocations to R code calling functions from the Bioconductor *Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Introduce *Ranges to bedtools users -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a83b42b9a323f3f3e356bfa8bbc0fd85 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-helloranges", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:helloranges + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-helloranges + path: recipes/bioconductor-helloranges + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: HelloRangesData, BiocStyle, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-docopt run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-docopt + +source: + md5: ee369883249c5424d123a30d6f80a112 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Introduce *Ranges to bedtools users' - description: 'Translates bedtools command-line invocations to R code calling functions from the Bioconductor *Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:helloranges - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-helloranges - path: recipes/bioconductor-helloranges - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hellorangesdata/meta.yaml b/recipes/bioconductor-hellorangesdata/meta.yaml index 4b189bec162c2..62d564ffacfcf 100644 --- a/recipes/bioconductor-hellorangesdata/meta.yaml +++ b/recipes/bioconductor-hellorangesdata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "HelloRangesData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ae6ac65f3af7f41136eb6fb3558eb2a +about: + description: Provides the data that were used in the bedtools tutorial by Aaron Quinlan (http://quinlanlab.org/tutorials/bedtools/bedtools.html). Includes a subset of the DnaseI hypersensitivity data from "Maurano et al. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA. Science. 2012. Vol. 337 no. 6099 pp. 1190-1195." The rest of the tracks were originally downloaded from the UCSC table browser. See the HelloRanges vignette for a port of the bedtools tutorial to R. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Data for the HelloRanges tutorial vignette build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hellorangesdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: acda716ebef959e29b29129559d11134 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Data for the HelloRanges tutorial vignette' - description: 'Provides the data that were used in the bedtools tutorial by Aaron Quinlan (http://quinlanlab.org/tutorials/bedtools/bedtools.html). Includes a subset of the DnaseI hypersensitivity data from "Maurano et al. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA. Science. 2012. Vol. 337 no. 6099 pp. 1190-1195." The rest of the tracks were originally downloaded from the UCSC table browser. See the HelloRanges vignette for a port of the bedtools tutorial to R.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hellorangesdata/post-link.sh b/recipes/bioconductor-hellorangesdata/post-link.sh index 3a9fee9bcee90..04bab9b519c62 100644 --- a/recipes/bioconductor-hellorangesdata/post-link.sh +++ b/recipes/bioconductor-hellorangesdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hellorangesdata-1.28.0" +installBiocDataPackage.sh "hellorangesdata-1.32.0" diff --git a/recipes/bioconductor-help/meta.yaml b/recipes/bioconductor-help/meta.yaml index 02757fe4dc641..9a7eccb9c91b9 100644 --- a/recipes/bioconductor-help/meta.yaml +++ b/recipes/bioconductor-help/meta.yaml @@ -1,40 +1,22 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "HELP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Tools for HELP data analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d7a1038ee6eb5ec01393b39e30e028fe build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-help", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Tools for HELP data analysis' - description: 'The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:help @@ -44,3 +26,27 @@ extra: path: recipes/bioconductor-help version: 1.38.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + +source: + md5: 9163051930de1ef9ce1b2a57a1558c1e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-hem/meta.yaml b/recipes/bioconductor-hem/meta.yaml index d6fe622e155cb..063239f0cf14d 100644 --- a/recipes/bioconductor-hem/meta.yaml +++ b/recipes/bioconductor-hem/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "HEM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package fits heterogeneous error models for analysis of microarray data + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Heterogeneous error model for identification of differentially expressed genes under multiple conditions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ad1825d95504eaf9e2bcad8438816f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hem", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:hem + - doi:10.1093/bioinformatics/bth192 + parent_recipe: + name: bioconductor-hem + path: recipes/bioconductor-hem + version: 1.52.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: e0e9b1d77b9f1ecc095735724aa68ffe + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Heterogeneous error model for identification of differentially expressed genes under multiple conditions' - description: 'This package fits heterogeneous error models for analysis of microarray data' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:hem - - doi:10.1093/bioinformatics/bth192 - parent_recipe: - name: bioconductor-hem - path: recipes/bioconductor-hem - version: 1.52.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hermes/meta.yaml b/recipes/bioconductor-hermes/meta.yaml index 628da60c967f4..08f2b56d7befe 100644 --- a/recipes/bioconductor-hermes/meta.yaml +++ b/recipes/bioconductor-hermes/meta.yaml @@ -1,49 +1,51 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "hermes" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides classes and functions for quality control, filtering, normalization and differential expression analysis of pre-processed `RNA-seq` data. Data can be imported from `SummarizedExperiment` as well as `matrix` objects and can be annotated from `BioMart`. Filtering for genes without too low expression or containing required annotations, as well as filtering for samples with sufficient correlation to other samples or total number of reads is supported. The standard normalization methods including cpm, rpkm and tpm can be used, and 'DESeq2` as well as voom differential expression analyses are available. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Apache License 2.0 + summary: Preprocessing, analyzing, and reporting of RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: af1e1dd4bab597cfb7b0bd12a1e9e7dd build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hermes", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, DelayedArray, DT, grid, httr, knitr, rmarkdown, statmod, testthat (>= 2.0), vdiffr, withr + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, DelayedArray, DT, grid, httr, knitr, rmarkdown, statmod, testthat (>= 2.0), vdiffr requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - - 'r-checkmate >=2.1' + - r-checkmate >=2.1 - r-circlize - r-dplyr - r-envstats - - r-forcats + - r-forcats >=1.0.0 - r-ggfortify - r-ggplot2 - - 'r-ggrepel >=0.9' + - r-ggrepel >=0.9 - r-lifecycle - r-magrittr - r-matrixstats @@ -52,29 +54,30 @@ requirements: - r-rdpack - r-rlang - r-tidyr + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - - 'r-checkmate >=2.1' + - r-checkmate >=2.1 - r-circlize - r-dplyr - r-envstats - - r-forcats + - r-forcats >=1.0.0 - r-ggfortify - r-ggplot2 - - 'r-ggrepel >=0.9' + - r-ggrepel >=0.9 - r-lifecycle - r-magrittr - r-matrixstats @@ -83,13 +86,16 @@ requirements: - r-rdpack - r-rlang - r-tidyr + +source: + md5: 66f15d90a3af1663393f1904bbdd74f0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Apache License 2.0 | file LICENSE' - summary: 'Preprocessing, analyzing, and reporting of RNA-seq data' - description: 'Provides classes and functions for quality control, filtering, normalization and differential expression analysis of pre-processed RNA-seq data. Data can be imported from `SummarizedExperiment` as well as `matrix` objects and can be annotated from BioMart. Filtering for genes without too low expression or containing required annotations, as well as filtering for samples with sufficient correlation to other samples or total number of reads is supported. The standard normalization methods including `cpm`, `rpkm` and `tpm` can be used, and `DESeq2` as well as `voom` differential expression analyses are available.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-heron/meta.yaml b/recipes/bioconductor-heron/meta.yaml index abc4916803605..3f7de45360184 100644 --- a/recipes/bioconductor-heron/meta.yaml +++ b/recipes/bioconductor-heron/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "HERON" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: HERON is a software package for analyzing peptide binding array data. In addition to identifying significant binding probes, HERON also provides functions for finding epitopes (string of consecutive peptides within a protein). HERON also calculates significance on the probe, epitope, and protein level by employing meta p-value methods. HERON is designed for obtaining calls on the sample level and calculates fractions of hits for different conditions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Hierarchical Epitope pROtein biNding -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9c146a8d99bada338098732e1de5a5e2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-heron", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-data.table @@ -36,11 +38,11 @@ requirements: - r-metap - r-spdep run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-data.table @@ -49,13 +51,16 @@ requirements: - r-matrixstats - r-metap - r-spdep + +source: + md5: d41b40db5c26c69733c46f4396dfcf4c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Hierarchical Epitope pROtein biNding' - description: 'HERON is a software package for analyzing peptide binding array data. In addition to identifying significant binding probes, HERON also provides functions for finding epitopes (string of consecutive peptides within a protein). HERON also calculates significance on the probe, epitope, and protein level by employing meta p-value methods. HERON is designed for obtaining calls on the sample level and calculates fractions of hits for different conditions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-herper/meta.yaml b/recipes/bioconductor-herper/meta.yaml index 1ec27237788bd..1b9db3af73668 100644 --- a/recipes/bioconductor-herper/meta.yaml +++ b/recipes/bioconductor-herper/meta.yaml @@ -1,25 +1,24 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "Herper" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dad437a472cae186246d3cf0f6b44964 +about: + description: Many tools for data analysis are not available in R, but are present in public repositories like conda. The Herper package provides a comprehensive set of functions to interact with the conda package managament system. With Herper users can install, manage and run conda packages from the comfort of their R session. Herper also provides an ad-hoc approach to handling external system requirements for R packages. For people developing packages with python conda dependencies we recommend using basilisk (https://bioconductor.org/packages/release/bioc/html/basilisk.html) to internally support these system requirments pre-hoc. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: The Herper package is a simple toolset to install and manage conda packages and environments from R build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-herper", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, testthat, knitr, rmarkdown, seqCNA +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - r-base @@ -31,13 +30,14 @@ requirements: - r-reticulate - r-rjson - r-withr +source: + md5: 9f9111e2307d05fa4c12eca84ca524f5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'The Herper package is a simple toolset to install and manage conda packages and environments from R' - description: 'Many tools for data analysis are not available in R, but are present in public repositories like conda. The Herper package provides a comprehensive set of functions to interact with the conda package managament system. With Herper users can install, manage and run conda packages from the comfort of their R session. Herper also provides an ad-hoc approach to handling external system requirements for R packages. For people developing packages with python conda dependencies we recommend using basilisk (https://bioconductor.org/packages/release/bioc/html/basilisk.html) to internally support these system requirments pre-hoc.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgc/meta.yaml b/recipes/bioconductor-hgc/meta.yaml index 415c8beba464a..c0cd105257875 100644 --- a/recipes/bioconductor-hgc/meta.yaml +++ b/recipes/bioconductor-hgc/meta.yaml @@ -1,26 +1,32 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "HGC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: HGC (short for Hierarchical Graph-based Clustering) is an R package for conducting hierarchical clustering on large-scale single-cell RNA-seq (scRNA-seq) data. The key idea is to construct a dendrogram of cells on their shared nearest neighbor (SNN) graph. HGC provides functions for building graphs and for conducting hierarchical clustering on the graph. The users with old R version could visit https://github.com/XuegongLab/HGC/tree/HGC4oldRVersion to get HGC package built for R 3.6. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A fast hierarchical graph-based clustering method -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a8ac62af3106b62952c79c162937a3c build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgc", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-ape - r-base @@ -31,8 +37,8 @@ requirements: - r-mclust - r-patchwork - r-rann - - 'r-rcpp >=1.0.0' - - 'r-rcppeigen >=0.3.2.0' + - r-rcpp >=1.0.0 + - r-rcppeigen >=0.3.2.0 - libblas - liblapack run: @@ -45,19 +51,18 @@ requirements: - r-mclust - r-patchwork - r-rann - - 'r-rcpp >=1.0.0' - - 'r-rcppeigen >=0.3.2.0' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=1.0.0 + - r-rcppeigen >=0.3.2.0 + +source: + md5: 237909a41003377a1abf5bbd65de72ba + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'A fast hierarchical graph-based clustering method' - description: 'HGC (short for Hierarchical Graph-based Clustering) is an R package for conducting hierarchical clustering on large-scale single-cell RNA-seq (scRNA-seq) data. The key idea is to construct a dendrogram of cells on their shared nearest neighbor (SNN) graph. HGC provides functions for building graphs and for conducting hierarchical clustering on the graph. The users with old R version could visit https://github.com/XuegongLab/HGC/tree/HGC4oldRVersion to get HGC package built for R 3.6.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgfocus.db/meta.yaml b/recipes/bioconductor-hgfocus.db/meta.yaml index 7aed356288bfa..5e5e30ab2ef3a 100644 --- a/recipes/bioconductor-hgfocus.db/meta.yaml +++ b/recipes/bioconductor-hgfocus.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "hgfocus.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a6bee48c0aa947d3c7d25ef2c5a4d485 +about: + description: Affymetrix Affymetrix HG-Focus Array annotation data (chip hgfocus) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HG-Focus Array annotation data (chip hgfocus) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgfocus.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a6bee48c0aa947d3c7d25ef2c5a4d485 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HG-Focus Array annotation data (chip hgfocus)' - description: 'Affymetrix Affymetrix HG-Focus Array annotation data (chip hgfocus) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgfocuscdf/meta.yaml b/recipes/bioconductor-hgfocuscdf/meta.yaml index eff511fe7d21c..d0203efe97cb1 100644 --- a/recipes/bioconductor-hgfocuscdf/meta.yaml +++ b/recipes/bioconductor-hgfocuscdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgfocuscdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9883e53bfd9ddb9ad5f3a9c2e47bbd2c +about: + description: A package containing an environment representing the HG-Focus.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hgfocuscdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgfocuscdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9883e53bfd9ddb9ad5f3a9c2e47bbd2c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hgfocuscdf - description: 'A package containing an environment representing the HG-Focus.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgfocusprobe/meta.yaml b/recipes/bioconductor-hgfocusprobe/meta.yaml index 778b13ab99e1f..d674754276392 100644 --- a/recipes/bioconductor-hgfocusprobe/meta.yaml +++ b/recipes/bioconductor-hgfocusprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgfocusprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0a399ed276b89e3d80946b6cbbf167b4 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-Focus\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hgfocus build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgfocusprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0a399ed276b89e3d80946b6cbbf167b4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hgfocus' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-Focus\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133a.db/meta.yaml b/recipes/bioconductor-hgu133a.db/meta.yaml index 7f4d6907ae274..ce4de8735ebac 100644 --- a/recipes/bioconductor-hgu133a.db/meta.yaml +++ b/recipes/bioconductor-hgu133a.db/meta.yaml @@ -1,47 +1,53 @@ {% set version = "3.13.0" %} {% set name = "hgu133a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Affymetrix Affymetrix HG-U133A Array annotation data (chip hgu133a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HG-U133A Array annotation data (chip hgu133a) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 97675c27b13624bdfd760460dbca6bf0 build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133a.db", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-hgu133a.db + path: recipes/bioconductor-hgu133a.db + version: 3.2.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 97675c27b13624bdfd760460dbca6bf0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HG-U133A Array annotation data (chip hgu133a)' - description: 'Affymetrix Affymetrix HG-U133A Array annotation data (chip hgu133a) assembled using data from public repositories' -extra: - parent_recipe: - name: bioconductor-hgu133a.db - path: recipes/bioconductor-hgu133a.db - version: 3.2.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133a2.db/meta.yaml b/recipes/bioconductor-hgu133a2.db/meta.yaml index 4d8b4ac0c42dd..2a310a9cf0e7e 100644 --- a/recipes/bioconductor-hgu133a2.db/meta.yaml +++ b/recipes/bioconductor-hgu133a2.db/meta.yaml @@ -1,47 +1,53 @@ {% set version = "3.13.0" %} {% set name = "hgu133a2.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Affymetrix Affymetrix HG-U133A_2 Array annotation data (chip hgu133a2) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HG-U133A_2 Array annotation data (chip hgu133a2) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e3bf9c5c9941f5f378cbc3dbeb9919ee build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133a2.db", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-hgu133a2.db + path: recipes/bioconductor-hgu133a2.db + version: 3.2.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: e3bf9c5c9941f5f378cbc3dbeb9919ee + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HG-U133A_2 Array annotation data (chip hgu133a2)' - description: 'Affymetrix Affymetrix HG-U133A_2 Array annotation data (chip hgu133a2) assembled using data from public repositories' -extra: - parent_recipe: - name: bioconductor-hgu133a2.db - path: recipes/bioconductor-hgu133a2.db - version: 3.2.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133a2cdf/meta.yaml b/recipes/bioconductor-hgu133a2cdf/meta.yaml index f9a09d9b3bf33..64932dbaab49e 100644 --- a/recipes/bioconductor-hgu133a2cdf/meta.yaml +++ b/recipes/bioconductor-hgu133a2cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu133a2cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 566bc70f0bb94a376bf88f191a2f067e +about: + description: A package containing an environment representing the HG-U133A_2.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hgu133a2cdf build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133a2cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 566bc70f0bb94a376bf88f191a2f067e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hgu133a2cdf - description: 'A package containing an environment representing the HG-U133A_2.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133a2frmavecs/meta.yaml b/recipes/bioconductor-hgu133a2frmavecs/meta.yaml index 94e507f7794fa..13b21723e2a29 100644 --- a/recipes/bioconductor-hgu133a2frmavecs/meta.yaml +++ b/recipes/bioconductor-hgu133a2frmavecs/meta.yaml @@ -1,38 +1,38 @@ {% set version = "1.2.0" %} {% set name = "hgu133a2frmavecs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4bf8cf5cbaf288ce0a9618d764c87044 +about: + description: This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Vectors used by frma for microarrays of type hgu133a2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133a2frmavecs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4bf8cf5cbaf288ce0a9618d764c87044 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Vectors used by frma for microarrays of type hgu133a2' - description: 'This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133a2probe/meta.yaml b/recipes/bioconductor-hgu133a2probe/meta.yaml index 6ee5643b2e00d..56b00da0fccd0 100644 --- a/recipes/bioconductor-hgu133a2probe/meta.yaml +++ b/recipes/bioconductor-hgu133a2probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu133a2probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 736b43cfc37a297ccc0d30cb75fcc95a +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U133A\_2\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hgu133a2 build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133a2probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 736b43cfc37a297ccc0d30cb75fcc95a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hgu133a2' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U133A\_2\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133abarcodevecs/meta.yaml b/recipes/bioconductor-hgu133abarcodevecs/meta.yaml index c86306fc1565e..ade8f3b468f5c 100644 --- a/recipes/bioconductor-hgu133abarcodevecs/meta.yaml +++ b/recipes/bioconductor-hgu133abarcodevecs/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "hgu133abarcodevecs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4a6ec67e649f7ca004242fd860f79521 +about: + description: Data used by the barcode package for microarrays of type hgu133a. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: hgu133a data for barcode build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133abarcodevecs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 86e728d6eabf7c2b2d0629e4489ba140 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'hgu133a data for barcode' - description: 'Data used by the barcode package for microarrays of type hgu133a.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133abarcodevecs/post-link.sh b/recipes/bioconductor-hgu133abarcodevecs/post-link.sh index fba77b0ea4940..86453581b026d 100644 --- a/recipes/bioconductor-hgu133abarcodevecs/post-link.sh +++ b/recipes/bioconductor-hgu133abarcodevecs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hgu133abarcodevecs-1.40.0" +installBiocDataPackage.sh "hgu133abarcodevecs-1.44.0" diff --git a/recipes/bioconductor-hgu133acdf/meta.yaml b/recipes/bioconductor-hgu133acdf/meta.yaml index d4d21cf580157..741294419328b 100644 --- a/recipes/bioconductor-hgu133acdf/meta.yaml +++ b/recipes/bioconductor-hgu133acdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu133acdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d3e0e22b2d3943d26c94e7c01b91035c +about: + description: A package containing an environment representing the HG-U133A.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hgu133acdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133acdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d3e0e22b2d3943d26c94e7c01b91035c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hgu133acdf - description: 'A package containing an environment representing the HG-U133A.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133afrmavecs/meta.yaml b/recipes/bioconductor-hgu133afrmavecs/meta.yaml index 97d6ef809ddbb..b96198396aecf 100644 --- a/recipes/bioconductor-hgu133afrmavecs/meta.yaml +++ b/recipes/bioconductor-hgu133afrmavecs/meta.yaml @@ -1,38 +1,38 @@ {% set version = "1.5.0" %} {% set name = "hgu133afrmavecs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 85034ab02491f5b3699d210cef50812d +about: + description: This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Vectors used by frma for microarrays of type hgu133a build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133afrmavecs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 85034ab02491f5b3699d210cef50812d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Vectors used by frma for microarrays of type hgu133a' - description: 'This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133aprobe/meta.yaml b/recipes/bioconductor-hgu133aprobe/meta.yaml index 289e639bf7daa..f0e56f25f0767 100644 --- a/recipes/bioconductor-hgu133aprobe/meta.yaml +++ b/recipes/bioconductor-hgu133aprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu133aprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 76cd9c54b0a8a0240dbb0fc758959d62 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U133A\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hgu133a build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133aprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 76cd9c54b0a8a0240dbb0fc758959d62 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hgu133a' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U133A\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133atagcdf/meta.yaml b/recipes/bioconductor-hgu133atagcdf/meta.yaml index 96ad110b6ed05..147ab62f10396 100644 --- a/recipes/bioconductor-hgu133atagcdf/meta.yaml +++ b/recipes/bioconductor-hgu133atagcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu133atagcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 01f8809e0deb5b83f3f0decec881a1d8 +about: + description: A package containing an environment representing the HG-U133A_tag.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hgu133atagcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133atagcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 01f8809e0deb5b83f3f0decec881a1d8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hgu133atagcdf - description: 'A package containing an environment representing the HG-U133A_tag.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133atagprobe/meta.yaml b/recipes/bioconductor-hgu133atagprobe/meta.yaml index 26c2b3d196144..bc7a2dc627eef 100644 --- a/recipes/bioconductor-hgu133atagprobe/meta.yaml +++ b/recipes/bioconductor-hgu133atagprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu133atagprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 97aeaf9ac9450369cf030581b8ec5a53 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U133A\_tag\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hgu133atag build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133atagprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 97aeaf9ac9450369cf030581b8ec5a53 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hgu133atag' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U133A\_tag\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133b.db/meta.yaml b/recipes/bioconductor-hgu133b.db/meta.yaml index 1667653d2b6b0..475a9110c289d 100644 --- a/recipes/bioconductor-hgu133b.db/meta.yaml +++ b/recipes/bioconductor-hgu133b.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "hgu133b.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ff7930c99300c1022fde06ebe5c4a8cc +about: + description: Affymetrix Affymetrix HG-U133B Array annotation data (chip hgu133b) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HG-U133B Array annotation data (chip hgu133b) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133b.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ff7930c99300c1022fde06ebe5c4a8cc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HG-U133B Array annotation data (chip hgu133b)' - description: 'Affymetrix Affymetrix HG-U133B Array annotation data (chip hgu133b) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133bcdf/meta.yaml b/recipes/bioconductor-hgu133bcdf/meta.yaml index 0d9eb06173948..4d51378ced924 100644 --- a/recipes/bioconductor-hgu133bcdf/meta.yaml +++ b/recipes/bioconductor-hgu133bcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu133bcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 649aaa5e6275be6ee4d24d80ca390ea5 +about: + description: A package containing an environment representing the HG-U133B.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hgu133bcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133bcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 649aaa5e6275be6ee4d24d80ca390ea5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hgu133bcdf - description: 'A package containing an environment representing the HG-U133B.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133bprobe/meta.yaml b/recipes/bioconductor-hgu133bprobe/meta.yaml index ea232fc9d19a3..cb082176462de 100644 --- a/recipes/bioconductor-hgu133bprobe/meta.yaml +++ b/recipes/bioconductor-hgu133bprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu133bprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 203750510e51450e1267e08c241151c4 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U133B\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hgu133b build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133bprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 203750510e51450e1267e08c241151c4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hgu133b' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U133B\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133plus2.db/meta.yaml b/recipes/bioconductor-hgu133plus2.db/meta.yaml index cf1fe96b56771..1e199f22c5740 100644 --- a/recipes/bioconductor-hgu133plus2.db/meta.yaml +++ b/recipes/bioconductor-hgu133plus2.db/meta.yaml @@ -1,47 +1,53 @@ {% set version = "3.13.0" %} {% set name = "hgu133plus2.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 459fcf4880a9eaa25b373c5635fede3d build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133plus2.db", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-hgu133plus2.db + path: recipes/bioconductor-hgu133plus2.db + version: 3.2.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 459fcf4880a9eaa25b373c5635fede3d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2)' - description: 'Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data (chip hgu133plus2) assembled using data from public repositories' -extra: - parent_recipe: - name: bioconductor-hgu133plus2.db - path: recipes/bioconductor-hgu133plus2.db - version: 3.2.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133plus2barcodevecs/meta.yaml b/recipes/bioconductor-hgu133plus2barcodevecs/meta.yaml index cb5e8dfdb2d01..2d31ba346e9de 100644 --- a/recipes/bioconductor-hgu133plus2barcodevecs/meta.yaml +++ b/recipes/bioconductor-hgu133plus2barcodevecs/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "hgu133plus2barcodevecs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 624bad8617d806474bc9406dc3c22384 +about: + description: Data used by the barcode package for microarrays of type hgu133plus2. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: hgu133plus2 data for barcode build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133plus2barcodevecs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8e70491d7b0590fa84517fbb449ec2db + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'hgu133plus2 data for barcode' - description: 'Data used by the barcode package for microarrays of type hgu133plus2.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133plus2barcodevecs/post-link.sh b/recipes/bioconductor-hgu133plus2barcodevecs/post-link.sh index f44c331060ecf..ff266eb9bf368 100644 --- a/recipes/bioconductor-hgu133plus2barcodevecs/post-link.sh +++ b/recipes/bioconductor-hgu133plus2barcodevecs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hgu133plus2barcodevecs-1.40.0" +installBiocDataPackage.sh "hgu133plus2barcodevecs-1.44.0" diff --git a/recipes/bioconductor-hgu133plus2cdf/meta.yaml b/recipes/bioconductor-hgu133plus2cdf/meta.yaml index 9e57c07dda204..eea4d8fb6394f 100644 --- a/recipes/bioconductor-hgu133plus2cdf/meta.yaml +++ b/recipes/bioconductor-hgu133plus2cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu133plus2cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 284fef2f0b777d7b53451538ddd53de3 +about: + description: A package containing an environment representing the HG-U133_Plus_2.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hgu133plus2cdf build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133plus2cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 284fef2f0b777d7b53451538ddd53de3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hgu133plus2cdf - description: 'A package containing an environment representing the HG-U133_Plus_2.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133plus2cellscore/meta.yaml b/recipes/bioconductor-hgu133plus2cellscore/meta.yaml index 8d4b60ba2ced3..c6d3a2b821edf 100644 --- a/recipes/bioconductor-hgu133plus2cellscore/meta.yaml +++ b/recipes/bioconductor-hgu133plus2cellscore/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "hgu133plus2CellScore" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 486b7084ad0056c1031545af9c6dd515 +about: + description: The CellScore Standard Dataset contains expression data from a wide variety of human cells and tissues, which should be used as standard cell types in the calculation of the CellScore. All data was curated from public databases such as Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) or ArrayExpress (https://www.ebi.ac.uk/arrayexpress/). This standard dataset only contains data from the Affymetrix GeneChip Human Genome U133 Plus 2.0 microarrays. Samples were manually annotated using the database information or consulting the publications in which the datasets originated. The sample annotations are stored in the phenoData slot of the expressionSet object. Raw data (CEL files) were processed with the affy package to generate present/absent calls (mas5calls) and background-subtracted values, which were then normalized by the R-package yugene to yield the final expression values for the standard expression matrix. The annotation table for the microarray was retrieved from the BioC annotation package hgu133plus2. All data are stored in an expressionSet object. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: CellScore Standard Cell Types Expression Dataset [hgu133plus2] build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133plus2cellscore", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ece73161aa2c3ec43a558994e4a81dd1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'CellScore Standard Cell Types Expression Dataset [hgu133plus2]' - description: 'The CellScore Standard Dataset contains expression data from a wide variety of human cells and tissues, which should be used as standard cell types in the calculation of the CellScore. All data was curated from public databases such as Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) or ArrayExpress (https://www.ebi.ac.uk/arrayexpress/). This standard dataset only contains data from the Affymetrix GeneChip Human Genome U133 Plus 2.0 microarrays. Samples were manually annotated using the database information or consulting the publications in which the datasets originated. The sample annotations are stored in the phenoData slot of the expressionSet object. Raw data (CEL files) were processed with the affy package to generate present/absent calls (mas5calls) and background-subtracted values, which were then normalized by the R-package yugene to yield the final expression values for the standard expression matrix. The annotation table for the microarray was retrieved from the BioC annotation package hgu133plus2. All data are stored in an expressionSet object.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133plus2cellscore/post-link.sh b/recipes/bioconductor-hgu133plus2cellscore/post-link.sh index 5db37f89ca4fd..4460447bf7663 100644 --- a/recipes/bioconductor-hgu133plus2cellscore/post-link.sh +++ b/recipes/bioconductor-hgu133plus2cellscore/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hgu133plus2cellscore-1.22.0" +installBiocDataPackage.sh "hgu133plus2cellscore-1.26.0" diff --git a/recipes/bioconductor-hgu133plus2frmavecs/meta.yaml b/recipes/bioconductor-hgu133plus2frmavecs/meta.yaml index a4180048a8637..75b5190f45ace 100644 --- a/recipes/bioconductor-hgu133plus2frmavecs/meta.yaml +++ b/recipes/bioconductor-hgu133plus2frmavecs/meta.yaml @@ -1,38 +1,38 @@ {% set version = "1.5.0" %} {% set name = "hgu133plus2frmavecs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a4781cbcccc1ee17dfd16259f1c7bebc +about: + description: This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Vectors used by frma for microarrays of type hgu133plus2 build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133plus2frmavecs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a4781cbcccc1ee17dfd16259f1c7bebc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Vectors used by frma for microarrays of type hgu133plus2' - description: 'This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu133plus2probe/meta.yaml b/recipes/bioconductor-hgu133plus2probe/meta.yaml index 15f9e2c0e4cd0..3574246ef09de 100644 --- a/recipes/bioconductor-hgu133plus2probe/meta.yaml +++ b/recipes/bioconductor-hgu133plus2probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu133plus2probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7a244787a0269bc72732ac3d830f34dd +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U133\_Plus\_2\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hgu133plus2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu133plus2probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7a244787a0269bc72732ac3d830f34dd + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hgu133plus2' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U133\_Plus\_2\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu219.db/meta.yaml b/recipes/bioconductor-hgu219.db/meta.yaml index 6207dd4fbfcc9..f207c7cfadf0a 100644 --- a/recipes/bioconductor-hgu219.db/meta.yaml +++ b/recipes/bioconductor-hgu219.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "hgu219.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a4a0fd2ac170a75d8b17618615fcd7a0 +about: + description: Affymetrix Human Genome 219 Plate annotation data (chip hgu219) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Human Genome 219 Plate annotation data (chip hgu219) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu219.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a4a0fd2ac170a75d8b17618615fcd7a0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Human Genome 219 Plate annotation data (chip hgu219)' - description: 'Affymetrix Human Genome 219 Plate annotation data (chip hgu219) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu219cdf/meta.yaml b/recipes/bioconductor-hgu219cdf/meta.yaml index b692201bd81cd..34bdc910a8af5 100644 --- a/recipes/bioconductor-hgu219cdf/meta.yaml +++ b/recipes/bioconductor-hgu219cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu219cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 157a4280a9de960902260ab18f678949 +about: + description: A package containing an environment representing the HG-U219.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hgu219cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu219cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 157a4280a9de960902260ab18f678949 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hgu219cdf - description: 'A package containing an environment representing the HG-U219.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu219probe/meta.yaml b/recipes/bioconductor-hgu219probe/meta.yaml index ce6e47caba3dd..7e9ac0a94fe28 100644 --- a/recipes/bioconductor-hgu219probe/meta.yaml +++ b/recipes/bioconductor-hgu219probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu219probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c5bb2f7b2e0f8fa89e6a30befaee6497 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U219\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hgu219 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu219probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c5bb2f7b2e0f8fa89e6a30befaee6497 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hgu219' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U219\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu2beta7/meta.yaml b/recipes/bioconductor-hgu2beta7/meta.yaml index e96e80fe95558..5dd46a483ffbb 100644 --- a/recipes/bioconductor-hgu2beta7/meta.yaml +++ b/recipes/bioconductor-hgu2beta7/meta.yaml @@ -1,37 +1,37 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "hgu2beta7" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0643f49d27bf1dd6b73fb9192b23ebaa +about: + description: Annotation data file for hgu2beta7 assembled using data from public data repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: A data package containing annotation data for hgu2beta7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu2beta7", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4b1f0eca6477f5475ebdccb2c06f6634 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A data package containing annotation data for hgu2beta7' - description: 'Annotation data file for hgu2beta7 assembled using data from public data repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu2beta7/post-link.sh b/recipes/bioconductor-hgu2beta7/post-link.sh index 344f6120b8df6..c42848693fea6 100644 --- a/recipes/bioconductor-hgu2beta7/post-link.sh +++ b/recipes/bioconductor-hgu2beta7/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hgu2beta7-1.42.0" +installBiocDataPackage.sh "hgu2beta7-1.46.0" diff --git a/recipes/bioconductor-hgu95a.db/meta.yaml b/recipes/bioconductor-hgu95a.db/meta.yaml index 304c7640fc879..9b0b6f1a0edb7 100644 --- a/recipes/bioconductor-hgu95a.db/meta.yaml +++ b/recipes/bioconductor-hgu95a.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "hgu95a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b228ec0eded3ba9bccf033c2fff8f7b8 +about: + description: Affymetrix Affymetrix HG U95A Array annotation data (chip hgu95a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HG U95A Array annotation data (chip hgu95a) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu95a.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b228ec0eded3ba9bccf033c2fff8f7b8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HG U95A Array annotation data (chip hgu95a)' - description: 'Affymetrix Affymetrix HG U95A Array annotation data (chip hgu95a) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu95acdf/meta.yaml b/recipes/bioconductor-hgu95acdf/meta.yaml index 1b49083b8669c..810a17712927d 100644 --- a/recipes/bioconductor-hgu95acdf/meta.yaml +++ b/recipes/bioconductor-hgu95acdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu95acdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: afc999d77b1532154d45911ad15a5897 +about: + description: A package containing an environment representing the HG U95A.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hgu95acdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu95acdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: afc999d77b1532154d45911ad15a5897 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hgu95acdf - description: 'A package containing an environment representing the HG U95A.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu95aprobe/meta.yaml b/recipes/bioconductor-hgu95aprobe/meta.yaml index 0d469c84c6f9b..6676d8905e9ea 100644 --- a/recipes/bioconductor-hgu95aprobe/meta.yaml +++ b/recipes/bioconductor-hgu95aprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu95aprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 67d94ecdc1889acc19dafd19d26700a2 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG\_U95A\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hgu95a build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu95aprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 67d94ecdc1889acc19dafd19d26700a2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hgu95a' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG\_U95A\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu95av2.db/meta.yaml b/recipes/bioconductor-hgu95av2.db/meta.yaml index 3ff766aa5fb19..473145a248452 100644 --- a/recipes/bioconductor-hgu95av2.db/meta.yaml +++ b/recipes/bioconductor-hgu95av2.db/meta.yaml @@ -1,47 +1,53 @@ {% set version = "3.13.0" %} {% set name = "hgu95av2.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Affymetrix Affymetrix HG U95Av2 Array annotation data (chip hgu95av2) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HG U95Av2 Array annotation data (chip hgu95av2) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0ada3f3c2507992b94d2daa7de8b7fbf build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu95av2.db", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-hgu95av2.db + path: recipes/bioconductor-hgu95av2.db + version: 3.2.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 0ada3f3c2507992b94d2daa7de8b7fbf + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HG U95Av2 Array annotation data (chip hgu95av2)' - description: 'Affymetrix Affymetrix HG U95Av2 Array annotation data (chip hgu95av2) assembled using data from public repositories' -extra: - parent_recipe: - name: bioconductor-hgu95av2.db - path: recipes/bioconductor-hgu95av2.db - version: 3.2.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu95av2/meta.yaml b/recipes/bioconductor-hgu95av2/meta.yaml index 78e1d0a7807fd..5d319c1765cec 100644 --- a/recipes/bioconductor-hgu95av2/meta.yaml +++ b/recipes/bioconductor-hgu95av2/meta.yaml @@ -1,37 +1,37 @@ {% set version = "2.2.0" %} {% set name = "hgu95av2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b92585c0f43e91bd1abd234b9465a6a7 +about: + description: Affymetrix Human Genome U95 Set annotation data (hgu95av2) assembled using data from public data repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: The Artistic License, Version 2.0 + summary: Affymetrix Human Genome U95 Set Annotation Data (hgu95av2) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu95av2", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b92585c0f43e91bd1abd234b9465a6a7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'The Artistic License, Version 2.0' - summary: 'Affymetrix Human Genome U95 Set Annotation Data (hgu95av2)' - description: 'Affymetrix Human Genome U95 Set annotation data (hgu95av2) assembled using data from public data repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu95av2cdf/meta.yaml b/recipes/bioconductor-hgu95av2cdf/meta.yaml index 11a1128c63fc1..821acad35f2d0 100644 --- a/recipes/bioconductor-hgu95av2cdf/meta.yaml +++ b/recipes/bioconductor-hgu95av2cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu95av2cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 026bae2f76433593f75ca6c79bc9a9d0 +about: + description: A package containing an environment representing the HG U95Av2.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hgu95av2cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu95av2cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 026bae2f76433593f75ca6c79bc9a9d0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hgu95av2cdf - description: 'A package containing an environment representing the HG U95Av2.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu95av2probe/meta.yaml b/recipes/bioconductor-hgu95av2probe/meta.yaml index 8eb701c5659f3..a419de5a9973c 100644 --- a/recipes/bioconductor-hgu95av2probe/meta.yaml +++ b/recipes/bioconductor-hgu95av2probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu95av2probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d3efb56f7e7a264b633fac787a5a2b95 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG\_U95Av2\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hgu95av2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu95av2probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d3efb56f7e7a264b633fac787a5a2b95 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hgu95av2' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG\_U95Av2\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu95b.db/meta.yaml b/recipes/bioconductor-hgu95b.db/meta.yaml index ac0f7ed32a448..dbf7996d60396 100644 --- a/recipes/bioconductor-hgu95b.db/meta.yaml +++ b/recipes/bioconductor-hgu95b.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "hgu95b.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 12334c263cfd9f7dc835762b4661edc1 +about: + description: Affymetrix Affymetrix HG U95B Array annotation data (chip hgu95b) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HG U95B Array annotation data (chip hgu95b) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu95b.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 12334c263cfd9f7dc835762b4661edc1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HG U95B Array annotation data (chip hgu95b)' - description: 'Affymetrix Affymetrix HG U95B Array annotation data (chip hgu95b) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu95bcdf/meta.yaml b/recipes/bioconductor-hgu95bcdf/meta.yaml index 32b337096ddfa..161e1d6b1c4f7 100644 --- a/recipes/bioconductor-hgu95bcdf/meta.yaml +++ b/recipes/bioconductor-hgu95bcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu95bcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e6e56b7a107bb2df25b3c25a8191385d +about: + description: A package containing an environment representing the HG U95B.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hgu95bcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu95bcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e6e56b7a107bb2df25b3c25a8191385d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hgu95bcdf - description: 'A package containing an environment representing the HG U95B.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu95bprobe/meta.yaml b/recipes/bioconductor-hgu95bprobe/meta.yaml index c651f98a9e74e..a07d64abbf5a5 100644 --- a/recipes/bioconductor-hgu95bprobe/meta.yaml +++ b/recipes/bioconductor-hgu95bprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu95bprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 60dcb57fd402dc24d53ef9390c893cfc +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U95B\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hgu95b build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu95bprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 60dcb57fd402dc24d53ef9390c893cfc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hgu95b' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U95B\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu95c.db/meta.yaml b/recipes/bioconductor-hgu95c.db/meta.yaml index 5a2400c03379f..23eb55ce1c125 100644 --- a/recipes/bioconductor-hgu95c.db/meta.yaml +++ b/recipes/bioconductor-hgu95c.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "hgu95c.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 680cdfc3e63853ace2ec47caa00ded36 +about: + description: Affymetrix Affymetrix HG U95C Array annotation data (chip hgu95c) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HG U95C Array annotation data (chip hgu95c) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu95c.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 680cdfc3e63853ace2ec47caa00ded36 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HG U95C Array annotation data (chip hgu95c)' - description: 'Affymetrix Affymetrix HG U95C Array annotation data (chip hgu95c) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu95ccdf/meta.yaml b/recipes/bioconductor-hgu95ccdf/meta.yaml index 1ea680ebb03a3..740ea274c6c11 100644 --- a/recipes/bioconductor-hgu95ccdf/meta.yaml +++ b/recipes/bioconductor-hgu95ccdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu95ccdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 976151eac05c320aec7a24397a6b5806 +about: + description: A package containing an environment representing the HG U95C.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hgu95ccdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu95ccdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 976151eac05c320aec7a24397a6b5806 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hgu95ccdf - description: 'A package containing an environment representing the HG U95C.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu95cprobe/meta.yaml b/recipes/bioconductor-hgu95cprobe/meta.yaml index a111dd5f829b2..ea4514b9a162d 100644 --- a/recipes/bioconductor-hgu95cprobe/meta.yaml +++ b/recipes/bioconductor-hgu95cprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu95cprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3fe935a52c70105dc7a214174c946455 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U95C\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hgu95c build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu95cprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3fe935a52c70105dc7a214174c946455 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hgu95c' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U95C\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu95d.db/meta.yaml b/recipes/bioconductor-hgu95d.db/meta.yaml index 50de9e491ea14..9f74124d3a7d6 100644 --- a/recipes/bioconductor-hgu95d.db/meta.yaml +++ b/recipes/bioconductor-hgu95d.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "hgu95d.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 90ecf383640f6ab7314fa1babcdd5a0b +about: + description: Affymetrix Affymetrix HG U95D Array annotation data (chip hgu95d) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HG U95D Array annotation data (chip hgu95d) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu95d.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 90ecf383640f6ab7314fa1babcdd5a0b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HG U95D Array annotation data (chip hgu95d)' - description: 'Affymetrix Affymetrix HG U95D Array annotation data (chip hgu95d) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu95dcdf/meta.yaml b/recipes/bioconductor-hgu95dcdf/meta.yaml index 483baf4b30cfe..694d8071816c2 100644 --- a/recipes/bioconductor-hgu95dcdf/meta.yaml +++ b/recipes/bioconductor-hgu95dcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu95dcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 36e11ff001b1bec3f34ba7c93132ad6f +about: + description: A package containing an environment representing the HG U95D.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hgu95dcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu95dcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 36e11ff001b1bec3f34ba7c93132ad6f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hgu95dcdf - description: 'A package containing an environment representing the HG U95D.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu95dprobe/meta.yaml b/recipes/bioconductor-hgu95dprobe/meta.yaml index 030c64728d67d..d5f5323796825 100644 --- a/recipes/bioconductor-hgu95dprobe/meta.yaml +++ b/recipes/bioconductor-hgu95dprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu95dprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 165ce5029f49fc515b9ee0e6a6a29cb5 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U95D\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hgu95d build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu95dprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 165ce5029f49fc515b9ee0e6a6a29cb5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hgu95d' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U95D\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu95e.db/meta.yaml b/recipes/bioconductor-hgu95e.db/meta.yaml index 2a6007514b8b7..8f1788f02b488 100644 --- a/recipes/bioconductor-hgu95e.db/meta.yaml +++ b/recipes/bioconductor-hgu95e.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "hgu95e.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 116bd146279d19d50a7233bc61c22104 +about: + description: Affymetrix Affymetrix HG U95E Array annotation data (chip hgu95e) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HG U95E Array annotation data (chip hgu95e) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu95e.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 116bd146279d19d50a7233bc61c22104 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HG U95E Array annotation data (chip hgu95e)' - description: 'Affymetrix Affymetrix HG U95E Array annotation data (chip hgu95e) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu95ecdf/meta.yaml b/recipes/bioconductor-hgu95ecdf/meta.yaml index 909814914ac7e..414c6dcedb277 100644 --- a/recipes/bioconductor-hgu95ecdf/meta.yaml +++ b/recipes/bioconductor-hgu95ecdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu95ecdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fa27cfff62a38fc51640d797bd628105 +about: + description: A package containing an environment representing the HG U95E.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hgu95ecdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu95ecdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fa27cfff62a38fc51640d797bd628105 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hgu95ecdf - description: 'A package containing an environment representing the HG U95E.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgu95eprobe/meta.yaml b/recipes/bioconductor-hgu95eprobe/meta.yaml index e25fb81f9803c..3ba222bbdc712 100644 --- a/recipes/bioconductor-hgu95eprobe/meta.yaml +++ b/recipes/bioconductor-hgu95eprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hgu95eprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9e5407ab80c5bbb4065484be0b9c6191 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U95E\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hgu95e build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgu95eprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9e5407ab80c5bbb4065484be0b9c6191 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hgu95e' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U95E\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hguatlas13k.db/meta.yaml b/recipes/bioconductor-hguatlas13k.db/meta.yaml index 631974fa66149..10204c75c1102 100644 --- a/recipes/bioconductor-hguatlas13k.db/meta.yaml +++ b/recipes/bioconductor-hguatlas13k.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "hguatlas13k.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ab9ffe1a1de44c0f938129f193e7fb63 +about: + description: Clontech BD Atlas Long Oligos Human 13K annotation data (chip hguatlas13k) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Clontech BD Atlas Long Oligos Human 13K annotation data (chip hguatlas13k) build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hguatlas13k.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ab9ffe1a1de44c0f938129f193e7fb63 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Clontech BD Atlas Long Oligos Human 13K annotation data (chip hguatlas13k)' - description: 'Clontech BD Atlas Long Oligos Human 13K annotation data (chip hguatlas13k) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgubeta7.db/meta.yaml b/recipes/bioconductor-hgubeta7.db/meta.yaml index f952f59819473..cacb362ddf4aa 100644 --- a/recipes/bioconductor-hgubeta7.db/meta.yaml +++ b/recipes/bioconductor-hgubeta7.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "hgubeta7.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1b8b065f95d2089985f59f22dcabc824 +about: + description: Unknown annotation data (chip hgubeta7) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Unknown annotation data (chip hgubeta7) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgubeta7.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1b8b065f95d2089985f59f22dcabc824 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Unknown annotation data (chip hgubeta7)' - description: 'Unknown annotation data (chip hgubeta7) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgudkfz31.db/meta.yaml b/recipes/bioconductor-hgudkfz31.db/meta.yaml index 797b9e34dc787..b74589e4213b4 100644 --- a/recipes/bioconductor-hgudkfz31.db/meta.yaml +++ b/recipes/bioconductor-hgudkfz31.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "hguDKFZ31.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fa3ba493cebdac4253dea8fe5d58452b +about: + description: Unknown annotation data (chip hguDKFZ31) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Unknown annotation data (chip hguDKFZ31) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgudkfz31.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fa3ba493cebdac4253dea8fe5d58452b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Unknown annotation data (chip hguDKFZ31)' - description: 'Unknown annotation data (chip hguDKFZ31) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgug4100a.db/meta.yaml b/recipes/bioconductor-hgug4100a.db/meta.yaml index 25b4d28578ec5..dde99f7911e5e 100644 --- a/recipes/bioconductor-hgug4100a.db/meta.yaml +++ b/recipes/bioconductor-hgug4100a.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "hgug4100a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b7856928278a77d71f963410ea4f2376 +about: + description: Agilent Human 1 cDNA Microarray Kit annotation data (chip hgug4100a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Agilent Human 1 cDNA Microarray Kit annotation data (chip hgug4100a) build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgug4100a.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b7856928278a77d71f963410ea4f2376 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Agilent Human 1 cDNA Microarray Kit annotation data (chip hgug4100a)' - description: 'Agilent Human 1 cDNA Microarray Kit annotation data (chip hgug4100a) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgug4101a.db/meta.yaml b/recipes/bioconductor-hgug4101a.db/meta.yaml index bbddbf83684d0..f6f016136f616 100644 --- a/recipes/bioconductor-hgug4101a.db/meta.yaml +++ b/recipes/bioconductor-hgug4101a.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "hgug4101a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e4731217efbffd05d3ee7eec68ce0aa0 +about: + description: Agilent Human 2 cDNA Microarry Kit annotation data (chip hgug4101a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Agilent Human 2 cDNA Microarry Kit annotation data (chip hgug4101a) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgug4101a.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e4731217efbffd05d3ee7eec68ce0aa0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Agilent Human 2 cDNA Microarry Kit annotation data (chip hgug4101a)' - description: 'Agilent Human 2 cDNA Microarry Kit annotation data (chip hgug4101a) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgug4110b.db/meta.yaml b/recipes/bioconductor-hgug4110b.db/meta.yaml index 288b0336f7a3f..04d7ce4977e18 100644 --- a/recipes/bioconductor-hgug4110b.db/meta.yaml +++ b/recipes/bioconductor-hgug4110b.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "hgug4110b.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a9edcdbc121f22d4dec335a64598ff0e +about: + description: Agilent Human 1A (V2) annotation data (chip hgug4110b) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Agilent Human 1A (V2) annotation data (chip hgug4110b) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgug4110b.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a9edcdbc121f22d4dec335a64598ff0e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Agilent Human 1A (V2) annotation data (chip hgug4110b)' - description: 'Agilent Human 1A (V2) annotation data (chip hgug4110b) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgug4111a.db/meta.yaml b/recipes/bioconductor-hgug4111a.db/meta.yaml index 23c816d0468e7..91f06df4b067b 100644 --- a/recipes/bioconductor-hgug4111a.db/meta.yaml +++ b/recipes/bioconductor-hgug4111a.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "hgug4111a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a5f2c3b463915fa1ab0ca21e6b0f5840 +about: + description: Agilent Human 1B annotation data (chip hgug4111a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Agilent Human 1B annotation data (chip hgug4111a) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgug4111a.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a5f2c3b463915fa1ab0ca21e6b0f5840 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Agilent Human 1B annotation data (chip hgug4111a)' - description: 'Agilent Human 1B annotation data (chip hgug4111a) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgug4112a.db/meta.yaml b/recipes/bioconductor-hgug4112a.db/meta.yaml index 1d650ea7689f3..38d222a49d0db 100644 --- a/recipes/bioconductor-hgug4112a.db/meta.yaml +++ b/recipes/bioconductor-hgug4112a.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "hgug4112a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 67ecf8c887e2ebe1941cc51d0f5fb468 +about: + description: Agilent "Human Genome, Whole" annotation data (chip hgug4112a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Agilent "Human Genome, Whole" annotation data (chip hgug4112a) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgug4112a.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 67ecf8c887e2ebe1941cc51d0f5fb468 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Agilent "Human Genome, Whole" annotation data (chip hgug4112a)' - description: 'Agilent "Human Genome, Whole" annotation data (chip hgug4112a) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hgug4845a.db/meta.yaml b/recipes/bioconductor-hgug4845a.db/meta.yaml index 56bdebf753da7..6f4fec5ba506e 100644 --- a/recipes/bioconductor-hgug4845a.db/meta.yaml +++ b/recipes/bioconductor-hgug4845a.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "0.0.3" %} {% set name = "hgug4845a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 46133d7bcb6d8c24c026304e8ddd150d +about: + description: agilent AMADID 026652 annotation data (chip hgug4845a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: agilent AMADID 026652 annotation data (chip hgug4845a) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hgug4845a.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 46133d7bcb6d8c24c026304e8ddd150d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'agilent AMADID 026652 annotation data (chip hgug4845a)' - description: 'agilent AMADID 026652 annotation data (chip hgug4845a) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hguqiagenv3.db/meta.yaml b/recipes/bioconductor-hguqiagenv3.db/meta.yaml index a89094655e843..572a3b53e120e 100644 --- a/recipes/bioconductor-hguqiagenv3.db/meta.yaml +++ b/recipes/bioconductor-hguqiagenv3.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "hguqiagenv3.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 91ebb82e773ff799befdb8921b38e90e +about: + description: Qiagen Qiagen V3.0 oligo set annotation data (chip hguqiagenv3) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Qiagen Qiagen V3.0 oligo set annotation data (chip hguqiagenv3) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hguqiagenv3.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 91ebb82e773ff799befdb8921b38e90e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Qiagen Qiagen V3.0 oligo set annotation data (chip hguqiagenv3)' - description: 'Qiagen Qiagen V3.0 oligo set annotation data (chip hguqiagenv3) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hi16cod.db/meta.yaml b/recipes/bioconductor-hi16cod.db/meta.yaml index 6f2d6f8fea470..faed215504367 100644 --- a/recipes/bioconductor-hi16cod.db/meta.yaml +++ b/recipes/bioconductor-hi16cod.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.4.0" %} {% set name = "hi16cod.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: abdc77937e8d37fa5468691376ceb6a5 +about: + description: Codelink Human Inflammation 16 Bioarray annotation data (chip hi16cod) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Codelink Human Inflammation 16 Bioarray annotation data (chip hi16cod) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hi16cod.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: abdc77937e8d37fa5468691376ceb6a5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Codelink Human Inflammation 16 Bioarray annotation data (chip hi16cod)' - description: 'Codelink Human Inflammation 16 Bioarray annotation data (chip hi16cod) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hiannotator/meta.yaml b/recipes/bioconductor-hiannotator/meta.yaml index 2e398493417b3..a9bf7f012375c 100644 --- a/recipes/bioconductor-hiannotator/meta.yaml +++ b/recipes/bioconductor-hiannotator/meta.yaml @@ -1,30 +1,41 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "hiAnnotator" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'hiAnnotator contains set of functions which allow users to annotate a GRanges object with custom set of annotations. The basic philosophy of this package is to take two GRanges objects (query & subject) with common set of seqnames (i.e. chromosomes) and return associated annotation per seqnames and rows from the query matching seqnames and rows from the subject (i.e. genes or cpg islands). The package comes with three types of annotation functions which calculates if a position from query is: within a feature, near a feature, or count features in defined window sizes. Moreover, each function is equipped with parallel backend to utilize the foreach package. In addition, the package is equipped with wrapper functions, which finds appropriate columns needed to make a GRanges object from a common data frame.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Functions for annotating GRanges objects -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67e0fbd27bb6f634ccb9912642a2aeb6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hiannotator", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:hiannotator + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-hiannotator + path: recipes/bioconductor-hiannotator + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, doParallel, testthat, BiocGenerics, markdown requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-dplyr - r-foreach @@ -32,30 +43,25 @@ requirements: - r-iterators - r-scales run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-dplyr - r-foreach - r-ggplot2 - r-iterators - r-scales + +source: + md5: c2e1132d926b5ec2006fe37609b1ca16 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Functions for annotating GRanges objects' - description: 'hiAnnotator contains set of functions which allow users to annotate a GRanges object with custom set of annotations. The basic philosophy of this package is to take two GRanges objects (query & subject) with common set of seqnames (i.e. chromosomes) and return associated annotation per seqnames and rows from the query matching seqnames and rows from the subject (i.e. genes or cpg islands). The package comes with three types of annotation functions which calculates if a position from query is: within a feature, near a feature, or count features in defined window sizes. Moreover, each function is equipped with parallel backend to utilize the foreach package. In addition, the package is equipped with wrapper functions, which finds appropriate columns needed to make a GRanges object from a common data frame.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:hiannotator - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-hiannotator - path: recipes/bioconductor-hiannotator - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hibag/meta.yaml b/recipes/bioconductor-hibag/meta.yaml index 1c32235779499..52f55f1123c9f 100644 --- a/recipes/bioconductor-hibag/meta.yaml +++ b/recipes/bioconductor-hibag/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "HIBAG" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Imputes HLA classical alleles using GWAS SNP data, and it relies on a training set of HLA and SNP genotypes. HIBAG can be used by researchers with published parameter estimates instead of requiring access to large training sample datasets. It combines the concepts of attribute bagging, an ensemble classifier method, with haplotype inference for SNPs and HLA types. Attribute bagging is a technique which improves the accuracy and stability of classifier ensembles using bootstrap aggregating and random variable selection. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: HLA Genotype Imputation with Attribute Bagging -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80772de8231b22269fb6ee5401af8292 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hibag", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:hibag + parent_recipe: + name: bioconductor-hibag + path: recipes/bioconductor-hibag + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray, knitr, markdown, rmarkdown, Rsamtools # SystemRequirements: C++11, GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - - 'r-rcppparallel >=5.0.0' + - r-rcppparallel >=5.0.0 - libblas - liblapack run: - r-base - - 'r-rcppparallel >=5.0.0' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcppparallel >=5.0.0 + +source: + md5: aa87ab9f1d702618bef7f7fc52ea180b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'HLA Genotype Imputation with Attribute Bagging' - description: 'Imputes HLA classical alleles using GWAS SNP data, and it relies on a training set of HLA and SNP genotypes. HIBAG can be used by researchers with published parameter estimates instead of requiring access to large training sample datasets. It combines the concepts of attribute bagging, an ensemble classifier method, with haplotype inference for SNPs and HLA types. Attribute bagging is a technique which improves the accuracy and stability of classifier ensembles using bootstrap aggregating and random variable selection.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:hibag - parent_recipe: - name: bioconductor-hibag - path: recipes/bioconductor-hibag - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hibed/meta.yaml b/recipes/bioconductor-hibed/meta.yaml index 428afabbff047..36353e9e20128 100644 --- a/recipes/bioconductor-hibed/meta.yaml +++ b/recipes/bioconductor-hibed/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "HiBED" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Hierarchical deconvolution for extensive cell type resolution in the human brain using DNA methylation. The HiBED deconvolution estimates proportions up to 7 cell types (GABAergic neurons, glutamatergic neurons, astrocytes, microglial cells, oligodendrocytes, endothelial cells, and stromal cells) in bulk brain tissues. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: HiBED -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 282aec6967013cdaa790ff191e4139b4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hibed", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, IlluminaHumanMethylation450kmanifest requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-flowsorted.blood.epic >=2.6.0,<2.7.0' - - 'bioconductor-flowsorted.dlpfc.450k >=1.38.0,<1.39.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-flowsorted.blood.epic >=2.10.0,<2.11.0 + - bioconductor-flowsorted.dlpfc.450k >=1.42.0,<1.43.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-tibble run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-flowsorted.blood.epic >=2.6.0,<2.7.0' - - 'bioconductor-flowsorted.dlpfc.450k >=1.38.0,<1.39.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-flowsorted.blood.epic >=2.10.0,<2.11.0 + - bioconductor-flowsorted.dlpfc.450k >=1.42.0,<1.43.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-tibble - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 2858803aaed3e0110711dfb4246789bc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: HiBED - description: 'Hierarchical deconvolution for extensive cell type resolution in the human brain using DNA methylation. The HiBED deconvolution estimates proportions up to 7 cell types (GABAergic neurons, glutamatergic neurons, astrocytes, microglial cells, oligodendrocytes, endothelial cells, and stromal cells) in bulk brain tissues.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hibed/post-link.sh b/recipes/bioconductor-hibed/post-link.sh index f600caeca45ee..bafcb6220b278 100644 --- a/recipes/bioconductor-hibed/post-link.sh +++ b/recipes/bioconductor-hibed/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hibed-1.0.0" +installBiocDataPackage.sh "hibed-1.4.0" diff --git a/recipes/bioconductor-hicaggr/build.sh b/recipes/bioconductor-hicaggr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hicaggr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hicaggr/meta.yaml b/recipes/bioconductor-hicaggr/meta.yaml new file mode 100644 index 0000000000000..e539f70c1ac1f --- /dev/null +++ b/recipes/bioconductor-hicaggr/meta.yaml @@ -0,0 +1,90 @@ +{% set version = "1.2.0" %} +{% set name = "HicAggR" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a set of functions useful in the analysis of 3D genomic interactions. It includes the import of standard HiC data formats into R and HiC normalisation procedures. The main objective of this package is to improve the visualization and quantification of the analysis of HiC contacts through aggregation. The package allows to import 1D genomics data, such as peaks from ATACSeq, ChIPSeq, to create potential couples between features of interest under user-defined parameters such as distance between pairs of features of interest. It allows then the extraction of contact values from the HiC data for these couples and to perform Aggregated Peak Analysis (APA) for visualization, but also to compare normalized contact values between conditions. Overall the package allows to integrate 1D genomics data with 3D genomics data, providing an easy access to HiC contact values. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Set of 3D genomic interaction analysis tools + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hicaggr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: covr, tools, kableExtra (>= 1.3.4), knitr (>= 1.45), rmarkdown, testthat (>= 3.0.0), BiocFileCache (>= 2.6.1) +requirements: + + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-checkmate + - r-data.table + - r-dplyr + - r-ggplot2 + - r-gridextra + - r-matrix + - r-purrr + - r-reshape + - r-rlang + - r-strawr + - r-stringr + - r-tibble + - r-tidyr + - r-withr + + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-checkmate + - r-data.table + - r-dplyr + - r-ggplot2 + - r-gridextra + - r-matrix + - r-purrr + - r-reshape + - r-rlang + - r-strawr + - r-stringr + - r-tibble + - r-tidyr + - r-withr + +source: + md5: 0f8ad2187b6596e9b8cc747ed3dbddb6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-hicbricks/meta.yaml b/recipes/bioconductor-hicbricks/meta.yaml index 929d6db889cb6..47db63820ffd5 100644 --- a/recipes/bioconductor-hicbricks/meta.yaml +++ b/recipes/bioconductor-hicbricks/meta.yaml @@ -1,33 +1,36 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "HiCBricks" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: HiCBricks is a library designed for handling large high-resolution Hi-C datasets. Over the years, the Hi-C field has experienced a rapid increase in the size and complexity of datasets. HiCBricks is meant to overcome the challenges related to the analysis of such large datasets within the R environment. HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides an R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms. HiCBricks already incorporates example algorithms for calling domain boundaries and functions for high quality data visualization. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Framework for Storing and Accessing Hi-C Data Through HDF Files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c92df374e0660e328cbf53f181afd61 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hicbricks", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: + host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-curl - r-data.table @@ -43,13 +46,14 @@ requirements: - r-stringr - r-tibble - r-viridis + run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-curl - r-data.table @@ -65,13 +69,16 @@ requirements: - r-stringr - r-tibble - r-viridis + +source: + md5: 1b5c3f39d3a0b30bf78439e1cdc26eb6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Framework for Storing and Accessing Hi-C Data Through HDF Files' - description: 'HiCBricks is a library designed for handling large high-resolution Hi-C datasets. Over the years, the Hi-C field has experienced a rapid increase in the size and complexity of datasets. HiCBricks is meant to overcome the challenges related to the analysis of such large datasets within the R environment. HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides an R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms. HiCBricks already incorporates example algorithms for calling domain boundaries and functions for high quality data visualization.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hiccompare/meta.yaml b/recipes/bioconductor-hiccompare/meta.yaml index 2ad1ed7f62ae8..a9d26550ca1aa 100644 --- a/recipes/bioconductor-hiccompare/meta.yaml +++ b/recipes/bioconductor-hiccompare/meta.yaml @@ -1,33 +1,44 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "HiCcompare" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCcompare is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states.`HiCcompare` differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, `HiCcompare` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCcompare` also provides a simple yet robust method for detecting differences between Hi-C datasets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 'HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 081a94597115ed9f99e23930935648dd build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hiccompare", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:HiCcompare + - doi:10.1186/s12859-018-2288-x + parent_recipe: + name: bioconductor-hiccompare + path: recipes/bioconductor-hiccompare + version: 1.2.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, multiHiCcompare requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-dplyr @@ -38,12 +49,12 @@ requirements: - r-mgcv - r-pheatmap run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-dplyr @@ -53,21 +64,16 @@ requirements: - r-kernsmooth - r-mgcv - r-pheatmap + +source: + md5: e9eaa0683ae4dc4c726fbb16e343d15d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets' - description: 'HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCcompare is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states.`HiCcompare` differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, `HiCcompare` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCcompare` also provides a simple yet robust method for detecting differences between Hi-C datasets.' - license_file: LICENSE -extra: - identifiers: - - biotools:HiCcompare - - doi:10.1186/s12859-018-2288-x - parent_recipe: - name: bioconductor-hiccompare - path: recipes/bioconductor-hiccompare - version: 1.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hicdatahumanimr90/meta.yaml b/recipes/bioconductor-hicdatahumanimr90/meta.yaml index f9a4a366087d4..9b6ab5ae0476c 100644 --- a/recipes/bioconductor-hicdatahumanimr90/meta.yaml +++ b/recipes/bioconductor-hicdatahumanimr90/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "HiCDataHumanIMR90" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02854f68384130b0bcd3d0f84d94b856 +about: + description: The HiC data from Human Fibroblast IMR90 cell line (HindIII restriction) was retrieved from the GEO website, accession number GSE35156 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35156). The raw reads were processed as explained in Dixon et al. (Nature 2012). + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Human IMR90 Fibroblast HiC data from Dixon et al. 2012 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hicdatahumanimr90", max_pin="x.x") }}' - noarch: generic -# Suggests: HiTC +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: HiTC, BiocStyle requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6fa599b5b8d54523c6bb6dcd12d135a5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Human IMR90 Fibroblast HiC data from Dixon et al. 2012' - description: 'The HiC data from Human Fibroblast IMR90 cell line (HindIII restriction) was retrieved from the GEO website, accession number GSE35156 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35156). The raw reads were processed as explained in Dixon et al. (Nature 2012).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hicdatahumanimr90/post-link.sh b/recipes/bioconductor-hicdatahumanimr90/post-link.sh index 5079a3784185d..81aa7b5701f6a 100644 --- a/recipes/bioconductor-hicdatahumanimr90/post-link.sh +++ b/recipes/bioconductor-hicdatahumanimr90/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hicdatahumanimr90-1.22.0" +installBiocDataPackage.sh "hicdatahumanimr90-1.26.0" diff --git a/recipes/bioconductor-hicdatalymphoblast/meta.yaml b/recipes/bioconductor-hicdatalymphoblast/meta.yaml index 36a2e897eb980..9f51892467e2c 100644 --- a/recipes/bioconductor-hicdatalymphoblast/meta.yaml +++ b/recipes/bioconductor-hicdatalymphoblast/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "HiCDataLymphoblast" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4e51d696b30a37414375e6987c7ab59c +about: + description: The HiC data from human lymphoblastoid cell line (HindIII restriction) was retrieved from the sequence read archive and two ends of the paired reads were aligned separately with bowtie. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Human lymphoblastoid HiC data from Lieberman-Aiden et al. 2009 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hicdatalymphoblast", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: ShortRead requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 22efbfbd94821942a7e1c9e0e9df0db6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Human lymphoblastoid HiC data from Lieberman-Aiden et al. 2009' - description: 'The HiC data from human lymphoblastoid cell line (HindIII restriction) was retrieved from the sequence read archive and two ends of the paired reads were aligned separately with bowtie.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hicdatalymphoblast/post-link.sh b/recipes/bioconductor-hicdatalymphoblast/post-link.sh index acbb04bef68ba..ae6b49a4d816d 100644 --- a/recipes/bioconductor-hicdatalymphoblast/post-link.sh +++ b/recipes/bioconductor-hicdatalymphoblast/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hicdatalymphoblast-1.38.0" +installBiocDataPackage.sh "hicdatalymphoblast-1.42.0" diff --git a/recipes/bioconductor-hicdcplus/meta.yaml b/recipes/bioconductor-hicdcplus/meta.yaml index e014d6b12ff12..cd21eb1a95ac6 100644 --- a/recipes/bioconductor-hicdcplus/meta.yaml +++ b/recipes/bioconductor-hicdcplus/meta.yaml @@ -1,36 +1,44 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "HiCDCPlus" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. The HiC-DC+ (Hi-C/HiChIP direct caller plus) package enables principled statistical analysis of Hi-C and HiChIP data sets – including calling significant interactions within a single experiment and performing differential analysis between conditions given replicate experiments – to facilitate global integrative studies. HiC-DC+ estimates significant interactions in a Hi-C or HiChIP experiment directly from the raw contact matrix for each chromosome up to a specified genomic distance, binned by uniform genomic intervals or restriction enzyme fragments, by training a background model to account for random polymer ligation and systematic sources of read count variation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Hi-C Direct Caller Plus -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d129ae6d6c11f6f92e52399c46754b1f build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hicdcplus", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, RUnit, BiocGenerics, knitr, rmarkdown, HiTC, DESeq2, Matrix, BiocFileCache, rappdirs # SystemRequirements: JRE 8+ requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicinteractions >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-bbmle - r-data.table @@ -44,16 +52,18 @@ requirements: - r-tidyr - libblas - liblapack + - zlib + run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicinteractions >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-bbmle - r-data.table @@ -65,17 +75,16 @@ requirements: - r-rlang - r-tibble - r-tidyr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: e874749d4720ab9a0963a98ab1fdcc19 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Hi-C Direct Caller Plus' - description: 'Systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. The HiC-DC+ (Hi-C/HiChIP direct caller plus) package enables principled statistical analysis of Hi-C and HiChIP data sets – including calling significant interactions within a single experiment and performing differential analysis between conditions given replicate experiments – to facilitate global integrative studies. HiC-DC+ estimates significant interactions in a Hi-C or HiChIP experiment directly from the raw contact matrix for each chromosome up to a specified genomic distance, binned by uniform genomic intervals or restriction enzyme fragments, by training a background model to account for random polymer ligation and systematic sources of read count variation.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hicdoc/meta.yaml b/recipes/bioconductor-hicdoc/meta.yaml index 4fc805acafb41..a339fe899002b 100644 --- a/recipes/bioconductor-hicdoc/meta.yaml +++ b/recipes/bioconductor-hicdoc/meta.yaml @@ -1,36 +1,44 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "HiCDOC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'HiCDOC normalizes intrachromosomal Hi-C matrices, uses unsupervised learning to predict A/B compartments from multiple replicates, and detects significant compartment changes between experiment conditions. It provides a collection of functions assembled into a pipeline to filter and normalize the data, predict the compartments and visualize the results. It accepts several type of data: tabular `.tsv` files, Cooler `.cool` or `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: A/B compartment detection and differential analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 334df180a7e5e2851bbf6724e8537ffd build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hicdoc", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, BiocStyle, BiocManager, rhdf5 # SystemRequirements: C++11 requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-multihiccompare >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-multihiccompare >=1.24.0,<1.25.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-cowplot - r-data.table @@ -38,19 +46,21 @@ requirements: - r-gridextra - r-gtools - r-pbapply - - 'r-rcpp >=0.12.8' + - r-rcpp >=0.12.8 - libblas - liblapack + - zlib + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-multihiccompare >=1.20.0,<1.21.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-multihiccompare >=1.24.0,<1.25.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-cowplot - r-data.table @@ -58,18 +68,17 @@ requirements: - r-gridextra - r-gtools - r-pbapply - - 'r-rcpp >=0.12.8' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=0.12.8 + +source: + md5: d6f9e9565f7fd00b7cc8bc1689c2111d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'A/B compartment detection and differential analysis' - description: 'HiCDOC normalizes intrachromosomal Hi-C matrices, uses unsupervised learning to predict A/B compartments from multiple replicates, and detects significant compartment changes between experiment conditions. It provides a collection of functions assembled into a pipeline to filter and normalize the data, predict the compartments and visualize the results. It accepts several type of data: tabular `.tsv` files, Cooler `.cool` or `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hicexperiment/meta.yaml b/recipes/bioconductor-hicexperiment/meta.yaml index e0267b602fd7d..c98943319d526 100644 --- a/recipes/bioconductor-hicexperiment/meta.yaml +++ b/recipes/bioconductor-hicexperiment/meta.yaml @@ -1,63 +1,68 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "HiCExperiment" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: R generic interface to Hi-C contact matrices in `.(m)cool`, `.hic` or HiC-Pro derived formats, as well as other Hi-C processed file formats. Contact matrices can be partially parsed using a random access method, allowing a memory-efficient representation of Hi-C data in R. The `HiCExperiment` class stores the Hi-C contacts parsed from local contact matrix files. `HiCExperiment` instances can be further investigated in R using the `HiContacts` analysis package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Bioconductor class for interacting with Hi-C files in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98efc0440886cc84faef975a12f290a0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hicexperiment", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: HiContacts, HiContactsData, BiocFileCache, rtracklayer, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-matrix - r-strawr - r-vroom run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-matrix - r-strawr - r-vroom + +source: + md5: 78ff18f540ccf6d3459097f2575c3ef0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Bioconductor class for interacting with Hi-C files in R' - description: 'R generic interface to Hi-C contact matrices in `.(m)cool`, `.hic` or HiC-Pro derived formats, as well as other Hi-C processed file formats. Contact matrices can be partially parsed using a random access method, allowing a memory-efficient representation of Hi-C data in R. The `HiCExperiment` class stores the Hi-C contacts parsed from local contact matrix files. `HiCExperiment` instances can be further investigated in R using the `HiContacts` analysis package.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hicontacts/meta.yaml b/recipes/bioconductor-hicontacts/meta.yaml index 29ba194cc6150..cc5f30aab7b20 100644 --- a/recipes/bioconductor-hicontacts/meta.yaml +++ b/recipes/bioconductor-hicontacts/meta.yaml @@ -1,37 +1,40 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "HiContacts" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Analysing cool files in R with HiContacts -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f7f7341e5b4cbfcd13b04fadd9c472c7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hicontacts", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: HiContactsData, rtracklayer, GenomicFeatures, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra, patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hicexperiment >=1.6.0,<1.7.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -43,17 +46,18 @@ requirements: - r-stringr - r-tibble - r-tidyr + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hicexperiment >=1.6.0,<1.7.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -65,13 +69,16 @@ requirements: - r-stringr - r-tibble - r-tidyr + +source: + md5: 04024808b535cef83529e36f47032b54 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Analysing cool files in R with HiContacts' - description: 'HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hicontactsdata/meta.yaml b/recipes/bioconductor-hicontactsdata/meta.yaml index 02887a5d7f1f6..9b2c0ec21ea16 100644 --- a/recipes/bioconductor-hicontactsdata/meta.yaml +++ b/recipes/bioconductor-hicontactsdata/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "HiContactsData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bcd518f48342168f7a814a442cf9564c +about: + description: Provides a collection of Hi-C files (pairs, (m)cool and fastq). These datasets can be read into R and further investigated and visualized with the HiContacts package. Data includes yeast Hi-C data generated by the Koszul lab from the Pasteur Institute. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: HiContacts companion data package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hicontactsdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat, methods, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0798e7ca7fd4015c2885161ce8db285a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'HiContacts companion data package' - description: 'Provides a collection of Hi-C files (pairs, (m)cool and fastq). These datasets can be read into R and further investigated and visualized with the HiContacts package. Data includes yeast Hi-C data generated by the Koszul lab from the Pasteur Institute.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hicontactsdata/post-link.sh b/recipes/bioconductor-hicontactsdata/post-link.sh index 7b88fae0e188f..00c23740bd345 100644 --- a/recipes/bioconductor-hicontactsdata/post-link.sh +++ b/recipes/bioconductor-hicontactsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hicontactsdata-1.4.0" +installBiocDataPackage.sh "hicontactsdata-1.8.0" diff --git a/recipes/bioconductor-hicool/meta.yaml b/recipes/bioconductor-hicool/meta.yaml index e83c1ddf394de..a4946863aac1a 100644 --- a/recipes/bioconductor-hicool/meta.yaml +++ b/recipes/bioconductor-hicool/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "HiCool" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: HiCool provides an R interface to process and normalize Hi-C paired-end fastq reads into .(m)cool files. .(m)cool is a compact, indexed HDF5 file format specifically tailored for efficiently storing HiC-based data. On top of processing fastq reads, HiCool provides a convenient reporting function to generate shareable reports summarizing Hi-C experiments and including quality controls. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: HiCool -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 04aa2ef16336d5c43fc0a02291ba7887 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hicool", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: HiContacts, HiContactsData, AnnotationHub, BiocFileCache, BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hicexperiment >=1.6.0,<1.7.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-plotly @@ -39,13 +41,13 @@ requirements: - r-stringr - r-vroom run: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hicexperiment >=1.2.0,<1.3.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hicexperiment >=1.6.0,<1.7.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-plotly @@ -55,13 +57,16 @@ requirements: - r-sessioninfo - r-stringr - r-vroom + +source: + md5: e17b49313cd3d6d77cfb5c858a4e90fb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: HiCool - description: 'HiCool provides an R interface to process and normalize Hi-C paired-end fastq reads into .(m)cool files. .(m)cool is a compact, indexed HDF5 file format specifically tailored for efficiently storing HiC-based data. On top of processing fastq reads, HiCool provides a convenient reporting function to generate shareable reports summarizing Hi-C experiments and including quality controls.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hicvenndiagram/meta.yaml b/recipes/bioconductor-hicvenndiagram/meta.yaml index 1af9811467c2e..60b8dea9236f6 100644 --- a/recipes/bioconductor-hicvenndiagram/meta.yaml +++ b/recipes/bioconductor-hicvenndiagram/meta.yaml @@ -1,30 +1,35 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "hicVennDiagram" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package to generate high-resolution Venn and Upset plots for genomic interaction data from HiC, ChIA-PET, HiChIP, PLAC-Seq, Hi-TrAC, HiCAR and etc. The package generates plots specifically crafted to eliminate the deceptive visual representation caused by the counts method. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Venn Diagram for genomic interaction data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11577b64cc67b69e4b9d712a76cd3310 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hicvenndiagram", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, testthat, GenomicRanges, ChIPpeakAnno, grid + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, testthat, ChIPpeakAnno, grid, TxDb.Hsapiens.UCSC.hg38.knownGene requirements: host: - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-complexupset - r-eulerr @@ -33,9 +38,12 @@ requirements: - r-reshape2 - r-svglite run: - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-complexupset - r-eulerr @@ -43,13 +51,16 @@ requirements: - r-htmlwidgets - r-reshape2 - r-svglite + +source: + md5: 0a2b9d864d34d269d6dd47b00ac6e46a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Venn Diagram for genomic interaction data' - description: 'A package to generate high-resolution Venn and Upset plots for genomic interaction data from HiC, ChIA-PET, HiChIP, PLAC-Seq, Hi-TrAC, HiCAR and etc. The package generates plots specifically crafted to eliminate the deceptive visual representation caused by the counts method.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hiergwas/meta.yaml b/recipes/bioconductor-hiergwas/meta.yaml index 917a0f7876b4a..c678bec654627 100644 --- a/recipes/bioconductor-hiergwas/meta.yaml +++ b/recipes/bioconductor-hiergwas/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "hierGWAS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9f15cfa27c8d57b818fc7913d8a9093b +about: + description: Testing individual SNPs, as well as arbitrarily large groups of SNPs in GWA studies, using a joint model of all SNPs. The method controls the FWER, and provides an automatic, data-driven refinement of the SNP clusters to smaller groups or single markers. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Asessing statistical significance in predictive GWA studies build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hiergwas", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocGenerics, RUnit, MASS requirements: host: @@ -31,13 +30,14 @@ requirements: - r-fastcluster - r-fmsb - r-glmnet +source: + md5: bd862a09a6e77c3694ad2a58210610e7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Asessing statistical significance in predictive GWA studies' - description: 'Testing individual SNPs, as well as arbitrarily large groups of SNPs in GWA studies, using a joint model of all SNPs. The method controls the FWER, and provides an automatic, data-driven refinement of the SNP clusters to smaller groups or single markers.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hierinf/meta.yaml b/recipes/bioconductor-hierinf/meta.yaml index b55d1417ca221..39111cbc556aa 100644 --- a/recipes/bioconductor-hierinf/meta.yaml +++ b/recipes/bioconductor-hierinf/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "hierinf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 44446a50b3747865eadceabe415ce6f5 +about: + description: Tools to perform hierarchical inference for one or multiple studies / data sets based on high-dimensional multivariate (generalised) linear models. A possible application is to perform hierarchical inference for GWA studies to find significant groups or single SNPs (if the signal is strong) in a data-driven and automated procedure. The method is based on an efficient hierarchical multiple testing correction and controls the FWER. The functions can easily be run in parallel. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 | file LICENSE + license_file: LICENSE + summary: Hierarchical Inference build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hierinf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, MASS, testthat requirements: host: @@ -29,13 +28,14 @@ requirements: - r-base - r-fmsb - r-glmnet +source: + md5: ed51fa55cd6f4de5fe24920ce844f547 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 | file LICENSE' - summary: 'Hierarchical Inference' - description: 'Tools to perform hierarchical inference for one or multiple studies / data sets based on high-dimensional multivariate (generalised) linear models. A possible application is to perform hierarchical inference for GWA studies to find significant groups or single SNPs (if the signal is strong) in a data-driven and automated procedure. The method is based on an efficient hierarchical multiple testing correction and controls the FWER. The functions can easily be run in parallel.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-highlyreplicatedrnaseq/meta.yaml b/recipes/bioconductor-highlyreplicatedrnaseq/meta.yaml index 936d3d703dbea..e5958f34e888c 100644 --- a/recipes/bioconductor-highlyreplicatedrnaseq/meta.yaml +++ b/recipes/bioconductor-highlyreplicatedrnaseq/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "HighlyReplicatedRNASeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a397cddffb2dfea70943930b992ea7c0 +about: + description: Gene-level count matrix data for bulk RNA-seq dataset with many replicates. The data are provided as easy to use SummarizedExperiment objects. The source data that is made accessible through this package comes from https://github.com/bartongroup/profDGE48. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Collection of Bulk RNA-Seq Experiments With Many Replicates build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-highlyreplicatedrnaseq", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, BiocFileCache, knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 99ee0dea69d529c22e03384cc5a61941 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Collection of Bulk RNA-Seq Experiments With Many Replicates' - description: 'Gene-level count matrix data for bulk RNA-seq dataset with many replicates. The data are provided as easy to use SummarizedExperiment objects. The source data that is made accessible through this package comes from https://github.com/bartongroup/profDGE48.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-highlyreplicatedrnaseq/post-link.sh b/recipes/bioconductor-highlyreplicatedrnaseq/post-link.sh index fdd22acfec305..ffdad77ea6eef 100644 --- a/recipes/bioconductor-highlyreplicatedrnaseq/post-link.sh +++ b/recipes/bioconductor-highlyreplicatedrnaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "highlyreplicatedrnaseq-1.14.0" +installBiocDataPackage.sh "highlyreplicatedrnaseq-1.18.0" diff --git a/recipes/bioconductor-hiiragi2013/meta.yaml b/recipes/bioconductor-hiiragi2013/meta.yaml index 1db7f4d8b615d..96ef7a73621fc 100644 --- a/recipes/bioconductor-hiiragi2013/meta.yaml +++ b/recipes/bioconductor-hiiragi2013/meta.yaml @@ -1,33 +1,34 @@ -{% set version = "1.38.0" %} +{% set version = "1.41.0" %} {% set name = "Hiiragi2013" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881."' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dde13f333fe218976f71b626ed5eefa4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hiiragi2013", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ArrayExpress, BiocStyle requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-geneplotter >=1.80.0,<1.81.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-mouse4302.db >=3.13.0,<3.14.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-geneplotter >=1.84.0,<1.85.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-mouse4302.db >=3.13.0,<3.14.0 - r-base - r-boot - r-clue @@ -40,12 +41,12 @@ requirements: - r-rcolorbrewer - r-xtable run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-geneplotter >=1.80.0,<1.81.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-mouse4302.db >=3.13.0,<3.14.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-geneplotter >=1.84.0,<1.85.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-mouse4302.db >=3.13.0,<3.14.0 - r-base - r-boot - r-clue @@ -58,13 +59,17 @@ requirements: - r-rcolorbrewer - r-xtable - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 71c665b10052ac72002701dd45990dc7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages' - description: 'This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881."' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hiiragi2013/post-link.sh b/recipes/bioconductor-hiiragi2013/post-link.sh index 6c78d22253936..90c7266997c01 100644 --- a/recipes/bioconductor-hiiragi2013/post-link.sh +++ b/recipes/bioconductor-hiiragi2013/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hiiragi2013-1.38.0" +installBiocDataPackage.sh "hiiragi2013-1.41.0" diff --git a/recipes/bioconductor-hilbertcurve/meta.yaml b/recipes/bioconductor-hilbertcurve/meta.yaml index f707d6bb5a83d..e5df2d5064b77 100644 --- a/recipes/bioconductor-hilbertcurve/meta.yaml +++ b/recipes/bioconductor-hilbertcurve/meta.yaml @@ -1,49 +1,59 @@ -{% set version = "1.32.0" %} +{% set version = "2.0.0" %} {% set name = "HilbertCurve" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Hilbert curve is a type of space-filling curves that fold one dimensional axis into a two dimensional space, but with still preserves the locality. This package aims to provide an easy and flexible way to visualize data through Hilbert curve. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Making 2D Hilbert Curve -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 97eed8a87d8bb062c5d0b900823f6bcc build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hilbertcurve", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0), markdown, RColorBrewer, RCurl, GetoptLong, rmarkdown requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hilbertvis >=1.60.0,<1.61.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - - 'r-circlize >=0.3.3' + - r-circlize >=0.3.3 - r-png - r-polylabelr + - r-rcpp + - libblas + - liblapack run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hilbertvis >=1.60.0,<1.61.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - - 'r-circlize >=0.3.3' + - r-circlize >=0.3.3 - r-png - r-polylabelr + - r-rcpp + +source: + md5: b4aea3a4cfa4d8d022dc17a0d18311ac + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Making 2D Hilbert Curve' - description: 'Hilbert curve is a type of space-filling curves that fold one dimensional axis into a two dimensional space, but with still preserves the locality. This package aims to provide an easy and flexible way to visualize data through Hilbert curve.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hilbertvis/meta.yaml b/recipes/bioconductor-hilbertvis/meta.yaml index 9720dd65d60bf..1394f62de97e2 100644 --- a/recipes/bioconductor-hilbertvis/meta.yaml +++ b/recipes/bioconductor-hilbertvis/meta.yaml @@ -1,25 +1,41 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "HilbertVis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions to visualize long vectors of integer data by means of Hilbert curves + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Hilbert curve visualization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b30abc9c50034b41daf1399031d657e3 build: - number: 3 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hilbertvis", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:hilbertvis + - doi:10.1093/bioinformatics/btp152 + parent_recipe: + name: bioconductor-hilbertvis + path: recipes/bioconductor-hilbertvis + version: 1.38.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: IRanges, EBImage requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - r-lattice @@ -28,26 +44,16 @@ requirements: run: - r-base - r-lattice - build: - - {{ compiler('c') }} - - make + +source: + md5: 627ad4e5725a9044727aa1ef90e3da09 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Hilbert curve visualization' - description: 'Functions to visualize long vectors of integer data by means of Hilbert curves' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:hilbertvis - - doi:10.1093/bioinformatics/btp152 - parent_recipe: - name: bioconductor-hilbertvis - path: recipes/bioconductor-hilbertvis - version: 1.38.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hilbertvisgui/meta.yaml b/recipes/bioconductor-hilbertvisgui/meta.yaml index 4f51df3df8f16..085ff702d977c 100644 --- a/recipes/bioconductor-hilbertvisgui/meta.yaml +++ b/recipes/bioconductor-hilbertvisgui/meta.yaml @@ -1,46 +1,46 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "HilbertVisGUI" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e9e6a2cce82ff0dfcf0828ae7d123537 +about: + description: An interactive tool to visualize long vectors of integer data by means of Hilbert curves + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: HilbertVisGUI build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hilbertvisgui", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: lattice, IRanges # SystemRequirements: gtkmm-2.4, GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - - 'bioconductor-hilbertvis >=1.60.0,<1.61.0' + - bioconductor-hilbertvis >=1.64.0,<1.65.0 - r-base - libblas - liblapack run: - - 'bioconductor-hilbertvis >=1.60.0,<1.61.0' + - bioconductor-hilbertvis >=1.64.0,<1.65.0 - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make +source: + md5: dc316bebd3431b7778ab5c7acc27c52e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: HilbertVisGUI - description: 'An interactive tool to visualize long vectors of integer data by means of Hilbert curves' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hilda/meta.yaml b/recipes/bioconductor-hilda/meta.yaml index 903151efa8394..7fe50f204cf1c 100644 --- a/recipes/bioconductor-hilda/meta.yaml +++ b/recipes/bioconductor-hilda/meta.yaml @@ -1,35 +1,43 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "HiLDA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package built under the Bayesian framework of applying hierarchical latent Dirichlet allocation. It statistically tests whether the mutational exposures of mutational signatures (Shiraishi-model signatures) are different between two groups. The package also provides inference and visualization. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e1961cfe72082b160cafb7bed5376673 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hilda", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, BiocStyle # SystemRequirements: JAGS 4.0.0 requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-abind - r-base - r-cowplot @@ -41,15 +49,16 @@ requirements: - r-tidyr - libblas - liblapack + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-abind - r-base - r-cowplot @@ -59,17 +68,16 @@ requirements: - r-rcpp - r-stringr - r-tidyr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: fe37f0a9870a06f8c16ff8530e7fabfb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation' - description: 'A package built under the Bayesian framework of applying hierarchical latent Dirichlet allocation. It statistically tests whether the mutational exposures of mutational signatures (Shiraishi-model signatures) are different between two groups. The package also provides inference and visualization.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hipathia/meta.yaml b/recipes/bioconductor-hipathia/meta.yaml index 60ebebd0e0391..30b553550835e 100644 --- a/recipes/bioconductor-hipathia/meta.yaml +++ b/recipes/bioconductor-hipathia/meta.yaml @@ -1,40 +1,42 @@ -{% set version = "3.2.0" %} +{% set version = "3.6.0" %} {% set name = "hipathia" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Hipathia is a method for the computation of signal transduction along signaling pathways from transcriptomic data. The method is based on an iterative algorithm which is able to compute the signal intensity passing through the nodes of a network by taking into account the level of expression of each gene and the intensity of the signal arriving to it. It also provides a new approach to functional analysis allowing to compute the signal arriving to the functions annotated to each pathway. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'HiPathia: High-throughput Pathway Analysis' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 819d2eecca55d3d4708934bbe69e82a7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hipathia", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-coin - r-dplyr - r-ggplot2 - r-ggpubr - - 'r-igraph >=1.0.1' + - r-igraph >=1.0.1 - r-matrixstats - r-metbrewer - r-reshape2 @@ -42,32 +44,35 @@ requirements: - r-tibble - r-visnetwork run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-coin - r-dplyr - r-ggplot2 - r-ggpubr - - 'r-igraph >=1.0.1' + - r-igraph >=1.0.1 - r-matrixstats - r-metbrewer - r-reshape2 - r-servr - r-tibble - r-visnetwork + +source: + md5: 73997b57da0ca2a2759adeb5aca55b26 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'HiPathia: High-throughput Pathway Analysis' - description: 'Hipathia is a method for the computation of signal transduction along signaling pathways from transcriptomic data. The method is based on an iterative algorithm which is able to compute the signal intensity passing through the nodes of a network by taking into account the level of expression of each gene and the intensity of the signal arriving to it. It also provides a new approach to functional analysis allowing to compute the signal arriving to the functions annotated to each pathway.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hippo/meta.yaml b/recipes/bioconductor-hippo/meta.yaml index 6daf28263c519..c3cd57fcfe876 100644 --- a/recipes/bioconductor-hippo/meta.yaml +++ b/recipes/bioconductor-hippo/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "HIPPO" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: For scRNA-seq data, it selects features and clusters the cells simultaneously for single-cell UMI data. It has a novel feature selection method using the zero inflation instead of gene variance, and computationally faster than other existing methods since it only relies on PCA+Kmeans rather than graph-clustering or consensus clustering. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Heterogeneity-Induced Pre-Processing tOol -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6c249e5f8b3f2a0622642c945e8d0566 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hippo", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-dplyr - r-ggplot2 @@ -36,7 +38,7 @@ requirements: - r-rtsne - r-umap run: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-dplyr - r-ggplot2 @@ -49,13 +51,16 @@ requirements: - r-rlang - r-rtsne - r-umap + +source: + md5: 4c0625a3e2ca57bc7910711f3fa80931 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Heterogeneity-Induced Pre-Processing tOol' - description: 'For scRNA-seq data, it selects features and clusters the cells simultaneously for single-cell UMI data. It has a novel feature selection method using the zero inflation instead of gene variance, and computationally faster than other existing methods since it only relies on PCA+Kmeans rather than graph-clustering or consensus clustering.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hireadsprocessor/meta.yaml b/recipes/bioconductor-hireadsprocessor/meta.yaml index fa5d6a94b7947..9d841fdbf7999 100644 --- a/recipes/bioconductor-hireadsprocessor/meta.yaml +++ b/recipes/bioconductor-hireadsprocessor/meta.yaml @@ -1,56 +1,63 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "hiReadsProcessor" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: hiReadsProcessor contains set of functions which allow users to process LM-PCR products sequenced using any platform. Given an excel/txt file containing parameters for demultiplexing and sample metadata, the functions automate trimming of adaptors and identification of the genomic product. Genomic products are further processed for QC and abundance quantification. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Functions to process LM-PCR reads from 454/Illumina data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a194956515b40e5dc75f90cafdea5c6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hireadsprocessor", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, markdown # SystemRequirements: BLAT, UCSC hg18 in 2bit format for BLAT requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hiannotator >=1.36.0,<1.37.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hiannotator >=1.40.0,<1.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 - r-base - r-dplyr - r-readxl - r-soniclength run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hiannotator >=1.36.0,<1.37.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hiannotator >=1.40.0,<1.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 - r-base - r-dplyr - r-readxl - r-soniclength + +source: + md5: 209c5291932b6ef2978cb534f008d458 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Functions to process LM-PCR reads from 454/Illumina data' - description: 'hiReadsProcessor contains set of functions which allow users to process LM-PCR products sequenced using any platform. Given an excel/txt file containing parameters for demultiplexing and sample metadata, the functions automate trimming of adaptors and identification of the genomic product. Genomic products are further processed for QC and abundance quantification.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hireewas/meta.yaml b/recipes/bioconductor-hireewas/meta.yaml index 88bfdf68e2cc3..9fa4ea67c299f 100644 --- a/recipes/bioconductor-hireewas/meta.yaml +++ b/recipes/bioconductor-hireewas/meta.yaml @@ -1,25 +1,27 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "HIREewas" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fd57bb11c16b2d194d7950ce0d918899 +about: + description: In epigenome-wide association studies, the measured signals for each sample are a mixture of methylation profiles from different cell types. The current approaches to the association detection only claim whether a cytosine-phosphate-guanine (CpG) site is associated with the phenotype or not, but they cannot determine the cell type in which the risk-CpG site is affected by the phenotype. We propose a solid statistical method, HIgh REsolution (HIRE), which not only substantially improves the power of association detection at the aggregated level as compared to the existing methods but also enables the detection of risk-CpG sites for individual cell types. The "HIREewas" R package is to implement HIRE model in R. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hireewas", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, BiocGenerics requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - r-gplots @@ -30,16 +32,14 @@ requirements: - r-base - r-gplots - r-quadprog - build: - - {{ compiler('c') }} - - make +source: + md5: d3dbaa6596c88295115e17190d76ca06 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies' - description: 'In epigenome-wide association studies, the measured signals for each sample are a mixture of methylation profiles from different cell types. The current approaches to the association detection only claim whether a cytosine-phosphate-guanine (CpG) site is associated with the phenotype or not, but they cannot determine the cell type in which the risk-CpG site is affected by the phenotype. We propose a solid statistical method, HIgh REsolution (HIRE), which not only substantially improves the power of association detection at the aggregated level as compared to the existing methods but also enables the detection of risk-CpG sites for individual cell types. The "HIREewas" R package is to implement HIRE model in R.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hitc/meta.yaml b/recipes/bioconductor-hitc/meta.yaml index 6d1346745d845..5909bcfab4eb5 100644 --- a/recipes/bioconductor-hitc/meta.yaml +++ b/recipes/bioconductor-hitc/meta.yaml @@ -1,57 +1,63 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "HiTC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The HiTC package was developed to explore high-throughput 'C' data such as 5C or Hi-C. Dedicated R classes as well as standard methods for quality controls, normalization, visualization, and further analysis are also provided. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: High Throughput Chromosome Conformation Capture analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e530516c0386e2e9bb6ff9afbed5893f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hitc", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, HiCDataHumanIMR90 + +extra: + identifiers: + - biotools:hitc + parent_recipe: + name: bioconductor-hitc + path: recipes/bioconductor-hitc + version: 1.24.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, HiCDataHumanIMR90, BSgenome.Hsapiens.UCSC.hg18 requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-matrix - r-rcolorbrewer run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-matrix - r-rcolorbrewer + +source: + md5: ca7c15fd99bd6921a1317abd8591a363 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'High Throughput Chromosome Conformation Capture analysis' - description: 'The HiTC package was developed to explore high-throughput ''C'' data such as 5C or Hi-C. Dedicated R classes as well as standard methods for quality controls, normalization, visualization, and further analysis are also provided.' -extra: - identifiers: - - biotools:hitc - parent_recipe: - name: bioconductor-hitc - path: recipes/bioconductor-hitc - version: 1.24.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hivcdnavantwout03/meta.yaml b/recipes/bioconductor-hivcdnavantwout03/meta.yaml index 9f5b6824060b5..6c4241cc6c722 100644 --- a/recipes/bioconductor-hivcdnavantwout03/meta.yaml +++ b/recipes/bioconductor-hivcdnavantwout03/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "HIVcDNAvantWout03" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4936f53bb66cdf1983a8bcbcd667a188 +about: + description: The expression levels of approximately 4600 cellular RNA transcripts were assessed in CD4+ T cell lines at different times after infection with HIV-1BRU using DNA microarrays. This data corresponds to the first block of a 12 block array image (001030_08_1.GEL) in the first data set (2000095918 A) in the first experiment (CEM LAI vs HI-LAI 24hr). There are two data sets, which are part of a dye-swap experiment with replicates, representing the Cy3 (green) absorption intensities for channel 1 (hiv1raw) and the Cy5 (red) absorption intensities for channel 2 (hiv2raw). + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: T cell line infections with HIV-1 LAI (BRU) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hivcdnavantwout03", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d8a55d85bce20ea0197759f2da10a230 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'T cell line infections with HIV-1 LAI (BRU)' - description: 'The expression levels of approximately 4600 cellular RNA transcripts were assessed in CD4+ T cell lines at different times after infection with HIV-1BRU using DNA microarrays. This data corresponds to the first block of a 12 block array image (001030_08_1.GEL) in the first data set (2000095918 A) in the first experiment (CEM LAI vs HI-LAI 24hr). There are two data sets, which are part of a dye-swap experiment with replicates, representing the Cy3 (green) absorption intensities for channel 1 (hiv1raw) and the Cy5 (red) absorption intensities for channel 2 (hiv2raw).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hivcdnavantwout03/post-link.sh b/recipes/bioconductor-hivcdnavantwout03/post-link.sh index 0eb40797b7714..98e31abe812ad 100644 --- a/recipes/bioconductor-hivcdnavantwout03/post-link.sh +++ b/recipes/bioconductor-hivcdnavantwout03/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hivcdnavantwout03-1.42.0" +installBiocDataPackage.sh "hivcdnavantwout03-1.46.0" diff --git a/recipes/bioconductor-hivprtplus2cdf/meta.yaml b/recipes/bioconductor-hivprtplus2cdf/meta.yaml index 31d0377db8de7..d64fa34351f31 100644 --- a/recipes/bioconductor-hivprtplus2cdf/meta.yaml +++ b/recipes/bioconductor-hivprtplus2cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hivprtplus2cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 143d9c2f5f328786bae7bb8dc4daf261 +about: + description: A package containing an environment representing the HIV PRTPlus 2.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hivprtplus2cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hivprtplus2cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 143d9c2f5f328786bae7bb8dc4daf261 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hivprtplus2cdf - description: 'A package containing an environment representing the HIV PRTPlus 2.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hmdbquery/meta.yaml b/recipes/bioconductor-hmdbquery/meta.yaml index a34079bd13563..db4150f0cad09 100644 --- a/recipes/bioconductor-hmdbquery/meta.yaml +++ b/recipes/bioconductor-hmdbquery/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "hmdbQuery" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 32b8de26d3b369730bdd7c734da1be06 +about: + description: Define utilities for exploration of human metabolome database, including functions to retrieve specific metabolite entries and data snapshots with pairwise associations (metabolite-gene,-protein,-disease). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: utilities for exploration of human metabolome database build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hmdbquery", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, annotate, gwascat, testthat, rmarkdown requirements: host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-xml run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-xml +source: + md5: e26ff837a92d941a46413c8028b228d9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'utilities for exploration of human metabolome database' - description: 'Define utilities for exploration of human metabolome database, including functions to retrieve specific metabolite entries and data snapshots with pairwise associations (metabolite-gene,-protein,-disease).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hmmcopy/meta.yaml b/recipes/bioconductor-hmmcopy/meta.yaml index 6e18042be1c07..4e3c15a289084 100644 --- a/recipes/bioconductor-hmmcopy/meta.yaml +++ b/recipes/bioconductor-hmmcopy/meta.yaml @@ -1,44 +1,21 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "HMMcopy" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for furthur analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Copy number prediction with correction for GC and mappability bias for HTS data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4785371e1642cd191330693396010a6e build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hmmcopy", max_pin="x.x") }}' -requirements: - host: - - r-base - - 'r-data.table >=1.11.8' - - libblas - - liblapack - run: - - r-base - - 'r-data.table >=1.11.8' - build: - - {{ compiler('c') }} - - make -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Copy number prediction with correction for GC and mappability bias for HTS data' - description: 'Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for furthur analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: additional-platforms: - linux-aarch64 @@ -50,3 +27,32 @@ extra: path: recipes/bioconductor-hmmcopy version: 1.22.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + build: + - {{ compiler('c') }} + - make + host: + - r-base + - r-data.table >=1.11.8 + - libblas + - liblapack + run: + - r-base + - r-data.table >=1.11.8 + +source: + md5: b0b3054c45fe88b26718969395126799 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-hmp16sdata/meta.yaml b/recipes/bioconductor-hmp16sdata/meta.yaml index 36851b9076422..7d3450bc50b7c 100644 --- a/recipes/bioconductor-hmp16sdata/meta.yaml +++ b/recipes/bioconductor-hmp16sdata/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "HMP16SData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: HMP16SData is a Bioconductor ExperimentData package of the Human Microbiome Project (HMP) 16S rRNA sequencing data for variable regions 1–3 and 3–5. Raw data files are provided in the package as downloaded from the HMP Data Analysis and Coordination Center. Processed data is provided as SummarizedExperiment class objects via ExperimentHub. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: 16S rRNA Sequencing Data from the Human Microbiome Project -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a137f917000e15acffca9bb0baac8fbb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hmp16sdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, circlize, cowplot, dendextend, devtools, ggplot2, gridExtra, haven, phyloseq, rmarkdown, roxygen2, stats, testthat, tidyr requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-dplyr @@ -36,10 +37,10 @@ requirements: - r-stringr - r-tibble run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-dplyr @@ -50,13 +51,17 @@ requirements: - r-stringr - r-tibble - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 7dcdd859e777169f9dacff8369a65e15 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: '16S rRNA Sequencing Data from the Human Microbiome Project' - description: 'HMP16SData is a Bioconductor ExperimentData package of the Human Microbiome Project (HMP) 16S rRNA sequencing data for variable regions 1–3 and 3–5. Raw data files are provided in the package as downloaded from the HMP Data Analysis and Coordination Center. Processed data is provided as SummarizedExperiment class objects via ExperimentHub.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hmp16sdata/post-link.sh b/recipes/bioconductor-hmp16sdata/post-link.sh index 43a01f6fffd29..00ca81cfdca88 100644 --- a/recipes/bioconductor-hmp16sdata/post-link.sh +++ b/recipes/bioconductor-hmp16sdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hmp16sdata-1.22.0" +installBiocDataPackage.sh "hmp16sdata-1.26.0" diff --git a/recipes/bioconductor-hmp2data/meta.yaml b/recipes/bioconductor-hmp2data/meta.yaml index 0f1a1a16733fa..6ab7c4a5303c1 100644 --- a/recipes/bioconductor-hmp2data/meta.yaml +++ b/recipes/bioconductor-hmp2data/meta.yaml @@ -1,33 +1,34 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "HMP2Data" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: HMP2Data is a Bioconductor package of the Human Microbiome Project 2 (HMP2) 16S rRNA sequencing data. Processed data is provided as phyloseq, SummarizedExperiment, and MultiAssayExperiment class objects. Individual matrices and data.frames used for building these S4 class objects are also provided in the package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: 16s rRNA sequencing data from the Human Microbiome Project 2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f334416386d2c1af677494e1fd5743d6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hmp2data", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, cowplot, devtools, ggplot2, gridExtra, haven, rmarkdown, roxygen2, stats, testthat, tibble, UpSetR requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-data.table @@ -37,12 +38,12 @@ requirements: - r-magrittr - r-readr run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-data.table @@ -52,13 +53,17 @@ requirements: - r-magrittr - r-readr - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 6d8778e92c4375d4bc35c25ab174473d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: '16s rRNA sequencing data from the Human Microbiome Project 2' - description: 'HMP2Data is a Bioconductor package of the Human Microbiome Project 2 (HMP2) 16S rRNA sequencing data. Processed data is provided as phyloseq, SummarizedExperiment, and MultiAssayExperiment class objects. Individual matrices and data.frames used for building these S4 class objects are also provided in the package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hmp2data/post-link.sh b/recipes/bioconductor-hmp2data/post-link.sh index 22fac5c1ff254..6aa24b9c108d1 100644 --- a/recipes/bioconductor-hmp2data/post-link.sh +++ b/recipes/bioconductor-hmp2data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hmp2data-1.16.0" +installBiocDataPackage.sh "hmp2data-1.20.0" diff --git a/recipes/bioconductor-holofoodr/build.sh b/recipes/bioconductor-holofoodr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-holofoodr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-holofoodr/meta.yaml b/recipes/bioconductor-holofoodr/meta.yaml new file mode 100644 index 0000000000000..fc0f324e08e49 --- /dev/null +++ b/recipes/bioconductor-holofoodr/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "1.0.0" %} +{% set name = "HoloFoodR" %} +{% set bioc = "3.20" %} + +about: + description: Utility package to facilitate integration and analysis of EBI HoloFood data in R. This package streamlines access to the resource, allowing for direct loading of data into formats optimized for downstream analytics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 | file LICENSE + license_file: LICENSE + summary: R interface to EBI HoloFood resource + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-holofoodr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, knitr, rmarkdown, BiocStyle +requirements: + host: + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 + - r-base + - r-dplyr + - r-httr2 + - r-jsonlite + run: + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 + - r-base + - r-dplyr + - r-httr2 + - r-jsonlite + +source: + md5: c8dd93af0578c15fd5a7df1b5c8a997f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-homo.sapiens/meta.yaml b/recipes/bioconductor-homo.sapiens/meta.yaml index 4f0fdece86a13..cf7eb466df625 100644 --- a/recipes/bioconductor-homo.sapiens/meta.yaml +++ b/recipes/bioconductor-homo.sapiens/meta.yaml @@ -1,54 +1,60 @@ {% set version = "1.3.1" %} {% set name = "Homo.sapiens" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Contains the Homo.sapiens object to access data from several related annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for the Homo.sapiens object -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 653b60cfcdaefd171729115cd629b585 build: - number: 16 + noarch: generic + number: 17 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-homo.sapiens", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-homo.sapiens + path: recipes/bioconductor-homo.sapiens + version: 1.3.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-organismdbi >=1.48.0,<1.49.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-organismdbi >=1.48.0,<1.49.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 653b60cfcdaefd171729115cd629b585 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for the Homo.sapiens object' - description: 'Contains the Homo.sapiens object to access data from several related annotation packages.' -extra: - parent_recipe: - name: bioconductor-homo.sapiens - path: recipes/bioconductor-homo.sapiens - version: 1.3.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hoodscanr/meta.yaml b/recipes/bioconductor-hoodscanr/meta.yaml index 61cbf0679547a..398e86f4c87cd 100644 --- a/recipes/bioconductor-hoodscanr/meta.yaml +++ b/recipes/bioconductor-hoodscanr/meta.yaml @@ -1,64 +1,69 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "hoodscanR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. The package can result in cell-level neighborhood annotation output, along with funtions to perform neighborhood colocalization analysis and neighborhood-based cell clustering. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Spatial cellular neighbourhood scanning in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c5ac598990d1f80bfa526c576abc8d84 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hoodscanr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.0.0), BiocStyle requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-ggplot2 - r-knitr - r-rann - - 'r-rcpp >=1.0.9' + - r-rcpp >=1.0.9 - r-rlang - r-rmarkdown - r-scico - libblas - liblapack run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-ggplot2 - r-knitr - r-rann - - 'r-rcpp >=1.0.9' + - r-rcpp >=1.0.9 - r-rlang - r-rmarkdown - r-scico - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: c61ed5273654b20c204142213c309391 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Spatial cellular neighbourhood scanning in R' - description: 'hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. The package can result in cell-level neighborhood annotation output, along with funtions to perform neighborhood colocalization analysis and neighborhood-based cell clustering.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hopach/meta.yaml b/recipes/bioconductor-hopach/meta.yaml index e515605dc2dc5..5442629b949b0 100644 --- a/recipes/bioconductor-hopach/meta.yaml +++ b/recipes/bioconductor-hopach/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "2.62.0" %} +{% set version = "2.66.0" %} {% set name = "hopach" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0310e9a4e3a34dfe2bb4edf0dbb38b16 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hopach", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:hopach + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-hopach + path: recipes/bioconductor-hopach + version: 2.40.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-cluster - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-cluster - build: - - {{ compiler('c') }} - - make + +source: + md5: 2307d00e135d616ac702514600985980 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)' - description: 'The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:hopach - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-hopach - path: recipes/bioconductor-hopach - version: 2.40.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hpaanalyze/meta.yaml b/recipes/bioconductor-hpaanalyze/meta.yaml index 73545f1379178..4ba065c80f202 100644 --- a/recipes/bioconductor-hpaanalyze/meta.yaml +++ b/recipes/bioconductor-hpaanalyze/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "HPAanalyze" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provide functions for retrieving, exploratory analyzing and visualizing the Human Protein Atlas data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Retrieve and analyze data from the Human Protein Atlas -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0916d6c86a23a3c136b3d0f1de2a25f4 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hpaanalyze", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, markdown, devtools, BiocStyle requirements: host: @@ -37,13 +39,16 @@ requirements: - r-openxlsx - r-tibble - r-xml2 + +source: + md5: f1857dcb95235213758524c18cb642b7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Retrieve and analyze data from the Human Protein Atlas' - description: 'Provide functions for retrieving, exploratory analyzing and visualizing the Human Protein Atlas data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hpannot/meta.yaml b/recipes/bioconductor-hpannot/meta.yaml index 0f3297ff458a5..6b486a9189cf3 100644 --- a/recipes/bioconductor-hpannot/meta.yaml +++ b/recipes/bioconductor-hpannot/meta.yaml @@ -1,24 +1,23 @@ {% set version = "1.1.0" %} {% set name = "hpAnnot" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fbc94a00b0f33b41bc5ff53fbe060663 +about: + description: Package containing example and annotation data for Hipathia package. Hipathia is a method for the computation of signal transduction along signaling pathways from transcriptomic data. The method is based on an iterative algorithm which is able to compute the signal intensity passing through the nodes of a network by taking into account the level of expression of each gene and the intensity of the signal arriving to it. It also provides a new approach to functional analysis allowing to compute the signal arriving to the functions annotated to each pathway. Hipathia depends on this package to be functional. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Anotation package for Hipathia package build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hpannot", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fbc94a00b0f33b41bc5ff53fbe060663 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: GPL-2 - summary: 'Anotation package for Hipathia package' - description: 'Package containing example and annotation data for Hipathia package. Hipathia is a method for the computation of signal transduction along signaling pathways from transcriptomic data. The method is based on an iterative algorithm which is able to compute the signal intensity passing through the nodes of a network by taking into account the level of expression of each gene and the intensity of the signal arriving to it. It also provides a new approach to functional analysis allowing to compute the signal arriving to the functions annotated to each pathway. Hipathia depends on this package to be functional.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hpar/meta.yaml b/recipes/bioconductor-hpar/meta.yaml index a49dd41f591c0..a43f40c927f37 100644 --- a/recipes/bioconductor-hpar/meta.yaml +++ b/recipes/bioconductor-hpar/meta.yaml @@ -1,40 +1,21 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "hpar" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The hpar package provides a simple R interface to and data from the Human Protein Atlas project. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Human Protein Atlas in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f970b068a2112cd8bf1a8dfb7d29d86a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hpar", max_pin="x.x") }}' - noarch: generic -# Suggests: org.Hs.eg.db, GO.db, AnnotationDbi, knitr, BiocStyle, testthat, rmarkdown, dplyr, DT -requirements: - host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - r-base - run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Human Protein Atlas in R' - description: 'The hpar package provides a simple R interface to and data from the Human Protein Atlas project.' + extra: identifiers: - biotools:hpar @@ -44,3 +25,28 @@ extra: path: recipes/bioconductor-hpar version: 1.22.2 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: org.Hs.eg.db, GO.db, AnnotationDbi, knitr, BiocStyle, testthat, rmarkdown, dplyr, DT +requirements: + host: + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - r-base + run: + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - r-base + +source: + md5: 6677e6756e4f9ba4131f8bf1e7dfbf73 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-hpip/meta.yaml b/recipes/bioconductor-hpip/meta.yaml index a97924166d6b7..6405158d94f2d 100644 --- a/recipes/bioconductor-hpip/meta.yaml +++ b/recipes/bioconductor-hpip/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "HPiP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: HPiP (Host-Pathogen Interaction Prediction) uses an ensemble learning algorithm for prediction of host-pathogen protein-protein interactions (HP-PPIs) using structural and physicochemical descriptors computed from amino acid-composition of host and pathogen proteins.The proposed package can effectively address data shortages and data unavailability for HP-PPI network reconstructions. Moreover, establishing computational frameworks in that regard will reveal mechanistic insights into infectious diseases and suggest potential HP-PPI targets, thus narrowing down the range of possible candidates for subsequent wet-lab experimental validations. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Host-Pathogen Interaction Prediction -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cbf5bf4735e100b22b184490854f8427 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hpip", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, colorspace, e1071, kernlab, ranger, SummarizedExperiment, Biostrings, randomForest, gprofiler2, gridExtra, ggthemes, BiocStyle, BiocGenerics, RUnit, tools, knitr requirements: host: - r-base - r-caret - r-corrplot - - 'r-dplyr >=1.0.6' + - r-dplyr >=1.0.6 - r-ggplot2 - - 'r-httr >=1.4.2' + - r-httr >=1.4.2 - r-igraph - r-magrittr - r-mcl @@ -43,9 +45,9 @@ requirements: - r-base - r-caret - r-corrplot - - 'r-dplyr >=1.0.6' + - r-dplyr >=1.0.6 - r-ggplot2 - - 'r-httr >=1.4.2' + - r-httr >=1.4.2 - r-igraph - r-magrittr - r-mcl @@ -57,13 +59,16 @@ requirements: - r-stringr - r-tibble - r-tidyr + +source: + md5: 2704b380252bc6db2d60f9354a2e7f47 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Host-Pathogen Interaction Prediction' - description: 'HPiP (Host-Pathogen Interaction Prediction) uses an ensemble learning algorithm for prediction of host-pathogen protein-protein interactions (HP-PPIs) using structural and physicochemical descriptors computed from amino acid-composition of host and pathogen proteins.The proposed package can effectively address data shortages and data unavailability for HP-PPI network reconstructions. Moreover, establishing computational frameworks in that regard will reveal mechanistic insights into infectious diseases and suggest potential HP-PPI targets, thus narrowing down the range of possible candidates for subsequent wet-lab experimental validations.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hpo.db/build_failure.linux-64.yaml b/recipes/bioconductor-hpo.db/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..9e223cb52ff2c --- /dev/null +++ b/recipes/bioconductor-hpo.db/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 92e0b99f8f31cbf7ee6247b3cc9b017c57c91b84ee51375d28cbf3cc4c228ada # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + During startup - Warning message: + Setting LC_TIME failed, using "C" + During startup - Warning message: + Setting LC_TIME failed, using "C" + Error: package or namespace load failed for HPO.db: + .onLoad failed in loadNamespace() for 'HPO.db', details: + call: NULL + error: Public + Resource removed on: 2024-05-02 + Error: loading failed + Execution halted + + stderr: dirname -- /opt/conda/conda-bld/bioconductor-hpo.db_1734770876917/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/installBiocDataPackage.sh + SCRIPT_DIR=/opt/conda/conda-bld/bioconductor-hpo.db_1734770876917/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/../share/bioconductor-data-packages + json=/opt/conda/conda-bld/bioconductor-hpo.db_1734770876917/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/../share/bioconductor-data-packages/dataURLs.json + yq '."hpo.db-0.99.2".fn' /opt/conda/conda-bld/bioconductor-hpo.db_1734770876917/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/../share/bioconductor-data-packages/dataURLs.json + FN='"HPO.db_0.99.2.tar.gz"' + IFS= + read -r value + yq '."hpo.db-0.99.2".urls[]' /opt/conda/conda-bld/bioconductor-hpo.db_1734770876917/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/../share/bioconductor-data-packages/dataURLs.json + URLS=($value) + IFS= + read -r value + URLS=($value) + IFS= + read -r value + URLS=($value) + IFS= + read -r value + yq '."hpo.db-0.99.2".md5' /opt/conda/conda-bld/bioconductor-hpo.db_1734770876917/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/../share/bioconductor-data-packages/dataURLs.json + MD5='"977cfb31ff344c58fd2dd0a2c6b765ab"' + STAGING=/opt/conda/conda-bld/bioconductor-hpo.db_1734770876917/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/share/hpo.db-0.99.2 + mkdir -p /opt/conda/conda-bld/bioconductor-hpo.db_1734770876917/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/share/hpo.db-0.99.2 + TARBALL='/opt/conda/conda-bld/bioconductor-hpo.db_1734770876917/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/share/hpo.db-0.99.2/"HPO.db_0.99.2.tar.gz"' + SUCCESS=0 + for URL in '${URLS[@]}' + echo '"https://bioconductor.org/packages/3.20/data/annotation/src/contrib/HPO.db_0.99.2.tar.gz"' + tr -d '"' + URL=https://bioconductor.org/packages/3.20/data/annotation/src/contrib/HPO.db_0.99.2.tar.gz + echo '"977cfb31ff344c58fd2dd0a2c6b765ab"' + tr -d '"' + MD5=977cfb31ff344c58fd2dd0a2c6b765ab + curl -L https://bioconductor.org/packages/3.20/data/annotation/src/contrib/HPO.db_0.99.2.tar.gz + % Total % Received % Xferd Average Speed Time Time Time Current + Dload Upload Total Spent Left Speed + + 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 + 100 24377 100 24377 0 0 75684 0 --:--:-- --:--:-- --:--:-- 75704 + [[ 0 == 0 ]] + uname -s + [[ Linux == \L\i\n\u\x ]] + md5sum -c + SUCCESS=1 + break + [[ 1 != 1 ]] + R CMD INSTALL --library=/opt/conda/conda-bld/bioconductor-hpo.db_1734770876917/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/R/library '/opt/conda/conda-bld/bioconductor-hpo.db_1734770876917/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/share/hpo.db-0.99.2/"HPO.db_0.99.2.tar.gz"' + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing *source* package HPO.db ... + ** using staged installation + ** R + ** inst + ** byte-compile and prepare package for lazy loading + ** help + *** installing help indices + ** building package indices + ** installing vignettes + ** testing if installed package can be loaded from temporary location + ERROR: loading failed + * removing /opt/conda/conda-bld/bioconductor-hpo.db_1734770876917/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/R/library/HPO.db + + return code: 1 + + kwargs: + {} + + : + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3462, in test + environ.create_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1060, in create_env + "too short in" in str(exc) + File "/opt/conda/lib/python3.10/site-packages/conda/__init__.py", line 130, in __str__ + return "\n".join(str(e) for e in self.errors) "\n" + File "/opt/conda/lib/python3.10/site-packages/conda/__init__.py", line 130, in + return "\n".join(str(e) for e in self.errors) "\n" + File "/opt/conda/lib/python3.10/site-packages/conda/__init__.py", line 83, in __str__ + return str(self.message % self._kwargs) + ValueError: unsupported format character 'T' (0x54) at index 4667 +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-hpo.db/meta.yaml b/recipes/bioconductor-hpo.db/meta.yaml index 64e2223e94fa9..8524bfcc99c9f 100644 --- a/recipes/bioconductor-hpo.db/meta.yaml +++ b/recipes/bioconductor-hpo.db/meta.yaml @@ -1,46 +1,51 @@ {% set version = "0.99.2" %} {% set name = "HPO.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Human Phenotype Ontology (HPO) was developed to create a consistent description of gene products with disease perspectives, and is essential for supporting functional genomics in disease context. Accurate disease descriptions can discover new relationships between genes and disease, and new functions for previous uncharacteried genes and alleles.We have developed the [DOSE](https://bioconductor.org/packages/DOSE/) package for semantic similarity analysis and disease enrichment analysis, and `DOSE` import an Bioconductor package 'DO.db' to get the relationship(such as parent and child) between MPO terms. But `DO.db` hasn't been updated for years, and a lot of semantic information is [missing](https://github.com/YuLab-SMU/DOSE/issues/57). So we developed the new package `HPO.db` for Human Human Phenotype Ontology annotation. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: A set of annotation maps describing the entire Human Phenotype Ontology -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 977cfb31ff344c58fd2dd0a2c6b765ab build: - number: 0 + noarch: generic + number: 1 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hpo.db", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base - r-dbi - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 977cfb31ff344c58fd2dd0a2c6b765ab + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A set of annotation maps describing the entire Human Phenotype Ontology' - description: 'Human Phenotype Ontology (HPO) was developed to create a consistent description of gene products with disease perspectives, and is essential for supporting functional genomics in disease context. Accurate disease descriptions can discover new relationships between genes and disease, and new functions for previous uncharacteried genes and alleles.We have developed the [DOSE](https://bioconductor.org/packages/DOSE/) package for semantic similarity analysis and disease enrichment analysis, and `DOSE` import an Bioconductor package ''DO.db'' to get the relationship(such as parent and child) between MPO terms. But `DO.db` hasn''t been updated for years, and a lot of semantic information is [missing](https://github.com/YuLab-SMU/DOSE/issues/57). So we developed the new package `HPO.db` for Human Human Phenotype Ontology annotation.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hs25kresogen.db/meta.yaml b/recipes/bioconductor-hs25kresogen.db/meta.yaml index 6c8d7424a4441..4b2adf638d4e0 100644 --- a/recipes/bioconductor-hs25kresogen.db/meta.yaml +++ b/recipes/bioconductor-hs25kresogen.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "2.5.0" %} {% set name = "hs25kresogen.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a3800d072ce0e5f6f5d8299538b99cca +about: + description: RNG_MRC Human Pangenomic 25k Set annotation data (chip hs25kresogen) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: RNG_MRC Human Pangenomic 25k Set annotation data (chip hs25kresogen) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hs25kresogen.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a3800d072ce0e5f6f5d8299538b99cca + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'RNG_MRC Human Pangenomic 25k Set annotation data (chip hs25kresogen)' - description: 'RNG_MRC Human Pangenomic 25k Set annotation data (chip hs25kresogen) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hs6ug171.db/meta.yaml b/recipes/bioconductor-hs6ug171.db/meta.yaml index 17b3f570c6ea2..52066bc857b5c 100644 --- a/recipes/bioconductor-hs6ug171.db/meta.yaml +++ b/recipes/bioconductor-hs6ug171.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "Hs6UG171.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7aaf8a2441941f70247275c93735ed3b +about: + description: A package containing metadata for Hs6UG171 arrays assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: A package containing metadata for Hs6UG171 arrays build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hs6ug171.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7aaf8a2441941f70247275c93735ed3b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A package containing metadata for Hs6UG171 arrays' - description: 'A package containing metadata for Hs6UG171 arrays assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hsagilentdesign026652.db/meta.yaml b/recipes/bioconductor-hsagilentdesign026652.db/meta.yaml index d5d0b53d117d3..2bc39de85de75 100644 --- a/recipes/bioconductor-hsagilentdesign026652.db/meta.yaml +++ b/recipes/bioconductor-hsagilentdesign026652.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "HsAgilentDesign026652.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dcd2c748bf9d7c002611cd5cf2ff38c0 +about: + description: Agilent Chips that use Agilent design number 026652 annotation data (chip HsAgilentDesign026652) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Agilent Chips that use Agilent design number 026652 annotation data (chip HsAgilentDesign026652) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hsagilentdesign026652.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: dcd2c748bf9d7c002611cd5cf2ff38c0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Agilent Chips that use Agilent design number 026652 annotation data (chip HsAgilentDesign026652)' - description: 'Agilent Chips that use Agilent design number 026652 annotation data (chip HsAgilentDesign026652) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hsmmsinglecell/meta.yaml b/recipes/bioconductor-hsmmsinglecell/meta.yaml index 642e145c87cf4..f7c344610687c 100644 --- a/recipes/bioconductor-hsmmsinglecell/meta.yaml +++ b/recipes/bioconductor-hsmmsinglecell/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "HSMMSingleCell" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dae440cd20110d25cd699a9a792ac4b8 +about: + description: Skeletal myoblasts undergo a well-characterized sequence of morphological and transcriptional changes during differentiation. In this experiment, primary human skeletal muscle myoblasts (HSMM) were expanded under high mitogen conditions (GM) and then differentiated by switching to low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several hundred cells taken over a time-course of serum-induced differentiation. Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hsmmsinglecell", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-hsmmsinglecell + path: recipes/bioconductor-hsmmsinglecell + version: 0.114.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 81add770e941f389d38651577056a14e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)' - description: 'Skeletal myoblasts undergo a well-characterized sequence of morphological and transcriptional changes during differentiation. In this experiment, primary human skeletal muscle myoblasts (HSMM) were expanded under high mitogen conditions (GM) and then differentiated by switching to low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several hundred cells taken over a time-course of serum-induced differentiation. Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell.' -extra: - parent_recipe: - name: bioconductor-hsmmsinglecell - path: recipes/bioconductor-hsmmsinglecell - version: 0.114.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hsmmsinglecell/post-link.sh b/recipes/bioconductor-hsmmsinglecell/post-link.sh index eac2f6e837b9c..5b6796d324544 100644 --- a/recipes/bioconductor-hsmmsinglecell/post-link.sh +++ b/recipes/bioconductor-hsmmsinglecell/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "hsmmsinglecell-1.22.0" +installBiocDataPackage.sh "hsmmsinglecell-1.26.0" diff --git a/recipes/bioconductor-hspec/meta.yaml b/recipes/bioconductor-hspec/meta.yaml index cdb859d14a07b..0c4e0ff348f79 100644 --- a/recipes/bioconductor-hspec/meta.yaml +++ b/recipes/bioconductor-hspec/meta.yaml @@ -1,40 +1,40 @@ {% set version = "0.99.1" %} {% set name = "Hspec" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ade3e3147c8f0086e9be2312cccdfeb +about: + description: A package containing an environment representing the HGU133Plus2_Hs_Hspec.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Hspec build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hspec", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0ade3e3147c8f0086e9be2312cccdfeb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: Hspec - description: 'A package containing an environment representing the HGU133Plus2_Hs_Hspec.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hspeccdf/meta.yaml b/recipes/bioconductor-hspeccdf/meta.yaml index 9d7ecbfd4107f..7fec23a253957 100644 --- a/recipes/bioconductor-hspeccdf/meta.yaml +++ b/recipes/bioconductor-hspeccdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "0.99.1" %} {% set name = "hspeccdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 89f81adf91094710558ce6aec79fc7fd +about: + description: A package containing an environment representing the HGU133Plus2_Hs_Hspec.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hspeccdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hspeccdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 89f81adf91094710558ce6aec79fc7fd + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hspeccdf - description: 'A package containing an environment representing the HGU133Plus2_Hs_Hspec.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hta20probeset.db/meta.yaml b/recipes/bioconductor-hta20probeset.db/meta.yaml index 8954764a4ca49..474aaf15dbabe 100644 --- a/recipes/bioconductor-hta20probeset.db/meta.yaml +++ b/recipes/bioconductor-hta20probeset.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "hta20probeset.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8cc15bb71f3c2776015e55a2d7df2c2f +about: + description: Affymetrix hta20 annotation data (chip hta20probeset) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix hta20 annotation data (chip hta20probeset) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hta20probeset.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8cc15bb71f3c2776015e55a2d7df2c2f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix hta20 annotation data (chip hta20probeset)' - description: 'Affymetrix hta20 annotation data (chip hta20probeset) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hta20transcriptcluster.db/meta.yaml b/recipes/bioconductor-hta20transcriptcluster.db/meta.yaml index e8c9ccf5eb116..1ffdcd9795e4f 100644 --- a/recipes/bioconductor-hta20transcriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hta20transcriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "hta20transcriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9debbc190cc5f9f0ad97fbc452fe7025 +about: + description: Affymetrix hta20 annotation data (chip hta20transcriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix hta20 annotation data (chip hta20transcriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hta20transcriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9debbc190cc5f9f0ad97fbc452fe7025 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix hta20 annotation data (chip hta20transcriptcluster)' - description: 'Affymetrix hta20 annotation data (chip hta20transcriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hthgu133a.db/meta.yaml b/recipes/bioconductor-hthgu133a.db/meta.yaml index 726b1974b31d6..784a8595e7fdd 100644 --- a/recipes/bioconductor-hthgu133a.db/meta.yaml +++ b/recipes/bioconductor-hthgu133a.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "hthgu133a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 769ed088760102b61edfb73454d4c642 +about: + description: Affymetrix Affymetrix HT_HG-U133A Array annotation data (chip hthgu133a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HT_HG-U133A Array annotation data (chip hthgu133a) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hthgu133a.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 769ed088760102b61edfb73454d4c642 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HT_HG-U133A Array annotation data (chip hthgu133a)' - description: 'Affymetrix Affymetrix HT_HG-U133A Array annotation data (chip hthgu133a) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hthgu133acdf/meta.yaml b/recipes/bioconductor-hthgu133acdf/meta.yaml index beceffbf2be85..4980ef96cb7ed 100644 --- a/recipes/bioconductor-hthgu133acdf/meta.yaml +++ b/recipes/bioconductor-hthgu133acdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hthgu133acdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b92e543867f1f0c08bfa9299e123d608 +about: + description: A package containing an environment representing the HT_HG-U133A.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hthgu133acdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hthgu133acdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b92e543867f1f0c08bfa9299e123d608 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hthgu133acdf - description: 'A package containing an environment representing the HT_HG-U133A.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hthgu133afrmavecs/meta.yaml b/recipes/bioconductor-hthgu133afrmavecs/meta.yaml index c0d9ce5809f99..4fc9128603fed 100644 --- a/recipes/bioconductor-hthgu133afrmavecs/meta.yaml +++ b/recipes/bioconductor-hthgu133afrmavecs/meta.yaml @@ -1,38 +1,38 @@ {% set version = "1.3.0" %} {% set name = "hthgu133afrmavecs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: be3f3d67a94dca3b080c184fba5ff6d8 +about: + description: This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Vectors used by frma for microarrays of type hthgu133a build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hthgu133afrmavecs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: be3f3d67a94dca3b080c184fba5ff6d8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Vectors used by frma for microarrays of type hthgu133a' - description: 'This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hthgu133aprobe/meta.yaml b/recipes/bioconductor-hthgu133aprobe/meta.yaml index e97081613b6ed..15cd2a13e7097 100644 --- a/recipes/bioconductor-hthgu133aprobe/meta.yaml +++ b/recipes/bioconductor-hthgu133aprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hthgu133aprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cdc17ea670719f055ee75bea1415c754 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_HG-U133A\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hthgu133a build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hthgu133aprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: cdc17ea670719f055ee75bea1415c754 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hthgu133a' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_HG-U133A\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hthgu133b.db/meta.yaml b/recipes/bioconductor-hthgu133b.db/meta.yaml index 3f1e467464b75..d8b76a658e1b2 100644 --- a/recipes/bioconductor-hthgu133b.db/meta.yaml +++ b/recipes/bioconductor-hthgu133b.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "hthgu133b.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8501401a7385e28173ea7b60aa3bf3d2 +about: + description: Affymetrix Affymetrix HT_HG-U133B Array annotation data (chip hthgu133b) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HT_HG-U133B Array annotation data (chip hthgu133b) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hthgu133b.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8501401a7385e28173ea7b60aa3bf3d2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HT_HG-U133B Array annotation data (chip hthgu133b)' - description: 'Affymetrix Affymetrix HT_HG-U133B Array annotation data (chip hthgu133b) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hthgu133bcdf/meta.yaml b/recipes/bioconductor-hthgu133bcdf/meta.yaml index de3ebaee98b4e..926017df16f65 100644 --- a/recipes/bioconductor-hthgu133bcdf/meta.yaml +++ b/recipes/bioconductor-hthgu133bcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hthgu133bcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 935ae53fb168d9c7890d71020ef4c366 +about: + description: A package containing an environment representing the HT_HG-U133B.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hthgu133bcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hthgu133bcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 935ae53fb168d9c7890d71020ef4c366 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hthgu133bcdf - description: 'A package containing an environment representing the HT_HG-U133B.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hthgu133bprobe/meta.yaml b/recipes/bioconductor-hthgu133bprobe/meta.yaml index 4cb19a19a6c5e..20b7bde90bb15 100644 --- a/recipes/bioconductor-hthgu133bprobe/meta.yaml +++ b/recipes/bioconductor-hthgu133bprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hthgu133bprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8a2e306638a81fdec3b10a014c04c6b9 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_HG-U133B\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hthgu133b build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hthgu133bprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8a2e306638a81fdec3b10a014c04c6b9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hthgu133b' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_HG-U133B\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hthgu133plusa.db/meta.yaml b/recipes/bioconductor-hthgu133plusa.db/meta.yaml index b6fdded12559a..4bbe9ddc76df6 100644 --- a/recipes/bioconductor-hthgu133plusa.db/meta.yaml +++ b/recipes/bioconductor-hthgu133plusa.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "hthgu133plusa.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 477cb32e1d8eb6da894486ad810b4232 +about: + description: Affymetrix Affymetrix HT_HG-U133_Plus_A Array annotation data (chip hthgu133plusa) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HT_HG-U133_Plus_A Array annotation data (chip hthgu133plusa) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hthgu133plusa.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 477cb32e1d8eb6da894486ad810b4232 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HT_HG-U133_Plus_A Array annotation data (chip hthgu133plusa)' - description: 'Affymetrix Affymetrix HT_HG-U133_Plus_A Array annotation data (chip hthgu133plusa) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hthgu133plusb.db/meta.yaml b/recipes/bioconductor-hthgu133plusb.db/meta.yaml index 091a03b1a4e40..b0a144016c53f 100644 --- a/recipes/bioconductor-hthgu133plusb.db/meta.yaml +++ b/recipes/bioconductor-hthgu133plusb.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "hthgu133plusb.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f3214792ba174598b0559937f46de937 +about: + description: Affymetrix Affymetrix HT_HG-U133_Plus_B Array annotation data (chip hthgu133plusb) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HT_HG-U133_Plus_B Array annotation data (chip hthgu133plusb) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hthgu133plusb.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f3214792ba174598b0559937f46de937 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HT_HG-U133_Plus_B Array annotation data (chip hthgu133plusb)' - description: 'Affymetrix Affymetrix HT_HG-U133_Plus_B Array annotation data (chip hthgu133plusb) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hthgu133pluspm.db/meta.yaml b/recipes/bioconductor-hthgu133pluspm.db/meta.yaml index b7b803fc73c0b..65f350a2e3c00 100644 --- a/recipes/bioconductor-hthgu133pluspm.db/meta.yaml +++ b/recipes/bioconductor-hthgu133pluspm.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "hthgu133pluspm.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b0b3cb0174608d5705ae6c80dac02e3c +about: + description: Affymetrix Affymetrix HT_HG-U133_Plus_PM Array annotation data (chip hthgu133pluspm) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HT_HG-U133_Plus_PM Array annotation data (chip hthgu133pluspm) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hthgu133pluspm.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b0b3cb0174608d5705ae6c80dac02e3c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HT_HG-U133_Plus_PM Array annotation data (chip hthgu133pluspm)' - description: 'Affymetrix Affymetrix HT_HG-U133_Plus_PM Array annotation data (chip hthgu133pluspm) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hthgu133pluspmcdf/meta.yaml b/recipes/bioconductor-hthgu133pluspmcdf/meta.yaml index a4bcc1b6c3e99..5469a18106e8e 100644 --- a/recipes/bioconductor-hthgu133pluspmcdf/meta.yaml +++ b/recipes/bioconductor-hthgu133pluspmcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hthgu133pluspmcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 56d15101d59decac7811caa15b349a9c +about: + description: A package containing an environment representing the HT_HG-U133_Plus_PM.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hthgu133pluspmcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hthgu133pluspmcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 56d15101d59decac7811caa15b349a9c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hthgu133pluspmcdf - description: 'A package containing an environment representing the HT_HG-U133_Plus_PM.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hthgu133pluspmprobe/meta.yaml b/recipes/bioconductor-hthgu133pluspmprobe/meta.yaml index 4906c52b78aba..054cb03cc76cb 100644 --- a/recipes/bioconductor-hthgu133pluspmprobe/meta.yaml +++ b/recipes/bioconductor-hthgu133pluspmprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hthgu133pluspmprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 74713e822a689007892d0eb92dbd456b +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_HG-U133\_Plus\_PM\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hthgu133pluspm build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hthgu133pluspmprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 74713e822a689007892d0eb92dbd456b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hthgu133pluspm' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_HG-U133\_Plus\_PM\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-htmg430a.db/meta.yaml b/recipes/bioconductor-htmg430a.db/meta.yaml index e8fbd4bfd804b..2c866a0614a4c 100644 --- a/recipes/bioconductor-htmg430a.db/meta.yaml +++ b/recipes/bioconductor-htmg430a.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "htmg430a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 171e457946a6b485b2ebd928b233abb3 +about: + description: Affymetrix Affymetrix HT_MG-430A Array annotation data (chip htmg430a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HT_MG-430A Array annotation data (chip htmg430a) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-htmg430a.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 171e457946a6b485b2ebd928b233abb3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HT_MG-430A Array annotation data (chip htmg430a)' - description: 'Affymetrix Affymetrix HT_MG-430A Array annotation data (chip htmg430a) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-htmg430acdf/meta.yaml b/recipes/bioconductor-htmg430acdf/meta.yaml index 4e08e47255617..963d48e7a9a95 100644 --- a/recipes/bioconductor-htmg430acdf/meta.yaml +++ b/recipes/bioconductor-htmg430acdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "htmg430acdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aef7a3c3af7d2624ee6fc6f2d22472e2 +about: + description: A package containing an environment representing the HT_MG-430A.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: htmg430acdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-htmg430acdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: aef7a3c3af7d2624ee6fc6f2d22472e2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: htmg430acdf - description: 'A package containing an environment representing the HT_MG-430A.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-htmg430aprobe/meta.yaml b/recipes/bioconductor-htmg430aprobe/meta.yaml index 6c1055bf656d9..7b3c79c3840a1 100644 --- a/recipes/bioconductor-htmg430aprobe/meta.yaml +++ b/recipes/bioconductor-htmg430aprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "htmg430aprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e50cc49b8887b6ef8ee1152ec12d5010 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_MG-430A\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type htmg430a build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-htmg430aprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e50cc49b8887b6ef8ee1152ec12d5010 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type htmg430a' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_MG-430A\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-htmg430b.db/meta.yaml b/recipes/bioconductor-htmg430b.db/meta.yaml index 24cdd2d9eedb8..c24710c4ea155 100644 --- a/recipes/bioconductor-htmg430b.db/meta.yaml +++ b/recipes/bioconductor-htmg430b.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "htmg430b.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 70849a636e972a9be604a3320d3bd814 +about: + description: Affymetrix Affymetrix HT_MG-430B Array annotation data (chip htmg430b) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HT_MG-430B Array annotation data (chip htmg430b) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-htmg430b.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 70849a636e972a9be604a3320d3bd814 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HT_MG-430B Array annotation data (chip htmg430b)' - description: 'Affymetrix Affymetrix HT_MG-430B Array annotation data (chip htmg430b) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-htmg430bcdf/meta.yaml b/recipes/bioconductor-htmg430bcdf/meta.yaml index b404825d00bc8..e3d2dc98b090c 100644 --- a/recipes/bioconductor-htmg430bcdf/meta.yaml +++ b/recipes/bioconductor-htmg430bcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "htmg430bcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 53cc1408504a5f07b5655aa46b969157 +about: + description: A package containing an environment representing the HT_MG-430B.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: htmg430bcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-htmg430bcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 53cc1408504a5f07b5655aa46b969157 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: htmg430bcdf - description: 'A package containing an environment representing the HT_MG-430B.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-htmg430bprobe/meta.yaml b/recipes/bioconductor-htmg430bprobe/meta.yaml index bcfd9933555af..ae2c1a32b6152 100644 --- a/recipes/bioconductor-htmg430bprobe/meta.yaml +++ b/recipes/bioconductor-htmg430bprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "htmg430bprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f0e3eb56925d786762dee0c2dc82b530 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_MG-430B\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type htmg430b build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-htmg430bprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f0e3eb56925d786762dee0c2dc82b530 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type htmg430b' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_MG-430B\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-htmg430pm.db/meta.yaml b/recipes/bioconductor-htmg430pm.db/meta.yaml index b5ad88deeedc5..01401ef9eef8e 100644 --- a/recipes/bioconductor-htmg430pm.db/meta.yaml +++ b/recipes/bioconductor-htmg430pm.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "htmg430pm.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f89738ce2e33d1c626aa2d15cd28a49b +about: + description: Affymetrix Affymetrix HT_MG-430_PM Array annotation data (chip htmg430pm) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HT_MG-430_PM Array annotation data (chip htmg430pm) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-htmg430pm.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f89738ce2e33d1c626aa2d15cd28a49b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HT_MG-430_PM Array annotation data (chip htmg430pm)' - description: 'Affymetrix Affymetrix HT_MG-430_PM Array annotation data (chip htmg430pm) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-htmg430pmcdf/meta.yaml b/recipes/bioconductor-htmg430pmcdf/meta.yaml index 02705c76b099c..1b7d33e7839a5 100644 --- a/recipes/bioconductor-htmg430pmcdf/meta.yaml +++ b/recipes/bioconductor-htmg430pmcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "htmg430pmcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 016a54b47adbbed7db989787646a0084 +about: + description: A package containing an environment representing the HT_MG-430_PM.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: htmg430pmcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-htmg430pmcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 016a54b47adbbed7db989787646a0084 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: htmg430pmcdf - description: 'A package containing an environment representing the HT_MG-430_PM.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-htmg430pmprobe/meta.yaml b/recipes/bioconductor-htmg430pmprobe/meta.yaml index cd3aa90766fbd..569781c64ab6f 100644 --- a/recipes/bioconductor-htmg430pmprobe/meta.yaml +++ b/recipes/bioconductor-htmg430pmprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "htmg430pmprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f0e053fcc0ca4b5f8c539fc0a3fcb076 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_MG-430\_PM\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type htmg430pm build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-htmg430pmprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f0e053fcc0ca4b5f8c539fc0a3fcb076 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type htmg430pm' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_MG-430\_PM\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-htrat230pm.db/meta.yaml b/recipes/bioconductor-htrat230pm.db/meta.yaml index 949dfe5fa1ff5..5fef5bcb52d4c 100644 --- a/recipes/bioconductor-htrat230pm.db/meta.yaml +++ b/recipes/bioconductor-htrat230pm.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "htrat230pm.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 46ed50806c568bf269fe4c51d3df3955 +about: + description: Affymetrix Affymetrix HT_Rat230_PM Array annotation data (chip htrat230pm) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HT_Rat230_PM Array annotation data (chip htrat230pm) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-htrat230pm.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 46ed50806c568bf269fe4c51d3df3955 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HT_Rat230_PM Array annotation data (chip htrat230pm)' - description: 'Affymetrix Affymetrix HT_Rat230_PM Array annotation data (chip htrat230pm) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-htrat230pmcdf/meta.yaml b/recipes/bioconductor-htrat230pmcdf/meta.yaml index fc6ec741ec909..333d32758594b 100644 --- a/recipes/bioconductor-htrat230pmcdf/meta.yaml +++ b/recipes/bioconductor-htrat230pmcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "htrat230pmcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c6683d16e8aacccd326f7a7eebb79b98 +about: + description: A package containing an environment representing the HT_Rat230_PM.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: htrat230pmcdf build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-htrat230pmcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c6683d16e8aacccd326f7a7eebb79b98 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: htrat230pmcdf - description: 'A package containing an environment representing the HT_Rat230_PM.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-htrat230pmprobe/meta.yaml b/recipes/bioconductor-htrat230pmprobe/meta.yaml index b1e1040532964..4868ebbf1cb32 100644 --- a/recipes/bioconductor-htrat230pmprobe/meta.yaml +++ b/recipes/bioconductor-htrat230pmprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "htrat230pmprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e4deeca2dc406367ac4a347e370267cf +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_Rat230\_PM\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type htrat230pm build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-htrat230pmprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e4deeca2dc406367ac4a347e370267cf + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type htrat230pm' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_Rat230\_PM\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-htratfocus.db/meta.yaml b/recipes/bioconductor-htratfocus.db/meta.yaml index a270b55119363..e3e3dfb74e967 100644 --- a/recipes/bioconductor-htratfocus.db/meta.yaml +++ b/recipes/bioconductor-htratfocus.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "htratfocus.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 88be90edb1acb31faedde0b66b27a150 +about: + description: Affymetrix Affymetrix HT_Rat-Focus Array annotation data (chip htratfocus) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix HT_Rat-Focus Array annotation data (chip htratfocus) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-htratfocus.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 88be90edb1acb31faedde0b66b27a150 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix HT_Rat-Focus Array annotation data (chip htratfocus)' - description: 'Affymetrix Affymetrix HT_Rat-Focus Array annotation data (chip htratfocus) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-htratfocuscdf/meta.yaml b/recipes/bioconductor-htratfocuscdf/meta.yaml index e0495aa07b0d0..daffbc694b2b2 100644 --- a/recipes/bioconductor-htratfocuscdf/meta.yaml +++ b/recipes/bioconductor-htratfocuscdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "htratfocuscdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 04b4952f7d8b607a7eb0f779c08c57dc +about: + description: A package containing an environment representing the HT_Rat-Focus.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: htratfocuscdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-htratfocuscdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 04b4952f7d8b607a7eb0f779c08c57dc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: htratfocuscdf - description: 'A package containing an environment representing the HT_Rat-Focus.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-htratfocusprobe/meta.yaml b/recipes/bioconductor-htratfocusprobe/meta.yaml index e79a05ee51073..308eee69c44d2 100644 --- a/recipes/bioconductor-htratfocusprobe/meta.yaml +++ b/recipes/bioconductor-htratfocusprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "htratfocusprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 26a0963d8aff314a4a1f2c47e9147a8a +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_Rat-Focus\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type htratfocus build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-htratfocusprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 26a0963d8aff314a4a1f2c47e9147a8a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type htratfocus' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_Rat-Focus\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-htsfilter/meta.yaml b/recipes/bioconductor-htsfilter/meta.yaml index 84f5596a79d3c..e3260f7fc8e41 100644 --- a/recipes/bioconductor-htsfilter/meta.yaml +++ b/recipes/bioconductor-htsfilter/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "HTSFilter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6eb5ebe090ac02b5a0099f63f3e6ccc6 +about: + description: This package implements a filtering procedure for replicated transcriptome sequencing data based on a global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Filter replicated high-throughput transcriptome sequencing data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-htsfilter", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: EDASeq, testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 - r-base +source: + md5: 54a2338151f8950f9557785c3a02fc98 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Filter replicated high-throughput transcriptome sequencing data' - description: 'This package implements a filtering procedure for replicated transcriptome sequencing data based on a global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hu35ksuba.db/meta.yaml b/recipes/bioconductor-hu35ksuba.db/meta.yaml index aa6d56d193767..209531c52f7e2 100644 --- a/recipes/bioconductor-hu35ksuba.db/meta.yaml +++ b/recipes/bioconductor-hu35ksuba.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "hu35ksuba.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4c2306a80f26bacb6172e84c896ef911 +about: + description: Affymetrix Affymetrix Hu35KsubA Array annotation data (chip hu35ksuba) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Hu35KsubA Array annotation data (chip hu35ksuba) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hu35ksuba.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4c2306a80f26bacb6172e84c896ef911 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Hu35KsubA Array annotation data (chip hu35ksuba)' - description: 'Affymetrix Affymetrix Hu35KsubA Array annotation data (chip hu35ksuba) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hu35ksubacdf/meta.yaml b/recipes/bioconductor-hu35ksubacdf/meta.yaml index 6e0051e83251d..c1985558f1393 100644 --- a/recipes/bioconductor-hu35ksubacdf/meta.yaml +++ b/recipes/bioconductor-hu35ksubacdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubacdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c8b82c4755eb62818ca0dbf22de5d25e +about: + description: A package containing an environment representing the Hu35KsubA.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hu35ksubacdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hu35ksubacdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c8b82c4755eb62818ca0dbf22de5d25e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hu35ksubacdf - description: 'A package containing an environment representing the Hu35KsubA.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hu35ksubaprobe/meta.yaml b/recipes/bioconductor-hu35ksubaprobe/meta.yaml index 27ff012919986..9d7c09c190d15 100644 --- a/recipes/bioconductor-hu35ksubaprobe/meta.yaml +++ b/recipes/bioconductor-hu35ksubaprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubaprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 49bd19ec3b6404211f2e410e473fa644 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Hu35KsubA\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hu35ksuba build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hu35ksubaprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 49bd19ec3b6404211f2e410e473fa644 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hu35ksuba' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Hu35KsubA\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hu35ksubb.db/meta.yaml b/recipes/bioconductor-hu35ksubb.db/meta.yaml index 26b4effc29790..30a4dc01b6cdf 100644 --- a/recipes/bioconductor-hu35ksubb.db/meta.yaml +++ b/recipes/bioconductor-hu35ksubb.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "hu35ksubb.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b82ece4860eddff8010faecaae802312 +about: + description: Affymetrix Affymetrix Hu35KsubB Array annotation data (chip hu35ksubb) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Hu35KsubB Array annotation data (chip hu35ksubb) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hu35ksubb.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b82ece4860eddff8010faecaae802312 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Hu35KsubB Array annotation data (chip hu35ksubb)' - description: 'Affymetrix Affymetrix Hu35KsubB Array annotation data (chip hu35ksubb) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hu35ksubbcdf/meta.yaml b/recipes/bioconductor-hu35ksubbcdf/meta.yaml index 058b2d719b0ab..9e1d9d061a151 100644 --- a/recipes/bioconductor-hu35ksubbcdf/meta.yaml +++ b/recipes/bioconductor-hu35ksubbcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubbcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d873b6c521e926b331f799baf10a4e13 +about: + description: A package containing an environment representing the Hu35KsubB.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hu35ksubbcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hu35ksubbcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d873b6c521e926b331f799baf10a4e13 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hu35ksubbcdf - description: 'A package containing an environment representing the Hu35KsubB.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hu35ksubbprobe/meta.yaml b/recipes/bioconductor-hu35ksubbprobe/meta.yaml index f268e43a45ffd..8211ecf52d65c 100644 --- a/recipes/bioconductor-hu35ksubbprobe/meta.yaml +++ b/recipes/bioconductor-hu35ksubbprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubbprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0a63051d0faf38a56f17d5865cbed9b1 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Hu35KsubB\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hu35ksubb build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hu35ksubbprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0a63051d0faf38a56f17d5865cbed9b1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hu35ksubb' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Hu35KsubB\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hu35ksubc.db/meta.yaml b/recipes/bioconductor-hu35ksubc.db/meta.yaml index 12eff013b1335..7958869d8a9d1 100644 --- a/recipes/bioconductor-hu35ksubc.db/meta.yaml +++ b/recipes/bioconductor-hu35ksubc.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "hu35ksubc.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 57e60b8d025e0e8cf7ac2b355111cf2d +about: + description: Affymetrix Affymetrix Hu35KsubC Array annotation data (chip hu35ksubc) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Hu35KsubC Array annotation data (chip hu35ksubc) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hu35ksubc.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 57e60b8d025e0e8cf7ac2b355111cf2d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Hu35KsubC Array annotation data (chip hu35ksubc)' - description: 'Affymetrix Affymetrix Hu35KsubC Array annotation data (chip hu35ksubc) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hu35ksubccdf/meta.yaml b/recipes/bioconductor-hu35ksubccdf/meta.yaml index e74f1c9802053..5481d99f31c39 100644 --- a/recipes/bioconductor-hu35ksubccdf/meta.yaml +++ b/recipes/bioconductor-hu35ksubccdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubccdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: de96e69680c5f8747c99d170272d7c3c +about: + description: A package containing an environment representing the Hu35KsubC.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hu35ksubccdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hu35ksubccdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: de96e69680c5f8747c99d170272d7c3c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hu35ksubccdf - description: 'A package containing an environment representing the Hu35KsubC.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hu35ksubcprobe/meta.yaml b/recipes/bioconductor-hu35ksubcprobe/meta.yaml index e34a24730e4a9..103c1618ec820 100644 --- a/recipes/bioconductor-hu35ksubcprobe/meta.yaml +++ b/recipes/bioconductor-hu35ksubcprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubcprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b10453ea061b09172192bd21baa9083d +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Hu35KsubC\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hu35ksubc build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hu35ksubcprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b10453ea061b09172192bd21baa9083d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hu35ksubc' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Hu35KsubC\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hu35ksubd.db/meta.yaml b/recipes/bioconductor-hu35ksubd.db/meta.yaml index 1e4d5c25aa532..72c3c203005b9 100644 --- a/recipes/bioconductor-hu35ksubd.db/meta.yaml +++ b/recipes/bioconductor-hu35ksubd.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "hu35ksubd.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5ce6b6ede0f9733fd4dc527a28114327 +about: + description: Affymetrix Affymetrix Hu35KsubD Array annotation data (chip hu35ksubd) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Hu35KsubD Array annotation data (chip hu35ksubd) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hu35ksubd.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5ce6b6ede0f9733fd4dc527a28114327 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Hu35KsubD Array annotation data (chip hu35ksubd)' - description: 'Affymetrix Affymetrix Hu35KsubD Array annotation data (chip hu35ksubd) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hu35ksubdcdf/meta.yaml b/recipes/bioconductor-hu35ksubdcdf/meta.yaml index bc47065d4bc5e..b0466df3dd760 100644 --- a/recipes/bioconductor-hu35ksubdcdf/meta.yaml +++ b/recipes/bioconductor-hu35ksubdcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubdcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6f6423426969f306fb0d5171e75b5380 +about: + description: A package containing an environment representing the Hu35KsubD.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hu35ksubdcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hu35ksubdcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6f6423426969f306fb0d5171e75b5380 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hu35ksubdcdf - description: 'A package containing an environment representing the Hu35KsubD.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hu35ksubdprobe/meta.yaml b/recipes/bioconductor-hu35ksubdprobe/meta.yaml index aecbeb343c4d5..418dae94afe2e 100644 --- a/recipes/bioconductor-hu35ksubdprobe/meta.yaml +++ b/recipes/bioconductor-hu35ksubdprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hu35ksubdprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 430a9b8ccd646d8cb06e6c1d750eec23 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Hu35KsubD\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hu35ksubd build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hu35ksubdprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 430a9b8ccd646d8cb06e6c1d750eec23 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hu35ksubd' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Hu35KsubD\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hu6800.db/meta.yaml b/recipes/bioconductor-hu6800.db/meta.yaml index b0075ffaca4fd..f213a5daf7388 100644 --- a/recipes/bioconductor-hu6800.db/meta.yaml +++ b/recipes/bioconductor-hu6800.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "hu6800.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aa1cb6c107dee6d2ed1929b48aa831e9 +about: + description: Affymetrix Affymetrix Hu6800 Array annotation data (chip hu6800) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Hu6800 Array annotation data (chip hu6800) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hu6800.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: aa1cb6c107dee6d2ed1929b48aa831e9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Hu6800 Array annotation data (chip hu6800)' - description: 'Affymetrix Affymetrix Hu6800 Array annotation data (chip hu6800) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hu6800cdf/meta.yaml b/recipes/bioconductor-hu6800cdf/meta.yaml index e614aa6fa22fa..8d6dcb817abf9 100644 --- a/recipes/bioconductor-hu6800cdf/meta.yaml +++ b/recipes/bioconductor-hu6800cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hu6800cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fa2b2ab8f3aba517c63ad2e65873d2f0 +about: + description: A package containing an environment representing the Hu6800.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hu6800cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hu6800cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fa2b2ab8f3aba517c63ad2e65873d2f0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hu6800cdf - description: 'A package containing an environment representing the Hu6800.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hu6800probe/meta.yaml b/recipes/bioconductor-hu6800probe/meta.yaml index f27bcb41f1371..b66651cb9a510 100644 --- a/recipes/bioconductor-hu6800probe/meta.yaml +++ b/recipes/bioconductor-hu6800probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hu6800probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7a2383bd870cbc0628c210174e911250 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Hu6800\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hu6800 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hu6800probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7a2383bd870cbc0628c210174e911250 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hu6800' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Hu6800\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hu6800subacdf/meta.yaml b/recipes/bioconductor-hu6800subacdf/meta.yaml index 14d7f881b2a7e..41f3a186b38c1 100644 --- a/recipes/bioconductor-hu6800subacdf/meta.yaml +++ b/recipes/bioconductor-hu6800subacdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hu6800subacdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9e8ec301e066e400564976cd9750297e +about: + description: A package containing an environment representing the Hu6800subA.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hu6800subacdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hu6800subacdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9e8ec301e066e400564976cd9750297e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hu6800subacdf - description: 'A package containing an environment representing the Hu6800subA.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hu6800subbcdf/meta.yaml b/recipes/bioconductor-hu6800subbcdf/meta.yaml index 2d20ea344463a..acedbec551d65 100644 --- a/recipes/bioconductor-hu6800subbcdf/meta.yaml +++ b/recipes/bioconductor-hu6800subbcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hu6800subbcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 529aad5e4e73594c8cb66274d7e4adc5 +about: + description: A package containing an environment representing the Hu6800subB.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hu6800subbcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hu6800subbcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 529aad5e4e73594c8cb66274d7e4adc5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hu6800subbcdf - description: 'A package containing an environment representing the Hu6800subB.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hu6800subccdf/meta.yaml b/recipes/bioconductor-hu6800subccdf/meta.yaml index 85db4b5ce728c..e538c3a1262bd 100644 --- a/recipes/bioconductor-hu6800subccdf/meta.yaml +++ b/recipes/bioconductor-hu6800subccdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hu6800subccdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 020fe3a6bdf44efbde15432b968433e8 +about: + description: A package containing an environment representing the Hu6800subC.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hu6800subccdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hu6800subccdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 020fe3a6bdf44efbde15432b968433e8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hu6800subccdf - description: 'A package containing an environment representing the Hu6800subC.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hu6800subdcdf/meta.yaml b/recipes/bioconductor-hu6800subdcdf/meta.yaml index f3b36b1e7d49c..c542e74221230 100644 --- a/recipes/bioconductor-hu6800subdcdf/meta.yaml +++ b/recipes/bioconductor-hu6800subdcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hu6800subdcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7966c21babb23e18cca4faafc8720f0a +about: + description: A package containing an environment representing the Hu6800subD.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hu6800subdcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hu6800subdcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7966c21babb23e18cca4faafc8720f0a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hu6800subdcdf - description: 'A package containing an environment representing the Hu6800subD.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hubmapr/build.sh b/recipes/bioconductor-hubmapr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hubmapr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hubmapr/meta.yaml b/recipes/bioconductor-hubmapr/meta.yaml new file mode 100644 index 0000000000000..965cbc5a3e3b8 --- /dev/null +++ b/recipes/bioconductor-hubmapr/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "0.99.6" %} +{% set name = "HuBMAPR" %} +{% set bioc = "3.20" %} + +about: + description: '''HuBMAP'' provides an open, global bio-molecular atlas of the human body at the cellular level. The `datasets()`, `samples()`, `donors()`, `publications()`, and `collections()` functions retrieves the information for each of these entity types. `*_details()` are available for individual entries of each entity type. `*_derived()` are available for retrieving derived datasets or samples for individual entries of each entity type. Data files can be accessed using `files_globus_url()`.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Interface to 'HuBMAP' + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hubmapr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat (>= 3.0.0), knitr, ggplot2, rmarkdown, BiocStyle +requirements: + host: + - r-base + - r-dplyr + - r-httr2 + - r-purrr + - r-rjsoncons + - r-rlang + - r-stringr + - r-tibble + - r-tidyr + - r-whisker + run: + - r-base + - r-dplyr + - r-httr2 + - r-purrr + - r-rjsoncons + - r-rlang + - r-stringr + - r-tibble + - r-tidyr + - r-whisker + +source: + md5: aca3cada99622535bbdc96a2c545f0eb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-hubpub/meta.yaml b/recipes/bioconductor-hubpub/meta.yaml index ce98d178e7182..1ca97363e1969 100644 --- a/recipes/bioconductor-hubpub/meta.yaml +++ b/recipes/bioconductor-hubpub/meta.yaml @@ -1,28 +1,29 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "HubPub" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: HubPub provides users with functionality to help with the Bioconductor Hub structures. The package provides the ability to create a skeleton of a Hub style package that the user can then populate with the necessary information. There are also functions to help add resources to the Hub package metadata files as well as publish data to the Bioconductor S3 bucket. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Utilities to create and use Bioconductor Hubs -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9595496f838fced99c75d9604456df25 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hubpub", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationHubData, ExperimentHubData, testthat, knitr, rmarkdown, BiocStyle, requirements: host: - - 'bioconductor-biocthis >=1.12.0,<1.13.0' + - bioconductor-biocthis >=1.16.0,<1.17.0 - r-available - r-aws.s3 - r-base @@ -31,7 +32,7 @@ requirements: - r-fs - r-usethis run: - - 'bioconductor-biocthis >=1.12.0,<1.13.0' + - bioconductor-biocthis >=1.16.0,<1.17.0 - r-available - r-aws.s3 - r-base @@ -39,12 +40,16 @@ requirements: - r-dplyr - r-fs - r-usethis + +source: + md5: 3a9913ba3d2dffa26ecb52faa33ee89c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Utilities to create and use Bioconductor Hubs' - description: 'HubPub provides users with functionality to help with the Bioconductor Hub structures. The package provides the ability to create a skeleton of a Hub style package that the user can then populate with the necessary information. There are also functions to help add resources to the Hub package metadata files as well as publish data to the Bioconductor S3 bucket.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-huex.1.0.st.v2frmavecs/meta.yaml b/recipes/bioconductor-huex.1.0.st.v2frmavecs/meta.yaml index f52623a6d6adc..388a1d3f651b8 100644 --- a/recipes/bioconductor-huex.1.0.st.v2frmavecs/meta.yaml +++ b/recipes/bioconductor-huex.1.0.st.v2frmavecs/meta.yaml @@ -1,38 +1,38 @@ {% set version = "1.1.0" %} {% set name = "huex.1.0.st.v2frmavecs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 982935d07b526ff555790e309fe4147e +about: + description: This package was created by frmaTools version 1.9.2. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Vectors used by frma for microarrays of type huex.1.0.st.v2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-huex.1.0.st.v2frmavecs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 982935d07b526ff555790e309fe4147e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Vectors used by frma for microarrays of type huex.1.0.st.v2' - description: 'This package was created by frmaTools version 1.9.2.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-huex10stprobeset.db/meta.yaml b/recipes/bioconductor-huex10stprobeset.db/meta.yaml index e46db4b591594..f7176a7f7a81f 100644 --- a/recipes/bioconductor-huex10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-huex10stprobeset.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "huex10stprobeset.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fda9fc7340aeda2564a76756d2b8d4d3 +about: + description: Affymetrix huex10 annotation data (chip huex10stprobeset) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix huex10 annotation data (chip huex10stprobeset) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-huex10stprobeset.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fda9fc7340aeda2564a76756d2b8d4d3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix huex10 annotation data (chip huex10stprobeset)' - description: 'Affymetrix huex10 annotation data (chip huex10stprobeset) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-huex10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-huex10sttranscriptcluster.db/meta.yaml index 466ce65126903..711270ea84de0 100644 --- a/recipes/bioconductor-huex10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-huex10sttranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "huex10sttranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0789a1e8ee4474bd64c2772eab0db247 +about: + description: Affymetrix huex10 annotation data (chip huex10sttranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix huex10 annotation data (chip huex10sttranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-huex10sttranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0789a1e8ee4474bd64c2772eab0db247 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix huex10 annotation data (chip huex10sttranscriptcluster)' - description: 'Affymetrix huex10 annotation data (chip huex10sttranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-huexexonprobesetlocation/meta.yaml b/recipes/bioconductor-huexexonprobesetlocation/meta.yaml index 5d2372d38e4b0..4dbb5b279fedd 100644 --- a/recipes/bioconductor-huexexonprobesetlocation/meta.yaml +++ b/recipes/bioconductor-huexexonprobesetlocation/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.15.0" %} {% set name = "HuExExonProbesetLocation" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11bf1b88d9e90711b4064497f611da4f +about: + description: This package was automatically created by package AnnotationForge version 1.7.17. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type HuEx build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-huexexonprobesetlocation", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 11bf1b88d9e90711b4064497f611da4f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type HuEx' - description: 'This package was automatically created by package AnnotationForge version 1.7.17. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-huexexonprobesetlocationhg18/meta.yaml b/recipes/bioconductor-huexexonprobesetlocationhg18/meta.yaml index eda440ed446a7..4844b257bd403 100644 --- a/recipes/bioconductor-huexexonprobesetlocationhg18/meta.yaml +++ b/recipes/bioconductor-huexexonprobesetlocationhg18/meta.yaml @@ -1,40 +1,40 @@ {% set version = "0.0.2" %} {% set name = "HuExExonProbesetLocationHg18" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bb00b7f5e4db2b04dca5951aa6bd073e +about: + description: This package was automatically created by package AnnotationDbi version 1.8.0. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible. Genome release hg18. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Exon-level probeset chromosome location for microarrays of type HuEx build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-huexexonprobesetlocationhg18", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bb00b7f5e4db2b04dca5951aa6bd073e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Exon-level probeset chromosome location for microarrays of type HuEx' - description: 'This package was automatically created by package AnnotationDbi version 1.8.0. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible. Genome release hg18.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-huexexonprobesetlocationhg19/meta.yaml b/recipes/bioconductor-huexexonprobesetlocationhg19/meta.yaml index e74f60f8e47af..02eeb5ec77038 100644 --- a/recipes/bioconductor-huexexonprobesetlocationhg19/meta.yaml +++ b/recipes/bioconductor-huexexonprobesetlocationhg19/meta.yaml @@ -1,40 +1,40 @@ {% set version = "0.0.3" %} {% set name = "HuExExonProbesetLocationHg19" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a3843c95c82dc71a043d902961ba33a +about: + description: This package was automatically created by package AnnotationDbi version 1.11.8. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible. Genome release hg19. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Exon-level probeset chromosome location for microarrays of type HuEx build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-huexexonprobesetlocationhg19", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1a3843c95c82dc71a043d902961ba33a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Exon-level probeset chromosome location for microarrays of type HuEx' - description: 'This package was automatically created by package AnnotationDbi version 1.11.8. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible. Genome release hg19.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hugene.1.0.st.v1frmavecs/meta.yaml b/recipes/bioconductor-hugene.1.0.st.v1frmavecs/meta.yaml index f4e9cd4365fe4..9342b21645d11 100644 --- a/recipes/bioconductor-hugene.1.0.st.v1frmavecs/meta.yaml +++ b/recipes/bioconductor-hugene.1.0.st.v1frmavecs/meta.yaml @@ -1,38 +1,38 @@ {% set version = "1.1.0" %} {% set name = "hugene.1.0.st.v1frmavecs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 711a69e6fa6dd3737a90615222416dfc +about: + description: This package was created by frmaTools version 1.13.0. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Vectors used by frma for microarrays of type hugene.1.0.st.v1frmavecs build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hugene.1.0.st.v1frmavecs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 711a69e6fa6dd3737a90615222416dfc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Vectors used by frma for microarrays of type hugene.1.0.st.v1frmavecs' - description: 'This package was created by frmaTools version 1.13.0.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hugene10stprobeset.db/meta.yaml b/recipes/bioconductor-hugene10stprobeset.db/meta.yaml index f70af17a40af8..83f3f73f233c1 100644 --- a/recipes/bioconductor-hugene10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-hugene10stprobeset.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "hugene10stprobeset.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0a4a87d64564cbec1e4bb1f9e5a67add +about: + description: Affymetrix hugene10 annotation data (chip hugene10stprobeset) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix hugene10 annotation data (chip hugene10stprobeset) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hugene10stprobeset.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0a4a87d64564cbec1e4bb1f9e5a67add + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix hugene10 annotation data (chip hugene10stprobeset)' - description: 'Affymetrix hugene10 annotation data (chip hugene10stprobeset) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hugene10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene10sttranscriptcluster.db/meta.yaml index b7a09239b1a3a..7e37b70b2aee0 100644 --- a/recipes/bioconductor-hugene10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hugene10sttranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "hugene10sttranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a32fb5729d37e96f157b0a1085dff43e +about: + description: Affymetrix hugene10 annotation data (chip hugene10sttranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix hugene10 annotation data (chip hugene10sttranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hugene10sttranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a32fb5729d37e96f157b0a1085dff43e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix hugene10 annotation data (chip hugene10sttranscriptcluster)' - description: 'Affymetrix hugene10 annotation data (chip hugene10sttranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hugene10stv1cdf/meta.yaml b/recipes/bioconductor-hugene10stv1cdf/meta.yaml index bb829c36e72d1..65a7fd4af98b1 100644 --- a/recipes/bioconductor-hugene10stv1cdf/meta.yaml +++ b/recipes/bioconductor-hugene10stv1cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hugene10stv1cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f1fb1c7076ac40b9e709f18e645d6181 +about: + description: A package containing an environment representing the HuGene-1_0-st-v1.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: hugene10stv1cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hugene10stv1cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f1fb1c7076ac40b9e709f18e645d6181 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: hugene10stv1cdf - description: 'A package containing an environment representing the HuGene-1_0-st-v1.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hugene10stv1probe/meta.yaml b/recipes/bioconductor-hugene10stv1probe/meta.yaml index 8f44196d5f02b..f632c4c9f0579 100644 --- a/recipes/bioconductor-hugene10stv1probe/meta.yaml +++ b/recipes/bioconductor-hugene10stv1probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "hugene10stv1probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6ed3c17dd026acf008658a5994044c62 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HuGene-1\_0-st-v1\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type hugene10stv1 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hugene10stv1probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6ed3c17dd026acf008658a5994044c62 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type hugene10stv1' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HuGene-1\_0-st-v1\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hugene11stprobeset.db/meta.yaml b/recipes/bioconductor-hugene11stprobeset.db/meta.yaml index a66804c1c2f9b..2ff4c23014898 100644 --- a/recipes/bioconductor-hugene11stprobeset.db/meta.yaml +++ b/recipes/bioconductor-hugene11stprobeset.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "hugene11stprobeset.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4d22ec32dedd6c8603d5f545faeb4ba4 +about: + description: Affymetrix hugene11 annotation data (chip hugene11stprobeset) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix hugene11 annotation data (chip hugene11stprobeset) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hugene11stprobeset.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4d22ec32dedd6c8603d5f545faeb4ba4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix hugene11 annotation data (chip hugene11stprobeset)' - description: 'Affymetrix hugene11 annotation data (chip hugene11stprobeset) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hugene11sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene11sttranscriptcluster.db/meta.yaml index ea292b35aa0c2..38c48cf20f263 100644 --- a/recipes/bioconductor-hugene11sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hugene11sttranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "hugene11sttranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7fed70c4bd904655459a41b5667f7c23 +about: + description: Affymetrix hugene11 annotation data (chip hugene11sttranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix hugene11 annotation data (chip hugene11sttranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hugene11sttranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7fed70c4bd904655459a41b5667f7c23 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix hugene11 annotation data (chip hugene11sttranscriptcluster)' - description: 'Affymetrix hugene11 annotation data (chip hugene11sttranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hugene20stprobeset.db/meta.yaml b/recipes/bioconductor-hugene20stprobeset.db/meta.yaml index 8a24073d3fade..0c7a2490cd058 100644 --- a/recipes/bioconductor-hugene20stprobeset.db/meta.yaml +++ b/recipes/bioconductor-hugene20stprobeset.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "hugene20stprobeset.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bf7909fc41a80da59099327a6d9abb57 +about: + description: Affymetrix hugene20 annotation data (chip hugene20stprobeset) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix hugene20 annotation data (chip hugene20stprobeset) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hugene20stprobeset.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bf7909fc41a80da59099327a6d9abb57 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix hugene20 annotation data (chip hugene20stprobeset)' - description: 'Affymetrix hugene20 annotation data (chip hugene20stprobeset) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hugene20sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene20sttranscriptcluster.db/meta.yaml index 761de8398ee20..62b0033139e8e 100644 --- a/recipes/bioconductor-hugene20sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hugene20sttranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "hugene20sttranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0b929a3a959662e8a7265f58b81b4e35 +about: + description: Affymetrix hugene20 annotation data (chip hugene20sttranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix hugene20 annotation data (chip hugene20sttranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hugene20sttranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0b929a3a959662e8a7265f58b81b4e35 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix hugene20 annotation data (chip hugene20sttranscriptcluster)' - description: 'Affymetrix hugene20 annotation data (chip hugene20sttranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hugene21stprobeset.db/meta.yaml b/recipes/bioconductor-hugene21stprobeset.db/meta.yaml index e76e57e758538..b72ceb42c23b4 100644 --- a/recipes/bioconductor-hugene21stprobeset.db/meta.yaml +++ b/recipes/bioconductor-hugene21stprobeset.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "hugene21stprobeset.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2b816dca48d0b2e1a946469b8d85d257 +about: + description: Affymetrix hugene21 annotation data (chip hugene21stprobeset) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix hugene21 annotation data (chip hugene21stprobeset) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hugene21stprobeset.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2b816dca48d0b2e1a946469b8d85d257 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix hugene21 annotation data (chip hugene21stprobeset)' - description: 'Affymetrix hugene21 annotation data (chip hugene21stprobeset) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hugene21sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene21sttranscriptcluster.db/meta.yaml index e6f8ab5591590..644ed848ecb76 100644 --- a/recipes/bioconductor-hugene21sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-hugene21sttranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "hugene21sttranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ca90de6093bbad760abfcf0cfeada830 +about: + description: Affymetrix hugene21 annotation data (chip hugene21sttranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix hugene21 annotation data (chip hugene21sttranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hugene21sttranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ca90de6093bbad760abfcf0cfeada830 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix hugene21 annotation data (chip hugene21sttranscriptcluster)' - description: 'Affymetrix hugene21 annotation data (chip hugene21sttranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-human.db0/meta.yaml b/recipes/bioconductor-human.db0/meta.yaml index 4e65c14b082c3..a9d3ed1343b3e 100644 --- a/recipes/bioconductor-human.db0/meta.yaml +++ b/recipes/bioconductor-human.db0/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "human.db0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e3b04d46f0618785b37fb84bb899295e +about: + description: Base annotation databases for human, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Level Annotation databases for human build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-human.db0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1e484144eaebbc7b654640a105c8dea4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Level Annotation databases for human' - description: 'Base annotation databases for human, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-human.db0/post-link.sh b/recipes/bioconductor-human.db0/post-link.sh index ec096e9328845..2002b3414b3d3 100644 --- a/recipes/bioconductor-human.db0/post-link.sh +++ b/recipes/bioconductor-human.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "human.db0-3.18.0" +installBiocDataPackage.sh "human.db0-3.20.0" diff --git a/recipes/bioconductor-human1mduov3bcrlmm/meta.yaml b/recipes/bioconductor-human1mduov3bcrlmm/meta.yaml index d5179e02efca6..2fa6f892b27ee 100644 --- a/recipes/bioconductor-human1mduov3bcrlmm/meta.yaml +++ b/recipes/bioconductor-human1mduov3bcrlmm/meta.yaml @@ -1,37 +1,37 @@ {% set version = "1.0.4" %} {% set name = "human1mduov3bCrlmm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ff9f1e8bcc6348d6777bbb982ae0325 +about: + description: Package with metadata for genotyping Illumina 1M Duo arrays using the 'crlmm' package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Metadata for fast genotyping with the 'crlmm' package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-human1mduov3bcrlmm", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0ff9f1e8bcc6348d6777bbb982ae0325 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Metadata for fast genotyping with the ''crlmm'' package' - description: 'Package with metadata for genotyping Illumina 1M Duo arrays using the ''crlmm'' package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-human1mv1ccrlmm/meta.yaml b/recipes/bioconductor-human1mv1ccrlmm/meta.yaml index 31b085def1cd8..74ee285789833 100644 --- a/recipes/bioconductor-human1mv1ccrlmm/meta.yaml +++ b/recipes/bioconductor-human1mv1ccrlmm/meta.yaml @@ -1,37 +1,37 @@ {% set version = "1.0.3" %} {% set name = "human1mv1cCrlmm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b9f638c7b0ede50cb070f1bae85eb4dc +about: + description: Package with metadata fast genotyping Illumina 1M arrays using the 'crlmm' package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Metadata for fast genotyping with the 'crlmm' package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-human1mv1ccrlmm", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b9f638c7b0ede50cb070f1bae85eb4dc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Metadata for fast genotyping with the ''crlmm'' package' - description: 'Package with metadata fast genotyping Illumina 1M arrays using the ''crlmm'' package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-human370quadv3ccrlmm/meta.yaml b/recipes/bioconductor-human370quadv3ccrlmm/meta.yaml index 6d828cffe3c89..c3b58132071fb 100644 --- a/recipes/bioconductor-human370quadv3ccrlmm/meta.yaml +++ b/recipes/bioconductor-human370quadv3ccrlmm/meta.yaml @@ -1,37 +1,37 @@ {% set version = "1.0.3" %} {% set name = "human370quadv3cCrlmm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 33c3ccc3793ed95647418b746a5177f9 +about: + description: Package with metadata for genotyping Illumina 370kQuad arrays using the 'crlmm' package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Metadata for fast genotyping with the 'crlmm' package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-human370quadv3ccrlmm", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 33c3ccc3793ed95647418b746a5177f9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Metadata for fast genotyping with the ''crlmm'' package' - description: 'Package with metadata for genotyping Illumina 370kQuad arrays using the ''crlmm'' package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-human370v1ccrlmm/meta.yaml b/recipes/bioconductor-human370v1ccrlmm/meta.yaml index 36f4345a136f5..0e971089926eb 100644 --- a/recipes/bioconductor-human370v1ccrlmm/meta.yaml +++ b/recipes/bioconductor-human370v1ccrlmm/meta.yaml @@ -1,37 +1,37 @@ {% set version = "1.0.2" %} {% set name = "human370v1cCrlmm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ec4192f533faee2b14484de02548075 +about: + description: Package with metadata for genotyping Illumina 370k arrays using the 'crlmm' package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Metadata for fast genotyping with the 'crlmm' package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-human370v1ccrlmm", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9ec4192f533faee2b14484de02548075 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Metadata for fast genotyping with the ''crlmm'' package' - description: 'Package with metadata for genotyping Illumina 370k arrays using the ''crlmm'' package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-human550v3bcrlmm/meta.yaml b/recipes/bioconductor-human550v3bcrlmm/meta.yaml index 7c0d212370923..02fd0ad11e276 100644 --- a/recipes/bioconductor-human550v3bcrlmm/meta.yaml +++ b/recipes/bioconductor-human550v3bcrlmm/meta.yaml @@ -1,37 +1,37 @@ {% set version = "1.0.4" %} {% set name = "human550v3bCrlmm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20e6b008fab5e1084354c87ad50d18a8 +about: + description: Package with metadata for genotyping Illumina 550k arrays using the 'crlmm' package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Metadata for fast genotyping with the 'crlmm' package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-human550v3bcrlmm", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 20e6b008fab5e1084354c87ad50d18a8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Metadata for fast genotyping with the ''crlmm'' package' - description: 'Package with metadata for genotyping Illumina 550k arrays using the ''crlmm'' package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-human610quadv1bcrlmm/meta.yaml b/recipes/bioconductor-human610quadv1bcrlmm/meta.yaml index 9c38228c1a8c5..b729ffdbe32e9 100644 --- a/recipes/bioconductor-human610quadv1bcrlmm/meta.yaml +++ b/recipes/bioconductor-human610quadv1bcrlmm/meta.yaml @@ -1,37 +1,37 @@ {% set version = "1.0.3" %} {% set name = "human610quadv1bCrlmm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 609cf09410774e084ee6a3286652bb1a +about: + description: Package with metadata for genotyping Illumina 610kQuad arrays using the 'crlmm' package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Metadata for fast genotyping with the 'crlmm' package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-human610quadv1bcrlmm", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 609cf09410774e084ee6a3286652bb1a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Metadata for fast genotyping with the ''crlmm'' package' - description: 'Package with metadata for genotyping Illumina 610kQuad arrays using the ''crlmm'' package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-human650v3acrlmm/meta.yaml b/recipes/bioconductor-human650v3acrlmm/meta.yaml index 9808f0f0abf83..6c6368006631c 100644 --- a/recipes/bioconductor-human650v3acrlmm/meta.yaml +++ b/recipes/bioconductor-human650v3acrlmm/meta.yaml @@ -1,37 +1,37 @@ {% set version = "1.0.3" %} {% set name = "human650v3aCrlmm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4b0de367ccc0f7499dcffe21ef1893c2 +about: + description: Package with metadata for genotyping Illumina 650k arrays using the 'crlmm' package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Metadata for fast genotyping with the 'crlmm' package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-human650v3acrlmm", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4b0de367ccc0f7499dcffe21ef1893c2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Metadata for fast genotyping with the ''crlmm'' package' - description: 'Package with metadata for genotyping Illumina 650k arrays using the ''crlmm'' package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-human660quadv1acrlmm/meta.yaml b/recipes/bioconductor-human660quadv1acrlmm/meta.yaml index fd3e90ca86186..36bb5645ea66a 100644 --- a/recipes/bioconductor-human660quadv1acrlmm/meta.yaml +++ b/recipes/bioconductor-human660quadv1acrlmm/meta.yaml @@ -1,37 +1,37 @@ {% set version = "1.0.3" %} {% set name = "human660quadv1aCrlmm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5fd2d94a462e150c888f13c5c0975c36 +about: + description: Package with metadata for genotyping Illumina 660kQuad arrays using the 'crlmm' package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Metadata for fast genotyping with the 'crlmm' package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-human660quadv1acrlmm", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5fd2d94a462e150c888f13c5c0975c36 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Metadata for fast genotyping with the ''crlmm'' package' - description: 'Package with metadata for genotyping Illumina 660kQuad arrays using the ''crlmm'' package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-humanaffydata/meta.yaml b/recipes/bioconductor-humanaffydata/meta.yaml index c746ebbe83689..95564fd70d17f 100644 --- a/recipes/bioconductor-humanaffydata/meta.yaml +++ b/recipes/bioconductor-humanaffydata/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "HumanAffyData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11341e772169b7141b9bd22161e14417 +about: + description: Re-analysis of human gene expression data generated on the Affymetrix HG U133PlusV2 (EH176) and Affymetrix HG U133A (EH177) platforms. The original data were normalized using robust multiarray averaging (RMA) to obtain an integrated gene expression atlas across diverse biological sample types and conditions. The entire compendia comprisee 9395 arrays for EH176 and 5372 arrays for EH177. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: GEO accession GSE64985 and ArrayExpress accession E-MTAB-62 as ExpressionSet objects build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-humanaffydata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: abaf3ed8ff9db09d86de2a6f5f364e54 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'GEO accession GSE64985 and ArrayExpress accession E-MTAB-62 as ExpressionSet objects' - description: 'Re-analysis of human gene expression data generated on the Affymetrix HG U133PlusV2 (EH176) and Affymetrix HG U133A (EH177) platforms. The original data were normalized using robust multiarray averaging (RMA) to obtain an integrated gene expression atlas across diverse biological sample types and conditions. The entire compendia comprisee 9395 arrays for EH176 and 5372 arrays for EH177.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-humanaffydata/post-link.sh b/recipes/bioconductor-humanaffydata/post-link.sh index 596705396fd7e..31b8e5f6152d8 100644 --- a/recipes/bioconductor-humanaffydata/post-link.sh +++ b/recipes/bioconductor-humanaffydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "humanaffydata-1.28.0" +installBiocDataPackage.sh "humanaffydata-1.32.0" diff --git a/recipes/bioconductor-humanchrloc/meta.yaml b/recipes/bioconductor-humanchrloc/meta.yaml index e535202d4443c..e0f3fb8238139 100644 --- a/recipes/bioconductor-humanchrloc/meta.yaml +++ b/recipes/bioconductor-humanchrloc/meta.yaml @@ -1,37 +1,37 @@ {% set version = "2.1.6" %} {% set name = "humanCHRLOC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 113450c0822000c9b4e8a0141cf4b819 +about: + description: Annotation data file for humanCHRLOC assembled using data from public data repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: The Artistic License, Version 2.0 + summary: A data package containing annotation data for humanCHRLOC build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-humanchrloc", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 113450c0822000c9b4e8a0141cf4b819 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'The Artistic License, Version 2.0' - summary: 'A data package containing annotation data for humanCHRLOC' - description: 'Annotation data file for humanCHRLOC assembled using data from public data repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-humancytosnp12v2p1hcrlmm/meta.yaml b/recipes/bioconductor-humancytosnp12v2p1hcrlmm/meta.yaml index 00664a6615e8e..ccde993e18659 100644 --- a/recipes/bioconductor-humancytosnp12v2p1hcrlmm/meta.yaml +++ b/recipes/bioconductor-humancytosnp12v2p1hcrlmm/meta.yaml @@ -1,37 +1,37 @@ {% set version = "1.0.1" %} {% set name = "humancytosnp12v2p1hCrlmm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: edf80245ddb28afb9fbaa6668187bf3a +about: + description: Package with metadata for genotyping Illumina CytoSNP 12 arrays using the 'crlmm' package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Metadata for fast genotyping with the 'crlmm' package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-humancytosnp12v2p1hcrlmm", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: edf80245ddb28afb9fbaa6668187bf3a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Metadata for fast genotyping with the ''crlmm'' package' - description: 'Package with metadata for genotyping Illumina CytoSNP 12 arrays using the ''crlmm'' package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-humanomni1quadv1bcrlmm/meta.yaml b/recipes/bioconductor-humanomni1quadv1bcrlmm/meta.yaml index 7b086ab8634cb..d098732e31b62 100644 --- a/recipes/bioconductor-humanomni1quadv1bcrlmm/meta.yaml +++ b/recipes/bioconductor-humanomni1quadv1bcrlmm/meta.yaml @@ -1,37 +1,37 @@ {% set version = "1.0.3" %} {% set name = "humanomni1quadv1bCrlmm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e81b2603f37d4cda3f28cd69a7296a23 +about: + description: Package with metadata for genotyping Illumina Omni1 Quad arrays using the 'crlmm' package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Metadata for fast genotyping with the 'crlmm' package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-humanomni1quadv1bcrlmm", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e81b2603f37d4cda3f28cd69a7296a23 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Metadata for fast genotyping with the ''crlmm'' package' - description: 'Package with metadata for genotyping Illumina Omni1 Quad arrays using the ''crlmm'' package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-humanomni25quadv1bcrlmm/meta.yaml b/recipes/bioconductor-humanomni25quadv1bcrlmm/meta.yaml index ea1f4ab912275..4ea75a69bc14c 100644 --- a/recipes/bioconductor-humanomni25quadv1bcrlmm/meta.yaml +++ b/recipes/bioconductor-humanomni25quadv1bcrlmm/meta.yaml @@ -1,37 +1,37 @@ {% set version = "1.0.2" %} {% set name = "humanomni25quadv1bCrlmm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2ee1fa7bf712d7f81a167079c975d49f +about: + description: Package with metadata for genotyping Illumina Omni2.5 Quad arrays using the 'crlmm' package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Metadata for fast genotyping with the 'crlmm' package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-humanomni25quadv1bcrlmm", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2ee1fa7bf712d7f81a167079c975d49f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Metadata for fast genotyping with the ''crlmm'' package' - description: 'Package with metadata for genotyping Illumina Omni2.5 Quad arrays using the ''crlmm'' package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-humanomni5quadv1bcrlmm/meta.yaml b/recipes/bioconductor-humanomni5quadv1bcrlmm/meta.yaml index f90cbd61ccc35..4086da23e9ccd 100644 --- a/recipes/bioconductor-humanomni5quadv1bcrlmm/meta.yaml +++ b/recipes/bioconductor-humanomni5quadv1bcrlmm/meta.yaml @@ -1,37 +1,37 @@ {% set version = "1.0.0" %} {% set name = "humanomni5quadv1bCrlmm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ac4d6867c3d5590a6308d6edff0912b +about: + description: Package with metadata for genotyping Illumina Omni5 Quad arrays using the 'crlmm' package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Metadata for fast genotyping with the 'crlmm' package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-humanomni5quadv1bcrlmm", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3ac4d6867c3d5590a6308d6edff0912b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Metadata for fast genotyping with the ''crlmm'' package' - description: 'Package with metadata for genotyping Illumina Omni5 Quad arrays using the ''crlmm'' package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-humanomniexpress12v1bcrlmm/meta.yaml b/recipes/bioconductor-humanomniexpress12v1bcrlmm/meta.yaml index b15927786e117..18dcc512d580b 100644 --- a/recipes/bioconductor-humanomniexpress12v1bcrlmm/meta.yaml +++ b/recipes/bioconductor-humanomniexpress12v1bcrlmm/meta.yaml @@ -1,37 +1,37 @@ {% set version = "1.0.1" %} {% set name = "humanomniexpress12v1bCrlmm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: abdb730fc230db669e588e024ee7624b +about: + description: Package with metadata for genotyping Illumina Omni Express 12 arrays using the 'crlmm' package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Metadata for fast genotyping with the 'crlmm' package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-humanomniexpress12v1bcrlmm", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: abdb730fc230db669e588e024ee7624b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Metadata for fast genotyping with the ''crlmm'' package' - description: 'Package with metadata for genotyping Illumina Omni Express 12 arrays using the ''crlmm'' package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-humanstemcell/meta.yaml b/recipes/bioconductor-humanstemcell/meta.yaml index c0d2b5a0d197e..9cc513bcc5b81 100644 --- a/recipes/bioconductor-humanstemcell/meta.yaml +++ b/recipes/bioconductor-humanstemcell/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "0.42.0" %} +{% set version = "0.46.0" %} {% set name = "humanStemCell" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: be6367d8fa19187d644247ed8795eb0e +about: + description: 'Affymetrix time course experiment on human stem cells (two time points: undifferentiated and differentiated).' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Human Stem Cells time course experiment build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-humanstemcell", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-hgu133plus2.db >=3.13.0,<3.14.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-hgu133plus2.db >=3.13.0,<3.14.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4531bfaff7e8e167ce039037db799cd6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Human Stem Cells time course experiment' - description: 'Affymetrix time course experiment on human stem cells (two time points: undifferentiated and differentiated).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-humanstemcell/post-link.sh b/recipes/bioconductor-humanstemcell/post-link.sh index 959dc8dc69bda..a6d12f5287464 100644 --- a/recipes/bioconductor-humanstemcell/post-link.sh +++ b/recipes/bioconductor-humanstemcell/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "humanstemcell-0.42.0" +installBiocDataPackage.sh "humanstemcell-0.46.0" diff --git a/recipes/bioconductor-hummingbird/meta.yaml b/recipes/bioconductor-hummingbird/meta.yaml index 506999c697083..8578ec2ef98b1 100644 --- a/recipes/bioconductor-hummingbird/meta.yaml +++ b/recipes/bioconductor-hummingbird/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "hummingbird" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package for detecting differential methylation. It exploits a Bayesian hidden Markov model that incorporates location dependence among genomic loci, unlike most existing methods that assume independence among observations. Bayesian priors are applied to permit information sharing across an entire chromosome for improved power of detection. The direct output of our software package is the best sequence of methylation states, eliminating the use of a subjective, and most of the time an arbitrary, threshold of p-value for determining significance. At last, our methodology does not require replication in either or both of the two comparison groups. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Bayesian Hidden Markov Model for the detection of differentially methylated regions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3f2788dadae0f811072b04866fc9e5ed build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hummingbird", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: bf02b3569b0ee7a436ad13d0489dde96 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Bayesian Hidden Markov Model for the detection of differentially methylated regions' - description: 'A package for detecting differential methylation. It exploits a Bayesian hidden Markov model that incorporates location dependence among genomic loci, unlike most existing methods that assume independence among observations. Bayesian priors are applied to permit information sharing across an entire chromosome for improved power of detection. The direct output of our software package is the best sequence of methylation states, eliminating the use of a subjective, and most of the time an arbitrary, threshold of p-value for determining significance. At last, our methodology does not require replication in either or both of the two comparison groups.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-huo22.db/meta.yaml b/recipes/bioconductor-huo22.db/meta.yaml index b0ae8869cbd58..746864552a2cc 100644 --- a/recipes/bioconductor-huo22.db/meta.yaml +++ b/recipes/bioconductor-huo22.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "HuO22.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ddabf6c01f94c1dfd6ab35b40852828a +about: + description: FHCRC Genomics Shared Resource HuO22 Annotation Data (HuO22) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: FHCRC Genomics Shared Resource HuO22 Annotation Data (HuO22) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-huo22.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ddabf6c01f94c1dfd6ab35b40852828a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'FHCRC Genomics Shared Resource HuO22 Annotation Data (HuO22)' - description: 'FHCRC Genomics Shared Resource HuO22 Annotation Data (HuO22) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hwgcod.db/meta.yaml b/recipes/bioconductor-hwgcod.db/meta.yaml index dfb997797f058..fe2b83ca8c33c 100644 --- a/recipes/bioconductor-hwgcod.db/meta.yaml +++ b/recipes/bioconductor-hwgcod.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.4.0" %} {% set name = "hwgcod.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a46bf1a242853bbab26351a11b18030a +about: + description: Codelink Human Whole Genome Bioarray (~55 000 human genes) annotation data (chip hwgcod) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Codelink Human Whole Genome Bioarray (~55 000 human genes) annotation data (chip hwgcod) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hwgcod.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a46bf1a242853bbab26351a11b18030a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Codelink Human Whole Genome Bioarray (~55 000 human genes) annotation data (chip hwgcod)' - description: 'Codelink Human Whole Genome Bioarray (~55 000 human genes) annotation data (chip hwgcod) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hybridexpress/build.sh b/recipes/bioconductor-hybridexpress/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hybridexpress/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hybridexpress/meta.yaml b/recipes/bioconductor-hybridexpress/meta.yaml new file mode 100644 index 0000000000000..3669f2c763b4c --- /dev/null +++ b/recipes/bioconductor-hybridexpress/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.2.0" %} +{% set name = "HybridExpress" %} +{% set bioc = "3.20" %} + +about: + description: HybridExpress can be used to perform comparative transcriptomics analysis of hybrids (or allopolyploids) relative to their progenitor species. The package features functions to perform exploratory analyses of sample grouping, identify differentially expressed genes in hybrids relative to their progenitors, classify genes in expression categories (N = 12) and classes (N = 5), and perform functional analyses. We also provide users with graphical functions for the seamless creation of publication-ready figures that are commonly used in the literature. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Comparative analysis of RNA-seq data for hybrids and their progenitors + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-hybridexpress", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-ggplot2 + - r-patchwork + - r-rcolorbrewer + - r-rlang + run: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-ggplot2 + - r-patchwork + - r-rcolorbrewer + - r-rlang + +source: + md5: 358b7186b8e1d4ba19006e34bfa81a2e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-hybridmtest/meta.yaml b/recipes/bioconductor-hybridmtest/meta.yaml index 009114237f60b..bb38b2037ea92 100644 --- a/recipes/bioconductor-hybridmtest/meta.yaml +++ b/recipes/bioconductor-hybridmtest/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "HybridMTest" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Performs hybrid multiple testing that incorporates method selection and assumption evaluations into the analysis using empirical Bayes probability (EBP) estimates obtained by Grenander density estimation. For instance, for 3-group comparison analysis, Hybrid Multiple testing considers EBPs as weighted EBPs between F-test and H-test with EBPs from Shapiro Wilk test of normality as weigth. Instead of just using EBPs from F-test only or using H-test only, this methodology combines both types of EBPs through EBPs from Shapiro Wilk test of normality. This methodology uses then the law of total EBPs. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL Version 2 or later + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Hybrid Multiple Testing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a2b1764b0e458f82e6055a3ebdf90933 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hybridmtest", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:hybridmtest + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-hybridmtest + path: recipes/bioconductor-hybridmtest + version: 1.24.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-fdrtool - r-mass - r-survival run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-fdrtool - r-mass - r-survival + +source: + md5: 489ba94cda0e85739b28525b73ef2520 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL Version 2 or later' - summary: 'Hybrid Multiple Testing' - description: 'Performs hybrid multiple testing that incorporates method selection and assumption evaluations into the analysis using empirical Bayes probability (EBP) estimates obtained by Grenander density estimation. For instance, for 3-group comparison analysis, Hybrid Multiple testing considers EBPs as weighted EBPs between F-test and H-test with EBPs from Shapiro Wilk test of normality as weigth. Instead of just using EBPs from F-test only or using H-test only, this methodology combines both types of EBPs through EBPs from Shapiro Wilk test of normality. This methodology uses then the law of total EBPs.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:hybridmtest - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-hybridmtest - path: recipes/bioconductor-hybridmtest - version: 1.24.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hyper/meta.yaml b/recipes/bioconductor-hyper/meta.yaml index 99a5d17a40f21..46de2609e59fa 100644 --- a/recipes/bioconductor-hyper/meta.yaml +++ b/recipes/bioconductor-hyper/meta.yaml @@ -1,28 +1,31 @@ -{% set version = "2.0.0" %} +{% set version = "2.4.0" %} {% set name = "hypeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An R Package for Geneset Enrichment Workflows. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: An R Package For Geneset Enrichment Workflows -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d2de417437ab81645e7d4702021f349f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hyper", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: tidyverse, devtools, testthat, knitr requirements: + host: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 - r-base - r-dplyr - r-ggforce @@ -44,8 +47,9 @@ requirements: - r-shiny - r-stringr - r-visnetwork + run: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 - r-base - r-dplyr - r-ggforce @@ -67,13 +71,16 @@ requirements: - r-shiny - r-stringr - r-visnetwork + +source: + md5: 1f821fa3ca250670831f6b5cab2a07ca + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'An R Package For Geneset Enrichment Workflows' - description: 'An R Package for Geneset Enrichment Workflows.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hyperdraw/meta.yaml b/recipes/bioconductor-hyperdraw/meta.yaml index 85de9545d1190..fa5e24bdd17db 100644 --- a/recipes/bioconductor-hyperdraw/meta.yaml +++ b/recipes/bioconductor-hyperdraw/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "1.54.0" %} +{% set version = "1.58.0" %} {% set name = "hyperdraw" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions for visualizing hypergraphs. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Visualizing Hypergaphs -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2b1ec2cf9ea920a241f821baa08bb393 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hyperdraw", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:hyperdraw + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-hyperdraw + path: recipes/bioconductor-hyperdraw + version: 1.32.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # SystemRequirements: graphviz requirements: host: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-hypergraph >=1.74.0,<1.75.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-hypergraph >=1.78.0,<1.79.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - graphviz run: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-hypergraph >=1.74.0,<1.75.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-hypergraph >=1.78.0,<1.79.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - graphviz + +source: + md5: abab7727a13aa50695376ac33b4ae504 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Visualizing Hypergaphs' - description: 'Functions for visualizing hypergraphs.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:hyperdraw - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-hyperdraw - path: recipes/bioconductor-hyperdraw - version: 1.32.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-hypergraph/meta.yaml b/recipes/bioconductor-hypergraph/meta.yaml index b46a9d8bbdee9..bf283221a5eaa 100644 --- a/recipes/bioconductor-hypergraph/meta.yaml +++ b/recipes/bioconductor-hypergraph/meta.yaml @@ -1,40 +1,21 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "hypergraph" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package that implements some simple capabilities for representing and manipulating hypergraphs. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: A package providing hypergraph data structures -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e97653a8503ba0bcb6da1dbdf1a3552b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-hypergraph", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocGenerics, RUnit -requirements: - host: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - r-base - run: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A package providing hypergraph data structures' - description: 'A package that implements some simple capabilities for representing and manipulating hypergraphs.' + extra: identifiers: - biotools:hypergraph @@ -44,3 +25,28 @@ extra: path: recipes/bioconductor-hypergraph version: 1.52.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocGenerics, RUnit +requirements: + host: + - bioconductor-graph >=1.84.0,<1.85.0 + - r-base + run: + - bioconductor-graph >=1.84.0,<1.85.0 + - r-base + +source: + md5: 664ea291a51db1bed4d8433759c6a43a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-iaseq/meta.yaml b/recipes/bioconductor-iaseq/meta.yaml index 45a697e239e4e..eb881b506c0b8 100644 --- a/recipes/bioconductor-iaseq/meta.yaml +++ b/recipes/bioconductor-iaseq/meta.yaml @@ -1,38 +1,20 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "iASeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3086632b16254c5b1f22c4f376bd43a7 +about: + description: It fits correlation motif model to multiple RNAseq or ChIPseq studies to improve detection of allele-specific events and describe correlation patterns across studies. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'iASeq: integrating multiple sequencing datasets for detecting allele-specific events' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-iaseq", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'iASeq: integrating multiple sequencing datasets for detecting allele-specific events' - description: 'It fits correlation motif model to multiple RNAseq or ChIPseq studies to improve detection of allele-specific events and describe correlation patterns across studies.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' extra: identifiers: - biotools:iaseq @@ -41,4 +23,22 @@ extra: name: bioconductor-iaseq path: recipes/bioconductor-iaseq version: 1.26.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +requirements: + host: + - r-base + run: + - r-base +source: + md5: d34b9d842ac1e44587242916ab97db12 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-iasva/meta.yaml b/recipes/bioconductor-iasva/meta.yaml index 500fa9d1f76ca..d7cc5e6eb6267 100644 --- a/recipes/bioconductor-iasva/meta.yaml +++ b/recipes/bioconductor-iasva/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "iasva" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a52a31d7564e175a288943ae77b22a93 +about: + description: Iteratively Adjusted Surrogate Variable Analysis (IA-SVA) is a statistical framework to uncover hidden sources of variation even when these sources are correlated. IA-SVA provides a flexible methodology to i) identify a hidden factor for unwanted heterogeneity while adjusting for all known factors; ii) test the significance of the putative hidden factor for explaining the unmodeled variation in the data; and iii), if significant, use the estimated factor as an additional known factor in the next iteration to uncover further hidden factors. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Iteratively Adjusted Surrogate Variable Analysis build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-iasva", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, testthat, rmarkdown, sva, Rtsne, pheatmap, corrplot, DescTools, RColorBrewer requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-irlba run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-irlba +source: + md5: da507e8b7a5bcc1915ecfd09fd77161b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Iteratively Adjusted Surrogate Variable Analysis' - description: 'Iteratively Adjusted Surrogate Variable Analysis (IA-SVA) is a statistical framework to uncover hidden sources of variation even when these sources are correlated. IA-SVA provides a flexible methodology to i) identify a hidden factor for unwanted heterogeneity while adjusting for all known factors; ii) test the significance of the putative hidden factor for explaining the unmodeled variation in the data; and iii), if significant, use the estimated factor as an additional known factor in the next iteration to uncover further hidden factors.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ibbig/meta.yaml b/recipes/bioconductor-ibbig/meta.yaml index 3ed3cdcd3bd2e..cbd580daca9d0 100644 --- a/recipes/bioconductor-ibbig/meta.yaml +++ b/recipes/bioconductor-ibbig/meta.yaml @@ -1,25 +1,29 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "iBBiG" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: iBBiG is a bi-clustering algorithm which is optimizes for binary data analysis. We apply it to meta-gene set analysis of large numbers of gene expression datasets. The iterative algorithm extracts groups of phenotypes from multiple studies that are associated with similar gene sets. iBBiG does not require prior knowledge of the number or scale of clusters and allows discovery of clusters with diverse sizes + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Iterative Binary Biclustering of Genesets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6114f0b7d488fd60923a6607bf2d59f2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ibbig", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: methods requirements: + build: + - {{ compiler('c') }} + - make host: - r-ade4 - r-base @@ -32,15 +36,16 @@ requirements: - r-base - r-biclust - r-xtable - build: - - {{ compiler('c') }} - - make + +source: + md5: fabeab25598836dca5bfba9401c1aa32 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Iterative Binary Biclustering of Genesets' - description: 'iBBiG is a bi-clustering algorithm which is optimizes for binary data analysis. We apply it to meta-gene set analysis of large numbers of gene expression datasets. The iterative algorithm extracts groups of phenotypes from multiple studies that are associated with similar gene sets. iBBiG does not require prior knowledge of the number or scale of clusters and allows discovery of clusters with diverse sizes' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ibh/meta.yaml b/recipes/bioconductor-ibh/meta.yaml index 9af60c615d1d4..bea18dedb5397 100644 --- a/recipes/bioconductor-ibh/meta.yaml +++ b/recipes/bioconductor-ibh/meta.yaml @@ -1,41 +1,22 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "ibh" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains methods for calculating Interaction Based Homogeneity to evaluate fitness of gene lists to an interaction network which is useful for evaluation of clustering results and gene list analysis. BioGRID interactions are used in the calculation. The user can also provide their own interactions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Interaction Based Homogeneity for Evaluating Gene Lists -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3c87bb1083990548eb09c4e43459ba1f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ibh", max_pin="x.x") }}' - noarch: generic -# Suggests: yeastCC, stats -requirements: - host: - - 'bioconductor-simpintlists >=1.38.0,<1.39.0' - - r-base - run: - - 'bioconductor-simpintlists >=1.38.0,<1.39.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Interaction Based Homogeneity for Evaluating Gene Lists' - description: 'This package contains methods for calculating Interaction Based Homogeneity to evaluate fitness of gene lists to an interaction network which is useful for evaluation of clustering results and gene list analysis. BioGRID interactions are used in the calculation. The user can also provide their own interactions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:ibh @@ -45,3 +26,28 @@ extra: path: recipes/bioconductor-ibh version: 1.28.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: yeastCC, stats +requirements: + host: + - bioconductor-simpintlists >=1.42.0,<1.43.0 + - r-base + run: + - bioconductor-simpintlists >=1.42.0,<1.43.0 + - r-base + +source: + md5: c028c9f17de8180f8724f8e3b252911d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-ibmq/meta.yaml b/recipes/bioconductor-ibmq/meta.yaml index e1827d8126305..6b628b979070c 100644 --- a/recipes/bioconductor-ibmq/meta.yaml +++ b/recipes/bioconductor-ibmq/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "iBMQ" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: integrated Bayesian Modeling of eQTL data + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: integrated Bayesian Modeling of eQTL data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9737c0aee38670491b2f29f73dcb743c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ibmq", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:ibmq + - usegalaxy-eu:ibmq + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # SystemRequirements: GSL and OpenMP requirements: + build: + - {{ compiler('c') }} + - automake + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - - 'r-ggplot2 >=0.9.2' + - r-ggplot2 >=0.9.2 - libblas - liblapack - gsl run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - - 'r-ggplot2 >=0.9.2' + - r-ggplot2 >=0.9.2 - gsl - build: - - {{ compiler('c') }} - - automake - - make + +source: + md5: 5c74bb448bbe373bb37798c411de7037 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'integrated Bayesian Modeling of eQTL data' - description: 'integrated Bayesian Modeling of eQTL data' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} - - usegalaxy-eu:{{ name|lower }} diff --git a/recipes/bioconductor-icare/meta.yaml b/recipes/bioconductor-icare/meta.yaml index aded7a26c7465..9de5fa737ec52 100644 --- a/recipes/bioconductor-icare/meta.yaml +++ b/recipes/bioconductor-icare/meta.yaml @@ -1,25 +1,36 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "iCARE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An R package to build, validate and apply absolute risk models + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Individualized Coherent Absolute Risk Estimation (iCARE) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9230befcb5d16fdc72a6f87b50397789 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-icare", max_pin="x.x") }}' + +extra: + parent_recipe: + name: bioconductor-icare + path: recipes/bioconductor-icare + version: 1.10.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - r-gtools @@ -32,21 +43,16 @@ requirements: - r-gtools - r-hmisc - r-plotrix - build: - - {{ compiler('c') }} - - make + +source: + md5: 9d8145140886876660aeaa921fd14a47 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)' - description: 'An R package to compute Individualized Coherent Absolute Risk Estimators.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-icare - path: recipes/bioconductor-icare - version: 1.10.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-icens/meta.yaml b/recipes/bioconductor-icens/meta.yaml index ee1fb6954e914..3a73632c2c733 100644 --- a/recipes/bioconductor-icens/meta.yaml +++ b/recipes/bioconductor-icens/meta.yaml @@ -1,24 +1,34 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "Icens" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Many functions for computing the NPMLE for censored and truncated data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: NPMLE for Censored and Truncated Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 07481f23c5b4fdfe9ff465e5a57e33c2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-icens", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:icens + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-icens + path: recipes/bioconductor-icens + version: 1.52.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -26,20 +36,16 @@ requirements: run: - r-base - r-survival + +source: + md5: a9c2a7c2a240d00ef9baa1100daabf5c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'NPMLE for Censored and Truncated Data' - description: 'Many functions for computing the NPMLE for censored and truncated data.' -extra: - identifiers: - - biotools:icens - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-icens - path: recipes/bioconductor-icens - version: 1.52.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-icetea/meta.yaml b/recipes/bioconductor-icetea/meta.yaml index 916fb97d57978..455bd69dea573 100644 --- a/recipes/bioconductor-icetea/meta.yaml +++ b/recipes/bioconductor-icetea/meta.yaml @@ -1,75 +1,82 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "icetea" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: icetea (Integrating Cap Enrichment with Transcript Expression Analysis) provides functions for end-to-end analysis of multiple 5'-profiling methods such as CAGE, RAMPAGE and MAPCap, beginning from raw reads to detection of transcription start sites using replicates. It also allows performing differential TSS detection between group of samples, therefore, integrating the mRNA cap enrichment information with transcript expression analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Integrating Cap Enrichment with Transcript Expression Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2e7e3e32b56771089cefcc4295456e49 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-icetea", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, Rsubread (>= 1.29.0), testthat requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-csaw >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene >=3.12.0,<3.13.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-csaw >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene >=3.12.0,<3.13.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-ggplot2 + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-csaw >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene >=3.12.0,<3.13.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-csaw >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene >=3.12.0,<3.13.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-ggplot2 + +source: + md5: ddac69b3713d80d69e4a1966c8e64410 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Integrating Cap Enrichment with Transcript Expression Analysis' - description: 'icetea (Integrating Cap Enrichment with Transcript Expression Analysis) provides functions for end-to-end analysis of multiple 5''-profiling methods such as CAGE, RAMPAGE and MAPCap, beginning from raw reads to detection of transcription start sites using replicates. It also allows performing differential TSS detection between group of samples, therefore, integrating the mRNA cap enrichment information with transcript expression analysis.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-icheck/meta.yaml b/recipes/bioconductor-icheck/meta.yaml index 51520bfa018ee..fcb43de66c9a3 100644 --- a/recipes/bioconductor-icheck/meta.yaml +++ b/recipes/bioconductor-icheck/meta.yaml @@ -1,32 +1,45 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "iCheck" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: QC pipeline and data analysis tools for high-dimensional Illumina mRNA expression data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4404db494985157058a6af6d8c29b0c1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-icheck", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-geneselectmmd >=2.46.0,<2.47.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-geneselectmmd >=2.50.0,<2.51.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-lumi >=2.58.0,<2.59.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-gplots - r-lmtest @@ -35,12 +48,12 @@ requirements: - r-rgl - r-scatterplot3d run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-geneselectmmd >=2.46.0,<2.47.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-geneselectmmd >=2.50.0,<2.51.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-lumi >=2.58.0,<2.59.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-gplots - r-lmtest @@ -48,23 +61,16 @@ requirements: - r-randomforest - r-rgl - r-scatterplot3d - build: - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - xorg-libxfixes # [linux] + +source: + md5: bff5b73dc24f3a509cac0c6d18c1fc46 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data' - description: 'QC pipeline and data analysis tools for high-dimensional Illumina mRNA expression data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ichip/meta.yaml b/recipes/bioconductor-ichip/meta.yaml index 6a06380a203bd..0664816f80fd1 100644 --- a/recipes/bioconductor-ichip/meta.yaml +++ b/recipes/bioconductor-ichip/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.56.0" %} +{% set version = "1.60.0" %} {% set name = "iChip" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Hidden Ising models are implemented to identify enriched genomic regions in ChIP-chip data. They can be used to analyze the data from multiple platforms (e.g., Affymetrix, Agilent, and NimbleGen), and the data with single to multiple replicates. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d50d8db2c1de02e8a1df4de992aa64f4 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ichip", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:ichip + - doi:10.1093/bioinformatics/btq032 + parent_recipe: + name: bioconductor-ichip + path: recipes/bioconductor-ichip + version: 1.34.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - libblas - liblapack run: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: e2f8c25bb34a748e937e8d4c85f2d1db + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models' - description: 'Hidden Ising models are implemented to identify enriched genomic regions in ChIP-chip data. They can be used to analyze the data from multiple platforms (e.g., Affymetrix, Agilent, and NimbleGen), and the data with single to multiple replicates.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:ichip - - doi:10.1093/bioinformatics/btq032 - parent_recipe: - name: bioconductor-ichip - path: recipes/bioconductor-ichip - version: 1.34.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-iclusterplus/build.sh b/recipes/bioconductor-iclusterplus/build.sh index 0f7012ed24200..c1d13421f5f1e 100644 --- a/recipes/bioconductor-iclusterplus/build.sh +++ b/recipes/bioconductor-iclusterplus/build.sh @@ -8,5 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -autoreconf -fi $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iclusterplus/build_failure.linux-64.yaml b/recipes/bioconductor-iclusterplus/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0acb8f908518f --- /dev/null +++ b/recipes/bioconductor-iclusterplus/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c0f0faf47f5c80e0741ba499252c600b59f5a9d44b9fed2b5e25336242f23728 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + + source tree in: /opt/conda/conda-bld/bioconductor-iclusterplus_1734187731650/work + export PREFIX=/opt/conda/conda-bld/bioconductor-iclusterplus_1734187731650/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-iclusterplus_1734187731650/_build_env + export SRC_DIR=/opt/conda/conda-bld/bioconductor-iclusterplus_1734187731650/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gfortran_linux-64.sh made the following environmental changes: + DEBUG_FFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -I$BUILD_PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -ffunction-sections -pipe + DEBUG_FORTRANFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -I$BUILD_PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -ffunction-sections -pipe + F77=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gfortran + F90=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gfortran + F95=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-f95 + FC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gfortran + FC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gfortran + FFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -I$BUILD_PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -I$BUILD_PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gfortran + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-iclusterplus_1734187731650/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/R/library + * installing *source* package iClusterPlus ... + ** package iClusterPlus successfully unpacked and MD5 sums checked + ** using staged installation + This package has only been tested with gfortran. + So some checks are needed. + R_HOME is $PREFIX/lib/R + Attempting to determine R_ARCH... + R_ARCH is + Attempting to detect how R was configured for Fortran 90.... + Unsupported Fortran 90 compiler or Fortran 90 + compilers unavailable! Stop! + ERROR: configuration failed for package iClusterPlus + * removing /opt/conda/conda-bld/bioconductor-iclusterplus_1734187731650/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/R/library/iClusterPlus + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-iclusterplus_1734187731650/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-iclusterplus_1734187731650/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-iclusterplus/build_failure.linux-aarch64.yaml b/recipes/bioconductor-iclusterplus/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..604d3b3c12b79 --- /dev/null +++ b/recipes/bioconductor-iclusterplus/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c0f0faf47f5c80e0741ba499252c600b59f5a9d44b9fed2b5e25336242f23728 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + + source tree in: /opt/conda/conda-bld/bioconductor-iclusterplus_1734185867868/work + export PREFIX=/opt/conda/conda-bld/bioconductor-iclusterplus_1734185867868/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-iclusterplus_1734185867868/_build_env + export SRC_DIR=/opt/conda/conda-bld/bioconductor-iclusterplus_1734185867868/work + INFO: activate-binutils_linux-aarch64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strip + INFO: activate-gcc_linux-aarch64.sh made the following environmental changes: + BUILD=aarch64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc + CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=aarch64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=aarch64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib + HOST=aarch64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_aarch64_conda_cos7_linux_gnu + build_alias=aarch64-conda-linux-gnu + host_alias=aarch64-conda-linux-gnu + -BUILD=aarch64-conda_cos7-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gfortran_linux-aarch64.sh made the following environmental changes: + DEBUG_FFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -I$BUILD_PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ftree-vectorize -fPIC -fstack-protector-strong -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fvar-tracking-assignments -pipe + DEBUG_FORTRANFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -I$BUILD_PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ftree-vectorize -fPIC -fstack-protector-strong -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fvar-tracking-assignments -pipe + F77=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gfortran + F90=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gfortran + F95=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-f95 + FC=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gfortran + FC_FOR_BUILD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gfortran + FFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -I$BUILD_PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -I$BUILD_PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gfortran + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-iclusterplus_1734185867868/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/R/library + * installing *source* package iClusterPlus ... + ** package iClusterPlus successfully unpacked and MD5 sums checked + ** using staged installation + This package has only been tested with gfortran. + So some checks are needed. + R_HOME is $PREFIX/lib/R + Attempting to determine R_ARCH... + R_ARCH is + Attempting to detect how R was configured for Fortran 90.... + Unsupported Fortran 90 compiler or Fortran 90 + compilers unavailable! Stop! + ERROR: configuration failed for package iClusterPlus + * removing /opt/conda/conda-bld/bioconductor-iclusterplus_1734185867868/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/R/library/iClusterPlus + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-iclusterplus_1734185867868/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-iclusterplus_1734185867868/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-iclusterplus/build_failure.osx-64.yaml b/recipes/bioconductor-iclusterplus/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..4f1cbe803cd47 --- /dev/null +++ b/recipes/bioconductor-iclusterplus/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c0f0faf47f5c80e0741ba499252c600b59f5a9d44b9fed2b5e25336242f23728 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-iclusterplus_1734185521886/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-iclusterplus_1734185521886/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-iclusterplus_1734185521886/work + INFO: activate-gfortran_osx-64.sh made the following environmental changes: + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate-gfortran_osx-64.sh made the following environmental changes: + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + GFORTRAN=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + -DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + -DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + -FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + -GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-iclusterplus-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + This package has only been tested with gfortran. + So some checks are needed. + R_HOME is $PREFIX/lib/R + Attempting to determine R_ARCH... + R_ARCH is + Attempting to detect how R was configured for Fortran 90.... + Unsupported Fortran 90 compiler or Fortran 90 + compilers unavailable! Stop! +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-iclusterplus/meta.yaml b/recipes/bioconductor-iclusterplus/meta.yaml index 0426fabc27f70..ad555d8dc48d9 100644 --- a/recipes/bioconductor-iclusterplus/meta.yaml +++ b/recipes/bioconductor-iclusterplus/meta.yaml @@ -1,48 +1,52 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "iClusterPlus" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Integrative clustering of multiple genomic data using a joint latent variable model. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Integrative clustering of multi-type genomic data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 133b682823ec6ab41f6f6579413d461d - patches: - - 0001-Detect-compiler-with-gfortran-suffix.patch build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-iclusterplus", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics requirements: + build: + - {{ compiler('c') }} + - {{ compiler('fortran') }} + - automake + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - {{ compiler('fortran') }} - - automake - - autoconf - - make + +source: + md5: 65bf4787b2705f9d30c243e2abbb068b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Integrative clustering of multi-type genomic data' - description: 'Integrative clustering of multiple genomic data using a joint latent variable model.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-icnv/meta.yaml b/recipes/bioconductor-icnv/meta.yaml index b1c5eb62c6e2d..15360d7bae528 100644 --- a/recipes/bioconductor-icnv/meta.yaml +++ b/recipes/bioconductor-icnv/meta.yaml @@ -1,28 +1,36 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "iCNV" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Integrative copy number variation (CNV) detection from multiple platform and experimental design. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Integrated Copy Number Variation detection -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ff1415b4764c18a3609c4eb3b6d65a30 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-icnv", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-icnv + path: recipes/bioconductor-icnv + version: 1.2.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, WES.1KG.WUGSC requirements: host: - - 'bioconductor-codex >=1.34.0,<1.35.0' + - bioconductor-codex >=1.38.0,<1.39.0 - r-base - r-data.table - r-dplyr @@ -32,7 +40,7 @@ requirements: - r-tidyr - r-truncnorm run: - - 'bioconductor-codex >=1.34.0,<1.35.0' + - bioconductor-codex >=1.38.0,<1.39.0 - r-base - r-data.table - r-dplyr @@ -41,18 +49,16 @@ requirements: - r-rlang - r-tidyr - r-truncnorm + +source: + md5: 06031b0e2f77cbcb9e48635b698084b8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Integrated Copy Number Variation detection' - description: 'Integrative copy number variation (CNV) detection from multiple platform and experimental design.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - parent_recipe: - name: bioconductor-icnv - path: recipes/bioconductor-icnv - version: 1.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-icobra/meta.yaml b/recipes/bioconductor-icobra/meta.yaml index 0a0ef086aa674..abd3544ef6245 100644 --- a/recipes/bioconductor-icobra/meta.yaml +++ b/recipes/bioconductor-icobra/meta.yaml @@ -1,68 +1,76 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "iCOBRA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. Various types of performance plots can be generated programmatically. The package also contains a shiny application for interactive exploration of results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Comparison and Visualization of Ranking and Assignment Methods -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dc297e102e2b6ee717a494f652a6d6bf build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-icobra", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:icobra + parent_recipe: + name: bioconductor-icobra + path: recipes/bioconductor-icobra + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-dplyr - r-dt - - 'r-ggplot2 >=2.0.0' + - r-ggplot2 >=3.4.0 - r-markdown - r-reshape2 + - r-rlang - r-rocr - r-scales - - 'r-shiny >=0.9.1.9008' + - r-shiny >=0.9.1.9008 - r-shinybs - r-shinydashboard - r-upsetr run: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-dplyr - r-dt - - 'r-ggplot2 >=2.0.0' + - r-ggplot2 >=3.4.0 - r-markdown - r-reshape2 + - r-rlang - r-rocr - r-scales - - 'r-shiny >=0.9.1.9008' + - r-shiny >=0.9.1.9008 - r-shinybs - r-shinydashboard - r-upsetr + +source: + md5: 01d6f84334605ccc0d8247572e9c9695 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Comparison and Visualization of Ranking and Assignment Methods' - description: 'This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. Various types of performance plots can be generated programmatically. The package also contains a shiny application for interactive exploration of results.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:icobra - parent_recipe: - name: bioconductor-icobra - path: recipes/bioconductor-icobra - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ideal/build_failure.linux-64.yaml b/recipes/bioconductor-ideal/build_failure.linux-64.yaml deleted file mode 100644 index 19d2276079b9f..0000000000000 --- a/recipes/bioconductor-ideal/build_failure.linux-64.yaml +++ /dev/null @@ -1,106 +0,0 @@ -recipe_sha: 67de6b5cdabab9789f4141c7b4df882eca324c62877eb622c009398c5cadd390 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: |- - dependency issue -log: |2- - - Leaving build/test directories: - Work: - /opt/conda/conda-bld/work - Test: - /opt/conda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl - Build: - source activate /opt/conda/conda-bld/_build_env - - - Traceback (most recent call last): - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action - t = self.solve(specs) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - r-plotly - - r-shinyace - - r-shinybs - - r-upsetr - - bioconductor-limma >=3.58.0,<3.59.0 - - r-rintrojs - - r-base64enc - - bioconductor-iranges >=2.36.0,<2.37.0 - - bioconductor-goseq >=1.54.0,<1.55.0 - - bioconductor-s4vectors >=0.40.0,<0.41.0 - - r-gplots - - r-rentrez - - bioconductor-topgo >=2.54.0,<2.55.0 - - r-base 4.3.* - - r-shinydashboard - - bioconductor-deseq2 >=1.42.0,<1.43.0 - - bioconductor-go.db >=3.18.0,<3.19.0 - - bioconductor-genomicranges >=1.54.0,<1.55.0 - - r-heatmaply - - r-knitr - - r-shiny >=0.12.0 - - bioconductor-gostats >=2.68.0,<2.69.0 - - r-dplyr - - bioconductor-pcaexplorer >=2.28.0,<2.29.0 - - bioconductor-biocparallel >=1.36.0,<1.37.0 - - r-dt - - r-ggplot2 >=2.0.0 - - r-ggrepel - - bioconductor-annotationdbi >=1.64.0,<1.65.0 - - bioconductor-ihw >=1.30.0,<1.31.0 - - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 - - r-stringr - - r-pheatmap - - r-rlang - - r-rmarkdown - - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested bioconductor-ihw >=1.30.0,<1.31.0 - - - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build - output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs - for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set - conda_packages = finalize_outputs_pass( - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass - fm = finalize_metadata( - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata - build_unsat, host_unsat = add_upstream_pins(m, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins - host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files - deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies - actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-ihw[version='>=1.30.0,<1.31.0']")} -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-ideal/meta.yaml b/recipes/bioconductor-ideal/meta.yaml index 3cbe305f544a5..efbdfd6001094 100644 --- a/recipes/bioconductor-ideal/meta.yaml +++ b/recipes/bioconductor-ideal/meta.yaml @@ -1,46 +1,55 @@ -{% set version = "1.26.0" %} +{% set version = "2.0.0" %} {% set name = "ideal" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package. Support for reproducibility of the whole analysis is provided by means of a template report which gets automatically compiled and can be stored/shared. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Interactive Differential Expression AnaLysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d4714305a9be71a4b4c71da0fb624148 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ideal", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, edgeR + +extra: + parent_recipe: + name: bioconductor-ideal + path: recipes/bioconductor-ideal + version: 1.4.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, htmltools, edgeR requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-goseq >=1.54.0,<1.55.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-ihw >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-pcaexplorer >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-goseq >=1.58.0,<1.59.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-ihw >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-mosdef >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-base - r-base64enc - r-dplyr - r-dt - - 'r-ggplot2 >=2.0.0' + - r-ggplot2 >=2.0.0 - r-ggrepel - r-gplots - r-heatmaply @@ -51,32 +60,33 @@ requirements: - r-rintrojs - r-rlang - r-rmarkdown - - 'r-shiny >=0.12.0' + - r-shiny >=0.12.0 - r-shinyace - r-shinybs - r-shinydashboard - r-stringr - r-upsetr + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-goseq >=1.54.0,<1.55.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-ihw >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-pcaexplorer >=2.28.0,<2.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-goseq >=1.58.0,<1.59.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-ihw >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-mosdef >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-base - r-base64enc - r-dplyr - r-dt - - 'r-ggplot2 >=2.0.0' + - r-ggplot2 >=2.0.0 - r-ggrepel - r-gplots - r-heatmaply @@ -87,24 +97,22 @@ requirements: - r-rintrojs - r-rlang - r-rmarkdown - - 'r-shiny >=0.12.0' + - r-shiny >=0.12.0 - r-shinyace - r-shinybs - r-shinydashboard - r-stringr - r-upsetr + +source: + md5: cf4dfd814f77ebd496c3de75eb7b7b3f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Interactive Differential Expression AnaLysis' - description: 'This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-ideal - path: recipes/bioconductor-ideal - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ideoviz/meta.yaml b/recipes/bioconductor-ideoviz/meta.yaml index 3e85ceeaf3c0f..3bc8fb872789d 100644 --- a/recipes/bioconductor-ideoviz/meta.yaml +++ b/recipes/bioconductor-ideoviz/meta.yaml @@ -1,56 +1,62 @@ -{% set version = "1.37.0" %} +{% set version = "1.42.0" %} {% set name = "IdeoViz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Plots data associated with arbitrary genomic intervals along chromosomal ideogram. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Plots data (continuous/discrete) along chromosomal ideogram -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 187ebcc3f7a11124ebbe137722672ffc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ideoviz", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:ideoviz + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ideoviz + path: recipes/bioconductor-ideoviz + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-rcolorbrewer + +source: + md5: ee20eec11c0b72dcf1edac17b6a1f507 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Plots data (continuous/discrete) along chromosomal ideogram' - description: 'Plots data associated with arbitrary genomic intervals along chromosomal ideogram.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:ideoviz - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-ideoviz - path: recipes/bioconductor-ideoviz - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-idiogram/meta.yaml b/recipes/bioconductor-idiogram/meta.yaml index 6fa4e077bdb2d..67cdf793ad149 100644 --- a/recipes/bioconductor-idiogram/meta.yaml +++ b/recipes/bioconductor-idiogram/meta.yaml @@ -1,51 +1,57 @@ -{% set version = "1.78.0" %} +{% set version = "1.82.0" %} {% set name = "idiogram" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package for plotting genomic data by chromosomal location + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: idiogram -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2ee94ac9719c77f8a2f6b691662a7909 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-idiogram", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:idiogram + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-idiogram + path: recipes/bioconductor-idiogram + version: 1.56.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: hu6800.db, hgu95av2.db, golubEsets requirements: host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-plotrix run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-plotrix + +source: + md5: 12e658f262aa8be1e682a1e1d5ab3dfa + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: idiogram - description: 'A package for plotting genomic data by chromosomal location' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:idiogram - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-idiogram - path: recipes/bioconductor-idiogram - version: 1.56.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-idpr/meta.yaml b/recipes/bioconductor-idpr/meta.yaml index 3450da1b12fbd..65e3f4bdf7d92 100644 --- a/recipes/bioconductor-idpr/meta.yaml +++ b/recipes/bioconductor-idpr/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "idpr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: '‘idpr’ aims to integrate tools for the computational analysis of intrinsically disordered proteins (IDPs) within R. This package is used to identify known characteristics of IDPs for a sequence of interest with easily reported and dynamic results. Additionally, this package includes tools for IDP-based sequence analysis to be used in conjunction with other R packages. Described in McFadden WM & Yanowitz JL (2022). "idpr: A package for profiling and analyzing Intrinsically Disordered Proteins in R." PloS one, 17(4), e0266929. .' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Profiling and Analyzing Intrinsically Disordered Proteins in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 16fb786981b0e04b0d094c4867303555 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-idpr", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, msa, ape, testthat, seqinr + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, pwalign, msa, ape, testthat, seqinr requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - - 'r-dplyr >=0.8.5' - - 'r-ggplot2 >=3.3.0' - - 'r-jsonlite >=1.6.1' - - 'r-magrittr >=1.5' - - 'r-plyr >=1.8.6' - - 'r-rlang >=0.4.6' + - r-dplyr >=0.8.5 + - r-ggplot2 >=3.3.0 + - r-jsonlite >=1.6.1 + - r-magrittr >=1.5 + - r-plyr >=1.8.6 + - r-rlang >=0.4.6 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - - 'r-dplyr >=0.8.5' - - 'r-ggplot2 >=3.3.0' - - 'r-jsonlite >=1.6.1' - - 'r-magrittr >=1.5' - - 'r-plyr >=1.8.6' - - 'r-rlang >=0.4.6' + - r-dplyr >=0.8.5 + - r-ggplot2 >=3.3.0 + - r-jsonlite >=1.6.1 + - r-magrittr >=1.5 + - r-plyr >=1.8.6 + - r-rlang >=0.4.6 + +source: + md5: 737a8df73b7fe876f517a85936d4cb6d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 3)' - summary: 'Profiling and Analyzing Intrinsically Disordered Proteins in R' - description: '‘idpr’ aims to integrate tools for the computational analysis of intrinsically disordered proteins (IDPs) within R. This package is used to identify known characteristics of IDPs for a sequence of interest with easily reported and dynamic results. Additionally, this package includes tools for IDP-based sequence analysis to be used in conjunction with other R packages. Described in McFadden WM & Yanowitz JL (2022). "idpr: A package for profiling and analyzing Intrinsically Disordered Proteins in R." PloS one, 17(4), e0266929. .' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-idr2d/meta.yaml b/recipes/bioconductor-idr2d/meta.yaml index f2c297502502b..8fda4bf64d48c 100644 --- a/recipes/bioconductor-idr2d/meta.yaml +++ b/recipes/bioconductor-idr2d/meta.yaml @@ -1,60 +1,65 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "idr2d" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A tool to measure reproducibility between genomic experiments that produce two-dimensional peaks (interactions between peaks), such as ChIA-PET, HiChIP, and HiC. idr2d is an extension of the original idr package, which is intended for (one-dimensional) ChIP-seq peaks. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Irreproducible Discovery Rate for Genomic Interactions Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6662b2b18dc8c6029ad40099c5fcd6a7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-idr2d", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: DT (>= 0.4), htmltools (>= 0.3.6), knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) # SystemRequirements: Python (>= 3.5.0), hic-straw requirements: host: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - - 'r-dplyr >=0.7.6' - - 'r-futile.logger >=1.4.3' - - 'r-ggplot2 >=3.1.1' - - 'r-idr >=1.2' - - 'r-magrittr >=1.5' - - 'r-reticulate >=1.13' - - 'r-scales >=1.0.0' - - 'r-stringr >=1.3.1' + - r-dplyr >=0.7.6 + - r-futile.logger >=1.4.3 + - r-ggplot2 >=3.1.1 + - r-idr >=1.2 + - r-magrittr >=1.5 + - r-reticulate >=1.13 + - r-scales >=1.0.0 + - r-stringr >=1.3.1 run: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - - 'r-dplyr >=0.7.6' - - 'r-futile.logger >=1.4.3' - - 'r-ggplot2 >=3.1.1' - - 'r-idr >=1.2' - - 'r-magrittr >=1.5' - - 'r-reticulate >=1.13' - - 'r-scales >=1.0.0' - - 'r-stringr >=1.3.1' + - r-dplyr >=0.7.6 + - r-futile.logger >=1.4.3 + - r-ggplot2 >=3.1.1 + - r-idr >=1.2 + - r-magrittr >=1.5 + - r-reticulate >=1.13 + - r-scales >=1.0.0 + - r-stringr >=1.3.1 + +source: + md5: 1338e503482c45b1a05bb0dcda720276 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Irreproducible Discovery Rate for Genomic Interactions Data' - description: 'A tool to measure reproducibility between genomic experiments that produce two-dimensional peaks (interactions between peaks), such as ChIA-PET, HiChIP, and HiC. idr2d is an extension of the original idr package, which is intended for (one-dimensional) ChIP-seq peaks.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ifaa/meta.yaml b/recipes/bioconductor-ifaa/meta.yaml index 59789aaa6e7d1..39ba18fc280d6 100644 --- a/recipes/bioconductor-ifaa/meta.yaml +++ b/recipes/bioconductor-ifaa/meta.yaml @@ -1,63 +1,68 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "IFAA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package offers a robust approach to make inference on the association of covariates with the absolute abundance (AA) of microbiome in an ecosystem. It can be also directly applied to relative abundance (RA) data to make inference on AA because the ratio of two RA is equal to the ratio of their AA. This algorithm can estimate and test the associations of interest while adjusting for potential confounders. The estimates of this method have easy interpretation like a typical regression analysis. High-dimensional covariates are handled with regularization and it is implemented by parallel computing. False discovery rate is automatically controlled by this approach. Zeros do not need to be imputed by a positive value for the analysis. The IFAA package also offers the 'MZILN' function for estimating and testing associations of abundance ratios with covariates. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Robust Inference for Absolute Abundance in Microbiome Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 393ac86513ddc9adf474c654b5127394 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ifaa", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-desctools - - 'r-doparallel >=1.0.11' + - r-doparallel >=1.0.11 - r-dorng - - 'r-foreach >=1.4.3' + - r-foreach >=1.4.3 - r-glmnet - - 'r-hdci >=1.0-2' + - r-hdci >=1.0-2 - r-mathjaxr - - 'r-matrix >=1.4-0' + - r-matrix >=1.4-0 - r-matrixextra - r-parallelly - r-stringr run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-desctools - - 'r-doparallel >=1.0.11' + - r-doparallel >=1.0.11 - r-dorng - - 'r-foreach >=1.4.3' + - r-foreach >=1.4.3 - r-glmnet - - 'r-hdci >=1.0-2' + - r-hdci >=1.0-2 - r-mathjaxr - - 'r-matrix >=1.4-0' + - r-matrix >=1.4-0 - r-matrixextra - r-parallelly - r-stringr + +source: + md5: 8fb0287945a2dc4a4d6ff969d6e2b1c0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Robust Inference for Absolute Abundance in Microbiome Analysis' - description: 'This package offers a robust approach to make inference on the association of covariates with the absolute abundance (AA) of microbiome in an ecosystem. It can be also directly applied to relative abundance (RA) data to make inference on AA because the ratio of two RA is equal to the ratio of their AA. This algorithm can estimate and test the associations of interest while adjusting for potential confounders. The estimates of this method have easy interpretation like a typical regression analysis. High-dimensional covariates are handled with regularization and it is implemented by parallel computing. False discovery rate is automatically controlled by this approach. Zeros do not need to be imputed by a positive value for the analysis. The IFAA package also offers the ''MZILN'' function for estimating and testing associations of abundance ratios with covariates.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-igc/meta.yaml b/recipes/bioconductor-igc/meta.yaml index f9eeb7f8b07b8..816a31270bd67 100644 --- a/recipes/bioconductor-igc/meta.yaml +++ b/recipes/bioconductor-igc/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "iGC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 14007fadd58eaea3e345ba53a279f783 +about: + description: This package is intended to identify differentially expressed genes driven by Copy Number Alterations from samples with both gene expression and CNA data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: An integrated analysis package of Gene expression and Copy number alteration build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-igc", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: @@ -29,13 +28,14 @@ requirements: - r-base - r-data.table - r-plyr +source: + md5: 460d9cb7d0e9f62b5ffde15215adc7b8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'An integrated analysis package of Gene expression and Copy number alteration' - description: 'This package is intended to identify differentially expressed genes driven by Copy Number Alterations from samples with both gene expression and CNA data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-iggeneusage/meta.yaml b/recipes/bioconductor-iggeneusage/meta.yaml index 23adf82cfe2f0..245edf31b7901 100644 --- a/recipes/bioconductor-iggeneusage/meta.yaml +++ b/recipes/bioconductor-iggeneusage/meta.yaml @@ -1,64 +1,69 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "IgGeneUsage" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Detection of biases in the usage of immunoglobulin (Ig) genes is an important task in immune repertoire profiling. IgGeneUsage detects aberrant Ig gene usage between biological conditions using a probabilistic model which is analyzed computationally by Bayes inference. With this IgGeneUsage also avoids some common problems related to the current practice of null-hypothesis significance testing. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Differential gene usage in immune repertoires -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 231f1af3465f435ca3bb099a93e51e5b build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-iggeneusage", max_pin="x.x") }}' -# Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, gridExtra, ggrepel + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, ggrepel, patchwork # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-bh >=1.66.0' - - 'r-rcpp >=0.12.0' - - 'r-rcppeigen >=0.3.3.3.0' - - 'r-rcppparallel >=5.0.1' - - 'r-reshape2 >=1.4.3' - - 'r-rstan >=2.18.1' - - 'r-rstantools >=2.2.0' - - 'r-stanheaders >=2.18.0' + - r-bh >=1.66.0 + - r-rcpp >=0.12.0 + - r-rcppeigen >=0.3.3.3.0 + - r-rcppparallel >=5.0.1 + - r-reshape2 >=1.4.3 + - r-rstan >=2.18.1 + - r-rstantools >=2.2.0 + - r-stanheaders >=2.18.0 - r-tidyr - libblas - liblapack run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-bh >=1.66.0' - - 'r-rcpp >=0.12.0' - - 'r-rcppeigen >=0.3.3.3.0' - - 'r-rcppparallel >=5.0.1' - - 'r-reshape2 >=1.4.3' - - 'r-rstan >=2.18.1' - - 'r-rstantools >=2.2.0' - - 'r-stanheaders >=2.18.0' + - r-bh >=1.66.0 + - r-rcpp >=0.12.0 + - r-rcppeigen >=0.3.3.3.0 + - r-rcppparallel >=5.0.1 + - r-reshape2 >=1.4.3 + - r-rstan >=2.18.1 + - r-rstantools >=2.2.0 + - r-stanheaders >=2.18.0 - r-tidyr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 0432bed8882294ef0ac0747430bbd02a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Differential gene usage in immune repertoires' - description: 'Detection of biases in the usage of immunoglobulin (Ig) genes is an important task in immune repertoire profiling. IgGeneUsage detects aberrant Ig gene usage between biological conditions using a probabilistic model which is analyzed computationally by Bayes inference. With this IgGeneUsage also avoids some common problems related to the current practice of null-hypothesis significance testing.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-igvr/meta.yaml b/recipes/bioconductor-igvr/meta.yaml index cb1fe14f9bcc1..3c8cea8bc2f82 100644 --- a/recipes/bioconductor-igvr/meta.yaml +++ b/recipes/bioconductor-igvr/meta.yaml @@ -1,55 +1,60 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "igvR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Access to igv.js, the Integrative Genomics Viewer running in a web browser. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 'igvR: integrative genomics viewer' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 318b9d244079439576763028e1731a18 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-igvr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocStyle, knitr, rmarkdown, MotifDb, seqLogo requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-browserviz >=2.24.0,<2.25.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-browserviz >=2.28.0,<2.29.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-httpuv - r-httr - r-rcolorbrewer run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-browserviz >=2.24.0,<2.25.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-browserviz >=2.28.0,<2.29.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-httpuv - r-httr - r-rcolorbrewer + +source: + md5: 63f7141145b7b23100a155e1f85c0916 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'igvR: integrative genomics viewer' - description: 'Access to igv.js, the Integrative Genomics Viewer running in a web browser.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ihw/build_failure.linux-64.yaml b/recipes/bioconductor-ihw/build_failure.linux-64.yaml deleted file mode 100644 index 49c95de2d51b7..0000000000000 --- a/recipes/bioconductor-ihw/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: df348495dada1a372be82599b073dacb131efa9c20367ac100389a77a59630c4 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - conda-forge/linux-64 [2K[1A[2K[0G[] 4.9s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.0s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.1s - conda-forge/linux-64 100%[2K[1A[2K[0G[] 5.2s - conda-forge/linux-64 100%[2K[1A[2K[0Gconda-forge/linux-64 - [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m - [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 2.2MB/s 0.0s - [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m - [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 2.2MB/s 0.0s - [?25hMamba failed to solve: - - bioconductor-lpsymphony >=1.30.0,<1.31.0 - - r-base 4.3.* - - r-slam - - r-fdrtool - - bioconductor-biocgenerics >=0.48.0,<0.49.0 - - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested bioconductor-lpsymphony >=1.30.0,<1.31.0 - - - - Leaving build/test directories: - Work: - /opt/conda/conda-bld/work - Test: - /opt/conda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl - Build: - source activate /opt/conda/conda-bld/_build_env - - - Traceback (most recent call last): - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action - t = self.solve(specs) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - bioconductor-lpsymphony >=1.30.0,<1.31.0 - - r-base 4.3.* - - r-slam - - r-fdrtool - - bioconductor-biocgenerics >=0.48.0,<0.49.0 - - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested bioconductor-lpsymphony >=1.30.0,<1.31.0 - - - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build - output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs - for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set - conda_packages = finalize_outputs_pass( - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass - fm = finalize_metadata( - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata - build_unsat, host_unsat = add_upstream_pins(m, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins - host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files - deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies - actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-lpsymphony[version='>=1.30.0,<1.31.0']")} -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-ihw/meta.yaml b/recipes/bioconductor-ihw/meta.yaml index 74e07fd5f88d8..47bcbe51761b1 100644 --- a/recipes/bioconductor-ihw/meta.yaml +++ b/recipes/bioconductor-ihw/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "IHW" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Independent hypothesis weighting (IHW) is a multiple testing procedure that increases power compared to the method of Benjamini and Hochberg by assigning data-driven weights to each hypothesis. The input to IHW is a two-column table of p-values and covariates. The covariate can be any continuous-valued or categorical variable that is thought to be informative on the statistical properties of each hypothesis test, while it is independent of the p-value under the null hypothesis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Independent Hypothesis Weighting -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa53165d5f689e8bfdebb02838ae9dab build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ihw", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:IHW + - doi:10.1038/nmeth.3885 + parent_recipe: + name: bioconductor-ihw + path: recipes/bioconductor-ihw + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat, Matrix, BiocStyle, knitr, rmarkdown, devtools requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-lpsymphony >=1.30.0,<1.31.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-lpsymphony >=1.34.0,<1.35.0 - r-base - r-fdrtool - r-slam run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-lpsymphony >=1.30.0,<1.31.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-lpsymphony >=1.34.0,<1.35.0 - r-base - r-fdrtool - r-slam + +source: + md5: d128f674729c18419d57cecbadb0c789 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Independent Hypothesis Weighting' - description: 'Independent hypothesis weighting (IHW) is a multiple testing procedure that increases power compared to the method of Benjamini and Hochberg by assigning data-driven weights to each hypothesis. The input to IHW is a two-column table of p-values and covariates. The covariate can be any continuous-valued or categorical variable that is thought to be informative on the statistical properties of each hypothesis test, while it is independent of the p-value under the null hypothesis.' -extra: - identifiers: - - biotools:IHW - - doi:10.1038/nmeth.3885 - parent_recipe: - name: bioconductor-ihw - path: recipes/bioconductor-ihw - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ihwpaper/build_failure.linux-64.yaml b/recipes/bioconductor-ihwpaper/build_failure.linux-64.yaml deleted file mode 100644 index 0d1d099182dc8..0000000000000 --- a/recipes/bioconductor-ihwpaper/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 366efc448b56ba6b7e86a876417279bedf04156e08c60e0c035fe672c82e0ddc # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - - r-ggplot2 - - libgcc-ng >=12 - - r-rcpp - - libstdcxx-ng >=12 - - bioconductor-biobase >=2.62.0,<2.63.0 - - r-fdrtool - - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested bioconductor-ihw >=1.30.0,<1.31.0 - - - - Leaving build/test directories: - Work: - /opt/conda/conda-bld/work - Test: - /opt/conda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl - Build: - source activate /opt/conda/conda-bld/_build_env - - - Traceback (most recent call last): - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action - t = self.solve(specs) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - bioconductor-biocparallel >=1.36.0,<1.37.0 - - bioconductor-biocgenerics >=0.48.0,<0.49.0 - - liblapack 3.9.* *netlib - - libblas 3.9.* *netlib - - bioconductor-deseq2 >=1.42.0,<1.43.0 - - r-dplyr - - r-base 4.3.* - - bioconductor-genefilter >=1.84.0,<1.85.0 - - bioconductor-ihw >=1.30.0,<1.31.0 - - bioconductor-qvalue >=2.34.0,<2.35.0 - - r-cowplot - - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 - - r-ggplot2 - - libgcc-ng >=12 - - r-rcpp - - libstdcxx-ng >=12 - - bioconductor-biobase >=2.62.0,<2.63.0 - - r-fdrtool - - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested bioconductor-ihw >=1.30.0,<1.31.0 - - - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build - output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs - for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set - conda_packages = finalize_outputs_pass( - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass - fm = finalize_metadata( - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata - build_unsat, host_unsat = add_upstream_pins(m, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins - host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files - deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies - actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-ihw[version='>=1.30.0,<1.31.0']")} -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-ihwpaper/build_failure.osx-64.yaml b/recipes/bioconductor-ihwpaper/build_failure.osx-64.yaml index e81f7f57656d0..e0f8af8f34cca 100644 --- a/recipes/bioconductor-ihwpaper/build_failure.osx-64.yaml +++ b/recipes/bioconductor-ihwpaper/build_failure.osx-64.yaml @@ -1,106 +1,104 @@ -recipe_sha: 366efc448b56ba6b7e86a876417279bedf04156e08c60e0c035fe672c82e0ddc # The commit at which this recipe failed to build. +recipe_sha: 5822332f7ff41c4641b6ad4f7202c7af53bf5029b2ef7b38e1f68ff71904fef3 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: |- - dependency issue log: |2- - - r-dplyr - - bioconductor-biocparallel >=1.36.0,<1.37.0 - - libcxx >=14 - - bioconductor-qvalue >=2.34.0,<2.35.0 - - bioconductor-biobase >=2.62.0,<2.63.0 - - bioconductor-genefilter >=1.84.0,<1.85.0 - - bioconductor-biocgenerics >=0.48.0,<0.49.0 - - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 - - r-cowplot - - with channels: - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested bioconductor-ihw >=1.30.0,<1.31.0 - - - - Leaving build/test directories: - Work: - /opt/mambaforge/envs/bioconda/conda-bld/work - Test: - /opt/mambaforge/envs/bioconda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/mambaforge/envs/bioconda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla - Build: - source activate /opt/mambaforge/envs/bioconda/conda-bld/_build_env + bioconductor-genefilter >=1.88.0,<1.89.0 is not installable because it requires + bioconductor-annotate >=1.84.0,<1.85.0 , which does not exist (perhaps a missing channel); + bioconductor-ihw >=1.34.0,<1.35.0 is not installable because it requires + bioconductor-lpsymphony >=1.34.0,<1.35.0 , which does not exist (perhaps a missing channel). + During handling of the above exception, another exception occurred: Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action - t = self.solve(specs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - r-ggplot2 - - bioconductor-ihw >=1.30.0,<1.31.0 - - liblapack 3.9.* *netlib - - bioconductor-deseq2 >=1.42.0,<1.43.0 - - libblas 3.9.* *netlib - - r-fdrtool - - r-rcpp - - r-base 4.3.* - - r-dplyr - - bioconductor-biocparallel >=1.36.0,<1.37.0 - - libcxx >=14 - - bioconductor-qvalue >=2.34.0,<2.35.0 - - bioconductor-biobase >=2.62.0,<2.63.0 - - bioconductor-genefilter >=1.84.0,<1.85.0 - - bioconductor-biocgenerics >=0.48.0,<0.49.0 - - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 - - r-cowplot - - with channels: - - conda-forge - - bioconda - - defaults + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec(">=1.34.0,<1.35.0"), MatchSpec("bioconductor-ihw==1.34.0=r44hdfd78af_0"), MatchSpec(">=1.84.0,<1.85.0"), MatchSpec("bioconductor-genefilter==1.88.0=r44hcacfdae_0")} + Encountered problems while solving: + - nothing provides bioconductor-annotate >=1.84.0,<1.85.0 needed by bioconductor-genefilter-1.88.0-r44hcacfdae_0 + - nothing provides bioconductor-lpsymphony >=1.34.0,<1.35.0 needed by bioconductor-ihw-1.34.0-r44hdfd78af_0 - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested bioconductor-ihw >=1.30.0,<1.31.0 - - + Could not solve for environment specs + The following packages are incompatible + bioconductor-genefilter >=1.88.0,<1.89.0 is not installable because it requires + bioconductor-annotate >=1.84.0,<1.85.0 , which does not exist (perhaps a missing channel); + bioconductor-ihw >=1.34.0,<1.35.0 is not installable because it requires + bioconductor-lpsymphony >=1.34.0,<1.35.0 , which does not exist (perhaps a missing channel). During handling of the above exception, another exception occurred: Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs - for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set conda_packages = finalize_outputs_pass( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass fm = finalize_metadata( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata - build_unsat, host_unsat = add_upstream_pins(m, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins - host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files - deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies - actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-ihw[version='>=1.30.0,<1.31.0']")} + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec(">=1.34.0,<1.35.0"), MatchSpec("bioconductor-ihw==1.34.0=r44hdfd78af_0"), MatchSpec(">=1.84.0,<1.85.0"), MatchSpec("bioconductor-genefilter==1.88.0=r44hcacfdae_0")} + Encountered problems while solving: + - nothing provides bioconductor-annotate >=1.84.0,<1.85.0 needed by bioconductor-genefilter-1.88.0-r44hcacfdae_0 + - nothing provides bioconductor-lpsymphony >=1.34.0,<1.35.0 needed by bioconductor-ihw-1.34.0-r44hdfd78af_0 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-genefilter >=1.88.0,<1.89.0 is not installable because it requires + bioconductor-annotate >=1.84.0,<1.85.0 , which does not exist (perhaps a missing channel); + bioconductor-ihw >=1.34.0,<1.35.0 is not installable because it requires + bioconductor-lpsymphony >=1.34.0,<1.35.0 , which does not exist (perhaps a missing channel). # Last 100 lines of the build log. diff --git a/recipes/bioconductor-ihwpaper/meta.yaml b/recipes/bioconductor-ihwpaper/meta.yaml index 4251fc13e6670..dcdaffe0bda7d 100644 --- a/recipes/bioconductor-ihwpaper/meta.yaml +++ b/recipes/bioconductor-ihwpaper/meta.yaml @@ -1,34 +1,39 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "IHWpaper" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package conveniently wraps all functions needed to reproduce the figures in the IHW paper (https://www.nature.com/articles/nmeth.3885) and the data analysis in https://rss.onlinelibrary.wiley.com/doi/10.1111/rssb.12411, cf. the arXiv preprint (http://arxiv.org/abs/1701.05179). Thus it is a companion package to the Bioconductor IHW package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Reproduce figures in IHW paper -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 21e65d900bf8e6015fd006fbf01237d5 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ihwpaper", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, RColorBrewer, wesanderson, scales, gridExtra, BiocStyle, knitr, rmarkdown, airway, locfdr, tidyr, latex2exp requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-ihw >=1.30.0,<1.31.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-ihw >=1.34.0,<1.35.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cowplot - r-dplyr @@ -38,14 +43,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-ihw >=1.30.0,<1.31.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-ihw >=1.34.0,<1.35.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cowplot - r-dplyr @@ -53,17 +58,17 @@ requirements: - r-ggplot2 - r-rcpp - curl - - 'bioconductor-data-packages >=20231203' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - bioconductor-data-packages >=20241103 + +source: + md5: a934c0fe5745d5172c0bc40d7fe67166 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Reproduce figures in IHW paper' - description: 'This package conveniently wraps all functions needed to reproduce the figures in the IHW paper (https://www.nature.com/articles/nmeth.3885) and the data analysis in https://rss.onlinelibrary.wiley.com/doi/10.1111/rssb.12411, cf. the arXiv preprint (http://arxiv.org/abs/1701.05179). Thus it is a companion package to the Bioconductor IHW package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ihwpaper/post-link.sh b/recipes/bioconductor-ihwpaper/post-link.sh index cceb85018f40b..628fe42341d63 100644 --- a/recipes/bioconductor-ihwpaper/post-link.sh +++ b/recipes/bioconductor-ihwpaper/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ihwpaper-1.30.0" +installBiocDataPackage.sh "ihwpaper-1.34.0" diff --git a/recipes/bioconductor-illumina450probevariants.db/meta.yaml b/recipes/bioconductor-illumina450probevariants.db/meta.yaml index 1458b848396e0..a3becd7e5b7db 100644 --- a/recipes/bioconductor-illumina450probevariants.db/meta.yaml +++ b/recipes/bioconductor-illumina450probevariants.db/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "Illumina450ProbeVariants.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ca34eec73a57e5f226b70a20ef706ee3 +about: + description: Includes details on variants for each probe on the 450k bead chip for each of the four populations (Asian, American, African and European) + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illumina450probevariants.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a439949b2c954d589bc6e56ba1d13b0a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes' - description: 'Includes details on variants for each probe on the 450k bead chip for each of the four populations (Asian, American, African and European)' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illumina450probevariants.db/post-link.sh b/recipes/bioconductor-illumina450probevariants.db/post-link.sh index 1d85e7fc79149..bd57824e4968d 100644 --- a/recipes/bioconductor-illumina450probevariants.db/post-link.sh +++ b/recipes/bioconductor-illumina450probevariants.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "illumina450probevariants.db-1.38.0" +installBiocDataPackage.sh "illumina450probevariants.db-1.42.0" diff --git a/recipes/bioconductor-illuminadatatestfiles/meta.yaml b/recipes/bioconductor-illuminadatatestfiles/meta.yaml index b9af46bf149a1..f4bb6b11e617b 100644 --- a/recipes/bioconductor-illuminadatatestfiles/meta.yaml +++ b/recipes/bioconductor-illuminadatatestfiles/meta.yaml @@ -1,37 +1,37 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "IlluminaDataTestFiles" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3afa4b143fbb1dd18b3a7acd8f2984b1 +about: + description: Example data for Illumina microarray output files, for testing purposes + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina microarray files (IDAT) for testing build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminadatatestfiles", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b7ef98a177e46103b696291264e4238e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina microarray files (IDAT) for testing' - description: 'Example data for Illumina microarray output files, for testing purposes' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminadatatestfiles/post-link.sh b/recipes/bioconductor-illuminadatatestfiles/post-link.sh index a8b688442f90a..c9104fc284889 100644 --- a/recipes/bioconductor-illuminadatatestfiles/post-link.sh +++ b/recipes/bioconductor-illuminadatatestfiles/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "illuminadatatestfiles-1.40.0" +installBiocDataPackage.sh "illuminadatatestfiles-1.44.0" diff --git a/recipes/bioconductor-illuminahumanmethylation27k.db/meta.yaml b/recipes/bioconductor-illuminahumanmethylation27k.db/meta.yaml index ae8bb8780986d..638b9a90a90af 100644 --- a/recipes/bioconductor-illuminahumanmethylation27k.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation27k.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "1.4.8" %} {% set name = "IlluminaHumanMethylation27k.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 70586bda9db01d598723bb439c315367 +about: + description: Illumina Illumina Human Methylation 27k annotation data (chip IlluminaHumanMethylation27k) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina Illumina Human Methylation 27k annotation data (chip IlluminaHumanMethylation27k) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylation27k.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 70586bda9db01d598723bb439c315367 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina Illumina Human Methylation 27k annotation data (chip IlluminaHumanMethylation27k)' - description: 'Illumina Illumina Human Methylation 27k annotation data (chip IlluminaHumanMethylation27k) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/meta.yaml index 7a1f7e62ecb9c..7812013451160 100644 --- a/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/meta.yaml @@ -1,39 +1,39 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylation27kanno.ilmn12.hg19" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 765851336506120467c2e3cc6beef7ed +about: + description: An annotation package for Illumina's EPIC methylation arrays. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation for Illumina's 27k methylation arrays build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 765851336506120467c2e3cc6beef7ed + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation for Illumina''s 27k methylation arrays' - description: 'An annotation package for Illumina''s EPIC methylation arrays.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminahumanmethylation27kmanifest/meta.yaml b/recipes/bioconductor-illuminahumanmethylation27kmanifest/meta.yaml index f08b35ab5f4d1..0ea2ac772bc99 100644 --- a/recipes/bioconductor-illuminahumanmethylation27kmanifest/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation27kmanifest/meta.yaml @@ -1,39 +1,39 @@ {% set version = "0.4.0" %} {% set name = "IlluminaHumanMethylation27kmanifest" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c4cdda637dccf85f193342c7262b02a6 +about: + description: Manifest for Illumina's 27k array data + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation for Illumina's 27k methylation arrays build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylation27kmanifest", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c4cdda637dccf85f193342c7262b02a6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation for Illumina''s 27k methylation arrays' - description: 'Manifest for Illumina''s 27k array data' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml index 263014c5c77c9..b6f8ee81a5af1 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml @@ -1,44 +1,44 @@ {% set version = "0.6.1" %} {% set name = "IlluminaHumanMethylation450kanno.ilmn12.hg19" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aeafc54d887b128ed265fa704a3efa42 +about: + description: Manifests and annotation for Illumina's 450k array data. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation for Illumina's 450k methylation arrays build: - number: 2 + noarch: generic + number: 3 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 + path: recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 + version: 0.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: aeafc54d887b128ed265fa704a3efa42 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation for Illumina''s 450k methylation arrays' - description: 'Manifests and annotation for Illumina''s 450k array data.' -extra: - parent_recipe: - name: bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 - path: recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 - version: 0.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml b/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml index 9c9f591b02e13..8258ed59f7e8a 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml @@ -1,44 +1,44 @@ {% set version = "0.4.0" %} {% set name = "IlluminaHumanMethylation450kmanifest" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 664d1f5a3892974334faa26757269509 +about: + description: Manifest for Illumina's 450k array data + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation for Illumina's 450k methylation arrays build: - number: 16 + noarch: generic + number: 17 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylation450kmanifest", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-illuminahumanmethylation450kmanifest + path: recipes/bioconductor-illuminahumanmethylation450kmanifest + version: 0.4.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 664d1f5a3892974334faa26757269509 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation for Illumina''s 450k methylation arrays' - description: 'Manifest for Illumina''s 450k array data' -extra: - parent_recipe: - name: bioconductor-illuminahumanmethylation450kmanifest - path: recipes/bioconductor-illuminahumanmethylation450kmanifest - version: 0.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminahumanmethylation450kprobe/meta.yaml b/recipes/bioconductor-illuminahumanmethylation450kprobe/meta.yaml index 19a1c6a35f21c..90948f944d423 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kprobe/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation450kprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.0.6" %} {% set name = "IlluminaHumanMethylation450kprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84c31861fcbaddbf2a9c500b8d8d767d +about: + description: Probe sequences from Illumina (ftp.illumina.com) for hm450 probes + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type IlluminaHumanMethylation450k build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylation450kprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 84c31861fcbaddbf2a9c500b8d8d767d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type IlluminaHumanMethylation450k' - description: 'Probe sequences from Illumina (ftp.illumina.com) for hm450 probes' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml index 54f90a3b90e8d..a75947d9cc8d4 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml @@ -1,44 +1,44 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylationEPICanno.ilm10b2.hg19" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6a8e2398a0f930aa7828a1412fb21e88 +about: + description: An annotation package for Illumina's EPIC methylation arrays. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation for Illumina's EPIC methylation arrays build: - number: 15 + noarch: generic + number: 16 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 + path: recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 + version: 0.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6a8e2398a0f930aa7828a1412fb21e88 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation for Illumina''s EPIC methylation arrays' - description: 'An annotation package for Illumina''s EPIC methylation arrays.' -extra: - parent_recipe: - name: bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 - path: recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 - version: 0.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml index 5f0e19275d213..250b5a2776041 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml @@ -1,44 +1,44 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylationEPICanno.ilm10b3.hg19" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2dac8e889486386eaea1bb7ce1beea2e +about: + description: An annotation package for Illumina's EPIC methylation arrays. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation for Illumina's EPIC methylation arrays build: - number: 15 + noarch: generic + number: 16 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19 + path: recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19 + version: 0.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2dac8e889486386eaea1bb7ce1beea2e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation for Illumina''s EPIC methylation arrays' - description: 'An annotation package for Illumina''s EPIC methylation arrays.' -extra: - parent_recipe: - name: bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19 - path: recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19 - version: 0.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml index 70a78787f09b0..f37c8ba513475 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml @@ -1,44 +1,44 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylationEPICanno.ilm10b4.hg19" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d0c05917bcbf9ba1e354380d4e17a77 +about: + description: An annotation package for Illumina's EPIC methylation arrays. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation for Illumina's EPIC methylation arrays build: - number: 15 + noarch: generic + number: 16 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 + path: recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 + version: 0.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2d0c05917bcbf9ba1e354380d4e17a77 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation for Illumina''s EPIC methylation arrays' - description: 'An annotation package for Illumina''s EPIC methylation arrays.' -extra: - parent_recipe: - name: bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 - path: recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 - version: 0.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml index 2f570b1de65ff..9f6162654d935 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml @@ -1,44 +1,44 @@ {% set version = "0.3.0" %} {% set name = "IlluminaHumanMethylationEPICmanifest" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c6b0268de177badfe0b8184002da7e16 +about: + description: A manifest package for Illumina's EPIC methylation arrays. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Manifest for Illumina's EPIC methylation arrays build: - number: 16 + noarch: generic + number: 17 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminahumanmethylationepicmanifest", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-illuminahumanmethylationepicmanifest + path: recipes/bioconductor-illuminahumanmethylationepicmanifest + version: 0.3.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c6b0268de177badfe0b8184002da7e16 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Manifest for Illumina''s EPIC methylation arrays' - description: 'A manifest package for Illumina''s EPIC methylation arrays.' -extra: - parent_recipe: - name: bioconductor-illuminahumanmethylationepicmanifest - path: recipes/bioconductor-illuminahumanmethylationepicmanifest - version: 0.3.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminahumanv1.db/meta.yaml b/recipes/bioconductor-illuminahumanv1.db/meta.yaml index cc147efd5d97d..b3c3b604496d4 100644 --- a/recipes/bioconductor-illuminahumanv1.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv1.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanv1.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2c362256b7be2861b8bf6e0d1fe46786 +about: + description: Illumina HumanWG6v1 annotation data (chip illuminaHumanv1) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina HumanWG6v1 annotation data (chip illuminaHumanv1) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminahumanv1.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2c362256b7be2861b8bf6e0d1fe46786 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina HumanWG6v1 annotation data (chip illuminaHumanv1)' - description: 'Illumina HumanWG6v1 annotation data (chip illuminaHumanv1) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminahumanv2.db/meta.yaml b/recipes/bioconductor-illuminahumanv2.db/meta.yaml index e86b530f95ba8..6cd32aa3b99e1 100644 --- a/recipes/bioconductor-illuminahumanv2.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv2.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanv2.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 006de5f671a9a68fb27a6b6bce39c555 +about: + description: Illumina HumanWG6v2 annotation data (chip illuminaHumanv2) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina HumanWG6v2 annotation data (chip illuminaHumanv2) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminahumanv2.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 006de5f671a9a68fb27a6b6bce39c555 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina HumanWG6v2 annotation data (chip illuminaHumanv2)' - description: 'Illumina HumanWG6v2 annotation data (chip illuminaHumanv2) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminahumanv2beadid.db/meta.yaml b/recipes/bioconductor-illuminahumanv2beadid.db/meta.yaml index b94e962adf513..e159c2762903b 100644 --- a/recipes/bioconductor-illuminahumanv2beadid.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv2beadid.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "1.8.0" %} {% set name = "illuminaHumanv2BeadID.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b5a2b2deaa9a9b245a141043e7bc5270 +about: + description: 'Illumina HumanWGv2 annotation data (chip illuminaHumanv2BeadID) assembled using data from public repositories to be used with data summarized from bead-level data with numeric ArrayAddressIDs as keys. Illumina probes with a No match or Bad quality score were removed prior to annotation. See http://www.compbio.group.cam.ac.uk/Resources/Annotation/index.html and Barbosa-Morais et al (2010) A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Research.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina HumanWGv2 annotation data (chip illuminaHumanv2BeadID) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminahumanv2beadid.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b5a2b2deaa9a9b245a141043e7bc5270 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina HumanWGv2 annotation data (chip illuminaHumanv2BeadID)' - description: 'Illumina HumanWGv2 annotation data (chip illuminaHumanv2BeadID) assembled using data from public repositories to be used with data summarized from bead-level data with numeric ArrayAddressIDs as keys. Illumina probes with a No match or Bad quality score were removed prior to annotation. See http://www.compbio.group.cam.ac.uk/Resources/Annotation/index.html and Barbosa-Morais et al (2010) A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Research.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminahumanv3.db/meta.yaml b/recipes/bioconductor-illuminahumanv3.db/meta.yaml index 004dc46800cdb..13035262efab3 100644 --- a/recipes/bioconductor-illuminahumanv3.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv3.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanv3.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7d9e7534f0b60f0e3e7473e545ef373d +about: + description: Illumina HumanHT12v3 annotation data (chip illuminaHumanv3) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina HumanHT12v3 annotation data (chip illuminaHumanv3) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminahumanv3.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7d9e7534f0b60f0e3e7473e545ef373d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina HumanHT12v3 annotation data (chip illuminaHumanv3)' - description: 'Illumina HumanHT12v3 annotation data (chip illuminaHumanv3) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminahumanv4.db/meta.yaml b/recipes/bioconductor-illuminahumanv4.db/meta.yaml index e40ca66f6cf27..b0ba609ba8260 100644 --- a/recipes/bioconductor-illuminahumanv4.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanv4.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanv4.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 42d554559ac0106dc71317ffaf466421 +about: + description: Illumina HumanHT12v4 annotation data (chip illuminaHumanv4) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina HumanHT12v4 annotation data (chip illuminaHumanv4) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminahumanv4.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 42d554559ac0106dc71317ffaf466421 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina HumanHT12v4 annotation data (chip illuminaHumanv4)' - description: 'Illumina HumanHT12v4 annotation data (chip illuminaHumanv4) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminahumanwgdaslv3.db/meta.yaml b/recipes/bioconductor-illuminahumanwgdaslv3.db/meta.yaml index dcb880875fc8c..d885ff638c16d 100644 --- a/recipes/bioconductor-illuminahumanwgdaslv3.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanwgdaslv3.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanWGDASLv3.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 32e8e24555c16f6d0148438d4a841ab8 +about: + description: Illumina HumanHT12WGDASLv3 annotation data (chip illuminaHumanWGDASLv3) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina HumanHT12WGDASLv3 annotation data (chip illuminaHumanWGDASLv3) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminahumanwgdaslv3.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 32e8e24555c16f6d0148438d4a841ab8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina HumanHT12WGDASLv3 annotation data (chip illuminaHumanWGDASLv3)' - description: 'Illumina HumanHT12WGDASLv3 annotation data (chip illuminaHumanWGDASLv3) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminahumanwgdaslv4.db/meta.yaml b/recipes/bioconductor-illuminahumanwgdaslv4.db/meta.yaml index da9c7a5e9aa5d..45aae48d3a099 100644 --- a/recipes/bioconductor-illuminahumanwgdaslv4.db/meta.yaml +++ b/recipes/bioconductor-illuminahumanwgdaslv4.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "1.26.0" %} {% set name = "illuminaHumanWGDASLv4.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4cc1f192de838f2b6c1b148706d354ca +about: + description: Illumina HumanWGDASLv4 annotation data (chip illuminaHumanWGDASLv4) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina HumanWGDASLv4 annotation data (chip illuminaHumanWGDASLv4) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminahumanwgdaslv4.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4cc1f192de838f2b6c1b148706d354ca + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina HumanWGDASLv4 annotation data (chip illuminaHumanWGDASLv4)' - description: 'Illumina HumanWGDASLv4 annotation data (chip illuminaHumanWGDASLv4) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminaio/meta.yaml b/recipes/bioconductor-illuminaio/meta.yaml index be0a242b5324f..e30ebf1c30e07 100644 --- a/recipes/bioconductor-illuminaio/meta.yaml +++ b/recipes/bioconductor-illuminaio/meta.yaml @@ -1,25 +1,40 @@ -{% set version = "0.44.0" %} +{% set version = "0.48.0" %} {% set name = "illuminaio" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for parsing Illumina's microarray output files, including IDAT. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Parsing Illumina Microarray Output Files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5bf0b60249c92ef8408564391a69a97d build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminaio", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:illuminaio + parent_recipe: + name: bioconductor-illuminaio + path: recipes/bioconductor-illuminaio + version: 0.22.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2), BiocStyle requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - r-base64 @@ -28,25 +43,16 @@ requirements: run: - r-base - r-base64 - build: - - {{ compiler('c') }} - - make + +source: + md5: 96c3a34369cebbffbd6e13da17d4344a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Parsing Illumina Microarray Output Files' - description: 'Tools for parsing Illumina''s microarray output files, including IDAT.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:illuminaio - parent_recipe: - name: bioconductor-illuminaio - path: recipes/bioconductor-illuminaio - version: 0.22.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminamousev1.db/meta.yaml b/recipes/bioconductor-illuminamousev1.db/meta.yaml index f0095683a0190..28ab80997bff2 100644 --- a/recipes/bioconductor-illuminamousev1.db/meta.yaml +++ b/recipes/bioconductor-illuminamousev1.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "1.26.0" %} {% set name = "illuminaMousev1.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 13818c3b9acabe75550492bbe638fc05 +about: + description: Illumina MouseWG6v1 annotation data (chip illuminaMousev1) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina MouseWG6v1 annotation data (chip illuminaMousev1) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminamousev1.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 13818c3b9acabe75550492bbe638fc05 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina MouseWG6v1 annotation data (chip illuminaMousev1)' - description: 'Illumina MouseWG6v1 annotation data (chip illuminaMousev1) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminamousev1p1.db/meta.yaml b/recipes/bioconductor-illuminamousev1p1.db/meta.yaml index e2dbd5a55ed59..7cb471a1418fb 100644 --- a/recipes/bioconductor-illuminamousev1p1.db/meta.yaml +++ b/recipes/bioconductor-illuminamousev1p1.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "1.26.0" %} {% set name = "illuminaMousev1p1.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f6a4af01480a6f8d1d2d9b9b64a2b073 +about: + description: Illumina MouseWG6v1p1 annotation data (chip illuminaMousev1p1) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina MouseWG6v1p1 annotation data (chip illuminaMousev1p1) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminamousev1p1.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f6a4af01480a6f8d1d2d9b9b64a2b073 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina MouseWG6v1p1 annotation data (chip illuminaMousev1p1)' - description: 'Illumina MouseWG6v1p1 annotation data (chip illuminaMousev1p1) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminamousev2.db/meta.yaml b/recipes/bioconductor-illuminamousev2.db/meta.yaml index 405b1d50f2aa1..faff26e621903 100644 --- a/recipes/bioconductor-illuminamousev2.db/meta.yaml +++ b/recipes/bioconductor-illuminamousev2.db/meta.yaml @@ -1,47 +1,53 @@ {% set version = "1.26.0" %} {% set name = "illuminaMousev2.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Illumina MouseWG6v2 annotation data (chip illuminaMousev2) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina MouseWG6v2 annotation data (chip illuminaMousev2) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fba228a71f264f976d8cdb035861974d build: - number: 17 + noarch: generic + number: 18 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminamousev2.db", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-illuminamousev2.db + path: recipes/bioconductor-illuminamousev2.db + version: 1.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: fba228a71f264f976d8cdb035861974d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina MouseWG6v2 annotation data (chip illuminaMousev2)' - description: 'Illumina MouseWG6v2 annotation data (chip illuminaMousev2) assembled using data from public repositories' -extra: - parent_recipe: - name: bioconductor-illuminamousev2.db - path: recipes/bioconductor-illuminamousev2.db - version: 1.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-illuminaratv1.db/meta.yaml b/recipes/bioconductor-illuminaratv1.db/meta.yaml index 68fc32da96338..5341ce947a3ee 100644 --- a/recipes/bioconductor-illuminaratv1.db/meta.yaml +++ b/recipes/bioconductor-illuminaratv1.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "1.26.0" %} {% set name = "illuminaRatv1.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5de2324d7b96c0cdb3301ef269341aa8 +about: + description: Illumina Ratv1 annotation data (chip illuminaRatv1) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina Ratv1 annotation data (chip illuminaRatv1) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-illuminaratv1.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5de2324d7b96c0cdb3301ef269341aa8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina Ratv1 annotation data (chip illuminaRatv1)' - description: 'Illumina Ratv1 annotation data (chip illuminaRatv1) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-iloreg/meta.yaml b/recipes/bioconductor-iloreg/meta.yaml index a6a8493c995e4..dc79fbe8d2eb8 100644 --- a/recipes/bioconductor-iloreg/meta.yaml +++ b/recipes/bioconductor-iloreg/meta.yaml @@ -1,29 +1,33 @@ -{% set version = "1.10.0" %} +{% set version = "1.16.0" %} {% set name = "ILoReg" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: ILoReg is a tool for identification of cell populations from scRNA-seq data. In particular, ILoReg is useful for finding cell populations with subtle transcriptomic differences. The method utilizes a self-supervised learning method, called Iteratitive Clustering Projection (ICP), to find cluster probabilities, which are used in noise reduction prior to PCA and the subsequent hierarchical clustering and t-SNE steps. Additionally, functions for differential expression analysis to find gene markers for the populations and gene expression visualization are provided. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b4425d7d9a6bc0201dcd9c1d0b1c98c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic -# Suggests: knitr, rmarkdown + run_exports: '{{ pin_subpackage("bioconductor-iloreg", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, BiocStyle requirements: + host: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-aricode - r-base - r-cluster @@ -47,10 +51,11 @@ requirements: - r-scales - r-sparsem - r-umap + run: - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-singlecellexperiment >=1.22.0,<1.23.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-aricode - r-base - r-cluster @@ -74,13 +79,16 @@ requirements: - r-scales - r-sparsem - r-umap + +source: + md5: 61adff20a5da2b5904280b6fca673407 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data' - description: 'ILoReg is a tool for identification of cell populations from scRNA-seq data. In particular, ILoReg is useful for finding cell populations with subtle transcriptomic differences. The method utilizes a self-supervised learning method, called Iteratitive Clustering Projection (ICP), to find cluster probabilities, which are used in noise reduction prior to PCA and the subsequent hierarchical clustering and t-SNE steps. Additionally, functions for differential expression analysis to find gene markers for the populations and gene expression visualization are provided.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-imas/meta.yaml b/recipes/bioconductor-imas/meta.yaml index 9000f1e30f504..344be10a72f8b 100644 --- a/recipes/bioconductor-imas/meta.yaml +++ b/recipes/bioconductor-imas/meta.yaml @@ -1,38 +1,47 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "IMAS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Integrative analysis of Multi-omics data for Alternative splicing. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Integrative analysis of Multi-omics data for Alternative Splicing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c86deaedf1d19981dbfcea7a3b53d331 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-imas", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-imas + path: recipes/bioconductor-imas + version: 1.4.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, RUnit requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-ivas >=2.22.0,<2.23.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-ivas >=2.26.0,<2.27.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-doparallel - r-foreach @@ -43,18 +52,19 @@ requirements: - r-lme4 - r-matrix - r-survival + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-ivas >=2.22.0,<2.23.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-ivas >=2.26.0,<2.27.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-doparallel - r-foreach @@ -65,18 +75,16 @@ requirements: - r-lme4 - r-matrix - r-survival + +source: + md5: 45a412d3daeabfefbdc1ef933977fcfe + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Integrative analysis of Multi-omics data for Alternative Splicing' - description: 'Integrative analysis of Multi-omics data for Alternative splicing.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - parent_recipe: - name: bioconductor-imas - path: recipes/bioconductor-imas - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-imcdatasets/meta.yaml b/recipes/bioconductor-imcdatasets/meta.yaml index 50be0d4514827..e1d54b637f048 100644 --- a/recipes/bioconductor-imcdatasets/meta.yaml +++ b/recipes/bioconductor-imcdatasets/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "imcdatasets" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The imcdatasets package provides access to publicly available IMC datasets. IMC is a technology that enables measurement of > 40 proteins from tissue sections. The generated images can be segmented to extract single cell data. Datasets typically consist of three elements: a SingleCellExperiment object containing single cell data, a CytoImageList object containing multichannel images and a CytoImageList object containing the cell masks that were used to extract the single cell data from the images.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Collection of publicly available imaging mass cytometry (IMC) datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6e687f10502d7d9d369c384e99977953 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-imcdatasets", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat requirements: host: - - 'bioconductor-cytomapper >=1.14.0,<1.15.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - bioconductor-cytomapper >=1.18.0,<1.19.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 - r-base run: - - 'bioconductor-cytomapper >=1.14.0,<1.15.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - bioconductor-cytomapper >=1.18.0,<1.19.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: c93de5b533351ab9d7414616e1d45d08 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Collection of publicly available imaging mass cytometry (IMC) datasets' - description: 'The imcdatasets package provides access to publicly available IMC datasets. IMC is a technology that enables measurement of > 40 proteins from tissue sections. The generated images can be segmented to extract single cell data. Datasets typically consist of three elements: a SingleCellExperiment object containing single cell data, a CytoImageList object containing multichannel images and a CytoImageList object containing the cell masks that were used to extract the single cell data from the images.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-imcdatasets/post-link.sh b/recipes/bioconductor-imcdatasets/post-link.sh index 12db5126d417b..bd1d42adaa4b3 100644 --- a/recipes/bioconductor-imcdatasets/post-link.sh +++ b/recipes/bioconductor-imcdatasets/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "imcdatasets-1.10.0" +installBiocDataPackage.sh "imcdatasets-1.14.0" diff --git a/recipes/bioconductor-imcrtools/meta.yaml b/recipes/bioconductor-imcrtools/meta.yaml index 50de270226360..7ae68a22baa94 100644 --- a/recipes/bioconductor-imcrtools/meta.yaml +++ b/recipes/bioconductor-imcrtools/meta.yaml @@ -1,37 +1,40 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "imcRtools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This R package supports the handling and analysis of imaging mass cytometry and other highly multiplexed imaging data. The main functionality includes reading in single-cell data after image segmentation and measurement, data formatting to perform channel spillover correction and a number of spatial analysis approaches. First, cell-cell interactions are detected via spatial graph construction; these graphs can be visualized with cells representing nodes and interactions representing edges. Furthermore, per cell, its direct neighbours are summarized to allow spatial clustering. Per image/grouping level, interactions between types of cells are counted, averaged and compared against random permutations. In that way, types of cells that interact more (attraction) or less (avoidance) frequently than expected by chance are detected. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Methods for imaging mass cytometry data analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 483b782cf0adc433cf956e4ca52c393c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-imcrtools", max_pin="x.x") }}' - noarch: generic -# Suggests: CATALYST, grid, BiocStyle, knitr, rmarkdown, markdown, testthat + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: CATALYST, grid, tidyr, BiocStyle, knitr, rmarkdown, markdown, testthat requirements: + host: - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-cytomapper >=1.14.0,<1.15.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-cytomapper >=1.18.0,<1.19.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-abind - r-base - r-concaveman @@ -45,6 +48,7 @@ requirements: - r-magrittr - r-pheatmap - r-readr + - r-rlang - r-rtriangle - r-sf - r-stringr @@ -52,17 +56,18 @@ requirements: - r-tidyselect - r-viridis - r-vroom + run: - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-cytomapper >=1.14.0,<1.15.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-cytomapper >=1.18.0,<1.19.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-abind - r-base - r-concaveman @@ -76,6 +81,7 @@ requirements: - r-magrittr - r-pheatmap - r-readr + - r-rlang - r-rtriangle - r-sf - r-stringr @@ -83,13 +89,16 @@ requirements: - r-tidyselect - r-viridis - r-vroom + +source: + md5: 05b80d9fcab29c6827e7a67cc17ab353 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Methods for imaging mass cytometry data analysis' - description: 'This R package supports the handling and analysis of imaging mass cytometry and other highly multiplexed imaging data. The main functionality includes reading in single-cell data after image segmentation and measurement, data formatting to perform channel spillover correction and a number of spatial analysis approaches. First, cell-cell interactions are detected via spatial graph construction; these graphs can be visualized with cells representing nodes and interactions representing edges. Furthermore, per cell, its direct neighbours are summarized to allow spatial clustering. Per image/grouping level, interactions between types of cells are counted, averaged and compared against random permutations. In that way, types of cells that interact more (attraction) or less (avoidance) frequently than expected by chance are detected.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-imman/meta.yaml b/recipes/bioconductor-imman/meta.yaml index 4a0b5412457fe..3d3d3f73e58f2 100644 --- a/recipes/bioconductor-imman/meta.yaml +++ b/recipes/bioconductor-imman/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "IMMAN" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6e3ac40584a93ea233ba0b082a4d79aa +about: + description: Reconstructing Interlog Protein Network (IPN) integrated from several Protein protein Interaction Networks (PPINs). Using this package, overlaying different PPINs to mine conserved common networks between diverse species will be applicable. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Interlog protein network reconstruction by Mapping and Mining ANalysis build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-imman", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-stringdb >=2.14.0,<2.15.0' + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-stringdb >=2.18.0,<2.19.0 - r-base - r-igraph - r-seqinr run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-stringdb >=2.14.0,<2.15.0' + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-stringdb >=2.18.0,<2.19.0 - r-base - r-igraph - r-seqinr +source: + md5: d24a18ee9927aa1357ea998c764711a9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Interlog protein network reconstruction by Mapping and Mining ANalysis' - description: 'Reconstructing Interlog Protein Network (IPN) integrated from several Protein protein Interaction Networks (PPINs). Using this package, overlaying different PPINs to mine conserved common networks between diverse species will be applicable.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-immunoclust/meta.yaml b/recipes/bioconductor-immunoclust/meta.yaml index 32861095ef561..76a08e835b56d 100644 --- a/recipes/bioconductor-immunoclust/meta.yaml +++ b/recipes/bioconductor-immunoclust/meta.yaml @@ -1,49 +1,51 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "immunoClust" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: immunoClust is a model based clustering approach for Flow Cytometry samples. The cell-events of single Flow Cytometry samples are modelled by a mixture of multinominal normal- or t-distributions. The cell-event clusters of several samples are modelled by a mixture of multinominal normal-distributions aiming stable co-clusters across these samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: immunoClust - Automated Pipeline for Population Detection in Flow Cytometry -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b83f47eaa19d45984b19f4071b455873 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-immunoclust", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, utils, testthat -# SystemRequirements: gsl requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-lattice - libblas - liblapack - - gsl run: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-lattice - - gsl - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 5b3098131f1d50cb13fa632992dbfddb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'immunoClust - Automated Pipeline for Population Detection in Flow Cytometry' - description: 'immunoClust is a model based clustering approach for Flow Cytometry samples. The cell-events of single Flow Cytometry samples are modelled by a mixture of multinominal normal- or t-distributions. The cell-event clusters of several samples are modelled by a mixture of multinominal normal-distributions aiming stable co-clusters across these samples.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-immunogenviewer/build.sh b/recipes/bioconductor-immunogenviewer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-immunogenviewer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-immunogenviewer/meta.yaml b/recipes/bioconductor-immunogenviewer/meta.yaml new file mode 100644 index 0000000000000..814e2d3e20ed3 --- /dev/null +++ b/recipes/bioconductor-immunogenviewer/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.0.0" %} +{% set name = "immunogenViewer" %} +{% set bioc = "3.20" %} + +about: + description: Plots protein properties and visualizes position of peptide immunogens within protein sequence. Allows evaluation of immunogens based on structural and functional annotations to infer suitability for antibody-based methods aiming to detect native proteins. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Apache License (>= 2) + summary: Visualization and evaluation of protein immunogens + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-immunogenviewer", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), DT +requirements: + host: + - bioconductor-uniprot.ws >=2.46.0,<2.47.0 + - r-base + - r-ggplot2 + - r-httr + - r-jsonlite + - r-patchwork + run: + - bioconductor-uniprot.ws >=2.46.0,<2.47.0 + - r-base + - r-ggplot2 + - r-httr + - r-jsonlite + - r-patchwork + +source: + md5: e8e74b422151cbe6d35e17e4f91ddbc3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-immunotation/meta.yaml b/recipes/bioconductor-immunotation/meta.yaml index eb969b28a159d..8590abea0a5e2 100644 --- a/recipes/bioconductor-immunotation/meta.yaml +++ b/recipes/bioconductor-immunotation/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "immunotation" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MHC (major histocompatibility complex) molecules are cell surface complexes that present antigens to T cells. The repertoire of antigens presented in a given genetic background largely depends on the sequence of the encoded MHC molecules, and thus, in humans, on the highly variable HLA (human leukocyte antigen) genes of the hyperpolymorphic HLA locus. More than 28,000 different HLA alleles have been reported, with significant differences in allele frequencies between human populations worldwide. Reproducible and consistent annotation of HLA alleles in large-scale bioinformatics workflows remains challenging, because the available reference databases and software tools often use different HLA naming schemes. The package immunotation provides tools for consistent annotation of HLA genes in typical immunoinformatics workflows such as for example the prediction of MHC-presented peptides in different human donors. Converter functions that provide mappings between different HLA naming schemes are based on the MHC restriction ontology (MRO). The package also provides automated access to HLA alleles frequencies in worldwide human reference populations stored in the Allele Frequency Net Database. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Tools for working with diverse immune genes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b05bb33e3987de27d181d8e44e468f62 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-immunotation", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, rmarkdown, BiocStyle, knitr, testthat, DT requirements: host: @@ -45,13 +47,16 @@ requirements: - r-stringr - r-tidyr - r-xml2 + +source: + md5: 3b496af731dee7e84ff52048d5116937 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Tools for working with diverse immune genes' - description: 'MHC (major histocompatibility complex) molecules are cell surface complexes that present antigens to T cells. The repertoire of antigens presented in a given genetic background largely depends on the sequence of the encoded MHC molecules, and thus, in humans, on the highly variable HLA (human leukocyte antigen) genes of the hyperpolymorphic HLA locus. More than 28,000 different HLA alleles have been reported, with significant differences in allele frequencies between human populations worldwide. Reproducible and consistent annotation of HLA alleles in large-scale bioinformatics workflows remains challenging, because the available reference databases and software tools often use different HLA naming schemes. The package immunotation provides tools for consistent annotation of HLA genes in typical immunoinformatics workflows such as for example the prediction of MHC-presented peptides in different human donors. Converter functions that provide mappings between different HLA naming schemes are based on the MHC restriction ontology (MRO). The package also provides automated access to HLA alleles frequencies in worldwide human reference populations stored in the Allele Frequency Net Database.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-impcdata/meta.yaml b/recipes/bioconductor-impcdata/meta.yaml index 6d8b9e6c09f7b..a886a0677338f 100644 --- a/recipes/bioconductor-impcdata/meta.yaml +++ b/recipes/bioconductor-impcdata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "IMPCdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c4a243d4a15f680abfb5d61a951c620d +about: + description: Package contains methods for data retrieval from IMPC Database. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Retrieves data from IMPC database build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-impcdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base @@ -26,13 +25,14 @@ requirements: run: - r-base - r-rjson +source: + md5: 40f6bfe3b3597ca0716dc08c8d2d86d2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Retrieves data from IMPC database' - description: 'Package contains methods for data retrieval from IMPC Database.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-impute/meta.yaml b/recipes/bioconductor-impute/meta.yaml index 95703fe1a101b..a84b6658a546e 100644 --- a/recipes/bioconductor-impute/meta.yaml +++ b/recipes/bioconductor-impute/meta.yaml @@ -1,43 +1,21 @@ -{% set version = "1.76.0" %} +{% set version = "1.80.0" %} {% set name = "impute" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Imputation for microarray data (currently KNN only) + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'impute: Imputation for microarray data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8e974dcc31c3507ebcc8984b2d7943f9 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-impute", max_pin="x.x") }}' -requirements: - host: - - r-base - - libblas - - liblapack - run: - - r-base - build: - - {{ compiler('c') }} - - {{ compiler('fortran') }} - - make -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'impute: Imputation for microarray data' - description: 'Imputation for microarray data (currently KNN only)' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + extra: additional-platforms: - linux-aarch64 @@ -49,3 +27,31 @@ extra: path: recipes/bioconductor-impute version: 1.54.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('fortran') }} + - make + host: + - r-base + - libblas + - liblapack + run: + - r-base + +source: + md5: 8d8453b24e87eec606c28c8d6181db8a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-indac.db/meta.yaml b/recipes/bioconductor-indac.db/meta.yaml index 280f0ef419b4f..05843af2c9f95 100644 --- a/recipes/bioconductor-indac.db/meta.yaml +++ b/recipes/bioconductor-indac.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "indac.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cba72edcf7278033151e0eac077d8ff8 +about: + description: INDAC FlyChip_long_oligonucleotide_002 (FL002) annotation data (chip indac) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: INDAC FlyChip_long_oligonucleotide_002 (FL002) annotation data (chip indac) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-indac.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.dm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.dm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.dm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: cba72edcf7278033151e0eac077d8ff8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'INDAC FlyChip_long_oligonucleotide_002 (FL002) annotation data (chip indac)' - description: 'INDAC FlyChip_long_oligonucleotide_002 (FL002) annotation data (chip indac) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-indeed/meta.yaml b/recipes/bioconductor-indeed/meta.yaml index 1e3e32686ddea..85d473879277d 100644 --- a/recipes/bioconductor-indeed/meta.yaml +++ b/recipes/bioconductor-indeed/meta.yaml @@ -1,49 +1,55 @@ -{% set version = "2.16.0" %} +{% set version = "2.20.0" %} {% set name = "INDEED" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'An R package for integrated differential expression and differential network analysis based on omic data for cancer biomarker discovery. Both correlation and partial correlation can be used to generate differential network to aid the traditional differential expression analysis to identify changes between biomolecules on both their expression and pairwise association levels. A detailed description of the methodology has been published in Methods journal (PMID: 27592383). An interactive visualization feature allows for the exploration and selection of candidate biomarkers.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 457badfae1608eb2c198b89526abe740 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-indeed", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-indeed + path: recipes/bioconductor-indeed + version: 1.0.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 2.0.0) requirements: host: - r-base - - 'r-devtools >=1.13.0' - - 'r-glasso >=1.8' - - 'r-igraph >=1.2.4' - - 'r-visnetwork >=2.0.6' + - r-devtools >=1.13.0 + - r-glasso >=1.8 + - r-igraph >=1.2.4 + - r-visnetwork >=2.0.6 run: - r-base - - 'r-devtools >=1.13.0' - - 'r-glasso >=1.8' - - 'r-igraph >=1.2.4' - - 'r-visnetwork >=2.0.6' + - r-devtools >=1.13.0 + - r-glasso >=1.8 + - r-igraph >=1.2.4 + - r-visnetwork >=2.0.6 + +source: + md5: bead8a561e0225c4447fd94c49cdb2c5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package' - description: 'An R package for integrated differential expression and differential network analysis based on omic data for cancer biomarker discovery. Both correlation and partial correlation can be used to generate differential network to aid the traditional differential expression analysis to identify changes between biomolecules on both their expression and pairwise association levels. A detailed description of the methodology has been published in Methods journal (PMID: 27592383). An interactive visualization feature allows for the exploration and selection of candidate biomarkers.' -extra: - parent_recipe: - name: bioconductor-indeed - path: recipes/bioconductor-indeed - version: 1.0.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-inetgrate/meta.yaml b/recipes/bioconductor-inetgrate/meta.yaml index 2e2f82d637edc..5fac382a62fa4 100644 --- a/recipes/bioconductor-inetgrate/meta.yaml +++ b/recipes/bioconductor-inetgrate/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "iNETgrate" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The iNETgrate package provides functions to build a correlation network in which nodes are genes. DNA methylation and gene expression data are integrated to define the connections between genes. This network is used to identify modules (clusters) of genes. The biological information in each of the resulting modules is represented by an eigengene. These biological signatures can be used as features e.g., for classification of patients into risk categories. The resulting biological signatures are very robust and give a holistic view of the underlying molecular changes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Integrates DNA methylation data with gene expression in a single gene network -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fb3e503060d4294162e8690a6bb41059 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-inetgrate", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, IlluminaHumanMethylation450kanno.ilmn12.hg19, AnnotationDbi, sesameData, TCGAbiolinks (>= 2.29.4) requirements: host: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-pigengene >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-homo.sapiens >=1.3.0,<1.4.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-pigengene >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-caret - r-glmnet @@ -40,12 +42,12 @@ requirements: - r-tidyselect - r-wgcna run: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-pigengene >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-homo.sapiens >=1.3.0,<1.4.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-pigengene >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-caret - r-glmnet @@ -57,13 +59,16 @@ requirements: - r-tidyr - r-tidyselect - r-wgcna + +source: + md5: cb056d979ec3c5bea91f047f40cdd502 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Integrates DNA methylation data with gene expression in a single gene network' - description: 'The iNETgrate package provides functions to build a correlation network in which nodes are genes. DNA methylation and gene expression data are integrated to define the connections between genes. This network is used to identify modules (clusters) of genes. The biological information in each of the resulting modules is represented by an eigengene. These biological signatures can be used as features e.g., for classification of patients into risk categories. The resulting biological signatures are very robust and give a holistic view of the underlying molecular changes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-infercnv/meta.yaml b/recipes/bioconductor-infercnv/meta.yaml index bc5498d7db6df..feb35807a8580 100644 --- a/recipes/bioconductor-infercnv/meta.yaml +++ b/recipes/bioconductor-infercnv/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "infercnv" %} -{% set bioc = "3.19" %} +{% set bioc = "3.20" %} + +about: + description: Using single-cell RNA-Seq expression to visualize CNV in cells. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_3_clause + file LICENSE + license_file: LICENSE + summary: Infer Copy Number Variation from Single-Cell RNA-Seq Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: cd7baf7107beee52484e70abc6a48edb09ec877f734226131336adffb14b28ba build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-infercnv", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat # SystemRequirements: JAGS 4.x.y requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'r-htmltools >=0.5.7' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-ape - r-argparse - r-base @@ -56,13 +58,13 @@ requirements: - r-rjags - r-seurat - r-tidyr - - 'jags 4.*.*' + - jags 4.*.* + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'r-htmltools >=0.5.7' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-ape - r-argparse - r-base @@ -91,14 +93,17 @@ requirements: - r-rjags - r-seurat - r-tidyr - - 'jags 4.*.*' + - jags 4.*.* + +source: + md5: f7c2ce4a64fbb3d68f38375f8a96f03e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_3_clause + file LICENSE' - summary: 'Infer Copy Number Variation from Single-Cell RNA-Seq Data' - description: 'Using single-cell RNA-Seq expression to visualize CNV in cells.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-infinityflow/build_failure.linux-64.yaml b/recipes/bioconductor-infinityflow/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..aaf03a2d4ff01 --- /dev/null +++ b/recipes/bioconductor-infinityflow/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 97757153e78ef815f6e2cfa7b52288e47a8eaaca33f7e259b02791d12b4595b6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec(">=3.5.0,<3.5.1.0a0"), MatchSpec("r-xgboost==0.80=mro350h255eb88_1")} + Encountered problems while solving: + - nothing provides mro-base >=3.5.0,<3.5.1.0a0 needed by r-xgboost-0.80-mro350h255eb88_1 + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-xgboost[0m is not installable because there are no viable options + [31mr-xgboost 0.80[0m would require + [31mmro-base >=3.5.0,<3.5.1.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-xgboost [0.80|0.81|0.82|0.90|1.0.2][0m would require + [31mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [0.82|0.90|...|1.4.0][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.0.2|1.1.1|...|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.4.0|1.4.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec(">=3.5.0,<3.5.1.0a0"), MatchSpec("r-xgboost==0.80=mro350h255eb88_1")} + Encountered problems while solving: + - nothing provides mro-base >=3.5.0,<3.5.1.0a0 needed by r-xgboost-0.80-mro350h255eb88_1 + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-xgboost[0m is not installable because there are no viable options + [31mr-xgboost 0.80[0m would require + [31mmro-base >=3.5.0,<3.5.1.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-xgboost [0.80|0.81|0.82|0.90|1.0.2][0m would require + [31mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [0.82|0.90|...|1.4.0][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.0.2|1.1.1|...|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.4.0|1.4.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-infinityflow/meta.yaml b/recipes/bioconductor-infinityflow/meta.yaml index f1047378cf0e6..a7a6ed50863d3 100644 --- a/recipes/bioconductor-infinityflow/meta.yaml +++ b/recipes/bioconductor-infinityflow/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "infinityFlow" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Pipeline to analyze and merge data files produced by BioLegend's LEGENDScreen or BD Human Cell Surface Marker Screening Panel (BD Lyoplates). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e65e5163632d9351a8a1f1bb30d74d8f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-infinityflow", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071 requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-generics - r-gtools @@ -34,8 +36,8 @@ requirements: - r-uwot - r-xgboost run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-generics - r-gtools @@ -45,13 +47,16 @@ requirements: - r-raster - r-uwot - r-xgboost + +source: + md5: 401db5ce8ade415fa555be18af55eae2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions' - description: 'Pipeline to analyze and merge data files produced by BioLegend''s LEGENDScreen or BD Human Cell Surface Marker Screening Panel (BD Lyoplates).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-informeasure/meta.yaml b/recipes/bioconductor-informeasure/meta.yaml index 796fc46a7b4dc..fd05490517d25 100644 --- a/recipes/bioconductor-informeasure/meta.yaml +++ b/recipes/bioconductor-informeasure/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.10.0" %} +{% set version = "1.16.0" %} {% set name = "Informeasure" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45288bfbafcd9e2087662f7cb9c57c0e +about: + description: This package consolidates a comprehensive set of information measurements, encompassing mutual information, conditional mutual information, interaction information, partial information decomposition, and part mutual information. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: R implementation of information measures build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic -# Suggests: knitr, rmarkdown, testthat, SummarizedExperiment + run_exports: '{{ pin_subpackage("bioconductor-informeasure", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), SummarizedExperiment requirements: host: - r-base @@ -26,13 +25,14 @@ requirements: run: - r-base - r-entropy +source: + md5: b52fbbdf221f0437533a025776f59940 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'R implementation of Information measures' - description: 'This package compiles most of the information measures currently available: mutual information, conditional mutual information, interaction information, partial information decomposition and part mutual information. All of these estimators can be used to quantify nonlinear dependence between variables in (biological regulatory) network inference. The first estimator is used to infer bivariate networks while the last four estimators are dedicated to analysis of trivariate networks.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-inpas/meta.yaml b/recipes/bioconductor-inpas/meta.yaml index 9d51c47ac6612..06f0ea60f1342 100644 --- a/recipes/bioconductor-inpas/meta.yaml +++ b/recipes/bioconductor-inpas/meta.yaml @@ -1,40 +1,43 @@ -{% set version = "2.10.0" %} +{% set version = "2.14.0" %} {% set name = "InPAS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Alternative polyadenylation (APA) is one of the important post- transcriptional regulation mechanisms which occurs in most human genes. InPAS facilitates the discovery of novel APA sites and the differential usage of APA sites from RNA-Seq data. It leverages cleanUpdTSeq to fine tune identified APA sites by removing false sites. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d11dbf3351e3fec486c3da1a61bf6050 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-inpas", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics,BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, knitr, markdown, rmarkdown, rtracklayer, RUnit, grDevices, TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-cleanupdtseq >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-cleanupdtseq >=1.44.0,<1.45.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-batchtools - r-depmixs4 @@ -48,20 +51,21 @@ requirements: - r-readr - r-reshape2 - r-rsqlite + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-cleanupdtseq >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-cleanupdtseq >=1.44.0,<1.45.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-batchtools - r-depmixs4 @@ -75,13 +79,16 @@ requirements: - r-readr - r-reshape2 - r-rsqlite + +source: + md5: f4983122d1db9dbbea961de3b5d6e9da + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data' - description: 'Alternative polyadenylation (APA) is one of the important post- transcriptional regulation mechanisms which occurs in most human genes. InPAS facilitates the discovery of novel APA sites and the differential usage of APA sites from RNA-Seq data. It leverages cleanUpdTSeq to fine tune identified APA sites by removing false sites.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-inpower/meta.yaml b/recipes/bioconductor-inpower/meta.yaml index 352b849653f39..79345c8c4b8af 100644 --- a/recipes/bioconductor-inpower/meta.yaml +++ b/recipes/bioconductor-inpower/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "INPower" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An R package for computing the number of susceptibility SNPs and power of future studies + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + file LICENSE + license_file: LICENSE + summary: An R package for computing the number of susceptibility SNPs -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3b769c08ded506c713da036c30fe4da9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-inpower", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:inpower + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-inpower + path: recipes/bioconductor-inpower + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics requirements: host: @@ -27,21 +38,16 @@ requirements: run: - r-base - r-mvtnorm + +source: + md5: 3970fbee033347e77144646d9e60c4cb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-2 + file LICENSE' - summary: 'An R package for computing the number of susceptibility SNPs' - description: 'An R package for computing the number of susceptibility SNPs and power of future studies' - license_file: LICENSE -extra: - identifiers: - - biotools:inpower - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-inpower - path: recipes/bioconductor-inpower - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-inspect/build_failure.linux-64.yaml b/recipes/bioconductor-inspect/build_failure.linux-64.yaml deleted file mode 100644 index 95ece71c08362..0000000000000 --- a/recipes/bioconductor-inspect/build_failure.linux-64.yaml +++ /dev/null @@ -1,33 +0,0 @@ -recipe_sha: b6bbddaaff8dbbb23dad96d68412111023807b708179b0d3fa28588e58a8759a # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -reason: |- - Error: object ‘read.xls’ is not exported by 'namespace:gdata' -category: |- - compiler error -log: |- - 14:32:11 BIOCONDA INFO (OUT) ERROR: lazy loading failed for package ‘INSPEcT’ - 14:32:11 BIOCONDA INFO (OUT) During startup - Warning message: - 14:32:11 BIOCONDA INFO (OUT) Setting LC_TIME failed, using "C" - 14:32:11 BIOCONDA INFO (OUT) Error: object ‘read.xls’ is not exported by 'namespace:gdata' - 14:32:11 BIOCONDA INFO (OUT) Execution halted - 14:32:11 BIOCONDA INFO (OUT) * removing ‘/opt/conda/conda-bld/bioconductor-inspect_1702304851717/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/INSPEcT’ - 14:32:12 BIOCONDA INFO (OUT) Traceback (most recent call last): - 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/bin/conda-mambabuild", line 10, in - 14:32:12 BIOCONDA INFO (OUT) sys.exit(main()) - 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - 14:32:12 BIOCONDA INFO (OUT) call_conda_build(action, config) - 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - 14:32:12 BIOCONDA INFO (OUT) result = api.build( - 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - 14:32:12 BIOCONDA INFO (OUT) return build_tree( - 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - 14:32:12 BIOCONDA INFO (OUT) packages_from_this = build(metadata, stats, - 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - 14:32:12 BIOCONDA INFO (OUT) utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - 14:32:12 BIOCONDA INFO (OUT) return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - 14:32:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - 14:32:12 BIOCONDA INFO (OUT) raise subprocess.CalledProcessError(proc.returncode, _args) - 14:32:12 BIOCONDA INFO (OUT) subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-inspect_1702304851717/work/conda_build.sh']' returned non-zero exit status 1. - 14:32:21 BIOCONDA ERROR COMMAND FAILED (exited with 1): docker run -t --net host --rm -v /tmp/tmp24i5m63r/build_script.bash:/opt/build_script.bash -v /opt/mambaforge/envs/bioconda/conda-bld/:/opt/host-conda-bld -v /home/runner/work/bioconda-recipes/bioconda-recipes/recipes/bioconductor-inspect:/opt/recipe -e LANG=C.UTF-8 -e HOST_USER_ID=1001 quay.io/bioconda/bioconda-utils-build-env-cos7:2.11.0 /bin/bash /opt/build_script.bash - diff --git a/recipes/bioconductor-inspect/meta.yaml b/recipes/bioconductor-inspect/meta.yaml index 8036e06f7ea1b..da3e1435273da 100644 --- a/recipes/bioconductor-inspect/meta.yaml +++ b/recipes/bioconductor-inspect/meta.yaml @@ -1,86 +1,94 @@ -{% set version = "1.31.0" %} +{% set version = "1.36.0" %} {% set name = "INSPEcT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: INSPEcT (INference of Synthesis, Processing and dEgradation rates from Transcriptomic data) RNA-seq data in time-course experiments or steady-state conditions, with or without the support of nascent RNA data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Modeling RNA synthesis, processing and degradation with RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e48ba19e529a7072f52817ecd08d2b9c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-inspect", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:inspect + parent_recipe: + name: bioconductor-inspect + path: recipes/bioconductor-inspect + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-plgem >=1.74.0,<1.75.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-plgem >=1.78.0,<1.79.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0 - r-base - r-desolve - - r-gdata - r-kernsmooth - r-proc + - r-readxl - r-rootsolve - r-shiny + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-plgem >=1.74.0,<1.75.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-plgem >=1.78.0,<1.79.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0 - r-base - r-desolve - - r-gdata - r-kernsmooth - r-proc + - r-readxl - r-rootsolve - r-shiny + +source: + md5: e0f1db4ffc949c4b4ed6d6b141d77f5e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Modeling RNA synthesis, processing and degradation with RNA-seq data' - description: 'INSPEcT (INference of Synthesis, Processing and dEgradation rates from Transcriptomic data) RNA-seq data in time-course experiments or steady-state conditions, with or without the support of nascent RNA data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:inspect - parent_recipe: - name: bioconductor-inspect - path: recipes/bioconductor-inspect - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-intact/meta.yaml b/recipes/bioconductor-intact/meta.yaml index a273c8c9b8cd1..71b69e7ed2a8a 100644 --- a/recipes/bioconductor-intact/meta.yaml +++ b/recipes/bioconductor-intact/meta.yaml @@ -1,43 +1,52 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "INTACT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package integrates colocalization probabilities from colocalization analysis with transcriptome-wide association study (TWAS) scan summary statistics to implicate genes that may be biologically relevant to a complex trait. The probabilistic framework implemented in this package constrains the TWAS scan z-score-based likelihood using a gene-level colocalization probability. Given gene set annotations, this package can estimate gene set enrichment using posterior probabilities from the TWAS-colocalization integration step. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d8646f4acb0cbb31ccf53a672818be40 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-intact", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - r-base - r-bdsmatrix + - r-ggplot2 - r-numderiv - r-squarem + - r-tidyr run: - r-base - r-bdsmatrix + - r-ggplot2 - r-numderiv - r-squarem + - r-tidyr + +source: + md5: 38788d2ac09f0322ffb9ddc03478cd46 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis' - description: 'This package integrates colocalization probabilities from colocalization analysis with transcriptome-wide association study (TWAS) scan summary statistics to implicate genes that may be biologically relevant to a complex trait. The probabilistic framework implemented in this package constrains the TWAS scan z-score-based likelihood using a gene-level colocalization probability. Given gene set annotations, this package can estimate gene set enrichment using posterior probabilities from the TWAS-colocalization integration step.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-intad/meta.yaml b/recipes/bioconductor-intad/meta.yaml index 754ba4a2adcb7..2e80d7cc67db9 100644 --- a/recipes/bioconductor-intad/meta.yaml +++ b/recipes/bioconductor-intad/meta.yaml @@ -1,61 +1,66 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "InTAD" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package is focused on the detection of correlation between expressed genes and selected epigenomic signals (i.e. enhancers obtained from ChIP-seq data) either within topologically associated domains (TADs) or between chromatin contact loop anchors. Various parameters can be controlled to investigate the influence of external factors and visualization plots are available for each analysis step. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Search for correlation between epigenetic signals and gene expression in TADs -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2502f954bc06e364560216eb972c18f7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-intad", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-ggpubr - r-mclust run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-ggpubr - r-mclust + +source: + md5: 16b624bc4b4796b628fc54d92facf54d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Search for correlation between epigenetic signals and gene expression in TADs' - description: 'The package is focused on the detection of correlation between expressed genes and selected epigenomic signals (i.e. enhancers obtained from ChIP-seq data) either within topologically associated domains (TADs) or between chromatin contact loop anchors. Various parameters can be controlled to investigate the influence of external factors and visualization plots are available for each analysis step.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-intansv/meta.yaml b/recipes/bioconductor-intansv/meta.yaml index 7b67061f38d88..3597bcb04cef1 100644 --- a/recipes/bioconductor-intansv/meta.yaml +++ b/recipes/bioconductor-intansv/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "intansv" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides efficient tools to read and integrate structural variations predicted by popular softwares. Annotation and visulation of structural variations are also implemented in the package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Integrative analysis of structural variations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d23f9f69f23ab113ea9ac7100cafb3f1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-intansv", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-plyr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-plyr + +source: + md5: 42e93dfa30ac57e5bc3b2aeee8036ec2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Integrative analysis of structural variations' - description: 'This package provides efficient tools to read and integrate structural variations predicted by popular softwares. Annotation and visulation of structural variations are also implemented in the package.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-interaccircos/meta.yaml b/recipes/bioconductor-interaccircos/meta.yaml index df5cf27ff94e8..60fc4cb195e19 100644 --- a/recipes/bioconductor-interaccircos/meta.yaml +++ b/recipes/bioconductor-interaccircos/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "interacCircos" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d97429da8da823bf80547b4ac8ca2505 +about: + description: Implement in an efficient approach to display the genomic data, relationship, information in an interactive circular genome(Circos) plot. 'interacCircos' are inspired by 'circosJS', 'BioCircos.js' and 'NG-Circos' and we integrate the modules of 'circosJS', 'BioCircos.js' and 'NG-Circos' into this R package, based on 'htmlwidgets' framework. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: The Generation of Interactive Circos Plot build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-interaccircos", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: @@ -31,13 +30,14 @@ requirements: - r-htmlwidgets - r-plyr - r-rcolorbrewer +source: + md5: a6899ee320ae109f491acb9a0aec156b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'The Generation of Interactive Circos Plot' - description: 'Implement in an efficient approach to display the genomic data, relationship, information in an interactive circular genome(Circos) plot. ''interacCircos'' are inspired by ''circosJS'', ''BioCircos.js'' and ''NG-Circos'' and we integrate the modules of ''circosJS'', ''BioCircos.js'' and ''NG-Circos'' into this R package, based on ''htmlwidgets'' framework.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-interactionset/meta.yaml b/recipes/bioconductor-interactionset/meta.yaml index b29bd02b58e82..c7907a64446ce 100644 --- a/recipes/bioconductor-interactionset/meta.yaml +++ b/recipes/bioconductor-interactionset/meta.yaml @@ -1,68 +1,74 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "InteractionSet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Base Classes for Storing Genomic Interaction Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 273175864f47083ba4b983c72ba0c1dc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-interactionset", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:interactionset + parent_recipe: + name: bioconductor-interactionset + path: recipes/bioconductor-interactionset + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocStyle # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 485a335d5aaa206938b323f6c8a4c18b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'Base Classes for Storing Genomic Interaction Data' - description: 'Provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:interactionset - parent_recipe: - name: bioconductor-interactionset - path: recipes/bioconductor-interactionset - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-interactivecomplexheatmap/meta.yaml b/recipes/bioconductor-interactivecomplexheatmap/meta.yaml index 1fc9f6c2b98ff..233eff53b2be1 100644 --- a/recipes/bioconductor-interactivecomplexheatmap/meta.yaml +++ b/recipes/bioconductor-interactivecomplexheatmap/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "InteractiveComplexHeatmap" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'This package can easily make heatmaps which are produced by the ComplexHeatmap package into interactive applications. It provides two types of interactivities: 1. on the interactive graphics device, and 2. on a Shiny app. It also provides functions for integrating the interactive heatmap widgets for more complex Shiny app development.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Make Interactive Complex Heatmaps -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 87fef3e4c9035cbfab5dc4a2242223dc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-interactivecomplexheatmap", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, EnrichedHeatmap, GenomicRanges, data.table, circlize, GenomicFeatures, tidyverse, tidyHeatmap, cluster, org.Hs.eg.db, simplifyEnrichment, GO.db, SC3, GOexpress, SingleCellExperiment, scater, gplots, pheatmap, airway, DESeq2, DT, cola, BiocManager, gridtext, HilbertCurve (>= 1.21.1), shinydashboard, SummarizedExperiment, pkgndep, ks requirements: host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-clisymbols - r-digest @@ -32,14 +34,14 @@ requirements: - r-getoptlong - r-htmltools - r-jsonlite - - 'r-kableextra >=1.3.1' + - r-kableextra >=1.3.1 - r-rcolorbrewer - r-shiny - r-svglite run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-clisymbols - r-digest @@ -47,17 +49,20 @@ requirements: - r-getoptlong - r-htmltools - r-jsonlite - - 'r-kableextra >=1.3.1' + - r-kableextra >=1.3.1 - r-rcolorbrewer - r-shiny - r-svglite + +source: + md5: 871186361b95d5712999615af449b969 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Make Interactive Complex Heatmaps' - description: 'This package can easily make heatmaps which are produced by the ComplexHeatmap package into interactive applications. It provides two types of interactivities: 1. on the interactive graphics device, and 2. on a Shiny app. It also provides functions for integrating the interactive heatmap widgets for more complex Shiny app development.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-interactivedisplay/build_failure.linux-64.yaml b/recipes/bioconductor-interactivedisplay/build_failure.linux-64.yaml index 9eba9918043d4..2a31049dc6cdc 100644 --- a/recipes/bioconductor-interactivedisplay/build_failure.linux-64.yaml +++ b/recipes/bioconductor-interactivedisplay/build_failure.linux-64.yaml @@ -1,73 +1,68 @@ -recipe_sha: 9c517fc772ed28be827019592f5023b076b81fbe7358c247a963d5f1d48acc90 # The commit at which this recipe failed to build. +recipe_sha: 2e953b34550b7c2560316e98934f32e431666d1521470ee9f04b8e9bd3d68747 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- - sysroot_linux-64: 2.12-he073ed8_16 conda-forge - tk: 8.6.13-noxft_h4845f30_101 conda-forge - tktable: 2.10-h0c5db8f_5 conda-forge - toml: 0.10.2-pyhd8ed1ab_0 conda-forge - tomlkit: 0.12.3-pyha770c72_0 conda-forge - tzdata: 2023c-h71feb2d_0 conda-forge - wheel: 0.42.0-pyhd8ed1ab_0 conda-forge - xmltodict: 0.13.0-pyhd8ed1ab_0 conda-forge - xorg-kbproto: 1.0.7-h7f98852_1002 conda-forge - xorg-libice: 1.1.1-hd590300_0 conda-forge - xorg-libsm: 1.2.4-h7391055_0 conda-forge - xorg-libx11: 1.8.7-h8ee46fc_0 conda-forge - xorg-libxau: 1.0.11-hd590300_0 conda-forge - xorg-libxdmcp: 1.1.3-h7f98852_0 conda-forge - xorg-libxext: 1.3.4-h0b41bf4_2 conda-forge - xorg-libxrender: 0.9.11-hd590300_0 conda-forge - xorg-libxt: 1.3.0-hd590300_1 conda-forge - xorg-renderproto: 0.11.1-h7f98852_1002 conda-forge - xorg-xextproto: 7.3.0-h0b41bf4_1003 conda-forge - xorg-xproto: 7.0.31-h7f98852_1007 conda-forge - xz: 5.2.6-h166bdaf_0 conda-forge - yaml: 0.2.5-h7f98852_2 conda-forge - yq: 3.2.3-pyhd8ed1ab_0 conda-forge - zlib: 1.2.13-hd590300_5 conda-forge - zstd: 1.5.5-hfc55251_0 conda-forge + - r-bslib 0.8.0 r44hc72bb7e_0 + - r-reshape2 1.4.4 r44h0d4f4ea_4 + - r-rsqlite 2.3.9 r44h93ab643_0 + - r-tibble 3.2.1 r44hdb488b9_3 + - bioconductor-genomeinfodb 1.42.0 r44hdfd78af_0 + - r-ggplot2 3.5.1 r44hc72bb7e_1 + - r-rmarkdown 2.29 r44hc72bb7e_0 + - r-shiny 1.10.0 r44h785f33e_0 + - bioconductor-biostrings 2.74.0 r44h3df3fcb_0 + - r-htmlwidgets 1.6.4 r44h785f33e_3 + - bioconductor-keggrest 1.46.0 r44hdfd78af_0 + - r-dt 0.33 r44hc72bb7e_1 + - bioconductor-annotationdbi 1.68.0 r44hdfd78af_0 + - bioconductor-interactivedisplaybase 1.44.0 r44hdfd78af_0 + - bioconductor-annotate 1.84.0 r44hdfd78af_0 + - bioconductor-genefilter 1.88.0 r44h81e381d_0 + - bioconductor-gseabase 1.68.0 r44hdfd78af_0 + - bioconductor-category 2.72.0 r44hdfd78af_0 + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - r-base >=4.4,<4.5.0a0 + - r-base >=4.4,<4.5.0a0 + - r-reshape2 + - r-shiny + - r-rcolorbrewer + - bioconductor-category >=2.72.0,<2.73.0 + - r-plyr + - r-gridsvg + - bioconductor-interactivedisplaybase >=1.44.0,<1.45.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - r-ggplot2 + - r-xml + test: + commands: + - $R -e "library('interactiveDisplay')" + about: + description: The interactiveDisplay package contains the methods needed to generate + interactive Shiny based display methods for Bioconductor objects. + home: https://bioconductor.org/packages/3.20/bioc/html/interactiveDisplay.html + license: Artistic-2.0 + summary: Package for enabling powerful shiny web displays of Bioconductor objects + extra: + copy_test_source_files: true + final: true + identifiers: + - biotools:interactivedisplay + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-interactivedisplay + path: recipes/bioconductor-interactivedisplay + version: 1.18.0 - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... - To install TinyTeX with tinytex::install_tinytex() the system must have a functional Perl - installation with a File::Find module. Most end-user systems will already satisfy this - requirement; however, some minimal contexts (e.g., containers) may not. Perl is available - via Conda Forge as the package perl. See https://github.com/rstudio/tinytex/issues/419 - - done - [34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m - [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.0MB/s 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 2.5MB/s 0.0s - [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m - [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 129.0 B @ 2.0MB/s 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 2.5MB/s 0.0s - [?25h - ## Package Plan ## - - environment location: /opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/_build_env - - - Source cache directory is: /opt/conda/conda-bld/src_cache - INFO:conda_build.source:Source cache directory is: /opt/conda/conda-bld/src_cache - Downloading source to cache: interactiveDisplay_1.40.0_4adec73e76.tar.gz - INFO:conda_build.source:Downloading source to cache: interactiveDisplay_1.40.0_4adec73e76.tar.gz - Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/interactiveDisplay_1.40.0.tar.gz - INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/interactiveDisplay_1.40.0.tar.gz - Success - INFO:conda_build.source:Success - Extracting download - source tree in: /opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/work - export PREFIX=/opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p - export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/_build_env - export SRC_DIR=/opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/work + source tree in: /opt/conda/conda-bld/bioconductor-interactivedisplay_1735589677364/work + export PREFIX=/opt/conda/conda-bld/bioconductor-interactivedisplay_1735589677364/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-interactivedisplay_1735589677364/_build_env + export SRC_DIR=/opt/conda/conda-bld/bioconductor-interactivedisplay_1735589677364/work During startup - Warning message: Setting LC_TIME failed, using "C" - * installing to library /opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library + * installing to library /opt/conda/conda-bld/bioconductor-interactivedisplay_1735589677364/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library * installing *source* package interactiveDisplay ... + ** package interactiveDisplay successfully unpacked and MD5 sums checked ** using staged installation ** R ** data @@ -82,23 +77,28 @@ log: |2- Error: unable to load R code in package interactiveDisplay Execution halted ERROR: lazy loading failed for package interactiveDisplay - * removing /opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/interactiveDisplay + * removing /opt/conda/conda-bld/bioconductor-interactivedisplay_1735589677364/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/interactiveDisplay Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-interactivedisplay_1703228514768/work/conda_build.sh']' returned non-zero exit status 1. + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-interactivedisplay_1735589677364/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-interactivedisplay_1735589677364/work/conda_build.sh']' returned non-zero exit status 1. # Last 100 lines of the build log. diff --git a/recipes/bioconductor-interactivedisplay/meta.yaml b/recipes/bioconductor-interactivedisplay/meta.yaml index d76299068acbc..20454caa98c75 100644 --- a/recipes/bioconductor-interactivedisplay/meta.yaml +++ b/recipes/bioconductor-interactivedisplay/meta.yaml @@ -1,31 +1,41 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "interactiveDisplay" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The interactiveDisplay package contains the methods needed to generate interactive Shiny based display methods for Bioconductor objects. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Package for enabling powerful shiny web displays of Bioconductor objects -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4adec73e763df3dc2e697e41bff3ead8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-interactivedisplay", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:interactivedisplay + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-interactivedisplay + path: recipes/bioconductor-interactivedisplay + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, hgu95av2.db, knitr, GenomicRanges, SummarizedExperiment, GOstats, ggbio, GO.db, Gviz, rtracklayer, metagenomeSeq, gplots, vegan, Biobase requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-category >=2.68.0,<2.69.0' - - 'bioconductor-interactivedisplaybase >=1.40.0,<1.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-category >=2.72.0,<2.73.0 + - bioconductor-interactivedisplaybase >=1.44.0,<1.45.0 - r-base - r-ggplot2 - r-gridsvg @@ -35,10 +45,10 @@ requirements: - r-shiny - r-xml run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-category >=2.68.0,<2.69.0' - - 'bioconductor-interactivedisplaybase >=1.40.0,<1.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-category >=2.72.0,<2.73.0 + - bioconductor-interactivedisplaybase >=1.44.0,<1.45.0 - r-base - r-ggplot2 - r-gridsvg @@ -47,20 +57,16 @@ requirements: - r-reshape2 - r-shiny - r-xml + +source: + md5: 1632e8f269ab0ca57340fa46eb5ce2bd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Package for enabling powerful shiny web displays of Bioconductor objects' - description: 'The interactiveDisplay package contains the methods needed to generate interactive Shiny based display methods for Bioconductor objects.' -extra: - identifiers: - - biotools:interactivedisplay - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-interactivedisplay - path: recipes/bioconductor-interactivedisplay - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-interactivedisplaybase/meta.yaml b/recipes/bioconductor-interactivedisplaybase/meta.yaml index 6457aaceb53ef..abdfc5227ec5f 100644 --- a/recipes/bioconductor-interactivedisplaybase/meta.yaml +++ b/recipes/bioconductor-interactivedisplaybase/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "interactiveDisplayBase" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The interactiveDisplayBase package contains the the basic methods needed to generate interactive Shiny based display methods for Bioconductor objects. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Base package for enabling powerful shiny web displays of Bioconductor objects -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ae8be7104ab2debe258b504bcd24e38 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-interactivedisplaybase", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:interactivedisplaybase + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-interactivedisplaybase + path: recipes/bioconductor-interactivedisplaybase + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, markdown requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-dt - r-shiny run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-dt - r-shiny + +source: + md5: d112e51307461b9955062ac0f67de40c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base package for enabling powerful shiny web displays of Bioconductor objects' - description: 'The interactiveDisplayBase package contains the the basic methods needed to generate interactive Shiny based display methods for Bioconductor objects.' -extra: - identifiers: - - biotools:interactivedisplaybase - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-interactivedisplaybase - path: recipes/bioconductor-interactivedisplaybase - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-intercellar/meta.yaml b/recipes/bioconductor-intercellar/meta.yaml index 81dde8f9efb34..436b24e732a7d 100644 --- a/recipes/bioconductor-intercellar/meta.yaml +++ b/recipes/bioconductor-intercellar/meta.yaml @@ -1,29 +1,32 @@ -{% set version = "2.8.0" %} +{% set version = "2.12.0" %} {% set name = "InterCellar" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: InterCellar is implemented as an R/Bioconductor Package containing a Shiny app that allows users to interactively analyze cell-cell communication from scRNA-seq data. Starting from precomputed ligand-receptor interactions, InterCellar provides filtering options, annotations and multiple visualizations to explore clusters, genes and functions. Finally, based on functional annotation from Gene Ontology and pathway databases, InterCellar implements data-driven analyses to investigate cell-cell communication in one or multiple conditions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 'InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a331a8a5f0161dd1e5afa2430660b785 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-intercellar", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite, processx, attempt, BiocStyle, httr requirements: + host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 - r-base - r-circlize - r-colorspace @@ -58,9 +61,10 @@ requirements: - r-umap - r-visnetwork - r-wordcloud2 + run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 - r-base - r-circlize - r-colorspace @@ -95,13 +99,16 @@ requirements: - r-umap - r-visnetwork - r-wordcloud2 + +source: + md5: 864c8fa51ec2091440caf5853f659865 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics' - description: 'InterCellar is implemented as an R/Bioconductor Package containing a Shiny app that allows users to interactively analyze cell-cell communication from scRNA-seq data. Starting from precomputed ligand-receptor interactions, InterCellar provides filtering options, annotations and multiple visualizations to explore clusters, genes and functions. Finally, based on functional annotation from Gene Ontology and pathway databases, InterCellar implements data-driven analyses to investigate cell-cell communication in one or multiple conditions.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-interest/meta.yaml b/recipes/bioconductor-interest/meta.yaml index 80b57c6986664..8166f08faf3c9 100644 --- a/recipes/bioconductor-interest/meta.yaml +++ b/recipes/bioconductor-interest/meta.yaml @@ -1,80 +1,90 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "IntEREst" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Intron-Exon Retention Estimator -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b9b473ea53b89a32487163ef6a664905 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-interest", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - doi:10.18129/B9.bioc.IntEREst + parent_recipe: + name: bioconductor-interest + path: recipes/bioconductor-interest + version: 1.4.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: clinfun, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-dexseq >=1.48.0,<1.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-seqlogo >=1.68.0,<1.69.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-dexseq >=1.52.0,<1.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicfiles >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqlogo >=1.72.0,<1.73.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-dbi - - r-rmysql + - r-rmariadb - r-seqinr + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-dexseq >=1.48.0,<1.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-seqlogo >=1.68.0,<1.69.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-dexseq >=1.52.0,<1.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicfiles >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqlogo >=1.72.0,<1.73.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-dbi - - r-rmysql + - r-rmariadb - r-seqinr + +source: + md5: dc9e7878b6baed74e9b8fd3bedaf4f9c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Intron-Exon Retention Estimator' - description: 'This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - doi:10.18129/B9.bioc.IntEREst - parent_recipe: - name: bioconductor-interest - path: recipes/bioconductor-interest - version: 1.4.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-intramirexplorer/meta.yaml b/recipes/bioconductor-intramirexplorer/meta.yaml index 8e70e8e286ee9..b1546ca23f428 100644 --- a/recipes/bioconductor-intramirexplorer/meta.yaml +++ b/recipes/bioconductor-intramirexplorer/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "IntramiRExploreR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e319d73695e5e1f12d9fc79896c49674 +about: + description: Intra-miR-ExploreR, an integrative miRNA target prediction bioinformatics tool, identifies targets combining expression and biophysical interactions of a given microRNA (miR). Using the tool, we have identified targets for 92 intragenic miRs in D. melanogaster, using available microarray expression data, from Affymetrix 1 and Affymetrix2 microarray array platforms, providing a global perspective of intragenic miR targets in Drosophila. Predicted targets are grouped according to biological functions using the DAVID Gene Ontology tool and are ranked based on a biologically relevant scoring system, enabling the user to identify functionally relevant targets for a given miR. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Predicting Targets for Drosophila Intragenic miRNAs build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-intramirexplorer", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat requirements: host: - - 'bioconductor-fgnet >=3.36.0,<3.37.0' + - bioconductor-fgnet >=3.40.0,<3.41.0 - r-base - - 'r-igraph >=1.0.1' - - 'r-knitr >=1.12.3' + - r-igraph >=1.0.1 + - r-knitr >=1.12.3 run: - - 'bioconductor-fgnet >=3.36.0,<3.37.0' + - bioconductor-fgnet >=3.40.0,<3.41.0 - r-base - - 'r-igraph >=1.0.1' - - 'r-knitr >=1.12.3' + - r-igraph >=1.0.1 + - r-knitr >=1.12.3 +source: + md5: d3e26768e1a3f263a05a1af5a0bbd81f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Predicting Targets for Drosophila Intragenic miRNAs' - description: 'Intra-miR-ExploreR, an integrative miRNA target prediction bioinformatics tool, identifies targets combining expression and biophysical interactions of a given microRNA (miR). Using the tool, we have identified targets for 92 intragenic miRs in D. melanogaster, using available microarray expression data, from Affymetrix 1 and Affymetrix2 microarray array platforms, providing a global perspective of intragenic miR targets in Drosophila. Predicted targets are grouped according to biological functions using the DAVID Gene Ontology tool and are ranked based on a biologically relevant scoring system, enabling the user to identify functionally relevant targets for a given miR.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ioniser/meta.yaml b/recipes/bioconductor-ioniser/meta.yaml index d6dce6d5af852..5e3e0c874b760 100644 --- a/recipes/bioconductor-ioniser/meta.yaml +++ b/recipes/bioconductor-ioniser/meta.yaml @@ -1,33 +1,44 @@ -{% set version = "2.26.0" %} +{% set version = "2.30.0" %} {% set name = "IONiseR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Quality Assessment Tools for Oxford Nanopore MinION data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 10a3ed3f75ba8be8989b90d197096b40 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ioniser", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:ioniser + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ioniser + path: recipes/bioconductor-ioniser + version: 2.4.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-bit64 - r-dplyr @@ -37,12 +48,12 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-bit64 - r-dplyr @@ -51,21 +62,16 @@ requirements: - r-stringr - r-tibble - r-tidyr + +source: + md5: 0ddc0fc53a430d8a6468ee55cfb05d93 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Quality Assessment Tools for Oxford Nanopore MinION data' - description: 'IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.' - license_file: LICENSE -extra: - identifiers: - - biotools:ioniser - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-ioniser - path: recipes/bioconductor-ioniser - version: 2.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ipath/meta.yaml b/recipes/bioconductor-ipath/meta.yaml index c942c0964afed..68c7e73524389 100644 --- a/recipes/bioconductor-ipath/meta.yaml +++ b/recipes/bioconductor-ipath/meta.yaml @@ -1,61 +1,66 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "iPath" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: iPath is the Bioconductor package used for calculating personalized pathway score and test the association with survival outcomes. Abundant single-gene biomarkers have been identified and used in the clinics. However, hundreds of oncogenes or tumor-suppressor genes are involved during the process of tumorigenesis. We believe individual-level expression patterns of pre-defined pathways or gene sets are better biomarkers than single genes. In this study, we devised a computational method named iPath to identify prognostic biomarker pathways, one sample at a time. To test its utility, we conducted a pan-cancer analysis across 14 cancer types from The Cancer Genome Atlas and demonstrated that iPath is capable of identifying highly predictive biomarkers for clinical outcomes, including overall survival, tumor subtypes, and tumor stage classifications. We found that pathway-based biomarkers are more robust and effective than single genes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: iPath pipeline for detecting perturbed pathways at individual level -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71bdeccc2d0192cd080c4c190831d792 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ipath", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, BiocStyle, knitr # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-ggplot2 - r-ggpubr - r-matrixstats - r-mclust - - 'r-rcpp >=1.0.5' + - r-rcpp >=1.0.5 - r-rcpparmadillo - r-survival - r-survminer - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-ggplot2 - r-ggpubr - r-matrixstats - r-mclust - - 'r-rcpp >=1.0.5' + - r-rcpp >=1.0.5 - r-rcpparmadillo - r-survival - r-survminer - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 0b959d8ba286bddf6b334ff5c64fa825 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'iPath pipeline for detecting perturbed pathways at individual level' - description: 'iPath is the Bioconductor package used for calculating personalized pathway score and test the association with survival outcomes. Abundant single-gene biomarkers have been identified and used in the clinics. However, hundreds of oncogenes or tumor-suppressor genes are involved during the process of tumorigenesis. We believe individual-level expression patterns of pre-defined pathways or gene sets are better biomarkers than single genes. In this study, we devised a computational method named iPath to identify prognostic biomarker pathways, one sample at a time. To test its utility, we conducted a pan-cancer analysis across 14 cancer types from The Cancer Genome Atlas and demonstrated that iPath is capable of identifying highly predictive biomarkers for clinical outcomes, including overall survival, tumor subtypes, and tumor stage classifications. We found that pathway-based biomarkers are more robust and effective than single genes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ipddb/meta.yaml b/recipes/bioconductor-ipddb/meta.yaml index 685bfe5c5e978..f65aba8d7c300 100644 --- a/recipes/bioconductor-ipddb/meta.yaml +++ b/recipes/bioconductor-ipddb/meta.yaml @@ -1,52 +1,57 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "ipdDb" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'All alleles from the IPD IMGT/HLA and IPD KIR database for Homo sapiens. Reference: Robinson J, Maccari G, Marsh SGE, Walter L, Blokhuis J, Bimber B, Parham P, De Groot NG, Bontrop RE, Guethlein LA, and Hammond JA KIR Nomenclature in non-human species Immunogenetics (2018), in preparation.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: IPD IMGT/HLA and IPD KIR database for Homo sapiens -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0346f5dcca05a1bfb117214c54f36524 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ipddb", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-assertthat - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-assertthat - r-base - r-dbi - r-rsqlite + +source: + md5: 7554c2d3c695d50f78e28847ec7c06a5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'IPD IMGT/HLA and IPD KIR database for Homo sapiens' - description: 'All alleles from the IPD IMGT/HLA and IPD KIR database for Homo sapiens. Reference: Robinson J, Maccari G, Marsh SGE, Walter L, Blokhuis J, Bimber B, Parham P, De Groot NG, Bontrop RE, Guethlein LA, and Hammond JA KIR Nomenclature in non-human species Immunogenetics (2018), in preparation.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ipo/meta.yaml b/recipes/bioconductor-ipo/meta.yaml index 85a6e762813ff..bbe72e5ea8ae2 100644 --- a/recipes/bioconductor-ipo/meta.yaml +++ b/recipes/bioconductor-ipo/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "IPO" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The outcome of XCMS data processing strongly depends on the parameter settings. IPO (`Isotopologue Parameter Optimization`) is a parameter optimization tool that is applicable for different kinds of samples and liquid chromatography coupled to high resolution mass spectrometry devices, fast and free of labeling steps. IPO uses natural, stable 13C isotopes to calculate a peak picking score. Retention time correction is optimized by minimizing the relative retention time differences within features and grouping parameters are optimized by maximizing the number of features showing exactly one peak from each injection of a pooled sample. The different parameter settings are achieved by design of experiment. The resulting scores are evaluated using response surface models. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + file LICENSE + license_file: LICENSE + summary: Automated Optimization of XCMS Data Processing parameters -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a1275d6f177754744bcceb9a8aed44a0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ipo", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:ipo + parent_recipe: + name: bioconductor-ipo + path: recipes/bioconductor-ipo + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-camera >=1.58.0,<1.59.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-camera >=1.62.0,<1.63.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base - r-rsm run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-camera >=1.58.0,<1.59.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-camera >=1.62.0,<1.63.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base - r-rsm + +source: + md5: a28289f80eb8b8ee01ac00c4f9f03876 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2) + file LICENSE' - summary: 'Automated Optimization of XCMS Data Processing parameters' - description: 'The outcome of XCMS data processing strongly depends on the parameter settings. IPO (`Isotopologue Parameter Optimization`) is a parameter optimization tool that is applicable for different kinds of samples and liquid chromatography coupled to high resolution mass spectrometry devices, fast and free of labeling steps. IPO uses natural, stable 13C isotopes to calculate a peak picking score. Retention time correction is optimized by minimizing the relative retention time differences within features and grouping parameters are optimized by maximizing the number of features showing exactly one peak from each injection of a pooled sample. The different parameter settings are achieved by design of experiment. The resulting scores are evaluated using response surface models.' - license_file: LICENSE -extra: - identifiers: - - biotools:ipo - parent_recipe: - name: bioconductor-ipo - path: recipes/bioconductor-ipo - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-iranges/meta.yaml b/recipes/bioconductor-iranges/meta.yaml index eba4471741a2e..61586fa852492 100644 --- a/recipes/bioconductor-iranges/meta.yaml +++ b/recipes/bioconductor-iranges/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "2.36.0" %} +{% set version = "2.40.0" %} {% set name = "IRanges" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Foundation of integer range manipulation in Bioconductor -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 87618d2e5ee94d7ab81d2e1c4d847120 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-iranges", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:iranges + parent_recipe: + name: bioconductor-iranges + path: recipes/bioconductor-iranges + version: 2.14.12 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: bc5e6f78cb6689f381db95d356128872 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Foundation of integer range manipulation in Bioconductor' - description: 'Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:iranges - parent_recipe: - name: bioconductor-iranges - path: recipes/bioconductor-iranges - version: 2.14.12 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-isee/meta.yaml b/recipes/bioconductor-isee/meta.yaml index 1cb011c60e377..f49977c018b24 100644 --- a/recipes/bioconductor-isee/meta.yaml +++ b/recipes/bioconductor-isee/meta.yaml @@ -1,32 +1,41 @@ -{% set version = "2.14.0" %} +{% set version = "2.18.0" %} {% set name = "iSEE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Interactive SummarizedExperiment Explorer -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e6d2be3afb9bc484d594cbd21887ec53 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-isee", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools + +extra: + parent_recipe: + name: bioconductor-isee + path: recipes/bioconductor-isee + version: 1.0.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools, GenomicRanges requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-colourpicker @@ -34,6 +43,7 @@ requirements: - r-ggplot2 - r-ggrepel - r-igraph + - r-listviewer - r-mgcv - r-rintrojs - r-shiny @@ -43,12 +53,13 @@ requirements: - r-shinywidgets - r-vipor - r-viridislite + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-colourpicker @@ -56,6 +67,7 @@ requirements: - r-ggplot2 - r-ggrepel - r-igraph + - r-listviewer - r-mgcv - r-rintrojs - r-shiny @@ -65,18 +77,16 @@ requirements: - r-shinywidgets - r-vipor - r-viridislite + +source: + md5: 610054ed8c9baa845d8ac58576cad743 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Interactive SummarizedExperiment Explorer' - description: 'Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-isee - path: recipes/bioconductor-isee - version: 1.0.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-iseede/meta.yaml b/recipes/bioconductor-iseede/meta.yaml index 68f2097a44e14..81ce0cacfb0fe 100644 --- a/recipes/bioconductor-iseede/meta.yaml +++ b/recipes/bioconductor-iseede/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "iSEEde" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of differential expression results. This package does not perform differential expression. Instead, it provides methods to embed precomputed differential expression results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: iSEE extension for panels related to differential expression analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d6215b9243635ed9dd3b6fcf5cbf166 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-iseede", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: airway, BiocStyle, covr, knitr, limma, org.Hs.eg.db, RefManageR, rmarkdown, scuttle, sessioninfo, statmod, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-isee >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-isee >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-shiny run: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-isee >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-isee >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-shiny + +source: + md5: ef63989cd800352207ea9004c2579544 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'iSEE extension for panels related to differential expression analysis' - description: 'This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of differential expression results. This package does not perform differential expression. Instead, it provides methods to embed precomputed differential expression results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-iseefier/build.sh b/recipes/bioconductor-iseefier/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-iseefier/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iseefier/meta.yaml b/recipes/bioconductor-iseefier/meta.yaml new file mode 100644 index 0000000000000..2f24e9bbf46d9 --- /dev/null +++ b/recipes/bioconductor-iseefier/meta.yaml @@ -0,0 +1,60 @@ +{% set version = "1.2.0" %} +{% set name = "iSEEfier" %} +{% set bioc = "3.20" %} + +about: + description: iSEEfier provides a set of functionality to quickly and intuitively create, inspect, and combine initial configuration objects. These can be conveniently passed in a straightforward manner to the function call to launch iSEE() with the specified configuration. This package currently works seamlessly with the sets of panels provided by the iSEE and iSEEu packages, but can be extended to accommodate the usage of any custom panel (e.g. from iSEEde, iSEEpathways, or any panel developed independently by the user). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Streamlining the creation of initial states for starting an iSEE instance + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iseefier", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, scater, scRNAseq, org.Mm.eg.db, scuttle, BiocStyle, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-isee >=2.18.0,<2.19.0 + - bioconductor-iseeu >=1.18.0,<1.19.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-ggplot2 + - r-igraph + - r-rlang + - r-visnetwork + run: + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-isee >=2.18.0,<2.19.0 + - bioconductor-iseeu >=1.18.0,<1.19.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-ggplot2 + - r-igraph + - r-rlang + - r-visnetwork + +source: + md5: b11503c5591e64502cae064f7ac5f708 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-iseehex/meta.yaml b/recipes/bioconductor-iseehex/meta.yaml index 45547ab3c80ac..66886548c2484 100644 --- a/recipes/bioconductor-iseehex/meta.yaml +++ b/recipes/bioconductor-iseehex/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "iSEEhex" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides panels summarising data points in hexagonal bins for `iSEE`. It is part of `iSEEu`, the iSEE universe of panels that extend the `iSEE` package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: iSEE extension for summarising data points in hexagonal bins -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9bc98dc14114c756f97c130adf061a4b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-iseehex", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), scRNAseq, scater requirements: host: - - 'bioconductor-isee >=2.14.0,<2.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-isee >=2.18.0,<2.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-hexbin - r-shiny run: - - 'bioconductor-isee >=2.14.0,<2.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-isee >=2.18.0,<2.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-hexbin - r-shiny + +source: + md5: 5436e4d62fe8747281aec6402f6544d4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'iSEE extension for summarising data points in hexagonal bins' - description: 'This package provides panels summarising data points in hexagonal bins for `iSEE`. It is part of `iSEEu`, the iSEE universe of panels that extend the `iSEE` package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-iseehub/meta.yaml b/recipes/bioconductor-iseehub/meta.yaml index 0a193959471a0..0935b5649a048 100644 --- a/recipes/bioconductor-iseehub/meta.yaml +++ b/recipes/bioconductor-iseehub/meta.yaml @@ -1,33 +1,34 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "iSEEhub" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package defines a custom landing page for an iSEE app interfacing with the Bioconductor ExperimentHub. The landing page allows users to browse the ExperimentHub, select a data set, download and cache it, and import it directly into a Bioconductor iSEE app. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: iSEE for the Bioconductor ExperimentHub -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ebb32da66242f608b83522fca1d9a62 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-iseehub", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), nullrangesData requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-isee >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-isee >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-biocmanager - r-dt @@ -36,12 +37,12 @@ requirements: - r-shinydashboard - r-shinyjs run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-isee >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-isee >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-biocmanager - r-dt @@ -49,12 +50,16 @@ requirements: - r-shiny - r-shinydashboard - r-shinyjs + +source: + md5: 523b657b491c77e31636c78ea5d50db0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'iSEE for the Bioconductor ExperimentHub' - description: 'This package defines a custom landing page for an iSEE app interfacing with the Bioconductor ExperimentHub. The landing page allows users to browse the ExperimentHub, select a data set, download and cache it, and import it directly into a Bioconductor iSEE app.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-iseeindex/meta.yaml b/recipes/bioconductor-iseeindex/meta.yaml index e795471cb94d1..f8fc417c0d9a2 100644 --- a/recipes/bioconductor-iseeindex/meta.yaml +++ b/recipes/bioconductor-iseeindex/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "iSEEindex" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides an interface to any collection of data sets within a single iSEE web-application. The main functionality of this package is to define a custom landing page allowing app maintainers to list a custom collection of data sets that users can selected from and directly load objects into an iSEE web-application. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: iSEE extension for a landing page to a custom collection of data sets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98a9141431a3206fd242b5b0b4056c41 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-iseeindex", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), yaml + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, markdown, scRNAseq, sessioninfo, testthat (>= 3.0.0), yaml requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-isee >=2.14.0,<2.15.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-isee >=2.18.0,<2.19.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dt - r-paws.storage @@ -36,10 +37,10 @@ requirements: - r-stringr - r-urltools run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-isee >=2.14.0,<2.15.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-isee >=2.18.0,<2.19.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dt - r-paws.storage @@ -49,12 +50,16 @@ requirements: - r-shinyjs - r-stringr - r-urltools + +source: + md5: 89858c285959d94b41f065c9973efa52 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'iSEE extension for a landing page to a custom collection of data sets' - description: 'This package provides an interface to any collection of data sets within a single iSEE web-application. The main functionality of this package is to define a custom landing page allowing app maintainers to list a custom collection of data sets that users can selected from and directly load objects into an iSEE web-application.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-iseepathways/meta.yaml b/recipes/bioconductor-iseepathways/meta.yaml index b1ecb82d75020..da8b37631e826 100644 --- a/recipes/bioconductor-iseepathways/meta.yaml +++ b/recipes/bioconductor-iseepathways/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "iSEEpathways" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of pathway analysis results. This package does not perform pathway analysis. Instead, it provides methods to embed precomputed pathway analysis results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: iSEE extension for panels related to pathway analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 52b84dcbd5e5ab0a6bbdc27120d7e86a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-iseepathways", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: airway, BiocStyle, covr, edgeR, fgsea, GO.db, iSEEde, knitr, org.Hs.eg.db, RefManageR, rmarkdown, scater, scuttle, sessioninfo, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-isee >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-isee >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-shiny - r-shinywidgets run: - - 'bioconductor-isee >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-isee >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-shiny - r-shinywidgets + +source: + md5: c92fd9a45f30200db5072ec7a61b0e05 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'iSEE extension for panels related to pathway analysis' - description: 'This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of pathway analysis results. This package does not perform pathway analysis. Instead, it provides methods to embed precomputed pathway analysis results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-iseetree/build.sh b/recipes/bioconductor-iseetree/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-iseetree/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iseetree/meta.yaml b/recipes/bioconductor-iseetree/meta.yaml new file mode 100644 index 0000000000000..4efa1b423409c --- /dev/null +++ b/recipes/bioconductor-iseetree/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.0.0" %} +{% set name = "iSEEtree" %} +{% set bioc = "3.20" %} + +about: + description: iSEEtree is an extension of iSEE for the TreeSummarizedExperiment. It leverages the functionality from the miaViz package for microbiome data visualisation to create panels that are specific for TreeSummarizedExperiment objects. Not surprisingly, it also depends on the generic panels from iSEE. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Interactive visualisation for microbiome data + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-iseetree", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: biomformat, BiocStyle, knitr, MGnifyR, RefManageR, remotes, rmarkdown, scater, testthat (>= 3.0.0), vegan +requirements: + host: + - bioconductor-isee >=2.18.0,<2.19.0 + - bioconductor-mia >=1.14.0,<1.15.0 + - bioconductor-miaviz >=1.14.0,<1.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 + - r-base + - r-shiny + - r-shinywidgets + run: + - bioconductor-isee >=2.18.0,<2.19.0 + - bioconductor-mia >=1.14.0,<1.15.0 + - bioconductor-miaviz >=1.14.0,<1.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 + - r-base + - r-shiny + - r-shinywidgets + +source: + md5: 745ee6b1394c38405f4b3660159ac465 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-iseeu/meta.yaml b/recipes/bioconductor-iseeu/meta.yaml index b0845ec64ecd3..353ba1d7c2435 100644 --- a/recipes/bioconductor-iseeu/meta.yaml +++ b/recipes/bioconductor-iseeu/meta.yaml @@ -1,59 +1,64 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "iSEEu" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: iSEEu (the iSEE universe) contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels, or modes allowing easy configuration of iSEE applications. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: iSEE Universe -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d9349d85759c37c8a971b4ffcebcecea build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-iseeu", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: scRNAseq, scater, scran, airway, edgeR, AnnotationDbi, org.Hs.eg.db, GO.db, KEGGREST, knitr, igraph, rmarkdown, BiocStyle, htmltools, Rtsne, uwot, testthat (>= 2.1.0), covr requirements: host: - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-isee >=2.14.0,<2.15.0' - - 'bioconductor-iseehex >=1.4.0,<1.5.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-isee >=2.18.0,<2.19.0 + - bioconductor-iseehex >=1.8.0,<1.9.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-colourpicker - r-dt - - 'r-ggplot2 >=3.4.0' + - r-ggplot2 >=3.4.0 - r-shiny - r-shinyace run: - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-isee >=2.14.0,<2.15.0' - - 'bioconductor-iseehex >=1.4.0,<1.5.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-isee >=2.18.0,<2.19.0 + - bioconductor-iseehex >=1.8.0,<1.9.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-colourpicker - r-dt - - 'r-ggplot2 >=3.4.0' + - r-ggplot2 >=3.4.0 - r-shiny - r-shinyace + +source: + md5: afafd1e9ccb493a2a6fd86ed07ef6b42 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'iSEE Universe' - description: 'iSEEu (the iSEE universe) contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels, or modes allowing easy configuration of iSEE applications.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-iseq/meta.yaml b/recipes/bioconductor-iseq/meta.yaml index 326c46a55f5f7..b53e281625b7c 100644 --- a/recipes/bioconductor-iseq/meta.yaml +++ b/recipes/bioconductor-iseq/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "1.54.0" %} +{% set version = "1.58.0" %} {% set name = "iSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Bayesian hidden Ising models are implemented to identify IP-enriched genomic regions from ChIP-seq data. They can be used to analyze ChIP-seq data with and without controls and replicates. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1798c4c248175516afc66ee7f45d5051 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-iseq", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:iseq + - doi:10.1111/j.1541-0420.2009.01379.x + parent_recipe: + name: bioconductor-iseq + path: recipes/bioconductor-iseq + version: 1.32.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: 2bc4f21bcd55e452770d0be195985880 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models' - description: 'Bayesian hidden Ising models are implemented to identify IP-enriched genomic regions from ChIP-seq data. They can be used to analyze ChIP-seq data with and without controls and replicates.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:iseq - - doi:10.1111/j.1541-0420.2009.01379.x - parent_recipe: - name: bioconductor-iseq - path: recipes/bioconductor-iseq - version: 1.32.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-islet/meta.yaml b/recipes/bioconductor-islet/meta.yaml index 78b454e10d2aa..74f39d5f38290 100644 --- a/recipes/bioconductor-islet/meta.yaml +++ b/recipes/bioconductor-islet/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "ISLET" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ISLET is a method to conduct signal deconvolution for general -omics data. It can estimate the individual-specific and cell-type-specific reference panels, when there are multiple samples observed from each subject. It takes the input of the observed mixture data (feature by sample matrix), and the cell type mixture proportions (sample by cell type matrix), and the sample-to-subject information. It can solve for the reference panel on the individual-basis and conduct test to identify cell-type-specific differential expression (csDE) genes. It also improves estimated cell type mixture proportions by integrating personalized reference panels. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Individual-Specific ceLl typE referencing Tool -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5cf5ae7df60062c1822ca64c3989a4e0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-islet", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, htmltools, RUnit, dplyr requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-abind - r-base - r-lme4 @@ -32,22 +34,25 @@ requirements: - r-nnls - r-purrr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-abind - r-base - r-lme4 - r-matrix - r-nnls - r-purrr + +source: + md5: dee7246f762794b535f67abf34b9a2d9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Individual-Specific ceLl typE referencing Tool' - description: 'ISLET is a method to conduct signal deconvolution for general -omics data. It can estimate the individual-specific and cell-type-specific reference panels, when there are multiple samples observed from each subject. It takes the input of the observed mixture data (feature by sample matrix), and the cell type mixture proportions (sample by cell type matrix), and the sample-to-subject information. It can solve for the reference panel on the individual-basis and conduct test to identify cell-type-specific differential expression (csDE) genes. It also improves estimated cell type mixture proportions by integrating personalized reference panels.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-isobar/meta.yaml b/recipes/bioconductor-isobar/meta.yaml index b900b92c86f60..d18df9c156ecc 100644 --- a/recipes/bioconductor-isobar/meta.yaml +++ b/recipes/bioconductor-isobar/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "isobar" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: isobar provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data labeled with isobaric tags, such as iTRAQ and TMT. Features modules for integrating and validating PTM-centric datasets (isobar-PTM). More information on http://www.ms-isobar.org. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2' + summary: Analysis and quantitation of isobarically tagged MSMS proteomics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bf7b66ee10cfc2f8b24f22642bbc395a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-isobar", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, DBI, MASS requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biomart >=2.62.0,<2.63.0 - r-base - r-distr - r-ggplot2 - r-plyr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biomart >=2.62.0,<2.63.0 - r-base - r-distr - r-ggplot2 - r-plyr + +source: + md5: 1d5e059f717cae9a8989a9b7a7f7b96d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-2 - summary: 'Analysis and quantitation of isobarically tagged MSMS proteomics data' - description: 'isobar provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data labeled with isobaric tags, such as iTRAQ and TMT. Features modules for integrating and validating PTM-centric datasets (isobar-PTM). More information on http://www.ms-isobar.org.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-isobayes/meta.yaml b/recipes/bioconductor-isobayes/meta.yaml index 39f49ed83d0d2..b7f62625a0e06 100644 --- a/recipes/bioconductor-isobayes/meta.yaml +++ b/recipes/bioconductor-isobayes/meta.yaml @@ -1,29 +1,35 @@ -{% set version = "1.0.1" %} +{% set version = "1.4.0" %} {% set name = "IsoBayes" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'IsoBayes is a Bayesian method to perform inference on single protein isoforms. Our approach infers the presence/absence of protein isoforms, and also estimates their abundance; additionally, it provides a measure of the uncertainty of these estimates, via: i) the posterior probability that a protein isoform is present in the sample; ii) a posterior credible interval of its abundance. IsoBayes inputs liquid cromatography mass spectrometry (MS) data, and can work with both PSM counts, and intensities. When available, trascript isoform abundances (i.e., TPMs) are also incorporated: TPMs are used to formulate an informative prior for the respective protein isoform relative abundance. We further identify isoforms where the relative abundance of proteins and transcripts significantly differ. We use a two-layer latent variable approach to model two sources of uncertainty typical of MS data: i) peptides may be erroneously detected (even when absent); ii) many peptides are compatible with multiple protein isoforms. In the first layer, we sample the presence/absence of each peptide based on its estimated probability of being mistakenly detected, also known as PEP (i.e., posterior error probability). In the second layer, for peptides that were estimated as being present, we allocate their abundance across the protein isoforms they map to. These two steps allow us to recover the presence and abundance of each protein isoform.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'IsoBayes: Single Isoform protein inference Method via Bayesian Analyses' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d9e1de9f5a1f8279117fde4cc997725d build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-isobayes", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, BiocStyle # SystemRequirements: C++17 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-doparallel @@ -38,8 +44,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-doparallel @@ -51,17 +57,16 @@ requirements: - r-iterators - r-rcpp - r-rcpparmadillo - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 8441343e4f5d5e49720a871d5a103b54 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'IsoBayes: Single Isoform protein inference Method via Bayesian Analyses' - description: 'IsoBayes is a Bayesian method to perform inference on single protein isoforms. Our approach infers the presence/absence of protein isoforms, and also estimates their abundance; additionally, it provides a measure of the uncertainty of these estimates, via: i) the posterior probability that a protein isoform is present in the sample; ii) a posterior credible interval of its abundance. IsoBayes inputs liquid cromatography mass spectrometry (MS) data, and can work with both PSM counts, and intensities. When available, trascript isoform abundances (i.e., TPMs) are also incorporated: TPMs are used to formulate an informative prior for the respective protein isoform relative abundance. We further identify isoforms where the relative abundance of proteins and transcripts significantly differ. We use a two-layer latent variable approach to model two sources of uncertainty typical of MS data: i) peptides may be erroneously detected (even when absent); ii) many peptides are compatible with multiple protein isoforms. In the first layer, we sample the presence/absence of each peptide based on its estimated probability of being mistakenly detected, also known as PEP (i.e., posterior error probability). In the second layer, for peptides that were estimated as being present, we allocate their abundance across the protein isoforms they map to. These two steps allow us to recover the presence and abundance of each protein isoform.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-isocorrector/meta.yaml b/recipes/bioconductor-isocorrector/meta.yaml index f21aefe95aded..6182c63c90e75 100644 --- a/recipes/bioconductor-isocorrector/meta.yaml +++ b/recipes/bioconductor-isocorrector/meta.yaml @@ -1,24 +1,32 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "IsoCorrectoR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'IsoCorrectoR performs the correction of mass spectrometry data from stable isotope labeling/tracing metabolomics experiments with regard to natural isotope abundance and tracer impurity. Data from both MS and MS/MS measurements can be corrected (with any tracer isotope: 13C, 15N, 18O...), as well as ultra-high resolution MS data from multiple-tracer experiments (e.g. 13C and 15N used simultaneously). See the Bioconductor package IsoCorrectoRGUI for a graphical user interface to IsoCorrectoR. NOTE: With R version 4.0.0, writing correction results to Excel files may currently not work on Windows. However, writing results to csv works as before.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ba3b19c2ad9ed8f9b7f6929c49828bb5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-isocorrector", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-isocorrector + path: recipes/bioconductor-isocorrector + version: 1.0.4 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: IsoCorrectoRGUI, knitr, rmarkdown, testthat, BiocStyle requirements: host: @@ -43,18 +51,16 @@ requirements: - r-stringr - r-tibble - r-writexls + +source: + md5: b2d0f007cc55788211373f20740d79a5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments' - description: 'IsoCorrectoR performs the correction of mass spectrometry data from stable isotope labeling/tracing metabolomics experiments with regard to natural isotope abundance and tracer impurity. Data from both MS and MS/MS measurements can be corrected (with any tracer isotope: 13C, 15N, 18O...), as well as ultra-high resolution MS data from multiple-tracer experiments (e.g. 13C and 15N used simultaneously). See the Bioconductor package IsoCorrectoRGUI for a graphical user interface to IsoCorrectoR. NOTE: With R version 4.0.0, writing correction results to Excel files may currently not work on Windows. However, writing results to csv works as before.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-isocorrector - path: recipes/bioconductor-isocorrector - version: 1.0.4 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-isocorrectorgui/meta.yaml b/recipes/bioconductor-isocorrectorgui/meta.yaml index 93ca3c9414cfc..fbca13de64083 100644 --- a/recipes/bioconductor-isocorrectorgui/meta.yaml +++ b/recipes/bioconductor-isocorrectorgui/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "IsoCorrectoRGUI" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f46ff7c7647616cced839067b9e1b39 +about: + description: 'IsoCorrectoRGUI is a Graphical User Interface for the IsoCorrectoR package. IsoCorrectoR performs the correction of mass spectrometry data from stable isotope labeling/tracing metabolomics experiments with regard to natural isotope abundance and tracer impurity. Data from both MS and MS/MS measurements can be corrected (with any tracer isotope: 13C, 15N, 18O...), as well as high resolution MS data from multiple-tracer experiments (e.g. 13C and 15N used simultaneously).' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Graphical User Interface for IsoCorrectoR build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-isocorrectorgui", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-isocorrector >=1.20.0,<1.21.0' + - bioconductor-isocorrector >=1.24.0,<1.25.0 - r-base - r-readxl - r-tcltk2 run: - - 'bioconductor-isocorrector >=1.20.0,<1.21.0' + - bioconductor-isocorrector >=1.24.0,<1.25.0 - r-base - r-readxl - r-tcltk2 +source: + md5: 1ba9ee16b27e3490b42099c37357da17 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Graphical User Interface for IsoCorrectoR' - description: 'IsoCorrectoRGUI is a Graphical User Interface for the IsoCorrectoR package. IsoCorrectoR performs the correction of mass spectrometry data from stable isotope labeling/tracing metabolomics experiments with regard to natural isotope abundance and tracer impurity. Data from both MS and MS/MS measurements can be corrected (with any tracer isotope: 13C, 15N, 18O...), as well as high resolution MS data from multiple-tracer experiments (e.g. 13C and 15N used simultaneously).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-isoformswitchanalyzer/meta.yaml b/recipes/bioconductor-isoformswitchanalyzer/meta.yaml index 83124db0611eb..70d756410f3ce 100644 --- a/recipes/bioconductor-isoformswitchanalyzer/meta.yaml +++ b/recipes/bioconductor-isoformswitchanalyzer/meta.yaml @@ -1,51 +1,68 @@ -{% set version = "2.2.0" %} +{% set version = "2.6.0" %} {% set name = "IsoformSwitchAnalyzeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6aad6b0133da9e103b4385ff31b7028c build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-isoformswitchanalyzer", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:IsoformSwitchAnalyzeR + - doi:10.1158/1541-7786.MCR-16-0459 + parent_recipe: + name: bioconductor-isoformswitchanalyzer + path: recipes/bioconductor-isoformswitchanalyzer + version: 1.2.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, rmarkdown requirements: + + build: + - {{ compiler('c') }} + - make + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-dexseq >=1.48.0,<1.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-pfamanalyzer >=1.2.0,<1.3.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-saturn >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' - - 'bioconductor-tximeta >=1.20.0,<1.21.0' - - 'bioconductor-tximport >=1.30.0,<1.31.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-dexseq >=1.52.0,<1.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-pfamanalyzer >=1.6.0,<1.7.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-saturn >=1.14.0,<1.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 + - bioconductor-tximeta >=1.24.0,<1.25.0 + - bioconductor-tximport >=1.34.0,<1.35.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-dbi - r-dplyr - r-futile.logger - - 'r-ggplot2 >=3.3.5' + - r-ggplot2 >=3.3.5 - r-gridextra - r-magrittr - r-plyr @@ -59,32 +76,34 @@ requirements: - r-venndiagram - libblas - liblapack + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-dexseq >=1.48.0,<1.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-pfamanalyzer >=1.2.0,<1.3.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-saturn >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' - - 'bioconductor-tximeta >=1.20.0,<1.21.0' - - 'bioconductor-tximport >=1.30.0,<1.31.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-dexseq >=1.52.0,<1.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-pfamanalyzer >=1.6.0,<1.7.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-saturn >=1.14.0,<1.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 + - bioconductor-tximeta >=1.24.0,<1.25.0 + - bioconductor-tximport >=1.34.0,<1.35.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-dbi - r-dplyr - r-futile.logger - - 'r-ggplot2 >=3.3.5' + - r-ggplot2 >=3.3.5 - r-gridextra - r-magrittr - r-plyr @@ -96,24 +115,16 @@ requirements: - r-tibble - r-tidyr - r-venndiagram - build: - - {{ compiler('c') }} - - make + +source: + md5: 7818e5233168673220445e38a823ce51 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data' - description: 'Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:IsoformSwitchAnalyzeR - - doi:10.1158/1541-7786.MCR-16-0459 - parent_recipe: - name: bioconductor-isoformswitchanalyzer - path: recipes/bioconductor-isoformswitchanalyzer - version: 1.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-isolde/build_failure.osx-64.yaml b/recipes/bioconductor-isolde/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..906a50980cf33 --- /dev/null +++ b/recipes/bioconductor-isolde/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5145c93976d11f09dd734bd9477bb6b90e65324dd23b991a8e7d2c1f58f4ddc0 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + description: This package provides ISoLDE a new method for identifying imprinted + genes. This method is dedicated to data arising from RNA sequencing technologies. + The ISoLDE package implements original statistical methodology described in the + publication below. + home: https://bioconductor.org/packages/3.20/bioc/html/ISoLDE.html + license: GPL (>= 2.0) + license_file: /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-isolde_1734212925497/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/R/share/licenses/GPL-3 + summary: Integrative Statistics of alleLe Dependent Expression + extra: + additional-platforms: + - linux-aarch64 + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-isolde_1734212925497/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-isolde_1734212925497/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-isolde_1734212925497/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-isolde_1734212925497/work + INFO: activate-gfortran_osx-64.sh made the following environmental changes: + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-isolde-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-isolde-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-isolde-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-isolde-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-isolde-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-isolde-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-isolde-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-isolde-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-isolde-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-isolde-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-isolde-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-isolde-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-isolde-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-isolde-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -I"$PREFIX/lib/R/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fopenmp -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c Isolde.c -o Isolde.o +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-isolde/meta.yaml b/recipes/bioconductor-isolde/meta.yaml index 15cbf7f4756b9..082c1b4a8f62e 100644 --- a/recipes/bioconductor-isolde/meta.yaml +++ b/recipes/bioconductor-isolde/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "ISoLDE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 448414b250ff7c903395638de3688411 +about: + description: This package provides ISoLDE a new method for identifying imprinted genes. This method is dedicated to data arising from RNA sequencing technologies. The ISoLDE package implements original statistical methodology described in the publication below. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2.0) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Integrative Statistics of alleLe Dependent Expression build: - skip: True # [osx] - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-isolde", max_pin="x.x") }}' +extra: + additional-platforms: + - linux-aarch64 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - make +source: + md5: 191e6a6d928c52508fb3f8be15ba9a34 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2.0)' - summary: 'Integrative Statistics of alleLe Dependent Expression' - description: 'This package provides ISoLDE a new method for identifying imprinted genes. This method is dedicated to data arising from RNA sequencing technologies. The ISoLDE package implements original statistical methodology described in the publication below.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-isomirs/meta.yaml b/recipes/bioconductor-isomirs/meta.yaml index f101815c26500..6dce80810b806 100644 --- a/recipes/bioconductor-isomirs/meta.yaml +++ b/recipes/bioconductor-isomirs/meta.yaml @@ -1,38 +1,49 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "isomiRs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Characterization of miRNAs and isomiRs, clustering and differential expression. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Analyze isomiRs and miRNAs from small RNA-seq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 95b301f966153c00b98359bb6a0986cd build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-isomirs", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:isomirs + - doi:10.1093/bioinformatics/btv632 + parent_recipe: + name: bioconductor-isomirs + path: recipes/bioconductor-isomirs + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, org.Mm.eg.db, targetscan.Hs.eg.db, pheatmap, BiocStyle, testthat requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-degreport >=1.38.0,<1.39.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - r-assertive.sets + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-degreport >=1.42.0,<1.43.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-broom - r-cluster @@ -50,18 +61,18 @@ requirements: - r-stringr - r-tibble - r-tidyr + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-degreport >=1.38.0,<1.39.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - r-assertive.sets + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-degreport >=1.42.0,<1.43.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-broom - r-cluster @@ -79,21 +90,16 @@ requirements: - r-stringr - r-tibble - r-tidyr + +source: + md5: 5664da8911aadc6a0c16a81710f3b9dc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Analyze isomiRs and miRNAs from small RNA-seq' - description: 'Characterization of miRNAs and isomiRs, clustering and differential expression.' - license_file: LICENSE -extra: - identifiers: - - biotools:isomirs - - doi:10.1093/bioinformatics/btv632 - parent_recipe: - name: bioconductor-isomirs - path: recipes/bioconductor-isomirs - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-italics/build_failure.linux-64.yaml b/recipes/bioconductor-italics/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..f3a1edc7fc1be --- /dev/null +++ b/recipes/bioconductor-italics/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a18e711e908e2bbd6e2dd212768c7fdc9fb876fd3ec9b1e1bf5fa71734e99a46 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-glad[version='>=2.70.0,<2.71.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-glad >=2.70.0,<2.71.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-glad >=2.70.0,<2.71.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-glad[version='>=2.70.0,<2.71.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-glad >=2.70.0,<2.71.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-glad >=2.70.0,<2.71.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-glad[version='>=2.70.0,<2.71.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-glad >=2.70.0,<2.71.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-glad >=2.70.0,<2.71.0 [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-italics/meta.yaml b/recipes/bioconductor-italics/meta.yaml index a6482e448f84b..564a1afbd1346 100644 --- a/recipes/bioconductor-italics/meta.yaml +++ b/recipes/bioconductor-italics/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "2.62.0" %} +{% set version = "2.66.0" %} {% set name = "ITALICS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: ITALICS -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 05a5c23fcec3a45b6ff9b36b66b89752 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-italics", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: pd.mapping50k.hind240, pd.mapping250k.sty, pd.mapping250k.nsp requirements: host: - - 'bioconductor-affxparser >=1.74.0,<1.75.0' - - 'bioconductor-glad >=2.66.0,<2.67.0' - - 'bioconductor-italicsdata >=2.40.0,<2.41.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-pd.mapping50k.xba240 >=3.12.0,<3.13.0' + - bioconductor-affxparser >=1.78.0,<1.79.0 + - bioconductor-glad >=2.70.0,<2.71.0 + - bioconductor-italicsdata >=2.44.0,<2.45.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-pd.mapping50k.xba240 >=3.12.0,<3.13.0 - r-base - r-dbi run: - - 'bioconductor-affxparser >=1.74.0,<1.75.0' - - 'bioconductor-glad >=2.66.0,<2.67.0' - - 'bioconductor-italicsdata >=2.40.0,<2.41.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-pd.mapping50k.xba240 >=3.12.0,<3.13.0' + - bioconductor-affxparser >=1.78.0,<1.79.0 + - bioconductor-glad >=2.70.0,<2.71.0 + - bioconductor-italicsdata >=2.44.0,<2.45.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-pd.mapping50k.xba240 >=3.12.0,<3.13.0 - r-base - r-dbi + +source: + md5: f7b1507617f9c1b4db24aab8499045e4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: ITALICS - description: 'A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-italicsdata/meta.yaml b/recipes/bioconductor-italicsdata/meta.yaml index 9a246291d9dd4..999c955215c6e 100644 --- a/recipes/bioconductor-italicsdata/meta.yaml +++ b/recipes/bioconductor-italicsdata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "2.40.0" %} +{% set version = "2.44.0" %} {% set name = "ITALICSData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e154526c43e11840acfd4c92ff1cee8f +about: + description: Data needed to use the ITALICS package + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: ITALICSData build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-italicsdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 90f027ec991724ac688d30ceb7a0b103 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL - summary: ITALICSData - description: 'Data needed to use the ITALICS package' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-italicsdata/post-link.sh b/recipes/bioconductor-italicsdata/post-link.sh index 606e7a5f75eef..7fc47bc69e489 100644 --- a/recipes/bioconductor-italicsdata/post-link.sh +++ b/recipes/bioconductor-italicsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "italicsdata-2.40.0" +installBiocDataPackage.sh "italicsdata-2.44.0" diff --git a/recipes/bioconductor-iterativebma/meta.yaml b/recipes/bioconductor-iterativebma/meta.yaml index 60232f6f7d1a5..ebf6d884aa288 100644 --- a/recipes/bioconductor-iterativebma/meta.yaml +++ b/recipes/bioconductor-iterativebma/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "iterativeBMA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The iterative Bayesian Model Averaging (BMA) algorithm is a variable selection and classification algorithm with an application of classifying 2-class microarray samples, as described in Yeung, Bumgarner and Raftery (Bioinformatics 2005, 21: 2394-2402).' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: The Iterative Bayesian Model Averaging (BMA) algorithm -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: be5e8911f1a2493bdf001fbe0a7cecfa build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-iterativebma", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:iterativebma + - doi:10.1186/gb-2008-9-7-r118 + parent_recipe: + name: bioconductor-iterativebma + path: recipes/bioconductor-iterativebma + version: 1.38.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-bma - r-leaps run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-bma - r-leaps + +source: + md5: 9c2fa4813ea36fed167414bdaa0bcb4a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'The Iterative Bayesian Model Averaging (BMA) algorithm' - description: 'The iterative Bayesian Model Averaging (BMA) algorithm is a variable selection and classification algorithm with an application of classifying 2-class microarray samples, as described in Yeung, Bumgarner and Raftery (Bioinformatics 2005, 21: 2394-2402).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:iterativebma - - doi:10.1186/gb-2008-9-7-r118 - parent_recipe: - name: bioconductor-iterativebma - path: recipes/bioconductor-iterativebma - version: 1.38.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-iterativebmasurv/meta.yaml b/recipes/bioconductor-iterativebmasurv/meta.yaml index 3d92067ce1446..36cc399491b4b 100644 --- a/recipes/bioconductor-iterativebmasurv/meta.yaml +++ b/recipes/bioconductor-iterativebmasurv/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "iterativeBMAsurv" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The iterative Bayesian Model Averaging (BMA) algorithm for survival analysis is a variable selection method for applying survival analysis to microarray data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d2ced120a3665f0ebb69a462a072ad63 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-iterativebmasurv", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:iterativebmasurv + - doi:10.1186/1471-2105-10-72 + parent_recipe: + name: bioconductor-iterativebmasurv + path: recipes/bioconductor-iterativebmasurv + version: 1.38.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -30,21 +41,16 @@ requirements: - r-bma - r-leaps - r-survival + +source: + md5: 734ab3dcd679f88158ce0cbbfa247072 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis' - description: 'The iterative Bayesian Model Averaging (BMA) algorithm for survival analysis is a variable selection method for applying survival analysis to microarray data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:iterativebmasurv - - doi:10.1186/1471-2105-10-72 - parent_recipe: - name: bioconductor-iterativebmasurv - path: recipes/bioconductor-iterativebmasurv - version: 1.38.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ivas/meta.yaml b/recipes/bioconductor-ivas/meta.yaml index 2759fdf777900..3cb382c0182cb 100644 --- a/recipes/bioconductor-ivas/meta.yaml +++ b/recipes/bioconductor-ivas/meta.yaml @@ -1,36 +1,47 @@ -{% set version = "2.22.0" %} +{% set version = "2.26.0" %} {% set name = "IVAS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Identification of genetic variants affecting alternative splicing. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Identification of genetic Variants affecting Alternative Splicing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bf3c824233bc6ad5feffc4463554f57f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ivas", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:ivas + - doi:10.1007/s13258-016-0466-7 + parent_recipe: + name: bioconductor-ivas + path: recipes/bioconductor-ivas + version: 2.0.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-doparallel - r-foreach @@ -39,15 +50,15 @@ requirements: - r-lme4 - r-matrix run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-doparallel - r-foreach @@ -55,21 +66,16 @@ requirements: - r-ggplot2 - r-lme4 - r-matrix + +source: + md5: 96350bba9881a0ee12ef3576e44372c6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Identification of genetic Variants affecting Alternative Splicing' - description: 'Identification of genetic variants affecting alternative splicing.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:ivas - - doi:10.1007/s13258-016-0466-7 - parent_recipe: - name: bioconductor-ivas - path: recipes/bioconductor-ivas - version: 2.0.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ivygapse/meta.yaml b/recipes/bioconductor-ivygapse/meta.yaml index cd26902f032a0..7de607ebfb1d8 100644 --- a/recipes/bioconductor-ivygapse/meta.yaml +++ b/recipes/bioconductor-ivygapse/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "ivygapSE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Define a SummarizedExperiment and exploratory app for Ivy-GAP glioblastoma image, expression, and clinical data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: A SummarizedExperiment for Ivy-GAP data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d58fa85c46a9447719fa06aa57cc217d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ivygapse", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, png, limma, grid, DT, randomForest, digest, testthat, rmarkdown, BiocStyle, magick, statmod, codetools requirements: host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-hwriter @@ -33,8 +34,8 @@ requirements: - r-survminer - r-upsetr run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-hwriter @@ -43,12 +44,16 @@ requirements: - r-survival - r-survminer - r-upsetr + +source: + md5: fad5a7d0a0eca3adce4fe6f88093d7a6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A SummarizedExperiment for Ivy-GAP data' - description: 'Define a SummarizedExperiment and exploratory app for Ivy-GAP glioblastoma image, expression, and clinical data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-iwtomics/meta.yaml b/recipes/bioconductor-iwtomics/meta.yaml index 4149664fdced6..d174a9aa56fa4 100644 --- a/recipes/bioconductor-iwtomics/meta.yaml +++ b/recipes/bioconductor-iwtomics/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "IWTomics" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Interval-Wise Testing for Omics Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f571644700ff672c2ac90aa49b611158 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-iwtomics", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-iwtomics + path: recipes/bioconductor-iwtomics + version: 1.4.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-fda - r-gtable - r-kernsmooth run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-fda - r-gtable - r-kernsmooth + +source: + md5: b027438ed02d8cf992321a4e3adc423c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Interval-Wise Testing for Omics Data' - description: 'Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-iwtomics - path: recipes/bioconductor-iwtomics - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-iyer517/meta.yaml b/recipes/bioconductor-iyer517/meta.yaml index 0f3cf9d1d1a9d..b2a1d078e5b3a 100644 --- a/recipes/bioconductor-iyer517/meta.yaml +++ b/recipes/bioconductor-iyer517/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "Iyer517" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 81226f1ad5acd16cff4c7371f37d1881 +about: + description: representation of public Iyer data from http://genome-www.stanford.edu/serum/clusters.html + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: exprSets for Iyer, Eisen et all 1999 Science paper build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-iyer517", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b9822faff0be8722db82a5e8340b9873 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'exprSets for Iyer, Eisen et all 1999 Science paper' - description: 'representation of public Iyer data from http://genome-www.stanford.edu/serum/clusters.html' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-iyer517/post-link.sh b/recipes/bioconductor-iyer517/post-link.sh index 6eb9d2b69a88b..a3c1bac26fd3a 100644 --- a/recipes/bioconductor-iyer517/post-link.sh +++ b/recipes/bioconductor-iyer517/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "iyer517-1.44.0" +installBiocDataPackage.sh "iyer517-1.48.0" diff --git a/recipes/bioconductor-jaspar2014/meta.yaml b/recipes/bioconductor-jaspar2014/meta.yaml index a7de5670f7d7f..4478ea107f0b1 100644 --- a/recipes/bioconductor-jaspar2014/meta.yaml +++ b/recipes/bioconductor-jaspar2014/meta.yaml @@ -1,45 +1,51 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "JASPAR2014" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Data package for JASPAR 2014. To search this databases, please use the package TFBSTools. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Data package for JASPAR -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ef536411db46944f6d5b9a23ee13be6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-jaspar2014", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-jaspar2014 + path: recipes/bioconductor-jaspar2014 + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: f69c9d61904b3a4279535d61c3ef9597 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Data package for JASPAR' - description: 'Data package for JASPAR 2014. To search this databases, please use the package TFBSTools.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - parent_recipe: - name: bioconductor-jaspar2014 - path: recipes/bioconductor-jaspar2014 - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-jaspar2014/post-link.sh b/recipes/bioconductor-jaspar2014/post-link.sh index 0e2548b04d68b..336a63111bb42 100644 --- a/recipes/bioconductor-jaspar2014/post-link.sh +++ b/recipes/bioconductor-jaspar2014/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "jaspar2014-1.38.0" +installBiocDataPackage.sh "jaspar2014-1.42.0" diff --git a/recipes/bioconductor-jaspar2016/meta.yaml b/recipes/bioconductor-jaspar2016/meta.yaml index 9085e136ba423..950a8e7f2c8fd 100644 --- a/recipes/bioconductor-jaspar2016/meta.yaml +++ b/recipes/bioconductor-jaspar2016/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "JASPAR2016" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2976e4678291944f664396385049180b +about: + description: Data package for JASPAR 2016. To search this databases, please use the package TFBSTools (>= 1.8.1). + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Data package for JASPAR 2016 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-jaspar2016", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-jaspar2016 + path: recipes/bioconductor-jaspar2016 + version: 1.8.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 15bad5cb473e295ea4c509c366f4568a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Data package for JASPAR 2016' - description: 'Data package for JASPAR 2016. To search this databases, please use the package TFBSTools (>= 1.8.1).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - parent_recipe: - name: bioconductor-jaspar2016 - path: recipes/bioconductor-jaspar2016 - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-jaspar2016/post-link.sh b/recipes/bioconductor-jaspar2016/post-link.sh index 692043bcfa04f..47a4e2cafa93b 100644 --- a/recipes/bioconductor-jaspar2016/post-link.sh +++ b/recipes/bioconductor-jaspar2016/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "jaspar2016-1.30.0" +installBiocDataPackage.sh "jaspar2016-1.34.0" diff --git a/recipes/bioconductor-jaspar2018/meta.yaml b/recipes/bioconductor-jaspar2018/meta.yaml index d6ddb786027d8..eb0359bf3e695 100644 --- a/recipes/bioconductor-jaspar2018/meta.yaml +++ b/recipes/bioconductor-jaspar2018/meta.yaml @@ -1,24 +1,28 @@ {% set version = "1.1.1" %} {% set name = "JASPAR2018" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d91fce6ea0dc9fa6a3be6ebc05c1af5d +about: + description: Data package for JASPAR 2018. To search this databases, please use the package TFBSTools (>= 1.15.6). + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Data package for JASPAR 2018 build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-jaspar2018", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-jaspar2018 + path: recipes/bioconductor-jaspar2018 + version: 1.1.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: TFBSTools (>= 1.15.6) requirements: host: @@ -26,19 +30,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d91fce6ea0dc9fa6a3be6ebc05c1af5d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: GPL-2 - summary: 'Data package for JASPAR 2018' - description: 'Data package for JASPAR 2018. To search this databases, please use the package TFBSTools (>= 1.15.6).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - parent_recipe: - name: bioconductor-jaspar2018 - path: recipes/bioconductor-jaspar2018 - version: 1.1.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-jaspar2020/meta.yaml b/recipes/bioconductor-jaspar2020/meta.yaml index 4fb9b4b049b1e..10b79aa3d6223 100644 --- a/recipes/bioconductor-jaspar2020/meta.yaml +++ b/recipes/bioconductor-jaspar2020/meta.yaml @@ -1,24 +1,23 @@ {% set version = "0.99.10" %} {% set name = "JASPAR2020" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bfcaf41ebf0935b8d146afd37719de2d +about: + description: Data package for JASPAR2020. To search this databases, please use the package TFBSTools (>= 1.23.1). + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Data package for JASPAR database (version 2020) build: - number: 7 + noarch: generic + number: 8 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-jaspar2020", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, TFBSTools (>= 1.23.1) requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bfcaf41ebf0935b8d146afd37719de2d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: GPL-2 - summary: 'Data package for JASPAR database (version 2020)' - description: 'Data package for JASPAR2020. To search this databases, please use the package TFBSTools (>= 1.23.1).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-jaspar2022/build_failure.linux-64.yaml b/recipes/bioconductor-jaspar2022/build_failure.linux-64.yaml deleted file mode 100644 index 12aa18bc75ecd..0000000000000 --- a/recipes/bioconductor-jaspar2022/build_failure.linux-64.yaml +++ /dev/null @@ -1,43 +0,0 @@ -recipe_sha: 686f49bcd245205318d59d6a520044055090f8bfdb5ed23f0ddd8ceb5b88b41e # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -reason: |- - ValueError: unsupported format character 'T' (0x54) at index 5523 -category: |- - compiler error -log: |- - 09:04:38 BIOCONDA INFO (OUT) ERROR: loading failed - 09:04:38 BIOCONDA INFO (OUT) * removing ‘/opt/conda/conda-bld/bioconductor-jaspar2022_1702026057787/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/R/library/JASPAR2022’ - 09:04:38 BIOCONDA INFO (OUT) - 09:04:38 BIOCONDA INFO (OUT) return code: 1 - 09:04:38 BIOCONDA INFO (OUT) - 09:04:38 BIOCONDA INFO (OUT) kwargs: - 09:04:38 BIOCONDA INFO (OUT) {} - 09:04:38 BIOCONDA INFO (OUT) - 09:04:38 BIOCONDA INFO (OUT) : - 09:04:38 BIOCONDA INFO (OUT) - 09:04:38 BIOCONDA INFO (OUT) During handling of the above exception, another exception occurred: - 09:04:38 BIOCONDA INFO (OUT) - 09:04:38 BIOCONDA INFO (OUT) Traceback (most recent call last): - 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/bin/conda-mambabuild", line 10, in - 09:04:38 BIOCONDA INFO (OUT) sys.exit(main()) - 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - 09:04:38 BIOCONDA INFO (OUT) call_conda_build(action, config) - 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - 09:04:38 BIOCONDA INFO (OUT) result = api.build( - 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - 09:04:38 BIOCONDA INFO (OUT) return build_tree( - 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3089, in build_tree - 09:04:38 BIOCONDA INFO (OUT) test(pkg, config=metadata.config.copy(), stats=stats) - 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2879, in test - 09:04:38 BIOCONDA INFO (OUT) environ.create_env(metadata.config.test_prefix, actions, config=metadata.config, - 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/environ.py", line 1068, in create_env - 09:04:38 BIOCONDA INFO (OUT) "too short in" in str(exc) - 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda/__init__.py", line 104, in __str__ - 09:04:38 BIOCONDA INFO (OUT) return "\n".join(str(e) for e in self.errors) + "\n" - 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda/__init__.py", line 104, in - 09:04:38 BIOCONDA INFO (OUT) return "\n".join(str(e) for e in self.errors) + "\n" - 09:04:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda/__init__.py", line 58, in __str__ - 09:04:38 BIOCONDA INFO (OUT) return str(self.message % self._kwargs) - 09:04:38 BIOCONDA INFO (OUT) ValueError: unsupported format character 'T' (0x54) at index 5523 - 09:04:47 BIOCONDA ERROR COMMAND FAILED (exited with 1): docker run -t --net host --rm -v /tmp/tmptio6n346/build_script.bash:/opt/build_script.bash -v /opt/mambaforge/envs/bioconda/conda-bld/:/opt/host-conda-bld -v /home/runner/work/bioconda-recipes/bioconda-recipes/recipes/bioconductor-jaspar2022:/opt/recipe -e LANG=C.UTF-8 -e HOST_USER_ID=1001 quay.io/bioconda/bioconda-utils-build-env-cos7:2.11.0 /bin/bash /opt/build_script.bash - diff --git a/recipes/bioconductor-jaspar2022/meta.yaml b/recipes/bioconductor-jaspar2022/meta.yaml index f9be32b043fea..8ed806ba279a4 100644 --- a/recipes/bioconductor-jaspar2022/meta.yaml +++ b/recipes/bioconductor-jaspar2022/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "0.99.7" %} +{% set version = "0.99.8" %} {% set name = "JASPAR2022" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 282af23228198a377fa9bd76c94dd5eb +about: + description: JASPAR is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. To search thisdatabases, please use the package TFBSTools (>= 1.31.2). + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Data package for JASPAR database (version 2022) build: - number: 2 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-jaspar2022", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle, TFBSTools (>= 1.31.2) requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f3ac6c35365f8d8f670adad6e30c3b2f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: GPL-2 - summary: 'Data package for JASPAR database (version 2022)' - description: 'JASPAR is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. To search thisdatabases, please use the package TFBSTools (>= 1.31.2).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-jaspar2022/post-link.sh b/recipes/bioconductor-jaspar2022/post-link.sh index 48a3c21d325a3..2c00249ee14d6 100644 --- a/recipes/bioconductor-jaspar2022/post-link.sh +++ b/recipes/bioconductor-jaspar2022/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "jaspar2022-0.99.7" +installBiocDataPackage.sh "jaspar2022-0.99.8" diff --git a/recipes/bioconductor-jaspar2024/meta.yaml b/recipes/bioconductor-jaspar2024/meta.yaml index 76fe59cb071b2..f816350ea7206 100644 --- a/recipes/bioconductor-jaspar2024/meta.yaml +++ b/recipes/bioconductor-jaspar2024/meta.yaml @@ -1,41 +1,41 @@ {% set version = "0.99.6" %} {% set name = "JASPAR2024" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9c8144547873a36473a5f9cad793f578 +about: + description: JASPAR (https://testjaspar.uio.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20 percent increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF-binding sites in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Data package for JASPAR database (version 2024) build: - number: 0 + noarch: generic + number: 1 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-jaspar2024", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle, RSQLite requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9c8144547873a36473a5f9cad793f578 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: GPL-2 - summary: 'Data package for JASPAR database (version 2024)' - description: 'JASPAR (https://testjaspar.uio.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20 percent increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF-binding sites in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-jazaerimetadata.db/meta.yaml b/recipes/bioconductor-jazaerimetadata.db/meta.yaml index 102a58956d8c4..997ba3ae81361 100644 --- a/recipes/bioconductor-jazaerimetadata.db/meta.yaml +++ b/recipes/bioconductor-jazaerimetadata.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "JazaeriMetaData.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3a154a74ac2acebe3471b039c9d9a4dc +about: + description: A data package containing annotation data for JazaeriMetaData assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: A data package containing annotation data for JazaeriMetaData build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-jazaerimetadata.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3a154a74ac2acebe3471b039c9d9a4dc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A data package containing annotation data for JazaeriMetaData' - description: 'A data package containing annotation data for JazaeriMetaData assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-karyoploter/meta.yaml b/recipes/bioconductor-karyoploter/meta.yaml index f19c5440e562c..dda0c9930275f 100644 --- a/recipes/bioconductor-karyoploter/meta.yaml +++ b/recipes/bioconductor-karyoploter/meta.yaml @@ -1,66 +1,71 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "karyoploteR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Plot customizable linear genomes displaying arbitrary data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b9fcbfd3b5d7f3349cce595751b31a41 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-karyoploter", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat, magrittr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Hs.eg.db, org.Mm.eg.db, pasillaBamSubset requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-bamsignals >=1.34.0,<1.35.0' - - 'bioconductor-biovizbase >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-regioner >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-bamsignals >=1.38.0,<1.39.0 + - bioconductor-biovizbase >=1.54.0,<1.55.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-regioner >=1.38.0,<1.39.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-bezier - r-digest - r-memoise run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-bamsignals >=1.34.0,<1.35.0' - - 'bioconductor-biovizbase >=1.50.0,<1.51.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-regioner >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-bamsignals >=1.38.0,<1.39.0 + - bioconductor-biovizbase >=1.54.0,<1.55.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-regioner >=1.38.0,<1.39.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-bezier - r-digest - r-memoise + +source: + md5: 3f215f2621d0dffa766884ea05b2737f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Plot customizable linear genomes displaying arbitrary data' - description: 'karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-katdetectr/meta.yaml b/recipes/bioconductor-katdetectr/meta.yaml index 3ee2e89e53520..855a6a2a57851 100644 --- a/recipes/bioconductor-katdetectr/meta.yaml +++ b/recipes/bioconductor-katdetectr/meta.yaml @@ -1,81 +1,90 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "katdetectr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Kataegis refers to the occurrence of regional hypermutation and is a phenomenon observed in a wide range of malignancies. Using changepoint detection katdetectr aims to identify putative kataegis foci from common data-formats housing genomic variants. Katdetectr has shown to be a robust package for the detection, characterization and visualization of kataegis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Detection, Characterization and Visualization of Kataegis in Sequencing Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7ae9895a26f752a9e8502913ef8ce410 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-katdetectr", max_pin="x.x") }}' - noarch: generic -# Suggests: scales (>= 1.2.0), knitr (>= 1.37), rmarkdown (>= 2.13), testthat (>= 3.0.0), BiocStyle (>= 2.26.0) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle (>= 2.26.0), knitr (>= 1.37), rmarkdown (>= 2.13), stats, testthat (>= 3.0.0) requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-maftools >=2.18.0,<2.19.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-maftools >=2.22.0,<2.23.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - - 'r-changepoint >=2.2.3' - - 'r-changepoint.np >=1.0.3' - - 'r-checkmate >=2.0.0' - - 'r-dplyr >=1.0.8' - - 'r-ggplot2 >=3.3.5' - - 'r-ggtext >=0.1.1' - - 'r-rdpack >=2.3.1' - - 'r-rlang >=1.0.2' - - 'r-tibble >=3.1.6' - - 'r-tidyr >=1.2.0' + - r-changepoint >=2.2.3 + - r-changepoint.np >=1.0.3 + - r-checkmate >=2.0.0 + - r-dplyr >=1.0.8 + - r-ggplot2 >=3.3.5 + - r-ggtext >=0.1.1 + - r-rdpack >=2.3.1 + - r-rlang >=1.0.2 + - r-scales >=1.2.0 + - r-tibble >=3.1.6 + - r-tidyr >=1.2.0 + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-maftools >=2.18.0,<2.19.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-maftools >=2.22.0,<2.23.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - - 'r-changepoint >=2.2.3' - - 'r-changepoint.np >=1.0.3' - - 'r-checkmate >=2.0.0' - - 'r-dplyr >=1.0.8' - - 'r-ggplot2 >=3.3.5' - - 'r-ggtext >=0.1.1' - - 'r-rdpack >=2.3.1' - - 'r-rlang >=1.0.2' - - 'r-tibble >=3.1.6' - - 'r-tidyr >=1.2.0' + - r-changepoint >=2.2.3 + - r-changepoint.np >=1.0.3 + - r-checkmate >=2.0.0 + - r-dplyr >=1.0.8 + - r-ggplot2 >=3.3.5 + - r-ggtext >=0.1.1 + - r-rdpack >=2.3.1 + - r-rlang >=1.0.2 + - r-scales >=1.2.0 + - r-tibble >=3.1.6 + - r-tidyr >=1.2.0 + +source: + md5: b82e34bb3c3d447ca1899d32dd214f1d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Detection, Characterization and Visualization of Kataegis in Sequencing Data' - description: 'Kataegis refers to the occurrence of regional hypermutation and is a phenomenon observed in a wide range of malignancies. Using changepoint detection katdetectr aims to identify putative kataegis foci from common data-formats housing genomic variants. Katdetectr has shown to be a robust package for the detection, characterization and visualization of kataegis.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-kboost/meta.yaml b/recipes/bioconductor-kboost/meta.yaml index 8c45d97eb7d3f..144d81278e750 100644 --- a/recipes/bioconductor-kboost/meta.yaml +++ b/recipes/bioconductor-kboost/meta.yaml @@ -1,37 +1,37 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "KBoost" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 853c93af3367a8af56b60aea8495f44b +about: + description: Reconstructing gene regulatory networks and transcription factor activity is crucial to understand biological processes and holds potential for developing personalized treatment. Yet, it is still an open problem as state-of-art algorithm are often not able to handle large amounts of data. Furthermore, many of the present methods predict numerous false positives and are unable to integrate other sources of information such as previously known interactions. Here we introduce KBoost, an algorithm that uses kernel PCA regression, boosting and Bayesian model averaging for fast and accurate reconstruction of gene regulatory networks. KBoost can also use a prior network built on previously known transcription factor targets. We have benchmarked KBoost using three different datasets against other high performing algorithms. The results show that our method compares favourably to other methods across datasets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 | GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Inference of gene regulatory networks from gene expression data build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-kboost", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, testthat requirements: host: - r-base run: - r-base +source: + md5: 4a2b4d297e7f50f34be5bae46abe46eb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-2 | GPL-3' - summary: 'Inference of gene regulatory networks from gene expression data' - description: 'Reconstructing gene regulatory networks and transcription factor activity is crucial to understand biological processes and holds potential for developing personalized treatment. Yet, it is still an open problem as state-of-art algorithm are often not able to handle large amounts of data. Furthermore, many of the present methods predict numerous false positives and are unable to integrate other sources of information such as previously known interactions. Here we introduce KBoost, an algorithm that uses kernel PCA regression, boosting and Bayesian model averaging for fast and accurate reconstruction of gene regulatory networks. KBoost can also use a prior network built on previously known transcription factor targets. We have benchmarked KBoost using three different datasets against other high performing algorithms. The results show that our method compares favourably to other methods across datasets.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-kcsmart/meta.yaml b/recipes/bioconductor-kcsmart/meta.yaml index e23a15eee3b25..c7fd69441046d 100644 --- a/recipes/bioconductor-kcsmart/meta.yaml +++ b/recipes/bioconductor-kcsmart/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "2.60.0" %} +{% set version = "2.64.0" %} {% set name = "KCsmart" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Multi sample aCGH analysis package using kernel convolution + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Multi sample aCGH analysis package using kernel convolution -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e50f547d912df8deb29537d5e27fc5d0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-kcsmart", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:kcsmart + - doi:10.1186/1756-0500-3-298 + parent_recipe: + name: bioconductor-kcsmart + path: recipes/bioconductor-kcsmart + version: 2.38.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-siggenes >=1.76.0,<1.77.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-siggenes >=1.80.0,<1.81.0 - r-base - r-kernsmooth run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-siggenes >=1.76.0,<1.77.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-siggenes >=1.80.0,<1.81.0 - r-base - r-kernsmooth + +source: + md5: a5f8500e44005b573292f1f49ffd6253 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Multi sample aCGH analysis package using kernel convolution' - description: 'Multi sample aCGH analysis package using kernel convolution' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:kcsmart - - doi:10.1186/1756-0500-3-298 - parent_recipe: - name: bioconductor-kcsmart - path: recipes/bioconductor-kcsmart - version: 2.38.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-kebabs/meta.yaml b/recipes/bioconductor-kebabs/meta.yaml index 5543552572b65..7f51e691f6e8a 100644 --- a/recipes/bioconductor-kebabs/meta.yaml +++ b/recipes/bioconductor-kebabs/meta.yaml @@ -1,71 +1,77 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "kebabs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The package provides functionality for kernel-based analysis of DNA, RNA, and amino acid sequences via SVM-based methods. As core functionality, kebabs implements following sequence kernels: spectrum kernel, mismatch kernel, gappy pair kernel, and motif kernel. Apart from an efficient implementation of standard position-independent functionality, the kernels are extended in a novel way to take the position of patterns into account for the similarity measure. Because of the flexibility of the kernel formulation, other kernels like the weighted degree kernel or the shifted weighted degree kernel with constant weighting of positions are included as special cases. An annotation-specific variant of the kernels uses annotation information placed along the sequence together with the patterns in the sequence. The package allows for the generation of a kernel matrix or an explicit feature representation in dense or sparse format for all available kernels which can be used with methods implemented in other R packages. With focus on SVM-based methods, kebabs provides a framework which simplifies the usage of existing SVM implementations in kernlab, e1071, and LiblineaR. Binary and multi-class classification as well as regression tasks can be used in a unified way without having to deal with the different functions, parameters, and formats of the selected SVM. As support for choosing hyperparameters, the package provides cross validation - including grouped cross validation, grid search and model selection functions. For easier biological interpretation of the results, the package computes feature weights for all SVMs and prediction profiles which show the contribution of individual sequence positions to the prediction result and indicate the relevance of sequence sections for the learning result and the underlying biological functions.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2.1) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Kernel-Based Analysis of Biological Sequences -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d6c4a16d9fd157b1e68acc8d4816017e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-kebabs", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:kebabs + parent_recipe: + name: bioconductor-kebabs + path: recipes/bioconductor-kebabs + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SparseM, Biobase, BiocGenerics, knitr requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-apcluster - r-base - r-e1071 - r-kernlab - r-liblinear - - 'r-matrix >=1.5-0' - - 'r-rcpp >=0.11.2' + - r-matrix >=1.5-0 + - r-rcpp >=0.11.2 - libblas - liblapack run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-apcluster - r-base - r-e1071 - r-kernlab - r-liblinear - - 'r-matrix >=1.5-0' - - 'r-rcpp >=0.11.2' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-matrix >=1.5-0 + - r-rcpp >=0.11.2 + +source: + md5: 81dc80097c4cba89240342b0ab426728 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'Kernel-Based Analysis Of Biological Sequences' - description: 'The package provides functionality for kernel-based analysis of DNA, RNA, and amino acid sequences via SVM-based methods. As core functionality, kebabs implements following sequence kernels: spectrum kernel, mismatch kernel, gappy pair kernel, and motif kernel. Apart from an efficient implementation of standard position-independent functionality, the kernels are extended in a novel way to take the position of patterns into account for the similarity measure. Because of the flexibility of the kernel formulation, other kernels like the weighted degree kernel or the shifted weighted degree kernel with constant weighting of positions are included as special cases. An annotation-specific variant of the kernels uses annotation information placed along the sequence together with the patterns in the sequence. The package allows for the generation of a kernel matrix or an explicit feature representation in dense or sparse format for all available kernels which can be used with methods implemented in other R packages. With focus on SVM-based methods, kebabs provides a framework which simplifies the usage of existing SVM implementations in kernlab, e1071, and LiblineaR. Binary and multi-class classification as well as regression tasks can be used in a unified way without having to deal with the different functions, parameters, and formats of the selected SVM. As support for choosing hyperparameters, the package provides cross validation - including grouped cross validation, grid search and model selection functions. For easier biological interpretation of the results, the package computes feature weights for all SVMs and prediction profiles which show the contribution of individual sequence positions to the prediction result and indicate the relevance of sequence sections for the learning result and the underlying biological functions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} - parent_recipe: - name: bioconductor-kebabs - path: recipes/bioconductor-kebabs - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-keggandmetacoredzpathwaysgeo/meta.yaml b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/meta.yaml index 184fb7d2a89ea..1488cc95e3037 100644 --- a/recipes/bioconductor-keggandmetacoredzpathwaysgeo/meta.yaml +++ b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "KEGGandMetacoreDzPathwaysGEO" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3a5180de47f1c28949b77db9f79b44ed +about: + description: This is a collection of 18 data sets for which the phenotype is a disease with a corresponding pathway in either KEGG or metacore database.This collection of datasets were used as gold standard in comparing gene set analysis methods. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Disease Datasets from GEO build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-keggandmetacoredzpathwaysgeo", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bc64484970f91516654ad091857f000b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Disease Datasets from GEO' - description: 'This is a collection of 18 data sets for which the phenotype is a disease with a corresponding pathway in either KEGG or metacore database.This collection of datasets were used as gold standard in comparing gene set analysis methods.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-keggandmetacoredzpathwaysgeo/post-link.sh b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/post-link.sh index 30e63a47b1f7d..9093f6197d516 100644 --- a/recipes/bioconductor-keggandmetacoredzpathwaysgeo/post-link.sh +++ b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "keggandmetacoredzpathwaysgeo-1.22.0" +installBiocDataPackage.sh "keggandmetacoredzpathwaysgeo-1.26.0" diff --git a/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml b/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml index 1cbbda4787238..7c4d30f66fc73 100644 --- a/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml +++ b/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml @@ -1,47 +1,53 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "KEGGdzPathwaysGEO" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This is a collection of 24 data sets for which the phenotype is a disease with a corresponding pathway in the KEGG database.This collection of datasets were used as gold standard in comparing gene set analysis methods by the PADOG package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: KEGG Disease Datasets from GEO -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f30f9ac05c04214d25a9d49fb4ce8bd build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-keggdzpathwaysgeo", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-keggdzpathwaysgeo + path: recipes/bioconductor-keggdzpathwaysgeo + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 2edbe2925b386b52a1fd7231d93d006b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'KEGG Disease Datasets from GEO' - description: 'This is a collection of 24 data sets for which the phenotype is a disease with a corresponding pathway in the KEGG database.This collection of datasets were used as gold standard in comparing gene set analysis methods by the PADOG package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - parent_recipe: - name: bioconductor-keggdzpathwaysgeo - path: recipes/bioconductor-keggdzpathwaysgeo - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh b/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh index 872a58fcfdea7..d08b2a683abeb 100644 --- a/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh +++ b/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "keggdzpathwaysgeo-1.40.0" +installBiocDataPackage.sh "keggdzpathwaysgeo-1.44.0" diff --git a/recipes/bioconductor-kegggraph/meta.yaml b/recipes/bioconductor-kegggraph/meta.yaml index d5e9a057135c4..f227cc6902caf 100644 --- a/recipes/bioconductor-kegggraph/meta.yaml +++ b/recipes/bioconductor-kegggraph/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.62.0" %} +{% set version = "1.66.0" %} {% set name = "KEGGgraph" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9a4fb63b5bab3eeb0af51af22fa2dc16 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-kegggraph", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:kegggraph + parent_recipe: + name: bioconductor-kegggraph + path: recipes/bioconductor-kegggraph + version: 1.40.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RBGL, testthat, RColorBrewer, org.Hs.eg.db, hgu133plus2.db, SPIA requirements: host: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-rcurl - - 'r-xml >=2.3-0' + - r-xml >=2.3-0 run: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-rcurl - - 'r-xml >=2.3-0' + - r-xml >=2.3-0 + +source: + md5: 81b027ccaf08ba3c8665bfa057d2be60 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor' - description: 'KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:kegggraph - parent_recipe: - name: bioconductor-kegggraph - path: recipes/bioconductor-kegggraph - version: 1.40.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-kegglincs/meta.yaml b/recipes/bioconductor-kegglincs/meta.yaml index f94dbdc65d52e..40c5c2f47991d 100644 --- a/recipes/bioconductor-kegglincs/meta.yaml +++ b/recipes/bioconductor-kegglincs/meta.yaml @@ -1,34 +1,45 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "KEGGlincs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: See what is going on 'under the hood' of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Visualize all edges within a KEGG pathway and overlay LINCS data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ef4b8d4652560f3e9fddb3209adb0dd build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-kegglincs", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:kegglincs + - doi:10.7490/f1000research.1113436.1 + parent_recipe: + name: bioconductor-kegglincs + path: recipes/bioconductor-kegglincs + version: 1.6.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocManager (>= 1.20.3), knitr, graph # SystemRequirements: Cytoscape (>= 3.3.0), Java (>= 8) requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-kodata >=1.28.0,<1.29.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-hgu133a.db >=3.13.0,<3.14.0 + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-kodata >=1.32.0,<1.33.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - r-gtools - r-httr @@ -36,14 +47,14 @@ requirements: - r-plyr - r-rjsonio - r-xml - - 'cytoscape >=3.3.0' + - cytoscape >=3.3.0 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-kodata >=1.28.0,<1.29.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-hgu133a.db >=3.13.0,<3.14.0 + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-kodata >=1.32.0,<1.33.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - r-gtools - r-httr @@ -51,22 +62,17 @@ requirements: - r-plyr - r-rjsonio - r-xml - - 'cytoscape >=3.3.0' + - cytoscape >=3.3.0 + +source: + md5: b18b0cbbe1a545bba3ff3930e345c9df + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Visualize all edges within a KEGG pathway and overlay LINCS data' - description: 'See what is going on ''under the hood'' of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:kegglincs - - doi:10.7490/f1000research.1113436.1 - parent_recipe: - name: bioconductor-kegglincs - path: recipes/bioconductor-kegglincs - version: 1.6.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-keggorthology/meta.yaml b/recipes/bioconductor-keggorthology/meta.yaml index 9d57eb0840070..6f4ee29b0a748 100644 --- a/recipes/bioconductor-keggorthology/meta.yaml +++ b/recipes/bioconductor-keggorthology/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "2.54.0" %} +{% set version = "2.58.0" %} {% set name = "keggorthology" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused with the KEGG ortholog IDs. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: graph support for KO, KEGG Orthology -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 56d510a339dd4fb984bad81624d83142 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-keggorthology", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:keggorthology + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-keggorthology + path: recipes/bioconductor-keggorthology + version: 2.32.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RBGL,ALL requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-hgu95av2.db >=3.13.0,<3.14.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-hgu95av2.db >=3.13.0,<3.14.0 - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-hgu95av2.db >=3.13.0,<3.14.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-hgu95av2.db >=3.13.0,<3.14.0 - r-base - r-dbi + +source: + md5: 5cd740f7ce22655579c8ae79d2ddbeab + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'graph support for KO, KEGG Orthology' - description: 'graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused with the KEGG ortholog IDs.' -extra: - identifiers: - - biotools:keggorthology - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-keggorthology - path: recipes/bioconductor-keggorthology - version: 2.32.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-keggrest/meta.yaml b/recipes/bioconductor-keggrest/meta.yaml index 3da5fe6a36e58..d05822b44a3dc 100644 --- a/recipes/bioconductor-keggrest/meta.yaml +++ b/recipes/bioconductor-keggrest/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "KEGGREST" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package that provides a client interface to the Kyoto Encyclopedia of Genes and Genomes (KEGG) REST API. Only for academic use by academic users belonging to academic institutions (see ). Note that KEGGREST is based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG (python package) by Aurelien Mazurie. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 805cb8808b0ffa6f57999b880337b504 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-keggrest", max_pin="x.x") }}' - noarch: generic -# Suggests: RUnit, BiocGenerics, knitr, markdown + +extra: + identifiers: + - biotools:keggrest + - doi:10.1007/s11845-015-1283-8 + parent_recipe: + name: bioconductor-keggrest + path: recipes/bioconductor-keggrest + version: 1.20.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RUnit, BiocGenerics, BiocStyle, knitr, markdown requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - r-httr - r-png run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - r-httr - r-png + +source: + md5: 700871ac08e548038a9986884d153360 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)' - description: 'A package that provides a client interface to the Kyoto Encyclopedia of Genes and Genomes (KEGG) REST server. Based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG (python package) by Aurelien Mazurie.' -extra: - identifiers: - - biotools:keggrest - - doi:10.1007/s11845-015-1283-8 - parent_recipe: - name: bioconductor-keggrest - path: recipes/bioconductor-keggrest - version: 1.20.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-kidpack/meta.yaml b/recipes/bioconductor-kidpack/meta.yaml index c56508e1335ec..7ff520aec244d 100644 --- a/recipes/bioconductor-kidpack/meta.yaml +++ b/recipes/bioconductor-kidpack/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "kidpack" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 26f5ad5fba1c63156e282d8eac7ac385 +about: + description: kidney microarray data + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: DKFZ kidney package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-kidpack", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 52f60c471d09226cba0e0938924b4bda + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'DKFZ kidney package' - description: 'kidney microarray data' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-kidpack/post-link.sh b/recipes/bioconductor-kidpack/post-link.sh index ac98a263cffef..2f28ac52cc5e6 100644 --- a/recipes/bioconductor-kidpack/post-link.sh +++ b/recipes/bioconductor-kidpack/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "kidpack-1.44.0" +installBiocDataPackage.sh "kidpack-1.48.0" diff --git a/recipes/bioconductor-kinswingr/meta.yaml b/recipes/bioconductor-kinswingr/meta.yaml index 8f1012a7708bc..8e294f4d97451 100644 --- a/recipes/bioconductor-kinswingr/meta.yaml +++ b/recipes/bioconductor-kinswingr/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "KinSwingR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fae1cbd6c179b4fdd5ac12a32ce50eb7 +about: + description: KinSwingR integrates phosphosite data derived from mass-spectrometry data and kinase-substrate predictions to predict kinase activity. Several functions allow the user to build PWM models of kinase-subtrates, statistically infer PWM:substrate matches, and integrate these data to infer kinase activity. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'KinSwingR: network-based kinase activity prediction' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-kinswingr", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-data.table - r-sqldf run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-data.table - r-sqldf +source: + md5: d2840bfa72275821b0a97376de449a57 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'KinSwingR: network-based kinase activity prediction' - description: 'KinSwingR integrates phosphosite data derived from mass-spectrometry data and kinase-substrate predictions to predict kinase activity. Several functions allow the user to build PWM models of kinase-subtrates, statistically infer PWM:substrate matches, and integrate these data to infer kinase activity.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-kmcut/build.sh b/recipes/bioconductor-kmcut/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-kmcut/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-kmcut/meta.yaml b/recipes/bioconductor-kmcut/meta.yaml new file mode 100644 index 0000000000000..5c75b62085cf2 --- /dev/null +++ b/recipes/bioconductor-kmcut/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.0.0" %} +{% set name = "kmcut" %} +{% set bioc = "3.20" %} + +about: + description: The purpose of the package is to identify prognostic biomarkers and an optimal numeric cutoff for each biomarker that can be used to stratify a group of test subjects (samples) into two sub-groups with significantly different survival (better vs. worse). The package was developed for the analysis of gene expression data, such as RNA-seq. However, it can be used with any quantitative variable that has a sufficiently large proportion of unique values. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Optimized Kaplan Meier analysis and identification and validation of prognostic biomarkers + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-kmcut", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, +requirements: + host: + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-doparallel + - r-foreach + - r-pracma + - r-survival + run: + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-doparallel + - r-foreach + - r-pracma + - r-survival + +source: + md5: 505c5a27bd7430ae58156933038d3f38 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-knowseq/meta.yaml b/recipes/bioconductor-knowseq/meta.yaml index b000d31472de7..bedd836cb4ca5 100644 --- a/recipes/bioconductor-knowseq/meta.yaml +++ b/recipes/bioconductor-knowseq/meta.yaml @@ -1,37 +1,40 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "KnowSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: KnowSeq proposes a novel methodology that comprises the most relevant steps in the Transcriptomic gene expression analysis. KnowSeq expects to serve as an integrative tool that allows to process and extract relevant biomarkers, as well as to assess them through a Machine Learning approaches. Finally, the last objective of KnowSeq is the biological knowledge extraction from the biomarkers (Gene Ontology enrichment, Pathway listing and Visualization and Evidences related to the addressed disease). Although the package allows analyzing all the data manually, the main strenght of KnowSeq is the possibilty of carrying out an automatic and intelligent HTML report that collect all the involved steps in one document. It is important to highligh that the pipeline is totally modular and flexible, hence it can be started from whichever of the different steps. KnowSeq expects to serve as a novel tool to help to the experts in the field to acquire robust knowledge and conclusions for the data and diseases to study. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b57c9661e3de8e27e79e3809a609acda build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-knowseq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: + host: - - 'bioconductor-cqn >=1.48.0,<1.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-cqn >=1.52.0,<1.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-caret - r-e1071 - - 'r-ggplot2 >=3.3.0' + - r-ggplot2 >=3.3.0 - r-gridextra - - 'r-hmisc >=4.4.0' + - r-hmisc >=4.4.0 - r-httr - r-jsonlite - r-kernlab @@ -43,17 +46,18 @@ requirements: - r-rmarkdown - r-stringr - r-xml + run: - - 'bioconductor-cqn >=1.48.0,<1.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-cqn >=1.52.0,<1.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-caret - r-e1071 - - 'r-ggplot2 >=3.3.0' + - r-ggplot2 >=3.3.0 - r-gridextra - - 'r-hmisc >=4.4.0' + - r-hmisc >=4.4.0 - r-httr - r-jsonlite - r-kernlab @@ -65,13 +69,16 @@ requirements: - r-rmarkdown - r-stringr - r-xml + +source: + md5: eee927957a3a83938ee054b3b6664eda + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'KnowSeq R/Bioc package The Smart Transcriptomic Pipeline' - description: 'KnowSeq proposes a novel methodology that comprises the most relevant steps in the Transcriptomic gene expression analysis. KnowSeq expects to serve as an integrative tool that allows to process and extract relevant biomarkers, as well as to assess them through a Machine Learning approaches. Finally, the last objective of KnowSeq is the biological knowledge extraction from the biomarkers (Gene Ontology enrichment, Pathway listing and Visualization and Evidences related to the addressed disease). Although the package allows analyzing all the data manually, the main strenght of KnowSeq is the possibilty of carrying out an automatic and intelligent HTML report that collect all the involved steps in one document. It is important to highligh that the pipeline is totally modular and flexible, hence it can be started from whichever of the different steps. KnowSeq expects to serve as a novel tool to help to the experts in the field to acquire robust knowledge and conclusions for the data and diseases to study.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-knowyourcg/build.sh b/recipes/bioconductor-knowyourcg/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-knowyourcg/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-knowyourcg/meta.yaml b/recipes/bioconductor-knowyourcg/meta.yaml new file mode 100644 index 0000000000000..7a3187b87fbd0 --- /dev/null +++ b/recipes/bioconductor-knowyourcg/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.2.0" %} +{% set name = "knowYourCG" %} +{% set bioc = "3.20" %} + +about: + description: knowYourCG automates the functional analysis of DNA methylation data. The package tests the enrichment of discrete CpG probes across thousands of curated biological and technical features. GSEA-like analysis can be performed on continuous methylation data query sets. knowYourCG can also take beta matrices as input to perform feature aggregation over the curated database sets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Functional analysis of DNA methylome datasets + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-knowyourcg", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat (>= 3.0.0), SummarizedExperiment, rmarkdown, knitr, sesame, gprofiler2 +requirements: + host: + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sesamedata >=1.24.0,<1.25.0 + - r-base + - r-dplyr + - r-reshape2 + - r-rlang + - r-stringr + run: + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sesamedata >=1.24.0,<1.25.0 + - r-base + - r-dplyr + - r-reshape2 + - r-rlang + - r-stringr + +source: + md5: 2bc64fc886cd4f244fc4c9e6d744bd80 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-kodata/meta.yaml b/recipes/bioconductor-kodata/meta.yaml index c6d97424dd478..85ef5448986bd 100644 --- a/recipes/bioconductor-kodata/meta.yaml +++ b/recipes/bioconductor-kodata/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "KOdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 40e099053eae889ad66256a94427ac54 +about: + description: Contains consensus genomic signatures (CGS) for experimental cell-line specific gene knock-outs as well as baseline gene expression data for a subset of experimental cell-lines. Intended for use with package KEGGlincs. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: LINCS Knock-Out Data Package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-kodata", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-kodata + path: recipes/bioconductor-kodata + version: 1.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b31e70b88fa60ec9a64d94fe6b2b487e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'LINCS Knock-Out Data Package' - description: 'Contains consensus genomic signatures (CGS) for experimental cell-line specific gene knock-outs as well as baseline gene expression data for a subset of experimental cell-lines. Intended for use with package KEGGlincs.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-kodata - path: recipes/bioconductor-kodata - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-kodata/post-link.sh b/recipes/bioconductor-kodata/post-link.sh index d0c7715575049..190dccf0fab49 100644 --- a/recipes/bioconductor-kodata/post-link.sh +++ b/recipes/bioconductor-kodata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "kodata-1.28.0" +installBiocDataPackage.sh "kodata-1.32.0" diff --git a/recipes/bioconductor-koinar/build.sh b/recipes/bioconductor-koinar/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-koinar/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-koinar/meta.yaml b/recipes/bioconductor-koinar/meta.yaml new file mode 100644 index 0000000000000..cdddd85fe8e10 --- /dev/null +++ b/recipes/bioconductor-koinar/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.0.0" %} +{% set name = "koinar" %} +{% set bioc = "3.20" %} + +about: + description: A client to simplify fetching predictions from the Koina web service. Koina is a model repository enabling the remote execution of models. Predictions are generated as a response to HTTP/S requests, the standard protocol used for nearly all web traffic. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Apache License 2.0 + summary: KoinaR - Remote machine learning inference using Koina +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-koinar", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: BiocManager, BiocStyle (>= 2.26), httptest, knitr, lattice, msdata, OrgMassSpecR, protViz, S4Vectors, Spectra, testthat, mzR +requirements: + host: + - r-base + - r-httr + - r-jsonlite + run: + - r-base + - r-httr + - r-jsonlite +source: + md5: fdede8485780d12b73b9bfa663c34023 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-lace/meta.yaml b/recipes/bioconductor-lace/meta.yaml index 40a6921d22e8c..ac231b0dbc416 100644 --- a/recipes/bioconductor-lace/meta.yaml +++ b/recipes/bioconductor-lace/meta.yaml @@ -1,29 +1,32 @@ -{% set version = "2.6.0" %} +{% set version = "2.10.0" %} {% set name = "LACE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: LACE is an algorithmic framework that processes single-cell somatic mutation profiles from cancer samples collected at different time points and in distinct experimental settings, to produce longitudinal models of cancer evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints, by maximizing a weighed likelihood function computed on multiple time points. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Longitudinal Analysis of Cancer Evolution (LACE) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d11f64211d10d293c2931b49765b5d61 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lace", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, BiocStyle, testthat, knitr, rmarkdown requirements: + host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bsplus - r-callr @@ -60,9 +63,10 @@ requirements: - r-stringr - r-svglite - r-tidyr + run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bsplus - r-callr @@ -99,13 +103,16 @@ requirements: - r-stringr - r-svglite - r-tidyr + +source: + md5: 2462e9b4d29170580cbb756e8c281a2f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Longitudinal Analysis of Cancer Evolution (LACE)' - description: 'LACE is an algorithmic framework that processes single-cell somatic mutation profiles from cancer samples collected at different time points and in distinct experimental settings, to produce longitudinal models of cancer evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints, by maximizing a weighed likelihood function computed on multiple time points.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lapmix/meta.yaml b/recipes/bioconductor-lapmix/meta.yaml index 76e3e6dc36bb5..5afaa855e9f5e 100644 --- a/recipes/bioconductor-lapmix/meta.yaml +++ b/recipes/bioconductor-lapmix/meta.yaml @@ -1,40 +1,22 @@ -{% set version = "1.68.0" %} +{% set version = "1.72.0" %} {% set name = "lapmix" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Laplace mixture modelling of microarray experiments. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes. The main purpose is to identify differentially expressed genes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Laplace Mixture Model in Microarray Experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5d2611d1b39b06b05ed64ffab459a5a9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lapmix", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Laplace Mixture Model in Microarray Experiments' - description: 'Laplace mixture modelling of microarray experiments. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes. The main purpose is to identify differentially expressed genes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:lapmix @@ -44,3 +26,27 @@ extra: path: recipes/bioconductor-lapmix version: 1.46.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + +source: + md5: c7c5fb52d888b23a23ba4049137cab60 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-lapointe.db/meta.yaml b/recipes/bioconductor-lapointe.db/meta.yaml index 2e19eca313c84..6714d903fa916 100644 --- a/recipes/bioconductor-lapointe.db/meta.yaml +++ b/recipes/bioconductor-lapointe.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "LAPOINTE.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 434b25ad7411201d8be6bb1a0463b387 +about: + description: A package containing metadata for LAPOINTE arrays assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: A package containing metadata for LAPOINTE arrays build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lapointe.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 434b25ad7411201d8be6bb1a0463b387 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A package containing metadata for LAPOINTE arrays' - description: 'A package containing metadata for LAPOINTE arrays assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lbe/meta.yaml b/recipes/bioconductor-lbe/meta.yaml index 5c71cafda8ca6..8a36e36bf8376 100644 --- a/recipes/bioconductor-lbe/meta.yaml +++ b/recipes/bioconductor-lbe/meta.yaml @@ -1,39 +1,20 @@ -{% set version = "1.70.0" %} +{% set version = "1.74.0" %} {% set name = "LBE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 36559f365f1dbd53056e6b43bc1e06e9 +about: + description: LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Estimation of the false discovery rate build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lbe", max_pin="x.x") }}' - noarch: generic -# Suggests: qvalue -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Estimation of the false discovery rate.' - description: 'LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' extra: identifiers: - biotools:lbe @@ -42,4 +23,23 @@ extra: name: bioconductor-lbe path: recipes/bioconductor-lbe version: 1.48.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: qvalue +requirements: + host: + - r-base + run: + - r-base +source: + md5: 407869685d2147e5aba11fb883f1e7a9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ldblock/meta.yaml b/recipes/bioconductor-ldblock/meta.yaml index 9863043358259..fe9d3d22acce1 100644 --- a/recipes/bioconductor-ldblock/meta.yaml +++ b/recipes/bioconductor-ldblock/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "ldblock" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 579c380a003913fde7767f15b47a6692 +about: + description: Define data structures for linkage disequilibrium measures in populations. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: data structures for linkage disequilibrium measures in populations build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ldblock", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: RUnit, knitr, BiocStyle, gwascat, rmarkdown, snpStats, VariantAnnotation, GenomeInfoDb, ensembldb, EnsDb.Hsapiens.v75, Rsamtools, GenomicFiles (>= 1.13.6) requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-httr - r-matrix - r-rlang run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-httr - r-matrix - r-rlang +source: + md5: 3f84d33f77d6672958a7ba420ec1ac8a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'data structures for linkage disequilibrium measures in populations' - description: 'Define data structures for linkage disequilibrium measures in populations.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lea/meta.yaml b/recipes/bioconductor-lea/meta.yaml index 51dd613a14f2e..d8e6f8a267231 100644 --- a/recipes/bioconductor-lea/meta.yaml +++ b/recipes/bioconductor-lea/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "3.14.0" %} +{% set version = "3.18.0" %} {% set name = "LEA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e32cbc2a97921f9b911eef1a5d1ef3d7 +about: + description: LEA is an R package dedicated to population genomics, landscape genomics and genotype-environment association tests. LEA can run analyses of population structure and genome-wide tests for local adaptation, and also performs imputation of missing genotypes. The package includes statistical methods for estimating ancestry coefficients from large genotypic matrices and for evaluating the number of ancestral populations (snmf). It performs statistical tests using latent factor mixed models for identifying genetic polymorphisms that exhibit association with environmental gradients or phenotypic traits (lfmm2). In addition, LEA computes values of genetic offset statistics based on new or predicted environments (genetic.gap, genetic.offset). LEA is mainly based on optimized programs that can scale with the dimensions of large data sets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'LEA: an R package for Landscape and Ecological Association Studies' build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lea", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - make +source: + md5: dc3a581a78477d4910e29a0f94d81c31 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'LEA: an R package for Landscape and Ecological Association Studies' - description: 'LEA is an R package dedicated to population genomics, landscape genomics and genotype-environment association tests. LEA can run analyses of population structure and genome-wide tests for local adaptation, and also performs imputation of missing genotypes. The package includes statistical methods for estimating ancestry coefficients from large genotypic matrices and for evaluating the number of ancestral populations (snmf). It performs statistical tests using latent factor mixed models for identifying genetic polymorphisms that exhibit association with environmental gradients or phenotypic traits (lfmm2). In addition, LEA computes values of genetic offset statistics based on new or predicted environments (genetic.gap, genetic.offset). LEA is mainly based on optimized programs that can scale with the dimensions of large data sets.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ledpred/meta.yaml b/recipes/bioconductor-ledpred/meta.yaml index add26d8b55ec8..885cd9f429b1b 100644 --- a/recipes/bioconductor-ledpred/meta.yaml +++ b/recipes/bioconductor-ledpred/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "LedPred" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package aims at creating a predictive model of regulatory sequences used to score unknown sequences based on the content of DNA motifs, next-generation sequencing (NGS) peaks and signals and other numerical scores of the sequences using supervised classification. The package contains a workflow based on the support vector machine (SVM) algorithm that maps features to sequences, optimize SVM parameters and feature number and creates a model that can be stored and used to score the regulatory potential of unknown sequences. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT | file LICENSE + license_file: LICENSE + summary: Learning from DNA to Predict Enhancers -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a083c0408938618b62557ece5682e61 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ledpred", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-akima - r-base - - 'r-e1071 >=1.6' + - r-e1071 >=1.6 - r-ggplot2 - r-irr - r-jsonlite @@ -35,7 +37,7 @@ requirements: run: - r-akima - r-base - - 'r-e1071 >=1.6' + - r-e1071 >=1.6 - r-ggplot2 - r-irr - r-jsonlite @@ -44,13 +46,16 @@ requirements: - r-rcurl - r-rocr - r-testthat + +source: + md5: 1cedd94401e0419dae5a6e8b22ae8a92 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT | file LICENSE' - summary: 'Learning from DNA to Predict Enhancers' - description: 'This package aims at creating a predictive model of regulatory sequences used to score unknown sequences based on the content of DNA motifs, next-generation sequencing (NGS) peaks and signals and other numerical scores of the sequences using supervised classification. The package contains a workflow based on the support vector machine (SVM) algorithm that maps features to sequences, optimize SVM parameters and feature number and creates a model that can be stored and used to score the regulatory potential of unknown sequences.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-leebamviews/meta.yaml b/recipes/bioconductor-leebamviews/meta.yaml index 23ddd91fec827..b451544ca6993 100644 --- a/recipes/bioconductor-leebamviews/meta.yaml +++ b/recipes/bioconductor-leebamviews/meta.yaml @@ -1,52 +1,57 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "leeBamViews" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: data from PMID 19096707; prototype for managing multiple NGS samples + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic 2.0 + summary: leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 58f7c7fdbb1f949f48924ac79d31b580 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-leebamviews", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: biomaRt, org.Sc.sgd.db, edgeR requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 80635485b599e011e632e0c9f82f6e88 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'Artistic 2.0' - summary: 'leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009' - description: 'data from PMID 19096707; prototype for managing multiple NGS samples' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-leebamviews/post-link.sh b/recipes/bioconductor-leebamviews/post-link.sh index f1275b766d7ad..be7b8bfb5bcb8 100644 --- a/recipes/bioconductor-leebamviews/post-link.sh +++ b/recipes/bioconductor-leebamviews/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "leebamviews-1.38.0" +installBiocDataPackage.sh "leebamviews-1.42.0" diff --git a/recipes/bioconductor-lefser/meta.yaml b/recipes/bioconductor-lefser/meta.yaml index e6ee9347ff280..d4f0d68d3e0ce 100644 --- a/recipes/bioconductor-lefser/meta.yaml +++ b/recipes/bioconductor-lefser/meta.yaml @@ -1,46 +1,65 @@ -{% set version = "1.12.1" %} +{% set version = "1.16.0" %} {% set name = "lefser" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: lefser is the R implementation of the popular microbiome biomarker discovery too, LEfSe. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers from two-level classes (and optional sub-classes). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: R implementation of the LEfSE method for microbiome biomarker discovery -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c3b2deaf4b58de1bb930164df11a388f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lefser", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, curatedMetagenomicData, BiocStyle, phyloseq, testthat, pkgdown, covr, withr + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, curatedMetagenomicData, BiocStyle, phyloseq, pkgdown, covr, withr requirements: host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-coin + - r-dplyr + - r-forcats - r-ggplot2 - r-mass + - r-stringr + - r-testthat + - r-tibble + - r-tidyr run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-coin + - r-dplyr + - r-forcats - r-ggplot2 - r-mass + - r-stringr + - r-testthat + - r-tibble + - r-tidyr + +source: + md5: 3e2b3ab61f31fe370694da47cfa6b4f8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'R implementation of the LEfSE method for microbiome biomarker discovery' - description: 'lefser is an implementation in R of the popular "LDA Effect Size (LEfSe)" method for microbiome biomarker discovery. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers of groups and sub-groups.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lemur/build_failure.osx-64.yaml b/recipes/bioconductor-lemur/build_failure.osx-64.yaml deleted file mode 100644 index 9beef668bed41..0000000000000 --- a/recipes/bioconductor-lemur/build_failure.osx-64.yaml +++ /dev/null @@ -1,106 +0,0 @@ -recipe_sha: 9ec1f5c47eca7b1c8d8b7db53ce0866846a9c61f157f39bec7526f0c5cbe3856 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: |- - dependency issue -log: |2- - - bioconductor-s4vectors >=0.40.0,<0.41.0 - - r-base 4.3.* - - bioconductor-matrixgenerics >=1.14.0,<1.15.0 - - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 - - with channels: - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - package bioconductor-summarizedexperiment-1.32.0-r43hdfd78af_0 requires r-base >=4.3,<4.4.0a0, but none of the providers can be installed - - - - Leaving build/test directories: - Work: - /opt/mambaforge/envs/bioconda/conda-bld/work - Test: - /opt/mambaforge/envs/bioconda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/mambaforge/envs/bioconda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla - Build: - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - source activate /opt/mambaforge/envs/bioconda/conda-bld/_build_env - - - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action - t = self.solve(specs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - bioconductor-hdf5array >=1.30.0,<1.31.0 - - r-rcpparmadillo - - r-rcpp - - r-harmony - - r-matrixstats - - r-vctrs - - liblapack 3.9.* *netlib - - bioconductor-delayedmatrixstats >=1.24.0,<1.25.0 - - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 - - libblas 3.9.* *netlib - - bioconductor-biocneighbors >=1.20.0,<1.21.0 - - libcxx >=14 - - bioconductor-biocgenerics >=0.48.0,<0.49.0 - - r-irlba - - r-matrix - - r-rlang - - bioconductor-limma >=3.58.0,<3.59.0 - - bioconductor-glmgampoi >=1.14.0,<1.15.0 - - bioconductor-s4vectors >=0.40.0,<0.41.0 - - r-base 4.3.* - - bioconductor-matrixgenerics >=1.14.0,<1.15.0 - - bioconductor-singlecellexperiment >=1.24.0,<1.25.0 - - with channels: - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - package bioconductor-summarizedexperiment-1.32.0-r43hdfd78af_0 requires r-base >=4.3,<4.4.0a0, but none of the providers can be installed - - - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build - output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs - for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set - conda_packages = finalize_outputs_pass( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass - fm = finalize_metadata( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata - build_unsat, host_unsat = add_upstream_pins(m, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins - host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files - deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies - actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("r-base[version='>=4.3,<4.4.0a0']"), MatchSpec("bioconductor-summarizedexperiment==1.32.0=r43hdfd78af_0")} -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-lemur/meta.yaml b/recipes/bioconductor-lemur/meta.yaml index 71c676e618440..9c0979d7fe84b 100644 --- a/recipes/bioconductor-lemur/meta.yaml +++ b/recipes/bioconductor-lemur/meta.yaml @@ -1,78 +1,86 @@ -{% set version = "1.0.4" %} +{% set version = "1.4.0" %} {% set name = "lemur" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Fit a latent embedding multivariate regression (LEMUR) model to multi-condition single-cell data. The model provides a parametric description of single-cell data measured with treatment vs. control or more complex experimental designs. The parametric model is used to (1) align conditions, (2) predict log fold changes between conditions for all cells, and (3) identify cell neighborhoods with consistent log fold changes. For those neighborhoods, a pseudobulked differential expression test is conducted to assess which genes are significantly changed. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Latent Embedding Multivariate Regression -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 76ef0d01a8f6f23e0f125274af96522d build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lemur", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.0.0), tidyverse, uwot, dplyr, edgeR, knitr, rmarkdown, BiocStyle requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-glmgampoi >=1.14.0,<1.15.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-glmgampoi >=1.18.0,<1.19.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - r-harmony + - r-harmony >=1.2.0 - r-irlba - r-matrix - r-matrixstats - r-rcpp - r-rcpparmadillo - - r-rlang - - r-vctrs + - r-rlang >=1.1.0 + - r-vctrs >=0.6.0 - libblas - liblapack + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-glmgampoi >=1.14.0,<1.15.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-glmgampoi >=1.18.0,<1.19.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - r-harmony + - r-harmony >=1.2.0 - r-irlba - r-matrix - r-matrixstats - r-rcpp - r-rcpparmadillo - - r-rlang - - r-vctrs - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rlang >=1.1.0 + - r-vctrs >=0.6.0 + +source: + md5: 96ec610bec9c5bd78d7c19c8f7e657d0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Latent Embedding Multivariate Regression' - description: 'Fit a latent embedding multivariate regression (LEMUR) model to multi-condition single-cell data. The model provides a parametric description of single-cell data measured with complex experimental designs. The parametric model is used to (1) align conditions, (2) predict log fold changes between conditions for all cells, and (3) identify cell neighborhoods with consistent log fold changes. For those neighborhoods, a pseudobulked differential expression test is conducted to assess which genes are significantly changed.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-les/meta.yaml b/recipes/bioconductor-les/meta.yaml index 2c610c014b1e5..eff678db63a30 100644 --- a/recipes/bioconductor-les/meta.yaml +++ b/recipes/bioconductor-les/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.52.0" %} +{% set version = "1.56.0" %} {% set name = "les" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The 'les' package estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identifying Differential Effects in Tiling Microarray Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b0418480f87e364b451a3f940bcdcb8c build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-les", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:les + - doi:10.1089/cmb.2008.0226 + parent_recipe: + name: bioconductor-les + path: recipes/bioconductor-les + version: 1.30.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biobase, limma requirements: host: @@ -33,21 +44,16 @@ requirements: - r-fdrtool - r-gplots - r-rcolorbrewer + +source: + md5: 4fdbde5acca03c52bc247e2c073fb4a2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Identifying Differential Effects in Tiling Microarray Data' - description: 'The ''les'' package estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:les - - doi:10.1089/cmb.2008.0226 - parent_recipe: - name: bioconductor-les - path: recipes/bioconductor-les - version: 1.30.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-leukemiaseset/meta.yaml b/recipes/bioconductor-leukemiaseset/meta.yaml index d3bfaf2adc95a..ae2a3f0f7c3fc 100644 --- a/recipes/bioconductor-leukemiaseset/meta.yaml +++ b/recipes/bioconductor-leukemiaseset/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "leukemiasEset" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f9e8274856b0d78de6da7ec0bce171f5 +about: + description: Expressionset containing gene expresion data from 60 bone marrow samples of patients with one of the four main types of leukemia (ALL, AML, CLL, CML) or non-leukemia. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Leukemia's microarray gene expression data (expressionSet). build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-leukemiaseset", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5adc5dcc59cbe7e760ae276724f98fad + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Leukemia''s microarray gene expression data (expressionSet).' - description: 'Expressionset containing gene expresion data from 60 bone marrow samples of patients with one of the four main types of leukemia (ALL, AML, CLL, CML) or non-leukemia.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-leukemiaseset/post-link.sh b/recipes/bioconductor-leukemiaseset/post-link.sh index f03618f99ae1e..bf5602bb04b74 100644 --- a/recipes/bioconductor-leukemiaseset/post-link.sh +++ b/recipes/bioconductor-leukemiaseset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "leukemiaseset-1.38.0" +installBiocDataPackage.sh "leukemiaseset-1.42.0" diff --git a/recipes/bioconductor-levi/meta.yaml b/recipes/bioconductor-levi/meta.yaml index 863283e9eb2fd..02bd06f2b49aa 100644 --- a/recipes/bioconductor-levi/meta.yaml +++ b/recipes/bioconductor-levi/meta.yaml @@ -1,74 +1,82 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "levi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The tool integrates data from biological networks with transcriptomes, displaying a heatmap with surface curves to evidence the altered regions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Landscape Expression Visualization Interface -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fff39f74d44cb186d14ebb591b3fa3a1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-levi", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, BiocStyle requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - r-base - - 'r-colorspace >=1.3-2' - - 'r-dplyr >=0.7.4' - - 'r-dt >=0.4' - - 'r-ggplot2 >=2.2.1' - - 'r-httr >=1.3.1' - - 'r-igraph >=1.2.1' + - r-colorspace >=1.3-2 + - r-dplyr >=0.7.4 + - r-dt >=0.4 + - r-ggplot2 >=2.2.1 + - r-httr >=1.3.1 + - r-igraph >=1.2.1 - r-knitr - - 'r-rcolorbrewer >=1.1-2' - - 'r-rcpp >=0.12.18' - - 'r-reshape2 >=1.4.3' + - r-rcolorbrewer >=1.1-2 + - r-rcpp >=0.12.18 + - r-reshape2 >=1.4.3 - r-rmarkdown - - 'r-shiny >=1.0.5' - - 'r-shinydashboard >=0.7.0' - - 'r-shinyjs >=1.0' + - r-shiny >=1.0.5 + - r-shinydashboard >=0.7.0 + - r-shinyjs >=1.0 - r-testthat - - 'r-xml2 >=1.2.0' + - r-xml2 >=1.2.0 - libblas - liblapack + run: - r-base - - 'r-colorspace >=1.3-2' - - 'r-dplyr >=0.7.4' - - 'r-dt >=0.4' - - 'r-ggplot2 >=2.2.1' - - 'r-httr >=1.3.1' - - 'r-igraph >=1.2.1' + - r-colorspace >=1.3-2 + - r-dplyr >=0.7.4 + - r-dt >=0.4 + - r-ggplot2 >=2.2.1 + - r-httr >=1.3.1 + - r-igraph >=1.2.1 - r-knitr - - 'r-rcolorbrewer >=1.1-2' - - 'r-rcpp >=0.12.18' - - 'r-reshape2 >=1.4.3' + - r-rcolorbrewer >=1.1-2 + - r-rcpp >=0.12.18 + - r-reshape2 >=1.4.3 - r-rmarkdown - - 'r-shiny >=1.0.5' - - 'r-shinydashboard >=0.7.0' - - 'r-shinyjs >=1.0' + - r-shiny >=1.0.5 + - r-shinydashboard >=0.7.0 + - r-shinyjs >=1.0 - r-testthat - - 'r-xml2 >=1.2.0' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-xml2 >=1.2.0 + +source: + md5: dd3e6a48e7e67f09ed134357f00fd6d4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Landscape Expression Visualization Interface' - description: 'The tool integrates data from biological networks with transcriptomes, displaying a heatmap with surface curves to evidence the altered regions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lfa/meta.yaml b/recipes/bioconductor-lfa/meta.yaml index ef404bf4b9e2b..990fec452ebf3 100644 --- a/recipes/bioconductor-lfa/meta.yaml +++ b/recipes/bioconductor-lfa/meta.yaml @@ -1,25 +1,39 @@ -{% set version = "2.2.0" %} +{% set version = "2.6.0" %} {% set name = "lfa" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Logistic Factor Analysis is a method for a PCA analogue on Binomial data via estimation of latent structure in the natural parameter. The main method estimates genetic population structure from genotype data. There are also methods for estimating individual-specific allele frequencies using the population structure. Lastly, a structured Hardy-Weinberg equilibrium (HWE) test is developed, which quantifies the goodness of fit of the genotype data to the estimated population structure, via the estimated individual-specific allele frequencies (all of which generalizes traditional HWE tests). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Logistic Factor Analysis for Categorical Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 83d3c5671422b432d992834ae675e020 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lfa", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:lfa + - doi:10.1093/bioinformatics/btv641 + parent_recipe: + name: bioconductor-lfa + path: recipes/bioconductor-lfa + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, ggplot2, testthat, BEDMatrix, genio requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - r-corpcor @@ -30,24 +44,16 @@ requirements: - r-base - r-corpcor - r-rspectra - build: - - {{ compiler('c') }} - - make + +source: + md5: 8cc986c57b3ea73343d7dba9e2e687ab + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Logistic Factor Analysis for Categorical Data' - description: 'Logistic Factor Analysis is a method for a PCA analogue on Binomial data via estimation of latent structure in the natural parameter. The main method estimates genetic population structure from genotype data. There are also methods for estimating individual-specific allele frequencies using the population structure. Lastly, a structured Hardy-Weinberg equilibrium (HWE) test is developed, which quantifies the goodness of fit of the genotype data to the estimated population structure, via the estimated individual-specific allele frequencies (all of which generalizes traditional HWE tests).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:lfa - - doi:10.1093/bioinformatics/btv641 - parent_recipe: - name: bioconductor-lfa - path: recipes/bioconductor-lfa - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-liebermanaidenhic2009/meta.yaml b/recipes/bioconductor-liebermanaidenhic2009/meta.yaml index d71d5f911cfaf..ac1be3e9593b3 100644 --- a/recipes/bioconductor-liebermanaidenhic2009/meta.yaml +++ b/recipes/bioconductor-liebermanaidenhic2009/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "0.40.0" %} +{% set version = "0.44.0" %} {% set name = "LiebermanAidenHiC2009" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 34818101f902d251b339864716cd2d1a +about: + description: 'This package provides data that were presented in the article "Comprehensive mapping of long-range interactions reveals folding principles of the human genome", Science 2009 Oct 9;326(5950):289-93. PMID: 19815776' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Selected data from the HiC paper of E. Lieberman-Aiden et al. in Science (2009) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-liebermanaidenhic2009", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-kernsmooth run: - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-kernsmooth - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 66667bb8dda5d64584a6fcb82c893d2d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Selected data from the HiC paper of E. Lieberman-Aiden et al. in Science (2009)' - description: 'This package provides data that were presented in the article "Comprehensive mapping of long-range interactions reveals folding principles of the human genome", Science 2009 Oct 9;326(5950):289-93. PMID: 19815776' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-liebermanaidenhic2009/post-link.sh b/recipes/bioconductor-liebermanaidenhic2009/post-link.sh index e899cf7938d0f..cd1bfe3d2e0e9 100644 --- a/recipes/bioconductor-liebermanaidenhic2009/post-link.sh +++ b/recipes/bioconductor-liebermanaidenhic2009/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "liebermanaidenhic2009-0.40.0" +installBiocDataPackage.sh "liebermanaidenhic2009-0.44.0" diff --git a/recipes/bioconductor-limma/meta.yaml b/recipes/bioconductor-limma/meta.yaml index 65bacae5a6963..42e9cd7074467 100644 --- a/recipes/bioconductor-limma/meta.yaml +++ b/recipes/bioconductor-limma/meta.yaml @@ -1,53 +1,61 @@ -{% set version = "3.58.1" %} +{% set version = "3.62.1" %} {% set name = "limma" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Data analysis, linear models and differential expression for omics data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Linear Models for Microarray and Omics Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f52a816d0d34b01f721654f90a1fb5f5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-limma", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:limma + - usegalaxy-eu:limma_voom + parent_recipe: + name: bioconductor-limma + path: recipes/bioconductor-limma + version: 3.36.5 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines, affy, AnnotationDbi, Biobase, BiocStyle, GO.db, illuminaio, org.Hs.eg.db, vsn requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - r-statmod - libblas - liblapack + - zlib + - liblzma-devel run: - r-base - r-statmod - build: - - {{ compiler('c') }} - - make + +source: + md5: 60f71c513c6724401b8d114b8d669e08 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Linear Models for Microarray Data' - description: 'Data analysis, linear models and differential expression for microarray data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:limma - - usegalaxy-eu:limma_voom - parent_recipe: - name: bioconductor-limma - path: recipes/bioconductor-limma - version: 3.36.5 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-limmagui/meta.yaml b/recipes/bioconductor-limmagui/meta.yaml index f6bc9994f2951..4aee0671e3f4d 100644 --- a/recipes/bioconductor-limmagui/meta.yaml +++ b/recipes/bioconductor-limmagui/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.78.0" %} +{% set version = "1.82.0" %} {% set name = "limmaGUI" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b0c7c34dfac5955d26908f730a73b880 +about: + description: A Graphical User Interface for differential expression analysis of two-color microarray data using the limma package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: GUI for limma Package With Two Color Microarrays build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-limmagui", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-r2html - r-tkrplot - r-xtable run: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-r2html - r-tkrplot - r-xtable +source: + md5: 72b40d4ee4d5828a47764c76dfc63358 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'GUI for limma Package With Two Color Microarrays' - description: 'A Graphical User Interface for differential expression analysis of two-color microarray data using the limma package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-limpca/build.sh b/recipes/bioconductor-limpca/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-limpca/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-limpca/meta.yaml b/recipes/bioconductor-limpca/meta.yaml new file mode 100644 index 0000000000000..09fd2956fde38 --- /dev/null +++ b/recipes/bioconductor-limpca/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "1.2.0" %} +{% set name = "limpca" %} +{% set bioc = "3.20" %} + +about: + description: This package has for objectives to provide a method to make Linear Models for high-dimensional designed data. limpca applies a GLM (General Linear Model) version of ASCA and APCA to analyse multivariate sample profiles generated by an experimental design. ASCA/APCA provide powerful visualization tools for multivariate structures in the space of each effect of the statistical model linked to the experimental design and contrarily to MANOVA, it can deal with mutlivariate datasets having more variables than observations. This method can handle unbalanced design. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: An R package for the linear modeling of high-dimensional designed data based on ASCA/APCA family of methods + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-limpca", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, pander, rmarkdown, car, gridExtra, knitr, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-doparallel + - r-dplyr + - r-ggplot2 + - r-ggrepel + - r-ggsci + - r-plyr + - r-reshape2 + - r-stringr + - r-tibble + - r-tidyr + - r-tidyverse + run: + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-doparallel + - r-dplyr + - r-ggplot2 + - r-ggrepel + - r-ggsci + - r-plyr + - r-reshape2 + - r-stringr + - r-tibble + - r-tidyr + - r-tidyverse + +source: + md5: 66755349b1e192c28860ffaa149308ef + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-lineagespot/meta.yaml b/recipes/bioconductor-lineagespot/meta.yaml index a0a3a46e80bc1..45e600f467bea 100644 --- a/recipes/bioconductor-lineagespot/meta.yaml +++ b/recipes/bioconductor-lineagespot/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "lineagespot" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Lineagespot is a framework written in R, and aims to identify SARS-CoV-2 related mutations based on a single (or a list) of variant(s) file(s) (i.e., variant calling format). The method can facilitate the detection of SARS-CoV-2 lineages in wastewater samples using next generation sequencing, and attempts to infer the potential distribution of the SARS-CoV-2 lineages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7a06bfea8fdf81ea88ebe7f4478607f6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lineagespot", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, RefManageR, rmarkdown, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-data.table - r-httr - r-stringr run: - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-data.table - r-httr - r-stringr + +source: + md5: 16869e44569c6f2e5fa2780ccbb0dfc2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing' - description: 'Lineagespot is a framework written in R, and aims to identify SARS-CoV-2 related mutations based on a single (or a list) of variant(s) file(s) (i.e., variant calling format). The method can facilitate the detection of SARS-CoV-2 lineages in wastewater samples using next generation sequencing, and attempts to infer the potential distribution of the SARS-CoV-2 lineages.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-linkhd/meta.yaml b/recipes/bioconductor-linkhd/meta.yaml index c4ba0e55eb6ef..5ddf36908b2a1 100644 --- a/recipes/bioconductor-linkhd/meta.yaml +++ b/recipes/bioconductor-linkhd/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "LinkHD" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Here we present Link-HD, an approach to integrate heterogeneous datasets, as a generalization of STATIS-ACT (“Structuration des Tableaux A Trois Indices de la Statistique–Analyse Conjointe de Tableaux”), a family of methods to join and compare information from multiple subspaces. However, STATIS-ACT has some drawbacks since it only allows continuous data and it is unable to establish relationships between samples and features. In order to tackle these constraints, we incorporate multiple distance options and a linear regression based Biplot model in order to stablish relationships between observations and variable and perform variable selection. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'LinkHD: a versatile framework to explore and integrate heterogeneous data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 64515bedacee602d8f8c92785e075039 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-linkhd", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: MASS (>= 7.3.0), knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 - r-base - r-cluster - r-data.table @@ -35,7 +37,7 @@ requirements: - r-scales - r-vegan run: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 - r-base - r-cluster - r-data.table @@ -47,13 +49,16 @@ requirements: - r-rio - r-scales - r-vegan + +source: + md5: 0ef4c9b91cad4f53b3f4442e413c6bd7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'LinkHD: a versatile framework to explore and integrate heterogeneous data' - description: 'Here we present Link-HD, an approach to integrate heterogeneous datasets, as a generalization of STATIS-ACT (“Structuration des Tableaux A Trois Indices de la Statistique–Analyse Conjointe de Tableaux”), a family of methods to join and compare information from multiple subspaces. However, STATIS-ACT has some drawbacks since it only allows continuous data and it is unable to establish relationships between samples and features. In order to tackle these constraints, we incorporate multiple distance options and a linear regression based Biplot model in order to stablish relationships between observations and variable and perform variable selection.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-linnorm/meta.yaml b/recipes/bioconductor-linnorm/meta.yaml index baa5b5fdfc69a..78c11c639b93d 100644 --- a/recipes/bioconductor-linnorm/meta.yaml +++ b/recipes/bioconductor-linnorm/meta.yaml @@ -1,27 +1,41 @@ -{% set version = "2.26.0" %} +{% set version = "2.30.0" %} {% set name = "Linnorm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Linnorm is an algorithm for normalizing and transforming RNA-seq, single cell RNA-seq, ChIP-seq count data or any large scale count data. It has been independently reviewed by Tian et al. on Nature Methods (https://doi.org/10.1038/s41592-019-0425-8). Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Linear model and normality based normalization and transformation method (Linnorm) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8fc0ff0d6e9c2d274137b0e99ce0f4a2 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-linnorm", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:linnorm + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, markdown, gplots, RColorBrewer, moments, testthat, matrixStats requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-amap - r-apcluster - r-base @@ -34,16 +48,17 @@ requirements: - r-igraph - r-mass - r-mclust - - 'r-rcpp >=0.12.2' - - 'r-rcpparmadillo >=0.8.100.1.0' + - r-rcpp >=0.12.2 + - r-rcpparmadillo >=0.8.100.1.0 - r-rtsne - r-statmod - r-vegan - r-zoo - libblas - liblapack + run: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-amap - r-apcluster - r-base @@ -56,28 +71,22 @@ requirements: - r-igraph - r-mass - r-mclust - - 'r-rcpp >=0.12.2' - - 'r-rcpparmadillo >=0.8.100.1.0' + - r-rcpp >=0.12.2 + - r-rcpparmadillo >=0.8.100.1.0 - r-rtsne - r-statmod - r-vegan - r-zoo - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 4adfc36d01bac9e486e4384f7e0f9976 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Linear model and normality based normalization and transformation method (Linnorm)' - description: 'Linnorm is an algorithm for normalizing and transforming RNA-seq, single cell RNA-seq, ChIP-seq count data or any large scale count data. It has been independently reviewed by Tian et al. on Nature Methods (https://doi.org/10.1038/s41592-019-0425-8). Linnorm can work with raw count, CPM, RPKM, FPKM and TPM.' - license_file: LICENSE + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-lintind/meta.yaml b/recipes/bioconductor-lintind/meta.yaml index 954eb5cb07f07..b8ea4496b0413 100644 --- a/recipes/bioconductor-lintind/meta.yaml +++ b/recipes/bioconductor-lintind/meta.yaml @@ -1,32 +1,36 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "LinTInd" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: When we combine gene-editing technology and sequencing technology, we need to reconstruct a lineage tree from alleles generated and calculate the similarity between each pair of groups. FindIndel() and IndelForm() function will help you align each read to reference sequence and generate scar form strings respectively. IndelIdents() function will help you to define a scar form for each cell or read. IndelPlot() function will help you to visualize the distribution of deletion and insertion. TagProcess() function will help you to extract indels for each cell or read. TagDist() function will help you to calculate the similarity between each pair of groups across the indwells they contain. BuildTree() function will help you to reconstruct a tree. PlotTree() function will help you to visualize the tree. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Lineage tracing by indels -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3dd8f8601ee8df3a0a53a02dc0c4d272 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lintind", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-ape - r-base - r-cowplot @@ -41,12 +45,14 @@ requirements: - r-rlist - r-stringdist - r-stringr + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-ape - r-base - r-cowplot @@ -61,13 +67,16 @@ requirements: - r-rlist - r-stringdist - r-stringr + +source: + md5: 92c6b3c5b5aa628fbc0e66ebe3bee94e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Lineage tracing by indels' - description: 'When we combine gene-editing technology and sequencing technology, we need to reconstruct a lineage tree from alleles generated and calculate the similarity between each pair of groups. FindIndel() and IndelForm() function will help you align each read to reference sequence and generate scar form strings respectively. IndelIdents() function will help you to define a scar form for each cell or read. IndelPlot() function will help you to visualize the distribution of deletion and insertion. TagProcess() function will help you to extract indels for each cell or read. TagDist() function will help you to calculate the similarity between each pair of groups across the indwells they contain. BuildTree() function will help you to reconstruct a tree. PlotTree() function will help you to visualize the tree.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lionessr/meta.yaml b/recipes/bioconductor-lionessr/meta.yaml index 6af7c447fb9c4..57185a3e32162 100644 --- a/recipes/bioconductor-lionessr/meta.yaml +++ b/recipes/bioconductor-lionessr/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "lionessR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4301a7fed98cbe717433fa80791ad9a6 +about: + description: LIONESS, or Linear Interpolation to Obtain Network Estimates for Single Samples, can be used to reconstruct single-sample networks (https://arxiv.org/abs/1505.06440). This code implements the LIONESS equation in the lioness function in R to reconstruct single-sample networks. The default network reconstruction method we use is based on Pearson correlation. However, lionessR can run on any network reconstruction algorithms that returns a complete, weighted adjacency matrix. lionessR works for both unipartite and bipartite networks. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Modeling networks for individual samples using LIONESS build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lionessr", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, igraph, reshape2, limma, requirements: host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base +source: + md5: cad6b9096224be2ad92b9abb98329a8e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Modeling networks for individual samples using LIONESS' - description: 'LIONESS, or Linear Interpolation to Obtain Network Estimates for Single Samples, can be used to reconstruct single-sample networks (https://arxiv.org/abs/1505.06440). This code implements the LIONESS equation in the lioness function in R to reconstruct single-sample networks. The default network reconstruction method we use is based on Pearson correlation. However, lionessR can run on any network reconstruction algorithms that returns a complete, weighted adjacency matrix. lionessR works for both unipartite and bipartite networks.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lipidr/meta.yaml b/recipes/bioconductor-lipidr/meta.yaml index 046cb235bf30f..39a3f873e8729 100644 --- a/recipes/bioconductor-lipidr/meta.yaml +++ b/recipes/bioconductor-lipidr/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "2.16.0" %} +{% set version = "2.20.0" %} {% set name = "lipidr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: lipidr an easy-to-use R package implementing a complete workflow for downstream analysis of targeted and untargeted lipidomics data. lipidomics results can be imported into lipidr as a numerical matrix or a Skyline export, allowing integration into current analysis frameworks. Data mining of lipidomics datasets is enabled through integration with Metabolomics Workbench API. lipidr allows data inspection, normalization, univariate and multivariate analysis, displaying informative visualizations. lipidr also implements a novel Lipid Set Enrichment Analysis (LSEA), harnessing molecular information such as lipid class, total chain length and unsaturation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Data Mining and Analysis of Lipidomics Datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 27b17acc2b4de0439304799e0a7cba2a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lipidr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, ggrepel, plotly, spelling, testthat requirements: host: - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-ropls >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-ropls >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-dplyr @@ -37,11 +39,11 @@ requirements: - r-rlang - r-tidyr run: - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-ropls >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-ropls >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-dplyr @@ -51,13 +53,16 @@ requirements: - r-magrittr - r-rlang - r-tidyr + +source: + md5: 3bba856da2703ced5be1ceb7323bc1ac + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Data Mining and Analysis of Lipidomics Datasets' - description: 'lipidr an easy-to-use R package implementing a complete workflow for downstream analysis of targeted and untargeted lipidomics data. lipidomics results can be imported into lipidr as a numerical matrix or a Skyline export, allowing integration into current analysis frameworks. Data mining of lipidomics datasets is enabled through integration with Metabolomics Workbench API. lipidr allows data inspection, normalization, univariate and multivariate analysis, displaying informative visualizations. lipidr also implements a novel Lipid Set Enrichment Analysis (LSEA), harnessing molecular information such as lipid class, total chain length and unsaturation.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-liquidassociation/meta.yaml b/recipes/bioconductor-liquidassociation/meta.yaml index 456d16ad1c383..5d7d946b45ff4 100644 --- a/recipes/bioconductor-liquidassociation/meta.yaml +++ b/recipes/bioconductor-liquidassociation/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.56.0" %} +{% set version = "1.60.0" %} {% set name = "LiquidAssociation" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package contains functions for calculate direct and model-based estimators for liquid association. It also provides functions for testing the existence of liquid association given a gene triplet data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: LiquidAssociation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b484ed119d8ef9ebb19bfd7497eb33af build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-liquidassociation", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:liquidassociation + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-liquidassociation + path: recipes/bioconductor-liquidassociation + version: 1.34.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' - - 'bioconductor-yeastcc >=1.42.0,<1.43.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-org.sc.sgd.db >=3.20.0,<3.21.0 + - bioconductor-yeastcc >=1.46.0,<1.47.0 - r-base - r-geepack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' - - 'bioconductor-yeastcc >=1.42.0,<1.43.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-org.sc.sgd.db >=3.20.0,<3.21.0 + - bioconductor-yeastcc >=1.46.0,<1.47.0 - r-base - r-geepack + +source: + md5: 121e25a4ac666df1847a58c6830aa4b2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=3)' - summary: LiquidAssociation - description: 'The package contains functions for calculate direct and model-based estimators for liquid association. It also provides functions for testing the existence of liquid association given a gene triplet data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:liquidassociation - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-liquidassociation - path: recipes/bioconductor-liquidassociation - version: 1.34.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lisaclust/meta.yaml b/recipes/bioconductor-lisaclust/meta.yaml index 0658217e488ff..11f5b61da958a 100644 --- a/recipes/bioconductor-lisaclust/meta.yaml +++ b/recipes/bioconductor-lisaclust/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.10.1" %} +{% set version = "1.14.0" %} {% set name = "lisaClust" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: lisaClust provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. This package can be used to provide a high-level summary of cell-type colocalization in multiplexed imaging data that has been segmented at a single-cell resolution. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'lisaClust: Clustering of Local Indicators of Spatial Association' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fa6fe90f1866b21dce3d34bb8471c9e1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lisaclust", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, SpatialDatasets requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-spicyr >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-spicyr >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-class - r-concaveman @@ -42,13 +44,13 @@ requirements: - r-spatstat.random - r-tidyr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-spicyr >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-spicyr >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-class - r-concaveman @@ -61,13 +63,16 @@ requirements: - r-spatstat.geom - r-spatstat.random - r-tidyr + +source: + md5: 76b4f3a611312094eed00c26b533c83a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'lisaClust: Clustering of Local Indicators of Spatial Association' - description: 'lisaClust provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. This package can be used to provide a high-level summary of cell-type colocalization in multiplexed imaging data that has been segmented at a single-cell resolution.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-listeretalbsseq/meta.yaml b/recipes/bioconductor-listeretalbsseq/meta.yaml index dee27377bbb58..257a21ee504d1 100644 --- a/recipes/bioconductor-listeretalbsseq/meta.yaml +++ b/recipes/bioconductor-listeretalbsseq/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "ListerEtAlBSseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 302e026ae021a5f26c149b5086569db1 +about: + description: Base resolution bisulfite sequencing data of Human DNA methylomes + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic 2.0 + summary: BS-seq data of H1 and IMR90 cell line excerpted from Lister et al. 2009 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-listeretalbsseq", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BSgenome.Hsapiens.UCSC.hg18 requirements: host: - - 'bioconductor-methylpipe >=1.36.0,<1.37.0' + - bioconductor-methylpipe >=1.40.0,<1.41.0 - r-base run: - - 'bioconductor-methylpipe >=1.36.0,<1.37.0' + - bioconductor-methylpipe >=1.40.0,<1.41.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c985f67b2cfdb549d614ae350ac50029 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'Artistic 2.0' - summary: 'BS-seq data of H1 and IMR90 cell line excerpted from Lister et al. 2009' - description: 'Base resolution bisulfite sequencing data of Human DNA methylomes' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-listeretalbsseq/post-link.sh b/recipes/bioconductor-listeretalbsseq/post-link.sh index 683046c9aced0..ae31ad6f604cb 100644 --- a/recipes/bioconductor-listeretalbsseq/post-link.sh +++ b/recipes/bioconductor-listeretalbsseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "listeretalbsseq-1.34.0" +installBiocDataPackage.sh "listeretalbsseq-1.38.0" diff --git a/recipes/bioconductor-lmdme/meta.yaml b/recipes/bioconductor-lmdme/meta.yaml index 3a621770cd470..0867b156f7b43 100644 --- a/recipes/bioconductor-lmdme/meta.yaml +++ b/recipes/bioconductor-lmdme/meta.yaml @@ -1,49 +1,55 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "lmdme" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'linear ANOVA decomposition of Multivariate Designed Experiments implementation based on limma lmFit. Features: i)Flexible formula type interface, ii) Fast limma based implementation, iii) p-values for each estimated coefficient levels in each factor, iv) F values for factor effects and v) plotting functions for PCA and PLS.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Linear Model decomposition for Designed Multivariate Experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9a1b98d738df482adb30496ac028b924 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lmdme", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:lmdme + parent_recipe: + name: bioconductor-lmdme + path: recipes/bioconductor-lmdme + version: 1.22.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-stemhypoxia >=1.38.0,<1.39.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-stemhypoxia >=1.42.0,<1.43.0 - r-base - r-pls run: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-stemhypoxia >=1.38.0,<1.39.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-stemhypoxia >=1.42.0,<1.43.0 - r-base - r-pls + +source: + md5: 68ca2b61743abd8fa7b70156cbb34009 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Linear Model decomposition for Designed Multivariate Experiments' - description: 'linear ANOVA decomposition of Multivariate Designed Experiments implementation based on limma lmFit. Features: i)Flexible formula type interface, ii) Fast limma based implementation, iii) p-values for each estimated coefficient levels in each factor, iv) F values for factor effects and v) plotting functions for PCA and PLS.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:lmdme - parent_recipe: - name: bioconductor-lmdme - path: recipes/bioconductor-lmdme - version: 1.22.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lobstahs/meta.yaml b/recipes/bioconductor-lobstahs/meta.yaml index eea31dbdaeae0..bd9930e07b560 100644 --- a/recipes/bioconductor-lobstahs/meta.yaml +++ b/recipes/bioconductor-lobstahs/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "LOBSTAHS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: LOBSTAHS is a multifunction package for screening, annotation, and putative identification of mass spectral features in large, HPLC-MS lipid datasets. In silico data for a wide range of lipids, oxidized lipids, and oxylipins can be generated from user-supplied structural criteria with a database generation function. LOBSTAHS then applies these databases to assign putative compound identities to features in any high-mass accuracy dataset that has been processed using xcms and CAMERA. Users can then apply a series of orthogonal screening criteria based on adduct ion formation patterns, chromatographic retention time, and other properties, to evaluate and assign confidence scores to this list of preliminary assignments. During the screening routine, LOBSTAHS rejects assignments that do not meet the specified criteria, identifies potential isomers and isobars, and assigns a variety of annotation codes to assist the user in evaluating the accuracy of each assignment. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + file LICENSE + license_file: LICENSE + summary: Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45092babf761359e504ae5ad71d21ab8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lobstahs", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:lobstahs + parent_recipe: + name: bioconductor-lobstahs + path: recipes/bioconductor-lobstahs + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: PtH2O2lipids, knitr, rmarkdown requirements: host: - - 'bioconductor-camera >=1.58.0,<1.59.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-camera >=1.62.0,<1.63.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base run: - - 'bioconductor-camera >=1.58.0,<1.59.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-camera >=1.62.0,<1.63.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base + +source: + md5: b475990b09baab38979a76a91b25537f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3) + file LICENSE' - summary: 'Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences' - description: 'LOBSTAHS is a multifunction package for screening, annotation, and putative identification of mass spectral features in large, HPLC-MS lipid datasets. In silico data for a wide range of lipids, oxidized lipids, and oxylipins can be generated from user-supplied structural criteria with a database generation function. LOBSTAHS then applies these databases to assign putative compound identities to features in any high-mass accuracy dataset that has been processed using xcms and CAMERA. Users can then apply a series of orthogonal screening criteria based on adduct ion formation patterns, chromatographic retention time, and other properties, to evaluate and assign confidence scores to this list of preliminary assignments. During the screening routine, LOBSTAHS rejects assignments that do not meet the specified criteria, identifies potential isomers and isobars, and assigns a variety of annotation codes to assist the user in evaluating the accuracy of each assignment.' - license_file: LICENSE -extra: - identifiers: - - biotools:lobstahs - parent_recipe: - name: bioconductor-lobstahs - path: recipes/bioconductor-lobstahs - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-loci2path/meta.yaml b/recipes/bioconductor-loci2path/meta.yaml index a8e5177b97e07..4fcf8a911d70b 100644 --- a/recipes/bioconductor-loci2path/meta.yaml +++ b/recipes/bioconductor-loci2path/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "loci2path" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: loci2path performs statistics-rigorous enrichment analysis of eQTLs in genomic regions of interest. Using eQTL collections provided by the Genotype-Tissue Expression (GTEx) project and pathway collections from MSigDB. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3527f58dccf385bbc6f71a4c659a37c5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-loci2path", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-pheatmap - r-rcolorbrewer - r-wordcloud run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-pheatmap - r-rcolorbrewer - r-wordcloud + +source: + md5: 7dad3e48f75d195a5ba147857d09c3c6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs' - description: 'loci2path performs statistics-rigorous enrichment analysis of eQTLs in genomic regions of interest. Using eQTL collections provided by the Genotype-Tissue Expression (GTEx) project and pathway collections from MSigDB.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-logicfs/meta.yaml b/recipes/bioconductor-logicfs/meta.yaml index 6824cb2b44a4e..e862cf92b059a 100644 --- a/recipes/bioconductor-logicfs/meta.yaml +++ b/recipes/bioconductor-logicfs/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "2.22.0" %} +{% set version = "2.26.0" %} {% set name = "logicFS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af46ee02e89efc5057af01be3f530a4f +about: + description: Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a bagging version of logic regression for classification. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Identification of SNP Interactions build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-logicfs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: genefilter, siggenes requirements: host: @@ -31,13 +30,14 @@ requirements: - r-logicreg - r-mcbiopi - r-survival +source: + md5: 1da216467b438745e9929edf5a695237 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'Identification of SNP Interactions' - description: 'Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a bagging version of logic regression for classification.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lola/meta.yaml b/recipes/bioconductor-lola/meta.yaml index 58d33f706a825..90ee267785b3b 100644 --- a/recipes/bioconductor-lola/meta.yaml +++ b/recipes/bioconductor-lola/meta.yaml @@ -1,57 +1,63 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "LOLA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides functions for testing overlap of sets of genomic regions with public and custom region set (genomic ranges) databases. This makes it possible to do automated enrichment analysis for genomic region sets, thus facilitating interpretation of functional genomics and epigenomics data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Locus overlap analysis for enrichment of genomic ranges -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e3ff8271b0433c6098fd7380af165742 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lola", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:lola + - doi:10.1093/bioinformatics/btv612 + parent_recipe: + name: bioconductor-lola + path: recipes/bioconductor-lola + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: parallel, testthat, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-reshape2 + +source: + md5: 0cfd669bec6dba4c4fe07b868bbb7df3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Locus overlap analysis for enrichment of genomic ranges' - description: 'Provides functions for testing overlap of sets of genomic regions with public and custom region set (genomic ranges) databases. This makes it possible to do automated enrichment analysis for genomic region sets, thus facilitating interpretation of functional genomics and epigenomics data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:lola - - doi:10.1093/bioinformatics/btv612 - parent_recipe: - name: bioconductor-lola - path: recipes/bioconductor-lola - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-loomexperiment/meta.yaml b/recipes/bioconductor-loomexperiment/meta.yaml index a46c9fe2eeebc..1f262fc964457 100644 --- a/recipes/bioconductor-loomexperiment/meta.yaml +++ b/recipes/bioconductor-loomexperiment/meta.yaml @@ -1,56 +1,61 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "LoomExperiment" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The LoomExperiment package provide a means to easily convert the Bioconductor "Experiment" classes to loom files and vice versa. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: LoomExperiment container -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f69aaf53b56cebfe748b8c0c029af481 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-loomexperiment", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr, rmarkdown, reticulate requirements: host: - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-stringr run: - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-stringr + +source: + md5: bf195d20618013613a8b911b800828f0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'LoomExperiment container' - description: 'The LoomExperiment package provide a means to easily convert the Bioconductor "Experiment" classes to loom files and vice versa.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lowmacaannotation/meta.yaml b/recipes/bioconductor-lowmacaannotation/meta.yaml index 5ad4a74a0e5db..e8b6ccbbf461c 100644 --- a/recipes/bioconductor-lowmacaannotation/meta.yaml +++ b/recipes/bioconductor-lowmacaannotation/meta.yaml @@ -1,24 +1,23 @@ {% set version = "0.99.3" %} {% set name = "LowMACAAnnotation" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e0d3fe7f30fe48aef9c4387eb5bacfa +about: + description: A package containing the data to run LowMACA package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: LowMACAAnnotation build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lowmacaannotation", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9e0d3fe7f30fe48aef9c4387eb5bacfa + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: GPL-3 - summary: LowMACAAnnotation - description: 'A package containing the data to run LowMACA package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lpe/meta.yaml b/recipes/bioconductor-lpe/meta.yaml index d286d7876465c..04bb6826942d4 100644 --- a/recipes/bioconductor-lpe/meta.yaml +++ b/recipes/bioconductor-lpe/meta.yaml @@ -1,38 +1,20 @@ -{% set version = "1.76.0" %} +{% set version = "1.80.0" %} {% set name = "LPE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9001fbe949f64e59e79de1f81bd4aa01 +about: + description: This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional 'BH' or 'BY' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Methods for analyzing microarray data using Local Pooled Error (LPE) method build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lpe", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Methods for analyzing microarray data using Local Pooled Error (LPE) method' - description: 'This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional ''BH'' or ''BY'' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' extra: identifiers: - biotools:lpe @@ -41,4 +23,22 @@ extra: name: bioconductor-lpe path: recipes/bioconductor-lpe version: 1.54.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +requirements: + host: + - r-base + run: + - r-base +source: + md5: d9b6f891378d49b442bdb39e0fa9b567 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lpnet/meta.yaml b/recipes/bioconductor-lpnet/meta.yaml index b0d2a9dd75db3..70cb9a785b787 100644 --- a/recipes/bioconductor-lpnet/meta.yaml +++ b/recipes/bioconductor-lpnet/meta.yaml @@ -1,45 +1,53 @@ -{% set version = "2.34.0" %} +{% set version = "2.38.0" %} {% set name = "lpNet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: lpNet aims at infering biological networks, in particular signaling and gene networks. For that it takes perturbation data, either steady-state or time-series, as input and generates an LP model which allows the inference of signaling networks. For parameter identification either leave-one-out cross-validation or stratified n-fold cross-validation can be used. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic License 2.0 + summary: Linear Programming Model for Network Inference -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b2aa2f27ba2f75f595f718f9c9f6e737 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lpnet", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:lpnet + - doi:10.1093/bioinformatics/btv327 + parent_recipe: + name: bioconductor-lpnet + path: recipes/bioconductor-lpnet + version: 2.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: + - bioconductor-kegggraph >=1.66.0,<1.67.0 - r-base - r-lpsolve run: + - bioconductor-kegggraph >=1.66.0,<1.67.0 - r-base - r-lpsolve + +source: + md5: 47317ca53357a4f5f86161dd4d49a342 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Artistic License 2.0' - summary: 'Linear Programming Model for Network Inference' - description: 'lpNet aims at infering biological networks, in particular signaling and gene networks. For that it takes perturbation data, either steady-state or time-series, as input and generates an LP model which allows the inference of signaling networks. For parameter identification either leave-one-out cross-validation or stratified n-fold cross-validation can be used.' -extra: - identifiers: - - biotools:lpnet - - doi:10.1093/bioinformatics/btv327 - parent_recipe: - name: bioconductor-lpnet - path: recipes/bioconductor-lpnet - version: 2.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lpsymphony/build.sh b/recipes/bioconductor-lpsymphony/build.sh index b12d3b6a8730e..c1d13421f5f1e 100644 --- a/recipes/bioconductor-lpsymphony/build.sh +++ b/recipes/bioconductor-lpsymphony/build.sh @@ -8,6 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -sed -i.bak "s/-TP//" src/SYMPHONY/SYMPHONY/configure.ac -sed -i.bak "s/-TP//" src/SYMPHONY/SYMPHONY/configure $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lpsymphony/build_failure.linux-64.yaml b/recipes/bioconductor-lpsymphony/build_failure.linux-64.yaml deleted file mode 100644 index 7895e96771c2c..0000000000000 --- a/recipes/bioconductor-lpsymphony/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: fc3c0b78a302a196c67dd12bb2d7378a8e0cfce2422bd52ac55af76b95b1b9c6 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - checking if $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c supports -c -o file.o... yes - checking whether the $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c linker ($BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld) supports shared libraries... yes - cat: ld.so.conf.d/*.conf: No such file or directory - checking dynamic linker characteristics... GNU/Linux ld.so - checking how to hardcode library paths into programs... immediate - appending configuration tag "F77" to libtool - checking if libtool supports shared libraries... yes - checking whether to build shared libraries... no - checking whether to build static libraries... yes - checking for x86_64-conda-linux-gnu-gfortran option to produce PIC... -fPIC - checking if x86_64-conda-linux-gnu-gfortran PIC flag -fPIC works... yes - checking if x86_64-conda-linux-gnu-gfortran static flag -static works... no - checking if x86_64-conda-linux-gnu-gfortran supports -c -o file.o... yes - checking whether the x86_64-conda-linux-gnu-gfortran linker ($BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld) supports shared libraries... yes - cat: ld.so.conf.d/*.conf: No such file or directory - checking dynamic linker characteristics... GNU/Linux ld.so - checking how to hardcode library paths into programs... immediate - configure: Build is "x86_64-conda-linux-gnu". - checking if library version is set... no - checking whether source of project Blas is available and should be compiled... no, source file ./ThirdParty/Blas/daxpy.f not available - checking whether source of project Lapack is available and should be compiled... no, source file ./ThirdParty/Lapack/LAPACK/SRC/dlarf.f not available - checking whether source of project Glpk is available and should be compiled... no, source file ./ThirdParty/Glpk/glpk/src/glplpx01.c not available - checking whether source of project Sample is available and should be compiled... no - checking whether source of project miblib3 is available and should be compiled... no - checking whether source of project CoinUtils is available and should be compiled... yes, source in CoinUtils - checking whether source of project Osi is available and should be compiled... yes, source in Osi - checking whether source of project Clp is available and should be compiled... yes, source in Clp - checking whether source of project Cgl is available and should be compiled... yes, source in Cgl - checking whether source of project DyLP is available and should be compiled... no - checking whether source of project Vol is available and should be compiled... no - checking whether source of project SYMPHONY is available and should be compiled... yes, source in SYMPHONY - checking whether Clp is required... yes - checking which command should be used to link input files... ln -s - configure: creating ./config.status - config.status: creating Makefile - config.status: executing depfiles commands - configure: configuring in CoinUtils - configure: running /bin/sh './configure' --prefix=$SRC_DIR/src/SYMPHONY '--enable-static' '--disable-shared' '--with-pic' '--with-application=no' '--disable-dependency-tracking' '--disable-zlib' '--disable-bzlib' '--disable-cplex-libcheck' '--disable-glpk-libcheck' '--disable-osl-libcheck' '--disable-soplex-libcheck' '--disable-xpress-libcheck' 'CFLAGS=-w -g -O2' 'CXXFLAGS=-w -g -O2' 'CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc' 'CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include' 'CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp' 'CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c' 'LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib' 'build_alias=x86_64-conda-linux-gnu' 'host_alias=x86_64-conda-linux-gnu' --cache-file=/dev/null --srcdir=. - configure: loading site script $SRC_DIR/src/SYMPHONY/share/config.site - checking build system type... x86_64-conda-linux-gnu - checking for svnversion... no - checking whether we want to compile in debug mode... no - checking for x86_64-conda-linux-gnu-gcc... $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - checking for C compiler default output file name... a.out - checking whether the C compiler works... yes - checking whether we are cross compiling... no - checking for suffix of executables... - checking for suffix of object files... o - checking whether we are using the GNU C compiler... yes - checking whether $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc accepts -g... yes - checking for $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc option to accept ANSI C... none needed - configure: C compiler options are: -w -g -O2 -DCOINUTILS_BUILD - checking for x86_64-conda-linux-gnu-g... $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - checking whether we are using the GNU C compiler... yes - checking whether $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c accepts -g... yes - checking whether C compiler $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c works... yes - configure: C compiler options are: -w -g -O2 -DCOINUTILS_BUILD - configure: Trying to determine Fortran compiler name - checking for x86_64-conda-linux-gnu-gfortran... x86_64-conda-linux-gnu-gfortran - checking for x86_64-conda-linux-gnu-gfortran... (cached) x86_64-conda-linux-gnu-gfortran - checking whether we are using the GNU Fortran 77 compiler... yes - checking whether x86_64-conda-linux-gnu-gfortran accepts -g... yes - configure: Fortran compiler options are: -O3 -pipe - checking how to get verbose linking output from x86_64-conda-linux-gnu-gfortran... -v - checking for Fortran libraries of x86_64-conda-linux-gnu-gfortran... -L$PREFIX/lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0 -L$PREFIX/bin/../lib/gcc -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../x86_64-conda-linux-gnu/lib/../lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../lib -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../x86_64-conda-linux-gnu/lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../.. -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/lib -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib -lgfortran -lm -lgcc_s -lquadmath - configure: Corrected Fortran libraries: -L$PREFIX/lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0 -L$PREFIX/bin/../lib/gcc -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../x86_64-conda-linux-gnu/lib/../lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../lib -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../../../x86_64-conda-linux-gnu/lib -L$PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/13.2.0/../../.. -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/lib -L$PREFIX/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib -lgfortran -lm -lquadmath - configure: error: linking to Fortran libraries from C fails - See config.log' for more details. - checking for dummy main to link with Fortran libraries... unknown - configure: error: /bin/sh './configure' failed for CoinUtils - ** libs - using C compiler: x86_64-conda-linux-gnu-c (conda-forge gcc 12.3.0-3) 12.3.0 - make[1]: Entering directory '$SRC_DIR/src/SYMPHONY' - Making all in CoinUtils - make[2]: *** No rule to make target 'all'. Stop. - make[2]: Entering directory '$SRC_DIR/src/SYMPHONY/CoinUtils' - make[2]: Leaving directory '$SRC_DIR/src/SYMPHONY/CoinUtils' - make[1]: *** [Makefile:324: all-recursive] Error 1 - make[1]: Leaving directory '$SRC_DIR/src/SYMPHONY' - make: *** [Makevars:14: SYMPHONY.ts] Error 2 - ERROR: compilation failed for package lpsymphony - * removing /opt/conda/conda-bld/bioconductor-lpsymphony_1703079915102/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/R/library/lpsymphony - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-lpsymphony_1703079915102/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-lpsymphony/build_failure.osx-64.yaml b/recipes/bioconductor-lpsymphony/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..7be4b20117207 --- /dev/null +++ b/recipes/bioconductor-lpsymphony/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: a2b5507af7bf831c6d854cf116ff70fd6a6c9ba91db46664cea2f8ce35c77703 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-lpsymphony_1734455465033/work/conda_build.sh']' returned non-zero exit status 1. + configure: running /bin/sh './configure' --prefix=$SRC_DIR/src/SYMPHONY 'CC=x86_64-apple-darwin13.4.0-clang' 'CXX=x86_64-apple-darwin13.4.0-clang' 'CFLAGS=-w -g -O2' 'CXXFLAGS=-w -g -O2' '--enable-static' '--disable-shared' '--with-pic' '--with-application=no' '--disable-dependency-tracking' '--disable-zlib' '--disable-bzlib' '--disable-openmp' '--disable-cplex-libcheck' '--disable-glpk-libcheck' '--disable-osl-libcheck' '--disable-soplex-libcheck' '--disable-xpress-libcheck' 'CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13' 'CPP=x86_64-apple-darwin13.4.0-clang-cpp' 'F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran' 'FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-lpsymphony-1.34.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix' 'LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib' 'build_alias=x86_64-apple-darwin13.4.0' 'host_alias=x86_64-apple-darwin13.4.0' --cache-file=/dev/null --srcdir=. + checking build system type... x86_64-apple-darwin13.4.0 + checking for svnversion... no + checking whether we want to compile in debug mode... no + checking for x86_64-apple-darwin13.4.0-clang... x86_64-apple-darwin13.4.0-clang + checking for C compiler default output file name... a.out + checking whether the C compiler works... yes + checking whether we are cross compiling... no + checking for suffix of executables... + checking for suffix of object files... o + checking whether we are using the GNU C compiler... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking for x86_64-apple-darwin13.4.0-clang option to accept ANSI C... none needed + configure: C compiler options are: -w -g -O2 -DSYMPHONY_BUILD + checking for x86_64-apple-darwin13.4.0-clang... x86_64-apple-darwin13.4.0-clang + checking whether we are using the GNU C compiler... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking whether C compiler x86_64-apple-darwin13.4.0-clang works... yes + configure: C compiler options are: -w -g -O2 -DSYMPHONY_BUILD + checking for egrep... grep -E + checking whether ln -s works... yes + checking for a BSD-compatible install... /usr/bin/install -c + checking whether build environment is sane... yes + checking for gawk... no + checking for mawk... no + checking for nawk... no + checking for awk... awk + checking whether make sets $(MAKE)... yes + checking for style of include used by make... GNU + checking dependency style of x86_64-apple-darwin13.4.0-clang... none + checking dependency style of x86_64-apple-darwin13.4.0-clang... none + checking whether to enable maintainer-specific portions of Makefiles... no + configure: Using libtool script in directory .. + checking if library version is set... 9:10:6 + checking for x86_64-apple-darwin13.4.0-pkg-config... no + checking for pkg-config... pkg-config + checking pkg-config is at least version 0.16.0... yes + checking for COIN-OR package CoinDepend... yes: 2.10.6 + checking for COIN-OR package Clp... yes: 1.16.6 + checking for COIN-OR package DyLP... not given: Package 'osi-dylp' not found + checking for COIN-OR package Vol... not given: Package 'osi-vol' not found + checking for COIN-OR package Cgl... yes: 0.59.4 + checking for COIN-OR package OsiTests... yes: 0.107.4 + checking for COIN-OR package Sample... not given: Package 'coindatasample' not found + checking for COIN-OR package Netlib... not given: Package 'coindatanetlib' not found + checking for COIN-OR package Miplib3... not given: Package 'coindatamiplib3' not found + checking for COIN-OR package Cpx... not given: Package 'osi-cplex' not found + checking for COIN-OR package Glpk... not given: Package 'osi-glpk' not found + checking for COIN-OR package Msk... not given: Package 'osi-mosek' not found + checking for COIN-OR package Xpr... not given: Package 'osi-xpress' not found + checking for SYMPHONY default solver... Clp + checking whether to compile with gmpl... no + checking whether to compile application library... no + checking if user provides library for Pvm... no + checking whether this is a VPATH configuration... no + checking which command should be used to link input files... ln -s + configure: creating ./config.status + config.status: creating Makefile + config.status: creating src/Makefile + config.status: creating src/OsiSym/Makefile + config.status: creating test/Makefile + config.status: creating Examples/Makefile + config.status: creating Applications/Makefile.Applications + config.status: creating Applications/CNRP/Makefile + config.status: creating Applications/MATCH/Makefile + config.status: creating Applications/MCKP/Makefile + config.status: creating Applications/MPP/Makefile + config.status: creating Applications/SPP/Makefile + config.status: creating Applications/SPPCUTS/Makefile + config.status: creating Applications/USER/Makefile + config.status: creating Applications/VRP/Makefile + config.status: creating symphony.pc + config.status: creating symphony-app.pc + config.status: creating symphony-uninstalled.pc + config.status: creating osi-sym.pc + config.status: creating osi-sym-uninstalled.pc + config.status: creating include/config.h + config.status: creating include/config_sym.h + config.status: executing depfiles commands + configure: In case of trouble, first consult the troubleshooting page at https://projects.coin-or.org/BuildTools/wiki/user-troubleshooting + configure: Configuration of SYMPHONY successful + configure: In case of trouble, first consult the troubleshooting page at https://projects.coin-or.org/BuildTools/wiki/user-troubleshooting + configure: Main configuration of SYMPHONY successful + make[1]: Entering directory '$SRC_DIR/src/SYMPHONY' + Making all in CoinUtils + make[2]: Entering directory '$SRC_DIR/src/SYMPHONY/CoinUtils' + Making all in src + make[3]: Entering directory '$SRC_DIR/src/SYMPHONY/CoinUtils/src' + make all-am + make[4]: Entering directory '$SRC_DIR/src/SYMPHONY/CoinUtils/src' + /bin/sh ../../libtool --tag=CXX --mode=compile x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -Iecho . -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -w -g -O2 -DCOINUTILS_BUILD -c -o CoinAlloc.lo CoinAlloc.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -w -g -O2 -DCOINUTILS_BUILD -c CoinAlloc.cpp -fno-common -DPIC -o CoinAlloc.o + /bin/sh ../../libtool --tag=CXX --mode=compile x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -Iecho . -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -w -g -O2 -DCOINUTILS_BUILD -c -o CoinBuild.lo CoinBuild.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -w -g -O2 -DCOINUTILS_BUILD -c CoinBuild.cpp -fno-common -DPIC -o CoinBuild.o + make[4]: Leaving directory '$SRC_DIR/src/SYMPHONY/CoinUtils/src' + make[3]: Leaving directory '$SRC_DIR/src/SYMPHONY/CoinUtils/src' + make[2]: Leaving directory '$SRC_DIR/src/SYMPHONY/CoinUtils' + make[1]: Leaving directory '$SRC_DIR/src/SYMPHONY' +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/bioconductor-lpsymphony/meta.yaml b/recipes/bioconductor-lpsymphony/meta.yaml index 141bac727f2ab..0f7adb579aeac 100644 --- a/recipes/bioconductor-lpsymphony/meta.yaml +++ b/recipes/bioconductor-lpsymphony/meta.yaml @@ -1,51 +1,58 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "lpsymphony" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package was derived from Rsymphony_0.1-17 from CRAN. These packages provide an R interface to SYMPHONY, an open-source linear programming solver written in C++. The main difference between this package and Rsymphony is that it includes the solver source code (SYMPHONY version 5.6), while Rsymphony expects to find header and library files on the users' system. Thus the intention of lpsymphony is to provide an easy to install interface to SYMPHONY. For Windows, precompiled DLLs are included in this package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: EPL + summary: Symphony integer linear programming solver in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 106ec54272f27574ea1eea2d5721d7e4 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lpsymphony", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:lpsymphony + - doi:10.1007/0-387-23529-9_5 + parent_recipe: + name: bioconductor-lpsymphony + path: recipes/bioconductor-lpsymphony + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, testthat # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - {{ compiler('fortran') }} + - automake + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 54ce27cefa98d444f06b137ba5ca4a70 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: EPL - summary: 'Symphony integer linear programming solver in R' - description: 'This package was derived from Rsymphony_0.1-17 from CRAN. These packages provide an R interface to SYMPHONY, an open-source linear programming solver written in C++. The main difference between this package and Rsymphony is that it includes the solver source code (SYMPHONY version 5.6), while Rsymphony expects to find header and library files on the users'' system. Thus the intention of lpsymphony is to provide an easy to install interface to SYMPHONY. For Windows, precompiled DLLs are included in this package.' -extra: - identifiers: - - biotools:lpsymphony - - doi:10.1007/0-387-23529-9_5 - parent_recipe: - name: bioconductor-lpsymphony - path: recipes/bioconductor-lpsymphony - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lrbasedbi/meta.yaml b/recipes/bioconductor-lrbasedbi/meta.yaml index ea0d85aceaab3..369a0e911f375 100644 --- a/recipes/bioconductor-lrbasedbi/meta.yaml +++ b/recipes/bioconductor-lrbasedbi/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "2.12.0" %} +{% set version = "2.16.0" %} {% set name = "LRBaseDbi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ed780d2b26059691bd1a1e859ca5003 +about: + description: Interface to construct LRBase package (LRBase.XXX.eg.db). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: DBI to construct LRBase-related package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lrbasedbi", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, BiocStyle +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: testthat, BiocStyle, AnnotationHub requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-dbi - r-rsqlite +source: + md5: f2b87b49059d28ca959d1acc0c02ed5a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'DBI to construct LRBase-related package' - description: 'Interface to construct LRBase package (LRBase.XXX.eg.db).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lrcell/meta.yaml b/recipes/bioconductor-lrcell/meta.yaml index e7c109ef9e482..d9c7e7364b071 100644 --- a/recipes/bioconductor-lrcell/meta.yaml +++ b/recipes/bioconductor-lrcell/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "LRcell" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The goal of LRcell is to identify specific sub-cell types that drives the changes observed in a bulk RNA-seq differential gene expression experiment. To achieve this, LRcell utilizes sets of cell marker genes acquired from single-cell RNA-sequencing (scRNA-seq) as indicators for various cell types in the tissue of interest. Next, for each cell type, using its marker genes as indicators, we apply Logistic Regression on the complete set of genes with differential expression p-values to calculate a cell-type significance p-value. Finally, these p-values are compared to predict which one(s) are likely to be responsible for the differential gene expression pattern observed in the bulk RNA-seq experiments. LRcell is inspired by the LRpath[@sartor2009lrpath] algorithm developed by Sartor et al., originally designed for pathway/gene set enrichment analysis. LRcell contains three major components: LRcell analysis, plot generation and marker gene selection. All modules in this package are written in R. This package also provides marker genes in the Prefrontal Cortex (pFC) human brain region, human PBMC and nine mouse brain regions (Frontal Cortex, Cerebellum, Globus Pallidus, Hippocampus, Entopeduncular, Posterior Cortex, Striatum, Substantia Nigra and Thalamus).' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Differential cell type change analysis using Logistic/linear Regression -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 845d68fab279d4a81933621a81085179 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lrcell", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: LRcellTypeMarkers, BiocStyle, knitr, rmarkdown, roxygen2, testthat requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - r-dplyr - r-ggplot2 - r-ggrepel - r-magrittr run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - r-dplyr - r-ggplot2 - r-ggrepel - r-magrittr + +source: + md5: aa1d6c9b1bf3fdf273f65a932096671e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Differential cell type change analysis using Logistic/linear Regression' - description: 'The goal of LRcell is to identify specific sub-cell types that drives the changes observed in a bulk RNA-seq differential gene expression experiment. To achieve this, LRcell utilizes sets of cell marker genes acquired from single-cell RNA-sequencing (scRNA-seq) as indicators for various cell types in the tissue of interest. Next, for each cell type, using its marker genes as indicators, we apply Logistic Regression on the complete set of genes with differential expression p-values to calculate a cell-type significance p-value. Finally, these p-values are compared to predict which one(s) are likely to be responsible for the differential gene expression pattern observed in the bulk RNA-seq experiments. LRcell is inspired by the LRpath[@sartor2009lrpath] algorithm developed by Sartor et al., originally designed for pathway/gene set enrichment analysis. LRcell contains three major components: LRcell analysis, plot generation and marker gene selection. All modules in this package are written in R. This package also provides marker genes in the Prefrontal Cortex (pFC) human brain region, human PBMC and nine mouse brain regions (Frontal Cortex, Cerebellum, Globus Pallidus, Hippocampus, Entopeduncular, Posterior Cortex, Striatum, Substantia Nigra and Thalamus).' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lrcelltypemarkers/meta.yaml b/recipes/bioconductor-lrcelltypemarkers/meta.yaml index ab499894e1e20..33fb7f62f1e0f 100644 --- a/recipes/bioconductor-lrcelltypemarkers/meta.yaml +++ b/recipes/bioconductor-lrcelltypemarkers/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "LRcellTypeMarkers" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5731667b56b631291d22a830d212f04 +about: + description: 'This is an external ExperimentData package for LRcell. This data package contains the gene enrichment scores calculated from scRNA-seq dataset which indicates the gene enrichment of each cell type in certain brain region. LRcell package is used to identify specific sub-cell types that drives the changes observed in a bulk RNA-seq differential gene expression experiment. For more details, please visit: https://github.com/marvinquiet/LRcell.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Marker gene information for LRcell R Bioconductor package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lrcelltypemarkers", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: LRcell, BiocStyle, knitr, rmarkdown, roxygen2, testthat requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1acc45444ff327ed8d97526b019d5369 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Marker gene information for LRcell R Bioconductor package' - description: 'This is an external ExperimentData package for LRcell. This data package contains the gene enrichment scores calculated from scRNA-seq dataset which indicates the gene enrichment of each cell type in certain brain region. LRcell package is used to identify specific sub-cell types that drives the changes observed in a bulk RNA-seq differential gene expression experiment. For more details, please visit: https://github.com/marvinquiet/LRcell.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lrcelltypemarkers/post-link.sh b/recipes/bioconductor-lrcelltypemarkers/post-link.sh index 5ea30236a697f..4ab48e7b36228 100644 --- a/recipes/bioconductor-lrcelltypemarkers/post-link.sh +++ b/recipes/bioconductor-lrcelltypemarkers/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "lrcelltypemarkers-1.10.0" +installBiocDataPackage.sh "lrcelltypemarkers-1.14.0" diff --git a/recipes/bioconductor-lumi/meta.yaml b/recipes/bioconductor-lumi/meta.yaml index 1511bffa3477a..bf6fe85746466 100644 --- a/recipes/bioconductor-lumi/meta.yaml +++ b/recipes/bioconductor-lumi/meta.yaml @@ -1,74 +1,80 @@ -{% set version = "2.54.0" %} +{% set version = "2.58.0" %} {% set name = "lumi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 59fdd5b0a2e145d7a8772635121bb2ec build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lumi", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:lumi + parent_recipe: + name: bioconductor-lumi + path: recipes/bioconductor-lumi + version: 2.32.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-methylumi >=2.48.0,<2.49.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-methylumi >=2.52.0,<2.53.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-dbi - r-kernsmooth - r-lattice - r-mass - - 'r-mgcv >=1.4-0' + - r-mgcv >=1.4-0 - r-nleqslv - r-rsqlite run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-methylumi >=2.48.0,<2.49.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-methylumi >=2.52.0,<2.53.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-dbi - r-kernsmooth - r-lattice - r-mass - - 'r-mgcv >=1.4-0' + - r-mgcv >=1.4-0 - r-nleqslv - r-rsqlite + +source: + md5: 13058207143b550e73ad6b4b0dcf9a6d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'BeadArray Specific Methods for Illumina Methylation and Expression Microarrays' - description: 'The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:lumi - parent_recipe: - name: bioconductor-lumi - path: recipes/bioconductor-lumi - version: 2.32.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lumibarnes/meta.yaml b/recipes/bioconductor-lumibarnes/meta.yaml index a83dcd4119b6d..3434b3464d022 100644 --- a/recipes/bioconductor-lumibarnes/meta.yaml +++ b/recipes/bioconductor-lumibarnes/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "lumiBarnes" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2be75f5470fd60f9919045fc8147b613 +about: + description: The Barnes benchmark dataset can be used to evaluate the algorithms for Illumina microarrays. It measured a titration series of two human tissues, blood and placenta, and includes six samples with the titration ratio of blood and placenta as 100:0, 95:5, 75:25, 50:50, 25:75 and 0:100. The samples were hybridized on HumanRef-8 BeadChip (Illumina, Inc) in duplicate. The data is loaded as an LumiBatch Object (see documents in the lumi package). + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Barnes Benchmark Illumina Tissues Titration Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lumibarnes", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-lumi >=2.58.0,<2.59.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-lumi >=2.58.0,<2.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a91894c192736dabcdd81493fd693d6a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Barnes Benchmark Illumina Tissues Titration Data' - description: 'The Barnes benchmark dataset can be used to evaluate the algorithms for Illumina microarrays. It measured a titration series of two human tissues, blood and placenta, and includes six samples with the titration ratio of blood and placenta as 100:0, 95:5, 75:25, 50:50, 25:75 and 0:100. The samples were hybridized on HumanRef-8 BeadChip (Illumina, Inc) in duplicate. The data is loaded as an LumiBatch Object (see documents in the lumi package).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lumibarnes/post-link.sh b/recipes/bioconductor-lumibarnes/post-link.sh index 96d26854e3ad0..8d0872137e267 100644 --- a/recipes/bioconductor-lumibarnes/post-link.sh +++ b/recipes/bioconductor-lumibarnes/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "lumibarnes-1.42.0" +installBiocDataPackage.sh "lumibarnes-1.46.0" diff --git a/recipes/bioconductor-lumihumanall.db/meta.yaml b/recipes/bioconductor-lumihumanall.db/meta.yaml index e61a5dd476ab5..3e8e354bc722b 100644 --- a/recipes/bioconductor-lumihumanall.db/meta.yaml +++ b/recipes/bioconductor-lumihumanall.db/meta.yaml @@ -1,47 +1,53 @@ {% set version = "1.22.0" %} {% set name = "lumiHumanAll.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Illumina Human Illumina expression annotation data (chip lumiHumanAll) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina Human Illumina expression annotation data (chip lumiHumanAll) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ce7e219b50833ceab203f0bbfb11d917 build: - number: 15 + noarch: generic + number: 16 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lumihumanall.db", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-lumihumanall.db + path: recipes/bioconductor-lumihumanall.db + version: 1.22.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: ce7e219b50833ceab203f0bbfb11d917 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina Human Illumina expression annotation data (chip lumiHumanAll)' - description: 'Illumina Human Illumina expression annotation data (chip lumiHumanAll) assembled using data from public repositories' -extra: - parent_recipe: - name: bioconductor-lumihumanall.db - path: recipes/bioconductor-lumihumanall.db - version: 1.22.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lumihumanidmapping/meta.yaml b/recipes/bioconductor-lumihumanidmapping/meta.yaml index 6a28062e422f4..ad9d5c5551940 100644 --- a/recipes/bioconductor-lumihumanidmapping/meta.yaml +++ b/recipes/bioconductor-lumihumanidmapping/meta.yaml @@ -1,43 +1,43 @@ {% set version = "1.10.1" %} {% set name = "lumiHumanIDMapping" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 007e5aa2f1596cc08d888ba6dce7148a +about: + description: This package includes mappings information between different types of Illumina IDs of Illumina Human chips and nuIDs. It also includes mappings of all nuIDs included in Illumina Human chips to RefSeq IDs with mapping qualities information. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: The Artistic License, Version 2.0 + summary: Illumina Identifier mapping for Human build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lumihumanidmapping", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-lumi >=2.58.0,<2.59.0 - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-lumi >=2.58.0,<2.59.0 - r-base - r-dbi - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 007e5aa2f1596cc08d888ba6dce7148a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'The Artistic License, Version 2.0' - summary: 'Illumina Identifier mapping for Human' - description: 'This package includes mappings information between different types of Illumina IDs of Illumina Human chips and nuIDs. It also includes mappings of all nuIDs included in Illumina Human chips to RefSeq IDs with mapping qualities information.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lumimouseall.db/meta.yaml b/recipes/bioconductor-lumimouseall.db/meta.yaml index 7046c1ded1218..9101c7f2868b6 100644 --- a/recipes/bioconductor-lumimouseall.db/meta.yaml +++ b/recipes/bioconductor-lumimouseall.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "1.22.0" %} {% set name = "lumiMouseAll.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6f12330377aaddc83bfa9c37477b999e +about: + description: Illumina Mouse Illumina expression annotation data (chip lumiMouseAll) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina Mouse Illumina expression annotation data (chip lumiMouseAll) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lumimouseall.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6f12330377aaddc83bfa9c37477b999e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina Mouse Illumina expression annotation data (chip lumiMouseAll)' - description: 'Illumina Mouse Illumina expression annotation data (chip lumiMouseAll) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lumimouseidmapping/meta.yaml b/recipes/bioconductor-lumimouseidmapping/meta.yaml index 4d70e4fb54cf8..a7c38cc16e9d1 100644 --- a/recipes/bioconductor-lumimouseidmapping/meta.yaml +++ b/recipes/bioconductor-lumimouseidmapping/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.10.0" %} {% set name = "lumiMouseIDMapping" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 305aba80ebf6ef4c26899302ea9e50e8 +about: + description: This package includes mappings information between different types of Illumina IDs of Illumina Mouse chips and nuIDs. It also includes mappings of all nuIDs included in Illumina Mouse chips to RefSeq IDs with mapping qualities information. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: The Artistic License, Version 2.0 + summary: Illumina Identifier mapping for Mouse build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lumimouseidmapping", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-lumi >=2.58.0,<2.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-lumi >=2.58.0,<2.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 305aba80ebf6ef4c26899302ea9e50e8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'The Artistic License, Version 2.0' - summary: 'Illumina Identifier mapping for Mouse' - description: 'This package includes mappings information between different types of Illumina IDs of Illumina Mouse chips and nuIDs. It also includes mappings of all nuIDs included in Illumina Mouse chips to RefSeq IDs with mapping qualities information.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lumiratall.db/meta.yaml b/recipes/bioconductor-lumiratall.db/meta.yaml index 2bec6ec9618a5..fd7b59ee81c6e 100644 --- a/recipes/bioconductor-lumiratall.db/meta.yaml +++ b/recipes/bioconductor-lumiratall.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "1.22.0" %} {% set name = "lumiRatAll.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 65027624574d5e33f18b0a54a54f4be9 +about: + description: Illumina Rat Illumina expression annotation data (chip lumiRatAll) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Illumina Rat Illumina expression annotation data (chip lumiRatAll) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lumiratall.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 65027624574d5e33f18b0a54a54f4be9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Illumina Rat Illumina expression annotation data (chip lumiRatAll)' - description: 'Illumina Rat Illumina expression annotation data (chip lumiRatAll) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lumiratidmapping/meta.yaml b/recipes/bioconductor-lumiratidmapping/meta.yaml index fa2629353e6c9..013ff87b134be 100644 --- a/recipes/bioconductor-lumiratidmapping/meta.yaml +++ b/recipes/bioconductor-lumiratidmapping/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.10.0" %} {% set name = "lumiRatIDMapping" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1122fc25e3fff62678bed36f9d7b5709 +about: + description: This package includes mappings information between different types of Illumina IDs of Illumina Rat chips and nuIDs. It also includes mappings of all nuIDs included in Illumina Rat chips to RefSeq IDs with mapping qualities information. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: The Artistic License, Version 2.0 + summary: Illumina Identifier mapping for Rat build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lumiratidmapping", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-lumi >=2.58.0,<2.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-lumi >=2.58.0,<2.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1122fc25e3fff62678bed36f9d7b5709 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'The Artistic License, Version 2.0' - summary: 'Illumina Identifier mapping for Rat' - description: 'This package includes mappings information between different types of Illumina IDs of Illumina Rat chips and nuIDs. It also includes mappings of all nuIDs included in Illumina Rat chips to RefSeq IDs with mapping qualities information.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml b/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml index 5af4751df9291..32e7806bba579 100644 --- a/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml +++ b/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "LungCancerACvsSCCGEO" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f353aa0cc36dc25e67cdf1ba0738985e +about: + description: This package contains 30 Affymetrix CEL files for 7 Adenocarcinoma (AC) and 8 Squamous cell carcinoma (SCC) lung cancer samples taken at random from 3 GEO datasets (GSE10245, GSE18842 and GSE2109) and other 15 samples from a dataset produced by the organizers of the IMPROVER Diagnostic Signature Challenge available from GEO (GSE43580). + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A lung cancer dataset that can be used with maPredictDSC package for developing outcome prediction models from Affymetrix CEL files. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lungcanceracvssccgeo", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-lungcanceracvssccgeo + path: recipes/bioconductor-lungcanceracvssccgeo + version: 1.16.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e6408dab179c36800a5a9f501c20b6f5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'A lung cancer dataset that can be used with maPredictDSC package for developing outcome prediction models from Affymetrix CEL files.' - description: 'This package contains 30 Affymetrix CEL files for 7 Adenocarcinoma (AC) and 8 Squamous cell carcinoma (SCC) lung cancer samples taken at random from 3 GEO datasets (GSE10245, GSE18842 and GSE2109) and other 15 samples from a dataset produced by the organizers of the IMPROVER Diagnostic Signature Challenge available from GEO (GSE43580).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - parent_recipe: - name: bioconductor-lungcanceracvssccgeo - path: recipes/bioconductor-lungcanceracvssccgeo - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh b/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh index b44b1fa903eb7..ad06dc7fa4c29 100644 --- a/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh +++ b/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "lungcanceracvssccgeo-1.38.0" +installBiocDataPackage.sh "lungcanceracvssccgeo-1.42.0" diff --git a/recipes/bioconductor-lungcancerlines/meta.yaml b/recipes/bioconductor-lungcancerlines/meta.yaml index a54b8590d329e..e29eb48540ec2 100644 --- a/recipes/bioconductor-lungcancerlines/meta.yaml +++ b/recipes/bioconductor-lungcancerlines/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "0.40.0" %} +{% set version = "0.44.0" %} {% set name = "LungCancerLines" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 17b67ca0eac14ef832832b949972b277 +about: + description: 'Reads from an RNA-seq experiment between two lung cancer cell lines: H1993 (met) and H2073 (primary). The reads are stored as Fastq files and are meant for use with the TP53Genome object in the gmapR package.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Reads from Two Lung Cancer Cell Lines build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lungcancerlines", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base run: - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: cbedb747be0dc1ed37072304b42e29cb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Reads from Two Lung Cancer Cell Lines' - description: 'Reads from an RNA-seq experiment between two lung cancer cell lines: H1993 (met) and H2073 (primary). The reads are stored as Fastq files and are meant for use with the TP53Genome object in the gmapR package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lungcancerlines/post-link.sh b/recipes/bioconductor-lungcancerlines/post-link.sh index 3191b811f3162..3210efae129ec 100644 --- a/recipes/bioconductor-lungcancerlines/post-link.sh +++ b/recipes/bioconductor-lungcancerlines/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "lungcancerlines-0.40.0" +installBiocDataPackage.sh "lungcancerlines-0.44.0" diff --git a/recipes/bioconductor-lungexpression/meta.yaml b/recipes/bioconductor-lungexpression/meta.yaml index 13240159ee3d6..9dc91e8309a7d 100644 --- a/recipes/bioconductor-lungexpression/meta.yaml +++ b/recipes/bioconductor-lungexpression/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "0.40.0" %} +{% set version = "0.44.0" %} {% set name = "lungExpression" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 35eab717cb2e24c92faf417ad7fb9cb8 +about: + description: Data from three large lung cancer studies provided as ExpressionSets + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: ExpressionSets for Parmigiani et al., 2004 Clinical Cancer Research paper build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lungexpression", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 51b928a75488636d40016a51e9fe0f40 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'ExpressionSets for Parmigiani et al., 2004 Clinical Cancer Research paper' - description: 'Data from three large lung cancer studies provided as ExpressionSets' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lungexpression/post-link.sh b/recipes/bioconductor-lungexpression/post-link.sh index a98eb220db162..f10c290a058bb 100644 --- a/recipes/bioconductor-lungexpression/post-link.sh +++ b/recipes/bioconductor-lungexpression/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "lungexpression-0.40.0" +installBiocDataPackage.sh "lungexpression-0.44.0" diff --git a/recipes/bioconductor-lute/build.sh b/recipes/bioconductor-lute/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-lute/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lute/meta.yaml b/recipes/bioconductor-lute/meta.yaml new file mode 100644 index 0000000000000..04eb81b49835d --- /dev/null +++ b/recipes/bioconductor-lute/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.2.0" %} +{% set name = "lute" %} +{% set bioc = "3.20" %} + +about: + description: Provides a framework for adjustment on cell type size when performing bulk transcripomics deconvolution. The main framework function provides a means of reference normalization using cell size scale factors. It allows for marker selection and deconvolution using non-negative least squares (NNLS) by default. The framework is extensible for other marker selection and deconvolution algorithms, and users may reuse the generics, methods, and classes for these when developing new algorithms. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Framework for cell size scale factor normalized bulk transcriptomics deconvolution experiments + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-lute", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: nnls, knitr, testthat, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub, DelayedMatrixStats, BisqueRNA, DelayedArray +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-dplyr + - r-ggplot2 + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-dplyr + - r-ggplot2 + +source: + md5: 475ee58dc340d0877d41ef644ea0b957 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-lydata/meta.yaml b/recipes/bioconductor-lydata/meta.yaml index 5bd099c210424..eba0d7d1915f5 100644 --- a/recipes/bioconductor-lydata/meta.yaml +++ b/recipes/bioconductor-lydata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "lydata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4541ec0aad2bbee135b19b0bed4ea0af +about: + description: Raw data downloaded from GEO for the compound LY294002. Raw data is from multiple platforms from Affymetrix and Illumina. This data is used to illustrate the cross-platform meta-analysis of microarray data using the crossmeta package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Example Dataset for crossmeta Package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lydata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1f492ef0a9ea66a511aef7b9c0fc8ce8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Example Dataset for crossmeta Package' - description: 'Raw data downloaded from GEO for the compound LY294002. Raw data is from multiple platforms from Affymetrix and Illumina. This data is used to illustrate the cross-platform meta-analysis of microarray data using the crossmeta package.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lydata/post-link.sh b/recipes/bioconductor-lydata/post-link.sh index 1e814b39963f5..5d75f7e2bc7f2 100644 --- a/recipes/bioconductor-lydata/post-link.sh +++ b/recipes/bioconductor-lydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "lydata-1.28.0" +installBiocDataPackage.sh "lydata-1.32.0" diff --git a/recipes/bioconductor-lymphoseq/meta.yaml b/recipes/bioconductor-lymphoseq/meta.yaml index 444c73883de46..234f7d41783f1 100644 --- a/recipes/bioconductor-lymphoseq/meta.yaml +++ b/recipes/bioconductor-lymphoseq/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "LymphoSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This R package analyzes high-throughput sequencing of T and B cell receptor complementarity determining region 3 (CDR3) sequences generated by Adaptive Biotechnologies' ImmunoSEQ assay. Its input comes from tab-separated value (.tsv) files exported from the ImmunoSEQ analyzer. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Analyze high-throughput sequencing of T and B cell receptors -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c7a311767150648a29d45e5cd5ee5c30 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lymphoseq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, pheatmap, wordcloud, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-lymphoseqdb >=0.99.0,<0.100.0' - - 'bioconductor-msa >=1.34.0,<1.35.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-lymphoseqdb >=0.99.0,<0.100.0 + - bioconductor-msa >=1.38.0,<1.39.0 - r-base - r-circlize - r-data.table @@ -40,10 +41,10 @@ requirements: - r-upsetr - r-venndiagram run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-lymphoseqdb >=0.99.0,<0.100.0' - - 'bioconductor-msa >=1.34.0,<1.35.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-lymphoseqdb >=0.99.0,<0.100.0 + - bioconductor-msa >=1.38.0,<1.39.0 - r-base - r-circlize - r-data.table @@ -57,12 +58,16 @@ requirements: - r-stringdist - r-upsetr - r-venndiagram + +source: + md5: 53552e65477bcc40ea242470f988d262 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Analyze high-throughput sequencing of T and B cell receptors' - description: 'This R package analyzes high-throughput sequencing of T and B cell receptor complementarity determining region 3 (CDR3) sequences generated by Adaptive Biotechnologies'' ImmunoSEQ assay. Its input comes from tab-separated value (.tsv) files exported from the ImmunoSEQ analyzer.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-lymphoseqdb/meta.yaml b/recipes/bioconductor-lymphoseqdb/meta.yaml index 9ae31ac173cd1..b31cf594f8227 100644 --- a/recipes/bioconductor-lymphoseqdb/meta.yaml +++ b/recipes/bioconductor-lymphoseqdb/meta.yaml @@ -1,37 +1,37 @@ {% set version = "0.99.2" %} {% set name = "LymphoSeqDB" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 22fc0dc2439ef497982a5ffddda1e418 +about: + description: This package provides annotation databases that support the package LymphoSeq. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: LymphoSeq annotation databases build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-lymphoseqdb", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 22fc0dc2439ef497982a5ffddda1e418 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'LymphoSeq annotation databases' - description: 'This package provides annotation databases that support the package LymphoSeq.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-m10kcod.db/meta.yaml b/recipes/bioconductor-m10kcod.db/meta.yaml index 82e91d08de883..995e20b2dd2ec 100644 --- a/recipes/bioconductor-m10kcod.db/meta.yaml +++ b/recipes/bioconductor-m10kcod.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.4.0" %} {% set name = "m10kcod.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 04811628e4b37cd6d24e0b2a17d79ab8 +about: + description: Codelink UniSet Mouse I Bioarray (~10 000 mouse gene targets) annotation data (chip m10kcod) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Codelink UniSet Mouse I Bioarray (~10 000 mouse gene targets) annotation data (chip m10kcod) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-m10kcod.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 04811628e4b37cd6d24e0b2a17d79ab8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Codelink UniSet Mouse I Bioarray (~10 000 mouse gene targets) annotation data (chip m10kcod)' - description: 'Codelink UniSet Mouse I Bioarray (~10 000 mouse gene targets) annotation data (chip m10kcod) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-m20kcod.db/meta.yaml b/recipes/bioconductor-m20kcod.db/meta.yaml index 6f7477b00a514..4f170f3bba5ff 100644 --- a/recipes/bioconductor-m20kcod.db/meta.yaml +++ b/recipes/bioconductor-m20kcod.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.4.0" %} {% set name = "m20kcod.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f2f734fb41e1ae4e949abf09687733bf +about: + description: Codelink UniSet Mouse 20k I Bioarray annotation data (chip m20kcod) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Codelink UniSet Mouse 20k I Bioarray annotation data (chip m20kcod) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ - run_exports: '{{ pin_subpackage("bioconductor-m20kcod.db", max_pin="x") }}' - noarch: generic + run_exports: '{{ pin_subpackage("bioconductor-m20kcod.db", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - bioconductor-data-packages >=20231202 + - bioconductor-data-packages >=20241103 +source: + md5: f2f734fb41e1ae4e949abf09687733bf + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Codelink UniSet Mouse 20k I Bioarray annotation data (chip m20kcod)' - description: 'Codelink UniSet Mouse 20k I Bioarray annotation data (chip m20kcod) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-m3c/meta.yaml b/recipes/bioconductor-m3c/meta.yaml index d5ae69bc55ced..342e6e5713cd8 100644 --- a/recipes/bioconductor-m3c/meta.yaml +++ b/recipes/bioconductor-m3c/meta.yaml @@ -1,24 +1,32 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "M3C" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: M3C is a consensus clustering algorithm that uses a Monte Carlo simulation to eliminate overestimation of K and can reject the null hypothesis K=1. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + summary: Monte Carlo Reference-based Consensus Clustering -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e04534528d39712026e9b1de15a12c3d build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-m3c", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-m3c + path: recipes/bioconductor-m3c + version: 1.4.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: @@ -45,18 +53,16 @@ requirements: - r-matrixcalc - r-rtsne - r-umap + +source: + md5: c8f3dbe2542a596b4fda621e4c9a80b9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3 - summary: 'Monte Carlo Reference-based Consensus Clustering' - description: 'M3C is a consensus clustering algorithm that uses a Monte Carlo simulation to eliminate overestimation of K and can reject the null hypothesis K=1.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' -extra: - parent_recipe: - name: bioconductor-m3c - path: recipes/bioconductor-m3c - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-m3dexampledata/meta.yaml b/recipes/bioconductor-m3dexampledata/meta.yaml index f1420a70bec4e..3f070fcccb5bc 100644 --- a/recipes/bioconductor-m3dexampledata/meta.yaml +++ b/recipes/bioconductor-m3dexampledata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "M3DExampleData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6988767aab7572ae3e701fd6854c061f +about: + description: Example data for M3Drop package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: M3Drop Example Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-m3dexampledata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b277ae479790377a52b91adb72f9f916 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'M3Drop Example Data' - description: 'Example data for M3Drop package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-m3dexampledata/post-link.sh b/recipes/bioconductor-m3dexampledata/post-link.sh index 72da968afa952..7282a5444b9f0 100644 --- a/recipes/bioconductor-m3dexampledata/post-link.sh +++ b/recipes/bioconductor-m3dexampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "m3dexampledata-1.28.0" +installBiocDataPackage.sh "m3dexampledata-1.32.0" diff --git a/recipes/bioconductor-m3drop/meta.yaml b/recipes/bioconductor-m3drop/meta.yaml index 29a92577f3e60..8bda05821275d 100644 --- a/recipes/bioconductor-m3drop/meta.yaml +++ b/recipes/bioconductor-m3drop/meta.yaml @@ -1,27 +1,39 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "M3Drop" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package fits a model to the pattern of dropouts in single-cell RNASeq data. This model is used as a null to identify significantly variable (i.e. differentially expressed) genes for use in downstream analysis, such as clustering cells. Also includes an method for calculating exact Pearson residuals in UMI-tagged data using a library-size aware negative binomial model. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Michaelis-Menten Modelling of Dropouts in single-cell RNASeq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad347f93f1a297543e7ab0e74437dd4d build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-m3drop", max_pin="x.x") }}' - noarch: generic -# Suggests: ROCR, knitr, M3DExampleData, scater, SingleCellExperiment, monocle, Seurat, Biobase + +extra: + identifiers: + - biotools:m3drop + - doi:10.1002/1873-3468.12684 + parent_recipe: + name: bioconductor-m3drop + path: recipes/bioconductor-m3drop + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: ROCR, knitr, M3DExampleData, SingleCellExperiment, Seurat, Biobase requirements: host: + - bioconductor-scater >=1.34.0,<1.35.0 - r-base - r-bbmle - r-gplots @@ -34,6 +46,7 @@ requirements: - r-reldist - r-statmod run: + - bioconductor-scater >=1.34.0,<1.35.0 - r-base - r-bbmle - r-gplots @@ -45,21 +58,16 @@ requirements: - r-rcolorbrewer - r-reldist - r-statmod + +source: + md5: 65a23be10bdfae99a3245ad2f1c10ba8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Michaelis-Menten Modelling of Dropouts in single-cell RNASeq' - description: 'This package fits a Michaelis-Menten model to the pattern of dropouts in single-cell RNASeq data. This model is used as a null to identify significantly variable (i.e. differentially expressed) genes for use in downstream analysis, such as clustering cells.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:m3drop - - doi:10.1002/1873-3468.12684 - parent_recipe: - name: bioconductor-m3drop - path: recipes/bioconductor-m3drop - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-m6aboost/meta.yaml b/recipes/bioconductor-m6aboost/meta.yaml index 929ee2436e646..553abc36ad560 100644 --- a/recipes/bioconductor-m6aboost/meta.yaml +++ b/recipes/bioconductor-m6aboost/meta.yaml @@ -1,54 +1,59 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "m6Aboost" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package can help user to run the m6Aboost model on their own miCLIP2 data. The package includes functions to assign the read counts and get the features to run the m6Aboost model. The miCLIP2 data should be stored in a GRanges object. More details can be found in the vignette. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: m6Aboost -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 17bd39bcc17e45a0bb22be3e2e15c533 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-m6aboost", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-adabag - r-base - r-dplyr run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-adabag - r-base - r-dplyr + +source: + md5: d6bd9364bcdd08b8c8d34dfe4c8e521e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: m6Aboost - description: 'This package can help user to run the m6Aboost model on their own miCLIP2 data. The package includes functions to assign the read counts and get the features to run the m6Aboost model. The miCLIP2 data should be stored in a GRanges object. More details can be found in the vignette.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-macorrplot/meta.yaml b/recipes/bioconductor-macorrplot/meta.yaml index 26005f13bc3d4..504b71caa51be 100644 --- a/recipes/bioconductor-macorrplot/meta.yaml +++ b/recipes/bioconductor-macorrplot/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.72.0" %} +{% set version = "1.76.0" %} {% set name = "maCorrPlot" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Graphically displays correlation in microarray data that is due to insufficient normalization + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Visualize artificial correlation in microarray data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d4be51b04e4ff3e09aff6643eeed215 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-macorrplot", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:macorrplot + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-macorrplot + path: recipes/bioconductor-macorrplot + version: 1.50.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -26,21 +37,16 @@ requirements: run: - r-base - r-lattice + +source: + md5: 131553e83d70b83c6770f29d77850e8d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Visualize artificial correlation in microarray data' - description: 'Graphically displays correlation in microarray data that is due to insufficient normalization' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:macorrplot - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-macorrplot - path: recipes/bioconductor-macorrplot - version: 1.50.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-macrophage/meta.yaml b/recipes/bioconductor-macrophage/meta.yaml index 54570f039c559..40b22b0582f38 100644 --- a/recipes/bioconductor-macrophage/meta.yaml +++ b/recipes/bioconductor-macrophage/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "macrophage" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5f83cf12d699a285cd228119b1d95cf0 +about: + description: This package provides the output of running Salmon on a set of 24 RNA-seq samples from Alasoo, et al. "Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response", published in Nature Genetics, January 2018. For details on version numbers and how the samples were processed see the package vignette. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Human macrophage immune response build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-macrophage", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, markdown requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0782d719de282a1fb033344185c2d3ff + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Human macrophage immune response' - description: 'This package provides the output of running Salmon on a set of 24 RNA-seq samples from Alasoo, et al. "Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response", published in Nature Genetics, January 2018. For details on version numbers and how the samples were processed see the package vignette.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-macrophage/post-link.sh b/recipes/bioconductor-macrophage/post-link.sh index 07ecd9410ed61..5e9c6518da90a 100644 --- a/recipes/bioconductor-macrophage/post-link.sh +++ b/recipes/bioconductor-macrophage/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "macrophage-1.18.0" +installBiocDataPackage.sh "macrophage-1.22.0" diff --git a/recipes/bioconductor-macsdata/meta.yaml b/recipes/bioconductor-macsdata/meta.yaml index 9b6e64baa9952..3b7e9bbaf4aa8 100644 --- a/recipes/bioconductor-macsdata/meta.yaml +++ b/recipes/bioconductor-macsdata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "MACSdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d10f4fe6b20d5c09148b8011fb3183f +about: + description: 'Test datasets from the MACS3 test examples are use in the examples of the `MACSr` package. All 9 datasets are uploaded to the `ExperimentHub`. The original data can be found at: https://github.com/macs3-project/MACS/.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Test datasets for the MACSr package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-macsdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ad077b7b288ff5fec2b011453af70aad + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Test datasets for the MACSr package' - description: 'Test datasets from the MACS3 test examples are use in the examples of the `MACSr` package. All 9 datasets are uploaded to the `ExperimentHub`. The original data can be found at: https://github.com/macs3-project/MACS/.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-macsdata/post-link.sh b/recipes/bioconductor-macsdata/post-link.sh index 5b08e731f2aa8..279052d5ac107 100644 --- a/recipes/bioconductor-macsdata/post-link.sh +++ b/recipes/bioconductor-macsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "macsdata-1.10.0" +installBiocDataPackage.sh "macsdata-1.14.0" diff --git a/recipes/bioconductor-macsquantifyr/meta.yaml b/recipes/bioconductor-macsquantifyr/meta.yaml index d34ebb85df598..ec2ca4a8f0f21 100644 --- a/recipes/bioconductor-macsquantifyr/meta.yaml +++ b/recipes/bioconductor-macsquantifyr/meta.yaml @@ -1,24 +1,25 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "MACSQuantifyR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Automatically process the metadata of MACSQuantify FACS sorter. It runs multiple modules: i) imports of raw file and graphical selection of duplicates in well plate, ii) computes statistics on data and iii) can compute combination index.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Fast treatment of MACSQuantify FACS data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b0bc5dd3ddff22c28356a8af09704f82 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-macsquantifyr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, R.utils, spelling requirements: host: @@ -47,12 +48,16 @@ requirements: - r-rmarkdown - r-rvest - r-xml2 + +source: + md5: 64a9696488ec0270610f2c7aef146080 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Fast treatment of MACSQuantify FACS data' - description: 'Automatically process the metadata of MACSQuantify FACS sorter. It runs multiple modules: i) imports of raw file and graphical selection of duplicates in well plate, ii) computes statistics on data and iii) can compute combination index.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-macsr/meta.yaml b/recipes/bioconductor-macsr/meta.yaml index 69879b8a4a240..8a6631128e62a 100644 --- a/recipes/bioconductor-macsr/meta.yaml +++ b/recipes/bioconductor-macsr/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "MACSr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The Model-based Analysis of ChIP-Seq (MACS) is a widely used toolkit for identifying transcript factor binding sites. This package is an R wrapper of the lastest MACS3. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_3_clause + file LICENSE + license_file: LICENSE + summary: 'MACS: Model-based Analysis for ChIP-Seq' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bab4dacc8d41a2a47798bc740181f014 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-macsr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocStyle, MACSdata requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-reticulate run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-reticulate + +source: + md5: b8fc522dac1cde77a5c38c39c7228d7a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_3_clause + file LICENSE' - summary: 'MACS: Model-based Analysis for ChIP-Seq' - description: 'The Model-based Analysis of ChIP-Seq (MACS) is a widely used toolkit for identifying transcript factor binding sites. This package is an R wrapper of the lastest MACS3.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-made4/meta.yaml b/recipes/bioconductor-made4/meta.yaml index 924483d6772f8..bc89491690c6d 100644 --- a/recipes/bioconductor-made4/meta.yaml +++ b/recipes/bioconductor-made4/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.76.0" %} +{% set version = "1.80.0" %} {% set name = "made4" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Multivariate data analysis and graphical display of microarray data. Functions include for supervised dimension reduction (between group analysis) and joint dimension reduction of 2 datasets (coinertia analysis). It contains functions that require R package ade4. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Multivariate analysis of microarray data using ADE4 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ae8a8a420c5f5ebd8a729767baf0a762 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-made4", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:made4 + parent_recipe: + name: bioconductor-made4 + path: recipes/bioconductor-made4 + version: 1.54.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: affy, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-ade4 - r-base - r-gplots - r-rcolorbrewer - r-scatterplot3d run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-ade4 - r-base - r-gplots - r-rcolorbrewer - r-scatterplot3d + +source: + md5: 7669d7276ff623c318b6337c6776512e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Multivariate analysis of microarray data using ADE4' - description: 'Multivariate data analysis and graphical display of microarray data. Functions include for supervised dimension reduction (between group analysis) and joint dimension reduction of 2 datasets (coinertia analysis). It contains functions that require R package ade4.' -extra: - identifiers: - - biotools:made4 - parent_recipe: - name: bioconductor-made4 - path: recipes/bioconductor-made4 - version: 1.54.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-madseq/meta.yaml b/recipes/bioconductor-madseq/meta.yaml index 54bf4e92bbf41..260b0707fba49 100644 --- a/recipes/bioconductor-madseq/meta.yaml +++ b/recipes/bioconductor-madseq/meta.yaml @@ -1,81 +1,87 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "MADSEQ" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The MADSEQ package provides a group of hierarchical Bayeisan models for the detection of mosaic aneuploidy, the inference of the type of aneuploidy and also for the quantification of the fraction of aneuploid cells in the sample. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL(>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c64d51251670d105945b18d12dcd5fec build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-madseq", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:madseq + - doi:10.1101/142299 + parent_recipe: + name: bioconductor-madseq + path: recipes/bioconductor-madseq + version: 1.6.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-coda - - 'r-rjags >=4.6' + - r-rjags >=4.6 - r-vcfr - r-vgam run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-coda - - 'r-rjags >=4.6' + - r-rjags >=4.6 - r-vcfr - r-vgam + +source: + md5: dbce51bd9e630dafc96e5d542a53a6b3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL(>=2) - summary: 'Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data' - description: 'The MADSEQ package provides a group of hierarchical Bayeisan models for the detection of mosaic aneuploidy, the inference of the type of aneuploidy and also for the quantification of the fraction of aneuploid cells in the sample.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:madseq - - doi:10.1101/142299 - parent_recipe: - name: bioconductor-madseq - path: recipes/bioconductor-madseq - version: 1.6.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/meta.yaml index 2b6aa7f5d2729..2d6a011e50d68 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/meta.yaml @@ -1,50 +1,55 @@ {% set version = "3.10.0" %} {% set name = "MafDb.1Kgenomes.phase1.GRCh38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Store minor allele frequency data from the Phase 1 of the 1000 Genomes Project for the human genome version GRCh38. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Minor allele frequency data from 1000 Genomes Phase 1 for GRCh38 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a20471906a41678ce710879e92d2a9dc build: - number: 9 + noarch: generic + number: 10 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mafdb.1kgenomes.phase1.grch38", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: a20471906a41678ce710879e92d2a9dc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Minor allele frequency data from 1000 Genomes Phase 1 for GRCh38' - description: 'Store minor allele frequency data from the Phase 1 of the 1000 Genomes Project for the human genome version GRCh38.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/meta.yaml index 370e667cdc070..eed896c785a15 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/meta.yaml @@ -1,50 +1,55 @@ {% set version = "3.10.0" %} {% set name = "MafDb.1Kgenomes.phase1.hs37d5" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Store minor allele frequency data from the Phase 1 of the 1000 Genomes Project for the human genome version hs37d5. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Minor allele frequency data from 1000 Genomes Phase 1 for hs37d5 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ece6b758ca0e1a8a307b5cd5829671f4 build: - number: 9 + noarch: generic + number: 10 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mafdb.1kgenomes.phase1.hs37d5", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: ece6b758ca0e1a8a307b5cd5829671f4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Minor allele frequency data from 1000 Genomes Phase 1 for hs37d5' - description: 'Store minor allele frequency data from the Phase 1 of the 1000 Genomes Project for the human genome version hs37d5.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/meta.yaml index 1db40c302708a..9fa8bdbe7fd2c 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/meta.yaml @@ -1,50 +1,55 @@ {% set version = "3.10.0" %} {% set name = "MafDb.1Kgenomes.phase3.GRCh38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Store minor allele frequency data from the Phase 3 of the 1000 Genomes Project for the human genome version GRCh38. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Minor allele frequency data from 1000 Genomes Phase 3 for GRCh38 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee57d9cb6a1748932407d20b9bffd8a2 build: - number: 9 + noarch: generic + number: 10 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mafdb.1kgenomes.phase3.grch38", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: ee57d9cb6a1748932407d20b9bffd8a2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Minor allele frequency data from 1000 Genomes Phase 3 for GRCh38' - description: 'Store minor allele frequency data from the Phase 3 of the 1000 Genomes Project for the human genome version GRCh38.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/meta.yaml index e5eef7f32a86d..ca7b98ca322ce 100644 --- a/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/meta.yaml @@ -1,50 +1,55 @@ {% set version = "3.10.0" %} {% set name = "MafDb.1Kgenomes.phase3.hs37d5" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Store minor allele frequency data from the Phase 3 of the 1000 Genomes Project for the human genome version hs37d5. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Minor allele frequency data from 1000 Genomes Phase 3 for hs37d5 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ac3cbbf52eb2026f067a4f42c6654555 build: - number: 9 + noarch: generic + number: 10 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mafdb.1kgenomes.phase3.hs37d5", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: ac3cbbf52eb2026f067a4f42c6654555 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Minor allele frequency data from 1000 Genomes Phase 3 for hs37d5' - description: 'Store minor allele frequency data from the Phase 3 of the 1000 Genomes Project for the human genome version hs37d5.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mafdb.exac.r1.0.grch38/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.grch38/meta.yaml index a96f0e68085a4..4b1e5ea78f7a8 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.exac.r1.0.grch38/meta.yaml @@ -1,50 +1,55 @@ {% set version = "3.10.0" %} {% set name = "MafDb.ExAC.r1.0.GRCh38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0) for the human genome version GRCh38. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Minor allele frequency data from ExAC release 1.0 for GRCh38 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 303332c918996d8cb3e7b7c74d694dd1 build: - number: 9 + noarch: generic + number: 10 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mafdb.exac.r1.0.grch38", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 303332c918996d8cb3e7b7c74d694dd1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Minor allele frequency data from ExAC release 1.0 for GRCh38' - description: 'Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0) for the human genome version GRCh38.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/meta.yaml index 8ee13e3ac78c2..761bc6cbec536 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/meta.yaml @@ -1,50 +1,55 @@ {% set version = "3.10.0" %} {% set name = "MafDb.ExAC.r1.0.hs37d5" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0) for the human genome version hs37d5. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Minor allele frequency data from ExAC release 1.0 for hs37d5 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d523554a2b0eb296bada9d33a78eefc build: - number: 9 + noarch: generic + number: 10 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mafdb.exac.r1.0.hs37d5", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 4d523554a2b0eb296bada9d33a78eefc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Minor allele frequency data from ExAC release 1.0 for hs37d5' - description: 'Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0) for the human genome version hs37d5.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/meta.yaml index acc4810915163..87483a75d0d8c 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/meta.yaml @@ -1,50 +1,55 @@ {% set version = "3.10.0" %} {% set name = "MafDb.ExAC.r1.0.nonTCGA.GRCh38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0 subset of nonTCGA exomes) for the human genome version GRCh38. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Minor allele frequency data from ExAC release 1.0 subset of nonTCGA exomes for GRCh38 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf447f59cc8b1cd7ca395fd3fe6e4730 build: - number: 9 + noarch: generic + number: 10 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mafdb.exac.r1.0.nontcga.grch38", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: cf447f59cc8b1cd7ca395fd3fe6e4730 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Minor allele frequency data from ExAC release 1.0 subset of nonTCGA exomes for GRCh38' - description: 'Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0 subset of nonTCGA exomes) for the human genome version GRCh38.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/meta.yaml index 4e474b21e0b3f..955656ee1950d 100644 --- a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/meta.yaml @@ -1,50 +1,55 @@ {% set version = "3.10.0" %} {% set name = "MafDb.ExAC.r1.0.nonTCGA.hs37d5" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0 subset of nonTCGA exomes) for the human genome version hs37d5. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Minor allele frequency data from ExAC release 1.0 subset of nonTCGA exomes for hs37d5 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: da3a699e9776b0b769b3bc1e9fb742f0 build: - number: 9 + noarch: generic + number: 10 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mafdb.exac.r1.0.nontcga.hs37d5", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: da3a699e9776b0b769b3bc1e9fb742f0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Minor allele frequency data from ExAC release 1.0 subset of nonTCGA exomes for hs37d5' - description: 'Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0 subset of nonTCGA exomes) for the human genome version hs37d5.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/meta.yaml b/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/meta.yaml index 6a2aeb3790b7b..d12550166ba62 100644 --- a/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.gnomad.r2.1.grch38/meta.yaml @@ -1,50 +1,55 @@ {% set version = "3.10.0" %} {% set name = "MafDb.gnomAD.r2.1.GRCh38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Store minor allele frequency data from the Genome Aggregation Database (gnomAD release 2.1) for the human genome version GRCh38. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Minor allele frequency data from gnomAD release 2.1 for GRCh38 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e842b24476aeb834f57f9302a36ea18 build: + noarch: generic number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mafdb.gnomad.r2.1.grch38", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 0e842b24476aeb834f57f9302a36ea18 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Minor allele frequency data from gnomAD release 2.1 for GRCh38' - description: 'Store minor allele frequency data from the Genome Aggregation Database (gnomAD release 2.1) for the human genome version GRCh38.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/meta.yaml index e55b30222e669..521453ace46e3 100644 --- a/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/meta.yaml @@ -1,50 +1,55 @@ {% set version = "3.10.0" %} {% set name = "MafDb.gnomAD.r2.1.hs37d5" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Store minor allele frequency data from the Genome Aggregation Database (gnomAD release 2.1) for the human genome version hs37d5. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Minor allele frequency data from gnomAD release 2.1 for hs37d5 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 12221c461930ae1ecfe925943a619d56 build: + noarch: generic number: 7 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mafdb.gnomad.r2.1.hs37d5", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 12221c461930ae1ecfe925943a619d56 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Minor allele frequency data from gnomAD release 2.1 for hs37d5' - description: 'Store minor allele frequency data from the Genome Aggregation Database (gnomAD release 2.1) for the human genome version hs37d5.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/meta.yaml b/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/meta.yaml index 0a1f9568b4c16..f4880a5fe7943 100644 --- a/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/meta.yaml +++ b/recipes/bioconductor-mafdb.gnomadex.r2.1.grch38/meta.yaml @@ -1,50 +1,55 @@ {% set version = "3.10.0" %} {% set name = "MafDb.gnomADex.r2.1.GRCh38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Store minor allele frequency data from the Genome Aggregation Database (gnomAD exomes release 2.1) for the human genome version GRCh38. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Minor allele frequency data from gnomAD exomes release 2.1 for GRCh38 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a0ab5b74997669fabb8aecfd9ef7f767 build: - number: 9 + noarch: generic + number: 10 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mafdb.gnomadex.r2.1.grch38", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: a0ab5b74997669fabb8aecfd9ef7f767 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Minor allele frequency data from gnomAD exomes release 2.1 for GRCh38' - description: 'Store minor allele frequency data from the Genome Aggregation Database (gnomAD exomes release 2.1) for the human genome version GRCh38.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/meta.yaml index 9c24dd865ddc8..4d6af0e2f2645 100644 --- a/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/meta.yaml +++ b/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/meta.yaml @@ -1,50 +1,55 @@ {% set version = "3.10.0" %} {% set name = "MafDb.gnomADex.r2.1.hs37d5" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Store minor allele frequency data from the Genome Aggregation Database (gnomAD exomes release 2.1) for the human genome version hs37d5. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Minor allele frequency data from gnomAD exomes release 2.1 for hs37d5 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ca4d742571687a13906d99cea2dbf1f build: - number: 9 + noarch: generic + number: 10 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mafdb.gnomadex.r2.1.hs37d5", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 6ca4d742571687a13906d99cea2dbf1f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Minor allele frequency data from gnomAD exomes release 2.1 for hs37d5' - description: 'Store minor allele frequency data from the Genome Aggregation Database (gnomAD exomes release 2.1) for the human genome version hs37d5.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mafdb.topmed.freeze5.hg19/meta.yaml b/recipes/bioconductor-mafdb.topmed.freeze5.hg19/meta.yaml index 06fdf2b8407e8..6c4441959f680 100644 --- a/recipes/bioconductor-mafdb.topmed.freeze5.hg19/meta.yaml +++ b/recipes/bioconductor-mafdb.topmed.freeze5.hg19/meta.yaml @@ -1,50 +1,55 @@ {% set version = "3.10.0" %} {% set name = "MafDb.TOPMed.freeze5.hg19" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Store minor allele frequency data from NHLBI TOPMed for the human genome version hg19. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Minor allele frequency data from TOPMed for hg19 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7fdb58eb69187ade189689da58ca6266 build: - number: 9 + noarch: generic + number: 10 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mafdb.topmed.freeze5.hg19", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 7fdb58eb69187ade189689da58ca6266 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Minor allele frequency data from TOPMed for hg19' - description: 'Store minor allele frequency data from NHLBI TOPMed for the human genome version hg19.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mafdb.topmed.freeze5.hg38/meta.yaml b/recipes/bioconductor-mafdb.topmed.freeze5.hg38/meta.yaml index 485f8cd9f87c6..8430821fc9e22 100644 --- a/recipes/bioconductor-mafdb.topmed.freeze5.hg38/meta.yaml +++ b/recipes/bioconductor-mafdb.topmed.freeze5.hg38/meta.yaml @@ -1,50 +1,55 @@ {% set version = "3.10.0" %} {% set name = "MafDb.TOPMed.freeze5.hg38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Store minor allele frequency data from NHLBI TOPMed for the human genome version hg38. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Minor allele frequency data from TOPMed for hg38 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3355623fde26b83dfd346a32829f073 build: - number: 9 + noarch: generic + number: 10 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mafdb.topmed.freeze5.hg38", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: a3355623fde26b83dfd346a32829f073 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Minor allele frequency data from TOPMed for hg38' - description: 'Store minor allele frequency data from NHLBI TOPMed for the human genome version hg38.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-maftools/meta.yaml b/recipes/bioconductor-maftools/meta.yaml index ef10236192193..f28d79e2ed0ff 100644 --- a/recipes/bioconductor-maftools/meta.yaml +++ b/recipes/bioconductor-maftools/meta.yaml @@ -1,64 +1,74 @@ -{% set version = "2.18.0" %} +{% set version = "2.22.0" %} {% set name = "maftools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Summarize, Analyze and Visualize MAF Files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3dadc2b7f6f1693ae23a41b61f541db4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-maftools", max_pin="x.x") }}' -# Suggests: berryFunctions, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr, mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment, rmarkdown, S4Vectors, pheatmap, curl + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:maftools + - usegalaxy-eu:maftools + parent_recipe: + name: bioconductor-maftools + path: recipes/bioconductor-maftools + version: 1.6.15 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: berryFunctions, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr, mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment, rmarkdown, S4Vectors, curl # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-data.table + - r-pheatmap - r-rcolorbrewer - r-survival - libblas - liblapack + - zlib + - liblzma-devel run: - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-data.table + - r-pheatmap - r-rcolorbrewer - r-survival - build: - - {{ compiler('c') }} - - make + +source: + md5: 46734cb554e493255927202f63c58b5f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Summarize, Analyze and Visualize MAF Files' - description: 'Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.' - license_file: LICENSE -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} - - usegalaxy-eu:{{ name|lower }} - parent_recipe: - name: bioconductor-maftools - path: recipes/bioconductor-maftools - version: 1.6.15 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-magar/meta.yaml b/recipes/bioconductor-magar/meta.yaml index e87b79b60d97d..77bbcab229d82 100644 --- a/recipes/bioconductor-magar/meta.yaml +++ b/recipes/bioconductor-magar/meta.yaml @@ -1,33 +1,36 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "MAGAR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: '"Methylation-Aware Genotype Association in R" (MAGAR) computes methQTL from DNA methylation and genotyping data from matched samples. MAGAR uses a linear modeling stragety to call CpGs/SNPs that are methQTLs. MAGAR accounts for the local correlation structure of CpGs.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 27ccb3bf6acaabe9b9d29b52f9d98213 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-magar", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil, rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools, BiocGenerics, BiocManager requirements: host: - - 'bioconductor-crlmm >=1.60.0,<1.61.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-rnbeads >=2.20.0,<2.21.0' - - 'bioconductor-rnbeads.hg19 >=1.34.0,<1.35.0' - - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - bioconductor-crlmm >=1.64.0,<1.65.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-rnbeads >=2.24.0,<2.25.0 + - bioconductor-rnbeads.hg19 >=1.38.0,<1.39.0 + - bioconductor-rnbeads.hg38 >=1.38.0,<1.39.0 + - bioconductor-snpstats >=1.56.0,<1.57.0 - r-argparse - r-base - r-bigstatsr @@ -41,12 +44,13 @@ requirements: - r-rjson - r-upsetr run: - - 'bioconductor-crlmm >=1.60.0,<1.61.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-rnbeads >=2.20.0,<2.21.0' - - 'bioconductor-rnbeads.hg19 >=1.34.0,<1.35.0' - - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - bioconductor-crlmm >=1.64.0,<1.65.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-rnbeads >=2.24.0,<2.25.0 + - bioconductor-rnbeads.hg19 >=1.38.0,<1.39.0 + - bioconductor-rnbeads.hg38 >=1.38.0,<1.39.0 + - bioconductor-snpstats >=1.56.0,<1.57.0 - r-argparse - r-base - r-bigstatsr @@ -59,13 +63,16 @@ requirements: - r-reshape2 - r-rjson - r-upsetr + +source: + md5: a54d3ada0dda135fabf355780623abe0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data' - description: '"Methylation-Aware Genotype Association in R" (MAGAR) computes methQTL from DNA methylation and genotyping data from matched samples. MAGAR uses a linear modeling stragety to call CpGs/SNPs that are methQTLs. MAGAR accounts for the local correlation structure of CpGs.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mageckflute/meta.yaml b/recipes/bioconductor-mageckflute/meta.yaml index 3a485e0d36c7c..ce95cbcbdac45 100644 --- a/recipes/bioconductor-mageckflute/meta.yaml +++ b/recipes/bioconductor-mageckflute/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "2.6.0" %} +{% set version = "2.9.0" %} {% set name = "MAGeCKFlute" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CRISPR (clustered regularly interspaced short palindrome repeats) coupled with nuclease Cas9 (CRISPR/Cas9) screens represent a promising technology to systematically evaluate gene functions. Data analysis for CRISPR/Cas9 screens is a critical process that includes identifying screen hits and exploring biological functions for these hits in downstream analysis. We have previously developed two algorithms, MAGeCK and MAGeCK-VISPR, to analyze CRISPR/Cas9 screen data in various scenarios. These two algorithms allow users to perform quality control, read count generation and normalization, and calculate beta score to evaluate gene selection performance. In downstream analysis, the biological functional analysis is required for understanding biological functions of these identified genes with different screening purposes. Here, We developed MAGeCKFlute for supporting downstream analysis. MAGeCKFlute provides several strategies to remove potential biases within sgRNA-level read counts and gene-level beta scores. The downstream analysis with the package includes identifying essential, non-essential, and target-associated genes, and performing biological functional category analysis, pathway enrichment analysis and protein complex enrichment analysis of these genes. The package also visualizes genes in multiple ways to benefit users exploring screening data. Collectively, MAGeCKFlute enables accurate identification of essential, non-essential, and targeted genes, as well as their related biological functions. This vignette explains the use of the package and demonstrates typical workflows. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 09a3c95fe59a959ce069f5ad56e75276 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mageckflute", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: biomaRt, BiocStyle, dendextend, graphics, knitr, pheatmap, png, scales, sva, BiocManager requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-depmap >=1.16.0,<1.17.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - - 'bioconductor-pathview >=1.42.0,<1.43.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-depmap >=1.20.0,<1.21.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 + - bioconductor-pathview >=1.46.0,<1.47.0 - r-base - r-ggplot2 - r-ggrepel @@ -35,25 +37,28 @@ requirements: - r-msigdbr - r-reshape2 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-depmap >=1.16.0,<1.17.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - - 'bioconductor-pathview >=1.42.0,<1.43.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-depmap >=1.20.0,<1.21.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 + - bioconductor-pathview >=1.46.0,<1.47.0 - r-base - r-ggplot2 - r-ggrepel - r-gridextra - r-msigdbr - r-reshape2 + +source: + md5: 09a221017ca0e42c35bdbde86aa15a00 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=3)' - summary: 'Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens' - description: 'CRISPR (clustered regularly interspaced short palindrome repeats) coupled with nuclease Cas9 (CRISPR/Cas9) screens represent a promising technology to systematically evaluate gene functions. Data analysis for CRISPR/Cas9 screens is a critical process that includes identifying screen hits and exploring biological functions for these hits in downstream analysis. We have previously developed two algorithms, MAGeCK and MAGeCK-VISPR, to analyze CRISPR/Cas9 screen data in various scenarios. These two algorithms allow users to perform quality control, read count generation and normalization, and calculate beta score to evaluate gene selection performance. In downstream analysis, the biological functional analysis is required for understanding biological functions of these identified genes with different screening purposes. Here, We developed MAGeCKFlute for supporting downstream analysis. MAGeCKFlute provides several strategies to remove potential biases within sgRNA-level read counts and gene-level beta scores. The downstream analysis with the package includes identifying essential, non-essential, and target-associated genes, and performing biological functional category analysis, pathway enrichment analysis and protein complex enrichment analysis of these genes. The package also visualizes genes in multiple ways to benefit users exploring screening data. Collectively, MAGeCKFlute enables accurate identification of essential, non-essential, and targeted genes, as well as their related biological functions. This vignette explains the use of the package and demonstrates typical workflows.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-magpie/meta.yaml b/recipes/bioconductor-magpie/meta.yaml index 9b8edec7aca44..5598bb572e672 100644 --- a/recipes/bioconductor-magpie/meta.yaml +++ b/recipes/bioconductor-magpie/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "magpie" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package aims to perform power analysis for the MeRIP-seq study. It calculates FDR, FDC, power, and precision under various study design parameters, including but not limited to sample size, sequencing depth, and testing method. It can also output results into .xlsx files or produce corresponding figures of choice. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: MeRIP-Seq data Analysis for Genomic Power Investigation and Evaluation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 019cf9b038353b96851fe65fa55f3d08 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-magpie", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, kableExtra, RUnit, TBX20BamSubset, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-tress >=1.8.0,<1.9.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-tress >=1.12.0,<1.13.0 - r-aod - r-base - r-matrix @@ -40,16 +42,16 @@ requirements: - r-rcolorbrewer - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-tress >=1.8.0,<1.9.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-tress >=1.12.0,<1.13.0 - r-aod - r-base - r-matrix @@ -57,13 +59,16 @@ requirements: - r-openxlsx - r-rcolorbrewer - r-reshape2 + +source: + md5: a2d8cace71fdb5936f5e1eda05cf9989 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'MeRIP-Seq data Analysis for Genomic Power Investigation and Evaluation' - description: 'This package aims to perform power analysis for the MeRIP-seq study. It calculates FDR, FDC, power, and precision under various study design parameters, including but not limited to sample size, sequencing depth, and testing method. It can also output results into .xlsx files or produce corresponding figures of choice.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-magrene/meta.yaml b/recipes/bioconductor-magrene/meta.yaml index 54cc0f1df97ec..a34067d13b148 100644 --- a/recipes/bioconductor-magrene/meta.yaml +++ b/recipes/bioconductor-magrene/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "magrene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7d02392d3081830451c4fae90ed50177 +about: + description: magrene allows the identification and analysis of graph motifs in (duplicated) gene regulatory networks (GRNs), including lambda, V, PPI V, delta, and bifan motifs. GRNs can be tested for motif enrichment by comparing motif frequencies to a null distribution generated from degree-preserving simulated GRNs. Motif frequencies can be analyzed in the context of gene duplications to explore the impact of small-scale and whole-genome duplications on gene regulatory networks. Finally, users can calculate interaction similarity for gene pairs based on the Sorensen-Dice similarity index. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Motif Analysis In Gene Regulatory Networks build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-magrene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, covr, knitr, rmarkdown, ggplot2, sessioninfo, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base +source: + md5: e091291ec9d04bc620b1bdde157221e2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Motif Analysis In Gene Regulatory Networks' - description: 'magrene allows the identification and analysis of graph motifs in (duplicated) gene regulatory networks (GRNs), including lambda, V, PPI V, delta, and bifan motifs. GRNs can be tested for motif enrichment by comparing motif frequencies to a null distribution generated from degree-preserving simulated GRNs. Motif frequencies can be analyzed in the context of gene duplications to explore the impact of small-scale and whole-genome duplications on gene regulatory networks. Finally, users can calculate interaction similarity for gene pairs based on the Sorensen-Dice similarity index.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mai/meta.yaml b/recipes/bioconductor-mai/meta.yaml index e1039188b4612..fda258ac453bb 100644 --- a/recipes/bioconductor-mai/meta.yaml +++ b/recipes/bioconductor-mai/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "MAI" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A two-step approach to imputing missing data in metabolomics. Step 1 uses a random forest classifier to classify missing values as either Missing Completely at Random/Missing At Random (MCAR/MAR) or Missing Not At Random (MNAR). MCAR/MAR are combined because it is often difficult to distinguish these two missing types in metabolomics data. Step 2 imputes the missing values based on the classified missing mechanisms, using the appropriate imputation algorithms. Imputation algorithms tested and available for MCAR/MAR include Bayesian Principal Component Analysis (BPCA), Multiple Imputation No-Skip K-Nearest Neighbors (Multi_nsKNN), and Random Forest. Imputation algorithms tested and available for MNAR include nsKNN and a single imputation approach for imputation of metabolites where left-censoring is present. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Mechanism-Aware Imputation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ac8dbd997d58657f8ed6b64f5cdee7a9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mai", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-caret - r-doparallel @@ -35,9 +37,9 @@ requirements: - r-missforest - r-tidyverse run: - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-caret - r-doparallel @@ -47,13 +49,16 @@ requirements: - r-future.apply - r-missforest - r-tidyverse + +source: + md5: 4b3f2448e7b085778a262cd2fbeda1e0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Mechanism-Aware Imputation' - description: 'A two-step approach to imputing missing data in metabolomics. Step 1 uses a random forest classifier to classify missing values as either Missing Completely at Random/Missing At Random (MCAR/MAR) or Missing Not At Random (MNAR). MCAR/MAR are combined because it is often difficult to distinguish these two missing types in metabolomics data. Step 2 imputes the missing values based on the classified missing mechanisms, using the appropriate imputation algorithms. Imputation algorithms tested and available for MCAR/MAR include Bayesian Principal Component Analysis (BPCA), Multiple Imputation No-Skip K-Nearest Neighbors (Multi_nsKNN), and Random Forest. Imputation algorithms tested and available for MNAR include nsKNN and a single imputation approach for imputation of metabolites where left-censoring is present.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mait/meta.yaml b/recipes/bioconductor-mait/meta.yaml index f55befffc79c5..b104e5854e9b3 100644 --- a/recipes/bioconductor-mait/meta.yaml +++ b/recipes/bioconductor-mait/meta.yaml @@ -1,28 +1,43 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "MAIT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The MAIT package contains functions to perform end-to-end statistical analysis of LC/MS Metabolomic Data. Special emphasis is put on peak annotation and in modular function design of the functions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Statistical Analysis of Metabolomic Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f32e9e8e908202848634b26a5ece4d8f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mait", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:mait + parent_recipe: + name: bioconductor-mait + path: recipes/bioconductor-mait + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: faahKO requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - - 'bioconductor-camera >=1.58.0,<1.59.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-camera >=1.62.0,<1.63.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-agricolae - r-base - r-caret @@ -36,8 +51,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-camera >=1.58.0,<1.59.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-camera >=1.62.0,<1.63.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-agricolae - r-base - r-caret @@ -48,25 +63,16 @@ requirements: - r-pls - r-plsgenomics - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} + +source: + md5: f16bfab6fa3d3e7fed16b9f6d186ecc2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2.0-only - summary: 'Statistical Analysis of Metabolomic Data' - description: 'The MAIT package contains functions to perform end-to-end statistical analysis of LC/MS Metabolomic Data. Special emphasis is put on peak annotation and in modular function design of the functions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} - parent_recipe: - name: bioconductor-mait - path: recipes/bioconductor-mait - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-maizecdf/meta.yaml b/recipes/bioconductor-maizecdf/meta.yaml index d836b954f6903..f5445dceb208f 100644 --- a/recipes/bioconductor-maizecdf/meta.yaml +++ b/recipes/bioconductor-maizecdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "maizecdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f9dec9e46688d96daf1e07d4e815afb4 +about: + description: A package containing an environment representing the Maize.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: maizecdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-maizecdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f9dec9e46688d96daf1e07d4e815afb4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: maizecdf - description: 'A package containing an environment representing the Maize.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-maizeprobe/meta.yaml b/recipes/bioconductor-maizeprobe/meta.yaml index 3c8eb2bfe896a..6568f159704d4 100644 --- a/recipes/bioconductor-maizeprobe/meta.yaml +++ b/recipes/bioconductor-maizeprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "maizeprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ef7ba47de2346b3552621263399c05d1 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Maize\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type maize build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-maizeprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ef7ba47de2346b3552621263399c05d1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type maize' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Maize\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-makecdfenv/meta.yaml b/recipes/bioconductor-makecdfenv/meta.yaml index 2271860f8f2bc..1b84f9f174351 100644 --- a/recipes/bioconductor-makecdfenv/meta.yaml +++ b/recipes/bioconductor-makecdfenv/meta.yaml @@ -1,57 +1,63 @@ -{% set version = "1.78.0" %} +{% set version = "1.82.0" %} {% set name = "makecdfenv" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: CDF Environment Maker -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b5c8877fd5b09fbb4d3656490fa7eb64 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-makecdfenv", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:makecdfenv + - doi:10.1186/1471-2105-13-56 + parent_recipe: + name: bioconductor-makecdfenv + path: recipes/bioconductor-makecdfenv + version: 1.56.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - automake + - make host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - libblas - liblapack run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - build: - - {{ compiler('c') }} - - automake - - make + +source: + md5: 8fea48d8169003c7436fc406fe5e3ac1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'CDF Environment Maker' - description: 'This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:makecdfenv - - doi:10.1186/1471-2105-13-56 - parent_recipe: - name: bioconductor-makecdfenv - path: recipes/bioconductor-makecdfenv - version: 1.56.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-malaria.db0/meta.yaml b/recipes/bioconductor-malaria.db0/meta.yaml index ddff973edf6fe..5a5512996b52b 100644 --- a/recipes/bioconductor-malaria.db0/meta.yaml +++ b/recipes/bioconductor-malaria.db0/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "malaria.db0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6f71b4ac69ae5237f3f5e1337d5073d7 +about: + description: Base annotation databases for malaria, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Level Annotation databases for malaria build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-malaria.db0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fbcf1c6f5d5a6a2c33ab9a3200c51166 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Level Annotation databases for malaria' - description: 'Base annotation databases for malaria, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-malaria.db0/post-link.sh b/recipes/bioconductor-malaria.db0/post-link.sh index 723835d617cfb..c08a328ca436e 100644 --- a/recipes/bioconductor-malaria.db0/post-link.sh +++ b/recipes/bioconductor-malaria.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "malaria.db0-3.18.0" +installBiocDataPackage.sh "malaria.db0-3.20.0" diff --git a/recipes/bioconductor-mammaprintdata/meta.yaml b/recipes/bioconductor-mammaprintdata/meta.yaml index 0ad3e9e516f38..cc689238356ca 100644 --- a/recipes/bioconductor-mammaprintdata/meta.yaml +++ b/recipes/bioconductor-mammaprintdata/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "mammaPrintData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 08b3249a36d5f165a933bfab5eb05a2a +about: + description: Gene expression data for the two breast cancer cohorts published by Glas and Buyse in 2006. This cohorts were used to implement and validate the mammaPrint breast cancer test. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: RGLists from the Glas and Buyse breast cancer studies build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mammaprintdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: Biobase, readxl, limma requirements: host: @@ -26,13 +24,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 698b5dfa798c98b7d8478b23fbfeb560 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'RGLists from the Glas and Buyse breast cancer studies' - description: 'Gene expression data for the two breast cancer cohorts published by Glas and Buyse in 2006. This cohorts were used to implement and validate the mammaPrint breast cancer test.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mammaprintdata/post-link.sh b/recipes/bioconductor-mammaprintdata/post-link.sh index ee220d325a5a0..83c283d9c0926 100644 --- a/recipes/bioconductor-mammaprintdata/post-link.sh +++ b/recipes/bioconductor-mammaprintdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mammaprintdata-1.38.0" +installBiocDataPackage.sh "mammaprintdata-1.42.0" diff --git a/recipes/bioconductor-manor/meta.yaml b/recipes/bioconductor-manor/meta.yaml index 0b48ee35d2fea..af1e942b4f180 100644 --- a/recipes/bioconductor-manor/meta.yaml +++ b/recipes/bioconductor-manor/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "MANOR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a2d915a1904045acbe371b10102c8512 +about: + description: Importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: CGH Micro-Array NORmalization build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-manor", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, bookdown requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-glad >=2.66.0,<2.67.0' + - bioconductor-glad >=2.70.0,<2.71.0 - r-base - libblas - liblapack run: - - 'bioconductor-glad >=2.66.0,<2.67.0' + - bioconductor-glad >=2.70.0,<2.71.0 - r-base - build: - - {{ compiler('c') }} - - make +source: + md5: 24220ee4180315752bbfef71dcaae920 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'CGH Micro-Array NORmalization' - description: 'Importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mantelcorr/meta.yaml b/recipes/bioconductor-mantelcorr/meta.yaml index 5fe60a98bbc56..ba6305bdd5d47 100644 --- a/recipes/bioconductor-mantelcorr/meta.yaml +++ b/recipes/bioconductor-mantelcorr/meta.yaml @@ -1,38 +1,20 @@ -{% set version = "1.72.0" %} +{% set version = "1.76.0" %} {% set name = "MantelCorr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ef5ee0a329a4cf218c340e9289fea32 +about: + description: Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Compute Mantel Cluster Correlations build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mantelcorr", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Compute Mantel Cluster Correlations' - description: 'Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: identifiers: - biotools:mantelcorr @@ -41,4 +23,22 @@ extra: name: bioconductor-mantelcorr path: recipes/bioconductor-mantelcorr version: 1.50.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +requirements: + host: + - r-base + run: + - r-base +source: + md5: d323b5d644189314130a7481019e198e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mapfx/build.sh b/recipes/bioconductor-mapfx/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mapfx/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mapfx/build_failure.linux-64.yaml b/recipes/bioconductor-mapfx/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0e3fd2bb858eb --- /dev/null +++ b/recipes/bioconductor-mapfx/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 56a2cf4abcbb3eee1381faceaa3d780f0b03bf014377fdf1b6c39b0de88e6c78 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-icellr[0m does not exist (perhaps a typo or a missing channel); + [31mr-xgboost[0m is not installable because there are no viable options + [31mr-xgboost 0.80[0m would require + [31mmro-base >=3.5.0,<3.5.1.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-xgboost [0.80|0.81|0.82|0.90|1.0.2][0m would require + [31mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [0.82|0.90|...|1.4.0][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.0.2|1.1.1|...|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.4.0|1.4.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-icellr"), MatchSpec("r-xgboost==0.80=mro350h255eb88_1"), MatchSpec(">=3.5.0,<3.5.1.0a0")} + Encountered problems while solving: + - nothing provides requested r-icellr + - nothing provides mro-base >=3.5.0,<3.5.1.0a0 needed by r-xgboost-0.80-mro350h255eb88_1 + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-icellr[0m does not exist (perhaps a typo or a missing channel); + [31mr-xgboost[0m is not installable because there are no viable options + [31mr-xgboost 0.80[0m would require + [31mmro-base >=3.5.0,<3.5.1.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-xgboost [0.80|0.81|0.82|0.90|1.0.2][0m would require + [31mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [0.82|0.90|...|1.4.0][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.0.2|1.1.1|...|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.4.0|1.4.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. +category: |- + dependency issue diff --git a/recipes/bioconductor-mapfx/meta.yaml b/recipes/bioconductor-mapfx/meta.yaml new file mode 100644 index 0000000000000..386a29ec3c256 --- /dev/null +++ b/recipes/bioconductor-mapfx/meta.yaml @@ -0,0 +1,78 @@ +{% set version = "1.2.0" %} +{% set name = "MAPFX" %} +{% set bioc = "3.20" %} + +about: + description: MAPFX is an end-to-end toolbox that pre-processes the raw data from MPC experiments (e.g., BioLegend's LEGENDScreen and BD Lyoplates assays), and further imputes the ‘missing’ infinity markers in the wells without those measurements. The pipeline starts by performing background correction on raw intensities to remove the noise from electronic baseline restoration and fluorescence compensation by adapting a normal-exponential convolution model. Unwanted technical variation, from sources such as well effects, is then removed using a log-normal model with plate, column, and row factors, after which infinity markers are imputed using the informative backbone markers as predictors. The completed dataset can then be used for clustering and other statistical analyses. Additionally, MAPFX can be used to normalise data from FFC assays as well. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'MAssively Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massively-Parallel Cytometry Experiments' + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mapfx", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, testthat +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - r-base + - r-circlize + - r-cowplot + - r-e1071 + - r-ggplot2 + - r-glmnetutils + - r-gtools + - r-icellr + - r-igraph + - r-pbapply + - r-rcolorbrewer + - r-reshape2 + - r-rfast + - r-stringr + - r-uwot + - r-xgboost + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - r-base + - r-circlize + - r-cowplot + - r-e1071 + - r-ggplot2 + - r-glmnetutils + - r-gtools + - r-icellr + - r-igraph + - r-pbapply + - r-rcolorbrewer + - r-reshape2 + - r-rfast + - r-stringr + - r-uwot + - r-xgboost + +source: + md5: 9d71addcff5b12f2961af7a87ba796ac + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-mapredictdsc/meta.yaml b/recipes/bioconductor-mapredictdsc/meta.yaml index 88e0feda89173..34433c0f6d3ec 100644 --- a/recipes/bioconductor-mapredictdsc/meta.yaml +++ b/recipes/bioconductor-mapredictdsc/meta.yaml @@ -1,34 +1,45 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "maPredictDSC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements the classification pipeline of the best overall team (Team221) in the IMPROVER Diagnostic Signature Challenge. Additional functionality is added to compare 27 combinations of data preprocessing, feature selection and classifier types. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Diagnostic Signature Challenge' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b2a491a7c799fcc0efcaed0b3067aa66 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mapredictdsc", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:mapredictdsc + - doi:10.1093/bioinformatics/btt492 + parent_recipe: + name: bioconductor-mapredictdsc + path: recipes/bioconductor-mapredictdsc + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: parallel requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-gcrma >=2.74.0,<2.75.0' - - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-lungcanceracvssccgeo >=1.38.0,<1.39.0' - - 'bioconductor-roc >=1.78.0,<1.79.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-gcrma >=2.78.0,<2.79.0 + - bioconductor-hgu133plus2.db >=3.13.0,<3.14.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-lungcanceracvssccgeo >=1.42.0,<1.43.0 + - bioconductor-roc >=1.82.0,<1.83.0 - r-base - r-caret - r-class @@ -36,34 +47,29 @@ requirements: - r-mass - r-rocr run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-gcrma >=2.74.0,<2.75.0' - - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-lungcanceracvssccgeo >=1.38.0,<1.39.0' - - 'bioconductor-roc >=1.78.0,<1.79.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-gcrma >=2.78.0,<2.79.0 + - bioconductor-hgu133plus2.db >=3.13.0,<3.14.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-lungcanceracvssccgeo >=1.42.0,<1.43.0 + - bioconductor-roc >=1.82.0,<1.83.0 - r-base - r-caret - r-class - r-e1071 - r-mass - r-rocr + +source: + md5: 82667d2efe4e487d74f046e066000822 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Diagnostic Signature Challenge' - description: 'This package implements the classification pipeline of the best overall team (Team221) in the IMPROVER Diagnostic Signature Challenge. Additional functionality is added to compare 27 combinations of data preprocessing, feature selection and classifier types.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:mapredictdsc - - doi:10.1093/bioinformatics/btt492 - parent_recipe: - name: bioconductor-mapredictdsc - path: recipes/bioconductor-mapredictdsc - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mapscape/meta.yaml b/recipes/bioconductor-mapscape/meta.yaml index d0af3af41f6ed..65a623330e806 100644 --- a/recipes/bioconductor-mapscape/meta.yaml +++ b/recipes/bioconductor-mapscape/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "mapscape" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dc197aa43e86dc49fef0d85d2ead252c +about: + description: 'MapScape integrates clonal prevalence, clonal hierarchy, anatomic and mutational information to provide interactive visualization of spatial clonal evolution. There are four inputs to MapScape: (i) the clonal phylogeny, (ii) clonal prevalences, (iii) an image reference, which may be a medical image or drawing and (iv) pixel locations for each sample on the referenced image. Optionally, MapScape can accept a data table of mutations for each clone and their variant allele frequencies in each sample. The output of MapScape consists of a cropped anatomical image surrounded by two representations of each tumour sample. The first, a cellular aggregate, visually displays the prevalence of each clone. The second shows a skeleton of the clonal phylogeny while highlighting only those clones present in the sample. Together, these representations enable the analyst to visualize the distribution of clones throughout anatomic space.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: mapscape build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mapscape", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: - r-base - - 'r-base64enc >=0.1-3' - - 'r-htmlwidgets >=0.5' - - 'r-jsonlite >=0.9.19' - - 'r-stringr >=1.0.0' + - r-base64enc >=0.1-3 + - r-htmlwidgets >=0.5 + - r-jsonlite >=0.9.19 + - r-stringr >=1.0.0 run: - r-base - - 'r-base64enc >=0.1-3' - - 'r-htmlwidgets >=0.5' - - 'r-jsonlite >=0.9.19' - - 'r-stringr >=1.0.0' + - r-base64enc >=0.1-3 + - r-htmlwidgets >=0.5 + - r-jsonlite >=0.9.19 + - r-stringr >=1.0.0 +source: + md5: 772729f3de7a3a1dacc272002a80bc46 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: mapscape - description: 'MapScape integrates clonal prevalence, clonal hierarchy, anatomic and mutational information to provide interactive visualization of spatial clonal evolution. There are four inputs to MapScape: (i) the clonal phylogeny, (ii) clonal prevalences, (iii) an image reference, which may be a medical image or drawing and (iv) pixel locations for each sample on the referenced image. Optionally, MapScape can accept a data table of mutations for each clone and their variant allele frequencies in each sample. The output of MapScape consists of a cropped anatomical image surrounded by two representations of each tumour sample. The first, a cellular aggregate, visually displays the prevalence of each clone. The second shows a skeleton of the clonal phylogeny while highlighting only those clones present in the sample. Together, these representations enable the analyst to visualize the distribution of clones throughout anatomic space.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-maqcexpression4plex/meta.yaml b/recipes/bioconductor-maqcexpression4plex/meta.yaml index 58945237d3ad0..fee5992f1716e 100644 --- a/recipes/bioconductor-maqcexpression4plex/meta.yaml +++ b/recipes/bioconductor-maqcexpression4plex/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "maqcExpression4plex" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8312b7fbcba763a33630effb8c3b5f10 +about: + description: Data from human (HG18) 4plex NimbleGen array. It has 24k genes with 3 60mer probes per gene. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Sample Expression Data - MAQC / HG18 - NimbleGen build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-maqcexpression4plex", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: oligo, pdInfoBuilder requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 898e52d569cdc046e620e674ece0104f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL - summary: 'Sample Expression Data - MAQC / HG18 - NimbleGen' - description: 'Data from human (HG18) 4plex NimbleGen array. It has 24k genes with 3 60mer probes per gene.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-maqcexpression4plex/post-link.sh b/recipes/bioconductor-maqcexpression4plex/post-link.sh index 8a868702a088b..f6fef4c056844 100644 --- a/recipes/bioconductor-maqcexpression4plex/post-link.sh +++ b/recipes/bioconductor-maqcexpression4plex/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "maqcexpression4plex-1.46.0" +installBiocDataPackage.sh "maqcexpression4plex-1.50.0" diff --git a/recipes/bioconductor-maqcsubset/meta.yaml b/recipes/bioconductor-maqcsubset/meta.yaml index 4f5f9467649c3..19ab23c0ab6d7 100644 --- a/recipes/bioconductor-maqcsubset/meta.yaml +++ b/recipes/bioconductor-maqcsubset/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "MAQCsubset" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5757c11a1af2150b8fd17c3a8b8b0c0c +about: + description: Data Package automatically created on Sun Nov 19 15:59:29 2006. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: 'Experimental Data Package: MAQCsubset' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-maqcsubset", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: genefilter, codelink requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-lumi >=2.58.0,<2.59.0 - r-base run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-lumi >=2.58.0,<2.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c65a03cafbb8d0d6a644a491d0516f7a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Experimental Data Package: MAQCsubset' - description: 'Data Package automatically created on Sun Nov 19 15:59:29 2006.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-maqcsubset/post-link.sh b/recipes/bioconductor-maqcsubset/post-link.sh index 2e61448c5748c..ba45f02153341 100644 --- a/recipes/bioconductor-maqcsubset/post-link.sh +++ b/recipes/bioconductor-maqcsubset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "maqcsubset-1.40.0" +installBiocDataPackage.sh "maqcsubset-1.44.0" diff --git a/recipes/bioconductor-mariner/meta.yaml b/recipes/bioconductor-mariner/meta.yaml index faa6324855fb2..1a4306692dacb 100644 --- a/recipes/bioconductor-mariner/meta.yaml +++ b/recipes/bioconductor-mariner/meta.yaml @@ -1,40 +1,43 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "mariner" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for manipulating paired ranges and working with Hi-C data in R. Functionality includes manipulating/merging paired regions, generating paired ranges, extracting/aggregating interactions from `.hic` files, and visualizing the results. Designed for compatibility with plotgardener for visualization. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'Mariner: Explore the Hi-Cs' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6ed30878d03b8a17e8e7c4ee17218893 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mariner", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat (>= 3.0.0), dplyr, rmarkdown, ExperimentHub, marinerData requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-plotgardener >=1.8.0,<1.9.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-plotgardener >=1.12.0,<1.13.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-abind - r-assertthat - r-base @@ -48,21 +51,22 @@ requirements: - r-purrr - r-rcolorbrewer - r-rlang - - 'r-strawr >=0.0.91' + - r-strawr >=0.0.91 + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-plotgardener >=1.8.0,<1.9.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-plotgardener >=1.12.0,<1.13.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-abind - r-assertthat - r-base @@ -76,14 +80,17 @@ requirements: - r-purrr - r-rcolorbrewer - r-rlang - - 'r-strawr >=0.0.91' + - r-strawr >=0.0.91 + +source: + md5: 90a36f8615cf24c1fca3a47bd87d756c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Mariner: Explore the Hi-Cs' - description: 'Tools for manipulating paired ranges and working with Hi-C data in R. Functionality includes manipulating/merging paired regions, generating paired ranges, extracting/aggregating interactions from `.hic` files, and visualizing the results. Designed for compatibility with plotgardener for visualization.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-marinerdata/meta.yaml b/recipes/bioconductor-marinerdata/meta.yaml index 1f58a93bd6ba5..bdf65f5938f0f 100644 --- a/recipes/bioconductor-marinerdata/meta.yaml +++ b/recipes/bioconductor-marinerdata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "marinerData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7875113ebb6baaaed6eb6fc762ba92ca +about: + description: Subsampled Hi-C in HEK cells expressing the NHA9 fusion with an F to S mutated IDR ("FS") or without any mutations to the IDR ("Wildtype" or "WT"). These files are used for testing mariner functions and some examples. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: ExperimentHub data for the mariner package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-marinerdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a107161ab0d78f794f5088aa17e219bc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'ExperimentHub data for the mariner package' - description: 'Subsampled Hi-C in HEK cells expressing the NHA9 fusion with an F to S mutated IDR ("FS") or without any mutations to the IDR ("Wildtype" or "WT"). These files are used for testing mariner functions and some examples.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-marinerdata/post-link.sh b/recipes/bioconductor-marinerdata/post-link.sh index a1f63c4a9a63d..e0c4eb8377953 100644 --- a/recipes/bioconductor-marinerdata/post-link.sh +++ b/recipes/bioconductor-marinerdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "marinerdata-1.2.0" +installBiocDataPackage.sh "marinerdata-1.6.0" diff --git a/recipes/bioconductor-marr/meta.yaml b/recipes/bioconductor-marr/meta.yaml index cb6168d37a922..eaba69442749e 100644 --- a/recipes/bioconductor-marr/meta.yaml +++ b/recipes/bioconductor-marr/meta.yaml @@ -1,28 +1,34 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "marr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: marr (Maximum Rank Reproducibility) is a nonparametric approach that detects reproducible signals using a maximal rank statistic for high-dimensional biological data. In this R package, we implement functions that measures the reproducibility of features per sample pair and sample pairs per feature in high-dimensional biological replicate experiments. The user-friendly plot functions in this package also plot histograms of the reproducibility of features per sample pair and sample pairs per feature. Furthermore, our approach also allows the users to select optimal filtering threshold values for the identification of reproducible features and sample pairs based on output visualization checks (histograms). This package also provides the subset of data filtered by reproducible features and/or sample pairs. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Maximum rank reproducibility -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3b839d77065c34ddb5f5c2a8eee277ea build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-marr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat, covr requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -32,25 +38,24 @@ requirements: - libblas - liblapack run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 - r-magrittr - r-rcpp - r-rlang - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 7a46f4aa55fc69f9620700c0021981fc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Maximum rank reproducibility' - description: 'marr (Maximum Rank Reproducibility) is a nonparametric approach that detects reproducible signals using a maximal rank statistic for high-dimensional biological data. In this R package, we implement functions that measures the reproducibility of features per sample pair and sample pairs per feature in high-dimensional biological replicate experiments. The user-friendly plot functions in this package also plot histograms of the reproducibility of features per sample pair and sample pairs per feature. Furthermore, our approach also allows the users to select optimal filtering threshold values for the identification of reproducible features and sample pairs based on output visualization checks (histograms). This package also provides the subset of data filtered by reproducible features and/or sample pairs.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-marray/meta.yaml b/recipes/bioconductor-marray/meta.yaml index d4701902cbd9a..47be28ddaa9b9 100644 --- a/recipes/bioconductor-marray/meta.yaml +++ b/recipes/bioconductor-marray/meta.yaml @@ -1,41 +1,22 @@ -{% set version = "1.80.0" %} +{% set version = "1.84.0" %} {% set name = "marray" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Exploratory analysis for two-color spotted microarray data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 569b373e346d36964430d249d075cf07 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-marray", max_pin="x.x") }}' - noarch: generic -# Suggests: tkWidgets -requirements: - host: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - r-base - run: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Exploratory analysis for two-color spotted microarray data' - description: 'Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + extra: identifiers: - biotools:marray @@ -45,3 +26,28 @@ extra: path: recipes/bioconductor-marray version: 1.58.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: tkWidgets +requirements: + host: + - bioconductor-limma >=3.62.0,<3.63.0 + - r-base + run: + - bioconductor-limma >=3.62.0,<3.63.0 + - r-base + +source: + md5: 14968534582d73d85a4e171a01a5b028 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-martini/meta.yaml b/recipes/bioconductor-martini/meta.yaml index 59fd53e07ccc9..fe69995614e7c 100644 --- a/recipes/bioconductor-martini/meta.yaml +++ b/recipes/bioconductor-martini/meta.yaml @@ -1,61 +1,66 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "martini" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: martini deals with the low power inherent to GWAS studies by using prior knowledge represented as a network. SNPs are the vertices of the network, and the edges represent biological relationships between them (genomic adjacency, belonging to the same gene, physical interaction between protein products). The network is scanned using SConES, which looks for groups of SNPs maximally associated with the phenotype, that form a close subnetwork. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: GWAS Incorporating Networks -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 85e3366daf7ac24c0f50261fafe8b274 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-martini", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:martini + - usegalaxy-eu:martini + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: biomaRt (>= 2.34.1), circlize (>= 0.4.11), STRINGdb (>= 2.2.0), httr (>= 1.2.1), IRanges (>= 2.8.2), S4Vectors (>= 0.12.2), knitr, testthat, readr, rmarkdown requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - bioconductor-snpstats >=1.56.0,<1.57.0 - r-base - - 'r-igraph >=1.0.1' + - r-igraph >=1.0.1 - r-matrix - - 'r-memoise >=2.0.0' - - 'r-rcpp >=0.12.8' - - 'r-rcppeigen >=0.3.3.5.0' + - r-memoise >=2.0.0 + - r-rcpp >=0.12.8 + - r-rcppeigen >=0.3.3.5.0 - libblas - liblapack run: - - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - bioconductor-snpstats >=1.56.0,<1.57.0 - r-base - - 'r-igraph >=1.0.1' + - r-igraph >=1.0.1 - r-matrix - - 'r-memoise >=2.0.0' - - 'r-rcpp >=0.12.8' - - 'r-rcppeigen >=0.3.3.5.0' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-memoise >=2.0.0 + - r-rcpp >=0.12.8 + - r-rcppeigen >=0.3.3.5.0 + +source: + md5: 51f7d27f462e045af0b38101d05fc03f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'GWAS Incorporating Networks' - description: 'martini deals with the low power inherent to GWAS studies by using prior knowledge represented as a network. SNPs are the vertices of the network, and the edges represent biological relationships between them (genomic adjacency, belonging to the same gene, physical interaction between protein products). The network is scanned using SConES, which looks for groups of SNPs maximally associated with the phenotype, that form a close subnetwork.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} - - usegalaxy-eu:{{ name|lower }} + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-maser/meta.yaml b/recipes/bioconductor-maser/meta.yaml index 984e5476ff7d0..dbc1f4a1b568a 100644 --- a/recipes/bioconductor-maser/meta.yaml +++ b/recipes/bioconductor-maser/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "maser" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events generated by rMATS. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Mapping Alternative Splicing Events to pRoteins -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 43be20847a05369476ccdb91cdd6ad4e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-maser", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocStyle, AnnotationHub requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-data.table - r-dplyr @@ -35,25 +37,28 @@ requirements: - r-ggplot2 - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-data.table - r-dplyr - r-dt - r-ggplot2 - r-reshape2 + +source: + md5: 3d6656a6fba252ab4aec75511aa696d5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Mapping Alternative Splicing Events to pRoteins' - description: 'This package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events generated by rMATS.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-masigpro/meta.yaml b/recipes/bioconductor-masigpro/meta.yaml index 92ad4b2047ab2..2a7c12d786ae2 100644 --- a/recipes/bioconductor-masigpro/meta.yaml +++ b/recipes/bioconductor-masigpro/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "maSigPro" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Significant Gene Expression Profile Differences in Time Course Gene Expression Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ab91a6a10122c6d1f28fee40be32c2b8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-masigpro", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:masigpro + - doi:10.1093/bioinformatics/btu333 + parent_recipe: + name: bioconductor-masigpro + path: recipes/bioconductor-masigpro + version: 1.52.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-mass - r-mclust - r-venn run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-mass - r-mclust - r-venn + +source: + md5: 32c1a89c087b895aa37bdf79a9036f2a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Significant Gene Expression Profile Differences in Time Course Gene Expression Data' - description: 'maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:masigpro - - doi:10.1093/bioinformatics/btu333 - parent_recipe: - name: bioconductor-masigpro - path: recipes/bioconductor-masigpro - version: 1.52.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-maskbad/meta.yaml b/recipes/bioconductor-maskbad/meta.yaml index e7cfd10db732a..c43aea35fbacf 100644 --- a/recipes/bioconductor-maskbad/meta.yaml +++ b/recipes/bioconductor-maskbad/meta.yaml @@ -1,43 +1,22 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "maskBAD" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package includes functions to analyze and mask microarray expression data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Masking probes with binding affinity differences -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a5fc8482a4370f32fde7bc2b3e302c77 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-maskbad", max_pin="x.x") }}' - noarch: generic -# Suggests: hgu95av2probe, hgu95av2cdf -requirements: - host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-gcrma >=2.74.0,<2.75.0' - - r-base - run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-gcrma >=2.74.0,<2.75.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Masking probes with binding affinity differences' - description: 'Package includes functions to analyze and mask microarray expression data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:maskbad @@ -47,3 +26,30 @@ extra: path: recipes/bioconductor-maskbad version: 1.24.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: hgu95av2probe, hgu95av2cdf +requirements: + host: + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-gcrma >=2.78.0,<2.79.0 + - r-base + run: + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-gcrma >=2.78.0,<2.79.0 + - r-base + +source: + md5: ab35a6e1afaadcd2f3db4d4fcb05630f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-massarray/meta.yaml b/recipes/bioconductor-massarray/meta.yaml index 0afae7ac8c0e7..6af6b875604c2 100644 --- a/recipes/bioconductor-massarray/meta.yaml +++ b/recipes/bioconductor-massarray/meta.yaml @@ -1,38 +1,20 @@ -{% set version = "1.54.0" %} +{% set version = "1.58.0" %} {% set name = "MassArray" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 028fea456ce2e5b3820ad6dc0d1989c1 +about: + description: This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom's MassArray platform. The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package. Additionally, automatic SNP-detection can be used to flag potentially confounded data from specific CG sites. Visualization includes barplots of methylation data as well as UCSC Genome Browser-compatible BED tracks. Multiple assays can be positionally combined for integrated analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Analytical Tools for MassArray Data build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-massarray", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Analytical Tools for MassArray Data' - description: 'This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom''s MassArray platform. The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package. Additionally, automatic SNP-detection can be used to flag potentially confounded data from specific CG sites. Visualization includes barplots of methylation data as well as UCSC Genome Browser-compatible BED tracks. Multiple assays can be positionally combined for integrated analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: identifiers: - biotools:massarray @@ -41,4 +23,22 @@ extra: name: bioconductor-massarray path: recipes/bioconductor-massarray version: 1.34.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +requirements: + host: + - r-base + run: + - r-base +source: + md5: ef8f67686045bc38410b3a22386a4993 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-massir/meta.yaml b/recipes/bioconductor-massir/meta.yaml index dbf9731aa509d..503724263ebf6 100644 --- a/recipes/bioconductor-massir/meta.yaml +++ b/recipes/bioconductor-massir/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "massiR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Predicts the sex of samples in gene expression microarray datasets + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'massiR: MicroArray Sample Sex Identifier' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f2dda0fb78f776b416af77100e902b55 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-massir", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:massir + parent_recipe: + name: bioconductor-massir + path: recipes/bioconductor-massir + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: biomaRt, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-cluster - r-diptest - r-gplots run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-cluster - r-diptest - r-gplots + +source: + md5: 0ae4c4073d8e5c456a706d4c843193e0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'massiR: MicroArray Sample Sex Identifier' - description: 'Predicts the sex of samples in gene expression microarray datasets' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:massir - parent_recipe: - name: bioconductor-massir - path: recipes/bioconductor-massir - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-massspecwavelet/meta.yaml b/recipes/bioconductor-massspecwavelet/meta.yaml index f8ad82d1d808a..4a087c51446c9 100644 --- a/recipes/bioconductor-massspecwavelet/meta.yaml +++ b/recipes/bioconductor-massspecwavelet/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.68.0" %} +{% set version = "1.72.0" %} {% set name = "MassSpecWavelet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Peak Detection in Mass Spectrometry data is one of the important preprocessing steps. The performance of peak detection affects subsequent processes, including protein identification, profile alignment and biomarker identification. Using Continuous Wavelet Transform (CWT), this package provides a reliable algorithm for peak detection that does not require any type of smoothing or previous baseline correction method, providing more consistent results for different spectra. See = 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Peak Detection for Mass Spectrometry data using wavelet-based algorithms -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 387636ea7c674fe339c56a8af3458f8a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-massspecwavelet", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:massspecwavelet + parent_recipe: + name: bioconductor-massspecwavelet + path: recipes/bioconductor-massspecwavelet + version: 1.46.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: signal, waveslim, BiocStyle, knitr, rmarkdown, RUnit, bench requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: 354eea90e997824d5812d14c0fc0a588 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'Peak Detection for Mass Spectrometry data using wavelet-based algorithms' - description: 'Peak Detection in Mass Spectrometry data is one of the important preprocessing steps. The performance of peak detection affects subsequent processes, including protein identification, profile alignment and biomarker identification. Using Continuous Wavelet Transform (CWT), this package provides a reliable algorithm for peak detection that does not require any type of smoothing or previous baseline correction method, providing more consistent results for different spectra. See = 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Model-based Analysis of Single Cell Transcriptomics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b2d5c6a33243cdf9c2e4440ba4bf1da build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mast", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:mast + - doi:10.1186/s13059-015-0844-5 + parent_recipe: + name: bioconductor-mast + path: recipes/bioconductor-mast + version: 1.6.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, lme4(>= 1.0), blme, roxygen2(> 6.0.0), numDeriv, car, gdata, lattice, GGally, GSEABase, NMF, TxDb.Hsapiens.UCSC.hg19.knownGene, rsvd, limma, RColorBrewer, BiocStyle, scater, DelayedArray, HDF5Array, zinbwave, dplyr requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-abind - r-base - r-data.table @@ -37,11 +48,11 @@ requirements: - r-reshape2 - r-stringr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-abind - r-base - r-data.table @@ -51,21 +62,16 @@ requirements: - r-progress - r-reshape2 - r-stringr + +source: + md5: 107286d9011330ac96cf5f6a1c0662a8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL(>= 2)' - summary: 'Model-based Analysis of Single Cell Transcriptomics' - description: 'Methods and models for handling zero-inflated single cell assay data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:mast - - doi:10.1186/s13059-015-0844-5 - parent_recipe: - name: bioconductor-mast - path: recipes/bioconductor-mast - version: 1.6.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mastr/meta.yaml b/recipes/bioconductor-mastr/meta.yaml index d13e915d95790..9df0a3ac9a265 100644 --- a/recipes/bioconductor-mastr/meta.yaml +++ b/recipes/bioconductor-mastr/meta.yaml @@ -1,36 +1,38 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "mastR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: mastR is an R package designed for automated screening of signatures of interest for specific research questions. The package is developed for generating refined lists of signature genes from multiple group comparisons based on the results from edgeR and limma differential expression (DE) analysis workflow. It also takes into account the background noise of tissue-specificity, which is often ignored by other marker generation tools. This package is particularly useful for the identification of group markers in various biological and medical applications, including cancer research and developmental biology. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Markers Automated Screening Tool in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: be4cab3fb29097cb5dd34ee7ba1ce228 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mastr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocManager, BiocStyle, BisqueRNA, clusterProfiler, ComplexHeatmap, depmap, enrichplot, ggrepel, ggvenn, gridExtra, jsonlite, knitr, rmarkdown, RobustRankAggreg, rvest, scuttle, singscore, splatter, testthat (>= 3.0.0), UpSetR requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-msigdb >=1.10.0,<1.11.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-msigdb >=1.14.0,<1.15.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -40,15 +42,15 @@ requirements: - r-seuratobject - r-tidyr run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-msigdb >=1.10.0,<1.11.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-msigdb >=1.14.0,<1.15.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -57,13 +59,16 @@ requirements: - r-patchwork - r-seuratobject - r-tidyr + +source: + md5: ef996ab3532927e3c4f825aac2d741e1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Markers Automated Screening Tool in R' - description: 'mastR is an R package designed for automated screening of signatures of interest for specific research questions. The package is developed for generating refined lists of signature genes from multiple group comparisons based on the results from edgeR and limma differential expression (DE) analysis workflow. It also takes into account the background noise of tissue-specificity, which is often ignored by other marker generation tools. This package is particularly useful for the identification of group markers in various biological and medical applications, including cancer research and developmental biology.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-matchbox/meta.yaml b/recipes/bioconductor-matchbox/meta.yaml index 0cb5c684cdaaa..a94f1a88d9c62 100644 --- a/recipes/bioconductor-matchbox/meta.yaml +++ b/recipes/bioconductor-matchbox/meta.yaml @@ -1,35 +1,35 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "matchBox" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b6e4b10ee38f433d1bce146a089a44ec +about: + description: The matchBox package enables comparing ranked vectors of features, merging multiple datasets, removing redundant features, using CAT-plots and Venn diagrams, and computing statistical significance. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-matchbox", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base +source: + md5: fb95c93ad0608089b8d5f3f3ad20d5d6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis.' - description: 'The matchBox package enables comparing ranked vectors of features, merging multiple datasets, removing redundant features, using CAT-plots and Venn diagrams, and computing statistical significance.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-matrixgenerics/meta.yaml b/recipes/bioconductor-matrixgenerics/meta.yaml index 8438fa63d3154..a78b506413629 100644 --- a/recipes/bioconductor-matrixgenerics/meta.yaml +++ b/recipes/bioconductor-matrixgenerics/meta.yaml @@ -1,37 +1,38 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "MatrixGenerics" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 18c3a5cc993ca5c2ad48dde1813105e6 +about: + description: S4 generic functions modeled after the 'matrixStats' API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects build: - number: 3 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-matrixgenerics", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: Matrix, sparseMatrixStats, SparseArray, DelayedArray, DelayedMatrixStats, SummarizedExperiment, testthat (>= 2.1.0) requirements: host: - r-base - - 'r-matrixstats >=1.0.0' + - r-matrixstats >=1.4.1 run: - r-base - - 'r-matrixstats >=1.0.0' + - r-matrixstats >=1.4.1 +source: + md5: be0b5a464be94a86963f7c1c30c8c3da + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects' - description: 'S4 generic functions modeled after the ''matrixStats'' API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities.' + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-matrixqcvis/meta.yaml b/recipes/bioconductor-matrixqcvis/meta.yaml index 39bd88b0aa423..a571a283230c6 100644 --- a/recipes/bioconductor-matrixqcvis/meta.yaml +++ b/recipes/bioconductor-matrixqcvis/meta.yaml @@ -1,89 +1,100 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "MatrixQCvis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval. We present here the MatrixQCvis package, which provides shiny-based interactive visualization of data quality metrics at the per-sample and per-feature level. It is broadly applicable to quantitative omics data types that come in matrix-like format (features x samples). It enables the detection of low-quality samples, drifts, outliers and batch effects in data sets. Visualizations include amongst others bar- and violin plots of the (count/intensity) values, mean vs standard deviation plots, MA plots, empirical cumulative distribution function (ECDF) plots, visualizations of the distances between samples, and multiple types of dimension reduction plots. Furthermore, MatrixQCvis allows for differential expression analysis based on the limma (moderated t-tests) and proDA (Wald tests) packages. MatrixQCvis builds upon the popular Bioconductor SummarizedExperiment S4 class and enables thus the facile integration into existing workflows. The package is especially tailored towards metabolomics and proteomics mass spectrometry data, but also allows to assess the data quality of other data types that can be represented in a SummarizedExperiment object. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Shiny-based interactive data-quality exploration for omics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 21f91ace512d3afadd5fe42e93ba7fe9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-matrixqcvis", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocGenerics (>= 0.37.4), BiocStyle (>= 2.19.2), hexbin (>= 1.28.2), jpeg (>= 0.1-10), knitr (>= 1.33), statmod (>= 1.5.0), testthat (>= 3.0.2) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocGenerics (>= 0.37.4), BiocStyle (>= 2.19.2), hexbin (>= 1.28.2), httr (>= 1.4.7), jpeg (>= 0.1-10), knitr (>= 1.33), statmod (>= 1.5.0), testthat (>= 3.0.2) requirements: + host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-proda >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-proda >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-base - - 'r-dplyr >=1.0.5' - - 'r-ggplot2 >=3.3.3' - - 'r-hmisc >=4.5-0' - - 'r-htmlwidgets >=1.5.3' - - 'r-imputelcmd >=2.0' - - 'r-mass >=7.3-58.1' - - 'r-plotly >=4.9.3' - - 'r-rlang >=0.4.10' - - 'r-rmarkdown >=2.7' - - 'r-rtsne >=0.15' - - 'r-shiny >=1.6.0' - - 'r-shinydashboard >=0.7.1' - - 'r-shinyhelper >=0.3.2' - - 'r-shinyjs >=2.0.0' - - 'r-tibble >=3.1.1' - - 'r-tidyr >=1.1.3' - - 'r-umap >=0.2.7.0' - - 'r-upsetr >=1.4.0' + - r-dplyr >=1.0.5 + - r-dt >=0.33 + - r-ggplot2 >=3.3.3 + - r-hmisc >=4.5-0 + - r-htmlwidgets >=1.5.3 + - r-imputelcmd >=2.0 + - r-mass >=7.3-58.1 + - r-plotly >=4.9.3 + - r-rlang >=0.4.10 + - r-rmarkdown >=2.7 + - r-rtsne >=0.15 + - r-shiny >=1.6.0 + - r-shinydashboard >=0.7.1 + - r-shinyhelper >=0.3.2 + - r-shinyjs >=2.0.0 + - r-tibble >=3.1.1 + - r-tidyr >=1.1.3 + - r-umap >=0.2.7.0 + - r-upsetr >=1.4.0 + run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-proda >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-proda >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-base - - 'r-dplyr >=1.0.5' - - 'r-ggplot2 >=3.3.3' - - 'r-hmisc >=4.5-0' - - 'r-htmlwidgets >=1.5.3' - - 'r-imputelcmd >=2.0' - - 'r-mass >=7.3-58.1' - - 'r-plotly >=4.9.3' - - 'r-rlang >=0.4.10' - - 'r-rmarkdown >=2.7' - - 'r-rtsne >=0.15' - - 'r-shiny >=1.6.0' - - 'r-shinydashboard >=0.7.1' - - 'r-shinyhelper >=0.3.2' - - 'r-shinyjs >=2.0.0' - - 'r-tibble >=3.1.1' - - 'r-tidyr >=1.1.3' - - 'r-umap >=0.2.7.0' - - 'r-upsetr >=1.4.0' + - r-dplyr >=1.0.5 + - r-dt >=0.33 + - r-ggplot2 >=3.3.3 + - r-hmisc >=4.5-0 + - r-htmlwidgets >=1.5.3 + - r-imputelcmd >=2.0 + - r-mass >=7.3-58.1 + - r-plotly >=4.9.3 + - r-rlang >=0.4.10 + - r-rmarkdown >=2.7 + - r-rtsne >=0.15 + - r-shiny >=1.6.0 + - r-shinydashboard >=0.7.1 + - r-shinyhelper >=0.3.2 + - r-shinyjs >=2.0.0 + - r-tibble >=3.1.1 + - r-tidyr >=1.1.3 + - r-umap >=0.2.7.0 + - r-upsetr >=1.4.0 + +source: + md5: 83cc9e7b8aea4637ea87723a51ab28d3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Shiny-based interactive data-quality exploration for omics data' - description: 'Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval. We present here the MatrixQCvis package, which provides shiny-based interactive visualization of data quality metrics at the per-sample and per-feature level. It is broadly applicable to quantitative omics data types that come in matrix-like format (features x samples). It enables the detection of low-quality samples, drifts, outliers and batch effects in data sets. Visualizations include amongst others bar- and violin plots of the (count/intensity) values, mean vs standard deviation plots, MA plots, empirical cumulative distribution function (ECDF) plots, visualizations of the distances between samples, and multiple types of dimension reduction plots. Furthermore, MatrixQCvis allows for differential expression analysis based on the limma (moderated t-tests) and proDA (Wald tests) packages. MatrixQCvis builds upon the popular Bioconductor SummarizedExperiment S4 class and enables thus the facile integration into existing workflows. The package is especially tailored towards metabolomics and proteomics mass spectrometry data, but also allows to assess the data quality of other data types that can be represented in a SummarizedExperiment object.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-matrixrider/build_failure.osx-64.yaml b/recipes/bioconductor-matrixrider/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..7aeef645af291 --- /dev/null +++ b/recipes/bioconductor-matrixrider/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: d9a3087a221cb9071a9945fa608c90fb96477c1b9da1a89c0164feb173537483 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Encountered problems while solving: + - nothing provides bioconductor-annotate >=1.84.0,<1.85.0 needed by bioconductor-cner-1.42.0-r44h2f393c0_0 + + Could not solve for environment specs + The following package could not be installed + bioconductor-tfbstools >=1.44.0,<1.45.0 is not installable because it requires + bioconductor-cner >=1.42.0,<1.43.0 , which requires + bioconductor-annotate >=1.84.0,<1.85.0 , which does not exist (perhaps a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-cner==1.42.0=r44h2f393c0_0"), MatchSpec(">=1.84.0,<1.85.0")} + Encountered problems while solving: + - nothing provides bioconductor-annotate >=1.84.0,<1.85.0 needed by bioconductor-cner-1.42.0-r44h2f393c0_0 + + Could not solve for environment specs + The following package could not be installed + bioconductor-tfbstools >=1.44.0,<1.45.0 is not installable because it requires + bioconductor-cner >=1.42.0,<1.43.0 , which requires + bioconductor-annotate >=1.84.0,<1.85.0 , which does not exist (perhaps a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-cner==1.42.0=r44h2f393c0_0"), MatchSpec(">=1.84.0,<1.85.0")} + Encountered problems while solving: + - nothing provides bioconductor-annotate >=1.84.0,<1.85.0 needed by bioconductor-cner-1.42.0-r44h2f393c0_0 + + Could not solve for environment specs + The following package could not be installed + bioconductor-tfbstools >=1.44.0,<1.45.0 is not installable because it requires + bioconductor-cner >=1.42.0,<1.43.0 , which requires + bioconductor-annotate >=1.84.0,<1.85.0 , which does not exist (perhaps a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-matrixrider/meta.yaml b/recipes/bioconductor-matrixrider/meta.yaml index 89be4c1d9d40e..4091b999ebadd 100644 --- a/recipes/bioconductor-matrixrider/meta.yaml +++ b/recipes/bioconductor-matrixrider/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "MatrixRider" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Calculates a single number for a whole sequence that reflects the propensity of a DNA binding protein to interact with it. The DNA binding protein has to be described with a PFM matrix, for example gotten from Jaspar. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Obtain total affinity and occupancies for binding site matrices on a given sequence -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2de2ee8befc7dcf6b84ea6630a0c089f build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-matrixrider", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, BiocStyle, JASPAR2014 requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-tfbstools >=1.44.0,<1.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-tfbstools >=1.44.0,<1.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: c692494f512007aa6e8508555a2f4a70 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Obtain total affinity and occupancies for binding site matrices on a given sequence' - description: 'Calculates a single number for a whole sequence that reflects the propensity of a DNA binding protein to interact with it. The DNA binding protein has to be described with a PFM matrix, for example gotten from Jaspar.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-matter/meta.yaml b/recipes/bioconductor-matter/meta.yaml index 631bf8eaa0512..af956f74ff39e 100644 --- a/recipes/bioconductor-matter/meta.yaml +++ b/recipes/bioconductor-matter/meta.yaml @@ -1,63 +1,70 @@ -{% set version = "2.4.0" %} +{% set version = "2.8.0" %} {% set name = "matter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Toolbox for larger-than-memory scientific computing and visualization, providing efficient out-of-core data structures using files or shared memory, for dense and sparse vectors, matrices, and arrays, with applications to nonuniformly sampled signals and images. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 | file LICENSE + license_file: LICENSE + summary: Out-of-core statistical computing and signal processing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 08919bc0df5442e0916ee7cffbc23003 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-matter", max_pin="x.x") }}' -# Suggests: BiocStyle, knitr, testthat + +extra: + identifiers: + - biotools:matter + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-matter + path: recipes/bioconductor-matter + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, testthat, plotly requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 - r-base - - r-biglm + - r-bh - r-digest - r-irlba - r-matrix - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 - r-base - - r-biglm + - r-bh - r-digest - r-irlba - r-matrix - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: a88ddbb17b4cee347e387880d46e6658 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Out-of-memory dense and sparse signal arrays' - description: 'Memory-efficient file-based data structures for dense and sparse vectors, matrices, arrays, and lists with applications to nonuniformly sampled signals and spectra.' -extra: - identifiers: - - biotools:matter - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-matter - path: recipes/bioconductor-matter - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mbamethyl/meta.yaml b/recipes/bioconductor-mbamethyl/meta.yaml index d76d4dc6cc97c..c0de4cb76076c 100644 --- a/recipes/bioconductor-mbamethyl/meta.yaml +++ b/recipes/bioconductor-mbamethyl/meta.yaml @@ -1,37 +1,19 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "MBAmethyl" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0b6ac0d76525c156606d08bcbf606709 +about: + description: This package provides a function for reconstructing DNA methylation values from raw measurements. It iteratively implements the group fused lars to smooth related-by-location methylation values and the constrained least squares to remove probe affinity effect across multiple sequences. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Model-based analysis of DNA methylation data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mbamethyl", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Model-based analysis of DNA methylation data' - description: 'This package provides a function for reconstructing DNA methylation values from raw measurements. It iteratively implements the group fused lars to smooth related-by-location methylation values and the constrained least squares to remove probe affinity effect across multiple sequences.' extra: identifiers: - biotools:mbamethyl @@ -40,4 +22,22 @@ extra: name: bioconductor-mbamethyl path: recipes/bioconductor-mbamethyl version: 1.14.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +requirements: + host: + - r-base + run: + - r-base +source: + md5: c2a206e48019dbb7e521593e2d2992e6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mbased/meta.yaml b/recipes/bioconductor-mbased/meta.yaml index 02ada98f3ea95..d684f5dcb3048 100644 --- a/recipes/bioconductor-mbased/meta.yaml +++ b/recipes/bioconductor-mbased/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "MBASED" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package implements MBASED algorithm for detecting allele-specific gene expression from RNA count data, where allele counts at individual loci (SNVs) are integrated into a gene-specific measure of ASE, and utilizes simulations to appropriately assess the statistical significance of observed ASE. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 441d95c8a2670c6d5fd3488ed33aad2d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mbased", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:mbased + - doi:10.1186/s13059-014-0405-3 + parent_recipe: + name: bioconductor-mbased + path: recipes/bioconductor-mbased + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-runit run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-runit + +source: + md5: 95deb036649a95ed2a395c573c22b93c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection' - description: 'The package implements MBASED algorithm for detecting allele-specific gene expression from RNA count data, where allele counts at individual loci (SNVs) are integrated into a gene-specific measure of ASE, and utilizes simulations to appropriately assess the statistical significance of observed ASE.' -extra: - identifiers: - - biotools:mbased - - doi:10.1186/s13059-014-0405-3 - parent_recipe: - name: bioconductor-mbased - path: recipes/bioconductor-mbased - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mbcb/meta.yaml b/recipes/bioconductor-mbcb/meta.yaml index 10a541c33c679..8901f1a4200a5 100644 --- a/recipes/bioconductor-mbcb/meta.yaml +++ b/recipes/bioconductor-mbcb/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.56.0" %} +{% set version = "1.60.0" %} {% set name = "MBCB" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 51a88491b8d5872a1088def3f6113466 +about: + description: This package provides a model-based background correction method, which incorporates the negative control beads to pre-process Illumina BeadArray data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: MBCB (Model-based Background Correction for Beadarray) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mbcb", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-tcltk2 run: - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-tcltk2 +source: + md5: 083dda1a76d23a0e162baa2ed3c3da97 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'MBCB (Model-based Background Correction for Beadarray)' - description: 'This package provides a model-based background correction method, which incorporates the negative control beads to pre-process Illumina BeadArray data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mbecs/meta.yaml b/recipes/bioconductor-mbecs/meta.yaml index 027ca183cf4f5..579de50ddf335 100644 --- a/recipes/bioconductor-mbecs/meta.yaml +++ b/recipes/bioconductor-mbecs/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "MBECS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The Microbiome Batch Effect Correction Suite (MBECS) provides a set of functions to evaluate and mitigate unwated noise due to processing in batches. To that end it incorporates a host of batch correcting algorithms (BECA) from various packages. In addition it offers a correction and reporting pipeline that provides a preliminary look at the characteristics of a data-set before and after correcting for batch effects. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Evaluation and correction of batch effects in microbiome data-sets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5e7481e4bcd7fc20a2251635324035a4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mbecs", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, markdown, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-cluster - r-dplyr @@ -41,9 +42,9 @@ requirements: - r-tidyr - r-vegan run: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-cluster - r-dplyr @@ -59,12 +60,16 @@ requirements: - r-tibble - r-tidyr - r-vegan + +source: + md5: cbd4d415284fcb3e70279bb89899162e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Evaluation and correction of batch effects in microbiome data-sets' - description: 'The Microbiome Batch Effect Correction Suite (MBECS) provides a set of functions to evaluate and mitigate unwated noise due to processing in batches. To that end it incorporates a host of batch correcting algorithms (BECA) from various packages. In addition it offers a correction and reporting pipeline that provides a preliminary look at the characteristics of a data-set before and after correcting for batch effects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mbkmeans/meta.yaml b/recipes/bioconductor-mbkmeans/meta.yaml index 2f6a287d2b940..0878c77eda401 100644 --- a/recipes/bioconductor-mbkmeans/meta.yaml +++ b/recipes/bioconductor-mbkmeans/meta.yaml @@ -1,72 +1,78 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "mbkmeans" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implements the mini-batch k-means algorithm for large datasets, including support for on-disk data representation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Mini-batch K-means Clustering for Single-Cell RNA-seq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1bd55f0f927fea250caa1a8264e3013c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mbkmeans", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:mbkmeans + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData, scater, DelayedMatrixStats, bluster, knitr, testthat, rmarkdown # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-benchmarkme - r-clusterr - r-matrix - r-rcpp - - 'r-rcpparmadillo >=0.7.2' + - r-rcpparmadillo >=0.7.2 - libblas - liblapack run: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-benchmarkme - r-clusterr - r-matrix - r-rcpp - - 'r-rcpparmadillo >=0.7.2' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpparmadillo >=0.7.2 + +source: + md5: c27bacbb29b27caf53212c975408f116 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Mini-batch K-means Clustering for Single-Cell RNA-seq' - description: 'Implements the mini-batch k-means algorithm for large datasets, including support for on-disk data representation.' - license_file: LICENSE + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} \ No newline at end of file diff --git a/recipes/bioconductor-mbpcr/meta.yaml b/recipes/bioconductor-mbpcr/meta.yaml index bdcd2d19a5648..5da1f6496c6f7 100644 --- a/recipes/bioconductor-mbpcr/meta.yaml +++ b/recipes/bioconductor-mbpcr/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.56.0" %} +{% set version = "1.60.0" %} {% set name = "mBPCR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d48a3fd5a04c61ce96aa4da34d364a2 +about: + description: It contains functions for estimating the DNA copy number profile using mBPCR with the aim of detecting regions with copy number changes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Bayesian Piecewise Constant Regression for DNA copy number estimation build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mbpcr", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: xtable requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gwastools >=1.48.0,<1.49.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gwastools >=1.52.0,<1.53.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gwastools >=1.48.0,<1.49.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gwastools >=1.52.0,<1.53.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base +source: + md5: 98b189af08186dcf5449ace77edd37bd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Bayesian Piecewise Constant Regression for DNA copy number estimation' - description: 'It contains functions for estimating the DNA copy number profile using mBPCR with the aim of detecting regions with copy number changes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mbqn/meta.yaml b/recipes/bioconductor-mbqn/meta.yaml index 37d730a8cbee4..c3f7c05c3ecdc 100644 --- a/recipes/bioconductor-mbqn/meta.yaml +++ b/recipes/bioconductor-mbqn/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "2.14.0" %} +{% set version = "2.18.0" %} {% set name = "MBQN" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Modified quantile normalization for omics or other matrix-like data distorted in location and scale. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Mean/Median-balanced quantile normalization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e48e4ebcd3b69b82559496b66ca4cf44 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mbqn", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-paireddata @@ -34,10 +36,10 @@ requirements: - r-rmarkdown - r-xml2 run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-paireddata @@ -45,13 +47,16 @@ requirements: - r-rcurl - r-rmarkdown - r-xml2 + +source: + md5: b29ea005e3011f3cd678d258265e5156 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Mean/Median-balanced quantile normalization' - description: 'Modified quantile normalization for omics or other matrix-like data distorted in location and scale.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mbttest/meta.yaml b/recipes/bioconductor-mbttest/meta.yaml index a9891797e564b..a00bbe1805b2f 100644 --- a/recipes/bioconductor-mbttest/meta.yaml +++ b/recipes/bioconductor-mbttest/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "MBttest" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MBttest method was developed from beta t-test method of Baggerly et al(2003). Compared to baySeq (Hard castle and Kelly 2010), DESeq (Anders and Huber 2010) and exact test (Robinson and Smyth 2007, 2008) and the GLM of McCarthy et al(2012), MBttest is of high work efficiency,that is, it has high power, high conservativeness of FDR estimation and high stability. MBttest is suit- able to transcriptomic data, tag data, SAGE data (count data) from small samples or a few replicate libraries. It can be used to identify genes, mRNA isoforms or tags differentially expressed between two conditions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Multiple Beta t-Tests -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 35c603063456aab63ffa0ebfc67a3c16 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mbttest", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:mbttest + - doi:10.1371/journal.pone.0123658 + parent_recipe: + name: bioconductor-mbttest + path: recipes/bioconductor-mbttest + version: 1.8.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, BiocGenerics requirements: host: @@ -29,21 +40,16 @@ requirements: - r-base - r-gplots - r-gtools + +source: + md5: 7c3452a6b2d42731cc87975fa109fc80 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Multiple Beta t-Tests' - description: 'MBttest method was developed from beta t-test method of Baggerly et al(2003). Compared to baySeq (Hard castle and Kelly 2010), DESeq (Anders and Huber 2010) and exact test (Robinson and Smyth 2007, 2008) and the GLM of McCarthy et al(2012), MBttest is of high work efficiency,that is, it has high power, high conservativeness of FDR estimation and high stability. MBttest is suit- able to transcriptomic data, tag data, SAGE data (count data) from small samples or a few replicate libraries. It can be used to identify genes, mRNA isoforms or tags differentially expressed between two conditions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:mbttest - - doi:10.1371/journal.pone.0123658 - parent_recipe: - name: bioconductor-mbttest - path: recipes/bioconductor-mbttest - version: 1.8.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mcbiclust/meta.yaml b/recipes/bioconductor-mcbiclust/meta.yaml index ba83c329537ca..3edd8e27b3c5a 100644 --- a/recipes/bioconductor-mcbiclust/meta.yaml +++ b/recipes/bioconductor-mcbiclust/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "MCbiclust" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Massive correlating biclusters for gene expression data and associated methods -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dd042cb41360eec094ff9596439d3aa6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mcbiclust", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr, pander, devtools, testthat, GSVA requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - r-cluster - r-ggally @@ -33,23 +35,26 @@ requirements: - r-scales - r-wgcna run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - r-cluster - r-ggally - r-ggplot2 - r-scales - r-wgcna + +source: + md5: 660766da15e1bc39c473133cf7be9edd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Massive correlating biclusters for gene expression data and associated methods' - description: 'Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mcseadata/meta.yaml b/recipes/bioconductor-mcseadata/meta.yaml index 08f1aea183985..8bd11b8cb5eb5 100644 --- a/recipes/bioconductor-mcseadata/meta.yaml +++ b/recipes/bioconductor-mcseadata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.1" %} {% set name = "mCSEAdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11f8150e223a0e8d8fa5b9b8dedaa374 +about: + description: Data objects necessary to some mCSEA package functions. There are also example data objects to illustrate mCSEA package functionality. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Data package for mCSEA package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mcseadata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241231 +source: + md5: 1081e2c4a6e4e868c409a7ec19cb515a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Data package for mCSEA package' - description: 'Data objects necessary to some mCSEA package functions. There are also example data objects to illustrate mCSEA package functionality.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mcseadata/post-link.sh b/recipes/bioconductor-mcseadata/post-link.sh index eddebf7dac4c4..297d6a11f8117 100644 --- a/recipes/bioconductor-mcseadata/post-link.sh +++ b/recipes/bioconductor-mcseadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mcseadata-1.22.0" +installBiocDataPackage.sh "mcseadata-1.26.1" diff --git a/recipes/bioconductor-mcsurvdata/meta.yaml b/recipes/bioconductor-mcsurvdata/meta.yaml index 07bb985fda8c3..b49f00d9d9530 100644 --- a/recipes/bioconductor-mcsurvdata/meta.yaml +++ b/recipes/bioconductor-mcsurvdata/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "mcsurvdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0299258c7610f3675dc0b9f8e333eefa +about: + description: This package stores two merged expressionSet objects that contain the gene expression profile and clinical information of -a- six breast cancer cohorts and -b- four colorectal cancer cohorts. Breast cancer data are employed in the vignette of the hrunbiased package for survival analysis of gene signatures. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Meta cohort survival data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mcsurvdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9195686975c6647629ceed2276471756 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Meta cohort survival data' - description: 'This package stores two merged expressionSet objects that contain the gene expression profile and clinical information of -a- six breast cancer cohorts and -b- four colorectal cancer cohorts. Breast cancer data are employed in the vignette of the hrunbiased package for survival analysis of gene signatures.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mcsurvdata/post-link.sh b/recipes/bioconductor-mcsurvdata/post-link.sh index 2585fbcb3d43f..cc237f57b4ca6 100644 --- a/recipes/bioconductor-mcsurvdata/post-link.sh +++ b/recipes/bioconductor-mcsurvdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mcsurvdata-1.20.0" +installBiocDataPackage.sh "mcsurvdata-1.24.0" diff --git a/recipes/bioconductor-mdp/meta.yaml b/recipes/bioconductor-mdp/meta.yaml index b0c34a1dd0fdb..8ae0f0c8c75de 100644 --- a/recipes/bioconductor-mdp/meta.yaml +++ b/recipes/bioconductor-mdp/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "mdp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a947b52acd7f930a3babcdb4e429bb0c +about: + description: The Molecular Degree of Perturbation webtool quantifies the heterogeneity of samples. It takes a data.frame of omic data that contains at least two classes (control and test) and assigns a score to all samples based on how perturbed they are compared to the controls. It is based on the Molecular Distance to Health (Pankla et al. 2009), and expands on this algorithm by adding the options to calculate the z-score using the modified z-score (using median absolute deviation), change the z-score zeroing threshold, and look at genes that are most perturbed in the test versus control classes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mdp", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat, knitr, rmarkdown, fgsea, BiocManager requirements: host: @@ -29,13 +28,14 @@ requirements: - r-base - r-ggplot2 - r-gridextra +source: + md5: d888e64a082aeb561e95a1a2cb79231d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls' - description: 'The Molecular Degree of Perturbation webtool quantifies the heterogeneity of samples. It takes a data.frame of omic data that contains at least two classes (control and test) and assigns a score to all samples based on how perturbed they are compared to the controls. It is based on the Molecular Distance to Health (Pankla et al. 2009), and expands on this algorithm by adding the options to calculate the z-score using the modified z-score (using median absolute deviation), change the z-score zeroing threshold, and look at genes that are most perturbed in the test versus control classes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mdqc/meta.yaml b/recipes/bioconductor-mdqc/meta.yaml index 1ffa27337522e..eff736ea4783c 100644 --- a/recipes/bioconductor-mdqc/meta.yaml +++ b/recipes/bioconductor-mdqc/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.64.0" %} +{% set version = "1.68.0" %} {% set name = "mdqc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MDQC is a multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Mahalanobis Distance Quality Control for microarrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a9dd8adf71b5fe15b4b5b444f0b43110 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mdqc", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:mdqc + - doi:10.1093/bioinformatics/btm487 + parent_recipe: + name: bioconductor-mdqc + path: recipes/bioconductor-mdqc + version: 1.42.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -28,21 +39,16 @@ requirements: - r-base - r-cluster - r-mass + +source: + md5: f277ca29f77be3efbbc0ed040ca57c5c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'Mahalanobis Distance Quality Control for microarrays' - description: 'MDQC is a multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array''s quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:mdqc - - doi:10.1093/bioinformatics/btm487 - parent_recipe: - name: bioconductor-mdqc - path: recipes/bioconductor-mdqc - version: 1.42.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mdts/meta.yaml b/recipes/bioconductor-mdts/meta.yaml index 4f9602a0f22b3..35f4f3a173e6f 100644 --- a/recipes/bioconductor-mdts/meta.yaml +++ b/recipes/bioconductor-mdts/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "MDTS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package for the detection of de novo copy number deletions in targeted sequencing of trios with high sensitivity and positive predictive value. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Detection of de novo deletion in targeted sequencing trios -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a9ab8fa7a5e9ef7dcdb28fb553b895f6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mdts", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-stringr run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-stringr + +source: + md5: f480419541d2377398b84f7e7114a74f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Detection of de novo deletion in targeted sequencing trios' - description: 'A package for the detection of de novo copy number deletions in targeted sequencing of trios with high sensitivity and positive predictive value.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-meal/meta.yaml b/recipes/bioconductor-meal/meta.yaml index 3ab450a08d105..0fb501c016995 100644 --- a/recipes/bioconductor-meal/meta.yaml +++ b/recipes/bioconductor-meal/meta.yaml @@ -1,70 +1,75 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "MEAL" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package to integrate methylation and expression data. It can also perform methylation or expression analysis alone. Several plotting functionalities are included as well as a new region analysis based on redundancy analysis. Effect of SNPs on a region can also be estimated. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Perform methylation analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f157edf85ba036b17edb728a44e2e519 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-meal", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData, BiocStyle, rmarkdown, brgedata requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-missmethyl >=1.36.0,<1.37.0' - - 'bioconductor-multidataset >=1.30.0,<1.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-missmethyl >=1.40.0,<1.41.0 + - bioconductor-multidataset >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-ggplot2 >=2.0.0' + - r-ggplot2 >=2.0.0 - r-isva - r-matrixstats - r-permute - r-smartsva - r-vegan run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-missmethyl >=1.36.0,<1.37.0' - - 'bioconductor-multidataset >=1.30.0,<1.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-missmethyl >=1.40.0,<1.41.0 + - bioconductor-multidataset >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-ggplot2 >=2.0.0' + - r-ggplot2 >=2.0.0 - r-isva - r-matrixstats - r-permute - r-smartsva - r-vegan + +source: + md5: d8296355d2f4244ff3f49b7afe2dc562 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Perform methylation analysis' - description: 'Package to integrate methylation and expression data. It can also perform methylation or expression analysis alone. Several plotting functionalities are included as well as a new region analysis based on redundancy analysis. Effect of SNPs on a region can also be estimated.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-measurementerror.cor/meta.yaml b/recipes/bioconductor-measurementerror.cor/meta.yaml index a008cdd80f4d1..fcc428a6817f4 100644 --- a/recipes/bioconductor-measurementerror.cor/meta.yaml +++ b/recipes/bioconductor-measurementerror.cor/meta.yaml @@ -1,38 +1,20 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "MeasurementError.cor" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7de3f5ca3749a7b1e80fdfa66204a252 +about: + description: Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Measurement Error model estimate for correlation coefficient build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-measurementerror.cor", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Measurement Error model estimate for correlation coefficient' - description: 'Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' extra: identifiers: - biotools:measurementerror.cor @@ -41,4 +23,22 @@ extra: name: bioconductor-measurementerror.cor path: recipes/bioconductor-measurementerror.cor version: 1.52.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +requirements: + host: + - r-base + run: + - r-base +source: + md5: 6f63025944c35b4663e33452890f3a01 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-meat/meta.yaml b/recipes/bioconductor-meat/meta.yaml index 084d2922cfced..525815e821bec 100644 --- a/recipes/bioconductor-meat/meta.yaml +++ b/recipes/bioconductor-meat/meta.yaml @@ -1,57 +1,62 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "MEAT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package estimates epigenetic age in skeletal muscle, using DNA methylation data generated with the Illumina Infinium technology (HM27, HM450 and HMEPIC). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Muscle Epigenetic Age Test -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea3f3041f0bdfab3844cea85f8d28c9b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-meat", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, markdown, rmarkdown, BiocStyle, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-watermelon >=2.8.0,<2.9.0' + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-watermelon >=2.12.0,<2.13.0 - r-base - r-dplyr - - 'r-dynamictreecut >=1.63' - - 'r-glmnet >=2.0' - - 'r-rpmm >=1.25' + - r-dynamictreecut >=1.63 + - r-glmnet >=2.0 + - r-rpmm >=1.25 - r-stringr - r-tibble run: - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-watermelon >=2.8.0,<2.9.0' + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-watermelon >=2.12.0,<2.13.0 - r-base - r-dplyr - - 'r-dynamictreecut >=1.63' - - 'r-glmnet >=2.0' - - 'r-rpmm >=1.25' + - r-dynamictreecut >=1.63 + - r-glmnet >=2.0 + - r-rpmm >=1.25 - r-stringr - r-tibble + +source: + md5: 627f3f2501cb213070b3a30f58429175 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Muscle Epigenetic Age Test' - description: 'This package estimates epigenetic age in skeletal muscle, using DNA methylation data generated with the Illumina Infinium technology (HM27, HM450 and HMEPIC).' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-meb/meta.yaml b/recipes/bioconductor-meb/meta.yaml index fbe884a83a68b..db37f37e5e418 100644 --- a/recipes/bioconductor-meb/meta.yaml +++ b/recipes/bioconductor-meb/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "MEB" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a method to identify differential expression genes in the same or different species. Given that non-DE genes have some similarities in features, a scaling-free minimum enclosing ball (SFMEB) model is built to cover those non-DE genes in feature space, then those DE genes, which are enormously different from non-DE genes, being regarded as outliers and rejected outside the ball. The method on this package is described in the article 'A minimum enclosing ball method to detect differential expression genes for RNA-seq data'. The SFMEB method is extended to the scMEB method that considering two or more potential types of cells or unknown labels scRNA-seq dataset DEGs identification. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A normalization-invariant minimum enclosing ball method to detect differentially expressed genes for RNA-seq and scRNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b1785984524fee5b32976a5e768037d6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-meb", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr,rmarkdown,BiocStyle requirements: host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-e1071 - r-wrswor run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-e1071 - r-wrswor + +source: + md5: 0176c4c63698de986c3185635a451ce3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'A normalization-invariant minimum enclosing ball method to detect differentially expressed genes for RNA-seq and scRNA-seq data' - description: 'This package provides a method to identify differential expression genes in the same or different species. Given that non-DE genes have some similarities in features, a scaling-free minimum enclosing ball (SFMEB) model is built to cover those non-DE genes in feature space, then those DE genes, which are enormously different from non-DE genes, being regarded as outliers and rejected outside the ball. The method on this package is described in the article ''A minimum enclosing ball method to detect differential expression genes for RNA-seq data''. The SFMEB method is extended to the scMEB method that considering two or more potential types of cells or unknown labels scRNA-seq dataset DEGs identification.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-medicagocdf/meta.yaml b/recipes/bioconductor-medicagocdf/meta.yaml index 4f18d4e92ad67..ac4f235f83555 100644 --- a/recipes/bioconductor-medicagocdf/meta.yaml +++ b/recipes/bioconductor-medicagocdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "medicagocdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1fbb2e4c070344d18e65f1b3993867db +about: + description: A package containing an environment representing the Medicago.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: medicagocdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-medicagocdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1fbb2e4c070344d18e65f1b3993867db + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: medicagocdf - description: 'A package containing an environment representing the Medicago.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-medicagoprobe/meta.yaml b/recipes/bioconductor-medicagoprobe/meta.yaml index 64886de29099e..b02f6f686d3ea 100644 --- a/recipes/bioconductor-medicagoprobe/meta.yaml +++ b/recipes/bioconductor-medicagoprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "medicagoprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 83b9887ad2ed26c704b0ca7115e5838d +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Medicago\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type medicago build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-medicagoprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 83b9887ad2ed26c704b0ca7115e5838d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type medicago' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Medicago\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-medips/meta.yaml b/recipes/bioconductor-medips/meta.yaml index fa842250f78ce..a2054d87addec 100644 --- a/recipes/bioconductor-medips/meta.yaml +++ b/recipes/bioconductor-medips/meta.yaml @@ -1,66 +1,72 @@ -{% set version = "1.54.0" %} +{% set version = "1.58.0" %} {% set name = "MEDIPS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of any kind of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential coverage between groups of samples and saturation and correlation analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: DNA IP-seq data analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 088394b1864d37eba7ed1064a9d671e9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-medips", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:medips + parent_recipe: + name: bioconductor-medips + path: recipes/bioconductor-medips + version: 1.32.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, BiocStyle requirements: host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-gtools run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-gtools + +source: + md5: f7ae115e9d7ee63573d8524bfa559829 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'DNA IP-seq data analysis' - description: 'MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of any kind of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential coverage between groups of samples and saturation and correlation analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:medips - parent_recipe: - name: bioconductor-medips - path: recipes/bioconductor-medips - version: 1.32.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-medipsdata/meta.yaml b/recipes/bioconductor-medipsdata/meta.yaml index 898fea78b24ec..dd0b86b42b5ea 100644 --- a/recipes/bioconductor-medipsdata/meta.yaml +++ b/recipes/bioconductor-medipsdata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "MEDIPSData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7b329ecedb2e9911b92ad669856abf2b +about: + description: Example data for MEDIPS and QSEA packages, consisting of chromosome 22 MeDIP and control/Input sample data. Additionally, the package contains MeDIP seq data from 3 NSCLC samples and adjacent normal tissue (chr 20-22). All data has been aligned to human genome hg19. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Example data for MEDIPS and QSEA packages build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-medipsdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7c0968e7c9e258a93e85879626e3e08a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Example data for MEDIPS and QSEA packages' - description: 'Example data for MEDIPS and QSEA packages, consisting of chromosome 22 MeDIP and control/Input sample data. Additionally, the package contains MeDIP seq data from 3 NSCLC samples and adjacent normal tissue (chr 20-22). All data has been aligned to human genome hg19.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-medipsdata/post-link.sh b/recipes/bioconductor-medipsdata/post-link.sh index 82ae17809dfbd..04162e69f1908 100644 --- a/recipes/bioconductor-medipsdata/post-link.sh +++ b/recipes/bioconductor-medipsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "medipsdata-1.38.0" +installBiocDataPackage.sh "medipsdata-1.42.0" diff --git a/recipes/bioconductor-medme/meta.yaml b/recipes/bioconductor-medme/meta.yaml index 83cc34d658330..d367ade8030e6 100644 --- a/recipes/bioconductor-medme/meta.yaml +++ b/recipes/bioconductor-medme/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.62.0" %} +{% set version = "1.66.0" %} {% set name = "MEDME" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Modelling Experimental Data from MeDIP Enrichment -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 03868c2e2f04af9c9f33d48cc6abed08 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-medme", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:medme + - doi:10.1101/gr.080721.108 + parent_recipe: + name: bioconductor-medme + path: recipes/bioconductor-medme + version: 1.40.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Hsapiens.UCSC.hg18, BSgenome.Mmusculus.UCSC.mm9 requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - r-drc - r-mass - libblas - liblapack run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - r-drc - r-mass - build: - - {{ compiler('c') }} - - make + +source: + md5: 83044db7ff26673430e82547931cb89e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Modelling Experimental Data from MeDIP Enrichment' - description: 'MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:medme - - doi:10.1101/gr.080721.108 - parent_recipe: - name: bioconductor-medme - path: recipes/bioconductor-medme - version: 1.40.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-meebodata/meta.yaml b/recipes/bioconductor-meebodata/meta.yaml index 4f4e1ad5b8435..3876667560017 100644 --- a/recipes/bioconductor-meebodata/meta.yaml +++ b/recipes/bioconductor-meebodata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "MEEBOdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd3b9bb8a918c9497903f6274f323904 +about: + description: R objects describing the MEEBO set. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: MEEBO set and MEEBO controls. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-meebodata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 85b931867f6b8761f474e911d7632f86 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'MEEBO set and MEEBO controls.' - description: 'R objects describing the MEEBO set.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-meebodata/post-link.sh b/recipes/bioconductor-meebodata/post-link.sh index f406ddac9857c..65598a5278266 100644 --- a/recipes/bioconductor-meebodata/post-link.sh +++ b/recipes/bioconductor-meebodata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "meebodata-1.40.0" +installBiocDataPackage.sh "meebodata-1.44.0" diff --git a/recipes/bioconductor-megadepth/meta.yaml b/recipes/bioconductor-megadepth/meta.yaml index c3dc6063d66e7..f58222d95ff0f 100644 --- a/recipes/bioconductor-megadepth/meta.yaml +++ b/recipes/bioconductor-megadepth/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "megadepth" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides an R interface to Megadepth by Christopher Wilks available at https://github.com/ChristopherWilks/megadepth. It is particularly useful for computing the coverage of a set of genomic regions across bigWig or BAM files. With this package, you can build base-pair coverage matrices for regions or annotations of your choice from BigWig files. Megadepth was used to create the raw files provided by https://bioconductor.org/packages/recount3. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'megadepth: BigWig and BAM related utilities' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5fa04f9d4075030126388db419378304 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-megadepth", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: covr, knitr, BiocStyle, sessioninfo, rmarkdown, rtracklayer, derfinder, GenomeInfoDb, tools, RefManageR, testthat # SystemRequirements: megadepth () requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-cmdfun - r-dplyr @@ -32,7 +33,7 @@ requirements: - r-readr - r-xfun run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-cmdfun - r-dplyr @@ -40,12 +41,16 @@ requirements: - r-magrittr - r-readr - r-xfun + +source: + md5: afbcaad3f9b031a65f0febdfcc2b4276 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'megadepth: BigWig and BAM related utilities' - description: 'This package provides an R interface to Megadepth by Christopher Wilks available at https://github.com/ChristopherWilks/megadepth. It is particularly useful for computing the coverage of a set of genomic regions across bigWig or BAM files. With this package, you can build base-pair coverage matrices for regions or annotations of your choice from BigWig files. Megadepth was used to create the raw files provided by https://bioconductor.org/packages/recount3.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-meigor/meta.yaml b/recipes/bioconductor-meigor/meta.yaml index d721e4cb5dbca..68906d18a1461 100644 --- a/recipes/bioconductor-meigor/meta.yaml +++ b/recipes/bioconductor-meigor/meta.yaml @@ -1,52 +1,59 @@ -{% set version = "1.33.0" %} +{% set version = "1.40.0" %} {% set name = "MEIGOR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: MEIGOR provides a comprehensive environment for performing global optimization tasks in bioinformatics and systems biology. It leverages advanced metaheuristic algorithms to efficiently search the solution space and is specifically tailored to handle the complexity and high-dimensionality of biological datasets. This package supports various optimization routines and is integrated with Bioconductor's infrastructure for a seamless analysis workflow. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: MEIGOR - MEtaheuristics for bIoinformatics Global Optimization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8c4d636efa888a0984f7e385aa5acf5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic -# Suggests: CellNOptR, knitr + run_exports: '{{ pin_subpackage("bioconductor-meigor", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:meigor + - doi:10.1186/1471-2105-15-136 + parent_recipe: + name: bioconductor-meigor + path: recipes/bioconductor-meigor + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: CellNOptR, knitr, BiocStyle requirements: host: - - 'bioconductor-cnorode >=1.42.0,<1.43.0' + - bioconductor-cnorode >=1.48.0,<1.49.0 - r-base - r-desolve - r-rsolnp - r-snowfall run: - - 'bioconductor-cnorode >=1.42.0,<1.43.0' + - bioconductor-cnorode >=1.48.0,<1.49.0 - r-base - r-desolve - r-rsolnp - r-snowfall + +source: + md5: 0dbaa957e4f6f08b24ae29007b73518f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'MEIGO - MEtaheuristics for bIoinformatics Global Optimization' - description: 'Global Optimization' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:meigor - - doi:10.1186/1471-2105-15-136 - parent_recipe: - name: bioconductor-meigor - path: recipes/bioconductor-meigor - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-melissa/meta.yaml b/recipes/bioconductor-melissa/meta.yaml index c69b137991ec8..6e01b39429b74 100644 --- a/recipes/bioconductor-melissa/meta.yaml +++ b/recipes/bioconductor-melissa/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "Melissa" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Melissa is a Baysian probabilistic model for jointly clustering and imputing single cell methylomes. This is done by taking into account local correlations via a Generalised Linear Model approach and global similarities using a mixture modelling approach. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 | file LICENSE + license_file: LICENSE + summary: Bayesian clustering and imputationa of single cell methylomes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 25f975650bec04b62c6e022b11cc33c6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-melissa", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-bprmeth >=1.28.0,<1.29.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-bprmeth >=1.32.0,<1.33.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-assertthat - r-base - r-cowplot @@ -40,9 +42,9 @@ requirements: - r-rocr - r-truncnorm run: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-bprmeth >=1.28.0,<1.29.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-bprmeth >=1.32.0,<1.33.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-assertthat - r-base - r-cowplot @@ -57,13 +59,16 @@ requirements: - r-mvtnorm - r-rocr - r-truncnorm + +source: + md5: b7a6bb222c251ee539e97e177faf325f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 | file LICENSE' - summary: 'Bayesian clustering and imputationa of single cell methylomes' - description: 'Melissa is a Baysian probabilistic model for jointly clustering and imputing single cell methylomes. This is done by taking into account local correlations via a Generalised Linear Model approach and global similarities using a mixture modelling approach.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-memes/meta.yaml b/recipes/bioconductor-memes/meta.yaml index eb689687be72c..b5ff3db53613d 100644 --- a/recipes/bioconductor-memes/meta.yaml +++ b/recipes/bioconductor-memes/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "memes" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A seamless interface to the MEME Suite family of tools for motif analysis. 'memes' provides data aware utilities for using GRanges objects as entrypoints to motif analysis, data structures for examining & editing motif lists, and novel data visualizations. 'memes' functions and data structures are amenable to both base R and tidyverse workflows. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: motif matching, comparison, and de novo discovery using the MEME Suite -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c9b7baebb9608344040a4dc38a05dea3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-memes", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: cowplot, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Dmelanogaster.UCSC.dm6, forcats, testthat (>= 2.1.0), knitr, MotifDb, pheatmap, PMCMRplus, plyranges (>= 1.9.1), rmarkdown, covr # SystemRequirements: Meme Suite (v5.3.3 or above) requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-universalmotif >=1.20.0,<1.21.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-universalmotif >=1.24.0,<1.25.0 - r-base - - 'r-cmdfun >=1.0.2' + - r-cmdfun >=1.0.2 - r-dplyr - r-ggplot2 - r-ggseqlogo @@ -43,11 +45,11 @@ requirements: - r-usethis - r-xml2 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-universalmotif >=1.20.0,<1.21.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-universalmotif >=1.24.0,<1.25.0 - r-base - - 'r-cmdfun >=1.0.2' + - r-cmdfun >=1.0.2 - r-dplyr - r-ggplot2 - r-ggseqlogo @@ -62,13 +64,16 @@ requirements: - r-tidyr - r-usethis - r-xml2 + +source: + md5: ca85fcf4bbc792484859320c12a8bde7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'motif matching, comparison, and de novo discovery using the MEME Suite' - description: 'A seamless interface to the MEME Suite family of tools for motif analysis. ''memes'' provides data aware utilities for using GRanges objects as entrypoints to motif analysis, data structures for examining & editing motif lists, and novel data visualizations. ''memes'' functions and data structures are amenable to both base R and tidyverse workflows.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-merfishdata/meta.yaml b/recipes/bioconductor-merfishdata/meta.yaml index 70f5bd162ef8c..1795d1e4f1f80 100644 --- a/recipes/bioconductor-merfishdata/meta.yaml +++ b/recipes/bioconductor-merfishdata/meta.yaml @@ -1,54 +1,61 @@ -{% set version = "1.4.1" %} +{% set version = "1.8.0" %} {% set name = "MerfishData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MerfishData is an ExperimentHub package that serves publicly available datasets obtained with Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH). MERFISH is a massively multiplexed single-molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells. The scope of the package is to provide MERFISH data for benchmarking and analysis. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Collection of public MERFISH datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 05369f89c4e1a15bdab1ce5174facbe4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-merfishdata", max_pin="x.x") }}' - noarch: generic -# Suggests: grid, ggplot2, ggpubr, knitr, rmarkdown, testthat, BiocStyle, DropletUtils + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: grid, ggplot2, ggpubr, knitr, rmarkdown, scater, scattermore, terra, testthat, BiocStyle, DropletUtils requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-bumpymatrix >=1.14.0,<1.15.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-bumpymatrix >=1.14.0,<1.15.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20250104 + +source: + md5: 86f043a416a009f9fd1ebb30f8a83360 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Collection of public MERFISH datasets' - description: 'MerfishData is an ExperimentHub package that serves publicly available datasets obtained with Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH). MERFISH is a massively multiplexed single-molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells. The scope of the package is to provide MERFISH data for benchmarking and analysis.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-merfishdata/post-link.sh b/recipes/bioconductor-merfishdata/post-link.sh index d616f8e059879..d3e980aff352d 100644 --- a/recipes/bioconductor-merfishdata/post-link.sh +++ b/recipes/bioconductor-merfishdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "merfishdata-1.4.1" +installBiocDataPackage.sh "merfishdata-1.8.0" diff --git a/recipes/bioconductor-mergeomics/meta.yaml b/recipes/bioconductor-mergeomics/meta.yaml index 5284a10f7d961..43ec8f152a728 100644 --- a/recipes/bioconductor-mergeomics/meta.yaml +++ b/recipes/bioconductor-mergeomics/meta.yaml @@ -1,39 +1,20 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "Mergeomics" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b8f5bc8cf54fa99df988a83c71737d3 +about: + description: The Mergeomics pipeline serves as a flexible framework for integrating multidimensional omics-disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. It includes two main parts, 1) Marker set enrichment analysis (MSEA); 2) Weighted Key Driver Analysis (wKDA). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Integrative network analysis of omics data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mergeomics", max_pin="x.x") }}' - noarch: generic -# Suggests: RUnit, BiocGenerics -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Integrative network analysis of omics data' - description: 'The Mergeomics pipeline serves as a flexible framework for integrating multidimensional omics-disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. It includes two main parts, 1) Marker set enrichment analysis (MSEA); 2) Weighted Key Driver Analysis (wKDA).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: identifiers: - biotools:mergeomics @@ -42,4 +23,23 @@ extra: name: bioconductor-mergeomics path: recipes/bioconductor-mergeomics version: 1.8.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: RUnit, BiocGenerics +requirements: + host: + - r-base + run: + - r-base +source: + md5: cbed7a299eb2d105e14405c156a621a9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-meshdbi/meta.yaml b/recipes/bioconductor-meshdbi/meta.yaml index 05e67cd414ef0..06e8cd18be86f 100644 --- a/recipes/bioconductor-meshdbi/meta.yaml +++ b/recipes/bioconductor-meshdbi/meta.yaml @@ -1,49 +1,55 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "MeSHDbi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package is unified implementation of MeSH.db, MeSH.AOR.db, and MeSH.PCR.db and also is interface to construct Gene-MeSH package (MeSH.XXX.eg.db). loadMeSHDbiPkg import sqlite file and generate MeSH.XXX.eg.db. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: DBI to construct MeSH-related package from sqlite file -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: edb738bd5c18f7017ebd13bd0cce9d2f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-meshdbi", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:meshdbi + parent_recipe: + name: bioconductor-meshdbi + path: recipes/bioconductor-meshdbi + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-rsqlite + +source: + md5: 01ca9060868de87892da25d6822b982d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'DBI to construct MeSH-related package from sqlite file' - description: 'The package is unified implementation of MeSH.db, MeSH.AOR.db, and MeSH.PCR.db and also is interface to construct Gene-MeSH package (MeSH.XXX.eg.db). loadMeSHDbiPkg import sqlite file and generate MeSH.XXX.eg.db.' -extra: - identifiers: - - biotools:meshdbi - parent_recipe: - name: bioconductor-meshdbi - path: recipes/bioconductor-meshdbi - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-meshes/meta.yaml b/recipes/bioconductor-meshes/meta.yaml index 860286dd24bc5..f213d28df31ba 100644 --- a/recipes/bioconductor-meshes/meta.yaml +++ b/recipes/bioconductor-meshes/meta.yaml @@ -1,52 +1,21 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "meshes" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MeSH (Medical Subject Headings) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH terms were associated by Entrez Gene ID by three methods, gendoo, gene2pubmed and RBBH. This association is fundamental for enrichment and semantic analyses. meshes supports enrichment analysis (over-representation and gene set enrichment analysis) of gene list or whole expression profile. The semantic comparisons of MeSH terms provide quantitative ways to compute similarities between genes and gene groups. meshes implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively and supports more than 70 species. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: MeSH Enrichment and Semantic analyses -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 90be6eeeb3ced1146ddcba48e2ec6c6e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-meshes", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, prettydoc -requirements: - host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - - 'bioconductor-meshdbi >=1.38.0,<1.39.0' - - r-base - - r-yulab.utils - run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - - 'bioconductor-meshdbi >=1.38.0,<1.39.0' - - r-base - - r-yulab.utils -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'MeSH Enrichment and Semantic analyses' - description: 'MeSH (Medical Subject Headings) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH terms were associated by Entrez Gene ID by three methods, gendoo, gene2pubmed and RBBH. This association is fundamental for enrichment and semantic analyses. meshes supports enrichment analysis (over-representation and gene set enrichment analysis) of gene list or whole expression profile. The semantic comparisons of MeSH terms provide quantitative ways to compute similarities between genes and gene groups. meshes implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively and supports more than 70 species.' + extra: identifiers: - biotools:meshes @@ -56,3 +25,40 @@ extra: path: recipes/bioconductor-meshes version: 1.6.1 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, prettydoc +requirements: + host: + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 + - bioconductor-gosemsim >=2.32.0,<2.33.0 + - bioconductor-meshdbi >=1.42.0,<1.43.0 + - r-base + - r-yulab.utils >=0.1.5 + run: + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 + - bioconductor-gosemsim >=2.32.0,<2.33.0 + - bioconductor-meshdbi >=1.42.0,<1.43.0 + - r-base + - r-yulab.utils >=0.1.5 + +source: + md5: 67f774a48cecf5173121fff150972d54 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-meshr/meta.yaml b/recipes/bioconductor-meshr/meta.yaml index 529a0bdbb3121..263844e0d2007 100644 --- a/recipes/bioconductor-meshr/meta.yaml +++ b/recipes/bioconductor-meshr/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "2.8.0" %} +{% set version = "2.12.0" %} {% set name = "meshr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A set of annotation maps describing the entire MeSH assembled using data from MeSH. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Tools for conducting enrichment analysis of MeSH -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7809b970dabdb3c42112e6b3aad5b75b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-meshr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-category >=2.68.0,<2.69.0' - - 'bioconductor-meshdbi >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-category >=2.72.0,<2.73.0 + - bioconductor-meshdbi >=1.42.0,<1.43.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-fdrtool - r-knitr @@ -33,23 +34,27 @@ requirements: - r-rmarkdown - r-rsqlite run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-category >=2.68.0,<2.69.0' - - 'bioconductor-meshdbi >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-category >=2.72.0,<2.73.0 + - bioconductor-meshdbi >=1.42.0,<1.43.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-fdrtool - r-knitr - r-markdown - r-rmarkdown - r-rsqlite + +source: + md5: bd7179596eddb8790f09d35bbb4dbc2f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Tools for conducting enrichment analysis of MeSH' - description: 'A set of annotation maps describing the entire MeSH assembled using data from MeSH.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-meskit/meta.yaml b/recipes/bioconductor-meskit/meta.yaml index df270a05c0104..9e8f3aa432340 100644 --- a/recipes/bioconductor-meskit/meta.yaml +++ b/recipes/bioconductor-meskit/meta.yaml @@ -1,33 +1,41 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "MesKit" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MesKit provides commonly used analysis and visualization modules based on mutational data generated by multi-region sequencing (MRS). This package allows to depict mutational profiles, measure heterogeneity within or between tumors from the same patient, track evolutionary dynamics, as well as characterize mutational patterns on different levels. Shiny application was also developed for a need of GUI-based analysis. As a handy tool, MesKit can facilitate the interpretation of tumor heterogeneity and the understanding of evolutionary relationship between regions in MRS study. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 909ad92f34384c66c0e86f0f13ff7e71 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-meskit", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-meskit + path: recipes/bioconductor-meskit + version: 0.99.16 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: shiny, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), org.Hs.eg.db, clusterProfiler, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'r-ape >=5.4.1' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-ape >=5.4.1 - r-base - r-circlize - r-cowplot @@ -40,14 +48,14 @@ requirements: - r-phangorn - r-pracma - r-rcolorbrewer - - 'r-tidyr >=1.0.0' + - r-tidyr >=1.0.0 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'r-ape >=5.4.1' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-ape >=5.4.1 - r-base - r-circlize - r-cowplot @@ -60,19 +68,17 @@ requirements: - r-phangorn - r-pracma - r-rcolorbrewer - - 'r-tidyr >=1.0.0' + - r-tidyr >=1.0.0 + +source: + md5: 950350f211e6021c931b25ff2df92c32 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations' - description: 'MesKit provides commonly used analysis and visualization modules based on mutational data generated by multi-region sequencing (MRS). This package allows to depict mutational profiles, measure heterogeneity within or between tumors from the same patient, track evolutionary dynamics, as well as characterize mutational patterns on different levels. Shiny application was also developed for a need of GUI-based analysis. As a handy tool, MesKit can facilitate the interpretation of tumor heterogeneity and the understanding of evolutionary relationship between regions in MRS study.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-meskit - path: recipes/bioconductor-meskit - version: 0.99.16 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-messina/build_failure.osx-64.yaml b/recipes/bioconductor-messina/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..e64fb06b32763 --- /dev/null +++ b/recipes/bioconductor-messina/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 4f438e7ce54a12be04e5f6ee54f152570181f37644762386b542a443263f4caa # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-messina-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-messina-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-messina-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-messina-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-messina-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-messina-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-messina-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-messina-1.42.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c Classifier.cpp -o Classifier.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c Data.cpp -o Data.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c crossval.cpp -o crossval.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c errors.cpp -o errors.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c init.cpp -o init.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c messinaExtern.cpp -o messinaExtern.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L$PREFIX/lib/R/lib -Wl,-dead_strip_dylibs -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o messina.so Classifier.o Data.o RcppExports.o crossval.o errors.o init.o messinaExtern.o -L$PREFIX/lib/R/lib -lR -Wl,-framework -Wl,CoreFoundation + + Resource usage statistics from building bioconductor-messina: + Process count: 7 + CPU time: Sys=0:00:03.8, User=0:00:21.1 + Memory: 301.3M + Disk usage: 3.2K + Time elapsed: 0:00:46.7 + + + Packaging bioconductor-messina + Packaging bioconductor-messina-1.42.0-r44h35d7169_0 + + number of files: 29 + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + Fixing linking of messina.so in /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-messina_1734237173161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/messina/libs/messina.so + New link location is lib/R/library/messina/libs/messina.so + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2765, in build + newly_built_packages = bundlers[pkg_type]( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1874, in bundle_conda + files = post_process_files(metadata, initial_files) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1653, in post_process_files + post_build(m, new_files, build_python=python) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1759, in post_build + post_process_shared_lib(m, f, prefix_files, host_prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1635, in post_process_shared_lib + mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 488, in mk_relative_osx + existing_rpaths = macho.get_rpaths(path, build_prefix=prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 252, in get_rpaths + dylib_loads = otool(path, build_prefix, is_rpath) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 221, in otool + lines = check_output([otool, "-l", path], stderr=STDOUT).decode("utf-8") + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 421, in check_output + return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 526, in run + raise CalledProcessError(retcode, process.args, + subprocess.CalledProcessError: Command '['/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-messina_1734237173161/_build_env/bin/llvm-otool', '-l', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-messina_1734237173161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/messina/libs/messina.so']' died with . +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-messina/meta.yaml b/recipes/bioconductor-messina/meta.yaml index 48739dc5c9b95..b9fe926625f37 100644 --- a/recipes/bioconductor-messina/meta.yaml +++ b/recipes/bioconductor-messina/meta.yaml @@ -1,58 +1,64 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "messina" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Messina is a collection of algorithms for constructing optimally robust single-gene classifiers, and for identifying differential expression in the presence of outliers or unknown sample subgroups. The methods have application in identifying lead features to develop into clinical tests (both diagnostic and prognostic), and in identifying differential expression when a fraction of samples show unusual patterns of expression. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: EPL (>= 1.0) + summary: Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ad9cfdec37597c8a312b49085f1ff124 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-messina", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:messina + parent_recipe: + name: bioconductor-messina + path: recipes/bioconductor-messina + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>= 2.22.0), BiocStyle requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - - 'r-foreach >=1.4.1' - - 'r-ggplot2 >=0.9.3.1' - - 'r-plyr >=1.8' - - 'r-rcpp >=0.11.1' - - 'r-survival >=2.37-4' + - r-foreach >=1.4.1 + - r-ggplot2 >=0.9.3.1 + - r-plyr >=1.8 + - r-rcpp >=0.11.1 + - r-survival >=2.37-4 - libblas - liblapack run: - r-base - - 'r-foreach >=1.4.1' - - 'r-ggplot2 >=0.9.3.1' - - 'r-plyr >=1.8' - - 'r-rcpp >=0.11.1' - - 'r-survival >=2.37-4' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-foreach >=1.4.1 + - r-ggplot2 >=0.9.3.1 + - r-plyr >=1.8 + - r-rcpp >=0.11.1 + - r-survival >=2.37-4 + +source: + md5: c9284a0cefc50cf77b2b8e8ccb7f4588 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'EPL (>= 1.0)' - summary: 'Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems' - description: 'Messina is a collection of algorithms for constructing optimally robust single-gene classifiers, and for identifying differential expression in the presence of outliers or unknown sample subgroups. The methods have application in identifying lead features to develop into clinical tests (both diagnostic and prognostic), and in identifying differential expression when a fraction of samples show unusual patterns of expression.' -extra: - identifiers: - - biotools:messina - parent_recipe: - name: bioconductor-messina - path: recipes/bioconductor-messina - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metabcombiner/meta.yaml b/recipes/bioconductor-metabcombiner/meta.yaml index 9b9563bf04b9f..29d5ccb5faee2 100644 --- a/recipes/bioconductor-metabcombiner/meta.yaml +++ b/recipes/bioconductor-metabcombiner/meta.yaml @@ -1,30 +1,35 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "metabCombiner" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package aligns LC-HRMS metabolomics datasets acquired from biologically similar specimens analyzed under similar, but not necessarily identical, conditions. Peak-picked and simply aligned metabolomics feature tables (consisting of m/z, rt, and per-sample abundance measurements, plus optional identifiers & adduct annotations) are accepted as input. The package outputs a combined table of feature pair alignments, organized into groups of similar m/z, and ranked by a similarity score. Input tables are assumed to be acquired using similar (but not necessarily identical) analytical methods. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Method for Combining LC-MS Metabolomics Feature Measurements -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9840a8f7cdc657e21d3ebc2a7b6b68b2 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metabcombiner", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-caret - - 'r-dplyr >=1.0' + - r-dplyr >=1.0 - r-matrixstats - r-mgcv - r-rlang @@ -32,24 +37,24 @@ requirements: - libblas - liblapack run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-caret - - 'r-dplyr >=1.0' + - r-dplyr >=1.0 - r-matrixstats - r-mgcv - r-rlang - r-tidyr - build: - - {{ compiler('c') }} - - make + +source: + md5: c252f40df99df7472acac7159df5bc96 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Method for Combining LC-MS Metabolomics Feature Measurements' - description: 'This package aligns LC-HRMS metabolomics datasets acquired from biologically similar specimens analyzed under similar, but not necessarily identical, conditions. Peak-picked and simply aligned metabolomics feature tables (consisting of m/z, rt, and per-sample abundance measurements, plus optional identifiers & adduct annotations) are accepted as input. The package outputs a combined table of feature pair alignments, organized into groups of similar m/z, and ranked by a similarity score. Input tables are assumed to be acquired using similar (but not necessarily identical) analytical methods.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metabinr/meta.yaml b/recipes/bioconductor-metabinr/meta.yaml index 67899dd2e1f85..4367c9c466f40 100644 --- a/recipes/bioconductor-metabinr/meta.yaml +++ b/recipes/bioconductor-metabinr/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "metabinR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7080ae8eac49640aeae95bda1185ac7d +about: + description: Provide functions for performing abundance and compositional based binning on metagenomic samples, directly from FASTA or FASTQ files. Functions are implemented in Java and called via rJava. Parallel implementation that operates directly on input FASTA/FASTQ files for fast execution. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Abundance and Compositional Based Binning of Metagenomes build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metabinr", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, cvms, data.table, dplyr, ggplot2, gridExtra, knitr, R.utils, rmarkdown, sabre, spelling, testthat (>= 3.0.0) # SystemRequirements: Java (>= 8) requirements: @@ -30,13 +29,14 @@ requirements: - r-base - r-rjava - openjdk +source: + md5: 5ecee6cce174068c7c3f1eb3700327ea + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Abundance and Compositional Based Binning of Metagenomes' - description: 'Provide functions for performing abundance and compositional based binning on metagenomic samples, directly from FASTA or FASTQ files. Functions are implemented in Java and called via rJava. Parallel implementation that operates directly on input FASTA/FASTQ files for fast execution.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metaboannotation/meta.yaml b/recipes/bioconductor-metaboannotation/meta.yaml index 4664b5262cd69..623083e6fa2f0 100644 --- a/recipes/bioconductor-metaboannotation/meta.yaml +++ b/recipes/bioconductor-metaboannotation/meta.yaml @@ -1,58 +1,63 @@ -{% set version = "1.6.1" %} +{% set version = "1.10.0" %} {% set name = "MetaboAnnotation" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: High level functions to assist in annotation of (metabolomics) data sets. These include functions to perform simple tentative annotations based on mass matching but also functions to consider m/z and retention times for annotation of LC-MS features given that respective reference values are available. In addition, the function provides high-level functions to simplify matching of LC-MS/MS spectra against spectral libraries and objects and functionality to represent and manage such matched data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Utilities for Annotation of Metabolomics Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fee181fc1795a1e2bde1d1e551f1a45e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metaboannotation", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, msdata, BiocStyle, rmarkdown, plotly, shiny, shinyjs, DT, microbenchmark, mzR requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-compounddb >=1.6.0,<1.7.0' - - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-qfeatures >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-compounddb >=1.10.0,<1.11.0 + - bioconductor-metabocoreutils >=1.14.0,<1.15.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-qfeatures >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-compounddb >=1.6.0,<1.7.0' - - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-qfeatures >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-compounddb >=1.10.0,<1.11.0 + - bioconductor-metabocoreutils >=1.14.0,<1.15.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-qfeatures >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + +source: + md5: 5220af7284f5d8b782230028ba1406fe + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Utilities for Annotation of Metabolomics Data' - description: 'High level functions to assist in annotation of (metabolomics) data sets. These include functions to perform simple tentative annotations based on mass matching but also functions to consider m/z and retention times for annotation of LC-MS features given that respective reference values are available. In addition, the function provides high-level functions to simplify matching of LC-MS/MS spectra against spectral libraries and objects and functionality to represent and manage such matched data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metabocoreutils/meta.yaml b/recipes/bioconductor-metabocoreutils/meta.yaml index a73ae28540ebe..5c269e72ae02a 100644 --- a/recipes/bioconductor-metabocoreutils/meta.yaml +++ b/recipes/bioconductor-metabocoreutils/meta.yaml @@ -1,38 +1,40 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "MetaboCoreUtils" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e4b834af09aa89158b64b8586d4d15c4 +about: + description: MetaboCoreUtils defines metabolomics-related core functionality provided as low-level functions to allow a data structure-independent usage across various R packages. This includes functions to calculate between ion (adduct) and compound mass-to-charge ratios and masses or functions to work with chemical formulas. The package provides also a set of adduct definitions and information on some commercially available internal standard mixes commonly used in MS experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Core Utils for Metabolomics Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metabocoreutils", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, testthat, knitr, rmarkdown +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: BiocStyle, testthat, knitr, rmarkdown, robustbase requirements: host: - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 - r-base run: - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 - r-base +source: + md5: 76392967ed18baf8cf0eaf7d98bdcbec + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Core Utils for Metabolomics Data' - description: 'MetaboCoreUtils defines metabolomics-related core functionality provided as low-level functions to allow a data structure-independent usage across various R packages. This includes functions to calculate between ion (adduct) and compound mass-to-charge ratios and masses or functions to work with chemical formulas. The package provides also a set of adduct definitions and information on some commercially available internal standard mixes commonly used in MS experiments.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metaboliteidmapping/meta.yaml b/recipes/bioconductor-metaboliteidmapping/meta.yaml index e248f2cb8aadb..af17f0d97da01 100644 --- a/recipes/bioconductor-metaboliteidmapping/meta.yaml +++ b/recipes/bioconductor-metaboliteidmapping/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.0.0" %} {% set name = "metaboliteIDmapping" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bd78ec373ce90fac1a10d2c64c462e77 +about: + description: The package provides a comprehensive mapping table of nine different Metabolite ID formats and their common name. The data has been collected and merged from four publicly available source, including HMDB, Comptox Dashboard, ChEBI, and the graphite Bioconductor R package. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Mapping of Metabolite IDs from Different Sources build: - number: 5 + noarch: generic + number: 6 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metaboliteidmapping", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: magrittr, graphite, dplyr, tidyr, tibble, rappdirs, XML, readxl, stringr, utils, knitr, sets, R.utils, readr, conflicted, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bd78ec373ce90fac1a10d2c64c462e77 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: GPL-3 - summary: 'Mapping of Metabolite IDs from Different Sources' - description: 'The package provides a comprehensive mapping table of nine different Metabolite ID formats and their common name. The data has been collected and merged from four publicly available source, including HMDB, Comptox Dashboard, ChEBI, and the graphite Bioconductor R package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metabolomicsworkbenchr/meta.yaml b/recipes/bioconductor-metabolomicsworkbenchr/meta.yaml index d4c21164ee6d0..abc25c616efbe 100644 --- a/recipes/bioconductor-metabolomicsworkbenchr/meta.yaml +++ b/recipes/bioconductor-metabolomicsworkbenchr/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "metabolomicsWorkbenchR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functions for interfacing with the Metabolomics Workbench RESTful API. Study, compound, protein and gene information can be searched for using the API. Methods to obtain study data in common Bioconductor formats such as SummarizedExperiment and MultiAssayExperiment are also included. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Metabolomics Workbench in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e8485177f5ad463ff6a0f6e573e74fb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metabolomicsworkbenchr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, covr, knitr, HDF5Array, httptest, rmarkdown, structToolbox, testthat, pmp, grid, png requirements: host: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-struct >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-struct >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-httr - r-jsonlite run: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-struct >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-struct >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-httr - r-jsonlite + +source: + md5: 4370275467c24b894e5a3d9374b29bec + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Metabolomics Workbench in R' - description: 'This package provides functions for interfacing with the Metabolomics Workbench RESTful API. Study, compound, protein and gene information can be searched for using the API. Methods to obtain study data in common Bioconductor formats such as SummarizedExperiment and MultiAssayExperiment are also included.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metabomxtr/meta.yaml b/recipes/bioconductor-metabomxtr/meta.yaml index 1ab86aa0f3f66..b3eb8db771eb4 100644 --- a/recipes/bioconductor-metabomxtr/meta.yaml +++ b/recipes/bioconductor-metabomxtr/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "metabomxtr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The functions in this package return optimized parameter estimates and log likelihoods for mixture models of truncated data with normal or lognormal distributions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A package to run mixture models for truncated metabolomics data with normal or lognormal distributions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ec247e3fe8099096d1bfcc8fff93f08d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metabomxtr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: xtable, reshape2 requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base - r-formula - r-ggplot2 - r-optimx - r-plyr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base - r-formula - r-ggplot2 - r-optimx - r-plyr + +source: + md5: 0708d3d272c142694abe37ae3abf7964 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'A package to run mixture models for truncated metabolomics data with normal or lognormal distributions' - description: 'The functions in this package return optimized parameter estimates and log likelihoods for mixture models of truncated data with normal or lognormal distributions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metabosignal/build_failure.linux-64.yaml b/recipes/bioconductor-metabosignal/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..fe437b77661e6 --- /dev/null +++ b/recipes/bioconductor-metabosignal/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a5114a9096d63443cf807ed229a595b9b6616c4df7631c7bb7777b6259430be7 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [31mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [31mbioconductor-ensembldb >=2.26.0,<2.27.0 [0m, which requires + [31mbioconductor-annotationdbi >=1.64.0,<1.65.0 [0m, which conflicts with any installable versions previously reported; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-ensdb.hsapiens.v75==2.99.0=r3.4.1_0"), MatchSpec("r-base=3.4.1")} + Encountered problems while solving: + - package bioconductor-ensdb.hsapiens.v75-2.99.0-r3.4.1_0 requires r-base 3.4.1*, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-annotationdbi >=1.68.0,<1.69.0 [0m is requested and can be installed; + [32mbioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0 [0m is installable with the potential options + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mr-base 3.4.1* [0m, which can be installed; + [31mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [31mbioconductor-ensembldb >=2.4.1,<2.6.0 [0m, which requires + [31mbioconductor-annotationdbi >=1.42.1,<1.44.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [31mbioconductor-ensembldb >=2.6.0,<2.7.0 [0m, which requires + [31mbioconductor-annotationdbi >=1.44.0,<1.45.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [31mbioconductor-ensembldb >=2.8.0,<2.9.0 [0m, which requires + [31mbioconductor-annotationdbi >=1.46.0,<1.47.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [31mbioconductor-ensembldb >=2.10.0,<2.11.0 [0m, which requires + [31mbioconductor-annotationdbi >=1.48.0,<1.49.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [31mbioconductor-ensembldb >=2.12.0,<2.13.0 [0m, which requires + [31mbioconductor-annotationdbi >=1.50.0,<1.51.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [31mbioconductor-ensembldb >=2.14.0,<2.15.0 [0m, which requires + [31mbioconductor-annotationdbi >=1.52.0,<1.53.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [31mbioconductor-ensembldb >=2.16.0,<2.17.0 [0m, which requires + [31mbioconductor-annotationdbi >=1.54.0,<1.55.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [31mbioconductor-ensembldb >=2.18.0,<2.19.0 [0m, which requires + [31mbioconductor-annotationdbi >=1.56.0,<1.57.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [31mbioconductor-ensembldb >=2.22.0,<2.23.0 [0m, which requires + [31mbioconductor-annotationdbi >=1.60.0,<1.61.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [31mbioconductor-ensembldb >=2.24.0,<2.25.0 [0m, which requires + [31mbioconductor-annotationdbi >=1.62.0,<1.63.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [31mbioconductor-ensembldb >=2.26.0,<2.27.0 [0m, which requires + [31mbioconductor-annotationdbi >=1.64.0,<1.65.0 [0m, which conflicts with any installable versions previously reported; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-metabosignal/meta.yaml b/recipes/bioconductor-metabosignal/meta.yaml index 01f312d812830..3b4f56b8c196f 100644 --- a/recipes/bioconductor-metabosignal/meta.yaml +++ b/recipes/bioconductor-metabosignal/meta.yaml @@ -1,66 +1,72 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "MetaboSignal" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8f1dc09626a1881461f987e726078bf build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metabosignal", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:metabosignal + parent_recipe: + name: bioconductor-metabosignal + path: recipes/bioconductor-metabosignal + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0' - - 'bioconductor-hpar >=1.44.0,<1.45.0' - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-mwastools >=1.26.0,<1.27.0' - - 'bioconductor-mygene >=1.38.0,<1.39.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0 + - bioconductor-hpar >=1.48.0,<1.49.0 + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-mwastools >=1.30.0,<1.31.0 + - bioconductor-mygene >=1.42.0,<1.43.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - r-igraph - r-rcurl run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0' - - 'bioconductor-hpar >=1.44.0,<1.45.0' - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-mwastools >=1.26.0,<1.27.0' - - 'bioconductor-mygene >=1.38.0,<1.39.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0 + - bioconductor-hpar >=1.48.0,<1.49.0 + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-mwastools >=1.30.0,<1.31.0 + - bioconductor-mygene >=1.42.0,<1.43.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - r-igraph - r-rcurl + +source: + md5: 1a7667ef13119d45cd58ff155f911042 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways' - description: 'MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:metabosignal - parent_recipe: - name: bioconductor-metabosignal - path: recipes/bioconductor-metabosignal - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metacca/meta.yaml b/recipes/bioconductor-metacca/meta.yaml index 851175efd2c07..529543b1b51e3 100644 --- a/recipes/bioconductor-metacca/meta.yaml +++ b/recipes/bioconductor-metacca/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "metaCCA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d5be58f253912b275964a681a508234d +about: + description: metaCCA performs multivariate analysis of a single or multiple GWAS based on univariate regression coefficients. It allows multivariate representation of both phenotype and genotype. metaCCA extends the statistical technique of canonical correlation analysis to the setting where original individual-level records are not available, and employs a covariance shrinkage algorithm to achieve robustness. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metacca", max_pin="x.x") }}' - noarch: generic +extra: + identifiers: + - biotools:metacca + parent_recipe: + name: bioconductor-metacca + path: recipes/bioconductor-metacca + version: 1.8.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr requirements: host: - r-base run: - r-base +source: + md5: 61e5e91a9b098d14828dd5a786499da1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis' - description: 'metaCCA performs multivariate analysis of a single or multiple GWAS based on univariate regression coefficients. It allows multivariate representation of both phenotype and genotype. metaCCA extends the statistical technique of canonical correlation analysis to the setting where original individual-level records are not available, and employs a covariance shrinkage algorithm to achieve robustness.' - license_file: LICENSE -extra: - identifiers: - - biotools:metacca - parent_recipe: - name: bioconductor-metacca - path: recipes/bioconductor-metacca - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metacyto/meta.yaml b/recipes/bioconductor-metacyto/meta.yaml index e7c7260f307a2..727210dc74710 100644 --- a/recipes/bioconductor-metacyto/meta.yaml +++ b/recipes/bioconductor-metacyto/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "MetaCyto" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functions for preprocessing, automated gating and meta-analysis of cytometry data. It also provides functions that facilitate the collection of cytometry data from the ImmPort database. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'MetaCyto: A package for meta-analysis of cytometry data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0cd04a831a226a35bdeb881c03d30193 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metacyto", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, dplyr, rmarkdown requirements: host: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowsom >=2.10.0,<2.11.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowsom >=2.14.0,<2.15.0 - r-base - r-cluster - r-fastcluster - r-ggplot2 - r-metafor - - 'r-tidyr >=0.7' + - r-tidyr >=0.7 run: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowsom >=2.10.0,<2.11.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowsom >=2.14.0,<2.15.0 - r-base - r-cluster - r-fastcluster - r-ggplot2 - r-metafor - - 'r-tidyr >=0.7' + - r-tidyr >=0.7 + +source: + md5: 5f8aea732c6486f8f34586b41c0be7b5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'MetaCyto: A package for meta-analysis of cytometry data' - description: 'This package provides functions for preprocessing, automated gating and meta-analysis of cytometry data. It also provides functions that facilitate the collection of cytometry data from the ImmPort database.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metagene2/meta.yaml b/recipes/bioconductor-metagene2/meta.yaml index 7b828dbbaba57..93d57845069e1 100644 --- a/recipes/bioconductor-metagene2/meta.yaml +++ b/recipes/bioconductor-metagene2/meta.yaml @@ -1,64 +1,69 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "metagene2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package produces metagene plots to compare coverages of sequencing experiments at selected groups of genomic regions. It can be used for such analyses as assessing the binding of DNA-interacting proteins at promoter regions or surveying antisense transcription over the length of a gene. The metagene2 package can manage all aspects of the analysis, from normalization of coverages to plot facetting according to experimental metadata. Bootstraping analysis is used to provide confidence intervals of per-sample mean coverages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: A package to produce metagene plots -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: adef0ffd2a7cec30870a2b66eb2cb4f9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metagene2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-data.table - r-dplyr - r-ggplot2 - r-magrittr - r-purrr - - 'r-r6 >=2.0' + - r-r6 >=2.0 - r-reshape2 run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-data.table - r-dplyr - r-ggplot2 - r-magrittr - r-purrr - - 'r-r6 >=2.0' + - r-r6 >=2.0 - r-reshape2 + +source: + md5: 3f00b08254a2d4b76e1c053953817793 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A package to produce metagene plots' - description: 'This package produces metagene plots to compare coverages of sequencing experiments at selected groups of genomic regions. It can be used for such analyses as assessing the binding of DNA-interacting proteins at promoter regions or surveying antisense transcription over the length of a gene. The metagene2 package can manage all aspects of the analysis, from normalization of coverages to plot facetting according to experimental metadata. Bootstraping analysis is used to provide confidence intervals of per-sample mean coverages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metagxbreast/meta.yaml b/recipes/bioconductor-metagxbreast/meta.yaml index 969e8d8c535ba..4d0d4cc11a7b5 100644 --- a/recipes/bioconductor-metagxbreast/meta.yaml +++ b/recipes/bioconductor-metagxbreast/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "MetaGxBreast" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A collection of Breast Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Apache License (>= 2) + summary: Transcriptomic Breast Cancer Datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e711302482bca1429de5fe2e5276c788 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metagxbreast", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, xtable, tinytex requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-lattice run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-lattice - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 6022b5352915c1777c7c600ffc2cc86c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'Apache License (>= 2)' - summary: 'Transcriptomic Breast Cancer Datasets' - description: 'A collection of Breast Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metagxbreast/post-link.sh b/recipes/bioconductor-metagxbreast/post-link.sh index e04b480c25fb1..bddebb0974f2b 100644 --- a/recipes/bioconductor-metagxbreast/post-link.sh +++ b/recipes/bioconductor-metagxbreast/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "metagxbreast-1.22.0" +installBiocDataPackage.sh "metagxbreast-1.26.0" diff --git a/recipes/bioconductor-metagxovarian/meta.yaml b/recipes/bioconductor-metagxovarian/meta.yaml index a6cf76c8d62c9..66dd93df5bbba 100644 --- a/recipes/bioconductor-metagxovarian/meta.yaml +++ b/recipes/bioconductor-metagxovarian/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "MetaGxOvarian" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A collection of Ovarian Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Transcriptomic Ovarian Cancer Datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f76dc6c912d3a8936f81509ba6559286 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metagxovarian", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, xtable, rmarkdown, knitr, BiocStyle, markdown requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-lattice run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-lattice - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: aa02381feac47d0d6a29bfa33249caf1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Transcriptomic Ovarian Cancer Datasets' - description: 'A collection of Ovarian Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metagxovarian/post-link.sh b/recipes/bioconductor-metagxovarian/post-link.sh index a592b878de955..34806a38f8126 100644 --- a/recipes/bioconductor-metagxovarian/post-link.sh +++ b/recipes/bioconductor-metagxovarian/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "metagxovarian-1.22.0" +installBiocDataPackage.sh "metagxovarian-1.26.0" diff --git a/recipes/bioconductor-metagxpancreas/meta.yaml b/recipes/bioconductor-metagxpancreas/meta.yaml index 0486ab5f27c80..dcad35c2ab181 100644 --- a/recipes/bioconductor-metagxpancreas/meta.yaml +++ b/recipes/bioconductor-metagxpancreas/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "MetaGxPancreas" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A collection of pancreatic Cancer transcriptomic datasets that are part of the MetaGxData package compendium. This package contains multiple pancreas cancer datasets that have been downloaded from various resources and turned into SummarizedExperiment objects. The details of how the authors normalized the data can be found in the experiment data section of the objects. Additionally, the location the data was obtained from can be found in the url variables of the experiment data portion of each SE. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Transcriptomic Pancreatic Cancer Datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0c1764dc18a9a180b2121649c98a26a1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metagxpancreas", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, BiocStyle, rmarkdown, markdown requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: a662c1634949436c2fe455a8d59abb07 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Transcriptomic Pancreatic Cancer Datasets' - description: 'A collection of pancreatic Cancer transcriptomic datasets that are part of the MetaGxData package compendium. This package contains multiple pancreas cancer datasets that have been downloaded from various resources and turned into SummarizedExperiment objects. The details of how the authors normalized the data can be found in the experiment data section of the objects. Additionally, the location the data was obtained from can be found in the url variables of the experiment data portion of each SE.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metagxpancreas/post-link.sh b/recipes/bioconductor-metagxpancreas/post-link.sh index 325b7237840e4..26e496ae8ed81 100644 --- a/recipes/bioconductor-metagxpancreas/post-link.sh +++ b/recipes/bioconductor-metagxpancreas/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "metagxpancreas-1.22.0" +installBiocDataPackage.sh "metagxpancreas-1.26.0" diff --git a/recipes/bioconductor-metahdep/build_failure.osx-64.yaml b/recipes/bioconductor-metahdep/build_failure.osx-64.yaml index 8f5e1414fd2f4..a72eb56c38761 100644 --- a/recipes/bioconductor-metahdep/build_failure.osx-64.yaml +++ b/recipes/bioconductor-metahdep/build_failure.osx-64.yaml @@ -1,35 +1,60 @@ -recipe_sha: 7d681cfa3280b3e2180df68fba6a82a10dab63dfb65f81b7020b5d2b80a134a9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: da639fed2430e20faa9a1d6785e1b6e4d67385ed7bf631de51139808f79e6603 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- +log: |2- + license: GPL-3 + license_file: /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-metahdep_1734216852036/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/share/licenses/GPL-3 + summary: Hierarchical Dependence in Meta-Analysis + extra: + copy_test_source_files: true + final: true + identifiers: + - biotools:metahdep + - doi:10.1093/bioinformatics/btp468 + parent_recipe: + name: bioconductor-metahdep + path: recipes/bioconductor-metahdep + version: 1.38.0 + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-metahdep_1734216852036/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-metahdep_1734216852036/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-metahdep_1734216852036/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-metahdep_1734216852036/work + INFO: activate-gfortran_osx-64.sh made the following environmental changes: + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.64.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.64.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.58.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.58.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.64.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.64.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as CC=x86_64-apple-darwin13.4.0-clang CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.58.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.64.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.58.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.64.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -38,7 +63,7 @@ log: |- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -53,56 +78,27 @@ log: |- INFO: activate_clangxx_osx-64.sh made the following environmental changes: CLANGXX=x86_64-apple-darwin13.4.0-clang CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.58.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.64.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.58.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.64.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix INFO: activate_clang_osx-64.sh made the following environmental changes: CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.64.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.64.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.64.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.64.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.64.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-metahdep-1.64.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - * installing to library /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-metahdep_1689833451644/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library - * installing *source* package metahdep ... - ** using staged installation - ** libs - using C compiler: clang version 15.0.7 - using SDK: - x86_64-apple-darwin13.4.0-clang -I"$PREFIX/lib/R/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1689263077211/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c metahdep.c -o metahdep.o - metahdep.c:471:79: error: incompatible pointer to integer conversion passing 'const char *' to parameter of type 'char' [-Wint-conversion] - index = metan_binary_search_unique(name_list, sort_index, R_old_names, j, CHAR(STRING_ELT(R_old_chipsets, j)), i); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-metahdep_1689833451644/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/include/Rinternals.h:197:17: note: expanded from macro 'CHAR' - #define CHAR(x) R_CHAR(x) - ^~~~~~~~~ - metahdep.c:372:103: note: passing argument to parameter 'chipset_name' here - SEXP metan_binary_search_unique(SEXP name_list, SEXP sort_index, SEXP gene_name, int gene_index, char chipset_name, int study_num) - ^ - 1 error generated. - make: *** [/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-metahdep_1689833451644/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/etc/Makeconf:193: metahdep.o] Error 1 - ERROR: compilation failed for package metahdep - * removing /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-metahdep_1689833451644/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/metahdep - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-metahdep_1689833451644/work/conda_build.sh']' returned non-zero exit status 1. + x86_64-apple-darwin13.4.0-clang -I"$PREFIX/lib/R/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c metahdep.c -o metahdep.o # Last 100 lines of the build log. -reason: |- - 19:17:50 BIOCONDA INFO (ERR) metahdep.c:471:79: error: incompatible pointer to integer conversion passing 'const char *' to parameter of type 'char' [-Wint-conversion] -category: |- - compiler error diff --git a/recipes/bioconductor-metahdep/meta.yaml b/recipes/bioconductor-metahdep/meta.yaml index c8dc23a250052..20998b3c3eea4 100644 --- a/recipes/bioconductor-metahdep/meta.yaml +++ b/recipes/bioconductor-metahdep/meta.yaml @@ -1,49 +1,55 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "metahdep" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Hierarchical Dependence in Meta-Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 578b66621982372185989aa8559f8293 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metahdep", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:metahdep + - doi:10.1093/bioinformatics/btp468 + parent_recipe: + name: bioconductor-metahdep + path: recipes/bioconductor-metahdep + version: 1.38.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: affyPLM requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: caaf064d7e18803a472e8fccfc255c58 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Hierarchical Dependence in Meta-Analysis' - description: 'Tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:metahdep - - doi:10.1093/bioinformatics/btp468 - parent_recipe: - name: bioconductor-metahdep - path: recipes/bioconductor-metahdep - version: 1.38.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metams/meta.yaml b/recipes/bioconductor-metams/meta.yaml index af42016d642d6..b97f09caff873 100644 --- a/recipes/bioconductor-metams/meta.yaml +++ b/recipes/bioconductor-metams/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "metaMS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MS-based metabolomics data processing and compound annotation pipeline. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: MS-based metabolomics annotation pipeline -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c26507515ab859aa42dbea4acc8cacc3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metams", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:metams + parent_recipe: + name: bioconductor-metams + path: recipes/bioconductor-metams + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: metaMSdata, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-camera >=1.58.0,<1.59.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-camera >=1.62.0,<1.63.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base - r-matrix - r-robustbase run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-camera >=1.58.0,<1.59.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-camera >=1.62.0,<1.63.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base - r-matrix - r-robustbase + +source: + md5: f83ed753222affdaaa30a48cdd250c76 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'MS-based metabolomics annotation pipeline' - description: 'MS-based metabolomics data processing and compound annotation pipeline.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:metams - parent_recipe: - name: bioconductor-metams - path: recipes/bioconductor-metams - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metamsdata/meta.yaml b/recipes/bioconductor-metamsdata/meta.yaml index b6730e4cfe2c3..a1e359bbf7879 100644 --- a/recipes/bioconductor-metamsdata/meta.yaml +++ b/recipes/bioconductor-metamsdata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "metaMSdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa7ca09c8f43104cb85f69fda0a1fc1a +about: + description: Example CDF data for the metaMS package + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Example CDF data for the metaMS package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metamsdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a7a51ec5456a74897baff56060a85fae + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Example CDF data for the metaMS package' - description: 'Example CDF data for the metaMS package' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metamsdata/post-link.sh b/recipes/bioconductor-metamsdata/post-link.sh index 6e2a1a56a7ab7..066a937699a2f 100644 --- a/recipes/bioconductor-metamsdata/post-link.sh +++ b/recipes/bioconductor-metamsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "metamsdata-1.38.0" +installBiocDataPackage.sh "metamsdata-1.42.0" diff --git a/recipes/bioconductor-metaneighbor/meta.yaml b/recipes/bioconductor-metaneighbor/meta.yaml index cdd31dff18139..0c79b61cf43b9 100644 --- a/recipes/bioconductor-metaneighbor/meta.yaml +++ b/recipes/bioconductor-metaneighbor/meta.yaml @@ -1,61 +1,66 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "MetaNeighbor" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MetaNeighbor allows users to quantify cell type replicability across datasets using neighbor voting. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Single cell replicability analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4b42a5bac6ac46bdff32c5cce84e448d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metaneighbor", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr (>= 1.17), rmarkdown (>= 1.6), testthat (>= 1.0.2), UpSetR requirements: host: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-beanplot >=1.2' + - r-beanplot >=1.2 - r-dplyr - r-ggplot2 - - 'r-gplots >=3.0.1' + - r-gplots >=3.0.1 - r-igraph - - 'r-matrix >=1.2' - - 'r-matrixstats >=0.54' - - 'r-rcolorbrewer >=1.1.2' + - r-matrix >=1.2 + - r-matrixstats >=0.54 + - r-rcolorbrewer >=1.1.2 - r-tibble - r-tidyr run: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-beanplot >=1.2' + - r-beanplot >=1.2 - r-dplyr - r-ggplot2 - - 'r-gplots >=3.0.1' + - r-gplots >=3.0.1 - r-igraph - - 'r-matrix >=1.2' - - 'r-matrixstats >=0.54' - - 'r-rcolorbrewer >=1.1.2' + - r-matrix >=1.2 + - r-matrixstats >=0.54 + - r-rcolorbrewer >=1.1.2 - r-tibble - r-tidyr + +source: + md5: 52c2fb3ee0727af453d43816a2c91f13 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Single cell replicability analysis' - description: 'MetaNeighbor allows users to quantify cell type replicability across datasets using neighbor voting.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metaphor/meta.yaml b/recipes/bioconductor-metaphor/meta.yaml index ee6d1a43d5289..4c9490b02589d 100644 --- a/recipes/bioconductor-metaphor/meta.yaml +++ b/recipes/bioconductor-metaphor/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "MetaPhOR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'MetaPhOR was developed to enable users to assess metabolic dysregulation using transcriptomic-level data (RNA-sequencing and Microarray data) and produce publication-quality figures. A list of differentially expressed genes (DEGs), which includes fold change and p value, from DESeq2 or limma, can be used as input, with sample size for MetaPhOR, and will produce a data frame of scores for each KEGG pathway. These scores represent the magnitude and direction of transcriptional change within the pathway, along with estimated p-values.MetaPhOR then uses these scores to visualize metabolic profiles within and between samples through a variety of mechanisms, including: bubble plots, heatmaps, and pathway models.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Metabolic Pathway Analysis of RNA -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 311e286126427130d127b23a77b3b6f4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metaphor", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, kableExtra # SystemRequirements: Cytoscape (>= 3.9.0) for the cytoPath() examples requirements: host: - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 - r-base - r-ggplot2 - r-ggrepel @@ -32,20 +33,24 @@ requirements: - r-recordlinkage - r-stringr run: - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 - r-base - r-ggplot2 - r-ggrepel - r-pheatmap - r-recordlinkage - r-stringr + +source: + md5: 1f0bda4f5f0a9ee2b6aa60ee4cd6ffab + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Metabolic Pathway Analysis of RNA' - description: 'MetaPhOR was developed to enable users to assess metabolic dysregulation using transcriptomic-level data (RNA-sequencing and Microarray data) and produce publication-quality figures. A list of differentially expressed genes (DEGs), which includes fold change and p value, from DESeq2 or limma, can be used as input, with sample size for MetaPhOR, and will produce a data frame of scores for each KEGG pathway. These scores represent the magnitude and direction of transcriptional change within the pathway, along with estimated p-values.MetaPhOR then uses these scores to visualize metabolic profiles within and between samples through a variety of mechanisms, including: bubble plots, heatmaps, and pathway models.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metapod/meta.yaml b/recipes/bioconductor-metapod/meta.yaml index 6753ccc9e4516..36f3edbc727f3 100644 --- a/recipes/bioconductor-metapod/meta.yaml +++ b/recipes/bioconductor-metapod/meta.yaml @@ -1,26 +1,36 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "metapod" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implements a variety of methods for combining p-values in differential analyses of genome-scale datasets. Functions can combine p-values across different tests in the same analysis (e.g., genomic windows in ChIP-seq, exons in RNA-seq) or for corresponding tests across separate analyses (e.g., replicated comparisons, effect of different treatment conditions). Support is provided for handling log-transformed input p-values, missing values and weighting where appropriate. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Meta-Analyses on P-Values of Differential Analyses -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 49bf3f5df3f99c0d4068224a8f51eacc build: - number: 3 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metapod", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, BiocStyle, rmarkdown # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-rcpp @@ -29,20 +39,16 @@ requirements: run: - r-base - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 5b2fb0fb730e8294a67c9eeb8c8a6f30 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Meta-Analyses on P-Values of Differential Analyses' - description: 'Implements a variety of methods for combining p-values in differential analyses of genome-scale datasets. Functions can combine p-values across different tests in the same analysis (e.g., genomic windows in ChIP-seq, exons in RNA-seq) or for corresponding tests across separate analyses (e.g., replicated comparisons, effect of different treatment conditions). Support is provided for handling log-transformed input p-values, missing values and weighting where appropriate.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 diff --git a/recipes/bioconductor-metapone/meta.yaml b/recipes/bioconductor-metapone/meta.yaml index 491d13b08b3c4..807a42295ab76 100644 --- a/recipes/bioconductor-metapone/meta.yaml +++ b/recipes/bioconductor-metapone/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "metapone" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package conducts pathway testing from untargetted metabolomics data. It requires the user to supply feature-level test results, from case-control testing, regression, or other suitable feature-level tests for the study design. Weights are given to metabolic features based on how many metabolites they could potentially match to. The package can combine positive and negative mode results in pathway tests. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Conducts pathway test of metabolomics data using a weighted permutation test -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d53938772148968f88fab10130dbc905 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metapone", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 - r-base - r-fdrtool - r-fields @@ -31,20 +32,24 @@ requirements: - r-ggrepel - r-markdown run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 - r-base - r-fdrtool - r-fields - r-ggplot2 - r-ggrepel - r-markdown + +source: + md5: ba431a307ba12da07cef26b969edccd5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Conducts pathway test of metabolomics data using a weighted permutation test' - description: 'The package conducts pathway testing from untargetted metabolomics data. It requires the user to supply feature-level test results, from case-control testing, regression, or other suitable feature-level tests for the study design. Weights are given to metabolic features based on how many metabolites they could potentially match to. The package can combine positive and negative mode results in pathway tests.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metascope/build_failure.linux-64.yaml b/recipes/bioconductor-metascope/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..1f42bad8431d1 --- /dev/null +++ b/recipes/bioconductor-metascope/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5ab65cb815f5bab5bc94b091460c4268b3f0422cf2ad13757a3191d37e142d42 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Encountered problems while solving: + - nothing provides requested bioconductor-rbowtie2 >=2.12.0,<2.13.0 + - nothing provides requested bioconductor-rsamtools >=2.22.0,<2.23.0 + + Could not solve for environment specs + The following packages are incompatible + [31mbioconductor-rbowtie2 >=2.12.0,<2.13.0 [0m does not exist (perhaps a typo or a missing channel); + [31mbioconductor-rsamtools >=2.22.0,<2.23.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rsamtools[version='>=2.22.0,<2.23.0']"), MatchSpec("bioconductor-rbowtie2[version='>=2.12.0,<2.13.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rbowtie2 >=2.12.0,<2.13.0 + - nothing provides requested bioconductor-rsamtools >=2.22.0,<2.23.0 + + Could not solve for environment specs + The following packages are incompatible + [31mbioconductor-rbowtie2 >=2.12.0,<2.13.0 [0m does not exist (perhaps a typo or a missing channel); + [31mbioconductor-rsamtools >=2.22.0,<2.23.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rsamtools[version='>=2.22.0,<2.23.0']"), MatchSpec("bioconductor-rbowtie2[version='>=2.12.0,<2.13.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rbowtie2 >=2.12.0,<2.13.0 + - nothing provides requested bioconductor-rsamtools >=2.22.0,<2.23.0 + + Could not solve for environment specs + The following packages are incompatible + [31mbioconductor-rbowtie2 >=2.12.0,<2.13.0 [0m does not exist (perhaps a typo or a missing channel); + [31mbioconductor-rsamtools >=2.22.0,<2.23.0 [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-metascope/meta.yaml b/recipes/bioconductor-metascope/meta.yaml index 4e41830dd7494..3ed7b00f573af 100644 --- a/recipes/bioconductor-metascope/meta.yaml +++ b/recipes/bioconductor-metascope/meta.yaml @@ -1,75 +1,82 @@ -{% set version = "1.2.0" %} +{% set version = "1.5.4" %} {% set name = "MetaScope" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains tools and methods for preprocessing microbiome data. Functionality includes library generation, demultiplexing, alignment, and microbe identification. It is in part an R translation of the PathoScope 2.0 pipeline. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3e9dbacc12fa3bd332773ffa95325f0b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metascope", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, biomformat, knitr, lintr, plyr, R.utils, rmarkdown, Rsubread, spelling, sys, testthat, usethis + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: animalcules, BiocStyle, biomformat, GenomicRanges, IRanges, knitr, lintr, plyr, R.utils, rmarkdown, Rsubread, spelling, sys, taxonomizr, testthat, usethis requirements: + host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-rbowtie2 >=2.12.0,<2.13.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-dplyr - r-ggplot2 - r-magrittr - r-matrix - - r-qlcmatrix - r-readr - r-rlang - r-stringr - r-taxize + - r-tibble - r-tidyr + run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-rbowtie2 >=2.12.0,<2.13.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-dplyr - r-ggplot2 - r-magrittr - r-matrix - - r-qlcmatrix - r-readr - r-rlang - r-stringr - r-taxize + - r-tibble - r-tidyr - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: d3f60d78fb0987fa182b408d6a83fe8b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data' - description: 'This package contains tools and methods for preprocessing microbiome data. Functionality includes library generation, demultiplexing, alignment, and microbe identification. It is in part an R translation of the PathoScope 2.0 pipeline.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metascope/post-link.sh b/recipes/bioconductor-metascope/post-link.sh index e3bd6b90fb0e0..8753879c30aaa 100644 --- a/recipes/bioconductor-metascope/post-link.sh +++ b/recipes/bioconductor-metascope/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "metascope-1.2.0" +installBiocDataPackage.sh "metascope-1.5.4" diff --git a/recipes/bioconductor-metaseq/meta.yaml b/recipes/bioconductor-metaseq/meta.yaml index 8aafac7b3bdf8..2f8b20ffdfb16 100644 --- a/recipes/bioconductor-metaseq/meta.yaml +++ b/recipes/bioconductor-metaseq/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "metaSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Meta-analysis of RNA-Seq count data in multiple studies -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8c3ee60501395cc86ecda6817d0d5439 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metaseq", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:metaseq + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-metaseq + path: recipes/bioconductor-metaseq + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - - 'bioconductor-noiseq >=2.46.0,<2.47.0' + - bioconductor-noiseq >=2.50.0,<2.51.0 - r-base - r-rcpp - r-snow - libblas - liblapack run: - - 'bioconductor-noiseq >=2.46.0,<2.47.0' + - bioconductor-noiseq >=2.50.0,<2.51.0 - r-base - r-rcpp - r-snow - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} + +source: + md5: be93adc0d88b6db57cf47d684bdd7c68 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Meta-analysis of RNA-Seq count data in multiple studies' - description: 'The probabilities by one-sided NOISeq are combined by Fisher''s method or Stouffer''s method' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:metaseq - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-metaseq - path: recipes/bioconductor-metaseq - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metaseqr2/build.sh b/recipes/bioconductor-metaseqr2/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-metaseqr2/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metaseqr2/meta.yaml b/recipes/bioconductor-metaseqr2/meta.yaml new file mode 100644 index 0000000000000..b6dfca3b972bc --- /dev/null +++ b/recipes/bioconductor-metaseqr2/meta.yaml @@ -0,0 +1,245 @@ +{% set version = "1.18.0" %} +{% set name = "metaseqR2" %} +{% set bioc = "3.20" %} + +about: + description: Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metaseqr2", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, BiocManager, BSgenome, knitr, RMySQL, RUnit +requirements: + + build: + - {{ compiler('c') }} + - make + + host: + + - bioconductor-absseq >=1.60.0,<1.61.0 + + - bioconductor-biobase >=2.66.0,<2.67.0 + + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + + - bioconductor-biocparallel >=1.40.0,<1.41.0 + + - bioconductor-biomart >=2.62.0,<2.63.0 + + - bioconductor-biostrings >=2.74.0,<2.75.0 + + - bioconductor-deseq2 >=1.46.0,<1.47.0 + + - bioconductor-dss >=2.54.0,<2.55.0 + + - bioconductor-edaseq >=2.40.0,<2.41.0 + + - bioconductor-edger >=4.4.0,<4.5.0 + + - bioconductor-genefilter >=1.88.0,<1.89.0 + + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + + - bioconductor-genomicranges >=1.58.0,<1.59.0 + + - bioconductor-iranges >=2.40.0,<2.41.0 + + - bioconductor-limma >=3.62.0,<3.63.0 + + - bioconductor-qvalue >=2.38.0,<2.39.0 + + - bioconductor-rsamtools >=2.22.0,<2.23.0 + + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + + - bioconductor-s4vectors >=0.44.0,<0.45.0 + + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + + - bioconductor-survcomp >=1.56.0,<1.57.0 + + - bioconductor-txdbmaker >=1.2.0,<1.3.0 + + - bioconductor-vsn >=3.74.0,<3.75.0 + + - r-base + + - r-corrplot + + - r-dt + + - r-gplots + + - r-harmonicmeanp + + - r-heatmaply + + - r-htmltools + + - r-httr + + - r-jsonlite + + - r-lattice + + - r-locfit + + - r-log4r + + - r-magrittr + + - r-mass + + - r-matrix + + - r-nbpseq + + - r-pander + + - r-rmarkdown + + - r-rmdformats + + - r-rsqlite + + - r-stringr + + - r-venndiagram + + - r-yaml + + - r-zoo + + - libblas + + - liblapack + + run: + + - bioconductor-absseq >=1.60.0,<1.61.0 + + - bioconductor-biobase >=2.66.0,<2.67.0 + + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + + - bioconductor-biocparallel >=1.40.0,<1.41.0 + + - bioconductor-biomart >=2.62.0,<2.63.0 + + - bioconductor-biostrings >=2.74.0,<2.75.0 + + - bioconductor-deseq2 >=1.46.0,<1.47.0 + + - bioconductor-dss >=2.54.0,<2.55.0 + + - bioconductor-edaseq >=2.40.0,<2.41.0 + + - bioconductor-edger >=4.4.0,<4.5.0 + + - bioconductor-genefilter >=1.88.0,<1.89.0 + + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + + - bioconductor-genomicranges >=1.58.0,<1.59.0 + + - bioconductor-iranges >=2.40.0,<2.41.0 + + - bioconductor-limma >=3.62.0,<3.63.0 + + - bioconductor-qvalue >=2.38.0,<2.39.0 + + - bioconductor-rsamtools >=2.22.0,<2.23.0 + + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + + - bioconductor-s4vectors >=0.44.0,<0.45.0 + + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + + - bioconductor-survcomp >=1.56.0,<1.57.0 + + - bioconductor-txdbmaker >=1.2.0,<1.3.0 + + - bioconductor-vsn >=3.74.0,<3.75.0 + + - r-base + + - r-corrplot + + - r-dt + + - r-gplots + + - r-harmonicmeanp + + - r-heatmaply + + - r-htmltools + + - r-httr + + - r-jsonlite + + - r-lattice + + - r-locfit + + - r-log4r + + - r-magrittr + + - r-mass + + - r-matrix + + - r-nbpseq + + - r-pander + + - r-rmarkdown + + - r-rmdformats + + - r-rsqlite + + - r-stringr + + - r-venndiagram + + - r-yaml + + - r-zoo + +source: + md5: 63be3ca96bdfbeb4262124fe5f8fa4a2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-metcirc/meta.yaml b/recipes/bioconductor-metcirc/meta.yaml index c70232ee98cfa..30dfd53966d1d 100644 --- a/recipes/bioconductor-metcirc/meta.yaml +++ b/recipes/bioconductor-metcirc/meta.yaml @@ -1,55 +1,22 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "MetCirc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MetCirc comprises a workflow to interactively explore high-resolution MS/MS metabolomics data. MetCirc uses the Spectra object infrastructure defined in the package Spectra that stores MS/MS spectra. MetCirc offers functionality to calculate similarity between precursors based on the normalised dot product, neutral losses or user-defined functions and visualise similarities in a circular layout. Within the interactive framework the user can annotate MS/MS features based on their similarity to (known) related MS/MS features. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c21a385245acf6911f5c762093ea6e0b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metcirc", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocGenerics, graphics (>= 3.5), grDevices (>= 3.5), knitr (>= 1.11), testthat (>= 2.2.1) -requirements: - host: - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' - - 'r-amap >=0.8' - - r-base - - 'r-circlize >=0.3.9' - - 'r-ggplot2 >=3.2.1' - - 'r-scales >=0.3.0' - - 'r-shiny >=1.0.0' - run: - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' - - 'r-amap >=0.8' - - r-base - - 'r-circlize >=0.3.9' - - 'r-ggplot2 >=3.2.1' - - 'r-scales >=0.3.0' - - 'r-shiny >=1.0.0' -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics data' - description: 'MetCirc comprises a workflow to interactively explore high-resolution MS/MS metabolomics data. MetCirc uses the Spectra object infrastructure defined in the package Spectra that stores MS/MS spectra. MetCirc offers functionality to calculate similarity between precursors based on the normalised dot product, neutral losses or user-defined functions and visualise similarities in a circular layout. Within the interactive framework the user can annotate MS/MS features based on their similarity to (known) related MS/MS features.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:metcirc @@ -59,3 +26,42 @@ extra: path: recipes/bioconductor-metcirc version: 1.12.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocGenerics, graphics (>= 4.4), grDevices (>= 4.4), knitr (>= 1.48), testthat (>= 3.2.1.1) +requirements: + host: + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 + - r-amap >=0.8 + - r-base + - r-circlize >=0.4.16 + - r-ggplot2 >=3.5.1 + - r-scales >=1.3.0 + - r-shiny >=1.8.1.1 + run: + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 + - r-amap >=0.8 + - r-base + - r-circlize >=0.4.16 + - r-ggplot2 >=3.5.1 + - r-scales >=1.3.0 + - r-shiny >=1.8.1.1 + +source: + md5: e94760cb48342a59a9e4bfece8819176 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-methimpute/meta.yaml b/recipes/bioconductor-methimpute/meta.yaml index 65d687e154683..f268b837fd16a 100644 --- a/recipes/bioconductor-methimpute/meta.yaml +++ b/recipes/bioconductor-methimpute/meta.yaml @@ -1,64 +1,70 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "methimpute" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements functions for calling methylation for all cytosines in the genome. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Imputation-guided re-construction of complete methylomes from WGBS data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7b2a598d7391c33c4ba82639616077e6 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methimpute", max_pin="x.x") }}' + +extra: + parent_recipe: + name: bioconductor-methimpute + path: recipes/bioconductor-methimpute + version: 1.4.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-data.table - r-ggplot2 - r-minpack.lm - - 'r-rcpp >=0.12.4.5' + - r-rcpp >=0.12.4.5 - r-reshape2 - libblas - liblapack run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-data.table - r-ggplot2 - r-minpack.lm - - 'r-rcpp >=0.12.4.5' + - r-rcpp >=0.12.4.5 - r-reshape2 - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 5a7c64502af590d30eb3f937d9fb748d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Imputation-guided re-construction of complete methylomes from WGBS data' - description: 'This package implements functions for calling methylation for all cytosines in the genome.' -extra: - parent_recipe: - name: bioconductor-methimpute - path: recipes/bioconductor-methimpute - version: 1.4.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methinheritsim/meta.yaml b/recipes/bioconductor-methinheritsim/meta.yaml index d131c38563f89..676b190076fd1 100644 --- a/recipes/bioconductor-methinheritsim/meta.yaml +++ b/recipes/bioconductor-methinheritsim/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "methInheritSim" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Simulate a multigeneration methylation case versus control experiment with inheritance relation using a real control dataset. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Simulating Whole-Genome Inherited Bisulphite Sequencing Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c695628dcb686ee7e6a3f4ee134481ff build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methinheritsim", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, RUnit, methylInheritance requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-methylkit >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-methylkit >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-msm run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-methylkit >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-methylkit >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-msm + +source: + md5: c5c9e518658133356a0375b044db6f10 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Simulating Whole-Genome Inherited Bisulphite Sequencing Data' - description: 'Simulate a multigeneration methylation case versus control experiment with inheritance relation using a real control dataset.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methped/meta.yaml b/recipes/bioconductor-methped/meta.yaml index ab47c7a890944..23b716eb16308 100644 --- a/recipes/bioconductor-methped/meta.yaml +++ b/recipes/bioconductor-methped/meta.yaml @@ -1,49 +1,55 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "MethPed" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Classification of pediatric tumors into biologically defined subtypes is challenging and multifaceted approaches are needed. For this aim, we developed a diagnostic classifier based on DNA methylation profiles. We offer MethPed as an easy-to-use toolbox that allows researchers and clinical diagnosticians to test single samples as well as large cohorts for subclass prediction of pediatric brain tumors. The current version of MethPed can classify the following tumor diagnoses/subgroups: Diffuse Intrinsic Pontine Glioma (DIPG), Ependymoma, Embryonal tumors with multilayered rosettes (ETMR), Glioblastoma (GBM), Medulloblastoma (MB) - Group 3 (MB_Gr3), Group 4 (MB_Gr3), Group WNT (MB_WNT), Group SHH (MB_SHH) and Pilocytic Astrocytoma (PiloAstro).' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 57b633da5d8548342b0a2071efe3c04d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methped", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:methped + - doi:10.1186/s13148-015-0103-3 + parent_recipe: + name: bioconductor-methped + path: recipes/bioconductor-methped + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, markdown, impute requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-randomforest run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-randomforest + +source: + md5: 181fbe7f9413884ea5adac4fe74f1f99 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes' - description: 'Classification of pediatric tumors into biologically defined subtypes is challenging and multifaceted approaches are needed. For this aim, we developed a diagnostic classifier based on DNA methylation profiles. We offer MethPed as an easy-to-use toolbox that allows researchers and clinical diagnosticians to test single samples as well as large cohorts for subclass prediction of pediatric brain tumors. The current version of MethPed can classify the following tumor diagnoses/subgroups: Diffuse Intrinsic Pontine Glioma (DIPG), Ependymoma, Embryonal tumors with multilayered rosettes (ETMR), Glioblastoma (GBM), Medulloblastoma (MB) - Group 3 (MB_Gr3), Group 4 (MB_Gr3), Group WNT (MB_WNT), Group SHH (MB_SHH) and Pilocytic Astrocytoma (PiloAstro).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:methped - - doi:10.1186/s13148-015-0103-3 - parent_recipe: - name: bioconductor-methped - path: recipes/bioconductor-methped - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methrix/meta.yaml b/recipes/bioconductor-methrix/meta.yaml index bd7c11532203f..3089158998ea1 100644 --- a/recipes/bioconductor-methrix/meta.yaml +++ b/recipes/bioconductor-methrix/meta.yaml @@ -1,61 +1,66 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "methrix" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Bedgraph files generated by Bisulfite pipelines often come in various flavors. Critical downstream step requires summarization of these files into methylation/coverage matrices. This step of data aggregation is done by Methrix, including many other useful downstream functions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Fast and efficient summarization of generic bedGraph files from Bisufite sequencing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7bdda59fc802fc09d10ca9a4916cfe94 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methrix", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, BSgenome.Hsapiens.UCSC.hg19, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-data.table >=1.12.4' + - r-data.table >=1.12.4 - r-ggplot2 - r-matrixstats run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-data.table >=1.12.4' + - r-data.table >=1.12.4 - r-ggplot2 - r-matrixstats + +source: + md5: d5a1bcccf94805215885bf668a24a421 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Fast and efficient summarization of generic bedGraph files from Bisufite sequencing' - description: 'Bedgraph files generated by Bisulfite pipelines often come in various flavors. Critical downstream step requires summarization of these files into methylation/coverage matrices. This step of data aggregation is done by Methrix, including many other useful downstream functions.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methtargetedngs/meta.yaml b/recipes/bioconductor-methtargetedngs/meta.yaml index fb49f0aa6445e..cce9b164aede3 100644 --- a/recipes/bioconductor-methtargetedngs/meta.yaml +++ b/recipes/bioconductor-methtargetedngs/meta.yaml @@ -1,54 +1,62 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "MethTargetedNGS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Perform step by step methylation analysis of Next Generation Sequencing data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Perform Methylation Analysis on Next Generation Sequencing Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0bce9edc9682a9ca23653409301d7225 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methtargetedngs", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:methtargetedngs + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-methtargetedngs + path: recipes/bioconductor-methtargetedngs + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # SystemRequirements: HMMER3 requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 - r-base - r-gplots - r-seqinr - r-stringr - - 'hmmer >=3' + - hmmer >=3 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 - r-base - r-gplots - r-seqinr - r-stringr - - 'hmmer >=3' + - hmmer >=3 + +source: + md5: a8d565caedbbee4c1e3028b13b58f6c6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Perform Methylation Analysis on Next Generation Sequencing Data' - description: 'Perform step by step methylation analysis of Next Generation Sequencing data.' -extra: - identifiers: - - biotools:methtargetedngs - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-methtargetedngs - path: recipes/bioconductor-methtargetedngs - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methylaid/meta.yaml b/recipes/bioconductor-methylaid/meta.yaml index d6bdffb88c0f7..6761dd63d0391 100644 --- a/recipes/bioconductor-methylaid/meta.yaml +++ b/recipes/bioconductor-methylaid/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "MethylAid" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A visual and interactive web application using RStudio's shiny package. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Visual and interactive quality control of large Illumina DNA Methylation array data sets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e5139726d6384208be410a794ba6388 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methylaid", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-gridbase @@ -35,11 +37,11 @@ requirements: - r-rcolorbrewer - r-shiny run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-gridbase @@ -47,13 +49,16 @@ requirements: - r-matrixstats - r-rcolorbrewer - r-shiny + +source: + md5: 9f94767e837e9b31a3fae0855698343d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Visual and interactive quality control of large Illumina DNA Methylation array data sets' - description: 'A visual and interactive web application using RStudio''s shiny package. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methylaiddata/meta.yaml b/recipes/bioconductor-methylaiddata/meta.yaml index 9d93dbaa10899..59f93e286e7dc 100644 --- a/recipes/bioconductor-methylaiddata/meta.yaml +++ b/recipes/bioconductor-methylaiddata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "MethylAidData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 95cc72b436067e4a8046564381101e04 +about: + description: A data package containing summarized Illumina 450k array data on 2800 samples and summarized EPIC data for 2620 samples. The data can be use as a background data set in the interactive application. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: MethylAid-summarized data for 2800 Illumina 450k array samples and 2620 EPIC array samples build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methylaiddata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC requirements: host: - - 'bioconductor-methylaid >=1.36.0,<1.37.0' + - bioconductor-methylaid >=1.40.0,<1.41.0 - r-base run: - - 'bioconductor-methylaid >=1.36.0,<1.37.0' + - bioconductor-methylaid >=1.40.0,<1.41.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8790cb85810d6013ce273669a726c75e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'MethylAid-summarized data for 2800 Illumina 450k array samples and 2620 EPIC array samples' - description: 'A data package containing summarized Illumina 450k array data on 2800 samples and summarized EPIC data for 2620 samples. The data can be use as a background data set in the interactive application.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methylaiddata/post-link.sh b/recipes/bioconductor-methylaiddata/post-link.sh index 05ddd59e85e4c..d62e0be1bbc35 100644 --- a/recipes/bioconductor-methylaiddata/post-link.sh +++ b/recipes/bioconductor-methylaiddata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "methylaiddata-1.34.0" +installBiocDataPackage.sh "methylaiddata-1.38.0" diff --git a/recipes/bioconductor-methylcc/meta.yaml b/recipes/bioconductor-methylcc/meta.yaml index 55e496807a54b..f891b20f5d495 100644 --- a/recipes/bioconductor-methylcc/meta.yaml +++ b/recipes/bioconductor-methylcc/meta.yaml @@ -1,67 +1,72 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "methylCC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A tool to estimate the cell composition of DNA methylation whole blood sample measured on any platform technology (microarray and sequencing). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Estimate the cell composition of whole blood in DNA methylation samples -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 77566e7338f615ca5305d6e00465908b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methylcc", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-bsseq >=1.38.0,<1.39.0' - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-flowsorted.blood.450k >=1.40.0,<1.41.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-bsseq >=1.42.0,<1.43.0 + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-flowsorted.blood.450k >=1.44.0,<1.45.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-magrittr - r-quadprog run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-bsseq >=1.38.0,<1.39.0' - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-flowsorted.blood.450k >=1.40.0,<1.41.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-bsseq >=1.42.0,<1.43.0 + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-flowsorted.blood.450k >=1.44.0,<1.45.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-magrittr - r-quadprog + +source: + md5: 0cbe8d66d84cf953afdc8c2352b9b1b4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Estimate the cell composition of whole blood in DNA methylation samples' - description: 'A tool to estimate the cell composition of DNA methylation whole blood sample measured on any platform technology (microarray and sequencing).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methylclock/meta.yaml b/recipes/bioconductor-methylclock/meta.yaml index 16024462c189f..314d8f6974109 100644 --- a/recipes/bioconductor-methylclock/meta.yaml +++ b/recipes/bioconductor-methylclock/meta.yaml @@ -1,33 +1,41 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "methylclock" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'This package allows to estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks. Chronological DNAm age (in years) : Horvath''s clock, Hannum''s clock, BNN, Horvath''s skin+blood clock, PedBE clock and Wu''s clock. Gestational DNAm age : Knight''s clock, Bohlin''s clock, Mayne''s clock and Lee''s clocks. Biological DNAm clocks : Levine''s clock and Telomere Length''s clock.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Methylclock - DNA methylation-based clocks -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b6151e23d6086f38d6489dcc277c81c9 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methylclock", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, GEOquery, rmarkdown requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-methylclockdata >=1.10.0,<1.11.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-planet >=1.10.0,<1.11.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-methylclockdata >=1.14.0,<1.15.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-planet >=1.14.0,<1.15.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-devtools - r-dplyr @@ -38,21 +46,22 @@ requirements: - r-gridextra - r-performanceanalytics - r-quadprog - - 'r-rcpp >=1.0.6' + - r-rcpp >=1.0.6 - r-rpmm - r-tibble - r-tidyr - r-tidyverse - libblas - liblapack + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-methylclockdata >=1.10.0,<1.11.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-planet >=1.10.0,<1.11.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-methylclockdata >=1.14.0,<1.15.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-planet >=1.14.0,<1.15.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-devtools - r-dplyr @@ -63,22 +72,21 @@ requirements: - r-gridextra - r-performanceanalytics - r-quadprog - - 'r-rcpp >=1.0.6' + - r-rcpp >=1.0.6 - r-rpmm - r-tibble - r-tidyr - r-tidyverse - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 61d2f452c0d86f49888d77bf94b7afa0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Methylclock - DNA methylation-based clocks' - description: 'This package allows to estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks. Chronological DNAm age (in years) : Horvath''s clock, Hannum''s clock, BNN, Horvath''s skin+blood clock, PedBE clock and Wu''s clock. Gestational DNAm age : Knight''s clock, Bohlin''s clock, Mayne''s clock and Lee''s clocks. Biological DNAm clocks : Levine''s clock and Telomere Length''s clock.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methylclockdata/meta.yaml b/recipes/bioconductor-methylclockdata/meta.yaml index 771be08cf1782..36c786068cb89 100644 --- a/recipes/bioconductor-methylclockdata/meta.yaml +++ b/recipes/bioconductor-methylclockdata/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "methylclockData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 633d9cc6c028025090e12004484fada1 +about: + description: Collection of 9 datasets, andrews and bakulski cord blood, blood gse35069, blood gse35069 chen, blood gse35069 complete, combined cord blood, cord bloo d gse68456, gervin and lyle cord blood, guintivano dlpfc and saliva gse48472". Data downloaded from [meffil](https://github.com/perishky/meffil/). Data used to estimate cell counts using Extrinsic epigenetic age acceleration (EEAA) method Collection of 12 datasets to use with MethylClock package to estimate chronological and gestational DNA methylationwith estimators to use wit different methylation clocks + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Data for methylclock package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methylclockdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-experimenthubdata >=1.28.0,<1.29.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-experimenthubdata >=1.32.0,<1.33.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-experimenthubdata >=1.28.0,<1.29.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-experimenthubdata >=1.32.0,<1.33.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ad071093db338056dbd6cf1951640286 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Data for methylclock package' - description: 'Collection of 9 datasets, andrews and bakulski cord blood, blood gse35069, blood gse35069 chen, blood gse35069 complete, combined cord blood, cord bloo d gse68456, gervin and lyle cord blood, guintivano dlpfc and saliva gse48472". Data downloaded from [meffil](https://github.com/perishky/meffil/). Data used to estimate cell counts using Extrinsic epigenetic age acceleration (EEAA) method Collection of 12 datasets to use with MethylClock package to estimate chronological and gestational DNA methylationwith estimators to use wit different methylation clocks' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methylclockdata/post-link.sh b/recipes/bioconductor-methylclockdata/post-link.sh index 16f98ea792eb3..1fb4602823cf0 100644 --- a/recipes/bioconductor-methylclockdata/post-link.sh +++ b/recipes/bioconductor-methylclockdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "methylclockdata-1.10.0" +installBiocDataPackage.sh "methylclockdata-1.14.0" diff --git a/recipes/bioconductor-methylgsa/meta.yaml b/recipes/bioconductor-methylgsa/meta.yaml index 9858e7286e22e..90c863e7f93a6 100644 --- a/recipes/bioconductor-methylgsa/meta.yaml +++ b/recipes/bioconductor-methylgsa/meta.yaml @@ -1,63 +1,68 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "methylGSA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The main functions for methylGSA are methylglm and methylRRA. methylGSA implements logistic regression adjusting number of probes as a covariate. methylRRA adjusts multiple p-values of each gene by Robust Rank Aggregation. For more detailed help information, please see the vignette. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Gene Set Analysis Using the Outcome of Differential Methylation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e802fab6abc1a9bac64bc36dd588c19d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methylgsa", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, enrichplot requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-missmethyl >=1.36.0,<1.37.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0 + - bioconductor-missmethyl >=1.40.0,<1.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-reactome.db >=1.89.0,<1.90.0 - r-base - r-ggplot2 - r-robustrankaggreg - r-shiny - r-stringr run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-missmethyl >=1.36.0,<1.37.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0 + - bioconductor-missmethyl >=1.40.0,<1.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-reactome.db >=1.89.0,<1.90.0 - r-base - r-ggplot2 - r-robustrankaggreg - r-shiny - r-stringr + +source: + md5: 42c3e90fd0fe7b2787b15b99c5835771 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Gene Set Analysis Using the Outcome of Differential Methylation' - description: 'The main functions for methylGSA are methylglm and methylRRA. methylGSA implements logistic regression adjusting number of probes as a covariate. methylRRA adjusts multiple p-values of each gene by Robust Rank Aggregation. For more detailed help information, please see the vignette.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methylimp2/build.sh b/recipes/bioconductor-methylimp2/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-methylimp2/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-methylimp2/meta.yaml b/recipes/bioconductor-methylimp2/meta.yaml new file mode 100644 index 0000000000000..357a812ce440f --- /dev/null +++ b/recipes/bioconductor-methylimp2/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.2.0" %} +{% set name = "methyLImp2" %} +{% set bioc = "3.20" %} + +about: + description: This package allows to estimate missing values in DNA methylation data. methyLImp method is based on linear regression since methylation levels show a high degree of inter-sample correlation. Implementation is parallelised over chromosomes since probes on different chromosomes are usually independent. Mini-batch approach to reduce the runtime in case of large number of samples is available. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Missing value estimation of DNA methylation data +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-methylimp2", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: BiocStyle, knitr, rmarkdown, spelling, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-champdata >=2.38.0,<2.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-corpcor + run: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-champdata >=2.38.0,<2.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-corpcor +source: + md5: 5ccde94b54c5ca73e1765c3e3fb31169 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-methylinheritance/meta.yaml b/recipes/bioconductor-methylinheritance/meta.yaml index c3fcbcbda2b35..eaa0a8dda3f49 100644 --- a/recipes/bioconductor-methylinheritance/meta.yaml +++ b/recipes/bioconductor-methylinheritance/meta.yaml @@ -1,52 +1,57 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "methylInheritance" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Permutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0242605800daea10c810fa356cb2cf0c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methylinheritance", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit, methInheritSim requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-methylkit >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-methylkit >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-gridextra - r-rebus run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-methylkit >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-methylkit >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-gridextra - r-rebus + +source: + md5: 1ee0a93516c8802eba1d5758931fe7d4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect' - description: 'Permutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methylkit/meta.yaml b/recipes/bioconductor-methylkit/meta.yaml index a0eb42e2b27ef..99e75e43c69e5 100644 --- a/recipes/bioconductor-methylkit/meta.yaml +++ b/recipes/bioconductor-methylkit/meta.yaml @@ -1,40 +1,57 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "methylKit" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Methylation calling can be performed directly from Bismark aligned BAM files. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: DNA methylation analysis from high-throughput bisulfite sequencing results -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5e21ca2558b439a2f542492eeec0f99d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methylkit", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:methylkit + parent_recipe: + name: bioconductor-methylkit + path: recipes/bioconductor-methylkit + version: 1.6.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager # SystemRequirements: GNU make requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-fastseg >=1.48.0,<1.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-fastseg >=1.52.0,<1.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - - 'r-data.table >=1.9.6' + - r-data.table >=1.9.6 - r-emdbook - r-gtools - r-kernsmooth @@ -44,20 +61,23 @@ requirements: - r-rcpp - libblas - liblapack + - zlib + - liblzma-devel + run: - - 'bioconductor-fastseg >=1.48.0,<1.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-fastseg >=1.52.0,<1.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - - 'r-data.table >=1.9.6' + - r-data.table >=1.9.6 - r-emdbook - r-gtools - r-kernsmooth @@ -65,25 +85,16 @@ requirements: - r-mgcv - r-r.utils - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 569d9049779250a340f2543af4bdd088 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'DNA methylation analysis from high-throughput bisulfite sequencing results' - description: 'methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Methylation calling can be performed directly from Bismark aligned BAM files.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:methylkit - parent_recipe: - name: bioconductor-methylkit - path: recipes/bioconductor-methylkit - version: 1.6.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methylmix/meta.yaml b/recipes/bioconductor-methylmix/meta.yaml index 80533398aa225..6275e82492866 100644 --- a/recipes/bioconductor-methylmix/meta.yaml +++ b/recipes/bioconductor-methylmix/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "2.32.0" %} +{% set version = "2.36.0" %} {% set name = "MethylMix" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'MethylMix is an algorithm implemented to identify hyper and hypomethylated genes for a disease. MethylMix is based on a beta mixture model to identify methylation states and compares them with the normal DNA methylation state. MethylMix uses a novel statistic, the Differential Methylation value or DM-value defined as the difference of a methylation state with the normal methylation state. Finally, matched gene expression data is used to identify, besides differential, functional methylation states by focusing on methylation changes that effect gene expression. References: Gevaert 0. MethylMix: an R package for identifying DNA methylation-driven genes. Bioinformatics (Oxford, England). 2015;31(11):1839-41. doi:10.1093/bioinformatics/btv020. Gevaert O, Tibshirani R, Plevritis SK. Pancancer analysis of DNA methylation-driven genes using MethylMix. Genome Biology. 2015;16(1):17. doi:10.1186/s13059-014-0579-8.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'MethylMix: Identifying methylation driven cancer genes' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a716254f6aff8e65daf63cdcd939704 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methylmix", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-data.table - r-digest @@ -34,8 +36,8 @@ requirements: - r-rcurl - r-rpmm run: - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-data.table - r-digest @@ -45,13 +47,16 @@ requirements: - r-rcolorbrewer - r-rcurl - r-rpmm + +source: + md5: 9b79302bb00794b653e9a28742e0449e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'MethylMix: Identifying methylation driven cancer genes' - description: 'MethylMix is an algorithm implemented to identify hyper and hypomethylated genes for a disease. MethylMix is based on a beta mixture model to identify methylation states and compares them with the normal DNA methylation state. MethylMix uses a novel statistic, the Differential Methylation value or DM-value defined as the difference of a methylation state with the normal methylation state. Finally, matched gene expression data is used to identify, besides differential, functional methylation states by focusing on methylation changes that effect gene expression. References: Gevaert 0. MethylMix: an R package for identifying DNA methylation-driven genes. Bioinformatics (Oxford, England). 2015;31(11):1839-41. doi:10.1093/bioinformatics/btv020. Gevaert O, Tibshirani R, Plevritis SK. Pancancer analysis of DNA methylation-driven genes using MethylMix. Genome Biology. 2015;16(1):17. doi:10.1186/s13059-014-0579-8.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methylmnm/meta.yaml b/recipes/bioconductor-methylmnm/meta.yaml index ffae70e36fd4a..fe65b130da639 100644 --- a/recipes/bioconductor-methylmnm/meta.yaml +++ b/recipes/bioconductor-methylmnm/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "methylMnM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: To give the exactly p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: detect different methylation level (DMR) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d6c83c4fa30daea5b1c91e70f67c6b5 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methylmnm", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:methylmnm + - doi:10.1101/gr.156539.113 + parent_recipe: + name: bioconductor-methylmnm + path: recipes/bioconductor-methylmnm + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-edger >=4.0.0,<4.1.0' + - bioconductor-edger >=4.4.0,<4.5.0 - r-base - r-statmod - libblas - liblapack run: - - 'bioconductor-edger >=4.0.0,<4.1.0' + - bioconductor-edger >=4.4.0,<4.5.0 - r-base - r-statmod - build: - - {{ compiler('c') }} - - make + +source: + md5: 23ff1dc1c980c3bf3664854fcff99599 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'detect different methylation level (DMR)' - description: 'To give the exactly p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparation.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:methylmnm - - doi:10.1101/gr.156539.113 - parent_recipe: - name: bioconductor-methylmnm - path: recipes/bioconductor-methylmnm - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methylpipe/meta.yaml b/recipes/bioconductor-methylpipe/meta.yaml index e26a21bb9abad..8259fb29e5974 100644 --- a/recipes/bioconductor-methylpipe/meta.yaml +++ b/recipes/bioconductor-methylpipe/meta.yaml @@ -1,76 +1,82 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "methylPipe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Memory efficient analysis of base resolution DNA methylation data in both the CpG and non-CpG sequence context. Integration of DNA methylation data derived from any methodology providing base- or low-resolution data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL(>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Base resolution DNA methylation data analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bd41f308a3d5e58c4e05ce38c28f17f9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methylpipe", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:methylpipe + parent_recipe: + name: bioconductor-methylpipe + path: recipes/bioconductor-methylpipe + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-marray >=1.84.0,<1.85.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-gplots - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-marray >=1.84.0,<1.85.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-gplots - build: - - {{ compiler('c') }} - - make + +source: + md5: 65ac07ced2d2d93fb7a1b81e70383189 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-or-later - summary: 'Base resolution DNA methylation data analysis' - description: 'Memory efficient analysis of base resolution DNA methylation data in both the CpG and non-CpG sequence context. Integration of DNA methylation data derived from any methodology providing base- or low-resolution data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:methylpipe - parent_recipe: - name: bioconductor-methylpipe - path: recipes/bioconductor-methylpipe - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methylscaper/meta.yaml b/recipes/bioconductor-methylscaper/meta.yaml index 2dd87a797efc1..d4ba759ad48a5 100644 --- a/recipes/bioconductor-methylscaper/meta.yaml +++ b/recipes/bioconductor-methylscaper/meta.yaml @@ -1,30 +1,33 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "methylscaper" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: methylscaper is an R package for processing and visualizing data jointly profiling methylation and chromatin accessibility (MAPit, NOMe-seq, scNMT-seq, nanoNOMe, etc.). The package supports both single-cell and single-molecule data, and a common interface for jointly visualizing both data types through the generation of ordered representational methylation-state matrices. The Shiny app allows for an interactive seriation process of refinement and re-weighting that optimally orders the cells or DNA molecules to discover methylation patterns and nucleosome positioning. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Visualization of Methylation Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0fae72e2aac98ec4a55d8aa4343039ba build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methylscaper", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, devtools, R.utils requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-rfast @@ -34,9 +37,10 @@ requirements: - r-shinyfiles - r-shinyjs run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-rfast @@ -45,13 +49,16 @@ requirements: - r-shiny - r-shinyfiles - r-shinyjs + +source: + md5: ce8efbce696cc7f66100c0d92108cf62 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Visualization of Methylation Data' - description: 'methylscaper is an R package for processing and visualizing data jointly profiling methylation and chromatin accessibility (MAPit, NOMe-seq, scNMT-seq, nanoNOMe, etc.). The package supports both single-cell and single-molecule data, and a common interface for jointly visualizing both data types through the generation of ordered representational methylation-state matrices. The Shiny app allows for an interactive seriation process of refinement and re-weighting that optimally orders the cells or DNA molecules to discover methylation patterns and nucleosome positioning.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methylseekr/meta.yaml b/recipes/bioconductor-methylseekr/meta.yaml index 49c54a3395fbc..1edd9393e85bc 100644 --- a/recipes/bioconductor-methylseekr/meta.yaml +++ b/recipes/bioconductor-methylseekr/meta.yaml @@ -1,56 +1,62 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "MethylSeekR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This is a package for the discovery of regulatory regions from Bis-seq data + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Segmentation of Bis-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02bba9cfe7502e55a26e0ac76ba63457 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methylseekr", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:methylseekr + parent_recipe: + name: bioconductor-methylseekr + path: recipes/bioconductor-methylseekr + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Hsapiens.UCSC.hg18 requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-geneplotter >=1.80.0,<1.81.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-geneplotter >=1.84.0,<1.85.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - - 'r-mhsmm >=0.4.4' + - r-mhsmm >=0.4.4 run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-geneplotter >=1.80.0,<1.81.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-geneplotter >=1.84.0,<1.85.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - - 'r-mhsmm >=0.4.4' + - r-mhsmm >=0.4.4 + +source: + md5: b57f523a0de8f9a9c810e6b84625224c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Segmentation of Bis-seq data' - description: 'This is a package for the discovery of regulatory regions from Bis-seq data' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:methylseekr - parent_recipe: - name: bioconductor-methylseekr - path: recipes/bioconductor-methylseekr - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methylseqdata/meta.yaml b/recipes/bioconductor-methylseqdata/meta.yaml index 136355ee746c8..b15fadf952563 100644 --- a/recipes/bioconductor-methylseqdata/meta.yaml +++ b/recipes/bioconductor-methylseqdata/meta.yaml @@ -1,54 +1,59 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "MethylSeqData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Base-level (i.e. cytosine-level) counts for a collection of public bisulfite-seq datasets (e.g., WGBS and RRBS), provided as SummarizedExperiment objects with sample- and base-level metadata. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: CC0 + summary: Collection of Public DNA Methylation Sequencing Datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ded280784f55a6ebec42069160de26ad build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methylseqdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocFileCache, BiocStyle, data.table, knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 16f7382e59811b9cead8c141c39d0b5f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: CC0 - summary: 'Collection of Public DNA Methylation Sequencing Datasets' - description: 'Base-level (i.e. cytosine-level) counts for a collection of public bisulfite-seq datasets (e.g., WGBS and RRBS), provided as SummarizedExperiment objects with sample- and base-level metadata.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methylseqdata/post-link.sh b/recipes/bioconductor-methylseqdata/post-link.sh index a095ba9151fb9..2cdd717183025 100644 --- a/recipes/bioconductor-methylseqdata/post-link.sh +++ b/recipes/bioconductor-methylseqdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "methylseqdata-1.12.0" +installBiocDataPackage.sh "methylseqdata-1.16.0" diff --git a/recipes/bioconductor-methylsig/meta.yaml b/recipes/bioconductor-methylsig/meta.yaml index cd481a00b8dcc..2f9fa4607b739 100644 --- a/recipes/bioconductor-methylsig/meta.yaml +++ b/recipes/bioconductor-methylsig/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.12.0" %} +{% set version = "1.18.0" %} {% set name = "methylSig" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: MethylSig is a package for testing for differentially methylated cytosines (DMCs) or regions (DMRs) in whole-genome bisulfite sequencing (WGBS) or reduced representation bisulfite sequencing (RRBS) experiments. MethylSig uses a beta binomial model to test for significant differences between groups of samples. Several options exist for either site-specific or sliding window tests, and variance estimation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'MethylSig: Differential Methylation Testing for WGBS and RRBS Data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 12a8c7f9fdec964b1e4decf7681c1e88 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic + run_exports: '{{ pin_subpackage("bioconductor-methylsig", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr requirements: host: - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-dss >=2.48.0,<2.49.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - bioconductor-bsseq >=1.42.0,<1.43.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-dss >=2.54.0,<2.55.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-bsseq >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.26.0,<0.27.0' - - 'bioconductor-delayedmatrixstats >=1.22.0,<1.23.0' - - 'bioconductor-dss >=2.48.0,<2.49.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-iranges >=2.34.0,<2.35.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' + - bioconductor-bsseq >=1.42.0,<1.43.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-dss >=2.54.0,<2.55.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base + +source: + md5: 778774751ccacfdc083584d3478820cf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'MethylSig: Differential Methylation Testing for WGBS and RRBS Data' - description: 'MethylSig is a package for testing for differentially methylated cytosines (DMCs) or regions (DMRs) in whole-genome bisulfite sequencing (WGBS) or reduced representation bisulfite sequencing (RRBS) experiments. MethylSig uses a beta binomial model to test for significant differences between groups of samples. Several options exist for either site-specific or sliding window tests, and variance estimation.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-methylumi/meta.yaml b/recipes/bioconductor-methylumi/meta.yaml index 52c8312d6006e..cf7720d07caa7 100644 --- a/recipes/bioconductor-methylumi/meta.yaml +++ b/recipes/bioconductor-methylumi/meta.yaml @@ -1,83 +1,91 @@ -{% set version = "2.48.0" %} +{% set version = "2.52.0" %} {% set name = "methylumi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Handle Illumina methylation data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eb3792c8c9c2a778cf41e9bb7b95232b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-methylumi", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:methylumi + - doi:10.1186/1471-2164-14-293 + parent_recipe: + name: bioconductor-methylumi + path: recipes/bioconductor-methylumi + version: 2.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr requirements: + host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-fdb.infiniummethylation.hg19 >=2.2.0,<2.3.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-fdb.infiniummethylation.hg19 >=2.2.0,<2.3.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-lattice - r-matrixstats - r-reshape2 - r-scales + run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-fdb.infiniummethylation.hg19 >=2.2.0,<2.3.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-fdb.infiniummethylation.hg19 >=2.2.0,<2.3.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-lattice - r-matrixstats - r-reshape2 - r-scales + +source: + md5: c0c0bf506cee589cad3dd25dbf771106 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Handle Illumina methylation data' - description: 'This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:methylumi - - doi:10.1186/1471-2164-14-293 - parent_recipe: - name: bioconductor-methylumi - path: recipes/bioconductor-methylumi - version: 2.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metid/meta.yaml b/recipes/bioconductor-metid/meta.yaml index 3b7cbc31f2086..8f5000208e440 100644 --- a/recipes/bioconductor-metid/meta.yaml +++ b/recipes/bioconductor-metid/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "MetID" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package uses an innovative network-based approach that will enhance our ability to determine the identities of significant ions detected by LC-MS. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Network-based prioritization of putative metabolite IDs -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 873920da0ab3c4e6a3bcd9e580097b86 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metid", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr (>= 1.19), rmarkdown (>= 1.8) requirements: host: - - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - bioconductor-chemminer >=3.58.0,<3.59.0 - r-base - - 'r-devtools >=1.13.0' - - 'r-igraph >=1.2.1' - - 'r-matrix >=1.2-12' - - 'r-stringr >=1.3.0' + - r-devtools >=1.13.0 + - r-igraph >=1.2.1 + - r-matrix >=1.2-12 + - r-stringr >=1.3.0 run: - - 'bioconductor-chemminer >=3.54.0,<3.55.0' + - bioconductor-chemminer >=3.58.0,<3.59.0 - r-base - - 'r-devtools >=1.13.0' - - 'r-igraph >=1.2.1' - - 'r-matrix >=1.2-12' - - 'r-stringr >=1.3.0' + - r-devtools >=1.13.0 + - r-igraph >=1.2.1 + - r-matrix >=1.2-12 + - r-stringr >=1.3.0 + +source: + md5: 8778c3a8e0f7f73850b9fbc0daf71776 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Network-based prioritization of putative metabolite IDs' - description: 'This package uses an innovative network-based approach that will enhance our ability to determine the identities of significant ions detected by LC-MS.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-metmashr/build.sh b/recipes/bioconductor-metmashr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-metmashr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metmashr/meta.yaml b/recipes/bioconductor-metmashr/meta.yaml new file mode 100644 index 0000000000000..c7cbb38122f86 --- /dev/null +++ b/recipes/bioconductor-metmashr/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.0.0" %} +{% set name = "MetMashR" %} +{% set bioc = "3.20" %} + +about: + description: A package to merge, filter sort, organise and otherwise mash together metabolite annotation tables. Metabolite annotations can be imported from multiple sources (software) and combined using workflow steps based on S4 class templates derived from the `struct` package. Other modular workflow steps such as filtering, merging, splitting, normalisation and rest-api queries are included. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Metabolite Mashing with R + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-metmashr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: covr, httptest, knitr, rmarkdown, testthat (>= 3.0.0), rgoslin, DT, RSQLite, CompoundDb, BiocStyle, BiocFileCache, msPurity, ChemmineOB, rsvg, metabolomicsWorkbenchR, KEGGREST, plyr, magick, structToolbox, RVenn, ggVennDiagram, patchwork, XML, GO.db, tidytext, tidyr, tidyselect, ComplexUpset, jsonlite, openxlsx +requirements: + host: + - bioconductor-struct >=1.18.0,<1.19.0 + - r-base + - r-cowplot + - r-dplyr + - r-ggplot2 + - r-ggthemes + - r-httr + - r-rlang + - r-scales + run: + - bioconductor-struct >=1.18.0,<1.19.0 + - r-base + - r-cowplot + - r-dplyr + - r-ggplot2 + - r-ggthemes + - r-httr + - r-rlang + - r-scales + +source: + md5: e76782f219e073986b675cb10171f990 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-metnet/meta.yaml b/recipes/bioconductor-metnet/meta.yaml index 78ede31d4fedc..6bc728daa979f 100644 --- a/recipes/bioconductor-metnet/meta.yaml +++ b/recipes/bioconductor-metnet/meta.yaml @@ -1,67 +1,72 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "MetNet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MetNet contains functionality to infer metabolic network topologies from quantitative data and high-resolution mass/charge information. Using statistical models (including correlation, mutual information, regression and Bayes statistics) and quantitative data (intensity values of features) adjacency matrices are inferred that can be combined to a consensus matrix. Mass differences calculated between mass/charge values of features will be matched against a data frame of supplied mass/charge differences referring to transformations of enzymatic activities. In a third step, the two levels of information are combined to form a adjacency matrix inferred from both quantitative and structure information. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Inferring metabolic networks from untargeted high-resolution mass spectrometry data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e03ec28e1272f094758907923a0226f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-metnet", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), glmnet (>= 4.1-1), igraph (>= 1.1.2), knitr (>= 1.11), rmarkdown (>= 1.15), testthat (>= 2.2.1), Spectra (>= 1.4.1), MsCoreUtils (>= 1.6.0) requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genie3 >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genie3 >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-bnlearn >=4.3' - - 'r-corpcor >=1.6.10' - - 'r-dplyr >=1.0.3' - - 'r-genenet >=1.2.15' - - 'r-ggplot2 >=3.3.3' - - 'r-parmigene >=1.0.2' - - 'r-psych >=2.1.6' - - 'r-rlang >=0.4.10' - - 'r-stabs >=0.6' - - 'r-tibble >=3.0.5' - - 'r-tidyr >=1.1.2' + - r-bnlearn >=4.3 + - r-corpcor >=1.6.10 + - r-dplyr >=1.0.3 + - r-genenet >=1.2.15 + - r-ggplot2 >=3.3.3 + - r-parmigene >=1.0.2 + - r-psych >=2.1.6 + - r-rlang >=0.4.10 + - r-stabs >=0.6 + - r-tibble >=3.0.5 + - r-tidyr >=1.1.2 run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genie3 >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genie3 >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-bnlearn >=4.3' - - 'r-corpcor >=1.6.10' - - 'r-dplyr >=1.0.3' - - 'r-genenet >=1.2.15' - - 'r-ggplot2 >=3.3.3' - - 'r-parmigene >=1.0.2' - - 'r-psych >=2.1.6' - - 'r-rlang >=0.4.10' - - 'r-stabs >=0.6' - - 'r-tibble >=3.0.5' - - 'r-tidyr >=1.1.2' + - r-bnlearn >=4.3 + - r-corpcor >=1.6.10 + - r-dplyr >=1.0.3 + - r-genenet >=1.2.15 + - r-ggplot2 >=3.3.3 + - r-parmigene >=1.0.2 + - r-psych >=2.1.6 + - r-rlang >=0.4.10 + - r-stabs >=0.6 + - r-tibble >=3.0.5 + - r-tidyr >=1.1.2 + +source: + md5: 561bf20994efd996100121f021e95955 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Inferring metabolic networks from untargeted high-resolution mass spectrometry data' - description: 'MetNet contains functionality to infer metabolic network topologies from quantitative data and high-resolution mass/charge information. Using statistical models (including correlation, mutual information, regression and Bayes statistics) and quantitative data (intensity values of features) adjacency matrices are inferred that can be combined to a consensus matrix. Mass differences calculated between mass/charge values of features will be matched against a data frame of supplied mass/charge differences referring to transformations of enzymatic activities. In a third step, the two levels of information are combined to form a adjacency matrix inferred from both quantitative and structure information.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mfa/meta.yaml b/recipes/bioconductor-mfa/meta.yaml index 5da35eaca5908..59fbcaa67bb52 100644 --- a/recipes/bioconductor-mfa/meta.yaml +++ b/recipes/bioconductor-mfa/meta.yaml @@ -1,27 +1,33 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "mfa" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MFA models genomic bifurcations using a Bayesian hierarchical mixture of factor analysers. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 37fa2e82d83636458e9a20cc72069dcd build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mfa", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-coda - r-dplyr @@ -35,7 +41,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-coda - r-dplyr @@ -46,17 +52,16 @@ requirements: - r-mcmcpack - r-rcpp - r-tibble - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: fdd4337cce5b79f16b1e621eebc3322b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations' - description: 'MFA models genomic bifurcations using a Bayesian hierarchical mixture of factor analysers.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mfuzz/meta.yaml b/recipes/bioconductor-mfuzz/meta.yaml index a85698f9f0ed3..98cc37ee8fe37 100644 --- a/recipes/bioconductor-mfuzz/meta.yaml +++ b/recipes/bioconductor-mfuzz/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "2.62.0" %} +{% set version = "2.66.0" %} {% set name = "Mfuzz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 03a765bd452d34b166f85cdfee8063ae +about: + description: The Mfuzz package implements noise-robust soft clustering of omics time-series data, including transcriptomic, proteomic or metabolomic data. It is based on the use of c-means clustering. For convenience, it includes a graphical user interface. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Soft clustering of omics time series data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mfuzz", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: marray requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-tkwidgets >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-tkwidgets >=1.84.0,<1.85.0 - r-base - r-e1071 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-tkwidgets >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-tkwidgets >=1.84.0,<1.85.0 - r-base - r-e1071 +source: + md5: 8eef6e78c19a6446ffbad684c49b65e7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Soft clustering of time series gene expression data' - description: 'Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgfm/meta.yaml b/recipes/bioconductor-mgfm/meta.yaml index 7b05b8cea6a81..b8020187c2e7e 100644 --- a/recipes/bioconductor-mgfm/meta.yaml +++ b/recipes/bioconductor-mgfm/meta.yaml @@ -1,43 +1,22 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "MGFM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package is designed to detect marker genes from Microarray gene expression data sets + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Marker Gene Finder in Microarray gene expression data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 893a9f574fe4e023d3c4d3b99d58ae78 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgfm", max_pin="x.x") }}' - noarch: generic -# Suggests: hgu133a.db -requirements: - host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - r-base - run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Marker Gene Finder in Microarray gene expression data' - description: 'The package is designed to detect marker genes from Microarray gene expression data sets' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:mgfm @@ -47,3 +26,30 @@ extra: path: recipes/bioconductor-mgfm version: 1.14.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: hgu133a.db +requirements: + host: + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - r-base + run: + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - r-base + +source: + md5: 98be25e57ca7e51f52feded3d94f4b9c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-mgfr/meta.yaml b/recipes/bioconductor-mgfr/meta.yaml index 988ffb8e7853e..19f755f9a4a80 100644 --- a/recipes/bioconductor-mgfr/meta.yaml +++ b/recipes/bioconductor-mgfr/meta.yaml @@ -1,42 +1,22 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "MGFR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package is designed to detect marker genes from RNA-seq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Marker Gene Finder in RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73cad34ad523499dbdcfb3746b519b48 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgfr", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - r-base - run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Marker Gene Finder in RNA-seq data' - description: 'The package is designed to detect marker genes from RNA-seq data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:mgfr @@ -46,3 +26,29 @@ extra: path: recipes/bioconductor-mgfr version: 1.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - r-base + run: + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - r-base + +source: + md5: 7405099a21b45e004571720c66a10664 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-mgnifyr/build.sh b/recipes/bioconductor-mgnifyr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mgnifyr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mgnifyr/meta.yaml b/recipes/bioconductor-mgnifyr/meta.yaml new file mode 100644 index 0000000000000..12342a69c1415 --- /dev/null +++ b/recipes/bioconductor-mgnifyr/meta.yaml @@ -0,0 +1,68 @@ +{% set version = "1.2.0" %} +{% set name = "MGnifyR" %} +{% set bioc = "3.20" %} + +about: + description: Utility package to facilitate integration and analysis of EBI MGnify data in R. The package can be used to import microbial data for instance into TreeSummarizedExperiment (TreeSE). In TreeSE format, the data is directly compatible with miaverse framework. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 | file LICENSE + license_file: LICENSE + summary: R interface to EBI MGnify metagenomics resource + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mgnifyr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: biomformat, broom, ggplot2, knitr, rmarkdown, testthat, xml2, BiocStyle, miaViz, vegan, scater, phyloseq, magick +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-mia >=1.14.0,<1.15.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 + - r-ape + - r-base + - r-dplyr + - r-httr + - r-plyr + - r-reshape2 + - r-tidyjson + - r-urltools + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-mia >=1.14.0,<1.15.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 + - r-ape + - r-base + - r-dplyr + - r-httr + - r-plyr + - r-reshape2 + - r-tidyjson + - r-urltools + +source: + md5: 143609852e2afe5335d345320e3c29ec + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-mgsa/meta.yaml b/recipes/bioconductor-mgsa/meta.yaml index b41a7de444713..d5ee90cb7c8c4 100644 --- a/recipes/bioconductor-mgsa/meta.yaml +++ b/recipes/bioconductor-mgsa/meta.yaml @@ -1,25 +1,41 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "mgsa" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Model-based Gene Set Analysis (MGSA) is a Bayesian modeling approach for gene set enrichment. The package mgsa implements MGSA and tools to use MGSA together with the Gene Ontology. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Model-based gene set analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1a0667a9a3b9c3e973a47a49249b08db build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgsa", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:mgsa + - doi:10.1093/nar/gkq045 + parent_recipe: + name: bioconductor-mgsa + path: recipes/bioconductor-mgsa + version: 1.28.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: DBI, RSQLite, GO.db, testthat requirements: + build: + - {{ compiler('c') }} + - automake + - make host: - r-base - r-gplots @@ -28,26 +44,16 @@ requirements: run: - r-base - r-gplots - build: - - {{ compiler('c') }} - - automake - - make + +source: + md5: 697df1e213746a4582d9d684e06318b7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Model-based gene set analysis' - description: 'Model-based Gene Set Analysis (MGSA) is a Bayesian modeling approach for gene set enrichment. The package mgsa implements MGSA and tools to use MGSA together with the Gene Ontology.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:mgsa - - doi:10.1093/nar/gkq045 - parent_recipe: - name: bioconductor-mgsa - path: recipes/bioconductor-mgsa - version: 1.28.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgu74a.db/meta.yaml b/recipes/bioconductor-mgu74a.db/meta.yaml index c2dd2b0ae3b6f..88655fa4bd2e9 100644 --- a/recipes/bioconductor-mgu74a.db/meta.yaml +++ b/recipes/bioconductor-mgu74a.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "mgu74a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9fb75c159c50e2ae316ee5a8abe1a48c +about: + description: Affymetrix Affymetrix MG_U74A Array annotation data (chip mgu74a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix MG_U74A Array annotation data (chip mgu74a) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgu74a.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9fb75c159c50e2ae316ee5a8abe1a48c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix MG_U74A Array annotation data (chip mgu74a)' - description: 'Affymetrix Affymetrix MG_U74A Array annotation data (chip mgu74a) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgu74acdf/meta.yaml b/recipes/bioconductor-mgu74acdf/meta.yaml index 6d1e5d9376af7..70c0999411eae 100644 --- a/recipes/bioconductor-mgu74acdf/meta.yaml +++ b/recipes/bioconductor-mgu74acdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mgu74acdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ed6e86398e51c7b0ddca4431797ecbc0 +about: + description: A package containing an environment representing the MG_U74A.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mgu74acdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgu74acdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ed6e86398e51c7b0ddca4431797ecbc0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mgu74acdf - description: 'A package containing an environment representing the MG_U74A.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgu74aprobe/meta.yaml b/recipes/bioconductor-mgu74aprobe/meta.yaml index 01606e9b7cee0..22f272ebcc804 100644 --- a/recipes/bioconductor-mgu74aprobe/meta.yaml +++ b/recipes/bioconductor-mgu74aprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mgu74aprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7fea6d44856203e6293e0cd9fe1ad066 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74A\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type mgu74a build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgu74aprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7fea6d44856203e6293e0cd9fe1ad066 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type mgu74a' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74A\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgu74av2.db/meta.yaml b/recipes/bioconductor-mgu74av2.db/meta.yaml index 405b9aa9777a8..e341addf4c1ad 100644 --- a/recipes/bioconductor-mgu74av2.db/meta.yaml +++ b/recipes/bioconductor-mgu74av2.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "mgu74av2.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3205856d0c7725acded5238415e907bc +about: + description: Affymetrix Affymetrix MG_U74Av2 Array annotation data (chip mgu74av2) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix MG_U74Av2 Array annotation data (chip mgu74av2) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgu74av2.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3205856d0c7725acded5238415e907bc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix MG_U74Av2 Array annotation data (chip mgu74av2)' - description: 'Affymetrix Affymetrix MG_U74Av2 Array annotation data (chip mgu74av2) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgu74av2cdf/meta.yaml b/recipes/bioconductor-mgu74av2cdf/meta.yaml index e72145c2c0482..9fea0dc04c1e1 100644 --- a/recipes/bioconductor-mgu74av2cdf/meta.yaml +++ b/recipes/bioconductor-mgu74av2cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mgu74av2cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 35e2abb9fbfd68d90dc32a2faae00c95 +about: + description: A package containing an environment representing the MG_U74Av2.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mgu74av2cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgu74av2cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 35e2abb9fbfd68d90dc32a2faae00c95 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mgu74av2cdf - description: 'A package containing an environment representing the MG_U74Av2.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgu74av2probe/meta.yaml b/recipes/bioconductor-mgu74av2probe/meta.yaml index 8e2e4ecec00f0..5fe5f99742d3e 100644 --- a/recipes/bioconductor-mgu74av2probe/meta.yaml +++ b/recipes/bioconductor-mgu74av2probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mgu74av2probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ac540b0e26b14a411740233b02d3e11c +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74Av2\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type mgu74av2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgu74av2probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ac540b0e26b14a411740233b02d3e11c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type mgu74av2' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74Av2\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgu74b.db/meta.yaml b/recipes/bioconductor-mgu74b.db/meta.yaml index 3063cdc54e8e1..a6ce6ce37ab3e 100644 --- a/recipes/bioconductor-mgu74b.db/meta.yaml +++ b/recipes/bioconductor-mgu74b.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "mgu74b.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 205577a6e41d56910f221ffb940ee25b +about: + description: Affymetrix Affymetrix MG_U74B Array annotation data (chip mgu74b) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix MG_U74B Array annotation data (chip mgu74b) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgu74b.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 205577a6e41d56910f221ffb940ee25b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix MG_U74B Array annotation data (chip mgu74b)' - description: 'Affymetrix Affymetrix MG_U74B Array annotation data (chip mgu74b) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgu74bcdf/meta.yaml b/recipes/bioconductor-mgu74bcdf/meta.yaml index f44812422b044..7211cdb1d0563 100644 --- a/recipes/bioconductor-mgu74bcdf/meta.yaml +++ b/recipes/bioconductor-mgu74bcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mgu74bcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a1f0f98f29d34a421622447252113e1e +about: + description: A package containing an environment representing the MG_U74B.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mgu74bcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgu74bcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a1f0f98f29d34a421622447252113e1e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mgu74bcdf - description: 'A package containing an environment representing the MG_U74B.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgu74bprobe/meta.yaml b/recipes/bioconductor-mgu74bprobe/meta.yaml index 29fd25ee76e40..5fb5d346f5dcb 100644 --- a/recipes/bioconductor-mgu74bprobe/meta.yaml +++ b/recipes/bioconductor-mgu74bprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mgu74bprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 224d606e6fc87592d387dbaabe5cd353 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74B\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type mgu74b build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgu74bprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 224d606e6fc87592d387dbaabe5cd353 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type mgu74b' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74B\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgu74bv2.db/meta.yaml b/recipes/bioconductor-mgu74bv2.db/meta.yaml index 84c103d1c0982..a266bd3c35808 100644 --- a/recipes/bioconductor-mgu74bv2.db/meta.yaml +++ b/recipes/bioconductor-mgu74bv2.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "mgu74bv2.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4ec0fbed7343f0578ef11e2330d0d12a +about: + description: Affymetrix Affymetrix MG_U74Bv2 Array annotation data (chip mgu74bv2) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix MG_U74Bv2 Array annotation data (chip mgu74bv2) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgu74bv2.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4ec0fbed7343f0578ef11e2330d0d12a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix MG_U74Bv2 Array annotation data (chip mgu74bv2)' - description: 'Affymetrix Affymetrix MG_U74Bv2 Array annotation data (chip mgu74bv2) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgu74bv2cdf/meta.yaml b/recipes/bioconductor-mgu74bv2cdf/meta.yaml index 1e5b584de6c4a..16bc83c1f644f 100644 --- a/recipes/bioconductor-mgu74bv2cdf/meta.yaml +++ b/recipes/bioconductor-mgu74bv2cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mgu74bv2cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 45c48d11af03633dc10f8682b7ad74c5 +about: + description: A package containing an environment representing the MG_U74Bv2.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mgu74bv2cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgu74bv2cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 45c48d11af03633dc10f8682b7ad74c5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mgu74bv2cdf - description: 'A package containing an environment representing the MG_U74Bv2.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgu74bv2probe/meta.yaml b/recipes/bioconductor-mgu74bv2probe/meta.yaml index 2c0bd49a0fabb..e5d0c9b7cbee6 100644 --- a/recipes/bioconductor-mgu74bv2probe/meta.yaml +++ b/recipes/bioconductor-mgu74bv2probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mgu74bv2probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f6a12f88ea3c43a3e885c7e9b3fd03d2 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74Bv2\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type mgu74bv2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgu74bv2probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f6a12f88ea3c43a3e885c7e9b3fd03d2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type mgu74bv2' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74Bv2\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgu74c.db/meta.yaml b/recipes/bioconductor-mgu74c.db/meta.yaml index f645da667a7cf..2d2788756e256 100644 --- a/recipes/bioconductor-mgu74c.db/meta.yaml +++ b/recipes/bioconductor-mgu74c.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "mgu74c.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6c4f183e6ed5f0b5735596e7544746ae +about: + description: Affymetrix Affymetrix MG_U74C Array annotation data (chip mgu74c) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix MG_U74C Array annotation data (chip mgu74c) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgu74c.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6c4f183e6ed5f0b5735596e7544746ae + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix MG_U74C Array annotation data (chip mgu74c)' - description: 'Affymetrix Affymetrix MG_U74C Array annotation data (chip mgu74c) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgu74ccdf/meta.yaml b/recipes/bioconductor-mgu74ccdf/meta.yaml index 80c910bd5ffb7..eadd03ea47c2a 100644 --- a/recipes/bioconductor-mgu74ccdf/meta.yaml +++ b/recipes/bioconductor-mgu74ccdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mgu74ccdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 172e626b0e3072edc65c4efff35fe998 +about: + description: A package containing an environment representing the MG_U74C.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mgu74ccdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgu74ccdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 172e626b0e3072edc65c4efff35fe998 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mgu74ccdf - description: 'A package containing an environment representing the MG_U74C.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgu74cprobe/meta.yaml b/recipes/bioconductor-mgu74cprobe/meta.yaml index 2e2b2ca35ed51..5cbf0e3285483 100644 --- a/recipes/bioconductor-mgu74cprobe/meta.yaml +++ b/recipes/bioconductor-mgu74cprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mgu74cprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 186992992708f0071fd552ef92b9e25c +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74C\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type mgu74c build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgu74cprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 186992992708f0071fd552ef92b9e25c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type mgu74c' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74C\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgu74cv2.db/meta.yaml b/recipes/bioconductor-mgu74cv2.db/meta.yaml index 997784f9be6fd..bc376cad18b89 100644 --- a/recipes/bioconductor-mgu74cv2.db/meta.yaml +++ b/recipes/bioconductor-mgu74cv2.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "mgu74cv2.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1f860dfbf4400ede54eb30d9a70ec131 +about: + description: Affymetrix Affymetrix MG_U74Cv2 Array annotation data (chip mgu74cv2) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix MG_U74Cv2 Array annotation data (chip mgu74cv2) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgu74cv2.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1f860dfbf4400ede54eb30d9a70ec131 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix MG_U74Cv2 Array annotation data (chip mgu74cv2)' - description: 'Affymetrix Affymetrix MG_U74Cv2 Array annotation data (chip mgu74cv2) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgu74cv2cdf/meta.yaml b/recipes/bioconductor-mgu74cv2cdf/meta.yaml index e03108fc7e228..59f2747d0b721 100644 --- a/recipes/bioconductor-mgu74cv2cdf/meta.yaml +++ b/recipes/bioconductor-mgu74cv2cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mgu74cv2cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9ef62b4b28f97770859db24393a07ed5 +about: + description: A package containing an environment representing the MG_U74Cv2.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mgu74cv2cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgu74cv2cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9ef62b4b28f97770859db24393a07ed5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mgu74cv2cdf - description: 'A package containing an environment representing the MG_U74Cv2.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgu74cv2probe/meta.yaml b/recipes/bioconductor-mgu74cv2probe/meta.yaml index ca9038a77b902..70dc54c2864d0 100644 --- a/recipes/bioconductor-mgu74cv2probe/meta.yaml +++ b/recipes/bioconductor-mgu74cv2probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mgu74cv2probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0373496c817a1c1a153114047cfa7c5b +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74Cv2\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type mgu74cv2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgu74cv2probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0373496c817a1c1a153114047cfa7c5b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type mgu74cv2' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74Cv2\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mguatlas5k.db/meta.yaml b/recipes/bioconductor-mguatlas5k.db/meta.yaml index 22485ecde8e5b..4e0d557a0cc77 100644 --- a/recipes/bioconductor-mguatlas5k.db/meta.yaml +++ b/recipes/bioconductor-mguatlas5k.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "mguatlas5k.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 826093fe7228c08962aff36ad89af28e +about: + description: Clontech BD Atlas Long Oligos Mouse 5K annotation data (chip mguatlas5k) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Clontech BD Atlas Long Oligos Mouse 5K annotation data (chip mguatlas5k) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mguatlas5k.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 826093fe7228c08962aff36ad89af28e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Clontech BD Atlas Long Oligos Mouse 5K annotation data (chip mguatlas5k)' - description: 'Clontech BD Atlas Long Oligos Mouse 5K annotation data (chip mguatlas5k) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgug4104a.db/meta.yaml b/recipes/bioconductor-mgug4104a.db/meta.yaml index 23f2e33b36284..851adfde04f99 100644 --- a/recipes/bioconductor-mgug4104a.db/meta.yaml +++ b/recipes/bioconductor-mgug4104a.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "mgug4104a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7b1cef094a226257cd657ed8d61e9ef1 +about: + description: Agilent annotation data (chip mgug4104a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Agilent annotation data (chip mgug4104a) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgug4104a.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7b1cef094a226257cd657ed8d61e9ef1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Agilent annotation data (chip mgug4104a)' - description: 'Agilent annotation data (chip mgug4104a) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgug4120a.db/meta.yaml b/recipes/bioconductor-mgug4120a.db/meta.yaml index 5029a19397f6f..bfacca7f96c74 100644 --- a/recipes/bioconductor-mgug4120a.db/meta.yaml +++ b/recipes/bioconductor-mgug4120a.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "mgug4120a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bb57e8b2efe3d038ec2a0ace0313a4e7 +about: + description: Agilent annotation data (chip mgug4120a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Agilent annotation data (chip mgug4120a) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgug4120a.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bb57e8b2efe3d038ec2a0ace0313a4e7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Agilent annotation data (chip mgug4120a)' - description: 'Agilent annotation data (chip mgug4120a) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgug4121a.db/meta.yaml b/recipes/bioconductor-mgug4121a.db/meta.yaml index f58dbc5d4a23b..11c4a6afc66c2 100644 --- a/recipes/bioconductor-mgug4121a.db/meta.yaml +++ b/recipes/bioconductor-mgug4121a.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "mgug4121a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6b5cc321d5175356c383b91e30e120b7 +about: + description: Agilent Mouse annotation data (chip mgug4121a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Agilent Mouse annotation data (chip mgug4121a) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgug4121a.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6b5cc321d5175356c383b91e30e120b7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Agilent Mouse annotation data (chip mgug4121a)' - description: 'Agilent Mouse annotation data (chip mgug4121a) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mgug4122a.db/meta.yaml b/recipes/bioconductor-mgug4122a.db/meta.yaml index f28449f09300b..877f63868a955 100644 --- a/recipes/bioconductor-mgug4122a.db/meta.yaml +++ b/recipes/bioconductor-mgug4122a.db/meta.yaml @@ -1,47 +1,53 @@ {% set version = "3.2.3" %} {% set name = "mgug4122a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Agilent "Mouse Genome, Whole" annotation data (chip mgug4122a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Agilent "Mouse Genome, Whole" annotation data (chip mgug4122a) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5fcdce909ac1c0ccbf06bf6411f6fe52 build: - number: 17 + noarch: generic + number: 18 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mgug4122a.db", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-mgug4122a.db + path: recipes/bioconductor-mgug4122a.db + version: 3.2.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 5fcdce909ac1c0ccbf06bf6411f6fe52 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Agilent "Mouse Genome, Whole" annotation data (chip mgug4122a)' - description: 'Agilent "Mouse Genome, Whole" annotation data (chip mgug4122a) assembled using data from public repositories' -extra: - parent_recipe: - name: bioconductor-mgug4122a.db - path: recipes/bioconductor-mgug4122a.db - version: 3.2.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mi16cod.db/meta.yaml b/recipes/bioconductor-mi16cod.db/meta.yaml index 8fb4d0203848f..2f53bed2a9865 100644 --- a/recipes/bioconductor-mi16cod.db/meta.yaml +++ b/recipes/bioconductor-mi16cod.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.4.0" %} {% set name = "mi16cod.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f3a8e6f45ce5c298c1b1c5b32bf2630c +about: + description: Codelink Mouse Inflammation 16 Bioarray annotation data (chip mi16cod) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Codelink Mouse Inflammation 16 Bioarray annotation data (chip mi16cod) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mi16cod.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f3a8e6f45ce5c298c1b1c5b32bf2630c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Codelink Mouse Inflammation 16 Bioarray annotation data (chip mi16cod)' - description: 'Codelink Mouse Inflammation 16 Bioarray annotation data (chip mi16cod) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mia/meta.yaml b/recipes/bioconductor-mia/meta.yaml index 919a3676af018..1ba3367823e21 100644 --- a/recipes/bioconductor-mia/meta.yaml +++ b/recipes/bioconductor-mia/meta.yaml @@ -1,87 +1,98 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "mia" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: mia implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure. Data wrangling and analysis in the context of taxonomic data is the main scope. Additional functions for common task are implemented such as community indices calculation and summarization. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 | file LICENSE + license_file: LICENSE + summary: Microbiome analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 73446335fd354444f38c4e8cf793d520 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mia", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, knitr, patchwork, BiocStyle, yaml, phyloseq, dada2, stringr, biomformat, reldist, ade4, microbiomeDataSets, rmarkdown + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: ade4, BiocStyle, biomformat, dada2, knitr, miaViz, microbiomeDataSets, NMF, patchwork, phyloseq, reldist, rhdf5, rmarkdown, stringr, testthat, topicdoc, topicmodels, yaml requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bluster >=1.12.0,<1.13.0' - - 'bioconductor-decipher >=2.30.0,<2.31.0' - - 'bioconductor-decontam >=1.22.0,<1.23.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-dirichletmultinomial >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bluster >=1.16.0,<1.17.0 + - bioconductor-decipher >=3.2.0,<3.3.0 + - bioconductor-decontam >=1.26.0,<1.27.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-dirichletmultinomial >=1.48.0,<1.49.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 - r-ape - r-base - r-dplyr - r-mass + - r-mediation + - r-rbiom - r-rlang - r-tibble - r-tidyr - r-vegan + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bluster >=1.12.0,<1.13.0' - - 'bioconductor-decipher >=2.30.0,<2.31.0' - - 'bioconductor-decontam >=1.22.0,<1.23.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-dirichletmultinomial >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bluster >=1.16.0,<1.17.0 + - bioconductor-decipher >=3.2.0,<3.3.0 + - bioconductor-decontam >=1.26.0,<1.27.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-dirichletmultinomial >=1.48.0,<1.49.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 - r-ape - r-base - r-dplyr - r-mass + - r-mediation + - r-rbiom - r-rlang - r-tibble - r-tidyr - r-vegan + +source: + md5: 235e96191a12bd939ddc50d8f6246925 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Artistic-2.0 | file LICENSE' - summary: 'Microbiome analysis' - description: 'mia implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure. Data wrangling and analysis in the context of taxonomic data is the main scope. Additional functions for common task are implemented such as community indices calculation and summarization.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-miasim/meta.yaml b/recipes/bioconductor-miasim/meta.yaml index 01006e0284875..47b624c81ef96 100644 --- a/recipes/bioconductor-miasim/meta.yaml +++ b/recipes/bioconductor-miasim/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "miaSim" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell's Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to (Tree)SummarizedExperiment objects. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 | file LICENSE + license_file: LICENSE + summary: Microbiome Data Simulation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0867c6e7b7cae5acbfd6154b8af06d41 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-miasim", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ape, cluster, foreach, doParallel, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy requirements: host: - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 - r-base - r-desolve - r-powerlaw run: - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 - r-base - r-desolve - r-powerlaw + +source: + md5: 63f5e34abd70ce9d9b6e15fe645b02cd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Artistic-2.0 | file LICENSE' - summary: 'Microbiome Data Simulation' - description: 'Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell''s Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to (Tree)SummarizedExperiment objects.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-miaviz/meta.yaml b/recipes/bioconductor-miaviz/meta.yaml index 5d98581a6690d..561aeff88d4f3 100644 --- a/recipes/bioconductor-miaviz/meta.yaml +++ b/recipes/bioconductor-miaviz/meta.yaml @@ -1,85 +1,94 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "miaViz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The miaViz package implements functions to visualize TreeSummarizedExperiment objects especially in the context of microbiome analysis. Part of the mia family of R/Bioconductor packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 | file LICENSE + license_file: LICENSE + summary: Microbiome Analysis Plotting and Visualization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8388770fbcfce7b95040dc84f02938bc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-miaviz", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, BiocStyle, testthat, patchwork, vegan, microbiomeDataSets, bluster + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, BiocStyle, testthat, patchwork, vegan, bluster, ComplexHeatmap, circlize requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-dirichletmultinomial >=1.44.0,<1.45.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-mia >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-dirichletmultinomial >=1.48.0,<1.49.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-mia >=1.14.0,<1.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 - r-ape - r-base - r-dplyr - r-ggnewscale - r-ggplot2 - - 'r-ggraph >=2.0' + - r-ggraph >=2.0 - r-ggrepel - r-purrr - r-rlang - r-tibble - r-tidygraph - r-tidyr + - r-tidytext - r-tidytree - r-viridis + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-dirichletmultinomial >=1.44.0,<1.45.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-mia >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-dirichletmultinomial >=1.48.0,<1.49.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-mia >=1.14.0,<1.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 - r-ape - r-base - r-dplyr - r-ggnewscale - r-ggplot2 - - 'r-ggraph >=2.0' + - r-ggraph >=2.0 - r-ggrepel - r-purrr - r-rlang - r-tibble - r-tidygraph - r-tidyr + - r-tidytext - r-tidytree - r-viridis + +source: + md5: c47b4360b420f306ec1ef3c68a17c4a0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Artistic-2.0 | file LICENSE' - summary: 'Microbiome Analysis Plotting and Visualization' - description: 'The miaViz package implements functions to visualize TreeSummarizedExperiment objects especially in the context of microbiome analysis. Part of the mia family of R/Bioconductor packages.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-michip/meta.yaml b/recipes/bioconductor-michip/meta.yaml index cafafc492b65d..218e9dd0f86b3 100644 --- a/recipes/bioconductor-michip/meta.yaml +++ b/recipes/bioconductor-michip/meta.yaml @@ -1,40 +1,22 @@ -{% set version = "1.56.0" %} +{% set version = "1.60.0" %} {% set name = "MiChip" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package takes the MiChip miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse MiChip hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by other BioConductor packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: MiChip Parsing and Summarizing Functions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 28daafdf6588314a9fad7a75b1671c10 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-michip", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'MiChip Parsing and Summarizing Functions' - description: 'This package takes the MiChip miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse MiChip hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by other BioConductor packages.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:michip @@ -44,3 +26,27 @@ extra: path: recipes/bioconductor-michip version: 1.34.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + +source: + md5: b41d75f030af603bb06d2f85e19d198c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-microbiome/meta.yaml b/recipes/bioconductor-microbiome/meta.yaml index 1a8d53b4a4491..fb37a9088e3d0 100644 --- a/recipes/bioconductor-microbiome/meta.yaml +++ b/recipes/bioconductor-microbiome/meta.yaml @@ -1,29 +1,37 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "microbiome" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Utilities for microbiome analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_2_clause + file LICENSE + license_file: LICENSE + summary: Microbiome Analytics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2d185cf8b8bf7d23f295dee1af621a0f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-microbiome", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-microbiome + path: recipes/bioconductor-microbiome + version: 1.2.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 - r-base - r-compositions - r-dplyr @@ -35,8 +43,8 @@ requirements: - r-tidyr - r-vegan run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 - r-base - r-compositions - r-dplyr @@ -47,18 +55,16 @@ requirements: - r-tibble - r-tidyr - r-vegan + +source: + md5: 25d79565e12d9b23303b8631b926497a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_2_clause + file LICENSE' - summary: 'Microbiome Analytics' - description: 'Utilities for microbiome analysis.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-microbiome - path: recipes/bioconductor-microbiome - version: 1.2.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-microbiomebenchmarkdata/meta.yaml b/recipes/bioconductor-microbiomebenchmarkdata/meta.yaml index 4738a600749e6..220d6b4f554c0 100644 --- a/recipes/bioconductor-microbiomebenchmarkdata/meta.yaml +++ b/recipes/bioconductor-microbiomebenchmarkdata/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "MicrobiomeBenchmarkData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The MicrobiomeBenchmarkData package provides functionality to access microbiome datasets suitable for benchmarking. These datasets have some biological truth, which allows to have expected results for comparison. The datasets come from various published sources and are provided as TreeSummarizedExperiment objects. Currently, only datasets suitable for benchmarking differential abundance methods are available. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Datasets for benchmarking in microbiome research -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c6c791669de95bf2dc108798770ea5be build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-microbiomebenchmarkdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0), mia, ggplot2, tidyr, dplyr, magrittr, tibble, purrr requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 - r-ape - r-base run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 - r-ape - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: f0c2276607641ceeab25744f8b83fad9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Datasets for benchmarking in microbiome research' - description: 'The MicrobiomeBenchmarkData package provides functionality to access microbiome datasets suitable for benchmarking. These datasets have some biological truth, which allows to have expected results for comparison. The datasets come from various published sources and are provided as TreeSummarizedExperiment objects. Currently, only datasets suitable for benchmarking differential abundance methods are available.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-microbiomebenchmarkdata/post-link.sh b/recipes/bioconductor-microbiomebenchmarkdata/post-link.sh index b41c09486c6b4..3710d87cca0b2 100644 --- a/recipes/bioconductor-microbiomebenchmarkdata/post-link.sh +++ b/recipes/bioconductor-microbiomebenchmarkdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "microbiomebenchmarkdata-1.4.0" +installBiocDataPackage.sh "microbiomebenchmarkdata-1.8.0" diff --git a/recipes/bioconductor-microbiomedatasets/meta.yaml b/recipes/bioconductor-microbiomedatasets/meta.yaml index 4fcdb8454b7a9..c2c83ba2eedb9 100644 --- a/recipes/bioconductor-microbiomedatasets/meta.yaml +++ b/recipes/bioconductor-microbiomedatasets/meta.yaml @@ -1,52 +1,57 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "microbiomeDataSets" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: microbiomeDataSets is a collection of microbiome datasets loaded from Bioconductor'S ExperimentHub infrastructure. The datasets serve as reference for workflows and vignettes published adjacent to the microbiome analysis tools on Bioconductor. Additional datasets can be added overtime and additions from authors are welcome. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: CC0 + summary: Experiment Hub based microbiome datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90cd4bb36dafcef8f6eb0e0232afdcd0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-microbiomedatasets", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 - r-ape - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 - r-ape - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: df3b92fa8bb2edd4cb6b98d4d6215542 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: CC0 - summary: 'Experiment Hub based microbiome datasets' - description: 'microbiomeDataSets is a collection of microbiome datasets loaded from Bioconductor''S ExperimentHub infrastructure. The datasets serve as reference for workflows and vignettes published adjacent to the microbiome analysis tools on Bioconductor. Additional datasets can be added overtime and additions from authors are welcome.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-microbiomedatasets/post-link.sh b/recipes/bioconductor-microbiomedatasets/post-link.sh index a7009b824d2c1..f22375a1e50e3 100644 --- a/recipes/bioconductor-microbiomedatasets/post-link.sh +++ b/recipes/bioconductor-microbiomedatasets/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "microbiomedatasets-1.10.0" +installBiocDataPackage.sh "microbiomedatasets-1.14.0" diff --git a/recipes/bioconductor-microbiomeprofiler/meta.yaml b/recipes/bioconductor-microbiomeprofiler/meta.yaml index 7a31e5d435166..622d8dfd50268 100644 --- a/recipes/bioconductor-microbiomeprofiler/meta.yaml +++ b/recipes/bioconductor-microbiomeprofiler/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "MicrobiomeProfiler" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This is an R/shiny package to perform functional enrichment analysis for microbiome data. This package was based on clusterProfiler. Moreover, MicrobiomeProfiler support KEGG enrichment analysis, COG enrichment analysis, Microbe-Disease association enrichment analysis, Metabo-Pathway analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: An R/shiny package for microbiome functional enrichment analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 47851ff17ed03e5b448a09513c7bf122 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-microbiomeprofiler", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, testthat (>= 3.0.0), prettydoc requirements: host: - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 - r-base - r-config - r-dt @@ -32,12 +34,13 @@ requirements: - r-gson - r-htmltools - r-magrittr - - 'r-shiny >=1.6.0' + - r-shiny >=1.6.0 - r-shinycustomloader - r-shinywidgets + - r-yulab.utils run: - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 - r-base - r-config - r-dt @@ -46,16 +49,20 @@ requirements: - r-gson - r-htmltools - r-magrittr - - 'r-shiny >=1.6.0' + - r-shiny >=1.6.0 - r-shinycustomloader - r-shinywidgets + - r-yulab.utils + +source: + md5: 2807b5fe05f24e95d6a30e2e64182621 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'An R/shiny package for microbiome functional enrichment analysis' - description: 'This is an R/shiny package to perform functional enrichment analysis for microbiome data. This package was based on clusterProfiler. Moreover, MicrobiomeProfiler support KEGG enrichment analysis, COG enrichment analysis, Microbe-Disease association enrichment analysis, Metabo-Pathway analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-microbiotaprocess/meta.yaml b/recipes/bioconductor-microbiotaprocess/meta.yaml index 448857a29ab05..8fa9697f651c0 100644 --- a/recipes/bioconductor-microbiotaprocess/meta.yaml +++ b/recipes/bioconductor-microbiotaprocess/meta.yaml @@ -1,32 +1,35 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "MicrobiotaProcess" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MicrobiotaProcess is an R package for analysis, visualization and biomarker discovery of microbial datasets. It introduces MPSE class, this make it more interoperable with the existing computing ecosystem. Moreover, it introduces a tidy microbiome data structure paradigm and analysis grammar. It provides a wide variety of microbiome data analysis procedures under the unified and common framework (tidy-like framework). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3.0) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 104b99004b64b664131ddea6462cbabc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-microbiotaprocess", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, ggupset, ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial, ggpp, BiocManager requirements: + host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-ggtreeextra >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treeio >=1.26.0,<1.27.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-ggtreeextra >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treeio >=1.30.0,<1.31.0 - r-ape - r-base - r-cli @@ -35,7 +38,7 @@ requirements: - r-dplyr - r-dtplyr - r-foreach - - 'r-ggfun >=0.1.1' + - r-ggfun >=0.1.1 - r-ggplot2 - r-ggrepel - r-ggsignif @@ -49,15 +52,16 @@ requirements: - r-tibble - r-tidyr - r-tidyselect - - 'r-tidytree >=0.4.2' + - r-tidytree >=0.4.2 - r-vegan - r-zoo + run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-ggtreeextra >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treeio >=1.26.0,<1.27.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-ggtreeextra >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treeio >=1.30.0,<1.31.0 - r-ape - r-base - r-cli @@ -66,7 +70,7 @@ requirements: - r-dplyr - r-dtplyr - r-foreach - - 'r-ggfun >=0.1.1' + - r-ggfun >=0.1.1 - r-ggplot2 - r-ggrepel - r-ggsignif @@ -80,16 +84,19 @@ requirements: - r-tibble - r-tidyr - r-tidyselect - - 'r-tidytree >=0.4.2' + - r-tidytree >=0.4.2 - r-vegan - r-zoo + +source: + md5: 44b21e324ef11a355d79de51f78126fd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3.0)' - summary: 'A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework' - description: 'MicrobiotaProcess is an R package for analysis, visualization and biomarker discovery of microbial datasets. It introduces MPSE class, this make it more interoperable with the existing computing ecosystem. Moreover, it introduces a tidy microbiome data structure paradigm and analysis grammar. It provides a wide variety of microbiome data analysis procedures under the unified and common framework (tidy-like framework).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-microrna/meta.yaml b/recipes/bioconductor-microrna/meta.yaml index cc92ab37669ca..c69d2b56441b6 100644 --- a/recipes/bioconductor-microrna/meta.yaml +++ b/recipes/bioconductor-microrna/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "microRNA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Different data resources for microRNAs and some functions for manipulating them. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Data and functions for dealing with microRNAs -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 04b7af542581242a8e6ba5d4f19c14ca build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-microrna", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:microrna + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-microrna + path: recipes/bioconductor-microrna + version: 1.38.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: ecbbe0f4a76950c5b26cfa4e5102f120 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Data and functions for dealing with microRNAs' - description: 'Different data resources for microRNAs and some functions for manipulating them.' -extra: - identifiers: - - biotools:microrna - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-microrna - path: recipes/bioconductor-microrna - version: 1.38.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-micrornaome/meta.yaml b/recipes/bioconductor-micrornaome/meta.yaml index 20251ad808f38..4a29f275b3fb1 100644 --- a/recipes/bioconductor-micrornaome/meta.yaml +++ b/recipes/bioconductor-micrornaome/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "microRNAome" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 12d3baf395e82975bbcacfb9ff61a715 +about: + description: 'This package provides a SummarizedExperiment object of read counts for microRNAs across tissues, cell-types, and cancer cell-lines. The read count matrix was prepared and provided by the author of the study: Towards the human cellular microRNAome.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: SummarizedExperiment for the microRNAome project build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-micrornaome", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocGenerics, RUnit requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e1eeee6effefa7c38c24ac14ccdbb9c1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'SummarizedExperiment for the microRNAome project' - description: 'This package provides a SummarizedExperiment object of read counts for microRNAs across tissues, cell-types, and cancer cell-lines. The read count matrix was prepared and provided by the author of the study: Towards the human cellular microRNAome.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-micrornaome/post-link.sh b/recipes/bioconductor-micrornaome/post-link.sh index 2c965f7636c8d..13b22f0e943d6 100644 --- a/recipes/bioconductor-micrornaome/post-link.sh +++ b/recipes/bioconductor-micrornaome/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "micrornaome-1.24.0" +installBiocDataPackage.sh "micrornaome-1.28.0" diff --git a/recipes/bioconductor-microstasis/meta.yaml b/recipes/bioconductor-microstasis/meta.yaml index 52e1c42705ee5..c77c5f5642e30 100644 --- a/recipes/bioconductor-microstasis/meta.yaml +++ b/recipes/bioconductor-microstasis/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "microSTASIS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The toolkit 'µSTASIS', or microSTASIS, has been developed for the stability analysis of microbiota in a temporal framework by leveraging on iterative clustering. Concretely, the core function uses Hartigan-Wong k-means algorithm as many times as possible for stressing out paired samples from the same individuals to test if they remain together for multiple numbers of clusters over a whole data set of individuals. Moreover, the package includes multiple functions to subset samples from paired times, validate the results or visualize the output. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Microbiota STability ASsessment via Iterative cluStering -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7b9b67613eb5e6b69918dffc9d4060d8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-microstasis", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, gghighlight, knitr, rmarkdown, methods, RefManageR, sessioninfo, SingleCellExperiment, SummarizedExperiment, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 - r-base - r-ggplot2 - r-ggside - r-rlang - r-stringr run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-treesummarizedexperiment >=2.10.0,<2.11.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 - r-base - r-ggplot2 - r-ggside - r-rlang - r-stringr + +source: + md5: aa143ed7e2e787173f15f326de7bdbb8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Microbiota STability ASsessment via Iterative cluStering' - description: 'The toolkit ''µSTASIS'', or microSTASIS, has been developed for the stability analysis of microbiota in a temporal framework by leveraging on iterative clustering. Concretely, the core function uses Hartigan-Wong k-means algorithm as many times as possible for stressing out paired samples from the same individuals to test if they remain together for multiple numbers of clusters over a whole data set of individuals. Moreover, the package includes multiple functions to subset samples from paired times, validate the results or visualize the output.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-micsqtl/build_failure.linux-64.yaml b/recipes/bioconductor-micsqtl/build_failure.linux-64.yaml deleted file mode 100644 index 3fe5e63aee6a4..0000000000000 --- a/recipes/bioconductor-micsqtl/build_failure.linux-64.yaml +++ /dev/null @@ -1,106 +0,0 @@ -recipe_sha: 48da45ce49c1641d3245866b89ddd5bb41be17df6a5b307fcbb400bb8ebd78e7 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: |- - dependency issue -log: |2- - - r-ggplot2 - - r-tca - - r-glue - - bioconductor-biocparallel >=1.36.0,<1.37.0 - - r-dirmult - - r-nnls - - r-magrittr - - r-purrr - - r-base 4.3.* - - r-ggridges - - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested r-tca - - - - Leaving build/test directories: - Work: - /opt/conda/conda-bld/work - Test: - /opt/conda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl - Build: - source activate /opt/conda/conda-bld/_build_env - - - Traceback (most recent call last): - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action - t = self.solve(specs) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - bioconductor-toast >=1.16.0,<1.17.0 - - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 - - bioconductor-s4vectors >=0.40.0,<0.41.0 - - r-ggpubr - - r-ggplot2 - - r-tca - - r-glue - - bioconductor-biocparallel >=1.36.0,<1.37.0 - - r-dirmult - - r-nnls - - r-magrittr - - r-purrr - - r-base 4.3.* - - r-ggridges - - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested r-tca - - - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build - output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs - for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set - conda_packages = finalize_outputs_pass( - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass - fm = finalize_metadata( - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata - build_unsat, host_unsat = add_upstream_pins(m, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins - host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files - deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies - actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-tca")} -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-micsqtl/meta.yaml b/recipes/bioconductor-micsqtl/meta.yaml index 33eb7aa2e58cf..ead8f8b8c777d 100644 --- a/recipes/bioconductor-micsqtl/meta.yaml +++ b/recipes/bioconductor-micsqtl/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "MICSQTL" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Our pipeline, MICSQTL, utilizes scRNA-seq reference and bulk transcriptomes to estimate cellular composition in the matched bulk proteomes. The expression of genes and proteins at either bulk level or cell type level can be integrated by Angle-based Joint and Individual Variation Explained (AJIVE) framework. Meanwhile, MICSQTL can perform cell-type-specic quantitative trait loci (QTL) mapping to proteins or transcripts based on the input of bulk expression data and the estimated cellular composition per molecule type, without the need for single cell sequencing. We use matched transcriptome-proteome from human brain frontal cortex tissue samples to demonstrate the input and output of our tool. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec49e08df014da6955d2b6ab7dc77d3b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-micsqtl", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.0.0), rmarkdown, knitr, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-toast >=1.16.0,<1.17.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-toast >=1.20.0,<1.21.0 - r-base - r-dirmult - r-ggplot2 @@ -37,10 +39,10 @@ requirements: - r-purrr - r-tca run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-toast >=1.16.0,<1.17.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-toast >=1.20.0,<1.21.0 - r-base - r-dirmult - r-ggplot2 @@ -51,13 +53,16 @@ requirements: - r-nnls - r-purrr - r-tca + +source: + md5: 09eaf773ad8d3777ca46e06d1afcdab9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci)' - description: 'Our pipeline, MICSQTL, utilizes scRNA-seq reference and bulk transcriptomes to estimate cellular composition in the matched bulk proteomes. The expression of genes and proteins at either bulk level or cell type level can be integrated by Angle-based Joint and Individual Variation Explained (AJIVE) framework. Meanwhile, MICSQTL can perform cell-type-specic quantitative trait loci (QTL) mapping to proteins or transcripts based on the input of bulk expression data and the estimated cellular composition per molecule type, without the need for single cell sequencing. We use matched transcriptome-proteome from human brain frontal cortex tissue samples to demonstrate the input and output of our tool.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-midashla/meta.yaml b/recipes/bioconductor-midashla/meta.yaml index 99330f8c5b329..0a6be887af08b 100644 --- a/recipes/bioconductor-midashla/meta.yaml +++ b/recipes/bioconductor-midashla/meta.yaml @@ -1,66 +1,71 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "midasHLA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MiDAS is a R package for immunogenetics data transformation and statistical analysis. MiDAS accepts input data in the form of HLA alleles and KIR types, and can transform it into biologically meaningful variables, enabling HLA amino acid fine mapping, analyses of HLA evolutionary divergence, KIR gene presence, as well as validated HLA-KIR interactions. Further, it allows comprehensive statistical association analysis workflows with phenotypes of diverse measurement scales. MiDAS closes a gap between the inference of immunogenetic variation and its efficient utilization to make relevant discoveries related to T cell, Natural Killer cell, and disease biology. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENCE + summary: R package for immunogenomics data handling and association analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7d77f1bda1bff8d67de91e02cb985519 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-midashla", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: broom.mixed (>= 0.2.4), cowplot (>= 1.0.0), devtools (>= 2.0.1), ggplot2 (>= 3.1.0), ggpubr (>= 0.2.5), rmarkdown, seqinr (>= 3.4-5), survival (>= 2.43-3), testthat (>= 2.0.1), tidyr (>= 1.1.2) requirements: host: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'r-assertthat >=0.2.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-assertthat >=0.2.0 - r-base - - 'r-broom >=0.5.1' - - 'r-dplyr >=0.8.0.1' - - 'r-formattable >=0.2.0.1' - - 'r-hardyweinberg >=1.6.3' - - 'r-kableextra >=1.1.0' - - 'r-knitr >=1.21' - - 'r-magrittr >=1.5' - - 'r-qdaptools >=1.3.3' - - 'r-rlang >=0.3.1' - - 'r-stringi >=1.2.4' - - 'r-tibble >=2.0.1' + - r-broom >=0.5.1 + - r-dplyr >=0.8.0.1 + - r-formattable >=0.2.0.1 + - r-hardyweinberg >=1.6.3 + - r-kableextra >=1.1.0 + - r-knitr >=1.21 + - r-magrittr >=1.5 + - r-qdaptools >=1.3.3 + - r-rlang >=0.3.1 + - r-stringi >=1.2.4 + - r-tibble >=2.0.1 run: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'r-assertthat >=0.2.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-assertthat >=0.2.0 - r-base - - 'r-broom >=0.5.1' - - 'r-dplyr >=0.8.0.1' - - 'r-formattable >=0.2.0.1' - - 'r-hardyweinberg >=1.6.3' - - 'r-kableextra >=1.1.0' - - 'r-knitr >=1.21' - - 'r-magrittr >=1.5' - - 'r-qdaptools >=1.3.3' - - 'r-rlang >=0.3.1' - - 'r-stringi >=1.2.4' - - 'r-tibble >=2.0.1' + - r-broom >=0.5.1 + - r-dplyr >=0.8.0.1 + - r-formattable >=0.2.0.1 + - r-hardyweinberg >=1.6.3 + - r-kableextra >=1.1.0 + - r-knitr >=1.21 + - r-magrittr >=1.5 + - r-qdaptools >=1.3.3 + - r-rlang >=0.3.1 + - r-stringi >=1.2.4 + - r-tibble >=2.0.1 + +source: + md5: 7def111fdc9b4877e6c530366f4d8def + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENCE' - summary: 'R package for immunogenomics data handling and association analysis' - description: 'MiDAS is a R package for immunogenetics data transformation and statistical analysis. MiDAS accepts input data in the form of HLA alleles and KIR types, and can transform it into biologically meaningful variables, enabling HLA amino acid fine mapping, analyses of HLA evolutionary divergence, KIR gene presence, as well as validated HLA-KIR interactions. Further, it allows comprehensive statistical association analysis workflows with phenotypes of diverse measurement scales. MiDAS closes a gap between the inference of immunogenetic variation and its efficient utilization to make relevant discoveries related to T cell, Natural Killer cell, and disease biology.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-milor/meta.yaml b/recipes/bioconductor-milor/meta.yaml index 85f159f4f472b..3cbf6aaf1d23b 100644 --- a/recipes/bioconductor-milor/meta.yaml +++ b/recipes/bioconductor-milor/meta.yaml @@ -1,36 +1,44 @@ -{% set version = "1.10.0" %} +{% set version = "2.2.0" %} {% set name = "miloR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Milo performs single-cell differential abundance testing. Cell states are modelled as representative neighbourhoods on a nearest neighbour graph. Hypothesis testing is performed using either a negative bionomial generalized linear model or negative binomial generalized linear mixed model. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Differential neighbourhood abundance testing on a graph -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ab9a4a2fe26786cd8fef69354bfa08f build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-milor", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, MASS, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, scuttle, BiocStyle, MouseGastrulationData, MouseThymusAgeing, magick, RCurl, curl, graphics + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, scuttle, BiocStyle, MouseGastrulationData, MouseThymusAgeing, magick, RCurl, MASS, curl, scRNAseq, graphics, sparseMatrixStats requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cowplot - r-dplyr @@ -41,23 +49,33 @@ requirements: - r-gtools - r-igraph - r-irlba - - 'r-matrix >=1.3-0' + - r-matrix >=1.3-0 - r-matrixstats + - r-numderiv - r-patchwork + - r-pracma - r-rcolorbrewer + - r-rcpp + - r-rcpparmadillo + - r-rcppeigen + - r-rcppml - r-stringr - r-tibble - r-tidyr + - libblas + - liblapack + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cowplot - r-dplyr @@ -68,20 +86,29 @@ requirements: - r-gtools - r-igraph - r-irlba - - 'r-matrix >=1.3-0' + - r-matrix >=1.3-0 - r-matrixstats + - r-numderiv - r-patchwork + - r-pracma - r-rcolorbrewer + - r-rcpp + - r-rcpparmadillo + - r-rcppeigen + - r-rcppml - r-stringr - r-tibble - r-tidyr + +source: + md5: dd33732ab19ad0bf8206fb392e6e9c62 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Differential neighbourhood abundance testing on a graph' - description: 'Milo performs single-cell differential abundance testing. Cell states are modelled as representative neighbourhoods on a nearest neighbour graph. Hypothesis testing is performed using a negative bionomial generalized linear model.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mimager/meta.yaml b/recipes/bioconductor-mimager/meta.yaml index 648f2f64bb6d4..37275066843d7 100644 --- a/recipes/bioconductor-mimager/meta.yaml +++ b/recipes/bioconductor-mimager/meta.yaml @@ -1,59 +1,64 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "mimager" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Easily visualize and inspect microarrays for spatial artifacts. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 'mimager: The Microarray Imager' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2a9eaf36345d24dc2d44a65c1f8640a0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mimager", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind, affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1 requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affyplm >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affyplm >=1.82.0,<1.83.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dbi - r-gtable - r-scales run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affyplm >=1.78.0,<1.79.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affyplm >=1.82.0,<1.83.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dbi - r-gtable - r-scales + +source: + md5: 9e4f6d3ac5d7a6d4c41480f2adb9f3b6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'mimager: The Microarray Imager' - description: 'Easily visualize and inspect microarrays for spatial artifacts.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mina/meta.yaml b/recipes/bioconductor-mina/meta.yaml index 1f816fb2b240f..25a0509fb4789 100644 --- a/recipes/bioconductor-mina/meta.yaml +++ b/recipes/bioconductor-mina/meta.yaml @@ -1,25 +1,31 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "mina" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An increasing number of microbiome datasets have been generated and analyzed with the help of rapidly developing sequencing technologies. At present, analysis of taxonomic profiling data is mainly conducted using composition-based methods, which ignores interactions between community members. Besides this, a lack of efficient ways to compare microbial interaction networks limited the study of community dynamics. To better understand how community diversity is affected by complex interactions between its members, we developed a framework (Microbial community dIversity and Network Analysis, mina), a comprehensive framework for microbial community diversity analysis and network comparison. By defining and integrating network-derived community features, we greatly reduce noise-to-signal ratio for diversity analyses. A bootstrap and permutation-based method was implemented to assess community network dissimilarities and extract discriminative features in a statistically principled way. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Microbial community dIversity and Network Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d6578736bef864eef8f89958a849137b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mina", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-apcluster - r-base @@ -56,17 +62,16 @@ requirements: - r-reshape2 - r-rspectra - r-stringr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 7dc755ac67f493187d858b9e27f43882 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL - summary: 'Microbial community dIversity and Network Analysis' - description: 'An increasing number of microbiome datasets have been generated and analyzed with the help of rapidly developing sequencing technologies. At present, analysis of taxonomic profiling data is mainly conducted using composition-based methods, which ignores interactions between community members. Besides this, a lack of efficient ways to compare microbial interaction networks limited the study of community dynamics. To better understand how community diversity is affected by complex interactions between its members, we developed a framework (Microbial community dIversity and Network Analysis, mina), a comprehensive framework for microbial community diversity analysis and network comparison. By defining and integrating network-derived community features, we greatly reduce noise-to-signal ratio for diversity analyses. A bootstrap and permutation-based method was implemented to assess community network dissimilarities and extract discriminative features in a statistically principled way.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mineica/meta.yaml b/recipes/bioconductor-mineica/meta.yaml index 4f8e58766912f..eb16a20fd003e 100644 --- a/recipes/bioconductor-mineica/meta.yaml +++ b/recipes/bioconductor-mineica/meta.yaml @@ -1,38 +1,50 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "MineICA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The goal of MineICA is to perform Independent Component Analysis (ICA) on multiple transcriptome datasets, integrating additional data (e.g molecular, clinical and pathological). This Integrative ICA helps the biological interpretation of the components by studying their association with variables (e.g sample annotations) and gene sets, and enables the comparison of components from different datasets using correlation-based graph. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Analysis of an ICA decomposition obtained on genomics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d08aa74cfe4d20f4ad26235e0695d555 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mineica", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:mineica + - doi:10.1155/2014/213656 + parent_recipe: + name: bioconductor-mineica + path: recipes/bioconductor-mineica + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX, future, future.apply requirements: + host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' - - 'bioconductor-lumihumanall.db >=1.22.0,<1.23.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-lumi >=2.58.0,<2.59.0 + - bioconductor-lumihumanall.db >=1.22.0,<1.23.0 + - bioconductor-marray >=1.84.0,<1.85.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-cluster - r-colorspace @@ -49,18 +61,19 @@ requirements: - r-rcolorbrewer - r-scales - r-xtable + run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' - - 'bioconductor-lumihumanall.db >=1.22.0,<1.23.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-lumi >=2.58.0,<2.59.0 + - bioconductor-lumihumanall.db >=1.22.0,<1.23.0 + - bioconductor-marray >=1.84.0,<1.85.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-cluster - r-colorspace @@ -77,21 +90,16 @@ requirements: - r-rcolorbrewer - r-scales - r-xtable + +source: + md5: 7de548fd73a9b82a26405a3b77872a53 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Analysis of an ICA decomposition obtained on genomics data' - description: 'The goal of MineICA is to perform Independent Component Analysis (ICA) on multiple transcriptome datasets, integrating additional data (e.g molecular, clinical and pathological). This Integrative ICA helps the biological interpretation of the components by studying their association with variables (e.g sample annotations) and gene sets, and enables the comparison of components from different datasets using correlation-based graph.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:mineica - - doi:10.1155/2014/213656 - parent_recipe: - name: bioconductor-mineica - path: recipes/bioconductor-mineica - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-minet/meta.yaml b/recipes/bioconductor-minet/meta.yaml index 2695fcc76aaa2..d5d8fae341c63 100644 --- a/recipes/bioconductor-minet/meta.yaml +++ b/recipes/bioconductor-minet/meta.yaml @@ -1,24 +1,40 @@ -{% set version = "3.60.0" %} +{% set version = "3.64.0" %} {% set name = "minet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements various algorithms for inferring mutual information networks from data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Mutual Information NETworks -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8aaab67519352be115568a301e98ef99 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-minet", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:minet + - doi:10.1186/1471-2105-9-461 + parent_recipe: + name: bioconductor-minet + path: recipes/bioconductor-minet + version: 3.38.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-infotheo @@ -27,26 +43,16 @@ requirements: run: - r-base - r-infotheo - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 022eb3117a32dfa1688624c98af7d5d9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Mutual Information NETworks' - description: 'This package implements various algorithms for inferring mutual information networks from data.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:minet - - doi:10.1186/1471-2105-9-461 - parent_recipe: - name: bioconductor-minet - path: recipes/bioconductor-minet - version: 3.38.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-minfi/meta.yaml b/recipes/bioconductor-minfi/meta.yaml index 9c09bfd03b090..1992b6189baa6 100644 --- a/recipes/bioconductor-minfi/meta.yaml +++ b/recipes/bioconductor-minfi/meta.yaml @@ -1,47 +1,56 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "minfi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools to analyze & visualize Illumina Infinium methylation arrays. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Analyze Illumina Infinium DNA methylation arrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3c1998eee0aabbfab3c3796c82339a18 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-minfi", max_pin="x.x") }}' - noarch: generic +extra: + identifiers: + - biotools:minfi + parent_recipe: + name: bioconductor-minfi + path: recipes/bioconductor-minfi + version: 1.26.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-siggenes >=1.76.0,<1.77.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'r-base >=4.3,<4.4.0a0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-siggenes >=1.80.0,<1.81.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base - r-beanplot - r-data.table - r-lattice @@ -52,28 +61,28 @@ requirements: - r-quadprog - r-rcolorbrewer - r-reshape - - 'openblas =0.3.3' + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-siggenes >=1.76.0,<1.77.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'r-base >=4.3,<4.4.0a0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-siggenes >=1.80.0,<1.81.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base - r-beanplot - r-data.table - r-lattice @@ -84,20 +93,16 @@ requirements: - r-quadprog - r-rcolorbrewer - r-reshape - - 'openblas =0.3.3' + +source: + md5: 57c03de4a9c35f98a7b8d1e3e9b7150c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Analyze Illumina Infinium DNA methylation arrays' - description: 'Tools to analyze & visualize Illumina Infinium methylation arrays.' -extra: - identifiers: - - biotools:minfi - parent_recipe: - name: bioconductor-minfi - path: recipes/bioconductor-minfi - version: 1.26.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-minfidata/meta.yaml b/recipes/bioconductor-minfidata/meta.yaml index f41037aeece26..9ee48b93a84ce 100644 --- a/recipes/bioconductor-minfidata/meta.yaml +++ b/recipes/bioconductor-minfidata/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "0.48.0" %} +{% set version = "0.52.0" %} {% set name = "minfiData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1ca7578aeab1a54db146c443870be6e7 +about: + description: Data from 6 samples across 2 groups from 450k methylation arrays. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Example data for the Illumina Methylation 450k array build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-minfidata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0 + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0 + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8a4cef6c4c950cfa8c6484c289a084c1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Example data for the Illumina Methylation 450k array' - description: 'Data from 6 samples across 2 groups from 450k methylation arrays.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-minfidata/post-link.sh b/recipes/bioconductor-minfidata/post-link.sh index 7dbdb4780ea5f..c67e0c1943adf 100644 --- a/recipes/bioconductor-minfidata/post-link.sh +++ b/recipes/bioconductor-minfidata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "minfidata-0.48.0" +installBiocDataPackage.sh "minfidata-0.52.0" diff --git a/recipes/bioconductor-minfidataepic/meta.yaml b/recipes/bioconductor-minfidataepic/meta.yaml index d9429ed793030..65c89a771f355 100644 --- a/recipes/bioconductor-minfidataepic/meta.yaml +++ b/recipes/bioconductor-minfidataepic/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "minfiDataEPIC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bcb0b01d571c5308e02db4c6b5c0d1ce +about: + description: Data from 3 technical replicates of the cell line GM12878 from the EPIC methylation array. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Example data for the Illumina Methylation EPIC array build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-minfidataepic", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0 + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0 + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ee3086e570c8bb7a0283e30d3e9d06a6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Example data for the Illumina Methylation EPIC array' - description: 'Data from 3 technical replicates of the cell line GM12878 from the EPIC methylation array.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-minfidataepic/post-link.sh b/recipes/bioconductor-minfidataepic/post-link.sh index 506358fd0d0de..f23e4518314e4 100644 --- a/recipes/bioconductor-minfidataepic/post-link.sh +++ b/recipes/bioconductor-minfidataepic/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "minfidataepic-1.28.0" +installBiocDataPackage.sh "minfidataepic-1.32.0" diff --git a/recipes/bioconductor-minimumdistance/meta.yaml b/recipes/bioconductor-minimumdistance/meta.yaml index 46b1638468be4..eec8fcb2f06c8 100644 --- a/recipes/bioconductor-minimumdistance/meta.yaml +++ b/recipes/bioconductor-minimumdistance/meta.yaml @@ -1,38 +1,48 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "MinimumDistance" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Analysis of de novo copy number variants in trios from high-dimensional genotyping platforms. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: A Package for De Novo CNV Detection in Case-Parent Trios -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ab96e788a4152b80b7a685f3fc8fcd9c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-minimumdistance", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:minimumdistance + - doi:10.1186/1471-2105-13-330 + parent_recipe: + name: bioconductor-minimumdistance + path: recipes/bioconductor-minimumdistance + version: 1.24.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-vanillaice >=1.64.0,<1.65.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-vanillaice >=1.68.0,<1.69.0 - r-base - r-data.table - r-ff @@ -40,37 +50,33 @@ requirements: - r-lattice - r-matrixstats run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-vanillaice >=1.64.0,<1.65.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-vanillaice >=1.68.0,<1.69.0 - r-base - r-data.table - r-ff - r-foreach - r-lattice - r-matrixstats + +source: + md5: 06a608c74974ed1e1f297a3b84e914a9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A Package for De Novo CNV Detection in Case-Parent Trios' - description: 'Analysis of de novo copy number variants in trios from high-dimensional genotyping platforms.' -extra: - identifiers: - - biotools:minimumdistance - - doi:10.1186/1471-2105-13-330 - parent_recipe: - name: bioconductor-minimumdistance - path: recipes/bioconductor-minimumdistance - version: 1.24.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-minionsummarydata/meta.yaml b/recipes/bioconductor-minionsummarydata/meta.yaml index f09a52c37ecc6..859af2e0cab4b 100644 --- a/recipes/bioconductor-minionsummarydata/meta.yaml +++ b/recipes/bioconductor-minionsummarydata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "minionSummaryData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1679c45541b2d76094c3894abe9c011d +about: + description: Summarised MinION sequencing data for Salmonella Typhi published by Ashton et al. in 2015. Three replicate runs are each provided as Fast5Summary objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Summarised MinION sequencing data published by Ashton et al. 2015 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-minionsummarydata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 46fb1c1bc260bfa260fc0935ca887972 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Summarised MinION sequencing data published by Ashton et al. 2015' - description: 'Summarised MinION sequencing data for Salmonella Typhi published by Ashton et al. in 2015. Three replicate runs are each provided as Fast5Summary objects.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-minionsummarydata/post-link.sh b/recipes/bioconductor-minionsummarydata/post-link.sh index 9e9250e8eedd7..76f270271bf56 100644 --- a/recipes/bioconductor-minionsummarydata/post-link.sh +++ b/recipes/bioconductor-minionsummarydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "minionsummarydata-1.32.0" +installBiocDataPackage.sh "minionsummarydata-1.36.0" diff --git a/recipes/bioconductor-mipp/meta.yaml b/recipes/bioconductor-mipp/meta.yaml index 50af592ccbaa4..36a2e5628b566 100644 --- a/recipes/bioconductor-mipp/meta.yaml +++ b/recipes/bioconductor-mipp/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "MiPP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package finds optimal sets of genes that seperate samples into two or more classes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Misclassification Penalized Posterior Classification -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ce412e2a72891fcc7969faee078b2be3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mipp", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:mipp + - doi:10.1093/bioinformatics/bti1020 + parent_recipe: + name: bioconductor-mipp + path: recipes/bioconductor-mipp + version: 1.52.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-e1071 - r-mass run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-e1071 - r-mass + +source: + md5: aa0c3c94f8573215b719dd25561c45b3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Misclassification Penalized Posterior Classification' - description: 'This package finds optimal sets of genes that seperate samples into two or more classes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:mipp - - doi:10.1093/bioinformatics/bti1020 - parent_recipe: - name: bioconductor-mipp - path: recipes/bioconductor-mipp - version: 1.52.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-miqc/meta.yaml b/recipes/bioconductor-miqc/meta.yaml index 6c084decec07f..9e3621cdf8ea7 100644 --- a/recipes/bioconductor-miqc/meta.yaml +++ b/recipes/bioconductor-miqc/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "miQC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e1246c2b5dcb83059d6887b35db543a0 +about: + description: Single-cell RNA-sequencing (scRNA-seq) has made it possible to profile gene expression in tissues at high resolution. An important preprocessing step prior to performing downstream analyses is to identify and remove cells with poor or degraded sample quality using quality control (QC) metrics. Two widely used QC metrics to identify a ‘low-quality’ cell are (i) if the cell includes a high proportion of reads that map to mitochondrial DNA encoded genes (mtDNA) and (ii) if a small number of genes are detected. miQC is data-driven QC metric that jointly models both the proportion of reads mapping to mtDNA and the number of detected genes with mixture models in a probabilistic framework to predict the low-quality cells in a given dataset. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_3_clause + file LICENSE + license_file: LICENSE + summary: Flexible, probabilistic metrics for quality control of scRNA-seq data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-miqc", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: scRNAseq, scater, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-flexmix - r-ggplot2 run: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-flexmix - r-ggplot2 +source: + md5: 0792aac601eccb65fe462680371452b2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_3_clause + file LICENSE' - summary: 'Flexible, probabilistic metrics for quality control of scRNA-seq data' - description: 'Single-cell RNA-sequencing (scRNA-seq) has made it possible to profile gene expression in tissues at high resolution. An important preprocessing step prior to performing downstream analyses is to identify and remove cells with poor or degraded sample quality using quality control (QC) metrics. Two widely used QC metrics to identify a ‘low-quality’ cell are (i) if the cell includes a high proportion of reads that map to mitochondrial DNA encoded genes (mtDNA) and (ii) if a small number of genes are detected. miQC is data-driven QC metric that jointly models both the proportion of reads mapping to mtDNA and the number of detected genes with mixture models in a probabilistic framework to predict the low-quality cells in a given dataset.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mira/meta.yaml b/recipes/bioconductor-mira/meta.yaml index 93e25f1a9c765..d9fbe301ca193 100644 --- a/recipes/bioconductor-mira/meta.yaml +++ b/recipes/bioconductor-mira/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "MIRA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: DNA methylation contains information about the regulatory state of the cell. MIRA aggregates genome-scale DNA methylation data into a DNA methylation profile for a given region set with shared biological annotation. Using this profile, MIRA infers and scores the collective regulatory activity for the region set. MIRA facilitates regulatory analysis in situations where classical regulatory assays would be difficult and allows public sources of region sets to be leveraged for novel insight into the regulatory state of DNA methylation datasets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Methylation-Based Inference of Regulatory Activity -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 670cb42f275d260b28e0e2d140cacda2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mira", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsseq >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsseq >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-ggplot2 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsseq >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsseq >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-ggplot2 + +source: + md5: e5cc9c99f4b1b812446d3aa457e83f97 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Methylation-Based Inference of Regulatory Activity' - description: 'DNA methylation contains information about the regulatory state of the cell. MIRA aggregates genome-scale DNA methylation data into a DNA methylation profile for a given region set with shared biological annotation. Using this profile, MIRA infers and scores the collective regulatory activity for the region set. MIRA facilitates regulatory analysis in situations where classical regulatory assays would be difficult and allows public sources of region sets to be leveraged for novel insight into the regulatory state of DNA methylation datasets.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mirage/meta.yaml b/recipes/bioconductor-mirage/meta.yaml index 45a443bde1f58..c2857f7d25ad1 100644 --- a/recipes/bioconductor-mirage/meta.yaml +++ b/recipes/bioconductor-mirage/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "MiRaGE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package contains functions for inferece of target gene regulation by miRNA, based on only target gene expression profile. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: MiRNA Ranking by Gene Expression -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c86c12c042052eb4d558bdff55e8c47a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mirage", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:mirage + parent_recipe: + name: bioconductor-mirage + path: recipes/bioconductor-mirage + version: 1.22.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>= 1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell, IRanges, GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-biocmanager run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-biocmanager + +source: + md5: e13ad9fdad2deeee94e0395bfb34e182 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL - summary: 'MiRNA Ranking by Gene Expression' - description: 'The package contains functions for inferece of target gene regulation by miRNA, based on only target gene expression profile.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:mirage - parent_recipe: - name: bioconductor-mirage - path: recipes/bioconductor-mirage - version: 1.22.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mirbase.db/meta.yaml b/recipes/bioconductor-mirbase.db/meta.yaml index a51ede2582bcd..45640a59cd88e 100644 --- a/recipes/bioconductor-mirbase.db/meta.yaml +++ b/recipes/bioconductor-mirbase.db/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.2.0" %} {% set name = "mirbase.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 316bc12cee8c2dd9240b7fc30cd1619e +about: + description: 'miRBase: the microRNA database assembled using data from miRBase (http://www.mirbase.org/).' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: 'miRBase: the microRNA database' build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mirbase.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 316bc12cee8c2dd9240b7fc30cd1619e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'miRBase: the microRNA database' - description: 'miRBase: the microRNA database assembled using data from miRBase (http://www.mirbase.org/).' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mirbaseconverter/meta.yaml b/recipes/bioconductor-mirbaseconverter/meta.yaml index 49f8e79f49ee0..d0ef3f93bcf3b 100644 --- a/recipes/bioconductor-mirbaseconverter/meta.yaml +++ b/recipes/bioconductor-mirbaseconverter/meta.yaml @@ -1,36 +1,37 @@ -{% set version = "1.24.0" %} +{% set version = "1.30.0" %} {% set name = "miRBaseConverter" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0164410dd1aea8865c0b1f6821572c14 +about: + description: A comprehensive tool for converting and retrieving the miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. It can process a huge number of miRNAs in a short time without other depends. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versions build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic + run_exports: '{{ pin_subpackage("bioconductor-mirbaseconverter", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils, rmarkdown requirements: host: - r-base run: - r-base +source: + md5: 1be1455324a0b495727373e719e29026 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versions' - description: 'A comprehensive tool for converting and retrieving the miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. It can process a huge number of miRNAs in a short time without other depends.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mirbaseversions.db/meta.yaml b/recipes/bioconductor-mirbaseversions.db/meta.yaml index a66ca195291ed..43a3e929fb8f9 100644 --- a/recipes/bioconductor-mirbaseversions.db/meta.yaml +++ b/recipes/bioconductor-mirbaseversions.db/meta.yaml @@ -1,51 +1,57 @@ {% set version = "1.1.0" %} {% set name = "miRBaseVersions.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Annotation package containing all available miRNA names from 22 versions (data from http://www.mirbase.org/). + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Collection of mature miRNA names of 22 different miRBase release versions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9944ab7a474f84a40100c56298f9cb77 build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mirbaseversions.db", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-mirbaseversions.db + path: recipes/bioconductor-mirbaseversions.db + version: 1.1.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, annotate requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - r-dbi - r-gtools - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - r-dbi - r-gtools - r-rsqlite - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 9944ab7a474f84a40100c56298f9cb77 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Collection of mature miRNA names of 22 different miRBase release versions' - description: 'Annotation package containing all available miRNA names from 22 versions (data from http://www.mirbase.org/).' -extra: - parent_recipe: - name: bioconductor-mirbaseversions.db - path: recipes/bioconductor-mirbaseversions.db - version: 1.1.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mircomp/meta.yaml b/recipes/bioconductor-mircomp/meta.yaml index 465227f2e2975..cbcbb5b9521b4 100644 --- a/recipes/bioconductor-mircomp/meta.yaml +++ b/recipes/bioconductor-mircomp/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "miRcomp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 06b97d8829ca13b60dd4869a48b684ab +about: + description: Based on a large miRNA dilution study, this package provides tools to read in the raw amplification data and use these data to assess the performance of methods that estimate expression from the amplification curves. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 | file LICENSE + license_file: LICENSE + summary: Tools to assess and compare miRNA expression estimatation methods build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mircomp", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-mircompdata >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-mircompdata >=1.36.0,<1.37.0 - r-base - r-kernsmooth run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-mircompdata >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-mircompdata >=1.36.0,<1.37.0 - r-base - r-kernsmooth +source: + md5: f2dc7026533a1b60c30f91180486bdf4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 | file LICENSE' - summary: 'Tools to assess and compare miRNA expression estimatation methods' - description: 'Based on a large miRNA dilution study, this package provides tools to read in the raw amplification data and use these data to assess the performance of methods that estimate expression from the amplification curves.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mircompdata/meta.yaml b/recipes/bioconductor-mircompdata/meta.yaml index 95ae5ae333c25..871a9c5aeb5bc 100644 --- a/recipes/bioconductor-mircompdata/meta.yaml +++ b/recipes/bioconductor-mircompdata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "miRcompData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0b091222ebe8ac1a3a2c59384931393b +about: + description: Raw amplification data from a large microRNA mixture / dilution study. These data are used by the miRcomp package to assess the performance of methods that estimate expression from the amplification curves. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 | file LICENSE + license_file: LICENSE + summary: Data used in the miRcomp package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mircompdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c4ca934e422f56d80d298f8f51a82aa8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL-3 | file LICENSE' - summary: 'Data used in the miRcomp package' - description: 'Raw amplification data from a large microRNA mixture / dilution study. These data are used by the miRcomp package to assess the performance of methods that estimate expression from the amplification curves.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mircompdata/post-link.sh b/recipes/bioconductor-mircompdata/post-link.sh index 5d104e9b53a6d..4f395a24df514 100644 --- a/recipes/bioconductor-mircompdata/post-link.sh +++ b/recipes/bioconductor-mircompdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mircompdata-1.32.0" +installBiocDataPackage.sh "mircompdata-1.36.0" diff --git a/recipes/bioconductor-mirintegrator/meta.yaml b/recipes/bioconductor-mirintegrator/meta.yaml index e122769fc894f..bcbf1d5d40874 100644 --- a/recipes/bioconductor-mirintegrator/meta.yaml +++ b/recipes/bioconductor-mirintegrator/meta.yaml @@ -1,57 +1,63 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "mirIntegrator" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for augmenting signaling pathways to perform pathway analysis of microRNA and mRNA expression levels. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Integrating microRNA expression into signaling pathways for pathway analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ec5789f159dfc3880ce8369af20c27a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mirintegrator", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:mirintegrator + - doi:10.1038/srep29251 + parent_recipe: + name: bioconductor-mirintegrator + path: recipes/bioconductor-mirintegrator + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-rontotools >=2.30.0,<2.31.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-rontotools >=2.34.0,<2.35.0 - r-base - r-ggplot2 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-rontotools >=2.30.0,<2.31.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-rontotools >=2.34.0,<2.35.0 - r-base - r-ggplot2 + +source: + md5: 489c20455b69a6f0abea9c44beb8e91c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=3)' - summary: 'Integrating microRNA expression into signaling pathways for pathway analysis' - description: 'Tools for augmenting signaling pathways to perform pathway analysis of microRNA and mRNA expression levels.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:mirintegrator - - doi:10.1038/srep29251 - parent_recipe: - name: bioconductor-mirintegrator - path: recipes/bioconductor-mirintegrator - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mirit/build.sh b/recipes/bioconductor-mirit/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mirit/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mirit/build_failure.linux-64.yaml b/recipes/bioconductor-mirit/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..729b7024dacc2 --- /dev/null +++ b/recipes/bioconductor-mirit/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: 3796e0536723ffbd5b636c6caddf1ce1532c7e2763035b17558c097c8e1164fb # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Encountered problems while solving: + - nothing provides requested r-genekitr + - nothing provides requested r-geneset + + Could not solve for environment specs + The following packages are incompatible + [31mr-genekitr[0m does not exist (perhaps a typo or a missing channel); + [31mr-geneset[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-geneset"), MatchSpec("r-genekitr")} + Encountered problems while solving: + - nothing provides requested r-genekitr + - nothing provides requested r-geneset + + Could not solve for environment specs + The following packages are incompatible + [31mr-genekitr[0m does not exist (perhaps a typo or a missing channel); + [31mr-geneset[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-geneset"), MatchSpec("r-genekitr")} + Encountered problems while solving: + - nothing provides requested r-genekitr + - nothing provides requested r-geneset + + Could not solve for environment specs + The following packages are incompatible + [31mr-genekitr[0m does not exist (perhaps a typo or a missing channel); + [31mr-geneset[0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. +reason: |- + needs r-genekitr and r-geneset to be added to conda-forge +category: |- + dependency issue diff --git a/recipes/bioconductor-mirit/build_failure.osx-64.yaml b/recipes/bioconductor-mirit/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..22d7db650ee07 --- /dev/null +++ b/recipes/bioconductor-mirit/build_failure.osx-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: 3796e0536723ffbd5b636c6caddf1ce1532c7e2763035b17558c097c8e1164fb # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Encountered problems while solving: + - nothing provides requested r-genekitr + - nothing provides requested r-geneset + + Could not solve for environment specs + The following packages are incompatible + r-genekitr does not exist (perhaps a typo or a missing channel); + r-geneset does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("r-geneset"), MatchSpec("r-genekitr")} + Encountered problems while solving: + - nothing provides requested r-genekitr + - nothing provides requested r-geneset + + Could not solve for environment specs + The following packages are incompatible + r-genekitr does not exist (perhaps a typo or a missing channel); + r-geneset does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("r-geneset"), MatchSpec("r-genekitr")} + Encountered problems while solving: + - nothing provides requested r-genekitr + - nothing provides requested r-geneset + + Could not solve for environment specs + The following packages are incompatible + r-genekitr does not exist (perhaps a typo or a missing channel); + r-geneset does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. +reason: |- + needs r-genekitr and r-geneset to be added to conda-forge +category: |- + dependency issue diff --git a/recipes/bioconductor-mirit/meta.yaml b/recipes/bioconductor-mirit/meta.yaml new file mode 100644 index 0000000000000..9f9626381224a --- /dev/null +++ b/recipes/bioconductor-mirit/meta.yaml @@ -0,0 +1,86 @@ +{% set version = "1.2.0" %} +{% set name = "MIRit" %} +{% set bioc = "3.20" %} + +about: + description: MIRit is an R package that provides several methods for investigating the relationships between miRNAs and genes in different biological conditions. In particular, MIRit allows to explore the functions of dysregulated miRNAs, and makes it possible to identify miRNA-gene regulatory axes that control biological pathways, thus enabling the users to unveil the complexity of miRNA biology. MIRit is an all-in-one framework that aims to help researchers in all the central aspects of an integrative miRNA-mRNA analyses, from differential expression analysis to network characterization. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Integrate microRNA and gene expression to decipher pathway complexity + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirit", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, biomaRt, BSgenome.Hsapiens.UCSC.hg38, GenomicRanges, ggrepel, ggridges, Gviz, gwasrapidd, knitr, MonoPoly, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0) +requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + + host: + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-graphite >=1.52.0,<1.53.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - r-base + - r-genekitr + - r-geneset + - r-ggplot2 + - r-ggpubr + - r-httr + - r-rcpp + - r-rlang + - libblas + - liblapack + + run: + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-graphite >=1.52.0,<1.53.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - r-base + - r-genekitr + - r-geneset + - r-ggplot2 + - r-ggpubr + - r-httr + - r-rcpp + - r-rlang + +source: + md5: 337ea67055b96bac0c5d5e20cc146cdb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-mirlab/meta.yaml b/recipes/bioconductor-mirlab/meta.yaml index 02d028c863d44..dc53c807f627b 100644 --- a/recipes/bioconductor-mirlab/meta.yaml +++ b/recipes/bioconductor-mirlab/meta.yaml @@ -1,35 +1,38 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "miRLAB" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provide tools exploring miRNA-mRNA relationships, including popular miRNA target prediction methods, ensemble methods that integrate individual methods, functions to get data from online resources, functions to validate the results, and functions to conduct enrichment analyses. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Dry lab for exploring miRNA-mRNA relationships -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3347a99a17fc2caade03a35471a79ad0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mirlab", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr,BiocGenerics, AnnotationDbi,RUnit,rmarkdown requirements: + host: - - 'bioconductor-category >=2.68.0,<2.69.0' - - 'bioconductor-ctc >=1.76.0,<1.77.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tcgabiolinks >=2.30.0,<2.31.0' + - bioconductor-category >=2.72.0,<2.73.0 + - bioconductor-ctc >=1.80.0,<1.81.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tcgabiolinks >=2.34.0,<2.35.0 - r-base - r-dplyr - r-energy @@ -42,15 +45,16 @@ requirements: - r-pcalg - r-rcurl - r-stringr + run: - - 'bioconductor-category >=2.68.0,<2.69.0' - - 'bioconductor-ctc >=1.76.0,<1.77.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tcgabiolinks >=2.30.0,<2.31.0' + - bioconductor-category >=2.72.0,<2.73.0 + - bioconductor-ctc >=1.80.0,<1.81.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tcgabiolinks >=2.34.0,<2.35.0 - r-base - r-dplyr - r-energy @@ -63,13 +67,16 @@ requirements: - r-pcalg - r-rcurl - r-stringr + +source: + md5: 1f3860b3bbf7168a19ff63930870bf1d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Dry lab for exploring miRNA-mRNA relationships' - description: 'Provide tools exploring miRNA-mRNA relationships, including popular miRNA target prediction methods, ensemble methods that integrate individual methods, functions to get data from online resources, functions to validate the results, and functions to conduct enrichment analyses.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mirna102xgaincdf/meta.yaml b/recipes/bioconductor-mirna102xgaincdf/meta.yaml index c2998928a01d0..396f94edee5ee 100644 --- a/recipes/bioconductor-mirna102xgaincdf/meta.yaml +++ b/recipes/bioconductor-mirna102xgaincdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mirna102xgaincdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9091a45c2ac15c2de0263743ab334f97 +about: + description: A package containing an environment representing the miRNA-1_0_2Xgain.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mirna102xgaincdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mirna102xgaincdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9091a45c2ac15c2de0263743ab334f97 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mirna102xgaincdf - description: 'A package containing an environment representing the miRNA-1_0_2Xgain.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mirna10cdf/meta.yaml b/recipes/bioconductor-mirna10cdf/meta.yaml index 657e2d588c9fe..21a4f4b1fb75e 100644 --- a/recipes/bioconductor-mirna10cdf/meta.yaml +++ b/recipes/bioconductor-mirna10cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mirna10cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 814da2a2e298e132f4db0b2e8ab814be +about: + description: A package containing an environment representing the miRNA-1_0.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mirna10cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mirna10cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 814da2a2e298e132f4db0b2e8ab814be + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mirna10cdf - description: 'A package containing an environment representing the miRNA-1_0.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mirna10probe/meta.yaml b/recipes/bioconductor-mirna10probe/meta.yaml index ad500280b4d55..52e3ab7e701f6 100644 --- a/recipes/bioconductor-mirna10probe/meta.yaml +++ b/recipes/bioconductor-mirna10probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mirna10probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8bfa6cdfeee1c563b4881214bd5d4ce1 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was miRNA-1\_0\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type mirna10 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mirna10probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8bfa6cdfeee1c563b4881214bd5d4ce1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type mirna10' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was miRNA-1\_0\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mirna20cdf/meta.yaml b/recipes/bioconductor-mirna20cdf/meta.yaml index 3d81b3981f94a..ef81873acde5a 100644 --- a/recipes/bioconductor-mirna20cdf/meta.yaml +++ b/recipes/bioconductor-mirna20cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mirna20cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 56f7807673ff108427ae7f6bdf85ae1c +about: + description: A package containing an environment representing the miRNA-2_0.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mirna20cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mirna20cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 56f7807673ff108427ae7f6bdf85ae1c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mirna20cdf - description: 'A package containing an environment representing the miRNA-2_0.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mirnameconverter/meta.yaml b/recipes/bioconductor-mirnameconverter/meta.yaml index 5e214021c777c..73707ae1916e9 100644 --- a/recipes/bioconductor-mirnameconverter/meta.yaml +++ b/recipes/bioconductor-mirnameconverter/meta.yaml @@ -1,51 +1,57 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "miRNAmeConverter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Translating mature miRNA names to different miRBase versions, sequence retrieval, checking names for validity and detecting miRBase version of a given set of names (data from http://www.mirbase.org/). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Convert miRNA Names to Different miRBase Versions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cfc6563f669ecbc03292cccba919fe05 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mirnameconverter", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:mirnameconverter + parent_recipe: + name: bioconductor-mirnameconverter + path: recipes/bioconductor-mirnameconverter + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: methods, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-mirbaseversions.db >=1.1.0,<1.2.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-mirbaseversions.db >=1.1.0,<1.2.0 - r-base - r-dbi - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-mirbaseversions.db >=1.1.0,<1.2.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-mirbaseversions.db >=1.1.0,<1.2.0 - r-base - r-dbi - r-reshape2 + +source: + md5: a86fef391cf4cc0bbe7868c65c9641b7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Convert miRNA Names to Different miRBase Versions' - description: 'Translating mature miRNA names to different miRBase versions, sequence retrieval, checking names for validity and detecting miRBase version of a given set of names (data from http://www.mirbase.org/).' -extra: - identifiers: - - biotools:mirnameconverter - parent_recipe: - name: bioconductor-mirnameconverter - path: recipes/bioconductor-mirnameconverter - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mirnapath/meta.yaml b/recipes/bioconductor-mirnapath/meta.yaml index 9438bd5588098..671af69b88e61 100644 --- a/recipes/bioconductor-mirnapath/meta.yaml +++ b/recipes/bioconductor-mirnapath/meta.yaml @@ -1,38 +1,20 @@ -{% set version = "1.62.0" %} +{% set version = "1.66.0" %} {% set name = "miRNApath" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94aad8a3b57b070cb5c559d9d1f14726 +about: + description: This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-2.1 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2.1' + summary: 'miRNApath: Pathway Enrichment for miRNA Expression Data' build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mirnapath", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-2.1 - summary: 'miRNApath: Pathway Enrichment for miRNA Expression Data' - description: 'This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2.1' extra: identifiers: - biotools:mirnapath @@ -40,4 +22,22 @@ extra: name: bioconductor-mirnapath path: recipes/bioconductor-mirnapath version: 1.40.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +requirements: + host: + - r-base + run: + - r-base +source: + md5: 52bfe4f43f6707c465da3e1fb4fe4ff4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mirnatap.db/meta.yaml b/recipes/bioconductor-mirnatap.db/meta.yaml index b8f95f3419969..bd97aafb5606c 100644 --- a/recipes/bioconductor-mirnatap.db/meta.yaml +++ b/recipes/bioconductor-mirnatap.db/meta.yaml @@ -1,51 +1,57 @@ {% set version = "0.99.10" %} {% set name = "miRNAtap.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package holds the database for miRNAtap. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Data for miRNAtap -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 48010280b68d6f1ddbff3b374132ce0a build: - number: 15 + noarch: generic + number: 16 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mirnatap.db", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-mirnatap.db + path: recipes/bioconductor-mirnatap.db + version: 0.99.10 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-mirnatap >=1.36.0,<1.37.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-mirnatap >=1.40.0,<1.41.0 - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-mirnatap >=1.36.0,<1.37.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-mirnatap >=1.40.0,<1.41.0 - r-base - r-dbi - r-rsqlite - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 48010280b68d6f1ddbff3b374132ce0a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: GPL-2 - summary: 'Data for miRNAtap' - description: 'This package holds the database for miRNAtap.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - parent_recipe: - name: bioconductor-mirnatap.db - path: recipes/bioconductor-mirnatap.db - version: 0.99.10 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mirnatap/meta.yaml b/recipes/bioconductor-mirnatap/meta.yaml index 6a542792493d7..4cf50b46e501f 100644 --- a/recipes/bioconductor-mirnatap/meta.yaml +++ b/recipes/bioconductor-mirnatap/meta.yaml @@ -1,28 +1,39 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "miRNAtap" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package facilitates implementation of workflows requiring miRNA predictions, it allows to integrate ranked miRNA target predictions from multiple sources available online and aggregate them with various methods which improves quality of predictions above any of the single sources. Currently predictions are available for Homo sapiens, Mus musculus and Rattus norvegicus (the last one through homology translation). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'miRNAtap: microRNA Targets - Aggregated Predictions' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f09289c10d9e5e916cc1b95e79bf504f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mirnatap", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:mirnatap + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-mirnatap + path: recipes/bioconductor-mirnatap + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: topGO, org.Hs.eg.db, miRNAtap.db, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - r-dbi - r-plyr @@ -30,28 +41,23 @@ requirements: - r-sqldf - r-stringr run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - r-dbi - r-plyr - r-rsqlite - r-sqldf - r-stringr + +source: + md5: 9b2e4fb40170fc5f9fab2dfd964a3ac0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'miRNAtap: microRNA Targets - Aggregated Predictions' - description: 'The package facilitates implementation of workflows requiring miRNA predictions, it allows to integrate ranked miRNA target predictions from multiple sources available online and aggregate them with various methods which improves quality of predictions above any of the single sources. Currently predictions are available for Homo sapiens, Mus musculus and Rattus norvegicus (the last one through homology translation).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:mirnatap - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-mirnatap - path: recipes/bioconductor-mirnatap - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mirnatarget/meta.yaml b/recipes/bioconductor-mirnatarget/meta.yaml index 130d1f40deaf8..51f016cf7ab30 100644 --- a/recipes/bioconductor-mirnatarget/meta.yaml +++ b/recipes/bioconductor-mirnatarget/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "miRNATarget" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f1988a96af5f0232abfbe507854d49bb +about: + description: gene target tabale of miRNA for human/mouse used for MiRaGE package + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: gene target tabale of miRNA for human/mouse used for MiRaGE package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mirnatarget", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c31b5caacb79947f7bc47db42c9931d0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL - summary: 'gene target tabale of miRNA for human/mouse used for MiRaGE package' - description: 'gene target tabale of miRNA for human/mouse used for MiRaGE package' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mirnatarget/post-link.sh b/recipes/bioconductor-mirnatarget/post-link.sh index cca9ffdc3448c..0a8d32f8e123c 100644 --- a/recipes/bioconductor-mirnatarget/post-link.sh +++ b/recipes/bioconductor-mirnatarget/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mirnatarget-1.40.0" +installBiocDataPackage.sh "mirnatarget-1.44.0" diff --git a/recipes/bioconductor-mirsm/meta.yaml b/recipes/bioconductor-mirsm/meta.yaml index 5f42f6f233970..ff9deaca29451 100644 --- a/recipes/bioconductor-mirsm/meta.yaml +++ b/recipes/bioconductor-mirsm/meta.yaml @@ -1,34 +1,45 @@ -{% set version = "1.18.0" %} +{% set version = "2.2.0" %} {% set name = "miRSM" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: The package aims to identify miRNA sponge or ceRNA modules in heterogeneous data. It provides several functions to study miRNA sponge modules at single-sample and multi-sample levels, including popular methods for inferring gene modules (candidate miRNA sponge or ceRNA modules), and two functions to identify miRNA sponge modules at single-sample and multi-sample levels, as well as several functions to conduct modular analysis of miRNA sponge modules. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Inferring miRNA sponge modules in heterogeneous data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2c9037736a60c1bbcd546542c1d70f41 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirsm", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-bicare >=1.58.0,<1.59.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-fabia >=2.46.0,<2.47.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-ibbig >=1.44.0,<1.45.0' - - 'bioconductor-mirsponger >=2.4.0,<2.5.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rqubic >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - bioconductor-bicare >=1.64.0,<1.65.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-fabia >=2.52.0,<2.53.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-ibbig >=1.50.0,<1.51.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-reactomepa >=1.50.0,<1.51.0 + - bioconductor-rqubic >=1.52.0,<1.53.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bibitr - r-biclust @@ -53,16 +64,19 @@ requirements: - r-wgcna - libblas - liblapack + run: - - 'bioconductor-bicare >=1.58.0,<1.59.0' - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-fabia >=2.46.0,<2.47.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-ibbig >=1.44.0,<1.45.0' - - 'bioconductor-mirsponger >=2.4.0,<2.5.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-rqubic >=1.46.0,<1.47.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - bioconductor-bicare >=1.64.0,<1.65.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-fabia >=2.52.0,<2.53.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-ibbig >=1.50.0,<1.51.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-reactomepa >=1.50.0,<1.51.0 + - bioconductor-rqubic >=1.52.0,<1.53.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bibitr - r-biclust @@ -85,17 +99,16 @@ requirements: - r-sombrero - r-subspace - r-wgcna - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: c6816f0e2fc48787e1c66416261129b6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Inferring miRNA sponge modules in heterogeneous data' - description: 'The package aims to identify miRNA sponge modules in heterogeneous data. It provides several functions to study miRNA sponge modules, including popular methods for inferring gene modules (candidate miRNA sponge modules), and a function to identify miRNA sponge modules, as well as several functions to conduct modular analysis of miRNA sponge modules.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mirsponger/meta.yaml b/recipes/bioconductor-mirsponger/meta.yaml index 9d12a53a9292c..6f0183119ff59 100644 --- a/recipes/bioconductor-mirsponger/meta.yaml +++ b/recipes/bioconductor-mirsponger/meta.yaml @@ -1,30 +1,37 @@ -{% set version = "2.4.0" %} +{% set version = "2.10.0" %} {% set name = "miRspongeR" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: This package provides several functions to explore miRNA sponge (also called ceRNA or miRNA decoy) regulation from putative miRNA-target interactions or/and transcriptomics data (including bulk, single-cell and spatial gene expression data). It provides eight popular methods for identifying miRNA sponge interactions, and an integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of miRNA sponge modules, and conduct survival analysis of miRNA sponge modules. By using a sample control variable strategy, it provides a function to infer sample-specific miRNA sponge interactions. In terms of sample-specific miRNA sponge interactions, it implements three similarity methods to construct sample-sample correlation network. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identification and analysis of miRNA sponge regulation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 52c6fe3ed5a289fd16c2e8c549402eb8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mirsponger", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactomepa >=1.44.0,<1.45.0' - - 'bioconductor-sponge >=1.22.0,<1.23.0' + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-reactomepa >=1.50.0,<1.51.0 + - bioconductor-sponge >=1.28.0,<1.29.0 - r-base - r-corpcor - r-doparallel @@ -37,11 +44,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-clusterprofiler >=4.8.0,<4.9.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-org.hs.eg.db >=3.17.0,<3.18.0' - - 'bioconductor-reactomepa >=1.44.0,<1.45.0' - - 'bioconductor-sponge >=1.22.0,<1.23.0' + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-reactomepa >=1.50.0,<1.51.0 + - bioconductor-sponge >=1.28.0,<1.29.0 - r-base - r-corpcor - r-doparallel @@ -51,17 +58,16 @@ requirements: - r-mcl - r-rcpp - r-survival - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: cf7c860e44629876bb7c4d6cacc6635f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Identification and analysis of miRNA sponge regulation' - description: 'This package provides several functions to explore miRNA sponge (also called ceRNA or miRNA decoy) regulation from putative miRNA-target interactions or/and transcriptomics data (including bulk, single-cell and spatial gene expression data). It provides eight popular methods for identifying miRNA sponge interactions, and an integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of miRNA sponge modules, and conduct survival analysis of miRNA sponge modules. By using a sample control variable strategy, it provides a function to infer sample-specific miRNA sponge interactions. In terms of sample-specific miRNA sponge interactions, it implements three similarity methods to construct sample-sample correlation network.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mirtarrnaseq/meta.yaml b/recipes/bioconductor-mirtarrnaseq/meta.yaml index 5a9e793f0b0a7..87602f6b5fc28 100644 --- a/recipes/bioconductor-mirtarrnaseq/meta.yaml +++ b/recipes/bioconductor-mirtarrnaseq/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "mirTarRnaSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis. This package utilizes expression or differential expression mRNA and miRNA sequencing results and performs interactive correlation and various GLMs (Regular GLM, Multivariate GLM, and Interaction GLMs ) analysis between mRNA and miRNA expriments. These experiments can be time point experiments, and or condition expriments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: mirTarRnaSeq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b8cac8c363bddb02eb97e6009bb91f4e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mirtarrnaseq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, R.cache, SPONGE requirements: host: @@ -51,13 +53,16 @@ requirements: - r-r.utils - r-reshape2 - r-viridis + +source: + md5: 95e5955842da376ae7ebb10ca1702857 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: mirTarRnaSeq - description: 'mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis. This package utilizes expression or differential expression mRNA and miRNA sequencing results and performs interactive correlation and various GLMs (Regular GLM, Multivariate GLM, and Interaction GLMs ) analysis between mRNA and miRNA expriments. These experiments can be time point experiments, and or condition expriments.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-missmethyl/meta.yaml b/recipes/bioconductor-missmethyl/meta.yaml index 73c8b2a6314ae..fb14e51b1946a 100644 --- a/recipes/bioconductor-missmethyl/meta.yaml +++ b/recipes/bioconductor-missmethyl/meta.yaml @@ -1,84 +1,96 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "missMethyl" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Normalisation, testing for differential variability and differential methylation and gene set testing for data from Illumina's Infinium HumanMethylation arrays. The normalisation procedure is subset-quantile within-array normalisation (SWAN), which allows Infinium I and II type probes on a single array to be normalised together. The test for differential variability is based on an empirical Bayes version of Levene's test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array, as well as taking into account multi-gene associated probes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Analysing Illumina HumanMethylation BeadChip Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4773cfc60c545bb0a04dac0b6cc0ac4e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-missmethyl", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:missmethyl + parent_recipe: + name: bioconductor-missmethyl + path: recipes/bioconductor-missmethyl + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData, DMRcate, ExperimentHub requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-methylumi >=2.48.0,<2.49.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0 + - bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0 + - bioconductor-illuminahumanmethylationepicv2anno.20a1.hg38 >=1.0.0,<1.1.0 + - bioconductor-illuminahumanmethylationepicv2manifest >=1.0.0,<1.1.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-methylumi >=2.52.0,<2.53.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-biasedurn - r-ruv - r-statmod - r-stringr + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-methylumi >=2.48.0,<2.49.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0 + - bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0 + - bioconductor-illuminahumanmethylationepicv2anno.20a1.hg38 >=1.0.0,<1.1.0 + - bioconductor-illuminahumanmethylationepicv2manifest >=1.0.0,<1.1.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-methylumi >=2.52.0,<2.53.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-biasedurn - r-ruv - r-statmod - r-stringr + +source: + md5: 272949b145733e053fc29fe54ad7672d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Analysing Illumina HumanMethylation BeadChip Data' - description: 'Normalisation, testing for differential variability and differential methylation and gene set testing for data from Illumina''s Infinium HumanMethylation arrays. The normalisation procedure is subset-quantile within-array normalisation (SWAN), which allows Infinium I and II type probes on a single array to be normalised together. The test for differential variability is based on an empirical Bayes version of Levene''s test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array, as well as taking into account multi-gene associated probes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:missmethyl - parent_recipe: - name: bioconductor-missmethyl - path: recipes/bioconductor-missmethyl - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-missrows/meta.yaml b/recipes/bioconductor-missrows/meta.yaml index 95759b50cdab7..81e68a0d9f6d1 100644 --- a/recipes/bioconductor-missrows/meta.yaml +++ b/recipes/bioconductor-missrows/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "missRows" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The missRows package implements the MI-MFA method to deal with missing individuals ('biological units') in multi-omics data integration. The MI-MFA method generates multiple imputed datasets from a Multiple Factor Analysis model, then the yield results are combined in a single consensus solution. The package provides functions for estimating coordinates of individuals and variables, imputing missing individuals, and various diagnostic plots to inspect the pattern of missingness and visualize the uncertainty due to missing values. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Handling Missing Individuals in Multi-Omics Data Integration -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d076124257e06505c39064a9dcddd695 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-missrows", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-gtools - r-plyr run: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-gtools - r-plyr + +source: + md5: adaa57514a428d540e2415112524e666 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Handling Missing Individuals in Multi-Omics Data Integration' - description: 'The missRows package implements the MI-MFA method to deal with missing individuals (''biological units'') in multi-omics data integration. The MI-MFA method generates multiple imputed datasets from a Multiple Factor Analysis model, then the yield results are combined in a single consensus solution. The package provides functions for estimating coordinates of individuals and variables, imputing missing individuals, and various diagnostic plots to inspect the pattern of missingness and visualize the uncertainty due to missing values.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mistyr/meta.yaml b/recipes/bioconductor-mistyr/meta.yaml index ab71622892ea4..8bdeed268cd6f 100644 --- a/recipes/bioconductor-mistyr/meta.yaml +++ b/recipes/bioconductor-mistyr/meta.yaml @@ -1,26 +1,29 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "mistyR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: mistyR is an implementation of the Multiview Intercellular SpaTialmodeling framework (MISTy). MISTy is an explainable machine learning framework for knowledge extraction and analysis of single-cell, highly multiplexed, spatially resolved data. MISTy facilitates an in-depth understanding of marker interactions by profiling the intra- and intercellular relationships. MISTy is a flexible framework able to process a custom number of views. Each of these views can describe a different spatial context, i.e., define a relationship among the observed expressions of the markers, such as intracellular regulation or paracrine regulation, but also, the views can also capture cell-type specific relationships, capture relations between functional footprints or focus on relations between different anatomical regions. Each MISTy view is considered as a potential source of variability in the measured marker expressions. Each MISTy view is then analyzed for its contribution to the total expression of each marker and is explained in terms of the interactions with other measurements that led to the observed contribution. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Multiview Intercellular SpaTial modeling framework -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f21483e1d8c9575d0c27a9fa544cfb3c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mistyr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, covr, earth, future, igraph (>= 1.2.7), iml, kernlab, knitr, MASS, rmarkdown, RSNNS, testthat (>= 3.0.0), xgboost requirements: + host: - r-assertthat - r-base @@ -28,22 +31,23 @@ requirements: - r-deldir - r-digest - r-distances - - 'r-dplyr >=1.1.0' + - r-dplyr >=1.1.0 - r-filelock - - 'r-furrr >=0.2.0' + - r-furrr >=0.2.0 - r-ggplot2 - r-purrr - r-r.utils - r-ranger - - 'r-readr >=2.0.0' + - r-readr >=2.0.0 - r-ridge - r-rlang - r-rlist - r-stringr - r-tibble - r-tidyr - - 'r-tidyselect >=1.2.0' + - r-tidyselect >=1.2.0 - r-withr + run: - r-assertthat - r-base @@ -51,29 +55,32 @@ requirements: - r-deldir - r-digest - r-distances - - 'r-dplyr >=1.1.0' + - r-dplyr >=1.1.0 - r-filelock - - 'r-furrr >=0.2.0' + - r-furrr >=0.2.0 - r-ggplot2 - r-purrr - r-r.utils - r-ranger - - 'r-readr >=2.0.0' + - r-readr >=2.0.0 - r-ridge - r-rlang - r-rlist - r-stringr - r-tibble - r-tidyr - - 'r-tidyselect >=1.2.0' + - r-tidyselect >=1.2.0 - r-withr + +source: + md5: 94b404f8a6094afe2761ba69b3c59648 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Multiview Intercellular SpaTial modeling framework' - description: 'mistyR is an implementation of the Multiview Intercellular SpaTialmodeling framework (MISTy). MISTy is an explainable machine learning framework for knowledge extraction and analysis of single-cell, highly multiplexed, spatially resolved data. MISTy facilitates an in-depth understanding of marker interactions by profiling the intra- and intercellular relationships. MISTy is a flexible framework able to process a custom number of views. Each of these views can describe a different spatial context, i.e., define a relationship among the observed expressions of the markers, such as intracellular regulation or paracrine regulation, but also, the views can also capture cell-type specific relationships, capture relations between functional footprints or focus on relations between different anatomical regions. Each MISTy view is considered as a potential source of variability in the measured marker expressions. Each MISTy view is then analyzed for its contribution to the total expression of each marker and is explained in terms of the interactions with other measurements that led to the observed contribution.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mitoclone2/build_failure.osx-64.yaml b/recipes/bioconductor-mitoclone2/build_failure.osx-64.yaml index 6dc0ac91eab34..23d7925a28d1e 100644 --- a/recipes/bioconductor-mitoclone2/build_failure.osx-64.yaml +++ b/recipes/bioconductor-mitoclone2/build_failure.osx-64.yaml @@ -1,106 +1,104 @@ -recipe_sha: 60f475e5bda7669f78635653dbdbbc6ac8818393a7bc525552f7d723c69c6571 # The commit at which this recipe failed to build. +recipe_sha: 787ac308427f8dedf02196e6cb5bca8fb238b6fc715a584df1027ad9c933e49d # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: |- - source download error log: |2- - tapi: 1100.0.11-h9ce4665_0 conda-forge - tk: 8.6.13-h1abcd95_1 conda-forge - tktable: 2.10-ha166976_5 conda-forge - toml: 0.10.2-pyhd8ed1ab_0 conda-forge - tomlkit: 0.12.3-pyha770c72_0 conda-forge - tzdata: 2023c-h71feb2d_0 conda-forge - xmltodict: 0.13.0-pyhd8ed1ab_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - yaml: 0.2.5-h0d85af4_2 conda-forge - yq: 3.2.3-pyhd8ed1ab_0 conda-forge - zlib: 1.2.13-h8a1eda9_5 conda-forge - zstd: 1.5.5-h829000d_0 conda-forge + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-mitoclone2_1735824931402/work/conda_build.sh']' returned non-zero exit status 1. - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld - Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-mitoclone2-1.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + The above exception was the direct cause of the following exception: - ## Package Plan ## - - environment location: /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-mitoclone2_1703020590195/_build_env - - - The following NEW packages will be INSTALLED: - - ca-certificates: 2023.11.17-h8857fd0_0 conda-forge - cctools_osx-64: 973.0.1-habff3f6_15 conda-forge - clang: 15.0.7-hac416ee_4 conda-forge - clang-15: 15.0.7-default_h6b1ee41_4 conda-forge - clang_impl_osx-64: 15.0.7-h03d6864_7 conda-forge - clang_osx-64: 15.0.7-hb91bd55_7 conda-forge - clangxx: 15.0.7-default_h6b1ee41_4 conda-forge - clangxx_impl_osx-64: 15.0.7-h2133e9c_7 conda-forge - clangxx_osx-64: 15.0.7-hb91bd55_7 conda-forge - compiler-rt: 15.0.7-ha38d28d_2 conda-forge - compiler-rt_osx-64: 15.0.7-ha38d28d_2 conda-forge - icu: 73.2-hf5e326d_0 conda-forge - ld64_osx-64: 609-h0fd476b_15 conda-forge - libclang-cpp15: 15.0.7-default_h6b1ee41_4 conda-forge - libcxx: 16.0.6-hd57cbcb_0 conda-forge - libiconv: 1.17-hd75f5a5_2 conda-forge - libllvm15: 15.0.7-hbedff68_4 conda-forge - libxml2: 2.12.3-hc0ae0f7_0 conda-forge - libzlib: 1.2.13-h8a1eda9_5 conda-forge - llvm-tools: 15.0.7-hbedff68_4 conda-forge - make: 4.3-h22f3db7_1 conda-forge - openssl: 3.2.0-hd75f5a5_1 conda-forge - sigtool: 0.1.3-h88f4db0_0 conda-forge - tapi: 1100.0.11-h9ce4665_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - zstd: 1.5.5-h829000d_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - INFO:conda_build.source:Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - Downloading source to cache: mitoClone2_1.8.1_22c58ba6ed.tar.gz - INFO:conda_build.source:Downloading source to cache: mitoClone2_1.8.1_22c58ba6ed.tar.gz - Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/mitoClone2_1.8.1.tar.gz - INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.18/bioc/src/contrib/mitoClone2_1.8.1.tar.gz - Success - INFO:conda_build.source:Success - Extracting download - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/bioconductor-mitoclone2/gamma.patch - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/bioconductor-mitoclone2/gamma.patch with args: - ['-Np1', '-i', '/var/folders/qv/pdh5wsgn0lq3dp77zj602b5c0000gn/T/tmpz0brhpff/gamma.patch.native', '--binary'] - checking file inst/SCITEpkg/findBestTrees.cpp - Hunk #1 succeeded at 55 (offset 2 lines). - Hunk #2 FAILED at 97. - Hunk #3 succeeded at 264 (offset 2 lines). - 1 out of 3 hunks FAILED - checking file inst/SCITEpkg/mcmc.cpp - Hunk #1 FAILED at 41. - Hunk #2 succeeded at 98 (offset 2 lines). - Hunk #3 succeeded at 121 (offset 2 lines). - 1 out of 3 hunks FAILED - checking file inst/SCITEpkg/mcmc.h - Hunk #1 FAILED at 8. - 1 out of 1 hunk FAILED - Warning: failed to download source. If building, will try again after downloading recipe dependencies. - Error was: - Command '['/opt/mambaforge/envs/bioconda/bin/patch', '--no-backup-if-mismatch', '--batch', '-Np1', '-i', '/var/folders/qv/pdh5wsgn0lq3dp77zj602b5c0000gn/T/tmpz0brhpff/gamma.patch.native', '--binary', '--dry-run']' returned non-zero exit status 1. Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-mitoclone2-1.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2125, in build - try_download(m, no_download_source=False, raise_error=True) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 663, in try_download - raise RuntimeError("Failed to download or patch source. Please see build log for info.") - RuntimeError: Failed to download or patch source. Please see build log for info. + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-mitoclone2-1.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-mitoclone2-1.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-mitoclone2_1735824931402/work/conda_build.sh']' returned non-zero exit status 1. + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-mitoclone2-1.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-mitoclone2-1.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-mitoclone2-1.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-mitoclone2-1.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-mitoclone2-1.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-mitoclone2-1.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-mitoclone2-1.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-mitoclone2-1.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-mitoclone2-1.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-mitoclone2-1.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -std=gnu17 -D_FILE_OFFSET_BITS=64 ../inst/SCITEpkg/*.cpp -o scite # Last 100 lines of the build log. diff --git a/recipes/bioconductor-mitoclone2/meta.yaml b/recipes/bioconductor-mitoclone2/meta.yaml index 5d35d4e370509..4d0cb97d9a3b3 100644 --- a/recipes/bioconductor-mitoclone2/meta.yaml +++ b/recipes/bioconductor-mitoclone2/meta.yaml @@ -1,59 +1,64 @@ -{% set version = "1.8.1" %} +{% set version = "1.12.0" %} {% set name = "mitoClone2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package primarily identifies variants in mitochondrial genomes from BAM alignment files. It filters these variants to remove RNA editing events then estimates their evolutionary relationship (i.e. their phylogenetic tree) and groups single cells into clones. It also visualizes the mutations and providing additional genomic context. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 22c58ba6ed0a51f10714551935477355 - patches: - - gamma.patch build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mitoclone2", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, Biostrings, testthat # SystemRequirements: GNU make, PhISCS (optional) requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-deepsnv >=1.48.0,<1.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-deepsnv >=1.52.0,<1.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-pheatmap - r-reshape2 - libblas - liblapack + - zlib + - liblzma-devel run: - - 'bioconductor-deepsnv >=1.48.0,<1.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-deepsnv >=1.52.0,<1.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-pheatmap - r-reshape2 - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 1200b6872a85870476f9b188177175a4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations' - description: 'This package primarily identifies variants in mitochondrial genomes from BAM alignment files. It filters these variants to remove RNA editing events then estimates their evolutionary relationship (i.e. their phylogenetic tree) and groups single cells into clones. It also visualizes the mutations and providing additional genomic context.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mixomics/build.sh b/recipes/bioconductor-mixomics/build.sh index c1d13421f5f1e..497f7b5bdb678 100644 --- a/recipes/bioconductor-mixomics/build.sh +++ b/recipes/bioconductor-mixomics/build.sh @@ -8,4 +8,5 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars +export LD_LIBRARY_PATH=${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mixomics/meta.yaml b/recipes/bioconductor-mixomics/meta.yaml index d86404b99b5ef..ad799dd35f9ad 100644 --- a/recipes/bioconductor-mixomics/meta.yaml +++ b/recipes/bioconductor-mixomics/meta.yaml @@ -1,28 +1,41 @@ -{% set version = "6.26.0" %} +{% set version = "6.30.0" %} {% set name = "mixOmics" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include variants of generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Omics Data Integration Project -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d735d1aec6a3576238256244e87031ff build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mixomics", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, testthat, rgl + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, testthat, microbenchmark, magick requirements: + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-corpcor - r-dplyr @@ -30,6 +43,7 @@ requirements: - r-ggplot2 - r-ggrepel - r-gridextra + - r-gsignal - r-igraph - r-lattice - r-mass @@ -37,9 +51,10 @@ requirements: - r-rarpack - r-rcolorbrewer - r-reshape2 + - r-rgl - r-tidyr run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-corpcor - r-dplyr @@ -47,6 +62,7 @@ requirements: - r-ggplot2 - r-ggrepel - r-gridextra + - r-gsignal - r-igraph - r-lattice - r-mass @@ -54,14 +70,18 @@ requirements: - r-rarpack - r-rcolorbrewer - r-reshape2 + - r-rgl - r-tidyr + +source: + md5: bc07fef3c1ce86dbad92753050c4742e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Omics Data Integration Project' - description: 'Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include variants of generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mlinterfaces/meta.yaml b/recipes/bioconductor-mlinterfaces/meta.yaml index fe32e07d825f8..4a3d7770c4abb 100644 --- a/recipes/bioconductor-mlinterfaces/meta.yaml +++ b/recipes/bioconductor-mlinterfaces/meta.yaml @@ -1,31 +1,47 @@ -{% set version = "1.82.0" %} +{% set version = "1.86.0" %} {% set name = "MLInterfaces" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Uniform interfaces to R machine learning procedures for data in Bioconductor containers -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: acb5f91abaa05ef8c6b156b2cc7df846 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mlinterfaces", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:mlinterfaces + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-mlinterfaces + path: recipes/bioconductor-mlinterfaces + version: 1.60.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party, klaR, BiocStyle, knitr, testthat requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-fpc @@ -42,15 +58,16 @@ requirements: - r-rpart - r-sfsmisc - r-shiny - - 'r-threejs >=0.2.2' + - r-threejs >=0.2.2 - libblas - liblapack + run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-fpc @@ -67,25 +84,17 @@ requirements: - r-rpart - r-sfsmisc - r-shiny - - 'r-threejs >=0.2.2' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} + - r-threejs >=0.2.2 + +source: + md5: f90df9372acaba53b404582b1fd12368 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Uniform interfaces to R machine learning procedures for data in Bioconductor containers' - description: 'This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:mlinterfaces - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-mlinterfaces - path: recipes/bioconductor-mlinterfaces - version: 1.60.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mlp/meta.yaml b/recipes/bioconductor-mlp/meta.yaml index 2a506c09f0e69..0ea334cbde741 100644 --- a/recipes/bioconductor-mlp/meta.yaml +++ b/recipes/bioconductor-mlp/meta.yaml @@ -1,49 +1,55 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "MLP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Pathway analysis based on p-values associated to genes from a genes expression analysis of interest. Utility functions enable to extract pathways from the Gene Ontology Biological Process (GOBP), Molecular Function (GOMF) and Cellular Component (GOCC), Kyoto Encyclopedia of Genes of Genomes (KEGG) and Reactome databases. Methodology, and helper functions to display the results as a table, barplot of pathway significance, Gene Ontology graph and pathway significance are available. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Mean Log P Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ed5a850807679b4baa1c5d4d88f48d6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mlp", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:mlp + - doi:10.1007/978-3-642-24007-2_12 + parent_recipe: + name: bioconductor-mlp + path: recipes/bioconductor-mlp + version: 1.28.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, org.Mmu.eg.db, KEGGREST, annotate, Rgraphviz, GOstats, graph, limma, mouse4302.db, reactome.db requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - r-gplots run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - r-gplots + +source: + md5: 6f60b1fac9054df7ae085f24f5556ce0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Mean Log P Analysis' - description: 'Pathway analysis based on p-values associated to genes from a genes expression analysis of interest. Utility functions enable to extract pathways from the Gene Ontology Biological Process (GOBP), Molecular Function (GOMF) and Cellular Component (GOCC), Kyoto Encyclopedia of Genes of Genomes (KEGG) and Reactome databases. Methodology, and helper functions to display the results as a table, barplot of pathway significance, Gene Ontology graph and pathway significance are available.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:mlp - - doi:10.1007/978-3-642-24007-2_12 - parent_recipe: - name: bioconductor-mlp - path: recipes/bioconductor-mlp - version: 1.28.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mlseq/meta.yaml b/recipes/bioconductor-mlseq/meta.yaml index f6a2d8f85b768..67d1693d27376 100644 --- a/recipes/bioconductor-mlseq/meta.yaml +++ b/recipes/bioconductor-mlseq/meta.yaml @@ -1,33 +1,44 @@ -{% set version = "2.20.0" %} +{% set version = "2.24.0" %} {% set name = "MLSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package applies several machine learning methods, including SVM, bagSVM, Random Forest and CART to RNA-Seq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL(>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Machine Learning Interface for RNA-Seq Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 07ebcff7e7a474bc21b783a6ebc2605b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mlseq", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:mlseq + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-mlseq + path: recipes/bioconductor-mlseq + version: 1.20.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, e1071, kernlab requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-sseq >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-sseq >=1.44.0,<1.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-caret - r-foreach @@ -38,12 +49,12 @@ requirements: - r-venndiagram - r-xtable run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-sseq >=1.40.0,<1.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-sseq >=1.44.0,<1.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-caret - r-foreach @@ -53,21 +64,16 @@ requirements: - r-testthat - r-venndiagram - r-xtable + +source: + md5: 402677688472631e3a8e9d4c70b98154 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL(>=2) - summary: 'Machine Learning Interface for RNA-Seq Data' - description: 'This package applies several machine learning methods, including SVM, bagSVM, Random Forest and CART to RNA-Seq data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:mlseq - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-mlseq - path: recipes/bioconductor-mlseq - version: 1.20.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mm24kresogen.db/meta.yaml b/recipes/bioconductor-mm24kresogen.db/meta.yaml index 13b54d2ee5b24..15e3ff4c20330 100644 --- a/recipes/bioconductor-mm24kresogen.db/meta.yaml +++ b/recipes/bioconductor-mm24kresogen.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "2.5.0" %} {% set name = "mm24kresogen.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 437f5d4bc225ee500af1ecc2d4da472b +about: + description: RNG_MRC Mouse Pangenomic 24k Set annotation data (chip mm24kresogen) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: RNG_MRC Mouse Pangenomic 24k Set annotation data (chip mm24kresogen) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mm24kresogen.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 437f5d4bc225ee500af1ecc2d4da472b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'RNG_MRC Mouse Pangenomic 24k Set annotation data (chip mm24kresogen)' - description: 'RNG_MRC Mouse Pangenomic 24k Set annotation data (chip mm24kresogen) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mmagilentdesign026655.db/meta.yaml b/recipes/bioconductor-mmagilentdesign026655.db/meta.yaml index 316ebba0491be..d29020782efe3 100644 --- a/recipes/bioconductor-mmagilentdesign026655.db/meta.yaml +++ b/recipes/bioconductor-mmagilentdesign026655.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "MmAgilentDesign026655.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ef619bd2c74f22ea4f3c2b2c4131fe9 +about: + description: Agilent Chips that use Agilent design number 026655 annotation data (chip MmAgilentDesign026655) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Agilent Chips that use Agilent design number 026655 annotation data (chip MmAgilentDesign026655) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mmagilentdesign026655.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7ef619bd2c74f22ea4f3c2b2c4131fe9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Agilent Chips that use Agilent design number 026655 annotation data (chip MmAgilentDesign026655)' - description: 'Agilent Chips that use Agilent design number 026655 annotation data (chip MmAgilentDesign026655) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mmdiff2/meta.yaml b/recipes/bioconductor-mmdiff2/meta.yaml index ad1ed95691e31..24c897fdefb5d 100644 --- a/recipes/bioconductor-mmdiff2/meta.yaml +++ b/recipes/bioconductor-mmdiff2/meta.yaml @@ -1,64 +1,70 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "MMDiff2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package detects statistically significant differences between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Statistical Testing for ChIP-Seq data sets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d14e03f2d5842c403a50c41f30c82d1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mmdiff2", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:mmdiff2 + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-mmdiff2 + path: recipes/bioconductor-mmdiff2 + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-locfit - r-rcolorbrewer - r-shiny run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-locfit - r-rcolorbrewer - r-shiny + +source: + md5: 8ed419214cc72589bcb6a2ef82979593 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Statistical Testing for ChIP-Seq data sets' - description: 'This package detects statistically significant differences between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD).' -extra: - identifiers: - - biotools:mmdiff2 - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-mmdiff2 - path: recipes/bioconductor-mmdiff2 - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mmdiffbamsubset/meta.yaml b/recipes/bioconductor-mmdiffbamsubset/meta.yaml index c8687b937206b..2da9941622427 100644 --- a/recipes/bioconductor-mmdiffbamsubset/meta.yaml +++ b/recipes/bioconductor-mmdiffbamsubset/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "MMDiffBamSubset" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0becc66301b49b58a99efa19577ee27c +about: + description: Subset of BAM files, including WT_2.bam, Null_2.bam, Resc_2.bam, Input.bam from the "Cfp1" experiment (see Clouaire et al., Genes Dev. 2012). Data is available under ArrayExpress accession numbers E-ERAD-79. Additionally, corresponding subset of peaks called by MACS + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Example ChIP-Seq data for the MMDiff package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mmdiffbamsubset", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: MMDiff2 requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d8195c879ffc8680c7eb2b3ca6dd690d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Example ChIP-Seq data for the MMDiff package' - description: 'Subset of BAM files, including WT_2.bam, Null_2.bam, Resc_2.bam, Input.bam from the "Cfp1" experiment (see Clouaire et al., Genes Dev. 2012). Data is available under ArrayExpress accession numbers E-ERAD-79. Additionally, corresponding subset of peaks called by MACS' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mmdiffbamsubset/post-link.sh b/recipes/bioconductor-mmdiffbamsubset/post-link.sh index 41d02cf30eea3..f278b9ebbaaa8 100644 --- a/recipes/bioconductor-mmdiffbamsubset/post-link.sh +++ b/recipes/bioconductor-mmdiffbamsubset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mmdiffbamsubset-1.38.0" +installBiocDataPackage.sh "mmdiffbamsubset-1.42.0" diff --git a/recipes/bioconductor-mnem/meta.yaml b/recipes/bioconductor-mnem/meta.yaml index ecf09bdc62142..c5ebd1a29dda7 100644 --- a/recipes/bioconductor-mnem/meta.yaml +++ b/recipes/bioconductor-mnem/meta.yaml @@ -1,29 +1,43 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "mnem" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Mixture Nested Effects Models (mnem) is an extension of Nested Effects Models and allows for the analysis of single cell perturbation data provided by methods like Perturb-Seq (Dixit et al., 2016) or Crop-Seq (Datlinger et al., 2017). In those experiments each of many cells is perturbed by a knock-down of a specific gene, i.e. several cells are perturbed by a knock-down of gene A, several by a knock-down of gene B, ... and so forth. The observed read-out has to be multi-trait and in the case of the Perturb-/Crop-Seq gene are expression profiles for each cell. mnem uses a mixture model to simultaneously cluster the cell population into k clusters and and infer k networks causally linking the perturbed genes for each cluster. The mixture components are inferred via an expectation maximization algorithm. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Mixture Nested Effects Models -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 630cb52a48148dc82038613aacb4e834 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mnem", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:mnem + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM, BiocStyle requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-linnorm >=2.26.0,<2.27.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-linnorm >=2.30.0,<2.31.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-cluster - r-data.table @@ -40,10 +54,11 @@ requirements: - r-wesanderson - libblas - liblapack + run: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-linnorm >=2.26.0,<2.27.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-linnorm >=2.30.0,<2.31.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-cluster - r-data.table @@ -58,22 +73,16 @@ requirements: - r-snowfall - r-tsne - r-wesanderson - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 2d7b90c117bdab6211ab3f7901b1165b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'Mixture Nested Effects Models' - description: 'Mixture Nested Effects Models (mnem) is an extension of Nested Effects Models and allows for the analysis of single cell perturbation data provided by methods like Perturb-Seq (Dixit et al., 2016) or Crop-Seq (Datlinger et al., 2017). In those experiments each of many cells is perturbed by a knock-down of a specific gene, i.e. several cells are perturbed by a knock-down of gene A, several by a knock-down of gene B, ... and so forth. The observed read-out has to be multi-trait and in the case of the Perturb-/Crop-Seq gene are expression profiles for each cell. mnem uses a mixture model to simultaneously cluster the cell population into k clusters and and infer k networks causally linking the perturbed genes for each cluster. The mixture components are inferred via an expectation maximization algorithm.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-moanin/meta.yaml b/recipes/bioconductor-moanin/meta.yaml index 896119d5f8400..050e2be8b0e10 100644 --- a/recipes/bioconductor-moanin/meta.yaml +++ b/recipes/bioconductor-moanin/meta.yaml @@ -1,61 +1,66 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "moanin" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Simple and efficient workflow for time-course gene expression data, built on publictly available open-source projects hosted on CRAN and bioconductor. moanin provides helper functions for all the steps required for analysing time-course data using functional data analysis: (1) functional modeling of the timecourse data; (2) differential expression analysis; (3) clustering; (4) downstream analysis.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD 3-clause License + file LICENSE + license_file: LICENSE + summary: An R Package for Time Course RNASeq Data Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 74f0ff5d927d538a2b41cdc9c1ee9fd9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-moanin", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 1.0.0), timecoursedata, knitr, rmarkdown, markdown, covr, BiocStyle requirements: host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-base - r-clusterr - - 'r-mass >=1.0.0' + - r-mass >=1.0.0 - r-matrixstats - r-nmi - r-reshape2 - r-viridis - r-zoo run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-base - r-clusterr - - 'r-mass >=1.0.0' + - r-mass >=1.0.0 - r-matrixstats - r-nmi - r-reshape2 - r-viridis - r-zoo + +source: + md5: 9305678333042c7e9d0c98121bd4e3f8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD 3-clause License + file LICENSE' - summary: 'An R Package for Time Course RNASeq Data Analysis' - description: 'Simple and efficient workflow for time-course gene expression data, built on publictly available open-source projects hosted on CRAN and bioconductor. moanin provides helper functions for all the steps required for analysing time-course data using functional data analysis: (1) functional modeling of the timecourse data; (2) differential expression analysis; (3) clustering; (4) downstream analysis.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mobilerna/build.sh b/recipes/bioconductor-mobilerna/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mobilerna/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mobilerna/build_failure.linux-64.yaml b/recipes/bioconductor-mobilerna/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..9ad35da7239b5 --- /dev/null +++ b/recipes/bioconductor-mobilerna/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: ad9871e830efada844db453a3d0d5d5808e618743382e7b3778be0c61a3df139 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-simdesign")} + Encountered problems while solving: + - nothing provides requested r-simdesign + + Could not solve for environment specs + The following package could not be installed + [31mr-simdesign[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-simdesign")} + Encountered problems while solving: + - nothing provides requested r-simdesign + + Could not solve for environment specs + The following package could not be installed + [31mr-simdesign[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-simdesign")} + Encountered problems while solving: + - nothing provides requested r-simdesign + + Could not solve for environment specs + The following package could not be installed + [31mr-simdesign[0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-mobilerna/meta.yaml b/recipes/bioconductor-mobilerna/meta.yaml new file mode 100644 index 0000000000000..2aefb443b9d0b --- /dev/null +++ b/recipes/bioconductor-mobilerna/meta.yaml @@ -0,0 +1,93 @@ +{% set version = "1.2.0" %} +{% set name = "mobileRNA" %} +{% set bioc = "3.20" %} + +about: + description: Genomic analysis can be utilised to identify differences between RNA populations in two conditions, both in production and abundance. This includes the identification of RNAs produced by multiple genomes within a biological system. For example, RNA produced by pathogens within a host or mobile RNAs in plant graft systems. The mobileRNA package provides methods to pre-process, analyse and visualise the sRNA and mRNA populations based on the premise of mapping reads to all genotypes at the same time. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 'mobileRNA: Investigate the RNA mobilome & population-scale changes' + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mobilerna", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, BiocStyle +# SystemRequirements: GNU make, ShortStack (>= 4.0), HTSeq, HISAT2, SAMtools, Conda +requirements: + + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-bioseq + - r-data.table + - r-dplyr + - r-ggplot2 + - r-ggrepel + - r-pheatmap + - r-progress + - r-rcolorbrewer + - r-reticulate + - r-rlang + - r-scales + - r-simdesign + - r-tidyr + - r-tidyselect + + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-bioseq + - r-data.table + - r-dplyr + - r-ggplot2 + - r-ggrepel + - r-pheatmap + - r-progress + - r-rcolorbrewer + - r-reticulate + - r-rlang + - r-scales + - r-simdesign + - r-tidyr + - r-tidyselect + +source: + md5: e3aecfdd0bceaef68b290500e62024dd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-moda/build_failure.linux-64.yaml b/recipes/bioconductor-moda/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..643f3b0b856cc --- /dev/null +++ b/recipes/bioconductor-moda/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 87245b135c6c2ab447b78ac1d2eda1a970f4d7b8a94488d5338e24fbff9e5df3 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [31mr-wgcna 1.71[0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna [1.71|1.73][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("3.3.1*"), MatchSpec("r-wgcna==1.51=r3.3.1_0")} + Encountered problems while solving: + - nothing provides r-base 3.3.1* needed by r-wgcna-1.51-r3.3.1_0 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-amountain >=1.32.0,<1.33.0 [0m is installable and it requires + [32mgsl >=2.7,<2.8.0a0 [0m, which can be installed; + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-wgcna[0m is not installable because there are no viable options + [31mr-wgcna 1.51[0m would require + [31mr-base 3.3.1* [0m, which does not exist (perhaps a missing channel); + [31mr-wgcna 1.51[0m would require + [31mr-base 3.3.2* [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna [1.51|1.61|1.64_1][0m would require + [31mr-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ][0m but there are no viable options + [31mr-base 3.4.1[0m conflicts with any installable versions previously reported; + [31mr-base [3.4.1|3.5.1][0m would require + [31mgsl >=2.2.1,<2.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna [1.64_1|1.66|1.67|1.68][0m would require + [31mr-base >=3.5.1,<3.5.2.0a0 [0m but there are no viable options + [31mr-base [3.4.1|3.5.1][0m, which cannot be installed (as previously explained); + [31mr-base [3.5.1|3.6.1|3.6.2][0m would require + [31mgsl >=2.5,<2.6.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-base 3.5.1[0m would require + [31mgsl >=2.4,<2.5.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-base 3.5.1[0m conflicts with any installable versions previously reported; + [31mr-wgcna [1.68|1.69][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m but there are no viable options + [31mr-base [3.5.1|3.6.1|3.6.2][0m, which cannot be installed (as previously explained); + [31mr-base [3.6.2|3.6.3|...|4.1.1][0m would require + [31mgsl >=2.6,<2.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna 1.69[0m would require + [31mr-base >=4.0,<4.1.0a0 [0m but there are no viable options + [31mr-base [3.6.2|3.6.3|...|4.1.1][0m, which cannot be installed (as previously explained); + [31mr-base 4.0.5[0m conflicts with any installable versions previously reported; + [31mr-wgcna [1.69|1.71][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m but there are no viable options + [31mr-base [3.6.2|3.6.3|...|4.1.1][0m, which cannot be installed (as previously explained); + [31mr-base [4.1.1|4.1.2|4.1.3][0m conflicts with any installable versions previously reported; + [31mr-wgcna 1.71[0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna [1.71|1.73][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-moda/meta.yaml b/recipes/bioconductor-moda/meta.yaml index f0c112fc22b46..e5c785ea03cf6 100644 --- a/recipes/bioconductor-moda/meta.yaml +++ b/recipes/bioconductor-moda/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "MODA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MODA can be used to estimate and construct condition-specific gene co-expression networks, and identify differentially expressed subnetworks as conserved or condition specific modules which are potentially associated with relevant biological processes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'MODA: MOdule Differential Analysis for weighted gene co-expression network' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f48d76fbd7f8905725dbd2db1bc6fee build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-moda", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-amountain >=1.28.0,<1.29.0' + - bioconductor-amountain >=1.32.0,<1.33.0 - r-base - r-cluster - r-dynamictreecut @@ -30,20 +32,23 @@ requirements: - r-rcolorbrewer - r-wgcna run: - - 'bioconductor-amountain >=1.28.0,<1.29.0' + - bioconductor-amountain >=1.32.0,<1.33.0 - r-base - r-cluster - r-dynamictreecut - r-igraph - r-rcolorbrewer - r-wgcna + +source: + md5: 51db43cd631c9cc2a3811982ab9001df + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'MODA: MOdule Differential Analysis for weighted gene co-expression network' - description: 'MODA can be used to estimate and construct condition-specific gene co-expression networks, and identify differentially expressed subnetworks as conserved or condition specific modules which are potentially associated with relevant biological processes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-modcon/meta.yaml b/recipes/bioconductor-modcon/meta.yaml index b45ecc4ebeb3c..c80c2d50594cb 100644 --- a/recipes/bioconductor-modcon/meta.yaml +++ b/recipes/bioconductor-modcon/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "ModCon" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bdb0634e890917a01325519cf6e53f90 +about: + description: Collection of functions to calculate a nucleotide sequence surrounding for splice donors sites to either activate or repress donor usage. The proposed alternative nucleotide sequence encodes the same amino acid and could be applied e.g. in reporter systems to silence or activate cryptic splice donor sites. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Modifying splice site usage by changing the mRNP code, while maintaining the genetic code build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-modcon", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat, knitr, rmarkdown, dplyr, shinycssloaders, shiny, shinyFiles, shinydashboard, shinyjs # SystemRequirements: Perl requirements: host: - r-base - r-data.table - - 'perl >=5.6.0' + - perl >=5.6.0 run: - r-base - r-data.table - - 'perl >=5.6.0' + - perl >=5.6.0 +source: + md5: 14c390fdeaf314a5bccb90fa0b8a13a1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Modifying splice site usage by changing the mRNP code, while maintaining the genetic code' - description: 'Collection of functions to calculate a nucleotide sequence surrounding for splice donors sites to either activate or repress donor usage. The proposed alternative nucleotide sequence encodes the same amino acid and could be applied e.g. in reporter systems to silence or activate cryptic splice donor sites.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-modstrings/meta.yaml b/recipes/bioconductor-modstrings/meta.yaml index 41aab942018f8..9b6306cb5bc13 100644 --- a/recipes/bioconductor-modstrings/meta.yaml +++ b/recipes/bioconductor-modstrings/meta.yaml @@ -1,54 +1,59 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "Modstrings" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Representing nucleotide modifications in a nucleotide sequence is usually done via special characters from a number of sources. This represents a challenge to work with in R and the Biostrings package. The Modstrings package implements this functionallity for RNA and DNA sequences containing modified nucleotides by translating the character internally in order to work with the infrastructure of the Biostrings package. For this the ModRNAString and ModDNAString classes and derivates and functions to construct and modify these objects despite the encoding issues are implemenented. In addition the conversion from sequences to list like location information (and the reverse operation) is implemented as well. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Working with modified nucleotide sequences -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 04e7bccc20c165b4d1317e995a0b1de2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-modstrings", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-crayon - r-stringi - r-stringr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-crayon - r-stringi - r-stringr + +source: + md5: ceebce9c77fa42d7339085ceacec85d2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Working with modified nucleotide sequences' - description: 'Representing nucleotide modifications in a nucleotide sequence is usually done via special characters from a number of sources. This represents a challenge to work with in R and the Biostrings package. The Modstrings package implements this functionallity for RNA and DNA sequences containing modified nucleotides by translating the character internally in order to work with the infrastructure of the Biostrings package. For this the ModRNAString and ModDNAString classes and derivates and functions to construct and modify these objects despite the encoding issues are implemenented. In addition the conversion from sequences to list like location information (and the reverse operation) is implemented as well.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-moe430a.db/meta.yaml b/recipes/bioconductor-moe430a.db/meta.yaml index 07af16105b075..9747033a8538a 100644 --- a/recipes/bioconductor-moe430a.db/meta.yaml +++ b/recipes/bioconductor-moe430a.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "moe430a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2bcdace3c55437bc8428b99064e486b1 +about: + description: Affymetrix Affymetrix MOE430A Array annotation data (chip moe430a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix MOE430A Array annotation data (chip moe430a) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-moe430a.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2bcdace3c55437bc8428b99064e486b1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix MOE430A Array annotation data (chip moe430a)' - description: 'Affymetrix Affymetrix MOE430A Array annotation data (chip moe430a) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-moe430acdf/meta.yaml b/recipes/bioconductor-moe430acdf/meta.yaml index 269ad39177873..8ec6df79b6489 100644 --- a/recipes/bioconductor-moe430acdf/meta.yaml +++ b/recipes/bioconductor-moe430acdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "moe430acdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b03f1295fc483f0d782a4615e8ca0137 +about: + description: A package containing an environment representing the MOE430A.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: moe430acdf build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-moe430acdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b03f1295fc483f0d782a4615e8ca0137 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: moe430acdf - description: 'A package containing an environment representing the MOE430A.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-moe430aprobe/meta.yaml b/recipes/bioconductor-moe430aprobe/meta.yaml index bb37dab84d098..1c1d32b2fae2b 100644 --- a/recipes/bioconductor-moe430aprobe/meta.yaml +++ b/recipes/bioconductor-moe430aprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "moe430aprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0aa83189d04599a65211d1a2f0a51c8f +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MOE430A\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type moe430a build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-moe430aprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0aa83189d04599a65211d1a2f0a51c8f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type moe430a' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MOE430A\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-moe430b.db/meta.yaml b/recipes/bioconductor-moe430b.db/meta.yaml index 1ca12a8892d3c..563bd242754a3 100644 --- a/recipes/bioconductor-moe430b.db/meta.yaml +++ b/recipes/bioconductor-moe430b.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "moe430b.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2d8a80b9d3342fb943087cc327c824e7 +about: + description: Affymetrix Affymetrix MOE430B Array annotation data (chip moe430b) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix MOE430B Array annotation data (chip moe430b) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-moe430b.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2d8a80b9d3342fb943087cc327c824e7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix MOE430B Array annotation data (chip moe430b)' - description: 'Affymetrix Affymetrix MOE430B Array annotation data (chip moe430b) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-moe430bcdf/meta.yaml b/recipes/bioconductor-moe430bcdf/meta.yaml index e59a11f6dde96..4e2557e28371e 100644 --- a/recipes/bioconductor-moe430bcdf/meta.yaml +++ b/recipes/bioconductor-moe430bcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "moe430bcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b7112dcf8ccfe4e079ca67ff62046f2e +about: + description: A package containing an environment representing the MOE430B.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: moe430bcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-moe430bcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b7112dcf8ccfe4e079ca67ff62046f2e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: moe430bcdf - description: 'A package containing an environment representing the MOE430B.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-moe430bprobe/meta.yaml b/recipes/bioconductor-moe430bprobe/meta.yaml index cc36302889064..938d325227e2d 100644 --- a/recipes/bioconductor-moe430bprobe/meta.yaml +++ b/recipes/bioconductor-moe430bprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "moe430bprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1368e6f4225babe7a693ccd39a3a436a +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MOE430B\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type moe430b build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-moe430bprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1368e6f4225babe7a693ccd39a3a436a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type moe430b' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MOE430B\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-moex10stprobeset.db/meta.yaml b/recipes/bioconductor-moex10stprobeset.db/meta.yaml index cfb5fa806324b..57608558132fd 100644 --- a/recipes/bioconductor-moex10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-moex10stprobeset.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "moex10stprobeset.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b1c12c80a4424e2854beab9dc796cb00 +about: + description: Affymetrix moex10 annotation data (chip moex10stprobeset) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix moex10 annotation data (chip moex10stprobeset) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-moex10stprobeset.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b1c12c80a4424e2854beab9dc796cb00 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix moex10 annotation data (chip moex10stprobeset)' - description: 'Affymetrix moex10 annotation data (chip moex10stprobeset) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-moex10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-moex10sttranscriptcluster.db/meta.yaml index 224ad7a7dc909..1930fa68e75fc 100644 --- a/recipes/bioconductor-moex10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-moex10sttranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "moex10sttranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bc3357b3c77ab7bf1dfb66f5f7da36ec +about: + description: Affymetrix moex10 annotation data (chip moex10sttranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix moex10 annotation data (chip moex10sttranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-moex10sttranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bc3357b3c77ab7bf1dfb66f5f7da36ec + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix moex10 annotation data (chip moex10sttranscriptcluster)' - description: 'Affymetrix moex10 annotation data (chip moex10sttranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-moexexonprobesetlocation/meta.yaml b/recipes/bioconductor-moexexonprobesetlocation/meta.yaml index 60209c1317491..d21e755008dc7 100644 --- a/recipes/bioconductor-moexexonprobesetlocation/meta.yaml +++ b/recipes/bioconductor-moexexonprobesetlocation/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.15.0" %} {% set name = "MoExExonProbesetLocation" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 07eea205fce2a8cf4585fa7e71fb0057 +about: + description: This package was automatically created by package AnnotationForge version 1.7.17. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type MoEx build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-moexexonprobesetlocation", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 07eea205fce2a8cf4585fa7e71fb0057 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type MoEx' - description: 'This package was automatically created by package AnnotationForge version 1.7.17. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mofa2/meta.yaml b/recipes/bioconductor-mofa2/meta.yaml index 5040a7de17019..494e649d833e4 100644 --- a/recipes/bioconductor-mofa2/meta.yaml +++ b/recipes/bioconductor-mofa2/meta.yaml @@ -1,31 +1,38 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "MOFA2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The MOFA2 package contains a collection of tools for training and analysing multi-omic factor analysis (MOFA). MOFA is a probabilistic factor model that aims to identify principal axes of variation from data sets that can comprise multiple omic layers and/or groups of samples. Additional time or space information on the samples can be incorporated using the MEFISTO framework, which is part of MOFA2. Downstream analysis functions to inspect molecular features underlying each factor, vizualisation, imputation etc are available. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Multi-Omics Factor Analysis v2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ce3c0d9a65e9e3f18d387af8a86ef6e build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mofa2", max_pin="x.x") }}' -# Suggests: knitr, testthat, Seurat, ggpubr, foreach, psych, MultiAssayExperiment, SummarizedExperiment, SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown, data.table, tidyverse, BiocStyle, Matrix, markdown + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, testthat, Seurat, SeuratObject, ggpubr, foreach, psych, MultiAssayExperiment, SummarizedExperiment, SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown, data.table, tidyverse, BiocStyle, Matrix, markdown # SystemRequirements: Python (>=3), numpy, pandas, h5py, scipy, argparse, sklearn, mofapy2 requirements: + + build: + - automake + - make + host: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 - r-base - r-corrplot - r-cowplot @@ -42,11 +49,12 @@ requirements: - r-stringi - r-tidyr - r-uwot + run: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 - r-base - r-corrplot - r-cowplot @@ -63,16 +71,16 @@ requirements: - r-stringi - r-tidyr - r-uwot - build: - - automake - - make + +source: + md5: aa84acedfadae2954706a4bdc6cf4658 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Multi-Omics Factor Analysis v2' - description: 'The MOFA2 package contains a collection of tools for training and analysing multi-omic factor analysis (MOFA). MOFA is a probabilistic factor model that aims to identify principal axes of variation from data sets that can comprise multiple omic layers and/or groups of samples. Additional time or space information on the samples can be incorporated using the MEFISTO framework, which is part of MOFA2. Downstream analysis functions to inspect molecular features underlying each factor, vizualisation, imputation etc are available.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mofadata/meta.yaml b/recipes/bioconductor-mofadata/meta.yaml index 3105056f66ed7..4f4f7eb2f93e2 100644 --- a/recipes/bioconductor-mofadata/meta.yaml +++ b/recipes/bioconductor-mofadata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "MOFAdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 23e46e209a43d7e62cfd6accc6a6fb44 +about: + description: A collection of datasets to accompany the R package MOFA and illustrate running and analysing MOFA models. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Data package for Multi-Omics Factor Analysis (MOFA) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mofadata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, MultiAssayExperiment, rmarkdown, BiocStyle requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3f8a0f3d03b4fa72d75a782592539c5c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL-3 - summary: 'Data package for Multi-Omics Factor Analysis (MOFA)' - description: 'A collection of datasets to accompany the R package MOFA and illustrate running and analysing MOFA models.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mofadata/post-link.sh b/recipes/bioconductor-mofadata/post-link.sh index b927a90f23c04..7244434aa33b9 100644 --- a/recipes/bioconductor-mofadata/post-link.sh +++ b/recipes/bioconductor-mofadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mofadata-1.18.0" +installBiocDataPackage.sh "mofadata-1.22.0" diff --git a/recipes/bioconductor-mogamun/meta.yaml b/recipes/bioconductor-mogamun/meta.yaml index ec048725b40a6..fd35bc2e5cc75 100644 --- a/recipes/bioconductor-mogamun/meta.yaml +++ b/recipes/bioconductor-mogamun/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "MOGAMUN" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MOGAMUN is a multi-objective genetic algorithm that identifies active modules in a multiplex biological network. This allows analyzing different biological networks at the same time. MOGAMUN is based on NSGA-II (Non-Dominated Sorting Genetic Algorithm, version II), which we adapted to work on networks. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: 'MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e2d5c06b9fc3d7e294b154f7efb83b3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mogamun", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, markdown requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 - r-base - r-igraph - r-runit - r-stringr run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 - r-base - r-igraph - r-runit - r-stringr + +source: + md5: b6dfd4f6110f13c6adb22756466025aa + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks' - description: 'MOGAMUN is a multi-objective genetic algorithm that identifies active modules in a multiplex biological network. This allows analyzing different biological networks at the same time. MOGAMUN is based on NSGA-II (Non-Dominated Sorting Genetic Algorithm, version II), which we adapted to work on networks.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mogene.1.0.st.v1frmavecs/meta.yaml b/recipes/bioconductor-mogene.1.0.st.v1frmavecs/meta.yaml index 99400c2a549a3..f72f9e9674aa4 100644 --- a/recipes/bioconductor-mogene.1.0.st.v1frmavecs/meta.yaml +++ b/recipes/bioconductor-mogene.1.0.st.v1frmavecs/meta.yaml @@ -1,38 +1,38 @@ {% set version = "1.1.0" %} {% set name = "mogene.1.0.st.v1frmavecs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b46f76903d0f19b85e8fa30347813ff5 +about: + description: This package was created by frmaTools version 1.13.0. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Vectors used by frma for microarrays of type mogene.1.0.st.v1frmavecs build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mogene.1.0.st.v1frmavecs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b46f76903d0f19b85e8fa30347813ff5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Vectors used by frma for microarrays of type mogene.1.0.st.v1frmavecs' - description: 'This package was created by frmaTools version 1.13.0.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mogene10stprobeset.db/meta.yaml b/recipes/bioconductor-mogene10stprobeset.db/meta.yaml index 98460dd552e38..d3fabf7c05204 100644 --- a/recipes/bioconductor-mogene10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-mogene10stprobeset.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "mogene10stprobeset.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 570d4cf3fcc42d1e9b54237b9e4eb5f7 +about: + description: Affymetrix mogene10 annotation data (chip mogene10stprobeset) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix mogene10 annotation data (chip mogene10stprobeset) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mogene10stprobeset.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 570d4cf3fcc42d1e9b54237b9e4eb5f7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix mogene10 annotation data (chip mogene10stprobeset)' - description: 'Affymetrix mogene10 annotation data (chip mogene10stprobeset) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mogene10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene10sttranscriptcluster.db/meta.yaml index b7365dee5c39e..bfa650f2f59df 100644 --- a/recipes/bioconductor-mogene10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mogene10sttranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "mogene10sttranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9553a8ecefad2baa7241c6b6bb8013f5 +about: + description: Affymetrix mogene10 annotation data (chip mogene10sttranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix mogene10 annotation data (chip mogene10sttranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mogene10sttranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9553a8ecefad2baa7241c6b6bb8013f5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix mogene10 annotation data (chip mogene10sttranscriptcluster)' - description: 'Affymetrix mogene10 annotation data (chip mogene10sttranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mogene10stv1cdf/meta.yaml b/recipes/bioconductor-mogene10stv1cdf/meta.yaml index 842e7b799689e..22f61da38b947 100644 --- a/recipes/bioconductor-mogene10stv1cdf/meta.yaml +++ b/recipes/bioconductor-mogene10stv1cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mogene10stv1cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9c0271f5d6493290fc47f041a8c3f925 +about: + description: A package containing an environment representing the MoGene-1_0-st-v1.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mogene10stv1cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mogene10stv1cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9c0271f5d6493290fc47f041a8c3f925 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mogene10stv1cdf - description: 'A package containing an environment representing the MoGene-1_0-st-v1.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mogene10stv1probe/meta.yaml b/recipes/bioconductor-mogene10stv1probe/meta.yaml index 7df09b6409c4e..74c60822cdb0b 100644 --- a/recipes/bioconductor-mogene10stv1probe/meta.yaml +++ b/recipes/bioconductor-mogene10stv1probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mogene10stv1probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 63cba1e2a0edee9f201267057fddb0fa +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MoGene-1\_0-st-v1\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type mogene10stv1 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mogene10stv1probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 63cba1e2a0edee9f201267057fddb0fa + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type mogene10stv1' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MoGene-1\_0-st-v1\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mogene11stprobeset.db/meta.yaml b/recipes/bioconductor-mogene11stprobeset.db/meta.yaml index d6a7c91a56257..8135aba00aac5 100644 --- a/recipes/bioconductor-mogene11stprobeset.db/meta.yaml +++ b/recipes/bioconductor-mogene11stprobeset.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "mogene11stprobeset.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1fba63da3f550e814a58c09d24d61cc0 +about: + description: Affymetrix mogene11 annotation data (chip mogene11stprobeset) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix mogene11 annotation data (chip mogene11stprobeset) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mogene11stprobeset.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1fba63da3f550e814a58c09d24d61cc0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix mogene11 annotation data (chip mogene11stprobeset)' - description: 'Affymetrix mogene11 annotation data (chip mogene11stprobeset) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mogene11sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene11sttranscriptcluster.db/meta.yaml index e973216aa7b66..efb95fe0b8bc3 100644 --- a/recipes/bioconductor-mogene11sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mogene11sttranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "mogene11sttranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2a3bf07a4794e2349b7d09368dcb7d18 +about: + description: Affymetrix mogene11 annotation data (chip mogene11sttranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix mogene11 annotation data (chip mogene11sttranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mogene11sttranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2a3bf07a4794e2349b7d09368dcb7d18 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix mogene11 annotation data (chip mogene11sttranscriptcluster)' - description: 'Affymetrix mogene11 annotation data (chip mogene11sttranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mogene20stprobeset.db/meta.yaml b/recipes/bioconductor-mogene20stprobeset.db/meta.yaml index d2fae2f15b125..483cb9ddfc4e2 100644 --- a/recipes/bioconductor-mogene20stprobeset.db/meta.yaml +++ b/recipes/bioconductor-mogene20stprobeset.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "mogene20stprobeset.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a64ddbf33e4f2b96301452e808d0e81a +about: + description: Affymetrix mogene20 annotation data (chip mogene20stprobeset) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix mogene20 annotation data (chip mogene20stprobeset) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mogene20stprobeset.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a64ddbf33e4f2b96301452e808d0e81a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix mogene20 annotation data (chip mogene20stprobeset)' - description: 'Affymetrix mogene20 annotation data (chip mogene20stprobeset) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mogene20sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene20sttranscriptcluster.db/meta.yaml index 192560f9dbc55..5bc77e5cad43e 100644 --- a/recipes/bioconductor-mogene20sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mogene20sttranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "mogene20sttranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e00e56d47bd19169875690e8e2129156 +about: + description: Affymetrix mogene20 annotation data (chip mogene20sttranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix mogene20 annotation data (chip mogene20sttranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mogene20sttranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e00e56d47bd19169875690e8e2129156 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix mogene20 annotation data (chip mogene20sttranscriptcluster)' - description: 'Affymetrix mogene20 annotation data (chip mogene20sttranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mogene21stprobeset.db/meta.yaml b/recipes/bioconductor-mogene21stprobeset.db/meta.yaml index fae2795386efa..0108ee357d8ae 100644 --- a/recipes/bioconductor-mogene21stprobeset.db/meta.yaml +++ b/recipes/bioconductor-mogene21stprobeset.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "mogene21stprobeset.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d6b3c352329b46493a20f6c27db05d43 +about: + description: Affymetrix mogene21 annotation data (chip mogene21stprobeset) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix mogene21 annotation data (chip mogene21stprobeset) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mogene21stprobeset.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d6b3c352329b46493a20f6c27db05d43 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix mogene21 annotation data (chip mogene21stprobeset)' - description: 'Affymetrix mogene21 annotation data (chip mogene21stprobeset) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mogene21sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene21sttranscriptcluster.db/meta.yaml index d36ffcbf36338..12a71fbcbbb3d 100644 --- a/recipes/bioconductor-mogene21sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mogene21sttranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "mogene21sttranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 10aaecc97bf06bfe770496b99612837a +about: + description: Affymetrix mogene21 annotation data (chip mogene21sttranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix mogene21 annotation data (chip mogene21sttranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mogene21sttranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 10aaecc97bf06bfe770496b99612837a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix mogene21 annotation data (chip mogene21sttranscriptcluster)' - description: 'Affymetrix mogene21 annotation data (chip mogene21sttranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mogsa/meta.yaml b/recipes/bioconductor-mogsa/meta.yaml index d9ec395d1b4f8..2c6913333580d 100644 --- a/recipes/bioconductor-mogsa/meta.yaml +++ b/recipes/bioconductor-mogsa/meta.yaml @@ -1,55 +1,60 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "mogsa" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provide a method for doing gene set analysis based on multiple omics data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Multiple omics data integrative clustering and gene set analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 177b003a38a7dc7ce3fb238369d1b6e7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mogsa", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, org.Hs.eg.db requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-graphite >=1.48.0,<1.49.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-graphite >=1.52.0,<1.53.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 - r-base - r-cluster - r-corpcor - r-gplots - r-svd run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-graphite >=1.48.0,<1.49.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-graphite >=1.52.0,<1.53.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 - r-base - r-cluster - r-corpcor - r-gplots - r-svd + +source: + md5: 42a2dd385ffc90a674b3ea1c2453b497 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Multiple omics data integrative clustering and gene set analysis' - description: 'This package provide a method for doing gene set analysis based on multiple omics data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-moleculeexperiment/meta.yaml b/recipes/bioconductor-moleculeexperiment/meta.yaml index 995c26bed8b41..43c1164335eeb 100644 --- a/recipes/bioconductor-moleculeexperiment/meta.yaml +++ b/recipes/bioconductor-moleculeexperiment/meta.yaml @@ -1,36 +1,38 @@ -{% set version = "1.2.2" %} +{% set version = "1.6.0" %} {% set name = "MoleculeExperiment" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MoleculeExperiment contains functions to create and work with objects from the new MoleculeExperiment class. We introduce this class for analysing molecule-based spatial transcriptomics data (e.g., Xenium by 10X, Cosmx SMI by Nanostring, and Merscope by Vizgen). This allows researchers to analyse spatial transcriptomics data at the molecule level, and to have standardised data formats accross vendors. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Prioritising a molecule-level storage of Spatial Transcriptomics Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d8fef705349bc9464ae152cd47bb9a58 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-moleculeexperiment", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 - r-base - r-cli - r-data.table - - 'r-dplyr >=1.1.1' + - r-dplyr >=1.1.1 - r-ggplot2 - r-magrittr - r-matrix @@ -39,15 +41,15 @@ requirements: - r-rlang - r-terra run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 - r-base - r-cli - r-data.table - - 'r-dplyr >=1.1.1' + - r-dplyr >=1.1.1 - r-ggplot2 - r-magrittr - r-matrix @@ -55,13 +57,16 @@ requirements: - r-rjson - r-rlang - r-terra + +source: + md5: cfe686e0c6e5cc5d890c56b519d5642d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Prioritising a molecule-level storage of Spatial Transcriptomics Data' - description: 'MoleculeExperiment contains functions to create and work with objects from the new MoleculeExperiment class. We introduce this class for analysing molecule-based spatial transcriptomics data (e.g., Xenium by 10X, Cosmx SMI by Nanostring, and Merscope by Vizgen). This allows researchers to analyse spatial transcriptomics data at the molecule level, and to have standardised data formats accross vendors.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-moma/meta.yaml b/recipes/bioconductor-moma/meta.yaml index 82fa380418cee..3777f5708df12 100644 --- a/recipes/bioconductor-moma/meta.yaml +++ b/recipes/bioconductor-moma/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "MOMA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements the inference of candidate master regulator proteins from multi-omics' data (MOMA) algorithm, as well as ancillary analysis and visualization functions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Multi Omic Master Regulator Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ce4cf6dab5fea53127b5b980756ef5db build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-moma", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, viper requirements: host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - r-circlize - r-cluster @@ -40,9 +42,9 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - r-circlize - r-cluster @@ -57,13 +59,16 @@ requirements: - r-stringr - r-tibble - r-tidyr + +source: + md5: 723ca93b14f8f8514315b94a47c6eb72 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Multi Omic Master Regulator Analysis' - description: 'This package implements the inference of candidate master regulator proteins from multi-omics'' data (MOMA) algorithm, as well as ancillary analysis and visualization functions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-monalisa/meta.yaml b/recipes/bioconductor-monalisa/meta.yaml index a8dbdc4c4bbc7..ec5de0c5e34f0 100644 --- a/recipes/bioconductor-monalisa/meta.yaml +++ b/recipes/bioconductor-monalisa/meta.yaml @@ -1,69 +1,76 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "monaLisa" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Useful functions to work with sequence motifs in the analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility or expression. Functions to produce informative visualizations of the obtained results are also provided. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Binned Motif Enrichment Analysis and Visualization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fc86eb3743fc47252a4420cd850ead9e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-monalisa", max_pin="x.x") }}' - noarch: generic -# Suggests: JASPAR2020, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown, testthat, BiocStyle, gridExtra + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: JASPAR2020, JASPAR2024, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown, testthat, BiocStyle, gridExtra requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tfbstools >=1.44.0,<1.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-circlize - r-glmnet + - r-rsqlite - r-stabs - r-vioplot run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tfbstools >=1.40.0,<1.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tfbstools >=1.44.0,<1.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-circlize - r-glmnet + - r-rsqlite - r-stabs - r-vioplot + +source: + md5: 6fcf806ce164367488b93818d2bd9461 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Binned Motif Enrichment Analysis and Visualization' - description: 'Useful functions to work with sequence motifs in the analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility or expression. Functions to produce informative visualizations of the obtained results are also provided.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-monocle/build_failure.osx-64.yaml b/recipes/bioconductor-monocle/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..6b3bd19765dbf --- /dev/null +++ b/recipes/bioconductor-monocle/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: e340e38e864df08918bbbdea4245d6f6b18516b3fde690f6981df4606061a84a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec(">=1.84.0,<1.85.0"), MatchSpec("bioconductor-biocviews==1.74.0=r44hdfd78af_0"), MatchSpec("bioconductor-limma==3.62.0=r44h2f393c0_0"), MatchSpec("r-base[version='>=4.4,<4.5.0a0']")} + Encountered problems while solving: + - nothing provides bioconductor-graph >=1.84.0,<1.85.0 needed by bioconductor-biocviews-1.74.0-r44hdfd78af_0 + - package bioconductor-limma-3.62.0-r44h2f393c0_0 requires r-base >=4.4,<4.5.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + bioconductor-biocviews >=1.74.0,<1.75.0 is not installable because it requires + bioconductor-graph >=1.84.0,<1.85.0 , which does not exist (perhaps a missing channel); + bioconductor-limma >=3.62.0,<3.63.0 is installable and it requires + r-base >=4.4,<4.5.0a0 , which can be installed; + r-leidenbase >=0.1.9 is not installable because there are no viable options + r-leidenbase 0.1.12 would require + r-base >=4.2,<4.3.0a0 , which conflicts with any installable versions previously reported; + r-leidenbase [0.1.18|0.1.27] would require + r-base >=4.3,<4.4.0a0 , which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec(">=1.84.0,<1.85.0"), MatchSpec("bioconductor-biocviews==1.74.0=r44hdfd78af_0"), MatchSpec("bioconductor-limma==3.62.0=r44h2f393c0_0"), MatchSpec("r-base[version='>=4.4,<4.5.0a0']")} + Encountered problems while solving: + - nothing provides bioconductor-graph >=1.84.0,<1.85.0 needed by bioconductor-biocviews-1.74.0-r44hdfd78af_0 + - package bioconductor-limma-3.62.0-r44h2f393c0_0 requires r-base >=4.4,<4.5.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + bioconductor-biocviews >=1.74.0,<1.75.0 is not installable because it requires + bioconductor-graph >=1.84.0,<1.85.0 , which does not exist (perhaps a missing channel); + bioconductor-limma >=3.62.0,<3.63.0 is installable and it requires + r-base >=4.4,<4.5.0a0 , which can be installed; + r-leidenbase >=0.1.9 is not installable because there are no viable options + r-leidenbase 0.1.12 would require + r-base >=4.2,<4.3.0a0 , which conflicts with any installable versions previously reported; + r-leidenbase [0.1.18|0.1.27] would require + r-base >=4.3,<4.4.0a0 , which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. +category: |- + dependency issue diff --git a/recipes/bioconductor-monocle/meta.yaml b/recipes/bioconductor-monocle/meta.yaml index 0d97d8b9d68ad..d069b04584ee5 100644 --- a/recipes/bioconductor-monocle/meta.yaml +++ b/recipes/bioconductor-monocle/meta.yaml @@ -1,110 +1,117 @@ -{% set version = "2.30.0" %} +{% set version = "2.34.0" %} {% set name = "monocle" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8b3a3d5cd2698b4cef4396c388250658 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-monocle", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:monocle + parent_recipe: + name: bioconductor-monocle + path: recipes/bioconductor-monocle + version: 2.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocviews >=1.70.0,<1.71.0' - - 'bioconductor-hsmmsinglecell >=1.22.0,<1.23.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocviews >=1.74.0,<1.75.0 + - bioconductor-hsmmsinglecell >=1.26.0,<1.27.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-cluster - r-combinat - - 'r-ddrtree >=0.1.4' + - r-ddrtree >=0.1.4 - r-dplyr - r-fastica - - 'r-ggplot2 >=1.0.0' - - 'r-igraph >=1.0.1' - - 'r-irlba >=2.0.0' - - 'r-leidenbase >=0.1.9' + - r-ggplot2 >=1.0.0 + - r-igraph >=1.0.1 + - r-irlba >=2.0.0 + - r-leidenbase >=0.1.9 - r-mass - - 'r-matrix >=1.2-6' + - r-matrix >=1.2-6 - r-matrixstats - r-pheatmap - r-plyr - r-proxy - - r-qlcmatrix - - 'r-rann >=2.5' - - 'r-rcpp >=0.12.0' + - r-rann >=2.5 + - r-rcpp >=0.12.0 - r-reshape2 - r-rtsne - r-slam - r-stringr - r-tibble - - 'r-vgam >=1.0-6' + - r-vgam >=1.0-6 - r-viridis - libblas - liblapack + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocviews >=1.70.0,<1.71.0' - - 'bioconductor-hsmmsinglecell >=1.22.0,<1.23.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocviews >=1.74.0,<1.75.0 + - bioconductor-hsmmsinglecell >=1.26.0,<1.27.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-cluster - r-combinat - - 'r-ddrtree >=0.1.4' + - r-ddrtree >=0.1.4 - r-dplyr - r-fastica - - 'r-ggplot2 >=1.0.0' - - 'r-igraph >=1.0.1' - - 'r-irlba >=2.0.0' - - 'r-leidenbase >=0.1.9' + - r-ggplot2 >=1.0.0 + - r-igraph >=1.0.1 + - r-irlba >=2.0.0 + - r-leidenbase >=0.1.9 - r-mass - - 'r-matrix >=1.2-6' + - r-matrix >=1.2-6 - r-matrixstats - r-pheatmap - r-plyr - r-proxy - - r-qlcmatrix - - 'r-rann >=2.5' - - 'r-rcpp >=0.12.0' + - r-rann >=2.5 + - r-rcpp >=0.12.0 - r-reshape2 - r-rtsne - r-slam - r-stringr - r-tibble - - 'r-vgam >=1.0-6' + - r-vgam >=1.0-6 - r-viridis - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 6be2330eb42a8c8c4692d96aac05fb3d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq' - description: 'Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:monocle - parent_recipe: - name: bioconductor-monocle - path: recipes/bioconductor-monocle - version: 2.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-moonlight2r/meta.yaml b/recipes/bioconductor-moonlight2r/meta.yaml index 0bfdabb5af5a6..7e101cba74c93 100644 --- a/recipes/bioconductor-moonlight2r/meta.yaml +++ b/recipes/bioconductor-moonlight2r/meta.yaml @@ -1,37 +1,55 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "Moonlight2R" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role (notably oncogenes and tumor suppressors). We present an updated version of the R/bioconductor package called MoonlightR, namely Moonlight2R, which returns a list of candidate driver genes for specific cancer types on the basis of omics data integration. The Moonlight framework contains a primary layer where gene expression data and information about biological processes are integrated to predict genes called oncogenic mediators, divided into putative tumor suppressors and putative oncogenes. This is done through functional enrichment analyses, gene regulatory networks and upstream regulator analyses to score the importance of well-known biological processes with respect to the studied cancer type. By evaluating the effect of the oncogenic mediators on biological processes or through random forests, the primary layer predicts two putative roles for the oncogenic mediators: i) tumor suppressor genes (TSGs) and ii) oncogenes (OCGs). As gene expression data alone is not enough to explain the deregulation of the genes, a second layer of evidence is needed. We have automated the integration of a secondary mutational layer through new functionalities in Moonlight2R. These functionalities analyze mutations in the cancer cohort and classifies these into driver and passenger mutations using the driver mutation prediction tool, CScape-somatic. Those oncogenic mediators with at least one driver mutation are retained as the driver genes. As a consequence, this methodology does not only identify genes playing a dual role (e.g. TSG in one cancer type and OCG in another) but also helps in elucidating the biological processes underlying their specific roles. In particular, Moonlight2R can be used to discover OCGs and TSGs in the same cancer type. This may for instance help in answering the question whether some genes change role between early stages (I, II) and late stages (III, IV). In the future, this analysis could be useful to determine the causes of different resistances to chemotherapeutic treatments.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identify oncogenes and tumor suppressor genes from omics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45af1bc580f9231cb2a83eae7517d3b8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-moonlight2r", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), devtools, roxygen2, png # SystemRequirements: CScapeSomatic requirements: + + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] + host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-epimix >=1.8.0,<1.9.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-circlize - r-doparallel @@ -39,6 +57,7 @@ requirements: - r-easypubmed - r-foreach - r-fuzzyjoin + - r-ggplot2 - r-gplots - r-hiver - r-magrittr @@ -54,16 +73,20 @@ requirements: - r-tibble - r-tidyheatmap - r-tidyr + run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-epimix >=1.8.0,<1.9.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-circlize - r-doparallel @@ -71,6 +94,7 @@ requirements: - r-easypubmed - r-foreach - r-fuzzyjoin + - r-ggplot2 - r-gplots - r-hiver - r-magrittr @@ -86,23 +110,16 @@ requirements: - r-tibble - r-tidyheatmap - r-tidyr - build: - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - xorg-libxfixes # [linux] + +source: + md5: 96842c4ab79b82de4ee8a43d1cc10976 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Identify oncogenes and tumor suppressor genes from omics data' - description: 'The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role (notably oncogenes and tumor suppressors). We present an updated version of the R/bioconductor package called MoonlightR, namely Moonlight2R, which returns a list of candidate driver genes for specific cancer types on the basis of omics data integration. The Moonlight framework contains a primary layer where gene expression data and information about biological processes are integrated to predict genes called oncogenic mediators, divided into putative tumor suppressors and putative oncogenes. This is done through functional enrichment analyses, gene regulatory networks and upstream regulator analyses to score the importance of well-known biological processes with respect to the studied cancer type. By evaluating the effect of the oncogenic mediators on biological processes or through random forests, the primary layer predicts two putative roles for the oncogenic mediators: i) tumor suppressor genes (TSGs) and ii) oncogenes (OCGs). As gene expression data alone is not enough to explain the deregulation of the genes, a second layer of evidence is needed. We have automated the integration of a secondary mutational layer through new functionalities in Moonlight2R. These functionalities analyze mutations in the cancer cohort and classifies these into driver and passenger mutations using the driver mutation prediction tool, CScape-somatic. Those oncogenic mediators with at least one driver mutation are retained as the driver genes. As a consequence, this methodology does not only identify genes playing a dual role (e.g. TSG in one cancer type and OCG in another) but also helps in elucidating the biological processes underlying their specific roles. In particular, Moonlight2R can be used to discover OCGs and TSGs in the same cancer type. This may for instance help in answering the question whether some genes change role between early stages (I, II) and late stages (III, IV). In the future, this analysis could be useful to determine the causes of different resistances to chemotherapeutic treatments.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-moonlightr/meta.yaml b/recipes/bioconductor-moonlightr/meta.yaml index c20170c048746..ee9cfe6a2355e 100644 --- a/recipes/bioconductor-moonlightr/meta.yaml +++ b/recipes/bioconductor-moonlightr/meta.yaml @@ -1,34 +1,47 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "MoonlightR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Motivation: The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role (notably oncogenes and tumor suppressors). Results: We present an R/bioconductor package called MoonlightR which returns a list of candidate driver genes for specific cancer types on the basis of TCGA expression data. The method first infers gene regulatory networks and then carries out a functional enrichment analysis (FEA) (implementing an upstream regulator analysis, URA) to score the importance of well-known biological processes with respect to the studied cancer type. Eventually, by means of random forests, MoonlightR predicts two specific roles for the candidate driver genes: i) tumor suppressor genes (TSGs) and ii) oncogenes (OCGs). As a consequence, this methodology does not only identify genes playing a dual role (e.g. TSG in one cancer type and OCG in another) but also helps in elucidating the biological processes underlying their specific roles. In particular, MoonlightR can be used to discover OCGs and TSGs in the same cancer type. This may help in answering the question whether some genes change role between early stages (I, II) and late stages (III, IV) in breast cancer. In the future, this analysis could be useful to determine the causes of different resistances to chemotherapeutic treatments.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identify oncogenes and tumor suppressor genes from omics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2a389ad9b7fe5ffc5e2c47717eb0b4c0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-moonlightr", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png, edgeR requirements: + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tcgabiolinks >=2.30.0,<2.31.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tcgabiolinks >=2.34.0,<2.35.0 - r-base - r-circlize - r-doparallel @@ -40,13 +53,13 @@ requirements: - r-rcolorbrewer - r-rismed run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tcgabiolinks >=2.30.0,<2.31.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tcgabiolinks >=2.34.0,<2.35.0 - r-base - r-circlize - r-doparallel @@ -57,23 +70,16 @@ requirements: - r-randomforest - r-rcolorbrewer - r-rismed - build: - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - xorg-libxfixes # [linux] + +source: + md5: 2667f0a5fd689b9e47a535e8d6e623be + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Identify oncogenes and tumor suppressor genes from omics data' - description: 'Motivation: The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role (notably oncogenes and tumor suppressors). Results: We present an R/bioconductor package called MoonlightR which returns a list of candidate driver genes for specific cancer types on the basis of TCGA expression data. The method first infers gene regulatory networks and then carries out a functional enrichment analysis (FEA) (implementing an upstream regulator analysis, URA) to score the importance of well-known biological processes with respect to the studied cancer type. Eventually, by means of random forests, MoonlightR predicts two specific roles for the candidate driver genes: i) tumor suppressor genes (TSGs) and ii) oncogenes (OCGs). As a consequence, this methodology does not only identify genes playing a dual role (e.g. TSG in one cancer type and OCG in another) but also helps in elucidating the biological processes underlying their specific roles. In particular, MoonlightR can be used to discover OCGs and TSGs in the same cancer type. This may help in answering the question whether some genes change role between early stages (I, II) and late stages (III, IV) in breast cancer. In the future, this analysis could be useful to determine the causes of different resistances to chemotherapeutic treatments.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mosaics/meta.yaml b/recipes/bioconductor-mosaics/meta.yaml index a9598eaacbb9c..978df396dedbb 100644 --- a/recipes/bioconductor-mosaics/meta.yaml +++ b/recipes/bioconductor-mosaics/meta.yaml @@ -1,71 +1,77 @@ -{% set version = "2.40.0" %} +{% set version = "2.44.0" %} {% set name = "mosaics" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functions for fitting MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data of transcription factor binding and histone modification. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0648fcfd9fd595974e0602fbb2a37cac build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mosaics", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:mosaics + - doi:10.1198/jasa.2011.ap09706 + parent_recipe: + name: bioconductor-mosaics + path: recipes/bioconductor-mosaics + version: 2.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: mosaicsExample # SystemRequirements: Perl requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-lattice - r-mass - r-rcpp - libblas - liblapack - - 'perl >=5.6.0' + - perl >=5.6.0 run: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-lattice - r-mass - r-rcpp - - 'perl >=5.6.0' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - perl >=5.6.0 + +source: + md5: 0171a569a0d8f960055be2c6f9d269a0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)' - description: 'This package provides functions for fitting MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data of transcription factor binding and histone modification.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:mosaics - - doi:10.1198/jasa.2011.ap09706 - parent_recipe: - name: bioconductor-mosaics - path: recipes/bioconductor-mosaics - version: 2.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mosaicsexample/meta.yaml b/recipes/bioconductor-mosaicsexample/meta.yaml index ff93401dec058..0eb5b4a1c60f2 100644 --- a/recipes/bioconductor-mosaicsexample/meta.yaml +++ b/recipes/bioconductor-mosaicsexample/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "mosaicsExample" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8852ad56f152a138367e7630b6b21efb +about: + description: Data for the mosaics package, consisting of (1) chromosome 22 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding and H3K4me3 modification in MCF7 cell line from ENCODE database (HG19) and (2) chromosome 21 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding, with mappability, GC content, and sequence ambiguity scores of human genome HG18. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Example data for the mosaics package, which implements MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data for transcription factor binding and histone modification build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mosaicsexample", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8e41d96ae8a0d1cc915db718a0dfd2a7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Example data for the mosaics package, which implements MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data for transcription factor binding and histone modification' - description: 'Data for the mosaics package, consisting of (1) chromosome 22 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding and H3K4me3 modification in MCF7 cell line from ENCODE database (HG19) and (2) chromosome 21 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding, with mappability, GC content, and sequence ambiguity scores of human genome HG18.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mosaicsexample/post-link.sh b/recipes/bioconductor-mosaicsexample/post-link.sh index b88c16fdb3cce..309b982fd486d 100644 --- a/recipes/bioconductor-mosaicsexample/post-link.sh +++ b/recipes/bioconductor-mosaicsexample/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mosaicsexample-1.40.0" +installBiocDataPackage.sh "mosaicsexample-1.44.0" diff --git a/recipes/bioconductor-mosbi/meta.yaml b/recipes/bioconductor-mosbi/meta.yaml index 4206531beddd4..28cc474c436ac 100644 --- a/recipes/bioconductor-mosbi/meta.yaml +++ b/recipes/bioconductor-mosbi/meta.yaml @@ -1,29 +1,35 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "mosbi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering). MoSBi provides standardized interfaces for biclustering results and can combine their results with a multi-algorithm ensemble approach to compute robust ensemble biclusters on molecular omics data. This is done by computing similarity networks of biclusters and filtering for overlaps using a custom error model. After that, the louvain modularity it used to extract bicluster communities from the similarity network, which can then be converted to ensemble biclusters. Additionally, MoSBi includes several network visualization methods to give an intuitive and scalable overview of the results. MoSBi comes with several biclustering algorithms, but can be easily extended to new biclustering algorithms. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + file LICENSE + license_file: LICENSE + summary: Molecular Signature identification using Biclustering -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f34159f8140d9fe59ea7fe2546e9cdce build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mosbi", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat (>= 3.0.0) # SystemRequirements: C++17, GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-fabia >=2.48.0,<2.49.0' - - 'bioconductor-qubic >=1.30.0,<1.31.0' + - bioconductor-fabia >=2.52.0,<2.53.0 + - bioconductor-qubic >=1.34.0,<1.35.0 - r-akmbiclust - r-base - r-bh @@ -37,8 +43,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-fabia >=2.48.0,<2.49.0' - - 'bioconductor-qubic >=1.30.0,<1.31.0' + - bioconductor-fabia >=2.52.0,<2.53.0 + - bioconductor-qubic >=1.34.0,<1.35.0 - r-akmbiclust - r-base - r-bh @@ -49,17 +55,16 @@ requirements: - r-rcpp - r-rcppparallel - r-xml2 - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 1e4037cfe8ee2351fcb55e3079b8804c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'AGPL-3 + file LICENSE' - summary: 'Molecular Signature identification using Biclustering' - description: 'This package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering). MoSBi provides standardized interfaces for biclustering results and can combine their results with a multi-algorithm ensemble approach to compute robust ensemble biclusters on molecular omics data. This is done by computing similarity networks of biclusters and filtering for overlaps using a custom error model. After that, the louvain modularity it used to extract bicluster communities from the similarity network, which can then be converted to ensemble biclusters. Additionally, MoSBi includes several network visualization methods to give an intuitive and scalable overview of the results. MoSBi comes with several biclustering algorithms, but can be easily extended to new biclustering algorithms.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mosclip/build.sh b/recipes/bioconductor-mosclip/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mosclip/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mosclip/build_failure.linux-64.yaml b/recipes/bioconductor-mosclip/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..bfa2f6b1de666 --- /dev/null +++ b/recipes/bioconductor-mosclip/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: c96457b131554dcc9c9d7d06d9863d45250edecc08406f95054d0f6c0619021e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Encountered problems while solving: + - nothing provides requested r-coxrobust + - nothing provides requested r-superexacttest + + Could not solve for environment specs + The following packages are incompatible + [31mr-coxrobust[0m does not exist (perhaps a typo or a missing channel); + [31mr-superexacttest[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-coxrobust"), MatchSpec("r-superexacttest")} + Encountered problems while solving: + - nothing provides requested r-coxrobust + - nothing provides requested r-superexacttest + + Could not solve for environment specs + The following packages are incompatible + [31mr-coxrobust[0m does not exist (perhaps a typo or a missing channel); + [31mr-superexacttest[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-coxrobust"), MatchSpec("r-superexacttest")} + Encountered problems while solving: + - nothing provides requested r-coxrobust + - nothing provides requested r-superexacttest + + Could not solve for environment specs + The following packages are incompatible + [31mr-coxrobust[0m does not exist (perhaps a typo or a missing channel); + [31mr-superexacttest[0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. +reason: |- + needs r-coxrobust and r-superexacttest to be added to conda-forge +category: |- + dependency issue diff --git a/recipes/bioconductor-mosclip/build_failure.osx-64.yaml b/recipes/bioconductor-mosclip/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..23adc1b2c2ad4 --- /dev/null +++ b/recipes/bioconductor-mosclip/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: c96457b131554dcc9c9d7d06d9863d45250edecc08406f95054d0f6c0619021e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + needs r-coxrobust and r-superexacttest to be added to conda-forge +category: |- + dependency issue diff --git a/recipes/bioconductor-mosclip/meta.yaml b/recipes/bioconductor-mosclip/meta.yaml new file mode 100644 index 0000000000000..583c93bbd7bab --- /dev/null +++ b/recipes/bioconductor-mosclip/meta.yaml @@ -0,0 +1,98 @@ +{% set version = "1.0.0" %} +{% set name = "MOSClip" %} +{% set bioc = "3.20" %} + +about: + description: 'Topological pathway analysis tool able to integrate multi-omics data. It finds survival-associated modules or significant modules for two-class analysis. This tool have two main methods: pathway tests and module tests. The latter method allows the user to dig inside the pathways itself.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + summary: Multi Omics Survival Clip + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mosclip", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RUnit, BiocGenerics, MASS, BiocStyle, knitr, EDASeq, rmarkdown, kableExtra, testthat (>= 3.0.0) +requirements: + + host: + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-graphite >=1.52.0,<1.53.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-qpgraph >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-checkmate + - r-circlize + - r-corpcor + - r-coxrobust + - r-elasticnet + - r-factominer + - r-ggplot2 + - r-ggplotify + - r-grbase + - r-gridextra + - r-igraph + - r-matrix + - r-nbclust + - r-pheatmap + - r-rcolorbrewer + - r-reshape + - r-superexacttest + - r-survival + - r-survminer + + run: + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-graphite >=1.52.0,<1.53.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-qpgraph >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-checkmate + - r-circlize + - r-corpcor + - r-coxrobust + - r-elasticnet + - r-factominer + - r-ggplot2 + - r-ggplotify + - r-grbase + - r-gridextra + - r-igraph + - r-matrix + - r-nbclust + - r-pheatmap + - r-rcolorbrewer + - r-reshape + - r-superexacttest + - r-survival + - r-survminer + +source: + md5: b02d6a00f99b9b6932d68d84781456ee + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-mosdef/build.sh b/recipes/bioconductor-mosdef/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mosdef/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mosdef/build_failure.osx-64.yaml b/recipes/bioconductor-mosdef/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..10692f4e23907 --- /dev/null +++ b/recipes/bioconductor-mosdef/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 6faea2d3343138f5187b5d04b1c9e257e85cdc99c786fa4506391e769590261f # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + clusterprofiler needs to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-mosdef/meta.yaml b/recipes/bioconductor-mosdef/meta.yaml new file mode 100644 index 0000000000000..1d7ad100e1420 --- /dev/null +++ b/recipes/bioconductor-mosdef/meta.yaml @@ -0,0 +1,74 @@ +{% set version = "1.2.0" %} +{% set name = "mosdef" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functionality to run a number of tasks in the differential expression analysis workflow. This encompasses the most widely used steps, from running various enrichment analysis tools with a unified interface to creating plots and beautifying table components linking to external websites and databases. This streamlines the generation of comprehensive analysis reports. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: MOSt frequently used and useful Differential Expression Functions + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mosdef", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, macrophage, org.Hs.eg.db, GeneTonic, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg38.knownGene, BiocStyle +requirements: + host: + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-goseq >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-topgo >=2.58.0,<2.59.0 + - r-base + - r-dt + - r-ggforce + - r-ggplot2 + - r-ggrepel + - r-htmltools + - r-rcolorbrewer + - r-rlang + - r-scales + run: + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-goseq >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-topgo >=2.58.0,<2.59.0 + - r-base + - r-dt + - r-ggforce + - r-ggplot2 + - r-ggrepel + - r-htmltools + - r-rcolorbrewer + - r-rlang + - r-scales + +source: + md5: 23db710f63347d36f046d8c46a8d3022 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-mosim/meta.yaml b/recipes/bioconductor-mosim/meta.yaml index b7ae429633a46..b746d40f4551d 100644 --- a/recipes/bioconductor-mosim/meta.yaml +++ b/recipes/bioconductor-mosim/meta.yaml @@ -1,69 +1,84 @@ -{% set version = "1.16.0" %} +{% set version = "2.2.0" %} {% set name = "MOSim" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MOSim package simulates multi-omic experiments that mimic regulatory mechanisms within the cell, allowing flexible experimental design including time course and multiple groups. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Multi-Omics Simulation (MOSim) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67f131b000a6d50361f61b4a78835d47 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mosim", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, knitr, rmarkdown, BiocStyle + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, knitr, rmarkdown, codetools, BiocStyle, stats, utils, purrr, scales, tibble, tidyr, Biobase, scater, SingleCellExperiment, decor, markdown, Rsamtools, igraph, leiden, bluster requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scran >=1.34.0,<1.35.0 - r-base + - r-cpp11 - r-dplyr - r-ggplot2 - r-hiddenmarkov - r-lazyeval - r-matrixstats - - r-purrr + - r-rcpp - r-rlang - - r-scales + - r-seurat + - r-signac - r-stringi - r-stringr - - r-tibble - - r-tidyr - r-zoo + - libblas + - liblapack + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scran >=1.34.0,<1.35.0 - r-base + - r-cpp11 - r-dplyr - r-ggplot2 - r-hiddenmarkov - r-lazyeval - r-matrixstats - - r-purrr + - r-rcpp - r-rlang - - r-scales + - r-seurat + - r-signac - r-stringi - r-stringr - - r-tibble - - r-tidyr - r-zoo + +source: + md5: 38533e929ac399f2bd03d8518ebe3653 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Multi-Omics Simulation (MOSim)' - description: 'MOSim package simulates multi-omic experiments that mimic regulatory mechanisms within the cell, allowing flexible experimental design including time course and multiple groups.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-motif2site/meta.yaml b/recipes/bioconductor-motif2site/meta.yaml index d941340b40832..5f95747c80b08 100644 --- a/recipes/bioconductor-motif2site/meta.yaml +++ b/recipes/bioconductor-motif2site/meta.yaml @@ -1,59 +1,64 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "Motif2Site" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Detect binding sites using motifs IUPAC sequence or bed coordinates and ChIP-seq experiments in bed or bam format. Combine/compare binding sites across experiments, tissues, or conditions. All normalization and differential steps are done using TMM-GLM method. Signal decomposition is done by setting motifs as the centers of the mixture of normal distribution curves. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e8228f1deb42f2d4b3867a90a6eba14c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-motif2site", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805 requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-mass - r-mixtools run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-mass - r-mixtools + +source: + md5: 8b19397baf4e352f178fcd3812800112 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions' - description: 'Detect binding sites using motifs IUPAC sequence or bed coordinates and ChIP-seq experiments in bed or bam format. Combine/compare binding sites across experiments, tissues, or conditions. All normalization and differential steps are done using TMM-GLM method. Signal decomposition is done by setting motifs as the centers of the mixture of normal distribution curves.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-motifbreakr/build_failure.linux-64.yaml b/recipes/bioconductor-motifbreakr/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..60f722c3ece3b --- /dev/null +++ b/recipes/bioconductor-motifbreakr/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 813fb2366551e9c206ecd2365106df9092f49f0c6e2b1df6bed06953be62563b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-bsicons")} + Encountered problems while solving: + - nothing provides requested r-bsicons + + Could not solve for environment specs + The following package could not be installed + [31mr-bsicons[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-bsicons")} + Encountered problems while solving: + - nothing provides requested r-bsicons + + Could not solve for environment specs + The following package could not be installed + [31mr-bsicons[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-bsicons")} + Encountered problems while solving: + - nothing provides requested r-bsicons + + Could not solve for environment specs + The following package could not be installed + [31mr-bsicons[0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-motifbreakr/meta.yaml b/recipes/bioconductor-motifbreakr/meta.yaml index ac68355c1531a..5a576e828ff4a 100644 --- a/recipes/bioconductor-motifbreakr/meta.yaml +++ b/recipes/bioconductor-motifbreakr/meta.yaml @@ -1,78 +1,102 @@ -{% set version = "2.16.0" %} +{% set version = "2.20.0" %} {% set name = "motifbreakR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: We introduce motifbreakR, which allows the biologist to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. MotifbreakR is both flexible and extensible over previous offerings; giving a choice of algorithms for interrogation of genomes with motifs from public sources that users can choose from; these are 1) a weighted-sum probability matrix, 2) log-probabilities, and 3) weighted by relative entropy. MotifbreakR can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor (currently there are 32 species, a total of 109 versions). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fd2ed6098a4bade8948f237753404006 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-motifbreakr", max_pin="x.x") }}' - noarch: generic -# Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP155.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle + +extra: + identifiers: + - biotools:motifbreakr + parent_recipe: + name: bioconductor-motifbreakr + path: recipes/bioconductor-motifbreakr + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP155.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Hsapiens.NCBI.GRCh38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Hsapiens.UCSC.hg38 requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-motifdb >=1.44.0,<1.45.0' - - 'bioconductor-motifstack >=1.46.0,<1.47.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-motifdb >=1.48.0,<1.49.0 + - bioconductor-motifstack >=1.50.0,<1.51.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base + - r-bsicons + - r-bslib + - r-dt - r-matrixstats + - r-shiny - r-stringr - r-tfmpvalue + - r-vroom + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-motifdb >=1.44.0,<1.45.0' - - 'bioconductor-motifstack >=1.46.0,<1.47.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-motifdb >=1.48.0,<1.49.0 + - bioconductor-motifstack >=1.50.0,<1.51.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base + - r-bsicons + - r-bslib + - r-dt - r-matrixstats + - r-shiny - r-stringr - r-tfmpvalue + - r-vroom + +source: + md5: 86c5acab3930ad2ef42208fea74e05ba + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites' - description: 'We introduce motifbreakR, which allows the biologist to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. MotifbreakR is both flexible and extensible over previous offerings; giving a choice of algorithms for interrogation of genomes with motifs from public sources that users can choose from; these are 1) a weighted-sum probability matrix, 2) log-probabilities, and 3) weighted by relative entropy. MotifbreakR can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor (currently there are 32 species, a total of 109 versions).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:motifbreakr - parent_recipe: - name: bioconductor-motifbreakr - path: recipes/bioconductor-motifbreakr - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-motifcounter/meta.yaml b/recipes/bioconductor-motifcounter/meta.yaml index a8167142b3b79..cdfe16665420f 100644 --- a/recipes/bioconductor-motifcounter/meta.yaml +++ b/recipes/bioconductor-motifcounter/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "motifcounter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: '''motifcounter'' provides motif matching, motif counting and motif enrichment functionality based on position frequency matrices. The main features of the packages include the utilization of higher-order background models and accounting for self-overlapping motif matches when determining motif enrichment. The background model allows to capture dinucleotide (or higher-order nucleotide) composition adequately which may reduced model biases and misleading results compared to using simple GC background models. When conducting a motif enrichment analysis based on the motif match count, the package relies on a compound Poisson distribution or alternatively a combinatorial model. These distribution account for self-overlapping motif structures as exemplified by repeat-like or palindromic motifs, and allow to determine the p-value and fold-enrichment for a set of observed motif matches.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: R package for analysing TFBSs in DNA sequences -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f093ba4ac3fe6bcf19d9d46bfb084290 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-motifcounter", max_pin="x.x") }}' + +extra: + parent_recipe: + name: bioconductor-motifcounter + path: recipes/bioconductor-motifcounter + version: 1.4.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: c4e221aed09cf31e91c28a4a7bfdbfb2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'R package for analysing TFBSs in DNA sequences' - description: '''motifcounter'' provides motif matching, motif counting and motif enrichment functionality based on position frequency matrices. The main features of the packages include the utilization of higher-order background models and accounting for self-overlapping motif matches when determining motif enrichment. The background model allows to capture dinucleotide (or higher-order nucleotide) composition adequately which may reduced model biases and misleading results compared to using simple GC background models. When conducting a motif enrichment analysis based on the motif match count, the package relies on a compound Poisson distribution or alternatively a combinatorial model. These distribution account for self-overlapping motif structures as exemplified by repeat-like or palindromic motifs, and allow to determine the p-value and fold-enrichment for a set of observed motif matches.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - parent_recipe: - name: bioconductor-motifcounter - path: recipes/bioconductor-motifcounter - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-motifdb/meta.yaml b/recipes/bioconductor-motifdb/meta.yaml index ccbbed4686d7d..53d022c36eeed 100644 --- a/recipes/bioconductor-motifdb/meta.yaml +++ b/recipes/bioconductor-motifdb/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "MotifDb" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 | file LICENSE + license_file: LICENSE + summary: An Annotated Collection of Protein-DNA Binding Sequence Motifs -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0aa63f3bc133dc0fa6c8cf88ebae383b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-motifdb", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:motifdb + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-motifdb + path: recipes/bioconductor-motifdb + version: 1.22.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR, markdown requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-splitstackshape run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-splitstackshape + +source: + md5: 58da75ad34570e7934c4eebd1bd8afa3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Artistic-2.0 | file LICENSE' - summary: 'An Annotated Collection of Protein-DNA Binding Sequence Motifs' - description: 'More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.' - license_file: LICENSE -extra: - identifiers: - - biotools:motifdb - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-motifdb - path: recipes/bioconductor-motifdb - version: 1.22.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-motifmatchr/meta.yaml b/recipes/bioconductor-motifmatchr/meta.yaml index 273956ac97380..c07c646ecba3a 100644 --- a/recipes/bioconductor-motifmatchr/meta.yaml +++ b/recipes/bioconductor-motifmatchr/meta.yaml @@ -1,36 +1,48 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "motifmatchr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Quickly find motif matches for many motifs and many sequences. Wraps C++ code from the MOODS motif calling library, which was developed by Pasi Rastas, Janne Korhonen, and Petri Martinmäki. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Fast Motif Matching in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 23c63cb97f5e359a4fb9e5e6751e037d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-motifmatchr", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:motifmatchr + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tfbstools >=1.44.0,<1.45.0 - r-base - r-matrix - r-rcpp @@ -38,35 +50,29 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tfbstools >=1.44.0,<1.45.0 - r-base - r-matrix - r-rcpp - r-rcpparmadillo - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 4c3cf75a0c77cc0e12170f4a9fec7dc4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-only + file LICENSE' - summary: 'Fast Motif Matching in R' - description: 'Quickly find motif matches for many motifs and many sequences. Wraps C++ code from the MOODS motif calling library, which was developed by Pasi Rastas, Janne Korhonen, and Petri Martinmäki.' - license_file: LICENSE + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name }} \ No newline at end of file diff --git a/recipes/bioconductor-motifstack/meta.yaml b/recipes/bioconductor-motifstack/meta.yaml index 2475f81526c68..2844b3a1e6d8e 100644 --- a/recipes/bioconductor-motifstack/meta.yaml +++ b/recipes/bioconductor-motifstack/meta.yaml @@ -1,57 +1,63 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "motifStack" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b3306b32c8722e6d63ee1a37165a572e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-motifstack", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:motifstack + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-motifstack + path: recipes/bioconductor-motifstack + version: 1.24.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Cairo, grImport, grImport2, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr, RUnit, rmarkdown, JASPAR2020 requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-tfbstools >=1.44.0,<1.45.0 - r-ade4 - r-base - r-ggplot2 - r-htmlwidgets - r-xml run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-tfbstools >=1.44.0,<1.45.0 - r-ade4 - r-base - r-ggplot2 - r-htmlwidgets - r-xml + +source: + md5: c3d5c6ef197f3ebce4eb1f95ee0e0208 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Plot stacked logos for single or multiple DNA, RNA and amino acid sequence' - description: 'The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:motifstack - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-motifstack - path: recipes/bioconductor-motifstack - version: 1.24.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-motiftestr/build.sh b/recipes/bioconductor-motiftestr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-motiftestr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-motiftestr/meta.yaml b/recipes/bioconductor-motiftestr/meta.yaml new file mode 100644 index 0000000000000..2025019e40893 --- /dev/null +++ b/recipes/bioconductor-motiftestr/meta.yaml @@ -0,0 +1,64 @@ +{% set version = "1.2.1" %} +{% set name = "motifTestR" %} +{% set bioc = "3.20" %} + +about: + description: Taking a set of sequence motifs as PWMs, test a set of sequences for over-representation of these motifs, as well as any positional features within the set of motifs. Enrichment analysis can be undertaken using multiple statistical approaches. The package also contains core functions to prepare data for analysis, and to visualise results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Perform key tests for binding motifs in sequence data + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-motiftestr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, extraChIPs, ggdendro, knitr, MotifDb, rmarkdown, rtracklayer, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-universalmotif >=1.24.0,<1.25.0 + - r-base + - r-ggplot2 >=3.5.0 + - r-harmonicmeanp + - r-matrixstats + - r-patchwork + - r-rlang + run: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-universalmotif >=1.24.0,<1.25.0 + - r-base + - r-ggplot2 >=3.5.0 + - r-harmonicmeanp + - r-matrixstats + - r-patchwork + - r-rlang + +source: + md5: 6844bc3b6698b2187e4ce76abc672022 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-mouse.db0/meta.yaml b/recipes/bioconductor-mouse.db0/meta.yaml index ae26bfd28f0fd..6726e5206c9d8 100644 --- a/recipes/bioconductor-mouse.db0/meta.yaml +++ b/recipes/bioconductor-mouse.db0/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "mouse.db0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1ef6bb1d25e53443871e0e8c975b36c0 +about: + description: Base annotation databases for mouse, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Level Annotation databases for mouse build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mouse.db0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9790c803e9b9c2a74e2b711991a27009 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Level Annotation databases for mouse' - description: 'Base annotation databases for mouse, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mouse.db0/post-link.sh b/recipes/bioconductor-mouse.db0/post-link.sh index b17f1a0a17b14..fd1a89101f07e 100644 --- a/recipes/bioconductor-mouse.db0/post-link.sh +++ b/recipes/bioconductor-mouse.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mouse.db0-3.18.0" +installBiocDataPackage.sh "mouse.db0-3.20.0" diff --git a/recipes/bioconductor-mouse4302.db/meta.yaml b/recipes/bioconductor-mouse4302.db/meta.yaml index 0a61e3af5ee7a..0276f1c4f19a9 100644 --- a/recipes/bioconductor-mouse4302.db/meta.yaml +++ b/recipes/bioconductor-mouse4302.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "mouse4302.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4ecaa53d32faca4199ba712c0e8ee570 +about: + description: Affymetrix Affymetrix Mouse430_2 Array annotation data (chip mouse4302) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Mouse430_2 Array annotation data (chip mouse4302) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mouse4302.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4ecaa53d32faca4199ba712c0e8ee570 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Mouse430_2 Array annotation data (chip mouse4302)' - description: 'Affymetrix Affymetrix Mouse430_2 Array annotation data (chip mouse4302) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mouse4302barcodevecs/meta.yaml b/recipes/bioconductor-mouse4302barcodevecs/meta.yaml index 027726e25334e..4591bfc3bbc04 100644 --- a/recipes/bioconductor-mouse4302barcodevecs/meta.yaml +++ b/recipes/bioconductor-mouse4302barcodevecs/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "mouse4302barcodevecs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 365757fba17dae1ed483e184d2c9fcdb +about: + description: Data used by the barcode package for microarrays of type mouse4302. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: mouse4302 data for barcode build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mouse4302barcodevecs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9f4d2c9dfa9224f36db3c05fa37d8a85 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'mouse4302 data for barcode' - description: 'Data used by the barcode package for microarrays of type mouse4302.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mouse4302barcodevecs/post-link.sh b/recipes/bioconductor-mouse4302barcodevecs/post-link.sh index ed7160125db4e..1c7e33f7723f8 100644 --- a/recipes/bioconductor-mouse4302barcodevecs/post-link.sh +++ b/recipes/bioconductor-mouse4302barcodevecs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mouse4302barcodevecs-1.40.0" +installBiocDataPackage.sh "mouse4302barcodevecs-1.44.0" diff --git a/recipes/bioconductor-mouse4302cdf/meta.yaml b/recipes/bioconductor-mouse4302cdf/meta.yaml index 57eb77636c347..d9e75a03a9c14 100644 --- a/recipes/bioconductor-mouse4302cdf/meta.yaml +++ b/recipes/bioconductor-mouse4302cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mouse4302cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bda3463613f958de35c58777db05cec2 +about: + description: A package containing an environment representing the Mouse430_2.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mouse4302cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mouse4302cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bda3463613f958de35c58777db05cec2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mouse4302cdf - description: 'A package containing an environment representing the Mouse430_2.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mouse4302frmavecs/meta.yaml b/recipes/bioconductor-mouse4302frmavecs/meta.yaml index 22c8cdff80066..05c36bc8ab668 100644 --- a/recipes/bioconductor-mouse4302frmavecs/meta.yaml +++ b/recipes/bioconductor-mouse4302frmavecs/meta.yaml @@ -1,38 +1,38 @@ {% set version = "1.5.0" %} {% set name = "mouse4302frmavecs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ec144b381abbe54d696356c1c124e372 +about: + description: This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Vectors used by frma for microarrays of type mouse4302 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mouse4302frmavecs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ec144b381abbe54d696356c1c124e372 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Vectors used by frma for microarrays of type mouse4302' - description: 'This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mouse4302probe/meta.yaml b/recipes/bioconductor-mouse4302probe/meta.yaml index 6da34b4b12cbc..607664e0ec916 100644 --- a/recipes/bioconductor-mouse4302probe/meta.yaml +++ b/recipes/bioconductor-mouse4302probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mouse4302probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7116787a7db241a545e79e419a8cfa0d +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Mouse430\_2\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type mouse4302 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mouse4302probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7116787a7db241a545e79e419a8cfa0d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type mouse4302' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Mouse430\_2\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mouse430a2.db/meta.yaml b/recipes/bioconductor-mouse430a2.db/meta.yaml index 29f8490359d73..833ba8c4eff69 100644 --- a/recipes/bioconductor-mouse430a2.db/meta.yaml +++ b/recipes/bioconductor-mouse430a2.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "mouse430a2.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0f1d053517af5f973f3cc49289cca1e5 +about: + description: Affymetrix Affymetrix Mouse430A_2 Array annotation data (chip mouse430a2) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Mouse430A_2 Array annotation data (chip mouse430a2) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mouse430a2.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0f1d053517af5f973f3cc49289cca1e5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Mouse430A_2 Array annotation data (chip mouse430a2)' - description: 'Affymetrix Affymetrix Mouse430A_2 Array annotation data (chip mouse430a2) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mouse430a2cdf/meta.yaml b/recipes/bioconductor-mouse430a2cdf/meta.yaml index e6b2a4871edaf..df5b3ab5792c7 100644 --- a/recipes/bioconductor-mouse430a2cdf/meta.yaml +++ b/recipes/bioconductor-mouse430a2cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mouse430a2cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1114c0415d1200bc21ad205e0830b075 +about: + description: A package containing an environment representing the Mouse430A_2.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mouse430a2cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mouse430a2cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1114c0415d1200bc21ad205e0830b075 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mouse430a2cdf - description: 'A package containing an environment representing the Mouse430A_2.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mouse430a2frmavecs/meta.yaml b/recipes/bioconductor-mouse430a2frmavecs/meta.yaml index 885f3133c6c45..f64920e31755e 100644 --- a/recipes/bioconductor-mouse430a2frmavecs/meta.yaml +++ b/recipes/bioconductor-mouse430a2frmavecs/meta.yaml @@ -1,38 +1,38 @@ {% set version = "1.3.0" %} {% set name = "mouse430a2frmavecs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3bcb8de9182bbb8de5d560748eafa0cc +about: + description: This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Vectors used by frma for microarrays of type mouse430a2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mouse430a2frmavecs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3bcb8de9182bbb8de5d560748eafa0cc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Vectors used by frma for microarrays of type mouse430a2' - description: 'This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mouse430a2probe/meta.yaml b/recipes/bioconductor-mouse430a2probe/meta.yaml index 9891dca3ac191..046667b685742 100644 --- a/recipes/bioconductor-mouse430a2probe/meta.yaml +++ b/recipes/bioconductor-mouse430a2probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mouse430a2probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bb3c34477d4fcf03a539772011118795 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Mouse430A\_2\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type mouse430a2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mouse430a2probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bb3c34477d4fcf03a539772011118795 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type mouse430a2' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Mouse430A\_2\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mousechrloc/meta.yaml b/recipes/bioconductor-mousechrloc/meta.yaml index 97f1bb6f99725..f19fc2b3df06f 100644 --- a/recipes/bioconductor-mousechrloc/meta.yaml +++ b/recipes/bioconductor-mousechrloc/meta.yaml @@ -1,37 +1,37 @@ {% set version = "2.1.6" %} {% set name = "mouseCHRLOC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0b81d7391e628cc355af4de3c5585a5f +about: + description: Annotation data file for mouseCHRLOC assembled using data from public data repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: The Artistic License, Version 2.0 + summary: A data package containing annotation data for mouseCHRLOC build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mousechrloc", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0b81d7391e628cc355af4de3c5585a5f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'The Artistic License, Version 2.0' - summary: 'A data package containing annotation data for mouseCHRLOC' - description: 'Annotation data file for mouseCHRLOC assembled using data from public data repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mousefm/meta.yaml b/recipes/bioconductor-mousefm/meta.yaml index c7958d978dad0..9759051bdc87f 100644 --- a/recipes/bioconductor-mousefm/meta.yaml +++ b/recipes/bioconductor-mousefm/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "MouseFM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides methods for genetic finemapping in inbred mice by taking advantage of their very high homozygosity rate (>95%). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: In-silico methods for genetic finemapping in inbred mice -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02947a619a95abf1ad58bb781953a22d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mousefm", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-curl - r-data.table @@ -39,10 +41,10 @@ requirements: - r-scales - r-tidyr run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-curl - r-data.table @@ -55,13 +57,16 @@ requirements: - r-rlist - r-scales - r-tidyr + +source: + md5: c847a523a2c49aa62f263f09662a8d10 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'In-silico methods for genetic finemapping in inbred mice' - description: 'This package provides methods for genetic finemapping in inbred mice by taking advantage of their very high homozygosity rate (>95%).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mousegastrulationdata/build_failure.linux-64.yaml b/recipes/bioconductor-mousegastrulationdata/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..22551c38ecafc --- /dev/null +++ b/recipes/bioconductor-mousegastrulationdata/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a68664bf348a14a3b16c035d8c817730fd3d46772bed36a9952521c4d6d69979 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-pillar: 1.10.0-r44hc72bb7e_0 conda-forge + r-pkgconfig: 2.0.3-r44hc72bb7e_4 conda-forge + r-plogr: 0.2.0-r44hc72bb7e_1006 conda-forge + r-png: 0.1_8-r44h21f035c_2 conda-forge + r-purrr: 1.0.2-r44hdb488b9_1 conda-forge + r-r6: 2.5.1-r44hc72bb7e_3 conda-forge + r-rappdirs: 0.3.3-r44hb1dbf0f_3 conda-forge + r-rcpp: 1.0.13_1-r44h93ab643_0 conda-forge + r-rjson: 0.2.23-r44h93ab643_0 conda-forge + r-rlang: 1.1.4-r44ha18555a_1 conda-forge + r-rsqlite: 2.3.9-r44h93ab643_0 conda-forge + r-stringi: 1.8.4-r44h33cde33_3 conda-forge + r-stringr: 1.5.1-r44h785f33e_1 conda-forge + r-sys: 3.4.3-r44h2b5f3a1_0 conda-forge + r-tibble: 3.2.1-r44hdb488b9_3 conda-forge + r-tidyr: 1.3.1-r44h0d4f4ea_1 conda-forge + r-tidyselect: 1.2.1-r44hc72bb7e_1 conda-forge + r-utf8: 1.2.4-r44hb1dbf0f_1 conda-forge + r-vctrs: 0.6.5-r44h0d4f4ea_1 conda-forge + r-withr: 3.0.2-r44hc72bb7e_0 conda-forge + r-yaml: 2.3.10-r44hdb488b9_0 conda-forge + rav1e: 0.6.6-he8a937b_2 conda-forge + readline: 8.2-h8228510_1 conda-forge + sed: 4.8-he412f7d_0 conda-forge + setuptools: 75.6.0-pyhff2d567_1 conda-forge + svt-av1: 2.3.0-h5888daf_0 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tktable: 2.10-h8bc8fbc_6 conda-forge + toml: 0.10.2-pyhd8ed1ab_1 conda-forge + tomlkit: 0.13.2-pyha770c72_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + x265: 3.5-h924138e_3 conda-forge + xmltodict: 0.14.2-pyhd8ed1ab_1 conda-forge + xorg-libice: 1.1.2-hb9d3cd8_0 conda-forge + xorg-libsm: 1.2.5-he73a12e_0 conda-forge + xorg-libx11: 1.8.10-h4f16b4b_1 conda-forge + xorg-libxau: 1.0.12-hb9d3cd8_0 conda-forge + xorg-libxdmcp: 1.1.5-hb9d3cd8_0 conda-forge + xorg-libxext: 1.3.6-hb9d3cd8_0 conda-forge + xorg-libxrender: 0.9.12-hb9d3cd8_0 conda-forge + xorg-libxt: 1.3.1-hb9d3cd8_0 conda-forge + yaml: 0.2.5-h7f98852_2 conda-forge + yq: 3.4.3-pyhd8ed1ab_1 conda-forge + zlib: 1.3.1-hb9d3cd8_2 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... + + done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: MouseGastrulationData_1.19.0_16126f4e92.tar.gz + Downloading https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MouseGastrulationData_1.19.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.073291 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioconductor.org/packages/3.20/bioc/src/contrib/Archive/MouseGastrulationData/MouseGastrulationData_1.19.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.041880 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioarchive.galaxyproject.org/MouseGastrulationData_1.19.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.215766 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://depot.galaxyproject.org/software/bioconductor-mousegastrulationdata/bioconductor-mousegastrulationdata_1.19.0_src_all.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.240805 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download https://depot.galaxyproject.org/software/bioconductor-mousegastrulationdata/bioconductor-mousegastrulationdata_1.19.0_src_all.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-mousegastrulationdata/meta.yaml b/recipes/bioconductor-mousegastrulationdata/meta.yaml index c6470676bb06c..3fcb26dad5592 100644 --- a/recipes/bioconductor-mousegastrulationdata/meta.yaml +++ b/recipes/bioconductor-mousegastrulationdata/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.16.0" %} +{% set version = "1.19.0" %} {% set name = "MouseGastrulationData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides processed and raw count data for single-cell RNA sequencing, single-cell ATAC-seq, and seqFISH (spatial transcriptomic) experiments performed along a timecourse of mouse gastrulation and early organogenesis. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Single-Cell -omics Data across Mouse Gastrulation and Early Organogenesis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4af06fb157942c6cfd9f24494bd7ae1f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mousegastrulationdata", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bumpymatrix >=1.14.0,<1.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bumpymatrix >=1.10.0,<1.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bumpymatrix >=1.14.0,<1.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 16126f4e927357245915ba465dcd34e3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Single-Cell -omics Data across Mouse Gastrulation and Early Organogenesis' - description: 'Provides processed and raw count data for single-cell RNA sequencing, single-cell ATAC-seq, and seqFISH (spatial transcriptomic) experiments performed along a timecourse of mouse gastrulation and early organogenesis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mousegastrulationdata/post-link.sh b/recipes/bioconductor-mousegastrulationdata/post-link.sh index 62b2c9b8a5dae..03f3f76c1895a 100644 --- a/recipes/bioconductor-mousegastrulationdata/post-link.sh +++ b/recipes/bioconductor-mousegastrulationdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mousegastrulationdata-1.16.0" +installBiocDataPackage.sh "mousegastrulationdata-1.19.0" diff --git a/recipes/bioconductor-mousethymusageing/build_failure.linux-64.yaml b/recipes/bioconductor-mousethymusageing/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..f975f2e79c137 --- /dev/null +++ b/recipes/bioconductor-mousethymusageing/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c5d5956304f06beb0d4e6739fd9f42d25612cd2dcd9e8fcf7567fa7b394ab929 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-lattice: 0.22_6-r44hb1dbf0f_1 conda-forge + r-lifecycle: 1.0.4-r44hc72bb7e_1 conda-forge + r-magrittr: 2.0.3-r44hb1dbf0f_3 conda-forge + r-matrix: 1.6_5-r44he966344_1 conda-forge + r-matrixstats: 1.4.1-r44h2b5f3a1_0 conda-forge + r-memoise: 2.0.1-r44hc72bb7e_3 conda-forge + r-mime: 0.12-r44hb1dbf0f_3 conda-forge + r-openssl: 2.2.2-r44he8289e2_0 conda-forge + r-pillar: 1.10.0-r44hc72bb7e_0 conda-forge + r-pkgconfig: 2.0.3-r44hc72bb7e_4 conda-forge + r-plogr: 0.2.0-r44hc72bb7e_1006 conda-forge + r-png: 0.1_8-r44h21f035c_2 conda-forge + r-purrr: 1.0.2-r44hdb488b9_1 conda-forge + r-r6: 2.5.1-r44hc72bb7e_3 conda-forge + r-rappdirs: 0.3.3-r44hb1dbf0f_3 conda-forge + r-rlang: 1.1.4-r44ha18555a_1 conda-forge + r-rsqlite: 2.3.9-r44h93ab643_0 conda-forge + r-stringi: 1.8.4-r44h33cde33_3 conda-forge + r-stringr: 1.5.1-r44h785f33e_1 conda-forge + r-sys: 3.4.3-r44h2b5f3a1_0 conda-forge + r-tibble: 3.2.1-r44hdb488b9_3 conda-forge + r-tidyr: 1.3.1-r44h0d4f4ea_1 conda-forge + r-tidyselect: 1.2.1-r44hc72bb7e_1 conda-forge + r-utf8: 1.2.4-r44hb1dbf0f_1 conda-forge + r-vctrs: 0.6.5-r44h0d4f4ea_1 conda-forge + r-withr: 3.0.2-r44hc72bb7e_0 conda-forge + r-yaml: 2.3.10-r44hdb488b9_0 conda-forge + readline: 8.2-h8228510_1 conda-forge + sed: 4.8-he412f7d_0 conda-forge + setuptools: 75.6.0-pyhff2d567_1 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tktable: 2.10-h8bc8fbc_6 conda-forge + toml: 0.10.2-pyhd8ed1ab_1 conda-forge + tomlkit: 0.13.2-pyha770c72_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + xmltodict: 0.14.2-pyhd8ed1ab_1 conda-forge + xorg-libice: 1.1.2-hb9d3cd8_0 conda-forge + xorg-libsm: 1.2.5-he73a12e_0 conda-forge + xorg-libx11: 1.8.10-h4f16b4b_1 conda-forge + xorg-libxau: 1.0.12-hb9d3cd8_0 conda-forge + xorg-libxdmcp: 1.1.5-hb9d3cd8_0 conda-forge + xorg-libxext: 1.3.6-hb9d3cd8_0 conda-forge + xorg-libxrender: 0.9.12-hb9d3cd8_0 conda-forge + xorg-libxt: 1.3.1-hb9d3cd8_0 conda-forge + yaml: 0.2.5-h7f98852_2 conda-forge + yq: 3.4.3-pyhd8ed1ab_1 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: MouseThymusAgeing_1.13.0_99ea897822.tar.gz + Downloading https://bioconductor.org/packages/3.20/data/experiment/src/contrib/MouseThymusAgeing_1.13.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.102745 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioconductor.org/packages/3.20/bioc/src/contrib/Archive/MouseThymusAgeing/MouseThymusAgeing_1.13.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.136019 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioarchive.galaxyproject.org/MouseThymusAgeing_1.13.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.663985 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://depot.galaxyproject.org/software/bioconductor-mousethymusageing/bioconductor-mousethymusageing_1.13.0_src_all.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.757429 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download https://depot.galaxyproject.org/software/bioconductor-mousethymusageing/bioconductor-mousethymusageing_1.13.0_src_all.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-mousethymusageing/meta.yaml b/recipes/bioconductor-mousethymusageing/meta.yaml index 0f159f50427ac..e93527e8d8fa3 100644 --- a/recipes/bioconductor-mousethymusageing/meta.yaml +++ b/recipes/bioconductor-mousethymusageing/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.10.0" %} +{% set version = "1.13.0" %} {% set name = "MouseThymusAgeing" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides data access to counts matrices and meta-data for single-cell RNA sequencing data of thymic epithlial cells across mouse ageing using SMARTseq2 and 10X Genommics chemistries. Access is provided as a data package via ExperimentHub. It is designed to facilitate the re-use of data from Baran-Gale _et al._ in a consistent format that includes relevant and informative meta-data. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Single-cell Transcriptomics Data of the Ageing Mouse Thymus -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf1889c22fa9e5ac5899a4d911907a90 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mousethymusageing", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, scuttle, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 99ea8978220d8b887a917005eb990533 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Single-cell Transcriptomics Data of the Ageing Mouse Thymus' - description: 'This package provides data access to counts matrices and meta-data for single-cell RNA sequencing data of thymic epithlial cells across mouse ageing using SMARTseq2 and 10X Genommics chemistries. Access is provided as a data package via ExperimentHub. It is designed to facilitate the re-use of data from Baran-Gale _et al._ in a consistent format that includes relevant and informative meta-data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mousethymusageing/post-link.sh b/recipes/bioconductor-mousethymusageing/post-link.sh index f63c5f266662c..791ce287d6f5b 100644 --- a/recipes/bioconductor-mousethymusageing/post-link.sh +++ b/recipes/bioconductor-mousethymusageing/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mousethymusageing-1.10.0" +installBiocDataPackage.sh "mousethymusageing-1.13.0" diff --git a/recipes/bioconductor-mpac/build.sh b/recipes/bioconductor-mpac/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mpac/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mpac/meta.yaml b/recipes/bioconductor-mpac/meta.yaml new file mode 100644 index 0000000000000..f43de0def20d5 --- /dev/null +++ b/recipes/bioconductor-mpac/meta.yaml @@ -0,0 +1,66 @@ +{% set version = "1.0.0" %} +{% set name = "MPAC" %} +{% set bioc = "3.20" %} + +about: + description: Multi-omic Pathway Analysis of Cancer (MPAC), integrates multi-omic data for understanding cancer mechanisms. It predicts novel patient groups with distinct pathway profiles as well as identifying key pathway proteins with potential clinical associations. From CNA and RNA-seq data, it determines genes’ DNA and RNA states (i.e., repressed, normal, or activated), which serve as the input for PARADIGM to calculate Inferred Pathway Levels (IPLs). It also permutes DNA and RNA states to create a background distribution to filter IPLs as a way to remove events observed by chance. It provides multiple methods for downstream analysis and visualization. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Multi-omic Pathway Analysis of Cancer + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-mpac", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: rmarkdown, knitr, svglite, bookdown(>= 0.34), testthat (>= 3.0.0) +requirements: + host: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-bluster >=1.16.0,<1.17.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-data.table >=1.14.2 + - r-fitdistrplus >=1.1 + - r-igraph >=1.4.3 + run: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-bluster >=1.16.0,<1.17.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-data.table >=1.14.2 + - r-fitdistrplus >=1.1 + - r-igraph >=1.4.3 + +source: + md5: 4994c148ede020434eaecc9788f38f04 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-mpedbarray.db/meta.yaml b/recipes/bioconductor-mpedbarray.db/meta.yaml index b919b9c2456b9..e0574f3f685aa 100644 --- a/recipes/bioconductor-mpedbarray.db/meta.yaml +++ b/recipes/bioconductor-mpedbarray.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "mpedbarray.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7bcd1fee1554b6f8844c9bf30b7db4ef +about: + description: FHCRC Nelson Lab mpedbarray Annotation Data (mpedbarray) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: FHCRC Nelson Lab mpedbarray Annotation Data (mpedbarray) build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mpedbarray.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7bcd1fee1554b6f8844c9bf30b7db4ef + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'FHCRC Nelson Lab mpedbarray Annotation Data (mpedbarray)' - description: 'FHCRC Nelson Lab mpedbarray Annotation Data (mpedbarray) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mpfe/meta.yaml b/recipes/bioconductor-mpfe/meta.yaml index b632910f132e4..115721cdcfa68 100644 --- a/recipes/bioconductor-mpfe/meta.yaml +++ b/recipes/bioconductor-mpfe/meta.yaml @@ -1,38 +1,20 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "MPFE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4f86c179f9bc43d1e16295df91c07cb8 +about: + description: Estimate distribution of methylation patterns from a table of counts from a bisulphite sequencing experiment given a non-conversion rate and read error rate. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mpfe", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data' - description: 'Estimate distribution of methylation patterns from a table of counts from a bisulphite sequencing experiment given a non-conversion rate and read error rate.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: identifiers: - biotools:mpfe @@ -41,4 +23,22 @@ extra: name: bioconductor-mpfe path: recipes/bioconductor-mpfe version: 1.16.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +requirements: + host: + - r-base + run: + - r-base +source: + md5: 70bd38ef543a0b93b02105297efbc151 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mpo.db/meta.yaml b/recipes/bioconductor-mpo.db/meta.yaml index 1e7309a1611e8..ee88e012b2660 100644 --- a/recipes/bioconductor-mpo.db/meta.yaml +++ b/recipes/bioconductor-mpo.db/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "0.99.7" %} +{% set version = "0.99.8" %} {% set name = "MPO.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: We have developed the human disease ontology R package HDO.db, which provides the semantic relationship between human diseases. Relying on the DOSE and GOSemSim packages we developed, we can carry out disease enrichment and semantic similarity analyses. Many biological studies are achieved through mouse models, and a large number of data indicate the association between genotypes and phenotypes or diseases. The study of model organisms can be transformed into useful knowledge about normal human biology and disease to facilitate treatment and early screening for diseases. Organism-specific genotype-phenotypic associations can be applied to cross-species phenotypic studies to clarify previously unknown phenotypic connections in other species. Using the same principle to diseases can identify genetic associations and even help to identify disease associations that are not obvious. Therefore, as a supplement to HDO.db and DOSE, we developed mouse phenotypic ontology R package MPO.db. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: A set of annotation maps describing the Mouse Phenotype Ontology -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f1b83d5d03d69a82ca2b9e7179b537f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mpo.db", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base - r-dbi - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: fd9bff2a147bbef37b58cef85ec79488 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A set of annotation maps describing the Mouse Phenotype Ontology' - description: 'We have developed the human disease ontology R package HDO.db, which provides the semantic relationship between human diseases. Relying on the DOSE and GOSemSim packages we developed, we can carry out disease enrichment and semantic similarity analyses. Many biological studies are achieved through mouse models, and a large number of data indicate the association between genotypes and phenotypes or diseases. The study of model organisms can be transformed into useful knowledge about normal human biology and disease to facilitate treatment and early screening for diseases. Organism-specific genotype-phenotypic associations can be applied to cross-species phenotypic studies to clarify previously unknown phenotypic connections in other species. Using the same principle to diseases can identify genetic associations and even help to identify disease associations that are not obvious. Therefore, as a supplement to HDO.db and DOSE, we developed mouse phenotypic ontology R package MPO.db.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mpo.db/post-link.sh b/recipes/bioconductor-mpo.db/post-link.sh index e54b8c62eb857..952bc78a079b7 100644 --- a/recipes/bioconductor-mpo.db/post-link.sh +++ b/recipes/bioconductor-mpo.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mpo.db-0.99.7" +installBiocDataPackage.sh "mpo.db-0.99.8" diff --git a/recipes/bioconductor-mpra/meta.yaml b/recipes/bioconductor-mpra/meta.yaml index 3f22c781079ee..aae859e15f36a 100644 --- a/recipes/bioconductor-mpra/meta.yaml +++ b/recipes/bioconductor-mpra/meta.yaml @@ -2,47 +2,52 @@ {% set name = "mpra" %} {% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7de08f36d1319293d1e7134bc698a546 +about: + description: Tools for data management, count preprocessing, and differential analysis in massively parallel report assays (MPRA). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Analyze massively parallel reporter assays + build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mpra", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.48.0' - - 'bioconductor-limma >=3.58.0' - - 'bioconductor-s4vectors >=0.40.0' - - 'bioconductor-summarizedexperiment >=1.32.0' - - 'r-base <4.4' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base - r-scales - r-statmod run: - - 'bioconductor-biocgenerics >=0.48.0' - - 'bioconductor-limma >=3.58.0' - - 'bioconductor-s4vectors >=0.40.0' - - 'bioconductor-summarizedexperiment >=1.32.0' - - 'r-base <4.4' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base - r-scales - r-statmod + +source: + md5: 7de08f36d1319293d1e7134bc698a546 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Analyze massively parallel reporter assays' - description: 'Tools for data management, count preprocessing, and differential analysis in massively parallel report assays (MPRA).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mpranalyze/meta.yaml b/recipes/bioconductor-mpranalyze/meta.yaml index d750c44c0fcf3..266dfa28a77ff 100644 --- a/recipes/bioconductor-mpranalyze/meta.yaml +++ b/recipes/bioconductor-mpranalyze/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "MPRAnalyze" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 63ae4121bc319692b51499a1b151dffc +about: + description: MPRAnalyze provides statistical framework for the analysis of data generated by Massively Parallel Reporter Assays (MPRAs), used to directly measure enhancer activity. MPRAnalyze can be used for quantification of enhancer activity, classification of active enhancers and comparative analyses of enhancer activity between conditions. MPRAnalyze construct a nested pair of generalized linear models (GLMs) to relate the DNA and RNA observations, easily adjustable to various experimental designs and conditions, and provides a set of rigorous statistical testig schemes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Statistical Analysis of MPRA data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mpranalyze", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-progress run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-progress +source: + md5: 5ac27d7a340e6d560836e63f88576189 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Statistical Analysis of MPRA data' - description: 'MPRAnalyze provides statistical framework for the analysis of data generated by Massively Parallel Reporter Assays (MPRAs), used to directly measure enhancer activity. MPRAnalyze can be used for quantification of enhancer activity, classification of active enhancers and comparative analyses of enhancer activity between conditions. MPRAnalyze construct a nested pair of generalized linear models (GLMs) to relate the DNA and RNA observations, easily adjustable to various experimental designs and conditions, and provides a set of rigorous statistical testig schemes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/faqcs/build_failure.osx-64.yaml b/recipes/bioconductor-msa/build_failure.osx-64.yaml similarity index 58% rename from recipes/faqcs/build_failure.osx-64.yaml rename to recipes/bioconductor-msa/build_failure.osx-64.yaml index 355b8c5709076..cada1771f9a35 100644 --- a/recipes/faqcs/build_failure.osx-64.yaml +++ b/recipes/bioconductor-msa/build_failure.osx-64.yaml @@ -1,54 +1,59 @@ -recipe_sha: 75dbf71ff4651d6a783a9d37c2ddc4ed5950198de6ba39b79d8d43a463b31a53 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 0ae07e342fce3a1c5cbe4cdb762f381e5753b54dc571dd063d8119bf94020c6c # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - 1 error generated. - make: *** [Makefile:18: FaQCs.o] Error 1 - Extracting download - Traceback (most recent call last): - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/faqcs_1717509739648/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/faqcs_1717509739648/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/faqcs_1717509739648/_build_env - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/faqcs_1717509739648/work +log: |2- + commands: + - $R -e "library('msa')" + about: + description: The 'msa' package provides a unified R/Bioconductor interface to the + multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All + three algorithms are integrated in the package, therefore, they do not depend + on any external software tools and are available for all major platforms. The + multiple sequence alignment algorithms are complemented by a function for pretty-printing + multiple sequence alignments using the LaTeX package TeXshade. + home: https://bioconductor.org/packages/3.20/bioc/html/msa.html + license: GPL (>= 2) + license_file: /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-msa_1734695160029/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/R/share/licenses/GPL-3 + summary: Multiple Sequence Alignment + extra: + additional-platforms: + - linux-aarch64 + copy_test_source_files: true + final: true + identifiers: + - biotools:msa + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-msa_1734695160029/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-msa_1734695160029/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-msa_1734695160029/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-msa_1734695160029/work INFO: activate-gfortran_osx-64.sh made the following environmental changes: - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/faqcs-2.10 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments - DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/faqcs-2.10 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-msa-1.38.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-msa-1.38.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/faqcs-2.10 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/faqcs-2.10 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-msa-1.38.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-msa-1.38.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as CC=x86_64-apple-darwin13.4.0-clang CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/faqcs_1717509739648/work/conda_build.sh']' returned non-zero exit status 2. - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/faqcs-2.10 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-msa-1.38.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/faqcs-2.10 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-msa-1.38.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool LD=x86_64-apple-darwin13.4.0-ld @@ -56,7 +61,7 @@ log: |- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -65,7 +70,7 @@ log: |- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -80,25 +85,22 @@ log: |- INFO: activate_clangxx_osx-64.sh made the following environmental changes: CLANGXX=x86_64-apple-darwin13.4.0-clang CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/faqcs-2.10 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-msa-1.38.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/faqcs-2.10 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-msa-1.38.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix INFO: activate_clang_osx-64.sh made the following environmental changes: CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang INFO: activate_clangxx_osx-64.sh made the following environmental changes: CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - Installing FaQCs for OSX. - x86_64-apple-darwin13.4.0-clang -O3 -Wall -std=c0x -msse2 -DATA16 -I. -c fastq.cpp - x86_64-apple-darwin13.4.0-clang -O3 -Wall -std=c0x -msse2 -DATA16 -I. -c options.cpp - x86_64-apple-darwin13.4.0-clang -O3 -Wall -std=c0x -msse2 -DATA16 -I. -c file_util.cpp - x86_64-apple-darwin13.4.0-clang -O3 -Wall -std=c0x -msse2 -DATA16 -I. -c trim.cpp - x86_64-apple-darwin13.4.0-clang -O3 -Wall -std=c0x -msse2 -DATA16 -I. -c plot.cpp - x86_64-apple-darwin13.4.0-clang -O3 -Wall -std=c0x -msse2 -DATA16 -I. -c seq_overlap.cpp - x86_64-apple-darwin13.4.0-clang -O3 -Wall -std=c0x -msse2 -DATA16 -I. -c FaQCs.cpp + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -I"./gc-8.2.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c R_init_msa.cpp -o R_init_msa.o # Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/bioconductor-msa/meta.yaml b/recipes/bioconductor-msa/meta.yaml index 3b02f9e8d1d8f..68d51152254ea 100644 --- a/recipes/bioconductor-msa/meta.yaml +++ b/recipes/bioconductor-msa/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "msa" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Multiple Sequence Alignment -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 78eba41452ffe497e1a7c72116335b3e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msa", max_pin="x.x") }}' -# Suggests: Biobase, knitr, seqinr, ape (>= 5.1), phangorn + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:msa + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-rcpp >=0.11.1' + - r-rcpp >=0.11.1 - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-rcpp >=0.11.1' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + - r-rcpp >=0.11.1 + +source: + md5: b0876e877edd9fd49356b20229f9424f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Multiple Sequence Alignment' - description: 'The ''msa'' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-msa2dist/meta.yaml b/recipes/bioconductor-msa2dist/meta.yaml index 64b19c561480a..798fad55c2476 100644 --- a/recipes/bioconductor-msa2dist/meta.yaml +++ b/recipes/bioconductor-msa2dist/meta.yaml @@ -1,30 +1,39 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "MSA2dist" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calcualtions which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calculates pairwise IUPAC distances. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a0d1c303af72c93a1810488010c2e6f build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msa2dist", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle # SystemRequirements: C++11 requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 - r-ape - r-base - r-doparallel @@ -40,10 +49,12 @@ requirements: - r-tidyr - libblas - liblapack + run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 - r-ape - r-base - r-doparallel @@ -57,17 +68,16 @@ requirements: - r-stringr - r-tibble - r-tidyr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: a7b7b619a8a9eacfca84d05e1499b4dc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis' - description: 'MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calcualtions which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calculates pairwise IUPAC distances.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msbackendmassbank/meta.yaml b/recipes/bioconductor-msbackendmassbank/meta.yaml index dc48b7c227b93..815724eea3023 100644 --- a/recipes/bioconductor-msbackendmassbank/meta.yaml +++ b/recipes/bioconductor-msbackendmassbank/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.10.1" %} +{% set version = "1.14.0" %} {% set name = "MsBackendMassbank" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Mass spectrometry (MS) data backend supporting import and export of MS/MS library spectra from MassBank record files. Different backends are available that allow handling of data in plain MassBank text file format or allow also to interact directly with MassBank SQL databases. Objects from this package are supposed to be used with the Spectra Bioconductor package. This package thus adds MassBank support to the Spectra package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Mass Spectrometry Data Backend for MassBank record Files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a929aebecff77108bc62891bc397f057 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msbackendmassbank", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 - r-base - r-dbi run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 - r-base - r-dbi + +source: + md5: c15b437f5527f5efbe3e2fe33ece5bda + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Mass Spectrometry Data Backend for MassBank record Files' - description: 'Mass spectrometry (MS) data backend supporting import and export of MS/MS library spectra from MassBank record files. Different backends are available that allow handling of data in plain MassBank text file format or allow also to interact directly with MassBank SQL databases. Objects from this package are supposed to be used with the Spectra Bioconductor package. This package thus adds MassBank support to the Spectra package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msbackendmetabolights/build.sh b/recipes/bioconductor-msbackendmetabolights/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-msbackendmetabolights/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msbackendmetabolights/meta.yaml b/recipes/bioconductor-msbackendmetabolights/meta.yaml new file mode 100644 index 0000000000000..25bf90761c1fd --- /dev/null +++ b/recipes/bioconductor-msbackendmetabolights/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.0.0" %} +{% set name = "MsBackendMetaboLights" %} +{% set bioc = "3.20" %} + +about: + description: MetaboLights is one of the main public repositories for storage of metabolomics experiments, which includes analysis results as well as raw data. The MsBackendMetaboLights package provides functionality to retrieve and represent mass spectrometry (MS) data from MetaboLights. Data files are downloaded and cached locally avoiding repetitive downloads. MS data from metabolomics experiments can thus be directly and seamlessly integrated into R-based analysis workflows with the Spectra and MsBackendMetaboLights package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Retrieve Mass Spectrometry Data from MetaboLights + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-msbackendmetabolights", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, rmarkdown, mzR, knitr, BiocStyle +requirements: + host: + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 + - r-base + - r-curl + run: + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 + - r-base + - r-curl + +source: + md5: f036a1c6240ed398087a23be6152f4c5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-msbackendmgf/meta.yaml b/recipes/bioconductor-msbackendmgf/meta.yaml index 87335b6ed47d8..6d3b9a8bf2b75 100644 --- a/recipes/bioconductor-msbackendmgf/meta.yaml +++ b/recipes/bioconductor-msbackendmgf/meta.yaml @@ -1,46 +1,53 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "MsBackendMgf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Mass spectrometry (MS) data backend supporting import and export of MS/MS spectra data from Mascot Generic Format (mgf) files. Objects defined in this package are supposed to be used with the Spectra Bioconductor package. This package thus adds mgf file support to the Spectra package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8b5cc0b0f9c2da6222c217ae8a4c44f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msbackendmgf", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 - r-base run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 - r-base + +source: + md5: a05648360c4648fd8ca90ec0a4856092 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files' - description: 'Mass spectrometry (MS) data backend supporting import and export of MS/MS spectra data from Mascot Generic Format (mgf) files. Objects defined in this package are supposed to be used with the Spectra Bioconductor package. This package thus adds mgf file support to the Spectra package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msbackendmsp/meta.yaml b/recipes/bioconductor-msbackendmsp/meta.yaml index 34df8b380d30c..e04dc6dacfb8a 100644 --- a/recipes/bioconductor-msbackendmsp/meta.yaml +++ b/recipes/bioconductor-msbackendmsp/meta.yaml @@ -1,46 +1,53 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "MsBackendMsp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Mass spectrometry (MS) data backend supporting import and handling of MS/MS spectra from NIST MSP Format (msp) files. Import of data from files with different MSP *flavours* is supported. Objects from this package add support for MSP files to Bioconductor's Spectra package. This package is thus not supposed to be used without the Spectra package that provides a complete infrastructure for MS data handling. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Mass Spectrometry Data Backend for NIST msp Files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 805d831547106b2f232bb9eda75172bc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msbackendmsp", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 - r-base run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 - r-base + +source: + md5: cd1d33e6c98c6cc2900a0e3dbf857275 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Mass Spectrometry Data Backend for NIST msp Files' - description: 'Mass spectrometry (MS) data backend supporting import and handling of MS/MS spectra from NIST MSP Format (msp) files. Import of data from files with different MSP *flavours* is supported. Objects from this package add support for MSP files to Bioconductor''s Spectra package. This package is thus not supposed to be used without the Spectra package that provides a complete infrastructure for MS data handling.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msbackendrawfilereader/build_failure.linux-64.yaml b/recipes/bioconductor-msbackendrawfilereader/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..8000aceefa4f0 --- /dev/null +++ b/recipes/bioconductor-msbackendrawfilereader/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 940156279581d437bcc19d7a0980942df2516374986c42568d53955a4154c17e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rawrr[version='>=1.14.0,<1.15.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rawrr >=1.14.0,<1.15.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rawrr >=1.14.0,<1.15.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rawrr[version='>=1.14.0,<1.15.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rawrr >=1.14.0,<1.15.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rawrr >=1.14.0,<1.15.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rawrr[version='>=1.14.0,<1.15.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rawrr >=1.14.0,<1.15.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rawrr >=1.14.0,<1.15.0 [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-msbackendrawfilereader/meta.yaml b/recipes/bioconductor-msbackendrawfilereader/meta.yaml index ebd428e4ee072..d6435a762dcc8 100644 --- a/recipes/bioconductor-msbackendrawfilereader/meta.yaml +++ b/recipes/bioconductor-msbackendrawfilereader/meta.yaml @@ -1,50 +1,57 @@ -{% set version = "1.8.1" %} +{% set version = "1.12.0" %} {% set name = "MsBackendRawFileReader" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: implements a MsBackend for the Spectra package using Thermo Fisher Scientific's NewRawFileReader .Net libraries. The package is generalizing the functionality introduced by the rawrr package Methods defined in this package are supposed to extend the Spectra Bioconductor package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b933c2e4fbd38b9cc8298a9cb397b5ad build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msbackendrawfilereader", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle (>= 2.5), ExperimentHub, MsBackendMgf, knitr, lattice, mzR, protViz (>= 0.7), rmarkdown, tartare (>= 1.5), testthat # SystemRequirements: mono-runtime 4.x or higher (including System.Data library) on Linux/macOS, .Net Framework (>= 4.5.1) on Microsoft Windows. requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-rawrr >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-rawrr >=1.14.0,<1.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 - r-base run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-rawrr >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-rawrr >=1.14.0,<1.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 - r-base + +source: + md5: b572fa8fcb5d29ece30da3539d5eba91 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files' - description: 'implements a MsBackend for the Spectra package using Thermo Fisher Scientific''s NewRawFileReader .Net libraries. The package is generalizing the functionality introduced by the rawrr package Methods defined in this package are supposed to extend the Spectra Bioconductor package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msbackendsql/meta.yaml b/recipes/bioconductor-msbackendsql/meta.yaml index ebd150923cd74..829ea783ddfff 100644 --- a/recipes/bioconductor-msbackendsql/meta.yaml +++ b/recipes/bioconductor-msbackendsql/meta.yaml @@ -1,56 +1,61 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "MsBackendSql" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SQL-based mass spectrometry (MS) data backend supporting also storange and handling of very large data sets. Objects from this package are supposed to be used with the Spectra Bioconductor package. Through the MsBackendSql with its minimal memory footprint, this package thus provides an alternative MS data representation for very large or remote MS data sets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: SQL-based Mass Spectrometry Data Backend -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c5d7c6ce9c877e7c0bbbc1b63a71eb70 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msbackendsql", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, msdata, rmarkdown, microbenchmark, mzR requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 - r-base - r-data.table - r-dbi - r-progress run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 - r-base - r-data.table - r-dbi - r-progress + +source: + md5: 8c744daa8fc956b4c7c99e1e4998f5db + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'SQL-based Mass Spectrometry Data Backend' - description: 'SQL-based mass spectrometry (MS) data backend supporting also storange and handling of very large data sets. Objects from this package are supposed to be used with the Spectra Bioconductor package. Through the MsBackendSql with its minimal memory footprint, this package thus provides an alternative MS data representation for very large or remote MS data sets.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mscoreutils/meta.yaml b/recipes/bioconductor-mscoreutils/meta.yaml index e3dad78d9e43e..05071c083edb3 100644 --- a/recipes/bioconductor-mscoreutils/meta.yaml +++ b/recipes/bioconductor-mscoreutils/meta.yaml @@ -1,27 +1,39 @@ -{% set version = "1.14.1" %} +{% set version = "1.18.0" %} {% set name = "MsCoreUtils" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MsCoreUtils defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning, baseline estimation), quantitative aggregation functions (median polish, robust summarisation, ...), missing data imputation, data normalisation (quantiles, vsn, ...), misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Core Utils for Mass Spectrometry Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 163cc129bc77ed033c124fed5bf7d9ca build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mscoreutils", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:mscoreutils + - usegalaxy-eu:mscoreutils + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD, impute, norm, pcaMethods, vsn, Matrix, preprocessCore, missForest requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-clue - r-mass @@ -29,28 +41,21 @@ requirements: - libblas - liblapack run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-clue - r-mass - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 61311736dc7f409221abbac6dad1732a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Core Utils for Mass Spectrometry Data' - description: 'MsCoreUtils defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning), quantitative aggregation functions (median polish, robust summarisation, ...), missing data imputation, data normalisation (quantiles, vsn, ...) as well as misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.' - -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} - - usegalaxy-eu:{{ name|lower }} + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msd16s/build_failure.linux-64.yaml b/recipes/bioconductor-msd16s/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..c444f675167ec --- /dev/null +++ b/recipes/bioconductor-msd16s/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 2108030817e7f131f893b1782301c2977f8442fecfa67e6b6135f287d8ad9a1e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: metagenomeseq 1.47 Not ready for BioC 3.20 +category: dependency issue +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-metagenomeseq[version='>=1.47.0,<1.48.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-metagenomeseq >=1.47.0,<1.48.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-metagenomeseq >=1.47.0,<1.48.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-metagenomeseq[version='>=1.47.0,<1.48.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-metagenomeseq >=1.47.0,<1.48.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-metagenomeseq >=1.47.0,<1.48.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-metagenomeseq[version='>=1.47.0,<1.48.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-metagenomeseq >=1.47.0,<1.48.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-metagenomeseq >=1.47.0,<1.48.0 [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-msd16s/meta.yaml b/recipes/bioconductor-msd16s/meta.yaml index 093763b193ce2..b438185e51910 100644 --- a/recipes/bioconductor-msd16s/meta.yaml +++ b/recipes/bioconductor-msd16s/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.22.0" %} +{% set version = "1.25.0" %} {% set name = "msd16s" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fddb80467192bbe28bb92599941be5d3 +about: + description: Gut 16S sequencing expression data from 992 healthy and moderate-to-severe diarrhetic samples used in 'Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition'. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Healthy and moderate to severe diarrhea 16S expression data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msd16s", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-metagenomeseq >=1.47.0,<1.48.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-metagenomeseq >=1.43.0,<1.44.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-metagenomeseq >=1.47.0,<1.48.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2f1e1f51527fd43615f898bc898357d1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Healthy and moderate to severe diarrhea 16S expression data' - description: 'Gut 16S sequencing expression data from 992 healthy and moderate-to-severe diarrhetic samples used in ''Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition''.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msd16s/post-link.sh b/recipes/bioconductor-msd16s/post-link.sh index 62fa20ab286f1..8839f78157d75 100644 --- a/recipes/bioconductor-msd16s/post-link.sh +++ b/recipes/bioconductor-msd16s/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "msd16s-1.22.0" +installBiocDataPackage.sh "msd16s-1.25.0" diff --git a/recipes/bioconductor-msdata/meta.yaml b/recipes/bioconductor-msdata/meta.yaml index a93c158772cf0..ee6a003c00526 100644 --- a/recipes/bioconductor-msdata/meta.yaml +++ b/recipes/bioconductor-msdata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "0.42.0" %} +{% set version = "0.46.0" %} {% set name = "msdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3ef7fea0866799a767fb8ac2d1da0a16 +about: + description: Ion Trap positive ionization mode data in mzML file format. Subset from 500-850 m/z and 1190-1310 seconds, incl. MS2 and MS3, intensity threshold 100.000. Extracts from FTICR Apex III, m/z 400-450. Subset of UPLC - Bruker micrOTOFq data, both mzML and mz5. LC-MSMS and MRM files from proteomics experiments. PSI mzIdentML example files for various search engines. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Various Mass Spectrometry raw data example files build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: xcms, mzR, MSnbase requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241220 +source: + md5: 280e355d2ab77124dcf82cf8625e1c4f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Various Mass Spectrometry raw data example files' - description: 'Ion Trap positive ionization mode data in mzML file format. Subset from 500-850 m/z and 1190-1310 seconds, incl. MS2 and MS3, intensity threshold 100.000. Extracts from FTICR Apex III, m/z 400-450. Subset of UPLC - Bruker micrOTOFq data, both mzML and mz5. LC-MSMS and MRM files from proteomics experiments. PSI mzIdentML example files for various search engines.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msdata/post-link.sh b/recipes/bioconductor-msdata/post-link.sh index d125e3b63b591..f40085637e008 100644 --- a/recipes/bioconductor-msdata/post-link.sh +++ b/recipes/bioconductor-msdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "msdata-0.42.0" +installBiocDataPackage.sh "msdata-0.46.0" diff --git a/recipes/bioconductor-msdatahub/meta.yaml b/recipes/bioconductor-msdatahub/meta.yaml index 2e0d17ac40a1a..3749136e1a200 100644 --- a/recipes/bioconductor-msdatahub/meta.yaml +++ b/recipes/bioconductor-msdatahub/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "MsDataHub" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f355465b6b3994491364cbe994e4488d +about: + description: The MsDataHub package uses the ExperimentHub infrastructure to distribute raw mass spectrometry data files, peptide spectrum matches or quantitative data from proteomics and metabolomics experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Mass Spectrometry Data on ExperimentHub build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msdatahub", max_pin="x.x") }}' - noarch: generic -# Suggests: ExperimentHubData, DT, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), Spectra, mzR, PSMatch, QFeatures +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: ExperimentHubData, DT, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), Spectra, mzR, PSMatch, QFeatures (>= 1.13.3) requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base +source: + md5: 315760cb18f34292e0349572be2492d3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Mass Spectrometry Data on ExperimentHub' - description: 'The MsDataHub package uses the ExperimentHub infrastructure to distribute raw mass spectrometry data files, peptide spectrum matches or quantitative data from proteomics and metabolomics experiments.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msexperiment/meta.yaml b/recipes/bioconductor-msexperiment/meta.yaml index 13793f29ea8ce..f8b0359827f86 100644 --- a/recipes/bioconductor-msexperiment/meta.yaml +++ b/recipes/bioconductor-msexperiment/meta.yaml @@ -1,48 +1,57 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "MsExperiment" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Infrastructure to store and manage all aspects related to a complete proteomics or metabolomics mass spectrometry (MS) experiment. The MsExperiment package provides light-weight and flexible containers for MS experiments building on the new MS infrastructure provided by the Spectra, QFeatures and related packages. Along with raw data representations, links to original data files and sample annotations, additional metadata or annotations can also be stored within the MsExperiment container. To guarantee maximum flexibility only minimal constraints are put on the type and content of the data within the containers. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Infrastructure for Mass Spectrometry Experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b248141f2ad9d5421d067b7f90a4c87e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msexperiment", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown, rpx, mzR, msdata + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown, rpx, mzR, msdata, MsBackendSql (>= 1.3.2), RSQLite requirements: host: - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-qfeatures >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-qfeatures >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + - r-dbi run: - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-qfeatures >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-qfeatures >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + - r-dbi + +source: + md5: 5b2dd4750bc74cf3ec8f7748b6f21891 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Infrastructure for Mass Spectrometry Experiments' - description: 'Infrastructure to store and manage all aspects related to a complete proteomics or metabolomics mass spectrometry (MS) experiment. The MsExperiment package provides light-weight and flexible containers for MS experiments building on the new MS infrastructure provided by the Spectra, QFeatures and related packages. Along with raw data representations, links to original data files and sample annotations, additional metadata or annotations can also be stored within the MsExperiment container. To guarantee maximum flexibility only minimal constraints are put on the type and content of the data within the containers.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msfeatures/meta.yaml b/recipes/bioconductor-msfeatures/meta.yaml index f2f78d9cab20a..8976eed00d9db 100644 --- a/recipes/bioconductor-msfeatures/meta.yaml +++ b/recipes/bioconductor-msfeatures/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "MsFeatures" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 326a08270ef7c22e636f1fed4cf569b6 +about: + description: The MsFeature package defines functionality for Mass Spectrometry features. This includes functions to group (LC-MS) features based on some of their properties, such as retention time (coeluting features), or correlation of signals across samples. This packge hence allows to group features, and its results can be used as an input for the `QFeatures` package which allows to aggregate abundance levels of features within each group. This package defines concepts and functions for base and common data types, implementations for more specific data types are expected to be implemented in the respective packages (such as e.g. `xcms`). All functionality of this package is implemented in a modular way which allows combination of different grouping approaches and enables its re-use in other R packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Functionality for Mass Spectrometry Features build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msfeatures", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat, roxygen2, BiocStyle, pheatmap, knitr, rmarkdown requirements: host: - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base +source: + md5: 5461d524e676b4fb7d8b25d892d344db + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Functionality for Mass Spectrometry Features' - description: 'The MsFeature package defines functionality for Mass Spectrometry features. This includes functions to group (LC-MS) features based on some of their properties, such as retention time (coeluting features), or correlation of signals across samples. This packge hence allows to group features, and its results can be used as an input for the `QFeatures` package which allows to aggregate abundance levels of features within each group. This package defines concepts and functions for base and common data types, implementations for more specific data types are expected to be implemented in the respective packages (such as e.g. `xcms`). All functionality of this package is implemented in a modular way which allows combination of different grouping approaches and enables its re-use in other R packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msgbsr/meta.yaml b/recipes/bioconductor-msgbsr/meta.yaml index 945baebb54043..43149d82a41c1 100644 --- a/recipes/bioconductor-msgbsr/meta.yaml +++ b/recipes/bioconductor-msgbsr/meta.yaml @@ -1,67 +1,72 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "msgbsR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Pipeline for the anaysis of a MS-GBS experiment. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 41ae41a9216ffbe0ee9c51a91f89112c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msgbsr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: roxygen2, BSgenome.Rnorvegicus.UCSC.rn6 requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-easyrnaseq >=2.38.0,<2.39.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-easyrnaseq >=2.42.0,<2.43.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-plyr - r-r.utils run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-easyrnaseq >=2.38.0,<2.39.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-easyrnaseq >=2.42.0,<2.43.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-plyr - r-r.utils + +source: + md5: ed106032ca1ecb64cef04cb06a4a49b5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions' - description: 'Pipeline for the anaysis of a MS-GBS experiment.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msigdb/meta.yaml b/recipes/bioconductor-msigdb/meta.yaml index 04f7f6cf90356..b616aca1f9c02 100644 --- a/recipes/bioconductor-msigdb/meta.yaml +++ b/recipes/bioconductor-msigdb/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "msigdb" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides the Molecular Signatures Database (MSigDB) in a R accessible objects. Signatures are stored in GeneSet class objects form the GSEABase package and the entire database is stored in a GeneSetCollection object. These data are then hosted on the ExperimentHub. Data used in this package was obtained from the MSigDB of the Broad Institute. Metadata for each gene set is stored along with the gene set in the GeneSet class object. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: CC BY 4.0 + summary: An ExperimentHub Package for the Molecular Signatures Database (MSigDB) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eb5822dab5f9ad68cc5a46beaf626de0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msigdb", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: singscore, vissE, knitr, prettydoc, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocFileCache, GO.db, stringr, limma requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241231 + +source: + md5: 1c8a6d642d596cc654fa254d9cef809e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'CC BY 4.0' - summary: 'An ExperimentHub Package for the Molecular Signatures Database (MSigDB)' - description: 'This package provides the Molecular Signatures Database (MSigDB) in a R accessible objects. Signatures are stored in GeneSet class objects form the GSEABase package and the entire database is stored in a GeneSetCollection object. These data are then hosted on the ExperimentHub. Data used in this package was obtained from the MSigDB of the Broad Institute. Metadata for each gene set is stored along with the gene set in the GeneSet class object.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msigdb/post-link.sh b/recipes/bioconductor-msigdb/post-link.sh index 62fbfe5ec1ef4..dd0ce5dc022b1 100644 --- a/recipes/bioconductor-msigdb/post-link.sh +++ b/recipes/bioconductor-msigdb/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "msigdb-1.10.0" +installBiocDataPackage.sh "msigdb-1.14.0" diff --git a/recipes/bioconductor-msimpute/meta.yaml b/recipes/bioconductor-msimpute/meta.yaml index 3da17fd266353..6222e03236315 100644 --- a/recipes/bioconductor-msimpute/meta.yaml +++ b/recipes/bioconductor-msimpute/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "msImpute" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MsImpute is a package for imputation of peptide intensity in proteomics experiments. It additionally contains tools for MAR/MNAR diagnosis and assessment of distortions to the probability distribution of the data post imputation. The missing values are imputed by low-rank approximation of the underlying data matrix if they are MAR (method = "v2"), by Barycenter approach if missingness is MNAR ("v2-mnar"), or by Peptide Identity Propagation (PIP). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Imputation of label-free mass spectrometry peptides -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 493d744acd5f63e07590f22b2ce0eea2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msimpute", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD # SystemRequirements: python requirements: host: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-scran >=1.34.0,<1.35.0 - r-base - r-data.table - r-dplyr @@ -36,8 +38,8 @@ requirements: - r-softimpute - r-tidyr run: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-scran >=1.34.0,<1.35.0 - r-base - r-data.table - r-dplyr @@ -48,13 +50,16 @@ requirements: - r-reticulate - r-softimpute - r-tidyr + +source: + md5: d61fb8e995cf111bd63651bef4ddf496 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Imputation of label-free mass spectrometry peptides' - description: 'MsImpute is a package for imputation of peptide intensity in proteomics experiments. It additionally contains tools for MAR/MNAR diagnosis and assessment of distortions to the probability distribution of the data post imputation. The missing values are imputed by low-rank approximation of the underlying data matrix if they are MAR (method = "v2"), by Barycenter approach if missingness is MNAR ("v2-mnar"), or by Peptide Identity Propagation (PIP).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mslp/meta.yaml b/recipes/bioconductor-mslp/meta.yaml index cffb95da2b231..8d80cf2581157 100644 --- a/recipes/bioconductor-mslp/meta.yaml +++ b/recipes/bioconductor-mslp/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "mslp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An integrated pipeline to predict the potential synthetic lethality partners (SLPs) of tumour mutations, based on gene expression, mutation profiling and cell line genetic screens data. It has builtd-in support for data from cBioPortal. The primary SLPs correlating with muations in WT and compensating for the loss of function of mutations are predicted by random forest based methods (GENIE3) and Rank Products, respectively. Genetic screens are employed to identfy consensus SLPs leads to reduced cell viability when perturbed. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Predict synthetic lethal partners of tumour mutations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8d78607401143e315c9ad75923a0c9c5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mslp", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, doFuture, future, knitr, rmarkdown, roxygen2, tinytest requirements: host: - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rankprod >=3.28.0,<3.29.0' + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rankprod >=3.32.0,<3.33.0 - r-base - - 'r-data.table >=1.13.0' + - r-data.table >=1.13.0 - r-dorng - r-fmsb - r-foreach @@ -33,23 +35,26 @@ requirements: - r-proc - r-randomforest run: - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rankprod >=3.28.0,<3.29.0' + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rankprod >=3.32.0,<3.33.0 - r-base - - 'r-data.table >=1.13.0' + - r-data.table >=1.13.0 - r-dorng - r-fmsb - r-foreach - r-magrittr - r-proc - r-randomforest + +source: + md5: d1daaf0f5a6170eed32cc5462d94ee47 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Predict synthetic lethal partners of tumour mutations' - description: 'An integrated pipeline to predict the potential synthetic lethality partners (SLPs) of tumour mutations, based on gene expression, mutation profiling and cell line genetic screens data. It has builtd-in support for data from cBioPortal. The primary SLPs correlating with muations in WT and compensating for the loss of function of mutations are predicted by random forest based methods (GENIE3) and Rank Products, respectively. Genetic screens are employed to identfy consensus SLPs leads to reduced cell viability when perturbed.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msmb/meta.yaml b/recipes/bioconductor-msmb/meta.yaml index 75d847b490453..734a8fd15046c 100644 --- a/recipes/bioconductor-msmb/meta.yaml +++ b/recipes/bioconductor-msmb/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "MSMB" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bc2942708f54a40d59ce7e41daff7df0 +about: + description: Data sets for the book 'Modern Statistics for Modern Biology', S.P. Holmes and W. Huber. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Data sets for the book 'Modern Statistics for Biology' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msmb", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, BiocStyle requirements: host: @@ -28,14 +27,15 @@ requirements: - r-base - r-tibble - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5167cfe5c0b53d2cc730be93fb20218c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Data sets for the book ''Modern Statistics for Biology''' - description: 'Data sets for the book ''Modern Statistics for Modern Biology'', S.P. Holmes and W. Huber.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msmb/post-link.sh b/recipes/bioconductor-msmb/post-link.sh index 3244b61f86248..773005e5ad0df 100644 --- a/recipes/bioconductor-msmb/post-link.sh +++ b/recipes/bioconductor-msmb/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "msmb-1.20.0" +installBiocDataPackage.sh "msmb-1.24.0" diff --git a/recipes/bioconductor-msmseda/meta.yaml b/recipes/bioconductor-msmseda/meta.yaml index 71435d318c253..d664bb0478fa1 100644 --- a/recipes/bioconductor-msmseda/meta.yaml +++ b/recipes/bioconductor-msmseda/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "msmsEDA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Exploratory data analysis to assess the quality of a set of LC-MS/MS experiments, and visualize de influence of the involved factors. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Exploratory Data Analysis of LC-MS/MS data by spectral counts -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d2350677044dfea55c25faa434894cb2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msmseda", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:msmseda + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-msmseda + path: recipes/bioconductor-msmseda + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - bioconductor-msnbase >=2.32.0,<2.33.0 - r-base - r-gplots - r-mass - r-rcolorbrewer run: - - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - bioconductor-msnbase >=2.32.0,<2.33.0 - r-base - r-gplots - r-mass - r-rcolorbrewer + +source: + md5: a07c4428032e5672527fc72139d9af74 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Exploratory Data Analysis of LC-MS/MS data by spectral counts' - description: 'Exploratory data analysis to assess the quality of a set of LC-MS/MS experiments, and visualize de influence of the involved factors.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:msmseda - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-msmseda - path: recipes/bioconductor-msmseda - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msmstests/meta.yaml b/recipes/bioconductor-msmstests/meta.yaml index f842cafcbe067..92b0f130f92fb 100644 --- a/recipes/bioconductor-msmstests/meta.yaml +++ b/recipes/bioconductor-msmstests/meta.yaml @@ -1,49 +1,56 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "msmsTests" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR package.The three models admit blocking factors to control for nuissance variables.To assure a good level of reproducibility a post-test filter is available, where we may set the minimum effect size considered biologicaly relevant, and the minimum expression of the most abundant condition.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: LC-MS/MS Differential Expression Tests -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90c08df612ce3e4608ab3b9fa048764a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msmstests", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-msmstests + path: recipes/bioconductor-msmstests + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: xtable requirements: host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-msmseda >=1.40.0,<1.41.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-msmseda >=1.44.0,<1.45.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-msmseda >=1.40.0,<1.41.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-msmseda >=1.44.0,<1.45.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base + +source: + md5: abde5f7510d8e0461e5f030124a99ed3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'LC-MS/MS Differential Expression Tests' - description: 'Statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR package.The three models admit blocking factors to control for nuissance variables.To assure a good level of reproducibility a post-test filter is available, where we may set the minimum effect size considered biologicaly relevant, and the minimum expression of the most abundant condition.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - parent_recipe: - name: bioconductor-msmstests - path: recipes/bioconductor-msmstests - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msnbase/meta.yaml b/recipes/bioconductor-msnbase/meta.yaml index 9ee30e970c999..5d815d568b1e1 100644 --- a/recipes/bioconductor-msnbase/meta.yaml +++ b/recipes/bioconductor-msnbase/meta.yaml @@ -1,94 +1,103 @@ -{% set version = "2.28.1" %} +{% set version = "2.32.0" %} {% set name = "MSnbase" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Functions and Classes for Mass Spectrometry and Proteomics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d3cbd696e9ca193ec9bdc4722f2ac49 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msnbase", max_pin="x.x") }}' -# Suggests: testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.7.1), msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny, magrittr, SummarizedExperiment + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:msnbase + parent_recipe: + name: bioconductor-msnbase + path: recipes/bioconductor-msnbase + version: 2.6.4 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.43.3), magick, msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, XML, shiny, magrittr, SummarizedExperiment requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-mzid >=1.40.0,<1.41.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-mzid >=1.44.0,<1.45.0 + - bioconductor-mzr >=2.40.0,<2.41.0 + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-psmatch >=1.10.0,<1.11.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-base - r-digest - r-ggplot2 - r-lattice - - 'r-maldiquant >=1.16' + - r-maldiquant >=1.16 - r-mass - r-plyr - r-rcpp - r-scales - - r-xml - libblas - liblapack + run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-mzid >=1.40.0,<1.41.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-mzid >=1.44.0,<1.45.0 + - bioconductor-mzr >=2.40.0,<2.41.0 + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-psmatch >=1.10.0,<1.11.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-base - r-digest - r-ggplot2 - r-lattice - - 'r-maldiquant >=1.16' + - r-maldiquant >=1.16 - r-mass - r-plyr - r-rcpp - r-scales - - r-xml - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: c9ddc0c7d42dbfa22cff5683a41a27de + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Functions and Classes for Mass Spectrometry and Proteomics' - description: 'MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:msnbase - parent_recipe: - name: bioconductor-msnbase - path: recipes/bioconductor-msnbase - version: 2.6.4 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msnid/meta.yaml b/recipes/bioconductor-msnid/meta.yaml index 2c78af9e2fe61..5c57370a7ff00 100644 --- a/recipes/bioconductor-msnid/meta.yaml +++ b/recipes/bioconductor-msnid/meta.yaml @@ -1,36 +1,51 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "MSnID" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. Also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e0491fe4f99deb1c0128ab4dcde8f3f3 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msnid", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:msnid + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-msnid + path: recipes/bioconductor-msnid + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-msmstests >=1.40.0,<1.41.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-mzid >=1.40.0,<1.41.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-msmstests >=1.44.0,<1.45.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-mzid >=1.44.0,<1.45.0 + - bioconductor-mzr >=2.40.0,<2.41.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 - r-base - r-data.table - r-doparallel @@ -49,18 +64,19 @@ requirements: - r-xtable - libblas - liblapack + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-msmstests >=1.40.0,<1.41.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-mzid >=1.40.0,<1.41.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-msmstests >=1.44.0,<1.45.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-mzid >=1.44.0,<1.45.0 + - bioconductor-mzr >=2.40.0,<2.41.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 - r-base - r-data.table - r-doparallel @@ -77,23 +93,16 @@ requirements: - r-stringr - r-tibble - r-xtable - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} + +source: + md5: d9352491f61b466b73346733d8e2c3f4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications' - description: 'Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. Also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.' -extra: - identifiers: - - biotools:msnid - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-msnid - path: recipes/bioconductor-msnid - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msprep/meta.yaml b/recipes/bioconductor-msprep/meta.yaml index a6f5d896e023c..7cbacc9a5162a 100644 --- a/recipes/bioconductor-msprep/meta.yaml +++ b/recipes/bioconductor-msprep/meta.yaml @@ -1,65 +1,70 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "MSPrep" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package performs summarization of replicates, filtering by frequency, several different options for imputing missing data, and a variety of options for transforming, batch correcting, and normalizing data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Package for Summarizing, Filtering, Imputing, and Normalizing Metabolomics Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 65036a0ebe0b1280a2c4666c263a6e5f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msprep", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 1.0.2) requirements: host: - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-crmn - - 'r-dplyr >=0.7' + - r-dplyr >=0.7 - r-magrittr - r-missforest - r-rlang - r-stringr - - 'r-tibble >=1.2' + - r-tibble >=1.2 - r-tidyr - r-vim run: - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-crmn - - 'r-dplyr >=0.7' + - r-dplyr >=0.7 - r-magrittr - r-missforest - r-rlang - r-stringr - - 'r-tibble >=1.2' + - r-tibble >=1.2 - r-tidyr - r-vim + +source: + md5: a2b1d61abb6952ece54996955b432914 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Package for Summarizing, Filtering, Imputing, and Normalizing Metabolomics Data' - description: 'Package performs summarization of replicates, filtering by frequency, several different options for imputing missing data, and a variety of options for transforming, batch correcting, and normalizing data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mspurity/meta.yaml b/recipes/bioconductor-mspurity/meta.yaml index 3dcb43f28b697..53bed454247f7 100644 --- a/recipes/bioconductor-mspurity/meta.yaml +++ b/recipes/bioconductor-mspurity/meta.yaml @@ -1,27 +1,41 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "msPurity" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'msPurity R package was developed to: 1) Assess the spectral quality of fragmentation spectra by evaluating the "precursor ion purity". 2) Process fragmentation spectra. 3) Perform spectral matching. What is precursor ion purity? -What we call "Precursor ion purity" is a measure of the contribution of a selected precursor peak in an isolation window used for fragmentation. The simple calculation involves dividing the intensity of the selected precursor peak by the total intensity of the isolation window. When assessing MS/MS spectra this calculation is done before and after the MS/MS scan of interest and the purity is interpolated at the recorded time of the MS/MS acquisition. Additionally, isotopic peaks can be removed, low abundance peaks are removed that are thought to have limited contribution to the resulting MS/MS spectra and the isolation efficiency of the mass spectrometer can be used to normalise the intensities used for the calculation.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0a29b8f3eacf707bf9791d50df53083a build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mspurity", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:mspurity + - doi:10.1021/acs.analchem.6b04358 + parent_recipe: + name: bioconductor-mspurity + path: recipes/bioconductor-mspurity + version: 1.6.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA, RPostgres, RMySQL requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - - 'bioconductor-mzr >=2.36.0,<2.37.0' + - bioconductor-mzr >=2.40.0,<2.41.0 - r-base - r-dbi - r-dbplyr @@ -39,7 +53,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-mzr >=2.36.0,<2.37.0' + - bioconductor-mzr >=2.40.0,<2.41.0 - r-base - r-dbi - r-dbplyr @@ -54,24 +68,16 @@ requirements: - r-reshape2 - r-rsqlite - r-stringr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} + +source: + md5: 9ee3a37b16cd9b35ace687b729c012f4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics' - description: 'msPurity R package was developed to: 1) Assess the spectral quality of fragmentation spectra by evaluating the "precursor ion purity". 2) Process fragmentation spectra. 3) Perform spectral matching. What is precursor ion purity? -What we call "Precursor ion purity" is a measure of the contribution of a selected precursor peak in an isolation window used for fragmentation. The simple calculation involves dividing the intensity of the selected precursor peak by the total intensity of the isolation window. When assessing MS/MS spectra this calculation is done before and after the MS/MS scan of interest and the purity is interpolated at the recorded time of the MS/MS acquisition. Additionally, isotopic peaks can be removed, low abundance peaks are removed that are thought to have limited contribution to the resulting MS/MS spectra and the isolation efficiency of the mass spectrometer can be used to normalise the intensities used for the calculation.' - license_file: LICENSE -extra: - identifiers: - - biotools:mspurity - - doi:10.1021/acs.analchem.6b04358 - parent_recipe: - name: bioconductor-mspurity - path: recipes/bioconductor-mspurity - version: 1.6.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mspuritydata/meta.yaml b/recipes/bioconductor-mspuritydata/meta.yaml index 52332729fbed8..a3f13ebc12a97 100644 --- a/recipes/bioconductor-mspuritydata/meta.yaml +++ b/recipes/bioconductor-mspuritydata/meta.yaml @@ -1,24 +1,28 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "msPurityData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6c86343515cbb9f81131baa3f25659f0 +about: + description: Fragmentation spectral libraries and data to test the msPurity package + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Fragmentation spectral libraries and data to test the msPurity package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mspuritydata", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-mspuritydata + path: recipes/bioconductor-mspuritydata + version: 1.8.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr requirements: host: @@ -26,19 +30,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c167bd73ab7483ee04320b8a18824b03 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Fragmentation spectral libraries and data to test the msPurity package' - description: 'Fragmentation spectral libraries and data to test the msPurity package' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-mspuritydata - path: recipes/bioconductor-mspuritydata - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mspuritydata/post-link.sh b/recipes/bioconductor-mspuritydata/post-link.sh index 7b9e5d412b057..f698d248a4b83 100644 --- a/recipes/bioconductor-mspuritydata/post-link.sh +++ b/recipes/bioconductor-mspuritydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mspuritydata-1.30.0" +installBiocDataPackage.sh "mspuritydata-1.34.0" diff --git a/recipes/bioconductor-msqc1/meta.yaml b/recipes/bioconductor-msqc1/meta.yaml index b1e92a856601d..91274bb82d0bc 100644 --- a/recipes/bioconductor-msqc1/meta.yaml +++ b/recipes/bioconductor-msqc1/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "msqc1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a95a760a0c0ef5e8053acee1d59170a4 +about: + description: contains eight technical replicate data set and a three replicate dilution series of the MS Qual/Quant Quality Control Mix standard sample (Sigma-Aldrich, Buchs, Switzerland) measured on five different mass spectrometer platforms at the Functional Genomics Center Zurich. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Sigma mix MSQC1 data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msqc1", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat, specL (>= 1.2) requirements: host: @@ -28,14 +27,15 @@ requirements: - r-base - r-lattice - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: db71d1e332bca83be8180f47fab9bd14 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL - summary: 'Sigma mix MSQC1 data' - description: 'contains eight technical replicate data set and a three replicate dilution series of the MS Qual/Quant Quality Control Mix standard sample (Sigma-Aldrich, Buchs, Switzerland) measured on five different mass spectrometer platforms at the Functional Genomics Center Zurich.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msqc1/post-link.sh b/recipes/bioconductor-msqc1/post-link.sh index 7c052c8f8c306..6753e7715c48e 100644 --- a/recipes/bioconductor-msqc1/post-link.sh +++ b/recipes/bioconductor-msqc1/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "msqc1-1.30.0" +installBiocDataPackage.sh "msqc1-1.34.0" diff --git a/recipes/bioconductor-msqrob2/meta.yaml b/recipes/bioconductor-msqrob2/meta.yaml index 5084c4368d7b3..819fc8217d7cf 100644 --- a/recipes/bioconductor-msqrob2/meta.yaml +++ b/recipes/bioconductor-msqrob2/meta.yaml @@ -1,32 +1,33 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "msqrob2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: msqrob2 provides a robust linear mixed model framework for assessing differential abundance in MS-based Quantitative proteomics experiments. Our workflows can start from raw peptide intensities or summarised protein expression values. The model parameter estimates can be stabilized by ridge regression, empirical Bayes variance estimation and robust M-estimation. msqrob2's hurde workflow can handle missing data without having to rely on hard-to-verify imputation assumptions, and, outcompetes state-of-the-art methods with and without imputation for both high and low missingness. It builds on QFeature infrastructure for quantitative mass spectrometry data to store the model results together with the raw data and preprocessed data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Robust statistical inference for quantitative LC-MS proteomics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b2c0046b0c67c24dd7d94eeb22fea3a8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msqrob2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: multcomp, gridExtra, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown, testthat, tidyverse, plotly, msdata, MSnbase, matrixStats, MsCoreUtils, covr requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-qfeatures >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-qfeatures >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-codetools - r-lme4 @@ -34,23 +35,27 @@ requirements: - r-matrix - r-purrr run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-qfeatures >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-qfeatures >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-codetools - r-lme4 - r-mass - r-matrix - r-purrr + +source: + md5: 2b4681f68211250f3fbd3e73ec0ad4a6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Robust statistical inference for quantitative LC-MS proteomics' - description: 'msqrob2 provides a robust linear mixed model framework for assessing differential abundance in MS-based Quantitative proteomics experiments. Our workflows can start from raw peptide intensities or summarised protein expression values. The model parameter estimates can be stabilized by ridge regression, empirical Bayes variance estimation and robust M-estimation. msqrob2''s hurde workflow can handle missing data without having to rely on hard-to-verify imputation assumptions, and, outcompetes state-of-the-art methods with and without imputation for both high and low missingness. It builds on QFeature infrastructure for quantitative mass spectrometry data to store the model results together with the raw data and preprocessed data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msquality/meta.yaml b/recipes/bioconductor-msquality/meta.yaml index 541bf61068252..38f63468ab936 100644 --- a/recipes/bioconductor-msquality/meta.yaml +++ b/recipes/bioconductor-msquality/meta.yaml @@ -1,65 +1,72 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "MsQuality" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The MsQuality provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics defined by the Human Proteom Organization-Proteomics Standards Initiative (HUPO-PSI). These metrics quantify the quality of spectral raw files using a controlled vocabulary. The package is especially addressed towards users that acquire mass spectrometry data on a large scale (e.g. data sets from clinical settings consisting of several thousands of samples). The MsQuality package allows to calculate low-level quality metrics that require minimum information on mass spectrometry data: retention time, m/z values, and associated intensities. MsQuality relies on the Spectra package, or alternatively the MsExperiment package, and its infrastructure to store spectral data.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: MsQuality - Quality metric calculation from Spectra and MsExperiment objects -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d8e2101f472e8fc93bfa275db511982 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msquality", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), dplyr (>= 1.0.5), knitr (>= 1.11), mzR (>= 2.32.0), rmarkdown (>= 2.7), S4Vectors (>= 0.29.17), testthat (>= 2.2.1) requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-msdata >=0.42.0,<0.43.0' - - 'bioconductor-msexperiment >=1.4.0,<1.5.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-msdata >=0.46.0,<0.47.0 + - bioconductor-msexperiment >=1.8.0,<1.9.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-spectra >=1.16.0,<1.17.0 - r-base - - 'r-ggplot2 >=3.3.5' - - 'r-htmlwidgets >=1.5.3' - - 'r-plotly >=4.9.4.1' - - 'r-rmzqc >=0.5.0' - - 'r-shiny >=1.6.0' - - 'r-shinydashboard >=0.7.1' - - 'r-stringr >=1.4.0' - - 'r-tibble >=3.1.4' - - 'r-tidyr >=1.1.3' + - r-ggplot2 >=3.3.5 + - r-htmlwidgets >=1.5.3 + - r-plotly >=4.9.4.1 + - r-rlang >=1.1.1 + - r-rmzqc >=0.5.0 + - r-shiny >=1.6.0 + - r-shinydashboard >=0.7.1 + - r-stringr >=1.4.0 + - r-tibble >=3.1.4 + - r-tidyr >=1.1.3 run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-msdata >=0.42.0,<0.43.0' - - 'bioconductor-msexperiment >=1.4.0,<1.5.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-msdata >=0.46.0,<0.47.0 + - bioconductor-msexperiment >=1.8.0,<1.9.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-spectra >=1.16.0,<1.17.0 - r-base - - 'r-ggplot2 >=3.3.5' - - 'r-htmlwidgets >=1.5.3' - - 'r-plotly >=4.9.4.1' - - 'r-rmzqc >=0.5.0' - - 'r-shiny >=1.6.0' - - 'r-shinydashboard >=0.7.1' - - 'r-stringr >=1.4.0' - - 'r-tibble >=3.1.4' - - 'r-tidyr >=1.1.3' + - r-ggplot2 >=3.3.5 + - r-htmlwidgets >=1.5.3 + - r-plotly >=4.9.4.1 + - r-rlang >=1.1.1 + - r-rmzqc >=0.5.0 + - r-shiny >=1.6.0 + - r-shinydashboard >=0.7.1 + - r-stringr >=1.4.0 + - r-tibble >=3.1.4 + - r-tidyr >=1.1.3 + +source: + md5: 4f5ec7a8df26bc6542bb6d3f2a7b9a6b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'MsQuality - Quality metric calculation from Spectra and MsExperiment objects' - description: 'The MsQuality provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics defined by the Human Proteom Organization-Proteomics Standards Initiative (HUPO-PSI). These metrics quantify the quality of spectral raw files using a controlled vocabulary. The package is especially addressed towards users that acquire mass spectrometry data on a large scale (e.g. data sets from clinical settings consisting of several thousands of samples). The MsQuality package allows to calculate low-level quality metrics that require minimum information on mass spectrometry data: retention time, m/z values, and associated intensities. MsQuality relies on the Spectra package, or alternatively the MsExperiment package, and its infrastructure to store spectral data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msstats/meta.yaml b/recipes/bioconductor-msstats/meta.yaml index 16e7cd6050d08..fdec240ceb2d3 100644 --- a/recipes/bioconductor-msstats/meta.yaml +++ b/recipes/bioconductor-msstats/meta.yaml @@ -1,80 +1,93 @@ -{% set version = "4.10.0" %} +{% set version = "4.14.0" %} {% set name = "MSstats" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A set of tools for statistical relative protein significance analysis in DDA, SRM and DIA experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fac3a495f2e627a75b10a9b941d3674d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msstats", max_pin="x.x") }}' -# Suggests: BiocStyle, knitr, rmarkdown, tinytest, covr, markdown + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:msstats + parent_recipe: + name: bioconductor-msstats + path: recipes/bioconductor-msstats + version: 3.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, tinytest, covr, markdown, mockery requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' - - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-marray >=1.84.0,<1.85.0 + - bioconductor-msstatsconvert >=1.16.0,<1.17.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-checkmate - r-data.table - r-ggplot2 - r-ggrepel - r-gplots + - r-htmltools - r-lme4 - r-mass + - r-plotly - r-rcpp - r-rcpparmadillo - r-statmod - r-survival - libblas - liblapack + run: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' - - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-marray >=1.84.0,<1.85.0 + - bioconductor-msstatsconvert >=1.16.0,<1.17.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-checkmate - r-data.table - r-ggplot2 - r-ggrepel - r-gplots + - r-htmltools - r-lme4 - r-mass + - r-plotly - r-rcpp - r-rcpparmadillo - r-statmod - r-survival - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: abb7d32f3e6b04a3353c31f64d250ba7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments' - description: 'A set of tools for statistical relative protein significance analysis in DDA, SRM and DIA experiments.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:msstats - parent_recipe: - name: bioconductor-msstats - path: recipes/bioconductor-msstats - version: 3.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msstatsbig/meta.yaml b/recipes/bioconductor-msstatsbig/meta.yaml index 18aabd0559ba2..c255d567c5e5f 100644 --- a/recipes/bioconductor-msstatsbig/meta.yaml +++ b/recipes/bioconductor-msstatsbig/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "MSstatsBig" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MSstats package provide tools for preprocessing, summarization and differential analysis of mass spectrometry (MS) proteomics data. Recently, some MS protocols enable acquisition of data sets that result in larger than memory quantitative data. MSstats functions are not able to process such data. MSstatsBig package provides additional converter functions that enable processing larger than memory data sets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: MSstats Preprocessing for Larger than Memory Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a53de589b47964296160c6fb8aaeb3b4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msstatsbig", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-msstats >=4.10.0,<4.11.0' - - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - bioconductor-msstats >=4.14.0,<4.15.0 + - bioconductor-msstatsconvert >=1.16.0,<1.17.0 - r-arrow - r-base - r-dbi @@ -31,20 +32,24 @@ requirements: - r-readr - r-sparklyr run: - - 'bioconductor-msstats >=4.10.0,<4.11.0' - - 'bioconductor-msstatsconvert >=1.12.0,<1.13.0' + - bioconductor-msstats >=4.14.0,<4.15.0 + - bioconductor-msstatsconvert >=1.16.0,<1.17.0 - r-arrow - r-base - r-dbi - r-dplyr - r-readr - r-sparklyr + +source: + md5: f3cf3db1d4b71e96112666fabfbdb172 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'MSstats Preprocessing for Larger than Memory Data' - description: 'MSstats package provide tools for preprocessing, summarization and differential analysis of mass spectrometry (MS) proteomics data. Recently, some MS protocols enable acquisition of data sets that result in larger than memory quantitative data. MSstats functions are not able to process such data. MSstatsBig package provides additional converter functions that enable processing larger than memory data sets.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msstatsconvert/meta.yaml b/recipes/bioconductor-msstatsconvert/meta.yaml index f5eb9823683aa..9c6516f5e5a56 100644 --- a/recipes/bioconductor-msstatsconvert/meta.yaml +++ b/recipes/bioconductor-msstatsconvert/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "MSstatsConvert" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a8b79ba830db5296c2d3f589b398b7f +about: + description: MSstatsConvert provides tools for importing reports of Mass Spectrometry data processing tools into R format suitable for statistical analysis using the MSstats and MSstatsTMT packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msstatsconvert", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: tinytest, covr, knitr, rmarkdown requirements: host: @@ -33,12 +31,14 @@ requirements: - r-data.table - r-log4r - r-stringi +source: + md5: a684228ee2dd985547a0876549c25e2f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format' - description: 'MSstatsConvert provides tools for importing reports of Mass Spectrometry data processing tools into R format suitable for statistical analysis using the MSstats and MSstatsTMT packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msstatslobd/meta.yaml b/recipes/bioconductor-msstatslobd/meta.yaml index a464e413da1ea..1c4fa9fc295cb 100644 --- a/recipes/bioconductor-msstatslobd/meta.yaml +++ b/recipes/bioconductor-msstatslobd/meta.yaml @@ -1,25 +1,29 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "MSstatsLOBD" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The MSstatsLOBD package allows calculation and visualization of limit of blac (LOB) and limit of detection (LOD). We define the LOB as the highest apparent concentration of a peptide expected when replicates of a blank sample containing no peptides are measured. The LOD is defined as the measured concentration value for which the probability of falsely claiming the absence of a peptide in the sample is 0.05, given a probability 0.05 of falsely claiming its presence. These functionalities were previously a part of the MSstats package. The methodology is described in Galitzine (2018) . + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1d67c5813cb057b72100d71487c26f64 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msstatslobd", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - r-base - r-ggplot2 @@ -32,15 +36,16 @@ requirements: - r-ggplot2 - r-minpack.lm - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} + +source: + md5: 6d7e14a6035c0e417dbb473156e4b90b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)' - description: 'The MSstatsLOBD package allows calculation and visualization of limit of blac (LOB) and limit of detection (LOD). We define the LOB as the highest apparent concentration of a peptide expected when replicates of a blank sample containing no peptides are measured. The LOD is defined as the measured concentration value for which the probability of falsely claiming the absence of a peptide in the sample is 0.05, given a probability 0.05 of falsely claiming its presence. These functionalities were previously a part of the MSstats package. The methodology is described in Galitzine (2018) .' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msstatsqc/meta.yaml b/recipes/bioconductor-msstatsqc/meta.yaml index fd453766efc47..914330dead4c1 100644 --- a/recipes/bioconductor-msstatsqc/meta.yaml +++ b/recipes/bioconductor-msstatsqc/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "2.20.0" %} +{% set version = "2.24.0" %} {% set name = "MSstatsQC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MSstatsQC is an R package which provides longitudinal system suitability monitoring and quality control tools for proteomic experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic License 2.0 + summary: Longitudinal system suitability monitoring and quality control for proteomic experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9328babd37ae774a13dff37e38088339 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msstatsqc", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-msstatsqc + path: recipes/bioconductor-msstatsqc + version: 2.0.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr,rmarkdown, testthat, RforProteomics requirements: host: - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-qcmetrics >=1.40.0,<1.41.0' + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-qcmetrics >=1.44.0,<1.45.0 - r-base - r-dplyr - r-ggextra - r-ggplot2 - r-plotly run: - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-qcmetrics >=1.40.0,<1.41.0' + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-qcmetrics >=1.44.0,<1.45.0 - r-base - r-dplyr - r-ggextra - r-ggplot2 - r-plotly + +source: + md5: b6b4b784a37b007476612961d003097d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Artistic License 2.0' - summary: 'Longitudinal system suitability monitoring and quality control for proteomic experiments' - description: 'MSstatsQC is an R package which provides longitudinal system suitability monitoring and quality control tools for proteomic experiments.' -extra: - parent_recipe: - name: bioconductor-msstatsqc - path: recipes/bioconductor-msstatsqc - version: 2.0.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-msstatsqcgui/meta.yaml b/recipes/bioconductor-msstatsqcgui/meta.yaml index acb4bf4a02184..647b09c2446fd 100644 --- a/recipes/bioconductor-msstatsqcgui/meta.yaml +++ b/recipes/bioconductor-msstatsqcgui/meta.yaml @@ -1,28 +1,35 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "MSstatsQCgui" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MSstatsQCgui is a Shiny app which provides longitudinal system suitability monitoring and quality control tools for proteomic experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic License 2.0 + summary: A graphical user interface for MSstatsQC package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1e648f2226907f737e1d7e71a375f01c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-msstatsqcgui", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-msstatsqcgui + path: recipes/bioconductor-msstatsqcgui + version: 1.2.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: host: - - 'bioconductor-msstatsqc >=2.20.0,<2.21.0' + - bioconductor-msstatsqc >=2.24.0,<2.25.0 - r-base - r-dplyr - r-ggextra @@ -30,24 +37,23 @@ requirements: - r-plotly - r-shiny run: - - 'bioconductor-msstatsqc >=2.20.0,<2.21.0' + - bioconductor-msstatsqc >=2.24.0,<2.25.0 - r-base - r-dplyr - r-ggextra - r-gridextra - r-plotly - r-shiny + +source: + md5: d788a5c9a6e00f4681e60f76b0301a39 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Artistic License 2.0' - summary: 'A graphical user interface for MSstatsQC package' - description: 'MSstatsQCgui is a Shiny app which provides longitudinal system suitability monitoring and quality control tools for proteomic experiments.' -extra: - parent_recipe: - name: bioconductor-msstatsqcgui - path: recipes/bioconductor-msstatsqcgui - version: 1.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mta10probeset.db/meta.yaml b/recipes/bioconductor-mta10probeset.db/meta.yaml index 6e88a7ceb061d..66e2acea518f2 100644 --- a/recipes/bioconductor-mta10probeset.db/meta.yaml +++ b/recipes/bioconductor-mta10probeset.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "mta10probeset.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 84517c6b354690cd72ccefbe3b39d8e1 +about: + description: Affymetrix mta10 annotation data (chip mta10probeset) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix mta10 annotation data (chip mta10probeset) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mta10probeset.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 84517c6b354690cd72ccefbe3b39d8e1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix mta10 annotation data (chip mta10probeset)' - description: 'Affymetrix mta10 annotation data (chip mta10probeset) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mta10transcriptcluster.db/meta.yaml b/recipes/bioconductor-mta10transcriptcluster.db/meta.yaml index 9a39f45852b4d..6864c9241b014 100644 --- a/recipes/bioconductor-mta10transcriptcluster.db/meta.yaml +++ b/recipes/bioconductor-mta10transcriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "mta10transcriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bfd13b16b71ac2cfc82f40f2d102892b +about: + description: Affymetrix mta10 annotation data (chip mta10transcriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix mta10 annotation data (chip mta10transcriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mta10transcriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bfd13b16b71ac2cfc82f40f2d102892b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix mta10 annotation data (chip mta10transcriptcluster)' - description: 'Affymetrix mta10 annotation data (chip mta10transcriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mtbls2/meta.yaml b/recipes/bioconductor-mtbls2/meta.yaml index fb928253ee251..7e67777b358ca 100644 --- a/recipes/bioconductor-mtbls2/meta.yaml +++ b/recipes/bioconductor-mtbls2/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "mtbls2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 820109836c79f398ea5b82f5887b7fea +about: + description: Indole-3-acetaldoxime (IAOx) represents an early intermediate of the biosynthesis of a variety of indolic secondary metabolites including the phytoanticipin indol-3-ylmethyl glucosinolate and the phytoalexin camalexin (3-thiazol-2'-yl-indole). Arabidopsis thaliana cyp79B2 cyp79B3 double knockout plants are completely impaired in the conversion of tryptophan to indole-3-acetaldoxime and do not accumulate IAOx-derived metabolites any longer. Consequently, comparative analysis of wild-type and cyp79B2 cyp79B3 plant lines has the potential to explore the complete range of IAOx-derived indolic secondary metabolites. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: CC0 + summary: 'MetaboLights MTBLS2: Comparative LC/MS-based profiling of silver nitrate-treated Arabidopsis thaliana leaves of wild-type and cyp79B2 cyp79B3 double knockout plants. Böttcher et al. (2004)' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mtbls2", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: xcms (>= 3.13.8), CAMERA, Risa (>= 1.0.0), knitr, Heatplus, pcaMethods, sp, rmarkdown requirements: host: @@ -26,13 +24,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 79a28f68b38f98d6ce03a37e9c345eca + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: CC0 - summary: 'MetaboLights MTBLS2: Comparative LC/MS-based profiling of silver nitrate-treated Arabidopsis thaliana leaves of wild-type and cyp79B2 cyp79B3 double knockout plants. Böttcher et al. (2004)' - description: 'Indole-3-acetaldoxime (IAOx) represents an early intermediate of the biosynthesis of a variety of indolic secondary metabolites including the phytoanticipin indol-3-ylmethyl glucosinolate and the phytoalexin camalexin (3-thiazol-2''-yl-indole). Arabidopsis thaliana cyp79B2 cyp79B3 double knockout plants are completely impaired in the conversion of tryptophan to indole-3-acetaldoxime and do not accumulate IAOx-derived metabolites any longer. Consequently, comparative analysis of wild-type and cyp79B2 cyp79B3 plant lines has the potential to explore the complete range of IAOx-derived indolic secondary metabolites.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mtbls2/post-link.sh b/recipes/bioconductor-mtbls2/post-link.sh index 0ef2e910328f4..e9fd1fccc89bc 100644 --- a/recipes/bioconductor-mtbls2/post-link.sh +++ b/recipes/bioconductor-mtbls2/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mtbls2-1.32.0" +installBiocDataPackage.sh "mtbls2-1.36.0" diff --git a/recipes/bioconductor-mu11ksuba.db/meta.yaml b/recipes/bioconductor-mu11ksuba.db/meta.yaml index b55de485fc588..7bfa1a8cf6a24 100644 --- a/recipes/bioconductor-mu11ksuba.db/meta.yaml +++ b/recipes/bioconductor-mu11ksuba.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "mu11ksuba.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 73d80611d1eaf8ee1eb37ebc469d97e9 +about: + description: Affymetrix Affymetrix Mu11KsubA Array annotation data (chip mu11ksuba) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Mu11KsubA Array annotation data (chip mu11ksuba) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mu11ksuba.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 73d80611d1eaf8ee1eb37ebc469d97e9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Mu11KsubA Array annotation data (chip mu11ksuba)' - description: 'Affymetrix Affymetrix Mu11KsubA Array annotation data (chip mu11ksuba) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mu11ksubacdf/meta.yaml b/recipes/bioconductor-mu11ksubacdf/meta.yaml index b59ac2145b73a..210ec751e4bfe 100644 --- a/recipes/bioconductor-mu11ksubacdf/meta.yaml +++ b/recipes/bioconductor-mu11ksubacdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mu11ksubacdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 52fb8ac56435775022fb62f40efafd22 +about: + description: A package containing an environment representing the Mu11KsubA.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mu11ksubacdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mu11ksubacdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 52fb8ac56435775022fb62f40efafd22 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mu11ksubacdf - description: 'A package containing an environment representing the Mu11KsubA.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mu11ksubaprobe/meta.yaml b/recipes/bioconductor-mu11ksubaprobe/meta.yaml index dcedba4948626..f5dc19febeb15 100644 --- a/recipes/bioconductor-mu11ksubaprobe/meta.yaml +++ b/recipes/bioconductor-mu11ksubaprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mu11ksubaprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 813cd0750cca6ff0cfb696b83286177e +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Mu11KsubA\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type mu11ksuba build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mu11ksubaprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 813cd0750cca6ff0cfb696b83286177e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type mu11ksuba' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Mu11KsubA\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mu11ksubb.db/meta.yaml b/recipes/bioconductor-mu11ksubb.db/meta.yaml index 63bb7d8ea3a05..226bddca7c9a3 100644 --- a/recipes/bioconductor-mu11ksubb.db/meta.yaml +++ b/recipes/bioconductor-mu11ksubb.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "mu11ksubb.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2b61d911c3595843e80041949cb79b41 +about: + description: Affymetrix Affymetrix Mu11KsubB Array annotation data (chip mu11ksubb) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Mu11KsubB Array annotation data (chip mu11ksubb) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mu11ksubb.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2b61d911c3595843e80041949cb79b41 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Mu11KsubB Array annotation data (chip mu11ksubb)' - description: 'Affymetrix Affymetrix Mu11KsubB Array annotation data (chip mu11ksubb) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mu11ksubbcdf/meta.yaml b/recipes/bioconductor-mu11ksubbcdf/meta.yaml index c998c26278a66..d042fcb6631de 100644 --- a/recipes/bioconductor-mu11ksubbcdf/meta.yaml +++ b/recipes/bioconductor-mu11ksubbcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mu11ksubbcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f9691ea74e19dfe57bf6cca6ed396947 +about: + description: A package containing an environment representing the Mu11KsubB.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mu11ksubbcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mu11ksubbcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f9691ea74e19dfe57bf6cca6ed396947 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mu11ksubbcdf - description: 'A package containing an environment representing the Mu11KsubB.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mu11ksubbprobe/meta.yaml b/recipes/bioconductor-mu11ksubbprobe/meta.yaml index 8b5ab818deb4d..c8c17762e0406 100644 --- a/recipes/bioconductor-mu11ksubbprobe/meta.yaml +++ b/recipes/bioconductor-mu11ksubbprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mu11ksubbprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 28d162e18e4e16e3c6db47195d2ea0ac +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Mu11KsubB\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type mu11ksubb build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mu11ksubbprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 28d162e18e4e16e3c6db47195d2ea0ac + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type mu11ksubb' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Mu11KsubB\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mu15v1.db/meta.yaml b/recipes/bioconductor-mu15v1.db/meta.yaml index 74f2380efbe7e..6ec9141dc2243 100644 --- a/recipes/bioconductor-mu15v1.db/meta.yaml +++ b/recipes/bioconductor-mu15v1.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "Mu15v1.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e9297b5fe223b046bc65dc6ea0b4376d +about: + description: FHCRC Genomics Shared Resource Mu15v1 Annotation Data (Mu15v1) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: FHCRC Genomics Shared Resource Mu15v1 Annotation Data (Mu15v1) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mu15v1.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e9297b5fe223b046bc65dc6ea0b4376d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'FHCRC Genomics Shared Resource Mu15v1 Annotation Data (Mu15v1)' - description: 'FHCRC Genomics Shared Resource Mu15v1 Annotation Data (Mu15v1) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mu19ksuba.db/meta.yaml b/recipes/bioconductor-mu19ksuba.db/meta.yaml index 35416f946ef4e..d0fe05b034ae5 100644 --- a/recipes/bioconductor-mu19ksuba.db/meta.yaml +++ b/recipes/bioconductor-mu19ksuba.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "mu19ksuba.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c057d8793f2db914a93d2e1f5a3af178 +about: + description: Affymetrix Affymetrix Mu19KsubA Array annotation data (chip mu19ksuba) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Mu19KsubA Array annotation data (chip mu19ksuba) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mu19ksuba.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c057d8793f2db914a93d2e1f5a3af178 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Mu19KsubA Array annotation data (chip mu19ksuba)' - description: 'Affymetrix Affymetrix Mu19KsubA Array annotation data (chip mu19ksuba) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mu19ksubacdf/meta.yaml b/recipes/bioconductor-mu19ksubacdf/meta.yaml index 795c51c9e9101..c43f1d09f3ecd 100644 --- a/recipes/bioconductor-mu19ksubacdf/meta.yaml +++ b/recipes/bioconductor-mu19ksubacdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mu19ksubacdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 83a9e7a3bac665b655786e66dbd77848 +about: + description: A package containing an environment representing the Mu19KsubA.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mu19ksubacdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mu19ksubacdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 83a9e7a3bac665b655786e66dbd77848 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mu19ksubacdf - description: 'A package containing an environment representing the Mu19KsubA.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mu19ksubb.db/meta.yaml b/recipes/bioconductor-mu19ksubb.db/meta.yaml index 0dcbb94ef24d0..09b3119573b06 100644 --- a/recipes/bioconductor-mu19ksubb.db/meta.yaml +++ b/recipes/bioconductor-mu19ksubb.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "mu19ksubb.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1b177a3b5626c825c91e7c25e0acd897 +about: + description: Affymetrix Affymetrix Mu19KsubB Array annotation data (chip mu19ksubb) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Mu19KsubB Array annotation data (chip mu19ksubb) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mu19ksubb.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1b177a3b5626c825c91e7c25e0acd897 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Mu19KsubB Array annotation data (chip mu19ksubb)' - description: 'Affymetrix Affymetrix Mu19KsubB Array annotation data (chip mu19ksubb) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mu19ksubbcdf/meta.yaml b/recipes/bioconductor-mu19ksubbcdf/meta.yaml index f36b278a44c54..b615e85eb860d 100644 --- a/recipes/bioconductor-mu19ksubbcdf/meta.yaml +++ b/recipes/bioconductor-mu19ksubbcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mu19ksubbcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 35e5ebcb4cb51950a85c1e3622bb39f0 +about: + description: A package containing an environment representing the Mu19KsubB.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mu19ksubbcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mu19ksubbcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 35e5ebcb4cb51950a85c1e3622bb39f0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mu19ksubbcdf - description: 'A package containing an environment representing the Mu19KsubB.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mu19ksubc.db/meta.yaml b/recipes/bioconductor-mu19ksubc.db/meta.yaml index 2a6ec8567e56b..a9ee7141a7f0a 100644 --- a/recipes/bioconductor-mu19ksubc.db/meta.yaml +++ b/recipes/bioconductor-mu19ksubc.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "mu19ksubc.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bef37c9cd01032e9f1fb177a1af8cba4 +about: + description: Affymetrix Affymetrix Mu19KsubC Array annotation data (chip mu19ksubc) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Mu19KsubC Array annotation data (chip mu19ksubc) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mu19ksubc.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bef37c9cd01032e9f1fb177a1af8cba4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Mu19KsubC Array annotation data (chip mu19ksubc)' - description: 'Affymetrix Affymetrix Mu19KsubC Array annotation data (chip mu19ksubc) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mu19ksubccdf/meta.yaml b/recipes/bioconductor-mu19ksubccdf/meta.yaml index a36c87e66abc3..a8158ea7cad85 100644 --- a/recipes/bioconductor-mu19ksubccdf/meta.yaml +++ b/recipes/bioconductor-mu19ksubccdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mu19ksubccdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e53ef2716f88022e5e41e2cd857fc2a3 +about: + description: A package containing an environment representing the Mu19KsubC.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mu19ksubccdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mu19ksubccdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e53ef2716f88022e5e41e2cd857fc2a3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mu19ksubccdf - description: 'A package containing an environment representing the Mu19KsubC.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mu22v3.db/meta.yaml b/recipes/bioconductor-mu22v3.db/meta.yaml index 2f51fdab19768..ee74e3ecdf81e 100644 --- a/recipes/bioconductor-mu22v3.db/meta.yaml +++ b/recipes/bioconductor-mu22v3.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "Mu22v3.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 44aaebe909be9b0108256194c55cf6fb +about: + description: FHCRC Genomics Shared Resource Mu22v3 Annotation Data (Mu22v3) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: FHCRC Genomics Shared Resource Mu22v3 Annotation Data (Mu22v3) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mu22v3.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 44aaebe909be9b0108256194c55cf6fb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'FHCRC Genomics Shared Resource Mu22v3 Annotation Data (Mu22v3)' - description: 'FHCRC Genomics Shared Resource Mu22v3 Annotation Data (Mu22v3) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mu6500subacdf/meta.yaml b/recipes/bioconductor-mu6500subacdf/meta.yaml index 70ad8c1a4d40a..d9b7af335c4e5 100644 --- a/recipes/bioconductor-mu6500subacdf/meta.yaml +++ b/recipes/bioconductor-mu6500subacdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mu6500subacdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e72152fc4bae307e3858160e018b7f92 +about: + description: A package containing an environment representing the Mu6500subA.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mu6500subacdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mu6500subacdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e72152fc4bae307e3858160e018b7f92 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mu6500subacdf - description: 'A package containing an environment representing the Mu6500subA.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mu6500subbcdf/meta.yaml b/recipes/bioconductor-mu6500subbcdf/meta.yaml index 3d1466e9f7e83..b27f87c7a7dcc 100644 --- a/recipes/bioconductor-mu6500subbcdf/meta.yaml +++ b/recipes/bioconductor-mu6500subbcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mu6500subbcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5000bea2a018b4b6ec05cda111438bc1 +about: + description: A package containing an environment representing the Mu6500subB.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mu6500subbcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mu6500subbcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5000bea2a018b4b6ec05cda111438bc1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mu6500subbcdf - description: 'A package containing an environment representing the Mu6500subB.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mu6500subccdf/meta.yaml b/recipes/bioconductor-mu6500subccdf/meta.yaml index 7d7b7e16103de..c87e0672f39d3 100644 --- a/recipes/bioconductor-mu6500subccdf/meta.yaml +++ b/recipes/bioconductor-mu6500subccdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mu6500subccdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c7cbbe6c70a0a3ae11600ad6c0e540c1 +about: + description: A package containing an environment representing the Mu6500subC.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mu6500subccdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mu6500subccdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c7cbbe6c70a0a3ae11600ad6c0e540c1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mu6500subccdf - description: 'A package containing an environment representing the Mu6500subC.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mu6500subdcdf/meta.yaml b/recipes/bioconductor-mu6500subdcdf/meta.yaml index 33e237d79d7f6..fa6c4b6400209 100644 --- a/recipes/bioconductor-mu6500subdcdf/meta.yaml +++ b/recipes/bioconductor-mu6500subdcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "mu6500subdcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a614674e8bc60fefd8520dd25d45f8d0 +about: + description: A package containing an environment representing the Mu6500subD.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: mu6500subdcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mu6500subdcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a614674e8bc60fefd8520dd25d45f8d0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: mu6500subdcdf - description: 'A package containing an environment representing the Mu6500subD.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mudata/meta.yaml b/recipes/bioconductor-mudata/meta.yaml index bf39d295640fb..db187754cfce1 100644 --- a/recipes/bioconductor-mudata/meta.yaml +++ b/recipes/bioconductor-mudata/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "MuData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Save MultiAssayExperiments to h5mu files supported by muon and mudata. Muon is a Python framework for multimodal omics data analysis. It uses an HDF5-based format for data storage. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Serialization for MultiAssayExperiment Objects -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 10ef702e87a5f0517e59c1ccb96b08dc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mudata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: HDF5Array, rmarkdown, knitr, fs, testthat, BiocStyle, covr, SingleCellMultiModal, CiteFuse, scater requirements: host: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix run: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix + +source: + md5: 110a67684c75c4825fefd5a6e40e6983 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Serialization for MultiAssayExperiment Objects' - description: 'Save MultiAssayExperiments to h5mu files supported by muon and mudata. Muon is a Python framework for multimodal omics data analysis. It uses an HDF5-based format for data storage.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mugaexampledata/meta.yaml b/recipes/bioconductor-mugaexampledata/meta.yaml index 4141815c412fb..c4dd30a3232b5 100644 --- a/recipes/bioconductor-mugaexampledata/meta.yaml +++ b/recipes/bioconductor-mugaexampledata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "MUGAExampleData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b7fe2c7ad41486695fb78263a8c9a854 +about: + description: This package contains example data for the MUGA array that is used by the R package DOQTL. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Example {M}ouse {U}niversal {G}enotyping {A}rray data for genome reconstruction and quantitative trait locus mapping. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mugaexampledata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d5088f4c87dbb3d54790d75dd7402dcc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Example {M}ouse {U}niversal {G}enotyping {A}rray data for genome reconstruction and quantitative trait locus mapping.' - description: 'This package contains example data for the MUGA array that is used by the R package DOQTL.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mugaexampledata/post-link.sh b/recipes/bioconductor-mugaexampledata/post-link.sh index 36035835faa9e..206c03f895ff7 100644 --- a/recipes/bioconductor-mugaexampledata/post-link.sh +++ b/recipes/bioconductor-mugaexampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mugaexampledata-1.22.0" +installBiocDataPackage.sh "mugaexampledata-1.26.0" diff --git a/recipes/bioconductor-mulcom/meta.yaml b/recipes/bioconductor-mulcom/meta.yaml index 87516158ebe13..7a377a8bfe600 100644 --- a/recipes/bioconductor-mulcom/meta.yaml +++ b/recipes/bioconductor-mulcom/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "1.52.0" %} +{% set version = "1.56.0" %} {% set name = "Mulcom" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Identification of differentially expressed genes and false discovery rate (FDR) calculation by Multiple Comparison test. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Calculates Mulcom test -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 87375077f62104b18567db2e68a07488 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mulcom", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:mulcom + - doi:10.1186/1471-2105-12-382 + parent_recipe: + name: bioconductor-mulcom + path: recipes/bioconductor-mulcom + version: 1.30.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-fields - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-fields - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 33131944ade2295ecf3d31f83c4e8730 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Calculates Mulcom test' - description: 'Identification of differentially expressed genes and false discovery rate (FDR) calculation by Multiple Comparison test.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:mulcom - - doi:10.1186/1471-2105-12-382 - parent_recipe: - name: bioconductor-mulcom - path: recipes/bioconductor-mulcom - version: 1.30.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-multiassayexperiment/meta.yaml b/recipes/bioconductor-multiassayexperiment/meta.yaml index d65438bca2711..fb7eb61bd79f2 100644 --- a/recipes/bioconductor-multiassayexperiment/meta.yaml +++ b/recipes/bioconductor-multiassayexperiment/meta.yaml @@ -1,62 +1,68 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "MultiAssayExperiment" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Harmonize data management of multiple experimental assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Software for the integration of multi-omics experiments in Bioconductor -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 01844376cd208e33797b236e2e65fd77 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-multiassayexperiment", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, HDF5Array (>= 1.19.17), knitr, maftools (>= 2.7.10), rmarkdown, R.rsp, RaggedExperiment, UpSetR, survival, survminer, testthat + +extra: + identifiers: + - biotools:multiassayexperiment + - doi:10.1101/144774 + parent_recipe: + name: bioconductor-multiassayexperiment + path: recipes/bioconductor-multiassayexperiment + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, HDF5Array, knitr, maftools, R.rsp, RaggedExperiment, reshape2, rmarkdown, survival, survminer, testthat, UpSetR requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-tidyr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-tidyr + +source: + md5: b9674137dd18833e44e30dfaea04a49f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Software for the integration of multi-omics experiments in Bioconductor' - description: 'MultiAssayExperiment harmonizes data management of multiple experimental assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis.' -extra: - identifiers: - - biotools:multiassayexperiment - - doi:10.1101/144774 - parent_recipe: - name: bioconductor-multiassayexperiment - path: recipes/bioconductor-multiassayexperiment - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-multibac/meta.yaml b/recipes/bioconductor-multibac/meta.yaml index 56235ddd1ac34..e28ace8a389ae 100644 --- a/recipes/bioconductor-multibac/meta.yaml +++ b/recipes/bioconductor-multibac/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "MultiBaC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MultiBaC is a strategy to correct batch effects from multiomic datasets distributed across different labs or data acquisition events. MultiBaC is the first Batch effect correction algorithm that dealing with batch effect correction in multiomics datasets. MultiBaC is able to remove batch effects across different omics generated within separate batches provided that at least one common omic data type is included in all the batches considered. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Multiomic Batch effect Correction -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5585e9f823074db09f44221063a3e64b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-multibac", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, devtools requirements: host: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-ropls >=1.34.0,<1.35.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-ropls >=1.38.0,<1.39.0 - r-base - r-ggplot2 - r-matrix - r-plotrix run: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-ropls >=1.34.0,<1.35.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-ropls >=1.38.0,<1.39.0 - r-base - r-ggplot2 - r-matrix - r-plotrix + +source: + md5: ed7bb1f0f8b5f8ffb720d9ac13da14f9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Multiomic Batch effect Correction' - description: 'MultiBaC is a strategy to correct batch effects from multiomic datasets distributed across different labs or data acquisition events. MultiBaC is the first Batch effect correction algorithm that dealing with batch effect correction in multiomics datasets. MultiBaC is able to remove batch effects across different omics generated within separate batches provided that at least one common omic data type is included in all the batches considered.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-multiclust/meta.yaml b/recipes/bioconductor-multiclust/meta.yaml index 93e1c54ad3fec..0da0817ff9bf0 100644 --- a/recipes/bioconductor-multiclust/meta.yaml +++ b/recipes/bioconductor-multiclust/meta.yaml @@ -1,28 +1,39 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "multiClust" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Clustering is carried out to identify patterns in transcriptomics profiles to determine clinically relevant subgroups of patients. Feature (gene) selection is a critical and an integral part of the process. Currently, there are many feature selection and clustering methods to identify the relevant genes and perform clustering of samples. However, choosing an appropriate methodology is difficult. In addition, extensive feature selection methods have not been supported by the available packages. Hence, we developed an integrative R-package called multiClust that allows researchers to experiment with the choice of combination of methods for gene selection and clustering with ease. Using multiClust, we identified the best performing clustering methodology in the context of clinical outcome. Our observations demonstrate that simple methods such as variance-based ranking perform well on the majority of data sets, provided that the appropriate number of genes is selected. However, different gene ranking and selection methods remain relevant as no methodology works for all studies. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 86c305cad6c68f0a1850f056dad9615e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-multiclust", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:multiclust + - doi:10.4137/cin.s38000 + parent_recipe: + name: bioconductor-multiclust + path: recipes/bioconductor-multiclust + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery requirements: host: - - 'bioconductor-ctc >=1.76.0,<1.77.0' + - bioconductor-ctc >=1.80.0,<1.81.0 - r-amap - r-base - r-cluster @@ -30,28 +41,23 @@ requirements: - r-mclust - r-survival run: - - 'bioconductor-ctc >=1.76.0,<1.77.0' + - bioconductor-ctc >=1.80.0,<1.81.0 - r-amap - r-base - r-cluster - r-dendextend - r-mclust - r-survival + +source: + md5: 18e55be6961025228cbaa4694f815647 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles' - description: 'Clustering is carried out to identify patterns in transcriptomics profiles to determine clinically relevant subgroups of patients. Feature (gene) selection is a critical and an integral part of the process. Currently, there are many feature selection and clustering methods to identify the relevant genes and perform clustering of samples. However, choosing an appropriate methodology is difficult. In addition, extensive feature selection methods have not been supported by the available packages. Hence, we developed an integrative R-package called multiClust that allows researchers to experiment with the choice of combination of methods for gene selection and clustering with ease. Using multiClust, we identified the best performing clustering methodology in the context of clinical outcome. Our observations demonstrate that simple methods such as variance-based ranking perform well on the majority of data sets, provided that the appropriate number of genes is selected. However, different gene ranking and selection methods remain relevant as no methodology works for all studies.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:multiclust - - doi:10.4137/cin.s38000 - parent_recipe: - name: bioconductor-multiclust - path: recipes/bioconductor-multiclust - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-multicrispr/meta.yaml b/recipes/bioconductor-multicrispr/meta.yaml index fe725d944bd47..e486d66d59b73 100644 --- a/recipes/bioconductor-multicrispr/meta.yaml +++ b/recipes/bioconductor-multicrispr/meta.yaml @@ -1,43 +1,40 @@ -{% set version = "1.12.3" %} +{% set version = "1.16.0" %} {% set name = "multicrispr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is for designing Crispr/Cas9 and Prime Editing experiments. It contains functions to (1) define and transform genomic targets, (2) find spacers (4) count offtarget (mis)matches, and (5) compute Doench2016/2014 targeting efficiency. Care has been taken for multicrispr to scale well towards large target sets, enabling the design of large Crispr/Cas9 libraries. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Multi-locus multi-purpose Crispr/Cas design -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d0bbc847e39772348376d944c884290a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-multicrispr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer1, ensembldb, IRanges, knitr, magick, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-crisprseek >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-karyoploter >=1.28.0,<1.29.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-rbowtie >=1.42.0,<1.43.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - r-assertive.base - - r-assertive.files - - r-assertive.numbers - - r-assertive.reflection - - r-assertive.sets + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-crisprseek >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-karyoploter >=1.32.0,<1.33.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-rbowtie >=1.46.0,<1.47.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-data.table - r-ggplot2 @@ -47,22 +44,17 @@ requirements: - r-tidyr - r-tidyselect run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-crisprseek >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-karyoploter >=1.28.0,<1.29.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-rbowtie >=1.42.0,<1.43.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - r-assertive.base - - r-assertive.files - - r-assertive.numbers - - r-assertive.reflection - - r-assertive.sets + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-crisprseek >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-karyoploter >=1.32.0,<1.33.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-rbowtie >=1.46.0,<1.47.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-data.table - r-ggplot2 @@ -71,13 +63,16 @@ requirements: - r-stringi - r-tidyr - r-tidyselect + +source: + md5: 3d1620d4b9306dafaf2896b1f3b9a10e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Multi-locus multi-purpose Crispr/Cas design' - description: 'This package is for designing Crispr/Cas9 and Prime Editing experiments. It contains functions to (1) define and transform genomic targets, (2) find spacers (4) count offtarget (mis)matches, and (5) compute Doench2016/2014 targeting efficiency. Care has been taken for multicrispr to scale well towards large target sets, enabling the design of large Crispr/Cas9 libraries.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-multidataset/meta.yaml b/recipes/bioconductor-multidataset/meta.yaml index 8cbbdbf9d333b..138493c7bc2cb 100644 --- a/recipes/bioconductor-multidataset/meta.yaml +++ b/recipes/bioconductor-multidataset/meta.yaml @@ -1,64 +1,70 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "MultiDataSet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for integrating multi omics data sets and ResultSet is a container for omics results. This package contains base classes for MEAL and rexposome packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Implementation of MultiDataSet and ResultSet -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 304e6d8ccbb54c446f43f2df5e13f530 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-multidataset", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:multidataset + parent_recipe: + name: bioconductor-multidataset + path: recipes/bioconductor-multidataset + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: brgedata, minfi, minfiData, knitr, rmarkdown, testthat, omicade4, iClusterPlus, GEOquery, MultiAssayExperiment, BiocStyle, RaggedExperiment requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-ggrepel - r-qqman run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-ggrepel - r-qqman + +source: + md5: 861a7a8948822c1a156cdd7b7880c7d3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Implementation of MultiDataSet and ResultSet' - description: 'Implementation of the BRGE''s (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for integrating multi omics data sets and ResultSet is a container for omics results. This package contains base classes for MEAL and rexposome packages.' - license_file: LICENSE -extra: - identifiers: - - biotools:multidataset - parent_recipe: - name: bioconductor-multidataset - path: recipes/bioconductor-multidataset - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-multigsea/meta.yaml b/recipes/bioconductor-multigsea/meta.yaml index 52e09755c08a2..96a51e1241d19 100644 --- a/recipes/bioconductor-multigsea/meta.yaml +++ b/recipes/bioconductor-multigsea/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "multiGSEA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Extracted features from pathways derived from 8 different databases (KEGG, Reactome, Biocarta, etc.) can be used on transcriptomic, proteomic, and/or metabolomic level to calculate a combined GSEA-based enrichment score. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Combining GSEA-based pathway enrichment with multi omics data integration -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4f22605155c363e634e9a2ca6afae5c3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-multigsea", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Ss.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Xl.eg.db, org.Cf.eg.db, knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-graphite >=1.48.0,<1.49.0' - - 'bioconductor-metaboliteidmapping >=1.0.0,<1.1.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-graphite >=1.52.0,<1.53.0 + - bioconductor-metaboliteidmapping >=1.0.0,<1.1.0 - r-base - r-dplyr - r-magrittr @@ -33,23 +35,26 @@ requirements: - r-rappdirs - r-rlang run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-graphite >=1.48.0,<1.49.0' - - 'bioconductor-metaboliteidmapping >=1.0.0,<1.1.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-graphite >=1.52.0,<1.53.0 + - bioconductor-metaboliteidmapping >=1.0.0,<1.1.0 - r-base - r-dplyr - r-magrittr - r-metap - r-rappdirs - r-rlang + +source: + md5: 3f8ae904b1d893e0e4b63df77f9d1378 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Combining GSEA-based pathway enrichment with multi omics data integration' - description: 'Extracted features from pathways derived from 8 different databases (KEGG, Reactome, Biocarta, etc.) can be used on transcriptomic, proteomic, and/or metabolomic level to calculate a combined GSEA-based enrichment score.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-multihiccompare/meta.yaml b/recipes/bioconductor-multihiccompare/meta.yaml index d25d76d5d4fc4..60005bcdf8b6c 100644 --- a/recipes/bioconductor-multihiccompare/meta.yaml +++ b/recipes/bioconductor-multihiccompare/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "multiHiCcompare" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: multiHiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. This extension of the original HiCcompare package now allows for Hi-C experiments with more than 2 groups and multiple samples per group. multiHiCcompare operates on processed Hi-C data in the form of sparse upper triangular matrices. It accepts four column (chromosome, region1, region2, IF) tab-separated text files storing chromatin interaction matrices. multiHiCcompare provides cyclic loess and fast loess (fastlo) methods adapted to jointly normalizing Hi-C data. Additionally, it provides a general linear model (GLM) framework adapting the edgeR package to detect differences in Hi-C data in a distance dependent manner. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 04512b7be1f12fa8bfb32a13dbbb408f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-multihiccompare", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hiccompare >=1.24.0,<1.25.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomeinfodbdata >=1.2.0,<1.3.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hiccompare >=1.28.0,<1.29.0 - r-aggregation - r-base - r-data.table @@ -36,12 +38,12 @@ requirements: - r-pheatmap - r-qqman run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hiccompare >=1.24.0,<1.25.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomeinfodbdata >=1.2.0,<1.3.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hiccompare >=1.28.0,<1.29.0 - r-aggregation - r-base - r-data.table @@ -49,13 +51,16 @@ requirements: - r-pbapply - r-pheatmap - r-qqman + +source: + md5: c228019c62fe855dba77509be8019f07 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available' - description: 'multiHiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. This extension of the original HiCcompare package now allows for Hi-C experiments with more than 2 groups and multiple samples per group. multiHiCcompare operates on processed Hi-C data in the form of sparse upper triangular matrices. It accepts four column (chromosome, region1, region2, IF) tab-separated text files storing chromatin interaction matrices. multiHiCcompare provides cyclic loess and fast loess (fastlo) methods adapted to jointly normalizing Hi-C data. Additionally, it provides a general linear model (GLM) framework adapting the edgeR package to detect differences in Hi-C data in a distance dependent manner.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-multimed/meta.yaml b/recipes/bioconductor-multimed/meta.yaml index 0efc3b4e5acb4..dc4d53660b5c8 100644 --- a/recipes/bioconductor-multimed/meta.yaml +++ b/recipes/bioconductor-multimed/meta.yaml @@ -1,39 +1,20 @@ -{% set version = "2.24.0" %} +{% set version = "2.28.0" %} {% set name = "MultiMed" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 019bc5d7be15d1688b3b5df7b87246f7 +about: + description: Implements methods for testing multiple mediators + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + file LICENSE + license_file: LICENSE + summary: Testing multiple biological mediators simultaneously build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-multimed", max_pin="x.x") }}' - noarch: generic -# Suggests: RUnit, BiocGenerics -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2) + file LICENSE' - summary: 'Testing multiple biological mediators simultaneously' - description: 'Implements methods for testing multiple mediators' - license_file: LICENSE extra: identifiers: - biotools:multimed @@ -42,4 +23,23 @@ extra: name: bioconductor-multimed path: recipes/bioconductor-multimed version: 2.2.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: RUnit, BiocGenerics +requirements: + host: + - r-base + run: + - r-base +source: + md5: 0b351652af73cc1dce50f98ff1bb422b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-multimir/meta.yaml b/recipes/bioconductor-multimir/meta.yaml index f62e261c71752..448ee7e4c72fa 100644 --- a/recipes/bioconductor-multimir/meta.yaml +++ b/recipes/bioconductor-multimir/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "multiMiR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A collection of microRNAs/targets from external resources, including validated microRNA-target databases (miRecords, miRTarBase and TarBase), predicted microRNA-target databases (DIANA-microT, ElMMo, MicroCosm, miRanda, miRDB, PicTar, PITA and TargetScan) and microRNA-disease/drug databases (miR2Disease, Pharmaco-miR VerSe and PhenomiR). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Integration of multiple microRNA-target databases with their disease and drug associations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7102f312557b010d184bac5dea6e5009 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-multimir", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2) requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-dplyr - - 'r-purrr >=0.2.2' + - r-purrr >=0.2.2 - r-rcurl - - 'r-tibble >=1.2' + - r-tibble >=2.0 - r-xml run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-dplyr - - 'r-purrr >=0.2.2' + - r-purrr >=0.2.2 - r-rcurl - - 'r-tibble >=1.2' + - r-tibble >=2.0 - r-xml + +source: + md5: b99c3f147f539b220544149f38b69f10 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Integration of multiple microRNA-target databases with their disease and drug associations' - description: 'A collection of microRNAs/targets from external resources, including validated microRNA-target databases (miRecords, miRTarBase and TarBase), predicted microRNA-target databases (DIANA-microT, ElMMo, MicroCosm, miRanda, miRDB, PicTar, PITA and TargetScan) and microRNA-disease/drug databases (miR2Disease, Pharmaco-miR VerSe and PhenomiR).' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-multimodalexperiment/meta.yaml b/recipes/bioconductor-multimodalexperiment/meta.yaml index 4e86eba270849..4a74c776161a4 100644 --- a/recipes/bioconductor-multimodalexperiment/meta.yaml +++ b/recipes/bioconductor-multimodalexperiment/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "MultimodalExperiment" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 376186ba5972df1b6d4be9dc69253a61 +about: + description: MultimodalExperiment is an S4 class that integrates bulk and single-cell experiment data; it is optimally storage-efficient, and its methods are exceptionally fast. It effortlessly represents multimodal data of any nature and features normalized experiment, subject, sample, and cell annotations, which are related to underlying biological experiments through maps. Its coordination methods are opt-in and employ database-like join operations internally to deliver fast and flexible management of multimodal data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Integrative Bulk and Single-Cell Experiment Container build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-multimodalexperiment", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base +source: + md5: 48415565bbd9cb96dd8d264d58c7d034 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Integrative Bulk and Single-Cell Experiment Container' - description: 'MultimodalExperiment is an S4 class that integrates bulk and single-cell experiment data; it is optimally storage-efficient, and its methods are exceptionally fast. It effortlessly represents multimodal data of any nature and features normalized experiment, subject, sample, and cell annotations, which are related to underlying biological experiments through maps. Its coordination methods are opt-in and employ database-like join operations internally to deliver fast and flexible management of multimodal data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-multirnaflow/build_failure.linux-64.yaml b/recipes/bioconductor-multirnaflow/build_failure.linux-64.yaml deleted file mode 100644 index 8506b569378e7..0000000000000 --- a/recipes/bioconductor-multirnaflow/build_failure.linux-64.yaml +++ /dev/null @@ -1,6 +0,0 @@ -recipe_sha: bb62d3b200f33f1ffccfa82f8214efabe8d38de5aa2a4135bccc1e17878148d7 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -reason: |- - package r-plot3drgl-1.0.4-r43h6115d3f_0 is excluded by strict repo priority -category: |- - dependency issue diff --git a/recipes/bioconductor-multirnaflow/meta.yaml b/recipes/bioconductor-multirnaflow/meta.yaml index 46b7f0655ed98..24210c4828edf 100644 --- a/recipes/bioconductor-multirnaflow/meta.yaml +++ b/recipes/bioconductor-multirnaflow/meta.yaml @@ -1,72 +1,32 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "MultiRNAflow" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Our R package MultiRNAflow provides an easy to use unified framework allowing to automatically make both unsupervised and supervised (DE) analysis for datasets with an arbitrary number of biological conditions and time points. In particular, our code makes a deep downstream analysis of DE information, e.g. identifying temporal patterns across biological conditions and DE genes which are specific to a biological condition for each time. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 | file LICENSE + license_file: LICENSE + summary: An R package for integrated analysis of temporal RNA-seq data with multiple biological conditions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cefc109896f4cb34b4ee6a09ae966f42 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-multirnaflow", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics (>= 0.40.0), BiocStyle, e1071 (>= 1.7.12), knitr, rmarkdown, testthat (>= 3.0.0) requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-mfuzz >=2.62.0,<2.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - r-base - - 'r-factoextra >=1.0.7' - - 'r-factominer >=2.6' - - 'r-ggalluvial >=0.12.3' - - 'r-ggplot2 >=3.4.0' - - 'r-ggrepel >=0.9.2' - - 'r-ggsci >=2.9' - - 'r-gprofiler2 >=0.2.1' - - 'r-plot3d >=1.4' - - 'r-plot3drgl >=1.0.3' - - 'r-plyr >=1.8.8' - - 'r-rcolorbrewer >=1.1.3' - - 'r-reshape2 >=1.4.4' - - 'r-rlang >=1.1.1' - - 'r-scales >=1.2.1' - - 'r-upsetr >=1.4.0' - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-mfuzz >=2.62.0,<2.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - r-base - - 'r-factoextra >=1.0.7' - - 'r-factominer >=2.6' - - 'r-ggalluvial >=0.12.3' - - 'r-ggplot2 >=3.4.0' - - 'r-ggrepel >=0.9.2' - - 'r-ggsci >=2.9' - - 'r-gprofiler2 >=0.2.1' - - 'r-plot3d >=1.4' - - 'r-plot3drgl >=1.0.3' - - 'r-plyr >=1.8.8' - - 'r-rcolorbrewer >=1.1.3' - - 'r-reshape2 >=1.4.4' - - 'r-rlang >=1.1.1' - - 'r-scales >=1.2.1' - - 'r-upsetr >=1.4.0' build: - {{ cdt('mesa-libgl-devel') }} # [linux] - {{ cdt('mesa-dri-drivers') }} # [linux] @@ -74,16 +34,54 @@ requirements: - {{ cdt('libxdamage') }} # [linux] - {{ cdt('libxxf86vm') }} # [linux] - xorg-libxfixes # [linux] + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-mfuzz >=2.66.0,<2.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-factoextra >=1.0.7 + - r-factominer >=2.6 + - r-ggalluvial >=0.12.3 + - r-ggplot2 >=3.4.0 + - r-ggplotify >=0.1.2 + - r-ggrepel >=0.9.2 + - r-gprofiler2 >=0.2.1 + - r-plot3d >=1.4 + - r-plot3drgl >=1.0.3 + - r-reshape2 >=1.4.4 + - r-upsetr >=1.4.0 + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-mfuzz >=2.66.0,<2.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-factoextra >=1.0.7 + - r-factominer >=2.6 + - r-ggalluvial >=0.12.3 + - r-ggplot2 >=3.4.0 + - r-ggplotify >=0.1.2 + - r-ggrepel >=0.9.2 + - r-gprofiler2 >=0.2.1 + - r-plot3d >=1.4 + - r-plot3drgl >=1.0.3 + - r-reshape2 >=1.4.4 + - r-upsetr >=1.4.0 + +source: + md5: 8f256be5013d735dbf6a5d2d0a258cf9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 | file LICENSE' - summary: 'An R package for analysing RNA-seq raw counts with several biological conditions and different time points' - description: 'Our R package MultiRNAflow provides an easy to use unified framework allowing to automatically make both unsupervised and supervised (DE) analysis for datasets with an arbitrary number of biological conditions and time points. In particular, our code makes a deep downstream analysis of DE information, e.g. identifying temporal patterns across biological conditions and DE genes which are specific to a biological condition for each time.' - license_file: LICENSE -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-multiscan/meta.yaml b/recipes/bioconductor-multiscan/meta.yaml index 703917f5a7eb5..56050beaa69ee 100644 --- a/recipes/bioconductor-multiscan/meta.yaml +++ b/recipes/bioconductor-multiscan/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.62.0" %} +{% set version = "1.66.0" %} {% set name = "multiscan" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Estimates gene expressions from several laser scans of the same microarray + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: R package for combining multiple scans -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 58243690ff05bdbd30da46ea01e409a3 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-multiscan", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:multiscan + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-multiscan + path: recipes/bioconductor-multiscan + version: 1.40.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: 0e811fc5a4799629af8e512c5b9f0f7d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'R package for combining multiple scans' - description: 'Estimates gene expressions from several laser scans of the same microarray' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:multiscan - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-multiscan - path: recipes/bioconductor-multiscan - version: 1.40.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-multistateqtl/build.sh b/recipes/bioconductor-multistateqtl/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-multistateqtl/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-multistateqtl/meta.yaml b/recipes/bioconductor-multistateqtl/meta.yaml new file mode 100644 index 0000000000000..4055286978fd4 --- /dev/null +++ b/recipes/bioconductor-multistateqtl/meta.yaml @@ -0,0 +1,70 @@ +{% set version = "1.2.0" %} +{% set name = "multistateQTL" %} +{% set bioc = "3.20" %} + +about: + description: A collection of tools for doing various analyses of multi-state QTL data, with a focus on visualization and interpretation. The package 'multistateQTL' contains functions which can remove or impute missing data, identify significant associations, as well as categorise features into global, multi-state or unique. The analysis results are stored in a 'QTLExperiment' object, which is based on the 'SummarisedExperiment' framework. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Toolkit for the analysis of multi-state QTL data + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-multistateqtl", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, BiocStyle, knitr, covr, rmarkdown +requirements: + host: + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-qtlexperiment >=1.4.0,<1.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-circlize + - r-collapse + - r-data.table + - r-dplyr + - r-fitdistrplus + - r-ggplot2 + - r-mashr + - r-matrixstats + - r-tidyr + - r-viridis + run: + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-qtlexperiment >=1.4.0,<1.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-circlize + - r-collapse + - r-data.table + - r-dplyr + - r-fitdistrplus + - r-ggplot2 + - r-mashr + - r-matrixstats + - r-tidyr + - r-viridis + +source: + md5: c87735e1416b5b079b5d34e8d61e7906 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-multiwgcna/meta.yaml b/recipes/bioconductor-multiwgcna/meta.yaml index b40ef3418752f..a8b01f3a0ae0b 100644 --- a/recipes/bioconductor-multiwgcna/meta.yaml +++ b/recipes/bioconductor-multiwgcna/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "multiWGCNA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An R package for deeping mining gene co-expression networks in multi-trait expression data. Provides functions for analyzing, comparing, and visualizing WGCNA networks across conditions. multiWGCNA was designed to handle the common case where there are multiple biologically meaningful sample traits, such as disease vs wildtype across development or anatomical region. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: multiWGCNA -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b8f70e9496cf73238aa3ba3c08cb81fa build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-multiwgcna", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, doParallel, ExperimentHub, knitr, markdown, rmarkdown, testthat (>= 3.0.0), vegan requirements: host: - - 'bioconductor-dcanr >=1.18.0,<1.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-dcanr >=1.22.0,<1.23.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cowplot - r-data.table @@ -40,8 +42,8 @@ requirements: - r-stringr - r-wgcna run: - - 'bioconductor-dcanr >=1.18.0,<1.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-dcanr >=1.22.0,<1.23.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cowplot - r-data.table @@ -57,13 +59,16 @@ requirements: - r-scales - r-stringr - r-wgcna + +source: + md5: 64ba3fa001a82baae932cb76dc19a515 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: multiWGCNA - description: 'An R package for deeping mining gene co-expression networks in multi-trait expression data. Provides functions for analyzing, comparing, and visualizing WGCNA networks across conditions. multiWGCNA was designed to handle the common case where there are multiple biologically meaningful sample traits, such as disease vs wildtype across development or anatomical region.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-multtest/meta.yaml b/recipes/bioconductor-multtest/meta.yaml index 9a08836c83130..04f6c474f2afd 100644 --- a/recipes/bioconductor-multtest/meta.yaml +++ b/recipes/bioconductor-multtest/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "2.58.0" %} +{% set version = "2.62.0" %} {% set name = "multtest" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Resampling-based multiple hypothesis testing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7d81a8460781f4a86f01a9df5fcf50d7 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-multtest", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:multtest + - doi:10.1007/0-387-29362-0_15 + parent_recipe: + name: bioconductor-multtest + path: recipes/bioconductor-multtest + version: 2.36.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: snow requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-mass - r-survival - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-mass - r-survival - build: - - {{ compiler('c') }} - - make + +source: + md5: ea043ffe972fb0592853ebe0496666c9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3-only - summary: 'Resampling-based multiple hypothesis testing' - description: 'Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:multtest - - doi:10.1007/0-387-29362-0_15 - parent_recipe: - name: bioconductor-multtest - path: recipes/bioconductor-multtest - version: 2.36.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mumosa/meta.yaml b/recipes/bioconductor-mumosa/meta.yaml index 8030f8a98140c..2bd18cdda5f35 100644 --- a/recipes/bioconductor-mumosa/meta.yaml +++ b/recipes/bioconductor-mumosa/meta.yaml @@ -1,75 +1,82 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "mumosa" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Assorted utilities for multi-modal analyses of single-cell datasets. Includes functions to combine multiple modalities for downstream analysis, perform MNN-based batch correction across multiple modalities, and to compute correlations between assay values for different modalities. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Multi-Modal Single-Cell Analysis Methods -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 634ea9c4fce9573e5da8297886d4b699 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mumosa", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, BiocStyle, rmarkdown, scater, bluster, DropletUtils, scRNAseq requirements: + host: - - 'bioconductor-batchelor >=1.18.0,<1.19.0' - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-metapod >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-batchelor >=1.22.0,<1.23.0 + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-metapod >=1.14.0,<1.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scaledmatrix >=1.14.0,<1.15.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-igraph - r-matrix - r-uwot + run: - - 'bioconductor-batchelor >=1.18.0,<1.19.0' - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-metapod >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-batchelor >=1.22.0,<1.23.0 + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-metapod >=1.14.0,<1.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scaledmatrix >=1.14.0,<1.15.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-igraph - r-matrix - r-uwot + +source: + md5: f5c40b8e3382234436ada72b62b910b5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Multi-Modal Single-Cell Analysis Methods' - description: 'Assorted utilities for multi-modal analyses of single-cell datasets. Includes functions to combine multiple modalities for downstream analysis, perform MNN-based batch correction across multiple modalities, and to compute correlations between assay values for different modalities.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mungesumstats/meta.yaml b/recipes/bioconductor-mungesumstats/meta.yaml index b1efda96dcf54..07d6424815c95 100644 --- a/recipes/bioconductor-mungesumstats/meta.yaml +++ b/recipes/bioconductor-mungesumstats/meta.yaml @@ -1,34 +1,35 @@ -{% set version = "1.10.1" %} +{% set version = "1.14.1" %} {% set name = "MungeSumstats" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The *MungeSumstats* package is designed to facilitate the standardisation of GWAS summary statistics. It reformats inputted summary statisitics to include SNP, CHR, BP and can look up these values if any are missing. It also pefrorms dozens of QC and filtering steps to ensure high data quality and minimise inter-study differences. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Standardise summary statistics from GWAS -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9164f3e5c8e7612c387b35bff82dc4cc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mungesumstats", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR, BiocStyle, covr, Rsamtools, MatrixGenerics, badger, BiocParallel, GenomicFiles requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-data.table - r-dplyr @@ -40,13 +41,13 @@ requirements: - r-rcurl - r-stringr run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-data.table - r-dplyr @@ -57,12 +58,16 @@ requirements: - r-r.utils - r-rcurl - r-stringr + +source: + md5: 67f1b35796c6f1a605748560bfc3997c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Standardise summary statistics from GWAS' - description: 'The *MungeSumstats* package is designed to facilitate the standardisation of GWAS summary statistics. It reformats inputted summary statisitics to include SNP, CHR, BP and can look up these values if any are missing. It also pefrorms dozens of QC and filtering steps to ensure high data quality and minimise inter-study differences.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mus.musculus/meta.yaml b/recipes/bioconductor-mus.musculus/meta.yaml index 59c522bbcc842..f23933ce83b50 100644 --- a/recipes/bioconductor-mus.musculus/meta.yaml +++ b/recipes/bioconductor-mus.musculus/meta.yaml @@ -1,49 +1,54 @@ {% set version = "1.3.1" %} {% set name = "Mus.musculus" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Contains the Mus.musculus object to access data from several related annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for the Mus.musculus object -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b8defe64c2dd308a88d1ac7a4ce04b9 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mus.musculus", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-organismdbi >=1.48.0,<1.49.0 + - bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-organismdbi >=1.48.0,<1.49.0 + - bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 1b8defe64c2dd308a88d1ac7a4ce04b9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for the Mus.musculus object' - description: 'Contains the Mus.musculus object to access data from several related annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-muscdata/meta.yaml b/recipes/bioconductor-muscdata/meta.yaml index 9db11d8026d1c..1061b42594643 100644 --- a/recipes/bioconductor-muscdata/meta.yaml +++ b/recipes/bioconductor-muscdata/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "muscData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f34c376f88f97c98d4aac5490b45bc24 +about: + description: Data package containing a collection of multi-sample multi-group scRNA-seq datasets in SingleCellExperiment Bioconductor object format. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Multi-sample multi-group scRNA-seq data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-muscdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, dplyr, DropletUtils, knitr, GEOquery, Matrix, matrixStats, methods, muscat, rmarkdown, R.utils, readxl, scater, scds, Seurat requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20250104 +source: + md5: 157c067dfb062ac305f9e79a6fb42bd1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Multi-sample multi-group scRNA-seq data' - description: 'Data package containing a collection of multi-sample multi-group scRNA-seq datasets in SingleCellExperiment Bioconductor object format.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-muscdata/post-link.sh b/recipes/bioconductor-muscdata/post-link.sh index 87addac2bf682..408608f8f5056 100644 --- a/recipes/bioconductor-muscdata/post-link.sh +++ b/recipes/bioconductor-muscdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "muscdata-1.16.0" +installBiocDataPackage.sh "muscdata-1.20.0" diff --git a/recipes/bioconductor-muscle/meta.yaml b/recipes/bioconductor-muscle/meta.yaml index c75199b874840..feb5395a32621 100644 --- a/recipes/bioconductor-muscle/meta.yaml +++ b/recipes/bioconductor-muscle/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "3.44.0" %} +{% set version = "3.48.0" %} {% set name = "muscle" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 159745260e624c7aeb3d2e0deeef99ab +about: + description: MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Unlimited + summary: Multiple Sequence Alignment with MUSCLE build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-muscle", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make +source: + md5: 7ad249c5ec6b866d70ae0a0d47a62eb1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Unlimited - summary: 'Multiple Sequence Alignment with MUSCLE' - description: 'MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-musicatk/build_failure.linux-64.yaml b/recipes/bioconductor-musicatk/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..05fd4c2901fb9 --- /dev/null +++ b/recipes/bioconductor-musicatk/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: 437fa6c76fd7bd49c0fa3a2df753cb3183aba2f080ced5011b3b3ead5109694c # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-conclust")} + Encountered problems while solving: + - nothing provides requested r-conclust + + Could not solve for environment specs + The following package could not be installed + [31mr-conclust[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-conclust")} + Encountered problems while solving: + - nothing provides requested r-conclust + + Could not solve for environment specs + The following package could not be installed + [31mr-conclust[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-conclust")} + Encountered problems while solving: + - nothing provides requested r-conclust + + Could not solve for environment specs + The following package could not be installed + [31mr-conclust[0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. +reason: |- + needs r-conclust added to conda-forge +category: |- + dependency issue diff --git a/recipes/bioconductor-musicatk/build_failure.osx-64.yaml b/recipes/bioconductor-musicatk/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..1af12916ae8a1 --- /dev/null +++ b/recipes/bioconductor-musicatk/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 437fa6c76fd7bd49c0fa3a2df753cb3183aba2f080ced5011b3b3ead5109694c # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + needs r-conclust added to conda-forge +category: |- + dependency issue diff --git a/recipes/bioconductor-musicatk/meta.yaml b/recipes/bioconductor-musicatk/meta.yaml index 3bbcc539d032f..332279fc7b2ac 100644 --- a/recipes/bioconductor-musicatk/meta.yaml +++ b/recipes/bioconductor-musicatk/meta.yaml @@ -1,125 +1,230 @@ -{% set version = "1.12.0" %} +{% set version = "2.0.0" %} {% set name = "musicatk" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Mutational signatures are carcinogenic exposures or aberrant cellular processes that can cause alterations to the genome. We created musicatk (MUtational SIgnature Comprehensive Analysis ToolKit) to address shortcomings in versatility and ease of use in other pre-existing computational tools. Although many different types of mutational data have been generated, current software packages do not have a flexible framework to allow users to mix and match different types of mutations in the mutational signature inference process. Musicatk enables users to count and combine multiple mutation types, including SBS, DBS, and indels. Musicatk calculates replication strand, transcription strand and combinations of these features along with discovery from unique and proprietary genomic feature associated with any mutation type. Musicatk also implements several methods for discovery of new signatures as well as methods to infer exposure given an existing set of signatures. Musicatk provides functions for visualization and downstream exploratory analysis including the ability to compare signatures between cohorts and find matching signatures in COSMIC V2 or COSMIC V3. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Mutational Signature Comprehensive Analysis Toolkit -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 50869915aff9dd79823e05b4ae163bc6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-musicatk", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: TCGAbiolinks, shinyBS, shinyalert, shinybusy, shinydashboard, shinyjs, shinyjqui, sortable, testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr, shinyWidgets, cowplot, withr requirements: + host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-decomptumor2sig >=2.18.0,<2.19.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-maftools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + + - bioconductor-biostrings >=2.74.0,<2.75.0 + + - bioconductor-bsgenome >=1.74.0,<1.75.0 + + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + + - bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0 + + - bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0 + + - bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0 + + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + + - bioconductor-decomptumor2sig >=2.22.0,<2.23.0 + + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + + - bioconductor-genomicranges >=1.58.0,<1.59.0 + + - bioconductor-iranges >=2.40.0,<2.41.0 + + - bioconductor-maftools >=2.22.0,<2.23.0 + + - bioconductor-s4vectors >=0.44.0,<0.45.0 + + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 + + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - r-base + - r-cluster + + - r-conclust + - r-data.table - - r-deconstructsigs + - r-dplyr + - r-factoextra + - r-ggplot2 + - r-ggpubr + - r-ggrepel + - r-gridextra + - r-gtools + - r-magrittr + - r-mass + + - r-matrix >=1.6.1 + - r-matrixtests + - r-mcmcprecision + - r-nmf + - r-philentropy + - r-plotly + - r-rlang + + - r-scales + - r-shiny + - r-stringi + - r-stringr + - r-tibble + - r-tidyr + - r-tidyverse + - r-topicmodels + - r-uwot + run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-decomptumor2sig >=2.18.0,<2.19.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-maftools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + + - bioconductor-biostrings >=2.74.0,<2.75.0 + + - bioconductor-bsgenome >=1.74.0,<1.75.0 + + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + + - bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0 + + - bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0 + + - bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0 + + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + + - bioconductor-decomptumor2sig >=2.22.0,<2.23.0 + + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + + - bioconductor-genomicranges >=1.58.0,<1.59.0 + + - bioconductor-iranges >=2.40.0,<2.41.0 + + - bioconductor-maftools >=2.22.0,<2.23.0 + + - bioconductor-s4vectors >=0.44.0,<0.45.0 + + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 + + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - r-base + - r-cluster + + - r-conclust + - r-data.table - - r-deconstructsigs + - r-dplyr + - r-factoextra + - r-ggplot2 + - r-ggpubr + - r-ggrepel + - r-gridextra + - r-gtools + - r-magrittr + - r-mass + + - r-matrix >=1.6.1 + - r-matrixtests + - r-mcmcprecision + - r-nmf + - r-philentropy + - r-plotly + - r-rlang + + - r-scales + - r-shiny + - r-stringi + - r-stringr + - r-tibble + - r-tidyr + - r-tidyverse + - r-topicmodels + - r-uwot + +source: + md5: cfe4828f24432a9ae59b6d7e45d58d8e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'Mutational Signature Comprehensive Analysis Toolkit' - description: 'Mutational signatures are carcinogenic exposures or aberrant cellular processes that can cause alterations to the genome. We created musicatk (MUtational SIgnature Comprehensive Analysis ToolKit) to address shortcomings in versatility and ease of use in other pre-existing computational tools. Although many different types of mutational data have been generated, current software packages do not have a flexible framework to allow users to mix and match different types of mutations in the mutational signature inference process. Musicatk enables users to count and combine multiple mutation types, including SBS, DBS, and indels. Musicatk calculates replication strand, transcription strand and combinations of these features along with discovery from unique and proprietary genomic feature associated with any mutation type. Musicatk also implements several methods for discovery of new signatures as well as methods to infer exposure given an existing set of signatures. Musicatk provides functions for visualization and downstream exploratory analysis including the ability to compare signatures between cohorts and find matching signatures in COSMIC V2 or COSMIC V3.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mutationalpatterns/meta.yaml b/recipes/bioconductor-mutationalpatterns/meta.yaml index 78b54176ec5de..0c9161a379435 100644 --- a/recipes/bioconductor-mutationalpatterns/meta.yaml +++ b/recipes/bioconductor-mutationalpatterns/meta.yaml @@ -1,84 +1,92 @@ -{% set version = "3.12.0" %} +{% set version = "3.16.0" %} {% set name = "MutationalPatterns" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Mutational processes leave characteristic footprints in genomic DNA. This package provides a comprehensive set of flexible functions that allows researchers to easily evaluate and visualize a multitude of mutational patterns in base substitution catalogues of e.g. healthy samples, tumour samples, or DNA-repair deficient cells. The package covers a wide range of patterns including: mutational signatures, transcriptional and replicative strand bias, lesion segregation, genomic distribution and association with genomic features, which are collectively meaningful for studying the activity of mutational processes. The package works with single nucleotide variants (SNVs), insertions and deletions (Indels), double base substitutions (DBSs) and larger multi base substitutions (MBSs). The package provides functionalities for both extracting mutational signatures de novo and determining the contribution of previously identified mutational signatures on a single sample level. MutationalPatterns integrates with common R genomic analysis workflows and allows easy association with (publicly available) annotation data.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Comprehensive genome-wide analysis of mutational processes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6c800e4f89957108a1b4ab1d3a2b4cb6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mutationalpatterns", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-mutationalpatterns + path: recipes/bioconductor-mutationalpatterns + version: 1.6.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), BiocStyle (>= 2.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), biomaRt (>= 2.28.0), gridExtra (>= 2.2.1), rtracklayer (>= 1.32.2), ccfindR (>= 1.6.0), GenomicFeatures, AnnotationDbi, testthat, knitr, rmarkdown requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - - 'r-cowplot >=0.9.2' - - 'r-dplyr >=0.8.3' - - 'r-ggalluvial >=0.12.2' - - 'r-ggdendro >=0.1-20' - - 'r-ggplot2 >=2.1.0' - - 'r-magrittr >=1.5' - - 'r-nmf >=0.20.6' - - 'r-pracma >=1.8.8' - - 'r-purrr >=0.3.2' + - r-cowplot >=0.9.2 + - r-dplyr >=0.8.3 + - r-ggalluvial >=0.12.2 + - r-ggdendro >=0.1-20 + - r-ggplot2 >=2.1.0 + - r-magrittr >=1.5 + - r-nmf >=0.20.6 + - r-pracma >=1.8.8 + - r-purrr >=0.3.2 - r-rcolorbrewer - - 'r-stringr >=1.4.0' - - 'r-tibble >=2.1.3' - - 'r-tidyr >=1.0.0' + - r-stringr >=1.4.0 + - r-tibble >=2.1.3 + - r-tidyr >=1.0.0 + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - - 'r-cowplot >=0.9.2' - - 'r-dplyr >=0.8.3' - - 'r-ggalluvial >=0.12.2' - - 'r-ggdendro >=0.1-20' - - 'r-ggplot2 >=2.1.0' - - 'r-magrittr >=1.5' - - 'r-nmf >=0.20.6' - - 'r-pracma >=1.8.8' - - 'r-purrr >=0.3.2' + - r-cowplot >=0.9.2 + - r-dplyr >=0.8.3 + - r-ggalluvial >=0.12.2 + - r-ggdendro >=0.1-20 + - r-ggplot2 >=2.1.0 + - r-magrittr >=1.5 + - r-nmf >=0.20.6 + - r-pracma >=1.8.8 + - r-purrr >=0.3.2 - r-rcolorbrewer - - 'r-stringr >=1.4.0' - - 'r-tibble >=2.1.3' - - 'r-tidyr >=1.0.0' + - r-stringr >=1.4.0 + - r-tibble >=2.1.3 + - r-tidyr >=1.0.0 + +source: + md5: bf6f909ef82ca63bbc39f0f380681f2e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Comprehensive genome-wide analysis of mutational processes' - description: 'Mutational processes leave characteristic footprints in genomic DNA. This package provides a comprehensive set of flexible functions that allows researchers to easily evaluate and visualize a multitude of mutational patterns in base substitution catalogues of e.g. healthy samples, tumour samples, or DNA-repair deficient cells. The package covers a wide range of patterns including: mutational signatures, transcriptional and replicative strand bias, lesion segregation, genomic distribution and association with genomic features, which are collectively meaningful for studying the activity of mutational processes. The package works with single nucleotide variants (SNVs), insertions and deletions (Indels), double base substitutions (DBSs) and larger multi base substitutions (MBSs). The package provides functionalities for both extracting mutational signatures de novo and determining the contribution of previously identified mutational signatures on a single sample level. MutationalPatterns integrates with common R genomic analysis workflows and allows easy association with (publicly available) annotation data.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-mutationalpatterns - path: recipes/bioconductor-mutationalpatterns - version: 1.6.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mvcclass/meta.yaml b/recipes/bioconductor-mvcclass/meta.yaml index dc8edbb507c49..b05cbab7a4dc2 100644 --- a/recipes/bioconductor-mvcclass/meta.yaml +++ b/recipes/bioconductor-mvcclass/meta.yaml @@ -1,38 +1,20 @@ -{% set version = "1.76.0" %} +{% set version = "1.80.0" %} {% set name = "MVCClass" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2ef3331b86ae7981a2ab3323386caf61 +about: + description: Creates classes used in model-view-controller (MVC) design + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Model-View-Controller (MVC) Classes build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mvcclass", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Model-View-Controller (MVC) Classes' - description: 'Creates classes used in model-view-controller (MVC) design' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' extra: identifiers: - biotools:mvcclass @@ -41,4 +23,22 @@ extra: name: bioconductor-mvcclass path: recipes/bioconductor-mvcclass version: 1.54.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +requirements: + host: + - r-base + run: + - r-base +source: + md5: a8ce7fca6f05d4da5d4025891e82c51c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mvoutdata/meta.yaml b/recipes/bioconductor-mvoutdata/meta.yaml index a0a5517d19240..b25f07a03b6d7 100644 --- a/recipes/bioconductor-mvoutdata/meta.yaml +++ b/recipes/bioconductor-mvoutdata/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "mvoutData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: abca7ca8ae7729ed8f146d0083aa9757 +about: + description: affy and illumina raw data for assessing outlier detector performance + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: affy and illumina raw data for assessing outlier detector performance build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mvoutdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-lumi >=2.58.0,<2.59.0 - r-base run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-lumi >=2.58.0,<2.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20250101 +source: + md5: 313c7e57d9a26a53342aa415b0370cbd + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'affy and illumina raw data for assessing outlier detector performance' - description: 'affy and illumina raw data for assessing outlier detector performance' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mvoutdata/post-link.sh b/recipes/bioconductor-mvoutdata/post-link.sh index c258bd7e17567..e9e5578ef15ab 100644 --- a/recipes/bioconductor-mvoutdata/post-link.sh +++ b/recipes/bioconductor-mvoutdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "mvoutdata-1.38.0" +installBiocDataPackage.sh "mvoutdata-1.42.0" diff --git a/recipes/bioconductor-mwastools/meta.yaml b/recipes/bioconductor-mwastools/meta.yaml index 75f809f1bc281..cb2ed5050572a 100644 --- a/recipes/bioconductor-mwastools/meta.yaml +++ b/recipes/bioconductor-mwastools/meta.yaml @@ -1,32 +1,39 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "MWASTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'MWASTools provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: CC BY-NC-ND 4.0 + summary: 'MWASTools: an integrated pipeline to perform metabolome-wide association studies' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4af3f3512a794c7944a27bfad640aa81 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mwastools", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-mwastools + path: recipes/bioconductor-mwastools + version: 1.4.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-boot - r-car @@ -37,11 +44,11 @@ requirements: - r-ppcor - r-rcurl run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-boot - r-car @@ -51,17 +58,16 @@ requirements: - r-igraph - r-ppcor - r-rcurl + +source: + md5: 919802ea963bcf315a070eea285d5283 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'CC BY-NC-ND 4.0' - summary: 'MWASTools: an integrated pipeline to perform metabolome-wide association studies' - description: 'MWASTools provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results.' -extra: - parent_recipe: - name: bioconductor-mwastools - path: recipes/bioconductor-mwastools - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mwgcod.db/meta.yaml b/recipes/bioconductor-mwgcod.db/meta.yaml index e5a5c3839be7b..28c73489e2667 100644 --- a/recipes/bioconductor-mwgcod.db/meta.yaml +++ b/recipes/bioconductor-mwgcod.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.4.0" %} {% set name = "mwgcod.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3d6e2af6b05d6e07a212c043dc9d37c4 +about: + description: Codelink Mouse Whole Genome Bioarray (~36 000 mouse gene targets) annotation data (chip mwgcod) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Codelink Mouse Whole Genome Bioarray (~36 000 mouse gene targets) annotation data (chip mwgcod) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mwgcod.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3d6e2af6b05d6e07a212c043dc9d37c4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Codelink Mouse Whole Genome Bioarray (~36 000 mouse gene targets) annotation data (chip mwgcod)' - description: 'Codelink Mouse Whole Genome Bioarray (~36 000 mouse gene targets) annotation data (chip mwgcod) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mygene/meta.yaml b/recipes/bioconductor-mygene/meta.yaml index a48b4d7634c6f..a0793f7eba0f2 100644 --- a/recipes/bioconductor-mygene/meta.yaml +++ b/recipes/bioconductor-mygene/meta.yaml @@ -1,58 +1,66 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "mygene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MyGene.Info_ provides simple-to-use REST web services to query/retrieve gene annotation data. It's designed with simplicity and performance emphasized. *mygene*, is an easy-to-use R wrapper to access MyGene.Info_ services. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Access MyGene.Info_ services -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 01ebbd87d5d6b57ca6987eef9c3ae95a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mygene", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:mygene + - doi:10.1101/009333 + parent_recipe: + name: bioconductor-mygene + path: recipes/bioconductor-mygene + version: 1.16.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle requirements: host: - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-hmisc - - 'r-httr >=0.3' - - 'r-jsonlite >=0.9.7' + - r-httr >=0.3 + - r-jsonlite >=0.9.7 - r-plyr - r-sqldf run: - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-hmisc - - 'r-httr >=0.3' - - 'r-jsonlite >=0.9.7' + - r-httr >=0.3 + - r-jsonlite >=0.9.7 - r-plyr - r-sqldf + +source: + md5: f53f04381d0b954109c518d4d4876f96 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Access MyGene.Info_ services' - description: 'MyGene.Info_ provides simple-to-use REST web services to query/retrieve gene annotation data. It''s designed with simplicity and performance emphasized. *mygene*, is an easy-to-use R wrapper to access MyGene.Info_ services.' -extra: - identifiers: - - biotools:mygene - - doi:10.1101/009333 - parent_recipe: - name: bioconductor-mygene - path: recipes/bioconductor-mygene - version: 1.16.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-myvariant/meta.yaml b/recipes/bioconductor-myvariant/meta.yaml index bfcdcd49ceb7b..e7bc863571d04 100644 --- a/recipes/bioconductor-myvariant/meta.yaml +++ b/recipes/bioconductor-myvariant/meta.yaml @@ -1,30 +1,40 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "myvariant" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: MyVariant.info is a comprehensive aggregation of variant annotation resources. myvariant is a wrapper for querying MyVariant.info services + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Accesses MyVariant.info variant query and annotation services -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 110e5245914806eb225bad404727124f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-myvariant", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:myvariant + - doi:10.1101/035667 + parent_recipe: + name: bioconductor-myvariant + path: recipes/bioconductor-myvariant + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle requirements: host: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-hmisc - r-httr @@ -32,29 +42,25 @@ requirements: - r-magrittr - r-plyr run: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-hmisc - r-httr - r-jsonlite - r-magrittr - r-plyr + +source: + md5: aa962af64065d70827f09a7388869286 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Accesses MyVariant.info variant query and annotation services' - description: 'MyVariant.info is a comprehensive aggregation of variant annotation resources. myvariant is a wrapper for querying MyVariant.info services' -extra: - identifiers: - - biotools:myvariant - - doi:10.1101/035667 - parent_recipe: - name: bioconductor-myvariant - path: recipes/bioconductor-myvariant - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mzid/meta.yaml b/recipes/bioconductor-mzid/meta.yaml index 52a34ad7b0de9..c72410f412e36 100644 --- a/recipes/bioconductor-mzid/meta.yaml +++ b/recipes/bioconductor-mzid/meta.yaml @@ -1,28 +1,39 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "mzID" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less 'pretty' output than a vendor specific parser. Please contact the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quickly. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: An mzIdentML parser for R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8ede9a6260d4b9aa70edd19838e3c80c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mzid", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:mzid + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-mzid + path: recipes/bioconductor-mzid + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat requirements: host: - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - bioconductor-protgenerics >=1.38.0,<1.39.0 - r-base - r-doparallel - r-foreach @@ -30,28 +41,23 @@ requirements: - r-plyr - r-xml run: - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' + - bioconductor-protgenerics >=1.38.0,<1.39.0 - r-base - r-doparallel - r-foreach - r-iterators - r-plyr - r-xml + +source: + md5: 3df562afb53b11d4b7f38aa6716f3f99 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'An mzIdentML parser for R' - description: 'A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less ''pretty'' output than a vendor specific parser. Please contact the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quickly.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:mzid - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-mzid - path: recipes/bioconductor-mzid - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-mzr/meta.yaml b/recipes/bioconductor-mzr/meta.yaml index 9a63146869b81..5db8225a3b3fc 100644 --- a/recipes/bioconductor-mzr/meta.yaml +++ b/recipes/bioconductor-mzr/meta.yaml @@ -1,64 +1,70 @@ -{% set version = "2.36.0" %} +{% set version = "2.40.0" %} {% set name = "mzR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a subset of the proteowizard library for mzXML, mzML and mzIdentML. The netCDF reading code has previously been used in XCMS. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aae8b88db5fd49675b653b861702800e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-mzr", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:mzr + parent_recipe: + name: bioconductor-mzr + path: recipes/bioconductor-mzr + version: 2.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML, rmarkdown # SystemRequirements: C++11, GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 - r-base - r-ncdf4 - - 'r-rcpp >=0.10.1' + - r-rcpp >=0.10.1 - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 - r-base - r-ncdf4 - - 'r-rcpp >=0.10.1' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + - r-rcpp >=0.10.1 + +source: + md5: d1139d459bfd5b65bb24669ea8e1a387 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)' - description: 'mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a subset of the proteowizard library for mzXML, mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:mzr - parent_recipe: - name: bioconductor-mzr - path: recipes/bioconductor-mzr - version: 2.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nadfinder/meta.yaml b/recipes/bioconductor-nadfinder/meta.yaml index fef35a4d2ebc1..6b08d2ad4b7f2 100644 --- a/recipes/bioconductor-nadfinder/meta.yaml +++ b/recipes/bioconductor-nadfinder/meta.yaml @@ -1,78 +1,84 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "NADfinder" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Nucleolus is an important structure inside the nucleus in eukaryotic cells. It is the site for transcribing rDNA into rRNA and for assembling ribosomes, aka ribosome biogenesis. In addition, nucleoli are dynamic hubs through which numerous proteins shuttle and contact specific non-rDNA genomic loci. Deep sequencing analyses of DNA associated with isolated nucleoli (NAD- seq) have shown that specific loci, termed nucleolus- associated domains (NADs) form frequent three- dimensional associations with nucleoli. NAD-seq has been used to study the biological functions of NAD and the dynamics of NAD distribution during embryonic stem cell (ESC) differentiation. Here, we developed a Bioconductor package NADfinder for bioinformatic analysis of the NAD-seq data, including baseline correction, smoothing, normalization, peak calling, and annotation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Call wide peaks for sequencing data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d60f5020a7e46305fafc626c59a11851 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nadfinder", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-nadfinder + path: recipes/bioconductor-nadfinder + version: 1.4.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat, BiocManager, rmarkdown requirements: host: - - 'bioconductor-atacseqqc >=1.26.0,<1.27.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-csaw >=1.36.0,<1.37.0' - - 'bioconductor-empiricalbrownsmethod >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-trackviewer >=1.38.0,<1.39.0' + - bioconductor-atacseqqc >=1.30.0,<1.31.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-csaw >=1.40.0,<1.41.0 + - bioconductor-empiricalbrownsmethod >=1.34.0,<1.35.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-trackviewer >=1.42.0,<1.43.0 - r-base - r-baseline - r-corrplot - r-metap - r-signal run: - - 'bioconductor-atacseqqc >=1.26.0,<1.27.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-csaw >=1.36.0,<1.37.0' - - 'bioconductor-empiricalbrownsmethod >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-trackviewer >=1.38.0,<1.39.0' + - bioconductor-atacseqqc >=1.30.0,<1.31.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-csaw >=1.40.0,<1.41.0 + - bioconductor-empiricalbrownsmethod >=1.34.0,<1.35.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-trackviewer >=1.42.0,<1.43.0 - r-base - r-baseline - r-corrplot - r-metap - r-signal + +source: + md5: 75fcb8ce2a5bedab332b7407603b6516 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Call wide peaks for sequencing data' - description: 'Nucleolus is an important structure inside the nucleus in eukaryotic cells. It is the site for transcribing rDNA into rRNA and for assembling ribosomes, aka ribosome biogenesis. In addition, nucleoli are dynamic hubs through which numerous proteins shuttle and contact specific non-rDNA genomic loci. Deep sequencing analyses of DNA associated with isolated nucleoli (NAD- seq) have shown that specific loci, termed nucleolus- associated domains (NADs) form frequent three- dimensional associations with nucleoli. NAD-seq has been used to study the biological functions of NAD and the dynamics of NAD distribution during embryonic stem cell (ESC) differentiation. Here, we developed a Bioconductor package NADfinder for bioinformatic analysis of the NAD-seq data, including baseline correction, smoothing, normalization, peak calling, and annotation.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-nadfinder - path: recipes/bioconductor-nadfinder - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nanomethviz/build_failure.linux-64.yaml b/recipes/bioconductor-nanomethviz/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..09fbb69e25aa2 --- /dev/null +++ b/recipes/bioconductor-nanomethviz/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: bf8a669213667a4fc410ba87463e8ff32438af3134767a12246207080163ce11 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + description: NanoMethViz is a toolkit for visualising methylation data from Oxford + Nanopore sequencing. It can be used to explore methylation patterns from reads + derived from Oxford Nanopore direct DNA sequencing with methylation called by + callers including nanopolish, f5c and megalodon. The plots in this package allow + the visualisation of methylation profiles aggregated over experimental groups + and across classes of genomic features. + home: https://bioconductor.org/packages/3.20/bioc/html/NanoMethViz.html + license: Apache License (>= 2.0) + summary: Visualise methylation data from Oxford Nanopore sequencing + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/conda/conda-bld/bioconductor-nanomethviz_1735166811180/work + export PREFIX=/opt/conda/conda-bld/bioconductor-nanomethviz_1735166811180/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-nanomethviz_1735166811180/_build_env + export SRC_DIR=/opt/conda/conda-bld/bioconductor-nanomethviz_1735166811180/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-nanomethviz-3.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-nanomethviz-3.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-nanomethviz-3.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-nanomethviz-3.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-nanomethviz_1735166811180/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/R/library + * installing *source* package NanoMethViz ... + ** package NanoMethViz successfully unpacked and MD5 sums checked + ** using staged installation + ** libs + Error: C20 standard requested but CXX20 is not defined + * removing /opt/conda/conda-bld/bioconductor-nanomethviz_1735166811180/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/R/library/NanoMethViz + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-nanomethviz_1735166811180/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-nanomethviz_1735166811180/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-nanomethviz/meta.yaml b/recipes/bioconductor-nanomethviz/meta.yaml index 94a584c8be8d5..6722bf4baae0e 100644 --- a/recipes/bioconductor-nanomethviz/meta.yaml +++ b/recipes/bioconductor-nanomethviz/meta.yaml @@ -1,49 +1,55 @@ -{% set version = "2.8.1" %} +{% set version = "3.2.0" %} {% set name = "NanoMethViz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing. It can be used to explore methylation patterns from reads derived from Oxford Nanopore direct DNA sequencing with methylation called by callers including nanopolish, f5c and megalodon. The plots in this package allow the visualisation of methylation profiles aggregated over experimental groups and across classes of genomic features. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Apache License (>= 2.0) + summary: Visualise methylation data from Oxford Nanopore sequencing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ddef080c0bf460814f94f28ee5f98d5 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nanomethviz", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, DSS, Mus.musculus (>= 1.3.1), Homo.sapiens (>= 1.3.1), org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm39.refGene, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0), covr -# SystemRequirements: C++17 +# SystemRequirements: C++20 requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsseq >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsseq >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-assertthat - r-base - r-cli - - 'r-cpp11 >=0.2.5' - - r-data.table + - r-cpp11 >=0.2.5 - r-dbscan - r-dplyr - r-e1071 - r-forcats - r-fs - - 'r-ggplot2 >=3.4.0' + - r-ggplot2 >=3.4.0 - r-ggrastr - r-glue - r-patchwork @@ -52,37 +58,36 @@ requirements: - r-rcpp - r-readr - r-rlang - - 'r-scales >=1.2.0' - - r-scico + - r-scales >=1.2.0 - r-stringr - r-tibble - r-tidyr - r-withr - libblas - liblapack + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsseq >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsseq >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-assertthat - r-base - r-cli - - 'r-cpp11 >=0.2.5' - - r-data.table + - r-cpp11 >=0.2.5 - r-dbscan - r-dplyr - r-e1071 - r-forcats - r-fs - - 'r-ggplot2 >=3.4.0' + - r-ggplot2 >=3.4.0 - r-ggrastr - r-glue - r-patchwork @@ -91,22 +96,21 @@ requirements: - r-rcpp - r-readr - r-rlang - - 'r-scales >=1.2.0' - - r-scico + - r-scales >=1.2.0 - r-stringr - r-tibble - r-tidyr - r-withr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 37353e2801348c57a5e4e067bb7d9468 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Apache License (>= 2.0)' - summary: 'Visualise methlation data from Oxford Nanopore sequencing' - description: 'NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing. It can be used to explore methylation patterns from reads derived from Oxford Nanopore direct DNA sequencing with methylation called by callers including nanopolish, f5c and megalodon. The plots in this package allow the visualisation of methylation profiles aggregated over experimental groups and across classes of genomic features.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nanoporernaseq/build_failure.linux-64.yaml b/recipes/bioconductor-nanoporernaseq/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..76cb6289796f3 --- /dev/null +++ b/recipes/bioconductor-nanoporernaseq/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 71d2226171b9993387cb2fef6f7ea78e0907d2467a77fd371f663c50ce9944cf # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-glue: 1.8.0-r44h2b5f3a1_0 conda-forge + r-httr: 1.4.7-r44hc72bb7e_1 conda-forge + r-jsonlite: 1.8.9-r44h2b5f3a1_0 conda-forge + r-lifecycle: 1.0.4-r44hc72bb7e_1 conda-forge + r-magrittr: 2.0.3-r44hb1dbf0f_3 conda-forge + r-memoise: 2.0.1-r44hc72bb7e_3 conda-forge + r-mime: 0.12-r44hb1dbf0f_3 conda-forge + r-openssl: 2.2.2-r44he8289e2_0 conda-forge + r-pillar: 1.10.0-r44hc72bb7e_0 conda-forge + r-pkgconfig: 2.0.3-r44hc72bb7e_4 conda-forge + r-plogr: 0.2.0-r44hc72bb7e_1006 conda-forge + r-png: 0.1_8-r44h21f035c_2 conda-forge + r-purrr: 1.0.2-r44hdb488b9_1 conda-forge + r-r6: 2.5.1-r44hc72bb7e_3 conda-forge + r-rappdirs: 0.3.3-r44hb1dbf0f_3 conda-forge + r-rlang: 1.1.4-r44ha18555a_1 conda-forge + r-rsqlite: 2.3.9-r44h93ab643_0 conda-forge + r-stringi: 1.8.4-r44h33cde33_3 conda-forge + r-stringr: 1.5.1-r44h785f33e_1 conda-forge + r-sys: 3.4.3-r44h2b5f3a1_0 conda-forge + r-tibble: 3.2.1-r44hdb488b9_3 conda-forge + r-tidyr: 1.3.1-r44h0d4f4ea_1 conda-forge + r-tidyselect: 1.2.1-r44hc72bb7e_1 conda-forge + r-utf8: 1.2.4-r44hb1dbf0f_1 conda-forge + r-vctrs: 0.6.5-r44h0d4f4ea_1 conda-forge + r-withr: 3.0.2-r44hc72bb7e_0 conda-forge + r-yaml: 2.3.10-r44hdb488b9_0 conda-forge + readline: 8.2-h8228510_1 conda-forge + sed: 4.8-he412f7d_0 conda-forge + setuptools: 75.6.0-pyhff2d567_1 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tktable: 2.10-h8bc8fbc_6 conda-forge + toml: 0.10.2-pyhd8ed1ab_1 conda-forge + tomlkit: 0.13.2-pyha770c72_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + xmltodict: 0.14.2-pyhd8ed1ab_1 conda-forge + xorg-libice: 1.1.2-hb9d3cd8_0 conda-forge + xorg-libsm: 1.2.5-he73a12e_0 conda-forge + xorg-libx11: 1.8.10-h4f16b4b_1 conda-forge + xorg-libxau: 1.0.12-hb9d3cd8_0 conda-forge + xorg-libxdmcp: 1.1.5-hb9d3cd8_0 conda-forge + xorg-libxext: 1.3.6-hb9d3cd8_0 conda-forge + xorg-libxrender: 0.9.12-hb9d3cd8_0 conda-forge + xorg-libxt: 1.3.1-hb9d3cd8_0 conda-forge + yaml: 0.2.5-h7f98852_2 conda-forge + yq: 3.4.3-pyhd8ed1ab_1 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: NanoporeRNASeq_1.15.0_62af5121b9.tar.gz + Downloading https://bioconductor.org/packages/3.20/data/experiment/src/contrib/NanoporeRNASeq_1.15.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.140916 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioconductor.org/packages/3.20/bioc/src/contrib/Archive/NanoporeRNASeq/NanoporeRNASeq_1.15.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.132874 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioarchive.galaxyproject.org/NanoporeRNASeq_1.15.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.568765 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://depot.galaxyproject.org/software/bioconductor-nanoporernaseq/bioconductor-nanoporernaseq_1.15.0_src_all.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.473374 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download https://depot.galaxyproject.org/software/bioconductor-nanoporernaseq/bioconductor-nanoporernaseq_1.15.0_src_all.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-nanoporernaseq/meta.yaml b/recipes/bioconductor-nanoporernaseq/meta.yaml index 262cf057ce809..e69f5b66a0df7 100644 --- a/recipes/bioconductor-nanoporernaseq/meta.yaml +++ b/recipes/bioconductor-nanoporernaseq/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.12.0" %} +{% set version = "1.15.0" %} {% set name = "NanoporeRNASeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eca12ebcd403efd53e1b38d5f03f2027 +about: + description: The NanoporeRNASeq package contains long read RNA-Seq data generated using Oxford Nanopore Sequencing. The data consists of 6 samples from two human cell lines (K562 and MCF7) that were generated by the SG-NEx project. Each of these cell lines has three replicates, with 1 direct RNA sequencing data and 2 cDNA sequencing data. Reads are aligned to chromosome 22 (Grch38) and stored as bam files. The original data is from the SG-NEx project. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Nanopore RNA-Seq Example data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nanoporernaseq", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, bambu, ggbio, BSgenome.Hsapiens.NCBI.GRCh38, circlize, ComplexHeatmap, apeglm, rlang, rmarkdown, GenomicAlignments, Rsamtools requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 62af5121b9015934e82a2cafeae598a2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Nanopore RNA-Seq Example data' - description: 'The NanoporeRNASeq package contains long read RNA-Seq data generated using Oxford Nanopore Sequencing. The data consists of 6 samples from two human cell lines (K562 and MCF7) that were generated by the SG-NEx project. Each of these cell lines has three replicates, with 1 direct RNA sequencing data and 2 cDNA sequencing data. Reads are aligned to chromosome 22 (Grch38) and stored as bam files. The original data is from the SG-NEx project.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nanoporernaseq/post-link.sh b/recipes/bioconductor-nanoporernaseq/post-link.sh index cb6624b6a8d06..876723946db8f 100644 --- a/recipes/bioconductor-nanoporernaseq/post-link.sh +++ b/recipes/bioconductor-nanoporernaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "nanoporernaseq-1.12.0" +installBiocDataPackage.sh "nanoporernaseq-1.15.0" diff --git a/recipes/bioconductor-nanostringdiff/meta.yaml b/recipes/bioconductor-nanostringdiff/meta.yaml index ed2b6dc1d1f75..60e54b129c9dd 100644 --- a/recipes/bioconductor-nanostringdiff/meta.yaml +++ b/recipes/bioconductor-nanostringdiff/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "NanoStringDiff" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This Package utilizes a generalized linear model(GLM) of the negative binomial family to characterize count data and allows for multi-factor design. NanoStrongDiff incorporate size factors, calculated from positive controls and housekeeping controls, and background level, obtained from negative controls, in the model framework so that all the normalization information provided by NanoString nCounter Analyzer is fully utilized. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Differential Expression Analysis of NanoString nCounter Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3614c5bcf8aeea002875aa005d746092 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nanostringdiff", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-matrixstats - r-rcpp - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-matrixstats - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 28069ba4127a6aed423d6bf100885c6e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL - summary: 'Differential Expression Analysis of NanoString nCounter Data' - description: 'This Package utilizes a generalized linear model(GLM) of the negative binomial family to characterize count data and allows for multi-factor design. NanoStrongDiff incorporate size factors, calculated from positive controls and housekeeping controls, and background level, obtained from negative controls, in the model framework so that all the normalization information provided by NanoString nCounter Analyzer is fully utilized.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nanostringnctools/meta.yaml b/recipes/bioconductor-nanostringnctools/meta.yaml index 8e2ae08e86524..f903a6a595d96 100644 --- a/recipes/bioconductor-nanostringnctools/meta.yaml +++ b/recipes/bioconductor-nanostringnctools/meta.yaml @@ -1,32 +1,33 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "NanoStringNCTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for NanoString Technologies nCounter Technology. Provides support for reading RCC files into an ExpressionSet derived object. Also includes methods for QC and normalizaztion of NanoString data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + summary: NanoString nCounter Tools -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 97985a577c04cc2d7c19d00f2bd8e1d1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nanostringnctools", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: biovizBase, ggbio, RUnit, rmarkdown, knitr, qpdf requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggbeeswarm - r-ggiraph @@ -35,11 +36,11 @@ requirements: - r-pheatmap - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggbeeswarm - r-ggiraph @@ -47,12 +48,16 @@ requirements: - r-ggthemes - r-pheatmap - r-rcolorbrewer + +source: + md5: f593b22f668fc055c6220cd732864cf4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: MIT - summary: 'NanoString nCounter Tools' - description: 'Tools for NanoString Technologies nCounter Technology. Provides support for reading RCC files into an ExpressionSet derived object. Also includes methods for QC and normalizaztion of NanoString data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nanotube/meta.yaml b/recipes/bioconductor-nanotube/meta.yaml index 9a1e127227387..57352aaf98896 100644 --- a/recipes/bioconductor-nanotube/meta.yaml +++ b/recipes/bioconductor-nanotube/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "NanoTube" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: NanoTube includes functions for the processing, quality control, analysis, and visualization of NanoString nCounter data. Analysis functions include differential analysis and gene set analysis methods, as well as postprocessing steps to help understand the results. Additional functions are included to enable interoperability with other Bioconductor NanoString data analysis packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: An Easy Pipeline for NanoString nCounter Data Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 524cdc55bcaf670d538be8f6c2f06c11 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nanotube", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly, rlang, rmarkdown, ruv, RUVSeq, shiny, testthat, xlsx requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-ggplot2 - r-reshape run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-ggplot2 - r-reshape + +source: + md5: 12888ce680c2f393f73f11a1df7f3cb3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'An Easy Pipeline for NanoString nCounter Data Analysis' - description: 'NanoTube includes functions for the processing, quality control, analysis, and visualization of NanoString nCounter data. Analysis functions include differential analysis and gene set analysis methods, as well as postprocessing steps to help understand the results. Additional functions are included to enable interoperability with other Bioconductor NanoString data analysis packages.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nanotubes/meta.yaml b/recipes/bioconductor-nanotubes/meta.yaml index 3af73d0c984a9..e1f65d59d419b 100644 --- a/recipes/bioconductor-nanotubes/meta.yaml +++ b/recipes/bioconductor-nanotubes/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "nanotubes" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ff283cb49c319a357c22e17d2df22715 +about: + description: Cap Analysis of Gene Expression (CAGE) data from "Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo" by Bornholdt et al. supplied as CAGE Transcription Start Sites (CTSSs). + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Mouse nanotube CAGE data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nanotubes", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer, CAGEfightR requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e12d5b3c6facf1c6aa320715282de427 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Mouse nanotube CAGE data' - description: 'Cap Analysis of Gene Expression (CAGE) data from "Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo" by Bornholdt et al. supplied as CAGE Transcription Start Sites (CTSSs).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nanotubes/post-link.sh b/recipes/bioconductor-nanotubes/post-link.sh index b2fb9f7b15f26..1017cabf8ecdb 100644 --- a/recipes/bioconductor-nanotubes/post-link.sh +++ b/recipes/bioconductor-nanotubes/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "nanotubes-1.18.0" +installBiocDataPackage.sh "nanotubes-1.22.0" diff --git a/recipes/bioconductor-nbamseq/meta.yaml b/recipes/bioconductor-nbamseq/meta.yaml index 4476179efd3cd..8db6005ae26ca 100644 --- a/recipes/bioconductor-nbamseq/meta.yaml +++ b/recipes/bioconductor-nbamseq/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "NBAMSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: High-throughput sequencing experiments followed by differential expression analysis is a widely used approach to detect genomic biomarkers. A fundamental step in differential expression analysis is to model the association between gene counts and covariates of interest. NBAMSeq a flexible statistical model based on the generalized additive model and allows for information sharing across genes in variance estimation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Negative Binomial Additive Model for RNA-Seq Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45181f95a38937784da7cbad4d416811 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nbamseq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, ggplot2 requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-mgcv >=1.8-24' + - r-mgcv >=1.8-24 run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-mgcv >=1.8-24' + - r-mgcv >=1.8-24 + +source: + md5: 9ac3de6a0dece162a3e824e71207811e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Negative Binomial Additive Model for RNA-Seq Data' - description: 'High-throughput sequencing experiments followed by differential expression analysis is a widely used approach to detect genomic biomarkers. A fundamental step in differential expression analysis is to model the association between gene counts and covariates of interest. NBAMSeq a flexible statistical model based on the generalized additive model and allows for information sharing across genes in variance estimation.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ncdfflow/meta.yaml b/recipes/bioconductor-ncdfflow/meta.yaml index 976e9392a7934..40e50fd0ae44d 100644 --- a/recipes/bioconductor-ncdfflow/meta.yaml +++ b/recipes/bioconductor-ncdfflow/meta.yaml @@ -1,64 +1,71 @@ -{% set version = "2.48.0" %} +{% set version = "2.52.0" %} {% set name = "ncdfFlow" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides HDF5 storage based methods and functions for manipulation of flow cytometry data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3.0-only + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 974c454443e3ed6c243aed7395f28911 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ncdfflow", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:ncdfflow + - doi:10.1016/j.copbio.2012.09.003 + parent_recipe: + name: bioconductor-ncdfflow + path: recipes/bioconductor-ncdfflow + version: 2.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat,parallel,flowStats,knitr requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-bh - r-cpp11 - libblas - liblapack + - zlib run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-bh - r-cpp11 - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: d67423b40637d81fccdf25642a6ae33b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3.0-only - summary: 'ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.' - description: 'Provides HDF5 storage based methods and functions for manipulation of flow cytometry data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:ncdfflow - - doi:10.1016/j.copbio.2012.09.003 - parent_recipe: - name: bioconductor-ncdfflow - path: recipes/bioconductor-ncdfflow - version: 2.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ncgtw/meta.yaml b/recipes/bioconductor-ncgtw/meta.yaml index c74112360f5e6..3c1677c55ebb4 100644 --- a/recipes/bioconductor-ncgtw/meta.yaml +++ b/recipes/bioconductor-ncgtw/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "ncGTW" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The purpose of ncGTW is to help XCMS for LC-MS data alignment. Currently, ncGTW can detect the misaligned feature groups by XCMS, and the user can choose to realign these feature groups by ncGTW or not. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea33321b03c3751afd04234fd7fbcda3 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ncgtw", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, testthat, rmarkdown requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 6f38bb92656caf6a7910e3266da17355 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Alignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection' - description: 'The purpose of ncGTW is to help XCMS for LC-MS data alignment. Currently, ncGTW can detect the misaligned feature groups by XCMS, and the user can choose to realign these feature groups by ncGTW or not.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ncigraph/meta.yaml b/recipes/bioconductor-ncigraph/meta.yaml index 090a8f728c23d..cf479026969de 100644 --- a/recipes/bioconductor-ncigraph/meta.yaml +++ b/recipes/bioconductor-ncigraph/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "NCIgraph" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides various methods to load the pathways from the NCI Pathways Database in R graph objects and to re-format them. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Pathways from the NCI Pathways Database -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed568ded26dce9e64d5f38606e65c13d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ncigraph", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:ncigraph + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ncigraph + path: recipes/bioconductor-ncigraph + version: 1.28.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Rgraphviz requirements: host: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 - r-base - r-r.oo run: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 - r-base - r-r.oo + +source: + md5: 39ef54003713b1eddd5262eee4628033 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Pathways from the NCI Pathways Database' - description: 'Provides various methods to load the pathways from the NCI Pathways Database in R graph objects and to re-format them.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:ncigraph - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-ncigraph - path: recipes/bioconductor-ncigraph - version: 1.28.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ncigraphdata/meta.yaml b/recipes/bioconductor-ncigraphdata/meta.yaml index 91195f389e417..487e2110a9ebe 100644 --- a/recipes/bioconductor-ncigraphdata/meta.yaml +++ b/recipes/bioconductor-ncigraphdata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "NCIgraphData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f144169473d42fafb1966986dcf15628 +about: + description: Provides pathways from the NCI Pathways Database as R graph objects + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Data for the NCIgraph software package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ncigraphdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: Rgraphviz requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 10459d011efb985487e297cbe4b9ffac + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Data for the NCIgraph software package' - description: 'Provides pathways from the NCI Pathways Database as R graph objects' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ncigraphdata/post-link.sh b/recipes/bioconductor-ncigraphdata/post-link.sh index 2c15cc4502b3a..86014748c2c32 100644 --- a/recipes/bioconductor-ncigraphdata/post-link.sh +++ b/recipes/bioconductor-ncigraphdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ncigraphdata-1.38.0" +installBiocDataPackage.sh "ncigraphdata-1.42.0" diff --git a/recipes/bioconductor-ncrnatools/meta.yaml b/recipes/bioconductor-ncrnatools/meta.yaml index 0be79f82b0b3b..3ffa5d5b27cd4 100644 --- a/recipes/bioconductor-ncrnatools/meta.yaml +++ b/recipes/bioconductor-ncrnatools/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "ncRNAtools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ncRNAtools provides a set of basic tools for handling and analyzing non-coding RNAs. These include tools to access the RNAcentral database and to predict and visualize the secondary structure of non-coding RNAs. The package also provides tools to read, write and interconvert the file formats most commonly used for representing such secondary structures. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: An R toolkit for non-coding RNA -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4e6f2f3809ca2cfe114ecc2c63f1d3dc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ncrnatools", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-httr - r-xml2 run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-httr - r-xml2 + +source: + md5: 65232d5ff400589d895ca1fac017e932 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'An R toolkit for non-coding RNA' - description: 'ncRNAtools provides a set of basic tools for handling and analyzing non-coding RNAs. These include tools to access the RNAcentral database and to predict and visualize the secondary structure of non-coding RNAs. The package also provides tools to read, write and interconvert the file formats most commonly used for representing such secondary structures.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ndexr/meta.yaml b/recipes/bioconductor-ndexr/meta.yaml index e78c598266f08..61824972f8e3c 100644 --- a/recipes/bioconductor-ndexr/meta.yaml +++ b/recipes/bioconductor-ndexr/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "ndexr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package offers an interface to NDEx servers, e.g. the public server at http://ndexbio.org/. It can retrieve and save networks via the API. Networks are offered as RCX object and as igraph representation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_3_clause + file LICENSE + license_file: LICENSE + summary: NDEx R client library -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: caa87487f3e0c062aa6b56b1dc6f70a0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ndexr", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-ndexr + path: recipes/bioconductor-ndexr + version: 1.2.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-rcx >=1.6.0,<1.7.0' + - bioconductor-rcx >=1.10.0,<1.11.0 - r-base - r-httr - r-jsonlite - r-plyr - r-tidyr run: - - 'bioconductor-rcx >=1.6.0,<1.7.0' + - bioconductor-rcx >=1.10.0,<1.11.0 - r-base - r-httr - r-jsonlite - r-plyr - r-tidyr + +source: + md5: 212ecbc3605714b0c940b9ba81448b2d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_3_clause + file LICENSE' - summary: 'NDEx R client library' - description: 'This package offers an interface to NDEx servers, e.g. the public server at http://ndexbio.org/. It can retrieve and save networks via the API. Networks are offered as RCX object and as igraph representation.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-ndexr - path: recipes/bioconductor-ndexr - version: 1.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nearbynding/meta.yaml b/recipes/bioconductor-nearbynding/meta.yaml index 5344eaad1760f..099e1302e0fb2 100644 --- a/recipes/bioconductor-nearbynding/meta.yaml +++ b/recipes/bioconductor-nearbynding/meta.yaml @@ -1,37 +1,38 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "nearBynding" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides a pipeline to discern RNA structure at and proximal to the site of protein binding within regions of the transcriptome defined by the user. CLIP protein-binding data can be input as either aligned BAM or peak-called bedGraph files. RNA structure can either be predicted internally from sequence or users have the option to input their own RNA structure data. RNA structure binding profiles can be visually and quantitatively compared across multiple formats. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Discern RNA structure proximal to protein binding -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2bcc4459fa78c6327ee2708f06da54db build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nearbynding", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown # SystemRequirements: bedtools (>= 2.28.0), Stereogene (>= v2.22), CapR (>= 1.1.1) requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 - r-base - r-dplyr - r-ggplot2 @@ -42,15 +43,15 @@ requirements: - r-rlang - r-transport run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 - r-base - r-dplyr - r-ggplot2 @@ -60,12 +61,16 @@ requirements: - r-r.utils - r-rlang - r-transport + +source: + md5: 8fb74f690601087b29f556c9f6a41943 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Discern RNA structure proximal to protein binding' - description: 'Provides a pipeline to discern RNA structure at and proximal to the site of protein binding within regions of the transcriptome defined by the user. CLIP protein-binding data can be input as either aligned BAM or peak-called bedGraph files. RNA structure can either be predicted internally from sequence or users have the option to input their own RNA structure data. RNA structure binding profiles can be visually and quantitatively compared across multiple formats.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nebulosa/meta.yaml b/recipes/bioconductor-nebulosa/meta.yaml index 7ee5a8801e91d..f6ad86d470290 100644 --- a/recipes/bioconductor-nebulosa/meta.yaml +++ b/recipes/bioconductor-nebulosa/meta.yaml @@ -1,51 +1,58 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "Nebulosa" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a enhanced visualization of single-cell data based on gene-weighted density estimation. Nebulosa recovers the signal from dropped-out features and allows the inspection of the joint expression from multiple features (e.g. genes). Seurat and SingleCellExperiment objects can be used within Nebulosa. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e71c21bbda87365578a49f21dd915fa4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nebulosa", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils, igraph, BiocFileCache, SeuratObject + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils, igraph, BiocFileCache, Seurat requirements: host: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 + - r-ggrastr - r-ks - r-matrix - r-patchwork - - r-seurat + - r-seuratobject run: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 + - r-ggrastr - r-ks - r-matrix - r-patchwork - - r-seurat + - r-seuratobject + +source: + md5: 7693058a1cf85b5d099559b2639cde2c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation' - description: 'This package provides a enhanced visualization of single-cell data based on gene-weighted density estimation. Nebulosa recovers the signal from dropped-out features and allows the inspection of the joint expression from multiple features (e.g. genes). Seurat and SingleCellExperiment objects can be used within Nebulosa.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nempi/build_failure.linux-64.yaml b/recipes/bioconductor-nempi/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..edab33b7f1212 --- /dev/null +++ b/recipes/bioconductor-nempi/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: 22f415dd745b6124db32809ba6c20d9ea5d56889edbfc75395317f60e5beb54b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-epinem[version='>=1.30.0,<1.31.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-epinem >=1.30.0,<1.31.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-epinem >=1.30.0,<1.31.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-epinem[version='>=1.30.0,<1.31.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-epinem >=1.30.0,<1.31.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-epinem >=1.30.0,<1.31.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-epinem[version='>=1.30.0,<1.31.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-epinem >=1.30.0,<1.31.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-epinem >=1.30.0,<1.31.0 [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. +reason: |- + needs bioconductor-epinem to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-nempi/build_failure.osx-64.yaml b/recipes/bioconductor-nempi/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..0952e678bcf07 --- /dev/null +++ b/recipes/bioconductor-nempi/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 22f415dd745b6124db32809ba6c20d9ea5d56889edbfc75395317f60e5beb54b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + needs bioconductor-epinem to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-nempi/meta.yaml b/recipes/bioconductor-nempi/meta.yaml index 35ac5c2778196..7abff7038086d 100644 --- a/recipes/bioconductor-nempi/meta.yaml +++ b/recipes/bioconductor-nempi/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "nempi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Takes as input an incomplete perturbation profile and differential gene expression in log odds and infers unobserved perturbations and augments observed ones. The inference is done by iteratively inferring a network from the perturbations and inferring perturbations from the network. The network inference is done by Nested Effects Models. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Inferring unobserved perturbations from gene expression data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1180e323b8f109079a74702ef7159cda build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nempi", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocGenerics, rmarkdown, RUnit, BiocStyle requirements: host: - - 'bioconductor-epinem >=1.26.0,<1.27.0' - - 'bioconductor-mnem >=1.18.0,<1.19.0' + - bioconductor-epinem >=1.30.0,<1.31.0 + - bioconductor-mnem >=1.22.0,<1.23.0 - r-base - r-e1071 - r-matrixstats @@ -31,21 +33,24 @@ requirements: - r-nnet - r-randomforest run: - - 'bioconductor-epinem >=1.26.0,<1.27.0' - - 'bioconductor-mnem >=1.18.0,<1.19.0' + - bioconductor-epinem >=1.30.0,<1.31.0 + - bioconductor-mnem >=1.22.0,<1.23.0 - r-base - r-e1071 - r-matrixstats - r-naturalsort - r-nnet - r-randomforest + +source: + md5: 4ddadcdb8dda0bd40d87344ec2cd3139 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Inferring unobserved perturbations from gene expression data' - description: 'Takes as input an incomplete perturbation profile and differential gene expression in log odds and infers unobserved perturbations and augments observed ones. The inference is done by iteratively inferring a network from the perturbations and inferring perturbations from the network. The network inference is done by Nested Effects Models.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nestlink/meta.yaml b/recipes/bioconductor-nestlink/meta.yaml index 7547790cc430c..9d6f5d80dc606 100644 --- a/recipes/bioconductor-nestlink/meta.yaml +++ b/recipes/bioconductor-nestlink/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "NestLink" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides next-generation sequencing (NGS) and mass spectrometry (MS) sample data, code snippets and replication material used for developing NestLink. The NestLink approach is a protein binder selection and identification technology able to biophysically characterize thousands of library members at once without handling individual clones at any stage of the process. Data were acquired on NGS and MS platforms at the Functional Genomics Center Zurich. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: NestLink an R data package to guide through Engineered Peptide Barcodes for In-Depth Analyzes of Binding Protein Ensembles -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11cd94f5bd8b38cf261ae3346a283e81 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nestlink", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle (>= 2.2), DT, ggplot2, knitr, rmarkdown, testthat, specL, lattice, scales requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - - 'r-gplots >=3.0' - - 'r-protviz >=0.4' + - r-gplots >=3.0 + - r-protviz >=0.4 run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - - 'r-gplots >=3.0' - - 'r-protviz >=0.4' + - r-gplots >=3.0 + - r-protviz >=0.4 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20250104 + +source: + md5: 3fc4cdd3cb28a6f27b3be814b3e9334d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL - summary: 'NestLink an R data package to guide through Engineered Peptide Barcodes for In-Depth Analyzes of Binding Protein Ensembles' - description: 'Provides next-generation sequencing (NGS) and mass spectrometry (MS) sample data, code snippets and replication material used for developing NestLink. The NestLink approach is a protein binder selection and identification technology able to biophysically characterize thousands of library members at once without handling individual clones at any stage of the process. Data were acquired on NGS and MS platforms at the Functional Genomics Center Zurich.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nestlink/post-link.sh b/recipes/bioconductor-nestlink/post-link.sh index e4c21fc4a1132..2598e6f9839fd 100644 --- a/recipes/bioconductor-nestlink/post-link.sh +++ b/recipes/bioconductor-nestlink/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "nestlink-1.18.0" +installBiocDataPackage.sh "nestlink-1.22.0" diff --git a/recipes/bioconductor-netactivity/meta.yaml b/recipes/bioconductor-netactivity/meta.yaml index 78e371d72f461..fd041253faa4e 100644 --- a/recipes/bioconductor-netactivity/meta.yaml +++ b/recipes/bioconductor-netactivity/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "NetActivity" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: '#'' NetActivity enables to compute gene set scores from previously trained sparsely-connected autoencoders. The package contains a function to prepare the data (`prepareSummarizedExperiment`) and a function to compute the gene set scores (`computeGeneSetScores`). The package `NetActivityData` contains different pre-trained models to be directly applied to the data. Alternatively, the users might use the package to compute gene set scores using custom models.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Compute gene set scores from a deep learning framework -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3493b441d888adf6d3a089936bbeafd6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-netactivity", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0), tidyverse requirements: host: - - 'bioconductor-airway >=1.22.0,<1.23.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-netactivitydata >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-airway >=1.26.0,<1.27.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-netactivitydata >=1.8.0,<1.9.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-airway >=1.22.0,<1.23.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-netactivitydata >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-airway >=1.26.0,<1.27.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-netactivitydata >=1.8.0,<1.9.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + +source: + md5: aee224387f9df720b12309541d2953c7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Compute gene set scores from a deep learning framework' - description: '#'' NetActivity enables to compute gene set scores from previously trained sparsely-connected autoencoders. The package contains a function to prepare the data (`prepareSummarizedExperiment`) and a function to compute the gene set scores (`computeGeneSetScores`). The package `NetActivityData` contains different pre-trained models to be directly applied to the data. Alternatively, the users might use the package to compute gene set scores using custom models.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-netactivitydata/meta.yaml b/recipes/bioconductor-netactivitydata/meta.yaml index eb4cf6502a8c5..69624c08c4657 100644 --- a/recipes/bioconductor-netactivitydata/meta.yaml +++ b/recipes/bioconductor-netactivitydata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "NetActivityData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3805046d14d13afc30a0f082952f200 +about: + description: This package contains the weights from pre-trained shallow sparsely-connected autoencoders. This data is required for getting the gene set scores with NetActivity package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Data required for getting the gene set scores with NetActivity package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-netactivitydata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 48e57fff0a0666f0e03312f686825c25 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Data required for getting the gene set scores with NetActivity package' - description: 'This package contains the weights from pre-trained shallow sparsely-connected autoencoders. This data is required for getting the gene set scores with NetActivity package.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-netactivitydata/post-link.sh b/recipes/bioconductor-netactivitydata/post-link.sh index 945e66b43cd20..160de27a13e8a 100644 --- a/recipes/bioconductor-netactivitydata/post-link.sh +++ b/recipes/bioconductor-netactivitydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "netactivitydata-1.4.0" +installBiocDataPackage.sh "netactivitydata-1.8.0" diff --git a/recipes/bioconductor-netboost/meta.yaml b/recipes/bioconductor-netboost/meta.yaml index 827401588e5f8..c6ca1cb55c42a 100644 --- a/recipes/bioconductor-netboost/meta.yaml +++ b/recipes/bioconductor-netboost/meta.yaml @@ -1,29 +1,36 @@ -{% set version = "2.10.0" %} +{% set version = "2.14.0" %} {% set name = "netboost" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Boosting supported network analysis for high-dimensional omics applications. This package comes bundled with the MC-UPGMA clustering package by Yaniv Loewenstein. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Network Analysis Supported by Boosting -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d21f645a3fe85c35ff9b9127bce1fbca build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-netboost", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown # SystemRequirements: GNU make, Bash, Perl, Gzip requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-impute >=1.80.0,<1.81.0 - r-base - r-colorspace - r-dynamictreecut @@ -34,8 +41,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-impute >=1.80.0,<1.81.0 - r-base - r-colorspace - r-dynamictreecut @@ -43,18 +50,16 @@ requirements: - r-rcpp - r-rcppparallel - r-wgcna - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 24b404583b12464b5cc270a6cd1a0cd9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Network Analysis Supported by Boosting' - description: 'Boosting supported network analysis for high-dimensional omics applications. This package comes bundled with the MC-UPGMA clustering package by Yaniv Loewenstein.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nethet/meta.yaml b/recipes/bioconductor-nethet/meta.yaml index fa9f00d135eb1..54ea49689aa84 100644 --- a/recipes/bioconductor-nethet/meta.yaml +++ b/recipes/bioconductor-nethet/meta.yaml @@ -1,28 +1,33 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "nethet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package nethet is an implementation of statistical solid methodology enabling the analysis of network heterogeneity from high-dimensional data. It combines several implementations of recent statistical innovations useful for estimation and comparison of networks in a heterogeneous, high-dimensional setting. In particular, we provide code for formal two-sample testing in Gaussian graphical models (differential network and GGM-GSA; Stadler and Mukherjee, 2013, 2014) and make a novel network-based clustering algorithm available (mixed graphical lasso, Stadler and Mukherjee, 2013). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A bioconductor package for high-dimensional exploration of biological network heterogeneity -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 35bc35cf08904b721563aa54e486cc95 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nethet", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, xtable, BiocStyle, testthat requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base - r-compquadform - r-genenet @@ -39,8 +44,8 @@ requirements: - libblas - liblapack run: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base - r-compquadform - r-genenet @@ -54,16 +59,16 @@ requirements: - r-mclust - r-mvtnorm - r-network - build: - - {{ compiler('c') }} - - make + +source: + md5: 4775425acafec422168d1e53f9102d2e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'A bioconductor package for high-dimensional exploration of biological network heterogeneity' - description: 'Package nethet is an implementation of statistical solid methodology enabling the analysis of network heterogeneity from high-dimensional data. It combines several implementations of recent statistical innovations useful for estimation and comparison of networks in a heterogeneous, high-dimensional setting. In particular, we provide code for formal two-sample testing in Gaussian graphical models (differential network and GGM-GSA; Stadler and Mukherjee, 2013, 2014) and make a novel network-based clustering algorithm available (mixed graphical lasso, Stadler and Mukherjee, 2013).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-netpathminer/meta.yaml b/recipes/bioconductor-netpathminer/meta.yaml index 32eed2ae8d2b5..a37ea1410126a 100644 --- a/recipes/bioconductor-netpathminer/meta.yaml +++ b/recipes/bioconductor-netpathminer/meta.yaml @@ -1,55 +1,63 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "NetPathMiner" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: NetPathMiner is a general framework for network path mining using genome-scale networks. It constructs networks from KGML, SBML and BioPAX files, providing three network representations, metabolic, reaction and gene representations. NetPathMiner finds active paths and applies machine learning methods to summarize found paths for easy interpretation. It also provides static and interactive visualizations of networks and paths to aid manual investigation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: NetPathMiner for Biological Network Construction, Path Mining and Visualization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91cc0601961f682fcf1a2bed61eb6438 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-netpathminer", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:netpathminer + parent_recipe: + name: bioconductor-netpathminer + path: recipes/bioconductor-netpathminer + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle # SystemRequirements: libxml2, libSBML (>= 5.5) requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - r-base - - 'r-igraph >=1.0' + - r-igraph >=1.0 - libblas - liblapack - libxml2 + - zlib + - liblzma-devel run: - r-base - - 'r-igraph >=1.0' + - r-igraph >=1.0 - libxml2 - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 029f09aab87add082c84c57fb292859d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'NetPathMiner for Biological Network Construction, Path Mining and Visualization' - description: 'NetPathMiner is a general framework for network path mining using genome-scale networks. It constructs networks from KGML, SBML and BioPAX files, providing three network representations, metabolic, reaction and gene representations. NetPathMiner finds active paths and applies machine learning methods to summarize found paths for easy interpretation. It also provides static and interactive visualizations of networks and paths to aid manual investigation.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:netpathminer - parent_recipe: - name: bioconductor-netpathminer - path: recipes/bioconductor-netpathminer - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-netprior/meta.yaml b/recipes/bioconductor-netprior/meta.yaml index 146dd2bda1f80..307c83fc5e10a 100644 --- a/recipes/bioconductor-netprior/meta.yaml +++ b/recipes/bioconductor-netprior/meta.yaml @@ -1,24 +1,32 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "netprioR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A model for semi-supervised prioritisation of genes integrating network data, phenotypes and additional prior knowledge about TP and TN gene labels from the literature or experts. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A model for network-based prioritisation of genes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e4023edbe230057c85ae74d90f59fd1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-netprior", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-netprior + path: recipes/bioconductor-netprior + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, pander requirements: host: @@ -41,18 +49,16 @@ requirements: - r-matrix - r-proc - r-sparsemvn + +source: + md5: cbc8a4af4a2a607b46750d3c23c62349 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'A model for network-based prioritisation of genes' - description: 'A model for semi-supervised prioritisation of genes integrating network data, phenotypes and additional prior knowledge about TP and TN gene labels from the literature or experts.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-netprior - path: recipes/bioconductor-netprior - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-netresponse/meta.yaml b/recipes/bioconductor-netresponse/meta.yaml index 8f03e8e1a4efd..544cd7021f0b6 100644 --- a/recipes/bioconductor-netresponse/meta.yaml +++ b/recipes/bioconductor-netresponse/meta.yaml @@ -1,31 +1,42 @@ -{% set version = "1.62.0" %} +{% set version = "1.66.0" %} {% set name = "netresponse" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Algorithms for functional network analysis. Includes an implementation of a variational Dirichlet process Gaussian mixture model for nonparametric mixture modeling. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Functional Network Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 990c864cea311427d5af5f854edf4041 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-netresponse", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:netresponse + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-minet >=3.60.0,<3.61.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-minet >=3.64.0,<3.65.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-ggplot2 - r-igraph @@ -37,11 +48,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-minet >=3.60.0,<3.61.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-minet >=3.64.0,<3.65.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-ggplot2 - r-igraph @@ -50,22 +61,16 @@ requirements: - r-rcolorbrewer - r-reshape2 - r-rmarkdown - build: - - {{ compiler('c') }} - - make + +source: + md5: e20c3007cae4033b71198709e0240d4a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'Functional Network Analysis' - description: 'Algorithms for functional network analysis. Includes an implementation of a variational Dirichlet process Gaussian mixture model for nonparametric mixture modeling.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-netsam/meta.yaml b/recipes/bioconductor-netsam/meta.yaml index 7bdf23012be6b..ded4b35cb2697 100644 --- a/recipes/bioconductor-netsam/meta.yaml +++ b/recipes/bioconductor-netsam/meta.yaml @@ -1,59 +1,64 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "NetSAM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The NetSAM (Network Seriation and Modularization) package takes an edge-list representation of a weighted or unweighted network as an input, performs network seriation and modularization analysis, and generates as files that can be used as an input for the one-dimensional network visualization tool NetGestalt (http://www.netgestalt.org) or other network analysis. The NetSAM package can also generate correlation network (e.g. co-expression network) based on the input matrix data, perform seriation and modularization analysis for the correlation network and calculate the associations between the sample features and modules or identify the associated GO terms for the modules. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Network Seriation And Modularization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8248bae56028b8d8ee872cb007cbd7f5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-netsam", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, org.Sc.sgd.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dr.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.At.tair.db, rmarkdown, knitr, markdown requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-go.db >=3.20.0,<3.21.0 - r-base - - 'r-dbi >=0.5-1' - - 'r-doparallel >=1.0.10' - - 'r-foreach >=1.4.0' - - 'r-igraph >=0.6-1' - - 'r-r2html >=2.2.0' - - 'r-seriation >=1.0-6' - - 'r-survival >=2.37-7' - - 'r-wgcna >=1.34.0' + - r-dbi >=0.5-1 + - r-doparallel >=1.0.10 + - r-foreach >=1.4.0 + - r-igraph >=2.0.0 + - r-r2html >=2.2.0 + - r-seriation >=1.0-6 + - r-survival >=2.37-7 + - r-wgcna >=1.34.0 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-go.db >=3.20.0,<3.21.0 - r-base - - 'r-dbi >=0.5-1' - - 'r-doparallel >=1.0.10' - - 'r-foreach >=1.4.0' - - 'r-igraph >=0.6-1' - - 'r-r2html >=2.2.0' - - 'r-seriation >=1.0-6' - - 'r-survival >=2.37-7' - - 'r-wgcna >=1.34.0' + - r-dbi >=0.5-1 + - r-doparallel >=1.0.10 + - r-foreach >=1.4.0 + - r-igraph >=2.0.0 + - r-r2html >=2.2.0 + - r-seriation >=1.0-6 + - r-survival >=2.37-7 + - r-wgcna >=1.34.0 + +source: + md5: f4ef7a137f29d1af4a083e569ced22bd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Network Seriation And Modularization' - description: 'The NetSAM (Network Seriation and Modularization) package takes an edge-list representation of a weighted or unweighted network as an input, performs network seriation and modularization analysis, and generates as files that can be used as an input for the one-dimensional network visualization tool NetGestalt (http://www.netgestalt.org) or other network analysis. The NetSAM package can also generate correlation network (e.g. co-expression network) based on the input matrix data, perform seriation and modularization analysis for the correlation network and calculate the associations between the sample features and modules or identify the associated GO terms for the modules.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-netsmooth/meta.yaml b/recipes/bioconductor-netsmooth/meta.yaml index 8ba8209e5b286..fc8741d6d855d 100644 --- a/recipes/bioconductor-netsmooth/meta.yaml +++ b/recipes/bioconductor-netsmooth/meta.yaml @@ -1,57 +1,62 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "netSmooth" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: netSmooth is an R package for network smoothing of single cell RNA sequencing data. Using bio networks such as protein-protein interactions as priors for gene co-expression, netsmooth improves cell type identification from noisy, sparse scRNAseq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Network smoothing for scRNAseq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 074a02c5cf8d32c2111268513d8404c5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-netsmooth", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot requirements: host: - - 'bioconductor-clusterexperiment >=2.22.0,<2.23.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-clusterexperiment >=2.26.0,<2.27.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-data.table - r-entropy - r-matrix run: - - 'bioconductor-clusterexperiment >=2.22.0,<2.23.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-clusterexperiment >=2.26.0,<2.27.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-data.table - r-entropy - r-matrix + +source: + md5: 3663bc72d4b0ec48f3c85c1b2dd0f64f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Network smoothing for scRNAseq' - description: 'netSmooth is an R package for network smoothing of single cell RNA sequencing data. Using bio networks such as protein-protein interactions as priors for gene co-expression, netsmooth improves cell type identification from noisy, sparse scRNAseq data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-netzoor/meta.yaml b/recipes/bioconductor-netzoor/meta.yaml index 6091f5648d7f6..0ff52d0329e47 100644 --- a/recipes/bioconductor-netzoor/meta.yaml +++ b/recipes/bioconductor-netzoor/meta.yaml @@ -1,36 +1,39 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "netZooR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: netZooR unifies the implementations of several Network Zoo methods (netzoo, netzoo.github.io) into a single package by creating interfaces between network inference and network analysis methods. Currently, the package has 3 methods for network inference including PANDA and its optimized implementation OTTER (network reconstruction using mutliple lines of biological evidence), LIONESS (single-sample network inference), and EGRET (genotype-specific networks). Network analysis methods include CONDOR (community detection), ALPACA (differential community detection), CRANE (significance estimation of differential modules), MONSTER (estimation of network transition states). In addition, YARN allows to process gene expresssion data for tissue-specific analyses and SAMBAR infers missing mutation data based on pathway information. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Unified methods for the inference and analysis of gene regulatory networks -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f4adb3763df2df201212073e34bab10 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-netzoor", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 2.1.0), knitr, rmarkdown, pkgdown requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-pandar >=1.34.0,<1.35.0' - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - - 'bioconductor-stringdb >=2.14.0,<2.15.0' - - 'bioconductor-yarn >=1.28.0,<1.29.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-pandar >=1.38.0,<1.39.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 + - bioconductor-stringdb >=2.18.0,<2.19.0 + - bioconductor-yarn >=1.32.0,<1.33.0 - r-assertthat - r-base - r-data.table @@ -53,16 +56,17 @@ requirements: - r-tidyr - r-vegan - r-viridislite + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-pandar >=1.34.0,<1.35.0' - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - - 'bioconductor-stringdb >=2.14.0,<2.15.0' - - 'bioconductor-yarn >=1.28.0,<1.29.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-pandar >=1.38.0,<1.39.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 + - bioconductor-stringdb >=2.18.0,<2.19.0 + - bioconductor-yarn >=1.32.0,<1.33.0 - r-assertthat - r-base - r-data.table @@ -85,13 +89,16 @@ requirements: - r-tidyr - r-vegan - r-viridislite + +source: + md5: dcb15929eca8b8b2db4a935e9c204f77 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Unified methods for the inference and analysis of gene regulatory networks' - description: 'netZooR unifies the implementations of several Network Zoo methods (netzoo, netzoo.github.io) into a single package by creating interfaces between network inference and network analysis methods. Currently, the package has 3 methods for network inference including PANDA and its optimized implementation OTTER (network reconstruction using mutliple lines of biological evidence), LIONESS (single-sample network inference), and EGRET (genotype-specific networks). Network analysis methods include CONDOR (community detection), ALPACA (differential community detection), CRANE (significance estimation of differential modules), MONSTER (estimation of network transition states). In addition, YARN allows to process gene expresssion data for tissue-specific analyses and SAMBAR infers missing mutation data based on pathway information.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-neve2006/meta.yaml b/recipes/bioconductor-neve2006/meta.yaml index 42228ba33d521..fe2b002e5c3f3 100644 --- a/recipes/bioconductor-neve2006/meta.yaml +++ b/recipes/bioconductor-neve2006/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "0.40.0" %} +{% set version = "0.44.0" %} {% set name = "Neve2006" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1feec2f09bac8c69ba9df5ea29e7e08c +about: + description: Experimental organization of combined expression and CGH data + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: expression and CGH data on breast cancer cell lines build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-neve2006", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-hgu133a.db >=3.13.0,<3.14.0 - r-base run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-hgu133a.db >=3.13.0,<3.14.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2728c25e8357e4a82c70e4f6a82b492d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'expression and CGH data on breast cancer cell lines' - description: 'Experimental organization of combined expression and CGH data' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-neve2006/post-link.sh b/recipes/bioconductor-neve2006/post-link.sh index 24e05c66b69e3..fb489a1566b22 100644 --- a/recipes/bioconductor-neve2006/post-link.sh +++ b/recipes/bioconductor-neve2006/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "neve2006-0.40.0" +installBiocDataPackage.sh "neve2006-0.44.0" diff --git a/recipes/bioconductor-newwave/meta.yaml b/recipes/bioconductor-newwave/meta.yaml index 72507f5c6eb2b..7a470eef9598e 100644 --- a/recipes/bioconductor-newwave/meta.yaml +++ b/recipes/bioconductor-newwave/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "NewWave" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A model designed for dimensionality reduction and batch effect removal for scRNA-seq data. It is designed to be massively parallelizable using shared objects that prevent memory duplication, and it can be used with different mini-batch approaches in order to reduce time consumption. It assumes a negative binomial distribution for the data with a dispersion parameter that can be both commonwise across gene both genewise. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Negative binomial model for scRNA-seq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed222f643c357c84a7eb8534aa7b3a91 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-newwave", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr requirements: host: - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-sharedobject >=1.16.0,<1.17.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-sharedobject >=1.20.0,<1.21.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-irlba - r-matrix run: - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-sharedobject >=1.16.0,<1.17.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-sharedobject >=1.20.0,<1.21.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-irlba - r-matrix + +source: + md5: 9305cd86b7d16a7a16ff447d6c1123bb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Negative binomial model for scRNA-seq' - description: 'A model designed for dimensionality reduction and batch effect removal for scRNA-seq data. It is designed to be massively parallelizable using shared objects that prevent memory duplication, and it can be used with different mini-batch approaches in order to reduce time consumption. It assumes a negative binomial distribution for the data with a dispersion parameter that can be both commonwise across gene both genewise.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ngscopydata/meta.yaml b/recipes/bioconductor-ngscopydata/meta.yaml index 68de821e7a0fb..9e8540cc86ca0 100644 --- a/recipes/bioconductor-ngscopydata/meta.yaml +++ b/recipes/bioconductor-ngscopydata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "NGScopyData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ba77cf672a331e4c9dd90b26f41b5c6 +about: + description: Subset of BAM files of human lung tumor and pooled normal samples by targeted panel sequencing. [Zhao et al 2014. Targeted Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using the University of North Carolina (UNC) Sequencing Assay Captures Most Previously Described Genetic Aberrations in NSCLC. In preparation.] Each sample is a 10 percent random subsample drawn from the original sequencing data. The pooled normal sample has been rescaled accroding to the total number of normal samples in the "pool". Here provided is the subsampled data on chr6 (hg19). + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Subset of BAM files of human tumor and pooled normal sequencing data (Zhao et al. 2014) for the NGScopy package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ngscopydata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 765a3d0f4a4c7faae9cfae3d1275f233 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Subset of BAM files of human tumor and pooled normal sequencing data (Zhao et al. 2014) for the NGScopy package' - description: 'Subset of BAM files of human lung tumor and pooled normal samples by targeted panel sequencing. [Zhao et al 2014. Targeted Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using the University of North Carolina (UNC) Sequencing Assay Captures Most Previously Described Genetic Aberrations in NSCLC. In preparation.] Each sample is a 10 percent random subsample drawn from the original sequencing data. The pooled normal sample has been rescaled accroding to the total number of normal samples in the "pool". Here provided is the subsampled data on chr6 (hg19).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ngscopydata/post-link.sh b/recipes/bioconductor-ngscopydata/post-link.sh index 362855219f4b3..0933fce5fa284 100644 --- a/recipes/bioconductor-ngscopydata/post-link.sh +++ b/recipes/bioconductor-ngscopydata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ngscopydata-1.22.0" +installBiocDataPackage.sh "ngscopydata-1.26.0" diff --git a/recipes/bioconductor-ngsreports/meta.yaml b/recipes/bioconductor-ngsreports/meta.yaml index 185ed58b5bdcb..6af0e6d887dd1 100644 --- a/recipes/bioconductor-ngsreports/meta.yaml +++ b/recipes/bioconductor-ngsreports/meta.yaml @@ -1,85 +1,86 @@ -{% set version = "2.4.0" %} +{% set version = "2.8.0" %} {% set name = "ngsReports" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides methods and object classes for parsing FastQC reports and output summaries from other NGS tools into R. As well as parsing files, multiple plotting methods have been implemented for visualising the parsed data. Plots can be generated as static ggplot objects or interactive plotly objects. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Load FastqQC reports and other NGS related files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c2d8c1f7a1869275420e05125fb1b420 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ngsreports", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, Cairo, knitr, testthat, truncnorm + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, Cairo, DT, knitr, pander, readr, testthat, truncnorm requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - r-checkmate - - 'r-dplyr >=1.1.0' - - r-dt + - r-dplyr >=1.1.0 - r-forcats - r-ggdendro - - 'r-ggplot2 >=3.4.0' + - r-ggplot2 >=3.5.0 - r-jsonlite - r-lifecycle - r-lubridate - - r-pander - - 'r-patchwork >=1.1.1' - - 'r-plotly >=4.9.4' - - r-readr + - r-patchwork >=1.1.1 + - r-plotly >=4.9.4 - r-reshape2 - r-rlang - r-rmarkdown - r-scales - r-stringr - - 'r-tibble >=1.3.1' + - r-tibble >=1.3.1 - r-tidyr - - 'r-tidyselect >=0.2.3' + - r-tidyselect >=0.2.3 - r-zoo + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - r-checkmate - - 'r-dplyr >=1.1.0' - - r-dt + - r-dplyr >=1.1.0 - r-forcats - r-ggdendro - - 'r-ggplot2 >=3.4.0' + - r-ggplot2 >=3.5.0 - r-jsonlite - r-lifecycle - r-lubridate - - r-pander - - 'r-patchwork >=1.1.1' - - 'r-plotly >=4.9.4' - - r-readr + - r-patchwork >=1.1.1 + - r-plotly >=4.9.4 - r-reshape2 - r-rlang - r-rmarkdown - r-scales - r-stringr - - 'r-tibble >=1.3.1' + - r-tibble >=1.3.1 - r-tidyr - - 'r-tidyselect >=0.2.3' + - r-tidyselect >=0.2.3 - r-zoo + +source: + md5: 3229a9d9554cc366b1095c3ba2118f84 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Load FastqQC reports and other NGS related files' - description: 'This package provides methods and object classes for parsing FastQC reports and output summaries from other NGS tools into R. As well as parsing files, multiple plotting methods have been implemented for visualising the parsed data. Plots can be generated as static ggplot objects or interactive plotly objects.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nipalsmcia/meta.yaml b/recipes/bioconductor-nipalsmcia/meta.yaml index bfba119094b74..2442f6493eac9 100644 --- a/recipes/bioconductor-nipalsmcia/meta.yaml +++ b/recipes/bioconductor-nipalsmcia/meta.yaml @@ -1,57 +1,62 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "nipalsMCIA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Computes Multiple Co-Inertia Analysis (MCIA), a dimensionality reduction (jDR) algorithm, for a multi-block dataset using a modification to the Nonlinear Iterative Partial Least Squares method (NIPALS) proposed in (Hanafi et. al, 2010). Allows multiple options for row- and table-level preprocessing, and speeds up computation of variance explained. Vignettes detail application to bulk- and single cell- multi-omics studies. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Multiple Co-Inertia Analysis via the NIPALS Method -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0558d05ea61523c6fcaed9d8ed9b0ded build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nipalsmcia", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, circlize, ggpubr, KernSmooth, knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>= 4.0.0), spatstat.explore, stringr, survival, tidyverse, testthat (>= 3.0.0) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocFileCache, BiocStyle, circlize, ggpubr, KernSmooth, knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>= 4.0.0), spatstat.explore, stringr, survival, tidyverse, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - - 'r-ggplot2 >=3.0.0' + - r-ggplot2 >=3.0.0 - r-pracma - r-rlang - r-rspectra - r-scales run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - - 'r-ggplot2 >=3.0.0' + - r-ggplot2 >=3.0.0 - r-pracma - r-rlang - r-rspectra - r-scales + +source: + md5: 188157c4292195321f1c4506fe50094d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Multiple Co-Inertia Analysis via the NIPALS Method' - description: 'Computes Multiple Co-Inertia Analysis (MCIA), a dimensionality reduction (jDR) algorithm, for a multi-block dataset using a modification to the Nonlinear Iterative Partial Least Squares method (NIPALS) proposed in (Hanafi et. al, 2010). Allows multiple options for row- and table-level preprocessing, and speeds up computation of variance explained. Vignettes detail application to bulk- and single cell- multi-omics studies.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nnnorm/meta.yaml b/recipes/bioconductor-nnnorm/meta.yaml index ed154d75e8173..f59b24d09b2c0 100644 --- a/recipes/bioconductor-nnnorm/meta.yaml +++ b/recipes/bioconductor-nnnorm/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "2.66.0" %} +{% set version = "2.70.0" %} {% set name = "nnNorm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Spatial and intensity based normalization of cDNA microarray data based on robust neural nets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f6e41106fc2afb44568c00dce1a36670 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nnnorm", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:nnnorm + - doi:10.1093/bioinformatics/bti397 + parent_recipe: + name: bioconductor-nnnorm + path: recipes/bioconductor-nnnorm + version: 2.44.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-marray >=1.84.0,<1.85.0 - r-base - r-nnet run: - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-marray >=1.84.0,<1.85.0 - r-base - r-nnet + +source: + md5: 9b96328c86619f69f34dc5e6123049ae + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Spatial and intensity based normalization of cDNA microarray data based on robust neural nets' - description: 'This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:nnnorm - - doi:10.1093/bioinformatics/bti397 - parent_recipe: - name: bioconductor-nnnorm - path: recipes/bioconductor-nnnorm - version: 2.44.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nnsvg/meta.yaml b/recipes/bioconductor-nnsvg/meta.yaml index b04d39476984c..d3d8dae6dad7f 100644 --- a/recipes/bioconductor-nnsvg/meta.yaml +++ b/recipes/bioconductor-nnsvg/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "nnSVG" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. The method is based on nearest-neighbor Gaussian processes and uses the BRISC algorithm for model fitting and parameter estimation. Allows identification and ranking of SVGs with flexible length scales across a tissue slide or within spatial domains defined by covariates. Scales linearly with the number of spatial locations and can be applied to datasets containing thousands or more spatial locations. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Scalable identification of spatially variable genes in spatially-resolved transcriptomics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4af169b12d944eff8ee9d9e3063ff5ea build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nnsvg", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, STexampleData, WeberDivechaLCdata, scran, ggplot2, testthat requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-brisc - r-matrix - r-matrixstats run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-brisc - r-matrix - r-matrixstats + +source: + md5: f6f9e616f7afeacdd159320811fd1b0a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Scalable identification of spatially variable genes in spatially-resolved transcriptomics data' - description: 'Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. The method is based on nearest-neighbor Gaussian processes and uses the BRISC algorithm for model fitting and parameter estimation. Allows identification and ranking of SVGs with flexible length scales across a tissue slide or within spatial domains defined by covariates. Scales linearly with the number of spatial locations and can be applied to datasets containing thousands or more spatial locations.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-noiseq/meta.yaml b/recipes/bioconductor-noiseq/meta.yaml index 675fe63b421b6..352e89d228107 100644 --- a/recipes/bioconductor-noiseq/meta.yaml +++ b/recipes/bioconductor-noiseq/meta.yaml @@ -1,41 +1,21 @@ -{% set version = "2.46.0" %} +{% set version = "2.50.0" %} {% set name = "NOISeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Analysis of RNA-seq expression data or other similar kind of data. Exploratory plots to evualuate saturation, count distribution, expression per chromosome, type of detected features, features length, etc. Differential expression between two experimental conditions with no parametric assumptions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Exploratory analysis and differential expression for RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e7ea859871f96aa68269efa3a1e7dd46 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-noiseq", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base - - 'r-matrix >=1.2' - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base - - 'r-matrix >=1.2' -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Exploratory analysis and differential expression for RNA-seq data' - description: 'Analysis of RNA-seq expression data or other similar kind of data. Exploratory plots to evualuate saturation, count distribution, expression per chromosome, type of detected features, features length, etc. Differential expression between two experimental conditions with no parametric assumptions.' + extra: identifiers: - biotools:noiseq @@ -44,3 +24,29 @@ extra: path: recipes/bioconductor-noiseq version: 2.24.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + - r-matrix >=1.2 + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + - r-matrix >=1.2 + +source: + md5: 58a62af2eac8bcc4c9e76238fd2d94a2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-norce/meta.yaml b/recipes/bioconductor-norce/meta.yaml index 8aea0cd7dd50e..065532f86a565 100644 --- a/recipes/bioconductor-norce/meta.yaml +++ b/recipes/bioconductor-norce/meta.yaml @@ -1,41 +1,44 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "NoRCE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint to a functional association. We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 'NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e3a1a53f9c68bc68ab881bd49e28ecb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-norce", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Dmelanogaster.UCSC.dm6.ensGene, testthat,TxDb.Celegans.UCSC.ce11.refGene,rmarkdown, TxDb.Rnorvegicus.UCSC.rn6.refGene,TxDb.Hsapiens.UCSC.hg19.knownGene, org.Mm.eg.db, org.Rn.eg.db,org.Hs.eg.db,org.Dr.eg.db,BiocGenerics, org.Sc.sgd.db, org.Ce.eg.db,org.Dm.eg.db, methods,markdown requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-rwikipathways >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-reactome.db >=1.89.0,<1.90.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-rwikipathways >=1.26.0,<1.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-dbi - r-dbplyr @@ -49,21 +52,22 @@ requirements: - r-rsqlite - r-stringr - r-tidyr + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-rwikipathways >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-reactome.db >=1.89.0,<1.90.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-rwikipathways >=1.26.0,<1.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-dbi - r-dbplyr @@ -77,13 +81,16 @@ requirements: - r-rsqlite - r-stringr - r-tidyr + +source: + md5: 82b2d03cddbc73312ebcacc52b089d8d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment' - description: 'While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint to a functional association. We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-normalize450k/meta.yaml b/recipes/bioconductor-normalize450k/meta.yaml index d3980f100fdc2..99eea240b7277 100644 --- a/recipes/bioconductor-normalize450k/meta.yaml +++ b/recipes/bioconductor-normalize450k/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "normalize450K" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5ea0fdcbdd43103b5ee941c96fe43fa +about: + description: Precise measurements are important for epigenome-wide studies investigating DNA methylation in whole blood samples, where effect sizes are expected to be small in magnitude. The 450K platform is often affected by batch effects and proper preprocessing is recommended. This package provides functions to read and normalize 450K '.idat' files. The normalization corrects for dye bias and biases related to signal intensity and methylation of probes using local regression. No adjustment for probe type bias is performed to avoid the trade-off of precision for accuracy of beta-values. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_2_clause + file LICENSE + license_file: LICENSE + summary: Preprocessing of Illumina Infinium 450K data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-normalize450k", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 - r-base - r-quadprog run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 - r-base - r-quadprog +source: + md5: da95bdde1f294e05d1d8005f859b8a0a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_2_clause + file LICENSE' - summary: 'Preprocessing of Illumina Infinium 450K data' - description: 'Precise measurements are important for epigenome-wide studies investigating DNA methylation in whole blood samples, where effect sizes are expected to be small in magnitude. The 450K platform is often affected by batch effects and proper preprocessing is recommended. This package provides functions to read and normalize 450K ''.idat'' files. The normalization corrects for dye bias and biases related to signal intensity and methylation of probes using local regression. No adjustment for probe type bias is performed to avoid the trade-off of precision for accuracy of beta-values.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-normalyzerde/meta.yaml b/recipes/bioconductor-normalyzerde/meta.yaml index 73ac8ed4eadf9..580698e5c8f3c 100644 --- a/recipes/bioconductor-normalyzerde/meta.yaml +++ b/recipes/bioconductor-normalyzerde/meta.yaml @@ -1,32 +1,32 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "NormalyzerDE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: NormalyzerDE provides screening of normalization methods for LC-MS based expression data. It calculates a range of normalized matrices using both existing approaches and a novel time-segmented approach, calculates performance measures and generates an evaluation report. Furthermore, it provides an easy utility for Limma- or ANOVA- based differential expression analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Evaluation of normalization methods and calculation of differential expression analysis statistics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e55d57346b59dbd8b317a263e4b413b0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-normalyzerde", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-ape - r-base - r-car @@ -35,11 +35,10 @@ requirements: - r-mass - r-matrixstats run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-ape - r-base - r-car @@ -47,12 +46,16 @@ requirements: - r-ggplot2 - r-mass - r-matrixstats + +source: + md5: db6dd9d11430295bc7625fb5b260019e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Evaluation of normalization methods and calculation of differential expression analysis statistics' - description: 'NormalyzerDE provides screening of normalization methods for LC-MS based expression data. It calculates a range of normalized matrices using both existing approaches and a novel time-segmented approach, calculates performance measures and generates an evaluation report. Furthermore, it provides an easy utility for Limma- or ANOVA- based differential expression analysis.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-normqpcr/meta.yaml b/recipes/bioconductor-normqpcr/meta.yaml index 79afa3c7882ff..408f447e54467 100644 --- a/recipes/bioconductor-normqpcr/meta.yaml +++ b/recipes/bioconductor-normqpcr/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "NormqPCR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions for the selection of optimal reference genes and the normalisation of real-time quantitative PCR data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Functions for normalisation of RT-qPCR data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 379e7395ad03c0d57dffa7331748e253 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-normqpcr", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-readqpcr >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-readqpcr >=1.52.0,<1.53.0 - r-base - r-qpcr - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-readqpcr >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-readqpcr >=1.52.0,<1.53.0 - r-base - r-qpcr - r-rcolorbrewer - build: - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - xorg-libxfixes # [linux] + +source: + md5: 23b072389ca09a8e54da8857c772cb46 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'Functions for normalisation of RT-qPCR data' - description: 'Functions for the selection of optimal reference genes and the normalisation of real-time quantitative PCR data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-normr/meta.yaml b/recipes/bioconductor-normr/meta.yaml index 7e2b0dacc4662..9e5fefcf5c0e4 100644 --- a/recipes/bioconductor-normr/meta.yaml +++ b/recipes/bioconductor-normr/meta.yaml @@ -1,57 +1,62 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "normr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Robust normalization and difference calling procedures for ChIP-seq and alike data. Read counts are modeled jointly as a binomial mixture model with a user-specified number of components. A fitted background estimate accounts for the effect of enrichment in certain regions and, therefore, represents an appropriate null hypothesis. This robust background is used to identify significantly enriched or depleted regions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Normalization and difference calling in ChIP-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 06d294d5935656789cc44341eca46620 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-normr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat (>= 1.0), knitr, rmarkdown # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-bamsignals >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-bamsignals >=1.38.0,<1.39.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - - 'r-rcpp >=0.11' + - r-rcpp >=0.11 - libblas - liblapack run: - - 'bioconductor-bamsignals >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-bamsignals >=1.38.0,<1.39.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - - 'r-rcpp >=0.11' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=0.11 + +source: + md5: 7dc63258eb167eda7294e40ea7ae6aa2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Normalization and difference calling in ChIP-seq data' - description: 'Robust normalization and difference calling procedures for ChIP-seq and alike data. Read counts are modeled jointly as a binomial mixture model with a user-specified number of components. A fitted background estimate accounts for the effect of enrichment in certain regions and, therefore, represents an appropriate null hypothesis. This robust background is used to identify significantly enriched or depleted regions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-norway981.db/meta.yaml b/recipes/bioconductor-norway981.db/meta.yaml index 71d94b527398a..e5cf158d5f68e 100644 --- a/recipes/bioconductor-norway981.db/meta.yaml +++ b/recipes/bioconductor-norway981.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "Norway981.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 85367390919bba9018438585e59fbb87 +about: + description: Norway981 http://genome-www5.stanford.edu/ Annotation Data (Norway981) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Norway981 http://genome-www5.stanford.edu/ Annotation Data (Norway981) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-norway981.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 85367390919bba9018438585e59fbb87 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Norway981 http://genome-www5.stanford.edu/ Annotation Data (Norway981)' - description: 'Norway981 http://genome-www5.stanford.edu/ Annotation Data (Norway981) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nparc/meta.yaml b/recipes/bioconductor-nparc/meta.yaml index 0c5bebf6db5c1..27c51cd36f663 100644 --- a/recipes/bioconductor-nparc/meta.yaml +++ b/recipes/bioconductor-nparc/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "NPARC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Perform non-parametric analysis of response curves as described by Childs, Bach, Franken et al. (2019): Non-parametric analysis of thermal proteome profiles reveals novel drug-binding proteins.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Non-parametric analysis of response curves for thermal proteome profiling experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b49f408fb60e58d3c62cfd2d5d4809cb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nparc", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, devtools, knitr, rprojroot, rmarkdown, ggplot2, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-broom - r-dplyr @@ -31,7 +33,7 @@ requirements: - r-rlang - r-tidyr run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-broom - r-dplyr @@ -39,13 +41,16 @@ requirements: - r-mass - r-rlang - r-tidyr + +source: + md5: d72813fe5c5b69ffe12e88e548c013cc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Non-parametric analysis of response curves for thermal proteome profiling experiments' - description: 'Perform non-parametric analysis of response curves as described by Childs, Bach, Franken et al. (2019): Non-parametric analysis of thermal proteome profiles reveals novel drug-binding proteins.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-npgsea/meta.yaml b/recipes/bioconductor-npgsea/meta.yaml index 908e3b860253b..a25845ed264e5 100644 --- a/recipes/bioconductor-npgsea/meta.yaml +++ b/recipes/bioconductor-npgsea/meta.yaml @@ -1,49 +1,55 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "npGSEA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Current gene set enrichment methods rely upon permutations for inference. These approaches are computationally expensive and have minimum achievable p-values based on the number of permutations, not on the actual observed statistics. We have derived three parametric approximations to the permutation distributions of two gene set enrichment test statistics. We are able to reduce the computational burden and granularity issues of permutation testing with our method, which is implemented in this package. npGSEA calculates gene set enrichment statistics and p-values without the computational cost of permutations. It is applicable in settings where one or many gene sets are of interest. There are also built-in plotting functions to help users visualize results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 82d2208fe4478a1d5423940daa7128be build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-npgsea", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:npgsea + parent_recipe: + name: bioconductor-npgsea + path: recipes/bioconductor-npgsea + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 - r-base + +source: + md5: f6148e3dd59ae51db08a01279ae93d97 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)' - description: 'Current gene set enrichment methods rely upon permutations for inference. These approaches are computationally expensive and have minimum achievable p-values based on the number of permutations, not on the actual observed statistics. We have derived three parametric approximations to the permutation distributions of two gene set enrichment test statistics. We are able to reduce the computational burden and granularity issues of permutation testing with our method, which is implemented in this package. npGSEA calculates gene set enrichment statistics and p-values without the computational cost of permutations. It is applicable in settings where one or many gene sets are of interest. There are also built-in plotting functions to help users visualize results.' -extra: - identifiers: - - biotools:npgsea - parent_recipe: - name: bioconductor-npgsea - path: recipes/bioconductor-npgsea - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ntw/meta.yaml b/recipes/bioconductor-ntw/meta.yaml index 61ef8840dc598..11a13ba3776bc 100644 --- a/recipes/bioconductor-ntw/meta.yaml +++ b/recipes/bioconductor-ntw/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.52.0" %} +{% set version = "1.56.0" %} {% set name = "NTW" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package predicts the gene-gene interaction network and identifies the direct transcriptional targets of the perturbation using an ODE (Ordinary Differential Equation) based method. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Predict gene network using an Ordinary Differential Equation (ODE) based method -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c64df447dfa43cbb3bf97922655ff516 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ntw", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:ntw + - doi:10.1093/bioinformatics/btq629 + parent_recipe: + name: bioconductor-ntw + path: recipes/bioconductor-ntw + version: 1.30.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -26,21 +37,16 @@ requirements: run: - r-base - r-mvtnorm + +source: + md5: 7b43e4f87881a4c275859cc8a2865eb8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Predict gene network using an Ordinary Differential Equation (ODE) based method' - description: 'This package predicts the gene-gene interaction network and identifies the direct transcriptional targets of the perturbation using an ODE (Ordinary Differential Equation) based method.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:ntw - - doi:10.1093/bioinformatics/btq629 - parent_recipe: - name: bioconductor-ntw - path: recipes/bioconductor-ntw - version: 1.30.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nucleosim/meta.yaml b/recipes/bioconductor-nucleosim/meta.yaml index 3bfd2f9382492..b5c6531073198 100644 --- a/recipes/bioconductor-nucleosim/meta.yaml +++ b/recipes/bioconductor-nucleosim/meta.yaml @@ -1,42 +1,21 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "nucleoSim" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'This package can generate a synthetic map with reads covering the nucleosome regions as well as a synthetic map with forward and reverse reads emulating next-generation sequencing. The synthetic hybridization data of “Tiling Arrays” can also be generated. The user has choice between three different distributions for the read positioning: Normal, Student and Uniform. In addition, a visualization tool is provided to explore the synthetic nucleosome maps.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Generate synthetic nucleosome maps -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b1b994c654ce500e414a8a7caea5162f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nucleosim", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, testthat -requirements: - host: - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - r-base - run: - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Generate synthetic nucleosome maps' - description: 'This package can generate a synthetic map with reads covering the nucleosome regions as well as a synthetic map with forward and reverse reads emulating next-generation sequencing. The synthetic hybridization data of “Tiling Arrays” can also be generated. The user has choice between three different distributions for the read positioning: Normal, Student and Uniform. In addition, a visualization tool is provided to explore the synthetic nucleosome maps.' + extra: identifiers: - biotools:nucleosim @@ -46,3 +25,30 @@ extra: path: recipes/bioconductor-nucleosim version: 1.8.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, testthat +requirements: + host: + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + run: + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + +source: + md5: d698b8ac01221cfe5b6436b343e009b9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-nucler/meta.yaml b/recipes/bioconductor-nucler/meta.yaml index 340e91083a435..f57badb2f55b8 100644 --- a/recipes/bioconductor-nucler/meta.yaml +++ b/recipes/bioconductor-nucler/meta.yaml @@ -1,68 +1,74 @@ -{% set version = "2.34.0" %} +{% set version = "2.38.0" %} {% set name = "nucleR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Nucleosome positioning for Tiling Arrays and NGS experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Nucleosome positioning package for R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 854586c378515ad6e2eefe2e1a09f394 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nucler", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:nucler + parent_recipe: + name: bioconductor-nucler + path: recipes/bioconductor-nucler + version: 2.12.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-dplyr - r-ggplot2 - r-magrittr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-dplyr - r-ggplot2 - r-magrittr + +source: + md5: c9ecea8141ff8e57601715ce4427da2f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 3)' - summary: 'Nucleosome positioning package for R' - description: 'Nucleosome positioning for Tiling Arrays and NGS experiments.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:nucler - parent_recipe: - name: bioconductor-nucler - path: recipes/bioconductor-nucler - version: 2.12.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nucpos/meta.yaml b/recipes/bioconductor-nucpos/meta.yaml index 4bc66b50e3842..72e168b1ef097 100644 --- a/recipes/bioconductor-nucpos/meta.yaml +++ b/recipes/bioconductor-nucpos/meta.yaml @@ -1,37 +1,37 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "nuCpos" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b029b2678c784645c2198f00093bd923 +about: + description: 'nuCpos, a derivative of NuPoP, is an R package for prediction of nucleosome positions. nuCpos calculates local and whole nucleosomal histone binding affinity (HBA) scores for a given 147-bp sequence. Note: This package was designed to demonstrate the use of chemical maps in prediction. As the parental package NuPoP now provides chemical-map-based prediction, the function for dHMM-based prediction was removed from this package. nuCpos continues to provide functions for HBA calculation.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: An R package for prediction of nucleosome positions build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nucpos", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: NuPoP, Biostrings, testthat requirements: host: - r-base run: - r-base +source: + md5: 99e983e13fa6b7e2307f04f97ea9a1e5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'An R package for prediction of nucleosome positions' - description: 'nuCpos, a derivative of NuPoP, is an R package for prediction of nucleosome positions. nuCpos calculates local and whole nucleosomal histone binding affinity (HBA) scores for a given 147-bp sequence. Note: This package was designed to demonstrate the use of chemical maps in prediction. As the parental package NuPoP now provides chemical-map-based prediction, the function for dHMM-based prediction was removed from this package. nuCpos continues to provide functions for HBA calculation.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nugohs1a520180.db/meta.yaml b/recipes/bioconductor-nugohs1a520180.db/meta.yaml index b418a0f7208e0..75cdf18c39175 100644 --- a/recipes/bioconductor-nugohs1a520180.db/meta.yaml +++ b/recipes/bioconductor-nugohs1a520180.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.4.0" %} {% set name = "nugohs1a520180.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f83701b35b07e69e1ad503b546bb5eaf +about: + description: Affymetrix nugohs1a520180 annotation data (chip nugohs1a520180) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix nugohs1a520180 annotation data (chip nugohs1a520180) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nugohs1a520180.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f83701b35b07e69e1ad503b546bb5eaf + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix nugohs1a520180 annotation data (chip nugohs1a520180)' - description: 'Affymetrix nugohs1a520180 annotation data (chip nugohs1a520180) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nugohs1a520180cdf/meta.yaml b/recipes/bioconductor-nugohs1a520180cdf/meta.yaml index f90749d9e7a72..6be3aee5cf58c 100644 --- a/recipes/bioconductor-nugohs1a520180cdf/meta.yaml +++ b/recipes/bioconductor-nugohs1a520180cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "3.4.0" %} {% set name = "nugohs1a520180cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aa152658a4a801cc0edb552a98aee841 +about: + description: A package containing an environment representing the NuGO_Hs1a520180.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: nugohs1a520180cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nugohs1a520180cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: aa152658a4a801cc0edb552a98aee841 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: nugohs1a520180cdf - description: 'A package containing an environment representing the NuGO_Hs1a520180.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nugohs1a520180probe/meta.yaml b/recipes/bioconductor-nugohs1a520180probe/meta.yaml index f0bd987761f56..ab4b9ec434f11 100644 --- a/recipes/bioconductor-nugohs1a520180probe/meta.yaml +++ b/recipes/bioconductor-nugohs1a520180probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "3.4.0" %} {% set name = "nugohs1a520180probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6acf20ac4a799eaae97d0a64426d6ac3 +about: + description: This package was automatically created by package AnnotationForge version 1.11.20. The probe sequence data was obtained from http://www.affymetrix.com. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type nugohs1a520180 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nugohs1a520180probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6acf20ac4a799eaae97d0a64426d6ac3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type nugohs1a520180' - description: 'This package was automatically created by package AnnotationForge version 1.11.20. The probe sequence data was obtained from http://www.affymetrix.com.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nugomm1a520177.db/meta.yaml b/recipes/bioconductor-nugomm1a520177.db/meta.yaml index 7be86d928b24d..70ebbc2f1671b 100644 --- a/recipes/bioconductor-nugomm1a520177.db/meta.yaml +++ b/recipes/bioconductor-nugomm1a520177.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.4.0" %} {% set name = "nugomm1a520177.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 99f69ea2cbb80a79bedee99e3d726e50 +about: + description: Affymetrix nugomm1a520177 annotation data (chip nugomm1a520177) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix nugomm1a520177 annotation data (chip nugomm1a520177) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nugomm1a520177.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 99f69ea2cbb80a79bedee99e3d726e50 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix nugomm1a520177 annotation data (chip nugomm1a520177)' - description: 'Affymetrix nugomm1a520177 annotation data (chip nugomm1a520177) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nugomm1a520177cdf/meta.yaml b/recipes/bioconductor-nugomm1a520177cdf/meta.yaml index 6e57813681d86..e8a8ff1c4baf8 100644 --- a/recipes/bioconductor-nugomm1a520177cdf/meta.yaml +++ b/recipes/bioconductor-nugomm1a520177cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "3.4.0" %} {% set name = "nugomm1a520177cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fc60c2018580decaea30f09de55142fb +about: + description: A package containing an environment representing the NuGO_Mm1a520177.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: nugomm1a520177cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nugomm1a520177cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fc60c2018580decaea30f09de55142fb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: nugomm1a520177cdf - description: 'A package containing an environment representing the NuGO_Mm1a520177.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nugomm1a520177probe/meta.yaml b/recipes/bioconductor-nugomm1a520177probe/meta.yaml index 1d994b823856e..f3816521f33cb 100644 --- a/recipes/bioconductor-nugomm1a520177probe/meta.yaml +++ b/recipes/bioconductor-nugomm1a520177probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "3.4.0" %} {% set name = "nugomm1a520177probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7fa974389ad2be6ebda8810496221a9b +about: + description: This package was automatically created by package AnnotationForge version 1.11.20. The probe sequence data was obtained from http://www.affymetrix.com. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type nugomm1a520177 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nugomm1a520177probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7fa974389ad2be6ebda8810496221a9b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type nugomm1a520177' - description: 'This package was automatically created by package AnnotationForge version 1.11.20. The probe sequence data was obtained from http://www.affymetrix.com.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nullranges/meta.yaml b/recipes/bioconductor-nullranges/meta.yaml index 61ea19b4a06cf..cedc37bd8c715 100644 --- a/recipes/bioconductor-nullranges/meta.yaml +++ b/recipes/bioconductor-nullranges/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "nullranges" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrap samples of ranges (using the block bootstrap framework of Bickel et al 2010), or sets of control ranges that are matched across one or more covariates. nullranges is designed to be inter-operable with other packages for analysis of genomic overlap enrichment, including the plyranges Bioconductor package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Generation of null ranges via bootstrapping or covariate matching -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6ee32a46c332cfeefa89ebc2b32608bf build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nullranges", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, ks, DNAcopy, RcppHMM, AnnotationHub, ExperimentHub, nullrangesData, excluderanges, ensembldb, EnsDb.Hsapiens.v86, BSgenome.Hsapiens.UCSC.hg38, patchwork, plotgardener, dplyr, purrr, magrittr, tidyr, cobalt, DiagrammeR, tidySummarizedExperiment requirements: host: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-ggplot2 @@ -36,12 +38,12 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-ggplot2 @@ -49,13 +51,16 @@ requirements: - r-progress - r-rlang - r-scales + +source: + md5: eac86b21c9afba0e6c976fb6073e9e8d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Generation of null ranges via bootstrapping or covariate matching' - description: 'Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrap samples of ranges (using the block bootstrap framework of Bickel et al 2010), or sets of control ranges that are matched across one or more covariates. nullranges is designed to be inter-operable with other packages for analysis of genomic overlap enrichment, including the plyranges Bioconductor package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nullrangesdata/meta.yaml b/recipes/bioconductor-nullrangesdata/meta.yaml index 357383664f328..bb7160b41b6ba 100644 --- a/recipes/bioconductor-nullrangesdata/meta.yaml +++ b/recipes/bioconductor-nullrangesdata/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "nullrangesData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c8b4cf63d70a2577251c03c093c014b1 +about: + description: Provides datasets for the nullranges package vignette, in particular example datasets for DNase hypersensitivity sites (DHS), CTCF binding sites, and CTCF genomic interactions. These are used to demonstrate generation of null hypothesis feature sets, either through block bootstrapping or matching, in the nullranges vignette. For more details, see the data object man pages, and the R scripts for object construction provided within the package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: ExperimentHub datasets for the nullranges package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nullrangesdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5fc9168190de6f06922ed63027aba161 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'ExperimentHub datasets for the nullranges package' - description: 'Provides datasets for the nullranges package vignette, in particular example datasets for DNase hypersensitivity sites (DHS), CTCF binding sites, and CTCF genomic interactions. These are used to demonstrate generation of null hypothesis feature sets, either through block bootstrapping or matching, in the nullranges vignette. For more details, see the data object man pages, and the R scripts for object construction provided within the package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nullrangesdata/post-link.sh b/recipes/bioconductor-nullrangesdata/post-link.sh index 56c49a53ff303..700ce6ede07bf 100644 --- a/recipes/bioconductor-nullrangesdata/post-link.sh +++ b/recipes/bioconductor-nullrangesdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "nullrangesdata-1.8.0" +installBiocDataPackage.sh "nullrangesdata-1.12.0" diff --git a/recipes/bioconductor-nupop/meta.yaml b/recipes/bioconductor-nupop/meta.yaml index 95a7ccb26204e..59dd25f1bc931 100644 --- a/recipes/bioconductor-nupop/meta.yaml +++ b/recipes/bioconductor-nupop/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "2.10.0" %} +{% set version = "2.14.0" %} {% set name = "NuPoP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 65372d828848fa588584e42324762643 +about: + description: 'NuPoP is an R package for Nucleosome Positioning Prediction.This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available at https://github.com/jipingw. The Fortran codes have complete functonality as the R package. Note: NuPoP has two separate functions for prediction of nucleosome positioning, one for MNase-map trained models and the other for chemical map-trained models. The latter was implemented for four species including yeast, S.pombe, mouse and human, trained based on our recent publications. We noticed there is another package nuCpos by another group for prediction of nucleosome positioning trained with chemicals. A report to compare recent versions of NuPoP with nuCpos can be found at https://github.com/jiping/NuPoP_doc. Some more information can be found and will be posted at https://github.com/jipingw/NuPoP.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: An R package for nucleosome positioning prediction build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nupop", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: + build: + - {{ compiler('c') }} + - {{ compiler('fortran') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - {{ compiler('fortran') }} - - make +source: + md5: f78251e4d6e4d71b766f2b87ba2d5266 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'An R package for nucleosome positioning prediction' - description: 'NuPoP is an R package for Nucleosome Positioning Prediction.This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available at https://github.com/jipingw. The Fortran codes have complete functonality as the R package. Note: NuPoP has two separate functions for prediction of nucleosome positioning, one for MNase-map trained models and the other for chemical map-trained models. The latter was implemented for four species including yeast, S.pombe, mouse and human, trained based on our recent publications. We noticed there is another package nuCpos by another group for prediction of nucleosome positioning trained with chemicals. A report to compare recent versions of NuPoP with nuCpos can be found at https://github.com/jiping/NuPoP_doc. Some more information can be found and will be posted at https://github.com/jipingw/NuPoP.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nxtirfdata/meta.yaml b/recipes/bioconductor-nxtirfdata/meta.yaml index 60c0e2b69d5f7..1334f67e56efb 100644 --- a/recipes/bioconductor-nxtirfdata/meta.yaml +++ b/recipes/bioconductor-nxtirfdata/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "NxtIRFdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: NxtIRFdata is a companion package for SpliceWiz, an interactive analysis and visualization tool for alternative splicing quantitation (including intron retention) for RNA-seq BAM files. NxtIRFdata contains Mappability files required for the generation of human and mouse references. NxtIRFdata also contains a synthetic genome reference and example BAM files used to demonstrate SpliceWiz's functionality. BAM files are based on 6 samples from the Leucegene dataset provided by NCBI Gene Expression Omnibus under accession number GSE67039. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Data for NxtIRF -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d9c35f12650fe6e2eb413224b3590dc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-nxtirfdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.0.0), knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-r.utils run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-r.utils - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 74ae8288457bfc954fecd85de9b16580 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Data for NxtIRF' - description: 'NxtIRFdata is a companion package for SpliceWiz, an interactive analysis and visualization tool for alternative splicing quantitation (including intron retention) for RNA-seq BAM files. NxtIRFdata contains Mappability files required for the generation of human and mouse references. NxtIRFdata also contains a synthetic genome reference and example BAM files used to demonstrate SpliceWiz''s functionality. BAM files are based on 6 samples from the Leucegene dataset provided by NCBI Gene Expression Omnibus under accession number GSE67039.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-nxtirfdata/post-link.sh b/recipes/bioconductor-nxtirfdata/post-link.sh index bc8f830b35b74..b9cbd545bb1e9 100644 --- a/recipes/bioconductor-nxtirfdata/post-link.sh +++ b/recipes/bioconductor-nxtirfdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "nxtirfdata-1.8.0" +installBiocDataPackage.sh "nxtirfdata-1.12.0" diff --git a/recipes/bioconductor-obmiti/meta.yaml b/recipes/bioconductor-obmiti/meta.yaml index a995f44ec42d3..a169317e2cba2 100644 --- a/recipes/bioconductor-obmiti/meta.yaml +++ b/recipes/bioconductor-obmiti/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "ObMiTi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0510665a5231cd3109d19478e4aadbd9 +about: + description: The package provide RNA-seq count for 2 strains of mus musclus; Wild type and Ob/Ob. Each strain was divided into two groups, and each group received either chow diet or high fat diet. RNA expression was measured after 20 weeks in 7 tissues. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Ob/ob Mice Data on Normal and High Fat Diet build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-obmiti", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocManager, GenomicFeatures, S4Vectors, devtools, testthat requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c207988f479ca296dbc34cab5399e2d7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Ob/ob Mice Data on Normal and High Fat Diet' - description: 'The package provide RNA-seq count for 2 strains of mus musclus; Wild type and Ob/Ob. Each strain was divided into two groups, and each group received either chow diet or high fat diet. RNA expression was measured after 20 weeks in 7 tissues.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-obmiti/post-link.sh b/recipes/bioconductor-obmiti/post-link.sh index 03b4d1416cd34..f157e1752ca81 100644 --- a/recipes/bioconductor-obmiti/post-link.sh +++ b/recipes/bioconductor-obmiti/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "obmiti-1.10.0" +installBiocDataPackage.sh "obmiti-1.14.0" diff --git a/recipes/bioconductor-occugene/meta.yaml b/recipes/bioconductor-occugene/meta.yaml index f5f74d87be869..eab27c9abbeb1 100644 --- a/recipes/bioconductor-occugene/meta.yaml +++ b/recipes/bioconductor-occugene/meta.yaml @@ -1,38 +1,20 @@ -{% set version = "1.62.0" %} +{% set version = "1.66.0" %} {% set name = "occugene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 264da1422714d735ac474b414e57a2a9 +about: + description: Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Functions for Multinomial Occupancy Distribution build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-occugene", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Functions for Multinomial Occupancy Distribution' - description: 'Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: identifiers: - biotools:occugene @@ -41,4 +23,22 @@ extra: name: bioconductor-occugene path: recipes/bioconductor-occugene version: 1.40.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +requirements: + host: + - r-base + run: + - r-base +source: + md5: 8b0b5ae61b8723d7e7df5ab057874281 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ocplus/meta.yaml b/recipes/bioconductor-ocplus/meta.yaml index 5dd736c909f68..92bf487ef4341 100644 --- a/recipes/bioconductor-ocplus/meta.yaml +++ b/recipes/bioconductor-ocplus/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.76.0" %} +{% set version = "1.80.0" %} {% set name = "OCplus" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8093ec3c635bc4ba57d27f42c6c85c48 +about: + description: This package allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Operating characteristics plus sample size and local fdr for microarray experiments build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ocplus", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base - r-interp run: - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base - r-interp +source: + md5: e3474563932be47dd46824f752f51a0a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Operating characteristics plus sample size and local fdr for microarray experiments' - description: 'This package allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-oct4/meta.yaml b/recipes/bioconductor-oct4/meta.yaml index 14a38304a08b0..1a82d17332f5c 100644 --- a/recipes/bioconductor-oct4/meta.yaml +++ b/recipes/bioconductor-oct4/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "oct4" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1b6bbc6300c74c038689c7fb5b7d5eb2 +about: + description: This package provides the output of running Salmon on a set of 12 RNA-seq samples from King & Klose, "The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells", published in eLIFE, March 2017. For details on version numbers and how the samples were processed see the package vignette. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Conditional knockdown of OCT4 in mouse ESCs build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-oct4", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, markdown requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9a2784c2fdbf88a19542be9870628f76 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Conditional knockdown of OCT4 in mouse ESCs' - description: 'This package provides the output of running Salmon on a set of 12 RNA-seq samples from King & Klose, "The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells", published in eLIFE, March 2017. For details on version numbers and how the samples were processed see the package vignette.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-oct4/post-link.sh b/recipes/bioconductor-oct4/post-link.sh index b3235662475f3..3a1913db964d9 100644 --- a/recipes/bioconductor-oct4/post-link.sh +++ b/recipes/bioconductor-oct4/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "oct4-1.18.0" +installBiocDataPackage.sh "oct4-1.22.0" diff --git a/recipes/bioconductor-octad.db/meta.yaml b/recipes/bioconductor-octad.db/meta.yaml index a4fa56d807f6c..7f539cca7bcd8 100644 --- a/recipes/bioconductor-octad.db/meta.yaml +++ b/recipes/bioconductor-octad.db/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "octad.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ef8723031fea32015ee26dbf30d2c8ba +about: + description: Open Cancer TherApeutic Discovery (OCTAD) package implies sRGES approach for the drug discovery. The essential idea is to identify drugs that reverse the gene expression signature of a disease by tamping down over-expressed genes and stimulating weakly expressed ones. The following package contains all required precomputed data for whole OCTAD pipeline computation. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Open Cancer TherApeutic Discovery (OCTAD) database build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-octad.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0afebff9d9a140dbdb280de68a39cc0e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Open Cancer TherApeutic Discovery (OCTAD) database' - description: 'Open Cancer TherApeutic Discovery (OCTAD) package implies sRGES approach for the drug discovery. The essential idea is to identify drugs that reverse the gene expression signature of a disease by tamping down over-expressed genes and stimulating weakly expressed ones. The following package contains all required precomputed data for whole OCTAD pipeline computation.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-octad.db/post-link.sh b/recipes/bioconductor-octad.db/post-link.sh index 2b1a3295db9c8..382103db64aa0 100644 --- a/recipes/bioconductor-octad.db/post-link.sh +++ b/recipes/bioconductor-octad.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "octad.db-1.4.0" +installBiocDataPackage.sh "octad.db-1.8.0" diff --git a/recipes/bioconductor-octad/meta.yaml b/recipes/bioconductor-octad/meta.yaml index 5247c0dddb66c..bee91ce59aee4 100644 --- a/recipes/bioconductor-octad/meta.yaml +++ b/recipes/bioconductor-octad/meta.yaml @@ -1,39 +1,41 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "octad" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: OCTAD provides a platform for virtually screening compounds targeting precise cancer patient groups. The essential idea is to identify drugs that reverse the gene expression signature of disease by tamping down over-expressed genes and stimulating weakly expressed ones. The package offers deep-learning based reference tissue selection, disease gene expression signature creation, pathway enrichment analysis, drug reversal potency scoring, cancer cell line selection, drug enrichment analysis and in silico hit validation. It currently covers ~20,000 patient tissue samples covering 50 cancer types, and expression profiles for ~12,000 distinct compounds. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Open Cancer TherApeutic Discovery (OCTAD) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 65dcd54e4646d61afcfb9afc90108ba4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-octad", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: + host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edaseq >=2.36.0,<2.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-gsva >=1.50.0,<1.51.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-octad.db >=1.4.0,<1.5.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-ruvseq >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edaseq >=2.40.0,<2.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-gsva >=2.0.0,<2.1.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-octad.db >=1.8.0,<1.9.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-ruvseq >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-dplyr @@ -43,21 +45,23 @@ requirements: - r-httr - r-magrittr - r-plotly + - r-qpdf - r-reshape2 - r-rfast + run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edaseq >=2.36.0,<2.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-gsva >=1.50.0,<1.51.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-octad.db >=1.4.0,<1.5.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-ruvseq >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edaseq >=2.40.0,<2.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-gsva >=2.0.0,<2.1.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-octad.db >=1.8.0,<1.9.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-ruvseq >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-dplyr @@ -67,14 +71,19 @@ requirements: - r-httr - r-magrittr - r-plotly + - r-qpdf - r-reshape2 - r-rfast + +source: + md5: f1bd72460f38e4ef66241fa979e2a6cc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Open Cancer TherApeutic Discovery (OCTAD)' - description: 'OCTAD provides a platform for virtually screening compounds targeting precise cancer patient groups. The essential idea is to identify drugs that reverse the gene expression signature of disease by tamping down over-expressed genes and stimulating weakly expressed ones. The package offers deep-learning based reference tissue selection, disease gene expression signature creation, pathway enrichment analysis, drug reversal potency scoring, cancer cell line selection, drug enrichment analysis and in silico hit validation. It currently covers ~20,000 patient tissue samples covering 50 cancer types, and expression profiles for ~12,000 distinct compounds.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-odseq/meta.yaml b/recipes/bioconductor-odseq/meta.yaml index 15f186744d094..5558f5fae9068 100644 --- a/recipes/bioconductor-odseq/meta.yaml +++ b/recipes/bioconductor-odseq/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "odseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5eac4befb045c1d0531b13501f3aa880 +about: + description: Performs outlier detection of sequences in a multiple sequence alignment using bootstrap of predefined distance metrics. Outlier sequences can make downstream analyses unreliable or make the alignments less accurate while they are being constructed. This package implements the OD-seq algorithm proposed by Jehl et al (doi 10.1186/s12859-015-0702-1) for aligned sequences and a variant using string kernels for unaligned sequences. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Outlier detection in multiple sequence alignments build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-odseq", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr(>= 1.11) requirements: host: - - 'bioconductor-kebabs >=1.36.0,<1.37.0' - - 'bioconductor-msa >=1.34.0,<1.35.0' + - bioconductor-kebabs >=1.40.0,<1.41.0 + - bioconductor-msa >=1.38.0,<1.39.0 - r-base - - 'r-mclust >=5.1' + - r-mclust >=5.1 run: - - 'bioconductor-kebabs >=1.36.0,<1.37.0' - - 'bioconductor-msa >=1.34.0,<1.35.0' + - bioconductor-kebabs >=1.40.0,<1.41.0 + - bioconductor-msa >=1.38.0,<1.39.0 - r-base - - 'r-mclust >=5.1' + - r-mclust >=5.1 +source: + md5: ea5e4ffe41599b6a3ecd6c801c28254a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Outlier detection in multiple sequence alignments' - description: 'Performs outlier detection of sequences in a multiple sequence alignment using bootstrap of predefined distance metrics. Outlier sequences can make downstream analyses unreliable or make the alignments less accurate while they are being constructed. This package implements the OD-seq algorithm proposed by Jehl et al (doi 10.1186/s12859-015-0702-1) for aligned sequences and a variant using string kernels for unaligned sequences.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ogre/meta.yaml b/recipes/bioconductor-ogre/meta.yaml index 31154fe4bd61b..53fa55cd01a13 100644 --- a/recipes/bioconductor-ogre/meta.yaml +++ b/recipes/bioconductor-ogre/meta.yaml @@ -1,34 +1,35 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "OGRE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: OGRE calculates overlap between user defined genomic region datasets. Any regions can be supplied i.e. genes, SNPs, or reads from sequencing experiments. Key numbers help analyse the extend of overlaps which can also be visualized at a genomic level. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Calculate, visualize and analyse overlap between genomic regions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cff18fd2eda3eb1e67e9f7739fb9e773 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ogre", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.0.0), knitr (>= 1.36), rmarkdown (>= 2.11) requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-assertthat - r-base - r-data.table @@ -40,13 +41,13 @@ requirements: - r-shinyfiles - r-tidyr run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-assertthat - r-base - r-data.table @@ -57,12 +58,16 @@ requirements: - r-shinydashboard - r-shinyfiles - r-tidyr + +source: + md5: 4bd09d598eb2be1c4fced58fc417b8fd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Calculate, visualize and analyse overlap between genomic regions' - description: 'OGRE calculates overlap between user defined genomic region datasets. Any regions can be supplied i.e. genes, SNPs, or reads from sequencing experiments. Key numbers help analyse the extend of overlaps which can also be visualized at a genomic level.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-oligo/meta.yaml b/recipes/bioconductor-oligo/meta.yaml index b3a0210da009e..8201650efa79b 100644 --- a/recipes/bioconductor-oligo/meta.yaml +++ b/recipes/bioconductor-oligo/meta.yaml @@ -1,70 +1,77 @@ -{% set version = "1.66.0" %} +{% set version = "1.70.0" %} {% set name = "oligo" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Preprocessing tools for oligonucleotide arrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3ba99dedbe0ebca2fcaa81a400777469 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-oligo", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:oligo + parent_recipe: + name: bioconductor-oligo + path: recipes/bioconductor-oligo + version: 1.44.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, ACME, RCurl requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-affxparser >=1.74.0,<1.75.0' - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-affxparser >=1.78.0,<1.79.0 + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - - 'r-dbi >=0.3.1' + - r-dbi >=0.3.1 - r-ff - - 'r-rsqlite >=1.0.0' + - r-rsqlite >=1.0.0 - libblas - liblapack + - zlib run: - - 'bioconductor-affxparser >=1.74.0,<1.75.0' - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-affxparser >=1.78.0,<1.79.0 + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - - 'r-dbi >=0.3.1' + - r-dbi >=0.3.1 - r-ff - - 'r-rsqlite >=1.0.0' - build: - - {{ compiler('c') }} - - make + - r-rsqlite >=1.0.0 + +source: + md5: 7596c63194f0bf3e58feaa2a854c2061 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'Preprocessing tools for oligonucleotide arrays' - description: 'A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:oligo - parent_recipe: - name: bioconductor-oligo - path: recipes/bioconductor-oligo - version: 1.44.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-oligoclasses/meta.yaml b/recipes/bioconductor-oligoclasses/meta.yaml index f580b7d23a33d..d07ad120b376c 100644 --- a/recipes/bioconductor-oligoclasses/meta.yaml +++ b/recipes/bioconductor-oligoclasses/meta.yaml @@ -1,35 +1,46 @@ -{% set version = "1.64.0" %} +{% set version = "1.68.0" %} {% set name = "oligoClasses" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Classes for high-throughput arrays supported by oligo and crlmm -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 379f1364d7159e2456c9310556e990e6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-oligoclasses", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:oligoclasses + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-oligoclasses + path: recipes/bioconductor-oligoclasses + version: 1.42.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6), RUnit, human370v1cCrlmm, VanillaICE, crlmm requirements: host: - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-biocmanager - r-dbi @@ -37,35 +48,30 @@ requirements: - r-foreach - r-rsqlite run: - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-biocmanager - r-dbi - r-ff - r-foreach - r-rsqlite + +source: + md5: 229a43bcae2583337fc02593fba76b41 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Classes for high-throughput arrays supported by oligo and crlmm' - description: 'This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:oligoclasses - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-oligoclasses - path: recipes/bioconductor-oligoclasses - version: 1.42.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-oligodata/meta.yaml b/recipes/bioconductor-oligodata/meta.yaml index 3359689fb98fc..1d74504bf9e10 100644 --- a/recipes/bioconductor-oligodata/meta.yaml +++ b/recipes/bioconductor-oligodata/meta.yaml @@ -1,41 +1,41 @@ {% set version = "1.8.0" %} {% set name = "oligoData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9625cfd4b31bb575c4029a0632a7ee12 +about: + description: 'Dataset samples (Affymetrix: Expression, Gene, Exon, SNP; NimbleGen: Expression, Tiling) to be used with the oligo package.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Dataset samples for the oligo package build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-oligodata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: pd.hg.u95av2, pd.huex.1.0.st.v2, pd.mapping50k.xba240, pd.hg18.60mer.expr, pd.2006.07.18.hg18.refseq.promoter, pd.hugene.1.0.st.v1 requirements: host: - - 'bioconductor-oligo >=1.66.0,<1.67.0' + - bioconductor-oligo >=1.70.0,<1.71.0 - r-base run: - - 'bioconductor-oligo >=1.66.0,<1.67.0' + - bioconductor-oligo >=1.70.0,<1.71.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9625cfd4b31bb575c4029a0632a7ee12 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'Dataset samples for the oligo package' - description: 'Dataset samples (Affymetrix: Expression, Gene, Exon, SNP; NimbleGen: Expression, Tiling) to be used with the oligo package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-olin/meta.yaml b/recipes/bioconductor-olin/meta.yaml index 90100d3abd625..3e81e2cfe4ebf 100644 --- a/recipes/bioconductor-olin/meta.yaml +++ b/recipes/bioconductor-olin/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.80.0" %} +{% set version = "1.84.0" %} {% set name = "OLIN" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Optimized local intensity-dependent normalisation of two-color microarrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3a6ce43e9272204280a346c20012f710 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-olin", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:olin + parent_recipe: + name: bioconductor-olin + path: recipes/bioconductor-olin + version: 1.58.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: convert requirements: host: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-marray >=1.84.0,<1.85.0 - r-base - r-locfit run: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-marray >=1.84.0,<1.85.0 - r-base - r-locfit + +source: + md5: 6db425fd29cdbd12bce61e9be6cf7878 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Optimized local intensity-dependent normalisation of two-color microarrays' - description: 'Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:olin - parent_recipe: - name: bioconductor-olin - path: recipes/bioconductor-olin - version: 1.58.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-olingui/meta.yaml b/recipes/bioconductor-olingui/meta.yaml index 229943f4192e8..53a459e097552 100644 --- a/recipes/bioconductor-olingui/meta.yaml +++ b/recipes/bioconductor-olingui/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.76.0" %} +{% set version = "1.80.0" %} {% set name = "OLINgui" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f960cc922153099a7b7a6e7ee939d9f +about: + description: Graphical user interface for the OLIN package + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Graphical user interface for OLIN build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-olingui", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-marray >=1.80.0,<1.81.0' - - 'bioconductor-olin >=1.80.0,<1.81.0' - - 'bioconductor-tkwidgets >=1.80.0,<1.81.0' - - 'bioconductor-widgettools >=1.80.0,<1.81.0' + - bioconductor-marray >=1.84.0,<1.85.0 + - bioconductor-olin >=1.84.0,<1.85.0 + - bioconductor-tkwidgets >=1.84.0,<1.85.0 + - bioconductor-widgettools >=1.84.0,<1.85.0 - r-base run: - - 'bioconductor-marray >=1.80.0,<1.81.0' - - 'bioconductor-olin >=1.80.0,<1.81.0' - - 'bioconductor-tkwidgets >=1.80.0,<1.81.0' - - 'bioconductor-widgettools >=1.80.0,<1.81.0' + - bioconductor-marray >=1.84.0,<1.85.0 + - bioconductor-olin >=1.84.0,<1.85.0 + - bioconductor-tkwidgets >=1.84.0,<1.85.0 + - bioconductor-widgettools >=1.84.0,<1.85.0 - r-base +source: + md5: 9cabba294a5208ce6bcb4872f9d3618e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Graphical user interface for OLIN' - description: 'Graphical user interface for the OLIN package' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-omada/meta.yaml b/recipes/bioconductor-omada/meta.yaml index 009cfe955a23d..c46ceaa6e5c3d 100644 --- a/recipes/bioconductor-omada/meta.yaml +++ b/recipes/bioconductor-omada/meta.yaml @@ -1,63 +1,68 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "omada" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Symptomatic heterogeneity in complex diseases reveals differences in molecular states that need to be investigated. However, selecting the numerous parameters of an exploratory clustering analysis in RNA profiling studies requires deep understanding of machine learning and extensive computational experimentation. Tools that assist with such decisions without prior field knowledge are nonexistent and further gene association analyses need to be performed independently. We have developed a suite of tools to automate these processes and make robust unsupervised clustering of transcriptomic data more accessible through automated machine learning based functions. The efficiency of each tool was tested with four datasets characterised by different expression signal strengths. Our toolkit’s decisions reflected the real number of stable partitions in datasets where the subgroups are discernible. Even in datasets with less clear biological distinctions, stable subgroups with different expression profiles and clinical associations were found. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Machine learning tools for automated transcriptome clustering analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d214fdb20c51cbce86bf1d34c59cb84b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-omada", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, testthat requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - r-base - - 'r-clvalid >=0.7' - - 'r-dicer >=0.6.0' - - 'r-dplyr >=1.0.7' - - 'r-fpc >=2.2-9' - - 'r-genieclust >=1.1.3' - - 'r-ggplot2 >=3.3.5' - - 'r-glmnet >=4.1.3' - - 'r-kernlab >=0.9-29' - - 'r-pdfcluster >=1.0-3' - - 'r-rcpp >=1.0.7' - - 'r-reshape >=0.8.8' + - r-clvalid >=0.7 + - r-dicer >=0.6.0 + - r-dplyr >=1.0.7 + - r-fpc >=2.2-9 + - r-genieclust >=1.1.3 + - r-ggplot2 >=3.3.5 + - r-glmnet >=4.1.3 + - r-kernlab >=0.9-29 + - r-pdfcluster >=1.0-3 + - r-rcpp >=1.0.7 + - r-reshape >=0.8.8 - libblas - liblapack run: - r-base - - 'r-clvalid >=0.7' - - 'r-dicer >=0.6.0' - - 'r-dplyr >=1.0.7' - - 'r-fpc >=2.2-9' - - 'r-genieclust >=1.1.3' - - 'r-ggplot2 >=3.3.5' - - 'r-glmnet >=4.1.3' - - 'r-kernlab >=0.9-29' - - 'r-pdfcluster >=1.0-3' - - 'r-rcpp >=1.0.7' - - 'r-reshape >=0.8.8' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} + - r-clvalid >=0.7 + - r-dicer >=0.6.0 + - r-dplyr >=1.0.7 + - r-fpc >=2.2-9 + - r-genieclust >=1.1.3 + - r-ggplot2 >=3.3.5 + - r-glmnet >=4.1.3 + - r-kernlab >=0.9-29 + - r-pdfcluster >=1.0-3 + - r-rcpp >=1.0.7 + - r-reshape >=0.8.8 + +source: + md5: c0ddb89b287d5c6efd9788f289e5710b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Machine learning tools for automated transcriptome clustering analysis' - description: 'Symptomatic heterogeneity in complex diseases reveals differences in molecular states that need to be investigated. However, selecting the numerous parameters of an exploratory clustering analysis in RNA profiling studies requires deep understanding of machine learning and extensive computational experimentation. Tools that assist with such decisions without prior field knowledge are nonexistent and further gene association analyses need to be performed independently. We have developed a suite of tools to automate these processes and make robust unsupervised clustering of transcriptomic data more accessible through automated machine learning based functions. The efficiency of each tool was tested with four datasets characterised by different expression signal strengths. Our toolkit’s decisions reflected the real number of stable partitions in datasets where the subgroups are discernible. Even in datasets with less clear biological distinctions, stable subgroups with different expression profiles and clinical associations were found.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-omadb/meta.yaml b/recipes/bioconductor-omadb/meta.yaml index 2f326296a255a..1f9d11324feb6 100644 --- a/recipes/bioconductor-omadb/meta.yaml +++ b/recipes/bioconductor-omadb/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "2.18.0" %} +{% set version = "2.22.0" %} {% set name = "OmaDB" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package for the orthology prediction data download from OMA database. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: R wrapper for the OMA REST API -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4bfced261f7429c6e881e05dc45ec0d3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-omadb", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-ape - r-base - - 'r-httr >=1.2.1' + - r-httr >=1.2.1 - r-jsonlite - - 'r-plyr >=1.8.4' + - r-plyr >=1.8.4 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-ape - r-base - - 'r-httr >=1.2.1' + - r-httr >=1.2.1 - r-jsonlite - - 'r-plyr >=1.8.4' + - r-plyr >=1.8.4 + +source: + md5: 5d4b7990636e3351fc11565b225a95cb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'R wrapper for the OMA REST API' - description: 'A package for the orthology prediction data download from OMA database.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-omicade4/meta.yaml b/recipes/bioconductor-omicade4/meta.yaml index d1459a945c810..b83b516fc2689 100644 --- a/recipes/bioconductor-omicade4/meta.yaml +++ b/recipes/bioconductor-omicade4/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "omicade4" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package performes multiple co-inertia analysis of omics datasets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Multiple co-inertia analysis of omics datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ed6de2f603d54a9ad262ff62784818a2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-omicade4", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:omicade4 + parent_recipe: + name: bioconductor-omicade4 + path: recipes/bioconductor-omicade4 + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-made4 >=1.76.0,<1.77.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-made4 >=1.80.0,<1.81.0 - r-ade4 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-made4 >=1.76.0,<1.77.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-made4 >=1.80.0,<1.81.0 - r-ade4 - r-base + +source: + md5: d7b95beb9870ee7b4c0dc94d99473563 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Multiple co-inertia analysis of omics datasets' - description: 'This package performes multiple co-inertia analysis of omics datasets.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:omicade4 - parent_recipe: - name: bioconductor-omicade4 - path: recipes/bioconductor-omicade4 - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-omiccircos/meta.yaml b/recipes/bioconductor-omiccircos/meta.yaml index 38a85dda1eaff..036d434616a00 100644 --- a/recipes/bioconductor-omiccircos/meta.yaml +++ b/recipes/bioconductor-omiccircos/meta.yaml @@ -1,40 +1,22 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "OmicCircos" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: OmicCircos is an R application and package for generating high-quality circular plots for omics data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: High-quality circular visualization of omics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7d77b9a00853d3e6fec869012ce33daf build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-omiccircos", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - r-base - run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'High-quality circular visualization of omics data' - description: 'OmicCircos is an R application and package for generating high-quality circular plots for omics data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + extra: identifiers: - biotools:omiccircos @@ -44,3 +26,27 @@ extra: path: recipes/bioconductor-omiccircos version: 1.18.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - r-base + run: + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - r-base + +source: + md5: 7228c6cb7c274ce1f772ded22e631132 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-omicplotr/meta.yaml b/recipes/bioconductor-omicplotr/meta.yaml index f4321b6264bdd..f2f7d2d9398d6 100644 --- a/recipes/bioconductor-omicplotr/meta.yaml +++ b/recipes/bioconductor-omicplotr/meta.yaml @@ -1,27 +1,29 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "omicplotR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A Shiny app for visual exploration of omic datasets as compositions, and differential abundance analysis using ALDEx2. Useful for exploring RNA-seq, meta-RNA-seq, 16s rRNA gene sequencing with visualizations such as principal component analysis biplots (coloured using metadata for visualizing each variable), dendrograms and stacked bar plots, and effect plots (ALDEx2). Input is a table of counts and metadata file (if metadata exists), with options to filter data by count or by metadata to remove low counts, or to visualize select samples according to selected metadata. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Visual Exploration of Omic Datasets Using a Shiny App -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1ab1c2e82c98f8086b4dba4f65a613e7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-omicplotr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-aldex2 >=1.34.0,<1.35.0' + - bioconductor-aldex2 >=1.38.0,<1.39.0 - r-base - r-compositions - r-dt @@ -33,7 +35,7 @@ requirements: - r-vegan - r-zcompositions run: - - 'bioconductor-aldex2 >=1.34.0,<1.35.0' + - bioconductor-aldex2 >=1.38.0,<1.39.0 - r-base - r-compositions - r-dt @@ -44,13 +46,16 @@ requirements: - r-shiny - r-vegan - r-zcompositions + +source: + md5: 7b0ad7d06e38d89369d2b4b38fcd4f60 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Visual Exploration of Omic Datasets Using a Shiny App' - description: 'A Shiny app for visual exploration of omic datasets as compositions, and differential abundance analysis using ALDEx2. Useful for exploring RNA-seq, meta-RNA-seq, 16s rRNA gene sequencing with visualizations such as principal component analysis biplots (coloured using metadata for visualizing each variable), dendrograms and stacked bar plots, and effect plots (ALDEx2). Input is a table of counts and metadata file (if metadata exists), with options to filter data by count or by metadata to remove low counts, or to visualize select samples according to selected metadata.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-omicrexposome/meta.yaml b/recipes/bioconductor-omicrexposome/meta.yaml index b6b78aeaefd18..254aaecd72a4a 100644 --- a/recipes/bioconductor-omicrexposome/meta.yaml +++ b/recipes/bioconductor-omicrexposome/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.24.2" %} +{% set version = "1.28.0" %} {% set name = "omicRexposome" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: omicRexposome systematizes the association evaluation between exposures and omic data, taking advantage of MultiDataSet for coordinated data management, rexposome for exposome data definition and limma for association testing. Also to perform data integration mixing exposome and omic data using multi co-inherent analysis (omicade4) and multi-canonical correlation analysis (PMA). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Exposome and omic data associatin and integration analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3b7a896124164c0dd282c91c79d2db00 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-omicrexposome", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, snpStats, brgedata requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multidataset >=1.30.0,<1.31.0' - - 'bioconductor-omicade4 >=1.42.0,<1.43.0' - - 'bioconductor-rexposome >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multidataset >=1.34.0,<1.35.0 + - bioconductor-omicade4 >=1.46.0,<1.47.0 + - bioconductor-rexposome >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-ggplot2 - r-ggrepel @@ -38,13 +40,13 @@ requirements: - r-smartsva - r-stringr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multidataset >=1.30.0,<1.31.0' - - 'bioconductor-omicade4 >=1.42.0,<1.43.0' - - 'bioconductor-rexposome >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multidataset >=1.34.0,<1.35.0 + - bioconductor-omicade4 >=1.46.0,<1.47.0 + - bioconductor-rexposome >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-ggplot2 - r-ggrepel @@ -53,13 +55,16 @@ requirements: - r-pma - r-smartsva - r-stringr + +source: + md5: d3370377256db6c688b4bfd8c411d227 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Exposome and omic data associatin and integration analysis' - description: 'omicRexposome systematizes the association evaluation between exposures and omic data, taking advantage of MultiDataSet for coordinated data management, rexposome for exposome data definition and limma for association testing. Also to perform data integration mixing exposome and omic data using multi co-inherent analysis (omicade4) and multi-canonical correlation analysis (PMA).' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-omicsmlrepor/build.sh b/recipes/bioconductor-omicsmlrepor/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-omicsmlrepor/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-omicsmlrepor/meta.yaml b/recipes/bioconductor-omicsmlrepor/meta.yaml new file mode 100644 index 0000000000000..02ebd7835dc79 --- /dev/null +++ b/recipes/bioconductor-omicsmlrepor/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "1.0.0" %} +{% set name = "OmicsMLRepoR" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functions to browse the harmonized metadata for large omics databases. This package also supports data navigation if the metadata incorporates ontology. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Search harmonized metadata created under the OmicsMLRepo project + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omicsmlrepor", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: arrow, knitr, BiocStyle, curatedMetagenomicData, testthat (>= 3.0.0), cBioPortalData +requirements: + host: + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-rols >=3.2.0,<3.3.0 + - r-base + - r-data.tree + - r-diagrammer + - r-dplyr + - r-jsonlite + - r-lubridate + - r-plyr + - r-readr + - r-rlang + - r-stringr + - r-tibble + - r-tidyr + run: + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-rols >=3.2.0,<3.3.0 + - r-base + - r-data.tree + - r-diagrammer + - r-dplyr + - r-jsonlite + - r-lubridate + - r-plyr + - r-readr + - r-rlang + - r-stringr + - r-tibble + - r-tidyr + +source: + md5: e559bc10da4e08d10e8fe597195b2d89 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-omicspca/meta.yaml b/recipes/bioconductor-omicspca/meta.yaml index 3dfa436153af2..42c66a8d3dfc3 100644 --- a/recipes/bioconductor-omicspca/meta.yaml +++ b/recipes/bioconductor-omicspca/meta.yaml @@ -1,33 +1,52 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "OMICsPCA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: OMICsPCA is an analysis pipeline designed to integrate multi OMICs experiments done on various subjects (e.g. Cell lines, individuals), treatments (e.g. disease/control) or time points and to analyse such integrated data from various various angles and perspectives. In it's core OMICsPCA uses Principal Component Analysis (PCA) to integrate multiomics experiments from various sources and thus has ability to over data insufficiency issues by using the ingegrated data as representatives. OMICsPCA can be used in various application including analysis of overall distribution of OMICs assays across various samples /individuals /time points; grouping assays by user-defined conditions; identification of source of variation, similarity/dissimilarity between assays, variables or individuals. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d115069df9bde574c2439532f584f19a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-omicspca", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + parent_recipe: + name: bioconductor-omicspca + path: recipes/bioconductor-omicspca + version: 1.0.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, RUnit, BiocGenerics requirements: + + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] + host: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-helloranges >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-omicspcadata >=1.20.0,<1.21.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-helloranges >=1.32.0,<1.33.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-omicspcadata >=1.24.0,<1.25.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-cluster - r-clvalid @@ -48,13 +67,14 @@ requirements: - r-rgl - r-rmarkdown - r-tidyr + run: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-helloranges >=1.28.0,<1.29.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-omicspcadata >=1.20.0,<1.21.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-helloranges >=1.32.0,<1.33.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-omicspcadata >=1.24.0,<1.25.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-cluster - r-clvalid @@ -75,27 +95,16 @@ requirements: - r-rgl - r-rmarkdown - r-tidyr - build: - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - xorg-libxfixes # [linux] + +source: + md5: b7eb63118eba26ae612b275ed8720ab2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples' - description: 'OMICsPCA is an analysis pipeline designed to integrate multi OMICs experiments done on various subjects (e.g. Cell lines, individuals), treatments (e.g. disease/control) or time points and to analyse such integrated data from various various angles and perspectives. In it''s core OMICsPCA uses Principal Component Analysis (PCA) to integrate multiomics experiments from various sources and thus has ability to over data insufficiency issues by using the ingegrated data as representatives. OMICsPCA can be used in various application including analysis of overall distribution of OMICs assays across various samples /individuals /time points; grouping assays by user-defined conditions; identification of source of variation, similarity/dissimilarity between assays, variables or individuals.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - container: - extended-base: true - parent_recipe: - name: bioconductor-omicspca - path: recipes/bioconductor-omicspca - version: 1.0.0 + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-omicspcadata/meta.yaml b/recipes/bioconductor-omicspcadata/meta.yaml index 463dedac14b20..547655626bfc7 100644 --- a/recipes/bioconductor-omicspcadata/meta.yaml +++ b/recipes/bioconductor-omicspcadata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "OMICsPCAdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ba3167fdf846cb80aea07162b88c9b73 +about: + description: Supporting data for package OMICsPCA + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Supporting data for package OMICsPCA build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-omicspcadata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, kableExtra, rmarkdown requirements: host: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 - r-base run: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0662aa06eb12503247db63f9eb7589b2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Supporting data for package OMICsPCA' - description: 'Supporting data for package OMICsPCA' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-omicspcadata/post-link.sh b/recipes/bioconductor-omicspcadata/post-link.sh index ca5c61ccc8b1f..0076ddcf63ee6 100644 --- a/recipes/bioconductor-omicspcadata/post-link.sh +++ b/recipes/bioconductor-omicspcadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "omicspcadata-1.20.0" +installBiocDataPackage.sh "omicspcadata-1.24.0" diff --git a/recipes/bioconductor-omicsprint/meta.yaml b/recipes/bioconductor-omicsprint/meta.yaml index 43008f464b26c..1028222edfea3 100644 --- a/recipes/bioconductor-omicsprint/meta.yaml +++ b/recipes/bioconductor-omicsprint/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "omicsPrint" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: omicsPrint provides functionality for cross omic genetic fingerprinting, for example, to verify sample relationships between multiple omics data types, i.e. genomic, transcriptomic and epigenetic (DNA methylation). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Cross omic genetic fingerprinting -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4e45c908441cedfc0dac097c558e61f1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-omicsprint", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-omicsprint + path: recipes/bioconductor-omicsprint + version: 1.2.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats requirements: host: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-raggedexperiment >=1.30.0,<1.31.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-mass - r-matrixstats run: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-raggedexperiment >=1.30.0,<1.31.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-mass - r-matrixstats + +source: + md5: 234532209b31f4c589480bdd498ca702 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Cross omic genetic fingerprinting' - description: 'omicsPrint provides functionality for cross omic genetic fingerprinting, for example, to verify sample relationships between multiple omics data types, i.e. genomic, transcriptomic and epigenetic (DNA methylation).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-omicsprint - path: recipes/bioconductor-omicsprint - version: 1.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-omicsviewer/build_failure.linux-64.yaml b/recipes/bioconductor-omicsviewer/build_failure.linux-64.yaml deleted file mode 100644 index 42c095bbef5d2..0000000000000 --- a/recipes/bioconductor-omicsviewer/build_failure.linux-64.yaml +++ /dev/null @@ -1,108 +0,0 @@ -recipe_sha: 239d6bdc75a778a6447bf4fc3495c2f506b1d9b087b303660bddf9344473faef # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -reason: |- - r-flatxml 0.1.1 would require r-base >=4.2,<4.3.0a0, which conflicts with any installable versions previously reported; -category: |- - dependency issue -log: |- - - - package bioconductor-summarizedexperiment-1.32.0-r43hdfd78af_0 requires bioconductor-delayedarray >=0.28.0,<0.29.0, but none of the providers can be installed - - - - Leaving build/test directories: - Work: - /opt/conda/conda-bld/work - Test: - /opt/conda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl - Build: - source activate /opt/conda/conda-bld/_build_env - - - Traceback (most recent call last): - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action - t = self.solve(specs) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - r-ggplot2 - - r-matrixstats - - r-fastmatch - - r-psych - - r-rsqlite - - bioconductor-summarizedexperiment >=1.32.0,<1.33.0 - - r-rocr - - r-survminer - - r-matrix - - r-shinybusy - - r-htmlwidgets - - r-rcolorbrewer - - bioconductor-fgsea >=1.28.0,<1.29.0 - - r-networkd3 - - r-dt - - r-shinyjs - - r-plotly - - bioconductor-s4vectors >=0.40.0,<0.41.0 - - r-ggseqlogo - - r-curl - - r-flatxml - - r-shinythemes - - r-httr - - r-shinywidgets - - r-reshape2 - - r-shiny - - r-base 4.3.* - - r-openxlsx - - r-stringr - - bioconductor-biobase >=2.62.0,<2.63.0 - - r-shinycssloaders - - r-survival - - r-beeswarm - - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - package bioconductor-summarizedexperiment-1.32.0-r43hdfd78af_0 requires bioconductor-delayedarray >=0.28.0,<0.29.0, but none of the providers can be installed - - - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build - output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs - for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set - conda_packages = finalize_outputs_pass( - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass - fm = finalize_metadata( - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata - build_unsat, host_unsat = add_upstream_pins(m, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins - host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files - deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies - actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-summarizedexperiment==1.32.0=r43hdfd78af_0"), MatchSpec("bioconductor-delayedarray[version='>=0.28.0,<0.29.0']")} -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-omicsviewer/meta.yaml b/recipes/bioconductor-omicsviewer/meta.yaml index bc96b7d767299..5c18640bed284 100644 --- a/recipes/bioconductor-omicsviewer/meta.yaml +++ b/recipes/bioconductor-omicsviewer/meta.yaml @@ -1,34 +1,38 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "omicsViewer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: omicsViewer visualizes ExpressionSet (or SummarizedExperiment) in an interactive way. The omicsViewer has a separate back- and front-end. In the back-end, users need to prepare an ExpressionSet that contains all the necessary information for the downstream data interpretation. Some extra requirements on the headers of phenotype data or feature data are imposed so that the provided information can be clearly recognized by the front-end, at the same time, keep a minimum modification on the existing ExpressionSet object. The pure dependency on R/Bioconductor guarantees maximum flexibility in the statistical analysis in the back-end. Once the ExpressionSet is prepared, it can be visualized using the front-end, implemented by shiny and plotly. Both features and samples could be selected from (data) tables or graphs (scatter plot/heatmap). Different types of analyses, such as enrichment analysis (using Bioconductor package fgsea or fisher's exact test) and STRING network analysis, will be performed on the fly and the results are visualized simultaneously. When a subset of samples and a phenotype variable is selected, a significance test on means (t-test or ranked based test; when phenotype variable is quantitative) or test of independence (chi-square or fisher’s exact test; when phenotype data is categorical) will be performed to test the association between the phenotype of interest with the selected samples. Additionally, other analyses can be easily added as extra shiny modules. Therefore, omicsViewer will greatly facilitate data exploration, many different hypotheses can be explored in a short time without the need for knowledge of R. In addition, the resulting data could be easily shared using a shiny server. Otherwise, a standalone version of omicsViewer together with designated omics data could be easily created by integrating it with portable R, which can be shared with collaborators or submitted as supplementary data together with a manuscript. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Interactive and explorative visualization of SummarizedExperssionSet or ExpressionSet using omicsViewer -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7d650ff242a133610199a574a29abfde build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-omicsviewer", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, unittest requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-beeswarm - r-curl + - r-drc - r-dt - r-fastmatch - r-flatxml @@ -55,14 +59,16 @@ requirements: - r-stringr - r-survival - r-survminer + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-beeswarm - r-curl + - r-drc - r-dt - r-fastmatch - r-flatxml @@ -89,13 +95,16 @@ requirements: - r-stringr - r-survival - r-survminer + +source: + md5: 239148f41b6a545addcf27cf6489fe14 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Interactive and explorative visualization of SummarizedExperssionSet or ExpressionSet using omicsViewer' - description: 'omicsViewer visualizes ExpressionSet (or SummarizedExperiment) in an interactive way. The omicsViewer has a separate back- and front-end. In the back-end, users need to prepare an ExpressionSet that contains all the necessary information for the downstream data interpretation. Some extra requirements on the headers of phenotype data or feature data are imposed so that the provided information can be clearly recognized by the front-end, at the same time, keep a minimum modification on the existing ExpressionSet object. The pure dependency on R/Bioconductor guarantees maximum flexibility in the statistical analysis in the back-end. Once the ExpressionSet is prepared, it can be visualized using the front-end, implemented by shiny and plotly. Both features and samples could be selected from (data) tables or graphs (scatter plot/heatmap). Different types of analyses, such as enrichment analysis (using Bioconductor package fgsea or fisher''s exact test) and STRING network analysis, will be performed on the fly and the results are visualized simultaneously. When a subset of samples and a phenotype variable is selected, a significance test on means (t-test or ranked based test; when phenotype variable is quantitative) or test of independence (chi-square or fisher’s exact test; when phenotype data is categorical) will be performed to test the association between the phenotype of interest with the selected samples. Additionally, other analyses can be easily added as extra shiny modules. Therefore, omicsViewer will greatly facilitate data exploration, many different hypotheses can be explored in a short time without the need for knowledge of R. In addition, the resulting data could be easily shared using a shiny server. Otherwise, a standalone version of omicsViewer together with designated omics data could be easily created by integrating it with portable R, which can be shared with collaborators or submitted as supplementary data together with a manuscript.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-omixer/meta.yaml b/recipes/bioconductor-omixer/meta.yaml index 5a6e3c4aa6eb1..0ca2c9a209476 100644 --- a/recipes/bioconductor-omixer/meta.yaml +++ b/recipes/bioconductor-omixer/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "Omixer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Omixer - an Bioconductor package for multivariate and reproducible sample randomization, which ensures optimal sample distribution across batches with well-documented methods. It outputs lab-friendly sample layouts, reducing the risk of sample mixups when manually pipetting randomized samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 'Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6360569495c662f2c34c86dbd7387f4a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-omixer", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, magick, testthat requirements: host: @@ -43,13 +45,16 @@ requirements: - r-stringr - r-tibble - r-tidyselect + +source: + md5: de7855603ccf8805e895b4b1368098be + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies' - description: 'Omixer - an Bioconductor package for multivariate and reproducible sample randomization, which ensures optimal sample distribution across batches with well-documented methods. It outputs lab-friendly sample layouts, reducing the risk of sample mixups when manually pipetting randomized samples.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-omnipathr/build_failure.linux-64.yaml b/recipes/bioconductor-omnipathr/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..8b2f9d2602e94 --- /dev/null +++ b/recipes/bioconductor-omnipathr/build_failure.linux-64.yaml @@ -0,0 +1,4 @@ +recipe_sha: d550b12df7e1890bd5d8eec3d0b7ebe7e1df5bef0254ffe5715504b72e5817ba # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + error removing tempfile at end of build diff --git a/recipes/bioconductor-omnipathr/build_failure.osx-64.yaml b/recipes/bioconductor-omnipathr/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..8b2f9d2602e94 --- /dev/null +++ b/recipes/bioconductor-omnipathr/build_failure.osx-64.yaml @@ -0,0 +1,4 @@ +recipe_sha: d550b12df7e1890bd5d8eec3d0b7ebe7e1df5bef0254ffe5715504b72e5817ba # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + error removing tempfile at end of build diff --git a/recipes/bioconductor-omnipathr/meta.yaml b/recipes/bioconductor-omnipathr/meta.yaml index e3b362d4d7544..683001121413f 100644 --- a/recipes/bioconductor-omnipathr/meta.yaml +++ b/recipes/bioconductor-omnipathr/meta.yaml @@ -1,33 +1,36 @@ -{% set version = "3.10.1" %} +{% set version = "3.14.0" %} {% set name = "OmnipathR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A client for the OmniPath web service (https://www.omnipathdb.org) and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation `nichenetr` (available only on github). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: OmniPath web service client and more -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c51296b40e8d580f14dc3ff6839495f6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-omnipathr", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, biomaRt, bookdown, dnet, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, sigmajs, smoof, supraHex, testthat + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, bookdown, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, R.matlab, sigmajs, smoof, supraHex, testthat requirements: + host: - r-base - r-checkmate - r-crayon - r-curl - r-digest - - 'r-dplyr >=1.1.0' + - r-dplyr >=1.1.0 - r-httr - r-igraph - r-jsonlite @@ -37,27 +40,33 @@ requirements: - r-magrittr - r-progress - r-purrr + - r-r.utils - r-rappdirs - - 'r-readr >=2.0.0' + - r-readr >=2.0.0 - r-readxl - r-rlang - r-rmarkdown + - r-rsqlite - r-rvest - r-stringi - r-stringr - r-tibble - r-tidyr - r-tidyselect + - r-vctrs - r-withr + - r-xml - r-xml2 - r-yaml + - r-zip + run: - r-base - r-checkmate - r-crayon - r-curl - r-digest - - 'r-dplyr >=1.1.0' + - r-dplyr >=1.1.0 - r-httr - r-igraph - r-jsonlite @@ -67,28 +76,35 @@ requirements: - r-magrittr - r-progress - r-purrr + - r-r.utils - r-rappdirs - - 'r-readr >=2.0.0' + - r-readr >=2.0.0 - r-readxl - r-rlang - r-rmarkdown + - r-rsqlite - r-rvest - r-stringi - r-stringr - r-tibble - r-tidyr - r-tidyselect + - r-vctrs - r-withr + - r-xml - r-xml2 - r-yaml + - r-zip + +source: + md5: d2e2da1697eb72a8c6313883043682ca + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "options(omnipath.logfile=''none''); library(''{{ name }}'')"' - - find /tmp -name omnipathr-log -exec rm -rf {} + -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'OmniPath web service client and more' - description: 'A client for the OmniPath web service (https://www.omnipathdb.org) and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation `nichenetr` (available only on github).' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ompbam/meta.yaml b/recipes/bioconductor-ompbam/meta.yaml index 87ebc1481b424..b2b49e4c58791 100644 --- a/recipes/bioconductor-ompbam/meta.yaml +++ b/recipes/bioconductor-ompbam/meta.yaml @@ -1,45 +1,43 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "ompBAM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e9d31ddcad0b4bb4acb30ad970a0cd5 +about: + description: This packages provides C++ header files for developers wishing to create R packages that processes BAM files. ompBAM automates file access, memory management, and handling of multiple threads 'behind the scenes', so developers can focus on creating domain-specific functionality. The included vignette contains detailed documentation of this API, including quick-start instructions to create a new ompBAM-based package, and step-by-step explanation of the functionality behind the example packaged included within ompBAM. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: C++ Library for OpenMP-based multi-threaded sequential profiling of Binary Alignment Map (BAM) files build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ompbam", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis, desc, testthat (>= 3.0.0) requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - r-base - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} +source: + md5: d88dc9ccb61fdc23ad3660bffa5d78f6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'C++ Library for OpenMP-based multi-threaded sequential profiling of Binary Alignment Map (BAM) files' - description: 'This packages provides C++ header files for developers wishing to create R packages that processes BAM files. ompBAM automates file access, memory management, and handling of multiple threads ''behind the scenes'', so developers can focus on creating domain-specific functionality. The included vignette contains detailed documentation of this API, including quick-start instructions to create a new ompBAM-based package, and step-by-step explanation of the functionality behind the example packaged included within ompBAM.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-omxplore/build.sh b/recipes/bioconductor-omxplore/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-omxplore/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-omxplore/meta.yaml b/recipes/bioconductor-omxplore/meta.yaml new file mode 100644 index 0000000000000..9b270cd19ccdc --- /dev/null +++ b/recipes/bioconductor-omxplore/meta.yaml @@ -0,0 +1,85 @@ +{% set version = "1.0.0" %} +{% set name = "omXplore" %} +{% set bioc = "3.20" %} + +about: + description: This package contains a collection of functions (written as shiny modules) for the visualisation and the statistical analysis of omics data. These plots can be displayed individually or embedded in a global Shiny module. Additionaly, it is possible to integrate third party modules to the main interface of the package omXplore. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Vizualization tools for 'omics' datasets with R + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-omxplore", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, BiocStyle, testthat, Matrix, graph +requirements: + + host: + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-psmatch >=1.10.0,<1.11.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-dendextend + - r-dplyr + - r-dt + - r-factoextra + - r-factominer + - r-gplots + - r-highcharter + - r-htmlwidgets + - r-rcolorbrewer + - r-shiny + - r-shinybs + - r-shinyjqui + - r-shinyjs + - r-tibble + - r-tidyr + - r-vioplot + - r-visnetwork + + run: + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-psmatch >=1.10.0,<1.11.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-dendextend + - r-dplyr + - r-dt + - r-factoextra + - r-factominer + - r-gplots + - r-highcharter + - r-htmlwidgets + - r-rcolorbrewer + - r-shiny + - r-shinybs + - r-shinyjqui + - r-shinyjs + - r-tibble + - r-tidyr + - r-vioplot + - r-visnetwork + +source: + md5: 6bd0ad2004166ccda4a844f210277b61 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-onassisjavalibs/meta.yaml b/recipes/bioconductor-onassisjavalibs/meta.yaml index d2c32d35b58e1..2570326f5b07c 100644 --- a/recipes/bioconductor-onassisjavalibs/meta.yaml +++ b/recipes/bioconductor-onassisjavalibs/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "OnassisJavaLibs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 88d86bc7e7d339146ba7ea689c2d8080 +about: + description: A package that contains java libraries to call conceptmapper and compute semnatic similarity from R + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: OnassisJavaLibs, java libraries to run conceptmapper and semantic similarity build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-onassisjavalibs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, rmarkdown, knitr # SystemRequirements: Java (>= 1.8) requirements: @@ -30,15 +29,16 @@ requirements: - r-base - r-rjava - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 - openjdk +source: + md5: 835d47c58d358149eaf643a280345200 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'OnassisJavaLibs, java libraries to run conceptmapper and semantic similarity' - description: 'A package that contains java libraries to call conceptmapper and compute semnatic similarity from R' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-onassisjavalibs/post-link.sh b/recipes/bioconductor-onassisjavalibs/post-link.sh index 2e98dfca3f0c9..2511be1c83ad6 100644 --- a/recipes/bioconductor-onassisjavalibs/post-link.sh +++ b/recipes/bioconductor-onassisjavalibs/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "onassisjavalibs-1.24.0" +installBiocDataPackage.sh "onassisjavalibs-1.28.0" diff --git a/recipes/bioconductor-oncomix/meta.yaml b/recipes/bioconductor-oncomix/meta.yaml index e3d50be1cdf3e..a756a58b7dd96 100644 --- a/recipes/bioconductor-oncomix/meta.yaml +++ b/recipes/bioconductor-oncomix/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "oncomix" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package helps identify mRNAs that are overexpressed in subsets of tumors relative to normal tissue. Ideal inputs would be paired tumor-normal data from the same tissue from many patients (>15 pairs). This unsupervised approach relies on the observation that oncogenes are characteristically overexpressed in only a subset of tumors in the population, and may help identify oncogene candidates purely based on differences in mRNA expression between previously unknown subtypes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dd6381604152d7cb96f7c592e8f82ab7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-oncomix", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, RMySQL requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-ggrepel - r-mclust - r-rcolorbrewer run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-ggrepel - r-mclust - r-rcolorbrewer + +source: + md5: 7cdd25fe248dec0a8676f980bf6f313a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data' - description: 'This package helps identify mRNAs that are overexpressed in subsets of tumors relative to normal tissue. Ideal inputs would be paired tumor-normal data from the same tissue from many patients (>15 pairs). This unsupervised approach relies on the observation that oncogenes are characteristically overexpressed in only a subset of tumors in the population, and may help identify oncogene candidates purely based on differences in mRNA expression between previously unknown subtypes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-oncoscanr/meta.yaml b/recipes/bioconductor-oncoscanr/meta.yaml index 84d19dea331fa..a125e7ee7dc42 100644 --- a/recipes/bioconductor-oncoscanr/meta.yaml +++ b/recipes/bioconductor-oncoscanr/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "oncoscanR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The software uses the copy number segments from a text file and identifies all chromosome arms that are globally altered and computes various genome-wide scores. The following HRD scores (characteristic of BRCA-mutated cancers) are included: LST, HR-LOH, nLST and gLOH. the package is tailored for the ThermoFisher Oncoscan assay analyzed with their Chromosome Alteration Suite (ChAS) but can be adapted to any input.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Secondary analyses of CNV data (HRD and more) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 48aee6850c94c299417e75cf74418b01 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-oncoscanr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.1.4), jsonlite, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-magrittr - r-readr run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-magrittr - r-readr + +source: + md5: 41a3ad0c018823770001a20a8a1625ac + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Secondary analyses of CNV data (HRD and more)' - description: 'The software uses the copy number segments from a text file and identifies all chromosome arms that are globally altered and computes various genome-wide scores. The following HRD scores (characteristic of BRCA-mutated cancers) are included: LST, HR-LOH, nLST and gLOH. the package is tailored for the ThermoFisher Oncoscan assay analyzed with their Chromosome Alteration Suite (ChAS) but can be adapted to any input.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-oncoscore/meta.yaml b/recipes/bioconductor-oncoscore/meta.yaml index f85345b846e04..00fefd2483fae 100644 --- a/recipes/bioconductor-oncoscore/meta.yaml +++ b/recipes/bioconductor-oncoscore/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "OncoScore" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5b61a8738f91d4c8ff214b38878a8564 +about: + description: OncoScore is a tool to measure the association of genes to cancer based on citation frequencies in biomedical literature. The score is evaluated from PubMed literature by dynamically updatable web queries. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: A tool to identify potentially oncogenic genes build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-oncoscore", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocGenerics, BiocStyle, knitr, testthat, requirements: host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' + - bioconductor-biomart >=2.62.0,<2.63.0 - r-base run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' + - bioconductor-biomart >=2.62.0,<2.63.0 - r-base +source: + md5: a4e704ceb3b771c4d00acf54f7f10f61 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'A tool to identify potentially oncogenic genes' - description: 'OncoScore is a tool to measure the association of genes to cancer based on citation frequencies in biomedical literature. The score is evaluated from PubMed literature by dynamically updatable web queries.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-oncosimulr/build.sh b/recipes/bioconductor-oncosimulr/build.sh index ac78ea511ccf4..c1d13421f5f1e 100644 --- a/recipes/bioconductor-oncosimulr/build.sh +++ b/recipes/bioconductor-oncosimulr/build.sh @@ -8,7 +8,4 @@ CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -if [[ $OSTYPE == "darwin"* ]]; then - sed -i.bak "s/OncoSimulR.so/OncoSimulR.dylib/g" src/install.libs.R -fi $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-oncosimulr/meta.yaml b/recipes/bioconductor-oncosimulr/meta.yaml index daa4bec2d291d..e1d667c5ef86a 100644 --- a/recipes/bioconductor-oncosimulr/meta.yaml +++ b/recipes/bioconductor-oncosimulr/meta.yaml @@ -1,28 +1,42 @@ -{% set version = "4.4.0" %} +{% set version = "4.8.0" %} {% set name = "OncoSimulR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Functions for forward population genetic simulation in asexual populations, with special focus on cancer progression. Fitness can be an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, order restrictions in mutation accumulation, and order effects. Fitness (including just birth, just death, or both birth and death) can also be a function of the relative and absolute frequencies of other genotypes (i.e., frequency-dependent fitness). Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). Simulating multi-species scenarios and therapeutic interventions, including adaptive therapy, is also possible. Simulations use continuous-time models and can include driver and passenger genes and modules. Also included are functions for: simulating random DAGs of the type found in Oncogenetic Trees, Conjunctive Bayesian Networks, and other cancer progression models; plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling; plotting the parent-child relationships of the clones; generating random fitness landscapes (Rough Mount Fuji, House of Cards, additive, NK, Ising, and Eggbox models) and plotting them.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Forward Genetic Simulation of Cancer Progression with Epistasis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9b908040a100f075d4f2493ec3c1fa85 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-oncosimulr", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:oncosimulr + parent_recipe: + name: bioconductor-oncosimulr + path: recipes/bioconductor-oncosimulr + version: 2.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-car - r-data.table @@ -32,14 +46,14 @@ requirements: - r-gtools - r-igraph - r-rcolorbrewer - - 'r-rcpp >=0.12.4' + - r-rcpp >=0.12.4 - r-smatr - r-stringr - libblas - liblapack run: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-car - r-data.table @@ -49,27 +63,19 @@ requirements: - r-gtools - r-igraph - r-rcolorbrewer - - 'r-rcpp >=0.12.4' + - r-rcpp >=0.12.4 - r-smatr - r-stringr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 0ee28418fe4a4fff5393eb1eaf472e50 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Forward Genetic Simulation of Cancer Progression with Epistasis' - description: 'Functions for forward population genetic simulation in asexual populations, with special focus on cancer progression. Fitness can be an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, order restrictions in mutation accumulation, and order effects. Fitness (including just birth, just death, or both birth and death) can also be a function of the relative and absolute frequencies of other genotypes (i.e., frequency-dependent fitness). Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). Simulating multi-species scenarios and therapeutic interventions, including adaptive therapy, is also possible. Simulations use continuous-time models and can include driver and passenger genes and modules. Also included are functions for: simulating random DAGs of the type found in Oncogenetic Trees, Conjunctive Bayesian Networks, and other cancer progression models; plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling; plotting the parent-child relationships of the clones; generating random fitness landscapes (Rough Mount Fuji, House of Cards, additive, NK, Ising, and Eggbox models) and plotting them.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:oncosimulr - parent_recipe: - name: bioconductor-oncosimulr - path: recipes/bioconductor-oncosimulr - version: 2.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-onlinefdr/meta.yaml b/recipes/bioconductor-onlinefdr/meta.yaml index 24c6eefdc5faf..c7e5c0eae72f2 100644 --- a/recipes/bioconductor-onlinefdr/meta.yaml +++ b/recipes/bioconductor-onlinefdr/meta.yaml @@ -1,25 +1,31 @@ -{% set version = "2.10.0" %} +{% set version = "2.14.0" %} {% set name = "onlineFDR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package allows users to control the false discovery rate (FDR) or familywise error rate (FWER) for online multiple hypothesis testing, where hypotheses arrive in a stream. In this framework, a null hypothesis is rejected based on the evidence against it and on the previous rejection decisions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Online error rate control -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1fcb84d6fd99c3f48d43c07adc29f256 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-onlinefdr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, covr requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-progress @@ -32,17 +38,16 @@ requirements: - r-progress - r-rcpp - r-rcppprogress - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: f3afcfebc4b2762b11a24fe1010d5a5a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Online error rate control' - description: 'This package allows users to control the false discovery rate (FDR) or familywise error rate (FWER) for online multiple hypothesis testing, where hypotheses arrive in a stream. In this framework, a null hypothesis is rejected based on the evidence against it and on the previous rejection decisions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ontoproc/meta.yaml b/recipes/bioconductor-ontoproc/meta.yaml index ebdd3376d7bee..729978daa9b0e 100644 --- a/recipes/bioconductor-ontoproc/meta.yaml +++ b/recipes/bioconductor-ontoproc/meta.yaml @@ -1,64 +1,77 @@ -{% set version = "1.24.0" %} +{% set version = "2.0.0" %} {% set name = "ontoProc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN. We provide snapshots of key ontologies for terms about cells, cell lines, chemical compounds, and anatomy, to help analyze genome-scale experiments, particularly cell x compound screens. Another purpose is to strengthen development of compelling use cases for richer interfaces to emerging ontologies. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: processing of ontologies of anatomy, cell lines, and so on -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 157cb78951de651c6be909aef51480a5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ontoproc", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, celldex, rmarkdown, AnnotationDbi + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, celldex, rmarkdown, AnnotationDbi, magick requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-dt + - r-httr - r-igraph - r-magrittr - r-ontologyindex - r-ontologyplot + - r-r.utils + - r-reticulate - r-shiny run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-dt + - r-httr - r-igraph - r-magrittr - r-ontologyindex - r-ontologyplot + - r-r.utils + - r-reticulate - r-shiny + +source: + md5: 0d1f9051f2943dc3ad512175573297bf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'processing of ontologies of anatomy, cell lines, and so on' - description: 'Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN. We provide snapshots of key ontologies for terms about cells, cell lines, chemical compounds, and anatomy, to help analyze genome-scale experiments, particularly cell x compound screens. Another purpose is to strengthen development of compelling use cases for richer interfaces to emerging ontologies.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ontoprocdata/meta.yaml b/recipes/bioconductor-ontoprocdata/meta.yaml index b0247d4b82b11..7eadcb79dadbc 100644 --- a/recipes/bioconductor-ontoprocdata/meta.yaml +++ b/recipes/bioconductor-ontoprocdata/meta.yaml @@ -1,24 +1,22 @@ {% set version = "0.99.9901" %} {% set name = "ontoProcData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d4160c1fc853db468ce73c7fe62ca00f +about: + description: This package manages rda files of multiple ontologies that are used in the ontoProc package. These ontologies were originally downloaded as owl or obo files and converted into Rda files. The files were downloaded at various times but most of them were downloaded on August 08 2022. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: A data package for ontoProc build: - number: 2 + noarch: generic + number: 3 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ontoprocdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat (>= 3.0.0), AnnotationHub, utils, knitr, rmarkdown requirements: host: @@ -26,13 +24,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d4160c1fc853db468ce73c7fe62ca00f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A data package for ontoProc' - description: 'This package manages rda files of multiple ontologies that are used in the ontoProc package. These ontologies were originally downloaded as owl or obo files and converted into Rda files. The files were downloaded at various times but most of them were downloaded on August 08 2022.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-opencyto/meta.yaml b/recipes/bioconductor-opencyto/meta.yaml index 6c2923914d7d3..762d0d9393e50 100644 --- a/recipes/bioconductor-opencyto/meta.yaml +++ b/recipes/bioconductor-opencyto/meta.yaml @@ -1,35 +1,47 @@ -{% set version = "2.14.0" %} +{% set version = "2.18.0" %} {% set name = "openCyto" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3.0-only + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Hierarchical Gating Pipeline for flow cytometry data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 04a62bb1960f008fc218686296a3118d build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-opencyto", max_pin="x.x") }}' + +extra: + parent_recipe: + name: bioconductor-opencyto + path: recipes/bioconductor-opencyto + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2), MASS requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-flowclust >=3.40.0,<3.41.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowviz >=1.66.0,<1.67.0' - - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-flowclust >=3.44.0,<3.45.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowviz >=1.70.0,<1.71.0 + - bioconductor-flowworkspace >=4.18.0,<4.19.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-ncdfflow >=2.52.0,<2.53.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 - r-base - r-bh - r-cpp11 @@ -38,36 +50,30 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-flowclust >=3.40.0,<3.41.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowviz >=1.66.0,<1.67.0' - - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-ncdfflow >=2.48.0,<2.49.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-flowclust >=3.44.0,<3.45.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowviz >=1.70.0,<1.71.0 + - bioconductor-flowworkspace >=4.18.0,<4.19.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-ncdfflow >=2.52.0,<2.53.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 - r-base - r-bh - r-cpp11 - r-data.table - r-rcolorbrewer - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 5d9c6a6851d56037f75a9369838768d4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3.0-only - summary: 'Hierarchical Gating Pipeline for flow cytometry data' - description: 'This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-opencyto - path: recipes/bioconductor-opencyto - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-openprimer/meta.yaml b/recipes/bioconductor-openprimer/meta.yaml index e7ebaf881fc1c..baffa8754434c 100644 --- a/recipes/bioconductor-openprimer/meta.yaml +++ b/recipes/bioconductor-openprimer/meta.yaml @@ -1,94 +1,97 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "openPrimeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An implementation of methods for designing, evaluating, and comparing primer sets for multiplex PCR. Primers are designed by solving a set cover problem such that the number of covered template sequences is maximized with the smallest possible set of primers. To guarantee that high-quality primers are generated, only primers fulfilling constraints on their physicochemical properties are selected. A Shiny app providing a user interface for the functionalities of this package is provided by the 'openPrimeRui' package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Multiplex PCR Primer Design and Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e3fe2285d832b192c7054a36e2aedc6b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-openprimer", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 1.0.2), knitr (>= 1.13), rmarkdown (>= 1.0), devtools (>= 1.12.0), doParallel (>= 1.0.10), pander (>= 0.6.0), learnr (>= 0.9) # SystemRequirements: MAFFT (>= 7.305), OligoArrayAux (>= 3.8), ViennaRNA (>= 2.4.1), MELTING (>= 5.1.1), Pandoc (>= 1.12.3) requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-decipher >=2.30.0,<2.31.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'r-ape >=3.5' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-decipher >=3.2.0,<3.3.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-ape >=3.5 - r-base - - 'r-digest >=0.6.9' - - 'r-distr >=2.6' - - 'r-distrex >=2.6' - - 'r-dplyr >=0.5.0' - - 'r-fitdistrplus >=1.0-7' - - 'r-foreach >=1.4.3' - - 'r-ggplot2 >=2.1.0' - - 'r-hmisc >=3.17-4' - - 'r-lpsolveapi >=5.5.2.0-17' - - 'r-magrittr >=1.5' - - 'r-openxlsx >=4.0.17' - - 'r-plyr >=1.8.4' - - 'r-rcolorbrewer >=1.1-2' - - 'r-reshape2 >=1.4.1' - - 'r-scales >=0.4.0' - - 'r-seqinr >=3.3-3' - - 'r-stringdist >=0.9.4.1' - - 'r-stringr >=1.0.0' - - 'r-uniqtag >=1.0' - - 'r-xml >=3.98-1.4' - - 'mafft >=7.305' + - r-digest >=0.6.9 + - r-dplyr >=0.5.0 + - r-foreach >=1.4.3 + - r-ggplot2 >=2.1.0 + - r-hmisc >=3.17-4 + - r-lpsolveapi >=5.5.2.0-17 + - r-magrittr >=1.5 + - r-openxlsx >=4.0.17 + - r-plyr >=1.8.4 + - r-rcolorbrewer >=1.1-2 + - r-reshape2 >=1.4.1 + - r-scales >=0.4.0 + - r-seqinr >=3.3-3 + - r-stringdist >=0.9.4.1 + - r-stringr >=1.0.0 + - r-uniqtag >=1.0 + - r-xml >=3.98-1.4 + - mafft >=7.305 + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-decipher >=2.30.0,<2.31.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'r-ape >=3.5' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-decipher >=3.2.0,<3.3.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-ape >=3.5 - r-base - - 'r-digest >=0.6.9' - - 'r-distr >=2.6' - - 'r-distrex >=2.6' - - 'r-dplyr >=0.5.0' - - 'r-fitdistrplus >=1.0-7' - - 'r-foreach >=1.4.3' - - 'r-ggplot2 >=2.1.0' - - 'r-hmisc >=3.17-4' - - 'r-lpsolveapi >=5.5.2.0-17' - - 'r-magrittr >=1.5' - - 'r-openxlsx >=4.0.17' - - 'r-plyr >=1.8.4' - - 'r-rcolorbrewer >=1.1-2' - - 'r-reshape2 >=1.4.1' - - 'r-scales >=0.4.0' - - 'r-seqinr >=3.3-3' - - 'r-stringdist >=0.9.4.1' - - 'r-stringr >=1.0.0' - - 'r-uniqtag >=1.0' - - 'r-xml >=3.98-1.4' - - 'mafft >=7.305' + - r-digest >=0.6.9 + - r-dplyr >=0.5.0 + - r-foreach >=1.4.3 + - r-ggplot2 >=2.1.0 + - r-hmisc >=3.17-4 + - r-lpsolveapi >=5.5.2.0-17 + - r-magrittr >=1.5 + - r-openxlsx >=4.0.17 + - r-plyr >=1.8.4 + - r-rcolorbrewer >=1.1-2 + - r-reshape2 >=1.4.1 + - r-scales >=0.4.0 + - r-seqinr >=3.3-3 + - r-stringdist >=0.9.4.1 + - r-stringr >=1.0.0 + - r-uniqtag >=1.0 + - r-xml >=3.98-1.4 + - mafft >=7.305 + +source: + md5: fb47d3362b75d0f8561bcfaa9e06b370 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Multiplex PCR Primer Design and Analysis' - description: 'An implementation of methods for designing, evaluating, and comparing primer sets for multiplex PCR. Primers are designed by solving a set cover problem such that the number of covered template sequences is maximized with the smallest possible set of primers. To guarantee that high-quality primers are generated, only primers fulfilling constraints on their physicochemical properties are selected. A Shiny app providing a user interface for the functionalities of this package is provided by the ''openPrimeRui'' package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-openstats/meta.yaml b/recipes/bioconductor-openstats/meta.yaml index f78c9bcdf4b49..d14f7c315ff68 100644 --- a/recipes/bioconductor-openstats/meta.yaml +++ b/recipes/bioconductor-openstats/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "OpenStats" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package contains several methods for statistical analysis of genotype to phenotype association in high-throughput screening pipelines. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e8a0fcd25ca1377c5bce5068bfaabff build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-openstats", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown requirements: host: @@ -43,13 +45,16 @@ requirements: - r-nlme - r-rlist - r-summarytools + +source: + md5: e33e1d076d50e2aa90f24e43e60ab884 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association' - description: 'Package contains several methods for statistical analysis of genotype to phenotype association in high-throughput screening pipelines.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-operonhumanv3.db/meta.yaml b/recipes/bioconductor-operonhumanv3.db/meta.yaml index c1bf73b30fa4b..8b6e00b744306 100644 --- a/recipes/bioconductor-operonhumanv3.db/meta.yaml +++ b/recipes/bioconductor-operonhumanv3.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "OperonHumanV3.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 648da5d4d63c6c8327f6035ee09f2b65 +about: + description: FHCRC Nelson Lab OperonHumanV3 Annotation Data (OperonHumanV3) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: FHCRC Nelson Lab OperonHumanV3 Annotation Data (OperonHumanV3) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-operonhumanv3.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 648da5d4d63c6c8327f6035ee09f2b65 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'FHCRC Nelson Lab OperonHumanV3 Annotation Data (OperonHumanV3)' - description: 'FHCRC Nelson Lab OperonHumanV3 Annotation Data (OperonHumanV3) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-opossom/meta.yaml b/recipes/bioconductor-opossom/meta.yaml index 131a22582ed1a..c254d4d4bc520 100644 --- a/recipes/bioconductor-opossom/meta.yaml +++ b/recipes/bioconductor-opossom/meta.yaml @@ -1,33 +1,39 @@ -{% set version = "2.20.0" %} +{% set version = "2.24.0" %} {% set name = "oposSOM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package translates microarray expression data into metadata of reduced dimension. It provides various sample-centered and group-centered visualizations, sample similarity analyses and functional enrichment analyses. The underlying SOM algorithm combines feature clustering, multidimensional scaling and dimension reduction, along with strong visualization capabilities. It enables extraction and description of functional expression modules inherent in the data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Comprehensive analysis of transcriptome data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a5660824c13db2ae8bf7b79aa7c529f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-opossom", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-ape - r-base - r-fastica - r-fdrtool - - 'r-igraph >=1.0.0' + - r-igraph >=1.0.0 - r-pixmap - r-png - r-rcpp @@ -39,14 +45,14 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-ape - r-base - r-fastica - r-fdrtool - - 'r-igraph >=1.0.0' + - r-igraph >=1.0.0 - r-pixmap - r-png - r-rcpp @@ -55,17 +61,16 @@ requirements: - r-scatterplot3d - r-tsne - r-xml - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 205b90618691057e82de1a844fb89ce9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Comprehensive analysis of transcriptome data' - description: 'This package translates microarray expression data into metadata of reduced dimension. It provides various sample-centered and group-centered visualizations, sample similarity analyses and functional enrichment analyses. The underlying SOM algorithm combines feature clustering, multidimensional scaling and dimension reduction, along with strong visualization capabilities. It enables extraction and description of functional expression modules inherent in the data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-oppar/meta.yaml b/recipes/bioconductor-oppar/meta.yaml index 9546c106c3853..ac44ed61c524f 100644 --- a/recipes/bioconductor-oppar/meta.yaml +++ b/recipes/bioconductor-oppar/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "oppar" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The R implementation of mCOPA package published by Wang et al. (2012). Oppar provides methods for Cancer Outlier profile Analysis. Although initially developed to detect outlier genes in cancer studies, methods presented in oppar can be used for outlier profile analysis in general. In addition, tools are provided for gene set enrichment and pathway analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Outlier profile and pathway analysis in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 21adf37b9236cf860009e709f63d5e30 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-oppar", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:oppar + parent_recipe: + name: bioconductor-oppar + path: recipes/bioconductor-oppar + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-gsva >=1.50.0,<1.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-gsva >=2.0.0,<2.1.0 - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-gsva >=1.50.0,<1.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-gsva >=2.0.0,<2.1.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: e37dc8f9b0b4e20e8821273244032fbb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Outlier profile and pathway analysis in R' - description: 'The R implementation of mCOPA package published by Wang et al. (2012). Oppar provides methods for Cancer Outlier profile Analysis. Although initially developed to detect outlier genes in cancer studies, methods presented in oppar can be used for outlier profile analysis in general. In addition, tools are provided for gene set enrichment and pathway analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:oppar - parent_recipe: - name: bioconductor-oppar - path: recipes/bioconductor-oppar - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-oppti/meta.yaml b/recipes/bioconductor-oppti/meta.yaml index ceb9efd135c77..e5f2293d87de9 100644 --- a/recipes/bioconductor-oppti/meta.yaml +++ b/recipes/bioconductor-oppti/meta.yaml @@ -1,28 +1,29 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "oppti" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The aim of oppti is to analyze protein (and phosphosite) expressions to find outlying markers for each sample in the given cohort(s) for the discovery of personalized actionable targets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + summary: Outlier Protein and Phosphosite Target Identifier -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8f995db99b66e966a96b8ce150c956a7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-oppti", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: markdown requirements: host: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-devtools - r-ggplot2 @@ -32,7 +33,7 @@ requirements: - r-rcolorbrewer - r-reshape run: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-devtools - r-ggplot2 @@ -41,12 +42,16 @@ requirements: - r-pheatmap - r-rcolorbrewer - r-reshape + +source: + md5: 45fd42bff6b3e6b28e0d95e5e9542b9b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: MIT - summary: 'Outlier Protein and Phosphosite Target Identifier' - description: 'The aim of oppti is to analyze protein (and phosphosite) expressions to find outlying markers for each sample in the given cohort(s) for the discovery of personalized actionable targets.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-optimalflow/meta.yaml b/recipes/bioconductor-optimalflow/meta.yaml index 992876df6f621..e21b10a3d8e39 100644 --- a/recipes/bioconductor-optimalflow/meta.yaml +++ b/recipes/bioconductor-optimalflow/meta.yaml @@ -1,29 +1,41 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "optimalFlow" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Optimal-transport techniques applied to supervised flow cytometry gating. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: optimalFlow -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c66127dc23a70fdcfd651543ea596329 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-optimalflow", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, rmarkdown, magick requirements: + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] host: - - 'bioconductor-flowmeans >=1.62.0,<1.63.0' - - 'bioconductor-optimalflowdata >=1.14.0,<1.15.0' + - bioconductor-flowmeans >=1.66.0,<1.67.0 + - bioconductor-optimalflowdata >=1.18.0,<1.19.0 - r-base - r-dbscan - r-doparallel @@ -33,12 +45,12 @@ requirements: - r-randomforest - r-rfast - r-rgl - - 'r-rlang >=0.4.0' + - r-rlang >=0.4.0 - r-robustbase - r-transport run: - - 'bioconductor-flowmeans >=1.62.0,<1.63.0' - - 'bioconductor-optimalflowdata >=1.14.0,<1.15.0' + - bioconductor-flowmeans >=1.66.0,<1.67.0 + - bioconductor-optimalflowdata >=1.18.0,<1.19.0 - r-base - r-dbscan - r-doparallel @@ -48,25 +60,19 @@ requirements: - r-randomforest - r-rfast - r-rgl - - 'r-rlang >=0.4.0' + - r-rlang >=0.4.0 - r-robustbase - r-transport - build: - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - xorg-libxfixes # [linux] + +source: + md5: 579f1d7205f12db20a358183f5de3a49 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: optimalFlow - description: 'Optimal-transport techniques applied to supervised flow cytometry gating.' -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-optimalflowdata/meta.yaml b/recipes/bioconductor-optimalflowdata/meta.yaml index d65bee9574e4b..09e7f91cf8bec 100644 --- a/recipes/bioconductor-optimalflowdata/meta.yaml +++ b/recipes/bioconductor-optimalflowdata/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "optimalFlowData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 790ea8af88ecf90abafdef9a7c4abb08 +about: + description: Data files used as examples and for testing of the software provided in the optimalFlow package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: optimalFlowData build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-optimalflowdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, BiocStyle, rmarkdown, magick requirements: host: @@ -26,13 +24,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 55a3488bbc6c8f1d9caac07a42a513fb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: optimalFlowData - description: 'Data files used as examples and for testing of the software provided in the optimalFlow package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-optimalflowdata/post-link.sh b/recipes/bioconductor-optimalflowdata/post-link.sh index 0a5ec1a8c8c2a..e5320ff69669f 100644 --- a/recipes/bioconductor-optimalflowdata/post-link.sh +++ b/recipes/bioconductor-optimalflowdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "optimalflowdata-1.14.0" +installBiocDataPackage.sh "optimalflowdata-1.18.0" diff --git a/recipes/bioconductor-opweight/meta.yaml b/recipes/bioconductor-opweight/meta.yaml index cd88a4afed9cd..ade709fb48a7a 100644 --- a/recipes/bioconductor-opweight/meta.yaml +++ b/recipes/bioconductor-opweight/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "OPWeight" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 83d9a0007e617f317f9424a4c228c50a +about: + description: This package perform weighted-pvalue based multiple hypothesis test and provides corresponding information such as ranking probability, weight, significant tests, etc . To conduct this testing procedure, the testing method apply a probabilistic relationship between the test rank and the corresponding test effect size. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Optimal p-value weighting with independent information build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-opweight", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2, gridExtra, knitr, Matrix, rmarkdown, scales, testthat requirements: host: - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - r-mass - r-tibble run: - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - r-mass - r-tibble +source: + md5: 3026e8c32704c0d2e14dfc572cf6c6bf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Optimal p-value weighting with independent information' - description: 'This package perform weighted-pvalue based multiple hypothesis test and provides corresponding information such as ranking probability, weight, significant tests, etc . To conduct this testing procedure, the testing method apply a probabilistic relationship between the test rank and the corresponding test effect size.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-orderedlist/meta.yaml b/recipes/bioconductor-orderedlist/meta.yaml index 6be59704a0e91..657237fdeb9a0 100644 --- a/recipes/bioconductor-orderedlist/meta.yaml +++ b/recipes/bioconductor-orderedlist/meta.yaml @@ -1,42 +1,22 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "OrderedList" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Detection of similarities between ordered lists of genes. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Similarities of Ordered Gene Lists -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d8239906b10a2630dc25ab749903a511 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-orderedlist", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-twilight >=1.78.0,<1.79.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-twilight >=1.78.0,<1.79.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Similarities of Ordered Gene Lists' - description: 'Detection of similarities between ordered lists of genes. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:orderedlist @@ -46,3 +26,29 @@ extra: path: recipes/bioconductor-orderedlist version: 1.52.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-twilight >=1.82.0,<1.83.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-twilight >=1.82.0,<1.83.0 + - r-base + +source: + md5: a2d2376888bc05bad547774c9777729b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-orfhunter/build_failure.osx-64.yaml b/recipes/bioconductor-orfhunter/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..7a048660af3b0 --- /dev/null +++ b/recipes/bioconductor-orfhunter/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: d979282dd93dc880f2618966284a7679c0e3c32de29a44ef75befde8e89ef83e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("3.3.1*"), MatchSpec("bioconductor-bsgenome==1.40.1=r3.3.1_0")} + Encountered problems while solving: + - nothing provides r 3.3.1* needed by bioconductor-bsgenome-1.40.1-r3.3.1_0 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0 is not installable because there are no viable options + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.1 would require + bioconductor-bsgenome >=1.35.16 with the potential options + bioconductor-bsgenome 1.74.0 would require + r-base >=4.4,<4.5.0a0 , which can be installed; + bioconductor-bsgenome [1.38.0|1.42.0|1.44.2|1.46.0] conflicts with any installable versions previously reported; + bioconductor-bsgenome [1.40.1|1.42.0] would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-bsgenome 1.48.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.50.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.52.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.54.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.56.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.58.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.60.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.62.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.66.1 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.66.3 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.68.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.70.1 conflicts with any installable versions previously reported; + r-base 3.3.2* , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.1 would require + bioconductor-bsgenome >=1.35.16 with the potential options + bioconductor-bsgenome 1.74.0, which can be installed (as previously explained); + bioconductor-bsgenome [1.38.0|1.42.0|1.44.2|1.46.0] conflicts with any installable versions previously reported; + bioconductor-bsgenome [1.40.1|1.42.0], which cannot be installed (as previously explained); + bioconductor-bsgenome 1.48.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.50.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.52.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.54.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.56.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.58.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.60.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.62.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.66.1 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.66.3 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.68.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.70.1 conflicts with any installable versions previously reported; + r-base 3.4.1* , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.1 would require + bioconductor-bsgenome >=1.48.0,<1.50.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.1 would require + bioconductor-bsgenome >=1.50.0,<1.51.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.1 would require + bioconductor-bsgenome >=1.52.0,<1.53.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.1 would require + bioconductor-bsgenome >=1.54.0,<1.55.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.3 would require + bioconductor-bsgenome >=1.56.0,<1.57.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.3 would require + bioconductor-bsgenome >=1.58.0,<1.59.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.3 would require + bioconductor-bsgenome >=1.60.0,<1.61.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.4 would require + bioconductor-bsgenome >=1.62.0,<1.63.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.4 would require + bioconductor-bsgenome >=1.66.0,<1.67.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.5 would require + bioconductor-bsgenome >=1.66.2,<1.67.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.5 would require + bioconductor-bsgenome >=1.68.0,<1.69.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.5 would require + bioconductor-bsgenome >=1.70.0,<1.71.0 , which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-orfhunter/meta.yaml b/recipes/bioconductor-orfhunter/meta.yaml index 239909d4356a3..1a733dddba3b8 100644 --- a/recipes/bioconductor-orfhunter/meta.yaml +++ b/recipes/bioconductor-orfhunter/meta.yaml @@ -1,59 +1,64 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "ORFhunteR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF) in a large set of RNA molecules. It efficiently implements the machine learning model based on vectorization of nucleotide sequences and the random forest classification algorithm. The ORFhunteR package consists of a set of functions written in the R language in conjunction with C++. The efficiency of the package was confirmed by the examples of the analysis of RNA molecules from the NCBI RefSeq and Ensembl databases. The package can be used in basic and applied biomedical research related to the study of the transcriptome of normal as well as altered (for example, cancer) human cells. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT License + summary: Predict open reading frames in nucleotide sequences -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c9e57a998b0746df96e6d173d75fd032 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-orfhunter", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, rmarkdown requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-data.table - r-peptides - r-randomforest - - 'r-rcpp >=1.0.3' + - r-rcpp >=1.0.3 - r-stringr - r-xfun - libblas - liblapack run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-data.table - r-peptides - r-randomforest - - 'r-rcpp >=1.0.3' + - r-rcpp >=1.0.3 - r-stringr - r-xfun - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: df49de36ebe05483dddc8d59f998f190 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT License' - summary: 'Predict open reading frames in nucleotide sequences' - description: 'The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF) in a large set of RNA molecules. It efficiently implements the machine learning model based on vectorization of nucleotide sequences and the random forest classification algorithm. The ORFhunteR package consists of a set of functions written in the R language in conjunction with C++. The efficiency of the package was confirmed by the examples of the analysis of RNA molecules from the NCBI RefSeq and Ensembl databases. The package can be used in basic and applied biomedical research related to the study of the transcriptome of normal as well as altered (for example, cancer) human cells.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-orfik/meta.yaml b/recipes/bioconductor-orfik/meta.yaml index 3a5075e7dd6ce..eb09c202110e7 100644 --- a/recipes/bioconductor-orfik/meta.yaml +++ b/recipes/bioconductor-orfik/meta.yaml @@ -1,106 +1,112 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "ORFik" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: R package for analysis of transcript and translation features through manipulation of sequence data and NGS data like Ribo-Seq, RNA-Seq, TCP-Seq and CAGE. It is generalized in the sense that any transcript region can be analysed, as the name hints to it was made with investigation of ribosomal patterns over Open Reading Frames (ORFs) as it's primary use case. ORFik is extremely fast through use of C++, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CAGE-Seq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for whole genomes and much more. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Open Reading Frames in Genomics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80a8144faafb88fcd9745dcfce492512 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-orfik", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, rmarkdown, knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19 requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - - r-biomartr - - 'r-cowplot >=1.0.0' - - r-curl - - 'r-data.table >=1.11.8' - - r-downloader - - 'r-fst >=0.9.2' - - 'r-ggplot2 >=2.2.1' - - 'r-gridextra >=2.3' - - 'r-httr >=1.3.0' + - r-biomartr >=1.0.7 + - r-cowplot >=1.0.0 + - r-data.table >=1.11.8 + - r-fst >=0.9.2 + - r-ggplot2 >=2.2.1 + - r-gridextra >=2.3 + - r-httr >=1.3.0 - r-jsonlite - r-r.utils - - 'r-rcpp >=1.0.0' - - r-rcurl + - r-rcpp >=1.0.0 - r-withr - r-xml - - 'r-xml2 >=1.2.0' + - r-xml2 >=1.2.0 - libblas - liblapack + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - - r-biomartr - - 'r-cowplot >=1.0.0' - - r-curl - - 'r-data.table >=1.11.8' - - r-downloader - - 'r-fst >=0.9.2' - - 'r-ggplot2 >=2.2.1' - - 'r-gridextra >=2.3' - - 'r-httr >=1.3.0' + - r-biomartr >=1.0.7 + - r-cowplot >=1.0.0 + - r-data.table >=1.11.8 + - r-fst >=0.9.2 + - r-ggplot2 >=2.2.1 + - r-gridextra >=2.3 + - r-httr >=1.3.0 - r-jsonlite - r-r.utils - - 'r-rcpp >=1.0.0' - - r-rcurl + - r-rcpp >=1.0.0 - r-withr - r-xml - - 'r-xml2 >=1.2.0' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-xml2 >=1.2.0 + +source: + md5: 94095b7968555d15eebcb011c9d9ed0b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Open Reading Frames in Genomics' - description: 'R package for analysis of transcript and translation features through manipulation of sequence data and NGS data like Ribo-Seq, RNA-Seq, TCP-Seq and CAGE. It is generalized in the sense that any transcript region can be analysed, as the name hints to it was made with investigation of ribosomal patterns over Open Reading Frames (ORFs) as it''s primary use case. ORFik is extremely fast through use of C++, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CAGE-Seq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for whole genomes and much more.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.ag.eg.db/meta.yaml b/recipes/bioconductor-org.ag.eg.db/meta.yaml index 6a62269c6da3b..d40b364dd2325 100644 --- a/recipes/bioconductor-org.ag.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ag.eg.db/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "org.Ag.eg.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a67c309f5472338fd47fe43ff20ce2e5 +about: + description: Genome wide annotation for Anopheles, primarily based on mapping using Entrez Gene identifiers. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome wide annotation for Anopheles build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-org.ag.eg.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b7bba2a1eee2f69084937f03d993d3ba + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome wide annotation for Anopheles' - description: 'Genome wide annotation for Anopheles, primarily based on mapping using Entrez Gene identifiers.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.ag.eg.db/post-link.sh b/recipes/bioconductor-org.ag.eg.db/post-link.sh index 914a57fe474f6..d0608807ec9e6 100644 --- a/recipes/bioconductor-org.ag.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ag.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.ag.eg.db-3.18.0" +installBiocDataPackage.sh "org.ag.eg.db-3.20.0" diff --git a/recipes/bioconductor-org.at.tair.db/meta.yaml b/recipes/bioconductor-org.at.tair.db/meta.yaml index 6ed40899b87cc..a1202044a49c8 100644 --- a/recipes/bioconductor-org.at.tair.db/meta.yaml +++ b/recipes/bioconductor-org.at.tair.db/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "org.At.tair.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d6161b859de99eaeadebc0e03ae9c68 +about: + description: Genome wide annotation for Arabidopsis, primarily based on mapping using TAIR identifiers. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome wide annotation for Arabidopsis build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-org.at.tair.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5f9cfc458b0af5cd4e6a2db04d304f13 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome wide annotation for Arabidopsis' - description: 'Genome wide annotation for Arabidopsis, primarily based on mapping using TAIR identifiers.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.at.tair.db/post-link.sh b/recipes/bioconductor-org.at.tair.db/post-link.sh index 4fbdf92ea3f91..2abee3e44e020 100644 --- a/recipes/bioconductor-org.at.tair.db/post-link.sh +++ b/recipes/bioconductor-org.at.tair.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.at.tair.db-3.18.0" +installBiocDataPackage.sh "org.at.tair.db-3.20.0" diff --git a/recipes/bioconductor-org.bt.eg.db/meta.yaml b/recipes/bioconductor-org.bt.eg.db/meta.yaml index c0fef6c777d07..b04bc858c3d89 100644 --- a/recipes/bioconductor-org.bt.eg.db/meta.yaml +++ b/recipes/bioconductor-org.bt.eg.db/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "org.Bt.eg.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 23fd8017323c86930c50d596204bad54 +about: + description: Genome wide annotation for Bovine, primarily based on mapping using Entrez Gene identifiers. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome wide annotation for Bovine build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-org.bt.eg.db", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-org.bt.eg.db + path: recipes/bioconductor-org.bt.eg.db + version: 3.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9eea3d6ba55f61524a04aafb1be83356 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome wide annotation for Bovine' - description: 'Genome wide annotation for Bovine, primarily based on mapping using Entrez Gene identifiers.' -extra: - parent_recipe: - name: bioconductor-org.bt.eg.db - path: recipes/bioconductor-org.bt.eg.db - version: 3.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.bt.eg.db/post-link.sh b/recipes/bioconductor-org.bt.eg.db/post-link.sh index cd489eb184530..73bba48149ae0 100644 --- a/recipes/bioconductor-org.bt.eg.db/post-link.sh +++ b/recipes/bioconductor-org.bt.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.bt.eg.db-3.18.0" +installBiocDataPackage.sh "org.bt.eg.db-3.20.0" diff --git a/recipes/bioconductor-org.ce.eg.db/meta.yaml b/recipes/bioconductor-org.ce.eg.db/meta.yaml index 495acc87d6521..b3416c333d1bc 100644 --- a/recipes/bioconductor-org.ce.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ce.eg.db/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "org.Ce.eg.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 441a5efb4649a1201b5552b14c1f1cef +about: + description: Genome wide annotation for Worm, primarily based on mapping using Entrez Gene identifiers. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome wide annotation for Worm build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-org.ce.eg.db", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-org.ce.eg.db + path: recipes/bioconductor-org.ce.eg.db + version: 3.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3b3cbc21c9f362b436ba4a80d9824da4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome wide annotation for Worm' - description: 'Genome wide annotation for Worm, primarily based on mapping using Entrez Gene identifiers.' -extra: - parent_recipe: - name: bioconductor-org.ce.eg.db - path: recipes/bioconductor-org.ce.eg.db - version: 3.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.ce.eg.db/post-link.sh b/recipes/bioconductor-org.ce.eg.db/post-link.sh index 2bdc66737e6a1..6f5e4facb4bd0 100644 --- a/recipes/bioconductor-org.ce.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ce.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.ce.eg.db-3.18.0" +installBiocDataPackage.sh "org.ce.eg.db-3.20.0" diff --git a/recipes/bioconductor-org.cf.eg.db/meta.yaml b/recipes/bioconductor-org.cf.eg.db/meta.yaml index 67f62fb8f70c8..e8d7e621f91b3 100644 --- a/recipes/bioconductor-org.cf.eg.db/meta.yaml +++ b/recipes/bioconductor-org.cf.eg.db/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "org.Cf.eg.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 038d08c046a81218a31ff8db0877dd15 +about: + description: Genome wide annotation for Canine, primarily based on mapping using Entrez Gene identifiers. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome wide annotation for Canine build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-org.cf.eg.db", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-org.cf.eg.db + path: recipes/bioconductor-org.cf.eg.db + version: 3.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 85da47fb3b35030884cf5b14940015d8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome wide annotation for Canine' - description: 'Genome wide annotation for Canine, primarily based on mapping using Entrez Gene identifiers.' -extra: - parent_recipe: - name: bioconductor-org.cf.eg.db - path: recipes/bioconductor-org.cf.eg.db - version: 3.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.cf.eg.db/post-link.sh b/recipes/bioconductor-org.cf.eg.db/post-link.sh index 06faa06376c83..ed62a13f676d2 100644 --- a/recipes/bioconductor-org.cf.eg.db/post-link.sh +++ b/recipes/bioconductor-org.cf.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.cf.eg.db-3.18.0" +installBiocDataPackage.sh "org.cf.eg.db-3.20.0" diff --git a/recipes/bioconductor-org.dm.eg.db/meta.yaml b/recipes/bioconductor-org.dm.eg.db/meta.yaml index f5b192c04a705..641715039a4df 100644 --- a/recipes/bioconductor-org.dm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.dm.eg.db/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "org.Dm.eg.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 92577ed3bc5d76b78905169eebfebe7d +about: + description: Genome wide annotation for Fly, primarily based on mapping using Entrez Gene identifiers. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome wide annotation for Fly build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-org.dm.eg.db", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-org.dm.eg.db + path: recipes/bioconductor-org.dm.eg.db + version: 3.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 29d33ed6c67a4562038f549dab8d536e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome wide annotation for Fly' - description: 'Genome wide annotation for Fly, primarily based on mapping using Entrez Gene identifiers.' -extra: - parent_recipe: - name: bioconductor-org.dm.eg.db - path: recipes/bioconductor-org.dm.eg.db - version: 3.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.dm.eg.db/post-link.sh b/recipes/bioconductor-org.dm.eg.db/post-link.sh index d0c3e58bb8bf4..d58aca497f698 100644 --- a/recipes/bioconductor-org.dm.eg.db/post-link.sh +++ b/recipes/bioconductor-org.dm.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.dm.eg.db-3.18.0" +installBiocDataPackage.sh "org.dm.eg.db-3.20.0" diff --git a/recipes/bioconductor-org.dr.eg.db/meta.yaml b/recipes/bioconductor-org.dr.eg.db/meta.yaml index 38cae1002a138..6c0b6cbee9878 100644 --- a/recipes/bioconductor-org.dr.eg.db/meta.yaml +++ b/recipes/bioconductor-org.dr.eg.db/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "org.Dr.eg.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cfea28c45f2f34c675975eacbe861a5f +about: + description: Genome wide annotation for Zebrafish, primarily based on mapping using Entrez Gene identifiers. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome wide annotation for Zebrafish build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-org.dr.eg.db", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-org.dr.eg.db + path: recipes/bioconductor-org.dr.eg.db + version: 3.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e0c8b01442611df62c594b5552bd1a29 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome wide annotation for Zebrafish' - description: 'Genome wide annotation for Zebrafish, primarily based on mapping using Entrez Gene identifiers.' -extra: - parent_recipe: - name: bioconductor-org.dr.eg.db - path: recipes/bioconductor-org.dr.eg.db - version: 3.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.dr.eg.db/post-link.sh b/recipes/bioconductor-org.dr.eg.db/post-link.sh index f65f46693b80e..93b107c4199fa 100644 --- a/recipes/bioconductor-org.dr.eg.db/post-link.sh +++ b/recipes/bioconductor-org.dr.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.dr.eg.db-3.18.0" +installBiocDataPackage.sh "org.dr.eg.db-3.20.0" diff --git a/recipes/bioconductor-org.eck12.eg.db/meta.yaml b/recipes/bioconductor-org.eck12.eg.db/meta.yaml index 496eac6758b52..434c80a19aef5 100644 --- a/recipes/bioconductor-org.eck12.eg.db/meta.yaml +++ b/recipes/bioconductor-org.eck12.eg.db/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "org.EcK12.eg.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 50d3d3ca9efec212eae3a920b00750a3 +about: + description: Genome wide annotation for E coli strain K12, primarily based on mapping using Entrez Gene identifiers. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome wide annotation for E coli strain K12 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-org.eck12.eg.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ee62df51636d67d2b3a29cd758c37251 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome wide annotation for E coli strain K12' - description: 'Genome wide annotation for E coli strain K12, primarily based on mapping using Entrez Gene identifiers.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.eck12.eg.db/post-link.sh b/recipes/bioconductor-org.eck12.eg.db/post-link.sh index ebfed362951d8..8f8adf0192998 100644 --- a/recipes/bioconductor-org.eck12.eg.db/post-link.sh +++ b/recipes/bioconductor-org.eck12.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.eck12.eg.db-3.18.0" +installBiocDataPackage.sh "org.eck12.eg.db-3.20.0" diff --git a/recipes/bioconductor-org.ecsakai.eg.db/meta.yaml b/recipes/bioconductor-org.ecsakai.eg.db/meta.yaml index d251c5b30c35e..7e555f94ea4ea 100644 --- a/recipes/bioconductor-org.ecsakai.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ecsakai.eg.db/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "org.EcSakai.eg.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f26ffa55ce30fc8caa64f826207ac61 +about: + description: Genome wide annotation for E coli strain Sakai, primarily based on mapping using Entrez Gene identifiers. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome wide annotation for E coli strain Sakai build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-org.ecsakai.eg.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 85c37f3ed2ee6a80e54e1020c0895404 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome wide annotation for E coli strain Sakai' - description: 'Genome wide annotation for E coli strain Sakai, primarily based on mapping using Entrez Gene identifiers.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.ecsakai.eg.db/post-link.sh b/recipes/bioconductor-org.ecsakai.eg.db/post-link.sh index 8ec1c9f68fb4b..c63b526d25df7 100644 --- a/recipes/bioconductor-org.ecsakai.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ecsakai.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.ecsakai.eg.db-3.18.0" +installBiocDataPackage.sh "org.ecsakai.eg.db-3.20.0" diff --git a/recipes/bioconductor-org.gg.eg.db/meta.yaml b/recipes/bioconductor-org.gg.eg.db/meta.yaml index 4e11232145408..34b5397fcf82d 100644 --- a/recipes/bioconductor-org.gg.eg.db/meta.yaml +++ b/recipes/bioconductor-org.gg.eg.db/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "org.Gg.eg.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ebcbfb0baeee3332a2a07aeae2402a9 +about: + description: Genome wide annotation for Chicken, primarily based on mapping using Entrez Gene identifiers. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome wide annotation for Chicken build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-org.gg.eg.db", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-org.gg.eg.db + path: recipes/bioconductor-org.gg.eg.db + version: 3.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c9a62fecb11dd4dc0b34392f354ffe5a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome wide annotation for Chicken' - description: 'Genome wide annotation for Chicken, primarily based on mapping using Entrez Gene identifiers.' -extra: - parent_recipe: - name: bioconductor-org.gg.eg.db - path: recipes/bioconductor-org.gg.eg.db - version: 3.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.gg.eg.db/post-link.sh b/recipes/bioconductor-org.gg.eg.db/post-link.sh index 19ca51f5ad61d..82a2ddf1ee956 100644 --- a/recipes/bioconductor-org.gg.eg.db/post-link.sh +++ b/recipes/bioconductor-org.gg.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.gg.eg.db-3.18.0" +installBiocDataPackage.sh "org.gg.eg.db-3.20.0" diff --git a/recipes/bioconductor-org.hs.eg.db/meta.yaml b/recipes/bioconductor-org.hs.eg.db/meta.yaml index 2aaffdc1eb4a7..28fa8808d1537 100644 --- a/recipes/bioconductor-org.hs.eg.db/meta.yaml +++ b/recipes/bioconductor-org.hs.eg.db/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "org.Hs.eg.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e1f74b9d0c541b5678a0d88f6a8ec847 +about: + description: Genome wide annotation for Human, primarily based on mapping using Entrez Gene identifiers. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome wide annotation for Human build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-org.hs.eg.db", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-org.hs.eg.db + path: recipes/bioconductor-org.hs.eg.db + version: 3.11.1 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 191276f1fde82d731babe624c7a9063f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome wide annotation for Human' - description: 'Genome wide annotation for Human, primarily based on mapping using Entrez Gene identifiers.' -extra: - parent_recipe: - name: bioconductor-org.hs.eg.db - path: recipes/bioconductor-org.hs.eg.db - version: 3.11.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.hs.eg.db/post-link.sh b/recipes/bioconductor-org.hs.eg.db/post-link.sh index 88931ccb51392..62f0a0473545e 100644 --- a/recipes/bioconductor-org.hs.eg.db/post-link.sh +++ b/recipes/bioconductor-org.hs.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.hs.eg.db-3.18.0" +installBiocDataPackage.sh "org.hs.eg.db-3.20.0" diff --git a/recipes/bioconductor-org.mm.eg.db/meta.yaml b/recipes/bioconductor-org.mm.eg.db/meta.yaml index 9d5b8774b3b7a..ac45cc70f7774 100644 --- a/recipes/bioconductor-org.mm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.mm.eg.db/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "org.Mm.eg.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bd95e1ff46f764fff51acc60b249fe95 +about: + description: Genome wide annotation for Mouse, primarily based on mapping using Entrez Gene identifiers. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome wide annotation for Mouse build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-org.mm.eg.db", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-org.mm.eg.db + path: recipes/bioconductor-org.mm.eg.db + version: 3.11.1 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 63357791b48f3fc181edd8c772ee6f94 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome wide annotation for Mouse' - description: 'Genome wide annotation for Mouse, primarily based on mapping using Entrez Gene identifiers.' -extra: - parent_recipe: - name: bioconductor-org.mm.eg.db - path: recipes/bioconductor-org.mm.eg.db - version: 3.11.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.mm.eg.db/post-link.sh b/recipes/bioconductor-org.mm.eg.db/post-link.sh index ea3b970a24917..43e11fb01369a 100644 --- a/recipes/bioconductor-org.mm.eg.db/post-link.sh +++ b/recipes/bioconductor-org.mm.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.mm.eg.db-3.18.0" +installBiocDataPackage.sh "org.mm.eg.db-3.20.0" diff --git a/recipes/bioconductor-org.mmu.eg.db/meta.yaml b/recipes/bioconductor-org.mmu.eg.db/meta.yaml index 408a76b274591..5f76ff4cdef93 100644 --- a/recipes/bioconductor-org.mmu.eg.db/meta.yaml +++ b/recipes/bioconductor-org.mmu.eg.db/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "org.Mmu.eg.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45a35940d0d1ab91b2b262a8666afa53 +about: + description: Genome wide annotation for Rhesus, primarily based on mapping using Entrez Gene identifiers. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome wide annotation for Rhesus build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-org.mmu.eg.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7c23ce0a276f52e0c34029b9094da1db + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome wide annotation for Rhesus' - description: 'Genome wide annotation for Rhesus, primarily based on mapping using Entrez Gene identifiers.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.mmu.eg.db/post-link.sh b/recipes/bioconductor-org.mmu.eg.db/post-link.sh index 017b895a9759c..97481ae225e8e 100644 --- a/recipes/bioconductor-org.mmu.eg.db/post-link.sh +++ b/recipes/bioconductor-org.mmu.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.mmu.eg.db-3.18.0" +installBiocDataPackage.sh "org.mmu.eg.db-3.20.0" diff --git a/recipes/bioconductor-org.mxanthus.db/meta.yaml b/recipes/bioconductor-org.mxanthus.db/meta.yaml index 558a2aefd9d12..583015c256f79 100644 --- a/recipes/bioconductor-org.mxanthus.db/meta.yaml +++ b/recipes/bioconductor-org.mxanthus.db/meta.yaml @@ -1,46 +1,51 @@ {% set version = "1.0.27" %} {% set name = "org.Mxanthus.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Genome wide annotation for Myxococcus xanthus DK 1622, primarily based on mapping using Gene identifiers. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome wide annotation for Myxococcus xanthus DK 1622 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e493814c41401de383b4f6e0f3d39619 build: - number: 9 + noarch: generic + number: 10 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-org.mxanthus.db", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: DBI, RUnit, clusterProfiler, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 929fa3dd8c5e1fdbcdbcbcd468845798 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome wide annotation for Myxococcus xanthus DK 1622' - description: 'Genome wide annotation for Myxococcus xanthus DK 1622, primarily based on mapping using Gene identifiers.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.pt.eg.db/meta.yaml b/recipes/bioconductor-org.pt.eg.db/meta.yaml index b98e9dd870761..b8a0463a67905 100644 --- a/recipes/bioconductor-org.pt.eg.db/meta.yaml +++ b/recipes/bioconductor-org.pt.eg.db/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "org.Pt.eg.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d6672365e68ece6415e2736f40bf096c +about: + description: Genome wide annotation for Chimp, primarily based on mapping using Entrez Gene identifiers. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome wide annotation for Chimp build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-org.pt.eg.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3385bff8e6ccc1693fa90b41e2d37826 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome wide annotation for Chimp' - description: 'Genome wide annotation for Chimp, primarily based on mapping using Entrez Gene identifiers.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.pt.eg.db/post-link.sh b/recipes/bioconductor-org.pt.eg.db/post-link.sh index 9bcd0492d2c7f..dbe5e6528a3ad 100644 --- a/recipes/bioconductor-org.pt.eg.db/post-link.sh +++ b/recipes/bioconductor-org.pt.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.pt.eg.db-3.18.0" +installBiocDataPackage.sh "org.pt.eg.db-3.20.0" diff --git a/recipes/bioconductor-org.rn.eg.db/meta.yaml b/recipes/bioconductor-org.rn.eg.db/meta.yaml index aa8ee6cf68f8d..40276f2f22179 100644 --- a/recipes/bioconductor-org.rn.eg.db/meta.yaml +++ b/recipes/bioconductor-org.rn.eg.db/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "org.Rn.eg.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1ff92cec0fc2cbd5b3055d1153526ce3 +about: + description: Genome wide annotation for Rat, primarily based on mapping using Entrez Gene identifiers. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome wide annotation for Rat build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-org.rn.eg.db", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-org.rn.eg.db + path: recipes/bioconductor-org.rn.eg.db + version: 3.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b3c38250a9c848390589cbecd663fc69 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome wide annotation for Rat' - description: 'Genome wide annotation for Rat, primarily based on mapping using Entrez Gene identifiers.' -extra: - parent_recipe: - name: bioconductor-org.rn.eg.db - path: recipes/bioconductor-org.rn.eg.db - version: 3.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.rn.eg.db/post-link.sh b/recipes/bioconductor-org.rn.eg.db/post-link.sh index 58dd4a7343f2b..fa84e6ac2ed38 100644 --- a/recipes/bioconductor-org.rn.eg.db/post-link.sh +++ b/recipes/bioconductor-org.rn.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.rn.eg.db-3.18.0" +installBiocDataPackage.sh "org.rn.eg.db-3.20.0" diff --git a/recipes/bioconductor-org.sc.sgd.db/meta.yaml b/recipes/bioconductor-org.sc.sgd.db/meta.yaml index 278039220b5c7..563e1cc3a2df0 100644 --- a/recipes/bioconductor-org.sc.sgd.db/meta.yaml +++ b/recipes/bioconductor-org.sc.sgd.db/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "org.Sc.sgd.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd83de7109be623e7a294a47ca65f160 +about: + description: Genome wide annotation for Yeast, primarily based on mapping using ORF identifiers from SGD. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome wide annotation for Yeast build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-org.sc.sgd.db", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-org.sc.sgd.db + path: recipes/bioconductor-org.sc.sgd.db + version: 3.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bbd0c3aa1aa0277c0a72d504042f9eea + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome wide annotation for Yeast' - description: 'Genome wide annotation for Yeast, primarily based on mapping using ORF identifiers from SGD.' -extra: - parent_recipe: - name: bioconductor-org.sc.sgd.db - path: recipes/bioconductor-org.sc.sgd.db - version: 3.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.sc.sgd.db/post-link.sh b/recipes/bioconductor-org.sc.sgd.db/post-link.sh index ad3c38e6e585e..93da590777a36 100644 --- a/recipes/bioconductor-org.sc.sgd.db/post-link.sh +++ b/recipes/bioconductor-org.sc.sgd.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.sc.sgd.db-3.18.0" +installBiocDataPackage.sh "org.sc.sgd.db-3.20.0" diff --git a/recipes/bioconductor-org.ss.eg.db/meta.yaml b/recipes/bioconductor-org.ss.eg.db/meta.yaml index 6e7b63562d155..d6e5781063f09 100644 --- a/recipes/bioconductor-org.ss.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ss.eg.db/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "org.Ss.eg.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f9b32c76d23f9195df7a7eb6529f3340 +about: + description: Genome wide annotation for Pig, primarily based on mapping using Entrez Gene identifiers. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome wide annotation for Pig build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-org.ss.eg.db", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-org.ss.eg.db + path: recipes/bioconductor-org.ss.eg.db + version: 3.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bbcc19e949a008100b54f4d336a55be3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome wide annotation for Pig' - description: 'Genome wide annotation for Pig, primarily based on mapping using Entrez Gene identifiers.' -extra: - parent_recipe: - name: bioconductor-org.ss.eg.db - path: recipes/bioconductor-org.ss.eg.db - version: 3.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.ss.eg.db/post-link.sh b/recipes/bioconductor-org.ss.eg.db/post-link.sh index 5696d4ac5b715..b2186306e9813 100644 --- a/recipes/bioconductor-org.ss.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ss.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.ss.eg.db-3.18.0" +installBiocDataPackage.sh "org.ss.eg.db-3.20.0" diff --git a/recipes/bioconductor-org.xl.eg.db/meta.yaml b/recipes/bioconductor-org.xl.eg.db/meta.yaml index 48b5a78fe55b9..c901c0dbe1a2d 100644 --- a/recipes/bioconductor-org.xl.eg.db/meta.yaml +++ b/recipes/bioconductor-org.xl.eg.db/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "org.Xl.eg.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bbea76a4373d8b51048029b83c591aca +about: + description: Genome wide annotation for Xenopus, primarily based on mapping using Entrez Gene identifiers. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Genome wide annotation for Xenopus build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-org.xl.eg.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4fb37259b7169c9b62b605604f3fc0de + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Genome wide annotation for Xenopus' - description: 'Genome wide annotation for Xenopus, primarily based on mapping using Entrez Gene identifiers.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-org.xl.eg.db/post-link.sh b/recipes/bioconductor-org.xl.eg.db/post-link.sh index d079ec990a1cf..95a5cf0ddc411 100644 --- a/recipes/bioconductor-org.xl.eg.db/post-link.sh +++ b/recipes/bioconductor-org.xl.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "org.xl.eg.db-3.18.0" +installBiocDataPackage.sh "org.xl.eg.db-3.20.0" diff --git a/recipes/bioconductor-organism.dplyr/meta.yaml b/recipes/bioconductor-organism.dplyr/meta.yaml index 2ccba681f13c0..862d21e40e830 100644 --- a/recipes/bioconductor-organism.dplyr/meta.yaml +++ b/recipes/bioconductor-organism.dplyr/meta.yaml @@ -1,64 +1,69 @@ -{% set version = "1.30.1" %} +{% set version = "1.34.0" %} {% set name = "Organism.dplyr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides an alternative interface to Bioconductor 'annotation' resources, in particular the gene identifier mapping functionality of the 'org' packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the 'TxDb' packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: dplyr-based Access to Bioconductor Annotation Resources -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b16c25c3ee5abafa1007a9c7bd731801 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-organism.dplyr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, magick, BiocStyle, ggplot2 requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dbi - r-dbplyr - - 'r-dplyr >=0.7.0' + - r-dplyr >=0.7.0 - r-rlang - r-rsqlite - r-tibble run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dbi - r-dbplyr - - 'r-dplyr >=0.7.0' + - r-dplyr >=0.7.0 - r-rlang - r-rsqlite - r-tibble + +source: + md5: 8a1d2e6e78f6224a4b84509b8f660d8b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'dplyr-based Access to Bioconductor Annotation Resources' - description: 'This package provides an alternative interface to Bioconductor ''annotation'' resources, in particular the gene identifier mapping functionality of the ''org'' packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the ''TxDb'' packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-organismdbi/meta.yaml b/recipes/bioconductor-organismdbi/meta.yaml index 3424eb8e53508..c49c429f1c73c 100644 --- a/recipes/bioconductor-organismdbi/meta.yaml +++ b/recipes/bioconductor-organismdbi/meta.yaml @@ -1,66 +1,74 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "OrganismDbi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Software to enable the smooth interfacing of different database packages -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d6c3ba042e4e0b6ecf5fa27fc344a82 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-organismdbi", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:organismdbi + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-organismdbi + path: recipes/bioconductor-organismdbi + version: 1.22.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, mirbase.db, rtracklayer, biomaRt, RUnit, RMariaDB, BiocStyle, knitr requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-biocmanager - r-dbi run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-biocmanager - r-dbi + +source: + md5: b9af4a5f4ce821aa7b62511b9c28f08f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Software to enable the smooth interfacing of different database packages' - description: 'The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.' -extra: - identifiers: - - biotools:organismdbi - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-organismdbi - path: recipes/bioconductor-organismdbi - version: 1.22.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-orthogene/meta.yaml b/recipes/bioconductor-orthogene/meta.yaml index 5fb52c90803da..c8c43bbafd899 100644 --- a/recipes/bioconductor-orthogene/meta.yaml +++ b/recipes/bioconductor-orthogene/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "orthogene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: '`orthogene` is an R package for easy mapping of orthologous genes across hundreds of species. It pulls up-to-date gene ortholog mappings across **700+ organisms**. It also provides various utility functions to aggregate/expand common objects (e.g. data.frames, gene expression matrices, lists) using **1:1**, **many:1**, **1:many** or **many:many** gene mappings, both within- and between-species.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Interspecies gene mapping -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f3597fa7ce02e2e32ee6cebb20f67c08 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-orthogene", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rworkflows, remotes, knitr, BiocStyle, markdown, rmarkdown, testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape, phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB requirements: host: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 - r-babelgene - r-base - r-data.table @@ -38,8 +40,8 @@ requirements: - r-patchwork - r-repmis run: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 - r-babelgene - r-base - r-data.table @@ -53,13 +55,16 @@ requirements: - r-matrix - r-patchwork - r-repmis + +source: + md5: bab026b422920faf5d5263fa2dfa3c51 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Interspecies gene mapping' - description: '`orthogene` is an R package for easy mapping of orthologous genes across hundreds of species. It pulls up-to-date gene ortholog mappings across **700+ organisms**. It also provides various utility functions to aggregate/expand common objects (e.g. data.frames, gene expression matrices, lists) using **1:1**, **many:1**, **1:many** or **many:many** gene mappings, both within- and between-species.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-orthology.eg.db/meta.yaml b/recipes/bioconductor-orthology.eg.db/meta.yaml index b4bceecfb8d50..c7f46ea40e5b1 100644 --- a/recipes/bioconductor-orthology.eg.db/meta.yaml +++ b/recipes/bioconductor-orthology.eg.db/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "Orthology.eg.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1e53a6a144a5074544cbe166ad241012 +about: + description: Orthology mapping package, based on data from NCBI, using NCBI Gene IDs and Taxonomy IDs. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Orthology mapping package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-orthology.eg.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 09c5048fda8f1df91892305c09f38227 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Orthology mapping package' - description: 'Orthology mapping package, based on data from NCBI, using NCBI Gene IDs and Taxonomy IDs.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-orthology.eg.db/post-link.sh b/recipes/bioconductor-orthology.eg.db/post-link.sh index 62dc891778772..11d4a3b145bd1 100644 --- a/recipes/bioconductor-orthology.eg.db/post-link.sh +++ b/recipes/bioconductor-orthology.eg.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "orthology.eg.db-3.18.0" +installBiocDataPackage.sh "orthology.eg.db-3.20.0" diff --git a/recipes/bioconductor-orthos/meta.yaml b/recipes/bioconductor-orthos/meta.yaml index 638a68a53caf2..d9a2a0c91288d 100644 --- a/recipes/bioconductor-orthos/meta.yaml +++ b/recipes/bioconductor-orthos/meta.yaml @@ -1,36 +1,39 @@ -{% set version = "1.0.1" %} +{% set version = "1.4.0" %} {% set name = "orthos" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: '`orthos` decomposes RNA-seq contrasts, for example obtained from a gene knock-out or compound treatment experiment, into unspecific and experiment-specific components. Original and decomposed contrasts can be efficiently queried against a large database of contrasts (derived from ARCHS4, https://maayanlab.cloud/archs4/) to identify similar experiments. `orthos` furthermore provides plotting functions to visualize the results of such a search for similar contrasts.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: '`orthos` is an R package for variance decomposition using conditional variational auto-encoders' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c35d515c0e956e4207b00db662192707 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-orthos", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocManager, BiocStyle, htmltools, knitr, rmarkdown, testthat (>= 3.0.0) requirements: + host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-orthosdata >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-orthosdata >=1.4.0,<1.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-colorspace - r-cowplot @@ -45,16 +48,17 @@ requirements: - r-rlang - r-tensorflow - r-tidyr + run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-orthosdata >=1.0.0,<1.1.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-orthosdata >=1.4.0,<1.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-colorspace - r-cowplot @@ -69,13 +73,16 @@ requirements: - r-rlang - r-tensorflow - r-tidyr + +source: + md5: c785f8e2372aaad8f3f9b418d152ddb7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: '`orthos` is an R package for variance decomposition using conditional variational auto-encoders' - description: '`orthos` decomposes RNA-seq contrasts, for example obtained from a gene knock-out or compound treatment experiment, into unspecific and experiment-specific components. Original and decomposed contrasts can be efficiently queried against a large database of contrasts (derived from ARCHS4, https://maayanlab.cloud/archs4/) to identify similar experiments. `orthos` furthermore provides plotting functions to visualize the results of such a search for similar contrasts.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-orthosdata/meta.yaml b/recipes/bioconductor-orthosdata/meta.yaml index 8aca3fc0ed845..90584be1e9078 100644 --- a/recipes/bioconductor-orthosdata/meta.yaml +++ b/recipes/bioconductor-orthosdata/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "orthosData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: '`orthosData` is the companion ExperimentData package to the `orthos` R package for mechanistic studies using differential gene expression experiments. It provides functions for retrieval from ExperimentHub and local caching of the models and datasets used internally in orthos.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Data for the orthos package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7970587455fa5197daf1f6b640b7f688 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-orthosdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, ggplot2, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-stringr run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-stringr - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 31ec483008cbe76b4ad674381133bb91 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Data for the orthos package' - description: '`orthosData` is the companion ExperimentData package to the `orthos` R package for mechanistic studies using differential gene expression experiments. It provides functions for retrieval from ExperimentHub and local caching of the models and datasets used internally in orthos.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-orthosdata/post-link.sh b/recipes/bioconductor-orthosdata/post-link.sh index 5c3cfd2f32ffc..6a336d0d12824 100644 --- a/recipes/bioconductor-orthosdata/post-link.sh +++ b/recipes/bioconductor-orthosdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "orthosdata-1.0.0" +installBiocDataPackage.sh "orthosdata-1.4.0" diff --git a/recipes/bioconductor-osat/meta.yaml b/recipes/bioconductor-osat/meta.yaml index 8b31b07c069f0..48a6965d9113a 100644 --- a/recipes/bioconductor-osat/meta.yaml +++ b/recipes/bioconductor-osat/meta.yaml @@ -1,38 +1,19 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "OSAT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 64bba183cfa8a211960d891cb5ee3ddb +about: + description: A sizable genomics study such as microarray often involves the use of multiple batches (groups) of experiment due to practical complication. To minimize batch effects, a careful experiment design should ensure the even distribution of biological groups and confounding factors across batches. OSAT (Optimal Sample Assignment Tool) is developed to facilitate the allocation of collected samples to different batches. With minimum steps, it produces setup that optimizes the even distribution of samples in groups of biological interest into different batches, reducing the confounding or correlation between batches and the biological variables of interest. It can also optimize the even distribution of confounding factors across batches. Our tool can handle challenging instances where incomplete and unbalanced sample collections are involved as well as ideal balanced RCBD. OSAT provides a number of predefined layout for some of the most commonly used genomics platform. Related paper can be find at http://www.biomedcentral.com/1471-2164/13/689 . + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'OSAT: Optimal Sample Assignment Tool' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-osat", max_pin="x.x") }}' - noarch: generic -# Suggests: xtable, Biobase -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'OSAT: Optimal Sample Assignment Tool' - description: 'A sizable genomics study such as microarray often involves the use of multiple batches (groups) of experiment due to practical complication. To minimize batch effects, a careful experiment design should ensure the even distribution of biological groups and confounding factors across batches. OSAT (Optimal Sample Assignment Tool) is developed to facilitate the allocation of collected samples to different batches. With minimum steps, it produces setup that optimizes the even distribution of samples in groups of biological interest into different batches, reducing the confounding or correlation between batches and the biological variables of interest. It can also optimize the even distribution of confounding factors across batches. Our tool can handle challenging instances where incomplete and unbalanced sample collections are involved as well as ideal balanced RCBD. OSAT provides a number of predefined layout for some of the most commonly used genomics platform. Related paper can be find at http://www.biomedcentral.com/1471-2164/13/689 .' extra: identifiers: - biotools:osat @@ -41,4 +22,23 @@ extra: name: bioconductor-osat path: recipes/bioconductor-osat version: 1.28.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: xtable, Biobase +requirements: + host: + - r-base + run: + - r-base +source: + md5: a074e20f248c79235e4780281c50e59c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-oscope/meta.yaml b/recipes/bioconductor-oscope/meta.yaml index d854e94085c0f..69b150de6274e 100644 --- a/recipes/bioconductor-oscope/meta.yaml +++ b/recipes/bioconductor-oscope/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "Oscope" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Oscope is a statistical pipeline developed to identifying and recovering the base cycle profiles of oscillating genes in an unsynchronized single cell RNA-seq experiment. The Oscope pipeline includes three modules: a sine model module to search for candidate oscillator pairs; a K-medoids clustering module to cluster candidate oscillators into groups; and an extended nearest insertion module to recover the base cycle order for each oscillator group.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96a8fc6730b6d493d352d74032c4b3d3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-oscope", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:oscope + - doi:10.1038/nmeth.3549 + parent_recipe: + name: bioconductor-oscope + path: recipes/bioconductor-oscope + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-ebseq >=2.0.0,<2.1.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-ebseq >=2.4.0,<2.5.0 - r-base - r-cluster - r-testthat run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-ebseq >=2.0.0,<2.1.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-ebseq >=2.4.0,<2.5.0 - r-base - r-cluster - r-testthat + +source: + md5: ee7801c0823b7ee339d43affc78c4244 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq' - description: 'Oscope is a statistical pipeline developed to identifying and recovering the base cycle profiles of oscillating genes in an unsynchronized single cell RNA-seq experiment. The Oscope pipeline includes three modules: a sine model module to search for candidate oscillator pairs; a K-medoids clustering module to cluster candidate oscillators into groups; and an extended nearest insertion module to recover the base cycle order for each oscillator group.' -extra: - identifiers: - - biotools:oscope - - doi:10.1038/nmeth.3549 - parent_recipe: - name: bioconductor-oscope - path: recipes/bioconductor-oscope - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-otubase/meta.yaml b/recipes/bioconductor-otubase/meta.yaml index b6a36eb811848..0b4626ecb140f 100644 --- a/recipes/bioconductor-otubase/meta.yaml +++ b/recipes/bioconductor-otubase/meta.yaml @@ -1,54 +1,61 @@ -{% set version = "1.52.0" %} +{% set version = "1.56.0" %} {% set name = "OTUbase" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides a platform for Operational Taxonomic Unit based analysis + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Provides structure and functions for the analysis of OTU data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 612c0f07995eb5cc0f753eb6750e5216 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-otubase", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:otubase + - doi:10.1093/bioinformatics/btr196 + parent_recipe: + name: bioconductor-otubase + path: recipes/bioconductor-otubase + version: 1.30.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-vegan run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-vegan + +source: + md5: c491f0ebead69ba34f79d6e24674683b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Provides structure and functions for the analysis of OTU data' - description: 'Provides a platform for Operational Taxonomic Unit based analysis' -extra: - identifiers: - - biotools:otubase - - doi:10.1093/bioinformatics/btr196 - parent_recipe: - name: bioconductor-otubase - path: recipes/bioconductor-otubase - version: 1.30.0 + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-outrider/meta.yaml b/recipes/bioconductor-outrider/meta.yaml index 84fc0e04082f1..ef8d1a184aa76 100644 --- a/recipes/bioconductor-outrider/meta.yaml +++ b/recipes/bioconductor-outrider/meta.yaml @@ -1,36 +1,50 @@ -{% set version = "1.20.1" %} +{% set version = "1.24.0" %} {% set name = "OUTRIDER" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Identification of aberrant gene expression in RNA-seq data. Read count expectations are modeled by an autoencoder to control for confounders in the data. Given these expectations, the RNA-seq read counts are assumed to follow a negative binomial distribution with a gene-specific dispersion. Outliers are then identified as read counts that significantly deviate from this distribution. Furthermore, OUTRIDER provides useful plotting functions to analyze and visualize the results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: OUTRIDER - OUTlier in RNA-Seq fInDER -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://github.com/gagneurlab/{{ name }}/archive/refs/tags/{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6406872685b1e9b329c55d07fc82237b build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-outrider", max_pin="x.x") }}' -# Suggests: testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr + +extra: + parent_recipe: + name: bioconductor-outrider + path: recipes/bioconductor-outrider + version: 1.1.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr, GenomeInfoDb, ggbio, biovizBase requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-bbmisc - r-data.table @@ -50,16 +64,18 @@ requirements: - r-scales - libblas - liblapack + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-bbmisc - r-data.table @@ -77,22 +93,16 @@ requirements: - r-rcpparmadillo - r-reshape2 - r-scales - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: ecb42761f893c9a73a6a0195fa4ff84f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'OUTRIDER - OUTlier in RNA-Seq fInDER' - description: 'Identification of aberrant gene expression in RNA-seq data. Read count expectations are modeled by an autoencoder to control for confounders in the data. Given these expectations, the RNA-seq read counts are assumed to follow a negative binomial distribution with a gene-specific dispersion. Outliers are then identified as read counts that significantly deviate from this distribution. Furthermore, OUTRIDER provides useful plotting functions to analyze and visualize the results.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-outrider - path: recipes/bioconductor-outrider - version: 1.1.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-outsplice/meta.yaml b/recipes/bioconductor-outsplice/meta.yaml index 88b5efe5ba59d..c92ef8e3d244f 100644 --- a/recipes/bioconductor-outsplice/meta.yaml +++ b/recipes/bioconductor-outsplice/meta.yaml @@ -1,55 +1,58 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "OutSplice" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An easy to use tool that can compare splicing events in tumor and normal tissue samples using either a user generated matrix, or data from The Cancer Genome Atlas (TCGA). This package generates a matrix of splicing outliers that are significantly over or underexpressed in tumors samples compared to normal denoted by chromosome location. The package also will calculate the splicing burden in each tumor and characterize the types of splicing events that occur. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Comparison of Splicing Events between Tumor and Normal Samples -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7a55735983a79681a2bbcd567c9f0c53 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-outsplice", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-repitools >=1.48.0,<1.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-repitools >=1.48.0,<1.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 - r-base + +source: + md5: 6a74e00206c137f0e08703cc06a114fc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Comparison of Splicing Events between Tumor and Normal Samples' - description: 'An easy to use tool that can compare splicing events in tumor and normal tissue samples using either a user generated matrix, or data from The Cancer Genome Atlas (TCGA). This package generates a matrix of splicing outliers that are significantly over or underexpressed in tumors samples compared to normal denoted by chromosome location. The package also will calculate the splicing burden in each tumor and characterize the types of splicing events that occur.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-oveseg/meta.yaml b/recipes/bioconductor-oveseg/meta.yaml index 9f062d2d0697a..c0d3cd1f5f44a 100644 --- a/recipes/bioconductor-oveseg/meta.yaml +++ b/recipes/bioconductor-oveseg/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "OVESEG" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An R package for multiple-group comparison to detect tissue/cell-specific marker genes among subtypes. It provides functions to compute OVESEG-test statistics, derive component weights in the mixture null distribution model and estimate p-values from weightedly aggregated permutations. Obtained posterior probabilities of component null hypotheses can also portrait all kinds of upregulation patterns among subtypes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: OVESEG-test to detect tissue/cell-specific markers -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2a1ac203dcd19e6c511d4bcefa0cee45 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-oveseg", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-fdrtool - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-fdrtool - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: b22162ecd69e07b60941994010ca08d0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'OVESEG-test to detect tissue/cell-specific markers' - description: 'An R package for multiple-group comparison to detect tissue/cell-specific marker genes among subtypes. It provides functions to compute OVESEG-test statistics, derive component weights in the mixture null distribution model and estimate p-values from weightedly aggregated permutations. Obtained posterior probabilities of component null hypotheses can also portrait all kinds of upregulation patterns among subtypes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-paa/meta.yaml b/recipes/bioconductor-paa/meta.yaml index e433b71cba99c..1ed27aedefa6f 100644 --- a/recipes/bioconductor-paa/meta.yaml +++ b/recipes/bioconductor-paa/meta.yaml @@ -1,29 +1,35 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "PAA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: PAA imports single color (protein) microarray data that has been saved in gpr file format - esp. ProtoArray data. After preprocessing (background correction, batch filtering, normalization) univariate feature preselection is performed (e.g., using the "minimum M statistic" approach - hereinafter referred to as "mMs"). Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. Therefore, either a frequency-based backwards elimination aproach or ensemble feature selection can be used. PAA provides a complete toolbox of analysis tools including several different plots for results examination and evaluation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_3_clause + file LICENSE + license_file: LICENSE + summary: PAA (Protein Array Analyzer) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4968ea3bfbaa5edd0e6d00dcbe93a6d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-paa", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, RUnit, BiocGenerics, vsn # SystemRequirements: C++ software package Random Jungle requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-e1071 - r-gplots @@ -31,13 +37,13 @@ requirements: - r-mass - r-mrmre - r-randomforest - - 'r-rcpp >=0.11.6' + - r-rcpp >=0.11.6 - r-rocr - libblas - liblapack run: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-e1071 - r-gplots @@ -45,19 +51,18 @@ requirements: - r-mass - r-mrmre - r-randomforest - - 'r-rcpp >=0.11.6' + - r-rcpp >=0.11.6 - r-rocr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 730153dfb6e7a37f522a59102b5a9f45 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_3_clause + file LICENSE' - summary: 'PAA (Protein Array Analyzer)' - description: 'PAA imports single color (protein) microarray data that has been saved in gpr file format - esp. ProtoArray data. After preprocessing (background correction, batch filtering, normalization) univariate feature preselection is performed (e.g., using the "minimum M statistic" approach - hereinafter referred to as "mMs"). Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. Therefore, either a frequency-based backwards elimination aproach or ensemble feature selection can be used. PAA provides a complete toolbox of analysis tools including several different plots for results examination and evaluation.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-packfinder/meta.yaml b/recipes/bioconductor-packfinder/meta.yaml index f973e5d16efa5..79bf93069466f 100644 --- a/recipes/bioconductor-packfinder/meta.yaml +++ b/recipes/bioconductor-packfinder/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "packFinder" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Algorithm and tools for in silico pack-TYPE transposon discovery. Filters a given genome for properties unique to DNA transposons and provides tools for the investigation of returned matches. Sequences are input in DNAString format, and ranges are returned as a dataframe (in the format returned by as.dataframe(GRanges)). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: de novo Annotation of Pack-TYPE Transposable Elements -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8c2f41158644b4d04136910e0ce39af8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-packfinder", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: biomartr, knitr, rmarkdown, testthat, dendextend, biocViews, BiocCheck, BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-ape - r-base - r-kmer run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-ape - r-base - r-kmer + +source: + md5: e15388b9f159eaf6ca8e36bd95474ce5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'de novo Annotation of Pack-TYPE Transposable Elements' - description: 'Algorithm and tools for in silico pack-TYPE transposon discovery. Filters a given genome for properties unique to DNA transposons and provides tools for the investigation of returned matches. Sequences are input in DNAString format, and ranges are returned as a dataframe (in the format returned by as.dataframe(GRanges)).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-padma/meta.yaml b/recipes/bioconductor-padma/meta.yaml index b61afc3f54526..b67da8edb0785 100644 --- a/recipes/bioconductor-padma/meta.yaml +++ b/recipes/bioconductor-padma/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "padma" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 126a8aec3057f8ccc5a435c5435adfc0 +about: + description: Use multiple factor analysis to calculate individualized pathway-centric scores of deviation with respect to the sampled population based on multi-omic assays (e.g., RNA-seq, copy number alterations, methylation, etc). Graphical and numerical outputs are provided to identify highly aberrant individuals for a particular pathway of interest, as well as the gene and omics drivers of aberrant multi-omic profiles. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-padma", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, BiocStyle, knitr, rmarkdown, KEGGREST, missMDA, ggplot2, ggrepel, car, cowplot +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: testthat, BiocStyle, knitr, rmarkdown, KEGGREST, missMDA, ggplot2, ggrepel, car, cowplot, reshape2 requirements: host: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-factominer run: - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-factominer +source: + md5: 75e80f0887d9aa13f4c9ce5c76b034f0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=3)' - summary: 'Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis' - description: 'Use multiple factor analysis to calculate individualized pathway-centric scores of deviation with respect to the sampled population based on multi-omic assays (e.g., RNA-seq, copy number alterations, methylation, etc). Graphical and numerical outputs are provided to identify highly aberrant individuals for a particular pathway of interest, as well as the gene and omics drivers of aberrant multi-omic profiles.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-padog/meta.yaml b/recipes/bioconductor-padog/meta.yaml index a248a46b7416c..bbfd4e6f44ae9 100644 --- a/recipes/bioconductor-padog/meta.yaml +++ b/recipes/bioconductor-padog/meta.yaml @@ -1,67 +1,73 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "PADOG" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements a general purpose gene set analysis method called PADOG that downplays the importance of genes that apear often accross the sets of genes to be analyzed. The package provides also a benchmark for gene set analysis methods in terms of sensitivity and ranking using 24 public datasets from KEGGdzPathwaysGEO package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Pathway Analysis with Down-weighting of Overlapping Genes (PADOG) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ca2c1e477f0ef2d2be1eaf52570dd8c4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-padog", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:padog + - doi:10.1186/1471-2105-13-136 + parent_recipe: + name: bioconductor-padog + path: recipes/bioconductor-padog + version: 1.22.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: doParallel, parallel requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-keggdzpathwaysgeo >=1.40.0,<1.41.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-hgu133a.db >=3.13.0,<3.14.0 + - bioconductor-hgu133plus2.db >=3.13.0,<3.14.0 + - bioconductor-keggdzpathwaysgeo >=1.44.0,<1.45.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-dorng - r-foreach - r-gsa - r-nlme run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - - 'bioconductor-hgu133plus2.db >=3.13.0,<3.14.0' - - 'bioconductor-keggdzpathwaysgeo >=1.40.0,<1.41.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-hgu133a.db >=3.13.0,<3.14.0 + - bioconductor-hgu133plus2.db >=3.13.0,<3.14.0 + - bioconductor-keggdzpathwaysgeo >=1.44.0,<1.45.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-dorng - r-foreach - r-gsa - r-nlme + +source: + md5: 9ef04a05c70159caaa3f1c37db9fb786 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)' - description: 'This package implements a general purpose gene set analysis method called PADOG that downplays the importance of genes that apear often accross the sets of genes to be analyzed. The package provides also a benchmark for gene set analysis methods in terms of sensitivity and ranking using 24 public datasets from KEGGdzPathwaysGEO package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:padog - - doi:10.1186/1471-2105-13-136 - parent_recipe: - name: bioconductor-padog - path: recipes/bioconductor-padog - version: 1.22.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-paeg1acdf/meta.yaml b/recipes/bioconductor-paeg1acdf/meta.yaml index 83f68341ac443..79b13a02100cb 100644 --- a/recipes/bioconductor-paeg1acdf/meta.yaml +++ b/recipes/bioconductor-paeg1acdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "paeg1acdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 73af974112051db0f715518393e84726 +about: + description: A package containing an environment representing the Pae_G1a.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: paeg1acdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-paeg1acdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 73af974112051db0f715518393e84726 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: paeg1acdf - description: 'A package containing an environment representing the Pae_G1a.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-paeg1aprobe/meta.yaml b/recipes/bioconductor-paeg1aprobe/meta.yaml index 52fa2ca8579b2..2dc6055093c7f 100644 --- a/recipes/bioconductor-paeg1aprobe/meta.yaml +++ b/recipes/bioconductor-paeg1aprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "paeg1aprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 493fa1fc7b92a78c8114b65038113c42 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was P\_aeg1a\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type paeg1a build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-paeg1aprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 493fa1fc7b92a78c8114b65038113c42 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type paeg1a' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was P\_aeg1a\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pagerank/meta.yaml b/recipes/bioconductor-pagerank/meta.yaml index fadcf0f1bd68e..25b17167e1142 100644 --- a/recipes/bioconductor-pagerank/meta.yaml +++ b/recipes/bioconductor-pagerank/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "pageRank" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 05578860ad3f7021d25c6c07953218ea +about: + description: Implemented temporal PageRank analysis as defined by Rozenshtein and Gionis. Implemented multiplex PageRank as defined by Halu et al. Applied temporal and multiplex PageRank in gene regulatory network analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Temporal and Multiplex PageRank for Gene Regulatory Network Analysis build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pagerank", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: bcellViper, BSgenome.Hsapiens.UCSC.hg19, JASPAR2018, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, TFBSTools, GenomicFeatures, annotate requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-motifmatchr >=1.28.0,<1.29.0 - r-base - r-igraph run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-motifmatchr >=1.28.0,<1.29.0 - r-base - r-igraph +source: + md5: fc6281ec2506531166320bac8deaf9f4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Temporal and Multiplex PageRank for Gene Regulatory Network Analysis' - description: 'Implemented temporal PageRank analysis as defined by Rozenshtein and Gionis. Implemented multiplex PageRank as defined by Halu et al. Applied temporal and multiplex PageRank in gene regulatory network analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pairadise/meta.yaml b/recipes/bioconductor-pairadise/meta.yaml index da305a20a0c68..e2906cad7f03e 100644 --- a/recipes/bioconductor-pairadise/meta.yaml +++ b/recipes/bioconductor-pairadise/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "PAIRADISE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements the PAIRADISE procedure for detecting differential isoform expression between matched replicates in paired RNA-Seq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 'PAIRADISE: Paired analysis of differential isoform expression' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2a3889d2380363b7a9b0ee3c75ef0891 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pairadise", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-abind - r-base - r-nloptr run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-abind - r-base - r-nloptr + +source: + md5: 618c12ea22bbeb79dc178a7abc5d7f46 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'PAIRADISE: Paired analysis of differential isoform expression' - description: 'This package implements the PAIRADISE procedure for detecting differential isoform expression between matched replicates in paired RNA-Seq data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-paircompviz/meta.yaml b/recipes/bioconductor-paircompviz/meta.yaml index 1a78dfad94d52..9de87a0494cc3 100644 --- a/recipes/bioconductor-paircompviz/meta.yaml +++ b/recipes/bioconductor-paircompviz/meta.yaml @@ -1,41 +1,22 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "paircompviz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides visualization of the results from the multiple (i.e. pairwise) comparison tests such as pairwise.t.test, pairwise.prop.test or pairwise.wilcox.test. The groups being compared are visualized as nodes in Hasse diagram. Such approach enables very clear and vivid depiction of which group is significantly greater than which others, especially if comparing a large number of groups. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=3.0) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Multiple comparison test visualization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e9c57c7305e15062d9258019fed12f3e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-paircompviz", max_pin="x.x") }}' - noarch: generic -# Suggests: multcomp, reshape, rpart, plyr, xtable -requirements: - host: - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - r-base - run: - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=3.0)' - summary: 'Multiple comparison test visualization' - description: 'This package provides visualization of the results from the multiple (i.e. pairwise) comparison tests such as pairwise.t.test, pairwise.prop.test or pairwise.wilcox.test. The groups being compared are visualized as nodes in Hasse diagram. Such approach enables very clear and vivid depiction of which group is significantly greater than which others, especially if comparing a large number of groups.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:paircompviz @@ -45,3 +26,28 @@ extra: path: recipes/bioconductor-paircompviz version: 1.18.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: multcomp, reshape, rpart, plyr, xtable +requirements: + host: + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - r-base + run: + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - r-base + +source: + md5: 658cb578043ab33e3a9174aac376f469 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-pairedgsea/meta.yaml b/recipes/bioconductor-pairedgsea/meta.yaml index f5f6ebb5140ba..4c61d4ea9b834 100644 --- a/recipes/bioconductor-pairedgsea/meta.yaml +++ b/recipes/bioconductor-pairedgsea/meta.yaml @@ -1,57 +1,62 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "pairedGSEA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: pairedGSEA makes it simple to run a paired Differential Gene Expression (DGE) and Differencital Gene Splicing (DGS) analysis. The package allows you to store intermediate results for further investiation, if desired. pairedGSEA comes with a wrapper function for running an Over-Representation Analysis (ORA) and functionalities for plotting the results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Paired DGE and DGS analysis for gene set enrichment analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 591cbbc31b4eab5064ef39c4b8133fa5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pairedgsea", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: writexl, readxl, readr, rhdf5, msigdbr, plotly, testthat (>= 3.0.0), knitr, rmarkdown, covr, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-dexseq >=1.48.0,<1.49.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-dexseq >=1.52.0,<1.53.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-aggregation - r-base - r-ggplot2 run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-dexseq >=1.48.0,<1.49.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-dexseq >=1.52.0,<1.53.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-aggregation - r-base - r-ggplot2 + +source: + md5: d182fc70ccc15823d971e759d93a8ad9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Paired DGE and DGS analysis for gene set enrichment analysis' - description: 'pairedGSEA makes it simple to run a paired Differential Gene Expression (DGE) and Differencital Gene Splicing (DGS) analysis. The package allows you to store intermediate results for further investiation, if desired. pairedGSEA comes with a wrapper function for running an Over-Representation Analysis (ORA) and functionalities for plotting the results.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pairkat/meta.yaml b/recipes/bioconductor-pairkat/meta.yaml index 88e9611ce00c4..7020d9dc023a7 100644 --- a/recipes/bioconductor-pairkat/meta.yaml +++ b/recipes/bioconductor-pairkat/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "pairkat" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: PaIRKAT is model framework for assessing statistical relationships between networks of metabolites (pathways) and an outcome of interest (phenotype). PaIRKAT queries the KEGG database to determine interactions between metabolites from which network connectivity is constructed. This model framework improves testing power on high dimensional data by including graph topography in the kernel machine regression setting. Studies on high dimensional data can struggle to include the complex relationships between variables. The semi-parametric kernel machine regression model is a powerful tool for capturing these types of relationships. They provide a framework for testing for relationships between outcomes of interest and high dimensional data such as metabolomic, genomic, or proteomic pathways. PaIRKAT uses known biological connections between high dimensional variables by representing them as edges of ‘graphs’ or ‘networks.’ It is common for nodes (e.g. metabolites) to be disconnected from all others within the graph, which leads to meaningful decreases in testing power whether or not the graph information is included. We include a graph regularization or ‘smoothing’ approach for managing this issue. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: PaIRKAT -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 030b0f4ea6e9f71adf6769ca9b16cae0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pairkat", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, BiocStyle, dplyr requirements: host: - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-compquadform - r-data.table @@ -31,21 +33,24 @@ requirements: - r-magrittr - r-tibble run: - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-compquadform - r-data.table - r-igraph - r-magrittr - r-tibble + +source: + md5: 6ab8d367b12423c055cb38d1990187e9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: PaIRKAT - description: 'PaIRKAT is model framework for assessing statistical relationships between networks of metabolites (pathways) and an outcome of interest (phenotype). PaIRKAT queries the KEGG database to determine interactions between metabolites from which network connectivity is constructed. This model framework improves testing power on high dimensional data by including graph topography in the kernel machine regression setting. Studies on high dimensional data can struggle to include the complex relationships between variables. The semi-parametric kernel machine regression model is a powerful tool for capturing these types of relationships. They provide a framework for testing for relationships between outcomes of interest and high dimensional data such as metabolomic, genomic, or proteomic pathways. PaIRKAT uses known biological connections between high dimensional variables by representing them as edges of ‘graphs’ or ‘networks.’ It is common for nodes (e.g. metabolites) to be disconnected from all others within the graph, which leads to meaningful decreases in testing power whether or not the graph information is included. We include a graph regularization or ‘smoothing’ approach for managing this issue.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pandar/meta.yaml b/recipes/bioconductor-pandar/meta.yaml index b750dee69940d..efd48ab19efb3 100644 --- a/recipes/bioconductor-pandar/meta.yaml +++ b/recipes/bioconductor-pandar/meta.yaml @@ -1,29 +1,39 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "pandaR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Runs PANDA, an algorithm for discovering novel network structure by combining information from multiple complementary data sources. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: PANDA Algorithm -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 203422d8a9df096677530f57bffe9e9c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pandar", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:pandar + parent_recipe: + name: bioconductor-pandar + path: recipes/bioconductor-pandar + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-ggplot2 - r-hexbin @@ -33,8 +43,8 @@ requirements: - r-reshape - r-runit run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-ggplot2 - r-hexbin @@ -43,20 +53,16 @@ requirements: - r-plyr - r-reshape - r-runit + +source: + md5: 40aa0b375f4120aa905b319a6197cd29 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'PANDA Algorithm' - description: 'Runs PANDA, an algorithm for discovering novel network structure by combining information from multiple complementary data sources.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:pandar - parent_recipe: - name: bioconductor-pandar - path: recipes/bioconductor-pandar - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-panelcn.mops/meta.yaml b/recipes/bioconductor-panelcn.mops/meta.yaml index a1f76cb47c1ad..54ff852e4419a 100644 --- a/recipes/bioconductor-panelcn.mops/meta.yaml +++ b/recipes/bioconductor-panelcn.mops/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "panelcn.mops" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CNV detection tool for targeted NGS panel data. Extension of the cn.mops package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2.0) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: CNV detection tool for targeted NGS panel data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c40de00a870c4b693e6312b7d2110b96 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-panelcn.mops", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, RUnit, BiocGenerics requirements: host: - - 'bioconductor-cn.mops >=1.48.0,<1.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-cn.mops >=1.52.0,<1.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-cn.mops >=1.48.0,<1.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-cn.mops >=1.52.0,<1.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base + +source: + md5: 1425ba75b76fd0a303300cf90d14e5d0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2.0)' - summary: 'CNV detection tool for targeted NGS panel data' - description: 'CNV detection tool for targeted NGS panel data. Extension of the cn.mops package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-panomir/meta.yaml b/recipes/bioconductor-panomir/meta.yaml index 0ded484f43400..6bc3dcefd782c 100644 --- a/recipes/bioconductor-panomir/meta.yaml +++ b/recipes/bioconductor-panomir/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "PanomiR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: PanomiR is a package to detect miRNAs that target groups of pathways from gene expression data. This package provides functionality for generating pathway activity profiles, determining differentially activated pathways between user-specified conditions, determining clusters of pathways via the PCxN package, and generating miRNAs targeting clusters of pathways. These function can be used separately or sequentially to analyze RNA-Seq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Detection of miRNAs that regulate interacting groups of pathways -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8f96cdc267551107e69e8cb260a05c0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-panomir", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-dplyr - r-forcats @@ -37,11 +39,11 @@ requirements: - r-tibble - r-withr run: - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-base - r-dplyr - r-forcats @@ -51,13 +53,16 @@ requirements: - r-rlang - r-tibble - r-withr + +source: + md5: 96e2c9bf2bd7d1d628a360579b66a77d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Detection of miRNAs that regulate interacting groups of pathways' - description: 'PanomiR is a package to detect miRNAs that target groups of pathways from gene expression data. This package provides functionality for generating pathway activity profiles, determining differentially activated pathways between user-specified conditions, determining clusters of pathways via the PCxN package, and generating miRNAs targeting clusters of pathways. These function can be used separately or sequentially to analyze RNA-Seq data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-panp/meta.yaml b/recipes/bioconductor-panp/meta.yaml index 88b59b7b344ae..fb807813e7f9c 100644 --- a/recipes/bioconductor-panp/meta.yaml +++ b/recipes/bioconductor-panp/meta.yaml @@ -1,43 +1,22 @@ -{% set version = "1.72.0" %} +{% set version = "1.76.0" %} {% set name = "panp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Presence-Absence Calls from Negative Strand Matching Probesets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1cc532873dbc4e2cde6c04ca995545db build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-panp", max_pin="x.x") }}' - noarch: generic -# Suggests: gcrma -requirements: - host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base - run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Presence-Absence Calls from Negative Strand Matching Probesets' - description: 'A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:panp @@ -47,3 +26,30 @@ extra: path: recipes/bioconductor-panp version: 1.50.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: gcrma +requirements: + host: + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + run: + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + +source: + md5: f36d65252a6f9a5773a88a721a1fb976 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-panr/meta.yaml b/recipes/bioconductor-panr/meta.yaml index 5a1a71d18d317..3ac35f2c9adbb 100644 --- a/recipes/bioconductor-panr/meta.yaml +++ b/recipes/bioconductor-panr/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "PANR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides S4 classes and methods for inferring functional gene networks with edges encoding posterior beliefs of gene association types and nodes encoding perturbation effects. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: accc5472b6656e95d885960d9f1ecee3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-panr", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:panr + - doi:10.1371/journal.pcbi.1002566 + parent_recipe: + name: bioconductor-panr + path: recipes/bioconductor-panr + version: 1.28.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: snow requirements: host: - - 'bioconductor-reder >=2.6.0,<2.7.0' + - bioconductor-reder >=3.2.0,<3.3.0 - r-base - r-igraph - r-mass - r-pvclust run: - - 'bioconductor-reder >=2.6.0,<2.7.0' + - bioconductor-reder >=3.2.0,<3.3.0 - r-base - r-igraph - r-mass - r-pvclust + +source: + md5: 2b53dd76ced348d4cf0a191051886c42 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations' - description: 'This package provides S4 classes and methods for inferring functional gene networks with edges encoding posterior beliefs of gene association types and nodes encoding perturbation effects.' -extra: - identifiers: - - biotools:panr - - doi:10.1371/journal.pcbi.1002566 - parent_recipe: - name: bioconductor-panr - path: recipes/bioconductor-panr - version: 1.28.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-panther.db/meta.yaml b/recipes/bioconductor-panther.db/meta.yaml index 9f4277d05f21e..58123ccdbdbad 100644 --- a/recipes/bioconductor-panther.db/meta.yaml +++ b/recipes/bioconductor-panther.db/meta.yaml @@ -1,51 +1,57 @@ {% set version = "1.0.12" %} {% set name = "PANTHER.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A set of annotation maps describing the entire Gene Ontology assembled using data from PANTHER. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: A set of annotation maps describing the entire PANTHER Gene Ontology -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: edafd1c94f2f1cf3975f525fae7a9b83 build: - number: 0 + noarch: generic + number: 1 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-panther.db", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-panther.db + path: recipes/bioconductor-panther.db + version: 1.0.4 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit,knitr,BiocStyle,rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base - r-rsqlite - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: edafd1c94f2f1cf3975f525fae7a9b83 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A set of annotation maps describing the entire PANTHER Gene Ontology' - description: 'A set of annotation maps describing the entire Gene Ontology assembled using data from PANTHER.' -extra: - parent_recipe: - name: bioconductor-panther.db - path: recipes/bioconductor-panther.db - version: 1.0.4 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-parathyroidse/build_failure.linux-64.yaml b/recipes/bioconductor-parathyroidse/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..e3f2138c1c10d --- /dev/null +++ b/recipes/bioconductor-parathyroidse/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 49b2b76e1e0c1b0b781be315c5f435bc2bf4519c1a66133cfcc731086590ee18 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + libzlib: 1.3.1-hb9d3cd8_2 conda-forge + make: 4.4.1-hb9d3cd8_2 conda-forge + ncurses: 6.5-he02047a_1 conda-forge + oniguruma: 6.9.9-hd590300_0 conda-forge + openssl: 3.4.0-hb9d3cd8_0 conda-forge + pango: 1.54.0-h861ebed_4 conda-forge + pcre2: 10.44-hba22ea6_2 conda-forge + pip: 24.3.1-pyh145f28c_2 conda-forge + pixman: 0.44.2-h29eaf8c_0 conda-forge + pthread-stubs: 0.4-hb9d3cd8_1002 conda-forge + python: 3.13.1-ha99a958_102_cp313 conda-forge + python_abi: 3.13-5_cp313 conda-forge + pyyaml: 6.0.2-py313h536fd9c_1 conda-forge + r-abind: 1.4_5-r44hc72bb7e_1006 conda-forge + r-askpass: 1.2.1-r44h2b5f3a1_0 conda-forge + r-base: 4.4.2-hc737e89_2 conda-forge + r-crayon: 1.5.3-r44hc72bb7e_1 conda-forge + r-curl: 6.0.1-r44h2700575_0 conda-forge + r-httr: 1.4.7-r44hc72bb7e_1 conda-forge + r-jsonlite: 1.8.9-r44h2b5f3a1_0 conda-forge + r-lattice: 0.22_6-r44hb1dbf0f_1 conda-forge + r-matrix: 1.6_5-r44he966344_1 conda-forge + r-matrixstats: 1.4.1-r44h2b5f3a1_0 conda-forge + r-mime: 0.12-r44hb1dbf0f_3 conda-forge + r-openssl: 2.2.2-r44he8289e2_0 conda-forge + r-r6: 2.5.1-r44hc72bb7e_3 conda-forge + r-sys: 3.4.3-r44h2b5f3a1_0 conda-forge + readline: 8.2-h8228510_1 conda-forge + sed: 4.8-he412f7d_0 conda-forge + setuptools: 75.6.0-pyhff2d567_1 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tktable: 2.10-h8bc8fbc_6 conda-forge + toml: 0.10.2-pyhd8ed1ab_1 conda-forge + tomlkit: 0.13.2-pyha770c72_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + xmltodict: 0.14.2-pyhd8ed1ab_1 conda-forge + xorg-libice: 1.1.2-hb9d3cd8_0 conda-forge + xorg-libsm: 1.2.5-he73a12e_0 conda-forge + xorg-libx11: 1.8.10-h4f16b4b_1 conda-forge + xorg-libxau: 1.0.12-hb9d3cd8_0 conda-forge + xorg-libxdmcp: 1.1.5-hb9d3cd8_0 conda-forge + xorg-libxext: 1.3.6-hb9d3cd8_0 conda-forge + xorg-libxrender: 0.9.12-hb9d3cd8_0 conda-forge + xorg-libxt: 1.3.1-hb9d3cd8_0 conda-forge + yaml: 0.2.5-h7f98852_2 conda-forge + yq: 3.4.3-pyhd8ed1ab_1 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: parathyroidSE_1.43.0_1e65ae1c86.tar.gz + Downloading https://bioconductor.org/packages/3.20/data/experiment/src/contrib/parathyroidSE_1.43.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.248807 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioconductor.org/packages/3.20/bioc/src/contrib/Archive/parathyroidSE/parathyroidSE_1.43.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.139484 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioarchive.galaxyproject.org/parathyroidSE_1.43.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.689157 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://depot.galaxyproject.org/software/bioconductor-parathyroidse/bioconductor-parathyroidse_1.43.0_src_all.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.438659 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download https://depot.galaxyproject.org/software/bioconductor-parathyroidse/bioconductor-parathyroidse_1.43.0_src_all.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-parathyroidse/meta.yaml b/recipes/bioconductor-parathyroidse/meta.yaml index a43c027d7671f..e504ad097f1c4 100644 --- a/recipes/bioconductor-parathyroidse/meta.yaml +++ b/recipes/bioconductor-parathyroidse/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.40.0" %} +{% set version = "1.43.0" %} {% set name = "parathyroidSE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e4d06f888feb4015273e20b14f8ee37a +about: + description: 'This package provides RangedSummarizedExperiment objects of read counts in genes and exonic parts for paired-end RNA-Seq data from experiments on primary cultures of parathyroid tumors. The data were presented in the article "Evidence of a Functional Estrogen Receptor in Parathyroid Adenomas" by Haglund F, Ma R, Huss M, Sulaiman L, Lu M, Nilsson IL, Hoog A, Juhlin CC, Hartman J, Larsson C, J Clin Endocrinol Metab. jc.2012-2484, Epub 2012 Sep 28, PMID: 23024189. The sequencing was performed on tumor cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control). One control sample was omitted by the paper authors due to low quality. The package vignette describes the creation of the object from raw sequencing data provided by NCBI Gene Expression Omnibus under accession number GSE37211. The gene and exon features are the GRCh37 Ensembl annotations.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: RangedSummarizedExperiment for RNA-Seq of primary cultures of parathyroid tumors by Haglund et al., J Clin Endocrinol Metab 2012. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-parathyroidse", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: Rsamtools, GenomicAlignments, GEOquery, SRAdb, GenomicFeatures, BiocStyle requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1e65ae1c86ad412e58b32b4d4c697486 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'RangedSummarizedExperiment for RNA-Seq of primary cultures of parathyroid tumors by Haglund et al., J Clin Endocrinol Metab 2012.' - description: 'This package provides RangedSummarizedExperiment objects of read counts in genes and exonic parts for paired-end RNA-Seq data from experiments on primary cultures of parathyroid tumors. The data were presented in the article "Evidence of a Functional Estrogen Receptor in Parathyroid Adenomas" by Haglund F, Ma R, Huss M, Sulaiman L, Lu M, Nilsson IL, Hoog A, Juhlin CC, Hartman J, Larsson C, J Clin Endocrinol Metab. jc.2012-2484, Epub 2012 Sep 28, PMID: 23024189. The sequencing was performed on tumor cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control). One control sample was omitted by the paper authors due to low quality. The package vignette describes the creation of the object from raw sequencing data provided by NCBI Gene Expression Omnibus under accession number GSE37211. The gene and exon features are the GRCh37 Ensembl annotations.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-parathyroidse/post-link.sh b/recipes/bioconductor-parathyroidse/post-link.sh index 170c351577c93..52dc85f6c85c8 100644 --- a/recipes/bioconductor-parathyroidse/post-link.sh +++ b/recipes/bioconductor-parathyroidse/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "parathyroidse-1.40.0" +installBiocDataPackage.sh "parathyroidse-1.43.0" diff --git a/recipes/bioconductor-parglms/meta.yaml b/recipes/bioconductor-parglms/meta.yaml index ddeebc825c183..f3b3e34625043 100644 --- a/recipes/bioconductor-parglms/meta.yaml +++ b/recipes/bioconductor-parglms/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "parglms" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0d6a2dc756389064b9be38e755e1a24b +about: + description: This package provides support for parallelized estimation of GLMs/GEEs, catering for dispersed data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: support for parallelized estimation of GLMs/GEEs build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-parglms", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges, gwascat, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-batchjobs - r-doparallel - r-foreach run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-batchjobs - r-doparallel - r-foreach +source: + md5: 3472a411a84595ceec22c75f4992caeb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'support for parallelized estimation of GLMs/GEEs' - description: 'This package provides support for parallelized estimation of GLMs/GEEs, catering for dispersed data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-parody/meta.yaml b/recipes/bioconductor-parody/meta.yaml index c39b7ed701f61..34f82b1fd2960 100644 --- a/recipes/bioconductor-parody/meta.yaml +++ b/recipes/bioconductor-parody/meta.yaml @@ -1,38 +1,19 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "parody" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b466cc7b30f33e1854daac921ec9dc87 +about: + description: Provide routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Parametric And Resistant Outlier DYtection build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-parody", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, BiocStyle, testthat, rmarkdown -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Parametric And Resistant Outlier DYtection' - description: 'Provide routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics.' extra: identifiers: - biotools:parody @@ -41,4 +22,23 @@ extra: name: bioconductor-parody path: recipes/bioconductor-parody version: 1.38.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: knitr, BiocStyle, testthat, rmarkdown +requirements: + host: + - r-base + run: + - r-base +source: + md5: 8f2aba829a626c88195193cba243d6de + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-partcnv/meta.yaml b/recipes/bioconductor-partcnv/meta.yaml index b464c8fbd145d..2f0bab5dac03a 100644 --- a/recipes/bioconductor-partcnv/meta.yaml +++ b/recipes/bioconductor-partcnv/meta.yaml @@ -1,51 +1,58 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "partCNV" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package uses a statistical framework for rapid and accurate detection of aneuploid cells with local copy number deletion or amplification. Our method uses an EM algorithm with mixtures of Poisson distributions while incorporating cytogenetics information (e.g., regional deletion or amplification) to guide the classification (partCNV). When applicable, we further improve the accuracy by integrating a Hidden Markov Model for feature selection (partCNVH). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Infer locally aneuploid cells using single cell RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e004f2129cbb1fe1e84e33cf223c06f6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-partcnv", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, rmarkdown, knitr, IRanges, testthat (>= 3.0.0) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: rmarkdown, knitr, IRanges, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-data.table - r-depmixs4 - r-magrittr - r-seurat run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-data.table - r-depmixs4 - r-magrittr - r-seurat + +source: + md5: 38b2a9c8ba2b0072bd80170e683d94b2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Infer locally aneuploid cells using single cell RNA-seq data' - description: 'This package uses a statistical framework for rapid and accurate detection of aneuploid cells with local copy number deletion or amplification. Our method uses an EM algorithm with mixtures of Poisson distributions while incorporating cytogenetics information (e.g., regional deletion or amplification) to guide the classification (partCNV). When applicable, we further improve the accuracy by integrating a Hidden Markov Model for feature selection (partCNVH).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-partheenmetadata.db/meta.yaml b/recipes/bioconductor-partheenmetadata.db/meta.yaml index 174c5d3e8a5fe..1e10a468dea73 100644 --- a/recipes/bioconductor-partheenmetadata.db/meta.yaml +++ b/recipes/bioconductor-partheenmetadata.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "PartheenMetaData.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c9fd27e13a341b9aba9a235a67ce978 +about: + description: PartheenMetaData http://swegene.onk.lu.se Annotation Data (PartheenMetaData) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: PartheenMetaData http://swegene.onk.lu.se Annotation Data (PartheenMetaData) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-partheenmetadata.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1c9fd27e13a341b9aba9a235a67ce978 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'PartheenMetaData http://swegene.onk.lu.se Annotation Data (PartheenMetaData)' - description: 'PartheenMetaData http://swegene.onk.lu.se Annotation Data (PartheenMetaData) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pasilla/meta.yaml b/recipes/bioconductor-pasilla/meta.yaml index cbe7571ac3d4a..6a77819d06e43 100644 --- a/recipes/bioconductor-pasilla/meta.yaml +++ b/recipes/bioconductor-pasilla/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "pasilla" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e1fbdd57136d8a29edd1e0164dc2412e +about: + description: 'This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article "Conservation of an RNA regulatory map between Drosophila and mammals" by Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR, Genome Res. 2011 Feb;21(2):193-202, Epub 2010 Oct 4, PMID: 20921232. The experiment studied the effect of RNAi knockdown of Pasilla, the Drosophila melanogaster ortholog of mammalian NOVA1 and NOVA2, on the transcriptome. The package vignette describes how the data provided here were derived from the RNA-Seq read sequence data that are provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pasilla", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: rmarkdown, BiocStyle, knitr, roxygen2 requirements: host: - - 'bioconductor-dexseq >=1.48.0,<1.49.0' + - bioconductor-dexseq >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-dexseq >=1.48.0,<1.49.0' + - bioconductor-dexseq >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241231 +source: + md5: b1521054ce2e43ced5de491d1ea26e8b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011.' - description: 'This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article "Conservation of an RNA regulatory map between Drosophila and mammals" by Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR, Genome Res. 2011 Feb;21(2):193-202, Epub 2010 Oct 4, PMID: 20921232. The experiment studied the effect of RNAi knockdown of Pasilla, the Drosophila melanogaster ortholog of mammalian NOVA1 and NOVA2, on the transcriptome. The package vignette describes how the data provided here were derived from the RNA-Seq read sequence data that are provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pasilla/post-link.sh b/recipes/bioconductor-pasilla/post-link.sh index d7bfc5e712bc6..47cb149815920 100644 --- a/recipes/bioconductor-pasilla/post-link.sh +++ b/recipes/bioconductor-pasilla/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pasilla-1.30.0" +installBiocDataPackage.sh "pasilla-1.34.0" diff --git a/recipes/bioconductor-pasillabamsubset/meta.yaml b/recipes/bioconductor-pasillabamsubset/meta.yaml index a7095742aa73c..7cb618f23746a 100644 --- a/recipes/bioconductor-pasillabamsubset/meta.yaml +++ b/recipes/bioconductor-pasillabamsubset/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "0.40.0" %} +{% set version = "0.44.0" %} {% set name = "pasillaBamSubset" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8fd05eac2d37650e157871908cbaf306 +about: + description: Subset of BAM files untreated1.bam (single-end reads) and untreated3.bam (paired-end reads) from "Pasilla" experiment (Pasilla knock-down by Brooks et al., Genome Research 2011). See the vignette in the pasilla data package for how BAM files untreated1.bam and untreated3.bam were obtained from the RNA-Seq read sequence data that is provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. Also contains the DNA sequence for fly chromosome 4 to which the reads can be mapped. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Subset of BAM files from "Pasilla" experiment build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pasillabamsubset", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: pasilla requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6c11c77d7bfecf2e07d1de5153c6f36f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Subset of BAM files from "Pasilla" experiment' - description: 'Subset of BAM files untreated1.bam (single-end reads) and untreated3.bam (paired-end reads) from "Pasilla" experiment (Pasilla knock-down by Brooks et al., Genome Research 2011). See the vignette in the pasilla data package for how BAM files untreated1.bam and untreated3.bam were obtained from the RNA-Seq read sequence data that is provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. Also contains the DNA sequence for fly chromosome 4 to which the reads can be mapped.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pasillabamsubset/post-link.sh b/recipes/bioconductor-pasillabamsubset/post-link.sh index 6e8d22f6eff32..132bfe061c1b5 100644 --- a/recipes/bioconductor-pasillabamsubset/post-link.sh +++ b/recipes/bioconductor-pasillabamsubset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pasillabamsubset-0.40.0" +installBiocDataPackage.sh "pasillabamsubset-0.44.0" diff --git a/recipes/bioconductor-pasillatranscriptexpr/build_failure.linux-64.yaml b/recipes/bioconductor-pasillatranscriptexpr/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..92b0c136d23c7 --- /dev/null +++ b/recipes/bioconductor-pasillatranscriptexpr/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 53b7ad3c85612158aa1b778ac3f96ec1f94d3b5946f2b7777b82a00ca393ff7a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + URLS=($value) + IFS= + read -r value + URLS=($value) + IFS= + read -r value + yq '."pasillatranscriptexpr-1.33.0".md5' /opt/conda/conda-bld/bioconductor-pasillatranscriptexpr_1734535284811/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/bin/../share/bioconductor-data-packages/dataURLs.json + MD5='"90e4ec9cc4a2e56e8d096d3d45b6f5b0"' + STAGING=/opt/conda/conda-bld/bioconductor-pasillatranscriptexpr_1734535284811/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/share/pasillatranscriptexpr-1.33.0 + mkdir -p /opt/conda/conda-bld/bioconductor-pasillatranscriptexpr_1734535284811/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/share/pasillatranscriptexpr-1.33.0 + TARBALL='/opt/conda/conda-bld/bioconductor-pasillatranscriptexpr_1734535284811/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/share/pasillatranscriptexpr-1.33.0/"PasillaTranscriptExpr_1.33.0.tar.gz"' + SUCCESS=0 + for URL in '${URLS[@]}' + echo '"https://bioconductor.org/packages/3.20/data/experiment/src/contrib/PasillaTranscriptExpr_1.33.0.tar.gz"' + tr -d '"' + URL=https://bioconductor.org/packages/3.20/data/experiment/src/contrib/PasillaTranscriptExpr_1.33.0.tar.gz + echo '"90e4ec9cc4a2e56e8d096d3d45b6f5b0"' + tr -d '"' + MD5=90e4ec9cc4a2e56e8d096d3d45b6f5b0 + curl -L https://bioconductor.org/packages/3.20/data/experiment/src/contrib/PasillaTranscriptExpr_1.33.0.tar.gz + % Total % Received % Xferd Average Speed Time Time Time Current + Dload Upload Total Spent Left Speed + + 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 + 100 10888 100 10888 0 0 61601 0 --:--:-- --:--:-- --:--:-- 61863 + [[ 0 == 0 ]] + uname -s + [[ Linux == \L\i\n\u\x ]] + md5sum -c + md5sum: WARNING: 1 computed checksum did NOT match + for URL in '${URLS[@]}' + echo '"https://bioarchive.galaxyproject.org/PasillaTranscriptExpr_1.33.0.tar.gz"' + tr -d '"' + URL=https://bioarchive.galaxyproject.org/PasillaTranscriptExpr_1.33.0.tar.gz + echo 90e4ec9cc4a2e56e8d096d3d45b6f5b0 + tr -d '"' + MD5=90e4ec9cc4a2e56e8d096d3d45b6f5b0 + curl -L https://bioarchive.galaxyproject.org/PasillaTranscriptExpr_1.33.0.tar.gz + % Total % Received % Xferd Average Speed Time Time Time Current + Dload Upload Total Spent Left Speed + + 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 + 100 153 100 153 0 0 623 0 --:--:-- --:--:-- --:--:-- 624 + [[ 0 == 0 ]] + uname -s + [[ Linux == \L\i\n\u\x ]] + md5sum -c + md5sum: WARNING: 1 computed checksum did NOT match + for URL in '${URLS[@]}' + echo '"https://depot.galaxyproject.org/software/bioconductor-pasillatranscriptexpr/bioconductor-pasillatranscriptexpr_1.33.0_src_all.tar.gz"' + tr -d '"' + URL=https://depot.galaxyproject.org/software/bioconductor-pasillatranscriptexpr/bioconductor-pasillatranscriptexpr_1.33.0_src_all.tar.gz + echo 90e4ec9cc4a2e56e8d096d3d45b6f5b0 + tr -d '"' + MD5=90e4ec9cc4a2e56e8d096d3d45b6f5b0 + curl -L https://depot.galaxyproject.org/software/bioconductor-pasillatranscriptexpr/bioconductor-pasillatranscriptexpr_1.33.0_src_all.tar.gz + % Total % Received % Xferd Average Speed Time Time Time Current + Dload Upload Total Spent Left Speed + + 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 + 100 153 100 153 0 0 814 0 --:--:-- --:--:-- --:--:-- 818 + [[ 0 == 0 ]] + uname -s + [[ Linux == \L\i\n\u\x ]] + md5sum -c + md5sum: WARNING: 1 computed checksum did NOT match + [[ 0 != 1 ]] + echo 'ERROR: post-link.sh was unable to download any of the following URLs with the md5sum 90e4ec9cc4a2e56e8d096d3d45b6f5b0:' + printf '%s\n' '"https://bioconductor.org/packages/3.20/data/experiment/src/contrib/PasillaTranscriptExpr_1.33.0.tar.gz"' '"https://bioarchive.galaxyproject.org/PasillaTranscriptExpr_1.33.0.tar.gz"' '"https://depot.galaxyproject.org/software/bioconductor-pasillatranscriptexpr/bioconductor-pasillatranscriptexpr_1.33.0_src_all.tar.gz"' + exit 1 + + return code: 1 + + kwargs: + {} + + : + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3462, in test + environ.create_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1060, in create_env + "too short in" in str(exc) + File "/opt/conda/lib/python3.10/site-packages/conda/__init__.py", line 130, in __str__ + return "\n".join(str(e) for e in self.errors) "\n" + File "/opt/conda/lib/python3.10/site-packages/conda/__init__.py", line 130, in + return "\n".join(str(e) for e in self.errors) "\n" + File "/opt/conda/lib/python3.10/site-packages/conda/__init__.py", line 83, in __str__ + return str(self.message % self._kwargs) + ValueError: unsupported format character 'T' (0x54) at index 5578 +# Last 100 lines of the build log. +category: |- + checksum mismatch diff --git a/recipes/bioconductor-pasillatranscriptexpr/meta.yaml b/recipes/bioconductor-pasillatranscriptexpr/meta.yaml index befc4ad24b21e..d3b94775d554a 100644 --- a/recipes/bioconductor-pasillatranscriptexpr/meta.yaml +++ b/recipes/bioconductor-pasillatranscriptexpr/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "PasillaTranscriptExpr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7d1d8c852fff7d80c11e8ab79dae7487 +about: + description: Provides kallisto workflow and transcript expression of RNA-Seq data from Brooks et al. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Data package with transcript expression obtained with kallisto from pasilla knock-down RNA-Seq data from Brooks et al. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pasillatranscriptexpr", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: rtracklayer, BiocStyle, knitr, testthat requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e997161d6ee94ee6a080e6b9a1665572 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Data package with transcript expression obtained with kallisto from pasilla knock-down RNA-Seq data from Brooks et al.' - description: 'Provides kallisto workflow and transcript expression of RNA-Seq data from Brooks et al.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pasillatranscriptexpr/post-link.sh b/recipes/bioconductor-pasillatranscriptexpr/post-link.sh index 4bb80603c4361..bf543dfb086a9 100644 --- a/recipes/bioconductor-pasillatranscriptexpr/post-link.sh +++ b/recipes/bioconductor-pasillatranscriptexpr/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pasillatranscriptexpr-1.30.0" +installBiocDataPackage.sh "pasillatranscriptexpr-1.33.0" diff --git a/recipes/bioconductor-past/meta.yaml b/recipes/bioconductor-past/meta.yaml index a2f50e875b09f..53f63b6834c7e 100644 --- a/recipes/bioconductor-past/meta.yaml +++ b/recipes/bioconductor-past/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "PAST" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: PAST takes GWAS output and assigns SNPs to genes, uses those genes to find pathways associated with the genes, and plots pathways based on significance. Implements methods for reading GWAS input data, finding genes associated with SNPs, calculating enrichment score and significance of pathways, and plotting pathways. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=3) + file LICENSE + license_file: LICENSE + summary: Pathway Association Study Tool (PAST) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9af26fa0c8f74a586f23905b9b2408c3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-past", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-doparallel - r-dplyr @@ -34,10 +36,10 @@ requirements: - r-iterators - r-rlang run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-doparallel - r-dplyr @@ -45,13 +47,16 @@ requirements: - r-ggplot2 - r-iterators - r-rlang + +source: + md5: 54eaa7a9f021f23adaaf4d3fe492599a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=3) + file LICENSE' - summary: 'Pathway Association Study Tool (PAST)' - description: 'PAST takes GWAS output and assigns SNPs to genes, uses those genes to find pathways associated with the genes, and plots pathways based on significance. Implements methods for reading GWAS input data, finding genes associated with SNPs, calculating enrichment score and significance of pathways, and plotting pathways.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-path2ppi/meta.yaml b/recipes/bioconductor-path2ppi/meta.yaml index 0153df53f02fd..8705ecea6e6d2 100644 --- a/recipes/bioconductor-path2ppi/meta.yaml +++ b/recipes/bioconductor-path2ppi/meta.yaml @@ -1,46 +1,52 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "Path2PPI" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package to predict protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available. Path2PPI predicts PPI networks based on sets of proteins which can belong to a certain pathway from well-established model organisms. It helps to combine and transfer information of a certain pathway or biological process from several reference organisms to one target organism. Path2PPI only depends on the sequence similarity of the involved proteins. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Prediction of pathway-related protein-protein interaction networks -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4fcd4d73b05e2167ecdfb79aadfe8722 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-path2ppi", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:path2ppi + parent_recipe: + name: bioconductor-path2ppi + path: recipes/bioconductor-path2ppi + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle requirements: host: - r-base - - 'r-igraph >=1.0.1' + - r-igraph >=1.0.1 run: - r-base - - 'r-igraph >=1.0.1' + - r-igraph >=1.0.1 + +source: + md5: 3413bff2fed7639111b56a8f46469c6d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Prediction of pathway-related protein-protein interaction networks' - description: 'Package to predict protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available. Path2PPI predicts PPI networks based on sets of proteins which can belong to a certain pathway from well-established model organisms. It helps to combine and transfer information of a certain pathway or biological process from several reference organisms to one target organism. Path2PPI only depends on the sequence similarity of the involved proteins.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:path2ppi - parent_recipe: - name: bioconductor-path2ppi - path: recipes/bioconductor-path2ppi - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pathifier/meta.yaml b/recipes/bioconductor-pathifier/meta.yaml index 818306e1cb392..d3edf31e6b645 100644 --- a/recipes/bioconductor-pathifier/meta.yaml +++ b/recipes/bioconductor-pathifier/meta.yaml @@ -1,47 +1,53 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "pathifier" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-1.0 + summary: Quantify deregulation of pathways in cancer -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 344576d367c4da46c28918be3de3f65e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pathifier", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:pathifier + - doi:10.1073/pnas.1219651110 + parent_recipe: + name: bioconductor-pathifier + path: recipes/bioconductor-pathifier + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base - - 'r-princurve >=2.0.4' + - r-princurve >=2.0.4 - r-r.oo run: - r-base - - 'r-princurve >=2.0.4' + - r-princurve >=2.0.4 - r-r.oo + +source: + md5: 3c0885c767a75ce4dd73eab001e2d2fe + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-1.0 - summary: 'Quantify deregulation of pathways in cancer' - description: 'Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample.' -extra: - identifiers: - - biotools:pathifier - - doi:10.1073/pnas.1219651110 - parent_recipe: - name: bioconductor-pathifier - path: recipes/bioconductor-pathifier - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pathlinkr/build.sh b/recipes/bioconductor-pathlinkr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pathlinkr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pathlinkr/build_failure.linux-64.yaml b/recipes/bioconductor-pathlinkr/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..a489962f630d1 --- /dev/null +++ b/recipes/bioconductor-pathlinkr/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: 4690a9bd93625e33857867d88e4e1c2a968689a44c82a73f5b5c93ebf07e97ba # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Encountered problems while solving: + - nothing provides requested bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - nothing provides requested r-sigora + + Could not solve for environment specs + The following packages are incompatible + [31mbioconductor-clusterprofiler >=4.14.0,<4.15.0 [0m does not exist (perhaps a typo or a missing channel); + [31mr-sigora[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-sigora"), MatchSpec("bioconductor-clusterprofiler[version='>=4.14.0,<4.15.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - nothing provides requested r-sigora + + Could not solve for environment specs + The following packages are incompatible + [31mbioconductor-clusterprofiler >=4.14.0,<4.15.0 [0m does not exist (perhaps a typo or a missing channel); + [31mr-sigora[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-sigora"), MatchSpec("bioconductor-clusterprofiler[version='>=4.14.0,<4.15.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - nothing provides requested r-sigora + + Could not solve for environment specs + The following packages are incompatible + [31mbioconductor-clusterprofiler >=4.14.0,<4.15.0 [0m does not exist (perhaps a typo or a missing channel); + [31mr-sigora[0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. +reason: |- + needs r-sigora and r-slam to be added to bioconda +category: |- + dependency issue diff --git a/recipes/bioconductor-pathlinkr/build_failure.osx-64.yaml b/recipes/bioconductor-pathlinkr/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..ac248a1523362 --- /dev/null +++ b/recipes/bioconductor-pathlinkr/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 4690a9bd93625e33857867d88e4e1c2a968689a44c82a73f5b5c93ebf07e97ba # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + needs r-sigora and r-slam to be added to bioconda +category: |- + dependency issue diff --git a/recipes/bioconductor-pathlinkr/meta.yaml b/recipes/bioconductor-pathlinkr/meta.yaml new file mode 100644 index 0000000000000..723f62e4f608d --- /dev/null +++ b/recipes/bioconductor-pathlinkr/meta.yaml @@ -0,0 +1,82 @@ +{% set version = "1.2.0" %} +{% set name = "pathlinkR" %} +{% set bioc = "3.20" %} + +about: + description: pathlinkR is an R package designed to facilitate analysis of RNA-Seq results. Specifically, our aim with pathlinkR was to provide a number of tools which take a list of DE genes and perform different analyses on them, aiding with the interpretation of results. Functions are included to perform pathway enrichment, with muliplte databases supported, and tools for visualizing these results. Genes can also be used to create and plot protein-protein interaction networks, all from inside of R. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Analyze and interpret RNA-Seq results + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pathlinkr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: AnnotationDbi, BiocStyle, biomaRt, covr, DESeq2, jsonlite, knitr, org.Hs.eg.db, rmarkdown, scales, testthat (>= 3.0.0), vdiffr +requirements: + + host: + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - r-base + - r-circlize + - r-dplyr + - r-ggforce + - r-ggplot2 + - r-ggpubr + - r-ggraph + - r-ggrepel + - r-igraph + - r-purrr + - r-sigora + - r-stringr + - r-tibble + - r-tidygraph + - r-tidyr + - r-vegan + - r-visnetwork + + run: + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - r-base + - r-circlize + - r-dplyr + - r-ggforce + - r-ggplot2 + - r-ggpubr + - r-ggraph + - r-ggrepel + - r-igraph + - r-purrr + - r-sigora + - r-stringr + - r-tibble + - r-tidygraph + - r-tidyr + - r-vegan + - r-visnetwork + +source: + md5: a3e081ba43d136a2ccc20e5ff8cfb9d6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-pathnet/meta.yaml b/recipes/bioconductor-pathnet/meta.yaml index a65c695e30d6d..526547dd71f1d 100644 --- a/recipes/bioconductor-pathnet/meta.yaml +++ b/recipes/bioconductor-pathnet/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "PathNet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 13ca247b602840ebfaea9f1e9a5839aa +about: + description: 'PathNet uses topological information present in pathways and differential expression levels of genes (obtained from microarray experiment) to identify pathways that are 1) significantly enriched and 2) associated with each other in the context of differential expression. The algorithm is described in: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J. Source Code for Biology and Medicine 2012 Sep 24;7(1):10.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: An R package for pathway analysis using topological information build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pathnet", max_pin="x.x") }}' - noarch: generic +extra: + identifiers: + - biotools:pathnet + parent_recipe: + name: bioconductor-pathnet + path: recipes/bioconductor-pathnet + version: 1.20.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: PathNetData, RUnit, BiocGenerics requirements: host: - r-base run: - r-base +source: + md5: c0a06ae5c507dd59f904efaac6bf24f6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'An R package for pathway analysis using topological information' - description: 'PathNet uses topological information present in pathways and differential expression levels of genes (obtained from microarray experiment) to identify pathways that are 1) significantly enriched and 2) associated with each other in the context of differential expression. The algorithm is described in: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J. Source Code for Biology and Medicine 2012 Sep 24;7(1):10.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:pathnet - parent_recipe: - name: bioconductor-pathnet - path: recipes/bioconductor-pathnet - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pathnetdata/meta.yaml b/recipes/bioconductor-pathnetdata/meta.yaml index cea53f8bb3615..9fceb2b9710a1 100644 --- a/recipes/bioconductor-pathnetdata/meta.yaml +++ b/recipes/bioconductor-pathnetdata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "PathNetData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d72e955b33c92f1703ae072ec788c1d9 +about: + description: 'This package contains the data employed in the vignette of the PathNet package. These data belong to the following publication: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J., Source Code for Biology and Medicine 2012 Sep 24;7(1):10.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Experimental data for the PathNet package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pathnetdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a253ad75c30b3b91a5069d7f270d16da + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Experimental data for the PathNet package' - description: 'This package contains the data employed in the vignette of the PathNet package. These data belong to the following publication: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J., Source Code for Biology and Medicine 2012 Sep 24;7(1):10.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pathnetdata/post-link.sh b/recipes/bioconductor-pathnetdata/post-link.sh index c51f9a25a4d1a..2bf934578ba49 100644 --- a/recipes/bioconductor-pathnetdata/post-link.sh +++ b/recipes/bioconductor-pathnetdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pathnetdata-1.38.0" +installBiocDataPackage.sh "pathnetdata-1.42.0" diff --git a/recipes/bioconductor-pathostat/meta.yaml b/recipes/bioconductor-pathostat/meta.yaml index adc375d616f15..55645affc65be 100644 --- a/recipes/bioconductor-pathostat/meta.yaml +++ b/recipes/bioconductor-pathostat/meta.yaml @@ -1,33 +1,45 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "PathoStat" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: PathoStat Statistical Microbiome Analysis Package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fd391aaf46df86a1608019bd2454d67f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pathostat", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:pathostat + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-pathostat + path: recipes/bioconductor-pathostat + version: 1.6.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, testthat requirements: + host: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 - r-ape - r-base - r-corpcor @@ -52,13 +64,14 @@ requirements: - r-vegan - r-webshot - r-xml + run: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 - r-ape - r-base - r-corpcor @@ -83,21 +96,16 @@ requirements: - r-vegan - r-webshot - r-xml + +source: + md5: 1b3b6228ce2911d30e8b1421979e4d6c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'PathoStat Statistical Microbiome Analysis Package' - description: 'The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:pathostat - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-pathostat - path: recipes/bioconductor-pathostat - version: 1.6.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pathrender/meta.yaml b/recipes/bioconductor-pathrender/meta.yaml index 8f6884f8bfe86..044b088d86fdc 100644 --- a/recipes/bioconductor-pathrender/meta.yaml +++ b/recipes/bioconductor-pathrender/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.70.0" %} +{% set version = "1.74.0" %} {% set name = "pathRender" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: build graphs from pathway databases, render them by Rgraphviz. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Render molecular pathways -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0796d30e763067880a67ed2435d2ac26 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pathrender", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:pathrender + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-pathrender + path: recipes/bioconductor-pathrender + version: 1.48.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ALL, hgu95av2.db requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-cmap >=1.15.0,<1.16.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-cmap >=1.15.0,<1.16.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-rcolorbrewer run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-cmap >=1.15.0,<1.16.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-cmap >=1.15.0,<1.16.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-rcolorbrewer + +source: + md5: b51336cbfc6edb8c13706fbc52332b87 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Render molecular pathways' - description: 'build graphs from pathway databases, render them by Rgraphviz.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:pathrender - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-pathrender - path: recipes/bioconductor-pathrender - version: 1.48.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pathview/meta.yaml b/recipes/bioconductor-pathview/meta.yaml index 939a3d3b6bded..407d3f03321f6 100644 --- a/recipes/bioconductor-pathview/meta.yaml +++ b/recipes/bioconductor-pathview/meta.yaml @@ -1,60 +1,66 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "pathview" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=3.0) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: a tool set for pathway based data integration and visualization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5e17ceee29bb13083a2b11be28edacb0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pathview", max_pin="x.x") }}' - noarch: generic -# Suggests: gage, org.Mm.eg.db, RUnit, BiocGenerics + +extra: + identifiers: + - biotools:pathview + parent_recipe: + name: bioconductor-pathview + path: recipes/bioconductor-pathview + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: gage, org.Mm.eg.db, org.EcK12.eg.db, RUnit, BiocGenerics requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-png - r-xml run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-png - r-xml + +source: + md5: 3cb3d45ea299c1d3d947cfd06b61b75e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=3.0)' - summary: 'a tool set for pathway based data integration and visualization' - description: 'Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:pathview - parent_recipe: - name: bioconductor-pathview - path: recipes/bioconductor-pathview - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pathwaypca/meta.yaml b/recipes/bioconductor-pathwaypca/meta.yaml index caaad95452bb9..d53a52800c5c5 100644 --- a/recipes/bioconductor-pathwaypca/meta.yaml +++ b/recipes/bioconductor-pathwaypca/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "pathwayPCA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 100ae90b68c015f8e344da1d3a2a4863 +about: + description: 'pathwayPCA is an integrative analysis tool that implements the principal component analysis (PCA) based pathway analysis approaches described in Chen et al. (2008), Chen et al. (2010), and Chen (2011). pathwayPCA allows users to: (1) Test pathway association with binary, continuous, or survival phenotypes. (2) Extract relevant genes in the pathways using the SuperPCA and AES-PCA approaches. (3) Compute principal components (PCs) based on the selected genes. These estimated latent variables represent pathway activities for individual subjects, which can then be used to perform integrative pathway analysis, such as multi-omics analysis. (4) Extract relevant genes that drive pathway significance as well as data corresponding to these relevant genes for additional in-depth analysis. (5) Perform analyses with enhanced computational efficiency with parallel computing and enhanced data safety with S4-class data objects. (6) Analyze studies with complex experimental designs, with multiple covariates, and with interaction effects, e.g., testing whether pathway association with clinical phenotype is different between male and female subjects. Citations: Chen et al. (2008) ; Chen et al. (2010) ; and Chen (2011) .' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pathwaypca", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: airway, circlize, grDevices, knitr, RCurl, reshape2, rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse requirements: host: @@ -29,13 +28,14 @@ requirements: - r-base - r-lars - r-survival +source: + md5: 0129956bd4573766d7168fcbf6d7d9a1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection' - description: 'pathwayPCA is an integrative analysis tool that implements the principal component analysis (PCA) based pathway analysis approaches described in Chen et al. (2008), Chen et al. (2010), and Chen (2011). pathwayPCA allows users to: (1) Test pathway association with binary, continuous, or survival phenotypes. (2) Extract relevant genes in the pathways using the SuperPCA and AES-PCA approaches. (3) Compute principal components (PCs) based on the selected genes. These estimated latent variables represent pathway activities for individual subjects, which can then be used to perform integrative pathway analysis, such as multi-omics analysis. (4) Extract relevant genes that drive pathway significance as well as data corresponding to these relevant genes for additional in-depth analysis. (5) Perform analyses with enhanced computational efficiency with parallel computing and enhanced data safety with S4-class data objects. (6) Analyze studies with complex experimental designs, with multiple covariates, and with interaction effects, e.g., testing whether pathway association with clinical phenotype is different between male and female subjects. Citations: Chen et al. (2008) ; Chen et al. (2010) ; and Chen (2011) .' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pcaexplorer/build_failure.linux-64.yaml b/recipes/bioconductor-pcaexplorer/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0c39f44ac7be9 --- /dev/null +++ b/recipes/bioconductor-pcaexplorer/build_failure.linux-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: b0b44b20bd26a2af878a0b157d22d505fcd19cbd2e02328a5e2edfb16151bbd1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bioconductor-mosdef needs to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-pcaexplorer/build_failure.osx-64.yaml b/recipes/bioconductor-pcaexplorer/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..0c39f44ac7be9 --- /dev/null +++ b/recipes/bioconductor-pcaexplorer/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: b0b44b20bd26a2af878a0b157d22d505fcd19cbd2e02328a5e2edfb16151bbd1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bioconductor-mosdef needs to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-pcaexplorer/meta.yaml b/recipes/bioconductor-pcaexplorer/meta.yaml index 9c16c5e3fce55..87625a49d7a8c 100644 --- a/recipes/bioconductor-pcaexplorer/meta.yaml +++ b/recipes/bioconductor-pcaexplorer/meta.yaml @@ -1,43 +1,56 @@ -{% set version = "2.28.0" %} +{% set version = "3.0.0" %} {% set name = "pcaExplorer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functionality for interactive visualization of RNA-seq datasets based on Principal Components Analysis. The methods provided allow for quick information extraction and effective data exploration. A Shiny application encapsulates the whole analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Interactive Visualization of RNA-seq Data Using a Principal Components Approach -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 622f43cef60e783c51d59ed8624019d8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pcaexplorer", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:pcaexplorer + - doi:10.18547/gcb.2017.vol3.iss1.e39 + parent_recipe: + name: bioconductor-pcaexplorer + path: recipes/bioconductor-pcaexplorer + version: 2.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, htmltools requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-mosdef >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-base - r-base64enc - r-dt - - 'r-ggplot2 >=2.0.0' + - r-ggplot2 >=2.0.0 - r-ggrepel - r-heatmaply - r-knitr @@ -47,29 +60,31 @@ requirements: - r-plyr - r-rmarkdown - r-scales - - 'r-shiny >=0.12.0' + - r-shiny >=0.12.0 - r-shinyace - r-shinybs - r-shinydashboard - r-threejs - r-tidyr + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-mosdef >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-base - r-base64enc - r-dt - - 'r-ggplot2 >=2.0.0' + - r-ggplot2 >=2.0.0 - r-ggrepel - r-heatmaply - r-knitr @@ -79,27 +94,22 @@ requirements: - r-plyr - r-rmarkdown - r-scales - - 'r-shiny >=0.12.0' + - r-shiny >=0.12.0 - r-shinyace - r-shinybs - r-shinydashboard - r-threejs - r-tidyr + +source: + md5: 64cb44bfb288c2133de1239dcd94db59 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Interactive Visualization of RNA-seq Data Using a Principal Components Approach' - description: 'This package provides functionality for interactive visualization of RNA-seq datasets based on Principal Components Analysis. The methods provided allow for quick information extraction and effective data exploration. A Shiny application encapsulates the whole analysis.' - license_file: LICENSE -extra: - identifiers: - - biotools:pcaexplorer - - doi:10.18547/gcb.2017.vol3.iss1.e39 - parent_recipe: - name: bioconductor-pcaexplorer - path: recipes/bioconductor-pcaexplorer - version: 2.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pcamethods/meta.yaml b/recipes/bioconductor-pcamethods/meta.yaml index a206627ebca74..734803376656f 100644 --- a/recipes/bioconductor-pcamethods/meta.yaml +++ b/recipes/bioconductor-pcamethods/meta.yaml @@ -1,61 +1,67 @@ -{% set version = "1.94.0" %} +{% set version = "1.98.0" %} {% set name = "pcaMethods" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results. Initiated at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A collection of PCA methods -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a989ad925a9852f55eb5e4d16d1529d0 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pcamethods", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:pcamethods + - doi:10.1093/bioinformatics/btm069 + parent_recipe: + name: bioconductor-pcamethods + path: recipes/bioconductor-pcamethods + version: 1.72.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: matrixStats, lattice, ggplot2 # SystemRequirements: Rcpp requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-mass - - 'r-rcpp >=0.11.3' + - r-rcpp >=0.11.3 - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-mass - - 'r-rcpp >=0.11.3' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=0.11.3 + +source: + md5: deabf6bd06e91898d6308319cbda0573 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'A collection of PCA methods' - description: 'Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results. Initiated at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:pcamethods - - doi:10.1093/bioinformatics/btm069 - parent_recipe: - name: bioconductor-pcamethods - path: recipes/bioconductor-pcamethods - version: 1.72.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pcan/meta.yaml b/recipes/bioconductor-pcan/meta.yaml index 47cee63d9eee6..a6c8ce9676f5e 100644 --- a/recipes/bioconductor-pcan/meta.yaml +++ b/recipes/bioconductor-pcan/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "PCAN" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94596d43854d98aee2e6da198147772b +about: + description: Phenotypes comparison based on a pathway consensus approach. Assess the relationship between candidate genes and a set of phenotypes based on additional genes related to the candidate (e.g. Pathways or network neighbors). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: CC BY-NC-ND 4.0 + summary: Phenotype Consensus ANalysis (PCAN) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pcan", max_pin="x.x") }}' - noarch: generic +extra: + identifiers: + - biotools:pcan + parent_recipe: + name: bioconductor-pcan + path: recipes/bioconductor-pcan + version: 1.8.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base +source: + md5: aba965b2eda8d1c84e5de4c29ba06a0e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'CC BY-NC-ND 4.0' - summary: 'Phenotype Consensus ANalysis (PCAN)' - description: 'Phenotypes comparison based on a pathway consensus approach. Assess the relationship between candidate genes and a set of phenotypes based on additional genes related to the candidate (e.g. Pathways or network neighbors).' -extra: - identifiers: - - biotools:pcan - parent_recipe: - name: bioconductor-pcan - path: recipes/bioconductor-pcan - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pcatools/meta.yaml b/recipes/bioconductor-pcatools/meta.yaml index eabd07294dc9a..81b292a90315d 100644 --- a/recipes/bioconductor-pcatools/meta.yaml +++ b/recipes/bioconductor-pcatools/meta.yaml @@ -1,32 +1,38 @@ -{% set version = "2.14.0" %} +{% set version = "2.18.0" %} {% set name = "PCAtools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Principal Component Analysis (PCA) is a very powerful technique that has wide applicability in data science, bioinformatics, and further afield. It was initially developed to analyse large volumes of data in order to tease out the differences/relationships between the logical entities being analysed. It extracts the fundamental structure of the data without the need to build any model to represent it. This 'summary' of the data is arrived at through a process of reduction that can transform the large number of variables into a lesser number that are uncorrelated (i.e. the 'principal components'), while at the same time being capable of easy interpretation on the original data. PCAtools provides functions for data exploration via PCA, and allows the user to generate publication-ready figures. PCA is performed via BiocSingular - users can also identify optimal number of principal components via different metrics, such as elbow method and Horn's parallel analysis, which has relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high dimensional mass cytometry data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'PCAtools: Everything Principal Components Analysis' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 316c693617402890169745a37dfaead6 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pcatools", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, scran, BiocGenerics, knitr, Biobase, GEOquery, hgu133a.db, ggplotify, beachmat, RMTstat, ggalt, DESeq2, airway, org.Hs.eg.db, magrittr, rmarkdown # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 - r-base - r-bh - r-cowplot @@ -40,11 +46,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 - r-base - r-bh - r-cowplot @@ -55,17 +61,16 @@ requirements: - r-matrix - r-rcpp - r-reshape2 - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 2b1d8c22e21a62e7c04162fb6a6a24b5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'PCAtools: Everything Principal Components Analysis' - description: 'Principal Component Analysis (PCA) is a very powerful technique that has wide applicability in data science, bioinformatics, and further afield. It was initially developed to analyse large volumes of data in order to tease out the differences/relationships between the logical entities being analysed. It extracts the fundamental structure of the data without the need to build any model to represent it. This ''summary'' of the data is arrived at through a process of reduction that can transform the large number of variables into a lesser number that are uncorrelated (i.e. the ''principal components''), while at the same time being capable of easy interpretation on the original data. PCAtools provides functions for data exploration via PCA, and allows the user to generate publication-ready figures. PCA is performed via BiocSingular - users can also identify optimal number of principal components via different metrics, such as elbow method and Horn''s parallel analysis, which has relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high dimensional mass cytometry data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pchicdata/meta.yaml b/recipes/bioconductor-pchicdata/meta.yaml index ab00c43103068..e75ed7451718e 100644 --- a/recipes/bioconductor-pchicdata/meta.yaml +++ b/recipes/bioconductor-pchicdata/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "PCHiCdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8791902075a44ae03c0366150aa3f61e +about: + description: Subsets of Promoter Capture Hi-C data conveniently packaged for Chicago users. Data includes interactions detected for chromosomes 20 and 21 in GM12878 cells and for chromosomes 18 and 19 in mESC. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Promoter Capture Hi-C data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pchicdata", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-pchicdata + path: recipes/bioconductor-pchicdata + version: 1.8.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat, BiocStyle, knitr requirements: host: - - 'bioconductor-chicago >=1.30.0,<1.31.0' + - bioconductor-chicago >=1.34.0,<1.35.0 - r-base run: - - 'bioconductor-chicago >=1.30.0,<1.31.0' + - bioconductor-chicago >=1.34.0,<1.35.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 77d9d2d9ac8fb77a6c4824c15a0cac64 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Promoter Capture Hi-C data' - description: 'Subsets of Promoter Capture Hi-C data conveniently packaged for Chicago users. Data includes interactions detected for chromosomes 20 and 21 in GM12878 cells and for chromosomes 18 and 19 in mESC.' -extra: - parent_recipe: - name: bioconductor-pchicdata - path: recipes/bioconductor-pchicdata - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pchicdata/post-link.sh b/recipes/bioconductor-pchicdata/post-link.sh index 3ab10ccd183c5..98a45027c3852 100644 --- a/recipes/bioconductor-pchicdata/post-link.sh +++ b/recipes/bioconductor-pchicdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pchicdata-1.30.0" +installBiocDataPackage.sh "pchicdata-1.34.0" diff --git a/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/meta.yaml b/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/meta.yaml index d5211fafad4a4..00991a7011aa8 100644 --- a/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/meta.yaml +++ b/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/meta.yaml @@ -1,49 +1,54 @@ {% set version = "0.99.4" %} {% set name = "pd.081229.hg18.promoter.medip.hx1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for NimbleGen 081229_hg18_promoter_medip_hx1 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for NimbleGen 081229_hg18_promoter_medip_hx1 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f3c240fa0d4503e94047be5ee323856b build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.081229.hg18.promoter.medip.hx1", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base - r-dbi - - 'r-rsqlite >=0.7-1' + - r-rsqlite >=0.7-1 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base - r-dbi - - 'r-rsqlite >=0.7-1' + - r-rsqlite >=0.7-1 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: f3c240fa0d4503e94047be5ee323856b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for NimbleGen 081229_hg18_promoter_medip_hx1' - description: 'Platform Design Info for NimbleGen 081229_hg18_promoter_medip_hx1' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/meta.yaml b/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/meta.yaml index 608d949b2763d..73fd126945405 100644 --- a/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/meta.yaml +++ b/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/meta.yaml @@ -1,49 +1,54 @@ {% set version = "1.8.1" %} {% set name = "pd.2006.07.18.hg18.refseq.promoter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for NimbleGen 2006-07-18_hg18_refseq_promoter + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for NimbleGen 2006-07-18_hg18_refseq_promoter -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 00838332d75b82d212078a9957f495df build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.2006.07.18.hg18.refseq.promoter", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base - r-dbi - - 'r-rsqlite >=0.11.1' + - r-rsqlite >=0.11.1 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base - r-dbi - - 'r-rsqlite >=0.11.1' + - r-rsqlite >=0.11.1 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 00838332d75b82d212078a9957f495df + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for NimbleGen 2006-07-18_hg18_refseq_promoter' - description: 'Platform Design Info for NimbleGen 2006-07-18_hg18_refseq_promoter' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/meta.yaml b/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/meta.yaml index fa0edeb2bdc22..980e01198d11a 100644 --- a/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/meta.yaml +++ b/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/meta.yaml @@ -1,49 +1,54 @@ {% set version = "0.99.3" %} {% set name = "pd.2006.07.18.mm8.refseq.promoter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for NimbleGen 2006-07-18_mm8_refseq_promoter + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for NimbleGen 2006-07-18_mm8_refseq_promoter -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 084b0a6759fd96d1bc775dd4c66c42b0 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.2006.07.18.mm8.refseq.promoter", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base - r-dbi - - 'r-rsqlite >=0.7-1' + - r-rsqlite >=0.7-1 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base - r-dbi - - 'r-rsqlite >=0.7-1' + - r-rsqlite >=0.7-1 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 084b0a6759fd96d1bc775dd4c66c42b0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for NimbleGen 2006-07-18_mm8_refseq_promoter' - description: 'Platform Design Info for NimbleGen 2006-07-18_mm8_refseq_promoter' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/meta.yaml b/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/meta.yaml index fc6ff228ae8d5..8bd621f56051a 100644 --- a/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/meta.yaml +++ b/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/meta.yaml @@ -1,49 +1,54 @@ {% set version = "0.99.3" %} {% set name = "pd.2006.10.31.rn34.refseq.promoter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for NimbleGen 2006-10-31_rn34_refseq_promoter + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for NimbleGen 2006-10-31_rn34_refseq_promoter -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ab5bb767ad29b213e5a969a5fc51ee7d build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.2006.10.31.rn34.refseq.promoter", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base - r-dbi - - 'r-rsqlite >=0.7-1' + - r-rsqlite >=0.7-1 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base - r-dbi - - 'r-rsqlite >=0.7-1' + - r-rsqlite >=0.7-1 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: ab5bb767ad29b213e5a969a5fc51ee7d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for NimbleGen 2006-10-31_rn34_refseq_promoter' - description: 'Platform Design Info for NimbleGen 2006-10-31_rn34_refseq_promoter' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.ag/meta.yaml b/recipes/bioconductor-pd.ag/meta.yaml index 28b10f01dcf8b..ed9de887fd43f 100644 --- a/recipes/bioconductor-pd.ag/meta.yaml +++ b/recipes/bioconductor-pd.ag/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.ag" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name AG + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name AG -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 21fb288536568ff010ad4847b671f9d6 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.ag", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 21fb288536568ff010ad4847b671f9d6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name AG' - description: 'Platform Design Info for The Manufacturer''s Name AG' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.aragene.1.0.st/meta.yaml b/recipes/bioconductor-pd.aragene.1.0.st/meta.yaml index 626b8d0f92db1..a8022d66747da 100644 --- a/recipes/bioconductor-pd.aragene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.aragene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.aragene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix AraGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix AraGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ff87a0793fd4b713c4a45b6c1d4a4977 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.aragene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: ff87a0793fd4b713c4a45b6c1d4a4977 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix AraGene-1_0-st' - description: 'Platform Design Info for Affymetrix AraGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.aragene.1.1.st/meta.yaml b/recipes/bioconductor-pd.aragene.1.1.st/meta.yaml index 5393c826fa919..a17d40d861dea 100644 --- a/recipes/bioconductor-pd.aragene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.aragene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.aragene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix AraGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix AraGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 828ad790eb2495e396d7fcd9bcbf9133 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.aragene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 828ad790eb2495e396d7fcd9bcbf9133 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix AraGene-1_1-st' - description: 'Platform Design Info for Affymetrix AraGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.atdschip.tiling/meta.yaml b/recipes/bioconductor-pd.atdschip.tiling/meta.yaml index 998de9d485df6..c7bfa01107fc3 100644 --- a/recipes/bioconductor-pd.atdschip.tiling/meta.yaml +++ b/recipes/bioconductor-pd.atdschip.tiling/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "0.40.0" %} +{% set version = "0.44.0" %} {% set name = "pd.atdschip.tiling" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix Atdschip_tiling + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix Atdschip_tiling -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a81ffdc7dfb8eb04e09ec133db77d0d4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.atdschip.tiling", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dbi - - 'r-rsqlite >=0.10.0' + - r-rsqlite >=0.10.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dbi - - 'r-rsqlite >=0.10.0' + - r-rsqlite >=0.10.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 738e3686e09fe6833e550da18e79328a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix Atdschip_tiling' - description: 'Platform Design Info for Affymetrix Atdschip_tiling' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.atdschip.tiling/post-link.sh b/recipes/bioconductor-pd.atdschip.tiling/post-link.sh index 3b973708641a2..d5cd517364f06 100644 --- a/recipes/bioconductor-pd.atdschip.tiling/post-link.sh +++ b/recipes/bioconductor-pd.atdschip.tiling/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pd.atdschip.tiling-0.40.0" +installBiocDataPackage.sh "pd.atdschip.tiling-0.44.0" diff --git a/recipes/bioconductor-pd.ath1.121501/meta.yaml b/recipes/bioconductor-pd.ath1.121501/meta.yaml index 994ab7c1fec7b..1f3a554a5a5df 100644 --- a/recipes/bioconductor-pd.ath1.121501/meta.yaml +++ b/recipes/bioconductor-pd.ath1.121501/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.ath1.121501" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name ATH1-121501 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name ATH1-121501 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d7ed8640f0deac552e0083a091e72a72 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.ath1.121501", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: d7ed8640f0deac552e0083a091e72a72 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name ATH1-121501' - description: 'Platform Design Info for The Manufacturer''s Name ATH1-121501' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.barley1/meta.yaml b/recipes/bioconductor-pd.barley1/meta.yaml index de7dce84ec276..6bdec493c64e0 100644 --- a/recipes/bioconductor-pd.barley1/meta.yaml +++ b/recipes/bioconductor-pd.barley1/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.barley1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Barley1 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Barley1 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b8d11f5ad42e75f7a91931b46d449c1a build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.barley1", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: b8d11f5ad42e75f7a91931b46d449c1a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Barley1' - description: 'Platform Design Info for The Manufacturer''s Name Barley1' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.bovgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.bovgene.1.0.st/meta.yaml index 4d35be7142cfe..22ff7976effc2 100644 --- a/recipes/bioconductor-pd.bovgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.bovgene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.bovgene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix BovGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix BovGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6e9747d13aee7825722562ccc49ad35f build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.bovgene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 6e9747d13aee7825722562ccc49ad35f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix BovGene-1_0-st' - description: 'Platform Design Info for Affymetrix BovGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.bovgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.bovgene.1.1.st/meta.yaml index 8ff60cbe49df0..2032c1c2a137f 100644 --- a/recipes/bioconductor-pd.bovgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.bovgene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.bovgene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix BovGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix BovGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 342246c0a76755fcca458cd723b3e98e build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.bovgene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 342246c0a76755fcca458cd723b3e98e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix BovGene-1_1-st' - description: 'Platform Design Info for Affymetrix BovGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.bovine/meta.yaml b/recipes/bioconductor-pd.bovine/meta.yaml index 74ee2b7d78929..63746099127f5 100644 --- a/recipes/bioconductor-pd.bovine/meta.yaml +++ b/recipes/bioconductor-pd.bovine/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.bovine" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Bovine + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Bovine -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6c7026dba53b54b547b1f1e135d043b3 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.bovine", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 6c7026dba53b54b547b1f1e135d043b3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Bovine' - description: 'Platform Design Info for The Manufacturer''s Name Bovine' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.bsubtilis/meta.yaml b/recipes/bioconductor-pd.bsubtilis/meta.yaml index a22e19c9d4fdf..5d3688a81ebb1 100644 --- a/recipes/bioconductor-pd.bsubtilis/meta.yaml +++ b/recipes/bioconductor-pd.bsubtilis/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.bsubtilis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Bsubtilis + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Bsubtilis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2261d8b0ec178beb432d71eafd90ec9a build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.bsubtilis", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 2261d8b0ec178beb432d71eafd90ec9a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Bsubtilis' - description: 'Platform Design Info for The Manufacturer''s Name Bsubtilis' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.cangene.1.0.st/meta.yaml b/recipes/bioconductor-pd.cangene.1.0.st/meta.yaml index be8e5256dd995..44bc9e0ad459f 100644 --- a/recipes/bioconductor-pd.cangene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.cangene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.cangene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix CanGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix CanGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0a39d6378193e3f7d31a7210f6766eaf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.cangene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 0a39d6378193e3f7d31a7210f6766eaf + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix CanGene-1_0-st' - description: 'Platform Design Info for Affymetrix CanGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.cangene.1.1.st/meta.yaml b/recipes/bioconductor-pd.cangene.1.1.st/meta.yaml index a37c378d3bfbc..b1ac8ace8611d 100644 --- a/recipes/bioconductor-pd.cangene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.cangene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.cangene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix CanGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix CanGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 946074601e7bee72f3b3dd6ae6b3bc33 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.cangene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 946074601e7bee72f3b3dd6ae6b3bc33 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix CanGene-1_1-st' - description: 'Platform Design Info for Affymetrix CanGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.canine.2/meta.yaml b/recipes/bioconductor-pd.canine.2/meta.yaml index 41ddf9797e74f..2482c3e3ac332 100644 --- a/recipes/bioconductor-pd.canine.2/meta.yaml +++ b/recipes/bioconductor-pd.canine.2/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.canine.2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Canine_2 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Canine_2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bc918d1953a3c7ac7168b60a53405a93 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.canine.2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: bc918d1953a3c7ac7168b60a53405a93 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Canine_2' - description: 'Platform Design Info for The Manufacturer''s Name Canine_2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.canine/meta.yaml b/recipes/bioconductor-pd.canine/meta.yaml index e825b40089dc5..93f94ad16cd94 100644 --- a/recipes/bioconductor-pd.canine/meta.yaml +++ b/recipes/bioconductor-pd.canine/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.canine" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Canine + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Canine -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5b40fe9e40d0b7f36d338e413d121ba7 build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.canine", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 5b40fe9e40d0b7f36d338e413d121ba7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Canine' - description: 'Platform Design Info for The Manufacturer''s Name Canine' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.celegans/meta.yaml b/recipes/bioconductor-pd.celegans/meta.yaml index c905fedbbd292..98e523d8cfade 100644 --- a/recipes/bioconductor-pd.celegans/meta.yaml +++ b/recipes/bioconductor-pd.celegans/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.celegans" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Celegans + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Celegans -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b90ea2e071522bb340c103a1c8270205 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.celegans", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: b90ea2e071522bb340c103a1c8270205 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Celegans' - description: 'Platform Design Info for The Manufacturer''s Name Celegans' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.charm.hg18.example/meta.yaml b/recipes/bioconductor-pd.charm.hg18.example/meta.yaml index 86ae0af9f5bd9..3a3151fb33f94 100644 --- a/recipes/bioconductor-pd.charm.hg18.example/meta.yaml +++ b/recipes/bioconductor-pd.charm.hg18.example/meta.yaml @@ -1,49 +1,54 @@ {% set version = "0.99.4" %} {% set name = "pd.charm.hg18.example" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for NimbleGen charm_hg18_example + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for NimbleGen charm_hg18_example -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e201d4281a23c202f57bae1135e226b4 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.charm.hg18.example", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base - r-dbi - - 'r-rsqlite >=0.7-1' + - r-rsqlite >=0.7-1 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base - r-dbi - - 'r-rsqlite >=0.7-1' + - r-rsqlite >=0.7-1 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: e201d4281a23c202f57bae1135e226b4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for NimbleGen charm_hg18_example' - description: 'Platform Design Info for NimbleGen charm_hg18_example' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.chicken/meta.yaml b/recipes/bioconductor-pd.chicken/meta.yaml index 8a7c80e514a6c..5f6fdc126ea61 100644 --- a/recipes/bioconductor-pd.chicken/meta.yaml +++ b/recipes/bioconductor-pd.chicken/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.chicken" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Chicken + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Chicken -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: af79b6d0910621910e72ea374499e5eb build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.chicken", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: af79b6d0910621910e72ea374499e5eb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Chicken' - description: 'Platform Design Info for The Manufacturer''s Name Chicken' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.chigene.1.0.st/meta.yaml b/recipes/bioconductor-pd.chigene.1.0.st/meta.yaml index 566afb7f346b2..aa921a986d9a4 100644 --- a/recipes/bioconductor-pd.chigene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.chigene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.chigene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix ChiGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix ChiGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e37cb047678fabb1801109d4efd16773 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.chigene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: e37cb047678fabb1801109d4efd16773 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix ChiGene-1_0-st' - description: 'Platform Design Info for Affymetrix ChiGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.chigene.1.1.st/meta.yaml b/recipes/bioconductor-pd.chigene.1.1.st/meta.yaml index 8db3bb63df879..be078f6307e12 100644 --- a/recipes/bioconductor-pd.chigene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.chigene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.chigene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix ChiGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix ChiGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bec602b45961607f5a4571977d54e015 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.chigene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: bec602b45961607f5a4571977d54e015 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix ChiGene-1_1-st' - description: 'Platform Design Info for Affymetrix ChiGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.chogene.2.0.st/meta.yaml b/recipes/bioconductor-pd.chogene.2.0.st/meta.yaml index 839f379c0b0a9..64c6b4fa579fd 100644 --- a/recipes/bioconductor-pd.chogene.2.0.st/meta.yaml +++ b/recipes/bioconductor-pd.chogene.2.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.chogene.2.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix CHOGene-2_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix CHOGene-2_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 641718e3d172838185a200bac3d32433 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.chogene.2.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 641718e3d172838185a200bac3d32433 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix CHOGene-2_0-st' - description: 'Platform Design Info for Affymetrix CHOGene-2_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.chogene.2.1.st/meta.yaml b/recipes/bioconductor-pd.chogene.2.1.st/meta.yaml index 5a6d320121240..8500d129b4c15 100644 --- a/recipes/bioconductor-pd.chogene.2.1.st/meta.yaml +++ b/recipes/bioconductor-pd.chogene.2.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.chogene.2.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix CHOGene-2_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix CHOGene-2_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ed25825e58a514cdde70b961bce9b4d7 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.chogene.2.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: ed25825e58a514cdde70b961bce9b4d7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix CHOGene-2_1-st' - description: 'Platform Design Info for Affymetrix CHOGene-2_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.citrus/meta.yaml b/recipes/bioconductor-pd.citrus/meta.yaml index ff50b6ed856a3..53225592cd4aa 100644 --- a/recipes/bioconductor-pd.citrus/meta.yaml +++ b/recipes/bioconductor-pd.citrus/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.citrus" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Citrus + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Citrus -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dee9b3298b84e7dd5152f48ad449b15a build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.citrus", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: dee9b3298b84e7dd5152f48ad449b15a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Citrus' - description: 'Platform Design Info for The Manufacturer''s Name Citrus' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.clariom.d.human/meta.yaml b/recipes/bioconductor-pd.clariom.d.human/meta.yaml index 69c689cf4964b..da90d1bc78497 100644 --- a/recipes/bioconductor-pd.clariom.d.human/meta.yaml +++ b/recipes/bioconductor-pd.clariom.d.human/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.d.human" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix Clariom_D_Human + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix Clariom_D_Human -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9d3505af53cc7c99980f29c527f0f37d build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.d.human", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 9d3505af53cc7c99980f29c527f0f37d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix Clariom_D_Human' - description: 'Platform Design Info for Affymetrix Clariom_D_Human' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.clariom.s.human.ht/meta.yaml b/recipes/bioconductor-pd.clariom.s.human.ht/meta.yaml index aa251a19d8271..5b17f27076c45 100644 --- a/recipes/bioconductor-pd.clariom.s.human.ht/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.human.ht/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.human.ht" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix Clariom_S_Human_HT + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix Clariom_S_Human_HT -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 90f910bea1b1aeb550a3f1bdd91d1a06 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.s.human.ht", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 90f910bea1b1aeb550a3f1bdd91d1a06 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix Clariom_S_Human_HT' - description: 'Platform Design Info for Affymetrix Clariom_S_Human_HT' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.clariom.s.human/meta.yaml b/recipes/bioconductor-pd.clariom.s.human/meta.yaml index 883abafec76d4..a5415dd753511 100644 --- a/recipes/bioconductor-pd.clariom.s.human/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.human/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.human" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix Clariom_S_Human + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix Clariom_S_Human -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 797afe8a6a8041453a34ced3cce34884 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.s.human", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 797afe8a6a8041453a34ced3cce34884 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix Clariom_S_Human' - description: 'Platform Design Info for Affymetrix Clariom_S_Human' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.clariom.s.mouse.ht/meta.yaml b/recipes/bioconductor-pd.clariom.s.mouse.ht/meta.yaml index 01a66173dfb16..e9daeb01b7ca9 100644 --- a/recipes/bioconductor-pd.clariom.s.mouse.ht/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.mouse.ht/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.mouse.ht" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix Clariom_S_Mouse_HT + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix Clariom_S_Mouse_HT -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9cb6f77cf9666a0d54e1eacb904fd57c build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.s.mouse.ht", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 9cb6f77cf9666a0d54e1eacb904fd57c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix Clariom_S_Mouse_HT' - description: 'Platform Design Info for Affymetrix Clariom_S_Mouse_HT' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.clariom.s.mouse/meta.yaml b/recipes/bioconductor-pd.clariom.s.mouse/meta.yaml index 6339960068e70..612b278554d72 100644 --- a/recipes/bioconductor-pd.clariom.s.mouse/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.mouse/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.mouse" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix Clariom_S_Mouse + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix Clariom_S_Mouse -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e3e4ce2b22a78faf525dd6c0c0b2a42d build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.s.mouse", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: e3e4ce2b22a78faf525dd6c0c0b2a42d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix Clariom_S_Mouse' - description: 'Platform Design Info for Affymetrix Clariom_S_Mouse' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.clariom.s.rat.ht/meta.yaml b/recipes/bioconductor-pd.clariom.s.rat.ht/meta.yaml index 057c509ee1c90..4fa52dd185d2d 100644 --- a/recipes/bioconductor-pd.clariom.s.rat.ht/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.rat.ht/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.rat.ht" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix Clariom_S_Rat_HT + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix Clariom_S_Rat_HT -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: be901eb9e8830f3e5bedf154189a3743 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.s.rat.ht", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: be901eb9e8830f3e5bedf154189a3743 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix Clariom_S_Rat_HT' - description: 'Platform Design Info for Affymetrix Clariom_S_Rat_HT' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.clariom.s.rat/meta.yaml b/recipes/bioconductor-pd.clariom.s.rat/meta.yaml index 92289bca2dfa0..e47495a193bb8 100644 --- a/recipes/bioconductor-pd.clariom.s.rat/meta.yaml +++ b/recipes/bioconductor-pd.clariom.s.rat/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.clariom.s.rat" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix Clariom_S_Rat + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix Clariom_S_Rat -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: be464b3eaea8eb8bdbcca6047fce4dea build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.clariom.s.rat", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: be464b3eaea8eb8bdbcca6047fce4dea + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix Clariom_S_Rat' - description: 'Platform Design Info for Affymetrix Clariom_S_Rat' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.cotton/meta.yaml b/recipes/bioconductor-pd.cotton/meta.yaml index b086689a2b42f..7c06ce2b0d53e 100644 --- a/recipes/bioconductor-pd.cotton/meta.yaml +++ b/recipes/bioconductor-pd.cotton/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.cotton" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Cotton + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Cotton -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 78c408902bcefb8c695119767534b393 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.cotton", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 78c408902bcefb8c695119767534b393 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Cotton' - description: 'Platform Design Info for The Manufacturer''s Name Cotton' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.cyngene.1.0.st/meta.yaml b/recipes/bioconductor-pd.cyngene.1.0.st/meta.yaml index 63fe0e2e116cf..069769b4a3380 100644 --- a/recipes/bioconductor-pd.cyngene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.cyngene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.cyngene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix CynGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix CynGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 784fac6cc92a0fe46dae32c9b737812a build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.cyngene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 784fac6cc92a0fe46dae32c9b737812a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix CynGene-1_0-st' - description: 'Platform Design Info for Affymetrix CynGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.cyngene.1.1.st/meta.yaml b/recipes/bioconductor-pd.cyngene.1.1.st/meta.yaml index ee76fadc3b263..b9b6191a03dd7 100644 --- a/recipes/bioconductor-pd.cyngene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.cyngene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.cyngene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix CynGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix CynGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a6217267e3e08a15f70c600918c7d4f6 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.cyngene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: a6217267e3e08a15f70c600918c7d4f6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix CynGene-1_1-st' - description: 'Platform Design Info for Affymetrix CynGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.cyrgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.cyrgene.1.0.st/meta.yaml index 9862258a4d044..f40931d7939e3 100644 --- a/recipes/bioconductor-pd.cyrgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.cyrgene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.cyrgene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix CyRGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix CyRGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 63228c07d3d16d6c62e9c0e83f10a855 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.cyrgene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 63228c07d3d16d6c62e9c0e83f10a855 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix CyRGene-1_0-st' - description: 'Platform Design Info for Affymetrix CyRGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.cyrgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.cyrgene.1.1.st/meta.yaml index e0cf4deb6049c..dfa27ff61f99a 100644 --- a/recipes/bioconductor-pd.cyrgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.cyrgene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.cyrgene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix CyRGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix CyRGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dbe3bb580b96aaddcc597de45159320d build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.cyrgene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: dbe3bb580b96aaddcc597de45159320d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix CyRGene-1_1-st' - description: 'Platform Design Info for Affymetrix CyRGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.cytogenetics.array/meta.yaml b/recipes/bioconductor-pd.cytogenetics.array/meta.yaml index cc6d19032f9c6..25d5cb25ab2f4 100644 --- a/recipes/bioconductor-pd.cytogenetics.array/meta.yaml +++ b/recipes/bioconductor-pd.cytogenetics.array/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.cytogenetics.array" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix Cytogenetics_Array + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix Cytogenetics_Array -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8c359ff56a9a558d370dc9a6a54218e0 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.cytogenetics.array", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 8c359ff56a9a558d370dc9a6a54218e0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix Cytogenetics_Array' - description: 'Platform Design Info for Affymetrix Cytogenetics_Array' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.drogene.1.0.st/meta.yaml b/recipes/bioconductor-pd.drogene.1.0.st/meta.yaml index 00cff01593c5b..b14163bce48a9 100644 --- a/recipes/bioconductor-pd.drogene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.drogene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.drogene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix DroGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix DroGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 67f92a97a5b78a95693edfdd32b67e93 build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.drogene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 67f92a97a5b78a95693edfdd32b67e93 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix DroGene-1_0-st' - description: 'Platform Design Info for Affymetrix DroGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.drogene.1.1.st/meta.yaml b/recipes/bioconductor-pd.drogene.1.1.st/meta.yaml index 3f2c2a0e4aea8..664f8e5716a45 100644 --- a/recipes/bioconductor-pd.drogene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.drogene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.drogene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix DroGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix DroGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5c63236ea91390d49dbabea63a48f0a2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.drogene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 5c63236ea91390d49dbabea63a48f0a2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix DroGene-1_1-st' - description: 'Platform Design Info for Affymetrix DroGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.drosgenome1/meta.yaml b/recipes/bioconductor-pd.drosgenome1/meta.yaml index e6a9cb0bbd747..fd94cd43dd8d0 100644 --- a/recipes/bioconductor-pd.drosgenome1/meta.yaml +++ b/recipes/bioconductor-pd.drosgenome1/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.drosgenome1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name DrosGenome1 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name DrosGenome1 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 59c1a37a7d6a43fc70ff8756bf1195ef build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.drosgenome1", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 59c1a37a7d6a43fc70ff8756bf1195ef + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name DrosGenome1' - description: 'Platform Design Info for The Manufacturer''s Name DrosGenome1' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.drosophila.2/meta.yaml b/recipes/bioconductor-pd.drosophila.2/meta.yaml index ce040c054161a..13a8c19aaf5f7 100644 --- a/recipes/bioconductor-pd.drosophila.2/meta.yaml +++ b/recipes/bioconductor-pd.drosophila.2/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.drosophila.2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Drosophila_2 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Drosophila_2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ddb821e35e722af8dcf0807c6da4fac1 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.drosophila.2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: ddb821e35e722af8dcf0807c6da4fac1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Drosophila_2' - description: 'Platform Design Info for The Manufacturer''s Name Drosophila_2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.e.coli.2/meta.yaml b/recipes/bioconductor-pd.e.coli.2/meta.yaml index 65befa3aa9ca4..9ed82e9b8ae3b 100644 --- a/recipes/bioconductor-pd.e.coli.2/meta.yaml +++ b/recipes/bioconductor-pd.e.coli.2/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.e.coli.2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name E_coli_2 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name E_coli_2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9176faa60a0c252a815b2a74d2f63dd4 build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.e.coli.2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 9176faa60a0c252a815b2a74d2f63dd4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name E_coli_2' - description: 'Platform Design Info for The Manufacturer''s Name E_coli_2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.ecoli.asv2/meta.yaml b/recipes/bioconductor-pd.ecoli.asv2/meta.yaml index 9bff540ced298..9bce0c5541ce2 100644 --- a/recipes/bioconductor-pd.ecoli.asv2/meta.yaml +++ b/recipes/bioconductor-pd.ecoli.asv2/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.ecoli.asv2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Ecoli_ASv2 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Ecoli_ASv2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d789ddf5a178a9a50c5587ee3ab294a4 build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.ecoli.asv2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: d789ddf5a178a9a50c5587ee3ab294a4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Ecoli_ASv2' - description: 'Platform Design Info for The Manufacturer''s Name Ecoli_ASv2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.ecoli/meta.yaml b/recipes/bioconductor-pd.ecoli/meta.yaml index faee4d2687af3..28d89d11e956e 100644 --- a/recipes/bioconductor-pd.ecoli/meta.yaml +++ b/recipes/bioconductor-pd.ecoli/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.ecoli" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Ecoli + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Ecoli -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 077e91b2567a32780305f0fb6b126fe9 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.ecoli", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 077e91b2567a32780305f0fb6b126fe9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Ecoli' - description: 'Platform Design Info for The Manufacturer''s Name Ecoli' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.elegene.1.0.st/meta.yaml b/recipes/bioconductor-pd.elegene.1.0.st/meta.yaml index dea66c5327058..52f46435dd52f 100644 --- a/recipes/bioconductor-pd.elegene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.elegene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.elegene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix EleGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix EleGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b6110c58d5964703c7117e5e0668c901 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.elegene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: b6110c58d5964703c7117e5e0668c901 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix EleGene-1_0-st' - description: 'Platform Design Info for Affymetrix EleGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.elegene.1.1.st/meta.yaml b/recipes/bioconductor-pd.elegene.1.1.st/meta.yaml index cf32b4ff695a2..e59715dc6aaf3 100644 --- a/recipes/bioconductor-pd.elegene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.elegene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.elegene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix EleGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix EleGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1dbe166ea347a5a7e240db925d2081c7 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.elegene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 1dbe166ea347a5a7e240db925d2081c7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix EleGene-1_1-st' - description: 'Platform Design Info for Affymetrix EleGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.equgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.equgene.1.0.st/meta.yaml index 2ec09700424d3..fa1b10ba50391 100644 --- a/recipes/bioconductor-pd.equgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.equgene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.equgene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix EquGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix EquGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3448f36fdb899f04702be37ffab4c4c7 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.equgene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 3448f36fdb899f04702be37ffab4c4c7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix EquGene-1_0-st' - description: 'Platform Design Info for Affymetrix EquGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.equgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.equgene.1.1.st/meta.yaml index f5976ac239916..5ce0ff0d96fa2 100644 --- a/recipes/bioconductor-pd.equgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.equgene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.equgene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix EquGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix EquGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bed32525513ce25f14d433ce805e7d6c build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.equgene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: bed32525513ce25f14d433ce805e7d6c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix EquGene-1_1-st' - description: 'Platform Design Info for Affymetrix EquGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.feinberg.hg18.me.hx1/meta.yaml b/recipes/bioconductor-pd.feinberg.hg18.me.hx1/meta.yaml index fcc901394bc1c..be2fc085dae8c 100644 --- a/recipes/bioconductor-pd.feinberg.hg18.me.hx1/meta.yaml +++ b/recipes/bioconductor-pd.feinberg.hg18.me.hx1/meta.yaml @@ -1,49 +1,54 @@ {% set version = "0.99.3" %} {% set name = "pd.feinberg.hg18.me.hx1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for NimbleGen feinberg_hg18_me_hx1 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for NimbleGen feinberg_hg18_me_hx1 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b6eeaf79671bab6f597965009516ce57 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.feinberg.hg18.me.hx1", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base - r-dbi - - 'r-rsqlite >=0.7-1' + - r-rsqlite >=0.7-1 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base - r-dbi - - 'r-rsqlite >=0.7-1' + - r-rsqlite >=0.7-1 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: b6eeaf79671bab6f597965009516ce57 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for NimbleGen feinberg_hg18_me_hx1' - description: 'Platform Design Info for NimbleGen feinberg_hg18_me_hx1' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.feinberg.mm8.me.hx1/meta.yaml b/recipes/bioconductor-pd.feinberg.mm8.me.hx1/meta.yaml index 941ef51cff169..d3b3309671f9b 100644 --- a/recipes/bioconductor-pd.feinberg.mm8.me.hx1/meta.yaml +++ b/recipes/bioconductor-pd.feinberg.mm8.me.hx1/meta.yaml @@ -1,49 +1,54 @@ {% set version = "0.99.3" %} {% set name = "pd.feinberg.mm8.me.hx1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for NimbleGen feinberg_mm8_me_hx1 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for NimbleGen feinberg_mm8_me_hx1 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7332102b69fc9ee087f52d3cdc311d00 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.feinberg.mm8.me.hx1", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base - r-dbi - - 'r-rsqlite >=0.7-1' + - r-rsqlite >=0.7-1 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base - r-dbi - - 'r-rsqlite >=0.7-1' + - r-rsqlite >=0.7-1 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 7332102b69fc9ee087f52d3cdc311d00 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for NimbleGen feinberg_mm8_me_hx1' - description: 'Platform Design Info for NimbleGen feinberg_mm8_me_hx1' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.felgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.felgene.1.0.st/meta.yaml index 96ca01bb821b7..8a12117142038 100644 --- a/recipes/bioconductor-pd.felgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.felgene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.felgene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix FelGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix FelGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b7ac0a5cbde5f248aac5d0a7422bd88d build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.felgene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: b7ac0a5cbde5f248aac5d0a7422bd88d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix FelGene-1_0-st' - description: 'Platform Design Info for Affymetrix FelGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.felgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.felgene.1.1.st/meta.yaml index aa2ec52c8c490..1453f30ba1dd7 100644 --- a/recipes/bioconductor-pd.felgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.felgene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.felgene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix FelGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix FelGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 734807a7f3608f6c44c76df7eee04c99 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.felgene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 734807a7f3608f6c44c76df7eee04c99 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix FelGene-1_1-st' - description: 'Platform Design Info for Affymetrix FelGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.fingene.1.0.st/meta.yaml b/recipes/bioconductor-pd.fingene.1.0.st/meta.yaml index aac9805b9a463..188c77d6261cc 100644 --- a/recipes/bioconductor-pd.fingene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.fingene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.fingene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix FinGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix FinGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b79e4f8a52cad3b62e32401bbe74603d build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.fingene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: b79e4f8a52cad3b62e32401bbe74603d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix FinGene-1_0-st' - description: 'Platform Design Info for Affymetrix FinGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.fingene.1.1.st/meta.yaml b/recipes/bioconductor-pd.fingene.1.1.st/meta.yaml index 543282bb74fc8..532de0e6202d7 100644 --- a/recipes/bioconductor-pd.fingene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.fingene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.fingene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix FinGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix FinGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 29030b14a0e8f8073874fb694a8c0c09 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.fingene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 29030b14a0e8f8073874fb694a8c0c09 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix FinGene-1_1-st' - description: 'Platform Design Info for Affymetrix FinGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.genomewidesnp.5/meta.yaml b/recipes/bioconductor-pd.genomewidesnp.5/meta.yaml index a9f3b15e3ee6d..25d8a5b3f1667 100644 --- a/recipes/bioconductor-pd.genomewidesnp.5/meta.yaml +++ b/recipes/bioconductor-pd.genomewidesnp.5/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.genomewidesnp.5" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix GenomeWideSNP_5 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix GenomeWideSNP_5 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d02255c861e82fca6a7445ada0c69e5d build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.genomewidesnp.5", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: d02255c861e82fca6a7445ada0c69e5d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix GenomeWideSNP_5' - description: 'Platform Design Info for Affymetrix GenomeWideSNP_5' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.genomewidesnp.6/meta.yaml b/recipes/bioconductor-pd.genomewidesnp.6/meta.yaml index b6b0437fd72fd..47db32a5eec95 100644 --- a/recipes/bioconductor-pd.genomewidesnp.6/meta.yaml +++ b/recipes/bioconductor-pd.genomewidesnp.6/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.genomewidesnp.6" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix GenomeWideSNP_6 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix GenomeWideSNP_6 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6e5369234e251c763f4f6c0220fbcb0c build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.genomewidesnp.6", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 6e5369234e251c763f4f6c0220fbcb0c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix GenomeWideSNP_6' - description: 'Platform Design Info for Affymetrix GenomeWideSNP_6' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.guigene.1.0.st/meta.yaml b/recipes/bioconductor-pd.guigene.1.0.st/meta.yaml index d1840016e0d28..fa12a396bbeaa 100644 --- a/recipes/bioconductor-pd.guigene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.guigene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.guigene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix GuiGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix GuiGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 29fe31499931836af72ddd0c7d06acfa build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.guigene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 29fe31499931836af72ddd0c7d06acfa + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix GuiGene-1_0-st' - description: 'Platform Design Info for Affymetrix GuiGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.guigene.1.1.st/meta.yaml b/recipes/bioconductor-pd.guigene.1.1.st/meta.yaml index 6c1aedcc5bf9d..c3b1b1d4d211a 100644 --- a/recipes/bioconductor-pd.guigene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.guigene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.guigene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix GuiGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix GuiGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aa3e0389c596a3676322104de5ad2358 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.guigene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: aa3e0389c596a3676322104de5ad2358 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix GuiGene-1_1-st' - description: 'Platform Design Info for Affymetrix GuiGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hc.g110/meta.yaml b/recipes/bioconductor-pd.hc.g110/meta.yaml index dce97b5d9dd19..10d40f43613da 100644 --- a/recipes/bioconductor-pd.hc.g110/meta.yaml +++ b/recipes/bioconductor-pd.hc.g110/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.hc.g110" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name HC_G110 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name HC_G110 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5c5418c588ed28e2fa088c7952c48b91 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hc.g110", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 5c5418c588ed28e2fa088c7952c48b91 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name HC_G110' - description: 'Platform Design Info for The Manufacturer''s Name HC_G110' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hg.focus/meta.yaml b/recipes/bioconductor-pd.hg.focus/meta.yaml index 07333501d804f..227b5816fce08 100644 --- a/recipes/bioconductor-pd.hg.focus/meta.yaml +++ b/recipes/bioconductor-pd.hg.focus/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.focus" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name HG-Focus + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name HG-Focus -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a89f344ae7ff8061a8e7968f155f4bcf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hg.focus", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: a89f344ae7ff8061a8e7968f155f4bcf + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name HG-Focus' - description: 'Platform Design Info for The Manufacturer''s Name HG-Focus' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hg.u133.plus.2/meta.yaml b/recipes/bioconductor-pd.hg.u133.plus.2/meta.yaml index 7c7d03a5cbfbd..eeb494b8198e2 100644 --- a/recipes/bioconductor-pd.hg.u133.plus.2/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133.plus.2/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133.plus.2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name HG-U133_Plus_2 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name HG-U133_Plus_2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8a87aa63c04e84266962bdde5226c06c build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u133.plus.2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 8a87aa63c04e84266962bdde5226c06c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name HG-U133_Plus_2' - description: 'Platform Design Info for The Manufacturer''s Name HG-U133_Plus_2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hg.u133a.2/meta.yaml b/recipes/bioconductor-pd.hg.u133a.2/meta.yaml index aa934add79651..29214d2be852b 100644 --- a/recipes/bioconductor-pd.hg.u133a.2/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133a.2/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133a.2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name HG-U133A_2 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name HG-U133A_2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a7941473bf081831fad4f4412023d9ee build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u133a.2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: a7941473bf081831fad4f4412023d9ee + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name HG-U133A_2' - description: 'Platform Design Info for The Manufacturer''s Name HG-U133A_2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hg.u133a.tag/meta.yaml b/recipes/bioconductor-pd.hg.u133a.tag/meta.yaml index 966e51ee906c8..ca9f5f032b7f2 100644 --- a/recipes/bioconductor-pd.hg.u133a.tag/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133a.tag/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133a.tag" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name HG-U133A_tag + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name HG-U133A_tag -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e090383098d6e1062b290889fba065d5 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u133a.tag", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: e090383098d6e1062b290889fba065d5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name HG-U133A_tag' - description: 'Platform Design Info for The Manufacturer''s Name HG-U133A_tag' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hg.u133a/meta.yaml b/recipes/bioconductor-pd.hg.u133a/meta.yaml index fd20c37e93ead..08debd8fb71d2 100644 --- a/recipes/bioconductor-pd.hg.u133a/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133a/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133a" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name HG-U133A + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name HG-U133A -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 05b4521f65ab294a5040a0c60198d22c build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u133a", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 05b4521f65ab294a5040a0c60198d22c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name HG-U133A' - description: 'Platform Design Info for The Manufacturer''s Name HG-U133A' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hg.u133b/meta.yaml b/recipes/bioconductor-pd.hg.u133b/meta.yaml index 4bfe9bab4a6e3..6c15738e78441 100644 --- a/recipes/bioconductor-pd.hg.u133b/meta.yaml +++ b/recipes/bioconductor-pd.hg.u133b/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u133b" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name HG-U133B + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name HG-U133B -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c5eac82ad7480571b9f2b442b4a8faa6 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u133b", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: c5eac82ad7480571b9f2b442b4a8faa6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name HG-U133B' - description: 'Platform Design Info for The Manufacturer''s Name HG-U133B' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hg.u219/meta.yaml b/recipes/bioconductor-pd.hg.u219/meta.yaml index f55dc3f703be2..8d3611d23fb31 100644 --- a/recipes/bioconductor-pd.hg.u219/meta.yaml +++ b/recipes/bioconductor-pd.hg.u219/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u219" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name HG-U219 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name HG-U219 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dab073d315af47ff3001c72a6d1e7972 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u219", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: dab073d315af47ff3001c72a6d1e7972 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name HG-U219' - description: 'Platform Design Info for The Manufacturer''s Name HG-U219' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hg.u95a/meta.yaml b/recipes/bioconductor-pd.hg.u95a/meta.yaml index e66160602d507..285c7670c1301 100644 --- a/recipes/bioconductor-pd.hg.u95a/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95a/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95a" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name HG U95A + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name HG U95A -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a9ad7d6a085e0e3ed7623902e7810da0 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u95a", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: a9ad7d6a085e0e3ed7623902e7810da0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name HG U95A' - description: 'Platform Design Info for The Manufacturer''s Name HG U95A' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hg.u95av2/meta.yaml b/recipes/bioconductor-pd.hg.u95av2/meta.yaml index 95848bb127f5f..a8b40586567b8 100644 --- a/recipes/bioconductor-pd.hg.u95av2/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95av2/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95av2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name HG U95Av2 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name HG U95Av2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3a4182b529bc07ec91277a95b1462468 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u95av2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 3a4182b529bc07ec91277a95b1462468 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name HG U95Av2' - description: 'Platform Design Info for The Manufacturer''s Name HG U95Av2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hg.u95b/meta.yaml b/recipes/bioconductor-pd.hg.u95b/meta.yaml index 8d252d62d20d3..00710c982afdb 100644 --- a/recipes/bioconductor-pd.hg.u95b/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95b/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95b" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name HG U95B + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name HG U95B -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a7f10f91e920e191c5009fac8ca79c24 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u95b", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: a7f10f91e920e191c5009fac8ca79c24 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name HG U95B' - description: 'Platform Design Info for The Manufacturer''s Name HG U95B' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hg.u95c/meta.yaml b/recipes/bioconductor-pd.hg.u95c/meta.yaml index b498166f902ea..e16dad44e8d65 100644 --- a/recipes/bioconductor-pd.hg.u95c/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95c/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95c" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name HG U95C + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name HG U95C -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 85655bf7a9ecd7aaa867e05899c5e3e4 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u95c", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 85655bf7a9ecd7aaa867e05899c5e3e4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name HG U95C' - description: 'Platform Design Info for The Manufacturer''s Name HG U95C' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hg.u95d/meta.yaml b/recipes/bioconductor-pd.hg.u95d/meta.yaml index ee978c70f173e..4f20ba6918f76 100644 --- a/recipes/bioconductor-pd.hg.u95d/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95d/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95d" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name HG U95D + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name HG U95D -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 946701ecfc9cccb46aaeb57a4d6fe1c5 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u95d", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 946701ecfc9cccb46aaeb57a4d6fe1c5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name HG U95D' - description: 'Platform Design Info for The Manufacturer''s Name HG U95D' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hg.u95e/meta.yaml b/recipes/bioconductor-pd.hg.u95e/meta.yaml index 51b85127f3579..4315e9644cc77 100644 --- a/recipes/bioconductor-pd.hg.u95e/meta.yaml +++ b/recipes/bioconductor-pd.hg.u95e/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.hg.u95e" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name HG U95E + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name HG U95E -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9295e2fd1b4be6ff58477ea5a5de45ee build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hg.u95e", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 9295e2fd1b4be6ff58477ea5a5de45ee + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name HG U95E' - description: 'Platform Design Info for The Manufacturer''s Name HG U95E' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hg18.60mer.expr/meta.yaml b/recipes/bioconductor-pd.hg18.60mer.expr/meta.yaml index c94697cfd3954..b1d4351c4b2b2 100644 --- a/recipes/bioconductor-pd.hg18.60mer.expr/meta.yaml +++ b/recipes/bioconductor-pd.hg18.60mer.expr/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.hg18.60mer.expr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for NimbleGen hg18_60mer_expr + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for NimbleGen hg18_60mer_expr -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ee8d3813f74edce4e796933aa63999fb build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hg18.60mer.expr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: ee8d3813f74edce4e796933aa63999fb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for NimbleGen hg18_60mer_expr' - description: 'Platform Design Info for NimbleGen hg18_60mer_expr' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.ht.hg.u133.plus.pm/meta.yaml b/recipes/bioconductor-pd.ht.hg.u133.plus.pm/meta.yaml index f8c8caeeabca3..9cb44c3f8ec43 100644 --- a/recipes/bioconductor-pd.ht.hg.u133.plus.pm/meta.yaml +++ b/recipes/bioconductor-pd.ht.hg.u133.plus.pm/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.ht.hg.u133.plus.pm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name HT_HG-U133_Plus_PM + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name HT_HG-U133_Plus_PM -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5b1c3dd0ab3f8b21154982c197512a7c build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.ht.hg.u133.plus.pm", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 5b1c3dd0ab3f8b21154982c197512a7c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name HT_HG-U133_Plus_PM' - description: 'Platform Design Info for The Manufacturer''s Name HT_HG-U133_Plus_PM' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.ht.hg.u133a/meta.yaml b/recipes/bioconductor-pd.ht.hg.u133a/meta.yaml index 10d4330dd368f..b0febab4ea9a5 100644 --- a/recipes/bioconductor-pd.ht.hg.u133a/meta.yaml +++ b/recipes/bioconductor-pd.ht.hg.u133a/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.ht.hg.u133a" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name HT_HG-U133A + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name HT_HG-U133A -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 80a82f43083f95e1e9f5e2e2da2e288e build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.ht.hg.u133a", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 80a82f43083f95e1e9f5e2e2da2e288e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name HT_HG-U133A' - description: 'Platform Design Info for The Manufacturer''s Name HT_HG-U133A' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.ht.mg.430a/meta.yaml b/recipes/bioconductor-pd.ht.mg.430a/meta.yaml index 0ffa3f528e690..6291cce422fe5 100644 --- a/recipes/bioconductor-pd.ht.mg.430a/meta.yaml +++ b/recipes/bioconductor-pd.ht.mg.430a/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.ht.mg.430a" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name HT_MG-430A + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name HT_MG-430A -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 65ea4fae22d21ad70998ba3ea034dcc0 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.ht.mg.430a", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 65ea4fae22d21ad70998ba3ea034dcc0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name HT_MG-430A' - description: 'Platform Design Info for The Manufacturer''s Name HT_MG-430A' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hta.2.0/meta.yaml b/recipes/bioconductor-pd.hta.2.0/meta.yaml index 7e82318382efb..1fc9c8a8fee0b 100644 --- a/recipes/bioconductor-pd.hta.2.0/meta.yaml +++ b/recipes/bioconductor-pd.hta.2.0/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.2" %} {% set name = "pd.hta.2.0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix HTA-2_0 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix HTA-2_0 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8e13f85ece49c38da73eaf7b2247f5f0 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hta.2.0", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 8e13f85ece49c38da73eaf7b2247f5f0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix HTA-2_0' - description: 'Platform Design Info for Affymetrix HTA-2_0' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hu6800/meta.yaml b/recipes/bioconductor-pd.hu6800/meta.yaml index 9cb8265192e77..3d24c4d8bd22c 100644 --- a/recipes/bioconductor-pd.hu6800/meta.yaml +++ b/recipes/bioconductor-pd.hu6800/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.hu6800" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Hu6800 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Hu6800 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9a3a3edde6d6f31b9e90dc32aa68875d build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hu6800", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 9a3a3edde6d6f31b9e90dc32aa68875d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Hu6800' - description: 'Platform Design Info for The Manufacturer''s Name Hu6800' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.huex.1.0.st.v2/meta.yaml b/recipes/bioconductor-pd.huex.1.0.st.v2/meta.yaml index 92f4d90dcf4f9..aea8e8d079858 100644 --- a/recipes/bioconductor-pd.huex.1.0.st.v2/meta.yaml +++ b/recipes/bioconductor-pd.huex.1.0.st.v2/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.huex.1.0.st.v2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix HuEx-1_0-st-v2 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix HuEx-1_0-st-v2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f4c4836c53447890b75b012efbdef3e9 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.huex.1.0.st.v2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: f4c4836c53447890b75b012efbdef3e9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix HuEx-1_0-st-v2' - description: 'Platform Design Info for Affymetrix HuEx-1_0-st-v2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hugene.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.hugene.1.0.st.v1/meta.yaml index a6b0f80043946..9740420aeea37 100644 --- a/recipes/bioconductor-pd.hugene.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.hugene.1.0.st.v1/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.hugene.1.0.st.v1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix HuGene-1_0-st-v1 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix HuGene-1_0-st-v1 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8cb24c351aee5bf216180e4b19742506 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hugene.1.0.st.v1", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 8cb24c351aee5bf216180e4b19742506 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix HuGene-1_0-st-v1' - description: 'Platform Design Info for Affymetrix HuGene-1_0-st-v1' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hugene.1.1.st.v1/meta.yaml b/recipes/bioconductor-pd.hugene.1.1.st.v1/meta.yaml index bc8bf2b9c2ee4..a4872aa2b9317 100644 --- a/recipes/bioconductor-pd.hugene.1.1.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.hugene.1.1.st.v1/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.hugene.1.1.st.v1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix HuGene-1_1-st-v1 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix HuGene-1_1-st-v1 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7a17ee4f7d258792be1d21be7d03deb0 build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hugene.1.1.st.v1", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 7a17ee4f7d258792be1d21be7d03deb0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix HuGene-1_1-st-v1' - description: 'Platform Design Info for Affymetrix HuGene-1_1-st-v1' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hugene.2.0.st/meta.yaml b/recipes/bioconductor-pd.hugene.2.0.st/meta.yaml index aded0828efe02..b4723da892cb4 100644 --- a/recipes/bioconductor-pd.hugene.2.0.st/meta.yaml +++ b/recipes/bioconductor-pd.hugene.2.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.hugene.2.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix HuGene-2_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix HuGene-2_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e484209aa0c2a839c3445d91c1a799ce build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hugene.2.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: e484209aa0c2a839c3445d91c1a799ce + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix HuGene-2_0-st' - description: 'Platform Design Info for Affymetrix HuGene-2_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.hugene.2.1.st/meta.yaml b/recipes/bioconductor-pd.hugene.2.1.st/meta.yaml index 4ba83c112fde7..0eff3fd4b5cd6 100644 --- a/recipes/bioconductor-pd.hugene.2.1.st/meta.yaml +++ b/recipes/bioconductor-pd.hugene.2.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.hugene.2.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix HuGene-2_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix HuGene-2_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 164227f10b87f87059e4ae27b40f5238 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.hugene.2.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 164227f10b87f87059e4ae27b40f5238 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix HuGene-2_1-st' - description: 'Platform Design Info for Affymetrix HuGene-2_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.maize/meta.yaml b/recipes/bioconductor-pd.maize/meta.yaml index 6acdd12194b41..2a398ff078432 100644 --- a/recipes/bioconductor-pd.maize/meta.yaml +++ b/recipes/bioconductor-pd.maize/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.maize" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Maize + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Maize -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a1689518c8525d3dfa97e870f90b7a7b build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.maize", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: a1689518c8525d3dfa97e870f90b7a7b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Maize' - description: 'Platform Design Info for The Manufacturer''s Name Maize' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mapping250k.nsp/meta.yaml b/recipes/bioconductor-pd.mapping250k.nsp/meta.yaml index d662313ff247e..da4c9c61a3d92 100644 --- a/recipes/bioconductor-pd.mapping250k.nsp/meta.yaml +++ b/recipes/bioconductor-pd.mapping250k.nsp/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.mapping250k.nsp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix Mapping250K_Nsp + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix Mapping250K_Nsp -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2786d00e1d621a9c415a599b4afe838b build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mapping250k.nsp", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 2786d00e1d621a9c415a599b4afe838b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix Mapping250K_Nsp' - description: 'Platform Design Info for Affymetrix Mapping250K_Nsp' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mapping250k.sty/meta.yaml b/recipes/bioconductor-pd.mapping250k.sty/meta.yaml index 431d2f563a670..1185a8f8745d1 100644 --- a/recipes/bioconductor-pd.mapping250k.sty/meta.yaml +++ b/recipes/bioconductor-pd.mapping250k.sty/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.mapping250k.sty" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix Mapping250K_Sty + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix Mapping250K_Sty -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0db5992855eaf9b8f61f8bc2e57ef347 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mapping250k.sty", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 0db5992855eaf9b8f61f8bc2e57ef347 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix Mapping250K_Sty' - description: 'Platform Design Info for Affymetrix Mapping250K_Sty' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mapping50k.hind240/meta.yaml b/recipes/bioconductor-pd.mapping50k.hind240/meta.yaml index 22b5b5394c56e..c16bcc83fdeb1 100644 --- a/recipes/bioconductor-pd.mapping50k.hind240/meta.yaml +++ b/recipes/bioconductor-pd.mapping50k.hind240/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.mapping50k.hind240" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix Mapping50K_Hind240 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix Mapping50K_Hind240 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 83615dcb01eb381f0c69e07504809094 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mapping50k.hind240", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 83615dcb01eb381f0c69e07504809094 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix Mapping50K_Hind240' - description: 'Platform Design Info for Affymetrix Mapping50K_Hind240' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mapping50k.xba240/meta.yaml b/recipes/bioconductor-pd.mapping50k.xba240/meta.yaml index 351f1e536040b..b6a73774385ae 100644 --- a/recipes/bioconductor-pd.mapping50k.xba240/meta.yaml +++ b/recipes/bioconductor-pd.mapping50k.xba240/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.mapping50k.xba240" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix Mapping50K_Xba240 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix Mapping50K_Xba240 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eb0f9250fe0d7b590ca9938fee88f2e7 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mapping50k.xba240", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: eb0f9250fe0d7b590ca9938fee88f2e7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix Mapping50K_Xba240' - description: 'Platform Design Info for Affymetrix Mapping50K_Xba240' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.margene.1.0.st/meta.yaml b/recipes/bioconductor-pd.margene.1.0.st/meta.yaml index 6300298e4726a..54c1bf41e7463 100644 --- a/recipes/bioconductor-pd.margene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.margene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.margene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix MarGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix MarGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f670b192e4b453f13bb7cae154b5de42 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.margene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: f670b192e4b453f13bb7cae154b5de42 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix MarGene-1_0-st' - description: 'Platform Design Info for Affymetrix MarGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.margene.1.1.st/meta.yaml b/recipes/bioconductor-pd.margene.1.1.st/meta.yaml index 4a7d544a718bf..ba6cabfdbd80c 100644 --- a/recipes/bioconductor-pd.margene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.margene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.margene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix MarGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix MarGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: efd71aeb9c5ab36c2ddeccf9cb66ddec build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.margene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: efd71aeb9c5ab36c2ddeccf9cb66ddec + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix MarGene-1_1-st' - description: 'Platform Design Info for Affymetrix MarGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.medgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.medgene.1.0.st/meta.yaml index 408d867813d22..1e73365ffa3f8 100644 --- a/recipes/bioconductor-pd.medgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.medgene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.medgene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix MedGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix MedGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2a0048ccd5310ec5c45bb691f3c25885 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.medgene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 2a0048ccd5310ec5c45bb691f3c25885 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix MedGene-1_0-st' - description: 'Platform Design Info for Affymetrix MedGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.medgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.medgene.1.1.st/meta.yaml index f519411548246..2ec14f7d450a4 100644 --- a/recipes/bioconductor-pd.medgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.medgene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.medgene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix MedGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix MedGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d96894cfea509734af62110311100142 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.medgene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: d96894cfea509734af62110311100142 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix MedGene-1_1-st' - description: 'Platform Design Info for Affymetrix MedGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.medicago/meta.yaml b/recipes/bioconductor-pd.medicago/meta.yaml index 769fa2b2e172b..c5a5de9e24b96 100644 --- a/recipes/bioconductor-pd.medicago/meta.yaml +++ b/recipes/bioconductor-pd.medicago/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.medicago" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Medicago + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Medicago -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0e3f00777919374619a9dc8244167068 build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.medicago", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 0e3f00777919374619a9dc8244167068 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Medicago' - description: 'Platform Design Info for The Manufacturer''s Name Medicago' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mg.u74a/meta.yaml b/recipes/bioconductor-pd.mg.u74a/meta.yaml index e94ef1d820d7e..485c558911a54 100644 --- a/recipes/bioconductor-pd.mg.u74a/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74a/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74a" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name MG_U74A + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name MG_U74A -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a855c7d2b80e9b8f9bbc1a3f83aca799 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mg.u74a", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: a855c7d2b80e9b8f9bbc1a3f83aca799 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name MG_U74A' - description: 'Platform Design Info for The Manufacturer''s Name MG_U74A' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mg.u74av2/meta.yaml b/recipes/bioconductor-pd.mg.u74av2/meta.yaml index 12c4b3403f631..543675daa02e9 100644 --- a/recipes/bioconductor-pd.mg.u74av2/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74av2/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74av2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name MG_U74Av2 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name MG_U74Av2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 01c6e4da9c2ad0f1939482284dd5b421 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mg.u74av2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 01c6e4da9c2ad0f1939482284dd5b421 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name MG_U74Av2' - description: 'Platform Design Info for The Manufacturer''s Name MG_U74Av2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mg.u74b/meta.yaml b/recipes/bioconductor-pd.mg.u74b/meta.yaml index d3a265d3115ec..5775a094c86bd 100644 --- a/recipes/bioconductor-pd.mg.u74b/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74b/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74b" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name MG_U74B + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name MG_U74B -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 47bb81abaceba6dfaab3e0987f28706c build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mg.u74b", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 47bb81abaceba6dfaab3e0987f28706c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name MG_U74B' - description: 'Platform Design Info for The Manufacturer''s Name MG_U74B' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mg.u74bv2/meta.yaml b/recipes/bioconductor-pd.mg.u74bv2/meta.yaml index 3cba6e2bcbf62..5027f919f3037 100644 --- a/recipes/bioconductor-pd.mg.u74bv2/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74bv2/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74bv2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name MG_U74Bv2 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name MG_U74Bv2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dbb6cd5b16bd5cafbf654744bc2d5c5c build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mg.u74bv2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: dbb6cd5b16bd5cafbf654744bc2d5c5c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name MG_U74Bv2' - description: 'Platform Design Info for The Manufacturer''s Name MG_U74Bv2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mg.u74c/meta.yaml b/recipes/bioconductor-pd.mg.u74c/meta.yaml index d34eec569ed78..ec65ae8f50ace 100644 --- a/recipes/bioconductor-pd.mg.u74c/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74c/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74c" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name MG_U74C + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name MG_U74C -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 01f10eae99481f03d1d5a6a2c2f01733 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mg.u74c", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 01f10eae99481f03d1d5a6a2c2f01733 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name MG_U74C' - description: 'Platform Design Info for The Manufacturer''s Name MG_U74C' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mg.u74cv2/meta.yaml b/recipes/bioconductor-pd.mg.u74cv2/meta.yaml index dded57370137e..051bd3c636e52 100644 --- a/recipes/bioconductor-pd.mg.u74cv2/meta.yaml +++ b/recipes/bioconductor-pd.mg.u74cv2/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.mg.u74cv2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name MG_U74Cv2 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name MG_U74Cv2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b60943b90b95a24fcf93f8c245fd88be build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mg.u74cv2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: b60943b90b95a24fcf93f8c245fd88be + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name MG_U74Cv2' - description: 'Platform Design Info for The Manufacturer''s Name MG_U74Cv2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mirna.1.0/meta.yaml b/recipes/bioconductor-pd.mirna.1.0/meta.yaml index cc8a6f4292057..aa2ce42b100dc 100644 --- a/recipes/bioconductor-pd.mirna.1.0/meta.yaml +++ b/recipes/bioconductor-pd.mirna.1.0/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.mirna.1.0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name miRNA-1_0 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name miRNA-1_0 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8dfeb82a9da6d6f73e5fb716a2867a34 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mirna.1.0", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 8dfeb82a9da6d6f73e5fb716a2867a34 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name miRNA-1_0' - description: 'Platform Design Info for The Manufacturer''s Name miRNA-1_0' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mirna.2.0/meta.yaml b/recipes/bioconductor-pd.mirna.2.0/meta.yaml index 39fb38a4ddbc3..ac990d012107f 100644 --- a/recipes/bioconductor-pd.mirna.2.0/meta.yaml +++ b/recipes/bioconductor-pd.mirna.2.0/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.mirna.2.0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix miRNA-2_0 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix miRNA-2_0 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: aab53cbc62fbd7727ca0303aeb1dca13 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mirna.2.0", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: aab53cbc62fbd7727ca0303aeb1dca13 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix miRNA-2_0' - description: 'Platform Design Info for Affymetrix miRNA-2_0' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mirna.3.0/meta.yaml b/recipes/bioconductor-pd.mirna.3.0/meta.yaml index 1fa7ec6d77b92..148e1d11d8459 100644 --- a/recipes/bioconductor-pd.mirna.3.0/meta.yaml +++ b/recipes/bioconductor-pd.mirna.3.0/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.mirna.3.0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix miRNA-3_0 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix miRNA-3_0 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1265f1969c618b3b5121e6a77ba57009 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mirna.3.0", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 1265f1969c618b3b5121e6a77ba57009 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix miRNA-3_0' - description: 'Platform Design Info for Affymetrix miRNA-3_0' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mirna.3.1/meta.yaml b/recipes/bioconductor-pd.mirna.3.1/meta.yaml index 5efcf883ca1ee..1d49a8f61c06d 100644 --- a/recipes/bioconductor-pd.mirna.3.1/meta.yaml +++ b/recipes/bioconductor-pd.mirna.3.1/meta.yaml @@ -1,49 +1,54 @@ {% set version = "3.8.1" %} {% set name = "pd.mirna.3.1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix miRNA-3_1 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix miRNA-3_1 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 296b3584ee5e9416c9018353d3e29c6c build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mirna.3.1", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base - r-dbi - - 'r-rsqlite >=0.11.1' + - r-rsqlite >=0.11.1 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base - r-dbi - - 'r-rsqlite >=0.11.1' + - r-rsqlite >=0.11.1 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 296b3584ee5e9416c9018353d3e29c6c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix miRNA-3_1' - description: 'Platform Design Info for Affymetrix miRNA-3_1' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mirna.4.0/meta.yaml b/recipes/bioconductor-pd.mirna.4.0/meta.yaml index a3ad36ee6f9cf..c7cb91defc09f 100644 --- a/recipes/bioconductor-pd.mirna.4.0/meta.yaml +++ b/recipes/bioconductor-pd.mirna.4.0/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.mirna.4.0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix miRNA-4_0 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix miRNA-4_0 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cae1a18c02aaa20a2f05172103e9d938 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mirna.4.0", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: cae1a18c02aaa20a2f05172103e9d938 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix miRNA-4_0' - description: 'Platform Design Info for Affymetrix miRNA-4_0' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.moe430a/meta.yaml b/recipes/bioconductor-pd.moe430a/meta.yaml index e9ab0dd8f57dd..ad571d2e11fdc 100644 --- a/recipes/bioconductor-pd.moe430a/meta.yaml +++ b/recipes/bioconductor-pd.moe430a/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.moe430a" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name MOE430A + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name MOE430A -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f9a7cb62140e42c2a82177548a1c73fb build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.moe430a", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: f9a7cb62140e42c2a82177548a1c73fb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name MOE430A' - description: 'Platform Design Info for The Manufacturer''s Name MOE430A' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.moe430b/meta.yaml b/recipes/bioconductor-pd.moe430b/meta.yaml index 72a0e356ab58c..2d118501d1ec9 100644 --- a/recipes/bioconductor-pd.moe430b/meta.yaml +++ b/recipes/bioconductor-pd.moe430b/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.moe430b" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name MOE430B + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name MOE430B -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c19d2ee5e7e87703cf73afa33a5f3156 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.moe430b", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: c19d2ee5e7e87703cf73afa33a5f3156 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name MOE430B' - description: 'Platform Design Info for The Manufacturer''s Name MOE430B' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.moex.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.moex.1.0.st.v1/meta.yaml index d83f930bddeed..3d2a2acd8456a 100644 --- a/recipes/bioconductor-pd.moex.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.moex.1.0.st.v1/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.moex.1.0.st.v1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix MoEx-1_0-st-v1 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix MoEx-1_0-st-v1 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 57427e63b2d44258c12d796eada1897b build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.moex.1.0.st.v1", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 57427e63b2d44258c12d796eada1897b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix MoEx-1_0-st-v1' - description: 'Platform Design Info for Affymetrix MoEx-1_0-st-v1' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mogene.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.mogene.1.0.st.v1/meta.yaml index 890fc6f4cb1c6..1382af3965446 100644 --- a/recipes/bioconductor-pd.mogene.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.mogene.1.0.st.v1/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.mogene.1.0.st.v1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix MoGene-1_0-st-v1 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix MoGene-1_0-st-v1 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c3767385af3b9a120c777adb6d6e3364 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mogene.1.0.st.v1", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: c3767385af3b9a120c777adb6d6e3364 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix MoGene-1_0-st-v1' - description: 'Platform Design Info for Affymetrix MoGene-1_0-st-v1' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mogene.1.1.st.v1/meta.yaml b/recipes/bioconductor-pd.mogene.1.1.st.v1/meta.yaml index 09713fc997bd3..76f0ac423c272 100644 --- a/recipes/bioconductor-pd.mogene.1.1.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.mogene.1.1.st.v1/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.mogene.1.1.st.v1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix MoGene-1_1-st-v1 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix MoGene-1_1-st-v1 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3d6c5d29e4d8a0b0152e109b68f82c37 build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mogene.1.1.st.v1", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 3d6c5d29e4d8a0b0152e109b68f82c37 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix MoGene-1_1-st-v1' - description: 'Platform Design Info for Affymetrix MoGene-1_1-st-v1' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mogene.2.0.st/meta.yaml b/recipes/bioconductor-pd.mogene.2.0.st/meta.yaml index 9c9a7d684131a..03b2c6b5b7114 100644 --- a/recipes/bioconductor-pd.mogene.2.0.st/meta.yaml +++ b/recipes/bioconductor-pd.mogene.2.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.mogene.2.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix MoGene-2_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix MoGene-2_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 71326d6bd85de02490171696f923d053 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mogene.2.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 71326d6bd85de02490171696f923d053 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix MoGene-2_0-st' - description: 'Platform Design Info for Affymetrix MoGene-2_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mogene.2.1.st/meta.yaml b/recipes/bioconductor-pd.mogene.2.1.st/meta.yaml index 499af455820e9..05e328ef53842 100644 --- a/recipes/bioconductor-pd.mogene.2.1.st/meta.yaml +++ b/recipes/bioconductor-pd.mogene.2.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.mogene.2.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix MoGene-2_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix MoGene-2_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2c7fc5644eae98359cb945ff16d072a2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mogene.2.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 2c7fc5644eae98359cb945ff16d072a2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix MoGene-2_1-st' - description: 'Platform Design Info for Affymetrix MoGene-2_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mouse430.2/meta.yaml b/recipes/bioconductor-pd.mouse430.2/meta.yaml index 205b87d6bbb36..e922cdba2a0a0 100644 --- a/recipes/bioconductor-pd.mouse430.2/meta.yaml +++ b/recipes/bioconductor-pd.mouse430.2/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.mouse430.2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Mouse430_2 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Mouse430_2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7f37397a57b06d15101ef86fa6242ca4 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mouse430.2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 7f37397a57b06d15101ef86fa6242ca4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Mouse430_2' - description: 'Platform Design Info for The Manufacturer''s Name Mouse430_2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mouse430a.2/meta.yaml b/recipes/bioconductor-pd.mouse430a.2/meta.yaml index 328c8998bd334..5ac15482de81c 100644 --- a/recipes/bioconductor-pd.mouse430a.2/meta.yaml +++ b/recipes/bioconductor-pd.mouse430a.2/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.mouse430a.2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Mouse430A_2 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Mouse430A_2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0c28f564a1fa23f59c936d42c156796d build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mouse430a.2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 0c28f564a1fa23f59c936d42c156796d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Mouse430A_2' - description: 'Platform Design Info for The Manufacturer''s Name Mouse430A_2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mta.1.0/meta.yaml b/recipes/bioconductor-pd.mta.1.0/meta.yaml index 7deeae0d5bdfb..d2c070fff571c 100644 --- a/recipes/bioconductor-pd.mta.1.0/meta.yaml +++ b/recipes/bioconductor-pd.mta.1.0/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.mta.1.0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix MTA-1_0 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix MTA-1_0 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0f737b4f1f1353733e56e2df637f554b build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mta.1.0", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 0f737b4f1f1353733e56e2df637f554b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix MTA-1_0' - description: 'Platform Design Info for Affymetrix MTA-1_0' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mu11ksuba/meta.yaml b/recipes/bioconductor-pd.mu11ksuba/meta.yaml index 94eb4e26e996d..07e9263d53281 100644 --- a/recipes/bioconductor-pd.mu11ksuba/meta.yaml +++ b/recipes/bioconductor-pd.mu11ksuba/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.mu11ksuba" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Mu11KsubA + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Mu11KsubA -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 56be58b3f444ccb9572dc4c3882964b2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mu11ksuba", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 56be58b3f444ccb9572dc4c3882964b2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Mu11KsubA' - description: 'Platform Design Info for The Manufacturer''s Name Mu11KsubA' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.mu11ksubb/meta.yaml b/recipes/bioconductor-pd.mu11ksubb/meta.yaml index 11001e1c78fc9..3bcb4a1fd589a 100644 --- a/recipes/bioconductor-pd.mu11ksubb/meta.yaml +++ b/recipes/bioconductor-pd.mu11ksubb/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.mu11ksubb" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Mu11KsubB + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Mu11KsubB -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c45b0ebe777b99cec38499826cc1b457 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.mu11ksubb", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: c45b0ebe777b99cec38499826cc1b457 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Mu11KsubB' - description: 'Platform Design Info for The Manufacturer''s Name Mu11KsubB' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.nugo.hs1a520180/meta.yaml b/recipes/bioconductor-pd.nugo.hs1a520180/meta.yaml index 104d2cb3a3b15..e16d2930ce81d 100644 --- a/recipes/bioconductor-pd.nugo.hs1a520180/meta.yaml +++ b/recipes/bioconductor-pd.nugo.hs1a520180/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.4.0" %} {% set name = "pd.nugo.hs1a520180" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name NuGO_Hs1a520180 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name NuGO_Hs1a520180 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 88a836472f0f9aab2e1d54e4bad7d6af build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.nugo.hs1a520180", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 88a836472f0f9aab2e1d54e4bad7d6af + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name NuGO_Hs1a520180' - description: 'Platform Design Info for The Manufacturer''s Name NuGO_Hs1a520180' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.nugo.mm1a520177/meta.yaml b/recipes/bioconductor-pd.nugo.mm1a520177/meta.yaml index 3114b806849f1..61470082f9b78 100644 --- a/recipes/bioconductor-pd.nugo.mm1a520177/meta.yaml +++ b/recipes/bioconductor-pd.nugo.mm1a520177/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.4.0" %} {% set name = "pd.nugo.mm1a520177" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name NuGO_Mm1a520177 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name NuGO_Mm1a520177 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5cd64895eaddaf4cae1c48db9468c079 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.nugo.mm1a520177", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 5cd64895eaddaf4cae1c48db9468c079 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name NuGO_Mm1a520177' - description: 'Platform Design Info for The Manufacturer''s Name NuGO_Mm1a520177' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.ovigene.1.0.st/meta.yaml b/recipes/bioconductor-pd.ovigene.1.0.st/meta.yaml index 0127427f2b795..b6db8dfef1d87 100644 --- a/recipes/bioconductor-pd.ovigene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.ovigene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.ovigene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix OviGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix OviGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 88cfedfe10dd357539305051a69d31a1 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.ovigene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 88cfedfe10dd357539305051a69d31a1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix OviGene-1_0-st' - description: 'Platform Design Info for Affymetrix OviGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.ovigene.1.1.st/meta.yaml b/recipes/bioconductor-pd.ovigene.1.1.st/meta.yaml index 1c6bc4fd9fc71..d60a4d61eb158 100644 --- a/recipes/bioconductor-pd.ovigene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.ovigene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.ovigene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix OviGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix OviGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d6158cacd32a1892975fddd8dc8bb3f2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.ovigene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: d6158cacd32a1892975fddd8dc8bb3f2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix OviGene-1_1-st' - description: 'Platform Design Info for Affymetrix OviGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.pae.g1a/meta.yaml b/recipes/bioconductor-pd.pae.g1a/meta.yaml index 78b855cedb8e9..e6171a597e2e2 100644 --- a/recipes/bioconductor-pd.pae.g1a/meta.yaml +++ b/recipes/bioconductor-pd.pae.g1a/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.pae.g1a" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Pae_G1a + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Pae_G1a -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d96462eb35c63b30772bccae2a27a8cd build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.pae.g1a", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: d96462eb35c63b30772bccae2a27a8cd + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Pae_G1a' - description: 'Platform Design Info for The Manufacturer''s Name Pae_G1a' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.plasmodium.anopheles/meta.yaml b/recipes/bioconductor-pd.plasmodium.anopheles/meta.yaml index 5db40654cc0d4..d6d3ae6aebf3b 100644 --- a/recipes/bioconductor-pd.plasmodium.anopheles/meta.yaml +++ b/recipes/bioconductor-pd.plasmodium.anopheles/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.plasmodium.anopheles" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Plasmodium_Anopheles + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Plasmodium_Anopheles -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ae55b1451ceaed951f68213c0433f3d0 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.plasmodium.anopheles", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: ae55b1451ceaed951f68213c0433f3d0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Plasmodium_Anopheles' - description: 'Platform Design Info for The Manufacturer''s Name Plasmodium_Anopheles' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.poplar/meta.yaml b/recipes/bioconductor-pd.poplar/meta.yaml index 56d765944b6ab..662d84dc72012 100644 --- a/recipes/bioconductor-pd.poplar/meta.yaml +++ b/recipes/bioconductor-pd.poplar/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.poplar" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Poplar + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Poplar -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9c33b7528e5a47654aeacf61b71058a8 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.poplar", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 9c33b7528e5a47654aeacf61b71058a8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Poplar' - description: 'Platform Design Info for The Manufacturer''s Name Poplar' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.porcine/meta.yaml b/recipes/bioconductor-pd.porcine/meta.yaml index 3c508d25653f1..927429aaf614d 100644 --- a/recipes/bioconductor-pd.porcine/meta.yaml +++ b/recipes/bioconductor-pd.porcine/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.porcine" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Porcine + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Porcine -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5df404babadb1d6faef73e249c819a72 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.porcine", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 5df404babadb1d6faef73e249c819a72 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Porcine' - description: 'Platform Design Info for The Manufacturer''s Name Porcine' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.porgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.porgene.1.0.st/meta.yaml index 60c46a620aa02..c62393035d8cc 100644 --- a/recipes/bioconductor-pd.porgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.porgene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.porgene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix PorGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix PorGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 203fc56b0e2904fa7063c4a325e038f1 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.porgene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 203fc56b0e2904fa7063c4a325e038f1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix PorGene-1_0-st' - description: 'Platform Design Info for Affymetrix PorGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.porgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.porgene.1.1.st/meta.yaml index d719ca62d0871..813c0b04b12e7 100644 --- a/recipes/bioconductor-pd.porgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.porgene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.porgene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix PorGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix PorGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3a31d325861925a7428241207c461a1d build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.porgene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 3a31d325861925a7428241207c461a1d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix PorGene-1_1-st' - description: 'Platform Design Info for Affymetrix PorGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rabgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rabgene.1.0.st/meta.yaml index 2d107b381b133..b0e7384daf146 100644 --- a/recipes/bioconductor-pd.rabgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rabgene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.rabgene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix RabGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix RabGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7f1e33f4767a4c4653bdaff2b79989a0 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rabgene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 7f1e33f4767a4c4653bdaff2b79989a0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix RabGene-1_0-st' - description: 'Platform Design Info for Affymetrix RabGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rabgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rabgene.1.1.st/meta.yaml index 4695d505632f7..6d441188f8883 100644 --- a/recipes/bioconductor-pd.rabgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rabgene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.rabgene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix RabGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix RabGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2492695661309f5e6628612685460ee5 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rabgene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 2492695661309f5e6628612685460ee5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix RabGene-1_1-st' - description: 'Platform Design Info for Affymetrix RabGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rae230a/meta.yaml b/recipes/bioconductor-pd.rae230a/meta.yaml index 663454610c8b4..dec15a14a1564 100644 --- a/recipes/bioconductor-pd.rae230a/meta.yaml +++ b/recipes/bioconductor-pd.rae230a/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.rae230a" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name RAE230A + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name RAE230A -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fa4a1c29d3457b1db82b1010c5f72412 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rae230a", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: fa4a1c29d3457b1db82b1010c5f72412 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name RAE230A' - description: 'Platform Design Info for The Manufacturer''s Name RAE230A' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rae230b/meta.yaml b/recipes/bioconductor-pd.rae230b/meta.yaml index 46e25943b634f..61c60362fe0d3 100644 --- a/recipes/bioconductor-pd.rae230b/meta.yaml +++ b/recipes/bioconductor-pd.rae230b/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.rae230b" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name RAE230B + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name RAE230B -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 10e2e70bb7538119127cd65f636f93b6 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rae230b", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 10e2e70bb7538119127cd65f636f93b6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name RAE230B' - description: 'Platform Design Info for The Manufacturer''s Name RAE230B' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.raex.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.raex.1.0.st.v1/meta.yaml index 519e76f5d2ad1..dc34fe7544069 100644 --- a/recipes/bioconductor-pd.raex.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.raex.1.0.st.v1/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.raex.1.0.st.v1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix RaEx-1_0-st-v1 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix RaEx-1_0-st-v1 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e2160b549f63ffcc9222d88d82d4d393 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.raex.1.0.st.v1", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: e2160b549f63ffcc9222d88d82d4d393 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix RaEx-1_0-st-v1' - description: 'Platform Design Info for Affymetrix RaEx-1_0-st-v1' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.ragene.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.ragene.1.0.st.v1/meta.yaml index 83bbe9f667204..29c54d22c49ea 100644 --- a/recipes/bioconductor-pd.ragene.1.0.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.ragene.1.0.st.v1/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.ragene.1.0.st.v1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix RaGene-1_0-st-v1 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix RaGene-1_0-st-v1 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 122cb69603e705218d01d70f48e90cad build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.ragene.1.0.st.v1", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 122cb69603e705218d01d70f48e90cad + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix RaGene-1_0-st-v1' - description: 'Platform Design Info for Affymetrix RaGene-1_0-st-v1' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.ragene.1.1.st.v1/meta.yaml b/recipes/bioconductor-pd.ragene.1.1.st.v1/meta.yaml index 7acf2c90841f4..79cd89348568d 100644 --- a/recipes/bioconductor-pd.ragene.1.1.st.v1/meta.yaml +++ b/recipes/bioconductor-pd.ragene.1.1.st.v1/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.ragene.1.1.st.v1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix RaGene-1_1-st-v1 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix RaGene-1_1-st-v1 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7301ab6472849395ccb800c39807e969 build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.ragene.1.1.st.v1", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 7301ab6472849395ccb800c39807e969 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix RaGene-1_1-st-v1' - description: 'Platform Design Info for Affymetrix RaGene-1_1-st-v1' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.ragene.2.0.st/meta.yaml b/recipes/bioconductor-pd.ragene.2.0.st/meta.yaml index d353b093c0f97..0e743916f3a33 100644 --- a/recipes/bioconductor-pd.ragene.2.0.st/meta.yaml +++ b/recipes/bioconductor-pd.ragene.2.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.ragene.2.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix RaGene-2_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix RaGene-2_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 37157b09f009fef368b54e47711c313b build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.ragene.2.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 37157b09f009fef368b54e47711c313b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix RaGene-2_0-st' - description: 'Platform Design Info for Affymetrix RaGene-2_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.ragene.2.1.st/meta.yaml b/recipes/bioconductor-pd.ragene.2.1.st/meta.yaml index 97f536d4fe7f2..64d79065facd9 100644 --- a/recipes/bioconductor-pd.ragene.2.1.st/meta.yaml +++ b/recipes/bioconductor-pd.ragene.2.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.14.1" %} {% set name = "pd.ragene.2.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix RaGene-2_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix RaGene-2_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 53adfa5ff2c7e466da83b807dbc7b237 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.ragene.2.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 53adfa5ff2c7e466da83b807dbc7b237 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix RaGene-2_1-st' - description: 'Platform Design Info for Affymetrix RaGene-2_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rat230.2/meta.yaml b/recipes/bioconductor-pd.rat230.2/meta.yaml index b9a674841bfcf..35d3c638f880f 100644 --- a/recipes/bioconductor-pd.rat230.2/meta.yaml +++ b/recipes/bioconductor-pd.rat230.2/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.rat230.2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Rat230_2 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Rat230_2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 286b1a7868ef6c795ebeb6dd8a5d5920 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rat230.2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 286b1a7868ef6c795ebeb6dd8a5d5920 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Rat230_2' - description: 'Platform Design Info for The Manufacturer''s Name Rat230_2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rcngene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rcngene.1.0.st/meta.yaml index 9200e31904ff5..119019e0d48bd 100644 --- a/recipes/bioconductor-pd.rcngene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rcngene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.rcngene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix RCnGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix RCnGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9c7c5ef4d4f5ed92d9130d77a99a0685 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rcngene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 9c7c5ef4d4f5ed92d9130d77a99a0685 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix RCnGene-1_0-st' - description: 'Platform Design Info for Affymetrix RCnGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rcngene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rcngene.1.1.st/meta.yaml index d5109147ee4f8..7ff590a4dc3b8 100644 --- a/recipes/bioconductor-pd.rcngene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rcngene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.rcngene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix RCnGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix RCnGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9781549447d90b5423e820fff5cc6273 build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rcngene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 9781549447d90b5423e820fff5cc6273 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix RCnGene-1_1-st' - description: 'Platform Design Info for Affymetrix RCnGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rg.u34a/meta.yaml b/recipes/bioconductor-pd.rg.u34a/meta.yaml index 814b06a1e7993..71c22ec521973 100644 --- a/recipes/bioconductor-pd.rg.u34a/meta.yaml +++ b/recipes/bioconductor-pd.rg.u34a/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.rg.u34a" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name RG_U34A + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name RG_U34A -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ac3a6cc203dabb8faab85b97f1a7ae3c build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rg.u34a", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: ac3a6cc203dabb8faab85b97f1a7ae3c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name RG_U34A' - description: 'Platform Design Info for The Manufacturer''s Name RG_U34A' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rg.u34b/meta.yaml b/recipes/bioconductor-pd.rg.u34b/meta.yaml index 3bd194cf18f4d..0c25a3d0f663d 100644 --- a/recipes/bioconductor-pd.rg.u34b/meta.yaml +++ b/recipes/bioconductor-pd.rg.u34b/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.rg.u34b" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name RG_U34B + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name RG_U34B -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 757966b66795d388c7169816d31977ad build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rg.u34b", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 757966b66795d388c7169816d31977ad + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name RG_U34B' - description: 'Platform Design Info for The Manufacturer''s Name RG_U34B' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rg.u34c/meta.yaml b/recipes/bioconductor-pd.rg.u34c/meta.yaml index 0be8eaeea6991..d28100d68244d 100644 --- a/recipes/bioconductor-pd.rg.u34c/meta.yaml +++ b/recipes/bioconductor-pd.rg.u34c/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.rg.u34c" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name RG_U34C + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name RG_U34C -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bc9cb7b208972ac2901235bdabdee5b2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rg.u34c", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: bc9cb7b208972ac2901235bdabdee5b2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name RG_U34C' - description: 'Platform Design Info for The Manufacturer''s Name RG_U34C' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rhegene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rhegene.1.0.st/meta.yaml index 0b394c279d5fa..22a7b93b04a72 100644 --- a/recipes/bioconductor-pd.rhegene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rhegene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.rhegene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix RheGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix RheGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6469add6928e663529df4df98fcdd7a8 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rhegene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 6469add6928e663529df4df98fcdd7a8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix RheGene-1_0-st' - description: 'Platform Design Info for Affymetrix RheGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rhegene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rhegene.1.1.st/meta.yaml index 9f7b2da4be891..516a58aefee3a 100644 --- a/recipes/bioconductor-pd.rhegene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rhegene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.rhegene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix RheGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix RheGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4f63424ab52283a95731767dce6623cd build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rhegene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 4f63424ab52283a95731767dce6623cd + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix RheGene-1_1-st' - description: 'Platform Design Info for Affymetrix RheGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rhesus/meta.yaml b/recipes/bioconductor-pd.rhesus/meta.yaml index 168eb0a7c0836..11492367a0df6 100644 --- a/recipes/bioconductor-pd.rhesus/meta.yaml +++ b/recipes/bioconductor-pd.rhesus/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.rhesus" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Rhesus + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Rhesus -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 51efcfe1384ac956ff93bf0530965054 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rhesus", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 51efcfe1384ac956ff93bf0530965054 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Rhesus' - description: 'Platform Design Info for The Manufacturer''s Name Rhesus' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rice/meta.yaml b/recipes/bioconductor-pd.rice/meta.yaml index cc3172d469287..e4ab8c6b11724 100644 --- a/recipes/bioconductor-pd.rice/meta.yaml +++ b/recipes/bioconductor-pd.rice/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.rice" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Rice + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Rice -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9c456981b3d0b99a96ac6c71e3eb7c8a build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rice", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 9c456981b3d0b99a96ac6c71e3eb7c8a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Rice' - description: 'Platform Design Info for The Manufacturer''s Name Rice' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rjpgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rjpgene.1.0.st/meta.yaml index 6d55e5903b9cc..68c7c0f919c75 100644 --- a/recipes/bioconductor-pd.rjpgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rjpgene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.rjpgene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix RJpGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix RJpGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 066f5dbacc1110e42ce4d457ad3b9306 build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rjpgene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 066f5dbacc1110e42ce4d457ad3b9306 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix RJpGene-1_0-st' - description: 'Platform Design Info for Affymetrix RJpGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rjpgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rjpgene.1.1.st/meta.yaml index f1cce02ab6f8c..b918b0e494cc1 100644 --- a/recipes/bioconductor-pd.rjpgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rjpgene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.rjpgene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix RJpGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix RJpGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 265503774b15e0f4e71ac53a276a80f2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rjpgene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 265503774b15e0f4e71ac53a276a80f2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix RJpGene-1_1-st' - description: 'Platform Design Info for Affymetrix RJpGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rn.u34/meta.yaml b/recipes/bioconductor-pd.rn.u34/meta.yaml index 7ba2751df2778..884cef928f801 100644 --- a/recipes/bioconductor-pd.rn.u34/meta.yaml +++ b/recipes/bioconductor-pd.rn.u34/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.rn.u34" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name RN_U34 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name RN_U34 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1728c547f1383bffab330796505119ec build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rn.u34", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 1728c547f1383bffab330796505119ec + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name RN_U34' - description: 'Platform Design Info for The Manufacturer''s Name RN_U34' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rta.1.0/meta.yaml b/recipes/bioconductor-pd.rta.1.0/meta.yaml index 96549451b50b6..920ee2267050d 100644 --- a/recipes/bioconductor-pd.rta.1.0/meta.yaml +++ b/recipes/bioconductor-pd.rta.1.0/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.2" %} {% set name = "pd.rta.1.0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix RTA-1_0 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix RTA-1_0 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 90752a892a103c7fe4cd6c86e61a61db build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rta.1.0", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 90752a892a103c7fe4cd6c86e61a61db + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix RTA-1_0' - description: 'Platform Design Info for Affymetrix RTA-1_0' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rusgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rusgene.1.0.st/meta.yaml index 1377c31afcc2c..06999346b1b75 100644 --- a/recipes/bioconductor-pd.rusgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.rusgene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.rusgene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix RUSGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix RUSGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0b9b00fee58ef211e041395052344483 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rusgene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 0b9b00fee58ef211e041395052344483 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix RUSGene-1_0-st' - description: 'Platform Design Info for Affymetrix RUSGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.rusgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rusgene.1.1.st/meta.yaml index ce4353bf56c14..37f8d83a5343f 100644 --- a/recipes/bioconductor-pd.rusgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.rusgene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.rusgene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix RUSGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix RUSGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 228837c2de4a4b106806cb7f384564fa build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.rusgene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 228837c2de4a4b106806cb7f384564fa + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix RUSGene-1_1-st' - description: 'Platform Design Info for Affymetrix RUSGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.s.aureus/meta.yaml b/recipes/bioconductor-pd.s.aureus/meta.yaml index 7bb76e909c429..70f8ad77c3a92 100644 --- a/recipes/bioconductor-pd.s.aureus/meta.yaml +++ b/recipes/bioconductor-pd.s.aureus/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.s.aureus" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name S_aureus + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name S_aureus -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f173ae6e4316aaa2eafbde92d5868a5a build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.s.aureus", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: f173ae6e4316aaa2eafbde92d5868a5a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name S_aureus' - description: 'Platform Design Info for The Manufacturer''s Name S_aureus' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.soybean/meta.yaml b/recipes/bioconductor-pd.soybean/meta.yaml index 9a179dc85bbc3..dc4b8780979ec 100644 --- a/recipes/bioconductor-pd.soybean/meta.yaml +++ b/recipes/bioconductor-pd.soybean/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.soybean" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Soybean + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Soybean -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6dbe167be9d40c1d9096485afb4525f0 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.soybean", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 6dbe167be9d40c1d9096485afb4525f0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Soybean' - description: 'Platform Design Info for The Manufacturer''s Name Soybean' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.soygene.1.0.st/meta.yaml b/recipes/bioconductor-pd.soygene.1.0.st/meta.yaml index a347597e89b5a..fb53d525e9ba0 100644 --- a/recipes/bioconductor-pd.soygene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.soygene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.soygene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix SoyGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix SoyGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b264df0648ec35d04f91e0ef8e26ac95 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.soygene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: b264df0648ec35d04f91e0ef8e26ac95 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix SoyGene-1_0-st' - description: 'Platform Design Info for Affymetrix SoyGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.soygene.1.1.st/meta.yaml b/recipes/bioconductor-pd.soygene.1.1.st/meta.yaml index a1729ed3dabec..7c2c6a526b452 100644 --- a/recipes/bioconductor-pd.soygene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.soygene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.soygene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix SoyGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix SoyGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4a911a4a4b5de927fe6239e500a2993f build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.soygene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 4a911a4a4b5de927fe6239e500a2993f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix SoyGene-1_1-st' - description: 'Platform Design Info for Affymetrix SoyGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.sugar.cane/meta.yaml b/recipes/bioconductor-pd.sugar.cane/meta.yaml index 1ac46bfb035b6..5542389a922ec 100644 --- a/recipes/bioconductor-pd.sugar.cane/meta.yaml +++ b/recipes/bioconductor-pd.sugar.cane/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.sugar.cane" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Sugar_Cane + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Sugar_Cane -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bd7eb8b1a1c9ac77359358a5347330fb build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.sugar.cane", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: bd7eb8b1a1c9ac77359358a5347330fb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Sugar_Cane' - description: 'Platform Design Info for The Manufacturer''s Name Sugar_Cane' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.tomato/meta.yaml b/recipes/bioconductor-pd.tomato/meta.yaml index f934a7a17e110..abd7844528397 100644 --- a/recipes/bioconductor-pd.tomato/meta.yaml +++ b/recipes/bioconductor-pd.tomato/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.tomato" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Tomato + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Tomato -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ce78f6ee43d72e017608413dd4d50580 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.tomato", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: ce78f6ee43d72e017608413dd4d50580 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Tomato' - description: 'Platform Design Info for The Manufacturer''s Name Tomato' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.u133.x3p/meta.yaml b/recipes/bioconductor-pd.u133.x3p/meta.yaml index 8831a79d5d391..3e40af55420b7 100644 --- a/recipes/bioconductor-pd.u133.x3p/meta.yaml +++ b/recipes/bioconductor-pd.u133.x3p/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.u133.x3p" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name U133_X3P + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name U133_X3P -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e3f343e32273667f851e26d7b8a7a5db build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.u133.x3p", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: e3f343e32273667f851e26d7b8a7a5db + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name U133_X3P' - description: 'Platform Design Info for The Manufacturer''s Name U133_X3P' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.vitis.vinifera/meta.yaml b/recipes/bioconductor-pd.vitis.vinifera/meta.yaml index 65c61d4bfd7fd..35de1eb6e63cb 100644 --- a/recipes/bioconductor-pd.vitis.vinifera/meta.yaml +++ b/recipes/bioconductor-pd.vitis.vinifera/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.vitis.vinifera" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Vitis_Vinifera + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Vitis_Vinifera -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 104a8ac33a9baa25a61f953679795696 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.vitis.vinifera", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 104a8ac33a9baa25a61f953679795696 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Vitis_Vinifera' - description: 'Platform Design Info for The Manufacturer''s Name Vitis_Vinifera' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.wheat/meta.yaml b/recipes/bioconductor-pd.wheat/meta.yaml index 2880ec9932dab..a8ff9cf41d828 100644 --- a/recipes/bioconductor-pd.wheat/meta.yaml +++ b/recipes/bioconductor-pd.wheat/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.wheat" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name wheat + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name wheat -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 38a7183c8d3b874cf62391a9e9169bb9 build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.wheat", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 38a7183c8d3b874cf62391a9e9169bb9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name wheat' - description: 'Platform Design Info for The Manufacturer''s Name wheat' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.x.laevis.2/meta.yaml b/recipes/bioconductor-pd.x.laevis.2/meta.yaml index 85c3ad7eb268f..0aea7bd1977f8 100644 --- a/recipes/bioconductor-pd.x.laevis.2/meta.yaml +++ b/recipes/bioconductor-pd.x.laevis.2/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.x.laevis.2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name X_laevis_2 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name X_laevis_2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 32416957e3cdc11ad4dbfcd9141ff113 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.x.laevis.2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 32416957e3cdc11ad4dbfcd9141ff113 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name X_laevis_2' - description: 'Platform Design Info for The Manufacturer''s Name X_laevis_2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.x.tropicalis/meta.yaml b/recipes/bioconductor-pd.x.tropicalis/meta.yaml index 6670ccd4bafab..ee4ebedf81582 100644 --- a/recipes/bioconductor-pd.x.tropicalis/meta.yaml +++ b/recipes/bioconductor-pd.x.tropicalis/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.x.tropicalis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name X_tropicalis + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name X_tropicalis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 79a4de91831e4b0153495e12b9c6e8d3 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.x.tropicalis", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 79a4de91831e4b0153495e12b9c6e8d3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name X_tropicalis' - description: 'Platform Design Info for The Manufacturer''s Name X_tropicalis' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.xenopus.laevis/meta.yaml b/recipes/bioconductor-pd.xenopus.laevis/meta.yaml index 95dc899a279f5..13df9be54045d 100644 --- a/recipes/bioconductor-pd.xenopus.laevis/meta.yaml +++ b/recipes/bioconductor-pd.xenopus.laevis/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.xenopus.laevis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Xenopus_laevis + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Xenopus_laevis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6d5c2c9e8e3891770b1c6e9dcd823c0d build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.xenopus.laevis", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 6d5c2c9e8e3891770b1c6e9dcd823c0d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Xenopus_laevis' - description: 'Platform Design Info for The Manufacturer''s Name Xenopus_laevis' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.yeast.2/meta.yaml b/recipes/bioconductor-pd.yeast.2/meta.yaml index 26d834b6f5f33..a93f111f85e9d 100644 --- a/recipes/bioconductor-pd.yeast.2/meta.yaml +++ b/recipes/bioconductor-pd.yeast.2/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.yeast.2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Yeast_2 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Yeast_2 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 780f5139ee9cda46c9e38122538ce129 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.yeast.2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 780f5139ee9cda46c9e38122538ce129 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Yeast_2' - description: 'Platform Design Info for The Manufacturer''s Name Yeast_2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.yg.s98/meta.yaml b/recipes/bioconductor-pd.yg.s98/meta.yaml index 9747d83c970c7..79003cb2fcb2f 100644 --- a/recipes/bioconductor-pd.yg.s98/meta.yaml +++ b/recipes/bioconductor-pd.yg.s98/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.yg.s98" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name YG_S98 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name YG_S98 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: caec3e8f29918f078b2dc7c76f4a74e2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.yg.s98", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: caec3e8f29918f078b2dc7c76f4a74e2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name YG_S98' - description: 'Platform Design Info for The Manufacturer''s Name YG_S98' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.zebgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.zebgene.1.0.st/meta.yaml index 3bb4402a2e409..1d318d9c22851 100644 --- a/recipes/bioconductor-pd.zebgene.1.0.st/meta.yaml +++ b/recipes/bioconductor-pd.zebgene.1.0.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.zebgene.1.0.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix ZebGene-1_0-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix ZebGene-1_0-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 54fcf757b8069e95dd7e2f3ff74ae050 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.zebgene.1.0.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 54fcf757b8069e95dd7e2f3ff74ae050 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix ZebGene-1_0-st' - description: 'Platform Design Info for Affymetrix ZebGene-1_0-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.zebgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.zebgene.1.1.st/meta.yaml index bb23b5798ea1e..be68d570cd652 100644 --- a/recipes/bioconductor-pd.zebgene.1.1.st/meta.yaml +++ b/recipes/bioconductor-pd.zebgene.1.1.st/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.zebgene.1.1.st" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for Affymetrix ZebGene-1_1-st + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for Affymetrix ZebGene-1_1-st -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d87028cd9024bc33be518635cf2f48fc build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.zebgene.1.1.st", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: d87028cd9024bc33be518635cf2f48fc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for Affymetrix ZebGene-1_1-st' - description: 'Platform Design Info for Affymetrix ZebGene-1_1-st' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pd.zebrafish/meta.yaml b/recipes/bioconductor-pd.zebrafish/meta.yaml index c747bdcc950f4..cca3eee1ba631 100644 --- a/recipes/bioconductor-pd.zebrafish/meta.yaml +++ b/recipes/bioconductor-pd.zebrafish/meta.yaml @@ -1,51 +1,56 @@ {% set version = "3.12.0" %} {% set name = "pd.zebrafish" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Platform Design Info for The Manufacturer's Name Zebrafish + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Info for The Manufacturer's Name Zebrafish -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 101f09a9d9304d1d8fbcc7f4812897b1 build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pd.zebrafish", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 101f09a9d9304d1d8fbcc7f4812897b1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Info for The Manufacturer''s Name Zebrafish' - description: 'Platform Design Info for The Manufacturer''s Name Zebrafish' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pdinfobuilder/meta.yaml b/recipes/bioconductor-pdinfobuilder/meta.yaml index b94711d5f3961..cfa1997dcd043 100644 --- a/recipes/bioconductor-pdinfobuilder/meta.yaml +++ b/recipes/bioconductor-pdinfobuilder/meta.yaml @@ -1,67 +1,73 @@ -{% set version = "1.66.0" %} +{% set version = "1.70.0" %} {% set name = "pdInfoBuilder" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Platform Design Information Package Builder -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67c0c8df22f95792e50c1e6c4b6eba2a build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pdinfobuilder", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:pdinfobuilder + - doi:10.1093/bioinformatics/btq431 + parent_recipe: + name: bioconductor-pdinfobuilder + path: recipes/bioconductor-pdinfobuilder + version: 1.44.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-affxparser >=1.74.0,<1.75.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-affxparser >=1.78.0,<1.79.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 - libblas - liblapack run: - - 'bioconductor-affxparser >=1.74.0,<1.75.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-affxparser >=1.78.0,<1.79.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-dbi >=0.3.1' - - 'r-rsqlite >=1.0.0' - build: - - {{ compiler('c') }} - - make + - r-dbi >=0.3.1 + - r-rsqlite >=1.0.0 + +source: + md5: 82dec35ff40abd56837f90a2242da52c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Platform Design Information Package Builder' - description: 'Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg.' -extra: - identifiers: - - biotools:pdinfobuilder - - doi:10.1093/bioinformatics/btq431 - parent_recipe: - name: bioconductor-pdinfobuilder - path: recipes/bioconductor-pdinfobuilder - version: 1.44.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-peacoqc/meta.yaml b/recipes/bioconductor-peacoqc/meta.yaml index 2a019595f29fb..41fa0e27d1acb 100644 --- a/recipes/bioconductor-peacoqc/meta.yaml +++ b/recipes/bioconductor-peacoqc/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "PeacoQC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This is a package that includes pre-processing and quality control functions that can remove margin events, compensate and transform the data and that will use PeacoQCSignalStability for quality control. This last function will first detect peaks in each channel of the flowframe. It will remove anomalies based on the IsolationTree function and the MAD outlier detection method. This package can be used for both flow- and mass cytometry data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Peak-based selection of high quality cytometry data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fa296e0522b97273b692874b5ec23b97 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-peacoqc", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowworkspace >=4.18.0,<4.19.0 - r-base - r-circlize - r-ggplot2 - r-gridextra - r-plyr run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-flowworkspace >=4.14.0,<4.15.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-flowworkspace >=4.18.0,<4.19.0 - r-base - r-circlize - r-ggplot2 - r-gridextra - r-plyr + +source: + md5: decb90e9768d8e8f8a422a2b7cee0196 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=3)' - summary: 'Peak-based selection of high quality cytometry data' - description: 'This is a package that includes pre-processing and quality control functions that can remove margin events, compensate and transform the data and that will use PeacoQCSignalStability for quality control. This last function will first detect peaks in each channel of the flowframe. It will remove anomalies based on the IsolationTree function and the MAD outlier detection method. This package can be used for both flow- and mass cytometry data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-peakpanther/meta.yaml b/recipes/bioconductor-peakpanther/meta.yaml index d56a1978bcd39..107d9e455122e 100644 --- a/recipes/bioconductor-peakpanther/meta.yaml +++ b/recipes/bioconductor-peakpanther/meta.yaml @@ -1,69 +1,76 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "peakPantheR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An automated pipeline for the detection, integration and reporting of predefined features across a large number of mass spectrometry data files. It enables the real time annotation of multiple compounds in a single file, or the parallel annotation of multiple compounds in multiple files. A graphical user interface as well as command line functions will assist in assessing the quality of annotation and update fitting parameters until a satisfactory result is obtained. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Peak Picking and Annotation of High Resolution Experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9753434861181af826b86fbc734b5850 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-peakpanther", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, devtools, faahKO, msdata, knitr, rmarkdown, pander, BiocStyle requirements: host: - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-mzr >=2.40.0,<2.41.0 - r-base - r-bslib - - 'r-doparallel >=1.0.11' - - 'r-dt >=0.15' - - 'r-foreach >=1.4.4' - - 'r-ggplot2 >=3.3.0' - - 'r-gridextra >=2.3' + - r-doparallel >=1.0.11 + - r-dt >=0.15 + - r-foreach >=1.4.4 + - r-ggplot2 >=3.5.0 + - r-gridextra >=2.3 - r-lubridate - - 'r-minpack.lm >=1.2.1' - - 'r-pracma >=2.2.3' - - 'r-scales >=0.5.0' - - 'r-shiny >=1.0.5' - - 'r-shinycssloaders >=1.0.0' - - 'r-stringr >=1.2.0' - - 'r-xml >=3.98.1.10' + - r-minpack.lm >=1.2.1 + - r-pracma >=2.2.3 + - r-scales >=0.5.0 + - r-shiny >=1.0.5 + - r-shinycssloaders >=1.0.0 + - r-stringr >=1.2.0 + - r-svglite >=2.1.1 + - r-xml >=3.98.1.10 run: - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-mzr >=2.40.0,<2.41.0 - r-base - r-bslib - - 'r-doparallel >=1.0.11' - - 'r-dt >=0.15' - - 'r-foreach >=1.4.4' - - 'r-ggplot2 >=3.3.0' - - 'r-gridextra >=2.3' + - r-doparallel >=1.0.11 + - r-dt >=0.15 + - r-foreach >=1.4.4 + - r-ggplot2 >=3.5.0 + - r-gridextra >=2.3 - r-lubridate - - 'r-minpack.lm >=1.2.1' - - 'r-pracma >=2.2.3' - - 'r-scales >=0.5.0' - - 'r-shiny >=1.0.5' - - 'r-shinycssloaders >=1.0.0' - - 'r-stringr >=1.2.0' - - 'r-xml >=3.98.1.10' + - r-minpack.lm >=1.2.1 + - r-pracma >=2.2.3 + - r-scales >=0.5.0 + - r-shiny >=1.0.5 + - r-shinycssloaders >=1.0.0 + - r-stringr >=1.2.0 + - r-svglite >=2.1.1 + - r-xml >=3.98.1.10 + +source: + md5: dd5dffdd9397ba01ab9d25d3dc075a28 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Peak Picking and Annotation of High Resolution Experiments' - description: 'An automated pipeline for the detection, integration and reporting of predefined features across a large number of mass spectrometry data files. It enables the real time annotation of multiple compounds in a single file, or the parallel annotation of multiple compounds in multiple files. A graphical user interface as well as command line functions will assist in assessing the quality of annotation and update fitting parameters until a satisfactory result is obtained.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-peca/meta.yaml b/recipes/bioconductor-peca/meta.yaml index 5605c4a16cf73..be9bca1c8bf81 100644 --- a/recipes/bioconductor-peca/meta.yaml +++ b/recipes/bioconductor-peca/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "PECA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Calculates Probe-level Expression Change Averages (PECA) to identify differential expression in Affymetrix gene expression microarray studies or in proteomic studies using peptide-level mesurements respectively. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Probe-level Expression Change Averaging -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43aed7fc555cb6ccbf70335add80f6dc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-peca", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:peca + - doi:10.1007/978-1-4939-6518-2_11 + parent_recipe: + name: bioconductor-peca + path: recipes/bioconductor-peca + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SpikeIn requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-rots >=1.30.0,<1.31.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-rots >=1.34.0,<1.35.0 - r-aroma.affymetrix - r-aroma.core - r-base run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-rots >=1.30.0,<1.31.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-rots >=1.34.0,<1.35.0 - r-aroma.affymetrix - r-aroma.core - r-base + +source: + md5: b1d1585740b1854dcd7e764988d55426 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Probe-level Expression Change Averaging' - description: 'Calculates Probe-level Expression Change Averages (PECA) to identify differential expression in Affymetrix gene expression microarray studies or in proteomic studies using peptide-level mesurements respectively.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:peca - - doi:10.1007/978-1-4939-6518-2_11 - parent_recipe: - name: bioconductor-peca - path: recipes/bioconductor-peca - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-peco/meta.yaml b/recipes/bioconductor-peco/meta.yaml index 42ee30969da6a..0b264b6945d36 100644 --- a/recipes/bioconductor-peco/meta.yaml +++ b/recipes/bioconductor-peco/meta.yaml @@ -1,55 +1,60 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "peco" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Our approach provides a way to assign continuous cell cycle phase using scRNA-seq data, and consequently, allows to identify cyclic trend of gene expression levels along the cell cycle. This package provides method and training data, which includes scRNA-seq data collected from 6 individual cell lines of induced pluripotent stem cells (iPSCs), and also continuous cell cycle phase derived from FUCCI fluorescence imaging data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9a15c75c989ee10da1fb0ead1bbac99f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-peco", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-circular - r-conicfit - r-doparallel - r-foreach - - 'r-genlasso >=1.4' + - r-genlasso >=1.4 run: - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-circular - r-conicfit - r-doparallel - r-foreach - - 'r-genlasso >=1.4' + - r-genlasso >=1.4 + +source: + md5: 58812570a419d72ca35b1f647ff1dd59 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data' - description: 'Our approach provides a way to assign continuous cell cycle phase using scRNA-seq data, and consequently, allows to identify cyclic trend of gene expression levels along the cell cycle. This package provides method and training data, which includes scRNA-seq data collected from 6 individual cell lines of induced pluripotent stem cells (iPSCs), and also continuous cell cycle phase derived from FUCCI fluorescence imaging data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pedbarrayv10.db/meta.yaml b/recipes/bioconductor-pedbarrayv10.db/meta.yaml index 1c9fa8f5fbffa..cc45bf2f61b60 100644 --- a/recipes/bioconductor-pedbarrayv10.db/meta.yaml +++ b/recipes/bioconductor-pedbarrayv10.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "pedbarrayv10.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 25acc3bfee229015ecca1c7d688e5168 +about: + description: FHCRC Nelson Lab pedbarrayv10 Annotation Data (pedbarrayv10) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: FHCRC Nelson Lab pedbarrayv10 Annotation Data (pedbarrayv10) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pedbarrayv10.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 25acc3bfee229015ecca1c7d688e5168 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'FHCRC Nelson Lab pedbarrayv10 Annotation Data (pedbarrayv10)' - description: 'FHCRC Nelson Lab pedbarrayv10 Annotation Data (pedbarrayv10) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pedbarrayv9.db/meta.yaml b/recipes/bioconductor-pedbarrayv9.db/meta.yaml index 1d5180b7a344c..fa48fef90c013 100644 --- a/recipes/bioconductor-pedbarrayv9.db/meta.yaml +++ b/recipes/bioconductor-pedbarrayv9.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "pedbarrayv9.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: da4b2f9c0a672e0c9ee53f017bacaff7 +about: + description: FHCRC Nelson Lab pedbarrayv9 Annotation Data (pedbarrayv9) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: FHCRC Nelson Lab pedbarrayv9 Annotation Data (pedbarrayv9) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pedbarrayv9.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: da4b2f9c0a672e0c9ee53f017bacaff7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'FHCRC Nelson Lab pedbarrayv9 Annotation Data (pedbarrayv9)' - description: 'FHCRC Nelson Lab pedbarrayv9 Annotation Data (pedbarrayv9) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pedixplorer/build.sh b/recipes/bioconductor-pedixplorer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pedixplorer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pedixplorer/meta.yaml b/recipes/bioconductor-pedixplorer/meta.yaml new file mode 100644 index 0000000000000..eb36a98d160fa --- /dev/null +++ b/recipes/bioconductor-pedixplorer/meta.yaml @@ -0,0 +1,83 @@ +{% set version = "1.2.0" %} +{% set name = "Pedixplorer" %} +{% set bioc = "3.20" %} + +about: + description: Routines to handle family data with a Pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for Pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the Pedigree object with various criteria, and kinship for the X chromosome. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Pedigree Functions + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pedixplorer", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: diffviewer, testthat (>= 3.0.0), vdiffr, rmarkdown, BiocStyle, knitr, withr, qpdf, shinytest2, covr, devtools, R.devices, usethis, magick +requirements: + + host: + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-colourpicker + - r-data.table + - r-dplyr + - r-dt + - r-ggplot2 + - r-gridextra + - r-htmlwidgets + - r-matrix + - r-plotly + - r-plyr + - r-quadprog + - r-readxl + - r-scales + - r-shiny + - r-shinycssloaders + - r-shinytoastr + - r-shinywidgets + - r-stringr + - r-tidyr + + run: + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-colourpicker + - r-data.table + - r-dplyr + - r-dt + - r-ggplot2 + - r-gridextra + - r-htmlwidgets + - r-matrix + - r-plotly + - r-plyr + - r-quadprog + - r-readxl + - r-scales + - r-shiny + - r-shinycssloaders + - r-shinytoastr + - r-shinywidgets + - r-stringr + - r-tidyr + +source: + md5: 2330dc5620f1299f7d2f88f890cfdd0d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-pengls/meta.yaml b/recipes/bioconductor-pengls/meta.yaml index 641c32b81fdc8..9740338462b7c 100644 --- a/recipes/bioconductor-pengls/meta.yaml +++ b/recipes/bioconductor-pengls/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "pengls" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7b4703b0839f4e46a97e208289a69345 +about: + description: Combine generalised least squares methodology from the nlme package for dealing with autocorrelation with penalised least squares methods from the glmnet package to deal with high dimensionality. This pengls packages glues them together through an iterative loop. The resulting method is applicable to high dimensional datasets that exhibit autocorrelation, such as spatial or temporal data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Fit Penalised Generalised Least Squares models build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pengls", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr,rmarkdown,testthat requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-glmnet - r-nlme run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-glmnet - r-nlme +source: + md5: 04c4e31303c6eeda21cab2286a2a5f5e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Fit Penalised Generalised Least Squares models' - description: 'Combine generalised least squares methodology from the nlme package for dealing with autocorrelation with penalised least squares methods from the glmnet package to deal with high dimensionality. This pengls packages glues them together through an iterative loop. The resulting method is applicable to high dimensional datasets that exhibit autocorrelation, such as spatial or temporal data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pepdat/meta.yaml b/recipes/bioconductor-pepdat/meta.yaml index e632c11c7cf5c..282b81b5afa2f 100644 --- a/recipes/bioconductor-pepdat/meta.yaml +++ b/recipes/bioconductor-pepdat/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "pepDat" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ce373369604b54b15e5992ebe9355b9 +about: + description: Provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Peptide microarray data package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pepdat", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 36b1a23bdd2410788bba91e2c156e869 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Peptide microarray data package' - description: 'Provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pepdat/post-link.sh b/recipes/bioconductor-pepdat/post-link.sh index 18087b8b14b2d..f6e0c56129487 100644 --- a/recipes/bioconductor-pepdat/post-link.sh +++ b/recipes/bioconductor-pepdat/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pepdat-1.22.0" +installBiocDataPackage.sh "pepdat-1.26.0" diff --git a/recipes/bioconductor-pepsettest/build.sh b/recipes/bioconductor-pepsettest/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pepsettest/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pepsettest/meta.yaml b/recipes/bioconductor-pepsettest/meta.yaml new file mode 100644 index 0000000000000..b865d526ea16e --- /dev/null +++ b/recipes/bioconductor-pepsettest/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.0.0" %} +{% set name = "PepSetTest" %} +{% set bioc = "3.20" %} + +about: + description: Peptide Set Test (PepSetTest) is a peptide-centric strategy to infer differentially expressed proteins in LC-MS/MS proteomics data. This test detects coordinated changes in the expression of peptides originating from the same protein and compares these changes against the rest of the peptidome. Compared to traditional aggregation-based approaches, the peptide set test demonstrates improved statistical power, yet controlling the Type I error rate correctly in most cases. This test can be valuable for discovering novel biomarkers and prioritizing drug targets, especially when the direct application of statistical analysis to protein data fails to provide substantial insights. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Peptide Set Test + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pepsettest", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: statmod, BiocStyle, knitr, rmarkdown, tidyr +requirements: + host: + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-dplyr + - r-lme4 + - r-mass + - r-matrixstats + - r-reshape2 + - r-tibble + run: + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-dplyr + - r-lme4 + - r-mass + - r-matrixstats + - r-reshape2 + - r-tibble + +source: + md5: 34543a61d708ed84e035f27ff8634055 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-pepsnmr/meta.yaml b/recipes/bioconductor-pepsnmr/meta.yaml index 58ea6cbaff257..edce335f50c11 100644 --- a/recipes/bioconductor-pepsnmr/meta.yaml +++ b/recipes/bioconductor-pepsnmr/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "PepsNMR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides R functions for common pre-procssing steps that are applied on 1H-NMR data. It also provides a function to read the FID signals directly in the Bruker format. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 | file LICENSE + license_file: LICENSE + summary: Pre-process 1H-NMR FID signals -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: afd34a264a3af86ad7aec1d6163b0aab build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pepsnmr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, markdown, rmarkdown, BiocStyle, PepsNMRData requirements: host: @@ -37,13 +39,16 @@ requirements: - r-matrixstats - r-ptw - r-reshape2 + +source: + md5: 8d1c438587788266d1a15fb4a2e2373f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-2 | file LICENSE' - summary: 'Pre-process 1H-NMR FID signals' - description: 'This package provides R functions for common pre-procssing steps that are applied on 1H-NMR data. It also provides a function to read the FID signals directly in the Bruker format.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pepsnmrdata/meta.yaml b/recipes/bioconductor-pepsnmrdata/meta.yaml index bc0e5911ad73c..252df80118dd9 100644 --- a/recipes/bioconductor-pepsnmrdata/meta.yaml +++ b/recipes/bioconductor-pepsnmrdata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "PepsNMRData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96fc9090499b4460f72fb85a0428b357 +about: + description: This package contains all the datasets used in the PepsNMR package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 | file LICENSE + license_file: LICENSE + summary: Datasets for the PepsNMR package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pepsnmrdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, markdown, rmarkdown, BiocStyle requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 015d1ec6d08d8544d1d1c21de64d61ac + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL-2 | file LICENSE' - summary: 'Datasets for the PepsNMR package' - description: 'This package contains all the datasets used in the PepsNMR package.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pepsnmrdata/post-link.sh b/recipes/bioconductor-pepsnmrdata/post-link.sh index 31aa57da37b58..00d5e325421aa 100644 --- a/recipes/bioconductor-pepsnmrdata/post-link.sh +++ b/recipes/bioconductor-pepsnmrdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pepsnmrdata-1.20.0" +installBiocDataPackage.sh "pepsnmrdata-1.24.0" diff --git a/recipes/bioconductor-pepstat/meta.yaml b/recipes/bioconductor-pepstat/meta.yaml index 63ce17507e1e1..2100053ed58b9 100644 --- a/recipes/bioconductor-pepstat/meta.yaml +++ b/recipes/bioconductor-pepstat/meta.yaml @@ -1,60 +1,66 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "pepStat" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Statistical analysis of peptide microarrays + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Statistical analysis of peptide microarrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 031af81c6bcac97b7262d978bfda2392 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pepstat", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:pepstat + - doi:10.1007/978-1-4939-3037-1_10 + parent_recipe: + name: bioconductor-pepstat + path: recipes/bioconductor-pepstat + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: pepDat, Pviz, knitr, shiny requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-data.table - r-fields - r-ggplot2 - r-plyr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-data.table - r-fields - r-ggplot2 - r-plyr + +source: + md5: 1b6b83f0415ec64eaeb7c802f5c77ee3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Statistical analysis of peptide microarrays' - description: 'Statistical analysis of peptide microarrays' -extra: - identifiers: - - biotools:pepstat - - doi:10.1007/978-1-4939-3037-1_10 - parent_recipe: - name: bioconductor-pepstat - path: recipes/bioconductor-pepstat - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pepxmltab/meta.yaml b/recipes/bioconductor-pepxmltab/meta.yaml index 44ccd49357088..fae8d302990ab 100644 --- a/recipes/bioconductor-pepxmltab/meta.yaml +++ b/recipes/bioconductor-pepxmltab/meta.yaml @@ -1,40 +1,21 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "pepXMLTab" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Parsing pepXML files based one XML package. The package tries to handle pepXML files generated from different softwares. The output will be a peptide-spectrum-matching tabular file. The package also provide function to filter the PSMs based on FDR. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Parsing pepXML files and filter based on peptide FDR. -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71d6bcb41c5a79bc2cfdd375c6468250 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pepxmltab", max_pin="x.x") }}' - noarch: generic -# Suggests: RUnit, BiocGenerics -requirements: - host: - - r-base - - 'r-xml >=3.98-1.1' - run: - - r-base - - 'r-xml >=3.98-1.1' -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Parsing pepXML files and filter based on peptide FDR.' - description: 'Parsing pepXML files based one XML package. The package tries to handle pepXML files generated from different softwares. The output will be a peptide-spectrum-matching tabular file. The package also provide function to filter the PSMs based on FDR.' + extra: identifiers: - biotools:pepxmltab @@ -44,3 +25,28 @@ extra: path: recipes/bioconductor-pepxmltab version: 1.16.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RUnit, BiocGenerics +requirements: + host: + - r-base + - r-xml >=3.98-1.1 + run: + - r-base + - r-xml >=3.98-1.1 + +source: + md5: 79c519a5ba5c9e98a19b081a82dac5c7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-periodicdna/meta.yaml b/recipes/bioconductor-periodicdna/meta.yaml index d85c082208a88..61d861bb5d8c3 100644 --- a/recipes/bioconductor-periodicdna/meta.yaml +++ b/recipes/bioconductor-periodicdna/meta.yaml @@ -1,61 +1,66 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "periodicDNA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This R package helps the user identify k-mers (e.g. di- or tri-nucleotides) present periodically in a set of genomic loci (typically regulatory elements). The functions of this package provide a straightforward approach to find periodic occurrences of k-mers in DNA sequences, such as regulatory elements. It is not aimed at identifying motifs separated by a conserved distance; for this type of analysis, please visit MEME website. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Set of tools to identify periodic occurrences of k-mers in DNA sequences -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 60036578bc6ec2c45d1c4b57ae96ad03 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-periodicdna", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, reticulate, testthat, covr, knitr, rmarkdown, pkgdown requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cowplot - r-ggplot2 - r-magrittr - r-zoo run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cowplot - r-ggplot2 - r-magrittr - r-zoo + +source: + md5: 8a1bf41ba0fb05d726ed3da7d1213eab + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Set of tools to identify periodic occurrences of k-mers in DNA sequences' - description: 'This R package helps the user identify k-mers (e.g. di- or tri-nucleotides) present periodically in a set of genomic loci (typically regulatory elements). The functions of this package provide a straightforward approach to find periodic occurrences of k-mers in DNA sequences, such as regulatory elements. It is not aimed at identifying motifs separated by a conserved distance; for this type of analysis, please visit MEME website.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pfam.db/meta.yaml b/recipes/bioconductor-pfam.db/meta.yaml index d5113df6b0741..155c03c3c44aa 100644 --- a/recipes/bioconductor-pfam.db/meta.yaml +++ b/recipes/bioconductor-pfam.db/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "PFAM.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f98f5d1e5d335e6bbf1ea6426cde67bb +about: + description: A set of protein ID mappings for PFAM assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: A set of protein ID mappings for PFAM build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pfam.db", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-pfam.db + path: recipes/bioconductor-pfam.db + version: 3.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b5fd5c9c43685f2b45a3102b98673d36 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A set of protein ID mappings for PFAM' - description: 'A set of protein ID mappings for PFAM assembled using data from public repositories' -extra: - parent_recipe: - name: bioconductor-pfam.db - path: recipes/bioconductor-pfam.db - version: 3.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pfam.db/post-link.sh b/recipes/bioconductor-pfam.db/post-link.sh index c837f5c6d710e..1456f54d71e7c 100644 --- a/recipes/bioconductor-pfam.db/post-link.sh +++ b/recipes/bioconductor-pfam.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pfam.db-3.18.0" +installBiocDataPackage.sh "pfam.db-3.20.0" diff --git a/recipes/bioconductor-pfamanalyzer/meta.yaml b/recipes/bioconductor-pfamanalyzer/meta.yaml index d17c3a7853043..59133f757e09d 100644 --- a/recipes/bioconductor-pfamanalyzer/meta.yaml +++ b/recipes/bioconductor-pfamanalyzer/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "pfamAnalyzeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Protein domains is one of the most import annoation of proteins we have with the Pfam database/tool being (by far) the most used tool. This R package enables the user to read the pfam prediction from both webserver and stand-alone runs into R. We have recently shown most human protein domains exist as multiple distinct variants termed domain isotypes. Different domain isotypes are used in a cell, tissue, and disease-specific manner. Accordingly, we find that domain isotypes, compared to each other, modulate, or abolish the functionality of a protein domain. This R package enables the identification and classification of such domain isotypes from Pfam data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Identification of domain isotypes in pfam data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20159a7f365760efda4827ae6fff80d3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pfamanalyzer", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: host: @@ -35,13 +37,16 @@ requirements: - r-readr - r-stringr - r-tibble + +source: + md5: 35528049bbe6c0fe561287bc2a39c3e4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Identification of domain isotypes in pfam data' - description: 'Protein domains is one of the most import annoation of proteins we have with the Pfam database/tool being (by far) the most used tool. This R package enables the user to read the pfam prediction from both webserver and stand-alone runs into R. We have recently shown most human protein domains exist as multiple distinct variants termed domain isotypes. Different domain isotypes are used in a cell, tissue, and disease-specific manner. Accordingly, we find that domain isotypes, compared to each other, modulate, or abolish the functionality of a protein domain. This R package enables the identification and classification of such domain isotypes from Pfam data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pgca/meta.yaml b/recipes/bioconductor-pgca/meta.yaml index bccdf859ffd7e..edcb527bd07a3 100644 --- a/recipes/bioconductor-pgca/meta.yaml +++ b/recipes/bioconductor-pgca/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "pgca" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 43c58c5b347ebf060a9e6afdc8aa8e93 +about: + description: Protein Group Code Algorithm (PGCA) is a computationally inexpensive algorithm to merge protein summaries from multiple experimental quantitative proteomics data. The algorithm connects two or more groups with overlapping accession numbers. In some cases, pairwise groups are mutually exclusive but they may still be connected by another group (or set of groups) with overlapping accession numbers. Thus, groups created by PGCA from multiple experimental runs (i.e., global groups) are called "connected" groups. These identified global protein groups enable the analysis of quantitative data available for protein groups instead of unique protein identifiers. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pgca", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-pgca + path: recipes/bioconductor-pgca + version: 1.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, testthat, rmarkdown requirements: host: - r-base run: - r-base +source: + md5: ec5cae8e52979d852cabb6c45123c013 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'PGCA: An Algorithm to Link Protein Groups Created from MS/MS Data' - description: 'Protein Group Code Algorithm (PGCA) is a computationally inexpensive algorithm to merge protein summaries from multiple experimental quantitative proteomics data. The algorithm connects two or more groups with overlapping accession numbers. In some cases, pairwise groups are mutually exclusive but they may still be connected by another group (or set of groups) with overlapping accession numbers. Thus, groups created by PGCA from multiple experimental runs (i.e., global groups) are called "connected" groups. These identified global protein groups enable the analysis of quantitative data available for protein groups instead of unique protein identifiers.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-pgca - path: recipes/bioconductor-pgca - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pgxrpi/build.sh b/recipes/bioconductor-pgxrpi/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pgxrpi/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pgxrpi/meta.yaml b/recipes/bioconductor-pgxrpi/meta.yaml new file mode 100644 index 0000000000000..457448b9f8d70 --- /dev/null +++ b/recipes/bioconductor-pgxrpi/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.2.0" %} +{% set name = "pgxRpi" %} +{% set bioc = "3.20" %} + +about: + description: The package is an R wrapper for Progenetix REST API built upon the Beacon v2 protocol. Its purpose is to provide a seamless way for retrieving genomic data from Progenetix database—an open resource dedicated to curated oncogenomic profiles. Empowered by this package, users can effortlessly access and visualize data from Progenetix. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: R wrapper for Progenetix + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pgxrpi", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, rmarkdown, knitr, testthat +requirements: + host: + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-attempt + - r-base + - r-circlize + - r-dplyr + - r-future + - r-future.apply + - r-ggplot2 + - r-httr + - r-lubridate + - r-survival + - r-survminer + - r-yaml + run: + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-attempt + - r-base + - r-circlize + - r-dplyr + - r-future + - r-future.apply + - r-ggplot2 + - r-httr + - r-lubridate + - r-survival + - r-survminer + - r-yaml + +source: + md5: 620df9868488feac34c15f6bd7b45d7c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-phantasus/meta.yaml b/recipes/bioconductor-phantasus/meta.yaml index 12893d324c41d..754983ae1514a 100644 --- a/recipes/bioconductor-phantasus/meta.yaml +++ b/recipes/bioconductor-phantasus/meta.yaml @@ -1,40 +1,54 @@ -{% set version = "1.22.2" %} +{% set version = "1.26.0" %} {% set name = "phantasus" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Phantasus is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Visual and interactive gene expression analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 84c6e2dce18e76a3268130cdd236ba59 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-phantasus", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, BiocStyle, knitr, rmarkdown + +extra: + parent_recipe: + name: bioconductor-phantasus + path: recipes/bioconductor-phantasus + version: 1.2.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, BiocStyle, knitr, rmarkdown, org.Hs.eg.db, org.Mm.eg.db requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-apeglm >=1.28.0,<1.29.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-phantasuslite >=1.4.0,<1.5.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rhdf5client >=1.28.0,<1.29.0 - r-assertthat - r-base - r-ccapp + - r-config >=0.3.2 - r-curl - r-data.table + - r-fs - r-ggplot2 - r-gtable - r-htmltools @@ -49,20 +63,29 @@ requirements: - r-scales - r-stringr - r-svglite + - r-tidyr + - r-xml + - r-yaml + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-apeglm >=1.28.0,<1.29.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-phantasuslite >=1.4.0,<1.5.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rhdf5client >=1.28.0,<1.29.0 - r-assertthat - r-base - r-ccapp + - r-config >=0.3.2 - r-curl - r-data.table + - r-fs - r-ggplot2 - r-gtable - r-htmltools @@ -77,18 +100,19 @@ requirements: - r-scales - r-stringr - r-svglite + - r-tidyr + - r-xml + - r-yaml + +source: + md5: 0afe7f193e0bf54f8f9c0a120e5b26fc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Visual and interactive gene expression analysis' - description: 'Phantasus is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-phantasus - path: recipes/bioconductor-phantasus - version: 1.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-phantasuslite/meta.yaml b/recipes/bioconductor-phantasuslite/meta.yaml index 8f7dc38016eeb..7c1bcaa9663fd 100644 --- a/recipes/bioconductor-phantasuslite/meta.yaml +++ b/recipes/bioconductor-phantasuslite/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "phantasusLite" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: PhantasusLite – a lightweight package with helper functions of general interest extracted from phantasus package. In parituclar it simplifies working with public RNA-seq datasets from GEO by providing access to the remote HSDS repository with the precomputed gene counts from ARCHS4 and DEE2 projects. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Loading and annotation RNA-seq counts matrices -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5fe0e101ac53a89dd49e077d5fb4c07d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-phantasuslite", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rhdf5, GEOquery requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-rhdf5client >=1.24.0,<1.25.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-rhdf5client >=1.28.0,<1.29.0 - r-base - r-data.table - r-httr - r-stringr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-rhdf5client >=1.24.0,<1.25.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-rhdf5client >=1.28.0,<1.29.0 - r-base - r-data.table - r-httr - r-stringr + +source: + md5: d91992a4871bae09abfd2ac02147be76 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Loading and annotation RNA-Seq counts matrices' - description: 'PhantasusLite – a lightweight package with helper functions of general interest extracted from phantasus package. In parituclar it simplifies working with public RNA-seq datasets from GEO by providing access to the remote HSDS repository with the precomputed gene counts from ARCHS4 and DEE2 projects.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pharmacogx/meta.yaml b/recipes/bioconductor-pharmacogx/meta.yaml index b3ec539112cf6..e621e73834d18 100644 --- a/recipes/bioconductor-pharmacogx/meta.yaml +++ b/recipes/bioconductor-pharmacogx/meta.yaml @@ -1,33 +1,41 @@ -{% set version = "3.6.0" %} +{% set version = "3.10.0" %} {% set name = "PharmacoGx" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Analysis of Large-Scale Pharmacogenomic Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a786bf3c0ace641195cfb3b00823cda3 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pharmacogx", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown, BiocStyle, R.utils requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-coregx >=2.6.0,<2.7.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-coregx >=2.10.0,<2.11.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-boot - r-catools @@ -43,14 +51,15 @@ requirements: - r-reshape2 - libblas - liblapack + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-coregx >=2.6.0,<2.7.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-coregx >=2.10.0,<2.11.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-boot - r-catools @@ -64,17 +73,16 @@ requirements: - r-rcolorbrewer - r-rcpp - r-reshape2 - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 7bfe9e2192f852deabc62b213d837920 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Analysis of Large-Scale Pharmacogenomic Data' - description: 'Contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml b/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml index d94d17575001b..9b468b26847d1 100644 --- a/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml +++ b/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml @@ -1,54 +1,60 @@ {% set version = "3.7.2" %} {% set name = "phastCons100way.UCSC.hg19" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Store UCSC phastCons conservation scores for the human genome (hg19) calculated from multiple alignments with other 99 vertebrate species. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: UCSC phastCons conservation scores for hg19 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 65aa706a567f7e328dbba0095f995cf1 build: - number: 14 + noarch: generic + number: 15 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-phastcons100way.ucsc.hg19", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-phastcons100way.ucsc.hg19 + path: recipes/bioconductor-phastcons100way.ucsc.hg19 + version: 3.7.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 65aa706a567f7e328dbba0095f995cf1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'UCSC phastCons conservation scores for hg19' - description: 'Store UCSC phastCons conservation scores for the human genome (hg19) calculated from multiple alignments with other 99 vertebrate species.' -extra: - parent_recipe: - name: bioconductor-phastcons100way.ucsc.hg19 - path: recipes/bioconductor-phastcons100way.ucsc.hg19 - version: 3.7.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg38/meta.yaml b/recipes/bioconductor-phastcons100way.ucsc.hg38/meta.yaml index bfb7828fb7da6..a72c11ee135e0 100644 --- a/recipes/bioconductor-phastcons100way.ucsc.hg38/meta.yaml +++ b/recipes/bioconductor-phastcons100way.ucsc.hg38/meta.yaml @@ -1,49 +1,54 @@ {% set version = "3.7.1" %} {% set name = "phastCons100way.UCSC.hg38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Store UCSC phastCons conservation scores for the human genome (hg38) calculated from multiple alignments with other 99 vertebrate species. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: UCSC phastCons conservation scores for hg38 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 878c757f9270b3410d11e4e4a4213c8e build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-phastcons100way.ucsc.hg38", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 878c757f9270b3410d11e4e4a4213c8e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'UCSC phastCons conservation scores for hg38' - description: 'Store UCSC phastCons conservation scores for the human genome (hg38) calculated from multiple alignments with other 99 vertebrate species.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-phastcons30way.ucsc.hg38/meta.yaml b/recipes/bioconductor-phastcons30way.ucsc.hg38/meta.yaml index c1311660034c3..e474e4fa7e840 100644 --- a/recipes/bioconductor-phastcons30way.ucsc.hg38/meta.yaml +++ b/recipes/bioconductor-phastcons30way.ucsc.hg38/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "phastCons30way.UCSC.hg38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 754faee8463bc494c502540cb8f6ea8d +about: + description: Store phastCons30way.UCSC.hg38 AnnotationHub Resource Metadata. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: phastCons30way.UCSC.hg38 AnnotationHub Resource Metadata build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-phastcons30way.ucsc.hg38", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 754faee8463bc494c502540cb8f6ea8d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'phastCons30way.UCSC.hg38 AnnotationHub Resource Metadata' - description: 'Store phastCons30way.UCSC.hg38 AnnotationHub Resource Metadata.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-phastcons35way.ucsc.mm39/meta.yaml b/recipes/bioconductor-phastcons35way.ucsc.mm39/meta.yaml index 1cd646da27c64..8767a4c667007 100644 --- a/recipes/bioconductor-phastcons35way.ucsc.mm39/meta.yaml +++ b/recipes/bioconductor-phastcons35way.ucsc.mm39/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.16.0" %} {% set name = "phastCons35way.UCSC.mm39" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 83fc2a2265bc341b6a00064a1286b5bc +about: + description: Store UCSC phastCons mm39 conservation scores AnnotationHub Resource Metadata. Provide provenance and citation information for UCSC phastCons mm39 conservation score AnnotationHub resources. Illustrate in a vignette how to access those resources. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: UCSC phastCons mm39 conservation scores AnnotationHub Resource Metadata build: - number: 2 + noarch: generic + number: 3 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-phastcons35way.ucsc.mm39", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 83fc2a2265bc341b6a00064a1286b5bc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'UCSC phastCons mm39 conservation scores AnnotationHub Resource Metadata' - description: 'Store UCSC phastCons mm39 conservation scores AnnotationHub Resource Metadata. Provide provenance and citation information for UCSC phastCons mm39 conservation score AnnotationHub resources. Illustrate in a vignette how to access those resources.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-phastcons7way.ucsc.hg38/meta.yaml b/recipes/bioconductor-phastcons7way.ucsc.hg38/meta.yaml index 8584071542d60..870e6294f41d2 100644 --- a/recipes/bioconductor-phastcons7way.ucsc.hg38/meta.yaml +++ b/recipes/bioconductor-phastcons7way.ucsc.hg38/meta.yaml @@ -1,49 +1,54 @@ {% set version = "3.7.1" %} {% set name = "phastCons7way.UCSC.hg38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Store UCSC phastCons conservation scores for the human genome (hg38) calculated from multiple alignments with other 6 vertebrate species. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: UCSC phastCons conservation scores for hg38 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c2d87446b022c166c1c325ea2aef521d build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-phastcons7way.ucsc.hg38", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: c2d87446b022c166c1c325ea2aef521d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'UCSC phastCons conservation scores for hg38' - description: 'Store UCSC phastCons conservation scores for the human genome (hg38) calculated from multiple alignments with other 6 vertebrate species.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-phenogeneranker/meta.yaml b/recipes/bioconductor-phenogeneranker/meta.yaml index 930e12d2e9963..2cdd2c4949bc5 100644 --- a/recipes/bioconductor-phenogeneranker/meta.yaml +++ b/recipes/bioconductor-phenogeneranker/meta.yaml @@ -1,24 +1,25 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "PhenoGeneRanker" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is a gene/phenotype prioritization tool that utilizes multiplex heterogeneous gene phenotype network. PhenoGeneRanker allows multi-layer gene and phenotype networks. It also calculates empirical p-values of gene/phenotype ranking using random stratified sampling of genes/phenotypes based on their connectivity degree in the network. https://dl.acm.org/doi/10.1145/3307339.3342155. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Creative Commons Attribution 4.0 International License + summary: 'PhenoGeneRanker: A gene and phenotype prioritization tool' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a6530ed180fae6b4250bc56d3de24e19 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-phenogeneranker", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: @@ -35,12 +36,16 @@ requirements: - r-foreach - r-igraph - r-matrix + +source: + md5: 683940c76832fb1787df54d93e5778c8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Creative Commons Attribution 4.0 International License' - summary: 'PhenoGeneRanker: A gene and phenotype prioritization tool' - description: 'This package is a gene/phenotype prioritization tool that utilizes multiplex heterogeneous gene phenotype network. PhenoGeneRanker allows multi-layer gene and phenotype networks. It also calculates empirical p-values of gene/phenotype ranking using random stratified sampling of genes/phenotypes based on their connectivity degree in the network. https://dl.acm.org/doi/10.1145/3307339.3342155.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-phenomis/meta.yaml b/recipes/bioconductor-phenomis/meta.yaml index 7d1a1238da6ff..82659fc2e53eb 100644 --- a/recipes/bioconductor-phenomis/meta.yaml +++ b/recipes/bioconductor-phenomis/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "phenomis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The 'phenomis' package provides methods to perform post-processing (i.e. quality control and normalization) as well as univariate statistical analysis of single and multi-omics data sets. These methods include quality control metrics, signal drift and batch effect correction, intensity transformation, univariate hypothesis testing, but also clustering (as well as annotation of metabolomics data). The data are handled in the standard Bioconductor formats (i.e. SummarizedExperiment and MultiAssayExperiment for single and multi-omics datasets, respectively; the alternative ExpressionSet and MultiDataSet formats are also supported for convenience). As a result, all methods can be readily chained as workflows. The pipeline can be further enriched by multivariate analysis and feature selection, by using the 'ropls' and 'biosigner' packages, which support the same formats. Data can be conveniently imported from and exported to text files. Although the methods were initially targeted to metabolomics data, most of the methods can be applied to other types of omics data (e.g., transcriptomics, proteomics). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: CeCILL + summary: Postprocessing and univariate analysis of omics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6fc3be4aed9fead1f2038fb3d2837854 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-phenomis", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, BiocStyle, biosigner, CLL, knitr, omicade4, rmarkdown, testthat requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biodb >=1.10.0,<1.11.0' - - 'bioconductor-biodbchebi >=1.8.0,<1.9.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-multidataset >=1.30.0,<1.31.0' - - 'bioconductor-ropls >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biodb >=1.14.0,<1.15.0 + - bioconductor-biodbchebi >=1.12.0,<1.13.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-multidataset >=1.34.0,<1.35.0 + - bioconductor-ropls >=1.38.0,<1.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-futile.logger @@ -44,15 +46,16 @@ requirements: - r-tibble - r-tidyr - r-venndiagram + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biodb >=1.10.0,<1.11.0' - - 'bioconductor-biodbchebi >=1.8.0,<1.9.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-multidataset >=1.30.0,<1.31.0' - - 'bioconductor-ropls >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biodb >=1.14.0,<1.15.0 + - bioconductor-biodbchebi >=1.12.0,<1.13.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-multidataset >=1.34.0,<1.35.0 + - bioconductor-ropls >=1.38.0,<1.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-futile.logger @@ -67,12 +70,16 @@ requirements: - r-tibble - r-tidyr - r-venndiagram + +source: + md5: 73d059932bb380964ca38e2fa1a550a3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: CeCILL - summary: 'Postprocessing and univariate analysis of omics data' - description: 'The ''phenomis'' package provides methods to perform post-processing (i.e. quality control and normalization) as well as univariate statistical analysis of single and multi-omics data sets. These methods include quality control metrics, signal drift and batch effect correction, intensity transformation, univariate hypothesis testing, but also clustering (as well as annotation of metabolomics data). The data are handled in the standard Bioconductor formats (i.e. SummarizedExperiment and MultiAssayExperiment for single and multi-omics datasets, respectively; the alternative ExpressionSet and MultiDataSet formats are also supported for convenience). As a result, all methods can be readily chained as workflows. The pipeline can be further enriched by multivariate analysis and feature selection, by using the ''ropls'' and ''biosigner'' packages, which support the same formats. Data can be conveniently imported from and exported to text files. Although the methods were initially targeted to metabolomics data, most of the methods can be applied to other types of omics data (e.g., transcriptomics, proteomics).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-phenopath/meta.yaml b/recipes/bioconductor-phenopath/meta.yaml index bc3a0995ad613..55ba3dcaaf897 100644 --- a/recipes/bioconductor-phenopath/meta.yaml +++ b/recipes/bioconductor-phenopath/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "phenopath" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: PhenoPath infers genomic trajectories (pseudotimes) in the presence of heterogeneous genetic and environmental backgrounds and tests for interactions between them. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Apache License (== 2.0) + summary: Genomic trajectories with heterogeneous genetic and environmental backgrounds -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1bbbcb87efbf78aa39ee07851d27f498 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-phenopath", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, forcats, testthat, BiocStyle, SingleCellExperiment requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 - - 'r-rcpp >=0.12.8' + - r-rcpp >=0.12.8 - r-tibble - r-tidyr - libblas - liblapack run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 - - 'r-rcpp >=0.12.8' + - r-rcpp >=0.12.8 - r-tibble - r-tidyr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: a1b664ee2d6d064f9faa43b0d38ae7d0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Apache License (== 2.0)' - summary: 'Genomic trajectories with heterogeneous genetic and environmental backgrounds' - description: 'PhenoPath infers genomic trajectories (pseudotimes) in the presence of heterogeneous genetic and environmental backgrounds and tests for interactions between them.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-phenotest/meta.yaml b/recipes/bioconductor-phenotest/meta.yaml index 58b9a36220404..7a80e0b010ae9 100644 --- a/recipes/bioconductor-phenotest/meta.yaml +++ b/recipes/bioconductor-phenotest/meta.yaml @@ -1,38 +1,41 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "phenoTest" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools to test correlation between gene expression and phenotype in a way that is efficient, structured, fast and scalable. GSEA is also provided. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation. -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 20bd295654c25854160e8a1aad42d8e8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-phenotest", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: GSEABase, GO.db requirements: + host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-category >=2.68.0,<2.69.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-heatplus >=3.10.0,<3.11.0' - - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - - 'bioconductor-hopach >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-category >=2.72.0,<2.73.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-heatplus >=3.14.0,<3.15.0 + - bioconductor-hgu133a.db >=3.13.0,<3.14.0 + - bioconductor-hopach >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-bma - r-ellipse @@ -42,18 +45,19 @@ requirements: - r-mgcv - r-survival - r-xtable + run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-category >=2.68.0,<2.69.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-heatplus >=3.10.0,<3.11.0' - - 'bioconductor-hgu133a.db >=3.13.0,<3.14.0' - - 'bioconductor-hopach >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-category >=2.72.0,<2.73.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-heatplus >=3.14.0,<3.15.0 + - bioconductor-hgu133a.db >=3.13.0,<3.14.0 + - bioconductor-hopach >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-bma - r-ellipse @@ -63,13 +67,16 @@ requirements: - r-mgcv - r-survival - r-xtable + +source: + md5: f50a29738bfdbc6c2dc658ffcd9b2809 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.' - description: 'Tools to test correlation between gene expression and phenotype in a way that is efficient, structured, fast and scalable. GSEA is also provided.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-phenstat/meta.yaml b/recipes/bioconductor-phenstat/meta.yaml index c766d7ff7dc15..4550de798271f 100644 --- a/recipes/bioconductor-phenstat/meta.yaml +++ b/recipes/bioconductor-phenstat/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "2.38.0" %} +{% set version = "2.42.0" %} {% set name = "PhenStat" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package contains methods for statistical analysis of phenotypic data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Statistical analysis of phenotypic data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f28cba815b5f6e8b3350c926d1d05907 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-phenstat", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-car - r-corrplot @@ -38,7 +40,7 @@ requirements: - r-reshape - r-smoothwin run: - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-car - r-corrplot @@ -53,13 +55,16 @@ requirements: - r-pingr - r-reshape - r-smoothwin + +source: + md5: 4010a9dad5f281a3054993c2092ced7b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Statistical analysis of phenotypic data' - description: 'Package contains methods for statistical analysis of phenotypic data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-philr/meta.yaml b/recipes/bioconductor-philr/meta.yaml index 225cd7a47bc4c..e7b1025d08581 100644 --- a/recipes/bioconductor-philr/meta.yaml +++ b/recipes/bioconductor-philr/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "philr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: PhILR is short for Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). Specifically this package allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Phylogenetic partitioning based ILR transform for metagenomics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d55e931af78335bd6378fba38c5f54a8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-philr", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:philr + parent_recipe: + name: bioconductor-philr + path: recipes/bioconductor-philr + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq, SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr, mia requirements: host: - - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - bioconductor-ggtree >=3.14.0,<3.15.0 - r-ape - r-base - r-ggplot2 - r-phangorn - r-tidyr run: - - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - bioconductor-ggtree >=3.14.0,<3.15.0 - r-ape - r-base - r-ggplot2 - r-phangorn - r-tidyr + +source: + md5: e45ace4abfb591c0f37ab174248f6311 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Phylogenetic partitioning based ILR transform for metagenomics data' - description: 'PhILR is short for Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). Specifically this package allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:philr - parent_recipe: - name: bioconductor-philr - path: recipes/bioconductor-philr - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-phipdata/meta.yaml b/recipes/bioconductor-phipdata/meta.yaml index 2c96fe878d6dc..0201b6d4ed277 100644 --- a/recipes/bioconductor-phipdata/meta.yaml +++ b/recipes/bioconductor-phipdata/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "PhIPData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: PhIPData defines an S4 class for phage-immunoprecipitation sequencing (PhIP-seq) experiments. Buliding upon the RangedSummarizedExperiment class, PhIPData enables users to coordinate metadata with experimental data in analyses. Additionally, PhIPData provides specialized methods to subset and identify beads-only samples, subset objects using virus aliases, and use existing peptide libraries to populate object parameters. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Container for PhIP-Seq Experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fdb81e6f685727bbbe4584f42ca33797 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-phipdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr, withr requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cli run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cli + +source: + md5: 5d5422da85869a7cae252e397a1746b5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Container for PhIP-Seq Experiments' - description: 'PhIPData defines an S4 class for phage-immunoprecipitation sequencing (PhIP-seq) experiments. Buliding upon the RangedSummarizedExperiment class, PhIPData enables users to coordinate metadata with experimental data in analyses. Additionally, PhIPData provides specialized methods to subset and identify beads-only samples, subset objects using virus aliases, and use existing peptide libraries to populate object parameters.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-phosphonormalizer/meta.yaml b/recipes/bioconductor-phosphonormalizer/meta.yaml index 83fa2d9b82923..66be93eaf6221 100644 --- a/recipes/bioconductor-phosphonormalizer/meta.yaml +++ b/recipes/bioconductor-phosphonormalizer/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "phosphonormalizer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b0146ac595b90e20d854404e6fa427bb +about: + description: It uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Compensates for the bias introduced by median normalization in build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-phosphonormalizer", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, testthat requirements: host: @@ -29,13 +28,14 @@ requirements: - r-base - r-matrixstats - r-plyr +source: + md5: 73c2916d619e81a1b3801fbbac91b8bf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Compensates for the bias introduced by median normalization in' - description: 'It uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-phosr/meta.yaml b/recipes/bioconductor-phosr/meta.yaml index c27015e7252dc..3f45b316e4750 100644 --- a/recipes/bioconductor-phosr/meta.yaml +++ b/recipes/bioconductor-phosr/meta.yaml @@ -1,33 +1,36 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "PhosR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'PhosR is a package for the comprenhensive analysis of phosphoproteomic data. There are two major components to PhosR: processing and downstream analysis. PhosR consists of various processing tools for phosphoproteomics data including filtering, imputation, normalisation, and functional analysis for inferring active kinases and signalling pathways.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: A set of methods and tools for comprehensive analysis of phosphoproteomics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 49f34b9174257536ac2a912530d69d10 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-phosr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown, org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle, stringr, calibrate requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-dendextend @@ -47,13 +50,14 @@ requirements: - r-ruv - r-stringi - r-tidyr + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-dendextend @@ -73,13 +77,16 @@ requirements: - r-ruv - r-stringi - r-tidyr + +source: + md5: 6b1504d5397d33cb69cced260b89c781 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'A set of methods and tools for comprehensive analysis of phosphoproteomics data' - description: 'PhosR is a package for the comprenhensive analysis of phosphoproteomic data. There are two major components to PhosR: processing and downstream analysis. PhosR consists of various processing tools for phosphoproteomics data including filtering, imputation, normalisation, and functional analysis for inferring active kinases and signalling pathways.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-phylop35way.ucsc.mm39/meta.yaml b/recipes/bioconductor-phylop35way.ucsc.mm39/meta.yaml index 891cac36e766a..791e2b40e2c43 100644 --- a/recipes/bioconductor-phylop35way.ucsc.mm39/meta.yaml +++ b/recipes/bioconductor-phylop35way.ucsc.mm39/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.16.0" %} {% set name = "phyloP35way.UCSC.mm39" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2c34eef5f20eace04efd47673cdf1062 +about: + description: Store UCSC phyloP mm39 conservation scores AnnotationHub Resource Metadata. Provide provenance and citation information for UCSC phyloP mm39 conservation score AnnotationHub resources. Illustrate in a vignette how to access those resources. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: UCSC phyloP mm39 conservation scores AnnotationHub Resource Metadata build: - number: 2 + noarch: generic + number: 3 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-phylop35way.ucsc.mm39", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2c34eef5f20eace04efd47673cdf1062 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'UCSC phyloP mm39 conservation scores AnnotationHub Resource Metadata' - description: 'Store UCSC phyloP mm39 conservation scores AnnotationHub Resource Metadata. Provide provenance and citation information for UCSC phyloP mm39 conservation score AnnotationHub resources. Illustrate in a vignette how to access those resources.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-phyloprofile/meta.yaml b/recipes/bioconductor-phyloprofile/meta.yaml index c9851553e3706..3105e806d2754 100644 --- a/recipes/bioconductor-phyloprofile/meta.yaml +++ b/recipes/bioconductor-phyloprofile/meta.yaml @@ -1,87 +1,98 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "PhyloProfile" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic profiles, presence/absence patterns of genes over a set of species, are commonly used to trace the functional and evolutionary history of genes across species and time. With PhyloProfile we can enrich regular phylogenetic profiles with further data like sequence/structure similarity, to make phylogenetic profiling more meaningful. Besides the interactive visualisation powered by R-Shiny, the package offers a set of further analysis features to gain insights like the gene age estimation or core gene identification. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: PhyloProfile -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96200a149b95297ba34dee53963493a1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-phyloprofile", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, testthat + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, testthat, OmaDB requirements: + host: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-biodist >=1.74.0,<1.75.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-omadb >=2.18.0,<2.19.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-biodist >=1.78.0,<1.79.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-ape - r-base - r-colourpicker - r-data.table + - r-dplyr - r-dt - r-energy + - r-extrafont - r-ggplot2 - r-gridextra - r-pbapply - - r-plyr - r-rcolorbrewer - r-rcurl + - r-scattermore - r-shiny - r-shinybs - r-shinycssloaders - r-shinyfiles - r-shinyjs - r-stringr + - r-umap - r-xml2 - r-yaml - r-zoo + run: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-biodist >=1.74.0,<1.75.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-omadb >=2.18.0,<2.19.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-biodist >=1.78.0,<1.79.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-ape - r-base - r-colourpicker - r-data.table + - r-dplyr - r-dt - r-energy + - r-extrafont - r-ggplot2 - r-gridextra - r-pbapply - - r-plyr - r-rcolorbrewer - r-rcurl + - r-scattermore - r-shiny - r-shinybs - r-shinycssloaders - r-shinyfiles - r-shinyjs - r-stringr + - r-umap - r-xml2 - r-yaml - r-zoo + +source: + md5: 2b825262feec94b16469620e9089da0b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: PhyloProfile - description: 'PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic profiles, presence/absence patterns of genes over a set of species, are commonly used to trace the functional and evolutionary history of genes across species and time. With PhyloProfile we can enrich regular phylogenetic profiles with further data like sequence/structure similarity, to make phylogenetic profiling more meaningful. Besides the interactive visualisation powered by R-Shiny, the package offers a set of further analysis features to gain insights like the gene age estimation or core gene identification.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-phyloprofiledata/meta.yaml b/recipes/bioconductor-phyloprofiledata/meta.yaml index f08883286f7df..3e39b6d0db125 100644 --- a/recipes/bioconductor-phyloprofiledata/meta.yaml +++ b/recipes/bioconductor-phyloprofiledata/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "PhyloProfileData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 68dda32e9151c0aba4eb5b29c0313f83 +about: + description: Two experimental datasets to illustrate running and analysing phylogenetic profiles with PhyloProfile package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Data package for phylogenetic profile analysis using PhyloProfile tool build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-phyloprofiledata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, markdown requirements: host: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c90f4558af49b28657028abe5d402f4f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Data package for phylogenetic profile analysis using PhyloProfile tool' - description: 'Two experimental datasets to illustrate running and analysing phylogenetic profiles with PhyloProfile package.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-phyloprofiledata/post-link.sh b/recipes/bioconductor-phyloprofiledata/post-link.sh index 7f47b649e3562..2089589690444 100644 --- a/recipes/bioconductor-phyloprofiledata/post-link.sh +++ b/recipes/bioconductor-phyloprofiledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "phyloprofiledata-1.16.0" +installBiocDataPackage.sh "phyloprofiledata-1.20.0" diff --git a/recipes/bioconductor-phyloseq/meta.yaml b/recipes/bioconductor-phyloseq/meta.yaml index 816a5356e24c3..262713e4209d8 100644 --- a/recipes/bioconductor-phyloseq/meta.yaml +++ b/recipes/bioconductor-phyloseq/meta.yaml @@ -1,76 +1,82 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "phyloseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + summary: Handling and analysis of high-throughput microbiome census data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 335dc9dedba529ce34669dd881127e7c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-phyloseq", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:phyloseq + parent_recipe: + name: bioconductor-phyloseq + path: recipes/bioconductor-phyloseq + version: 1.24.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle (>= 2.4), DESeq2 (>= 1.16.1), genefilter (>= 1.58), knitr (>= 1.16), magrittr (>= 1.5), metagenomeSeq (>= 1.14), rmarkdown (>= 1.6), testthat (>= 1.0.2) requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomformat >=1.30.0,<1.31.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'r-ade4 >=1.7-4' - - 'r-ape >=5.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomformat >=1.34.0,<1.35.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - r-ade4 >=1.7-4 + - r-ape >=5.0 - r-base - - 'r-cluster >=2.0.4' - - 'r-data.table >=1.10.4' - - 'r-foreach >=1.4.3' - - 'r-ggplot2 >=2.1.0' - - 'r-igraph >=1.0.1' - - 'r-plyr >=1.8.3' - - 'r-reshape2 >=1.4.1' - - 'r-scales >=0.4.0' - - 'r-vegan >=2.5' + - r-cluster >=2.0.4 + - r-data.table >=1.10.4 + - r-foreach >=1.4.3 + - r-ggplot2 >=2.1.0 + - r-igraph >=1.0.1 + - r-plyr >=1.8.3 + - r-reshape2 >=1.4.1 + - r-scales >=0.4.0 + - r-vegan >=2.5 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomformat >=1.30.0,<1.31.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'r-ade4 >=1.7-4' - - 'r-ape >=5.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomformat >=1.34.0,<1.35.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - r-ade4 >=1.7-4 + - r-ape >=5.0 - r-base - - 'r-cluster >=2.0.4' - - 'r-data.table >=1.10.4' - - 'r-foreach >=1.4.3' - - 'r-ggplot2 >=2.1.0' - - 'r-igraph >=1.0.1' - - 'r-plyr >=1.8.3' - - 'r-reshape2 >=1.4.1' - - 'r-scales >=0.4.0' - - 'r-vegan >=2.5' + - r-cluster >=2.0.4 + - r-data.table >=1.10.4 + - r-foreach >=1.4.3 + - r-ggplot2 >=2.1.0 + - r-igraph >=1.0.1 + - r-plyr >=1.8.3 + - r-reshape2 >=1.4.1 + - r-scales >=0.4.0 + - r-vegan >=2.5 + +source: + md5: 3477ffc96686ac43d1dc7ce0bdbb647f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3 - summary: 'Handling and analysis of high-throughput microbiome census data' - description: 'phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' -extra: - identifiers: - - biotools:phyloseq - parent_recipe: - name: bioconductor-phyloseq - path: recipes/bioconductor-phyloseq - version: 1.24.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-piano/meta.yaml b/recipes/bioconductor-piano/meta.yaml index 947eddd07883a..5a5d9e2efe745 100644 --- a/recipes/bioconductor-piano/meta.yaml +++ b/recipes/bioconductor-piano/meta.yaml @@ -1,31 +1,41 @@ -{% set version = "2.18.0" %} +{% set version = "2.22.0" %} {% set name = "piano" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Piano performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. Furthermore, the Piano package contains functions for combining the results of multiple runs of gene set analyses. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Platform for integrative analysis of omics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 84b0ce2cca9fb11110bd82113e066e82 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-piano", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:piano + parent_recipe: + name: bioconductor-piano + path: recipes/bioconductor-piano + version: 1.20.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-marray >=1.84.0,<1.85.0 - r-base - r-dt - r-gplots @@ -38,10 +48,10 @@ requirements: - r-shinyjs - r-visnetwork run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-marray >=1.84.0,<1.85.0 - r-base - r-dt - r-gplots @@ -53,20 +63,16 @@ requirements: - r-shinydashboard - r-shinyjs - r-visnetwork + +source: + md5: 85e52c0b48f3fe7a528f2bbb96657ca5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Platform for integrative analysis of omics data' - description: 'Piano performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. Furthermore, the Piano package contains functions for combining the results of multiple runs of gene set analyses.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:piano - parent_recipe: - name: bioconductor-piano - path: recipes/bioconductor-piano - version: 1.20.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pickgene/meta.yaml b/recipes/bioconductor-pickgene/meta.yaml index 2ac35c4ab1be0..6c3c320d5bfb0 100644 --- a/recipes/bioconductor-pickgene/meta.yaml +++ b/recipes/bioconductor-pickgene/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "pickgene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions to Analyze Microarray (Gene Expression) Data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Adaptive Gene Picking for Microarray Expression Data Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 250b3649eff783447f1d2c34f67bf3ca build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pickgene", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:pickgene + - doi:10.1007/0-387-21679-0_13 + parent_recipe: + name: bioconductor-pickgene + path: recipes/bioconductor-pickgene + version: 1.52.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -26,21 +37,16 @@ requirements: run: - r-base - r-mass + +source: + md5: fbee43148f438f3eae46783d369b7aaf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Adaptive Gene Picking for Microarray Expression Data Analysis' - description: 'Functions to Analyze Microarray (Gene Expression) Data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:pickgene - - doi:10.1007/0-387-21679-0_13 - parent_recipe: - name: bioconductor-pickgene - path: recipes/bioconductor-pickgene - version: 1.52.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pics/meta.yaml b/recipes/bioconductor-pics/meta.yaml index 29900a517454a..9cb0e31ee7af6 100644 --- a/recipes/bioconductor-pics/meta.yaml +++ b/recipes/bioconductor-pics/meta.yaml @@ -1,59 +1,62 @@ -{% set version = "2.46.0" %} +{% set version = "2.50.0" %} {% set name = "PICS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Probabilistic inference of ChIP-seq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 04ed3fdb7f1db15654e9974438495e43 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pics", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:pics + parent_recipe: + name: bioconductor-pics + path: recipes/bioconductor-pics + version: 2.24.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rtracklayer, parallel, knitr -# SystemRequirements: gsl requirements: + build: + - {{ compiler('c') }} + - automake + - make host: - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - libblas - liblapack - - gsl run: - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - - gsl - build: - - {{ compiler('c') }} - - automake - - make + +source: + md5: f7ebf4a39521560959720e07325dc592 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Probabilistic inference of ChIP-seq' - description: 'Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.' -extra: - identifiers: - - biotools:pics - parent_recipe: - name: bioconductor-pics - path: recipes/bioconductor-pics - version: 2.24.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pig.db0/meta.yaml b/recipes/bioconductor-pig.db0/meta.yaml index 15e8ede99ee85..59424d305e2ee 100644 --- a/recipes/bioconductor-pig.db0/meta.yaml +++ b/recipes/bioconductor-pig.db0/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "pig.db0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 85aaccdbdb969825957db45db3fb7801 +about: + description: Base annotation databases for pig, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Level Annotation databases for pig build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pig.db0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a3941b9af7837e468df8f53546072c5f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Level Annotation databases for pig' - description: 'Base annotation databases for pig, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pig.db0/post-link.sh b/recipes/bioconductor-pig.db0/post-link.sh index ccf6ee98e3660..ea39b74eadc76 100644 --- a/recipes/bioconductor-pig.db0/post-link.sh +++ b/recipes/bioconductor-pig.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pig.db0-3.18.0" +installBiocDataPackage.sh "pig.db0-3.20.0" diff --git a/recipes/bioconductor-pigengene/meta.yaml b/recipes/bioconductor-pigengene/meta.yaml index 6200d1de33d16..7ff01a1f75dff 100644 --- a/recipes/bioconductor-pigengene/meta.yaml +++ b/recipes/bioconductor-pigengene/meta.yaml @@ -1,39 +1,42 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "Pigengene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Pigengene package provides an efficient way to infer biological signatures from gene expression profiles. The signatures are independent from the underlying platform, e.g., the input can be microarray or RNA Seq data. It can even infer the signatures using data from one platform, and evaluate them on the other. Pigengene identifies the modules (clusters) of highly coexpressed genes using coexpression network analysis, summarizes the biological information of each module in an eigengene, learns a Bayesian network that models the probabilistic dependencies between modules, and builds a decision tree based on the expression of eigengenes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Infers biological signatures from gene expression data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d7b090a6d6fad6cf62c987970663167 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pigengene", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: org.Hs.eg.db (>= 3.7.0), org.Mm.eg.db (>= 3.7.0), biomaRt (>= 2.30.0), knitr, AnnotationDbi, energy requirements: + host: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-reactomepa >=1.46.0,<1.47.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-reactomepa >=1.50.0,<1.51.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - - 'r-bnlearn >=4.7' - - 'r-c50 >=0.1.2' + - r-bnlearn >=4.7 + - r-c50 >=0.1.2 - r-dbi - r-dplyr - r-gdata @@ -42,21 +45,22 @@ requirements: - r-matrixstats - r-openxlsx - r-partykit - - 'r-pheatmap >=1.0.8' + - r-pheatmap >=1.0.8 - r-wgcna + run: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-reactomepa >=1.46.0,<1.47.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-reactomepa >=1.50.0,<1.51.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - - 'r-bnlearn >=4.7' - - 'r-c50 >=0.1.2' + - r-bnlearn >=4.7 + - r-c50 >=0.1.2 - r-dbi - r-dplyr - r-gdata @@ -65,15 +69,18 @@ requirements: - r-matrixstats - r-openxlsx - r-partykit - - 'r-pheatmap >=1.0.8' + - r-pheatmap >=1.0.8 - r-wgcna + +source: + md5: 593b50d56cfb5bc2f5f5c83aadb236e8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Infers biological signatures from gene expression data' - description: 'Pigengene package provides an efficient way to infer biological signatures from gene expression profiles. The signatures are independent from the underlying platform, e.g., the input can be microarray or RNA Seq data. It can even infer the signatures using data from one platform, and evaluate them on the other. Pigengene identifies the modules (clusters) of highly coexpressed genes using coexpression network analysis, summarizes the biological information of each module in an eigengene, learns a Bayesian network that models the probabilistic dependencies between modules, and builds a decision tree based on the expression of eigengenes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ping/build_failure.osx-64.yaml b/recipes/bioconductor-ping/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..75fab06de85ed --- /dev/null +++ b/recipes/bioconductor-ping/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: f1fd274266574337f0b21bc25cbeb0c6aac547eca6eff5cd6d13022405af4f83 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-genomeinfodbdata [1.2.1|1.2.2] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-genomeinfodbdata [1.2.10|1.2.11] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.3|1.2.4] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.6|1.2.7] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-genomeinfodbdata 1.2.9 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-ucsc.utils >=1.2.0,<1.3.0 is not installable because it requires + r-base >=4.4,<4.5.0a0 , which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("4.0.1==hcfea43d_1"), MatchSpec("clang==4.0.1=1")} + Encountered problems while solving: + - nothing provides compiler-rt 4.0.1 hcfea43d_1 needed by clang-4.0.1-1 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-genomeinfodbdata >=1.2.0,<1.3.0 is installable with the potential options + bioconductor-genomeinfodbdata [1.2.0|1.2.1] would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-genomeinfodbdata [1.2.1|1.2.2] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-genomeinfodbdata [1.2.10|1.2.11] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.3|1.2.4] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.6|1.2.7] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-genomeinfodbdata 1.2.9 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-ucsc.utils >=1.2.0,<1.3.0 is not installable because it requires + r-base >=4.4,<4.5.0a0 , which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-ping/meta.yaml b/recipes/bioconductor-ping/meta.yaml index 05e5b3f99f186..9fc563b3e249a 100644 --- a/recipes/bioconductor-ping/meta.yaml +++ b/recipes/bioconductor-ping/meta.yaml @@ -1,64 +1,70 @@ -{% set version = "2.46.0" %} +{% set version = "2.50.0" %} {% set name = "PING" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 703e11e3d890a3cf2b48c15d4c76ea87 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ping", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:ping + parent_recipe: + name: bioconductor-ping + path: recipes/bioconductor-ping + version: 2.24.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: parallel, ShortRead, rtracklayer requirements: + build: + - {{ compiler('c') }} + - automake + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-pics >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pics >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-fda - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-pics >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pics >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-fda - build: - - {{ compiler('c') }} - - automake - - make + +source: + md5: 8339c8918acb33c6c33786c409899dc8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data' - description: 'Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.' -extra: - identifiers: - - biotools:ping - parent_recipe: - name: bioconductor-ping - path: recipes/bioconductor-ping - version: 2.24.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pipecomp/build_failure.linux-64.yaml b/recipes/bioconductor-pipecomp/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..e2dcf9e0c8806 --- /dev/null +++ b/recipes/bioconductor-pipecomp/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: da04a7fa501e6e187cd1eaada8b5b4e7db5fbd2badeb885962d2eb672fef65f8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-ggrastr"), MatchSpec("bioconductor-scater==1.34.0=r44hdfd78af_0")} + Encountered problems while solving: + - package bioconductor-scater-1.34.0-r44hdfd78af_0 requires r-ggrastr, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-scater >=1.34.0,<1.35.0 [0m is installable and it requires + [32mr-ggrastr[0m with the potential options + [32mr-ggrastr 1.0.2[0m would require + [32mr-cairo >=1.5.9 [0m with the potential options + [32mr-cairo [1.5_10|1.5_11|1.5_12|1.5_9][0m would require + [32mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which can be installed; + [32mr-cairo [1.5_10|1.5_11|1.5_12|1.5_12.2][0m would require + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mr-cairo [1.5_12|1.5_12.2|1.5_14|1.5_15|1.6_0][0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-cairo [1.5_12.2|1.5_14|1.5_15|1.6_0][0m would require + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-cairo 1.5_9[0m would require + [32mr-base 3.3.2* [0m, which can be installed; + [32mr-cairo 1.5_9[0m would require + [32mr-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ][0m, which can be installed; + [32mr-cairo [1.6_0|1.6_1|1.6_2][0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mr-cairo [1.6_0|1.6_1|1.6_2][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mr-cairo 1.6_2[0m would require + [32micu >=75.1,<76.0a0 [0m, which can be installed; + [32mr-ggrastr [0.2.1|0.2.2|0.2.3][0m would require + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mr-ggrastr [0.2.1|0.2.2|0.2.3|1.0.0|1.0.1][0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-ggrastr [0.2.3|1.0.0|1.0.1|1.0.2][0m would require + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-ggrastr [1.0.1|1.0.2][0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mr-ggrastr 1.0.2[0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because there are no viable options + [31mr-base [4.4.0|4.4.1][0m would require + [31micu >=73.2,<74.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-base [4.4.1|4.4.2][0m would require + [32micu >=75.1,<76.0a0 [0m, which can be installed; + [32mr-randomcolor[0m is installable with the potential options + [32mr-randomcolor 1.1.0.1[0m would require + [32mr-v8[0m with the potential options + [32mr-v8 [2.3|3.0|3.0.1|3.0.2][0m would require + [32mr-base >=3.5,<3.6.0a0 [0m, which can be installed; + [32mr-v8 [2.3|3.0|...|3.4.2][0m would require + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mr-v8 [3.0.2|3.1.0|...|4.2.1][0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-v8 [3.4.2|3.5.0|...|4.3.0][0m would require + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-v8 [4.2.1|4.2.2|...|4.4.2][0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mr-v8 [4.3.0|4.3.1|...|5.0.1][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-v8 [4.4.2|5.0.0|5.0.1][0m would require + [31micu >=73.2,<74.0a0 [0m, which conflicts with any installable versions previously reported; + [32mr-randomcolor [1.1.0|1.1.0.1][0m would require + [32mr-base >=3.5,<3.6.0a0 [0m, which can be installed; + [32mr-randomcolor [1.1.0|1.1.0.1][0m would require + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mr-randomcolor 1.1.0.1[0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-randomcolor 1.1.0.1[0m would require + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-randomcolor 1.1.0.1[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mr-randomcolor 1.1.0.1[0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-pipecomp/meta.yaml b/recipes/bioconductor-pipecomp/meta.yaml index f2a38e18004db..8f52c8c80446b 100644 --- a/recipes/bioconductor-pipecomp/meta.yaml +++ b/recipes/bioconductor-pipecomp/meta.yaml @@ -1,34 +1,37 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "pipeComp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A simple framework to facilitate the comparison of pipelines involving various steps and parameters. The `pipelineDefinition` class represents pipelines as, minimally, a set of functions consecutively executed on the output of the previous one, and optionally accompanied by step-wise evaluation and aggregation functions. Given such an object, a set of alternative parameters/methods, and benchmark datasets, the `runPipeline` function then proceeds through all combinations arguments, avoiding recomputing the same step twice and compiling evaluations on the fly to avoid storing potentially large intermediate data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: pipeComp pipeline benchmarking framework -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ccc688331233bccee84104cbbb9b5d81 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pipecomp", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, rmarkdown requirements: + host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-aricode - r-base - r-circlize @@ -49,14 +52,15 @@ requirements: - r-seurat - r-uwot - r-viridislite + run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-aricode - r-base - r-circlize @@ -77,13 +81,16 @@ requirements: - r-seurat - r-uwot - r-viridislite + +source: + md5: 1d4f2ff01c4ebbb799909f65d77eb0e2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL - summary: 'pipeComp pipeline benchmarking framework' - description: 'A simple framework to facilitate the comparison of pipelines involving various steps and parameters. The `pipelineDefinition` class represents pipelines as, minimally, a set of functions consecutively executed on the output of the previous one, and optionally accompanied by step-wise evaluation and aggregation functions. Given such an object, a set of alternative parameters/methods, and benchmark datasets, the `runPipeline` function then proceeds through all combinations arguments, avoiding recomputing the same step twice and compiling evaluations on the fly to avoid storing potentially large intermediate data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pipeframe/meta.yaml b/recipes/bioconductor-pipeframe/meta.yaml index eab0329b0160a..3c433091b56c1 100644 --- a/recipes/bioconductor-pipeframe/meta.yaml +++ b/recipes/bioconductor-pipeframe/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "pipeFrame" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: pipeFrame is an R package for building a componentized bioinformatics pipeline. Each step in this pipeline is wrapped in the framework, so the connection among steps is created seamlessly and automatically. Users could focus more on fine-tuning arguments rather than spending a lot of time on transforming file format, passing task outputs to task inputs or installing the dependencies. Componentized step elements can be customized into other new pipelines flexibly as well. This pipeline can be split into several important functional steps, so it is much easier for users to understand the complex arguments from each step rather than parameter combination from the whole pipeline. At the same time, componentized pipeline can restart at the breakpoint and avoid rerunning the whole pipeline, which may save a lot of time for users on pipeline tuning or such issues as power off or process other interrupts. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Pipeline framework for bioinformatics in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 142f8d049aa03cec36050c2b0ccc87d9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pipeframe", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocManager, knitr, rtracklayer, testthat, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 - r-base - r-digest - r-magrittr - r-rmarkdown - r-visnetwork run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 - r-base - r-digest - r-magrittr - r-rmarkdown - r-visnetwork + +source: + md5: 9d76948ffbd0785e16f89c0eccbb63d4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Pipeline framework for bioinformatics in R' - description: 'pipeFrame is an R package for building a componentized bioinformatics pipeline. Each step in this pipeline is wrapped in the framework, so the connection among steps is created seamlessly and automatically. Users could focus more on fine-tuning arguments rather than spending a lot of time on transforming file format, passing task outputs to task inputs or installing the dependencies. Componentized step elements can be customized into other new pipelines flexibly as well. This pipeline can be split into several important functional steps, so it is much easier for users to understand the complex arguments from each step rather than parameter combination from the whole pipeline. At the same time, componentized pipeline can restart at the breakpoint and avoid rerunning the whole pipeline, which may save a lot of time for users on pipeline tuning or such issues as power off or process other interrupts.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pipets/build.sh b/recipes/bioconductor-pipets/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pipets/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pipets/meta.yaml b/recipes/bioconductor-pipets/meta.yaml new file mode 100644 index 0000000000000..3588373d4e245 --- /dev/null +++ b/recipes/bioconductor-pipets/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.2.0" %} +{% set name = "PIPETS" %} +{% set bioc = "3.20" %} + +about: + description: PIPETS provides statistically robust analysis for 3'-seq/term-seq data. It utilizes a sliding window approach to apply a Poisson Distribution test to identify genomic positions with termination read coverage that is significantly higher than the surrounding signal. PIPETS then condenses proximal signal and produces strand specific results that contain all significant termination peaks. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Poisson Identification of PEaks from Term-Seq data +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pipets", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - r-base + - r-dplyr + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - r-base + - r-dplyr +source: + md5: c7f07b225d88c0172f2f4c5afb6da639 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-pirat/build.sh b/recipes/bioconductor-pirat/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pirat/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pirat/meta.yaml b/recipes/bioconductor-pirat/meta.yaml new file mode 100644 index 0000000000000..4ac64433d9d63 --- /dev/null +++ b/recipes/bioconductor-pirat/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.0.0" %} +{% set name = "Pirat" %} +{% set bioc = "3.20" %} + +about: + description: Pirat enables the imputation of missing values (either MNARs or MCARs) in bottom-up LC-MS/MS proteomics data using a penalized maximum likelihood strategy. It does not require any parameter tuning, it models the instrument censorship from the data available. It accounts for sibling peptides correlations and it can leverage complementary transcriptomics measurements. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Precursor or Peptide Imputation under Random Truncation + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pirat", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, BiocStyle +requirements: + host: + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-ggplot2 + - r-invgamma + - r-mass + - r-progress + - r-reticulate + run: + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-ggplot2 + - r-invgamma + - r-mass + - r-progress + - r-reticulate + +source: + md5: c650b34a77e8db8355855b68b4480f58 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-piuma/build.sh b/recipes/bioconductor-piuma/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-piuma/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-piuma/meta.yaml b/recipes/bioconductor-piuma/meta.yaml new file mode 100644 index 0000000000000..6973f0f6a5671 --- /dev/null +++ b/recipes/bioconductor-piuma/meta.yaml @@ -0,0 +1,66 @@ +{% set version = "1.2.0" %} +{% set name = "PIUMA" %} +{% set bioc = "3.20" %} + +about: + description: The PIUMA package offers a tidy pipeline of Topological Data Analysis frameworks to identify and characterize communities in high and heterogeneous dimensional data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Phenotypes Identification Using Mapper from topological data Analysis + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-piuma", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, testthat, rmarkdown +requirements: + host: + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-cluster + - r-dbscan + - r-ggplot2 + - r-hmisc + - r-igraph + - r-kernlab + - r-patchwork + - r-scales + - r-tsne + - r-umap + - r-vegan + run: + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-cluster + - r-dbscan + - r-ggplot2 + - r-hmisc + - r-igraph + - r-kernlab + - r-patchwork + - r-scales + - r-tsne + - r-umap + - r-vegan + +source: + md5: 235a7f290e21fb985fccc55ce67bf3ce + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-planet/meta.yaml b/recipes/bioconductor-planet/meta.yaml index 3b2c110ad4fd1..b37fa31344f6c 100644 --- a/recipes/bioconductor-planet/meta.yaml +++ b/recipes/bioconductor-planet/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "planet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dbd74bc4dd3583d6ebbd871b251ecd6d +about: + description: This package contains R functions to predict biological variables to from placnetal DNA methylation data generated from infinium arrays. This includes inferring ethnicity/ancestry, gestational age, and cell composition from placental DNA methylation array (450k/850k) data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Placental DNA methylation analysis tools build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-planet", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: ggplot2, testthat, tidyr, scales, minfi, EpiDISH, knitr, rmarkdown requirements: host: @@ -31,13 +30,14 @@ requirements: - r-dplyr - r-magrittr - r-tibble +source: + md5: c8ee44e07f3e337f10e1cbbea40e7b53 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Placental DNA methylation analysis tools' - description: 'This package contains R functions to predict biological variables to from placnetal DNA methylation data generated from infinium arrays. This includes inferring ethnicity/ancestry, gestational age, and cell composition from placental DNA methylation array (450k/850k) data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-planttfhunter/meta.yaml b/recipes/bioconductor-planttfhunter/meta.yaml index 2d4836f3fc65b..1edd20a295661 100644 --- a/recipes/bioconductor-planttfhunter/meta.yaml +++ b/recipes/bioconductor-planttfhunter/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "planttfhunter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 94bf35ef27114ae40bdd4be243dfb8fe +about: + description: planttfhunter is used to identify plant transcription factors (TFs) from protein sequence data and classify them into families and subfamilies using the classification scheme implemented in PlantTFDB. TFs are identified using pre-built hidden Markov model profiles for DNA-binding domains. Then, auxiliary and forbidden domains are used with DNA-binding domains to classify TFs into families and subfamilies (when applicable). Currently, TFs can be classified in 58 different TF families/subfamilies. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identification and classification of plant transcription factors build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-planttfhunter", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, covr, sessioninfo, knitr, rmarkdown, testthat (>= 3.0.0) # SystemRequirements: HMMER requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base +source: + md5: 8d2aac7dd28d9c74019070fe692019b8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Identification and classification of plant transcription factors' - description: 'planttfhunter is used to identify plant transcription factors (TFs) from protein sequence data and classify them into families and subfamilies using the classification scheme implemented in PlantTFDB. TFs are identified using pre-built hidden Markov model profiles for DNA-binding domains. Then, auxiliary and forbidden domains are used with DNA-binding domains to classify TFs into families and subfamilies (when applicable). Currently, TFs can be classified in 58 different TF families/subfamilies.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-plasmodiumanophelescdf/meta.yaml b/recipes/bioconductor-plasmodiumanophelescdf/meta.yaml index 5ce91658cfd34..ac447a0c92cbf 100644 --- a/recipes/bioconductor-plasmodiumanophelescdf/meta.yaml +++ b/recipes/bioconductor-plasmodiumanophelescdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "plasmodiumanophelescdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 54c5c326977d6358c40cacf34cb2aca2 +about: + description: A package containing an environment representing the Plasmodium_Anopheles.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: plasmodiumanophelescdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-plasmodiumanophelescdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 54c5c326977d6358c40cacf34cb2aca2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: plasmodiumanophelescdf - description: 'A package containing an environment representing the Plasmodium_Anopheles.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-plasmodiumanophelesprobe/meta.yaml b/recipes/bioconductor-plasmodiumanophelesprobe/meta.yaml index 7a007c04ba9cd..5035b5babc1b6 100644 --- a/recipes/bioconductor-plasmodiumanophelesprobe/meta.yaml +++ b/recipes/bioconductor-plasmodiumanophelesprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "plasmodiumanophelesprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 281683dab923168c2eedb7b08c528935 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Plasmodium\_Anopheles\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type plasmodiumanopheles build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-plasmodiumanophelesprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 281683dab923168c2eedb7b08c528935 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type plasmodiumanopheles' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Plasmodium\_Anopheles\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-plasmut/meta.yaml b/recipes/bioconductor-plasmut/meta.yaml index 7af4ecae4a8c9..b5f4b717af841 100644 --- a/recipes/bioconductor-plasmut/meta.yaml +++ b/recipes/bioconductor-plasmut/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "plasmut" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8681d905157c0cbb8b46e48cbe4ecde9 +about: + description: A Bayesian method for quantifying the liklihood that a given plasma mutation arises from clonal hematopoesis or the underlying tumor. It requires sequencing data of the mutation in plasma and white blood cells with the number of distinct and mutant reads in both tissues. We implement a Monte Carlo importance sampling method to assess the likelihood that a mutation arises from the tumor relative to non-tumor origin. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Stratifying mutations observed in cell-free DNA and white blood cells as germline, hematopoietic, or somatic build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-plasmut", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, tidyverse, ggrepel, magrittr, qpdf, BiocStyle, biocViews, testthat (>= 3.0.0) requirements: host: @@ -29,12 +27,14 @@ requirements: - r-base - r-dplyr - r-tibble +source: + md5: 9708eb46f23bff31c138161f8d609237 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Stratifying mutations observed in cell-free DNA and white blood cells as germline, hematopoietic, or somatic' - description: 'A Bayesian method for quantifying the liklihood that a given plasma mutation arises from clonal hematopoesis or the underlying tumor. It requires sequencing data of the mutation in plasma and white blood cells with the number of distinct and mutant reads in both tissues. We implement a Monte Carlo importance sampling method to assess the likelihood that a mutation arises from the tumor relative to non-tumor origin.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-plgem/meta.yaml b/recipes/bioconductor-plgem/meta.yaml index 2bc338a763d0a..200a2fdf00a5c 100644 --- a/recipes/bioconductor-plgem/meta.yaml +++ b/recipes/bioconductor-plgem/meta.yaml @@ -1,47 +1,53 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "plgem" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The Power Law Global Error Model (PLGEM) has been shown to faithfully model the variance-versus-mean dependence that exists in a variety of genome-wide datasets, including microarray and proteomics data. The use of PLGEM has been shown to improve the detection of differentially expressed genes or proteins in these datasets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: caa3e3fe048da49643b34bde9fcb834a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-plgem", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:plgem + parent_recipe: + name: bioconductor-plgem + path: recipes/bioconductor-plgem + version: 1.52.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-mass run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-mass + +source: + md5: 235a48662a4348b2cf87f14e593f06da + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)' - description: 'The Power Law Global Error Model (PLGEM) has been shown to faithfully model the variance-versus-mean dependence that exists in a variety of genome-wide datasets, including microarray and proteomics data. The use of PLGEM has been shown to improve the detection of differentially expressed genes or proteins in these datasets.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:plgem - parent_recipe: - name: bioconductor-plgem - path: recipes/bioconductor-plgem - version: 1.52.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-plier/meta.yaml b/recipes/bioconductor-plier/meta.yaml index 55b9c161f346c..2d239afd17407 100644 --- a/recipes/bioconductor-plier/meta.yaml +++ b/recipes/bioconductor-plier/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "1.72.0" %} +{% set version = "1.76.0" %} {% set name = "plier" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Implements the Affymetrix PLIER algorithm -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f16a09bf8bccc7f5596d55ed0577a593 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-plier", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:plier + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-plier + path: recipes/bioconductor-plier + version: 1.50.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - libblas - liblapack run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: c0aaf65bd0daf8ea18d41ba2067aa100 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Implements the Affymetrix PLIER algorithm' - description: 'The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:plier - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-plier - path: recipes/bioconductor-plier - version: 1.50.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-plotgardener/meta.yaml b/recipes/bioconductor-plotgardener/meta.yaml index e7cb36e9c2ed0..5d1eb3bae0020 100644 --- a/recipes/bioconductor-plotgardener/meta.yaml +++ b/recipes/bioconductor-plotgardener/meta.yaml @@ -1,35 +1,45 @@ -{% set version = "1.8.1" %} +{% set version = "1.12.0" %} {% set name = "plotgardener" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Coordinate-Based Genomic Visualization Package for R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7459452ce71af8384d3df8340a7c3db0 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-plotgardener", max_pin="x.x") }}' -# Suggests: AnnotationDbi, AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures, GenomeInfoDb, GenomicRanges, ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer, plotgardenerData, pdftools, png, rmarkdown, scales, showtext, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: AnnotationDbi, AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures, ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer, plotgardenerData, pdftools, png, rmarkdown, scales, showtext, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 - r-base - r-curl - r-data.table - r-dplyr - r-ggplotify + - r-glue - r-purrr - r-rcolorbrewer - r-rcpp @@ -38,33 +48,35 @@ requirements: - r-withr - libblas - liblapack + run: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 - r-base - r-curl - r-data.table - r-dplyr - r-ggplotify + - r-glue - r-purrr - r-rcolorbrewer - r-rcpp - r-rlang - r-strawr - r-withr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 736a74f491008039018f254193f46aad + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Coordinate-Based Genomic Visualization Package for R' - description: 'Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-plotgardenerdata/meta.yaml b/recipes/bioconductor-plotgardenerdata/meta.yaml index 9a02df7d187eb..2c0a1358dbf9f 100644 --- a/recipes/bioconductor-plotgardenerdata/meta.yaml +++ b/recipes/bioconductor-plotgardenerdata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "plotgardenerData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96055b11818bd59c0c91977b34973608 +about: + description: This is a supplemental data package for the plotgardener package. Includes example datasets used in plotgardener vignettes and example raw data files. For details on how to use these datasets, see the plotgardener package vignettes. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Datasets and test data files for the plotgardener package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-plotgardenerdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: rmarkdown, knitr requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4404a379e2a65bf165af4d5e434341ca + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Datasets and test data files for the plotgardener package' - description: 'This is a supplemental data package for the plotgardener package. Includes example datasets used in plotgardener vignettes and example raw data files. For details on how to use these datasets, see the plotgardener package vignettes.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-plotgardenerdata/post-link.sh b/recipes/bioconductor-plotgardenerdata/post-link.sh index 44e9cf40f78cf..192ee13d0bc4a 100644 --- a/recipes/bioconductor-plotgardenerdata/post-link.sh +++ b/recipes/bioconductor-plotgardenerdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "plotgardenerdata-1.8.0" +installBiocDataPackage.sh "plotgardenerdata-1.12.0" diff --git a/recipes/bioconductor-plotgrouper/meta.yaml b/recipes/bioconductor-plotgrouper/meta.yaml index c6e6e6c5bff30..9bd3bddd792cd 100644 --- a/recipes/bioconductor-plotgrouper/meta.yaml +++ b/recipes/bioconductor-plotgrouper/meta.yaml @@ -1,78 +1,84 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "plotGrouper" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A shiny app-based GUI wrapper for ggplot with built-in statistical analysis. Import data from file and use dropdown menus and checkboxes to specify the plotting variables, graph type, and look of your plots. Once created, plots can be saved independently or stored in a report that can be saved as a pdf. If new data are added to the file, the report can be refreshed to include new data. Statistical tests can be selected and added to the graphs. Analysis of flow cytometry data is especially integrated with plotGrouper. Count data can be transformed to return the absolute number of cells in a sample (this feature requires inclusion of the number of beads per sample and information about any dilution performed). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Shiny app GUI wrapper for ggplot with built-in statistical analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aca262974325a32b1d28d58d28e4e012 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-plotgrouper", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-plotgrouper + path: recipes/bioconductor-plotgrouper + version: 1.0.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, htmltools, BiocStyle, rmarkdown, testthat requirements: host: - r-base - - 'r-colourpicker >=1.0' - - 'r-dplyr >=0.7.6' - - 'r-egg >=0.4.0' - - 'r-ggplot2 >=3.0.0' - - 'r-ggpubr >=0.1.8' - - 'r-gridextra >=2.3' - - 'r-gtable >=0.2.0' - - 'r-hmisc >=4.1.1' - - 'r-magrittr >=1.5' - - 'r-readr >=1.1.1' - - 'r-readxl >=1.1.0' - - 'r-rlang >=0.2.2' - - 'r-scales >=1.0.0' - - 'r-shiny >=1.1.0' - - 'r-shinythemes >=1.1.1' - - 'r-stringr >=1.3.1' - - 'r-tibble >=1.4.2' - - 'r-tidyr >=0.2.0' + - r-colourpicker >=1.0 + - r-dplyr >=0.7.6 + - r-egg >=0.4.0 + - r-ggplot2 >=3.0.0 + - r-ggpubr >=0.1.8 + - r-gridextra >=2.3 + - r-gtable >=0.2.0 + - r-hmisc >=4.1.1 + - r-magrittr >=1.5 + - r-readr >=1.1.1 + - r-readxl >=1.1.0 + - r-rlang >=0.2.2 + - r-scales >=1.0.0 + - r-shiny >=1.1.0 + - r-shinythemes >=1.1.1 + - r-stringr >=1.3.1 + - r-tibble >=1.4.2 + - r-tidyr >=0.2.0 run: - r-base - - 'r-colourpicker >=1.0' - - 'r-dplyr >=0.7.6' - - 'r-egg >=0.4.0' - - 'r-ggplot2 >=3.0.0' - - 'r-ggpubr >=0.1.8' - - 'r-gridextra >=2.3' - - 'r-gtable >=0.2.0' - - 'r-hmisc >=4.1.1' - - 'r-magrittr >=1.5' - - 'r-readr >=1.1.1' - - 'r-readxl >=1.1.0' - - 'r-rlang >=0.2.2' - - 'r-scales >=1.0.0' - - 'r-shiny >=1.1.0' - - 'r-shinythemes >=1.1.1' - - 'r-stringr >=1.3.1' - - 'r-tibble >=1.4.2' - - 'r-tidyr >=0.2.0' + - r-colourpicker >=1.0 + - r-dplyr >=0.7.6 + - r-egg >=0.4.0 + - r-ggplot2 >=3.0.0 + - r-ggpubr >=0.1.8 + - r-gridextra >=2.3 + - r-gtable >=0.2.0 + - r-hmisc >=4.1.1 + - r-magrittr >=1.5 + - r-readr >=1.1.1 + - r-readxl >=1.1.0 + - r-rlang >=0.2.2 + - r-scales >=1.0.0 + - r-shiny >=1.1.0 + - r-shinythemes >=1.1.1 + - r-stringr >=1.3.1 + - r-tibble >=1.4.2 + - r-tidyr >=0.2.0 + +source: + md5: aea8b8b1c39df16b3f41c97e8eec2bd6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Shiny app GUI wrapper for ggplot with built-in statistical analysis' - description: 'A shiny app-based GUI wrapper for ggplot with built-in statistical analysis. Import data from file and use dropdown menus and checkboxes to specify the plotting variables, graph type, and look of your plots. Once created, plots can be saved independently or stored in a report that can be saved as a pdf. If new data are added to the file, the report can be refreshed to include new data. Statistical tests can be selected and added to the graphs. Analysis of flow cytometry data is especially integrated with plotGrouper. Count data can be transformed to return the absolute number of cells in a sample (this feature requires inclusion of the number of beads per sample and information about any dilution performed).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-plotgrouper - path: recipes/bioconductor-plotgrouper - version: 1.0.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-plpe/meta.yaml b/recipes/bioconductor-plpe/meta.yaml index 5818330d03f6a..fab81545c904c 100644 --- a/recipes/bioconductor-plpe/meta.yaml +++ b/recipes/bioconductor-plpe/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.62.0" %} +{% set version = "1.66.0" %} {% set name = "PLPE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package performs tests for paired high-throughput data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Local Pooled Error Test for Differential Expression with Paired High-throughput Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a4887a4c08676e0ce69331caacc297e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-plpe", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:plpe + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-plpe + path: recipes/bioconductor-plpe + version: 1.40.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-lpe >=1.76.0,<1.77.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-lpe >=1.80.0,<1.81.0 - r-base - r-mass run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-lpe >=1.76.0,<1.77.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-lpe >=1.80.0,<1.81.0 - r-base - r-mass + +source: + md5: 9daa2dbc4eb9ee37c4c3d91c9c343754 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Local Pooled Error Test for Differential Expression with Paired High-throughput Data' - description: 'This package performs tests for paired high-throughput data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:plpe - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-plpe - path: recipes/bioconductor-plpe - version: 1.40.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-plsdabatch/build.sh b/recipes/bioconductor-plsdabatch/build.sh new file mode 100644 index 0000000000000..497f7b5bdb678 --- /dev/null +++ b/recipes/bioconductor-plsdabatch/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +export LD_LIBRARY_PATH=${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-plsdabatch/meta.yaml b/recipes/bioconductor-plsdabatch/meta.yaml new file mode 100644 index 0000000000000..64e37515c6582 --- /dev/null +++ b/recipes/bioconductor-plsdabatch/meta.yaml @@ -0,0 +1,79 @@ +{% set version = "1.2.0" %} +{% set name = "PLSDAbatch" %} +{% set bioc = "3.20" %} + +about: + description: A novel framework to correct for batch effects prior to any downstream analysis in microbiome data based on Projection to Latent Structures Discriminant Analysis. The main method is named “PLSDA-batch”. It first estimates treatment and batch variation with latent components, then subtracts batch-associated components from the data whilst preserving biological variation of interest. PLSDA-batch is highly suitable for microbiome data as it is non-parametric, multivariate and allows for ordination and data visualisation. Combined with centered log-ratio transformation for addressing uneven library sizes and compositional structure, PLSDA-batch addresses all characteristics of microbiome data that existing correction methods have ignored so far. Two other variants are proposed for 1/ unbalanced batch x treatment designs that are commonly encountered in studies with small sample sizes, and for 2/ selection of discriminative variables amongst treatment groups to avoid overfitting in classification problems. These two variants have widened the scope of applicability of PLSDA-batch to different data settings. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: PLSDA-batch + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plsdabatch", max_pin="x.x") }}' + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, testthat, badger +requirements: + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-mixomics >=6.30.0,<6.31.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 + - r-base + - r-ggplot2 + - r-ggpubr + - r-gridextra + - r-lmertest + - r-performance + - r-pheatmap + - r-rdpack + - r-scales + - r-vegan + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-mixomics >=6.30.0,<6.31.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 + - r-base + - r-ggplot2 + - r-ggpubr + - r-gridextra + - r-lmertest + - r-performance + - r-pheatmap + - r-rdpack + - r-scales + - r-vegan + +source: + md5: fecfcef01e7bfb9786857c0baf735fc0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-plyinteractions/meta.yaml b/recipes/bioconductor-plyinteractions/meta.yaml index 19e57bfea4e2f..85a8e400b4b0c 100644 --- a/recipes/bioconductor-plyinteractions/meta.yaml +++ b/recipes/bioconductor-plyinteractions/meta.yaml @@ -1,58 +1,63 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "plyinteractions" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Operate on `GInteractions` objects as tabular data using `dplyr`-like verbs. The functions and methods in `plyinteractions` provide a grammatical approach to manipulate `GInteractions`, to facilitate their integration in genomic analysis workflows. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Extending tidy verbs to genomic interactions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e072613b18768f43d832eaa32354bbc9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-plyinteractions", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: tidyverse, BSgenome.Mmusculus.UCSC.mm10, Biostrings, BiocParallel, scales, HiContactsData, rtracklayer, BiocStyle, covr, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), RefManageR requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-rlang - r-tibble - r-tidyselect run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-rlang - r-tibble - r-tidyselect + +source: + md5: 1dd6aab852245e89ebc7e2b1df6fff25 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Extending tidy verbs to genomic interactions' - description: 'Operate on `GInteractions` objects as tabular data using `dplyr`-like verbs. The functions and methods in `plyinteractions` provide a grammatical approach to manipulate `GInteractions`, to facilitate their integration in genomic analysis workflows.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-plyranges/meta.yaml b/recipes/bioconductor-plyranges/meta.yaml index b8bbe45eb1171..e1480cb7184b1 100644 --- a/recipes/bioconductor-plyranges/meta.yaml +++ b/recipes/bioconductor-plyranges/meta.yaml @@ -1,60 +1,65 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "plyranges" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A dplyr-like interface for interacting with the common Bioconductor classes Ranges and GenomicRanges. By providing a grammatical and consistent way of manipulating these classes their accessiblity for new Bioconductor users is hopefully increased. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: A fluent interface for manipulating GenomicRanges -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 23b74165be3c4a855e6a49d8c0f1bab1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-plyranges", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 2.1.0), HelloRanges, HelloRangesData, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset, covr, ggplot2 requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-magrittr - - 'r-rlang >=0.2.0' - - 'r-tidyselect >=1.0.0' + - r-rlang >=0.2.0 + - r-tidyselect >=1.0.0 run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-magrittr - - 'r-rlang >=0.2.0' - - 'r-tidyselect >=1.0.0' + - r-rlang >=0.2.0 + - r-tidyselect >=1.0.0 + +source: + md5: 4628fbdeada32e0241ec451f8460fe26 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A fluent interface for manipulating GenomicRanges' - description: 'A dplyr-like interface for interacting with the common Bioconductor classes Ranges and GenomicRanges. By providing a grammatical and consistent way of manipulating these classes their accessiblity for new Bioconductor users is hopefully increased.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-plyxp/build.sh b/recipes/bioconductor-plyxp/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-plyxp/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-plyxp/meta.yaml b/recipes/bioconductor-plyxp/meta.yaml new file mode 100644 index 0000000000000..8dd2c151dc04d --- /dev/null +++ b/recipes/bioconductor-plyxp/meta.yaml @@ -0,0 +1,68 @@ +{% set version = "1.0.0" %} +{% set name = "plyxp" %} +{% set bioc = "3.20" %} + +about: + description: The package provides `rlang` data masks for the SummarizedExperiment class. The enables the evaluation of unquoted expression in different contexts of the SummarizedExperiment object with optional access to other contexts. The goal for `plyxp` is for evaluation to feel like a data.frame object without ever needing to unwind to a rectangular data.frame. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Data masks for SummarizedExperiment enabling dplyr-like manipulation + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-plyxp", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: devtools, knitr, rmarkdown, testthat, airway, IRanges, here +requirements: + host: + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-cli + - r-dplyr + - r-glue + - r-pillar + - r-purrr + - r-rlang + - r-s7 + - r-tibble + - r-tidyr + - r-tidyselect + - r-vctrs + run: + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-cli + - r-dplyr + - r-glue + - r-pillar + - r-purrr + - r-rlang + - r-s7 + - r-tibble + - r-tidyr + - r-tidyselect + - r-vctrs + +source: + md5: 71d1158d4ed392f139db2dffff1f56c6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-pmm/meta.yaml b/recipes/bioconductor-pmm/meta.yaml index 370e01487e660..4b721461ffd00 100644 --- a/recipes/bioconductor-pmm/meta.yaml +++ b/recipes/bioconductor-pmm/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "pmm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The Parallel Mixed Model (PMM) approach is suitable for hit selection and cross-comparison of RNAi screens generated in experiments that are performed in parallel under several conditions. For example, we could think of the measurements or readouts from cells under RNAi knock-down, which are infected with several pathogens or which are grown from different cell lines. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Parallel Mixed Model -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 43957004fa9664b15f4bca34f7ea975e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pmm", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:pmm + - doi:10.3929/ethz-a-010607487 + parent_recipe: + name: bioconductor-pmm + path: recipes/bioconductor-pmm + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -26,21 +37,16 @@ requirements: run: - r-base - r-lme4 + +source: + md5: 5ad703726e26716dc8f63498d5c44003 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Parallel Mixed Model' - description: 'The Parallel Mixed Model (PMM) approach is suitable for hit selection and cross-comparison of RNAi screens generated in experiments that are performed in parallel under several conditions. For example, we could think of the measurements or readouts from cells under RNAi knock-down, which are infected with several pathogens or which are grown from different cell lines.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:pmm - - doi:10.3929/ethz-a-010607487 - parent_recipe: - name: bioconductor-pmm - path: recipes/bioconductor-pmm - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pmp/meta.yaml b/recipes/bioconductor-pmp/meta.yaml index ffe645d75fd11..6859271ff7616 100644 --- a/recipes/bioconductor-pmp/meta.yaml +++ b/recipes/bioconductor-pmp/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "pmp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Methods and tools for (pre-)processing of metabolomics datasets (i.e. peak matrices), including filtering, normalisation, missing value imputation, scaling, and signal drift and batch effect correction methods. Filtering methods are based on: the fraction of missing values (across samples or features); Relative Standard Deviation (RSD) calculated from the Quality Control (QC) samples; the blank samples. Normalisation methods include Probabilistic Quotient Normalisation (PQN) and normalisation to total signal intensity. A unified user interface for several commonly used missing value imputation algorithms is also provided. Supported methods are: k-nearest neighbours (knn), random forests (rf), Bayesian PCA missing value estimator (bpca), mean or median value of the given feature and a constant small value. The generalised logarithm (glog) transformation algorithm is available to stabilise the variance across low and high intensity mass spectral features. Finally, this package provides an implementation of the Quality Control-Robust Spline Correction (QCRSC) algorithm for signal drift and batch effect correction of mass spectrometry-based datasets.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Peak Matrix Processing and signal batch correction for metabolomics datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 07feec54f330f10904aae29238f79369 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pmp", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, covr, knitr, rmarkdown, BiocStyle, gridExtra, magick requirements: host: - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-matrixstats - r-missforest - r-reshape2 run: - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-matrixstats - r-missforest - r-reshape2 + +source: + md5: 23b438cc67facbb276de2d89970e2e2a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Peak Matrix Processing and signal batch correction for metabolomics datasets' - description: 'Methods and tools for (pre-)processing of metabolomics datasets (i.e. peak matrices), including filtering, normalisation, missing value imputation, scaling, and signal drift and batch effect correction methods. Filtering methods are based on: the fraction of missing values (across samples or features); Relative Standard Deviation (RSD) calculated from the Quality Control (QC) samples; the blank samples. Normalisation methods include Probabilistic Quotient Normalisation (PQN) and normalisation to total signal intensity. A unified user interface for several commonly used missing value imputation algorithms is also provided. Supported methods are: k-nearest neighbours (knn), random forests (rf), Bayesian PCA missing value estimator (bpca), mean or median value of the given feature and a constant small value. The generalised logarithm (glog) transformation algorithm is available to stabilise the variance across low and high intensity mass spectral features. Finally, this package provides an implementation of the Quality Control-Robust Spline Correction (QCRSC) algorithm for signal drift and batch effect correction of mass spectrometry-based datasets.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pocrcannotation.db/meta.yaml b/recipes/bioconductor-pocrcannotation.db/meta.yaml index 0918cbf3fda7b..9a3ad7e1e2624 100644 --- a/recipes/bioconductor-pocrcannotation.db/meta.yaml +++ b/recipes/bioconductor-pocrcannotation.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "POCRCannotation.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: da1d4dacc5fffb9c5dfea55649974aa5 +about: + description: A package containing metadata for POCRC arrays assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: A package containing metadata for POCRC arrays build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pocrcannotation.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: da1d4dacc5fffb9c5dfea55649974aa5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A package containing metadata for POCRC arrays' - description: 'A package containing metadata for POCRC arrays assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-podcall/meta.yaml b/recipes/bioconductor-podcall/meta.yaml index 9e63932878f83..555a0a5de65e3 100644 --- a/recipes/bioconductor-podcall/meta.yaml +++ b/recipes/bioconductor-podcall/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "PoDCall" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Reads files exported from 'QX Manager or QuantaSoft' containing amplitude values from a run of ddPCR (96 well plate) and robustly sets thresholds to determine positive droplets for each channel of each individual well. Concentration and normalized concentration in addition to other metrics is then calculated for each well. Results are returned as a table, optionally written to file, as well as optional plots (scatterplot and histogram) for both channels per well written to file. The package includes a shiny application which provides an interactive and user-friendly interface to the full functionality of PoDCall. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Positive Droplet Calling for DNA Methylation Droplet Digital PCR -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e079c4df0c773e27d396662c928ac51b build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-podcall", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: @@ -47,13 +49,16 @@ requirements: - r-rlist - r-shiny - r-shinyjs + +source: + md5: 1a527f296adf984ae99dd9c88002e630 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Positive Droplet Calling for DNA Methylation Droplet Digital PCR' - description: 'Reads files exported from ''QX Manager or QuantaSoft'' containing amplitude values from a run of ddPCR (96 well plate) and robustly sets thresholds to determine positive droplets for each channel of each individual well. Concentration and normalized concentration in addition to other metrics is then calculated for each well. Results are returned as a table, optionally written to file, as well as optional plots (scatterplot and histogram) for both channels per well written to file. The package includes a shiny application which provides an interactive and user-friendly interface to the full functionality of PoDCall.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-podkat/build_failure.linux-64.yaml b/recipes/bioconductor-podkat/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..23bac339faac9 --- /dev/null +++ b/recipes/bioconductor-podkat/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 445ebad842fc94fa5b4b3ebcebe14c9e19f4352e7d6abbb66fcf91f2a9a7e556 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-podkat-1.38.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-podkat-1.38.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-podkat-1.38.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-podkat_1735440411805/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library + * installing *source* package podkat ... + ** package podkat successfully unpacked and MD5 sums checked + ** using staged installation + ** libs + using C compiler: x86_64-conda-linux-gnu-c (conda-forge gcc 13.3.0-1) 13.3.0 + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c R_init_podkat.cpp -o R_init_podkat.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c bernoulliExact.cpp -o bernoulliExact.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c checkAndFixGenotype.cpp -o checkAndFixGenotype.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c cumMax.cpp -o cumMax.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c doubleMale.cpp -o doubleMale.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c kernels.cpp -o kernels.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c pValues.cpp -o pValues.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c partitionRegions.cpp -o partitionRegions.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c qfc.cpp -o qfc.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c readGenotypeMatrix.cpp -o readGenotypeMatrix.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c readVariantInfo.cpp -o readVariantInfo.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -shared -L$PREFIX/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -o podkat.so R_init_podkat.o bernoulliExact.o checkAndFixGenotype.o cumMax.o doubleMale.o kernels.o pValues.o partitionRegions.o qfc.o readGenotypeMatrix.o readVariantInfo.o $PREFIX/lib/R/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L$PREFIX/lib/R/lib -lR + /opt/conda/conda-bld/bioconductor-podkat_1735440411805/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -llzma: No such file or directory + /opt/conda/conda-bld/bioconductor-podkat_1735440411805/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lz: No such file or directory + collect2: error: ld returned 1 exit status + make: *** [/opt/conda/conda-bld/bioconductor-podkat_1735440411805/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/share/make/shlib.mk:10: podkat.so] Error 1 + ERROR: compilation failed for package podkat + * removing /opt/conda/conda-bld/bioconductor-podkat_1735440411805/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/podkat + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-podkat_1735440411805/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-podkat_1735440411805/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-podkat/meta.yaml b/recipes/bioconductor-podkat/meta.yaml index 9678b6fcdff8a..048fcc93f43b4 100644 --- a/recipes/bioconductor-podkat/meta.yaml +++ b/recipes/bioconductor-podkat/meta.yaml @@ -1,73 +1,79 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "podkat" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides an association test that is capable of dealing with very rare and even private variants. This is accomplished by a kernel-based approach that takes the positions of the variants into account. The test can be used for pre-processed matrix data, but also directly for variant data stored in VCF files. Association testing can be performed whole-genome, whole-exome, or restricted to pre-defined regions of interest. The test is complemented by tools for analyzing and visualizing the results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Position-Dependent Kernel Association Test -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b06fbdc3f282bde5ec8df0d062d3ecb6 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-podkat", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:podkat + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-podkat + path: recipes/bioconductor-podkat + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Hsapiens.UCSC.hg38.masked, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24), VariantAnnotation, SummarizedExperiment, knitr # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-matrix - - 'r-rcpp >=0.11.1' + - r-rcpp >=0.11.1 - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-matrix - - 'r-rcpp >=0.11.1' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=0.11.1 + +source: + md5: 339a50e2d51e843e80516cbd528ab445 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Position-Dependent Kernel Association Test' - description: 'This package provides an association test that is capable of dealing with very rare and even private variants. This is accomplished by a kernel-based approach that takes the positions of the variants into account. The test can be used for pre-processed matrix data, but also directly for variant data stored in VCF files. Association testing can be performed whole-genome, whole-exome, or restricted to pre-defined regions of interest. The test is complemented by tools for analyzing and visualizing the results.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:podkat - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-podkat - path: recipes/bioconductor-podkat - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pogos/meta.yaml b/recipes/bioconductor-pogos/meta.yaml index 426527de50e5d..da29749c4216c 100644 --- a/recipes/bioconductor-pogos/meta.yaml +++ b/recipes/bioconductor-pogos/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "pogos" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provide simple utilities for querying bhklab PharmacoDB, modeling API outputs, and integrating to cell and compound ontologies. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: PharmacOGenomics Ontology Support -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 14955bb127999aaa92633bc1ce3a1227 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pogos", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, DT, ontologyPlot, testthat, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-ontoproc >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-ontoproc >=2.0.0,<2.1.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - - 'r-httr >=1.3.1' - - 'r-rjson >=0.2.15' + - r-httr >=1.3.1 + - r-rjson >=0.2.15 - r-shiny run: - - 'bioconductor-ontoproc >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-ontoproc >=2.0.0,<2.1.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - - 'r-httr >=1.3.1' - - 'r-rjson >=0.2.15' + - r-httr >=1.3.1 + - r-rjson >=0.2.15 - r-shiny + +source: + md5: 6da640662f651bd117d93365c2776952 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'PharmacOGenomics Ontology Support' - description: 'Provide simple utilities for querying bhklab PharmacoDB, modeling API outputs, and integrating to cell and compound ontologies.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-polyphen.hsapiens.dbsnp131/meta.yaml b/recipes/bioconductor-polyphen.hsapiens.dbsnp131/meta.yaml index bd986aeb518f3..1445d5d7a377b 100644 --- a/recipes/bioconductor-polyphen.hsapiens.dbsnp131/meta.yaml +++ b/recipes/bioconductor-polyphen.hsapiens.dbsnp131/meta.yaml @@ -1,43 +1,43 @@ {% set version = "1.0.2" %} {% set name = "PolyPhen.Hsapiens.dbSNP131" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 763e9cd4afd97b36f7e659f5454ef61f +about: + description: Database of PolyPhen predictions for Homo sapiens dbSNP build 131 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: PolyPhen Predictions for Homo sapiens dbSNP build 131 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-polyphen.hsapiens.dbsnp131", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - - 'r-rsqlite >=0.11.0' + - r-rsqlite >=0.11.0 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - - 'r-rsqlite >=0.11.0' + - r-rsqlite >=0.11.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 763e9cd4afd97b36f7e659f5454ef61f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'PolyPhen Predictions for Homo sapiens dbSNP build 131' - description: 'Database of PolyPhen predictions for Homo sapiens dbSNP build 131' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-poma/meta.yaml b/recipes/bioconductor-poma/meta.yaml index fffe40d372e0b..deab3aafb7113 100644 --- a/recipes/bioconductor-poma/meta.yaml +++ b/recipes/bioconductor-poma/meta.yaml @@ -1,91 +1,118 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "POMA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The POMA package offers a comprehensive toolkit designed for omics data analysis, streamlining the process from initial visualization to final statistical analysis. Its primary goal is to simplify and unify the various steps involved in omics data processing, making it more accessible and manageable within a single, intuitive R package. Emphasizing on reproducibility and user-friendliness, POMA leverages the standardized SummarizedExperiment class from Bioconductor, ensuring seamless integration and compatibility with a wide array of Bioconductor tools. This approach guarantees maximum flexibility and replicability, making POMA an essential asset for researchers handling omics datasets. See https://github.com/pcastellanoescuder/POMAShiny. Paper: Castellano-Escuder et al. (2021) for more details.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Tools for Omics Data Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 89690c830c8b6120d4d436f05e34f4eb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-poma", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, covr, ggraph, knitr, patchwork, plotly, tidyverse, testthat (>= 2.3.2) + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, covr, ggraph, ggtext, knitr, patchwork, plotly, tidyverse, testthat (>= 2.3.2) requirements: + + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] + host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-mixomics >=6.26.0,<6.27.0' - - 'bioconductor-rankprod >=3.28.0,<3.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-mixomics >=6.30.0,<6.31.0 + - bioconductor-rankprod >=3.32.0,<3.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-broom - r-caret - r-dbscan - r-dplyr + - r-fsa + - r-ggcorrplot - r-ggplot2 - r-ggrepel - - 'r-glasso >=1.11' - r-glmnet + - r-janitor + - r-lme4 - r-magrittr + - r-mass + - r-msigdbr + - r-multcomp + - r-purrr - r-randomforest - - r-rmarkdown + - r-rlang - r-tibble - r-tidyr - r-uwot - r-vegan + run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-mixomics >=6.26.0,<6.27.0' - - 'bioconductor-rankprod >=3.28.0,<3.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-mixomics >=6.30.0,<6.31.0 + - bioconductor-rankprod >=3.32.0,<3.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-broom - r-caret - r-dbscan - r-dplyr + - r-fsa + - r-ggcorrplot - r-ggplot2 - r-ggrepel - - 'r-glasso >=1.11' - r-glmnet + - r-janitor + - r-lme4 - r-magrittr + - r-mass + - r-msigdbr + - r-multcomp + - r-purrr - r-randomforest - - r-rmarkdown + - r-rlang - r-tibble - r-tidyr - r-uwot - r-vegan - build: - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - xorg-libxfixes # [linux] + +source: + md5: d1f2cc9db15e981cab28d5dc0dbca5d8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Tools for Omics Data Analysis' - description: 'A reproducible and easy-to-use toolkit for visualization, pre-processing, exploration, and statistical analysis of omics datasets. The main aim of POMA is to enable a flexible data cleaning and statistical analysis processes in one comprehensible and user-friendly R package. This package has a Shiny app version called POMAShiny that implements all POMA functions. See https://github.com/pcastellanoescuder/POMAShiny. See Castellano-Escuder P, González-Domínguez R, Carmona-Pontaque F, et al. (2021) for more details.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-poplarcdf/meta.yaml b/recipes/bioconductor-poplarcdf/meta.yaml index abe70a10b697e..039d48119d493 100644 --- a/recipes/bioconductor-poplarcdf/meta.yaml +++ b/recipes/bioconductor-poplarcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "poplarcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 556e7f8f6f76436552d8044ef29279cb +about: + description: A package containing an environment representing the Poplar.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: poplarcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-poplarcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 556e7f8f6f76436552d8044ef29279cb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: poplarcdf - description: 'A package containing an environment representing the Poplar.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-poplarprobe/meta.yaml b/recipes/bioconductor-poplarprobe/meta.yaml index 8844ecc8570be..e31596c70675a 100644 --- a/recipes/bioconductor-poplarprobe/meta.yaml +++ b/recipes/bioconductor-poplarprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "poplarprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 87a608cd86084a06973a88e9b51f799a +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Poplar\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type poplar build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-poplarprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 87a608cd86084a06973a88e9b51f799a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type poplar' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Poplar\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-porcine.db/meta.yaml b/recipes/bioconductor-porcine.db/meta.yaml index 345d8a9eba876..80747fd6170ff 100644 --- a/recipes/bioconductor-porcine.db/meta.yaml +++ b/recipes/bioconductor-porcine.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "porcine.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4a86b3e696d267dca673b4e9276d6368 +about: + description: Affymetrix Affymetrix Porcine Array annotation data (chip porcine) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Porcine Array annotation data (chip porcine) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-porcine.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.ss.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.ss.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.ss.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.ss.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4a86b3e696d267dca673b4e9276d6368 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Porcine Array annotation data (chip porcine)' - description: 'Affymetrix Affymetrix Porcine Array annotation data (chip porcine) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-porcinecdf/meta.yaml b/recipes/bioconductor-porcinecdf/meta.yaml index 11979dc62adb7..42b94b12be1a6 100644 --- a/recipes/bioconductor-porcinecdf/meta.yaml +++ b/recipes/bioconductor-porcinecdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "porcinecdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 32a60b93829c06a935895fab0a469228 +about: + description: A package containing an environment representing the Porcine.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: porcinecdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-porcinecdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 32a60b93829c06a935895fab0a469228 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: porcinecdf - description: 'A package containing an environment representing the Porcine.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-porcineprobe/meta.yaml b/recipes/bioconductor-porcineprobe/meta.yaml index 5d0f2c7ddf24a..993de51481ea7 100644 --- a/recipes/bioconductor-porcineprobe/meta.yaml +++ b/recipes/bioconductor-porcineprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "porcineprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5ac483b6329a012d4c9954e3dee8869e +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Porcine\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type porcine build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-porcineprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5ac483b6329a012d4c9954e3dee8869e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type porcine' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Porcine\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-powertcr/meta.yaml b/recipes/bioconductor-powertcr/meta.yaml index 8df9efbe126d8..7b1e79002f45d 100644 --- a/recipes/bioconductor-powertcr/meta.yaml +++ b/recipes/bioconductor-powertcr/meta.yaml @@ -1,24 +1,25 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "powerTCR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a model for the clone size distribution of the TCR repertoire. Further, it permits comparative analysis of TCR repertoire libraries based on theoretical model fits. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Model-Based Comparative Analysis of the TCR Repertoire -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6033da999bfcba4c2e80a45e358c3855 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-powertcr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics requirements: host: @@ -43,12 +44,16 @@ requirements: - r-truncdist - r-vegan - r-vgam + +source: + md5: 5b229108f3b909eb2515ffd7b193dfcd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Model-Based Comparative Analysis of the TCR Repertoire' - description: 'This package provides a model for the clone size distribution of the TCR repertoire. Further, it permits comparative analysis of TCR repertoire libraries based on theoretical model fits.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-powsc/meta.yaml b/recipes/bioconductor-powsc/meta.yaml index 9d658ab0472af..ada49c7150fc0 100644 --- a/recipes/bioconductor-powsc/meta.yaml +++ b/recipes/bioconductor-powsc/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "POWSC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Determining the sample size for adequate power to detect statistical significance is a crucial step at the design stage for high-throughput experiments. Even though a number of methods and tools are available for sample size calculation for microarray and RNA-seq in the context of differential expression (DE), this topic in the field of single-cell RNA sequencing is understudied. Moreover, the unique data characteristics present in scRNA-seq such as sparsity and heterogeneity increase the challenge. We propose POWSC, a simulation-based method, to provide power evaluation and sample size recommendation for single-cell RNA sequencing DE analysis. POWSC consists of a data simulator that creates realistic expression data, and a power assessor that provides a comprehensive evaluation and visualization of the power and sample size relationship. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Simulation, power evaluation, and sample size recommendation for single cell RNA-seq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e2ed51f94e9a1b37aa91fe74a007f4d7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-powsc", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-mast >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-mast >=1.32.0,<1.33.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-pheatmap - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-mast >=1.28.0,<1.29.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-mast >=1.32.0,<1.33.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-pheatmap - r-rcolorbrewer + +source: + md5: a3392d3714360c056d5b04104ae1a41c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Simulation, power evaluation, and sample size recommendation for single cell RNA-seq' - description: 'Determining the sample size for adequate power to detect statistical significance is a crucial step at the design stage for high-throughput experiments. Even though a number of methods and tools are available for sample size calculation for microarray and RNA-seq in the context of differential expression (DE), this topic in the field of single-cell RNA sequencing is understudied. Moreover, the unique data characteristics present in scRNA-seq such as sparsity and heterogeneity increase the challenge. We propose POWSC, a simulation-based method, to provide power evaluation and sample size recommendation for single-cell RNA sequencing DE analysis. POWSC consists of a data simulator that creates realistic expression data, and a power assessor that provides a comprehensive evaluation and visualization of the power and sample size relationship.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ppcseq/meta.yaml b/recipes/bioconductor-ppcseq/meta.yaml index bb0514df5b5e6..5025ddd602c32 100644 --- a/recipes/bioconductor-ppcseq/meta.yaml +++ b/recipes/bioconductor-ppcseq/meta.yaml @@ -1,82 +1,90 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "ppcseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Relative transcript abundance has proven to be a valuable tool for understanding the function of genes in biological systems. For the differential analysis of transcript abundance using RNA sequencing data, the negative binomial model is by far the most frequently adopted. However, common methods that are based on a negative binomial model are not robust to extreme outliers, which we found to be abundant in public datasets. So far, no rigorous and probabilistic methods for detection of outliers have been developed for RNA sequencing data, leaving the identification mostly to visual inspection. Recent advances in Bayesian computation allow large-scale comparison of observed data against its theoretical distribution given in a statistical model. Here we propose ppcseq, a key quality-control tool for identifying transcripts that include outlier data points in differential expression analysis, which do not follow a negative binomial distribution. Applying ppcseq to analyse several publicly available datasets using popular tools, we show that from 3 to 10 percent of differentially abundant transcripts across algorithms and datasets had statistics inflated by the presence of outliers. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5a95706ac4269643dd1eb6efd4bccb67 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ppcseq", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, BiocStyle, rmarkdown # SystemRequirements: GNU make requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make + host: - - 'bioconductor-edger >=4.0.0,<4.1.0' + - bioconductor-edger >=4.4.0,<4.5.0 - r-base - r-benchmarkme - - 'r-bh >=1.66.0' + - r-bh >=1.66.0 - r-dplyr - r-foreach - r-ggplot2 - r-lifecycle - r-magrittr - r-purrr - - 'r-rcpp >=0.12.0' - - 'r-rcppeigen >=0.3.3.3.0' - - 'r-rcppparallel >=5.0.1' + - r-rcpp >=0.12.0 + - r-rcppeigen >=0.3.3.3.0 + - r-rcppparallel >=5.0.1 - r-rlang - - 'r-rstan >=2.18.1' - - 'r-rstantools >=2.1.1' - - 'r-stanheaders >=2.18.0' + - r-rstan >=2.18.1 + - r-rstantools >=2.1.1 + - r-stanheaders >=2.18.0 - r-tibble - r-tidybayes - - 'r-tidyr >=0.8.3.9000' + - r-tidyr >=0.8.3.9000 - libblas - liblapack + run: - - 'bioconductor-edger >=4.0.0,<4.1.0' + - bioconductor-edger >=4.4.0,<4.5.0 - r-base - r-benchmarkme - - 'r-bh >=1.66.0' + - r-bh >=1.66.0 - r-dplyr - r-foreach - r-ggplot2 - r-lifecycle - r-magrittr - r-purrr - - 'r-rcpp >=0.12.0' - - 'r-rcppeigen >=0.3.3.3.0' - - 'r-rcppparallel >=5.0.1' + - r-rcpp >=0.12.0 + - r-rcppeigen >=0.3.3.3.0 + - r-rcppparallel >=5.0.1 - r-rlang - - 'r-rstan >=2.18.1' - - 'r-rstantools >=2.1.1' - - 'r-stanheaders >=2.18.0' + - r-rstan >=2.18.1 + - r-rstantools >=2.1.1 + - r-stanheaders >=2.18.0 - r-tibble - r-tidybayes - - 'r-tidyr >=0.8.3.9000' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + - r-tidyr >=0.8.3.9000 + +source: + md5: 61ba747d87e8faa669273b348c31a957 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models' - description: 'Relative transcript abundance has proven to be a valuable tool for understanding the function of genes in biological systems. For the differential analysis of transcript abundance using RNA sequencing data, the negative binomial model is by far the most frequently adopted. However, common methods that are based on a negative binomial model are not robust to extreme outliers, which we found to be abundant in public datasets. So far, no rigorous and probabilistic methods for detection of outliers have been developed for RNA sequencing data, leaving the identification mostly to visual inspection. Recent advances in Bayesian computation allow large-scale comparison of observed data against its theoretical distribution given in a statistical model. Here we propose ppcseq, a key quality-control tool for identifying transcripts that include outlier data points in differential expression analysis, which do not follow a negative binomial distribution. Applying ppcseq to analyse several publicly available datasets using popular tools, we show that from 3 to 10 percent of differentially abundant transcripts across algorithms and datasets had statistics inflated by the presence of outliers.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ppinfer/meta.yaml b/recipes/bioconductor-ppinfer/meta.yaml index a413c32921519..74d7d0cf75824 100644 --- a/recipes/bioconductor-ppinfer/meta.yaml +++ b/recipes/bioconductor-ppinfer/meta.yaml @@ -1,56 +1,62 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "PPInfer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Interactions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn ushered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at identifying proteins closely related to some interesting proteins. A network based statistical learning method is used to infer the putative functions of proteins from the known functions of its neighboring proteins on a PPI network. This package identifies such proteins often involved in the same or similar biological functions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Inferring functionally related proteins using protein interaction networks -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f6b346ab6e0c90b546825aa50fb52b59 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ppinfer", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-ppinfer + path: recipes/bioconductor-ppinfer + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-stringdb >=2.14.0,<2.15.0' - - 'bioconductor-yeastexpdata >=0.48.0,<0.49.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-stringdb >=2.18.0,<2.19.0 + - bioconductor-yeastexpdata >=0.52.0,<0.53.0 - r-base - r-ggplot2 - r-httr - r-igraph - r-kernlab run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-stringdb >=2.14.0,<2.15.0' - - 'bioconductor-yeastexpdata >=0.48.0,<0.49.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-stringdb >=2.18.0,<2.19.0 + - bioconductor-yeastexpdata >=0.52.0,<0.53.0 - r-base - r-ggplot2 - r-httr - r-igraph - r-kernlab + +source: + md5: 0e25d7cc8b0dbcb8868a394bb5e17e9f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Inferring functionally related proteins using protein interaction networks' - description: 'Interactions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn ushered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at identifying proteins closely related to some interesting proteins. A network based statistical learning method is used to infer the putative functions of proteins from the known functions of its neighboring proteins on a PPI network. This package identifies such proteins often involved in the same or similar biological functions.' -extra: - parent_recipe: - name: bioconductor-ppinfer - path: recipes/bioconductor-ppinfer - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pqsfinder/meta.yaml b/recipes/bioconductor-pqsfinder/meta.yaml index d89644da4851d..1130aa274098f 100644 --- a/recipes/bioconductor-pqsfinder/meta.yaml +++ b/recipes/bioconductor-pqsfinder/meta.yaml @@ -1,63 +1,69 @@ -{% set version = "2.18.0" %} +{% set version = "2.22.0" %} {% set name = "pqsfinder" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Pqsfinder detects DNA and RNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, pqsfinder is able to detect G4s folded from imperfect G-runs containing bulges or mismatches or G4s having long loops. Pqsfinder also assigns an integer score to each hit that was fitted on G4 sequencing data and corresponds to expected stability of the folded G4. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_2_clause + file LICENSE + license_file: LICENSE + summary: Identification of potential quadruplex forming sequences -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c1201a86985850d5ace97c629e2d4864 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pqsfinder", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:pqsfinder + - doi:10.1093/bioinformatics/btv272 + parent_recipe: + name: bioconductor-pqsfinder + path: recipes/bioconductor-pqsfinder + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, Gviz, rtracklayer, ggplot2, BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi # SystemRequirements: GNU make, C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-bh >=1.78.0' - - 'r-rcpp >=0.12.3' + - r-bh >=1.78.0 + - r-rcpp >=0.12.3 - libblas - liblapack run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-bh >=1.78.0' - - 'r-rcpp >=0.12.3' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-bh >=1.78.0 + - r-rcpp >=0.12.3 + +source: + md5: 87856f6757808a26fbb5e0b77371ff0f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_2_clause + file LICENSE' - summary: 'Identification of potential quadruplex forming sequences' - description: 'Pqsfinder detects DNA and RNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, pqsfinder is able to detect G4s folded from imperfect G-runs containing bulges or mismatches or G4s having long loops. Pqsfinder also assigns an integer score to each hit that was fitted on G4 sequencing data and corresponds to expected stability of the folded G4.' - license_file: LICENSE -extra: - identifiers: - - biotools:pqsfinder - - doi:10.1093/bioinformatics/btv272 - parent_recipe: - name: bioconductor-pqsfinder - path: recipes/bioconductor-pqsfinder - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pram/meta.yaml b/recipes/bioconductor-pram/meta.yaml index 6e6332cc06696..179f0a31953fa 100644 --- a/recipes/bioconductor-pram/meta.yaml +++ b/recipes/bioconductor-pram/meta.yaml @@ -1,57 +1,62 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "pram" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Publicly available RNA-seq data is routinely used for retrospective analysis to elucidate new biology. Novel transcript discovery enabled by large collections of RNA-seq datasets has emerged as one of such analysis. To increase the power of transcript discovery from large collections of RNA-seq datasets, we developed a new R package named Pooling RNA-seq and Assembling Models (PRAM), which builds transcript models in intergenic regions from pooled RNA-seq datasets. This package includes functions for defining intergenic regions, extracting and pooling related RNA-seq alignments, predicting, selected, and evaluating transcript models. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Pooling RNA-seq datasets for assembling transcript models -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 129a8e2cbbf4abab07038d3b7899c58e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pram", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-data.table >=1.11.8' + - r-data.table >=1.11.8 run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-data.table >=1.11.8' + - r-data.table >=1.11.8 + +source: + md5: f82820adea535d68aaddc8555db22a73 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Pooling RNA-seq datasets for assembling transcript models' - description: 'Publicly available RNA-seq data is routinely used for retrospective analysis to elucidate new biology. Novel transcript discovery enabled by large collections of RNA-seq datasets has emerged as one of such analysis. To increase the power of transcript discovery from large collections of RNA-seq datasets, we developed a new R package named Pooling RNA-seq and Assembling Models (PRAM), which builds transcript models in intergenic regions from pooled RNA-seq datasets. This package includes functions for defining intergenic regions, extracting and pooling related RNA-seq alignments, predicting, selected, and evaluating transcript models.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-prebs/meta.yaml b/recipes/bioconductor-prebs/meta.yaml index 8be0337f23ffe..5c9d4a94b900d 100644 --- a/recipes/bioconductor-prebs/meta.yaml +++ b/recipes/bioconductor-prebs/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "prebs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The prebs package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA algorithm. The pipeline takes mapped reads in BAM format as an input and produces either gene expressions or original microarray probe set expressions as an output. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Probe region expression estimation for RNA-seq data for improved microarray comparability -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 847264218e6725926f1b56aacd09b541 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-prebs", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:prebs + parent_recipe: + name: bioconductor-prebs + path: recipes/bioconductor-prebs + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: prebsdata, hgu133plus2cdf, hgu133plus2probe requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rpa >=1.58.0,<1.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rpa >=1.62.0,<1.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rpa >=1.58.0,<1.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rpa >=1.62.0,<1.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base + +source: + md5: b96a4d47e6fcd79cc5887b2eb2268a74 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Probe region expression estimation for RNA-seq data for improved microarray comparability' - description: 'The prebs package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA algorithm. The pipeline takes mapped reads in BAM format as an input and produces either gene expressions or original microarray probe set expressions as an output.' -extra: - identifiers: - - biotools:prebs - parent_recipe: - name: bioconductor-prebs - path: recipes/bioconductor-prebs - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-prebsdata/meta.yaml b/recipes/bioconductor-prebsdata/meta.yaml index 1b3a2dde647b4..8d1b5b28b10fe 100644 --- a/recipes/bioconductor-prebsdata/meta.yaml +++ b/recipes/bioconductor-prebsdata/meta.yaml @@ -1,37 +1,37 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "prebsdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a1c6aee2732035357adc3e2cb99d6bcc +about: + description: 'This package contains data required to run examples in ''prebs'' package. The data files include: 1) Small sample bam files for demonstration purposes 2) Probe sequence mappings for Custom CDF (taken from http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp) 3) Probe sequence mappings for manufacturer''s CDF (manually created using bowtie)' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Data for 'prebs' package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-prebsdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fbab2ecd59d9a1dc6f3e106f8ad9ffc4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Data for ''prebs'' package' - description: 'This package contains data required to run examples in ''prebs'' package. The data files include: 1) Small sample bam files for demonstration purposes 2) Probe sequence mappings for Custom CDF (taken from http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp) 3) Probe sequence mappings for manufacturer''s CDF (manually created using bowtie)' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-prebsdata/post-link.sh b/recipes/bioconductor-prebsdata/post-link.sh index 816d1ef0dbdd3..ca1acf1b95b11 100644 --- a/recipes/bioconductor-prebsdata/post-link.sh +++ b/recipes/bioconductor-prebsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prebsdata-1.38.0" +installBiocDataPackage.sh "prebsdata-1.42.0" diff --git a/recipes/bioconductor-precisetad/meta.yaml b/recipes/bioconductor-precisetad/meta.yaml index 47324c027359e..fd6db09a5920c 100644 --- a/recipes/bioconductor-precisetad/meta.yaml +++ b/recipes/bioconductor-precisetad/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "preciseTAD" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: preciseTAD provides functions to predict the location of boundaries of topologically associated domains (TADs) and chromatin loops at base-level resolution. As an input, it takes BED-formatted genomic coordinates of domain boundaries detected from low-resolution Hi-C data, and coordinates of high-resolution genomic annotations from ENCODE or other consortia. preciseTAD employs several feature engineering strategies and resampling techniques to address class imbalance, and trains an optimized random forest model for predicting low-resolution domain boundaries. Translated on a base-level, preciseTAD predicts the probability for each base to be a boundary. Density-based clustering and scalable partitioning techniques are used to detect precise boundary regions and summit points. Compared with low-resolution boundaries, preciseTAD boundaries are highly enriched for CTCF, RAD21, SMC3, and ZNF143 signal and more conserved across cell lines. The pre-trained model can accurately predict boundaries in another cell line using CTCF, RAD21, SMC3, and ZNF143 annotation data for this cell line. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 'preciseTAD: A machine learning framework for precise TAD boundary prediction' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5e6495261bf370abf46d979aace7f363 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-precisetad", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, BiocCheck, BiocManager, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rcgh >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rcgh >=1.36.0,<1.37.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-caret - r-cluster @@ -40,10 +42,10 @@ requirements: - r-prroc - r-randomforest run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rcgh >=1.32.0,<1.33.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rcgh >=1.36.0,<1.37.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-caret - r-cluster @@ -57,13 +59,16 @@ requirements: - r-proc - r-prroc - r-randomforest + +source: + md5: 0e602de9d61c6d4364dd71c47098729e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'preciseTAD: A machine learning framework for precise TAD boundary prediction' - description: 'preciseTAD provides functions to predict the location of boundaries of topologically associated domains (TADs) and chromatin loops at base-level resolution. As an input, it takes BED-formatted genomic coordinates of domain boundaries detected from low-resolution Hi-C data, and coordinates of high-resolution genomic annotations from ENCODE or other consortia. preciseTAD employs several feature engineering strategies and resampling techniques to address class imbalance, and trains an optimized random forest model for predicting low-resolution domain boundaries. Translated on a base-level, preciseTAD predicts the probability for each base to be a boundary. Density-based clustering and scalable partitioning techniques are used to detect precise boundary regions and summit points. Compared with low-resolution boundaries, preciseTAD boundaries are highly enriched for CTCF, RAD21, SMC3, and ZNF143 signal and more conserved across cell lines. The pre-trained model can accurately predict boundaries in another cell line using CTCF, RAD21, SMC3, and ZNF143 annotation data for this cell line.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-precisetadhub/meta.yaml b/recipes/bioconductor-precisetadhub/meta.yaml index d4dc0c0f45d28..5a5cf13e5fcea 100644 --- a/recipes/bioconductor-precisetadhub/meta.yaml +++ b/recipes/bioconductor-precisetadhub/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "preciseTADhub" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bff4bbf0a4ac1abf21ff72ad4346795c +about: + description: 'An experimentdata package to supplement the preciseTAD package containing pre-trained models and the variable importances of each genomic annotation used to build the model parsed into list objects and available in ExperimentHub. In total, preciseTADhub provides access to n=84 random forest classification models optimized to predict TAD/chromatin loop boundary regions and stored as .RDS files. The value, n, comes from the fact that we considered l=2 cell lines {GM12878, K562}, g=2 ground truth boundaries {Arrowhead, Peakachu}, and c=21 autosomal chromosomes {CHR1, CHR2, ..., CHR22} (omitting CHR9). Furthermore, each object is itself a two-item list containing: (1) the model object, and (2) the variable importances for CTCF, RAD21, SMC3, and ZNF143 used to predict boundary regions. Each model is trained via a "holdout" strategy, in which data from chromosomes {CHR1, CHR2, ..., CHRi-1, CHRi+1, ..., CHR22} were used to build the model and the ith chromosome was reserved for testing. See https://doi.org/10.1101/2020.09.03.282186 for more detail on the model building strategy.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Pre-trained random forest models obtained using preciseTAD build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-precisetadhub", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, markdown, BiocStyle, preciseTAD requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 695ed7dbc12e20c3f6bd9484fdfb309b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Pre-trained random forest models obtained using preciseTAD' - description: 'An experimentdata package to supplement the preciseTAD package containing pre-trained models and the variable importances of each genomic annotation used to build the model parsed into list objects and available in ExperimentHub. In total, preciseTADhub provides access to n=84 random forest classification models optimized to predict TAD/chromatin loop boundary regions and stored as .RDS files. The value, n, comes from the fact that we considered l=2 cell lines {GM12878, K562}, g=2 ground truth boundaries {Arrowhead, Peakachu}, and c=21 autosomal chromosomes {CHR1, CHR2, ..., CHR22} (omitting CHR9). Furthermore, each object is itself a two-item list containing: (1) the model object, and (2) the variable importances for CTCF, RAD21, SMC3, and ZNF143 used to predict boundary regions. Each model is trained via a "holdout" strategy, in which data from chromosomes {CHR1, CHR2, ..., CHRi-1, CHRi+1, ..., CHR22} were used to build the model and the ith chromosome was reserved for testing. See https://doi.org/10.1101/2020.09.03.282186 for more detail on the model building strategy.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-precisetadhub/post-link.sh b/recipes/bioconductor-precisetadhub/post-link.sh index ff7494e2c8d04..e26179ee60e6a 100644 --- a/recipes/bioconductor-precisetadhub/post-link.sh +++ b/recipes/bioconductor-precisetadhub/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "precisetadhub-1.10.0" +installBiocDataPackage.sh "precisetadhub-1.14.0" diff --git a/recipes/bioconductor-preda/meta.yaml b/recipes/bioconductor-preda/meta.yaml index 2c12240a90381..694d79bf1890e 100644 --- a/recipes/bioconductor-preda/meta.yaml +++ b/recipes/bioconductor-preda/meta.yaml @@ -1,47 +1,22 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "PREDA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package for the position related analysis of quantitative functional genomics data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Position Related Data Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6f051dc3182b2d70715d84a12e39dd57 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-preda", max_pin="x.x") }}' - noarch: generic -# Suggests: quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata -requirements: - host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - r-base - - 'r-lokern >=1.0.9' - run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - r-base - - 'r-lokern >=1.0.9' -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Position Related Data Analysis' - description: 'Package for the position related analysis of quantitative functional genomics data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + extra: identifiers: - biotools:preda @@ -51,3 +26,34 @@ extra: path: recipes/bioconductor-preda version: 1.26.1 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata +requirements: + host: + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - r-base + - r-lokern >=1.0.9 + run: + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - r-base + - r-lokern >=1.0.9 + +source: + md5: bcdc80537f37f8daaba13323d8f378e2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-predasampledata/meta.yaml b/recipes/bioconductor-predasampledata/meta.yaml index 1d617501f624f..e7b9d10b85834 100644 --- a/recipes/bioconductor-predasampledata/meta.yaml +++ b/recipes/bioconductor-predasampledata/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "0.42.0" %} +{% set version = "0.46.0" %} {% set name = "PREDAsampledata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Sample data for PREDA package. (annotations objects synchronized with GeneAnnot custom CDFs version 2.2.0) + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: expression and copy number data on clear cell renal carcinoma samples -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5acce57384c00a56d658281ba4fa57e5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-predasampledata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: hgu133plus2.db, hgu133plus2cdf requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-preda >=1.48.0,<1.49.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-preda >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-preda >=1.48.0,<1.49.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-preda >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 05358c3ac8d86e34a872c1105f66fc33 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'expression and copy number data on clear cell renal carcinoma samples' - description: 'Sample data for PREDA package. (annotations objects synchronized with GeneAnnot custom CDFs version 2.2.0)' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-predasampledata/post-link.sh b/recipes/bioconductor-predasampledata/post-link.sh index abc7050325f76..c45ef6870ad28 100644 --- a/recipes/bioconductor-predasampledata/post-link.sh +++ b/recipes/bioconductor-predasampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "predasampledata-0.42.0" +installBiocDataPackage.sh "predasampledata-0.46.0" diff --git a/recipes/bioconductor-preprocesscore/meta.yaml b/recipes/bioconductor-preprocesscore/meta.yaml index 4d4b028c4d4a1..2b0218716e4ac 100644 --- a/recipes/bioconductor-preprocesscore/meta.yaml +++ b/recipes/bioconductor-preprocesscore/meta.yaml @@ -1,43 +1,21 @@ -{% set version = "1.64.0" %} +{% set version = "1.68.0" %} {% set name = "preprocessCore" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A library of core preprocessing routines. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: A collection of pre-processing functions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2116c6363074b59becdaf7a1e88caf91 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-preprocesscore", max_pin="x.x") }}' -requirements: - host: - - r-base - - libblas - - liblapack - run: - - r-base - build: - - {{ compiler('c') }} - - automake - - make -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'A collection of pre-processing functions' - description: 'A library of core preprocessing routines.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + extra: additional-platforms: - linux-aarch64 @@ -49,3 +27,31 @@ extra: path: recipes/bioconductor-preprocesscore version: 1.42.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + build: + - {{ compiler('c') }} + - automake + - make + host: + - r-base + - libblas + - liblapack + run: + - r-base + +source: + md5: 61afd1d17c726fe857064bd7d1e9da07 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-primeviewcdf/meta.yaml b/recipes/bioconductor-primeviewcdf/meta.yaml index 352d7095f852b..cbaa4f07a8fba 100644 --- a/recipes/bioconductor-primeviewcdf/meta.yaml +++ b/recipes/bioconductor-primeviewcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "primeviewcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 71e39a59a5907e9b8a8dba58d36eee50 +about: + description: A package containing an environment representing the PrimeView.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: primeviewcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-primeviewcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 71e39a59a5907e9b8a8dba58d36eee50 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: primeviewcdf - description: 'A package containing an environment representing the PrimeView.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-primeviewprobe/meta.yaml b/recipes/bioconductor-primeviewprobe/meta.yaml index 73bf4d160c889..bce2d7637344c 100644 --- a/recipes/bioconductor-primeviewprobe/meta.yaml +++ b/recipes/bioconductor-primeviewprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "primeviewprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 87cc56a8da4fb742ab1558ce1d3d26cc +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was PrimeView\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type primeview build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-primeviewprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 87cc56a8da4fb742ab1558ce1d3d26cc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type primeview' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was PrimeView\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-primirtss/meta.yaml b/recipes/bioconductor-primirtss/meta.yaml index 7ba8ad1cb4071..84bfb44195e41 100644 --- a/recipes/bioconductor-primirtss/meta.yaml +++ b/recipes/bioconductor-primirtss/meta.yaml @@ -1,80 +1,88 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "primirTSS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A fast, convenient tool to identify the TSSs of miRNAs by integrating the data of H3K4me3 and Pol II as well as combining the conservation level and sequence feature, provided within both command-line and graphical interfaces, which achieves a better performance than the previous non-cell-specific methods on miRNA TSSs. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Prediction of pri-miRNA Transcription Start Site -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ead295f564f0e3c4c9d9c8bfa568e745 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-primirtss", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-primirtss + path: recipes/bioconductor-primirtss + version: 1.0.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' - - 'bioconductor-phastcons100way.ucsc.hg38 >=3.7.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-jaspar2018 >=1.1.0,<1.2.0 + - bioconductor-phastcons100way.ucsc.hg38 >=3.7.0,<3.8.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-tfbstools >=1.44.0,<1.45.0 - r-base - - 'r-dplyr >=0.7.6' - - 'r-purrr >=0.2.5' - - 'r-r.utils >=2.6.0' - - 'r-shiny >=1.0.5' - - 'r-stringr >=1.3.1' - - 'r-tibble >=1.4.2' - - 'r-tidyr >=0.8.1' + - r-dplyr >=0.7.6 + - r-purrr >=0.2.5 + - r-r.utils >=2.6.0 + - r-shiny >=1.0.5 + - r-stringr >=1.3.1 + - r-tibble >=1.4.2 + - r-tidyr >=0.8.1 + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' - - 'bioconductor-phastcons100way.ucsc.hg38 >=3.7.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-jaspar2018 >=1.1.0,<1.2.0 + - bioconductor-phastcons100way.ucsc.hg38 >=3.7.0,<3.8.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-tfbstools >=1.44.0,<1.45.0 - r-base - - 'r-dplyr >=0.7.6' - - 'r-purrr >=0.2.5' - - 'r-r.utils >=2.6.0' - - 'r-shiny >=1.0.5' - - 'r-stringr >=1.3.1' - - 'r-tibble >=1.4.2' - - 'r-tidyr >=0.8.1' + - r-dplyr >=0.7.6 + - r-purrr >=0.2.5 + - r-r.utils >=2.6.0 + - r-shiny >=1.0.5 + - r-stringr >=1.3.1 + - r-tibble >=1.4.2 + - r-tidyr >=0.8.1 + +source: + md5: eba06a5e0b1ed70d47bae698fcb29d34 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Prediction of pri-miRNA Transcription Start Site' - description: 'A fast, convenient tool to identify the TSSs of miRNAs by integrating the data of H3K4me3 and Pol II as well as combining the conservation level and sequence feature, provided within both command-line and graphical interfaces, which achieves a better performance than the previous non-cell-specific methods on miRNA TSSs.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - parent_recipe: - name: bioconductor-primirtss - path: recipes/bioconductor-primirtss - version: 1.0.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-prince/meta.yaml b/recipes/bioconductor-prince/meta.yaml index f898336ea68c0..ba6b13f463a74 100644 --- a/recipes/bioconductor-prince/meta.yaml +++ b/recipes/bioconductor-prince/meta.yaml @@ -1,69 +1,74 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "PrInCE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: PrInCE (Predicting Interactomes from Co-Elution) uses a naive Bayes classifier trained on dataset-derived features to recover protein-protein interactions from co-elution chromatogram profiles. This package contains the R implementation of PrInCE. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Predicting Interactomes from Co-Elution -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98e7e0b9a7e620e0e4ab55436b5c289b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-prince", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 - r-base - - 'r-dplyr >=0.7.4' - - 'r-forecast >=8.2' - - 'r-hmisc >=4.0' - - 'r-liblinear >=2.10-8' - - 'r-magrittr >=1.5' - - 'r-naivebayes >=0.9.1' - - 'r-progress >=1.1.2' - - 'r-purrr >=0.2.4' - - 'r-ranger >=0.8.0' - - 'r-rdpack >=0.7' - - 'r-robustbase >=0.92-7' - - 'r-speedglm >=0.3-2' - - 'r-tester >=0.1.7' - - 'r-tidyr >=0.8.99' + - r-dplyr >=0.7.4 + - r-forecast >=8.2 + - r-hmisc >=4.0 + - r-liblinear >=2.10-8 + - r-magrittr >=1.5 + - r-naivebayes >=0.9.1 + - r-progress >=1.1.2 + - r-purrr >=0.2.4 + - r-ranger >=0.8.0 + - r-rdpack >=0.7 + - r-robustbase >=0.92-7 + - r-speedglm >=0.3-2 + - r-tester >=0.1.7 + - r-tidyr >=0.8.99 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 - r-base - - 'r-dplyr >=0.7.4' - - 'r-forecast >=8.2' - - 'r-hmisc >=4.0' - - 'r-liblinear >=2.10-8' - - 'r-magrittr >=1.5' - - 'r-naivebayes >=0.9.1' - - 'r-progress >=1.1.2' - - 'r-purrr >=0.2.4' - - 'r-ranger >=0.8.0' - - 'r-rdpack >=0.7' - - 'r-robustbase >=0.92-7' - - 'r-speedglm >=0.3-2' - - 'r-tester >=0.1.7' - - 'r-tidyr >=0.8.99' + - r-dplyr >=0.7.4 + - r-forecast >=8.2 + - r-hmisc >=4.0 + - r-liblinear >=2.10-8 + - r-magrittr >=1.5 + - r-naivebayes >=0.9.1 + - r-progress >=1.1.2 + - r-purrr >=0.2.4 + - r-ranger >=0.8.0 + - r-rdpack >=0.7 + - r-robustbase >=0.92-7 + - r-speedglm >=0.3-2 + - r-tester >=0.1.7 + - r-tidyr >=0.8.99 + +source: + md5: 5f31284d4bccefe998ac479eb21274cc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Predicting Interactomes from Co-Elution' - description: 'PrInCE (Predicting Interactomes from Co-Elution) uses a naive Bayes classifier trained on dataset-derived features to recover protein-protein interactions from co-elution chromatogram profiles. This package contains the R implementation of PrInCE.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-proactiv/meta.yaml b/recipes/bioconductor-proactiv/meta.yaml index 475fc41ef36eb..0db9f616ede3a 100644 --- a/recipes/bioconductor-proactiv/meta.yaml +++ b/recipes/bioconductor-proactiv/meta.yaml @@ -1,37 +1,40 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "proActiv" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Most human genes have multiple promoters that control the expression of different isoforms. The use of these alternative promoters enables the regulation of isoform expression pre-transcriptionally. Alternative promoters have been found to be important in a wide number of cell types and diseases. proActiv is an R package that enables the analysis of promoters from RNA-seq data. proActiv uses aligned reads as input, and generates counts and normalized promoter activity estimates for each annotated promoter. In particular, proActiv accepts junction files from TopHat2 or STAR or BAM files as inputs. These estimates can then be used to identify which promoter is active, which promoter is inactive, and which promoters change their activity across conditions. proActiv also allows visualization of promoter activity across conditions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Estimate Promoter Activity from RNA-Seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3aaa83b78fb2e017358c24ab185506ca build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-proactiv", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, rmarkdown, knitr, Rtsne, gridExtra requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-data.table - r-dplyr @@ -41,16 +44,17 @@ requirements: - r-scales - r-tibble run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-data.table - r-dplyr @@ -59,13 +63,16 @@ requirements: - r-rlang - r-scales - r-tibble + +source: + md5: 1985887def235d0035fc9334a804e4d6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Estimate Promoter Activity from RNA-Seq data' - description: 'Most human genes have multiple promoters that control the expression of different isoforms. The use of these alternative promoters enables the regulation of isoform expression pre-transcriptionally. Alternative promoters have been found to be important in a wide number of cell types and diseases. proActiv is an R package that enables the analysis of promoters from RNA-seq data. proActiv uses aligned reads as input, and generates counts and normalized promoter activity estimates for each annotated promoter. In particular, proActiv accepts junction files from TopHat2 or STAR or BAM files as inputs. These estimates can then be used to identify which promoter is active, which promoter is inactive, and which promoters change their activity across conditions. proActiv also allows visualization of promoter activity across conditions.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-probamr/meta.yaml b/recipes/bioconductor-probamr/meta.yaml index 2afdefe586872..0f032bdd8f6f4 100644 --- a/recipes/bioconductor-probamr/meta.yaml +++ b/recipes/bioconductor-probamr/meta.yaml @@ -1,50 +1,21 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "proBAMr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Mapping PSMs back to genome. The package builds SAM file from shotgun proteomics data The package also provides function to prepare annotation from GTF file. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Generating SAM file for PSMs in shotgun proteomics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0b5a894a54fb0d56f940b75e025c0d47 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-probamr", max_pin="x.x") }}' - noarch: generic -# Suggests: RUnit, BiocGenerics -requirements: - host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - r-base - run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Generating SAM file for PSMs in shotgun proteomics data' - description: 'Mapping PSMs back to genome. The package builds SAM file from shotgun proteomics data The package also provides function to prepare annotation from GTF file.' + extra: identifiers: - biotools:probamr @@ -54,3 +25,40 @@ extra: path: recipes/bioconductor-probamr version: 1.14.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RUnit, BiocGenerics +requirements: + host: + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 + - r-base + run: + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 + - r-base + +source: + md5: ead4c9156710d421662ce7cb1ef3db20 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-process/meta.yaml b/recipes/bioconductor-process/meta.yaml index 3d680a0f15bea..991e2551457a9 100644 --- a/recipes/bioconductor-process/meta.yaml +++ b/recipes/bioconductor-process/meta.yaml @@ -1,39 +1,21 @@ -{% set version = "1.78.0" %} +{% set version = "1.82.0" %} {% set name = "PROcess" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package for processing protein mass spectrometry data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Ciphergen SELDI-TOF Processing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9a9b6e6d31c1c45fb08e1f7cf00f0170 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-process", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-icens >=1.74.0,<1.75.0' - - r-base - run: - - 'bioconductor-icens >=1.74.0,<1.75.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Ciphergen SELDI-TOF Processing' - description: 'A package for processing protein mass spectrometry data.' + extra: identifiers: - biotools:process @@ -43,3 +25,27 @@ extra: path: recipes/bioconductor-process version: 1.58.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-icens >=1.78.0,<1.79.0 + - r-base + run: + - bioconductor-icens >=1.78.0,<1.79.0 + - r-base + +source: + md5: 4908c255d9a7568a935d9a9a104a1543 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-procoil/meta.yaml b/recipes/bioconductor-procoil/meta.yaml index c05235fe4603e..608e23749492a 100644 --- a/recipes/bioconductor-procoil/meta.yaml +++ b/recipes/bioconductor-procoil/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "2.30.0" %} +{% set version = "2.34.0" %} {% set name = "procoil" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package allows for predicting whether a coiled coil sequence (amino acid sequence plus heptad register) is more likely to form a dimer or more likely to form a trimer. Additionally to the prediction itself, a prediction profile is computed which allows for determining the strengths to which the individual residues are indicative for either class. Prediction profiles can also be visualized as curves or heatmaps. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Prediction of Oligomerization of Coiled Coil Proteins -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5536c056587bff646a606dec3437fa5d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-procoil", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:procoil + parent_recipe: + name: bioconductor-procoil + path: recipes/bioconductor-procoil + version: 2.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-kebabs >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-kebabs >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-kebabs >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-kebabs >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base + +source: + md5: 174fa33038e5cb51178d3a96f06a2c34 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Prediction of Oligomerization of Coiled Coil Proteins' - description: 'The package allows for predicting whether a coiled coil sequence (amino acid sequence plus heptad register) is more likely to form a dimer or more likely to form a trimer. Additionally to the prediction itself, a prediction profile is computed which allows for determining the strengths to which the individual residues are indicative for either class. Prediction profiles can also be visualized as curves or heatmaps.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:procoil - parent_recipe: - name: bioconductor-procoil - path: recipes/bioconductor-procoil - version: 2.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-proda/meta.yaml b/recipes/bioconductor-proda/meta.yaml index 5a6afff59963e..43b99b41f1bc1 100644 --- a/recipes/bioconductor-proda/meta.yaml +++ b/recipes/bioconductor-proda/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "proDA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 906f58f351f6a657aafcb3f6a670cc9f +about: + description: Account for missing values in label-free mass spectrometry data without imputation. The package implements a probabilistic dropout model that ensures that the information from observed and missing values are properly combined. It adds empirical Bayesian priors to increase power to detect differentially abundant proteins. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Differential Abundance Analysis of Label-Free Mass Spectrometry Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-proda", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat (>= 2.1.0), MSnbase, dplyr, stringr, readr, tidyr, tibble, limma, DEP, numDeriv, pheatmap, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-extradistr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-extradistr +source: + md5: 6dc679d6860842be9745f7e3f37353a7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Differential Abundance Analysis of Label-Free Mass Spectrometry Data' - description: 'Account for missing values in label-free mass spectrometry data without imputation. The package implements a probabilistic dropout model that ensures that the information from observed and missing values are properly combined. It adds empirical Bayesian priors to increase power to detect differentially abundant proteins.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-prodata/meta.yaml b/recipes/bioconductor-prodata/meta.yaml index 8b8c68696cd5a..14aa9a804a506 100644 --- a/recipes/bioconductor-prodata/meta.yaml +++ b/recipes/bioconductor-prodata/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "ProData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73f3449db86899c83d61173f6bd02a79 +about: + description: A data package of SELDI-TOF protein mass spectrometry data of 167 breast cancer and normal samples. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: SELDI-TOF data of Breast cancer samples build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-prodata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6ada21309a6f88bf79e69a563a8b4c86 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL - summary: 'SELDI-TOF data of Breast cancer samples' - description: 'A data package of SELDI-TOF protein mass spectrometry data of 167 breast cancer and normal samples.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-prodata/post-link.sh b/recipes/bioconductor-prodata/post-link.sh index fd3bd80e9d246..67dd34fb99a3f 100644 --- a/recipes/bioconductor-prodata/post-link.sh +++ b/recipes/bioconductor-prodata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prodata-1.40.0" +installBiocDataPackage.sh "prodata-1.44.0" diff --git a/recipes/bioconductor-profileplyr/meta.yaml b/recipes/bioconductor-profileplyr/meta.yaml index 760ca42727502..e71d7c0db0a26 100644 --- a/recipes/bioconductor-profileplyr/meta.yaml +++ b/recipes/bioconductor-profileplyr/meta.yaml @@ -1,48 +1,51 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "profileplyr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Quick and straightforward visualization of read signal over genomic intervals is key for generating hypotheses from sequencing data sets (e.g. ChIP-seq, ATAC-seq, bisulfite/methyl-seq). Many tools both inside and outside of R and Bioconductor are available to explore these types of data, and they typically start with a bigWig or BAM file and end with some representation of the signal (e.g. heatmap). profileplyr leverages many Bioconductor tools to allow for both flexibility and additional functionality in workflows that end with visualization of the read signal. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Visualization and annotation of read signal over genomic ranges with profileplyr -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bc6ac2ac1050660a2cb45a11ebbd1a67 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-profileplyr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat, knitr, rmarkdown, png, Cairo requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-chipseeker >=1.38.0,<1.39.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-enrichedheatmap >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rgreat >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-soggi >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-chipseeker >=1.42.0,<1.43.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-enrichedheatmap >=1.36.0,<1.37.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-rgreat >=2.8.0,<2.9.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-soggi >=1.38.0,<1.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 + - bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0 + - bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0 - r-base - r-circlize - r-dplyr @@ -54,28 +57,29 @@ requirements: - r-rlang - r-tidyr - r-tiff + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-chipseeker >=1.38.0,<1.39.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-enrichedheatmap >=1.32.0,<1.33.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rgreat >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-soggi >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-chipseeker >=1.42.0,<1.43.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-enrichedheatmap >=1.36.0,<1.37.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-rgreat >=2.8.0,<2.9.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-soggi >=1.38.0,<1.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 + - bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.10.0,<3.11.0 + - bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0 - r-base - r-circlize - r-dplyr @@ -87,13 +91,16 @@ requirements: - r-rlang - r-tidyr - r-tiff + +source: + md5: 338eed59007c3609827942b0a50b4311 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Visualization and annotation of read signal over genomic ranges with profileplyr' - description: 'Quick and straightforward visualization of read signal over genomic intervals is key for generating hypotheses from sequencing data sets (e.g. ChIP-seq, ATAC-seq, bisulfite/methyl-seq). Many tools both inside and outside of R and Bioconductor are available to explore these types of data, and they typically start with a bigWig or BAM file and end with some representation of the signal (e.g. heatmap). profileplyr leverages many Bioconductor tools to allow for both flexibility and additional functionality in workflows that end with visualization of the read signal.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-profilescoredist/meta.yaml b/recipes/bioconductor-profilescoredist/meta.yaml index 7be23f4741047..9670fa5866c09 100644 --- a/recipes/bioconductor-profilescoredist/meta.yaml +++ b/recipes/bioconductor-profilescoredist/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "profileScoreDist" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Regularization and score distributions for position count matrices. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Profile score distributions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 59d0f0bd369e20aa7be8352e5cf46830 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-profilescoredist", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, MotifDb requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 760fd2987f725358003c665c7930f8ce + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Profile score distributions' - description: 'Regularization and score distributions for position count matrices.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-progeny/meta.yaml b/recipes/bioconductor-progeny/meta.yaml index b6dfccddd3534..0dd7215e1bdbb 100644 --- a/recipes/bioconductor-progeny/meta.yaml +++ b/recipes/bioconductor-progeny/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "progeny" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: PROGENy is resource that leverages a large compendium of publicly available signaling perturbation experiments to yield a common core of pathway responsive genes for human and mouse. These, coupled with any statistical method, can be used to infer pathway activities from bulk or single-cell transcriptomics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Apache License (== 2.0) | file LICENSE + license_file: LICENSE + summary: Pathway RespOnsive GENes for activity inference from gene expression -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9798ea9424f4115b980496038619f009 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-progeny", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: airway, biomaRt, BiocFileCache, broom, Seurat, SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl, pheatmap, tibble, rmarkdown, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-decoupler >=2.8.0,<2.9.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-decoupler >=2.12.0,<2.13.0 - r-base - r-dplyr - r-ggplot2 @@ -32,8 +34,8 @@ requirements: - r-reshape2 - r-tidyr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-decoupler >=2.8.0,<2.9.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-decoupler >=2.12.0,<2.13.0 - r-base - r-dplyr - r-ggplot2 @@ -41,13 +43,16 @@ requirements: - r-gridextra - r-reshape2 - r-tidyr + +source: + md5: 98f76e162cce19fd43ab13251969b117 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Apache License (== 2.0) | file LICENSE' - summary: 'Pathway RespOnsive GENes for activity inference from gene expression' - description: 'PROGENy is resource that leverages a large compendium of publicly available signaling perturbation experiments to yield a common core of pathway responsive genes for human and mouse. These, coupled with any statistical method, can be used to infer pathway activities from bulk or single-cell transcriptomics.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-projectr/meta.yaml b/recipes/bioconductor-projectr/meta.yaml index b84111fbdebb1..2ce1383d3f76a 100644 --- a/recipes/bioconductor-projectr/meta.yaml +++ b/recipes/bioconductor-projectr/meta.yaml @@ -1,28 +1,32 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "projectR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (==2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7351d9a1c593186a6adb189ebd3ff9d2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-projectr", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, CoGAPS, gridExtra, grid, testthat, devtools, rmarkdown, knitr, rmarkdown, ComplexHeatmap, gplots + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, CoGAPS, gridExtra, grid, testthat, devtools, knitr, rmarkdown, ComplexHeatmap, gplots, SeuratObject requirements: + host: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-cluster - r-cowplot @@ -32,6 +36,7 @@ requirements: - r-ggrepel - r-matrix - r-matrixmodels + - r-msigdbr - r-nmf - r-rcolorbrewer - r-reshape2 @@ -40,8 +45,10 @@ requirements: - r-tsne - r-umap - r-viridis + run: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-cluster - r-cowplot @@ -51,6 +58,7 @@ requirements: - r-ggrepel - r-matrix - r-matrixmodels + - r-msigdbr - r-nmf - r-rcolorbrewer - r-reshape2 @@ -59,13 +67,16 @@ requirements: - r-tsne - r-umap - r-viridis + +source: + md5: 31626fd24bbeeaaf849ed5487f363a39 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (==2)' - summary: 'Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering' - description: 'Functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-proloc/meta.yaml b/recipes/bioconductor-proloc/meta.yaml index 230e1d8a522c7..ac8de4aec1706 100644 --- a/recipes/bioconductor-proloc/meta.yaml +++ b/recipes/bioconductor-proloc/meta.yaml @@ -1,32 +1,48 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "pRoloc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A unifying bioinformatics framework for spatial proteomics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 309ce5a09f91050bdf916ab18389d7a8 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-proloc", max_pin="x.x") }}' -# Suggests: testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.41.0), dplyr, akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape, magick + +extra: + identifiers: + - biotools:proloc + parent_recipe: + name: bioconductor-proloc + path: recipes/bioconductor-proloc + version: 1.20.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, rmarkdown, pRolocdata (>= 1.43.2), roxygen2, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.41.0), dplyr, akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape, magick requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-mlinterfaces >=1.82.0,<1.83.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-mlinterfaces >=1.86.0,<1.87.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 - r-base - r-caret - r-class @@ -42,7 +58,7 @@ requirements: - r-laplacesdemon - r-lattice - r-mass - - 'r-mclust >=4.3' + - r-mclust >=4.3 - r-mixtools - r-mvtnorm - r-nnet @@ -50,19 +66,20 @@ requirements: - r-proxy - r-randomforest - r-rcolorbrewer - - 'r-rcpp >=0.10.3' + - r-rcpp >=0.10.3 - r-rcpparmadillo - r-sampling - r-scales - libblas - liblapack + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-mlinterfaces >=1.82.0,<1.83.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-mlinterfaces >=1.86.0,<1.87.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 - r-base - r-caret - r-class @@ -78,7 +95,7 @@ requirements: - r-laplacesdemon - r-lattice - r-mass - - 'r-mclust >=4.3' + - r-mclust >=4.3 - r-mixtools - r-mvtnorm - r-nnet @@ -86,28 +103,20 @@ requirements: - r-proxy - r-randomforest - r-rcolorbrewer - - 'r-rcpp >=0.10.3' + - r-rcpp >=0.10.3 - r-rcpparmadillo - r-sampling - r-scales - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: af27cefbe17786019c650bd56840013e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'A unifying bioinformatics framework for spatial proteomics' - description: 'The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:proloc - parent_recipe: - name: bioconductor-proloc - path: recipes/bioconductor-proloc - version: 1.20.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-prolocdata/meta.yaml b/recipes/bioconductor-prolocdata/meta.yaml index fb5d1764fc6b7..fc810de2787d4 100644 --- a/recipes/bioconductor-prolocdata/meta.yaml +++ b/recipes/bioconductor-prolocdata/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "pRolocdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8aafd04221b21588077788ec79272e1a +about: + description: Mass-spectrometry based spatial proteomics data sets and protein complex separation data. Also contains the time course expression experiment from Mulvey et al. 2015. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Data accompanying the pRoloc package build: - number: 0 + noarch: generic + number: 1 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-prolocdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: pRoloc (>= 1.13.8), testthat, SummarizedExperiment requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20250104 +source: + md5: 3a5b9d9bf4fe38873a4b16eeb7f73d29 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Data accompanying the pRoloc package' - description: 'Mass-spectrometry based spatial proteomics data sets and protein complex separation data. Also contains the time course expression experiment from Mulvey et al. 2015.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-prolocdata/post-link.sh b/recipes/bioconductor-prolocdata/post-link.sh index 58c959a4f2622..a6b8be0896374 100644 --- a/recipes/bioconductor-prolocdata/post-link.sh +++ b/recipes/bioconductor-prolocdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prolocdata-1.40.0" +installBiocDataPackage.sh "prolocdata-1.44.0" diff --git a/recipes/bioconductor-prolocgui/meta.yaml b/recipes/bioconductor-prolocgui/meta.yaml index 92ba43b5a6797..c18a285aaf71b 100644 --- a/recipes/bioconductor-prolocgui/meta.yaml +++ b/recipes/bioconductor-prolocgui/meta.yaml @@ -1,77 +1,83 @@ -{% set version = "2.12.0" %} +{% set version = "2.16.0" %} {% set name = "pRolocGUI" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package pRolocGUI comprises functions to interactively visualise spatial proteomics data on the basis of pRoloc, pRolocdata and shiny. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Interactive visualisation of spatial proteomics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a9947bbed5501a1c2c68f7c35364c1da build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-prolocgui", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:prolocgui + - doi:10.1038/ncomms9992 + parent_recipe: + name: bioconductor-prolocgui + path: recipes/bioconductor-prolocgui + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-proloc >=1.42.0,<1.43.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-proloc >=1.46.0,<1.47.0 - r-base - r-colorspace - r-colourpicker - r-dplyr - - 'r-dt >=0.1.40' + - r-dt >=0.1.40 - r-ggplot2 - r-scales - - 'r-shiny >=0.9.1' + - r-shiny >=0.9.1 - r-shinydashboard - - 'r-shinydashboardplus >=2.0.0' + - r-shinydashboardplus >=2.0.0 - r-shinyhelper - r-shinyjs - r-shinywidgets run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-proloc >=1.42.0,<1.43.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-proloc >=1.46.0,<1.47.0 - r-base - r-colorspace - r-colourpicker - r-dplyr - - 'r-dt >=0.1.40' + - r-dt >=0.1.40 - r-ggplot2 - r-scales - - 'r-shiny >=0.9.1' + - r-shiny >=0.9.1 - r-shinydashboard - - 'r-shinydashboardplus >=2.0.0' + - r-shinydashboardplus >=2.0.0 - r-shinyhelper - r-shinyjs - r-shinywidgets + +source: + md5: 9caa7759371934f6e3b7b7b017135960 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Interactive visualisation of spatial proteomics data' - description: 'The package pRolocGUI comprises functions to interactively visualise spatial proteomics data on the basis of pRoloc, pRolocdata and shiny.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:prolocgui - - doi:10.1038/ncomms9992 - parent_recipe: - name: bioconductor-prolocgui - path: recipes/bioconductor-prolocgui - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-promise/meta.yaml b/recipes/bioconductor-promise/meta.yaml index 17795839b7288..7443e070a7acd 100644 --- a/recipes/bioconductor-promise/meta.yaml +++ b/recipes/bioconductor-promise/meta.yaml @@ -1,42 +1,22 @@ -{% set version = "1.54.0" %} +{% set version = "1.58.0" %} {% set name = "PROMISE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'A general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables as described in Pounds et. al. (2009) Bioinformatics 25: 2013-2019' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: PRojection Onto the Most Interesting Statistical Evidence -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad7b8b2fcd0ba52ad47eb9ff23097a4e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-promise", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'PRojection Onto the Most Interesting Statistical Evidence' - description: 'A general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables as described in Pounds et. al. (2009) Bioinformatics 25: 2013-2019' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:promise @@ -46,3 +26,29 @@ extra: path: recipes/bioconductor-promise version: 1.32.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - r-base + +source: + md5: 6783c7f3744cb92cd4f4305aab04882c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-prone/build.sh b/recipes/bioconductor-prone/build.sh new file mode 100644 index 0000000000000..497f7b5bdb678 --- /dev/null +++ b/recipes/bioconductor-prone/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +export LD_LIBRARY_PATH=${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-prone/meta.yaml b/recipes/bioconductor-prone/meta.yaml new file mode 100644 index 0000000000000..b205e470b87c2 --- /dev/null +++ b/recipes/bioconductor-prone/meta.yaml @@ -0,0 +1,124 @@ +{% set version = "1.0.0" %} +{% set name = "PRONE" %} +{% set bioc = "3.20" %} + +about: + description: High-throughput omics data are often affected by systematic biases introduced throughout all the steps of a clinical study, from sample collection to quantification. Normalization methods aim to adjust for these biases to make the actual biological signal more prominent. However, selecting an appropriate normalization method is challenging due to the wide range of available approaches. Therefore, a comparative evaluation of unnormalized and normalized data is essential in identifying an appropriate normalization strategy for a specific data set. This R package provides different functions for preprocessing, normalizing, and evaluating different normalization approaches. Furthermore, normalization methods can be evaluated on downstream steps, such as differential expression analysis and statistical enrichment analysis. Spike-in data sets with known ground truth and real-world data sets of biological experiments acquired by either tandem mass tag (TMT) or label-free quantification (LFQ) can be analyzed. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: The PROteomics Normalization Evaluator + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-prone", max_pin="x.x") }}' + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, DT +requirements: + + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] + + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-deqms >=1.24.0,<1.25.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-normalyzerde >=1.24.0,<1.25.0 + - bioconductor-poma >=1.16.0,<1.17.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-rots >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-vsn >=3.74.0,<3.75.0 + - r-base + - r-circlize + - r-complexupset + - r-data.table + - r-dendsort + - r-dplyr + - r-ggplot2 + - r-ggtext + - r-gprofiler2 + - r-gtools + - r-magrittr + - r-mass + - r-matrixstats + - r-plotroc + - r-purrr + - r-rcolorbrewer + - r-reshape2 + - r-scales + - r-stringr + - r-tibble + - r-tidyr + - r-upsetr + + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-deqms >=1.24.0,<1.25.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-normalyzerde >=1.24.0,<1.25.0 + - bioconductor-poma >=1.16.0,<1.17.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-rots >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-vsn >=3.74.0,<3.75.0 + - r-base + - r-circlize + - r-complexupset + - r-data.table + - r-dendsort + - r-dplyr + - r-ggplot2 + - r-ggtext + - r-gprofiler2 + - r-gtools + - r-magrittr + - r-mass + - r-matrixstats + - r-plotroc + - r-purrr + - r-rcolorbrewer + - r-reshape2 + - r-scales + - r-stringr + - r-tibble + - r-tidyr + - r-upsetr + +source: + md5: 424320061fdf0c594037698358512cb3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-proper/meta.yaml b/recipes/bioconductor-proper/meta.yaml index 4bb762b00bf39..41cf078e20da8 100644 --- a/recipes/bioconductor-proper/meta.yaml +++ b/recipes/bioconductor-proper/meta.yaml @@ -1,46 +1,52 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "PROPER" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provide simulation based methods for evaluating the statistical power in differential expression analysis from RNA-seq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: PROspective Power Evaluation for RNAseq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6f91ce4b3f5feee476a991fc1072c521 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-proper", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:proper + parent_recipe: + name: bioconductor-proper + path: recipes/bioconductor-proper + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle,DESeq2,DSS,knitr requirements: host: - - 'bioconductor-edger >=4.0.0,<4.1.0' + - bioconductor-edger >=4.4.0,<4.5.0 - r-base run: - - 'bioconductor-edger >=4.0.0,<4.1.0' + - bioconductor-edger >=4.4.0,<4.5.0 - r-base + +source: + md5: 015d560900231510bd434cbf6f7ca621 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL - summary: 'PROspective Power Evaluation for RNAseq' - description: 'This package provide simulation based methods for evaluating the statistical power in differential expression analysis from RNA-seq data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:proper - parent_recipe: - name: bioconductor-proper - path: recipes/bioconductor-proper - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-prostar/meta.yaml b/recipes/bioconductor-prostar/meta.yaml index 7833b98683be8..683619d040e75 100644 --- a/recipes/bioconductor-prostar/meta.yaml +++ b/recipes/bioconductor-prostar/meta.yaml @@ -1,29 +1,38 @@ -{% set version = "1.34.3" %} +{% set version = "1.38.0" %} {% set name = "Prostar" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a GUI interface for the DAPAR package. The package Prostar (Proteomics statistical analysis with R) is a Bioconductor distributed R package which provides all the necessary functions to analyze quantitative data from label-free proteomics experiments. Contrarily to most other similar R packages, it is endowed with rich and user-friendly graphical interfaces, so that no programming skill is required. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Provides a GUI for DAPAR -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ab3095af56a61bfe4fe81279dffcae21 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-prostar", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, BiocManager, testthat + +extra: + parent_recipe: + name: bioconductor-prostar + path: recipes/bioconductor-prostar + version: 1.14.7 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, BiocManager, testthat, knitr requirements: + host: - - 'bioconductor-dapar >=1.34.0,<1.35.0' - - 'bioconductor-dapardata >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-dapar >=1.38.0,<1.39.0 + - bioconductor-dapardata >=1.36.0,<1.37.0 - r-base - r-colourpicker - r-data.table @@ -34,8 +43,8 @@ requirements: - r-gtools - r-highcharter - r-htmlwidgets - - r-knitr - r-later + - r-markdown - r-promises - r-r.utils - r-rclipboard @@ -55,9 +64,11 @@ requirements: - r-vioplot - r-webshot - r-xml + run: - - 'bioconductor-dapar >=1.34.0,<1.35.0' - - 'bioconductor-dapardata >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-dapar >=1.38.0,<1.39.0 + - bioconductor-dapardata >=1.36.0,<1.37.0 - r-base - r-colourpicker - r-data.table @@ -68,8 +79,8 @@ requirements: - r-gtools - r-highcharter - r-htmlwidgets - - r-knitr - r-later + - r-markdown - r-promises - r-r.utils - r-rclipboard @@ -89,17 +100,16 @@ requirements: - r-vioplot - r-webshot - r-xml + +source: + md5: 961266fdb4f9d8a645906d02de047833 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Provides a GUI for DAPAR' - description: 'This package provides a GUI interface for the DAPAR package. The package Prostar (Proteomics statistical analysis with R) is a Bioconductor distributed R package which provides all the necessary functions to analyze quantitative data from label-free proteomics experiments. Contrarily to most other similar R packages, it is endowed with rich and user-friendly graphical interfaces, so that no programming skill is required.' -extra: - parent_recipe: - name: bioconductor-prostar - path: recipes/bioconductor-prostar - version: 1.14.7 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-prostatecancercamcap/meta.yaml b/recipes/bioconductor-prostatecancercamcap/meta.yaml index b01bd5c2727ae..fe10bc7696907 100644 --- a/recipes/bioconductor-prostatecancercamcap/meta.yaml +++ b/recipes/bioconductor-prostatecancercamcap/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "prostateCancerCamcap" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a27ee47f07162569e5e1e06ffd69886 +about: + description: A Bioconductor data package for the Ross-Adams (2015) Prostate Cancer dataset. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Prostate Cancer Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-prostatecancercamcap", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GEOquery requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5dfbd00d06352a039fbc0c1a91837731 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Prostate Cancer Data' - description: 'A Bioconductor data package for the Ross-Adams (2015) Prostate Cancer dataset.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-prostatecancercamcap/post-link.sh b/recipes/bioconductor-prostatecancercamcap/post-link.sh index 884e3a7cda119..1c1c2c098c1b8 100644 --- a/recipes/bioconductor-prostatecancercamcap/post-link.sh +++ b/recipes/bioconductor-prostatecancercamcap/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prostatecancercamcap-1.30.0" +installBiocDataPackage.sh "prostatecancercamcap-1.34.0" diff --git a/recipes/bioconductor-prostatecancergrasso/meta.yaml b/recipes/bioconductor-prostatecancergrasso/meta.yaml index 642718a61eedf..dc7ad3557c07f 100644 --- a/recipes/bioconductor-prostatecancergrasso/meta.yaml +++ b/recipes/bioconductor-prostatecancergrasso/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "prostateCancerGrasso" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c331c996d943a14687439dfdf37b8029 +about: + description: A Bioconductor data package for the Grasso (2012) Prostate Cancer dataset. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Prostate Cancer Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-prostatecancergrasso", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GEOquery requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7c020aa40d54f0633ed989b8de1126af + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Prostate Cancer Data' - description: 'A Bioconductor data package for the Grasso (2012) Prostate Cancer dataset.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-prostatecancergrasso/post-link.sh b/recipes/bioconductor-prostatecancergrasso/post-link.sh index 544c52ea34897..468e6050f689e 100644 --- a/recipes/bioconductor-prostatecancergrasso/post-link.sh +++ b/recipes/bioconductor-prostatecancergrasso/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prostatecancergrasso-1.30.0" +installBiocDataPackage.sh "prostatecancergrasso-1.34.0" diff --git a/recipes/bioconductor-prostatecancerstockholm/meta.yaml b/recipes/bioconductor-prostatecancerstockholm/meta.yaml index 483e6a2239ac4..96a6cfc811020 100644 --- a/recipes/bioconductor-prostatecancerstockholm/meta.yaml +++ b/recipes/bioconductor-prostatecancerstockholm/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "prostateCancerStockholm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 49326bf3b6f66be78fa1e6d6768b5538 +about: + description: A Bioconductor data package for the Stockholm dataset + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Prostate Cancer Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-prostatecancerstockholm", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GEOquery requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: dff545fcd888a091cdbce5b71aef45a9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Prostate Cancer Data' - description: 'A Bioconductor data package for the Stockholm dataset' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-prostatecancerstockholm/post-link.sh b/recipes/bioconductor-prostatecancerstockholm/post-link.sh index b347e68cf857d..606d7f30d4500 100644 --- a/recipes/bioconductor-prostatecancerstockholm/post-link.sh +++ b/recipes/bioconductor-prostatecancerstockholm/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prostatecancerstockholm-1.30.0" +installBiocDataPackage.sh "prostatecancerstockholm-1.34.0" diff --git a/recipes/bioconductor-prostatecancertaylor/meta.yaml b/recipes/bioconductor-prostatecancertaylor/meta.yaml index 00ac0962d4074..f32adfa479d94 100644 --- a/recipes/bioconductor-prostatecancertaylor/meta.yaml +++ b/recipes/bioconductor-prostatecancertaylor/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "prostateCancerTaylor" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c90ff79776e9a658d4cf05e9a29706a8 +about: + description: A Bioconductor data package for the Taylor et al (2010) dataset. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Prostate Cancer Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-prostatecancertaylor", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GEOquery, org.Hs.eg.db requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4f8e97c1c1a342e44b183018b870b508 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Prostate Cancer Data' - description: 'A Bioconductor data package for the Taylor et al (2010) dataset.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-prostatecancertaylor/post-link.sh b/recipes/bioconductor-prostatecancertaylor/post-link.sh index 814031af6bc79..aafca40afaf08 100644 --- a/recipes/bioconductor-prostatecancertaylor/post-link.sh +++ b/recipes/bioconductor-prostatecancertaylor/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prostatecancertaylor-1.30.0" +installBiocDataPackage.sh "prostatecancertaylor-1.34.0" diff --git a/recipes/bioconductor-prostatecancervarambally/meta.yaml b/recipes/bioconductor-prostatecancervarambally/meta.yaml index 65f3a1df66b5c..597d4a9951470 100644 --- a/recipes/bioconductor-prostatecancervarambally/meta.yaml +++ b/recipes/bioconductor-prostatecancervarambally/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "prostateCancerVarambally" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf8fc1872af8c5c2b47372ce94ed4c5c +about: + description: A Bioconductor data package for the Varambally dataset + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Prostate Cancer Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-prostatecancervarambally", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GEOquery requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fb2f47a16abe1e3bba18ad518a17815f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Prostate Cancer Data' - description: 'A Bioconductor data package for the Varambally dataset' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-prostatecancervarambally/post-link.sh b/recipes/bioconductor-prostatecancervarambally/post-link.sh index 6a6d1ca836881..38693228b2e3b 100644 --- a/recipes/bioconductor-prostatecancervarambally/post-link.sh +++ b/recipes/bioconductor-prostatecancervarambally/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "prostatecancervarambally-1.30.0" +installBiocDataPackage.sh "prostatecancervarambally-1.34.0" diff --git a/recipes/bioconductor-proteingymr/build_failure.linux-64.yaml b/recipes/bioconductor-proteingymr/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..1a11bd22d56cf --- /dev/null +++ b/recipes/bioconductor-proteingymr/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: fc4d3cb15f4c1f69041d6a1039d510b49bbeb7bfe9393c77028b3c3d4a5208ca # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-queryup")} + Encountered problems while solving: + - nothing provides requested r-queryup + + Could not solve for environment specs + The following package could not be installed + [31mr-queryup[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-queryup")} + Encountered problems while solving: + - nothing provides requested r-queryup + + Could not solve for environment specs + The following package could not be installed + [31mr-queryup[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-queryup")} + Encountered problems while solving: + - nothing provides requested r-queryup + + Could not solve for environment specs + The following package could not be installed + [31mr-queryup[0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-proteingymr/meta.yaml b/recipes/bioconductor-proteingymr/meta.yaml new file mode 100644 index 0000000000000..7c7f96134fbcd --- /dev/null +++ b/recipes/bioconductor-proteingymr/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.0.0" %} +{% set name = "ProteinGymR" %} +{% set bioc = "3.20" %} + +about: + description: The ProteinGymR package provides analysis-ready data resources from ProteinGym, generated by Notin et al., 2023. ProteinGym comprises a collection of benchmarks for evaluating the performance of models predicting the effect of point mutations. This package provides access to 1. Deep mutational scanning (DMS) scores from 217 assays measuring the impact of all possible amino acid substitutions across 186 proteins, 2. AlphaMissense pathogenicity scores for ~1.6 M substitutions in the ProteinGym DMS data, and 3. five performance metrics for 62 variant prediction models in a zero-shot setting. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Programmatic access to ProteinGym datasets in R/Bioconductor + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-proteingymr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: ComplexHeatmap, AnnotationHub, tibble, stringr, BiocStyle, knitr, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - r-base + - r-dplyr + - r-forcats + - r-ggdist + - r-gghalves + - r-ggplot2 + - r-purrr + - r-queryup + - r-spdl + - r-tidyr + - r-tidyselect + run: + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - r-base + - r-dplyr + - r-forcats + - r-ggdist + - r-gghalves + - r-ggplot2 + - r-purrr + - r-queryup + - r-spdl + - r-tidyr + - r-tidyselect + - curl + - bioconductor-data-packages >=20241103 + +source: + md5: d7be5eeec1cc0645e89670a68fcef3d3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-proteingymr/post-link.sh b/recipes/bioconductor-proteingymr/post-link.sh new file mode 100644 index 0000000000000..18b6007a9ea53 --- /dev/null +++ b/recipes/bioconductor-proteingymr/post-link.sh @@ -0,0 +1,2 @@ +#!/bin/bash +installBiocDataPackage.sh "proteingymr-1.0.0" diff --git a/recipes/bioconductor-proteingymr/pre-unlink.sh b/recipes/bioconductor-proteingymr/pre-unlink.sh new file mode 100644 index 0000000000000..8aa9dcd013cdb --- /dev/null +++ b/recipes/bioconductor-proteingymr/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ProteinGymR diff --git a/recipes/bioconductor-proteinprofiles/meta.yaml b/recipes/bioconductor-proteinprofiles/meta.yaml index ac403d2f66889..0c26a7956642d 100644 --- a/recipes/bioconductor-proteinprofiles/meta.yaml +++ b/recipes/bioconductor-proteinprofiles/meta.yaml @@ -1,37 +1,37 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "proteinProfiles" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 491483ff7b360413ae0eafa5ac07de14 +about: + description: Significance assessment for distance measures of time-course protein profiles + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Protein Profiling build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-proteinprofiles", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat requirements: host: - r-base run: - r-base +source: + md5: bd105d4f0730d834b3485b18a6244163 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Protein Profiling' - description: 'Significance assessment for distance measures of time-course protein profiles' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-proteodisco/meta.yaml b/recipes/bioconductor-proteodisco/meta.yaml index 6e6ba09dfda9e..242fa594a719c 100644 --- a/recipes/bioconductor-proteodisco/meta.yaml +++ b/recipes/bioconductor-proteodisco/meta.yaml @@ -1,73 +1,78 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "ProteoDisco" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (variant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences. The flexible workflow can be adopted to suit a myriad of research and experimental settings. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f69597248b6cbbdb2c1029a1dd3b39cd build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-proteodisco", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationDbi (>= 1.54.1), BSgenome (>= 1.60.0), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.3), BiocStyle (>= 2.20.1), DelayedArray (>= 0.18.0), devtools (>= 2.4.2), knitr (>= 1.33), matrixStats (>= 0.59.0), markdown (>= 1.1), org.Hs.eg.db (>= 3.13.0), purrr (>= 0.3.4), RCurl (>= 1.98.1.3), readr (>= 1.4.0), ggplot2 (>= 3.3.5), rmarkdown (>= 2.9), rtracklayer (>= 1.52.0), seqinr (>= 4.2.8), stringr (>= 1.4.0), reshape2 (>= 1.4.4), scales (>= 1.1.1), testthat (>= 3.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2) requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-cleaver >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-cleaver >=1.44.0,<1.45.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - - 'r-checkmate >=2.0.0' - - 'r-dplyr >=1.0.6' - - 'r-parallellogger >=2.0.1' - - 'r-plyr >=1.8.6' - - 'r-rlang >=0.4.11' - - 'r-tibble >=3.1.2' - - 'r-tidyr >=1.1.3' + - r-checkmate >=2.0.0 + - r-dplyr >=1.0.6 + - r-parallellogger >=2.0.1 + - r-plyr >=1.8.6 + - r-rlang >=0.4.11 + - r-tibble >=3.1.2 + - r-tidyr >=1.1.3 run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-cleaver >=1.40.0,<1.41.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-cleaver >=1.44.0,<1.45.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - - 'r-checkmate >=2.0.0' - - 'r-dplyr >=1.0.6' - - 'r-parallellogger >=2.0.1' - - 'r-plyr >=1.8.6' - - 'r-rlang >=0.4.11' - - 'r-tibble >=3.1.2' - - 'r-tidyr >=1.1.3' + - r-checkmate >=2.0.0 + - r-dplyr >=1.0.6 + - r-parallellogger >=2.0.1 + - r-plyr >=1.8.6 + - r-rlang >=0.4.11 + - r-tibble >=3.1.2 + - r-tidyr >=1.1.3 + +source: + md5: aef1788d8265e423bb2d6a4cc67fd317 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences' - description: 'ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (variant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences. The flexible workflow can be adopted to suit a myriad of research and experimental settings.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-proteomm/meta.yaml b/recipes/bioconductor-proteomm/meta.yaml index 18d262626a71c..982123c603314 100644 --- a/recipes/bioconductor-proteomm/meta.yaml +++ b/recipes/bioconductor-proteomm/meta.yaml @@ -1,28 +1,29 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "ProteoMM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ProteoMM is a statistical method to perform model-based peptide-level differential expression analysis of single or multiple datasets. For multiple datasets ProteoMM produces a single fold change and p-value for each protein across multiple datasets. ProteoMM provides functionality for normalization, missing value imputation and differential expression. Model-based peptide-level imputation and differential expression analysis component of package follows the analysis described in “A statistical framework for protein quantitation in bottom-up MS based proteomics" (Karpievitch et al. Bioinformatics 2009). EigenMS normalisation is implemented as described in "Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition." (Karpievitch et al. Bioinformatics 2009). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + summary: Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6497729c8cc0221c898927dcddeb00e0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-proteomm", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' + - bioconductor-biomart >=2.62.0,<2.63.0 - r-base - r-gdata - r-ggplot2 @@ -30,19 +31,23 @@ requirements: - r-gtools - r-matrixstats run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' + - bioconductor-biomart >=2.62.0,<2.63.0 - r-base - r-gdata - r-ggplot2 - r-ggrepel - r-gtools - r-matrixstats + +source: + md5: d8c89e655a1cabcc73d039ee15550a48 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: MIT - summary: 'Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform' - description: 'ProteoMM is a statistical method to perform model-based peptide-level differential expression analysis of single or multiple datasets. For multiple datasets ProteoMM produces a single fold change and p-value for each protein across multiple datasets. ProteoMM provides functionality for normalization, missing value imputation and differential expression. Model-based peptide-level imputation and differential expression analysis component of package follows the analysis described in “A statistical framework for protein quantitation in bottom-up MS based proteomics" (Karpievitch et al. Bioinformatics 2009). EigenMS normalisation is implemented as described in "Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition." (Karpievitch et al. Bioinformatics 2009).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-protgear/meta.yaml b/recipes/bioconductor-protgear/meta.yaml index 6d3a0b7331dc4..b54339dbfc771 100644 --- a/recipes/bioconductor-protgear/meta.yaml +++ b/recipes/bioconductor-protgear/meta.yaml @@ -1,99 +1,106 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "protGear" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A generic three-step pre-processing package for protein microarray data. This package contains different data pre-processing procedures to allow comparison of their performance.These steps are background correction, the coefficient of variation (CV) based filtering, batch correction and normalization. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Protein Micro Array Data Management and Interactive Visualization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: db63dca71894a3ebbf3b8b78512bccb4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-protgear", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: gridExtra (>= 2.3), png (>= 0.1-7) , magick (>= 2.7.3) , ggplotify (>= 0.1.0) , scales (>= 1.1.1) , shinythemes (>= 1.2.0) , shinyjs (>= 2.0.0) , shinyWidgets (>= 0.6.2) , shinycssloaders (>= 1.0.0) , shinyalert (>= 3.0.0) , shinyFiles (>= 0.9.1) , shinyFeedback (>= 0.3.0) requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-base - - 'r-data.table >=1.14.0' - - 'r-dplyr >=0.8.0' - - 'r-factoextra >=1.0.7' - - 'r-factominer >=2.4' - - 'r-flexdashboard >=0.5.2' - - 'r-ggally >=2.1.2' - - 'r-ggplot2 >=3.3.0' - - 'r-ggpubr >=0.4.0' - - 'r-gtools >=3.8.2' - - 'r-htmltools >=0.4.0' - - 'r-kendall >=2.2' - - 'r-knitr >=1.33' - - 'r-magrittr >=1.5' - - 'r-mass >=7.3' - - 'r-pheatmap >=1.0.12' - - 'r-plotly >=4.9.0' - - 'r-plyr >=1.8.6' - - 'r-purrr >=0.3.4' - - 'r-readr >=2.0.1' - - 'r-remotes >=2.4.0' - - 'r-rlang >=0.4.11' - - 'r-rmarkdown >=2.9' - - 'r-shiny >=1.0.0' - - 'r-shinydashboard >=0.7.1' - - 'r-styler >=1.6.1' - - 'r-tibble >=3.1.0' - - 'r-tidyr >=1.1.3' + - r-data.table >=1.14.0 + - r-dplyr >=0.8.0 + - r-factoextra >=1.0.7 + - r-factominer >=2.4 + - r-flexdashboard >=0.5.2 + - r-ggally >=2.1.2 + - r-ggplot2 >=3.3.0 + - r-ggpubr >=0.4.0 + - r-gtools >=3.8.2 + - r-htmltools >=0.4.0 + - r-kendall >=2.2 + - r-knitr >=1.33 + - r-magrittr >=1.5 + - r-mass >=7.3 + - r-pheatmap >=1.0.12 + - r-plotly >=4.9.0 + - r-plyr >=1.8.6 + - r-purrr >=0.3.4 + - r-readr >=2.0.1 + - r-remotes >=2.4.0 + - r-rlang >=0.4.11 + - r-rmarkdown >=2.9 + - r-shiny >=1.0.0 + - r-shinydashboard >=0.7.1 + - r-styler >=1.6.1 + - r-tibble >=3.1.0 + - r-tidyr >=1.1.3 + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-base - - 'r-data.table >=1.14.0' - - 'r-dplyr >=0.8.0' - - 'r-factoextra >=1.0.7' - - 'r-factominer >=2.4' - - 'r-flexdashboard >=0.5.2' - - 'r-ggally >=2.1.2' - - 'r-ggplot2 >=3.3.0' - - 'r-ggpubr >=0.4.0' - - 'r-gtools >=3.8.2' - - 'r-htmltools >=0.4.0' - - 'r-kendall >=2.2' - - 'r-knitr >=1.33' - - 'r-magrittr >=1.5' - - 'r-mass >=7.3' - - 'r-pheatmap >=1.0.12' - - 'r-plotly >=4.9.0' - - 'r-plyr >=1.8.6' - - 'r-purrr >=0.3.4' - - 'r-readr >=2.0.1' - - 'r-remotes >=2.4.0' - - 'r-rlang >=0.4.11' - - 'r-rmarkdown >=2.9' - - 'r-shiny >=1.0.0' - - 'r-shinydashboard >=0.7.1' - - 'r-styler >=1.6.1' - - 'r-tibble >=3.1.0' - - 'r-tidyr >=1.1.3' + - r-data.table >=1.14.0 + - r-dplyr >=0.8.0 + - r-factoextra >=1.0.7 + - r-factominer >=2.4 + - r-flexdashboard >=0.5.2 + - r-ggally >=2.1.2 + - r-ggplot2 >=3.3.0 + - r-ggpubr >=0.4.0 + - r-gtools >=3.8.2 + - r-htmltools >=0.4.0 + - r-kendall >=2.2 + - r-knitr >=1.33 + - r-magrittr >=1.5 + - r-mass >=7.3 + - r-pheatmap >=1.0.12 + - r-plotly >=4.9.0 + - r-plyr >=1.8.6 + - r-purrr >=0.3.4 + - r-readr >=2.0.1 + - r-remotes >=2.4.0 + - r-rlang >=0.4.11 + - r-rmarkdown >=2.9 + - r-shiny >=1.0.0 + - r-shinydashboard >=0.7.1 + - r-styler >=1.6.1 + - r-tibble >=3.1.0 + - r-tidyr >=1.1.3 + +source: + md5: 0a2cf4e8e146f432a0ac89e6a6dc2f24 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Protein Micro Array Data Management and Interactive Visualization' - description: 'A generic three-step pre-processing package for protein microarray data. This package contains different data pre-processing procedures to allow comparison of their performance.These steps are background correction, the coefficient of variation (CV) based filtering, batch correction and normalization.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-protgenerics/meta.yaml b/recipes/bioconductor-protgenerics/meta.yaml index ffe275e39ca5f..a6121b672bbd3 100644 --- a/recipes/bioconductor-protgenerics/meta.yaml +++ b/recipes/bioconductor-protgenerics/meta.yaml @@ -2,37 +2,20 @@ {% set name = "ProtGenerics" %} {% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e7211a9fa758ca6f1b701c86e892895 +about: + description: S4 generic functions and classes needed by Bioconductor proteomics packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Generic infrastructure for Bioconductor mass spectrometry packages + build: - number: 0 + noarch: generic + number: 1 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-protgenerics", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Generic infrastructure for Bioconductor mass spectrometry packages' - description: 'S4 generic functions and classes needed by Bioconductor proteomics packages.' + extra: identifiers: - biotools:protgenerics @@ -41,4 +24,22 @@ extra: name: bioconductor-protgenerics path: recipes/bioconductor-protgenerics version: 1.12.0 - +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: testthat +requirements: + host: + - r-base + run: + - r-base +source: + md5: 7e7211a9fa758ca6f1b701c86e892895 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" \ No newline at end of file diff --git a/recipes/bioconductor-psichomics/meta.yaml b/recipes/bioconductor-psichomics/meta.yaml index 34f50e50ef81c..212744fa95a6c 100644 --- a/recipes/bioconductor-psichomics/meta.yaml +++ b/recipes/bioconductor-psichomics/meta.yaml @@ -1,45 +1,53 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "psichomics" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8d6d1c34972e5d4b389d9263ab2077db build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-psichomics", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi, spelling requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-recount >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-recount >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-colourpicker - r-data.table - r-digest - r-dplyr - - 'r-dt >=0.2' + - r-dt >=0.2 - r-fastica - r-fastmatch - r-ggplot2 - r-ggrepel - - 'r-highcharter >=0.5.0' + - r-highcharter >=0.5.0 - r-htmltools - r-httr - r-jsonlite @@ -47,10 +55,10 @@ requirements: - r-plyr - r-purrr - r-r.utils - - 'r-rcpp >=0.12.14' + - r-rcpp >=0.12.14 - r-reshape2 - r-rfast - - 'r-shiny >=1.7.0' + - r-shiny >=1.7.0 - r-shinybs - r-shinyjs - r-stringr @@ -59,26 +67,27 @@ requirements: - r-xtable - libblas - liblapack + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-recount >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-recount >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-colourpicker - r-data.table - r-digest - r-dplyr - - 'r-dt >=0.2' + - r-dt >=0.2 - r-fastica - r-fastmatch - r-ggplot2 - r-ggrepel - - 'r-highcharter >=0.5.0' + - r-highcharter >=0.5.0 - r-htmltools - r-httr - r-jsonlite @@ -86,27 +95,26 @@ requirements: - r-plyr - r-purrr - r-r.utils - - 'r-rcpp >=0.12.14' + - r-rcpp >=0.12.14 - r-reshape2 - r-rfast - - 'r-shiny >=1.7.0' + - r-shiny >=1.7.0 - r-shinybs - r-shinyjs - r-stringr - r-survival - r-xml - r-xtable - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 1d4af111319c0d85c7f0143b718f35ae + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation' - description: 'Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-psmatch/meta.yaml b/recipes/bioconductor-psmatch/meta.yaml index 86c4f75515374..396c407d55a67 100644 --- a/recipes/bioconductor-psmatch/meta.yaml +++ b/recipes/bioconductor-psmatch/meta.yaml @@ -1,52 +1,57 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "PSMatch" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The PSMatch package helps proteomics practitioners to load, handle and manage Peptide Spectrum Matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and make informed decision about shared peptide filtering. The package also provides functions to calculate and visualise MS2 fragment ions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Handling and Managing Peptide Spectrum Matches -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4c63ca3d541af4e5925bcc2bde7d67ea build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-psmatch", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: msdata, rpx, mzID, mzR, Spectra, SummarizedExperiment, BiocStyle, rmarkdown, knitr, factoextra, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-qfeatures >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-qfeatures >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-igraph - r-matrix run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-qfeatures >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-qfeatures >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-igraph - r-matrix + +source: + md5: cf954495b58b7d4bb5af2b1f09f7f572 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Handling and Managing Peptide Spectrum Matches' - description: 'The PSMatch package helps proteomics practitioners to load, handle and manage Peptide Spectrum Matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and make informed decision about shared peptide filtering. The package also provides functions to calculate and visualise MS2 fragment ions.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ptairdata/meta.yaml b/recipes/bioconductor-ptairdata/meta.yaml index 47412396819e7..432175bde984f 100644 --- a/recipes/bioconductor-ptairdata/meta.yaml +++ b/recipes/bioconductor-ptairdata/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "ptairData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eea0fcfdd0047d72092a3b6beb326129 +about: + description: 'The package ptairData contains two raw datasets from Proton-Transfer-Reaction Time-of-Flight mass spectrometer acquisitions (PTR-TOF-MS), in the HDF5 format. One from the exhaled air of two volunteer healthy individuals with three replicates, and one from the cell culture headspace from two mycobacteria species and one control (culture medium only) with two replicates. Those datasets are used in the examples and in the vignette of the ptairMS package (PTR-TOF-MS data pre-processing). There are also used to gererate the ptrSet in the ptairMS data : exhaledPtrset and mycobacteriaSet' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: PTR-TOF-MS volatolomics raw datasets from exhaled air and cell culture headspace build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ptairdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - bioconductor-rhdf5 >=2.50.0,<2.51.0 - r-base - r-signal run: - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - bioconductor-rhdf5 >=2.50.0,<2.51.0 - r-base - r-signal - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0197eba91d104f6fad9cd91e98f7c03b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'PTR-TOF-MS volatolomics raw datasets from exhaled air and cell culture headspace' - description: 'The package ptairData contains two raw datasets from Proton-Transfer-Reaction Time-of-Flight mass spectrometer acquisitions (PTR-TOF-MS), in the HDF5 format. One from the exhaled air of two volunteer healthy individuals with three replicates, and one from the cell culture headspace from two mycobacteria species and one control (culture medium only) with two replicates. Those datasets are used in the examples and in the vignette of the ptairMS package (PTR-TOF-MS data pre-processing). There are also used to gererate the ptrSet in the ptairMS data : exhaledPtrset and mycobacteriaSet' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ptairdata/post-link.sh b/recipes/bioconductor-ptairdata/post-link.sh index 8d2982bffafe3..e479e75bfef0b 100644 --- a/recipes/bioconductor-ptairdata/post-link.sh +++ b/recipes/bioconductor-ptairdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ptairdata-1.10.0" +installBiocDataPackage.sh "ptairdata-1.14.0" diff --git a/recipes/bioconductor-ptairms/meta.yaml b/recipes/bioconductor-ptairms/meta.yaml index dbf733b5430bc..cc80a342ab277 100644 --- a/recipes/bioconductor-ptairms/meta.yaml +++ b/recipes/bioconductor-ptairms/meta.yaml @@ -1,29 +1,37 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "ptairMS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the 'sample by features' table of peak intensities in addition to the sample and feature metadata (as a singl= 2.1.0), ptairData, ropls requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 - r-base - r-bit64 - r-chron @@ -46,10 +54,11 @@ requirements: - r-signal - libblas - liblapack + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 - r-base - r-bit64 - r-chron @@ -70,17 +79,16 @@ requirements: - r-shiny - r-shinyscreenshot - r-signal - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 2197daf83bbc4b82563b65efaa58c890 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Pre-processing PTR-TOF-MS Data' - description: 'This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the ''sample by features'' table of peak intensities in addition to the sample and feature metadata (as a singl=1.58.0,<1.59.0' - - 'bioconductor-lobstahs >=1.28.0,<1.29.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-camera >=1.62.0,<1.63.0 + - bioconductor-lobstahs >=1.32.0,<1.33.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base run: - - 'bioconductor-camera >=1.58.0,<1.59.0' - - 'bioconductor-lobstahs >=1.28.0,<1.29.0' - - 'bioconductor-xcms >=4.0.0,<4.1.0' + - bioconductor-camera >=1.62.0,<1.63.0 + - bioconductor-lobstahs >=1.32.0,<1.33.0 + - bioconductor-xcms >=4.4.0,<4.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2136bebfb44a436fdb84d3e40f8bf23a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'P. tricornutum HPLC-ESI-MS Lipid Data from van Creveld et al. (2015)' - description: 'Annotated HPLC-ESI-MS lipid data in positive ionization mode from an experiment in which cultures of the marine diatom Phaeodactylum tricornutum were treated with various concentrations of hydrogen peroxide (H2O2) to induce oxidative stress. The experiment is described in Graff van Creveld, et al., 2015, "Early perturbation in mitochondria redox homeostasis in response to environmental stress predicts cell fate in diatoms," ISME Journal 9:385-395. PtH2O2lipids consists of two objects: A CAMERA xsAnnotate object (ptH2O2lipids$xsAnnotate) and LOBSTAHS LOBSet object (ptH2O2lipids$xsAnnotate$LOBSet). The LOBSet includes putative compound assignments from the default LOBSTAHS database. Isomer annotation is recorded in three other LOBSet slots.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pth2o2lipids/post-link.sh b/recipes/bioconductor-pth2o2lipids/post-link.sh index db6d6c3fc4d12..a717f7df252e1 100644 --- a/recipes/bioconductor-pth2o2lipids/post-link.sh +++ b/recipes/bioconductor-pth2o2lipids/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pth2o2lipids-1.28.0" +installBiocDataPackage.sh "pth2o2lipids-1.32.0" diff --git a/recipes/bioconductor-puma/meta.yaml b/recipes/bioconductor-puma/meta.yaml index 991e8eb47bf36..2411eddbb0791 100644 --- a/recipes/bioconductor-puma/meta.yaml +++ b/recipes/bioconductor-puma/meta.yaml @@ -1,60 +1,66 @@ -{% set version = "3.44.0" %} +{% set version = "3.48.0" %} {% set name = "puma" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Most analyses of Affymetrix GeneChip data (including tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0) are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. In additon to calculte gene expression from Affymetrix 3' arrays, puma also provides methods to process exon arrays and produces gene and isoform expression for alternative splicing study. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting functions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ed1d90c9c9b7751611b0f32edf0a1ffb build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-puma", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:puma + parent_recipe: + name: bioconductor-puma + path: recipes/bioconductor-puma + version: 3.22.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: pumadata, affydata, snow, limma, ROCR,annotate requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base - r-mclust - libblas - liblapack run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 - r-base - r-mclust - build: - - {{ compiler('c') }} - - make + +source: + md5: 6d7a6b96c444d8e8321bd9d616fb0950 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3'' arrays and exon arrays and Human Transcriptome Array 2.0)' - description: 'Most analyses of Affymetrix GeneChip data (including tranditional 3'' arrays and exon arrays and Human Transcriptome Array 2.0) are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. In additon to calculte gene expression from Affymetrix 3'' arrays, puma also provides methods to process exon arrays and produces gene and isoform expression for alternative splicing study. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting functions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:puma - parent_recipe: - name: bioconductor-puma - path: recipes/bioconductor-puma - version: 3.22.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pumadata/meta.yaml b/recipes/bioconductor-pumadata/meta.yaml index a621ddfcce813..1f665a5c6a69c 100644 --- a/recipes/bioconductor-pumadata/meta.yaml +++ b/recipes/bioconductor-pumadata/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "2.38.0" %} +{% set version = "2.42.0" %} {% set name = "pumadata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 811d6234d1d4e310beb7111601b157b7 +about: + description: This is a simple data package including various data sets derived from the estrogen data for use with the puma (Propagating Uncertainty in Microarray Analysis) package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Various data sets for use with the puma package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pumadata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-puma >=3.44.0,<3.45.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-puma >=3.48.0,<3.49.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-puma >=3.44.0,<3.45.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-puma >=3.48.0,<3.49.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1ea3a80569c46dd7c018c794284601f2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Various data sets for use with the puma package' - description: 'This is a simple data package including various data sets derived from the estrogen data for use with the puma (Propagating Uncertainty in Microarray Analysis) package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pumadata/post-link.sh b/recipes/bioconductor-pumadata/post-link.sh index 1b94fc5e7a3cf..15ede488a8579 100644 --- a/recipes/bioconductor-pumadata/post-link.sh +++ b/recipes/bioconductor-pumadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pumadata-2.38.0" +installBiocDataPackage.sh "pumadata-2.42.0" diff --git a/recipes/bioconductor-purecn/meta.yaml b/recipes/bioconductor-purecn/meta.yaml index a34ed6b085135..10335453c36f8 100644 --- a/recipes/bioconductor-purecn/meta.yaml +++ b/recipes/bioconductor-purecn/meta.yaml @@ -1,41 +1,53 @@ -{% set version = "2.8.1" %} +{% set version = "2.12.0" %} {% set name = "PureCN" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Copy number calling and SNV classification using targeted short read sequencing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d668ed7c332244073d26762dd291004f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-purecn", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:purecn + parent_recipe: + name: bioconductor-purecn + path: recipes/bioconductor-purecn + version: 1.13.1 + recipe_maintainers: + - roryk + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocParallel, BiocStyle, PSCBS, R.utils, TxDb.Hsapiens.UCSC.hg19.knownGene, covr, knitr, optparse, org.Hs.eg.db, jsonlite, markdown, rmarkdown, testthat requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-data.table - r-futile.logger @@ -45,21 +57,22 @@ requirements: - r-mclust - r-rcolorbrewer - r-vgam + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-data.table - r-futile.logger @@ -69,21 +82,16 @@ requirements: - r-mclust - r-rcolorbrewer - r-vgam + +source: + md5: e00cd4d68b2c9e0d03750f4d75e11991 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Copy number calling and SNV classification using targeted short read sequencing' - description: 'This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.' -extra: - identifiers: - - biotools:purecn - parent_recipe: - name: bioconductor-purecn - path: recipes/bioconductor-purecn - version: 1.13.1 - recipe_maintainers: - - roryk + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pvac/meta.yaml b/recipes/bioconductor-pvac/meta.yaml index 904378bd67a73..69da0901a41b9 100644 --- a/recipes/bioconductor-pvac/meta.yaml +++ b/recipes/bioconductor-pvac/meta.yaml @@ -1,43 +1,22 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "pvac" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2.0) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: PCA-based gene filtering for Affymetrix arrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ae148a3c65e5b6efc44cfea7d208d918 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pvac", max_pin="x.x") }}' - noarch: generic -# Suggests: pbapply, affydata, ALLMLL, genefilter -requirements: - host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base - run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2.0)' - summary: 'PCA-based gene filtering for Affymetrix arrays' - description: 'The package contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + extra: identifiers: - biotools:pvac @@ -47,3 +26,30 @@ extra: path: recipes/bioconductor-pvac version: 1.28.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: pbapply, affydata, ALLMLL, genefilter +requirements: + host: + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + run: + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + +source: + md5: 603f27796d2268e8695b19e1d6509627 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-pvca/meta.yaml b/recipes/bioconductor-pvca/meta.yaml index c02a34e9d4f84..d253bc2799b8a 100644 --- a/recipes/bioconductor-pvca/meta.yaml +++ b/recipes/bioconductor-pvca/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "pvca" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains the function to assess the batch sourcs by fitting all "sources" as random effects including two-way interaction terms in the Mixed Model(depends on lme4 package) to selected principal components, which were obtained from the original data correlation matrix. This package accompanies the book "Batch Effects and Noise in Microarray Experiements, chapter 12. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2.0) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Principal Variance Component Analysis (PVCA) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dcc72a578e6ec7d738fab213c4d27e20 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pvca", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:pvca + - doi:10.1002/9780470685983.ch12 + parent_recipe: + name: bioconductor-pvca + path: recipes/bioconductor-pvca + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: golubEsets requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-base - r-lme4 - r-matrix run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-base - r-lme4 - r-matrix + +source: + md5: a58e00010280d2a69984c0edb9263382 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2.0)' - summary: 'Principal Variance Component Analysis (PVCA)' - description: 'This package contains the function to assess the batch sourcs by fitting all "sources" as random effects including two-way interaction terms in the Mixed Model(depends on lme4 package) to selected principal components, which were obtained from the original data correlation matrix. This package accompanies the book "Batch Effects and Noise in Microarray Experiements, chapter 12.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:pvca - - doi:10.1002/9780470685983.ch12 - parent_recipe: - name: bioconductor-pvca - path: recipes/bioconductor-pvca - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pviz/meta.yaml b/recipes/bioconductor-pviz/meta.yaml index 83a82e5290e48..1b878a8db75ab 100644 --- a/recipes/bioconductor-pviz/meta.yaml +++ b/recipes/bioconductor-pviz/meta.yaml @@ -1,56 +1,62 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "Pviz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Pviz adapts the Gviz package for protein sequences and data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Peptide Annotation and Data Visualization using Gviz -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a1513067c6a873f9523f20eb85f2878 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pviz", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:pviz + - doi:10.1007/978-1-4939-3037-1_10 + parent_recipe: + name: bioconductor-pviz + path: recipes/bioconductor-pviz + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, pepDat requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-biovizbase >=1.50.0,<1.51.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-biovizbase >=1.54.0,<1.55.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-data.table run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-biovizbase >=1.50.0,<1.51.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-biovizbase >=1.54.0,<1.55.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-data.table + +source: + md5: a7a777df32c02f6ebdae9a899dce0ba8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Peptide Annotation and Data Visualization using Gviz' - description: 'Pviz adapts the Gviz package for protein sequences and data.' -extra: - identifiers: - - biotools:pviz - - doi:10.1007/978-1-4939-3037-1_10 - parent_recipe: - name: bioconductor-pviz - path: recipes/bioconductor-pviz - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pwalign/build.sh b/recipes/bioconductor-pwalign/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pwalign/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pwalign/meta.yaml b/recipes/bioconductor-pwalign/meta.yaml new file mode 100644 index 0000000000000..448659787c8cf --- /dev/null +++ b/recipes/bioconductor-pwalign/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.2.0" %} +{% set name = "pwalign" %} +{% set bioc = "3.20" %} + +about: + description: The two main functions in the package are pairwiseAlignment() and stringDist(). The former solves (Needleman-Wunsch) global alignment, (Smith-Waterman) local alignment, and (ends-free) overlap alignment problems. The latter computes the Levenshtein edit distance or pairwise alignment score matrix for a set of strings. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Perform pairwise sequence alignments + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-pwalign", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RUnit +requirements: + build: + - {{ compiler('c') }} + - make + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 + - r-base + - libblas + - liblapack + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 + - r-base + +source: + md5: 02e773c9593e0e9c8ce0b9b7bde3bdae + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + +extra: + additional-platforms: + - linux-aarch64 diff --git a/recipes/bioconductor-pwmenrich.dmelanogaster.background/meta.yaml b/recipes/bioconductor-pwmenrich.dmelanogaster.background/meta.yaml index 0fc2d9e14d907..92cd3be6242e2 100644 --- a/recipes/bioconductor-pwmenrich.dmelanogaster.background/meta.yaml +++ b/recipes/bioconductor-pwmenrich.dmelanogaster.background/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "4.36.0" %} +{% set version = "4.40.0" %} {% set name = "PWMEnrich.Dmelanogaster.background" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b671ba0cff5c0c6017fd3f72d0afc547 +about: + description: PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: D. melanogaster background for PWMEnrich build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pwmenrich.dmelanogaster.background", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-pwmenrich >=4.38.0,<4.39.0' + - bioconductor-pwmenrich >=4.42.0,<4.43.0 - r-base run: - - 'bioconductor-pwmenrich >=4.38.0,<4.39.0' + - bioconductor-pwmenrich >=4.42.0,<4.43.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a8ce5a506cb9ccc09eb0e2825728b13d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'D. melanogaster background for PWMEnrich' - description: 'PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pwmenrich.dmelanogaster.background/post-link.sh b/recipes/bioconductor-pwmenrich.dmelanogaster.background/post-link.sh index f9aedbea31b16..2a9247da15031 100644 --- a/recipes/bioconductor-pwmenrich.dmelanogaster.background/post-link.sh +++ b/recipes/bioconductor-pwmenrich.dmelanogaster.background/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pwmenrich.dmelanogaster.background-4.36.0" +installBiocDataPackage.sh "pwmenrich.dmelanogaster.background-4.40.0" diff --git a/recipes/bioconductor-pwmenrich.hsapiens.background/meta.yaml b/recipes/bioconductor-pwmenrich.hsapiens.background/meta.yaml index 2cc73594c1eb4..5637ab08155b7 100644 --- a/recipes/bioconductor-pwmenrich.hsapiens.background/meta.yaml +++ b/recipes/bioconductor-pwmenrich.hsapiens.background/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "4.36.0" %} +{% set version = "4.40.0" %} {% set name = "PWMEnrich.Hsapiens.background" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c7b177c29fc31c7546d4e7160a9b977 +about: + description: PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: H. sapiens background for PWMEnrich build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pwmenrich.hsapiens.background", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-pwmenrich >=4.38.0,<4.39.0' + - bioconductor-pwmenrich >=4.42.0,<4.43.0 - r-base run: - - 'bioconductor-pwmenrich >=4.38.0,<4.39.0' + - bioconductor-pwmenrich >=4.42.0,<4.43.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 53e1366ff04f7bb46e6e74958adabd0a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'H. sapiens background for PWMEnrich' - description: 'PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pwmenrich.hsapiens.background/post-link.sh b/recipes/bioconductor-pwmenrich.hsapiens.background/post-link.sh index 5fd33b45910e0..05fcddf13a313 100644 --- a/recipes/bioconductor-pwmenrich.hsapiens.background/post-link.sh +++ b/recipes/bioconductor-pwmenrich.hsapiens.background/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pwmenrich.hsapiens.background-4.36.0" +installBiocDataPackage.sh "pwmenrich.hsapiens.background-4.40.0" diff --git a/recipes/bioconductor-pwmenrich.mmusculus.background/meta.yaml b/recipes/bioconductor-pwmenrich.mmusculus.background/meta.yaml index 14f7a80059072..19c673a857de2 100644 --- a/recipes/bioconductor-pwmenrich.mmusculus.background/meta.yaml +++ b/recipes/bioconductor-pwmenrich.mmusculus.background/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "4.36.0" %} +{% set version = "4.40.0" %} {% set name = "PWMEnrich.Mmusculus.background" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d54401a941d1efe7148da2ddc714d65 +about: + description: PWMEnrich pre-compiled background objects for M.musculus (mouse) and MotifDb M. musculus motifs. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: M. musculus background for PWMEnrich build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pwmenrich.mmusculus.background", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-pwmenrich >=4.38.0,<4.39.0' + - bioconductor-pwmenrich >=4.42.0,<4.43.0 - r-base run: - - 'bioconductor-pwmenrich >=4.38.0,<4.39.0' + - bioconductor-pwmenrich >=4.42.0,<4.43.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b26f2429a164aa6030315248fc874210 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'M. musculus background for PWMEnrich' - description: 'PWMEnrich pre-compiled background objects for M.musculus (mouse) and MotifDb M. musculus motifs.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-pwmenrich.mmusculus.background/post-link.sh b/recipes/bioconductor-pwmenrich.mmusculus.background/post-link.sh index b583b5d163e55..6e29ce1a6fb7f 100644 --- a/recipes/bioconductor-pwmenrich.mmusculus.background/post-link.sh +++ b/recipes/bioconductor-pwmenrich.mmusculus.background/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "pwmenrich.mmusculus.background-4.36.0" +installBiocDataPackage.sh "pwmenrich.mmusculus.background-4.40.0" diff --git a/recipes/bioconductor-pwmenrich/meta.yaml b/recipes/bioconductor-pwmenrich/meta.yaml index e3e4139a4902f..faa5b9ba06550 100644 --- a/recipes/bioconductor-pwmenrich/meta.yaml +++ b/recipes/bioconductor-pwmenrich/meta.yaml @@ -1,57 +1,63 @@ -{% set version = "4.38.0" %} +{% set version = "4.42.0" %} {% set name = "PWMEnrich" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already known PWMs (e.g. from databases such as MotifDb), but the package also implements high-level functions for PWM scanning and visualisation. The package does not perform "de novo" motif discovery, but is instead focused on using motifs that are either experimentally derived or computationally constructed by other tools. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: PWM enrichment analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ced56cbfbab381f5736f4f58fe26b9f8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-pwmenrich", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:pwmenrich + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-pwmenrich + path: recipes/bioconductor-pwmenrich + version: 4.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: MotifDb, BSgenome, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqlogo >=1.72.0,<1.73.0 - r-base - r-evd - r-gdata run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqlogo >=1.72.0,<1.73.0 - r-base - r-evd - r-gdata + +source: + md5: 261788d0539274cf75100b2b390fd457 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'PWM enrichment analysis' - description: 'A toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already known PWMs (e.g. from databases such as MotifDb), but the package also implements high-level functions for PWM scanning and visualisation. The package does not perform "de novo" motif discovery, but is instead focused on using motifs that are either experimentally derived or computationally constructed by other tools.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:pwmenrich - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-pwmenrich - path: recipes/bioconductor-pwmenrich - version: 4.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qckitfastq/meta.yaml b/recipes/bioconductor-qckitfastq/meta.yaml index ecb59cbec82ca..be051e61fea49 100644 --- a/recipes/bioconductor-qckitfastq/meta.yaml +++ b/recipes/bioconductor-qckitfastq/meta.yaml @@ -1,32 +1,35 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "qckitfastq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Assessment of FASTQ file format with multiple metrics including quality score, sequence content, overrepresented sequence and Kmers. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: FASTQ Quality Control -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 60955b37d9eb0868da1c5ecd262334e8 - patches: - - shared_timed_mutex.patch build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qckitfastq", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, kableExtra, testthat # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-rseqan >=1.22.0,<1.23.0' - - 'bioconductor-seqtools >=1.36.0,<1.37.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-rseqan >=1.26.0,<1.27.0 + - bioconductor-seqtools >=1.40.0,<1.41.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-data.table - r-dplyr @@ -37,10 +40,12 @@ requirements: - r-rlang - libblas - liblapack + - zlib + - liblzma-devel run: - - 'bioconductor-rseqan >=1.22.0,<1.23.0' - - 'bioconductor-seqtools >=1.36.0,<1.37.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-rseqan >=1.26.0,<1.27.0 + - bioconductor-seqtools >=1.40.0,<1.41.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-data.table - r-dplyr @@ -49,16 +54,16 @@ requirements: - r-rcpp - r-reshape2 - r-rlang - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 77c0797c0e417c03aa5424bfb1d9ec15 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'FASTQ Quality Control' - description: 'Assessment of FASTQ file format with multiple metrics including quality score, sequence content, overrepresented sequence and Kmers.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qcmetrics/meta.yaml b/recipes/bioconductor-qcmetrics/meta.yaml index 2cdd85a42a547..3c278f20849a6 100644 --- a/recipes/bioconductor-qcmetrics/meta.yaml +++ b/recipes/bioconductor-qcmetrics/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "qcmetrics" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A Framework for Quality Control -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 68f2a395be6986c02f8473dbe25ed621 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qcmetrics", max_pin="x.x") }}' - noarch: generic -# Suggests: affy, MSnbase, ggplot2, lattice, mzR, BiocStyle, rmarkdown + +extra: + identifiers: + - biotools:qcmetrics + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-qcmetrics + path: recipes/bioconductor-qcmetrics + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: affy, MSnbase, ggplot2, lattice, mzR, BiocStyle, rmarkdown, markdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-knitr - r-pander - r-xtable run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-knitr - r-pander - r-xtable + +source: + md5: 0f6c1fe40d9d8be77b652646b2ed082c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'A Framework for Quality Control' - description: 'The package provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:qcmetrics - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-qcmetrics - path: recipes/bioconductor-qcmetrics - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qdnaseq.hg19/meta.yaml b/recipes/bioconductor-qdnaseq.hg19/meta.yaml index bd3148547dbbb..07946dc7c8916 100644 --- a/recipes/bioconductor-qdnaseq.hg19/meta.yaml +++ b/recipes/bioconductor-qdnaseq.hg19/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "QDNAseq.hg19" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2b663d8771f16d55db88ec3321942ead +about: + description: This package provides QDNAseq bin annotations for the human genome build hg19. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: QDNAseq bin annotation for hg19 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qdnaseq.hg19", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' + - bioconductor-qdnaseq >=1.42.0,<1.43.0 - r-base run: - - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' + - bioconductor-qdnaseq >=1.42.0,<1.43.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 465422a4f1297d961ebd5ed5be39228d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL - summary: 'QDNAseq bin annotation for hg19' - description: 'This package provides QDNAseq bin annotations for the human genome build hg19.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qdnaseq.hg19/post-link.sh b/recipes/bioconductor-qdnaseq.hg19/post-link.sh index f95428a20b4fd..e96e994bf28cc 100644 --- a/recipes/bioconductor-qdnaseq.hg19/post-link.sh +++ b/recipes/bioconductor-qdnaseq.hg19/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "qdnaseq.hg19-1.32.0" +installBiocDataPackage.sh "qdnaseq.hg19-1.36.0" diff --git a/recipes/bioconductor-qdnaseq.mm10/meta.yaml b/recipes/bioconductor-qdnaseq.mm10/meta.yaml index a14c48bb16146..431b214d855f3 100644 --- a/recipes/bioconductor-qdnaseq.mm10/meta.yaml +++ b/recipes/bioconductor-qdnaseq.mm10/meta.yaml @@ -1,45 +1,51 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "QDNAseq.mm10" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides QDNAseq bin annotations for the mouse genome build mm10. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Bin annotation mm10 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d7b80c2bec7146aec28384b7875acca build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qdnaseq.mm10", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-qdnaseq.mm10 + path: recipes/bioconductor-qdnaseq.mm10 + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' + - bioconductor-qdnaseq >=1.42.0,<1.43.0 - r-base run: - - 'bioconductor-qdnaseq >=1.38.0,<1.39.0' + - bioconductor-qdnaseq >=1.42.0,<1.43.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 777629429e38d4c424de62579fa35b3b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL - summary: 'Bin annotation mm10' - description: 'This package provides QDNAseq bin annotations for the mouse genome build mm10.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-qdnaseq.mm10 - path: recipes/bioconductor-qdnaseq.mm10 - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qdnaseq.mm10/post-link.sh b/recipes/bioconductor-qdnaseq.mm10/post-link.sh index 05c6fcc404271..2f767480e3fe5 100644 --- a/recipes/bioconductor-qdnaseq.mm10/post-link.sh +++ b/recipes/bioconductor-qdnaseq.mm10/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "qdnaseq.mm10-1.32.0" +installBiocDataPackage.sh "qdnaseq.mm10-1.36.0" diff --git a/recipes/bioconductor-qdnaseq/meta.yaml b/recipes/bioconductor-qdnaseq/meta.yaml index aae4b1e35a592..02c259b9f8a44 100644 --- a/recipes/bioconductor-qdnaseq/meta.yaml +++ b/recipes/bioconductor-qdnaseq/meta.yaml @@ -1,64 +1,70 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "QDNAseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Quantitative DNA sequencing for chromosomal aberrations. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Quantitative DNA Sequencing for Chromosomal Aberrations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 589b066b44091955991b4f66ac86b9ee build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qdnaseq", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:qdnaseq + parent_recipe: + name: bioconductor-qdnaseq + path: recipes/bioconductor-qdnaseq + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle (>= 1.8.0), BSgenome (>= 1.38.0), digest (>= 0.6.20), GenomeInfoDb (>= 1.6.0), future (>= 1.22.1), parallelly (>= 1.28.1), R.cache (>= 0.13.0), QDNAseq.hg19, QDNAseq.mm10 requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-cghbase >=1.62.0,<1.63.0' - - 'bioconductor-cghcall >=2.64.0,<2.65.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-cghbase >=1.66.0,<1.67.0 + - bioconductor-cghcall >=2.68.0,<2.69.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - - 'r-future.apply >=1.8.1' - - 'r-matrixstats >=0.60.0' - - 'r-r.utils >=2.9.0' + - r-future.apply >=1.8.1 + - r-matrixstats >=0.60.0 + - r-r.utils >=2.9.0 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-cghbase >=1.62.0,<1.63.0' - - 'bioconductor-cghcall >=2.64.0,<2.65.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-cghbase >=1.66.0,<1.67.0 + - bioconductor-cghcall >=2.68.0,<2.69.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - - 'r-future.apply >=1.8.1' - - 'r-matrixstats >=0.60.0' - - 'r-r.utils >=2.9.0' + - r-future.apply >=1.8.1 + - r-matrixstats >=0.60.0 + - r-r.utils >=2.9.0 + +source: + md5: 86d1bb0aad347d95853508b57aa97dc0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL - summary: 'Quantitative DNA Sequencing for Chromosomal Aberrations' - description: 'Quantitative DNA sequencing for chromosomal aberrations. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:qdnaseq - parent_recipe: - name: bioconductor-qdnaseq - path: recipes/bioconductor-qdnaseq - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qfeatures/meta.yaml b/recipes/bioconductor-qfeatures/meta.yaml index f071f392d180f..b466d56540c91 100644 --- a/recipes/bioconductor-qfeatures/meta.yaml +++ b/recipes/bioconductor-qfeatures/meta.yaml @@ -1,60 +1,71 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "QFeatures" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The QFeatures infrastructure enables the management and processing of quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manages quantitative data across different assay levels (such as peptide spectrum matches, peptides and proteins) in a coherent and tractable format. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Quantitative features for mass spectrometry data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6833061a024bb9783b7d9a85bc282a88 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qfeatures", max_pin="x.x") }}' - noarch: generic -# Suggests: SingleCellExperiment, Matrix, HDF5Array, msdata, ggplot2, gplots, dplyr, limma, DT, shiny, shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn, preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute, norm, ComplexHeatmap + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: SingleCellExperiment, MsDataHub (>= 1.3.3), Matrix, HDF5Array, msdata, ggplot2, gplots, dplyr, limma, DT, shiny, shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn, preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute, norm, ComplexHeatmap requirements: host: - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-igraph - r-lazyeval - r-plotly + - r-reshape2 + - r-tidyr + - r-tidyselect run: - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-igraph - r-lazyeval - r-plotly + - r-reshape2 + - r-tidyr + - r-tidyselect + +source: + md5: 6013e8d25e7c98cfca285254718744c3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Quantitative features for mass spectrometry data' - description: 'The QFeatures infrastructure enables the management and processing of quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manages quantitative data across different assay levels (such as peptide spectrum matches, peptides and proteins) in a coherent and tractable format.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qmtools/meta.yaml b/recipes/bioconductor-qmtools/meta.yaml index 8ec0b0553e167..e7d6ccedaa008 100644 --- a/recipes/bioconductor-qmtools/meta.yaml +++ b/recipes/bioconductor-qmtools/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "qmtools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The qmtools (quantitative metabolomics tools) package provides basic tools for processing quantitative metabolomics data with the standard SummarizedExperiment class. This includes functions for imputation, normalization, feature filtering, feature clustering, dimension-reduction, and visualization to help users prepare data for statistical analysis. This package also offers a convenient way to compute empirical Bayes statistics for which metabolic features are different between two sets of study samples. Several functions in this package could also be used in other types of omics data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Quantitative Metabolomics Data Processing Tools -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 941d7cbf1dc8c2622fe97bda18a2bf49 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qmtools", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Rtsne, missForest, vsn, pcaMethods, pls, MsFeatures, impute, imputeLCMD, nlme, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-heatmaply @@ -34,9 +36,9 @@ requirements: - r-scales - r-vim run: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-heatmaply @@ -45,13 +47,16 @@ requirements: - r-rlang - r-scales - r-vim + +source: + md5: 6faa442b1949dd6c8af47c5285b455a7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Quantitative Metabolomics Data Processing Tools' - description: 'The qmtools (quantitative metabolomics tools) package provides basic tools for processing quantitative metabolomics data with the standard SummarizedExperiment class. This includes functions for imputation, normalization, feature filtering, feature clustering, dimension-reduction, and visualization to help users prepare data for statistical analysis. This package also offers a convenient way to compute empirical Bayes statistics for which metabolic features are different between two sets of study samples. Several functions in this package could also be used in other types of omics data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qpcrnorm/meta.yaml b/recipes/bioconductor-qpcrnorm/meta.yaml index 72c295aba9034..b3c86b391c7cc 100644 --- a/recipes/bioconductor-qpcrnorm/meta.yaml +++ b/recipes/bioconductor-qpcrnorm/meta.yaml @@ -1,44 +1,22 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "qpcrNorm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package contains functions to perform normalization of high-throughput qPCR data. Basic functions for processing raw Ct data plus functions to generate diagnostic plots are also available. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Data-driven normalization strategies for high-throughput qPCR data. -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 43fa513309301e6d8e89fcef668c7b28 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qpcrnorm", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - r-base - run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'Data-driven normalization strategies for high-throughput qPCR data.' - description: 'The package contains functions to perform normalization of high-throughput qPCR data. Basic functions for processing raw Ct data plus functions to generate diagnostic plots are also available.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + extra: identifiers: - biotools:qpcrnorm @@ -48,3 +26,31 @@ extra: path: recipes/bioconductor-qpcrnorm version: 1.38.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - r-base + run: + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - r-base + +source: + md5: 673a5545cde0b6a35d479b1c41a92cb6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-qpgraph/meta.yaml b/recipes/bioconductor-qpgraph/meta.yaml index 46f6f4233d53b..f2e6827163570 100644 --- a/recipes/bioconductor-qpgraph/meta.yaml +++ b/recipes/bioconductor-qpgraph/meta.yaml @@ -1,79 +1,85 @@ -{% set version = "2.36.0" %} +{% set version = "2.40.0" %} {% set name = "qpgraph" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Estimate gene and eQTL networks from high-throughput expression and genotyping assays. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Estimation of genetic and molecular regulatory networks from high-throughput genomics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 10be7ba90f9349fb4de4aa84e6fecaa4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qpgraph", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:qpgraph + parent_recipe: + name: bioconductor-qpgraph + path: recipes/bioconductor-qpgraph + version: 2.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db, rlecuyer, snow, Category, GOstats requirements: + build: + - {{ compiler('c') }} + - automake + - make host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-matrix >=1.5-0' + - r-matrix >=1.5-0 - r-mvtnorm - r-qtl - libblas - liblapack run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-matrix >=1.5-0' + - r-matrix >=1.5-0 - r-mvtnorm - r-qtl - build: - - {{ compiler('c') }} - - automake - - make + +source: + md5: 3eb484fe295f35d5b0171573be8067a1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'Estimation of genetic and molecular regulatory networks from high-throughput genomics data' - description: 'Estimate gene and eQTL networks from high-throughput expression and genotyping assays.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:qpgraph - parent_recipe: - name: bioconductor-qpgraph - path: recipes/bioconductor-qpgraph - version: 2.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qplexanalyzer/meta.yaml b/recipes/bioconductor-qplexanalyzer/meta.yaml index 6b01c08b890cd..17b84aef49751 100644 --- a/recipes/bioconductor-qplexanalyzer/meta.yaml +++ b/recipes/bioconductor-qplexanalyzer/meta.yaml @@ -1,37 +1,40 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "qPLEXanalyzer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for TMT based quantitative proteomics data analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Tools for quantitative proteomics data analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d30edcfbf4e355e0c40bd7cf16d396fb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qplexanalyzer", max_pin="x.x") }}' - noarch: generic -# Suggests: gridExtra, knitr, qPLEXdata, rmarkdown, statmod, testthat, UniProt.ws, vdiffr + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: patchwork, knitr, qPLEXdata, rmarkdown, statmod, testthat, UniProt.ws, vdiffr requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-assertthat - r-base - - 'r-dplyr >=1.0.0' + - r-dplyr >=1.0.0 - r-ggdendro - r-ggplot2 - r-magrittr @@ -44,17 +47,18 @@ requirements: - r-tibble - r-tidyr - r-tidyselect + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 - r-assertthat - r-base - - 'r-dplyr >=1.0.0' + - r-dplyr >=1.0.0 - r-ggdendro - r-ggplot2 - r-magrittr @@ -67,13 +71,16 @@ requirements: - r-tibble - r-tidyr - r-tidyselect + +source: + md5: 079b6b261234e203346710c930541607 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Tools for quantitative proteomics data analysis' - description: 'Tools for TMT based quantitative proteomics data analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qplexdata/meta.yaml b/recipes/bioconductor-qplexdata/meta.yaml index d72d4ac30f891..8c34276610b3b 100644 --- a/recipes/bioconductor-qplexdata/meta.yaml +++ b/recipes/bioconductor-qplexdata/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "qPLEXdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: qPLEX-RIME and Full proteome TMT mass spectrometry datasets. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Data accompanying qPLEXanalyzer package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af947f54391fc79c81308890b1e95d96 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qplexdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: statmod requirements: host: - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-qplexanalyzer >=1.20.0,<1.21.0' + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-qplexanalyzer >=1.24.0,<1.25.0 - r-base - r-dplyr - r-knitr run: - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-qplexanalyzer >=1.20.0,<1.21.0' + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-qplexanalyzer >=1.24.0,<1.25.0 - r-base - r-dplyr - r-knitr - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 91470ae70dda6162161bd64ffb7cb9b2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Data accompanying qPLEXanalyzer package' - description: 'qPLEX-RIME and Full proteome TMT mass spectrometry datasets.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qplexdata/post-link.sh b/recipes/bioconductor-qplexdata/post-link.sh index 5bfe1edb7e282..a42c04b7763b5 100644 --- a/recipes/bioconductor-qplexdata/post-link.sh +++ b/recipes/bioconductor-qplexdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "qplexdata-1.20.0" +installBiocDataPackage.sh "qplexdata-1.24.0" diff --git a/recipes/bioconductor-qsea/meta.yaml b/recipes/bioconductor-qsea/meta.yaml index 9bafebacc6db4..5046a8c454856 100644 --- a/recipes/bioconductor-qsea/meta.yaml +++ b/recipes/bioconductor-qsea/meta.yaml @@ -1,76 +1,82 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "qsea" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: qsea (quantitative sequencing enrichment analysis) was developed as the successor of the MEDIPS package for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, qsea provides several functionalities for the analysis of other kinds of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential enrichment between groups of samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: IP-seq data analysis and vizualization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2891ba342f17500cee6391d1f388c3c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qsea", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:qsea + parent_recipe: + name: bioconductor-qsea + path: recipes/bioconductor-qsea + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle, knitr, rmarkdown, BiocManager, MASS requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hmmcopy >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hmmcopy >=1.48.0,<1.49.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-gtools - r-zoo - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hmmcopy >=1.44.0,<1.45.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hmmcopy >=1.48.0,<1.49.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-gtools - r-zoo - build: - - {{ compiler('c') }} - - make + +source: + md5: 2ad89b066e549ed52b4a0b6768235d19 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'IP-seq data analysis and vizualization' - description: 'qsea (quantitative sequencing enrichment analysis) was developed as the successor of the MEDIPS package for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, qsea provides several functionalities for the analysis of other kinds of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential enrichment between groups of samples.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:qsea - parent_recipe: - name: bioconductor-qsea - path: recipes/bioconductor-qsea - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qsmooth/meta.yaml b/recipes/bioconductor-qsmooth/meta.yaml index 659687e2f8c11..7de1103b0e2ee 100644 --- a/recipes/bioconductor-qsmooth/meta.yaml +++ b/recipes/bioconductor-qsmooth/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "qsmooth" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 471983d71a4b056b71b10fe15c3f7b1c +about: + description: 'Smooth quantile normalization is a generalization of quantile normalization, which is average of the two types of assumptions about the data generation process: quantile normalization and quantile normalization between groups.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Smooth quantile normalization build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qsmooth", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-hmisc run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-hmisc +source: + md5: 45909d751d39e66fd98d35c49930b013 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Smooth quantile normalization' - description: 'Smooth quantile normalization is a generalization of quantile normalization, which is average of the two types of assumptions about the data generation process: quantile normalization and quantile normalization between groups.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qsutils/meta.yaml b/recipes/bioconductor-qsutils/meta.yaml index 67ebd30438806..41d0ce67449f1 100644 --- a/recipes/bioconductor-qsutils/meta.yaml +++ b/recipes/bioconductor-qsutils/meta.yaml @@ -1,45 +1,52 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "QSutils" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Set of utility functions for viral quasispecies analysis with NGS data. Most functions are equally useful for metagenomic studies. There are three main types: (1) data manipulation and exploration—functions useful for converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and visualizing haplotype alignments. (2) diversity indices—functions to compute diversity and entropy, in which incidence, abundance, and functional indices are considered. (3) data simulation—functions useful for generating random viral quasispecies data.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Quasispecies Diversity -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3a1816762d5d0d26145c352281211f80 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qsutils", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, ggplot2 requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 - r-ape - r-base - r-psych run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 - r-ape - r-base - r-psych + +source: + md5: 3aa765bb40d4a7eb359417b658873ab1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Quasispecies Diversity' - description: 'Set of utility functions for viral quasispecies analysis with NGS data. Most functions are equally useful for metagenomic studies. There are three main types: (1) data manipulation and exploration—functions useful for converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and visualizing haplotype alignments. (2) diversity indices—functions to compute diversity and entropy, in which incidence, abundance, and functional indices are considered. (3) data simulation—functions useful for generating random viral quasispecies data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qsvar/meta.yaml b/recipes/bioconductor-qsvar/meta.yaml index 1da9a23ce0762..39e1488d38d33 100644 --- a/recipes/bioconductor-qsvar/meta.yaml +++ b/recipes/bioconductor-qsvar/meta.yaml @@ -1,42 +1,51 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "qsvaR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The qsvaR package contains functions for removing the effect of degration in rna-seq data from postmortem brain tissue. The package is equipped to help users generate principal components associated with degradation. The components can be used in differential expression analysis to remove the effects of degradation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Generate Quality Surrogate Variable Analysis for Degradation Correction -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e9531cc164f93967a5d5d0469d47f7c7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qsvar", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-ggplot2 + - r-rlang + - r-tidyverse run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-ggplot2 + - r-rlang + - r-tidyverse + +source: + md5: 4eb890505b4495bb6b0367eb191caac9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Generate Quality Surrogate Variable Analysis for Degradation Correction' - description: 'The qsvaR package contains functions for removing the effect of degration in rna-seq data from postmortem brain tissue. The package is equipped to help users generate principal components associated with degradation. The components can be used in differential expression analysis to remove the effects of degradation.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qtlexperiment/meta.yaml b/recipes/bioconductor-qtlexperiment/meta.yaml index d7d4285a69261..fa4e183f18028 100644 --- a/recipes/bioconductor-qtlexperiment/meta.yaml +++ b/recipes/bioconductor-qtlexperiment/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "QTLExperiment" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: QLTExperiment defines an S4 class for storing and manipulating summary statistics from QTL mapping experiments in one or more states. It is based on the 'SummarizedExperiment' class and contains functions for creating, merging, and subsetting objects. 'QTLExperiment' also stores experiment metadata and has checks in place to ensure that transformations apply correctly. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: S4 classes for QTL summary statistics and metadata -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fe7642e0952c4c68e5417906dfb66fb3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qtlexperiment", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr, rmarkdown, covr requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-ashr - r-base - r-checkmate @@ -35,9 +37,9 @@ requirements: - r-tidyr - r-vroom run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-ashr - r-base - r-checkmate @@ -47,13 +49,16 @@ requirements: - r-tibble - r-tidyr - r-vroom + +source: + md5: 1e23219a564067f8eeda2c2efa0d0f07 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'S4 classes for QTL summary statistics and metadata' - description: 'QLTExperiment defines an S4 class for storing and manipulating summary statistics from QTL mapping experiments in one or more states. It is based on the ''SummarizedExperiment'' class and contains functions for creating, merging, and subsetting objects. ''QTLExperiment'' also stores experiment metadata and has checks in place to ensure that transformations apply correctly.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qtlizer/meta.yaml b/recipes/bioconductor-qtlizer/meta.yaml index e151c4ba3c0fc..0633fc8b389fd 100644 --- a/recipes/bioconductor-qtlizer/meta.yaml +++ b/recipes/bioconductor-qtlizer/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "Qtlizer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea7e6227ebf6708e465681021fb77b19 +about: + description: This R package provides access to the Qtlizer web server. Qtlizer annotates lists of common small variants (mainly SNPs) and genes in humans with associated changes in gene expression using the most comprehensive database of published quantitative trait loci (QTLs). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Comprehensive QTL annotation of GWAS results build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qtlizer", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-curl - r-httr - r-stringi run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-curl - r-httr - r-stringi +source: + md5: 56fe72150af71d2cb37d3d56f52dc872 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Comprehensive QTL annotation of GWAS results' - description: 'This R package provides access to the Qtlizer web server. Qtlizer annotates lists of common small variants (mainly SNPs) and genes in humans with associated changes in gene expression using the most comprehensive database of published quantitative trait loci (QTLs).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-quantiseqr/meta.yaml b/recipes/bioconductor-quantiseqr/meta.yaml index 92068f91ebef4..c8903b52def10 100644 --- a/recipes/bioconductor-quantiseqr/meta.yaml +++ b/recipes/bioconductor-quantiseqr/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "quantiseqr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a streamlined workflow for the quanTIseq method, developed to perform the quantification of the Tumor Immune contexture from RNA-seq data. The quantification is performed against the TIL10 signature (dissecting the contributions of ten immune cell types), carefully crafted from a collection of human RNA-seq samples. The TIL10 signature has been extensively validated using simulated, flow cytometry, and immunohistochemistry data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Quantification of the Tumor Immune contexture from RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 34cd21d2e59e1f8f58001fdcc49eaf44 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-quantiseqr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery, knitr, macrophage, org.Hs.eg.db, reshape2, rmarkdown, testthat, tibble requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-limsolve @@ -32,22 +34,25 @@ requirements: - r-rlang - r-tidyr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-limsolve - r-mass - r-rlang - r-tidyr + +source: + md5: a9551c10906fbb2f456a906cea0ab952 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Quantification of the Tumor Immune contexture from RNA-seq data' - description: 'This package provides a streamlined workflow for the quanTIseq method, developed to perform the quantification of the Tumor Immune contexture from RNA-seq data. The quantification is performed against the TIL10 signature (dissecting the contributions of ten immune cell types), carefully crafted from a collection of human RNA-seq samples. The TIL10 signature has been extensively validated using simulated, flow cytometry, and immunohistochemistry data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-quantro/meta.yaml b/recipes/bioconductor-quantro/meta.yaml index 78285b4ad918e..da9868f838121 100644 --- a/recipes/bioconductor-quantro/meta.yaml +++ b/recipes/bioconductor-quantro/meta.yaml @@ -1,29 +1,39 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "quantro" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A test for when to use quantile normalization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3e7912df8d9bc50c461074539540f289 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-quantro", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:quantro + parent_recipe: + name: bioconductor-quantro + path: recipes/bioconductor-quantro + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - r-doparallel - r-foreach @@ -31,28 +41,24 @@ requirements: - r-iterators - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - r-doparallel - r-foreach - r-ggplot2 - r-iterators - r-rcolorbrewer + +source: + md5: c1794f92b5943531bcac5f5ab43b09d5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'A test for when to use quantile normalization' - description: 'A data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:quantro - parent_recipe: - name: bioconductor-quantro - path: recipes/bioconductor-quantro - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-quantsmooth/meta.yaml b/recipes/bioconductor-quantsmooth/meta.yaml index 3145b221ce689..c234819ad432d 100644 --- a/recipes/bioconductor-quantsmooth/meta.yaml +++ b/recipes/bioconductor-quantsmooth/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.68.0" %} +{% set version = "1.72.0" %} {% set name = "quantsmooth" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Implements quantile smoothing as introduced in: Quantile smoothing of array CGH data; Eilers PH, de Menezes RX; Bioinformatics. 2005 Apr 1;21(7):1146-53.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Quantile smoothing and genomic visualization of array data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cb47e0040fd219ad15aebf094dd379cd build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-quantsmooth", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:quantsmooth + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-quantsmooth + path: recipes/bioconductor-quantsmooth + version: 1.46.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -26,21 +37,16 @@ requirements: run: - r-base - r-quantreg + +source: + md5: 6e5d3e1ed3e05b786a8eb2418f28fb87 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Quantile smoothing and genomic visualization of array data' - description: 'Implements quantile smoothing as introduced in: Quantile smoothing of array CGH data; Eilers PH, de Menezes RX; Bioinformatics. 2005 Apr 1;21(7):1146-53.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:quantsmooth - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-quantsmooth - path: recipes/bioconductor-quantsmooth - version: 1.46.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-quasr/meta.yaml b/recipes/bioconductor-quasr/meta.yaml index c95104f9a8972..1e4d082e09bf2 100644 --- a/recipes/bioconductor-quasr/meta.yaml +++ b/recipes/bioconductor-quasr/meta.yaml @@ -1,84 +1,97 @@ -{% set version = "1.42.1" %} +{% set version = "1.46.0" %} {% set name = "QuasR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest. Read alignments are either generated through Rbowtie (data from DNA/ChIP/ATAC/Bis-seq experiments) or Rhisat2 (data from RNA-seq experiments that require spliced alignments), or can be provided in the form of bam files. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Quantify and Annotate Short Reads in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ace4fd8823c92add78b78c8e05b366aa build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-quasr", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:quasr + parent_recipe: + name: bioconductor-quasr + path: recipes/bioconductor-quasr + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Gviz, BiocStyle, GenomicAlignments, Rhisat2, knitr, rmarkdown, covr, testthat # SystemRequirements: GNU make requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rbowtie >=1.42.0,<1.43.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicfiles >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rbowtie >=1.46.0,<1.47.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - libblas - liblapack + - zlib + - liblzma-devel + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rbowtie >=1.42.0,<1.43.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicfiles >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rbowtie >=1.46.0,<1.47.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 4eff6784217d0261a50a17c0f53fff8c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Quantify and Annotate Short Reads in R' - description: 'This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:quasr - parent_recipe: - name: bioconductor-quasr - path: recipes/bioconductor-quasr - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-quaternaryprod/meta.yaml b/recipes/bioconductor-quaternaryprod/meta.yaml index 335557456ba9f..fb2afb76733da 100644 --- a/recipes/bioconductor-quaternaryprod/meta.yaml +++ b/recipes/bioconductor-quaternaryprod/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "QuaternaryProd" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: QuaternaryProd is an R package that performs causal reasoning on biological networks, including publicly available networks such as STRINGdb. QuaternaryProd is an open-source alternative to commercial products such as Inginuity Pathway Analysis. For a given a set of differentially expressed genes, QuaternaryProd computes the significance of upstream regulators in the network by performing causal reasoning using the Quaternary Dot Product Scoring Statistic (Quaternary Statistic), Ternary Dot product Scoring Statistic (Ternary Statistic) and Fisher's exact test (Enrichment test). The Quaternary Statistic handles signed, unsigned and ambiguous edges in the network. Ambiguity arises when the direction of causality is unknown, or when the source node (e.g., a protein) has edges with conflicting signs for the same target gene. On the other hand, the Ternary Statistic provides causal reasoning using the signed and unambiguous edges only. The Vignette provides more details on the Quaternary Statistic and illustrates an example of how to perform causal reasoning using STRINGdb. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 73dfc14934979c18429472a3d6870ece build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-quaternaryprod", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:quaternaryprod + parent_recipe: + name: bioconductor-quaternaryprod + path: recipes/bioconductor-quaternaryprod + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-dplyr - - 'r-rcpp >=0.11.3' - - 'r-yaml >=2.1.18' + - r-rcpp >=0.11.3 + - r-yaml >=2.1.18 - libblas - liblapack run: - r-base - r-dplyr - - 'r-rcpp >=0.11.3' - - 'r-yaml >=2.1.18' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=0.11.3 + - r-yaml >=2.1.18 + +source: + md5: 417634579f84142a57115113561bac01 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=3)' - summary: 'Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs' - description: 'QuaternaryProd is an R package that performs causal reasoning on biological networks, including publicly available networks such as STRINGdb. QuaternaryProd is an open-source alternative to commercial products such as Inginuity Pathway Analysis. For a given a set of differentially expressed genes, QuaternaryProd computes the significance of upstream regulators in the network by performing causal reasoning using the Quaternary Dot Product Scoring Statistic (Quaternary Statistic), Ternary Dot product Scoring Statistic (Ternary Statistic) and Fisher''s exact test (Enrichment test). The Quaternary Statistic handles signed, unsigned and ambiguous edges in the network. Ambiguity arises when the direction of causality is unknown, or when the source node (e.g., a protein) has edges with conflicting signs for the same target gene. On the other hand, the Ternary Statistic provides causal reasoning using the signed and unambiguous edges only. The Vignette provides more details on the Quaternary Statistic and illustrates an example of how to perform causal reasoning using STRINGdb.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:quaternaryprod - parent_recipe: - name: bioconductor-quaternaryprod - path: recipes/bioconductor-quaternaryprod - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qubic/meta.yaml b/recipes/bioconductor-qubic/meta.yaml index dfff731e76d06..af0054a4decbe 100644 --- a/recipes/bioconductor-qubic/meta.yaml +++ b/recipes/bioconductor-qubic/meta.yaml @@ -1,31 +1,37 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "QUBIC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The core function of this R package is to provide the implementation of the well-cited and well-reviewed QUBIC algorithm, aiming to deliver an effective and efficient biclustering capability. This package also includes the following related functions: (i) a qualitative representation of the input gene expression data, through a well-designed discretization way considering the underlying data property, which can be directly used in other biclustering programs; (ii) visualization of identified biclusters using heatmap in support of overall expression pattern analysis; (iii) bicluster-based co-expression network elucidation and visualization, where different correlation coefficient scores between a pair of genes are provided; and (iv) a generalize output format of biclusters and corresponding network can be freely downloaded so that a user can easily do following comprehensive functional enrichment analysis (e.g. DAVID) and advanced network visualization (e.g. Cytoscape).' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: CC BY-NC-ND 4.0 + file LICENSE + license_file: LICENSE + summary: An R package for qualitative biclustering in support of gene co-expression analyses -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 728f7aca6c2d2913d424694e9b31c41c build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qubic", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: QUBICdata, qgraph, fields, knitr, rmarkdown # SystemRequirements: C++11, Rtools (>= 3.1) requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-biclust - r-matrix - - 'r-rcpp >=0.11.0' + - r-rcpp >=0.11.0 - r-rcpparmadillo - libblas - liblapack @@ -33,19 +39,18 @@ requirements: - r-base - r-biclust - r-matrix - - 'r-rcpp >=0.11.0' + - r-rcpp >=0.11.0 - r-rcpparmadillo - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: f844837224467549b8492c833217f618 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'CC BY-NC-ND 4.0 + file LICENSE' - summary: 'An R package for qualitative biclustering in support of gene co-expression analyses' - description: 'The core function of this R package is to provide the implementation of the well-cited and well-reviewed QUBIC algorithm, aiming to deliver an effective and efficient biclustering capability. This package also includes the following related functions: (i) a qualitative representation of the input gene expression data, through a well-designed discretization way considering the underlying data property, which can be directly used in other biclustering programs; (ii) visualization of identified biclusters using heatmap in support of overall expression pattern analysis; (iii) bicluster-based co-expression network elucidation and visualization, where different correlation coefficient scores between a pair of genes are provided; and (iv) a generalize output format of biclusters and corresponding network can be freely downloaded so that a user can easily do following comprehensive functional enrichment analysis (e.g. DAVID) and advanced network visualization (e.g. Cytoscape).' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qubicdata/meta.yaml b/recipes/bioconductor-qubicdata/meta.yaml index 349cf66d0a19b..63b0145444af5 100644 --- a/recipes/bioconductor-qubicdata/meta.yaml +++ b/recipes/bioconductor-qubicdata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "QUBICdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0670dfaee6f8d532cf3506428a5932c1 +about: + description: The data employed in the vignette of the QUBIC package. These data belong to Many Microbe Microarrays Database and STRING v10. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Unlimited | file LICENSE + license_file: LICENSE + summary: Data employed in the vignette of the QUBIC package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qubicdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c69aac772f8adcd444c82b2fa37605e1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'Unlimited | file LICENSE' - summary: 'Data employed in the vignette of the QUBIC package' - description: 'The data employed in the vignette of the QUBIC package. These data belong to Many Microbe Microarrays Database and STRING v10.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qubicdata/post-link.sh b/recipes/bioconductor-qubicdata/post-link.sh index e44c7a49f8d46..75bbb3cc8b8a0 100644 --- a/recipes/bioconductor-qubicdata/post-link.sh +++ b/recipes/bioconductor-qubicdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "qubicdata-1.30.0" +installBiocDataPackage.sh "qubicdata-1.34.0" diff --git a/recipes/bioconductor-qusage/meta.yaml b/recipes/bioconductor-qusage/meta.yaml index b458324664fca..093f148f2b2a7 100644 --- a/recipes/bioconductor-qusage/meta.yaml +++ b/recipes/bioconductor-qusage/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "2.36.0" %} +{% set version = "2.40.0" %} {% set name = "qusage" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is an implementation the Quantitative Set Analysis for Gene Expression (QuSAGE) method described in (Yaari G. et al, Nucl Acids Res, 2013). This is a novel Gene Set Enrichment-type test, which is designed to provide a faster, more accurate, and easier to understand test for gene expression studies. qusage accounts for inter-gene correlations using the Variance Inflation Factor technique proposed by Wu et al. (Nucleic Acids Res, 2012). In addition, rather than simply evaluating the deviation from a null hypothesis with a single number (a P value), qusage quantifies gene set activity with a complete probability density function (PDF). From this PDF, P values and confidence intervals can be easily extracted. Preserving the PDF also allows for post-hoc analysis (e.g., pair-wise comparisons of gene set activity) while maintaining statistical traceability. Finally, while qusage is compatible with individual gene statistics from existing methods (e.g., LIMMA), a Welch-based method is implemented that is shown to improve specificity. The QuSAGE package also includes a mixed effects model implementation, as described in (Turner JA et al, BMC Bioinformatics, 2015), and a meta-analysis framework as described in (Meng H, et al. PLoS Comput Biol. 2019). For questions, contact Chris Bolen (cbolen1@gmail.com) or Steven Kleinstein (steven.kleinstein@yale.edu) + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'qusage: Quantitative Set Analysis for Gene Expression' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f4675daa1494bbf070a084d05a2e672b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qusage", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:qusage + parent_recipe: + name: bioconductor-qusage + path: recipes/bioconductor-qusage + version: 2.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-emmeans - r-fftw - r-nlme run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-emmeans - r-fftw - r-nlme + +source: + md5: 1d24ced931708e44e55e492594c65bd4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'qusage: Quantitative Set Analysis for Gene Expression' - description: 'This package is an implementation the Quantitative Set Analysis for Gene Expression (QuSAGE) method described in (Yaari G. et al, Nucl Acids Res, 2013). This is a novel Gene Set Enrichment-type test, which is designed to provide a faster, more accurate, and easier to understand test for gene expression studies. qusage accounts for inter-gene correlations using the Variance Inflation Factor technique proposed by Wu et al. (Nucleic Acids Res, 2012). In addition, rather than simply evaluating the deviation from a null hypothesis with a single number (a P value), qusage quantifies gene set activity with a complete probability density function (PDF). From this PDF, P values and confidence intervals can be easily extracted. Preserving the PDF also allows for post-hoc analysis (e.g., pair-wise comparisons of gene set activity) while maintaining statistical traceability. Finally, while qusage is compatible with individual gene statistics from existing methods (e.g., LIMMA), a Welch-based method is implemented that is shown to improve specificity. The QuSAGE package also includes a mixed effects model implementation, as described in (Turner JA et al, BMC Bioinformatics, 2015), and a meta-analysis framework as described in (Meng H, et al. PLoS Comput Biol. 2019). For questions, contact Chris Bolen (cbolen1@gmail.com) or Steven Kleinstein (steven.kleinstein@yale.edu)' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:qusage - parent_recipe: - name: bioconductor-qusage - path: recipes/bioconductor-qusage - version: 2.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-qvalue/meta.yaml b/recipes/bioconductor-qvalue/meta.yaml index 255657b20155b..ec516c900ab1e 100644 --- a/recipes/bioconductor-qvalue/meta.yaml +++ b/recipes/bioconductor-qvalue/meta.yaml @@ -1,24 +1,32 @@ -{% set version = "2.34.0" %} +{% set version = "2.38.0" %} {% set name = "qvalue" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test's p-value. Various plots are automatically generated, allowing one to make sensible significance cut-offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Q-value estimation for false discovery rate control -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d6d57a60a814587681cf438b4e6ee9bc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-qvalue", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-qvalue + path: recipes/bioconductor-qvalue + version: 2.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: host: @@ -29,18 +37,16 @@ requirements: - r-base - r-ggplot2 - r-reshape2 + +source: + md5: 5b0fe91fe7e412b4286f68ea98d900de + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Q-value estimation for false discovery rate control' - description: 'This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test''s p-value. Various plots are automatically generated, allowing one to make sensible significance cut-offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - parent_recipe: - name: bioconductor-qvalue - path: recipes/bioconductor-qvalue - version: 2.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-r10kcod.db/meta.yaml b/recipes/bioconductor-r10kcod.db/meta.yaml index fe56f9587a20a..4482595548504 100644 --- a/recipes/bioconductor-r10kcod.db/meta.yaml +++ b/recipes/bioconductor-r10kcod.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.4.0" %} {% set name = "r10kcod.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4a7a25fee64294cfb5adccaa6cf28772 +about: + description: Codelink UniSet Rat I Bioarray (~10 000 rat gene targets) annotation data (chip r10kcod) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Codelink UniSet Rat I Bioarray (~10 000 rat gene targets) annotation data (chip r10kcod) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-r10kcod.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4a7a25fee64294cfb5adccaa6cf28772 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Codelink UniSet Rat I Bioarray (~10 000 rat gene targets) annotation data (chip r10kcod)' - description: 'Codelink UniSet Rat I Bioarray (~10 000 rat gene targets) annotation data (chip r10kcod) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-r3cpet/build_failure.osx-64.yaml b/recipes/bioconductor-r3cpet/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c70bd323432fd --- /dev/null +++ b/recipes/bioconductor-r3cpet/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 7d9022348bcdf1398b61054a9ae366757c2c1d48ce59cd09c99e17483acf025f # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-genomeinfodbdata [1.2.1|1.2.2] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-genomeinfodbdata [1.2.10|1.2.11] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.3|1.2.4] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.6|1.2.7] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-genomeinfodbdata 1.2.9 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-ucsc.utils >=1.2.0,<1.3.0 is not installable because it requires + r-base >=4.4,<4.5.0a0 , which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("4.0.1==hcfea43d_1"), MatchSpec("clang==4.0.1=1")} + Encountered problems while solving: + - nothing provides compiler-rt 4.0.1 hcfea43d_1 needed by clang-4.0.1-1 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-genomeinfodbdata >=1.2.0,<1.3.0 is installable with the potential options + bioconductor-genomeinfodbdata [1.2.0|1.2.1] would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-genomeinfodbdata [1.2.1|1.2.2] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-genomeinfodbdata [1.2.10|1.2.11] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.3|1.2.4] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.6|1.2.7] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-genomeinfodbdata 1.2.9 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-ucsc.utils >=1.2.0,<1.3.0 is not installable because it requires + r-base >=4.4,<4.5.0a0 , which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-r3cpet/meta.yaml b/recipes/bioconductor-r3cpet/meta.yaml index 8e04b83625ff9..d201c73af1aa4 100644 --- a/recipes/bioconductor-r3cpet/meta.yaml +++ b/recipes/bioconductor-r3cpet/meta.yaml @@ -1,32 +1,38 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "R3CPET" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package provides a method to infer the set of proteins that are more probably to work together to maintain chormatin interaction given a ChIA-PET experiment results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: '3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4eaced963afa114068f2c36982e1add3 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-r3cpet", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, TxDb.Hsapiens.UCSC.hg19.knownGene, biovizBase, biomaRt, AnnotationDbi, org.Hs.eg.db, shiny, ChIPpeakAnno requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-clvalid - r-data.table @@ -34,18 +40,18 @@ requirements: - r-hmisc - r-igraph - r-pheatmap - - 'r-rcpp >=0.10.4' + - r-rcpp >=0.10.4 - r-rcurl - r-reshape2 - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-clvalid - r-data.table @@ -53,20 +59,19 @@ requirements: - r-hmisc - r-igraph - r-pheatmap - - 'r-rcpp >=0.10.4' + - r-rcpp >=0.10.4 - r-rcurl - r-reshape2 - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 79a135db58a5cd1c82c43e76864477a2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: '3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process' - description: 'The package provides a method to infer the set of proteins that are more probably to work together to maintain chormatin interaction given a ChIA-PET experiment results.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-r3cseq/meta.yaml b/recipes/bioconductor-r3cseq/meta.yaml index cf83b123ff451..9ec94c153b833 100644 --- a/recipes/bioconductor-r3cseq/meta.yaml +++ b/recipes/bioconductor-r3cseq/meta.yaml @@ -1,67 +1,73 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "r3Cseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is used for the analysis of long-range chromatin interactions from 3C-seq assay. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 548b2dc3319fc848c932bcb142edbd61 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-r3cseq", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:r3cseq + - doi:10.1093/nar/gkt373 + parent_recipe: + name: bioconductor-r3cseq + path: recipes/bioconductor-r3cseq + version: 1.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Rnorvegicus.UCSC.rn5.masked requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-data.table - r-rcolorbrewer - r-sqldf - r-vgam run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-data.table - r-rcolorbrewer - r-sqldf - r-vgam + +source: + md5: 3d417020d49202c768b329fcab182186 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)' - description: 'This package is used for the analysis of long-range chromatin interactions from 3C-seq assay.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:r3cseq - - doi:10.1093/nar/gkt373 - parent_recipe: - name: bioconductor-r3cseq - path: recipes/bioconductor-r3cseq - version: 1.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-r453plus1toolbox/meta.yaml b/recipes/bioconductor-r453plus1toolbox/meta.yaml index 8870d430d6725..4526a1b0b0736 100644 --- a/recipes/bioconductor-r453plus1toolbox/meta.yaml +++ b/recipes/bioconductor-r453plus1toolbox/meta.yaml @@ -1,73 +1,83 @@ -{% set version = "1.52.0" %} +{% set version = "1.56.0" %} {% set name = "R453Plus1Toolbox" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The R453Plus1 Toolbox comprises useful functions for the analysis of data generated by Roche's 454 sequencing platform. It adds functions for quality assurance as well as for annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. Further, a pipeline for the detection of structural variants is provided. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: A package for importing and analyzing data from Roche's Genome Sequencer System -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d7ad69c3b68b4a635129d296599c210 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-r453plus1toolbox", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rtracklayer, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2 requirements: + + build: + - {{ compiler('c') }} + - make + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-r2html - r-teachingdemos - r-xtable - libblas - liblapack + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-r2html - r-teachingdemos - r-xtable - build: - - {{ compiler('c') }} - - make + +source: + md5: 331007d5708e801a668dc0ee055186d4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'A package for importing and analyzing data from Roche''s Genome Sequencer System' - description: 'The R453Plus1 Toolbox comprises useful functions for the analysis of data generated by Roche''s 454 sequencing platform. It adds functions for quality assurance as well as for annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. Further, a pipeline for the detection of structural variants is provided.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-r4rna/meta.yaml b/recipes/bioconductor-r4rna/meta.yaml index 5cb61ea244f9a..17d95d230764b 100644 --- a/recipes/bioconductor-r4rna/meta.yaml +++ b/recipes/bioconductor-r4rna/meta.yaml @@ -1,40 +1,22 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "R4RNA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package for RNA basepair analysis, including the visualization of basepairs as arc diagrams for easy comparison and annotation of sequence and structure. Arc diagrams can additionally be projected onto multiple sequence alignments to assess basepair conservation and covariation, with numerical methods for computing statistics for each. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: An R package for RNA visualization and analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a77903559307ab481671650646dd85e5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-r4rna", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - r-base - run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'An R package for RNA visualization and analysis' - description: 'A package for RNA basepair analysis, including the visualization of basepairs as arc diagrams for easy comparison and annotation of sequence and structure. Arc diagrams can additionally be projected onto multiple sequence alignments to assess basepair conservation and covariation, with numerical methods for computing statistics for each.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:r4rna @@ -43,3 +25,27 @@ extra: path: recipes/bioconductor-r4rna version: 1.8.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - r-base + run: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - r-base + +source: + md5: 5247e6e2486ba1fc17303aade988df31 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-radiogx/meta.yaml b/recipes/bioconductor-radiogx/meta.yaml index 6aa2d3edaaaa0..46e369b1f2329 100644 --- a/recipes/bioconductor-radiogx/meta.yaml +++ b/recipes/bioconductor-radiogx/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "2.6.0" %} +{% set version = "2.10.0" %} {% set name = "RadioGx" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Computational tool box for radio-genomic analysis which integrates radio-response data, radio-biological modelling and comprehensive cell line annotations for hundreds of cancer cell lines. The ''RadioSet'' class enables creation and manipulation of standardized datasets including information about cancer cells lines, radio-response assays and dose-response indicators. Included methods allow fitting and plotting dose-response data using established radio-biological models along with quality control to validate results. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, references, as well as: Manem, V. et al (2018) .' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Analysis of Large-Scale Radio-Genomic Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a7e06ef2f71341c5252a5e2b874fdf17 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-radiogx", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, BiocStyle, knitr, pander, markdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-coregx >=2.6.0,<2.7.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-coregx >=2.10.0,<2.11.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-catools @@ -39,12 +41,12 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-coregx >=2.6.0,<2.7.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-coregx >=2.10.0,<2.11.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-catools @@ -55,13 +57,16 @@ requirements: - r-rcolorbrewer - r-reshape2 - r-scales + +source: + md5: 2319d4c0bbbbf909fa57592dc80e9557 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Analysis of Large-Scale Radio-Genomic Data' - description: 'Computational tool box for radio-genomic analysis which integrates radio-response data, radio-biological modelling and comprehensive cell line annotations for hundreds of cancer cell lines. The ''RadioSet'' class enables creation and manipulation of standardized datasets including information about cancer cells lines, radio-response assays and dose-response indicators. Included methods allow fitting and plotting dose-response data using established radio-biological models along with quality control to validate results. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, references, as well as: Manem, V. et al (2018) .' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rae230a.db/meta.yaml b/recipes/bioconductor-rae230a.db/meta.yaml index afeee8e0950b8..e50a7774b4870 100644 --- a/recipes/bioconductor-rae230a.db/meta.yaml +++ b/recipes/bioconductor-rae230a.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "rae230a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a2a80af1669fc038a64effbf5a4b246d +about: + description: Affymetrix Affymetrix RAE230A Array annotation data (chip rae230a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix RAE230A Array annotation data (chip rae230a) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rae230a.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a2a80af1669fc038a64effbf5a4b246d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix RAE230A Array annotation data (chip rae230a)' - description: 'Affymetrix Affymetrix RAE230A Array annotation data (chip rae230a) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rae230acdf/meta.yaml b/recipes/bioconductor-rae230acdf/meta.yaml index 650f0d564ab13..0e9662fcd7fad 100644 --- a/recipes/bioconductor-rae230acdf/meta.yaml +++ b/recipes/bioconductor-rae230acdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rae230acdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6f2281124e1be164d5fd599e84f6adbc +about: + description: A package containing an environment representing the RAE230A.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: rae230acdf build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rae230acdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6f2281124e1be164d5fd599e84f6adbc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: rae230acdf - description: 'A package containing an environment representing the RAE230A.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rae230aprobe/meta.yaml b/recipes/bioconductor-rae230aprobe/meta.yaml index b7441cbf4679b..142c5058235e4 100644 --- a/recipes/bioconductor-rae230aprobe/meta.yaml +++ b/recipes/bioconductor-rae230aprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rae230aprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6f2d77e1d9c1e3afb96ef78b3202bb0b +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RAE230A\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type rae230a build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rae230aprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6f2d77e1d9c1e3afb96ef78b3202bb0b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type rae230a' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RAE230A\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rae230b.db/meta.yaml b/recipes/bioconductor-rae230b.db/meta.yaml index 0273888d9117e..802b8a1c1dd39 100644 --- a/recipes/bioconductor-rae230b.db/meta.yaml +++ b/recipes/bioconductor-rae230b.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "rae230b.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4f0474ed22bf5ebd932dd6a4d9573551 +about: + description: Affymetrix Affymetrix RAE230B Array annotation data (chip rae230b) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix RAE230B Array annotation data (chip rae230b) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rae230b.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4f0474ed22bf5ebd932dd6a4d9573551 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix RAE230B Array annotation data (chip rae230b)' - description: 'Affymetrix Affymetrix RAE230B Array annotation data (chip rae230b) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rae230bcdf/meta.yaml b/recipes/bioconductor-rae230bcdf/meta.yaml index 38c382de21f3c..e25a7bd004015 100644 --- a/recipes/bioconductor-rae230bcdf/meta.yaml +++ b/recipes/bioconductor-rae230bcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rae230bcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bd61c17402e9c04be1000c16e0356618 +about: + description: A package containing an environment representing the RAE230B.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: rae230bcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rae230bcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bd61c17402e9c04be1000c16e0356618 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: rae230bcdf - description: 'A package containing an environment representing the RAE230B.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rae230bprobe/meta.yaml b/recipes/bioconductor-rae230bprobe/meta.yaml index 242c7cdb4229c..bd2086176a5eb 100644 --- a/recipes/bioconductor-rae230bprobe/meta.yaml +++ b/recipes/bioconductor-rae230bprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rae230bprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7bdb3a07e1f00de8ff510a69bdac4c53 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RAE230B\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type rae230b build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rae230bprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7bdb3a07e1f00de8ff510a69bdac4c53 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type rae230b' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RAE230B\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-raer/build_failure.linux-64.yaml b/recipes/bioconductor-raer/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..9daf1397eaca4 --- /dev/null +++ b/recipes/bioconductor-raer/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 72f898cc0c56d808703c4f153fa673e571e34b6a68572f6165985aa228b0b13d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-raer-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-raer-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-raer_1735520893014/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/R/library + * installing *source* package raer ... + ** package raer successfully unpacked and MD5 sums checked + ** using staged installation + ** libs + using C compiler: x86_64-conda-linux-gnu-cc (conda-forge gcc 13.3.0-1) 13.3.0 + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c init.c -o init.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c plp.c -o plp.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c plp_data.c -o plp_data.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c plp_utils.c -o plp_utils.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c regfile.c -o regfile.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c sc-plp.c -o sc-plp.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c utils.c -o utils.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ext/bcftools/bcftools-ext.c -o ext/bcftools/bcftools-ext.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ext/htsbox/htsbox-ext.c -o ext/htsbox/htsbox-ext.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rhtslib/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ext/samtools/samtools-ext.c -o ext/samtools/samtools-ext.o + During startup - Warning message: + Setting LC_TIME failed, using "C" + During startup - Warning message: + Setting LC_TIME failed, using "C" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -shared -L$PREFIX/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -o raer.so init.o plp.o plp_data.o plp_utils.o regfile.o sc-plp.o utils.o ext/bcftools/bcftools-ext.o ext/htsbox/htsbox-ext.o ext/samtools/samtools-ext.o $PREFIX/lib/R/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L$PREFIX/lib/R/lib -lR + /opt/conda/conda-bld/bioconductor-raer_1735520893014/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -llzma: No such file or directory + /opt/conda/conda-bld/bioconductor-raer_1735520893014/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lz: No such file or directory + collect2: error: ld returned 1 exit status + make: *** [/opt/conda/conda-bld/bioconductor-raer_1735520893014/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/R/share/make/shlib.mk:10: raer.so] Error 1 + ERROR: compilation failed for package raer + * removing /opt/conda/conda-bld/bioconductor-raer_1735520893014/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/R/library/raer + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-raer_1735520893014/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-raer_1735520893014/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-raer/meta.yaml b/recipes/bioconductor-raer/meta.yaml index 61beb51eb00aa..c7d77b46bf503 100644 --- a/recipes/bioconductor-raer/meta.yaml +++ b/recipes/bioconductor-raer/meta.yaml @@ -1,80 +1,84 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "raer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Toolkit for identification and statistical testing of RNA editing signals from within R. Provides support for identifying sites from bulk-RNA and single cell RNA-seq datasets, and general methods for extraction of allelic read counts from alignment files. Facilitates annotation and exploratory analysis of editing signals using Bioconductor packages and resources. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: RNA editing tools in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0b5c050626ce21756f90b4f9c967465b build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-raer", max_pin="x.x") }}' -# Suggests: testthat (>= 3.0.0), knitr, DESeq2, edgeR, limma, rmarkdown, BiocStyle, ComplexHeatmap, TxDb.Hsapiens.UCSC.hg38.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, BSgenome.Hsapiens.NCBI.GRCh38, scater, scran, scuttle, AnnotationHub, covr, raerdata + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat (>= 3.0.0), knitr, DESeq2, edgeR, limma, rmarkdown, BiocStyle, ComplexHeatmap, TxDb.Hsapiens.UCSC.hg38.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, BSgenome.Hsapiens.NCBI.GRCh38, scater, scran, scuttle, AnnotationHub, covr, raerdata, txdbmaker # SystemRequirements: GNU make requirements: + + build: + - {{ compiler('c') }} + - make + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cli - - r-data.table - r-matrix - - r-r.utils - libblas - liblapack + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cli - - r-data.table - r-matrix - - r-r.utils - build: - - {{ compiler('c') }} - - make + +source: + md5: 62a848362e80523d0a265dea6475555b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'RNA editing tools in R' - description: 'Toolkit for identification and statistical testing of RNA editing signals from within R. Provides support for identifying sites from bulk-RNA and single cell RNA-seq datasets, and general methods for extraction of allelic read counts from alignment files. Facilitates annotation and exploratory analysis of editing signals using Bioconductor packages and resources.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-raerdata/meta.yaml b/recipes/bioconductor-raerdata/meta.yaml index a93eb084ad4ba..21a1471d04682 100644 --- a/recipes/bioconductor-raerdata/meta.yaml +++ b/recipes/bioconductor-raerdata/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "raerdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: raerdata is an ExperimentHub package that provides a collection of files useful for demostrating functionality in the raer package. Datasets include 10x genomics scRNA-seq, bulk RNA-seq, and paired whole-genome and RNA-seq data. Additionally databases of human and mouse RNA editing sites are provided. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: A collection of datasets for use with raer package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8f250d12f89396f8d4351da5045cf22c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-raerdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: d23f3d1df443467be1f57d2e9c6f4deb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'A collection of datasets for use with raer package' - description: 'raerdata is an ExperimentHub package that provides a collection of files useful for demostrating functionality in the raer package. Datasets include 10x genomics scRNA-seq, bulk RNA-seq, and paired whole-genome and RNA-seq data. Additionally databases of human and mouse RNA editing sites are provided.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-raerdata/post-link.sh b/recipes/bioconductor-raerdata/post-link.sh index f8c5dd141a4fe..c44fb8133c841 100644 --- a/recipes/bioconductor-raerdata/post-link.sh +++ b/recipes/bioconductor-raerdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "raerdata-1.0.0" +installBiocDataPackage.sh "raerdata-1.4.0" diff --git a/recipes/bioconductor-raex10stprobeset.db/meta.yaml b/recipes/bioconductor-raex10stprobeset.db/meta.yaml index 27cc03aa38783..ef76ea26713f6 100644 --- a/recipes/bioconductor-raex10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-raex10stprobeset.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "raex10stprobeset.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a386809ea8da340f315e378fa329b3ac +about: + description: Affymetrix raex10 annotation data (chip raex10stprobeset) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix raex10 annotation data (chip raex10stprobeset) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-raex10stprobeset.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a386809ea8da340f315e378fa329b3ac + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix raex10 annotation data (chip raex10stprobeset)' - description: 'Affymetrix raex10 annotation data (chip raex10stprobeset) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-raex10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-raex10sttranscriptcluster.db/meta.yaml index 98b38f78e2267..2582e66131218 100644 --- a/recipes/bioconductor-raex10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-raex10sttranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "raex10sttranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3a0c511a1073c67172770bc3e4b842b5 +about: + description: Affymetrix raex10 annotation data (chip raex10sttranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix raex10 annotation data (chip raex10sttranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-raex10sttranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3a0c511a1073c67172770bc3e4b842b5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix raex10 annotation data (chip raex10sttranscriptcluster)' - description: 'Affymetrix raex10 annotation data (chip raex10sttranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-raexexonprobesetlocation/meta.yaml b/recipes/bioconductor-raexexonprobesetlocation/meta.yaml index 370160c4212b6..77301a924921e 100644 --- a/recipes/bioconductor-raexexonprobesetlocation/meta.yaml +++ b/recipes/bioconductor-raexexonprobesetlocation/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.15.0" %} {% set name = "RaExExonProbesetLocation" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d547bcd30685495283b32f0f86ecc79b +about: + description: This package was automatically created by package AnnotationForge version 1.7.17. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type RaEx build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-raexexonprobesetlocation", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d547bcd30685495283b32f0f86ecc79b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type RaEx' - description: 'This package was automatically created by package AnnotationForge version 1.7.17. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ragene10stprobeset.db/meta.yaml b/recipes/bioconductor-ragene10stprobeset.db/meta.yaml index d5ca4b4037b08..7ae5ab0cdd29f 100644 --- a/recipes/bioconductor-ragene10stprobeset.db/meta.yaml +++ b/recipes/bioconductor-ragene10stprobeset.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "ragene10stprobeset.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 358685c380b37027a064924069b9ee40 +about: + description: Affymetrix ragene10 annotation data (chip ragene10stprobeset) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix ragene10 annotation data (chip ragene10stprobeset) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ragene10stprobeset.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 358685c380b37027a064924069b9ee40 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix ragene10 annotation data (chip ragene10stprobeset)' - description: 'Affymetrix ragene10 annotation data (chip ragene10stprobeset) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ragene10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene10sttranscriptcluster.db/meta.yaml index 4169739b0d7d0..c32399aa697c7 100644 --- a/recipes/bioconductor-ragene10sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-ragene10sttranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "ragene10sttranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5ff95454493a72bfa2546d82d32fbec1 +about: + description: Affymetrix ragene10 annotation data (chip ragene10sttranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix ragene10 annotation data (chip ragene10sttranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ragene10sttranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5ff95454493a72bfa2546d82d32fbec1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix ragene10 annotation data (chip ragene10sttranscriptcluster)' - description: 'Affymetrix ragene10 annotation data (chip ragene10sttranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ragene10stv1cdf/meta.yaml b/recipes/bioconductor-ragene10stv1cdf/meta.yaml index f9095368dcbb5..c31ebd33cbac3 100644 --- a/recipes/bioconductor-ragene10stv1cdf/meta.yaml +++ b/recipes/bioconductor-ragene10stv1cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "ragene10stv1cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: df696e9dbf5b3f2761b6a0a5914be058 +about: + description: A package containing an environment representing the RaGene-1_0-st-v1.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: ragene10stv1cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ragene10stv1cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: df696e9dbf5b3f2761b6a0a5914be058 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: ragene10stv1cdf - description: 'A package containing an environment representing the RaGene-1_0-st-v1.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ragene10stv1probe/meta.yaml b/recipes/bioconductor-ragene10stv1probe/meta.yaml index 36db272a8a25c..27dfe937aa754 100644 --- a/recipes/bioconductor-ragene10stv1probe/meta.yaml +++ b/recipes/bioconductor-ragene10stv1probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "ragene10stv1probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 94978b6efb075aacf31ccdc8000e40fa +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RaGene-1\_0-st-v1\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type ragene10stv1 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ragene10stv1probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 94978b6efb075aacf31ccdc8000e40fa + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type ragene10stv1' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RaGene-1\_0-st-v1\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ragene11stprobeset.db/meta.yaml b/recipes/bioconductor-ragene11stprobeset.db/meta.yaml index 9605b8d84ad9a..6b2b4ca4363c2 100644 --- a/recipes/bioconductor-ragene11stprobeset.db/meta.yaml +++ b/recipes/bioconductor-ragene11stprobeset.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "ragene11stprobeset.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 86f7704c4852c514b3bc3221f7692ba3 +about: + description: Affymetrix ragene11 annotation data (chip ragene11stprobeset) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix ragene11 annotation data (chip ragene11stprobeset) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ragene11stprobeset.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 86f7704c4852c514b3bc3221f7692ba3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix ragene11 annotation data (chip ragene11stprobeset)' - description: 'Affymetrix ragene11 annotation data (chip ragene11stprobeset) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ragene11sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene11sttranscriptcluster.db/meta.yaml index a4a85cda35e82..919c210ed31cb 100644 --- a/recipes/bioconductor-ragene11sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-ragene11sttranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "ragene11sttranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f7fbe318547f911b520415a90b3440e9 +about: + description: Affymetrix ragene11 annotation data (chip ragene11sttranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix ragene11 annotation data (chip ragene11sttranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ragene11sttranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f7fbe318547f911b520415a90b3440e9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix ragene11 annotation data (chip ragene11sttranscriptcluster)' - description: 'Affymetrix ragene11 annotation data (chip ragene11sttranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ragene20stprobeset.db/meta.yaml b/recipes/bioconductor-ragene20stprobeset.db/meta.yaml index 67108c15a1dd4..a72d3501ed1e9 100644 --- a/recipes/bioconductor-ragene20stprobeset.db/meta.yaml +++ b/recipes/bioconductor-ragene20stprobeset.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "ragene20stprobeset.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 23a43899a22078f4c13b7b1d45176319 +about: + description: Affymetrix ragene20 annotation data (chip ragene20stprobeset) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix ragene20 annotation data (chip ragene20stprobeset) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ragene20stprobeset.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 23a43899a22078f4c13b7b1d45176319 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix ragene20 annotation data (chip ragene20stprobeset)' - description: 'Affymetrix ragene20 annotation data (chip ragene20stprobeset) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ragene20sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene20sttranscriptcluster.db/meta.yaml index 28fc801a28399..218b368a49275 100644 --- a/recipes/bioconductor-ragene20sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-ragene20sttranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "ragene20sttranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b44c5f6ac2b2e3eb4d820d08f7a38644 +about: + description: Affymetrix ragene20 annotation data (chip ragene20sttranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix ragene20 annotation data (chip ragene20sttranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ragene20sttranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b44c5f6ac2b2e3eb4d820d08f7a38644 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix ragene20 annotation data (chip ragene20sttranscriptcluster)' - description: 'Affymetrix ragene20 annotation data (chip ragene20sttranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ragene21stprobeset.db/meta.yaml b/recipes/bioconductor-ragene21stprobeset.db/meta.yaml index 0b4be17e863db..fcadbf2d04746 100644 --- a/recipes/bioconductor-ragene21stprobeset.db/meta.yaml +++ b/recipes/bioconductor-ragene21stprobeset.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "ragene21stprobeset.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6451885f99ce3873d5d4dbacdf968181 +about: + description: Affymetrix ragene21 annotation data (chip ragene21stprobeset) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix ragene21 annotation data (chip ragene21stprobeset) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ragene21stprobeset.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6451885f99ce3873d5d4dbacdf968181 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix ragene21 annotation data (chip ragene21stprobeset)' - description: 'Affymetrix ragene21 annotation data (chip ragene21stprobeset) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ragene21sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene21sttranscriptcluster.db/meta.yaml index 06c45bcb7dee6..e60d4a709b45f 100644 --- a/recipes/bioconductor-ragene21sttranscriptcluster.db/meta.yaml +++ b/recipes/bioconductor-ragene21sttranscriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "ragene21sttranscriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6ffe13e1594add0a5169b2083b608336 +about: + description: Affymetrix ragene21 annotation data (chip ragene21sttranscriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix ragene21 annotation data (chip ragene21sttranscriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ragene21sttranscriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6ffe13e1594add0a5169b2083b608336 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix ragene21 annotation data (chip ragene21sttranscriptcluster)' - description: 'Affymetrix ragene21 annotation data (chip ragene21sttranscriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-raggedexperiment/meta.yaml b/recipes/bioconductor-raggedexperiment/meta.yaml index 5caad78ba3f76..093b66317763d 100644 --- a/recipes/bioconductor-raggedexperiment/meta.yaml +++ b/recipes/bioconductor-raggedexperiment/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "RaggedExperiment" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns. The RaggedExperiment class derives from a GRangesList representation and provides a semblance of a rectangular dataset. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Representation of Sparse Experiments and Assays Across Samples -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5704ce0834ff2770c489c3882ef4acec build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-raggedexperiment", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-raggedexperiment + path: recipes/bioconductor-raggedexperiment + version: 1.4.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, MultiAssayExperiment requirements: host: - - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix run: - - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix + +source: + md5: aecd9d560431b4dbe85d945bd858bd30 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Representation of Sparse Experiments and Assays Across Samples' - description: 'This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns. The RaggedExperiment class derives from a GRangesList representation and provides a semblance of a rectangular dataset.' -extra: - parent_recipe: - name: bioconductor-raggedexperiment - path: recipes/bioconductor-raggedexperiment - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-raids/meta.yaml b/recipes/bioconductor-raids/meta.yaml index 507252a73a248..3641c8590f3d7 100644 --- a/recipes/bioconductor-raids/meta.yaml +++ b/recipes/bioconductor-raids/meta.yaml @@ -1,66 +1,75 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "RAIDS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'This package implements specialized algorithms that enable genetic ancestry inference from various cancer sequences sources (RNA, Exome and Whole-Genome sequences). This package also implements a simulation algorithm that generates synthetic cancer-derived data. This code and analysis pipeline was designed and developed for the following publication: Belleau, P et al. Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Apache License (>= 2) + summary: Accurate Inference of Genetic Ancestry from Cancer Sequences -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 768d047b002bb44e1178d69233878818 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-raids", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocStyle, withr, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-genesis >=2.32.0,<2.33.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-snprelate >=1.36.0,<1.37.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-genesis >=2.36.0,<2.37.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-snprelate >=1.40.0,<1.41.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-class + - r-ggplot2 - r-proc - r-rlang + - r-stringr run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-genesis >=2.32.0,<2.33.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-snprelate >=1.36.0,<1.37.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-genesis >=2.36.0,<2.37.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-snprelate >=1.40.0,<1.41.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-class + - r-ggplot2 - r-proc - r-rlang + - r-stringr + +source: + md5: 248ebb52129550059a96c3f92d39cafc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Apache License (>= 2)' - summary: 'Accurate Inference of Genetic Ancestry from Cancer Sequences' - description: 'This package implements specialized algorithms that enable genetic ancestry inference from various cancer sequences sources (RNA, Exome and Whole-Genome sequences). This package also implements a simulation algorithm that generates synthetic cancer-derived data. This code and analysis pipeline was designed and developed for the following publication: Belleau, P et al. Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rain/meta.yaml b/recipes/bioconductor-rain/meta.yaml index f06f49eb3f548..90cf50f1201dd 100644 --- a/recipes/bioconductor-rain/meta.yaml +++ b/recipes/bioconductor-rain/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "rain" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'This package uses non-parametric methods to detect rhythms in time series. It deals with outliers, missing values and is optimized for time series comprising 10-100 measurements. As it does not assume expect any distinct waveform it is optimal or detecting oscillating behavior (e.g. circadian or cell cycle) in e.g. genome- or proteome-wide biological measurements such as: micro arrays, proteome mass spectrometry, or metabolome measurements.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Rhythmicity Analysis Incorporating Non-parametric Methods -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e523c08337422230710fd1f2a5a392cd build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rain", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rain + parent_recipe: + name: bioconductor-rain + path: recipes/bioconductor-rain + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: lattice, BiocStyle requirements: host: - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base - r-gmp run: - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base - r-gmp + +source: + md5: 7fd347e176d9bfa00a7b48a169934b7a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Rhythmicity Analysis Incorporating Non-parametric Methods' - description: 'This package uses non-parametric methods to detect rhythms in time series. It deals with outliers, missing values and is optimized for time series comprising 10-100 measurements. As it does not assume expect any distinct waveform it is optimal or detecting oscillating behavior (e.g. circadian or cell cycle) in e.g. genome- or proteome-wide biological measurements such as: micro arrays, proteome mass spectrometry, or metabolome measurements.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:rain - parent_recipe: - name: bioconductor-rain - path: recipes/bioconductor-rain - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ramr/meta.yaml b/recipes/bioconductor-ramr/meta.yaml index 196dcea668264..87db8a53e85c4 100644 --- a/recipes/bioconductor-ramr/meta.yaml +++ b/recipes/bioconductor-ramr/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "ramr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ramr is an R package for detection of low-frequency aberrant methylation events in large data sets obtained by methylation profiling using array or high-throughput bisulfite sequencing. In addition, package provides functions to visualize found aberrantly methylated regions (AMRs), to generate sets of all possible regions to be used as reference sets for enrichment analysis, and to generate biologically relevant test data sets for performance evaluation of AMR/DMR search algorithms. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Detection of Rare Aberrantly Methylated Regions in Array and NGS Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6a6278f2ad74018661b9985eb978e90c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ramr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, knitr, rmarkdown, gridExtra, annotatr, LOLA, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-doparallel - r-dorng @@ -36,10 +37,10 @@ requirements: - r-matrixstats - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-doparallel - r-dorng @@ -49,12 +50,16 @@ requirements: - r-ggplot2 - r-matrixstats - r-reshape2 + +source: + md5: 45dfa15b6a3fc7acdf6ef9a5006b8cae + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Detection of Rare Aberrantly Methylated Regions in Array and NGS Data' - description: 'ramr is an R package for detection of low-frequency aberrant methylation events in large data sets obtained by methylation profiling using array or high-throughput bisulfite sequencing. In addition, package provides functions to visualize found aberrantly methylated regions (AMRs), to generate sets of all possible regions to be used as reference sets for enrichment analysis, and to generate biologically relevant test data sets for performance evaluation of AMR/DMR search algorithms.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ramwas/meta.yaml b/recipes/bioconductor-ramwas/meta.yaml index 233f285fb2a8e..7043f6a60026c 100644 --- a/recipes/bioconductor-ramwas/meta.yaml +++ b/recipes/bioconductor-ramwas/meta.yaml @@ -1,31 +1,36 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "ramwas" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'A complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association analysis with respect to phenotypes of interest while correcting for top PCs and known covariates, (6) annotation of significant findings, and (7) multi-marker analysis (methylation risk score) using elastic net. Additionally, RaMWAS include tools for joint analysis of methlyation and genotype data. This work is published in Bioinformatics, Shabalin et al. (2018) .' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ccbff0a1c4bd31c8ceb9d2641d6608d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ramwas", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, pander, BiocStyle, BSgenome.Ecoli.NCBI.20080805 requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-digest - r-filematrix @@ -34,26 +39,26 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-digest - r-filematrix - r-glmnet - r-kernsmooth - build: - - {{ compiler('c') }} - - make + +source: + md5: e27bd83b278844ef7cfbe09a4d49fcc6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms' - description: 'A complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association analysis with respect to phenotypes of interest while correcting for top PCs and known covariates, (6) annotation of significant findings, and (7) multi-marker analysis (methylation risk score) using elastic net. Additionally, RaMWAS include tools for joint analysis of methlyation and genotype data. This work is published in Bioinformatics, Shabalin et al. (2018) .' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-randpack/meta.yaml b/recipes/bioconductor-randpack/meta.yaml index 626ee120a1935..29148a7223bad 100644 --- a/recipes/bioconductor-randpack/meta.yaml +++ b/recipes/bioconductor-randpack/meta.yaml @@ -1,39 +1,21 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "randPack" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A suite of classes and functions for randomizing patients in clinical trials. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic 2.0 + summary: Randomization routines for Clinical Trials -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71791ade28f58d981a510c8b660ae1e7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-randpack", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Artistic 2.0' - summary: 'Randomization routines for Clinical Trials' - description: 'A suite of classes and functions for randomizing patients in clinical trials.' + extra: identifiers: - biotools:randpack @@ -43,3 +25,27 @@ extra: path: recipes/bioconductor-randpack version: 1.26.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - r-base + +source: + md5: 3b62e01dd95b189100960ee0c9691b7f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-randrotation/meta.yaml b/recipes/bioconductor-randrotation/meta.yaml index 5d4447925d490..191f11fa91b5e 100644 --- a/recipes/bioconductor-randrotation/meta.yaml +++ b/recipes/bioconductor-randrotation/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "randRotation" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a05faf1fe582450a789fc2d58960fa97 +about: + description: A collection of methods for performing random rotations on high-dimensional, normally distributed data (e.g. microarray or RNA-seq data) with batch structure. The random rotation approach allows exact testing of dependent test statistics with linear models following arbitrary batch effect correction methods. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Random Rotation Methods for High Dimensional Data with Batch Structure build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-randrotation", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, BiocParallel, lme4, nlme, rmarkdown, BiocStyle, testthat (>= 2.1.0), limma, sva requirements: host: - r-base - - 'r-rdpack >=0.7' + - r-rdpack >=0.7 run: - r-base - - 'r-rdpack >=0.7' + - r-rdpack >=0.7 +source: + md5: 4b11105b6e7ebcd4f91794541b888b1e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Random Rotation Methods for High Dimensional Data with Batch Structure' - description: 'A collection of methods for performing random rotations on high-dimensional, normally distributed data (e.g. microarray or RNA-seq data) with batch structure. The random rotation approach allows exact testing of dependent test statistics with linear models following arbitrary batch effect correction methods.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rankprod/meta.yaml b/recipes/bioconductor-rankprod/meta.yaml index 2ebbe68585c00..29bd43172adca 100644 --- a/recipes/bioconductor-rankprod/meta.yaml +++ b/recipes/bioconductor-rankprod/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "3.28.0" %} +{% set version = "3.32.0" %} {% set name = "RankProd" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp). The method can combine data sets from different origins (meta-analysis) to increase the power of the identification. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Rank Product method for identifying differentially expressed genes with application in meta-analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 39f3eba64601984ad265d91f3a150180 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rankprod", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rankprod + - doi:10.1093/bioinformatics/btl476 + parent_recipe: + name: bioconductor-rankprod + path: recipes/bioconductor-rankprod + version: 3.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -28,21 +39,16 @@ requirements: - r-base - r-gmp - r-rmpfr + +source: + md5: 1dac9aa5435507951740d1c58d8bf42b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Rank Product method for identifying differentially expressed genes with application in meta-analysis' - description: 'Non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp). The method can combine data sets from different origins (meta-analysis) to increase the power of the identification.' - license_file: LICENSE -extra: - identifiers: - - biotools:rankprod - - doi:10.1093/bioinformatics/btl476 - parent_recipe: - name: bioconductor-rankprod - path: recipes/bioconductor-rankprod - version: 3.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-raresim/meta.yaml b/recipes/bioconductor-raresim/meta.yaml index fdd6a7e5a167e..e91188262294c 100644 --- a/recipes/bioconductor-raresim/meta.yaml +++ b/recipes/bioconductor-raresim/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "RAREsim" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6ec5b86f348e2d4ffb365da80651041e +about: + description: Haplotype simulations of rare variant genetic data that emulates real data can be performed with RAREsim. RAREsim uses the expected number of variants in MAC bins - either as provided by default parameters or estimated from target data - and an abundance of rare variants as simulated HAPGEN2 to probabilistically prune variants. RAREsim produces haplotypes that emulate real sequencing data with respect to the total number of variants, allele frequency spectrum, haplotype structure, and variant annotation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Simulation of Rare Variant Genetic Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-raresim", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) requirements: host: @@ -27,13 +26,14 @@ requirements: run: - r-base - r-nloptr +source: + md5: 6a90455bf846efb071d61507b0f76c83 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Simulation of Rare Variant Genetic Data' - description: 'Haplotype simulations of rare variant genetic data that emulates real data can be performed with RAREsim. RAREsim uses the expected number of variants in MAC bins - either as provided by default parameters or estimated from target data - and an abundance of rare variants as simulated HAPGEN2 to probabilistically prune variants. RAREsim produces haplotypes that emulate real sequencing data with respect to the total number of variants, allele frequency spectrum, haplotype structure, and variant annotation.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rarevariantvis/build_failure.linux-64.yaml b/recipes/bioconductor-rarevariantvis/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..fafc57a0f2cc6 --- /dev/null +++ b/recipes/bioconductor-rarevariantvis/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 7f02742cc5f49c6b2f418ed50e6214f2a21cc1331c8e162d737959067a667411 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - nothing provides r 3.2.2* needed by bioconductor-txdb.hsapiens.ucsc.hg19.knowngene-3.2.2-r3.2.2_0 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-biocgenerics >=0.52.0,<0.53.0 [0m is installable and it requires + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 [0m is installable with the potential options + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [31mr-base 3.3.2* [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [31mr 3.2.2* [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [31mr-base 3.4.1* [0m, which conflicts with any installable versions previously reported; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [32mbioconductor-bsgenome >=1.48.0,<1.50.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [32mbioconductor-bsgenome >=1.50.0,<1.51.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [32mbioconductor-bsgenome >=1.52.0,<1.53.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [32mbioconductor-bsgenome >=1.54.0,<1.55.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [32mbioconductor-bsgenome >=1.56.0,<1.57.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [32mbioconductor-bsgenome >=1.58.0,<1.59.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [32mbioconductor-bsgenome >=1.60.0,<1.61.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [32mbioconductor-bsgenome >=1.62.0,<1.63.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [32mbioconductor-bsgenome >=1.66.0,<1.67.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [32mbioconductor-bsgenome >=1.68.0,<1.69.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [32mbioconductor-bsgenome >=1.70.0,<1.71.0 [0m, which can be installed; + [31mbioconductor-bsgenome >=1.74.0,<1.75.0 [0m is not installable because it conflicts with any installable versions previously reported; + [32mbioconductor-genomicfeatures >=1.58.0,<1.59.0 [0m is requested and can be installed; + [32mbioconductor-genomicscores >=2.18.0,<2.19.0 [0m is installable and it requires + [32mbioconductor-annotationhub >=3.14.0,<3.15.0 [0m, which requires + [32mbioconductor-biocversion >=3.20.0,<3.21.0 [0m, which requires + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [32mbioconductor-phastcons100way.ucsc.hg19 >=3.7.0,<3.8.0 [0m is installable with the potential options + [32mbioconductor-phastcons100way.ucsc.hg19 3.7.2[0m would require + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [32mbioconductor-phastcons100way.ucsc.hg19 3.7.2[0m would require + [32mbioconductor-bsgenome >=1.48.0,<1.50.0 [0m, which can be installed; + [32mbioconductor-phastcons100way.ucsc.hg19 3.7.2[0m would require + [32mbioconductor-bsgenome >=1.50.0,<1.51.0 [0m, which can be installed; + [32mbioconductor-phastcons100way.ucsc.hg19 3.7.2[0m would require + [32mbioconductor-bsgenome >=1.52.0,<1.53.0 [0m, which can be installed; + [32mbioconductor-phastcons100way.ucsc.hg19 3.7.2[0m would require + [32mbioconductor-bsgenome >=1.54.0,<1.55.0 [0m, which can be installed; + [32mbioconductor-phastcons100way.ucsc.hg19 3.7.2[0m would require + [32mbioconductor-bsgenome >=1.56.0,<1.57.0 [0m, which can be installed; + [32mbioconductor-phastcons100way.ucsc.hg19 3.7.2[0m would require + [32mbioconductor-bsgenome >=1.58.0,<1.59.0 [0m, which can be installed; + [32mbioconductor-phastcons100way.ucsc.hg19 3.7.2[0m would require + [32mbioconductor-bsgenome >=1.62.0,<1.63.0 [0m, which can be installed; + [32mbioconductor-phastcons100way.ucsc.hg19 3.7.2[0m would require + [32mbioconductor-bsgenome >=1.60.0,<1.61.0 [0m, which can be installed; + [32mbioconductor-phastcons100way.ucsc.hg19 3.7.2[0m would require + [32mbioconductor-bsgenome >=1.66.0,<1.67.0 [0m, which can be installed; + [32mbioconductor-phastcons100way.ucsc.hg19 3.7.2[0m would require + [32mbioconductor-bsgenome >=1.68.0,<1.69.0 [0m, which can be installed; + [32mbioconductor-phastcons100way.ucsc.hg19 3.7.2[0m would require + [32mbioconductor-bsgenome >=1.70.0,<1.71.0 [0m, which can be installed; + [31mbioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 [0m is not installable because there are no viable options + [31mbioconductor-txdb.hsapiens.ucsc.hg19.knowngene 3.2.2[0m would require + [31mr-base 3.3.2* [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.hsapiens.ucsc.hg19.knowngene 3.2.2[0m would require + [31mr 3.2.2* [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-txdb.hsapiens.ucsc.hg19.knowngene 3.2.2[0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-txdb.hsapiens.ucsc.hg19.knowngene 3.2.2[0m would require + [31mr-base 3.4.1* [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.hsapiens.ucsc.hg19.knowngene 3.2.2[0m would require + [31mbioconductor-genomicfeatures >=1.32.2,<1.34.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.hsapiens.ucsc.hg19.knowngene 3.2.2[0m would require + [31mbioconductor-genomicfeatures >=1.34.0,<1.35.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.hsapiens.ucsc.hg19.knowngene 3.2.2[0m would require + [31mbioconductor-genomicfeatures >=1.36.0,<1.37.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.hsapiens.ucsc.hg19.knowngene 3.2.2[0m would require + [31mbioconductor-genomicfeatures >=1.38.0,<1.39.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.hsapiens.ucsc.hg19.knowngene 3.2.2[0m would require + [31mbioconductor-genomicfeatures >=1.40.0,<1.41.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.hsapiens.ucsc.hg19.knowngene 3.2.2[0m would require + [31mbioconductor-genomicfeatures >=1.42.0,<1.43.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.hsapiens.ucsc.hg19.knowngene 3.2.2[0m would require + [31mbioconductor-genomicfeatures >=1.44.0,<1.45.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.hsapiens.ucsc.hg19.knowngene 3.2.2[0m would require + [31mbioconductor-genomicfeatures >=1.46.0,<1.47.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.hsapiens.ucsc.hg19.knowngene 3.2.2[0m would require + [31mbioconductor-genomicfeatures >=1.50.0,<1.51.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.hsapiens.ucsc.hg19.knowngene 3.2.2[0m would require + [31mbioconductor-genomicfeatures >=1.52.0,<1.53.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.hsapiens.ucsc.hg19.knowngene 3.2.2[0m would require + [31mbioconductor-genomicfeatures >=1.54.0,<1.55.0 [0m, which conflicts with any installable versions previously reported; + [32mr-base 4.4.* [0m is requested and can be installed. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-rarevariantvis/meta.yaml b/recipes/bioconductor-rarevariantvis/meta.yaml index a55ff5d23bcd9..83e2d8b6d883e 100644 --- a/recipes/bioconductor-rarevariantvis/meta.yaml +++ b/recipes/bioconductor-rarevariantvis/meta.yaml @@ -1,74 +1,80 @@ -{% set version = "2.30.0" %} +{% set version = "2.34.0" %} {% set name = "RareVariantVis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Second version of RareVariantVis package aims to provide comprehensive information about rare variants for your genome data. It annotates, filters and presents genomic variants (especially rare ones) in a global, per chromosome way. For discovered rare variants CRISPR guide RNAs are designed, so the user can plan further functional studies. Large structural variants, including copy number variants are also supported. Package accepts variants directly from variant caller - for example GATK or Speedseq. Output of package are lists of variants together with adequate visualization. Visualization of variants is performed in two ways - standard that outputs png figures and interactive that uses JavaScript d3 package. Interactive visualization allows to analyze trio/family data, for example in search for causative variants in rare Mendelian diseases, in point-and-click interface. The package includes homozygous region caller and allows to analyse whole human genomes in less than 30 minutes on a desktop computer. RareVariantVis disclosed novel causes of several rare monogenic disorders, including one with non-coding causative variant - keratolythic winter erythema. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: A suite for analysis of rare genomic variants in whole genome sequencing data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2157172a825bbc826d5c2f3d17a41987 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rarevariantvis", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rarevariantvis + - doi:10.1093/bioinformatics/btw359 + parent_recipe: + name: bioconductor-rarevariantvis + path: recipes/bioconductor-rarevariantvis + version: 2.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-phastcons100way.ucsc.hg19 >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-phastcons100way.ucsc.hg19 >=3.7.0,<3.8.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-googlevis - r-gtools run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-phastcons100way.ucsc.hg19 >=3.7.0,<3.8.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-phastcons100way.ucsc.hg19 >=3.7.0,<3.8.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-googlevis - r-gtools + +source: + md5: 5960585b1e7d21d079eee7d71c24a1ea + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A suite for analysis of rare genomic variants in whole genome sequencing data' - description: 'Second version of RareVariantVis package aims to provide comprehensive information about rare variants for your genome data. It annotates, filters and presents genomic variants (especially rare ones) in a global, per chromosome way. For discovered rare variants CRISPR guide RNAs are designed, so the user can plan further functional studies. Large structural variants, including copy number variants are also supported. Package accepts variants directly from variant caller - for example GATK or Speedseq. Output of package are lists of variants together with adequate visualization. Visualization of variants is performed in two ways - standard that outputs png figures and interactive that uses JavaScript d3 package. Interactive visualization allows to analyze trio/family data, for example in search for causative variants in rare Mendelian diseases, in point-and-click interface. The package includes homozygous region caller and allows to analyse whole human genomes in less than 30 minutes on a desktop computer. RareVariantVis disclosed novel causes of several rare monogenic disorders, including one with non-coding causative variant - keratolythic winter erythema.' -extra: - identifiers: - - biotools:rarevariantvis - - doi:10.1093/bioinformatics/btw359 - parent_recipe: - name: bioconductor-rarevariantvis - path: recipes/bioconductor-rarevariantvis - version: 2.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rarr/meta.yaml b/recipes/bioconductor-rarr/meta.yaml index 5f28e2f9eb0be..2c7642bc0ac97 100644 --- a/recipes/bioconductor-rarr/meta.yaml +++ b/recipes/bioconductor-rarr/meta.yaml @@ -1,27 +1,36 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "Rarr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The Zarr specification defines a format for chunked, compressed, N-dimensional arrays. It's design allows efficient access to subsets of the stored array, and supports both local and cloud storage systems. Rarr aims to implement this specifcation in R with minimal reliance on an external tools or libraries. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Read Zarr Files in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94af864ae3de3557840993a429944ea2 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rarr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, covr, knitr, tinytest, mockery # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 - r-base - r-httr - r-jsonlite @@ -30,25 +39,26 @@ requirements: - r-stringr - libblas - liblapack + - zlib run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 - r-base - r-httr - r-jsonlite - r-paws.storage - r-r.utils - r-stringr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: b8aaee77be85b5c1f1ef3e67321f9f64 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Read Zarr Files in R' - description: 'The Zarr specification defines a format for chunked, compressed, N-dimensional arrays. It''s design allows efficient access to subsets of the stored array, and supports both local and cloud storage systems. Rarr aims to implement this specifcation in R with minimal reliance on an external tools or libraries.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rat.db0/meta.yaml b/recipes/bioconductor-rat.db0/meta.yaml index 97008b6343456..7c9f57d6170e6 100644 --- a/recipes/bioconductor-rat.db0/meta.yaml +++ b/recipes/bioconductor-rat.db0/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "rat.db0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cde666f86ec7b61beb8cf1037511f977 +about: + description: Base annotation databases for rat, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Level Annotation databases for rat build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rat.db0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b183489f8247adea901952a51faea48e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Level Annotation databases for rat' - description: 'Base annotation databases for rat, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rat.db0/post-link.sh b/recipes/bioconductor-rat.db0/post-link.sh index b40a101d33dc3..7283f8d1378f7 100644 --- a/recipes/bioconductor-rat.db0/post-link.sh +++ b/recipes/bioconductor-rat.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rat.db0-3.18.0" +installBiocDataPackage.sh "rat.db0-3.20.0" diff --git a/recipes/bioconductor-rat2302.db/meta.yaml b/recipes/bioconductor-rat2302.db/meta.yaml index 2a342615aa394..c5e7afebf4b3f 100644 --- a/recipes/bioconductor-rat2302.db/meta.yaml +++ b/recipes/bioconductor-rat2302.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "rat2302.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b1404d8a16fec681f0fd682589a685ea +about: + description: Affymetrix Affymetrix Rat230_2 Array annotation data (chip rat2302) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Rat230_2 Array annotation data (chip rat2302) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rat2302.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b1404d8a16fec681f0fd682589a685ea + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Rat230_2 Array annotation data (chip rat2302)' - description: 'Affymetrix Affymetrix Rat230_2 Array annotation data (chip rat2302) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rat2302cdf/meta.yaml b/recipes/bioconductor-rat2302cdf/meta.yaml index 043a6a2d81dd8..4149da7ecfb34 100644 --- a/recipes/bioconductor-rat2302cdf/meta.yaml +++ b/recipes/bioconductor-rat2302cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rat2302cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a033730f79a11d45b4cd7e7c520f8052 +about: + description: A package containing an environment representing the Rat230_2.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: rat2302cdf build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rat2302cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a033730f79a11d45b4cd7e7c520f8052 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: rat2302cdf - description: 'A package containing an environment representing the Rat230_2.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rat2302frmavecs/meta.yaml b/recipes/bioconductor-rat2302frmavecs/meta.yaml index 5eb5dfee57f4f..99119178437a5 100644 --- a/recipes/bioconductor-rat2302frmavecs/meta.yaml +++ b/recipes/bioconductor-rat2302frmavecs/meta.yaml @@ -1,43 +1,43 @@ {% set version = "0.99.11" %} {% set name = "rat2302frmavecs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 44d9f00c2f3806899c6605d1ba274066 +about: + description: This package was created with the help of frmaTools version 1.24.0. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Vectors used by frma for microarrays of type rat2302rnentrezg build: - number: 11 + noarch: generic + number: 12 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rat2302frmavecs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-frma >=1.54.0,<1.55.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-frma >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-frma >=1.54.0,<1.55.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-frma >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 44d9f00c2f3806899c6605d1ba274066 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Vectors used by frma for microarrays of type rat2302rnentrezg' - description: 'This package was created with the help of frmaTools version 1.24.0.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rat2302probe/meta.yaml b/recipes/bioconductor-rat2302probe/meta.yaml index e2c76e6e9f797..0b8473802c6c7 100644 --- a/recipes/bioconductor-rat2302probe/meta.yaml +++ b/recipes/bioconductor-rat2302probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rat2302probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d1d9215e52b9e845cc4d7c902536e0d6 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Rat230\_2\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type rat2302 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rat2302probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d1d9215e52b9e845cc4d7c902536e0d6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type rat2302' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Rat230\_2\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ratchrloc/meta.yaml b/recipes/bioconductor-ratchrloc/meta.yaml index d3fe6a6509e9a..808b281449179 100644 --- a/recipes/bioconductor-ratchrloc/meta.yaml +++ b/recipes/bioconductor-ratchrloc/meta.yaml @@ -1,37 +1,37 @@ {% set version = "2.1.6" %} {% set name = "ratCHRLOC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6fecff4821a5a47e3bd38a2ff78173d5 +about: + description: Annotation data file for ratCHRLOC assembled using data from public data repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: The Artistic License, Version 2.0 + summary: A data package containing annotation data for ratCHRLOC build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ratchrloc", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6fecff4821a5a47e3bd38a2ff78173d5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'The Artistic License, Version 2.0' - summary: 'A data package containing annotation data for ratCHRLOC' - description: 'Annotation data file for ratCHRLOC assembled using data from public data repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rattoxfxcdf/meta.yaml b/recipes/bioconductor-rattoxfxcdf/meta.yaml index 73dd35e04127f..953c73f627f03 100644 --- a/recipes/bioconductor-rattoxfxcdf/meta.yaml +++ b/recipes/bioconductor-rattoxfxcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rattoxfxcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 912d0fa424615fcd92773ed174d5efdd +about: + description: A package containing an environment representing the RatToxFX.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: rattoxfxcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rattoxfxcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 912d0fa424615fcd92773ed174d5efdd + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: rattoxfxcdf - description: 'A package containing an environment representing the RatToxFX.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rattoxfxprobe/meta.yaml b/recipes/bioconductor-rattoxfxprobe/meta.yaml index f32aeb6966e55..aad28a6ad72f0 100644 --- a/recipes/bioconductor-rattoxfxprobe/meta.yaml +++ b/recipes/bioconductor-rattoxfxprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rattoxfxprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 202791c72e8c956b9854fa4d9ba67a24 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RatToxFX\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type rattoxfx build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rattoxfxprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 202791c72e8c956b9854fa4d9ba67a24 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type rattoxfx' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RatToxFX\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rattus.norvegicus/build_failure.linux-64.yaml b/recipes/bioconductor-rattus.norvegicus/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..6f82aad463bd1 --- /dev/null +++ b/recipes/bioconductor-rattus.norvegicus/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: e9beb74f9585c52a3f4df2908b1d5a552c378b3ebcf7febcb3ade4de5ba0637e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-annotationdbi[version='>=1.52.0,<1.53.0']"), MatchSpec("bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene==3.12.0=r40_0")} + Encountered problems while solving: + - package bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene-3.12.0-r40_0 requires bioconductor-annotationdbi >=1.52.0,<1.53.0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-annotationdbi >=1.68.0,<1.69.0 [0m is requested and can be installed; + [31mbioconductor-txdb.rnorvegicus.ucsc.rn5.refgene >=3.12.0,<3.13.0 [0m is not installable because there are no viable options + [31mbioconductor-txdb.rnorvegicus.ucsc.rn5.refgene 3.12.0[0m would require + [31mbioconductor-annotationdbi >=1.52.0,<1.53.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.rnorvegicus.ucsc.rn5.refgene 3.12.0[0m would require + [31mbioconductor-annotationdbi >=1.54.0,<1.55.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.rnorvegicus.ucsc.rn5.refgene 3.12.0[0m would require + [31mbioconductor-annotationdbi >=1.56.0,<1.57.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.rnorvegicus.ucsc.rn5.refgene 3.12.0[0m would require + [31mbioconductor-annotationdbi >=1.60.0,<1.61.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.rnorvegicus.ucsc.rn5.refgene 3.12.0[0m would require + [31mbioconductor-annotationdbi >=1.62.0,<1.63.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.rnorvegicus.ucsc.rn5.refgene 3.12.0[0m would require + [31mbioconductor-annotationdbi >=1.64.0,<1.65.0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-annotationdbi[version='>=1.52.0,<1.53.0']"), MatchSpec("bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene==3.12.0=r40_0")} + Encountered problems while solving: + - package bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene-3.12.0-r40_0 requires bioconductor-annotationdbi >=1.52.0,<1.53.0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-annotationdbi >=1.68.0,<1.69.0 [0m is requested and can be installed; + [31mbioconductor-txdb.rnorvegicus.ucsc.rn5.refgene >=3.12.0,<3.13.0 [0m is not installable because there are no viable options + [31mbioconductor-txdb.rnorvegicus.ucsc.rn5.refgene 3.12.0[0m would require + [31mbioconductor-annotationdbi >=1.52.0,<1.53.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.rnorvegicus.ucsc.rn5.refgene 3.12.0[0m would require + [31mbioconductor-annotationdbi >=1.54.0,<1.55.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.rnorvegicus.ucsc.rn5.refgene 3.12.0[0m would require + [31mbioconductor-annotationdbi >=1.56.0,<1.57.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.rnorvegicus.ucsc.rn5.refgene 3.12.0[0m would require + [31mbioconductor-annotationdbi >=1.60.0,<1.61.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.rnorvegicus.ucsc.rn5.refgene 3.12.0[0m would require + [31mbioconductor-annotationdbi >=1.62.0,<1.63.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-txdb.rnorvegicus.ucsc.rn5.refgene 3.12.0[0m would require + [31mbioconductor-annotationdbi >=1.64.0,<1.65.0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-rattus.norvegicus/meta.yaml b/recipes/bioconductor-rattus.norvegicus/meta.yaml index 3d57f0f02545d..904e6fef53a2e 100644 --- a/recipes/bioconductor-rattus.norvegicus/meta.yaml +++ b/recipes/bioconductor-rattus.norvegicus/meta.yaml @@ -1,49 +1,54 @@ {% set version = "1.3.1" %} {% set name = "Rattus.norvegicus" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Contains the Rattus.norvegicus object to access data from several related annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for the Rattus.norvegicus object -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5692fdeb0bc7f94e1db35f097cad99a9 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rattus.norvegicus", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - - 'bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene >=3.12.0,<3.13.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 + - bioconductor-organismdbi >=1.48.0,<1.49.0 + - bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene >=3.12.0,<3.13.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - - 'bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene >=3.12.0,<3.13.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 + - bioconductor-organismdbi >=1.48.0,<1.49.0 + - bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene >=3.12.0,<3.13.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 5692fdeb0bc7f94e1db35f097cad99a9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for the Rattus.norvegicus object' - description: 'Contains the Rattus.norvegicus object to access data from several related annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rawdiag/build.sh b/recipes/bioconductor-rawdiag/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rawdiag/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rawdiag/build_failure.linux-64.yaml b/recipes/bioconductor-rawdiag/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..97d80cb3b8855 --- /dev/null +++ b/recipes/bioconductor-rawdiag/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: 63ae8e6abc83b9781ace7583b9c022b892d34f08f4f48c4326864ee0fe2bf363 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rawrr[version='>=1.14.0,<1.15.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rawrr >=1.14.0,<1.15.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rawrr >=1.14.0,<1.15.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rawrr[version='>=1.14.0,<1.15.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rawrr >=1.14.0,<1.15.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rawrr >=1.14.0,<1.15.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rawrr[version='>=1.14.0,<1.15.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rawrr >=1.14.0,<1.15.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rawrr >=1.14.0,<1.15.0 [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. +reason: |- + needs bioconductor-rawrr to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-rawdiag/build_failure.osx-64.yaml b/recipes/bioconductor-rawdiag/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..a455cc2d57642 --- /dev/null +++ b/recipes/bioconductor-rawdiag/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 63ae8e6abc83b9781ace7583b9c022b892d34f08f4f48c4326864ee0fe2bf363 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + needs bioconductor-rawrr to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-rawdiag/meta.yaml b/recipes/bioconductor-rawdiag/meta.yaml new file mode 100644 index 0000000000000..f8030e3b85b51 --- /dev/null +++ b/recipes/bioconductor-rawdiag/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.2.0" %} +{% set name = "rawDiag" %} +{% set bioc = "3.20" %} + +about: + description: Optimizing methods for liquid chromatography coupled to mass spectrometry (LC-MS) poses a nontrivial challenge. The rawDiag package facilitates rational method optimization by generating MS operator-tailored diagnostic plots of scan-level metadata. The package is designed for use on the R shell or as a Shiny application on the Orbitrap instrument PC. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rawdiag", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle (>= 2.28), ExperimentHub, tartare, knitr, testthat +# SystemRequirements: mono 4.x or higher on OSX / Linux, .NET 4.x or higher on Windows, 'msbuild' and 'nuget' available in the path +requirements: + host: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-rawrr >=1.14.0,<1.15.0 + - r-base + - r-biocmanager + - r-dplyr + - r-ggplot2 >=3.4 + - r-hexbin + - r-htmltools + - r-reshape2 + - r-rlang + - r-scales + - r-shiny >=1.5 + run: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-rawrr >=1.14.0,<1.15.0 + - r-base + - r-biocmanager + - r-dplyr + - r-ggplot2 >=3.4 + - r-hexbin + - r-htmltools + - r-reshape2 + - r-rlang + - r-scales + - r-shiny >=1.5 + +source: + md5: 115692133b84a768ea91a43cac8abced + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-rawrr/build_failure.linux-64.yaml b/recipes/bioconductor-rawrr/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..2138008b3dfcd --- /dev/null +++ b/recipes/bioconductor-rawrr/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: a0d9a572039d03b50fba7af6e2bf47f501a5adbd49425536ef25524fa4349c36 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - xorg-libsm 1.2.5 he73a12e_0 + - xorg-libx11 1.8.10 h4f16b4b_1 + - xz 5.6.3 hbcc6ac9_1 + - zstd 1.5.6 ha6fb4c9_0 + - fontconfig 2.15.0 h7e30c49_1 + - gfortran_impl_linux-64 14.2.0 hc73f493_1 + - gxx_impl_linux-64 14.2.0 h2c03514_1 + - krb5 1.21.3 h659f571_0 + - libblas 3.9.0 25_linux64_openblas + - libglib 2.82.2 h2ff4ddf_0 + - libtiff 4.7.0 hc4654cb_2 + - xorg-libxext 1.3.6 hb9d3cd8_0 + - xorg-libxrender 0.9.12 hb9d3cd8_0 + - xorg-libxt 1.3.1 hb9d3cd8_0 + - cairo 1.18.2 h3394656_1 + - libcblas 3.9.0 25_linux64_openblas + - libcurl 8.11.1 h332b0f4_0 + - liblapack 3.9.0 25_linux64_openblas + - curl 8.11.1 h332b0f4_0 + - gsl 2.7 he838d99_0 + - harfbuzz 9.0.0 hda332d3_1 + - pango 1.54.0 h3a902e7_3 + - r-base 4.4.2 h64c9cd0_0 + run: + - r-base >=4.4,<4.5.0a0 + - r-base >=4.4,<4.5.0a0 + test: + commands: + - $R -e "library('rawrr')" + about: + description: This package wraps the functionality of the RawFileReader .NET assembly. + Within the R environment, spectra and chromatograms are represented by S3 objects. + The package provides basic functions to download and install the required third-party + libraries. The package is developed, tested, and used at the Functional Genomics + Center Zurich, Switzerland. + home: https://bioconductor.org/packages/3.20/bioc/html/rawrr.html + license: GPL-3 + license_file: /opt/conda/conda-bld/bioconductor-rawrr_1734295013414/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/R/share/licenses/GPL-3 + summary: Direct Access to Orbitrap Data and Beyond + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/conda/conda-bld/bioconductor-rawrr_1734295013414/work + export PREFIX=/opt/conda/conda-bld/bioconductor-rawrr_1734295013414/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-rawrr_1734295013414/_build_env + export SRC_DIR=/opt/conda/conda-bld/bioconductor-rawrr_1734295013414/work + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-rawrr_1734295013414/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/R/library + * installing *source* package rawrr ... + ** using staged installation + ** R + ** inst + ** byte-compile and prepare package for lazy loading + During startup - Warning message: + Setting LC_TIME failed, using "C" + ** help + *** installing help indices + ** building package indices + During startup - Warning message: + Setting LC_TIME failed, using "C" + ** installing vignettes + ** testing if installed package can be loaded from temporary location + During startup - Warning message: + Setting LC_TIME failed, using "C" + Error: package or namespace load failed for rawrr: + .onLoad failed in loadNamespace() for 'rawrr', details: + call: fun(libname, pkgname) + error: The cross platform, open source .NET framework (mono) is not available. + Consider to install 'apt-get install mono-runtime libmono-system-data4.0-cil -y' on Linux + ERROR: loading failed + or download/install from https://www.mono-project.com/. + Error: loading failed + Execution halted + * removing /opt/conda/conda-bld/bioconductor-rawrr_1734295013414/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/R/library/rawrr + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-rawrr_1734295013414/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-rawrr_1734295013414/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +reason: |- + needs mono +category: |- + dependency issue diff --git a/recipes/bioconductor-rawrr/build_failure.osx-64.yaml b/recipes/bioconductor-rawrr/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..fcbb9ee51e7f6 --- /dev/null +++ b/recipes/bioconductor-rawrr/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: a0d9a572039d03b50fba7af6e2bf47f501a5adbd49425536ef25524fa4349c36 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + needs mono +category: |- + dependency issue diff --git a/recipes/bioconductor-rawrr/meta.yaml b/recipes/bioconductor-rawrr/meta.yaml index 08f497e744570..1f84836e6d692 100644 --- a/recipes/bioconductor-rawrr/meta.yaml +++ b/recipes/bioconductor-rawrr/meta.yaml @@ -1,40 +1,38 @@ -{% set version = "1.10.2" %} +{% set version = "1.14.0" %} {% set name = "rawrr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 42213a8a733115af719162fc1a72d6a1 +about: + description: This package wraps the functionality of the RawFileReader .NET assembly. Within the R environment, spectra and chromatograms are represented by S3 objects. The package provides basic functions to download and install the required third-party libraries. The package is developed, tested, and used at the Functional Genomics Center Zurich, Switzerland. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Direct Access to Orbitrap Data and Beyond build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rawrr", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle (>= 2.5), ExperimentHub, knitr, protViz (>= 0.7), rmarkdown, tartare (>= 1.5), testthat # SystemRequirements: mono-runtime 4.x or higher (including System.Data library) on Linux/macOS, .Net Framework (>= 4.5.1) on Microsoft Windows. requirements: host: - r-base - - mono >=4.5.1 run: - r-base - - mono >=4.5.1 +source: + md5: 55a9376088cb6b3fe2a698aef0000063 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Direct Access to Orbitrap Data and Beyond' - description: 'This package wraps the functionality of the RawFileReader .NET assembly. Within the R environment, spectra and chromatograms are represented by S3 objects. The package provides basic functions to download and install the required third-party libraries. The package is developed, tested, and used at the Functional Genomics Center Zurich, Switzerland.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rbcbook1/meta.yaml b/recipes/bioconductor-rbcbook1/meta.yaml index 59907071a6fca..7dcba6d87e20f 100644 --- a/recipes/bioconductor-rbcbook1/meta.yaml +++ b/recipes/bioconductor-rbcbook1/meta.yaml @@ -1,49 +1,55 @@ -{% set version = "1.70.0" %} +{% set version = "1.74.0" %} {% set name = "RbcBook1" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: tools for building book + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Support for Springer monograph on Bioconductor -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 16f681613c1c4d309b032c64cfe18c4a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rbcbook1", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rbcbook1 + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rbcbook1 + path: recipes/bioconductor-rbcbook1 + version: 1.48.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-rpart run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-rpart + +source: + md5: 7753fb21d64b213fbae45060fb88b2bc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Support for Springer monograph on Bioconductor' - description: 'tools for building book' -extra: - identifiers: - - biotools:rbcbook1 - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-rbcbook1 - path: recipes/bioconductor-rbcbook1 - version: 1.48.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rbec/meta.yaml b/recipes/bioconductor-rbec/meta.yaml index 92930222940ff..ed52b005a0796 100644 --- a/recipes/bioconductor-rbec/meta.yaml +++ b/recipes/bioconductor-rbec/meta.yaml @@ -1,54 +1,59 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "Rbec" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Rbec is a adapted version of DADA2 for analyzing amplicon sequencing data from synthetic communities (SynComs), where the reference sequences for each strain exists. Rbec can not only accurately profile the microbial compositions in SynComs, but also predict the contaminants in SynCom samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: 'Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f295d8ade5faf2c0b770f2b075262116 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rbec", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-dada2 >=1.30.0,<1.31.0' + - bioconductor-dada2 >=1.34.0,<1.35.0 - r-base - r-doparallel - r-foreach - r-ggplot2 - - 'r-rcpp >=1.0.6' + - r-rcpp >=1.0.6 - r-readr - libblas - liblapack run: - - 'bioconductor-dada2 >=1.30.0,<1.31.0' + - bioconductor-dada2 >=1.34.0,<1.35.0 - r-base - r-doparallel - r-foreach - r-ggplot2 - - 'r-rcpp >=1.0.6' + - r-rcpp >=1.0.6 - r-readr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: b1d464bf92f81348c020054540cfe603 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities' - description: 'Rbec is a adapted version of DADA2 for analyzing amplicon sequencing data from synthetic communities (SynComs), where the reference sequences for each strain exists. Rbec can not only accurately profile the microbial compositions in SynComs, but also predict the contaminants in SynCom samples.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rbgl/meta.yaml b/recipes/bioconductor-rbgl/meta.yaml index 6dea29c5ac9ad..cb3eec93e1bad 100644 --- a/recipes/bioconductor-rbgl/meta.yaml +++ b/recipes/bioconductor-rbgl/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.78.0" %} +{% set version = "1.82.0" %} {% set name = "RBGL" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: An interface to the BOOST graph library -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a18b5ad5c49f058b6f65a2bd0a4274d1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rbgl", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:rbgl + - doi:10.1093/bioinformatics/bth458 + parent_recipe: + name: bioconductor-rbgl + path: recipes/bioconductor-rbgl + version: 1.56.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Rgraphviz, XML, RUnit, BiocGenerics, BiocStyle, knitr requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-bh - libblas - liblapack run: - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-bh - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 3c15ded2511af5c004e3e541d1a243f8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'An interface to the BOOST graph library' - description: 'A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:rbgl - - doi:10.1093/bioinformatics/bth458 - parent_recipe: - name: bioconductor-rbgl - path: recipes/bioconductor-rbgl - version: 1.56.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rbioformats/meta.yaml b/recipes/bioconductor-rbioformats/meta.yaml index 0b180c33b55f5..8fd396c652f82 100644 --- a/recipes/bioconductor-rbioformats/meta.yaml +++ b/recipes/bioconductor-rbioformats/meta.yaml @@ -1,46 +1,46 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "RBioFormats" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd83827dd164a9b44ba3d0d08fd77b38 +about: + description: An R package which interfaces the OME Bio-Formats Java library to allow reading of proprietary microscopy image data and metadata. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: R interface to Bio-Formats build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rbioformats", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, testthat, xml2 # SystemRequirements: Java (>= 1.7) requirements: host: - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-rjava >=0.9-6' + - r-rjava >=0.9-6 - openjdk run: - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-rjava >=0.9-6' + - r-rjava >=0.9-6 - openjdk +source: + md5: a376f226e64307c3b02230b87f0270f2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'R interface to Bio-Formats' - description: 'An R package which interfaces the OME Bio-Formats Java library to allow reading of proprietary microscopy image data and metadata.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rbioinf/meta.yaml b/recipes/bioconductor-rbioinf/meta.yaml index 9cf94f1be6a6b..ca762401cf06e 100644 --- a/recipes/bioconductor-rbioinf/meta.yaml +++ b/recipes/bioconductor-rbioinf/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.62.0" %} +{% set version = "1.66.0" %} {% set name = "RBioinf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions and datasets and examples to accompany the monograph R For Bioinformatics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: RBioinf -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec036823fe8f50106f37436eec716add build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rbioinf", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:rbioinf + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rbioinf + path: recipes/bioconductor-rbioinf + version: 1.40.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Rgraphviz requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - libblas - liblapack run: - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: 303fc235421e997fcfcaa5f4615bc90e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: RBioinf - description: 'Functions and datasets and examples to accompany the monograph R For Bioinformatics.' -extra: - identifiers: - - biotools:rbioinf - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-rbioinf - path: recipes/bioconductor-rbioinf - version: 1.40.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rbiopaxparser/meta.yaml b/recipes/bioconductor-rbiopaxparser/meta.yaml index b48a0a08c3e8a..99d234c77ae4d 100644 --- a/recipes/bioconductor-rbiopaxparser/meta.yaml +++ b/recipes/bioconductor-rbiopaxparser/meta.yaml @@ -1,24 +1,34 @@ -{% set version = "2.42.0" %} +{% set version = "2.46.0" %} {% set name = "rBiopaxParser" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Parses BioPax files and represents them in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 53e24a8896bf17bd56fe48d62427eb33 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rbiopaxparser", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rbiopaxparser + parent_recipe: + name: bioconductor-rbiopaxparser + path: recipes/bioconductor-rbiopaxparser + version: 2.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Rgraphviz, RCurl, graph, RUnit, BiocGenerics, RBGL, igraph requirements: host: @@ -29,20 +39,16 @@ requirements: - r-base - r-data.table - r-xml + +source: + md5: 8d29fadf37c6f8a0d5dbdd683db3e540 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Parses BioPax files and represents them in R' - description: 'Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:rbiopaxparser - parent_recipe: - name: bioconductor-rbiopaxparser - path: recipes/bioconductor-rbiopaxparser - version: 2.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rblast/build.sh b/recipes/bioconductor-rblast/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rblast/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rblast/meta.yaml b/recipes/bioconductor-rblast/meta.yaml new file mode 100644 index 0000000000000..5e95640ce71ff --- /dev/null +++ b/recipes/bioconductor-rblast/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.2.0" %} +{% set name = "rBLAST" %} +{% set bioc = "3.20" %} + +about: + description: Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: R Interface for the Basic Local Alignment Search Tool +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rblast", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: knitr, rmarkdown, testthat +# SystemRequirements: ncbi-blast+ +requirements: + host: + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - r-base + run: + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - r-base +source: + md5: bb818a89758192a34847b9f3c8071dde + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-rbm/meta.yaml b/recipes/bioconductor-rbm/meta.yaml index 216f62b73d664..ffe0b0667e253 100644 --- a/recipes/bioconductor-rbm/meta.yaml +++ b/recipes/bioconductor-rbm/meta.yaml @@ -1,42 +1,22 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "RBM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Use A Resampling-Based Empirical Bayes Approach to Assess Differential Expression in Two-Color Microarrays and RNA-Seq data sets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'RBM: a R package for microarray and RNA-Seq data analysis' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ae63966d6e9cfd1d3ce001f65a02abe build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rbm", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' - - r-base - run: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'RBM: a R package for microarray and RNA-Seq data analysis' - description: 'Use A Resampling-Based Empirical Bayes Approach to Assess Differential Expression in Two-Color Microarrays and RNA-Seq data sets.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:rbm @@ -46,3 +26,29 @@ extra: path: recipes/bioconductor-rbm version: 1.12.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-marray >=1.84.0,<1.85.0 + - r-base + run: + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-marray >=1.84.0,<1.85.0 + - r-base + +source: + md5: a1ce0bc981d4211829735494f172053e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-rbowtie/meta.yaml b/recipes/bioconductor-rbowtie/meta.yaml index 9263ed9e3b853..62d5188775a3b 100644 --- a/recipes/bioconductor-rbowtie/meta.yaml +++ b/recipes/bioconductor-rbowtie/meta.yaml @@ -1,51 +1,58 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "Rbowtie" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 | file LICENSE + license_file: LICENSE + summary: R bowtie wrapper -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 409fc50371b1eaf9be2af500aff05249 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rbowtie", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:rbowtie + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rbowtie + path: recipes/bioconductor-rbowtie + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, parallel, BiocStyle, knitr, rmarkdown # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - libblas - liblapack + - zlib run: - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: ec35e70cc07cf7e6756c4598af50f07d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Artistic-2.0 | file LICENSE' - summary: 'R bowtie wrapper' - description: 'This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.' - license_file: LICENSE -extra: - identifiers: - - biotools:rbowtie - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-rbowtie - path: recipes/bioconductor-rbowtie - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rbowtie2/build.sh b/recipes/bioconductor-rbowtie2/build.sh index e189fe0b69e5e..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rbowtie2/build.sh +++ b/recipes/bioconductor-rbowtie2/build.sh @@ -4,8 +4,8 @@ grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION mkdir -p ~/.R echo -e "CC=$CC FC=$FC -CXX=$CXX -I${PREFIX}/include -L${PREFIX}/lib +CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars -$R CMD INSTALL --build . +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rbowtie2/build_failure.linux-64.yaml b/recipes/bioconductor-rbowtie2/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..7402944f7d394 --- /dev/null +++ b/recipes/bioconductor-rbowtie2/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: 345eb4d8d9be90c4a86f7f5e0fafef5ef8744fbcdd5d451a5ba6e88bfe161be9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + export SRC_DIR=/opt/conda/conda-bld/bioconductor-rbowtie2_1735682658357/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-rbowtie2_1735682658357/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library + * installing *source* package Rbowtie2 ... + ** package Rbowtie2 successfully unpacked and MD5 sums checked + ** using staged installation + ** libs + mkdir -p ../inst + (cd adapterremoval && (make CXX="$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11" -f Makefile)) + make[1]: Entering directory '$SRC_DIR/src/adapterremoval' + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -O3 -pthread -DNDEBUG -c adapterset.cc + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -O3 -pthread -DNDEBUG -c alignment.cc + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -O3 -pthread -DNDEBUG -c argparse.cc + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -O3 -pthread -DNDEBUG -c debug.cc + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -O3 -pthread -DNDEBUG -c demultiplex.cc + In file included from demultiplex.h:31, + from demultiplex.cc:29: + fastq_io.h:30:10: fatal error: zlib.h: No such file or directory + 30 | #include + | ^~~~~~~~ + compilation terminated. + make[1]: *** [Makefile:46: demultiplex.o] Error 1 + make[1]: Leaving directory '$SRC_DIR/src/adapterremoval' + make: *** [Makefile:10: all] Error 2 + ERROR: compilation failed for package Rbowtie2 + * removing /opt/conda/conda-bld/bioconductor-rbowtie2_1735682658357/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/Rbowtie2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-rbowtie2_1735682658357/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-rbowtie2_1735682658357/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +reason: |- + zlib is somehow still being searched for in main system lib +category: |- + compiler error diff --git a/recipes/bioconductor-rbowtie2/build_failure.linux-aarch64.yaml b/recipes/bioconductor-rbowtie2/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..ec4e163460047 --- /dev/null +++ b/recipes/bioconductor-rbowtie2/build_failure.linux-aarch64.yaml @@ -0,0 +1,108 @@ +recipe_sha: 345eb4d8d9be90c4a86f7f5e0fafef5ef8744fbcdd5d451a5ba6e88bfe161be9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + export SRC_DIR=/opt/conda/conda-bld/bioconductor-rbowtie2_1736171538421/work + INFO: activate-binutils_linux-aarch64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strip + INFO: activate-gcc_linux-aarch64.sh made the following environmental changes: + BUILD=aarch64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc + CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=aarch64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=aarch64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib + HOST=aarch64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_aarch64_conda_cos7_linux_gnu + build_alias=aarch64-conda-linux-gnu + host_alias=aarch64-conda-linux-gnu + -BUILD=aarch64-conda_cos7-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-aarch64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-g + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-rbowtie2_1736171538421/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library + * installing *source* package Rbowtie2 ... + ** package Rbowtie2 successfully unpacked and MD5 sums checked + ** using staged installation + ** libs + mkdir -p ../inst + (cd adapterremoval && (make CXX="$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -std=gnu11" -f Makefile)) + make[1]: Entering directory '$SRC_DIR/src/adapterremoval' + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -std=gnu11 -O3 -pthread -DNDEBUG -c adapterset.cc + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -std=gnu11 -O3 -pthread -DNDEBUG -c alignment.cc + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -std=gnu11 -O3 -pthread -DNDEBUG -c argparse.cc + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -std=gnu11 -O3 -pthread -DNDEBUG -c debug.cc + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -std=gnu11 -O3 -pthread -DNDEBUG -c demultiplex.cc + In file included from demultiplex.h:31, + from demultiplex.cc:29: + fastq_io.h:30:10: fatal error: zlib.h: No such file or directory + 30 | #include + | ^~~~~~~~ + compilation terminated. + make[1]: *** [Makefile:46: demultiplex.o] Error 1 + make[1]: Leaving directory '$SRC_DIR/src/adapterremoval' + make: *** [Makefile:10: all] Error 2 + ERROR: compilation failed for package Rbowtie2 + * removing /opt/conda/conda-bld/bioconductor-rbowtie2_1736171538421/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/Rbowtie2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-rbowtie2_1736171538421/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-rbowtie2_1736171538421/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +reason: |- + zlib is somehow still being searched for in main system lib +category: |- + compiler error diff --git a/recipes/bioconductor-rbowtie2/build_failure.osx-64.yaml b/recipes/bioconductor-rbowtie2/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c63c7c3559076 --- /dev/null +++ b/recipes/bioconductor-rbowtie2/build_failure.osx-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: 345eb4d8d9be90c4a86f7f5e0fafef5ef8744fbcdd5d451a5ba6e88bfe161be9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + additional-platforms: + - linux-aarch64 + copy_test_source_files: true + final: true + identifiers: + - biotools:rbowtie2 + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rbowtie2_1735583266928/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rbowtie2_1735583266928/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rbowtie2_1735583266928/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rbowtie2_1735583266928/work + INFO: activate-gfortran_osx-64.sh made the following environmental changes: + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rbowtie2-2.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + mkdir -p ../inst + (cd adapterremoval && (make CXX="g -std=gnu11" -f Makefile)) + make[1]: Entering directory '$SRC_DIR/src/adapterremoval' + g -std=gnu11 -O3 -pthread -DNDEBUG -c adapterset.cc + make[1]: Leaving directory '$SRC_DIR/src/adapterremoval' +# Last 100 lines of the build log. +reason: |- + zlib is somehow still being searched for in main system lib +category: |- + compiler error diff --git a/recipes/bioconductor-rbowtie2/meta.yaml b/recipes/bioconductor-rbowtie2/meta.yaml index 37affc8af1f48..dcafda641582d 100644 --- a/recipes/bioconductor-rbowtie2/meta.yaml +++ b/recipes/bioconductor-rbowtie2/meta.yaml @@ -1,52 +1,59 @@ -{% set version = "2.8.0" %} +{% set version = "2.12.0" %} {% set name = "Rbowtie2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides an R wrapper of the popular bowtie2 sequencing reads aligner and AdapterRemoval, a convenient tool for rapid adapter trimming, identification, and read merging. The package contains wrapper functions that allow for genome indexing and alignment to those indexes. The package also allows for the creation of .bam files via Rsamtools. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: An R Wrapper for Bowtie2 and AdapterRemoval -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dbba503f3134fdb9c6521c060ec2d5fc build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rbowtie2", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:rbowtie2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat (>= 3.0.0), rmarkdown # SystemRequirements: C++11, GNU make, samtools requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-magrittr - libblas - liblapack + - zlib run: - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-magrittr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 8f768a243738cb290ab05e0699b70d80 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3.0-or-later' - summary: 'An R Wrapper for Bowtie2 and AdapterRemoval' - description: 'This package provides an R wrapper of the popular bowtie2 sequencing reads aligner and AdapterRemoval, a convenient tool for rapid adapter trimming, identification, and read merging. The package contains wrapper functions that allow for genome indexing and alignment to those indexes. The package also allows for the creation of .bam files via Rsamtools.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-rbsurv/meta.yaml b/recipes/bioconductor-rbsurv/meta.yaml index 399aaa8374e09..723b8270275c1 100644 --- a/recipes/bioconductor-rbsurv/meta.yaml +++ b/recipes/bioconductor-rbsurv/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "2.60.0" %} +{% set version = "2.64.0" %} {% set name = "rbsurv" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package selects genes associated with survival. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Robust likelihood-based survival modeling with microarray data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e2791c7a40004e031fd88e0995f4dc13 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rbsurv", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rbsurv + - doi:10.18637/jss.v029.i01 + parent_recipe: + name: bioconductor-rbsurv + path: recipes/bioconductor-rbsurv + version: 2.38.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-survival run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-survival + +source: + md5: c5c1b0485d5f9b2ea2053c30dcc709ee + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Robust likelihood-based survival modeling with microarray data' - description: 'This package selects genes associated with survival.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:rbsurv - - doi:10.18637/jss.v029.i01 - parent_recipe: - name: bioconductor-rbsurv - path: recipes/bioconductor-rbsurv - version: 2.38.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rbwa/build.sh b/recipes/bioconductor-rbwa/build.sh index 578c85ee502d7..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rbwa/build.sh +++ b/recipes/bioconductor-rbwa/build.sh @@ -2,9 +2,9 @@ mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION mkdir -p ~/.R -echo -e "CC=$CC -I${PREFIX}/include -L${PREFIX}/lib +echo -e "CC=$CC FC=$FC -CXX=$CXX -I${PREFIX}/include -L${PREFIX}/lib +CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars diff --git a/recipes/bioconductor-rbwa/build_failure.linux-64.yaml b/recipes/bioconductor-rbwa/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..9b6c651fbfd92 --- /dev/null +++ b/recipes/bioconductor-rbwa/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: dbc816f95c68f94afff89dad399dfa8e8f1a5b55d6ae403e695ff0fe99d65ef7 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + rope.c: In function 'rope_restore_node': + rope.c:282:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 282 | fread(&is_bottom, 1, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ + rope.c:283:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 283 | fread(&n, 2, 1, fp); + | ^~~~~~~~~~~~~~~~~~~ + rope.c:291:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 291 | fread(p[i].c, 8, 6, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~ + rope.c:292:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 292 | fread(q, 2, 1, fp); + | ^~~~~~~~~~~~~~~~~~ + rope.c:293:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 293 | fread(q 1, 1, *q, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~ + rope.c: In function 'rope_restore': + rope.c:312:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 312 | fread(&r->max_nodes, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + rope.c:313:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 313 | fread(&r->block_len, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c rle.c -o rle.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c is.c -o is.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwtindex.c -o bwtindex.o + ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwashm.c -o bwashm.o + bwashm.c: In function 'bwa_shm_stage': + bwashm.c:29:9: warning: ignoring return value of 'ftruncate' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | ftruncate(shmid, BWA_CTL_SIZE); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + bwashm.c:66:9: warning: ignoring return value of 'ftruncate' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | ftruncate(shmid, idx->l_mem); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwase.c -o bwase.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwaseqio.c -o bwaseqio.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwtgap.c -o bwtgap.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwtaln.c -o bwtaln.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bamlite.c -o bamlite.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwape.c -o bwape.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c kopen.c -o kopen.o + In file included from /opt/conda/conda-bld/bioconductor-rbwa_1735486699456/_build_env/x86_64-conda-linux-gnu/sysroot/usr/include/string.h:638, + from kopen.c:6: + In function 'strncpy', + inlined from 'cmd2argv' at kopen.c:248:2, + inlined from 'kopen' at kopen.c:306:13: + /opt/conda/conda-bld/bioconductor-rbwa_1735486699456/_build_env/x86_64-conda-linux-gnu/sysroot/usr/include/bits/string3.h:120:10: warning: '__builtin_strncpy' specified bound between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] + 120 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + In function 'cmd2argv', + inlined from 'kopen' at kopen.c:306:13: + kopen.c:247:32: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] + 247 | argv[0] = str = (char*)calloc(end - beg 1, 1); + | ^~~~~~~~~~~~~~~~~~~~~~~~ + In file included from /opt/conda/conda-bld/bioconductor-rbwa_1735486699456/_build_env/x86_64-conda-linux-gnu/sysroot/usr/include/bits/string2.h:1296, + from /opt/conda/conda-bld/bioconductor-rbwa_1735486699456/_build_env/x86_64-conda-linux-gnu/sysroot/usr/include/string.h:633: + /opt/conda/conda-bld/bioconductor-rbwa_1735486699456/_build_env/x86_64-conda-linux-gnu/sysroot/usr/include/stdlib.h: In function 'kopen': + /opt/conda/conda-bld/bioconductor-rbwa_1735486699456/_build_env/x86_64-conda-linux-gnu/sysroot/usr/include/stdlib.h:467:14: note: in a call to allocation function 'calloc' declared here + 467 | extern void *calloc (size_t __nmemb, size_t __size) + | ^~~~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c pemerge.c -o pemerge.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c maxk.c -o maxk.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwtsw2_core.c -o bwtsw2_core.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwtsw2_main.c -o bwtsw2_main.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwtsw2_aux.c -o bwtsw2_aux.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwt_lite.c -o bwt_lite.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwtsw2_chain.c -o bwtsw2_chain.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c fastmap.c -o fastmap.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwtsw2_pair.c -o bwtsw2_pair.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c main.c -o main.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt + /opt/conda/conda-bld/bioconductor-rbwa_1735486699456/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lz: No such file or directory + collect2: error: ld returned 1 exit status + make: *** [Makefile:45: bwa] Error 1 + ERROR: compilation failed for package Rbwa + * removing /opt/conda/conda-bld/bioconductor-rbwa_1735486699456/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/R/library/Rbwa + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-rbwa_1735486699456/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-rbwa_1735486699456/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +reason: |- + seems to be using system libraries, and zlib is not installed on system. +category: |- + compiler error diff --git a/recipes/bioconductor-rbwa/meta.yaml b/recipes/bioconductor-rbwa/meta.yaml index b777c8844fbd4..69533ba86821e 100644 --- a/recipes/bioconductor-rbwa/meta.yaml +++ b/recipes/bioconductor-rbwa/meta.yaml @@ -1,26 +1,28 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "Rbwa" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 036e0acc237e1249e5509df62d6c9968 +about: + description: Provides an R wrapper for BWA alignment algorithms. Both BWA-backtrack and BWA-MEM are available. Convenience function to build a BWA index from a reference genome is also provided. Currently not supported for Windows machines. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: R wrapper for BWA-backtrack and BWA-MEM aligners build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rbwa", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat, BiocStyle, knitr, rmarkdown # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - libblas @@ -28,16 +30,14 @@ requirements: - zlib run: - r-base - - zlib - build: - - {{ compiler('c') }} - - make +source: + md5: 6b903361122cbe4f67049f14cf3141ea + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'R wrapper for BWA-backtrack and BWA-MEM aligners' - description: 'Provides an R wrapper for BWA alignment algorithms. Both BWA-backtrack and BWA-MEM are available. Convenience function to build a BWA index from a reference genome is also provided. Currently not supported for Windows machines.' - license_file: LICENSE + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-rcas/meta.yaml b/recipes/bioconductor-rcas/meta.yaml index bfcfb29ffe1ef..d247298fb30f6 100644 --- a/recipes/bioconductor-rcas/meta.yaml +++ b/recipes/bioconductor-rcas/meta.yaml @@ -1,98 +1,108 @@ -{% set version = "1.28.2" %} +{% set version = "1.32.0" %} {% set name = "RCAS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: RCAS is an R/Bioconductor package designed as a generic reporting tool for the functional analysis of transcriptome-wide regions of interest detected by high-throughput experiments. Such transcriptomic regions could be, for instance, signal peaks detected by CLIP-Seq analysis for protein-RNA interaction sites, RNA modification sites (alias the epitranscriptome), CAGE-tag locations, or any other collection of query regions at the level of the transcriptome. RCAS produces in-depth annotation summaries and coverage profiles based on the distribution of the query regions with respect to transcript features (exons, introns, 5'/3' UTR regions, exon-intron boundaries, promoter regions). Moreover, RCAS can carry out functional enrichment analyses and discriminative motif discovery. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: RNA Centric Annotation System -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 379c5b756cc12ca37913f7b51d8d29eb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rcas", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rcas + parent_recipe: + name: bioconductor-rcas + path: recipes/bioconductor-rcas + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, covr, BiocManager # SystemRequirements: pandoc (>= 1.12.3) requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomation >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-genomation >=1.38.0,<1.39.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqlogo >=1.72.0,<1.73.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-cowplot - r-data.table - - 'r-dt >=0.2' + - r-dt >=0.2 - r-ggplot2 - - r-ggseqlogo - r-gprofiler2 - - 'r-knitr >=1.12.3' + - r-knitr >=1.12.3 - r-pbapply - r-pheatmap - - 'r-plotly >=4.5.2' + - r-plotly >=4.5.2 - r-plotrix - r-proxy - r-ranger - - 'r-rmarkdown >=0.9.5' + - r-rmarkdown >=0.9.5 - r-rsqlite - - 'pandoc >=1.12.3' + - pandoc >=1.12.3 + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomation >=1.34.0,<1.35.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-genomation >=1.38.0,<1.39.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqlogo >=1.72.0,<1.73.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-cowplot - r-data.table - - 'r-dt >=0.2' + - r-dt >=0.2 - r-ggplot2 - - r-ggseqlogo - r-gprofiler2 - - 'r-knitr >=1.12.3' + - r-knitr >=1.12.3 - r-pbapply - r-pheatmap - - 'r-plotly >=4.5.2' + - r-plotly >=4.5.2 - r-plotrix - r-proxy - r-ranger - - 'r-rmarkdown >=0.9.5' + - r-rmarkdown >=0.9.5 - r-rsqlite - - 'pandoc >=1.12.3' + - pandoc >=1.12.3 + +source: + md5: 328e8ba6ff2d09439eeda000470fcc09 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'RNA Centric Annotation System' - description: 'RCAS is an R/Bioconductor package designed as a generic reporting tool for the functional analysis of transcriptome-wide regions of interest detected by high-throughput experiments. Such transcriptomic regions could be, for instance, signal peaks detected by CLIP-Seq analysis for protein-RNA interaction sites, RNA modification sites (alias the epitranscriptome), CAGE-tag locations, or any other collection of query regions at the level of the transcriptome. RCAS produces in-depth annotation summaries and coverage profiles based on the distribution of the query regions with respect to transcript features (exons, introns, 5''/3'' UTR regions, exon-intron boundaries, promoter regions). Moreover, RCAS can carry out functional enrichment analyses and discriminative motif discovery.' -extra: - identifiers: - - biotools:rcas - parent_recipe: - name: bioconductor-rcas - path: recipes/bioconductor-rcas - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rcaspar/meta.yaml b/recipes/bioconductor-rcaspar/meta.yaml index 8d9c57743bd22..86c186df9f538 100644 --- a/recipes/bioconductor-rcaspar/meta.yaml +++ b/recipes/bioconductor-rcaspar/meta.yaml @@ -1,38 +1,20 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "RCASPAR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 54a7734c80b26a4b0080fbdeb583af02 +about: + description: 'The package is the R-version of the C-based software \bold{CASPAR} (Kaderali,2006: \url{http://bioinformatics.oxfordjournals.org/content/22/12/1495}). It is meant to help predict survival times in the presence of high-dimensional explanatory covariates. The model is a piecewise baseline hazard Cox regression model with an Lq-norm based prior that selects for the most important regression coefficients, and in turn the most relevant covariates for survival analysis. It was primarily tried on gene expression and aCGH data, but can be used on any other type of high-dimensional data and in disciplines other than biology and medicine.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A package for survival time prediction based on a piecewise baseline hazard Cox regression model. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rcaspar", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=3)' - summary: 'A package for survival time prediction based on a piecewise baseline hazard Cox regression model.' - description: 'The package is the R-version of the C-based software \bold{CASPAR} (Kaderali,2006: \url{http://bioinformatics.oxfordjournals.org/content/22/12/1495}). It is meant to help predict survival times in the presence of high-dimensional explanatory covariates. The model is a piecewise baseline hazard Cox regression model with an Lq-norm based prior that selects for the most important regression coefficients, and in turn the most relevant covariates for survival analysis. It was primarily tried on gene expression and aCGH data, but can be used on any other type of high-dimensional data and in disciplines other than biology and medicine.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: identifiers: - biotools:rcaspar @@ -41,4 +23,22 @@ extra: name: bioconductor-rcaspar path: recipes/bioconductor-rcaspar version: 1.26.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +requirements: + host: + - r-base + run: + - r-base +source: + md5: d6b29f80f202d281b777aea72b3e55b5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rcellminer/meta.yaml b/recipes/bioconductor-rcellminer/meta.yaml index 9ae4c09d89d57..f0f0a507e0815 100644 --- a/recipes/bioconductor-rcellminer/meta.yaml +++ b/recipes/bioconductor-rcellminer/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "2.24.0" %} +{% set version = "2.28.0" %} {% set name = "rcellminer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + file LICENSE + license_file: LICENSE + summary: 'rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e74fd74daff68802d805b6bc0336499d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rcellminer", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, RColorBrewer, sqldf, BiocGenerics, testthat, BiocStyle, jsonlite, heatmaply, glmnet, foreach, doSNOW, parallel, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-rcellminerdata >=2.24.0,<2.25.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-rcellminerdata >=2.28.0,<2.29.0 - r-base - r-ggplot2 - r-gplots - r-shiny - r-stringr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-rcellminerdata >=2.24.0,<2.25.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-rcellminerdata >=2.28.0,<2.29.0 - r-base - r-ggplot2 - r-gplots - r-shiny - r-stringr + +source: + md5: b947209ffa23ae0a8bc95c3e1f83fab4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL-3 + file LICENSE' - summary: 'rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines' - description: 'The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rcellminerdata/meta.yaml b/recipes/bioconductor-rcellminerdata/meta.yaml index 6d0d65c26be67..8c6656d00be39 100644 --- a/recipes/bioconductor-rcellminerdata/meta.yaml +++ b/recipes/bioconductor-rcellminerdata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "2.24.0" %} +{% set version = "2.28.0" %} {% set name = "rcellminerData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f45852d4eeb438b6a1feb156200b2bc +about: + description: The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL-3 + file LICENSE + license_file: LICENSE + summary: 'rcellminerData: Molecular Profiles and Drug Response for the NCI-60 Cell Lines' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rcellminerdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, testthat, BiocStyle, rcellminer, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bd3a4c4313595d2fdff46bcbafd61eca + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'LGPL-3 + file LICENSE' - summary: 'rcellminerData: Molecular Profiles and Drug Response for the NCI-60 Cell Lines' - description: 'The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rcellminerdata/post-link.sh b/recipes/bioconductor-rcellminerdata/post-link.sh index c6a6cbff8fe34..3ec20079ae0f0 100644 --- a/recipes/bioconductor-rcellminerdata/post-link.sh +++ b/recipes/bioconductor-rcellminerdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rcellminerdata-2.24.0" +installBiocDataPackage.sh "rcellminerdata-2.28.0" diff --git a/recipes/bioconductor-rcgh/meta.yaml b/recipes/bioconductor-rcgh/meta.yaml index add2e2dfda8d6..d6d8cee76f3c7 100644 --- a/recipes/bioconductor-rcgh/meta.yaml +++ b/recipes/bioconductor-rcgh/meta.yaml @@ -1,80 +1,86 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "rCGH" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A comprehensive pipeline for analyzing and interactively visualizing genomic profiles generated through commercial or custom aCGH arrays. As inputs, rCGH supports Agilent dual-color Feature Extraction files (.txt), from 44 to 400K, Affymetrix SNP6.0 and cytoScanHD probeset.txt, cychp.txt, and cnchp.txt files exported from ChAS or Affymetrix Power Tools. rCGH also supports custom arrays, provided data complies with the expected format. This package takes over all the steps required for individual genomic profiles analysis, from reading files to profiles segmentation and gene annotations. This package also provides several visualization functions (static or interactive) which facilitate individual profiles interpretation. Input files can be in compressed format, e.g. .bz2 or .gz. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80510d5207fb0ad5d517a99b35734621 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rcgh", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rcgh + - doi:10.1093/bioinformatics/btv718 + parent_recipe: + name: bioconductor-rcgh + path: recipes/bioconductor-rcgh + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, BiocGenerics, RUnit requirements: host: - - 'bioconductor-acgh >=1.80.0,<1.81.0' - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - bioconductor-acgh >=1.84.0,<1.85.0 + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 - r-base - r-ggplot2 - r-lattice - r-mclust - r-plyr - - 'r-shiny >=0.11.1' + - r-shiny >=0.11.1 run: - - 'bioconductor-acgh >=1.80.0,<1.81.0' - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - bioconductor-acgh >=1.84.0,<1.85.0 + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 - r-base - r-ggplot2 - r-lattice - r-mclust - r-plyr - - 'r-shiny >=0.11.1' + - r-shiny >=0.11.1 + +source: + md5: 2abd9fb5cfc57b8f4fd3f0b62ae92831 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data' - description: 'A comprehensive pipeline for analyzing and interactively visualizing genomic profiles generated through commercial or custom aCGH arrays. As inputs, rCGH supports Agilent dual-color Feature Extraction files (.txt), from 44 to 400K, Affymetrix SNP6.0 and cytoScanHD probeset.txt, cychp.txt, and cnchp.txt files exported from ChAS or Affymetrix Power Tools. rCGH also supports custom arrays, provided data complies with the expected format. This package takes over all the steps required for individual genomic profiles analysis, from reading files to profiles segmentation and gene annotations. This package also provides several visualization functions (static or interactive) which facilitate individual profiles interpretation. Input files can be in compressed format, e.g. .bz2 or .gz.' -extra: - identifiers: - - biotools:rcgh - - doi:10.1093/bioinformatics/btv718 - parent_recipe: - name: bioconductor-rcgh - path: recipes/bioconductor-rcgh - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/meta.yaml b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/meta.yaml index b884d5531ab95..c0d73d6ade63c 100644 --- a/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/meta.yaml +++ b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "RcisTarget.hg19.motifDBs.cisbpOnly.500bp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b8cdbfafeb9966332876fdf9be8dbb5a +about: + description: 'RcisTarget databases: Gene-based motif rankings and annotation to transcription factors. This package contains a subset of 4.6k motifs (cisbp motifs), scored only within 500bp upstream and the TSS. See RcisTarget tutorial to download the full databases, containing 20k motifs and search space up to 10kbp around the TSS.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: RcisTarget motif databases for human (hg19) - Subset of 4.6k motifs build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base @@ -27,14 +26,15 @@ requirements: - r-base - r-data.table - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f95b8be5e180ae1207c328a9255145f4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'RcisTarget motif databases for human (hg19) - Subset of 4.6k motifs' - description: 'RcisTarget databases: Gene-based motif rankings and annotation to transcription factors. This package contains a subset of 4.6k motifs (cisbp motifs), scored only within 500bp upstream and the TSS. See RcisTarget tutorial to download the full databases, containing 20k motifs and search space up to 10kbp around the TSS.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/post-link.sh b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/post-link.sh index 6674b4221ffd9..c681b06691b53 100644 --- a/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/post-link.sh +++ b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rcistarget.hg19.motifdbs.cisbponly.500bp-1.22.0" +installBiocDataPackage.sh "rcistarget.hg19.motifdbs.cisbponly.500bp-1.26.0" diff --git a/recipes/bioconductor-rcistarget/meta.yaml b/recipes/bioconductor-rcistarget/meta.yaml index 31c411b373592..c883fcd9a85d7 100644 --- a/recipes/bioconductor-rcistarget/meta.yaml +++ b/recipes/bioconductor-rcistarget/meta.yaml @@ -1,60 +1,68 @@ -{% set version = "1.20.0" %} +{% set version = "1.26.0" %} {% set name = "RcisTarget" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: RcisTarget identifies transcription factor binding motifs (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the transcription start site (TSS) of the genes in the gene-set. This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high Normalized Enrichment Score (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0f7605c0a9396d116b777b4954011027 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic + run_exports: '{{ pin_subpackage("bioconductor-rcistarget", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach, gplots, rtracklayer, igraph, knitr, RcisTarget.hg19.motifDBs.cisbpOnly.500bp, rmarkdown, testthat, visNetwork requirements: host: - - 'bioconductor-aucell >=1.22.0,<1.23.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'r-arrow >=2.0.0' + - bioconductor-aucell >=1.28.0,<1.29.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-arrow >=2.0.0 - r-base - r-data.table - r-dplyr - r-r.utils - r-tibble + - r-zoo run: - - 'bioconductor-aucell >=1.22.0,<1.23.0' - - 'bioconductor-biocgenerics >=0.46.0,<0.47.0' - - 'bioconductor-genomeinfodb >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.52.0,<1.53.0' - - 'bioconductor-gseabase >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' - - 'r-arrow >=2.0.0' + - bioconductor-aucell >=1.28.0,<1.29.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-arrow >=2.0.0 - r-base - r-data.table - r-dplyr - r-r.utils - r-tibble + - r-zoo + +source: + md5: 10124dd3e66007aa4e69635ff4a2055a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions' - description: 'RcisTarget identifies transcription factor binding motifs (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the transcription start site (TSS) of the genes in the gene-set. This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high Normalized Enrichment Score (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rcm/meta.yaml b/recipes/bioconductor-rcm/meta.yaml index 78a7ec4e17ce7..b033295ae8148 100644 --- a/recipes/bioconductor-rcm/meta.yaml +++ b/recipes/bioconductor-rcm/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "RCM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Combine ideas of log-linear analysis of contingency table, flexible response function estimation and empirical Bayes dispersion estimation for explorative visualization of microbiome datasets. The package includes unconstrained as well as constrained analysis. In addition, diagnostic plot to detect lack of fit are available. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Fit row-column association models with the negative binomial distribution for the microbiome -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2512426fe72a0dfede77816e98935ca1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rcm", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 - r-alabama - r-base - r-dbi - - 'r-ggplot2 >=2.2.1.9000' + - r-ggplot2 >=2.2.1.9000 - r-mass - r-nleqslv - r-rcolorbrewer @@ -36,12 +38,12 @@ requirements: - r-tseries - r-vgam run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 - r-alabama - r-base - r-dbi - - 'r-ggplot2 >=2.2.1.9000' + - r-ggplot2 >=2.2.1.9000 - r-mass - r-nleqslv - r-rcolorbrewer @@ -49,13 +51,16 @@ requirements: - r-tensor - r-tseries - r-vgam + +source: + md5: b9ae0db23764d294d38458ed9fae3014 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Fit row-column association models with the negative binomial distribution for the microbiome' - description: 'Combine ideas of log-linear analysis of contingency table, flexible response function estimation and empirical Bayes dispersion estimation for explorative visualization of microbiome datasets. The package includes unconstrained as well as constrained analysis. In addition, diagnostic plot to detect lack of fit are available.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rcollectl/meta.yaml b/recipes/bioconductor-rcollectl/meta.yaml index da65e37613492..ecd793898793e 100644 --- a/recipes/bioconductor-rcollectl/meta.yaml +++ b/recipes/bioconductor-rcollectl/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "Rcollectl" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 855c39cf9aece9c63b3febc0c0d5654b +about: + description: Provide functions to obtain instrumentation data on processes in a unix environment. Parse output of a collectl run. Vizualize aspects of system usage over time, with annotation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Help use collectl with R in Linux, to measure resource consumption in R processes build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rcollectl", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, BiocStyle, knitcitations, sessioninfo, rmarkdown, testthat, covr # SystemRequirements: collectl requirements: @@ -32,12 +30,14 @@ requirements: - r-ggplot2 - r-lubridate - r-processx +source: + md5: d556bceb7e9105aa481ae3dea2630674 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Help use collectl with R in Linux, to measure resource consumption in R processes' - description: 'Provide functions to obtain instrumentation data on processes in a unix environment. Parse output of a collectl run. Vizualize aspects of system usage over time, with annotation.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rcpi/meta.yaml b/recipes/bioconductor-rcpi/meta.yaml index 5da588cf6c1df..62fecebb62407 100644 --- a/recipes/bioconductor-rcpi/meta.yaml +++ b/recipes/bioconductor-rcpi/meta.yaml @@ -1,51 +1,58 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "Rcpi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 | file LICENSE + license_file: LICENSE + summary: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2f3697ca19200881f65d7d37f3d34e33 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rcpi", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-gosemsim >=2.32.0,<2.33.0 - r-base + - r-curl - r-doparallel - r-foreach - - r-rcurl - - r-rjson + - r-httr2 + - r-jsonlite - r-rlang run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-gosemsim >=2.32.0,<2.33.0 - r-base + - r-curl - r-doparallel - r-foreach - - r-rcurl - - r-rjson + - r-httr2 + - r-jsonlite - r-rlang + +source: + md5: 83acc5f4a67a80de2d3ff48c06ff7cb1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Artistic-2.0 | file LICENSE' - summary: 'Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery' - description: 'A molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rcsl/meta.yaml b/recipes/bioconductor-rcsl/meta.yaml index 304a744f83349..7f2f1b4ffbad7 100644 --- a/recipes/bioconductor-rcsl/meta.yaml +++ b/recipes/bioconductor-rcsl/meta.yaml @@ -1,50 +1,65 @@ -{% set version = "1.8.0" %} +{% set version = "1.14.0" %} {% set name = "RCSL" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: A novel clustering algorithm and toolkit RCSL (Rank Constrained Similarity Learning) to accurately identify various cell types using scRNA-seq data from a complex tissue. RCSL considers both lo-cal similarity and global similarity among the cells to discern the subtle differences among cells of the same type as well as larger differences among cells of different types. RCSL uses Spearman’s rank correlations of a cell’s expression vector with those of other cells to measure its global similar-ity, and adaptively learns neighbour representation of a cell as its local similarity. The overall similar-ity of a cell to other cells is a linear combination of its global similarity and local similarity. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Rank Constrained Similarity Learning for single cell RNA sequencing data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 014987c88b4b2941c8badfc38c37db2c build: number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic -# Suggests: knitr, rmarkdown, mclust, RcppAnnoy + run_exports: '{{ pin_subpackage("bioconductor-rcsl", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, knitr, BiocStyle, rmarkdown, mclust, tidyverse, tinytex requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} host: + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - - r-ggplot2 + - r-ggplot2 >=3.4.0 - r-igraph - r-nbclust - r-pracma + - r-rcpp >=0.11.0 - r-rcppannoy - r-rtsne - r-umap + - libblas + - liblapack run: + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - - r-ggplot2 + - r-ggplot2 >=3.4.0 - r-igraph - r-nbclust - r-pracma + - r-rcpp >=0.11.0 - r-rcppannoy - r-rtsne - r-umap + +source: + md5: 2624ecbd83fdbb8adbd2478ca9c59f40 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Rank Constrained Similarity Learning for single cell RNA sequencing data' - description: 'A novel clustering algorithm and toolkit RCSL (Rank Constrained Similarity Learning) to accurately identify various cell types using scRNA-seq data from a complex tissue. RCSL considers both lo-cal similarity and global similarity among the cells to discern the subtle differences among cells of the same type as well as larger differences among cells of different types. RCSL uses Spearman’s rank correlations of a cell’s expression vector with those of other cells to measure its global similar-ity, and adaptively learns neighbour representation of a cell as its local similarity. The overall similar-ity of a cell to other cells is a linear combination of its global similarity and local similarity.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rcwl/meta.yaml b/recipes/bioconductor-rcwl/meta.yaml index fbd644f83afd4..6603c8717c7b2 100644 --- a/recipes/bioconductor-rcwl/meta.yaml +++ b/recipes/bioconductor-rcwl/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "Rcwl" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The Common Workflow Language (CWL) is an open standard for development of data analysis workflows that is portable and scalable across different tools and working environments. Rcwl provides a simple way to wrap command line tools and build CWL data analysis pipelines programmatically within R. It increases the ease of usage, development, and maintenance of CWL pipelines. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 | file LICENSE + license_file: LICENSE + summary: An R interface to the Common Workflow Language -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f427ee3f7f5ba2458f8f97b694b48a85 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rcwl", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-batchtools - r-codetools @@ -33,9 +35,9 @@ requirements: - r-shiny - r-yaml run: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-batchtools - r-codetools @@ -43,13 +45,16 @@ requirements: - r-r.utils - r-shiny - r-yaml + +source: + md5: 0a5a5d1c4e6080eaa34d121a5e59fbc9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-2 | file LICENSE' - summary: 'An R interface to the Common Workflow Language' - description: 'The Common Workflow Language (CWL) is an open standard for development of data analysis workflows that is portable and scalable across different tools and working environments. Rcwl provides a simple way to wrap command line tools and build CWL data analysis pipelines programmatically within R. It increases the ease of usage, development, and maintenance of CWL pipelines.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rcwlpipelines/build_failure.linux-64.yaml b/recipes/bioconductor-rcwlpipelines/build_failure.linux-64.yaml deleted file mode 100644 index 6ae0fde6d9352..0000000000000 --- a/recipes/bioconductor-rcwlpipelines/build_failure.linux-64.yaml +++ /dev/null @@ -1,61 +0,0 @@ -recipe_sha: af004261d70c636e2d08ed30d7cbe6563df507346a88a94d377d6a64ee5d934a # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -reason: |- - package r-base-4.3.0-h0fc540b_0 requires icu >=72.1,<73.0a0, but none of the providers can be installed -category: |- - dependency issue -log: |- - 02:31:45 BIOCONDA INFO (OUT) RuntimeError: Solver could not find solution.Mamba failed to solve: - 02:31:45 BIOCONDA INFO (OUT) - r-base 4.3.* - 02:31:45 BIOCONDA INFO (OUT) - r-httr - 02:31:45 BIOCONDA INFO (OUT) - nodejs 14.* - 02:31:45 BIOCONDA INFO (OUT) - r-git2r - 02:31:45 BIOCONDA INFO (OUT) - bioconductor-s4vectors >=0.40.0,<0.41.0 - 02:31:45 BIOCONDA INFO (OUT) - r-rappdirs - 02:31:45 BIOCONDA INFO (OUT) - bioconductor-rcwl >=1.18.0,<1.19.0 - 02:31:45 BIOCONDA INFO (OUT) - bioconductor-biocfilecache >=2.10.0,<2.11.0 - 02:31:45 BIOCONDA INFO (OUT) - 02:31:45 BIOCONDA INFO (OUT) with channels: - 02:31:45 BIOCONDA INFO (OUT) - file:///opt/host-conda-bld - 02:31:45 BIOCONDA INFO (OUT) - conda-forge - 02:31:45 BIOCONDA INFO (OUT) - bioconda - 02:31:45 BIOCONDA INFO (OUT) - defaults - 02:31:45 BIOCONDA INFO (OUT) - 02:31:45 BIOCONDA INFO (OUT) The reported errors are: - 02:31:45 BIOCONDA INFO (OUT) - Encountered problems while solving: - 02:31:45 BIOCONDA INFO (OUT) - - package r-base-4.3.0-h0fc540b_0 requires icu >=72.1,<73.0a0, but none of the providers can be installed - 02:31:45 BIOCONDA INFO (OUT) - - 02:31:45 BIOCONDA INFO (OUT) - 02:31:45 BIOCONDA INFO (OUT) During handling of the above exception, another exception occurred: - 02:31:45 BIOCONDA INFO (OUT) - 02:31:45 BIOCONDA INFO (OUT) Traceback (most recent call last): - 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/bin/conda-mambabuild", line 10, in - 02:31:45 BIOCONDA INFO (OUT) sys.exit(main()) - 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - 02:31:45 BIOCONDA INFO (OUT) call_conda_build(action, config) - 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - 02:31:45 BIOCONDA INFO (OUT) result = api.build( - 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - 02:31:45 BIOCONDA INFO (OUT) return build_tree( - 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - 02:31:45 BIOCONDA INFO (OUT) packages_from_this = build(metadata, stats, - 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build - 02:31:45 BIOCONDA INFO (OUT) output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs - 02:31:45 BIOCONDA INFO (OUT) for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): - 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set - 02:31:45 BIOCONDA INFO (OUT) conda_packages = finalize_outputs_pass( - 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass - 02:31:45 BIOCONDA INFO (OUT) fm = finalize_metadata( - 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata - 02:31:45 BIOCONDA INFO (OUT) build_unsat, host_unsat = add_upstream_pins(m, - 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins - 02:31:45 BIOCONDA INFO (OUT) host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', - 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files - 02:31:45 BIOCONDA INFO (OUT) deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, - 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies - 02:31:45 BIOCONDA INFO (OUT) actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, - 02:31:45 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - 02:31:45 BIOCONDA INFO (OUT) raise err - 02:31:45 BIOCONDA INFO (OUT) conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-base==4.3.0=h0fc540b_0"), MatchSpec("icu[version='>=72.1,<73.0a0']")} - diff --git a/recipes/bioconductor-rcwlpipelines/meta.yaml b/recipes/bioconductor-rcwlpipelines/meta.yaml index f933217359628..b1414cc284bb8 100644 --- a/recipes/bioconductor-rcwlpipelines/meta.yaml +++ b/recipes/bioconductor-rcwlpipelines/meta.yaml @@ -1,52 +1,57 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "RcwlPipelines" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A collection of Bioinformatics tools and pipelines based on R and the Common Workflow Language. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Bioinformatics pipelines based on Rcwl -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ff1c2848694b09cc639a56009392cf3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rcwlpipelines", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocStyle # SystemRequirements: nodejs requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-rcwl >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-rcwl >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-git2r - r-httr - r-rappdirs - nodejs run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-rcwl >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-rcwl >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-git2r - r-httr - r-rappdirs - nodejs + +source: + md5: c94b429f4daa3fc5bc2f9dd0a0bee8eb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Bioinformatics pipelines based on Rcwl' - description: 'A collection of Bioinformatics tools and pipelines based on R and the Common Workflow Language.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rcx/meta.yaml b/recipes/bioconductor-rcx/meta.yaml index 63f9f80394e5d..a3d05a737f05a 100644 --- a/recipes/bioconductor-rcx/meta.yaml +++ b/recipes/bioconductor-rcx/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "RCX" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4fdd9c350200e6854c3ed1db44572826 +about: + description: Create, handle, validate, visualize and convert networks in the Cytoscape exchange (CX) format to standard data types and objects. The package also provides conversion to and from objects of iGraph and graphNEL. The CX format is also used by the NDEx platform, a online commons for biological networks, and the network visualization software Cytocape. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: R package implementing the Cytoscape Exchange (CX) format build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rcx", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, testthat, knitr, rmarkdown, base64enc, graph requirements: host: @@ -31,13 +30,14 @@ requirements: - r-igraph - r-jsonlite - r-plyr +source: + md5: fdec8869f3d06fc348f0a872824159ae + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'R package implementing the Cytoscape Exchange (CX) format' - description: 'Create, handle, validate, visualize and convert networks in the Cytoscape exchange (CX) format to standard data types and objects. The package also provides conversion to and from objects of iGraph and graphNEL. The CX format is also used by the NDEx platform, a online commons for biological networks, and the network visualization software Cytocape.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rcy3/meta.yaml b/recipes/bioconductor-rcy3/meta.yaml index e0c575aaae226..ee2e2268f5bb6 100644 --- a/recipes/bioconductor-rcy3/meta.yaml +++ b/recipes/bioconductor-rcy3/meta.yaml @@ -1,30 +1,38 @@ -{% set version = "2.22.1" %} +{% set version = "2.26.0" %} {% set name = "RCy3" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Functions to Access and Control Cytoscape -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d4f51eaf382ede111f69aefd2660e383 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rcy3", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-rcy3 + path: recipes/bioconductor-rcy3 + version: 2.0.88 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, igraph, grDevices # SystemRequirements: Cytoscape (>= 3.7.1), CyREST (>= 3.8.0) requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-base64enc - r-base64url @@ -40,10 +48,10 @@ requirements: - r-stringi - r-uuid - r-xml - - 'cytoscape >=3.7.1' + - cytoscape >=3.7.1 run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-base64enc - r-base64url @@ -59,19 +67,17 @@ requirements: - r-stringi - r-uuid - r-xml - - 'cytoscape >=3.7.1' + - cytoscape >=3.7.1 + +source: + md5: b6b75d115fce1878d5251f3fea1dfd3d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Functions to Access and Control Cytoscape' - description: 'Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-rcy3 - path: recipes/bioconductor-rcy3 - version: 2.0.88 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rcyjs/meta.yaml b/recipes/bioconductor-rcyjs/meta.yaml index d1b93b6a7c224..f56644b39e1da 100644 --- a/recipes/bioconductor-rcyjs/meta.yaml +++ b/recipes/bioconductor-rcyjs/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "2.24.0" %} +{% set version = "2.28.0" %} {% set name = "RCyjs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Interactive viewing and exploration of graphs, connecting R to Cytoscape.js, using websockets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Display and manipulate graphs in cytoscape.js -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b02526ea0ff36d61fdac395633bc4a4d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rcyjs", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-browserviz >=2.24.0,<2.25.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-browserviz >=2.28.0,<2.29.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-base64enc - - 'r-httpuv >=1.5.0' + - r-httpuv >=1.5.0 run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-browserviz >=2.24.0,<2.25.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-browserviz >=2.28.0,<2.29.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-base64enc - - 'r-httpuv >=1.5.0' + - r-httpuv >=1.5.0 + +source: + md5: 88082db73f4802d75c8ff1513e669cd1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Display and manipulate graphs in cytoscape.js' - description: 'Interactive viewing and exploration of graphs, connecting R to Cytoscape.js, using websockets.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rdisop/meta.yaml b/recipes/bioconductor-rdisop/meta.yaml index a2c7a9d73dcd3..2bdec38f31f5a 100644 --- a/recipes/bioconductor-rdisop/meta.yaml +++ b/recipes/bioconductor-rdisop/meta.yaml @@ -1,26 +1,39 @@ -{% set version = "1.62.0" %} +{% set version = "1.66.0" %} {% set name = "Rdisop" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: In high resolution mass spectrometry (HR-MS), the measured masses can be decomposed into potential element combinations (chemical sum formulas). Where additional mass/intensity information of respective isotopic peaks is available, decomposition can take this information into account to better rank the potential candidate sum formulas. To compare measured mass/intensity information with the theoretical distribution of candidate sum formulas, the latter needs to be calculated. This package implements fast algorithms to address both tasks, the calculation of isotopic distributions for arbitrary sum formulas (assuming a HR-MS resolution of roughly 30,000), and the ranked list of sum formulas fitting an observed peak or isotopic peak set. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Decomposition of Isotopic Patterns -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 508c96aaea70daa872ec75712570f6da build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rdisop", max_pin="x.x") }}' -# Suggests: RUnit + +extra: + parent_recipe: + name: bioconductor-rdisop + path: recipes/bioconductor-rdisop + version: 1.42.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, RUnit, testthat (>= 3.0.0) # SystemRequirements: None requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - r-base - r-rcpp @@ -29,23 +42,16 @@ requirements: run: - r-base - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 2c028e825b2eb802759a8005d318c009 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Decomposition of Isotopic Patterns' - description: 'Identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - parent_recipe: - name: bioconductor-rdisop - path: recipes/bioconductor-rdisop - version: 1.42.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rdrtoolbox/meta.yaml b/recipes/bioconductor-rdrtoolbox/meta.yaml index 8cf36b1c8d51c..19dd415107594 100644 --- a/recipes/bioconductor-rdrtoolbox/meta.yaml +++ b/recipes/bioconductor-rdrtoolbox/meta.yaml @@ -1,26 +1,39 @@ -{% set version = "1.52.0" %} +{% set version = "1.56.0" %} {% set name = "RDRToolbox" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package for nonlinear dimension reduction using the Isomap and LLE algorithm. It also includes a routine for computing the Davis-Bouldin-Index for cluster validation, a plotting tool and a data generator for microarray gene expression data and for the Swiss Roll dataset. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A package for nonlinear dimension reduction with Isomap and LLE. -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4b0e59a1ea48dd51e11d8d18666cf2d4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rdrtoolbox", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: golubEsets requirements: + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] host: - r-base - r-mass @@ -29,23 +42,16 @@ requirements: - r-base - r-mass - r-rgl - build: - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - xorg-libxfixes # [linux] + +source: + md5: 41bf57d357f7d8fbb7410bcab94bd9cb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'A package for nonlinear dimension reduction with Isomap and LLE.' - description: 'A package for nonlinear dimension reduction using the Isomap and LLE algorithm. It also includes a routine for computing the Davis-Bouldin-Index for cluster validation, a plotting tool and a data generator for microarray gene expression data and for the Swiss Roll dataset.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-reactome.db/meta.yaml b/recipes/bioconductor-reactome.db/meta.yaml index 242822e8bae25..f828f729666c2 100644 --- a/recipes/bioconductor-reactome.db/meta.yaml +++ b/recipes/bioconductor-reactome.db/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.86.2" %} +{% set version = "1.89.0" %} {% set name = "reactome.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ff56f3908b347cb18e3e4ccedf7f584e +about: + description: A set of annotation maps for reactome assembled using data from reactome. This package has been created by a third-party developer, and is not affiliated with the Reactome team. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: CC BY 4.0 + summary: A set of annotation maps for reactome build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-reactome.db", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-reactome.db + path: recipes/bioconductor-reactome.db + version: 1.64.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: RSQLite requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9cb7d59e83b3dfbe265d3264d880d5f2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'CC BY 4.0' - summary: 'A set of annotation maps for reactome' - description: 'A set of annotation maps for reactome assembled using data from reactome. This package has been created by a third-party developer, and is not affiliated with the Reactome team.' -extra: - parent_recipe: - name: bioconductor-reactome.db - path: recipes/bioconductor-reactome.db - version: 1.64.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-reactome.db/post-link.sh b/recipes/bioconductor-reactome.db/post-link.sh index 505cfbf3b984f..5d00dcc2499dc 100644 --- a/recipes/bioconductor-reactome.db/post-link.sh +++ b/recipes/bioconductor-reactome.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "reactome.db-1.86.2" +installBiocDataPackage.sh "reactome.db-1.89.0" diff --git a/recipes/bioconductor-reactomegsa.data/meta.yaml b/recipes/bioconductor-reactomegsa.data/meta.yaml index bec7f216b21da..0bf4714e6635d 100644 --- a/recipes/bioconductor-reactomegsa.data/meta.yaml +++ b/recipes/bioconductor-reactomegsa.data/meta.yaml @@ -1,45 +1,50 @@ -{% set version = "1.16.1" %} +{% set version = "1.20.0" %} {% set name = "ReactomeGSA.data" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Companion data sets to showcase the functionality of the ReactomeGSA package. This package contains proteomics and RNA-seq data of the melanoma B-cell induction study by Griss et al. and scRNA-seq data from Jerby-Arnon et al. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Companion data package for the ReactomeGSA package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bd236d4d4078f99ea5d473fde1ff065f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-reactomegsa.data", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-reactomegsa >=1.16.0,<1.17.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-reactomegsa >=1.20.0,<1.21.0 - r-base - r-seurat run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-reactomegsa >=1.16.0,<1.17.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-reactomegsa >=1.20.0,<1.21.0 - r-base - r-seurat - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: f81cfbbd26d41eb728363bdc5b8d2f8c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Companion data package for the ReactomeGSA package' - description: 'Companion data sets to showcase the functionality of the ReactomeGSA package. This package contains proteomics and RNA-seq data of the melanoma B-cell induction study by Griss et al. and scRNA-seq data from Jerby-Arnon et al.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-reactomegsa.data/post-link.sh b/recipes/bioconductor-reactomegsa.data/post-link.sh index 7105dd31e819c..3333b654daf26 100644 --- a/recipes/bioconductor-reactomegsa.data/post-link.sh +++ b/recipes/bioconductor-reactomegsa.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "reactomegsa.data-1.16.1" +installBiocDataPackage.sh "reactomegsa.data-1.20.0" diff --git a/recipes/bioconductor-reactomegsa/meta.yaml b/recipes/bioconductor-reactomegsa/meta.yaml index eca696e84304c..e669c39c2b6e5 100644 --- a/recipes/bioconductor-reactomegsa/meta.yaml +++ b/recipes/bioconductor-reactomegsa/meta.yaml @@ -1,27 +1,30 @@ -{% set version = "1.16.1" %} +{% set version = "1.20.0" %} {% set name = "ReactomeGSA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The ReactomeGSA packages uses Reactome's online analysis service to perform a multi-omics gene set analysis. The main advantage of this package is, that the retrieved results can be visualized using REACTOME's powerful webapplication. Since Reactome's analysis service also uses R to perfrom the actual gene set analysis you will get similar results when using the same packages (such as limma and edgeR) locally. Therefore, if you only require a gene set analysis, different packages are more suited. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Client for the Reactome Analysis Service for comparative multi-omics gene set analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c4ef9b68baf6957b7a3abf38bd4ffb39 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-reactomegsa", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, knitr, rmarkdown, ReactomeGSA.data, Biobase, devtools + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, knitr, rmarkdown, ReactomeGSA.data, devtools requirements: host: + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-dplyr - r-ggplot2 @@ -32,6 +35,7 @@ requirements: - r-rcolorbrewer - r-tidyr run: + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-dplyr - r-ggplot2 @@ -41,13 +45,16 @@ requirements: - r-progress - r-rcolorbrewer - r-tidyr + +source: + md5: 9ac75169cf50f17bee67fe2487c30a57 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Client for the Reactome Analysis Service for comparative multi-omics gene set analysis' - description: 'The ReactomeGSA packages uses Reactome''s online analysis service to perform a multi-omics gene set analysis. The main advantage of this package is, that the retrieved results can be visualized using REACTOME''s powerful webapplication. Since Reactome''s analysis service also uses R to perfrom the actual gene set analysis you will get similar results when using the same packages (such as limma and edgeR) locally. Therefore, if you only require a gene set analysis, different packages are more suited.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-reactomepa/meta.yaml b/recipes/bioconductor-reactomepa/meta.yaml index 7157cb19579aa..e69ab99f9fd5b 100644 --- a/recipes/bioconductor-reactomepa/meta.yaml +++ b/recipes/bioconductor-reactomepa/meta.yaml @@ -1,62 +1,70 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "ReactomePA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization. This package is not affiliated with the Reactome team. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Reactome Pathway Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c31f563d1848fd0bafdbedb6b7f9bb66 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-reactomepa", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:reactomepa + parent_recipe: + name: bioconductor-reactomepa + path: recipes/bioconductor-reactomepa + version: 1.24.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, clusterProfiler, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - - 'bioconductor-graphite >=1.48.0,<1.49.0' - - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 + - bioconductor-graphite >=1.52.0,<1.53.0 + - bioconductor-reactome.db >=1.89.0,<1.90.0 - r-base - - 'r-ggplot2 >=3.3.5' + - r-ggplot2 >=3.3.5 - r-ggraph - r-gson - r-igraph + - r-yulab.utils >=0.1.5 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - - 'bioconductor-graphite >=1.48.0,<1.49.0' - - 'bioconductor-reactome.db >=1.86.0,<1.87.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 + - bioconductor-graphite >=1.52.0,<1.53.0 + - bioconductor-reactome.db >=1.89.0,<1.90.0 - r-base - - 'r-ggplot2 >=3.3.5' + - r-ggplot2 >=3.3.5 - r-ggraph - r-gson - r-igraph + - r-yulab.utils >=0.1.5 + +source: + md5: 53e6b4f22aec5d9faf9f2cf3f07e55ae + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Reactome Pathway Analysis' - description: 'This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:reactomepa - parent_recipe: - name: bioconductor-reactomepa - path: recipes/bioconductor-reactomepa - version: 1.24.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-readqpcr/meta.yaml b/recipes/bioconductor-readqpcr/meta.yaml index 999355ab15670..ee58ee7c0bad5 100644 --- a/recipes/bioconductor-readqpcr/meta.yaml +++ b/recipes/bioconductor-readqpcr/meta.yaml @@ -1,46 +1,52 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "ReadqPCR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package provides functions to read raw RT-qPCR data of different platforms. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Read qPCR data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b92a0fe88b39abffbc0c46c36a76a8de build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-readqpcr", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:readqpcr + parent_recipe: + name: bioconductor-readqpcr + path: recipes/bioconductor-readqpcr + version: 1.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: qpcR requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base + +source: + md5: 5f14f25a5a7a20d73aff23a783fb6822 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'Read qPCR data' - description: 'The package provides functions to read raw RT-qPCR data of different platforms.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:readqpcr - parent_recipe: - name: bioconductor-readqpcr - path: recipes/bioconductor-readqpcr - version: 1.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rebet/meta.yaml b/recipes/bioconductor-rebet/meta.yaml index 8771d5bd544a0..cf5c1140a6444 100644 --- a/recipes/bioconductor-rebet/meta.yaml +++ b/recipes/bioconductor-rebet/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "REBET" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fc1e4bc02e112473630da74fce831189 +about: + description: There is an increasing focus to investigate the association between rare variants and diseases. The REBET package implements the subREgion-based BurdEn Test which is a powerful burden test that simultaneously identifies susceptibility loci and sub-regions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: The subREgion-based BurdEn Test (REBET) build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rebet", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: RUnit, BiocGenerics requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-asset >=2.20.0,<2.21.0' + - bioconductor-asset >=2.24.0,<2.25.0 - r-base - libblas - liblapack run: - - 'bioconductor-asset >=2.20.0,<2.21.0' + - bioconductor-asset >=2.24.0,<2.25.0 - r-base - build: - - {{ compiler('c') }} - - make +source: + md5: ddafdb1225d19db016e4acc664eec77f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'The subREgion-based BurdEn Test (REBET)' - description: 'There is an increasing focus to investigate the association between rare variants and diseases. The REBET package implements the subREgion-based BurdEn Test which is a powerful burden test that simultaneously identifies susceptibility loci and sub-regions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rebook/meta.yaml b/recipes/bioconductor-rebook/meta.yaml index 8ea103b7b63c5..1e3c9c20e656c 100644 --- a/recipes/bioconductor-rebook/meta.yaml +++ b/recipes/bioconductor-rebook/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "rebook" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides utilities to re-use content across chapters of a Bioconductor book. This is mostly based on functionality developed while writing the OSCA book, but generalized for potential use in other large books with heavy compute. Also contains some functions to assist book deployment. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Re-using Content in Bioconductor Books -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 05a8502e7f25563382e9e277b3199339 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rebook", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, igraph, XML, BiocManager, RCurl, bookdown, rappdirs, yaml, BiocParallel, OSCA.intro, OSCA.workflows requirements: host: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-dir.expiry >=1.10.0,<1.11.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-dir.expiry >=1.14.0,<1.15.0 - r-base - r-codedepends - r-filelock - - 'r-knitr >=1.32' + - r-knitr >=1.32 - r-rmarkdown run: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-dir.expiry >=1.10.0,<1.11.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-dir.expiry >=1.14.0,<1.15.0 - r-base - r-codedepends - r-filelock - - 'r-knitr >=1.32' + - r-knitr >=1.32 - r-rmarkdown + +source: + md5: 1a43fb79b3571524d0fbae53c3b3d4ee + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Re-using Content in Bioconductor Books' - description: 'Provides utilities to re-use content across chapters of a Bioconductor book. This is mostly based on functionality developed while writing the OSCA book, but generalized for potential use in other large books with heavy compute. Also contains some functions to assist book deployment.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-receptloss/meta.yaml b/recipes/bioconductor-receptloss/meta.yaml index 1dd994f66fc91..bd6a21f8f99b2 100644 --- a/recipes/bioconductor-receptloss/meta.yaml +++ b/recipes/bioconductor-receptloss/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "receptLoss" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: receptLoss identifies genes whose expression is lost in subsets of tumors relative to normal tissue. It is particularly well-suited in cases where the number of normal tissue samples is small, as the distribution of gene expression in normal tissue samples is approximated by a Gaussian. Originally designed for identifying nuclear hormone receptor expression loss but can be applied transcriptome wide as well. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3ccddd0181e8b78b843807d1378f86ef build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-receptloss", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat (>= 2.1.0), here requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 - r-magrittr - r-tidyr run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 - r-magrittr - r-tidyr + +source: + md5: d54134c825a4dab0483bcc572df24f5d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors' - description: 'receptLoss identifies genes whose expression is lost in subsets of tumors relative to normal tissue. It is particularly well-suited in cases where the number of normal tissue samples is small, as the distribution of gene expression in normal tissue samples is approximated by a Gaussian. Originally designed for identifying nuclear hormone receptor expression loss but can be applied transcriptome wide as well.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-reconsi/meta.yaml b/recipes/bioconductor-reconsi/meta.yaml index 7157b2fd15860..9e1db618e51d6 100644 --- a/recipes/bioconductor-reconsi/meta.yaml +++ b/recipes/bioconductor-reconsi/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "reconsi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Improves simultaneous inference under dependence of tests by estimating a collapsed null distribution through resampling. Accounting for the dependence between tests increases the power while reducing the variability of the false discovery proportion. This dependence is common in genomics applications, e.g. when combining flow cytometry measurements with microbiome sequence counts. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Resampling Collapsed Null Distributions for Simultaneous Inference -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 884019da85885289094a2aed95d18314 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-reconsi", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - bioconductor-phyloseq >=1.50.0,<1.51.0 - r-base - r-ggplot2 - r-ks @@ -30,20 +32,23 @@ requirements: - r-matrixstats - r-reshape2 run: - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - bioconductor-phyloseq >=1.50.0,<1.51.0 - r-base - r-ggplot2 - r-ks - r-matrix - r-matrixstats - r-reshape2 + +source: + md5: 2c0ca47c7f0dcbd2f683f5d5c69c365a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Resampling Collapsed Null Distributions for Simultaneous Inference' - description: 'Improves simultaneous inference under dependence of tests by estimating a collapsed null distribution through resampling. Accounting for the dependence between tests increases the power while reducing the variability of the false discovery proportion. This dependence is common in genomics applications, e.g. when combining flow cytometry measurements with microbiome sequence counts.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-recount/meta.yaml b/recipes/bioconductor-recount/meta.yaml index d016fb257b38b..fa0f2b162e346 100644 --- a/recipes/bioconductor-recount/meta.yaml +++ b/recipes/bioconductor-recount/meta.yaml @@ -1,65 +1,71 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "recount" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Explore and download data from the recount project -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 80d2f08ec7c30f139b1967db7cd07f7c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-recount", max_pin="x.x") }}' - noarch: generic -# Suggests: AnnotationDbi, BiocManager, BiocStyle (>= 2.5.19), DESeq2, sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures, knitr (>= 1.6), org.Hs.eg.db, RefManageR, regionReport (>= 1.9.4), rmarkdown (>= 0.9.5), testthat (>= 2.1.0), covr, pheatmap, DT, edgeR, ggplot2, RColorBrewer + +extra: + parent_recipe: + name: bioconductor-recount + path: recipes/bioconductor-recount + version: 1.6.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: AnnotationDbi, BiocManager, BiocStyle (>= 2.5.19), DESeq2, sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures, txdbmaker, knitr (>= 1.6), org.Hs.eg.db, RefManageR, regionReport (>= 1.9.4), rmarkdown (>= 0.9.5), testthat (>= 2.1.0), covr, pheatmap, DT, edgeR, ggplot2, RColorBrewer requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-derfinder >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-derfinder >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-downloader - r-rcurl - r-rentrez run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-derfinder >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-derfinder >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-downloader - r-rcurl - r-rentrez + +source: + md5: 173cd146ead4195e569d69b6531237da + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Explore and download data from the recount project' - description: 'Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.' -extra: - parent_recipe: - name: bioconductor-recount - path: recipes/bioconductor-recount - version: 1.6.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-recount3/meta.yaml b/recipes/bioconductor-recount3/meta.yaml index 4acc5addbf239..4c1c8f9aeaaee 100644 --- a/recipes/bioconductor-recount3/meta.yaml +++ b/recipes/bioconductor-recount3/meta.yaml @@ -1,32 +1,33 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "recount3" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The recount3 package enables access to a large amount of uniformly processed RNA-seq data from human and mouse. You can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level with sample metadata and QC statistics. In addition we provide access to sample coverage BigWig files. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Explore and download data from the recount3 project -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0e3b0229faa614fbbc49547e44b342d7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-recount3", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, covr, knitcitations, knitr, RefManageR, rmarkdown, testthat, pryr, interactiveDisplayBase, recount requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-httr @@ -34,23 +35,27 @@ requirements: - r-r.utils - r-sessioninfo run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-httr - r-matrix - r-r.utils - r-sessioninfo + +source: + md5: bc93fa96e743a69d2b0f79e398237a26 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Explore and download data from the recount3 project' - description: 'The recount3 package enables access to a large amount of uniformly processed RNA-seq data from human and mouse. You can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level with sample metadata and QC statistics. In addition we provide access to sample coverage BigWig files.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-recountmethylation/meta.yaml b/recipes/bioconductor-recountmethylation/meta.yaml index 8270e20eb93ab..92cdad1156b38 100644 --- a/recipes/bioconductor-recountmethylation/meta.yaml +++ b/recipes/bioconductor-recountmethylation/meta.yaml @@ -1,56 +1,61 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "recountmethylation" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Resources for cross-study analyses of public DNAm array data from NCBI GEO repo, produced using Illumina's Infinium HumanMethylation450K (HM450K) and MethylationEPIC (EPIC) platforms. Provided functions enable download, summary, and filtering of large compilation files. Vignettes detail background about file formats, example analyses, and more. Note the disclaimer on package load and consult the main manuscripts for further info. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Access and analyze public DNA methylation array data compilations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 56d6b1dcb581c96c3ee93c4def178a1c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-recountmethylation", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: minfiData, minfiDataEPIC, knitr, testthat, ggplot2, gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub requirements: host: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-r.utils - r-rcurl - r-reticulate run: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-r.utils - r-rcurl - r-reticulate + +source: + md5: bc6547f4dc230ade1e241686514d57dd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Access and analyze public DNA methylation array data compilations' - description: 'Resources for cross-study analyses of public DNAm array data from NCBI GEO repo, produced using Illumina''s Infinium HumanMethylation450K (HM450K) and MethylationEPIC (EPIC) platforms. Provided functions enable download, summary, and filtering of large compilation files. Vignettes detail background about file formats, example analyses, and more. Note the disclaimer on package load and consult the main manuscripts for further info.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-recoup/meta.yaml b/recipes/bioconductor-recoup/meta.yaml index 3d9060186612c..264382883cb18 100644 --- a/recipes/bioconductor-recoup/meta.yaml +++ b/recipes/bioconductor-recoup/meta.yaml @@ -1,39 +1,51 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "recoup" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: recoup calculates and plots signal profiles created from short sequence reads derived from Next Generation Sequencing technologies. The profiles provided are either sumarized curve profiles or heatmap profiles. Currently, recoup supports genomic profile plots for reads derived from ChIP-Seq and RNA-Seq experiments. The package uses ggplot2 and ComplexHeatmap graphics facilities for curve and heatmap coverage profiles respectively. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: An R package for the creation of complex genomic profile plots -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 021e00a6ca090381be16bf88e12eef05 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-recoup", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:recoup + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-recoup + path: recipes/bioconductor-recoup + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: grid, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocManager, BSgenome, RMySQL requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-circlize - r-ggplot2 @@ -41,39 +53,35 @@ requirements: - r-rsqlite - r-stringr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-circlize - r-ggplot2 - r-httr - r-rsqlite - r-stringr + +source: + md5: e706ef9dc0be3a41f2ebf9c6ef0cde4b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'An R package for the creation of complex genomic profile plots' - description: 'recoup calculates and plots signal profiles created from short sequence reads derived from Next Generation Sequencing technologies. The profiles provided are either sumarized curve profiles or heatmap profiles. Currently, recoup supports genomic profile plots for reads derived from ChIP-Seq and RNA-Seq experiments. The package uses ggplot2 and ComplexHeatmap graphics facilities for curve and heatmap coverage profiles respectively.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:recoup - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-recoup - path: recipes/bioconductor-recoup - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-reder/meta.yaml b/recipes/bioconductor-reder/meta.yaml index f41f96e824ee1..26a41d48c443e 100644 --- a/recipes/bioconductor-reder/meta.yaml +++ b/recipes/bioconductor-reder/meta.yaml @@ -1,47 +1,55 @@ -{% set version = "2.6.0" %} +{% set version = "3.2.0" %} {% set name = "RedeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: RedeR is an R-based package combined with a stand-alone Java application for interactive visualization and manipulation of nested networks. Graph, node, and edge attributes can be configured using either graphical or command-line methods, following igraph syntax rules. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Interactive visualization and manipulation of nested networks -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 033b5763d95dc222256a4ef85b7e3a99 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-reder", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, markdown, TreeAndLeaf + +extra: + identifiers: + - biotools:reder + parent_recipe: + name: bioconductor-reder + path: recipes/bioconductor-reder + version: 1.28.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, markdown, BiocStyle, TreeAndLeaf # SystemRequirements: Java Runtime Environment (Java>= 11) requirements: host: - r-base - r-igraph + - r-scales run: - r-base - r-igraph + - r-scales + +source: + md5: ef1c2425218353186e59818411cca25d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Interactive visualization and manipulation of nested networks' - description: 'RedeR is an R-based package combined with a stand-alone Java application for interactive visualization and manipulation of nested networks.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:reder - parent_recipe: - name: bioconductor-reder - path: recipes/bioconductor-reder - version: 1.28.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-redisparam/meta.yaml b/recipes/bioconductor-redisparam/meta.yaml index 1ae122c83be0f..85cee7febb798 100644 --- a/recipes/bioconductor-redisparam/meta.yaml +++ b/recipes/bioconductor-redisparam/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "RedisParam" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf24018f96bc9de6286d2806dfd7bfaa +about: + description: This package provides a Redis-based back-end for BiocParallel, enabling an alternative mechanism for distributed computation. The The 'manager' distributes tasks to a 'worker' pool through a central Redis server, rather than directly to workers as with other BiocParallel implementations. This means that the worker pool can change dynamically during job evaluation. All features of BiocParallel are supported, including reproducible random number streams, logging to the manager, and alternative 'load balancing' task distributions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Provide a 'redis' back-end for BiocParallel build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-redisparam", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: rmarkdown, knitr, testthat, BiocStyle # SystemRequirements: hiredis requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-futile.logger - r-redux - r-withr run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-futile.logger - r-redux - r-withr +source: + md5: 2afb7949c088cc8c661b205072bfc951 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Provide a ''redis'' back-end for BiocParallel' - description: 'This package provides a Redis-based back-end for BiocParallel, enabling an alternative mechanism for distributed computation. The The ''manager'' distributes tasks to a ''worker'' pool through a central Redis server, rather than directly to workers as with other BiocParallel implementations. This means that the worker pool can change dynamically during job evaluation. All features of BiocParallel are supported, including reproducible random number streams, logging to the manager, and alternative ''load balancing'' task distributions.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-redseq/meta.yaml b/recipes/bioconductor-redseq/meta.yaml index 452649f180224..7d5a46c58b67a 100644 --- a/recipes/bioconductor-redseq/meta.yaml +++ b/recipes/bioconductor-redseq/meta.yaml @@ -1,52 +1,57 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "REDseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Analysis of high-throughput sequencing data processed by restriction enzyme digestion -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f20e437ad9c48683bdaeda1825f87f85 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-redseq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.celegans.ucsc.ce2 >=1.4.0,<1.5.0' - - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.celegans.ucsc.ce2 >=1.4.0,<1.5.0 + - bioconductor-chippeakanno >=3.40.0,<3.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.celegans.ucsc.ce2 >=1.4.0,<1.5.0' - - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.celegans.ucsc.ce2 >=1.4.0,<1.5.0 + - bioconductor-chippeakanno >=3.40.0,<3.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base + +source: + md5: c84c3e86db14ef19355e4039acf08309 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Analysis of high-throughput sequencing data processed by restriction enzyme digestion' - description: 'The package includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-regenrich/meta.yaml b/recipes/bioconductor-regenrich/meta.yaml index a828d8b6fa8f4..10129b912537a 100644 --- a/recipes/bioconductor-regenrich/meta.yaml +++ b/recipes/bioconductor-regenrich/meta.yaml @@ -1,66 +1,74 @@ -{% set version = "1.10.0" %} +{% set version = "1.16.0" %} {% set name = "RegEnrich" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: 'This package is a pipeline to identify the key gene regulators in a biological process, for example in cell differentiation and in cell development after stimulation. There are four major steps in this pipeline: (1) differential expression analysis; (2) regulator-target network inference; (3) enrichment analysis; and (4) regulators scoring and ranking.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Gene regulator enrichment analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: afbd8028754ca907215ba26c3eae83f8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic + run_exports: '{{ pin_subpackage("bioconductor-regenrich", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: GEOquery, rmarkdown, knitr, BiocManager, testthat requirements: host: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocset >=1.14.0,<1.15.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocset >=1.20.0,<1.21.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - - 'r-ggplot2 >=2.2.0' + - r-ggplot2 >=2.2.0 - r-magrittr - r-randomforest - r-reshape2 - r-tibble - r-wgcna run: - - 'bioconductor-biocparallel >=1.34.0,<1.35.0' - - 'bioconductor-biocset >=1.14.0,<1.15.0' - - 'bioconductor-deseq2 >=1.40.0,<1.41.0' - - 'bioconductor-dose >=3.26.0,<3.27.0' - - 'bioconductor-fgsea >=1.26.0,<1.27.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-s4vectors >=0.38.0,<0.39.0' - - 'bioconductor-summarizedexperiment >=1.30.0,<1.31.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocset >=1.20.0,<1.21.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - - 'r-ggplot2 >=2.2.0' + - r-ggplot2 >=2.2.0 - r-magrittr - r-randomforest - r-reshape2 - r-tibble - r-wgcna + +source: + md5: f091133a6d86b9ae5114bbd3a96281bb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Gene regulator enrichment analysis' - description: 'This package is a pipeline to identify the key gene regulators in a biological process, for example in cell differentiation and in cell development after stimulation. There are four major steps in this pipeline: (1) differential expression analysis; (2) regulator-target network inference; (3) enrichment analysis; and (4) regulators scoring and ranking.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-regionalpcs/meta.yaml b/recipes/bioconductor-regionalpcs/meta.yaml index dfc7d8dcc70b5..52184cb1de4d3 100644 --- a/recipes/bioconductor-regionalpcs/meta.yaml +++ b/recipes/bioconductor-regionalpcs/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "regionalpcs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 37f0fc1370efacc719f72b419455096a +about: + description: Functions to summarize DNA methylation data using regional principal components. Regional principal components are computed using principal components analysis within genomic regions to summarize the variability in methylation levels across CpGs. The number of principal components is chosen using either the Marcenko-Pasteur or Gavish-Donoho method to identify relevant signal in the data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Summarizing Regional Methylation with Regional Principal Components Analysis build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-regionalpcs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, RMTstat, testthat (>= 3.0.0), BiocStyle, tidyr, minfiData, TxDb.Hsapiens.UCSC.hg19.knownGene, IRanges requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-pcatools >=2.14.0,<2.15.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-pcatools >=2.18.0,<2.19.0 - r-base - r-dplyr - r-tibble run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-pcatools >=2.14.0,<2.15.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-pcatools >=2.18.0,<2.19.0 - r-base - r-dplyr - r-tibble +source: + md5: 5bd633cf37f4f1e6510e072d95229143 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Summarizing Regional Methylation with Regional Principal Components Analysis' - description: 'Functions to summarize DNA methylation data using regional principal components. Regional principal components are computed using principal components analysis within genomic regions to summarize the variability in methylation levels across CpGs. The number of principal components is chosen using either the Marcenko-Pasteur or Gavish-Donoho method to identify relevant signal in the data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-regioner/meta.yaml b/recipes/bioconductor-regioner/meta.yaml index 0b0d546a5ab73..8c8cfab230b5b 100644 --- a/recipes/bioconductor-regioner/meta.yaml +++ b/recipes/bioconductor-regioner/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "regioneR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Association analysis of genomic regions based on permutation tests -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c2a9b6e46aa1aded948991c482cbf8a1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-regioner", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:regioner + parent_recipe: + name: bioconductor-regioner + path: recipes/bioconductor-regioner + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19.masked, testthat requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-memoise run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-memoise + +source: + md5: 5a11528b9d1d841c4a547a289e1b0788 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Association analysis of genomic regions based on permutation tests' - description: 'regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.' -extra: - identifiers: - - biotools:regioner - parent_recipe: - name: bioconductor-regioner - path: recipes/bioconductor-regioner - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-regionereloaded/meta.yaml b/recipes/bioconductor-regionereloaded/meta.yaml index c7131511ca7c5..7e1cfebabe1fe 100644 --- a/recipes/bioconductor-regionereloaded/meta.yaml +++ b/recipes/bioconductor-regionereloaded/meta.yaml @@ -1,28 +1,29 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "regioneReloaded" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: RegioneReloaded is a package that allows simultaneous analysis of associations between genomic region sets, enabling clustering of data and the creation of ready-to-publish graphs. It takes over and expands on all the features of its predecessor regioneR. It also incorporates a strategy to improve p-value calculations and normalize z-scores coming from multiple analysis to allow for their direct comparison. RegioneReloaded builds upon regioneR by adding new plotting functions for obtaining publication-ready graphs. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'RegioneReloaded: Multiple Association for Genomic Region Sets' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 38175e4bcc9ccb951f79fca8238897b2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-regionereloaded", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, BiocStyle, GenomeInfoDb, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-regioner >=1.34.0,<1.35.0' + - bioconductor-regioner >=1.38.0,<1.39.0 - r-base - r-cluster - r-ggplot2 @@ -33,7 +34,7 @@ requirements: - r-scales - r-umap run: - - 'bioconductor-regioner >=1.34.0,<1.35.0' + - bioconductor-regioner >=1.38.0,<1.39.0 - r-base - r-cluster - r-ggplot2 @@ -43,12 +44,16 @@ requirements: - r-rtsne - r-scales - r-umap + +source: + md5: 98c503cd7743188a9bc0ff1334206529 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'RegioneReloaded: Multiple Association for Genomic Region Sets' - description: 'RegioneReloaded is a package that allows simultaneous analysis of associations between genomic region sets, enabling clustering of data and the creation of ready-to-publish graphs. It takes over and expands on all the features of its predecessor regioneR. It also incorporates a strategy to improve p-value calculations and normalize z-scores coming from multiple analysis to allow for their direct comparison. RegioneReloaded builds upon regioneR by adding new plotting functions for obtaining publication-ready graphs.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-regionreport/meta.yaml b/recipes/bioconductor-regionreport/meta.yaml index 2b14e31961044..510c668f7d63d 100644 --- a/recipes/bioconductor-regionreport/meta.yaml +++ b/recipes/bioconductor-regionreport/meta.yaml @@ -1,60 +1,65 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "regionReport" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Generate HTML or PDF reports to explore a set of regions such as the results from annotation-agnostic expression analysis of RNA-seq data at base-pair resolution performed by derfinder. You can also create reports for DESeq2 or edgeR results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8ec5fb1e7db2235d543b2a9a6660a3b3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-regionreport", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocManager, biovizBase, bumphunter (>= 1.7.6), derfinderPlot (>= 1.29.1), sessioninfo, DT, edgeR, ggbio (>= 1.35.2), ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker requirements: host: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-deformats >=1.30.0,<1.31.0' - - 'bioconductor-derfinder >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-deformats >=1.34.0,<1.35.0 + - bioconductor-derfinder >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-knitr >=1.6' - - 'r-knitrbootstrap >=0.9.0' + - r-knitr >=1.6 + - r-knitrbootstrap >=0.9.0 - r-refmanager - - 'r-rmarkdown >=0.9.5' + - r-rmarkdown >=0.9.5 run: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-deformats >=1.30.0,<1.31.0' - - 'bioconductor-derfinder >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-deformats >=1.34.0,<1.35.0 + - bioconductor-derfinder >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-knitr >=1.6' - - 'r-knitrbootstrap >=0.9.0' + - r-knitr >=1.6 + - r-knitrbootstrap >=0.9.0 - r-refmanager - - 'r-rmarkdown >=0.9.5' + - r-rmarkdown >=0.9.5 + +source: + md5: be8e7ffb64f6f476fc9c5ce47b80f971 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results' - description: 'Generate HTML or PDF reports to explore a set of regions such as the results from annotation-agnostic expression analysis of RNA-seq data at base-pair resolution performed by derfinder. You can also create reports for DESeq2 or edgeR results.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-regparallel/meta.yaml b/recipes/bioconductor-regparallel/meta.yaml index c057ce329d0b4..4462408411514 100644 --- a/recipes/bioconductor-regparallel/meta.yaml +++ b/recipes/bioconductor-regparallel/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "RegParallel" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: In many analyses, a large amount of variables have to be tested independently against the trait/endpoint of interest, and also adjusted for covariates and confounding factors at the same time. The major bottleneck in these is the amount of time that it takes to complete these analyses. With RegParallel, a large number of tests can be performed simultaneously. On a 12-core system, 144 variables can be tested simultaneously, with 1000s of variables processed in a matter of seconds via 'nested' parallel processing. Works for logistic regression, linear regression, conditional logistic regression, Cox proportional hazards and survival models, and Bayesian logistic regression. Also caters for generalised linear models that utilise survey weights created by the 'survey' CRAN package and that utilise 'survey::svyglm'. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Standard regression functions in R enabled for parallel processing over large data-frames -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 68533561edc82ac22088ffdd6e988aad build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-regparallel", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, knitr, DESeq2, airway, magrittr, Biobase, GEOquery, biomaRt, survminer, survey, rmarkdown requirements: host: @@ -40,14 +42,17 @@ requirements: - r-stringr - r-survival - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: dc949c5ebd514bd0020a203585bba26b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Standard regression functions in R enabled for parallel processing over large data-frames' - description: 'In many analyses, a large amount of variables have to be tested independently against the trait/endpoint of interest, and also adjusted for covariates and confounding factors at the same time. The major bottleneck in these is the amount of time that it takes to complete these analyses. With RegParallel, a large number of tests can be performed simultaneously. On a 12-core system, 144 variables can be tested simultaneously, with 1000s of variables processed in a matter of seconds via ''nested'' parallel processing. Works for logistic regression, linear regression, conditional logistic regression, Cox proportional hazards and survival models, and Bayesian logistic regression. Also caters for generalised linear models that utilise survey weights created by the ''survey'' CRAN package and that utilise ''survey::svyglm''.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-regparallel/post-link.sh b/recipes/bioconductor-regparallel/post-link.sh index 72bade8afac71..c3b83322ed056 100644 --- a/recipes/bioconductor-regparallel/post-link.sh +++ b/recipes/bioconductor-regparallel/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "regparallel-1.20.0" +installBiocDataPackage.sh "regparallel-1.24.0" diff --git a/recipes/bioconductor-regsplice/meta.yaml b/recipes/bioconductor-regsplice/meta.yaml index 4c0ad8ce56a86..eb29c3810a668 100644 --- a/recipes/bioconductor-regsplice/meta.yaml +++ b/recipes/bioconductor-regsplice/meta.yaml @@ -1,57 +1,63 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "regsplice" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Statistical methods for detection of differential splicing (differential exon usage) in RNA-seq and exon microarray data, using L1-regularization (lasso) to improve power. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: L1-regularization based methods for detection of differential splicing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3f63d2e93b02aec3ed044e2c56938d12 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-regsplice", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:regsplice + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-regsplice + path: recipes/bioconductor-regsplice + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-glmnet - r-pbapply run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-glmnet - r-pbapply + +source: + md5: 2056541facad1da77268eefce16f9995 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'L1-regularization based methods for detection of differential splicing' - description: 'Statistical methods for detection of differential splicing (differential exon usage) in RNA-seq and exon microarray data, using L1-regularization (lasso) to improve power.' - license_file: LICENSE -extra: - identifiers: - - biotools:regsplice - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-regsplice - path: recipes/bioconductor-regsplice - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-regutools/meta.yaml b/recipes/bioconductor-regutools/meta.yaml index 84af8fe9dc688..85c39c97a9a8d 100644 --- a/recipes/bioconductor-regutools/meta.yaml +++ b/recipes/bioconductor-regutools/meta.yaml @@ -1,58 +1,63 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "regutools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: RegulonDB has collected, harmonized and centralized data from hundreds of experiments for nearly two decades and is considered a point of reference for transcriptional regulation in Escherichia coli K12. Here, we present the regutools R package to facilitate programmatic access to RegulonDB data in computational biology. regutools provides researchers with the possibility of writing reproducible workflows with automated queries to RegulonDB. The regutools package serves as a bridge between RegulonDB data and the Bioconductor ecosystem by reusing the data structures and statistical methods powered by other Bioconductor packages. We demonstrate the integration of regutools with Bioconductor by analyzing transcription factor DNA binding sites and transcriptional regulatory networks from RegulonDB. We anticipate that regutools will serve as a useful building block in our progress to further our understanding of gene regulatory networks. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'regutools: an R package for data extraction from RegulonDB' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f8b22dfa98af4304de7be1654159626a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-regutools", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 2.1.0), covr requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dbi - r-rsqlite + +source: + md5: d9b98dbb968dcdd93c48fe18bd7e2ac8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'regutools: an R package for data extraction from RegulonDB' - description: 'RegulonDB has collected, harmonized and centralized data from hundreds of experiments for nearly two decades and is considered a point of reference for transcriptional regulation in Escherichia coli K12. Here, we present the regutools R package to facilitate programmatic access to RegulonDB data in computational biology. regutools provides researchers with the possibility of writing reproducible workflows with automated queries to RegulonDB. The regutools package serves as a bridge between RegulonDB data and the Bioconductor ecosystem by reusing the data structures and statistical methods powered by other Bioconductor packages. We demonstrate the integration of regutools with Bioconductor by analyzing transcription factor DNA binding sites and transcriptional regulatory networks from RegulonDB. We anticipate that regutools will serve as a useful building block in our progress to further our understanding of gene regulatory networks.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-remp/meta.yaml b/recipes/bioconductor-remp/meta.yaml index d8706ceaf727c..54e22bd988ba8 100644 --- a/recipes/bioconductor-remp/meta.yaml +++ b/recipes/bioconductor-remp/meta.yaml @@ -1,41 +1,50 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "REMP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Machine learning-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Repetitive Element Methylation Prediction -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee8e5abfbef5fc5798de790cacbe2cfe build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-remp", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-remp + path: recipes/bioconductor-remp + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, minfiDataEPIC requirements: + host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-caret - r-doparallel @@ -45,21 +54,22 @@ requirements: - r-ranger - r-readr - r-settings + run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-caret - r-doparallel @@ -69,18 +79,16 @@ requirements: - r-ranger - r-readr - r-settings + +source: + md5: 4f14fb9db26661b7e3ae34a0264bd67e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Repetitive Element Methylation Prediction' - description: 'Machine learning-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-remp - path: recipes/bioconductor-remp - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-repitools/meta.yaml b/recipes/bioconductor-repitools/meta.yaml index c78c6b1bf1018..a2d12c6b35dcc 100644 --- a/recipes/bioconductor-repitools/meta.yaml +++ b/recipes/bioconductor-repitools/meta.yaml @@ -1,39 +1,54 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "Repitools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, BayMeth for quantifying methylation etc. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Epigenomic tools -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3388cac60efdea157e1975abc5dcccd2 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-repitools", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:repitools + parent_recipe: + name: bioconductor-repitools + path: recipes/bioconductor-repitools + version: 1.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ShortRead, BSgenome.Hsapiens.UCSC.hg18 requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-ringo >=1.66.0,<1.67.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cluster - r-gplots @@ -42,43 +57,36 @@ requirements: - r-rsolnp - libblas - liblapack + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-ringo >=1.66.0,<1.67.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cluster - r-gplots - r-gsmoothr - r-mass - r-rsolnp - build: - - {{ compiler('c') }} - - make + +source: + md5: 3b0d4ab302e58e688e9eccfaa6902df8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'Epigenomic tools' - description: 'Tools for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, BayMeth for quantifying methylation etc.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:repitools - parent_recipe: - name: bioconductor-repitools - path: recipes/bioconductor-repitools - version: 1.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-reportingtools/meta.yaml b/recipes/bioconductor-reportingtools/meta.yaml index c00a0944d468c..9fec28c4b086b 100644 --- a/recipes/bioconductor-reportingtools/meta.yaml +++ b/recipes/bioconductor-reportingtools/meta.yaml @@ -1,40 +1,50 @@ -{% set version = "2.42.2" %} +{% set version = "2.46.0" %} {% set name = "ReportingTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser. For more examples, please visit our site: http:// research-pub.gene.com/ReportingTools.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Tools for making reports in various formats -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f5adbf6b8570e232b9f3e98f75eab59 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-reportingtools", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:reportingtools + parent_recipe: + name: bioconductor-reportingtools + path: recipes/bioconductor-reportingtools + version: 2.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla, org.Sc.sgd.db, rmarkdown, markdown requirements: + host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-category >=2.68.0,<2.69.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-pfam.db >=3.18.0,<3.19.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-category >=2.72.0,<2.73.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-pfam.db >=3.20.0,<3.21.0 - r-base - r-ggplot2 - r-hwriter @@ -42,20 +52,21 @@ requirements: - r-lattice - r-r.utils - r-xml + run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-category >=2.68.0,<2.69.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-pfam.db >=3.18.0,<3.19.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-category >=2.72.0,<2.73.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-pfam.db >=3.20.0,<3.21.0 - r-base - r-ggplot2 - r-hwriter @@ -63,19 +74,16 @@ requirements: - r-lattice - r-r.utils - r-xml + +source: + md5: c16cb671104ea6cb9603b5b35c30392c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Tools for making reports in various formats' - description: 'The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser. For more examples, please visit our site: http:// research-pub.gene.com/ReportingTools.' -extra: - identifiers: - - biotools:reportingtools - parent_recipe: - name: bioconductor-reportingtools - path: recipes/bioconductor-reportingtools - version: 2.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-repviz/meta.yaml b/recipes/bioconductor-repviz/meta.yaml index eb6ecad3257e6..bed6b515690f0 100644 --- a/recipes/bioconductor-repviz/meta.yaml +++ b/recipes/bioconductor-repviz/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "RepViz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: RepViz enables the view of a genomic region in a simple and efficient way. RepViz allows simultaneous viewing of both intra- and intergroup variation in sequencing counts of the studied conditions, as well as their comparison to the output features (e.g. identified peaks) from user selected data analysis methods.The RepViz tool is primarily designed for chromatin data such as ChIP-seq and ATAC-seq, but can also be used with other sequencing data such as RNA-seq, or combinations of different types of genomic data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Replicate oriented Visualization of a genomic region -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a740655d18448d4fb24e37ff1c60820d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-repviz", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, testthat requirements: host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base + +source: + md5: 94101722411a12bff37c268534f4f4a0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Replicate oriented Visualization of a genomic region' - description: 'RepViz enables the view of a genomic region in a simple and efficient way. RepViz allows simultaneous viewing of both intra- and intergroup variation in sequencing counts of the studied conditions, as well as their comparison to the output features (e.g. identified peaks) from user selected data analysis methods.The RepViz tool is primarily designed for chromatin data such as ChIP-seq and ATAC-seq, but can also be used with other sequencing data such as RNA-seq, or combinations of different types of genomic data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-residualmatrix/meta.yaml b/recipes/bioconductor-residualmatrix/meta.yaml index aa7ea294a226e..138d533a246f4 100644 --- a/recipes/bioconductor-residualmatrix/meta.yaml +++ b/recipes/bioconductor-residualmatrix/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "ResidualMatrix" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 76eaee4311380f83265d9b5ecacd7e49 +about: + description: Provides delayed computation of a matrix of residuals after fitting a linear model to each column of an input matrix. Also supports partial computation of residuals where selected factors are to be preserved in the output matrix. Implements a number of efficient methods for operating on the delayed matrix of residuals, most notably matrix multiplication and calculation of row/column sums or means. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Creating a DelayedMatrix of Regression Residuals build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-residualmatrix", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular requirements: host: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-matrix run: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-matrix +source: + md5: 4b6ec484f681ceb2dead4a076bbec9af + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Creating a DelayedMatrix of Regression Residuals' - description: 'Provides delayed computation of a matrix of residuals after fitting a linear model to each column of an input matrix. Also supports partial computation of residuals where selected factors are to be preserved in the output matrix. Implements a number of efficient methods for operating on the delayed matrix of residuals, most notably matrix multiplication and calculation of row/column sums or means.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-resolve/meta.yaml b/recipes/bioconductor-resolve/meta.yaml index 3f516a9501e1f..a61c3edd4e97a 100644 --- a/recipes/bioconductor-resolve/meta.yaml +++ b/recipes/bioconductor-resolve/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "RESOLVE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Cancer is a genetic disease caused by somatic mutations in genes controlling key biological functions such as cellular growth and division. Such mutations may arise both through cell-intrinsic and exogenous processes, generating characteristic mutational patterns over the genome named mutational signatures. The study of mutational signatures have become a standard component of modern genomics studies, since it can reveal which (environmental and endogenous) mutagenic processes are active in a tumor, and may highlight markers for therapeutic response. Mutational signatures computational analysis presents many pitfalls. First, the task of determining the number of signatures is very complex and depends on heuristics. Second, several signatures have no clear etiology, casting doubt on them being computational artifacts rather than due to mutagenic processes. Last, approaches for signatures assignment are greatly influenced by the set of signatures used for the analysis. To overcome these limitations, we developed RESOLVE (Robust EStimation Of mutationaL signatures Via rEgularization), a framework that allows the efficient extraction and assignment of mutational signatures. RESOLVE implements a novel algorithm that enables (i) the efficient extraction, (ii) exposure estimation, and (iii) confidence assessment during the computational inference of mutational signatures. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: 'RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3dd3a656ed19f5faa759f4b37c459f53 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-resolve", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, BiocStyle, testthat, knitr requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.1000genomes.hs37d5 >=0.99.0,<0.100.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mutationalpatterns >=3.12.0,<3.13.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.1000genomes.hs37d5 >=0.99.0,<0.100.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mutationalpatterns >=3.16.0,<3.17.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-ggplot2 @@ -38,15 +40,16 @@ requirements: - r-lsa - r-nnls - r-reshape2 + - r-rhpcblasctl run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.1000genomes.hs37d5 >=0.99.0,<0.100.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-mutationalpatterns >=3.12.0,<3.13.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.1000genomes.hs37d5 >=0.99.0,<0.100.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-mutationalpatterns >=3.16.0,<3.17.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-ggplot2 @@ -55,13 +58,17 @@ requirements: - r-lsa - r-nnls - r-reshape2 + - r-rhpcblasctl + +source: + md5: dbd5f54b85966d066eb0ca4db3395a20 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes' - description: 'Cancer is a genetic disease caused by somatic mutations in genes controlling key biological functions such as cellular growth and division. Such mutations may arise both through cell-intrinsic and exogenous processes, generating characteristic mutational patterns over the genome named mutational signatures. The study of mutational signatures have become a standard component of modern genomics studies, since it can reveal which (environmental and endogenous) mutagenic processes are active in a tumor, and may highlight markers for therapeutic response. Mutational signatures computational analysis presents many pitfalls. First, the task of determining the number of signatures is very complex and depends on heuristics. Second, several signatures have no clear etiology, casting doubt on them being computational artifacts rather than due to mutagenic processes. Last, approaches for signatures assignment are greatly influenced by the set of signatures used for the analysis. To overcome these limitations, we developed RESOLVE (Robust EStimation Of mutationaL signatures Via rEgularization), a framework that allows the efficient extraction and assignment of mutational signatures. RESOLVE implements a novel algorithm that enables (i) the efficient extraction, (ii) exposure estimation, and (iii) confidence assessment during the computational inference of mutational signatures.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-retrofit/meta.yaml b/recipes/bioconductor-retrofit/meta.yaml index 82688026bb8d0..3c3c13dbd902c 100644 --- a/recipes/bioconductor-retrofit/meta.yaml +++ b/recipes/bioconductor-retrofit/meta.yaml @@ -1,25 +1,28 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "retrofit" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2b804a752a293f14495e94adb39df466 +about: + description: RETROFIT is a Bayesian non-negative matrix factorization framework to decompose cell type mixtures in ST data without using external single-cell expression references. RETROFIT outperforms existing reference-based methods in estimating cell type proportions and reconstructing gene expressions in simulations with varying spot size and sample heterogeneity, irrespective of the quality or availability of the single-cell reference. RETROFIT recapitulates known cell-type localization patterns in a Slide-seq dataset of mouse cerebellum without using any single-cell data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics' build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-retrofit", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat, DescTools, ggplot2, corrplot, cowplot, grid, colorspace, png, reshape2, pals, RCurl requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-rcpp @@ -28,17 +31,14 @@ requirements: run: - r-base - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make +source: + md5: d3fb30a061a10552e92ee052157b4ca4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics' - description: 'RETROFIT is a Bayesian non-negative matrix factorization framework to decompose cell type mixtures in ST data without using external single-cell expression references. RETROFIT outperforms existing reference-based methods in estimating cell type proportions and reconstructing gene expressions in simulations with varying spot size and sample heterogeneity, irrespective of the quality or availability of the single-cell reference. RETROFIT recapitulates known cell-type localization patterns in a Slide-seq dataset of mouse cerebellum without using any single-cell data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-reusedata/build_failure.linux-64.yaml b/recipes/bioconductor-reusedata/build_failure.linux-64.yaml deleted file mode 100644 index ecc86f7cff23e..0000000000000 --- a/recipes/bioconductor-reusedata/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 1370555a597842bfc527b0664421636a289d7b039c85298dda7098e9b36ad0b9 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 2.0MB/s 0.0s - [?25h[34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m - [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 ??.?MB @ ??.?MB/s 0 failed 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 2.0MB/s 0.0s - [?25hMamba failed to solve: - - bioconductor-basilisk >=1.14.0,<1.15.0 - - bioconductor-biocfilecache >=2.10.0,<2.11.0 - - bioconductor-rcwl >=1.18.0,<1.19.0 - - r-yaml - - bioconductor-s4vectors >=0.40.0,<0.41.0 - - r-base 4.3.* - - bioconductor-rcwlpipelines >=1.18.0,<1.19.0 - - r-jsonlite - - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested bioconductor-rcwlpipelines >=1.18.0,<1.19.0 - - - - Leaving build/test directories: - Work: - /opt/conda/conda-bld/work - Test: - /opt/conda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl - Build: - source activate /opt/conda/conda-bld/_build_env - - - Traceback (most recent call last): - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action - t = self.solve(specs) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - bioconductor-basilisk >=1.14.0,<1.15.0 - - bioconductor-biocfilecache >=2.10.0,<2.11.0 - - bioconductor-rcwl >=1.18.0,<1.19.0 - - r-yaml - - bioconductor-s4vectors >=0.40.0,<0.41.0 - - r-base 4.3.* - - bioconductor-rcwlpipelines >=1.18.0,<1.19.0 - - r-jsonlite - - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested bioconductor-rcwlpipelines >=1.18.0,<1.19.0 - - - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build - output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs - for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set - conda_packages = finalize_outputs_pass( - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass - fm = finalize_metadata( - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata - build_unsat, host_unsat = add_upstream_pins(m, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins - host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files - deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies - actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rcwlpipelines[version='>=1.18.0,<1.19.0']")} -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-reusedata/meta.yaml b/recipes/bioconductor-reusedata/meta.yaml index 3e52defa7ad81..a9b383a7d61df 100644 --- a/recipes/bioconductor-reusedata/meta.yaml +++ b/recipes/bioconductor-reusedata/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.2.2" %} +{% set version = "1.6.0" %} {% set name = "ReUseData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ReUseData is an _R/Bioconductor_ software tool to provide a systematic and versatile approach for standardized and reproducible data management. ReUseData facilitates transformation of shell or other ad hoc scripts for data preprocessing into workflow-based data recipes. Evaluation of data recipes generate curated data files in their generic formats (e.g., VCF, bed). Both recipes and data are cached using database infrastructure for easy data management and reuse. Prebuilt data recipes are available through ReUseData portal ("https://rcwl.org/dataRecipes/") with full annotation and user instructions. Pregenerated data are available through ReUseData cloud bucket that is directly downloadable through "getCloudData()". + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Reusable and reproducible Data Management -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c0041ec5d810d0d043c7375e04e78c06 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-reusedata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle requirements: host: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-rcwl >=1.18.0,<1.19.0' - - 'bioconductor-rcwlpipelines >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-rcwl >=1.22.0,<1.23.0 + - bioconductor-rcwlpipelines >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-jsonlite - r-yaml run: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-rcwl >=1.18.0,<1.19.0' - - 'bioconductor-rcwlpipelines >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-rcwl >=1.22.0,<1.23.0 + - bioconductor-rcwlpipelines >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-jsonlite - r-yaml + +source: + md5: c96d63fa9beb9571fd690ff5525f0713 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Reusable and reproducible Data Management' - description: 'ReUseData is an _R/Bioconductor_ software tool to provide a systematic and versatile approach for standardized and reproducible data management. ReUseData facilitates transformation of shell or other ad hoc scripts for data preprocessing into workflow-based data recipes. Evaluation of data recipes generate curated data files in their generic formats (e.g., VCF, bed). Both recipes and data are cached using database infrastructure for easy data management and reuse. Prebuilt data recipes are available through ReUseData portal ("https://rcwl.org/dataRecipes/") with full annotation and user instructions. Pregenerated data are available through ReUseData cloud bucket that is directly downloadable through "getCloudData()".' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rexposome/meta.yaml b/recipes/bioconductor-rexposome/meta.yaml index 83b17e2db684f..9e8e4503f14d0 100644 --- a/recipes/bioconductor-rexposome/meta.yaml +++ b/recipes/bioconductor-rexposome/meta.yaml @@ -1,29 +1,32 @@ -{% set version = "1.24.1" %} +{% set version = "1.28.0" %} {% set name = "rexposome" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package that allows to explore the exposome and to perform association analyses between exposures and health outcomes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Exposome exploration and outcome data analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5dec247e3db216fed87e97cbfbf254cc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rexposome", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: mclust, flexmix, testthat, BiocStyle, knitr, formatR, rmarkdown requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-circlize - r-corrplot @@ -45,9 +48,10 @@ requirements: - r-scales - r-scatterplot3d - r-stringr + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-circlize - r-corrplot @@ -69,13 +73,16 @@ requirements: - r-scales - r-scatterplot3d - r-stringr + +source: + md5: 2da6c4f78af706bbf12f8a47d0a03378 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Exposome exploration and outcome data analysis' - description: 'Package that allows to explore the exposome and to perform association analyses between exposures and health outcomes.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rfarm/build_failure.linux-64.yaml b/recipes/bioconductor-rfarm/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..cafc206898dbc --- /dev/null +++ b/recipes/bioconductor-rfarm/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 440751d4c3ec621b0a9e7ee75fc76b46be5847a6b78c2353e102db32c78d04b9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-rvest: 1.0.4-r44hc72bb7e_1 conda-forge + r-selectr: 0.4_2-r44hc72bb7e_4 conda-forge + r-stringi: 1.8.4-r44h33cde33_3 conda-forge + r-stringr: 1.5.1-r44h785f33e_1 conda-forge + r-sys: 3.4.3-r44h2b5f3a1_0 conda-forge + r-tibble: 3.2.1-r44hdb488b9_3 conda-forge + r-utf8: 1.2.4-r44hb1dbf0f_1 conda-forge + r-vctrs: 0.6.5-r44h0d4f4ea_1 conda-forge + r-withr: 3.0.2-r44hc72bb7e_0 conda-forge + r-xml2: 1.3.6-r44h8194278_2 conda-forge + rav1e: 0.6.6-he8a937b_2 conda-forge + readline: 8.2-h8228510_1 conda-forge + sed: 4.8-he412f7d_0 conda-forge + setuptools: 75.6.0-pyhff2d567_1 conda-forge + svt-av1: 2.3.0-h5888daf_0 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tktable: 2.10-h8bc8fbc_6 conda-forge + toml: 0.10.2-pyhd8ed1ab_1 conda-forge + tomlkit: 0.13.2-pyha770c72_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + x265: 3.5-h924138e_3 conda-forge + xmltodict: 0.14.2-pyhd8ed1ab_1 conda-forge + xorg-libice: 1.1.2-hb9d3cd8_0 conda-forge + xorg-libsm: 1.2.5-he73a12e_0 conda-forge + xorg-libx11: 1.8.10-h4f16b4b_1 conda-forge + xorg-libxau: 1.0.12-hb9d3cd8_0 conda-forge + xorg-libxdmcp: 1.1.5-hb9d3cd8_0 conda-forge + xorg-libxext: 1.3.6-hb9d3cd8_0 conda-forge + xorg-libxrender: 0.9.12-hb9d3cd8_0 conda-forge + xorg-libxt: 1.3.1-hb9d3cd8_0 conda-forge + yaml: 0.2.5-h7f98852_2 conda-forge + yq: 3.4.3-pyhd8ed1ab_1 conda-forge + zlib: 1.3.1-hb9d3cd8_2 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... + + done + export PREFIX=/opt/conda/conda-bld/bioconductor-rfarm_1734650451896/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold + export SRC_DIR=/opt/conda/conda-bld/bioconductor-rfarm_1734650451896/test_tmp + /opt/conda/conda-bld/bioconductor-rfarm_1734650451896/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/R -e 'library('\''rfaRm'\'')' + + R version 4.4.2 (2024-10-31) -- "Pile of Leaves" + Copyright (C) 2024 The R Foundation for Statistical Computing + Platform: x86_64-conda-linux-gnu + + R is free software and comes with ABSOLUTELY NO WARRANTY. + You are welcome to redistribute it under certain conditions. + Type 'license()' or 'licence()' for distribution details. + + Natural language support but running in an English locale + + R is a collaborative project with many contributors. + Type 'contributors()' for more information and + 'citation()' on how to cite R or R packages in publications. + + Type 'demo()' for some demos, 'help()' for on-line help, or + 'help.start()' for an HTML browser interface to help. + Type 'q()' to quit R. + + During startup - Warning message: + Setting LC_TIME failed, using "C" + > library('rfaRm') + Error: package or namespace load failed for rfaRm: + .onLoad failed in loadNamespace() for 'rfaRm', details: + call: readLines(clanMembershipCon) + error: cannot open the connection to 'https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/database_files/clan_membership.txt.gz' + In addition: Warning message: + In readLines(clanMembershipCon) : + URL 'https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/database_files/clan_membership.txt.gz': status was 'SSL connect error' + Execution halted + WARNING: Tests failed for bioconductor-rfarm-1.18.0-r44hdfd78af_0.tar.bz2 - moving package to /opt/conda/conda-bld/broken + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-rfarm_1734650451896/test_tmp/conda_test_runner.sh']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: bioconductor-rfarm-1.18.0-r44hdfd78af_0.tar.bz2 +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-rfarm/meta.yaml b/recipes/bioconductor-rfarm/meta.yaml index 0251337690723..6f7fd8ad565f9 100644 --- a/recipes/bioconductor-rfarm/meta.yaml +++ b/recipes/bioconductor-rfarm/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "rfaRm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: rfaRm provides a client interface to the Rfam database of RNA families. Data that can be retrieved include RNA families, secondary structure images, covariance models, sequences within each family, alignments leading to the identification of a family and secondary structures in the dot-bracket format. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: An R interface to the Rfam database -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c12fb6805f6eecba196474a4527f241a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rfarm", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics, RUnit requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-httr @@ -35,9 +37,9 @@ requirements: - r-stringi - r-xml2 run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-httr @@ -47,13 +49,16 @@ requirements: - r-rvest - r-stringi - r-xml2 + +source: + md5: fa2958c8284e8a5eaee4258da8074379 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'An R interface to the Rfam database' - description: 'rfaRm provides a client interface to the Rfam database of RNA families. Data that can be retrieved include RNA families, secondary structure images, covariance models, sequences within each family, alignments leading to the identification of a family and secondary structures in the dot-bracket format.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rfastp/meta.yaml b/recipes/bioconductor-rfastp/meta.yaml index 8acaaa9125710..d9365550cfdf8 100644 --- a/recipes/bioconductor-rfastp/meta.yaml +++ b/recipes/bioconductor-rfastp/meta.yaml @@ -1,29 +1,35 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "Rfastp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Rfastp is an R wrapper of fastp developed in c++. fastp performs quality control for fastq files. including low quality bases trimming, polyX trimming, adapter auto-detection and trimming, paired-end reads merging, UMI sequence/id handling. Rfastp can concatenate multiple files into one file (like shell command cat) and accept multiple files as input. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX trimming) and UMI Sequence Parsing). -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9f6903cb485151c4d3c368abf5193309 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rfastp", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat, knitr, rmarkdown # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-ggplot2 - r-rcpp @@ -31,25 +37,26 @@ requirements: - r-rjson - libblas - liblapack + - zlib + - liblzma-devel run: - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-ggplot2 - r-rcpp - r-reshape2 - r-rjson - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 32c7dac97e09175f4fe7941ccd764de9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX trimming) and UMI Sequence Parsing).' - description: 'Rfastp is an R wrapper of fastp developed in c++. fastp performs quality control for fastq files. including low quality bases trimming, polyX trimming, adapter auto-detection and trimming, paired-end reads merging, UMI sequence/id handling. Rfastp can concatenate multiple files into one file (like shell command cat) and accept multiple files as input.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rforproteomics/meta.yaml b/recipes/bioconductor-rforproteomics/meta.yaml index 4a0c7b03f4d54..89a7fd3f8da64 100644 --- a/recipes/bioconductor-rforproteomics/meta.yaml +++ b/recipes/bioconductor-rforproteomics/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "RforProteomics" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains code to illustrate the 'Using R and Bioconductor for proteomics data analysis' and 'Visualisation of proteomics data using R and Bioconductor' manuscripts. The vignettes describe the code and data needed to reproduce the examples and figures described in the paper and functionality for proteomics visualisation. It also contain various function to discover R software for mass spectrometry and proteomics. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d75aedb5902ea26a18e39da6848db4c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rforproteomics", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationDbi, rpx (>= 2.0.3), DT, knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, MALDIquant (>= 1.12), MALDIquantForeign, readBrukerFlexData, Rdisop, OrgMassSpecR, SummarizedExperiment, BRAIN, rols, hpar, GO.db, org.Hs.eg.db, e1071, biomaRt, RColorBrewer, ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, MSnID, msmsTests, msmsEDA, DEP, corrplot, beanplot, Heatplus, gplots, VennDiagram, protViz, genefilter, plotly, gridExtra, dplyr, lubridate, magick, cleaver requirements: host: - - 'bioconductor-biocviews >=1.70.0,<1.71.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - bioconductor-biocviews >=1.74.0,<1.75.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 - r-base - r-biocmanager - r-r.utils run: - - 'bioconductor-biocviews >=1.70.0,<1.71.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' + - bioconductor-biocviews >=1.74.0,<1.75.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 - r-base - r-biocmanager - r-r.utils - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 8c73b19d4642edded08e28a0c194d2e1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Companion package to the ''Using R and Bioconductor for proteomics data analysis'' publication' - description: 'This package contains code to illustrate the ''Using R and Bioconductor for proteomics data analysis'' and ''Visualisation of proteomics data using R and Bioconductor'' manuscripts. The vignettes describe the code and data needed to reproduce the examples and figures described in the paper and functionality for proteomics visualisation. It also contain various function to discover R software for mass spectrometry and proteomics.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rforproteomics/post-link.sh b/recipes/bioconductor-rforproteomics/post-link.sh index 8efbae4b8ad53..ef4bc4736c8bc 100644 --- a/recipes/bioconductor-rforproteomics/post-link.sh +++ b/recipes/bioconductor-rforproteomics/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rforproteomics-1.40.0" +installBiocDataPackage.sh "rforproteomics-1.44.0" diff --git a/recipes/bioconductor-rfpred/meta.yaml b/recipes/bioconductor-rfpred/meta.yaml index 3c6bb3e73f786..46144dd4e9ed8 100644 --- a/recipes/bioconductor-rfpred/meta.yaml +++ b/recipes/bioconductor-rfpred/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "rfPred" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Based on external numerous data files where rfPred scores are pre-calculated on all genomic positions of the human exome, the package gives rfPred scores to missense variants identified by the chromosome, the position (hg19 version), the referent and alternative nucleotids and the uniprot identifier of the protein. Note that for using the package, the user has to download the TabixFile and index (approximately 3.3 Go). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2 ) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Assign rfPred functional prediction scores to a missense variants list -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 125e88d593749d17979dfd08a67ea330 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rfpred", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:rfpred + - doi:10.1101/037127 + parent_recipe: + name: bioconductor-rfpred + path: recipes/bioconductor-rfpred + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-data.table - libblas - liblapack run: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-data.table - build: - - {{ compiler('c') }} - - make + +source: + md5: 92e824180ef6f21a8636166a146a56c0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2 )' - summary: 'Assign rfPred functional prediction scores to a missense variants list' - description: 'Based on external numerous data files where rfPred scores are pre-calculated on all genomic positions of the human exome, the package gives rfPred scores to missense variants identified by the chromosome, the position (hg19 version), the referent and alternative nucleotids and the uniprot identifier of the protein. Note that for using the package, the user has to download the TabixFile and index (approximately 3.3 Go).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:rfpred - - doi:10.1101/037127 - parent_recipe: - name: bioconductor-rfpred - path: recipes/bioconductor-rfpred - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgadem/meta.yaml b/recipes/bioconductor-rgadem/meta.yaml index 9ea5c84cd97c1..7fb65b98bb179 100644 --- a/recipes/bioconductor-rgadem/meta.yaml +++ b/recipes/bioconductor-rgadem/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "2.50.0" %} +{% set version = "2.54.0" %} {% set name = "rGADEM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data. It is an open-source R package, which is based on the GADEM software. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: de novo motif discovery -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 17a121fa91f30cba09ed9dbb6b318555 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgadem", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:rgadem + - doi:10.1371/journal.pone.0016432 + parent_recipe: + name: bioconductor-rgadem + path: recipes/bioconductor-rgadem + version: 2.28.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Hsapiens.UCSC.hg19, rtracklayer requirements: + build: + - {{ compiler('c') }} + - automake + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-seqlogo >=1.72.0,<1.73.0 - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-seqlogo >=1.72.0,<1.73.0 - r-base - build: - - {{ compiler('c') }} - - automake - - make + +source: + md5: 241489c941f013446526da273d7d6584 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'de novo motif discovery' - description: 'rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data. It is an open-source R package, which is based on the GADEM software.' -extra: - identifiers: - - biotools:rgadem - - doi:10.1371/journal.pone.0016432 - parent_recipe: - name: bioconductor-rgadem - path: recipes/bioconductor-rgadem - version: 2.28.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgenometracks/meta.yaml b/recipes/bioconductor-rgenometracks/meta.yaml index 56ab97b269241..f20a60ccc2e00 100644 --- a/recipes/bioconductor-rgenometracks/meta.yaml +++ b/recipes/bioconductor-rgenometracks/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "rGenomeTracks" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 860c81f62e3abf51de44d4dcdcdbfeef +about: + description: rGenomeTracks package leverages the power of pyGenomeTracks software with the interactivity of R. pyGenomeTracks is a python software that offers robust method for visualizing epigenetic data files like narrowPeak, Hic matrix, TADs and arcs, however though, here is no way currently to use it within R interactive session. rGenomeTracks wrapped the whole functionality of pyGenomeTracks with additional utilites to make to more pleasant for R users. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Integerated visualization of epigenomic data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgenometracks", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: rmarkdown, knitr, testthat (>= 3.0.0) # SystemRequirements: pyGenomeTracks (prefered to use install_pyGenomeTracks()) requirements: host: - - 'bioconductor-rgenometracksdata >=0.99.0,<0.100.0' + - bioconductor-rgenometracksdata >=0.99.0,<0.100.0 - r-base - r-imager - r-reticulate run: - - 'bioconductor-rgenometracksdata >=0.99.0,<0.100.0' + - bioconductor-rgenometracksdata >=0.99.0,<0.100.0 - r-base - r-imager - r-reticulate +source: + md5: 5aa4d66be2643587e0b63e95fbe28629 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Integerated visualization of epigenomic data' - description: 'rGenomeTracks package leverages the power of pyGenomeTracks software with the interactivity of R. pyGenomeTracks is a python software that offers robust method for visualizing epigenetic data files like narrowPeak, Hic matrix, TADs and arcs, however though, here is no way currently to use it within R interactive session. rGenomeTracks wrapped the whole functionality of pyGenomeTracks with additional utilites to make to more pleasant for R users.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgenometracksdata/meta.yaml b/recipes/bioconductor-rgenometracksdata/meta.yaml index f99c1c756acc0..e3d8fa290b956 100644 --- a/recipes/bioconductor-rgenometracksdata/meta.yaml +++ b/recipes/bioconductor-rgenometracksdata/meta.yaml @@ -1,41 +1,41 @@ {% set version = "0.99.0" %} {% set name = "rGenomeTracksData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 713103a8b4b4e48fa762ef589a43ffb8 +about: + description: rGenomeTracksData is a collection of data from pyGenomeTracks project. The purpose of this data is testing and demonstration of rGenomeTracks. This package include 14 sample file from different genomic and epigenomic file format. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Demonstration Data from rGenomeTracks Package build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgenometracksdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocManager, devtools requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 713103a8b4b4e48fa762ef589a43ffb8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Demonstration Data from rGenomeTracks Package' - description: 'rGenomeTracksData is a collection of data from pyGenomeTracks project. The purpose of this data is testing and demonstration of rGenomeTracks. This package include 14 sample file from different genomic and epigenomic file format.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgmqllib/meta.yaml b/recipes/bioconductor-rgmqllib/meta.yaml index 8807cc1353fdd..6962df7b5f6aa 100644 --- a/recipes/bioconductor-rgmqllib/meta.yaml +++ b/recipes/bioconductor-rgmqllib/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "RGMQLlib" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d8ad27b1fe0c5eff6135285db972cab2 +about: + description: A package that contains scala libraries to call GMQL from R used by RGMQL package. It contains a scalable data management engine written in Scala programming language. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: RGMQLlib, java libraries to run GMQL scala API build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgmqllib", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: @@ -26,13 +24,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 93c5a7fd1d93d309300ab5a679790507 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'RGMQLlib, java libraries to run GMQL scala API' - description: 'A package that contains scala libraries to call GMQL from R used by RGMQL package. It contains a scalable data management engine written in Scala programming language.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgmqllib/post-link.sh b/recipes/bioconductor-rgmqllib/post-link.sh index 1b73edc0605c1..c21b9b9830e55 100644 --- a/recipes/bioconductor-rgmqllib/post-link.sh +++ b/recipes/bioconductor-rgmqllib/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rgmqllib-1.22.0" +installBiocDataPackage.sh "rgmqllib-1.26.0" diff --git a/recipes/bioconductor-rgntx/meta.yaml b/recipes/bioconductor-rgntx/meta.yaml index 265575b96ae87..aebfbb8730487 100644 --- a/recipes/bioconductor-rgntx/meta.yaml +++ b/recipes/bioconductor-rgntx/meta.yaml @@ -1,52 +1,57 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "RgnTX" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: RgnTX allows the integration of transcriptome annotations so as to model the complex alternative splicing patterns. It supports the testing of transcriptome elements without clear isoform association, which is often the real scenario due to technical limitations. It involves functions that do permutaion test for evaluating association between features and transcriptome regions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ce438a2822a6541467c9781a3c48b26 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgntx", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-regioner >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-regioner >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 - r-base - r-ggplot2 run: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-regioner >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-regioner >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 - r-base - r-ggplot2 + +source: + md5: 5569e79d566959caaf9fa785838cde42 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity' - description: 'RgnTX allows the integration of transcriptome annotations so as to model the complex alternative splicing patterns. It supports the testing of transcriptome elements without clear isoform association, which is often the real scenario due to technical limitations. It involves functions that do permutaion test for evaluating association between features and transcriptome regions.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgoslin/meta.yaml b/recipes/bioconductor-rgoslin/meta.yaml index ed8b1ed6bb203..d22a8bdf0b90a 100644 --- a/recipes/bioconductor-rgoslin/meta.yaml +++ b/recipes/bioconductor-rgoslin/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "rgoslin" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The R implementation for the Grammar of Succint Lipid Nomenclature parses different short hand notation dialects for lipid names. It normalizes them to a standard name. It further provides calculated monoisotopic masses and sum formulas for each successfully parsed lipid name and supplements it with LIPID MAPS Category and Class information. Also, the structural level and further structural details about the head group, fatty acyls and functional groups are returned, where applicable. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Lipid Shorthand Name Parsing and Normalization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 211ef77e63cc8394ebc5eee33328cd08 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgoslin", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 2.1.0), BiocStyle, knitr, rmarkdown, kableExtra, BiocManager, stringr, stringi, ggplot2, tibble, lipidr requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-dplyr - - 'r-rcpp >=1.0.3' + - r-rcpp >=1.0.3 - libblas - liblapack run: - r-base - r-dplyr - - 'r-rcpp >=1.0.3' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=1.0.3 + +source: + md5: 4affb62b178e0dcc6453a7f34755e471 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Lipid Shorthand Name Parsing and Normalization' - description: 'The R implementation for the Grammar of Succint Lipid Nomenclature parses different short hand notation dialects for lipid names. It normalizes them to a standard name. It further provides calculated monoisotopic masses and sum formulas for each successfully parsed lipid name and supplements it with LIPID MAPS Category and Class information. Also, the structural level and further structural details about the head group, fatty acyls and functional groups are returned, where applicable.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgraph2js/meta.yaml b/recipes/bioconductor-rgraph2js/meta.yaml index 0212b86e5dd86..464f257dc29b3 100644 --- a/recipes/bioconductor-rgraph2js/meta.yaml +++ b/recipes/bioconductor-rgraph2js/meta.yaml @@ -1,56 +1,62 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "RGraph2js" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Generator of web pages which display interactive network/graph visualizations with D3js, jQuery and Raphael. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Convert a Graph into a D3js Script -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ccb2f26623270911ba855aa97e1269e1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgraph2js", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rgraph2js + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rgraph2js + path: recipes/bioconductor-rgraph2js + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocStyle, BiocGenerics, xtable, sna # SystemRequirements: jQuery, jQueryUI, qTip2, D3js and Raphael are required Javascript libraries made available via the online CDNJS service (http://cdnjs.cloudflare.com). requirements: host: - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-digest - r-rjson - r-whisker - jquery run: - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-digest - r-rjson - r-whisker - jquery + +source: + md5: 05152598c5c004db4823453285452209 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Convert a Graph into a D3js Script' - description: 'Generator of web pages which display interactive network/graph visualizations with D3js, jQuery and Raphael.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:rgraph2js - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-rgraph2js - path: recipes/bioconductor-rgraph2js - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgraphviz/meta.yaml b/recipes/bioconductor-rgraphviz/meta.yaml index 299076f3c8b84..b42b7ae98b1a6 100644 --- a/recipes/bioconductor-rgraphviz/meta.yaml +++ b/recipes/bioconductor-rgraphviz/meta.yaml @@ -1,51 +1,57 @@ -{% set version = "2.46.0" %} +{% set version = "2.50.0" %} {% set name = "Rgraphviz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: EPL + summary: Provides plotting capabilities for R graph objects -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b93e5d1c383b1e5cd06e4dec89a43ce8 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgraphviz", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:rgraphviz + - usegalaxy-eu:rgraphviz + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, XML # SystemRequirements: optionally Graphviz (>= 2.16) requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - libblas - liblapack run: - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 0e7b5c05caa3f2b31e26f04a26d4974b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: EPL - summary: 'Provides plotting capabilities for R graph objects' - description: 'Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} - - usegalaxy-eu:{{ name|lower }} + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgreat/meta.yaml b/recipes/bioconductor-rgreat/meta.yaml index 607172e832e2e..3f9a2d5f97eb7 100644 --- a/recipes/bioconductor-rgreat/meta.yaml +++ b/recipes/bioconductor-rgreat/meta.yaml @@ -1,43 +1,60 @@ -{% set version = "2.4.0" %} +{% set version = "2.8.0" %} {% set name = "rGREAT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: GREAT (Genomic Regions Enrichment of Annotations Tool) is a type of functional enrichment analysis directly performed on genomic regions. This package implements the GREAT algorithm (the local GREAT analysis), also it supports directly interacting with the GREAT web service (the online GREAT analysis). Both analysis can be viewed by a Shiny application. rGREAT by default supports more than 600 organisms and a large number of gene set collections, as well as self-provided gene sets and organisms from users. Additionally, it implements a general method for dealing with background regions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: GREAT Analysis - Functional Enrichment on Genomic Regions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 89ee57f3429887678846bba965ce84dc build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgreat", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:rgreat + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rgreat + path: recipes/bioconductor-rgreat + version: 1.12.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 0.3), knitr, rmarkdown, BiocManager, org.Mm.eg.db, msigdbr, KEGGREST, reactome.db requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 - r-base - r-circlize - r-digest - r-doparallel - r-dt - r-foreach - - 'r-getoptlong >=0.0.9' + - r-getoptlong >=0.0.9 - r-globaloptions - r-progress - r-rcolorbrewer @@ -47,24 +64,25 @@ requirements: - r-shiny - libblas - liblapack + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 - r-base - r-circlize - r-digest - r-doparallel - r-dt - r-foreach - - 'r-getoptlong >=0.0.9' + - r-getoptlong >=0.0.9 - r-globaloptions - r-progress - r-rcolorbrewer @@ -72,25 +90,16 @@ requirements: - r-rcurl - r-rjson - r-shiny - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 65306910d877fc9a7fadb33224ed9729 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'GREAT Analysis - Functional Enrichment on Genomic Regions' - description: 'GREAT (Genomic Regions Enrichment of Annotations Tool) is a type of functional enrichment analysis directly performed on genomic regions. This package implements the GREAT algorithm (the local GREAT analysis), also it supports directly interacting with the GREAT web service (the online GREAT analysis). Both analysis can be viewed by a Shiny application. rGREAT by default supports more than 600 organisms and a large number of gene set collections, as well as self-provided gene sets and organisms from users. Additionally, it implements a general method for dealing with background regions.' - license_file: LICENSE -extra: - identifiers: - - biotools:rgreat - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-rgreat - path: recipes/bioconductor-rgreat - version: 1.12.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgsea/meta.yaml b/recipes/bioconductor-rgsea/meta.yaml index 9042f59b32251..5e71552361c67 100644 --- a/recipes/bioconductor-rgsea/meta.yaml +++ b/recipes/bioconductor-rgsea/meta.yaml @@ -1,41 +1,22 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "RGSEA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Combining bootstrap aggregating and Gene set enrichment analysis (GSEA), RGSEA is a classfication algorithm with high robustness and no over-fitting problem. It performs well especially for the data generated from different exprements. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL(>=3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Random Gene Set Enrichment Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 426ab6d4dc463399d014c6e76c3f8c75 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgsea", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, GEOquery, knitr, RUnit -requirements: - host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - r-base - run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL(>=3) - summary: 'Random Gene Set Enrichment Analysis' - description: 'Combining bootstrap aggregating and Gene set enrichment analysis (GSEA), RGSEA is a classfication algorithm with high robustness and no over-fitting problem. It performs well especially for the data generated from different exprements.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:rgsea @@ -45,3 +26,28 @@ extra: path: recipes/bioconductor-rgsea version: 1.14.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, GEOquery, knitr, RUnit +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - r-base + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - r-base + +source: + md5: 08b1d6a2df3449e12fe7d0358fb62404 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-rgsepd/meta.yaml b/recipes/bioconductor-rgsepd/meta.yaml index c3b4954bb93cf..980dbe8de8b9f 100644 --- a/recipes/bioconductor-rgsepd/meta.yaml +++ b/recipes/bioconductor-rgsepd/meta.yaml @@ -1,61 +1,67 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "rgsepd" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at transcript IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Gene Set Enrichment / Projection Displays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0ca30d2f68c98bcc24cc5c5fbc5951b3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgsepd", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rgsepd + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rgsepd + path: recipes/bioconductor-rgsepd + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: boot, tools, BiocGenerics, knitr, xtable requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-goseq >=1.54.0,<1.55.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-goseq >=1.58.0,<1.59.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-gplots run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-goseq >=1.54.0,<1.55.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-goseq >=1.58.0,<1.59.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-gplots + +source: + md5: 8c4849c46cf35321625ef3e7b502def8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Gene Set Enrichment / Projection Displays' - description: 'R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at transcript IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:rgsepd - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-rgsepd - path: recipes/bioconductor-rgsepd - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgu34a.db/meta.yaml b/recipes/bioconductor-rgu34a.db/meta.yaml index 460be188747cf..d47547ec716f1 100644 --- a/recipes/bioconductor-rgu34a.db/meta.yaml +++ b/recipes/bioconductor-rgu34a.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "rgu34a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e99dc4c05360b49a2249cb5de0b1dd4e +about: + description: Affymetrix Affymetrix RG_U34A Array annotation data (chip rgu34a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix RG_U34A Array annotation data (chip rgu34a) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgu34a.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e99dc4c05360b49a2249cb5de0b1dd4e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix RG_U34A Array annotation data (chip rgu34a)' - description: 'Affymetrix Affymetrix RG_U34A Array annotation data (chip rgu34a) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgu34acdf/meta.yaml b/recipes/bioconductor-rgu34acdf/meta.yaml index 195b7856cd031..8fbcdb5aada5c 100644 --- a/recipes/bioconductor-rgu34acdf/meta.yaml +++ b/recipes/bioconductor-rgu34acdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rgu34acdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dcfa7ecce00e529f93809759ed837b8d +about: + description: A package containing an environment representing the RG_U34A.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: rgu34acdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgu34acdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: dcfa7ecce00e529f93809759ed837b8d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: rgu34acdf - description: 'A package containing an environment representing the RG_U34A.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgu34aprobe/meta.yaml b/recipes/bioconductor-rgu34aprobe/meta.yaml index 2e3ca3c13f057..1bcec3c6bb407 100644 --- a/recipes/bioconductor-rgu34aprobe/meta.yaml +++ b/recipes/bioconductor-rgu34aprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rgu34aprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 902aee259a2894fa8713c4bf9266c0e2 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RG-U34A\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type rgu34a build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgu34aprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 902aee259a2894fa8713c4bf9266c0e2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type rgu34a' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RG-U34A\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgu34b.db/meta.yaml b/recipes/bioconductor-rgu34b.db/meta.yaml index 2be3c456f72de..e654e576e4fdf 100644 --- a/recipes/bioconductor-rgu34b.db/meta.yaml +++ b/recipes/bioconductor-rgu34b.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "rgu34b.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5aeb80d5190bf2dcffa6b9264d3db33f +about: + description: Affymetrix Affymetrix RG_U34B Array annotation data (chip rgu34b) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix RG_U34B Array annotation data (chip rgu34b) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgu34b.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5aeb80d5190bf2dcffa6b9264d3db33f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix RG_U34B Array annotation data (chip rgu34b)' - description: 'Affymetrix Affymetrix RG_U34B Array annotation data (chip rgu34b) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgu34bcdf/meta.yaml b/recipes/bioconductor-rgu34bcdf/meta.yaml index c49a72cd0134b..1fb89a746da21 100644 --- a/recipes/bioconductor-rgu34bcdf/meta.yaml +++ b/recipes/bioconductor-rgu34bcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rgu34bcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 428b3a39f0d8addd7d863539b8cda6ea +about: + description: A package containing an environment representing the RG_U34B.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: rgu34bcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgu34bcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 428b3a39f0d8addd7d863539b8cda6ea + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: rgu34bcdf - description: 'A package containing an environment representing the RG_U34B.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgu34bprobe/meta.yaml b/recipes/bioconductor-rgu34bprobe/meta.yaml index 01e2a8f025744..38b15f53997c1 100644 --- a/recipes/bioconductor-rgu34bprobe/meta.yaml +++ b/recipes/bioconductor-rgu34bprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rgu34bprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2d6488309c5e54231a18e2ecf5608bb1 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RG-U34B\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type rgu34b build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgu34bprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2d6488309c5e54231a18e2ecf5608bb1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type rgu34b' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RG-U34B\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgu34c.db/meta.yaml b/recipes/bioconductor-rgu34c.db/meta.yaml index 61199d1900ac5..6f9c88d383943 100644 --- a/recipes/bioconductor-rgu34c.db/meta.yaml +++ b/recipes/bioconductor-rgu34c.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "rgu34c.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e19f250869a9894bc9d069a4baf39a3c +about: + description: Affymetrix Affymetrix RG_U34C Array annotation data (chip rgu34c) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix RG_U34C Array annotation data (chip rgu34c) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgu34c.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e19f250869a9894bc9d069a4baf39a3c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix RG_U34C Array annotation data (chip rgu34c)' - description: 'Affymetrix Affymetrix RG_U34C Array annotation data (chip rgu34c) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgu34ccdf/meta.yaml b/recipes/bioconductor-rgu34ccdf/meta.yaml index 8360de7865875..087952dc7ed41 100644 --- a/recipes/bioconductor-rgu34ccdf/meta.yaml +++ b/recipes/bioconductor-rgu34ccdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rgu34ccdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 556a7130086004d26095594da31c6410 +about: + description: A package containing an environment representing the RG_U34C.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: rgu34ccdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgu34ccdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 556a7130086004d26095594da31c6410 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: rgu34ccdf - description: 'A package containing an environment representing the RG_U34C.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgu34cprobe/meta.yaml b/recipes/bioconductor-rgu34cprobe/meta.yaml index 1d514934bc4ab..987c09c0cf302 100644 --- a/recipes/bioconductor-rgu34cprobe/meta.yaml +++ b/recipes/bioconductor-rgu34cprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rgu34cprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d1a6c433acd30b95fa7be89147105b74 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RG-U34C\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type rgu34c build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgu34cprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d1a6c433acd30b95fa7be89147105b74 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type rgu34c' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RG-U34C\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rguatlas4k.db/meta.yaml b/recipes/bioconductor-rguatlas4k.db/meta.yaml index e8a0ab33ef629..d68cac59bede3 100644 --- a/recipes/bioconductor-rguatlas4k.db/meta.yaml +++ b/recipes/bioconductor-rguatlas4k.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "rguatlas4k.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6a360676e08319ec5465c47c758110bd +about: + description: Clontech BD Atlas Long Oligos Rat 4K annotation data (chip rguatlas4k) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Clontech BD Atlas Long Oligos Rat 4K annotation data (chip rguatlas4k) build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rguatlas4k.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6a360676e08319ec5465c47c758110bd + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Clontech BD Atlas Long Oligos Rat 4K annotation data (chip rguatlas4k)' - description: 'Clontech BD Atlas Long Oligos Rat 4K annotation data (chip rguatlas4k) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgug4105a.db/meta.yaml b/recipes/bioconductor-rgug4105a.db/meta.yaml index 856bf606c03aa..50c0b34c06691 100644 --- a/recipes/bioconductor-rgug4105a.db/meta.yaml +++ b/recipes/bioconductor-rgug4105a.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "rgug4105a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3ccf354083ae36a7ae687fb8209c4e5b +about: + description: Agilent annotation data (chip rgug4105a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Agilent annotation data (chip rgug4105a) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgug4105a.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3ccf354083ae36a7ae687fb8209c4e5b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Agilent annotation data (chip rgug4105a)' - description: 'Agilent annotation data (chip rgug4105a) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgug4130a.db/meta.yaml b/recipes/bioconductor-rgug4130a.db/meta.yaml index 29321c986ab3a..9227781eb1bba 100644 --- a/recipes/bioconductor-rgug4130a.db/meta.yaml +++ b/recipes/bioconductor-rgug4130a.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "rgug4130a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 13643ac109aaf12590a5b6e379609b79 +about: + description: Agilent Rat annotation data (chip rgug4130a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Agilent Rat annotation data (chip rgug4130a) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgug4130a.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 13643ac109aaf12590a5b6e379609b79 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Agilent Rat annotation data (chip rgug4130a)' - description: 'Agilent Rat annotation data (chip rgug4130a) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rgug4131a.db/meta.yaml b/recipes/bioconductor-rgug4131a.db/meta.yaml index 1c64418da6bcc..024e1825699ac 100644 --- a/recipes/bioconductor-rgug4131a.db/meta.yaml +++ b/recipes/bioconductor-rgug4131a.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "rgug4131a.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1168d4906fb8ce60cbc0fa6cfa3b8ec6 +about: + description: Agilent "Rat Genome, Whole" annotation data (chip rgug4131a) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Agilent "Rat Genome, Whole" annotation data (chip rgug4131a) build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rgug4131a.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1168d4906fb8ce60cbc0fa6cfa3b8ec6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Agilent "Rat Genome, Whole" annotation data (chip rgug4131a)' - description: 'Agilent "Rat Genome, Whole" annotation data (chip rgug4131a) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml index a7b53b6eee845..5fe6647351258 100644 --- a/recipes/bioconductor-rhdf5/meta.yaml +++ b/recipes/bioconductor-rhdf5/meta.yaml @@ -1,58 +1,63 @@ -{% set version = "2.46.1" %} +{% set version = "2.50.0" %} {% set name = "rhdf5" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: R Interface to HDF5 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 947e662fe5f427ed0cc839e8049b431e build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rhdf5", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:rhdf5 + parent_recipe: + name: bioconductor-rhdf5 + path: recipes/bioconductor-rhdf5 + version: 2.24.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr, ggplot2, mockery, BiocParallel # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - - 'bioconductor-rhdf5filters >=1.14.0,<1.15.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-rhdf5filters >=1.18.0,<1.19.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 - r-base - libblas - liblapack + - zlib run: - - 'bioconductor-rhdf5filters >=1.14.0,<1.15.0' - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-rhdf5filters >=1.18.0,<1.19.0 + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 3b8b33f3ee9a260cceefab2911d1cd63 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'R Interface to HDF5' - description: 'This package provides an interface between HDF5 and R. HDF5''s main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:rhdf5 - parent_recipe: - name: bioconductor-rhdf5 - path: recipes/bioconductor-rhdf5 - version: 2.24.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rhdf5client/meta.yaml b/recipes/bioconductor-rhdf5client/meta.yaml index e9c92f1d8f081..b8843175c2a71 100644 --- a/recipes/bioconductor-rhdf5client/meta.yaml +++ b/recipes/bioconductor-rhdf5client/meta.yaml @@ -1,27 +1,31 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "rhdf5client" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functionality for reading data from HDF Scalable Data Service from within R. The HSDSArray function bridges from HSDS to the user via the DelayedArray interface. Bioconductor manages an open HSDS instance graciously provided by John Readey of the HDF Group. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Access HDF5 content from HDF Scalable Data Service -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9205b30177d59d75b7e544f795a90de5 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rhdf5client", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, BiocStyle, DT, rmarkdown requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 - r-base - r-data.table - r-httr @@ -29,20 +33,21 @@ requirements: - libblas - liblapack run: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 - r-base - r-data.table - r-httr - r-rjson - build: - - {{ compiler('c') }} - - make + +source: + md5: 61c367b6450eacb2dd7283daf399a80c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Access HDF5 content from HDF Scalable Data Service' - description: 'This package provides functionality for reading data from HDF Scalable Data Service from within R. The HSDSArray function bridges from HSDS to the user via the DelayedArray interface. Bioconductor manages an open HSDS instance graciously provided by John Readey of the HDF Group.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rhdf5filters/cc99_Makefile.in.patch b/recipes/bioconductor-rhdf5filters/cc99_Makefile.in.patch new file mode 100644 index 0000000000000..416bb66835315 --- /dev/null +++ b/recipes/bioconductor-rhdf5filters/cc99_Makefile.in.patch @@ -0,0 +1,51 @@ +On linux-aarch64 and osx-arm64, the CC99 is not found. Instead, set + +--- + +diff --git a/src/vbz/third_party/streamvbyte/Makefile.in b/src/vbz/third_party/streamvbyte/Makefile.in +index 11649f6..425418d 100644 +--- a/src/vbz/third_party/streamvbyte/Makefile.in ++++ b/src/vbz/third_party/streamvbyte/Makefile.in +@@ -13,7 +13,7 @@ PROCESSOR:=$(shell uname -m) + #CFLAGS = -fPIC -march=native -std=c99 -O3 -Wall -Wextra -pedantic -Wshadow + #endif + +-CFLAGS=$(PKG_C99FLAGS) $(PKG_CPICFLAGS) -Iinclude ++CFLAGS= -std=c99 $(PKG_C99FLAGS) $(PKG_CPICFLAGS) -Iinclude + + HEADERS=./include/streamvbyte.h ./include/streamvbytedelta.h ./include/streamvbyte_zigzag.h + +@@ -30,23 +30,23 @@ clean: + rm -f *.o libstreamvbyte.a + + streamvbyte_zigzag.o: ./src/streamvbyte_zigzag.c $(HEADERS) +- $(CC99) $(CFLAGS) -c ./src/streamvbyte_zigzag.c ++ $(CC) $(CFLAGS) -c ./src/streamvbyte_zigzag.c + + streamvbytedelta_encode.o: ./src/streamvbytedelta_encode.c $(HEADERS) +- $(CC99) $(CFLAGS) -c ./src/streamvbytedelta_encode.c ++ $(CC) $(CFLAGS) -c ./src/streamvbytedelta_encode.c + + streamvbytedelta_decode.o: ./src/streamvbytedelta_decode.c $(HEADERS) +- $(CC99) $(CFLAGS) -c ./src/streamvbytedelta_decode.c ++ $(CC) $(CFLAGS) -c ./src/streamvbytedelta_decode.c + + streamvbyte_0124_encode.o: ./src/streamvbyte_0124_encode.c $(HEADERS) +- $(CC99) $(CFLAGS) -c ./src/streamvbyte_0124_encode.c ++ $(CC) $(CFLAGS) -c ./src/streamvbyte_0124_encode.c + + streamvbyte_0124_decode.o: ./src/streamvbyte_0124_decode.c $(HEADERS) +- $(CC99) $(CFLAGS) -c ./src/streamvbyte_0124_decode.c ++ $(CC) $(CFLAGS) -c ./src/streamvbyte_0124_decode.c + + streamvbyte_decode.o: ./src/streamvbyte_decode.c $(HEADERS) +- $(CC99) $(CFLAGS) -c ./src/streamvbyte_decode.c ++ $(CC) $(CFLAGS) -c ./src/streamvbyte_decode.c + + streamvbyte_encode.o: ./src/streamvbyte_encode.c $(HEADERS) +- $(CC99) $(CFLAGS) -c ./src/streamvbyte_encode.c ++ $(CC) $(CFLAGS) -c ./src/streamvbyte_encode.c + +-- +2.46.0 + diff --git a/recipes/bioconductor-rhdf5filters/meta.yaml b/recipes/bioconductor-rhdf5filters/meta.yaml index b28d9aa1fb49b..cd7469129ae1e 100644 --- a/recipes/bioconductor-rhdf5filters/meta.yaml +++ b/recipes/bioconductor-rhdf5filters/meta.yaml @@ -1,51 +1,60 @@ -{% set version = "1.14.1" %} +{% set version = "1.18.0" %} {% set name = "rhdf5filters" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides a collection of additional compression filters for HDF5 datasets. The package is intended to provide seemless integration with rhdf5, however the compiled filters can also be used with external applications. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_2_clause + file LICENSE + license_file: LICENSE + summary: HDF5 Compression Filters -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3ecb2d30759fee6bde37bbb1f90fbf79 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rhdf5filters", max_pin="x.x") }}' -# Suggests: BiocStyle, knitr, rmarkdown, tinytest, rhdf5 (>= 2.34.0) + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:rhdf5filters + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, tinytest, rhdf5 (>= 2.47.7) # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 - r-base - libblas - liblapack + - zlib run: - - 'bioconductor-rhdf5lib >=1.24.0,<1.25.0' + - bioconductor-rhdf5lib >=1.28.0,<1.29.0 - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: b505519cacc6df4de9334c695ef2c205 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + patches: + - cc99_Makefile.in.patch # [not x86] + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_2_clause + file LICENSE' - summary: 'HDF5 Compression Filters' - description: 'Provides a collection of additional compression filters for HDF5 datasets. The package is intended to provide seemless integration with rhdf5, however the compiled filters can also be used with external applications.' - license_file: LICENSE -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name }} + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rhdf5lib/meta.yaml b/recipes/bioconductor-rhdf5lib/meta.yaml index 083cea6007bb4..3f1dd610208db 100644 --- a/recipes/bioconductor-rhdf5lib/meta.yaml +++ b/recipes/bioconductor-rhdf5lib/meta.yaml @@ -1,49 +1,56 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "Rhdf5lib" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides C and C++ hdf5 libraries. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: hdf5 library as an R package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 722160d55897324217ba8dc2cb60f3cd build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rhdf5lib", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + parent_recipe: + name: bioconductor-rhdf5lib + path: recipes/bioconductor-rhdf5lib + version: 1.2.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, tinytest, mockery # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - automake + - make host: - r-base - libblas - liblapack + - zlib run: - r-base - build: - - {{ compiler('c') }} - - automake - - make + +source: + md5: 2038bed88d3c7b81f8cc9caaf0b0a068 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'hdf5 library as an R package' - description: 'Provides C and C++ hdf5 libraries.' -extra: - additional-platforms: - - linux-aarch64 - parent_recipe: - name: bioconductor-rhdf5lib - path: recipes/bioconductor-rhdf5lib - version: 1.2.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rhesus.db0/meta.yaml b/recipes/bioconductor-rhesus.db0/meta.yaml index 72604a3cbf18b..b40b446bca0f9 100644 --- a/recipes/bioconductor-rhesus.db0/meta.yaml +++ b/recipes/bioconductor-rhesus.db0/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "rhesus.db0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 26d7aa426d23f0c64cb0918f90c32314 +about: + description: Base annotation databases for rhesus, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Level Annotation databases for rhesus build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rhesus.db0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 40063317ca33adad8023d1fe7c014970 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Level Annotation databases for rhesus' - description: 'Base annotation databases for rhesus, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rhesus.db0/post-link.sh b/recipes/bioconductor-rhesus.db0/post-link.sh index ff96f3afab411..25626c40f5fbe 100644 --- a/recipes/bioconductor-rhesus.db0/post-link.sh +++ b/recipes/bioconductor-rhesus.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rhesus.db0-3.18.0" +installBiocDataPackage.sh "rhesus.db0-3.20.0" diff --git a/recipes/bioconductor-rhesuscdf/meta.yaml b/recipes/bioconductor-rhesuscdf/meta.yaml index 5551420081edf..805550bd120f5 100644 --- a/recipes/bioconductor-rhesuscdf/meta.yaml +++ b/recipes/bioconductor-rhesuscdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rhesuscdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 994e16da5dd31bc2796d0da40aa2634f +about: + description: A package containing an environment representing the Rhesus.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: rhesuscdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rhesuscdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 994e16da5dd31bc2796d0da40aa2634f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: rhesuscdf - description: 'A package containing an environment representing the Rhesus.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rhesusprobe/meta.yaml b/recipes/bioconductor-rhesusprobe/meta.yaml index f06026d876a7c..c817081d34278 100644 --- a/recipes/bioconductor-rhesusprobe/meta.yaml +++ b/recipes/bioconductor-rhesusprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rhesusprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4169c1c997c4c08b027bc7489533e11e +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Rhesus\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type rhesus build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rhesusprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4169c1c997c4c08b027bc7489533e11e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type rhesus' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Rhesus\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rheumaticconditionwollbold/meta.yaml b/recipes/bioconductor-rheumaticconditionwollbold/meta.yaml index 52618980dd6d5..15789d735a723 100644 --- a/recipes/bioconductor-rheumaticconditionwollbold/meta.yaml +++ b/recipes/bioconductor-rheumaticconditionwollbold/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "rheumaticConditionWOLLBOLD" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8c8a5f56b923fe79c4a4902028d6fc5c +about: + description: Normalized gene expression data from rheumatic diseases from study published by Wollbold et al. in 2009, provided as an eSet. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Normalized gene expression dataset published by Wollbold et al. [2009] (WOLLBOLD). build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rheumaticconditionwollbold", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: genefilter, Biobase, hgu133plus2.db requirements: host: @@ -26,13 +24,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c9b78e6ccf15509071a4c8b6167eb3eb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Normalized gene expression dataset published by Wollbold et al. [2009] (WOLLBOLD).' - description: 'Normalized gene expression data from rheumatic diseases from study published by Wollbold et al. in 2009, provided as an eSet.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rheumaticconditionwollbold/post-link.sh b/recipes/bioconductor-rheumaticconditionwollbold/post-link.sh index 72f477eba6f72..388d37d2c53ae 100644 --- a/recipes/bioconductor-rheumaticconditionwollbold/post-link.sh +++ b/recipes/bioconductor-rheumaticconditionwollbold/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rheumaticconditionwollbold-1.40.0" +installBiocDataPackage.sh "rheumaticconditionwollbold-1.44.0" diff --git a/recipes/bioconductor-rhinotyper/build.sh b/recipes/bioconductor-rhinotyper/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rhinotyper/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rhinotyper/meta.yaml b/recipes/bioconductor-rhinotyper/meta.yaml new file mode 100644 index 0000000000000..68178b9601a6e --- /dev/null +++ b/recipes/bioconductor-rhinotyper/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.0" %} +{% set name = "rhinotypeR" %} +{% set bioc = "3.20" %} + +about: + description: '"rhinotypeR" is designed to automate the comparison of sequence data against prototype strains, streamlining the genotype assignment process. By implementing predefined pairwise distance thresholds, this package makes genotype assignment accessible to researchers and public health professionals. This tool enhances our epidemiological toolkit by enabling more efficient surveillance and analysis of rhinoviruses (RVs) and other viral pathogens with complex genomic landscapes. Additionally, "rhinotypeR" supports comprehensive visualization and analysis of single nucleotide polymorphisms (SNPs) and amino acid substitutions, facilitating in-depth genetic and evolutionary studies.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Rhinovirus genotyping +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rhinotyper", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: knitr, rmarkdown, BiocManager, BiocStyle, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - r-base + run: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - r-base +source: + md5: b0cb821c3bd76f66792d367677d8f0b4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-rhisat2/build_failure.osx-64.yaml b/recipes/bioconductor-rhisat2/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..fdc9d92101098 --- /dev/null +++ b/recipes/bioconductor-rhisat2/build_failure.osx-64.yaml @@ -0,0 +1,107 @@ +recipe_sha: 8c3a30622d17c4e1d0b86c6c3d0fef327c2d3563ea7c213237aa15d1819e817b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rhisat2-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rhisat2_1735585386962/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rhisat2-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rhisat2-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rhisat2_1735585386962/work/conda_build.sh']' returned non-zero exit status 1. + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rhisat2-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rhisat2-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rhisat2-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rhisat2-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rhisat2-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rhisat2-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rhisat2-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rhisat2-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rhisat2-1.22.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + /usr/bin/g -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -std=c11\"" -std=c11 \ + -fno-strict-aliasing -DHISAT2_VERSION="\"2.2.1\"" -DBUILD_HOST="\"Mac-1735576570564.local\"" -DBUILD_TIME="\"Mon Dec 30 19:06:04 UTC 2024\"" -DCOMPILER_VERSION="\"/usr/bin/g -v 2>&1 | tail -1\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DUSESIMDE -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ + -I. -I third_party \ + -o hisat2-build-s hisat2_build.cpp \ + ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ + -lpthread +# Last 100 lines of the build log. + +category: compiler error +reason: "'iostream' file not found" diff --git a/recipes/bioconductor-rhisat2/meta.yaml b/recipes/bioconductor-rhisat2/meta.yaml index 9bb4b0181af5c..8f6e39ecd12d9 100644 --- a/recipes/bioconductor-rhisat2/meta.yaml +++ b/recipes/bioconductor-rhisat2/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "Rhisat2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: R Wrapper for HISAT2 Aligner -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bcfb03ad1e10fa471b46f2b214ddbb2a build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rhisat2", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocStyle # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-sgseq >=1.36.0,<1.37.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-sgseq >=1.40.0,<1.41.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - libblas - liblapack run: - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-sgseq >=1.36.0,<1.37.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-sgseq >=1.40.0,<1.41.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: bbf4203f12d4fe54294b9c4fb71330f7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'R Wrapper for HISAT2 Aligner' - description: 'An R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rhtslib/arm_hwcap.patch b/recipes/bioconductor-rhtslib/arm_hwcap.patch new file mode 100644 index 0000000000000..691c0599ebee5 --- /dev/null +++ b/recipes/bioconductor-rhtslib/arm_hwcap.patch @@ -0,0 +1,20 @@ +Conda-forge's build environment on ARM uses sysroot_linux-aarch64 2.17, which +is based on glibc 2.17 so does not define HWCAP_* values on ARM. +Work around this by including the kernel header to get the desired values. + +See https://github.com/samtools/htscodecs/issues/88 +--- +diff --git a/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c b/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c +index 732d9f5..0592a78 100644 +--- a/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c ++++ b/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c +@@ -1011,6 +1011,8 @@ unsigned char *(*rans_dec_func(int do_simd, int order)) + + #if defined(__linux__) || defined(__FreeBSD__) + #include ++// Ensure ARM HWCAP_* values are defined even on old glibc ++#include + #elif defined(_WIN32) + #include + #endif + diff --git a/recipes/bioconductor-rhtslib/meta.yaml b/recipes/bioconductor-rhtslib/meta.yaml index 1965e9bb184d3..1b6f4455a8157 100644 --- a/recipes/bioconductor-rhtslib/meta.yaml +++ b/recipes/bioconductor-rhtslib/meta.yaml @@ -1,51 +1,61 @@ -{% set version = "2.4.0" %} +{% set version = "3.2.0" %} {% set name = "Rhtslib" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides version 1.18 of the 'HTSlib' C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib. Motivation and instructions for use of this package are in the vignette, vignette(package="Rhtslib", "Rhtslib"). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: HTSlib high-throughput sequencing library as an R package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8aa7fa3050a484702c3065c797948ba8 build: - number: 2 + number: 1 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rhtslib", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:rhtslib + - doi:10.1038/nmeth.3252 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle # SystemRequirements: libbz2 & liblzma & libcurl (with header files), GNU make requirements: + build: + - {{ compiler('c') }} + - automake + - make host: - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - libblas - liblapack + - zlib + - liblzma-devel run: - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - build: - - {{ compiler('c') }} - - automake - - make + +source: + md5: 1d8eabf0934373b61aca2dc20cab712b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + patches: + - arm_hwcap.patch + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'HTSlib high-throughput sequencing library as an R package' - description: 'This package provides version 1.15.1 of the ''HTSlib'' C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib. Motivation and instructions for use of this package are in the vignette, vignette(package="Rhtslib", "Rhtslib").' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:rhtslib - - doi:10.1038/nmeth.3252 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rhtslib/patch b/recipes/bioconductor-rhtslib/patch deleted file mode 100644 index bac065a6d530b..0000000000000 --- a/recipes/bioconductor-rhtslib/patch +++ /dev/null @@ -1,11 +0,0 @@ ---- src/htslib-1.7/Makefile.Rhtslib 2018-10-30 20:47:25.000000000 +0100 -+++ src/htslib-1.7/Makefile.Rhtslib 2018-10-30 20:47:25.000000000 +0100 -@@ -43,7 +43,7 @@ - #CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__ - CFLAGS = -g -Wall -O2 - EXTRA_CFLAGS_PIC = -fpic --LDFLAGS = -+LDFLAGS = "-L${PREFIX}/lib" - LIBS = $(htslib_default_libs) - - prefix = /usr/local diff --git a/recipes/bioconductor-rhtslib/rpath.patch b/recipes/bioconductor-rhtslib/rpath.patch deleted file mode 100644 index 6f62e59ed139b..0000000000000 --- a/recipes/bioconductor-rhtslib/rpath.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- src/Makevars 2016-10-12 07:06:31.000000000 -0500 -+++ src/Makevars.new 2017-01-24 14:26:30.000000000 -0600 -@@ -47,7 +47,7 @@ - cd $(HTSDIR)/ && ./configure --disable-dependency-tracking \ - --prefix="${R_PACKAGE_DIR}" \ - CC="${R_CC}" CFLAGS="${R_CFLAGS} ${R_CPICFLAGS}" \ -- LDFLAGS="${R_LDFLAGS}" CPPFLAGS="${R_CPPFLAGS}" CPP="${R_CPP}" -+ LDFLAGS="${R_LDFLAGS} -Wl,-rpath,${PREFIX}/lib" CPPFLAGS="${R_CPPFLAGS}" CPP="${R_CPP}" - @echo "buildling library..." - cd $(HTSDIR)/ && $(MAKE) - diff --git a/recipes/bioconductor-ri16cod.db/meta.yaml b/recipes/bioconductor-ri16cod.db/meta.yaml index 8bd8e75824883..ddda2327b062a 100644 --- a/recipes/bioconductor-ri16cod.db/meta.yaml +++ b/recipes/bioconductor-ri16cod.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.4.0" %} {% set name = "ri16cod.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cd01b429295fdbba21dbe566effacbdd +about: + description: Codelink Rat Inflammation 16 Bioarray annotation data (chip ri16cod) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Codelink Rat Inflammation 16 Bioarray annotation data (chip ri16cod) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ri16cod.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: cd01b429295fdbba21dbe566effacbdd + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Codelink Rat Inflammation 16 Bioarray annotation data (chip ri16cod)' - description: 'Codelink Rat Inflammation 16 Bioarray annotation data (chip ri16cod) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ribocrypt/meta.yaml b/recipes/bioconductor-ribocrypt/meta.yaml index 88ff4d20e3b05..7fa28d0331361 100644 --- a/recipes/bioconductor-ribocrypt/meta.yaml +++ b/recipes/bioconductor-ribocrypt/meta.yaml @@ -1,35 +1,38 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "RiboCrypt" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: R Package for interactive visualization and browsing NGS data. It contains a browser for both transcript and genomic coordinate view. In addition a QC and general metaplots are included, among others differential translation plots and gene expression plots. The package is still under development. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Interactive visualization in genomics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b5551bc35ad9798b4b1b401f7a08b280 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ribocrypt", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, rmarkdown, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19 requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-orfik >=1.22.0,<1.23.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-orfik >=1.26.0,<1.27.0 - r-base - r-bslib - r-data.table @@ -49,15 +52,16 @@ requirements: - r-shinyhelper - r-shinyjqui - r-stringr + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-orfik >=1.22.0,<1.23.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-orfik >=1.26.0,<1.27.0 - r-base - r-bslib - r-data.table @@ -77,13 +81,16 @@ requirements: - r-shinyhelper - r-shinyjqui - r-stringr + +source: + md5: 4216d254444fa2e4f3edd8a003ab3162 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Interactive visualization in genomics' - description: 'R Package for interactive visualization and browsing NGS data. It contains a browser for both transcript and genomic coordinate view. In addition a QC and general metaplots are included, among others differential translation plots and gene expression plots. The package is still under development.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ribodipa/meta.yaml b/recipes/bioconductor-ribodipa/meta.yaml index e581d9847010c..00b2c5e62fa52 100644 --- a/recipes/bioconductor-ribodipa/meta.yaml +++ b/recipes/bioconductor-ribodipa/meta.yaml @@ -1,36 +1,45 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "RiboDiPA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package performs differential pattern analysis for Ribo-seq data. It identifies genes with significantly different patterns in the ribosome footprint between two conditions. RiboDiPA contains five major components including bam file processing, P-site mapping, data binning, differential pattern analysis and footprint visualization. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Differential pattern analysis for Ribo-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0aab649d27962694300a1e3b42b9417d build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ribodipa", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-data.table - r-doparallel @@ -38,21 +47,23 @@ requirements: - r-foreach - r-ggplot2 - r-matrixstats - - 'r-rcpp >=1.0.2' + - r-rcpp >=1.0.2 - r-reldist - libblas - liblapack + run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-data.table - r-doparallel @@ -60,19 +71,18 @@ requirements: - r-foreach - r-ggplot2 - r-matrixstats - - 'r-rcpp >=1.0.2' + - r-rcpp >=1.0.2 - r-reldist - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: a3bd7b10e416c2f5cdb84fb5e1ba51d8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 3)' - summary: 'Differential pattern analysis for Ribo-seq data' - description: 'This package performs differential pattern analysis for Ribo-seq data. It identifies genes with significantly different patterns in the ribosome footprint between two conditions. RiboDiPA contains five major components including bam file processing, P-site mapping, data binning, differential pattern analysis and footprint visualization.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-riboprofiling/meta.yaml b/recipes/bioconductor-riboprofiling/meta.yaml index 51945ec4291e6..2c65fcbd47f41 100644 --- a/recipes/bioconductor-riboprofiling/meta.yaml +++ b/recipes/bioconductor-riboprofiling/meta.yaml @@ -1,38 +1,49 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "RiboProfiling" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of reads on CDS, 3''UTR, and 5''UTR, plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec32fb1993efa63a677422612e03ded7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-riboprofiling", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:riboprofiling + - doi:10.12688/f1000research.8964.1 + parent_recipe: + name: bioconductor-riboprofiling + path: recipes/bioconductor-riboprofiling + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-ggplot2 @@ -40,38 +51,33 @@ requirements: - r-reshape2 - r-sqldf run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-ggplot2 - r-plyr - r-reshape2 - r-sqldf + +source: + md5: 31099c07405aa0b838b71d20efced62b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation' - description: 'Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of reads on CDS, 3''UTR, and 5''UTR, plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:riboprofiling - - doi:10.12688/f1000research.8964.1 - parent_recipe: - name: bioconductor-riboprofiling - path: recipes/bioconductor-riboprofiling - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ribor/meta.yaml b/recipes/bioconductor-ribor/meta.yaml index d88e8a7571a55..f6da0d4a5841e 100644 --- a/recipes/bioconductor-ribor/meta.yaml +++ b/recipes/bioconductor-ribor/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "ribor" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The ribor package provides an R Interface for .ribo files. It provides functionality to read the .ribo file, which is of HDF5 format, and performs common analyses on its contents. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: An R Interface for Ribo Files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6d86ac039324d8fa1b6c708f42da44e2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ribor", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-ggplot2 @@ -32,8 +34,8 @@ requirements: - r-tidyr - r-yaml run: - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-ggplot2 @@ -41,13 +43,16 @@ requirements: - r-rlang - r-tidyr - r-yaml + +source: + md5: 6e05511565c53a49597d82f5786c7891 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'An R Interface for Ribo Files' - description: 'The ribor package provides an R Interface for .ribo files. It provides functionality to read the .ribo file, which is of HDF5 format, and performs common analyses on its contents.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-riboseqr/meta.yaml b/recipes/bioconductor-riboseqr/meta.yaml index 548f9398d22d6..116d18d3852e0 100644 --- a/recipes/bioconductor-riboseqr/meta.yaml +++ b/recipes/bioconductor-riboseqr/meta.yaml @@ -1,51 +1,58 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "riboSeqR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Analysis of sequencing data from ribosome profiling experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eb9c84e564128ad11960fac5955c4d2f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-riboseqr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, RUnit, BiocGenerics requirements: host: - - 'bioconductor-bayseq >=2.36.0,<2.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - bioconductor-bayseq >=2.40.0,<2.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqlogo >=1.72.0,<1.73.0 - r-abind - r-base run: - - 'bioconductor-bayseq >=2.36.0,<2.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - bioconductor-bayseq >=2.40.0,<2.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqlogo >=1.72.0,<1.73.0 - r-abind - r-base + +source: + md5: 4635ef611203db0cd52c6f64da120bf0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Analysis of sequencing data from ribosome profiling experiments' - description: 'Plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ribosomeprofilingqc/meta.yaml b/recipes/bioconductor-ribosomeprofilingqc/meta.yaml index a96b273f005a2..7f52177a5fa87 100644 --- a/recipes/bioconductor-ribosomeprofilingqc/meta.yaml +++ b/recipes/bioconductor-ribosomeprofilingqc/meta.yaml @@ -1,81 +1,92 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "ribosomeProfilingQC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Ribo-Seq (also named ribosome profiling or footprinting) measures translatome (unlike RNA-Seq, which sequences the transcriptome) by direct quantification of the ribosome-protected fragments (RPFs). This package provides the tools for quality assessment of ribosome profiling. In addition, it can preprocess Ribo-Seq data for subsequent differential analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=3) + file LICENSE + license_file: LICENSE + summary: Ribosome Profiling Quality Control -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f26a7222a62ed0c3462336d1c945cea6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ribosomeprofilingqc", max_pin="x.x") }}' - noarch: generic -# Suggests: RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, edgeR, limma, testthat, rmarkdown + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, edgeR, DESeq2, limma, ashr, testthat, rmarkdown, vsn, Biobase requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-edaseq >=2.36.0,<2.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-motifstack >=1.46.0,<1.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rsubread >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-ruvseq >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-edaseq >=2.40.0,<2.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-motifstack >=1.50.0,<1.51.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rsubread >=2.20.0,<2.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-ruvseq >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-cluster + - r-ggextra - r-ggfittext - r-ggplot2 - r-ggrepel - r-scales + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-edaseq >=2.36.0,<2.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-motifstack >=1.46.0,<1.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rsubread >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-ruvseq >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-edaseq >=2.40.0,<2.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-motifstack >=1.50.0,<1.51.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rsubread >=2.20.0,<2.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-ruvseq >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-cluster + - r-ggextra - r-ggfittext - r-ggplot2 - r-ggrepel - r-scales + +source: + md5: a3c34fd8292aea1d9c4e2c2e02a04cb1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=3) + file LICENSE' - summary: 'Ribosome Profiling Quality Control' - description: 'Ribo-Seq (also named ribosome profiling or footprinting) measures translatome (unlike RNA-Seq, which sequences the transcriptome) by direct quantification of the ribosome-protected fragments (RPFs). This package provides the tools for quality assessment of ribosome profiling. In addition, it can preprocess Ribo-Seq data for subsequent differential analysis.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ricecdf/meta.yaml b/recipes/bioconductor-ricecdf/meta.yaml index f47b3ea6adb91..d122497ef7097 100644 --- a/recipes/bioconductor-ricecdf/meta.yaml +++ b/recipes/bioconductor-ricecdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "ricecdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 51db6f51f4adcfb7f4940d07668db8b8 +about: + description: A package containing an environment representing the Rice.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: ricecdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ricecdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 51db6f51f4adcfb7f4940d07668db8b8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: ricecdf - description: 'A package containing an environment representing the Rice.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-riceprobe/meta.yaml b/recipes/bioconductor-riceprobe/meta.yaml index 297a6847aeceb..ad4cfe1a76e20 100644 --- a/recipes/bioconductor-riceprobe/meta.yaml +++ b/recipes/bioconductor-riceprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "riceprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2fac7746c343546cf30e6d54bc1e2019 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Rice\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type rice build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-riceprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2fac7746c343546cf30e6d54bc1e2019 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type rice' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Rice\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rifi/meta.yaml b/recipes/bioconductor-rifi/meta.yaml index 05ed25ea6941c..1a2efaf4a0b04 100644 --- a/recipes/bioconductor-rifi/meta.yaml +++ b/recipes/bioconductor-rifi/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "rifi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: '''rifi'' analyses data from rifampicin time series created by microarray or RNAseq. ''rifi'' is a transcriptome data analysis tool for the holistic identification of transcription and decay associated processes. The decay constants and the delay of the onset of decay is fitted for each probe/bin. Subsequently, probes/bins of equal properties are combined into segments by dynamic programming, independent of a existing genome annotation. This allows to detect transcript segments of different stability or transcriptional events within one annotated gene. In addition to the classic decay constant/half-life analysis, ''rifi'' detects processing sites, transcription pausing sites, internal transcription start sites in operons, sites of partial transcription termination in operons, identifies areas of likely transcriptional interference by the collision mechanism and gives an estimate of the transcription velocity. All data are integrated to give an estimate of continous transcriptional units, i.e. operons. Comprehensive output tables and visualizations of the full genome result and the individual fits for all probes/bins are produced.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: '''rifi'' analyses data from rifampicin time series created by microarray or RNAseq' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5d070b26ca40e04e4e3f9851853caa48 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rifi", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: DescTools, devtools, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-car - r-cowplot @@ -41,9 +43,9 @@ requirements: - r-stringr - r-tibble run: - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-car - r-cowplot @@ -59,13 +61,16 @@ requirements: - r-scales - r-stringr - r-tibble + +source: + md5: 9c1fda271448f428b30150b5c48f8607 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: '''rifi'' analyses data from rifampicin time series created by microarray or RNAseq' - description: '''rifi'' analyses data from rifampicin time series created by microarray or RNAseq. ''rifi'' is a transcriptome data analysis tool for the holistic identification of transcription and decay associated processes. The decay constants and the delay of the onset of decay is fitted for each probe/bin. Subsequently, probes/bins of equal properties are combined into segments by dynamic programming, independent of a existing genome annotation. This allows to detect transcript segments of different stability or transcriptional events within one annotated gene. In addition to the classic decay constant/half-life analysis, ''rifi'' detects processing sites, transcription pausing sites, internal transcription start sites in operons, sites of partial transcription termination in operons, identifies areas of likely transcriptional interference by the collision mechanism and gives an estimate of the transcription velocity. All data are integrated to give an estimate of continous transcriptional units, i.e. operons. Comprehensive output tables and visualizations of the full genome result and the individual fits for all probes/bins are produced.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rificomparative/meta.yaml b/recipes/bioconductor-rificomparative/meta.yaml index fd8f33a8cb823..893cc41bad1ef 100644 --- a/recipes/bioconductor-rificomparative/meta.yaml +++ b/recipes/bioconductor-rificomparative/meta.yaml @@ -1,31 +1,34 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "rifiComparative" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: '''rifiComparative'' is a continuation of rifi package. It compares two conditions output of rifi using half-life and mRNA at time 0 segments. As an input for the segmentation, the difference between half-life of both condtions and log2FC of the mRNA at time 0 are used. The package provides segmentation, statistics, summary table, fragments visualization and some additional useful plots for further anaylsis.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: '''rifiComparative'' compares the output of rifi from two different conditions.' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d371dc0f2b156f4565b09b7cfa5406e0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rificomparative", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: DescTools, knitr, rmarkdown, BiocStyle requirements: + host: - - 'bioconductor-dta >=2.48.0,<2.49.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-dta >=2.52.0,<2.53.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cowplot - r-devtools @@ -43,11 +46,12 @@ requirements: - r-stringr - r-tibble - r-writexl + run: - - 'bioconductor-dta >=2.48.0,<2.49.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-dta >=2.52.0,<2.53.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cowplot - r-devtools @@ -65,13 +69,16 @@ requirements: - r-stringr - r-tibble - r-writexl + +source: + md5: 5f76b5f9e57e55da53a99a5360140c62 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: '''rifiComparative'' compares the output of rifi from two different conditions.' - description: '''rifiComparative'' is a continuation of rifi package. It compares two conditions output of rifi using half-life and mRNA at time 0 segments. As an input for the segmentation, the difference between half-life of both condtions and log2FC of the mRNA at time 0 are used. The package provides segmentation, statistics, summary table, fragments visualization and some additional useful plots for further anaylsis.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rimmport/meta.yaml b/recipes/bioconductor-rimmport/meta.yaml index b64ed9ed2061d..a6917c49e46ff 100644 --- a/recipes/bioconductor-rimmport/meta.yaml +++ b/recipes/bioconductor-rimmport/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "RImmPort" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The RImmPort package simplifies access to ImmPort data for analysis in the R environment. It provides a standards-based interface to the ImmPort study data that is in a proprietary format. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'RImmPort: Enabling Ready-for-analysis Immunology Research Data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9a35da0a38439eee55d04ff8321ff09d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rimmport", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rimmport + - doi:10.1093/bioinformatics/btw719 + parent_recipe: + name: bioconductor-rimmport + path: recipes/bioconductor-rimmport + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: host: @@ -39,21 +50,16 @@ requirements: - r-reshape2 - r-rsqlite - r-sqldf + +source: + md5: c880a54538cd5f22795dd2dc27bd1114 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'RImmPort: Enabling Ready-for-analysis Immunology Research Data' - description: 'The RImmPort package simplifies access to ImmPort data for analysis in the R environment. It provides a standards-based interface to the ImmPort study data that is in a proprietary format.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:rimmport - - doi:10.1093/bioinformatics/btw719 - parent_recipe: - name: bioconductor-rimmport - path: recipes/bioconductor-rimmport - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ritan/build_failure.linux-64.yaml b/recipes/bioconductor-ritan/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..06ec32a05fd37 --- /dev/null +++ b/recipes/bioconductor-ritan/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: d87278a62a2daa882dd3085dfd496ae82c16e0112782e8f79ff15eb708a83764 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-bgeedb[version='>=2.32.0,<2.33.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-bgeedb >=2.32.0,<2.33.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-bgeedb >=2.32.0,<2.33.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-bgeedb[version='>=2.32.0,<2.33.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-bgeedb >=2.32.0,<2.33.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-bgeedb >=2.32.0,<2.33.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-bgeedb[version='>=2.32.0,<2.33.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-bgeedb >=2.32.0,<2.33.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-bgeedb >=2.32.0,<2.33.0 [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-ritan/meta.yaml b/recipes/bioconductor-ritan/meta.yaml index 3b41d1b6ab646..54f2d3a814406 100644 --- a/recipes/bioconductor-ritan/meta.yaml +++ b/recipes/bioconductor-ritan/meta.yaml @@ -1,34 +1,37 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "RITAN" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for comprehensive gene set enrichment and extraction of multi-resource high confidence subnetworks. RITAN facilitates bioinformatic tasks for enabling network biology research. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Rapid Integration of Term Annotation and Network resources -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d9b8cf771e70cd374ba72e63aa439865 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ritan", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, BgeeDB requirements: + host: - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-bgeedb >=2.28.0,<2.29.0' - - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-ritandata >=1.26.0,<1.27.0' - - 'bioconductor-stringdb >=2.14.0,<2.15.0' + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-bgeedb >=2.32.0,<2.33.0 + - bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-ritandata >=1.30.0,<1.31.0 + - bioconductor-stringdb >=2.18.0,<2.19.0 - r-base - r-dynamictreecut - r-ggplot2 @@ -45,14 +48,15 @@ requirements: - r-rcolorbrewer - r-reshape2 - r-sqldf + run: - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-bgeedb >=2.28.0,<2.29.0' - - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-ritandata >=1.26.0,<1.27.0' - - 'bioconductor-stringdb >=2.14.0,<2.15.0' + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-bgeedb >=2.32.0,<2.33.0 + - bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-ritandata >=1.30.0,<1.31.0 + - bioconductor-stringdb >=2.18.0,<2.19.0 - r-base - r-dynamictreecut - r-ggplot2 @@ -69,13 +73,16 @@ requirements: - r-rcolorbrewer - r-reshape2 - r-sqldf + +source: + md5: ccc0ac36181470a62acdb7be08aface6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Rapid Integration of Term Annotation and Network resources' - description: 'Tools for comprehensive gene set enrichment and extraction of multi-resource high confidence subnetworks. RITAN facilitates bioinformatic tasks for enabling network biology research.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ritandata/meta.yaml b/recipes/bioconductor-ritandata/meta.yaml index 5ca38c3c23f92..8d092a292a5a2 100644 --- a/recipes/bioconductor-ritandata/meta.yaml +++ b/recipes/bioconductor-ritandata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "RITANdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 12987879ef374ad399dd440a058b9a47 +about: + description: Data such as is contained in the two R data files in this package are required for the RITAN package examples. Users are highly encouraged to use their own or additional resources in conjunction with RITANdata. See the RITAN vignettes and RITAN.md for more information, such as gathering more up-to-date annotation data. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: This package contains reference annotation and network data sets build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ritandata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5636c146679aece62409941126b1b162 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'This package contains reference annotation and network data sets' - description: 'Data such as is contained in the two R data files in this package are required for the RITAN package examples. Users are highly encouraged to use their own or additional resources in conjunction with RITANdata. See the RITAN vignettes and RITAN.md for more information, such as gathering more up-to-date annotation data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ritandata/post-link.sh b/recipes/bioconductor-ritandata/post-link.sh index 41e2751e05e13..a3f950030eb07 100644 --- a/recipes/bioconductor-ritandata/post-link.sh +++ b/recipes/bioconductor-ritandata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ritandata-1.26.0" +installBiocDataPackage.sh "ritandata-1.30.0" diff --git a/recipes/bioconductor-river/meta.yaml b/recipes/bioconductor-river/meta.yaml index cf84189dac66b..467dc962ed510 100644 --- a/recipes/bioconductor-river/meta.yaml +++ b/recipes/bioconductor-river/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "RIVER" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7b8f82011a163ae4f4a31f2172d49124 +about: + description: An implementation of a probabilistic modeling framework that jointly analyzes personal genome and transcriptome data to estimate the probability that a variant has regulatory impact in that individual. It is based on a generative model that assumes that genomic annotations, such as the location of a variant with respect to regulatory elements, determine the prior probability that variant is a functional regulatory variant, which is an unobserved variable. The functional regulatory variant status then influences whether nearby genes are likely to display outlier levels of gene expression in that person. See the RIVER website for more information, documentation and examples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: R package for RIVER (RNA-Informed Variant Effect on Regulation) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-river", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-ggplot2 - r-glmnet - r-proc run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-ggplot2 - r-glmnet - r-proc +source: + md5: 06027af259a42a4baff99b729b703214 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'R package for RIVER (RNA-Informed Variant Effect on Regulation)' - description: 'An implementation of a probabilistic modeling framework that jointly analyzes personal genome and transcriptome data to estimate the probability that a variant has regulatory impact in that individual. It is based on a generative model that assumes that genomic annotations, such as the location of a variant with respect to regulatory elements, determine the prior probability that variant is a functional regulatory variant, which is an unobserved variable. The functional regulatory variant status then influences whether nearby genes are likely to display outlier levels of gene expression in that person. See the RIVER website for more information, documentation and examples.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml b/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml index 4c214aee9eaf1..e8182904d4f22 100644 --- a/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml +++ b/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml @@ -1,59 +1,63 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "RJMCMCNucleosomes" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package does nucleosome positioning using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cec0a46571d187963e019f18fff144f1 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rjmcmcnucleosomes", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, nucleoSim, RUnit -# SystemRequirements: Rcpp, gsl +# SystemRequirements: Rcpp requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-consensusseeker >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-consensusseeker >=1.34.0,<1.35.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-rcpp >=0.12.5' + - r-rcpp >=0.12.5 - libblas - liblapack - - gsl run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-consensusseeker >=1.30.0,<1.31.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-consensusseeker >=1.34.0,<1.35.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-rcpp >=0.12.5' - - gsl - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=0.12.5 + +source: + md5: bf76f59fa3d0f158997b9c90f9420aaf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)' - description: 'This package does nucleosome positioning using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.' + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-rlassocox/meta.yaml b/recipes/bioconductor-rlassocox/meta.yaml index 18539199c38bb..76924b44e4ebe 100644 --- a/recipes/bioconductor-rlassocox/meta.yaml +++ b/recipes/bioconductor-rlassocox/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "RLassoCox" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3f92bc442df2edc28546415bc716123b +about: + description: RLassoCox is a package that implements the RLasso-Cox model proposed by Wei Liu. The RLasso-Cox model integrates gene interaction information into the Lasso-Cox model for accurate survival prediction and survival biomarker discovery. It is based on the hypothesis that topologically important genes in the gene interaction network tend to have stable expression changes. The RLasso-Cox model uses random walk to evaluate the topological weight of genes, and then highlights topologically important genes to improve the generalization ability of the Lasso-Cox model. The RLasso-Cox model has the advantage of identifying small gene sets with high prognostic performance on independent datasets, which may play an important role in identifying robust survival biomarkers for various cancer types. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: A reweighted Lasso-Cox by integrating gene interaction information build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rlassocox", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr requirements: host: @@ -33,12 +31,14 @@ requirements: - r-igraph - r-matrix - r-survival +source: + md5: d1db688298e71f72ea0cfb4f24e85432 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A reweighted Lasso-Cox by integrating gene interaction information' - description: 'RLassoCox is a package that implements the RLasso-Cox model proposed by Wei Liu. The RLasso-Cox model integrates gene interaction information into the Lasso-Cox model for accurate survival prediction and survival biomarker discovery. It is based on the hypothesis that topologically important genes in the gene interaction network tend to have stable expression changes. The RLasso-Cox model uses random walk to evaluate the topological weight of genes, and then highlights topologically important genes to improve the generalization ability of the Lasso-Cox model. The RLasso-Cox model has the advantage of identifying small gene sets with high prognostic performance on independent datasets, which may play an important role in identifying robust survival biomarkers for various cancer types.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rlmm/meta.yaml b/recipes/bioconductor-rlmm/meta.yaml index f42b4445d98c7..9ab98f8fd5325 100644 --- a/recipes/bioconductor-rlmm/meta.yaml +++ b/recipes/bioconductor-rlmm/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.64.0" %} +{% set version = "1.68.0" %} {% set name = "RLMM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'A classification algorithm, based on a multi-chip, multi-SNP approach for Affymetrix SNP arrays. Using a large training sample where the genotype labels are known, this aglorithm will obtain more accurate classification results on new data. RLMM is based on a robust, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variation is removed through normalization. This model-based algorithm captures the similarities across genotype groups and probes, as well as thousands other SNPs for accurate classification. NOTE: 100K-Xba only at for now.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: A Genotype Calling Algorithm for Affymetrix SNP Arrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c43c967fab2a5e90059b26e46de345b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rlmm", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rlmm + - doi:10.1093/bioinformatics/bti741 + parent_recipe: + name: bioconductor-rlmm + path: recipes/bioconductor-rlmm + version: 1.42.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # SystemRequirements: Internal files Xba.CQV, Xba.regions (or other regions file) requirements: host: @@ -27,21 +38,16 @@ requirements: run: - r-base - r-mass + +source: + md5: 7f8b6b4bd9eb1d640055893d283d6b0a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'A Genotype Calling Algorithm for Affymetrix SNP Arrays' - description: 'A classification algorithm, based on a multi-chip, multi-SNP approach for Affymetrix SNP arrays. Using a large training sample where the genotype labels are known, this aglorithm will obtain more accurate classification results on new data. RLMM is based on a robust, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variation is removed through normalization. This model-based algorithm captures the similarities across genotype groups and probes, as well as thousands other SNPs for accurate classification. NOTE: 100K-Xba only at for now.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:rlmm - - doi:10.1093/bioinformatics/bti741 - parent_recipe: - name: bioconductor-rlmm - path: recipes/bioconductor-rlmm - version: 1.42.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rmagpie/meta.yaml b/recipes/bioconductor-rmagpie/meta.yaml index dbd9d4ffce38e..7195d14aa199d 100644 --- a/recipes/bioconductor-rmagpie/meta.yaml +++ b/recipes/bioconductor-rmagpie/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.58.0" %} +{% set version = "1.62.0" %} {% set name = "Rmagpie" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 939fbdcb38d890daf9880baea89c8685 +about: + description: Microarray Classification is designed for both biologists and statisticians. It offers the ability to train a classifier on a labelled microarray dataset and to then use that classifier to predict the class of new observations. A range of modern classifiers are available, including support vector machines (SVMs), nearest shrunken centroids (NSCs)... Advanced methods are provided to estimate the predictive error rate and to report the subset of genes which appear essential in discriminating between classes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: MicroArray Gene-expression-based Program In Error rate estimation build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rmagpie", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: xtable requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-e1071 - r-kernlab - r-pamr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-e1071 - r-kernlab - r-pamr +source: + md5: 28e2db2a1ed2acea51df1036ff00aa52 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'MicroArray Gene-expression-based Program In Error rate estimation' - description: 'Microarray Classification is designed for both biologists and statisticians. It offers the ability to train a classifier on a labelled microarray dataset and to then use that classifier to predict the class of new observations. A range of modern classifiers are available, including support vector machines (SVMs), nearest shrunken centroids (NSCs)... Advanced methods are provided to estimate the predictive error rate and to report the subset of genes which appear essential in discriminating between classes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rmassbank/build_failure.osx-64.yaml b/recipes/bioconductor-rmassbank/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..44e66781771de --- /dev/null +++ b/recipes/bioconductor-rmassbank/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 74621ebb122492aaffce5cffdd8c1beadf9dbee881b93413eae07c9692e888b5 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmassbank-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmassbank-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rmassbank_1734889625563/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmassbank-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rmassbank_1734889625563/work/conda_build.sh']' returned non-zero exit status 1. + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmassbank-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmassbank-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmassbank-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmassbank-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmassbank-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmassbank-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmassbank-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmassbank-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmassbank-3.16.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + Error: package or namespace load failed for Rcpp in library.dynam(lib, package, package.lib): + shared object Rcpp.dylib not found + Execution halted +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-rmassbank/meta.yaml b/recipes/bioconductor-rmassbank/meta.yaml index b45501cfdd4e3..f77da36ec9cb6 100644 --- a/recipes/bioconductor-rmassbank/meta.yaml +++ b/recipes/bioconductor-rmassbank/meta.yaml @@ -1,85 +1,103 @@ -{% set version = "3.12.0" %} +{% set version = "3.16.0" %} {% set name = "RMassBank" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Workflow to process tandem MS files and build MassBank records -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 59330cd723448b79eb751c6864e3dfbf build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rmassbank", max_pin="x.x") }}' -# Suggests: BiocStyle,gplots,RMassBankData (>= 1.33.1), xcms (>= 1.37.1), CAMERA, RUnit, knitr, rmarkdown + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, CAMERA, gplots, knitr, magick, rmarkdown, RMassBankData (>= 1.33.1), RUnit, xcms (>= 1.37.1) # SystemRequirements: OpenBabel requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-chemmineob >=1.40.0,<1.41.0' - - 'bioconductor-chemminer >=3.54.0,<3.55.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-chemminer >=3.58.0,<3.59.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-mzr >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-assertthat - r-base - r-data.table - r-digest + - r-dplyr - r-envipat - r-glue - r-httr + - r-httr2 - r-logger + - r-purrr - r-r.utils - r-rcdk - r-rcpp - r-readjdx + - r-readr - r-rjson + - r-tibble + - r-tidyselect - r-webchem - r-xml - r-yaml - libblas - liblapack - openbabel + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-chemmineob >=1.40.0,<1.41.0' - - 'bioconductor-chemminer >=3.54.0,<3.55.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-chemminer >=3.58.0,<3.59.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-mzr >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-assertthat - r-base - r-data.table - r-digest + - r-dplyr - r-envipat - r-glue - r-httr + - r-httr2 - r-logger + - r-purrr - r-r.utils - r-rcdk - r-rcpp - r-readjdx + - r-readr - r-rjson + - r-tibble + - r-tidyselect - r-webchem - r-xml - r-yaml - openbabel - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} + +source: + md5: 63db3f188ead6224735d06f429e1ea43 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Workflow to process tandem MS files and build MassBank records' - description: 'Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rmassbankdata/meta.yaml b/recipes/bioconductor-rmassbankdata/meta.yaml index add2a5313260a..75b42774b96e6 100644 --- a/recipes/bioconductor-rmassbankdata/meta.yaml +++ b/recipes/bioconductor-rmassbankdata/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "RMassBankData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ac6f883e962890eebb03c2368be8bcdc +about: + description: Example spectra, example compound list(s) and an example annotation list for a narcotics dataset; required to test RMassBank. The package is described in the man page for RMassBankData. Includes new XCMS test data. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Test dataset for RMassBank build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rmassbankdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: RMassBank requirements: host: @@ -26,13 +24,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d1aa782369d4a3b48f49343eaf62fe48 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Test dataset for RMassBank' - description: 'Example spectra, example compound list(s) and an example annotation list for a narcotics dataset; required to test RMassBank. The package is described in the man page for RMassBankData. Includes new XCMS test data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rmassbankdata/post-link.sh b/recipes/bioconductor-rmassbankdata/post-link.sh index fa1e79222fceb..471f74a901000 100644 --- a/recipes/bioconductor-rmassbankdata/post-link.sh +++ b/recipes/bioconductor-rmassbankdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rmassbankdata-1.40.0" +installBiocDataPackage.sh "rmassbankdata-1.44.0" diff --git a/recipes/bioconductor-rmelting/meta.yaml b/recipes/bioconductor-rmelting/meta.yaml index d3b27ada7ef61..27dcf284f7a51 100644 --- a/recipes/bioconductor-rmelting/meta.yaml +++ b/recipes/bioconductor-rmelting/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "rmelting" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a73d7dd41b3d77dce067644b04412e9d +about: + description: R interface to the MELTING 5 program (https://www.ebi.ac.uk/biomodels/tools/melting/) to compute melting temperatures of nucleic acid duplexes along with other thermodynamic parameters. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 | GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: R Interface to MELTING 5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rmelting", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: readxl, knitr, rmarkdown, reshape2, pander, testthat # SystemRequirements: Java requirements: host: - r-base - r-rdpack - - 'r-rjava >=0.9-8' + - r-rjava >=0.9-8 - openjdk run: - r-base - r-rdpack - - 'r-rjava >=0.9-8' + - r-rjava >=0.9-8 - openjdk +source: + md5: 79c4d4dc8accde517b50067ddbdacd16 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-2 | GPL-3' - summary: 'R Interface to MELTING 5' - description: 'R interface to the MELTING 5 program (https://www.ebi.ac.uk/biomodels/tools/melting/) to compute melting temperatures of nucleic acid duplexes along with other thermodynamic parameters.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rmir.hs.mirna/meta.yaml b/recipes/bioconductor-rmir.hs.mirna/meta.yaml index f38de5714e0ba..4169daaae656b 100644 --- a/recipes/bioconductor-rmir.hs.mirna/meta.yaml +++ b/recipes/bioconductor-rmir.hs.mirna/meta.yaml @@ -1,45 +1,45 @@ {% set version = "1.0.7" %} {% set name = "RmiR.Hs.miRNA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4aedac188382447d9907d2617aa2e8e6 +about: + description: Various databases of microRNA Targets + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: The Artistic License, Version 2.0 + summary: Various databases of microRNA Targets build: - number: 15 + noarch: generic + number: 16 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rmir.hs.mirna", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-rmir.hs.mirna + path: recipes/bioconductor-rmir.hs.mirna + version: 1.0.7 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: methods, hgug4112a.db requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4aedac188382447d9907d2617aa2e8e6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'The Artistic License, Version 2.0' - summary: 'Various databases of microRNA Targets' - description: 'Various databases of microRNA Targets' -extra: - parent_recipe: - name: bioconductor-rmir.hs.mirna - path: recipes/bioconductor-rmir.hs.mirna - version: 1.0.7 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rmir.hsa/meta.yaml b/recipes/bioconductor-rmir.hsa/meta.yaml index 0f5eb625023cc..5e43b8af4ec4e 100644 --- a/recipes/bioconductor-rmir.hsa/meta.yaml +++ b/recipes/bioconductor-rmir.hsa/meta.yaml @@ -1,40 +1,40 @@ {% set version = "1.0.5" %} {% set name = "RmiR.hsa" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f22a18d1a34d12f8fc4ba3daaf1379fd +about: + description: Various databases of microRNA Targets + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: The Artistic License, Version 2.0 + summary: Various databases of microRNA Targets build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rmir.hsa", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: methods, hgug4112a.db requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f22a18d1a34d12f8fc4ba3daaf1379fd + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'The Artistic License, Version 2.0' - summary: 'Various databases of microRNA Targets' - description: 'Various databases of microRNA Targets' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rmmquant/build_failure.osx-64.yaml b/recipes/bioconductor-rmmquant/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..a4c4863738953 --- /dev/null +++ b/recipes/bioconductor-rmmquant/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: d2d026299ba5593d9d8106c34f42b64073b693dc172658c3e06955b8a52d1cbf # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmmquant-1.24.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmmquant-1.24.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmmquant-1.24.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmmquant-1.24.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmmquant-1.24.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmmquant-1.24.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmmquant-1.24.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rmmquant-1.24.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o + x86_64-apple-darwin13.4.0-clang -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c mmquant_wrapper.cpp -o mmquant_wrapper.o + x86_64-apple-darwin13.4.0-clang -std=gnu11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L$PREFIX/lib/R/lib -Wl,-dead_strip_dylibs -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o Rmmquant.so RcppExports.o mmquant_wrapper.o -lz -L$PREFIX/lib/R/lib -lR -Wl,-framework -Wl,CoreFoundation + + Resource usage statistics from building bioconductor-rmmquant: + Process count: 6 + CPU time: Sys=0:00:02.1, User=0:00:31.8 + Memory: 1.0G + Disk usage: 3.2K + Time elapsed: 0:00:46.0 + + + Packaging bioconductor-rmmquant + Packaging bioconductor-rmmquant-1.24.0-r44hff34b7e_0 + + number of files: 34 + Fixing linking of Rmmquant.so in /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rmmquant_1735781552986/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/Rmmquant/libs/Rmmquant.so + Traceback (most recent call last): + New link location is lib/R/library/Rmmquant/libs/Rmmquant.so + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2765, in build + newly_built_packages = bundlers[pkg_type]( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1874, in bundle_conda + files = post_process_files(metadata, initial_files) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1653, in post_process_files + post_build(m, new_files, build_python=python) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1759, in post_build + post_process_shared_lib(m, f, prefix_files, host_prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1635, in post_process_shared_lib + mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 488, in mk_relative_osx + existing_rpaths = macho.get_rpaths(path, build_prefix=prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 252, in get_rpaths + dylib_loads = otool(path, build_prefix, is_rpath) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 221, in otool + lines = check_output([otool, "-l", path], stderr=STDOUT).decode("utf-8") + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 421, in check_output + return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 526, in run + raise CalledProcessError(retcode, process.args, + subprocess.CalledProcessError: Command '['/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rmmquant_1735781552986/_build_env/bin/llvm-otool', '-l', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rmmquant_1735781552986/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/Rmmquant/libs/Rmmquant.so']' died with . +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-rmmquant/meta.yaml b/recipes/bioconductor-rmmquant/meta.yaml index 5091be475916f..bb0adabb95bc9 100644 --- a/recipes/bioconductor-rmmquant/meta.yaml +++ b/recipes/bioconductor-rmmquant/meta.yaml @@ -1,65 +1,71 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "Rmmquant" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used, but all of them provide biased results. With Rmmquant, if a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes. Rmmquant is a drop-in replacement of the widely used tools findOverlaps and featureCounts that handles multi-mapping reads in an unabiased way. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: RNA-Seq multi-mapping Reads Quantification Tool -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8f12574d12fdfbb3ef7407666fb22a7b build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rmmquant", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-apeglm >=1.24.0,<1.25.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tbx20bamsubset >=1.38.0,<1.39.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' + - bioconductor-apeglm >=1.28.0,<1.29.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tbx20bamsubset >=1.42.0,<1.43.0 + - bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0 - r-base - r-devtools - - 'r-rcpp >=0.12.8' + - r-rcpp >=0.12.8 - libblas - liblapack + - zlib run: - - 'bioconductor-apeglm >=1.24.0,<1.25.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tbx20bamsubset >=1.38.0,<1.39.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' + - bioconductor-apeglm >=1.28.0,<1.29.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tbx20bamsubset >=1.42.0,<1.43.0 + - bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0 - r-base - r-devtools - - 'r-rcpp >=0.12.8' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=0.12.8 + +source: + md5: 963847e0892a9a7b11f628fadea1e82a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'RNA-Seq multi-mapping Reads Quantification Tool' - description: 'RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used, but all of them provide biased results. With Rmmquant, if a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes. Rmmquant is a drop-in replacement of the widely used tools findOverlaps and featureCounts that handles multi-mapping reads in an unabiased way.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnaagecalc/meta.yaml b/recipes/bioconductor-rnaagecalc/meta.yaml index dee8249e03b08..330a70a3854ea 100644 --- a/recipes/bioconductor-rnaagecalc/meta.yaml +++ b/recipes/bioconductor-rnaagecalc/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "RNAAgeCalc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: It has been shown that both DNA methylation and RNA transcription are linked to chronological age and age related diseases. Several estimators have been developed to predict human aging from DNA level and RNA level. Most of the human transcriptional age predictor are based on microarray data and limited to only a few tissues. To date, transcriptional studies on aging using RNASeq data from different human tissues is limited. The aim of this package is to provide a tool for across-tissue and tissue-specific transcriptional age calculation based on GTEx RNASeq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A multi-tissue transcriptional age calculator -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8601edc9bd38ec2387cd9cd9a78b0da8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnaagecalc", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-recount >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-recount >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-recount >=1.28.0,<1.29.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-recount >=1.32.0,<1.33.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 + +source: + md5: bb8c07d160976feccd3ab8a850b9cc26 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'A multi-tissue transcriptional age calculator' - description: 'It has been shown that both DNA methylation and RNA transcription are linked to chronological age and age related diseases. Several estimators have been developed to predict human aging from DNA level and RNA level. Most of the human transcriptional age predictor are based on microarray data and limited to only a few tissues. To date, transcriptional studies on aging using RNASeq data from different human tissues is limited. The aim of this package is to provide a tool for across-tissue and tissue-specific transcriptional age calculation based on GTEx RNASeq data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnadecay/meta.yaml b/recipes/bioconductor-rnadecay/meta.yaml index 084fa933beefc..6627eb85e052f 100644 --- a/recipes/bioconductor-rnadecay/meta.yaml +++ b/recipes/bioconductor-rnadecay/meta.yaml @@ -1,24 +1,37 @@ -{% set version = "1.19.0" %} +{% set version = "1.26.0" %} {% set name = "RNAdecay" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: 'RNA degradation is monitored through measurement of RNA abundance after inhibiting RNA synthesis. This package has functions and example scripts to facilitate (1) data normalization, (2) data modeling using constant decay rate or time-dependent decay rate models, (3) the evaluation of treatment or genotype effects, and (4) plotting of the data and models. Data Normalization: functions and scripts make easy the normalization to the initial (T0) RNA abundance, as well as a method to correct for artificial inflation of Reads per Million (RPM) abundance in global assessments as the total size of the RNA pool decreases. Modeling: Normalized data is then modeled using maximum likelihood to fit parameters. For making treatment or genotype comparisons (up to four), the modeling step models all possible treatment effects on each gene by repeating the modeling with constraints on the model parameters (i.e., the decay rate of treatments A and B are modeled once with them being equal and again allowing them to both vary independently). Model Selection: The AICc value is calculated for each model, and the model with the lowest AICc is chosen. Modeling results of selected models are then compiled into a single data frame. Graphical Plotting: functions are provided to easily visualize decay data model, or half-life distributions using ggplot2 package functions.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Maximum Likelihood Decay Modeling of RNA Degradation Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45ffe8fc9c250748a5beb7ade034b481 build: number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rnadecay", max_pin="x.x") }}' + +extra: + parent_recipe: + name: bioconductor-rnadecay + path: recipes/bioconductor-rnadecay + version: 1.2.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: parallel, knitr, reshape2, rmarkdown requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-ggplot2 @@ -35,22 +48,16 @@ requirements: - r-nloptr - r-scales - r-tmb - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 234bd79f217035934dc16605bca37397 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Maximum Likelihood Decay Modeling of RNA Degradation Data' - description: 'RNA degradation is monitored through measurement of RNA abundance after inhibiting RNA synthesis. This package has functions and example scripts to facilitate (1) data normalization, (2) data modeling using constant decay rate or time-dependent decay rate models, (3) the evaluation of treatment or genotype effects, and (4) plotting of the data and models. Data Normalization: functions and scripts make easy the normalization to the initial (T0) RNA abundance, as well as a method to correct for artificial inflation of Reads per Million (RPM) abundance in global assessments as the total size of the RNA pool decreases. Modeling: Normalized data is then modeled using maximum likelihood to fit parameters. For making treatment or genotype comparisons (up to four), the modeling step models all possible treatment effects on each gene by repeating the modeling with constraints on the model parameters (i.e., the decay rate of treatments A and B are modeled once with them being equal and again allowing them to both vary independently). Model Selection: The AICc value is calculated for each model, and the model with the lowest AICc is chosen. Modeling results of selected models are then compiled into a single data frame. Graphical Plotting: functions are provided to easily visualize decay data model, or half-life distributions using ggplot2 package functions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - parent_recipe: - name: bioconductor-rnadecay - path: recipes/bioconductor-rnadecay - version: 1.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnaeditr/meta.yaml b/recipes/bioconductor-rnaeditr/meta.yaml index cbbbde1bbbebf..dfe0c96c30774 100644 --- a/recipes/bioconductor-rnaeditr/meta.yaml +++ b/recipes/bioconductor-rnaeditr/meta.yaml @@ -1,57 +1,62 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "rnaEditr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: RNAeditr analyzes site-specific RNA editing events, as well as hyper-editing regions. The editing frequencies can be tested against binary, continuous or survival outcomes. Multiple covariate variables as well as interaction effects can also be incorporated in the statistical models. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Statistical analysis of RNA editing sites and hyper-editing regions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fb5365c7d12dcdc26838f4824e70a00d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnaeditr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-corrplot - r-logistf - r-plyr - r-survival run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bumphunter >=1.44.0,<1.45.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bumphunter >=1.48.0,<1.49.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-corrplot - r-logistf - r-plyr - r-survival + +source: + md5: 5e9cc8a9cb2460aa6efe45fb45cc1f50 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Statistical analysis of RNA editing sites and hyper-editing regions' - description: 'RNAeditr analyzes site-specific RNA editing events, as well as hyper-editing regions. The editing frequencies can be tested against binary, continuous or survival outcomes. Multiple covariate variables as well as interaction effects can also be incorporated in the statistical models.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnagilentdesign028282.db/meta.yaml b/recipes/bioconductor-rnagilentdesign028282.db/meta.yaml index 3fae561ac4294..e4fded1ecb6a3 100644 --- a/recipes/bioconductor-rnagilentdesign028282.db/meta.yaml +++ b/recipes/bioconductor-rnagilentdesign028282.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "RnAgilentDesign028282.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 72cafb0f7514a81f462acb3248e21aa9 +about: + description: Agilent Chips that use Agilent design number 028282 annotation data (chip RnAgilentDesign028282) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Agilent Chips that use Agilent design number 028282 annotation data (chip RnAgilentDesign028282) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnagilentdesign028282.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 72cafb0f7514a81f462acb3248e21aa9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Agilent Chips that use Agilent design number 028282 annotation data (chip RnAgilentDesign028282)' - description: 'Agilent Chips that use Agilent design number 028282 annotation data (chip RnAgilentDesign028282) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnainteractmapk/build_failure.linux-64.yaml b/recipes/bioconductor-rnainteractmapk/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..118c885c95153 --- /dev/null +++ b/recipes/bioconductor-rnainteractmapk/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 84488064f755b4aeabaef5b83751be1dfd61e74efd6afe5892b4ae2b856933fd # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: dependency issue +reason: bioconductor-rnainteract not available for 3.20 yet +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rnainteract[version='>=1.54.0,<1.55.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rnainteract >=1.54.0,<1.55.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rnainteract >=1.54.0,<1.55.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rnainteract[version='>=1.54.0,<1.55.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rnainteract >=1.54.0,<1.55.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rnainteract >=1.54.0,<1.55.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rnainteract[version='>=1.54.0,<1.55.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rnainteract >=1.54.0,<1.55.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rnainteract >=1.54.0,<1.55.0 [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-rnainteractmapk/meta.yaml b/recipes/bioconductor-rnainteractmapk/meta.yaml index 47e1b53a2be90..c07b2bd93209b 100644 --- a/recipes/bioconductor-rnainteractmapk/meta.yaml +++ b/recipes/bioconductor-rnainteractmapk/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "1.40.0" %} +{% set version = "1.41.0" %} {% set name = "RNAinteractMAPK" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package includes all data used in the paper -Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi- by Horn, Sandmann, Fischer et al.., Nat. Methods, 2011. The package vignette shows the R code to reproduce all figures in the paper. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c60bb748ed7dc37d409f5dde69354074 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnainteractmapk", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: qvalue requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-rnainteract >=1.50.0,<1.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-rnainteract >=1.54.0,<1.55.0 - r-base - r-fields - r-gdata @@ -32,9 +33,9 @@ requirements: - r-mass - r-sparselda run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-rnainteract >=1.50.0,<1.51.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-rnainteract >=1.54.0,<1.55.0 - r-base - r-fields - r-gdata @@ -42,13 +43,17 @@ requirements: - r-mass - r-sparselda - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 41bafca51c673429835afbcf60b89454 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi' - description: 'This package includes all data used in the paper -Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi- by Horn, Sandmann, Fischer et al.., Nat. Methods, 2011. The package vignette shows the R code to reproduce all figures in the paper.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnainteractmapk/post-link.sh b/recipes/bioconductor-rnainteractmapk/post-link.sh index d87f516db77a0..8463e8222ab39 100644 --- a/recipes/bioconductor-rnainteractmapk/post-link.sh +++ b/recipes/bioconductor-rnainteractmapk/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnainteractmapk-1.40.0" +installBiocDataPackage.sh "rnainteractmapk-1.41.0" diff --git a/recipes/bioconductor-rnamodr.alkanilineseq/meta.yaml b/recipes/bioconductor-rnamodr.alkanilineseq/meta.yaml index 93407ca9b47f1..84df8bbb210a7 100644 --- a/recipes/bioconductor-rnamodr.alkanilineseq/meta.yaml +++ b/recipes/bioconductor-rnamodr.alkanilineseq/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "RNAmodR.AlkAnilineSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: RNAmodR.AlkAnilineSeq implements the detection of m7G, m3C and D modifications on RNA from experimental data generated with the AlkAnilineSeq protocol. The package builds on the core functionality of the RNAmodR package to detect specific patterns of the modifications in high throughput sequencing data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Detection of m7G, m3C and D modification by AlkAnilineSeq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8d93c4a0a55346a6d47edb5f4c4438e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnamodr.alkanilineseq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, Biostrings, RNAmodR.Data requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rnamodr >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rnamodr >=1.20.0,<1.21.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rnamodr >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rnamodr >=1.20.0,<1.21.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base + +source: + md5: fa2a8c83e29b1895f93bff5ec487a784 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Detection of m7G, m3C and D modification by AlkAnilineSeq' - description: 'RNAmodR.AlkAnilineSeq implements the detection of m7G, m3C and D modifications on RNA from experimental data generated with the AlkAnilineSeq protocol. The package builds on the core functionality of the RNAmodR package to detect specific patterns of the modifications in high throughput sequencing data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnamodr.data/build_failure.linux-64.yaml b/recipes/bioconductor-rnamodr.data/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..dd68597f11c57 --- /dev/null +++ b/recipes/bioconductor-rnamodr.data/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: f7ec9e616f7fd1e78a67495c1f051318fdf84d00d2717ee694fd7c81f8c9002d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-ps: 1.8.1-r44h2b5f3a1_0 conda-forge + r-purrr: 1.0.2-r44hdb488b9_1 conda-forge + r-r6: 2.5.1-r44hc72bb7e_3 conda-forge + r-rappdirs: 0.3.3-r44hb1dbf0f_3 conda-forge + r-rcurl: 1.98_1.16-r44he8228da_1 conda-forge + r-restfulr: 0.0.15-r44h5ef9028_5 bioconda + r-rjson: 0.2.23-r44h93ab643_0 conda-forge + r-rlang: 1.1.4-r44ha18555a_1 conda-forge + r-rsqlite: 2.3.9-r44h93ab643_0 conda-forge + r-runit: 0.4.33-r44hc72bb7e_1 conda-forge + r-rvest: 1.0.4-r44hc72bb7e_1 conda-forge + r-selectr: 0.4_2-r44hc72bb7e_4 conda-forge + r-snow: 0.4_4-r44hc72bb7e_3 conda-forge + r-stringdist: 0.9.14-r44h2b5f3a1_0 conda-forge + r-stringi: 1.8.4-r44h33cde33_3 conda-forge + r-stringr: 1.5.1-r44h785f33e_1 conda-forge + r-sys: 3.4.3-r44h2b5f3a1_0 conda-forge + r-tibble: 3.2.1-r44hdb488b9_3 conda-forge + r-tidyr: 1.3.1-r44h0d4f4ea_1 conda-forge + r-tidyselect: 1.2.1-r44hc72bb7e_1 conda-forge + r-utf8: 1.2.4-r44hb1dbf0f_1 conda-forge + r-vctrs: 0.6.5-r44h0d4f4ea_1 conda-forge + r-withr: 3.0.2-r44hc72bb7e_0 conda-forge + r-xfun: 0.49-r44h93ab643_0 conda-forge + r-xml: 3.99_0.17-r44h5bae778_2 conda-forge + r-xml2: 1.3.6-r44h8194278_2 conda-forge + r-yaml: 2.3.10-r44hdb488b9_0 conda-forge + readline: 8.2-h8228510_1 conda-forge + sed: 4.8-he412f7d_0 conda-forge + setuptools: 75.6.0-pyhff2d567_1 conda-forge + sysroot_linux-64: 2.17-h0157908_18 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tktable: 2.10-h8bc8fbc_6 conda-forge + toml: 0.10.2-pyhd8ed1ab_1 conda-forge + tomlkit: 0.13.2-pyha770c72_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + xmltodict: 0.14.2-pyhd8ed1ab_1 conda-forge + xorg-libice: 1.1.2-hb9d3cd8_0 conda-forge + xorg-libsm: 1.2.5-he73a12e_0 conda-forge + xorg-libx11: 1.8.10-h4f16b4b_1 conda-forge + xorg-libxau: 1.0.12-hb9d3cd8_0 conda-forge + xorg-libxdmcp: 1.1.5-hb9d3cd8_0 conda-forge + xorg-libxext: 1.3.6-hb9d3cd8_0 conda-forge + xorg-libxrender: 0.9.12-hb9d3cd8_0 conda-forge + xorg-libxt: 1.3.1-hb9d3cd8_0 conda-forge + yaml: 0.2.5-h7f98852_2 conda-forge + yq: 3.4.3-pyhd8ed1ab_1 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: RNAmodR.Data_1.19.0_b8b56a5e31.tar.gz + Downloading https://bioconductor.org/packages/3.20/data/experiment/src/contrib/RNAmodR.Data_1.19.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.115326 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioconductor.org/packages/3.20/bioc/src/contrib/Archive/RNAmodR.Data/RNAmodR.Data_1.19.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.032725 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioarchive.galaxyproject.org/RNAmodR.Data_1.19.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.348237 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://depot.galaxyproject.org/software/bioconductor-rnamodr.data/bioconductor-rnamodr.data_1.19.0_src_all.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.154611 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download https://depot.galaxyproject.org/software/bioconductor-rnamodr.data/bioconductor-rnamodr.data_1.19.0_src_all.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-rnamodr.data/meta.yaml b/recipes/bioconductor-rnamodr.data/meta.yaml index beb72c08bfd72..e4211164d12f8 100644 --- a/recipes/bioconductor-rnamodr.data/meta.yaml +++ b/recipes/bioconductor-rnamodr.data/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.16.0" %} +{% set version = "1.19.0" %} {% set name = "RNAmodR.Data" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd4851e2f0c0a93c6d5a9163f542b07f +about: + description: RNAmodR.Data contains example data, which is used for vignettes and example workflows in the RNAmodR and dependent packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Example data for the RNAmodR package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnamodr.data", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle, GenomicRanges, sessioninfo, testthat requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-experimenthubdata >=1.28.0,<1.29.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-experimenthubdata >=1.32.0,<1.33.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-experimenthubdata >=1.28.0,<1.29.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-experimenthubdata >=1.32.0,<1.33.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b8b56a5e310771c78f3076d338eaeb02 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Example data for the RNAmodR package' - description: 'RNAmodR.Data contains example data, which is used for vignettes and example workflows in the RNAmodR and dependent packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnamodr.data/post-link.sh b/recipes/bioconductor-rnamodr.data/post-link.sh index 7991a62b289cf..defb00d49fdaf 100644 --- a/recipes/bioconductor-rnamodr.data/post-link.sh +++ b/recipes/bioconductor-rnamodr.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnamodr.data-1.16.0" +installBiocDataPackage.sh "rnamodr.data-1.19.0" diff --git a/recipes/bioconductor-rnamodr.ml/meta.yaml b/recipes/bioconductor-rnamodr.ml/meta.yaml index 1508ede453dec..65ae76b8eefde 100644 --- a/recipes/bioconductor-rnamodr.ml/meta.yaml +++ b/recipes/bioconductor-rnamodr.ml/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "RNAmodR.ML" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: RNAmodR.ML extend the functionality of the RNAmodR package and classical detection strategies towards detection through machine learning models. RNAmodR.ML provides classes, functions and an example workflow to establish a detection stratedy, which can be packaged. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Detecting patterns of post-transcriptional modifications using machine learning -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b82e119e7d8c2387b22f4b38d0985970 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnamodr.ml", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data, RNAmodR.AlkAnilineSeq, GenomicFeatures, Rsamtools, rtracklayer, keras requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rnamodr >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rnamodr >=1.20.0,<1.21.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ranger run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rnamodr >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rnamodr >=1.20.0,<1.21.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ranger + +source: + md5: 6869e376dfa0bdbc43899f3963029282 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Detecting patterns of post-transcriptional modifications using machine learning' - description: 'RNAmodR.ML extend the functionality of the RNAmodR package and classical detection strategies towards detection through machine learning models. RNAmodR.ML provides classes, functions and an example workflow to establish a detection stratedy, which can be packaged.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnamodr.ribomethseq/meta.yaml b/recipes/bioconductor-rnamodr.ribomethseq/meta.yaml index a6f3883a418a5..51dd198fb41e7 100644 --- a/recipes/bioconductor-rnamodr.ribomethseq/meta.yaml +++ b/recipes/bioconductor-rnamodr.ribomethseq/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "RNAmodR.RiboMethSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: RNAmodR.RiboMethSeq implements the detection of 2'-O methylations on RNA from experimental data generated with the RiboMethSeq protocol. The package builds on the core functionality of the RNAmodR package to detect specific patterns of the modifications in high throughput sequencing data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Detection of 2'-O methylations by RiboMethSeq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fc22b6332a4e89e33ff8921d9e54aac7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnamodr.ribomethseq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, RNAmodR.Data requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rnamodr >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rnamodr >=1.20.0,<1.21.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rnamodr >=1.16.0,<1.17.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rnamodr >=1.20.0,<1.21.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base + +source: + md5: a82549ffea70152b4e323ffb2ea69620 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Detection of 2''-O methylations by RiboMethSeq' - description: 'RNAmodR.RiboMethSeq implements the detection of 2''-O methylations on RNA from experimental data generated with the RiboMethSeq protocol. The package builds on the core functionality of the RNAmodR package to detect specific patterns of the modifications in high throughput sequencing data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnamodr/meta.yaml b/recipes/bioconductor-rnamodr/meta.yaml index 78ce0c695332d..d80a50faca3ae 100644 --- a/recipes/bioconductor-rnamodr/meta.yaml +++ b/recipes/bioconductor-rnamodr/meta.yaml @@ -1,41 +1,44 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "RNAmodR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: RNAmodR provides classes and workflows for loading/aggregation data from high througput sequencing aimed at detecting post-transcriptional modifications through analysis of specific patterns. In addition, utilities are provided to validate and visualize the results. The RNAmodR package provides a core functionality from which specific analysis strategies can be easily implemented as a seperate package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Detection of post-transcriptional modifications in high throughput sequencing data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ece4ec8fc16a95ec2ee8d9506283c57e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnamodr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-modstrings >=1.18.0,<1.19.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-modstrings >=1.22.0,<1.23.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-colorramps - r-ggplot2 @@ -43,21 +46,23 @@ requirements: - r-rcolorbrewer - r-reshape2 - r-rocr + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-modstrings >=1.18.0,<1.19.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-modstrings >=1.22.0,<1.23.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-colorramps - r-ggplot2 @@ -65,12 +70,16 @@ requirements: - r-rcolorbrewer - r-reshape2 - r-rocr + +source: + md5: 391d754edd4e3269fd8d604883b37b14 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Detection of post-transcriptional modifications in high throughput sequencing data' - description: 'RNAmodR provides classes and workflows for loading/aggregation data from high througput sequencing aimed at detecting post-transcriptional modifications through analysis of specific patterns. In addition, utilities are provided to validate and visualize the results. The RNAmodR package provides a core functionality from which specific analysis strategies can be easily implemented as a seperate package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnasense/meta.yaml b/recipes/bioconductor-rnasense/meta.yaml index f75925da2198c..c0c7469f45dab 100644 --- a/recipes/bioconductor-rnasense/meta.yaml +++ b/recipes/bioconductor-rnasense/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "RNAsense" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 514e6c09019b7f9116ddbedbdf514a5a +about: + description: RNA-sense tool compares RNA-seq time curves in two experimental conditions, i.e. wild-type and mutant, and works in three steps. At Step 1, it builds expression profile for each transcript in one condition (i.e. wild-type) and tests if the transcript abundance grows or decays significantly. Dynamic transcripts are then sorted to non-overlapping groups (time profiles) by the time point of switch up or down. At Step 2, RNA-sense outputs the groups of differentially expressed transcripts, which are up- or downregulated in the mutant compared to the wild-type at each time point. At Step 3, Correlations (Fisher's exact test) between the outputs of Step 1 (switch up- and switch down- time profile groups) and the outputs of Step2 (differentially expressed transcript groups) are calculated. The results of the correlation analysis are printed as two-dimensional color plot, with time profiles and differential expression groups at y- and x-axis, respectively, and facilitates the biological interpretation of the data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Analysis of Time-Resolved RNA-Seq Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnasense", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-nbpseq run: - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-nbpseq +source: + md5: 3607e197234601375c6c097c48d937fa + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Analysis of Time-Resolved RNA-Seq Data' - description: 'RNA-sense tool compares RNA-seq time curves in two experimental conditions, i.e. wild-type and mutant, and works in three steps. At Step 1, it builds expression profile for each transcript in one condition (i.e. wild-type) and tests if the transcript abundance grows or decays significantly. Dynamic transcripts are then sorted to non-overlapping groups (time profiles) by the time point of switch up or down. At Step 2, RNA-sense outputs the groups of differentially expressed transcripts, which are up- or downregulated in the mutant compared to the wild-type at each time point. At Step 3, Correlations (Fisher''s exact test) between the outputs of Step 1 (switch up- and switch down- time profile groups) and the outputs of Step2 (differentially expressed transcript groups) are calculated. The results of the correlation analysis are printed as two-dimensional color plot, with time profiles and differential expression groups at y- and x-axis, respectively, and facilitates the biological interpretation of the data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnaseqcomp/meta.yaml b/recipes/bioconductor-rnaseqcomp/meta.yaml index 874a5325d2799..159d9c45da57a 100644 --- a/recipes/bioconductor-rnaseqcomp/meta.yaml +++ b/recipes/bioconductor-rnaseqcomp/meta.yaml @@ -1,24 +1,34 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "rnaseqcomp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Several quantitative and visualized benchmarks for RNA-seq quantification pipelines. Two-condition quantifications for genes, transcripts, junctions or exons by each pipeline with necessary meta information should be organized into numeric matrices in order to proceed the evaluation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Benchmarks for RNA-seq Quantification Pipelines -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 2d0e9f4dd34f6746ff48994f8067f6f6 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnaseqcomp", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rnaseqcomp + parent_recipe: + name: bioconductor-rnaseqcomp + path: recipes/bioconductor-rnaseqcomp + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: host: @@ -27,20 +37,16 @@ requirements: run: - r-base - r-rcolorbrewer + +source: + md5: 43d09a0edafe42e83d9652ad5f8962ce + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Benchmarks for RNA-seq Quantification Pipelines' - description: 'Several quantitative and visualized benchmarks for RNA-seq quantification pipelines. Two-condition quantifications for genes, transcripts, junctions or exons by each pipeline with necessary meta information should be organized into numeric matrices in order to proceed the evaluation.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:rnaseqcomp - parent_recipe: - name: bioconductor-rnaseqcomp - path: recipes/bioconductor-rnaseqcomp - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnaseqcovarimpute/meta.yaml b/recipes/bioconductor-rnaseqcovarimpute/meta.yaml index 21a2e0ab62a71..d5141622f5666 100644 --- a/recipes/bioconductor-rnaseqcovarimpute/meta.yaml +++ b/recipes/bioconductor-rnaseqcovarimpute/meta.yaml @@ -1,31 +1,34 @@ -{% set version = "1.0.2" %} +{% set version = "1.4.0" %} {% set name = "RNAseqCovarImpute" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The RNAseqCovarImpute package makes linear model analysis for RNA sequencing read counts compatible with multiple imputation (MI) of missing covariates. A major problem with implementing MI in RNA sequencing studies is that the outcome data must be included in the imputation prediction models to avoid bias. This is difficult in omics studies with high-dimensional data. The first method we developed in the RNAseqCovarImpute package surmounts the problem of high-dimensional outcome data by binning genes into smaller groups to analyze pseudo-independently. This method implements covariate MI in gene expression studies by 1) randomly binning genes into smaller groups, 2) creating M imputed datasets separately within each bin, where the imputation predictor matrix includes all covariates and the log counts per million (CPM) for the genes within each bin, 3) estimating gene expression changes using `limma::voom` followed by `limma::lmFit` functions, separately on each M imputed dataset within each gene bin, 4) un-binning the gene sets and stacking the M sets of model results before applying the `limma::squeezeVar` function to apply a variance shrinking Bayesian procedure to each M set of model results, 5) pooling the results with Rubins’ rules to produce combined coefficients, standard errors, and P-values, and 6) adjusting P-values for multiplicity to account for false discovery rate (FDR). A faster method uses principal component analysis (PCA) to avoid binning genes while still retaining outcome information in the MI models. Binning genes into smaller groups requires that the MI and limma-voom analysis is run many times (typically hundreds). The more computationally efficient MI PCA method implements covariate MI in gene expression studies by 1) performing PCA on the log CPM values for all genes using the Bioconductor `PCAtools` package, 2) creating M imputed datasets where the imputation predictor matrix includes all covariates and the optimum number of PCs to retain (e.g., based on Horn’s parallel analysis or the number of PCs that account for >80% explained variation), 3) conducting the standard limma-voom pipeline with the `voom` followed by `lmFit` followed by `eBayes` functions on each M imputed dataset, 4) pooling the results with Rubins’ rules to produce combined coefficients, standard errors, and P-values, and 5) adjusting P-values for multiplicity to account for false discovery rate (FDR). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Impute Covariate Data in RNA Sequencing Studies -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 17d14273ae359562d3f0cbf1c45b10a7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnaseqcovarimpute", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, tidyr, stringr, testthat (>= 3.0.0) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, PCAtools, rmarkdown, tidyr, stringr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-dplyr - r-foreach @@ -33,23 +36,27 @@ requirements: - r-mice - r-rlang run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-dplyr - r-foreach - r-magrittr - r-mice - r-rlang + +source: + md5: 2b8770546c6f7feeacc2935c0db3065a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Impute Covariate Data in RNA Sequencing Studies' - description: 'The RNAseqCovarImpute package implements multiple imputation of missing covariates and differential gene expression analysis by: 1) Randomly binning genes into smaller groups, 2) Creating M imputed datasets separately within each bin, where the imputation predictor matrix includes all covariates and the log counts per million (CPM) for the genes within each bin, 3) Estimating gene expression changes using voom followed by lmFit functions, separately on each M imputed dataset within each gene bin, 4) Un-binning the gene sets and stacking the M sets of model results before applying the squeezeVar function to apply a variance shrinking Bayesian procedure to each M set of model results, 5) Pooling the results with Rubins’ rules to produce combined coefficients, standard errors, and P-values, and 6) Adjusting P-values for multiplicity to account for false discovery rate (FDR).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml index b3e826c19752f..e86bd585cc449 100644 --- a/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml +++ b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "0.40.0" %} +{% set version = "0.44.0" %} {% set name = "RNAseqData.HNRNPC.bam.chr14" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9bfb7faf3c8770b15f3cf15bb670162d +about: + description: The package contains 8 BAM files, 1 per sequencing run. Each BAM file was obtained by (1) aligning the reads (paired-end) to the full hg19 genome with TopHat2, and then (2) subsetting to keep only alignments on chr14. See accession number E-MTAB-1147 in the ArrayExpress database for details about the experiment, including links to the published study (by Zarnack et al., 2012) and to the FASTQ files. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: 'Aligned reads from RNAseq experiment: Transcription profiling by high throughput sequencing of HNRNPC knockdown and control HeLa cells' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnaseqdata.hnrnpc.bam.chr14", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicAlignments, BiocManager requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: aa012879d391a2c536ccaa7fb16862f7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Aligned reads from RNAseq experiment: Transcription profiling by high throughput sequencing of HNRNPC knockdown and control HeLa cells' - description: 'The package contains 8 BAM files, 1 per sequencing run. Each BAM file was obtained by (1) aligning the reads (paired-end) to the full hg19 genome with TopHat2, and then (2) subsetting to keep only alignments on chr14. See accession number E-MTAB-1147 in the ArrayExpress database for details about the experiment, including links to the published study (by Zarnack et al., 2012) and to the FASTQ files.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/post-link.sh b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/post-link.sh index 02be065d14f92..e1af41fc003d4 100644 --- a/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/post-link.sh +++ b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnaseqdata.hnrnpc.bam.chr14-0.40.0" +installBiocDataPackage.sh "rnaseqdata.hnrnpc.bam.chr14-0.44.0" diff --git a/recipes/bioconductor-rnaseqpower/meta.yaml b/recipes/bioconductor-rnaseqpower/meta.yaml index 50beb5be190ca..770df6ca61ccd 100644 --- a/recipes/bioconductor-rnaseqpower/meta.yaml +++ b/recipes/bioconductor-rnaseqpower/meta.yaml @@ -1,38 +1,20 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "RNASeqPower" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 38da142eb3ee64f2e7684ead27e4520f +about: + description: RNA-seq, sample size + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Sample size for RNAseq studies build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnaseqpower", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>=2)' - summary: 'Sample size for RNAseq studies' - description: 'RNA-seq, sample size' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' extra: identifiers: - biotools:rnaseqpower @@ -41,4 +23,22 @@ extra: name: bioconductor-rnaseqpower path: recipes/bioconductor-rnaseqpower version: 1.22.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +requirements: + host: + - r-base + run: + - r-base +source: + md5: 9ab53302908772115383389e5780aac6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnaseqsamplesize/meta.yaml b/recipes/bioconductor-rnaseqsamplesize/meta.yaml index 470e4efabe95e..7650abb211c2a 100644 --- a/recipes/bioconductor-rnaseqsamplesize/meta.yaml +++ b/recipes/bioconductor-rnaseqsamplesize/meta.yaml @@ -1,70 +1,75 @@ -{% set version = "2.12.0" %} +{% set version = "2.16.0" %} {% set name = "RnaSeqSampleSize" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: RnaSeqSampleSize package provides a sample size calculation method based on negative binomial model and the exact test for assessing differential expression analysis of RNA-seq data. It controls FDR for multiple testing and utilizes the average read count and dispersion distributions from real data to estimate a more reliable sample size. It is also equipped with several unique features, including estimation for interested genes or pathway, power curve visualization, and parameter optimization. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: RnaSeqSampleSize -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: faa40e62b53c345d9298c32310e6488c build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnaseqsamplesize", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, testthat requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-recount >=1.28.0,<1.29.0' - - 'bioconductor-rnaseqsamplesizedata >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-recount >=1.32.0,<1.33.0 + - bioconductor-rnaseqsamplesizedata >=1.38.0,<1.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 - r-ggpubr - r-heatmap3 - r-matlab - - 'r-rcpp >=0.11.2' + - r-rcpp >=0.11.2 - r-tidyr - r-tidyselect - libblas - liblapack run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-recount >=1.28.0,<1.29.0' - - 'bioconductor-rnaseqsamplesizedata >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-recount >=1.32.0,<1.33.0 + - bioconductor-rnaseqsamplesizedata >=1.38.0,<1.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 - r-ggpubr - r-heatmap3 - r-matlab - - 'r-rcpp >=0.11.2' + - r-rcpp >=0.11.2 - r-tidyr - r-tidyselect - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 4be5717671e4e3becac1dd4e8479545b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: RnaSeqSampleSize - description: 'RnaSeqSampleSize package provides a sample size calculation method based on negative binomial model and the exact test for assessing differential expression analysis of RNA-seq data. It controls FDR for multiple testing and utilizes the average read count and dispersion distributions from real data to estimate a more reliable sample size. It is also equipped with several unique features, including estimation for interested genes or pathway, power curve visualization, and parameter optimization.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml b/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml index d6d8fc2ab7470..829332bf22153 100644 --- a/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml +++ b/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml @@ -1,46 +1,52 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "RnaSeqSampleSizeData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: RnaSeqSampleSizeData package provides the read counts and dispersion distribution from real RNA-seq experiments. It can be used by RnaSeqSampleSize package to estimate sample size and power for RNA-seq experiment design. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: RnaSeqSampleSizeData -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a4edc47422b0be1d83521282c0599440 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnaseqsamplesizedata", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-rnaseqsamplesizedata + path: recipes/bioconductor-rnaseqsamplesizedata + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr requirements: host: - - 'bioconductor-edger >=4.0.0,<4.1.0' + - bioconductor-edger >=4.4.0,<4.5.0 - r-base run: - - 'bioconductor-edger >=4.0.0,<4.1.0' + - bioconductor-edger >=4.4.0,<4.5.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 806d652a73359e09fe4c124dacb85507 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: RnaSeqSampleSizeData - description: 'RnaSeqSampleSizeData package provides the read counts and dispersion distribution from real RNA-seq experiments. It can be used by RnaSeqSampleSize package to estimate sample size and power for RNA-seq experiment design.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-rnaseqsamplesizedata - path: recipes/bioconductor-rnaseqsamplesizedata - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnaseqsamplesizedata/post-link.sh b/recipes/bioconductor-rnaseqsamplesizedata/post-link.sh index 0b665148a7ee6..15becf1afffcb 100644 --- a/recipes/bioconductor-rnaseqsamplesizedata/post-link.sh +++ b/recipes/bioconductor-rnaseqsamplesizedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnaseqsamplesizedata-1.34.0" +installBiocDataPackage.sh "rnaseqsamplesizedata-1.38.0" diff --git a/recipes/bioconductor-rnbeads.hg19/meta.yaml b/recipes/bioconductor-rnbeads.hg19/meta.yaml index f712559b76362..15c2770e701a8 100644 --- a/recipes/bioconductor-rnbeads.hg19/meta.yaml +++ b/recipes/bioconductor-rnbeads.hg19/meta.yaml @@ -1,46 +1,52 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "RnBeads.hg19" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Automatically generated RnBeads annotation package for the assembly hg19. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: RnBeads.hg19 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 92612251679ba9c6d2b88b90838edf1c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnbeads.hg19", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-rnbeads.hg19 + path: recipes/bioconductor-rnbeads.hg19 + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: cb644f72ba6539bec603163702cd0162 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: RnBeads.hg19 - description: 'Automatically generated RnBeads annotation package for the assembly hg19.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-rnbeads.hg19 - path: recipes/bioconductor-rnbeads.hg19 - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnbeads.hg19/post-link.sh b/recipes/bioconductor-rnbeads.hg19/post-link.sh index b7529eae02133..cca518ab6869b 100644 --- a/recipes/bioconductor-rnbeads.hg19/post-link.sh +++ b/recipes/bioconductor-rnbeads.hg19/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnbeads.hg19-1.34.0" +installBiocDataPackage.sh "rnbeads.hg19-1.38.0" diff --git a/recipes/bioconductor-rnbeads.hg38/meta.yaml b/recipes/bioconductor-rnbeads.hg38/meta.yaml index 8baae260b3c7f..51491cc2d22c0 100644 --- a/recipes/bioconductor-rnbeads.hg38/meta.yaml +++ b/recipes/bioconductor-rnbeads.hg38/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "RnBeads.hg38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 44dd2d3ae3703e045016a34060a14b0a +about: + description: RnBeads annotation package for genome assembly hg38. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: RnBeads.hg38 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnbeads.hg38", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 43ecf19a9513772a76d0470d1dae9366 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: RnBeads.hg38 - description: 'Automatically generated RnBeads annotation package for the assembly hg38.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnbeads.hg38/post-link.sh b/recipes/bioconductor-rnbeads.hg38/post-link.sh index 7752ddaad438f..a7510a5e1a04b 100644 --- a/recipes/bioconductor-rnbeads.hg38/post-link.sh +++ b/recipes/bioconductor-rnbeads.hg38/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnbeads.hg38-1.34.0" +installBiocDataPackage.sh "rnbeads.hg38-1.38.0" diff --git a/recipes/bioconductor-rnbeads.mm10/meta.yaml b/recipes/bioconductor-rnbeads.mm10/meta.yaml index 6b68058cd1575..abd91e8a646cb 100644 --- a/recipes/bioconductor-rnbeads.mm10/meta.yaml +++ b/recipes/bioconductor-rnbeads.mm10/meta.yaml @@ -1,46 +1,52 @@ -{% set version = "2.10.0" %} +{% set version = "2.14.0" %} {% set name = "RnBeads.mm10" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Automatically generated RnBeads annotation package for the assembly mm10. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: RnBeads.mm10 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0c935572ce46183bc5a7aaea31ea2519 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnbeads.mm10", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-rnbeads.mm10 + path: recipes/bioconductor-rnbeads.mm10 + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: ccb483fc635f66ae10551ddb55bcbd3b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: RnBeads.mm10 - description: 'Automatically generated RnBeads annotation package for the assembly mm10.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-rnbeads.mm10 - path: recipes/bioconductor-rnbeads.mm10 - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnbeads.mm10/post-link.sh b/recipes/bioconductor-rnbeads.mm10/post-link.sh index f7a47eac3384f..415480e346352 100644 --- a/recipes/bioconductor-rnbeads.mm10/post-link.sh +++ b/recipes/bioconductor-rnbeads.mm10/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnbeads.mm10-2.10.0" +installBiocDataPackage.sh "rnbeads.mm10-2.14.0" diff --git a/recipes/bioconductor-rnbeads.mm9/meta.yaml b/recipes/bioconductor-rnbeads.mm9/meta.yaml index 0788e300ed3ab..4a416ecd44ca1 100644 --- a/recipes/bioconductor-rnbeads.mm9/meta.yaml +++ b/recipes/bioconductor-rnbeads.mm9/meta.yaml @@ -1,46 +1,52 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "RnBeads.mm9" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Automatically generated RnBeads annotation package for the assembly mm9. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: RnBeads.mm9 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 76f271051b1c542e5ac0da492777f933 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnbeads.mm9", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-rnbeads.mm9 + path: recipes/bioconductor-rnbeads.mm9 + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: caa3adcbf9caa032ac80937e9f93d1d3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: RnBeads.mm9 - description: 'Automatically generated RnBeads annotation package for the assembly mm9.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-rnbeads.mm9 - path: recipes/bioconductor-rnbeads.mm9 - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnbeads.mm9/post-link.sh b/recipes/bioconductor-rnbeads.mm9/post-link.sh index 6831e4e1b6ab5..4cf20a5e64e6a 100644 --- a/recipes/bioconductor-rnbeads.mm9/post-link.sh +++ b/recipes/bioconductor-rnbeads.mm9/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnbeads.mm9-1.34.0" +installBiocDataPackage.sh "rnbeads.mm9-1.38.0" diff --git a/recipes/bioconductor-rnbeads.rn5/meta.yaml b/recipes/bioconductor-rnbeads.rn5/meta.yaml index 82d6777b5462e..19606ac3f5080 100644 --- a/recipes/bioconductor-rnbeads.rn5/meta.yaml +++ b/recipes/bioconductor-rnbeads.rn5/meta.yaml @@ -1,46 +1,52 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "RnBeads.rn5" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Automatically generated RnBeads annotation package for the assembly rn5. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: RnBeads.rn5 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ed075717da62b68e7a9b47a14ac09a35 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnbeads.rn5", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-rnbeads.rn5 + path: recipes/bioconductor-rnbeads.rn5 + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: e07ef02cf744ae07ef1fa429005280f5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: RnBeads.rn5 - description: 'Automatically generated RnBeads annotation package for the assembly rn5.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-rnbeads.rn5 - path: recipes/bioconductor-rnbeads.rn5 - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnbeads.rn5/post-link.sh b/recipes/bioconductor-rnbeads.rn5/post-link.sh index a47dfa0ed34b1..b94e49f759f3f 100644 --- a/recipes/bioconductor-rnbeads.rn5/post-link.sh +++ b/recipes/bioconductor-rnbeads.rn5/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rnbeads.rn5-1.34.0" +installBiocDataPackage.sh "rnbeads.rn5-1.38.0" diff --git a/recipes/bioconductor-rnbeads/meta.yaml b/recipes/bioconductor-rnbeads/meta.yaml index 23bf5205b7e61..d00dda258dc0e 100644 --- a/recipes/bioconductor-rnbeads/meta.yaml +++ b/recipes/bioconductor-rnbeads/meta.yaml @@ -1,74 +1,80 @@ -{% set version = "2.20.0" %} +{% set version = "2.24.0" %} {% set name = "RnBeads" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: RnBeads -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 40a269bbbddeb407ca5c4545cb6852ff build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnbeads", max_pin="x.x") }}' - noarch: generic -# Suggests: Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RnBeads.hg19, RnBeads.mm9, XML, annotate, biomaRt, foreach, doParallel, ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue, argparse, glmnet, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit, MethylSeekR, sesame + +extra: + parent_recipe: + name: bioconductor-rnbeads + path: recipes/bioconductor-rnbeads + version: 1.12.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RnBeads.hg19, RnBeads.mm9, RnBeads.hg38, XML, annotate, biomaRt, foreach, doParallel, ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue, argparse, glmnet, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit, MethylSeekR, sesame requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-methylumi >=2.48.0,<2.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-methylumi >=2.52.0,<2.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cluster - r-ff - r-fields - - 'r-ggplot2 >=0.9.2' + - r-ggplot2 >=0.9.2 - r-gplots - r-gridextra - r-mass - r-matrixstats - r-plyr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-methylumi >=2.48.0,<2.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-methylumi >=2.52.0,<2.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cluster - r-ff - r-fields - - 'r-ggplot2 >=0.9.2' + - r-ggplot2 >=0.9.2 - r-gplots - r-gridextra - r-mass - r-matrixstats - r-plyr + +source: + md5: a59434a7e62b7cd71c227eefac1c3c36 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: RnBeads - description: 'RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-rnbeads - path: recipes/bioconductor-rnbeads - version: 1.12.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnits/meta.yaml b/recipes/bioconductor-rnits/meta.yaml index 64032849b40f0..721650b7ea2cd 100644 --- a/recipes/bioconductor-rnits/meta.yaml +++ b/recipes/bioconductor-rnits/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "Rnits" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: R/Bioconductor package for normalization, curve registration and inference in time course gene expression data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: R Normalization and Inference of Time Series data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4b767809cee3875eb2f7f991fba83771 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnits", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, GEOquery, stringr requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - r-boot - r-ggplot2 - r-reshape2 run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - r-boot - r-ggplot2 - r-reshape2 + +source: + md5: a2800d06ff629ccdf2f4eaaca7f9068e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'R Normalization and Inference of Time Series data' - description: 'R/Bioconductor package for normalization, curve registration and inference in time course gene expression data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnu34.db/meta.yaml b/recipes/bioconductor-rnu34.db/meta.yaml index bda66c2c787a1..eb6c2c2d532f9 100644 --- a/recipes/bioconductor-rnu34.db/meta.yaml +++ b/recipes/bioconductor-rnu34.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "rnu34.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7345817f2f26270779d2409b8a17a5bd +about: + description: Affymetrix Affymetrix RN_U34 Array annotation data (chip rnu34) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix RN_U34 Array annotation data (chip rnu34) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnu34.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7345817f2f26270779d2409b8a17a5bd + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix RN_U34 Array annotation data (chip rnu34)' - description: 'Affymetrix Affymetrix RN_U34 Array annotation data (chip rnu34) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnu34cdf/meta.yaml b/recipes/bioconductor-rnu34cdf/meta.yaml index 2611cd113cc77..b70e65b9d4e49 100644 --- a/recipes/bioconductor-rnu34cdf/meta.yaml +++ b/recipes/bioconductor-rnu34cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rnu34cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0f2564fc6ac89de4d779faf253f23ce3 +about: + description: A package containing an environment representing the RN_U34.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: rnu34cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnu34cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0f2564fc6ac89de4d779faf253f23ce3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: rnu34cdf - description: 'A package containing an environment representing the RN_U34.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rnu34probe/meta.yaml b/recipes/bioconductor-rnu34probe/meta.yaml index 7c8368ad92536..1d4a98f03d438 100644 --- a/recipes/bioconductor-rnu34probe/meta.yaml +++ b/recipes/bioconductor-rnu34probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rnu34probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c5ef9793a437f2bf990f6e84d31da0de +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RN-U34\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type rnu34 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rnu34probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c5ef9793a437f2bf990f6e84d31da0de + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type rnu34' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RN-U34\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-roar/meta.yaml b/recipes/bioconductor-roar/meta.yaml index 3e8eae075f595..d1d1c9e216cdd 100644 --- a/recipes/bioconductor-roar/meta.yaml +++ b/recipes/bioconductor-roar/meta.yaml @@ -1,55 +1,22 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "roar" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Identify preferential usage of APA sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identify differential APA usage from RNA-seq alignments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 563dcc245ffbc288c2e6ec9a9c138faa build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-roar", max_pin="x.x") }}' - noarch: generic -# Suggests: RNAseqData.HNRNPC.bam.chr14, testthat -requirements: - host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - r-base - run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Identify differential APA usage from RNA-seq alignments' - description: 'Identify preferential usage of APA sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:roar @@ -59,3 +26,42 @@ extra: path: recipes/bioconductor-roar version: 1.16.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RNAseqData.HNRNPC.bam.chr14, testthat +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + +source: + md5: f4506037026e7ca7e2c64752290768cf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-roastgsa/meta.yaml b/recipes/bioconductor-roastgsa/meta.yaml index 0f8d85c23ec25..fc857e3a6d15f 100644 --- a/recipes/bioconductor-roastgsa/meta.yaml +++ b/recipes/bioconductor-roastgsa/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "roastgsa" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements a variety of functions useful for gene set analysis using rotations to approximate the null distribution. It contributes with the implementation of seven test statistic scores that can be used with different goals and interpretations. Several functions are available to complement the statistical results with graphical representations. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Rotation based gene set analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 83d20d90ed18c719222042ae3d9f46d3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-roastgsa", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, GSEABenchmarkeR, EnrichmentBrowser, preprocessCore, DESeq2 requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-ggplot2 - r-gplots - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-ggplot2 - r-gplots - r-rcolorbrewer + +source: + md5: 082654cdda86a6de591abc1c71353c1c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Rotation based gene set analysis' - description: 'This package implements a variety of functions useful for gene set analysis using rotations to approximate the null distribution. It contributes with the implementation of seven test statistic scores that can be used with different goals and interpretations. Several functions are available to complement the statistical results with graphical representations.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-roberts2005annotation.db/meta.yaml b/recipes/bioconductor-roberts2005annotation.db/meta.yaml index 54bd6307c474c..f0b125454d35d 100644 --- a/recipes/bioconductor-roberts2005annotation.db/meta.yaml +++ b/recipes/bioconductor-roberts2005annotation.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "Roberts2005Annotation.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fb28aaf1a1e0c81cf936badc674b754a +about: + description: Roberts2005Annotation Annotation Data (Roberts2005Annotation) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Roberts2005Annotation Annotation Data (Roberts2005Annotation) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-roberts2005annotation.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fb28aaf1a1e0c81cf936badc674b754a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Roberts2005Annotation Annotation Data (Roberts2005Annotation)' - description: 'Roberts2005Annotation Annotation Data (Roberts2005Annotation) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-roc/meta.yaml b/recipes/bioconductor-roc/meta.yaml index 61a1d7d633cdd..c998001c598a2 100644 --- a/recipes/bioconductor-roc/meta.yaml +++ b/recipes/bioconductor-roc/meta.yaml @@ -1,25 +1,41 @@ -{% set version = "1.78.0" %} +{% set version = "1.82.0" %} {% set name = "ROC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provide utilities for ROC, with microarray focus. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: utilities for ROC, with microarray focus -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2b84dc68639bbe6dbc5e4b9eeb429dbb build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-roc", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:roc + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-roc + path: recipes/bioconductor-roc + version: 1.56.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, Biobase, BiocStyle requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-knitr @@ -28,26 +44,16 @@ requirements: run: - r-base - r-knitr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 4a2c9c81127df2c4fd0f6e2008462919 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'utilities for ROC, with microarray focus' - description: 'Provide utilities for ROC, with microarray focus.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:roc - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-roc - path: recipes/bioconductor-roc - version: 1.56.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rolde/meta.yaml b/recipes/bioconductor-rolde/meta.yaml index 839f45ba07b2e..89f22ec5fa76e 100644 --- a/recipes/bioconductor-rolde/meta.yaml +++ b/recipes/bioconductor-rolde/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "RolDE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: RolDE detects longitudinal differential expression between two conditions in noisy high-troughput data. Suitable even for data with a moderate amount of missing values.RolDE is a composite method, consisting of three independent modules with different approaches to detecting longitudinal differential expression. The combination of these diverse modules allows RolDE to robustly detect varying differences in longitudinal trends and expression levels in diverse data types and experimental settings. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'RolDE: Robust longitudinal Differential Expression' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 12c19e976fa6e9be2e9fa9a433690355 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rolde", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, printr, rmarkdown, testthat requirements: host: - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rots >=1.30.0,<1.31.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rots >=1.34.0,<1.35.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-doparallel - r-dorng @@ -33,9 +35,9 @@ requirements: - r-nlme - r-rngtools run: - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-rots >=1.30.0,<1.31.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-rots >=1.34.0,<1.35.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-doparallel - r-dorng @@ -43,13 +45,16 @@ requirements: - r-matrixstats - r-nlme - r-rngtools + +source: + md5: 36d0e8d7a7ed59c691e8ca4312cf0478 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'RolDE: Robust longitudinal Differential Expression' - description: 'RolDE detects longitudinal differential expression between two conditions in noisy high-troughput data. Suitable even for data with a moderate amount of missing values.RolDE is a composite method, consisting of three independent modules with different approaches to detecting longitudinal differential expression. The combination of these diverse modules allows RolDE to robustly detect varying differences in longitudinal trends and expression levels in diverse data types and experimental settings.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rols/meta.yaml b/recipes/bioconductor-rols/meta.yaml index caf228701c0ba..0b4aa792b2726 100644 --- a/recipes/bioconductor-rols/meta.yaml +++ b/recipes/bioconductor-rols/meta.yaml @@ -1,55 +1,59 @@ -{% set version = "2.30.0" %} +{% set version = "3.2.0" %} {% set name = "rols" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The rols package is an interface to the Ontology Lookup Service (OLS) to access and query hundred of ontolgies directly from R. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: An R interface to the Ontology Lookup Service -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ef7159fc8010e7a7a1c5ecf285b91fc8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rols", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rols + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rols + path: recipes/bioconductor-rols + version: 2.8.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19), testthat, lubridate, DT, rmarkdown, requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - - r-httr + - r-httr2 - r-jsonlite - - r-progress run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - - r-httr + - r-httr2 - r-jsonlite - - r-progress + +source: + md5: adf7e2ebfb9e1cc9d449a606aaa9768c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'An R interface to the Ontology Lookup Service' - description: 'The rols package is an interface to the Ontology Lookup Service (OLS) to access and query hundred of ontolgies directly from R.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:rols - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-rols - path: recipes/bioconductor-rols - version: 2.8.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rontotools/meta.yaml b/recipes/bioconductor-rontotools/meta.yaml index af20e2f7fb71a..6be54adc3a0e5 100644 --- a/recipes/bioconductor-rontotools/meta.yaml +++ b/recipes/bioconductor-rontotools/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "2.30.0" %} +{% set version = "2.34.0" %} {% set name = "ROntoTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Suite of tools for functional analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: CC BY-NC-ND 4.0 + file LICENSE + license_file: LICENSE + summary: R Onto-Tools suite -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 11764a125b9411a5b2d2ba20f4c64024 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rontotools", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rontotools + - doi:10.1109/JPROC.2016.2531000 + parent_recipe: + name: bioconductor-rontotools + path: recipes/bioconductor-rontotools + version: 2.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-boot run: - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-boot + +source: + md5: ebc83d02dc550f9673920bf52ee6ee1b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'CC BY-NC-ND 4.0 + file LICENSE' - summary: 'R Onto-Tools suite' - description: 'Suite of tools for functional analysis.' - license_file: LICENSE -extra: - identifiers: - - biotools:rontotools - - doi:10.1109/JPROC.2016.2531000 - parent_recipe: - name: bioconductor-rontotools - path: recipes/bioconductor-rontotools - version: 2.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ropls/meta.yaml b/recipes/bioconductor-ropls/meta.yaml index eda59d7bb9280..e60088ce7e6c1 100644 --- a/recipes/bioconductor-ropls/meta.yaml +++ b/recipes/bioconductor-ropls/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "ropls" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Latent variable modeling with Principal Component Analysis (PCA) and Partial Least Squares (PLS) are powerful methods for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. Orthogonal Partial Least Squares (OPLS) enables to separately model the variation correlated (predictive) to the factor of interest and the uncorrelated (orthogonal) variation. While performing similarly to PLS, OPLS facilitates interpretation. Successful applications of these chemometrics techniques include spectroscopic data such as Raman spectroscopy, nuclear magnetic resonance (NMR), mass spectrometry (MS) in metabolomics and proteomics, but also transcriptomics data. In addition to scores, loadings and weights plots, the package provides metrics and graphics to determine the optimal number of components (e.g. with the R2 and Q2 coefficients), check the validity of the model by permutation testing, detect outliers, and perform feature selection (e.g. with Variable Importance in Projection or regression coefficients). The package can be accessed via a user interface on the Workflow4Metabolomics.org online resource for computational metabolomics (built upon the Galaxy environment). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: CeCILL + summary: PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a1c4a1710eb179bb29f3831a5fe80849 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ropls", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocGenerics, BiocStyle, knitr, multtest, omicade4, rmarkdown, testthat + +extra: + identifiers: + - biotools:ropls + parent_recipe: + name: bioconductor-ropls + path: recipes/bioconductor-ropls + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocGenerics, BiocStyle, knitr, multtest, omicade4, phenomis, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-multidataset >=1.30.0,<1.31.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-multidataset >=1.34.0,<1.35.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-plotly run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-multidataset >=1.30.0,<1.31.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-multidataset >=1.34.0,<1.35.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-plotly + +source: + md5: e7e220266bf229dcbf1e8e18d0afe28c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: CeCILL - summary: 'PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data' - description: 'Latent variable modeling with Principal Component Analysis (PCA) and Partial Least Squares (PLS) are powerful methods for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. Orthogonal Partial Least Squares (OPLS) enables to separately model the variation correlated (predictive) to the factor of interest and the uncorrelated (orthogonal) variation. While performing similarly to PLS, OPLS facilitates interpretation. Successful applications of these chemometrics techniques include spectroscopic data such as Raman spectroscopy, nuclear magnetic resonance (NMR), mass spectrometry (MS) in metabolomics and proteomics, but also transcriptomics data. In addition to scores, loadings and weights plots, the package provides metrics and graphics to determine the optimal number of components (e.g. with the R2 and Q2 coefficients), check the validity of the model by permutation testing, detect outliers, and perform feature selection (e.g. with Variable Importance in Projection or regression coefficients). The package can be accessed via a user interface on the Workflow4Metabolomics.org online resource for computational metabolomics (built upon the Galaxy environment).' -extra: - identifiers: - - biotools:ropls - parent_recipe: - name: bioconductor-ropls - path: recipes/bioconductor-ropls - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-roseq/meta.yaml b/recipes/bioconductor-roseq/meta.yaml index 487093f51cc24..86c180b934a86 100644 --- a/recipes/bioconductor-roseq/meta.yaml +++ b/recipes/bioconductor-roseq/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "ROSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9af42531e92f5a535c6a139f0856e6e3 +about: + description: ROSeq - A rank based approach to modeling gene expression with filtered and normalized read count matrix. ROSeq takes filtered and normalized read matrix and cell-annotation/condition as input and determines the differentially expressed genes between the contrasting groups of single cells. One of the input parameters is the number of cores to be used. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-Seq data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-roseq", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, testthat, RUnit, BiocGenerics requirements: host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-pbmcapply run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-pbmcapply +source: + md5: c8bf453697a193df2e041152c9e64b2b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-Seq data' - description: 'ROSeq - A rank based approach to modeling gene expression with filtered and normalized read count matrix. ROSeq takes filtered and normalized read matrix and cell-annotation/condition as input and determines the differentially expressed genes between the contrasting groups of single cells. One of the input parameters is the number of cores to be used.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rots/meta.yaml b/recipes/bioconductor-rots/meta.yaml index 9ac10605af128..a93f95df4e76d 100644 --- a/recipes/bioconductor-rots/meta.yaml +++ b/recipes/bioconductor-rots/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "ROTS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Calculates the Reproducibility-Optimized Test Statistic (ROTS) for differential testing in omics data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Reproducibility-Optimized Test Statistic -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02d51e24e501790ad3049c1bb5b3f90b build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rots", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:rots + - doi:10.1109/tcbb.2007.1078 + parent_recipe: + name: bioconductor-rots + path: recipes/bioconductor-rots + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 4f180993ef115cb9c6e7f1f27b64d0ef + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Reproducibility-Optimized Test Statistic' - description: 'Calculates the Reproducibility-Optimized Test Statistic (ROTS) for differential testing in omics data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:rots - - doi:10.1109/tcbb.2007.1078 - parent_recipe: - name: bioconductor-rots - path: recipes/bioconductor-rots - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rpa/meta.yaml b/recipes/bioconductor-rpa/meta.yaml index f6f0aaf7b94d8..4dd594b7b0df9 100644 --- a/recipes/bioconductor-rpa/meta.yaml +++ b/recipes/bioconductor-rpa/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "1.58.0" %} +{% set version = "1.62.0" %} {% set name = "RPA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Probabilistic analysis of probe reliability and differential gene expression on short oligonucleotide arrays. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_2_clause + file LICENSE + license_file: LICENSE + summary: 'RPA: Robust Probabilistic Averaging for probe-level analysis' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea38f5a76b570c091b8f818c48c836cb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rpa", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rpa + parent_recipe: + name: bioconductor-rpa + path: recipes/bioconductor-rpa + version: 1.36.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, parallel requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 - r-base - r-rmarkdown run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 - r-base - r-rmarkdown + +source: + md5: caac0a78a269db4b0e272e18ca8ddb0f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_2_clause + file LICENSE' - summary: 'RPA: Robust Probabilistic Averaging for probe-level analysis' - description: 'Probabilistic analysis of probe reliability and differential gene expression on short oligonucleotide arrays.' - license_file: LICENSE -extra: - identifiers: - - biotools:rpa - parent_recipe: - name: bioconductor-rpa - path: recipes/bioconductor-rpa - version: 1.36.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rprimer/meta.yaml b/recipes/bioconductor-rprimer/meta.yaml index cf4019c640733..2e1e253b87825 100644 --- a/recipes/bioconductor-rprimer/meta.yaml +++ b/recipes/bioconductor-rprimer/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "rprimer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions, workflow, and a Shiny application for visualizing sequence conservation and designing degenerate primers, probes, and (RT)-(q/d)PCR assays from a multiple DNA sequence alignment. The results can be presented in data frame format and visualized as dashboard-like plots. For more information, please see the package vignette. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Design Degenerate Oligos from a Multiple DNA Sequence Alignment -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f866266895669cd0e898d1ffb0df86fa build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rprimer", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, covr, kableExtra, knitr, rmarkdown, styler, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-bslib - r-dt @@ -36,9 +38,9 @@ requirements: - r-shinycssloaders - r-shinyfeedback run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-bslib - r-dt @@ -49,13 +51,16 @@ requirements: - r-shiny - r-shinycssloaders - r-shinyfeedback + +source: + md5: 644134f1fa3fa1f38156cbbae27ef3f4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Design Degenerate Oligos from a Multiple DNA Sequence Alignment' - description: 'Functions, workflow, and a Shiny application for visualizing sequence conservation and designing degenerate primers, probes, and (RT)-(q/d)PCR assays from a multiple DNA sequence alignment. The results can be presented in data frame format and visualized as dashboard-like plots. For more information, please see the package vignette.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rprotobuflib/meta.yaml b/recipes/bioconductor-rprotobuflib/meta.yaml index 4d6cc29a5135a..03a0b817c1335 100644 --- a/recipes/bioconductor-rprotobuflib/meta.yaml +++ b/recipes/bioconductor-rprotobuflib/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "2.14.0" %} +{% set version = "2.18.0" %} {% set name = "RProtoBufLib" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides the headers and static library of Protocol buffers for other R packages to compile and link against. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_3_clause + summary: C++ headers and static libraries of Protocol buffers -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e7351127e6b19daaae94fcecc970292b build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rprotobuflib", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + parent_recipe: + name: bioconductor-rprotobuflib + path: recipes/bioconductor-rprotobuflib + version: 1.2.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 7de7917bb81b2f16b83661795e3f13bd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: BSD_3_clause - summary: 'C++ headers and static libraries of Protocol buffers' - description: 'This package provides the headers and static library of Protocol buffers for other R packages to compile and link against.' -extra: - additional-platforms: - - linux-aarch64 - parent_recipe: - name: bioconductor-rprotobuflib - path: recipes/bioconductor-rprotobuflib - version: 1.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rpx/meta.yaml b/recipes/bioconductor-rpx/meta.yaml index 95d2c560c7b95..9832152f1462d 100644 --- a/recipes/bioconductor-rpx/meta.yaml +++ b/recipes/bioconductor-rpx/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "2.10.0" %} +{% set version = "2.14.0" %} {% set name = "rpx" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The rpx package implements an interface to proteomics data submitted to the ProteomeXchange consortium. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: R Interface to the ProteomeXchange Repository -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7e3f2004892b6fb40746c0dcdd990a43 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rpx", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rpx + - doi:10.1038/nbt.2839 + parent_recipe: + name: bioconductor-rpx + path: recipes/bioconductor-rpx + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biostrings, BiocStyle, testthat, knitr, tibble, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base - r-curl - r-jsonlite - r-rcurl - r-xml2 run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-base - r-curl - r-jsonlite - r-rcurl - r-xml2 + +source: + md5: 24126081958186fa31a3f70954627ab1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'R Interface to the ProteomeXchange Repository' - description: 'The rpx package implements an interface to proteomics data submitted to the ProteomeXchange consortium.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:rpx - - doi:10.1038/nbt.2839 - parent_recipe: - name: bioconductor-rpx - path: recipes/bioconductor-rpx - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rqc/meta.yaml b/recipes/bioconductor-rqc/meta.yaml index c7e563d22e776..8278c44adaab4 100644 --- a/recipes/bioconductor-rqc/meta.yaml +++ b/recipes/bioconductor-rqc/meta.yaml @@ -1,78 +1,86 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "Rqc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Rqc is an optimised tool designed for quality control and assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Quality Control Tool for High-Throughput Sequencing Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 425dbc839b22b6af4d19ca20174c24c1 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rqc", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, testthat requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-biovizbase >=1.50.0,<1.51.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-biovizbase >=1.54.0,<1.55.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfiles >=1.42.0,<1.43.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-ggplot2 - - 'r-knitr >=1.7' + - r-knitr >=1.7 - r-markdown - r-plyr - - 'r-rcpp >=0.11.6' + - r-rcpp >=0.11.6 - r-reshape2 - r-shiny - libblas - liblapack + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-biovizbase >=1.50.0,<1.51.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-biovizbase >=1.54.0,<1.55.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfiles >=1.42.0,<1.43.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-base - r-ggplot2 - - 'r-knitr >=1.7' + - r-knitr >=1.7 - r-markdown - r-plyr - - 'r-rcpp >=0.11.6' + - r-rcpp >=0.11.6 - r-reshape2 - r-shiny - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: d7c52435ef38a762bdf10bc88b2a84d5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Quality Control Tool for High-Throughput Sequencing Data' - description: 'Rqc is an optimised tool designed for quality control and assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rqt/meta.yaml b/recipes/bioconductor-rqt/meta.yaml index b028572a28d95..c46d935fed18a 100644 --- a/recipes/bioconductor-rqt/meta.yaml +++ b/recipes/bioconductor-rqt/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "rqt" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Despite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see: "Gene-set association tests for next-generation sequencing data" by Lee et al (2016), Bioinformatics, 32(17), i611-i619, .' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'rqt: utilities for gene-level meta-analysis' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b6120899c4586c9dcfd093db762af1c8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rqt", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-ropls >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-ropls >=1.38.0,<1.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-car - r-compquadform @@ -33,8 +35,8 @@ requirements: - r-pls - r-runit run: - - 'bioconductor-ropls >=1.34.0,<1.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-ropls >=1.38.0,<1.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-car - r-compquadform @@ -43,13 +45,16 @@ requirements: - r-metap - r-pls - r-runit + +source: + md5: b9852546c427e3c9beab93ca0cbd28a9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL - summary: 'rqt: utilities for gene-level meta-analysis' - description: 'Despite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see: "Gene-set association tests for next-generation sequencing data" by Lee et al (2016), Bioinformatics, 32(17), i611-i619, .' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rqubic/meta.yaml b/recipes/bioconductor-rqubic/meta.yaml index a7d84df176096..b84b6a7e77ef4 100644 --- a/recipes/bioconductor-rqubic/meta.yaml +++ b/recipes/bioconductor-rqubic/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "rqubic" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements the QUBIC algorithm introduced by Li et al. for the qualitative biclustering with gene expression data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Qualitative biclustering algorithm for expression data analysis in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 018144d5ccfbe2df88a79212dedc2066 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rqubic", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RColorBrewer requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-biclust - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-biclust - build: - - {{ compiler('c') }} - - make + +source: + md5: d40e52edf078a301d33df897d1d77b48 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Qualitative biclustering algorithm for expression data analysis in R' - description: 'This package implements the QUBIC algorithm introduced by Li et al. for the qualitative biclustering with gene expression data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rrbsdata/meta.yaml b/recipes/bioconductor-rrbsdata/meta.yaml index eccd81fafefdc..e266f97a0462e 100644 --- a/recipes/bioconductor-rrbsdata/meta.yaml +++ b/recipes/bioconductor-rrbsdata/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "RRBSdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 04bcf0f0348dc54984ca9506773820ec +about: + description: RRBS data set comprising 12 samples with simulated differentially methylated regions (DMRs). + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: An RRBS data set with 12 samples and 10,000 simulated DMRs build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rrbsdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biseq >=1.42.0,<1.43.0' + - bioconductor-biseq >=1.46.0,<1.47.0 - r-base run: - - 'bioconductor-biseq >=1.42.0,<1.43.0' + - bioconductor-biseq >=1.46.0,<1.47.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ac09dd08a5f708241944185cac584cae + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL-3 - summary: 'An RRBS data set with 12 samples and 10,000 simulated DMRs' - description: 'RRBS data set comprising 12 samples with simulated differentially methylated regions (DMRs).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rrbsdata/post-link.sh b/recipes/bioconductor-rrbsdata/post-link.sh index 9daeae9d07b91..110a5b6fdc58b 100644 --- a/recipes/bioconductor-rrbsdata/post-link.sh +++ b/recipes/bioconductor-rrbsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rrbsdata-1.22.0" +installBiocDataPackage.sh "rrbsdata-1.26.0" diff --git a/recipes/bioconductor-rrdp/meta.yaml b/recipes/bioconductor-rrdp/meta.yaml index d4af9718a1b5b..ed916be1acae8 100644 --- a/recipes/bioconductor-rrdp/meta.yaml +++ b/recipes/bioconductor-rrdp/meta.yaml @@ -1,42 +1,22 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "rRDP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package installs and interfaces the naive Bayesian classifier for 16S rRNA sequences developed by the Ribosomal Database Project (RDP). With this package the classifier trained with the standard training set can be used or a custom classifier can be trained. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + file LICENSE + license_file: LICENSE + summary: Interface to the RDP Classifier -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a6dbbc2c3e31aa382c312202e85ce62 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rrdp", max_pin="x.x") }}' - noarch: generic -# Suggests: rRDPData -# SystemRequirements: Java JDK 1.4 or higher -requirements: - host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - r-base - run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-2 | file LICENSE' - summary: 'Interface to the RDP Classifier' - description: 'Seamlessly interfaces RDP classifier (version 2.9).' - license_file: LICENSE + extra: identifiers: - biotools:rrdp @@ -46,3 +26,31 @@ extra: path: recipes/bioconductor-rrdp version: 1.14.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: rRDPData, knitr, rmarkdown +# SystemRequirements: Java JDK 1.4 or higher +requirements: + host: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - r-base + - r-rjava + run: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - r-base + - r-rjava + +source: + md5: 2dc3e7d6baa2781859dbf38bc08ecbc5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-rrdpdata/meta.yaml b/recipes/bioconductor-rrdpdata/meta.yaml index e76d77d70c8d6..afe00a0b66d21 100644 --- a/recipes/bioconductor-rrdpdata/meta.yaml +++ b/recipes/bioconductor-rrdpdata/meta.yaml @@ -1,43 +1,40 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "rRDPData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ca56f1bf00bfaefb27c351ccc7346ae +about: + description: The package provides the data for the RDP Classifier 2.14 released in August 2023. It contains the latest bacterial and archaeal taxonomy training set No. 19 as described in Wang Q, Cole JR. 2024. Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification. Microbiol Resour Announc 0:e01063-23. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Databases for the Default RDP Classifier build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rrdpdata", max_pin="x.x") }}' - noarch: generic -# SystemRequirements: Java +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-rrdp >=1.36.0,<1.37.0' + - bioconductor-rrdp >=1.40.0,<1.41.0 - r-base - - openjdk run: - - 'bioconductor-rrdp >=1.36.0,<1.37.0' + - bioconductor-rrdp >=1.40.0,<1.41.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' - - openjdk + - bioconductor-data-packages >=20241103 +source: + md5: fa19b2b3f0f17eca244b65480bce1ddd + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Database for the Default RDP Classifier' - description: 'Database used by the default RDP Classifier' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rrdpdata/post-link.sh b/recipes/bioconductor-rrdpdata/post-link.sh index 529c560bd8bc7..df77fc391171e 100644 --- a/recipes/bioconductor-rrdpdata/post-link.sh +++ b/recipes/bioconductor-rrdpdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rrdpdata-1.22.0" +installBiocDataPackage.sh "rrdpdata-1.26.0" diff --git a/recipes/bioconductor-rrho/meta.yaml b/recipes/bioconductor-rrho/meta.yaml index 7873debb38070..8d89a0b1d7dc0 100644 --- a/recipes/bioconductor-rrho/meta.yaml +++ b/recipes/bioconductor-rrho/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "RRHO" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package is aimed at inference on the amount of agreement in two sorted lists using the Rank-Rank Hypergeometric Overlap test. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Inference on agreement between ordered lists -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 979e74a493ef06b25a98574facdd4c3f build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rrho", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rrho + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rrho + path: recipes/bioconductor-rrho + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: lattice requirements: host: @@ -27,21 +38,16 @@ requirements: run: - r-base - r-venndiagram + +source: + md5: acd367fc75b3b57bf9d3f14e55dcc043 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Inference on agreement between ordered lists' - description: 'The package is aimed at inference on the amount of agreement in two sorted lists using the Rank-Rank Hypergeometric Overlap test.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:rrho - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-rrho - path: recipes/bioconductor-rrho - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rrvgo/meta.yaml b/recipes/bioconductor-rrvgo/meta.yaml index f22c0df7d085d..ebbb045609eec 100644 --- a/recipes/bioconductor-rrvgo/meta.yaml +++ b/recipes/bioconductor-rrvgo/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "rrvgo" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Reduce + Visualize GO -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d84378ff00f99dfe761c41763a56315b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rrvgo", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), shinydashboard, DT, plotly, heatmaply, magrittr, utils, clusterProfiler, DOSE, slam, org.Ag.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-gosemsim >=2.32.0,<2.33.0 - r-base - r-ggplot2 - r-ggrepel @@ -35,9 +37,9 @@ requirements: - r-umap - r-wordcloud run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-gosemsim >=2.28.0,<2.29.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-gosemsim >=2.32.0,<2.33.0 - r-base - r-ggplot2 - r-ggrepel @@ -47,13 +49,16 @@ requirements: - r-treemap - r-umap - r-wordcloud + +source: + md5: 55c4e9d1f6bed0a9ca671085def08cb7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Reduce + Visualize GO' - description: 'Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rsamtools/meta.yaml b/recipes/bioconductor-rsamtools/meta.yaml index 55489dfd108c5..67889d9faf502 100644 --- a/recipes/bioconductor-rsamtools/meta.yaml +++ b/recipes/bioconductor-rsamtools/meta.yaml @@ -1,76 +1,83 @@ -{% set version = "2.18.0" %} +{% set version = "2.22.0" %} {% set name = "Rsamtools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 | file LICENSE + license_file: LICENSE + summary: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 63af2a7dd2513e992fd78b26ca2b3775 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rsamtools", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:rsamtools + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rsamtools + path: recipes/bioconductor-rsamtools + version: 1.32.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-bitops - libblas - liblapack + - zlib + - liblzma-devel run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-bitops - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make - - libcxx <=17 #[osx] + +source: + md5: a2863f9fd8439f30148428b1f2f20714 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Artistic-2.0 | file LICENSE' - summary: 'Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import' - description: 'This package provides an interface to the ''samtools'', ''bcftools'', and ''tabix'' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.' - license_file: LICENSE -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:rsamtools - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-rsamtools - path: recipes/bioconductor-rsamtools - version: 1.32.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rsbml/build_failure.linux-64.yaml b/recipes/bioconductor-rsbml/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..6f10cc2639de0 --- /dev/null +++ b/recipes/bioconductor-rsbml/build_failure.linux-64.yaml @@ -0,0 +1,107 @@ +recipe_sha: ecec315d275c7037e28817e172caaf8d2ccd8b0f0fa3b822fa0b77b7526cd6e6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + 68 | ASTNode_t *rmathml_ASTNode(SEXP sym); + | ^~~~~~~~~ + | ASTNode_h + rsbml.h:77:3: error: 'Layout_t' does not name a type; did you mean 'Layout_H__'? + 77 | Layout_t *LayoutModelPlugin_createLayout(LayoutModelPlugin_t *plugin); + | ^~~~~~~~ + | Layout_H__ + rsbml.h:79:3: error: 'Layout_t' does not name a type; did you mean 'Layout_H__'? + 79 | Layout_t *LayoutModelPlugin_getLayout(LayoutModelPlugin_t *plugin, + | ^~~~~~~~ + | Layout_H__ + rsbml.h:81:27: error: 'SBase_t' was not declared in this scope; did you mean 'libsbml::SBase_t'? + 81 | int SBase_enablePackage(SBase_t *sbase, const char *pkgURI, + | ^~~~~~~ + | libsbml::SBase_t + /opt/conda/conda-bld/bioconductor-rsbml_1735600653534/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/sbml/common/sbmlfwd.h:77:51: note: 'libsbml::SBase_t' declared here + 77 | typedef CLASS_OR_STRUCT SBase SBase_t; + | ^~~~~~~ + rsbml.h:81:36: error: 'sbase' was not declared in this scope + 81 | int SBase_enablePackage(SBase_t *sbase, const char *pkgURI, + | ^~~~~ + rsbml.h:81:43: error: expected primary-expression before 'const' + 81 | int SBase_enablePackage(SBase_t *sbase, const char *pkgURI, + | ^~~~~ + rsbml.h:82:27: error: expected primary-expression before 'const' + 82 | const char *pkgPrefix, Rboolean flag); + | ^~~~~ + rsbml.h:82:59: error: expected primary-expression before 'flag' + 82 | const char *pkgPrefix, Rboolean flag); + | ^~~~ + rsbml.h:82:63: error: expression list treated as compound expression in initializer [-fpermissive] + 82 | const char *pkgPrefix, Rboolean flag); + | ^ + layoutWrappers.cpp:6:1: error: 'Layout_t' does not name a type; did you mean 'Layout_H__'? + 6 | Layout_t *LayoutModelPlugin_createLayout(LayoutModelPlugin_t *plugin) { + | ^~~~~~~~ + | Layout_H__ + layoutWrappers.cpp: In function 'int LayoutModelPlugin_getNumLayouts(LayoutModelPlugin_t*)': + layoutWrappers.cpp:11:16: error: invalid use of incomplete type 'LayoutModelPlugin_t' {aka 'struct LayoutModelPlugin'} + 11 | return plugin->getNumLayouts(); + | ^~ + rsbml.h:76:18: note: forward declaration of 'LayoutModelPlugin_t' {aka 'struct LayoutModelPlugin'} + 76 | typedef struct LayoutModelPlugin LayoutModelPlugin_t; + | ^~~~~~~~~~~~~~~~~ + layoutWrappers.cpp: At global scope: + layoutWrappers.cpp:13:1: error: 'Layout_t' does not name a type; did you mean 'Layout_H__'? + 13 | Layout_t *LayoutModelPlugin_getLayout(LayoutModelPlugin_t *plugin, + | ^~~~~~~~ + | Layout_H__ + layoutWrappers.cpp:19:5: error: redefinition of 'int SBase_enablePackage' + 19 | int SBase_enablePackage(SBase_t *sbase, const char *pkgURI, + | ^~~~~~~~~~~~~~~~~~~ + rsbml.h:81:7: note: 'int SBase_enablePackage' previously defined here + 81 | int SBase_enablePackage(SBase_t *sbase, const char *pkgURI, + | ^~~~~~~~~~~~~~~~~~~ + layoutWrappers.cpp:19:25: error: 'SBase_t' was not declared in this scope; did you mean 'libsbml::SBase_t'? + 19 | int SBase_enablePackage(SBase_t *sbase, const char *pkgURI, + | ^~~~~~~ + | libsbml::SBase_t + /opt/conda/conda-bld/bioconductor-rsbml_1735600653534/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/sbml/common/sbmlfwd.h:77:51: note: 'libsbml::SBase_t' declared here + 77 | typedef CLASS_OR_STRUCT SBase SBase_t; + | ^~~~~~~ + layoutWrappers.cpp:19:34: error: 'sbase' was not declared in this scope + 19 | int SBase_enablePackage(SBase_t *sbase, const char *pkgURI, + | ^~~~~ + layoutWrappers.cpp:19:41: error: expected primary-expression before 'const' + 19 | int SBase_enablePackage(SBase_t *sbase, const char *pkgURI, + | ^~~~~ + layoutWrappers.cpp:20:25: error: expected primary-expression before 'const' + 20 | const char *pkgPrefix, Rboolean flag) + | ^~~~~ + layoutWrappers.cpp:20:57: error: expected primary-expression before 'flag' + 20 | const char *pkgPrefix, Rboolean flag) + | ^~~~ + make: *** [/opt/conda/conda-bld/bioconductor-rsbml_1735600653534/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/R/etc/Makeconf:204: layoutWrappers.o] Error 1 + ERROR: compilation failed for package rsbml + * removing /opt/conda/conda-bld/bioconductor-rsbml_1735600653534/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/R/library/rsbml + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-rsbml_1735600653534/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-rsbml_1735600653534/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + compiler error +reason: expected primary-expression before 'const' diff --git a/recipes/bioconductor-rsbml/build_failure.osx-64.yaml b/recipes/bioconductor-rsbml/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..74ba2a1da0604 --- /dev/null +++ b/recipes/bioconductor-rsbml/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: ecec315d275c7037e28817e172caaf8d2ccd8b0f0fa3b822fa0b77b7526cd6e6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + 76 | typedef struct LayoutModelPlugin LayoutModelPlugin_t; + | ^ + layoutWrappers.cpp:19:25: error: unknown type name 'SBase_t' + 19 | int SBase_enablePackage(SBase_t *sbase, const char *pkgURI, + | ^ + 13 errors generated. + make: *** [/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rsbml_1735854878400/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/R/etc/Makeconf:204: layoutWrappers.o] Error 1 + ERROR: compilation failed for package rsbml + * removing /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rsbml_1735854878400/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/R/library/rsbml + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-rsbml-2.64.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + checking for x86_64-apple-darwin13.4.0-pkg-config... no + checking for pkg-config... /usr/local/bin/pkg-config + checking pkg-config is at least version 0.9.0... yes + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + checking for LIBSBML... yes + configure: === Begin local SOSLib build === + checking for a BSD-compatible install... /usr/bin/install -c + checking whether build environment is sane... yes + checking for a thread-safe mkdir -p... config/install-sh -c -d + checking for gawk... no + checking for mawk... no + checking for nawk... no + checking for awk... awk + checking whether make sets $(MAKE)... yes + checking build system type... x86_64-apple-darwin13.4.0 + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + checking host system type... x86_64-apple-darwin13.4.0 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + checking for C compiler default output file name... a.out + checking whether the C compiler works... yes + checking whether we are cross compiling... no + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rsbml_1735854878400/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + checking for suffix of executables... + checking for suffix of object files... o + checking whether we are using the GNU C compiler... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + checking for style of include used by make... GNU + checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 + checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-rsbml_1735854878400/work/conda_build.sh']' returned non-zero exit status 1. + checking whether we are using the GNU C compiler... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking for x86_64-apple-darwin13.4.0-clang option to accept ISO C89... none needed + checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 + checking whether x86_64-apple-darwin13.4.0-clang accepts -fpic... yes + checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang-cpp + checking for x86_64-apple-darwin13.4.0-ranlib... x86_64-apple-darwin13.4.0-ranlib + checking for a BSD-compatible install... /usr/bin/install -c + checking whether make sets $(MAKE)... (cached) yes + checking for autoconf... $BUILD_PREFIX/bin/autoconf + checking for aclocal... $BUILD_PREFIX/bin/aclocal + checking for make... $BUILD_PREFIX/bin/make + checking for ar... /opt/mambaforge/envs/bioconda/bin/ar + checking for swig... swig + checking for perl... $BUILD_PREFIX/bin/perl + checking for x86_64-apple-darwin13.4.0-pkg-config... no + checking for pkg-config... /usr/local/bin/pkg-config + checking pkg-config is at least version 0.9.0... yes + checking for SBML... yes + checking for correct functioning of SBML... no: + CFLAGS=-g -O2 -pg -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -I$PREFIX/include -I$PREFIX/include/libxml2 + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LIBS=-lm -lstdc -L$PREFIX/lib -lsbml + configure: === End local SOSLib build === + configure: creating ./config.status + config.status: creating src/Makevars + x86_64-apple-darwin13.4.0-clang -I"$PREFIX/lib/R/include" -DNDEBUG -I$PREFIX/include -I$PREFIX/include/libxml2 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c StringMap.c -o StringMap.o + x86_64-apple-darwin13.4.0-clang -I"$PREFIX/lib/R/include" -DNDEBUG -I$PREFIX/include -I$PREFIX/include/libxml2 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c check.c -o check.o + x86_64-apple-darwin13.4.0-clang -I"$PREFIX/lib/R/include" -DNDEBUG -I$PREFIX/include -I$PREFIX/include/libxml2 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c doc.c -o doc.o + x86_64-apple-darwin13.4.0-clang -I"$PREFIX/lib/R/include" -DNDEBUG -I$PREFIX/include -I$PREFIX/include/libxml2 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c dom.c -o dom.o + x86_64-apple-darwin13.4.0-clang -I"$PREFIX/lib/R/include" -DNDEBUG -I$PREFIX/include -I$PREFIX/include/libxml2 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c graph.c -o graph.o + x86_64-apple-darwin13.4.0-clang -I"$PREFIX/lib/R/include" -DNDEBUG -I$PREFIX/include -I$PREFIX/include/libxml2 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c init.c -o init.o + x86_64-apple-darwin13.4.0-clang -I"$PREFIX/lib/R/include" -DNDEBUG -I$PREFIX/include -I$PREFIX/include/libxml2 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c io.c -o io.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I$PREFIX/include -I$PREFIX/include/libxml2 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c layoutWrappers.cpp -o layoutWrappers.o +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/bioconductor-rsbml/meta.yaml b/recipes/bioconductor-rsbml/meta.yaml index d79175c91dce7..5834dd2641440 100644 --- a/recipes/bioconductor-rsbml/meta.yaml +++ b/recipes/bioconductor-rsbml/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "2.60.0" %} +{% set version = "2.64.0" %} {% set name = "rsbml" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Links R to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects. Optionally links to the SBML ODE Solver Library (SOSLib) for simulating models. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: R support for SBML, using libsbml -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9e3df3c47a3bbb5b92bf55b478078d1f build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rsbml", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # SystemRequirements: libsbml (==5.10.2) requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - libblas - liblapack - - 'libsbml >=5.10.2' + - libsbml >=5.10.2 run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - - 'libsbml >=5.10.2' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + - libsbml >=5.10.2 + +source: + md5: c0f210dcdea4192cd5745ff9813b1a5b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'R support for SBML, using libsbml' - description: 'Links R to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects. Optionally links to the SBML ODE Solver Library (SOSLib) for simulating models.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rscudo/meta.yaml b/recipes/bioconductor-rscudo/meta.yaml index 0709bb86099e6..86b721d118004 100644 --- a/recipes/bioconductor-rscudo/meta.yaml +++ b/recipes/bioconductor-rscudo/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "rScudo" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SCUDO (Signature-based Clustering for Diagnostic Purposes) is a rank-based method for the analysis of gene expression profiles for diagnostic and classification purposes. It is based on the identification of sample-specific gene signatures composed of the most up- and down-regulated genes for that sample. Starting from gene expression data, functions in this package identify sample-specific gene signatures and use them to build a graph of samples. In this graph samples are joined by edges if they have a similar expression profile, according to a pre-computed similarity matrix. The similarity between the expression profiles of two samples is computed using a method similar to GSEA. The graph of samples can then be used to perform community clustering or to perform supervised classification of samples in a testing set. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Signature-based Clustering for Diagnostic Purposes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2ca44b84bbccb7ffdc9dc082d9a071ad build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rscudo", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret, e1071, parallel, doParallel requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-igraph - r-stringr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-igraph - r-stringr + +source: + md5: bfe6b848b97974bd3b093f5c0684b528 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Signature-based Clustering for Diagnostic Purposes' - description: 'SCUDO (Signature-based Clustering for Diagnostic Purposes) is a rank-based method for the analysis of gene expression profiles for diagnostic and classification purposes. It is based on the identification of sample-specific gene signatures composed of the most up- and down-regulated genes for that sample. Starting from gene expression data, functions in this package identify sample-specific gene signatures and use them to build a graph of samples. In this graph samples are joined by edges if they have a similar expression profile, according to a pre-computed similarity matrix. The similarity between the expression profiles of two samples is computed using a method similar to GSEA. The graph of samples can then be used to perform community clustering or to perform supervised classification of samples in a testing set.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rsemmed/meta.yaml b/recipes/bioconductor-rsemmed/meta.yaml index 1e8115b130485..df0508bfdaa7e 100644 --- a/recipes/bioconductor-rsemmed/meta.yaml +++ b/recipes/bioconductor-rsemmed/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "rsemmed" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 379f918582942443c9823373180a9978 +about: + description: A programmatic interface to the Semantic MEDLINE database. It provides functions for searching the database for concepts and finding paths between concepts. Path searching can also be tailored to user specifications, such as placing restrictions on concept types and the type of link between concepts. It also provides functions for summarizing and visualizing those paths. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: An interface to the Semantic MEDLINE database build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rsemmed", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat, knitr, BiocStyle, rmarkdown requirements: host: @@ -33,12 +31,14 @@ requirements: - r-igraph - r-magrittr - r-stringr +source: + md5: 61ec666b4025b52f5112dc4321fb1769 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'An interface to the Semantic MEDLINE database' - description: 'A programmatic interface to the Semantic MEDLINE database. It provides functions for searching the database for concepts and finding paths between concepts. Path searching can also be tailored to user specifications, such as placing restrictions on concept types and the type of link between concepts. It also provides functions for summarizing and visualizing those paths.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rseqan/meta.yaml b/recipes/bioconductor-rseqan/meta.yaml index 47423acccd913..aa212aba3f397 100644 --- a/recipes/bioconductor-rseqan/meta.yaml +++ b/recipes/bioconductor-rseqan/meta.yaml @@ -1,25 +1,28 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "RSeqAn" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 278ce2c8087516d02a4203bdcf9a6b9f +about: + description: Headers and some wrapper functions from the SeqAn C++ library for ease of usage in R. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_3_clause + file LICENSE + license_file: LICENSE + summary: R SeqAn build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rseqan", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, testthat requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-rcpp @@ -28,17 +31,14 @@ requirements: run: - r-base - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make +source: + md5: 41a1812a3db0e862af22935db17742a5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_3_clause + file LICENSE' - summary: 'R SeqAn' - description: 'Headers and some wrapper functions from the SeqAn C++ library for ease of usage in R.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rsubread/meta.yaml b/recipes/bioconductor-rsubread/meta.yaml index 486e6a8fe29c4..f7d00a38fc763 100644 --- a/recipes/bioconductor-rsubread/meta.yaml +++ b/recipes/bioconductor-rsubread/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "2.16.1" %} +{% set version = "2.20.0" %} {% set name = "Rsubread" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Mapping, quantification and variant analysis of sequencing data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec5687eb02901ff3b62915cf37aa48b4 build: - skip: True # [osx] number: 0 - run_exports: - - {{ pin_subpackage("bioconductor-rsubread", max_pin="x") }} rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("bioconductor-rsubread", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:rsubread + parent_recipe: + name: bioconductor-rsubread + path: recipes/bioconductor-rsubread + version: 1.30.9 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - automake + - make host: - r-base - r-matrix - libblas - liblapack + - zlib run: - r-base - r-matrix - build: - - {{ compiler('c') }} - - automake - - make + +source: + md5: ff51de2d85704503bda2039364d50130 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=3)' - summary: 'Mapping, quantification and variant analysis of sequencing data' - description: 'Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:rsubread - additional-platforms: - - linux-aarch64 - parent_recipe: - name: bioconductor-rsubread - path: recipes/bioconductor-rsubread - version: 1.30.9 + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-rsvsim/meta.yaml b/recipes/bioconductor-rsvsim/meta.yaml index 8a08b4435d024..37e5858c14cc0 100644 --- a/recipes/bioconductor-rsvsim/meta.yaml +++ b/recipes/bioconductor-rsvsim/meta.yaml @@ -1,47 +1,22 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "RSVSim" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: RSVSim is a package for the simulation of deletions, insertions, inversion, tandem-duplications and translocations of various sizes in any genome available as FASTA-file or BSgenome data package. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: 'RSVSim: an R/Bioconductor package for the simulation of structural variations' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ce59bfd8791d8b1bf0b4fa48ea37e31 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rsvsim", max_pin="x.x") }}' - noarch: generic -# Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer -requirements: - host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - r-base - run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'RSVSim: an R/Bioconductor package for the simulation of structural variations' - description: 'RSVSim is a package for the simulation of deletions, insertions, inversion, tandem-duplications and translocations of various sizes in any genome available as FASTA-file or BSgenome data package. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + extra: identifiers: - biotools:rsvsim @@ -51,3 +26,34 @@ extra: path: recipes/bioconductor-rsvsim version: 1.20.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer, pwalign +requirements: + host: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - r-base + run: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - r-base + +source: + md5: 6f231fbeeb1e93359dee86530dfbd7e0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-rsweep/meta.yaml b/recipes/bioconductor-rsweep/meta.yaml index 62261663a3374..2ce4c6f213abb 100644 --- a/recipes/bioconductor-rsweep/meta.yaml +++ b/recipes/bioconductor-rsweep/meta.yaml @@ -1,39 +1,45 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "rSWeeP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 42d80dcf3d267562e175115cdfd4c731 +about: + description: '"Spaced Words Projection (SWeeP)" is a method for representing biological sequences using vectors preserving inter-sequence comparability.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Spaced Words Projection (SWeeP) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rsweep", max_pin="x.x") }}' - noarch: generic -# Suggests: Biostrings, methods, knitr, rmarkdown, BiocStyle +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: Rtsne, ape, Seurat, knitr, rmarkdown, tictoc, BiocStyle, testthat (>= 3.0.0) requirements: host: + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - - r-pracma + - r-doparallel + - r-foreach + - r-stringi run: + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - - r-pracma + - r-doparallel + - r-foreach + - r-stringi +source: + md5: e9f05e3b0bad39fefd41f1fa4692ee2a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences' - description: 'The SWeeP method was developed to favor the analizes between amino acids sequences and to assist alignment free phylogenetic studies. This method is based on the concept of sparse words, which is applied in the scan of biological sequences and its the conversion in a matrix of ocurrences. Aiming the generation of low dimensional matrices of Amino Acid Sequence occurrences.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rta10probeset.db/meta.yaml b/recipes/bioconductor-rta10probeset.db/meta.yaml index 02c8c7bd97fab..735cbed975248 100644 --- a/recipes/bioconductor-rta10probeset.db/meta.yaml +++ b/recipes/bioconductor-rta10probeset.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "rta10probeset.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ce002623471eef89fb841f0bf3e7c9f8 +about: + description: Affymetrix rta10 annotation data (chip rta10probeset) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix rta10 annotation data (chip rta10probeset) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rta10probeset.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ce002623471eef89fb841f0bf3e7c9f8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix rta10 annotation data (chip rta10probeset)' - description: 'Affymetrix rta10 annotation data (chip rta10probeset) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rta10transcriptcluster.db/meta.yaml b/recipes/bioconductor-rta10transcriptcluster.db/meta.yaml index 2794ecc9761ab..d96053b24e025 100644 --- a/recipes/bioconductor-rta10transcriptcluster.db/meta.yaml +++ b/recipes/bioconductor-rta10transcriptcluster.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "8.8.0" %} {% set name = "rta10transcriptcluster.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 14ade3f4fca2d1091ccb28e7a777f3e5 +about: + description: Affymetrix rta10 annotation data (chip rta10transcriptcluster) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix rta10 annotation data (chip rta10transcriptcluster) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rta10transcriptcluster.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 14ade3f4fca2d1091ccb28e7a777f3e5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix rta10 annotation data (chip rta10transcriptcluster)' - description: 'Affymetrix rta10 annotation data (chip rta10transcriptcluster) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtca/meta.yaml b/recipes/bioconductor-rtca/meta.yaml index ab6f863af48a9..100437c0eee04 100644 --- a/recipes/bioconductor-rtca/meta.yaml +++ b/recipes/bioconductor-rtca/meta.yaml @@ -1,51 +1,57 @@ -{% set version = "1.54.0" %} +{% set version = "1.58.0" %} {% set name = "RTCA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Import, analyze and visualize data from Roche(R) xCELLigence RTCA systems. The package imports real-time cell electrical impedance data into R. As an alternative to commercial software shipped along the system, the Bioconductor package RTCA provides several unique transformation (normalization) strategies and various visualization tools. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Open-source toolkit to analyse data from xCELLigence System (RTCA) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8e1039d013ef1d5e08b48003ecffc25a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtca", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rtca + - doi:10.1016/j.compbiolchem.2013.12.004 + parent_recipe: + name: bioconductor-rtca + path: recipes/bioconductor-rtca + version: 1.32.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: xtable requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-gtools - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-gtools - r-rcolorbrewer + +source: + md5: 432ff93e50002d5471a2e8864a6e5f2a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'Open-source toolkit to analyse data from xCELLigence System (RTCA)' - description: 'Import, analyze and visualize data from Roche(R) xCELLigence RTCA systems. The package imports real-time cell electrical impedance data into R. As an alternative to commercial software shipped along the system, the Bioconductor package RTCA provides several unique transformation (normalization) strategies and various visualization tools.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:rtca - - doi:10.1016/j.compbiolchem.2013.12.004 - parent_recipe: - name: bioconductor-rtca - path: recipes/bioconductor-rtca - version: 1.32.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtcga.clinical/meta.yaml b/recipes/bioconductor-rtcga.clinical/meta.yaml index 0cbafa6e3191f..99598ff2e8ca5 100644 --- a/recipes/bioconductor-rtcga.clinical/meta.yaml +++ b/recipes/bioconductor-rtcga.clinical/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "20151101.32.0" %} +{% set version = "20151101.36.0" %} {% set name = "RTCGA.clinical" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9c32b8aef86c9ad34ea8c3672575d724 +about: + description: Package provides clinical datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Clinical data format is explained here https://wiki.nci.nih.gov/display/TCGA/Clinical+Data+Overview. Data from 2015-11-01 snapshot. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Clinical datasets from The Cancer Genome Atlas Project build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtcga.clinical", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: rmarkdown, knitr requirements: host: - - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - bioconductor-rtcga >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - bioconductor-rtcga >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: cccba079e0c1ad585e69e976dd71927b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Clinical datasets from The Cancer Genome Atlas Project' - description: 'Package provides clinical datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Clinical data format is explained here https://wiki.nci.nih.gov/display/TCGA/Clinical+Data+Overview. Data from 2015-11-01 snapshot.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtcga.clinical/post-link.sh b/recipes/bioconductor-rtcga.clinical/post-link.sh index a682ce0470fa4..39ffceeec6bf6 100644 --- a/recipes/bioconductor-rtcga.clinical/post-link.sh +++ b/recipes/bioconductor-rtcga.clinical/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.clinical-20151101.32.0" +installBiocDataPackage.sh "rtcga.clinical-20151101.36.0" diff --git a/recipes/bioconductor-rtcga.cnv/meta.yaml b/recipes/bioconductor-rtcga.cnv/meta.yaml index 2b0f7466f8e32..58b4571c8fa22 100644 --- a/recipes/bioconductor-rtcga.cnv/meta.yaml +++ b/recipes/bioconductor-rtcga.cnv/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "RTCGA.CNV" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 15267c2322da59ccd344657a28d2ba6a +about: + description: Package provides CNV (based on Merge snp) datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Retrieving +Data+Using+the+Data+Matrix. Data from 2015-11-01 snapshot. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: CNV (Copy-number variation) datasets from The Cancer Genome Atlas Project build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtcga.cnv", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - bioconductor-rtcga >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - bioconductor-rtcga >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bb5c72be005d63b713116dca5c820eb2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'CNV (Copy-number variation) datasets from The Cancer Genome Atlas Project' - description: 'Package provides CNV (based on Merge snp) datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Retrieving +Data+Using+the+Data+Matrix. Data from 2015-11-01 snapshot.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtcga.cnv/post-link.sh b/recipes/bioconductor-rtcga.cnv/post-link.sh index 046dd8d84df82..3ec3bfe0892a5 100644 --- a/recipes/bioconductor-rtcga.cnv/post-link.sh +++ b/recipes/bioconductor-rtcga.cnv/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.cnv-1.30.0" +installBiocDataPackage.sh "rtcga.cnv-1.34.0" diff --git a/recipes/bioconductor-rtcga.methylation/meta.yaml b/recipes/bioconductor-rtcga.methylation/meta.yaml index 60cb29db9aef4..c3b7569b3c536 100644 --- a/recipes/bioconductor-rtcga.methylation/meta.yaml +++ b/recipes/bioconductor-rtcga.methylation/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "RTCGA.methylation" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9d90704cb34a57878ef719348489c702 +about: + description: Package provides methylation (humanmethylation27) datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/DNA+methylation Data from 2015-11-01 snapshot. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Methylation datasets from The Cancer Genome Atlas Project build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtcga.methylation", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - bioconductor-rtcga >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - bioconductor-rtcga >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 604a06aaf5996979357d6a255ef8a48e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Methylation datasets from The Cancer Genome Atlas Project' - description: 'Package provides methylation (humanmethylation27) datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/DNA+methylation Data from 2015-11-01 snapshot.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtcga.methylation/post-link.sh b/recipes/bioconductor-rtcga.methylation/post-link.sh index 0149be259586a..3f37b1e8c09da 100644 --- a/recipes/bioconductor-rtcga.methylation/post-link.sh +++ b/recipes/bioconductor-rtcga.methylation/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.methylation-1.30.0" +installBiocDataPackage.sh "rtcga.methylation-1.34.0" diff --git a/recipes/bioconductor-rtcga.mirnaseq/meta.yaml b/recipes/bioconductor-rtcga.mirnaseq/meta.yaml index b3bc9acfe4918..0a0fb657d22f8 100644 --- a/recipes/bioconductor-rtcga.mirnaseq/meta.yaml +++ b/recipes/bioconductor-rtcga.mirnaseq/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "RTCGA.miRNASeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 744062c2f0db68a88e27db9d61929a79 +about: + description: Package provides miRNASeq datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/miRNASeq#miRNASeq-DataOverview Data from 2015-11-01 snapshot. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: miRNASeq datasets from The Cancer Genome Atlas Project build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtcga.mirnaseq", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - bioconductor-rtcga >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - bioconductor-rtcga >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 559ca4b4c3d24d5f545dbfc0649fdf84 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'miRNASeq datasets from The Cancer Genome Atlas Project' - description: 'Package provides miRNASeq datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/miRNASeq#miRNASeq-DataOverview Data from 2015-11-01 snapshot.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtcga.mirnaseq/post-link.sh b/recipes/bioconductor-rtcga.mirnaseq/post-link.sh index 4553a7939d834..5c26030097ab6 100644 --- a/recipes/bioconductor-rtcga.mirnaseq/post-link.sh +++ b/recipes/bioconductor-rtcga.mirnaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.mirnaseq-1.30.0" +installBiocDataPackage.sh "rtcga.mirnaseq-1.34.0" diff --git a/recipes/bioconductor-rtcga.mrna/meta.yaml b/recipes/bioconductor-rtcga.mrna/meta.yaml index 0fd9e1c2bc703..35aaa883ec92e 100644 --- a/recipes/bioconductor-rtcga.mrna/meta.yaml +++ b/recipes/bioconductor-rtcga.mrna/meta.yaml @@ -1,46 +1,52 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "RTCGA.mRNA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package provides mRNA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Gene+expression+data Data from 2015-11-01 snapshot. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: mRNA datasets from The Cancer Genome Atlas Project -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c9774207df355ef5945677d36e915103 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtcga.mrna", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-rtcga.mrna + path: recipes/bioconductor-rtcga.mrna + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - bioconductor-rtcga >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - bioconductor-rtcga >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 1adff9c1adfebeee25b3bd907467c3e5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'mRNA datasets from The Cancer Genome Atlas Project' - description: 'Package provides mRNA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Gene+expression+data Data from 2015-11-01 snapshot.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - parent_recipe: - name: bioconductor-rtcga.mrna - path: recipes/bioconductor-rtcga.mrna - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtcga.mrna/post-link.sh b/recipes/bioconductor-rtcga.mrna/post-link.sh index 75fe3ba6ceb43..117b260dfc630 100644 --- a/recipes/bioconductor-rtcga.mrna/post-link.sh +++ b/recipes/bioconductor-rtcga.mrna/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.mrna-1.30.0" +installBiocDataPackage.sh "rtcga.mrna-1.34.0" diff --git a/recipes/bioconductor-rtcga.mutations/meta.yaml b/recipes/bioconductor-rtcga.mutations/meta.yaml index dc0d506bc3755..87742a7188996 100644 --- a/recipes/bioconductor-rtcga.mutations/meta.yaml +++ b/recipes/bioconductor-rtcga.mutations/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "20151101.32.0" %} +{% set version = "20151101.36.0" %} {% set name = "RTCGA.mutations" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0740acb5a6a47fd9d1281ccaf80bafed +about: + description: Package provides mutations datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Mutations data format is explained here https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification. There is extra one column with patients' barcodes. Data from 2015-11-01 snapshot. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Mutations datasets from The Cancer Genome Atlas Project build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtcga.mutations", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - bioconductor-rtcga >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - bioconductor-rtcga >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b9efa7c97e496294c8867d9d6f615451 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Mutations datasets from The Cancer Genome Atlas Project' - description: 'Package provides mutations datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Mutations data format is explained here https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification. There is extra one column with patients'' barcodes. Data from 2015-11-01 snapshot.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtcga.mutations/post-link.sh b/recipes/bioconductor-rtcga.mutations/post-link.sh index 82133986d47de..e3512d55aa928 100644 --- a/recipes/bioconductor-rtcga.mutations/post-link.sh +++ b/recipes/bioconductor-rtcga.mutations/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.mutations-20151101.32.0" +installBiocDataPackage.sh "rtcga.mutations-20151101.36.0" diff --git a/recipes/bioconductor-rtcga.pancan12/meta.yaml b/recipes/bioconductor-rtcga.pancan12/meta.yaml index fed3714cbbb38..2bb211de6666a 100644 --- a/recipes/bioconductor-rtcga.pancan12/meta.yaml +++ b/recipes/bioconductor-rtcga.pancan12/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "RTCGA.PANCAN12" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8b0742d189afe05f47a2656556d85d0b +about: + description: Package provides clinical, expression, cnv and mutation data from Genome Cancer Browser. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: PanCan 12 from Genome Cancer Browser build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtcga.pancan12", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - bioconductor-rtcga >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - bioconductor-rtcga >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0efe506e10b90bfe638f397568f4ece9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'PanCan 12 from Genome Cancer Browser' - description: 'Package provides clinical, expression, cnv and mutation data from Genome Cancer Browser.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtcga.pancan12/post-link.sh b/recipes/bioconductor-rtcga.pancan12/post-link.sh index a5698c90619ab..45a8b0d04f7c4 100644 --- a/recipes/bioconductor-rtcga.pancan12/post-link.sh +++ b/recipes/bioconductor-rtcga.pancan12/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.pancan12-1.30.0" +installBiocDataPackage.sh "rtcga.pancan12-1.34.0" diff --git a/recipes/bioconductor-rtcga.rnaseq/meta.yaml b/recipes/bioconductor-rtcga.rnaseq/meta.yaml index 8d5fa4f1313d2..18f39c006b959 100644 --- a/recipes/bioconductor-rtcga.rnaseq/meta.yaml +++ b/recipes/bioconductor-rtcga.rnaseq/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "20151101.32.0" %} +{% set version = "20151101.36.0" %} {% set name = "RTCGA.rnaseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 47bee14c68ff4d1014677eca0ed969a9 +about: + description: Package provides rna-seq datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Rna-seq data format is explained here https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2. Data source is illumina hiseq Level 3 RSEM normalized expression data. Data from 2015-11-01 snapshot. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Rna-seq datasets from The Cancer Genome Atlas Project build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtcga.rnaseq", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - bioconductor-rtcga >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - bioconductor-rtcga >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 83acecb23e87c7b053d904279ada3512 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Rna-seq datasets from The Cancer Genome Atlas Project' - description: 'Package provides rna-seq datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Rna-seq data format is explained here https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2. Data source is illumina hiseq Level 3 RSEM normalized expression data. Data from 2015-11-01 snapshot.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtcga.rnaseq/post-link.sh b/recipes/bioconductor-rtcga.rnaseq/post-link.sh index 50935322d590a..a7540d158fe68 100644 --- a/recipes/bioconductor-rtcga.rnaseq/post-link.sh +++ b/recipes/bioconductor-rtcga.rnaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.rnaseq-20151101.32.0" +installBiocDataPackage.sh "rtcga.rnaseq-20151101.36.0" diff --git a/recipes/bioconductor-rtcga.rppa/meta.yaml b/recipes/bioconductor-rtcga.rppa/meta.yaml index 62d36b44246ca..7f3dd36351385 100644 --- a/recipes/bioconductor-rtcga.rppa/meta.yaml +++ b/recipes/bioconductor-rtcga.rppa/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "RTCGA.RPPA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5eccece412039d43cdf74aec284fa0d9 +about: + description: Package provides RPPA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Protein+Array +Data+Format+Specification?src=search + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: RPPA datasets from The Cancer Genome Atlas Project build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtcga.rppa", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - bioconductor-rtcga >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-rtcga >=1.32.0,<1.33.0' + - bioconductor-rtcga >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d1264823bcf1bb89103b73f31c00e376 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'RPPA datasets from The Cancer Genome Atlas Project' - description: 'Package provides RPPA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Protein+Array +Data+Format+Specification?src=search' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtcga.rppa/post-link.sh b/recipes/bioconductor-rtcga.rppa/post-link.sh index 382ca3c6abed1..9cd573bd22253 100644 --- a/recipes/bioconductor-rtcga.rppa/post-link.sh +++ b/recipes/bioconductor-rtcga.rppa/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "rtcga.rppa-1.30.0" +installBiocDataPackage.sh "rtcga.rppa-1.34.0" diff --git a/recipes/bioconductor-rtcga/meta.yaml b/recipes/bioconductor-rtcga/meta.yaml index 84fabac1dc0ff..eb121ce4e8f8c 100644 --- a/recipes/bioconductor-rtcga/meta.yaml +++ b/recipes/bioconductor-rtcga/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "RTCGA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The key is to understand genomics to improve cancer care. RTCGA package offers download and integration of the variety and volume of TCGA data using patient barcode key, what enables easier data possession. This may have an benefcial infuence on impact on development of science and improvement of patients' treatment. Furthermore, RTCGA package transforms TCGA data to tidy form which is convenient to use. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: The Cancer Genome Atlas Data Integration -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 97f413704d77f40ecbe00a1e0d25602d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtcga", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rtcga + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rtcga + path: recipes/bioconductor-rtcga + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: devtools, testthat, pander, Biobase, GenomicRanges, IRanges, S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, magrittr, tidyr requirements: host: @@ -61,21 +72,16 @@ requirements: - r-viridis - r-xml - r-xml2 + +source: + md5: 03057219eee1d04132b4e14add6a8a37 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'The Cancer Genome Atlas Data Integration' - description: 'The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The key is to understand genomics to improve cancer care. RTCGA package offers download and integration of the variety and volume of TCGA data using patient barcode key, what enables easier data possession. This may have an benefcial infuence on impact on development of science and improvement of patients'' treatment. Furthermore, RTCGA package transforms TCGA data to tidy form which is convenient to use.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:rtcga - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-rtcga - path: recipes/bioconductor-rtcga - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtcgatoolbox/meta.yaml b/recipes/bioconductor-rtcgatoolbox/meta.yaml index 22e51db05ee47..a3134f75c5614 100644 --- a/recipes/bioconductor-rtcgatoolbox/meta.yaml +++ b/recipes/bioconductor-rtcgatoolbox/meta.yaml @@ -1,35 +1,45 @@ -{% set version = "2.32.1" %} +{% set version = "2.36.0" %} {% set name = "RTCGAToolbox" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. We developed an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition, it can be integrated with other analysis pipelines for following data analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A new tool for exporting TCGA Firehose data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 002662ddf44b6ca3e771db3adcbda6d8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtcgatoolbox", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rtcgatoolbox + parent_recipe: + name: bioconductor-rtcgatoolbox + path: recipes/bioconductor-rtcgatoolbox + version: 2.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, Homo.sapiens, knitr, readr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tcgautils >=1.22.0,<1.23.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-raggedexperiment >=1.30.0,<1.31.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tcgautils >=1.26.0,<1.27.0 - r-base - r-data.table - r-httr @@ -38,14 +48,14 @@ requirements: - r-rvest - r-stringr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tcgautils >=1.22.0,<1.23.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-raggedexperiment >=1.30.0,<1.31.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tcgautils >=1.26.0,<1.27.0 - r-base - r-data.table - r-httr @@ -53,20 +63,16 @@ requirements: - r-rjsonio - r-rvest - r-stringr + +source: + md5: 8a19b80403d1ac8ad04b699bb29fd959 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'A new tool for exporting TCGA Firehose data' - description: 'Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. We developed an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition, it can be integrated with other analysis pipelines for following data analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:rtcgatoolbox - parent_recipe: - name: bioconductor-rtcgatoolbox - path: recipes/bioconductor-rtcgatoolbox - version: 2.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtn/meta.yaml b/recipes/bioconductor-rtn/meta.yaml index 31510ebec49e0..1548c374f4079 100644 --- a/recipes/bioconductor-rtn/meta.yaml +++ b/recipes/bioconductor-rtn/meta.yaml @@ -1,34 +1,35 @@ -{% set version = "2.26.0" %} +{% set version = "2.30.0" %} {% set name = "RTN" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A transcriptional regulatory network (TRN) consists of a collection of transcription factors (TFs) and the regulated target genes. TFs are regulators that recognize specific DNA sequences and guide the expression of the genome, either activating or repressing the expression the target genes. The set of genes controlled by the same TF forms a regulon. This package provides classes and methods for the reconstruction of TRNs and analysis of regulons. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3e79f58bcc4f0ac95a48819a0027028e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtn", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-minet >=3.60.0,<3.61.0' - - 'bioconductor-reder >=2.6.0,<2.7.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-viper >=1.36.0,<1.37.0' + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-minet >=3.64.0,<3.65.0 + - bioconductor-reder >=3.2.0,<3.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-viper >=1.40.0,<1.41.0 - r-base - r-car - r-data.table @@ -38,13 +39,13 @@ requirements: - r-pwr - r-snow run: - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-minet >=3.60.0,<3.61.0' - - 'bioconductor-reder >=2.6.0,<2.7.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-viper >=1.36.0,<1.37.0' + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-minet >=3.64.0,<3.65.0 + - bioconductor-reder >=3.2.0,<3.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-viper >=1.40.0,<1.41.0 - r-base - r-car - r-data.table @@ -53,12 +54,16 @@ requirements: - r-pheatmap - r-pwr - r-snow + +source: + md5: 3484f1a39b89baaf284fb2c439582bf3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons' - description: 'A transcriptional regulatory network (TRN) consists of a collection of transcription factors (TFs) and the regulated target genes. TFs are regulators that recognize specific DNA sequences and guide the expression of the genome, either activating or repressing the expression the target genes. The set of genes controlled by the same TF forms a regulon. This package provides classes and methods for the reconstruction of TRNs and analysis of regulons.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtnduals/meta.yaml b/recipes/bioconductor-rtnduals/meta.yaml index b9f3b2044cd8e..83171a7c770ec 100644 --- a/recipes/bioconductor-rtnduals/meta.yaml +++ b/recipes/bioconductor-rtnduals/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "RTNduals" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a4f986eb1a34493a1a577ea3546fe92 +about: + description: RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer 'dual regulons', a new concept that tests whether regulators can co-operate or compete in influencing targets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Analysis of co-regulation and inference of 'dual regulons' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtnduals", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics requirements: host: - - 'bioconductor-rtn >=2.26.0,<2.27.0' + - bioconductor-rtn >=2.30.0,<2.31.0 - r-base run: - - 'bioconductor-rtn >=2.26.0,<2.27.0' + - bioconductor-rtn >=2.30.0,<2.31.0 - r-base +source: + md5: 9905fa804241cc408b39a6b72503fc05 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Analysis of co-regulation and inference of ''dual regulons''' - description: 'RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer ''dual regulons'', a new concept that tests whether regulators can co-operate or compete in influencing targets.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtnsurvival/meta.yaml b/recipes/bioconductor-rtnsurvival/meta.yaml index 42c05a101eef4..e2d482bce9d00 100644 --- a/recipes/bioconductor-rtnsurvival/meta.yaml +++ b/recipes/bioconductor-rtnsurvival/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "RTNsurvival" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'RTNsurvival is a tool for integrating regulons generated by the RTN package with survival information. For a given regulon, the 2-tailed GSEA approach computes a differential Enrichment Score (dES) for each individual sample, and the dES distribution of all samples is then used to assess the survival statistics for the cohort. There are two main survival analysis workflows: a Cox Proportional Hazards approach used to model regulons as predictors of survival time, and a Kaplan-Meier analysis assessing the stratification of a cohort based on the regulon activity. All plots can be fine-tuned to the user''s specifications.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Survival analysis using transcriptional networks inferred by the RTN package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: db9d03eee81fed17fae3acb66a07893f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtnsurvival", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics requirements: host: - - 'bioconductor-rtn >=2.26.0,<2.27.0' - - 'bioconductor-rtnduals >=1.26.0,<1.27.0' + - bioconductor-rtn >=2.30.0,<2.31.0 + - bioconductor-rtnduals >=1.30.0,<1.31.0 - r-base - r-data.table - r-dunn.test @@ -34,8 +35,8 @@ requirements: - r-scales - r-survival run: - - 'bioconductor-rtn >=2.26.0,<2.27.0' - - 'bioconductor-rtnduals >=1.26.0,<1.27.0' + - bioconductor-rtn >=2.30.0,<2.31.0 + - bioconductor-rtnduals >=1.30.0,<1.31.0 - r-base - r-data.table - r-dunn.test @@ -45,12 +46,16 @@ requirements: - r-rcolorbrewer - r-scales - r-survival + +source: + md5: b00a4d74a034854f0b1170ab56e21e78 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Survival analysis using transcriptional networks inferred by the RTN package' - description: 'RTNsurvival is a tool for integrating regulons generated by the RTN package with survival information. For a given regulon, the 2-tailed GSEA approach computes a differential Enrichment Score (dES) for each individual sample, and the dES distribution of all samples is then used to assess the survival statistics for the cohort. There are two main survival analysis workflows: a Cox Proportional Hazards approach used to model regulons as predictors of survival time, and a Kaplan-Meier analysis assessing the stratification of a cohort based on the regulon activity. All plots can be fine-tuned to the user''s specifications.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtopper/meta.yaml b/recipes/bioconductor-rtopper/meta.yaml index 70748cb77078b..37d8fbe491508 100644 --- a/recipes/bioconductor-rtopper/meta.yaml +++ b/recipes/bioconductor-rtopper/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "RTopper" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: the RTopper package is designed to perform and integrate gene set enrichment results across multiple genomic platforms. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + file LICENSE + license_file: LICENSE + summary: This package is designed to perform Gene Set Analysis across multiple genomic platforms -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e551ec836b4c0743feabbd2deff66cb8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtopper", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rtopper + parent_recipe: + name: bioconductor-rtopper + path: recipes/bioconductor-rtopper + version: 1.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: org.Hs.eg.db, KEGGREST, GO.db requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multtest >=2.62.0,<2.63.0 - r-base + +source: + md5: 572d44333992c9d55db163dbaf59aad9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3) + file LICENSE' - summary: 'This package is designed to perform Gene Set Analysis across multiple genomic platforms' - description: 'the RTopper package is designed to perform and integrate gene set enrichment results across multiple genomic platforms.' - license_file: LICENSE -extra: - identifiers: - - biotools:rtopper - parent_recipe: - name: bioconductor-rtopper - path: recipes/bioconductor-rtopper - version: 1.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtpca/meta.yaml b/recipes/bioconductor-rtpca/meta.yaml index dc314446feed5..ad72fadcbe6c6 100644 --- a/recipes/bioconductor-rtpca/meta.yaml +++ b/recipes/bioconductor-rtpca/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "Rtpca" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: R package for performing thermal proximity co-aggregation analysis with thermal proteome profiling datasets to analyse protein complex assembly and (differential) protein-protein interactions across conditions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Thermal proximity co-aggregation with R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 671f34f1c510812fc37d66ed50378d75 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtpca", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, TPP, testthat, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-dplyr - r-fdrtool @@ -31,7 +33,7 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-dplyr - r-fdrtool @@ -39,13 +41,16 @@ requirements: - r-proc - r-tibble - r-tidyr + +source: + md5: 6a5f30e9ef1149d9572f6e3d4cf3cfd4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Thermal proximity co-aggregation with R' - description: 'R package for performing thermal proximity co-aggregation analysis with thermal proteome profiling datasets to analyse protein complex assembly and (differential) protein-protein interactions across conditions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtracklayer/meta.yaml b/recipes/bioconductor-rtracklayer/meta.yaml index 5e0eb2d16298a..921ab71ad8d5f 100644 --- a/recipes/bioconductor-rtracklayer/meta.yaml +++ b/recipes/bioconductor-rtracklayer/meta.yaml @@ -1,79 +1,88 @@ -{% set version = "1.62.0" %} +{% set version = "1.66.0" %} {% set name = "rtracklayer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + file LICENSE + license_file: LICENSE + summary: R interface to genome annotation files and the UCSC genome browser -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a16a9ca02e49808b38823899860abdb6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtracklayer", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:rtracklayer + parent_recipe: + name: bioconductor-rtracklayer + path: recipes/bioconductor-rtracklayer + version: 1.40.6 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit requirements: + build: + - {{ compiler('c') }} + - automake + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - - 'r-rcurl >=1.4-2' - - 'r-restfulr >=0.0.13' - - 'r-xml >=1.98-0' + - r-curl + - r-httr + - r-restfulr >=0.0.13 + - r-xml >=1.98-0 - libblas - liblapack + - zlib run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - - 'r-rcurl >=1.4-2' - - 'r-restfulr >=0.0.13' - - 'r-xml >=1.98-0' - build: - - {{ compiler('c') }} - - automake - - make + - r-curl + - r-httr + - r-restfulr >=0.0.13 + - r-xml >=1.98-0 + +source: + md5: a104b15f928583554639289984edec35 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Artistic-2.0 + file LICENSE' - summary: 'R interface to genome annotation files and the UCSC genome browser' - description: 'Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.' - license_file: LICENSE -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:rtracklayer - parent_recipe: - name: bioconductor-rtracklayer - path: recipes/bioconductor-rtracklayer - version: 1.40.6 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtreemix/meta.yaml b/recipes/bioconductor-rtreemix/meta.yaml index 3fcbf4f2015c1..aaf0e7345ab7b 100644 --- a/recipes/bioconductor-rtreemix/meta.yaml +++ b/recipes/bioconductor-rtreemix/meta.yaml @@ -1,56 +1,62 @@ -{% set version = "1.64.0" %} +{% set version = "1.68.0" %} {% set name = "Rtreemix" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Rtreemix is a package that offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. It includes functions for fitting the trees mixture models, likelihood computations, model comparisons, waiting time estimations, stability analysis, etc. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: 'Rtreemix: Mutagenetic trees mixture models.' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3a9bda84ad8cd784165f1b8ce1a43af7 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtreemix", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:rtreemix + - doi:10.1093/bioinformatics/btn410 + parent_recipe: + name: bioconductor-rtreemix + path: recipes/bioconductor-rtreemix + version: 1.42.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Rgraphviz requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-hmisc - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-hmisc - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 87e82c520ead56ce7deb2810a83feb40 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Rtreemix: Mutagenetic trees mixture models.' - description: 'Rtreemix is a package that offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. It includes functions for fitting the trees mixture models, likelihood computations, model comparisons, waiting time estimations, stability analysis, etc.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:rtreemix - - doi:10.1093/bioinformatics/btn410 - parent_recipe: - name: bioconductor-rtreemix - path: recipes/bioconductor-rtreemix - version: 1.42.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtrm/meta.yaml b/recipes/bioconductor-rtrm/meta.yaml index e12f221409eeb..cf36b96f10e4f 100644 --- a/recipes/bioconductor-rtrm/meta.yaml +++ b/recipes/bioconductor-rtrm/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "rTRM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: rTRM identifies transcriptional regulatory modules (TRMs) from protein-protein interaction networks. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2804488949a044166efe737d4e25d9ac build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtrm", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:rtrm + parent_recipe: + name: bioconductor-rtrm + path: recipes/bioconductor-rtrm + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - r-dbi - - 'r-igraph >=1.0' + - r-igraph >=1.0 - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - r-dbi - - 'r-igraph >=1.0' + - r-igraph >=1.0 - r-rsqlite + +source: + md5: 18daea52e386d0f963f647b18e7c89c7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks' - description: 'rTRM identifies transcriptional regulatory modules (TRMs) from protein-protein interaction networks.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:rtrm - parent_recipe: - name: bioconductor-rtrm - path: recipes/bioconductor-rtrm - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtrmui/meta.yaml b/recipes/bioconductor-rtrmui/meta.yaml index c92d5cb854754..29ee45785900f 100644 --- a/recipes/bioconductor-rtrmui/meta.yaml +++ b/recipes/bioconductor-rtrmui/meta.yaml @@ -1,48 +1,22 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "rTRMui" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a web interface to compute transcriptional regulatory modules with rTRM. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A shiny user interface for rTRM -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6e1589a0f3e51870f4eb71a0eb56d915 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtrmui", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-motifdb >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rtrm >=1.40.0,<1.41.0' - - r-base - - 'r-shiny >=0.9' - run: - - 'bioconductor-motifdb >=1.44.0,<1.45.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rtrm >=1.40.0,<1.41.0' - - r-base - - 'r-shiny >=0.9' -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'A shiny user interface for rTRM' - description: 'This package provides a web interface to compute transcriptional regulatory modules with rTRM.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:rtrmui @@ -52,3 +26,35 @@ extra: path: recipes/bioconductor-rtrmui version: 1.18.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-motifdb >=1.48.0,<1.49.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-rtrm >=1.44.0,<1.45.0 + - r-base + - r-shiny >=0.9 + run: + - bioconductor-motifdb >=1.48.0,<1.49.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-rtrm >=1.44.0,<1.45.0 + - r-base + - r-shiny >=0.9 + +source: + md5: 6f4baf596e1a9987e285330b3b04e046 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-rtu34.db/meta.yaml b/recipes/bioconductor-rtu34.db/meta.yaml index fc5ff8cdaf925..baf01dfe6b9c0 100644 --- a/recipes/bioconductor-rtu34.db/meta.yaml +++ b/recipes/bioconductor-rtu34.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "rtu34.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f46c4763627f1a9e00cdc9d0af8c5f2e +about: + description: Affymetrix Affymetrix RT_U34 Array annotation data (chip rtu34) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix RT_U34 Array annotation data (chip rtu34) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtu34.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f46c4763627f1a9e00cdc9d0af8c5f2e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix RT_U34 Array annotation data (chip rtu34)' - description: 'Affymetrix Affymetrix RT_U34 Array annotation data (chip rtu34) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtu34cdf/meta.yaml b/recipes/bioconductor-rtu34cdf/meta.yaml index 4c46f39a9d9c1..4cada2b5f2c37 100644 --- a/recipes/bioconductor-rtu34cdf/meta.yaml +++ b/recipes/bioconductor-rtu34cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rtu34cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 317abfcca319d01eb14f16efa6d91da1 +about: + description: A package containing an environment representing the RT_U34.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: rtu34cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtu34cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 317abfcca319d01eb14f16efa6d91da1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: rtu34cdf - description: 'A package containing an environment representing the RT_U34.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rtu34probe/meta.yaml b/recipes/bioconductor-rtu34probe/meta.yaml index 85fe1dcc09abf..853ce5af7b090 100644 --- a/recipes/bioconductor-rtu34probe/meta.yaml +++ b/recipes/bioconductor-rtu34probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "rtu34probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1778d857a61bf181b80b9fcf46ebd2c3 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RT-U34\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type rtu34 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rtu34probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1778d857a61bf181b80b9fcf46ebd2c3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type rtu34' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RT-U34\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-runibic/meta.yaml b/recipes/bioconductor-runibic/meta.yaml index 2880440cd9bb6..6086dd84f0f05 100644 --- a/recipes/bioconductor-runibic/meta.yaml +++ b/recipes/bioconductor-runibic/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "runibic" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements UbiBic algorithm in R. This biclustering algorithm for analysis of gene expression data was introduced by Zhenjia Wang et al. in 2016. It is currently considered the most promising biclustering method for identification of meaningful structures in complex and noisy data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 'runibic: row-based biclustering algorithm for analysis of gene expression data in R' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e67e1067d80c06f72208fca94d7a2e52 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-runibic", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, GEOquery, affy, airway, QUBIC # SystemRequirements: C++11, GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-biclust - - 'r-rcpp >=0.12.12' + - r-rcpp >=0.12.12 - r-testthat - libblas - liblapack run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-biclust - - 'r-rcpp >=0.12.12' + - r-rcpp >=0.12.12 - r-testthat - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 7741b1c71cce3fc9588e6d4665a18ff5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'runibic: row-based biclustering algorithm for analysis of gene expression data in R' - description: 'This package implements UbiBic algorithm in R. This biclustering algorithm for analysis of gene expression data was introduced by Zhenjia Wang et al. in 2016. It is currently considered the most promising biclustering method for identification of meaningful structures in complex and noisy data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ruvcorr/meta.yaml b/recipes/bioconductor-ruvcorr/meta.yaml index 2579d63c4c8d9..2e107c788026c 100644 --- a/recipes/bioconductor-ruvcorr/meta.yaml +++ b/recipes/bioconductor-ruvcorr/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "RUVcorr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: RUVcorr allows to apply global removal of unwanted variation (ridged version of RUV) to real and simulated gene expression data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Removal of unwanted variation for gene-gene correlations and related analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cfc2e185bc7d37f264843a6fa5ed7c6d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ruvcorr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, hgu133a2.db, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bladderbatch >=1.40.0,<1.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bladderbatch >=1.44.0,<1.45.0 - r-base - r-corrplot - r-gridextra @@ -33,8 +35,8 @@ requirements: - r-reshape2 - r-snowfall run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bladderbatch >=1.40.0,<1.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bladderbatch >=1.44.0,<1.45.0 - r-base - r-corrplot - r-gridextra @@ -43,13 +45,16 @@ requirements: - r-psych - r-reshape2 - r-snowfall + +source: + md5: f30e4a32f61a74390b0e101d16f3cfb2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Removal of unwanted variation for gene-gene correlations and related analysis' - description: 'RUVcorr allows to apply global removal of unwanted variation (ridged version of RUV) to real and simulated gene expression data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ruvnormalize/meta.yaml b/recipes/bioconductor-ruvnormalize/meta.yaml index 7c155c7112009..b8d13ac9a8f0b 100644 --- a/recipes/bioconductor-ruvnormalize/meta.yaml +++ b/recipes/bioconductor-ruvnormalize/meta.yaml @@ -1,42 +1,22 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "RUVnormalize" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: RUVnormalize is meant to remove unwanted variation from gene expression data when the factor of interest is not defined, e.g., to clean up a dataset for general use or to do any kind of unsupervised analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: RUV for normalization of expression array data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2d5d0d40d8720734dee3f8dc437c0756 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ruvnormalize", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-ruvnormalizedata >=1.22.0,<1.23.0' - - r-base - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-ruvnormalizedata >=1.22.0,<1.23.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'RUV for normalization of expression array data' - description: 'RUVnormalize is meant to remove unwanted variation from gene expression data when the factor of interest is not defined, e.g., to clean up a dataset for general use or to do any kind of unsupervised analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:ruvnormalize @@ -45,3 +25,29 @@ extra: path: recipes/bioconductor-ruvnormalize version: 1.14.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-ruvnormalizedata >=1.26.0,<1.27.0 + - r-base + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-ruvnormalizedata >=1.26.0,<1.27.0 + - r-base + +source: + md5: 1cc0f59467a2eba7cb2f4002f747c403 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-ruvnormalizedata/meta.yaml b/recipes/bioconductor-ruvnormalizedata/meta.yaml index b4d2035842550..80c13fc287feb 100644 --- a/recipes/bioconductor-ruvnormalizedata/meta.yaml +++ b/recipes/bioconductor-ruvnormalizedata/meta.yaml @@ -1,45 +1,51 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "RUVnormalizeData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Microarray gene expression data from the study of Vawter et al., 2004. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Gender data for the RUVnormalize package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d7104746a5cac16500870312dd769a6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ruvnormalizedata", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-ruvnormalizedata + path: recipes/bioconductor-ruvnormalizedata + version: 0.114.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 01b2d1a2ab2ff4433e5b3f64abdf3f43 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Gender data for the RUVnormalize package' - description: 'Microarray gene expression data from the study of Vawter et al., 2004.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-ruvnormalizedata - path: recipes/bioconductor-ruvnormalizedata - version: 0.114.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ruvnormalizedata/post-link.sh b/recipes/bioconductor-ruvnormalizedata/post-link.sh index 3d7a877bdd836..51f3890cee94d 100644 --- a/recipes/bioconductor-ruvnormalizedata/post-link.sh +++ b/recipes/bioconductor-ruvnormalizedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "ruvnormalizedata-1.22.0" +installBiocDataPackage.sh "ruvnormalizedata-1.26.0" diff --git a/recipes/bioconductor-ruvseq/meta.yaml b/recipes/bioconductor-ruvseq/meta.yaml index 2f25bffb6074b..83f04cb7e86b8 100644 --- a/recipes/bioconductor-ruvseq/meta.yaml +++ b/recipes/bioconductor-ruvseq/meta.yaml @@ -1,51 +1,57 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "RUVSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements the remove unwanted variation (RUV) methods of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Remove Unwanted Variation from RNA-Seq Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eebbc7e6520dc1fb18f5d8f66de7b739 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ruvseq", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:ruvseq + parent_recipe: + name: bioconductor-ruvseq + path: recipes/bioconductor-ruvseq + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2 requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-edaseq >=2.36.0,<2.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-edaseq >=2.40.0,<2.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 - r-base - r-mass run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-edaseq >=2.36.0,<2.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-edaseq >=2.40.0,<2.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 - r-base - r-mass + +source: + md5: 086e8941b21a0fba238044a475b925b7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Remove Unwanted Variation from RNA-Seq Data' - description: 'This package implements the remove unwanted variation (RUV) methods of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.' -extra: - identifiers: - - biotools:ruvseq - parent_recipe: - name: bioconductor-ruvseq - path: recipes/bioconductor-ruvseq - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rvisdiff/meta.yaml b/recipes/bioconductor-rvisdiff/meta.yaml index 5b328f86ae0db..95ac49f98c085 100644 --- a/recipes/bioconductor-rvisdiff/meta.yaml +++ b/recipes/bioconductor-rvisdiff/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "Rvisdiff" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3e3b8ccc9cb71388e2e7c17d60995cbe +about: + description: 'Creates a muti-graph web page which allows the interactive exploration of differential expression results. The graphical web interface presents results as a table which is integrated with five interactive graphs: MA-plot, volcano plot, box plot, lines plot and cluster heatmap. Graphical aspect and information represented in the graphs can be customized by means of user controls. Final graphics can be exported as PNG format.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 | GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Interactive Graphs for Differential Expression build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rvisdiff", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, DESeq2, limma, SummarizedExperiment, airway, BiocStyle, matrixTests, BiocManager requirements: host: - - 'bioconductor-edger >=4.0.0,<4.1.0' + - bioconductor-edger >=4.4.0,<4.5.0 - r-base run: - - 'bioconductor-edger >=4.0.0,<4.1.0' + - bioconductor-edger >=4.4.0,<4.5.0 - r-base +source: + md5: 4ba986d27d98c2d83005b9e6d69c0f32 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-2 | GPL-3' - summary: 'Interactive Graphs for Differential Expression' - description: 'Creates a muti-graph web page which allows the interactive exploration of differential expression results. The graphical web interface presents results as a table which is integrated with five interactive graphs: MA-plot, volcano plot, box plot, lines plot and cluster heatmap. Graphical aspect and information represented in the graphs can be customized by means of user controls. Final graphics can be exported as PNG format.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rvs/meta.yaml b/recipes/bioconductor-rvs/meta.yaml index 0439a11c2393c..0134b43007800 100644 --- a/recipes/bioconductor-rvs/meta.yaml +++ b/recipes/bioconductor-rvs/meta.yaml @@ -1,45 +1,52 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "RVS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Rare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Computes estimates of the probability of related individuals sharing a rare variant -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 209870dca9bf6ebc9831014045ddbd42 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rvs", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation requirements: host: - - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - bioconductor-snpstats >=1.56.0,<1.57.0 - r-base - r-genlib - r-grain - r-kinship2 + - r-r.utils run: - - 'bioconductor-snpstats >=1.52.0,<1.53.0' + - bioconductor-snpstats >=1.56.0,<1.57.0 - r-base - r-genlib - r-grain - r-kinship2 + - r-r.utils + +source: + md5: 01c75a05d91e9ae8d3058976f52671e2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Computes estimates of the probability of related individuals sharing a rare variant' - description: 'Rare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rwgcod.db/meta.yaml b/recipes/bioconductor-rwgcod.db/meta.yaml index 0fc2b8cb3aa76..e8c54462334c8 100644 --- a/recipes/bioconductor-rwgcod.db/meta.yaml +++ b/recipes/bioconductor-rwgcod.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.4.0" %} {% set name = "rwgcod.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c8d2fa81b6f03c4ee629a0883431e5fd +about: + description: Codelink Rat Whole Genome Bioarray (~34 000 rat gene targets) annotation data (chip rwgcod) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Codelink Rat Whole Genome Bioarray (~34 000 rat gene targets) annotation data (chip rwgcod) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rwgcod.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.rn.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.rn.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c8d2fa81b6f03c4ee629a0883431e5fd + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Codelink Rat Whole Genome Bioarray (~34 000 rat gene targets) annotation data (chip rwgcod)' - description: 'Codelink Rat Whole Genome Bioarray (~34 000 rat gene targets) annotation data (chip rwgcod) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-rwikipathways/meta.yaml b/recipes/bioconductor-rwikipathways/meta.yaml index f038e83886397..5dc03217eb1be 100644 --- a/recipes/bioconductor-rwikipathways/meta.yaml +++ b/recipes/bioconductor-rwikipathways/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.22.1" %} +{% set version = "1.26.0" %} {% set name = "rWikiPathways" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Use this package to interface with the WikiPathways API. It provides programmatic access to WikiPathways content in multiple data and image formats, including official monthly release files and convenient GMT read/write functions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: rWikiPathways - R client library for the WikiPathways API -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a836092dcb14297a316efeb45de307d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-rwikipathways", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: @@ -47,13 +49,16 @@ requirements: - r-stringr - r-tidyr - r-xml + +source: + md5: c726fe822b39d58fbbb070f81205e011 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'rWikiPathways - R client library for the WikiPathways API' - description: 'Use this package to interface with the WikiPathways API. It provides programmatic access to WikiPathways content in multiple data and image formats, including official monthly release files and convenient GMT read/write functions.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-s4arrays/meta.yaml b/recipes/bioconductor-s4arrays/meta.yaml index c70867b22c48d..c542714377563 100644 --- a/recipes/bioconductor-s4arrays/meta.yaml +++ b/recipes/bioconductor-s4arrays/meta.yaml @@ -1,29 +1,37 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "S4Arrays" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The S4Arrays package defines the Array virtual class to be extended by other S4 classes that wish to implement a container with an array-like semantic. It also provides: (1) low-level functionality meant to help the developer of such container to implement basic operations like display, subsetting, or coercion of their array-like objects to an ordinary matrix or array, and (2) a framework that facilitates block processing of array-like objects (typically on-disk objects).' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Foundation of array-like containers in Bioconductor -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c77474b839251d19d31708831de3c1bf build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-s4arrays", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocParallel, SparseArray (>= 0.0.4), DelayedArray, testthat, knitr, rmarkdown, BiocStyle requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-abind - r-base - r-crayon @@ -31,25 +39,23 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-abind - r-base - r-crayon - r-matrix - build: - - {{ compiler('c') }} - - make + +source: + md5: 0bdfca3df96ee46fa23a4913cbeccf9b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Foundation of array-like containers in Bioconductor' - description: 'The S4Arrays package defines the Array virtual class to be extended by other S4 classes that wish to implement a container with an array-like semantic. It also provides: (1) low-level functionality meant to help the developer of such container to implement basic operations like display, subsetting, or coercion of their array-like objects to an ordinary matrix or array, and (2) a framework that facilitates block processing of array-like objects (typically on-disk objects).' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 diff --git a/recipes/bioconductor-s4vectors/meta.yaml b/recipes/bioconductor-s4vectors/meta.yaml index dff5ef1152e05..486fa40a02fc0 100644 --- a/recipes/bioconductor-s4vectors/meta.yaml +++ b/recipes/bioconductor-s4vectors/meta.yaml @@ -1,44 +1,20 @@ -{% set version = "0.40.2" %} +{% set version = "0.44.0" %} {% set name = "S4Vectors" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, Factor, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Foundation of vector-like and list-like containers in Bioconductor -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ee94f4f6c25dcaf7a50f5814495310e3 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-s4vectors", max_pin="x.x") }}' -# Suggests: IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle, knitr -requirements: - host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - r-base - - libblas - - liblapack - run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - r-base - build: - - {{ compiler('c') }} - - make -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Foundation of vector-like and list-like containers in Bioconductor' - description: 'The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, Factor, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).' + extra: additional-platforms: - linux-aarch64 @@ -50,3 +26,33 @@ extra: path: recipes/bioconductor-s4vectors version: 0.18.3 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle, knitr +requirements: + build: + - {{ compiler('c') }} + - make + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - r-base + - libblas + - liblapack + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - r-base + +source: + md5: 6f87d627de90deccd2bc907b36d6d75d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-safe/meta.yaml b/recipes/bioconductor-safe/meta.yaml index 628005304fbab..f2f81b30aea2d 100644 --- a/recipes/bioconductor-safe/meta.yaml +++ b/recipes/bioconductor-safe/meta.yaml @@ -1,51 +1,57 @@ -{% set version = "3.42.0" %} +{% set version = "3.46.0" %} {% set name = "safe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SAFE is a resampling-based method for testing functional categories in gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Significance Analysis of Function and Expression -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 70cc344ddfe65a9d0f3a021c565a1e8e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-safe", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:safe + - doi:10.1093/bioinformatics/bti260 + parent_recipe: + name: bioconductor-safe + path: recipes/bioconductor-safe + version: 3.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-sparsem run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-sparsem + +source: + md5: 3483a0332c96f982bb8fc8cdae477eaa + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Significance Analysis of Function and Expression' - description: 'SAFE is a resampling-based method for testing functional categories in gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:safe - - doi:10.1093/bioinformatics/bti260 - parent_recipe: - name: bioconductor-safe - path: recipes/bioconductor-safe - version: 3.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sagenhaft/meta.yaml b/recipes/bioconductor-sagenhaft/meta.yaml index 678694684b10b..d31fddaf216aa 100644 --- a/recipes/bioconductor-sagenhaft/meta.yaml +++ b/recipes/bioconductor-sagenhaft/meta.yaml @@ -1,40 +1,22 @@ -{% set version = "1.72.0" %} +{% set version = "1.76.0" %} {% set name = "sagenhaft" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements several functions useful for analysis of gene expression data by sequencing tags as done in SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison. Sequencing error correction is implementing using an Expectation Maximization Algorithm based on a Mixture Model of tag counts. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Collection of functions for reading and comparing SAGE libraries -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4f27450a0e98b4f0f7396a784eb0e4e3 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sagenhaft", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - r-base - - 'r-sparsem >=0.73' - run: - - r-base - - 'r-sparsem >=0.73' -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Collection of functions for reading and comparing SAGE libraries' - description: 'This package implements several functions useful for analysis of gene expression data by sequencing tags as done in SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison. Sequencing error correction is implementing using an Expectation Maximization Algorithm based on a Mixture Model of tag counts.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:sagenhaft @@ -44,3 +26,27 @@ extra: path: recipes/bioconductor-sagenhaft version: 1.50.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - r-base + - r-sparsem >=0.73 + run: + - r-base + - r-sparsem >=0.73 + +source: + md5: 9546300f36a4c600915b430f7a982ce1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-saigegds/meta.yaml b/recipes/bioconductor-saigegds/meta.yaml index ff7383e3f09cc..5bbcb408c7e30 100644 --- a/recipes/bioconductor-saigegds/meta.yaml +++ b/recipes/bioconductor-saigegds/meta.yaml @@ -1,55 +1,64 @@ -{% set version = "2.2.0" %} +{% set version = "2.6.0" %} {% set name = "SAIGEgds" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Scalable implementation of generalized mixed models with highly optimized C++ implementation and integration with Genomic Data Structure (GDS) files. It is designed for single variant tests and set-based aggregate tests in large-scale Phenome-wide Association Studies (PheWAS) with millions of variants and samples, controlling for sample structure and case-control imbalance. The implementation is based on the SAIGE R package (v0.45, Zhou et al. 2018 and Zhou et al. 2020), and it is extended to include the state-of-the-art ACAT-O set-based tests. Benchmarks show that SAIGEgds is significantly faster than the SAIGE R package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d5792543f5eba866f022723bad21b67e build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-saigegds", max_pin="x.x") }}' -# Suggests: parallel, crayon, CompQuadForm, survey, SNPRelate, RUnit, knitr, markdown, rmarkdown, ggmanh, BiocGenerics + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: parallel, markdown, rmarkdown, crayon, SNPRelate, RUnit, knitr, ggmanh, BiocGenerics # SystemRequirements: C++11, GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-seqarray >=1.46.0,<1.47.0 - r-base + - r-compquadform - r-matrix - r-rcpp - r-rcpparmadillo - - 'r-rcppparallel >=5.0.0' + - r-rcppparallel >=5.0.0 + - r-survey - libblas - liblapack run: - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-seqarray >=1.46.0,<1.47.0 - r-base + - r-compquadform - r-matrix - r-rcpp - r-rcpparmadillo - - 'r-rcppparallel >=5.0.0' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcppparallel >=5.0.0 + - r-survey + +source: + md5: 6b3e2939d8ff51b9b7199227dabd6c73 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies' - description: 'Scalable implementation of generalized mixed models with highly optimized C++ implementation and integration with Genomic Data Structure (GDS) files. It is designed for single variant tests and set-based aggregate tests in large-scale Phenome-wide Association Studies (PheWAS) with millions of variants and samples, controlling for sample structure and case-control imbalance. The implementation is based on the SAIGE R package (v0.45, Zhou et al. 2018 and Zhou et al. 2020), and it is extended to include the state-of-the-art ACAT-O set-based tests. Benchmarks show that SAIGEgds is significantly faster than the SAIGE R package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sampleclassifier/meta.yaml b/recipes/bioconductor-sampleclassifier/meta.yaml index f2f2a849ce0a0..d6d20d0287a9d 100644 --- a/recipes/bioconductor-sampleclassifier/meta.yaml +++ b/recipes/bioconductor-sampleclassifier/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "sampleClassifier" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package is designed to classify microarray RNA-seq gene expression profiles. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Sample Classifier -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7f17cc7eb566dcd27148ee400491b6c7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sampleclassifier", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: sampleClassifierData, BiocStyle, hgu133a.db, hgu133plus2.db requirements: host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-mgfm >=1.36.0,<1.37.0' - - 'bioconductor-mgfr >=1.28.0,<1.29.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-mgfm >=1.40.0,<1.41.0 + - bioconductor-mgfr >=1.32.0,<1.33.0 - r-base - r-e1071 - r-ggplot2 run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-mgfm >=1.36.0,<1.37.0' - - 'bioconductor-mgfr >=1.28.0,<1.29.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-mgfm >=1.40.0,<1.41.0 + - bioconductor-mgfr >=1.32.0,<1.33.0 - r-base - r-e1071 - r-ggplot2 + +source: + md5: 2472d8a26d6f263d2633882d5c409b7e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Sample Classifier' - description: 'The package is designed to classify microarray RNA-seq gene expression profiles.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sampleclassifierdata/meta.yaml b/recipes/bioconductor-sampleclassifierdata/meta.yaml index a1b9746040b66..053ce0551da01 100644 --- a/recipes/bioconductor-sampleclassifierdata/meta.yaml +++ b/recipes/bioconductor-sampleclassifierdata/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "sampleClassifierData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 941790a92cde9051601206ed162f4151 +about: + description: This package contains two microarray and two RNA-seq datasets that have been preprocessed for use with the sampleClassifier package. The RNA-seq data are derived from Fagerberg et al. (2014) and the Illumina Body Map 2.0 data. The microarray data are derived from Roth et al. (2006) and Ge et al. (2005). + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Pre-processed data for use with the sampleClassifier package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sampleclassifierdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: dbda361a9401f68ae3935368e7555135 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Pre-processed data for use with the sampleClassifier package' - description: 'This package contains two microarray and two RNA-seq datasets that have been preprocessed for use with the sampleClassifier package. The RNA-seq data are derived from Fagerberg et al. (2014) and the Illumina Body Map 2.0 data. The microarray data are derived from Roth et al. (2006) and Ge et al. (2005).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sampleclassifierdata/post-link.sh b/recipes/bioconductor-sampleclassifierdata/post-link.sh index 9b49079caf80f..c64c666011a36 100644 --- a/recipes/bioconductor-sampleclassifierdata/post-link.sh +++ b/recipes/bioconductor-sampleclassifierdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "sampleclassifierdata-1.26.0" +installBiocDataPackage.sh "sampleclassifierdata-1.30.0" diff --git a/recipes/bioconductor-samspectral/meta.yaml b/recipes/bioconductor-samspectral/meta.yaml index 54499b23d8f09..5fd3abba31a70 100644 --- a/recipes/bioconductor-samspectral/meta.yaml +++ b/recipes/bioconductor-samspectral/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.56.0" %} +{% set version = "1.60.0" %} {% set name = "SamSPECTRAL" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2724bc54054c093fac88a672a6b173d6 +about: + description: Samples large data such that spectral clustering is possible while preserving density information in edge weights. More specifically, given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting "connected components" estimate biological cell populations in the data. See the vignette for more details on how to use this package, some illustrations, and simple examples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identifies cell population in flow cytometry data build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-samspectral", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - libblas - liblapack run: - r-base - build: - - {{ compiler('c') }} - - make +source: + md5: dc3da48feb16c796c61a290b9e10708f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Identifies cell population in flow cytometry data' - description: 'Samples large data such that spectral clustering is possible while preserving density information in edge weights. More specifically, given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting "connected components" estimate biological cell populations in the data. See the vignette for more details on how to use this package, some illustrations, and simple examples.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sangeranalyser/meta.yaml b/recipes/bioconductor-sangeranalyser/meta.yaml index 3b746fd6bf70d..6b671dd80e388 100644 --- a/recipes/bioconductor-sangeranalyser/meta.yaml +++ b/recipes/bioconductor-sangeranalyser/meta.yaml @@ -1,31 +1,35 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "sangeranalyseR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package builds on sangerseqR to allow users to create contigs from collections of Sanger sequencing reads. It provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. There is extensive online documentation, and the package can outputs detailed HTML reports, including chromatograms. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: da4a748e4e8a1eaba322abafbd7aedad build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sangeranalyser", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 2.1.0) requirements: + host: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-decipher >=2.30.0,<2.31.0' - - 'bioconductor-sangerseqr >=1.38.0,<1.39.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-decipher >=3.2.0,<3.3.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-sangerseqr >=1.42.0,<1.43.0 - r-ape - r-base - r-data.table @@ -33,13 +37,12 @@ requirements: - r-excelr - r-ggdendro - r-gridextra - - 'r-knitr >=1.33' + - r-knitr >=1.33 - r-logger - r-openxlsx - - r-phangorn - r-plotly - r-reshape2 - - 'r-rmarkdown >=2.9' + - r-rmarkdown >=2.9 - r-seqinr - r-shiny - r-shinycssloaders @@ -48,11 +51,13 @@ requirements: - r-shinywidgets - r-stringr - r-zeallot + run: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-decipher >=2.30.0,<2.31.0' - - 'bioconductor-sangerseqr >=1.38.0,<1.39.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-decipher >=3.2.0,<3.3.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-sangerseqr >=1.42.0,<1.43.0 - r-ape - r-base - r-data.table @@ -60,13 +65,12 @@ requirements: - r-excelr - r-ggdendro - r-gridextra - - 'r-knitr >=1.33' + - r-knitr >=1.33 - r-logger - r-openxlsx - - r-phangorn - r-plotly - r-reshape2 - - 'r-rmarkdown >=2.9' + - r-rmarkdown >=2.9 - r-seqinr - r-shiny - r-shinycssloaders @@ -75,13 +79,16 @@ requirements: - r-shinywidgets - r-stringr - r-zeallot + +source: + md5: c769810033a1ba71ac1833a2a9d9e254 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R' - description: 'This package builds on sangerseqR to allow users to create contigs from collections of Sanger sequencing reads. It provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. There is extensive online documentation, and the package can outputs detailed HTML reports, including chromatograms.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sangerseqr/meta.yaml b/recipes/bioconductor-sangerseqr/meta.yaml index adeddccc55773..6481cd28b9616 100644 --- a/recipes/bioconductor-sangerseqr/meta.yaml +++ b/recipes/bioconductor-sangerseqr/meta.yaml @@ -1,50 +1,58 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "sangerseqR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains several tools for analyzing Sanger Sequencing data files in R, including reading .scf and .ab1 files, making basecalls and plotting chromatograms. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Tools for Sanger Sequencing Data in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: efc55dbe39324b21b62910684962b86b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sangerseqr", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:sangerseqr + parent_recipe: + name: bioconductor-sangerseqr + path: recipes/bioconductor-sangerseqr + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 - r-base - r-shiny - r-stringr run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 - r-base - r-shiny - r-stringr + +source: + md5: f23125bae93ccaf24462cf34eb3aa323 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Tools for Sanger Sequencing Data in R' - description: 'This package contains several tools for analyzing Sanger Sequencing data files in R, including reading .scf and .ab1 files, making basecalls and plotting chromatograms.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:sangerseqr - parent_recipe: - name: bioconductor-sangerseqr - path: recipes/bioconductor-sangerseqr - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-santa/meta.yaml b/recipes/bioconductor-santa/meta.yaml index 5c73501ad8a78..c2c04a4301250 100644 --- a/recipes/bioconductor-santa/meta.yaml +++ b/recipes/bioconductor-santa/meta.yaml @@ -1,25 +1,27 @@ -{% set version = "2.38.0" %} +{% set version = "2.42.0" %} {% set name = "SANTA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b2b87312bb663905abbc444be13a056 +about: + description: This package provides methods for measuring the strength of association between a network and a phenotype. It does this by measuring clustering of the phenotype across the network (Knet). Vertices can also be individually ranked by their strength of association with high-weight vertices (Knode). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Spatial Analysis of Network Associations build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-santa", max_pin="x.x") }}' -# Suggests: BiocGenerics, BioNet, DLBCL, formatR, knitr, msm, org.Sc.sgd.db, markdown, rmarkdown, RUnit +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: BiocGenerics, BioNet, formatR, knitr, msm, org.Sc.sgd.db, markdown, rmarkdown, RUnit requirements: + build: + - {{ compiler('c') }} + - make host: - r-base - r-igraph @@ -30,16 +32,14 @@ requirements: - r-base - r-igraph - r-matrix - build: - - {{ compiler('c') }} - - make +source: + md5: 837afa9960831d36373b4b82d3443ebc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Spatial Analysis of Network Associations' - description: 'This package provides methods for measuring the strength of association between a network and a phenotype. It does this by measuring clustering of the phenotype across the network (Knet). Vertices can also be individually ranked by their strength of association with high-weight vertices (Knode).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sarc/meta.yaml b/recipes/bioconductor-sarc/meta.yaml index 168d1508d39d2..ede3d08d69b43 100644 --- a/recipes/bioconductor-sarc/meta.yaml +++ b/recipes/bioconductor-sarc/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "SARC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Imports a cov/coverage file (normalised read coverages from BAM files) and a cnv file (list of CNVs - similiar to a BED file) from WES/ WGS CNV (copy number variation) detection pipelines and utilises several metrics to weigh the likelihood of a sample containing a detected CNV being a true CNV or a false positive. Highly useful for diagnostic testing to filter out false positives to provide clinicians with fewer variants to interpret. SARC uniquely only used cov and csv (similiar to BED file) files which are the common CNV pipeline calling filetypes, and can be used as to supplement the Interactive Genome Browser (IGV) to generate many figures automatedly, which can be especially helpful in large cohorts with 100s-1000s of patients. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Statistical Analysis of Regions with CNVs -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b3ccd1bbc820bc93c4b13ec4e3ec9705 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sarc", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, kableExtra, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, Homo.sapiens, TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus, GenomicAlignments requirements: host: - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-raggedexperiment >=1.30.0,<1.31.0 - r-base - r-data.table - r-desctools @@ -41,12 +43,12 @@ requirements: - r-scales - r-tidyverse run: - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-plyranges >=1.22.0,<1.23.0' - - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-raggedexperiment >=1.30.0,<1.31.0 - r-base - r-data.table - r-desctools @@ -59,13 +61,16 @@ requirements: - r-reshape2 - r-scales - r-tidyverse + +source: + md5: e9da6decb3dcdfca23fcb7cef3cfe455 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Statistical Analysis of Regions with CNVs' - description: 'Imports a cov/coverage file (normalised read coverages from BAM files) and a cnv file (list of CNVs - similiar to a BED file) from WES/ WGS CNV (copy number variation) detection pipelines and utilises several metrics to weigh the likelihood of a sample containing a detected CNV being a true CNV or a false positive. Highly useful for diagnostic testing to filter out false positives to provide clinicians with fewer variants to interpret. SARC uniquely only used cov and csv (similiar to BED file) files which are the common CNV pipeline calling filetypes, and can be used as to supplement the Interactive Genome Browser (IGV) to generate many figures automatedly, which can be especially helpful in large cohorts with 100s-1000s of patients.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sarks/meta.yaml b/recipes/bioconductor-sarks/meta.yaml index 632d42d45814e..7b8d5e96921ca 100644 --- a/recipes/bioconductor-sarks/meta.yaml +++ b/recipes/bioconductor-sarks/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "sarks" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Suffix Array Kernel Smoothing (see https://academic.oup.com/bioinformatics/article-abstract/35/20/3944/5418797), or SArKS, identifies sequence motifs whose presence correlates with numeric scores (such as differential expression statistics) assigned to the sequences (such as gene promoters). SArKS smooths over sequence similarity, quantified by location within a suffix array based on the full set of input sequences. A second round of smoothing over spatial proximity within sequences reveals multi-motif domains. Discovered motifs can then be merged or extended based on adjacency within MMDs. False positive rates are estimated and controlled by permutation testing. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_3_clause + file LICENSE + license_file: LICENSE + summary: Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b6fc7553269237bea782582b858aaee5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sarks", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, ggplot2 # SystemRequirements: Java (>= 1.8) requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-binom - r-cluster - r-rjava - openjdk run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-binom - r-cluster - r-rjava - openjdk + +source: + md5: 52a4452437aa3323e71b492d069a99b5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_3_clause + file LICENSE' - summary: 'Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains' - description: 'Suffix Array Kernel Smoothing (see https://academic.oup.com/bioinformatics/article-abstract/35/20/3944/5418797), or SArKS, identifies sequence motifs whose presence correlates with numeric scores (such as differential expression statistics) assigned to the sequences (such as gene promoters). SArKS smooths over sequence similarity, quantified by location within a suffix array based on the full set of input sequences. A second round of smoothing over spatial proximity within sequences reveals multi-motif domains. Discovered motifs can then be merged or extended based on adjacency within MMDs. False positive rates are estimated and controlled by permutation testing.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-saser/build.sh b/recipes/bioconductor-saser/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-saser/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-saser/meta.yaml b/recipes/bioconductor-saser/meta.yaml new file mode 100644 index 0000000000000..4392b227b9f71 --- /dev/null +++ b/recipes/bioconductor-saser/meta.yaml @@ -0,0 +1,88 @@ +{% set version = "1.2.0" %} +{% set name = "saseR" %} +{% set bioc = "3.20" %} + +about: + description: 'saseR is a highly performant and fast framework for aberrant expression and splicing analyses. The main functions are: \itemize{ \item \code{\link{BamtoAspliCounts}} - Process BAM files to ASpli counts \item \code{\link{convertASpli}} - Get gene, bin or junction counts from ASpli SummarizedExperiment \item \code{\link{calculateOffsets}} - Create an offsets assays for aberrant expression or splicing analysis \item \code{\link{saseRfindEncodingDim}} - Estimate the optimal number of latent factors to include when estimating the mean expression \item \code{\link{saseRfit}} - Parameter estimation of the negative binomial distribution and compute p-values for aberrant expression and splicing } For information upon how to use these functions, check out our vignette at \url{https://github.com/statOmics/saseR/blob/main/vignettes/Vignette.Rmd} and the saseR paper: Segers, A. et al. (2023). Juggling offsets unlocks RNA-seq tools for fast scalable differential usage, aberrant splicing and expression analyses. bioRxiv. \url{https://doi.org/10.1101/2023.06.29.547014}.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Scalable Aberrant Splicing and Expression Retrieval + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-saser", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + + host: + - bioconductor-aspli >=2.16.0,<2.17.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-dexseq >=1.52.0,<1.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-data.table + - r-dplyr + - r-igraph + - r-knitr + - r-mass + - r-pracma + - r-precrec + - r-prroc + - r-rrcov + + run: + - bioconductor-aspli >=2.16.0,<2.17.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-dexseq >=1.52.0,<1.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-data.table + - r-dplyr + - r-igraph + - r-knitr + - r-mass + - r-pracma + - r-precrec + - r-prroc + - r-rrcov + +source: + md5: dcb28a0f27d7666b286394f28a1e2a71 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-saturn/meta.yaml b/recipes/bioconductor-saturn/meta.yaml index 56ea686073d4f..d64c68fce9e8b 100644 --- a/recipes/bioconductor-saturn/meta.yaml +++ b/recipes/bioconductor-saturn/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "satuRn" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: satuRn provides a higly performant and scalable framework for performing differential transcript usage analyses. The package consists of three main functions. The first function, fitDTU, fits quasi-binomial generalized linear models that model transcript usage in different groups of interest. The second function, testDTU, tests for differential usage of transcripts between groups of interest. Finally, plotDTU visualizes the usage profiles of transcripts in groups of interest. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a0826944ab0aee6ff42127fa7eebf43c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-saturn", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub, ensembldb, edgeR, DEXSeq, stageR, DelayedArray requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-boot - r-ggplot2 @@ -32,21 +33,25 @@ requirements: - r-matrix - r-pbapply run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-boot - r-ggplot2 - r-locfdr - r-matrix - r-pbapply + +source: + md5: 4be609ec2dd806f2e876cec9693cad2b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications' - description: 'satuRn provides a higly performant and scalable framework for performing differential transcript usage analyses. The package consists of three main functions. The first function, fitDTU, fits quasi-binomial generalized linear models that model transcript usage in different groups of interest. The second function, testDTU, tests for differential usage of transcripts between groups of interest. Finally, plotDTU visualizes the usage profiles of transcripts in groups of interest.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-saureuscdf/meta.yaml b/recipes/bioconductor-saureuscdf/meta.yaml index 63b9008ca29cf..61bee2fdad170 100644 --- a/recipes/bioconductor-saureuscdf/meta.yaml +++ b/recipes/bioconductor-saureuscdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "saureuscdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d01883e4c3dd99f32012e6dbab8cdb8b +about: + description: A package containing an environment representing the S_aureus.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: saureuscdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-saureuscdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d01883e4c3dd99f32012e6dbab8cdb8b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: saureuscdf - description: 'A package containing an environment representing the S_aureus.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-saureusprobe/meta.yaml b/recipes/bioconductor-saureusprobe/meta.yaml index 7346b9ecb2da6..08bf58d0f3866 100644 --- a/recipes/bioconductor-saureusprobe/meta.yaml +++ b/recipes/bioconductor-saureusprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "saureusprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eb4e91b10a536cbde4ecc08951ddf4d3 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was S\_aureus\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type saureus build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-saureusprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: eb4e91b10a536cbde4ecc08951ddf4d3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type saureus' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was S\_aureus\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sbgnview.data/meta.yaml b/recipes/bioconductor-sbgnview.data/meta.yaml index aba842e7df3b8..a47e0abf463f5 100644 --- a/recipes/bioconductor-sbgnview.data/meta.yaml +++ b/recipes/bioconductor-sbgnview.data/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "SBGNview.data" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7e1bce0dfbc48b3cdc023d88e2ea7d9a +about: + description: 'This package contains: 1. A microarray gene expression dataset from a human breast cancer study. 2. A RNA-Seq gene expression dataset from a mouse study on IFNG knockout. 3. ID mapping tables between gene IDs and SBGN-ML file glyph IDs. 4. Percent of orthologs detected in other species of the genes in a pathway. Cutoffs of this percentage for defining if a pathway exists in another species. 5. XML text of SBGN-ML files for all pre-collected pathways.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: AGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + summary: Supporting datasets for SBGNview package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sbgnview.data", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: SummarizedExperiment requirements: host: @@ -32,14 +31,15 @@ requirements: - r-knitr - r-rmarkdown - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bccffd0ac4bad51dd8d5d2f78b4a84a0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: AGPL-3 - summary: 'Supporting datasets for SBGNview package' - description: 'This package contains: 1. A microarray gene expression dataset from a human breast cancer study. 2. A RNA-Seq gene expression dataset from a mouse study on IFNG knockout. 3. ID mapping tables between gene IDs and SBGN-ML file glyph IDs. 4. Percent of orthologs detected in other species of the genes in a pathway. Cutoffs of this percentage for defining if a pathway exists in another species. 5. XML text of SBGN-ML files for all pre-collected pathways.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sbgnview.data/post-link.sh b/recipes/bioconductor-sbgnview.data/post-link.sh index b736f2bdd3bfd..0049230e3c380 100644 --- a/recipes/bioconductor-sbgnview.data/post-link.sh +++ b/recipes/bioconductor-sbgnview.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "sbgnview.data-1.16.0" +installBiocDataPackage.sh "sbgnview.data-1.20.0" diff --git a/recipes/bioconductor-sbgnview/meta.yaml b/recipes/bioconductor-sbgnview/meta.yaml index 8c50f540bbd86..30fce8cb2202a 100644 --- a/recipes/bioconductor-sbgnview/meta.yaml +++ b/recipes/bioconductor-sbgnview/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "SBGNview" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'SBGNview is a tool set for pathway based data visalization, integration and analysis. SBGNview is similar and complementary to the widely used Pathview, with the following key features: 1. Pathway definition by the widely adopted Systems Biology Graphical Notation (SBGN); 2. Supports multiple major pathway databases beyond KEGG (Reactome, MetaCyc, SMPDB, PANTHER, METACROP) and user defined pathways; 3. Covers 5,200 reference pathways and over 3,000 species by default; 4. Extensive graphics controls, including glyph and edge attributes, graph layout and sub-pathway highlight; 5. SBGN pathway data manipulation, processing, extraction and analysis.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + summary: '"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 785b51f08ce7b40f23b6e9168ce1d1af build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sbgnview", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, gage requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-pathview >=1.42.0,<1.43.0' - - 'bioconductor-sbgnview.data >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-pathview >=1.46.0,<1.47.0 + - bioconductor-sbgnview.data >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bookdown - r-httr @@ -37,11 +39,11 @@ requirements: - r-rsvg - r-xml2 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-pathview >=1.42.0,<1.43.0' - - 'bioconductor-sbgnview.data >=1.16.0,<1.17.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-pathview >=1.46.0,<1.47.0 + - bioconductor-sbgnview.data >=1.20.0,<1.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bookdown - r-httr @@ -51,13 +53,16 @@ requirements: - r-rmarkdown - r-rsvg - r-xml2 + +source: + md5: 254ed7863707573c5be6b8138351aef0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3 - summary: '"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"' - description: 'SBGNview is a tool set for pathway based data visalization, integration and analysis. SBGNview is similar and complementary to the widely used Pathview, with the following key features: 1. Pathway definition by the widely adopted Systems Biology Graphical Notation (SBGN); 2. Supports multiple major pathway databases beyond KEGG (Reactome, MetaCyc, SMPDB, PANTHER, METACROP) and user defined pathways; 3. Covers 5,200 reference pathways and over 3,000 species by default; 4. Extensive graphics controls, including glyph and edge attributes, graph layout and sub-pathway highlight; 5. SBGN pathway data manipulation, processing, extraction and analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sbmlr/meta.yaml b/recipes/bioconductor-sbmlr/meta.yaml index 2c7a8f8515985..df0e308a1d2fe 100644 --- a/recipes/bioconductor-sbmlr/meta.yaml +++ b/recipes/bioconductor-sbmlr/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.98.0" %} +{% set version = "2.2.0" %} {% set name = "SBMLR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 36433007d11730737942753523a9d91e +about: + description: This package contains a systems biology markup language (SBML) interface to R. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: SBML-R Interface and Analysis Tools build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sbmlr", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: rsbml requirements: host: @@ -29,13 +28,14 @@ requirements: - r-base - r-desolve - r-xml +source: + md5: 46faae1fb0b5e49168f88e8cb67ab6b0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'SBML-R Interface and Analysis Tools' - description: 'This package contains a systems biology markup language (SBML) interface to R.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sc3/meta.yaml b/recipes/bioconductor-sc3/meta.yaml index 87691107738fc..2d09d42764a76 100644 --- a/recipes/bioconductor-sc3/meta.yaml +++ b/recipes/bioconductor-sc3/meta.yaml @@ -1,30 +1,46 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "SC3" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A tool for unsupervised clustering and analysis of single cell RNA-Seq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Single-Cell Consensus Clustering -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c61e14eaf22ab5535ff11763d97e8c96 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sc3", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:sc3 + parent_recipe: + name: bioconductor-sc3 + path: recipes/bioconductor-sc3 + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, mclust, scater, BiocStyle requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-doparallel @@ -32,8 +48,8 @@ requirements: - r-e1071 - r-foreach - r-ggplot2 - - 'r-pheatmap >=1.0.8' - - 'r-rcpp >=0.11.1' + - r-pheatmap >=1.0.8 + - r-rcpp >=0.11.1 - r-rcpparmadillo - r-robustbase - r-rocr @@ -42,11 +58,12 @@ requirements: - r-writexls - libblas - liblapack + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-doparallel @@ -54,32 +71,24 @@ requirements: - r-e1071 - r-foreach - r-ggplot2 - - 'r-pheatmap >=1.0.8' - - 'r-rcpp >=0.11.1' + - r-pheatmap >=1.0.8 + - r-rcpp >=0.11.1 - r-rcpparmadillo - r-robustbase - r-rocr - r-rrcov - r-shiny - r-writexls - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 3608b0bf7724f32238239d885aa89a7d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Single-Cell Consensus Clustering' - description: 'A tool for unsupervised clustering and analysis of single cell RNA-Seq data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:sc3 - parent_recipe: - name: bioconductor-sc3 - path: recipes/bioconductor-sc3 - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scale4c/meta.yaml b/recipes/bioconductor-scale4c/meta.yaml index 114860f5f9880..1fbffb8a3ab3b 100644 --- a/recipes/bioconductor-scale4c/meta.yaml +++ b/recipes/bioconductor-scale4c/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "Scale4C" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7897932085759a05ad185eaec2afcd13 +about: + description: Scale4C is an R/Bioconductor package for scale-space transformation and visualization of 4C-seq data. The scale-space transformation is a multi-scale visualization technique to transform a 2D signal (e.g. 4C-seq reads on a genomic interval of choice) into a tesselation in the scale space (2D, genomic position x scale factor) by applying different smoothing kernels (Gauss, with increasing sigma). This transformation allows for explorative analysis and comparisons of the data's structure with other samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: 'Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scale4c", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-smoothie run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-smoothie +source: + md5: bcd8fcbb9e81f09cd4af4796cd6ba56a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data' - description: 'Scale4C is an R/Bioconductor package for scale-space transformation and visualization of 4C-seq data. The scale-space transformation is a multi-scale visualization technique to transform a 2D signal (e.g. 4C-seq reads on a genomic interval of choice) into a tesselation in the scale space (2D, genomic position x scale factor) by applying different smoothing kernels (Gauss, with increasing sigma). This transformation allows for explorative analysis and comparisons of the data''s structure with other samples.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scaledmatrix/meta.yaml b/recipes/bioconductor-scaledmatrix/meta.yaml index 2c06205107872..283f2e4887e68 100644 --- a/recipes/bioconductor-scaledmatrix/meta.yaml +++ b/recipes/bioconductor-scaledmatrix/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "ScaledMatrix" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 337f2af494241ac5def9fcae4dc12313 +about: + description: Provides delayed computation of a matrix of scaled and centered values. The result is equivalent to using the scale() function but avoids explicit realization of a dense matrix during block processing. This permits greater efficiency in common operations, most notably matrix multiplication. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Creating a DelayedMatrix of Scaled and Centered Values build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scaledmatrix", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular, DelayedMatrixStats requirements: host: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-matrix run: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-matrix +source: + md5: 763b5e7b3c5a90238ee676a2d1f9c7e0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Creating a DelayedMatrix of Scaled and Centered Values' - description: 'Provides delayed computation of a matrix of scaled and centered values. The result is equivalent to using the scale() function but avoids explicit realization of a dense matrix during block processing. This permits greater efficiency in common operations, most notably matrix multiplication.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scan.upc/meta.yaml b/recipes/bioconductor-scan.upc/meta.yaml index bc6fddb7ec4c6..875c992a5a57d 100644 --- a/recipes/bioconductor-scan.upc/meta.yaml +++ b/recipes/bioconductor-scan.upc/meta.yaml @@ -1,63 +1,69 @@ -{% set version = "2.44.0" %} +{% set version = "2.48.0" %} {% set name = "SCAN.UPC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SCAN is a microarray normalization method to facilitate personalized-medicine workflows. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The Universal exPression Codes (UPC) method is an extension of SCAN that estimates whether a given gene/transcript is active above background levels in a given sample. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + summary: Single-channel array normalization (SCAN) and Universal exPression Codes (UPC) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9da1b69c833d18db111112370bfe15ae build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scan.upc", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:scan.upc + parent_recipe: + name: bioconductor-scan.upc + path: recipes/bioconductor-scan.upc + version: 2.24.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: pd.hg.u95a requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-foreach - r-mass run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-affyio >=1.72.0,<1.73.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-geoquery >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-oligo >=1.66.0,<1.67.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-affyio >=1.76.0,<1.77.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-geoquery >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-oligo >=1.70.0,<1.71.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-foreach - r-mass + +source: + md5: 403a8b5b1d552f3d65597f0cd10975c4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: MIT - summary: 'Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)' - description: 'SCAN is a microarray normalization method to facilitate personalized-medicine workflows. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The Universal exPression Codes (UPC) method is an extension of SCAN that estimates whether a given gene/transcript is active above background levels in a given sample. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration.' -extra: - identifiers: - - biotools:scan.upc - parent_recipe: - name: bioconductor-scan.upc - path: recipes/bioconductor-scan.upc - version: 2.24.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scanmir/meta.yaml b/recipes/bioconductor-scanmir/meta.yaml index 97c1cf26883e9..86e692359aae4 100644 --- a/recipes/bioconductor-scanmir/meta.yaml +++ b/recipes/bioconductor-scanmir/meta.yaml @@ -1,59 +1,66 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "scanMiR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3' alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: scanMiR -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a08199f29933bb3b0d1e9336b1b46a76 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scanmir", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqlogo >=1.72.0,<1.73.0 - r-base - r-cowplot - r-data.table - r-ggplot2 - - r-ggseqlogo - r-stringi run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqlogo >=1.72.0,<1.73.0 - r-base - r-cowplot - r-data.table - r-ggplot2 - - r-ggseqlogo - r-stringi + +source: + md5: 0462c08dd1520af82e09351a0605a521 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: scanMiR - description: 'A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3'' alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scanmirapp/meta.yaml b/recipes/bioconductor-scanmirapp/meta.yaml index 247186ca2ad89..2adac16167936 100644 --- a/recipes/bioconductor-scanmirapp/meta.yaml +++ b/recipes/bioconductor-scanmirapp/meta.yaml @@ -1,41 +1,45 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "scanMiRApp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A shiny interface to the scanMiR package. The application enables the scanning of transcripts and custom sequences for miRNA binding sites, the visualization of KdModels and binding results, as well as browsing predicted repression data. In addition contains the IndexedFst class for fast indexed reading of large GenomicRanges or data.frames, and some utilities for facilitating scans and identifying enriched miRNA-target pairs. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: scanMiR shiny application -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 637ec69edde646093548d190325738fe build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scanmirapp", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn6 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Rnorvegicus.UCSC.rn6 requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scanmir >=1.8.0,<1.9.0' - - 'bioconductor-scanmirdata >=1.8.0,<1.9.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scanmir >=1.12.0,<1.13.0 + - bioconductor-scanmirdata >=1.12.0,<1.13.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-data.table - r-digest @@ -51,21 +55,23 @@ requirements: - r-shinydashboard - r-shinyjqui - r-waiter + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scanmir >=1.8.0,<1.9.0' - - 'bioconductor-scanmirdata >=1.8.0,<1.9.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scanmir >=1.12.0,<1.13.0 + - bioconductor-scanmirdata >=1.12.0,<1.13.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-data.table - r-digest @@ -81,13 +87,16 @@ requirements: - r-shinydashboard - r-shinyjqui - r-waiter + +source: + md5: 737b7abc0ac7def7215de0f2b99e7365 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'scanMiR shiny application' - description: 'A shiny interface to the scanMiR package. The application enables the scanning of transcripts and custom sequences for miRNA binding sites, the visualization of KdModels and binding results, as well as browsing predicted repression data. In addition contains the IndexedFst class for fast indexed reading of large GenomicRanges or data.frames, and some utilities for facilitating scans and identifying enriched miRNA-target pairs.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scanmirdata/meta.yaml b/recipes/bioconductor-scanmirdata/meta.yaml index 0deef63b6ab5b..27e88e24441d1 100644 --- a/recipes/bioconductor-scanmirdata/meta.yaml +++ b/recipes/bioconductor-scanmirdata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "scanMiRData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4c717492a3c85bbcf199873e35190219 +about: + description: This package contains companion data to the scanMiR package. It contains `KdModel` (miRNA 12-mer binding affinity models) collections corresponding to all human, mouse and rat mirbase miRNAs. See the scanMiR package for details. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: miRNA Affinity models for the scanMiR package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scanmirdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-scanmir >=1.8.0,<1.9.0' + - bioconductor-scanmir >=1.12.0,<1.13.0 - r-base run: - - 'bioconductor-scanmir >=1.8.0,<1.9.0' + - bioconductor-scanmir >=1.12.0,<1.13.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b003e73d86828d212a916bba13912ca6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'miRNA Affinity models for the scanMiR package' - description: 'This package contains companion data to the scanMiR package. It contains `KdModel` (miRNA 12-mer binding affinity models) collections corresponding to all human, mouse and rat mirbase miRNAs. See the scanMiR package for details.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scanmirdata/post-link.sh b/recipes/bioconductor-scanmirdata/post-link.sh index 38be41e8fc92c..68cb181008f94 100644 --- a/recipes/bioconductor-scanmirdata/post-link.sh +++ b/recipes/bioconductor-scanmirdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "scanmirdata-1.8.0" +installBiocDataPackage.sh "scanmirdata-1.12.0" diff --git a/recipes/bioconductor-scannotatr.models/meta.yaml b/recipes/bioconductor-scannotatr.models/meta.yaml index 6f96a2629007b..5e858aa84dfd9 100644 --- a/recipes/bioconductor-scannotatr.models/meta.yaml +++ b/recipes/bioconductor-scannotatr.models/meta.yaml @@ -1,24 +1,23 @@ {% set version = "0.99.10" %} {% set name = "scAnnotatR.models" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 77c6e16382645164d6413356c5ab52c5 +about: + description: Pretrained models for scAnnotatR package. These models can be used to automatically classify several (immune) cell types in human scRNA-seq data. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Pretrained models for scAnnotatR package build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scannotatr.models", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: scAnnotatR, knitr requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 77c6e16382645164d6413356c5ab52c5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Pretrained models for scAnnotatR package' - description: 'Pretrained models for scAnnotatR package. These models can be used to automatically classify several (immune) cell types in human scRNA-seq data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scannotatr/meta.yaml b/recipes/bioconductor-scannotatr/meta.yaml index cf184bb7c972c..ffe2d094eef11 100644 --- a/recipes/bioconductor-scannotatr/meta.yaml +++ b/recipes/bioconductor-scannotatr/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "scAnnotatR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package comprises a set of pretrained machine learning models to predict basic immune cell types. This enables all users to quickly get a first annotation of the cell types present in their dataset without requiring prior knowledge. scAnnotatR also allows users to train their own models to predict new cell types based on specific research needs. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Pretrained learning models for cell type prediction on single cell RNA-sequencing data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5474e416000bda50dc8273a09b41a54b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scannotatr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, scRNAseq, testthat requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-ape - r-base - r-caret @@ -37,9 +39,9 @@ requirements: - r-rocr - r-seurat run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-ape - r-base - r-caret @@ -51,13 +53,16 @@ requirements: - r-proc - r-rocr - r-seurat + +source: + md5: 3bd5234a9ccd7f826dde33664c488b87 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Pretrained learning models for cell type prediction on single cell RNA-sequencing data' - description: 'The package comprises a set of pretrained machine learning models to predict basic immune cell types. This enables all users to quickly get a first annotation of the cell types present in their dataset without requiring prior knowledge. scAnnotatR also allows users to train their own models to predict new cell types based on specific research needs.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scanvis/meta.yaml b/recipes/bioconductor-scanvis/meta.yaml index 507c7fb6aedb7..24727d025ae3a 100644 --- a/recipes/bioconductor-scanvis/meta.yaml +++ b/recipes/bioconductor-scanvis/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "SCANVIS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 36977f903eb019d8171d60519360cd9e +about: + description: SCANVIS is a set of annotation-dependent tools for analyzing splice junctions and their read support as predetermined by an alignment tool of choice (for example, STAR aligner). SCANVIS assesses each junction's relative read support (RRS) by relating to the context of local split reads aligning to annotated transcripts. SCANVIS also annotates each splice junction by indicating whether the junction is supported by annotation or not, and if not, what type of junction it is (e.g. exon skipping, alternative 5' or 3' events, Novel Exons). Unannotated junctions are also futher annotated by indicating whether it induces a frame shift or not. SCANVIS includes a visualization function to generate static sashimi-style plots depicting relative read support and number of split reads using arc thickness and arc heights, making it easy for users to spot well-supported junctions. These plots also clearly delineate unannotated junctions from annotated ones using designated color schemes, and users can also highlight splice junctions of choice. Variants and/or a read profile are also incoroporated into the plot if the user supplies variants in bed format and/or the BAM file. One further feature of the visualization function is that users can submit multiple samples of a certain disease or cohort to generate a single plot - this occurs via a "merge" function wherein junction details over multiple samples are merged to generate a single sashimi plot, which is useful when contrasting cohorots (eg. disease vs control). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scanvis", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-plotrix - r-rcurl run: - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-plotrix - r-rcurl +source: + md5: 8aae61c0614d456037d68f12b87be219 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions' - description: 'SCANVIS is a set of annotation-dependent tools for analyzing splice junctions and their read support as predetermined by an alignment tool of choice (for example, STAR aligner). SCANVIS assesses each junction''s relative read support (RRS) by relating to the context of local split reads aligning to annotated transcripts. SCANVIS also annotates each splice junction by indicating whether the junction is supported by annotation or not, and if not, what type of junction it is (e.g. exon skipping, alternative 5'' or 3'' events, Novel Exons). Unannotated junctions are also futher annotated by indicating whether it induces a frame shift or not. SCANVIS includes a visualization function to generate static sashimi-style plots depicting relative read support and number of split reads using arc thickness and arc heights, making it easy for users to spot well-supported junctions. These plots also clearly delineate unannotated junctions from annotated ones using designated color schemes, and users can also highlight splice junctions of choice. Variants and/or a read profile are also incoroporated into the plot if the user supplies variants in bed format and/or the BAM file. One further feature of the visualization function is that users can submit multiple samples of a certain disease or cohort to generate a single plot - this occurs via a "merge" function wherein junction details over multiple samples are merged to generate a single sashimi plot, which is useful when contrasting cohorots (eg. disease vs control).' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scarray.sat/meta.yaml b/recipes/bioconductor-scarray.sat/meta.yaml index b1f611aef2382..c1c24946f45d8 100644 --- a/recipes/bioconductor-scarray.sat/meta.yaml +++ b/recipes/bioconductor-scarray.sat/meta.yaml @@ -1,57 +1,64 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "SCArray.sat" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Extends the Seurat classes and functions to support Genomic Data Structure (GDS) files as a DelayedArray backend for data representation. It relies on the implementation of GDS-based DelayedMatrix in the SCArray package to represent single cell RNA-seq data. The common optimized algorithms leveraging GDS-based and single cell-specific DelayedMatrix (SC_GDSMatrix) are implemented in the SCArray package. SCArray.sat introduces a new SCArrayAssay class (derived from the Seurat Assay), which wraps raw counts, normalized expressions and scaled data matrix based on GDS-specific DelayedMatrix. It is designed to integrate seamlessly with the Seurat package to provide common data analysis in the SeuratObject-based workflow. Compared with Seurat, SCArray.sat significantly reduces the memory usage without downsampling and can be applied to very large datasets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Large-scale single-cell RNA-seq data analysis using GDS files and Seurat -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: da0366cd6f3cc83e7acc0a45bf2d2389 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scarray.sat", max_pin="x.x") }}' - noarch: generic -# Suggests: RUnit, knitr, markdown, rmarkdown, BiocStyle + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: future, RUnit, knitr, markdown, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scarray >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scarray >=1.14.0,<1.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-seurat >=4.0' - - 'r-seuratobject >=4.0' + - r-matrix + - r-seurat >=5.0 + - r-seuratobject >=5.0 run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scarray >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scarray >=1.14.0,<1.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-seurat >=4.0' - - 'r-seuratobject >=4.0' + - r-matrix + - r-seurat >=5.0 + - r-seuratobject >=5.0 + +source: + md5: a4fd7f15216b7396071b90d9cfb3b91b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Large-scale single-cell RNA-seq data analysis using GDS files and Seurat' - description: 'Extends the Seurat classes and functions to support Genomic Data Structure (GDS) files as a DelayedArray backend for data representation. It relies on the implementation of GDS-based DelayedMatrix in the SCArray package to represent single cell RNA-seq data. The common optimized algorithms leveraging GDS-based and single cell-specific DelayedMatrix (SC_GDSMatrix) are implemented in the SCArray package. SCArray.sat introduces a new SCArrayAssay class (derived from the Seurat Assay), which wraps raw counts, normalized expressions and scaled data matrix based on GDS-specific DelayedMatrix. It is designed to integrate seamlessly with the Seurat package to provide common data analysis in the SeuratObject-based workflow. Compared with Seurat, SCArray.sat significantly reduces the memory usage without downsampling and can be applied to very large datasets.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scarray/meta.yaml b/recipes/bioconductor-scarray/meta.yaml index 2253c7eb3d251..64270ba8efced 100644 --- a/recipes/bioconductor-scarray/meta.yaml +++ b/recipes/bioconductor-scarray/meta.yaml @@ -1,60 +1,67 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "SCArray" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides large-scale single-cell omics data manipulation using Genomic Data Structure (GDS) files. It combines dense and sparse matrices stored in GDS files and the Bioconductor infrastructure framework (SingleCellExperiment and DelayedArray) to provide out-of-memory data storage and large-scale manipulation using the R programming language. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Large-scale single-cell omics data manipulation with GDS files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c777bd1f1f52dd055b83830ed6da1f77 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scarray", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, scater, scuttle, uwot, RUnit, knitr, markdown, rmarkdown, rhdf5, HDF5Array requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 1b7148e404ab5f3820f470daf18b2e82 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Large-scale single-cell RNA-seq data manipulation with GDS files' - description: 'Provides large-scale single-cell RNA-seq data manipulation using Genomic Data Structure (GDS) files. It combines dense and sparse matrices stored in GDS files and the Bioconductor infrastructure framework (SingleCellExperiment and DelayedArray) to provide out-of-memory data storage and large-scale manipulation using the R programming language.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scatac.explorer/meta.yaml b/recipes/bioconductor-scatac.explorer/meta.yaml index dc04d869c90f5..1da68001bdc8b 100644 --- a/recipes/bioconductor-scatac.explorer/meta.yaml +++ b/recipes/bioconductor-scatac.explorer/meta.yaml @@ -1,48 +1,55 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.1" %} {% set name = "scATAC.Explorer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a tool to search and download a collection of publicly available single cell ATAC-seq datasets and their metadata. scATAC-Explorer aims to act as a single point of entry for users looking to study single cell ATAC-seq data. Users can quickly search available datasets using the metadata table and download datasets of interest for immediate analysis within R. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: A Collection of Single-cell ATAC Sequencing Datasets and Corresponding Metadata -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 80927899a83bb06d19b0f9800c183b36 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scatac.explorer", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-zellkonverter >=1.16.0,<1.17.0 - r-base - r-data.table - r-matrix run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-zellkonverter >=1.16.0,<1.17.0 - r-base - r-data.table - r-matrix - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20250104 + +source: + md5: e031fee987eb77af3299313b5a5f391b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A Collection of Single-cell ATAC Sequencing Datasets and Corresponding Metadata' - description: 'This package provides a tool to search and download a collection of publicly available single cell ATAC-seq datasets and their metadata. scATAC-Explorer aims to act as a single point of entry for users looking to study single cell ATAC-seq data. Users can quickly search available datasets using the metadata table and download datasets of interest for immediate analysis within R.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scatac.explorer/post-link.sh b/recipes/bioconductor-scatac.explorer/post-link.sh index e9ece7245fbbd..a8bb4e3c5d0e5 100644 --- a/recipes/bioconductor-scatac.explorer/post-link.sh +++ b/recipes/bioconductor-scatac.explorer/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "scatac.explorer-1.8.0" +installBiocDataPackage.sh "scatac.explorer-1.12.1" diff --git a/recipes/bioconductor-scater/meta.yaml b/recipes/bioconductor-scater/meta.yaml index 06196151e19c6..66aea8a5e9e1c 100644 --- a/recipes/bioconductor-scater/meta.yaml +++ b/recipes/bioconductor-scater/meta.yaml @@ -1,38 +1,50 @@ -{% set version = "1.30.1" %} +{% set version = "1.34.0" %} {% set name = "scater" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Single-Cell Analysis Toolkit for Gene Expression Data in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c161043392323318c01792e2de828ad5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scater", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, snifter, densvis, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore + +extra: + identifiers: + - biotools:scater + parent_recipe: + name: bioconductor-scater + path: recipes/bioconductor-scater + version: 1.8.4 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, DelayedMatrixStats, snifter, densvis, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore requirements: + host: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggbeeswarm - r-ggplot2 @@ -46,18 +58,20 @@ requirements: - r-rtsne - r-uwot - r-viridis + run: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggbeeswarm - r-ggplot2 @@ -71,20 +85,16 @@ requirements: - r-rtsne - r-uwot - r-viridis + +source: + md5: a9ee792d78c5f066f05a90247cd1aa6a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Single-Cell Analysis Toolkit for Gene Expression Data in R' - description: 'A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:scater - parent_recipe: - name: bioconductor-scater - path: recipes/bioconductor-scater - version: 1.8.4 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scatterhatch/meta.yaml b/recipes/bioconductor-scatterhatch/meta.yaml index 7d4048dd2cdaa..1561de4000a64 100644 --- a/recipes/bioconductor-scatterhatch/meta.yaml +++ b/recipes/bioconductor-scatterhatch/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "scatterHatch" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d86cfd4fa0820f65efd6085edc997eed +about: + description: The objective of this package is to efficiently create scatterplots where groups can be distinguished by color and texture. Visualizations in computational biology tend to have many groups making it difficult to distinguish between groups solely on color. Thus, this package is useful for increasing the accessibility of scatterplot visualizations to those with visual impairments such as color blindness. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Creates hatched patterns for scatterplots build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scatterhatch", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, testthat requirements: host: @@ -31,13 +30,14 @@ requirements: - r-ggplot2 - r-plyr - r-spatstat.geom +source: + md5: 082ffb512455bf34b7c607c584399074 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Creates hatched patterns for scatterplots' - description: 'The objective of this package is to efficiently create scatterplots where groups can be distinguished by color and texture. Visualizations in computational biology tend to have many groups making it difficult to distinguish between groups solely on color. Thus, this package is useful for increasing the accessibility of scatterplot visualizations to those with visual impairments such as color blindness.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scbfa/meta.yaml b/recipes/bioconductor-scbfa/meta.yaml index 9ab87c6d31b44..3ddd5da07c208 100644 --- a/recipes/bioconductor-scbfa/meta.yaml +++ b/recipes/bioconductor-scbfa/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "scBFA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is designed to model gene detection pattern of scRNA-seq through a binary factor analysis model. This model allows user to pass into a cell level covariate matrix X and gene level covariate matrix Q to account for nuisance variance(e.g batch effect), and it will output a low dimensional embedding matrix for downstream analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7729a460da97e96d4da3957b959149db build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scbfa", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, Rtsne requirements: host: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zinbwave >=1.24.0,<1.25.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zinbwave >=1.28.0,<1.29.0 - r-base - r-copula - r-ggplot2 @@ -33,23 +35,26 @@ requirements: - r-matrix - r-seurat run: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zinbwave >=1.24.0,<1.25.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zinbwave >=1.28.0,<1.29.0 - r-base - r-copula - r-ggplot2 - r-mass - r-matrix - r-seurat + +source: + md5: d8da099c3fe5f619b2b834eb458c14be + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq' - description: 'This package is designed to model gene detection pattern of scRNA-seq through a binary factor analysis model. This model allows user to pass into a cell level covariate matrix X and gene level covariate matrix Q to account for nuisance variance(e.g batch effect), and it will output a low dimensional embedding matrix for downstream analysis.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scbn/meta.yaml b/recipes/bioconductor-scbn/meta.yaml index 7da3092848b1b..49c31163a9ae1 100644 --- a/recipes/bioconductor-scbn/meta.yaml +++ b/recipes/bioconductor-scbn/meta.yaml @@ -1,37 +1,37 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "SCBN" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c58ee707d9418bd3374773e2675efad7 +about: + description: This package provides a scale based normalization (SCBN) method to identify genes with differential expression between different species. It takes into account the available knowledge of conserved orthologous genes and the hypothesis testing framework to detect differentially expressed orthologous genes. The method on this package are described in the article 'A statistical normalization method and differential expression analysis for RNA-seq data between different species' by Yan Zhou, Jiadi Zhu, Tiejun Tong, Junhui Wang, Bingqing Lin, Jun Zhang (2018, pending publication). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A statistical normalization method and differential expression analysis for RNA-seq data between different species build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scbn", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr,rmarkdown,BiocStyle,BiocManager requirements: host: - r-base run: - r-base +source: + md5: 091087bd3f6adc46eb6cd1ee2ab425c2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'A statistical normalization method and differential expression analysis for RNA-seq data between different species' - description: 'This package provides a scale based normalization (SCBN) method to identify genes with differential expression between different species. It takes into account the available knowledge of conserved orthologous genes and the hypothesis testing framework to detect differentially expressed orthologous genes. The method on this package are described in the article ''A statistical normalization method and differential expression analysis for RNA-seq data between different species'' by Yan Zhou, Jiadi Zhu, Tiejun Tong, Junhui Wang, Bingqing Lin, Jun Zhang (2018, pending publication).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scbubbletree/meta.yaml b/recipes/bioconductor-scbubbletree/meta.yaml index 785fc8a629766..a7b9c9a65d274 100644 --- a/recipes/bioconductor-scbubbletree/meta.yaml +++ b/recipes/bioconductor-scbubbletree/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "scBubbletree" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: scBubbletree is a quantitative method for the visual exploration of scRNA-seq data, preserving key biological properties such as local and global cell distances and cell density distributions across samples. It effectively resolves overplotting and enables the visualization of diverse cell attributes from multiomic single-cell experiments. Additionally, scBubbletree is user-friendly and integrates seamlessly with popular scRNA-seq analysis tools, facilitating comprehensive and intuitive data interpretation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Quantitative visual exploration of scRNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d64f38622d8aec6ebb23e81231710134 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scbubbletree", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, testthat, cluster, SingleCellExperiment # SystemRequirements: Python (>= 3.6), leidenalg (>= 0.8.2) requirements: host: - - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 - r-ape - r-base - - r-future - - r-future.apply + - r-dplyr - r-ggplot2 - r-patchwork - r-proxy @@ -35,24 +37,27 @@ requirements: - r-scales - r-seurat run: - - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 - r-ape - r-base - - r-future - - r-future.apply + - r-dplyr - r-ggplot2 - r-patchwork - r-proxy - r-reshape2 - r-scales - r-seurat + +source: + md5: 7dc4b512d5cdce8a4ca12cb8b10c352e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Quantitative visual exploration of scRNA-seq data' - description: 'scBubbletree is a quantitative method for visual exploration of scRNA-seq data. It preserves biologically meaningful properties of scRNA-seq data, such as local and global cell distances, as well as the density distribution of cells across the sample. scBubbletree is scalable and avoids the overplotting problem, and is able to visualize diverse cell attributes derived from multiomic single-cell experiments. Importantly, Importantly, scBubbletree is easy to use and to integrate with popular approaches for scRNA-seq data analysis.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sccb2/meta.yaml b/recipes/bioconductor-sccb2/meta.yaml index 50528ac515db8..f82e402d4f954 100644 --- a/recipes/bioconductor-sccb2/meta.yaml +++ b/recipes/bioconductor-sccb2/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "scCB2" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: scCB2 is an R package implementing CB2 for distinguishing real cells from empty droplets in droplet-based single cell RNA-seq experiments (especially for 10x Chromium). It is based on clustering similar barcodes and calculating Monte-Carlo p-value for each cluster to test against background distribution. This cluster-level test outperforms single-barcode-level tests in dealing with low count barcodes and homogeneous sequencing library, while keeping FDR well controlled. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aaa88ac58fbc1b32bfc514cc72109ada build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sccb2", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle, rmarkdown # SystemRequirements: C++11 requirements: host: - - 'bioconductor-dropletutils >=1.22.0,<1.23.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-dropletutils >=1.26.0,<1.27.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-doparallel - r-foreach @@ -35,24 +37,27 @@ requirements: - r-matrix - r-seurat run: - - 'bioconductor-dropletutils >=1.22.0,<1.23.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-dropletutils >=1.26.0,<1.27.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-doparallel - r-foreach - r-iterators - r-matrix - r-seurat + +source: + md5: c2c4b1521c5b877a1acca0004c8d7fb0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data' - description: 'scCB2 is an R package implementing CB2 for distinguishing real cells from empty droplets in droplet-based single cell RNA-seq experiments (especially for 10x Chromium). It is based on clustering similar barcodes and calculating Monte-Carlo p-value for each cluster to test against background distribution. This cluster-level test outperforms single-barcode-level tests in dealing with low count barcodes and homogeneous sequencing library, while keeping FDR well controlled.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scclassify/build_failure.linux-64.yaml b/recipes/bioconductor-scclassify/build_failure.linux-64.yaml deleted file mode 100644 index 0c17e3a10137a..0000000000000 --- a/recipes/bioconductor-scclassify/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 5d9ecd6df4ab307246d9923f365939c559cf85122664ccc27d4a9200bf32c6b7 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - - r-ggraph - - r-ggplot2 - - bioconductor-biocparallel >=1.36.0,<1.37.0 - - r-cluster - - r-base 4.3.* - - r-matrix - - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested bioconductor-cepo >=1.8.0,<1.9.0 - - - - Leaving build/test directories: - Work: - /opt/conda/conda-bld/work - Test: - /opt/conda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl - Build: - source activate /opt/conda/conda-bld/_build_env - - - Traceback (most recent call last): - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action - t = self.solve(specs) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - bioconductor-cepo >=1.8.0,<1.9.0 - - r-mixtools - - r-igraph - - r-proxyc - - bioconductor-limma >=3.58.0,<3.59.0 - - r-minpack.lm - - r-diptest - - r-mgcv - - bioconductor-s4vectors >=0.40.0,<0.41.0 - - r-statmod - - bioconductor-hopach >=2.62.0,<2.63.0 - - r-proxy - - r-ggraph - - r-ggplot2 - - bioconductor-biocparallel >=1.36.0,<1.37.0 - - r-cluster - - r-base 4.3.* - - r-matrix - - with channels: - - file:///opt/host-conda-bld - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested bioconductor-cepo >=1.8.0,<1.9.0 - - - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build - output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs - for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set - conda_packages = finalize_outputs_pass( - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass - fm = finalize_metadata( - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata - build_unsat, host_unsat = add_upstream_pins(m, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins - host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files - deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies - actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-cepo[version='>=1.8.0,<1.9.0']")} -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-scclassify/meta.yaml b/recipes/bioconductor-scclassify/meta.yaml index c466f33922a97..a7f05f1b89424 100644 --- a/recipes/bioconductor-scclassify/meta.yaml +++ b/recipes/bioconductor-scclassify/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "scClassify" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: scClassify is a multiscale classification framework for single-cell RNA-seq data based on ensemble learning and cell type hierarchies, enabling sample size estimation required for accurate cell type classification and joint classification of cells using multiple references. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'scClassify: single-cell Hierarchical Classification' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6268da69185981088025702610fd424c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scclassify", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, pkgdown requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-cepo >=1.8.0,<1.9.0' - - 'bioconductor-hopach >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-cepo >=1.12.0,<1.13.0 + - bioconductor-hopach >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cluster - r-diptest @@ -41,11 +43,11 @@ requirements: - r-proxyc - r-statmod run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-cepo >=1.8.0,<1.9.0' - - 'bioconductor-hopach >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-cepo >=1.12.0,<1.13.0 + - bioconductor-hopach >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cluster - r-diptest @@ -59,13 +61,16 @@ requirements: - r-proxy - r-proxyc - r-statmod + +source: + md5: 9cc6d31006c45bc4450c75942b39422f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'scClassify: single-cell Hierarchical Classification' - description: 'scClassify is a multiscale classification framework for single-cell RNA-seq data based on ensemble learning and cell type hierarchies, enabling sample size estimation required for accurate cell type classification and joint classification of cells using multiple references.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sccomp/build_failure.linux-64.yaml b/recipes/bioconductor-sccomp/build_failure.linux-64.yaml index f18015f5e5ff0..f62f820b404a8 100644 --- a/recipes/bioconductor-sccomp/build_failure.linux-64.yaml +++ b/recipes/bioconductor-sccomp/build_failure.linux-64.yaml @@ -1,6 +1,104 @@ -recipe_sha: c6c86a551617ab192acea3543c4da0aa9ddee063ff6e7204b82211c508530538 # The commit at which this recipe failed to build. +recipe_sha: f873681de3c0eb2fad42e38edf78453533787698269d82bfe6f7242e35dc1375 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -reason: |- - package r-rstan-2.32.3-r43h884c59f_0 is excluded by strict repo priority -category: |- - dependency issue +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-instantiate[version='>=0.2.3']")} + Encountered problems while solving: + - nothing provides requested r-instantiate >=0.2.3 + + Could not solve for environment specs + The following package could not be installed + [31mr-instantiate >=0.2.3 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-instantiate[version='>=0.2.3']")} + Encountered problems while solving: + - nothing provides requested r-instantiate >=0.2.3 + + Could not solve for environment specs + The following package could not be installed + [31mr-instantiate >=0.2.3 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-instantiate[version='>=0.2.3']")} + Encountered problems while solving: + - nothing provides requested r-instantiate >=0.2.3 + + Could not solve for environment specs + The following package could not be installed + [31mr-instantiate >=0.2.3 [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-sccomp/meta.yaml b/recipes/bioconductor-sccomp/meta.yaml index 60929b0dd67fd..a230f5941afe0 100644 --- a/recipes/bioconductor-sccomp/meta.yaml +++ b/recipes/bioconductor-sccomp/meta.yaml @@ -1,96 +1,93 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "sccomp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model can infer changes in tissue composition and heterogeneity, and can produce realistic data simulations based on any existing dataset. This model can also transfer knowledge from a large set of integrated datasets to increase accuracy further. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8a24adb07d155b94645a5f684e1455f6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sccomp", max_pin="x.x") }}' -# Suggests: BiocStyle, testthat (>= 3.0.0), markdown, knitr, tidyseurat, tidySingleCellExperiment, loo -# SystemRequirements: GNU make + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), markdown, knitr, loo, prettydoc, tidyseurat, tidySingleCellExperiment, bayesplot, posterior +# SystemRequirements: CmdStan (https://mc-stan.org/users/interfaces/cmdstan) requirements: + host: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - - 'r-bh >=1.66.0' - r-boot + - r-callr + - r-digest - r-dplyr - r-forcats + - r-fs - r-ggplot2 - r-ggrepel - r-glue + - r-instantiate >=0.2.3 - r-lifecycle - r-magrittr - r-patchwork - r-purrr - - 'r-rcpp >=0.12.0' - - 'r-rcppeigen >=0.3.3.3.0' - - 'r-rcppparallel >=5.0.1' - r-readr - r-rlang - - 'r-rstan >=2.26.0' - - 'r-rstantools >=2.1.1' - r-scales - r-seuratobject - - 'r-stanheaders >=2.26.0' - r-stringr - r-tibble - r-tidyr - r-tidyselect - - libblas - - liblapack + - r-withr + run: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - - 'r-bh >=1.66.0' - r-boot + - r-callr + - r-digest - r-dplyr - r-forcats + - r-fs - r-ggplot2 - r-ggrepel - r-glue + - r-instantiate >=0.2.3 - r-lifecycle - r-magrittr - r-patchwork - r-purrr - - 'r-rcpp >=0.12.0' - - 'r-rcppeigen >=0.3.3.3.0' - - 'r-rcppparallel >=5.0.1' - r-readr - r-rlang - - 'r-rstan >=2.26.0' - - 'r-rstantools >=2.1.1' - r-scales - r-seuratobject - - 'r-stanheaders >=2.26.0' - r-stringr - r-tibble - r-tidyr - r-tidyselect - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + - r-withr + +source: + md5: 763de87d7776c55e2321e17c85f433c7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data' - description: 'A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model can infer changes in tissue composition and heterogeneity, and can produce realistic data simulations based on any existing dataset. This model can also transfer knowledge from a large set of integrated datasets to increase accuracy further.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scdataviz/meta.yaml b/recipes/bioconductor-scdataviz/meta.yaml index 655232cf0f529..f8a9b291995df 100644 --- a/recipes/bioconductor-scdataviz/meta.yaml +++ b/recipes/bioconductor-scdataviz/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "scDataviz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: In the single cell World, which includes flow cytometry, mass cytometry, single-cell RNA-seq (scRNA-seq), and others, there is a need to improve data visualisation and to bring analysis capabilities to researchers even from non-technical backgrounds. scDataviz attempts to fit into this space, while also catering for advanced users. Additonally, due to the way that scDataviz is designed, which is based on SingleCellExperiment, it has a 'plug and play' feel, and immediately lends itself as flexibile and compatibile with studies that go beyond scDataviz. Finally, the graphics in scDataviz are generated via the ggplot engine, which means that users can 'add on' features to these with ease. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'scDataviz: single cell dataviz and downstream analyses' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71744390661cb39c6c12d920e7861d7f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scdataviz", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: PCAtools, cowplot, BiocGenerics, RUnit, knitr, kableExtra, rmarkdown requirements: host: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-corrplot - r-ggplot2 @@ -37,9 +39,9 @@ requirements: - r-seurat - r-umap run: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-corrplot - r-ggplot2 @@ -51,13 +53,16 @@ requirements: - r-scales - r-seurat - r-umap + +source: + md5: 323fdfdad14d30359b8b319c1caa81af + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'scDataviz: single cell dataviz and downstream analyses' - description: 'In the single cell World, which includes flow cytometry, mass cytometry, single-cell RNA-seq (scRNA-seq), and others, there is a need to improve data visualisation and to bring analysis capabilities to researchers even from non-technical backgrounds. scDataviz attempts to fit into this space, while also catering for advanced users. Additonally, due to the way that scDataviz is designed, which is based on SingleCellExperiment, it has a ''plug and play'' feel, and immediately lends itself as flexibile and compatibile with studies that go beyond scDataviz. Finally, the graphics in scDataviz are generated via the ggplot engine, which means that users can ''add on'' features to these with ease.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scdblfinder/build_failure.linux-64.yaml b/recipes/bioconductor-scdblfinder/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..ee20c71c7f718 --- /dev/null +++ b/recipes/bioconductor-scdblfinder/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 5f3c5f3507e520f4411cc51e45e40ed25ffbc14a9876c5dedb8c5a8b380c34eb # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec(">=3.5.0,<3.5.1.0a0"), MatchSpec("r-xgboost==0.80=mro350h255eb88_1")} + Encountered problems while solving: + - nothing provides mro-base >=3.5.0,<3.5.1.0a0 needed by r-xgboost-0.80-mro350h255eb88_1 + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-xgboost[0m is not installable because there are no viable options + [31mr-xgboost 0.80[0m would require + [31mmro-base >=3.5.0,<3.5.1.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-xgboost [0.80|0.81|0.82|0.90|1.0.2][0m would require + [31mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [0.82|0.90|...|1.4.0][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.0.2|1.1.1|...|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.4.0|1.4.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec(">=3.5.0,<3.5.1.0a0"), MatchSpec("r-xgboost==0.80=mro350h255eb88_1")} + Encountered problems while solving: + - nothing provides mro-base >=3.5.0,<3.5.1.0a0 needed by r-xgboost-0.80-mro350h255eb88_1 + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-xgboost[0m is not installable because there are no viable options + [31mr-xgboost 0.80[0m would require + [31mmro-base >=3.5.0,<3.5.1.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-xgboost [0.80|0.81|0.82|0.90|1.0.2][0m would require + [31mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [0.82|0.90|...|1.4.0][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.0.2|1.1.1|...|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.4.0|1.4.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. +category: |- + dependency issue diff --git a/recipes/bioconductor-scdblfinder/meta.yaml b/recipes/bioconductor-scdblfinder/meta.yaml index 42aaa31be2a5c..49d2c57a504d9 100644 --- a/recipes/bioconductor-scdblfinder/meta.yaml +++ b/recipes/bioconductor-scdblfinder/meta.yaml @@ -1,79 +1,86 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "scDblFinder" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The scDblFinder package gathers various methods for the detection and handling of doublets/multiplets in single-cell sequencing data (i.e. multiple cells captured within the same droplet or reaction volume). It includes methods formerly found in the scran package, the new fast and comprehensive scDblFinder method, and a reimplementation of the Amulet detection method for single-cell ATAC-seq. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: scDblFinder -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b833caa7cf87c1fb4cf9bf599f750ffa build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scdblfinder", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, viridisLite, mbkmeans requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-bluster >=1.12.0,<1.13.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-bluster >=1.16.0,<1.17.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-igraph - r-mass - r-matrix - r-xgboost + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-bluster >=1.12.0,<1.13.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-bluster >=1.16.0,<1.17.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-igraph - r-mass - r-matrix - r-xgboost + +source: + md5: 3643546da7a3961cb2a39e9ce689b013 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: scDblFinder - description: 'The scDblFinder package gathers various methods for the detection and handling of doublets/multiplets in single-cell sequencing data (i.e. multiple cells captured within the same droplet or reaction volume). It includes methods formerly found in the scran package, the new fast and comprehensive scDblFinder method, and a reimplementation of the Amulet detection method for single-cell ATAC-seq.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scdd/meta.yaml b/recipes/bioconductor-scdd/meta.yaml index 417177257b74a..6ae08a93b3462 100644 --- a/recipes/bioconductor-scdd/meta.yaml +++ b/recipes/bioconductor-scdd/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "scDD" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3c95209683b09f0584ab315a6fc1e779 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scdd", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, gridExtra requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-ebseq >=2.0.0,<2.1.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-ebseq >=2.4.0,<2.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-arm - r-base - r-fields @@ -35,25 +37,28 @@ requirements: - r-mclust - r-outliers run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-ebseq >=2.0.0,<2.1.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-ebseq >=2.4.0,<2.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-arm - r-base - r-fields - r-ggplot2 - r-mclust - r-outliers + +source: + md5: 15fb6dcf4a58c5560a54e791e4052840 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions' - description: 'This package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scddboost/build_failure.linux-64.yaml b/recipes/bioconductor-scddboost/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..560060fa00bb6 --- /dev/null +++ b/recipes/bioconductor-scddboost/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 0fced742b91f8841895cdc4276d59d7fb5bf95ff3eaeb57b7216697414448c97 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false>, 0>': + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false> >' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false> >' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/Block.h:172:103: required from 'class Eigen::internal::BlockImpl_dense, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false, false>' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/Block.h:154:7: required from 'class Eigen::BlockImpl, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false, Eigen::Dense>' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/Block.h:103:81: required from 'class Eigen::Block, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false>' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:380:43: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:31: required from 'static void Eigen::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Matrix; SrcXprType = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; Functor = Eigen::internal::assign_op; Weak = void]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:49: required from 'void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Matrix; Src = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; Func = assign_op]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:797:41: required from 'Derived& Eigen::PlainObjectBase::_set_noalias(const Eigen::DenseBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; Derived = Eigen::Matrix]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:594:19: required from 'Eigen::PlainObjectBase::PlainObjectBase(const Eigen::DenseBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; Derived = Eigen::Matrix]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:423:29: required from 'Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; _Scalar = double; int _Rows = -1; int _Cols = 1; int _Options = 0; int _MaxRows = -1; int _MaxCols = 1]' + derived.cpp:161:46: required from here + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] + 56 | >::type PacketReturnType; + | ^~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, const Eigen::Transpose, 1, -1, false> >, const Eigen::Block, -1, 1, true> >, 0>': + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, const Eigen::Transpose, 1, -1, false> >, const Eigen::Block, -1, 1, true> > >' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, const Eigen::Transpose, 1, -1, false> >, const Eigen::Block, -1, 1, true> > >' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:148:7: required from 'class Eigen::CwiseBinaryOpImpl, const Eigen::Transpose, 1, -1, false> >, const Eigen::Block, -1, 1, true>, Eigen::Dense>' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:77:7: required from 'class Eigen::CwiseBinaryOp, const Eigen::Transpose, 1, -1, false> >, const Eigen::Block, -1, 1, true> >' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:606:52: required from 'const Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::CoeffReturnType Eigen::internal::product_evaluator, ProductTag, Eigen::DenseShape, Eigen::DenseShape>::coeff(Eigen::Index, Eigen::Index) const [with Lhs = Eigen::Matrix; Rhs = Eigen::Matrix; int ProductTag = 8; typename Eigen::internal::traits::Lhs>::Scalar = double; typename Eigen::Product::Lhs = Eigen::Matrix; typename Eigen::internal::traits::Rhs>::Scalar = double; typename Eigen::Product::Rhs = Eigen::Matrix; CoeffReturnType = double; Eigen::Index = long int]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:654:63: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:332:31: required from 'Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const T&) [with T = Eigen::Product, Eigen::Matrix, 0>; _Scalar = double; int _Rows = -1; int _Cols = -1; int _Options = 0; int _MaxRows = -1; int _MaxCols = -1]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:850:41: required from 'void Eigen::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if::value, void*>::type) [with Dst = Eigen::Matrix; Src = Eigen::Product, Eigen::Matrix, 0>; Func = assign_op; typename enable_if::value, void*>::type = void*; typename evaluator_traits::Shape = Eigen::DenseShape]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836:18: required from 'void Eigen::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen::Matrix; Src = Eigen::Product, Eigen::Matrix, 0>]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:779:32: required from 'Derived& Eigen::PlainObjectBase::_set(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product, Eigen::Matrix, 0>; Derived = Eigen::Matrix]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:225:24: required from 'Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>& Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::operator=(const Eigen::DenseBase&) [with OtherDerived = Eigen::Product, Eigen::Matrix, 0>; _Scalar = double; int _Rows = -1; int _Cols = -1; int _Options = 0; int _MaxRows = -1; int _MaxCols = -1]' + derived.cpp:110:33: required from here + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false> >, 0>': + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false> > >' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false> > >' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/Transpose.h:118:37: required from 'class Eigen::TransposeImpl, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false>, Eigen::Dense>' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/Transpose.h:52:37: required from 'class Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false> >' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/Dot.h:50:23: required from 'static Eigen::internal::dot_nocheck::ResScalar Eigen::internal::dot_nocheck::run(const Eigen::MatrixBase&, const Eigen::MatrixBase&) [with T = Eigen::Block, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false>; U = Eigen::Block, -1, 1, true>; ResScalar = double]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/Dot.h:84:58: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:31: required from 'static void Eigen::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Matrix; SrcXprType = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; Functor = Eigen::internal::assign_op; Weak = void]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:49: required from 'void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Matrix; Src = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; Func = assign_op]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:797:41: required from 'Derived& Eigen::PlainObjectBase::_set_noalias(const Eigen::DenseBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; Derived = Eigen::Matrix]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:594:19: required from 'Eigen::PlainObjectBase::PlainObjectBase(const Eigen::DenseBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; Derived = Eigen::Matrix]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:423:29: required from 'Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; _Scalar = double; int _Rows = -1; int _Cols = 1; int _Options = 0; int _MaxRows = -1; int _MaxCols = 1]' + derived.cpp:161:46: required from here + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, const Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false> >, const Eigen::Block, -1, 1, true> >, 0>': + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, const Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false> >, const Eigen::Block, -1, 1, true> > >' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, const Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false> >, const Eigen::Block, -1, 1, true> > >' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:148:7: required from 'class Eigen::CwiseBinaryOpImpl, const Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false> >, const Eigen::Block, -1, 1, true>, Eigen::Dense>' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:77:7: required from 'class Eigen::CwiseBinaryOp, const Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false> >, const Eigen::Block, -1, 1, true> >' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/Dot.h:50:56: required from 'static Eigen::internal::dot_nocheck::ResScalar Eigen::internal::dot_nocheck::run(const Eigen::MatrixBase&, const Eigen::MatrixBase&) [with T = Eigen::Block, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false>; U = Eigen::Block, -1, 1, true>; ResScalar = double]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/Dot.h:84:58: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:31: required from 'static void Eigen::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Matrix; SrcXprType = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; Functor = Eigen::internal::assign_op; Weak = void]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:49: required from 'void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Matrix; Src = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; Func = assign_op]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:797:41: required from 'Derived& Eigen::PlainObjectBase::_set_noalias(const Eigen::DenseBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; Derived = Eigen::Matrix]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:594:19: required from 'Eigen::PlainObjectBase::PlainObjectBase(const Eigen::DenseBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; Derived = Eigen::Matrix]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:423:29: required from 'Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; _Scalar = double; int _Rows = -1; int _Cols = 1; int _Options = 0; int _MaxRows = -1; int _MaxCols = 1]' + derived.cpp:161:46: required from here + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h: In instantiation of 'struct Eigen::internal::evaluator, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false> >': + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:100:8: required from 'struct Eigen::internal::evaluator, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false> >' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:311:41: required from 'struct Eigen::internal::unary_evaluator, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false> >, Eigen::internal::IndexBased, double>' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:90:8: required from 'struct Eigen::internal::evaluator, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false> > >' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:100:8: required from 'struct Eigen::internal::evaluator, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false> > >' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:739:41: required from 'struct Eigen::internal::binary_evaluator, const Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Matrix >, 1, -1, false> >, const Eigen::Block, -1, 1, true> >, Eigen::internal::IndexBased, Eigen::internal::IndexBased, double, double>' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:722:8: [ skipping 17 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:31: required from 'static void Eigen::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Matrix; SrcXprType = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; Functor = Eigen::internal::assign_op; Weak = void]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:49: required from 'void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Matrix; Src = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; Func = assign_op]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:797:41: required from 'Derived& Eigen::PlainObjectBase::_set_noalias(const Eigen::DenseBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; Derived = Eigen::Matrix]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:594:19: required from 'Eigen::PlainObjectBase::PlainObjectBase(const Eigen::DenseBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; Derived = Eigen::Matrix]' + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:423:29: required from 'Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Product, Eigen::Matrix, 0> > >; _Scalar = double; int _Rows = -1; int _Cols = 1; int _Options = 0; int _MaxRows = -1; int _MaxCols = 1]' + derived.cpp:161:46: required from here + /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:1071:54: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] + 1071 | PacketAlignment = unpacket_traits::alignment, + | ^~~~~~~~~ + make: *** [/opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/etc/Makeconf:204: derived.o] Error 1 + ERROR: compilation failed for package scDDboost + * removing /opt/conda/conda-bld/bioconductor-scddboost_1735072154130/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/scDDboost + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-scddboost_1735072154130/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-scddboost_1735072154130/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-scddboost/build_failure.osx-64.yaml b/recipes/bioconductor-scddboost/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..ecfee69639391 --- /dev/null +++ b/recipes/bioconductor-scddboost/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 0fced742b91f8841895cdc4276d59d7fb5bf95ff3eaeb57b7216697414448c97 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-scddboost-1.8.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-scddboost_1734821707173/work/conda_build.sh']' returned non-zero exit status 1. + + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-scddboost-1.8.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-scddboost-1.8.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + AS=x86_64-apple-darwin13.4.0-as + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-scddboost-1.8.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-scddboost_1734821707173/work/conda_build.sh']' returned non-zero exit status 1. + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-scddboost-1.8.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-scddboost-1.8.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-scddboost-1.8.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-scddboost-1.8.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-scddboost-1.8.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-scddboost-1.8.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-scddboost-1.8.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-scddboost-1.8.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-scddboost-1.8.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -I'$PREFIX/lib/R/library/BH/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c DATA.cpp -o DATA.o + x86_64-apple-darwin13.4.0-clang -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -I'$PREFIX/lib/R/library/BH/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c Header.cpp -o Header.o + x86_64-apple-darwin13.4.0-clang -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -I'$PREFIX/lib/R/library/BH/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c derived.cpp -o derived.o +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-scddboost/meta.yaml b/recipes/bioconductor-scddboost/meta.yaml index 5268eed04fe71..2e477b6ed5a5e 100644 --- a/recipes/bioconductor-scddboost/meta.yaml +++ b/recipes/bioconductor-scddboost/meta.yaml @@ -1,65 +1,70 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "scDDboost" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: scDDboost is an R package to analyze changes in the distribution of single-cell expression data between two experimental conditions. Compared to other methods that assess differential expression, scDDboost benefits uniquely from information conveyed by the clustering of cells into cellular subtypes. Through a novel empirical Bayesian formulation it calculates gene-specific posterior probabilities that the marginal expression distribution is the same (or different) between the two conditions. The implementation in scDDboost treats gene-level expression data within each condition as a mixture of negative binomial distributions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A compositional model to assess expression changes from single-cell rna-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ac0cac5975ebe4025ea07ad00e132847 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scddboost", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat # SystemRequirements: c++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-ebseq >=2.0.0,<2.1.0' - - 'bioconductor-oscope >=1.32.0,<1.33.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-ebseq >=2.4.0,<2.5.0 + - bioconductor-oscope >=1.36.0,<1.37.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bh - r-cluster - r-ggplot2 - r-mclust - - 'r-rcpp >=0.12.11' - - 'r-rcppeigen >=0.3.2.9.0' + - r-rcpp >=0.12.11 + - r-rcppeigen >=0.3.2.9.0 - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-ebseq >=2.0.0,<2.1.0' - - 'bioconductor-oscope >=1.32.0,<1.33.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-ebseq >=2.4.0,<2.5.0 + - bioconductor-oscope >=1.36.0,<1.37.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bh - r-cluster - r-ggplot2 - r-mclust - - 'r-rcpp >=0.12.11' - - 'r-rcppeigen >=0.3.2.9.0' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=0.12.11 + - r-rcppeigen >=0.3.2.9.0 + +source: + md5: 888bd691549bf9be9f0c557fe50d29a4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'A compositional model to assess expression changes from single-cell rna-seq data' - description: 'scDDboost is an R package to analyze changes in the distribution of single-cell expression data between two experimental conditions. Compared to other methods that assess differential expression, scDDboost benefits uniquely from information conveyed by the clustering of cells into cellular subtypes. Through a novel empirical Bayesian formulation it calculates gene-specific posterior probabilities that the marginal expression distribution is the same (or different) between the two conditions. The implementation in scDDboost treats gene-level expression data within each condition as a mixture of negative binomial distributions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scde/meta.yaml b/recipes/bioconductor-scde/meta.yaml index f4b90ef2f8f2c..c931bfcd8f15d 100644 --- a/recipes/bioconductor-scde/meta.yaml +++ b/recipes/bioconductor-scde/meta.yaml @@ -1,29 +1,46 @@ -{% set version = "2.30.0" %} +{% set version = "2.34.0" %} {% set name = "scde" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The scde package implements a set of statistical methods for analyzing single-cell RNA-seq data. scde fits individual error models for single-cell RNA-seq measurements. These models can then be used for assessment of differential expression between groups of cells, as well as other types of analysis. The scde package also contains the pagoda framework which applies pathway and gene set overdispersion analysis to identify and characterize putative cell subpopulations based on transcriptional signatures. The overall approach to the differential expression analysis is detailed in the following publication: "Bayesian approach to single-cell differential expression analysis" (Kharchenko PV, Silberstein L, Scadden DT, Nature Methods, doi: 10.1038/nmeth.2967). The overall approach to subpopulation identification and characterization is detailed in the following pre-print: "Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis" (Fan J, Salathia N, Liu R, Kaeser G, Yung Y, Herman J, Kaper F, Fan JB, Zhang K, Chun J, and Kharchenko PV, Nature Methods, doi:10.1038/nmeth.3734).' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Single Cell Differential Expression -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ee4cb04c3a1431fb088d8681ff950d49 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scde", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:scde + - doi:10.1038/nmeth.2967 + parent_recipe: + name: bioconductor-scde + path: recipes/bioconductor-scde + version: 2.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-pcamethods >=1.98.0,<1.99.0 - r-base - r-cairo - r-extremes @@ -33,17 +50,18 @@ requirements: - r-nnet - r-quantreg - r-rcolorbrewer - - 'r-rcpp >=0.10.4' - - 'r-rcpparmadillo >=0.5.400.2.0' + - r-rcpp >=0.10.4 + - r-rcpparmadillo >=0.5.400.2.0 - r-rjson - r-rmtstat - r-rook - libblas - liblapack + run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-pcamethods >=1.98.0,<1.99.0 - r-base - r-cairo - r-extremes @@ -53,30 +71,21 @@ requirements: - r-nnet - r-quantreg - r-rcolorbrewer - - 'r-rcpp >=0.10.4' - - 'r-rcpparmadillo >=0.5.400.2.0' + - r-rcpp >=0.10.4 + - r-rcpparmadillo >=0.5.400.2.0 - r-rjson - r-rmtstat - r-rook - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 5011b4f51c2dea4d48dc891fcba77ee5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Single Cell Differential Expression' - description: 'The scde package implements a set of statistical methods for analyzing single-cell RNA-seq data. scde fits individual error models for single-cell RNA-seq measurements. These models can then be used for assessment of differential expression between groups of cells, as well as other types of analysis. The scde package also contains the pagoda framework which applies pathway and gene set overdispersion analysis to identify and characterize putative cell subpopulations based on transcriptional signatures. The overall approach to the differential expression analysis is detailed in the following publication: "Bayesian approach to single-cell differential expression analysis" (Kharchenko PV, Silberstein L, Scadden DT, Nature Methods, doi: 10.1038/nmeth.2967). The overall approach to subpopulation identification and characterization is detailed in the following pre-print: "Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis" (Fan J, Salathia N, Liu R, Kaeser G, Yung Y, Herman J, Kaper F, Fan JB, Zhang K, Chun J, and Kharchenko PV, Nature Methods, doi:10.1038/nmeth.3734).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:scde - - doi:10.1038/nmeth.2967 - parent_recipe: - name: bioconductor-scde - path: recipes/bioconductor-scde - version: 2.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scdesign3/meta.yaml b/recipes/bioconductor-scdesign3/meta.yaml index a5b20677348d3..09133302f7f92 100644 --- a/recipes/bioconductor-scdesign3/meta.yaml +++ b/recipes/bioconductor-scdesign3/meta.yaml @@ -1,31 +1,35 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "scDesign3" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning interpretable parameters from real data. Using a unified probabilistic model for single-cell and spatial omics data, scDesign3 infers biologically meaningful parameters; assesses the goodness-of-fit of inferred cell clusters, trajectories, and spatial locations; and generates in silico negative and positive controls for benchmarking computational tools. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84c2f07635607b2167f24750f952745a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scdesign3", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: mvnfast, igraph, knitr, rmarkdown, testthat (>= 3.0.0), RefManageR, sessioninfo, BiocStyle requirements: + host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + - r-coop - r-dplyr - r-gamlss - r-gamlss.dist @@ -38,14 +42,17 @@ requirements: - r-mvtnorm - r-pbmcapply - r-rvinecopulib + - r-sparsemvn - r-tibble - r-umap - r-viridis + run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + - r-coop - r-dplyr - r-gamlss - r-gamlss.dist @@ -58,16 +65,20 @@ requirements: - r-mvtnorm - r-pbmcapply - r-rvinecopulib + - r-sparsemvn - r-tibble - r-umap - r-viridis + +source: + md5: 7a2051e5737f93a928cfe0f983c7ba0f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics' - description: 'We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning interpretable parameters from real data. Using a unified probabilistic model for single-cell and spatial omics data, scDesign3 infers biologically meaningful parameters; assesses the goodness-of-fit of inferred cell clusters, trajectories, and spatial locations; and generates in silico negative and positive controls for benchmarking computational tools.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scdiagnostics/build.sh b/recipes/bioconductor-scdiagnostics/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scdiagnostics/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scdiagnostics/meta.yaml b/recipes/bioconductor-scdiagnostics/meta.yaml new file mode 100644 index 0000000000000..58bb64cfe54fb --- /dev/null +++ b/recipes/bioconductor-scdiagnostics/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.0.0" %} +{% set name = "scDiagnostics" %} +{% set bioc = "3.20" %} + +about: + description: The scDiagnostics package provides diagnostic plots to assess the quality of cell type assignments from single cell gene expression profiles. The implemented functionality allows to assess the reliability of cell type annotations, investigate gene expression patterns, and explore relationships between different cell types in query and reference datasets allowing users to detect potential misalignments between reference and query datasets. The package also provides visualization capabilities for diagnostics purposes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Cell type annotation diagnostics + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scdiagnostics", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: AUCell, BiocStyle, knitr, Matrix, rmarkdown, scran, scRNAseq, SingleR, celldex, scuttle, scater, dplyr, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-bluster >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-cramer + - r-ggplot2 + - r-ggridges + - r-isotree + - r-patchwork + - r-ranger + - r-rlang + - r-speedglm + - r-transport + run: + - bioconductor-bluster >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-cramer + - r-ggplot2 + - r-ggridges + - r-isotree + - r-patchwork + - r-ranger + - r-rlang + - r-speedglm + - r-transport + +source: + md5: 9c3175299b05983588f064916c420da8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-scdotplot/build.sh b/recipes/bioconductor-scdotplot/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scdotplot/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scdotplot/meta.yaml b/recipes/bioconductor-scdotplot/meta.yaml new file mode 100644 index 0000000000000..e53f4fbf80a25 --- /dev/null +++ b/recipes/bioconductor-scdotplot/meta.yaml @@ -0,0 +1,75 @@ +{% set version = "1.0.0" %} +{% set name = "scDotPlot" %} +{% set bioc = "3.20" %} + +about: + description: Dot plots of single-cell RNA-seq data allow for an examination of the relationships between cell groupings (e.g. clusters) and marker gene expression. The scDotPlot package offers a unified approach to perform a hierarchical clustering analysis and add annotations to the columns and/or rows of a scRNA-seq dot plot. It works with SingleCellExperiment and Seurat objects as well as data frames. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Cluster a Single-cell RNA-seq Dot Plot + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scdotplot", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: AnnotationDbi, BiocStyle, knitr, rmarkdown, scran, scRNAseq, scuttle, SeuratObject, testthat, vdiffr +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - r-aplot + - r-base + - r-cli + - r-dplyr + - r-ggplot2 + - r-ggsci + - r-magrittr + - r-purrr + - r-rlang + - r-scales + - r-seurat + - r-stringr + - r-tibble + - r-tidyr + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - r-aplot + - r-base + - r-cli + - r-dplyr + - r-ggplot2 + - r-ggsci + - r-magrittr + - r-purrr + - r-rlang + - r-scales + - r-seurat + - r-stringr + - r-tibble + - r-tidyr + +source: + md5: 3016f3b050f8246442354c35f6424f87 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-scds/build_failure.linux-64.yaml b/recipes/bioconductor-scds/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..1bb1ad4314eb0 --- /dev/null +++ b/recipes/bioconductor-scds/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: 0458a2d2b91cdced817f37925f10494429fd7ae7690cf757d421fcd14f0ee1b6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec(">=3.5.0,<3.5.1.0a0"), MatchSpec("r-xgboost==0.80=mro350h255eb88_1")} + Encountered problems while solving: + - nothing provides mro-base >=3.5.0,<3.5.1.0a0 needed by r-xgboost-0.80-mro350h255eb88_1 + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-xgboost[0m is not installable because there are no viable options + [31mr-xgboost 0.80[0m would require + [31mmro-base >=3.5.0,<3.5.1.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-xgboost [0.80|0.81|0.82|0.90|1.0.2][0m would require + [31mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [0.82|0.90|...|1.4.0][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.0.2|1.1.1|...|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.4.0|1.4.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec(">=3.5.0,<3.5.1.0a0"), MatchSpec("r-xgboost==0.80=mro350h255eb88_1")} + Encountered problems while solving: + - nothing provides mro-base >=3.5.0,<3.5.1.0a0 needed by r-xgboost-0.80-mro350h255eb88_1 + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-xgboost[0m is not installable because there are no viable options + [31mr-xgboost 0.80[0m would require + [31mmro-base >=3.5.0,<3.5.1.0a0 [0m, which does not exist (perhaps a missing channel); + [31mr-xgboost [0.80|0.81|0.82|0.90|1.0.2][0m would require + [31mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [0.82|0.90|...|1.4.0][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.0.2|1.1.1|...|1.6.2][0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.4.0|1.4.1|...|1.7.4][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.5.1|1.6.1|...|2.1.3][0m would require + [31m__cuda[0m, which is missing on the system; + [31mr-xgboost [1.6.2|1.7.0|...|2.0.3][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-xgboost [1.7.4|1.7.6|...|2.1.3][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. +reason: |- + needs updated r-xgboost package to be added to conda-forge (for R 4.4) +category: |- + dependency issue diff --git a/recipes/bioconductor-scds/build_failure.osx-64.yaml b/recipes/bioconductor-scds/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..148077fee0008 --- /dev/null +++ b/recipes/bioconductor-scds/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 0458a2d2b91cdced817f37925f10494429fd7ae7690cf757d421fcd14f0ee1b6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + needs updated r-xgboost package to be added to conda-forge (for R 4.4) +category: |- + dependency issue diff --git a/recipes/bioconductor-scds/meta.yaml b/recipes/bioconductor-scds/meta.yaml index 58c835c7336f2..0fb5fb7e0cb1e 100644 --- a/recipes/bioconductor-scds/meta.yaml +++ b/recipes/bioconductor-scds/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "scds" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: In single cell RNA sequencing (scRNA-seq) data combinations of cells are sometimes considered a single cell (doublets). The scds package provides methods to annotate doublets in scRNA-seq data computationally. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: df6bd91f4acdd6ea2e54d2f20f632cbf build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scds", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown requirements: host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-matrix - r-proc - r-xgboost run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-matrix - r-proc - r-xgboost + +source: + md5: ea1f46023a9499a5ed4b416f31fec655 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data' - description: 'In single cell RNA sequencing (scRNA-seq) data combinations of cells are sometimes considered a single cell (doublets). The scds package provides methods to annotate doublets in scRNA-seq data computationally.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scfa/meta.yaml b/recipes/bioconductor-scfa/meta.yaml index 1980760f8cd2b..7ff364b4f3f57 100644 --- a/recipes/bioconductor-scfa/meta.yaml +++ b/recipes/bioconductor-scfa/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "SCFA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Subtyping via Consensus Factor Analysis (SCFA) can efficiently remove noisy signals from consistent molecular patterns in multi-omics data. SCFA first uses an autoencoder to select only important features and then repeatedly performs factor analysis to represent the data with different numbers of factors. Using these representations, it can reliably identify cancer subtypes and accurately predict risk scores of patients. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: 'SCFA: Subtyping via Consensus Factor Analysis' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c4e7d00ff20faff6a8a14eddde8e7a84 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scfa", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-cluster - r-coro @@ -33,9 +35,9 @@ requirements: - r-psych - r-rhpcblasctl - r-survival - - 'r-torch >=0.3.0' + - r-torch >=0.3.0 run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-cluster - r-coro @@ -46,14 +48,17 @@ requirements: - r-psych - r-rhpcblasctl - r-survival - - 'r-torch >=0.3.0' + - r-torch >=0.3.0 + +source: + md5: 270f83e5c4aa3b5aa4754f384a439ca7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'SCFA: Subtyping via Consensus Factor Analysis' - description: 'Subtyping via Consensus Factor Analysis (SCFA) can efficiently remove noisy signals from consistent molecular patterns in multi-omics data. SCFA first uses an autoencoder to select only important features and then repeatedly performs factor analysis to represent the data with different numbers of factors. Using these representations, it can reliably identify cancer subtypes and accurately predict risk scores of patients.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scfeaturefilter/meta.yaml b/recipes/bioconductor-scfeaturefilter/meta.yaml index ce5324266d06b..a034921e82152 100644 --- a/recipes/bioconductor-scfeaturefilter/meta.yaml +++ b/recipes/bioconductor-scfeaturefilter/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "scFeatureFilter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An R implementation of the correlation-based method developed in the Joshi laboratory to analyse and filter processed single-cell RNAseq data. It returns a filtered version of the data containing only genes expression values unaffected by systematic noise. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: A correlation-based method for quality filtering of single-cell RNAseq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f642025d766eb2cd17f406126e6fe0ba build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scfeaturefilter", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-scfeaturefilter + path: recipes/bioconductor-scfeaturefilter + version: 1.2.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocStyle, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot requirements: host: - r-base - - 'r-dplyr >=0.7.3' - - 'r-ggplot2 >=2.1.0' - - 'r-magrittr >=1.5' - - 'r-rlang >=0.1.2' - - 'r-tibble >=1.3.4' + - r-dplyr >=0.7.3 + - r-ggplot2 >=2.1.0 + - r-magrittr >=1.5 + - r-rlang >=0.1.2 + - r-tibble >=1.3.4 run: - r-base - - 'r-dplyr >=0.7.3' - - 'r-ggplot2 >=2.1.0' - - 'r-magrittr >=1.5' - - 'r-rlang >=0.1.2' - - 'r-tibble >=1.3.4' + - r-dplyr >=0.7.3 + - r-ggplot2 >=2.1.0 + - r-magrittr >=1.5 + - r-rlang >=0.1.2 + - r-tibble >=1.3.4 + +source: + md5: 95ed10e4f805f9a9c00a963e143459d8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'A correlation-based method for quality filtering of single-cell RNAseq data' - description: 'An R implementation of the correlation-based method developed in the Joshi laboratory to analyse and filter processed single-cell RNAseq data. It returns a filtered version of the data containing only genes expression values unaffected by systematic noise.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-scfeaturefilter - path: recipes/bioconductor-scfeaturefilter - version: 1.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scfeatures/meta.yaml b/recipes/bioconductor-scfeatures/meta.yaml index 1b4a39426bc3a..0923a492aef87 100644 --- a/recipes/bioconductor-scfeatures/meta.yaml +++ b/recipes/bioconductor-scfeatures/meta.yaml @@ -1,39 +1,40 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "scFeatures" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: scFeatures constructs multi-view representations of single-cell and spatial data. scFeatures is a tool that generates multi-view representations of single-cell and spatial data through the construction of a total of 17 feature types. These features can then be used for a variety of analyses using other software in Biocondutor. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 00b3e1296507cdf60879fd6d112c1e53 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scfeatures", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, S4Vectors, survival, survminer, BiocStyle, ClassifyR, org.Hs.eg.db, clusterProfiler requirements: + host: - - 'bioconductor-aucell >=1.24.0,<1.25.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-ensdb.hsapiens.v79 >=2.99.0,<2.100.0' - - 'bioconductor-ensdb.mmusculus.v79 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-gsva >=1.50.0,<1.51.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-singlecellsignalr >=1.14.0,<1.15.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-aucell >=1.28.0,<1.29.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-ensdb.hsapiens.v79 >=2.99.0,<2.100.0 + - bioconductor-ensdb.mmusculus.v79 >=2.99.0,<2.100.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-gsva >=2.0.0,<2.1.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-singlecellsignalr >=1.18.0,<1.19.0 - r-ape - r-base - r-cli @@ -49,19 +50,18 @@ requirements: - r-spatstat.explore - r-spatstat.geom - r-tidyr + run: - - 'bioconductor-aucell >=1.24.0,<1.25.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-ensdb.hsapiens.v79 >=2.99.0,<2.100.0' - - 'bioconductor-ensdb.mmusculus.v79 >=2.99.0,<2.100.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-gsva >=1.50.0,<1.51.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-singlecellsignalr >=1.14.0,<1.15.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-aucell >=1.28.0,<1.29.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-ensdb.hsapiens.v79 >=2.99.0,<2.100.0 + - bioconductor-ensdb.mmusculus.v79 >=2.99.0,<2.100.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-gsva >=2.0.0,<2.1.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-singlecellsignalr >=1.18.0,<1.19.0 - r-ape - r-base - r-cli @@ -77,13 +77,16 @@ requirements: - r-spatstat.explore - r-spatstat.geom - r-tidyr + +source: + md5: df5ae072515e820cc5027911aae2e49a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction' - description: 'scFeatures constructs multi-view representations of single-cell and spatial data. scFeatures is a tool that generates multi-view representations of single-cell and spatial data through the construction of a total of 17 feature types. These features can then be used for a variety of analyses using other software in Biocondutor.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scgps/meta.yaml b/recipes/bioconductor-scgps/meta.yaml index c5ced940c31bd..799b57fe2ea63 100644 --- a/recipes/bioconductor-scgps/meta.yaml +++ b/recipes/bioconductor-scgps/meta.yaml @@ -1,37 +1,43 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "scGPS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The package implements two main algorithms to answer two key questions: a SCORE (Stable Clustering at Optimal REsolution) to find subpopulations, followed by scGPS to investigate the relationships between subpopulations.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d11fe3a4af0d56d3028d97c6090ccfb build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scgps", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown, RColorBrewer, ReactomePA, clusterProfiler, cowplot, org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne, BiocParallel, e1071, WGCNA, devtools, DOSE # SystemRequirements: GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-caret >=6.0' + - r-caret >=6.0 - r-dplyr - r-dynamictreecut - r-fastcluster - - 'r-ggplot2 >=2.2.1' - - 'r-glmnet >2.0' + - r-ggplot2 >=2.2.1 + - r-glmnet >2.0 - r-locfit - r-rcpp - r-rcpparmadillo @@ -39,31 +45,30 @@ requirements: - libblas - liblapack run: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-caret >=6.0' + - r-caret >=6.0 - r-dplyr - r-dynamictreecut - r-fastcluster - - 'r-ggplot2 >=2.2.1' - - 'r-glmnet >2.0' + - r-ggplot2 >=2.2.1 + - r-glmnet >2.0 - r-locfit - r-rcpp - r-rcpparmadillo - r-rcppparallel - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 656578131e67e1f49507007d41c7c772 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)' - description: 'The package implements two main algorithms to answer two key questions: a SCORE (Stable Clustering at Optimal REsolution) to find subpopulations, followed by scGPS to investigate the relationships between subpopulations.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-schex/meta.yaml b/recipes/bioconductor-schex/meta.yaml index c1c3dd9dbf16f..f568de4dd47c4 100644 --- a/recipes/bioconductor-schex/meta.yaml +++ b/recipes/bioconductor-schex/meta.yaml @@ -1,59 +1,60 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "schex" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Builds hexbin plots for variables and dimension reduction stored in single cell omics data such as SingleCellExperiment. The ideas used in this package are based on the excellent work of Dan Carr, Nicholas Lewin-Koh, Martin Maechler and Thomas Lumley. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Hexbin plots for single cell omics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5be5dd9c76b2ee49cc894a728b08e2e0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-schex", max_pin="x.x") }}' - noarch: generic -# Suggests: ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, shinydashboard, iSEE, igraph, scran + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, Seurat, shinydashboard, iSEE, igraph, scran, tibble, scuttle requirements: host: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-cluster - r-concaveman - r-dplyr - r-entropy - r-ggforce - - 'r-ggplot2 >=3.2.1' + - r-ggplot2 >=3.2.1 - r-hexbin - - r-scales - - r-seurat - - r-shiny + - r-rlang run: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-cluster - r-concaveman - r-dplyr - r-entropy - r-ggforce - - 'r-ggplot2 >=3.2.1' + - r-ggplot2 >=3.2.1 - r-hexbin - - r-scales - - r-seurat - - r-shiny + - r-rlang + +source: + md5: cfc765d08e235787112c320def671495 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Hexbin plots for single cell omics data' - description: 'Builds hexbin plots for variables and dimension reduction stored in single cell omics data such as SingleCellExperiment and SeuratObject. The ideas used in this package are based on the excellent work of Dan Carr, Nicholas Lewin-Koh, Martin Maechler and Thomas Lumley.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-schot/meta.yaml b/recipes/bioconductor-schot/meta.yaml index c35c587215b4b..fc57bccaecc5d 100644 --- a/recipes/bioconductor-schot/meta.yaml +++ b/recipes/bioconductor-schot/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "scHOT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Single cell Higher Order Testing (scHOT) is an R package that facilitates testing changes in higher order structure of gene expression along either a developmental trajectory or across space. scHOT is general and modular in nature, can be run in multiple data contexts such as along a continuous trajectory, between discrete groups, and over spatial orientations; as well as accommodate any higher order measurement such as variability or correlation. scHOT meaningfully adds to first order effect testing, such as differential expression, and provides a framework for interrogating higher order interactions from single cell data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: single-cell higher order testing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 75f460d2a6c2d8bee223b64a05eb6224 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-schot", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, markdown, rmarkdown, scater, scattermore, scales, matrixStats, deldir requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggforce - r-ggplot2 @@ -34,24 +36,27 @@ requirements: - r-matrix - r-reshape run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggforce - r-ggplot2 - r-igraph - r-matrix - r-reshape + +source: + md5: 07d76ef9e86a9cd78462437f1bf84196 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'single-cell higher order testing' - description: 'Single cell Higher Order Testing (scHOT) is an R package that facilitates testing changes in higher order structure of gene expression along either a developmental trajectory or across space. scHOT is general and modular in nature, can be run in multiple data contexts such as along a continuous trajectory, between discrete groups, and over spatial orientations; as well as accommodate any higher order measurement such as variability or correlation. scHOT meaningfully adds to first order effect testing, such as differential expression, and provides a framework for interrogating higher order interactions from single cell data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scider/meta.yaml b/recipes/bioconductor-scider/meta.yaml index 2dae5324cfcfe..150221c4b543b 100644 --- a/recipes/bioconductor-scider/meta.yaml +++ b/recipes/bioconductor-scider/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "scider" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: scider is a user-friendly R package providing functions to model the global density of cells in a slide of spatial transcriptomics data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. After modelling density, the package allows for serveral downstream analysis, including colocalization analysis, boundary detection analysis and differential density analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Spatial cell-type inter-correlation by density in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d20e0e846be7368da2613650b3834957 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scider", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: edgeR, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-igraph @@ -40,9 +42,9 @@ requirements: - r-spatstat.explore - r-spatstat.geom run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-igraph @@ -57,13 +59,16 @@ requirements: - r-shiny - r-spatstat.explore - r-spatstat.geom + +source: + md5: a97bda001a8ffbe4a5491691b675310a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Spatial cell-type inter-correlation by density in R' - description: 'scider is an user-friendly R package providing functions to model the global density of cells in a slide of spatial transcriptomics data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. After modelling density, the package allows for serveral downstream analysis, including colocalization analysis, boundary detection analysis and differential density analysis.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scifer/meta.yaml b/recipes/bioconductor-scifer/meta.yaml index 6f53163b0a43b..91a24e5243f66 100644 --- a/recipes/bioconductor-scifer/meta.yaml +++ b/recipes/bioconductor-scifer/meta.yaml @@ -1,69 +1,84 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "scifer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Have you ever index sorted cells in a 96 or 384-well plate and then sequenced using Sanger sequencing? If so, you probably had some struggles to either check the electropherogram of each cell sequenced manually, or when you tried to identify which cell was sorted where after sequencing the plate. Scifer was developed to solve this issue by performing basic quality control of Sanger sequences and merging flow cytometry data from probed single-cell sorted B cells with sequencing data. scifer can export summary tables, 'fasta' files, electropherograms for visual inspection, and generate reports. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 'Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 82fb184bec0c09d5f7067baf81f8fee1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scifer", max_pin="x.x") }}' - noarch: generic -# Suggests: fs, BiocStyle, testthat (>= 3.0.0) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocBaseUtils, fs, BiocStyle, testthat (>= 3.0.0) requirements: + host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-decipher >=2.30.0,<2.31.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-sangerseqr >=1.38.0,<1.39.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-basilisk.utils >=1.18.0,<1.19.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-decipher >=3.2.0,<3.3.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-sangerseqr >=1.42.0,<1.43.0 - r-base - r-data.table - r-dplyr - r-ggplot2 - r-gridextra + - r-here - r-kableextra - r-knitr - r-plyr + - r-reticulate - r-rlang - r-rmarkdown - r-scales - r-stringr - r-tibble + run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-decipher >=2.30.0,<2.31.0' - - 'bioconductor-flowcore >=2.14.0,<2.15.0' - - 'bioconductor-sangerseqr >=1.38.0,<1.39.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-basilisk.utils >=1.18.0,<1.19.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-decipher >=3.2.0,<3.3.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - bioconductor-sangerseqr >=1.42.0,<1.43.0 - r-base - r-data.table - r-dplyr - r-ggplot2 - r-gridextra + - r-here - r-kableextra - r-knitr - r-plyr + - r-reticulate - r-rlang - r-rmarkdown - r-scales - r-stringr - r-tibble + +source: + md5: 198aef728d59d2bb60481383fb140834 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences' - description: 'Have you ever index sorted cells in a 96 or 384-well plate and then sequenced using Sanger sequencing? If so, you probably had some struggles to either check the electropherogram of each cell sequenced manually, or when you tried to identify which cell was sorted where after sequencing the plate. Scifer was developed to solve this issue by performing basic quality control of Sanger sequences and merging flow cytometry data from probed single-cell sorted B cells with sequencing data. scifer can export summary tables, ''fasta'' files, electropherograms for visual inspection, and generate reports.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sclcbam/meta.yaml b/recipes/bioconductor-sclcbam/meta.yaml index 974fda737ce12..7f39f7c50f7c1 100644 --- a/recipes/bioconductor-sclcbam/meta.yaml +++ b/recipes/bioconductor-sclcbam/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "SCLCBam" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 660f11c1751b54cc942e91045884bfe6 +about: + description: Whole-exome sequencing data from a murine small-cell lung tumor; only contains data of chromosome 4. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Sequence data from chromosome 4 of a small-cell lung tumor build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sclcbam", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2e1013ff182c81e75551154d3849aa06 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Sequence data from chromosome 4 of a small-cell lung tumor' - description: 'Whole-exome sequencing data from a murine small-cell lung tumor; only contains data of chromosome 4.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sclcbam/post-link.sh b/recipes/bioconductor-sclcbam/post-link.sh index ebe08391743a4..fc98fef6129d6 100644 --- a/recipes/bioconductor-sclcbam/post-link.sh +++ b/recipes/bioconductor-sclcbam/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "sclcbam-1.34.0" +installBiocDataPackage.sh "sclcbam-1.38.0" diff --git a/recipes/bioconductor-scmap/meta.yaml b/recipes/bioconductor-scmap/meta.yaml index 747a349f39a63..1d097727ca134 100644 --- a/recipes/bioconductor-scmap/meta.yaml +++ b/recipes/bioconductor-scmap/meta.yaml @@ -1,31 +1,37 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "scmap" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Single-cell RNA-seq (scRNA-seq) is widely used to investigate the composition of complex tissues since the technology allows researchers to define cell-types using unsupervised clustering of the transcriptome. However, due to differences in experimental methods and computational analyses, it is often challenging to directly compare the cells identified in two different experiments. scmap is a method for projecting cells from a scRNA-seq experiment on to the cell-types or individual cells identified in a different experiment. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A tool for unsupervised projection of single cell RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: de159d16de109a02a1c7cb3c85418b58 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scmap", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-e1071 @@ -34,17 +40,17 @@ requirements: - r-matrixstats - r-proxy - r-randomforest - - 'r-rcpp >=0.12.12' + - r-rcpp >=0.12.12 - r-rcpparmadillo - r-reshape2 - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-e1071 @@ -53,20 +59,19 @@ requirements: - r-matrixstats - r-proxy - r-randomforest - - 'r-rcpp >=0.12.12' + - r-rcpp >=0.12.12 - r-rcpparmadillo - r-reshape2 - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: f6a5af5c1a78e5dcdcad2e20efc99bb3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'A tool for unsupervised projection of single cell RNA-seq data' - description: 'Single-cell RNA-seq (scRNA-seq) is widely used to investigate the composition of complex tissues since the technology allows researchers to define cell-types using unsupervised clustering of the transcriptome. However, due to differences in experimental methods and computational analyses, it is often challenging to directly compare the cells identified in two different experiments. scmap is a method for projecting cells from a scRNA-seq experiment on to the cell-types or individual cells identified in a different experiment.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scmerge/meta.yaml b/recipes/bioconductor-scmerge/meta.yaml index e33892f3dba5d..3850316f60b89 100644 --- a/recipes/bioconductor-scmerge/meta.yaml +++ b/recipes/bioconductor-scmerge/meta.yaml @@ -1,39 +1,41 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "scMerge" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Like all gene expression data, single-cell data suffers from batch effects and other unwanted variations that makes accurate biological interpretations difficult. The scMerge method leverages factor analysis, stably expressed genes (SEGs) and (pseudo-) replicates to remove unwanted variations and merge multiple single-cell data. This package contains all the necessary functions in the scMerge pipeline, including the identification of SEGs, replication-identification methods, and merging of single-cell data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'scMerge: Merging multiple batches of scRNA-seq data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d5b285890500ad5c781d33ab45282aca build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scmerge", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, proxy, testthat, badger requirements: host: - - 'bioconductor-batchelor >=1.18.0,<1.19.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-m3drop >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-batchelor >=1.22.0,<1.23.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-m3drop >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-cvtools @@ -42,18 +44,18 @@ requirements: - r-proxyc - r-ruv run: - - 'bioconductor-batchelor >=1.18.0,<1.19.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-m3drop >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-batchelor >=1.22.0,<1.23.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-m3drop >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-cvtools @@ -61,13 +63,16 @@ requirements: - r-igraph - r-proxyc - r-ruv + +source: + md5: 0ead2213629965114185276b50d3f4d7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'scMerge: Merging multiple batches of scRNA-seq data' - description: 'Like all gene expression data, single-cell data suffers from batch effects and other unwanted variations that makes accurate biological interpretations difficult. The scMerge method leverages factor analysis, stably expressed genes (SEGs) and (pseudo-) replicates to remove unwanted variations and merge multiple single-cell data. This package contains all the necessary functions in the scMerge pipeline, including the identification of SEGs, replication-identification methods, and merging of single-cell data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scmet/meta.yaml b/recipes/bioconductor-scmet/meta.yaml index 9a2d2fce9889a..875ac41566675 100644 --- a/recipes/bioconductor-scmet/meta.yaml +++ b/recipes/bioconductor-scmet/meta.yaml @@ -1,34 +1,43 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "scMET" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: High-throughput single-cell measurements of DNA methylomes can quantify methylation heterogeneity and uncover its role in gene regulation. However, technical limitations and sparse coverage can preclude this task. scMET is a hierarchical Bayesian model which overcomes sparsity, sharing information across cells and genomic features to robustly quantify genuine biological heterogeneity. scMET can identify highly variable features that drive epigenetic heterogeneity, and perform differential methylation and variability analyses. We illustrate how scMET facilitates the characterization of epigenetically distinct cell populations and how it enables the formulation of novel hypotheses on the epigenetic regulation of gene expression. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Bayesian modelling of cell-to-cell DNA methylation heterogeneity -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6420a2af7464f67eb676f06d20f9d5a6 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scmet", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown # SystemRequirements: GNU make requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make + host: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - - 'r-bh >=1.66.0' + - r-bh >=1.66.0 - r-coda - r-cowplot - r-data.table @@ -38,24 +47,25 @@ requirements: - r-mass - r-matrix - r-matrixstats - - 'r-rcpp >=1.0.0' - - 'r-rcppeigen >=0.3.3.3.0' - - 'r-rcppparallel >=5.0.1' - - 'r-rstan >=2.21.3' - - 'r-rstantools >=2.1.0' - - 'r-stanheaders >=2.21.0.7' + - r-rcpp >=1.0.0 + - r-rcppeigen >=0.3.3.3.0 + - r-rcppparallel >=5.0.1 + - r-rstan >=2.21.3 + - r-rstantools >=2.1.0 + - r-stanheaders >=2.21.0.7 - r-vgam - r-viridis - libblas - liblapack + run: - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - - 'r-bh >=1.66.0' + - r-bh >=1.66.0 - r-coda - r-cowplot - r-data.table @@ -65,26 +75,24 @@ requirements: - r-mass - r-matrix - r-matrixstats - - 'r-rcpp >=1.0.0' - - 'r-rcppeigen >=0.3.3.3.0' - - 'r-rcppparallel >=5.0.1' - - 'r-rstan >=2.21.3' - - 'r-rstantools >=2.1.0' - - 'r-stanheaders >=2.21.0.7' + - r-rcpp >=1.0.0 + - r-rcppeigen >=0.3.3.3.0 + - r-rcppparallel >=5.0.1 + - r-rstan >=2.21.3 + - r-rstantools >=2.1.0 + - r-stanheaders >=2.21.0.7 - r-vgam - r-viridis - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 454268faca57a0ade6352837704f5b15 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Bayesian modelling of cell-to-cell DNA methylation heterogeneity' - description: 'High-throughput single-cell measurements of DNA methylomes can quantify methylation heterogeneity and uncover its role in gene regulation. However, technical limitations and sparse coverage can preclude this task. scMET is a hierarchical Bayesian model which overcomes sparsity, sharing information across cells and genomic features to robustly quantify genuine biological heterogeneity. scMET can identify highly variable features that drive epigenetic heterogeneity, and perform differential methylation and variability analyses. We illustrate how scMET facilitates the characterization of epigenetically distinct cell populations and how it enables the formulation of novel hypotheses on the epigenetic regulation of gene expression.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scmeth/meta.yaml b/recipes/bioconductor-scmeth/meta.yaml index 97b16204b19f5..1678582c6f1e9 100644 --- a/recipes/bioconductor-scmeth/meta.yaml +++ b/recipes/bioconductor-scmeth/meta.yaml @@ -1,65 +1,70 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "scmeth" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions to analyze methylation data can be found here. Some functions are relevant for single cell methylation data but most other functions can be used for any methylation data. Highlight of this workflow is the comprehensive quality control report. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Functions to conduct quality control analysis in methylation data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 52beac81d58da27e01cc5e1a0b6584b2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scmeth", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, BiocGenerics, ggplot2, ggthemes requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-annotatr >=1.28.0,<1.29.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsseq >=1.38.0,<1.39.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-annotatr >=1.32.0,<1.33.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsseq >=1.42.0,<1.43.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dt - r-knitr - r-reshape2 - r-rmarkdown run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-annotatr >=1.28.0,<1.29.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsseq >=1.38.0,<1.39.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-annotatr >=1.32.0,<1.33.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsseq >=1.42.0,<1.43.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dt - r-knitr - r-reshape2 - r-rmarkdown + +source: + md5: 4a9841823c20b5a904aa0ccb3190d599 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Functions to conduct quality control analysis in methylation data' - description: 'Functions to analyze methylation data can be found here. Some functions are relevant for single cell methylation data but most other functions can be used for any methylation data. Highlight of this workflow is the comprehensive quality control report.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scmitomut/build.sh b/recipes/bioconductor-scmitomut/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scmitomut/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scmitomut/meta.yaml b/recipes/bioconductor-scmitomut/meta.yaml new file mode 100644 index 0000000000000..e28a334b0568f --- /dev/null +++ b/recipes/bioconductor-scmitomut/meta.yaml @@ -0,0 +1,70 @@ +{% set version = "1.2.0" %} +{% set name = "scMitoMut" %} +{% set bioc = "3.20" %} + +about: + description: This package is designed for calling lineage-informative mitochondrial mutations using single-cell sequencing data, such as scRNASeq and scATACSeq (preferably the latter due to RNA editing issues). It includes functions for mutation calling and visualization. Mutation calling is done using beta-binomial distribution. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Single-cell Mitochondrial Mutation Analysis Tool + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scmitomut", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM, R.utils +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 + - r-base + - r-data.table + - r-ggplot2 + - r-magrittr + - r-pheatmap + - r-plyr + - r-rcolorbrewer + - r-rcpp + - r-rcpparmadillo + - r-readr + - r-stringr + - libblas + - liblapack + run: + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 + - r-base + - r-data.table + - r-ggplot2 + - r-magrittr + - r-pheatmap + - r-plyr + - r-rcolorbrewer + - r-rcpp + - r-rcpparmadillo + - r-readr + - r-stringr + +source: + md5: 4add4309acee79623e5cdee0482242fc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-scmultiome/build_failure.linux-64.yaml b/recipes/bioconductor-scmultiome/build_failure.linux-64.yaml deleted file mode 100644 index 3225ddc538d53..0000000000000 --- a/recipes/bioconductor-scmultiome/build_failure.linux-64.yaml +++ /dev/null @@ -1,106 +0,0 @@ -recipe_sha: 6724b9796e501ce375d77f605eb535671bf9bee68ee4a9d1873f64c6432b2905 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: |- - dependency issue -log: |2- - - bioconductor-genomicranges >=1.52.0,<1.53.0 - - r-base 4.3.* - - bioconductor-multiassayexperiment >=1.26.0,<1.27.0 - - bioconductor-experimenthub >=2.8.0,<2.9.0 - - bioconductor-s4vectors >=0.38.0,<0.39.0 - - r-checkmate - - bioconductor-hdf5array >=1.28.0,<1.29.0 - - bioconductor-singlecellexperiment >=1.22.0,<1.23.0 - - bioconductor-delayedarray >=0.26.0,<0.27.0 - - bioconductor-rhdf5 >=2.44.0,<2.45.0 - - bioconductor-annotationhub >=3.8.0,<3.9.0 - - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 - - r-azurestor - - with channels: - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested r-azurestor - - - - Leaving build/test directories: - Work: - /opt/conda/conda-bld/work - Test: - /opt/conda/conda-bld/test_tmp - Leaving build/test environments: - Test: - source activate /opt/conda/conda-bld/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl - Build: - source activate /opt/conda/conda-bld/_build_env - - - Traceback (most recent call last): - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 141, in mamba_get_install_actions - solution = solver.solve_for_action(_specs, prefix) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 244, in solve_for_action - t = self.solve(specs) - File "/opt/conda/lib/python3.8/site-packages/boa/core/solver.py", line 234, in solve - raise RuntimeError("Solver could not find solution." error_string) - RuntimeError: Solver could not find solution.Mamba failed to solve: - - bioconductor-genomicranges >=1.52.0,<1.53.0 - - r-base 4.3.* - - bioconductor-multiassayexperiment >=1.26.0,<1.27.0 - - bioconductor-experimenthub >=2.8.0,<2.9.0 - - bioconductor-s4vectors >=0.38.0,<0.39.0 - - r-checkmate - - bioconductor-hdf5array >=1.28.0,<1.29.0 - - bioconductor-singlecellexperiment >=1.22.0,<1.23.0 - - bioconductor-delayedarray >=0.26.0,<0.27.0 - - bioconductor-rhdf5 >=2.44.0,<2.45.0 - - bioconductor-annotationhub >=3.8.0,<3.9.0 - - bioconductor-summarizedexperiment >=1.30.0,<1.31.0 - - r-azurestor - - with channels: - - conda-forge - - bioconda - - defaults - - The reported errors are: - - Encountered problems while solving: - - - nothing provides requested r-azurestor - - - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2038, in build - output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 787, in expand_outputs - for (output_dict, m) in deepcopy(_m).get_output_metadata_set(permit_unsatisfiable_variants=False): - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 2524, in get_output_metadata_set - conda_packages = finalize_outputs_pass( - File "/opt/conda/lib/python3.8/site-packages/conda_build/metadata.py", line 884, in finalize_outputs_pass - fm = finalize_metadata( - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 547, in finalize_metadata - build_unsat, host_unsat = add_upstream_pins(m, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 409, in add_upstream_pins - host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host', - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 374, in _read_upstream_pin_files - deps, actions, unsat = get_env_dependencies(m, env, m.config.variant, - File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 131, in get_env_dependencies - actions = environ.get_install_actions(tmpdir, tuple(dependencies), env, - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 150, in mamba_get_install_actions - raise err - conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-azurestor")} -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-scmultiome/meta.yaml b/recipes/bioconductor-scmultiome/meta.yaml index eaa4577ecd304..b1b808f26c1cb 100644 --- a/recipes/bioconductor-scmultiome/meta.yaml +++ b/recipes/bioconductor-scmultiome/meta.yaml @@ -1,62 +1,67 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "scMultiome" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Single cell multiome data, containing chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) information analyzed with the ArchR package and presented as MultiAssayExperiment objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: CC BY-SA 4.0 + summary: Collection of Public Single-Cell Multiome (scATAC + scRNAseq) Datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: db13145ffc5eb5430eee8ac7212e1b7d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scmultiome", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, IRanges, Matrix, knitr, rmarkdown, rstudioapi, testthat (>= 3.0.0), devtools, BiocStyle, ExperimentHubData requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-alabaster.matrix >=1.6.0,<1.7.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-azurestor - r-base - r-checkmate run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-alabaster.matrix >=1.6.0,<1.7.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-azurestor - r-base - r-checkmate - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 64a106794e0af59f4249dba3124aaed3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'CC BY-SA 4.0' - summary: 'Collection of Public Single-Cell Multiome (scATAC + scRNAseq) Datasets' - description: 'Single cell multiome data, containing chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) information analyzed with the ArchR package and presented as MultiAssayExperiment objects.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scmultiome/post-link.sh b/recipes/bioconductor-scmultiome/post-link.sh index 1324e5cb2e2c7..1a9c5a344c5cb 100644 --- a/recipes/bioconductor-scmultiome/post-link.sh +++ b/recipes/bioconductor-scmultiome/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "scmultiome-1.2.0" +installBiocDataPackage.sh "scmultiome-1.6.0" diff --git a/recipes/bioconductor-scmultisim/build.sh b/recipes/bioconductor-scmultisim/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scmultisim/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scmultisim/meta.yaml b/recipes/bioconductor-scmultisim/meta.yaml new file mode 100644 index 0000000000000..2adac1e0ae9dc --- /dev/null +++ b/recipes/bioconductor-scmultisim/meta.yaml @@ -0,0 +1,77 @@ +{% set version = "1.2.0" %} +{% set name = "scMultiSim" %} +{% set bioc = "3.20" %} + +about: + description: scMultiSim simulates paired single cell RNA-seq, single cell ATAC-seq and RNA velocity data, while incorporating mechanisms of gene regulatory networks, chromatin accessibility and cell-cell interactions. It allows users to tune various parameters controlling the amount of each biological factor, variation of gene-expression levels, the influence of chromatin accessibility on RNA sequence data, and so on. It can be used to benchmark various computational methods for single cell multi-omics data, and to assist in experimental design of wet-lab experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Simulation of Multi-Modality Single Cell Data Guided By Gene Regulatory Networks and Cell-Cell Interactions + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scmultisim", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, roxygen2, shiny, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-ape + - r-assertthat + - r-base + - r-crayon + - r-dplyr + - r-foreach + - r-ggplot2 + - r-gplots + - r-igraph + - r-kernelknn + - r-markdown + - r-mass + - r-matrixstats + - r-phytools + - r-rlang + - r-rtsne + - r-zeallot + run: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-ape + - r-assertthat + - r-base + - r-crayon + - r-dplyr + - r-foreach + - r-ggplot2 + - r-gplots + - r-igraph + - r-kernelknn + - r-markdown + - r-mass + - r-matrixstats + - r-phytools + - r-rlang + - r-rtsne + - r-zeallot + +source: + md5: ad7fee6876a5388c41fae6890079f95e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-scnorm/meta.yaml b/recipes/bioconductor-scnorm/meta.yaml index c4058c473a397..9a0858e699d8d 100644 --- a/recipes/bioconductor-scnorm/meta.yaml +++ b/recipes/bioconductor-scnorm/meta.yaml @@ -1,32 +1,40 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "SCnorm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements SCnorm — a method to normalize single-cell RNA-seq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Normalization of single cell RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cfac086eb57336e865c999c4c0b42a0c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scnorm", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-scnorm + path: recipes/bioconductor-scnorm + version: 1.2.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, devtools requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-data.table @@ -35,11 +43,11 @@ requirements: - r-moments - r-quantreg run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-data.table @@ -47,18 +55,16 @@ requirements: - r-ggplot2 - r-moments - r-quantreg + +source: + md5: 3243d13c27af322a2664ee0f094d755d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Normalization of single cell RNA-seq data' - description: 'This package implements SCnorm — a method to normalize single-cell RNA-seq data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-scnorm - path: recipes/bioconductor-scnorm - version: 1.2.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scone/meta.yaml b/recipes/bioconductor-scone/meta.yaml index 07e654e223342..e381b440d10fe 100644 --- a/recipes/bioconductor-scone/meta.yaml +++ b/recipes/bioconductor-scone/meta.yaml @@ -1,36 +1,40 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "scone" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Single Cell Overview of Normalized Expression data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0e7dd77999fc8cbf842fee6452c82a1b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scone", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData requirements: + host: - - 'bioconductor-aroma.light >=3.32.0,<3.33.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-ruvseq >=1.36.0,<1.37.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-aroma.light >=3.36.0,<3.37.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-ruvseq >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-boot - r-class @@ -44,16 +48,19 @@ requirements: - r-mixtools - r-rarpack - r-rcolorbrewer + run: - - 'bioconductor-aroma.light >=3.32.0,<3.33.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-ruvseq >=1.36.0,<1.37.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-aroma.light >=3.36.0,<3.37.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-ruvseq >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-boot - r-class @@ -67,12 +74,16 @@ requirements: - r-mixtools - r-rarpack - r-rcolorbrewer + +source: + md5: 98f2097f5c2cec8327af9125f51852e7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Single Cell Overview of Normalized Expression data' - description: 'SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sconify/meta.yaml b/recipes/bioconductor-sconify/meta.yaml index c166731eb09ff..b5b9cb2f718e0 100644 --- a/recipes/bioconductor-sconify/meta.yaml +++ b/recipes/bioconductor-sconify/meta.yaml @@ -1,28 +1,29 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "Sconify" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package does k-nearest neighbor based statistics and visualizations with flow and mass cytometery data. This gives tSNE maps"fold change" functionality and provides a data quality metric by assessing manifold overlap between fcs files expected to be the same. Other applications using this package include imputation, marker redundancy, and testing the relative information loss of lower dimension embeddings compared to the original manifold. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: A toolkit for performing KNN-based statistics for flow and mass cytometry data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61762bc5d7e8560ae818942a21da33a5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sconify", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-dplyr - r-fnn @@ -32,7 +33,7 @@ requirements: - r-rtsne - r-tibble run: - - 'bioconductor-flowcore >=2.14.0,<2.15.0' + - bioconductor-flowcore >=2.18.0,<2.19.0 - r-base - r-dplyr - r-fnn @@ -41,12 +42,16 @@ requirements: - r-readr - r-rtsne - r-tibble + +source: + md5: 8cd64b7a4ca0bcd04fb3aad9a7da3429 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A toolkit for performing KNN-based statistics for flow and mass cytometry data' - description: 'This package does k-nearest neighbor based statistics and visualizations with flow and mass cytometery data. This gives tSNE maps"fold change" functionality and provides a data quality metric by assessing manifold overlap between fcs files expected to be the same. Other applications using this package include imputation, marker redundancy, and testing the relative information loss of lower dimension embeddings compared to the original manifold.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scope/meta.yaml b/recipes/bioconductor-scope/meta.yaml index 3943cc3b77751..6360b1d7f44c5 100644 --- a/recipes/bioconductor-scope/meta.yaml +++ b/recipes/bioconductor-scope/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "SCOPE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Whole genome single-cell DNA sequencing (scDNA-seq) enables characterization of copy number profiles at the cellular level. This circumvents the averaging effects associated with bulk-tissue sequencing and has increased resolution yet decreased ambiguity in deconvolving cancer subclones and elucidating cancer evolutionary history. ScDNA-seq data is, however, sparse, noisy, and highly variable even within a homogeneous cell population, due to the biases and artifacts that are introduced during the library preparation and sequencing procedure. Here, we propose SCOPE, a normalization and copy number estimation method for scDNA-seq data. The distinguishing features of SCOPE include: (i) utilization of cell-specific Gini coefficients for quality controls and for identification of normal/diploid cells, which are further used as negative control samples in a Poisson latent factor model for normalization; (ii) modeling of GC content bias using an expectation-maximization algorithm embedded in the Poisson generalized linear models, which accounts for the different copy number states along the genome; (iii) a cross-sample iterative segmentation procedure to identify breakpoints that are shared across cells from the same genetic background.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A normalization and copy number estimation method for single-cell DNA sequencing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b8e4ce76717f217322282d378de1b3bd build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scope", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-desctools - r-doparallel @@ -39,29 +41,32 @@ requirements: - r-gplots - r-rcolorbrewer run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-dnacopy >=1.76.0,<1.77.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-dnacopy >=1.80.0,<1.81.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-desctools - r-doparallel - r-foreach - r-gplots - r-rcolorbrewer + +source: + md5: 9c3441b1dcb0f8a7f7cc20d12d534730 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'A normalization and copy number estimation method for single-cell DNA sequencing' - description: 'Whole genome single-cell DNA sequencing (scDNA-seq) enables characterization of copy number profiles at the cellular level. This circumvents the averaging effects associated with bulk-tissue sequencing and has increased resolution yet decreased ambiguity in deconvolving cancer subclones and elucidating cancer evolutionary history. ScDNA-seq data is, however, sparse, noisy, and highly variable even within a homogeneous cell population, due to the biases and artifacts that are introduced during the library preparation and sequencing procedure. Here, we propose SCOPE, a normalization and copy number estimation method for scDNA-seq data. The distinguishing features of SCOPE include: (i) utilization of cell-specific Gini coefficients for quality controls and for identification of normal/diploid cells, which are further used as negative control samples in a Poisson latent factor model for normalization; (ii) modeling of GC content bias using an expectation-maximization algorithm embedded in the Poisson generalized linear models, which accounts for the different copy number states along the genome; (iii) a cross-sample iterative segmentation procedure to identify breakpoints that are shared across cells from the same genetic background.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scoreinvhap/meta.yaml b/recipes/bioconductor-scoreinvhap/meta.yaml index 2ce9837a52775..db40c191a71fd 100644 --- a/recipes/bioconductor-scoreinvhap/meta.yaml +++ b/recipes/bioconductor-scoreinvhap/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "scoreInvHap" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'scoreInvHap can get the samples'' inversion status of known inversions. scoreInvHap uses SNP data as input and requires the following information about the inversion: genotype frequencies in the different haplotypes, R2 between the region SNPs and inversion status and heterozygote genotypes in the reference. The package include this data for 21 inversions.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Get inversion status in predefined regions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7505f8161571dcc7b9b752fc62dedce5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scoreinvhap", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-snpstats >=1.52.0,<1.53.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-snpstats >=1.56.0,<1.57.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-snpstats >=1.52.0,<1.53.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-snpstats >=1.56.0,<1.57.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base + +source: + md5: c12cfc5f84f75c3194003486aa5d7179 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Get inversion status in predefined regions' - description: 'scoreInvHap can get the samples'' inversion status of known inversions. scoreInvHap uses SNP data as input and requires the following information about the inversion: genotype frequencies in the different haplotypes, R2 between the region SNPs and inversion status and heterozygote genotypes in the reference. The package include this data for 21 inversions.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scoup/build.sh b/recipes/bioconductor-scoup/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scoup/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scoup/meta.yaml b/recipes/bioconductor-scoup/meta.yaml new file mode 100644 index 0000000000000..1fa407e6a919a --- /dev/null +++ b/recipes/bioconductor-scoup/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.0.0" %} +{% set name = "scoup" %} +{% set bioc = "3.20" %} + +about: + description: An elaborate molecular evolutionary framework that facilitates straightforward simulation of codon genetic sequences subjected to different degrees and/or patterns of Darwinian selection. The model was built upon the fitness landscape paradigm of Sewall Wright, as popularised by the mutation-selection model of Halpern and Bruno. This enabled realistic evolutionary process of living organisms to be reproduced seamlessly. For example, an Ornstein-Uhlenbeck fitness update algorithm is incorporated herein. Consequently, otherwise complex biological processes, such as the effect of the interplay between genetic drift and mutation on the inference of diversifying selection, may now be investigated with minimal effort. Frequency-dependent and deterministic fitness landscape update techniques are also available. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Simulate Codons with Darwinian Selection Modelled as an OU Process +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scoup", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: BiocManager, BiocStyle, bookdown, htmltools, knitr, testthat (>= 3.0.0), yaml +requirements: + host: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - r-base + - r-matrix + run: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - r-base + - r-matrix +source: + md5: 17986a009bc26f64976fde1c6bf17cff + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-scp/meta.yaml b/recipes/bioconductor-scp/meta.yaml index c349acb3dacba..3e01e163a3bba 100644 --- a/recipes/bioconductor-scp/meta.yaml +++ b/recipes/bioconductor-scp/meta.yaml @@ -1,54 +1,67 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "scp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics data. The package is an extension to the 'QFeatures' package and relies on 'SingleCellExpirement' to enable single-cell proteomics analyses. The package offers the user the functionality to process quantitative table (as generated by MaxQuant, Proteome Discoverer, and more) into data tables ready for downstream analysis and data visualization. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Mass Spectrometry-Based Single-Cell Proteomics Data Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c4f759cfb996e6150ecec65b7de3e343 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scp", max_pin="x.x") }}' - noarch: generic -# Suggests: scpdata, testthat, knitr, BiocStyle, rmarkdown, ggplot2, patchwork, impute, scater, sva, preprocessCore, vsn, uwot + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, BiocGenerics, MsDataHub (>= 1.3.3), impute, knitr, patchwork, preprocessCore, rmarkdown, scater, scpdata, sva, testthat, vdiffr, vsn, uwot requirements: host: - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-qfeatures >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-ihw >=1.34.0,<1.35.0 + - bioconductor-metapod >=1.14.0,<1.15.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-qfeatures >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - r-dplyr - - r-magrittr + - r-ggplot2 + - r-ggrepel - r-matrixstats + - r-nipals + - r-rcolorbrewer run: - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-qfeatures >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-ihw >=1.34.0,<1.35.0 + - bioconductor-metapod >=1.14.0,<1.15.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-qfeatures >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - r-dplyr - - r-magrittr + - r-ggplot2 + - r-ggrepel - r-matrixstats + - r-nipals + - r-rcolorbrewer + +source: + md5: 0216fe89610f6d2a2430695639439fd7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Mass Spectrometry-Based Single-Cell Proteomics Data Analysis' - description: 'Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics data. The package is an extension to the ''QFeatures'' package and relies on ''SingleCellExpirement'' to enable single-cell proteomics analyses. The package offers the user the functionality to process quantitative table (as generated by MaxQuant, Proteome Discoverer, and more) into data tables ready for downstream analysis and data visualization.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scpca/meta.yaml b/recipes/bioconductor-scpca/meta.yaml index 61a413188a29a..fb5d5ef408484 100644 --- a/recipes/bioconductor-scpca/meta.yaml +++ b/recipes/bioconductor-scpca/meta.yaml @@ -1,31 +1,34 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "scPCA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A toolbox for sparse contrastive principal component analysis (scPCA) of high-dimensional biological data. scPCA combines the stability and interpretability of sparse PCA with contrastive PCA's ability to disentangle biological signal from unwanted variation through the use of control data. Also implements and extends cPCA. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Sparse Contrastive Principal Component Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e7058ad8f079f25d21ae55911652d01d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scpca", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter, SingleCellExperiment, microbenchmark requirements: + host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-scaledmatrix >=1.14.0,<1.15.0 - r-assertthat - r-base - r-cluster @@ -42,11 +45,12 @@ requirements: - r-sparsepca - r-stringr - r-tibble + run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-scaledmatrix >=1.10.0,<1.11.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-scaledmatrix >=1.14.0,<1.15.0 - r-assertthat - r-base - r-cluster @@ -63,13 +67,16 @@ requirements: - r-sparsepca - r-stringr - r-tibble + +source: + md5: a3b9cac8e449f8898a5274fff7fd9f16 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Sparse Contrastive Principal Component Analysis' - description: 'A toolbox for sparse contrastive principal component analysis (scPCA) of high-dimensional biological data. scPCA combines the stability and interpretability of sparse PCA with contrastive PCA''s ability to disentangle biological signal from unwanted variation through the use of control data. Also implements and extends cPCA.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scpdata/meta.yaml b/recipes/bioconductor-scpdata/meta.yaml index cf133817eeedf..27c0dc1daadb9 100644 --- a/recipes/bioconductor-scpdata/meta.yaml +++ b/recipes/bioconductor-scpdata/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.10.0" %} +{% set version = "1.13.0" %} {% set name = "scpdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package disseminates mass spectrometry (MS)-based single-cell proteomics (SCP) datasets. The data were collected from published work and formatted using the `scp` data structure. The data sets contain quantitative information at spectrum, peptide and/or protein level for single cells or minute sample amounts. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Single-Cell Proteomics Data Package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eac9eae58fe9297359188c45a3dabd1f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scpdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: scp, magrittr, dplyr, knitr, BiocStyle, BiocCheck, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-qfeatures >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-qfeatures >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-qfeatures >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-qfeatures >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 9a026357adcb402892f64764ad09a6a6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Single-Cell Proteomics Data Package' - description: 'The package disseminates mass spectrometry (MS)-based single-cell proteomics (SCP) datasets. The data were collected from published work and formatted using the `scp` data structure. The data sets contain quantitative information at spectrum, peptide and/or protein level for single cells or minute sample amounts.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scpdata/post-link.sh b/recipes/bioconductor-scpdata/post-link.sh index 6e55327fbf91f..07d28113a981c 100644 --- a/recipes/bioconductor-scpdata/post-link.sh +++ b/recipes/bioconductor-scpdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "scpdata-1.10.0" +installBiocDataPackage.sh "scpdata-1.13.0" diff --git a/recipes/bioconductor-scpipe/meta.yaml b/recipes/bioconductor-scpipe/meta.yaml index 9efcbe7c1cace..33606e9642792 100644 --- a/recipes/bioconductor-scpipe/meta.yaml +++ b/recipes/bioconductor-scpipe/meta.yaml @@ -1,62 +1,74 @@ -{% set version = "2.2.0" %} +{% set version = "2.6.0" %} {% set name = "scPipe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A preprocessing pipeline for single cell RNA-seq/ATAC-seq data that starts from the fastq files and produces a feature count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Pipeline for single cell multi-omic data pre-processing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 477ce2b2da9cc1ae5365c3140d6ed566 build: - skip: True # [osx] number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scpipe", max_pin="x.x") }}' + +extra: + parent_recipe: + name: bioconductor-scpipe + path: recipes/bioconductor-scpipe + version: 1.2.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, DT, GenomicFeatures, grid, igraph, kableExtra, knitr, locStra, plotly, rmarkdown, RColorBrewer, readr, reshape2, RANN, shiny, scater (>= 1.11.0), testthat, xml2, umap # SystemRequirements: C++11, GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-dropletutils >=1.22.0,<1.23.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rsubread >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-dropletutils >=1.26.0,<1.27.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rsubread >=2.20.0,<2.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-data.table - r-dplyr - r-flexmix - r-ggally - r-ggplot2 - - 'r-glue >=1.3.0' + - r-glue >=1.3.0 - r-hash - r-magrittr - r-mass - - 'r-matrix >=1.5.0' + - r-matrix >=1.5.0 - r-mclust - r-purrr - - 'r-rcpp >=0.11.3' + - r-rcpp >=0.11.3 - r-reshape - r-reticulate - r-rlang @@ -66,44 +78,47 @@ requirements: - r-testthat - r-tibble - r-tidyr - - 'r-vctrs >=0.5.2' + - r-vctrs >=0.5.2 - libblas - liblapack + - zlib + - liblzma-devel + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-dropletutils >=1.22.0,<1.23.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rsubread >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-dropletutils >=1.26.0,<1.27.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rsubread >=2.20.0,<2.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-data.table - r-dplyr - r-flexmix - r-ggally - r-ggplot2 - - 'r-glue >=1.3.0' + - r-glue >=1.3.0 - r-hash - r-magrittr - r-mass - - 'r-matrix >=1.5.0' + - r-matrix >=1.5.0 - r-mclust - r-purrr - - 'r-rcpp >=0.11.3' + - r-rcpp >=0.11.3 - r-reshape - r-reticulate - r-rlang @@ -113,23 +128,18 @@ requirements: - r-testthat - r-tibble - r-tidyr - - 'r-vctrs >=0.5.2' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-vctrs >=0.5.2 + +source: + md5: e6ee5ea588aa24d6ae27300f8de7d8ff + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Pipeline for single cell multi-omic data pre-processing' - description: 'A preprocessing pipeline for single cell RNA-seq/ATAC-seq data that starts from the fastq files and produces a feature count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-scpipe - path: recipes/bioconductor-scpipe - version: 1.2.1 + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-scran/meta.yaml b/recipes/bioconductor-scran/meta.yaml index 1a024a2d84dca..edb50864f7b5d 100644 --- a/recipes/bioconductor-scran/meta.yaml +++ b/recipes/bioconductor-scran/meta.yaml @@ -1,41 +1,60 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "scran" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implements miscellaneous functions for interpretation of single-cell RNA-seq data. Methods are provided for assignment of cell cycle phase, detection of highly variable and significantly correlated genes, identification of marker genes, and other common tasks in routine single-cell analysis workflows. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Methods for Single-Cell RNA-Seq Data Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f8cc4c59dde80171927b115dc09592af build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scran", max_pin="x.x") }}' -# Suggests: testthat, BiocStyle, knitr, rmarkdown, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, monocle, Biobase, pheatmap, scater + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:scran + parent_recipe: + name: bioconductor-scran + path: recipes/bioconductor-scran + version: 1.8.4 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, BiocStyle, knitr, rmarkdown, DelayedMatrixStats, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, pheatmap, scater # SystemRequirements: C++11 requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-bluster >=1.12.0,<1.13.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-metapod >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-bluster >=1.16.0,<1.17.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-metapod >=1.14.0,<1.15.0 + - bioconductor-s4arrays >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bh - r-dqrng @@ -45,21 +64,23 @@ requirements: - r-statmod - libblas - liblapack + run: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-bluster >=1.12.0,<1.13.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-metapod >=1.10.0,<1.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-bluster >=1.16.0,<1.17.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-metapod >=1.14.0,<1.15.0 + - bioconductor-s4arrays >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bh - r-dqrng @@ -67,26 +88,16 @@ requirements: - r-matrix - r-rcpp - r-statmod - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: bac540bd32795a5cc1a0c1c0164a7b33 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'Methods for Single-Cell RNA-Seq Data Analysis' - description: 'Implements miscellaneous functions for interpretation of single-cell RNA-seq data. Methods are provided for assignment of cell cycle phase, detection of highly variable and significantly correlated genes, identification of marker genes, and other common tasks in routine single-cell analysis workflows.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:scran - parent_recipe: - name: bioconductor-scran - path: recipes/bioconductor-scran - version: 1.8.4 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scrapper/build.sh b/recipes/bioconductor-scrapper/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scrapper/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scrapper/build_failure.osx-64.yaml b/recipes/bioconductor-scrapper/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..62e2db7fbf3ad --- /dev/null +++ b/recipes/bioconductor-scrapper/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 87f80075848d9d40b705cd057e7be6b402749a21068b6e3886c5f5e9e83b5327 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-scrapper-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c adt_quality_control.cpp -o adt_quality_control.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c aggregate_across_cells.cpp -o aggregate_across_cells.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c build_snn_graph.cpp -o build_snn_graph.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c center_size_factors.cpp -o center_size_factors.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c choose_highly_variable_genes.cpp -o choose_highly_variable_genes.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c choose_pseudo_count.cpp -o choose_pseudo_count.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c cluster_graph.cpp -o cluster_graph.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c cluster_kmeans.cpp -o cluster_kmeans.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c combine_factors.cpp -o combine_factors.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c compute_clrm1_factors.cpp -o compute_clrm1_factors.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c correct_mnn.cpp -o correct_mnn.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c crispr_quality_control.cpp -o crispr_quality_control.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c fit_variance_trend.cpp -o fit_variance_trend.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c model_gene_variances.cpp -o model_gene_variances.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c normalize_counts.cpp -o normalize_counts.o + installing to /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-scrapper_1735947633316/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/00LOCK-work/00new/scrapper/libs + ** R + ** inst + ** byte-compile and prepare package for lazy loading + ** help + *** installing help indices + ** building package indices + ** installing vignettes + ** testing if installed package can be loaded from temporary location + ** checking absolute paths in shared objects and dynamic libraries + ** testing if installed package can be loaded from final location + ** testing if installed package keeps a record of temporary installation path + * creating tarball + packaged installation of scrapper as scrapper_1.0.0.tgz + * DONE (scrapper) + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c rna_quality_control.cpp -o rna_quality_control.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c run_pca.cpp -o run_pca.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c run_tsne.cpp -o run_tsne.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c run_umap.cpp -o run_umap.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c sanitize_size_factors.cpp -o sanitize_size_factors.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c scale_by_neighbors.cpp -o scale_by_neighbors.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c score_gene_set.cpp -o score_gene_set.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c score_markers.cpp -o score_markers.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c subsample_by_neighbors.cpp -o subsample_by_neighbors.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/assorthead/include' -I'$PREFIX/lib/R/library/beachmat/include' -I'$PREFIX/lib/R/library/BiocNeighbors/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c summarize_effects.cpp -o summarize_effects.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L$PREFIX/lib/R/lib -Wl,-dead_strip_dylibs -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o scrapper.so RcppExports.o adt_quality_control.o aggregate_across_cells.o build_snn_graph.o center_size_factors.o choose_highly_variable_genes.o choose_pseudo_count.o cluster_graph.o cluster_kmeans.o combine_factors.o compute_clrm1_factors.o correct_mnn.o crispr_quality_control.o fit_variance_trend.o model_gene_variances.o normalize_counts.o rna_quality_control.o run_pca.o run_tsne.o run_umap.o sanitize_size_factors.o scale_by_neighbors.o score_gene_set.o score_markers.o subsample_by_neighbors.o summarize_effects.o -L$PREFIX/lib/R/lib -lR -Wl,-framework -Wl,CoreFoundation + + Resource usage statistics from building bioconductor-scrapper: + Process count: 6 + CPU time: Sys=0:00:07.9, User=0:02:31.8 + Memory: 854.9M + Disk usage: 28.2K + Time elapsed: 0:03:21.6 + + + Packaging bioconductor-scrapper + Packaging bioconductor-scrapper-1.0.0-r44h35d7169_0 + + + + + number of files: 26 + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + Fixing linking of scrapper.so in /opt/mambaforge/envs/bioconda/conda-bld/bioconductor-scrapper_1735947633316/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/scrapper/libs/scrapper.so + New link location is lib/R/library/scrapper/libs/scrapper.so + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2765, in build + newly_built_packages = bundlers[pkg_type]( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1874, in bundle_conda + files = post_process_files(metadata, initial_files) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1653, in post_process_files + post_build(m, new_files, build_python=python) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1759, in post_build + post_process_shared_lib(m, f, prefix_files, host_prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1635, in post_process_shared_lib + mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 512, in mk_relative_osx + assert_relative_osx(path, host_prefix, build_prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 665, in assert_relative_osx + for name in macho.get_dylibs(path, tools_prefix): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 237, in get_dylibs + dylib_loads = otool(path, build_prefix, is_load_dylib) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 221, in otool + lines = check_output([otool, "-l", path], stderr=STDOUT).decode("utf-8") + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 421, in check_output + return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 526, in run + raise CalledProcessError(retcode, process.args, + subprocess.CalledProcessError: Command '['/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-scrapper_1735947633316/_build_env/bin/llvm-otool', '-l', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-scrapper_1735947633316/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/scrapper/libs/scrapper.so']' died with . +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-scrapper/meta.yaml b/recipes/bioconductor-scrapper/meta.yaml new file mode 100644 index 0000000000000..95eb8d7d92043 --- /dev/null +++ b/recipes/bioconductor-scrapper/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.0.0" %} +{% set name = "scrapper" %} +{% set bioc = "3.20" %} + +about: + description: Implements R bindings to C++ code for analyzing single-cell (expression) data, mostly from various libscran libraries. Each function performs an individual step in the single-cell analysis workflow, ranging from quality control to clustering and marker detection. It is mostly intended for other Bioconductor package developers to build more user-friendly end-to-end workflows. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Bindings to C++ Libraries for Single-Cell Analysis + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-scrapper", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, knitr, rmarkdown, BiocStyle, MatrixGenerics, sparseMatrixStats, Matrix, scRNAseq +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: + - bioconductor-assorthead >=1.0.0,<1.1.0 + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - r-base + - r-igraph + - r-rcpp + - libblas + - liblapack + run: + - bioconductor-assorthead >=1.0.0,<1.1.0 + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - r-base + - r-igraph + - r-rcpp + +source: + md5: 82e3c6e80451b9c0fe728edcb293667a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-screclassify/meta.yaml b/recipes/bioconductor-screclassify/meta.yaml index 6ab9c50202c44..cb0b720ab7ea4 100644 --- a/recipes/bioconductor-screclassify/meta.yaml +++ b/recipes/bioconductor-screclassify/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "scReClassify" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 722bce944db1f380df35d68a47c4bef7 +about: + description: A post hoc cell type classification tool to fine-tune cell type annotations generated by any cell type classification procedure with semi-supervised learning algorithm AdaSampling technique. The current version of scReClassify supports Support Vector Machine and Random Forest as a base classifier. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: 'scReClassify: post hoc cell type classification of single-cell RNA-seq data' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-screclassify", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr requirements: host: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-e1071 - r-randomforest run: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-e1071 - r-randomforest +source: + md5: 9cdca0d574ab1644788d0261f0c531ad + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'scReClassify: post hoc cell type classification of single-cell RNA-seq data' - description: 'A post hoc cell type classification tool to fine-tune cell type annotations generated by any cell type classification procedure with semi-supervised learning algorithm AdaSampling technique. The current version of scReClassify supports Support Vector Machine and Random Forest as a base classifier.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-screcover/meta.yaml b/recipes/bioconductor-screcover/meta.yaml index f0024c38fdf5e..ca97fa421167d 100644 --- a/recipes/bioconductor-screcover/meta.yaml +++ b/recipes/bioconductor-screcover/meta.yaml @@ -1,63 +1,68 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "scRecover" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: scRecover is an R package for imputation of single-cell RNA-seq (scRNA-seq) data. It will detect and impute dropout values in a scRNA-seq raw read counts matrix while keeping the real zeros unchanged, since there are both dropout zeros and real zeros in scRNA-seq data. By combination with scImpute, SAVER and MAGIC, scRecover not only detects dropout and real zeros at higher accuracy, but also improve the downstream clustering and visualization results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: scRecover for imputation of single-cell RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ebdc203b50818397a1856fdce417f10e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-screcover", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, SingleCellExperiment, testthat requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - - 'r-bbmle >=1.0.18' + - r-bbmle >=1.0.18 - r-doparallel - r-foreach - - 'r-gamlss >=4.4-0' + - r-gamlss >=4.4-0 - r-kernlab - - 'r-mass >=7.3-45' - - 'r-matrix >=1.2-14' + - r-mass >=7.3-45 + - r-matrix >=1.2-14 - r-penalized - - 'r-preseqr >=4.0.0' - - 'r-pscl >=1.4.9' + - r-preseqr >=4.0.0 + - r-pscl >=1.4.9 - r-rsvd - - 'r-saver >=1.1.1' + - r-saver >=1.1.1 run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - - 'r-bbmle >=1.0.18' + - r-bbmle >=1.0.18 - r-doparallel - r-foreach - - 'r-gamlss >=4.4-0' + - r-gamlss >=4.4-0 - r-kernlab - - 'r-mass >=7.3-45' - - 'r-matrix >=1.2-14' + - r-mass >=7.3-45 + - r-matrix >=1.2-14 - r-penalized - - 'r-preseqr >=4.0.0' - - 'r-pscl >=1.4.9' + - r-preseqr >=4.0.0 + - r-pscl >=1.4.9 - r-rsvd - - 'r-saver >=1.1.1' + - r-saver >=1.1.1 + +source: + md5: 50e417ce98131850e0320f6fc7e6af45 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL - summary: 'scRecover for imputation of single-cell RNA-seq data' - description: 'scRecover is an R package for imputation of single-cell RNA-seq (scRNA-seq) data. It will detect and impute dropout values in a scRNA-seq raw read counts matrix while keeping the real zeros unchanged, since there are both dropout zeros and real zeros in scRNA-seq data. By combination with scImpute, SAVER and MAGIC, scRecover not only detects dropout and real zeros at higher accuracy, but also improve the downstream clustering and visualization results.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-screencounter/build_failure.linux-64.yaml b/recipes/bioconductor-screencounter/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..90b71a9e965bf --- /dev/null +++ b/recipes/bioconductor-screencounter/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 9d82a5d5bb448a35918105ddc083b751da3f9b5299f99f14eae0efa465a49de4 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-screencounter-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-screencounter-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-screencounter-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-screencounter-1.6.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-screencounter_1734867954110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/R/library + * installing *source* package screenCounter ... + ** package screenCounter successfully unpacked and MD5 sums checked + ** using staged installation + ** libs + using C compiler: x86_64-conda-linux-gnu-c (conda-forge gcc 13.3.0-1) 13.3.0 + using C17 + x86_64-conda-linux-gnu-c -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I../inst/include -I'$PREFIX/lib/R/library/Rcpp/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o + x86_64-conda-linux-gnu-c -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I../inst/include -I'$PREFIX/lib/R/library/Rcpp/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c count_combo_barcodes_paired.cpp -o count_combo_barcodes_paired.o + count_combo_barcodes_paired.cpp: In function 'Rcpp::List count_combo_barcodes_paired(std::string, std::string, bool, int, Rcpp::CharacterVector, std::string, std::string, bool, int, Rcpp::CharacterVector, bool, bool, int)': + count_combo_barcodes_paired.cpp:73:13: error: 'SomeFileReader' is not a member of 'byteme'; did you mean 'RawFileReader'? + 73 | byteme::SomeFileReader reader1(path1.c_str()); + | ^~~~~~~~~~~~~~ + | RawFileReader + count_combo_barcodes_paired.cpp:76:13: error: 'SomeFileReader' is not a member of 'byteme'; did you mean 'RawFileReader'? + 76 | byteme::SomeFileReader reader2(path2.c_str()); + | ^~~~~~~~~~~~~~ + | RawFileReader + count_combo_barcodes_paired.cpp:83:51: error: 'reader1' was not declared in this scope + 83 | output = count_combo_barcodes_paired_<32>(reader1, constant1, reverse1, ptrs1, mismatches1, reader2, constant2, reverse2, ptrs2, mismatches2, randomized, use_first, nthreads); + | ^~~~~~~ + count_combo_barcodes_paired.cpp:83:101: error: 'reader2' was not declared in this scope + 83 | output = count_combo_barcodes_paired_<32>(reader1, constant1, reverse1, ptrs1, mismatches1, reader2, constant2, reverse2, ptrs2, mismatches2, randomized, use_first, nthreads); + | ^~~~~~~ + count_combo_barcodes_paired.cpp:85:51: error: 'reader1' was not declared in this scope + 85 | output = count_combo_barcodes_paired_<64>(reader1, constant1, reverse1, ptrs1, mismatches1, reader2, constant2, reverse2, ptrs2, mismatches2, randomized, use_first, nthreads); + | ^~~~~~~ + count_combo_barcodes_paired.cpp:85:101: error: 'reader2' was not declared in this scope + 85 | output = count_combo_barcodes_paired_<64>(reader1, constant1, reverse1, ptrs1, mismatches1, reader2, constant2, reverse2, ptrs2, mismatches2, randomized, use_first, nthreads); + | ^~~~~~~ + count_combo_barcodes_paired.cpp:87:52: error: 'reader1' was not declared in this scope + 87 | output = count_combo_barcodes_paired_<128>(reader1, constant1, reverse1, ptrs1, mismatches1, reader2, constant2, reverse2, ptrs2, mismatches2, randomized, use_first, nthreads); + | ^~~~~~~ + count_combo_barcodes_paired.cpp:87:102: error: 'reader2' was not declared in this scope + 87 | output = count_combo_barcodes_paired_<128>(reader1, constant1, reverse1, ptrs1, mismatches1, reader2, constant2, reverse2, ptrs2, mismatches2, randomized, use_first, nthreads); + | ^~~~~~~ + count_combo_barcodes_paired.cpp:89:52: error: 'reader1' was not declared in this scope + 89 | output = count_combo_barcodes_paired_<256>(reader1, constant1, reverse1, ptrs1, mismatches1, reader2, constant2, reverse2, ptrs2, mismatches2, randomized, use_first, nthreads); + | ^~~~~~~ + count_combo_barcodes_paired.cpp:89:102: error: 'reader2' was not declared in this scope + 89 | output = count_combo_barcodes_paired_<256>(reader1, constant1, reverse1, ptrs1, mismatches1, reader2, constant2, reverse2, ptrs2, mismatches2, randomized, use_first, nthreads); + | ^~~~~~~ + make: *** [/opt/conda/conda-bld/bioconductor-screencounter_1734867954110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/R/etc/Makeconf:204: count_combo_barcodes_paired.o] Error 1 + ERROR: compilation failed for package screenCounter + * removing /opt/conda/conda-bld/bioconductor-screencounter_1734867954110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/R/library/screenCounter + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-screencounter_1734867954110/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-screencounter_1734867954110/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-screencounter/meta.yaml b/recipes/bioconductor-screencounter/meta.yaml index d706b51cee9f4..7ec97b3ab8d60 100644 --- a/recipes/bioconductor-screencounter/meta.yaml +++ b/recipes/bioconductor-screencounter/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "screenCounter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides functions for counting reads from high-throughput sequencing screen data (e.g., CRISPR, shRNA) to quantify barcode abundance. Currently supports single barcodes in single- or paired-end data, and combinatorial barcodes in paired-end data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Counting Reads in High-Throughput Sequencing Screens -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 35bb89fb63853645e76facfc72e77522 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-screencounter", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown, testthat # SystemRequirements: C++17, GNU make requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 20a49381e47c9974f07ea9f8e4031584 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Counting Reads in High-Throughput Sequencing Screens' - description: 'Provides functions for counting reads from high-throughput sequencing screen data (e.g., CRISPR, shRNA) to quantify barcode abundance. Currently supports single barcodes in single- or paired-end data, and combinatorial barcodes in paired-end data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-screenr/meta.yaml b/recipes/bioconductor-screenr/meta.yaml index 34203b1646f65..7dde692521026 100644 --- a/recipes/bioconductor-screenr/meta.yaml +++ b/recipes/bioconductor-screenr/meta.yaml @@ -1,65 +1,70 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "ScreenR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ScreenR is a package suitable to perform hit identification in loss of function High Throughput Biological Screenings performed using barcoded shRNA-based libraries. ScreenR combines the computing power of software such as edgeR with the simplicity of use of the Tidyverse metapackage. ScreenR executes a pipeline able to find candidate hits from barcode counts, and integrates a wide range of visualization modes for each step of the analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Package to Perform High Throughput Biological Screening -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bb8bd3276b17f7e0d63de9c19e64473d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-screenr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown (>= 2.11), knitr (>= 1.37), testthat (>= 3.0.0), BiocStyle (>= 2.22.0), covr (>= 3.5) requirements: host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - - 'r-dplyr >=1.0' - - 'r-ggplot2 >=3.3' - - 'r-ggvenn >=0.1.9' - - 'r-magrittr >=1.0' - - 'r-patchwork >=1.1' - - 'r-purrr >=0.3.4' - - 'r-rlang >=0.4' - - 'r-scales >=1.1.1' - - 'r-stringr >=1.4' - - 'r-tibble >=3.1.6' - - 'r-tidyr >=1.2' - - 'r-tidyselect >=1.1.2' + - r-dplyr >=1.0 + - r-ggplot2 >=3.3 + - r-ggvenn >=0.1.9 + - r-magrittr >=1.0 + - r-patchwork >=1.1 + - r-purrr >=0.3.4 + - r-rlang >=0.4 + - r-scales >=1.1.1 + - r-stringr >=1.4 + - r-tibble >=3.1.6 + - r-tidyr >=1.2 + - r-tidyselect >=1.1.2 run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - - 'r-dplyr >=1.0' - - 'r-ggplot2 >=3.3' - - 'r-ggvenn >=0.1.9' - - 'r-magrittr >=1.0' - - 'r-patchwork >=1.1' - - 'r-purrr >=0.3.4' - - 'r-rlang >=0.4' - - 'r-scales >=1.1.1' - - 'r-stringr >=1.4' - - 'r-tibble >=3.1.6' - - 'r-tidyr >=1.2' - - 'r-tidyselect >=1.1.2' + - r-dplyr >=1.0 + - r-ggplot2 >=3.3 + - r-ggvenn >=0.1.9 + - r-magrittr >=1.0 + - r-patchwork >=1.1 + - r-purrr >=0.3.4 + - r-rlang >=0.4 + - r-scales >=1.1.1 + - r-stringr >=1.4 + - r-tibble >=3.1.6 + - r-tidyr >=1.2 + - r-tidyselect >=1.1.2 + +source: + md5: c2a515eaadacbe1c59c36a40814e5ab7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Package to Perform High Throughput Biological Screening' - description: 'ScreenR is a package suitable to perform hit identification in loss of function High Throughput Biological Screenings performed using barcoded shRNA-based libraries. ScreenR combines the computing power of software such as edgeR with the simplicity of use of the Tidyverse metapackage. ScreenR executes a pipeline able to find candidate hits from barcode counts, and integrates a wide range of visualization modes for each step of the analysis.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-screpertoire/build_failure.osx-64.yaml b/recipes/bioconductor-screpertoire/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..b0c119393a812 --- /dev/null +++ b/recipes/bioconductor-screpertoire/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 2096968ef5d37e9602cf6ca7b0b12359257e35c092e3ece4520f191723e8a1f1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-screpertoire-2.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-screpertoire_1734822443767/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-screpertoire_1734822443767/work/conda_build.sh']' returned non-zero exit status 1. + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-screpertoire-2.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-screpertoire-2.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-screpertoire-2.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-screpertoire-2.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-screpertoire-2.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-screpertoire-2.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-screpertoire-2.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-screpertoire-2.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-screpertoire-2.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c aaKmers.cpp -o aaKmers.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c constructConDfAndParseBCR.cpp -o constructConDfAndParseBCR.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c constructConDfAndparseTCR.cpp -o constructConDfAndparseTCR.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ntKmers.cpp -o ntKmers.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L$PREFIX/lib/R/lib -Wl,-dead_strip_dylibs -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o scRepertoire.so RcppExports.o aaKmers.o constructConDfAndParseBCR.o constructConDfAndparseTCR.o ntKmers.o -L$PREFIX/lib/R/lib -lR -Wl,-framework -Wl,CoreFoundation + Error in dyn.load(file, DLLpath = DLLpath, ...) : + unable to load shared object '$PREFIX/lib/R/library/iNEXT/libs/iNEXT.so': + dlopen($PREFIX/lib/R/library/iNEXT/libs/iNEXT.so, 0x0006): tried: '$PREFIX/lib/R/library/iNEXT/libs/iNEXT.so' (not a mach-o file), '/System/Volumes/Preboot/Cryptexes/OS/op + Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load + Execution halted +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-screpertoire/meta.yaml b/recipes/bioconductor-screpertoire/meta.yaml index e423553bb5630..d6d2240374505 100644 --- a/recipes/bioconductor-screpertoire/meta.yaml +++ b/recipes/bioconductor-screpertoire/meta.yaml @@ -1,71 +1,100 @@ -{% set version = "1.12.0" %} +{% set version = "2.2.0" %} {% set name = "scRepertoire" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: scRepertoire is a toolkit for processing and analyzing single-cell T-cell receptor (TCR) and immunoglobulin (Ig). The scRepertoire framework supports use of 10x, AIRR, BD, MiXCR, Omniscope, TRUST4, and WAT3R single-cell formats. The functionality includes basic clonal analyses, repertoire summaries, distance-based clustering and interaction with the popular Seurat and SingleCellExperiment/Bioconductor R workflows. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: A toolkit for single-cell immune receptor profiling -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3debd173702ebe6c551ba6c572a76c25 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-screpertoire", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, BiocStyle, circlize, scales, Seurat, scater + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocManager, BiocStyle, circlize, knitr, rmarkdown, scales, scater, Seurat, spelling, testthat (>= 3.0.0), vdiffr requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-powertcr >=1.22.0,<1.23.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - r-doparallel + - r-cubature - r-dplyr + - r-evmix - r-ggalluvial + - r-ggdendro - r-ggplot2 - r-ggraph + - r-hash - r-igraph + - r-inext - r-plyr + - r-quantreg + - r-rcpp - r-reshape2 + - r-rjson - r-rlang - r-seuratobject - r-stringdist - r-stringr - r-tidygraph - - r-vegan + - r-truncdist + - r-vgam + - libblas + - liblapack + run: - - 'bioconductor-powertcr >=1.22.0,<1.23.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - r-doparallel + - r-cubature - r-dplyr + - r-evmix - r-ggalluvial + - r-ggdendro - r-ggplot2 - r-ggraph + - r-hash - r-igraph + - r-inext - r-plyr + - r-quantreg + - r-rcpp - r-reshape2 + - r-rjson - r-rlang - r-seuratobject - r-stringdist - r-stringr - r-tidygraph - - r-vegan + - r-truncdist + - r-vgam + +source: + md5: eb321afd64fa19bda15b6e574b19ef7a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'A toolkit for single-cell immune receptor profiling' - description: 'scRepertoire was built to process data derived from the 10x Genomics Chromium Immune Profiling for both T-cell receptor (TCR) and immunoglobulin (Ig) enrichment workflows and subsequently interacts with the popular Seurat and SingleCellExperiment R packages. It also allows for general analysis of single-cell clonotype information without the use of expression information. The package functions as a wrapper for Startrac and powerTCR R packages.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scrnaseq/build_failure.osx-64.yaml b/recipes/bioconductor-scrnaseq/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..10b60a1bbb51d --- /dev/null +++ b/recipes/bioconductor-scrnaseq/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: d228e0d3b50470a92676c43c101532956fd173c478f6a5a7f8ac810fddc5fff6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bioconductor-alabaster.base needs to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-scrnaseq/meta.yaml b/recipes/bioconductor-scrnaseq/meta.yaml index 8ac4a0edce522..4dac85521bb53 100644 --- a/recipes/bioconductor-scrnaseq/meta.yaml +++ b/recipes/bioconductor-scrnaseq/meta.yaml @@ -1,63 +1,91 @@ -{% set version = "2.16.0" %} +{% set version = "2.20.0" %} {% set name = "scRNAseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: CC0 + summary: Collection of Public Single-Cell RNA-Seq Datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 55196cb10876aa15733c6a29ffc38100 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scrnaseq", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, BiocFileCache, testthat, rappdirs, tools + +extra: + parent_recipe: + name: bioconductor-scrnaseq + path: recipes/bioconductor-scrnaseq + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, testthat, jsonvalidate, BiocManager requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-alabaster.matrix >=1.6.0,<1.7.0 + - bioconductor-alabaster.sce >=1.6.0,<1.7.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gypsum >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + - r-dbi + - r-jsonlite + - r-matrix + - r-rsqlite + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-alabaster.base >=1.6.0,<1.7.0 + - bioconductor-alabaster.matrix >=1.6.0,<1.7.0 + - bioconductor-alabaster.sce >=1.6.0,<1.7.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gypsum >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + - r-dbi + - r-jsonlite + - r-matrix + - r-rsqlite - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 9712b05cec1dd4c33c67fffa06e3257d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: CC0 - summary: 'Collection of Public Single-Cell RNA-Seq Datasets' - description: 'Gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata.' -extra: - parent_recipe: - name: bioconductor-scrnaseq - path: recipes/bioconductor-scrnaseq - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scrnaseq/post-link.sh b/recipes/bioconductor-scrnaseq/post-link.sh index 25b040d1f3d7a..0221adb79f3f4 100644 --- a/recipes/bioconductor-scrnaseq/post-link.sh +++ b/recipes/bioconductor-scrnaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "scrnaseq-2.16.0" +installBiocDataPackage.sh "scrnaseq-2.20.0" diff --git a/recipes/bioconductor-scrnaseqapp/meta.yaml b/recipes/bioconductor-scrnaseqapp/meta.yaml index d31492b6be478..32fb339935373 100644 --- a/recipes/bioconductor-scrnaseqapp/meta.yaml +++ b/recipes/bioconductor-scrnaseqapp/meta.yaml @@ -1,113 +1,210 @@ -{% set version = "1.2.2" %} +{% set version = "1.6.0" %} {% set name = "scRNAseqApp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The scRNAseqApp is a Shiny app package designed for interactive visualization of single-cell data. It is an enhanced version derived from the ShinyCell, repackaged to accommodate multiple datasets. The app enables users to visualize data containing various types of information simultaneously, facilitating comprehensive analysis. Additionally, it includes a user management system to regulate database accessibility for different users. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A single-cell RNAseq Shiny app-package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a9b64e980a9e0acef5ab93a44a35e124 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scrnaseqapp", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, testthat, BiocStyle requirements: + host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-slingshot >=2.10.0,<2.11.0' + + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + + - bioconductor-genomicranges >=1.58.0,<1.59.0 + + - bioconductor-iranges >=2.40.0,<2.41.0 + + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + + - bioconductor-rsamtools >=2.22.0,<2.23.0 + + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + + - bioconductor-s4vectors >=0.44.0,<0.45.0 + + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + + - bioconductor-slingshot >=2.14.0,<2.15.0 + - r-base + - r-bibtex + - r-bslib + - r-circlize + + - r-colourpicker + - r-data.table + + - r-dbi + - r-dt + - r-ggdendro + - r-ggforce + - r-ggplot2 + - r-ggrepel + - r-ggridges + - r-gridextra - - r-hdf5r + - r-htmltools + - r-jsonlite + - r-magrittr + - r-patchwork + - r-plotly + - r-rcolorbrewer + - r-refmanager + + - r-rsqlite + - r-scales + - r-scrypt + - r-seurat + - r-seuratobject + - r-shiny + - r-shinyhelper + - r-shinymanager + - r-sortable + - r-xfun + - r-xml2 + run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-slingshot >=2.10.0,<2.11.0' + + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + + - bioconductor-genomicranges >=1.58.0,<1.59.0 + + - bioconductor-iranges >=2.40.0,<2.41.0 + + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + + - bioconductor-rsamtools >=2.22.0,<2.23.0 + + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + + - bioconductor-s4vectors >=0.44.0,<0.45.0 + + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + + - bioconductor-slingshot >=2.14.0,<2.15.0 + - r-base + - r-bibtex + - r-bslib + - r-circlize + + - r-colourpicker + - r-data.table + + - r-dbi + - r-dt + - r-ggdendro + - r-ggforce + - r-ggplot2 + - r-ggrepel + - r-ggridges + - r-gridextra - - r-hdf5r + - r-htmltools + - r-jsonlite + - r-magrittr + - r-patchwork + - r-plotly + - r-rcolorbrewer + - r-refmanager + + - r-rsqlite + - r-scales + - r-scrypt + - r-seurat + - r-seuratobject + - r-shiny + - r-shinyhelper + - r-shinymanager + - r-sortable + - r-xfun + - r-xml2 + +source: + md5: 7c98a1c5c3e90b1df917e94b08c7560b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'A single-cell RNAseq Shiny app-package' - description: 'scRNAseqApp is a Shiny app package that allows users to visualize single cell data interactively. It was modified from ShinyCell and repackaged to a tool to show multiple data. It can visulize the data with multiple information side by side.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scruff/meta.yaml b/recipes/bioconductor-scruff/meta.yaml index 51177f8c27686..10f74864c69ef 100644 --- a/recipes/bioconductor-scruff/meta.yaml +++ b/recipes/bioconductor-scruff/meta.yaml @@ -1,43 +1,47 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "scruff" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A pipeline which processes single cell RNA-seq (scRNA-seq) reads from CEL-seq and CEL-seq2 protocols. Demultiplex scRNA-seq FASTQ files, align reads to reference genome using Rsubread, and generate UMI filtered count matrix. Also provide visualizations of read alignments and pre- and post-alignment QC metrics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Single Cell RNA-Seq UMI Filtering Facilitator (scruff) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cd21598690887291d1540e0a827fb6cc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scruff", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rsubread >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rsubread >=2.20.0,<2.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-data.table - r-ggplot2 @@ -46,23 +50,25 @@ requirements: - r-plyr - r-scales - r-stringdist + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rsubread >=2.16.0,<2.17.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rsubread >=2.20.0,<2.21.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-data.table - r-ggplot2 @@ -71,13 +77,16 @@ requirements: - r-plyr - r-scales - r-stringdist + +source: + md5: f9a472c6e9a2f95b808e60231272f687 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Single Cell RNA-Seq UMI Filtering Facilitator (scruff)' - description: 'A pipeline which processes single cell RNA-seq (scRNA-seq) reads from CEL-seq and CEL-seq2 protocols. Demultiplex scRNA-seq FASTQ files, align reads to reference genome using Rsubread, and generate UMI filtered count matrix. Also provide visualizations of read alignments and pre- and post-alignment QC metrics.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scry/meta.yaml b/recipes/bioconductor-scry/meta.yaml index 741c3bb267ea5..3d9c094770f4f 100644 --- a/recipes/bioconductor-scry/meta.yaml +++ b/recipes/bioconductor-scry/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "scry" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Many modern biological datasets consist of small counts that are not well fit by standard linear-Gaussian methods such as principal component analysis. This package provides implementations of count-based feature selection and dimension reduction algorithms. These methods can be used to facilitate unsupervised analysis of any high-dimensional data such as single-cell RNA-seq. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Small-Count Analysis Methods for High-Dimensional Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: dbdcf37d35f52ba787d1d8d5f21e886e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scry", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, covr, DuoClustering2018, ggplot2, HDF5Array, knitr, markdown, rmarkdown, TENxPBMCData, testthat requirements: host: - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-glmpca >=0.2.0' + - r-glmpca >=0.2.0 - r-matrix run: - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-glmpca >=0.2.0' + - r-glmpca >=0.2.0 - r-matrix + +source: + md5: 707c3684c772110a0c1fdab3e7a1e38a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Small-Count Analysis Methods for High-Dimensional Data' - description: 'Many modern biological datasets consist of small counts that are not well fit by standard linear-Gaussian methods such as principal component analysis. This package provides implementations of count-based feature selection and dimension reduction algorithms. These methods can be used to facilitate unsupervised analysis of any high-dimensional data such as single-cell RNA-seq.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scshapes/meta.yaml b/recipes/bioconductor-scshapes/meta.yaml index d12d4297ae966..5954ac0271678 100644 --- a/recipes/bioconductor-scshapes/meta.yaml +++ b/recipes/bioconductor-scshapes/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "scShapes" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: We present a novel statistical framework for identifying differential distributions in single-cell RNA-sequencing (scRNA-seq) data between treatment conditions by modeling gene expression read counts using generalized linear models (GLMs). We model each gene independently under each treatment condition using error distributions Poisson (P), Negative Binomial (NB), Zero-inflated Poisson (ZIP) and Zero-inflated Negative Binomial (ZINB) with log link function and model based normalization for differences in sequencing depth. Since all four distributions considered in our framework belong to the same family of distributions, we first perform a Kolmogorov-Smirnov (KS) test to select genes belonging to the family of ZINB distributions. Genes passing the KS test will be then modeled using GLMs. Model selection is done by calculating the Bayesian Information Criterion (BIC) and likelihood ratio test (LRT) statistic. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A Statistical Framework for Modeling and Identifying Differential Distributions in Single-cell RNA-sequencing Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5a4954c320f7b1f30f8fbff6e9f5ad91 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scshapes", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-dgof - r-emdbook @@ -32,7 +34,7 @@ requirements: - r-pscl - r-vgam run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-dgof - r-emdbook @@ -41,13 +43,16 @@ requirements: - r-matrix - r-pscl - r-vgam + +source: + md5: 302294eba46ef3b09fafd9bd4cba4a9e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'A Statistical Framework for Modeling and Identifying Differential Distributions in Single-cell RNA-sequencing Data' - description: 'We present a novel statistical framework for identifying differential distributions in single-cell RNA-sequencing (scRNA-seq) data between treatment conditions by modeling gene expression read counts using generalized linear models (GLMs). We model each gene independently under each treatment condition using error distributions Poisson (P), Negative Binomial (NB), Zero-inflated Poisson (ZIP) and Zero-inflated Negative Binomial (ZINB) with log link function and model based normalization for differences in sequencing depth. Since all four distributions considered in our framework belong to the same family of distributions, we first perform a Kolmogorov-Smirnov (KS) test to select genes belonging to the family of ZINB distributions. Genes passing the KS test will be then modeled using GLMs. Model selection is done by calculating the Bayesian Information Criterion (BIC) and likelihood ratio test (LRT) statistic.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sctensor/meta.yaml b/recipes/bioconductor-sctensor/meta.yaml index a835706474c23..7a5267f247aae 100644 --- a/recipes/bioconductor-sctensor/meta.yaml +++ b/recipes/bioconductor-sctensor/meta.yaml @@ -1,100 +1,107 @@ -{% set version = "2.12.0" %} +{% set version = "2.16.0" %} {% set name = "scTensor" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The algorithm is based on the non-negative tucker decomposition (NTD2) of nnTensor. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cfbb59a88b526fe373aacf4b1b1a5a97 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sctensor", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens, AnnotationHub requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-category >=2.68.0,<2.69.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-meshdbi >=1.38.0,<1.39.0' - - 'bioconductor-meshr >=2.8.0,<2.9.0' - - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - - 'bioconductor-reactomepa >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-schex >=1.16.0,<1.17.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-category >=2.72.0,<2.73.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-meshdbi >=1.42.0,<1.43.0 + - bioconductor-meshr >=2.12.0,<2.13.0 + - bioconductor-reactome.db >=1.89.0,<1.90.0 + - bioconductor-reactomepa >=1.50.0,<1.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-schex >=1.20.0,<1.21.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-abind - r-base - r-biocmanager - - 'r-cctensor >=1.0.2' + - r-cctensor >=1.0.2 - r-checkmate - r-crayon - r-ggplot2 - r-heatmaply - r-igraph - r-knitr - - 'r-nntensor >=1.1.5' + - r-nntensor >=1.1.5 - r-outliers - r-plotly - r-plotrix - r-rmarkdown - r-rsqlite - - 'r-rtensor >=1.4.8' + - r-rtensor >=1.4.8 - r-tagcloud - r-visnetwork + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-category >=2.68.0,<2.69.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-meshdbi >=1.38.0,<1.39.0' - - 'bioconductor-meshr >=2.8.0,<2.9.0' - - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - - 'bioconductor-reactomepa >=1.46.0,<1.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-schex >=1.16.0,<1.17.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-category >=2.72.0,<2.73.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-meshdbi >=1.42.0,<1.43.0 + - bioconductor-meshr >=2.12.0,<2.13.0 + - bioconductor-reactome.db >=1.89.0,<1.90.0 + - bioconductor-reactomepa >=1.50.0,<1.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-schex >=1.20.0,<1.21.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-abind - r-base - r-biocmanager - - 'r-cctensor >=1.0.2' + - r-cctensor >=1.0.2 - r-checkmate - r-crayon - r-ggplot2 - r-heatmaply - r-igraph - r-knitr - - 'r-nntensor >=1.1.5' + - r-nntensor >=1.1.5 - r-outliers - r-plotly - r-plotrix - r-rmarkdown - r-rsqlite - - 'r-rtensor >=1.4.8' + - r-rtensor >=1.4.8 - r-tagcloud - r-visnetwork + +source: + md5: e55082b94f3ca78f04041ca3a86f4e64 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition' - description: 'The algorithm is based on the non-negative tucker decomposition (NTD2) of nnTensor.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sctgif/meta.yaml b/recipes/bioconductor-sctgif/meta.yaml index bc0285138b195..301c656b49d9d 100644 --- a/recipes/bioconductor-sctgif/meta.yaml +++ b/recipes/bioconductor-sctgif/meta.yaml @@ -1,33 +1,39 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "scTGIF" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: scTGIF connects the cells and the related gene functions without cell type label. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Cell type annotation for unannotated single-cell RNA-Seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7fcf2fd9ff8c1d34aaa64399fa876f3a build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sctgif", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-schex >=1.16.0,<1.17.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-schex >=1.20.0,<1.21.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-igraph @@ -43,14 +49,15 @@ requirements: - r-tibble - libblas - liblapack + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocstyle >=2.30.0,<2.31.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-schex >=1.16.0,<1.17.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocstyle >=2.34.0,<2.35.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-schex >=1.20.0,<1.21.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-igraph @@ -64,15 +71,16 @@ requirements: - r-scales - r-tagcloud - r-tibble - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} + +source: + md5: 6d66dfa6c5f610ac934bfd39a8cc3967 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Cell type annotation for unannotated single-cell RNA-Seq data' - description: 'scTGIF connects the cells and the related gene functions without cell type label.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scthi.data/meta.yaml b/recipes/bioconductor-scthi.data/meta.yaml index d2c6c62b7e0c1..00e3d3a68f0b8 100644 --- a/recipes/bioconductor-scthi.data/meta.yaml +++ b/recipes/bioconductor-scthi.data/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "scTHI.data" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1fd101f8dc30262c323bdfa79810f6f5 +about: + description: Data for the vignette and tutorial of the package scTHI. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: The package contains examples of single cell data used in vignettes and examples of the scTHI package; data contain both tumor cells and immune cells from public dataset of glioma build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scthi.data", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c4e56ab66669c550520df2fb0ad688b1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'The package contains examples of single cell data used in vignettes and examples of the scTHI package; data contain both tumor cells and immune cells from public dataset of glioma' - description: 'Data for the vignette and tutorial of the package scTHI.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scthi.data/post-link.sh b/recipes/bioconductor-scthi.data/post-link.sh index 7763769e34368..687496fc23297 100644 --- a/recipes/bioconductor-scthi.data/post-link.sh +++ b/recipes/bioconductor-scthi.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "scthi.data-1.14.0" +installBiocDataPackage.sh "scthi.data-1.18.0" diff --git a/recipes/bioconductor-scthi/meta.yaml b/recipes/bioconductor-scthi/meta.yaml index 1e0797b2c9961..fe1ec853bc39f 100644 --- a/recipes/bioconductor-scthi/meta.yaml +++ b/recipes/bioconductor-scthi/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "scTHI" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c90e49b0aaed73dd76437e5236607e06 +about: + description: scTHI is an R package to identify active pairs of ligand-receptors from single cells in order to study,among others, tumor-host interactions. scTHI contains a set of signatures to classify cells from the tumor microenvironment. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Indentification of significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scthi", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: scTHI.data, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-rtsne run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-rtsne +source: + md5: b2cfcf2cceabf2f1c7f21749898cfac3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Indentification of significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data' - description: 'scTHI is an R package to identify active pairs of ligand-receptors from single cells in order to study,among others, tumor-host interactions. scTHI contains a set of signatures to classify cells from the tumor microenvironment.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sctreeviz/meta.yaml b/recipes/bioconductor-sctreeviz/meta.yaml index b05fd3b6f86e7..0b1a2a5354fd2 100644 --- a/recipes/bioconductor-sctreeviz/meta.yaml +++ b/recipes/bioconductor-sctreeviz/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "scTreeViz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: scTreeViz provides classes to support interactive data aggregation and visualization of single cell RNA-seq datasets with hierarchies for e.g. cell clusters at different resolutions. The `TreeIndex` class provides methods to manage hierarchy and split the tree at a given resolution or across resolutions. The `TreeViz` class extends `SummarizedExperiment` and can performs quick aggregations on the count matrix defined by clusters. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9e1a317862ad079f52876f54d7160bde build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sctreeviz", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s, metagenomeSeq, epivizrStandalone, GenomeInfoDb requirements: + host: - - 'bioconductor-epivizr >=2.32.0,<2.33.0' - - 'bioconductor-epivizrdata >=1.30.0,<1.31.0' - - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-epivizr >=2.36.0,<2.37.0 + - bioconductor-epivizrdata >=1.34.0,<1.35.0 + - bioconductor-epivizrserver >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-clustree - r-data.table @@ -42,15 +44,16 @@ requirements: - r-rtsne - r-seurat - r-sys + run: - - 'bioconductor-epivizr >=2.32.0,<2.33.0' - - 'bioconductor-epivizrdata >=1.30.0,<1.31.0' - - 'bioconductor-epivizrserver >=1.30.0,<1.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-epivizr >=2.36.0,<2.37.0 + - bioconductor-epivizrdata >=1.34.0,<1.35.0 + - bioconductor-epivizrserver >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-clustree - r-data.table @@ -63,12 +66,16 @@ requirements: - r-rtsne - r-seurat - r-sys + +source: + md5: 8c96789f4dd4d0338e36fa08172d47d1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations' - description: 'scTreeViz provides classes to support interactive data aggregation and visualization of single cell RNA-seq datasets with hierarchies for e.g. cell clusters at different resolutions. The `TreeIndex` class provides methods to manage hierarchy and split the tree at a given resolution or across resolutions. The `TreeViz` class extends `SummarizedExperiment` and can performs quick aggregations on the count matrix defined by clusters.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-scuttle/meta.yaml b/recipes/bioconductor-scuttle/meta.yaml index a578d0cb4595c..bb01629da7f1a 100644 --- a/recipes/bioconductor-scuttle/meta.yaml +++ b/recipes/bioconductor-scuttle/meta.yaml @@ -1,70 +1,80 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "scuttle" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. Also provides some helper functions to assist development of other packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Single-Cell RNA-Seq Analysis Utilities -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b784ac30ef76b7c0cdac8b79be67b995 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scuttle", max_pin="x.x") }}' -# Suggests: BiocStyle, knitr, scRNAseq, rmarkdown, testthat, scran + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:scuttle + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, scRNAseq, rmarkdown, testthat, sparseMatrixStats, DelayedMatrixStats, scran # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4arrays >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4arrays >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: f10f6358407c2d4aa3457a6efebc6a93 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'Single-Cell RNA-Seq Analysis Utilities' - description: 'Provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. Also provides some helper functions to assist development of other packages.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-scvir/meta.yaml b/recipes/bioconductor-scvir/meta.yaml index 1c38e61212da1..d437a7e250cd6 100644 --- a/recipes/bioconductor-scvir/meta.yaml +++ b/recipes/bioconductor-scvir/meta.yaml @@ -1,58 +1,63 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "scviR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package defines interfaces from R to scvi-tools. A vignette works through the totalVI tutorial for analyzing CITE-seq data. Another vignette compares outputs of Chapter 12 of the OSCA book with analogous outputs based on totalVI quantifications. Future work will address other components of scvi-tools, with a focus on building understanding of probabilistic methods based on variational autoencoders. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: experimental inferface from R to scvi-tools -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 71d6c427fcc042ac8b011a31935641df build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-scvir", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, reshape2, ggplot2, rhdf5, BiocStyle requirements: host: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-pheatmap - r-reticulate - r-shiny run: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-pheatmap - r-reticulate - r-shiny + +source: + md5: f74a3316c36a41c893d5fb09c718a465 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'experimental inferface from R to scvi-tools' - description: 'This package defines interfaces from R to scvi-tools. A vignette works through the totalVI tutorial for analyzing CITE-seq data. Another vignette compares outputs of Chapter 12 of the OSCA book with analogous outputs based on totalVI quantifications. Future work will address other components of scvi-tools, with a focus on building understanding of probabilistic methods based on variational autoencoders.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sdams/meta.yaml b/recipes/bioconductor-sdams/meta.yaml index 8ad0a22e4f270..02d55f3243dd1 100644 --- a/recipes/bioconductor-sdams/meta.yaml +++ b/recipes/bioconductor-sdams/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "SDAMS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 27ac3a8046a94bf8473502ee2cd5afe1 +about: + description: This Package utilizes a Semi-parametric Differential Abundance/expression analysis (SDA) method for metabolomics and proteomics data from mass spectrometry as well as single-cell RNA sequencing data. SDA is able to robustly handle non-normally distributed data and provides a clear quantification of the effect size. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequencing Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sdams", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat requirements: host: - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-trust run: - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-trust +source: + md5: 00f019a01ecc97ee6585f066502dde93 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL - summary: 'Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequencing Data' - description: 'This Package utilizes a Semi-parametric Differential Abundance/expression analysis (SDA) method for metabolomics and proteomics data from mass spectrometry as well as single-cell RNA sequencing data. SDA is able to robustly handle non-normally distributed data and provides a clear quantification of the effect size.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-seahtrue/build.sh b/recipes/bioconductor-seahtrue/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-seahtrue/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-seahtrue/meta.yaml b/recipes/bioconductor-seahtrue/meta.yaml new file mode 100644 index 0000000000000..17267012a98a0 --- /dev/null +++ b/recipes/bioconductor-seahtrue/meta.yaml @@ -0,0 +1,85 @@ +{% set version = "1.0.0" %} +{% set name = "seahtrue" %} +{% set bioc = "3.20" %} + +about: + description: Seahtrue organizes oxygen consumption and extracellular acidification analysis data from experiments performed on an XF analyzer into structured nested tibbles.This allows for detailed processing of raw data and advanced data visualization and statistics. Seahtrue introduces an open and reproducible way to analyze these XF experiments. It uses file paths to .xlsx files. These .xlsx files are supplied by the userand are generated by the user in the Wave software from Agilent from the assay result files (.asyr). The .xlsx file contains different sheets of important data for the experiment; 1. Assay Information - Details about how the experiment was set up. 2. Rate Data - Information about the OCR and ECAR rates. 3. Raw Data - The original raw data collected during the experiment. 4. Calibration Data - Data related to calibrating the instrument. Seahtrue focuses on getting the specific data needed for analysis. Once this data is extracted, it is prepared for calculations through preprocessing. To make sure everything is accurate, both the initial data and the preprocessed data go through thorough checks. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Seahtrue revives XF data for structured data analysis + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-seahtrue", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle +requirements: + + host: + - r-base + - r-cli >=3.4.1 + - r-colorspace >=2.1.0 + - r-dplyr >=1.1.2 + - r-forcats >=1.0.0 + - r-ggplot2 >=3.5.0 + - r-ggridges >=0.5.6 + - r-glue >=1.6.2 + - r-janitor >=2.2.0 + - r-logger >=0.2.2 + - r-lubridate >=1.8.0 + - r-purrr >=0.3.5 + - r-rcolorbrewer >=1.1.3 + - r-readr >=2.1.5 + - r-readxl >=1.4.1 + - r-rlang >=1.0.0 + - r-scales >=1.3.0 + - r-stringr >=1.4.1 + - r-tibble >=3.1.8 + - r-tidyr >=1.3.0 + - r-tidyxl >=1.0.8 + - r-validate >=1.1.1 + + run: + - r-base + - r-cli >=3.4.1 + - r-colorspace >=2.1.0 + - r-dplyr >=1.1.2 + - r-forcats >=1.0.0 + - r-ggplot2 >=3.5.0 + - r-ggridges >=0.5.6 + - r-glue >=1.6.2 + - r-janitor >=2.2.0 + - r-logger >=0.2.2 + - r-lubridate >=1.8.0 + - r-purrr >=0.3.5 + - r-rcolorbrewer >=1.1.3 + - r-readr >=2.1.5 + - r-readxl >=1.4.1 + - r-rlang >=1.0.0 + - r-scales >=1.3.0 + - r-stringr >=1.4.1 + - r-tibble >=3.1.8 + - r-tidyr >=1.3.0 + - r-tidyxl >=1.0.8 + - r-validate >=1.1.1 + +source: + md5: bee1e14310733bbd79afb3af3894b05b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-sechm/meta.yaml b/recipes/bioconductor-sechm/meta.yaml index 5d3d35924430b..ceeb243408f70 100644 --- a/recipes/bioconductor-sechm/meta.yaml +++ b/recipes/bioconductor-sechm/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "sechm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: sechm provides a simple interface between SummarizedExperiment objects and the ComplexHeatmap package. It enables plotting annotated heatmaps from SE objects, with easy access to rowData and colData columns, and implements a number of features to make the generation of heatmaps easier and more flexible. These functionalities used to be part of the SEtools package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'sechm: Complex Heatmaps from a SummarizedExperiment' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6935a759779eaf70e1cbf3f22c7a1358 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sechm", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-matrixstats - r-randomcolor - r-seriation run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circlize - r-matrixstats - r-randomcolor - r-seriation + +source: + md5: c89224d13b5d6792fa4568f08b69081f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'sechm: Complex Heatmaps from a SummarizedExperiment' - description: 'sechm provides a simple interface between SummarizedExperiment objects and the ComplexHeatmap package. It enables plotting annotated heatmaps from SE objects, with easy access to rowData and colData columns, and implements a number of features to make the generation of heatmaps easier and more flexible. These functionalities used to be part of the SEtools package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-segmenter/meta.yaml b/recipes/bioconductor-segmenter/meta.yaml index 76cfdd42e39c9..fc294901c0c2e 100644 --- a/recipes/bioconductor-segmenter/meta.yaml +++ b/recipes/bioconductor-segmenter/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "segmenter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Chromatin segmentation analysis transforms ChIP-seq data into signals over the genome. The latter represents the observed states in a multivariate Markov model to predict the chromatin's underlying states. ChromHMM, written in Java, integrates histone modification datasets to learn the chromatin states de-novo. The goal of this package is to call chromHMM from within R, capture the output files in an S4 object and interface to other relevant Bioconductor analysis tools. In addition, segmenter provides functions to test, select and visualize the output of the segmentation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Perform Chromatin Segmentation Analysis in R by Calling ChromHMM -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8877dce2f35cc59e9c3d8b3fb38bf29e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-segmenter", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz requirements: host: - - 'bioconductor-bamsignals >=1.34.0,<1.35.0' - - 'bioconductor-chipseeker >=1.38.0,<1.39.0' - - 'bioconductor-chromhmmdata >=0.99.0,<0.100.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-bamsignals >=1.38.0,<1.39.0 + - bioconductor-chipseeker >=1.42.0,<1.43.0 + - bioconductor-chromhmmdata >=0.99.0,<0.100.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-bamsignals >=1.34.0,<1.35.0' - - 'bioconductor-chipseeker >=1.38.0,<1.39.0' - - 'bioconductor-chromhmmdata >=0.99.0,<0.100.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-bamsignals >=1.38.0,<1.39.0 + - bioconductor-chipseeker >=1.42.0,<1.43.0 + - bioconductor-chromhmmdata >=0.99.0,<0.100.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + +source: + md5: b6c2d7f5ad306fc10a3d4c6865c5668b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Perform Chromatin Segmentation Analysis in R by Calling ChromHMM' - description: 'Chromatin segmentation analysis transforms ChIP-seq data into signals over the genome. The latter represents the observed states in a multivariate Markov model to predict the chromatin''s underlying states. ChromHMM, written in Java, integrates histone modification datasets to learn the chromatin states de-novo. The goal of this package is to call chromHMM from within R, capture the output files in an S4 object and interface to other relevant Bioconductor analysis tools. In addition, segmenter provides functions to test, select and visualize the output of the segmentation.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-segmentseq/meta.yaml b/recipes/bioconductor-segmentseq/meta.yaml index e43eace8f35f7..f04edff815c2f 100644 --- a/recipes/bioconductor-segmentseq/meta.yaml +++ b/recipes/bioconductor-segmentseq/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "2.36.0" %} +{% set version = "2.40.0" %} {% set name = "segmentSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Methods for identifying small RNA loci from high-throughput sequencing data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f86ecc00eba08e4f13412c624d98697c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-segmentseq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, BiocGenerics requirements: host: - - 'bioconductor-bayseq >=2.36.0,<2.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-bayseq >=2.40.0,<2.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-abind - r-base run: - - 'bioconductor-bayseq >=2.36.0,<2.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' + - bioconductor-bayseq >=2.40.0,<2.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 - r-abind - r-base + +source: + md5: 27365cd159f6e2b16071be25219114e1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Methods for identifying small RNA loci from high-throughput sequencing data' - description: 'High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-selectksigs/meta.yaml b/recipes/bioconductor-selectksigs/meta.yaml index 15de6e1d4eb79..8c5112cdbc13c 100644 --- a/recipes/bioconductor-selectksigs/meta.yaml +++ b/recipes/bioconductor-selectksigs/meta.yaml @@ -1,27 +1,33 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "selectKSigs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A package to suggest the number of mutational signatures in a collection of somatic mutations using calculating the cross-validated perplexity score. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Selecting the number of mutational signatures using a perplexity-based measure and cross-validation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 95d84e53b480a52695c40071dfa9be68 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-selectksigs", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-hilda >=1.16.0,<1.17.0' + - bioconductor-hilda >=1.20.0,<1.21.0 - r-base - r-gtools - r-magrittr @@ -29,22 +35,21 @@ requirements: - libblas - liblapack run: - - 'bioconductor-hilda >=1.16.0,<1.17.0' + - bioconductor-hilda >=1.20.0,<1.21.0 - r-base - r-gtools - r-magrittr - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 5c94b8595503af2cc228959d5b8d68f3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Selecting the number of mutational signatures using a perplexity-based measure and cross-validation' - description: 'A package to suggest the number of mutational signatures in a collection of somatic mutations using calculating the cross-validated perplexity score.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-selex/meta.yaml b/recipes/bioconductor-selex/meta.yaml index f722404705424..5fc952d3accde 100644 --- a/recipes/bioconductor-selex/meta.yaml +++ b/recipes/bioconductor-selex/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "SELEX" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fdb39d601a2ce8c882e9a0e822ef014c +about: + description: Tools for quantifying DNA binding specificities based on SELEX-seq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Functions for analyzing SELEX-seq data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-selex", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # SystemRequirements: Java (>= 1.5) requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - - 'r-rjava >=0.5-0' + - r-rjava >=0.5-0 - openjdk run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - - 'r-rjava >=0.5-0' + - r-rjava >=0.5-0 - openjdk +source: + md5: 25034e2be1f002487837d965f3812b63 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Functions for analyzing SELEX-seq data' - description: 'Tools for quantifying DNA binding specificities based on SELEX-seq data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-semdist/meta.yaml b/recipes/bioconductor-semdist/meta.yaml index 4d76de2af60bc..7357d23e4f71d 100644 --- a/recipes/bioconductor-semdist/meta.yaml +++ b/recipes/bioconductor-semdist/meta.yaml @@ -1,45 +1,22 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "SemDist" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements methods to calculate information accretion for a given version of the gene ontology and uses this data to calculate remaining uncertainty, misinformation, and semantic similarity for given sets of predicted annotations and true annotations from a protein function predictor. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Information Accretion-based Function Predictor Evaluation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b95a04e7daaae24fb22f3b2a40b17f5f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-semdist", max_pin="x.x") }}' - noarch: generic -# Suggests: GOSemSim -requirements: - host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - r-base - run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Information Accretion-based Function Predictor Evaluation' - description: 'This package implements methods to calculate information accretion for a given version of the gene ontology and uses this data to calculate remaining uncertainty, misinformation, and semantic similarity for given sets of predicted annotations and true annotations from a protein function predictor.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:semdist @@ -49,3 +26,32 @@ extra: path: recipes/bioconductor-semdist version: 1.14.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: GOSemSim +requirements: + host: + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - r-base + run: + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - r-base + +source: + md5: f253ae30232aebcb7f34d1573d92d308 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-semisup/meta.yaml b/recipes/bioconductor-semisup/meta.yaml index e541f2fdda943..63823eea7fea9 100644 --- a/recipes/bioconductor-semisup/meta.yaml +++ b/recipes/bioconductor-semisup/meta.yaml @@ -1,24 +1,28 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "semisup" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fb3d32c07acbfadbbee01f9a6c8333fe +about: + description: Implements a parametric semi-supervised mixture model. The permutation test detects markers with main or interactive effects, without distinguishing them. Possible applications include genome-wide association analysis and differential expression analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Semi-Supervised Mixture Model build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-semisup", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-semisup + path: recipes/bioconductor-semisup + version: 1.4.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, testthat, SummarizedExperiment requirements: host: @@ -27,18 +31,14 @@ requirements: run: - r-base - r-vgam +source: + md5: 6c4a3b77b2d1403bf24cc9954c7f7148 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Semi-Supervised Mixture Model' - description: 'Implements a parametric semi-supervised mixture model. The permutation test detects markers with main or interactive effects, without distinguishing them. Possible applications include genome-wide association analysis and differential expression analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-semisup - path: recipes/bioconductor-semisup - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-seq.hotspot/meta.yaml b/recipes/bioconductor-seq.hotspot/meta.yaml index a2ea709167002..682cbcfba8a09 100644 --- a/recipes/bioconductor-seq.hotspot/meta.yaml +++ b/recipes/bioconductor-seq.hotspot/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "seq.hotSPOT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 37e04dc7e1bb05af58c50cb7701388c7 +about: + description: seq.hotSPOT provides a resource for designing effective sequencing panels to help improve mutation capture efficacy for ultradeep sequencing projects. Using SNV datasets, this package designs custom panels for any tissue of interest and identify the genomic regions likely to contain the most mutations. Establishing efficient targeted sequencing panels can allow researchers to study mutation burden in tissues at high depth without the economic burden of whole-exome or whole-genome sequencing. This tool was developed to make high-depth sequencing panels to study low-frequency clonal mutations in clinically normal and cancerous tissues. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Targeted sequencing panel design based on mutation hotspots build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-seq.hotspot", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: @@ -29,12 +27,14 @@ requirements: - r-base - r-hash - r-r.utils +source: + md5: 2a061f0311bfeaf86ed51a9cdc48b966 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Targeted sequencing panel design based on mutation hotspots' - description: 'seq.hotSPOT provides a resource for designing effective sequencing panels to help improve mutation capture efficacy for ultradeep sequencing projects. Using SNV datasets, this package designs custom panels for any tissue of interest and identify the genomic regions likely to contain the most mutations. Establishing efficient targeted sequencing panels can allow researchers to study mutation burden in tissues at high depth without the economic burden of whole-exome or whole-genome sequencing. This tool was developed to make high-depth sequencing panels to study low-frequency clonal mutations in clinically normal and cancerous tissues.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-seq2pathway.data/meta.yaml b/recipes/bioconductor-seq2pathway.data/meta.yaml index 8410739a77c65..57ca6e8f009a6 100644 --- a/recipes/bioconductor-seq2pathway.data/meta.yaml +++ b/recipes/bioconductor-seq2pathway.data/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "seq2pathway.data" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b0035ff986391159c1329eac9fb96661 +about: + description: Supporting data for the seq2patheway package. Includes modified gene sets from MsigDB and org.Hs.eg.db; gene locus definitions from GENCODE project. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: data set for R package seq2pathway build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-seq2pathway.data", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-seq2pathway.data + path: recipes/bioconductor-seq2pathway.data + version: 1.12.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 56fcfc87bf877f64ff1283275f37ab73 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'data set for R package seq2pathway' - description: 'Supporting data for the seq2patheway package. Includes modified gene sets from MsigDB and org.Hs.eg.db; gene locus definitions from GENCODE project.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-seq2pathway.data - path: recipes/bioconductor-seq2pathway.data - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-seq2pathway.data/post-link.sh b/recipes/bioconductor-seq2pathway.data/post-link.sh index 30b629ea74cff..a195e394e15ff 100644 --- a/recipes/bioconductor-seq2pathway.data/post-link.sh +++ b/recipes/bioconductor-seq2pathway.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "seq2pathway.data-1.34.0" +installBiocDataPackage.sh "seq2pathway.data-1.38.0" diff --git a/recipes/bioconductor-seq2pathway/build_failure.linux-64.yaml b/recipes/bioconductor-seq2pathway/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..72febe4f5333d --- /dev/null +++ b/recipes/bioconductor-seq2pathway/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: cbb1907acc8eb3691ebd82f22f0cd61374ca57f63692b4235e115c0aee63f3ed # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [31mr-base >=3.5.1,<3.5.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna [1.68|1.69][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna 1.69[0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna [1.69|1.71][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna 1.71[0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna 1.71[0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna [1.71|1.73][0m would require + [31mbioconductor-annotationdbi >=1.64.1,<1.65.0a0 [0m, which requires + [31mbioconductor-iranges >=2.36.0,<2.37.0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-wgcna==1.51=r3.3.1_0"), MatchSpec("3.3.1*")} + Encountered problems while solving: + - nothing provides r-base 3.3.1* needed by r-wgcna-1.51-r3.3.1_0 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-genomicranges >=1.58.0,<1.59.0 [0m is installable and it requires + [32mbioconductor-iranges >=2.40.0,<2.41.0 [0m, which can be installed; + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-wgcna[0m is not installable because there are no viable options + [31mr-wgcna 1.51[0m would require + [31mr-base 3.3.1* [0m, which does not exist (perhaps a missing channel); + [31mr-wgcna 1.51[0m would require + [31mr-base 3.3.2* [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna [1.51|1.61][0m would require + [31mr-base 3.4.1* [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna [1.64_1|1.66][0m would require + [31mbioconductor-annotationdbi >=1.42.0,<1.44.0 [0m, which requires + [31mbioconductor-iranges >=2.14.12,<2.16.0 [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna [1.66|1.67|1.68][0m would require + [31mr-base >=3.5.1,<3.5.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna [1.68|1.69][0m would require + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna 1.69[0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna [1.69|1.71][0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna 1.71[0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna 1.71[0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-wgcna [1.71|1.73][0m would require + [31mbioconductor-annotationdbi >=1.64.1,<1.65.0a0 [0m, which requires + [31mbioconductor-iranges >=2.36.0,<2.37.0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-seq2pathway/meta.yaml b/recipes/bioconductor-seq2pathway/meta.yaml index 4dbc70fe6e390..3818dd0f7dcae 100644 --- a/recipes/bioconductor-seq2pathway/meta.yaml +++ b/recipes/bioconductor-seq2pathway/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "seq2pathway" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Seq2pathway is a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data, consisting of "seq2gene" and "gene2path" components. The seq2gene links sequence-level measurements of genomic regions (including SNPs or point mutation coordinates) to gene-level scores, and the gene2pathway summarizes gene scores to pathway-scores for each sample. The seq2gene has the feasibility to assign both coding and non-exon regions to a broader range of neighboring genes than only the nearest one, thus facilitating the study of functional non-coding regions. The gene2pathway takes into account the quantity of significance for gene members within a pathway compared those outside a pathway. The output of seq2pathway is a general structure of quantitative pathway-level scores, thus allowing one to functional interpret such datasets as RNA-seq, ChIP-seq, GWAS, and derived from other next generational sequencing experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4aaa34232c40fdc31f493d67c72742c4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-seq2pathway", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:seq2pathway + parent_recipe: + name: bioconductor-seq2pathway + path: recipes/bioconductor-seq2pathway + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-seq2pathway.data >=1.34.0,<1.35.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-seq2pathway.data >=1.38.0,<1.39.0 - r-base - r-gsa - r-nnet - r-wgcna run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-seq2pathway.data >=1.34.0,<1.35.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-seq2pathway.data >=1.38.0,<1.39.0 - r-base - r-gsa - r-nnet - r-wgcna + +source: + md5: 250480b364466bf484e3a5a63e4dd65d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data' - description: 'Seq2pathway is a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data, consisting of "seq2gene" and "gene2path" components. The seq2gene links sequence-level measurements of genomic regions (including SNPs or point mutation coordinates) to gene-level scores, and the gene2pathway summarizes gene scores to pathway-scores for each sample. The seq2gene has the feasibility to assign both coding and non-exon regions to a broader range of neighboring genes than only the nearest one, thus facilitating the study of functional non-coding regions. The gene2pathway takes into account the quantity of significance for gene members within a pathway compared those outside a pathway. The output of seq2pathway is a general structure of quantitative pathway-level scores, thus allowing one to functional interpret such datasets as RNA-seq, ChIP-seq, GWAS, and derived from other next generational sequencing experiments.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:seq2pathway - parent_recipe: - name: bioconductor-seq2pathway - path: recipes/bioconductor-seq2pathway - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-seqarray/meta.yaml b/recipes/bioconductor-seqarray/meta.yaml index c533d2b4768d9..53f7fa0154218 100644 --- a/recipes/bioconductor-seqarray/meta.yaml +++ b/recipes/bioconductor-seqarray/meta.yaml @@ -1,60 +1,65 @@ -{% set version = "1.42.4" %} +{% set version = "1.46.0" %} {% set name = "SeqArray" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Data management of large-scale whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray GDS files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Data Management of Large-Scale Whole-Genome Sequence Variant Calls -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 607951cd78bea8ef1156be7aba41052f build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-seqarray", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:seqarray + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, markdown, rmarkdown, Rsamtools, VariantAnnotation requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 3cfd40aeb8399455e23b265f96b8f695 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3.0-only - summary: 'Data Management of Large-Scale Whole-Genome Sequence Variant Calls' - description: 'Data management of large-scale whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray GDS files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-seqc/meta.yaml b/recipes/bioconductor-seqc/meta.yaml index 6da322827d369..649deaa352e0b 100644 --- a/recipes/bioconductor-seqc/meta.yaml +++ b/recipes/bioconductor-seqc/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "seqc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 105a278c97aca90968641aec403c1219 +about: + description: The SEQC/MAQC-III Consortium has produced benchmark RNA-seq data for the assessment of RNA sequencing technologies and data analysis methods (Nat Biotechnol, 2014). Billions of sequence reads have been generated from ten different sequencing sites. This package contains the summarized read count data for ~2000 sequencing libraries. It also includes all the exon-exon junctions discovered from the study. TaqMan RT-PCR data for ~1000 genes and ERCC spike-in sequence data are included in this package as well. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: RNA-seq data generated from SEQC (MAQC-III) study build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-seqc", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 36346eaad47ac3ef20ae0b8979145247 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'RNA-seq data generated from SEQC (MAQC-III) study' - description: 'The SEQC/MAQC-III Consortium has produced benchmark RNA-seq data for the assessment of RNA sequencing technologies and data analysis methods (Nat Biotechnol, 2014). Billions of sequence reads have been generated from ten different sequencing sites. This package contains the summarized read count data for ~2000 sequencing libraries. It also includes all the exon-exon junctions discovered from the study. TaqMan RT-PCR data for ~1000 genes and ERCC spike-in sequence data are included in this package as well.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-seqc/post-link.sh b/recipes/bioconductor-seqc/post-link.sh index 9d67b6fc469d9..9206bb4ed3a00 100644 --- a/recipes/bioconductor-seqc/post-link.sh +++ b/recipes/bioconductor-seqc/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "seqc-1.36.0" +installBiocDataPackage.sh "seqc-1.40.0" diff --git a/recipes/bioconductor-seqcat/meta.yaml b/recipes/bioconductor-seqcat/meta.yaml index 4c3f9796fbf43..ac932c107ebdf 100644 --- a/recipes/bioconductor-seqcat/meta.yaml +++ b/recipes/bioconductor-seqcat/meta.yaml @@ -1,60 +1,65 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "seqCAT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The seqCAT package uses variant calling data (in the form of VCF files) from high throughput sequencing technologies to authenticate and validate the source, function and characteristics of biological samples used in scientific endeavours. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENCE + summary: High Throughput Sequencing Cell Authentication Toolkit -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a7694d3599501816a63d4b6e831af35d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-seqcat", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager requirements: host: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - - 'r-dplyr >=0.5.0' - - 'r-ggplot2 >=2.2.1' + - r-dplyr >=0.5.0 + - r-ggplot2 >=2.2.1 - r-rlang - - 'r-scales >=0.4.1' - - 'r-tidyr >=0.6.1' + - r-scales >=0.4.1 + - r-tidyr >=0.6.1 run: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - - 'r-dplyr >=0.5.0' - - 'r-ggplot2 >=2.2.1' + - r-dplyr >=0.5.0 + - r-ggplot2 >=2.2.1 - r-rlang - - 'r-scales >=0.4.1' - - 'r-tidyr >=0.6.1' + - r-scales >=0.4.1 + - r-tidyr >=0.6.1 + +source: + md5: 5b6197a98759a7cb4100d4bfcc37ca65 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENCE' - summary: 'High Throughput Sequencing Cell Authentication Toolkit' - description: 'The seqCAT package uses variant calling data (in the form of VCF files) from high throughput sequencing technologies to authenticate and validate the source, function and characteristics of biological samples used in scientific endeavours.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-seqcombo/meta.yaml b/recipes/bioconductor-seqcombo/meta.yaml index 4afa58a79f493..5360ac06b26e1 100644 --- a/recipes/bioconductor-seqcombo/meta.yaml +++ b/recipes/bioconductor-seqcombo/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "seqcombo" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 76a401edd5e5583a94ab3a1b599b7a78 +about: + description: Provides useful functions for visualizing virus reassortment events. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Visualization Tool for Genetic Reassortment build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-seqcombo", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: emojifont, knitr, rmarkdown, prettydoc, tibble requirements: host: @@ -31,12 +29,14 @@ requirements: - r-ggplot2 - r-igraph - r-yulab.utils +source: + md5: 57aaa841ba97972f5ea8272d9e354ace + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Visualization Tool for Genetic Reassortment' - description: 'Provides useful functions for visualizing virus reassortment events.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-seqgate/meta.yaml b/recipes/bioconductor-seqgate/meta.yaml index 5ca65b1d94bf3..041ca9268874a 100644 --- a/recipes/bioconductor-seqgate/meta.yaml +++ b/recipes/bioconductor-seqgate/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "SeqGate" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 786d9cf0f14de2b0056b9207daedbf45 +about: + description: Filtering of lowly expressed features (e.g. genes) is a common step before performing statistical analysis, but an arbitrary threshold is generally chosen. SeqGate implements a method that rationalize this step by the analysis of the distibution of counts in replicate samples. The gate is the threshold above which sequenced features can be considered as confidently quantified. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2.0) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Filtering of Lowly Expressed Features build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-seqgate", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-biocmanager run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-biocmanager +source: + md5: 0a1c3365067d26ef25b06a3fcb13a1f5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2.0)' - summary: 'Filtering of Lowly Expressed Features' - description: 'Filtering of lowly expressed features (e.g. genes) is a common step before performing statistical analysis, but an arbitrary threshold is generally chosen. SeqGate implements a method that rationalize this step by the analysis of the distibution of counts in replicate samples. The gate is the threshold above which sequenced features can be considered as confidently quantified.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-seqgsea/meta.yaml b/recipes/bioconductor-seqgsea/meta.yaml index 0d91107a888ec..8d2429a6b82f4 100644 --- a/recipes/bioconductor-seqgsea/meta.yaml +++ b/recipes/bioconductor-seqgsea/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "SeqGSEA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 13213924066a18535220d42938e923fa +about: + description: The package generally provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene's differential expression and splicing, respectively. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-seqgsea", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: GenomicRanges requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 - r-base - r-doparallel run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 - r-base - r-doparallel +source: + md5: 8aa3f3c9f25bec465e1388734a23784a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing' - description: 'The package generally provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene''s differential expression and splicing, respectively.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-seqlogo/meta.yaml b/recipes/bioconductor-seqlogo/meta.yaml index 7f32797f34d61..f251ddc31764c 100644 --- a/recipes/bioconductor-seqlogo/meta.yaml +++ b/recipes/bioconductor-seqlogo/meta.yaml @@ -1,39 +1,20 @@ -{% set version = "1.68.0" %} +{% set version = "1.72.0" %} {% set name = "seqLogo" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0771c35a7929a3e71aa5eebaf4a624ef +about: + description: seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Sequence logos for DNA sequence alignments build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-seqlogo", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, BiocStyle, rmarkdown, testthat -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'Sequence logos for DNA sequence alignments' - description: 'seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' extra: identifiers: - biotools:seqlogo @@ -42,4 +23,23 @@ extra: name: bioconductor-seqlogo path: recipes/bioconductor-seqlogo version: 1.46.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: knitr, BiocStyle, rmarkdown, testthat +requirements: + host: + - r-base + run: + - r-base +source: + md5: a4abef9336767a981efc4395fa831aea + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-seqpattern/meta.yaml b/recipes/bioconductor-seqpattern/meta.yaml index 78b4fabd8eb99..af62cad68e035 100644 --- a/recipes/bioconductor-seqpattern/meta.yaml +++ b/recipes/bioconductor-seqpattern/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "seqPattern" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Visualising oligonucleotide patterns and sequence motifs occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 90ef37347887673ee80f12fa953e02f3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-seqpattern", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:seqpattern + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-seqpattern + path: recipes/bioconductor-seqpattern + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-kernsmooth - r-plotrix run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-kernsmooth - r-plotrix + +source: + md5: dbdb048e7fc633edc7d941dfafbc8bca + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences' - description: 'Visualising oligonucleotide patterns and sequence motifs occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:seqpattern - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-seqpattern - path: recipes/bioconductor-seqpattern - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-seqsetvis/meta.yaml b/recipes/bioconductor-seqsetvis/meta.yaml index fce6340743e95..95bcca0c8f341 100644 --- a/recipes/bioconductor-seqsetvis/meta.yaml +++ b/recipes/bioconductor-seqsetvis/meta.yaml @@ -1,35 +1,38 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "seqsetvis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: seqsetvis enables the visualization and analysis of sets of genomic sites in next gen sequencing data. Although seqsetvis was designed for the comparison of mulitple ChIP-seq samples, this package is domain-agnostic and allows the processing of multiple genomic coordinate files (bed-like files) and signal files (bigwig files pileups from bam file). seqsetvis has multiple functions for fetching data from regions into a tidy format for analysis in data.table or tidyverse and visualization via ggplot2. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Set Based Visualizations for Next-Gen Sequencing Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0119c8a5e2475e3a0d35059b3c35dfd6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-seqsetvis", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, knitr, rmarkdown, testthat requirements: + host: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cowplot - r-data.table @@ -42,15 +45,16 @@ requirements: - r-rcolorbrewer - r-scales - r-upsetr + run: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cowplot - r-data.table @@ -63,13 +67,16 @@ requirements: - r-rcolorbrewer - r-scales - r-upsetr + +source: + md5: 596d00c266a2b595ef7118666963cf30 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Set Based Visualizations for Next-Gen Sequencing Data' - description: 'seqsetvis enables the visualization and analysis of sets of genomic sites in next gen sequencing data. Although seqsetvis was designed for the comparison of mulitple ChIP-seq samples, this package is domain-agnostic and allows the processing of multiple genomic coordinate files (bed-like files) and signal files (bigwig files pileups from bam file).' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-seqsqc/meta.yaml b/recipes/bioconductor-seqsqc/meta.yaml index dfcf859b73495..c3e03d0f27942 100644 --- a/recipes/bioconductor-seqsqc/meta.yaml +++ b/recipes/bioconductor-seqsqc/meta.yaml @@ -1,63 +1,68 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "SeqSQC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The SeqSQC is designed to identify problematic samples in NGS data, including samples with gender mismatch, contamination, cryptic relatedness, and population outlier. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A bioconductor package for sample quality check with next generation sequencing data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 10e877d23b5c1572319af0515baca2c1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-seqsqc", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-snprelate >=1.40.0,<1.41.0 - r-base - r-e1071 - r-ggally - r-ggplot2 - - r-rbokeh + - r-plotly - r-rcolorbrewer - r-reshape2 - r-rmarkdown run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-snprelate >=1.36.0,<1.37.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-snprelate >=1.40.0,<1.41.0 - r-base - r-e1071 - r-ggally - r-ggplot2 - - r-rbokeh + - r-plotly - r-rcolorbrewer - r-reshape2 - r-rmarkdown + +source: + md5: d3038a849a70cc2625cf2931230e0a2a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'A bioconductor package for sample quality check with next generation sequencing data' - description: 'The SeqSQC is designed to identify problematic samples in NGS data, including samples with gender mismatch, contamination, cryptic relatedness, and population outlier.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-seqtools/meta.yaml b/recipes/bioconductor-seqtools/meta.yaml index 93a07f90dca3c..04fdf3c726a29 100644 --- a/recipes/bioconductor-seqtools/meta.yaml +++ b/recipes/bioconductor-seqtools/meta.yaml @@ -1,50 +1,57 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "seqTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Analyze read length, phred scores and alphabet frequency and DNA k-mers on uncompressed and compressed fastq files. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Analysis of nucleotide, sequence and quality content on fastq files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: be9be6eb0ee1ff4ab001720970d68da8 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-seqtools", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:seqtools + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-seqtools + path: recipes/bioconductor-seqtools + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - libblas - liblapack + - zlib run: - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: ae732af0b68234893f0cb7852dbe64c7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Analysis of nucleotide, sequence and quality content on fastq files' - description: 'Analyze read length, phred scores and alphabet frequency and DNA k-mers on uncompressed and compressed fastq files.' -extra: - identifiers: - - biotools:seqtools - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-seqtools - path: recipes/bioconductor-seqtools - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-seqvartools/meta.yaml b/recipes/bioconductor-seqvartools/meta.yaml index cd40a732cfeb5..68829723be32c 100644 --- a/recipes/bioconductor-seqvartools/meta.yaml +++ b/recipes/bioconductor-seqvartools/meta.yaml @@ -1,59 +1,64 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "SeqVarTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Tools for variant data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 160f56cd78339c2e4d4b5c0766a47846 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-seqvartools", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, RUnit, stringr requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqarray >=1.46.0,<1.47.0 - r-base - r-data.table - r-gwasexacthw - r-logistf - r-matrix run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-seqarray >=1.42.0,<1.43.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqarray >=1.46.0,<1.47.0 - r-base - r-data.table - r-gwasexacthw - r-logistf - r-matrix + +source: + md5: 31e63d1f87278b6809aa14cb1c3a7d0e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Tools for variant data' - description: 'An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-serumstimulation/meta.yaml b/recipes/bioconductor-serumstimulation/meta.yaml index 7304fb6ceb832..cd12c54c3165c 100644 --- a/recipes/bioconductor-serumstimulation/meta.yaml +++ b/recipes/bioconductor-serumstimulation/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "serumStimulation" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d3f1a4e58f500d7e424eef0b22c05ad +about: + description: Contains 13 micro array data results from a serum stimulation experiment + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: serumStimulation is a data package which is used by examples in package pcaGoPromoter build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-serumstimulation", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9ae60ca2091b47da1d3d887067f89135 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'serumStimulation is a data package which is used by examples in package pcaGoPromoter' - description: 'Contains 13 micro array data results from a serum stimulation experiment' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-serumstimulation/post-link.sh b/recipes/bioconductor-serumstimulation/post-link.sh index f74707b1a8b74..ff4a4cd37789d 100644 --- a/recipes/bioconductor-serumstimulation/post-link.sh +++ b/recipes/bioconductor-serumstimulation/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "serumstimulation-1.38.0" +installBiocDataPackage.sh "serumstimulation-1.42.0" diff --git a/recipes/bioconductor-sesame/meta.yaml b/recipes/bioconductor-sesame/meta.yaml index bef67f6a17dd4..a48d812600faa 100644 --- a/recipes/bioconductor-sesame/meta.yaml +++ b/recipes/bioconductor-sesame/meta.yaml @@ -1,37 +1,38 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "sesame" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools For analyzing Illumina Infinium DNA methylation arrays. SeSAMe provides utilities to support analyses of multiple generations of Infinium DNA methylation BeadChips, including preprocessing, quality control, visualization and inference. SeSAMe features accurate detection calling, intelligent inference of ethnicity, sex and advanced quality control routines. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: SEnsible Step-wise Analysis of DNA MEthylation BeadChips -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9bb9cc07a6c773f324fdee69d75a8427 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sesame", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: scales, BiocManager, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, KernSmooth, pals requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-sesamedata >=1.20.0,<1.21.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sesamedata >=1.24.0,<1.25.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -40,18 +41,17 @@ requirements: - r-reshape2 - r-stringr - r-tibble - - 'r-wheatmap >=0.2.0' + - r-wheatmap >=0.2.0 run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-sesamedata >=1.20.0,<1.21.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sesamedata >=1.24.0,<1.25.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -60,14 +60,17 @@ requirements: - r-reshape2 - r-stringr - r-tibble - - 'r-wheatmap >=0.2.0' + - r-wheatmap >=0.2.0 + +source: + md5: 18b0d7200e2924b57ff218e52943c0d0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'SEnsible Step-wise Analysis of DNA MEthylation BeadChips' - description: 'Tools For analyzing Illumina Infinium DNA methylation arrays. SeSAMe provides utilities to support analyses of multiple generations of Infinium DNA methylation BeadChips, including preprocessing, quality control, visualization and inference. SeSAMe features accurate detection calling, intelligent inference of ethnicity, sex and advanced quality control routines.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sesamedata/meta.yaml b/recipes/bioconductor-sesamedata/meta.yaml index 48d75153c0584..e0e2a9dcd2c6a 100644 --- a/recipes/bioconductor-sesamedata/meta.yaml +++ b/recipes/bioconductor-sesamedata/meta.yaml @@ -1,54 +1,59 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "sesameData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides supporting annotation and test data for SeSAMe package. This includes chip tango addresses, mapping information, performance annotation, and trained predictor for Infinium array data. This package provides user access to essential annotation data for working with many generations of the Infinium DNA methylation array. Current we support human array (HM27, HM450, EPIC), mouse array (MM285) and the HorvathMethylChip40 (Mammal40) array. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Supporting Data for SeSAMe Package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4cd44c4f5307d2775d94f2051b9a7f46 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sesamedata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, sesame, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-readr - r-stringr run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-readr - r-stringr - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 0e78ee4d14094d812a39b12167c8d747 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Supporting Data for SeSAMe Package' - description: 'Provides supporting annotation and test data for SeSAMe package. This includes chip tango addresses, mapping information, performance annotation, and trained predictor for Infinium array data. This package provides user access to essential annotation data for working with many generations of the Infinium DNA methylation array. Current we support human array (HM27, HM450, EPIC), mouse array (MM285) and the HorvathMethylChip40 (Mammal40) array.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sesamedata/post-link.sh b/recipes/bioconductor-sesamedata/post-link.sh index f5cc75f5ec748..19b15bf7146c8 100644 --- a/recipes/bioconductor-sesamedata/post-link.sh +++ b/recipes/bioconductor-sesamedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "sesamedata-1.20.0" +installBiocDataPackage.sh "sesamedata-1.24.0" diff --git a/recipes/bioconductor-setools/meta.yaml b/recipes/bioconductor-setools/meta.yaml index 364be9dc5ca55..b7c30ad770be8 100644 --- a/recipes/bioconductor-setools/meta.yaml +++ b/recipes/bioconductor-setools/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "SEtools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This includes a set of convenience functions for working with the SummarizedExperiment class. Note that plotting functions historically in this package have been moved to the sechm package (see vignette for details). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'SEtools: tools for working with SummarizedExperiment' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4b6f28a6fdf032d51f29793f25729114 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-setools", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, ggplot2 requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-sechm >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sechm >=1.14.0,<1.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-circlize - r-data.table @@ -36,26 +38,29 @@ requirements: - r-openxlsx - r-pheatmap run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-sechm >=1.10.0,<1.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sechm >=1.14.0,<1.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-circlize - r-data.table - r-matrix - r-openxlsx - r-pheatmap + +source: + md5: 0157f338d5325713e2b2d7f299c7a5d4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL - summary: 'SEtools: tools for working with SummarizedExperiment' - description: 'This includes a set of convenience functions for working with the SummarizedExperiment class. Note that plotting functions historically in this package have been moved to the sechm package (see vignette for details).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sevenbridges/meta.yaml b/recipes/bioconductor-sevenbridges/meta.yaml index 66cb3290bcdbe..4cecb64cbb0ad 100644 --- a/recipes/bioconductor-sevenbridges/meta.yaml +++ b/recipes/bioconductor-sevenbridges/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "sevenbridges" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: R client and utilities for Seven Bridges platform API, from Cancer Genomics Cloud to other Seven Bridges supported platforms. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Apache License 2.0 | file LICENSE + license_file: LICENSE + summary: Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1c204add9c56d7518a5362b99111ec18 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sevenbridges", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, readr requirements: host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-curl - r-data.table @@ -34,7 +36,7 @@ requirements: - r-uuid - r-yaml run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-curl - r-data.table @@ -45,13 +47,16 @@ requirements: - r-stringr - r-uuid - r-yaml + +source: + md5: 72f0145f3fcdb5070afe3919368399c2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Apache License 2.0 | file LICENSE' - summary: 'Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R' - description: 'R client and utilities for Seven Bridges platform API, from Cancer Genomics Cloud to other Seven Bridges supported platforms.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sevenc/meta.yaml b/recipes/bioconductor-sevenc/meta.yaml index e56d3a0da93e1..0725195c5abab 100644 --- a/recipes/bioconductor-sevenc/meta.yaml +++ b/recipes/bioconductor-sevenc/meta.yaml @@ -1,59 +1,64 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "sevenC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Chromatin looping is an essential feature of eukaryotic genomes and can bring regulatory sequences, such as enhancers or transcription factor binding sites, in the close physical proximity of regulated target genes. Here, we provide sevenC, an R package that uses protein binding signals from ChIP-seq and sequence motif information to predict chromatin looping events. Cross-linking of proteins that bind close to loop anchors result in ChIP-seq signals at both anchor loci. These signals are used at CTCF motif pairs together with their distance and orientation to each other to predict whether they interact or not. The resulting chromatin loops might be used to associate enhancers or transcription factor binding sites (e.g., ChIP-seq peaks) to regulated target genes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 575914dcdfdff58d10d7e926182801b9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sevenc", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions, covr requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-boot >=1.3-20' - - 'r-data.table >=1.10.4' - - 'r-purrr >=0.2.2' - - 'r-readr >=1.1.0' + - r-boot >=1.3-20 + - r-data.table >=1.10.4 + - r-purrr >=0.2.2 + - r-readr >=1.1.0 run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-boot >=1.3-20' - - 'r-data.table >=1.10.4' - - 'r-purrr >=0.2.2' - - 'r-readr >=1.1.0' + - r-boot >=1.3-20 + - r-data.table >=1.10.4 + - r-purrr >=0.2.2 + - r-readr >=1.1.0 + +source: + md5: 4124d617aff47e59b6673c17d8c93dab + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs' - description: 'Chromatin looping is an essential feature of eukaryotic genomes and can bring regulatory sequences, such as enhancers or transcription factor binding sites, in the close physical proximity of regulated target genes. Here, we provide sevenC, an R package that uses protein binding signals from ChIP-seq and sequence motif information to predict chromatin looping events. Cross-linking of proteins that bind close to loop anchors result in ChIP-seq signals at both anchor loci. These signals are used at CTCF motif pairs together with their distance and orientation to each other to predict whether they interact or not. The resulting chromatin loops might be used to associate enhancers or transcription factor binding sites (e.g., ChIP-seq peaks) to regulated target genes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-seventygenedata/meta.yaml b/recipes/bioconductor-seventygenedata/meta.yaml index 076afa9211ab5..f74d3a182d96b 100644 --- a/recipes/bioconductor-seventygenedata/meta.yaml +++ b/recipes/bioconductor-seventygenedata/meta.yaml @@ -1,37 +1,38 @@ -{% set version = "1.36.1" %} +{% set version = "1.42.0" %} {% set name = "seventyGeneData" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f7c9703c12b845c5c2eb6cf583fb0f02 +about: + description: Gene expression data for the two breast cancer cohorts published by van't Veer and Van de Vijver in 2002. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: ExpressionSets from the van't Veer and Van de Vijver breast cancer studies build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic -# Suggests: Biobase, gdata, limma, breastCancerNKI + run_exports: '{{ pin_subpackage("bioconductor-seventygenedata", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: Biobase, limma, breastCancerNKI, knitr, rmarkdown, readxl, BiocStyle requirements: host: - r-base run: - r-base - curl - - bioconductor-data-packages >=20230706 + - bioconductor-data-packages >=20241103 +source: + md5: 0f1a3ab072300477276d2dc9bc5e16e4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'ExpressionSets from the van''t Veer and Van de Vijver breast cancer studies' - description: 'Gene expression data for the two breast cancer cohorts published by van''t Veer and Van de Vijver in 2002' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-seventygenedata/post-link.sh b/recipes/bioconductor-seventygenedata/post-link.sh index bf1389fdcbf8d..99cd8839b5890 100644 --- a/recipes/bioconductor-seventygenedata/post-link.sh +++ b/recipes/bioconductor-seventygenedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "seventygenedata-1.36.1" +installBiocDataPackage.sh "seventygenedata-1.42.0" diff --git a/recipes/bioconductor-sfedata/build_failure.linux-64.yaml b/recipes/bioconductor-sfedata/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..4ad2f6592cf6f --- /dev/null +++ b/recipes/bioconductor-sfedata/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: bfeb642d36afa3de5571c18a03b77c199ec0c9802ca33c145e701cddda3f9271 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-glue: 1.8.0-r44h2b5f3a1_0 conda-forge + r-httr: 1.4.7-r44hc72bb7e_1 conda-forge + r-jsonlite: 1.8.9-r44h2b5f3a1_0 conda-forge + r-lifecycle: 1.0.4-r44hc72bb7e_1 conda-forge + r-magrittr: 2.0.3-r44hb1dbf0f_3 conda-forge + r-memoise: 2.0.1-r44hc72bb7e_3 conda-forge + r-mime: 0.12-r44hb1dbf0f_3 conda-forge + r-openssl: 2.2.2-r44he8289e2_0 conda-forge + r-pillar: 1.10.0-r44hc72bb7e_0 conda-forge + r-pkgconfig: 2.0.3-r44hc72bb7e_4 conda-forge + r-plogr: 0.2.0-r44hc72bb7e_1006 conda-forge + r-png: 0.1_8-r44h21f035c_2 conda-forge + r-purrr: 1.0.2-r44hdb488b9_1 conda-forge + r-r6: 2.5.1-r44hc72bb7e_3 conda-forge + r-rappdirs: 0.3.3-r44hb1dbf0f_3 conda-forge + r-rlang: 1.1.4-r44ha18555a_1 conda-forge + r-rsqlite: 2.3.9-r44h93ab643_0 conda-forge + r-stringi: 1.8.4-r44h33cde33_3 conda-forge + r-stringr: 1.5.1-r44h785f33e_1 conda-forge + r-sys: 3.4.3-r44h2b5f3a1_0 conda-forge + r-tibble: 3.2.1-r44hdb488b9_3 conda-forge + r-tidyr: 1.3.1-r44h0d4f4ea_1 conda-forge + r-tidyselect: 1.2.1-r44hc72bb7e_1 conda-forge + r-utf8: 1.2.4-r44hb1dbf0f_1 conda-forge + r-vctrs: 0.6.5-r44h0d4f4ea_1 conda-forge + r-withr: 3.0.2-r44hc72bb7e_0 conda-forge + r-yaml: 2.3.10-r44hdb488b9_0 conda-forge + readline: 8.2-h8228510_1 conda-forge + sed: 4.8-he412f7d_0 conda-forge + setuptools: 75.6.0-pyhff2d567_1 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tktable: 2.10-h8bc8fbc_6 conda-forge + toml: 0.10.2-pyhd8ed1ab_1 conda-forge + tomlkit: 0.13.2-pyha770c72_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + xmltodict: 0.14.2-pyhd8ed1ab_1 conda-forge + xorg-libice: 1.1.2-hb9d3cd8_0 conda-forge + xorg-libsm: 1.2.5-he73a12e_0 conda-forge + xorg-libx11: 1.8.10-h4f16b4b_1 conda-forge + xorg-libxau: 1.0.12-hb9d3cd8_0 conda-forge + xorg-libxdmcp: 1.1.5-hb9d3cd8_0 conda-forge + xorg-libxext: 1.3.6-hb9d3cd8_0 conda-forge + xorg-libxrender: 0.9.12-hb9d3cd8_0 conda-forge + xorg-libxt: 1.3.1-hb9d3cd8_0 conda-forge + yaml: 0.2.5-h7f98852_2 conda-forge + yq: 3.4.3-pyhd8ed1ab_1 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: SFEData_1.8.0_0e1005c4fc.tar.gz + Downloading https://bioconductor.org/packages/3.20/data/experiment/src/contrib/SFEData_1.8.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.135770 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioconductor.org/packages/3.20/bioc/src/contrib/Archive/SFEData/SFEData_1.8.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.127597 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://bioarchive.galaxyproject.org/SFEData_1.8.0.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.702957 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Downloading https://depot.galaxyproject.org/software/bioconductor-sfedata/bioconductor-sfedata_1.8.0_src_all.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.661702 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download https://depot.galaxyproject.org/software/bioconductor-sfedata/bioconductor-sfedata_1.8.0_src_all.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-sfedata/meta.yaml b/recipes/bioconductor-sfedata/meta.yaml index 7b97631753e5d..ba303dd073476 100644 --- a/recipes/bioconductor-sfedata/meta.yaml +++ b/recipes/bioconductor-sfedata/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "SFEData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7f3376870c972cba309b26d52d24fcbb +about: + description: Example spatial transcriptomics datasets with Simple Feature annotations as SpatialFeatureExperiment objects. Technologies include Visium, slide-seq, Nanostring CoxMX, Vizgen MERFISH, and 10X Xenium. Tissues include mouse skeletal muscle, human melanoma metastasis, human lung, breast cancer, and mouse liver. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Example SpatialFeatureExperiment datasets build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sfedata", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, SpatialFeatureExperiment, testthat (>= 3.0.0) +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: BiocStyle, knitr, rmarkdown, SeuratObject, SpatialFeatureExperiment, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0e1005c4fc1b0ca2bef593cffedb87d3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Example SpatialFeatureExperiment datasets' - description: 'Example spatial transcriptomics datasets with Simple Feature annotations as SpatialFeatureExperiment objects. Technologies include Visium, slide-seq, Nanostring CoxMX, Vizgen MERFISH, and 10X Xenium. Tissues include mouse skeletal muscle, human melanoma metastasis, human lung, breast cancer, and mouse liver.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sfedata/post-link.sh b/recipes/bioconductor-sfedata/post-link.sh index f690a3a41ff4f..7e563e5b5791c 100644 --- a/recipes/bioconductor-sfedata/post-link.sh +++ b/recipes/bioconductor-sfedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "sfedata-1.4.0" +installBiocDataPackage.sh "sfedata-1.8.0" diff --git a/recipes/bioconductor-sgcp/meta.yaml b/recipes/bioconductor-sgcp/meta.yaml index eaaca7d8f94e0..fd93b38924672 100644 --- a/recipes/bioconductor-sgcp/meta.yaml +++ b/recipes/bioconductor-sgcp/meta.yaml @@ -1,35 +1,38 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "SGCP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SGC is a semi-supervised pipeline for gene clustering in gene co-expression networks. SGC consists of multiple novel steps that enable the computation of highly enriched modules in an unsupervised manner. But unlike all existing frameworks, it further incorporates a novel step that leverages Gene Ontology information in a semi-supervised clustering method that further improves the quality of the computed modules. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expression networks' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46986c7dd18ef80a29c389500ed5023b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sgcp", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, BiocManager + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, BiocManager, devtools, BiocStyle requirements: + host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-caret - r-desctools @@ -43,15 +46,16 @@ requirements: - r-reshape2 - r-rspectra - r-xtable + run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-gostats >=2.68.0,<2.69.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-gostats >=2.72.0,<2.73.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-caret - r-desctools @@ -65,13 +69,16 @@ requirements: - r-reshape2 - r-rspectra - r-xtable + +source: + md5: bc891da768259608cd73b693089ffa39 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expression networks' - description: 'SGC is a semi-supervised pipeline for gene clustering in gene co-expression networks. SGC consists of multiple novel steps that enable the computation of highly enriched modules in an unsupervised manner. But unlike all existing frameworks, it further incorporates a novel step that leverages Gene Ontology information in a semi-supervised clustering method that further improves the quality of the computed modules.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sgseq/meta.yaml b/recipes/bioconductor-sgseq/meta.yaml index a88e1160be342..3809b5ce0ec65 100644 --- a/recipes/bioconductor-sgseq/meta.yaml +++ b/recipes/bioconductor-sgseq/meta.yaml @@ -1,71 +1,77 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "SGSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SGSeq is a software package for analyzing splice events from RNA-seq data. Input data are RNA-seq reads mapped to a reference genome in BAM format. Genes are represented as a splice graph, which can be obtained from existing annotation or predicted from the mapped sequence reads. Splice events are identified from the graph and are quantified locally using structurally compatible reads at the start or end of each splice variant. The software includes functions for splice event prediction, quantification, visualization and interpretation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Splice event prediction and quantification from RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 874492401a4a17bf0836f9fa011f459a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sgseq", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:sgseq + parent_recipe: + name: bioconductor-sgseq + path: recipes/bioconductor-sgseq + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-igraph - r-runit run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-igraph - r-runit + +source: + md5: 516203d55f790ca154f4fe4b69591a43 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Splice event prediction and quantification from RNA-seq data' - description: 'SGSeq is a software package for analyzing splice events from RNA-seq data. Input data are RNA-seq reads mapped to a reference genome in BAM format. Genes are represented as a splice graph, which can be obtained from existing annotation or predicted from the mapped sequence reads. Splice events are identified from the graph and are quantified locally using structurally compatible reads at the start or end of each splice variant. The software includes functions for splice event prediction, quantification, visualization and interpretation.' -extra: - identifiers: - - biotools:sgseq - parent_recipe: - name: bioconductor-sgseq - path: recipes/bioconductor-sgseq - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sharedobject/meta.yaml b/recipes/bioconductor-sharedobject/meta.yaml index 849fb0abf9871..497c3b76e7e1e 100644 --- a/recipes/bioconductor-sharedobject/meta.yaml +++ b/recipes/bioconductor-sharedobject/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "SharedObject" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is developed for facilitating parallel computing in R. It is capable to create an R object in the shared memory space and share the data across multiple R processes. It avoids the overhead of memory dulplication and data transfer, which make sharing big data object across many clusters possible. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Sharing R objects across multiple R processes without memory duplication -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7c47265b6a5f61385088d6146c7e4879 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sharedobject", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, parallel, knitr, rmarkdown, BiocStyle # SystemRequirements: GNU make, C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-bh - r-rcpp - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-bh - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 72c88a08e6e3bed0f4b4c1fdcae274ec + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Sharing R objects across multiple R processes without memory duplication' - description: 'This package is developed for facilitating parallel computing in R. It is capable to create an R object in the shared memory space and share the data across multiple R processes. It avoids the overhead of memory dulplication and data transfer, which make sharing big data object across many clusters possible.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-shdz.db/meta.yaml b/recipes/bioconductor-shdz.db/meta.yaml index b7927519c0bdf..cdcd79385f21c 100644 --- a/recipes/bioconductor-shdz.db/meta.yaml +++ b/recipes/bioconductor-shdz.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "SHDZ.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 63c4439a272a5cd0c4746e9e53a7bdc7 +about: + description: SHDZ http://genome-www5.stanford.edu/ Annotation Data (SHDZ) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: SHDZ http://genome-www5.stanford.edu/ Annotation Data (SHDZ) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-shdz.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 63c4439a272a5cd0c4746e9e53a7bdc7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'SHDZ http://genome-www5.stanford.edu/ Annotation Data (SHDZ)' - description: 'SHDZ http://genome-www5.stanford.edu/ Annotation Data (SHDZ) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-shiny.gosling/build.sh b/recipes/bioconductor-shiny.gosling/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-shiny.gosling/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-shiny.gosling/meta.yaml b/recipes/bioconductor-shiny.gosling/meta.yaml new file mode 100644 index 0000000000000..2399fd3f89818 --- /dev/null +++ b/recipes/bioconductor-shiny.gosling/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.2.0" %} +{% set name = "shiny.gosling" %} +{% set bioc = "3.20" %} + +about: + description: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization. http://gosling-lang.org/. This R package is based on gosling.js. It uses R functions to create gosling plots that could be embedded onto R Shiny apps. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization for R and Shiny + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-shiny.gosling", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: config, covr, knitr, lintr, mockery (>= 0.4.3), rcmdcheck, rmarkdown, sessioninfo, spelling, testthat (>= 3.0.0), GenomicRanges, VariantAnnotation, StructuralVariantAnnotation, biovizBase, ggbio +requirements: + host: + - r-base + - r-digest + - r-fs + - r-htmltools + - r-jsonlite + - r-rjson + - r-rlang + - r-shiny + - r-shiny.react + run: + - r-base + - r-digest + - r-fs + - r-htmltools + - r-jsonlite + - r-rjson + - r-rlang + - r-shiny + - r-shiny.react + +source: + md5: daf1969e34ee8ff6c8f5e2bd65b3f780 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-shinyepico/meta.yaml b/recipes/bioconductor-shinyepico/meta.yaml index 352d8232c1e6f..622c7020684fe 100644 --- a/recipes/bioconductor-shinyepico/meta.yaml +++ b/recipes/bioconductor-shinyepico/meta.yaml @@ -1,85 +1,92 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "shinyepico" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: ShinyÉPICo is a graphical pipeline to analyze Illumina DNA methylation arrays (450k or EPIC). It allows to calculate differentially methylated positions and differentially methylated regions in a user-friendly interface. Moreover, it includes several options to export the results and obtain files to perform downstream analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + file LICENSE + license_file: LICENSE + summary: ShinyÉPICo -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 044010b7c6b7570adb28be7374473f82 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-shinyepico", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr (>= 1.30.0), mCSEA (>= 1.10.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICmanifest, testthat, minfiData, BiocStyle requirements: + host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - - 'r-data.table >=1.13.0' - - 'r-doparallel >=1.0.0' - - 'r-dplyr >=1.0.9' - - 'r-dt >=0.15.0' - - 'r-foreach >=1.5.0' - - 'r-ggplot2 >=3.3.0' - - 'r-gplots >=3.0.0' - - 'r-heatmaply >=1.1.0' - - 'r-plotly >=4.9.2' - - 'r-reshape2 >=1.4.0' - - 'r-rlang >=1.0.2' - - 'r-rmarkdown >=2.3.0' - - 'r-shiny >=1.5.0' - - 'r-shinycssloaders >=0.3.0' - - 'r-shinyjs >=1.1.0' - - 'r-shinythemes >=1.1.0' - - 'r-shinywidgets >=0.5.0' - - 'r-statmod >=1.4.0' - - 'r-tidyr >=1.2.0' - - 'r-zip >=2.1.0' + - r-data.table >=1.13.0 + - r-doparallel >=1.0.0 + - r-dplyr >=1.0.9 + - r-dt >=0.15.0 + - r-foreach >=1.5.0 + - r-ggplot2 >=3.3.0 + - r-gplots >=3.0.0 + - r-heatmaply >=1.1.0 + - r-plotly >=4.9.2 + - r-reshape2 >=1.4.0 + - r-rlang >=1.0.2 + - r-rmarkdown >=2.3.0 + - r-shiny >=1.5.0 + - r-shinycssloaders >=0.3.0 + - r-shinyjs >=1.1.0 + - r-shinythemes >=1.1.0 + - r-shinywidgets >=0.5.0 + - r-statmod >=1.4.0 + - r-tidyr >=1.2.0 + - r-zip >=2.1.0 + run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - - 'r-data.table >=1.13.0' - - 'r-doparallel >=1.0.0' - - 'r-dplyr >=1.0.9' - - 'r-dt >=0.15.0' - - 'r-foreach >=1.5.0' - - 'r-ggplot2 >=3.3.0' - - 'r-gplots >=3.0.0' - - 'r-heatmaply >=1.1.0' - - 'r-plotly >=4.9.2' - - 'r-reshape2 >=1.4.0' - - 'r-rlang >=1.0.2' - - 'r-rmarkdown >=2.3.0' - - 'r-shiny >=1.5.0' - - 'r-shinycssloaders >=0.3.0' - - 'r-shinyjs >=1.1.0' - - 'r-shinythemes >=1.1.0' - - 'r-shinywidgets >=0.5.0' - - 'r-statmod >=1.4.0' - - 'r-tidyr >=1.2.0' - - 'r-zip >=2.1.0' + - r-data.table >=1.13.0 + - r-doparallel >=1.0.0 + - r-dplyr >=1.0.9 + - r-dt >=0.15.0 + - r-foreach >=1.5.0 + - r-ggplot2 >=3.3.0 + - r-gplots >=3.0.0 + - r-heatmaply >=1.1.0 + - r-plotly >=4.9.2 + - r-reshape2 >=1.4.0 + - r-rlang >=1.0.2 + - r-rmarkdown >=2.3.0 + - r-shiny >=1.5.0 + - r-shinycssloaders >=0.3.0 + - r-shinyjs >=1.1.0 + - r-shinythemes >=1.1.0 + - r-shinywidgets >=0.5.0 + - r-statmod >=1.4.0 + - r-tidyr >=1.2.0 + - r-zip >=2.1.0 + +source: + md5: 134dc9e08350da1492af99fb7349567d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'AGPL-3 + file LICENSE' - summary: ShinyÉPICo - description: 'ShinyÉPICo is a graphical pipeline to analyze Illumina DNA methylation arrays (450k or EPIC). It allows to calculate differentially methylated positions and differentially methylated regions in a user-friendly interface. Moreover, it includes several options to export the results and obtain files to perform downstream analysis.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-shinymethyl/meta.yaml b/recipes/bioconductor-shinymethyl/meta.yaml index 09cdddcbcd8cc..f0c58f63c6140 100644 --- a/recipes/bioconductor-shinymethyl/meta.yaml +++ b/recipes/bioconductor-shinymethyl/meta.yaml @@ -1,57 +1,63 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "shinyMethyl" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Interactive visualization for Illumina methylation arrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 21f2fe819a72a5c4db3694a22dcda934 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-shinymethyl", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:shinymethyl + parent_recipe: + name: bioconductor-shinymethyl + path: recipes/bioconductor-shinymethyl + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: shinyMethylData, minfiData, BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - r-htmltools - r-rcolorbrewer - r-shiny run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-minfi >=1.52.0,<1.53.0 - r-base - r-htmltools - r-rcolorbrewer - r-shiny + +source: + md5: cf500be83d4657e46813a8d9102e3a26 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Interactive visualization for Illumina methylation arrays' - description: 'Interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported.' -extra: - identifiers: - - biotools:shinymethyl - parent_recipe: - name: bioconductor-shinymethyl - path: recipes/bioconductor-shinymethyl - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-shinymethyldata/meta.yaml b/recipes/bioconductor-shinymethyldata/meta.yaml index e41c94e7ad9f3..3a50733d7ccce 100644 --- a/recipes/bioconductor-shinymethyldata/meta.yaml +++ b/recipes/bioconductor-shinymethyldata/meta.yaml @@ -1,37 +1,37 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "shinyMethylData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46f32db849aaa1467d09b0a371769374 +about: + description: Extracted data from 369 TCGA Head and Neck Cancer DNA methylation samples. The extracted data serve as an example dataset for the package shinyMethyl. Original samples are from 450k methylation arrays, and were obtained from The Cancer Genome Atlas (TCGA). 310 samples are from tumor, 50 are matched normals and 9 are technical replicates of a control cell line. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Example dataset of input data for shinyMethyl build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-shinymethyldata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e27eb788611027ac6995ce44df9076f3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Example dataset of input data for shinyMethyl' - description: 'Extracted data from 369 TCGA Head and Neck Cancer DNA methylation samples. The extracted data serve as an example dataset for the package shinyMethyl. Original samples are from 450k methylation arrays, and were obtained from The Cancer Genome Atlas (TCGA). 310 samples are from tumor, 50 are matched normals and 9 are technical replicates of a control cell line.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-shinymethyldata/post-link.sh b/recipes/bioconductor-shinymethyldata/post-link.sh index 3d514dc1f7ffc..6c2dcb5709745 100644 --- a/recipes/bioconductor-shinymethyldata/post-link.sh +++ b/recipes/bioconductor-shinymethyldata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "shinymethyldata-1.22.0" +installBiocDataPackage.sh "shinymethyldata-1.26.0" diff --git a/recipes/bioconductor-shortread/meta.yaml b/recipes/bioconductor-shortread/meta.yaml index 139aace635d19..31781ce79e586 100644 --- a/recipes/bioconductor-shortread/meta.yaml +++ b/recipes/bioconductor-shortread/meta.yaml @@ -1,83 +1,93 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "ShortRead" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: FASTQ input and manipulation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 480786b1db8f8138a7a4e8c36f9bdfc4 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-shortread", max_pin="x.x") }}' -# Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:shortread + parent_recipe: + name: bioconductor-shortread + path: recipes/bioconductor-shortread + version: 1.38.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi, knitr requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-hwriter - r-lattice - r-latticeextra - libblas - liblapack + - zlib + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-hwriter - r-lattice - r-latticeextra - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 6550882a18baeb952edc082bd4aef6ec + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'FASTQ input and manipulation' - description: 'This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:shortread - parent_recipe: - name: bioconductor-shortread - path: recipes/bioconductor-shortread - version: 1.38.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-siamcat/meta.yaml b/recipes/bioconductor-siamcat/meta.yaml index d94c3be14962d..8492f1b84ebcc 100644 --- a/recipes/bioconductor-siamcat/meta.yaml +++ b/recipes/bioconductor-siamcat/meta.yaml @@ -1,28 +1,31 @@ -{% set version = "2.6.0" %} +{% set version = "2.10.0" %} {% set name = "SIAMCAT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Pipeline for Statistical Inference of Associations between Microbial Communities And host phenoTypes (SIAMCAT). A primary goal of analyzing microbiome data is to determine changes in community composition that are associated with environmental factors. In particular, linking human microbiome composition to host phenotypes such as diseases has become an area of intense research. For this, robust statistical modeling and biomarker extraction toolkits are crucially needed. SIAMCAT provides a full pipeline supporting data preprocessing, statistical association testing, statistical modeling (LASSO logistic regression) including tools for evaluation and interpretation of these models (such as cross validation, parameter selection, ROC analysis and diagnostic model plots). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Statistical Inference of Associations between Microbial Communities And host phenoTypes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 36938473e8b2bd9b269fae69ec312e8d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-siamcat", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr requirements: + host: - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - bioconductor-phyloseq >=1.50.0,<1.51.0 - r-base - r-beanplot - r-corrplot @@ -44,8 +47,9 @@ requirements: - r-rcolorbrewer - r-scales - r-stringr + run: - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' + - bioconductor-phyloseq >=1.50.0,<1.51.0 - r-base - r-beanplot - r-corrplot @@ -67,13 +71,16 @@ requirements: - r-rcolorbrewer - r-scales - r-stringr + +source: + md5: e2c0cfba5a48d7811ad976655f252e49 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Statistical Inference of Associations between Microbial Communities And host phenoTypes' - description: 'Pipeline for Statistical Inference of Associations between Microbial Communities And host phenoTypes (SIAMCAT). A primary goal of analyzing microbiome data is to determine changes in community composition that are associated with environmental factors. In particular, linking human microbiome composition to host phenotypes such as diseases has become an area of intense research. For this, robust statistical modeling and biomarker extraction toolkits are crucially needed. SIAMCAT provides a full pipeline supporting data preprocessing, statistical association testing, statistical modeling (LASSO logistic regression) including tools for evaluation and interpretation of these models (such as cross validation, parameter selection, ROC analysis and diagnostic model plots).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sictools/build_failure.linux-64.yaml b/recipes/bioconductor-sictools/build_failure.linux-64.yaml index c447c0a1d2387..f2c444ef54e0f 100644 --- a/recipes/bioconductor-sictools/build_failure.linux-64.yaml +++ b/recipes/bioconductor-sictools/build_failure.linux-64.yaml @@ -1,37 +1,104 @@ -recipe_sha: d0341aa6f0be4917a820c67382d360ac5f5e76815434d7cecb1769b617051f44 # The commit at which this recipe failed to build. +recipe_sha: 36ddd119734177ae07ec8ee8a74f99e7d99f608f847b0c8a73fb44dce4a59a4b # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -reason: |- - bgzf.h:33:10: fatal error: zlib.h: No such file or directory -category: |- - compiler error log: |- - 13:35:37 BIOCONDA INFO (OUT) In file included from bgzf.c:32: - 13:35:37 BIOCONDA INFO (OUT) bgzf.h:33:10: fatal error: zlib.h: No such file or directory - 13:35:37 BIOCONDA INFO (OUT) 33 | #include - 13:35:37 BIOCONDA INFO (OUT) | ^~~~~~~~ - 13:35:37 BIOCONDA INFO (OUT) compilation terminated. - 13:35:37 BIOCONDA INFO (OUT) make[2]: *** [Makefile:56: bgzf.o] Error 1 - 13:35:37 BIOCONDA INFO (OUT) make[2]: Leaving directory '$SRC_DIR/src' - 13:35:37 BIOCONDA INFO (OUT) make[1]: *** [Makefile:27: lib-recur] Error 1 - 13:35:37 BIOCONDA INFO (OUT) make[1]: Leaving directory '$SRC_DIR/src' - 13:35:37 BIOCONDA INFO (OUT) make: *** [Makefile:27: all-recur] Error 1 - 13:35:37 BIOCONDA INFO (OUT) ERROR: compilation failed for package ‘SICtools’ - 13:35:37 BIOCONDA INFO (OUT) * removing ‘/opt/conda/conda-bld/bioconductor-sictools_1702301527486/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/SICtools’ - 13:35:38 BIOCONDA INFO (OUT) Traceback (most recent call last): - 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/bin/conda-mambabuild", line 10, in - 13:35:38 BIOCONDA INFO (OUT) sys.exit(main()) - 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - 13:35:38 BIOCONDA INFO (OUT) call_conda_build(action, config) - 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - 13:35:38 BIOCONDA INFO (OUT) result = api.build( - 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - 13:35:38 BIOCONDA INFO (OUT) return build_tree( - 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - 13:35:38 BIOCONDA INFO (OUT) packages_from_this = build(metadata, stats, - 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - 13:35:38 BIOCONDA INFO (OUT) utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - 13:35:38 BIOCONDA INFO (OUT) return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - 13:35:38 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - 13:35:38 BIOCONDA INFO (OUT) raise subprocess.CalledProcessError(proc.returncode, _args) - 13:35:38 BIOCONDA INFO (OUT) subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-sictools_1702301527486/work/conda_build.sh']' returned non-zero exit status 1. + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/conda/conda-bld/bioconductor-sictools_1735948094404/work + export PREFIX=/opt/conda/conda-bld/bioconductor-sictools_1735948094404/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-sictools_1735948094404/_build_env + export SRC_DIR=/opt/conda/conda-bld/bioconductor-sictools_1735948094404/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-sictools-1.36.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-sictools-1.36.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-sictools_1735948094404/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library + * installing *source* package SICtools ... + ** package SICtools successfully unpacked and MD5 sums checked + ** using staged installation + ** libs + Makefile:24: warning: overriding recipe for target '.c.o' + /opt/conda/conda-bld/bioconductor-sictools_1735948094404/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/etc/Makeconf:197: warning: ignoring old recipe for target '.c.o' + make[1]: Entering directory '$SRC_DIR/src' + make[2]: Entering directory '$SRC_DIR/src' + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o + In file included from bgzf.c:32: + bgzf.h:33:10: fatal error: zlib.h: No such file or directory + 33 | #include + | ^~~~~~~~ + compilation terminated. + make[2]: *** [Makefile:56: bgzf.o] Error 1 + make[2]: Leaving directory '$SRC_DIR/src' + make[1]: *** [Makefile:27: lib-recur] Error 1 + make[1]: Leaving directory '$SRC_DIR/src' + make: *** [Makefile:27: all-recur] Error 1 + ERROR: compilation failed for package SICtools + * removing /opt/conda/conda-bld/bioconductor-sictools_1735948094404/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/SICtools + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-sictools_1735948094404/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-sictools_1735948094404/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-sictools/meta.yaml b/recipes/bioconductor-sictools/meta.yaml index 12a5dc2cb5ca8..93018890e8734 100644 --- a/recipes/bioconductor-sictools/meta.yaml +++ b/recipes/bioconductor-sictools/meta.yaml @@ -1,57 +1,63 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "SICtools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is to find SNV/Indel differences between two bam files with near relationship in a way of pairwise comparison thourgh each base position across the genome region of interest. The difference is inferred by fisher test and euclidean distance, the input of which is the base count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Find SNV/Indel differences between two bam files with near relationship -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1df54634cb8bc00e60963b0ca10886d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sictools", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, RUnit, BiocGenerics requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - - 'r-doparallel >=1.0.8' - - 'r-matrixstats >=0.10.0' - - 'r-plyr >=1.8.3' - - 'r-stringr >=0.6.2' + - r-doparallel >=1.0.8 + - r-matrixstats >=0.10.0 + - r-plyr >=1.8.3 + - r-stringr >=0.6.2 - libblas - liblapack + - zlib run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - - 'r-doparallel >=1.0.8' - - 'r-matrixstats >=0.10.0' - - 'r-plyr >=1.8.3' - - 'r-stringr >=0.6.2' - build: - - {{ compiler('c') }} - - make + - r-doparallel >=1.0.8 + - r-matrixstats >=0.10.0 + - r-plyr >=1.8.3 + - r-stringr >=0.6.2 + +source: + md5: 211832c3db57789ff2e090a1c344926c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Find SNV/Indel differences between two bam files with near relationship' - description: 'This package is to find SNV/Indel differences between two bam files with near relationship in a way of pairwise comparison thourgh each base position across the genome region of interest. The difference is inferred by fisher test and euclidean distance, the input of which is the base count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sift.hsapiens.dbsnp132/meta.yaml b/recipes/bioconductor-sift.hsapiens.dbsnp132/meta.yaml index 63f65568f82da..0bed768cbb09e 100644 --- a/recipes/bioconductor-sift.hsapiens.dbsnp132/meta.yaml +++ b/recipes/bioconductor-sift.hsapiens.dbsnp132/meta.yaml @@ -1,43 +1,43 @@ {% set version = "1.0.2" %} {% set name = "SIFT.Hsapiens.dbSNP132" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c374f0bf4c99357cfe99e0b192c00d75 +about: + description: Database of SIFT predictions for Homo sapiens dbSNP build 132 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: SIFT Predictions for Homo sapiens dbSNP build 132 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sift.hsapiens.dbsnp132", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - - 'r-rsqlite >=0.11.0' + - r-rsqlite >=0.11.0 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - - 'r-rsqlite >=0.11.0' + - r-rsqlite >=0.11.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c374f0bf4c99357cfe99e0b192c00d75 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'SIFT Predictions for Homo sapiens dbSNP build 132' - description: 'Database of SIFT predictions for Homo sapiens dbSNP build 132' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sift.hsapiens.dbsnp137/meta.yaml b/recipes/bioconductor-sift.hsapiens.dbsnp137/meta.yaml index f0f7108912e36..b72d581c7c905 100644 --- a/recipes/bioconductor-sift.hsapiens.dbsnp137/meta.yaml +++ b/recipes/bioconductor-sift.hsapiens.dbsnp137/meta.yaml @@ -1,43 +1,43 @@ {% set version = "1.0.0" %} {% set name = "SIFT.Hsapiens.dbSNP137" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3c3e73f826399af5ff368d1aab12cfd1 +about: + description: Database of PROVEAN/SIFT predictions for Homo sapiens dbSNP build 137 + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: PROVEAN/SIFT Predictions for Homo sapiens dbSNP build 137 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sift.hsapiens.dbsnp137", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - - 'r-rsqlite >=0.11.0' + - r-rsqlite >=0.11.0 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - - 'r-rsqlite >=0.11.0' + - r-rsqlite >=0.11.0 - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3c3e73f826399af5ff368d1aab12cfd1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'PROVEAN/SIFT Predictions for Homo sapiens dbSNP build 137' - description: 'Database of PROVEAN/SIFT predictions for Homo sapiens dbSNP build 137' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sigcheck/meta.yaml b/recipes/bioconductor-sigcheck/meta.yaml index d0bf27e007237..faa217ef6d835 100644 --- a/recipes/bioconductor-sigcheck/meta.yaml +++ b/recipes/bioconductor-sigcheck/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "2.34.0" %} +{% set version = "2.38.0" %} {% set name = "SigCheck" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: While gene signatures are frequently used to predict phenotypes (e.g. predict prognosis of cancer patients), it it not always clear how optimal or meaningful they are (cf David Venet, Jacques E. Dumont, and Vincent Detours' paper "Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome"). Based on suggestions in that paper, SigCheck accepts a data set (as an ExpressionSet) and a gene signature, and compares its performance on survival and/or classification tasks against a) random gene signatures of the same length; b) known, related and unrelated gene signatures; and c) permuted data and/or metadata. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0c956bbf06058a0a494f887fbdf6549f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sigcheck", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, breastCancerNKI, qusage requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-mlinterfaces >=1.82.0,<1.83.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-mlinterfaces >=1.86.0,<1.87.0 - r-base - r-e1071 - r-survival run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-mlinterfaces >=1.82.0,<1.83.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-mlinterfaces >=1.86.0,<1.87.0 - r-base - r-e1071 - r-survival + +source: + md5: bd93e43ae20c57f05c62df1361f7f914 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Check a gene signature''s prognostic performance against random signatures, known signatures, and permuted data/metadata' - description: 'While gene signatures are frequently used to predict phenotypes (e.g. predict prognosis of cancer patients), it it not always clear how optimal or meaningful they are (cf David Venet, Jacques E. Dumont, and Vincent Detours'' paper "Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome"). Based on suggestions in that paper, SigCheck accepts a data set (as an ExpressionSet) and a gene signature, and compares its performance on survival and/or classification tasks against a) random gene signatures of the same length; b) known, related and unrelated gene signatures; and c) permuted data and/or metadata.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sigfeature/meta.yaml b/recipes/bioconductor-sigfeature/meta.yaml index 9c09d518d848e..85af7e8ab6008 100644 --- a/recipes/bioconductor-sigfeature/meta.yaml +++ b/recipes/bioconductor-sigfeature/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "sigFeature" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a novel feature selection algorithm for binary classification using support vector machine recursive feature elimination SVM-RFE and t-statistic. In this feature selection process, the selected features are differentially significant between the two classes and also they are good classifier with higher degree of classification accuracy. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'sigFeature: Significant feature selection using SVM-RFE & t-statistic' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96249637034c39dc1924cd78c1a0ba58 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sigfeature", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocviews >=1.70.0,<1.71.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocviews >=1.74.0,<1.75.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-e1071 - r-matrix @@ -34,9 +36,9 @@ requirements: - r-rcolorbrewer - r-sparsem run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocviews >=1.70.0,<1.71.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocviews >=1.74.0,<1.75.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-e1071 - r-matrix @@ -45,13 +47,16 @@ requirements: - r-pheatmap - r-rcolorbrewer - r-sparsem + +source: + md5: 44db06bf580ea2d3a41785a52c5cf4e6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'sigFeature: Significant feature selection using SVM-RFE & t-statistic' - description: 'This package provides a novel feature selection algorithm for binary classification using support vector machine recursive feature elimination SVM-RFE and t-statistic. In this feature selection process, the selected features are differentially significant between the two classes and also they are good classifier with higher degree of classification accuracy.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sigfuge/meta.yaml b/recipes/bioconductor-sigfuge/meta.yaml index b5a313692d97c..92dc2d9a8cee9 100644 --- a/recipes/bioconductor-sigfuge/meta.yaml +++ b/recipes/bioconductor-sigfuge/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "SigFuge" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Algorithm for testing significance of clustering in RNA-seq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: SigFuge -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cb03ecb39c2df4b4f5e1b49f8ba5d594 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sigfuge", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:sigfuge + - doi:10.1093/nar/gku521 + parent_recipe: + name: bioconductor-sigfuge + path: recipes/bioconductor-sigfuge + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: org.Hs.eg.db, prebsdata, Rsamtools (>= 1.17.0), TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-ggplot2 - r-matlab - r-reshape - r-sigclust run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - r-ggplot2 - r-matlab - r-reshape - r-sigclust + +source: + md5: d721b007563cff93176dd80bf87f79b3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: SigFuge - description: 'Algorithm for testing significance of clustering in RNA-seq data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:sigfuge - - doi:10.1093/nar/gku521 - parent_recipe: - name: bioconductor-sigfuge - path: recipes/bioconductor-sigfuge - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-siggenes/meta.yaml b/recipes/bioconductor-siggenes/meta.yaml index 7b70075ae924b..aa752e2cf6cae 100644 --- a/recipes/bioconductor-siggenes/meta.yaml +++ b/recipes/bioconductor-siggenes/meta.yaml @@ -1,45 +1,22 @@ -{% set version = "1.76.0" %} +{% set version = "1.80.0" %} {% set name = "siggenes" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Multiple Testing using SAM and Efron's Empirical Bayes Approaches -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ae9899f2a3587a423169a27502868709 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-siggenes", max_pin="x.x") }}' - noarch: generic -# Suggests: affy, annotate, genefilter, KernSmooth -requirements: - host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - r-base - - 'r-scrime >=1.2.5' - run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - r-base - - 'r-scrime >=1.2.5' -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'Multiple Testing using SAM and Efron''s Empirical Bayes Approaches' - description: 'Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + extra: identifiers: - biotools:siggenes @@ -49,3 +26,32 @@ extra: path: recipes/bioconductor-siggenes version: 1.54.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: affy, annotate, genefilter, KernSmooth +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - r-base + - r-scrime >=1.2.5 + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - r-base + - r-scrime >=1.2.5 + +source: + md5: 9273fff292c699d7045af85d7b064917 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-sights/meta.yaml b/recipes/bioconductor-sights/meta.yaml index 6e11b18225760..da501c5a53e39 100644 --- a/recipes/bioconductor-sights/meta.yaml +++ b/recipes/bioconductor-sights/meta.yaml @@ -1,49 +1,22 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "sights" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SIGHTS is a suite of normalization methods, statistical tests, and diagnostic graphical tools for high throughput screening (HTS) assays. HTS assays use microtitre plates to screen large libraries of compounds for their biological, chemical, or biochemical activity. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 | file LICENSE + license_file: LICENSE + summary: Statistics and dIagnostic Graphs for HTS -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 566e869c884c7b12f1a42a9dbaeec05a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sights", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx -requirements: - host: - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - r-base - - 'r-ggplot2 >=2.0' - - 'r-lattice >=0.2' - - 'r-mass >=7.3' - - 'r-reshape2 >=1.4' - run: - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - r-base - - 'r-ggplot2 >=2.0' - - 'r-lattice >=0.2' - - 'r-mass >=7.3' - - 'r-reshape2 >=1.4' -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 | file LICENSE' - summary: 'Statistics and dIagnostic Graphs for HTS' - description: 'SIGHTS is a suite of normalization methods, statistical tests, and diagnostic graphical tools for high throughput screening (HTS) assays. HTS assays use microtitre plates to screen large libraries of compounds for their biological, chemical, or biochemical activity.' - license_file: LICENSE + extra: identifiers: - biotools:sights @@ -53,3 +26,36 @@ extra: path: recipes/bioconductor-sights version: 1.6.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx +requirements: + host: + - bioconductor-qvalue >=2.38.0,<2.39.0 + - r-base + - r-ggplot2 >=2.0 + - r-lattice >=0.2 + - r-mass >=7.3 + - r-reshape2 >=1.4 + run: + - bioconductor-qvalue >=2.38.0,<2.39.0 + - r-base + - r-ggplot2 >=2.0 + - r-lattice >=0.2 + - r-mass >=7.3 + - r-reshape2 >=1.4 + +source: + md5: fcb27503e3f774c56e849c62da44697f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-signaturesearch/build_failure.osx-64.yaml b/recipes/bioconductor-signaturesearch/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..39453b6331736 --- /dev/null +++ b/recipes/bioconductor-signaturesearch/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: e8eb0f430bfcde6822a2f8f2b50d6f43358adebd6daafbf4df87927e3cf47040 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-genomeinfodbdata [1.2.1|1.2.2] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-genomeinfodbdata [1.2.10|1.2.11] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.3|1.2.4] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.6|1.2.7] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-genomeinfodbdata 1.2.9 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-ucsc.utils >=1.2.0,<1.3.0 is not installable because it requires + r-base >=4.4,<4.5.0a0 , which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("clang==4.0.1=1"), MatchSpec("4.0.1==hcfea43d_1")} + Encountered problems while solving: + - nothing provides compiler-rt 4.0.1 hcfea43d_1 needed by clang-4.0.1-1 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-genomeinfodbdata >=1.2.0,<1.3.0 is installable with the potential options + bioconductor-genomeinfodbdata [1.2.0|1.2.1] would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-genomeinfodbdata [1.2.1|1.2.2] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-genomeinfodbdata [1.2.10|1.2.11] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.3|1.2.4] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.6|1.2.7] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-genomeinfodbdata 1.2.9 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-ucsc.utils >=1.2.0,<1.3.0 is not installable because it requires + r-base >=4.4,<4.5.0a0 , which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-signaturesearch/meta.yaml b/recipes/bioconductor-signaturesearch/meta.yaml index f1ab00dc3f3f6..2b2bd2b144396 100644 --- a/recipes/bioconductor-signaturesearch/meta.yaml +++ b/recipes/bioconductor-signaturesearch/meta.yaml @@ -1,42 +1,49 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "signatureSearch" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements algorithms and data structures for performing gene expression signature (GES) searches, and subsequently interpreting the results functionally with specialized enrichment methods. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9585172c7764e755ee67aee1c5a1adba build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-signaturesearch", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, rmarkdown, BiocStyle, signatureSearchData, DT # SystemRequirements: C++11 requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-reactome.db >=1.89.0,<1.90.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-dplyr @@ -53,22 +60,23 @@ requirements: - r-visnetwork - libblas - liblapack + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-clusterprofiler >=4.10.0,<4.11.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-fgsea >=1.28.0,<1.29.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-clusterprofiler >=4.14.0,<4.15.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-fgsea >=1.32.0,<1.33.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-reactome.db >=1.89.0,<1.90.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-dplyr @@ -83,16 +91,16 @@ requirements: - r-scales - r-tibble - r-visnetwork - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: bd5e9ae4a91a4a12e107f0ee13921b1e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Environment for Gene Expression Searching Combined with Functional Enrichment Analysis' - description: 'This package implements algorithms and data structures for performing gene expression signature (GES) searches, and subsequently interpreting the results functionally with specialized enrichment methods.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-signaturesearchdata/meta.yaml b/recipes/bioconductor-signaturesearchdata/meta.yaml index c53b81dce19ae..03a0d333c9c8b 100644 --- a/recipes/bioconductor-signaturesearchdata/meta.yaml +++ b/recipes/bioconductor-signaturesearchdata/meta.yaml @@ -1,54 +1,59 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "signatureSearchData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: CMAP/LINCS hdf5 databases and other annotations used for signatureSearch software package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Datasets for signatureSearch package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b30a7f1715a7525279c47db6df5ad995 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-signaturesearchdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 - r-base - r-dplyr - r-magrittr - r-r.utils run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 - r-base - r-dplyr - r-magrittr - r-r.utils - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 98c11cb295e59f4f3caae25cdc4d616e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Datasets for signatureSearch package' - description: 'CMAP/LINCS hdf5 databases and other annotations used for signatureSearch software package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-signaturesearchdata/post-link.sh b/recipes/bioconductor-signaturesearchdata/post-link.sh index 505a2c08ce197..3a7f20cf5bf4a 100644 --- a/recipes/bioconductor-signaturesearchdata/post-link.sh +++ b/recipes/bioconductor-signaturesearchdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "signaturesearchdata-1.16.0" +installBiocDataPackage.sh "signaturesearchdata-1.20.0" diff --git a/recipes/bioconductor-signer/meta.yaml b/recipes/bioconductor-signer/meta.yaml index 8c8f0364b486a..cbec96ee6072a 100644 --- a/recipes/bioconductor-signer/meta.yaml +++ b/recipes/bioconductor-signer/meta.yaml @@ -1,154 +1,271 @@ -{% set version = "2.4.0" %} +{% set version = "2.8.0" %} {% set name = "signeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The signeR package provides an empirical Bayesian approach to mutational signature discovery. It is designed to analyze single nucleotide variation (SNV) counts in cancer genomes, but can also be applied to other features as well. Functionalities to characterize signatures or genome samples according to exposure patterns are also provided. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Empirical Bayesian approach to mutational signature discovery -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 36ca120021611cebddf20efa74c6bbf7 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-signer", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:signer + parent_recipe: + name: bioconductor-signer + path: recipes/bioconductor-signer + version: 1.6.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, rmarkdown # SystemRequirements: C++11 requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + + - bioconductor-biostrings >=2.74.0,<2.75.0 + + - bioconductor-bsgenome >=1.74.0,<1.75.0 + + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + + - bioconductor-genomicranges >=1.58.0,<1.59.0 + + - bioconductor-iranges >=2.40.0,<2.41.0 + + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - r-ada + - r-base + - r-bsplus + - r-class + - r-clue + - r-cowplot + - r-dplyr + - r-dt + - r-e1071 + - r-future + - r-future.apply + - r-ggplot2 + - r-ggpubr + - r-glmnet + - r-kknn + - r-listenv + - r-magrittr + - r-mass + - r-maxstat + - r-nloptr + - r-nmf + - r-pheatmap + - r-pmcmrplus + - r-ppclust + - r-proc + - r-proxy + - r-pvclust + - r-randomforest + - r-rcolorbrewer + - r-rcpp - - 'r-rcpparmadillo >=0.7.100' + + - r-rcpparmadillo >=0.7.100 + - r-readr + - r-reshape2 + - r-scales + - r-shiny + - r-shinycssloaders + - r-shinydashboard + - r-shinywidgets + - r-survival + - r-survivalanalysis + - r-survminer + - r-tibble + - r-tidyr + - r-vgam + - libblas + - liblapack + run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + + - bioconductor-biostrings >=2.74.0,<2.75.0 + + - bioconductor-bsgenome >=1.74.0,<1.75.0 + + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + + - bioconductor-genomicranges >=1.58.0,<1.59.0 + + - bioconductor-iranges >=2.40.0,<2.41.0 + + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - r-ada + - r-base + - r-bsplus + - r-class + - r-clue + - r-cowplot + - r-dplyr + - r-dt + - r-e1071 + - r-future + - r-future.apply + - r-ggplot2 + - r-ggpubr + - r-glmnet + - r-kknn + - r-listenv + - r-magrittr + - r-mass + - r-maxstat + - r-nloptr + - r-nmf + - r-pheatmap + - r-pmcmrplus + - r-ppclust + - r-proc + - r-proxy + - r-pvclust + - r-randomforest + - r-rcolorbrewer + - r-rcpp - - 'r-rcpparmadillo >=0.7.100' + + - r-rcpparmadillo >=0.7.100 + - r-readr + - r-reshape2 + - r-scales + - r-shiny + - r-shinycssloaders + - r-shinydashboard + - r-shinywidgets + - r-survival + - r-survivalanalysis + - r-survminer + - r-tibble + - r-tidyr + - r-vgam - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 44ad74b94e8c65b23858d84d085ddd07 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Empirical Bayesian approach to mutational signature discovery' - description: 'The signeR package provides an empirical Bayesian approach to mutational signature discovery. It is designed to analyze single nucleotide variation (SNV) counts in cancer genomes, but can also be applied to other features as well. Functionalities to characterize signatures or genome samples according to exposure patterns are also provided.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:signer - parent_recipe: - name: bioconductor-signer - path: recipes/bioconductor-signer - version: 1.6.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sigspack/meta.yaml b/recipes/bioconductor-sigspack/meta.yaml index 4b9d64c027d97..e37f6360ad5a9 100644 --- a/recipes/bioconductor-sigspack/meta.yaml +++ b/recipes/bioconductor-sigspack/meta.yaml @@ -1,55 +1,60 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "SigsPack" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Single sample estimation of exposure to mutational signatures. Exposures to known mutational signatures are estimated for single samples, based on quadratic programming algorithms. Bootstrapping the input mutational catalogues provides estimations on the stability of these exposures. The effect of the sequence composition of mutational context can be taken into account by normalising the catalogues. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Mutational Signature Estimation for Single Samples -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5fde29d53a470944ef9a4ba82bcca75d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sigspack", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - - 'r-quadprog >=1.5-5' + - r-quadprog >=1.5-5 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - - 'r-quadprog >=1.5-5' + - r-quadprog >=1.5-5 + +source: + md5: f4107a1fa2e4d7dc1d6c9f875ea8604c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Mutational Signature Estimation for Single Samples' - description: 'Single sample estimation of exposure to mutational signatures. Exposures to known mutational signatures are estimated for single samples, based on quadratic programming algorithms. Bootstrapping the input mutational catalogues provides estimations on the stability of these exposures. The effect of the sequence composition of mutational context can be taken into account by normalising the catalogues.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sigsquared/meta.yaml b/recipes/bioconductor-sigsquared/meta.yaml index 2970f841bef59..607c8b0cc4e9c 100644 --- a/recipes/bioconductor-sigsquared/meta.yaml +++ b/recipes/bioconductor-sigsquared/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "sigsquared" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f7dfbb4c066df8fe146b2b73f8180195 +about: + description: By leveraging statistical properties (log-rank test for survival) of patient cohorts defined by binary thresholds, poor-prognosis patients are identified by the sigsquared package via optimization over a cost function reducing type I and II error. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL version 3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Gene signature generation for functionally validated signaling pathways build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sigsquared", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-survival run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-survival +source: + md5: e1807436779fc908917dacd8f237ef81 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL version 3' - summary: 'Gene signature generation for functionally validated signaling pathways' - description: 'By leveraging statistical properties (log-rank test for survival) of patient cohorts defined by binary thresholds, poor-prognosis patients are identified by the sigsquared package via optimization over a cost function reducing type I and II error.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sim/meta.yaml b/recipes/bioconductor-sim/meta.yaml index b5f1d18e0e31c..cfd20863e7def 100644 --- a/recipes/bioconductor-sim/meta.yaml +++ b/recipes/bioconductor-sim/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.72.0" %} +{% set version = "1.76.0" %} {% set name = "SIM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Finds associations between two human genomic datasets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Integrated Analysis on two human genomic datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 72c2ca38244f4d53842bece2abdfadee build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sim", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:sim + - doi:10.1186/1471-2105-10-203 + parent_recipe: + name: bioconductor-sim + path: recipes/bioconductor-sim + version: 1.50.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: biomaRt, RColorBrewer requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-globaltest >=5.56.0,<5.57.0' - - 'bioconductor-quantsmooth >=1.68.0,<1.69.0' + - bioconductor-globaltest >=5.60.0,<5.61.0 + - bioconductor-quantsmooth >=1.72.0,<1.73.0 - r-base - r-quantreg - libblas - liblapack run: - - 'bioconductor-globaltest >=5.56.0,<5.57.0' - - 'bioconductor-quantsmooth >=1.68.0,<1.69.0' + - bioconductor-globaltest >=5.60.0,<5.61.0 + - bioconductor-quantsmooth >=1.72.0,<1.73.0 - r-base - r-quantreg - build: - - {{ compiler('c') }} - - make + +source: + md5: ad97c8ac31f33a53a9bf7319c3abdf0a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Integrated Analysis on two human genomic datasets' - description: 'Finds associations between two human genomic datasets.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:sim - - doi:10.1186/1471-2105-10-203 - parent_recipe: - name: bioconductor-sim - path: recipes/bioconductor-sim - version: 1.50.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-simat/meta.yaml b/recipes/bioconductor-simat/meta.yaml index c8c53947eb7d9..64729938cf0d9 100644 --- a/recipes/bioconductor-simat/meta.yaml +++ b/recipes/bioconductor-simat/meta.yaml @@ -1,57 +1,63 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "SIMAT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a pipeline for analysis of GC-MS data acquired in selected ion monitoring (SIM) mode. The tool also provides a guidance in choosing appropriate fragments for the targets of interest by using an optimization algorithm. This is done by considering overlapping peaks from a provided library by the user. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: GC-SIM-MS data processing and alaysis tool -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4482fbb67b81a5c0c2ed553f6b44faa2 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-simat", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:simat + - doi:10.1186/s12859-015-0681-2 + parent_recipe: + name: bioconductor-simat + path: recipes/bioconductor-simat + version: 1.12.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - - 'bioconductor-mzr >=2.36.0,<2.37.0' + - bioconductor-mzr >=2.40.0,<2.41.0 - r-base - r-ggplot2 - - 'r-rcpp >=0.11.3' + - r-rcpp >=0.11.3 - r-reshape2 - libblas - liblapack run: - - 'bioconductor-mzr >=2.36.0,<2.37.0' + - bioconductor-mzr >=2.40.0,<2.41.0 - r-base - r-ggplot2 - - 'r-rcpp >=0.11.3' + - r-rcpp >=0.11.3 - r-reshape2 - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} + +source: + md5: 95fb0d70ca9802bf2a2efc703fa79dba + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'GC-SIM-MS data processing and alaysis tool' - description: 'This package provides a pipeline for analysis of GC-MS data acquired in selected ion monitoring (SIM) mode. The tool also provides a guidance in choosing appropriate fragments for the targets of interest by using an optimization algorithm. This is done by considering overlapping peaks from a provided library by the user.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:simat - - doi:10.1186/s12859-015-0681-2 - parent_recipe: - name: bioconductor-simat - path: recipes/bioconductor-simat - version: 1.12.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-simbenchdata/meta.yaml b/recipes/bioconductor-simbenchdata/meta.yaml index a21401c5931bd..95dee93989ee0 100644 --- a/recipes/bioconductor-simbenchdata/meta.yaml +++ b/recipes/bioconductor-simbenchdata/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "SimBenchData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c801056ea68c668cd98230e8956d551b +about: + description: The SimBenchData package contains a total of 35 single-cell RNA-seq datasets covering a wide range of data characteristics, including major sequencing protocols, multiple tissue types, and both human and mouse sources. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'SimBenchData: a collection of 35 single-cell RNA-seq data covering a wide range of data characteristics' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-simbenchdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, Seurat requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3a786d414a97f00b39d6ab12811996ff + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'SimBenchData: a collection of 35 single-cell RNA-seq data covering a wide range of data characteristics' - description: 'The SimBenchData package contains a total of 35 single-cell RNA-seq datasets covering a wide range of data characteristics, including major sequencing protocols, multiple tissue types, and both human and mouse sources.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-simbenchdata/post-link.sh b/recipes/bioconductor-simbenchdata/post-link.sh index 29b22974ec81f..3931d80482e04 100644 --- a/recipes/bioconductor-simbenchdata/post-link.sh +++ b/recipes/bioconductor-simbenchdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "simbenchdata-1.10.0" +installBiocDataPackage.sh "simbenchdata-1.14.0" diff --git a/recipes/bioconductor-simbu/meta.yaml b/recipes/bioconductor-simbu/meta.yaml index 122d2cdc3c9af..31514f620baca 100644 --- a/recipes/bioconductor-simbu/meta.yaml +++ b/recipes/bioconductor-simbu/meta.yaml @@ -1,65 +1,70 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "SimBu" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SimBu can be used to simulate bulk RNA-seq datasets with known cell type fractions. You can either use your own single-cell study for the simulation or the sfaira database. Different pre-defined simulation scenarios exist, as are options to run custom simulations. Additionally, expression values can be adapted by adding an mRNA bias, which produces more biologically relevant simulations. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Simulate Bulk RNA-seq Datasets from Single-Cell Datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 50f7ac0bde39513f3ca816495b7ec9fc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-simbu", max_pin="x.x") }}' - noarch: generic -# Suggests: curl, knitr, matrixStats, rmarkdown, Seurat, testthat (>= 3.0.0) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: curl, knitr, matrixStats, rmarkdown, Seurat (>= 5.0.0), SeuratObject (>= 5.0.0), testthat (>= 3.0.0) requirements: host: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-dplyr - r-ggplot2 - - 'r-matrix >=1.3.3' + - r-matrix >=1.3.3 - r-proxyc - r-rcolorbrewer - r-rcurl - r-reticulate - r-tidyr run: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - - 'bioconductor-sparsematrixstats >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-dplyr - r-ggplot2 - - 'r-matrix >=1.3.3' + - r-matrix >=1.3.3 - r-proxyc - r-rcolorbrewer - r-rcurl - r-reticulate - r-tidyr + +source: + md5: 6481bcae0136a8572d411c675417284f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Simulate Bulk RNA-seq Datasets from Single-Cell Datasets' - description: 'SimBu can be used to simulate bulk RNA-seq datasets with known cell type fractions. You can either use your own single-cell study for the simulation or the sfaira database. Different pre-defined simulation scenarios exist, as are options to run custom simulations. Additionally, expression values can be adapted by adding an mRNA bias, which produces more biologically relevant simulations.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-simd/meta.yaml b/recipes/bioconductor-simd/meta.yaml index a50dbbec80a87..124f7612ab8ea 100644 --- a/recipes/bioconductor-simd/meta.yaml +++ b/recipes/bioconductor-simd/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "SIMD" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides a inferential analysis method for detecting differentially expressed CpG sites in MeDIP-seq data. It uses statistical framework and EM algorithm, to identify differentially expressed CpG sites. The methods on this package are described in the article 'Methylation-level Inferences and Detection of Differential Methylation with Medip-seq Data' by Yan Zhou, Jiadi Zhu, Mingtao Zhao, Baoxue Zhang, Chunfu Jiang and Xiyan Yang (2018, pending publication). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3fa4a3f26b9c42aa5026f0a22956195b build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-simd", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr,rmarkdown requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-methylmnm >=1.40.0,<1.41.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-methylmnm >=1.44.0,<1.45.0 - r-base - r-statmod - libblas - liblapack run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-methylmnm >=1.40.0,<1.41.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-methylmnm >=1.44.0,<1.45.0 - r-base - r-statmod - build: - - {{ compiler('c') }} - - make + +source: + md5: eb3e40e49e40d33edc36976821de390b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site' - description: 'This package provides a inferential analysis method for detecting differentially expressed CpG sites in MeDIP-seq data. It uses statistical framework and EM algorithm, to identify differentially expressed CpG sites. The methods on this package are described in the article ''Methylation-level Inferences and Detection of Differential Methylation with Medip-seq Data'' by Yan Zhou, Jiadi Zhu, Mingtao Zhao, Baoxue Zhang, Chunfu Jiang and Xiyan Yang (2018, pending publication).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-simffpe/meta.yaml b/recipes/bioconductor-simffpe/meta.yaml index 8e72d0c1e17b1..a4b320899be49 100644 --- a/recipes/bioconductor-simffpe/meta.yaml +++ b/recipes/bioconductor-simffpe/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "SimFFPE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The NGS (Next-Generation Sequencing) reads from FFPE (Formalin-Fixed Paraffin-Embedded) samples contain numerous artifact chimeric reads (ACRS), which can lead to false positive structural variant calls. These ACRs are derived from the combination of two single-stranded DNA (ss-DNA) fragments with short reverse complementary regions (SRCRs). This package simulates these artifact chimeric reads as well as normal reads for FFPE samples on the whole genome / several chromosomes / large regions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: NGS Read Simulator for FFPE Tissue -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 95d6710ea184127f659f0c6f7786234c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-simffpe", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-doparallel - r-dplyr - r-foreach - r-truncnorm run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-doparallel - r-dplyr - r-foreach - r-truncnorm + +source: + md5: 12d6d7ebffbb39b585919105c63bc958 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'NGS Read Simulator for FFPE Tissue' - description: 'The NGS (Next-Generation Sequencing) reads from FFPE (Formalin-Fixed Paraffin-Embedded) samples contain numerous artifact chimeric reads (ACRS), which can lead to false positive structural variant calls. These ACRs are derived from the combination of two single-stranded DNA (ss-DNA) fragments with short reverse complementary regions (SRCRs). This package simulates these artifact chimeric reads as well as normal reads for FFPE samples on the whole genome / several chromosomes / large regions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-similarpeak/meta.yaml b/recipes/bioconductor-similarpeak/meta.yaml index 9f2da87d43c8c..8bd457257cefb 100644 --- a/recipes/bioconductor-similarpeak/meta.yaml +++ b/recipes/bioconductor-similarpeak/meta.yaml @@ -1,40 +1,21 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "similaRpeak" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package calculates metrics which quantify the level of similarity between ChIP-Seq profiles. More specifically, the package implements six pseudometrics specialized in pattern similarity detection in ChIP-Seq profiles. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Metrics to estimate a level of similarity between two ChIP-Seq profiles -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d91ba41941b12c9f93e77872e444c4d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-similarpeak", max_pin="x.x") }}' - noarch: generic -# Suggests: RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments, rtracklayer, rmarkdown, BiocStyle -requirements: - host: - - r-base - - 'r-r6 >=2.0' - run: - - r-base - - 'r-r6 >=2.0' -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Metrics to estimate a level of similarity between two ChIP-Seq profiles' - description: 'This package calculates metrics which quantify the level of similarity between ChIP-Seq profiles. More specifically, the package implements six pseudometrics specialized in pattern similarity detection in ChIP-Seq profiles.' + extra: identifiers: - biotools:similarpeak @@ -44,3 +25,28 @@ extra: path: recipes/bioconductor-similarpeak version: 1.12.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments, rtracklayer, rmarkdown, BiocStyle +requirements: + host: + - r-base + - r-r6 >=2.0 + run: + - r-base + - r-r6 >=2.0 + +source: + md5: 326a9c389d85c0e026cad982ae4aa5cd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-simlr/meta.yaml b/recipes/bioconductor-simlr/meta.yaml index ab2a37047dc77..06e76f236d343 100644 --- a/recipes/bioconductor-simlr/meta.yaml +++ b/recipes/bioconductor-simlr/meta.yaml @@ -1,25 +1,40 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "SIMLR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Single-cell RNA-seq technologies enable high throughput gene expression measurement of individual cells, and allow the discovery of heterogeneity within cell populations. Measurement of cell-to-cell gene expression similarity is critical for the identification, visualization and analysis of cell populations. However, single-cell data introduce challenges to conventional measures of gene expression similarity because of the high level of noise, outliers and dropouts. We develop a novel similarity-learning framework, SIMLR (Single-cell Interpretation via Multi-kernel LeaRning), which learns an appropriate distance metric from the data for dimension reduction, clustering and visualization. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Single-cell Interpretation via Multi-kernel LeaRning (SIMLR) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9692308a74c8781b41b55409edf594ce build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-simlr", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:simlr + - doi:10.1101/118901 + parent_recipe: + name: bioconductor-simlr + path: recipes/bioconductor-simlr + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, BiocStyle, testthat, knitr, igraph requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-matrix @@ -36,25 +51,16 @@ requirements: - r-rcpp - r-rcppannoy - r-rspectra - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 6add06309485ff6326731e6be60c0b46 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)' - description: 'Single-cell RNA-seq technologies enable high throughput gene expression measurement of individual cells, and allow the discovery of heterogeneity within cell populations. Measurement of cell-to-cell gene expression similarity is critical for the identification, visualization and analysis of cell populations. However, single-cell data introduce challenges to conventional measures of gene expression similarity because of the high level of noise, outliers and dropouts. We develop a novel similarity-learning framework, SIMLR (Single-cell Interpretation via Multi-kernel LeaRning), which learns an appropriate distance metric from the data for dimension reduction, clustering and visualization.' - license_file: LICENSE -extra: - identifiers: - - biotools:simlr - - doi:10.1101/118901 - parent_recipe: - name: bioconductor-simlr - path: recipes/bioconductor-simlr - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-simona/meta.yaml b/recipes/bioconductor-simona/meta.yaml index 7cbbb253de34d..3f7876bd61bda 100644 --- a/recipes/bioconductor-simona/meta.yaml +++ b/recipes/bioconductor-simona/meta.yaml @@ -1,29 +1,35 @@ -{% set version = "1.0.2" %} +{% set version = "1.4.0" %} {% set name = "simona" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements infrastructures for ontology analysis by offering efficient data structures, fast ontology traversal methods, and elegant visualizations. It provides a robust toolbox supporting over 70 methods for semantic similarity analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Semantic Similarity on Bio-Ontologies -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: be691f3b2b1908a5af3180d4c9e47232 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-simona", max_pin="x.x") }}' -# Suggests: knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png, InteractiveComplexHeatmap, UniProtKeywords, simplifyEnrichment, AnnotationHub, jsonlite # SystemRequirements: Perl, Java requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-circlize - r-getoptlong @@ -32,13 +38,14 @@ requirements: - r-matrixstats - r-polychrome - r-rcpp - - 'r-xml2 >=1.3.3' + - r-shiny + - r-xml2 >=1.3.3 - libblas - liblapack - - 'perl >=5.6.0' + - perl >=5.6.0 run: - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-circlize - r-getoptlong @@ -47,19 +54,19 @@ requirements: - r-matrixstats - r-polychrome - r-rcpp - - 'r-xml2 >=1.3.3' - - 'perl >=5.6.0' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-shiny + - r-xml2 >=1.3.3 + - perl >=5.6.0 + +source: + md5: b1e954e8f591b4440136f4b60280f1d9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Semantic Similarity in Bio-Ontologies' - description: 'This package implements infrastructures for ontology analysis by offering efficient data structures, fast ontology traversal methods, and elegant visualizations. It provides a robust toolbox supporting over 70 methods for semantic similarity analysis.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-simpic/build.sh b/recipes/bioconductor-simpic/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-simpic/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-simpic/meta.yaml b/recipes/bioconductor-simpic/meta.yaml new file mode 100644 index 0000000000000..31c9fc09bffa7 --- /dev/null +++ b/recipes/bioconductor-simpic/meta.yaml @@ -0,0 +1,66 @@ +{% set version = "1.2.0" %} +{% set name = "simPIC" %} +{% set bioc = "3.20" %} + +about: + description: simPIC is a package for simulating single-cell ATAC-seq count data. It provides a user-friendly, well documented interface for data simulation. Functions are provided for parameter estimation, realistic scATAC-seq data simulation, and comparing real and simulated datasets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'simPIC: flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data' + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-simpic", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-actuar + - r-base + - r-checkmate >=2.0.0 + - r-fitdistrplus + - r-matrix + - r-matrixstats + - r-rlang + - r-scales + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-actuar + - r-base + - r-checkmate >=2.0.0 + - r-fitdistrplus + - r-matrix + - r-matrixstats + - r-rlang + - r-scales + +source: + md5: cbab2494177921bb0d655613910b54a6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-simpintlists/meta.yaml b/recipes/bioconductor-simpintlists/meta.yaml index a51d0edccc031..1ccdb0c8779eb 100644 --- a/recipes/bioconductor-simpintlists/meta.yaml +++ b/recipes/bioconductor-simpintlists/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "simpIntLists" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9dbe0a1f390843a49bb11d05ac5f2e28 +about: + description: The package contains BioGRID interactions for arabidopsis(thale cress), c.elegans, fruit fly, human, mouse, yeast( budding yeast ) and S.pombe (fission yeast) . Entrez ids, official names and unique ids can be used to find proteins. The format of interactions are lists. For each gene/protein, there is an entry in the list with "name" containing name of the gene/protein and "interactors" containing the list of genes/proteins interacting with it. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: The package contains BioGRID interactions for various organisms in a simple format build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-simpintlists", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-simpintlists + path: recipes/bioconductor-simpintlists + version: 1.16.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 22e154a884965c1309c378abc80c602a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'The package contains BioGRID interactions for various organisms in a simple format' - description: 'The package contains BioGRID interactions for arabidopsis(thale cress), c.elegans, fruit fly, human, mouse, yeast( budding yeast ) and S.pombe (fission yeast) . Entrez ids, official names and unique ids can be used to find proteins. The format of interactions are lists. For each gene/protein, there is an entry in the list with "name" containing name of the gene/protein and "interactors" containing the list of genes/proteins interacting with it.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-simpintlists - path: recipes/bioconductor-simpintlists - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-simpintlists/post-link.sh b/recipes/bioconductor-simpintlists/post-link.sh index 20fa4fcd46724..28df2531eb1f8 100644 --- a/recipes/bioconductor-simpintlists/post-link.sh +++ b/recipes/bioconductor-simpintlists/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "simpintlists-1.38.0" +installBiocDataPackage.sh "simpintlists-1.42.0" diff --git a/recipes/bioconductor-simpleseg/meta.yaml b/recipes/bioconductor-simpleseg/meta.yaml index 37f94dc135935..7a0b6bfc08eb2 100644 --- a/recipes/bioconductor-simpleseg/meta.yaml +++ b/recipes/bioconductor-simpleseg/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "simpleSeg" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image. This allows for the features of cells such as marker expression and morphology to be extracted, stored and analysed. simpleSeg provides functionality for user friendly, watershed based segmentation on multiplexed cellular images in R based on the intensity of user specified protein marker channels. simpleSeg can also be used for the normalization of single cell data obtained from multiple images. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A package to perform simple cell segmentation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d0e40e9be3d3e9c8a16d0390040f3da8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-simpleseg", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat (>= 3.0.0), knitr, ggplot2 requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-cytomapper >=1.14.0,<1.15.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-cytomapper >=1.18.0,<1.19.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-spatstat.geom - r-terra run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-cytomapper >=1.14.0,<1.15.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-cytomapper >=1.18.0,<1.19.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-spatstat.geom - r-terra + +source: + md5: c65ea4225e3500fb4674ab0fbb189772 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'A package to perform simple cell segmentation' - description: 'Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image. This allows for the features of cells such as marker expression and morphology to be extracted, stored and analysed. simpleSeg provides functionality for user friendly, watershed based segmentation on multiplexed cellular images in R based on the intensity of user specified protein marker channels. simpleSeg can also be used for the normalization of single cell data obtained from multiple images.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-simplifyenrichment/meta.yaml b/recipes/bioconductor-simplifyenrichment/meta.yaml index 83eeed1cbd3c8..efdf870e939ec 100644 --- a/recipes/bioconductor-simplifyenrichment/meta.yaml +++ b/recipes/bioconductor-simplifyenrichment/meta.yaml @@ -1,71 +1,68 @@ -{% set version = "1.12.0" %} +{% set version = "2.0.0" %} {% set name = "simplifyEnrichment" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A new clustering algorithm, "binary cut", for clustering similarity matrices of functional terms is implemeted in this package. It also provides functions for visualizing, summarizing and comparing the clusterings. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Simplify Functional Enrichment Results -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d54c7188ca88dd43802296650e5b80e1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-simplifyenrichment", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, clusterProfiler, msigdbr, DOSE, DO.db, reactome.db, flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11), shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter, gridtext, fpc + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11), shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter, gridtext, fpc requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-simona >=1.4.0,<1.5.0 - r-base - r-circlize - r-clue - - 'r-cluster >=1.14.2' + - r-cluster >=1.14.2 - r-colorspace - r-digest - r-getoptlong - - 'r-globaloptions >=0.1.0' - - r-matrix - - r-proxyc + - r-globaloptions >=0.1.0 - r-slam - r-tm run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-simona >=1.4.0,<1.5.0 - r-base - r-circlize - r-clue - - 'r-cluster >=1.14.2' + - r-cluster >=1.14.2 - r-colorspace - r-digest - r-getoptlong - - 'r-globaloptions >=0.1.0' - - r-matrix - - r-proxyc + - r-globaloptions >=0.1.0 - r-slam - r-tm + +source: + md5: 57602d6e3858ec77d41291fd31f7d743 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Simplify Functional Enrichment Results' - description: 'A new clustering algorithm, "binary cut", for clustering similarity matrices of functional terms is implemeted in this package. It also provides functions for visualizing, summarizing and comparing the clusterings.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sincell/meta.yaml b/recipes/bioconductor-sincell/meta.yaml index f42dbd1131da1..a36b51a8d0578 100644 --- a/recipes/bioconductor-sincell/meta.yaml +++ b/recipes/bioconductor-sincell/meta.yaml @@ -1,25 +1,39 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "sincell" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Cell differentiation processes are achieved through a continuum of hierarchical intermediate cell-states that might be captured by single-cell RNA seq. Existing computational approaches for the assessment of cell-state hierarchies from single-cell data might be formalized under a general workflow composed of i) a metric to assess cell-to-cell similarities (combined or not with a dimensionality reduction step), and ii) a graph-building algorithm (optionally making use of a cells-clustering step). Sincell R package implements a methodological toolbox allowing flexible workflows under such framework. Furthermore, Sincell contributes new algorithms to provide cell-state hierarchies with statistical support while accounting for stochastic factors in single-cell RNA seq. Graphical representations and functional association tests are provided to interpret hierarchies. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 308aa15c851a99b7f345dbd0af122f07 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sincell", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:sincell + parent_recipe: + name: bioconductor-sincell + path: recipes/bioconductor-sincell + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, biomaRt, stringr, monocle requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-cluster @@ -30,7 +44,7 @@ requirements: - r-igraph - r-mass - r-proxy - - 'r-rcpp >=0.11.2' + - r-rcpp >=0.11.2 - r-reshape2 - r-rtsne - r-scatterplot3d @@ -48,30 +62,22 @@ requirements: - r-igraph - r-mass - r-proxy - - 'r-rcpp >=0.11.2' + - r-rcpp >=0.11.2 - r-reshape2 - r-rtsne - r-scatterplot3d - r-statmod - r-tsp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 20b8bd991b46ef01e3ceef836254899d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data' - description: 'Cell differentiation processes are achieved through a continuum of hierarchical intermediate cell-states that might be captured by single-cell RNA seq. Existing computational approaches for the assessment of cell-state hierarchies from single-cell data might be formalized under a general workflow composed of i) a metric to assess cell-to-cell similarities (combined or not with a dimensionality reduction step), and ii) a graph-building algorithm (optionally making use of a cells-clustering step). Sincell R package implements a methodological toolbox allowing flexible workflows under such framework. Furthermore, Sincell contributes new algorithms to provide cell-state hierarchies with statistical support while accounting for stochastic factors in single-cell RNA seq. Graphical representations and functional association tests are provided to interpret hierarchies.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:sincell - parent_recipe: - name: bioconductor-sincell - path: recipes/bioconductor-sincell - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-single.mtec.transcriptomes/meta.yaml b/recipes/bioconductor-single.mtec.transcriptomes/meta.yaml index d9ce115024fa4..ac222ecbd3557 100644 --- a/recipes/bioconductor-single.mtec.transcriptomes/meta.yaml +++ b/recipes/bioconductor-single.mtec.transcriptomes/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "Single.mTEC.Transcriptomes" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 574ee45ff1177688d68e6ae8295e67a2 +about: + description: 'This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data from the manuscript titled: Single-cell transcriptome analysis reveals coordinated ectopic-gene expression patterns in medullary thymic epithelial cells. This paper was published in Nature Immunology 16,933-941(2015). The data objects provided in this package has been pre-processed: the raw data files can be downloaded from ArrayExpress under the accession identifiers E-MTAB-3346 and E-MTAB-3624. The vignette of this data package provides a documented and reproducible workflow that includes the code that was used to generate each statistic and figure from the manuscript.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Single Cell Transcriptome Data and Analysis of Mouse mTEC cells build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-single.mtec.transcriptomes", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod, gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid, gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap, BiocStyle, knitr, BiocParallel requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5b2e48b74d9d995d70016366038e5a9d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Single Cell Transcriptome Data and Analysis of Mouse mTEC cells' - description: 'This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data from the manuscript titled: Single-cell transcriptome analysis reveals coordinated ectopic-gene expression patterns in medullary thymic epithelial cells. This paper was published in Nature Immunology 16,933-941(2015). The data objects provided in this package has been pre-processed: the raw data files can be downloaded from ArrayExpress under the accession identifiers E-MTAB-3346 and E-MTAB-3624. The vignette of this data package provides a documented and reproducible workflow that includes the code that was used to generate each statistic and figure from the manuscript.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-single.mtec.transcriptomes/post-link.sh b/recipes/bioconductor-single.mtec.transcriptomes/post-link.sh index c09b613681aa7..a9041eeecc78e 100644 --- a/recipes/bioconductor-single.mtec.transcriptomes/post-link.sh +++ b/recipes/bioconductor-single.mtec.transcriptomes/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "single.mtec.transcriptomes-1.30.0" +installBiocDataPackage.sh "single.mtec.transcriptomes-1.34.0" diff --git a/recipes/bioconductor-singlecellalleleexperiment/build.sh b/recipes/bioconductor-singlecellalleleexperiment/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-singlecellalleleexperiment/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-singlecellalleleexperiment/meta.yaml b/recipes/bioconductor-singlecellalleleexperiment/meta.yaml new file mode 100644 index 0000000000000..87381b04b9a5d --- /dev/null +++ b/recipes/bioconductor-singlecellalleleexperiment/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "1.2.0" %} +{% set name = "SingleCellAlleleExperiment" %} +{% set bioc = "3.20" %} + +about: + description: Defines a S4 class that is based on SingleCellExperiment. In addition to the usual gene layer the object can also store data for immune genes such as HLAs, Igs and KIRs at allele and functional level. The package is part of a workflow named single-cell ImmunoGenomic Diversity (scIGD), that firstly incorporates allele-aware quantification data for immune genes. This new data can then be used with the here implemented data structure and functionalities for further data handling and data analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: S4 Class for Single Cell Data with Allele and Functional Levels for Immune Genes + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-singlecellalleleexperiment", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: scaeData, knitr, rmarkdown, BiocStyle, scran, scater, scuttle, ggplot2, patchwork, org.Hs.eg.db, AnnotationDbi, DropletUtils, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-matrix + run: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-matrix + +source: + md5: 8071d08019c40f812d8f8d09531835e9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-singlecellexperiment/meta.yaml b/recipes/bioconductor-singlecellexperiment/meta.yaml index 3f8eefc75d7b5..ad4cd868a906c 100644 --- a/recipes/bioconductor-singlecellexperiment/meta.yaml +++ b/recipes/bioconductor-singlecellexperiment/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "SingleCellExperiment" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: S4 Classes for Single Cell Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef057b77f40efba992f311486e83448b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-singlecellexperiment", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-singlecellexperiment + path: recipes/bioconductor-singlecellexperiment + version: 1.2.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>= 2.9.1), Rtsne requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + +source: + md5: 2471847d91e0cd67873f5928daedbcd1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'S4 Classes for Single Cell Data' - description: 'Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-singlecellexperiment - path: recipes/bioconductor-singlecellexperiment - version: 1.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-singlecellmultimodal/meta.yaml b/recipes/bioconductor-singlecellmultimodal/meta.yaml index 7a3421ef82fa5..abf1a5635889e 100644 --- a/recipes/bioconductor-singlecellmultimodal/meta.yaml +++ b/recipes/bioconductor-singlecellmultimodal/meta.yaml @@ -1,60 +1,65 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "SingleCellMultiModal" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SingleCellMultiModal is an ExperimentHub package that serves multiple datasets obtained from GEO and other sources and represents them as MultiAssayExperiment objects. We provide several multi-modal datasets including scNMT, 10X Multiome, seqFISH, CITEseq, SCoPE2, and others. The scope of the package is is to provide data for benchmarking and analysis. To cite, use the 'citation' function and see . + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Integrating Multi-modal Single Cell Experiment datasets -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e397bc4fbd9ea63f6660758f01d01d38 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-singlecellmultimodal", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, ggplot2, knitr, RaggedExperiment, rmarkdown, scater, scran, UpSetR, uwot requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 61f436e43d8121f6eef92a6e9445e96f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Integrating Multi-modal Single Cell Experiment datasets' - description: 'SingleCellMultiModal is an ExperimentHub package that serves multiple datasets obtained from GEO and other sources and represents them as MultiAssayExperiment objects. We provide several multi-modal datasets including scNMT, 10X Multiome, seqFISH, CITEseq, SCoPE2, and others. The scope of the package is is to provide data for benchmarking and analysis.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-singlecellmultimodal/post-link.sh b/recipes/bioconductor-singlecellmultimodal/post-link.sh index a9af6b4051d35..3131932bee2b1 100644 --- a/recipes/bioconductor-singlecellmultimodal/post-link.sh +++ b/recipes/bioconductor-singlecellmultimodal/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "singlecellmultimodal-1.14.0" +installBiocDataPackage.sh "singlecellmultimodal-1.18.0" diff --git a/recipes/bioconductor-singlecellsignalr/meta.yaml b/recipes/bioconductor-singlecellsignalr/meta.yaml index 65343241fe4ed..6472badc80165 100644 --- a/recipes/bioconductor-singlecellsignalr/meta.yaml +++ b/recipes/bioconductor-singlecellsignalr/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "SingleCellSignalR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Allows single cell RNA seq data analysis, clustering, creates internal network and infers cell-cell interactions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Cell Signalling Using Single Cell RNAseq Data Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d00060a859db9cd8c87ce9673cc9d886 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-singlecellsignalr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-scran >=1.34.0,<1.35.0 - r-base - r-biocmanager - r-circlize @@ -37,10 +39,10 @@ requirements: - r-rtsne - r-stringr run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-scran >=1.34.0,<1.35.0 - r-base - r-biocmanager - r-circlize @@ -51,13 +53,16 @@ requirements: - r-pheatmap - r-rtsne - r-stringr + +source: + md5: 0e82613ffe044a13aff73b6929714472 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Cell Signalling Using Single Cell RNAseq Data Analysis' - description: 'Allows single cell RNA seq data analysis, clustering, creates internal network and infers cell-cell interactions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-singlecelltk/build_failure.linux-64.yaml b/recipes/bioconductor-singlecelltk/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..65138ddac6ea4 --- /dev/null +++ b/recipes/bioconductor-singlecelltk/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 3aba5b7f556ee445220a9f4bbb9b96e232d36b4f9593a922936e2539254dfc36 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-scdblfinder[version='>=1.20.0,<1.21.0']"), MatchSpec("bioconductor-gsvadata==1.42.0=r44hdfd78af_0"), MatchSpec("bioconductor-scater==1.34.0=r44hdfd78af_0"), MatchSpec("bioconductor-scds[version='>=1.22.0,<1.23.0']"), MatchSpec("bioconductor-hgu95a.db[version='>=3.13.0,<3.14.0']"), MatchSpec("r-ggrastr")} + Encountered problems while solving: + - nothing provides requested bioconductor-scdblfinder >=1.20.0,<1.21.0 + - nothing provides requested bioconductor-scds >=1.22.0,<1.23.0 + - package bioconductor-scater-1.34.0-r44hdfd78af_0 requires r-ggrastr, but none of the providers can be installed + - package bioconductor-gsvadata-1.42.0-r44hdfd78af_0 requires bioconductor-hgu95a.db >=3.13.0,<3.14.0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-annotationhub >=3.14.0,<3.15.0 [0m is installable and it requires + [32mbioconductor-annotationdbi >=1.68.0,<1.69.0 [0m, which can be installed; + [32mbioconductor-celda >=1.22.0,<1.23.0 [0m is installable and it requires + [32mbioconductor-scater >=1.34.0,<1.35.0 [0m, which requires + [32mr-ggrastr[0m with the potential options + [32mr-ggrastr 1.0.2[0m would require + [32mr-cairo >=1.5.9 [0m with the potential options + [32mr-cairo [1.5_10|1.5_11|1.5_12|1.5_9][0m would require + [32mr-base [>=3.5,<3.6.0a0 |>=3.5.1,<3.5.2.0a0 ][0m, which can be installed; + [32mr-cairo [1.5_10|1.5_11|1.5_12|1.5_12.2][0m would require + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mr-cairo [1.5_12|1.5_12.2|1.5_14|1.5_15|1.6_0][0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-cairo [1.5_12.2|1.5_14|1.5_15|1.6_0][0m would require + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-cairo 1.5_9[0m would require + [32mr-base 3.3.2* [0m, which can be installed; + [32mr-cairo 1.5_9[0m would require + [32mr-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ][0m, which can be installed; + [32mr-cairo [1.6_0|1.6_1|1.6_2][0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mr-cairo [1.6_0|1.6_1|1.6_2][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mr-cairo 1.6_2[0m would require + [32micu >=75.1,<76.0a0 [0m, which can be installed; + [32mr-ggrastr [0.2.1|0.2.2|0.2.3][0m would require + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mr-ggrastr [0.2.1|0.2.2|0.2.3|1.0.0|1.0.1][0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-ggrastr [0.2.3|1.0.0|1.0.1|1.0.2][0m would require + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-ggrastr [1.0.1|1.0.2][0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mr-ggrastr 1.0.2[0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mbioconductor-celldex >=1.16.0,<1.17.0 [0m is installable and it requires + [32mbioconductor-alabaster.base >=1.6.0,<1.7.0 [0m, which requires + [32mr-jsonvalidate[0m with the potential options + [32mr-jsonvalidate 1.3.2[0m would require + [32mr-v8[0m with the potential options + [32mr-v8 [2.3|3.0|3.0.1|3.0.2][0m would require + [32mr-base >=3.5,<3.6.0a0 [0m, which can be installed; + [32mr-v8 [2.3|3.0|...|3.4.2][0m would require + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mr-v8 [3.0.2|3.1.0|...|4.2.1][0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-v8 [3.4.2|3.5.0|...|4.3.0][0m would require + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-v8 [4.2.1|4.2.2|...|4.4.2][0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mr-v8 [4.3.0|4.3.1|...|5.0.1][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-v8 [4.4.2|5.0.0|5.0.1][0m would require + [31micu >=73.2,<74.0a0 [0m, which conflicts with any installable versions previously reported; + [32mr-jsonvalidate 1.1.0[0m would require + [32mr-base >=3.5,<3.6.0a0 [0m, which can be installed; + [32mr-jsonvalidate 1.1.0[0m would require + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mr-jsonvalidate [1.1.0|1.3.1|1.3.2][0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-jsonvalidate [1.1.0|1.3.1|1.3.2][0m would require + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-jsonvalidate 1.3.2[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mr-jsonvalidate 1.3.2[0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mbioconductor-gsvadata >=1.42.0,<1.43.0 [0m is not installable because it requires + [31mbioconductor-hgu95a.db >=3.13.0,<3.14.0 [0m but there are no viable options + [31mbioconductor-hgu95a.db 3.13.0[0m would require + [31mbioconductor-org.hs.eg.db >=3.20.0,<3.21.0 [0m, which requires + [31mr-base >=4.4,<4.5.0a0 [0m but there are no viable options + [31mr-base [4.4.0|4.4.1][0m would require + [31micu >=73.2,<74.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-base [4.4.1|4.4.2][0m would require + [32micu >=75.1,<76.0a0 [0m, which can be installed; + [31mbioconductor-hgu95a.db 3.13.0[0m would require + [31mbioconductor-annotationdbi >=1.56.0,<1.57.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-hgu95a.db 3.13.0[0m would require + [31mbioconductor-annotationdbi >=1.60.0,<1.61.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-hgu95a.db 3.13.0[0m would require + [31mbioconductor-annotationdbi >=1.62.0,<1.63.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-hgu95a.db 3.13.0[0m would require + [31mbioconductor-annotationdbi >=1.64.0,<1.65.0 [0m, which conflicts with any installable versions previously reported; + [32mbioconductor-scater >=1.34.0,<1.35.0 [0m, which can be installed (as previously explained); + [31mbioconductor-scdblfinder >=1.20.0,<1.21.0 [0m does not exist (perhaps a typo or a missing channel); + [31mbioconductor-scds >=1.22.0,<1.23.0 [0m does not exist (perhaps a typo or a missing channel); + [32mbioconductor-scrnaseq >=2.20.0,<2.21.0 [0m is installable and it requires + [32mbioconductor-alabaster.base >=1.6.0,<1.7.0 [0m, which can be installed (as previously explained); + [31mr-base 4.4.* [0m, which cannot be installed (as previously explained). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-singlecelltk/build_failure.osx-64.yaml b/recipes/bioconductor-singlecelltk/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..3c95d5e38b564 --- /dev/null +++ b/recipes/bioconductor-singlecelltk/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 3aba5b7f556ee445220a9f4bbb9b96e232d36b4f9593a922936e2539254dfc36 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + bioconductor-alabaster.base needs to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-singlecelltk/meta.yaml b/recipes/bioconductor-singlecelltk/meta.yaml index 9455db96d8260..2862b4421cf4a 100644 --- a/recipes/bioconductor-singlecelltk/meta.yaml +++ b/recipes/bioconductor-singlecelltk/meta.yaml @@ -1,199 +1,378 @@ -{% set version = "2.12.0" %} +{% set version = "2.16.0" %} {% set name = "singleCellTK" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The Single Cell Toolkit (SCTK) in the singleCellTK package provides an interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. SCTK allows users to seamlessly integrate tools from various packages at different stages of the analysis workflow. A general "a la carte" workflow gives users the ability access to multiple methods for data importing, calculation of general QC metrics, doublet detection, ambient RNA estimation and removal, filtering, normalization, batch correction or integration, dimensionality reduction, 2-D embedding, clustering, marker detection, differential expression, cell type labeling, pathway analysis, and data exporting. Curated workflows can be used to run Seurat and Celda. Streamlined quality control can be performed on the command line using the SCTK-QC pipeline. Users can analyze their data using commands in the R console or by using an interactive Shiny Graphical User Interface (GUI). Specific analyses or entire workflows can be summarized and shared with comprehensive HTML reports generated by Rmarkdown. Additional documentation and vignettes can be found at camplab.net/sctk. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5efaf76211a6a623f6657383677474bb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-singlecelltk", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, Rsubread, BiocStyle, knitr, lintr, spelling, org.Mm.eg.db, stringr, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics, RColorBrewer, fastmap (>= 1.1.0), harmony + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, Rsubread, BiocStyle, knitr, lintr, spelling, org.Mm.eg.db, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics, RColorBrewer, fastmap (>= 1.1.0), harmony, SeuratObject, optparse requirements: + host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-batchelor >=1.18.0,<1.19.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-celda >=1.18.0,<1.19.0' - - 'bioconductor-celldex >=1.12.0,<1.13.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-dropletutils >=1.22.0,<1.23.0' - - 'bioconductor-eds >=1.4.0,<1.5.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-gsva >=1.50.0,<1.51.0' - - 'bioconductor-gsvadata >=1.38.0,<1.39.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-mast >=1.28.0,<1.29.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scdblfinder >=1.16.0,<1.17.0' - - 'bioconductor-scds >=1.18.0,<1.19.0' - - 'bioconductor-scmerge >=1.18.0,<1.19.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-scrnaseq >=2.16.0,<2.17.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-singler >=2.4.0,<2.5.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' - - 'bioconductor-tenxpbmcdata >=1.20.0,<1.21.0' - - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' - - 'bioconductor-tscan >=1.40.0,<1.41.0' - - 'bioconductor-tximport >=1.30.0,<1.31.0' - - 'bioconductor-zellkonverter >=1.12.0,<1.13.0' - - 'bioconductor-zinbwave >=1.24.0,<1.25.0' + + - bioconductor-annotationhub >=3.14.0,<3.15.0 + + - bioconductor-batchelor >=1.22.0,<1.23.0 + + - bioconductor-biobase >=2.66.0,<2.67.0 + + - bioconductor-biocparallel >=1.40.0,<1.41.0 + + - bioconductor-celda >=1.22.0,<1.23.0 + + - bioconductor-celldex >=1.16.0,<1.17.0 + + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + + - bioconductor-delayedarray >=0.32.0,<0.33.0 + + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + + - bioconductor-deseq2 >=1.46.0,<1.47.0 + + - bioconductor-dropletutils >=1.26.0,<1.27.0 + + - bioconductor-eds >=1.8.0,<1.9.0 + + - bioconductor-ensembldb >=2.30.0,<2.31.0 + + - bioconductor-experimenthub >=2.14.0,<2.15.0 + + - bioconductor-ggtree >=3.14.0,<3.15.0 + + - bioconductor-gseabase >=1.68.0,<1.69.0 + + - bioconductor-gsva >=2.0.0,<2.1.0 + + - bioconductor-gsvadata >=1.42.0,<1.43.0 + + - bioconductor-limma >=3.62.0,<3.63.0 + + - bioconductor-mast >=1.32.0,<1.33.0 + + - bioconductor-multtest >=2.62.0,<2.63.0 + + - bioconductor-s4vectors >=0.44.0,<0.45.0 + + - bioconductor-scater >=1.34.0,<1.35.0 + + - bioconductor-scdblfinder >=1.20.0,<1.21.0 + + - bioconductor-scds >=1.22.0,<1.23.0 + + - bioconductor-scmerge >=1.22.0,<1.23.0 + + - bioconductor-scran >=1.34.0,<1.35.0 + + - bioconductor-scrnaseq >=2.20.0,<2.21.0 + + - bioconductor-scuttle >=1.16.0,<1.17.0 + + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + + - bioconductor-singler >=2.8.0,<2.9.0 + + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + + - bioconductor-sva >=3.54.0,<3.55.0 + + - bioconductor-tenxpbmcdata >=1.24.0,<1.25.0 + + - bioconductor-trajectoryutils >=1.14.0,<1.15.0 + + - bioconductor-tscan >=1.44.0,<1.45.0 + + - bioconductor-tximport >=1.34.0,<1.35.0 + + - bioconductor-zellkonverter >=1.16.0,<1.17.0 + + - bioconductor-zinbwave >=1.28.0,<1.29.0 + - r-anndata + - r-ape + - r-base + - r-circlize + - r-cluster + - r-colorspace + - r-colourpicker + - r-cowplot + - r-data.table + - r-dplyr + - r-dt - - 'r-enrichr >=3.2' + + - r-enrichr >=3.2 + - r-fields + - r-ggplot2 + - r-ggplotify + - r-ggrepel + - r-gridextra + - r-igraph + - r-kernsmooth + - r-magrittr - - 'r-matrix >=1.5-3' + + - r-matrix >=1.6-1 + - r-matrixstats + - r-metap + - r-msigdbr + - r-plotly + - r-plyr + - r-r.utils + - r-reshape2 - - 'r-reticulate >=1.14' + + - r-reticulate >=1.14 + - r-rlang + - r-rmarkdown + - r-rocr + - r-rtsne - - 'r-seurat >=3.1.3' + + - r-seurat >=3.1.3 + - r-shiny + - r-shinyalert + - r-shinycssloaders + - r-shinyjs + - r-soupx + + - r-stringr + - r-tibble - - 'r-vam >=0.5.3' + + - r-tidyr + + - r-vam >=0.5.3 + - r-withr + - r-yaml + run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-batchelor >=1.18.0,<1.19.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-celda >=1.18.0,<1.19.0' - - 'bioconductor-celldex >=1.12.0,<1.13.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-dropletutils >=1.22.0,<1.23.0' - - 'bioconductor-eds >=1.4.0,<1.5.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-gsva >=1.50.0,<1.51.0' - - 'bioconductor-gsvadata >=1.38.0,<1.39.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-mast >=1.28.0,<1.29.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scdblfinder >=1.16.0,<1.17.0' - - 'bioconductor-scds >=1.18.0,<1.19.0' - - 'bioconductor-scmerge >=1.18.0,<1.19.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-scrnaseq >=2.16.0,<2.17.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-singler >=2.4.0,<2.5.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' - - 'bioconductor-tenxpbmcdata >=1.20.0,<1.21.0' - - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' - - 'bioconductor-tscan >=1.40.0,<1.41.0' - - 'bioconductor-tximport >=1.30.0,<1.31.0' - - 'bioconductor-zellkonverter >=1.12.0,<1.13.0' - - 'bioconductor-zinbwave >=1.24.0,<1.25.0' + + - bioconductor-annotationhub >=3.14.0,<3.15.0 + + - bioconductor-batchelor >=1.22.0,<1.23.0 + + - bioconductor-biobase >=2.66.0,<2.67.0 + + - bioconductor-biocparallel >=1.40.0,<1.41.0 + + - bioconductor-celda >=1.22.0,<1.23.0 + + - bioconductor-celldex >=1.16.0,<1.17.0 + + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + + - bioconductor-delayedarray >=0.32.0,<0.33.0 + + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + + - bioconductor-deseq2 >=1.46.0,<1.47.0 + + - bioconductor-dropletutils >=1.26.0,<1.27.0 + + - bioconductor-eds >=1.8.0,<1.9.0 + + - bioconductor-ensembldb >=2.30.0,<2.31.0 + + - bioconductor-experimenthub >=2.14.0,<2.15.0 + + - bioconductor-ggtree >=3.14.0,<3.15.0 + + - bioconductor-gseabase >=1.68.0,<1.69.0 + + - bioconductor-gsva >=2.0.0,<2.1.0 + + - bioconductor-gsvadata >=1.42.0,<1.43.0 + + - bioconductor-limma >=3.62.0,<3.63.0 + + - bioconductor-mast >=1.32.0,<1.33.0 + + - bioconductor-multtest >=2.62.0,<2.63.0 + + - bioconductor-s4vectors >=0.44.0,<0.45.0 + + - bioconductor-scater >=1.34.0,<1.35.0 + + - bioconductor-scdblfinder >=1.20.0,<1.21.0 + + - bioconductor-scds >=1.22.0,<1.23.0 + + - bioconductor-scmerge >=1.22.0,<1.23.0 + + - bioconductor-scran >=1.34.0,<1.35.0 + + - bioconductor-scrnaseq >=2.20.0,<2.21.0 + + - bioconductor-scuttle >=1.16.0,<1.17.0 + + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + + - bioconductor-singler >=2.8.0,<2.9.0 + + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + + - bioconductor-sva >=3.54.0,<3.55.0 + + - bioconductor-tenxpbmcdata >=1.24.0,<1.25.0 + + - bioconductor-trajectoryutils >=1.14.0,<1.15.0 + + - bioconductor-tscan >=1.44.0,<1.45.0 + + - bioconductor-tximport >=1.34.0,<1.35.0 + + - bioconductor-zellkonverter >=1.16.0,<1.17.0 + + - bioconductor-zinbwave >=1.28.0,<1.29.0 + - r-anndata + - r-ape + - r-base + - r-circlize + - r-cluster + - r-colorspace + - r-colourpicker + - r-cowplot + - r-data.table + - r-dplyr + - r-dt - - 'r-enrichr >=3.2' + + - r-enrichr >=3.2 + - r-fields + - r-ggplot2 + - r-ggplotify + - r-ggrepel + - r-gridextra + - r-igraph + - r-kernsmooth + - r-magrittr - - 'r-matrix >=1.5-3' + + - r-matrix >=1.6-1 + - r-matrixstats + - r-metap + - r-msigdbr + - r-plotly + - r-plyr + - r-r.utils + - r-reshape2 - - 'r-reticulate >=1.14' + + - r-reticulate >=1.14 + - r-rlang + - r-rmarkdown + - r-rocr + - r-rtsne - - 'r-seurat >=3.1.3' + + - r-seurat >=3.1.3 + - r-shiny + - r-shinyalert + - r-shinycssloaders + - r-shinyjs + - r-soupx + + - r-stringr + - r-tibble - - 'r-vam >=0.5.3' + + - r-tidyr + + - r-vam >=0.5.3 + - r-withr + - r-yaml + +source: + md5: bb7bd2d338add88f67814720ea9b34b6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data' - description: 'The Single Cell Toolkit (SCTK) in the singleCellTK package provides an interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. SCTK allows users to seamlessly integrate tools from various packages at different stages of the analysis workflow. A general "a la carte" workflow gives users the ability access to multiple methods for data importing, calculation of general QC metrics, doublet detection, ambient RNA estimation and removal, filtering, normalization, batch correction or integration, dimensionality reduction, 2-D embedding, clustering, marker detection, differential expression, cell type labeling, pathway analysis, and data exporting. Curated workflows can be used to run Seurat and Celda. Streamlined quality control can be performed on the command line using the SCTK-QC pipeline. Users can analyze their data using commands in the R console or by using an interactive Shiny Graphical User Interface (GUI). Specific analyses or entire workflows can be summarized and shared with comprehensive HTML reports generated by Rmarkdown. Additional documentation and vignettes can be found at camplab.net/sctk.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-singlemoleculefootprinting/meta.yaml b/recipes/bioconductor-singlemoleculefootprinting/meta.yaml index 0a49754cd4e22..1ae5534d51a3f 100644 --- a/recipes/bioconductor-singlemoleculefootprinting/meta.yaml +++ b/recipes/bioconductor-singlemoleculefootprinting/meta.yaml @@ -1,57 +1,90 @@ -{% set version = "1.10.0" %} +{% set version = "2.0.0" %} {% set name = "SingleMoleculeFootprinting" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SingleMoleculeFootprinting provides functions to analyze Single Molecule Footprinting (SMF) data. Following the workflow exemplified in its vignette, the user will be able to perform basic data analysis of SMF data with minimal coding effort. Starting from an aligned bam file, we show how to perform quality controls over sequencing libraries, extract methylation information at the single molecule level accounting for the two possible kind of SMF experiments (single enzyme or double enzyme), classify single molecules based on their patterns of molecular occupancy, plot SMF information at a given genomic location. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Analysis tools for Single Molecule Footprinting (SMF) data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dcdbbace0f6394ce22397640da1dd03f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-singlemoleculefootprinting", max_pin="x.x") }}' - noarch: generic -# Suggests: BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, parallel, rmarkdown, readr, SingleMoleculeFootprintingData, testthat (>= 3.0.0) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, qs, rmarkdown, readr, SingleMoleculeFootprintingData, testthat (>= 3.0.0) requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-quasr >=1.42.0,<1.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-quasr >=1.46.0,<1.47.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - r-data.table + - r-dplyr + - r-ggplot2 + - r-ggpointdensity + - r-ggrepel + - r-matrix + - r-patchwork - r-plyr - r-rcolorbrewer + - r-rlang + - r-stringr + - r-tibble + - r-tidyr + - r-tidyverse + - r-viridis + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-quasr >=1.42.0,<1.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-quasr >=1.46.0,<1.47.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - r-data.table + - r-dplyr + - r-ggplot2 + - r-ggpointdensity + - r-ggrepel + - r-matrix + - r-patchwork - r-plyr - r-rcolorbrewer + - r-rlang + - r-stringr + - r-tibble + - r-tidyr + - r-tidyverse + - r-viridis + +source: + md5: ffcca6ebb15db8845361824fd1ffb92f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Analysis tools for Single Molecule Footprinting (SMF) data' - description: 'SingleMoleculeFootprinting is an R package providing functions to analyze Single Molecule Footprinting (SMF) data. Following the workflow exemplified in its vignette, the user will be able to perform basic data analysis of SMF data with minimal coding effort. Starting from an aligned bam file, we show how to perform quality controls over sequencing libraries, extract methylation information at the single molecule level accounting for the two possible kind of SMF experiments (single enzyme or double enzyme), classify single molecules based on their patterns of molecular occupancy, plot SMF information at a given genomic location' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-singlemoleculefootprintingdata/meta.yaml b/recipes/bioconductor-singlemoleculefootprintingdata/meta.yaml index 6a54bd67dd050..3fe3982f02559 100644 --- a/recipes/bioconductor-singlemoleculefootprintingdata/meta.yaml +++ b/recipes/bioconductor-singlemoleculefootprintingdata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "SingleMoleculeFootprintingData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 451ecbdbb964607afbbe3b778b290246 +about: + description: This Data package contains data objcets relevanat for the SingleMoleculeFootprinting package. More specifically, it contains one example of aligned sequencing data (.bam & .bai) necessary to run the SingleMoleculeFootprinting vignette. Additionally, we provide data that are essential for some functions to work correctly such as BaitCapture() and SampleCorrelation(). + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Data supporting the SingleMoleculeFootprinting pkg build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-singlemoleculefootprintingdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 202e6ff943df3b9150db62ee77671784 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Data supporting the SingleMoleculeFootprinting pkg' - description: 'This Data package contains data objcets relevanat for the SingleMoleculeFootprinting package. More specifically, it contains one example of aligned sequencing data (.bam & .bai) necessary to run the SingleMoleculeFootprinting vignette. Additionally, we provide data that are essential for some functions to work correctly such as BaitCapture() and SampleCorrelation().' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-singlemoleculefootprintingdata/post-link.sh b/recipes/bioconductor-singlemoleculefootprintingdata/post-link.sh index a016eff25036b..9747217f3ac57 100644 --- a/recipes/bioconductor-singlemoleculefootprintingdata/post-link.sh +++ b/recipes/bioconductor-singlemoleculefootprintingdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "singlemoleculefootprintingdata-1.10.0" +installBiocDataPackage.sh "singlemoleculefootprintingdata-1.14.0" diff --git a/recipes/bioconductor-singler/meta.yaml b/recipes/bioconductor-singler/meta.yaml index 8bf68ce82b2b1..bbb1fbafdea6e 100644 --- a/recipes/bioconductor-singler/meta.yaml +++ b/recipes/bioconductor-singler/meta.yaml @@ -1,63 +1,70 @@ -{% set version = "2.4.0" %} +{% set version = "2.8.0" %} {% set name = "SingleR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Reference-Based Single-Cell RNA-Seq Annotation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 83651106a9f823febc5859dff16b48a7 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-singler", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scater, scran, scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex # SystemRequirements: C++17 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-assorthead >=1.0.0,<1.1.0 + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-beachmat >=2.18.0,<2.19.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-assorthead >=1.0.0,<1.1.0 + - bioconductor-beachmat >=2.22.0,<2.23.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 9421b0d69afd536c1859d17557a79de1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Reference-Based Single-Cell RNA-Seq Annotation' - description: 'Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-singscore/meta.yaml b/recipes/bioconductor-singscore/meta.yaml index 9fb6b973e6177..83a369d7309b1 100644 --- a/recipes/bioconductor-singscore/meta.yaml +++ b/recipes/bioconductor-singscore/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "singscore" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A simple single-sample gene signature scoring method that uses rank-based statistics to analyze the sample's gene expression profile. It scores the expression activities of gene sets at a single-sample level. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Rank-based single-sample gene set scoring method -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c3ab598fd61c5bb54a842f9738133d24 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-singscore", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-ggrepel @@ -40,12 +42,12 @@ requirements: - r-reshape2 - r-tidyr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-ggrepel @@ -57,13 +59,16 @@ requirements: - r-reshape - r-reshape2 - r-tidyr + +source: + md5: 070e0e54e5c7abf22271db64323404f3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Rank-based single-sample gene set scoring method' - description: 'A simple single-sample gene signature scoring method that uses rank-based statistics to analyze the sample''s gene expression profile. It scores the expression activities of gene sets at a single-sample level.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sipsic/meta.yaml b/recipes/bioconductor-sipsic/meta.yaml index b7be8ce59689b..b731897e5caef 100644 --- a/recipes/bioconductor-sipsic/meta.yaml +++ b/recipes/bioconductor-sipsic/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "SiPSiC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e85e0e9b34b9a1e0a93dd653868061ef +about: + description: Infer biological pathway activity of cells from single-cell RNA-sequencing data by calculating a pathway score for each cell (pathway genes are specified by the user). It is recommended to have the data in Transcripts-Per-Million (TPM) or Counts-Per-Million (CPM) units for best results. Scores may change when adding cells to or removing cells off the data. SiPSiC stands for Single Pathway analysis in Single Cells. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Calculate Pathway Scores for Each Cell in scRNA-Seq Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sipsic", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-matrix run: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-matrix +source: + md5: 83dae26f17bd94c83b20cf42726a065d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Calculate Pathway Scores for Each Cell in scRNA-Seq Data' - description: 'Infer biological pathway activity of cells from single-cell RNA-sequencing data by calculating a pathway score for each cell (pathway genes are specified by the user). It is recommended to have the data in Transcripts-Per-Million (TPM) or Counts-Per-Million (CPM) units for best results. Scores may change when adding cells to or removing cells off the data. SiPSiC stands for Single Pathway analysis in Single Cells.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sitadela/meta.yaml b/recipes/bioconductor-sitadela/meta.yaml index 81f00ad65a55e..ac50dbe5a2272 100644 --- a/recipes/bioconductor-sitadela/meta.yaml +++ b/recipes/bioconductor-sitadela/meta.yaml @@ -1,60 +1,67 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "sitadela" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides an interface to build a unified database of genomic annotations and their coordinates (gene, transcript and exon levels). It is aimed to be used when simple tab-delimited annotations (or simple GRanges objects) are required instead of the more complex annotation Bioconductor packages. Also useful when combinatorial annotation elements are reuired, such as RefSeq coordinates with Ensembl biotypes. Finally, it can download, construct and handle annotations with versioned genes and transcripts (where available, e.g. RefSeq and latest Ensembl). This is particularly useful in precision medicine applications where the latter must be reported. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 109b3096c37f30906c8c009097e45c59 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sitadela", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, BSgenome, knitr, rmarkdown, RMySQL, RUnit requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-rsqlite run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-rsqlite + +source: + md5: 707012bd9511f0c66885f57ee1c177e7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms' - description: 'Provides an interface to build a unified database of genomic annotations and their coordinates (gene, transcript and exon levels). It is aimed to be used when simple tab-delimited annotations (or simple GRanges objects) are required instead of the more complex annotation Bioconductor packages. Also useful when combinatorial annotation elements are reuired, such as RefSeq coordinates with Ensembl biotypes. Finally, it can download, construct and handle annotations with versioned genes and transcripts (where available, e.g. RefSeq and latest Ensembl). This is particularly useful in precision medicine applications where the latter must be reported.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sitepath/meta.yaml b/recipes/bioconductor-sitepath/meta.yaml index 9470f4a08a362..caa73a3af046d 100644 --- a/recipes/bioconductor-sitepath/meta.yaml +++ b/recipes/bioconductor-sitepath/meta.yaml @@ -1,27 +1,33 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "sitePath" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Using site polymorphism is one of the ways to cluster DNA/protein sequences but it is possible for the sequences with the same polymorphism on a single site to be genetically distant. This package is aimed at clustering sequences using site polymorphism and their corresponding phylogenetic trees. By considering their location on the tree, only the structurally adjacent sequences will be clustered. However, the adjacent sequences may not necessarily have the same polymorphism. So a branch-and-bound like algorithm is used to minimize the entropy representing the purity of site polymorphism of each cluster. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Phylogeny-based sequence clustering with site polymorphism -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5742fbe513f4d3cec29d3d3ee714d13 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sitepath", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, devtools, knitr, magick, rmarkdown, testthat requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - bioconductor-ggtree >=3.14.0,<3.15.0 - r-ape - r-aplot - r-base @@ -35,7 +41,7 @@ requirements: - libblas - liblapack run: - - 'bioconductor-ggtree >=3.10.0,<3.11.0' + - bioconductor-ggtree >=3.14.0,<3.15.0 - r-ape - r-aplot - r-base @@ -46,17 +52,16 @@ requirements: - r-rcpp - r-seqinr - r-tidytree - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 63e88d5b3dc83e098747760bb340563a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Phylogeny-based sequence clustering with site polymorphism' - description: 'Using site polymorphism is one of the ways to cluster DNA/protein sequences but it is possible for the sequences with the same polymorphism on a single site to be genetically distant. This package is aimed at clustering sequences using site polymorphism and their corresponding phylogenetic trees. By considering their location on the tree, only the structurally adjacent sequences will be clustered. However, the adjacent sequences may not necessarily have the same polymorphism. So a branch-and-bound like algorithm is used to minimize the entropy representing the purity of site polymorphism of each cluster.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sizepower/meta.yaml b/recipes/bioconductor-sizepower/meta.yaml index bdcda1851859b..1572f476cbe7a 100644 --- a/recipes/bioconductor-sizepower/meta.yaml +++ b/recipes/bioconductor-sizepower/meta.yaml @@ -1,38 +1,20 @@ -{% set version = "1.72.0" %} +{% set version = "1.76.0" %} {% set name = "sizepower" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4edf7f08a26ccaa8ae0d08e17b6ef0cd +about: + description: This package has been prepared to assist users in computing either a sample size or power value for a microarray experimental study. The user is referred to the cited references for technical background on the methodology underpinning these calculations. This package provides support for five types of sample size and power calculations. These five types can be adapted in various ways to encompass many of the standard designs encountered in practice. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Sample Size and Power Calculation in Micorarray Studies build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sizepower", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Sample Size and Power Calculation in Micorarray Studies' - description: 'This package has been prepared to assist users in computing either a sample size or power value for a microarray experimental study. The user is referred to the cited references for technical background on the methodology underpinning these calculations. This package provides support for five types of sample size and power calculations. These five types can be adapted in various ways to encompass many of the standard designs encountered in practice.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' extra: identifiers: - biotools:sizepower @@ -41,4 +23,22 @@ extra: name: bioconductor-sizepower path: recipes/bioconductor-sizepower version: 1.50.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +requirements: + host: + - r-base + run: + - r-base +source: + md5: 53bba3b5f22b789f25f51d04692e3f3b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sketchr/build.sh b/recipes/bioconductor-sketchr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sketchr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sketchr/meta.yaml b/recipes/bioconductor-sketchr/meta.yaml new file mode 100644 index 0000000000000..bf3d8b723800e --- /dev/null +++ b/recipes/bioconductor-sketchr/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.2.0" %} +{% set name = "sketchR" %} +{% set bioc = "3.20" %} + +about: + description: Provides an R interface for various subsampling algorithms implemented in python packages. Currently, interfaces to the geosketch and scSampler python packages are implemented. In addition it also provides diagnostic plots to evaluate the subsampling. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: An R interface for python subsampling/sketching algorithms + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-sketchr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: rmarkdown, knitr, testthat (>= 3.0.0), TENxPBMCData, scuttle, scran, scater, SingleR, celldex, cowplot, SummarizedExperiment, beachmat.hdf5, BiocStyle, BiocManager, SingleCellExperiment +requirements: + host: + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - r-base + - r-dplyr + - r-ggplot2 + - r-reticulate + - r-rlang + - r-scales + run: + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - r-base + - r-dplyr + - r-ggplot2 + - r-reticulate + - r-rlang + - r-scales + +source: + md5: 8e0ff413b98f71050948bdaf582b5d8e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-skewr/meta.yaml b/recipes/bioconductor-skewr/meta.yaml index 4c0aea4605a0e..bec5c9c5cb6eb 100644 --- a/recipes/bioconductor-skewr/meta.yaml +++ b/recipes/bioconductor-skewr/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "skewr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The skewr package is a tool for visualizing the output of the Illumina Human Methylation 450k BeadChip to aid in quality control. It creates a panel of nine plots. Six of the plots represent the density of either the methylated intensity or the unmethylated intensity given by one of three subsets of the 485,577 total probes. These subsets include Type I-red, Type I-green, and Type II.The remaining three distributions give the density of the Beta-values for these same three subsets. Each of the nine plots optionally displays the distributions of the "rs" SNP probes and the probes associated with imprinted genes as series of 'tick' marks located above the x-axis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 083671e386afa1b9ec5766e6a8c50bba build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-skewr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: GEOquery, knitr, minfiData requirements: host: - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-methylumi >=2.48.0,<2.49.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-watermelon >=2.8.0,<2.9.0' + - bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0 + - bioconductor-methylumi >=2.52.0,<2.53.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-watermelon >=2.12.0,<2.13.0 - r-base - r-mixsmsn - r-rcolorbrewer run: - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' - - 'bioconductor-methylumi >=2.48.0,<2.49.0' - - 'bioconductor-minfi >=1.48.0,<1.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-watermelon >=2.8.0,<2.9.0' + - bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0 + - bioconductor-methylumi >=2.52.0,<2.53.0 + - bioconductor-minfi >=1.52.0,<1.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-watermelon >=2.12.0,<2.13.0 - r-base - r-mixsmsn - r-rcolorbrewer + +source: + md5: c360cf904dbc931e77d6ce9159ad01fc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Visualize Intensities Produced by Illumina''s Human Methylation 450k BeadChip' - description: 'The skewr package is a tool for visualizing the output of the Illumina Human Methylation 450k BeadChip to aid in quality control. It creates a panel of nine plots. Six of the plots represent the density of either the methylated intensity or the unmethylated intensity given by one of three subsets of the 485,577 total probes. These subsets include Type I-red, Type I-green, and Type II.The remaining three distributions give the density of the Beta-values for these same three subsets. Each of the nine plots optionally displays the distributions of the "rs" SNP probes and the probes associated with imprinted genes as series of ''tick'' marks located above the x-axis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-slalom/build_failure.osx-64.yaml b/recipes/bioconductor-slalom/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..55752d97c8dec --- /dev/null +++ b/recipes/bioconductor-slalom/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 09f5ad3402b333ed26a4fb52ef2726d72ddbf72e4040ab3f20ff7ecaffcfee4e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-slalom-1.28.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-slalom-1.28.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-slalom-1.28.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-slalom_1735280512703/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-slalom_1735280512703/work/conda_build.sh']' returned non-zero exit status 1. + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-slalom-1.28.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-slalom-1.28.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-slalom-1.28.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-slalom-1.28.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-slalom-1.28.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-slalom-1.28.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-slalom-1.28.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-slalom-1.28.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-slalom-1.28.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/BH/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/BH/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c slalom-classes.cpp -o slalom-classes.o +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-slalom/meta.yaml b/recipes/bioconductor-slalom/meta.yaml index 9a66e56b5ce25..50c263c681fde 100644 --- a/recipes/bioconductor-slalom/meta.yaml +++ b/recipes/bioconductor-slalom/meta.yaml @@ -1,58 +1,63 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "slalom" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: slalom is a scalable modelling framework for single-cell RNA-seq data that uses gene set annotations to dissect single-cell transcriptome heterogeneity, thereby allowing to identify biological drivers of cell-to-cell variability and model confounding factors. The method uses Bayesian factor analysis with a latent variable model to identify active pathways (selected by the user, e.g. KEGG pathways) that explain variation in a single-cell RNA-seq dataset. This an R/C++ implementation of the f-scLVM Python package. See the publication describing the method at https://doi.org/10.1186/s13059-017-1334-8. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cf8b2aec440cd0fd79260a1f0199db2f build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-slalom", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rhdf5, rmarkdown, scater, testthat requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bh - r-ggplot2 - - 'r-rcpp >=0.12.8' + - r-rcpp >=0.12.8 - r-rcpparmadillo - r-rsvd - libblas - liblapack run: - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-bh - r-ggplot2 - - 'r-rcpp >=0.12.8' + - r-rcpp >=0.12.8 - r-rcpparmadillo - r-rsvd - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: e9156957107ed916936ebd9c062336f4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data' - description: 'slalom is a scalable modelling framework for single-cell RNA-seq data that uses gene set annotations to dissect single-cell transcriptome heterogeneity, thereby allowing to identify biological drivers of cell-to-cell variability and model confounding factors. The method uses Bayesian factor analysis with a latent variable model to identify active pathways (selected by the user, e.g. KEGG pathways) that explain variation in a single-cell RNA-seq dataset. This an R/C++ implementation of the f-scLVM Python package. See the publication describing the method at https://doi.org/10.1186/s13059-017-1334-8.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-slingshot/meta.yaml b/recipes/bioconductor-slingshot/meta.yaml index 6031c6d4802c9..46555663dc7f5 100644 --- a/recipes/bioconductor-slingshot/meta.yaml +++ b/recipes/bioconductor-slingshot/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "2.10.0" %} +{% set version = "2.14.0" %} {% set name = "slingshot" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides functions for inferring continuous, branching lineage structures in low-dimensional data. Slingshot was designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering. It is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Tools for ordering single-cell sequencing -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 556fe5835a602547c3475065eb5c11d0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-slingshot", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, BiocStyle, clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr requirements: host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-trajectoryutils >=1.14.0,<1.15.0 - r-base - r-igraph - r-matrixstats - - 'r-princurve >=2.0.4' + - r-princurve >=2.0.4 run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-trajectoryutils >=1.14.0,<1.15.0 - r-base - r-igraph - r-matrixstats - - 'r-princurve >=2.0.4' + - r-princurve >=2.0.4 + +source: + md5: 127a8d3a7c6cb6521059f882b12a9c8e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Tools for ordering single-cell sequencing' - description: 'Provides functions for inferring continuous, branching lineage structures in low-dimensional data. Slingshot was designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering. It is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.' -extra: - container: - extended-base: true + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-slqpcr/meta.yaml b/recipes/bioconductor-slqpcr/meta.yaml index 51064b62afbb9..127859161439c 100644 --- a/recipes/bioconductor-slqpcr/meta.yaml +++ b/recipes/bioconductor-slqpcr/meta.yaml @@ -1,39 +1,20 @@ -{% set version = "1.68.0" %} +{% set version = "1.72.0" %} {% set name = "SLqPCR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 72759fb6b62f3852f458e695318c0f6f +about: + description: Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-slqpcr", max_pin="x.x") }}' - noarch: generic -# Suggests: RColorBrewer -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH' - description: 'Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: identifiers: - biotools:slqpcr @@ -42,4 +23,23 @@ extra: name: bioconductor-slqpcr path: recipes/bioconductor-slqpcr version: 1.46.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: RColorBrewer +requirements: + host: + - r-base + run: + - r-base +source: + md5: 7bf08a56b19db7f31c3c36e65a760b98 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-smad/meta.yaml b/recipes/bioconductor-smad/meta.yaml index 1fe978fb29b01..e05cb0aedc076 100644 --- a/recipes/bioconductor-smad/meta.yaml +++ b/recipes/bioconductor-smad/meta.yaml @@ -1,30 +1,36 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "SMAD" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Assigning probability scores to protein interactions captured in affinity purification mass spectrometry (AP-MS) expriments to infer protein-protein interactions. The output would facilitate non-specific background removal as contaminants are commonly found in AP-MS data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Statistical Modelling of AP-MS Data (SMAD) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 65f0eba6ed0bf086797b95b2c9da6dd6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-smad", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, BiocStyle requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-dplyr - - 'r-magrittr >=1.5' - - 'r-rcpp >=1.0.0' + - r-magrittr >=1.5 + - r-rcpp >=1.0.0 - r-rcppalgos - r-tidyr - libblas @@ -32,21 +38,20 @@ requirements: run: - r-base - r-dplyr - - 'r-magrittr >=1.5' - - 'r-rcpp >=1.0.0' + - r-magrittr >=1.5 + - r-rcpp >=1.0.0 - r-rcppalgos - r-tidyr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: aadca1bedea5db4730f49638cbc0bdd0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Statistical Modelling of AP-MS Data (SMAD)' - description: 'Assigning probability scores to protein interactions captured in affinity purification mass spectrometry (AP-MS) expriments to infer protein-protein interactions. The output would facilitate non-specific background removal as contaminants are commonly found in AP-MS data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-smartid/build.sh b/recipes/bioconductor-smartid/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-smartid/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-smartid/meta.yaml b/recipes/bioconductor-smartid/meta.yaml new file mode 100644 index 0000000000000..9236306087cd6 --- /dev/null +++ b/recipes/bioconductor-smartid/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.2.0" %} +{% set name = "smartid" %} +{% set bioc = "3.20" %} + +about: + description: This package enables automated selection of group specific signature, especially for rare population. The package is developed for generating specifc lists of signature genes based on Term Frequency-Inverse Document Frequency (TF-IDF) modified methods. It can also be used as a new gene-set scoring method or data transformation method. Multiple visualization functions are implemented in this package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Scoring and Marker Selection Method Based on Modified TF-IDF + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-smartid", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, dbscan, ggpubr, knitr, rmarkdown, scater, splatter, testthat (>= 3.0.0), tidytext, UpSetR +requirements: + host: + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-dplyr + - r-ggplot2 + - r-matrix + - r-mclust + - r-mixtools + - r-tidyr + run: + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-dplyr + - r-ggplot2 + - r-matrix + - r-mclust + - r-mixtools + - r-tidyr + +source: + md5: e34221de22ae4cbc80203960aaaaf335 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-smite/meta.yaml b/recipes/bioconductor-smite/meta.yaml index 84c7ff35a230a..e10737c3f038d 100644 --- a/recipes/bioconductor-smite/meta.yaml +++ b/recipes/bioconductor-smite/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "SMITE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package builds on the Epimods framework which facilitates finding weighted subnetworks ("modules") on Illumina Infinium 27k arrays using the SpinGlass algorithm, as implemented in the iGraph package. We have created a class of gene centric annotations associated with p-values and effect sizes and scores from any researchers prior statistical results to find functional modules. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Significance-based Modules Integrating the Transcriptome and Epigenome -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 47c578785a426c3c7850880ed58033e8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-smite", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:smite + - doi:10.1186/s12859-017-1477-3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-bionet >=1.62.0,<1.63.0' - - 'bioconductor-genelendatabase >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-goseq >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-bionet >=1.66.0,<1.67.0 + - bioconductor-genelendatabase >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-goseq >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-reactome.db >=1.89.0,<1.90.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-hmisc @@ -40,34 +47,33 @@ requirements: - r-plyr - r-scales run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-bionet >=1.62.0,<1.63.0' - - 'bioconductor-genelendatabase >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-goseq >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-reactome.db >=1.86.0,<1.87.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-bionet >=1.66.0,<1.67.0 + - bioconductor-genelendatabase >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-goseq >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-reactome.db >=1.89.0,<1.90.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-hmisc - r-igraph - r-plyr - r-scales + +source: + md5: 31df3cd19d2ba3d0a2453ab18a80b51c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Significance-based Modules Integrating the Transcriptome and Epigenome' - description: 'This package builds on the Epimods framework which facilitates finding weighted subnetworks ("modules") on Illumina Infinium 27k arrays using the SpinGlass algorithm, as implemented in the iGraph package. We have created a class of gene centric annotations associated with p-values and effect sizes and scores from any researchers prior statistical results to find functional modules.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:smite - - doi:10.1186/s12859-017-1477-3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-smokingmouse/meta.yaml b/recipes/bioconductor-smokingmouse/meta.yaml index 95d226795b7e7..71688a05c7140 100644 --- a/recipes/bioconductor-smokingmouse/meta.yaml +++ b/recipes/bioconductor-smokingmouse/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "smokingMouse" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0c2fad6bf0e911ae8c140c02bc29150e +about: + description: This is an ExperimentHub package that provides access to the data at the gene, exon, transcript and junction level used in the analyses of the smokingMouse project. See https://github.com/LieberInstitute/smokingMouse_Indirects. This datasets contain the expression counts of genes, transcripts, exons and exon-exon junctions across 208 mice samples from pup and adult brains and adult blood. They also contain relevant information of these samples and features, such as conditions, QC metrics and if they were used after filtering steps and also if the features were differently expressed in the different experiments. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Provides access to smokingMouse project data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-smokingmouse", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: ExperimentHub, AnnotationHubData, BiocStyle, covr, ExperimentHubData, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) requirements: host: @@ -26,13 +24,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7a530bd77d1c17a739dd2e070ed1f4b8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Provides access to smokingMouse project data' - description: 'This is an ExperimentHub package that provides access to the data at the gene, exon, transcript and junction level used in the analyses of the smokingMouse project. See https://github.com/LieberInstitute/smokingMouse_Indirects. This datasets contain the expression counts of genes, transcripts, exons and exon-exon junctions across 208 mice samples from pup and adult brains and adult blood. They also contain relevant information of these samples and features, such as conditions, QC metrics and if they were used after filtering steps and also if the features were differently expressed in the different experiments.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-smokingmouse/post-link.sh b/recipes/bioconductor-smokingmouse/post-link.sh index d023daf8a973e..2f6c6fef9a52d 100644 --- a/recipes/bioconductor-smokingmouse/post-link.sh +++ b/recipes/bioconductor-smokingmouse/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "smokingmouse-1.0.0" +installBiocDataPackage.sh "smokingmouse-1.4.0" diff --git a/recipes/bioconductor-smoothclust/build.sh b/recipes/bioconductor-smoothclust/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-smoothclust/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-smoothclust/meta.yaml b/recipes/bioconductor-smoothclust/meta.yaml new file mode 100644 index 0000000000000..6985199a7e3d4 --- /dev/null +++ b/recipes/bioconductor-smoothclust/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.2.0" %} +{% set name = "smoothclust" %} +{% set bioc = "3.20" %} + +about: + description: Method for segmentation of spatial domains and spatially-aware clustering in spatial transcriptomics data. The method generates spatial domains with smooth boundaries by smoothing gene expression profiles across neighboring spatial locations, followed by unsupervised clustering. Spatial domains consisting of consistent mixtures of cell types may then be further investigated by applying cell type compositional analyses or differential analyses. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: smoothclust +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-smoothclust", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: BiocStyle, knitr, STexampleData, scuttle, scran, scater, ggspavis, testthat +requirements: + host: + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-spdep + run: + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-spdep +source: + md5: 0f0e9229aea3dfa58353ce1ac4c0e662 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-snadata/meta.yaml b/recipes/bioconductor-snadata/meta.yaml index 326d0f4f2d6e1..7b755dc4d2c7c 100644 --- a/recipes/bioconductor-snadata/meta.yaml +++ b/recipes/bioconductor-snadata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "SNAData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bfbd447afa550db44aa1db55e227cc10 +about: + description: Data from Wasserman & Faust (1999) "Social Network Analysis" + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Social Networks Analysis Data Examples build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-snadata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: Rgraphviz requirements: host: - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-graph >=1.84.0,<1.85.0 - r-base run: - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 37724640b8892123d6e4fd6f426a2461 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Social Networks Analysis Data Examples' - description: 'Data from Wasserman & Faust (1999) "Social Network Analysis"' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-snadata/post-link.sh b/recipes/bioconductor-snadata/post-link.sh index 15572eae53e04..8ad48385b1415 100644 --- a/recipes/bioconductor-snadata/post-link.sh +++ b/recipes/bioconductor-snadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "snadata-1.48.0" +installBiocDataPackage.sh "snadata-1.52.0" diff --git a/recipes/bioconductor-snagee/meta.yaml b/recipes/bioconductor-snagee/meta.yaml index 88fa7034220c6..2515860e84b8c 100644 --- a/recipes/bioconductor-snagee/meta.yaml +++ b/recipes/bioconductor-snagee/meta.yaml @@ -1,40 +1,21 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "SNAGEE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Signal-to-Noise applied to Gene Expression Experiments. Signal-to-noise ratios can be used as a proxy for quality of gene expression studies and samples. The SNRs can be calculated on any gene expression data set as long as gene IDs are available, no access to the raw data files is necessary. This allows to flag problematic studies and samples in any public data set. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Signal-to-Noise applied to Gene Expression Experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: faadcab23b170f71a29ac7fd67b2a5d8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-snagee", max_pin="x.x") }}' - noarch: generic -# Suggests: ALL, hgu95av2.db -requirements: - host: - - 'bioconductor-snageedata >=1.38.0,<1.39.0' - - r-base - run: - - 'bioconductor-snageedata >=1.38.0,<1.39.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Signal-to-Noise applied to Gene Expression Experiments' - description: 'Signal-to-Noise applied to Gene Expression Experiments. Signal-to-noise ratios can be used as a proxy for quality of gene expression studies and samples. The SNRs can be calculated on any gene expression data set as long as gene IDs are available, no access to the raw data files is necessary. This allows to flag problematic studies and samples in any public data set.' + extra: identifiers: - biotools:snagee @@ -44,3 +25,28 @@ extra: path: recipes/bioconductor-snagee version: 1.20.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: ALL, hgu95av2.db +requirements: + host: + - bioconductor-snageedata >=1.42.0,<1.43.0 + - r-base + run: + - bioconductor-snageedata >=1.42.0,<1.43.0 + - r-base + +source: + md5: ca322a39ca0a32a55a45b53bfda91db9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-snageedata/meta.yaml b/recipes/bioconductor-snageedata/meta.yaml index 06c4621e7b240..adf68db18e777 100644 --- a/recipes/bioconductor-snageedata/meta.yaml +++ b/recipes/bioconductor-snageedata/meta.yaml @@ -1,24 +1,27 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "SNAGEEdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bfd0a2689cb9ac612cb2f8995c3a03d5 +about: + description: SNAGEE data - gene list and correlation matrix + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: SNAGEE data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-snageedata", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-snageedata + path: recipes/bioconductor-snageedata + version: 1.16.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: ALL, hgu95av2.db, SNAGEE requirements: host: @@ -26,18 +29,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ad1629bee4e1cb85c3dfe006369b272e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'SNAGEE data' - description: 'SNAGEE data - gene list and correlation matrix' -extra: - parent_recipe: - name: bioconductor-snageedata - path: recipes/bioconductor-snageedata - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-snageedata/post-link.sh b/recipes/bioconductor-snageedata/post-link.sh index 5e8bb8a522c3c..d0e034326dbd2 100644 --- a/recipes/bioconductor-snageedata/post-link.sh +++ b/recipes/bioconductor-snageedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "snageedata-1.38.0" +installBiocDataPackage.sh "snageedata-1.42.0" diff --git a/recipes/bioconductor-snapcount/meta.yaml b/recipes/bioconductor-snapcount/meta.yaml index e40c86fed787a..2190674bdb04e 100644 --- a/recipes/bioconductor-snapcount/meta.yaml +++ b/recipes/bioconductor-snapcount/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "snapcount" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: snapcount is a client interface to the Snaptron webservices which support querying by gene name or genomic region. Results include raw expression counts derived from alignment of RNA-seq samples and/or various summarized measures of expression across one or more regions/genes per-sample (e.g. percent spliced in). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8efa036bfe73acf9c31a279b3c365ae7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-snapcount", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocManager, bit64, covr, knitcitations, knitr (>= 1.6), devtools, BiocStyle (>= 2.5.19), rmarkdown (>= 0.9.5), testthat (>= 2.1.0) requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-data.table @@ -37,9 +39,9 @@ requirements: - r-rlang - r-stringr run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-data.table @@ -51,13 +53,16 @@ requirements: - r-r6 - r-rlang - r-stringr + +source: + md5: b03544b9f4295e499bc16b54f5b607d9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts' - description: 'snapcount is a client interface to the Snaptron webservices which support querying by gene name or genomic region. Results include raw expression counts derived from alignment of RNA-seq samples and/or various summarized measures of expression across one or more regions/genes per-sample (e.g. percent spliced in).' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-snifter/meta.yaml b/recipes/bioconductor-snifter/meta.yaml index 2da36a360a549..ef25029b6bb34 100644 --- a/recipes/bioconductor-snifter/meta.yaml +++ b/recipes/bioconductor-snifter/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "snifter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a6cfc8a05013cd2d050a1adba2b3fe4d +about: + description: Provides an R wrapper for the implementation of FI-tSNE from the python package openTNSE. See Poličar et al. (2019) and the algorithm described by Linderman et al. (2018) . + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: R wrapper for the python openTSNE library build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-snifter", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 - r-assertthat - r-base - r-irlba - r-reticulate run: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 - r-assertthat - r-base - r-irlba - r-reticulate +source: + md5: caef9a718d8c2b83f5ded7a99d64f4cf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'R wrapper for the python openTSNE library' - description: 'Provides an R wrapper for the implementation of FI-tSNE from the python package openTNSE. See Poličar et al. (2019) and the algorithm described by Linderman et al. (2018) .' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-snm/meta.yaml b/recipes/bioconductor-snm/meta.yaml index 16a1786338618..e0612809d46d1 100644 --- a/recipes/bioconductor-snm/meta.yaml +++ b/recipes/bioconductor-snm/meta.yaml @@ -1,47 +1,53 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "snm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SNM is a modeling strategy especially designed for normalizing high-throughput genomic data. The underlying premise of our approach is that your data is a function of what we refer to as study-specific variables. These variables are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Supervised Normalization of Microarrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 103ab8eb4cca35d12c53c48615ebd5da build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-snm", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:snm + parent_recipe: + name: bioconductor-snm + path: recipes/bioconductor-snm + version: 1.28.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base - r-corpcor - - 'r-lme4 >=1.0' + - r-lme4 >=1.0 run: - r-base - r-corpcor - - 'r-lme4 >=1.0' + - r-lme4 >=1.0 + +source: + md5: fabb2d7c590c489183587ead5e6da8b1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Supervised Normalization of Microarrays' - description: 'SNM is a modeling strategy especially designed for normalizing high-throughput genomic data. The underlying premise of our approach is that your data is a function of what we refer to as study-specific variables. These variables are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:snm - parent_recipe: - name: bioconductor-snm - path: recipes/bioconductor-snm - version: 1.28.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-snpediar/meta.yaml b/recipes/bioconductor-snpediar/meta.yaml index 163a5977bdb6d..ca11e034f075e 100644 --- a/recipes/bioconductor-snpediar/meta.yaml +++ b/recipes/bioconductor-snpediar/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "SNPediaR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SNPediaR provides some tools for downloading and parsing data from the SNPedia web site . The implemented functions allow users to import the wiki text available in SNPedia pages and to extract the most relevant information out of them. If some information in the downloaded pages is not automatically processed by the library functions, users can easily implement their own parsers to access it in an efficient way. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Query data from SNPedia -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 25d5eec5081ccfac687eba26102eb826 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-snpediar", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:snpediar + - doi:10.1007/978-1-4419-9863-7_1039 + parent_recipe: + name: bioconductor-snpediar + path: recipes/bioconductor-snpediar + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: @@ -29,21 +40,16 @@ requirements: - r-base - r-jsonlite - r-rcurl + +source: + md5: 158429720541b2c5e73d891b2393d308 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Query data from SNPedia' - description: 'SNPediaR provides some tools for downloading and parsing data from the SNPedia web site . The implemented functions allow users to import the wiki text available in SNPedia pages and to extract the most relevant information out of them. If some information in the downloaded pages is not automatically processed by the library functions, users can easily implement their own parsers to access it in an efficient way.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:snpediar - - doi:10.1007/978-1-4419-9863-7_1039 - parent_recipe: - name: bioconductor-snpediar - path: recipes/bioconductor-snpediar - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-snphood/meta.yaml b/recipes/bioconductor-snphood/meta.yaml index 9b8303698581a..68fe6cd820a7b 100644 --- a/recipes/bioconductor-snphood/meta.yaml +++ b/recipes/bioconductor-snphood/meta.yaml @@ -1,38 +1,50 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "SNPhood" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: To date, thousands of single nucleotide polymorphisms (SNPs) have been found to be associated with complex traits and diseases. However, the vast majority of these disease-associated SNPs lie in the non-coding part of the genome, and are likely to affect regulatory elements, such as enhancers and promoters, rather than function of a protein. Thus, to understand the molecular mechanisms underlying genetic traits and diseases, it becomes increasingly important to study the effect of a SNP on nearby molecular traits such as chromatin environment or transcription factor (TF) binding. Towards this aim, we developed SNPhood, a user-friendly *Bioconductor* R package to investigate and visualize the local neighborhood of a set of SNPs of interest for NGS data such as chromatin marks or transcription factor binding sites from ChIP-Seq or RNA- Seq experiments. SNPhood comprises a set of easy-to-use functions to extract, normalize and summarize reads for a genomic region, perform various data quality checks, normalize read counts using additional input files, and to cluster and visualize the regions according to the binding pattern. The regions around each SNP can be binned in a user-defined fashion to allow for analysis of very broad patterns as well as a detailed investigation of specific binding shapes. Furthermore, SNPhood supports the integration with genotype information to investigate and visualize genotype-specific binding patterns. Finally, SNPhood can be employed for determining, investigating, and visualizing allele-specific binding patterns around the SNPs of interest. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: 'SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5a30ae405bebdb97e51cb2782debcbf build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-snphood", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:snphood + - doi:10.1093/bioinformatics/btw127 + parent_recipe: + name: bioconductor-snphood + path: recipes/bioconductor-snphood + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-checkmate - r-cluster @@ -43,18 +55,19 @@ requirements: - r-rcolorbrewer - r-reshape2 - r-scales + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-checkmate - r-cluster @@ -65,21 +78,16 @@ requirements: - r-rcolorbrewer - r-reshape2 - r-scales + +source: + md5: 220cd6947cc7137ce0e436cf3b042232 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 3)' - summary: 'SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data' - description: 'To date, thousands of single nucleotide polymorphisms (SNPs) have been found to be associated with complex traits and diseases. However, the vast majority of these disease-associated SNPs lie in the non-coding part of the genome, and are likely to affect regulatory elements, such as enhancers and promoters, rather than function of a protein. Thus, to understand the molecular mechanisms underlying genetic traits and diseases, it becomes increasingly important to study the effect of a SNP on nearby molecular traits such as chromatin environment or transcription factor (TF) binding. Towards this aim, we developed SNPhood, a user-friendly *Bioconductor* R package to investigate and visualize the local neighborhood of a set of SNPs of interest for NGS data such as chromatin marks or transcription factor binding sites from ChIP-Seq or RNA- Seq experiments. SNPhood comprises a set of easy-to-use functions to extract, normalize and summarize reads for a genomic region, perform various data quality checks, normalize read counts using additional input files, and to cluster and visualize the regions according to the binding pattern. The regions around each SNP can be binned in a user-defined fashion to allow for analysis of very broad patterns as well as a detailed investigation of specific binding shapes. Furthermore, SNPhood supports the integration with genotype information to investigate and visualize genotype-specific binding patterns. Finally, SNPhood can be employed for determining, investigating, and visualizing allele-specific binding patterns around the SNPs of interest.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:snphood - - doi:10.1093/bioinformatics/btw127 - parent_recipe: - name: bioconductor-snphood - path: recipes/bioconductor-snphood - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-snphooddata/meta.yaml b/recipes/bioconductor-snphooddata/meta.yaml index b7e1b79ba3652..6f79507c5492d 100644 --- a/recipes/bioconductor-snphooddata/meta.yaml +++ b/recipes/bioconductor-snphooddata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "SNPhoodData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 72ac86008c225c71df946cc8a7de1fa1 +about: + description: This companion package for SNPhood provides some example datasets of a larger size than allowed for the SNPhood package. They include full and real-world examples for performing analyses with the SNPhood package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Additional and more complex example data for the SNPhood package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-snphooddata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle,knitr,rmarkdown requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 66d3827ba213bcbf04e5cde90529f975 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'LGPL (>= 3)' - summary: 'Additional and more complex example data for the SNPhood package' - description: 'This companion package for SNPhood provides some example datasets of a larger size than allowed for the SNPhood package. They include full and real-world examples for performing analyses with the SNPhood package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-snphooddata/post-link.sh b/recipes/bioconductor-snphooddata/post-link.sh index 7fd81f93fc969..6d424f3876f59 100644 --- a/recipes/bioconductor-snphooddata/post-link.sh +++ b/recipes/bioconductor-snphooddata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "snphooddata-1.32.0" +installBiocDataPackage.sh "snphooddata-1.36.0" diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml index 9e6b83fb2ab62..b37affdffd552 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml @@ -1,50 +1,55 @@ {% set version = "0.99.20" %} {% set name = "SNPlocs.Hsapiens.dbSNP144.GRCh37" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13. WARNING: Note that the GRCh37.p13 genome is a patched version of GRCh37. However the patch doesn''t alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be "injected" in BSgenome.Hsapiens.UCSC.hg19 and they will land at the correct position but this injection will exclude chrM (i.e. nothing will be injected in that sequence).' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: SNP locations for Homo sapiens (dbSNP Build 144) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bd338bb583cacc18f210e871dac79ebf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-snplocs.hsapiens.dbsnp144.grch37", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: bd338bb583cacc18f210e871dac79ebf + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'SNP locations for Homo sapiens (dbSNP Build 144)' - description: 'SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13. WARNING: Note that the GRCh37.p13 genome is a patched version of GRCh37. However the patch doesn''t alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be "injected" in BSgenome.Hsapiens.UCSC.hg19 and they will land at the correct position but this injection will exclude chrM (i.e. nothing will be injected in that sequence).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml index 62e24e4082892..c1d62002803b0 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml @@ -1,55 +1,61 @@ {% set version = "0.99.20" %} {% set name = "SNPlocs.Hsapiens.dbSNP144.GRCh38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 30, 2015, and contain SNPs mapped to reference genome GRCh38.p2 (a patched version of GRCh38 that doesn't alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: SNP locations for Homo sapiens (dbSNP Build 144) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 128c95e327adf72ae137fb5ae58270fc build: - number: 16 + noarch: generic + number: 17 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-snplocs.hsapiens.dbsnp144.grch38", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-snplocs.hsapiens.dbsnp144.grch38 + path: recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38 + version: 0.99.20 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 128c95e327adf72ae137fb5ae58270fc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'SNP locations for Homo sapiens (dbSNP Build 144)' - description: 'SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 30, 2015, and contain SNPs mapped to reference genome GRCh38.p2 (a patched version of GRCh38 that doesn''t alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38.' -extra: - parent_recipe: - name: bioconductor-snplocs.hsapiens.dbsnp144.grch38 - path: recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38 - version: 0.99.20 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/meta.yaml index f6a6fc11e513c..cd13c33066196 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/meta.yaml @@ -1,50 +1,55 @@ {% set version = "0.99.20" %} {% set name = "SNPlocs.Hsapiens.dbSNP149.GRCh38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 149. The source data files used for this package were created by NCBI between November 8-12, 2016, and contain SNPs mapped to reference genome GRCh38.p7 (a patched version of GRCh38 that doesn't alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: SNP locations for Homo sapiens (dbSNP Build 149) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8cf749a8649a53449066b54160a3745c build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-snplocs.hsapiens.dbsnp149.grch38", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 8cf749a8649a53449066b54160a3745c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'SNP locations for Homo sapiens (dbSNP Build 149)' - description: 'SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 149. The source data files used for this package were created by NCBI between November 8-12, 2016, and contain SNPs mapped to reference genome GRCh38.p7 (a patched version of GRCh38 that doesn''t alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/meta.yaml index f066bc2eeae6b..447b54896af06 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/meta.yaml @@ -1,50 +1,55 @@ {% set version = "0.99.20" %} {% set name = "SNPlocs.Hsapiens.dbSNP150.GRCh38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 150. The source data files used for this package were created by NCBI between March 12-14, 2017, and contain SNPs mapped to reference genome GRCh38.p7 (a patched version of GRCh38 that doesn't alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: SNP locations for Homo sapiens (dbSNP Build 150) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 575a7aaa9125d52ca0634b3ac586c9a7 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-snplocs.hsapiens.dbsnp150.grch38", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 575a7aaa9125d52ca0634b3ac586c9a7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'SNP locations for Homo sapiens (dbSNP Build 150)' - description: 'SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 150. The source data files used for this package were created by NCBI between March 12-14, 2017, and contain SNPs mapped to reference genome GRCh38.p7 (a patched version of GRCh38 that doesn''t alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch37/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch37/meta.yaml index 64217e319f370..5f015710d0232 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch37/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch37/meta.yaml @@ -1,50 +1,55 @@ {% set version = "0.99.24" %} {% set name = "SNPlocs.Hsapiens.dbSNP155.GRCh37" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The 929,496,192 SNPs in this package were extracted from the RefSNP JSON files for chromosomes 1-22, X, Y, and MT, located at https://ftp.ncbi.nih.gov/snp/archive/b155/JSON/ (these files were created by NCBI in May 2021). These SNPs can be "injected" in BSgenome.Hsapiens.UCSC.hg19. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Human SNP locations and alleles extracted from dbSNP Build 155 and placed on the GRCh37/hg19 assembly -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9473e23ffc7ae76e630a78324b245da8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-snplocs.hsapiens.dbsnp155.grch37", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 9473e23ffc7ae76e630a78324b245da8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Human SNP locations and alleles extracted from dbSNP Build 155 and placed on the GRCh37/hg19 assembly' - description: 'The 929,496,192 SNPs in this package were extracted from the RefSNP JSON files for chromosomes 1-22, X, Y, and MT, located at https://ftp.ncbi.nih.gov/snp/archive/b155/JSON/ (these files were created by NCBI in May 2021). These SNPs can be "injected" in BSgenome.Hsapiens.UCSC.hg19.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch38/meta.yaml index cfda415a59962..6e5c12a0a2b43 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch38/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch38/meta.yaml @@ -1,50 +1,55 @@ {% set version = "0.99.24" %} {% set name = "SNPlocs.Hsapiens.dbSNP155.GRCh38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The 949,021,448 SNPs in this package were extracted from the RefSNP JSON files for chromosomes 1-22, X, Y, and MT, located at https://ftp.ncbi.nih.gov/snp/archive/b155/JSON/ (these files were created by NCBI in May 2021). These SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or BSgenome.Hsapiens.UCSC.hg38. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Human SNP locations and alleles extracted from dbSNP Build 155 and placed on the GRCh38/hg38 assembly -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a16b7b1f940c3fcc8fd2d78f438fd25c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-snplocs.hsapiens.dbsnp155.grch38", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: a16b7b1f940c3fcc8fd2d78f438fd25c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Human SNP locations and alleles extracted from dbSNP Build 155 and placed on the GRCh38/hg38 assembly' - description: 'The 949,021,448 SNPs in this package were extracted from the RefSNP JSON files for chromosomes 1-22, X, Y, and MT, located at https://ftp.ncbi.nih.gov/snp/archive/b155/JSON/ (these files were created by NCBI in May 2021). These SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or BSgenome.Hsapiens.UCSC.hg38.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-snprelate/meta.yaml b/recipes/bioconductor-snprelate/meta.yaml index 2fac4055b5d28..87bde1de563fa 100644 --- a/recipes/bioconductor-snprelate/meta.yaml +++ b/recipes/bioconductor-snprelate/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "SNPRelate" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed an R package SNPRelate to provide a binary format for single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS format offers the efficient operations specifically designed for integers with two bits, since a SNP could occupy only two bits. SNPRelate is also designed to accelerate two key computations on SNP data using parallel computing for multi-core symmetric multiprocessing computer architectures: Principal Component Analysis (PCA) and relatedness analysis using Identity-By-Descent measures. The SNP GDS format is also used by the GWASTools package with the support of S4 classes and generic functions. The extended GDS format is implemented in the SeqArray package to support the storage of single nucleotide variations (SNVs), insertion/deletion polymorphism (indel) and structural variation calls in whole-genome and whole-exome variant data.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f4e5095c6b99014e02d770e7f4bd5617 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-snprelate", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:snprelate + parent_recipe: + name: bioconductor-snprelate + path: recipes/bioconductor-snprelate + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS, BiocGenerics requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - bioconductor-gdsfmt >=1.42.0,<1.43.0 - r-base - libblas - liblapack run: - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' + - bioconductor-gdsfmt >=1.42.0,<1.43.0 - r-base - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 977eb0e7932e79f2569cd69aefa52784 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3-only - summary: 'Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data' - description: 'Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed an R package SNPRelate to provide a binary format for single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS format offers the efficient operations specifically designed for integers with two bits, since a SNP could occupy only two bits. SNPRelate is also designed to accelerate two key computations on SNP data using parallel computing for multi-core symmetric multiprocessing computer architectures: Principal Component Analysis (PCA) and relatedness analysis using Identity-By-Descent measures. The SNP GDS format is also used by the GWASTools package with the support of S4 classes and generic functions. The extended GDS format is implemented in the SeqArray package to support the storage of single nucleotide variations (SNVs), insertion/deletion polymorphism (indel) and structural variation calls in whole-genome and whole-exome variant data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} - parent_recipe: - name: bioconductor-snprelate - path: recipes/bioconductor-snprelate - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-snpstats/meta.yaml b/recipes/bioconductor-snpstats/meta.yaml index 8843ee6bc567e..86bf67dff795f 100644 --- a/recipes/bioconductor-snpstats/meta.yaml +++ b/recipes/bioconductor-snpstats/meta.yaml @@ -1,59 +1,66 @@ -{% set version = "1.52.0" %} +{% set version = "1.56.0" %} {% set name = "snpStats" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: SnpMatrix and XSnpMatrix classes and methods -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0625c920470937a31fd278cf8bd8982a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-snpstats", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:snpstats + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-snpstats + path: recipes/bioconductor-snpstats + version: 1.30.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: hexbin requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-matrix - r-survival - libblas - liblapack + - zlib run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-matrix - r-survival - build: - - {{ compiler('c') }} - - make + +source: + md5: b473e5e0c8c7fa0ebc3353eb23acede3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3-only' - summary: 'SnpMatrix and XSnpMatrix classes and methods' - description: 'Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:snpstats - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-snpstats - path: recipes/bioconductor-snpstats - version: 1.30.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-soggi/meta.yaml b/recipes/bioconductor-soggi/meta.yaml index b4b76b787681f..23c42eb3e49be 100644 --- a/recipes/bioconductor-soggi/meta.yaml +++ b/recipes/bioconductor-soggi/meta.yaml @@ -1,75 +1,81 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "soGGi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The soGGi package provides a toolset to create genomic interval aggregate/summary plots of signal or motif occurence from BAM and bigWig files as well as PWM, rlelist, GRanges and GAlignments Bioconductor objects. soGGi allows for normalisation, transformation and arithmetic operation on and between summary plot objects as well as grouping and subsetting of plots by GRanges objects and user supplied metadata. Plots are created using the GGplot2 libary to allow user defined manipulation of the returned plot object. Coupled together, soGGi features a broad set of methods to visualise genomics data in the context of groups of genomic intervals such as genes, superenhancers and transcription factor binding events. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6b8a823ad7812fdda198d38b28c00f6f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-soggi", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:soggi + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-soggi + path: recipes/bioconductor-soggi + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-chipseq >=1.52.0,<1.53.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-chipseq >=1.56.0,<1.57.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-chipseq >=1.52.0,<1.53.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-chipseq >=1.56.0,<1.57.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-reshape2 + +source: + md5: 8400cc6bca42772adb6050fd6fd9b3bf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals' - description: 'The soGGi package provides a toolset to create genomic interval aggregate/summary plots of signal or motif occurence from BAM and bigWig files as well as PWM, rlelist, GRanges and GAlignments Bioconductor objects. soGGi allows for normalisation, transformation and arithmetic operation on and between summary plot objects as well as grouping and subsetting of plots by GRanges objects and user supplied metadata. Plots are created using the GGplot2 libary to allow user defined manipulation of the returned plot object. Coupled together, soGGi features a broad set of methods to visualise genomics data in the context of groups of genomic intervals such as genes, superenhancers and transcription factor binding events.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:soggi - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-soggi - path: recipes/bioconductor-soggi - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-somascan.db/meta.yaml b/recipes/bioconductor-somascan.db/meta.yaml index 06a3f52706efd..6323931d8322f 100644 --- a/recipes/bioconductor-somascan.db/meta.yaml +++ b/recipes/bioconductor-somascan.db/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "0.99.7" %} +{% set version = "0.99.10" %} {% set name = "SomaScan.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aa52f4f12dfb2f0aa4c7fe3633de4646 +about: + description: An R package providing extended biological annotations for the SomaScan Assay, a proteomics platform developed by SomaLogic Operating Co., Inc. The annotations in this package were assembled using data from public repositories. For more information about the SomaScan assay and its data, please reference the 'SomaLogic/SomaLogic-Data' GitHub repository. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Somalogic SomaScan Annotation Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-somascan.db", max_pin="x.x") }}' - noarch: generic -# Suggests: annotate, BiocStyle, dplyr, GO.db, hgu95av2.db, KEGGREST, knitr, rmarkdown, SomaDataIO, testthat (>= 3.0.0), withr +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: annotate, BiocStyle, dplyr, GO.db, KEGGREST, knitr, rmarkdown, SomaDataIO, testthat (>= 3.0.0), tibble, withr requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - r-dbi - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4a5ba80cc1038c6adeb887147e691ca8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Somalogic SomaScan Annotation Data' - description: 'An R package providing extended biological annotations for the SomaScan Assay, a proteomics platform developed by SomaLogic Operating Co., Inc. The annotations in this package were assembled using data from public repositories. For more information about the SomaScan assay and its data, please reference the ''SomaLogic/SomaLogic-Data'' GitHub repository.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-somascan.db/post-link.sh b/recipes/bioconductor-somascan.db/post-link.sh index 5a86e22124d74..59752baf12328 100644 --- a/recipes/bioconductor-somascan.db/post-link.sh +++ b/recipes/bioconductor-somascan.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "somascan.db-0.99.7" +installBiocDataPackage.sh "somascan.db-0.99.10" diff --git a/recipes/bioconductor-somaticadata/meta.yaml b/recipes/bioconductor-somaticadata/meta.yaml index 00bdf05078a09..2ef9e44250f07 100644 --- a/recipes/bioconductor-somaticadata/meta.yaml +++ b/recipes/bioconductor-somaticadata/meta.yaml @@ -1,37 +1,37 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "SomatiCAData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 31d9100d6b5fa5f95c59eda9995f2684 +about: + description: An example cancer whole genome sequencing data for the SomatiCA package + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: An example cancer whole genome sequencing data for the SomatiCA package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-somaticadata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5376764d2b06ef447b96d362e80f5ad1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'An example cancer whole genome sequencing data for the SomatiCA package' - description: 'An example cancer whole genome sequencing data for the SomatiCA package' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-somaticadata/post-link.sh b/recipes/bioconductor-somaticadata/post-link.sh index ae240efdbcd9e..384cd0bf6f4f2 100644 --- a/recipes/bioconductor-somaticadata/post-link.sh +++ b/recipes/bioconductor-somaticadata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "somaticadata-1.40.0" +installBiocDataPackage.sh "somaticadata-1.44.0" diff --git a/recipes/bioconductor-somaticcanceralterations/meta.yaml b/recipes/bioconductor-somaticcanceralterations/meta.yaml index 45d47329efb01..cb261f004ec70 100644 --- a/recipes/bioconductor-somaticcanceralterations/meta.yaml +++ b/recipes/bioconductor-somaticcanceralterations/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "SomaticCancerAlterations" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 77b2b0312705c2a9581cdf7aab591db8 +about: + description: Collection of somatic cancer alteration datasets + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Somatic Cancer Alterations build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-somaticcanceralterations", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat, ggbio, ggplot2, knitr requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 89c1936e44be3156ca5170d210806ad9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Somatic Cancer Alterations' - description: 'Collection of somatic cancer alteration datasets' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-somaticcanceralterations/post-link.sh b/recipes/bioconductor-somaticcanceralterations/post-link.sh index d63db0e4c80a7..5691d7209f5f7 100644 --- a/recipes/bioconductor-somaticcanceralterations/post-link.sh +++ b/recipes/bioconductor-somaticcanceralterations/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "somaticcanceralterations-1.38.0" +installBiocDataPackage.sh "somaticcanceralterations-1.42.0" diff --git a/recipes/bioconductor-somaticsignatures/meta.yaml b/recipes/bioconductor-somaticsignatures/meta.yaml index 9db50d019bf36..0b68ca966f61e 100644 --- a/recipes/bioconductor-somaticsignatures/meta.yaml +++ b/recipes/bioconductor-somaticsignatures/meta.yaml @@ -1,70 +1,76 @@ -{% set version = "2.38.0" %} +{% set version = "2.42.0" %} {% set name = "SomaticSignatures" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Somatic Signatures -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46d14334be0098323bc956bade5d5e9e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-somaticsignatures", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:somaticsignatures + parent_recipe: + name: bioconductor-somaticsignatures + path: recipes/bioconductor-somaticsignatures + version: 2.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, parallel, BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations, ggdendro, fastICA, sva requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-ggplot2 - r-nmf - r-proxy - r-reshape2 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-ggbio >=1.50.0,<1.51.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-pcamethods >=1.94.0,<1.95.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-ggbio >=1.54.0,<1.55.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pcamethods >=1.98.0,<1.99.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-ggplot2 - r-nmf - r-proxy - r-reshape2 + +source: + md5: 6ab3beb240433201b14846ada95b12f0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Somatic Signatures' - description: 'The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.' - license_file: LICENSE -extra: - identifiers: - - biotools:somaticsignatures - parent_recipe: - name: bioconductor-somaticsignatures - path: recipes/bioconductor-somaticsignatures - version: 2.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-soybeancdf/meta.yaml b/recipes/bioconductor-soybeancdf/meta.yaml index fa809e0be223a..52541309e2593 100644 --- a/recipes/bioconductor-soybeancdf/meta.yaml +++ b/recipes/bioconductor-soybeancdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "soybeancdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a18e0ba5dbcf2291bdec91091dc528e6 +about: + description: A package containing an environment representing the Soybean.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: soybeancdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-soybeancdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a18e0ba5dbcf2291bdec91091dc528e6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: soybeancdf - description: 'A package containing an environment representing the Soybean.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-soybeanprobe/meta.yaml b/recipes/bioconductor-soybeanprobe/meta.yaml index 37c26efb68ab5..7d342f886d5ee 100644 --- a/recipes/bioconductor-soybeanprobe/meta.yaml +++ b/recipes/bioconductor-soybeanprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "soybeanprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3057a5c387ff35b6c647c4db27041a13 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Soybean\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type soybean build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-soybeanprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3057a5c387ff35b6c647c4db27041a13 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type soybean' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Soybean\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spacemarkers/build.sh b/recipes/bioconductor-spacemarkers/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-spacemarkers/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-spacemarkers/meta.yaml b/recipes/bioconductor-spacemarkers/meta.yaml new file mode 100644 index 0000000000000..3ca487aec4b17 --- /dev/null +++ b/recipes/bioconductor-spacemarkers/meta.yaml @@ -0,0 +1,62 @@ +{% set version = "1.2.1" %} +{% set name = "SpaceMarkers" %} +{% set bioc = "3.20" %} + +about: + description: Spatial transcriptomic technologies have helped to resolve the connection between gene expression and the 2D orientation of tissues relative to each other. However, the limited single-cell resolution makes it difficult to highlight the most important molecular interactions in these tissues. SpaceMarkers, R/Bioconductor software, can help to find molecular interactions, by identifying genes associated with latent space interactions in spatial transcriptomics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Spatial Interaction Markers + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spacemarkers", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: data.table, devtools, dplyr, ggplot2, hrbrthemes, knitr, RColorBrewer, cowplot, readbitmap, rjson, rmarkdown, BiocStyle, testthat (>= 3.0.0), viridis, CoGAPS +requirements: + host: + - bioconductor-qvalue >=2.38.0,<2.39.0 + - r-ape + - r-base + - r-hdf5r + - r-jsonlite + - r-matrix + - r-matrixstats + - r-matrixtests + - r-rstatix + - r-spatstat.explore + - r-spatstat.geom + run: + - bioconductor-qvalue >=2.38.0,<2.39.0 + - r-ape + - r-base + - r-hdf5r + - r-jsonlite + - r-matrix + - r-matrixstats + - r-matrixtests + - r-rstatix + - r-spatstat.explore + - r-spatstat.geom + +source: + md5: 8545c5e1ff4727fd96fa0b1f268d1174 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-spaniel/meta.yaml b/recipes/bioconductor-spaniel/meta.yaml index 5dbb8445371d2..f418d898229ff 100644 --- a/recipes/bioconductor-spaniel/meta.yaml +++ b/recipes/bioconductor-spaniel/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "Spaniel" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Spaniel includes a series of tools to aid the quality control and analysis of Spatial Transcriptomics data. Spaniel can import data from either the original Spatial Transcriptomics system or 10X Visium technology. The package contains functions to create a SingleCellExperiment Seurat object and provides a method of loading a histologial image into R. The spanielPlot function allows visualisation of metrics contained within the S4 object overlaid onto the image of the tissue. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Spatial Transcriptomics Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fb29666756a1db567f16b5c72420de4c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spaniel", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, devtools requirements: host: - - 'bioconductor-dropletutils >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-dropletutils >=1.26.0,<1.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -39,12 +41,12 @@ requirements: - r-seurat - r-shiny run: - - 'bioconductor-dropletutils >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-dropletutils >=1.26.0,<1.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -55,13 +57,16 @@ requirements: - r-png - r-seurat - r-shiny + +source: + md5: daa499182a0877097e8db020ebeb0ec9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Spatial Transcriptomics Analysis' - description: 'Spaniel includes a series of tools to aid the quality control and analysis of Spatial Transcriptomics data. Spaniel can import data from either the original Spatial Transcriptomics system or 10X Visium technology. The package contains functions to create a SingleCellExperiment Seurat object and provides a method of loading a histologial image into R. The spanielPlot function allows visualisation of metrics contained within the S4 object overlaid onto the image of the tissue.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spanorm/build.sh b/recipes/bioconductor-spanorm/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-spanorm/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-spanorm/meta.yaml b/recipes/bioconductor-spanorm/meta.yaml new file mode 100644 index 0000000000000..c1a9b8f16359c --- /dev/null +++ b/recipes/bioconductor-spanorm/meta.yaml @@ -0,0 +1,64 @@ +{% set version = "1.0.0" %} +{% set name = "SpaNorm" %} +{% set bioc = "3.20" %} + +about: + description: This package implements the spatially aware library size normalisation algorithm, SpaNorm. SpaNorm normalises out library size effects while retaining biology through the modelling of smooth functions for each effect. Normalisation is performed in a gene- and cell-/spot- specific manner, yielding library size adjusted data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Spatially-aware normalisation for spatial transcriptomics data + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spanorm", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat (>= 3.0.0), knitr, rmarkdown, prettydoc, pkgdown, covr, BiocStyle, Seurat, patchwork, ggforce, ggnewscale +requirements: + host: + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-ggplot2 + - r-matrix + - r-matrixstats + - r-rlang + - r-seuratobject + run: + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scran >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-ggplot2 + - r-matrix + - r-matrixstats + - r-rlang + - r-seuratobject + +source: + md5: ddd91b1dfca25d18d77e1a375babaa72 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-sparrow/meta.yaml b/recipes/bioconductor-sparrow/meta.yaml index 5d45dc6ab1c96..94c98ce9afae7 100644 --- a/recipes/bioconductor-sparrow/meta.yaml +++ b/recipes/bioconductor-sparrow/meta.yaml @@ -1,71 +1,76 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "sparrow" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of results. Interactive exploration of GSEA results is enabled through a shiny app provided by a sparrow.shiny sibling package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Take command of set enrichment analyses through a unified interface -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 072ccf02fa2cc42410000f238dce492b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sparrow", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle, DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin, magrittr, matrixStats, msigdbr (>= 7.4.1), KernSmooth, knitr, PANTHER.db (>= 1.0.3), R.utils, reactome.db, rmarkdown, SummarizedExperiment, statmod, stringr, testthat, webshot requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocset >=1.16.0,<1.17.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'r-babelgene >=21.4' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocset >=1.20.0,<1.21.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - r-babelgene >=21.4 - r-base - r-checkmate - r-circlize - - 'r-data.table >=1.10.4' - - 'r-ggplot2 >=2.2.0' + - r-data.table >=1.10.4 + - r-ggplot2 >=2.2.0 - r-irlba - r-matrix - - 'r-plotly >=4.9.0' + - r-plotly >=4.9.0 - r-viridis run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocset >=1.16.0,<1.17.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'r-babelgene >=21.4' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocset >=1.20.0,<1.21.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - r-babelgene >=21.4 - r-base - r-checkmate - r-circlize - - 'r-data.table >=1.10.4' - - 'r-ggplot2 >=2.2.0' + - r-data.table >=1.10.4 + - r-ggplot2 >=2.2.0 - r-irlba - r-matrix - - 'r-plotly >=4.9.0' + - r-plotly >=4.9.0 - r-viridis + +source: + md5: 7107632bd91242c5c921235ba727e279 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Take command of set enrichment analyses through a unified interface' - description: 'Provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of results. Interactive exploration of GSEA results is enabled through a shiny app provided by a sparrow.shiny sibling package.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sparsearray/meta.yaml b/recipes/bioconductor-sparsearray/meta.yaml index 1ce3dc389f1af..447159a463d9c 100644 --- a/recipes/bioconductor-sparsearray/meta.yaml +++ b/recipes/bioconductor-sparsearray/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "1.2.2" %} +{% set version = "1.6.0" %} {% set name = "SparseArray" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The SparseArray package provides array-like containers for efficient in-memory representation of multidimensional sparse data in R (arrays and matrices). The package defines the SparseArray virtual class and two concrete subclasses: COO_SparseArray and SVT_SparseArray. Each subclass uses its own internal representation of the nonzero multidimensional data: the "COO layout" and the "SVT layout", respectively. SVT_SparseArray objects mimic as much as possible the behavior of ordinary matrix and array objects in base R. In particular, they suppport most of the "standard matrix and array API" defined in base R and in the matrixStats package from CRAN.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: High-performance sparse data representation and manipulation in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a73b2e316ce8135de81af01a9a9610ec build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sparsearray", max_pin="x.x") }}' -# Suggests: DelayedArray, testthat, knitr, rmarkdown, BiocStyle + +extra: + additional-platforms: + - linux-aarch64 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: HDF5Array, ExperimentHub, testthat, knitr, rmarkdown, BiocStyle requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4arrays >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4arrays >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-matrix - r-matrixstats - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4arrays >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4arrays >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-matrix - r-matrixstats - build: - - {{ compiler('c') }} - - make + +source: + md5: b57caafbc8b4ad3fa535a6b6180d0476 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Efficient in-memory representation of multidimensional sparse arrays' - description: 'The SparseArray package is an infrastructure package that provides an array-like container for efficient in-memory representation of multidimensional sparse data in R. The package defines the SparseArray virtual class and two concrete subclasses: COO_SparseArray and SVT_SparseArray. Each subclass uses its own internal representation of the nonzero multidimensional data, the "COO layout" and the "SVT layout", respectively. SVT_SparseArray objects mimic as much as possible the behavior of ordinary matrix and array objects in base R. In particular, they suppport most of the "standard matrix and array API" defined in base R and in the matrixStats package from CRAN.' + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 diff --git a/recipes/bioconductor-sparsematrixstats/meta.yaml b/recipes/bioconductor-sparsematrixstats/meta.yaml index b32bbcc2f9c2f..a2733d2451f0d 100644 --- a/recipes/bioconductor-sparsematrixstats/meta.yaml +++ b/recipes/bioconductor-sparsematrixstats/meta.yaml @@ -1,56 +1,62 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "sparseMatrixStats" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'High performance functions for row and column operations on sparse matrices. For example: col / rowMeans2, col / rowMedians, col / rowVars etc. Currently, the optimizations are limited to data in the column sparse format. This package is inspired by the matrixStats package by Henrik Bengtsson.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Summary Statistics for Rows and Columns of Sparse Matrices -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4319e6fb04b91467bd08cc4ce2ad609c build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sparsematrixstats", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:sparseMatrixStats + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 - r-base - r-matrix - - 'r-matrixstats >=0.60.0' + - r-matrixstats >=0.60.0 - r-rcpp - libblas - liblapack run: - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 - r-base - r-matrix - - 'r-matrixstats >=0.60.0' + - r-matrixstats >=0.60.0 - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 50096c9aa26a1cfd016375256c1c911a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Summary Statistics for Rows and Columns of Sparse Matrices' - description: 'High performance functions for row and column operations on sparse matrices. For example: col / rowMeans2, col / rowMedians, col / rowVars etc. Currently, the optimizations are limited to data in the column sparse format. This package is inspired by the matrixStats package by Henrik Bengtsson.' - license_file: LICENSE -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name }} + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sparsenetgls/meta.yaml b/recipes/bioconductor-sparsenetgls/meta.yaml index 9568b17a7c9b5..d53340e19afc7 100644 --- a/recipes/bioconductor-sparsenetgls/meta.yaml +++ b/recipes/bioconductor-sparsenetgls/meta.yaml @@ -1,24 +1,32 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "sparsenetgls" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package provides methods of combining the graph structure learning and generalized least squares regression to improve the regression estimation. The main function sparsenetgls() provides solutions for multivariate regression with Gaussian distributed dependant variables and explanatory variables utlizing multiple well-known graph structure learning approaches to estimating the precision matrix, and uses a penalized variance covariance matrix with a distance tuning parameter of the graph structure in deriving the sandwich estimators in generalized least squares (gls) regression. This package also provides functions for assessing a Gaussian graphical model which uses the penalized approach. It uses Receiver Operative Characteristics curve as a visualization tool in the assessment. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 32b8f3b9fe86b40386aee23ac4ea55fd build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sparsenetgls", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-sparsenetgls + path: recipes/bioconductor-sparsenetgls + version: 1.0.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0) # SystemRequirements: GNU make requirements: @@ -34,18 +42,16 @@ requirements: - r-huge - r-mass - r-matrix + +source: + md5: 6c4b26bf65d269e87001549230ddc640 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression' - description: 'The package provides methods of combining the graph structure learning and generalized least squares regression to improve the regression estimation. The main function sparsenetgls() provides solutions for multivariate regression with Gaussian distributed dependant variables and explanatory variables utlizing multiple well-known graph structure learning approaches to estimating the precision matrix, and uses a penalized variance covariance matrix with a distance tuning parameter of the graph structure in deriving the sandwich estimators in generalized least squares (gls) regression. This package also provides functions for assessing a Gaussian graphical model which uses the penalized approach. It uses Receiver Operative Characteristics curve as a visualization tool in the assessment.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-sparsenetgls - path: recipes/bioconductor-sparsenetgls - version: 1.0.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sparsesignatures/meta.yaml b/recipes/bioconductor-sparsesignatures/meta.yaml index 5f81cb9307a38..bc9c742cbcabd 100644 --- a/recipes/bioconductor-sparsesignatures/meta.yaml +++ b/recipes/bioconductor-sparsesignatures/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "2.12.0" %} +{% set version = "2.16.0" %} {% set name = "SparseSignatures" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Point mutations occurring in a genome can be divided into 96 categories based on the base being mutated, the base it is mutated into and its two flanking bases. Therefore, for any patient, it is possible to represent all the point mutations occurring in that patient's tumor as a vector of length 96, where each element represents the count of mutations for a given category in the patient. A mutational signature represents the pattern of mutations produced by a mutagen or mutagenic process inside the cell. Each signature can also be represented by a vector of length 96, where each element represents the probability that this particular mutagenic process generates a mutation of the 96 above mentioned categories. In this R package, we provide a set of functions to extract and visualize the mutational signatures that best explain the mutation counts of a large number of patients. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: SparseSignatures -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 832b206679a06252fa3b76f2700a70e9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sparsesignatures", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5, BiocStyle, testthat, knitr, requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-data.table - r-ggplot2 @@ -35,12 +37,13 @@ requirements: - r-nnlasso - r-nnls - r-reshape2 + - r-rhpcblasctl run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-data.table - r-ggplot2 @@ -49,13 +52,17 @@ requirements: - r-nnlasso - r-nnls - r-reshape2 + - r-rhpcblasctl + +source: + md5: 5e5ff1f13735b1f3d65c5b5a6ab20289 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: SparseSignatures - description: 'Point mutations occurring in a genome can be divided into 96 categories based on the base being mutated, the base it is mutated into and its two flanking bases. Therefore, for any patient, it is possible to represent all the point mutations occurring in that patient''s tumor as a vector of length 96, where each element represents the count of mutations for a given category in the patient. A mutational signature represents the pattern of mutations produced by a mutagen or mutagenic process inside the cell. Each signature can also be represented by a vector of length 96, where each element represents the probability that this particular mutagenic process generates a mutation of the 96 above mentioned categories. In this R package, we provide a set of functions to extract and visualize the mutational signatures that best explain the mutation counts of a large number of patients.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spasim/meta.yaml b/recipes/bioconductor-spasim/meta.yaml index 4189527c513c5..ef4a715c15b3f 100644 --- a/recipes/bioconductor-spasim/meta.yaml +++ b/recipes/bioconductor-spasim/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "spaSim" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A suite of functions for simulating spatial patterns of cells in tissue images. Output images are multitype point data in SingleCellExperiment format. Each point represents a cell, with its 2D locations and cell type. Potential cell patterns include background cells, tumour/immune cell clusters, immune rings, and blood/lymphatic vessels. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Spatial point data simulator for tissue images -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d69e70975aaaa9bffc5e52f95885e59c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spasim", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RefManageR, BiocStyle, knitr, testthat (>= 3.0.0), sessioninfo, rmarkdown, markdown requirements: host: - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -31,20 +32,24 @@ requirements: - r-spatstat.geom - r-spatstat.random run: - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 - r-rann - r-spatstat.geom - r-spatstat.random + +source: + md5: 4a3dbdeaaca0ec5a65d98a70385f7f5b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Spatial point data simulator for tissue images' - description: 'A suite of functions for simulating spatial patterns of cells in tissue images. Output images are multitype point data in SingleCellExperiment format. Each point represents a cell, with its 2D locations and cell type. Potential cell patterns include background cells, tumour/immune cell clusters, immune rings, and blood/lymphatic vessels.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spatialcpie/meta.yaml b/recipes/bioconductor-spatialcpie/meta.yaml index 2a26cea000a99..436516e5058be 100644 --- a/recipes/bioconductor-spatialcpie/meta.yaml +++ b/recipes/bioconductor-spatialcpie/meta.yaml @@ -1,81 +1,88 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "SpatialCPie" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SpatialCPie is an R package designed to facilitate cluster evaluation for spatial transcriptomics data by providing intuitive visualizations that display the relationships between clusters in order to guide the user during cluster identification and other downstream applications. The package is built around a shiny "gadget" to allow the exploration of the data with multiple plots in parallel and an interactive UI. The user can easily toggle between different cluster resolutions in order to choose the most appropriate visual cues. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Cluster analysis of Spatial Transcriptomics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f7f622f0a9e08b387870bddc9a52cfc2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spatialcpie", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle (>= 2.8.2), jpeg (>= 0.1-8), knitr (>= 1.20), rmarkdown (>= 1.10), testthat (>= 2.0.0) requirements: + host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-colorspace >=1.3-2' - - 'r-data.table >=1.12.2' - - 'r-digest >=0.6.21' - - 'r-dplyr >=0.7.6' - - 'r-ggforce >=0.3.0' - - 'r-ggiraph >=0.5.0' - - 'r-ggplot2 >=3.0.0' - - 'r-ggrepel >=0.8.0' - - 'r-igraph >=1.2.2' - - 'r-lpsolve >=5.6.13' - - 'r-purrr >=0.2.5' - - 'r-readr >=1.1.1' - - 'r-rlang >=0.2.2' - - 'r-shiny >=1.1.0' - - 'r-shinycssloaders >=0.2.0' - - 'r-shinyjs >=1.0' - - 'r-shinywidgets >=0.4.8' - - 'r-tibble >=1.4.2' - - 'r-tidyr >=0.8.1' - - 'r-tidyselect >=0.2.4' - - 'r-zeallot >=0.1.0' + - r-colorspace >=1.3-2 + - r-data.table >=1.12.2 + - r-digest >=0.6.21 + - r-dplyr >=0.7.6 + - r-ggforce >=0.3.0 + - r-ggiraph >=0.5.0 + - r-ggplot2 >=3.0.0 + - r-ggrepel >=0.8.0 + - r-igraph >=1.2.2 + - r-lpsolve >=5.6.13 + - r-purrr >=0.2.5 + - r-readr >=1.1.1 + - r-rlang >=0.2.2 + - r-shiny >=1.1.0 + - r-shinycssloaders >=0.2.0 + - r-shinyjs >=1.0 + - r-shinywidgets >=0.4.8 + - r-tibble >=1.4.2 + - r-tidyr >=0.8.1 + - r-tidyselect >=0.2.4 + - r-zeallot >=0.1.0 + run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-colorspace >=1.3-2' - - 'r-data.table >=1.12.2' - - 'r-digest >=0.6.21' - - 'r-dplyr >=0.7.6' - - 'r-ggforce >=0.3.0' - - 'r-ggiraph >=0.5.0' - - 'r-ggplot2 >=3.0.0' - - 'r-ggrepel >=0.8.0' - - 'r-igraph >=1.2.2' - - 'r-lpsolve >=5.6.13' - - 'r-purrr >=0.2.5' - - 'r-readr >=1.1.1' - - 'r-rlang >=0.2.2' - - 'r-shiny >=1.1.0' - - 'r-shinycssloaders >=0.2.0' - - 'r-shinyjs >=1.0' - - 'r-shinywidgets >=0.4.8' - - 'r-tibble >=1.4.2' - - 'r-tidyr >=0.8.1' - - 'r-tidyselect >=0.2.4' - - 'r-zeallot >=0.1.0' + - r-colorspace >=1.3-2 + - r-data.table >=1.12.2 + - r-digest >=0.6.21 + - r-dplyr >=0.7.6 + - r-ggforce >=0.3.0 + - r-ggiraph >=0.5.0 + - r-ggplot2 >=3.0.0 + - r-ggrepel >=0.8.0 + - r-igraph >=1.2.2 + - r-lpsolve >=5.6.13 + - r-purrr >=0.2.5 + - r-readr >=1.1.1 + - r-rlang >=0.2.2 + - r-shiny >=1.1.0 + - r-shinycssloaders >=0.2.0 + - r-shinyjs >=1.0 + - r-shinywidgets >=0.4.8 + - r-tibble >=1.4.2 + - r-tidyr >=0.8.1 + - r-tidyselect >=0.2.4 + - r-zeallot >=0.1.0 + +source: + md5: 785298a0c75b8c788c20cd5de7733a3c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Cluster analysis of Spatial Transcriptomics data' - description: 'SpatialCPie is an R package designed to facilitate cluster evaluation for spatial transcriptomics data by providing intuitive visualizations that display the relationships between clusters in order to guide the user during cluster identification and other downstream applications. The package is built around a shiny "gadget" to allow the exploration of the data with multiple plots in parallel and an interactive UI. The user can easily toggle between different cluster resolutions in order to choose the most appropriate visual cues.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spatialdatasets/meta.yaml b/recipes/bioconductor-spatialdatasets/meta.yaml index 59eeabf7949e9..70a9b0ac6fbe0 100644 --- a/recipes/bioconductor-spatialdatasets/meta.yaml +++ b/recipes/bioconductor-spatialdatasets/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "SpatialDatasets" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 36fd913ef0d7109d0be40afbc1255548 +about: + description: This is a collection of publically available spatial omics datasets. Where possible we have curated these datasets as either SpatialExperiments, MoleculeExperiments or CytoImageLists and included annotations of the sample characteristics. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Collection of spatial omics datasets build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spatialdatasets", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0d46aa02771cb1ca6428d46e88d89654 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Collection of spatial omics datasets' - description: 'This is a collection of publically available spatial omics datasets. Where possible we have curated these datasets as either SpatialExperiments, MoleculeExperiments or CytoImageLists and included annotations of the sample characteristics.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spatialdatasets/post-link.sh b/recipes/bioconductor-spatialdatasets/post-link.sh index 072e49b3171c7..40e1a3ad9f1d1 100644 --- a/recipes/bioconductor-spatialdatasets/post-link.sh +++ b/recipes/bioconductor-spatialdatasets/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "spatialdatasets-1.0.0" +installBiocDataPackage.sh "spatialdatasets-1.4.0" diff --git a/recipes/bioconductor-spatialde/meta.yaml b/recipes/bioconductor-spatialde/meta.yaml index 113377b6f586e..f41c57b269014 100644 --- a/recipes/bioconductor-spatialde/meta.yaml +++ b/recipes/bioconductor-spatialde/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "spatialDE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data. This package provides wrappers to use the Python SpatialDE library in R, using reticulate and basilisk. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: R wrapper for SpatialDE -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4227d5d446ef2399e1b325cfa7ef65b7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spatialde", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-checkmate - r-ggplot2 @@ -34,9 +36,9 @@ requirements: - r-reticulate - r-scales run: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-checkmate - r-ggplot2 @@ -45,13 +47,16 @@ requirements: - r-matrix - r-reticulate - r-scales + +source: + md5: af57deb100f4ad97c1591a3c2ddd2e11 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'R wrapper for SpatialDE' - description: 'SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data. This package provides wrappers to use the Python SpatialDE library in R, using reticulate and basilisk.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spatialdecon/meta.yaml b/recipes/bioconductor-spatialdecon/meta.yaml index dd83c38cceac5..87f51bfe993fe 100644 --- a/recipes/bioconductor-spatialdecon/meta.yaml +++ b/recipes/bioconductor-spatialdecon/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "SpatialDecon" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Using spatial or bulk gene expression data, estimates abundance of mixed cell types within each observation. Based on "Advances in mixed cell deconvolution enable quantification of cell types in spatial transcriptomic data", Danaher (2022). Designed for use with the NanoString GeoMx platform, but applicable to any gene expression data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Deconvolution of mixed cells from spatial and/or bulk gene expression data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3dd72587ea55dc018231523782d225f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spatialdecon", max_pin="x.x") }}' - noarch: generic -# Suggests: testthat, knitr, rmarkdown, qpdf + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, knitr, rmarkdown, qpdf, Seurat requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-geomxtools >=3.5.0,<3.6.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-geomxtools >=3.10.0,<3.11.0 - r-base - - 'r-lognormreg >=0.4' + - r-lognormreg >=0.4 - r-matrix - r-repmis - r-seuratobject run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-geomxtools >=3.5.0,<3.6.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-geomxtools >=3.10.0,<3.11.0 - r-base - - 'r-lognormreg >=0.4' + - r-lognormreg >=0.4 - r-matrix - r-repmis - r-seuratobject + +source: + md5: 1926c558a0c6dc9aed1ca4e2d84073e3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Deconvolution of mixed cells from spatial and/or bulk gene expression data' - description: 'Using spatial or bulk gene expression data, estimates abundance of mixed cell types within each observation. Based on "Advances in mixed cell deconvolution enable quantification of cell types in spatial transcriptomic data", Danaher (2022). Designed for use with the NanoString GeoMx platform, but applicable to any gene expression data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spatialdmelxsim/meta.yaml b/recipes/bioconductor-spatialdmelxsim/meta.yaml index 2e4dbaa680488..d5d3f4d81a925 100644 --- a/recipes/bioconductor-spatialdmelxsim/meta.yaml +++ b/recipes/bioconductor-spatialdmelxsim/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "spatialDmelxsim" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2fec38c7672022e76f2b7a7ba7b9a677 +about: + description: Spatial allelic expression counts from Combs & Fraser (2018), compiled into a SummarizedExperiment object. This package contains data of allelic expression counts of spatial slices of a fly embryo, a Drosophila melanogaster x Drosophila simulans cross. See the CITATION file for the data source, and the associated script for how the object was constructed from publicly available data. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Spatial allelic expression counts for fly cross embryo build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spatialdmelxsim", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3480463b7d6ea68d2755d643f65549be + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Spatial allelic expression counts for fly cross embryo' - description: 'Spatial allelic expression counts from Combs & Fraser (2018), compiled into a SummarizedExperiment object. This package contains data of allelic expression counts of spatial slices of a fly embryo, a Drosophila melanogaster x Drosophila simulans cross. See the CITATION file for the data source, and the associated script for how the object was constructed from publicly available data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spatialdmelxsim/post-link.sh b/recipes/bioconductor-spatialdmelxsim/post-link.sh index b6c6cfed4f1e5..cf4994ae8fb81 100644 --- a/recipes/bioconductor-spatialdmelxsim/post-link.sh +++ b/recipes/bioconductor-spatialdmelxsim/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "spatialdmelxsim-1.8.0" +installBiocDataPackage.sh "spatialdmelxsim-1.12.0" diff --git a/recipes/bioconductor-spatialexperiment/meta.yaml b/recipes/bioconductor-spatialexperiment/meta.yaml index 61e7e4da5902d..69eaebf4e93bb 100644 --- a/recipes/bioconductor-spatialexperiment/meta.yaml +++ b/recipes/bioconductor-spatialexperiment/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "SpatialExperiment" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordinates, images, and image metadata. A specialized constructor function is included for data from the 10x Genomics Visium platform. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: S4 Class for Spatially Resolved -omics Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7dbd7938c005104df763ecf3d016154f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spatialexperiment", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-magick - r-rjson run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-magick - r-rjson + +source: + md5: dd52315d7fcca2045bb553d952a15573 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'S4 Class for Spatially Resolved -omics Data' - description: 'Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordinates, images, and image metadata. A specialized constructor function is included for data from the 10x Genomics Visium platform.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spatialfeatureexperiment/meta.yaml b/recipes/bioconductor-spatialfeatureexperiment/meta.yaml index 72a314a96d05f..052470a2d88c7 100644 --- a/recipes/bioconductor-spatialfeatureexperiment/meta.yaml +++ b/recipes/bioconductor-spatialfeatureexperiment/meta.yaml @@ -1,62 +1,83 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "SpatialFeatureExperiment" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A new S4 class integrating Simple Features with the R package sf to bring geospatial data analysis methods based on vector data to spatial transcriptomics. Also implements management of spatial neighborhood graphs and geometric operations. This pakage builds upon SpatialExperiment and SingleCellExperiment, hence methods for these parent classes can still be used. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Integrating SpatialExperiment with Simple Features in sf -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 56d4ad5144861bea16c2f677e096ac75 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spatialfeatureexperiment", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, dplyr, DropletUtils, knitr, rhdf5, rmarkdown, sfarrow, SFEData, vroom, testthat (>= 3.0.0) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: arrow, BiocStyle, dplyr, knitr, RBioFormats, rhdf5, rmarkdown, scater, sfarrow, SFEData (>= 1.5.3), Seurat, SeuratObject, sparseMatrixStats, testthat (>= 3.0.0), tidyr, Voyager (>= 1.7.2), xml2 requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-dropletutils >=1.26.0,<1.27.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + - r-data.table + - r-lifecycle - r-matrix - r-rjson - r-rlang - r-sf - - 'r-spdep >=1.1-7' + - r-sfheaders + - r-spdep >=1.1-7 - r-terra + - r-zeallot + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-dropletutils >=1.26.0,<1.27.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + - r-data.table + - r-lifecycle - r-matrix - r-rjson - r-rlang - r-sf - - 'r-spdep >=1.1-7' + - r-sfheaders + - r-spdep >=1.1-7 - r-terra + - r-zeallot + +source: + md5: d2194357fbb7ff0f69305a15fae9c4bb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Integrating SpatialExperiment with Simple Features in sf' - description: 'A new S4 class integrating Simple Features with the R package sf to bring geospatial data analysis methods based on vector data to spatial transcriptomics. Also implements management of spatial neighborhood graphs and geometric operations. This pakage builds upon SpatialExperiment and SingleCellExperiment, hence methods for these parent classes can still be used.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spatialheatmap/meta.yaml b/recipes/bioconductor-spatialheatmap/meta.yaml index d4edc6ad928bf..41141edfa6878 100644 --- a/recipes/bioconductor-spatialheatmap/meta.yaml +++ b/recipes/bioconductor-spatialheatmap/meta.yaml @@ -1,41 +1,39 @@ -{% set version = "2.8.0" %} +{% set version = "2.12.0" %} {% set name = "spatialHeatmap" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The spatialHeatmap package offers the primary functionality for visualizing cell-, tissue- and organ-specific assay data in spatial anatomical images. Additionally, it provides extended functionalities for large-scale data mining routines and co-visualizing bulk and single-cell data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: spatialHeatmap -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2fe3c68f9bbfb419d0afd3d329e65747 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spatialheatmap", max_pin="x.x") }}' - noarch: generic -# Suggests: AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, distinct, dendextend, DT, dynamicTreeCut, flashClust, ggdendro, HDF5Array, htmltools, htmlwidgets, kableExtra, knitr, limma, magick, memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db, org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, plotly, rmarkdown, rols, rappdirs, RUnit, Rtsne, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, yaml + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, dendextend, DT, dynamicTreeCut, flashClust, gplots, ggdendro, HDF5Array, htmltools, htmlwidgets, kableExtra, knitr, limma, magick, memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db, org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, plotly, rmarkdown, rols, rappdirs, RUnit, Rtsne, rhdf5, scater, scuttle, scran, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, xlsx, yaml requirements: + host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-dplyr - r-ggplot2 - r-ggplotify - - r-gplots - r-gridextra - r-grimport - r-igraph @@ -44,24 +42,21 @@ requirements: - r-rsvg - r-shiny - r-shinydashboard - - 'r-spscomps >=0.3.3.0' + - r-spscomps >=0.3.3.0 - r-tibble - r-xml2 + run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scran >=1.30.0,<1.31.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-dplyr - r-ggplot2 - r-ggplotify - - r-gplots - r-gridextra - r-grimport - r-igraph @@ -70,15 +65,19 @@ requirements: - r-rsvg - r-shiny - r-shinydashboard - - 'r-spscomps >=0.3.3.0' + - r-spscomps >=0.3.3.0 - r-tibble - r-xml2 + +source: + md5: 498528cde13ba1c6810a8593d44a6b45 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: spatialHeatmap - description: 'The spatialHeatmap package offers the primary functionality for visualizing cell-, tissue- and organ-specific assay data in spatial anatomical images. Additionally, it provides extended functionalities for large-scale data mining routines and co-visualizing bulk and single-cell data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spatiallibd/meta.yaml b/recipes/bioconductor-spatiallibd/meta.yaml index 9c66105422f97..3648b12e77c32 100644 --- a/recipes/bioconductor-spatiallibd/meta.yaml +++ b/recipes/bioconductor-spatiallibd/meta.yaml @@ -1,45 +1,49 @@ -{% set version = "1.14.1" %} +{% set version = "1.18.0" %} {% set name = "spatialLIBD" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Inspect interactively the spatially-resolved transcriptomics data from the 10x Genomics Visium platform as well as data from the Maynard, Collado-Torres et al, Nature Neuroscience, 2021 project analyzed by Lieber Institute for Brain Development (LIBD) researchers and collaborators. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: 'spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cd8c85a03e555f2dfdeb1627f7087002 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spatiallibd", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager, lobstr, DropletUtils requirements: + host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-benchmarkme - r-cowplot + - r-dplyr - r-dt - r-fields - r-ggplot2 @@ -51,31 +55,35 @@ requirements: - r-plotly - r-png - r-rcolorbrewer + - r-rlang - r-sessioninfo - r-shiny - r-shinywidgets - r-statmod - r-tibble - r-viridislite + run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-benchmarkme - r-cowplot + - r-dplyr - r-dt - r-fields - r-ggplot2 @@ -87,6 +95,7 @@ requirements: - r-plotly - r-png - r-rcolorbrewer + - r-rlang - r-sessioninfo - r-shiny - r-shinywidgets @@ -94,13 +103,17 @@ requirements: - r-tibble - r-viridislite - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20250105 + +source: + md5: a261eafe19ca77ff46ca694974b64923 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data' - description: 'Inspect interactively the spatially-resolved transcriptomics data from the 10x Genomics Visium platform as well as data from the Maynard, Collado-Torres et al, Nature Neuroscience, 2021 project analyzed by Lieber Institute for Brain Development (LIBD) researchers and collaborators.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spatiallibd/post-link.sh b/recipes/bioconductor-spatiallibd/post-link.sh index 9ef1f36f1b430..d11d3bca727a2 100644 --- a/recipes/bioconductor-spatiallibd/post-link.sh +++ b/recipes/bioconductor-spatiallibd/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "spatiallibd-1.14.1" +installBiocDataPackage.sh "spatiallibd-1.18.0" diff --git a/recipes/bioconductor-spatialomicsoverlay/meta.yaml b/recipes/bioconductor-spatialomicsoverlay/meta.yaml index 8d46d91ef4271..5a4308e33ec66 100644 --- a/recipes/bioconductor-spatialomicsoverlay/meta.yaml +++ b/recipes/bioconductor-spatialomicsoverlay/meta.yaml @@ -1,33 +1,34 @@ -{% set version = "1.2.1" %} +{% set version = "1.6.0" %} {% set name = "SpatialOmicsOverlay" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools for NanoString Technologies GeoMx Technology. Package to easily graph on top of an OME-TIFF image. Plotting annotations can range from tissue segment to gene expression. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + summary: Spatial Overlay for Omic Data from Nanostring GeoMx Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 149a968f19aa22b57caca243b3480378 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spatialomicsoverlay", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr, sf requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-geomxtools >=3.5.0,<3.6.0' - - 'bioconductor-rbioformats >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-geomxtools >=3.10.0,<3.11.0 + - bioconductor-rbioformats >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-base64enc - r-data.table @@ -42,12 +43,12 @@ requirements: - r-stringr - r-xml run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-geomxtools >=3.5.0,<3.6.0' - - 'bioconductor-rbioformats >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-geomxtools >=3.10.0,<3.11.0 + - bioconductor-rbioformats >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-base64enc - r-data.table @@ -61,12 +62,16 @@ requirements: - r-scattermore - r-stringr - r-xml + +source: + md5: 91bb3a6361147d347e342ad042c71d15 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: MIT - summary: 'Spatial Overlay for Omic Data from Nanostring GeoMx Data' - description: 'Tools for NanoString Technologies GeoMx Technology. Package to easily graph on top of an OME-TIFF image. Plotting annotations can range from tissue segment to gene expression.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spatialsimgp/build.sh b/recipes/bioconductor-spatialsimgp/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-spatialsimgp/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-spatialsimgp/meta.yaml b/recipes/bioconductor-spatialsimgp/meta.yaml new file mode 100644 index 0000000000000..841d0791217ab --- /dev/null +++ b/recipes/bioconductor-spatialsimgp/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.0.0" %} +{% set name = "spatialSimGP" %} +{% set bioc = "3.20" %} + +about: + description: This packages simulates spatial transcriptomics data with the mean- variance relationship using a Gaussian Process model per gene. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Simulate Spatial Transcriptomics Data with the Mean-variance Relationship +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spatialsimgp", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: testthat (>= 3.0.0), STexampleData, ggplot2, knitr +requirements: + host: + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-mass + run: + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-mass +source: + md5: 29f0efd7408868e2022f28f9cf811c56 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-spatzie/meta.yaml b/recipes/bioconductor-spatzie/meta.yaml index 98199da5b24e6..756a2d86768b2 100644 --- a/recipes/bioconductor-spatzie/meta.yaml +++ b/recipes/bioconductor-spatzie/meta.yaml @@ -1,65 +1,70 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "spatzie" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Identifies motifs that are significantly co-enriched from enhancer-promoter interaction data. While enhancer-promoter annotation is commonly used to define groups of interaction anchors, spatzie also supports co-enrichment analysis between preprocessed interaction anchors. Supports BEDPE interaction data derived from genome-wide assays such as HiC, ChIA-PET, and HiChIP. Can also be used to look for differentially enriched motif pairs between two interaction experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identification of enriched motif pairs from chromatin interaction data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fa887a71329c75cde9ab0b1aaeb0d481 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spatzie", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocManager, Biostrings, knitr, pheatmap, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicinteractions >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-motifmatchr >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tfbstools >=1.44.0,<1.45.0 - r-base - r-ggplot2 - r-matrixstats run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicinteractions >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-motifmatchr >=1.24.0,<1.25.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tfbstools >=1.40.0,<1.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicinteractions >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-motifmatchr >=1.28.0,<1.29.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tfbstools >=1.44.0,<1.45.0 - r-base - r-ggplot2 - r-matrixstats + +source: + md5: 858deff331d847d4d386ac460d68dbe9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Identification of enriched motif pairs from chromatin interaction data' - description: 'Identifies motifs that are significantly co-enriched from enhancer-promoter interaction data. While enhancer-promoter annotation is commonly used to define groups of interaction anchors, spatzie also supports co-enrichment analysis between preprocessed interaction anchors. Supports BEDPE interaction data derived from genome-wide assays such as HiC, ChIA-PET, and HiChIP. Can also be used to look for differentially enriched motif pairs between two interaction experiments.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-speckle/meta.yaml b/recipes/bioconductor-speckle/meta.yaml index 76d5d70a76e25..5961c44ec0bb5 100644 --- a/recipes/bioconductor-speckle/meta.yaml +++ b/recipes/bioconductor-speckle/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "speckle" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The speckle package contains functions for the analysis of single cell RNA-seq data. The speckle package currently contains functions to analyse differences in cell type proportions. There are also functions to estimate the parameters of the Beta distribution based on a given counts matrix, and a function to normalise a counts matrix to the median library size. There are plotting functions to visualise cell type proportions and the mean-variance relationship in cell type proportions and counts. As our research into specialised analyses of single cell data continues we anticipate that the package will be updated with new functions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Statistical methods for analysing single cell RNA-seq data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4603cad300c83d6e6374e5989b5fe32a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-speckle", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, statmod, CellBench, scater, patchwork, jsonlite, vdiffr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-ggplot2 - r-seurat run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-ggplot2 - r-seurat + +source: + md5: 02df000664c70b6ee85aa74170cb6248 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Statistical methods for analysing single cell RNA-seq data' - description: 'The speckle package contains functions for the analysis of single cell RNA-seq data. The speckle package currently contains functions to analyse differences in cell type proportions. There are also functions to estimate the parameters of the Beta distribution based on a given counts matrix, and a function to normalise a counts matrix to the median library size. There are plotting functions to visualise cell type proportions and the mean-variance relationship in cell type proportions and counts. As our research into specialised analyses of single cell data continues we anticipate that the package will be updated with new functions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-specl/meta.yaml b/recipes/bioconductor-specl/meta.yaml index df05401abb956..3b4965c42c8d1 100644 --- a/recipes/bioconductor-specl/meta.yaml +++ b/recipes/bioconductor-specl/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "specL" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: provides a functions for generating spectra libraries that can be used for MRM SRM MS workflows in proteomics. The package provides a BiblioSpec reader, a function which can add the protein information using a FASTA formatted amino acid file, and an export method for using the created library in the Spectronaut software. The package is developed, tested and used at the Functional Genomics Center Zurich . + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a3a436585f26f8353106b030a26cbf98 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-specl", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:specl + parent_recipe: + name: bioconductor-specl + path: recipes/bioconductor-specl + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4) requirements: host: - r-base - - 'r-dbi >=0.5' - - 'r-protviz >=0.7' - - 'r-rsqlite >=1.1' - - 'r-seqinr >=3.3' + - r-dbi >=0.5 + - r-protviz >=0.7 + - r-rsqlite >=1.1 + - r-seqinr >=3.3 run: - r-base - - 'r-dbi >=0.5' - - 'r-protviz >=0.7' - - 'r-rsqlite >=1.1' - - 'r-seqinr >=3.3' + - r-dbi >=0.5 + - r-protviz >=0.7 + - r-rsqlite >=1.1 + - r-seqinr >=3.3 + +source: + md5: eefcc88f521d4c3e655f177f357c1755 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics' - description: 'provides a functions for generating spectra libraries that can be used for MRM SRM MS workflows in proteomics. The package provides a BiblioSpec reader, a function which can add the protein information using a FASTA formatted amino acid file, and an export method for using the created library in the Spectronaut software. The package is developed, tested and used at the Functional Genomics Center Zurich .' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:specl - parent_recipe: - name: bioconductor-specl - path: recipes/bioconductor-specl - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-specond/meta.yaml b/recipes/bioconductor-specond/meta.yaml index dce56f3e7bbba..8bcb52b8a5775 100644 --- a/recipes/bioconductor-specond/meta.yaml +++ b/recipes/bioconductor-specond/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "1.56.0" %} +{% set version = "1.60.0" %} {% set name = "SpeCond" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package performs a gene expression data analysis to detect condition-specific genes. Such genes are significantly up- or down-regulated in a small number of conditions. It does so by fitting a mixture of normal distributions to the expression values. Conditions can be environmental conditions, different tissues, organs or any other sources that you wish to compare in terms of gene expression. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Condition specific detection from expression data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f189b2d0a72f0fb1b7a99bd0b2bb73ab build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-specond", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:specond + - doi:10.1186/gb-2011-12-12-413 + parent_recipe: + name: bioconductor-specond + path: recipes/bioconductor-specond + version: 1.34.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-fields - - 'r-hwriter >=1.1' - - 'r-mclust >=3.3.1' + - r-hwriter >=1.1 + - r-mclust >=3.3.1 - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-fields - - 'r-hwriter >=1.1' - - 'r-mclust >=3.3.1' + - r-hwriter >=1.1 + - r-mclust >=3.3.1 - r-rcolorbrewer + +source: + md5: 4d69e75f9dba65f187a00c758b279777 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>=2)' - summary: 'Condition specific detection from expression data' - description: 'This package performs a gene expression data analysis to detect condition-specific genes. Such genes are significantly up- or down-regulated in a small number of conditions. It does so by fitting a mixture of normal distributions to the expression values. Conditions can be environmental conditions, different tissues, organs or any other sources that you wish to compare in terms of gene expression.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:specond - - doi:10.1186/gb-2011-12-12-413 - parent_recipe: - name: bioconductor-specond - path: recipes/bioconductor-specond - version: 1.34.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spectra/meta.yaml b/recipes/bioconductor-spectra/meta.yaml index dd269b5bb66be..79def2f048174 100644 --- a/recipes/bioconductor-spectra/meta.yaml +++ b/recipes/bioconductor-spectra/meta.yaml @@ -1,52 +1,57 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "Spectra" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Spectra Infrastructure for Mass Spectrometry Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 32589596593389b703c87d7a05479fe3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spectra", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr (>= 1.1.0), msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0), rmarkdown, vdiffr (>= 1.0.0), msentropy, patrick requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-metabocoreutils >=1.14.0,<1.15.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-fs run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-metabocoreutils >=1.10.0,<1.11.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-metabocoreutils >=1.14.0,<1.15.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-fs + +source: + md5: cb974efa2343f87a21128ee11b972932 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Spectra Infrastructure for Mass Spectrometry Data' - description: 'The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spectraltad/meta.yaml b/recipes/bioconductor-spectraltad/meta.yaml index dc69aaf8e4fd8..255af0daa867a 100644 --- a/recipes/bioconductor-spectraltad/meta.yaml +++ b/recipes/bioconductor-spectraltad/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "SpectralTAD" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SpectralTAD is an R package designed to identify Topologically Associated Domains (TADs) from Hi-C contact matrices. It uses a modified version of spectral clustering that uses a sliding window to quickly detect TADs. The function works on a range of different formats of contact matrices and returns a bed file of TAD coordinates. The method does not require users to adjust any parameters to work and gives them control over the number of hierarchical levels to be returned. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 'SpectralTAD: Hierarchical TAD detection using spectral clustering' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 359760e22303de30ab396fcc7d5938af build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spectraltad", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hiccompare >=1.24.0,<1.25.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hiccompare >=1.28.0,<1.29.0 - r-base - r-cluster - r-dplyr @@ -32,22 +34,25 @@ requirements: - r-matrix - r-primme run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hiccompare >=1.24.0,<1.25.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hiccompare >=1.28.0,<1.29.0 - r-base - r-cluster - r-dplyr - r-magrittr - r-matrix - r-primme + +source: + md5: f5297d7ebd86a1eaec9b83d278a2ddcb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'SpectralTAD: Hierarchical TAD detection using spectral clustering' - description: 'SpectralTAD is an R package designed to identify Topologically Associated Domains (TADs) from Hi-C contact matrices. It uses a modified version of spectral clustering that uses a sliding window to quickly detect TADs. The function works on a range of different formats of contact matrices and returns a bed file of TAD coordinates. The method does not require users to adjust any parameters to work and gives them control over the number of hierarchical levels to be returned.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spectraql/build.sh b/recipes/bioconductor-spectraql/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-spectraql/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-spectraql/meta.yaml b/recipes/bioconductor-spectraql/meta.yaml new file mode 100644 index 0000000000000..c7b8559952ee0 --- /dev/null +++ b/recipes/bioconductor-spectraql/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.0.0" %} +{% set name = "SpectraQL" %} +{% set bioc = "3.20" %} + +about: + description: The Mass Spec Query Language (MassQL) is a domain-specific language enabling to express a query and retrieve mass spectrometry (MS) data in a more natural and understandable way for MS users. It is inspired by SQL and is by design programming language agnostic. The SpectraQL package adds support for the MassQL query language to R, in particular to MS data represented by Spectra objects. Users can thus apply MassQL expressions to analyze and retrieve specific data from Spectra objects. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: MassQL support for Spectra +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spectraql", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: testthat, msdata (>= 0.19.3), roxygen2, rmarkdown, knitr, S4Vectors, BiocStyle, mzR +requirements: + host: + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-spectra >=1.16.0,<1.17.0 + - r-base + run: + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-spectra >=1.16.0,<1.17.0 + - r-base +source: + md5: b3ec1a2add5ab132d6231d37b54abde8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-spem/meta.yaml b/recipes/bioconductor-spem/meta.yaml index a841243035900..bd58a4b0c1dc0 100644 --- a/recipes/bioconductor-spem/meta.yaml +++ b/recipes/bioconductor-spem/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "SPEM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package can optimize the parameter in S-system models given time series data + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: S-system parameter estimation method -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2b0ef40bd2428559cf559dfeb2a384f3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spem", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:spem + - doi:10.1089/cmb.2011.0269 + parent_recipe: + name: bioconductor-spem + path: recipes/bioconductor-spem + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-rsolnp run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-rsolnp + +source: + md5: 9a07117ec17b2565c419c992935962c2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'S-system parameter estimation method' - description: 'This package can optimize the parameter in S-system models given time series data' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:spem - - doi:10.1089/cmb.2011.0269 - parent_recipe: - name: bioconductor-spem - path: recipes/bioconductor-spem - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spia/meta.yaml b/recipes/bioconductor-spia/meta.yaml index dc1d20edf94e0..a053fe943c505 100644 --- a/recipes/bioconductor-spia/meta.yaml +++ b/recipes/bioconductor-spia/meta.yaml @@ -1,41 +1,22 @@ -{% set version = "2.54.0" %} +{% set version = "2.58.0" %} {% set name = "SPIA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a03ed18c41344eb23d6836cb337b9dc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spia", max_pin="x.x") }}' - noarch: generic -# Suggests: graph, Rgraphviz, hgu133plus2.db -requirements: - host: - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - r-base - run: - - 'bioconductor-kegggraph >=1.62.0,<1.63.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations' - description: 'This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study.' - license_file: LICENSE + extra: identifiers: - biotools:spia @@ -45,3 +26,28 @@ extra: path: recipes/bioconductor-spia version: 2.32.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: graph, Rgraphviz, hgu133plus2.db +requirements: + host: + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - r-base + run: + - bioconductor-kegggraph >=1.66.0,<1.67.0 + - r-base + +source: + md5: 1ac84aa5495b39db8d7007b0970bc4a3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-spiat/meta.yaml b/recipes/bioconductor-spiat/meta.yaml index 584c9b01bc639..a955bd06e0ffa 100644 --- a/recipes/bioconductor-spiat/meta.yaml +++ b/recipes/bioconductor-spiat/meta.yaml @@ -1,77 +1,84 @@ -{% set version = "1.4.1" %} +{% set version = "1.8.0" %} {% set name = "SPIAT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + file LICENSE + license_file: LICENSE + summary: Spatial Image Analysis of Tissues -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 45342ea9b5cbfbc01e38d6c7b7866852 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spiat", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, plotly (>= 4.9.0), knitr, rmarkdown, pkgdown, testthat, graphics, alphahull, Rtsne, umap, ComplexHeatmap, elsa requirements: + host: - - 'bioconductor-dittoseq >=1.14.0,<1.15.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'r-apcluster >=1.4.7' + - bioconductor-dittoseq >=1.18.0,<1.19.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-apcluster >=1.4.7 - r-base - - 'r-dbscan >=1.1-5' - - 'r-dplyr >=0.8.3' - - 'r-ggplot2 >=3.2.1' - - 'r-gridextra >=2.3' - - 'r-gtools >=3.8.1' - - 'r-mmand >=1.5.4' - - 'r-pracma >=2.2.5' - - 'r-rann >=2.6.1' + - r-dbscan >=1.1-5 + - r-dplyr >=0.8.3 + - r-ggplot2 >=3.2.1 + - r-gridextra >=2.3 + - r-gtools >=3.8.1 + - r-mmand >=1.5.4 + - r-pracma >=2.2.5 + - r-rann >=2.6.1 - r-raster - - 'r-reshape2 >=1.4.3' + - r-reshape2 >=1.4.3 - r-rlang - r-sp - r-spatstat.explore - r-spatstat.geom - - 'r-tibble >=2.1.3' + - r-tibble >=2.1.3 - r-vroom + run: - - 'bioconductor-dittoseq >=1.14.0,<1.15.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'r-apcluster >=1.4.7' + - bioconductor-dittoseq >=1.18.0,<1.19.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-apcluster >=1.4.7 - r-base - - 'r-dbscan >=1.1-5' - - 'r-dplyr >=0.8.3' - - 'r-ggplot2 >=3.2.1' - - 'r-gridextra >=2.3' - - 'r-gtools >=3.8.1' - - 'r-mmand >=1.5.4' - - 'r-pracma >=2.2.5' - - 'r-rann >=2.6.1' + - r-dbscan >=1.1-5 + - r-dplyr >=0.8.3 + - r-ggplot2 >=3.2.1 + - r-gridextra >=2.3 + - r-gtools >=3.8.1 + - r-mmand >=1.5.4 + - r-pracma >=2.2.5 + - r-rann >=2.6.1 - r-raster - - 'r-reshape2 >=1.4.3' + - r-reshape2 >=1.4.3 - r-rlang - r-sp - r-spatstat.explore - r-spatstat.geom - - 'r-tibble >=2.1.3' + - r-tibble >=2.1.3 - r-vroom + +source: + md5: 3ab0f28822c6e3562763db99043222eb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Artistic-2.0 + file LICENSE' - summary: 'Spatial Image Analysis of Tissues' - description: 'SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spicyr/meta.yaml b/recipes/bioconductor-spicyr/meta.yaml index cac91262c0ec4..b0fa83f0a52c6 100644 --- a/recipes/bioconductor-spicyr/meta.yaml +++ b/recipes/bioconductor-spicyr/meta.yaml @@ -1,81 +1,96 @@ -{% set version = "1.14.2" %} +{% set version = "1.18.0" %} {% set name = "spicyR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The spicyR package provides a framework for performing inference on changes in spatial relationships between pairs of cell types for cell-resolution spatial omics technologies. spicyR consists of three primary steps: (i) summarizing the degree of spatial localization between pairs of cell types for each image; (ii) modelling the variability in localization summary statistics as a function of cell counts and (iii) testing for changes in spatial localizations associated with a response variable.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Spatial analysis of in situ cytometry data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 36cba4820e1206ad3a7220e0430b245f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spicyr", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, pkgdown, imcRtools + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: SpatialDatasets, BiocStyle, knitr, rmarkdown, pkgdown, imcRtools, testthat (>= 3.0.0) requirements: + host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-classifyr >=3.6.0,<3.7.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-classifyr >=3.10.0,<3.11.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + - r-cli - r-concaveman + - r-coxme - r-data.table - r-dplyr - r-ggforce + - r-ggh4x + - r-ggnewscale - r-ggplot2 + - r-ggthemes - r-lmertest - - r-mgcv + - r-magrittr - r-pheatmap - r-rlang - r-scam - r-spatstat.explore - r-spatstat.geom + - r-survival - r-tibble - r-tidyr + run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-classifyr >=3.6.0,<3.7.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-classifyr >=3.10.0,<3.11.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + - r-cli - r-concaveman + - r-coxme - r-data.table - r-dplyr - r-ggforce + - r-ggh4x + - r-ggnewscale - r-ggplot2 + - r-ggthemes - r-lmertest - - r-mgcv + - r-magrittr - r-pheatmap - r-rlang - r-scam - r-spatstat.explore - r-spatstat.geom + - r-survival - r-tibble - r-tidyr + +source: + md5: 649f74757f7202a610dc5895c2b4d349 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Spatial analysis of in situ cytometry data' - description: 'The spicyR package provides a framework for performing inference on changes in spatial relationships between pairs of cell types for cell-resolution spatial omics technologies. spicyR consists of three primary steps: (i) summarizing the degree of spatial localization between pairs of cell types for each image; (ii) modelling the variability in localization summary statistics as a function of cell counts and (iii) testing for changes in spatial localizations associated with a response variable.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spikein/meta.yaml b/recipes/bioconductor-spikein/meta.yaml index f995b553eabe6..85e1bdb1a3a9f 100644 --- a/recipes/bioconductor-spikein/meta.yaml +++ b/recipes/bioconductor-spikein/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "SpikeIn" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 439f9d2eda54024edb7c1c81862d74c8 +about: + description: Contains the HGU133 and HGU95 spikein experiment data. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Spike-In Experiment Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spikein", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' + - bioconductor-affy >=1.84.0,<1.85.0 - r-base run: - - 'bioconductor-affy >=1.80.0,<1.81.0' + - bioconductor-affy >=1.84.0,<1.85.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f3fe76424ae86180f43ef63bbeb06181 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Spike-In Experiment Data' - description: 'Contains the HGU133 and HGU95 spikein experiment data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spikein/post-link.sh b/recipes/bioconductor-spikein/post-link.sh index 2b5335dd03814..825dc56db2be4 100644 --- a/recipes/bioconductor-spikein/post-link.sh +++ b/recipes/bioconductor-spikein/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "spikein-1.44.0" +installBiocDataPackage.sh "spikein-1.48.0" diff --git a/recipes/bioconductor-spikeinsubset/meta.yaml b/recipes/bioconductor-spikeinsubset/meta.yaml index 1cbb90bd6c7ae..3cf218cdde929 100644 --- a/recipes/bioconductor-spikeinsubset/meta.yaml +++ b/recipes/bioconductor-spikeinsubset/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "SpikeInSubset" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0c9b5af679c89a1468c9a6f581202e2b +about: + description: Includes probe-level and expression data for the HGU133 and HGU95 spike-in experiments + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Part of Affymetrix's Spike-In Experiment Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spikeinsubset", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9f377e32d90cb3e23ae288363c767af7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Part of Affymetrix''s Spike-In Experiment Data' - description: 'Includes probe-level and expression data for the HGU133 and HGU95 spike-in experiments' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spikeinsubset/post-link.sh b/recipes/bioconductor-spikeinsubset/post-link.sh index 0c176d193c9ac..f46db738e4a19 100644 --- a/recipes/bioconductor-spikeinsubset/post-link.sh +++ b/recipes/bioconductor-spikeinsubset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "spikeinsubset-1.42.0" +installBiocDataPackage.sh "spikeinsubset-1.46.0" diff --git a/recipes/bioconductor-spikeli/meta.yaml b/recipes/bioconductor-spikeli/meta.yaml index eaaa49bf1b204..b3b18fe625944 100644 --- a/recipes/bioconductor-spikeli/meta.yaml +++ b/recipes/bioconductor-spikeli/meta.yaml @@ -1,38 +1,20 @@ -{% set version = "2.62.0" %} +{% set version = "2.66.0" %} {% set name = "spikeLI" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 15e5851707938b83c34b9d5667d62f79 +about: + description: SpikeLI is a package that performs the analysis of the Affymetrix spike-in data using the Langmuir Isotherm. The aim of this package is to show the advantages of a physical-chemistry based analysis of the Affymetrix microarray data compared to the traditional methods. The spike-in (or Latin square) data for the HGU95 and HGU133 chipsets have been downloaded from the Affymetrix web site. The model used in the spikeLI package is described in details in E. Carlon and T. Heim, Physica A 362, 433 (2006). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spikeli", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool' - description: 'SpikeLI is a package that performs the analysis of the Affymetrix spike-in data using the Langmuir Isotherm. The aim of this package is to show the advantages of a physical-chemistry based analysis of the Affymetrix microarray data compared to the traditional methods. The spike-in (or Latin square) data for the HGU95 and HGU133 chipsets have been downloaded from the Affymetrix web site. The model used in the spikeLI package is described in details in E. Carlon and T. Heim, Physica A 362, 433 (2006).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' extra: identifiers: - biotools:spikeli @@ -41,4 +23,22 @@ extra: name: bioconductor-spikeli path: recipes/bioconductor-spikeli version: 2.40.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +requirements: + host: + - r-base + run: + - r-base +source: + md5: ed4042921be4030d00fee6fee87a5a69 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spiky/meta.yaml b/recipes/bioconductor-spiky/meta.yaml index e7f1720f0e287..024d282082423 100644 --- a/recipes/bioconductor-spiky/meta.yaml +++ b/recipes/bioconductor-spiky/meta.yaml @@ -1,61 +1,66 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "spiky" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: spiky implements methods and model generation for cfMeDIP (cell-free methylated DNA immunoprecipitation) with spike-in controls. CfMeDIP is an enrichment protocol which avoids destructive conversion of scarce template, making it ideal as a "liquid biopsy," but creating certain challenges in comparing results across specimens, subjects, and experiments. The use of synthetic spike-in standard oligos allows diagnostics performed with cfMeDIP to quantitatively compare samples across subjects, experiments, and time points in both relative and absolute terms. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Spike-in calibration for cell-free MeDIP -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8f710d2ecca4f24247ab38805d665b41 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spiky", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: covr, testthat, rmarkdown, markdown, knitr, devtools, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-bamlss - r-base - r-blandaltmanleh - r-ggplot2 - r-scales run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-bamlss - r-base - r-blandaltmanleh - r-ggplot2 - r-scales + +source: + md5: fef6f93009bc9faef02d22ecb3d4ea08 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Spike-in calibration for cell-free MeDIP' - description: 'spiky implements methods and model generation for cfMeDIP (cell-free methylated DNA immunoprecipitation) with spike-in controls. CfMeDIP is an enrichment protocol which avoids destructive conversion of scarce template, making it ideal as a "liquid biopsy," but creating certain challenges in comparing results across specimens, subjects, and experiments. The use of synthetic spike-in standard oligos allows diagnostics performed with cfMeDIP to quantitatively compare samples across subjects, experiments, and time points in both relative and absolute terms.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spillr/build.sh b/recipes/bioconductor-spillr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-spillr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-spillr/meta.yaml b/recipes/bioconductor-spillr/meta.yaml new file mode 100644 index 0000000000000..05fce2906dc38 --- /dev/null +++ b/recipes/bioconductor-spillr/meta.yaml @@ -0,0 +1,60 @@ +{% set version = "1.2.0" %} +{% set name = "spillR" %} +{% set bioc = "3.20" %} + +about: + description: Channel interference in mass cytometry can cause spillover and may result in miscounting of protein markers. We develop a nonparametric finite mixture model and use the mixture components to estimate the probability of spillover. We implement our method using expectation-maximization to fit the mixture model. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Spillover Compensation in Mass Cytometry Data + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spillr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, cowplot, testthat (>= 3.0.0), BiocStyle, hexbin +requirements: + host: + - bioconductor-catalyst >=1.30.0,<1.31.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-dplyr + - r-ggplot2 + - r-spatstat.univar + - r-tibble + - r-tidyr + - r-tidyselect + run: + - bioconductor-catalyst >=1.30.0,<1.31.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-dplyr + - r-ggplot2 + - r-spatstat.univar + - r-tibble + - r-tidyr + - r-tidyselect + +source: + md5: d2ea4ee02e32592d0833fc25efb858e1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-spktools/meta.yaml b/recipes/bioconductor-spktools/meta.yaml index e82233da53f09..361047d11fbfa 100644 --- a/recipes/bioconductor-spktools/meta.yaml +++ b/recipes/bioconductor-spktools/meta.yaml @@ -1,51 +1,57 @@ -{% set version = "1.58.0" %} +{% set version = "1.62.0" %} {% set name = "spkTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package contains functions that can be used to compare expression measures on different array platforms. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Methods for Spike-in Arrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9cc7d56d0cf0eec1e65d47d262525ba1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spktools", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:spktools + - doi:10.1093/nar/gkn430 + parent_recipe: + name: bioconductor-spktools + path: recipes/bioconductor-spktools + version: 1.36.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: xtable requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-gtools - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-gtools - r-rcolorbrewer + +source: + md5: a1a83ff154c3c0c08103ed53c801919e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Methods for Spike-in Arrays' - description: 'The package contains functions that can be used to compare expression measures on different array platforms.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:spktools - - doi:10.1093/nar/gkn430 - parent_recipe: - name: bioconductor-spktools - path: recipes/bioconductor-spktools - version: 1.36.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-splatter/meta.yaml b/recipes/bioconductor-splatter/meta.yaml index 15276553de261..2a5ce6ef8499c 100644 --- a/recipes/bioconductor-splatter/meta.yaml +++ b/recipes/bioconductor-splatter/meta.yaml @@ -1,36 +1,44 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "splatter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Simple Simulation of Single-cell RNA Sequencing Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1afec799cae913802068b5b20b32a598 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-splatter", max_pin="x.x") }}' - noarch: generic -# Suggests: BASiCS (>= 1.7.10), BiocManager, BiocSingular, BiocStyle, Biostrings, covr, cowplot, GenomeInfoDb, GenomicRanges, ggplot2 (>= 3.4.0), IRanges, igraph, knitr, limSolve, lme4, magick, mfa, phenopath, progress, preprocessCore, pscl, rmarkdown, scales, scater (>= 1.15.16), scDD, scran, SparseDC, spelling, testthat, VariantAnnotation, zinbwave, + +extra: + parent_recipe: + name: bioconductor-splatter + path: recipes/bioconductor-splatter + version: 1.4.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BASiCS (>= 1.7.10), BiocManager, BiocSingular, BiocStyle, Biostrings, covr, cowplot, GenomeInfoDb, GenomicRanges, ggplot2 (>= 3.4.0), igraph, IRanges, knitr, limSolve, lme4, magick, mfa, phenopath, preprocessCore, progress, pscl, rmarkdown, scales, scater (>= 1.15.16), scDD, scran, SparseDC, spelling, testthat, VariantAnnotation, zinbwave requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-checkmate >=2.0.0' + - r-checkmate >=2.0.0 - r-crayon - r-fitdistrplus - r-locfit @@ -38,33 +46,31 @@ requirements: - r-rlang - r-withr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-checkmate >=2.0.0' + - r-checkmate >=2.0.0 - r-crayon - r-fitdistrplus - r-locfit - r-matrixstats - r-rlang - r-withr + +source: + md5: 1438027116db29475e3f719975194e34 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Simple Simulation of Single-cell RNA Sequencing Data' - description: 'Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-splatter - path: recipes/bioconductor-splatter - version: 1.4.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-splicewiz/meta.yaml b/recipes/bioconductor-splicewiz/meta.yaml index 9a264cf06a4ec..6e74ff8e14015 100644 --- a/recipes/bioconductor-splicewiz/meta.yaml +++ b/recipes/bioconductor-splicewiz/meta.yaml @@ -1,132 +1,238 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "SpliceWiz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging. SpliceWiz is a user-friendly and performance-optimized R package for AS analysis, by processing alignment BAM files to quantify read counts across splice junctions, IRFinder-based intron retention quantitation, and supports novel splicing event identification. We introduce a novel visualization for AS using normalized coverage, thereby allowing visualization of differential AS across conditions. SpliceWiz features a shiny-based GUI facilitating interactive data exploration of results including gene ontology enrichment. It is performance optimized with multi-threaded processing of BAM files and a new COV file format for fast recall of sequencing coverage. Overall, SpliceWiz streamlines AS analysis, enabling reliable identification of functionally relevant AS events for further characterization. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: interactive analysis and visualization of alternative splicing in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 95ad1603bebc847d12b7dc715aef923a build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-splicewiz", max_pin="x.x") }}' -# Suggests: knitr, rmarkdown, openssl, crayon, splines, testthat (>= 3.0.0), DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, fgsea, Rsubread + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, crayon, splines, testthat (>= 3.0.0), DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, AnnotationDbi, fgsea, Rsubread # SystemRequirements: C++11, GNU make requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make + host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-nxtirfdata >=1.8.0,<1.9.0' - - 'bioconductor-ompbam >=1.6.0,<1.7.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + + - bioconductor-annotationhub >=3.14.0,<3.15.0 + + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + + - bioconductor-biocparallel >=1.40.0,<1.41.0 + + - bioconductor-biostrings >=2.74.0,<2.75.0 + + - bioconductor-bsgenome >=1.74.0,<1.75.0 + + - bioconductor-delayedarray >=0.32.0,<0.33.0 + + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + + - bioconductor-genefilter >=1.88.0,<1.89.0 + + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + + - bioconductor-genomicranges >=1.58.0,<1.59.0 + + - bioconductor-hdf5array >=1.34.0,<1.35.0 + + - bioconductor-iranges >=2.40.0,<2.41.0 + + - bioconductor-nxtirfdata >=1.12.0,<1.13.0 + + - bioconductor-ompbam >=1.10.0,<1.11.0 + + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + + - bioconductor-s4vectors >=0.44.0,<0.45.0 + + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-data.table + - r-dt + - r-fst + - r-ggplot2 + - r-heatmaply + - r-htmltools + + - r-httr + - r-magrittr + - r-matrixstats + - r-patchwork + - r-pheatmap + - r-plotly + - r-progress + - r-r.utils + - r-rcolorbrewer - - 'r-rcpp >=1.0.5' + + - r-rcpp >=1.0.5 + - r-rcppprogress + - r-rhandsontable + + - r-rsqlite + - r-rvest + - r-scales + - r-shiny + - r-shinydashboard + - r-shinyfiles + - r-shinywidgets + - r-stringi + - libblas + - liblapack + - zlib + - liblzma-devel + run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-nxtirfdata >=1.8.0,<1.9.0' - - 'bioconductor-ompbam >=1.6.0,<1.7.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + + - bioconductor-annotationhub >=3.14.0,<3.15.0 + + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + + - bioconductor-biocparallel >=1.40.0,<1.41.0 + + - bioconductor-biostrings >=2.74.0,<2.75.0 + + - bioconductor-bsgenome >=1.74.0,<1.75.0 + + - bioconductor-delayedarray >=0.32.0,<0.33.0 + + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + + - bioconductor-genefilter >=1.88.0,<1.89.0 + + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + + - bioconductor-genomicranges >=1.58.0,<1.59.0 + + - bioconductor-hdf5array >=1.34.0,<1.35.0 + + - bioconductor-iranges >=2.40.0,<2.41.0 + + - bioconductor-nxtirfdata >=1.12.0,<1.13.0 + + - bioconductor-ompbam >=1.10.0,<1.11.0 + + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + + - bioconductor-s4vectors >=0.44.0,<0.45.0 + + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-data.table + - r-dt + - r-fst + - r-ggplot2 + - r-heatmaply + - r-htmltools + + - r-httr + - r-magrittr + - r-matrixstats + - r-patchwork + - r-pheatmap + - r-plotly + - r-progress + - r-r.utils + - r-rcolorbrewer - - 'r-rcpp >=1.0.5' + + - r-rcpp >=1.0.5 + - r-rcppprogress + - r-rhandsontable + + - r-rsqlite + - r-rvest + - r-scales + - r-shiny + - r-shinydashboard + - r-shinyfiles + - r-shinywidgets + - r-stringi - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + +source: + md5: 610351969ab7832e2ab4fae3aa691736 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Easy, optimized, and accurate alternative splicing analysis in R' - description: 'Reads and fragments aligned to splice junctions can be used to quantify alternative splicing events (ASE). However, overlapping ASEs can confound their quantification. SpliceWiz quantifies ASEs, calculating percent-spliced-in (PSI) using junction reads, and intron retention using IRFinder-based quantitation. Novel filters identify ASEs that are relatively less confounded by overlapping events, whereby PSIs can be calculated with higher confidence. SpliceWiz is ultra-fast, using multi-threaded processing of BAM files. It can be run using a graphical user or command line interfaces. GUI-based interactive visualization of differential ASEs, including novel group-based RNA-seq coverage visualization, simplifies short-read RNA-seq analysis in R.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-splicingfactory/meta.yaml b/recipes/bioconductor-splicingfactory/meta.yaml index 79a03bd119400..2c2be84a9112c 100644 --- a/recipes/bioconductor-splicingfactory/meta.yaml +++ b/recipes/bioconductor-splicingfactory/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "SplicingFactory" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 354167193190b04ec94fac9c097b4503 +about: + description: The SplicingFactory R package uses transcript-level expression values to analyze splicing diversity based on various statistical measures, like Shannon entropy or the Gini index. These measures can quantify transcript isoform diversity within samples or between conditions. Additionally, the package analyzes the isoform diversity data, looking for significant changes between conditions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Splicing Diversity Analysis for Transcriptome Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-splicingfactory", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat, knitr, rmarkdown, ggplot2, tidyr requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base +source: + md5: 5fb4a1d4f62f5b569978fb2582f3a9b4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Splicing Diversity Analysis for Transcriptome Data' - description: 'The SplicingFactory R package uses transcript-level expression values to analyze splicing diversity based on various statistical measures, like Shannon entropy or the Gini index. These measures can quantify transcript isoform diversity within samples or between conditions. Additionally, the package analyzes the isoform diversity data, looking for significant changes between conditions.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-splicinggraphs/meta.yaml b/recipes/bioconductor-splicinggraphs/meta.yaml index dd2329883597e..2260ad7fda317 100644 --- a/recipes/bioconductor-splicinggraphs/meta.yaml +++ b/recipes/bioconductor-splicinggraphs/meta.yaml @@ -1,68 +1,74 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "SplicingGraphs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA-seq reads to the edges of a set of splicing graphs, and to summarize them in different ways. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 04e2a057bc1c6935ee13333acdf5ba52 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-splicinggraphs", max_pin="x.x") }}' - noarch: generic -# Suggests: igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit + +extra: + identifiers: + - biotools:splicinggraphs + - doi:10.1093/bioinformatics/18.suppl_1.s181 + parent_recipe: + name: bioconductor-splicinggraphs + path: recipes/bioconductor-splicinggraphs + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: igraph, Gviz, txdbmaker, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-igraph run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rgraphviz >=2.50.0,<2.51.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-igraph + +source: + md5: 5c9b55ff8c3c07ae1739c5d29f9bdafd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them' - description: 'This package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA-seq reads to the edges of a set of splicing graphs, and to summarize them in different ways.' -extra: - identifiers: - - biotools:splicinggraphs - - doi:10.1093/bioinformatics/18.suppl_1.s181 - parent_recipe: - name: bioconductor-splicinggraphs - path: recipes/bioconductor-splicinggraphs - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-splinetimer/meta.yaml b/recipes/bioconductor-splinetimer/meta.yaml index 19a7f65b4f424..42f3d1a42bc1d 100644 --- a/recipes/bioconductor-splinetimer/meta.yaml +++ b/recipes/bioconductor-splinetimer/meta.yaml @@ -1,61 +1,67 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "splineTimeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functions for differential gene expression analysis of gene expression time-course data. Natural cubic spline regression models are used. Identified genes may further be used for pathway enrichment analysis and/or the reconstruction of time dependent gene regulatory association networks. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 09454e29df75ff3f9d9e3f2780fb5db6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-splinetimer", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:splinetimer + - doi:10.1371/journal.pone.0160791 + parent_recipe: + name: bioconductor-splinetimer + path: recipes/bioconductor-splinetimer + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-fis >=1.30.0,<1.31.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-fis >=1.34.0,<1.35.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - - 'r-genenet >=1.2.13' + - r-genenet >=1.2.13 - r-gtools - r-igraph - - 'r-longitudinal >=1.1.12' + - r-longitudinal >=1.1.12 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-fis >=1.30.0,<1.31.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-fis >=1.34.0,<1.35.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - - 'r-genenet >=1.2.13' + - r-genenet >=1.2.13 - r-gtools - r-igraph - - 'r-longitudinal >=1.1.12' + - r-longitudinal >=1.1.12 + +source: + md5: 31423c3cd6996cadd3237a0b500630b5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction' - description: 'This package provides functions for differential gene expression analysis of gene expression time-course data. Natural cubic spline regression models are used. Identified genes may further be used for pathway enrichment analysis and/or the reconstruction of time dependent gene regulatory association networks.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:splinetimer - - doi:10.1371/journal.pone.0160791 - parent_recipe: - name: bioconductor-splinetimer - path: recipes/bioconductor-splinetimer - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-splinter/build_failure.linux-64.yaml b/recipes/bioconductor-splinter/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..d49d3627468b6 --- /dev/null +++ b/recipes/bioconductor-splinter/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: b5634120f13e5b7b455d9f2021ef704c91c2d7c721d0678c40dacb778fb57ff4 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-bsgenome.mmusculus.ucsc.mm9==1.4.0=r3.2.2_0"), MatchSpec("3.2.2*")} + Encountered problems while solving: + - nothing provides r 3.2.2* needed by bioconductor-bsgenome.mmusculus.ucsc.mm9-1.4.0-r3.2.2_0 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-biostrings >=2.74.0,<2.75.0 [0m is requested and can be installed; + [32mbioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0 [0m is installable with the potential options + [32mbioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0[0m would require + [32mr-base 3.3.2* [0m, which can be installed; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0[0m would require + [31mr 3.2.2* [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0[0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [32mbioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0[0m would require + [32mr-base 3.4.1* [0m, which can be installed; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.48.0,<1.50.0 [0m, which requires + [31mbioconductor-biostrings >=2.48.0,<2.50.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.50.0,<1.51.0 [0m, which requires + [31mbioconductor-biostrings >=2.50.0,<2.51.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.52.0,<1.53.0 [0m, which requires + [31mbioconductor-biostrings >=2.52.0,<2.53.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.54.0,<1.55.0 [0m, which requires + [31mbioconductor-biostrings >=2.54.0,<2.55.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.58.0,<1.59.0 [0m, which requires + [31mbioconductor-biostrings >=2.58.0,<2.59.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.56.0,<1.57.0 [0m, which requires + [31mbioconductor-biostrings >=2.56.0,<2.57.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.60.0,<1.61.0 [0m, which requires + [31mbioconductor-biostrings >=2.60.0,<2.61.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.62.0,<1.63.0 [0m, which requires + [31mbioconductor-biostrings >=2.62.0,<2.63.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.66.0,<1.67.0 [0m, which requires + [31mbioconductor-biostrings >=2.66.0,<2.67.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.68.0,<1.69.0 [0m, which requires + [31mbioconductor-biostrings >=2.68.0,<2.69.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.mmusculus.ucsc.mm9 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.70.0,<1.71.0 [0m, which requires + [31mbioconductor-biostrings >=2.70.0,<2.71.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-genomicalignments >=1.42.0,<1.43.0 [0m is not installable because it requires + [31mbioconductor-summarizedexperiment >=1.36.0,<1.37.0 [0m, which requires + [31mbioconductor-delayedarray >=0.32.0,<0.33.0 [0m, which requires + [31mbioconductor-sparsearray >=1.6.0,<1.7.0 [0m, which requires + [31mr-base >=4.4,<4.5.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-splinter/meta.yaml b/recipes/bioconductor-splinter/meta.yaml index e96e229c81b4a..b570f362ccfe7 100644 --- a/recipes/bioconductor-splinter/meta.yaml +++ b/recipes/bioconductor-splinter/meta.yaml @@ -1,75 +1,83 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "SPLINTER" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Splice Interpreter of Transcripts -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f328ebcc0e4d27dee8a98c2e230bd8dc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-splinter", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown + +extra: + identifiers: + - biotools:splinter + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-splinter + path: recipes/bioconductor-splinter + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: txdbmaker, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqlogo >=1.72.0,<1.73.0 - r-base - r-ggplot2 - r-googlevis - r-plyr - r-stringr run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-seqlogo >=1.68.0,<1.69.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqlogo >=1.72.0,<1.73.0 - r-base - r-ggplot2 - r-googlevis - r-plyr - r-stringr + +source: + md5: 16b64c57fa376c2bd1fe45c4c30fc810 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Splice Interpreter of Transcripts' - description: 'Provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:splinter - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-splinter - path: recipes/bioconductor-splinter - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-splots/meta.yaml b/recipes/bioconductor-splots/meta.yaml index adc7ad8e35825..ee468cfd7d700 100644 --- a/recipes/bioconductor-splots/meta.yaml +++ b/recipes/bioconductor-splots/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.68.0" %} +{% set version = "1.72.0" %} {% set name = "splots" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is here to support legacy usages of it, but it should not be used for new code development. It provides a single function, plotScreen, for visualising data in microtitre plate or slide format. As a better alternative for such functionality, please consider the platetools package on CRAN (https://cran.r-project.org/package=platetools and https://github.com/Swarchal/platetools), or ggplot2 (geom_raster, facet_wrap) as exemplified in the vignette of this package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Visualization of high-throughput assays in microtitre plate or slide format -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5f497af3c7a5fcdbba178a1ff3b411b9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-splots", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:splots + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-splots + path: recipes/bioconductor-splots + version: 1.46.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, assertthat, HD2013SGI, dplyr, ggplot2 requirements: host: @@ -27,21 +38,16 @@ requirements: run: - r-base - r-rcolorbrewer + +source: + md5: 392b3bdf03e72c4ae1e0d619340917df + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Visualization of high-throughput assays in microtitre plate or slide format' - description: 'This package is here to support legacy usages of it, but it should not be used for new code development. It provides a single function, plotScreen, for visualising data in microtitre plate or slide format. As a better alternative for such functionality, please consider the platetools package on CRAN (https://cran.r-project.org/package=platetools and https://github.com/Swarchal/platetools), or ggplot2 (geom_raster, facet_wrap) as exemplified in the vignette of this package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:splots - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-splots - path: recipes/bioconductor-splots - version: 1.46.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sponge/meta.yaml b/recipes/bioconductor-sponge/meta.yaml index 23ecf3938c90d..bebfd1b82edc3 100644 --- a/recipes/bioconductor-sponge/meta.yaml +++ b/recipes/bioconductor-sponge/meta.yaml @@ -1,30 +1,33 @@ -{% set version = "1.22.0" %} +{% set version = "1.28.0" %} {% set name = "SPONGE" %} -{% set bioc = "3.17" %} +{% set bioc = "3.20" %} + +about: + description: 'This package provides methods to efficiently detect competitive endogeneous RNA interactions between two genes. Such interactions are mediated by one or several miRNAs such that both gene and miRNA expression data for a larger number of samples is needed as input. The SPONGE package now also includes spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Sparse Partial Correlations On Gene Expression -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4ec8bdffb258be839e469d1baa50c4e9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ - noarch: generic + run_exports: '{{ pin_subpackage("bioconductor-sponge", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra, digest, doParallel, bigmemory, GSVA requirements: + host: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-mirbaseconverter >=1.24.0,<1.25.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 - r-base - r-caret - r-cvms @@ -50,11 +53,11 @@ requirements: - r-tidyr - r-tidyverse - r-tnet + run: - - 'bioconductor-biobase >=2.60.0,<2.61.0' - - 'bioconductor-biomart >=2.56.0,<2.57.0' - - 'bioconductor-complexheatmap >=2.16.0,<2.17.0' - - 'bioconductor-mirbaseconverter >=1.24.0,<1.25.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 - r-base - r-caret - r-cvms @@ -80,13 +83,16 @@ requirements: - r-tidyr - r-tidyverse - r-tnet + +source: + md5: 2133e52cd4046b2fa7e40988ac2cdc0c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=3)' - summary: 'Sparse Partial Correlations On Gene Expression' - description: 'This package provides methods to efficiently detect competitive endogeneous RNA interactions between two genes. Such interactions are mediated by one or several miRNAs such that both gene and miRNA expression data for a larger number of samples is needed as input. The SPONGE package now also includes spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spoon/build.sh b/recipes/bioconductor-spoon/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-spoon/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-spoon/meta.yaml b/recipes/bioconductor-spoon/meta.yaml new file mode 100644 index 0000000000000..df3e44840babe --- /dev/null +++ b/recipes/bioconductor-spoon/meta.yaml @@ -0,0 +1,56 @@ +{% set version = "1.2.0" %} +{% set name = "spoon" %} +{% set bioc = "3.20" %} + +about: + description: This package addresses the mean-variance relationship in spatially resolved transcriptomics data. Precision weights are generated for individual observations using Empirical Bayes techniques. These weights are used to rescale the data and covariates, which are then used as input in spatially variable gene detection tools. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Address the Mean-variance Relationship in Spatial Transcriptomics Data + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-spoon", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: testthat, STexampleData, knitr +requirements: + host: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-nnsvg >=1.10.0,<1.11.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-brisc + - r-matrix + run: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-nnsvg >=1.10.0,<1.11.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-brisc + - r-matrix + +source: + md5: dbeb4e68770bfb719dc68dcab0c96364 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-spotclean/meta.yaml b/recipes/bioconductor-spotclean/meta.yaml index 8832e69eae5ea..790773284954d 100644 --- a/recipes/bioconductor-spotclean/meta.yaml +++ b/recipes/bioconductor-spotclean/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.4.1" %} +{% set version = "1.8.0" %} {% set name = "SpotClean" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case due to bleed from nearby spots, an artifact we refer to as spot swapping. SpotClean is able to estimate the contamination rate in observed data and decontaminate the spot swapping effect, thus increase the sensitivity and precision of downstream analyses. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: SpotClean adjusts for spot swapping in spatial transcriptomics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b6e7be89394d959837993f3fd385ad55 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spotclean", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils, spelling requirements: host: - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -38,10 +40,10 @@ requirements: - r-tibble - r-viridis run: - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -53,13 +55,16 @@ requirements: - r-seurat - r-tibble - r-viridis + +source: + md5: 9bd3112138af8c8398a05bd0befe71d6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'SpotClean adjusts for spot swapping in spatial transcriptomics data' - description: 'SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case due to bleed from nearby spots, an artifact we refer to as spot swapping. SpotClean is able to estimate the contamination rate in observed data and decontaminate the spot swapping effect, thus increase the sensitivity and precision of downstream analyses.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spotlight/meta.yaml b/recipes/bioconductor-spotlight/meta.yaml index a29d88c4d27da..231c4cc86bdfc 100644 --- a/recipes/bioconductor-spotlight/meta.yaml +++ b/recipes/bioconductor-spotlight/meta.yaml @@ -1,28 +1,31 @@ -{% set version = "1.6.3" %} +{% set version = "1.10.0" %} {% set name = "SPOTlight" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: '`SPOTlight`provides a method to deconvolute spatial transcriptomics spots using a seeded NMF approach along with visualization tools to assess the results. Spatially resolved gene expression profiles are key to understand tissue organization and function. However, novel spatial transcriptomics (ST) profiling techniques lack single-cell resolution and require a combination with single-cell RNA sequencing (scRNA-seq) information to deconvolute the spatially indexed datasets. Leveraging the strengths of both data types, we developed SPOTlight, a computational tool that enables the integration of ST with scRNA-seq data to infer the location of cell types and states within a complex tissue. SPOTlight is centered around a seeded non-negative matrix factorization (NMF) regression, initialized using cell-type marker genes and non-negative least squares (NNLS) to subsequently deconvolute ST capture locations (spots).' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: '`SPOTlight`: Spatial Transcriptomics Deconvolution' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 00759051612f8f17697afd03507d6d8c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spotlight", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, colorBlindness, DelayedArray, DropletUtils, ExperimentHub, ggcorrplot, grDevices, grid, igraph, jpeg, knitr, methods, png, rmarkdown, scater, scatterpie, scran, Seurat, SeuratObject, SpatialExperiment, SummarizedExperiment, S4Vectors, TabulaMurisSenisData, TENxVisiumData, testthat + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, colorBlindness, DelayedArray, DropletUtils, ExperimentHub, ggcorrplot, grDevices, grid, igraph, jpeg, knitr, methods, png, rmarkdown, scater, scatterpie, scran, SpatialExperiment, SummarizedExperiment, S4Vectors, TabulaMurisSenisData, TENxVisiumData, testthat requirements: host: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 - r-base - r-ggplot2 - r-matrix @@ -30,20 +33,24 @@ requirements: - r-nmf - r-nnls run: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsematrixstats >=1.18.0,<1.19.0 - r-base - r-ggplot2 - r-matrix - r-matrixstats - r-nmf - r-nnls + +source: + md5: 638290a97f214a906f347c6bb5a8c5dd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: '`SPOTlight`: Spatial Transcriptomics Deconvolution' - description: '`SPOTlight`provides a method to deconvolute spatial transcriptomics spots using a seeded NMF approach along with visualization tools to assess the results. Spatially resolved gene expression profiles are key to understand tissue organization and function. However, novel spatial transcriptomics (ST) profiling techniques lack single-cell resolution and require a combination with single-cell RNA sequencing (scRNA-seq) information to deconvolute the spatially indexed datasets. Leveraging the strengths of both data types, we developed SPOTlight, a computational tool that enables the integration of ST with scRNA-seq data to infer the location of cell types and states within a complex tissue. SPOTlight is centered around a seeded non-negative matrix factorization (NMF) regression, initialized using cell-type marker genes and non-negative least squares (NNLS) to subsequently deconvolute ST capture locations (spots).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spqn/meta.yaml b/recipes/bioconductor-spqn/meta.yaml index c6aa1696bc6a1..0c2ba7d3536de 100644 --- a/recipes/bioconductor-spqn/meta.yaml +++ b/recipes/bioconductor-spqn/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "spqn" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The spqn package implements spatial quantile normalization (SpQN). This method was developed to remove a mean-correlation relationship in correlation matrices built from gene expression data. It can serve as pre-processing step prior to a co-expression analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Spatial quantile normalization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 63599cd8ebe97287b176d98cb3d9de43 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spqn", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, tools, spqnData (>= 0.99.3), RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-ggridges - r-matrixstats run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-ggridges - r-matrixstats + +source: + md5: 9f6486af7313e8b6ceed1ffd6f91f0a3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Spatial quantile normalization' - description: 'The spqn package implements spatial quantile normalization (SpQN). This method was developed to remove a mean-correlation relationship in correlation matrices built from gene expression data. It can serve as pre-processing step prior to a co-expression analysis.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spqndata/meta.yaml b/recipes/bioconductor-spqndata/meta.yaml index efac37f68f5cb..5b39331c88cc1 100644 --- a/recipes/bioconductor-spqndata/meta.yaml +++ b/recipes/bioconductor-spqndata/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "spqnData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 453bf944ea40956afef2bd868f92d747 +about: + description: Bulk RNA-seq from GTEx on 4,000 randomly selected, expressed genes. Data has been processed for co-expression analysis. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Data for the spqn package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spqndata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8366c866aac67ef93786d2f59a98d015 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Data for the spqn package' - description: 'Bulk RNA-seq from GTEx on 4,000 randomly selected, expressed genes. Data has been processed for co-expression analysis.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-spqndata/post-link.sh b/recipes/bioconductor-spqndata/post-link.sh index 4468f52ef6133..b4c6a638418b2 100644 --- a/recipes/bioconductor-spqndata/post-link.sh +++ b/recipes/bioconductor-spqndata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "spqndata-1.14.0" +installBiocDataPackage.sh "spqndata-1.18.0" diff --git a/recipes/bioconductor-spsimseq/meta.yaml b/recipes/bioconductor-spsimseq/meta.yaml index e85f49127980d..7378bcd899b2c 100644 --- a/recipes/bioconductor-spsimseq/meta.yaml +++ b/recipes/bioconductor-spsimseq/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "SPsimSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SPsimSeq uses a specially designed exponential family for density estimation to constructs the distribution of gene expression levels from a given real RNA sequencing data (single-cell or bulk), and subsequently simulates a new dataset from the estimated marginal distributions using Gaussian-copulas to retain the dependence between genes. It allows simulation of multiple groups and batches with any required sample size and library size. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Semi-parametric simulation tool for bulk and single-cell RNA sequencing data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1ccc188618b92dcf94489a00d7faa5b4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-spsimseq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, LSD, testthat, BiocStyle requirements: host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-fitdistrplus - r-hmisc - r-mvtnorm - r-wgcna run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-phyloseq >=1.46.0,<1.47.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-fitdistrplus - r-hmisc - r-mvtnorm - r-wgcna + +source: + md5: 2130ee7f20b6c1f9cd2d8cbcae5e49c8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Semi-parametric simulation tool for bulk and single-cell RNA sequencing data' - description: 'SPsimSeq uses a specially designed exponential family for density estimation to constructs the distribution of gene expression levels from a given real RNA sequencing data (single-cell or bulk), and subsequently simulates a new dataset from the estimated marginal distributions using Gaussian-copulas to retain the dependence between genes. It allows simulation of multiple groups and batches with any required sample size and library size.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sqldataframe/meta.yaml b/recipes/bioconductor-sqldataframe/meta.yaml index 4ab1d6af33f2c..79ce22f0fb98c 100644 --- a/recipes/bioconductor-sqldataframe/meta.yaml +++ b/recipes/bioconductor-sqldataframe/meta.yaml @@ -1,53 +1,54 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "SQLDataFrame" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implements bindings for SQL tables that are compatible with Bioconductor S4 data structures, namely the DataFrame and DelayedArray. This allows SQL-derived data to be easily used inside other Bioconductor objects (e.g., SummarizedExperiments) while keeping everything on disk. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 3); File LICENSE + license_file: LICENSE + summary: Representation of SQL tables in DataFrame metaphor -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4153fe66ee281c087e77c6706a2b2faf build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sqldataframe", max_pin="x.x") }}' - noarch: generic -# Suggests: RMySQL, bigrquery, testthat, knitr, rmarkdown, DelayedArray, GenomicRanges + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dbi - - 'r-dbplyr >=1.4.0' - - 'r-dplyr >=0.8.0.1' - - r-lazyeval + - r-duckdb - r-rsqlite - - r-tibble run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dbi - - 'r-dbplyr >=1.4.0' - - 'r-dplyr >=0.8.0.1' - - r-lazyeval + - r-duckdb - r-rsqlite - - r-tibble + +source: + md5: 2448466a5203b92539fe0e1b7522379b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Representation of SQL database in DataFrame metaphor' - description: 'SQLDataFrame is developed to lazily represent and efficiently analyze SQL-based tables in _R_. SQLDataFrame supports common and familiar ''DataFrame'' operations such as ''['' subsetting, rbind, cbind, etc.. The internal implementation is based on the widely adopted dplyr grammar and SQL commands. In-memory datasets or plain text files (.txt, .csv, etc.) could also be easily converted into SQLDataFrames objects (which generates a new database on-disk).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-squallms/build.sh b/recipes/bioconductor-squallms/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-squallms/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-squallms/build_failure.linux-64.yaml b/recipes/bioconductor-squallms/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..044178d353fc6 --- /dev/null +++ b/recipes/bioconductor-squallms/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: f1047f790c07bfa20f7ad0930515944c982b405c0a24ff5630cb1e2e1d14500a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-rams")} + Encountered problems while solving: + - nothing provides requested r-rams + + Could not solve for environment specs + The following package could not be installed + [31mr-rams[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-rams")} + Encountered problems while solving: + - nothing provides requested r-rams + + Could not solve for environment specs + The following package could not be installed + [31mr-rams[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-rams")} + Encountered problems while solving: + - nothing provides requested r-rams + + Could not solve for environment specs + The following package could not be installed + [31mr-rams[0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-squallms/meta.yaml b/recipes/bioconductor-squallms/meta.yaml new file mode 100644 index 0000000000000..b6b858d299f7d --- /dev/null +++ b/recipes/bioconductor-squallms/meta.yaml @@ -0,0 +1,68 @@ +{% set version = "1.0.0" %} +{% set name = "squallms" %} +{% set bioc = "3.20" %} + +about: + description: squallms is a Bioconductor R package that implements a "semi-labeled" approach to untargeted mass spectrometry data. It pulls in raw data from mass-spec files to calculate several metrics that are then used to label MS features in bulk as high or low quality. These metrics of peak quality are then passed to a simple logistic model that produces a fully-labeled dataset suitable for downstream analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Speedy quality assurance via lasso labeling for LC-MS data + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-squallms", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-msexperiment >=1.8.0,<1.9.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-xcms >=4.4.0,<4.5.0 + - r-base + - r-caret + - r-data.table + - r-dplyr + - r-ggplot2 + - r-keys + - r-plotly + - r-rams + - r-shiny + - r-tibble + - r-tidyr + run: + - bioconductor-msexperiment >=1.8.0,<1.9.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-xcms >=4.4.0,<4.5.0 + - r-base + - r-caret + - r-data.table + - r-dplyr + - r-ggplot2 + - r-keys + - r-plotly + - r-rams + - r-shiny + - r-tibble + - r-tidyr + +source: + md5: 470efd3eef6b7b699f8c4aaa234e688c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-sracipe/meta.yaml b/recipes/bioconductor-sracipe/meta.yaml index 3b7c215452e39..7f62b9f222c25 100644 --- a/recipes/bioconductor-sracipe/meta.yaml +++ b/recipes/bioconductor-sracipe/meta.yaml @@ -1,29 +1,35 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "sRACIPE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: sRACIPE implements a randomization-based method for gene circuit modeling. It allows us to study the effect of both the gene expression noise and the parametric variation on any gene regulatory circuit (GRC) using only its topology, and simulates an ensemble of models with random kinetic parameters at multiple noise levels. Statistical analysis of the generated gene expressions reveals the basin of attraction and stability of various phenotypic states and their changes associated with intrinsic and extrinsic noises. sRACIPE provides a holistic picture to evaluate the effects of both the stochastic nature of cellular processes and the parametric variation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Systems biology tool to simulate gene regulatory circuits -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 84a1b79b944741fc6ecab26168020841 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sracipe", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, rmarkdown, tinytest, doFuture requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-gplots @@ -38,9 +44,9 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-gplots @@ -52,17 +58,16 @@ requirements: - r-reshape2 - r-umap - r-visnetwork - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 44e5d2919a826491f03b1180974b4098 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Systems biology tool to simulate gene regulatory circuits' - description: 'sRACIPE implements a randomization-based method for gene circuit modeling. It allows us to study the effect of both the gene expression noise and the parametric variation on any gene regulatory circuit (GRC) using only its topology, and simulates an ensemble of models with random kinetic parameters at multiple noise levels. Statistical analysis of the generated gene expressions reveals the basin of attraction and stability of various phenotypic states and their changes associated with intrinsic and extrinsic noises. sRACIPE provides a holistic picture to evaluate the effects of both the stochastic nature of cellular processes and the parametric variation.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sscu/meta.yaml b/recipes/bioconductor-sscu/meta.yaml index 2d4fb8c20013f..43928cfd5d484 100644 --- a/recipes/bioconductor-sscu/meta.yaml +++ b/recipes/bioconductor-sscu/meta.yaml @@ -1,45 +1,22 @@ -{% set version = "2.32.0" %} +{% set version = "2.36.0" %} {% set name = "sscu" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package calculates the indexes for selective stength in codon usage in bacteria species. (1) The package can calculate the strength of selected codon usage bias (sscu, also named as s_index) based on Paul Sharp's method. The method take into account of background mutation rate, and focus only on four pairs of codons with universal translational advantages in all bacterial species. Thus the sscu index is comparable among different species. (2) The package can detect the strength of translational accuracy selection by Akashi's test. The test tabulating all codons into four categories with the feature as conserved/variable amino acids and optimal/non-optimal codons. (3) Optimal codon lists (selected codons) can be calculated by either op_highly function (by using the highly expressed genes compared with all genes to identify optimal codons), or op_corre_CodonW/op_corre_NCprime function (by correlative method developed by Hershberg & Petrov). Users will have a list of optimal codons for further analysis, such as input to the Akashi's test. (4) The detailed codon usage information, such as RSCU value, number of optimal codons in the highly/all gene set, as well as the genomic gc3 value, can be calculate by the optimal_codon_statistics and genomic_gc3 function. (5) Furthermore, we added one test function low_frequency_op in the package. The function try to find the low frequency optimal codons, among all the optimal codons identified by the op_highly function. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Strength of Selected Codon Usage -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3856e06321ac866e2664573b452c6a85 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sscu", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown -requirements: - host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - r-base - - 'r-seqinr >=3.1-3' - run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - r-base - - 'r-seqinr >=3.1-3' -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Strength of Selected Codon Usage' - description: 'The package calculates the indexes for selective stength in codon usage in bacteria species. (1) The package can calculate the strength of selected codon usage bias (sscu, also named as s_index) based on Paul Sharp''s method. The method take into account of background mutation rate, and focus only on four pairs of codons with universal translational advantages in all bacterial species. Thus the sscu index is comparable among different species. (2) The package can detect the strength of translational accuracy selection by Akashi''s test. The test tabulating all codons into four categories with the feature as conserved/variable amino acids and optimal/non-optimal codons. (3) Optimal codon lists (selected codons) can be calculated by either op_highly function (by using the highly expressed genes compared with all genes to identify optimal codons), or op_corre_CodonW/op_corre_NCprime function (by correlative method developed by Hershberg & Petrov). Users will have a list of optimal codons for further analysis, such as input to the Akashi''s test. (4) The detailed codon usage information, such as RSCU value, number of optimal codons in the highly/all gene set, as well as the genomic gc3 value, can be calculate by the optimal_codon_statistics and genomic_gc3 function. (5) Furthermore, we added one test function low_frequency_op in the package. The function try to find the low frequency optimal codons, among all the optimal codons identified by the op_highly function.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:sscu @@ -49,3 +26,32 @@ extra: path: recipes/bioconductor-sscu version: 2.10.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - r-base + - r-seqinr >=3.1-3 + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - r-base + - r-seqinr >=3.1-3 + +source: + md5: 6c8a2699eccbfa005a3f640275b8936d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-sseq/meta.yaml b/recipes/bioconductor-sseq/meta.yaml index 2ecb6cdba2b18..ba7555be7a0f0 100644 --- a/recipes/bioconductor-sseq/meta.yaml +++ b/recipes/bioconductor-sseq/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "sSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The purpose of this package is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are shrunk towards an estimated target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9276919acd944871a6e05a8dbeed6b9f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sseq", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:sseq + - doi:10.1093/bioinformatics/btt143 + parent_recipe: + name: bioconductor-sseq + path: recipes/bioconductor-sseq + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -28,21 +39,16 @@ requirements: - r-base - r-catools - r-rcolorbrewer + +source: + md5: f53027265f3d855adb218783bdc23f3a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size' - description: 'The purpose of this package is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are shrunk towards an estimated target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:sseq - - doi:10.1093/bioinformatics/btt143 - parent_recipe: - name: bioconductor-sseq - path: recipes/bioconductor-sseq - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ssize/meta.yaml b/recipes/bioconductor-ssize/meta.yaml index e7e2942a52185..747653a0c8d1e 100644 --- a/recipes/bioconductor-ssize/meta.yaml +++ b/recipes/bioconductor-ssize/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.76.0" %} +{% set version = "1.80.0" %} {% set name = "ssize" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions for computing and displaying sample size information for gene expression arrays. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Estimate Microarray Sample Size -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b61fbe78b68fecd3090e1c658a284b83 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ssize", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:ssize + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ssize + path: recipes/bioconductor-ssize + version: 1.54.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -28,21 +39,16 @@ requirements: - r-base - r-gdata - r-xtable + +source: + md5: 7655a80644294da2d9b1daffb06917b7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Estimate Microarray Sample Size' - description: 'Functions for computing and displaying sample size information for gene expression arrays.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:ssize - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-ssize - path: recipes/bioconductor-ssize - version: 1.54.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ssnappy/meta.yaml b/recipes/bioconductor-ssnappy/meta.yaml index 5b49df2a9511a..7206776ae743e 100644 --- a/recipes/bioconductor-ssnappy/meta.yaml +++ b/recipes/bioconductor-ssnappy/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.6.1" %} +{% set version = "1.10.0" %} {% set name = "sSNAPPY" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A single sample pathway perturbation testing method for RNA-seq data. The method propagates changes in gene expression down gene-set topologies to compute single-sample directional pathway perturbation scores that reflect potential direction of change. Perturbation scores can be used to test significance of pathway perturbation at both individual-sample and treatment levels. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Single Sample directioNAl Pathway Perturbation analYsis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 15f7a550e110c069710c3f6572a06e83 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ssnappy", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools, knitr, pander, patchwork, rmarkdown, spelling, testthat (>= 3.0.0), tidyverse # SystemRequirements: C++11 requirements: host: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-graphite >=1.48.0,<1.49.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-graphite >=1.52.0,<1.53.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-dplyr >=1.1' + - r-dplyr >=1.1 - r-ggforce - r-ggplot2 - r-ggraph @@ -42,12 +44,12 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-graphite >=1.48.0,<1.49.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-graphite >=1.52.0,<1.53.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-dplyr >=1.1' + - r-dplyr >=1.1 - r-ggforce - r-ggplot2 - r-ggraph @@ -60,13 +62,16 @@ requirements: - r-stringr - r-tibble - r-tidyr + +source: + md5: 19c4be1cf2891d0fe3497ebb4bfcbf2f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Single Sample directioNAl Pathway Perturbation analYsis' - description: 'A single sample pathway perturbation testing method for RNA-seq data. The method propagates changes in gene expression down gene-set topologies to compute single-sample directional pathway perturbation scores that reflect potential direction of change. Perturbation scores can be used to test significance of pathway perturbation at both individual-sample and treatment levels.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sspaths/meta.yaml b/recipes/bioconductor-sspaths/meta.yaml index e7f074e25161c..f8587acb4b1e8 100644 --- a/recipes/bioconductor-sspaths/meta.yaml +++ b/recipes/bioconductor-sspaths/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "ssPATHS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 121909c57596e3cd0d817cac2deb22c9 +about: + description: This package generates pathway scores from expression data for single samples after training on a reference cohort. The score is generated by taking the expression of a gene set (pathway) from a reference cohort and performing linear discriminant analysis to distinguish samples in the cohort that have the pathway augmented and not. The separating hyperplane is then used to score new samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 'ssPATHS: Single Sample PATHway Score' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sspaths", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: ggplot2, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dml - r-mess - r-rocr run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dml - r-mess - r-rocr +source: + md5: 01957efa93b77612a47d0955356653a0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'ssPATHS: Single Sample PATHway Score' - description: 'This package generates pathway scores from expression data for single samples after training on a reference cohort. The score is generated by taking the expression of a gene set (pathway) from a reference cohort and performing linear discriminant analysis to distinguish samples in the cohort that have the pathway augmented and not. The separating hyperplane is then used to score new samples.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ssrch/meta.yaml b/recipes/bioconductor-ssrch/meta.yaml index b3495f2f86488..9c8b6c5a80962 100644 --- a/recipes/bioconductor-ssrch/meta.yaml +++ b/recipes/bioconductor-ssrch/meta.yaml @@ -1,24 +1,22 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "ssrch" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 095c153ce56b89d040c929a8c1af6840 +about: + description: Demonstrate tokenization and a search gadget for collections of CSV files. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: a simple search engine build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ssrch", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, testthat, rmarkdown, BiocStyle requirements: host: @@ -29,12 +27,14 @@ requirements: - r-base - r-dt - r-shiny +source: + md5: 50c6e553985475d718389f6923691ef0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'a simple search engine' - description: 'Demonstrate tokenization and a search gadget for collections of CSV files.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ssviz/meta.yaml b/recipes/bioconductor-ssviz/meta.yaml index 87ac9b79c48bf..80c526c037659 100644 --- a/recipes/bioconductor-ssviz/meta.yaml +++ b/recipes/bioconductor-ssviz/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "ssviz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Small RNA sequencing viewer + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A small RNA-seq visualizer and analysis toolkit -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 00bd4a7d6a57af51b74187993bdf84c4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ssviz", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:ssviz + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ssviz + path: recipes/bioconductor-ssviz + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-ggplot2 - r-rcolorbrewer - r-reshape run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-ggplot2 - r-rcolorbrewer - r-reshape + +source: + md5: 5a9f304b4fdae1b67425470948684237 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'A small RNA-seq visualizer and analysis toolkit' - description: 'Small RNA sequencing viewer' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:ssviz - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-ssviz - path: recipes/bioconductor-ssviz - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-stabmap/build.sh b/recipes/bioconductor-stabmap/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-stabmap/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-stabmap/meta.yaml b/recipes/bioconductor-stabmap/meta.yaml new file mode 100644 index 0000000000000..d6f1f6d465049 --- /dev/null +++ b/recipes/bioconductor-stabmap/meta.yaml @@ -0,0 +1,64 @@ +{% set version = "1.0.0" %} +{% set name = "StabMap" %} +{% set bioc = "3.20" %} + +about: + description: StabMap performs single cell mosaic data integration by first building a mosaic data topology, and for each reference dataset, traverses the topology to project and predict data onto a common embedding. Mosaic data should be provided in a list format, with all relevant features included in the data matrices within each list object. The output of stabMap is a joint low-dimensional embedding taking into account all available relevant features. Expression imputation can also be performed using the StabMap embedding and any of the original data matrices for given reference and query cell lists. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Stabilised mosaic single cell data integration using unshared features + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-stabmap", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: scran, scater, knitr, UpSetR, gridExtra, SingleCellMultiModal, BiocStyle, magrittr, testthat (>= 3.0.0), purrr, sparseMatrixStats +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-abind + - r-base + - r-igraph + - r-mass + - r-matrix + - r-slam + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-abind + - r-base + - r-igraph + - r-mass + - r-matrix + - r-slam + +source: + md5: d6f3b17a6b922b54b815d22481ed956f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-stager/meta.yaml b/recipes/bioconductor-stager/meta.yaml index afdbee6634400..bfe04989444c7 100644 --- a/recipes/bioconductor-stager/meta.yaml +++ b/recipes/bioconductor-stager/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "stageR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cdbf6ab3c35c3e019b0ce786ad85eb38 +about: + description: The stageR package allows automated stage-wise analysis of high-throughput gene expression data. The method is published in Genome Biology at https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0 + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GNU General Public License version 3 + summary: 'stageR: stage-wise analysis of high throughput gene expression data in R' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-stager", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma, DEXSeq, testthat requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base +source: + md5: 00122ad1bc1040fc4eb4e3430d9bb8ef + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GNU General Public License version 3' - summary: 'stageR: stage-wise analysis of high throughput gene expression data in R' - description: 'The stageR package allows automated stage-wise analysis of high-throughput gene expression data. The method is published in Genome Biology at https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-standr/meta.yaml b/recipes/bioconductor-standr/meta.yaml index c54e0c516383c..b73ac41ba099c 100644 --- a/recipes/bioconductor-standr/meta.yaml +++ b/recipes/bioconductor-standr/meta.yaml @@ -1,36 +1,39 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "standR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. standR allows data inspection, quality control, normalization, batch correction and evaluation with informative visualizations. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Spatial transcriptome analyses of Nanostring's DSP data in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94e29a2001fbb9d0bfa1488ae7039aa7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-standr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, ExperimentHub, rmarkdown, scater, uwot, ggpubr, ggrepel, cluster, testthat (>= 3.0.0) requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-ruvseq >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-ruvseq >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggalluvial @@ -42,16 +45,17 @@ requirements: - r-ruv - r-tibble - r-tidyr + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-ruvseq >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-ruvseq >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggalluvial @@ -63,13 +67,16 @@ requirements: - r-ruv - r-tibble - r-tidyr + +source: + md5: db56e912a06aba49932192a6206fcc55 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Spatial transcriptome analyses of Nanostring''s DSP data in R' - description: 'standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring''s GeoMX DSP data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. standR allows data inspection, quality control, normalization, batch correction and evaluation with informative visualizations.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-stategra/meta.yaml b/recipes/bioconductor-stategra/meta.yaml index 21e069eaf1b45..0799f52f29549 100644 --- a/recipes/bioconductor-stategra/meta.yaml +++ b/recipes/bioconductor-stategra/meta.yaml @@ -1,31 +1,42 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "STATegRa" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Classes and tools for multi-omics data integration. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Classes and methods for multi-omics data integration -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: be42ca7786d4b038ad3f706492c74022 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-stategra", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:stategra + - doi:10.14806/ej.20.a.768 + parent_recipe: + name: bioconductor-stategra + path: recipes/bioconductor-stategra + version: 1.16.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>= 1.3), roxygen2, doSNOW requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-calibrate - r-foreach @@ -34,10 +45,10 @@ requirements: - r-gridextra - r-mass run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-calibrate - r-foreach @@ -45,21 +56,16 @@ requirements: - r-gplots - r-gridextra - r-mass + +source: + md5: 5bc7c8398540e93911f698c4e5c411ab + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Classes and methods for multi-omics data integration' - description: 'Classes and tools for multi-omics data integration.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:stategra - - doi:10.14806/ej.20.a.768 - parent_recipe: - name: bioconductor-stategra - path: recipes/bioconductor-stategra - version: 1.16.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-statial/meta.yaml b/recipes/bioconductor-statial/meta.yaml index d414780320fc2..0dea6f4f92c5c 100644 --- a/recipes/bioconductor-statial/meta.yaml +++ b/recipes/bioconductor-statial/meta.yaml @@ -1,34 +1,39 @@ -{% set version = "1.4.5" %} +{% set version = "1.8.0" %} {% set name = "Statial" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Statial is a suite of functions for identifying changes in cell state. The functionality provided by Statial provides robust quantification of cell type localisation which are invariant to changes in tissue structure. In addition to this Statial uncovers changes in marker expression associated with varying levels of localisation. These features can be used to explore how the structure and function of different cell types may be altered by the agents they are surrounded with. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A package to identify changes in cell state relative to spatial associations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e7151f23bb952401803e4d239390c210 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-statial", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, testthat (>= 3.0.0), ClassifyR, spicyR, ggsurvfit, lisaClust, survival requirements: + host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treekor >=1.14.0,<1.15.0 - r-base + - r-cluster - r-concaveman - r-data.table - r-dplyr @@ -43,14 +48,17 @@ requirements: - r-tibble - r-tidyr - r-tidyselect + run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treekor >=1.14.0,<1.15.0 - r-base + - r-cluster - r-concaveman - r-data.table - r-dplyr @@ -65,13 +73,16 @@ requirements: - r-tibble - r-tidyr - r-tidyselect + +source: + md5: 2ea52b3f2cf7b4b8a0968030fd9c9d7c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'A package to identify changes in cell state relative to spatial associations' - description: 'Statial is a suite of functions for identifying changes in cell state. The functionality provided by Statial provides robust quantification of cell type localisation which are invariant to changes in tissue structure. In addition to this Statial uncovers changes in marker expression associated with varying levels of localisation. These features can be used to explore how the structure and function of different cell types may be altered by the agents they are surrounded with.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-stattarget/meta.yaml b/recipes/bioconductor-stattarget/meta.yaml index c3b72f32f6d1c..09ac6fc328885 100644 --- a/recipes/bioconductor-stattarget/meta.yaml +++ b/recipes/bioconductor-stattarget/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "statTarget" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A streamlined tool provides a graphical user interface for quality control based signal drift correction (QC-RFSC), integration of data from multi-batch MS-based experiments, and the comprehensive statistical analysis in metabolomics and proteomics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Statistical Analysis of Molecular Profiles -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a504e674b8756201ca93b590dd0b078 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-stattarget", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-roc >=1.78.0,<1.79.0' + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-roc >=1.82.0,<1.83.0 - r-base - r-pdist - r-pls @@ -31,21 +33,24 @@ requirements: - r-randomforest - r-rrcov run: - - 'bioconductor-impute >=1.76.0,<1.77.0' - - 'bioconductor-roc >=1.78.0,<1.79.0' + - bioconductor-impute >=1.80.0,<1.81.0 + - bioconductor-roc >=1.82.0,<1.83.0 - r-base - r-pdist - r-pls - r-plyr - r-randomforest - r-rrcov + +source: + md5: 24eb1ce2f644e9802d398f46eeb04612 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 3)' - summary: 'Statistical Analysis of Molecular Profiles' - description: 'A streamlined tool provides a graphical user interface for quality control based signal drift correction (QC-RFSC), integration of data from multi-batch MS-based experiments, and the comprehensive statistical analysis in metabolomics and proteomics.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-stemhypoxia/meta.yaml b/recipes/bioconductor-stemhypoxia/meta.yaml index 1bf4c404eb5a3..8faff5172469c 100644 --- a/recipes/bioconductor-stemhypoxia/meta.yaml +++ b/recipes/bioconductor-stemhypoxia/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "stemHypoxia" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 22ec9d76cac05ac7118873f7815225ba +about: + description: Expression profiling using microarray technology to prove if 'Hypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells to Functional Endothelium' by Prado-Lopez et al. (2010) Stem Cells 28:407-418. Full data available at Gene Expression Omnibus series GSE37761. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Differentiation of Human Embryonic Stem Cells under Hypoxia gene expression dataset by Prado-Lopez et al. (2010) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-stemhypoxia", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-stemhypoxia + path: recipes/bioconductor-stemhypoxia + version: 1.16.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 49bf6a9e4b05c1ae7841672ab7484457 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Differentiation of Human Embryonic Stem Cells under Hypoxia gene expression dataset by Prado-Lopez et al. (2010)' - description: 'Expression profiling using microarray technology to prove if ''Hypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells to Functional Endothelium'' by Prado-Lopez et al. (2010) Stem Cells 28:407-418. Full data available at Gene Expression Omnibus series GSE37761.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-stemhypoxia - path: recipes/bioconductor-stemhypoxia - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-stemhypoxia/post-link.sh b/recipes/bioconductor-stemhypoxia/post-link.sh index 519f3ce64e7b7..e6ea1394cc1d9 100644 --- a/recipes/bioconductor-stemhypoxia/post-link.sh +++ b/recipes/bioconductor-stemhypoxia/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "stemhypoxia-1.38.0" +installBiocDataPackage.sh "stemhypoxia-1.42.0" diff --git a/recipes/bioconductor-stepnorm/meta.yaml b/recipes/bioconductor-stepnorm/meta.yaml index a109683e28058..985af44e3f6dc 100644 --- a/recipes/bioconductor-stepnorm/meta.yaml +++ b/recipes/bioconductor-stepnorm/meta.yaml @@ -1,48 +1,54 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "stepNorm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Stepwise normalization functions for cDNA microarray data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Stepwise normalization functions for cDNA microarrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a8f357efcff85a6d723734d6e0a91ba0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-stepnorm", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:stepnorm + - doi:10.1109/IEMBS.2004.1403830 + parent_recipe: + name: bioconductor-stepnorm + path: recipes/bioconductor-stepnorm + version: 1.52.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-marray >=1.84.0,<1.85.0 - r-base - r-mass run: - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-marray >=1.84.0,<1.85.0 - r-base - r-mass + +source: + md5: 9ef9c6ad62abc7dc28acf07af56173d0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Stepwise normalization functions for cDNA microarrays' - description: 'Stepwise normalization functions for cDNA microarray data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:stepnorm - - doi:10.1109/IEMBS.2004.1403830 - parent_recipe: - name: bioconductor-stepnorm - path: recipes/bioconductor-stepnorm - version: 1.52.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-stexampledata/meta.yaml b/recipes/bioconductor-stexampledata/meta.yaml index 422e84e76f070..ba10308505e72 100644 --- a/recipes/bioconductor-stexampledata/meta.yaml +++ b/recipes/bioconductor-stexampledata/meta.yaml @@ -1,43 +1,45 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "STexampleData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5fa4bfb2e58e7f6bbcd957aa1aa7e938 +about: + description: Collection of spatial transcriptomics datasets stored in SpatialExperiment Bioconductor format, for use in examples, demonstrations, and tutorials. The datasets are from several different platforms and have been sourced from various publicly available sources. Several datasets include images and/or reference annotation labels. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Collection of spatial transcriptomics datasets in SpatialExperiment Bioconductor format build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-stexampledata", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, BumpyMatrix +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: BiocStyle, knitr, rmarkdown, BumpyMatrix, HDF5Array requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 20e089ef88575b871a5e0edc17c520ca + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Collection of spatially-resolved transcriptomics datasets in SpatialExperiment Bioconductor format' - description: 'Collection of spatially-resolved transcriptomics (SRT) datasets in SpatialExperiment Bioconductor format, for use in examples, demonstrations, and tutorials. The datasets are from several different SRT platforms and have been sourced from various publicly available sources. Several datasets include images and/or ground truth annotation labels.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-stexampledata/post-link.sh b/recipes/bioconductor-stexampledata/post-link.sh index 6dea914d714c1..a8e2494eeb295 100644 --- a/recipes/bioconductor-stexampledata/post-link.sh +++ b/recipes/bioconductor-stexampledata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "stexampledata-1.10.0" +installBiocDataPackage.sh "stexampledata-1.14.0" diff --git a/recipes/bioconductor-stjoincount/meta.yaml b/recipes/bioconductor-stjoincount/meta.yaml index 38b3392c1fcd2..1877fca735fed 100644 --- a/recipes/bioconductor-stjoincount/meta.yaml +++ b/recipes/bioconductor-stjoincount/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "stJoincount" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: stJoincount facilitates the application of join count analysis to spatial transcriptomic data generated from the 10x Genomics Visium platform. This tool first converts a labeled spatial tissue map into a raster object, in which each spatial feature is represented by a pixel coded by label assignment. This process includes automatic calculation of optimal raster resolution and extent for the sample. A neighbors list is then created from the rasterized sample, in which adjacent and diagonal neighbors for each pixel are identified. After adding binary spatial weights to the neighbors list, a multi-categorical join count analysis is performed to tabulate "joins" between all possible combinations of label pairs. The function returns the observed join counts, the expected count under conditions of spatial randomness, and the variance calculated under non-free sampling. The z-score is then calculated as the difference between observed and expected counts, divided by the square root of the variance. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: stJoincount - Join count statistic for quantifying spatial correlation between clusters -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 85dd3f81a773ede72a70185cb4132d2b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-stjoincount", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -34,8 +36,8 @@ requirements: - r-sp - r-spdep run: - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 @@ -45,13 +47,16 @@ requirements: - r-seurat - r-sp - r-spdep + +source: + md5: 94c4eeaaa629a3a0f2ddf84ed2f602bb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'stJoincount - Join count statistic for quantifying spatial correlation between clusters' - description: 'stJoincount facilitates the application of join count analysis to spatial transcriptomic data generated from the 10x Genomics Visium platform. This tool first converts a labeled spatial tissue map into a raster object, in which each spatial feature is represented by a pixel coded by label assignment. This process includes automatic calculation of optimal raster resolution and extent for the sample. A neighbors list is then created from the rasterized sample, in which adjacent and diagonal neighbors for each pixel are identified. After adding binary spatial weights to the neighbors list, a multi-categorical join count analysis is performed to tabulate "joins" between all possible combinations of label pairs. The function returns the observed join counts, the expected count under conditions of spatial randomness, and the variance calculated under non-free sampling. The z-score is then calculated as the difference between observed and expected counts, divided by the square root of the variance.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-strandcheckr/meta.yaml b/recipes/bioconductor-strandcheckr/meta.yaml index 21ce40d74e7fd..0f1ae056acc1b 100644 --- a/recipes/bioconductor-strandcheckr/meta.yaml +++ b/recipes/bioconductor-strandcheckr/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "strandCheckR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package aims to quantify and remove putative double strand DNA from a strand-specific RNA sample. There are also options and methods to plot the positive/negative proportions of all sliding windows, which allow users to have an idea of how much the sample was contaminated and the appropriate threshold to be used for filtering. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Calculate strandness information of a bam file -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d9544940bb53aa96ca4e14fda712581d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-strandcheckr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 - r-base - r-dplyr - r-ggplot2 @@ -39,14 +41,14 @@ requirements: - r-rmarkdown - r-stringr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 - r-base - r-dplyr - r-ggplot2 @@ -55,13 +57,16 @@ requirements: - r-reshape2 - r-rmarkdown - r-stringr + +source: + md5: 283cae7cd525c8d9709468b7e0e87378 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Calculate strandness information of a bam file' - description: 'This package aims to quantify and remove putative double strand DNA from a strand-specific RNA sample. There are also options and methods to plot the positive/negative proportions of all sliding windows, which allow users to have an idea of how much the sample was contaminated and the appropriate threshold to be used for filtering.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-streamer/meta.yaml b/recipes/bioconductor-streamer/meta.yaml index b98467148e69a..e86c500952bf3 100644 --- a/recipes/bioconductor-streamer/meta.yaml +++ b/recipes/bioconductor-streamer/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "Streamer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Large data files can be difficult to work with in R, where data generally resides in memory. This package encourages a style of programming where data is 'streamed' from disk into R via a `producer' and through a series of `consumers' that, typically reduce the original data to a manageable size. The package provides useful Producer and Consumer stream components for operations such as data input, sampling, indexing, and transformation; see package?Streamer for details. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Enabling stream processing of large files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d41ea52d04a44b0705846078ffe3b1e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-streamer", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:streamer + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-streamer + path: recipes/bioconductor-streamer + version: 1.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 - r-base - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: a8f1d72c63f0700f2bb954f4fd549238 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Enabling stream processing of large files' - description: 'Large data files can be difficult to work with in R, where data generally resides in memory. This package encourages a style of programming where data is ''streamed'' from disk into R via a `producer'' and through a series of `consumers'' that, typically reduce the original data to a manageable size. The package provides useful Producer and Consumer stream components for operations such as data input, sampling, indexing, and transformation; see package?Streamer for details.' -extra: - identifiers: - - biotools:streamer - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-streamer - path: recipes/bioconductor-streamer - version: 1.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-stringdb/meta.yaml b/recipes/bioconductor-stringdb/meta.yaml index 64027a236667d..3d9651e98dd69 100644 --- a/recipes/bioconductor-stringdb/meta.yaml +++ b/recipes/bioconductor-stringdb/meta.yaml @@ -1,62 +1,68 @@ -{% set version = "2.14.0" %} +{% set version = "2.18.0" %} {% set name = "STRINGdb" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The STRINGdb package provides a R interface to the STRING protein-protein interactions database (https://string-db.org). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: STRINGdb - Protein-Protein Interaction Networks and Functional Enrichment Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6dc5819519574f0656e4b811e4618db7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-stringdb", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:stringdb + parent_recipe: + name: bioconductor-stringdb + path: recipes/bioconductor-stringdb + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocGenerics requirements: host: - r-base - r-gplots - r-hash + - r-httr - r-igraph - r-plotrix - r-plyr - r-png - r-rcolorbrewer - - r-rcurl - r-sqldf run: - r-base - r-gplots - r-hash + - r-httr - r-igraph - r-plotrix - r-plyr - r-png - r-rcolorbrewer - - r-rcurl - r-sqldf + +source: + md5: 9b150c10f4fe0f8f195cd6cdd8e99d62 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'STRINGdb - Protein-Protein Interaction Networks and Functional Enrichment Analysis' - description: 'The STRINGdb package provides a R interface to the STRING protein-protein interactions database (https://string-db.org).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:stringdb - parent_recipe: - name: bioconductor-stringdb - path: recipes/bioconductor-stringdb - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-struct/meta.yaml b/recipes/bioconductor-struct/meta.yaml index 6436c5e2462f7..b83f046743db8 100644 --- a/recipes/bioconductor-struct/meta.yaml +++ b/recipes/bioconductor-struct/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "struct" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Defines and includes a set of class-based templates for developing and implementing data processing and analysis workflows, with a strong emphasis on statistics and machine learning. The templates can be used and where needed extended to 'wrap' tools and methods from other packages into a common standardised structure to allow for effective and fast integration. Model objects can be combined into sequences, and sequences nested in iterators using overloaded operators to simplify and improve readability of the code. Ontology lookup has been integrated and implemented to provide standardised definitions for methods, inputs and outputs wrapped using the class-based templates. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Statistics in R Using Class-based Templates -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ef5fb8febc9f7bfed87fba9bc24cbebc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-struct", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, rstudioapi, rmarkdown, covr, BiocStyle, openxlsx, ggplot2, magick requirements: host: - - 'bioconductor-rols >=2.30.0,<2.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-rols >=3.2.0,<3.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-knitr - r-ontologyindex run: - - 'bioconductor-rols >=2.30.0,<2.31.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-rols >=3.2.0,<3.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-knitr - r-ontologyindex + +source: + md5: f3ff24c246719c62f81a273629f33ee3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Statistics in R Using Class-based Templates' - description: 'Defines and includes a set of class-based templates for developing and implementing data processing and analysis workflows, with a strong emphasis on statistics and machine learning. The templates can be used and where needed extended to ''wrap'' tools and methods from other packages into a common standardised structure to allow for effective and fast integration. Model objects can be combined into sequences, and sequences nested in iterators using overloaded operators to simplify and improve readability of the code. Ontology lookup has been integrated and implemented to provide standardised definitions for methods, inputs and outputs wrapped using the class-based templates.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-structstrings/meta.yaml b/recipes/bioconductor-structstrings/meta.yaml index adcd3be37235e..c08be0c10feab 100644 --- a/recipes/bioconductor-structstrings/meta.yaml +++ b/recipes/bioconductor-structstrings/meta.yaml @@ -1,31 +1,35 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "Structstrings" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Implementation of the dot bracket annotations with Biostrings -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d4afbd61a5546b52947869b7912eecb build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-structstrings", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-crayon - r-stringi @@ -33,24 +37,25 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-crayon - r-stringi - r-stringr - build: - - {{ compiler('c') }} - - make + +source: + md5: bd98e8f1849fb554204d616c3fb3f540 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Implementation of the dot bracket annotations with Biostrings' - description: 'The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-structtoolbox/meta.yaml b/recipes/bioconductor-structtoolbox/meta.yaml index 4a6d887b6e887..60c63f509399a 100644 --- a/recipes/bioconductor-structtoolbox/meta.yaml +++ b/recipes/bioconductor-structtoolbox/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "structToolbox" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An extensive set of data (pre-)processing and analysis methods and tools for metabolomics and other omics, with a strong emphasis on statistics and machine learning. This toolbox allows the user to build extensive and standardised workflows for data analysis. The methods and tools have been implemented using class-based templates provided by the struct (Statistics in R Using Class-based Templates) package. The toolbox includes pre-processing methods (e.g. signal drift and batch correction, normalisation, missing value imputation and scaling), univariate (e.g. ttest, various forms of ANOVA, Kruskal–Wallis test and more) and multivariate statistical methods (e.g. PCA and PLS, including cross-validation and permutation testing) as well as machine learning methods (e.g. Support Vector Machines). The STATistics Ontology (STATO) has been integrated and implemented to provide standardised definitions for the different methods, inputs and outputs. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Data processing & analysis tools for Metabolomics and other omics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d6e4aa6631f797571a7ec07348cfbd30 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-structtoolbox", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: agricolae, BiocFileCache, BiocStyle, car, covr, cowplot, e1071, emmeans, ggdendro, knitr, magick, nlme, openxlsx, pls, pmp, reshape2, ropls, rmarkdown, Rtsne, testthat, rappdirs requirements: host: - - 'bioconductor-struct >=1.14.0,<1.15.0' + - bioconductor-struct >=1.18.0,<1.19.0 - r-base - r-ggplot2 - r-ggthemes @@ -30,20 +32,23 @@ requirements: - r-scales - r-sp run: - - 'bioconductor-struct >=1.14.0,<1.15.0' + - bioconductor-struct >=1.18.0,<1.19.0 - r-base - r-ggplot2 - r-ggthemes - r-gridextra - r-scales - r-sp + +source: + md5: afd1a6cef078298e385bf9281b1543bf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Data processing & analysis tools for Metabolomics and other omics' - description: 'An extensive set of data (pre-)processing and analysis methods and tools for metabolomics and other omics, with a strong emphasis on statistics and machine learning. This toolbox allows the user to build extensive and standardised workflows for data analysis. The methods and tools have been implemented using class-based templates provided by the struct (Statistics in R Using Class-based Templates) package. The toolbox includes pre-processing methods (e.g. signal drift and batch correction, normalisation, missing value imputation and scaling), univariate (e.g. ttest, various forms of ANOVA, Kruskal–Wallis test and more) and multivariate statistical methods (e.g. PCA and PLS, including cross-validation and permutation testing) as well as machine learning methods (e.g. Support Vector Machines). The STATistics Ontology (STATO) has been integrated and implemented to provide standardised definitions for the different methods, inputs and outputs.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-structuralvariantannotation/meta.yaml b/recipes/bioconductor-structuralvariantannotation/meta.yaml index 33f925708abe9..8da2097336b7a 100644 --- a/recipes/bioconductor-structuralvariantannotation/meta.yaml +++ b/recipes/bioconductor-structuralvariantannotation/meta.yaml @@ -1,65 +1,72 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "StructuralVariantAnnotation" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: StructuralVariantAnnotation provides a framework for analysis of structural variants within the Bioconductor ecosystem. This package contains contains useful helper functions for dealing with structural variants in VCF format. The packages contains functions for parsing VCFs from a number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Variant annotations for structural variants -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d72d8c88083ed0fc9319afa075360841 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-structuralvariantannotation", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ggplot2, devtools, testthat (>= 2.1.0), roxygen2, rmarkdown, tidyverse, knitr, ggbio, biovizBase, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-assertthat - r-base - r-dplyr - r-rlang - r-stringr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-assertthat - r-base - r-dplyr - r-rlang - r-stringr + +source: + md5: 9072d77c242f802f7440da1838bf4a03 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Variant annotations for structural variants' - description: 'StructuralVariantAnnotation provides a framework for analysis of structural variants within the Bioconductor ecosystem. This package contains contains useful helper functions for dealing with structural variants in VCF format. The packages contains functions for parsing VCFs from a number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-subcellbarcode/meta.yaml b/recipes/bioconductor-subcellbarcode/meta.yaml index e6f6ea30837ae..92291cb8196cf 100644 --- a/recipes/bioconductor-subcellbarcode/meta.yaml +++ b/recipes/bioconductor-subcellbarcode/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "SubCellBarCode" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Mass-Spectrometry based spatial proteomics have enabled the proteome-wide mapping of protein subcellular localization (Orre et al. 2019, Molecular Cell). SubCellBarCode R package robustly classifies proteins into corresponding subcellular localization. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9b3f34495b8132c4cbdc426e27ffc740 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-subcellbarcode", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - r-caret - r-e1071 @@ -34,8 +36,8 @@ requirements: - r-rtsne - r-scatterplot3d run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - r-caret - r-e1071 @@ -45,13 +47,16 @@ requirements: - r-networkd3 - r-rtsne - r-scatterplot3d + +source: + md5: 7284f839c7f0c486fd3f48bd199b0392 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome' - description: 'Mass-Spectrometry based spatial proteomics have enabled the proteome-wide mapping of protein subcellular localization (Orre et al. 2019, Molecular Cell). SubCellBarCode R package robustly classifies proteins into corresponding subcellular localization.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-subseq/meta.yaml b/recipes/bioconductor-subseq/meta.yaml index f482cf4d343f7..c778439ab1caf 100644 --- a/recipes/bioconductor-subseq/meta.yaml +++ b/recipes/bioconductor-subseq/meta.yaml @@ -1,29 +1,40 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "subSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Subsampling of high throughput sequencing count data for use in experiment design and analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Subsampling of high-throughput sequencing count data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 81acfd896fc4e8c52e50475dca2c1519 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-subseq", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:subseq + - doi:10.1093/bioinformatics/btu552 + parent_recipe: + name: bioconductor-subseq + path: recipes/bioconductor-subseq + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - r-data.table - r-digest @@ -32,8 +43,8 @@ requirements: - r-magrittr - r-tidyr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - r-data.table - r-digest @@ -41,21 +52,16 @@ requirements: - r-ggplot2 - r-magrittr - r-tidyr + +source: + md5: 4ebb7e76f3dab82e2cba34adeed4b8b7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Subsampling of high-throughput sequencing count data' - description: 'Subsampling of high throughput sequencing count data for use in experiment design and analysis.' - license_file: LICENSE -extra: - identifiers: - - biotools:subseq - - doi:10.1093/bioinformatics/btu552 - parent_recipe: - name: bioconductor-subseq - path: recipes/bioconductor-subseq - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sugarcanecdf/meta.yaml b/recipes/bioconductor-sugarcanecdf/meta.yaml index f35923e94468a..b767be1f57c65 100644 --- a/recipes/bioconductor-sugarcanecdf/meta.yaml +++ b/recipes/bioconductor-sugarcanecdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "sugarcanecdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f66d51868068f83d3693d3cb05be418a +about: + description: A package containing an environment representing the Sugar_Cane.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: sugarcanecdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sugarcanecdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f66d51868068f83d3693d3cb05be418a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: sugarcanecdf - description: 'A package containing an environment representing the Sugar_Cane.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sugarcaneprobe/meta.yaml b/recipes/bioconductor-sugarcaneprobe/meta.yaml index 206f4292a4db3..fe9fca9d900e6 100644 --- a/recipes/bioconductor-sugarcaneprobe/meta.yaml +++ b/recipes/bioconductor-sugarcaneprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "sugarcaneprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 66c101ac73e9235d258b9f996c42778e +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Sugar\_Cane\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type sugarcane build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sugarcaneprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 66c101ac73e9235d258b9f996c42778e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type sugarcane' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Sugar\_Cane\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-suitor/meta.yaml b/recipes/bioconductor-suitor/meta.yaml index 2c3b4b7017d9d..abcee425210fb 100644 --- a/recipes/bioconductor-suitor/meta.yaml +++ b/recipes/bioconductor-suitor/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "SUITOR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5f4a5ea607ef7551025cf8b425d20bc7 +about: + description: An unsupervised cross-validation method to select the optimal number of mutational signatures. A data set of mutational counts is split into training and validation data.Signatures are estimated in the training data and then used to predict the mutations in the validation data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Selecting the number of mutational signatures through cross-validation build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-suitor", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: devtools, MutationalPatterns, RUnit, BiocManager, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-ggplot2 - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-ggplot2 - build: - - {{ compiler('c') }} - - make +source: + md5: 1780e3240f4b4d5644da6feb41eb5c45 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Selecting the number of mutational signatures through cross-validation' - description: 'An unsupervised cross-validation method to select the optimal number of mutational signatures. A data set of mutational counts is split into training and validation data.Signatures are estimated in the training data and then used to predict the mutations in the validation data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-summarizedexperiment/meta.yaml b/recipes/bioconductor-summarizedexperiment/meta.yaml index 26284256593de..7d3dd98df336f 100644 --- a/recipes/bioconductor-summarizedexperiment/meta.yaml +++ b/recipes/bioconductor-summarizedexperiment/meta.yaml @@ -1,64 +1,70 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "SummarizedExperiment" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: A container (S4 class) for matrix-like assays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cf4b430247b40acb2be8e6c9ecf3aac7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-summarizedexperiment", max_pin="x.x") }}' - noarch: generic -# Suggests: HDF5Array (>= 1.7.5), annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, jsonlite, rhdf5, airway (>= 1.15.1), BiocStyle, knitr, rmarkdown, RUnit, testthat, digest + +extra: + identifiers: + - biotools:summarizedexperiment + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-summarizedexperiment + path: recipes/bioconductor-summarizedexperiment + version: 1.10.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: jsonlite, rhdf5, HDF5Array (>= 1.7.5), annotate, AnnotationDbi, GenomicFeatures, SparseArray, SingleCellExperiment, TxDb.Hsapiens.UCSC.hg19.knownGene, hgu95av2.db, airway (>= 1.15.1), BiocStyle, knitr, rmarkdown, RUnit, testthat, digest requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4arrays >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4arrays >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-matrix run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4arrays >=1.2.0,<1.3.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4arrays >=1.6.0,<1.7.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-matrix + +source: + md5: c1925961cb5cec2af5f5ed843128b5cc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'SummarizedExperiment container' - description: 'The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.' -extra: - identifiers: - - biotools:summarizedexperiment - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-summarizedexperiment - path: recipes/bioconductor-summarizedexperiment - version: 1.10.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-summix/build_failure.linux-64.yaml b/recipes/bioconductor-summix/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..12531d6599166 --- /dev/null +++ b/recipes/bioconductor-summix/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 0d8431efa4ec783e97329d34413857a3d169c0c4955b9730fbcbd14353077a74 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-bedassle")} + Encountered problems while solving: + - nothing provides requested r-bedassle + + Could not solve for environment specs + The following package could not be installed + [31mr-bedassle[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-bedassle")} + Encountered problems while solving: + - nothing provides requested r-bedassle + + Could not solve for environment specs + The following package could not be installed + [31mr-bedassle[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-bedassle")} + Encountered problems while solving: + - nothing provides requested r-bedassle + + Could not solve for environment specs + The following package could not be installed + [31mr-bedassle[0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-summix/meta.yaml b/recipes/bioconductor-summix/meta.yaml index 9426ca82a1bea..328bfe7fea0fb 100644 --- a/recipes/bioconductor-summix/meta.yaml +++ b/recipes/bioconductor-summix/meta.yaml @@ -1,39 +1,60 @@ -{% set version = "2.8.0" %} +{% set version = "2.12.0" %} {% set name = "Summix" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package contains the Summix2 method for estimating and adjusting for substructure in genetic summary allele frequency data. The function summix() estimates reference group proportions using a mixture model. The adjAF() function produces adjusted allele frequencies for an observed group with reference group proportions matching a target individual or sample. The summix_local() function estimates local ancestry mixture proportions and performs selection scans in genetic summary data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 'Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 74d3140f7f5db9a648955b81abdfb769 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-summix", max_pin="x.x") }}' - noarch: generic -# Suggests: rmarkdown, markdown, knitr + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: rmarkdown, markdown, knitr, testthat (>= 3.0.0) requirements: host: - r-base + - r-bedassle + - r-dplyr + - r-magrittr - r-nloptr + - r-randomcolor + - r-scales + - r-tibble + - r-tidyselect + - r-visnetwork run: - r-base + - r-bedassle + - r-dplyr + - r-magrittr - r-nloptr + - r-randomcolor + - r-scales + - r-tibble + - r-tidyselect + - r-visnetwork + +source: + md5: 7fe653455de7f81c916b60eab39de2d2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Summix: A method to estimate and adjust for population structure in genetic summary data' - description: 'This package contains the Summix method for estimating and adjusting for ancestry in genetic summary allele frequency data. The function summix estimates reference ancestry proportions using a mixture model. The adjAF function produces ancestry adjusted allele frequencies for an observed sample with ancestry proportions matching a target person or sample.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-supersigs/meta.yaml b/recipes/bioconductor-supersigs/meta.yaml index 7eb7f89d459f7..ead8fe5999c13 100644 --- a/recipes/bioconductor-supersigs/meta.yaml +++ b/recipes/bioconductor-supersigs/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "supersigs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Generate SuperSigs (supervised mutational signatures) from single nucleotide variants in the cancer genome. Functions included in the package allow the user to learn supervised mutational signatures from their data and apply them to new data. The methodology is based on the one described in Afsari (2021, ELife). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Supervised mutational signatures -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 35df3e9fd0272854b23baf15d93d300f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-supersigs", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, testthat, VariantAnnotation requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-caret @@ -32,8 +34,8 @@ requirements: - r-rsample - r-tidyr run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-caret @@ -41,13 +43,16 @@ requirements: - r-rlang - r-rsample - r-tidyr + +source: + md5: d3254207082434d37928637038425006 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Supervised mutational signatures' - description: 'Generate SuperSigs (supervised mutational signatures) from single nucleotide variants in the cancer genome. Functions included in the package allow the user to learn supervised mutational signatures from their data and apply them to new data. The methodology is based on the one described in Afsari (2021, ELife).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-surfaltr/meta.yaml b/recipes/bioconductor-surfaltr/meta.yaml index fec35c9c96474..79469ca466a7a 100644 --- a/recipes/bioconductor-surfaltr/meta.yaml +++ b/recipes/bioconductor-surfaltr/meta.yaml @@ -1,61 +1,66 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "surfaltr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Cell surface proteins form a major fraction of the druggable proteome and can be used for tissue-specific delivery of oligonucleotide/cell-based therapeutics. Alternatively spliced surface protein isoforms have been shown to differ in their subcellular localization and/or their transmembrane (TM) topology. Surface proteins are hydrophobic and remain difficult to study thereby necessitating the use of TM topology prediction methods such as TMHMM and Phobius. However, there exists a need for bioinformatic approaches to streamline batch processing of isoforms for comparing and visualizing topologies. To address this gap, we have developed an R package, surfaltr. It pairs inputted isoforms, either known alternatively spliced or novel, with their APPRIS annotated principal counterparts, predicts their TM topologies using TMHMM or Phobius, and generates a customizable graphical output. Further, surfaltr facilitates the prioritization of biologically diverse isoform pairs through the incorporation of three different ranking metrics and through protein alignment functions. Citations for programs mentioned here can be found in the vignette. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 69ea67dd32fffa5376607fa6fa5c7e9f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-surfaltr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, devtools, kableExtra requirements: host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-msa >=1.34.0,<1.35.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-msa >=1.38.0,<1.39.0 - r-base - - 'r-dplyr >=1.0.6' - - 'r-ggplot2 >=3.3.2' - - 'r-httr >=1.4.2' - - 'r-protr >=1.6-2' - - 'r-readr >=1.4.0' - - 'r-seqinr >=4.2-5' - - 'r-stringr >=1.4.0' - - 'r-testthat >=3.0.0' - - 'r-xml2 >=1.3.2' + - r-dplyr >=1.0.6 + - r-ggplot2 >=3.3.2 + - r-httr >=1.4.2 + - r-protr >=1.6-2 + - r-readr >=1.4.0 + - r-seqinr >=4.2-5 + - r-stringr >=1.4.0 + - r-testthat >=3.0.0 + - r-xml2 >=1.3.2 run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-msa >=1.34.0,<1.35.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-msa >=1.38.0,<1.39.0 - r-base - - 'r-dplyr >=1.0.6' - - 'r-ggplot2 >=3.3.2' - - 'r-httr >=1.4.2' - - 'r-protr >=1.6-2' - - 'r-readr >=1.4.0' - - 'r-seqinr >=4.2-5' - - 'r-stringr >=1.4.0' - - 'r-testthat >=3.0.0' - - 'r-xml2 >=1.3.2' + - r-dplyr >=1.0.6 + - r-ggplot2 >=3.3.2 + - r-httr >=1.4.2 + - r-protr >=1.6-2 + - r-readr >=1.4.0 + - r-seqinr >=4.2-5 + - r-stringr >=1.4.0 + - r-testthat >=3.0.0 + - r-xml2 >=1.3.2 + +source: + md5: 263c7833ebcf3511da69f39336453990 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr' - description: 'Cell surface proteins form a major fraction of the druggable proteome and can be used for tissue-specific delivery of oligonucleotide/cell-based therapeutics. Alternatively spliced surface protein isoforms have been shown to differ in their subcellular localization and/or their transmembrane (TM) topology. Surface proteins are hydrophobic and remain difficult to study thereby necessitating the use of TM topology prediction methods such as TMHMM and Phobius. However, there exists a need for bioinformatic approaches to streamline batch processing of isoforms for comparing and visualizing topologies. To address this gap, we have developed an R package, surfaltr. It pairs inputted isoforms, either known alternatively spliced or novel, with their APPRIS annotated principal counterparts, predicts their TM topologies using TMHMM or Phobius, and generates a customizable graphical output. Further, surfaltr facilitates the prioritization of biologically diverse isoform pairs through the incorporation of three different ranking metrics and through protein alignment functions. Citations for programs mentioned here can be found in the vignette.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-survclust/build.sh b/recipes/bioconductor-survclust/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-survclust/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-survclust/meta.yaml b/recipes/bioconductor-survclust/meta.yaml new file mode 100644 index 0000000000000..d534a3190284b --- /dev/null +++ b/recipes/bioconductor-survclust/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.0.0" %} +{% set name = "survClust" %} +{% set bioc = "3.20" %} + +about: + description: survClust is an outcome weighted integrative clustering algorithm used to classify multi-omic samples on their available time to event information. The resulting clusters are cross-validated to avoid over overfitting and output classification of samples that are molecularly distinct and clinically meaningful. It takes in binary (mutation) as well as continuous data (other omic types). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Identification Of Clinically Relevant Genomic Subtypes Using Outcome Weighted Learning + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-survclust", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, testthat (>= 3.0.0), gplots, htmltools, BiocParallel +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - r-base + - r-pdist + - r-rcpp + - r-survival + - libblas + - liblapack + run: + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - r-base + - r-pdist + - r-rcpp + - r-survival + +source: + md5: ea7b5d530a1188fe7133b5be851ee739 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-survcomp/meta.yaml b/recipes/bioconductor-survcomp/meta.yaml index 52adadac760d3..810db29bcf712 100644 --- a/recipes/bioconductor-survcomp/meta.yaml +++ b/recipes/bioconductor-survcomp/meta.yaml @@ -1,25 +1,38 @@ -{% set version = "1.52.0" %} +{% set version = "1.56.0" %} {% set name = "survcomp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Assessment and Comparison for Performance of Risk Prediction (Survival) Models. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Performance Assessment and Comparison for Survival Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5026589c50042751474d3474dc24847d build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-survcomp", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:survcomp + parent_recipe: + name: bioconductor-survcomp + path: recipes/bioconductor-survcomp + version: 1.30.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Hmisc, clinfun, xtable, Biobase, BiocManager requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-bootstrap @@ -42,23 +55,16 @@ requirements: - r-suppdists - r-survival - r-survivalroc - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: d1c0e8e9725b9bff15c03e5911af86a9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Performance Assessment and Comparison for Survival Analysis' - description: 'Assessment and Comparison for Performance of Risk Prediction (Survival) Models.' -extra: - identifiers: - - biotools:survcomp - parent_recipe: - name: bioconductor-survcomp - path: recipes/bioconductor-survcomp - version: 1.30.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-survtype/meta.yaml b/recipes/bioconductor-survtype/meta.yaml index 1d4612397856c..baa278443d95f 100644 --- a/recipes/bioconductor-survtype/meta.yaml +++ b/recipes/bioconductor-survtype/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "survtype" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Subtypes are defined as groups of samples that have distinct molecular and clinical features. Genomic data can be analyzed for discovering patient subtypes, associated with clinical data, especially for survival information. This package is aimed to identify subtypes that are both clinically relevant and biologically meaningful. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Subtype Identification with Survival Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e939bd3726a715cb0a817d0541ff86ab build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-survtype", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: maftools, scales, knitr, rmarkdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-clustvarsel - r-pheatmap - r-survival - r-survminer run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-clustvarsel - r-pheatmap - r-survival - r-survminer + +source: + md5: 3a0e70ad72d6a9fe1752e6f8f05fe7cc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Subtype Identification with Survival Data' - description: 'Subtypes are defined as groups of samples that have distinct molecular and clinical features. Genomic data can be analyzed for discovering patient subtypes, associated with clinical data, especially for survival information. This package is aimed to identify subtypes that are both clinically relevant and biologically meaningful.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-sva/meta.yaml b/recipes/bioconductor-sva/meta.yaml index 6f654ea41dd4b..8d26fca77016f 100644 --- a/recipes/bioconductor-sva/meta.yaml +++ b/recipes/bioconductor-sva/meta.yaml @@ -1,62 +1,68 @@ -{% set version = "3.50.0" %} +{% set version = "3.54.0" %} {% set name = "sva" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high-dimensional data (like gene expression/RNA sequencing/methylation/brain imaging data) that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise. The sva package can be used to remove artifacts in three ways: (1) identifying and estimating surrogate variables for unknown sources of variation in high-throughput experiments (Leek and Storey 2007 PLoS Genetics,2008 PNAS), (2) directly removing known batch effects using ComBat (Johnson et al. 2007 Biostatistics) and (3) removing batch effects with known control probes (Leek 2014 biorXiv). Removing batch effects and using surrogate variables in differential expression analysis have been shown to reduce dependence, stabilize error rate estimates, and improve reproducibility, see (Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews Genetics).' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Surrogate Variable Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8c42cd3e23be4d24f072d98394931552 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-sva", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:sva + - doi:10.1371/journal.pgen.0030161 + parent_recipe: + name: bioconductor-sva + path: recipes/bioconductor-sva + version: 3.28.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-matrixstats - r-mgcv - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-matrixstats - r-mgcv - build: - - {{ compiler('c') }} - - make + +source: + md5: e3f926939855e9fc04006b67a322eeb9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Surrogate Variable Analysis' - description: 'The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high-dimensional data (like gene expression/RNA sequencing/methylation/brain imaging data) that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise. The sva package can be used to remove artifacts in three ways: (1) identifying and estimating surrogate variables for unknown sources of variation in high-throughput experiments (Leek and Storey 2007 PLoS Genetics,2008 PNAS), (2) directly removing known batch effects using ComBat (Johnson et al. 2007 Biostatistics) and (3) removing batch effects with known control probes (Leek 2014 biorXiv). Removing batch effects and using surrogate variables in differential expression analysis have been shown to reduce dependence, stabilize error rate estimates, and improve reproducibility, see (Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews Genetics).' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:sva - - doi:10.1371/journal.pgen.0030161 - parent_recipe: - name: bioconductor-sva - path: recipes/bioconductor-sva - version: 3.28.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-svanumt/meta.yaml b/recipes/bioconductor-svanumt/meta.yaml index 03b3aa0e409af..3eebfe10463f6 100644 --- a/recipes/bioconductor-svanumt/meta.yaml +++ b/recipes/bioconductor-svanumt/meta.yaml @@ -1,63 +1,70 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "svaNUMT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: svaNUMT contains functions for detecting NUMT events from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies NUMTs by nuclear-mitochondrial breakend junctions. The main function reports candidate NUMTs if there is a pair of valid insertion sites found on the nuclear genome within a certain distance threshold. The candidate NUMTs are reported by events. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: NUMT detection from structural variant calls -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1f25f8632f0e52d0826ee0b1b8a1fe28 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-svanumt", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, readr, plyranges, circlize, IRanges, SummarizedExperiment, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-structuralvariantannotation >=1.18.0,<1.19.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-structuralvariantannotation >=1.22.0,<1.23.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-assertthat - r-base - r-dplyr - r-rlang - r-stringr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-structuralvariantannotation >=1.18.0,<1.19.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-structuralvariantannotation >=1.22.0,<1.23.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-assertthat - r-base - r-dplyr - r-rlang - r-stringr + +source: + md5: 52fe243524484bd3036c694f0e38934d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'NUMT detection from structural variant calls' - description: 'svaNUMT contains functions for detecting NUMT events from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies NUMTs by nuclear-mitochondrial breakend junctions. The main function reports candidate NUMTs if there is a pair of valid insertion sites found on the nuclear genome within a certain distance threshold. The candidate NUMTs are reported by events.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-svaretro/meta.yaml b/recipes/bioconductor-svaretro/meta.yaml index 176e5ea539cc2..0f1602569c569 100644 --- a/recipes/bioconductor-svaretro/meta.yaml +++ b/recipes/bioconductor-svaretro/meta.yaml @@ -1,63 +1,68 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "svaRetro" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: svaRetro contains functions for detecting retrotransposed transcripts (RTs) from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies RTs by exon-exon junctions and insertion sites. The candidate RTs are reported by events and annotated with information of the inserted transcripts. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Retrotransposed transcript detection from structural variants -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 56da2ed056a7078a5d9f2883885d5be5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-svaretro", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, BiocStyle, plyranges, circlize, tictoc, IRanges, stats, SummarizedExperiment, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-structuralvariantannotation >=1.18.0,<1.19.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-structuralvariantannotation >=1.22.0,<1.23.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-assertthat - r-base - r-dplyr - r-rlang - r-stringr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-structuralvariantannotation >=1.18.0,<1.19.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-structuralvariantannotation >=1.22.0,<1.23.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-assertthat - r-base - r-dplyr - r-rlang - r-stringr + +source: + md5: 39b0fcccb2b528ff6053d46acbbacfda + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Retrotransposed transcript detection from structural variants' - description: 'svaRetro contains functions for detecting retrotransposed transcripts (RTs) from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies RTs by exon-exon junctions and insertion sites. The candidate RTs are reported by events and annotated with information of the inserted transcripts.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-svm2crmdata/meta.yaml b/recipes/bioconductor-svm2crmdata/meta.yaml index 7e8ea729d45d5..bbcaece3076c1 100644 --- a/recipes/bioconductor-svm2crmdata/meta.yaml +++ b/recipes/bioconductor-svm2crmdata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "SVM2CRMdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ce0c6615bfbb9a5a7cf4eeab0bd6199d +about: + description: An example dataset for use with the SVM2CRM package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: An example dataset for use with the SVM2CRM package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-svm2crmdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0a323250bb842533ddf675228e0ff0b7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'LGPL (>= 2)' - summary: 'An example dataset for use with the SVM2CRM package' - description: 'An example dataset for use with the SVM2CRM package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-svm2crmdata/post-link.sh b/recipes/bioconductor-svm2crmdata/post-link.sh index b48dec842f852..6aedca8ad5856 100644 --- a/recipes/bioconductor-svm2crmdata/post-link.sh +++ b/recipes/bioconductor-svm2crmdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "svm2crmdata-1.34.0" +installBiocDataPackage.sh "svm2crmdata-1.38.0" diff --git a/recipes/bioconductor-svmdo/meta.yaml b/recipes/bioconductor-svmdo/meta.yaml index 81368ffa43b1b..04548da1d68bc 100644 --- a/recipes/bioconductor-svmdo/meta.yaml +++ b/recipes/bioconductor-svmdo/meta.yaml @@ -1,73 +1,82 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "SVMDO" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: It is an easy-to-use GUI using disease information for detecting tumor/normal sample discriminating gene sets from differentially expressed genes. Our approach is based on an iterative algorithm filtering genes with disease ontology enrichment analysis and wilk and wilks lambda criterion connected to SVM classification model construction. Along with gene set extraction, SVMDO also provides individual prognostic marker detection. The algorithm is designed for FPKM and RPKM normalized RNA-Seq transcriptome datasets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Identification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by Disease Ontology -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3edf50ad6544537845fe263bb490b9e5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-svmdo", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, testthat (>= 3.1.6), BiocStyle + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.1.6) requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-bsda >=1.2.1' - - 'r-caret >=6.0-93' - - 'r-catools >=1.18.2' - - 'r-data.table >=1.14.6' - - 'r-dplyr >=1.0.10' - - 'r-e1071 >=1.7-12' - - 'r-golem >=0.3.5' - - 'r-klar >=1.7-1' - - 'r-nortest >=1.0-4' - - 'r-shiny >=1.7.4' - - 'r-shinyfiles >=0.9.3' - - 'r-shinytitle >=0.1.0' - - 'r-sjmisc >=2.8.9' - - 'r-survival >=3.4-0' + - r-bsda >=1.2.1 + - r-caret >=6.0-93 + - r-catools >=1.18.2 + - r-data.table >=1.14.6 + - r-dplyr >=1.0.10 + - r-dt >=0.33.0 + - r-e1071 >=1.7-12 + - r-golem >=0.3.5 + - r-klar >=1.7-1 + - r-nortest >=1.0-4 + - r-shiny >=1.7.4 + - r-shinyfiles >=0.9.3 + - r-shinytitle >=0.1.0 + - r-sjmisc >=2.8.9 + - r-survival >=3.4-0 + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-bsda >=1.2.1' - - 'r-caret >=6.0-93' - - 'r-catools >=1.18.2' - - 'r-data.table >=1.14.6' - - 'r-dplyr >=1.0.10' - - 'r-e1071 >=1.7-12' - - 'r-golem >=0.3.5' - - 'r-klar >=1.7-1' - - 'r-nortest >=1.0-4' - - 'r-shiny >=1.7.4' - - 'r-shinyfiles >=0.9.3' - - 'r-shinytitle >=0.1.0' - - 'r-sjmisc >=2.8.9' - - 'r-survival >=3.4-0' + - r-bsda >=1.2.1 + - r-caret >=6.0-93 + - r-catools >=1.18.2 + - r-data.table >=1.14.6 + - r-dplyr >=1.0.10 + - r-dt >=0.33.0 + - r-e1071 >=1.7-12 + - r-golem >=0.3.5 + - r-klar >=1.7-1 + - r-nortest >=1.0-4 + - r-shiny >=1.7.4 + - r-shinyfiles >=0.9.3 + - r-shinytitle >=0.1.0 + - r-sjmisc >=2.8.9 + - r-survival >=3.4-0 + +source: + md5: 82f1c21363960db074b2a7d67410b4f3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Identification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by Disease Ontology' - description: 'It is an easy-to-use GUI using disease information for detecting tumor/normal sample discriminating gene sets from differentially expressed genes. Our approach is based on an iterative algorithm filtering genes with disease ontology enrichment analysis and wilk’s lambda criterion connected to SVM classification model construction. Along with gene set extraction, SVMDO also provides individual prognostic marker detection. The algorithm is designed for FPKM and RPKM normalized RNA-Seq transcriptome datasets.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-swath2stats/meta.yaml b/recipes/bioconductor-swath2stats/meta.yaml index 8a7eef17ac912..f6a3d90d5bfae 100644 --- a/recipes/bioconductor-swath2stats/meta.yaml +++ b/recipes/bioconductor-swath2stats/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "SWATH2stats" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Transform and Filter SWATH Data for Statistical Packages -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3853f9f81af8bc0732ff0e2ceaf43441 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-swath2stats", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:swath2stats + parent_recipe: + name: bioconductor-swath2stats + path: recipes/bioconductor-swath2stats + version: 1.10.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' + - bioconductor-biomart >=2.62.0,<2.63.0 - r-base - r-data.table - r-ggplot2 - r-reshape2 run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' + - bioconductor-biomart >=2.62.0,<2.63.0 - r-base - r-data.table - r-ggplot2 - r-reshape2 + +source: + md5: 39357a6c5cf510962679418ecc1d4e95 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Transform and Filter SWATH Data for Statistical Packages' - description: 'This package is intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:swath2stats - parent_recipe: - name: bioconductor-swath2stats - path: recipes/bioconductor-swath2stats - version: 1.10.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-swathxtend/meta.yaml b/recipes/bioconductor-swathxtend/meta.yaml index 23a30c62141a5..8e3cc8a92547b 100644 --- a/recipes/bioconductor-swathxtend/meta.yaml +++ b/recipes/bioconductor-swathxtend/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "2.24.0" %} +{% set version = "2.28.0" %} {% set name = "SwathXtend" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Contains utility functions for integrating spectral libraries for SWATH and statistical data analysis for SWATH generated data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: SWATH extended library generation and statistical data analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 64b04f78ca92078b9ad63cee65bf012f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-swathxtend", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:swathxtend + - doi:10.1074/mcp.M115.055558 + parent_recipe: + name: bioconductor-swathxtend + path: recipes/bioconductor-swathxtend + version: 2.2.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - r-base @@ -32,21 +43,16 @@ requirements: - r-lattice - r-openxlsx - r-venndiagram + +source: + md5: 81247ec78a84f9b29b5a3c995d80305a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'SWATH extended library generation and statistical data analysis' - description: 'Contains utility functions for integrating spectral libraries for SWATH and statistical data analysis for SWATH generated data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:swathxtend - - doi:10.1074/mcp.M115.055558 - parent_recipe: - name: bioconductor-swathxtend - path: recipes/bioconductor-swathxtend - version: 2.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-swfdr/meta.yaml b/recipes/bioconductor-swfdr/meta.yaml index 5b1503ab08784..f83faa961c14b 100644 --- a/recipes/bioconductor-swfdr/meta.yaml +++ b/recipes/bioconductor-swfdr/meta.yaml @@ -1,37 +1,37 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "swfdr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f873820993a9785dbca1c825b291abfb +about: + description: This package allows users to estimate the science-wise false discovery rate from Jager and Leek, "Empirical estimates suggest most published medical research is true," 2013, Biostatistics, using an EM approach due to the presence of rounding and censoring. It also allows users to estimate the false discovery rate conditional on covariates, using a regression framework, as per Boca and Leek, "A direct approach to estimating false discovery rates conditional on covariates," 2018, PeerJ. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Estimation of the science-wise false discovery rate and the false discovery rate conditional on covariates build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-swfdr", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2, rmarkdown, testthat requirements: host: - r-base run: - r-base +source: + md5: df5515b6f5248314e0bf2b3d9796a675 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Estimation of the science-wise false discovery rate and the false discovery rate conditional on covariates' - description: 'This package allows users to estimate the science-wise false discovery rate from Jager and Leek, "Empirical estimates suggest most published medical research is true," 2013, Biostatistics, using an EM approach due to the presence of rounding and censoring. It also allows users to estimate the false discovery rate conditional on covariates, using a regression framework, as per Boca and Leek, "A direct approach to estimating false discovery rates conditional on covariates," 2018, PeerJ.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-switchbox/meta.yaml b/recipes/bioconductor-switchbox/meta.yaml index a1db6b69845ce..2883a21397fe6 100644 --- a/recipes/bioconductor-switchbox/meta.yaml +++ b/recipes/bioconductor-switchbox/meta.yaml @@ -1,24 +1,38 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "switchBox" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package offer different classifiers based on comparisons of pair of features (TSP), using various decision rules (e.g., majority wins principle). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 29de2be8446a4f686acf75635f1539b9 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-switchbox", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:switchbox + parent_recipe: + name: bioconductor-switchbox + path: recipes/bioconductor-switchbox + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-gplots @@ -29,24 +43,16 @@ requirements: - r-base - r-gplots - r-proc - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 40863cfc22c022ed150b48004f33ac0b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm' - description: 'The package offer different classifiers based on comparisons of pair of features (TSP), using various decision rules (e.g., majority wins principle).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:switchbox - parent_recipe: - name: bioconductor-switchbox - path: recipes/bioconductor-switchbox - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-switchde/meta.yaml b/recipes/bioconductor-switchde/meta.yaml index 7bd82e5a01c55..1a470b9107181 100644 --- a/recipes/bioconductor-switchde/meta.yaml +++ b/recipes/bioconductor-switchde/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "switchde" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Inference and detection of switch-like differential expression across single-cell RNA-seq trajectories. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Switch-like differential expression across single-cell trajectories -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9017dd3162508b4412c30ae21eef9328 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-switchde", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:switchde + - doi:10.1093/bioinformatics/btw798 + parent_recipe: + name: bioconductor-switchde + path: recipes/bioconductor-switchde + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr requirements: host: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 run: - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-ggplot2 + +source: + md5: 4319e9c79cdf7e5bfa480360966646dc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Switch-like differential expression across single-cell trajectories' - description: 'Inference and detection of switch-like differential expression across single-cell RNA-seq trajectories.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:switchde - - doi:10.1093/bioinformatics/btw798 - parent_recipe: - name: bioconductor-switchde - path: recipes/bioconductor-switchde - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-synapsis/meta.yaml b/recipes/bioconductor-synapsis/meta.yaml index 448748a38bafa..1cc7bb7cc5d03 100644 --- a/recipes/bioconductor-synapsis/meta.yaml +++ b/recipes/bioconductor-synapsis/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "synapsis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 592572937da010f5fbd70fb7fc8e80d6 +about: + description: Synapsis is a Bioconductor software package for automated (unbiased and reproducible) analysis of meiotic immunofluorescence datasets. The primary functions of the software can i) identify cells in meiotic prophase that are labelled by a synaptonemal complex axis or central element protein, ii) isolate individual synaptonemal complexes and measure their physical length, iii) quantify foci and co-localise them with synaptonemal complexes, iv) measure interference between synaptonemal complex-associated foci. The software has applications that extend to multiple species and to the analysis of other proteins that label meiotic prophase chromosomes. The software converts meiotic immunofluorescence images into R data frames that are compatible with machine learning methods. Given a set of microscopy images of meiotic spread slides, synapsis crops images around individual single cells, counts colocalising foci on strands on a per cell basis, and measures the distance between foci on any given strand. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: An R package to automate the analysis of double-strand break repair during meiosis build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-synapsis", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, tidyverse, BiocStyle requirements: host: - - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - bioconductor-ebimage >=4.48.0,<4.49.0 - r-base run: - - 'bioconductor-ebimage >=4.44.0,<4.45.0' + - bioconductor-ebimage >=4.48.0,<4.49.0 - r-base +source: + md5: e54d1506f16b37444a3553ec38c4f4a8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'An R package to automate the analysis of double-strand break repair during meiosis' - description: 'Synapsis is a Bioconductor software package for automated (unbiased and reproducible) analysis of meiotic immunofluorescence datasets. The primary functions of the software can i) identify cells in meiotic prophase that are labelled by a synaptonemal complex axis or central element protein, ii) isolate individual synaptonemal complexes and measure their physical length, iii) quantify foci and co-localise them with synaptonemal complexes, iv) measure interference between synaptonemal complex-associated foci. The software has applications that extend to multiple species and to the analysis of other proteins that label meiotic prophase chromosomes. The software converts meiotic immunofluorescence images into R data frames that are compatible with machine learning methods. Given a set of microscopy images of meiotic spread slides, synapsis crops images around individual single cells, counts colocalising foci on strands on a per cell basis, and measures the distance between foci on any given strand.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-synapter/meta.yaml b/recipes/bioconductor-synapter/meta.yaml index 74524f15fc539..04844a55943ab 100644 --- a/recipes/bioconductor-synapter/meta.yaml +++ b/recipes/bioconductor-synapter/meta.yaml @@ -1,57 +1,62 @@ -{% set version = "2.26.0" %} +{% set version = "2.30.0" %} {% set name = "synapter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The synapter package provides functionality to reanalyse label-free proteomics data acquired on a Synapt G2 mass spectrometer. One or several runs, possibly processed with additional ion mobility separation to increase identification accuracy can be combined to other quantitation files to maximise identification and quantitation accuracy. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Label-free data analysis pipeline for optimal identification and quantitation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a6c9ade32fbe35d5cb85adc0e9a5322c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-synapter", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: synapterdata (>= 1.13.2), xtable, testthat (>= 0.8), BRAIN, BiocStyle, knitr requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-cleaver >=1.40.0,<1.41.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-cleaver >=1.44.0,<1.45.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - r-lattice - r-rcolorbrewer - - 'r-readr >=0.2' - - 'r-rmarkdown >=1.0' + - r-readr >=0.2 + - r-rmarkdown >=1.0 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-cleaver >=1.40.0,<1.41.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-cleaver >=1.44.0,<1.45.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - r-lattice - r-rcolorbrewer - - 'r-readr >=0.2' - - 'r-rmarkdown >=1.0' + - r-readr >=0.2 + - r-rmarkdown >=1.0 + +source: + md5: a98619ff1d4662fcadb83e7b2370b934 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Label-free data analysis pipeline for optimal identification and quantitation' - description: 'The synapter package provides functionality to reanalyse label-free proteomics data acquired on a Synapt G2 mass spectrometer. One or several runs, possibly processed with additional ion mobility separation to increase identification accuracy can be combined to other quantitation files to maximise identification and quantitation accuracy.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-synapterdata/meta.yaml b/recipes/bioconductor-synapterdata/meta.yaml index a49f7875e36cd..c9c702a0a0535 100644 --- a/recipes/bioconductor-synapterdata/meta.yaml +++ b/recipes/bioconductor-synapterdata/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "synapterdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 255aa756f0b6c0c1d95cdfbc889a67a2 +about: + description: Data independant acquisition of UPS1 protein mix in an E. coli background obtained on a Waters Synapt G2 instrument. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Data accompanying the synapter package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-synapterdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-synapter >=2.26.0,<2.27.0' + - bioconductor-synapter >=2.30.0,<2.31.0 - r-base run: - - 'bioconductor-synapter >=2.26.0,<2.27.0' + - bioconductor-synapter >=2.30.0,<2.31.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e13319e22eff32d961f703684f9a23dc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Data accompanying the synapter package' - description: 'Data independant acquisition of UPS1 protein mix in an E. coli background obtained on a Waters Synapt G2 instrument.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-synapterdata/post-link.sh b/recipes/bioconductor-synapterdata/post-link.sh index a426a8749af10..649d97606868f 100644 --- a/recipes/bioconductor-synapterdata/post-link.sh +++ b/recipes/bioconductor-synapterdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "synapterdata-1.40.0" +installBiocDataPackage.sh "synapterdata-1.44.0" diff --git a/recipes/bioconductor-synaptome.data/meta.yaml b/recipes/bioconductor-synaptome.data/meta.yaml index d7106934d6d10..2b4e3f9aed097 100644 --- a/recipes/bioconductor-synaptome.data/meta.yaml +++ b/recipes/bioconductor-synaptome.data/meta.yaml @@ -1,40 +1,40 @@ {% set version = "0.99.6" %} {% set name = "synaptome.data" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4388c63219782a9aa3e384fcdb51ed47 +about: + description: The package provides access to the copy of the Synaptic proteome database. It was designed as an accompaniment for Synaptome.DB package. Database provides information for specific synaptic genes and allows building the protein-protein interaction graph for gene sets, synaptic compartments, and brain regions. In the current update we added 6 more synaptic proteome studies, which resulted in total of 64 studies. We introduced Synaptic Vesicle as a separate compartment. We also added coding mutations for Autistic Spectral disorder and Epilepsy collected from publicly available databases. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: AnnotationData for Synaptome.DB package build: - number: 2 + noarch: generic + number: 3 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-synaptome.data", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4388c63219782a9aa3e384fcdb51ed47 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'AnnotationData for Synaptome.DB package' - description: 'The package provides access to the copy of the Synaptic proteome database. It was designed as an accompaniment for Synaptome.DB package. Database provides information for specific synaptic genes and allows building the protein-protein interaction graph for gene sets, synaptic compartments, and brain regions. In the current update we added 6 more synaptic proteome studies, which resulted in total of 64 studies. We introduced Synaptic Vesicle as a separate compartment. We also added coding mutations for Autistic Spectral disorder and Epilepsy collected from publicly available databases.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-synaptome.db/meta.yaml b/recipes/bioconductor-synaptome.db/meta.yaml index 1ee54ad6b3834..506b7a91fad21 100644 --- a/recipes/bioconductor-synaptome.db/meta.yaml +++ b/recipes/bioconductor-synaptome.db/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "0.99.15" %} +{% set version = "0.99.16" %} {% set name = "synaptome.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package contains local copy of the Synaptic proteome database. On top of this it provide a set of utility R functions to query and analyse its content. It allows extraction of information for specific genes and building the protein-protein interaction graph for gene sets, synaptic compartments, and brain regions. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Synamptosome Proteome Database -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 7ed11d61ac8dca86372eeec59b5ab03b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-synaptome.db", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, pander, testthat, devtools, markdown, ggplot2 requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-synaptome.data >=0.99.0,<0.100.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-synaptome.data >=0.99.0,<0.100.0 - r-base - r-dbi - r-dbplyr @@ -32,8 +33,8 @@ requirements: - r-rdpack - r-rsqlite run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-synaptome.data >=0.99.0,<0.100.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-synaptome.data >=0.99.0,<0.100.0 - r-base - r-dbi - r-dbplyr @@ -42,13 +43,17 @@ requirements: - r-rdpack - r-rsqlite - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: f59812004d1b9b433203dab3b41d10f7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Synamptosome Proteome Database' - description: 'The package contains local copy of the Synaptic proteome database. On top of this it provide a set of utility R functions to query and analyse its content. It allows extraction of information for specific genes and building the protein-protein interaction graph for gene sets, synaptic compartments, and brain regions.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-synaptome.db/post-link.sh b/recipes/bioconductor-synaptome.db/post-link.sh index f2b7062f649b3..8c929d5fd67cf 100644 --- a/recipes/bioconductor-synaptome.db/post-link.sh +++ b/recipes/bioconductor-synaptome.db/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "synaptome.db-0.99.15" +installBiocDataPackage.sh "synaptome.db-0.99.16" diff --git a/recipes/bioconductor-synergyfinder/meta.yaml b/recipes/bioconductor-synergyfinder/meta.yaml index 9eb18914024ce..85a3a676f0e5c 100644 --- a/recipes/bioconductor-synergyfinder/meta.yaml +++ b/recipes/bioconductor-synergyfinder/meta.yaml @@ -1,86 +1,21 @@ -{% set version = "3.10.0" %} +{% set version = "3.14.0" %} {% set name = "synergyfinder" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Efficient implementations for analyzing pre-clinical multiple drug combination datasets. It provides efficient implementations for 1.the popular synergy scoring models, including HSA, Loewe, Bliss, and ZIP to quantify the degree of drug combination synergy; 2. higher order drug combination data analysis and synergy landscape visualization for unlimited number of drugs in a combination; 3. statistical analysis of drug combination synergy and sensitivity with confidence intervals and p-values; 4. synergy barometer for harmonizing multiple synergy scoring methods to provide a consensus metric of synergy; 5. evaluation of synergy and sensitivity simultaneously to provide an unbiased interpretation of the clinical potential of the drug combinations. Based on this package, we also provide a web application (http://www.synergyfinder.org) for users who prefer graphical user interface. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Mozilla Public License 2.0 + summary: Calculate and Visualize Synergy Scores for Drug Combinations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8b511fc821bd8e8b344a439f5c641a72 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-synergyfinder", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown -requirements: - host: - - r-base - - 'r-dplyr >=1.0.3' - - 'r-drc >=3.0-1' - - 'r-furrr >=0.2.2' - - 'r-future >=1.21.0' - - 'r-ggforce >=0.3.2' - - 'r-ggplot2 >=3.3.3' - - 'r-ggrepel >=0.9.1' - - 'r-gstat >=2.0-6' - - 'r-kriging >=1.1' - - 'r-lattice >=0.20-41' - - 'r-magrittr >=2.0.1' - - 'r-metr >=0.9.1' - - 'r-mice >=3.13.0' - - 'r-nleqslv >=3.3.2' - - 'r-pbapply >=1.4-3' - - 'r-plotly >=4.9.3' - - 'r-purrr >=0.3.4' - - 'r-reshape2 >=1.4.4' - - 'r-sp >=1.4-5' - - 'r-spatialextremes >=2.0-9' - - 'r-stringr >=1.4.0' - - 'r-tidyr >=1.1.2' - - 'r-tidyverse >=1.3.0' - - 'r-vegan >=2.5-7' - run: - - r-base - - 'r-dplyr >=1.0.3' - - 'r-drc >=3.0-1' - - 'r-furrr >=0.2.2' - - 'r-future >=1.21.0' - - 'r-ggforce >=0.3.2' - - 'r-ggplot2 >=3.3.3' - - 'r-ggrepel >=0.9.1' - - 'r-gstat >=2.0-6' - - 'r-kriging >=1.1' - - 'r-lattice >=0.20-41' - - 'r-magrittr >=2.0.1' - - 'r-metr >=0.9.1' - - 'r-mice >=3.13.0' - - 'r-nleqslv >=3.3.2' - - 'r-pbapply >=1.4-3' - - 'r-plotly >=4.9.3' - - 'r-purrr >=0.3.4' - - 'r-reshape2 >=1.4.4' - - 'r-sp >=1.4-5' - - 'r-spatialextremes >=2.0-9' - - 'r-stringr >=1.4.0' - - 'r-tidyr >=1.1.2' - - 'r-tidyverse >=1.3.0' - - 'r-vegan >=2.5-7' -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Mozilla Public License 2.0' - summary: 'Calculate and Visualize Synergy Scores for Drug Combinations' - description: 'Efficient implementations for analyzing pre-clinical multiple drug combination datasets. It provides efficient implementations for 1.the popular synergy scoring models, including HSA, Loewe, Bliss, and ZIP to quantify the degree of drug combination synergy; 2. higher order drug combination data analysis and synergy landscape visualization for unlimited number of drugs in a combination; 3. statistical analysis of drug combination synergy and sensitivity with confidence intervals and p-values; 4. synergy barometer for harmonizing multiple synergy scoring methods to provide a consensus metric of synergy; 5. evaluation of synergy and sensitivity simultaneously to provide an unbiased interpretation of the clinical potential of the drug combinations. Based on this package, we also provide a web application (http://www.synergyfinder.org) for users who prefer graphical user interface.' + extra: identifiers: - biotools:synergyfinder @@ -90,3 +25,76 @@ extra: path: recipes/bioconductor-synergyfinder version: 1.6.1 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown +requirements: + + host: + - r-base + - r-dplyr >=1.0.3 + - r-drc >=3.0-1 + - r-furrr >=0.2.2 + - r-future >=1.21.0 + - r-ggforce >=0.3.2 + - r-ggplot2 >=3.3.3 + - r-ggrepel >=0.9.1 + - r-gstat >=2.0-6 + - r-kriging >=1.1 + - r-lattice >=0.20-41 + - r-magrittr >=2.0.1 + - r-metr >=0.9.1 + - r-mice >=3.13.0 + - r-nleqslv >=3.3.2 + - r-pbapply >=1.4-3 + - r-plotly >=4.9.3 + - r-purrr >=0.3.4 + - r-reshape2 >=1.4.4 + - r-sp >=1.4-5 + - r-spatialextremes >=2.0-9 + - r-stringr >=1.4.0 + - r-tidyr >=1.1.2 + - r-tidyverse >=1.3.0 + - r-vegan >=2.5-7 + + run: + - r-base + - r-dplyr >=1.0.3 + - r-drc >=3.0-1 + - r-furrr >=0.2.2 + - r-future >=1.21.0 + - r-ggforce >=0.3.2 + - r-ggplot2 >=3.3.3 + - r-ggrepel >=0.9.1 + - r-gstat >=2.0-6 + - r-kriging >=1.1 + - r-lattice >=0.20-41 + - r-magrittr >=2.0.1 + - r-metr >=0.9.1 + - r-mice >=3.13.0 + - r-nleqslv >=3.3.2 + - r-pbapply >=1.4-3 + - r-plotly >=4.9.3 + - r-purrr >=0.3.4 + - r-reshape2 >=1.4.4 + - r-sp >=1.4-5 + - r-spatialextremes >=2.0-9 + - r-stringr >=1.4.0 + - r-tidyr >=1.1.2 + - r-tidyverse >=1.3.0 + - r-vegan >=2.5-7 + +source: + md5: 6e3bef765805bc8dc28f55ae23b26747 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-synextend/build_failure.linux-64.yaml b/recipes/bioconductor-synextend/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..82d2a0ce0dc86 --- /dev/null +++ b/recipes/bioconductor-synextend/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5156e6101132e6e8fa12079a9dd18cd38853122cabb3d28cd4b0d290a08e4f2f # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-synextend-1.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bioconductor-synextend-1.18.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/bioconductor-synextend_1734707193120/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library + * installing *source* package SynExtend ... + ** package SynExtend successfully unpacked and MD5 sums checked + ** using staged installation + ** libs + using C compiler: x86_64-conda-linux-gnu-cc (conda-forge gcc 13.3.0-1) 13.3.0 + sh: --version: command not found + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c CDend.c -o CDend.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c CShuffle.c -o CShuffle.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c HungarianAlgo.c -o HungarianAlgo.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c MoranI.c -o MoranI.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c NucleotideCounts.c -o NucleotideCounts.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c OnDiskLP.c -o OnDiskLP.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c PrefixTrie.c -o PrefixTrie.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c R_init_synextend.c -o R_init_synextend.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RandomForest.c -o RandomForest.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c SEutils.c -o SEutils.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c XORRand.c -o XORRand.o + fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c _fortran_tabulate.f95 -o _fortran_tabulate.o + make: fpic: No such file or directory + make: [/opt/conda/conda-bld/bioconductor-synextend_1734707193120/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/etc/Makeconf:223: _fortran_tabulate.o] Error 127 (ignored) + fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c _fortran_utils.f95 -o _fortran_utils.o + make: fpic: No such file or directory + make: [/opt/conda/conda-bld/bioconductor-synextend_1734707193120/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/etc/Makeconf:223: _fortran_utils.o] Error 127 (ignored) + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c calcMIR2C.c -o calcMIR2C.o + fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c cart_fort.f95 -o cart_fort.o + make: fpic: No such file or directory + make: [/opt/conda/conda-bld/bioconductor-synextend_1734707193120/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/etc/Makeconf:223: cart_fort.o] Error 127 (ignored) + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fopenmp -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c dendrapply.c -o dendrapply.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -shared -L$PREFIX/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -o SynExtend.so CDend.o CShuffle.o HungarianAlgo.o MoranI.o NucleotideCounts.o OnDiskLP.o PrefixTrie.o R_init_synextend.o RandomForest.o SEutils.o XORRand.o _fortran_tabulate.o _fortran_utils.o calcMIR2C.o cart_fort.o dendrapply.o -fopenmp -lgfortran -lm -lquadmath -L$PREFIX/lib/R/lib -lR + /opt/conda/conda-bld/bioconductor-synextend_1734707193120/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find _fortran_tabulate.o: No such file or directory + /opt/conda/conda-bld/bioconductor-synextend_1734707193120/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find _fortran_utils.o: No such file or directory + /opt/conda/conda-bld/bioconductor-synextend_1734707193120/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find cart_fort.o: No such file or directory + collect2: error: ld returned 1 exit status + make: *** [/opt/conda/conda-bld/bioconductor-synextend_1734707193120/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/share/make/shlib.mk:10: SynExtend.so] Error 1 + ERROR: compilation failed for package SynExtend + * removing /opt/conda/conda-bld/bioconductor-synextend_1734707193120/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/SynExtend + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-synextend_1734707193120/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-synextend_1734707193120/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-synextend/meta.yaml b/recipes/bioconductor-synextend/meta.yaml index f46ea364894f7..60bebea92b53d 100644 --- a/recipes/bioconductor-synextend/meta.yaml +++ b/recipes/bioconductor-synextend/meta.yaml @@ -1,49 +1,58 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "SynExtend" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Shared order between genomic sequences provide a great deal of information. Synteny objects produced by the R package DECIPHER provides quantitative information about that shared order. SynExtend provides tools for extracting information from Synteny objects. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Tools for Working With Synteny Objects -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f7ee0b985a06dbd6040329dd264648f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-synextend", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, igraph, markdown, rmarkdown requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-decipher >=2.30.0,<2.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-decipher >=3.2.0,<3.3.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base + - r-dbi + - r-rsqlite - libblas - liblapack run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-decipher >=2.30.0,<2.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-decipher >=3.2.0,<3.3.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - build: - - {{ compiler('c') }} - - make + - r-dbi + - r-rsqlite + +source: + md5: eb6add489f08d6f63e015f582a5ac59b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Tools for Working With Synteny Objects' - description: 'Shared order between genomic sequences provide a great deal of information. Synteny objects produced by the R package DECIPHER provides quantitative information about that shared order. SynExtend provides tools for extracting information from Synteny objects.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-synlet/meta.yaml b/recipes/bioconductor-synlet/meta.yaml index 42f0e6cfbeb87..5471363401ce7 100644 --- a/recipes/bioconductor-synlet/meta.yaml +++ b/recipes/bioconductor-synlet/meta.yaml @@ -1,28 +1,39 @@ -{% set version = "2.2.0" %} +{% set version = "2.6.0" %} {% set name = "synlet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Select hits from synthetic lethal RNAi screen data. For example, there are two identical celllines except one gene is knocked-down in one cellline. The interest is to find genes that lead to stronger lethal effect when they are knocked-down further by siRNA. Quality control and various visualisation tools are implemented. Four different algorithms could be used to pick up the interesting hits. This package is designed based on 384 wells plates, but may apply to other platforms with proper configuration. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Hits Selection for Synthetic Lethal RNAi Screen Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f56c634faaae3a0de5e46d18e6617d11 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-synlet", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:synlet + - doi:10.1101/043570 + parent_recipe: + name: bioconductor-synlet + path: recipes/bioconductor-synlet + version: 1.10.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-rankprod >=3.28.0,<3.29.0' + - bioconductor-rankprod >=3.32.0,<3.33.0 - r-base - r-data.table - r-ggplot2 @@ -30,28 +41,23 @@ requirements: - r-patchwork - r-rcolorbrewer run: - - 'bioconductor-rankprod >=3.28.0,<3.29.0' + - bioconductor-rankprod >=3.32.0,<3.33.0 - r-base - r-data.table - r-ggplot2 - r-magrittr - r-patchwork - r-rcolorbrewer + +source: + md5: 070bb69d84f70bd96a82cc605068381b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Hits Selection for Synthetic Lethal RNAi Screen Data' - description: 'Select hits from synthetic lethal RNAi screen data. For example, there are two identical celllines except one gene is knocked-down in one cellline. The interest is to find genes that lead to stronger lethal effect when they are knocked-down further by siRNA. Quality control and various visualisation tools are implemented. Four different algorithms could be used to pick up the interesting hits. This package is designed based on 384 wells plates, but may apply to other platforms with proper configuration.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:synlet - - doi:10.1101/043570 - parent_recipe: - name: bioconductor-synlet - path: recipes/bioconductor-synlet - version: 1.10.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-synmut/meta.yaml b/recipes/bioconductor-synmut/meta.yaml index e2cd14510aeba..16a2b8ca4ec33 100644 --- a/recipes/bioconductor-synmut/meta.yaml +++ b/recipes/bioconductor-synmut/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "SynMut" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 485dd0770e2c64ad7ace9a3edf957fe8 +about: + description: There are increasing demands on designing virus mutants with specific dinucleotide or codon composition. This tool can take both dinucleotide preference and/or codon usage bias into account while designing mutants. It is a powerful tool for in silico designs of DNA sequence mutants. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-synmut", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc, glue requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - r-seqinr - r-stringr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - r-seqinr - r-stringr +source: + md5: 0b5f7e13d2845a7a0a7e73be5b21c640 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'SynMut: Designing Synonymously Mutated Sequences with Different Genomic Signatures' - description: 'There are increasing demands on designing virus mutants with specific dinucleotide or codon composition. This tool can take both dinucleotide preference and/or codon usage bias into account while designing mutants. It is a powerful tool for in silico designs of DNA sequence mutants.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-syntenet/meta.yaml b/recipes/bioconductor-syntenet/meta.yaml index 58a7b99d243ea..3ea232f93d6c2 100644 --- a/recipes/bioconductor-syntenet/meta.yaml +++ b/recipes/bioconductor-syntenet/meta.yaml @@ -1,70 +1,73 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "syntenet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm, which was ported to this package with the Rcpp framework for R and C++ integration. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform: i. network clustering; ii. phylogenomic profiling (by identifying which species contain which clusters) and; iii. microsynteny-based phylogeny reconstruction with maximum likelihood.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Inference And Analysis Of Synteny Networks -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ab56b637f74d79cfba3dd6aab80b7ac9 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-syntenet", max_pin="x.x") }}' -# Suggests: BiocStyle, ggtree, labdsv, covr, knitr, rmarkdown, testthat (>= 3.0.0), xml2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, ggtree, labdsv, covr, knitr, rmarkdown, testthat (>= 3.0.0), xml2, networkD3 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-ggnetwork - r-ggplot2 - r-igraph - r-intergraph - - r-networkd3 - r-pheatmap - r-rcolorbrewer - - 'r-rcpp >=1.0.8' + - r-rcpp >=1.0.8 - r-rlang - r-testthat - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 - r-base - r-ggnetwork - r-ggplot2 - r-igraph - r-intergraph - - r-networkd3 - r-pheatmap - r-rcolorbrewer - - 'r-rcpp >=1.0.8' + - r-rcpp >=1.0.8 - r-rlang - r-testthat - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: d43f9996496ecd4cf2de0933f5226ca6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Inference And Analysis Of Synteny Networks' - description: 'syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm, which was ported to this package with the Rcpp framework for R and C++ integration. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform: i. network clustering; ii. phylogenomic profiling (by identifying which species contain which clusters) and; iii. microsynteny-based phylogeny reconstruction with maximum likelihood.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-systempiper/meta.yaml b/recipes/bioconductor-systempiper/meta.yaml index 2690b4fb73a2c..b02d90713e6f4 100644 --- a/recipes/bioconductor-systempiper/meta.yaml +++ b/recipes/bioconductor-systempiper/meta.yaml @@ -1,35 +1,44 @@ -{% set version = "2.8.0" %} +{% set version = "2.12.0" %} {% set name = "systemPipeR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: systemPipeR is a multipurpose data analysis workflow environment that unifies R with command-line tools. It enables scientists to analyze many types of large- or small-scale data on local or distributed computer systems with a high level of reproducibility, scalability and portability. At its core is a command-line interface (CLI) that adopts the Common Workflow Language (CWL). This design allows users to choose for each analysis step the optimal R or command-line software. It supports both end-to-end and partial execution of workflows with built-in restart functionalities. Efficient management of complex analysis tasks is accomplished by a flexible workflow control container class. Handling of large numbers of input samples and experimental designs is facilitated by consistent sample annotation mechanisms. As a multi-purpose workflow toolkit, systemPipeR enables users to run existing workflows, customize them or design entirely new ones while taking advantage of widely adopted data structures within the Bioconductor ecosystem. Another important core functionality is the generation of reproducible scientific analysis and technical reports. For result interpretation, systemPipeR offers a wide range of plotting functionality, while an associated Shiny App offers many useful functionalities for interactive result exploration. The vignettes linked from this page include (1) a general introduction, (2) a description of technical details, and (3) a collection of workflow templates. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'systemPipeR: Workflow Environment for Data Analysis and Report Generation' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 67456347870d6c358e1209658cb930d2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-systempiper", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, systemPipeRdata, GenomicAlignments, grid, dplyr, testthat, rjson, annotate, AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT, rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools, GenomicFeatures (>= 1.31.3), VariantAnnotation (>= 1.25.11) + +extra: + identifiers: + - biotools:systempiper + parent_recipe: + name: bioconductor-systempiper + path: recipes/bioconductor-systempiper + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, systemPipeRdata, GenomicAlignments, grid, dplyr, testthat, rjson, annotate, AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT, rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools, GenomicFeatures, txdbmaker, VariantAnnotation (>= 1.25.11) # SystemRequirements: systemPipeR can be used to run external command-line software (e.g. short read aligners), but the corresponding tool needs to be installed on a system. requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-crayon - r-ggplot2 @@ -38,13 +47,13 @@ requirements: - r-stringr - r-yaml run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-crayon - r-ggplot2 @@ -52,19 +61,16 @@ requirements: - r-magrittr - r-stringr - r-yaml + +source: + md5: cc9cef185e84097abc4a6bb73036a50d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'systemPipeR: workflow management and report generation environment' - description: 'systemPipeR is a multipurpose data analysis workflow environment that unifies R with command-line tools. It enables scientists to analyze many types of large- or small-scale data on local or distributed computer systems with a high level of reproducibility, scalability and portability. At its core is a command-line interface (CLI) that adopts the Common Workflow Language (CWL). This design allows users to choose for each analysis step the optimal R or command-line software. It supports both end-to-end and partial execution of workflows with built-in restart functionalities. Efficient management of complex analysis tasks is accomplished by a flexible workflow control container class. Handling of large numbers of input samples and experimental designs is facilitated by consistent sample annotation mechanisms. As a multi-purpose workflow toolkit, systemPipeR enables users to run existing workflows, customize them or design entirely new ones while taking advantage of widely adopted data structures within the Bioconductor ecosystem. Another important core functionality is the generation of reproducible scientific analysis and technical reports. For result interpretation, systemPipeR offers a wide range of plotting functionality, while an associated Shiny App offers many useful functionalities for interactive result exploration. The vignettes linked from this page include (1) a general introduction, (2) a description of technical details, and (3) a collection of workflow templates.' -extra: - identifiers: - - biotools:systempiper - parent_recipe: - name: bioconductor-systempiper - path: recipes/bioconductor-systempiper - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-systempiperdata/meta.yaml b/recipes/bioconductor-systempiperdata/meta.yaml index 40deed2560a71..3e45a3f81620c 100644 --- a/recipes/bioconductor-systempiperdata/meta.yaml +++ b/recipes/bioconductor-systempiperdata/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "2.6.0" %} +{% set version = "2.10.0" %} {% set name = "systemPipeRdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: systemPipeRdata complements the systemPipeR workflow management system (WMS) by offering a collection of pre-designed data analysis workflow templates. These templates are easily accessible and can be readily loaded onto a user's system with a single command. Once loaded, the WMS can immediately utilize these templates for efficient end-to-end analysis, serving a wide range of data analysis needs. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: 'systemPipeRdata: Workflow templates and sample data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1af59929fb95c3a017b88fce32a4c833 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-systempiperdata", max_pin="x.x") }}' - noarch: generic -# Suggests: GenomicFeatures, GenomicRanges, IRanges, Rsamtools, ShortRead, rtracklayer, RUnit, BiocStyle, knitr, rmarkdown, systemPipeR + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: GenomicFeatures, GenomicRanges, IRanges, Rsamtools, ShortRead, rtracklayer, RUnit, BiocStyle, knitr, rmarkdown, systemPipeR, kableExtra, magrittr, dplyr requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - r-jsonlite - r-remotes run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 - r-base - r-jsonlite - r-remotes - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 73820a7b33a8d1df288467179c3d96cc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'systemPipeRdata: Workflow templates and sample data' - description: 'systemPipeRdata is a helper package to generate with a single command NGS workflow templates that are intended to be used by its parent package systemPipeR. The latter is an environment for building end-to-end analysis pipelines with automated report generation for next generation sequence (NGS) applications such as RNA-Seq, RIBO-Seq, ChIP-Seq, VAR-Seq and many others. Detailed examples for using systemPipeRdata are given in systemPipeR''s overview vignette.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-systempiperdata/post-link.sh b/recipes/bioconductor-systempiperdata/post-link.sh index 5e959d6d140be..095298880023e 100644 --- a/recipes/bioconductor-systempiperdata/post-link.sh +++ b/recipes/bioconductor-systempiperdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "systempiperdata-2.6.0" +installBiocDataPackage.sh "systempiperdata-2.10.0" diff --git a/recipes/bioconductor-systempipeshiny/meta.yaml b/recipes/bioconductor-systempipeshiny/meta.yaml index 6a0d1fa4130e8..b9e2ee52f6588 100644 --- a/recipes/bioconductor-systempipeshiny/meta.yaml +++ b/recipes/bioconductor-systempipeshiny/meta.yaml @@ -1,33 +1,36 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "systemPipeShiny" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'systemPipeShiny (SPS) extends the widely used systemPipeR (SPR) workflow environment with a versatile graphical user interface provided by a Shiny App. This allows non-R users, such as experimentalists, to run many systemPipeR’s workflow designs, control, and visualization functionalities interactively without requiring knowledge of R. Most importantly, SPS has been designed as a general purpose framework for interacting with other R packages in an intuitive manner. Like most Shiny Apps, SPS can be used on both local computers as well as centralized server-based deployments that can be accessed remotely as a public web service for using SPR’s functionalities with community and/or private data. The framework can integrate many core packages from the R/Bioconductor ecosystem. Examples of SPS’ current functionalities include: (a) interactive creation of experimental designs and metadata using an easy to use tabular editor or file uploader; (b) visualization of workflow topologies combined with auto-generation of R Markdown preview for interactively designed workflows; (d) access to a wide range of data processing routines; (e) and an extendable set of visualization functionalities. Complex visual results can be managed on a ''Canvas Workbench’ allowing users to organize and to compare plots in an efficient manner combined with a session snapshot feature to continue work at a later time. The present suite of pre-configured visualization examples. The modular design of SPR makes it easy to design custom functions without any knowledge of Shiny, as well as extending the environment in the future with contributions from the community.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'systemPipeShiny: An Interactive Framework for Workflow Management and Visualization' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8880796c4c2bf213ffa98df7f3f8d164 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-systempipeshiny", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr, rmarkdown, systemPipeR (>= 2.2.0), systemPipeRdata (>= 2.0.0), rhandsontable, zip, callr, pushbar, fs, readr, R.utils, DESeq2, SummarizedExperiment, glmpca, pheatmap, grid, ape, Rtsne, UpSetR, tidyr, esquisse (>= 1.1.0), cicerone requirements: + host: - r-assertthat - r-base - r-bsplus - r-crayon - r-dplyr - - 'r-drawer >=0.2' + - r-drawer >=0.2 - r-dt - r-ggplot2 - r-glue @@ -39,29 +42,30 @@ requirements: - r-rlang - r-rsqlite - r-rstudioapi - - 'r-shiny >=1.6.0' + - r-shiny >=1.6.0 - r-shinyace - r-shinydashboard - - 'r-shinydashboardplus >=2.0.0' + - r-shinydashboardplus >=2.0.0 - r-shinyfiles - r-shinyjqui - r-shinyjs - r-shinytoastr - r-shinywidgets - - 'r-spscomps >=0.3.3' - - 'r-spsutil >=0.2.2' + - r-spscomps >=0.3.3 + - r-spsutil >=0.2.2 - r-stringr - r-styler - r-tibble - - 'r-vroom >=1.3.1' + - r-vroom >=1.3.1 - r-yaml + run: - r-assertthat - r-base - r-bsplus - r-crayon - r-dplyr - - 'r-drawer >=0.2' + - r-drawer >=0.2 - r-dt - r-ggplot2 - r-glue @@ -73,29 +77,32 @@ requirements: - r-rlang - r-rsqlite - r-rstudioapi - - 'r-shiny >=1.6.0' + - r-shiny >=1.6.0 - r-shinyace - r-shinydashboard - - 'r-shinydashboardplus >=2.0.0' + - r-shinydashboardplus >=2.0.0 - r-shinyfiles - r-shinyjqui - r-shinyjs - r-shinytoastr - r-shinywidgets - - 'r-spscomps >=0.3.3' - - 'r-spsutil >=0.2.2' + - r-spscomps >=0.3.3 + - r-spsutil >=0.2.2 - r-stringr - r-styler - r-tibble - - 'r-vroom >=1.3.1' + - r-vroom >=1.3.1 - r-yaml + +source: + md5: dc9a1d1a008674c8a9fc3f716810a73f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'systemPipeShiny: An Interactive Framework for Workflow Management and Visualization' - description: 'systemPipeShiny (SPS) extends the widely used systemPipeR (SPR) workflow environment with a versatile graphical user interface provided by a Shiny App. This allows non-R users, such as experimentalists, to run many systemPipeR’s workflow designs, control, and visualization functionalities interactively without requiring knowledge of R. Most importantly, SPS has been designed as a general purpose framework for interacting with other R packages in an intuitive manner. Like most Shiny Apps, SPS can be used on both local computers as well as centralized server-based deployments that can be accessed remotely as a public web service for using SPR’s functionalities with community and/or private data. The framework can integrate many core packages from the R/Bioconductor ecosystem. Examples of SPS’ current functionalities include: (a) interactive creation of experimental designs and metadata using an easy to use tabular editor or file uploader; (b) visualization of workflow topologies combined with auto-generation of R Markdown preview for interactively designed workflows; (d) access to a wide range of data processing routines; (e) and an extendable set of visualization functionalities. Complex visual results can be managed on a ''Canvas Workbench’ allowing users to organize and to compare plots in an efficient manner combined with a session snapshot feature to continue work at a later time. The present suite of pre-configured visualization examples. The modular design of SPR makes it easy to design custom functions without any knowledge of Shiny, as well as extending the environment in the future with contributions from the community.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-systempipetools/meta.yaml b/recipes/bioconductor-systempipetools/meta.yaml index f406794a6855d..2889a7988da8b 100644 --- a/recipes/bioconductor-systempipetools/meta.yaml +++ b/recipes/bioconductor-systempipetools/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "systemPipeTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: systemPipeTools package extends the widely used systemPipeR (SPR) workflow environment with an enhanced toolkit for data visualization, including utilities to automate the data visualizaton for analysis of differentially expressed genes (DEGs). systemPipeTools provides data transformation and data exploration functions via scatterplots, hierarchical clustering heatMaps, principal component analysis, multidimensional scaling, generalized principal components, t-Distributed Stochastic Neighbor embedding (t-SNE), and MA and volcano plots. All these utilities can be integrated with the modular design of the systemPipeR environment that allows users to easily substitute any of these features and/or custom with alternatives. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Tools for data visualization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e0f74af8b351b49c68cbfed4e9e00adc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-systempipetools", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: systemPipeR, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocGenerics, Biostrings, methods requirements: host: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-ape - r-base - r-dplyr @@ -39,9 +40,9 @@ requirements: - r-rtsne - r-tibble run: - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-ape - r-base - r-dplyr @@ -55,12 +56,16 @@ requirements: - r-plotly - r-rtsne - r-tibble + +source: + md5: 6a14f23733dc113d07a860f495035ebf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Tools for data visualization' - description: 'systemPipeTools package extends the widely used systemPipeR (SPR) workflow environment with an enhanced toolkit for data visualization, including utilities to automate the data visualizaton for analysis of differentially expressed genes (DEGs). systemPipeTools provides data transformation and data exploration functions via scatterplots, hierarchical clustering heatMaps, principal component analysis, multidimensional scaling, generalized principal components, t-Distributed Stochastic Neighbor embedding (t-SNE), and MA and volcano plots. All these utilities can be integrated with the modular design of the systemPipeR environment that allows users to easily substitute any of these features and/or custom with alternatives.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tabulamurisdata/meta.yaml b/recipes/bioconductor-tabulamurisdata/meta.yaml index c226941259d34..3f9a7ef379d13 100644 --- a/recipes/bioconductor-tabulamurisdata/meta.yaml +++ b/recipes/bioconductor-tabulamurisdata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "TabulaMurisData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 39c27cc6646ea3bcdb4637a226b219b8 +about: + description: Access to processed 10x (droplet) and SmartSeq2 (on FACS-sorted cells) single-cell RNA-seq data from the Tabula Muris consortium (http://tabula-muris.ds.czbiohub.org/). + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 10x And SmartSeq2 Data From The Tabula Muris Consortium build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tabulamurisdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran, scater, iSEE, testthat requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c1bd6839155817b5f01874ac53fe91cd + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: '10x And SmartSeq2 Data From The Tabula Muris Consortium' - description: 'Access to processed 10x (droplet) and SmartSeq2 (on FACS-sorted cells) single-cell RNA-seq data from the Tabula Muris consortium (http://tabula-muris.ds.czbiohub.org/).' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tabulamurisdata/post-link.sh b/recipes/bioconductor-tabulamurisdata/post-link.sh index fb80612c77662..ff16c87da69d0 100644 --- a/recipes/bioconductor-tabulamurisdata/post-link.sh +++ b/recipes/bioconductor-tabulamurisdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tabulamurisdata-1.20.0" +installBiocDataPackage.sh "tabulamurisdata-1.24.0" diff --git a/recipes/bioconductor-tabulamurissenisdata/meta.yaml b/recipes/bioconductor-tabulamurissenisdata/meta.yaml index 0a4e957526051..84cc2f6a7ecc5 100644 --- a/recipes/bioconductor-tabulamurissenisdata/meta.yaml +++ b/recipes/bioconductor-tabulamurissenisdata/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "TabulaMurisSenisData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides access to RNA-seq data generated by the Tabula Muris Senis project via the Bioconductor project. The data is made available without restrictions by the Chan Zuckerberg Biohub. It is provided here without further processing, collected in the form of SingleCellExperiment objects. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Bulk and single-cell RNA-seq data from the Tabula Muris Senis project -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6d6120b18adce70e943a3da8e0e577b2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tabulamurissenisdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ggplot2, testthat, knitr, rmarkdown, iSEE, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-gdata run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-gdata - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 3335145c932f9c89f2ba43b229209575 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Bulk and single-cell RNA-seq data from the Tabula Muris Senis project' - description: 'This package provides access to RNA-seq data generated by the Tabula Muris Senis project via the Bioconductor project. The data is made available without restrictions by the Chan Zuckerberg Biohub. It is provided here without further processing, collected in the form of SingleCellExperiment objects.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tabulamurissenisdata/post-link.sh b/recipes/bioconductor-tabulamurissenisdata/post-link.sh index 946a2b411a203..f4a6b16e1e196 100644 --- a/recipes/bioconductor-tabulamurissenisdata/post-link.sh +++ b/recipes/bioconductor-tabulamurissenisdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tabulamurissenisdata-1.8.0" +installBiocDataPackage.sh "tabulamurissenisdata-1.12.0" diff --git a/recipes/bioconductor-tadar/meta.yaml b/recipes/bioconductor-tadar/meta.yaml index a4d1aea0a2232..0407e420b22d4 100644 --- a/recipes/bioconductor-tadar/meta.yaml +++ b/recipes/bioconductor-tadar/meta.yaml @@ -1,59 +1,64 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "tadar" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functions to standardise the analysis of Differential Allelic Representation (DAR). DAR compromises the integrity of Differential Expression analysis results as it can bias expression, influencing the classification of genes (or transcripts) as being differentially expressed. DAR analysis results in an easy-to-interpret value between 0 and 1 for each genetic feature of interest, where 0 represents identical allelic representation and 1 represents complete diversity. This metric can be used to identify features prone to false-positive calls in Differential Expression analysis, and can be leveraged with statistical methods to alleviate the impact of such artefacts on RNA-seq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Transcriptome Analysis of Differential Allelic Representation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 88c91583a351bef3f3d8ca38b51c0c04 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tadar", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, covr, knitr, limma, rmarkdown, testthat (>= 3.0.0), tidyverse requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-ggplot2 - r-rlang run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-ggplot2 - r-rlang + +source: + md5: 2befd08cefb1a79c02ba456de5d8ef2a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Transcriptome Analysis of Differential Allelic Representation' - description: 'This package provides functions to standardise the analysis of Differential Allelic Representation (DAR). DAR compromises the integrity of Differential Expression analysis results as it can bias expression, influencing the classification of genes (or transcripts) as being differentially expressed. DAR analysis results in an easy-to-interpret value between 0 and 1 for each genetic feature of interest, where 0 represents identical allelic representation and 1 represents complete diversity. This metric can be used to identify features prone to false-positive calls in Differential Expression analysis, and can be leveraged with statistical methods to alleviate the impact of such artefacts on RNA-seq data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tadcompare/meta.yaml b/recipes/bioconductor-tadcompare/meta.yaml index db49b519eb40d..ee00c4fe1e444 100644 --- a/recipes/bioconductor-tadcompare/meta.yaml +++ b/recipes/bioconductor-tadcompare/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "TADCompare" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: TADCompare is an R package designed to identify and characterize differential Topologically Associated Domains (TADs) between multiple Hi-C contact matrices. It contains functions for finding differential TADs between two datasets, finding differential TADs over time and identifying consensus TADs across multiple matrices. It takes all of the main types of HiC input and returns simple, comprehensive, easy to analyze results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 'TADCompare: Identification and characterization of differential TADs' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 92966a38a0c202cfe7dbd09bb83b23b1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tadcompare", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr, pheatmap, rGREAT, SpectralTAD + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr, pheatmap, SpectralTAD, magick, qpdf requirements: host: - - 'bioconductor-hiccompare >=1.24.0,<1.25.0' + - bioconductor-hiccompare >=1.28.0,<1.29.0 - r-base - r-cluster - r-cowplot @@ -36,7 +38,7 @@ requirements: - r-reshape2 - r-tidyr run: - - 'bioconductor-hiccompare >=1.24.0,<1.25.0' + - bioconductor-hiccompare >=1.28.0,<1.29.0 - r-base - r-cluster - r-cowplot @@ -49,13 +51,16 @@ requirements: - r-rcolorbrewer - r-reshape2 - r-tidyr + +source: + md5: e29de1e58e0c613f54bf3766dc171b12 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'TADCompare: Identification and characterization of differential TADs' - description: 'TADCompare is an R package designed to identify and characterize differential Topologically Associated Domains (TADs) between multiple Hi-C contact matrices. It contains functions for finding differential TADs between two datasets, finding differential TADs over time and identifying consensus TADs across multiple matrices. It takes all of the main types of HiC input and returns simple, comprehensive, easy to analyze results.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tanggle/meta.yaml b/recipes/bioconductor-tanggle/meta.yaml index f1e803a007b94..32a0b2b802e8e 100644 --- a/recipes/bioconductor-tanggle/meta.yaml +++ b/recipes/bioconductor-tanggle/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "tanggle" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d23bc70f7c920e00bb14a3d05e8cfdea +about: + description: Offers functions for plotting split (or implicit) networks (unrooted, undirected) and explicit networks (rooted, directed) with reticulations extending. 'ggtree' and using functions from 'ape' and 'phangorn'. It extends the 'ggtree' package [@Yu2017] to allow the visualization of phylogenetic networks using the 'ggplot2' syntax. It offers an alternative to the plot functions already available in 'ape' Paradis and Schliep (2019) and 'phangorn' Schliep (2011) . + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Visualization of Phylogenetic Networks build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tanggle", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: tinytest, BiocStyle, ggimage, knitr, rmarkdown requirements: host: - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'r-ape >=5.0' + - bioconductor-ggtree >=3.14.0,<3.15.0 + - r-ape >=5.0 - r-base - - 'r-ggplot2 >=2.2.0' - - 'r-phangorn >=2.5' + - r-ggplot2 >=2.2.0 + - r-phangorn >=2.5 run: - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'r-ape >=5.0' + - bioconductor-ggtree >=3.14.0,<3.15.0 + - r-ape >=5.0 - r-base - - 'r-ggplot2 >=2.2.0' - - 'r-phangorn >=2.5' + - r-ggplot2 >=2.2.0 + - r-phangorn >=2.5 +source: + md5: 9e7144ca413bc859d0ff745b16baabf1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Visualization of Phylogenetic Networks' - description: 'Offers functions for plotting split (or implicit) networks (unrooted, undirected) and explicit networks (rooted, directed) with reticulations extending. ''ggtree'' and using functions from ''ape'' and ''phangorn''. It extends the ''ggtree'' package [@Yu2017] to allow the visualization of phylogenetic networks using the ''ggplot2'' syntax. It offers an alternative to the plot functions already available in ''ape'' Paradis and Schliep (2019) and ''phangorn'' Schliep (2011) .' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tapseq/meta.yaml b/recipes/bioconductor-tapseq/meta.yaml index 39c94bc15447d..59f6761f234ea 100644 --- a/recipes/bioconductor-tapseq/meta.yaml +++ b/recipes/bioconductor-tapseq/meta.yaml @@ -1,62 +1,67 @@ -{% set version = "1.14.1" %} +{% set version = "1.18.0" %} {% set name = "TAPseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using Primer3. Potential off-targets can be estimated with BLAST. Requires working installations of Primer3 and BLASTn. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Targeted scRNA-seq primer design for TAP-seq -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 423853e9c2015594d616f9315d5c217d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tapseq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer, BiocStyle # SystemRequirements: Primer3 (>= 2.5.0), BLAST+ (>=2.6.0) requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-tidyr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-dplyr - r-tidyr + +source: + md5: 5e66107f5a03eecda7bfddb3a6a750b8 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Targeted scRNA-seq primer design for TAP-seq' - description: 'Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using Primer3. Potential off-targets can be estimated with BLAST. Requires working installations of Primer3 and BLASTn.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-target/meta.yaml b/recipes/bioconductor-target/meta.yaml index 9a6b3f33d033d..df896aab4b6f2 100644 --- a/recipes/bioconductor-target/meta.yaml +++ b/recipes/bioconductor-target/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "target" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Implement the BETA algorithm for infering direct target genes from DNA-binding and perturbation expression data Wang et al. (2013) . Extend the algorithm to predict the combined function of two DNA-binding elements from comprable binding and expression data.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Predict Combined Function of Transcription Factors -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 96ca9fa7bed738941cd930b5e7491bc2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-target", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 2.1.0), knitr, rmarkdown, shinytest, shinyBS, covr requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-matrixstats - r-shiny run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-matrixstats - r-shiny + +source: + md5: 35ca55252ec0cc3a5da05590a8ccb559 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Predict Combined Function of Transcription Factors' - description: 'Implement the BETA algorithm for infering direct target genes from DNA-binding and perturbation expression data Wang et al. (2013) . Extend the algorithm to predict the combined function of two DNA-binding elements from comprable binding and expression data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-targetdecoy/meta.yaml b/recipes/bioconductor-targetdecoy/meta.yaml index a48d89bad2795..703635ca85af6 100644 --- a/recipes/bioconductor-targetdecoy/meta.yaml +++ b/recipes/bioconductor-targetdecoy/meta.yaml @@ -1,48 +1,53 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "TargetDecoy" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A first step in the data analysis of Mass Spectrometry (MS) based proteomics data is to identify peptides and proteins. With this respect the huge number of experimental mass spectra typically have to be assigned to theoretical peptides derived from a sequence database. Search engines are used for this purpose. These tools compare each of the observed spectra to all candidate theoretical spectra derived from the sequence data base and calculate a score for each comparison. The observed spectrum is then assigned to the theoretical peptide with the best score, which is also referred to as the peptide to spectrum match (PSM). It is of course crucial for the downstream analysis to evaluate the quality of these matches. Therefore False Discovery Rate (FDR) control is used to return a reliable list PSMs. The FDR, however, requires a good characterisation of the score distribution of PSMs that are matched to the wrong peptide (bad target hits). In proteomics, the target decoy approach (TDA) is typically used for this purpose. The TDA method matches the spectra to a database of real (targets) and nonsense peptides (decoys). A popular approach to generate these decoys is to reverse the target database. Hence, all the PSMs that match to a decoy are known to be bad hits and the distribution of their scores are used to estimate the distribution of the bad scoring target PSMs. A crucial assumption of the TDA is that the decoy PSM hits have similar properties as bad target hits so that the decoy PSM scores are a good simulation of the target PSM scores. Users, however, typically do not evaluate these assumptions. To this end we developed TargetDecoy to generate diagnostic plots to evaluate the quality of the target decoy method. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Diagnostic Plots to Evaluate the Target Decoy Approach -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ff49065b40e049f06bbe1ad9c74200fc build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-targetdecoy", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, msdata, sessioninfo, rmarkdown, gridExtra, testthat (>= 3.0.0), covr requirements: host: - - 'bioconductor-mzid >=1.40.0,<1.41.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' + - bioconductor-mzid >=1.44.0,<1.45.0 + - bioconductor-mzr >=2.40.0,<2.41.0 - r-base - r-ggplot2 - r-ggpubr - r-miniui - r-shiny run: - - 'bioconductor-mzid >=1.40.0,<1.41.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' + - bioconductor-mzid >=1.44.0,<1.45.0 + - bioconductor-mzr >=2.40.0,<2.41.0 - r-base - r-ggplot2 - r-ggpubr - r-miniui - r-shiny + +source: + md5: 7d744a8c777e75469e6a56a03a09e55e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Diagnostic Plots to Evaluate the Target Decoy Approach' - description: 'A first step in the data analysis of Mass Spectrometry (MS) based proteomics data is to identify peptides and proteins. With this respect the huge number of experimental mass spectra typically have to be assigned to theoretical peptides derived from a sequence database. Search engines are used for this purpose. These tools compare each of the observed spectra to all candidate theoretical spectra derived from the sequence data base and calculate a score for each comparison. The observed spectrum is then assigned to the theoretical peptide with the best score, which is also referred to as the peptide to spectrum match (PSM). It is of course crucial for the downstream analysis to evaluate the quality of these matches. Therefore False Discovery Rate (FDR) control is used to return a reliable list PSMs. The FDR, however, requires a good characterisation of the score distribution of PSMs that are matched to the wrong peptide (bad target hits). In proteomics, the target decoy approach (TDA) is typically used for this purpose. The TDA method matches the spectra to a database of real (targets) and nonsense peptides (decoys). A popular approach to generate these decoys is to reverse the target database. Hence, all the PSMs that match to a decoy are known to be bad hits and the distribution of their scores are used to estimate the distribution of the bad scoring target PSMs. A crucial assumption of the TDA is that the decoy PSM hits have similar properties as bad target hits so that the decoy PSM scores are a good simulation of the target PSM scores. Users, however, typically do not evaluate these assumptions. To this end we developed TargetDecoy to generate diagnostic plots to evaluate the quality of the target decoy method.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml b/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml index 1a5256aad3781..a7e544fffb6f4 100644 --- a/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml +++ b/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml @@ -1,45 +1,51 @@ {% set version = "0.6.1" %} {% set name = "targetscan.Hs.eg.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: TargetScan miRNA target predictions for human assembled using data from the TargetScan website. TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA. Also identified are sites with mismatches in the seed region that are compensated by conserved 3' pairing. In mammals, predictions are ranked based on the predicted efficacy of targeting as calculated using the context scores of the sites. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: TargetScan miRNA target predictions for human -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d10569315400f6c1b95ad2688632b6de build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-targetscan.hs.eg.db", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-targetscan.hs.eg.db + path: recipes/bioconductor-targetscan.hs.eg.db + version: 0.6.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: d10569315400f6c1b95ad2688632b6de + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'TargetScan miRNA target predictions for human' - description: 'TargetScan miRNA target predictions for human assembled using data from the TargetScan website. TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA. Also identified are sites with mismatches in the seed region that are compensated by conserved 3'' pairing. In mammals, predictions are ranked based on the predicted efficacy of targeting as calculated using the context scores of the sites.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-targetscan.hs.eg.db - path: recipes/bioconductor-targetscan.hs.eg.db - version: 0.6.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-targetscan.mm.eg.db/meta.yaml b/recipes/bioconductor-targetscan.mm.eg.db/meta.yaml index 0a4db556725a7..05709d36f52e1 100644 --- a/recipes/bioconductor-targetscan.mm.eg.db/meta.yaml +++ b/recipes/bioconductor-targetscan.mm.eg.db/meta.yaml @@ -1,40 +1,40 @@ {% set version = "0.6.1" %} {% set name = "targetscan.Mm.eg.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1830815c9d1383739f1ff152da0508c5 +about: + description: TargetScan miRNA target predictions for mouse assembled using data from the TargetScan website. TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA. Also identified are sites with mismatches in the seed region that are compensated by conserved 3' pairing. In mammals, predictions are ranked based on the predicted efficacy of targeting as calculated using the context scores of the sites. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: TargetScan miRNA target predictions for mouse build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-targetscan.mm.eg.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1830815c9d1383739f1ff152da0508c5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'TargetScan miRNA target predictions for mouse' - description: 'TargetScan miRNA target predictions for mouse assembled using data from the TargetScan website. TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA. Also identified are sites with mismatches in the seed region that are compensated by conserved 3'' pairing. In mammals, predictions are ranked based on the predicted efficacy of targeting as calculated using the context scores of the sites.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-targetscore/meta.yaml b/recipes/bioconductor-targetscore/meta.yaml index b57d457d83c63..16260185a454d 100644 --- a/recipes/bioconductor-targetscore/meta.yaml +++ b/recipes/bioconductor-targetscore/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "TargetScore" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. Variaitonal Bayesian Gaussian mixture model (VB-GMM) is applied to log fold-changes and sequence scores to obtain the posteriors of latent variable being the miRNA targets. The final targetScore is computed as the sigmoid-transformed fold-change weighted by the averaged posteriors of target components over all of the features. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 92d3b6ca138c6c3081262a758ec63766 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-targetscore", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:targetscore + - doi:10.1093/bioinformatics/btt599 + parent_recipe: + name: bioconductor-targetscore + path: recipes/bioconductor-targetscore + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: TargetScoreData, gplots, Biobase, GEOquery requirements: host: @@ -29,21 +40,16 @@ requirements: - r-base - r-matrix - r-pracma + +source: + md5: 9bbc21c6a5d206ba977b0c4cdd9a7bfe + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information' - description: 'Infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. Variaitonal Bayesian Gaussian mixture model (VB-GMM) is applied to log fold-changes and sequence scores to obtain the posteriors of latent variable being the miRNA targets. The final targetScore is computed as the sigmoid-transformed fold-change weighted by the averaged posteriors of target components over all of the features.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:targetscore - - doi:10.1093/bioinformatics/btt599 - parent_recipe: - name: bioconductor-targetscore - path: recipes/bioconductor-targetscore - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-targetscoredata/meta.yaml b/recipes/bioconductor-targetscoredata/meta.yaml index 2da4addce3f26..09e831758eb7d 100644 --- a/recipes/bioconductor-targetscoredata/meta.yaml +++ b/recipes/bioconductor-targetscoredata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "TargetScoreData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61084f230f2c3dedb27988867f07f50f +about: + description: Precompiled and processed miRNA-overexpression fold-changes from 84 Gene Expression Omnibus (GEO) series corresponding to 6 platforms, 77 human cells or tissues, and 113 distinct miRNAs. Accompanied with the data, we also included in this package the sequence feature scores from TargetScanHuman 6.1 including the context+ score and the probabilities of conserved targeting for each miRNA-mRNA interaction. Thus, the user can use these static sequence-based scores together with user-supplied tissue/cell-specific fold-change due to miRNA overexpression to predict miRNA targets using the package TargetScore (download separately) + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: TargetScoreData build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-targetscoredata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: TargetScore, gplots requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3fac4abe234ab4439fd08e5a8d8c7035 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: TargetScoreData - description: 'Precompiled and processed miRNA-overexpression fold-changes from 84 Gene Expression Omnibus (GEO) series corresponding to 6 platforms, 77 human cells or tissues, and 113 distinct miRNAs. Accompanied with the data, we also included in this package the sequence feature scores from TargetScanHuman 6.1 including the context+ score and the probabilities of conserved targeting for each miRNA-mRNA interaction. Thus, the user can use these static sequence-based scores together with user-supplied tissue/cell-specific fold-change due to miRNA overexpression to predict miRNA targets using the package TargetScore (download separately)' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-targetscoredata/post-link.sh b/recipes/bioconductor-targetscoredata/post-link.sh index 80e2477b8de59..3d7a3f0eeff36 100644 --- a/recipes/bioconductor-targetscoredata/post-link.sh +++ b/recipes/bioconductor-targetscoredata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "targetscoredata-1.38.0" +installBiocDataPackage.sh "targetscoredata-1.42.0" diff --git a/recipes/bioconductor-targetsearch/meta.yaml b/recipes/bioconductor-targetsearch/meta.yaml index c554006c9e67c..068f87ba7cc4f 100644 --- a/recipes/bioconductor-targetsearch/meta.yaml +++ b/recipes/bioconductor-targetsearch/meta.yaml @@ -1,25 +1,27 @@ -{% set version = "2.4.1" %} +{% set version = "2.8.0" %} {% set name = "TargetSearch" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 652009cfa3df492780c9ea45715df0b9 +about: + description: This packages provides a flexible, fast and accurate method for targeted pre-processing of GC-MS data. The user provides a (often very large) set of GC chromatograms and a metabolite library of targets. The package will automatically search those targets in the chromatograms resulting in a data matrix that can be used for further data analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A package for the analysis of GC-MS metabolite profiling data build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-targetsearch", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: TargetSearchData, BiocStyle, knitr, tinytest requirements: + build: + - {{ compiler('c') }} + - make host: - r-assertthat - r-base @@ -30,16 +32,14 @@ requirements: - r-assertthat - r-base - r-ncdf4 - build: - - {{ compiler('c') }} - - make +source: + md5: d0d868cbde6b3ca682569e3541ccc4aa + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'A package for the analysis of GC-MS metabolite profiling data' - description: 'This packages provides a flexible, fast and accurate method for targeted pre-processing of GC-MS data. The user provides a (often very large) set of GC chromatograms and a metabolite library of targets. The package will automatically search those targets in the chromatograms resulting in a data matrix that can be used for further data analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-targetsearchdata/meta.yaml b/recipes/bioconductor-targetsearchdata/meta.yaml index df32deec7a9b3..18bc08cff8b2f 100644 --- a/recipes/bioconductor-targetsearchdata/meta.yaml +++ b/recipes/bioconductor-targetsearchdata/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "TargetSearchData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 96bbec70706d8adcf4ee321261620d79 +about: + description: Example files of GC-MS data for the TargetSearch Package. The package contains raw NetCDF files from a E.coli salt stress experiment, extracted peak lists, and sample metadata required for a GC-MS analysis. The raw data has been restricted for demonstration purposes. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Example GC-MS data for TargetSearch Package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-targetsearchdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ed882cf4fe96e35cb9be14e429a9acfc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Example GC-MS data for TargetSearch Package' - description: 'Example files of GC-MS data for the TargetSearch Package. The package contains raw NetCDF files from a E.coli salt stress experiment, extracted peak lists, and sample metadata required for a GC-MS analysis. The raw data has been restricted for demonstration purposes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-targetsearchdata/post-link.sh b/recipes/bioconductor-targetsearchdata/post-link.sh index 1f74c111549e7..4308f46d686eb 100644 --- a/recipes/bioconductor-targetsearchdata/post-link.sh +++ b/recipes/bioconductor-targetsearchdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "targetsearchdata-1.40.0" +installBiocDataPackage.sh "targetsearchdata-1.44.0" diff --git a/recipes/bioconductor-tartare/meta.yaml b/recipes/bioconductor-tartare/meta.yaml index 880886341b0d0..3ad340ce6a063 100644 --- a/recipes/bioconductor-tartare/meta.yaml +++ b/recipes/bioconductor-tartare/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "tartare" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 869743e16f05bc962de518ca925750d8 +about: + description: Provides raw files recorded on different Liquid Chromatography Mass Spectrometry (LC-MS) instruments. All included MS instruments are manufactured by Thermo Fisher Scientific and belong to the Orbitrap Tribrid or Q Exactive Orbitrap family of instruments. Despite their common origin and shared hardware components, e.g., Orbitrap mass analyser, the above instruments tend to write data in different "dialects" in a shared binary file format (.raw). The intention behind tartare is to provide complex but slim real-world files that can be used to make code robust with respect to this diversity. In other words, it is intended for enhanced unit testing. The package is considered to be used with the rawrr package and the Spectra MsBackends. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Raw ground spectra recorded on Thermo Fisher Scientific mass spectrometers build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tartare", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat, tools requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6eeeb4d2495f54d9ea03ec88a99d6124 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Raw ground spectra recorded on Thermo Fisher Scientific mass spectrometers' - description: 'Provides raw files recorded on different Liquid Chromatography Mass Spectrometry (LC-MS) instruments. All included MS instruments are manufactured by Thermo Fisher Scientific and belong to the Orbitrap Tribrid or Q Exactive Orbitrap family of instruments. Despite their common origin and shared hardware components, e.g., Orbitrap mass analyser, the above instruments tend to write data in different "dialects" in a shared binary file format (.raw). The intention behind tartare is to provide complex but slim real-world files that can be used to make code robust with respect to this diversity. In other words, it is intended for enhanced unit testing. The package is considered to be used with the rawrr package and the Spectra MsBackends.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tartare/post-link.sh b/recipes/bioconductor-tartare/post-link.sh index 0017d5f89c426..a4aab98252a1f 100644 --- a/recipes/bioconductor-tartare/post-link.sh +++ b/recipes/bioconductor-tartare/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tartare-1.16.0" +installBiocDataPackage.sh "tartare-1.20.0" diff --git a/recipes/bioconductor-tbx20bamsubset/meta.yaml b/recipes/bioconductor-tbx20bamsubset/meta.yaml index 18a9421aaee7e..5c78562ce977b 100644 --- a/recipes/bioconductor-tbx20bamsubset/meta.yaml +++ b/recipes/bioconductor-tbx20bamsubset/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "TBX20BamSubset" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c158901ec6203e85569c600efb335ccf +about: + description: Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. A subset of the RNA-Seq data. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Subset of BAM files from the "TBX20" experiment build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tbx20bamsubset", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-xtable run: - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-xtable - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c4621f88eceaa2b24655558964790f51 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Subset of BAM files from the "TBX20" experiment' - description: 'Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. A subset of the RNA-Seq data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tbx20bamsubset/post-link.sh b/recipes/bioconductor-tbx20bamsubset/post-link.sh index 7c52406af39b8..426cb3b5a4214 100644 --- a/recipes/bioconductor-tbx20bamsubset/post-link.sh +++ b/recipes/bioconductor-tbx20bamsubset/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tbx20bamsubset-1.38.0" +installBiocDataPackage.sh "tbx20bamsubset-1.42.0" diff --git a/recipes/bioconductor-tcc/meta.yaml b/recipes/bioconductor-tcc/meta.yaml index a070ac06036b2..1162055ac9db4 100644 --- a/recipes/bioconductor-tcc/meta.yaml +++ b/recipes/bioconductor-tcc/meta.yaml @@ -1,45 +1,43 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "TCC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e36a17d628a68654296227603e0678da +about: + description: This package provides a series of functions for performing differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in depended packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'TCC: Differential expression analysis for tag count data with robust normalization strategies' build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tcc", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-bayseq >=2.36.0,<2.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-roc >=1.78.0,<1.79.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-roc >=1.82.0,<1.83.0 - r-base run: - - 'bioconductor-bayseq >=2.36.0,<2.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-roc >=1.78.0,<1.79.0' + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-roc >=1.82.0,<1.83.0 - r-base +source: + md5: dd5ee19edca147016b7bb36a0172e65c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'TCC: Differential expression analysis for tag count data with robust normalization strategies' - description: 'This package provides a series of functions for performing differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in depended packages.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tcgabiolinks/meta.yaml b/recipes/bioconductor-tcgabiolinks/meta.yaml index a5d528634ec4a..ce4357e6b3b1a 100644 --- a/recipes/bioconductor-tcgabiolinks/meta.yaml +++ b/recipes/bioconductor-tcgabiolinks/meta.yaml @@ -1,91 +1,99 @@ -{% set version = "2.30.0" %} +{% set version = "2.34.0" %} {% set name = "TCGAbiolinks" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91536d6234ebd992dac8102393c363d0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tcgabiolinks", max_pin="x.x") }}' - noarch: generic -# Suggests: jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, dnet, Biobase, affy, testthat, sesame, AnnotationHub, ExperimentHub, pathview, clusterProfiler, Seurat, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph, supraHex, limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3), scales, grid + +extra: + identifiers: + - biotools:tcgabiolinks + - doi:10.1093/nar/gkv1507 + parent_recipe: + name: bioconductor-tcgabiolinks + path: recipes/bioconductor-tcgabiolinks + version: 2.8.4 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, Biobase, affy, testthat, sesame, AnnotationHub, ExperimentHub, pathview, clusterProfiler, Seurat, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph, supraHex, limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3), scales, grid, DT requirements: + host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tcgabiolinksgui.data >=1.22.0,<1.23.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tcgabiolinksgui.data >=1.26.0,<1.27.0 - r-base - r-data.table - - 'r-downloader >=0.4' + - r-downloader >=0.4 - r-dplyr - r-ggplot2 - - 'r-httr >=1.2.1' - - 'r-jsonlite >=1.0.0' + - r-httr >=1.2.1 + - r-jsonlite >=1.0.0 - r-knitr - r-plyr - r-purrr - r-r.utils - r-readr - - 'r-rvest >=0.3.0' - - 'r-stringr >=1.0.0' + - r-rvest >=0.3.0 + - r-stringr >=1.0.0 - r-tibble - r-tidyr - - 'r-xml >=3.98.0' + - r-xml >=3.98.0 - r-xml2 + run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tcgabiolinksgui.data >=1.22.0,<1.23.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tcgabiolinksgui.data >=1.26.0,<1.27.0 - r-base - r-data.table - - 'r-downloader >=0.4' + - r-downloader >=0.4 - r-dplyr - r-ggplot2 - - 'r-httr >=1.2.1' - - 'r-jsonlite >=1.0.0' + - r-httr >=1.2.1 + - r-jsonlite >=1.0.0 - r-knitr - r-plyr - r-purrr - r-r.utils - r-readr - - 'r-rvest >=0.3.0' - - 'r-stringr >=1.0.0' + - r-rvest >=0.3.0 + - r-stringr >=1.0.0 - r-tibble - r-tidyr - - 'r-xml >=3.98.0' + - r-xml >=3.98.0 - r-xml2 + +source: + md5: 76e1f792f8f2f2479f4d521ce22c34a5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data' - description: 'The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:tcgabiolinks - - doi:10.1093/nar/gkv1507 - parent_recipe: - name: bioconductor-tcgabiolinks - path: recipes/bioconductor-tcgabiolinks - version: 2.8.4 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tcgabiolinksgui.data/meta.yaml b/recipes/bioconductor-tcgabiolinksgui.data/meta.yaml index a599989612e1c..42d9812caadad 100644 --- a/recipes/bioconductor-tcgabiolinksgui.data/meta.yaml +++ b/recipes/bioconductor-tcgabiolinksgui.data/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "TCGAbiolinksGUI.data" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bd2042c0064583d666364a52ce3be17e +about: + description: Supporting data for the TCGAbiolinksGUI package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Data for the TCGAbiolinksGUI package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tcgabiolinksgui.data", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, readr, DT requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 280de6c6b0ebc043613aa8fd5e79d2b5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Data for the TCGAbiolinksGUI package' - description: 'Supporting data for the TCGAbiolinksGUI package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tcgabiolinksgui.data/post-link.sh b/recipes/bioconductor-tcgabiolinksgui.data/post-link.sh index 3ce61f3013f98..000ac822030ac 100644 --- a/recipes/bioconductor-tcgabiolinksgui.data/post-link.sh +++ b/recipes/bioconductor-tcgabiolinksgui.data/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tcgabiolinksgui.data-1.22.0" +installBiocDataPackage.sh "tcgabiolinksgui.data-1.26.0" diff --git a/recipes/bioconductor-tcgacrcmirna/meta.yaml b/recipes/bioconductor-tcgacrcmirna/meta.yaml index d5aa585eae22e..51f295927e1c3 100644 --- a/recipes/bioconductor-tcgacrcmirna/meta.yaml +++ b/recipes/bioconductor-tcgacrcmirna/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "TCGAcrcmiRNA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 451d09b5ec341d7e92211a1d42c35947 +about: + description: colorectal cancer miRNA profile provided by TCGA + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: TCGA CRC 450 miRNA dataset build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tcgacrcmirna", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 987fb490cde2a7c1387a03ce1a38efe8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'TCGA CRC 450 miRNA dataset' - description: 'colorectal cancer miRNA profile provided by TCGA' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tcgacrcmirna/post-link.sh b/recipes/bioconductor-tcgacrcmirna/post-link.sh index 8c432e9a0c322..e2dfca04d2997 100644 --- a/recipes/bioconductor-tcgacrcmirna/post-link.sh +++ b/recipes/bioconductor-tcgacrcmirna/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tcgacrcmirna-1.22.0" +installBiocDataPackage.sh "tcgacrcmirna-1.26.0" diff --git a/recipes/bioconductor-tcgacrcmrna/meta.yaml b/recipes/bioconductor-tcgacrcmrna/meta.yaml index e4c24ff6fed90..ade298a9a9399 100644 --- a/recipes/bioconductor-tcgacrcmrna/meta.yaml +++ b/recipes/bioconductor-tcgacrcmrna/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "TCGAcrcmRNA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bb9300e6ad6e4e5435a31487fdc22ed6 +about: + description: colorectal cancer mRNA profile provided by TCGA + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: TCGA CRC 450 mRNA dataset build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tcgacrcmrna", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: da22bfc5ef7e6cf3b67e3bd4b9ccdb03 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'TCGA CRC 450 mRNA dataset' - description: 'colorectal cancer mRNA profile provided by TCGA' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tcgacrcmrna/post-link.sh b/recipes/bioconductor-tcgacrcmrna/post-link.sh index 53b5ac1ad6709..523bd78d05eb7 100644 --- a/recipes/bioconductor-tcgacrcmrna/post-link.sh +++ b/recipes/bioconductor-tcgacrcmrna/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tcgacrcmrna-1.22.0" +installBiocDataPackage.sh "tcgacrcmrna-1.26.0" diff --git a/recipes/bioconductor-tcgamethylation450k/meta.yaml b/recipes/bioconductor-tcgamethylation450k/meta.yaml index 521516a508d02..e765814ef9bda 100644 --- a/recipes/bioconductor-tcgamethylation450k/meta.yaml +++ b/recipes/bioconductor-tcgamethylation450k/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "TCGAMethylation450k" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e913aa3b85d5cd1d0b27a346daf8c9ee +about: + description: The Cancer Genome Atlas (TCGA) is applying genomics technologies to over 20 different types of cancer. This package contains a small set of 450k array data in idat format. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: The Cancer Genome Atlas Illumina 450k methylation example data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tcgamethylation450k", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 14bf9c5d9f61ad9f29b0e6fdf1a76506 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'The Cancer Genome Atlas Illumina 450k methylation example data' - description: 'The Cancer Genome Atlas (TCGA) is applying genomics technologies to over 20 different types of cancer. This package contains a small set of 450k array data in idat format.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tcgamethylation450k/post-link.sh b/recipes/bioconductor-tcgamethylation450k/post-link.sh index 7b0a1b521a206..ce29367bb9107 100644 --- a/recipes/bioconductor-tcgamethylation450k/post-link.sh +++ b/recipes/bioconductor-tcgamethylation450k/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tcgamethylation450k-1.38.0" +installBiocDataPackage.sh "tcgamethylation450k-1.42.0" diff --git a/recipes/bioconductor-tcgautils/meta.yaml b/recipes/bioconductor-tcgautils/meta.yaml index 472458d809d70..d5aabffa80c98 100644 --- a/recipes/bioconductor-tcgautils/meta.yaml +++ b/recipes/bioconductor-tcgautils/meta.yaml @@ -1,66 +1,71 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "TCGAutils" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable. Exported functions include those that import data from flat files into Bioconductor objects, convert row annotations, and identifier translation via the GDC API. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: TCGA utility functions for data management -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 33d917253a210382a92537383bb4ee4f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tcgautils", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationHub, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, httr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, mirbase.db, org.Hs.eg.db, RColorBrewer, readr, rmarkdown, RTCGAToolbox (>= 2.17.4), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicdatacommons >=1.26.0,<1.27.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicdatacommons >=1.30.0,<1.31.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-raggedexperiment >=1.30.0,<1.31.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-rvest - r-stringr - r-xml2 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicdatacommons >=1.26.0,<1.27.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicdatacommons >=1.30.0,<1.31.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-raggedexperiment >=1.30.0,<1.31.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-rvest - r-stringr - r-xml2 + +source: + md5: ca884d60032295841410c8b3d5afd8d1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'TCGA utility functions for data management' - description: 'A suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable. Exported functions include those that import data from flat files into Bioconductor objects, convert row annotations, and identifier translation via the GDC API.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tcgaworkflowdata/meta.yaml b/recipes/bioconductor-tcgaworkflowdata/meta.yaml index 8987d3058c1b2..a3fc03f905c0e 100644 --- a/recipes/bioconductor-tcgaworkflowdata/meta.yaml +++ b/recipes/bioconductor-tcgaworkflowdata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "TCGAWorkflowData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cbba498f1922aeedadf96a1911a81751 +about: + description: 'This experimental data package contains 11 data sets necessary to follow the "TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages".' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Data for TCGA Workflow build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tcgaworkflowdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, pander, testthat, BiocStyle requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5d7066d5244562eb269a1c8bef037a30 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Data for TCGA Workflow' - description: 'This experimental data package contains 11 data sets necessary to follow the "TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages".' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tcgaworkflowdata/post-link.sh b/recipes/bioconductor-tcgaworkflowdata/post-link.sh index 1f5635c08afec..41ea18b2957eb 100644 --- a/recipes/bioconductor-tcgaworkflowdata/post-link.sh +++ b/recipes/bioconductor-tcgaworkflowdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tcgaworkflowdata-1.26.0" +installBiocDataPackage.sh "tcgaworkflowdata-1.30.0" diff --git a/recipes/bioconductor-tcseq/meta.yaml b/recipes/bioconductor-tcseq/meta.yaml index 59a57399ee0d5..c6aae4f2b9d32 100644 --- a/recipes/bioconductor-tcseq/meta.yaml +++ b/recipes/bioconductor-tcseq/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "TCseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Quantitative and differential analysis of epigenomic and transcriptomic time course sequencing data, clustering analysis and visualization of the temporal patterns of time course data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Time course sequencing data analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f5b63a6d1b40c82f8ddc86cc2abdb89b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tcseq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-e1071 @@ -36,26 +38,29 @@ requirements: - r-locfit - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cluster - r-e1071 - r-ggplot2 - r-locfit - r-reshape2 + +source: + md5: 1d475ecc4e2b6536dd0c7ac0740a4aa2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Time course sequencing data analysis' - description: 'Quantitative and differential analysis of epigenomic and transcriptomic time course sequencing data, clustering analysis and visualization of the temporal patterns of time course data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tdbasedufe/meta.yaml b/recipes/bioconductor-tdbasedufe/meta.yaml index 52baeee1720db..6d5d6eb30d0c4 100644 --- a/recipes/bioconductor-tdbasedufe/meta.yaml +++ b/recipes/bioconductor-tdbasedufe/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "TDbasedUFE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. It can perform unsupervised feature extraction. It uses tensor decomposition. It is applicable to gene expression, DNA methylation, and histone modification etc. It can perform multiomics analysis. It is also potentially applicable to single cell omics data sets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Tensor Decomposition Based Unsupervised Feature Extraction -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5557e1128d1d6ffab09670bf90b8947c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tdbasedufe", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-mofadata >=1.18.0,<1.19.0' - - 'bioconductor-tximport >=1.30.0,<1.31.0' - - 'bioconductor-tximportdata >=1.30.0,<1.31.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-mofadata >=1.22.0,<1.23.0 + - bioconductor-tximport >=1.34.0,<1.35.0 + - bioconductor-tximportdata >=1.34.0,<1.35.0 - r-base - r-readr - r-rtensor - r-shiny run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-mofadata >=1.18.0,<1.19.0' - - 'bioconductor-tximport >=1.30.0,<1.31.0' - - 'bioconductor-tximportdata >=1.30.0,<1.31.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-mofadata >=1.22.0,<1.23.0 + - bioconductor-tximport >=1.34.0,<1.35.0 + - bioconductor-tximportdata >=1.34.0,<1.35.0 - r-base - r-readr - r-rtensor - r-shiny + +source: + md5: c4aa77cf0d230a62932048868d3317c3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Tensor Decomposition Based Unsupervised Feature Extraction' - description: 'This is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. It can perform unsupervised feature extraction. It uses tensor decomposition. It is applicable to gene expression, DNA methylation, and histone modification etc. It can perform multiomics analysis. It is also potentially applicable to single cell omics data sets.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tdbasedufeadv/meta.yaml b/recipes/bioconductor-tdbasedufeadv/meta.yaml index 3ec6ded747c03..7b0d3a2498990 100644 --- a/recipes/bioconductor-tdbasedufeadv/meta.yaml +++ b/recipes/bioconductor-tdbasedufeadv/meta.yaml @@ -1,59 +1,64 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "TDbasedUFEadv" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This is an advanced version of TDbasedUFE, which is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. In contrast to TDbasedUFE which can perform simple the feature selection and the multiomics analyses, this package can perform more complicated and advanced features, but they are not so popularly required. Only users who require more specific features can make use of its functionality. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Advanced package of tensor decomposition based unsupervised feature extraction -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6f873403b62f756c6b8424cfeb2409c9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tdbasedufeadv", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat (>= 3.0.0), RTCGA.rnaseq, RTCGA.clinical, BiocStyle, MOFAdata requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtcga >=1.32.0,<1.33.0' - - 'bioconductor-stringdb >=2.14.0,<2.15.0' - - 'bioconductor-tdbasedufe >=1.2.0,<1.3.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtcga >=1.36.0,<1.37.0 + - bioconductor-stringdb >=2.18.0,<2.19.0 + - bioconductor-tdbasedufe >=1.6.0,<1.7.0 - r-base - r-enrichr - r-hash - r-rtensor - r-shiny run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-dose >=3.28.0,<3.29.0' - - 'bioconductor-enrichplot >=1.22.0,<1.23.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rtcga >=1.32.0,<1.33.0' - - 'bioconductor-stringdb >=2.14.0,<2.15.0' - - 'bioconductor-tdbasedufe >=1.2.0,<1.3.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-dose >=4.0.0,<4.1.0 + - bioconductor-enrichplot >=1.26.0,<1.27.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rtcga >=1.36.0,<1.37.0 + - bioconductor-stringdb >=2.18.0,<2.19.0 + - bioconductor-tdbasedufe >=1.6.0,<1.7.0 - r-base - r-enrichr - r-hash - r-rtensor - r-shiny + +source: + md5: c05ba77ef7e6572f3039df8041a12d5e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Advanced package of tensor decomposition based unsupervised feature extraction' - description: 'This is an advanced version of TDbasedUFE, which is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. In contrast to TDbasedUFE which can perform simple the feature selection and the multiomics analyses, this package can perform more complicated and advanced features, but they are not so popularly required. Only users who require more specific features can make use of its functionality.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tekrabber/meta.yaml b/recipes/bioconductor-tekrabber/meta.yaml index 14842af5d7cd6..34b7d1895c556 100644 --- a/recipes/bioconductor-tekrabber/meta.yaml +++ b/recipes/bioconductor-tekrabber/meta.yaml @@ -1,56 +1,69 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "TEKRABber" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: TEKRABber is made to provide a user-friendly pipeline for comparing orthologs and transposable elements (TEs) between two species. It considers the orthology confidence between two species from BioMart to normalize expression counts and detect differentially expressed orthologs/TEs. Then it provides one to one correlation analysis for desired orthologs and TEs. There is also an app function to have a first insight on the result. Users can prepare orthologs/TEs RNA-seq expression data by their own preference to run TEKRABber following the data structure mentioned in the vignettes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>=3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: An R package estimates the correlations of orthologs and transposable elements between two species -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 145026d8a5e02ec94f8a2a1f5405851e build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tekrabber", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, bslib, ggplot2, ggpubr, plotly, rmarkdown, shiny, knitr, testthat (>= 3.0.0) requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-apeglm >=1.24.0,<1.25.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-scbn >=1.20.0,<1.21.0' + - bioconductor-apeglm >=1.28.0,<1.29.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-scbn >=1.24.0,<1.25.0 - r-base + - r-doparallel - r-dplyr + - r-foreach - r-magrittr - - 'r-rcpp >=1.0.7' + - r-rcpp >=1.0.7 - libblas - liblapack run: - - 'bioconductor-apeglm >=1.24.0,<1.25.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-scbn >=1.20.0,<1.21.0' + - bioconductor-apeglm >=1.28.0,<1.29.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-scbn >=1.24.0,<1.25.0 - r-base + - r-doparallel - r-dplyr + - r-foreach - r-magrittr - - 'r-rcpp >=1.0.7' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=1.0.7 + +source: + md5: 06eae4ec275e8f28223fa119009b3dc6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>=3)' - summary: 'An R package estimates the correlations of orthologs and transposable elements between two species' - description: 'TEKRABber is made to provide a user-friendly pipeline for comparing orthologs and transposable elements (TEs) between two species. It considers the orthology confidence between two species from BioMart to normalize expression counts and detect differentially expressed orthologs/TEs. Then it provides one to one correlation analysis for desired orthologs and TEs. There is also an app function to have a first insight on the result. Users can prepare orthologs/TEs RNA-seq expression data by their own preference to run TEKRABber following the data structure mentioned in the vignettes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tenxbraindata/meta.yaml b/recipes/bioconductor-tenxbraindata/meta.yaml index 58bd199e51f1a..52317debf721f 100644 --- a/recipes/bioconductor-tenxbraindata/meta.yaml +++ b/recipes/bioconductor-tenxbraindata/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "TENxBrainData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Single-cell RNA-seq data for 1.3 million brain cells from E18 mice, generated by 10X Genomics. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: CC BY 4.0 + summary: Data from the 10X 1.3 Million Brain Cell Study -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1fa1b93ab8d144b860c83dc5741490a0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tenxbraindata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel, data.table, rmarkdown requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: c75922e698f3cfea4aeceff12647f0c4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'CC BY 4.0' - summary: 'Data from the 10X 1.3 Million Brain Cell Study' - description: 'Single-cell RNA-seq data for 1.3 million brain cells from E18 mice, generated by 10X Genomics.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tenxbraindata/post-link.sh b/recipes/bioconductor-tenxbraindata/post-link.sh index 5358e416f4cff..37fafc3fae14a 100644 --- a/recipes/bioconductor-tenxbraindata/post-link.sh +++ b/recipes/bioconductor-tenxbraindata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tenxbraindata-1.22.0" +installBiocDataPackage.sh "tenxbraindata-1.26.0" diff --git a/recipes/bioconductor-tenxbusdata/meta.yaml b/recipes/bioconductor-tenxbusdata/meta.yaml index 6b7ec47703e37..94ff22cc986f9 100644 --- a/recipes/bioconductor-tenxbusdata/meta.yaml +++ b/recipes/bioconductor-tenxbusdata/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "TENxBUSData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 35be2bd3c806b055fc9463e8f135dd32 +about: + description: Download Barcode, UMI, and Set (BUS) format of 10x datasets from within R. This package accompanies the package BUSpaRse, which can load BUS format into R as a sparse matrix, and which has utility functions related to using the C++ command line package bustools. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: BSD_2_clause + file LICENSE + license_file: LICENSE + summary: Single cell dataset from 10x in BUS format build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tenxbusdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d06d50a0967cda65a36e27a32d2e6c6e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'BSD_2_clause + file LICENSE' - summary: 'Single cell dataset from 10x in BUS format' - description: 'Download Barcode, UMI, and Set (BUS) format of 10x datasets from within R. This package accompanies the package BUSpaRse, which can load BUS format into R as a sparse matrix, and which has utility functions related to using the C++ command line package bustools.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tenxbusdata/post-link.sh b/recipes/bioconductor-tenxbusdata/post-link.sh index dc2ed75ffb6a5..610a9b9536df1 100644 --- a/recipes/bioconductor-tenxbusdata/post-link.sh +++ b/recipes/bioconductor-tenxbusdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tenxbusdata-1.16.0" +installBiocDataPackage.sh "tenxbusdata-1.20.0" diff --git a/recipes/bioconductor-tenxio/meta.yaml b/recipes/bioconductor-tenxio/meta.yaml index d48c1bc5f0f43..b30280e1cac5b 100644 --- a/recipes/bioconductor-tenxio/meta.yaml +++ b/recipes/bioconductor-tenxio/meta.yaml @@ -1,62 +1,71 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "TENxIO" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides a structured S4 approach to importing data files from the 10X pipelines. It mainly supports Single Cell Multiome ATAC + Gene Expression data among other data types. The main Bioconductor data representations used are SingleCellExperiment and RaggedExperiment. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Import methods for 10X Genomics files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 98a845f55877d89b82b9a153fe54a41f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tenxio", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, DropletTestFiles, ExperimentHub, HDF5Array, knitr, RaggedExperiment, rhdf5, rmarkdown, Rsamtools, tinytest + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, DropletTestFiles, ExperimentHub, knitr, RaggedExperiment (>= 1.29.5), rmarkdown, Rsamtools, tinytest requirements: host: - - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-r.utils - r-rcurl - r-readr run: - - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocio >=1.12.0,<1.13.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-r.utils - r-rcurl - r-readr + +source: + md5: 0854922fae1e35bb49259bf1139ac34f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Import methods for 10X Genomics files' - description: 'Provides a structured S4 approach to importing data files from the 10X pipelines. It mainly supports Single Cell Multiome ATAC + Gene Expression data among other data types. The main Bioconductor data representations used are SingleCellExperiment and RaggedExperiment.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tenxpbmcdata/meta.yaml b/recipes/bioconductor-tenxpbmcdata/meta.yaml index 7b29159a6f5b5..3488a6aad6316 100644 --- a/recipes/bioconductor-tenxpbmcdata/meta.yaml +++ b/recipes/bioconductor-tenxpbmcdata/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "TENxPBMCData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Single-cell RNA-seq data for on PBMC cells, generated by 10X Genomics. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: CC BY 4.0 + summary: PBMC data from 10X Genomics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3e6c961a01998667f37de542858dbc09 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tenxpbmcdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, BiocStyle, snow, BiocFileCache, BiocParallel requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 15f610613ce383ac323033ee5a8f42c5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'CC BY 4.0' - summary: 'PBMC data from 10X Genomics' - description: 'Single-cell RNA-seq data for on PBMC cells, generated by 10X Genomics.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tenxpbmcdata/post-link.sh b/recipes/bioconductor-tenxpbmcdata/post-link.sh index eb9fbb18d674f..0d2e8f0fd7f79 100644 --- a/recipes/bioconductor-tenxpbmcdata/post-link.sh +++ b/recipes/bioconductor-tenxpbmcdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tenxpbmcdata-1.20.0" +installBiocDataPackage.sh "tenxpbmcdata-1.24.0" diff --git a/recipes/bioconductor-tenxplore/meta.yaml b/recipes/bioconductor-tenxplore/meta.yaml index f2c5019b0eebf..13da080262383 100644 --- a/recipes/bioconductor-tenxplore/meta.yaml +++ b/recipes/bioconductor-tenxplore/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "tenXplore" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Perform ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 13e1778f8b644661a521bb832af6e7d6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tenxplore", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: org.Hs.eg.db, testthat, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-ontoproc >=1.24.0,<1.25.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-restfulse >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-ontoproc >=2.0.0,<2.1.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrixstats - r-shiny run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-ontoproc >=1.24.0,<1.25.0' - - 'bioconductor-org.mm.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-restfulse >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-ontoproc >=2.0.0,<2.1.0 + - bioconductor-org.mm.eg.db >=3.20.0,<3.21.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrixstats - r-shiny + +source: + md5: 683f80423aaf423f134f0d20050ce418 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics' - description: 'Perform ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tenxvisiumdata/meta.yaml b/recipes/bioconductor-tenxvisiumdata/meta.yaml index 6c8051114d57a..b518f2567e1d9 100644 --- a/recipes/bioconductor-tenxvisiumdata/meta.yaml +++ b/recipes/bioconductor-tenxvisiumdata/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "TENxVisiumData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f578add429847efff027a61b1749b9b4 +about: + description: 'Collection of Visium spatial gene expression datasets by 10X Genomics, formatted into objects of class SpatialExperiment. Data cover various organisms and tissues, and include: single- and multi-section experiments, as well as single sections subjected to both whole transcriptome and targeted panel analysis. Datasets may be used for testing of and as examples in packages, for tutorials and workflow demonstrations, or similar purposes.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Visium spatial gene expression data by 10X Genomics build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tenxvisiumdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 51c4de649c20eb710f34c5e6803f98ed + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Visium spatial gene expression data by 10X Genomics' - description: 'Collection of Visium spatial gene expression datasets by 10X Genomics, formatted into objects of class SpatialExperiment. Data cover various organisms and tissues, and include: single- and multi-section experiments, as well as single sections subjected to both whole transcriptome and targeted panel analysis. Datasets may be used for testing of and as examples in packages, for tutorials and workflow demonstrations, or similar purposes.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tenxvisiumdata/post-link.sh b/recipes/bioconductor-tenxvisiumdata/post-link.sh index 1921065bf2398..e5142991e490b 100644 --- a/recipes/bioconductor-tenxvisiumdata/post-link.sh +++ b/recipes/bioconductor-tenxvisiumdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tenxvisiumdata-1.10.0" +installBiocDataPackage.sh "tenxvisiumdata-1.14.0" diff --git a/recipes/bioconductor-teqc/meta.yaml b/recipes/bioconductor-teqc/meta.yaml index 062c2e16d092a..aa2229d642166 100644 --- a/recipes/bioconductor-teqc/meta.yaml +++ b/recipes/bioconductor-teqc/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "4.24.0" %} +{% set version = "4.28.0" %} {% set name = "TEQC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Target capture experiments combine hybridization-based (in solution or on microarrays) capture and enrichment of genomic regions of interest (e.g. the exome) with high throughput sequencing of the captured DNA fragments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Quality control for target capture experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 02976837ccda44f13a0a43b9de17ea81 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-teqc", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:teqc + - doi:10.1093/bioinformatics/btr122 + parent_recipe: + name: bioconductor-teqc + path: recipes/bioconductor-teqc + version: 4.2.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-hwriter run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-hwriter + +source: + md5: 60434b2b1bef39f9c4d9392c9e24ab4a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Quality control for target capture experiments' - description: 'Target capture experiments combine hybridization-based (in solution or on microarrays) capture and enrichment of genomic regions of interest (e.g. the exome) with high throughput sequencing of the captured DNA fragments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:teqc - - doi:10.1093/bioinformatics/btr122 - parent_recipe: - name: bioconductor-teqc - path: recipes/bioconductor-teqc - version: 4.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ternarynet/meta.yaml b/recipes/bioconductor-ternarynet/meta.yaml index bd39c481f7479..fc4c4d5cef157 100644 --- a/recipes/bioconductor-ternarynet/meta.yaml +++ b/recipes/bioconductor-ternarynet/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "1.46.0" %} +{% set version = "1.50.0" %} {% set name = "ternarynet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Gene-regulatory network (GRN) modeling seeks to infer dependencies between genes and thereby provide insight into the regulatory relationships that exist within a cell. This package provides a computational Bayesian approach to GRN estimation from perturbation experiments using a ternary network model, in which gene expression is discretized into one of 3 states: up, unchanged, or down). The ternarynet package includes a parallel implementation of the replica exchange Monte Carlo algorithm for fitting network models, using MPI.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Ternary Network Estimation -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1ee0ac867354eedf8cf756d94be52589 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ternarynet", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:ternarynet + parent_recipe: + name: bioconductor-ternarynet + path: recipes/bioconductor-ternarynet + version: 1.24.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-igraph - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 - r-base - r-igraph - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 7078cae2daf1530cfdfaebb85b7aada7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Ternary Network Estimation' - description: 'Gene-regulatory network (GRN) modeling seeks to infer dependencies between genes and thereby provide insight into the regulatory relationships that exist within a cell. This package provides a computational Bayesian approach to GRN estimation from perturbation experiments using a ternary network model, in which gene expression is discretized into one of 3 states: up, unchanged, or down). The ternarynet package includes a parallel implementation of the replica exchange Monte Carlo algorithm for fitting network models, using MPI.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:ternarynet - parent_recipe: - name: bioconductor-ternarynet - path: recipes/bioconductor-ternarynet - version: 1.24.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-terratcgadata/meta.yaml b/recipes/bioconductor-terratcgadata/meta.yaml index d5498e1fc2f25..5c353f41f4dba 100644 --- a/recipes/bioconductor-terratcgadata/meta.yaml +++ b/recipes/bioconductor-terratcgadata/meta.yaml @@ -1,56 +1,63 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "terraTCGAdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Leverage the existing open access TCGA data on Terra with well-established Bioconductor infrastructure. Make use of the Terra data model without learning its complexities. With a few functions, you can copy / download and generate a MultiAssayExperiment from the TCGA example workspaces provided by Terra. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: OpenAccess TCGA Data on Terra as MultiAssayExperiment -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b5803a78627bbe874b8cd8ae0a147979 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-terratcgadata", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, BiocStyle, withr, testthat (>= 3.0.0) + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: AnVILBase, knitr, rmarkdown, BiocStyle, withr, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-anvil >=1.14.0,<1.15.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-tcgautils >=1.22.0,<1.23.0' + - bioconductor-anvil >=1.18.0,<1.19.0 + - bioconductor-anvilgcp >=1.0.0,<1.1.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-raggedexperiment >=1.30.0,<1.31.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-tcgautils >=1.26.0,<1.27.0 - r-base - r-dplyr - r-readr - r-tidyr run: - - 'bioconductor-anvil >=1.14.0,<1.15.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-raggedexperiment >=1.26.0,<1.27.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-tcgautils >=1.22.0,<1.23.0' + - bioconductor-anvil >=1.18.0,<1.19.0 + - bioconductor-anvilgcp >=1.0.0,<1.1.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-raggedexperiment >=1.30.0,<1.31.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-tcgautils >=1.26.0,<1.27.0 - r-base - r-dplyr - r-readr - r-tidyr + +source: + md5: ae543b0934e758b48fb1924aca28a519 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'OpenAccess TCGA Data on Terra as MultiAssayExperiment' - description: 'Leverage the existing open access TCGA data on Terra with well-established Bioconductor infrastructure. Make use of the Terra data model without learning its complexities. With a few functions, you can copy / download and generate a MultiAssayExperiment from the TCGA example workspaces provided by Terra.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-test1cdf/meta.yaml b/recipes/bioconductor-test1cdf/meta.yaml index 9cf00a9e907da..67e636fb733ae 100644 --- a/recipes/bioconductor-test1cdf/meta.yaml +++ b/recipes/bioconductor-test1cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "test1cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8c94708b49ccc7bbf127485155970b9b +about: + description: A package containing an environment representing the Test1.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: test1cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-test1cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8c94708b49ccc7bbf127485155970b9b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: test1cdf - description: 'A package containing an environment representing the Test1.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-test2cdf/meta.yaml b/recipes/bioconductor-test2cdf/meta.yaml index 74ae9fa6eb04c..094de6d84f61a 100644 --- a/recipes/bioconductor-test2cdf/meta.yaml +++ b/recipes/bioconductor-test2cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "test2cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0d1c20d6450dfc83d62214be9dc46b5f +about: + description: A package containing an environment representing the Test2.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: test2cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-test2cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0d1c20d6450dfc83d62214be9dc46b5f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: test2cdf - description: 'A package containing an environment representing the Test2.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-test3cdf/meta.yaml b/recipes/bioconductor-test3cdf/meta.yaml index 4f62a9f138b91..aac648b7f8b7d 100644 --- a/recipes/bioconductor-test3cdf/meta.yaml +++ b/recipes/bioconductor-test3cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "test3cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9904e7fa6599f68400a9b77d0caa159a +about: + description: A package containing an environment representing the Test3.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: test3cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-test3cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9904e7fa6599f68400a9b77d0caa159a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: test3cdf - description: 'A package containing an environment representing the Test3.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-test3probe/meta.yaml b/recipes/bioconductor-test3probe/meta.yaml index 4cf7c7451737f..539badf8c61dc 100644 --- a/recipes/bioconductor-test3probe/meta.yaml +++ b/recipes/bioconductor-test3probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "test3probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ffcbfee4e5c486fd03b2b9b64820340c +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Test3\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type test3 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-test3probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ffcbfee4e5c486fd03b2b9b64820340c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type test3' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Test3\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tfarm/meta.yaml b/recipes/bioconductor-tfarm/meta.yaml index f68855b990209..53260244b1a6a 100644 --- a/recipes/bioconductor-tfarm/meta.yaml +++ b/recipes/bioconductor-tfarm/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "TFARM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: It searches for relevant associations of transcription factors with a transcription factor target, in specific genomic regions. It also allows to evaluate the Importance Index distribution of transcription factors (and combinations of transcription factors) in association rules. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Transcription Factors Association Rules Miner -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bf2876d47da6baa42642dc5492ef7a94 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tfarm", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, plyr requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-arules - r-base - r-fields - r-gplots - r-stringr run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-arules - r-base - r-fields - r-gplots - r-stringr + +source: + md5: 6dced9e6abf5b4abd26d88cb913ef4b7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Transcription Factors Association Rules Miner' - description: 'It searches for relevant associations of transcription factors with a transcription factor target, in specific genomic regions. It also allows to evaluate the Importance Index distribution of transcription factors (and combinations of transcription factors) in association rules.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tfbstools/meta.yaml b/recipes/bioconductor-tfbstools/meta.yaml index 7d4d315b0df18..0157317537d23 100644 --- a/recipes/bioconductor-tfbstools/meta.yaml +++ b/recipes/bioconductor-tfbstools/meta.yaml @@ -1,90 +1,101 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "TFBSTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Software Package for Transcription Factor Binding Site (TFBS) Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f2395c8153c4820e3cebb53a9eda94d6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tfbstools", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:tfbstools + parent_recipe: + name: bioconductor-tfbstools + path: recipes/bioconductor-tfbstools + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle(>= 1.7.7), JASPAR2014(>= 1.4.0), knitr(>= 1.11), testthat, JASPAR2016(>= 1.0.0), JASPAR2018(>= 1.0.0), rmarkdown requirements: + + build: + - {{ compiler('c') }} + - make + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-cner >=1.38.0,<1.39.0' - - 'bioconductor-dirichletmultinomial >=1.44.0,<1.45.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-seqlogo >=1.68.0,<1.69.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-cner >=1.42.0,<1.43.0 + - bioconductor-dirichletmultinomial >=1.48.0,<1.49.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqlogo >=1.72.0,<1.73.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - - 'r-catools >=1.17.1' - - 'r-dbi >=0.6' - - 'r-gtools >=3.5.0' - - 'r-rsqlite >=1.0.0' - - 'r-tfmpvalue >=0.0.5' - - 'r-xml >=3.98-1.3' + - r-catools >=1.17.1 + - r-dbi >=0.6 + - r-gtools >=3.5.0 + - r-rsqlite >=1.0.0 + - r-tfmpvalue >=0.0.5 + - r-xml >=3.98-1.3 - libblas - liblapack + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-cner >=1.38.0,<1.39.0' - - 'bioconductor-dirichletmultinomial >=1.44.0,<1.45.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-seqlogo >=1.68.0,<1.69.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-cner >=1.42.0,<1.43.0 + - bioconductor-dirichletmultinomial >=1.48.0,<1.49.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqlogo >=1.72.0,<1.73.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - - 'r-catools >=1.17.1' - - 'r-dbi >=0.6' - - 'r-gtools >=3.5.0' - - 'r-rsqlite >=1.0.0' - - 'r-tfmpvalue >=0.0.5' - - 'r-xml >=3.98-1.3' - build: - - {{ compiler('c') }} - - make + - r-catools >=1.17.1 + - r-dbi >=0.6 + - r-gtools >=3.5.0 + - r-rsqlite >=1.0.0 + - r-tfmpvalue >=0.0.5 + - r-xml >=3.98-1.3 + +source: + md5: 6a911dc2eaa79f199041039488ed7271 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2.0-only - summary: 'Software Package for Transcription Factor Binding Site (TFBS) Analysis' - description: 'TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:tfbstools - parent_recipe: - name: bioconductor-tfbstools - path: recipes/bioconductor-tfbstools - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tfea.chip/meta.yaml b/recipes/bioconductor-tfea.chip/meta.yaml index de5695cd80ca7..9f6b118d7be3d 100644 --- a/recipes/bioconductor-tfea.chip/meta.yaml +++ b/recipes/bioconductor-tfea.chip/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "TFEA.ChIP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Package to analize transcription factor enrichment in a gene set using data from ChIP-Seq experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Analyze Transcription Factor Enrichment -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 86f7ae5bb16ceaf9fbdc01d0cc606c42 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tfea.chip", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2, DESeq2, BiocGenerics, ggrepel, rcompanion, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit requirements: host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - r-dplyr - r-r.utils run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - r-dplyr - r-r.utils + +source: + md5: e6bf364a3389c915a5027ea027ca8c39 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Analyze Transcription Factor Enrichment' - description: 'Package to analize transcription factor enrichment in a gene set using data from ChIP-Seq experiments.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tfhaz/meta.yaml b/recipes/bioconductor-tfhaz/meta.yaml index 62729c28422f7..db491a9ededbc 100644 --- a/recipes/bioconductor-tfhaz/meta.yaml +++ b/recipes/bioconductor-tfhaz/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "TFHAZ" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4befbb77bb7eb52b220a2472010cab25 +about: + description: It finds trascription factor (TF) high accumulation DNA zones, i.e., regions along the genome where there is a high presence of different transcription factors. Starting from a dataset containing the genomic positions of TF binding regions, for each base of the selected chromosome the accumulation of TFs is computed. Three different types of accumulation (TF, region and base accumulation) are available, together with the possibility of considering, in the single base accumulation computing, the TFs present not only in that single base, but also in its neighborhood, within a window of a given width. Two different methods for the search of TF high accumulation DNA zones, called "binding regions" and "overlaps", are available. In addition, some functions are provided in order to analyze, visualize and compare results obtained with different input parameters. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Transcription Factor High Accumulation Zones build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tfhaz", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-orfik >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-orfik >=1.26.0,<1.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-orfik >=1.22.0,<1.23.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-orfik >=1.26.0,<1.27.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base +source: + md5: 29a6535d42b79a71321cff6eafe5bf4c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Transcription Factor High Accumulation Zones' - description: 'It finds trascription factor (TF) high accumulation DNA zones, i.e., regions along the genome where there is a high presence of different transcription factors. Starting from a dataset containing the genomic positions of TF binding regions, for each base of the selected chromosome the accumulation of TFs is computed. Three different types of accumulation (TF, region and base accumulation) are available, together with the possibility of considering, in the single base accumulation computing, the TFs present not only in that single base, but also in its neighborhood, within a window of a given width. Two different methods for the search of TF high accumulation DNA zones, called "binding regions" and "overlaps", are available. In addition, some functions are provided in order to analyze, visualize and compare results obtained with different input parameters.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tfutils/meta.yaml b/recipes/bioconductor-tfutils/meta.yaml index e81f9833f5aea..28bb1d6b16a6d 100644 --- a/recipes/bioconductor-tfutils/meta.yaml +++ b/recipes/bioconductor-tfutils/meta.yaml @@ -1,32 +1,33 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "TFutils" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package helps users to work with TF metadata from various sources. Significant catalogs of TFs and classifications thereof are made available. Tools for working with motif scans are also provided. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: TFutils -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a2e83bbaafa0e47d7dbbd17385bd15fb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tfutils", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, data.table, testthat, AnnotationFilter, Biobase, GenomicFeatures, GenomicRanges, Gviz, IRanges, S4Vectors, EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db, GenomicFiles, GenomeInfoDb, SummarizedExperiment, UpSetR, ggplot2, png, gwascat, MotifDb, motifStack, RColorBrewer, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-dplyr - r-dt @@ -37,11 +38,11 @@ requirements: - r-rjson - r-shiny run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 - r-base - r-dplyr - r-dt @@ -51,12 +52,16 @@ requirements: - r-readxl - r-rjson - r-shiny + +source: + md5: f8019e25c3516fae7eaa121adfb3d215 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: TFutils - description: 'This package helps users to work with TF metadata from various sources. Significant catalogs of TFs and classifications thereof are made available. Tools for working with motif scans are also provided.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tidybulk/meta.yaml b/recipes/bioconductor-tidybulk/meta.yaml index af300d3308e74..c75d4849ea452 100644 --- a/recipes/bioconductor-tidybulk/meta.yaml +++ b/recipes/bioconductor-tidybulk/meta.yaml @@ -1,34 +1,37 @@ -{% set version = "1.14.2" %} +{% set version = "1.18.0" %} {% set name = "tidybulk" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This is a collection of utility functions that allow to perform exploration of and calculations to RNA sequencing data, in a modular, pipe-friendly and tidy fashion. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Brings transcriptomics to the tidyverse -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e1a43f9392049059ec6b67930277df16 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tidybulk", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, testthat, vctrs, AnnotationDbi, BiocManager, Rsubread, e1071, edgeR, limma, org.Hs.eg.db, org.Mm.eg.db, sva, GGally, knitr, qpdf, covr, Seurat, KernSmooth, Rtsne, ggplot2, widyr, clusterProfiler, msigdbr, DESeq2, broom, survival, boot, betareg, tidyHeatmap, pasilla, ggrepel, devtools, functional, survminer, tidySummarizedExperiment, markdown, uwot, matrixStats, igraph, EGSEA, IRanges, here, glmmSeq, pbapply, pbmcapply, lme4, glmmTMB, MASS + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, testthat, vctrs, AnnotationDbi, BiocManager, Rsubread, e1071, edgeR, limma, org.Hs.eg.db, org.Mm.eg.db, sva, GGally, knitr, qpdf, covr, Seurat, KernSmooth, Rtsne, ggplot2, widyr, clusterProfiler, msigdbr, DESeq2, broom, survival, boot, betareg, tidyHeatmap, pasilla, ggrepel, devtools, functional, survminer, tidySummarizedExperiment, markdown, uwot, matrixStats, igraph, EGSEA, IRanges, here, glmmSeq, pbapply, pbmcapply, lme4, glmmTMB, MASS, pkgconfig requirements: + host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-crayon - - 'r-dplyr >=1.1.0' + - r-dplyr >=1.1.0 - r-lifecycle - r-magrittr - r-matrix @@ -41,15 +44,16 @@ requirements: - r-tibble - r-tidyr - r-tidyselect - - 'r-ttservice >=0.3.6' + - r-ttservice >=0.3.6 + run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-crayon - - 'r-dplyr >=1.1.0' + - r-dplyr >=1.1.0 - r-lifecycle - r-magrittr - r-matrix @@ -62,14 +66,17 @@ requirements: - r-tibble - r-tidyr - r-tidyselect - - 'r-ttservice >=0.3.6' + - r-ttservice >=0.3.6 + +source: + md5: 541de0cbf7fbb2350db6e6980aea09dc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Brings transcriptomics to the tidyverse' - description: 'This is a collection of utility functions that allow to perform exploration of and calculations to RNA sequencing data, in a modular, pipe-friendly and tidy fashion.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tidycoverage/build.sh b/recipes/bioconductor-tidycoverage/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tidycoverage/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tidycoverage/meta.yaml b/recipes/bioconductor-tidycoverage/meta.yaml new file mode 100644 index 0000000000000..734da2cdfbb67 --- /dev/null +++ b/recipes/bioconductor-tidycoverage/meta.yaml @@ -0,0 +1,78 @@ +{% set version = "1.2.0" %} +{% set name = "tidyCoverage" %} +{% set bioc = "3.20" %} + +about: + description: '`tidyCoverage` framework enables tidy manipulation of collections of genomic tracks and features using `tidySummarizedExperiment` methods. It facilitates the extraction, aggregation and visualization of genomic coverage over individual or thousands of genomic loci, relying on `CoverageExperiment` and `AggregatedCoverage` classes. This accelerates the integration of genomic track data in genomic analysis workflows.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Extract and aggregate genomic coverage over features of interest + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tidycoverage", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: tidySummarizedExperiment, plyranges, TxDb.Hsapiens.UCSC.hg19.knownGene, AnnotationHub, GenomicFeatures, BiocStyle, hues, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-cli + - r-dplyr + - r-fansi + - r-ggplot2 + - r-pillar + - r-purrr + - r-rlang + - r-scales + - r-tidyr + - r-vctrs + run: + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-cli + - r-dplyr + - r-fansi + - r-ggplot2 + - r-pillar + - r-purrr + - r-rlang + - r-scales + - r-tidyr + - r-vctrs + +source: + md5: 96101741eac2f891b86dd0ac830711d1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-tidyflowcore/build.sh b/recipes/bioconductor-tidyflowcore/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tidyflowcore/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tidyflowcore/meta.yaml b/recipes/bioconductor-tidyflowcore/meta.yaml new file mode 100644 index 0000000000000..1e3ecf11bc9f7 --- /dev/null +++ b/recipes/bioconductor-tidyflowcore/meta.yaml @@ -0,0 +1,60 @@ +{% set version = "1.0.0" %} +{% set name = "tidyFlowCore" %} +{% set bioc = "3.20" %} + +about: + description: tidyFlowCore bridges the gap between flow cytometry analysis using the flowCore Bioconductor package and the tidy data principles advocated by the tidyverse. It provides a suite of dplyr-, ggplot2-, and tidyr-like verbs specifically designed for working with flowFrame and flowSet objects as if they were tibbles; however, your data remain flowCore data structures under this layer of abstraction. tidyFlowCore enables intuitive and streamlined analysis workflows that can leverage both the Bioconductor and tidyverse ecosystems for cytometry data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: 'tidyFlowCore: Bringing flowCore to the tidyverse' + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tidyflowcore", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, HDCytoData, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - r-base + - r-dplyr + - r-ggplot2 + - r-purrr + - r-rlang + - r-stringr + - r-tibble + - r-tidyr + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-flowcore >=2.18.0,<2.19.0 + - r-base + - r-dplyr + - r-ggplot2 + - r-purrr + - r-rlang + - r-stringr + - r-tibble + - r-tidyr + +source: + md5: 0baac8dd29cd2db4d57ec8c32a3ef9f9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-tidyomics/build.sh b/recipes/bioconductor-tidyomics/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tidyomics/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tidyomics/meta.yaml b/recipes/bioconductor-tidyomics/meta.yaml new file mode 100644 index 0000000000000..b9579a460b30c --- /dev/null +++ b/recipes/bioconductor-tidyomics/meta.yaml @@ -0,0 +1,62 @@ +{% set version = "1.2.0" %} +{% set name = "tidyomics" %} +{% set bioc = "3.20" %} + +about: + description: The tidyomics ecosystem is a set of packages for ’omic data analysis that work together in harmony; they share common data representations and API design, consistent with the tidyverse ecosystem. The tidyomics package is designed to make it easy to install and load core packages from the tidyomics ecosystem with a single command. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Easily install and load the tidyomics ecosystem + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tidyomics", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: tidyr, dplyr, tibble, ggplot2, mockr (>= 0.2.0), knitr (>= 1.41), rmarkdown (>= 2.20), testthat (>= 3.1.6) +requirements: + host: + - bioconductor-nullranges >=1.12.0,<1.13.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-tidybulk >=1.18.0,<1.19.0 + - bioconductor-tidysinglecellexperiment >=1.16.0,<1.17.0 + - bioconductor-tidysummarizedexperiment >=1.16.0,<1.17.0 + - r-base + - r-cli + - r-purrr + - r-rlang + - r-stringr + - r-tidyseurat + run: + - bioconductor-nullranges >=1.12.0,<1.13.0 + - bioconductor-plyranges >=1.26.0,<1.27.0 + - bioconductor-tidybulk >=1.18.0,<1.19.0 + - bioconductor-tidysinglecellexperiment >=1.16.0,<1.17.0 + - bioconductor-tidysummarizedexperiment >=1.16.0,<1.17.0 + - r-base + - r-cli + - r-purrr + - r-rlang + - r-stringr + - r-tidyseurat + +source: + md5: 59f073a0b34a0ba4046cf86cb98cb70f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-tidysbml/build.sh b/recipes/bioconductor-tidysbml/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tidysbml/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tidysbml/meta.yaml b/recipes/bioconductor-tidysbml/meta.yaml new file mode 100644 index 0000000000000..eb19f6d84c21c --- /dev/null +++ b/recipes/bioconductor-tidysbml/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.0.0" %} +{% set name = "tidysbml" %} +{% set bioc = "3.20" %} + +about: + description: Starting from one SBML file, it extracts information from each listOfCompartments, listOfSpecies and listOfReactions element by saving them into data frames. Each table provides one row for each entity (i.e. either compartment, species, reaction or speciesReference) and one set of columns for the attributes, one column for the content of the 'notes' subelement and one set of columns for the content of the 'annotation' subelement. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: CC BY 4.0 + summary: Extract SBML's data into dataframes +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tidysbml", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: rmarkdown, knitr, BiocStyle, biomaRt, RCy3, testthat (>= 3.0.0) +requirements: + host: + - r-base + - r-xml2 + run: + - r-base + - r-xml2 +source: + md5: 772b32a8717e0a1f51e75bfe73cd600b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-tidysinglecellexperiment/meta.yaml b/recipes/bioconductor-tidysinglecellexperiment/meta.yaml index e37d659138088..453117b99bf0e 100644 --- a/recipes/bioconductor-tidysinglecellexperiment/meta.yaml +++ b/recipes/bioconductor-tidysinglecellexperiment/meta.yaml @@ -1,30 +1,33 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "tidySingleCellExperiment" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: '''tidySingleCellExperiment'' is an adapter that abstracts the ''SingleCellExperiment'' container in the form of a ''tibble''. This allows *tidy* data manipulation, nesting, and plotting. For example, a ''tidySingleCellExperiment'' is directly compatible with functions from ''tidyverse'' packages `dplyr` and `tidyr`, as well as plotting with `ggplot2` and `plotly`. In addition, the package provides various utility functions specific to single-cell omics data analysis (e.g., aggregation of cell-level data to pseudobulks).' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Brings SingleCellExperiment to the Tidyverse -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4f0e61cb23c56df988e1a731a452eb2d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tidysinglecellexperiment", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, testthat, knitr, rmarkdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, uwot, celldex, dittoSeq + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, testthat, knitr, markdown, rmarkdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, uwot, celldex, dittoSeq, plotly requirements: + host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cli - r-dplyr @@ -36,19 +39,19 @@ requirements: - r-matrix - r-pillar - r-pkgconfig - - r-plotly - r-purrr - r-rlang - r-stringr - r-tibble - r-tidyr - r-tidyselect - - 'r-ttservice >=0.3.8' + - r-ttservice >=0.4.0 - r-vctrs + run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cli - r-dplyr @@ -60,22 +63,24 @@ requirements: - r-matrix - r-pillar - r-pkgconfig - - r-plotly - r-purrr - r-rlang - r-stringr - r-tibble - r-tidyr - r-tidyselect - - 'r-ttservice >=0.3.8' + - r-ttservice >=0.4.0 - r-vctrs + +source: + md5: d4789a8d368dbd07c161f290251c9051 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Brings SingleCellExperiment to the Tidyverse' - description: '''tidySingleCellExperiment'' is an adapter that abstracts the ''SingleCellExperiment'' container in the form of a ''tibble''. This allows *tidy* data manipulation, nesting, and plotting. For example, a ''tidySingleCellExperiment'' is directly compatible with functions from ''tidyverse'' packages `dplyr` and `tidyr`, as well as plotting with `ggplot2` and `plotly`. In addition, the package provides various utility functions specific to single-cell omics data analysis (e.g., aggregation of cell-level data to pseudobulks).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tidyspatialexperiment/build.sh b/recipes/bioconductor-tidyspatialexperiment/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tidyspatialexperiment/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tidyspatialexperiment/meta.yaml b/recipes/bioconductor-tidyspatialexperiment/meta.yaml new file mode 100644 index 0000000000000..dcddc69be8cf7 --- /dev/null +++ b/recipes/bioconductor-tidyspatialexperiment/meta.yaml @@ -0,0 +1,96 @@ +{% set version = "1.2.0" %} +{% set name = "tidySpatialExperiment" %} +{% set bioc = "3.20" %} + +about: + description: tidySpatialExperiment provides a bridge between the SpatialExperiment package and the tidyverse ecosystem. It creates an invisible layer that allows you to interact with a SpatialExperiment object as if it were a tibble; enabling the use of functions from dplyr, tidyr, ggplot2 and plotly. But, underneath, your data remains a SpatialExperiment object. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: SpatialExperiment with tidy principles + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tidyspatialexperiment", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, testthat, knitr, markdown, scater, igraph, cowplot, DropletUtils, tidySummarizedExperiment +requirements: + + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tidysinglecellexperiment >=1.16.0,<1.17.0 + - r-base + - r-cli + - r-dplyr + - r-fansi + - r-ggplot2 + - r-lifecycle + - r-magick + - r-matrix + - r-pillar + - r-pkgconfig + - r-plotly + - r-purrr + - r-rlang + - r-shiny + - r-stringr + - r-tibble + - r-tidygate >=1.0.13 + - r-tidyr + - r-tidyselect + - r-ttservice + - r-vctrs + + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tidysinglecellexperiment >=1.16.0,<1.17.0 + - r-base + - r-cli + - r-dplyr + - r-fansi + - r-ggplot2 + - r-lifecycle + - r-magick + - r-matrix + - r-pillar + - r-pkgconfig + - r-plotly + - r-purrr + - r-rlang + - r-shiny + - r-stringr + - r-tibble + - r-tidygate >=1.0.13 + - r-tidyr + - r-tidyselect + - r-ttservice + - r-vctrs + +source: + md5: b44123484c7c4f4e920b18585084098c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-tidysummarizedexperiment/meta.yaml b/recipes/bioconductor-tidysummarizedexperiment/meta.yaml index e1c10a2c75d43..5fa9973454750 100644 --- a/recipes/bioconductor-tidysummarizedexperiment/meta.yaml +++ b/recipes/bioconductor-tidysummarizedexperiment/meta.yaml @@ -1,29 +1,32 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "tidySummarizedExperiment" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The tidySummarizedExperiment package provides a set of tools for creating and manipulating tidy data representations of SummarizedExperiment objects. SummarizedExperiment is a widely used data structure in bioinformatics for storing high-throughput genomic data, such as gene expression or DNA sequencing data. The tidySummarizedExperiment package introduces a tidy framework for working with SummarizedExperiment objects. It allows users to convert their data into a tidy format, where each observation is a row and each variable is a column. This tidy representation simplifies data manipulation, integration with other tidyverse packages, and enables seamless integration with the broader ecosystem of tidy tools for data analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Brings SummarizedExperiment to the Tidyverse -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a7962f90a1d5e582e22a5c6e1f5e46da build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tidysummarizedexperiment", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle, testthat, knitr, markdown + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, testthat, knitr, markdown, rmarkdown, plotly requirements: + host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cli - r-dplyr @@ -34,18 +37,18 @@ requirements: - r-magrittr - r-pillar - r-pkgconfig - - r-plotly - r-purrr - r-rlang - r-stringr - - 'r-tibble >=3.0.4' + - r-tibble >=3.0.4 - r-tidyr - r-tidyselect - - r-ttservice + - r-ttservice >=0.4.0 - r-vctrs + run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cli - r-dplyr @@ -56,22 +59,24 @@ requirements: - r-magrittr - r-pillar - r-pkgconfig - - r-plotly - r-purrr - r-rlang - r-stringr - - 'r-tibble >=3.0.4' + - r-tibble >=3.0.4 - r-tidyr - r-tidyselect - - r-ttservice + - r-ttservice >=0.4.0 - r-vctrs + +source: + md5: 5c41c06e535eaf3c387dccd53e64e008 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Brings SummarizedExperiment to the Tidyverse' - description: 'The tidySummarizedExperiment package provides a set of tools for creating and manipulating tidy data representations of SummarizedExperiment objects. SummarizedExperiment is a widely used data structure in bioinformatics for storing high-throughput genomic data, such as gene expression or DNA sequencing data. The tidySummarizedExperiment package introduces a tidy framework for working with SummarizedExperiment objects. It allows users to convert their data into a tidy format, where each observation is a row and each variable is a column. This tidy representation simplifies data manipulation, integration with other tidyverse packages, and enables seamless integration with the broader ecosystem of tidy tools for data analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tidytof/build.sh b/recipes/bioconductor-tidytof/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tidytof/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tidytof/meta.yaml b/recipes/bioconductor-tidytof/meta.yaml new file mode 100644 index 0000000000000..c2865eedeefe4 --- /dev/null +++ b/recipes/bioconductor-tidytof/meta.yaml @@ -0,0 +1,90 @@ +{% set version = "1.0.0" %} +{% set name = "tidytof" %} +{% set bioc = "3.20" %} + +about: + description: This package implements an interactive, scientific analysis pipeline for high-dimensional cytometry data built using tidy data principles. It is specifically designed to play well with both the tidyverse and Bioconductor software ecosystems, with functionality for reading/writing data files, data cleaning, preprocessing, clustering, visualization, modeling, and other quality-of-life functions. tidytof implements a "grammar" of high-dimensional cytometry data analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Analyze High-dimensional Cytometry Data Using Tidy Data Principles + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tidytof", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: ConsensusClusterPlus, Biobase, broom, covr, diffcyt, emdist, FlowSOM, forcats, ggrepel, HDCytoData, knitr, markdown, philentropy, rmarkdown, Rtsne, statmod, SummarizedExperiment, testthat (>= 3.0.0), lmerTest, lme4, ggridges, spelling, scattermore, preprocessCore, SingleCellExperiment, Seurat, SeuratObject, embed, rsample, BiocGenerics +requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + + host: + - bioconductor-flowcore >=2.18.0,<2.19.0 + - r-base + - r-doparallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-ggraph + - r-glmnet + - r-purrr + - r-rcpp + - r-rcpphnsw + - r-readr + - r-recipes + - r-rlang + - r-stringr + - r-survival + - r-tibble + - r-tidygraph + - r-tidyr + - r-tidyselect + - r-yardstick + - libblas + - liblapack + + run: + - bioconductor-flowcore >=2.18.0,<2.19.0 + - r-base + - r-doparallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-ggraph + - r-glmnet + - r-purrr + - r-rcpp + - r-rcpphnsw + - r-readr + - r-recipes + - r-rlang + - r-stringr + - r-survival + - r-tibble + - r-tidygraph + - r-tidyr + - r-tidyselect + - r-yardstick + +source: + md5: d305e4dcfc65ceb6cca503201099dace + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-tigre/meta.yaml b/recipes/bioconductor-tigre/meta.yaml index 3d755d26318d8..ae3ae7b147799 100644 --- a/recipes/bioconductor-tigre/meta.yaml +++ b/recipes/bioconductor-tigre/meta.yaml @@ -1,30 +1,43 @@ -{% set version = "1.56.0" %} +{% set version = "1.60.0" %} {% set name = "tigre" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The tigre package implements our methodology of Gaussian process differential equation models for analysis of gene expression time series from single input motif networks. The package can be used for inferring unobserved transcription factor (TF) protein concentrations from expression measurements of known target genes, or for ranking candidate targets of a TF. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + summary: Transcription factor Inference through Gaussian process Reconstruction of Expression -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d6bc46b9552c8c910c05c2ab705710d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tigre", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:tigre + parent_recipe: + name: bioconductor-tigre + path: recipes/bioconductor-tigre + version: 1.34.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: drosgenome1.db, puma, lumi, BiocStyle, BiocManager requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-dbi - r-gplots @@ -32,31 +45,24 @@ requirements: - libblas - liblapack run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-dbi - r-gplots - r-rsqlite - build: - - {{ compiler('c') }} - - make + +source: + md5: 6440f9f077076a9606e5470ad8456d7d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3 - summary: 'Transcription factor Inference through Gaussian process Reconstruction of Expression' - description: 'The tigre package implements our methodology of Gaussian process differential equation models for analysis of gene expression time series from single input motif networks. The package can be used for inferring unobserved transcription factor (TF) protein concentrations from expression measurements of known target genes, or for ranking candidate targets of a TF.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' -extra: - identifiers: - - biotools:tigre - parent_recipe: - name: bioconductor-tigre - path: recipes/bioconductor-tigre - version: 1.34.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tiledbarray/meta.yaml b/recipes/bioconductor-tiledbarray/meta.yaml index 64c48ae9123a5..24a3749bed242 100644 --- a/recipes/bioconductor-tiledbarray/meta.yaml +++ b/recipes/bioconductor-tiledbarray/meta.yaml @@ -1,50 +1,45 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "TileDBArray" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7bb6ef67d882031ac2ebfcb3c1873dd2 +about: + description: Implements a DelayedArray backend for reading and writing dense or sparse arrays in the TileDB format. The resulting TileDBArrays are compatible with all Bioconductor pipelines that can accept DelayedArray instances. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Using TileDB as a DelayedArray Backend build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tiledbarray", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat requirements: host: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 - r-base - - r-rcpp - r-tiledb - - libblas - - liblapack run: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 - r-base - - r-rcpp - r-tiledb - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make +source: + md5: 4dc4bd304d350bd324cc751f646244ba + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Using TileDB as a DelayedArray Backend' - description: 'Implements a DelayedArray backend for reading and writing dense or sparse arrays in the TileDB format. The resulting TileDBArrays are compatible with all Bioconductor pipelines that can accept DelayedArray instances.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tilingarray/meta.yaml b/recipes/bioconductor-tilingarray/meta.yaml index 1cc59e0adddee..899b0a16eda5b 100644 --- a/recipes/bioconductor-tilingarray/meta.yaml +++ b/recipes/bioconductor-tilingarray/meta.yaml @@ -1,29 +1,33 @@ -{% set version = "1.80.0" %} +{% set version = "1.84.0" %} {% set name = "tilingArray" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The package provides functionality that can be useful for the analysis of high-density tiling microarray data (such as from Affymetrix genechips) for measuring transcript abundance and architecture. The main functionalities of the package are: 1. the class ''segmentation'' for representing partitionings of a linear series of data; 2. the function ''segment'' for fitting piecewise constant models using a dynamic programming algorithm that is both fast and exact; 3. the function ''confint'' for calculating confidence intervals using the strucchange package; 4. the function ''plotAlongChrom'' for generating pretty plots; 5. the function ''normalizeByReference'' for probe-sequence dependent response adjustment from a (set of) reference hybridizations.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Transcript mapping with high-density oligonucleotide tiling arrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ef9c26009f7990175b320386fcfeeb5c build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tilingarray", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-base - r-pixmap - r-rcolorbrewer @@ -31,23 +35,24 @@ requirements: - libblas - liblapack run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-base - r-pixmap - r-rcolorbrewer - r-strucchange - build: - - {{ compiler('c') }} - - make + +source: + md5: cc6bb59da38ff62ab1eb6522e255bd22 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Transcript mapping with high-density oligonucleotide tiling arrays' - description: 'The package provides functionality that can be useful for the analysis of high-density tiling microarray data (such as from Affymetrix genechips) for measuring transcript abundance and architecture. The main functionalities of the package are: 1. the class ''segmentation'' for representing partitionings of a linear series of data; 2. the function ''segment'' for fitting piecewise constant models using a dynamic programming algorithm that is both fast and exact; 3. the function ''confint'' for calculating confidence intervals using the strucchange package; 4. the function ''plotAlongChrom'' for generating pretty plots; 5. the function ''normalizeByReference'' for probe-sequence dependent response adjustment from a (set of) reference hybridizations.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-timecourse/meta.yaml b/recipes/bioconductor-timecourse/meta.yaml index dac5e6130e637..da7f0a6e2472e 100644 --- a/recipes/bioconductor-timecourse/meta.yaml +++ b/recipes/bioconductor-timecourse/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "timecourse" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functions for data analysis and graphical displays for developmental microarray time course data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Statistical Analysis for Developmental Microarray Time Course Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4a760d4bcf875bb5c0069cbef4a1af32 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-timecourse", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:timecourse + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-timecourse + path: recipes/bioconductor-timecourse + version: 1.52.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-marray >=1.84.0,<1.85.0 - r-base - r-mass run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-marray >=1.84.0,<1.85.0 - r-base - r-mass + +source: + md5: e1b47aacb78e70b3d78bc8920b527635 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Statistical Analysis for Developmental Microarray Time Course Data' - description: 'Functions for data analysis and graphical displays for developmental microarray time course data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:timecourse - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-timecourse - path: recipes/bioconductor-timecourse - version: 1.52.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-timecoursedata/meta.yaml b/recipes/bioconductor-timecoursedata/meta.yaml index 96f0a9f45922b..f6cddbc306889 100644 --- a/recipes/bioconductor-timecoursedata/meta.yaml +++ b/recipes/bioconductor-timecoursedata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "timecoursedata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a5b9f962c12d69003eff9b6949d2b0af +about: + description: This data package contains timecourse gene expression data sets. The first dataset, from Shoemaker et al, consists of microarray samples from lung tissue of mice exposed to different influenzy strains from 14 timepoints. The two other datasets are leaf and root samples from sorghum crops exposed to pre- and post-flowering drought stress and a control condition, sampled across the plants lifetime. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: BSD 3-clause License + file LICENSE + license_file: LICENSE + summary: A data package for timecourse RNA-seq and microarray gene expression data sets build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-timecoursedata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: testthat (>= 1.0.0), knitr, rmarkdown, markdown, covr, BiocStyle requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 28f66d8ccee52d67473922f1e417c78d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'BSD 3-clause License + file LICENSE' - summary: 'A data package for timecourse RNA-seq and microarray gene expression data sets' - description: 'This data package contains timecourse gene expression data sets. The first dataset, from Shoemaker et al, consists of microarray samples from lung tissue of mice exposed to different influenzy strains from 14 timepoints. The two other datasets are leaf and root samples from sorghum crops exposed to pre- and post-flowering drought stress and a control condition, sampled across the plants lifetime.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-timecoursedata/post-link.sh b/recipes/bioconductor-timecoursedata/post-link.sh index 4e773c67621b2..76a030ee81e6d 100644 --- a/recipes/bioconductor-timecoursedata/post-link.sh +++ b/recipes/bioconductor-timecoursedata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "timecoursedata-1.12.0" +installBiocDataPackage.sh "timecoursedata-1.16.0" diff --git a/recipes/bioconductor-timeomics/meta.yaml b/recipes/bioconductor-timeomics/meta.yaml index 9c8c950e0f52f..d841470ad6890 100644 --- a/recipes/bioconductor-timeomics/meta.yaml +++ b/recipes/bioconductor-timeomics/meta.yaml @@ -1,29 +1,43 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "timeOmics" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'timeOmics is a generic data-driven framework to integrate multi-Omics longitudinal data measured on the same biological samples and select key temporal features with strong associations within the same sample group. The main steps of timeOmics are: 1. Plaform and time-specific normalization and filtering steps; 2. Modelling each biological into one time expression profile; 3. Clustering features with the same expression profile over time; 4. Post-hoc validation step.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Time-Course Multi-Omics data integration -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ddea6709cf6d8d977b998f458e7938fb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-timeomics", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse, igraph, gplots requirements: + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] host: - - 'bioconductor-mixomics >=6.26.0,<6.27.0' + - bioconductor-mixomics >=6.30.0,<6.31.0 - r-base + - r-checkmate - r-dplyr - r-ggplot2 - r-ggrepel @@ -35,8 +49,9 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-mixomics >=6.26.0,<6.27.0' + - bioconductor-mixomics >=6.30.0,<6.31.0 - r-base + - r-checkmate - r-dplyr - r-ggplot2 - r-ggrepel @@ -47,23 +62,16 @@ requirements: - r-stringr - r-tibble - r-tidyr - build: - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - xorg-libxfixes # [linux] + +source: + md5: 051c5b8a48e338b1dfe161fe9ced080a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Time-Course Multi-Omics data integration' - description: 'timeOmics is a generic data-driven framework to integrate multi-Omics longitudinal data measured on the same biological samples and select key temporal features with strong associations within the same sample group. The main steps of timeOmics are: 1. Plaform and time-specific normalization and filtering steps; 2. Modelling each biological into one time expression profile; 3. Clustering features with the same expression profile over time; 4. Post-hoc validation step.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-timerquant/meta.yaml b/recipes/bioconductor-timerquant/meta.yaml index 1a46726437cd3..9c4b85ca4aabc 100644 --- a/recipes/bioconductor-timerquant/meta.yaml +++ b/recipes/bioconductor-timerquant/meta.yaml @@ -1,24 +1,25 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "TimerQuant" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Supplementary Data package for tandem timer methods paper by Barry et al. (2015) including TimerQuant shiny applications. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Timer Quantification -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7033d0ae9a0731af8bafecbbfa5398c8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-timerquant", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, reshape2, knitr, shinyBS requirements: host: @@ -38,13 +39,17 @@ requirements: - r-locfit - r-shiny - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: ba7baf3dc9562fe7c00adae7f5fe1ad2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Timer Quantification' - description: 'Supplementary Data package for tandem timer methods paper by Barry et al. (2015) including TimerQuant shiny applications.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-timerquant/post-link.sh b/recipes/bioconductor-timerquant/post-link.sh index c834f2b1641a0..90e3d1418a081 100644 --- a/recipes/bioconductor-timerquant/post-link.sh +++ b/recipes/bioconductor-timerquant/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "timerquant-1.32.0" +installBiocDataPackage.sh "timerquant-1.36.0" diff --git a/recipes/bioconductor-timescape/meta.yaml b/recipes/bioconductor-timescape/meta.yaml index 2b92ef17d1383..413bbe5c27116 100644 --- a/recipes/bioconductor-timescape/meta.yaml +++ b/recipes/bioconductor-timescape/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "timescape" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'TimeScape is an automated tool for navigating temporal clonal evolution data. The key attributes of this implementation involve the enumeration of clones, their evolutionary relationships and their shifting dynamics over time. TimeScape requires two inputs: (i) the clonal phylogeny and (ii) the clonal prevalences. Optionally, TimeScape accepts a data table of targeted mutations observed in each clone and their allele prevalences over time. The output is the TimeScape plot showing clonal prevalence vertically, time horizontally, and the plot height optionally encoding tumour volume during tumour-shrinking events. At each sampling time point (denoted by a faint white line), the height of each clone accurately reflects its proportionate prevalence. These prevalences form the anchors for bezier curves that visually represent the dynamic transitions between time points.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Patient Clonal Timescapes -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1a409bde946cb8ed4c7e8e6a334158de build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-timescape", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - r-base - - 'r-dplyr >=0.4.3' - - 'r-gtools >=3.5.0' - - 'r-htmlwidgets >=0.5' - - 'r-jsonlite >=0.9.19' - - 'r-stringr >=1.0.0' + - r-dplyr >=0.4.3 + - r-gtools >=3.5.0 + - r-htmlwidgets >=0.5 + - r-jsonlite >=0.9.19 + - r-stringr >=1.0.0 run: - r-base - - 'r-dplyr >=0.4.3' - - 'r-gtools >=3.5.0' - - 'r-htmlwidgets >=0.5' - - 'r-jsonlite >=0.9.19' - - 'r-stringr >=1.0.0' + - r-dplyr >=0.4.3 + - r-gtools >=3.5.0 + - r-htmlwidgets >=0.5 + - r-jsonlite >=0.9.19 + - r-stringr >=1.0.0 + +source: + md5: 1272e4ab325b69c4a073637bca02efad + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Patient Clonal Timescapes' - description: 'TimeScape is an automated tool for navigating temporal clonal evolution data. The key attributes of this implementation involve the enumeration of clones, their evolutionary relationships and their shifting dynamics over time. TimeScape requires two inputs: (i) the clonal phylogeny and (ii) the clonal prevalences. Optionally, TimeScape accepts a data table of targeted mutations observed in each clone and their allele prevalences over time. The output is the TimeScape plot showing clonal prevalence vertically, time horizontally, and the plot height optionally encoding tumour volume during tumour-shrinking events. At each sampling time point (denoted by a faint white line), the height of each clone accurately reflects its proportionate prevalence. These prevalences form the anchors for bezier curves that visually represent the dynamic transitions between time points.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tin/meta.yaml b/recipes/bioconductor-tin/meta.yaml index 1acc38ee9a11d..d4d29c6bf980b 100644 --- a/recipes/bioconductor-tin/meta.yaml +++ b/recipes/bioconductor-tin/meta.yaml @@ -1,28 +1,38 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "TIN" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The TIN package implements a set of tools for transcriptome instability analysis based on exon expression profiles. Deviating exon usage is studied in the context of splicing factors to analyse to what degree transcriptome instability is correlated to splicing factor expression. In the transcriptome instability correlation analysis, the data is compared to both random permutations of alternative splicing scores and expression of random gene sets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Transcriptome instability analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 33dbf5f6f5fada307f20f5a9b8d6f8a8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tin", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:tin + - doi:10.4137/CIN.S31363 + parent_recipe: + name: bioconductor-tin + path: recipes/bioconductor-tin + version: 1.12.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, aroma.light, affxparser, RUnit, BiocGenerics requirements: host: - - 'bioconductor-impute >=1.76.0,<1.77.0' + - bioconductor-impute >=1.80.0,<1.81.0 - r-aroma.affymetrix - r-base - r-data.table @@ -30,27 +40,23 @@ requirements: - r-stringr - r-wgcna run: - - 'bioconductor-impute >=1.76.0,<1.77.0' + - bioconductor-impute >=1.80.0,<1.81.0 - r-aroma.affymetrix - r-base - r-data.table - r-squash - r-stringr - r-wgcna + +source: + md5: f63cd84da454fa397ab8936a2dbded8d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Transcriptome instability analysis' - description: 'The TIN package implements a set of tools for transcriptome instability analysis based on exon expression profiles. Deviating exon usage is studied in the context of splicing factors to analyse to what degree transcriptome instability is correlated to splicing factor expression. In the transcriptome instability correlation analysis, the data is compared to both random permutations of alternative splicing scores and expression of random gene sets.' -extra: - identifiers: - - biotools:tin - - doi:10.4137/CIN.S31363 - parent_recipe: - name: bioconductor-tin - path: recipes/bioconductor-tin - version: 1.12.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tinesath1cdf/meta.yaml b/recipes/bioconductor-tinesath1cdf/meta.yaml index 73e31ef2a3a0c..fe7325de5d494 100644 --- a/recipes/bioconductor-tinesath1cdf/meta.yaml +++ b/recipes/bioconductor-tinesath1cdf/meta.yaml @@ -1,37 +1,37 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "tinesath1cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a58177f0ed4976f52370b35e13818ce3 +about: + description: A package containing an environment represeting the newcdf/tinesATH1.cdf.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: tinesath1cdf build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tinesath1cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7876f5f8916518557139bfd5dab1f4f3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: tinesath1cdf - description: 'A package containing an environment represeting the newcdf/tinesATH1.cdf.cdf file.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tinesath1cdf/post-link.sh b/recipes/bioconductor-tinesath1cdf/post-link.sh index 12e58ab694e6c..4cd9964113679 100644 --- a/recipes/bioconductor-tinesath1cdf/post-link.sh +++ b/recipes/bioconductor-tinesath1cdf/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tinesath1cdf-1.40.0" +installBiocDataPackage.sh "tinesath1cdf-1.44.0" diff --git a/recipes/bioconductor-tinesath1probe/meta.yaml b/recipes/bioconductor-tinesath1probe/meta.yaml index 6f2f2c78341f2..f88e1b498643e 100644 --- a/recipes/bioconductor-tinesath1probe/meta.yaml +++ b/recipes/bioconductor-tinesath1probe/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "tinesath1probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: abd9396a4f17a0044018702394b62933 +about: + description: This package was automatically created by package matchprobes version 1.4.0. The probe sequence data was obtained from http://www.affymetrix.com. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type tinesath1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tinesath1probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b62b0add44a447b6c38c051cf70aa87c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type tinesath1' - description: 'This package was automatically created by package matchprobes version 1.4.0. The probe sequence data was obtained from http://www.affymetrix.com.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tinesath1probe/post-link.sh b/recipes/bioconductor-tinesath1probe/post-link.sh index 1e35a8d90f622..0ffff7ed2c2b1 100644 --- a/recipes/bioconductor-tinesath1probe/post-link.sh +++ b/recipes/bioconductor-tinesath1probe/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tinesath1probe-1.40.0" +installBiocDataPackage.sh "tinesath1probe-1.44.0" diff --git a/recipes/bioconductor-tissueenrich/meta.yaml b/recipes/bioconductor-tissueenrich/meta.yaml index e98619fb7169a..f470971d24c35 100644 --- a/recipes/bioconductor-tissueenrich/meta.yaml +++ b/recipes/bioconductor-tissueenrich/meta.yaml @@ -1,54 +1,58 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "TissueEnrich" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The TissueEnrich package is used to calculate enrichment of tissue-specific genes in a set of input genes. For example, the user can input the most highly expressed genes from RNA-Seq data, or gene co-expression modules to determine which tissue-specific genes are enriched in those datasets. Tissue-specific genes were defined by processing RNA-Seq data from the Human Protein Atlas (HPA) (Uhlén et al. 2015), GTEx (Ardlie et al. 2015), and mouse ENCODE (Shen et al. 2012) using the algorithm from the HPA (Uhlén et al. 2015).The hypergeometric test is being used to determine if the tissue-specific genes are enriched among the input genes. Along with tissue-specific gene enrichment, the TissueEnrich package can also be used to define tissue-specific genes from expression datasets provided by the user, which can then be used to calculate tissue-specific gene enrichments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Tissue-specific gene enrichment analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5cc00925f523a6d82b216343e7f4b81a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tissueenrich", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-tissueenrich + path: recipes/bioconductor-tissueenrich + version: 1.0.7 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-dplyr >=0.7.3' - - 'r-ensurer >=1.1.0' - - 'r-ggplot2 >=2.2.1' - - 'r-tidyr >=0.8.0' + - r-dplyr >=0.7.3 + - r-ggplot2 >=2.2.1 + - r-tidyr >=0.8.0 run: - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-dplyr >=0.7.3' - - 'r-ensurer >=1.1.0' - - 'r-ggplot2 >=2.2.1' - - 'r-tidyr >=0.8.0' + - r-dplyr >=0.7.3 + - r-ggplot2 >=2.2.1 + - r-tidyr >=0.8.0 + +source: + md5: a5e44caa8db0d86ab6657533fb022638 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Tissue-specific gene enrichment analysis' - description: 'The TissueEnrich package is used to calculate enrichment of tissue-specific genes in a set of input genes. For example, the user can input the most highly expressed genes from RNA-Seq data, or gene co-expression modules to determine which tissue-specific genes are enriched in those datasets. Tissue-specific genes were defined by processing RNA-Seq data from the Human Protein Atlas (HPA) (Uhlén et al. 2015), GTEx (Ardlie et al. 2015), and mouse ENCODE (Shen et al. 2012) using the algorithm from the HPA (Uhlén et al. 2015).The hypergeometric test is being used to determine if the tissue-specific genes are enriched among the input genes. Along with tissue-specific gene enrichment, the TissueEnrich package can also be used to define tissue-specific genes from expression datasets provided by the user, which can then be used to calculate tissue-specific gene enrichments.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-tissueenrich - path: recipes/bioconductor-tissueenrich - version: 1.0.7 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tissuetreg/meta.yaml b/recipes/bioconductor-tissuetreg/meta.yaml index 78f702a37065e..7ea1bb249cefd 100644 --- a/recipes/bioconductor-tissuetreg/meta.yaml +++ b/recipes/bioconductor-tissuetreg/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "tissueTreg" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5d975c08b7a19af832c4468ecb04c58b +about: + description: 'The package provides ready to use epigenomes (obtained from TWGBS) and transcriptomes (RNA-seq) from various tissues as obtained in the study (Delacher and Imbusch 2017, PMID: 28783152). Regulatory T cells (Treg cells) perform two distinct functions: they maintain self-tolerance, and they support organ homeostasis by differentiating into specialized tissue Treg cells. The underlying dataset characterises the epigenetic and transcriptomic modifications for specialized tissue Treg cells.' + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: TWGBS and RNA-seq data from tissue T regulatory cells from mice build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tissuetreg", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq, SummarizedExperiment, ggplot2, reshape2 requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6d508115f45fe5ec1faf5349c9497e7d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'TWGBS and RNA-seq data from tissue T regulatory cells from mice' - description: 'The package provides ready to use epigenomes (obtained from TWGBS) and transcriptomes (RNA-seq) from various tissues as obtained in the study (Delacher and Imbusch 2017, PMID: 28783152). Regulatory T cells (Treg cells) perform two distinct functions: they maintain self-tolerance, and they support organ homeostasis by differentiating into specialized tissue Treg cells. The underlying dataset characterises the epigenetic and transcriptomic modifications for specialized tissue Treg cells.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tissuetreg/post-link.sh b/recipes/bioconductor-tissuetreg/post-link.sh index 407a1fd8a9db4..9404e07b56b37 100644 --- a/recipes/bioconductor-tissuetreg/post-link.sh +++ b/recipes/bioconductor-tissuetreg/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tissuetreg-1.22.0" +installBiocDataPackage.sh "tissuetreg-1.26.0" diff --git a/recipes/bioconductor-titancna/build_failure.osx-64.yaml b/recipes/bioconductor-titancna/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..9a06ece104d97 --- /dev/null +++ b/recipes/bioconductor-titancna/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5313341597836d4761d789ee6cff7b0878081ce23f92f98808f4907655085403 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec(">=1.58.0,<1.59.0"), MatchSpec("bioconductor-variantannotation==1.52.0=r44h2f393c0_0")} + Encountered problems while solving: + - nothing provides bioconductor-genomicfeatures >=1.58.0,<1.59.0 needed by bioconductor-variantannotation-1.52.0-r44h2f393c0_0 + + Could not solve for environment specs + The following package could not be installed + bioconductor-variantannotation >=1.52.0,<1.53.0 is not installable because it requires + bioconductor-genomicfeatures >=1.58.0,<1.59.0 , which does not exist (perhaps a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec(">=1.58.0,<1.59.0"), MatchSpec("bioconductor-variantannotation==1.52.0=r44h2f393c0_0")} + Encountered problems while solving: + - nothing provides bioconductor-genomicfeatures >=1.58.0,<1.59.0 needed by bioconductor-variantannotation-1.52.0-r44h2f393c0_0 + + Could not solve for environment specs + The following package could not be installed + bioconductor-variantannotation >=1.52.0,<1.53.0 is not installable because it requires + bioconductor-genomicfeatures >=1.58.0,<1.59.0 , which does not exist (perhaps a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec(">=1.58.0,<1.59.0"), MatchSpec("bioconductor-variantannotation==1.52.0=r44h2f393c0_0")} + Encountered problems while solving: + - nothing provides bioconductor-genomicfeatures >=1.58.0,<1.59.0 needed by bioconductor-variantannotation-1.52.0-r44h2f393c0_0 + + Could not solve for environment specs + The following package could not be installed + bioconductor-variantannotation >=1.52.0,<1.53.0 is not installable because it requires + bioconductor-genomicfeatures >=1.58.0,<1.59.0 , which does not exist (perhaps a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-titancna/meta.yaml b/recipes/bioconductor-titancna/meta.yaml index 05bd29c21bf16..a7d2273e9bcff 100644 --- a/recipes/bioconductor-titancna/meta.yaml +++ b/recipes/bioconductor-titancna/meta.yaml @@ -1,63 +1,69 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "TitanCNA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalence of clonal clusters in tumour whole genome sequencing data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Subclonal copy number and LOH prediction from whole genome sequencing of tumours -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ce40de587ae35a22c583019e6a85dbc6 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-titancna", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:titancna + parent_recipe: + name: bioconductor-titancna + path: recipes/bioconductor-titancna + version: 1.19.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - - 'r-data.table >=1.10.4' - - 'r-dplyr >=0.5.0' - - 'r-foreach >=1.4.3' + - r-data.table >=1.10.4 + - r-dplyr >=0.5.0 + - r-foreach >=1.4.3 - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - - 'r-data.table >=1.10.4' - - 'r-dplyr >=0.5.0' - - 'r-foreach >=1.4.3' - build: - - {{ compiler('c') }} - - make + - r-data.table >=1.10.4 + - r-dplyr >=0.5.0 + - r-foreach >=1.4.3 + +source: + md5: b3089ac06d09aa847f7baabaad759821 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Subclonal copy number and LOH prediction from whole genome sequencing of tumours' - description: 'Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalence of clonal clusters in tumour whole genome sequencing data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:titancna - parent_recipe: - name: bioconductor-titancna - path: recipes/bioconductor-titancna - version: 1.19.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tkwidgets/meta.yaml b/recipes/bioconductor-tkwidgets/meta.yaml index 81145b1f4f180..565cec37a6d49 100644 --- a/recipes/bioconductor-tkwidgets/meta.yaml +++ b/recipes/bioconductor-tkwidgets/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.80.0" %} +{% set version = "1.84.0" %} {% set name = "tkWidgets" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 044f7f3666426cbac3929eb9af1ce9d8 +about: + description: Widgets to provide user interfaces. tcltk should have been installed for the widgets to run. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: R based tk widgets build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tkwidgets", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: Biobase, hgu95av2 requirements: host: - - 'bioconductor-dyndoc >=1.80.0,<1.81.0' - - 'bioconductor-widgettools >=1.80.0,<1.81.0' + - bioconductor-dyndoc >=1.84.0,<1.85.0 + - bioconductor-widgettools >=1.84.0,<1.85.0 - r-base run: - - 'bioconductor-dyndoc >=1.80.0,<1.81.0' - - 'bioconductor-widgettools >=1.80.0,<1.81.0' + - bioconductor-dyndoc >=1.84.0,<1.85.0 + - bioconductor-widgettools >=1.84.0,<1.85.0 - r-base +source: + md5: 4dab35f753e3ecc76300812082567cf0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'R based tk widgets' - description: 'Widgets to provide user interfaces. tcltk should have been installed for the widgets to run.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tloh/meta.yaml b/recipes/bioconductor-tloh/meta.yaml index 72917842a802d..1a9eeeeb407f6 100644 --- a/recipes/bioconductor-tloh/meta.yaml +++ b/recipes/bioconductor-tloh/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "tLOH" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: tLOH, or transcriptomicsLOH, assesses evidence for loss of heterozygosity (LOH) in pre-processed spatial transcriptomics data. This tool requires spatial transcriptomics cluster and allele count information at likely heterozygous single-nucleotide polymorphism (SNP) positions in VCF format. Bayes factors are calculated at each SNP to determine likelihood of potential loss of heterozygosity event. Two plotting functions are included to visualize allele fraction and aggregated Bayes factor per chromosome. Data generated with the 10X Genomics Visium Spatial Gene Expression platform must be pre-processed to obtain an individual sample VCF with columns for each cluster. Required fields are allele depth (AD) with counts for reference/alternative alleles and read depth (DP). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1693fc28c2855f1af11159ec1051e2df build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tloh", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-bestnormalize - r-data.table @@ -36,9 +38,9 @@ requirements: - r-scales - r-stringr run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-bestnormalize - r-data.table @@ -49,13 +51,16 @@ requirements: - r-purrr - r-scales - r-stringr + +source: + md5: 99855940a5a855cc39bc937ef6f50f53 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations' - description: 'tLOH, or transcriptomicsLOH, assesses evidence for loss of heterozygosity (LOH) in pre-processed spatial transcriptomics data. This tool requires spatial transcriptomics cluster and allele count information at likely heterozygous single-nucleotide polymorphism (SNP) positions in VCF format. Bayes factors are calculated at each SNP to determine likelihood of potential loss of heterozygosity event. Two plotting functions are included to visualize allele fraction and aggregated Bayes factor per chromosome. Data generated with the 10X Genomics Visium Spatial Gene Expression platform must be pre-processed to obtain an individual sample VCF with columns for each cluster. Required fields are allele depth (AD) with counts for reference/alternative alleles and read depth (DP).' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tmexplorer/meta.yaml b/recipes/bioconductor-tmexplorer/meta.yaml index 016c668957311..c687d3114dfcf 100644 --- a/recipes/bioconductor-tmexplorer/meta.yaml +++ b/recipes/bioconductor-tmexplorer/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "TMExplorer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 48b11be99739e61f54d9b442af739d49 +about: + description: This package provides a tool to search and download a collection of tumour microenvironment single-cell RNA sequencing datasets and their metadata. TMExplorer aims to act as a single point of entry for users looking to study the tumour microenvironment at the single cell level. Users can quickly search available datasets using the metadata table and then download the ones they are interested in for analysis. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: A Collection of Tumour Microenvironment Single-cell RNA Sequencing Datasets and Corresponding Metadata build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tmexplorer", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-matrix run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-base - r-matrix - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6554fe5db5049cfe19f9b9f7d3f662c2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A Collection of Tumour Microenvironment Single-cell RNA Sequencing Datasets and Corresponding Metadata' - description: 'This package provides a tool to search and download a collection of tumour microenvironment single-cell RNA sequencing datasets and their metadata. TMExplorer aims to act as a single point of entry for users looking to study the tumour microenvironment at the single cell level. Users can quickly search available datasets using the metadata table and then download the ones they are interested in for analysis.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tmexplorer/post-link.sh b/recipes/bioconductor-tmexplorer/post-link.sh index 7bb935ca65385..7cd69aaa51f03 100644 --- a/recipes/bioconductor-tmexplorer/post-link.sh +++ b/recipes/bioconductor-tmexplorer/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tmexplorer-1.12.0" +installBiocDataPackage.sh "tmexplorer-1.16.0" diff --git a/recipes/bioconductor-tmixclust/meta.yaml b/recipes/bioconductor-tmixclust/meta.yaml index 4542db2ccca41..2f5c99b005c60 100644 --- a/recipes/bioconductor-tmixclust/meta.yaml +++ b/recipes/bioconductor-tmixclust/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "TMixClust" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implementation of a clustering method for time series gene expression data based on mixed-effects models with Gaussian variables and non-parametric cubic splines estimation. The method can robustly account for the high levels of noise present in typical gene expression time series datasets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3e0e6852e806722f305ed45332c23179 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tmixclust", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-spem >=1.42.0,<1.43.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-spem >=1.46.0,<1.47.0 - r-base - r-cluster - r-flexclust @@ -32,22 +34,25 @@ requirements: - r-mvtnorm - r-zoo run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-spem >=1.42.0,<1.43.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-spem >=1.46.0,<1.47.0 - r-base - r-cluster - r-flexclust - r-gss - r-mvtnorm - r-zoo + +source: + md5: ebab6e8362666c78cde53e6dcbf29a23 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines' - description: 'Implementation of a clustering method for time series gene expression data based on mixed-effects models with Gaussian variables and non-parametric cubic splines estimation. The method can robustly account for the high levels of noise present in typical gene expression time series datasets.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tmsig/build.sh b/recipes/bioconductor-tmsig/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tmsig/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tmsig/meta.yaml b/recipes/bioconductor-tmsig/meta.yaml new file mode 100644 index 0000000000000..475b247df073c --- /dev/null +++ b/recipes/bioconductor-tmsig/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "1.0.0" %} +{% set name = "TMSig" %} +{% set bioc = "3.20" %} + +about: + description: The TMSig package contains tools to prepare, analyze, and visualize named lists of sets, with an emphasis on molecular signatures (such as gene or kinase sets). It includes fast, memory efficient functions to construct sparse incidence and similarity matrices and filter, cluster, invert, and decompose sets. Additionally, bubble heatmaps can be created to visualize the results of any differential or molecular signatures analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Tools for Molecular Signatures + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tmsig", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - r-base + - r-circlize + - r-data.table + - r-matrix + run: + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - r-base + - r-circlize + - r-data.table + - r-matrix + +source: + md5: ebfbc13d259a7ab298ed4a808ba69aae + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-tnt/meta.yaml b/recipes/bioconductor-tnt/meta.yaml index eb73b9746ce6e..89f773d88d2d3 100644 --- a/recipes/bioconductor-tnt/meta.yaml +++ b/recipes/bioconductor-tnt/meta.yaml @@ -1,55 +1,60 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "TnT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A R interface to the TnT javascript library (https://github.com/ tntvis) to provide interactive and flexible visualization of track-based genomic data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + summary: Interactive Visualization for Genomic Features -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1afe4c0018eb0c5026c72dcfe2120045 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tnt", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: GenomicFeatures, shiny, BiocManager, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-htmlwidgets - r-jsonlite - r-knitr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-htmlwidgets - r-jsonlite - r-knitr + +source: + md5: 0b42f4d15542b2a0a4d9e7f7db95c9bd + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3 - summary: 'Interactive Visualization for Genomic Features' - description: 'A R interface to the TnT javascript library (https://github.com/ tntvis) to provide interactive and flexible visualization of track-based genomic data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-toast/meta.yaml b/recipes/bioconductor-toast/meta.yaml index 45a9580d13cd1..62518642b381a 100644 --- a/recipes/bioconductor-toast/meta.yaml +++ b/recipes/bioconductor-toast/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "TOAST" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is devoted to analyzing high-throughput data (e.g. gene expression microarray, DNA methylation microarray, RNA-seq) from complex tissues. Current functionalities include 1. detect cell-type specific or cross-cell type differential signals 2. tree-based differential analysis 3. improve variable selection in reference-free deconvolution 4. partial reference-free deconvolution with prior knowledge. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Tools for the analysis of heterogeneous tissues -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7161d25bca2e95e8f83aea1f7d0bba6d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-toast", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, gplots, matrixStats, Matrix requirements: host: - - 'bioconductor-epidish >=2.18.0,<2.19.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-epidish >=2.22.0,<2.23.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-corpcor - r-doparallel @@ -34,9 +36,9 @@ requirements: - r-quadprog - r-tidyr run: - - 'bioconductor-epidish >=2.18.0,<2.19.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-epidish >=2.22.0,<2.23.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-corpcor - r-doparallel @@ -45,13 +47,16 @@ requirements: - r-nnls - r-quadprog - r-tidyr + +source: + md5: c912d3bf2b4154775188ab78f35dc5b7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Tools for the analysis of heterogeneous tissues' - description: 'This package is devoted to analyzing high-throughput data (e.g. gene expression microarray, DNA methylation microarray, RNA-seq) from complex tissues. Current functionalities include 1. detect cell-type specific or cross-cell type differential signals 2. tree-based differential analysis 3. improve variable selection in reference-free deconvolution 4. partial reference-free deconvolution with prior knowledge.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tofsimsdata/meta.yaml b/recipes/bioconductor-tofsimsdata/meta.yaml index d77787901bee4..38c11defef20a 100644 --- a/recipes/bioconductor-tofsimsdata/meta.yaml +++ b/recipes/bioconductor-tofsimsdata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "tofsimsData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 57fe35de7b03ee4f3ca07540949a6b5e +about: + description: This packages contains data to be used with the 'tofsims' package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Import, process and analysis of ToF-SIMS imaging data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tofsimsdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, tools requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 820073aaa32a9664721c1245015c78db + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-3 - summary: 'Import, process and analysis of ToF-SIMS imaging data' - description: 'This packages contains data to be used with the ''tofsims'' package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tofsimsdata/post-link.sh b/recipes/bioconductor-tofsimsdata/post-link.sh index 2165ad029b1c3..ae158abd45112 100644 --- a/recipes/bioconductor-tofsimsdata/post-link.sh +++ b/recipes/bioconductor-tofsimsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tofsimsdata-1.30.0" +installBiocDataPackage.sh "tofsimsdata-1.34.0" diff --git a/recipes/bioconductor-tomatocdf/meta.yaml b/recipes/bioconductor-tomatocdf/meta.yaml index 18ad431e15afa..3640fdcde6349 100644 --- a/recipes/bioconductor-tomatocdf/meta.yaml +++ b/recipes/bioconductor-tomatocdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "tomatocdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 200efc0637788d4bd3263fc9183c1aa6 +about: + description: A package containing an environment representing the Tomato.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: tomatocdf build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tomatocdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 200efc0637788d4bd3263fc9183c1aa6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: tomatocdf - description: 'A package containing an environment representing the Tomato.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tomatoprobe/meta.yaml b/recipes/bioconductor-tomatoprobe/meta.yaml index da018906e552d..75a6e3a021109 100644 --- a/recipes/bioconductor-tomatoprobe/meta.yaml +++ b/recipes/bioconductor-tomatoprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "tomatoprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 72020469f35c19399fd0be9eaffd8e77 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Tomato\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type tomato build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tomatoprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 72020469f35c19399fd0be9eaffd8e77 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type tomato' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Tomato\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tomoda/meta.yaml b/recipes/bioconductor-tomoda/meta.yaml index ef22967e0bd24..903daf73be7e7 100644 --- a/recipes/bioconductor-tomoda/meta.yaml +++ b/recipes/bioconductor-tomoda/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "tomoda" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'This package provides many easy-to-use methods to analyze and visualize tomo-seq data. The tomo-seq technique is based on cryosectioning of tissue and performing RNA-seq on consecutive sections. (Reference: Kruse F, Junker JP, van Oudenaarden A, Bakkers J. Tomo-seq: A method to obtain genome-wide expression data with spatial resolution. Methods Cell Biol. 2016;135:299-307. doi:10.1016/bs.mcb.2016.01.006) The main purpose of the package is to find zones with similar transcriptional profiles and spatially expressed genes in a tomo-seq sample. Several visulization functions are available to create easy-to-modify plots.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Tomo-seq data analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 49b8009bc1e0c7c7567b75be6fbde6c4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tomoda", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-ggrepel @@ -31,7 +33,7 @@ requirements: - r-rtsne - r-umap run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggplot2 - r-ggrepel @@ -39,13 +41,16 @@ requirements: - r-reshape2 - r-rtsne - r-umap + +source: + md5: 75962e098028f25bf9ff184650535c5b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Tomo-seq data analysis' - description: 'This package provides many easy-to-use methods to analyze and visualize tomo-seq data. The tomo-seq technique is based on cryosectioning of tissue and performing RNA-seq on consecutive sections. (Reference: Kruse F, Junker JP, van Oudenaarden A, Bakkers J. Tomo-seq: A method to obtain genome-wide expression data with spatial resolution. Methods Cell Biol. 2016;135:299-307. doi:10.1016/bs.mcb.2016.01.006) The main purpose of the package is to find zones with similar transcriptional profiles and spatially expressed genes in a tomo-seq sample. Several visulization functions are available to create easy-to-modify plots.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tomoseqr/meta.yaml b/recipes/bioconductor-tomoseqr/meta.yaml index 10dee3d515805..217fab6000ad7 100644 --- a/recipes/bioconductor-tomoseqr/meta.yaml +++ b/recipes/bioconductor-tomoseqr/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "tomoseqr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: '`tomoseqr` is an R package for analyzing Tomo-seq data. Tomo-seq is a genome-wide RNA tomography method that combines combining high-throughput RNA sequencing with cryosectioning for spatially resolved transcriptomics. `tomoseqr` reconstructs 3D expression patterns from tomo-seq data and visualizes the reconstructed 3D expression patterns.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: R Package for Analyzing Tomo-seq Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b881e4b272396cc4696d840658ec0ef5 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tomoseqr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-animation - r-base - r-dplyr @@ -34,7 +36,7 @@ requirements: - r-stringr - r-tibble run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 - r-animation - r-base - r-dplyr @@ -45,13 +47,16 @@ requirements: - r-shiny - r-stringr - r-tibble + +source: + md5: 103b5393aaa6ab1dc037f20f36ae9d5f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'R Package for Analyzing Tomo-seq Data' - description: '`tomoseqr` is an R package for analyzing Tomo-seq data. Tomo-seq is a genome-wide RNA tomography method that combines combining high-throughput RNA sequencing with cryosectioning for spatially resolved transcriptomics. `tomoseqr` reconstructs 3D expression patterns from tomo-seq data and visualizes the reconstructed 3D expression patterns.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-top/meta.yaml b/recipes/bioconductor-top/meta.yaml index 47810af59cec0..7c93ecdd44601 100644 --- a/recipes/bioconductor-top/meta.yaml +++ b/recipes/bioconductor-top/meta.yaml @@ -1,29 +1,32 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "TOP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: TOP constructs a transferable model across gene expression platforms for prospective experiments. Such a transferable model can be trained to make predictions on independent validation data with an accuracy that is similar to a re-substituted model. The TOP procedure also has the flexibility to be adapted to suit the most common clinical response variables, including linear response, binomial and Cox PH models. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: TOP Constructs Transferable Model Across Gene Expression Platforms -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af6712369d58630bdcc2b05d7dc06b52 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-top", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, Biobase, curatedOvarianData, ggbeeswarm, ggsci, survminer, tidyverse requirements: + host: - - 'bioconductor-classifyr >=3.6.0,<3.7.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-classifyr >=3.10.0,<3.11.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-assertthat - r-base - r-caret @@ -50,9 +53,10 @@ requirements: - r-tibble - r-tidygraph - r-tidyr + run: - - 'bioconductor-classifyr >=3.6.0,<3.7.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-classifyr >=3.10.0,<3.11.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-assertthat - r-base - r-caret @@ -79,13 +83,16 @@ requirements: - r-tibble - r-tidygraph - r-tidyr + +source: + md5: 637187784f8b187f173cd3e6b9fab5aa + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'TOP Constructs Transferable Model Across Gene Expression Platforms' - description: 'TOP constructs a transferable model across gene expression platforms for prospective experiments. Such a transferable model can be trained to make predictions on independent validation data with an accuracy that is similar to a re-substituted model. The TOP procedure also has the flexibility to be adapted to suit the most common clinical response variables, including linear response, binomial and Cox PH models.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-topconfects/meta.yaml b/recipes/bioconductor-topconfects/meta.yaml index eb8e8b3ac1e1d..ca0df00b26871 100644 --- a/recipes/bioconductor-topconfects/meta.yaml +++ b/recipes/bioconductor-topconfects/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "topconfects" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 222a043b78c72f00d0dee0d6658d9284 +about: + description: Rank results by confident effect sizes, while maintaining False Discovery Rate and False Coverage-statement Rate control. Topconfects is an alternative presentation of TREAT results with improved usability, eliminating p-values and instead providing confidence bounds. The main application is differential gene expression analysis, providing genes ranked in order of confident log2 fold change, but it can be applied to any collection of effect sizes with associated standard errors. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-2.1 | file LICENSE + license_file: LICENSE + summary: Top Confident Effect Sizes build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-topconfects", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr, rmarkdown, BiocStyle requirements: host: @@ -29,13 +28,14 @@ requirements: - r-assertthat - r-base - r-ggplot2 +source: + md5: 5274ff47d2961095b6046e34ac3f135e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL-2.1 | file LICENSE' - summary: 'Top Confident Effect Sizes' - description: 'Rank results by confident effect sizes, while maintaining False Discovery Rate and False Coverage-statement Rate control. Topconfects is an alternative presentation of TREAT results with improved usability, eliminating p-values and instead providing confidence bounds. The main application is differential gene expression analysis, providing genes ranked in order of confident log2 fold change, but it can be applied to any collection of effect sizes with associated standard errors.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-topdownr/meta.yaml b/recipes/bioconductor-topdownr/meta.yaml index ae46358e6c952..3cc11a13f29cf 100644 --- a/recipes/bioconductor-topdownr/meta.yaml +++ b/recipes/bioconductor-topdownr/meta.yaml @@ -1,55 +1,62 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "topdownr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Investigation of Fragmentation Conditions in Top-Down Proteomics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9aa08f9983d77f0794cd1cce6c1b8085 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-topdownr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: topdownrdata (>= 0.2), knitr, rmarkdown, ranger, testthat, BiocStyle, xml2 requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-mzr >=2.40.0,<2.41.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-psmatch >=1.10.0,<1.11.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-ggplot2 >=2.2.1' - - 'r-matrix >=1.4-2' + - r-ggplot2 >=2.2.1 + - r-matrix >=1.4-2 run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-mzr >=2.40.0,<2.41.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-psmatch >=1.10.0,<1.11.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-ggplot2 >=2.2.1' - - 'r-matrix >=1.4-2' + - r-ggplot2 >=2.2.1 + - r-matrix >=1.4-2 + +source: + md5: e0a33bb1c0b72675e6de935c8455124b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Investigation of Fragmentation Conditions in Top-Down Proteomics' - description: 'The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-topdownrdata/meta.yaml b/recipes/bioconductor-topdownrdata/meta.yaml index fd7e915295c84..73be8ce13b6f2 100644 --- a/recipes/bioconductor-topdownrdata/meta.yaml +++ b/recipes/bioconductor-topdownrdata/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "topdownrdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 28e746b858956bea0967344bfe363e7d +about: + description: Example data for the topdownr package generated on a Thermo Orbitrap Fusion Lumos MS device. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Example Files for the topdownr R Package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-topdownrdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-topdownr >=1.24.0,<1.25.0' + - bioconductor-topdownr >=1.28.0,<1.29.0 - r-base run: - - 'bioconductor-topdownr >=1.24.0,<1.25.0' + - bioconductor-topdownr >=1.28.0,<1.29.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c74335a0fdebf3646e25eac76164738b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Example Files for the topdownr R Package' - description: 'Example data for the topdownr package generated on a Thermo Orbitrap Fusion Lumos MS device.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-topdownrdata/post-link.sh b/recipes/bioconductor-topdownrdata/post-link.sh index b9614922d0e2b..d3031e61c1886 100644 --- a/recipes/bioconductor-topdownrdata/post-link.sh +++ b/recipes/bioconductor-topdownrdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "topdownrdata-1.24.0" +installBiocDataPackage.sh "topdownrdata-1.28.0" diff --git a/recipes/bioconductor-topgo/meta.yaml b/recipes/bioconductor-topgo/meta.yaml index 1f934d3e45795..72652b5f86b96 100644 --- a/recipes/bioconductor-topgo/meta.yaml +++ b/recipes/bioconductor-topgo/meta.yaml @@ -1,63 +1,69 @@ -{% set version = "2.54.0" %} +{% set version = "2.58.0" %} {% set name = "topGO" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Enrichment Analysis for Gene Ontology -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 62aeda25dfb89dfd466ddc749e52a422 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-topgo", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:topgo + - doi:10.1093/bioinformatics/btl140 + parent_recipe: + name: bioconductor-topgo + path: recipes/bioconductor-topgo + version: 2.32.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-dbi - r-lattice - r-matrixstats - - 'r-sparsem >=0.73' + - r-sparsem >=0.73 run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-go.db >=3.18.0,<3.19.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-go.db >=3.20.0,<3.21.0 + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - r-dbi - r-lattice - r-matrixstats - - 'r-sparsem >=0.73' + - r-sparsem >=0.73 + +source: + md5: 72cfe77fe47fae85d8d1ee82dc417140 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Enrichment Analysis for Gene Ontology' - description: 'topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:topgo - - doi:10.1093/bioinformatics/btl140 - parent_recipe: - name: bioconductor-topgo - path: recipes/bioconductor-topgo - version: 2.32.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-toxicogx/meta.yaml b/recipes/bioconductor-toxicogx/meta.yaml index 94042954f8fd5..0dc5aafcb00fb 100644 --- a/recipes/bioconductor-toxicogx/meta.yaml +++ b/recipes/bioconductor-toxicogx/meta.yaml @@ -1,34 +1,37 @@ -{% set version = "2.6.0" %} +{% set version = "2.10.0" %} {% set name = "ToxicoGx" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Contains a set of functions to perform large-scale analysis of toxicogenomic data, providing a standardized data structure to hold information relevant to annotation, visualization and statistical analysis of toxicogenomic data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Analysis of Large-Scale Toxico-Genomic Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2be22f48c0e155c94f9af6e6157a0333 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-toxicogx", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rmarkdown, testthat, BiocStyle, knitr, tinytex, devtools, PharmacoGx, xtable, markdown requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-coregx >=2.6.0,<2.7.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-coregx >=2.10.0,<2.11.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-catools @@ -42,14 +45,15 @@ requirements: - r-scales - r-tibble - r-tidyr + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-coregx >=2.6.0,<2.7.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-coregx >=2.10.0,<2.11.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-assertthat - r-base - r-catools @@ -63,13 +67,16 @@ requirements: - r-scales - r-tibble - r-tidyr + +source: + md5: 3676baa7b45579fdbd24f9c3a9fafbe7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Analysis of Large-Scale Toxico-Genomic Data' - description: 'Contains a set of functions to perform large-scale analysis of toxicogenomic data, providing a standardized data structure to hold information relevant to annotation, visualization and statistical analysis of toxicogenomic data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tpp/meta.yaml b/recipes/bioconductor-tpp/meta.yaml index 573be703abd26..5dc6370a61deb 100644 --- a/recipes/bioconductor-tpp/meta.yaml +++ b/recipes/bioconductor-tpp/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "3.30.0" %} +{% set version = "3.34.0" %} {% set name = "TPP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Analyze thermal proteome profiling (TPP) experiments with varying temperatures (TR) or compound concentrations (CCR). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Analyze thermal proteome profiling (TPP) experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4a0ea50f7969045d710d3bfef371af62 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tpp", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biobroom >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biobroom >=1.38.0,<1.39.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-broom - r-data.table @@ -39,7 +41,7 @@ requirements: - r-mass - r-mefa - r-nls2 - - 'r-openxlsx >=2.4.0' + - r-openxlsx >=2.4.0 - r-plyr - r-purrr - r-rcolorbrewer @@ -51,10 +53,11 @@ requirements: - r-tidyr - r-venndiagram - r-vgam + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biobroom >=1.34.0,<1.35.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biobroom >=1.38.0,<1.39.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-broom - r-data.table @@ -69,7 +72,7 @@ requirements: - r-mass - r-mefa - r-nls2 - - 'r-openxlsx >=2.4.0' + - r-openxlsx >=2.4.0 - r-plyr - r-purrr - r-rcolorbrewer @@ -81,12 +84,16 @@ requirements: - r-tidyr - r-venndiagram - r-vgam + +source: + md5: 4ac7e43263f1a1c5e6040a0a12a651f4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Analyze thermal proteome profiling (TPP) experiments' - description: 'Analyze thermal proteome profiling (TPP) experiments with varying temperatures (TR) or compound concentrations (CCR).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tpp2d/meta.yaml b/recipes/bioconductor-tpp2d/meta.yaml index c7c16fb5161cc..c4bb1a927e9db 100644 --- a/recipes/bioconductor-tpp2d/meta.yaml +++ b/recipes/bioconductor-tpp2d/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "TPP2D" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Detection of ligand-protein interactions from 2D thermal profiles (DLPTP), Performs an FDR-controlled analysis of 2D-TPP experiments by functional analysis of dose-response curves across temperatures. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Detection of ligand-protein interactions from 2D thermal profiles (DLPTP) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b10330822e1c629c04c568ab155b4ee1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tpp2d", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-doparallel - r-dplyr @@ -35,8 +37,8 @@ requirements: - r-stringr - r-tidyr run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-doparallel - r-dplyr @@ -47,13 +49,16 @@ requirements: - r-rcurl - r-stringr - r-tidyr + +source: + md5: dcb01b04448cdf8ad8f2444a7d961716 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Detection of ligand-protein interactions from 2D thermal profiles (DLPTP)' - description: 'Detection of ligand-protein interactions from 2D thermal profiles (DLPTP), Performs an FDR-controlled analysis of 2D-TPP experiments by functional analysis of dose-response curves across temperatures.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tpsvg/build.sh b/recipes/bioconductor-tpsvg/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tpsvg/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tpsvg/meta.yaml b/recipes/bioconductor-tpsvg/meta.yaml new file mode 100644 index 0000000000000..440efe8dae356 --- /dev/null +++ b/recipes/bioconductor-tpsvg/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "1.2.0" %} +{% set name = "tpSVG" %} +{% set bioc = "3.20" %} + +about: + description: The goal of `tpSVG` is to detect and visualize spatial variation in the gene expression for spatially resolved transcriptomics data analysis. Specifically, `tpSVG` introduces a family of count-based models, with generalizable parametric assumptions such as Poisson distribution or negative binomial distribution. In addition, comparing to currently available count-based model for spatially resolved data analysis, the `tpSVG` models improves computational time, and hence greatly improves the applicability of count-based models in SRT data analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Thin plate models to detect spatially variable genes + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-tpsvg", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr, nnSVG, rmarkdown, scran, scuttle, STexampleData, escheR, ggpubr, colorspace, BumpyMatrix, sessioninfo, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-mgcv + run: + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-mgcv + +source: + md5: ddf3de53aea89392cfe8e6f0b8231cc2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-tracktables/meta.yaml b/recipes/bioconductor-tracktables/meta.yaml index 58b77cb8dd7a6..26778facac3a4 100644 --- a/recipes/bioconductor-tracktables/meta.yaml +++ b/recipes/bioconductor-tracktables/meta.yaml @@ -1,61 +1,67 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "tracktables" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Methods to create complex IGV genome browser sessions and dynamic IGV reports in HTML pages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Build IGV tracks and HTML reports -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0726840a7d7c0252dc163cfe065cefa0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tracktables", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:tracktables + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-tracktables + path: recipes/bioconductor-tracktables + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-rcolorbrewer - r-stringr - r-tractor.base - r-xml run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-rcolorbrewer - r-stringr - r-tractor.base - r-xml + +source: + md5: f9df323cc6a53fd11d9e7ec57d245426 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Build IGV tracks and HTML reports' - description: 'Methods to create complex IGV genome browser sessions and dynamic IGV reports in HTML pages.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:tracktables - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-tracktables - path: recipes/bioconductor-tracktables - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-trackviewer/meta.yaml b/recipes/bioconductor-trackviewer/meta.yaml index fa2657452ff77..88bf5bb72e538 100644 --- a/recipes/bioconductor-trackviewer/meta.yaml +++ b/recipes/bioconductor-trackviewer/meta.yaml @@ -1,85 +1,87 @@ -{% set version = "1.38.1" %} +{% set version = "1.42.0" %} {% set name = "trackViewer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c0004e0bdb49b5d051e486f73a79a245 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-trackviewer", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:trackviewer + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-trackviewer + path: recipes/bioconductor-trackviewer + version: 1.16.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools, rmarkdown, motifStack requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-grimport - r-htmlwidgets - - r-plotrix - r-scales - r-strawr run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-interactionset >=1.30.0,<1.31.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-interactionset >=1.34.0,<1.35.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base - r-grimport - r-htmlwidgets - - r-plotrix - r-scales - r-strawr + +source: + md5: 3287391dbe336650a318e360bf192258 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data' - description: 'Visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:trackviewer - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-trackviewer - path: recipes/bioconductor-trackviewer - version: 1.16.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tradeseq/meta.yaml b/recipes/bioconductor-tradeseq/meta.yaml index cc3a8829e413c..d4947b50eae0b 100644 --- a/recipes/bioconductor-tradeseq/meta.yaml +++ b/recipes/bioconductor-tradeseq/meta.yaml @@ -1,35 +1,38 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "tradeSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: tradeSeq provides a flexible method for fitting regression models that can be used to find genes that are differentially expressed along one or multiple lineages in a trajectory. Based on the fitted models, it uses a variety of tests suited to answer different questions of interest, e.g. the discovery of genes for which expression is associated with pseudotime, or which are differentially expressed (in a specific region) along the trajectory. It fits a negative binomial generalized additive model (GAM) for each gene, and performs inference on the parameters of the GAM. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: trajectory-based differential expression analysis for sequencing data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5de25ecb5472b592837cd3937ff467c7 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tradeseq", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, covr, clusterExperiment, DelayedMatrixStats requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-slingshot >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-slingshot >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-trajectoryutils >=1.14.0,<1.15.0 - r-base - r-ggplot2 - r-igraph @@ -43,15 +46,16 @@ requirements: - r-rcolorbrewer - r-tibble - r-viridis + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-slingshot >=2.10.0,<2.11.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-slingshot >=2.14.0,<2.15.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-trajectoryutils >=1.14.0,<1.15.0 - r-base - r-ggplot2 - r-igraph @@ -65,13 +69,16 @@ requirements: - r-rcolorbrewer - r-tibble - r-viridis + +source: + md5: ea65f3a3d11bc27c09659c3817221e1f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'trajectory-based differential expression analysis for sequencing data' - description: 'tradeSeq provides a flexible method for fitting regression models that can be used to find genes that are differentially expressed along one or multiple lineages in a trajectory. Based on the fitted models, it uses a variety of tests suited to answer different questions of interest, e.g. the discovery of genes for which expression is associated with pseudotime, or which are differentially expressed (in a specific region) along the trajectory. It fits a negative binomial generalized additive model (GAM) for each gene, and performs inference on the parameters of the GAM.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-trajectorygeometry/meta.yaml b/recipes/bioconductor-trajectorygeometry/meta.yaml index b8e7e01e6f772..ea0e1bc89efb0 100644 --- a/recipes/bioconductor-trajectorygeometry/meta.yaml +++ b/recipes/bioconductor-trajectorygeometry/meta.yaml @@ -1,26 +1,39 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "TrajectoryGeometry" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Given a time series or pseudo-times series of gene expression data, we might wish to know: Do the changes in gene expression in these data exhibit directionality? Are there turning points in this directionality. Do different subsets of the data move in different directions? This package uses spherical geometry to probe these sorts of questions. In particular, if we are looking at (say) the first n dimensions of the PCA of gene expression, directionality can be detected as the clustering of points on the (n-1)-dimensional sphere.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a955410c20ec9cbae97e2d60a8c9b46f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-trajectorygeometry", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: dplyr, knitr, RColorBrewer, rmarkdown requirements: + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] host: - r-base - r-ggplot2 @@ -31,23 +44,16 @@ requirements: - r-ggplot2 - r-pracma - r-rgl - build: - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - xorg-libxfixes # [linux] + +source: + md5: a3f57410d5856a776942e0ff6ad94529 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns' - description: 'Given a time series or pseudo-times series of gene expression data, we might wish to know: Do the changes in gene expression in these data exhibit directionality? Are there turning points in this directionality. Do different subsets of the data move in different directions? This package uses spherical geometry to probe these sorts of questions. In particular, if we are looking at (say) the first n dimensions of the PCA of gene expression, directionality can be detected as the clustering of points on the (n-1)-dimensional sphere.' - license_file: LICENSE -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-trajectoryutils/meta.yaml b/recipes/bioconductor-trajectoryutils/meta.yaml index b5d17afac2d84..44cb8edda3f8a 100644 --- a/recipes/bioconductor-trajectoryutils/meta.yaml +++ b/recipes/bioconductor-trajectoryutils/meta.yaml @@ -1,47 +1,52 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "TrajectoryUtils" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implements low-level utilities for single-cell trajectory analysis, primarily intended for re-use inside higher-level packages. Include a function to create a cluster-level minimum spanning tree and data structures to hold pseudotime inference results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Single-Cell Trajectory Analysis Utilities -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8d29813e2befc86d418f15a3e594f37b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-trajectoryutils", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocNeighbors, DelayedArray, DelayedMatrixStats, BiocParallel, testthat, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-igraph - r-matrix run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-igraph - r-matrix + +source: + md5: b11dcc19508bac859068d2b9a1a777f7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Single-Cell Trajectory Analysis Utilities' - description: 'Implements low-level utilities for single-cell trajectory analysis, primarily intended for re-use inside higher-level packages. Include a function to create a cluster-level minimum spanning tree and data structures to hold pseudotime inference results.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-transcriptogramer/meta.yaml b/recipes/bioconductor-transcriptogramer/meta.yaml index 987323d84bf10..86b4e91d15859 100644 --- a/recipes/bioconductor-transcriptogramer/meta.yaml +++ b/recipes/bioconductor-transcriptogramer/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "transcriptogramer" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: R package for transcriptional analysis based on transcriptograms, a method to analyze transcriptomes that projects expression values on a set of ordered proteins, arranged such that the probability that gene products participate in the same metabolic pathway exponentially decreases with the increase of the distance between two proteins of the ordering. Transcriptograms are, hence, genome wide gene expression profiles that provide a global view for the cellular metabolism, while indicating gene sets whose expressions are altered. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Transcriptional analysis based on transcriptograms -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6c6b8c13ec29ef0e6e5552cbbd49f14d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-transcriptogramer", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics # SystemRequirements: Java Runtime Environment (>= 6) requirements: host: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-reder >=2.6.0,<2.7.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-reder >=3.2.0,<3.3.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-base - r-data.table - r-dosnow @@ -38,10 +40,10 @@ requirements: - r-tidyr - openjdk run: - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-reder >=2.6.0,<2.7.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-reder >=3.2.0,<3.3.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-base - r-data.table - r-dosnow @@ -52,13 +54,16 @@ requirements: - r-snow - r-tidyr - openjdk + +source: + md5: 2f7f7d83e608fb6bc81873a9c8ca7c8b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Transcriptional analysis based on transcriptograms' - description: 'R package for transcriptional analysis based on transcriptograms, a method to analyze transcriptomes that projects expression values on a set of ordered proteins, arranged such that the probability that gene products participate in the same metabolic pathway exponentially decreases with the increase of the distance between two proteins of the ordering. Transcriptograms are, hence, genome wide gene expression profiles that provide a global view for the cellular metabolism, while indicating gene sets whose expressions are altered.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-transcriptr/meta.yaml b/recipes/bioconductor-transcriptr/meta.yaml index 9dbdcebc52b50..a8364bdd924ed 100644 --- a/recipes/bioconductor-transcriptr/meta.yaml +++ b/recipes/bioconductor-transcriptr/meta.yaml @@ -1,37 +1,48 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "transcriptR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The differences in the RNA types being sequenced have an impact on the resulting sequencing profiles. mRNA-seq data is enriched with reads derived from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial broader coverage of both exonic and intronic regions. The presence of intronic reads in GRO-seq type of data makes it possible to use it to computationally identify and quantify all de novo continuous regions of transcription distributed across the genome. This type of data, however, is more challenging to interpret and less common practice compared to mRNA-seq. One of the challenges for primary transcript detection concerns the simultaneous transcription of closely spaced genes, which needs to be properly divided into individually transcribed units. The R package transcriptR combines RNA-seq data with ChIP-seq data of histone modifications that mark active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to overcome this challenge. The advantage of this approach over the use of, for example, gene annotations is that this approach is data driven and therefore able to deal also with novel and case specific events. Furthermore, the integration of ChIP- and RNA-seq data allows the identification all known and novel active transcription start sites within a given sample. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a60b381f153539a74fa743f4f5edac43 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-transcriptr", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:transcriptr + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-transcriptr + path: recipes/bioconductor-transcriptr + version: 1.8.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-chipseq >=1.52.0,<1.53.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-chipseq >=1.56.0,<1.57.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-caret - r-e1071 @@ -39,37 +50,32 @@ requirements: - r-proc - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-chipseq >=1.52.0,<1.53.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-chipseq >=1.56.0,<1.57.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-caret - r-e1071 - r-ggplot2 - r-proc - r-reshape2 + +source: + md5: c2f448fb6e65d2b2993795655d79272f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification' - description: 'The differences in the RNA types being sequenced have an impact on the resulting sequencing profiles. mRNA-seq data is enriched with reads derived from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial broader coverage of both exonic and intronic regions. The presence of intronic reads in GRO-seq type of data makes it possible to use it to computationally identify and quantify all de novo continuous regions of transcription distributed across the genome. This type of data, however, is more challenging to interpret and less common practice compared to mRNA-seq. One of the challenges for primary transcript detection concerns the simultaneous transcription of closely spaced genes, which needs to be properly divided into individually transcribed units. The R package transcriptR combines RNA-seq data with ChIP-seq data of histone modifications that mark active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to overcome this challenge. The advantage of this approach over the use of, for example, gene annotations is that this approach is data driven and therefore able to deal also with novel and case specific events. Furthermore, the integration of ChIP- and RNA-seq data allows the identification all known and novel active transcription start sites within a given sample.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:transcriptr - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-transcriptr - path: recipes/bioconductor-transcriptr - version: 1.8.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-transformgampoi/meta.yaml b/recipes/bioconductor-transformgampoi/meta.yaml index baecaa012883b..ea685f914f155 100644 --- a/recipes/bioconductor-transformgampoi/meta.yaml +++ b/recipes/bioconductor-transformgampoi/meta.yaml @@ -1,56 +1,61 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "transformGamPoi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Variance-stabilizing transformations help with the analysis of heteroskedastic data (i.e., data where the variance is not constant, like count data). This package provide two types of variance stabilizing transformations: (1) methods based on the delta method (e.g., ''acosh'', ''log(x+1)''), (2) model residual based (Pearson and randomized quantile residuals).' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Variance Stabilizing Transformation for Gamma-Poisson Models -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ec9683fa0efb74c2fae2e8721f265f0b build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-transformgampoi", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, TENxPBMCData, scran, knitr, rmarkdown, BiocStyle requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-glmgampoi >=1.14.0,<1.15.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-glmgampoi >=1.18.0,<1.19.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-rcpp - libblas - liblapack run: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-glmgampoi >=1.14.0,<1.15.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-glmgampoi >=1.18.0,<1.19.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 5186c6b39f3d58d7a86be0807a59ce4e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Variance Stabilizing Transformation for Gamma-Poisson Models' - description: 'Variance-stabilizing transformations help with the analysis of heteroskedastic data (i.e., data where the variance is not constant, like count data). This package provide two types of variance stabilizing transformations: (1) methods based on the delta method (e.g., ''acosh'', ''log(x+1)''), (2) model residual based (Pearson and randomized quantile residuals).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-transite/meta.yaml b/recipes/bioconductor-transite/meta.yaml index a5da73a5f57c1..c2f574988d00a 100644 --- a/recipes/bioconductor-transite/meta.yaml +++ b/recipes/bioconductor-transite/meta.yaml @@ -1,63 +1,66 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "transite" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: transite is a computational method that allows comprehensive analysis of the regulatory role of RNA-binding proteins in various cellular processes by leveraging preexisting gene expression data and current knowledge of binding preferences of RNA-binding proteins. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: RNA-binding protein motif analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 14ac71ed8ae01023f28aaed2d93f83b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-transite", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) # SystemRequirements: C++11 requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - - 'r-dplyr >=0.7.6' - - 'r-ggplot2 >=3.0.0' - - 'r-ggseqlogo >=0.1' - - 'r-gridextra >=2.3' - - 'r-rcpp >=1.0.4.8' - - 'r-scales >=1.0.0' - - 'r-tfmpvalue >=0.0.8' + - r-dplyr >=0.7.6 + - r-ggplot2 >=3.0.0 + - r-gridextra >=2.3 + - r-rcpp >=1.0.4.8 + - r-scales >=1.0.0 + - r-tfmpvalue >=0.0.8 - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - - 'r-dplyr >=0.7.6' - - 'r-ggplot2 >=3.0.0' - - 'r-ggseqlogo >=0.1' - - 'r-gridextra >=2.3' - - 'r-rcpp >=1.0.4.8' - - 'r-scales >=1.0.0' - - 'r-tfmpvalue >=0.0.8' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-dplyr >=0.7.6 + - r-ggplot2 >=3.0.0 + - r-gridextra >=2.3 + - r-rcpp >=1.0.4.8 + - r-scales >=1.0.0 + - r-tfmpvalue >=0.0.8 + +source: + md5: bf4806708f88dd36f55e12337f207d90 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'RNA-binding protein motif analysis' - description: 'transite is a computational method that allows comprehensive analysis of the regulatory role of RNA-binding proteins in various cellular processes by leveraging preexisting gene expression data and current knowledge of binding preferences of RNA-binding proteins.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-translatome/meta.yaml b/recipes/bioconductor-translatome/meta.yaml index 500e767a03429..eb94b6d625b57 100644 --- a/recipes/bioconductor-translatome/meta.yaml +++ b/recipes/bioconductor-translatome/meta.yaml @@ -1,60 +1,65 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "tRanslatome" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions (treated vs. untreated, diseased vs. normal, mutant vs. wild-type) among different levels of gene expression (transcriptome ,translatome, proteome), using several statistical methods: Rank Product, Translational Efficiency, t-test, Limma, ANOTA, DESeq, edgeR. Possibility to plot the results with scatterplots, histograms, MA plots, standard deviation (SD) plots, coefficient of variation (CV) plots. Detection of significantly enriched post-transcriptional regulatory factors (RBPs, miRNAs, etc) and Gene Ontology terms in the lists of DEGs previously identified for the two expression levels. Comparison of GO terms enriched only in one of the levels or in both. Calculation of the semantic similarity score between the lists of enriched GO terms coming from the two expression levels. Visual examination and comparison of the enriched terms with heatmaps, radar plots and barplots.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Comparison between multiple levels of gene expression -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6dabe57675cc4250a3b38f9d309a6816 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-translatome", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-anota >=1.50.0,<1.51.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - - 'bioconductor-heatplus >=3.10.0,<3.11.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rankprod >=3.28.0,<3.29.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-anota >=1.54.0,<1.55.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-gosemsim >=2.32.0,<2.33.0 + - bioconductor-heatplus >=3.14.0,<3.15.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rankprod >=3.32.0,<3.33.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-base - r-gplots - r-plotrix run: - - 'bioconductor-anota >=1.50.0,<1.51.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-gosemsim >=2.28.0,<2.29.0' - - 'bioconductor-heatplus >=3.10.0,<3.11.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rankprod >=3.28.0,<3.29.0' - - 'bioconductor-topgo >=2.54.0,<2.55.0' + - bioconductor-anota >=1.54.0,<1.55.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-gosemsim >=2.32.0,<2.33.0 + - bioconductor-heatplus >=3.14.0,<3.15.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rankprod >=3.32.0,<3.33.0 + - bioconductor-topgo >=2.58.0,<2.59.0 - r-base - r-gplots - r-plotrix + +source: + md5: 74c6e18af8084fe233af48116b8ce0d5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Comparison between multiple levels of gene expression' - description: 'Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions (treated vs. untreated, diseased vs. normal, mutant vs. wild-type) among different levels of gene expression (transcriptome ,translatome, proteome), using several statistical methods: Rank Product, Translational Efficiency, t-test, Limma, ANOTA, DESeq, edgeR. Possibility to plot the results with scatterplots, histograms, MA plots, standard deviation (SD) plots, coefficient of variation (CV) plots. Detection of significantly enriched post-transcriptional regulatory factors (RBPs, miRNAs, etc) and Gene Ontology terms in the lists of DEGs previously identified for the two expression levels. Comparison of GO terms enriched only in one of the levels or in both. Calculation of the semantic similarity score between the lists of enriched GO terms coming from the two expression levels. Visual examination and comparison of the enriched terms with heatmaps, radar plots and barplots.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-transmogr/build.sh b/recipes/bioconductor-transmogr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-transmogr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-transmogr/meta.yaml b/recipes/bioconductor-transmogr/meta.yaml new file mode 100644 index 0000000000000..11c934d8537ca --- /dev/null +++ b/recipes/bioconductor-transmogr/meta.yaml @@ -0,0 +1,74 @@ +{% set version = "1.2.0" %} +{% set name = "transmogR" %} +{% set bioc = "3.20" %} + +about: + description: transmogR provides the tools needed to crate a new reference genome or reference transcriptome, using a set of variants. Variants can be any combination of SNPs, Insertions and Deletions. The intended use-case is to enable creation of variant-modified reference transcriptomes for incorporation into transcriptomic pseudo-alignment workflows, such as salmon. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Modify a set of reference sequences using a set of variants + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-transmogr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, ComplexUpset, extraChIPs, InteractionSet, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0) +requirements: + host: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - r-base + - r-dplyr + - r-ggplot2 >=3.5.0 + - r-jsonlite + - r-matrixstats + - r-rlang + - r-scales + - r-vroom + run: + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - r-base + - r-dplyr + - r-ggplot2 >=3.5.0 + - r-jsonlite + - r-matrixstats + - r-rlang + - r-scales + - r-vroom + +source: + md5: 2d6335a477d4abb86dbea222cf38fe74 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-transomics2cytoscape/meta.yaml b/recipes/bioconductor-transomics2cytoscape/meta.yaml index 656868a7687e9..72d5a07e7d5b2 100644 --- a/recipes/bioconductor-transomics2cytoscape/meta.yaml +++ b/recipes/bioconductor-transomics2cytoscape/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "transomics2cytoscape" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: transomics2cytoscape generates a file for 3D transomics visualization by providing input that specifies the IDs of multiple KEGG pathway layers, their corresponding Z-axis heights, and an input that represents the edges between the pathway layers. The edges are used, for example, to describe the relationships between kinase on a pathway and enzyme on another pathway. This package automates creation of a transomics network as shown in the figure in Yugi.2014 (https://doi.org/10.1016/j.celrep.2014.07.021) using Cytoscape automation (https://doi.org/10.1186/s13059-019-1758-4). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: A tool set for 3D Trans-Omic network visualization with Cytoscape -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 17325dd51ab6dfcc10dff97e98be6e91 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-transomics2cytoscape", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, roxygen2, knitr, BiocStyle, rmarkdown # SystemRequirements: Cytoscape >= 3.10.0 requirements: host: - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 - r-base - r-dplyr - r-pbapply - r-purrr - r-tibble run: - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-rcy3 >=2.22.0,<2.23.0' + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-rcy3 >=2.26.0,<2.27.0 - r-base - r-dplyr - r-pbapply - r-purrr - r-tibble + +source: + md5: cb6bf8cc64f438a03e2058a3082437ee + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A tool set for 3D Trans-Omic network visualization with Cytoscape' - description: 'transomics2cytoscape generates a file for 3D transomics visualization by providing input that specifies the IDs of multiple KEGG pathway layers, their corresponding Z-axis heights, and an input that represents the edges between the pathway layers. The edges are used, for example, to describe the relationships between kinase on a pathway and enzyme on another pathway. This package automates creation of a transomics network as shown in the figure in Yugi.2014 (https://doi.org/10.1016/j.celrep.2014.07.021) using Cytoscape automation (https://doi.org/10.1186/s13059-019-1758-4).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-traser/meta.yaml b/recipes/bioconductor-traser/meta.yaml index cc53d2c42bb9d..cb98951919fcf 100644 --- a/recipes/bioconductor-traser/meta.yaml +++ b/recipes/bioconductor-traser/meta.yaml @@ -1,45 +1,22 @@ -{% set version = "1.32.0" %} +{% set version = "1.36.0" %} {% set name = "traseR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: traseR performs GWAS trait-associated SNP enrichment analyses in genomic intervals using different hypothesis testing approaches, also provides various functionalities to explore and visualize the results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: GWAS trait-associated SNP enrichment analyses in genomic intervals -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2af018d9562b672f6701de644617856b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-traser", max_pin="x.x") }}' - noarch: generic -# Suggests: BiocStyle,RUnit, BiocGenerics -requirements: - host: - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - r-base - run: - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL - summary: 'GWAS trait-associated SNP enrichment analyses in genomic intervals' - description: 'traseR performs GWAS trait-associated SNP enrichment analyses in genomic intervals using different hypothesis testing approaches, also provides various functionalities to explore and visualize the results.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:traser @@ -49,3 +26,32 @@ extra: path: recipes/bioconductor-traser version: 1.10.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle,RUnit, BiocGenerics +requirements: + host: + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - r-base + run: + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - r-base + +source: + md5: d2588680c4fd2ec7dc9c8095ed3fa139 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-treeandleaf/meta.yaml b/recipes/bioconductor-treeandleaf/meta.yaml index f5ae24bf9b602..bd2b294d557d8 100644 --- a/recipes/bioconductor-treeandleaf/meta.yaml +++ b/recipes/bioconductor-treeandleaf/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "TreeAndLeaf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 066beb0c7f15d3b6a853bcb68c682f73 +about: + description: The TreeAndLeaf package combines unrooted and force-directed graph algorithms in order to layout binary trees, aiming to represent multiple layers of information onto dendrogram leaves. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Displaying binary trees with focus on dendrogram leaves build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-treeandleaf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr, geneplast, ggtree, ggplot2, dplyr, dendextend, RColorBrewer requirements: host: - - 'bioconductor-reder >=2.6.0,<2.7.0' + - bioconductor-reder >=3.2.0,<3.3.0 - r-ape - r-base - r-igraph run: - - 'bioconductor-reder >=2.6.0,<2.7.0' + - bioconductor-reder >=3.2.0,<3.3.0 - r-ape - r-base - r-igraph +source: + md5: 5c6bb392e15eafc4ec4c3fab3cd9d85b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Displaying binary trees with focus on dendrogram leaves' - description: 'The TreeAndLeaf package combines unrooted and force-directed graph algorithms in order to layout binary trees, aiming to represent multiple layers of information onto dendrogram leaves.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-treeclimbr/build.sh b/recipes/bioconductor-treeclimbr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-treeclimbr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-treeclimbr/meta.yaml b/recipes/bioconductor-treeclimbr/meta.yaml new file mode 100644 index 0000000000000..116a14ddec201 --- /dev/null +++ b/recipes/bioconductor-treeclimbr/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.2.0" %} +{% set name = "treeclimbR" %} +{% set bioc = "3.20" %} + +about: + description: The arrangement of hypotheses in a hierarchical structure appears in many research fields and often indicates different resolutions at which data can be viewed. This raises the question of which resolution level the signal should best be interpreted on. treeclimbR provides a flexible method to select optimal resolution levels (potentially different levels in different parts of the tree), rather than cutting the tree at an arbitrary level. treeclimbR uses a tuning parameter to generate candidate resolutions and from these selects the optimal one. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: An algorithm to find optimal signal levels in a tree + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-treeclimbr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, scales, testthat (>= 3.0.0), BiocStyle +requirements: + host: + - bioconductor-diffcyt >=1.26.0,<1.27.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 + - r-ape + - r-base + - r-dirmult + - r-dplyr + - r-ggnewscale + - r-ggplot2 >=3.4.0 + - r-rlang + - r-tibble + - r-tidyr + - r-viridis + run: + - bioconductor-diffcyt >=1.26.0,<1.27.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treesummarizedexperiment >=2.14.0,<2.15.0 + - r-ape + - r-base + - r-dirmult + - r-dplyr + - r-ggnewscale + - r-ggplot2 >=3.4.0 + - r-rlang + - r-tibble + - r-tidyr + - r-viridis + +source: + md5: 45a0a13d84ae8f136cc00d4a565015f1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-treeio/meta.yaml b/recipes/bioconductor-treeio/meta.yaml index f7107d562170d..4b9ef385056c4 100644 --- a/recipes/bioconductor-treeio/meta.yaml +++ b/recipes/bioconductor-treeio/meta.yaml @@ -1,25 +1,32 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "treeio" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: '''treeio'' is an R package to make it easier to import and store phylogenetic tree with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Classes and Functions for Phylogenetic Tree Input and Output -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 583758f88bf0d8efa0749407f4183567 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-treeio", max_pin="x.x") }}' - noarch: generic -# Suggests: Biostrings, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, testthat, tidyr, vroom, xml2, yaml, purrr, cli + +extra: + parent_recipe: + name: bioconductor-treeio + path: recipes/bioconductor-treeio + version: 1.4.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml requirements: host: - r-ape @@ -29,7 +36,8 @@ requirements: - r-magrittr - r-rlang - r-tibble - - 'r-tidytree >=0.4.5' + - r-tidytree >=0.4.5 + - r-yulab.utils >=0.1.6 run: - r-ape - r-base @@ -38,18 +46,18 @@ requirements: - r-magrittr - r-rlang - r-tibble - - 'r-tidytree >=0.4.5' + - r-tidytree >=0.4.5 + - r-yulab.utils >=0.1.6 + +source: + md5: ccf737f20029fdf856c800fc831686ba + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Classes and Functions for Phylogenetic Tree Input and Output' - description: '''treeio'' is an R package to make it easier to import and store phylogenetic tree with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.' -extra: - parent_recipe: - name: bioconductor-treeio - path: recipes/bioconductor-treeio - version: 1.4.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-treekor/meta.yaml b/recipes/bioconductor-treekor/meta.yaml index 4eb3c5f1947e7..5692c39ffa4a4 100644 --- a/recipes/bioconductor-treekor/meta.yaml +++ b/recipes/bioconductor-treekor/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "treekoR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'treekoR is a novel framework that aims to utilise the hierarchical nature of single cell cytometry data to find robust and interpretable associations between cell subsets and patient clinical end points. These associations are aimed to recapitulate the nested proportions prevalent in workflows inovlving manual gating, which are often overlooked in workflows using automatic clustering to identify cell populations. We developed treekoR to: Derive a hierarchical tree structure of cell clusters; quantify a cell types as a proportion relative to all cells in a sample (%total), and, as the proportion relative to a parent population (%parent); perform significance testing using the calculated proportions; and provide an interactive html visualisation to help highlight key results.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c1b9ce26aa6252f5cb1fe9cd07c3245f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-treekor", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, CATALYST, testthat (>= 3.0.0) requirements: host: - - 'bioconductor-diffcyt >=1.22.0,<1.23.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-hopach >=2.62.0,<2.63.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-diffcyt >=1.26.0,<1.27.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-hopach >=2.66.0,<2.67.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-ape - r-base - r-data.table @@ -38,11 +40,11 @@ requirements: - r-patchwork - r-tidyr run: - - 'bioconductor-diffcyt >=1.22.0,<1.23.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-ggtree >=3.10.0,<3.11.0' - - 'bioconductor-hopach >=2.62.0,<2.63.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' + - bioconductor-diffcyt >=1.26.0,<1.27.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-ggtree >=3.14.0,<3.15.0 + - bioconductor-hopach >=2.66.0,<2.67.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 - r-ape - r-base - r-data.table @@ -53,13 +55,16 @@ requirements: - r-multcomp - r-patchwork - r-tidyr + +source: + md5: 7f15a7694060c880fe93a8f511ebf0ad + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations' - description: 'treekoR is a novel framework that aims to utilise the hierarchical nature of single cell cytometry data to find robust and interpretable associations between cell subsets and patient clinical end points. These associations are aimed to recapitulate the nested proportions prevalent in workflows inovlving manual gating, which are often overlooked in workflows using automatic clustering to identify cell populations. We developed treekoR to: Derive a hierarchical tree structure of cell clusters; quantify a cell types as a proportion relative to all cells in a sample (%total), and, as the proportion relative to a parent population (%parent); perform significance testing using the calculated proportions; and provide an interactive html visualisation to help highlight key results.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-treesummarizedexperiment/meta.yaml b/recipes/bioconductor-treesummarizedexperiment/meta.yaml index c507405f02a1b..8fe8f86991442 100644 --- a/recipes/bioconductor-treesummarizedexperiment/meta.yaml +++ b/recipes/bioconductor-treesummarizedexperiment/meta.yaml @@ -1,59 +1,64 @@ -{% set version = "2.10.0" %} +{% set version = "2.14.0" %} {% set name = "TreeSummarizedExperiment" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: TreeSummarizedExperiment has extended SingleCellExperiment to include hierarchical information on the rows or columns of the rectangular data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'TreeSummarizedExperiment: a S4 Class for Data with Tree Structures' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 595842345af9cb4136aea17bdfdceb3f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-treesummarizedexperiment", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treeio >=1.26.0,<1.27.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treeio >=1.30.0,<1.31.0 - r-ape - r-base - r-dplyr - r-rlang run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-treeio >=1.26.0,<1.27.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-treeio >=1.30.0,<1.31.0 - r-ape - r-base - r-dplyr - r-rlang + +source: + md5: bd46085b0be9cc8e40959bf6cb91e9e5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'TreeSummarizedExperiment: a S4 Class for Data with Tree Structures' - description: 'TreeSummarizedExperiment has extended SingleCellExperiment to include hierarchical information on the rows or columns of the rectangular data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-treg/meta.yaml b/recipes/bioconductor-treg/meta.yaml index dfeb2c614796a..7163c48dac349 100644 --- a/recipes/bioconductor-treg/meta.yaml +++ b/recipes/bioconductor-treg/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "TREG" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d76ba3f3707e1810e6491d04013d6e7b +about: + description: RNA abundance and cell size parameters could improve RNA-seq deconvolution algorithms to more accurately estimate cell type proportions given the different cell type transcription activity levels. A Total RNA Expression Gene (TREG) can facilitate estimating total RNA content using single molecule fluorescent in situ hybridization (smFISH). We developed a data-driven approach using a measure of expression invariance to find candidate TREGs in postmortem human brain single nucleus RNA-seq. This R package implements the method for identifying candidate TREGs from snRNA-seq data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-treg", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap, sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0), tibble, tidyr, SingleCellExperiment requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-purrr - r-rafalib run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-purrr - r-rafalib +source: + md5: 871bb50be403533bc358bbf9c96e0df4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data' - description: 'RNA abundance and cell size parameters could improve RNA-seq deconvolution algorithms to more accurately estimate cell type proportions given the different cell type transcription activity levels. A Total RNA Expression Gene (TREG) can facilitate estimating total RNA content using single molecule fluorescent in situ hybridization (smFISH). We developed a data-driven approach using a measure of expression invariance to find candidate TREGs in postmortem human brain single nucleus RNA-seq. This R package implements the method for identifying candidate TREGs from snRNA-seq data.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-trendy/meta.yaml b/recipes/bioconductor-trendy/meta.yaml index aab3bd13ca6aa..024bebc31a01a 100644 --- a/recipes/bioconductor-trendy/meta.yaml +++ b/recipes/bioconductor-trendy/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.24.1" %} +{% set version = "1.28.0" %} {% set name = "Trendy" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Trendy implements segmented (or breakpoint) regression models to estimate breakpoints which represent changes in expression for each feature/gene in high throughput data with ordered conditions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Breakpoint analysis of time-course expression data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 00e5de9c46c116f4adc3caf3708608df build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-trendy", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, devtools requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dt - r-gplots @@ -33,9 +35,9 @@ requirements: - r-shiny - r-shinyfiles run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dt - r-gplots @@ -43,13 +45,16 @@ requirements: - r-segmented - r-shiny - r-shinyfiles + +source: + md5: 1be4ac1ab9b1041edb1d7af06bb1d02d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Breakpoint analysis of time-course expression data' - description: 'Trendy implements segmented (or breakpoint) regression models to estimate breakpoints which represent changes in expression for each feature/gene in high throughput data with ordered conditions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tress/meta.yaml b/recipes/bioconductor-tress/meta.yaml index a3e9ebd429ed9..9085c845a10fe 100644 --- a/recipes/bioconductor-tress/meta.yaml +++ b/recipes/bioconductor-tress/meta.yaml @@ -1,55 +1,60 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "TRESS" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is devoted to analyzing MeRIP-seq data. Current functionalities include 1. detect transcriptome wide m6A methylation regions 2. detect transcriptome wide differential m6A methylation regions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Toolbox for mRNA epigenetics sequencing analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f0a0a2bbb1b989970231d8ac23ecfaaa build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tress", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown,BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-matrix - r-matrixstats run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-matrix - r-matrixstats + +source: + md5: ad975d7de228c509578fe53447f39858 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Toolbox for mRNA epigenetics sequencing analysis' - description: 'This package is devoted to analyzing MeRIP-seq data. Current functionalities include 1. detect transcriptome wide m6A methylation regions 2. detect transcriptome wide differential m6A methylation regions.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tricycle/meta.yaml b/recipes/bioconductor-tricycle/meta.yaml index e1fdcf85c0706..b741cc8c45de3 100644 --- a/recipes/bioconductor-tricycle/meta.yaml +++ b/recipes/bioconductor-tricycle/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "tricycle" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package contains functions to infer and visualize cell cycle process using Single Cell RNASeq data. It exploits the idea of transfer learning, projecting new data to the previous learned biologically interpretable space. We provide a pre-learned cell cycle space, which could be used to infer cell cycle time of human and mouse single cell samples. In addition, we also offer functions to visualize cell cycle time on different embeddings and functions to build new reference. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'tricycle: Transferable Representation and Inference of cell cycle' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6a6a35c0a2cd9f279395e046b98a79f6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tricycle", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats, cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circular - r-dplyr @@ -37,13 +39,13 @@ requirements: - r-rcolorbrewer - r-scattermore run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-circular - r-dplyr @@ -51,13 +53,16 @@ requirements: - r-ggplot2 - r-rcolorbrewer - r-scattermore + +source: + md5: 15ce99cc65cd81d70f2665e9be4d0e1f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'tricycle: Transferable Representation and Inference of cell cycle' - description: 'The package contains functions to infer and visualize cell cycle process using Single Cell RNASeq data. It exploits the idea of transfer learning, projecting new data to the previous learned biologically interpretable space. We provide a pre-learned cell cycle space, which could be used to infer cell cycle time of human and mouse single cell samples. In addition, we also offer functions to visualize cell cycle time on different embeddings and functions to build new reference.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-trigger/meta.yaml b/recipes/bioconductor-trigger/meta.yaml index e17c679057855..47af7e5fab330 100644 --- a/recipes/bioconductor-trigger/meta.yaml +++ b/recipes/bioconductor-trigger/meta.yaml @@ -1,56 +1,62 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "trigger" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'This R package provides tools for the statistical analysis of integrative genomic data that involve some combination of: genotypes, high-dimensional intermediate traits (e.g., gene expression, protein abundance), and higher-order traits (phenotypes). The package includes functions to: (1) construct global linkage maps between genetic markers and gene expression; (2) analyze multiple-locus linkage (epistasis) for gene expression; (3) quantify the proportion of genome-wide variation explained by each locus and identify eQTL hotspots; (4) estimate pair-wise causal gene regulatory probabilities and construct gene regulatory networks; and (5) identify causal genes for a quantitative trait of interest.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Transcriptional Regulatory Inference from Genetics of Gene ExpRession -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d8cb2a76223f510ff08d9dcbf1d6210c build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-trigger", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:trigger + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-trigger + path: recipes/bioconductor-trigger + version: 1.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-corpcor - r-qtl - libblas - liblapack run: - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-sva >=3.50.0,<3.51.0' + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-sva >=3.54.0,<3.55.0 - r-base - r-corpcor - r-qtl - build: - - {{ compiler('c') }} - - make + +source: + md5: 3dc2d7cb59a817fd8e4b495da591cd5b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Transcriptional Regulatory Inference from Genetics of Gene ExpRession' - description: 'This R package provides tools for the statistical analysis of integrative genomic data that involve some combination of: genotypes, high-dimensional intermediate traits (e.g., gene expression, protein abundance), and higher-order traits (phenotypes). The package includes functions to: (1) construct global linkage maps between genetic markers and gene expression; (2) analyze multiple-locus linkage (epistasis) for gene expression; (3) quantify the proportion of genome-wide variation explained by each locus and identify eQTL hotspots; (4) estimate pair-wise causal gene regulatory probabilities and construct gene regulatory networks; and (5) identify causal genes for a quantitative trait of interest.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:trigger - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-trigger - path: recipes/bioconductor-trigger - version: 1.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-trio/meta.yaml b/recipes/bioconductor-trio/meta.yaml index 26c7056d86138..0697cdb2fc661 100644 --- a/recipes/bioconductor-trio/meta.yaml +++ b/recipes/bioconductor-trio/meta.yaml @@ -1,51 +1,57 @@ -{% set version = "3.40.0" %} +{% set version = "3.44.0" %} {% set name = "trio" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2' + summary: Testing of SNPs and SNP Interactions in Case-Parent Trio Studies -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cd87ad1a66fe181df937dd7a8edfda56 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-trio", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:trio + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-trio + path: recipes/bioconductor-trio + version: 3.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation requirements: host: - - 'bioconductor-siggenes >=1.76.0,<1.77.0' + - bioconductor-siggenes >=1.80.0,<1.81.0 - r-base - - 'r-logicreg >=1.6.1' + - r-logicreg >=1.6.1 - r-survival run: - - 'bioconductor-siggenes >=1.76.0,<1.77.0' + - bioconductor-siggenes >=1.80.0,<1.81.0 - r-base - - 'r-logicreg >=1.6.1' + - r-logicreg >=1.6.1 - r-survival + +source: + md5: 83111e31722700dfda35078c2f1e0881 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-2 - summary: 'Testing of SNPs and SNP Interactions in Case-Parent Trio Studies' - description: 'Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2' -extra: - identifiers: - - biotools:trio - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-trio - path: recipes/bioconductor-trio - version: 3.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-triplex/meta.yaml b/recipes/bioconductor-triplex/meta.yaml index 008158d2d995b..9cd90ece3dfb5 100644 --- a/recipes/bioconductor-triplex/meta.yaml +++ b/recipes/bioconductor-triplex/meta.yaml @@ -1,58 +1,64 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "triplex" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many cannonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_2_clause + file LICENSE + license_file: LICENSE + summary: Search and visualize intramolecular triplex-forming sequences in DNA -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: c66a6990486e7a4873b256d08eff9933 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-triplex", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:triplex + parent_recipe: + name: bioconductor-triplex + path: recipes/bioconductor-triplex + version: 1.20.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - libblas - liblapack run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: f79045e31ca1fd2b14b293bc7ee4d348 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'BSD_2_clause + file LICENSE' - summary: 'Search and visualize intramolecular triplex-forming sequences in DNA' - description: 'This package provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many cannonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.' - license_file: LICENSE -extra: - identifiers: - - biotools:triplex - parent_recipe: - name: bioconductor-triplex - path: recipes/bioconductor-triplex - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tripr/meta.yaml b/recipes/bioconductor-tripr/meta.yaml index 727c7544b3cdb..7d17b44e5a17f 100644 --- a/recipes/bioconductor-tripr/meta.yaml +++ b/recipes/bioconductor-tripr/meta.yaml @@ -1,69 +1,76 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "tripr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: TRIP is a software framework that provides analytics services on antigen receptor (B cell receptor immunoglobulin, BcR IG | T cell receptor, TR) gene sequence data. It is a web application written in R Shiny. It takes as input the output files of the IMGT/HighV-Quest tool. Users can select to analyze the data from each of the input samples separately, or the combined data files from all samples and visualize the results accordingly. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: T-cell Receptor/Immunoglobulin Profiler (TRIP) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 6682fcae99b44178612cdf8ebc48d045 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tripr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, shinycssloaders, tidyverse, BiocManager, Biostrings, xtable, rlist, motifStack, knitr, rmarkdown, testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis, pryr requirements: host: - r-base - - 'r-config >=0.3.1' + - r-config >=0.3.1 - r-data.table - r-dplyr - r-dt - - 'r-golem >=0.3.1' + - r-golem >=0.3.1 - r-gridextra - r-plot3d - r-plotly - r-plyr - r-rcolorbrewer - - 'r-shiny >=1.6.0' + - r-shiny >=1.6.0 - r-shinybs - r-shinyfiles - r-shinyjs - r-stringdist - r-stringr + - r-vegan run: - r-base - - 'r-config >=0.3.1' + - r-config >=0.3.1 - r-data.table - r-dplyr - r-dt - - 'r-golem >=0.3.1' + - r-golem >=0.3.1 - r-gridextra - r-plot3d - r-plotly - r-plyr - r-rcolorbrewer - - 'r-shiny >=1.6.0' + - r-shiny >=1.6.0 - r-shinybs - r-shinyfiles - r-shinyjs - r-stringdist - r-stringr + - r-vegan + +source: + md5: 053e834fb2828c7529f0466945850a65 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'T-cell Receptor/Immunoglobulin Profiler (TRIP)' - description: 'TRIP is a software framework that provides analytics services on antigen receptor (B cell receptor immunoglobulin, BcR IG | T cell receptor, TR) gene sequence data. It is a web application written in R Shiny. It takes as input the output files of the IMGT/HighV-Quest tool. Users can select to analyze the data from each of the input samples separately, or the combined data files from all samples and visualize the results accordingly.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-trna/meta.yaml b/recipes/bioconductor-trna/meta.yaml index 1c6f912b7393d..c17f98ec1d914 100644 --- a/recipes/bioconductor-trna/meta.yaml +++ b/recipes/bioconductor-trna/meta.yaml @@ -1,59 +1,64 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "tRNA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The tRNA package allows tRNA sequences and structures to be accessed and used for subsetting. In addition, it provides visualization tools to compare feature parameters of multiple tRNA sets and correlate them to additional data. The tRNA package uses GRanges objects as inputs requiring only few additional column data sets. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Analyzing tRNA sequences and structures -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 52f5648075d6e9b6cb9ca2db65b5509f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-trna", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-modstrings >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-structstrings >=1.18.0,<1.19.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-modstrings >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-structstrings >=1.22.0,<1.23.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-ggplot2 - r-scales - r-stringr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-modstrings >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-structstrings >=1.18.0,<1.19.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-modstrings >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-structstrings >=1.22.0,<1.23.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-ggplot2 - r-scales - r-stringr + +source: + md5: 7661d1f0f9f4fe017b3f01dd093849ba + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Analyzing tRNA sequences and structures' - description: 'The tRNA package allows tRNA sequences and structures to be accessed and used for subsetting. In addition, it provides visualization tools to compare feature parameters of multiple tRNA sets and correlate them to additional data. The tRNA package uses GRanges objects as inputs requiring only few additional column data sets.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-trnadbimport/meta.yaml b/recipes/bioconductor-trnadbimport/meta.yaml index 4306e7ec1e88a..81538f69a87dd 100644 --- a/recipes/bioconductor-trnadbimport/meta.yaml +++ b/recipes/bioconductor-trnadbimport/meta.yaml @@ -1,59 +1,62 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "tRNAdbImport" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: tRNAdbImport imports the entries of the tRNAdb and mtRNAdb (http://trna.bioinf.uni-leipzig.de) as GRanges object. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Importing from tRNAdb and mitotRNAdb as GRanges objects -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4610dcee69d8555572652b0193cc5cd3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-trnadbimport", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocGenerics, knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-modstrings >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-structstrings >=1.18.0,<1.19.0' - - 'bioconductor-trna >=1.20.0,<1.21.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-modstrings >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-structstrings >=1.22.0,<1.23.0 + - bioconductor-trna >=1.24.0,<1.25.0 - r-base - - r-httr + - r-httr2 - r-stringr - r-xml2 run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-modstrings >=1.18.0,<1.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-structstrings >=1.18.0,<1.19.0' - - 'bioconductor-trna >=1.20.0,<1.21.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-modstrings >=1.22.0,<1.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-structstrings >=1.22.0,<1.23.0 + - bioconductor-trna >=1.24.0,<1.25.0 - r-base - - r-httr + - r-httr2 - r-stringr - r-xml2 + +source: + md5: 05c490998d3a1d2a552747d44958b6a0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Importing from tRNAdb and mitotRNAdb as GRanges objects' - description: 'tRNAdbImport imports the entries of the tRNAdb and mtRNAdb (http://trna.bioinf.uni-leipzig.de) as GRanges object.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-trnascanimport/meta.yaml b/recipes/bioconductor-trnascanimport/meta.yaml index 87b8afa53958f..846e0f165bfd5 100644 --- a/recipes/bioconductor-trnascanimport/meta.yaml +++ b/recipes/bioconductor-trnascanimport/meta.yaml @@ -1,63 +1,68 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "tRNAscanImport" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package imports the result of tRNAscan-SE as a GRanges object. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Importing a tRNAscan-SE result file as GRanges object -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 49f872c7de9b6cba139c7758330efa8c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-trnascanimport", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2, BSgenome.Scerevisiae.UCSC.sacCer3 requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-structstrings >=1.18.0,<1.19.0' - - 'bioconductor-trna >=1.20.0,<1.21.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-structstrings >=1.22.0,<1.23.0 + - bioconductor-trna >=1.24.0,<1.25.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-stringr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-structstrings >=1.18.0,<1.19.0' - - 'bioconductor-trna >=1.20.0,<1.21.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-structstrings >=1.22.0,<1.23.0 + - bioconductor-trna >=1.24.0,<1.25.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-stringr + +source: + md5: 0fd1ac0528a87f31893b2436bb053d05 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Importing a tRNAscan-SE result file as GRanges object' - description: 'The package imports the result of tRNAscan-SE as a GRanges object.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tronco/meta.yaml b/recipes/bioconductor-tronco/meta.yaml index 58d3d0dadd395..dee025cc8c8e7 100644 --- a/recipes/bioconductor-tronco/meta.yaml +++ b/recipes/bioconductor-tronco/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "2.34.0" %} +{% set version = "2.38.0" %} {% set name = "TRONCO" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The TRONCO (TRanslational ONCOlogy) R package collects algorithms to infer progression models via the approach of Suppes-Bayes Causal Network, both from an ensemble of tumors (cross-sectional samples) and within an individual patient (multi-region or single-cell samples). The package provides parallel implementation of algorithms that process binary matrices where each row represents a tumor sample and each column a single-nucleotide or a structural variant driving the progression; a 0/1 value models the absence/presence of that alteration in the sample. The tool can import data from plain, MAF or GISTIC format files, and can fetch it from the cBioPortal for cancer genomics. Functions for data manipulation and visualization are provided, as well as functions to import/export such data to other bioinformatics tools for, e.g, clustering or detection of mutually exclusive alterations. Inferred models can be visualized and tested for their confidence via bootstrap and cross-validation. TRONCO is used for the implementation of the Pipeline for Cancer Inference (PICNIC). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: TRONCO, an R package for TRanslational ONCOlogy -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e137e734d0e5552bdcaa25ccdd4df08 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tronco", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways, magick requirements: host: - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-bnlearn - r-circlize @@ -38,7 +40,7 @@ requirements: - r-scales - r-xtable run: - - 'bioconductor-rgraphviz >=2.46.0,<2.47.0' + - bioconductor-rgraphviz >=2.50.0,<2.51.0 - r-base - r-bnlearn - r-circlize @@ -53,13 +55,16 @@ requirements: - r-rcolorbrewer - r-scales - r-xtable + +source: + md5: 6c77921cf34dca7158964df2d35b8fd4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'TRONCO, an R package for TRanslational ONCOlogy' - description: 'The TRONCO (TRanslational ONCOlogy) R package collects algorithms to infer progression models via the approach of Suppes-Bayes Causal Network, both from an ensemble of tumors (cross-sectional samples) and within an individual patient (multi-region or single-cell samples). The package provides parallel implementation of algorithms that process binary matrices where each row represents a tumor sample and each column a single-nucleotide or a structural variant driving the progression; a 0/1 value models the absence/presence of that alteration in the sample. The tool can import data from plain, MAF or GISTIC format files, and can fetch it from the cBioPortal for cancer genomics. Functions for data manipulation and visualization are provided, as well as functions to import/export such data to other bioinformatics tools for, e.g, clustering or detection of mutually exclusive alterations. Inferred models can be visualized and tested for their confidence via bootstrap and cross-validation. TRONCO is used for the implementation of the Pipeline for Cancer Inference (PICNIC).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tsar/meta.yaml b/recipes/bioconductor-tsar/meta.yaml index b6aae8910eb01..7e7b54230b2c4 100644 --- a/recipes/bioconductor-tsar/meta.yaml +++ b/recipes/bioconductor-tsar/meta.yaml @@ -1,69 +1,74 @@ -{% set version = "1.0.0" %} +{% set version = "1.4.0" %} {% set name = "TSAR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package automates analysis workflow for Thermal Shift Analysis (TSA) data. Processing, analyzing, and visualizing data through both shiny applications and command lines. Package aims to simplify data analysis and offer front to end workflow, from raw data to multiple trial analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: AGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + summary: Thermal Shift Analysis in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7cc8589151c5b03e247590bbd7dc04dd build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tsar", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat (>= 3.0.0) requirements: host: - r-base - - 'r-dplyr >=1.0.7' - - 'r-ggplot2 >=3.3.5' - - 'r-ggpubr >=0.4.0' - - 'r-jsonlite >=1.8.7' - - 'r-magrittr >=2.0.3' - - 'r-mgcv >=1.8.38' - - 'r-minpack.lm >=1.2.3' - - 'r-openxlsx >=4.2.5.2' - - 'r-plotly >=4.10.2' - - 'r-readxl >=1.4.0' - - 'r-rhandsontable >=0.3.8' - - 'r-shiny >=1.7.4.1' - - 'r-shinyjs >=2.1.0' - - 'r-shinywidgets >=0.7.6' - - 'r-stringr >=1.4.0' - - 'r-tidyr >=1.1.4' + - r-dplyr >=1.0.7 + - r-ggplot2 >=3.3.5 + - r-ggpubr >=0.4.0 + - r-jsonlite >=1.8.7 + - r-magrittr >=2.0.3 + - r-mgcv >=1.8.38 + - r-minpack.lm >=1.2.3 + - r-openxlsx >=4.2.5.2 + - r-plotly >=4.10.2 + - r-readxl >=1.4.0 + - r-rhandsontable >=0.3.8 + - r-shiny >=1.7.4.1 + - r-shinyjs >=2.1.0 + - r-shinywidgets >=0.7.6 + - r-stringr >=1.4.0 + - r-tidyr >=1.1.4 run: - r-base - - 'r-dplyr >=1.0.7' - - 'r-ggplot2 >=3.3.5' - - 'r-ggpubr >=0.4.0' - - 'r-jsonlite >=1.8.7' - - 'r-magrittr >=2.0.3' - - 'r-mgcv >=1.8.38' - - 'r-minpack.lm >=1.2.3' - - 'r-openxlsx >=4.2.5.2' - - 'r-plotly >=4.10.2' - - 'r-readxl >=1.4.0' - - 'r-rhandsontable >=0.3.8' - - 'r-shiny >=1.7.4.1' - - 'r-shinyjs >=2.1.0' - - 'r-shinywidgets >=0.7.6' - - 'r-stringr >=1.4.0' - - 'r-tidyr >=1.1.4' + - r-dplyr >=1.0.7 + - r-ggplot2 >=3.3.5 + - r-ggpubr >=0.4.0 + - r-jsonlite >=1.8.7 + - r-magrittr >=2.0.3 + - r-mgcv >=1.8.38 + - r-minpack.lm >=1.2.3 + - r-openxlsx >=4.2.5.2 + - r-plotly >=4.10.2 + - r-readxl >=1.4.0 + - r-rhandsontable >=0.3.8 + - r-shiny >=1.7.4.1 + - r-shinyjs >=2.1.0 + - r-shinywidgets >=0.7.6 + - r-stringr >=1.4.0 + - r-tidyr >=1.1.4 + +source: + md5: 841c30e0dfaafc18f334079e604b927b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3 - summary: 'Thermal Shift Analysis in R' - description: 'This package automates analysis workflow for Thermal Shift Analysis (TSAS) data. Processing, analyzing, and visualizing data through both shiny applications and command lines. Package aims to simplify data analysis and offer front to end workflow, from raw data to multiple trial analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tscan/meta.yaml b/recipes/bioconductor-tscan/meta.yaml index 2ea54e7791685..3b820a6e458c5 100644 --- a/recipes/bioconductor-tscan/meta.yaml +++ b/recipes/bioconductor-tscan/meta.yaml @@ -1,32 +1,44 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "TSCAN" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides methods to perform trajectory analysis based on a minimum spanning tree constructed from cluster centroids. Computes pseudotemporal cell orderings by mapping cells in each cluster (or new cells) to the closest edge in the tree. Uses linear modelling to identify differentially expressed genes along each path through the tree. Several plotting and interactive visualization functions are also implemented. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL(>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Tools for Single-Cell Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 018be0d6197c80dbf2ce7832a3f9c49d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tscan", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:tscan + - doi:10.1093/nar/gkw430 + parent_recipe: + name: bioconductor-tscan + path: recipes/bioconductor-tscan + version: 1.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor requirements: host: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-trajectoryutils >=1.14.0,<1.15.0 - r-base - r-combinat - r-fastica @@ -39,11 +51,12 @@ requirements: - r-plyr - r-shiny run: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-trajectoryutils >=1.10.0,<1.11.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-sparsearray >=1.6.0,<1.7.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-trajectoryutils >=1.14.0,<1.15.0 - r-base - r-combinat - r-fastica @@ -55,21 +68,16 @@ requirements: - r-mgcv - r-plyr - r-shiny + +source: + md5: 83c3b6fdbf6d1bb0c5d656fe23e6a049 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL(>=2) - summary: 'Tools for Single-Cell Analysis' - description: 'Provides methods to perform trajectory analysis based on a minimum spanning tree constructed from cluster centroids. Computes pseudotemporal cell orderings by mapping cells in each cluster (or new cells) to the closest edge in the tree. Uses linear modelling to identify differentially expressed genes along each path through the tree. Several plotting and interactive visualization functions are also implemented.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:tscan - - doi:10.1093/nar/gkw430 - parent_recipe: - name: bioconductor-tscan - path: recipes/bioconductor-tscan - version: 1.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ttgsea/meta.yaml b/recipes/bioconductor-ttgsea/meta.yaml index 9266a10fd6ed4..aa1709563d334 100644 --- a/recipes/bioconductor-ttgsea/meta.yaml +++ b/recipes/bioconductor-ttgsea/meta.yaml @@ -1,24 +1,25 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "ttgsea" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Functional enrichment analysis methods such as gene set enrichment analysis (GSEA) have been widely used for analyzing gene expression data. GSEA is a powerful method to infer results of gene expression data at a level of gene sets by calculating enrichment scores for predefined sets of genes. GSEA depends on the availability and accuracy of gene sets. There are overlaps between terms of gene sets or categories because multiple terms may exist for a single biological process, and it can thus lead to redundancy within enriched terms. In other words, the sets of related terms are overlapping. Using deep learning, this pakage is aimed to predict enrichment scores for unique tokens or words from text in names of gene sets to resolve this overlapping set issue. Furthermore, we can coin a new term by combining tokens and find its enrichment score by predicting such a combined tokens. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Tokenizing Text of Gene Set Enrichment Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0b38c9baea88905217b9ed667c80c26f build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ttgsea", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: fgsea, knitr, testthat, reticulate, rmarkdown requirements: host: @@ -43,12 +44,16 @@ requirements: - r-textstem - r-tm - r-tokenizers + +source: + md5: 71966a32afcb3d6e8c8d7c27faaedb39 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Tokenizing Text of Gene Set Enrichment Analysis' - description: 'Functional enrichment analysis methods such as gene set enrichment analysis (GSEA) have been widely used for analyzing gene expression data. GSEA is a powerful method to infer results of gene expression data at a level of gene sets by calculating enrichment scores for predefined sets of genes. GSEA depends on the availability and accuracy of gene sets. There are overlaps between terms of gene sets or categories because multiple terms may exist for a single biological process, and it can thus lead to redundancy within enriched terms. In other words, the sets of related terms are overlapping. Using deep learning, this pakage is aimed to predict enrichment scores for unique tokens or words from text in names of gene sets to resolve this overlapping set issue. Furthermore, we can coin a new term by combining tokens and find its enrichment score by predicting such a combined tokens.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ttmap/meta.yaml b/recipes/bioconductor-ttmap/meta.yaml index bcb28bc41745f..6220ec69e5dd2 100644 --- a/recipes/bioconductor-ttmap/meta.yaml +++ b/recipes/bioconductor-ttmap/meta.yaml @@ -1,55 +1,61 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "TTMap" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: TTMap is a clustering method that groups together samples with the same deviation in comparison to a control group. It is specially useful when the data is small. It is parameter free. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'Two-Tier Mapper: a clustering tool based on topological data analysis' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9fb52b78486eff55cc91ef0f8116633b build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ttmap", max_pin="x.x") }}' - noarch: generic + +extra: + container: + extended-base: yes + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, airway requirements: + build: + - {{ cdt('mesa-libgl-devel') }} # [linux] + - {{ cdt('mesa-dri-drivers') }} # [linux] + - {{ cdt('libselinux') }} # [linux] + - {{ cdt('libxdamage') }} # [linux] + - {{ cdt('libxxf86vm') }} # [linux] + - xorg-libxfixes # [linux] host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-colorramps - r-rgl run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-colorramps - r-rgl - build: - - {{ cdt('mesa-libgl-devel') }} # [linux] - - {{ cdt('mesa-dri-drivers') }} # [linux] - - {{ cdt('libselinux') }} # [linux] - - {{ cdt('libxdamage') }} # [linux] - - {{ cdt('libxxf86vm') }} # [linux] - - xorg-libxfixes # [linux] + +source: + md5: a1e721f30241ac80a7cbb95440a99f5a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - 'LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Two-Tier Mapper: a clustering tool based on topological data analysis' - description: 'TTMap is a clustering method that groups together samples with the same deviation in comparison to a control group. It is specially useful when the data is small. It is parameter free.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - container: - extended-base: true + - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib" $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tuberculosis/meta.yaml b/recipes/bioconductor-tuberculosis/meta.yaml index 019d16095c2ba..d28c68abf8dbe 100644 --- a/recipes/bioconductor-tuberculosis/meta.yaml +++ b/recipes/bioconductor-tuberculosis/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "tuberculosis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The tuberculosis R/Bioconductor package features tuberculosis gene expression data for machine learning. All human samples from GEO that did not come from cell lines, were not taken postmortem, and did not feature recombination have been included. The package has more than 10,000 samples from both microarray and sequencing studies that have been processed from raw data through a hyper-standardized, reproducible pipeline. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Tuberculosis Gene Expression Data for Machine Learning -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 154cd343b8fba727ecf80a671a6a112d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tuberculosis", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, ggplot2, hrbrthemes, knitr, readr, rmarkdown, scater, usethis, utils requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-magrittr @@ -35,10 +36,10 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-dplyr - r-magrittr @@ -48,13 +49,17 @@ requirements: - r-tibble - r-tidyr - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 232d8eebba6c53dead1fd5025f806613 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Tuberculosis Gene Expression Data for Machine Learning' - description: 'The tuberculosis R/Bioconductor package features tuberculosis gene expression data for machine learning. All human samples from GEO that did not come from cell lines, were not taken postmortem, and did not feature recombination have been included. The package has more than 10,000 samples from both microarray and sequencing studies that have been processed from raw data through a hyper-standardized, reproducible pipeline.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tuberculosis/post-link.sh b/recipes/bioconductor-tuberculosis/post-link.sh index 387c3ba762b5d..ae42695c2dd9d 100644 --- a/recipes/bioconductor-tuberculosis/post-link.sh +++ b/recipes/bioconductor-tuberculosis/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tuberculosis-1.8.0" +installBiocDataPackage.sh "tuberculosis-1.12.0" diff --git a/recipes/bioconductor-tumourmethdata/meta.yaml b/recipes/bioconductor-tumourmethdata/meta.yaml index 0258769ad47df..f349abbfe5351 100644 --- a/recipes/bioconductor-tumourmethdata/meta.yaml +++ b/recipes/bioconductor-tumourmethdata/meta.yaml @@ -1,50 +1,55 @@ -{% set version = "1.0.0" %} +{% set version = "1.3.0" %} {% set name = "TumourMethData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: TumourMethData collects tumour methylation data from a variety of different tumour types (and also matching normal samples where available) and produced with different technologies (e.g. WGBS, RRBS and methylation arrays) and provides them as RangedSummarizedExperiments. This facilitates easy extraction of methylation data for regions of interest across different tumour types and studies. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: A Collection of DNA Methylation Datasets for Human Tumour Samples and Matching Normal Samples -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7b4ba6a8a59379a3b7f368e6c26fa0a6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tumourmethdata", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: ggplot2, knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-r.utils run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-hdf5array >=1.30.0,<1.31.0' - - 'bioconductor-rhdf5 >=2.46.0,<2.47.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-rhdf5 >=2.50.0,<2.51.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-r.utils - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 33c0ff42d0fbc47bb824bd29b06c34f2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'A Collection of DNA Methylation Datasets for Human Tumour Samples and Matching Normal Samples' - description: 'TumourMethData collects tumour methylation data from a variety of different tumour types (and also matching normal samples where available) and produced with different technologies (e.g. WGBS, RRBS and methylation arrays) and provides them as RangedSummarizedExperiments. This facilitates easy extraction of methylation data for regions of interest across different tumour types and studies.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tumourmethdata/post-link.sh b/recipes/bioconductor-tumourmethdata/post-link.sh index 8e6c2a8a145a1..25850c624a223 100644 --- a/recipes/bioconductor-tumourmethdata/post-link.sh +++ b/recipes/bioconductor-tumourmethdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tumourmethdata-1.0.0" +installBiocDataPackage.sh "tumourmethdata-1.3.0" diff --git a/recipes/bioconductor-turbonorm/meta.yaml b/recipes/bioconductor-turbonorm/meta.yaml index 0818a2addd0ac..3ff54ced48a44 100644 --- a/recipes/bioconductor-turbonorm/meta.yaml +++ b/recipes/bioconductor-turbonorm/meta.yaml @@ -1,58 +1,64 @@ -{% set version = "1.50.0" %} +{% set version = "1.54.0" %} {% set name = "TurboNorm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A fast scatterplot smoother based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: A fast scatterplot smoother suitable for microarray normalization -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6df6da83bc36e4ce202d91888feaafa7 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-turbonorm", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:turbonorm + parent_recipe: + name: bioconductor-turbonorm + path: recipes/bioconductor-turbonorm + version: 1.28.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, affydata, hgu95av2cdf requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-convert >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-convert >=1.82.0,<1.83.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-marray >=1.84.0,<1.85.0 - r-base - r-lattice - libblas - liblapack run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-convert >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-marray >=1.80.0,<1.81.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-convert >=1.82.0,<1.83.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-marray >=1.84.0,<1.85.0 - r-base - r-lattice - build: - - {{ compiler('c') }} - - make + +source: + md5: 5baa780a371fb0fda681b73cb0ae58ba + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'A fast scatterplot smoother suitable for microarray normalization' - description: 'A fast scatterplot smoother based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:turbonorm - parent_recipe: - name: bioconductor-turbonorm - path: recipes/bioconductor-turbonorm - version: 1.28.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tvtb/meta.yaml b/recipes/bioconductor-tvtb/meta.yaml index 6955abe0f5030..9c9c0ad5291ad 100644 --- a/recipes/bioconductor-tvtb/meta.yaml +++ b/recipes/bioconductor-tvtb/meta.yaml @@ -1,72 +1,75 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "TVTB" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'TVTB: The VCF Tool Box' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 64da00f3c21bf3f9a82dc32e451395a1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tvtb", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT (>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>= 1.12), rmarkdown, testthat, covr, pander requirements: host: - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-ensemblvep >=1.44.0,<1.45.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-ggally - r-ggplot2 - r-reshape2 run: - - 'bioconductor-annotationfilter >=1.26.0,<1.27.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-ensemblvep >=1.44.0,<1.45.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-annotationfilter >=1.30.0,<1.31.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-ggally - r-ggplot2 - r-reshape2 + +source: + md5: 4a894a5b07664da57bec0755d610513d + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'TVTB: The VCF Tool Box' - description: 'The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tweedeseq/meta.yaml b/recipes/bioconductor-tweedeseq/meta.yaml index 2005ab0221e0d..fa44ab116a5ae 100644 --- a/recipes/bioconductor-tweedeseq/meta.yaml +++ b/recipes/bioconductor-tweedeseq/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "tweeDEseq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Differential expression analysis of RNA-seq using the Poisson-Tweedie (PT) family of distributions. PT distributions are described by a mean, a dispersion and a shape parameter and include Poisson and NB distributions, among others, as particular cases. An important feature of this family is that, while the Negative Binomial (NB) distribution only allows a quadratic mean-variance relationship, the PT distributions generalizes this relationship to any orde. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: RNA-seq data analysis using the Poisson-Tweedie family of distributions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1a919ba1b3c5709068bc126336b77826 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tweedeseq", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:tweedeseq + parent_recipe: + name: bioconductor-tweedeseq + path: recipes/bioconductor-tweedeseq + version: 1.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: tweeDEseqCountData, xtable requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-cqn >=1.48.0,<1.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-cqn >=1.52.0,<1.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-mass - - 'r-rcpp >=1.0.10' + - r-rcpp >=1.0.10 - libblas - liblapack run: - - 'bioconductor-cqn >=1.48.0,<1.49.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-cqn >=1.52.0,<1.53.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-mass - - 'r-rcpp >=1.0.10' - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + - r-rcpp >=1.0.10 + +source: + md5: ff5a78e57b13d4e38bdf925b89a7b238 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'RNA-seq data analysis using the Poisson-Tweedie family of distributions' - description: 'Differential expression analysis of RNA-seq using the Poisson-Tweedie (PT) family of distributions. PT distributions are described by a mean, a dispersion and a shape parameter and include Poisson and NB distributions, among others, as particular cases. An important feature of this family is that, while the Negative Binomial (NB) distribution only allows a quadratic mean-variance relationship, the PT distributions generalizes this relationship to any orde.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:tweedeseq - parent_recipe: - name: bioconductor-tweedeseq - path: recipes/bioconductor-tweedeseq - version: 1.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tweedeseqcountdata/build_failure.linux-64.yaml b/recipes/bioconductor-tweedeseqcountdata/build_failure.linux-64.yaml index 3e36ab5993f41..1541581dfcc88 100644 --- a/recipes/bioconductor-tweedeseqcountdata/build_failure.linux-64.yaml +++ b/recipes/bioconductor-tweedeseqcountdata/build_failure.linux-64.yaml @@ -1,44 +1,104 @@ -recipe_sha: e9ea10dec9b205dbce587c85515bdb5db1c152a2def749ed83d0b124ea0cec27 # The commit at which this recipe failed to build. +recipe_sha: ee498d349f43dcbd4d62652c198bdfcfecbc32acb2aeaab36f89e2786c880675 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -reason: |- - WARNING:conda_build.build:No files or script found for output bioconductor-tweedeseqcountdata -category: |- - source download error -log: |- - 08:56:10 BIOCONDA INFO (OUT) Downloading https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tweeDEseqCountData_1.40.0.tar.gz - 08:56:10 BIOCONDA INFO (OUT) INFO:conda_build.source:Downloading https://bioconductor.org/packages/3.18/data/experiment/src/contrib/tweeDEseqCountData_1.40.0.tar.gz - 08:56:11 BIOCONDA INFO (OUT) Success - 08:56:11 BIOCONDA INFO (OUT) INFO:conda_build.source:Success - 08:56:11 BIOCONDA INFO (OUT) Extracting download - 08:56:11 BIOCONDA INFO (OUT) source tree in: /opt/conda/conda-bld/bioconductor-tweedeseqcountdata_1702025598887/work - 08:56:11 BIOCONDA INFO (OUT) Packaging bioconductor-tweedeseqcountdata - 08:56:11 BIOCONDA INFO (OUT) INFO:conda_build.build:Packaging bioconductor-tweedeseqcountdata - 08:56:11 BIOCONDA INFO (OUT) Packaging bioconductor-tweedeseqcountdata-1.40.0-r43hdfd78af_0 - 08:56:11 BIOCONDA INFO (OUT) INFO:conda_build.build:Packaging bioconductor-tweedeseqcountdata-1.40.0-r43hdfd78af_0 - 08:56:11 BIOCONDA INFO (OUT) No files or script found for output bioconductor-tweedeseqcountdata - 08:56:11 BIOCONDA INFO (OUT) WARNING:conda_build.build:No files or script found for output bioconductor-tweedeseqcountdata - 08:56:12 BIOCONDA INFO (OUT) number of files: 2 - 08:56:12 BIOCONDA INFO (OUT) Fixing permissions - 08:56:12 BIOCONDA INFO (OUT) Traceback (most recent call last): - 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/bin/conda-mambabuild", line 10, in - 08:56:12 BIOCONDA INFO (OUT) sys.exit(main()) - 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - 08:56:12 BIOCONDA INFO (OUT) call_conda_build(action, config) - 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - 08:56:12 BIOCONDA INFO (OUT) result = api.build( - 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - 08:56:12 BIOCONDA INFO (OUT) return build_tree( - 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - 08:56:12 BIOCONDA INFO (OUT) packages_from_this = build(metadata, stats, - 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2358, in build - 08:56:12 BIOCONDA INFO (OUT) newly_built_packages = bundlers[pkg_type](output_d, m, env, stats) - 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 1672, in bundle_conda - 08:56:12 BIOCONDA INFO (OUT) output['checksums'] = create_info_files(metadata, replacements, files, prefix=metadata.config.host_prefix) - 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 1272, in create_info_files - 08:56:12 BIOCONDA INFO (OUT) copy_license(m) - 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 762, in copy_license - 08:56:12 BIOCONDA INFO (OUT) generic_copy(m, "license", "license_file") - 08:56:12 BIOCONDA INFO (OUT) File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 800, in generic_copy - 08:56:12 BIOCONDA INFO (OUT) raise ValueError( - 08:56:12 BIOCONDA INFO (OUT) ValueError: License file given in about/license_file (/opt/recipe/LICENSE) does not exist in source root dir or in recipe root dir (with meta.yaml) - .08:56:20 BIOCONDA ERROR COMMAND FAILED (exited with 1): docker run -t --net host --rm -v /tmp/tmpbp4seh01/build_script.bash:/opt/build_script.bash -v /opt/mambaforge/envs/bioconda/conda-bld/:/opt/host-conda-bld -v /home/runner/work/bioconda-recipes/bioconda-recipes/recipes/bioconductor-tweedeseqcountdata:/opt/recipe -e LANG=C.UTF-8 -e HOST_USER_ID=1001 quay.io/bioconda/bioconda-utils-build-env-cos7:2.11.0 /bin/bash /opt/build_script.bash +log: |2- + - libiconv 1.17 hd590300_2 + - libjpeg-turbo 3.0.0 hd590300_1 + - libpng 1.6.44 hadc24fc_0 + - libsanitizer 14.2.0 h2a3dede_1 + - libssh2 1.11.1 hf672d98_0 + - libstdcxx-ng 14.2.0 h4852527_1 + - libuuid 2.38.1 h0b41bf4_0 + - libwebp-base 1.4.0 hd590300_0 + - libxcb 1.17.0 h8a09558_0 + - ncurses 6.5 he02047a_1 + - pixman 0.44.2 h29eaf8c_0 + - sed 4.8 he412f7d_0 + - tk 8.6.13 noxft_h4845f30_101 + - bwidget 1.10.1 ha770c72_0 + - freetype 2.12.1 h267a509_2 + - gcc_impl_linux-64 14.2.0 h6b349bd_1 + - graphite2 1.3.13 h59595ed_1003 + - icu 75.1 he02047a_0 + - lerc 4.0.0 h27087fc_0 + - libedit 3.1.20191231 he28a2e2_2 + - libgfortran-ng 14.2.0 h69a702a_1 + - libnghttp2 1.64.0 h161d5f1_0 + - libopenblas 0.3.28 pthreads_h94d23a6_1 + - pcre2 10.44 hba22ea6_2 + - readline 8.2 h8228510_1 + - tktable 2.10 h8bc8fbc_6 + - xorg-libsm 1.2.5 he73a12e_0 + - xorg-libx11 1.8.10 h4f16b4b_1 + - zstd 1.5.6 ha6fb4c9_0 + - fontconfig 2.15.0 h7e30c49_1 + - gfortran_impl_linux-64 14.2.0 hc73f493_1 + - gxx_impl_linux-64 14.2.0 h2c03514_1 + - krb5 1.21.3 h659f571_0 + - libblas 3.9.0 26_linux64_openblas + - libglib 2.82.2 h2ff4ddf_0 + - libtiff 4.7.0 hd9ff511_3 + - xorg-libxext 1.3.6 hb9d3cd8_0 + - xorg-libxrender 0.9.12 hb9d3cd8_0 + - xorg-libxt 1.3.1 hb9d3cd8_0 + - cairo 1.18.2 h3394656_1 + - libcblas 3.9.0 26_linux64_openblas + - libcurl 8.11.1 h332b0f4_0 + - liblapack 3.9.0 26_linux64_openblas + - curl 8.11.1 h332b0f4_0 + - gsl 2.7 he838d99_0 + - harfbuzz 9.0.0 hda332d3_1 + - pango 1.54.0 h3a902e7_3 + - r-base 4.4.2 hc737e89_2 + - bioconductor-biocgenerics 0.52.0 r44hdfd78af_0 + - bioconductor-biobase 2.66.0 r44h3df3fcb_0 + run: + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-data-packages >=20241103 + - curl + - r-base >=4.4,<4.5.0a0 + - r-base >=4.4,<4.5.0a0 + test: + commands: + - $R -e "library('tweeDEseqCountData')" + about: + description: RNA-seq count data from Pickrell et al. (2010) employed to illustrate + the use of the Poisson-Tweedie family of distributions with the tweeDEseq package. + home: https://bioconductor.org/packages/3.20/data/experiment/html/tweeDEseqCountData.html + license: MIT file LICENSE + license_file: LICENSE + summary: RNA-seq count data employed in the vignette of the tweeDEseq package + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/conda/conda-bld/bioconductor-tweedeseqcountdata_1734490379298/work + Packaging bioconductor-tweedeseqcountdata + Packaging bioconductor-tweedeseqcountdata-1.44.0-r44hdfd78af_0 + WARNING: No files or script found for output bioconductor-tweedeseqcountdata + WARNING: The install/build script(s) for bioconductor-tweedeseqcountdata deleted the following files (from dependencies) from the prefix: + ['lib/gcc/x86_64-conda-linux-gnu/14.2.0/libhwasan.so'] + This will cause the post-link checks to mis-report. Please try not to delete and files (DSOs in particular) from the prefix + number of files: 2 + Fixing permissions + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2765, in build + newly_built_packages = bundlers[pkg_type]( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 1889, in bundle_conda + output["checksums"] = create_info_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 1406, in create_info_files + copy_license(m) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 829, in copy_license + generic_copy(m, "license", "license_file") + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 868, in generic_copy + raise ValueError( + ValueError: License file given in about/license_file (/opt/recipe/LICENSE) does not exist in source root dir or in recipe root dir (with meta.yaml) +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-tweedeseqcountdata/meta.yaml b/recipes/bioconductor-tweedeseqcountdata/meta.yaml index 4cec84b4097ed..080fbe482acc0 100644 --- a/recipes/bioconductor-tweedeseqcountdata/meta.yaml +++ b/recipes/bioconductor-tweedeseqcountdata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "tweeDEseqCountData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d63e819cedf93ffbe115ed518bc9feaf +about: + description: RNA-seq count data from Pickrell et al. (2010) employed to illustrate the use of the Poisson-Tweedie family of distributions with the tweeDEseq package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: RNA-seq count data employed in the vignette of the tweeDEseq package build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tweedeseqcountdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d948402ffc023b37cf2347865a1f1e2e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'RNA-seq count data employed in the vignette of the tweeDEseq package' - description: 'RNA-seq count data from Pickrell et al. (2010) employed to illustrate the use of the Poisson-Tweedie family of distributions with the tweeDEseq package.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tweedeseqcountdata/post-link.sh b/recipes/bioconductor-tweedeseqcountdata/post-link.sh index 5418d98cd3da2..e330caa56db35 100644 --- a/recipes/bioconductor-tweedeseqcountdata/post-link.sh +++ b/recipes/bioconductor-tweedeseqcountdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tweedeseqcountdata-1.40.0" +installBiocDataPackage.sh "tweedeseqcountdata-1.44.0" diff --git a/recipes/bioconductor-twilight/meta.yaml b/recipes/bioconductor-twilight/meta.yaml index 42a74a2994831..db07a37514a89 100644 --- a/recipes/bioconductor-twilight/meta.yaml +++ b/recipes/bioconductor-twilight/meta.yaml @@ -1,51 +1,57 @@ -{% set version = "1.78.0" %} +{% set version = "1.82.0" %} {% set name = "twilight" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'In a typical microarray setting with gene expression data observed under two conditions, the local false discovery rate describes the probability that a gene is not differentially expressed between the two conditions given its corrresponding observed score or p-value level. The resulting curve of p-values versus local false discovery rate offers an insight into the twilight zone between clear differential and clear non-differential gene expression. Package ''twilight'' contains two main functions: Function twilight.pval performs a two-condition test on differences in means for a given input matrix or expression set and computes permutation based p-values. Function twilight performs a stochastic downhill search to estimate local false discovery rates and effect size distributions. The package further provides means to filter for permutations that describe the null distribution correctly. Using filtered permutations, the influence of hidden confounders could be diminished.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Estimation of local false discovery rate -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fa6b01126ace9423edfc04757f6392b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-twilight", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:twilight + - doi:10.1093/bioinformatics/bti436 + parent_recipe: + name: bioconductor-twilight + path: recipes/bioconductor-twilight + version: 1.56.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: 75f8082dc238fcb07aa7a6793303681f + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Estimation of local false discovery rate' - description: 'In a typical microarray setting with gene expression data observed under two conditions, the local false discovery rate describes the probability that a gene is not differentially expressed between the two conditions given its corrresponding observed score or p-value level. The resulting curve of p-values versus local false discovery rate offers an insight into the twilight zone between clear differential and clear non-differential gene expression. Package ''twilight'' contains two main functions: Function twilight.pval performs a two-condition test on differences in means for a given input matrix or expression set and computes permutation based p-values. Function twilight performs a stochastic downhill search to estimate local false discovery rates and effect size distributions. The package further provides means to filter for permutations that describe the null distribution correctly. Using filtered permutations, the influence of hidden confounders could be diminished.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:twilight - - doi:10.1093/bioinformatics/bti436 - parent_recipe: - name: bioconductor-twilight - path: recipes/bioconductor-twilight - version: 1.56.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-twoddpcr/meta.yaml b/recipes/bioconductor-twoddpcr/meta.yaml index 1de09201d6a1c..9d9c48120312d 100644 --- a/recipes/bioconductor-twoddpcr/meta.yaml +++ b/recipes/bioconductor-twoddpcr/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "twoddpcr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The twoddpcr package takes Droplet Digital PCR (ddPCR) droplet amplitude data from Bio-Rad's QuantaSoft and can classify the droplets. A summary of the positive/negative droplet counts can be generated, which can then be used to estimate the number of molecules using the Poisson distribution. This is the first open source package that facilitates the automatic classification of general two channel ddPCR data. Previous work includes 'definetherain' (Jones et al., 2014) and 'ddpcRquant' (Trypsteen et al., 2015) which both handle one channel ddPCR experiments only. The 'ddpcr' package available on CRAN (Attali et al., 2016) supports automatic gating of a specific class of two channel ddPCR experiments only. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: bbdb2cd12a3bd6f756b700d1216043ee build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-twoddpcr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-class - r-ggplot2 @@ -31,7 +33,7 @@ requirements: - r-scales - r-shiny run: - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-class - r-ggplot2 @@ -39,13 +41,16 @@ requirements: - r-rcolorbrewer - r-scales - r-shiny + +source: + md5: abc589fb8cc635143ba88bcf487d295b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules' - description: 'The twoddpcr package takes Droplet Digital PCR (ddPCR) droplet amplitude data from Bio-Rad''s QuantaSoft and can classify the droplets. A summary of the positive/negative droplet counts can be generated, which can then be used to estimate the number of molecules using the Poisson distribution. This is the first open source package that facilitates the automatic classification of general two channel ddPCR data. Previous work includes ''definetherain'' (Jones et al., 2014) and ''ddpcRquant'' (Trypsteen et al., 2015) which both handle one channel ddPCR experiments only. The ''ddpcr'' package available on CRAN (Attali et al., 2016) supports automatic gating of a specific class of two channel ddPCR experiments only.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txcutr/meta.yaml b/recipes/bioconductor-txcutr/meta.yaml index 0e45c92ea1d02..17466ade6290b 100644 --- a/recipes/bioconductor-txcutr/meta.yaml +++ b/recipes/bioconductor-txcutr/meta.yaml @@ -1,55 +1,62 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "txcutr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Various mRNA sequencing library preparation methods generate sequencing reads specifically from the transcript ends. Analyses that focus on quantification of isoform usage from such data can be aided by using truncated versions of transcriptome annotations, both at the alignment or pseudo-alignment stage, as well as in downstream analysis. This package implements some convenience methods for readily generating such truncated annotations and their corresponding sequences. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Transcriptome CUTteR -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 10d81d02156a45cebc08845455180010 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txcutr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RefManageR, BiocStyle, knitr, sessioninfo, rmarkdown, testthat (>= 3.0.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, BSgenome.Scerevisiae.UCSC.sacCer3 requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 - r-base + +source: + md5: 0a905e26a0a6785cb4917b6ff9435613 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Transcriptome CUTteR' - description: 'Various mRNA sequencing library preparation methods generate sequencing reads specifically from the transcript ends. Analyses that focus on quantification of isoform usage from such data can be aided by using truncated versions of transcriptome annotations, both at the alignment or pseudo-alignment stage, as well as in downstream analysis. This package implements some convenience methods for readily generating such truncated annotations and their corresponding sequences.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/meta.yaml b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/meta.yaml index a6886a0920dd4..df59b310d9d2c 100644 --- a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/meta.yaml +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.0.1" %} {% set name = "TxDb.Athaliana.BioMart.plantsmart22" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3bab54295e300fedba99eef521220e50 +about: + description: Exposes an annotation databases generated from BioMart by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.athaliana.biomart.plantsmart22", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3bab54295e300fedba99eef521220e50 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from BioMart by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/meta.yaml b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/meta.yaml index eda07b96d60d3..941e3d4245fe8 100644 --- a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/meta.yaml +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.1.3" %} {% set name = "TxDb.Athaliana.BioMart.plantsmart25" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eb007c07317b9717c76949e5ed999978 +about: + description: Exposes an annotation databases generated from BioMart by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.athaliana.biomart.plantsmart25", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: eb007c07317b9717c76949e5ed999978 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from BioMart by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/meta.yaml b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/meta.yaml index 63dab73960eb5..29f45699d3938 100644 --- a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/meta.yaml +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Athaliana.BioMart.plantsmart28" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9ed52284f01e08fc382db179b544bb17 +about: + description: Exposes an annotation databases generated from BioMart by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.athaliana.biomart.plantsmart28", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9ed52284f01e08fc382db179b544bb17 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from BioMart by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart51/meta.yaml b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart51/meta.yaml index d69be5548db43..2d85e305e0026 100644 --- a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart51/meta.yaml +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart51/meta.yaml @@ -1,41 +1,41 @@ {% set version = "0.99.0" %} {% set name = "TxDb.Athaliana.BioMart.plantsmart51" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c623af555537bfd9958f8f9573308103 +about: + description: 'Exposes an annotation databases generated from BioMart by exposing these as TxDb objects. This package is for Arabidopsis thaliana (taxID: 3702). The BioMart plantsmart release number is 51.' + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.athaliana.biomart.plantsmart51", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c623af555537bfd9958f8f9573308103 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from BioMart by exposing these as TxDb objects. This package is for Arabidopsis thaliana (taxID: 3702). The BioMart plantsmart release number is 51.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/meta.yaml b/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/meta.yaml index 4a642c4756fcb..0b30493d16254 100644 --- a/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Btaurus.UCSC.bosTau8.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2112b91fbecabf9c89d1b0a48d88ce03 +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 7 + noarch: generic + number: 8 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.btaurus.ucsc.bostau8.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2112b91fbecabf9c89d1b0a48d88ce03 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.btaurus.ucsc.bostau9.refgene/meta.yaml b/recipes/bioconductor-txdb.btaurus.ucsc.bostau9.refgene/meta.yaml index a6ba08db8eca3..014c8aec2be1b 100644 --- a/recipes/bioconductor-txdb.btaurus.ucsc.bostau9.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.btaurus.ucsc.bostau9.refgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.10.0" %} {% set name = "TxDb.Btaurus.UCSC.bosTau9.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fe443d123b0b788e1e450f4e60036788 +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 9 + noarch: generic + number: 10 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.btaurus.ucsc.bostau9.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fe443d123b0b788e1e450f4e60036788 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/meta.yaml b/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/meta.yaml index b4921754ff83d..2aeffb839bfe5 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce11.ensgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.15.0" %} {% set name = "TxDb.Celegans.UCSC.ce11.ensGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1b4d61d06ac8acb27e57d1fafc5b79ce +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 2 + noarch: generic + number: 3 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.celegans.ucsc.ce11.ensgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1b4d61d06ac8acb27e57d1fafc5b79ce + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml index 25dfa74d6898a..2a65ea71e56bc 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml @@ -1,46 +1,52 @@ {% set version = "3.4.6" %} {% set name = "TxDb.Celegans.UCSC.ce11.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3765169432e745aff5e85afd239066ca build: - number: 11 + noarch: generic + number: 12 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.celegans.ucsc.ce11.refgene", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-txdb.celegans.ucsc.ce11.refgene + path: recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene + version: 3.4.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 3765169432e745aff5e85afd239066ca + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' -extra: - parent_recipe: - name: bioconductor-txdb.celegans.ucsc.ce11.refgene - path: recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene - version: 3.4.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml index 039511fff6c9e..97d83f69f6f24 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml @@ -1,46 +1,52 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Celegans.UCSC.ce6.ensGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 215c2edd440a3df8229fe6a75b431aa8 build: - number: 16 + noarch: generic + number: 17 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.celegans.ucsc.ce6.ensgene", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-txdb.celegans.ucsc.ce6.ensgene + path: recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene + version: 3.2.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 215c2edd440a3df8229fe6a75b431aa8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' -extra: - parent_recipe: - name: bioconductor-txdb.celegans.ucsc.ce6.ensgene - path: recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene - version: 3.2.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/meta.yaml b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/meta.yaml index 18ad135c029fc..3ece4f0729118 100644 --- a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.11.0" %} {% set name = "TxDb.Cfamiliaris.UCSC.canFam3.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bf6af84c14a30ad5d01f3678246b1180 +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 8 + noarch: generic + number: 9 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bf6af84c14a30ad5d01f3678246b1180 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene/meta.yaml b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene/meta.yaml index b46d02cb2c06d..b13d261217522 100644 --- a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.14.0" %} {% set name = "TxDb.Cfamiliaris.UCSC.canFam4.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0b47072fa79cf8e99f8563002a0998cb +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.cfamiliaris.ucsc.canfam4.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0b47072fa79cf8e99f8563002a0998cb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene/meta.yaml b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene/meta.yaml index ddec9ac42b39b..cc0da3df80494 100644 --- a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.14.0" %} {% set name = "TxDb.Cfamiliaris.UCSC.canFam5.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fc3d84569c092b74e5e0bccb785db8b6 +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.cfamiliaris.ucsc.canfam5.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fc3d84569c092b74e5e0bccb785db8b6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene/meta.yaml b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene/meta.yaml index 59b9744aeb5b0..b9efa13109679 100644 --- a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.17.0" %} {% set name = "TxDb.Cfamiliaris.UCSC.canFam6.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9279204329323191fbb72717a57b13aa +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 1 + noarch: generic + number: 2 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.cfamiliaris.ucsc.canfam6.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9279204329323191fbb72717a57b13aa + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml index d1f4e9fba8f5e..a9bd2fc8a2b3e 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml @@ -1,46 +1,52 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Dmelanogaster.UCSC.dm3.ensGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 46b7ffe0c516edf8a2a3b5d78e0d8b67 build: - number: 17 + noarch: generic + number: 18 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene + path: recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene + version: 3.2.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 46b7ffe0c516edf8a2a3b5d78e0d8b67 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' -extra: - parent_recipe: - name: bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene - path: recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene - version: 3.2.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml index e336c647d474a..c65c09b78a324 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml @@ -1,46 +1,52 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Dmelanogaster.UCSC.dm6.ensGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bec18a1fb2768347e907e3171d5332ca build: - number: 7 + noarch: generic + number: 8 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene + path: recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene + version: 3.4.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: bec18a1fb2768347e907e3171d5332ca + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' -extra: - parent_recipe: - name: bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene - path: recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene - version: 3.4.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml index fca8354c5912c..4e333445cda54 100644 --- a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml @@ -1,46 +1,52 @@ {% set version = "3.4.6" %} {% set name = "TxDb.Drerio.UCSC.danRer10.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: fef9bbec3809e1b69991516988f146fb build: - number: 11 + noarch: generic + number: 12 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.drerio.ucsc.danrer10.refgene", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-txdb.drerio.ucsc.danrer10.refgene + path: recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene + version: 3.4.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: fef9bbec3809e1b69991516988f146fb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' -extra: - parent_recipe: - name: bioconductor-txdb.drerio.ucsc.danrer10.refgene - path: recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene - version: 3.4.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/meta.yaml b/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/meta.yaml index f95557448c480..11c7ebd79eca6 100644 --- a/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.drerio.ucsc.danrer11.refgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.4.6" %} {% set name = "TxDb.Drerio.UCSC.danRer11.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3d4ded4cec068a807b8b86b31389b677 +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 11 + noarch: generic + number: 12 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.drerio.ucsc.danrer11.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3d4ded4cec068a807b8b86b31389b677 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/meta.yaml b/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/meta.yaml index a4d1e1a9d9a08..2ca8945ba52b2 100644 --- a/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Ggallus.UCSC.galGal4.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d50eb467227cd9077a7a690ae6934d11 +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 7 + noarch: generic + number: 8 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.ggallus.ucsc.galgal4.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d50eb467227cd9077a7a690ae6934d11 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/meta.yaml b/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/meta.yaml index c539c071a4343..00ba7c6e499a5 100644 --- a/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Ggallus.UCSC.galGal5.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0df53cd4f8e29705df75867a427de56e +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 7 + noarch: generic + number: 8 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.ggallus.ucsc.galgal5.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0df53cd4f8e29705df75867a427de56e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.ggallus.ucsc.galgal6.refgene/meta.yaml b/recipes/bioconductor-txdb.ggallus.ucsc.galgal6.refgene/meta.yaml index 9a465cc414e93..2f37a9be935da 100644 --- a/recipes/bioconductor-txdb.ggallus.ucsc.galgal6.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ggallus.ucsc.galgal6.refgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.10.0" %} {% set name = "TxDb.Ggallus.UCSC.galGal6.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4d81026ecb786abf1fe0cb548238214c +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 9 + noarch: generic + number: 10 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.ggallus.ucsc.galgal6.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4d81026ecb786abf1fe0cb548238214c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.hsapiens.biomart.igis/meta.yaml b/recipes/bioconductor-txdb.hsapiens.biomart.igis/meta.yaml index 3dbd6d642a0c9..f0d27192ca41f 100644 --- a/recipes/bioconductor-txdb.hsapiens.biomart.igis/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.biomart.igis/meta.yaml @@ -1,41 +1,41 @@ {% set version = "2.3.2" %} {% set name = "TxDb.Hsapiens.BioMart.igis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 75b793928d29bcd3f069b5986bc2cfae +about: + description: Exposes an annotation databases generated from BioMart by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.hsapiens.biomart.igis", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 75b793928d29bcd3f069b5986bc2cfae + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from BioMart by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml index 1e389329cbe79..1c7f21a77757a 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml @@ -1,46 +1,52 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Hsapiens.UCSC.hg18.knownGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: e8b32a672e87345c72bb30be73d1e2d6 build: - number: 16 + noarch: generic + number: 17 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.hsapiens.ucsc.hg18.knowngene", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-txdb.hsapiens.ucsc.hg18.knowngene + path: recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene + version: 3.2.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: e8b32a672e87345c72bb30be73d1e2d6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' -extra: - parent_recipe: - name: bioconductor-txdb.hsapiens.ucsc.hg18.knowngene - path: recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene - version: 3.2.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml index 09de8f7c38a1f..90d1016923e86 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml @@ -1,46 +1,52 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Hsapiens.UCSC.hg19.knownGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 61be88a81433958571b57d0952be48a0 build: - number: 16 + noarch: generic + number: 17 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.hsapiens.ucsc.hg19.knowngene", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-txdb.hsapiens.ucsc.hg19.knowngene + path: recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene + version: 3.2.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 61be88a81433958571b57d0952be48a0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' -extra: - parent_recipe: - name: bioconductor-txdb.hsapiens.ucsc.hg19.knowngene - path: recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene - version: 3.2.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml index 4559792f7c905..a8d8ebb86cabb 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml @@ -1,46 +1,52 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a0d61cd90639c40b3d0bb6bdb043cf12 build: - number: 18 + noarch: generic + number: 19 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts + path: recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts + version: 3.2.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: a0d61cd90639c40b3d0bb6bdb043cf12 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' -extra: - parent_recipe: - name: bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts - path: recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts - version: 3.2.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml index 618385aa5a855..905fcfb0b7208 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml @@ -1,46 +1,52 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "TxDb.Hsapiens.UCSC.hg38.knownGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2344dbd2878c82c6c860ed6529a700b2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.hsapiens.ucsc.hg38.knowngene", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-txdb.hsapiens.ucsc.hg38.knowngene + path: recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene + version: 3.4.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 416c5b08453bcfa1687dc06c15af3fa7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' -extra: - parent_recipe: - name: bioconductor-txdb.hsapiens.ucsc.hg38.knowngene - path: recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene - version: 3.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh index 7e845c2497808..8307f9d66e944 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "txdb.hsapiens.ucsc.hg38.knowngene-3.18.0" +installBiocDataPackage.sh "txdb.hsapiens.ucsc.hg38.knowngene-3.20.0" diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/meta.yaml index fbea99b3dbea6..28a246bf18f5f 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "3.18.0" %} +{% set version = "3.19.0" %} {% set name = "TxDb.Hsapiens.UCSC.hg38.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7ec982095ea795b99d53b6549d7ba4d4 +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.hsapiens.ucsc.hg38.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b5b5034f8674fafd9bd5a352264fc0a5 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/post-link.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/post-link.sh index 165899b5e92d6..937338c547640 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.refgene/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "txdb.hsapiens.ucsc.hg38.refgene-3.18.0" +installBiocDataPackage.sh "txdb.hsapiens.ucsc.hg38.refgene-3.19.0" diff --git a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene/meta.yaml b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene/meta.yaml index 71ee0e7b1156c..a63bd74575162 100644 --- a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.14.0" %} {% set name = "TxDb.Mmulatta.UCSC.rheMac10.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 81b01b07d87ae91b4d9a269a2baf616e +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.mmulatta.ucsc.rhemac10.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 81b01b07d87ae91b4d9a269a2baf616e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/meta.yaml b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/meta.yaml index 0534539bc09fe..1ccddb864b759 100644 --- a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Mmulatta.UCSC.rheMac3.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: db84a9e85d613635d74002f11df41e1f +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 7 + noarch: generic + number: 8 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: db84a9e85d613635d74002f11df41e1f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/meta.yaml b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/meta.yaml index bc41e0d7a744b..c55c47bd39340 100644 --- a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Mmulatta.UCSC.rheMac8.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8437e0a05ffd28b667c7b740e0db68a7 +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 7 + noarch: generic + number: 8 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8437e0a05ffd28b667c7b740e0db68a7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml index d32fc6e7daded..48257b633ff62 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml @@ -1,46 +1,52 @@ {% set version = "3.4.0" %} {% set name = "TxDb.Mmusculus.UCSC.mm10.ensGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 88d65b714d1f86b456aee2b8524e9d84 build: - number: 17 + noarch: generic + number: 18 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.mmusculus.ucsc.mm10.ensgene", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-txdb.mmusculus.ucsc.mm10.ensgene + path: recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene + version: 3.4.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 88d65b714d1f86b456aee2b8524e9d84 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' -extra: - parent_recipe: - name: bioconductor-txdb.mmusculus.ucsc.mm10.ensgene - path: recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene - version: 3.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml index 1466d7f497572..0a57fdd7d7ba0 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml @@ -1,46 +1,52 @@ {% set version = "3.10.0" %} {% set name = "TxDb.Mmusculus.UCSC.mm10.knownGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 129b610bf05ec77451731196baa55bcc build: - number: 9 + noarch: generic + number: 10 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.mmusculus.ucsc.mm10.knowngene", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-txdb.mmusculus.ucsc.mm10.knowngene + path: recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene + version: 3.4.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 129b610bf05ec77451731196baa55bcc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' -extra: - parent_recipe: - name: bioconductor-txdb.mmusculus.ucsc.mm10.knowngene - path: recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene - version: 3.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/meta.yaml index 7d5fc68376690..b2db5eb22f72d 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "TxDb.Mmusculus.UCSC.mm39.knownGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5ceb110ce3327d44f45bf5118ec7f3af +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.mmusculus.ucsc.mm39.knowngene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 59d302d11980ad599da45918d2891242 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/post-link.sh b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/post-link.sh index 40c86bb8d84f5..2c637cd9e2369 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.knowngene/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "txdb.mmusculus.ucsc.mm39.knowngene-3.18.0" +installBiocDataPackage.sh "txdb.mmusculus.ucsc.mm39.knowngene-3.20.0" diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/meta.yaml index 9734f2b6f61c1..4efff907c5bea 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "3.18.0" %} +{% set version = "3.19.0" %} {% set name = "TxDb.Mmusculus.UCSC.mm39.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2fd64557d5f1bade11432b666c63f33a +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.mmusculus.ucsc.mm39.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 2c2c41adc8b05f6353ee7ae744cdbd98 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/post-link.sh b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/post-link.sh index 039d2293e91ed..3bb27d7e68798 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm39.refgene/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "txdb.mmusculus.ucsc.mm39.refgene-3.18.0" +installBiocDataPackage.sh "txdb.mmusculus.ucsc.mm39.refgene-3.19.0" diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml index 4b3641897a188..43d4627f7e90c 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml @@ -1,46 +1,52 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Mmusculus.UCSC.mm9.knownGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cb72af039b011033477363bda8ed9104 build: - number: 16 + noarch: generic + number: 17 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.mmusculus.ucsc.mm9.knowngene", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-txdb.mmusculus.ucsc.mm9.knowngene + path: recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene + version: 3.2.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: cb72af039b011033477363bda8ed9104 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' -extra: - parent_recipe: - name: bioconductor-txdb.mmusculus.ucsc.mm9.knowngene - path: recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene - version: 3.2.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/meta.yaml b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/meta.yaml index 45f0301d0133b..9cca02bffb815 100644 --- a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Ptroglodytes.UCSC.panTro4.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9bdd3ba81561550f50250368d7d52eaa +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 7 + noarch: generic + number: 8 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9bdd3ba81561550f50250368d7d52eaa + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/meta.yaml b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/meta.yaml index e46a4701dd0a3..42fde4c7f26a3 100644 --- a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Ptroglodytes.UCSC.panTro5.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 76ee1d253d1c8e54c12e8d5b9db93303 +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 7 + noarch: generic + number: 8 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 76ee1d253d1c8e54c12e8d5b9db93303 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene/meta.yaml b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene/meta.yaml index 7e50c87b44421..ee5ed8a027fb5 100644 --- a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.10.0" %} {% set name = "TxDb.Ptroglodytes.UCSC.panTro6.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 48a88973fe0e5117cadd5c816a46e6e9 +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 9 + noarch: generic + number: 10 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.ptroglodytes.ucsc.pantro6.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 48a88973fe0e5117cadd5c816a46e6e9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/meta.yaml index 072131a10520b..4fc78e0173dc4 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/meta.yaml @@ -1,41 +1,41 @@ {% set version = "2.3.2" %} {% set name = "TxDb.Rnorvegicus.BioMart.igis" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: eaf695f63cd021074d68c76d148cdfb7 +about: + description: Exposes an annotation databases generated from BioMart by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.rnorvegicus.biomart.igis", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: eaf695f63cd021074d68c76d148cdfb7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from BioMart by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml index 87c5843fcb54e..f7180990c5f45 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml @@ -1,46 +1,52 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn4.ensGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6bf2ebc522c2828c036e52b2028792c1 build: - number: 16 + noarch: generic + number: 17 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene + path: recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene + version: 3.2.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 6bf2ebc522c2828c036e52b2028792c1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' -extra: - parent_recipe: - name: bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene - path: recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene - version: 3.2.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml index 7a4c200fb093a..285a7085401af 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml @@ -1,46 +1,52 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn5.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8a93a15b37bf73e5c529c976c4561537 build: - number: 7 + noarch: generic + number: 8 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene + path: recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene + version: 3.4.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 8a93a15b37bf73e5c529c976c4561537 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' -extra: - parent_recipe: - name: bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene - path: recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene - version: 3.4.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq/meta.yaml index a891c74d515a3..e3ecf4890e5d9 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn6.ncbiRefSeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6660ee000fbc956541728c6dadf1fca7 +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 7 + noarch: generic + number: 8 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.rnorvegicus.ucsc.rn6.ncbirefseq", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 6660ee000fbc956541728c6dadf1fca7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml index 18c8a1da4b97b..bc3ce5303a57f 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml @@ -1,46 +1,52 @@ {% set version = "3.4.6" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn6.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea525daa75bcf165eb24f6e93f4dbf6c build: - number: 11 + noarch: generic + number: 12 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene + path: recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene + version: 3.4.3 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: ea525daa75bcf165eb24f6e93f4dbf6c + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' -extra: - parent_recipe: - name: bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene - path: recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene - version: 3.4.3 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene/meta.yaml index 50c4b8f2e2f3f..4c196c1ee2642 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.15.0" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn7.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 589dc0f8f4c6ee8f5ed11aeb95a74a7d +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 2 + noarch: generic + number: 3 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.rnorvegicus.ucsc.rn7.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 589dc0f8f4c6ee8f5ed11aeb95a74a7d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml index 15d753d9f15d2..b8ca5185db0d7 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml @@ -1,46 +1,52 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Scerevisiae.UCSC.sacCer2.sgdGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 8ce83ef2ba6cfc69f9b4435a0a047819 build: - number: 19 + noarch: generic + number: 20 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene + path: recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene + version: 3.2.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 8ce83ef2ba6cfc69f9b4435a0a047819 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' -extra: - parent_recipe: - name: bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene - path: recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene - version: 3.2.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml index c404797fc5a6d..22e172502c5ee 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml @@ -1,46 +1,52 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Scerevisiae.UCSC.sacCer3.sgdGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: afb23b3265730b9e59c2f07ab37cc3a0 build: - number: 22 + noarch: generic + number: 23 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene + path: recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene + version: 3.2.2 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: afb23b3265730b9e59c2f07ab37cc3a0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' -extra: - parent_recipe: - name: bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene - path: recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene - version: 3.2.2 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/meta.yaml b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/meta.yaml index 0aac7bae47394..a7acd94f76674 100644 --- a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Sscrofa.UCSC.susScr11.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a6c5a2c402ad904a2f55099e391d18de +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 7 + noarch: generic + number: 8 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.sscrofa.ucsc.susscr11.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a6c5a2c402ad904a2f55099e391d18de + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/meta.yaml b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/meta.yaml index dafdf280b2985..bec572ced39e8 100644 --- a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/meta.yaml @@ -1,41 +1,41 @@ {% set version = "3.12.0" %} {% set name = "TxDb.Sscrofa.UCSC.susScr3.refGene" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 981602dc706e545d5acdf7590e222ca7 +about: + description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation package for TxDb object(s) build: - number: 7 + noarch: generic + number: 8 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-txdb.sscrofa.ucsc.susscr3.refgene", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 981602dc706e545d5acdf7590e222ca7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation package for TxDb object(s)' - description: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-txdbmaker/build.sh b/recipes/bioconductor-txdbmaker/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-txdbmaker/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-txdbmaker/meta.yaml b/recipes/bioconductor-txdbmaker/meta.yaml new file mode 100644 index 0000000000000..c484529abda28 --- /dev/null +++ b/recipes/bioconductor-txdbmaker/meta.yaml @@ -0,0 +1,73 @@ +{% set version = "1.2.0" %} +{% set name = "txdbmaker" %} +{% set bioc = "3.20" %} + +about: + description: A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and to import them in a TxDb object. TxDb objects are implemented in the GenomicFeatures package, together with flexible methods for extracting the desired features in convenient formats. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Tools for making TxDb objects from genomic annotations + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-txdbmaker", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RMariaDB, mirbase.db, ensembldb, RUnit, BiocStyle, knitr +requirements: + host: + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-ucsc.utils >=1.2.0,<1.3.0 + - r-base + - r-dbi + - r-httr + - r-rjson + - r-rsqlite >=2.0 + run: + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-ucsc.utils >=1.2.0,<1.3.0 + - r-base + - r-dbi + - r-httr + - r-rjson + - r-rsqlite >=2.0 + +source: + md5: f4e67ca04838483142710473015b5ef3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-tximeta/meta.yaml b/recipes/bioconductor-tximeta/meta.yaml index 1195350a6e9cc..7525540929e34 100644 --- a/recipes/bioconductor-tximeta/meta.yaml +++ b/recipes/bioconductor-tximeta/meta.yaml @@ -1,74 +1,80 @@ -{% set version = "1.20.1" %} +{% set version = "1.24.0" %} {% set name = "tximeta" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Transcript quantification import from Salmon and other quantifiers with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Transcript Quantification Import with Automatic Metadata -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 20a7fe1f7efc9be9ab420325932b8c0b build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tximeta", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-tximeta + path: recipes/bioconductor-tximeta + version: 1.0.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, fishpond, edgeR, limma, devtools requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.0.0,<2.46.1' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tximport >=1.30.0,<1.31.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 + - bioconductor-tximport >=1.34.0,<1.35.0 - r-base - r-jsonlite - r-matrix - r-tibble run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-ensembldb >=2.26.0,<2.27.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rhdf5 >=2.0.0,<2.46.1' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-tximport >=1.30.0,<1.31.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-ensembldb >=2.30.0,<2.31.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdbmaker >=1.2.0,<1.3.0 + - bioconductor-tximport >=1.34.0,<1.35.0 - r-base - r-jsonlite - r-matrix - r-tibble + +source: + md5: bd4f17024e7ddfe3c007e5726deef378 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Transcript Quantification Import with Automatic Metadata' - description: 'Transcript quantification import from Salmon and other quantifiers with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - parent_recipe: - name: bioconductor-tximeta - path: recipes/bioconductor-tximeta - version: 1.0.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tximport/meta.yaml b/recipes/bioconductor-tximport/meta.yaml index 0cac1468cec2d..c9e2b05289cb3 100644 --- a/recipes/bioconductor-tximport/meta.yaml +++ b/recipes/bioconductor-tximport/meta.yaml @@ -1,39 +1,22 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "tximport" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Import and summarize transcript-level estimates for transcript- and gene-level analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8bbe549dafbf5b0dfe626f327910a893 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tximport", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow, limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>=2)' - summary: 'Import and summarize transcript-level estimates for transcript- and gene-level analysis' - description: 'Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + extra: identifiers: - biotools:tximport @@ -44,3 +27,26 @@ extra: recipe-maintainers: - roryk +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow, limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds +requirements: + host: + - r-base + run: + - r-base + +source: + md5: 52012454226f0012bdbfd86f71ed2343 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-tximportdata/meta.yaml b/recipes/bioconductor-tximportdata/meta.yaml index 67efaa786b0ac..e606db63c6488 100644 --- a/recipes/bioconductor-tximportdata/meta.yaml +++ b/recipes/bioconductor-tximportdata/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.30.0" %} +{% set version = "1.34.0" %} {% set name = "tximportData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 4494d764fc087333e5c04ee7977c85c8 +about: + description: This package provides the output of running various transcript abundance quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The quantifiers were Cufflinks, RSEM, kallisto, Salmon and Sailfish. alevin example output is also included. Forr details on version numbers, sample information, and details on calls, see the package vignette. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: tximportData build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-tximportdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, markdown requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fc6bbc67c32e7eac6e11b68af9343745 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: tximportData - description: 'This package provides the output of running various transcript abundance quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The quantifiers were Cufflinks, RSEM, kallisto, Salmon and Sailfish. alevin example output is also included. Forr details on version numbers, sample information, and details on calls, see the package vignette.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-tximportdata/post-link.sh b/recipes/bioconductor-tximportdata/post-link.sh index d17909a301ad8..004f7e24398dd 100644 --- a/recipes/bioconductor-tximportdata/post-link.sh +++ b/recipes/bioconductor-tximportdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "tximportdata-1.30.0" +installBiocDataPackage.sh "tximportdata-1.34.0" diff --git a/recipes/bioconductor-u133aaofav2cdf/meta.yaml b/recipes/bioconductor-u133aaofav2cdf/meta.yaml index 68e66f5114324..eed49959dd305 100644 --- a/recipes/bioconductor-u133aaofav2cdf/meta.yaml +++ b/recipes/bioconductor-u133aaofav2cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "u133aaofav2cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 716483ddb6664b8b7f0c58cd21136e8b +about: + description: A package containing an environment representing the U133AAofAv2.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: u133aaofav2cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-u133aaofav2cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 716483ddb6664b8b7f0c58cd21136e8b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: u133aaofav2cdf - description: 'A package containing an environment representing the U133AAofAv2.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-u133x3p.db/meta.yaml b/recipes/bioconductor-u133x3p.db/meta.yaml index 141cf64856d0d..074ad71cb222d 100644 --- a/recipes/bioconductor-u133x3p.db/meta.yaml +++ b/recipes/bioconductor-u133x3p.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "u133x3p.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1a36a09dc64b94728bf6ac75600b40c6 +about: + description: Affymetrix Human X3P Array annotation data (chip u133x3p) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Human X3P Array annotation data (chip u133x3p) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-u133x3p.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 1a36a09dc64b94728bf6ac75600b40c6 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Human X3P Array annotation data (chip u133x3p)' - description: 'Affymetrix Human X3P Array annotation data (chip u133x3p) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-u133x3pcdf/meta.yaml b/recipes/bioconductor-u133x3pcdf/meta.yaml index c14b372731fdb..d3491694a1151 100644 --- a/recipes/bioconductor-u133x3pcdf/meta.yaml +++ b/recipes/bioconductor-u133x3pcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "u133x3pcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ee4e62041bc8c63813e8cf8400ece2f3 +about: + description: A package containing an environment representing the U133_X3P.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: u133x3pcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-u133x3pcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ee4e62041bc8c63813e8cf8400ece2f3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: u133x3pcdf - description: 'A package containing an environment representing the U133_X3P.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-u133x3pprobe/meta.yaml b/recipes/bioconductor-u133x3pprobe/meta.yaml index 2d940a22ec63b..1bcfa3117171b 100644 --- a/recipes/bioconductor-u133x3pprobe/meta.yaml +++ b/recipes/bioconductor-u133x3pprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "u133x3pprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 81e2b00985688160805147bef0c638be +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was U133\_X3P\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type u133x3p build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-u133x3pprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 81e2b00985688160805147bef0c638be + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type u133x3p' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was U133\_X3P\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ucell/meta.yaml b/recipes/bioconductor-ucell/meta.yaml index 584900adb879c..33bb2cd7d6091 100644 --- a/recipes/bioconductor-ucell/meta.yaml +++ b/recipes/bioconductor-ucell/meta.yaml @@ -1,49 +1,54 @@ -{% set version = "2.6.2" %} +{% set version = "2.10.1" %} {% set name = "UCell" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: UCell is a package for evaluating gene signatures in single-cell datasets. UCell signature scores, based on the Mann-Whitney U statistic, are robust to dataset size and heterogeneity, and their calculation demands less computing time and memory than other available methods, enabling the processing of large datasets in a few minutes even on machines with limited computing power. UCell can be applied to any single-cell data matrix, and includes functions to directly interact with SingleCellExperiment and Seurat objects. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + file LICENSE + license_file: LICENSE + summary: Rank-based signature enrichment analysis for single-cell data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c02318fc6a9ac12b0d902460be5204d4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ucell", max_pin="x.x") }}' - noarch: generic -# Suggests: Seurat, scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, knitr, rmarkdown + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, Seurat(>= 5.0.0), SeuratObject(>= 5.0.0), knitr, rmarkdown requirements: host: - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-data.table >=1.13.6' + - r-data.table >=1.13.6 - r-matrix run: - - 'bioconductor-biocneighbors >=1.20.0,<1.21.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocneighbors >=2.0.0,<2.1.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - - 'r-data.table >=1.13.6' + - r-data.table >=1.13.6 - r-matrix + +source: + md5: cc478a720dd4686878be30ca05aa0aed + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 + file LICENSE' - summary: 'Rank-based signature enrichment analysis for single-cell data' - description: 'UCell is a package for evaluating gene signatures in single-cell datasets. UCell signature scores, based on the Mann-Whitney U statistic, are robust to dataset size and heterogeneity, and their calculation demands less computing time and memory than other available methods, enabling the processing of large datasets in a few minutes even on machines with limited computing power. UCell can be applied to any single-cell data matrix, and includes functions to directly interact with SingleCellExperiment and Seurat objects.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ucsc.utils/build.sh b/recipes/bioconductor-ucsc.utils/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ucsc.utils/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ucsc.utils/meta.yaml b/recipes/bioconductor-ucsc.utils/meta.yaml new file mode 100644 index 0000000000000..af98fd038174a --- /dev/null +++ b/recipes/bioconductor-ucsc.utils/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.2.0" %} +{% set name = "UCSC.utils" %} +{% set bioc = "3.20" %} + +about: + description: A set of low-level utilities to retrieve data from the UCSC Genome Browser. Most functions in the package access the data via the UCSC REST API but some of them query the UCSC MySQL server directly. Note that the primary purpose of the package is to support higher-level functionalities implemented in downstream packages like GenomeInfoDb or txdbmaker. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Low-level utilities to retrieve data from the UCSC Genome Browser +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-ucsc.utils", max_pin="x.x") }}' +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: DBI, RMariaDB, GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle +requirements: + host: + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-httr + - r-jsonlite + run: + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - r-base + - r-httr + - r-jsonlite +source: + md5: ab12a0427231a9578aba56dc73049730 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-ucscrepeatmasker/meta.yaml b/recipes/bioconductor-ucscrepeatmasker/meta.yaml index 732e819f62c2b..79b37b56f99f6 100644 --- a/recipes/bioconductor-ucscrepeatmasker/meta.yaml +++ b/recipes/bioconductor-ucscrepeatmasker/meta.yaml @@ -1,46 +1,51 @@ {% set version = "3.15.2" %} {% set name = "UCSCRepeatMasker" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Store UCSC RepeatMasker AnnotationHub resource metadata. Provide provenance and citation information for UCSC RepeatMasker AnnotationHub resources. Illustrate in a vignette how to access those resources. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: UCSC RepeatMasker AnnotationHub resource metadata -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ad19a6fbd936e478af88fa21bc918a29 build: - number: 2 + noarch: generic + number: 3 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ucscrepeatmasker", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 - r-base - r-rcurl - r-xml run: - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 - r-base - r-rcurl - r-xml - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: ad19a6fbd936e478af88fa21bc918a29 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'UCSC RepeatMasker AnnotationHub resource metadata' - description: 'Store UCSC RepeatMasker AnnotationHub resource metadata. Provide provenance and citation information for UCSC RepeatMasker AnnotationHub resources. Illustrate in a vignette how to access those resources.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ularcirc/meta.yaml b/recipes/bioconductor-ularcirc/meta.yaml index 1007d484742c7..74f31035468f0 100644 --- a/recipes/bioconductor-ularcirc/meta.yaml +++ b/recipes/bioconductor-ularcirc/meta.yaml @@ -1,43 +1,46 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "Ularcirc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Ularcirc reads in STAR aligned splice junction files and provides visualisation and analysis tools for splicing analysis. Users can assess backsplice junctions and forward canonical junctions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dee64401e02d9e5884a6399d7ab122b2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ularcirc", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene requirements: + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-mirbase.db >=1.2.0,<1.3.0' - - 'bioconductor-organism.dplyr >=1.30.0,<1.31.0' - - 'bioconductor-plotgardener >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomeinfodbdata >=1.2.0,<1.3.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-mirbase.db >=1.2.0,<1.3.0 + - bioconductor-organism.dplyr >=1.34.0,<1.35.0 + - bioconductor-plotgardener >=1.12.0,<1.13.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-data.table >=1.9.4' + - r-data.table >=1.9.4 - r-dt - r-ggplot2 - r-ggrepel @@ -49,23 +52,24 @@ requirements: - r-shinyfiles - r-shinyjs - r-yaml + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-annotationhub >=3.10.0,<3.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-mirbase.db >=1.2.0,<1.3.0' - - 'bioconductor-organism.dplyr >=1.30.0,<1.31.0' - - 'bioconductor-plotgardener >=1.8.0,<1.9.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-annotationhub >=3.14.0,<3.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomeinfodbdata >=1.2.0,<1.3.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-mirbase.db >=1.2.0,<1.3.0 + - bioconductor-organism.dplyr >=1.34.0,<1.35.0 + - bioconductor-plotgardener >=1.12.0,<1.13.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-data.table >=1.9.4' + - r-data.table >=1.9.4 - r-dt - r-ggplot2 - r-ggrepel @@ -77,13 +81,16 @@ requirements: - r-shinyfiles - r-shinyjs - r-yaml + +source: + md5: 4a5c0c8939991b46d98ae2f52b06fc1b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)' - description: 'Ularcirc reads in STAR aligned splice junction files and provides visualisation and analysis tools for splicing analysis. Users can assess backsplice junctions and forward canonical junctions.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-umi4cats/build_failure.linux-64.yaml b/recipes/bioconductor-umi4cats/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..708601a6b4a85 --- /dev/null +++ b/recipes/bioconductor-umi4cats/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 7cf44df95c097a1c5d9f2e5fb4aa9f064a9cabb491fc53d87f88c665b36f7570 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rbowtie2[version='>=2.12.0,<2.13.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rbowtie2 >=2.12.0,<2.13.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rbowtie2 >=2.12.0,<2.13.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rbowtie2[version='>=2.12.0,<2.13.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rbowtie2 >=2.12.0,<2.13.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rbowtie2 >=2.12.0,<2.13.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rbowtie2[version='>=2.12.0,<2.13.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-rbowtie2 >=2.12.0,<2.13.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-rbowtie2 >=2.12.0,<2.13.0 [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-umi4cats/meta.yaml b/recipes/bioconductor-umi4cats/meta.yaml index caa73d85038c4..18927cf7a824f 100644 --- a/recipes/bioconductor-umi4cats/meta.yaml +++ b/recipes/bioconductor-umi4cats/meta.yaml @@ -1,46 +1,48 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "UMI4Cats" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: UMI-4C is a technique that allows characterization of 3D chromatin interactions with a bait of interest, taking advantage of a sonication step to produce unique molecular identifiers (UMIs) that help remove duplication bias, thus allowing a better differential comparsion of chromatin interactions between conditions. This package allows processing of UMI-4C data, starting from FastQ files provided by the sequencing facility. It provides two statistical methods for detecting differential contacts and includes a visualization function to plot integrated information from a UMI-4C assay. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bfadc67d7452919fe1e4a63684692442 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-umi4cats", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat requirements: + host: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' - - 'bioconductor-regioner >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rbowtie2 >=2.12.0,<2.13.0 + - bioconductor-regioner >=1.38.0,<1.39.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 - r-base - r-cowplot - r-dplyr @@ -56,26 +58,27 @@ requirements: - r-scales - r-stringr - r-zoo + run: - - 'bioconductor-annotate >=1.80.0,<1.81.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-rbowtie2 >=2.8.0,<2.9.0' - - 'bioconductor-regioner >=1.34.0,<1.35.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-shortread >=1.60.0,<1.61.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - bioconductor-annotate >=1.84.0,<1.85.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-rbowtie2 >=2.12.0,<2.13.0 + - bioconductor-regioner >=1.38.0,<1.39.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-shortread >=1.64.0,<1.65.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 - r-base - r-cowplot - r-dplyr @@ -91,12 +94,16 @@ requirements: - r-scales - r-stringr - r-zoo + +source: + md5: a61dba7091223da967bf03c427f81fe4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data' - description: 'UMI-4C is a technique that allows characterization of 3D chromatin interactions with a bait of interest, taking advantage of a sonication step to produce unique molecular identifiers (UMIs) that help remove duplication bias, thus allowing a better differential comparsion of chromatin interactions between conditions. This package allows processing of UMI-4C data, starting from FastQ files provided by the sequencing facility. It provides two statistical methods for detecting differential contacts and includes a visualization function to plot integrated information from a UMI-4C assay.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-uncoverapplib/build_failure.linux-64.yaml b/recipes/bioconductor-uncoverapplib/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..dc5bbd8c0c602 --- /dev/null +++ b/recipes/bioconductor-uncoverapplib/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5694638dfcc1ef8a574f62f6b4d6ebaff258581282b5093b5d4f48dd17328af6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-ensdb.hsapiens.v86==2.99.0=r351_0"), MatchSpec("bioconductor-ensembldb[version='>=2.30.0,<2.31.0']"), MatchSpec("bioconductor-gviz==1.50.0=r44hdfd78af_0")} + Encountered problems while solving: + - package bioconductor-ensdb.hsapiens.v86-2.99.0-r351_0 requires bioconductor-ensembldb >=2.6.0,<2.7.0, but none of the providers can be installed + - package bioconductor-gviz-1.50.0-r44hdfd78af_0 requires bioconductor-ensembldb >=2.30.0,<2.31.0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0 [0m is installable with the potential options + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mr-base 3.4.1* [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.4.1,<2.6.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.6.0,<2.7.0 [0m, which requires + [32mbioconductor-genomicranges >=1.34.0,<1.35.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.8.0,<2.9.0 [0m, which requires + [32mbioconductor-genomicranges >=1.36.0,<1.37.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.10.0,<2.11.0 [0m, which requires + [32mbioconductor-genomicranges >=1.38.0,<1.39.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.12.0,<2.13.0 [0m, which requires + [32mbioconductor-genomicranges >=1.40.0,<1.41.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.14.0,<2.15.0 [0m, which requires + [32mbioconductor-genomicranges >=1.42.0,<1.43.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.16.0,<2.17.0 [0m, which requires + [32mbioconductor-genomicranges >=1.44.0,<1.45.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.18.0,<2.19.0 [0m, which requires + [32mbioconductor-genomicranges >=1.46.0,<1.47.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.22.0,<2.23.0 [0m, which requires + [32mbioconductor-genomicranges >=1.50.0,<1.51.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.24.0,<2.25.0 [0m, which requires + [32mbioconductor-genomicranges >=1.52.0,<1.53.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.26.0,<2.27.0 [0m, which requires + [32mbioconductor-genomicranges >=1.54.0,<1.55.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0 [0m is installable with the potential options + [32mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.6.0,<2.7.0 [0m, which can be installed (as previously explained); + [32mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.8.0,<2.9.0 [0m, which can be installed (as previously explained); + [32mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.10.0,<2.11.0 [0m, which can be installed (as previously explained); + [32mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.12.0,<2.13.0 [0m, which can be installed (as previously explained); + [32mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.14.0,<2.15.0 [0m, which can be installed (as previously explained); + [32mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.16.0,<2.17.0 [0m, which can be installed (as previously explained); + [32mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.18.0,<2.19.0 [0m, which can be installed (as previously explained); + [32mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.22.0,<2.23.0 [0m, which can be installed (as previously explained); + [32mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.24.0,<2.25.0 [0m, which can be installed (as previously explained); + [32mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.26.0,<2.27.0 [0m, which can be installed (as previously explained); + [31mbioconductor-genomicranges >=1.58.0,<1.59.0 [0m is not installable because it conflicts with any installable versions previously reported; + [31mbioconductor-gviz >=1.50.0,<1.51.0 [0m is not installable because it requires + [31mbioconductor-ensembldb >=2.30.0,<2.31.0 [0m, which conflicts with any installable versions previously reported; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-uncoverapplib/meta.yaml b/recipes/bioconductor-uncoverapplib/meta.yaml index 1a28223113b02..3cbb4095362e4 100644 --- a/recipes/bioconductor-uncoverapplib/meta.yaml +++ b/recipes/bioconductor-uncoverapplib/meta.yaml @@ -1,39 +1,42 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "uncoverappLib" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'a Shiny application containing a suite of graphical and statistical tools to support clinical assessment of low coverage regions.It displays three web pages each providing a different analysis module: Coverage analysis, calculate AF by allele frequency app and binomial distribution. uncoverAPP provides a statisticl summary of coverage given target file or genes name.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Interactive graphical application for clinical assessment of sequence coverage at the base-pair level -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2aa395f92e95d5ff7e67612c6a2c0021 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-uncoverapplib", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, testthat, rmarkdown, dplyr requirements: + host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0' - - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0 + - bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-homo.sapiens >=1.3.0,<1.4.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-organismdbi >=1.48.0,<1.49.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 - r-base - r-condformat - r-dt @@ -48,19 +51,20 @@ requirements: - r-shinyjs - r-shinywidgets - r-stringr + run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0' - - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' - - 'bioconductor-org.hs.eg.db >=3.18.0,<3.19.0' - - 'bioconductor-organismdbi >=1.44.0,<1.45.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.18.0,<3.19.0' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0 + - bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-homo.sapiens >=1.3.0,<1.4.0 + - bioconductor-org.hs.eg.db >=3.20.0,<3.21.0 + - bioconductor-organismdbi >=1.48.0,<1.49.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.20.0,<3.21.0 - r-base - r-condformat - r-dt @@ -75,13 +79,16 @@ requirements: - r-shinyjs - r-shinywidgets - r-stringr + +source: + md5: 4e0a3240f0c1fda8a2010f0db9f3c721 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Interactive graphical application for clinical assessment of sequence coverage at the base-pair level' - description: 'a Shiny application containing a suite of graphical and statistical tools to support clinical assessment of low coverage regions.It displays three web pages each providing a different analysis module: Coverage analysis, calculate AF by allele frequency app and binomial distribution. uncoverAPP provides a statisticl summary of coverage given target file or genes name.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-undo/meta.yaml b/recipes/bioconductor-undo/meta.yaml index f214965e0b298..1f258d57bc401 100644 --- a/recipes/bioconductor-undo/meta.yaml +++ b/recipes/bioconductor-undo/meta.yaml @@ -1,54 +1,60 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "UNDO" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: UNDO is an R package for unsupervised deconvolution of tumor and stromal mixed expression data. It detects marker genes and deconvolutes the mixing expression data without any prior knowledge. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a94665c036a09fbf3728f0a1ad220dfa build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-undo", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:undo + - doi:10.1093/bioinformatics/btu607 + parent_recipe: + name: bioconductor-undo + path: recipes/bioconductor-undo + version: 1.22.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-boot - r-mass - r-nnls run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-boot - r-mass - r-nnls + +source: + md5: de9d4e4fc46f7474d274b53a4b9fd200 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions' - description: 'UNDO is an R package for unsupervised deconvolution of tumor and stromal mixed expression data. It detects marker genes and deconvolutes the mixing expression data without any prior knowledge.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:undo - - doi:10.1093/bioinformatics/btu607 - parent_recipe: - name: bioconductor-undo - path: recipes/bioconductor-undo - version: 1.22.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-unifiedwmwqpcr/meta.yaml b/recipes/bioconductor-unifiedwmwqpcr/meta.yaml index 9c7b8e08be53a..51b8a25e8d048 100644 --- a/recipes/bioconductor-unifiedwmwqpcr/meta.yaml +++ b/recipes/bioconductor-unifiedwmwqpcr/meta.yaml @@ -1,42 +1,22 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "unifiedWMWqPCR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>=2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d9a09d196f72dc2246328247851dd24a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-unifiedwmwqpcr", max_pin="x.x") }}' - noarch: generic -requirements: - host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-htqpcr >=1.56.0,<1.57.0' - - r-base - run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-htqpcr >=1.56.0,<1.57.0' - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' - summary: 'Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data' - description: 'This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + extra: identifiers: - biotools:unifiedwmwqpcr @@ -45,3 +25,29 @@ extra: path: recipes/bioconductor-unifiedwmwqpcr version: 1.16.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - r-base + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - r-base + +source: + md5: ae72e34d44270475ef2b483734894719 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-uniprot.ws/meta.yaml b/recipes/bioconductor-uniprot.ws/meta.yaml index 07e01957f1b4c..c8314e06336cd 100644 --- a/recipes/bioconductor-uniprot.ws/meta.yaml +++ b/recipes/bioconductor-uniprot.ws/meta.yaml @@ -1,31 +1,41 @@ -{% set version = "2.42.0" %} +{% set version = "2.46.0" %} {% set name = "UniProt.ws" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. This package provides a collection of functions for retrieving, processing, and re-packaging UniProt web services. The package makes use of UniProt's modernized REST API and allows mapping of identifiers accross different databases. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: R Interface to UniProt Web Services -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 47d9ee4038c5dcaf66229e4e1e07c052 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-uniprot.ws", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:uniprot.ws + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-uniprot.ws + path: recipes/bioconductor-uniprot.ws + version: 2.20.4 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-httpcache - r-httr @@ -34,10 +44,10 @@ requirements: - r-rjsoncons - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biocbaseutils >=1.4.0,<1.5.0' - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 - r-base - r-httpcache - r-httr @@ -45,20 +55,16 @@ requirements: - r-progress - r-rjsoncons - r-rsqlite + +source: + md5: 0d984ebed3ba57d6ad6ada3640f1965e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'R Interface to UniProt Web Services' - description: 'The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. This package provides a collection of functions for retrieving, processing, and re-packaging UniProt web services. The package makes use of UniProt''s modernized REST API and allows mapping of identifiers accross different databases.' -extra: - identifiers: - - biotools:uniprot.ws - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-uniprot.ws - path: recipes/bioconductor-uniprot.ws - version: 2.20.4 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-uniprotkeywords/meta.yaml b/recipes/bioconductor-uniprotkeywords/meta.yaml index e997cfd605a01..7f137bc32782a 100644 --- a/recipes/bioconductor-uniprotkeywords/meta.yaml +++ b/recipes/bioconductor-uniprotkeywords/meta.yaml @@ -1,24 +1,23 @@ {% set version = "0.99.7" %} {% set name = "UniProtKeywords" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: b2cda32dda256fb0d110192e194af838 +about: + description: UniProt database provides a list of controlled vocabulary represented as keywords for genes or proteins. This is useful for summarizing gene functions in a compact way. This package provides data of keywords hierarchy and gene-keyword relations. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Keywords from UniProt Database build: - number: 0 + noarch: generic + number: 1 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-uniprotkeywords", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, markdown, testthat requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b2cda32dda256fb0d110192e194af838 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Keywords from UniProt Database' - description: 'UniProt database provides a list of controlled vocabulary represented as keywords for genes or proteins. This is useful for summarizing gene functions in a compact way. This package provides data of keywords hierarchy and gene-keyword relations.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-uniquorn/meta.yaml b/recipes/bioconductor-uniquorn/meta.yaml index 3bcbea9f536d0..13859c9206bc2 100644 --- a/recipes/bioconductor-uniquorn/meta.yaml +++ b/recipes/bioconductor-uniquorn/meta.yaml @@ -1,30 +1,40 @@ -{% set version = "2.22.0" %} +{% set version = "2.26.0" %} {% set name = "Uniquorn" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: '''Uniquorn'' enables users to identify cancer cell lines. Cancer cell line misidentification and cross-contamination reprents a significant challenge for cancer researchers. The identification is vital and in the frame of this package based on the locations/ loci of somatic and germline mutations/ variations. The input format is vcf/ vcf.gz and the files have to contain a single cancer cell line sample (i.e. a single member/genotype/gt column in the vcf file).' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Identification of cancer cell lines based on their weighted mutational/ variational fingerprint -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 63658e23af6991784cdd4b038f2d1268 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-uniquorn", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:uniquorn + - doi:10.18632/oncotarget.16110 + parent_recipe: + name: bioconductor-uniquorn + path: recipes/bioconductor-uniquorn + version: 2.0.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, BiocGenerics requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-data.table - r-doparallel @@ -33,9 +43,9 @@ requirements: - r-stringr - r-writexls run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-data.table - r-doparallel @@ -43,20 +53,16 @@ requirements: - r-r.utils - r-stringr - r-writexls + +source: + md5: 55300f5e8b47cb80f27b9eddf671a8b4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Identification of cancer cell lines based on their weighted mutational/ variational fingerprint' - description: '''Uniquorn'' enables users to identify cancer cell lines. Cancer cell line misidentification and cross-contamination reprents a significant challenge for cancer researchers. The identification is vital and in the frame of this package based on the locations/ loci of somatic and germline mutations/ variations. The input format is vcf/ vcf.gz and the files have to contain a single cancer cell line sample (i.e. a single member/genotype/gt column in the vcf file).' -extra: - identifiers: - - biotools:uniquorn - - doi:10.18632/oncotarget.16110 - parent_recipe: - name: bioconductor-uniquorn - path: recipes/bioconductor-uniquorn - version: 2.0.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-universalmotif/meta.yaml b/recipes/bioconductor-universalmotif/meta.yaml index 3e87affe747df..0b09ca0519ad0 100644 --- a/recipes/bioconductor-universalmotif/meta.yaml +++ b/recipes/bioconductor-universalmotif/meta.yaml @@ -1,31 +1,43 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "universalmotif" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Allows for importing most common motif types into R for use by functions provided by other Bioconductor motif-related packages. Motifs can be exported into most major motif formats from various classes as defined by other Bioconductor packages. A suite of motif and sequence manipulation and analysis functions are included, including enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Import, Modify, and Export Motifs with R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fe680a8d988fce6bfde0af9fdce148de build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-universalmotif", max_pin="x.x") }}' + +extra: + parent_recipe: + name: bioconductor-universalmotif + path: recipes/bioconductor-universalmotif + version: 1.0.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-mass @@ -36,11 +48,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-ggplot2 - r-mass @@ -48,22 +60,16 @@ requirements: - r-rcppthread - r-rlang - r-yaml - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: d0c9b19cc79537e1b4530bddbf061cd5 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Import, Modify, and Export Motifs with R' - description: 'Allows for importing most common motif types into R for use by functions provided by other Bioconductor motif-related packages. Motifs can be exported into most major motif formats from various classes as defined by other Bioconductor packages. A suite of motif and sequence manipulation and analysis functions are included, including enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-universalmotif - path: recipes/bioconductor-universalmotif - version: 1.0.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-updateobject/meta.yaml b/recipes/bioconductor-updateobject/meta.yaml index 0ac250a75a4ef..6775768601fdc 100644 --- a/recipes/bioconductor-updateobject/meta.yaml +++ b/recipes/bioconductor-updateobject/meta.yaml @@ -1,43 +1,43 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "updateObject" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0d69cbbcd4bd9c5f31d905a47f6af212 +about: + description: A set of tools built around updateObject() to work with old serialized S4 instances. The package is primarily useful to package maintainers who want to update the serialized S4 instances included in their package. This is still work-in-progress. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Find/fix old serialized S4 instances build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-updateobject", max_pin="x.x") }}' - noarch: generic -# Suggests: GenomicRanges, SummarizedExperiment, InteractionSet, SingleCellExperiment, MultiAssayExperiment, TimiRGeN, testthat, knitr, rmarkdown, BiocStyle +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: GenomicRanges, SummarizedExperiment, InteractionSet, SingleCellExperiment, MultiAssayExperiment, BiSeq, testthat, knitr, rmarkdown, BiocStyle # SystemRequirements: git requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-digest run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-digest +source: + md5: 86c72e4e2732b9d7ca541898464d0fff + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Find/fix old serialized S4 instances' - description: 'A set of tools built around updateObject() to work with old serialized S4 instances. The package is primarily useful to package maintainers who want to update the serialized S4 instances included in their package. This is still work-in-progress.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-updhmm/build.sh b/recipes/bioconductor-updhmm/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-updhmm/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-updhmm/build_failure.linux-64.yaml b/recipes/bioconductor-updhmm/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..7983cd54e8f98 --- /dev/null +++ b/recipes/bioconductor-updhmm/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 3b58a1e3ed2924d8400340ffc4788b4fb850f72f7b43881ddf85781c7eb836bd # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-hmm")} + Encountered problems while solving: + - nothing provides requested r-hmm + + Could not solve for environment specs + The following package could not be installed + [31mr-hmm[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-hmm")} + Encountered problems while solving: + - nothing provides requested r-hmm + + Could not solve for environment specs + The following package could not be installed + [31mr-hmm[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-hmm")} + Encountered problems while solving: + - nothing provides requested r-hmm + + Could not solve for environment specs + The following package could not be installed + [31mr-hmm[0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-updhmm/meta.yaml b/recipes/bioconductor-updhmm/meta.yaml new file mode 100644 index 0000000000000..f9f2426e3b4a5 --- /dev/null +++ b/recipes/bioconductor-updhmm/meta.yaml @@ -0,0 +1,52 @@ +{% set version = "1.2.0" %} +{% set name = "UPDhmm" %} +{% set bioc = "3.20" %} + +about: + description: Uniparental disomy (UPD) is a genetic condition where an individual inherits both copies of a chromosome or part of it from one parent, rather than one copy from each parent. This package contains a HMM for detecting UPDs through HTS (High Throughput Sequencing) data from trio assays. By analyzing the genotypes in the trio, the model infers a hidden state (normal, father isodisomy, mother isodisomy, father heterodisomy and mother heterodisomy). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Detecting Uniparental Disomy through NGS trio data + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-updhmm", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, testthat (>= 2.1.0), BiocStyle, rmarkdown, markdown, karyoploteR, regioneR, dplyr +requirements: + host: + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - r-base + - r-hmm + run: + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - r-base + - r-hmm + +source: + md5: 0c02f01bfb84fea6abe640011d94321e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-usort/meta.yaml b/recipes/bioconductor-usort/meta.yaml index 5783b25934ca6..d8cd36376fb1e 100644 --- a/recipes/bioconductor-usort/meta.yaml +++ b/recipes/bioconductor-usort/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "uSORT" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package is designed to uncover the intrinsic cell progression path from single-cell RNA-seq data. It incorporates data pre-processing, preliminary PCA gene selection, preliminary cell ordering, feature selection, refined cell ordering, and post-analysis interpretation and visualization. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'uSORT: A self-refining ordering pipeline for gene selection' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0c89e7d86bb2f37b99ce32989b121110 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-usort", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, RUnit, testthat, ggplot2 requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-monocle >=2.30.0,<2.31.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-monocle >=2.34.0,<2.35.0 - r-base - r-cluster - r-fpc @@ -36,9 +37,9 @@ requirements: - r-rspectra - r-vgam run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-monocle >=2.30.0,<2.31.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-monocle >=2.34.0,<2.35.0 - r-base - r-cluster - r-fpc @@ -49,12 +50,16 @@ requirements: - r-rann - r-rspectra - r-vgam + +source: + md5: 53d1a0d6245f450da73f7bcf7eb7a733 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'uSORT: A self-refining ordering pipeline for gene selection' - description: 'This package is designed to uncover the intrinsic cell progression path from single-cell RNA-seq data. It incorporates data pre-processing, preliminary PCA gene selection, preliminary cell ordering, feature selection, refined cell ordering, and post-analysis interpretation and visualization.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-vaexprs/meta.yaml b/recipes/bioconductor-vaexprs/meta.yaml index 41a54d8a833b0..0c77e1b0a2fd0 100644 --- a/recipes/bioconductor-vaexprs/meta.yaml +++ b/recipes/bioconductor-vaexprs/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "VAExprs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A fundamental problem in biomedical research is the low number of observations, mostly due to a lack of available biosamples, prohibitive costs, or ethical reasons. By augmenting a few real observations with artificially generated samples, their analysis could lead to more robust and higher reproducible. One possible solution to the problem is the use of generative models, which are statistical models of data that attempt to capture the entire probability distribution from the observations. Using the variational autoencoder (VAE), a well-known deep generative model, this package is aimed to generate samples with gene expression data, especially for single-cell RNA-seq data. Furthermore, the VAE can use conditioning to produce specific cell types or subpopulations. The conditional VAE (CVAE) allows us to create targeted samples rather than completely random ones. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Generating Samples of Gene Expression Data with Variational Autoencoders -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 6f9ed6eba476abd7908d6849381b545c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-vaexprs", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SC3, knitr, testthat, reticulate, rmarkdown requirements: host: - - 'bioconductor-deeppincs >=1.10.0,<1.11.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deeppincs >=1.14.0,<1.15.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-catencoders - r-diagrammer @@ -34,10 +35,10 @@ requirements: - r-purrr - r-tensorflow run: - - 'bioconductor-deeppincs >=1.10.0,<1.11.0' - - 'bioconductor-scater >=1.30.0,<1.31.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-deeppincs >=1.14.0,<1.15.0 + - bioconductor-scater >=1.34.0,<1.35.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-catencoders - r-diagrammer @@ -45,12 +46,16 @@ requirements: - r-mclust - r-purrr - r-tensorflow + +source: + md5: 21f2c80e58e4fcece263dde33e380f1a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Generating Samples of Gene Expression Data with Variational Autoencoders' - description: 'A fundamental problem in biomedical research is the low number of observations, mostly due to a lack of available biosamples, prohibitive costs, or ethical reasons. By augmenting a few real observations with artificially generated samples, their analysis could lead to more robust and higher reproducible. One possible solution to the problem is the use of generative models, which are statistical models of data that attempt to capture the entire probability distribution from the observations. Using the variational autoencoder (VAE), a well-known deep generative model, this package is aimed to generate samples with gene expression data, especially for single-cell RNA-seq data. Furthermore, the VAE can use conditioning to produce specific cell types or subpopulations. The conditional VAE (CVAE) allows us to create targeted samples rather than completely random ones.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-vanillaice/meta.yaml b/recipes/bioconductor-vanillaice/meta.yaml index ef2b66554d491..3ad5368ccdc8d 100644 --- a/recipes/bioconductor-vanillaice/meta.yaml +++ b/recipes/bioconductor-vanillaice/meta.yaml @@ -1,37 +1,50 @@ -{% set version = "1.64.0" %} +{% set version = "1.68.0" %} {% set name = "VanillaICE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Hidden Markov Models for characterizing chromosomal alteration in high throughput SNP arrays. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2' + summary: A Hidden Markov Model for high throughput genotyping arrays -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 557131c410cc7474d15a4cc9a7d940de build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-vanillaice", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:vanillaice + parent_recipe: + name: bioconductor-vanillaice + path: recipes/bioconductor-vanillaice + version: 1.42.4 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, human610quadv1bCrlmm requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' - - 'bioconductor-crlmm >=1.60.0,<1.61.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0 + - bioconductor-crlmm >=1.64.0,<1.65.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-foreach @@ -40,39 +53,32 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' - - 'bioconductor-crlmm >=1.60.0,<1.61.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-oligoclasses >=1.64.0,<1.65.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0 + - bioconductor-crlmm >=1.64.0,<1.65.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-oligoclasses >=1.68.0,<1.69.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-foreach - r-lattice - r-matrixstats - build: - - {{ compiler('c') }} - - make + +source: + md5: 9130d891ab83de99a24d612d3d5e6e31 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-2 - summary: 'A Hidden Markov Model for high throughput genotyping arrays' - description: 'Hidden Markov Models for characterizing chromosomal alteration in high throughput SNP arrays.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2' -extra: - identifiers: - - biotools:vanillaice - parent_recipe: - name: bioconductor-vanillaice - path: recipes/bioconductor-vanillaice - version: 1.42.4 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-varcon/meta.yaml b/recipes/bioconductor-varcon/meta.yaml index 409d0dc24a003..345efe7e496c5 100644 --- a/recipes/bioconductor-varcon/meta.yaml +++ b/recipes/bioconductor-varcon/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "VarCon" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: VarCon is an R package which converts the positional information from the annotation of an single nucleotide variation (SNV) (either referring to the coding sequence or the reference genomic sequence). It retrieves the genomic reference sequence around the position of the single nucleotide variation. To asses, whether the SNV could potentially influence binding of splicing regulatory proteins VarCon calcualtes the HEXplorer score as an estimation. Besides, VarCon additionally reports splice site strengths of splice sites within the retrieved genomic sequence and any changes due to the SNV. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'VarCon: an R package for retrieving neighboring nucleotides of an SNV' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 843e95d7843d7611c222d8cbca8814b1 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-varcon", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-ggplot2 - r-shiny - r-shinycssloaders - r-shinyfiles run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 - r-base - r-ggplot2 - r-shiny - r-shinycssloaders - r-shinyfiles + +source: + md5: c76771827e1a75ae9f21264daaa49662 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'VarCon: an R package for retrieving neighboring nucleotides of an SNV' - description: 'VarCon is an R package which converts the positional information from the annotation of an single nucleotide variation (SNV) (either referring to the coding sequence or the reference genomic sequence). It retrieves the genomic reference sequence around the position of the single nucleotide variation. To asses, whether the SNV could potentially influence binding of splicing regulatory proteins VarCon calcualtes the HEXplorer score as an estimation. Besides, VarCon additionally reports splice site strengths of splice sites within the retrieved genomic sequence and any changes due to the SNV.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-variancepartition/meta.yaml b/recipes/bioconductor-variancepartition/meta.yaml index ff40c729611e6..8e1745140ddcc 100644 --- a/recipes/bioconductor-variancepartition/meta.yaml +++ b/recipes/bioconductor-variancepartition/meta.yaml @@ -1,30 +1,41 @@ -{% set version = "1.32.2" %} +{% set version = "1.36.2" %} {% set name = "variancePartition" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Quantify and interpret multiple sources of biological and technical variation in gene expression experiments. Uses a linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables. Includes dream differential expression analysis for repeated measures. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Quantify and interpret drivers of variation in multilevel gene expression experiments -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 75a8e840769ba62b9f175c73aba9c99a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-variancepartition", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:variancepartition + parent_recipe: + name: bioconductor-variancepartition + path: recipes/bioconductor-variancepartition + version: 1.10.4 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, cowplot, Rfast, zenith, statmod, BiocGenerics, r2glmm, readr requirements: + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-limma >=3.62.1,<3.63.0 - r-aod - r-base - r-corpcor @@ -32,22 +43,23 @@ requirements: - r-ggplot2 - r-gplots - r-iterators - - 'r-lme4 >=1.1.33' + - r-lme4 >=1.1.33 - r-lmertest - r-mass - - 'r-matrix >=1.4.0' + - r-matrix >=1.4.0 - r-matrixstats - - 'r-pbkrtest >=0.4-4' + - r-pbkrtest >=0.4-4 - r-rdpack - - 'r-remacor >=0.0.15' + - r-remacor >=0.0.15 - r-reshape2 - r-rhpcblasctl - r-rlang - r-scales + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-limma >=3.62.1,<3.63.0 - r-aod - r-base - r-corpcor @@ -55,32 +67,28 @@ requirements: - r-ggplot2 - r-gplots - r-iterators - - 'r-lme4 >=1.1.33' + - r-lme4 >=1.1.33 - r-lmertest - r-mass - - 'r-matrix >=1.4.0' + - r-matrix >=1.4.0 - r-matrixstats - - 'r-pbkrtest >=0.4-4' + - r-pbkrtest >=0.4-4 - r-rdpack - - 'r-remacor >=0.0.15' + - r-remacor >=0.0.15 - r-reshape2 - r-rhpcblasctl - r-rlang - r-scales + +source: + md5: 62e7d3308e7ace9f711bc4903e7edd02 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Quantify and interpret drivers of variation in multilevel gene expression experiments' - description: 'Quantify and interpret multiple sources of biological and technical variation in gene expression experiments. Uses a linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables. Includes dream differential expression analysis for repeated measures.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:variancepartition - parent_recipe: - name: bioconductor-variancepartition - path: recipes/bioconductor-variancepartition - version: 1.10.4 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-variantannotation/meta.yaml b/recipes/bioconductor-variantannotation/meta.yaml index 009efb72b17ce..314149e7e604c 100644 --- a/recipes/bioconductor-variantannotation/meta.yaml +++ b/recipes/bioconductor-variantannotation/meta.yaml @@ -1,86 +1,97 @@ -{% set version = "1.48.1" %} +{% set version = "1.52.0" %} {% set name = "VariantAnnotation" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Annotate variants, compute amino acid coding changes, predict coding outcomes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Annotation of Genetic Variants -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 39b6f4907fe37495a903c338e6d4cc73 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-variantannotation", max_pin="x.x") }}' -# Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle, knitr + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:variantannotation + parent_recipe: + name: bioconductor-variantannotation + path: recipes/bioconductor-variantannotation + version: 1.26.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle, knitr, magick, jsonlite, httr, rjsoncons # SystemRequirements: GNU make requirements: + + build: + - {{ compiler('c') }} + - make + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-xvector >=0.46.0,<0.47.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-dbi - libblas - liblapack + - zlib + - liblzma-devel + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-matrixgenerics >=1.14.0,<1.15.0' - - 'bioconductor-rhtslib >=2.4.0,<2.5.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-rhtslib >=3.2.0,<3.3.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-xvector >=0.46.0,<0.47.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 - r-base - r-dbi - build: - - {{ compiler('c') }} - - make + +source: + md5: dd78ea409fc16978cf2d87763e3b808e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Annotation of Genetic Variants' - description: 'Annotate variants, compute amino acid coding changes, predict coding outcomes.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:variantannotation - parent_recipe: - name: bioconductor-variantannotation - path: recipes/bioconductor-variantannotation - version: 1.26.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-variantexperiment/meta.yaml b/recipes/bioconductor-variantexperiment/meta.yaml index d996d1d7f6948..1c6f46e597c43 100644 --- a/recipes/bioconductor-variantexperiment/meta.yaml +++ b/recipes/bioconductor-variantexperiment/meta.yaml @@ -1,59 +1,64 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "VariantExperiment" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: VariantExperiment is a Bioconductor package for saving data in VCF/GDS format into RangedSummarizedExperiment object. The high-throughput genetic/genomic data are saved in GDSArray objects. The annotation data for features/samples are saved in DelayedDataFrame format with mono-dimensional GDSArray in each column. The on-disk representation of both assay data and annotation data achieves on-disk reading and processing and saves memory space significantly. The interface of RangedSummarizedExperiment data format enables easy and common manipulations for high-throughput genetic/genomic data with common SummarizedExperiment metaphor in R and Bioconductor. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: cfa81c58331066ea4f23ce2ba29fa114 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-variantexperiment", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, knitr, rmarkdown, markdown, BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayeddataframe >=1.18.0,<1.19.0' - - 'bioconductor-gdsarray >=1.22.0,<1.23.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-seqarray >=1.42.0,<1.43.0' - - 'bioconductor-snprelate >=1.36.0,<1.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayeddataframe >=1.22.0,<1.23.0 + - bioconductor-gdsarray >=1.26.0,<1.27.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqarray >=1.46.0,<1.47.0 + - bioconductor-snprelate >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayeddataframe >=1.18.0,<1.19.0' - - 'bioconductor-gdsarray >=1.22.0,<1.23.0' - - 'bioconductor-gdsfmt >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-seqarray >=1.42.0,<1.43.0' - - 'bioconductor-snprelate >=1.36.0,<1.37.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayeddataframe >=1.22.0,<1.23.0 + - bioconductor-gdsarray >=1.26.0,<1.27.0 + - bioconductor-gdsfmt >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-seqarray >=1.46.0,<1.47.0 + - bioconductor-snprelate >=1.40.0,<1.41.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base + +source: + md5: c4c1b7d10f9226bb6a48853b1645385b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend' - description: 'VariantExperiment is a Bioconductor package for saving data in VCF/GDS format into RangedSummarizedExperiment object. The high-throughput genetic/genomic data are saved in GDSArray objects. The annotation data for features/samples are saved in DelayedDataFrame format with mono-dimensional GDSArray in each column. The on-disk representation of both assay data and annotation data achieves on-disk reading and processing and saves memory space significantly. The interface of RangedSummarizedExperiment data format enables easy and common manipulations for high-throughput genetic/genomic data with common SummarizedExperiment metaphor in R and Bioconductor.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-variantfiltering/build_failure.osx-64.yaml b/recipes/bioconductor-variantfiltering/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..a720c83a30c37 --- /dev/null +++ b/recipes/bioconductor-variantfiltering/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 07f50ed4eb9cd711c34309f6dfe723f347dee6c6fc5e524016561e001f94e03c # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-genomeinfodbdata [1.2.1|1.2.2] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-genomeinfodbdata [1.2.10|1.2.11] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.3|1.2.4] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.6|1.2.7] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-genomeinfodbdata 1.2.9 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-ucsc.utils >=1.2.0,<1.3.0 is not installable because it requires + r-base >=4.4,<4.5.0a0 , which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("clang==4.0.1=1"), MatchSpec("4.0.1==hcfea43d_1")} + Encountered problems while solving: + - nothing provides compiler-rt 4.0.1 hcfea43d_1 needed by clang-4.0.1-1 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-genomeinfodbdata >=1.2.0,<1.3.0 is installable with the potential options + bioconductor-genomeinfodbdata [1.2.0|1.2.1] would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-genomeinfodbdata [1.2.1|1.2.2] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-genomeinfodbdata [1.2.10|1.2.11] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.3|1.2.4] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-genomeinfodbdata [1.2.6|1.2.7] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-genomeinfodbdata 1.2.9 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-ucsc.utils >=1.2.0,<1.3.0 is not installable because it requires + r-base >=4.4,<4.5.0a0 , which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-variantfiltering/meta.yaml b/recipes/bioconductor-variantfiltering/meta.yaml index 339238b836f34..1f9a2bf51f93a 100644 --- a/recipes/bioconductor-variantfiltering/meta.yaml +++ b/recipes/bioconductor-variantfiltering/meta.yaml @@ -1,45 +1,60 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "VariantFiltering" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Filtering of coding and non-coding genetic variants -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: af4ddac4cfb857eea4db9309da6de07d build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-variantfiltering", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:variantfiltering + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-variantfiltering + path: recipes/bioconductor-variantfiltering + version: 1.16.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RUnit, BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137 requirements: + + build: + - {{ compiler('c') }} + - make + host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-dt - r-shiny @@ -48,49 +63,43 @@ requirements: - r-shinytree - libblas - liblapack + run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-genomicscores >=2.14.0,<2.15.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-gviz >=1.46.0,<1.47.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rbgl >=1.78.0,<1.79.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' - - 'bioconductor-xvector >=0.42.0,<0.43.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-genomicscores >=2.18.0,<2.19.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-gviz >=1.50.0,<1.51.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rbgl >=1.82.0,<1.83.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 + - bioconductor-xvector >=0.46.0,<0.47.0 - r-base - r-dt - r-shiny - r-shinyjs - r-shinythemes - r-shinytree - build: - - {{ compiler('c') }} - - make + +source: + md5: 476ffb544e139f8c781219772ca94edb + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Filtering of coding and non-coding genetic variants' - description: 'Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.' -extra: - identifiers: - - biotools:variantfiltering - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-variantfiltering - path: recipes/bioconductor-variantfiltering - version: 1.16.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-varianttools/meta.yaml b/recipes/bioconductor-varianttools/meta.yaml index 6a504d7d03da0..48bf27a527bcc 100644 --- a/recipes/bioconductor-varianttools/meta.yaml +++ b/recipes/bioconductor-varianttools/meta.yaml @@ -1,72 +1,78 @@ -{% set version = "1.44.0" %} +{% set version = "1.48.0" %} {% set name = "VariantTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Explore, diagnose, and compare variant calls using filters. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Tools for Exploratory Analysis of Variant Calls -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 34afccb56ff143a33019bdd8f2e356ca build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-varianttools", max_pin="x.x") }}' - noarch: generic -# Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>= 1.21.3), TxDb.Hsapiens.UCSC.hg19.knownGene + +extra: + identifiers: + - biotools:varianttools + - doi:10.1101/027227 + parent_recipe: + name: bioconductor-varianttools + path: recipes/bioconductor-varianttools + version: 1.22.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>= 1.21.3), TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-matrix run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-matrix + +source: + md5: f6c19154d3f135e8a0eaf32f6c0bc12c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Tools for Exploratory Analysis of Variant Calls' - description: 'Explore, diagnose, and compare variant calls using filters.' -extra: - identifiers: - - biotools:varianttools - - doi:10.1101/027227 - parent_recipe: - name: bioconductor-varianttools - path: recipes/bioconductor-varianttools - version: 1.22.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-varianttoolsdata/meta.yaml b/recipes/bioconductor-varianttoolsdata/meta.yaml index a8a952360d6fc..e3108eb9c0cdb 100644 --- a/recipes/bioconductor-varianttoolsdata/meta.yaml +++ b/recipes/bioconductor-varianttoolsdata/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "VariantToolsData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a85757ce237b03b0480f01488a78879b +about: + description: Data from the sequencing of a 50/50 mixture of HapMap trio samples NA12878 (CEU) and NA19240 (YRI), subset to the TP53 region. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Data for the VariantTools tutorial build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-varianttoolsdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: VariantTools (>= 1.3.4), gmapR (>= 1.3.3), BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 00072c40be7324743e9a1d9f7507a743 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Data for the VariantTools tutorial' - description: 'Data from the sequencing of a 50/50 mixture of HapMap trio samples NA12878 (CEU) and NA19240 (YRI), subset to the TP53 region.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-varianttoolsdata/post-link.sh b/recipes/bioconductor-varianttoolsdata/post-link.sh index 7c1ae1c238049..59f3a16f99ed0 100644 --- a/recipes/bioconductor-varianttoolsdata/post-link.sh +++ b/recipes/bioconductor-varianttoolsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "varianttoolsdata-1.26.0" +installBiocDataPackage.sh "varianttoolsdata-1.30.0" diff --git a/recipes/bioconductor-vasp/meta.yaml b/recipes/bioconductor-vasp/meta.yaml index b3e673476385f..4c5b597264b97 100644 --- a/recipes/bioconductor-vasp/meta.yaml +++ b/recipes/bioconductor-vasp/meta.yaml @@ -1,55 +1,60 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "VaSP" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Discovery of genome-wide variable alternative splicing events from short-read RNA-seq data and visualizations of gene splicing information for publication-quality multi-panel figures in a population. (Warning: The visualizing function is removed due to the dependent package Sushi deprecated. If you want to use it, please change back to an older version.)' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2.0) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Quantification and Visualization of Variations of Splicing in Population -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 5fddc833bc7dd84dfb16e030fe966cd3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-vasp", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-ballgown >=2.34.0,<2.35.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-ballgown >=2.38.0,<2.39.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cluster - r-matrixstats run: - - 'bioconductor-ballgown >=2.34.0,<2.35.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-ballgown >=2.38.0,<2.39.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cluster - r-matrixstats + +source: + md5: 7adc829474be248c6792bf9d210a7bd7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2.0)' - summary: 'Quantification and Visualization of Variations of Splicing in Population' - description: 'Discovery of genome-wide variable alternative splicing events from short-read RNA-seq data and visualizations of gene splicing information for publication-quality multi-panel figures in a population. (Warning: The visualizing function is removed due to the dependent package Sushi deprecated. If you want to use it, please change back to an older version.)' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-vbmp/meta.yaml b/recipes/bioconductor-vbmp/meta.yaml index ce99b5aa8630f..f1dcd2839d4dc 100644 --- a/recipes/bioconductor-vbmp/meta.yaml +++ b/recipes/bioconductor-vbmp/meta.yaml @@ -1,39 +1,20 @@ -{% set version = "1.70.0" %} +{% set version = "1.74.0" %} {% set name = "vbmp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b7d2a0a9950dd7ecdbcea5ffdfbd853c +about: + description: Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the full posterior. This software also incorporates feature weighting by means of Automatic Relevance Determination. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Variational Bayesian Multinomial Probit Regression build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-vbmp", max_pin="x.x") }}' - noarch: generic -# Suggests: Biobase (>= 2.5.5), statmod -requirements: - host: - - r-base - run: - - r-base -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Variational Bayesian Multinomial Probit Regression' - description: 'Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the full posterior. This software also incorporates feature weighting by means of Automatic Relevance Determination.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: identifiers: - biotools:vbmp @@ -42,4 +23,23 @@ extra: name: bioconductor-vbmp path: recipes/bioconductor-vbmp version: 1.48.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: Biobase (>= 2.5.5), statmod +requirements: + host: + - r-base + run: + - r-base +source: + md5: 8e3b858522daf1a1e68a7aad26421977 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz +test: + commands: + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-vcfarray/meta.yaml b/recipes/bioconductor-vcfarray/meta.yaml index b97fe14953639..93106b36503f0 100644 --- a/recipes/bioconductor-vcfarray/meta.yaml +++ b/recipes/bioconductor-vcfarray/meta.yaml @@ -1,51 +1,56 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "VCFArray" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: VCFArray extends the DelayedArray to represent VCF data entries as array-like objects with on-disk / remote VCF file as backend. Data entries from VCF files, including info fields, FORMAT fields, and the fixed columns (REF, ALT, QUAL, FILTER) could be converted into VCFArray instances with different dimensions. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Representing on-disk / remote VCF files as array-like objects -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e101fbb3c6c6b57d792527a6c720654 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-vcfarray", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomicfiles >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomicfiles >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomicfiles >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base + +source: + md5: dfa387127317ca8b0b0faafef76804e6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Representing on-disk / remote VCF files as array-like objects' - description: 'VCFArray extends the DelayedArray to represent VCF data entries as array-like objects with on-disk / remote VCF file as backend. Data entries from VCF files, including info fields, FORMAT fields, and the fixed columns (REF, ALT, QUAL, FILTER) could be converted into VCFArray instances with different dimensions.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-vdjdive/meta.yaml b/recipes/bioconductor-vdjdive/meta.yaml index 9f4d20bf8610f..d313d020f95ed 100644 --- a/recipes/bioconductor-vdjdive/meta.yaml +++ b/recipes/bioconductor-vdjdive/meta.yaml @@ -1,31 +1,36 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "VDJdive" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functions for handling and analyzing immune receptor repertoire data, such as produced by the CellRanger V(D)J pipeline. This includes reading the data into R, merging it with paired single-cell data, quantifying clonotype abundances, calculating diversity metrics, and producing common plots. It implements the E-M Algorithm for clonotype assignment, along with other methods, which makes use of ambiguous cells for improved quantification. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Analysis Tools for 10X V(D)J Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 938051376344953e02e510f65d156939 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-vdjdive", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: breakaway, covr, knitr, rmarkdown, testthat, BiocStyle requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cowplot - r-ggplot2 @@ -36,11 +41,11 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cowplot - r-ggplot2 @@ -48,16 +53,16 @@ requirements: - r-matrix - r-rcolorbrewer - r-rcpp - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: e36bca9c91ac3f6a9499e622ee72c775 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Analysis Tools for 10X V(D)J Data' - description: 'This package provides functions for handling and analyzing immune receptor repertoire data, such as produced by the CellRanger V(D)J pipeline. This includes reading the data into R, merging it with paired single-cell data, quantifying clonotype abundances, calculating diversity metrics, and producing common plots. It implements the E-M Algorithm for clonotype assignment, along with other methods, which makes use of ambiguous cells for improved quantification.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-vectrapolarisdata/meta.yaml b/recipes/bioconductor-vectrapolarisdata/meta.yaml index 5c6b9f5915e33..40aaf57f99e93 100644 --- a/recipes/bioconductor-vectrapolarisdata/meta.yaml +++ b/recipes/bioconductor-vectrapolarisdata/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "VectraPolarisData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea2006b85e374e76fbd70ca8b0819072 +about: + description: Provides two multiplex imaging datasets collected on Vectra instruments at the University of Colorado Anschutz Medical Campus. Data are provided as a Spatial Experiment objects. Data is provided in tabular form and has been segmented and phenotyped using Inform software. Raw .tiff files are not included. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Vectra Polaris and Vectra 3 multiplex single-cell imaging data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-vectrapolarisdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown, dplyr requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9a68d6def6946fea171b63621c349a0b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Vectra Polaris and Vectra 3 multiplex single-cell imaging data' - description: 'Provides two multiplex imaging datasets collected on Vectra instruments at the University of Colorado Anschutz Medical Campus. Data are provided as a Spatial Experiment objects. Data is provided in tabular form and has been segmented and phenotyped using Inform software. Raw .tiff files are not included.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-vectrapolarisdata/post-link.sh b/recipes/bioconductor-vectrapolarisdata/post-link.sh index 2f937fb860681..d9c5eee15da86 100644 --- a/recipes/bioconductor-vectrapolarisdata/post-link.sh +++ b/recipes/bioconductor-vectrapolarisdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "vectrapolarisdata-1.6.0" +installBiocDataPackage.sh "vectrapolarisdata-1.10.0" diff --git a/recipes/bioconductor-vegamc/meta.yaml b/recipes/bioconductor-vegamc/meta.yaml index d21a2211e6724..bcb37a359698c 100644 --- a/recipes/bioconductor-vegamc/meta.yaml +++ b/recipes/bioconductor-vegamc/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "3.40.0" %} +{% set version = "3.44.0" %} {% set name = "VegaMC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. VegaMC performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, VegaMC produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: 'VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0e02ae3375b7bed5ca1ed7011b60f180 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-vegamc", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:vegamc + - doi:10.1093/bioinformatics/bts453 + parent_recipe: + name: bioconductor-vegamc + path: recipes/bioconductor-vegamc + version: 3.18.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biomart >=2.62.0,<2.63.0 - r-base - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biomart >=2.62.0,<2.63.0 - r-base - build: - - {{ compiler('c') }} - - make + +source: + md5: 56d81745f2bcce03cfbd36035be34587 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer' - description: 'This package enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. VegaMC performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, VegaMC produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:vegamc - - doi:10.1093/bioinformatics/bts453 - parent_recipe: - name: bioconductor-vegamc - path: recipes/bioconductor-vegamc - version: 3.18.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-velociraptor/meta.yaml b/recipes/bioconductor-velociraptor/meta.yaml index 85b401a821df5..09d5075e9b381 100644 --- a/recipes/bioconductor-velociraptor/meta.yaml +++ b/recipes/bioconductor-velociraptor/meta.yaml @@ -1,61 +1,66 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "velociraptor" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides Bioconductor-friendly wrappers for RNA velocity calculations in single-cell RNA-seq data. We use the basilisk package to manage Conda environments, and the zellkonverter package to convert data structures between SingleCellExperiment (R) and AnnData (Python). The information produced by the velocity methods is stored in the various components of the SingleCellExperiment class. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Toolkit for Single-Cell Velocity -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d2c16e280b1957ef3989e5d02f4f0b5d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-velociraptor", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat, knitr, rmarkdown, pkgdown, scran, scater, scRNAseq, Rtsne, graphics, grDevices, ggplot2, cowplot, GGally, patchwork, metR requirements: host: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zellkonverter >=1.12.0,<1.13.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zellkonverter >=1.16.0,<1.17.0 - r-base - r-matrix - r-reticulate run: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-biocsingular >=1.18.0,<1.19.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-scuttle >=1.12.0,<1.13.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-zellkonverter >=1.12.0,<1.13.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-biocsingular >=1.22.0,<1.23.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-scuttle >=1.16.0,<1.17.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-zellkonverter >=1.16.0,<1.17.0 - r-base - r-matrix - r-reticulate + +source: + md5: fd40fd69025725daf863b9c0bcfe46b6 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Toolkit for Single-Cell Velocity' - description: 'This package provides Bioconductor-friendly wrappers for RNA velocity calculations in single-cell RNA-seq data. We use the basilisk package to manage Conda environments, and the zellkonverter package to convert data structures between SingleCellExperiment (R) and AnnData (Python). The information produced by the velocity methods is stored in the various components of the SingleCellExperiment class.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-veloviz/meta.yaml b/recipes/bioconductor-veloviz/meta.yaml index 8fa3402c305e9..4de0ceffb3e51 100644 --- a/recipes/bioconductor-veloviz/meta.yaml +++ b/recipes/bioconductor-veloviz/meta.yaml @@ -1,25 +1,31 @@ -{% set version = "1.8.0" %} +{% set version = "1.12.0" %} {% set name = "veloviz" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: VeloViz uses each cell’s current observed and predicted future transcriptional states inferred from RNA velocity analysis to build a nearest neighbor graph between cells in the population. Edges are then pruned based on a cosine correlation threshold and/or a distance threshold and the resulting graph is visualized using a force-directed graph layout algorithm. VeloViz can help ensure that relationships between cell states are reflected in the 2D embedding, allowing for more reliable representation of underlying cellular trajectories. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: 'VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 54c6f9e5fd6275be8b999a2c949cf6bb build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-veloviz", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - r-base - r-igraph @@ -36,17 +42,16 @@ requirements: - r-mgcv - r-rcpp - r-rspectra - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: a8ffce477dd8f292384581007676310a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories' - description: 'VeloViz uses each cell’s current observed and predicted future transcriptional states inferred from RNA velocity analysis to build a nearest neighbor graph between cells in the population. Edges are then pruned based on a cosine correlation threshold and/or a distance threshold and the resulting graph is visualized using a force-directed graph layout algorithm. VeloViz can help ensure that relationships between cell states are reflected in the 2D embedding, allowing for more reliable representation of underlying cellular trajectories.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-venndetail/meta.yaml b/recipes/bioconductor-venndetail/meta.yaml index 42c138436e3dd..0d3c51528fecc 100644 --- a/recipes/bioconductor-venndetail/meta.yaml +++ b/recipes/bioconductor-venndetail/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "VennDetail" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A set of functions to generate high-resolution Venn,Vennpie plot,extract and combine details of these subsets with user datasets in data frame is available. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: A package for visualization and extract details -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: be9c3506e9707fe42642ea413c0873a6 build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-venndetail", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat, markdown requirements: host: @@ -41,13 +43,16 @@ requirements: - r-tibble - r-upsetr - r-venndiagram + +source: + md5: b33219812581c7f136ca5fb0fad9f585 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'A package for visualization and extract details' - description: 'A set of functions to generate high-resolution Venn,Vennpie plot,extract and combine details of these subsets with user datasets in data frame is available.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-verso/meta.yaml b/recipes/bioconductor-verso/meta.yaml index f142090d335ed..693e7ad386c5c 100644 --- a/recipes/bioconductor-verso/meta.yaml +++ b/recipes/bioconductor-verso/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "VERSO" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dcc0220c3f10bb1efaaa360448547771 +about: + description: Mutations that rapidly accumulate in viral genomes during a pandemic can be used to track the evolution of the virus and, accordingly, unravel the viral infection network. To this extent, sequencing samples of the virus can be employed to estimate models from genomic epidemiology and may serve, for instance, to estimate the proportion of undetected infected people by uncovering cryptic transmissions, as well as to predict likely trends in the number of infected, hospitalized, dead and recovered people. VERSO is an algorithmic framework that processes variants profiles from viral samples to produce phylogenetic models of viral evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints, by maximizing a log-likelihood function. VERSO includes two separate and subsequent steps; in this package we provide an R implementation of VERSO STEP 1. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Viral Evolution ReconStructiOn (VERSO) build: - number: 1 + noarch: generic + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-verso", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocGenerics, BiocStyle, testthat, knitr requirements: host: @@ -31,13 +30,14 @@ requirements: - r-base - r-data.tree - r-rfast +source: + md5: 6a867220991a119efc8c402960fd85c7 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Viral Evolution ReconStructiOn (VERSO)' - description: 'Mutations that rapidly accumulate in viral genomes during a pandemic can be used to track the evolution of the virus and, accordingly, unravel the viral infection network. To this extent, sequencing samples of the virus can be employed to estimate models from genomic epidemiology and may serve, for instance, to estimate the proportion of undetected infected people by uncovering cryptic transmissions, as well as to predict likely trends in the number of infected, hospitalized, dead and recovered people. VERSO is an algorithmic framework that processes variants profiles from viral samples to produce phylogenetic models of viral evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints, by maximizing a log-likelihood function. VERSO includes two separate and subsequent steps; in this package we provide an R implementation of VERSO STEP 1.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-vidger/meta.yaml b/recipes/bioconductor-vidger/meta.yaml index 6104b533f8e4e..f4fefa2babf64 100644 --- a/recipes/bioconductor-vidger/meta.yaml +++ b/recipes/bioconductor-vidger/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "vidger" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The aim of vidger is to rapidly generate information-rich visualizations for the interpretation of differential gene expression results from three widely-used tools: Cuffdiff, DESeq2, and edgeR.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 | file LICENSE + license_file: LICENSE + summary: Create rapid visualizations of RNAseq data in R -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 01029a545153064095a804a7e9093231 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-vidger", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggally - r-ggplot2 @@ -36,10 +38,10 @@ requirements: - r-scales - r-tidyr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggally - r-ggplot2 @@ -49,13 +51,16 @@ requirements: - r-rmarkdown - r-scales - r-tidyr + +source: + md5: d459258deb55f30911ad22bd309917c9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 | file LICENSE' - summary: 'Create rapid visualizations of RNAseq data in R' - description: 'The aim of vidger is to rapidly generate information-rich visualizations for the interpretation of differential gene expression results from three widely-used tools: Cuffdiff, DESeq2, and edgeR.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-viper/meta.yaml b/recipes/bioconductor-viper/meta.yaml index d7cc28cd92f69..c18c7ca23944f 100644 --- a/recipes/bioconductor-viper/meta.yaml +++ b/recipes/bioconductor-viper/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.36.0" %} +{% set version = "1.40.0" %} {% set name = "viper" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Inference of protein activity from gene expression data, including the VIPER and msVIPER algorithms + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: file LICENSE + license_file: LICENSE + summary: Virtual Inference of Protein-activity by Enriched Regulon analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0d7f13a212bc6fc5d7cf2213a1bfbdb0 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-viper", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:viper + parent_recipe: + name: bioconductor-viper + path: recipes/bioconductor-viper + version: 1.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: bcellViper requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-e1071 - r-kernsmooth - r-mixtools run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - r-e1071 - r-kernsmooth - r-mixtools + +source: + md5: 03f5022274388eca503bcf1f54ede7da + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'file LICENSE' - summary: 'Virtual Inference of Protein-activity by Enriched Regulon analysis' - description: 'Inference of protein activity from gene expression data, including the VIPER and msVIPER algorithms' - license_file: LICENSE -extra: - identifiers: - - biotools:viper - parent_recipe: - name: bioconductor-viper - path: recipes/bioconductor-viper - version: 1.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-visiumio/build.sh b/recipes/bioconductor-visiumio/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-visiumio/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-visiumio/meta.yaml b/recipes/bioconductor-visiumio/meta.yaml new file mode 100644 index 0000000000000..e21a555994e8c --- /dev/null +++ b/recipes/bioconductor-visiumio/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.2.0" %} +{% set name = "VisiumIO" %} +{% set bioc = "3.20" %} + +about: + description: The package allows users to readily import spatial data obtained from either the 10X website or from the Space Ranger pipeline. Supported formats include tar.gz, h5, and mtx files. Multiple files can be imported at once with *List type of functions. The package represents data mainly as SpatialExperiment objects. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Import Visium data from the 10X Space Ranger pipeline + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-visiumio", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: arrow, BiocStyle, knitr, rmarkdown, tinytest +requirements: + host: + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tenxio >=1.8.0,<1.9.0 + - r-base + - r-jsonlite + run: + - bioconductor-biocbaseutils >=1.8.0,<1.9.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocio >=1.16.0,<1.17.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tenxio >=1.8.0,<1.9.0 + - r-base + - r-jsonlite + +source: + md5: 8481b7a76d9f43e7c7f2285a189cd152 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-visse/meta.yaml b/recipes/bioconductor-visse/meta.yaml index f9e749668920d..26361dcd4ee46 100644 --- a/recipes/bioconductor-visse/meta.yaml +++ b/recipes/bioconductor-visse/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "vissE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package enables the interpretation and analysis of results from a gene set enrichment analysis using network-based and text-mining approaches. Most enrichment analyses result in large lists of significant gene sets that are difficult to interpret. Tools in this package help build a similarity-based network of significant gene sets from a gene set enrichment analysis that can then be investigated for their biological function using text-mining approaches. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Visualising Set Enrichment Analysis Results -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1c5018fd43f416ebc2d035a143877154 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-visse", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore, knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr requirements: host: - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-msigdb >=1.10.0,<1.11.0' + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-msigdb >=1.14.0,<1.15.0 - r-base - r-ggforce - r-ggplot2 @@ -40,8 +42,8 @@ requirements: - r-tidygraph - r-tm run: - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-msigdb >=1.10.0,<1.11.0' + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-msigdb >=1.14.0,<1.15.0 - r-base - r-ggforce - r-ggplot2 @@ -57,13 +59,16 @@ requirements: - r-textstem - r-tidygraph - r-tm + +source: + md5: 07e33163eb61ab6d823b565a43e3475a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Visualising Set Enrichment Analysis Results' - description: 'This package enables the interpretation and analysis of results from a gene set enrichment analysis using network-based and text-mining approaches. Most enrichment analyses result in large lists of significant gene sets that are difficult to interpret. Tools in this package help build a similarity-based network of significant gene sets from a gene set enrichment analysis that can then be investigated for their biological function using text-mining approaches.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-vitisviniferacdf/meta.yaml b/recipes/bioconductor-vitisviniferacdf/meta.yaml index 700763f7b9e4a..ba30431d6b67e 100644 --- a/recipes/bioconductor-vitisviniferacdf/meta.yaml +++ b/recipes/bioconductor-vitisviniferacdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "vitisviniferacdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8eb491f3ffa3ff0814f5c155787ae160 +about: + description: A package containing an environment representing the Vitis_Vinifera.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: vitisviniferacdf build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-vitisviniferacdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 8eb491f3ffa3ff0814f5c155787ae160 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: vitisviniferacdf - description: 'A package containing an environment representing the Vitis_Vinifera.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-vitisviniferaprobe/meta.yaml b/recipes/bioconductor-vitisviniferaprobe/meta.yaml index 6c147fb71d4de..0750b67445388 100644 --- a/recipes/bioconductor-vitisviniferaprobe/meta.yaml +++ b/recipes/bioconductor-vitisviniferaprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "vitisviniferaprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 386c0d5e37896d073ac20970e88b3160 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Vitis\_Vinifera\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type vitisvinifera build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-vitisviniferaprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 386c0d5e37896d073ac20970e88b3160 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type vitisvinifera' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Vitis\_Vinifera\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-voyager/meta.yaml b/recipes/bioconductor-voyager/meta.yaml index 805d9605955ad..ecef331683d4c 100644 --- a/recipes/bioconductor-voyager/meta.yaml +++ b/recipes/bioconductor-voyager/meta.yaml @@ -1,40 +1,44 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.1" %} {% set name = "Voyager" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: SpatialFeatureExperiment (SFE) is a new S4 class for working with spatial single-cell genomics data. The voyager package implements basic exploratory spatial data analysis (ESDA) methods for SFE. Univariate methods include univariate global spatial ESDA methods such as Moran's I, permutation testing for Moran's I, and correlograms. Bivariate methods include Lee's L and cross variogram. Multivariate methods include MULTISPATI PCA and multivariate local Geary's C recently developed by Anselin. The Voyager package also implements plotting functions to plot SFE data and ESDA results. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: From geospatial to spatial omics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 1cc32e63cf1c410d82c2cd1a26f9f929 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-voyager", max_pin="x.x") }}' - noarch: generic -# Suggests: automap, BiocSingular, BiocStyle, cowplot, ExperimentHub, ggh4x, gstat, hexbin, knitr, pheatmap, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, vroom + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: arrow, automap, BiocSingular, BiocStyle, cowplot, data.table, EBImage, ExperimentHub, ggh4x, gstat, hexbin, knitr, pheatmap, RBioFormats, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, xml2 requirements: + host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bluster >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-spatialfeatureexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bluster >=1.16.0,<1.17.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-spatialfeatureexperiment >=1.8.0,<1.9.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggnewscale - - 'r-ggplot2 >=3.4.0' + - r-ggplot2 >=3.4.0 - r-lifecycle - r-matrix - r-matrixstats + - r-memuse - r-patchwork - r-rlang - r-rspectra @@ -43,20 +47,24 @@ requirements: - r-sf - r-spdep - r-terra + - r-zeallot + run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-bluster >=1.12.0,<1.13.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' - - 'bioconductor-spatialfeatureexperiment >=1.4.0,<1.5.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-bluster >=1.16.0,<1.17.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-spatialfeatureexperiment >=1.8.0,<1.9.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-ggnewscale - - 'r-ggplot2 >=3.4.0' + - r-ggplot2 >=3.4.0 - r-lifecycle - r-matrix - r-matrixstats + - r-memuse - r-patchwork - r-rlang - r-rspectra @@ -65,12 +73,17 @@ requirements: - r-sf - r-spdep - r-terra + - r-zeallot + +source: + md5: 9b6f91a4b44f8820daaad795059eb572 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'From geospatial to spatial omics' - description: 'SpatialFeatureExperiment (SFE) is a new S4 class for working with spatial single-cell genomics data. The voyager package implements basic exploratory spatial data analysis (ESDA) methods for SFE. Univariate methods include univariate global spatial ESDA methods such as Moran''s I, permutation testing for Moran''s I, and correlograms. Bivariate methods include Lee''s L and cross variogram. Multivariate methods include MULTISPATI PCA and multivariate local Geary''s C recently developed by Anselin. The Voyager package also implements plotting functions to plot SFE data and ESDA results.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-vplotr/meta.yaml b/recipes/bioconductor-vplotr/meta.yaml index 60b10ff4e2b2e..53bb61e56c5cb 100644 --- a/recipes/bioconductor-vplotr/meta.yaml +++ b/recipes/bioconductor-vplotr/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.12.1" %} +{% set version = "1.16.0" %} {% set name = "VplotR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The pattern of digestion and protection from DNA nucleases such as DNAse I, micrococcal nuclease, and Tn5 transposase can be used to infer the location of associated proteins. This package contains useful functions to analyze patterns of paired-end sequencing fragment density. VplotR facilitates the generation of V-plots and footprint profiles over single or aggregated genomic loci of interest. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 3) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Set of tools to make V-plots and compute footprint profiles -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 91af0fd39cd72be94b7f5d674d9e494f build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-vplotr", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown requirements: host: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cowplot - r-ggplot2 @@ -36,12 +38,12 @@ requirements: - r-reshape2 - r-zoo run: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-cowplot - r-ggplot2 @@ -49,13 +51,16 @@ requirements: - r-rcolorbrewer - r-reshape2 - r-zoo + +source: + md5: 6158b3c841b45bf9e09ebb91b183ef19 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' - summary: 'Set of tools to make V-plots and compute footprint profiles' - description: 'The pattern of digestion and protection from DNA nucleases such as DNAse I, micrococcal nuclease, and Tn5 transposase can be used to infer the location of associated proteins. This package contains useful functions to analyze patterns of paired-end sequencing fragment density. VplotR facilitates the generation of V-plots and footprint profiles over single or aggregated genomic loci of interest.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-vsclust/meta.yaml b/recipes/bioconductor-vsclust/meta.yaml index 7ba0555dd39b9..a72c1ce8f56c1 100644 --- a/recipes/bioconductor-vsclust/meta.yaml +++ b/recipes/bioconductor-vsclust/meta.yaml @@ -1,29 +1,35 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "vsclust" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Feature-based variance-sensitive clustering of omics data. Optimizes cluster assignment by taking into account individual feature variance. Includes several modules for statistical testing, clustering and enrichment analysis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Feature-based variance-sensitive quantitative clustering -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0c492a6d65d0b230211a0f95706b51a4 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-vsclust", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle, clusterProfiler requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - r-matrixstats - r-rcpp @@ -31,24 +37,23 @@ requirements: - libblas - liblapack run: - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 - r-base - r-matrixstats - r-rcpp - r-shiny - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 5c1a8e08525ed6e692ef423a14d5e9e9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Feature-based variance-sensitive quantitative clustering' - description: 'Feature-based variance-sensitive clustering of omics data. Optimizes cluster assignment by taking into account individual feature variance. Includes several modules for statistical testing, clustering and enrichment analysis.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-vsn/meta.yaml b/recipes/bioconductor-vsn/meta.yaml index 073be9e2252d4..c778553501f27 100644 --- a/recipes/bioconductor-vsn/meta.yaml +++ b/recipes/bioconductor-vsn/meta.yaml @@ -1,59 +1,65 @@ -{% set version = "3.70.0" %} +{% set version = "3.74.0" %} {% set name = "vsn" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package implements a method for normalising microarray intensities from single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Variance stabilization and calibration for microarray data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1c9484f361b22f76135af5567306f0c6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-vsn", max_pin="x.x") }}' + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:vsn + parent_recipe: + name: bioconductor-vsn + path: recipes/bioconductor-vsn + version: 3.48.1 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat requirements: + build: + - {{ compiler('c') }} + - make host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-ggplot2 - r-lattice - libblas - liblapack run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-ggplot2 - r-lattice - build: - - {{ compiler('c') }} - - make + +source: + md5: dbffe4c2a84f437962fd43c987bd35b4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Variance stabilization and calibration for microarray data' - description: 'The package implements a method for normalising microarray intensities from single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.' -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:vsn - parent_recipe: - name: bioconductor-vsn - path: recipes/bioconductor-vsn - version: 3.48.1 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-vtpnet/meta.yaml b/recipes/bioconductor-vtpnet/meta.yaml index 5c0307387b96c..98a001aec90cd 100644 --- a/recipes/bioconductor-vtpnet/meta.yaml +++ b/recipes/bioconductor-vtpnet/meta.yaml @@ -1,46 +1,51 @@ -{% set version = "0.42.0" %} +{% set version = "0.46.0" %} {% set name = "vtpnet" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: variant-transcription factor-phenotype networks, inspired by Maurano et al., Science (2012), PMID 22955828 + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: variant-transcription factor-phenotype networks -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a3a08b447e9ce26fafeed6fe2c515e10 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-vtpnet", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: MotifDb, VariantAnnotation, Rgraphviz requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-gwascat >=2.34.0,<2.35.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-gwascat >=2.38.0,<2.39.0 - r-base - r-doparallel - r-foreach run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-graph >=1.80.0,<1.81.0' - - 'bioconductor-gwascat >=2.34.0,<2.35.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-graph >=1.84.0,<1.85.0 + - bioconductor-gwascat >=2.38.0,<2.39.0 - r-base - r-doparallel - r-foreach + +source: + md5: 7610d60696d5680e3776f07cf0d644fc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'variant-transcription factor-phenotype networks' - description: 'variant-transcription factor-phenotype networks, inspired by Maurano et al., Science (2012), PMID 22955828' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-vulcan/meta.yaml b/recipes/bioconductor-vulcan/meta.yaml index 37d48d05d6a20..373ac04564c97 100644 --- a/recipes/bioconductor-vulcan/meta.yaml +++ b/recipes/bioconductor-vulcan/meta.yaml @@ -1,36 +1,38 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "vulcan" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'Vulcan (VirtUaL ChIP-Seq Analysis through Networks) is a package that interrogates gene regulatory networks to infer cofactors significantly enriched in a differential binding signature coming from ChIP-Seq data. In order to do so, our package combines strategies from different BioConductor packages: DESeq for data normalization, ChIPpeakAnno and DiffBind for annotation and definition of ChIP-Seq genomic peaks, csaw to define optimal peak width and viper for applying a regulatory network over a differential binding signature.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: VirtUaL ChIP-Seq data Analysis using Networks -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0e0bf7a1e9b866d535489e7c37f2e19d build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-vulcan", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: vulcandata requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' - - 'bioconductor-csaw >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-diffbind >=3.12.0,<3.13.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-viper >=1.36.0,<1.37.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-chippeakanno >=3.40.0,<3.41.0 + - bioconductor-csaw >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-diffbind >=3.16.0,<3.17.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-viper >=1.40.0,<1.41.0 - r-base - r-catools - r-gplots @@ -38,28 +40,31 @@ requirements: - r-wordcloud - r-zoo run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-chippeakanno >=3.36.0,<3.37.0' - - 'bioconductor-csaw >=1.36.0,<1.37.0' - - 'bioconductor-deseq2 >=1.42.0,<1.43.0' - - 'bioconductor-diffbind >=3.12.0,<3.13.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - - 'bioconductor-viper >=1.36.0,<1.37.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-chippeakanno >=3.40.0,<3.41.0 + - bioconductor-csaw >=1.40.0,<1.41.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-diffbind >=3.16.0,<3.17.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0 + - bioconductor-viper >=1.40.0,<1.41.0 - r-base - r-catools - r-gplots - r-locfit - r-wordcloud - r-zoo + +source: + md5: 2fc8872a1ee68ebf6b7df05b194d7f0b + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'VirtUaL ChIP-Seq data Analysis using Networks' - description: 'Vulcan (VirtUaL ChIP-Seq Analysis through Networks) is a package that interrogates gene regulatory networks to infer cofactors significantly enriched in a differential binding signature coming from ChIP-Seq data. In order to do so, our package combines strategies from different BioConductor packages: DESeq for data normalization, ChIPpeakAnno and DiffBind for annotation and definition of ChIP-Seq genomic peaks, csaw to define optimal peak width and viper for applying a regulatory network over a differential binding signature.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-vulcandata/meta.yaml b/recipes/bioconductor-vulcandata/meta.yaml index c63ea516eec1c..3fa507b0a5827 100644 --- a/recipes/bioconductor-vulcandata/meta.yaml +++ b/recipes/bioconductor-vulcandata/meta.yaml @@ -1,38 +1,39 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "vulcandata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: cd95ea7ac7f2b9edfd46c1ffccb7c3c1 +about: + description: This package provides a dummy regulatory network and ChIP-Seq dataset for running examples in the vulcan package + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: VirtUaL ChIP-Seq data Analysis using Networks, dummy dataset build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-vulcandata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' +# Suggests: viper requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 967ff4f5f3eeef805d666b70f3659a5e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: LGPL-3 - summary: 'VirtUaL ChIP-Seq data Analysis using Networks, dummy dataset' - description: 'This package provides a dummy regulatory network and ChIP-Seq dataset for running examples in the vulcan package' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-vulcandata/post-link.sh b/recipes/bioconductor-vulcandata/post-link.sh index 29950d9bb1d51..2581e2948beee 100644 --- a/recipes/bioconductor-vulcandata/post-link.sh +++ b/recipes/bioconductor-vulcandata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "vulcandata-1.24.0" +installBiocDataPackage.sh "vulcandata-1.28.0" diff --git a/recipes/bioconductor-waddr/meta.yaml b/recipes/bioconductor-waddr/meta.yaml index c7bc5ff14d5ed..e4ff858ed9803 100644 --- a/recipes/bioconductor-waddr/meta.yaml +++ b/recipes/bioconductor-waddr/meta.yaml @@ -1,56 +1,61 @@ -{% set version = "1.16.0" %} +{% set version = "1.20.0" %} {% set name = "waddR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The package offers statistical tests based on the 2-Wasserstein distance for detecting and characterizing differences between two distributions given in the form of samples. Functions for calculating the 2-Wasserstein distance and testing for differential distributions are provided, as well as a specifically tailored test for differential expression in single-cell RNA sequencing data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Statistical tests for detecting differential distributions based on the 2-Wasserstein distance -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 97a692c918d531e3d872dc17141cd112 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-waddr", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, devtools, testthat, roxygen2, rprojroot, rmarkdown, scater requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'r-arm >=1.10-1' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - r-arm >=1.10-1 - r-base - r-eva - - 'r-rcpp >=1.0.1' + - r-rcpp >=1.0.1 - r-rcpparmadillo - libblas - liblapack run: - - 'bioconductor-biocfilecache >=2.10.0,<2.11.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'r-arm >=1.10-1' + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - r-arm >=1.10-1 - r-base - r-eva - - 'r-rcpp >=1.0.1' + - r-rcpp >=1.0.1 - r-rcpparmadillo - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 3bb00eacd4724bb28f8e73592e5daf3a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Statistical tests for detecting differential distributions based on the 2-Wasserstein distance' - description: 'The package offers statistical tests based on the 2-Wasserstein distance for detecting and characterizing differences between two distributions given in the form of samples. Functions for calculating the 2-Wasserstein distance and testing for differential distributions are provided, as well as a specifically tailored test for differential expression in single-cell RNA sequencing data.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-watermelon/meta.yaml b/recipes/bioconductor-watermelon/meta.yaml index b6fb1b65082bf..0bdac187e8a3c 100644 --- a/recipes/bioconductor-watermelon/meta.yaml +++ b/recipes/bioconductor-watermelon/meta.yaml @@ -1,60 +1,66 @@ -{% set version = "2.8.0" %} +{% set version = "2.12.0" %} {% set name = "wateRmelon" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Illumina DNA methylation array normalization and metrics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dd08402958a5cc50170669a5f17e44f6 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-watermelon", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:watermelon + parent_recipe: + name: bioconductor-watermelon + path: recipes/bioconductor-watermelon + version: 1.24.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BiocStyle, knitr, rmarkdown, IlluminaHumanMethylationEPICmanifest, irlba, FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' - - 'bioconductor-methylumi >=2.48.0,<2.49.0' - - 'bioconductor-roc >=1.78.0,<1.79.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-lumi >=2.58.0,<2.59.0 + - bioconductor-methylumi >=2.52.0,<2.53.0 + - bioconductor-roc >=1.82.0,<1.83.0 - r-base - r-matrixstats run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' - - 'bioconductor-illuminaio >=0.44.0,<0.45.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-lumi >=2.54.0,<2.55.0' - - 'bioconductor-methylumi >=2.48.0,<2.49.0' - - 'bioconductor-roc >=1.78.0,<1.79.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0 + - bioconductor-illuminaio >=0.48.0,<0.49.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-lumi >=2.58.0,<2.59.0 + - bioconductor-methylumi >=2.52.0,<2.53.0 + - bioconductor-roc >=1.82.0,<1.83.0 - r-base - r-matrixstats + +source: + md5: 3044edac0be669399cdb295bb084c4f2 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Illumina 450 and EPIC methylation array normalization and metrics' - description: '15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:watermelon - parent_recipe: - name: bioconductor-watermelon - path: recipes/bioconductor-watermelon - version: 1.24.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-wavcluster/meta.yaml b/recipes/bioconductor-wavcluster/meta.yaml index db62a8f56c5cf..c91c9db9320a2 100644 --- a/recipes/bioconductor-wavcluster/meta.yaml +++ b/recipes/bioconductor-wavcluster/meta.yaml @@ -1,35 +1,45 @@ -{% set version = "2.36.0" %} +{% set version = "2.40.0" %} {% set name = "wavClusteR" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The package provides an integrated pipeline for the analysis of PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from sequencing errors, SNPs and additional non-experimental sources by a non- parametric mixture model. The protein binding sites (clusters) are then resolved at high resolution and cluster statistics are estimated using a rigorous Bayesian framework. Post-processing of the results, data export for UCSC genome browser visualization and motif search analysis are provided. In addition, the package allows to integrate RNA-Seq data to estimate the False Discovery Rate of cluster detection. Key functions support parallel multicore computing. Note: while wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other NGS data obtained from experimental procedures that induce nucleotide substitutions (e.g. BisSeq).' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9177c657b31b1abaac94079e658a9c18 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-wavcluster", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:wavcluster + parent_recipe: + name: bioconductor-wavcluster + path: recipes/bioconductor-wavcluster + version: 2.14.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-foreach - r-ggplot2 @@ -38,14 +48,14 @@ requirements: - r-seqinr - r-stringr run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-genomicfeatures >=1.54.0,<1.55.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-genomicfeatures >=1.58.0,<1.59.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-foreach - r-ggplot2 @@ -53,20 +63,16 @@ requirements: - r-mclust - r-seqinr - r-stringr + +source: + md5: 92908cb5bab0691bc0d767fe5c000dbc + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data' - description: 'The package provides an integrated pipeline for the analysis of PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from sequencing errors, SNPs and additional non-experimental sources by a non- parametric mixture model. The protein binding sites (clusters) are then resolved at high resolution and cluster statistics are estimated using a rigorous Bayesian framework. Post-processing of the results, data export for UCSC genome browser visualization and motif search analysis are provided. In addition, the package allows to integrate RNA-Seq data to estimate the False Discovery Rate of cluster detection. Key functions support parallel multicore computing. Note: while wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other NGS data obtained from experimental procedures that induce nucleotide substitutions (e.g. BisSeq).' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:wavcluster - parent_recipe: - name: bioconductor-wavcluster - path: recipes/bioconductor-wavcluster - version: 2.14.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-weaver/meta.yaml b/recipes/bioconductor-weaver/meta.yaml index 4eac9e85fb718..d18a56645a9fc 100644 --- a/recipes/bioconductor-weaver/meta.yaml +++ b/recipes/bioconductor-weaver/meta.yaml @@ -1,24 +1,35 @@ -{% set version = "1.68.0" %} +{% set version = "1.72.0" %} {% set name = "weaver" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is included. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Tools and extensions for processing Sweave documents -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 629d19681872923f14b50543d833c1ba build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-weaver", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:weaver + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-weaver + path: recipes/bioconductor-weaver + version: 1.46.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: codetools requirements: host: @@ -29,21 +40,16 @@ requirements: - r-base - r-codetools - r-digest + +source: + md5: 15bf2732731e607cd0d341e870d2aaa4 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Tools and extensions for processing Sweave documents' - description: 'This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is included.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' -extra: - identifiers: - - biotools:weaver - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-weaver - path: recipes/bioconductor-weaver - version: 1.46.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-webbioc/meta.yaml b/recipes/bioconductor-webbioc/meta.yaml index 2186052bfbd19..292ce13fc8ba1 100644 --- a/recipes/bioconductor-webbioc/meta.yaml +++ b/recipes/bioconductor-webbioc/meta.yaml @@ -1,61 +1,67 @@ -{% set version = "1.74.0" %} +{% set version = "1.78.0" %} {% set name = "webbioc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: An integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. (Currently only Affymetrix oligonucleotide analysis is supported.) + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Bioconductor Web Interface -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 59774accefb60098cdf15cfcd1cda508 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-webbioc", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:webbioc + - doi:10.1007/0-387-29362-0_18 + parent_recipe: + name: bioconductor-webbioc + path: recipes/bioconductor-webbioc + version: 1.52.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # SystemRequirements: Unix, Perl (>= 5.6.0), Netpbm requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-annaffy >=1.74.0,<1.75.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gcrma >=2.74.0,<2.75.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-annaffy >=1.78.0,<1.79.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gcrma >=2.78.0,<2.79.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-base - r-biocmanager run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-annaffy >=1.74.0,<1.75.0' - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-gcrma >=2.74.0,<2.75.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-qvalue >=2.34.0,<2.35.0' - - 'bioconductor-vsn >=3.70.0,<3.71.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-annaffy >=1.78.0,<1.79.0 + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-gcrma >=2.78.0,<2.79.0 + - bioconductor-multtest >=2.62.0,<2.63.0 + - bioconductor-qvalue >=2.38.0,<2.39.0 + - bioconductor-vsn >=3.74.0,<3.75.0 - r-base - r-biocmanager + +source: + md5: d6783454c4d55a9364bbcd1dedefefce + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Bioconductor Web Interface' - description: 'An integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. (Currently only Affymetrix oligonucleotide analysis is supported.)' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:webbioc - - doi:10.1007/0-387-29362-0_18 - parent_recipe: - name: bioconductor-webbioc - path: recipes/bioconductor-webbioc - version: 1.52.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-weberdivechalcdata/meta.yaml b/recipes/bioconductor-weberdivechalcdata/meta.yaml index c4b66627150c2..a0b55df2983a5 100644 --- a/recipes/bioconductor-weberdivechalcdata/meta.yaml +++ b/recipes/bioconductor-weberdivechalcdata/meta.yaml @@ -1,45 +1,45 @@ -{% set version = "1.4.0" %} +{% set version = "1.8.0" %} {% set name = "WeberDivechaLCdata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 3b75c693f86ed228e2b7816872cfe4b7 +about: + description: Spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from the locus coeruleus (LC) in postmortem human brain samples. Data were generated with the 10x Genomics Visium SRT and 10x Genomics Chromium snRNA-seq platforms. Datasets are stored in SpatialExperiment and SingleCellExperiment formats. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Spatially-resolved transcriptomics and single-nucleus RNA-sequencing data from the locus coeruleus (LC) in postmortem human brain samples build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-weberdivechalcdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-spatialexperiment >=1.12.0,<1.13.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: c8a89a9a75b7249249905d8f2e5dc775 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Spatially-resolved transcriptomics and single-nucleus RNA-sequencing data from the locus coeruleus (LC) in postmortem human brain samples' - description: 'Spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from the locus coeruleus (LC) in postmortem human brain samples. Data were generated with the 10x Genomics Visium SRT and 10x Genomics Chromium snRNA-seq platforms. Datasets are stored in SpatialExperiment and SingleCellExperiment formats.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-weberdivechalcdata/post-link.sh b/recipes/bioconductor-weberdivechalcdata/post-link.sh index 7776be0617620..0cd20342ab07f 100644 --- a/recipes/bioconductor-weberdivechalcdata/post-link.sh +++ b/recipes/bioconductor-weberdivechalcdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "weberdivechalcdata-1.4.0" +installBiocDataPackage.sh "weberdivechalcdata-1.8.0" diff --git a/recipes/bioconductor-weitrix/meta.yaml b/recipes/bioconductor-weitrix/meta.yaml index eb99b763485c2..5a7c976a28211 100644 --- a/recipes/bioconductor-weitrix/meta.yaml +++ b/recipes/bioconductor-weitrix/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "weitrix" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Data type and tools for working with matrices having precision weights and missing data. This package provides a common representation and tools that can be used with many types of high-throughput data. The meaning of the weights is compatible with usage in the base R function "lm" and the package "limma". Calibrate weights to account for known predictors of precision. Find rows with excess variability. Perform differential testing and find rows with the largest confident differences. Find PCA-like components of variation even with many missing values, rotated so that individual components may be meaningfully interpreted. DelayedArray matrices and BiocParallel are supported. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-2.1 | file LICENSE + license_file: LICENSE + summary: Tools for matrices with precision weights, test and explore weighted or sparse data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 101d61858d3d388a1396212f7ef5332e build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-weitrix", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR, EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi, ComplexHeatmap, patchwork, testthat (>= 2.1.0) requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-topconfects >=1.18.0,<1.19.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-topconfects >=1.22.0,<1.23.0 - r-assertthat - r-base - r-ckmeans.1d.dp @@ -42,14 +44,14 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-delayedmatrixstats >=1.24.0,<1.25.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' - - 'bioconductor-topconfects >=1.18.0,<1.19.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-topconfects >=1.22.0,<1.23.0 - r-assertthat - r-base - r-ckmeans.1d.dp @@ -61,13 +63,16 @@ requirements: - r-rhpcblasctl - r-rlang - r-scales + +source: + md5: 13edf3fff909f635ca5c7f9ce03f2cce + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL-2.1 | file LICENSE' - summary: 'Tools for matrices with precision weights, test and explore weighted or sparse data' - description: 'Data type and tools for working with matrices having precision weights and missing data. This package provides a common representation and tools that can be used with many types of high-throughput data. The meaning of the weights is compatible with usage in the base R function "lm" and the package "limma". Calibrate weights to account for known predictors of precision. Find rows with excess variability. Perform differential testing and find rows with the largest confident differences. Find PCA-like components of variation even with many missing values, rotated so that individual components may be meaningfully interpreted. DelayedArray matrices and BiocParallel are supported.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-wes.1kg.wugsc/meta.yaml b/recipes/bioconductor-wes.1kg.wugsc/meta.yaml index 755106b9959f2..f954e347075d4 100644 --- a/recipes/bioconductor-wes.1kg.wugsc/meta.yaml +++ b/recipes/bioconductor-wes.1kg.wugsc/meta.yaml @@ -1,38 +1,38 @@ -{% set version = "1.34.0" %} +{% set version = "1.38.0" %} {% set name = "WES.1KG.WUGSC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a0a3d230e27342090638ec4868756e5a +about: + description: The assembled .bam files of whole exome sequencing data from the 1000 Genomes Project. 46 samples sequenced by the Washington University Genome Sequencing Center are included. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Whole Exome Sequencing (WES) of chromosome 22 401st to 500th exon from the 1000 Genomes (1KG) Project by the Washington University Genome Sequencing Center (WUGSC). build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-wes.1kg.wugsc", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5fab1142aa178a13bf1f056d9db5d8bb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Whole Exome Sequencing (WES) of chromosome 22 401st to 500th exon from the 1000 Genomes (1KG) Project by the Washington University Genome Sequencing Center (WUGSC).' - description: 'The assembled .bam files of whole exome sequencing data from the 1000 Genomes Project. 46 samples sequenced by the Washington University Genome Sequencing Center are included.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-wes.1kg.wugsc/post-link.sh b/recipes/bioconductor-wes.1kg.wugsc/post-link.sh index 379916e93aea6..20f82787b0c9d 100644 --- a/recipes/bioconductor-wes.1kg.wugsc/post-link.sh +++ b/recipes/bioconductor-wes.1kg.wugsc/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "wes.1kg.wugsc-1.34.0" +installBiocDataPackage.sh "wes.1kg.wugsc-1.38.0" diff --git a/recipes/bioconductor-wgsmapp/meta.yaml b/recipes/bioconductor-wgsmapp/meta.yaml index 004433757f803..304bd82d005d2 100644 --- a/recipes/bioconductor-wgsmapp/meta.yaml +++ b/recipes/bioconductor-wgsmapp/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.14.0" %} +{% set version = "1.18.0" %} {% set name = "WGSmapp" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: dfc3f5a82d532551e2d6c21b11c99566 +about: + description: This package provides whole-genome mappability tracks on human hg19/hg38 assembly. We employed the 100-mers mappability track from the ENCODE Project and computed weighted average of the mappability scores if multiple ENCODE regions overlap with the same bin. “Blacklist” bins, including segmental duplication regions and gaps in reference assembly from telomere, centromere, and/or heterochromatin regions are included. The dataset consists of three assembled .bam files of single-cell whole genome sequencing from 10X for illustration purposes. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Mappability tracks of Whole-genome Sequencing from the ENCODE Project build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-wgsmapp", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base run: - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' + - bioconductor-genomicranges >=1.58.0,<1.59.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b6b076672a568d3e456f3a934d444c3f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'Mappability tracks of Whole-genome Sequencing from the ENCODE Project' - description: 'This package provides whole-genome mappability tracks on human hg19/hg38 assembly. We employed the 100-mers mappability track from the ENCODE Project and computed weighted average of the mappability scores if multiple ENCODE regions overlap with the same bin. “Blacklist” bins, including segmental duplication regions and gaps in reference assembly from telomere, centromere, and/or heterochromatin regions are included. The dataset consists of three assembled .bam files of single-cell whole genome sequencing from 10X for illustration purposes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-wgsmapp/post-link.sh b/recipes/bioconductor-wgsmapp/post-link.sh index 72a7d5958caa4..23357183da7f9 100644 --- a/recipes/bioconductor-wgsmapp/post-link.sh +++ b/recipes/bioconductor-wgsmapp/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "wgsmapp-1.14.0" +installBiocDataPackage.sh "wgsmapp-1.18.0" diff --git a/recipes/bioconductor-wheatcdf/meta.yaml b/recipes/bioconductor-wheatcdf/meta.yaml index e48303b1fdecd..29ff506c77a3d 100644 --- a/recipes/bioconductor-wheatcdf/meta.yaml +++ b/recipes/bioconductor-wheatcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "wheatcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0abeeeb9700b8d93a1a83769bdd8480f +about: + description: A package containing an environment representing the wheat.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: wheatcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-wheatcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0abeeeb9700b8d93a1a83769bdd8480f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: wheatcdf - description: 'A package containing an environment representing the wheat.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-wheatprobe/meta.yaml b/recipes/bioconductor-wheatprobe/meta.yaml index a8a7d02b42958..1d7411bfead37 100644 --- a/recipes/bioconductor-wheatprobe/meta.yaml +++ b/recipes/bioconductor-wheatprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "wheatprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: b602d5050239850515be9dce12286360 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was wheat\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type wheat build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-wheatprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: b602d5050239850515be9dce12286360 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type wheat' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was wheat\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-widgettools/meta.yaml b/recipes/bioconductor-widgettools/meta.yaml index 9bd762908f52b..ca32c6ccece9d 100644 --- a/recipes/bioconductor-widgettools/meta.yaml +++ b/recipes/bioconductor-widgettools/meta.yaml @@ -1,37 +1,37 @@ -{% set version = "1.80.0" %} +{% set version = "1.84.0" %} {% set name = "widgetTools" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bb5358a7e064436aa744ffb098a9c0ec +about: + description: This packages contains tools to support the construction of tcltk widgets + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Creates an interactive tcltk widget build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-widgettools", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: Biobase requirements: host: - r-base run: - r-base +source: + md5: 83e16ec98e823d13ae3f359047fda205 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL - summary: 'Creates an interactive tcltk widget' - description: 'This packages contains tools to support the construction of tcltk widgets' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-wiggleplotr/meta.yaml b/recipes/bioconductor-wiggleplotr/meta.yaml index b8dcd748549bb..a01240edb7a0c 100644 --- a/recipes/bioconductor-wiggleplotr/meta.yaml +++ b/recipes/bioconductor-wiggleplotr/meta.yaml @@ -1,61 +1,67 @@ -{% set version = "1.26.0" %} +{% set version = "1.30.0" %} {% set name = "wiggleplotr" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools to visualise read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualisation of exonic read coverage. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Apache License 2.0 + summary: Make read coverage plots from BigWig files -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9e05d485ba51bf035918d23e686e60ba build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-wiggleplotr", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-wiggleplotr + path: recipes/bioconductor-wiggleplotr + version: 1.4.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter requirements: host: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-assertthat - r-base - r-cowplot - r-dplyr - - 'r-ggplot2 >=2.2.0' + - r-ggplot2 >=2.2.0 - r-purrr run: - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rtracklayer >=1.62.0,<1.63.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rtracklayer >=1.66.0,<1.67.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-assertthat - r-base - r-cowplot - r-dplyr - - 'r-ggplot2 >=2.2.0' + - r-ggplot2 >=2.2.0 - r-purrr + +source: + md5: 99582d2550bfa201b05f20898b1f7519 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Apache License 2.0' - summary: 'Make read coverage plots from BigWig files' - description: 'Tools to visualise read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualisation of exonic read coverage.' -extra: - parent_recipe: - name: bioconductor-wiggleplotr - path: recipes/bioconductor-wiggleplotr - version: 1.4.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-worm.db0/meta.yaml b/recipes/bioconductor-worm.db0/meta.yaml index 18bb7a5e84082..5769318ca5cae 100644 --- a/recipes/bioconductor-worm.db0/meta.yaml +++ b/recipes/bioconductor-worm.db0/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "worm.db0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 67be1277b5ae184558259ac720a5741e +about: + description: Base annotation databases for worm, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Level Annotation databases for worm build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-worm.db0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 4d526e85bb77f45595eaa31861a0ea3d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Level Annotation databases for worm' - description: 'Base annotation databases for worm, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-worm.db0/post-link.sh b/recipes/bioconductor-worm.db0/post-link.sh index 58e6b26a5f6a0..047a185d72ae5 100644 --- a/recipes/bioconductor-worm.db0/post-link.sh +++ b/recipes/bioconductor-worm.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "worm.db0-3.18.0" +installBiocDataPackage.sh "worm.db0-3.20.0" diff --git a/recipes/bioconductor-wpm/meta.yaml b/recipes/bioconductor-wpm/meta.yaml index 38ed8c9815556..fd7a31f1161f7 100644 --- a/recipes/bioconductor-wpm/meta.yaml +++ b/recipes/bioconductor-wpm/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.12.0" %} +{% set version = "1.16.0" %} {% set name = "wpm" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: 'The Well-Plate Maker (WPM) is a shiny application deployed as an R package. Functions for a command-line/script use are also available. The WPM allows users to generate well plate maps to carry out their experiments while improving the handling of batch effects. In particular, it helps controlling the "plate effect" thanks to its ability to randomize samples over multiple well plates. The algorithm for placing the samples is inspired by the backtracking algorithm: the samples are placed at random while respecting specific spatial constraints.' + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Well Plate Maker -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 44df6efb278049a19cefea84cb8a8b64 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-wpm", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: MSnbase, testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cli - r-config @@ -40,8 +41,8 @@ requirements: - r-shinywidgets - r-stringr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cli - r-config @@ -57,12 +58,16 @@ requirements: - r-shinydashboard - r-shinywidgets - r-stringr + +source: + md5: 6283bd8b65b3a3937f44d7f2d8d1d96e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Well Plate Maker' - description: 'The Well-Plate Maker (WPM) is a shiny application deployed as an R package. Functions for a command-line/script use are also available. The WPM allows users to generate well plate maps to carry out their experiments while improving the handling of batch effects. In particular, it helps controlling the "plate effect" thanks to its ability to randomize samples over multiple well plates. The algorithm for placing the samples is inspired by the backtracking algorithm: the samples are placed at random while respecting specific spatial constraints.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-wppi/build_failure.linux-64.yaml b/recipes/bioconductor-wppi/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0de9f729f83eb --- /dev/null +++ b/recipes/bioconductor-wppi/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: 24a1c2da82d1de5af54016e9c73f48a5341c90c417fc151fa33a879d41a98755 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-omnipathr[version='>=3.14.0,<3.15.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-omnipathr >=3.14.0,<3.15.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-omnipathr >=3.14.0,<3.15.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-omnipathr[version='>=3.14.0,<3.15.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-omnipathr >=3.14.0,<3.15.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-omnipathr >=3.14.0,<3.15.0 [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-omnipathr[version='>=3.14.0,<3.15.0']")} + Encountered problems while solving: + - nothing provides requested bioconductor-omnipathr >=3.14.0,<3.15.0 + + Could not solve for environment specs + The following package could not be installed + [31mbioconductor-omnipathr >=3.14.0,<3.15.0 [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. +reason: |- + needs bioconductor-omnipathr to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-wppi/build_failure.osx-64.yaml b/recipes/bioconductor-wppi/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..6c3b4070e1b50 --- /dev/null +++ b/recipes/bioconductor-wppi/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: 24a1c2da82d1de5af54016e9c73f48a5341c90c417fc151fa33a879d41a98755 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + needs bioconductor-omnipathr to be fixed +category: |- + dependency issue diff --git a/recipes/bioconductor-wppi/meta.yaml b/recipes/bioconductor-wppi/meta.yaml index b3d8b9e3382a3..dc54e194c23e4 100644 --- a/recipes/bioconductor-wppi/meta.yaml +++ b/recipes/bioconductor-wppi/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "wppi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Protein-protein interaction data is essential for omics data analysis and modeling. Database knowledge is general, not specific for cell type, physiological condition or any other context determining which connections are functional and contribute to the signaling. Functional annotations such as Gene Ontology and Human Phenotype Ontology might help to evaluate the relevance of interactions. This package predicts functional relevance of protein-protein interactions based on functional annotations such as Human Protein Ontology and Gene Ontology, and prioritizes genes based on network topology, functional scores and a path search algorithm. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Weighting protein-protein interactions -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 1de428cfbb93be33d9e71b0415937cd9 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-wppi", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, testthat, rmarkdown requirements: host: - - 'bioconductor-omnipathr >=3.10.0,<3.11.0' + - bioconductor-omnipathr >=3.14.0,<3.15.0 - r-base - r-dplyr - r-igraph @@ -36,7 +38,7 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-omnipathr >=3.10.0,<3.11.0' + - bioconductor-omnipathr >=3.14.0,<3.15.0 - r-base - r-dplyr - r-igraph @@ -49,12 +51,16 @@ requirements: - r-rlang - r-tibble - r-tidyr + +source: + md5: 50536f6d414ee0272f3804880f4c8aca + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - $R -e "options(omnipath.logfile=''none''); library(''{{ name }}'')" && find /tmp -name omnipathr-log -exec rm -rf {} + || true -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Weighting protein-protein interactions' - description: 'Protein-protein interaction data is essential for omics data analysis and modeling. Database knowledge is general, not specific for cell type, physiological condition or any other context determining which connections are functional and contribute to the signaling. Functional annotations such as Gene Ontology and Human Phenotype Ontology might help to evaluate the relevance of interactions. This package predicts functional relevance of protein-protein interactions based on functional annotations such as Human Protein Ontology and Gene Ontology, and prioritizes genes based on network topology, functional scores and a path search algorithm.' - license_file: LICENSE + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-wrench/meta.yaml b/recipes/bioconductor-wrench/meta.yaml index 8117dd068c109..f216e643dc131 100644 --- a/recipes/bioconductor-wrench/meta.yaml +++ b/recipes/bioconductor-wrench/meta.yaml @@ -1,42 +1,42 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "Wrench" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 18e9fb2840f0002f41be3799688e2b1f +about: + description: Wrench is a package for normalization sparse genomic count data, like that arising from 16s metagenomic surveys. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Wrench normalization for sparse count data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-wrench", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR requirements: host: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-locfit - r-matrixstats run: - - 'bioconductor-limma >=3.58.0,<3.59.0' + - bioconductor-limma >=3.62.0,<3.63.0 - r-base - r-locfit - r-matrixstats +source: + md5: a766c7f09aefdfa4c5178fc67e85d975 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Wrench normalization for sparse count data' - description: 'Wrench is a package for normalization sparse genomic count data, like that arising from 16s metagenomic surveys.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-xcms/meta.yaml b/recipes/bioconductor-xcms/meta.yaml index b007033ba5110..d3f442fd303d8 100644 --- a/recipes/bioconductor-xcms/meta.yaml +++ b/recipes/bioconductor-xcms/meta.yaml @@ -1,89 +1,92 @@ -{% set version = "4.0.0" %} +{% set version = "4.4.0" %} {% set name = "xcms" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL (>= 2) + file LICENSE + license_file: LICENSE + summary: LC-MS and GC-MS Data Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 194314f3a5b94121a4007b58b17182b1 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xcms", max_pin="x.x") }}' -# Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>= 0.25.1), ncdf4, testthat, pander, rmarkdown, MALDIquant, pheatmap, MsBackendMgf, MetaboCoreUtils, signal + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:xcms + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>= 0.25.1), ncdf4, testthat (>= 3.1.9), pander, rmarkdown, MALDIquant, pheatmap, RANN, multtest, MsBackendMgf, signal, mgcv requirements: + + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-massspecwavelet >=1.68.0,<1.69.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-msexperiment >=1.4.0,<1.5.0' - - 'bioconductor-msfeatures >=1.10.0,<1.11.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-massspecwavelet >=1.72.0,<1.73.0 + - bioconductor-metabocoreutils >=1.14.0,<1.15.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-msexperiment >=1.8.0,<1.9.0 + - bioconductor-msfeatures >=1.14.0,<1.15.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-mzr >=2.40.0,<2.41.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-lattice - - r-plyr - r-progress - - r-rann - r-rcolorbrewer - - r-robustbase - libblas - liblapack + run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-massspecwavelet >=1.68.0,<1.69.0' - - 'bioconductor-mscoreutils >=1.14.0,<1.15.0' - - 'bioconductor-msexperiment >=1.4.0,<1.5.0' - - 'bioconductor-msfeatures >=1.10.0,<1.11.0' - - 'bioconductor-msnbase >=2.28.0,<2.29.0' - - 'bioconductor-multtest >=2.58.0,<2.59.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' - - 'bioconductor-protgenerics >=1.34.0,<1.35.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-spectra >=1.12.0,<1.13.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-massspecwavelet >=1.72.0,<1.73.0 + - bioconductor-metabocoreutils >=1.14.0,<1.15.0 + - bioconductor-mscoreutils >=1.18.0,<1.19.0 + - bioconductor-msexperiment >=1.8.0,<1.9.0 + - bioconductor-msfeatures >=1.14.0,<1.15.0 + - bioconductor-msnbase >=2.32.0,<2.33.0 + - bioconductor-mzr >=2.40.0,<2.41.0 + - bioconductor-protgenerics >=1.38.0,<1.39.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-spectra >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-lattice - - r-plyr - r-progress - - r-rann - r-rcolorbrewer - - r-robustbase - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: caedc8f009885cab5b270bbba406f782 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-2.0-or-later + file LICENSE' - summary: 'LC-MS and GC-MS Data Analysis' - description: 'Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.' - license_file: LICENSE + - $R -e "library('{{ name }}')" -extra: - additional-platforms: - - linux-aarch64 - identifiers: - - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-xcore/meta.yaml b/recipes/bioconductor-xcore/meta.yaml index f83edf02082ee..cf7f9b55af62b 100644 --- a/recipes/bioconductor-xcore/meta.yaml +++ b/recipes/bioconductor-xcore/meta.yaml @@ -1,59 +1,64 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "xcore" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: xcore is an R package for transcription factor activity modeling based on known molecular signatures and user's gene expression data. Accompanying xcoredata package provides a collection of molecular signatures, constructed from publicly available ChiP-seq experiments. xcore use ridge regression to model changes in expression as a linear combination of molecular signatures and find their unknown activities. Obtained, estimates can be further tested for significance to select molecular signatures with the highest predicted effect on the observed expression changes. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: xcore expression regulators inference -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 4dd79b63bd7ff46aaa1b84dade889db2 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xcore", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: AnnotationHub (>= 3.0.2), BiocGenerics (>= 0.38.0), BiocParallel (>= 1.28), BiocStyle (>= 2.20.2), data.table (>= 1.14.0), devtools (>= 2.4.2), doParallel (>= 1.0.16), ExperimentHub (>= 2.2.0), knitr (>= 1.37), pheatmap (>= 1.0.12), proxy (>= 0.4.26), ridge (>= 3.0), rmarkdown (>= 2.11), rtracklayer (>= 1.52.0), testthat (>= 3.0.0), usethis (>= 2.0.1), xcoredata requirements: host: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-foreach >=1.5.1' - - 'r-glmnet >=4.1.2' - - 'r-iterators >=1.0.13' - - 'r-magrittr >=2.0.1' - - 'r-matrix >=1.3.4' + - r-foreach >=1.5.1 + - r-glmnet >=4.1.2 + - r-iterators >=1.0.13 + - r-magrittr >=2.0.1 + - r-matrix >=1.3.4 run: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-multiassayexperiment >=1.28.0,<1.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-multiassayexperiment >=1.32.0,<1.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - - 'r-foreach >=1.5.1' - - 'r-glmnet >=4.1.2' - - 'r-iterators >=1.0.13' - - 'r-magrittr >=2.0.1' - - 'r-matrix >=1.3.4' + - r-foreach >=1.5.1 + - r-glmnet >=4.1.2 + - r-iterators >=1.0.13 + - r-magrittr >=2.0.1 + - r-matrix >=1.3.4 + +source: + md5: 1f25b26360120ca184ece31f704c8daa + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'xcore expression regulators inference' - description: 'xcore is an R package for transcription factor activity modeling based on known molecular signatures and user''s gene expression data. Accompanying xcoredata package provides a collection of molecular signatures, constructed from publicly available ChiP-seq experiments. xcore use ridge regression to model changes in expression as a linear combination of molecular signatures and find their unknown activities. Obtained, estimates can be further tested for significance to select molecular signatures with the highest predicted effect on the observed expression changes.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-xcoredata/meta.yaml b/recipes/bioconductor-xcoredata/meta.yaml index d095f18812f83..5dfb6e2ec0e85 100644 --- a/recipes/bioconductor-xcoredata/meta.yaml +++ b/recipes/bioconductor-xcoredata/meta.yaml @@ -1,41 +1,41 @@ -{% set version = "1.6.0" %} +{% set version = "1.10.0" %} {% set name = "xcoredata" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 214626bfcbb5d66445324f6e367142c7 +about: + description: Provides data to use with xcore package. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: data package for xcore build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xcoredata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocGenerics (>= 0.40.0), data.table (>= 1.14.2), GenomeInfoDb (>= 1.30.0), GenomicRanges (>= 1.46.1), IRanges (>= 2.28.0), knitr (>= 1.37), rmarkdown (>= 2.11), Matrix (>= 1.3.4), stringr (>= 1.4.0), S4Vectors (>= 0.32.3), TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.14.0), xcore requirements: host: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base run: - - 'bioconductor-experimenthub >=2.10.0,<2.11.0' + - bioconductor-experimenthub >=2.14.0,<2.15.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 7ef4acfdabec19615e077d46749c32be + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL-2 - summary: 'data package for xcore' - description: 'Provides data to use with xcore package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-xcoredata/post-link.sh b/recipes/bioconductor-xcoredata/post-link.sh index fc698f3463f09..f660e19af82b1 100644 --- a/recipes/bioconductor-xcoredata/post-link.sh +++ b/recipes/bioconductor-xcoredata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "xcoredata-1.6.0" +installBiocDataPackage.sh "xcoredata-1.10.0" diff --git a/recipes/bioconductor-xde/meta.yaml b/recipes/bioconductor-xde/meta.yaml index 925ec6e74d9ad..3fbf2f90a99e0 100644 --- a/recipes/bioconductor-xde/meta.yaml +++ b/recipes/bioconductor-xde/meta.yaml @@ -1,31 +1,45 @@ -{% set version = "2.48.0" %} +{% set version = "2.52.0" %} {% set name = "XDE" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Multi-level model for cross-study detection of differential gene expression. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2' + summary: 'XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: aaf179de92edd3a7105c0fe20254f3d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xde", max_pin="x.x") }}' + +extra: + identifiers: + - biotools:xde + parent_recipe: + name: bioconductor-xde + path: recipes/bioconductor-xde + version: 2.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: MASS, RUnit requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-genemeta >=1.74.0,<1.75.0' - - 'bioconductor-siggenes >=1.76.0,<1.77.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-genemeta >=1.78.0,<1.79.0 + - bioconductor-siggenes >=1.80.0,<1.81.0 - r-base - r-gtools - r-mvtnorm @@ -33,33 +47,25 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-genemeta >=1.74.0,<1.75.0' - - 'bioconductor-siggenes >=1.76.0,<1.77.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-genemeta >=1.78.0,<1.79.0 + - bioconductor-siggenes >=1.80.0,<1.81.0 - r-base - r-gtools - r-mvtnorm - r-rcolorbrewer - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: fe568ba86902936804b630a579e8c5c0 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-2 - summary: 'XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression' - description: 'Multi-level model for cross-study detection of differential gene expression.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-2' -extra: - identifiers: - - biotools:xde - parent_recipe: - name: bioconductor-xde - path: recipes/bioconductor-xde - version: 2.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-xenlite/build.sh b/recipes/bioconductor-xenlite/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-xenlite/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-xenlite/meta.yaml b/recipes/bioconductor-xenlite/meta.yaml new file mode 100644 index 0000000000000..b925d4a412c81 --- /dev/null +++ b/recipes/bioconductor-xenlite/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "1.0.0" %} +{% set name = "xenLite" %} +{% set bioc = "3.20" %} + +about: + description: Define a relatively light class for managing Xenium data using Bioconductor. Address use of parquet for coordinates, SpatialExperiment for assay and sample data. Address serialization and use of cloud storage. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Simple classes and methods for managing Xenium datasets + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-xenlite", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, testthat, BiocStyle, yesno, terra, SpatialFeatureExperiment, SFEData, tiff +requirements: + host: + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tenxio >=1.8.0,<1.9.0 + - r-arrow + - r-base + - r-dplyr + - r-ggplot2 + - r-matrix + - r-shiny + run: + - bioconductor-biocfilecache >=2.14.0,<2.15.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-hdf5array >=1.34.0,<1.35.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-spatialexperiment >=1.16.0,<1.17.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - bioconductor-tenxio >=1.8.0,<1.9.0 + - r-arrow + - r-base + - r-dplyr + - r-ggplot2 + - r-matrix + - r-shiny + +source: + md5: 5660f5e80fbd23c85fa3bf39fe7abb50 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-xenopus.db0/meta.yaml b/recipes/bioconductor-xenopus.db0/meta.yaml index 43ceb31511611..bf44c87fc214b 100644 --- a/recipes/bioconductor-xenopus.db0/meta.yaml +++ b/recipes/bioconductor-xenopus.db0/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "xenopus.db0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 67b245b456f21672e70fa0690d7e8410 +about: + description: Base annotation databases for xenopus, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Level Annotation databases for xenopus build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xenopus.db0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: aeaf9b5fddc97f1c79ef98ff452b4858 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Level Annotation databases for xenopus' - description: 'Base annotation databases for xenopus, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-xenopus.db0/post-link.sh b/recipes/bioconductor-xenopus.db0/post-link.sh index f0f7cb9144929..b7750219bb0e5 100644 --- a/recipes/bioconductor-xenopus.db0/post-link.sh +++ b/recipes/bioconductor-xenopus.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "xenopus.db0-3.18.0" +installBiocDataPackage.sh "xenopus.db0-3.20.0" diff --git a/recipes/bioconductor-xenopuslaeviscdf/meta.yaml b/recipes/bioconductor-xenopuslaeviscdf/meta.yaml index 567de4b026944..e7bb9f46e9755 100644 --- a/recipes/bioconductor-xenopuslaeviscdf/meta.yaml +++ b/recipes/bioconductor-xenopuslaeviscdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "xenopuslaeviscdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9d09ff76471ae60faf71090e0638f240 +about: + description: A package containing an environment representing the Xenopus_laevis.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: xenopuslaeviscdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xenopuslaeviscdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9d09ff76471ae60faf71090e0638f240 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: xenopuslaeviscdf - description: 'A package containing an environment representing the Xenopus_laevis.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-xenopuslaevisprobe/meta.yaml b/recipes/bioconductor-xenopuslaevisprobe/meta.yaml index 25b78155e0d34..4c3db79d2c370 100644 --- a/recipes/bioconductor-xenopuslaevisprobe/meta.yaml +++ b/recipes/bioconductor-xenopuslaevisprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "xenopuslaevisprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 06a25268a5ab57bddf28bbb364ea977b +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Xenopus\_laevis\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type xenopuslaevis build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xenopuslaevisprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 06a25268a5ab57bddf28bbb364ea977b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type xenopuslaevis' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Xenopus\_laevis\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-xeva/meta.yaml b/recipes/bioconductor-xeva/meta.yaml index 26be5b11abecf..64f72a203373a 100644 --- a/recipes/bioconductor-xeva/meta.yaml +++ b/recipes/bioconductor-xeva/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.18.0" %} +{% set version = "1.22.0" %} {% set name = "Xeva" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The Xeva package provides efficient and powerful functions for patient-drived xenograft (PDX) based pharmacogenomic data analysis. This package contains a set of functions to perform analysis of patient-derived xenograft data. This package was developed by the BHKLab, for further information please see our documentation. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Analysis of patient-derived xenograft (PDX) data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 94733e069395be524fa2d7254f9c2c5c build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xeva", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-pharmacogx >=3.6.0,<3.7.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-pharmacogx >=3.10.0,<3.11.0 - r-base - r-bbmisc - r-doparallel @@ -34,9 +36,9 @@ requirements: - r-rmisc - r-scales run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-pharmacogx >=3.6.0,<3.7.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-pharmacogx >=3.10.0,<3.11.0 - r-base - r-bbmisc - r-doparallel @@ -45,13 +47,16 @@ requirements: - r-nlme - r-rmisc - r-scales + +source: + md5: 190d7a6b0353ecc5d58ca13191f7e8f3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Analysis of patient-derived xenograft (PDX) data' - description: 'The Xeva package provides efficient and powerful functions for patient-drived xenograft (PDX) based pharmacogenomic data analysis. This package contains a set of functions to perform analysis of patient-derived xenograft data. This package was developed by the BHKLab, for further information please see our documentation.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-xhybcasneuf/meta.yaml b/recipes/bioconductor-xhybcasneuf/meta.yaml index 82aa53006c4fa..206d5b88c7862 100644 --- a/recipes/bioconductor-xhybcasneuf/meta.yaml +++ b/recipes/bioconductor-xhybcasneuf/meta.yaml @@ -1,45 +1,50 @@ -{% set version = "1.40.0" %} +{% set version = "1.44.0" %} {% set name = "XhybCasneuf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Cross-hybridisation study on the ATH1 Affymetrix GeneChip + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: EBI/PSB cross-hybridisation study package -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f3e6306b5c05fb026e36e4c60656e25a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xhybcasneuf", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + requirements: host: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-ath1121501cdf >=2.18.0,<2.19.0' - - 'bioconductor-tinesath1cdf >=1.40.0,<1.41.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-ath1121501cdf >=2.18.0,<2.19.0 + - bioconductor-tinesath1cdf >=1.44.0,<1.45.0 - r-base - r-rcolorbrewer run: - - 'bioconductor-affy >=1.80.0,<1.81.0' - - 'bioconductor-ath1121501cdf >=2.18.0,<2.19.0' - - 'bioconductor-tinesath1cdf >=1.40.0,<1.41.0' + - bioconductor-affy >=1.84.0,<1.85.0 + - bioconductor-ath1121501cdf >=2.18.0,<2.19.0 + - bioconductor-tinesath1cdf >=1.44.0,<1.45.0 - r-base - r-rcolorbrewer - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: ef8eb72da053078342f2468969e41db2 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'EBI/PSB cross-hybridisation study package' - description: 'Cross-hybridisation study on the ATH1 Affymetrix GeneChip' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-xhybcasneuf/post-link.sh b/recipes/bioconductor-xhybcasneuf/post-link.sh index 40faf39513b0d..9dd574a533dc0 100644 --- a/recipes/bioconductor-xhybcasneuf/post-link.sh +++ b/recipes/bioconductor-xhybcasneuf/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "xhybcasneuf-1.40.0" +installBiocDataPackage.sh "xhybcasneuf-1.44.0" diff --git a/recipes/bioconductor-xina/meta.yaml b/recipes/bioconductor-xina/meta.yaml index 727ba242c837e..f2a18432dab17 100644 --- a/recipes/bioconductor-xina/meta.yaml +++ b/recipes/bioconductor-xina/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.20.0" %} +{% set version = "1.24.0" %} {% set name = "XINA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The aim of XINA is to determine which proteins exhibit similar patterns within and across experimental conditions, since proteins with co-abundance patterns may have common molecular functions. XINA imports multiple datasets, tags dataset in silico, and combines the data for subsequent subgrouping into multiple clusters. The result is a single output depicting the variation across all conditions. XINA, not only extracts coabundance profiles within and across experiments, but also incorporates protein-protein interaction databases and integrative resources such as KEGG to infer interactors and molecular functions, respectively, and produces intuitive graphical outputs. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f6a090d9e94032485c8c42a6c985b223 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xina", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-stringdb >=2.14.0,<2.15.0' + - bioconductor-stringdb >=2.18.0,<2.19.0 - r-alluvial - r-base - r-ggplot2 @@ -31,7 +33,7 @@ requirements: - r-mclust - r-plyr run: - - 'bioconductor-stringdb >=2.14.0,<2.15.0' + - bioconductor-stringdb >=2.18.0,<2.19.0 - r-alluvial - r-base - r-ggplot2 @@ -39,13 +41,16 @@ requirements: - r-igraph - r-mclust - r-plyr + +source: + md5: 6e59c3086e76875d4422a3379a3db929 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis' - description: 'The aim of XINA is to determine which proteins exhibit similar patterns within and across experimental conditions, since proteins with co-abundance patterns may have common molecular functions. XINA imports multiple datasets, tags dataset in silico, and combines the data for subsequent subgrouping into multiple clusters. The result is a single output depicting the variation across all conditions. XINA, not only extracts coabundance profiles within and across experiments, but also incorporates protein-protein interaction databases and integrative resources such as KEGG to infer interactors and molecular functions, respectively, and produces intuitive graphical outputs.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-xlaevis.db/meta.yaml b/recipes/bioconductor-xlaevis.db/meta.yaml index cc34275d94283..5cc74fe61d70a 100644 --- a/recipes/bioconductor-xlaevis.db/meta.yaml +++ b/recipes/bioconductor-xlaevis.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.2.3" %} {% set name = "xlaevis.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: deaffe47b4ee48a7edb159d8104dc241 +about: + description: Affymetrix Xenopus laevis annotation data (chip xlaevis) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Xenopus laevis annotation data (chip xlaevis) build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xlaevis.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.xl.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.xl.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.xl.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.xl.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: deaffe47b4ee48a7edb159d8104dc241 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Xenopus laevis annotation data (chip xlaevis)' - description: 'Affymetrix Xenopus laevis annotation data (chip xlaevis) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-xlaevis2cdf/meta.yaml b/recipes/bioconductor-xlaevis2cdf/meta.yaml index 80adc6f158546..d5c08a5bfc572 100644 --- a/recipes/bioconductor-xlaevis2cdf/meta.yaml +++ b/recipes/bioconductor-xlaevis2cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "xlaevis2cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 9e4a80d66397299b4e66a8d6715ca4aa +about: + description: A package containing an environment representing the X_laevis_2.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: xlaevis2cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xlaevis2cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9e4a80d66397299b4e66a8d6715ca4aa + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: xlaevis2cdf - description: 'A package containing an environment representing the X_laevis_2.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-xlaevis2probe/meta.yaml b/recipes/bioconductor-xlaevis2probe/meta.yaml index 1cba9aafeeb01..096a8dcc2289d 100644 --- a/recipes/bioconductor-xlaevis2probe/meta.yaml +++ b/recipes/bioconductor-xlaevis2probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "xlaevis2probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d86f8a05e106eb3123435da233ff851d +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was X\_laevis\_2\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type xlaevis2 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xlaevis2probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d86f8a05e106eb3123435da233ff851d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type xlaevis2' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was X\_laevis\_2\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-xmapbridge/meta.yaml b/recipes/bioconductor-xmapbridge/meta.yaml index 8a8a6245590fd..0a9c3e2f6f0c2 100644 --- a/recipes/bioconductor-xmapbridge/meta.yaml +++ b/recipes/bioconductor-xmapbridge/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.60.0" %} +{% set version = "1.64.0" %} {% set name = "xmapbridge" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 8b07bc6daa0d9dad8943ef442076eb5e +about: + description: xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: LGPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Export plotting files to the xmapBridge for visualisation in X:Map build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xmapbridge", max_pin="x.x") }}' - noarch: generic +extra: + identifiers: + - biotools:xmapbridge + parent_recipe: + name: bioconductor-xmapbridge + path: recipes/bioconductor-xmapbridge + version: 1.38.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: RUnit, RColorBrewer requirements: host: - r-base run: - r-base +source: + md5: e7eb4c88f4e7e8b2dd65ffe8acc7014e + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 - summary: 'Export plotting files to the xmapBridge for visualisation in X:Map' - description: 'xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' -extra: - identifiers: - - biotools:xmapbridge - parent_recipe: - name: bioconductor-xmapbridge - path: recipes/bioconductor-xmapbridge - version: 1.38.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-xnastring/meta.yaml b/recipes/bioconductor-xnastring/meta.yaml index b489f8d737902..bb892406fe402 100644 --- a/recipes/bioconductor-xnastring/meta.yaml +++ b/recipes/bioconductor-xnastring/meta.yaml @@ -1,31 +1,38 @@ -{% set version = "1.10.0" %} +{% set version = "1.14.0" %} {% set name = "XNAString" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The XNAString package allows for description of base sequences and associated chemical modifications in a single object. XNAString is able to capture single stranded, as well as double stranded molecules. Chemical modifications are represented as independent strings associated with different features of the molecules (base sequence, sugar sequence, backbone sequence, modifications) and can be read or written to a HELM notation. It also enables secondary structure prediction using RNAfold from ViennaRNA. XNAString is designed to be efficient representation of nucleic-acid based therapeutics, therefore it stores information about target sequences and provides interface for matching and alignment functions from Biostrings and pwalign packages. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Efficient Manipulation of Modified Oligonucleotide Sequences -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: d09bf1b8eba2843f2b6285d353fb51bc build: number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xnastring", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat, BSgenome.Hsapiens.UCSC.hg38, pander requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-formattable @@ -36,11 +43,12 @@ requirements: - libblas - liblapack run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-pwalign >=1.2.0,<1.3.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - r-data.table - r-formattable @@ -48,17 +56,16 @@ requirements: - r-rcpp - r-stringi - r-stringr - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make + +source: + md5: 9227299ff22cd0c02824cd16fcfca7b1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Efficient Manipulation of Modified Oligonucleotide Sequences' - description: 'The XNAString package allows for description of base sequences and associated chemical modifications in a single object. XNAString is able to capture single stranded, as well as double stranded molecules. Chemical modifications are represented as independent strings associated with different features of the molecules (base sequence, sugar sequence, backbone sequence, modifications) and can be read or written to a HELM notation. It also enables secondary structure prediction using RNAfold from ViennaRNA. XNAString is designed to be efficient representation of nucleic-acid based therapeutics, therefore it stores information about target sequences and provides interface for matching and alignment functions from Biostrings package.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/meta.yaml b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/meta.yaml index ebe23beba3511..31f146200fa9a 100644 --- a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/meta.yaml +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/meta.yaml @@ -1,50 +1,55 @@ {% set version = "0.99.12" %} {% set name = "XtraSNPlocs.Hsapiens.dbSNP144.GRCh37" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Extra SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13 (a patched version of GRCh37 that doesn't alter chromosomes 1-22, X, Y, MT). While the SNPlocs.Hsapiens.dbSNP144.GRCh37 package contains only molecular variations of class "snp", this package contains molecular variations of other classes (in-del, heterozygous, microsatellite, named-locus, no-variation, mixed, and multinucleotide-polymorphism). + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Extra SNP locations for Homo sapiens (dbSNP Build 144) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 758d024c50d2349036dc27cc689b4e5a build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP144.GRCh37 requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 758d024c50d2349036dc27cc689b4e5a + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Extra SNP locations for Homo sapiens (dbSNP Build 144)' - description: 'Extra SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13 (a patched version of GRCh37 that doesn''t alter chromosomes 1-22, X, Y, MT). While the SNPlocs.Hsapiens.dbSNP144.GRCh37 package contains only molecular variations of class "snp", this package contains molecular variations of other classes (in-del, heterozygous, microsatellite, named-locus, no-variation, mixed, and multinucleotide-polymorphism).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml index ac390b39412d5..8ac9ea97c12ff 100644 --- a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml @@ -1,50 +1,55 @@ {% set version = "0.99.12" %} {% set name = "XtraSNPlocs.Hsapiens.dbSNP144.GRCh38" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Extra SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 30, 2015, and contain SNPs mapped to reference genome GRCh38.p2 (a patched version of GRCh38 that doesn't alter chromosomes 1-22, X, Y, MT). While the SNPlocs.Hsapiens.dbSNP144.GRCh38 package contains only molecular variations of class "snp", this package contains molecular variations of other classes (in-del, heterozygous, microsatellite, named-locus, no-variation, mixed, and multinucleotide-polymorphism). + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Extra SNP locations for Homo sapiens (dbSNP Build 144) -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c617aa805c7ecf60ee9283eb3c51b1c7 build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38, SNPlocs.Hsapiens.dbSNP144.GRCh38 requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-bsgenome >=1.70.0,<1.71.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-bsgenome >=1.74.0,<1.75.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: c617aa805c7ecf60ee9283eb3c51b1c7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Extra SNP locations for Homo sapiens (dbSNP Build 144)' - description: 'Extra SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 30, 2015, and contain SNPs mapped to reference genome GRCh38.p2 (a patched version of GRCh38 that doesn''t alter chromosomes 1-22, X, Y, MT). While the SNPlocs.Hsapiens.dbSNP144.GRCh38 package contains only molecular variations of class "snp", this package contains molecular variations of other classes (in-del, heterozygous, microsatellite, named-locus, no-variation, mixed, and multinucleotide-polymorphism).' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-xtropicaliscdf/meta.yaml b/recipes/bioconductor-xtropicaliscdf/meta.yaml index 117cb678fcdff..af1499caff537 100644 --- a/recipes/bioconductor-xtropicaliscdf/meta.yaml +++ b/recipes/bioconductor-xtropicaliscdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "xtropicaliscdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 253e3cde76a393789e124f395820e947 +about: + description: A package containing an environment representing the X_tropicalis.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: xtropicaliscdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xtropicaliscdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 253e3cde76a393789e124f395820e947 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: xtropicaliscdf - description: 'A package containing an environment representing the X_tropicalis.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-xtropicalisprobe/meta.yaml b/recipes/bioconductor-xtropicalisprobe/meta.yaml index d9ebdd7601d4a..3dc3bea8c9ba7 100644 --- a/recipes/bioconductor-xtropicalisprobe/meta.yaml +++ b/recipes/bioconductor-xtropicalisprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "xtropicalisprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 43d15a7e12edaec1bb5f24b87498b599 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was X\_tropicalis\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type xtropicalis build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xtropicalisprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 43d15a7e12edaec1bb5f24b87498b599 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type xtropicalis' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was X\_tropicalis\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-xvector/meta.yaml b/recipes/bioconductor-xvector/meta.yaml index 8d926876d14e2..8e4f4032ff078 100644 --- a/recipes/bioconductor-xvector/meta.yaml +++ b/recipes/bioconductor-xvector/meta.yaml @@ -1,50 +1,20 @@ -{% set version = "0.42.0" %} +{% set version = "0.46.0" %} {% set name = "XVector" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides memory efficient S4 classes for storing sequences "externally" (e.g. behind an R external pointer, or on disk). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Foundation of external vector representation and manipulation in Bioconductor -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: f126998c6b563132e51ea31c3995c6b9 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-xvector", max_pin="x.x") }}' -# Suggests: Biostrings, drosophila2probe, RUnit -requirements: - host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - - r-base - - libblas - - liblapack - run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-zlibbioc >=1.48.0,<1.49.0' - - r-base - build: - - {{ compiler('c') }} - - make -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Foundation of external vector representation and manipulation in Bioconductor' - description: 'Provides memory efficient S4 classes for storing sequences "externally" (e.g. behind an R external pointer, or on disk).' + extra: additional-platforms: - linux-aarch64 @@ -56,3 +26,40 @@ extra: path: recipes/bioconductor-xvector version: 0.20.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: Biostrings, drosophila2probe, RUnit +requirements: + build: + - {{ compiler('c') }} + - make + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 + - r-base + - libblas + - liblapack + - zlib + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-zlibbioc >=1.52.0,<1.53.0 + - r-base + +source: + md5: 038527773e20903db8e40a7cfa44ab27 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-yamss/meta.yaml b/recipes/bioconductor-yamss/meta.yaml index 7c64564193b38..77cc544e2f5a3 100644 --- a/recipes/bioconductor-yamss/meta.yaml +++ b/recipes/bioconductor-yamss/meta.yaml @@ -1,61 +1,67 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "yamss" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Tools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis. At the core of these methods is a peak detection phase that pools information across all samples simultaneously. This is in contrast to other methods that detect peaks in a sample-by-sample basis. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Tools for high-throughput metabolomics -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: a60cfddcf6749fc165badbe9a0f8a311 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-yamss", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:yamss + parent_recipe: + name: bioconductor-yamss + path: recipes/bioconductor-yamss + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-mzr >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-matrix run: - - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - - 'bioconductor-ebimage >=4.44.0,<4.45.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-mzr >=2.36.0,<2.37.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-ebimage >=4.48.0,<4.49.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-mzr >=2.40.0,<2.41.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-data.table - r-matrix + +source: + md5: 181c1a5cf080d93476fd59b643e70424 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Tools for high-throughput metabolomics' - description: 'Tools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.' -extra: - identifiers: - - biotools:yamss - parent_recipe: - name: bioconductor-yamss - path: recipes/bioconductor-yamss - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-yapsa/build_failure.linux-64.yaml b/recipes/bioconductor-yapsa/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..446ca217b5fb8 --- /dev/null +++ b/recipes/bioconductor-yapsa/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a5e038a106aceeeed2a94c6b912127f3c222e43f4e2a9bda45715759a6ce77f5 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-bsgenome.hsapiens.ucsc.hg19==1.4.0=r3.2.2_0"), MatchSpec("3.2.2*")} + Encountered problems while solving: + - nothing provides r 3.2.2* needed by bioconductor-bsgenome.hsapiens.ucsc.hg19-1.4.0-r3.2.2_0 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-biostrings >=2.74.0,<2.75.0 [0m is requested and can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 [0m is installable with the potential options + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [32mr-base 3.3.2* [0m, which can be installed; + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [31mr 3.2.2* [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [32mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [32mr-base 3.4.1* [0m, which can be installed; + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.48.0,<1.50.0 [0m, which requires + [31mbioconductor-biostrings >=2.48.0,<2.50.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.50.0,<1.51.0 [0m, which requires + [31mbioconductor-biostrings >=2.50.0,<2.51.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.52.0,<1.53.0 [0m, which requires + [31mbioconductor-biostrings >=2.52.0,<2.53.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.0[0m would require + [31mbioconductor-bsgenome >=1.54.0,<1.55.0 [0m, which requires + [31mbioconductor-biostrings >=2.54.0,<2.55.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.56.0,<1.57.0 [0m, which requires + [31mbioconductor-biostrings >=2.56.0,<2.57.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.58.0,<1.59.0 [0m, which requires + [31mbioconductor-biostrings >=2.58.0,<2.59.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.60.0,<1.61.0 [0m, which requires + [31mbioconductor-biostrings >=2.60.0,<2.61.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.62.0,<1.63.0 [0m, which requires + [31mbioconductor-biostrings >=2.62.0,<2.63.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.66.0,<1.67.0 [0m, which requires + [31mbioconductor-biostrings >=2.66.0,<2.67.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.68.0,<1.69.0 [0m, which requires + [31mbioconductor-biostrings >=2.68.0,<2.69.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-bsgenome.hsapiens.ucsc.hg19 1.4.3[0m would require + [31mbioconductor-bsgenome >=1.70.0,<1.71.0 [0m, which requires + [31mbioconductor-biostrings >=2.70.0,<2.71.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-somaticsignatures >=2.42.0,<2.43.0 [0m is not installable because it requires + [31mbioconductor-ggbio >=1.54.0,<1.55.0 [0m, which requires + [31mbioconductor-organismdbi >=1.48.0,<1.49.0 [0m, which requires + [31mbioconductor-txdbmaker >=1.2.0,<1.3.0 [0m, which requires + [31mbioconductor-biomart >=2.62.0,<2.63.0 [0m, which requires + [31mbioconductor-biocfilecache >=2.14.0,<2.15.0 [0m, which requires + [31mr-base >=4.4,<4.5.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bioconductor-yapsa/meta.yaml b/recipes/bioconductor-yapsa/meta.yaml index ddef2c91d0bb8..0d911973797ac 100644 --- a/recipes/bioconductor-yapsa/meta.yaml +++ b/recipes/bioconductor-yapsa/meta.yaml @@ -1,36 +1,48 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "YAPSA" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package provides functions and routines for supervised analyses of mutational signatures (i.e., the signatures have to be known, cf. L. Alexandrov et al., Nature 2013 and L. Alexandrov et al., Bioaxiv 2018). In particular, the family of functions LCD (LCD = linear combination decomposition) can use optimal signature-specific cutoffs which takes care of different detectability of the different signatures. Moreover, the package provides different sets of mutational signatures, including the COSMIC and PCAWG SNV signatures and the PCAWG Indel signatures; the latter infering that with YAPSA, the concept of supervised analysis of mutational signatures is extended to Indel signatures. YAPSA also provides confidence intervals as computed by profile likelihoods and can perform signature analysis on a stratified mutational catalogue (SMC = stratify mutational catalogue) in order to analyze enrichment and depletion patterns for the signatures in different strata. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Yet Another Package for Signature Analysis -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7da75a0c0eabc79012aeb87c9a6e9582 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-yapsa", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:yapsa + - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-yapsa + path: recipes/bioconductor-yapsa + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: + host: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gtrellis >=1.34.0,<1.35.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-somaticsignatures >=2.38.0,<2.39.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gtrellis >=1.38.0,<1.39.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-somaticsignatures >=2.42.0,<2.43.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-circlize - r-corrplot @@ -46,16 +58,17 @@ requirements: - r-pmcmrplus - r-pracma - r-reshape2 + run: - - 'bioconductor-biostrings >=2.70.0,<2.71.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' - - 'bioconductor-complexheatmap >=2.18.0,<2.19.0' - - 'bioconductor-genomeinfodb >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-gtrellis >=1.34.0,<1.35.0' - - 'bioconductor-keggrest >=1.42.0,<1.43.0' - - 'bioconductor-somaticsignatures >=2.38.0,<2.39.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-biostrings >=2.74.0,<2.75.0 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0 + - bioconductor-complexheatmap >=2.22.0,<2.23.0 + - bioconductor-genomeinfodb >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-gtrellis >=1.38.0,<1.39.0 + - bioconductor-keggrest >=1.46.0,<1.47.0 + - bioconductor-somaticsignatures >=2.42.0,<2.43.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-circlize - r-corrplot @@ -71,21 +84,16 @@ requirements: - r-pmcmrplus - r-pracma - r-reshape2 + +source: + md5: 92dfb8587ec502a082056070b49d2d2c + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 - summary: 'Yet Another Package for Signature Analysis' - description: 'This package provides functions and routines for supervised analyses of mutational signatures (i.e., the signatures have to be known, cf. L. Alexandrov et al., Nature 2013 and L. Alexandrov et al., Bioaxiv 2018). In particular, the family of functions LCD (LCD = linear combination decomposition) can use optimal signature-specific cutoffs which takes care of different detectability of the different signatures. Moreover, the package provides different sets of mutational signatures, including the COSMIC and PCAWG SNV signatures and the PCAWG Indel signatures; the latter infering that with YAPSA, the concept of supervised analysis of mutational signatures is extended to Indel signatures. YAPSA also provides confidence intervals as computed by profile likelihoods and can perform signature analysis on a stratified mutational catalogue (SMC = stratify mutational catalogue) in order to analyze enrichment and depletion patterns for the signatures in different strata.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - identifiers: - - biotools:yapsa - - doi:10.1038/nmeth.3252 - parent_recipe: - name: bioconductor-yapsa - path: recipes/bioconductor-yapsa - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-yarn/meta.yaml b/recipes/bioconductor-yarn/meta.yaml index 2ac85ac689142..e1d85e06cf7ab 100644 --- a/recipes/bioconductor-yarn/meta.yaml +++ b/recipes/bioconductor-yarn/meta.yaml @@ -1,33 +1,43 @@ -{% set version = "1.28.0" %} +{% set version = "1.32.0" %} {% set name = "yarn" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Expedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: 'YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization' -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 90baa3de55a308d7deef0f913c6fdef8 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-yarn", max_pin="x.x") }}' - noarch: generic + +extra: + identifiers: + - biotools:yarn + - doi:10.1101/086587 + parent_recipe: + name: bioconductor-yarn + path: recipes/bioconductor-yarn + version: 1.6.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, rmarkdown, testthat (>= 0.8) requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-quantro >=1.36.0,<1.37.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-quantro >=1.40.0,<1.41.0 - r-base - r-downloader - r-gplots @@ -35,32 +45,28 @@ requirements: - r-rcolorbrewer - r-readr run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' - - 'bioconductor-biomart >=2.58.0,<2.59.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-preprocesscore >=1.64.0,<1.65.0' - - 'bioconductor-quantro >=1.36.0,<1.37.0' + - bioconductor-biobase >=2.66.0,<2.67.0 + - bioconductor-biomart >=2.62.0,<2.63.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-preprocesscore >=1.68.0,<1.69.0 + - bioconductor-quantro >=1.40.0,<1.41.0 - r-base - r-downloader - r-gplots - r-matrixstats - r-rcolorbrewer - r-readr + +source: + md5: 2c103371278e4ba17ebd22de0f45d5c3 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization' - description: 'Expedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.' -extra: - identifiers: - - biotools:yarn - - doi:10.1101/086587 - parent_recipe: - name: bioconductor-yarn - path: recipes/bioconductor-yarn - version: 1.6.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ye6100subacdf/meta.yaml b/recipes/bioconductor-ye6100subacdf/meta.yaml index 987121a33ff2b..fa6c72ba62697 100644 --- a/recipes/bioconductor-ye6100subacdf/meta.yaml +++ b/recipes/bioconductor-ye6100subacdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "ye6100subacdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 27bd71410956bfe8bffc8de14b85bdb0 +about: + description: A package containing an environment representing the Ye6100subA.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: ye6100subacdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ye6100subacdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 27bd71410956bfe8bffc8de14b85bdb0 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: ye6100subacdf - description: 'A package containing an environment representing the Ye6100subA.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ye6100subbcdf/meta.yaml b/recipes/bioconductor-ye6100subbcdf/meta.yaml index e0bfba3fe6699..aa0d7b28dc58a 100644 --- a/recipes/bioconductor-ye6100subbcdf/meta.yaml +++ b/recipes/bioconductor-ye6100subbcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "ye6100subbcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ee9ec4bd941940745bad538d79bfeab4 +about: + description: A package containing an environment representing the Ye6100subB.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: ye6100subbcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ye6100subbcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ee9ec4bd941940745bad538d79bfeab4 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: ye6100subbcdf - description: 'A package containing an environment representing the Ye6100subB.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ye6100subccdf/meta.yaml b/recipes/bioconductor-ye6100subccdf/meta.yaml index ff6863fba3546..186bd5746aba8 100644 --- a/recipes/bioconductor-ye6100subccdf/meta.yaml +++ b/recipes/bioconductor-ye6100subccdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "ye6100subccdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: fcdfed29a695fe53b62bacfe13dfe0c1 +about: + description: A package containing an environment representing the Ye6100subC.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: ye6100subccdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ye6100subccdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: fcdfed29a695fe53b62bacfe13dfe0c1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: ye6100subccdf - description: 'A package containing an environment representing the Ye6100subC.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ye6100subdcdf/meta.yaml b/recipes/bioconductor-ye6100subdcdf/meta.yaml index 03e5320b76673..525aed398f27b 100644 --- a/recipes/bioconductor-ye6100subdcdf/meta.yaml +++ b/recipes/bioconductor-ye6100subdcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "ye6100subdcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 521b501ddbcdc680c3d27b5b201029b1 +about: + description: A package containing an environment representing the Ye6100subD.CDF file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: ye6100subdcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ye6100subdcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 521b501ddbcdc680c3d27b5b201029b1 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: ye6100subdcdf - description: 'A package containing an environment representing the Ye6100subD.CDF file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-yeast.db0/meta.yaml b/recipes/bioconductor-yeast.db0/meta.yaml index b98f59b289457..0e9c3ddd88909 100644 --- a/recipes/bioconductor-yeast.db0/meta.yaml +++ b/recipes/bioconductor-yeast.db0/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "yeast.db0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 483043596daee94866843e6a43dcf538 +about: + description: Base annotation databases for yeast, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Level Annotation databases for yeast build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-yeast.db0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 579b93c0d1d3aa777f771cb25478d55f + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Level Annotation databases for yeast' - description: 'Base annotation databases for yeast, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-yeast.db0/post-link.sh b/recipes/bioconductor-yeast.db0/post-link.sh index 84300e3c77c28..f2ca9add66d13 100644 --- a/recipes/bioconductor-yeast.db0/post-link.sh +++ b/recipes/bioconductor-yeast.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "yeast.db0-3.18.0" +installBiocDataPackage.sh "yeast.db0-3.20.0" diff --git a/recipes/bioconductor-yeast2.db/meta.yaml b/recipes/bioconductor-yeast2.db/meta.yaml index 8a430b81ad727..d5fd58161a08c 100644 --- a/recipes/bioconductor-yeast2.db/meta.yaml +++ b/recipes/bioconductor-yeast2.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "yeast2.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: add5784349cde4d01b75ea4472d25597 +about: + description: Affymetrix Affymetrix Yeast_2 Array annotation data (chip yeast2) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Yeast_2 Array annotation data (chip yeast2) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-yeast2.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.sc.sgd.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.sc.sgd.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: add5784349cde4d01b75ea4472d25597 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Yeast_2 Array annotation data (chip yeast2)' - description: 'Affymetrix Affymetrix Yeast_2 Array annotation data (chip yeast2) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-yeast2cdf/meta.yaml b/recipes/bioconductor-yeast2cdf/meta.yaml index af701c9f658c7..eeff660cfb973 100644 --- a/recipes/bioconductor-yeast2cdf/meta.yaml +++ b/recipes/bioconductor-yeast2cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "yeast2cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 0a718d78ae56bef9bad8168123038ac8 +about: + description: A package containing an environment representing the Yeast_2.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: yeast2cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-yeast2cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 0a718d78ae56bef9bad8168123038ac8 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: yeast2cdf - description: 'A package containing an environment representing the Yeast_2.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-yeast2probe/meta.yaml b/recipes/bioconductor-yeast2probe/meta.yaml index 9e744a4c6cd0b..b57a1f28a388a 100644 --- a/recipes/bioconductor-yeast2probe/meta.yaml +++ b/recipes/bioconductor-yeast2probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "yeast2probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 3f52a2b7bd379624bc2966ca28c9ddf9 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Yeast\_2\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type yeast2 build: - number: 13 + noarch: generic + number: 14 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-yeast2probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 3f52a2b7bd379624bc2966ca28c9ddf9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type yeast2' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Yeast\_2\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-yeastcc/meta.yaml b/recipes/bioconductor-yeastcc/meta.yaml index 51737465e21ea..b25dc85f1b660 100644 --- a/recipes/bioconductor-yeastcc/meta.yaml +++ b/recipes/bioconductor-yeastcc/meta.yaml @@ -1,44 +1,44 @@ -{% set version = "1.42.0" %} +{% set version = "1.46.0" %} {% set name = "yeastCC" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 847d9bba73cb25f458f608c2cd6bf0e8 +about: + description: ExpressionSet for Spellman et al. (1998) yeast cell cycle microarray experiment + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Spellman et al. (1998) and Pramila/Breeden (2006) yeast cell cycle microarray data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-yeastcc", max_pin="x.x") }}' - noarch: generic +extra: + parent_recipe: + name: bioconductor-yeastcc + path: recipes/bioconductor-yeastcc + version: 1.20.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base run: - - 'bioconductor-biobase >=2.62.0,<2.63.0' + - bioconductor-biobase >=2.66.0,<2.67.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 5748a2de9c433d4f49c28744fef17e67 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Spellman et al. (1998) and Pramila/Breeden (2006) yeast cell cycle microarray data' - description: 'ExpressionSet for Spellman et al. (1998) yeast cell cycle microarray experiment' -extra: - parent_recipe: - name: bioconductor-yeastcc - path: recipes/bioconductor-yeastcc - version: 1.20.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-yeastcc/post-link.sh b/recipes/bioconductor-yeastcc/post-link.sh index 5cfa549de6683..ee0c65973bd68 100644 --- a/recipes/bioconductor-yeastcc/post-link.sh +++ b/recipes/bioconductor-yeastcc/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "yeastcc-1.42.0" +installBiocDataPackage.sh "yeastcc-1.46.0" diff --git a/recipes/bioconductor-yeastexpdata/meta.yaml b/recipes/bioconductor-yeastexpdata/meta.yaml index e659778f8d1c3..f22291d1dae39 100644 --- a/recipes/bioconductor-yeastexpdata/meta.yaml +++ b/recipes/bioconductor-yeastexpdata/meta.yaml @@ -1,46 +1,52 @@ -{% set version = "0.48.0" %} +{% set version = "0.52.0" %} {% set name = "yeastExpData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: A collection of different sets of experimental data from yeast. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Yeast Experimental Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 7cd63808a957defe831bf3e9d3ef4789 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-yeastexpdata", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-yeastexpdata + path: recipes/bioconductor-yeastexpdata + version: 0.26.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db requirements: host: - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-graph >=1.84.0,<1.85.0 - r-base run: - - 'bioconductor-graph >=1.80.0,<1.81.0' + - bioconductor-graph >=1.84.0,<1.85.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 + +source: + md5: 2298a34217fed5055d1526e3d72c1231 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL - summary: 'Yeast Experimental Data' - description: 'A collection of different sets of experimental data from yeast.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' -extra: - parent_recipe: - name: bioconductor-yeastexpdata - path: recipes/bioconductor-yeastexpdata - version: 0.26.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-yeastexpdata/post-link.sh b/recipes/bioconductor-yeastexpdata/post-link.sh index 60ca33cf64171..8f65f63698a7b 100644 --- a/recipes/bioconductor-yeastexpdata/post-link.sh +++ b/recipes/bioconductor-yeastexpdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "yeastexpdata-0.48.0" +installBiocDataPackage.sh "yeastexpdata-0.52.0" diff --git a/recipes/bioconductor-yeastgsdata/meta.yaml b/recipes/bioconductor-yeastgsdata/meta.yaml index ae9c7079330f7..2a9717ee5ecaf 100644 --- a/recipes/bioconductor-yeastgsdata/meta.yaml +++ b/recipes/bioconductor-yeastgsdata/meta.yaml @@ -1,37 +1,37 @@ -{% set version = "0.40.0" %} +{% set version = "0.44.0" %} {% set name = "yeastGSData" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: bc455a9ecd3eb2652f887026841b3c69 +about: + description: A collection of so-called gold (and other) standard data sets + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Yeast Gold Standard Data build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-yeastgsdata", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: bc968a47f5247e09b8a88af9d8289cbb + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Yeast Gold Standard Data' - description: 'A collection of so-called gold (and other) standard data sets' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-yeastgsdata/post-link.sh b/recipes/bioconductor-yeastgsdata/post-link.sh index 20a72ee7a6dc7..68b70e9d7d04f 100644 --- a/recipes/bioconductor-yeastgsdata/post-link.sh +++ b/recipes/bioconductor-yeastgsdata/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "yeastgsdata-0.40.0" +installBiocDataPackage.sh "yeastgsdata-0.44.0" diff --git a/recipes/bioconductor-yeastnagalakshmi/meta.yaml b/recipes/bioconductor-yeastnagalakshmi/meta.yaml index 1fdc69c9ba943..c8ae2795eacdd 100644 --- a/recipes/bioconductor-yeastnagalakshmi/meta.yaml +++ b/recipes/bioconductor-yeastnagalakshmi/meta.yaml @@ -1,37 +1,37 @@ -{% set version = "1.38.0" %} +{% set version = "1.42.0" %} {% set name = "yeastNagalakshmi" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: ea5068bf2b4053452f416c56ab32736a +about: + description: The yeast genome data was retrieved from the sequence read archive, aligned with bwa, and converted to BAM format with samtools. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: Artistic-2.0 + summary: Yeast genome RNA sequencing data based on Nagalakshmi et. al. build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-yeastnagalakshmi", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ce6fc59baa125ba08237e40b8be636dc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Yeast genome RNA sequencing data based on Nagalakshmi et. al.' - description: 'The yeast genome data was retrieved from the sequence read archive, aligned with bwa, and converted to BAM format with samtools.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-yeastnagalakshmi/post-link.sh b/recipes/bioconductor-yeastnagalakshmi/post-link.sh index 38aeeac70d388..546fa25ce0483 100644 --- a/recipes/bioconductor-yeastnagalakshmi/post-link.sh +++ b/recipes/bioconductor-yeastnagalakshmi/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "yeastnagalakshmi-1.38.0" +installBiocDataPackage.sh "yeastnagalakshmi-1.42.0" diff --git a/recipes/bioconductor-yeastrnaseq/meta.yaml b/recipes/bioconductor-yeastrnaseq/meta.yaml index 267ad94c02c79..070f95186d75b 100644 --- a/recipes/bioconductor-yeastrnaseq/meta.yaml +++ b/recipes/bioconductor-yeastrnaseq/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "0.40.0" %} +{% set version = "0.44.0" %} {% set name = "yeastRNASeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 2344deacf993b96e1709ad96b710471f +about: + description: A selection of RNA-Seq data from a yeast transcriptome experiment. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Yeast RNA-Seq Experimental Data from Lee et al. 2008 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-yeastrnaseq", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: Biobase, ShortRead, IRanges requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9d6061c54c1265775e1dd58a26822cde + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL - summary: 'Yeast RNA-Seq Experimental Data from Lee et al. 2008' - description: 'A selection of RNA-Seq data from a yeast transcriptome experiment.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-yeastrnaseq/post-link.sh b/recipes/bioconductor-yeastrnaseq/post-link.sh index 5e55679c515cb..14bc416e87075 100644 --- a/recipes/bioconductor-yeastrnaseq/post-link.sh +++ b/recipes/bioconductor-yeastrnaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "yeastrnaseq-0.40.0" +installBiocDataPackage.sh "yeastrnaseq-0.44.0" diff --git a/recipes/bioconductor-ygs98.db/meta.yaml b/recipes/bioconductor-ygs98.db/meta.yaml index a2127800e3fe5..7cff4cc08270c 100644 --- a/recipes/bioconductor-ygs98.db/meta.yaml +++ b/recipes/bioconductor-ygs98.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "ygs98.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: d21c0dc1ee0f7512ae921a501b425fd3 +about: + description: Affymetrix Affymetrix YG_S98 Array annotation data (chip ygs98) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix YG_S98 Array annotation data (chip ygs98) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ygs98.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.sc.sgd.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.sc.sgd.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.sc.sgd.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: d21c0dc1ee0f7512ae921a501b425fd3 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix YG_S98 Array annotation data (chip ygs98)' - description: 'Affymetrix Affymetrix YG_S98 Array annotation data (chip ygs98) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ygs98cdf/meta.yaml b/recipes/bioconductor-ygs98cdf/meta.yaml index 3fe615142da63..6e08a5f82e7b9 100644 --- a/recipes/bioconductor-ygs98cdf/meta.yaml +++ b/recipes/bioconductor-ygs98cdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "ygs98cdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: ec7df7564cf28e093646325ec55baf1e +about: + description: A package containing an environment representing the YG_S98.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: ygs98cdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ygs98cdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: ec7df7564cf28e093646325ec55baf1e + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: ygs98cdf - description: 'A package containing an environment representing the YG_S98.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ygs98frmavecs/meta.yaml b/recipes/bioconductor-ygs98frmavecs/meta.yaml index aa59611da9db5..ee77c9647684c 100644 --- a/recipes/bioconductor-ygs98frmavecs/meta.yaml +++ b/recipes/bioconductor-ygs98frmavecs/meta.yaml @@ -1,38 +1,38 @@ {% set version = "1.3.0" %} {% set name = "ygs98frmavecs" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e78c8447eb381b91dafb2f9688da39dc +about: + description: This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: GPL (>= 2) + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Vectors used by frma for microarrays of type ygs98 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ygs98frmavecs", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - r-base run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: e78c8447eb381b91dafb2f9688da39dc + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Vectors used by frma for microarrays of type ygs98' - description: 'This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-ygs98probe/meta.yaml b/recipes/bioconductor-ygs98probe/meta.yaml index 727f6b9cb5c26..c3c9141d34a77 100644 --- a/recipes/bioconductor-ygs98probe/meta.yaml +++ b/recipes/bioconductor-ygs98probe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "ygs98probe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f40f21d7074818a4ee74a45b5533e89d +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was YG-S98\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type ygs98 build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-ygs98probe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: f40f21d7074818a4ee74a45b5533e89d + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type ygs98' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was YG-S98\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-zebrafish.db/meta.yaml b/recipes/bioconductor-zebrafish.db/meta.yaml index a67f14aba8f67..9e7ed3ed59e07 100644 --- a/recipes/bioconductor-zebrafish.db/meta.yaml +++ b/recipes/bioconductor-zebrafish.db/meta.yaml @@ -1,42 +1,42 @@ {% set version = "3.13.0" %} {% set name = "zebrafish.db" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 64e40a61e81ac9397affb09880846559 +about: + description: Affymetrix Affymetrix Zebrafish Array annotation data (chip zebrafish) assembled using data from public repositories + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Affymetrix Affymetrix Zebrafish Array annotation data (chip zebrafish) build: - number: 4 + noarch: generic + number: 5 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-zebrafish.db", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.dr.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.dr.eg.db >=3.20.0,<3.21.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' - - 'bioconductor-org.dr.eg.db >=3.18.0,<3.19.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 + - bioconductor-org.dr.eg.db >=3.20.0,<3.21.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 64e40a61e81ac9397affb09880846559 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Affymetrix Affymetrix Zebrafish Array annotation data (chip zebrafish)' - description: 'Affymetrix Affymetrix Zebrafish Array annotation data (chip zebrafish) assembled using data from public repositories' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-zebrafish.db0/meta.yaml b/recipes/bioconductor-zebrafish.db0/meta.yaml index 47615e4211032..e6b0501759ae9 100644 --- a/recipes/bioconductor-zebrafish.db0/meta.yaml +++ b/recipes/bioconductor-zebrafish.db0/meta.yaml @@ -1,39 +1,39 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "zebrafish.db0" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5da71e369e2b538fe276cd58b511ebab +about: + description: Base annotation databases for zebrafish, intended ONLY to be used by AnnotationDbi to produce regular annotation packages. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: Artistic-2.0 + summary: Base Level Annotation databases for zebrafish build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-zebrafish.db0", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: a1d3664debe24db9c7c610717d2650b9 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Base Level Annotation databases for zebrafish' - description: 'Base annotation databases for zebrafish, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-zebrafish.db0/post-link.sh b/recipes/bioconductor-zebrafish.db0/post-link.sh index 9c2fee9d13f61..ce16d2933b7cb 100644 --- a/recipes/bioconductor-zebrafish.db0/post-link.sh +++ b/recipes/bioconductor-zebrafish.db0/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "zebrafish.db0-3.18.0" +installBiocDataPackage.sh "zebrafish.db0-3.20.0" diff --git a/recipes/bioconductor-zebrafishcdf/meta.yaml b/recipes/bioconductor-zebrafishcdf/meta.yaml index fe5266cf6ca7e..5024bb785ec4a 100644 --- a/recipes/bioconductor-zebrafishcdf/meta.yaml +++ b/recipes/bioconductor-zebrafishcdf/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "zebrafishcdf" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 04edbb632600c97610b86423c2d850e7 +about: + description: A package containing an environment representing the Zebrafish.cdf file. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: zebrafishcdf build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-zebrafishcdf", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 04edbb632600c97610b86423c2d850e7 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: zebrafishcdf - description: 'A package containing an environment representing the Zebrafish.cdf file.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-zebrafishprobe/meta.yaml b/recipes/bioconductor-zebrafishprobe/meta.yaml index a1f043e4c626b..b2443a67c88ca 100644 --- a/recipes/bioconductor-zebrafishprobe/meta.yaml +++ b/recipes/bioconductor-zebrafishprobe/meta.yaml @@ -1,40 +1,40 @@ {% set version = "2.18.0" %} {% set name = "zebrafishprobe" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: eea2747859afa763addc7313ab0a2452 +about: + description: This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Zebrafish\_probe\_tab. + home: https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html + license: LGPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + summary: Probe sequence data for microarrays of type zebrafish build: - number: 12 + noarch: generic + number: 13 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-zebrafishprobe", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' requirements: host: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base run: - - 'bioconductor-annotationdbi >=1.64.0,<1.65.0' + - bioconductor-annotationdbi >=1.68.0,<1.69.0 - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: eea2747859afa763addc7313ab0a2452 + url: + - https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' - license: LGPL - summary: 'Probe sequence data for microarrays of type zebrafish' - description: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Zebrafish\_probe\_tab.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-zebrafishrnaseq/meta.yaml b/recipes/bioconductor-zebrafishrnaseq/meta.yaml index 64a3e534df264..0b7e0c5c09226 100644 --- a/recipes/bioconductor-zebrafishrnaseq/meta.yaml +++ b/recipes/bioconductor-zebrafishrnaseq/meta.yaml @@ -1,24 +1,23 @@ -{% set version = "1.22.0" %} +{% set version = "1.26.0" %} {% set name = "zebrafishRNASeq" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c1fcbadec1b25e4b28483c015f7ab35c +about: + description: Gene-level read counts from RNA-Seq for gallein-treated and control zebrafish. + home: https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html + license: GPL + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + summary: Zebrafish RNA-Seq Experimental Data from Ferreira et al. (2014) build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-zebrafishrnaseq", max_pin="x.x") }}' - noarch: generic +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' # Suggests: BiocStyle, knitr requirements: host: @@ -26,14 +25,15 @@ requirements: run: - r-base - curl - - 'bioconductor-data-packages >=20231203' + - bioconductor-data-packages >=20241103 +source: + md5: 9efd43091fe0990c57a8fc8f5414885b + url: + - https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' - license: GPL - summary: 'Zebrafish RNA-Seq Experimental Data from Ferreira et al. (2014)' - description: 'Gene-level read counts from RNA-Seq for gallein-treated and control zebrafish.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-zebrafishrnaseq/post-link.sh b/recipes/bioconductor-zebrafishrnaseq/post-link.sh index 48e9432717478..414f3ad6867e0 100644 --- a/recipes/bioconductor-zebrafishrnaseq/post-link.sh +++ b/recipes/bioconductor-zebrafishrnaseq/post-link.sh @@ -1,2 +1,2 @@ #!/bin/bash -installBiocDataPackage.sh "zebrafishrnaseq-1.22.0" +installBiocDataPackage.sh "zebrafishrnaseq-1.26.0" diff --git a/recipes/bioconductor-zellkonverter/meta.yaml b/recipes/bioconductor-zellkonverter/meta.yaml index 779bd0a947f9a..15b562b2c969e 100644 --- a/recipes/bioconductor-zellkonverter/meta.yaml +++ b/recipes/bioconductor-zellkonverter/meta.yaml @@ -1,53 +1,58 @@ -{% set version = "1.12.1" %} +{% set version = "1.16.0" %} {% set name = "zellkonverter" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Provides methods to convert between Python AnnData objects and SingleCellExperiment objects. These are primarily intended for use by downstream Bioconductor packages that wrap Python methods for single-cell data analysis. It also includes functions to read and write H5AD files used for saving AnnData objects to disk. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: MIT + file LICENSE + license_file: LICENSE + summary: Conversion Between scRNA-seq Objects -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 5ba05cd62d95057a39c194a5084c551a build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-zellkonverter", max_pin="x.x") }}' - noarch: generic -# Suggests: anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr, pkgload, rmarkdown, rhdf5 (>= 2.45.1), scRNAseq, spelling, testthat, withr + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr, pkgload, rhdf5 (>= 2.45.1), rmarkdown, scRNAseq, spelling, testthat, withr requirements: host: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cli - r-matrix - r-reticulate run: - - 'bioconductor-basilisk >=1.14.0,<1.15.0' - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-s4vectors >=0.40.0,<0.41.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-basilisk >=1.18.0,<1.19.0 + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-s4vectors >=0.44.0,<0.45.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-cli - r-matrix - r-reticulate + +source: + md5: 34d82f13141a2b95f51a9492a693f86a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + file LICENSE' - summary: 'Conversion Between scRNA-seq Objects' - description: 'Provides methods to convert between Python AnnData objects and SingleCellExperiment objects. These are primarily intended for use by downstream Bioconductor packages that wrap Python methods for single-cell data analysis. It also includes functions to read and write H5AD files used for saving AnnData objects to disk.' - license_file: LICENSE + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-zenith/meta.yaml b/recipes/bioconductor-zenith/meta.yaml index 20b3c23ba110d..9ed8230e91550 100644 --- a/recipes/bioconductor-zenith/meta.yaml +++ b/recipes/bioconductor-zenith/meta.yaml @@ -1,58 +1,63 @@ -{% set version = "1.4.2" %} +{% set version = "1.8.0" %} {% set name = "zenith" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Zenith performs gene set analysis on the result of differential expression using linear (mixed) modeling with dream by considering the correlation between gene expression traits. This package implements the camera method from the limma package proposed by Wu and Smyth (2012). Zenith is a simple extension of camera to be compatible with linear mixed models implemented in variancePartition::dream(). + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Gene set analysis following differential expression using linear (mixed) modeling with dream -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: 60c9729fb2407d62a1ea15b1aa5ee0eb build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-zenith", max_pin="x.x") }}' - noarch: generic + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: BiocStyle, BiocGenerics, knitr, pander, rmarkdown, tweeDEseqCountData, edgeR, kableExtra, RUnit requirements: host: - - 'bioconductor-enrichmentbrowser >=2.32.0,<2.33.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-variancepartition >=1.32.0,<1.33.0' + - bioconductor-enrichmentbrowser >=2.36.0,<2.37.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-variancepartition >=1.36.0,<1.37.0 - r-base - r-ggplot2 - - 'r-msigdbr >=7.5.1' + - r-msigdbr >=7.5.1 - r-progress - r-rdpack - r-reshape2 - r-rfast - r-tidyr run: - - 'bioconductor-enrichmentbrowser >=2.32.0,<2.33.0' - - 'bioconductor-gseabase >=1.64.0,<1.65.0' - - 'bioconductor-limma >=3.58.0,<3.59.0' - - 'bioconductor-variancepartition >=1.32.0,<1.33.0' + - bioconductor-enrichmentbrowser >=2.36.0,<2.37.0 + - bioconductor-gseabase >=1.68.0,<1.69.0 + - bioconductor-limma >=3.62.0,<3.63.0 + - bioconductor-variancepartition >=1.36.0,<1.37.0 - r-base - r-ggplot2 - - 'r-msigdbr >=7.5.1' + - r-msigdbr >=7.5.1 - r-progress - r-rdpack - r-reshape2 - r-rfast - r-tidyr + +source: + md5: 65211ac331b8038c97aca4f4f8508a56 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Gene set analysis following differential expression using linear (mixed) modeling with dream' - description: 'Zenith performs gene set analysis on the result of differential expression using linear (mixed) modeling with dream by considering the correlation between gene expression traits. This package implements the camera method from the limma package proposed by Wu and Smyth (2012). Zenith is a simple extension of camera to be compatible with linear mixed models implemented in variancePartition::dream().' + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-zfpkm/meta.yaml b/recipes/bioconductor-zfpkm/meta.yaml index 0624f38a002d1..cebec4ef21823 100644 --- a/recipes/bioconductor-zfpkm/meta.yaml +++ b/recipes/bioconductor-zfpkm/meta.yaml @@ -1,52 +1,58 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "zFPKM" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113). Reference recommends using zFPKM > -3 to select expressed genes. Validated with encode open/closed chromosome data. Works well for gene level data using FPKM or TPM. Does not appear to calibrate well for transcript level data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-3 | file LICENSE + license_file: LICENSE + summary: A suite of functions to facilitate zFPKM transformations -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: a167e99447d7fd6b5081152a7d4472a4 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-zfpkm", max_pin="x.x") }}' - noarch: generic + +extra: + parent_recipe: + name: bioconductor-zfpkm + path: recipes/bioconductor-zfpkm + version: 1.2.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + # Suggests: knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown requirements: host: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-checkmate - r-dplyr - r-ggplot2 - r-tidyr run: - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-checkmate - r-dplyr - r-ggplot2 - r-tidyr + +source: + md5: 23e8817a9278e74bb04290d4ab9f56f9 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-3 | file LICENSE' - summary: 'A suite of functions to facilitate zFPKM transformations' - description: 'Perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113). Reference recommends using zFPKM > -3 to select expressed genes. Validated with encode open/closed chromosome data. Works well for gene level data using FPKM or TPM. Does not appear to calibrate well for transcript level data.' - license_file: LICENSE -extra: - parent_recipe: - name: bioconductor-zfpkm - path: recipes/bioconductor-zfpkm - version: 1.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-zinbwave/meta.yaml b/recipes/bioconductor-zinbwave/meta.yaml index 2dec8b8225d7f..7ca1b8ff8f8a0 100644 --- a/recipes/bioconductor-zinbwave/meta.yaml +++ b/recipes/bioconductor-zinbwave/meta.yaml @@ -1,58 +1,64 @@ -{% set version = "1.24.0" %} +{% set version = "1.28.0" %} {% set name = "zinbwave" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + summary: Zero-Inflated Negative Binomial Model for RNA-Seq Data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: e909f5d76f0ce0b7d65358ee0f80b1f3 build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-zinbwave", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2 + +extra: + identifiers: + - biotools:zinbwave + - doi:10.1038/s41467-017-02554-5 + parent_recipe: + name: bioconductor-zinbwave + path: recipes/bioconductor-zinbwave + version: 1.2.0 + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2, sparseMatrixStats requirements: host: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-softimpute run: - - 'bioconductor-biocparallel >=1.36.0,<1.37.0' - - 'bioconductor-edger >=4.0.0,<4.1.0' - - 'bioconductor-genefilter >=1.84.0,<1.85.0' - - 'bioconductor-singlecellexperiment >=1.24.0,<1.25.0' - - 'bioconductor-summarizedexperiment >=1.32.0,<1.33.0' + - bioconductor-biocparallel >=1.40.0,<1.41.0 + - bioconductor-edger >=4.4.0,<4.5.0 + - bioconductor-genefilter >=1.88.0,<1.89.0 + - bioconductor-singlecellexperiment >=1.28.0,<1.29.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 - r-base - r-matrix - r-softimpute + +source: + md5: 5d06238e82140e84ab57b0f0800d96bf + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 - summary: 'Zero-Inflated Negative Binomial Model for RNA-Seq Data' - description: 'Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data.' -extra: - identifiers: - - biotools:zinbwave - - doi:10.1038/s41467-017-02554-5 - parent_recipe: - name: bioconductor-zinbwave - path: recipes/bioconductor-zinbwave - version: 1.2.0 + - $R -e "library('{{ name }}')" diff --git a/recipes/bioconductor-zitools/build.sh b/recipes/bioconductor-zitools/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-zitools/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-zitools/meta.yaml b/recipes/bioconductor-zitools/meta.yaml new file mode 100644 index 0000000000000..db09275c4b2d8 --- /dev/null +++ b/recipes/bioconductor-zitools/meta.yaml @@ -0,0 +1,72 @@ +{% set version = "1.0.0" %} +{% set name = "zitools" %} +{% set bioc = "3.20" %} + +about: + description: zitools allows for zero inflated count data analysis by either using down-weighting of excess zeros or by replacing an appropriate proportion of excess zeros with NA. Through overloading frequently used statistical functions (such as mean, median, standard deviation), plotting functions (such as boxplots or heatmap) or differential abundance tests, it allows a wide range of downstream analyses for zero-inflated data in a less biased manner. This becomes applicable in the context of microbiome analyses, where the data is often overdispersed and zero-inflated, therefore making data analysis extremly challenging. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: BSD_3_clause + file LICENSE + license_file: LICENSE + summary: Analysis of zero-inflated count data + +build: + noarch: generic + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: '{{ pin_subpackage("bioconductor-zitools", max_pin="x.x") }}' + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), tidyverse, microbiome +requirements: + host: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-dplyr + - r-ggplot2 + - r-magrittr + - r-matrixstats + - r-pscl + - r-rcolorbrewer + - r-reshape2 + - r-tibble + - r-tidyr + - r-vgam + run: + - bioconductor-biocgenerics >=0.52.0,<0.53.0 + - bioconductor-deseq2 >=1.46.0,<1.47.0 + - bioconductor-matrixgenerics >=1.18.0,<1.19.0 + - bioconductor-phyloseq >=1.50.0,<1.51.0 + - bioconductor-summarizedexperiment >=1.36.0,<1.37.0 + - r-base + - r-dplyr + - r-ggplot2 + - r-magrittr + - r-matrixstats + - r-pscl + - r-rcolorbrewer + - r-reshape2 + - r-tibble + - r-tidyr + - r-vgam + +source: + md5: eb9b1c5201f609132929b2a323dc9c1a + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-zlibbioc/meta.yaml b/recipes/bioconductor-zlibbioc/meta.yaml index dfd70cebb4ab0..e960752e0dff7 100644 --- a/recipes/bioconductor-zlibbioc/meta.yaml +++ b/recipes/bioconductor-zlibbioc/meta.yaml @@ -1,44 +1,21 @@ -{% set version = "1.48.0" %} +{% set version = "1.52.0" %} {% set name = "zlibbioc" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means (most Linux and Mac users should have system-level access to zlib, and no direct need for this package). See the vignette for instructions on use. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: Artistic-2.0 + file LICENSE + license_file: LICENSE + summary: An R packaged zlib-1.2.5 -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: babdaf77bc9e9e8218fa07d643f31730 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-zlibbioc", max_pin="x.x") }}' -# Suggests: BiocStyle -requirements: - host: - - r-base - - libblas - - liblapack - run: - - r-base - build: - - {{ compiler('c') }} - - automake - - make -test: - commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Artistic-2.0 + file LICENSE' - summary: 'An R packaged zlib-1.2.5' - description: 'This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means (most Linux and Mac users should have system-level access to zlib, and no direct need for this package). See the vignette for instructions on use.' - license_file: LICENSE + extra: additional-platforms: - linux-aarch64 @@ -50,3 +27,32 @@ extra: path: recipes/bioconductor-zlibbioc version: 1.26.0 +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: BiocStyle, knitr +requirements: + build: + - {{ compiler('c') }} + - automake + - make + host: + - r-base + - libblas + - liblapack + run: + - r-base + +source: + md5: a8a1ac34bfefde2d1ec682600be874a1 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz + +test: + commands: + - $R -e "library('{{ name }}')" + diff --git a/recipes/bioconductor-zygositypredictor/meta.yaml b/recipes/bioconductor-zygositypredictor/meta.yaml index 6ed4225df0b9b..84d91f64f3c74 100644 --- a/recipes/bioconductor-zygositypredictor/meta.yaml +++ b/recipes/bioconductor-zygositypredictor/meta.yaml @@ -1,59 +1,72 @@ -{% set version = "1.2.0" %} +{% set version = "1.6.0" %} {% set name = "ZygosityPredictor" %} -{% set bioc = "3.18" %} +{% set bioc = "3.20" %} + +about: + description: The ZygosityPredictor allows to predict how many copies of a gene are affected by small variants. In addition to the basic calculations of the affected copy number of a variant, the Zygosity-Predictor can integrate the influence of several variants on a gene and ultimately make a statement if and how many wild-type copies of the gene are left. This information proves to be of particular use in the context of translational medicine. For example, in cancer genomes, the Zygosity-Predictor can address whether unmutated copies of tumor-suppressor genes are present. Beyond this, it is possible to make this statement for all genes of an organism. The Zygosity-Predictor was primarily developed to handle SNVs and INDELs (later addressed as small-variants) of somatic and germline origin. In order not to overlook severe effects outside of the small-variant context, it has been extended with the assessment of large scale deletions, which cause losses of whole genes or parts of them. + home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html + license: GPL-2 + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + summary: Package for prediction of zygosity for variants/genes in NGS data -package: - name: 'bioconductor-{{ name|lower }}' - version: '{{ version }}' -source: - url: - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: c201664f307a2cf422119e2fa87759cf build: + noarch: generic number: 0 rpaths: - lib/R/lib/ - lib/ run_exports: '{{ pin_subpackage("bioconductor-zygositypredictor", max_pin="x.x") }}' - noarch: generic -# Suggests: knitr, rmarkdown, testthat, BiocStyle + +package: + name: bioconductor-{{ name|lower }} + version: '{{ version }}' + +# Suggests: rmarkdown, testthat, BiocStyle requirements: host: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-dplyr - r-igraph + - r-knitr + - r-magrittr - r-purrr + - r-readr + - r-rlang - r-stringr - r-tibble run: - - 'bioconductor-delayedarray >=0.28.0,<0.29.0' - - 'bioconductor-genomicalignments >=1.38.0,<1.39.0' - - 'bioconductor-genomicranges >=1.54.0,<1.55.0' - - 'bioconductor-iranges >=2.36.0,<2.37.0' - - 'bioconductor-rsamtools >=2.18.0,<2.19.0' - - 'bioconductor-variantannotation >=1.48.0,<1.49.0' + - bioconductor-delayedarray >=0.32.0,<0.33.0 + - bioconductor-genomicalignments >=1.42.0,<1.43.0 + - bioconductor-genomicranges >=1.58.0,<1.59.0 + - bioconductor-iranges >=2.40.0,<2.41.0 + - bioconductor-rsamtools >=2.22.0,<2.23.0 + - bioconductor-variantannotation >=1.52.0,<1.53.0 - r-base - r-dplyr - r-igraph + - r-knitr + - r-magrittr - r-purrr + - r-readr + - r-rlang - r-stringr - r-tibble + +source: + md5: ea68947d05bf3b8ba399155f1fbf4c08 + url: + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz + - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz + test: commands: - - '$R -e "library(''{{ name }}'')"' -about: - home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 - summary: 'Package for prediction of zygosity for variants/genes in NGS data' - description: 'The ZygosityPredictor allows to predict how many copies of a gene are affected by small variants. In addition to the basic calculations of the affected copy number of a variant, the Zygosity-Predictor can integrate the influence of several variants on a gene and ultimately make a statement if and how many wild-type copies of the gene are left. This information proves to be of particular use in the context of translational medicine. For example, in cancer genomes, the Zygosity-Predictor can address whether unmutated copies of tumor-suppressor genes are present. Beyond this, it is possible to make this statement for all genes of an organism. The Zygosity-Predictor was primarily developed to handle SNVs and INDELs (later addressed as small-variants) of somatic and germline origin. In order not to overlook severe effects outside of the small-variant context, it has been extended with the assessment of large scale deletions, which cause losses of whole genes or parts of them.' - license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' + - $R -e "library('{{ name }}')" diff --git a/recipes/biodiff/meta.yaml b/recipes/biodiff/meta.yaml index 16894433a7adb..c4c6c9eae06c6 100644 --- a/recipes/biodiff/meta.yaml +++ b/recipes/biodiff/meta.yaml @@ -11,7 +11,7 @@ source: - osx.patch build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/biolite-tools/build_failure.osx-64.yaml b/recipes/biolite-tools/build_failure.osx-64.yaml index c6a46a775f13b..62793ce53ab04 100644 --- a/recipes/biolite-tools/build_failure.osx-64.yaml +++ b/recipes/biolite-tools/build_failure.osx-64.yaml @@ -1,6 +1,92 @@ -recipe_sha: 15c0495246aaa80ea6a578b7bfd53667b6f631ab485e9ede8fee9d3088150873 # The commit at which this recipe failed to build. +recipe_sha: d9036fac8e4a3c6146d4c284d2b1999d2d1d5e7aa6df21efa1133599ba5fd5d4 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/biolite-tools-0.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/biolite-tools-0.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + checking for a BSD-compatible install... /usr/bin/install -c + checking whether build environment is sane... yes + checking for a thread-safe mkdir -p... ./install-sh -c -d + checking for gawk... no + checking for mawk... no + checking for nawk... no + checking for awk... awk + checking whether make sets $(MAKE)... yes + checking whether make supports nested variables... yes + checking whether make supports nested variables... (cached) yes + checking build system type... x86_64-apple-darwin13.4.0 + checking host system type... x86_64-apple-darwin13.4.0 + checking whether make sets $(MAKE)... (cached) yes + checking for x86_64-apple-darwin13.4.0-ranlib... x86_64-apple-darwin13.4.0-ranlib + checking whether the C compiler works... yes + checking for C compiler default output file name... a.out + checking for suffix of executables... + checking whether we are cross compiling... no + checking for suffix of object files... o + checking whether we are using the GNU C compiler... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking for style of include used by make... GNU + checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 + checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang -E + checking for grep that handles long lines and -e... /usr/bin/grep + checking for egrep... /usr/bin/grep -E + checking for ANSI C header files... yes + checking for sys/types.h... yes + checking for sys/stat.h... yes + checking for stdlib.h... yes + checking for string.h... yes + checking for memory.h... yes + checking for strings.h... yes + checking for inttypes.h... yes + checking for stdint.h... yes + checking for unistd.h... yes + checking limits.h usability... yes + checking limits.h presence... yes + checking for limits.h... yes + checking for stdlib.h... (cached) yes + checking for string.h... (cached) yes + checking for unistd.h... (cached) yes + checking unordered_map usability... yes + checking unordered_map presence... yes + checking for unordered_map... yes + checking tr1/unordered_map usability... no + checking tr1/unordered_map presence... no + checking for tr1/unordered_map... no + checking unordered_set usability... yes + checking unordered_set presence... yes + checking for unordered_set... yes + checking tr1/unordered_set usability... no + checking tr1/unordered_set presence... no + checking for tr1/unordered_set... no + checking for stdbool.h that conforms to C99... no + checking for _Bool... no + checking for size_t... yes + checking for stdlib.h... (cached) yes + checking for GNU libc compatible malloc... (cached) yes + checking for sqrt... yes + checking for strrchr... yes + checking for strtoul... yes + checking that generated files are newer than configure... done + configure: creating ./config.status + config.status: creating Makefile + config.status: creating src/Makefile + config.status: creating config.h + config.status: executing depfiles commands + + Summary: + + Build OS: Darwin 22.6.0 x86_64 + Build host: Mac-1733850328615.local + Install dir: $PREFIX + C compiler: x86_64-apple-darwin13.4.0-clang (version: clang version 18.1.8) + CXXFLAGS = -I$PREFIX/include + LDFLAGS = -L$PREFIX/lib + LIBS = -lz + + make all-recursive + make[1]: Entering directory '$SRC_DIR' Making all in src make[2]: Entering directory '$SRC_DIR/src' CXX seqio.o @@ -13,92 +99,6 @@ log: |- CXX interleave.o CXX pair_reads.o CXX randomize.o - randomize.cpp:99:3: warning: 'random_shuffle>' is deprecated [-Wdeprecated-declarations] - random_shuffle(order.begin(), order.end()); - ^ - /opt/mambaforge/envs/bioconda/conda-bld/biolite-tools_1685352358324/_build_env/bin/../include/c/v1/__algorithm/shuffle.h:97:23: note: 'random_shuffle>' has been explicitly marked deprecated here - _LIBCPP_HIDE_FROM_ABI _LIBCPP_DEPRECATED_IN_CXX14 void - ^ - /opt/mambaforge/envs/bioconda/conda-bld/biolite-tools_1685352358324/_build_env/bin/../include/c/v1/__config:868:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX14' - # define _LIBCPP_DEPRECATED_IN_CXX14 _LIBCPP_DEPRECATED - ^ - /opt/mambaforge/envs/bioconda/conda-bld/biolite-tools_1685352358324/_build_env/bin/../include/c/v1/__config:847:49: note: expanded from macro '_LIBCPP_DEPRECATED' - # define _LIBCPP_DEPRECATED __attribute__((deprecated)) - ^ - CXX insert_stats.o - 1 warning generated. - CXX pileup_stats.o - CXX threshold.o - AR libseqio.a - CXXLD bl-coverage - CXXLD bl-exclude - CXXLD bl-filter-illumina - CXXLD bl-fasta2fastq - CXXLD bl-fastq2fasta - CXXLD bl-interleave - CXXLD bl-pair-reads - CXXLD bl-randomize - CXXLD bl-insert-stats - CXXLD bl-pileup-stats - CXXLD bl-threshold - make[2]: Leaving directory '$SRC_DIR/src' - make[2]: Entering directory '$SRC_DIR' - make[2]: Leaving directory '$SRC_DIR' - make[1]: Leaving directory '$SRC_DIR' - Making install in src - make[1]: Entering directory '$SRC_DIR/src' - make[2]: Entering directory '$SRC_DIR/src' - .././install-sh -c -d '$PREFIX/bin' - /usr/bin/install -c bl-coverage bl-exclude bl-filter-illumina bl-fasta2fastq bl-fastq2fasta bl-interleave bl-pair-reads bl-randomize bl-insert-stats bl-pileup-stats bl-threshold '$PREFIX/bin' - make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '$SRC_DIR/src' - make[1]: Leaving directory '$SRC_DIR/src' - make[1]: Entering directory '$SRC_DIR' - make[2]: Entering directory '$SRC_DIR' - make[2]: Nothing to be done for 'install-exec-am'. - make[2]: Nothing to be done for 'install-data-am'. - make[2]: Leaving directory '$SRC_DIR' make[1]: Leaving directory '$SRC_DIR' - - Resource usage statistics from building biolite-tools: - Process count: 11 - CPU time: Sys=0:00:01.3, User=0:00:09.2 - Memory: 141.0M - Disk usage: 14.6K - Time elapsed: 0:00:33.4 - - - Packaging biolite-tools - INFO:conda_build.build:Packaging biolite-tools - Packaging biolite-tools-0.4.0-hdf58011_8 - INFO:conda_build.build:Packaging biolite-tools-0.4.0-hdf58011_8 - number of files: 11 - error: /opt/mambaforge/envs/bioconda/conda-bld/biolite-tools_1685352358324/_build_env/bin/x86_64-apple-darwin13.4.0-install_name_tool: changing install names or rpaths can't be redone for: /opt/mambaforge/envs/bioconda/conda-bld/biolite-tools_1685352358324/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/bin/bl-pileup-stats (for architecture x86_64) because larger updated load commands do not fit (the program must be relinked, and you may need to use -headerpad or -headerpad_max_install_names) - - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2358, in build - newly_built_packages = bundlers[pkg_type](output_d, m, env, stats) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 1659, in bundle_conda - files = post_process_files(metadata, initial_files) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 1505, in post_process_files - post_build(m, new_files, build_python=python) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/post.py", line 1318, in post_build - post_process_shared_lib(m, f, prefix_files, host_prefix) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/post.py", line 1266, in post_process_shared_lib - mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/post.py", line 416, in mk_relative_osx - macho.add_rpath(path, rpath_new, build_prefix=prefix, verbose=True) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/os_utils/macho.py", line 268, in add_rpath - raise RuntimeError("install_name_tool failed with exit status %d" - RuntimeError: install_name_tool failed with exit status 1 # Last 100 lines of the build log. diff --git a/recipes/biolite-tools/meta.yaml b/recipes/biolite-tools/meta.yaml index 8390912fa515b..01eaafe17c92f 100644 --- a/recipes/biolite-tools/meta.yaml +++ b/recipes/biolite-tools/meta.yaml @@ -9,7 +9,7 @@ source: sha256: b2e08caa65d1bf0914a910fa2e90fa5757d0e2ddd0f2e4ec41dbd5682dab3093 build: - number: 8 + number: 9 requirements: build: diff --git a/recipes/biscuit/meta.yaml b/recipes/biscuit/meta.yaml index 21a22964ef728..f9f3e3f6f354c 100644 --- a/recipes/biscuit/meta.yaml +++ b/recipes/biscuit/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('biscuit', max_pin='x') }} diff --git a/recipes/bitmapperbs/meta.yaml b/recipes/bitmapperbs/meta.yaml index 963488f59c7e9..22f687744c10d 100644 --- a/recipes/bitmapperbs/meta.yaml +++ b/recipes/bitmapperbs/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 5 + number: 6 skip: True # [osx] source: diff --git a/recipes/blast/meta.yaml b/recipes/blast/meta.yaml index 141c4970cd638..db02079cafc62 100644 --- a/recipes/blast/meta.yaml +++ b/recipes/blast/meta.yaml @@ -16,7 +16,7 @@ source: - update_configsub.patch build: - number: 3 + number: 4 run_exports: # Now, the point releases seem to be only bugfixes at least (but this definitely was not the # case up to v2.2.31) diff --git a/recipes/blastalign/build_failure.linux-64.yaml b/recipes/blastalign/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..081947086d366 --- /dev/null +++ b/recipes/blastalign/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: b5bf8a322e67d1f4e608c9c457f1d25ea8b7778c06b27dce731c7206de45a1a2 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + 2024-12-14T21:48:11 linux-aarch64 Writing pre-patch repodata + 2024-12-14T21:48:11 linux-aarch64 Applying patch instructions + 2024-12-14T21:48:11 linux-aarch64 Writing patched repodata + 2024-12-14T21:48:11 linux-aarch64 Building current_repodata subset + 2024-12-14T21:48:11 linux-aarch64 Writing current_repodata subset + 2024-12-14T21:48:11 linux-aarch64 Writing index HTML + 2024-12-14T21:48:11 Subdir: noarch Gathering repodata + 2024-12-14T21:48:11 noarch Writing pre-patch repodata + 2024-12-14T21:48:11 noarch Applying patch instructions + 2024-12-14T21:48:11 noarch Writing patched repodata + 2024-12-14T21:48:11 noarch Building current_repodata subset + 2024-12-14T21:48:11 noarch Writing current_repodata subset + 2024-12-14T21:48:11 noarch Writing index HTML + /opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (/opt/recipe/meta.yaml). + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml + Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for blastalign + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['blastalign-1.4-h7b50bb2_9.tar.bz2'] + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/blastalign_1734212891888/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/blastalign_1734212891888/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.43-h4bf12b8_2 conda-forge + binutils_linux-64: 2.43-h4852527_2 conda-forge + gcc_impl_linux-64: 13.3.0-hfea6d02_1 conda-forge + gcc_linux-64: 13.3.0-hc28eda2_7 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libsanitizer: 13.3.0-heb74ff8_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: BlastAlign_20cd6895dc.tar + Downloading https://drive.google.com/uc?export=download&id=1Z0bt8vHRyR6QsEway1LxJjYIgM_E-j_f + Success + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 125, in download_to_cache + raise RuntimeError( + RuntimeError: SHA256 mismatch: 'a03d8d51bf7f24e72eb81afde811e4dd1d26841395f742aaba216b7f3e1a3399' != '20cd6895dc949d3aeafd14dcf18f2678d9ed24fdcaeddd9ace3e9862d84f106d' +# Last 100 lines of the build log. diff --git a/recipes/blastalign/meta.yaml b/recipes/blastalign/meta.yaml index 535812469a755..0f9de22326a4e 100644 --- a/recipes/blastalign/meta.yaml +++ b/recipes/blastalign/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.4" build: - number: 8 + number: 9 skip: True # [osx] source: diff --git a/recipes/blend-bio/build_failure.osx-64.yaml b/recipes/blend-bio/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..ab48cfdf303dd --- /dev/null +++ b/recipes/blend-bio/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: b3bb6ba15f055a42c2a359a2270536b4a1c0e1a106619c617af82258e120df91 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - tapi 1300.6.5 h390ca13_0 + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/blend-bio_1733987527292/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + - clangxx 18.1.8 default_h179603d_5 + - cctools_osx-64 1010.6 h00edd4c_2 + - clang_osx-64 18.1.8 h7e5c614_23 + - llvm-tools-18 18.1.8 h9ce406d_2 + host: + - libzlib 1.3.1 hd23fc13_2 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + - zlib 1.3.1 hd23fc13_2 + run: + - libzlib >=1.3.1,<2.0a0 + - zlib + test: + commands: + - blend -h + about: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/blend-bio_1733987527292/work/conda_build.sh']' returned non-zero exit status 2. + home: https://github.com/CMU-SAFARI/BLEND + license: MIT + license_file: LICENSE + summary: BLEND is a Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy + Seed Matches in Genome Analysis + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/blend-bio_1733987527292/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/blend-bio_1733987527292/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/blend-bio_1733987527292/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/blend-bio_1733987527292/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/blend-bio-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/blend-bio-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + x86_64-apple-darwin13.4.0-clang -c -g -Wall -O2 -Wc-compat -march=native -mavx2 -msse4.1 -L$PREFIX/lib -DHAVE_KALLOC -I$PREFIX/include main.c -o main.o + x86_64-apple-darwin13.4.0-clang -c -g -Wall -O2 -Wc-compat -march=native -mavx2 -msse4.1 -L$PREFIX/lib -DHAVE_KALLOC -I$PREFIX/include kthread.c -o kthread.o + x86_64-apple-darwin13.4.0-clang -c -g -Wall -O2 -Wc-compat -march=native -mavx2 -msse4.1 -L$PREFIX/lib -DHAVE_KALLOC -I$PREFIX/include kalloc.c -o kalloc.o + x86_64-apple-darwin13.4.0-clang -c -g -Wall -O2 -Wc-compat -march=native -mavx2 -msse4.1 -L$PREFIX/lib -DHAVE_KALLOC -I$PREFIX/include misc.c -o misc.o + x86_64-apple-darwin13.4.0-clang -c -g -Wall -O2 -Wc-compat -march=native -mavx2 -msse4.1 -L$PREFIX/lib -DHAVE_KALLOC -I$PREFIX/include bseq.c -o bseq.o + x86_64-apple-darwin13.4.0-clang -c -g -Wall -O2 -Wc-compat -march=native -mavx2 -msse4.1 -L$PREFIX/lib -DHAVE_KALLOC -I$PREFIX/include sketch.c -o sketch.o + x86_64-apple-darwin13.4.0-clang -c -g -Wall -O2 -Wc-compat -march=native -mavx2 -msse4.1 -L$PREFIX/lib -DHAVE_KALLOC -I$PREFIX/include sdust.c -o sdust.o + x86_64-apple-darwin13.4.0-clang -c -g -Wall -O2 -Wc-compat -march=native -mavx2 -msse4.1 -L$PREFIX/lib -DHAVE_KALLOC -I$PREFIX/include options.c -o options.o + x86_64-apple-darwin13.4.0-clang -c -g -Wall -O2 -Wc-compat -march=native -mavx2 -msse4.1 -L$PREFIX/lib -DHAVE_KALLOC -I$PREFIX/include index.c -o index.o +# Last 100 lines of the build log. diff --git a/recipes/blend-bio/meta.yaml b/recipes/blend-bio/meta.yaml index b14b5ce0aa51c..072c56d90bea2 100644 --- a/recipes/blend-bio/meta.yaml +++ b/recipes/blend-bio/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 8aa82c2f3bd829429095be7ca1dfd2e242a0c2df04d5dc0c48c8a8c09c911bc3 build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/blockbuster/meta.yaml b/recipes/blockbuster/meta.yaml index 8cde2a28361e4..01d35a9b33753 100644 --- a/recipes/blockbuster/meta.yaml +++ b/recipes/blockbuster/meta.yaml @@ -7,7 +7,7 @@ source: url: https://github.com/bgruening/download_store/raw/master/blockbuster/blockbuster-0.0.1.1.tar.gz build: - number: 7 + number: 8 requirements: build: diff --git a/recipes/blockclust/meta.yaml b/recipes/blockclust/meta.yaml index 37a9ec34be55b..d65e46c7c9cfe 100644 --- a/recipes/blockclust/meta.yaml +++ b/recipes/blockclust/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 80ee2b32085b93966254083574b2bf3988771ffe28d73775be96a16cfda5579b build: - number: 1 + number: 2 skip: True # [osx or py2k] run_exports: - {{ pin_subpackage('blockclust', max_pin="x") }} diff --git a/recipes/bloocoo/build_failure.osx-64.yaml b/recipes/bloocoo/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c495e9372aad1 --- /dev/null +++ b/recipes/bloocoo/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c623e9dd0b2830823eabf66b95763d6d22bcefe4b2e7c6cba10676d0453321fb # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + -- Looking for alarm + -- Looking for alarm - found + -- Looking for fork + -- Looking for fork - found + -- Looking for frexpf + -- Looking for frexpf - found + -- Looking for frexpl + -- Looking for frexpl - found + -- Looking for gethostname + -- Looking for gethostname - found + -- Looking for getpwuid + -- Looking for getpwuid - found + -- Looking for getrusage + -- Looking for getrusage - found + -- Looking for lstat + -- Looking for lstat - found + -- Looking for rand_r + -- Looking for rand_r - found + -- Looking for random + -- Looking for random - found + -- Looking for setsysinfo + -- Looking for setsysinfo - not found + -- Looking for signal + -- Looking for signal - found + -- Looking for longjmp + -- Looking for longjmp - found + -- Looking for setjmp + -- Looking for setjmp - found + -- Looking for siglongjmp + -- Looking for siglongjmp - found + -- Looking for sigsetjmp + -- Looking for sigsetjmp - found + -- Looking for sigaction + -- Looking for sigaction - found + -- Looking for sigprocmask + -- Looking for sigprocmask - found + -- Looking for snprintf + -- Looking for snprintf - found + -- Looking for srandom + -- Looking for srandom - found + -- Looking for strdup + -- Looking for strdup - found + -- Looking for symlink + -- Looking for symlink - found + -- Looking for system + -- Looking for system - found + -- Looking for vasprintf + -- Looking for vasprintf - found + -- Looking for waitpid + -- Looking for waitpid - found + -- Looking for vsnprintf + -- Looking for vsnprintf - found + -- Performing Other Test VSNPRINTF_WORKS - Success + -- Looking for tzname + -- Looking for tzname - found + -- Performing Other Test LONE_COLON - Failed + -- Performing Other Test HAVE_ATTRIBUTE - Success + -- Performing Other Test HAVE_C99_FUNC - Success + -- Performing Other Test HAVE_FUNCTION - Success + -- Performing Other Test HAVE_C99_DESIGNATED_INITIALIZER - Success + -- Performing Other Test SYSTEM_SCOPE_THREADS - Success + -- Performing Other Test HAVE_SOCKLEN_T - Success + -- Performing Other Test CXX_HAVE_OFFSETOF - Success + -- Performing CXX Test OLD_HEADER_FILENAME - Failed + -- Performing CXX Test H5_NO_NAMESPACE - Failed + -- Performing CXX Test H5_NO_STD - Failed + -- Performing CXX Test BOOL_NOTDEFINED - Failed + -- Performing CXX Test NO_STATIC_CAST - Failed + -- Performing TEST_DIRECT_VFD_WORKS... no + -- Performing Other Test INLINE_TEST_inline - Success + -- Performing Other Test INLINE_TEST___inline__ - Success + -- Performing Other Test INLINE_TEST___inline - Success + -- Checking for appropriate format for 64 bit long: + -- Checking for apropriate format for 64 bit long: found "ll" + -- checking IF converting from long double to integers is accurate... yes + -- Checking IF converting from long double to integers works... no + -- checking IF accurately converting from integers to long double... yes + -- Checking IF accurately converting unsigned long to float values... no + -- Checking IF accurately converting unsigned long long to floating-point values... no + -- Checking IF accurately roundup converting floating-point to unsigned long long values... no + -- Checking IF correctly converting long double to unsigned int values... no + -- Checking IF compiling unsigned long long to floating-point typecasts work... yes + -- Checking IF compiling long long to floating-point typecasts work... yes + -- Checking IF converting unsigned long long to long double with precision... no + -- Checking IF overflows normally converting floating-point to integer values... no + -- Checking IF your system converts long double to (unsigned) long values with special algorithm... no + -- Checking IF your system can convert (unsigned) long to long double values with special algorithm... no + -- Checking IF correctly converting long double to (unsigned) long long values... no + -- Checking IF correctly converting (unsigned) long long to long double values... no + -- Checking IF your system generates wrong code for log2 routine... no + -- Checking IF alignment restrictions are strictly enforced... yes + -- Could NOT find ZLIB (missing: ZLIB_DIR) + -- Found ZLIB: $PREFIX/lib/libz.dylib (found version "1.3.1") + -- Filter ZLIB is ON + -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) + -- Configuring done (71.5s) + -- Generating done (0.2s) + -- Build files have been written to: $SRC_DIR/build + [ 0%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5detect.dir/H5detect.c.o + [ 1%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5make_libsettings.dir/H5make_libsettings.c.o +# Last 100 lines of the build log. diff --git a/recipes/bloocoo/meta.yaml b/recipes/bloocoo/meta.yaml index f1daf3de547a3..51d2a2a8046b4 100644 --- a/recipes/bloocoo/meta.yaml +++ b/recipes/bloocoo/meta.yaml @@ -12,7 +12,7 @@ source: - 0001-Remove-superfluous-template-keyword-in-debruijn--impl.patch build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/bloomfiltertrie/meta.yaml b/recipes/bloomfiltertrie/meta.yaml index b13b7f8f005bb..026644d53c65b 100644 --- a/recipes/bloomfiltertrie/meta.yaml +++ b/recipes/bloomfiltertrie/meta.yaml @@ -12,7 +12,7 @@ source: - popcnt.patch build: - number: 5 + number: 6 skip: true # [osx] requirements: diff --git a/recipes/bmfilter/meta.yaml b/recipes/bmfilter/meta.yaml index a9c4f1c22e76d..c600b54957bed 100644 --- a/recipes/bmfilter/meta.yaml +++ b/recipes/bmfilter/meta.yaml @@ -13,7 +13,7 @@ source: md5: ef79071be499ed23e9f3a19c9c323775 # [osx] build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('bmfilter', max_pin="x") }} diff --git a/recipes/bmtool/meta.yaml b/recipes/bmtool/meta.yaml index f64a02e196bf0..dd2abbe49ecd1 100644 --- a/recipes/bmtool/meta.yaml +++ b/recipes/bmtool/meta.yaml @@ -13,7 +13,7 @@ source: md5: 43f112115af7ef2a28c6a64b31374c12 # [osx] build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('bmtool', max_pin="x") }} @@ -36,4 +36,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/boms/meta.yaml b/recipes/boms/meta.yaml index bb3cc10f65f7b..ac36177d5262e 100644 --- a/recipes/boms/meta.yaml +++ b/recipes/boms/meta.yaml @@ -14,7 +14,7 @@ build: - {{ pin_subpackage('boms', max_pin="x.x") }} skip: true # [osx or py<39] script: {{ PYTHON }} -m pip install . -vv --no-build-isolation - number: 1 + number: 2 requirements: build: diff --git a/recipes/booster/meta.yaml b/recipes/booster/meta.yaml index 428940471918e..f556f21af138c 100644 --- a/recipes/booster/meta.yaml +++ b/recipes/booster/meta.yaml @@ -9,7 +9,7 @@ source: sha256: eee92b91c98d3fccb2b94201dfdc775d1c381d22c5953240562b8de20e763e18 build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/bowtie/meta.yaml b/recipes/bowtie/meta.yaml index fb9765f3543a7..50cdf450226b6 100644 --- a/recipes/bowtie/meta.yaml +++ b/recipes/bowtie/meta.yaml @@ -13,7 +13,7 @@ source: build: skip: True # [py<30] - number: 9 + number: 10 run_exports: - {{ pin_subpackage("bowtie", max_pin="x.x") }} diff --git a/recipes/bowtie2/meta.yaml b/recipes/bowtie2/meta.yaml index 64a7124009d3a..09cb9b1fe35f1 100644 --- a/recipes/bowtie2/meta.yaml +++ b/recipes/bowtie2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 841a6a60111b690c11d1e123cb5c11560b4cd1502b5cee7e394fd50f83e74e13 build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage('bowtie2', max_pin="x") }} diff --git a/recipes/bpp-phyl/meta.yaml b/recipes/bpp-phyl/meta.yaml index 59d0808163650..ec4b5e2d0f9d2 100644 --- a/recipes/bpp-phyl/meta.yaml +++ b/recipes/bpp-phyl/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://github.com/BioPP/{{ name }}/archive/v{{ version }}.tar.gz diff --git a/recipes/bpp-popgen/meta.yaml b/recipes/bpp-popgen/meta.yaml index 22475866820dc..dfa66f455be07 100644 --- a/recipes/bpp-popgen/meta.yaml +++ b/recipes/bpp-popgen/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://github.com/BioPP/{{ name }}/archive/v{{ version }}.tar.gz diff --git a/recipes/bpp-seq/meta.yaml b/recipes/bpp-seq/meta.yaml index 82e8510b83817..ac51b419f3890 100644 --- a/recipes/bpp-seq/meta.yaml +++ b/recipes/bpp-seq/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://github.com/BioPP/{{ name }}/archive/v{{ version }}.tar.gz diff --git a/recipes/bracken/meta.yaml b/recipes/bracken/meta.yaml index d8380c4172c2c..d1892f997aced 100644 --- a/recipes/bracken/meta.yaml +++ b/recipes/bracken/meta.yaml @@ -14,7 +14,7 @@ source: - py3.patch build: - number: 1 + number: 2 skip: True # [osx and x86_64] run_exports: - {{ pin_subpackage('bracken', max_pin="x") }} diff --git a/recipes/breakdancer/build_failure.linux-64.yaml b/recipes/breakdancer/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..4a59011e58d0f --- /dev/null +++ b/recipes/breakdancer/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c1e898541bfa7816c2510a40454f502b7916aa000964c66fb5dd1b5100ecd449 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Fixing permissions + INFO :: Time taken to mark (prefix) + 0 replacements in 0 files was 0.01 seconds + Files containing CONDA_PREFIX + ----------------------------- + bin/breakdancer-max (binary): Patching + bin/samtools (binary): Patching + lib/breakdancer-maxunstable/bam2cfg.pl (text): Patching + WARNING: Importing conda-verify failed. Please be sure to test your packages. conda install conda-verify to make this message go away. + TEST START: /opt/conda/conda-bld/linux-64/breakdancer-1.4.5-pl5321h3e6c209_12.tar.bz2 + Renaming work directory '/opt/conda/conda-bld/breakdancer_1734365745767/work' to '/opt/conda/conda-bld/breakdancer_1734365745767/work_moved_breakdancer-1.4.5-pl5321h3e6c209_12_linux-64' + shutil.move(work)=/opt/conda/conda-bld/breakdancer_1734365745767/work, dest=/opt/conda/conda-bld/breakdancer_1734365745767/work_moved_breakdancer-1.4.5-pl5321h3e6c209_12_linux-64) + Reloading output folder (local, file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/breakdancer_1734365745767/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + breakdancer: 1.4.5-pl5321h3e6c209_12 local + font-ttf-dejavu-sans-mono: 2.37-hab24e00_0 conda-forge + font-ttf-inconsolata: 3.000-h77eed37_0 conda-forge + font-ttf-source-code-pro: 2.038-h77eed37_0 conda-forge + font-ttf-ubuntu: 0.83-h77eed37_3 conda-forge + fontconfig: 2.15.0-h7e30c49_1 conda-forge + fonts-conda-ecosystem: 1-0 conda-forge + fonts-conda-forge: 1-0 conda-forge + freetype: 2.12.1-h267a509_2 conda-forge + icu: 75.1-he02047a_0 conda-forge + lerc: 4.0.0-h27087fc_0 conda-forge + libdeflate: 1.22-hb9d3cd8_0 conda-forge + libexpat: 2.6.4-h5888daf_0 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-ng: 14.2.0-h69a702a_1 conda-forge + libgd: 2.3.3-hd3e95f3_10 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libjpeg-turbo: 3.0.0-hd590300_1 conda-forge + liblzma: 5.6.3-hb9d3cd8_1 conda-forge + libpng: 1.6.44-hadc24fc_0 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-ng: 14.2.0-h4852527_1 conda-forge + libtiff: 4.7.0-hc4654cb_2 conda-forge + libuuid: 2.38.1-h0b41bf4_0 conda-forge + libwebp-base: 1.4.0-hd590300_0 conda-forge + libxcrypt: 4.4.36-hd590300_1 conda-forge + libzlib: 1.3.1-hb9d3cd8_2 conda-forge + ncurses: 6.5-he02047a_1 conda-forge + perl: 5.32.1-7_hd590300_perl5 conda-forge + perl-exporter-tiny: 1.002002-pl5321hd8ed1ab_0 conda-forge + perl-gd: 2.56-0 bioconda + perl-gdgraph: 1.54-pl5321hdfd78af_1 bioconda + perl-gdgraph-histogram: 1.1-pl5321hdfd78af_4 bioconda + perl-gdtextutil: 0.86-pl5321h7b50bb2_9 bioconda + perl-list-moreutils: 0.430-pl5321hdfd78af_0 bioconda + perl-list-moreutils-xs: 0.430-pl5321h7b50bb2_4 file:///opt/host-conda-bld + perl-math-cdf: 0.1-pl5321h7b50bb2_11 bioconda + perl-statistics-descriptive: 3.0801-pl5321hdfd78af_0 bioconda + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + export PREFIX=/opt/conda/conda-bld/breakdancer_1734365745767/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export SRC_DIR=/opt/conda/conda-bld/breakdancer_1734365745767/test_tmp + breakdancer-max + grep 'Usage: breakdancer-max' + Usage: breakdancer-max + bam2cfg.pl + grep Usage + WARNING: Tests failed for breakdancer-1.4.5-pl5321h3e6c209_12.tar.bz2 - moving package to /opt/conda/conda-bld/broken + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/breakdancer_1734365745767/test_tmp/conda_test_runner.sh']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: breakdancer-1.4.5-pl5321h3e6c209_12.tar.bz2 +# Last 100 lines of the build log. diff --git a/recipes/breakdancer/meta.yaml b/recipes/breakdancer/meta.yaml index d767de21d90ba..6752c45cc8fba 100644 --- a/recipes/breakdancer/meta.yaml +++ b/recipes/breakdancer/meta.yaml @@ -17,7 +17,7 @@ source: build: skip: True # [osx] - number: 11 + number: 12 requirements: build: diff --git a/recipes/breseq/meta.yaml b/recipes/breseq/meta.yaml index bc10a5dbbd9ac..9612132cb7fd9 100644 --- a/recipes/breseq/meta.yaml +++ b/recipes/breseq/meta.yaml @@ -9,7 +9,7 @@ source: sha256: "39b35e246ecd2b497c82a99765ca4d78a0400bc4a7518b7506b140229ccc0247" build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('breseq', max_pin="x.x") }} diff --git a/recipes/bs_call/build_failure.osx-64.yaml b/recipes/bs_call/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c91d761de386b --- /dev/null +++ b/recipes/bs_call/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 1c74c7e69f4b9f23d3b37b854c28ac5551a37124c049bb7b21be9f7cc2ac3f5d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_error.c -o ../build/gt_error.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_mm.c -o ../build/gt_mm.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_fm.c -o ../build/gt_fm.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_profiler.c -o ../build/gt_profiler.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_ihash.c -o ../build/gt_ihash.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_shash.c -o ../build/gt_shash.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_vector.c -o ../build/gt_vector.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_string.c -o ../build/gt_string.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_attributes.c -o ../build/gt_attributes.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_dna_string.c -o ../build/gt_dna_string.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_dna_read.c -o ../build/gt_dna_read.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_compact_dna_string.c -o ../build/gt_compact_dna_string.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_template.c -o ../build/gt_template.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_alignment.c -o ../build/gt_alignment.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_map.c -o ../build/gt_map.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_misms.c -o ../build/gt_misms.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_template_utils.c -o ../build/gt_template_utils.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_alignment_utils.c -o ../build/gt_alignment_utils.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_counters_utils.c -o ../build/gt_counters_utils.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_map_metrics.c -o ../build/gt_map_metrics.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_map_align.c -o ../build/gt_map_align.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_map_score.c -o ../build/gt_map_score.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_map_utils.c -o ../build/gt_map_utils.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_sequence_archive.c -o ../build/gt_sequence_archive.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_segmented_sequence.c -o ../build/gt_segmented_sequence.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_input_file.c -o ../build/gt_input_file.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_buffered_input_file.c -o ../build/gt_buffered_input_file.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_input_parser.c -o ../build/gt_input_parser.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_input_map_parser.c -o ../build/gt_input_map_parser.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_input_fasta_parser.c -o ../build/gt_input_fasta_parser.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_input_generic_parser.c -o ../build/gt_input_generic_parser.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_input_map_utils.c -o ../build/gt_input_map_utils.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_pipe_io.c -o ../build/gt_pipe_io.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_input_sam_parser.c -o ../build/gt_input_sam_parser.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_sam_attributes.c -o ../build/gt_sam_attributes.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_buffered_output_file.c -o ../build/gt_buffered_output_file.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_output_file.c -o ../build/gt_output_file.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_generic_printer.c -o ../build/gt_generic_printer.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_output_buffer.c -o ../build/gt_output_buffer.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_output_printer.c -o ../build/gt_output_printer.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_output_map.c -o ../build/gt_output_map.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_output_fasta.c -o ../build/gt_output_fasta.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_output_sam.c -o ../build/gt_output_sam.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_output_generic_printer.c -o ../build/gt_output_generic_printer.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_stats.c -o ../build/gt_stats.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_gemIdx_loader.c -o ../build/gt_gemIdx_loader.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_gtf.c -o ../build/gt_gtf.o + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -D__LINUX__ -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../resources/include -I$PREFIX/include -c gt_json.c -o ../build/gt_json.o + ar -rcs ../lib/libgemtools.a ../build/*.o + make[2]: Leaving directory '$SRC_DIR/GEMTools/src' + make[1]: Leaving directory '$SRC_DIR/GEMTools' + make --directory=src + make[1]: Entering directory '$SRC_DIR/src' + mkdir -p ../bin + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../GEMTools/include -I../GEMTools/resources/include -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o bs_call.o bs_call.c + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../GEMTools/include -I../GEMTools/resources/include -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o genotype_model.o genotype_model.c + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -DNDEBUG -DGT_NO_CONSISTENCY_CHECKS -O3 -I../include -I../GEMTools/include -I../GEMTools/resources/include -I$PREFIX/include -o ../bin/bs_call bs_call.o genotype_model.o -L../GEMTools/lib -lgemtools -lgsl -lgslcblas -lm -L$PREFIX/lib -lpthread -lz -lbz2 + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -O3 -I../include -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o dbSNP_idx.o dbSNP_idx.c + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -O3 -I../include -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o dbSNP_compress.o dbSNP_compress.c + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -O3 -I../include -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o dbSNP_utils.o dbSNP_utils.c + x86_64-apple-darwin13.4.0-clang -fPIC -Wall -DHAVE_ZLIB -DHAVE_BZLIB -O3 -I../include -I$PREFIX/include -o ../bin/dbSNP_idx dbSNP_idx.o dbSNP_compress.o dbSNP_utils.o -L$PREFIX/lib -lm + make[1]: Leaving directory '$SRC_DIR/src' + + Resource usage statistics from building bs_call: + Process count: 6 + CPU time: Sys=0:00:00.3, User=0:00:01.4 + Memory: 71.2M + Disk usage: 9.8K + Time elapsed: 0:00:25.3 + + + Packaging bs_call + Packaging bs_call-2.02-h74acf98_9 + error: /opt/mambaforge/envs/bioconda/conda-bld/bs_call_1733989152218/_build_env/bin/x86_64-apple-darwin13.4.0-install_name_tool: changing install names or rpaths can't be redone for: /opt/mambaforge/envs/bioconda/conda-bld/bs_call_1733989152218/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/bin/dbSNP_idx (for architecture x86_64) because larger updated load commands do not fit (the program must be relinked, and you may need to use -headerpad or -headerpad_max_install_names) + + number of files: 2 + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2765, in build + newly_built_packages = bundlers[pkg_type]( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1874, in bundle_conda + files = post_process_files(metadata, initial_files) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1653, in post_process_files + post_build(m, new_files, build_python=python) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1759, in post_build + post_process_shared_lib(m, f, prefix_files, host_prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1635, in post_process_shared_lib + mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 498, in mk_relative_osx + macho.add_rpath(path, rpath_new, build_prefix=prefix, verbose=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 297, in add_rpath + raise RuntimeError("install_name_tool failed with exit status %d" % code) + RuntimeError: install_name_tool failed with exit status 1 +# Last 100 lines of the build log. diff --git a/recipes/bs_call/meta.yaml b/recipes/bs_call/meta.yaml index eeb4b12b323a8..529ef2c2267b4 100644 --- a/recipes/bs_call/meta.yaml +++ b/recipes/bs_call/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 8 + number: 9 requirements: build: diff --git a/recipes/bsmap/build_failure.linux-64.yaml b/recipes/bsmap/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..b901d46aa36dd --- /dev/null +++ b/recipes/bsmap/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: ac315c56b5195494365d0b3d519a486b13414db0d8f69b993c9707f891766c12 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("zlib=1.2"), MatchSpec("python==2.7.12=0")} + Encountered problems while solving: + - package python-2.7.12-0 requires zlib 1.2.*, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mlibzlib >=1.3.1,<2.0a0 [0m is installable with the potential options + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_0[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [31mpython 2.7.* [0m is not installable because there are no viable options + [31mpython [2.7.12|2.7.13][0m would require + [31mzlib 1.2.* [0m, which conflicts with any installable versions previously reported; + [31mpython 2.7.14[0m would require + [31mzlib 1.2.8 [0m, which conflicts with any installable versions previously reported; + [31mpython [2.7.14|2.7.15][0m would require + [31mzlib [1.2.11 |1.2.11.* ][0m, which conflicts with any installable versions previously reported; + [31mpython 2.7.15[0m would require + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("zlib=1.2"), MatchSpec("python==2.7.12=0")} + Encountered problems while solving: + - package python-2.7.12-0 requires zlib 1.2.*, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mlibzlib >=1.3.1,<2.0a0 [0m is installable with the potential options + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_0[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [31mpython 2.7.* [0m is not installable because there are no viable options + [31mpython [2.7.12|2.7.13][0m would require + [31mzlib 1.2.* [0m, which conflicts with any installable versions previously reported; + [31mpython 2.7.14[0m would require + [31mzlib 1.2.8 [0m, which conflicts with any installable versions previously reported; + [31mpython [2.7.14|2.7.15][0m would require + [31mzlib [1.2.11 |1.2.11.* ][0m, which conflicts with any installable versions previously reported; + [31mpython 2.7.15[0m would require + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/bsmap/meta.yaml b/recipes/bsmap/meta.yaml index 2ca3e7b1ea0b4..060364a02ab19 100644 --- a/recipes/bsmap/meta.yaml +++ b/recipes/bsmap/meta.yaml @@ -18,7 +18,7 @@ source: build: skip: True # [osx] - number: 5 + number: 6 requirements: build: diff --git a/recipes/btllib/meta.yaml b/recipes/btllib/meta.yaml index c106b65e155e0..72fbc68e1cb80 100644 --- a/recipes/btllib/meta.yaml +++ b/recipes/btllib/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 31e7124e1cda9eea6f27b654258a7f8d3dea83c828f0b2e8e847faf1c5296aa3 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('btllib', max_pin="x") }} diff --git a/recipes/btrim/meta.yaml b/recipes/btrim/meta.yaml index 55ba3cdf891a4..b60000e0bfab7 100644 --- a/recipes/btrim/meta.yaml +++ b/recipes/btrim/meta.yaml @@ -12,7 +12,7 @@ source: - 0001-fix-push_back-initializer_list-and-abs-from-uint.patch build: - number: 6 + number: 7 skip: true # [osx] requirements: diff --git a/recipes/bustools/meta.yaml b/recipes/bustools/meta.yaml index 7e114c40dd6d9..208b36ea8476c 100644 --- a/recipes/bustools/meta.yaml +++ b/recipes/bustools/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 829d7ca129b4c4911cae35bc2b87cac5d3a7845387b9a6487765aec84108d732 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('bustools', max_pin="x.x") }} diff --git a/recipes/bwa-aln-interactive/meta.yaml b/recipes/bwa-aln-interactive/meta.yaml index 14d6175ede952..375b299c6b288 100644 --- a/recipes/bwa-aln-interactive/meta.yaml +++ b/recipes/bwa-aln-interactive/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage("bwa-aln-interactive", max_pin="x.x") }} diff --git a/recipes/bwa-meme/build_failure.linux-64.yaml b/recipes/bwa-meme/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..4606103817c87 --- /dev/null +++ b/recipes/bwa-meme/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a4138472bb3ac3a509f98d73a55851e2f8f7512d60fa05872d3a579decd87550 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/memset_s.o safeclib/memset_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strisalphanumeric_s.o safeclib/strisalphanumeric_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wcpcpy_s.o safeclib/wcpcpy_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/memzero16_s.o safeclib/memzero16_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strisascii_s.o safeclib/strisascii_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wcscat_s.o safeclib/wcscat_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/memzero32_s.o safeclib/memzero32_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strisdigit_s.o safeclib/strisdigit_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wcscpy_s.o safeclib/wcscpy_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + src/bwtindex.cpp: In function 'void bwt_bwtupdate_core(bwt_t*)': + src/bwtindex.cpp:185:95: warning: ISO C forbids converting a string constant to 'char*' [-Wwrite-strings] + 185 | memcpy_bwamem(buf k, sizeof(bwtint_t) * 4, c, sizeof(bwtint_t) * 4, __FILE__, __LINE__); + | ^~~~~~~~ + src/bwtindex.cpp:192:79: warning: ISO C forbids converting a string constant to 'char*' [-Wwrite-strings] + 192 | memcpy_bwamem(buf k, sizeof(bwtint_t) * 4, c, sizeof(bwtint_t) * 4, __FILE__, __LINE__); + | ^~~~~~~~ + src/bwtindex.cpp: In function 'int bwa_index(int, char**)': + src/bwtindex.cpp:276:32: warning: invalid conversion from 'void*' to 'char*' [-fpermissive] + 276 | prefix = malloc(strnlen_s(argv[optind], PATH_MAX) 4); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | + | void* + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/memzero_s.o safeclib/memzero_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + src/bwtindex.cpp: In function 'int bwa_idx_build_Learned_index(const char*, const char*, int)': + src/bwtindex.cpp:371:31: warning: invalid conversion from 'const char*' to 'char*' [-fpermissive] + 371 | buildSAandLEP(prefix, num_threads); + | ^~~~~~ + | | + | const char* + In file included from src/bwtindex.cpp:43: + src/Learnedindex.h:35:27: note: initializing argument 1 of 'void buildSAandLEP(char*, int)' + 35 | void buildSAandLEP( char* prefix, int num_threads); + | ~~~~~~^~~~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strishex_s.o safeclib/strishex_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wcsncat_s.o safeclib/wcsncat_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strislowercase_s.o safeclib/strislowercase_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wcsncpy_s.o safeclib/wcsncpy_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/safe_mem_constraint.o safeclib/safe_mem_constraint.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strismixedcase_s.o safeclib/strismixedcase_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wcsnlen_s.o safeclib/wcsnlen_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strispassword_s.o safeclib/strispassword_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wmemcmp_s.o safeclib/wmemcmp_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/safe_str_constraint.o safeclib/safe_str_constraint.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strisuppercase_s.o safeclib/strisuppercase_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wmemcpy_s.o safeclib/wmemcpy_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strlastchar_s.o safeclib/strlastchar_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wmemmove_s.o safeclib/wmemmove_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/snprintf_support.o safeclib/snprintf_support.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + ar rcs libbwa.a src/fastmap.o src/main.o src/utils.o src/memcpy_bwamem.o src/kthread.o src/kstring.o src/ksw.o src/bwt.o src/ertindex.o src/Learnedindex.o src/bntseq.o src/bwamem.o src/ertseeding.o src/LearnedIndex_seeding.o src/profiling.o src/bandedSWA.o src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o src/bwamem_extra.o src/bwtbuild.o src/QSufSort.o src/bwt_gen.o src/rope.o src/rle.o src/is.o src/kopen.o src/bwtindex.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security + ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o + make[2]: Leaving directory '$SRC_DIR/ext/safestringlib' + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bwa-meme-1.0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -O3 -fpermissive -fopenmp -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -fopenmp -msse -msse2 -msse3 -mssse3 -msse4.1 src/main.o libbwa.a -DMODE=1 -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -Imimalloc/include -Wl,-whole-archive build/mimalloc/libmimalloc.a -Wl,-no-whole-archive -lrt -o bwa-meme_mode1.sse41 + /opt/conda/conda-bld/bwa-meme_1734150155172/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lz: No such file or directory + collect2: error: ld returned 1 exit status + make[1]: *** [Makefile:162: bwa-meme_mode1.sse41] Error 1 + make[1]: Leaving directory '$SRC_DIR' + make: *** [Makefile:123: multi] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bwa-meme_1734150155172/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bwa-meme_1734150155172/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/bwa-meme/meta.yaml b/recipes/bwa-meme/meta.yaml index 2fea8fddc46ac..7971bc49adbdc 100644 --- a/recipes/bwa-meme/meta.yaml +++ b/recipes/bwa-meme/meta.yaml @@ -10,7 +10,7 @@ source: build: - number: 2 + number: 3 # Compilation fails on OSX: # ext/safestringlib/include/safe_mem_lib.h:100:16: error: conflicting types for 'memset_s' # extern errno_t memset_s(void *dest, rsize_t dmax, uint8_t value); diff --git a/recipes/bwa/0.7.3a/meta.yaml b/recipes/bwa/0.7.3a/meta.yaml index 46556d99027a1..3d799f8d05233 100644 --- a/recipes/bwa/0.7.3a/meta.yaml +++ b/recipes/bwa/0.7.3a/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 9 + number: 10 source: url: http://downloads.sourceforge.net/project/bio-bwa/bwa-{{ version }}.tar.bz2 diff --git a/recipes/bwa/0.7.4/meta.yaml b/recipes/bwa/0.7.4/meta.yaml index f4ab9efd0f9b1..9ea4587a0072e 100644 --- a/recipes/bwa/0.7.4/meta.yaml +++ b/recipes/bwa/0.7.4/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 7 + number: 8 source: url: http://downloads.sourceforge.net/project/bio-bwa/bwa-{{ version }}.tar.bz2 diff --git a/recipes/bwa/0.7.8/meta.yaml b/recipes/bwa/0.7.8/meta.yaml index 54bb549c0c0a0..3d4eae25a5ed8 100644 --- a/recipes/bwa/0.7.8/meta.yaml +++ b/recipes/bwa/0.7.8/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 9 + number: 10 source: url: http://downloads.sourceforge.net/project/bio-bwa/bwa-{{ version }}.tar.bz2 diff --git a/recipes/bwa/meta.yaml b/recipes/bwa/meta.yaml index 2262ce914671c..62ea27d805e5f 100644 --- a/recipes/bwa/meta.yaml +++ b/recipes/bwa/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage("bwa", max_pin="x.x") }} diff --git a/recipes/bwapy/meta.yaml b/recipes/bwapy/meta.yaml index 6349f877323dd..a37413e5cdd89 100644 --- a/recipes/bwapy/meta.yaml +++ b/recipes/bwapy/meta.yaml @@ -10,7 +10,7 @@ source: folder: bwa build: - number: 8 + number: 9 # imp was removed from python 3.12 skip: true # [py == 312 ] run_exports: diff --git a/recipes/bwise/build_failure.linux-64.yaml b/recipes/bwise/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..dcddb5cda9e22 --- /dev/null +++ b/recipes/bwise/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: b9be3a2f89caca0667b53e206a49a235e084c344d38624db09f5c2905a77a7af # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bwise-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bwise-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bwise-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bwise-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -o n50.o -c N50.cpp -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bwise-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -L$PREFIX/lib -lz + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -o n50 n50.o -L$PREFIX/lib -flto -fopenmp -lz + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -o sequencesToNumbers.o -c sequencesToNumbers.cpp -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bwise-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -L$PREFIX/lib -lz + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -o sequencesToNumbers sequencesToNumbers.o -L$PREFIX/lib -flto -fopenmp -lz + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -o numbersToSequences.o -c numbersToSequences.cpp -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bwise-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -L$PREFIX/lib -lz + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -o numbersToSequences numbersToSequences.o -L$PREFIX/lib -flto -fopenmp -lz + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -o numbersFilter.o -c numbersFilter.cpp -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bwise-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -L$PREFIX/lib -lz + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -o numbersFilter numbersFilter.o -L$PREFIX/lib -flto -fopenmp -lz + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -o simulator.o -c simulator.cpp -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bwise-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -L$PREFIX/lib -lz + simulator.cpp:14:1: error: 'uint32_t' does not name a type + 14 | uint32_t xs(uint32_t& y){ + | ^~~~~~~~ + simulator.cpp:5:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + 4 | #include + |#include + 5 | + simulator.cpp: In function 'char randNucle(char)': + simulator.cpp:22:17: error: 'xs' was not declared in this scope + 22 | switch (xs(seed)%4){ + | ^~ + simulator.cpp: In function 'int main(int, char**)': + simulator.cpp:72:25: error: 'uint64_t' was not declared in this scope + 72 | uint64_t nucProduced(0); + | ^~~~~~~~ + simulator.cpp:72:25: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + simulator.cpp:73:31: error: 'nucProduced' was not declared in this scope + 73 | while(nucProduced<(uint64_t)(coverage*ref.size())){ + | ^~~~~~~~~~~ + simulator.cpp:78:41: error: expected ';' before 'position' + 78 | uint64_t position=xs(seed)%ref.size(); + | ^~~~~~~~~ + | ; + simulator.cpp:80:36: error: 'position' was not declared in this scope + 80 | if(positionlength<=ref.size()){ + | ^~~~~~~~ + simulator.cpp:87:52: error: 'xs' was not declared in this scope + 87 | if(xs(seed)%errorRate==0){ + | ^~ + make: *** [makefile:27: simulator.o] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bwise_1734236554617/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bwise_1734236554617/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/bwise/meta.yaml b/recipes/bwise/meta.yaml index 6f421237f6f61..9102b2bef8d91 100644 --- a/recipes/bwise/meta.yaml +++ b/recipes/bwise/meta.yaml @@ -10,7 +10,7 @@ source: sha256: daca421f91e9b3a4c272b46665df2e681d0068bb53fde86f41f04a2637f4f91d build: - number: 3 + number: 4 skip: true # [osx] requirements: diff --git a/recipes/bwread/build_failure.osx-64.yaml b/recipes/bwread/build_failure.osx-64.yaml deleted file mode 100644 index f798559bff6dc..0000000000000 --- a/recipes/bwread/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: d4a1a31409c2e433d027814944f03df2f929f892fd27f10073f7abfed231289e # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - sorted_nearest [>=0.0.28 |>=0.0.30 ] with the potential options - sorted_nearest [0.0.28|0.0.29|0.0.30|0.0.31] would require - python >=2.7,<2.8.0a0 , which can be installed; - sorted_nearest [0.0.28|0.0.29|0.0.30|0.0.31] would require - python >=3.6,<3.7.0a0 , which can be installed; - sorted_nearest [0.0.28|0.0.29|0.0.30|0.0.31] would require - python >=3.7,<3.8.0a0 , which can be installed; - sorted_nearest [0.0.31|0.0.32|0.0.33|0.0.37] would require - python_abi 2.7.* *_cp27m, which can be installed; - sorted_nearest [0.0.31|0.0.32|0.0.33|0.0.37] would require - python_abi 3.6.* *_cp36m, which can be installed; - sorted_nearest [0.0.31|0.0.32|0.0.33|0.0.37] would require - python_abi 3.7.* *_cp37m, which can be installed; - sorted_nearest [0.0.31|0.0.32|0.0.33|0.0.37|0.0.39] would require - python_abi 3.8.* *_cp38, which can be installed; - sorted_nearest [0.0.32|0.0.33|0.0.37|0.0.39] would require - python_abi 3.9.* *_cp39, which can be installed; - sorted_nearest [0.0.37|0.0.39] would require - python_abi 3.10.* *_cp310, which can be installed; - pyranges [0.0.125|0.0.127|0.0.128|0.0.129] would require - sorted_nearest >=0.0.33 , which can be installed (as previously explained); - python_abi 3.12.* *_cp312 is not installable because it requires - python 3.12.* *_cpython, which conflicts with any installable versions previously reported. - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2409, in build - create_build_envs(top_level_pkg, notest) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2247, in create_build_envs - raise e - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2220, in create_build_envs - environ.get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions - precs = _install_actions(prefix, index, specs)["LINK"] - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions - txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction - unlink_precs, link_precs = self.solve_for_diff( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff - final_precs = self.solve_final_state( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state - out_state = self._solving_loop(in_state, out_state, index) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop - solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt - new_conflicts = self._maybe_raise_for_problems( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems - self._maybe_raise_for_conda_build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build - raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("sorted_nearest[version='>=0.0.28']"), MatchSpec("pyranges==0.0.53=py_0")} - Encountered problems while solving: - - package pyranges-0.0.53-py_0 requires sorted_nearest >=0.0.28, but none of the providers can be installed - - Could not solve for environment specs - The following packages are incompatible - pyranges is installable with the potential options - pyranges [0.0.39|0.0.40|...|0.0.52] would require - python >=3.7,<3.8.0a0 , which can be installed; - pyranges [0.0.51|0.0.52] would require - python >=3.6,<3.7.0a0 , which can be installed; - pyranges [0.0.100|0.0.101|...|0.0.99] would require - sorted_nearest [>=0.0.28 |>=0.0.30 ] with the potential options - sorted_nearest [0.0.28|0.0.29|0.0.30|0.0.31] would require - python >=2.7,<2.8.0a0 , which can be installed; - sorted_nearest [0.0.28|0.0.29|0.0.30|0.0.31] would require - python >=3.6,<3.7.0a0 , which can be installed; - sorted_nearest [0.0.28|0.0.29|0.0.30|0.0.31] would require - python >=3.7,<3.8.0a0 , which can be installed; - sorted_nearest [0.0.31|0.0.32|0.0.33|0.0.37] would require - python_abi 2.7.* *_cp27m, which can be installed; - sorted_nearest [0.0.31|0.0.32|0.0.33|0.0.37] would require - python_abi 3.6.* *_cp36m, which can be installed; - sorted_nearest [0.0.31|0.0.32|0.0.33|0.0.37] would require - python_abi 3.7.* *_cp37m, which can be installed; - sorted_nearest [0.0.31|0.0.32|0.0.33|0.0.37|0.0.39] would require - python_abi 3.8.* *_cp38, which can be installed; - sorted_nearest [0.0.32|0.0.33|0.0.37|0.0.39] would require - python_abi 3.9.* *_cp39, which can be installed; - sorted_nearest [0.0.37|0.0.39] would require - python_abi 3.10.* *_cp310, which can be installed; - pyranges [0.0.125|0.0.127|0.0.128|0.0.129] would require - sorted_nearest >=0.0.33 , which can be installed (as previously explained); - python_abi 3.12.* *_cp312 is not installable because it requires - python 3.12.* *_cpython, which conflicts with any installable versions previously reported. -# Last 100 lines of the build log. diff --git a/recipes/bwread/meta.yaml b/recipes/bwread/meta.yaml index ad36e15aa5884..566627bc93bf9 100644 --- a/recipes/bwread/meta.yaml +++ b/recipes/bwread/meta.yaml @@ -10,7 +10,7 @@ source: sha256: a6f524baf85a8c10c0de8e1d5874467816a32dccaa7b9f2b571c99ed6c449b16 build: - number: 2 + number: 3 skip: True # [py27] script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" diff --git a/recipes/bx-python/meta.yaml b/recipes/bx-python/meta.yaml index 187536a7dee88..05169815fee75 100644 --- a/recipes/bx-python/meta.yaml +++ b/recipes/bx-python/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 script: - {{ PYTHON }} setup.py build_ext --force # [py<39] - {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv diff --git a/recipes/bxtools/meta.yaml b/recipes/bxtools/meta.yaml index 7320b3ef9c2d7..8b30df9b27aca 100644 --- a/recipes/bxtools/meta.yaml +++ b/recipes/bxtools/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 5 + number: 6 source: - url: https://github.com/walaj/bxtools/archive/{{ version }}.tar.gz diff --git a/recipes/cafe/4.2.1/meta.yaml b/recipes/cafe/4.2.1/meta.yaml index 3a28753b593e4..69b5b13044517 100644 --- a/recipes/cafe/4.2.1/meta.yaml +++ b/recipes/cafe/4.2.1/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 skip: True # [osx] requirements: diff --git a/recipes/cafe/meta.yaml b/recipes/cafe/meta.yaml index 09aead5b1a062..b92f721ab5951 100644 --- a/recipes/cafe/meta.yaml +++ b/recipes/cafe/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('cafe', max_pin="x.x") }} diff --git a/recipes/cage/meta.yaml b/recipes/cage/meta.yaml index c5ec5e4c7cce3..8cf2107e6e445 100644 --- a/recipes/cage/meta.yaml +++ b/recipes/cage/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 135abb4c769f8668e56e1f7c82bf98c68eccc3b387cd3b99baf18d851bd93d96 build: - number: 7 + number: 8 skip: True # [osx] requirements: diff --git a/recipes/cagee/build_failure.linux-64.yaml b/recipes/cagee/build_failure.linux-64.yaml deleted file mode 100644 index c5bf0c7244cda..0000000000000 --- a/recipes/cagee/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 63c9f58ae1d69e1262c2050a7d41496015d116ea463d5a35bc6e705de11441ba # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - export LDFLAGS=-L/opt/conda/conda-bld/cagee_1685350677756/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib - LDFLAGS=-L/opt/conda/conda-bld/cagee_1685350677756/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib - export MKL_THREADING_LAYER=GNU - MKL_THREADING_LAYER=GNU - export CFLAGS=-I/opt/conda/conda-bld/cagee_1685350677756/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include - CFLAGS=-I/opt/conda/conda-bld/cagee_1685350677756/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include - export CPATH=/opt/conda/conda-bld/cagee_1685350677756/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include - CPATH=/opt/conda/conda-bld/cagee_1685350677756/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include - mkdir -p build - cd build - cmake -DCMAKE_PREFIX_PATH:PATH=/opt/conda/conda-bld/cagee_1685350677756/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho -DCMAKE_INSTALL_PREFIX:PATH=/opt/conda/conda-bld/cagee_1685350677756/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho -DCMAKE_BUILD_TYPE=Release .. - -- The C compiler identification is GNU 12.2.0 - -- The CXX compiler identification is GNU 12.2.0 - -- Detecting C compiler ABI info - -- Detecting C compiler ABI info - done - -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - skipped - -- Detecting C compile features - -- Detecting C compile features - done - -- Detecting CXX compiler ABI info - -- Detecting CXX compiler ABI info - done - -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - skipped - -- Detecting CXX compile features - -- Detecting CXX compile features - done - -- Looking for getopt.h - -- Looking for getopt.h - found - -- Found Boost: $PREFIX/lib/cmake/Boost-1.78.0/BoostConfig.cmake (found version "1.78.0") found components: program_options - -- Found ZLIB: $PREFIX/lib/libz.so (found version "1.2.13") - -- Found OpenMP_C: -fopenmp (found version "4.5") - -- Found OpenMP_CXX: -fopenmp (found version "4.5") - -- Found OpenMP: TRUE (found version "4.5") - -- Configuring done (1.1s) - -- Generating done (0.0s) - -- Build files have been written to: $SRC_DIR/build - make - [ 3%] Building CXX object CMakeFiles/cagee.dir/main.cpp.o - [ 6%] Building CXX object CMakeFiles/cagee.dir/src/cagee.cpp.o - [ 9%] Building CXX object CMakeFiles/cagee.dir/src/DiffMat.cpp.o - [ 12%] Building CXX object CMakeFiles/cagee.dir/src/core.cpp.o - [ 15%] Building CXX object CMakeFiles/cagee.dir/src/gamma_core.cpp.o - /opt/conda/conda-bld/cagee_1685350677756/work/src/gamma_core.cpp: In member function 'std::vector gamma_model::get_posterior_probabilities(std::vector)': - /opt/conda/conda-bld/cagee_1685350677756/work/src/gamma_core.cpp:123:93: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = divides; _Tp = double]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 123 | transform(numerators.begin(), numerators.end(), posterior_probabilities.begin(), bind2nd(divides(), denominator)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - In file included from /opt/conda/conda-bld/cagee_1685350677756/_build_env/x86_64-conda-linux-gnu/include/c/12.2.0/bits/stl_function.h:1438, - from /opt/conda/conda-bld/cagee_1685350677756/_build_env/x86_64-conda-linux-gnu/include/c/12.2.0/string:48, - from /opt/conda/conda-bld/cagee_1685350677756/_build_env/x86_64-conda-linux-gnu/include/c/12.2.0/bits/locale_classes.h:40, - from /opt/conda/conda-bld/cagee_1685350677756/_build_env/x86_64-conda-linux-gnu/include/c/12.2.0/bits/ios_base.h:41, - from /opt/conda/conda-bld/cagee_1685350677756/_build_env/x86_64-conda-linux-gnu/include/c/12.2.0/iomanip:40, - from /opt/conda/conda-bld/cagee_1685350677756/work/src/gamma_core.cpp:3: - /opt/conda/conda-bld/cagee_1685350677756/_build_env/x86_64-conda-linux-gnu/include/c/12.2.0/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ - [ 18%] Building CXX object CMakeFiles/cagee.dir/src/sigma.cpp.o - /opt/conda/conda-bld/cagee_1685350677756/work/src/sigma.cpp: In function 'void DOCTEST_ANON_FUNC_0()': - /opt/conda/conda-bld/cagee_1685350677756/work/src/sigma.cpp:62:5: error: 'unique_ptr' was not declared in this scope - 62 | unique_ptr p_tree(parse_newick("(A:1,B:3):7")); - | ^~~~~~~~~~ - /opt/conda/conda-bld/cagee_1685350677756/work/src/sigma.cpp:11:1: note: 'std::unique_ptr' is defined in header ''; did you forget to '#include '? - 10 | #include "gene_transcript.h" - |#include - 11 | - /opt/conda/conda-bld/cagee_1685350677756/work/src/sigma.cpp:62:21: error: expected primary-expression before '>' token - 62 | unique_ptr p_tree(parse_newick("(A:1,B:3):7")); - | ^ - /opt/conda/conda-bld/cagee_1685350677756/work/src/sigma.cpp:62:23: error: there are no arguments to 'p_tree' that depend on a template parameter, so a declaration of 'p_tree' must be available [-fpermissive] - 62 | unique_ptr p_tree(parse_newick("(A:1,B:3):7")); - | ^~~~~~ - /opt/conda/conda-bld/cagee_1685350677756/work/src/sigma.cpp:62:23: note: (if you use '-fpermissive', G will accept your code, but allowing the use of an undeclared name is deprecated) - /opt/conda/conda-bld/cagee_1685350677756/work/src/sigma.cpp: In function 'void DOCTEST_ANON_FUNC_1()': - /opt/conda/conda-bld/cagee_1685350677756/work/src/sigma.cpp:79:5: error: 'unique_ptr' was not declared in this scope - 79 | unique_ptr p_tree(parse_newick("(A:1,B:3):7")); - | ^~~~~~~~~~ - /opt/conda/conda-bld/cagee_1685350677756/work/src/sigma.cpp:79:5: note: 'std::unique_ptr' is defined in header ''; did you forget to '#include '? - /opt/conda/conda-bld/cagee_1685350677756/work/src/sigma.cpp:79:21: error: expected primary-expression before '>' token - 79 | unique_ptr p_tree(parse_newick("(A:1,B:3):7")); - | ^ - /opt/conda/conda-bld/cagee_1685350677756/work/src/sigma.cpp:79:23: error: there are no arguments to 'p_tree' that depend on a template parameter, so a declaration of 'p_tree' must be available [-fpermissive] - 79 | unique_ptr p_tree(parse_newick("(A:1,B:3):7")); - | ^~~~~~ - make[2]: *** [CMakeFiles/cagee.dir/build.make:146: CMakeFiles/cagee.dir/src/sigma.cpp.o] Error 1 - make[1]: *** [CMakeFiles/Makefile2:103: CMakeFiles/cagee.dir/all] Error 2 - make: *** [Makefile:156: all] Error 2 - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cagee_1685350677756/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/cagee/meta.yaml b/recipes/cagee/meta.yaml index cdc593579ee6c..10126cf484213 100755 --- a/recipes/cagee/meta.yaml +++ b/recipes/cagee/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('cagee', max_pin="x") }} diff --git a/recipes/calib/build_failure.linux-64.yaml b/recipes/calib/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0ad76426465c8 --- /dev/null +++ b/recipes/calib/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 62889312e2c7e6e313b9866f45f76dffba0b1f30bade5c3e5a379cd28124bbf1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + clustering/cluster.cc:327:26: error: expected ';' before 'current_node' + 327 | node_id_t current_node = opened.top(); + | ^~~~~~~~~~~~~ + | ; + clustering/cluster.cc:328:24: error: request for member 'pop' in 'opened', which is of non-class type 'int' + 328 | opened.pop(); + | ^~~ + clustering/cluster.cc:329:40: error: 'current_node' was not declared in this scope + 329 | node_to_cluster_vector[current_node] = cluster_count; + | ^~~~~~~~~~~~ + clustering/cluster.cc:330:31: error: expected ';' before 'neighbor' + 330 | for (node_id_t neighbor: (*graph_ptr)[current_node]) { + | ^~~~~~~~~ + | ; + clustering/cluster.cc:337:13: error: expected primary-expression before '}' token + 337 | } + | ^ + clustering/cluster.cc:336:18: error: expected ';' before '}' token + 336 | } + | ^ + | ; + 337 | } + | ~ + clustering/cluster.cc:337:13: error: expected primary-expression before '}' token + 337 | } + | ^ + clustering/cluster.cc:336:18: error: expected ')' before '}' token + 336 | } + | ^ + | ) + 337 | } + | ~ + clustering/cluster.cc:330:21: note: to match this '(' + 330 | for (node_id_t neighbor: (*graph_ptr)[current_node]) { + | ^ + clustering/cluster.cc:337:13: error: expected primary-expression before '}' token + 337 | } + | ^ + clustering/cluster.cc: In function 'void output_clusters()': + clustering/cluster.cc:361:9: error: 'read_id_t' was not declared in this scope + 361 | read_id_t current_read = 0; + | ^~~~~~~~~ + clustering/cluster.cc:412:13: error: 'node_id_t' was not declared in this scope + 412 | node_id_t current_read_node = read_to_node_vector[current_read]; + | ^~~~~~~~~ + clustering/cluster.cc:413:48: error: 'current_read_node' was not declared in this scope + 413 | clusters << node_to_cluster_vector[current_read_node] << "\t" << current_read_node << "\t" << current_read << "\t"; + | ^~~~~~~~~~~~~~~~~ + clustering/cluster.cc:413:107: error: 'current_read' was not declared in this scope + 413 | clusters << node_to_cluster_vector[current_read_node] << "\t" << current_read_node << "\t" << current_read << "\t"; + | ^~~~~~~~~~~~ + clustering/cluster.cc:420:9: error: 'read_id_t' was not declared in this scope + 420 | read_id_t current_read = 0; + | ^~~~~~~~~ + clustering/cluster.cc:425:33: error: 'cluster_count' was not declared in this scope + 425 | cout << "There are " << cluster_count << " clusters\n"; + | ^~~~~~~~~~~~~ + clustering/cluster.cc:426:53: error: 'read_count' was not declared in this scope; did you mean 'thread_count'? + 426 | temp_out_count = (unsigned long) ceil(float(read_count)/float(min_records_per_tmp_file)); + | ^~~~~~~~~~ + | thread_count + clustering/cluster.cc:471:13: error: 'node_id_t' was not declared in this scope + 471 | node_id_t current_read_node = read_to_node_vector[current_read]; + | ^~~~~~~~~ + clustering/cluster.cc:472:65: error: 'current_read_node' was not declared in this scope + 472 | size_t current_temp_out_id = node_to_cluster_vector[current_read_node] % temp_out_count; + | ^~~~~~~~~~~~~~~~~ + clustering/cluster.cc:473:134: error: 'current_read' was not declared in this scope + 473 | temp_out_files[current_temp_out_id] << node_to_cluster_vector[current_read_node] << "\t" << current_read_node << "\t" << current_read << "\t"; + | ^~~~~~~~~~~~ + clustering/cluster.cc:478:37: error: request for member 'swap' in '0', which is of non-class type 'read_id_to_node_id_vector' {aka 'int'} + 478 | read_id_to_node_id_vector().swap(read_to_node_vector); + | ^~~~ + clustering/cluster.cc:479:40: error: request for member 'swap' in '0', which is of non-class type 'node_id_to_cluster_id_vector' {aka 'int'} + 479 | node_id_to_cluster_id_vector().swap(node_to_cluster_vector); + | ^~~~ + make: *** [Makefile:127: clustering/cluster.o] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/calib_1733978571591/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/calib_1733978571591/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/calib/build_failure.osx-64.yaml b/recipes/calib/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..1feb0a185219d --- /dev/null +++ b/recipes/calib/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 62889312e2c7e6e313b9866f45f76dffba0b1f30bade5c3e5a379cd28124bbf1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - liblzma 5.6.3 hd471939_1 + - libedit 3.1.20191231 h0678c8f_2 + - make 4.4.1 h00291cd_2 + - libiconv 1.17 hd75f5a5_2 + - xz-tools 5.6.3 hd471939_1 + - libcurl 8.8.0 hf9fcc65_1 + - libclang-cpp18.1 18.1.7 default_h4c8afb6_0 + - ld64_osx-64 711 had5d0d3_0 + - libev 4.33 h10d778d_2 + - ca-certificates 2024.8.30 h8857fd0_0 + - compiler-rt 18.1.7 h734a56e_0 + - zstd 1.5.6 h915ae27_0 + - llvm-tools 18.1.7 hd5e122f_0 + - c-ares 1.34.3 hf13058a_1 + - compiler-rt_osx-64 18.1.7 h7312ed1_0 + - clangxx_impl_osx-64 18.1.7 h5c1d95e_16 + - rhash 1.4.3 h0dc2134_2 + - tapi 1100.0.11 h9ce4665_0 + - liblzma-devel 5.6.3 hd471939_1 + - libxml2 2.12.7 h3e169fe_1 + host: + - libcxx 19.1.5 hf95d169_0 + - libzlib 1.3.1 hd23fc13_2 + - zlib 1.3.1 hd23fc13_2 + run: + - libzlib >=1.3.1,<2.0a0 + - libcxx >=17 + - zlib + test: + commands: + - calib --help + - calib_cons --help + about: + home: https://github.com/vpc-ccg/calib + license: MIT + license_file: LICENSE + summary: Clustering without alignment using (locality sensitive hashing) LSH and + MinHashing of barcoded reads + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/calib_1733985558105/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/calib_1733985558105/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/calib_1733985558105/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/calib_1733985558105/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/calib-0.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/calib-0.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/calib-0.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/calib-0.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + Making clustering/cluster.o + -std=c11 -pthread -I clustering/ -lz -Wall -Wextra -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + + -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + x86_64-apple-darwin13.4.0-clang -std=c11 -pthread -I clustering/ -lz -Wall -Wextra -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -O2 -c clustering/cluster.cc -o clustering/cluster.o +# Last 100 lines of the build log. diff --git a/recipes/calib/meta.yaml b/recipes/calib/meta.yaml index ae73a65df8cca..86549b3b2cb46 100644 --- a/recipes/calib/meta.yaml +++ b/recipes/calib/meta.yaml @@ -20,7 +20,7 @@ source: folder: consensus/spoa_v1.1.3/vendor/googletest build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/callerpp/meta.yaml b/recipes/callerpp/meta.yaml index 2379233d1c0f6..9a3d8962db3a7 100644 --- a/recipes/callerpp/meta.yaml +++ b/recipes/callerpp/meta.yaml @@ -10,7 +10,7 @@ source: sha256: d2d3b233164fe28f056e4cfea0518122ec8aefddf6f30e7c84f6b1827154ae3e build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/cancerit-allelecount/build_failure.linux-64.yaml b/recipes/cancerit-allelecount/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..033d9ddbbb3ae --- /dev/null +++ b/recipes/cancerit-allelecount/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 8c0dab5e4962203d2853394f7b5ec1035407e562311568e70e45e89a87a969f8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cancerit-allelecount-4.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cancerit-allelecount-4.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + export LIBRARY_PATH=/opt/conda/conda-bld/cancerit-allelecount_1734294747219/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib + LIBRARY_PATH=/opt/conda/conda-bld/cancerit-allelecount_1734294747219/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib + export INCPATH=/opt/conda/conda-bld/cancerit-allelecount_1734294747219/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include + INCPATH=/opt/conda/conda-bld/cancerit-allelecount_1734294747219/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include + cd /opt/conda/conda-bld/cancerit-allelecount_1734294747219/work/c + mkdir bin + sed -i 's/CC = gcc /compiler = ${CC} /g' Makefile + sed -i 's/$(CC) /$(compiler) /g' Makefile + sed -i 's#HTSLOC?=$(HTSLIB)#HTSLOC=${PREFIX}/lib#g' Makefile + sed -i 's#prefix=?/usr/local#prefix=${PREFIX}#g' Makefile + make -j 4 'OPTINC=-I/opt/conda/conda-bld/cancerit-allelecount_1734294747219/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include -L/opt/conda/conda-bld/cancerit-allelecount_1734294747219/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib' + rm -f ./src/*.o *~ ./bin/alleleCounter ./bin/* ./tests/tests_log ./tests/bam_access_tests ./src/*.gcda ./src/*.gcov ./src/*.gcno *.gcda *.gcov *.gcno ./tests/*.gcda ./tests/*.gcov ./tests/*.gcno + mkdir -p ./bin + mkdir -p ./htslib_tmp + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + #Do some magic to ensure we compile ALLELECOUNT with the static libhts.a rather than libhts.so + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O3 -DALLELECOUNTER_VERSION='"4.3.0"' -g -Wall -I/usr/local//include -Isrc/ -I$PREFIX/include -L$PREFIX/lib -rdynamic -c src/bam_access.c -o src/bam_access.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -I/usr/local//include -Isrc/ -I$PREFIX/include -L$PREFIX/lib -rdynamic ./src/bam_access.o -L./htslib_tmp -lhts -lpthread -lz -lbz2 -llzma -lm -ldl -L/usr/local//lib -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib tests/bam_access_tests.c -o tests/bam_access_tests + ln -fs $PREFIX/lib/libhts.a ./htslib_tmp/libhts.a + remove tmp hts location + rm -rf ./htslib_tmp + tests/bam_access_tests.c: In function 'test_bam_access_get_position_base_counts': + tests/bam_access_tests.c:45:13: warning: variable 'res' set but not used [-Wunused-but-set-variable] + 45 | int res = bam_access_get_position_base_counts(chr,pos,stats,0,NULL); + | ^~~ + /opt/conda/conda-bld/cancerit-allelecount_1734294747219/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find ./src/bam_access.o: No such file or directory + collect2: error: ld returned 1 exit status + make: *** [: tests/bam_access_tests] Error 1 + make: *** Waiting for unfinished jobs.... + src/bam_access.c: In function 'pileupCounts': + src/bam_access.c:132:70: warning: 'pre_b' may be used uninitialized [-Wmaybe-uninitialized] + 132 | if(!(p->is_del) && qual >= min_base_qual && (absent || pre_b != c)){ + | ~~~~~~~~^~~~~~~~~~~~~~ + src/bam_access.c:124:25: note: 'pre_b' was declared here + 124 | uint8_t pre_b; + | ^~~~~ + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cancerit-allelecount_1734294747219/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cancerit-allelecount_1734294747219/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/cancerit-allelecount/build_failure.linux-aarch64.yaml b/recipes/cancerit-allelecount/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..56fce4e02cdb3 --- /dev/null +++ b/recipes/cancerit-allelecount/build_failure.linux-aarch64.yaml @@ -0,0 +1,107 @@ +recipe_sha: 8c0dab5e4962203d2853394f7b5ec1035407e562311568e70e45e89a87a969f8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + LD_GOLD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strip + INFO: activate-gcc_linux-aarch64.sh made the following environmental changes: + BUILD=aarch64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc + CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cancerit-allelecount-4.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=aarch64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=aarch64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cancerit-allelecount-4.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib + HOST=aarch64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_aarch64_conda_cos7_linux_gnu + build_alias=aarch64-conda-linux-gnu + host_alias=aarch64-conda-linux-gnu + -BUILD=aarch64-conda_cos7-linux-gnu + -CONDA_BUILD_SYSROOT= + export LIBRARY_PATH=/opt/conda/conda-bld/cancerit-allelecount_1736171446459/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib + LIBRARY_PATH=/opt/conda/conda-bld/cancerit-allelecount_1736171446459/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib + export INCPATH=/opt/conda/conda-bld/cancerit-allelecount_1736171446459/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include + INCPATH=/opt/conda/conda-bld/cancerit-allelecount_1736171446459/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include + cd /opt/conda/conda-bld/cancerit-allelecount_1736171446459/work/c + mkdir bin + sed -i 's/CC = gcc /compiler = ${CC} /g' Makefile + sed -i 's/$(CC) /$(compiler) /g' Makefile + sed -i 's#HTSLOC?=$(HTSLIB)#HTSLOC=${PREFIX}/lib#g' Makefile + sed -i 's#prefix=?/usr/local#prefix=${PREFIX}#g' Makefile + make -j 4 'OPTINC=-I/opt/conda/conda-bld/cancerit-allelecount_1736171446459/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include -L/opt/conda/conda-bld/cancerit-allelecount_1736171446459/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib' + rm -f ./src/*.o *~ ./bin/alleleCounter ./bin/* ./tests/tests_log ./tests/bam_access_tests ./src/*.gcda ./src/*.gcov ./src/*.gcno *.gcda *.gcov *.gcno ./tests/*.gcda ./tests/*.gcov ./tests/*.gcno + mkdir -p ./bin + mkdir -p ./htslib_tmp + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + #Do some magic to ensure we compile ALLELECOUNT with the static libhts.a rather than libhts.so + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O3 -DALLELECOUNTER_VERSION='"4.3.0"' -g -Wall -I/usr/local//include -Isrc/ -I$PREFIX/include -L$PREFIX/lib -rdynamic -c src/bam_access.c -o src/bam_access.o + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -g -Wall -I/usr/local//include -Isrc/ -I$PREFIX/include -L$PREFIX/lib -rdynamic ./src/bam_access.o -L./htslib_tmp -lhts -lpthread -lz -lbz2 -llzma -lm -ldl -L/usr/local//lib -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib tests/bam_access_tests.c -o tests/bam_access_tests + ln -fs $PREFIX/lib/libhts.a ./htslib_tmp/libhts.a + remove tmp hts location + rm -rf ./htslib_tmp + tests/bam_access_tests.c: In function 'test_bam_access_get_position_base_counts': + tests/bam_access_tests.c:45:13: warning: variable 'res' set but not used [-Wunused-but-set-variable] + 45 | int res = bam_access_get_position_base_counts(chr,pos,stats,0,NULL); + | ^~~ + /opt/conda/conda-bld/cancerit-allelecount_1736171446459/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: cannot find ./src/bam_access.o: No such file or directory + collect2: error: ld returned 1 exit status + make: *** [: tests/bam_access_tests] Error 1 + make: *** Waiting for unfinished jobs.... + src/bam_access.c: In function 'pileupCounts': + src/bam_access.c:132:70: warning: 'pre_b' may be used uninitialized [-Wmaybe-uninitialized] + 132 | if(!(p->is_del) && qual >= min_base_qual && (absent || pre_b != c)){ + | ~~~~~~~~^~~~~~~~~~~~~~ + src/bam_access.c:124:25: note: 'pre_b' was declared here + 124 | uint8_t pre_b; + | ^~~~~ + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cancerit-allelecount_1736171446459/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cancerit-allelecount_1736171446459/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error +reason: cannot find ./src/bam_access.o No such file or directory diff --git a/recipes/cancerit-allelecount/meta.yaml b/recipes/cancerit-allelecount/meta.yaml index b86b40f7fad2f..da80762f052b3 100644 --- a/recipes/cancerit-allelecount/meta.yaml +++ b/recipes/cancerit-allelecount/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 5363ae12c2385c962728336a4498b1a29c9eaa3d4a24492d0debf897771cfd3c build: - number: 7 + number: 8 skip: True # [osx] run_exports: - {{ pin_subpackage('cancerit-allelecount', max_pin='x') }} diff --git a/recipes/canopy/meta.yaml b/recipes/canopy/meta.yaml index 8906c6773dc28..b4b2edd902014 100644 --- a/recipes/canopy/meta.yaml +++ b/recipes/canopy/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 6ea391021dc81ff1981bb69b0ec27a56a17bd23e01c25a27b86808366d62061f build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/cansam/meta.yaml b/recipes/cansam/meta.yaml index ce3c66befc14a..7969a64280f38 100644 --- a/recipes/cansam/meta.yaml +++ b/recipes/cansam/meta.yaml @@ -7,7 +7,7 @@ source: md5: 46adf65a926a56fb90760e08fead3261 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('cansam', max_pin=None) }} diff --git a/recipes/carnac-lr/meta.yaml b/recipes/carnac-lr/meta.yaml index 88e73700e213f..676687341da62 100644 --- a/recipes/carnac-lr/meta.yaml +++ b/recipes/carnac-lr/meta.yaml @@ -14,7 +14,7 @@ source: - python_path.patch build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/carpedeam/build_failure.linux-64.yaml b/recipes/carpedeam/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..70fadb3fc14e6 --- /dev/null +++ b/recipes/carpedeam/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 3cd3611839f9dfc2f3681c843367c769f087fe911dce12044abb62fca0fa9243 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [ 34%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/carpedeam-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/cover.c + [ 34%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/carpedeam-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/fastcover.c + [ 35%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o + [ 35%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/carpedeam-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/zdict.c + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/carpedeam-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/divsufsort.c + [ 35%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/carpedeam-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/deprecated/zbuff_common.c + [ 36%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/carpedeam-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/deprecated/zbuff_compress.c + [ 36%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/carpedeam-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/deprecated/zbuff_decompress.c + [ 36%] Linking C static library libzstd.a + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/cmake -P CMakeFiles/libzstd_static.dir/cmake_clean_target.cmake + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/cmake -E cmake_link_script CMakeFiles/libzstd_static.dir/link.txt --verbose=1 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar qc libzstd.a CMakeFiles/libzstd_static.dir/__/__/__/lib/common/entropy_common.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/fse_decompress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/threading.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/pool.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/zstd_common.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/error_private.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/xxhash.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/hist.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/fse_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/huf_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstdmt_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_fast.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_double_fast.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_lazy.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_opt.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_ldm.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/huf_decompress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress_block.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_ddict.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib libzstd.a + make[2]: Leaving directory '$SRC_DIR/build' + [ 36%] Built target libzstd_static + make -f lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build.make lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/depend + make[2]: Entering directory '$SRC_DIR/build' + cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR/lib/mmseqs/src $SRC_DIR/build $SRC_DIR/build/lib/mmseqs/src $SRC_DIR/build/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/DependInfo.cmake "--color=" + make[2]: Leaving directory '$SRC_DIR/build' + make -f lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build.make lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build + make[2]: Entering directory '$SRC_DIR/build' + [ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o + [ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o + [ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o + [ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/carpedeam-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/Alignment.cpp + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/carpedeam-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/Main.cpp + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/carpedeam-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/CompressedA3M.cpp + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/carpedeam-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/Matcher.cpp + [ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/carpedeam-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/MsaFilter.cpp + [ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/carpedeam-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/MultipleAlignment.cpp + In file included from /opt/conda/conda-bld/carpedeam_1733977940403/work/lib/mmseqs/src/commons/Debug.h:5, + from /opt/conda/conda-bld/carpedeam_1733977940403/work/lib/mmseqs/src/alignment/MsaFilter.cpp:5: + /opt/conda/conda-bld/carpedeam_1733977940403/work/lib/mmseqs/src/commons/Util.h:89:12: error: 'uint64_t' does not name a type + 89 | static uint64_t getL2CacheSize(); + | ^~~~~~~~ + /opt/conda/conda-bld/carpedeam_1733977940403/work/lib/mmseqs/src/commons/Util.h:11:1: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + 10 | #include "MMseqsMPI.h" + |#include + 11 | + /opt/conda/conda-bld/carpedeam_1733977940403/work/lib/mmseqs/src/commons/Util.h:362:12: error: 'uint64_t' does not name a type + 362 | static uint64_t revComplement(const uint64_t kmer, const int k); + | ^~~~~~~~ + /opt/conda/conda-bld/carpedeam_1733977940403/work/lib/mmseqs/src/commons/Util.h:362:12: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/carpedeam_1733977940403/work/lib/mmseqs/src/commons/Debug.h: In constructor 'Debug::Progress::Progress()': + /opt/conda/conda-bld/carpedeam_1733977940403/work/lib/mmseqs/src/commons/Debug.h:169:69: error: 'SIZE_MAX' was not declared in this scope + 169 | Progress() : currentPos(0), prevPrintedId(0), totalEntries(SIZE_MAX){ + | ^~~~~~~~ + /opt/conda/conda-bld/carpedeam_1733977940403/work/lib/mmseqs/src/commons/Debug.h:12:1: note: 'SIZE_MAX' is defined in header ''; did you forget to '#include '? + 11 | #include + |#include + 12 | + /opt/conda/conda-bld/carpedeam_1733977940403/work/lib/mmseqs/src/commons/Debug.h: In member function 'void Debug::Progress::updateProgress()': + /opt/conda/conda-bld/carpedeam_1733977940403/work/lib/mmseqs/src/commons/Debug.h:184:34: error: 'SIZE_MAX' was not declared in this scope + 184 | if(totalEntries==SIZE_MAX) { + | ^~~~~~~~ + /opt/conda/conda-bld/carpedeam_1733977940403/work/lib/mmseqs/src/commons/Debug.h:184:34: note: 'SIZE_MAX' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/carpedeam_1733977940403/work/lib/mmseqs/src/commons/Debug.h:218:34: error: 'SIZE_MAX' was not declared in this scope + 218 | if(totalEntries==SIZE_MAX){ + | ^~~~~~~~ + /opt/conda/conda-bld/carpedeam_1733977940403/work/lib/mmseqs/src/commons/Debug.h:218:34: note: 'SIZE_MAX' is defined in header ''; did you forget to '#include '? + [ 39%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/carpedeam-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/PSSMCalculator.cpp + make[2]: *** [lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build.make:135: lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o] Error 1 + make[2]: *** Waiting for unfinished jobs.... + make[2]: Leaving directory '$SRC_DIR/build' + make[1]: *** [CMakeFiles/Makefile2:1026: lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/all] Error 2 + make[1]: Leaving directory '$SRC_DIR/build' + make: *** [Makefile:136: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/carpedeam_1733977940403/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/carpedeam_1733977940403/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/carpedeam/meta.yaml b/recipes/carpedeam/meta.yaml index 59691207623a8..3ee9df60349b0 100644 --- a/recipes/carpedeam/meta.yaml +++ b/recipes/carpedeam/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version|replace("-", ".") }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('carpedeam', max_pin="x.x") }} diff --git a/recipes/cassiopee/build_failure.linux-64.yaml b/recipes/cassiopee/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..79eb95101be74 --- /dev/null +++ b/recipes/cassiopee/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: bef5f0e60eaff31b34ff0963c3e1be8e085900ee919d0d6baeac7b44de727b14 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:1656:11: error: 'uint32' does not name a type; did you mean 'uint32_t'? + 1656 | virtual uint32 LogSize() = 0; + | ^~~~~~ + | uint32_t + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:1662:26: error: expected initializer before '*' token + 1662 | extern GLOG_EXPORT Logger* GetLogger(LogSeverity level); + | ^ + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:1667:8: error: two or more data types in declaration of 'SetLogger' + 1667 | extern GLOG_EXPORT void SetLogger(LogSeverity level, Logger* logger); + | ^~~~~~~~~~~ + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:1667:35: error: 'LogSeverity' was not declared in this scope; did you mean 'google::LogSeverity'? + 1667 | extern GLOG_EXPORT void SetLogger(LogSeverity level, Logger* logger); + | ^~~~~~~~~~~ + | google::LogSeverity + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/log_severity.h:62:6: note: 'google::LogSeverity' declared here + 62 | enum LogSeverity { + | ^~~~~~~~~~~ + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:1667:54: error: 'Logger' was not declared in this scope; did you mean 'base::Logger'? + 1667 | extern GLOG_EXPORT void SetLogger(LogSeverity level, Logger* logger); + | ^~~~~~ + | base::Logger + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:1628:19: note: 'base::Logger' declared here + 1628 | class GLOG_EXPORT Logger { + | ^~~~~~ + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:1667:62: error: 'logger' was not declared in this scope + 1667 | extern GLOG_EXPORT void SetLogger(LogSeverity level, Logger* logger); + | ^~~~~~ + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:1669:1: error: expected declaration before '}' token + 1669 | } // namespace base + | ^ + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:1672:30: error: expected initializer before ':' token + 1672 | class GLOG_EXPORT NullStream : public LogMessage::LogStream { + | ^ + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:1697:8: error: 'NullStream' does not name a type + 1697 | inline NullStream& operator<<(NullStream& str, const T&) { + | ^~~~~~~~~~ + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:1703:35: error: expected initializer before ':' token + 1703 | class GLOG_EXPORT NullStreamFatal : public NullStream { + | ^ + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:1727:1: error: two or more data types in declaration of 'InstallFailureSignalHandler' + 1727 | GLOG_EXPORT void InstallFailureSignalHandler(); + | ^~~~~~~~~~~ + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:1730:1: error: two or more data types in declaration of 'IsFailureSignalHandlerInstalled' + 1730 | GLOG_EXPORT bool IsFailureSignalHandlerInstalled(); + | ^~~~~~~~~~~ + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:1736:1: error: two or more data types in declaration of 'InstallFailureWriter' + 1736 | GLOG_EXPORT void InstallFailureWriter(void (*writer)(const char* data, + | ^~~~~~~~~~~ + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:1740:25: error: expected initializer before 'GetStackTrace' + 1740 | GLOG_EXPORT std::string GetStackTrace(); + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:1742:1: error: expected declaration before '}' token + 1742 | } // namespace google + | ^ + /opt/conda/conda-bld/cassiopee_1734063569925/work/src/cassiopee.cxx: In constructor 'CassieIndexer::CassieIndexer(const char*)': + /opt/conda/conda-bld/cassiopee_1734063569925/work/src/cassiopee.cxx:511:9: error: 'LogMessageFatal' is not a member of 'google'; did you mean 'LogMessageTime'? + 511 | LOG(FATAL) << "Error: " << path << " could not be opened for reading!" ; + | ^~~ + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h: In instantiation of 'std::unique_ptr > google::logging::MakeCheckOpString(const T1&, const T2&, const char*) [with T1 = int; T2 = int]': + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:737:1: required from 'std::unique_ptr > google::logging::Check_EQImpl(const T1&, const T2&, const char*) [with T1 = int; T2 = int]' + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:737:1: required from here + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:710:25: error: 'MakeCheckOpValueString' was not declared in this scope; did you mean 'google::logging::internal::MakeCheckOpValueString'? + 710 | MakeCheckOpValueString(comb.ForVar1(), v1); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ + | google::logging::internal::MakeCheckOpValueString + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:653:13: note: 'google::logging::internal::MakeCheckOpValueString' declared here + 653 | inline void MakeCheckOpValueString(std::ostream* os, const T& v) { + | ^~~~~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:711:25: error: 'MakeCheckOpValueString' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation + 711 | MakeCheckOpValueString(comb.ForVar2(), v2); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/cassiopee_1734063569925/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/glog/logging.h:710:25: note: 'MakeCheckOpValueString' declared here, later in the translation unit + 710 | MakeCheckOpValueString(comb.ForVar1(), v1); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ + make[2]: *** [src/CMakeFiles/cassie.dir/build.make:79: src/CMakeFiles/cassie.dir/cassiopee.cxx.o] Error 1 + make[1]: *** [CMakeFiles/Makefile2:163: src/CMakeFiles/cassie.dir/all] Error 2 + make: *** [Makefile:146: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cassiopee_1734063569925/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cassiopee_1734063569925/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/cassiopee/build_failure.osx-64.yaml b/recipes/cassiopee/build_failure.osx-64.yaml index 9914ba234d248..7e408f5e7b8b8 100644 --- a/recipes/cassiopee/build_failure.osx-64.yaml +++ b/recipes/cassiopee/build_failure.osx-64.yaml @@ -1,20 +1,35 @@ -recipe_sha: 51bbcd4a9b8308a55e32b84f7d357d77b0c8fd587d6903e70c8000a68552e440 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: bef5f0e60eaff31b34ff0963c3e1be8e085900ee919d0d6baeac7b44de727b14 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - make: *** [Makefile:146: all] Error 2 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/cassiopee_1717516351394/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/cassiopee_1717516351394/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/cassiopee_1717516351394/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/cassiopee_1717516351394/work +log: |2- + - libboost-python 1.85.0 py312h44e70fa_2 + - libboost-python-devel 1.85.0 py312h0be7463_2 + - boost 1.85.0 h0be7463_2 + run: + - icu >=73.2,<74.0a0 + - glog >=0.7.1,<0.8.0a0 + - zlib + - boost + - bzip2 >=1.0.8,<2.0a0 + - libzlib >=1.3.1,<2.0a0 + - libcxx >=18 + test: + commands: + - cassiopee -h + about: + home: https://github.com/osallou/cassiopee-c + license: GPL-3 + license_file: LICENSE + summary: scan an input genomic sequence (dna/rna/protein) and search for a subsequence + with exact match or allowing substitutions (Hamming distance) and/or insertion/deletions + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/cassiopee_1734023590048/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/cassiopee_1734023590048/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/cassiopee_1734023590048/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/cassiopee_1734023590048/work INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as @@ -23,19 +38,13 @@ log: |- CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cassiopee-1.0.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - packages_from_this = build( - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/cassiopee_1717516351394/work/conda_build.sh']' returned non-zero exit status 2. + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cassiopee-1.0.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool @@ -44,7 +53,7 @@ log: |- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -53,7 +62,7 @@ log: |- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -71,8 +80,8 @@ log: |- CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cassiopee-1.0.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cassiopee-1.0.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - -- The C compiler identification is Clang 16.0.6 - -- The CXX compiler identification is Clang 16.0.6 + -- The C compiler identification is Clang 18.1.8 + -- The CXX compiler identification is Clang 18.1.8 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped @@ -85,20 +94,11 @@ log: |- -- Detecting CXX compile features - done -- Found Boost: $PREFIX/include (found version "1.85.0") found components: iostreams serialization regex -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) - -- Found OpenMP_C: -fopenmp=libomp (found version "5.0") - -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.0") - -- Found OpenMP: TRUE (found version "5.0") - -- Configuring done (4.8s) - -- Generating done (0.1s) + -- Found OpenMP_C: -fopenmp=libomp (found version "5.1") + -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.1") + -- Found OpenMP: TRUE (found version "5.1") + -- Configuring done (5.6s) + -- Generating done (0.2s) -- Build files have been written to: $SRC_DIR [ 12%] Building CXX object src/CMakeFiles/cassie.dir/cassiopee.cxx.o - [ 25%] Linking CXX shared library ../lib/libcassie.dylib - [ 25%] Built target cassie - [ 37%] Building CXX object src/CMakeFiles/cassiopee.dir/cassie.cxx.o - [ 50%] Linking CXX executable ../bin/cassiopee - [ 50%] Built target cassiopee - [ 62%] Building CXX object src/CMakeFiles/cassiopeeknife.dir/knife.cxx.o - [ 75%] Linking CXX executable ../bin/cassiopeeknife - [ 75%] Built target cassiopeeknife - [ 87%] Building CXX object test/CMakeFiles/test_cassiopee.dir/test.cxx.o # Last 100 lines of the build log. diff --git a/recipes/cassiopee/meta.yaml b/recipes/cassiopee/meta.yaml index 4a81a492cb454..de5bbd2f6d745 100644 --- a/recipes/cassiopee/meta.yaml +++ b/recipes/cassiopee/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.0.9" build: - number: 7 + number: 8 source: url: https://github.com/osallou/cassiopee-c/archive/1.0.9.tar.gz diff --git a/recipes/cassiopeia/meta.yaml b/recipes/cassiopeia/meta.yaml index 7d7254e282891..db6986fe20e1f 100644 --- a/recipes/cassiopeia/meta.yaml +++ b/recipes/cassiopeia/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 28ae7495152683f5733222255056a1e7b2f7a51e1cee2f23f0d9f8ae5f4c3742 build: - number: 1 + number: 2 entry_points: - cassiopeia-preprocess = cassiopeia.preprocess.cassiopeia_preprocess:main script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir --use-pep517 diff --git a/recipes/ccphylo/meta.yaml b/recipes/ccphylo/meta.yaml index 0389348f01e25..d4275172ca8f9 100644 --- a/recipes/ccphylo/meta.yaml +++ b/recipes/ccphylo/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/cd-hit-auxtools/meta.yaml b/recipes/cd-hit-auxtools/meta.yaml index f1bd4cf511298..15a42fece9feb 100644 --- a/recipes/cd-hit-auxtools/meta.yaml +++ b/recipes/cd-hit-auxtools/meta.yaml @@ -12,7 +12,7 @@ source: - 0001-Append-compiler-linker-flags.patch build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/cd-hit/meta.yaml b/recipes/cd-hit/meta.yaml index b46294a67d0a4..3e1247df5b2d6 100644 --- a/recipes/cd-hit/meta.yaml +++ b/recipes/cd-hit/meta.yaml @@ -12,7 +12,7 @@ source: - cd-hit.patch build: - number: 11 + number: 12 run_exports: - {{ pin_subpackage('cd-hit', max_pin="x") }} diff --git a/recipes/cdbtools/build_failure.linux-64.yaml b/recipes/cdbtools/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..16a50476600c0 --- /dev/null +++ b/recipes/cdbtools/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 5ef946c139d122b97a7ac5e1df75cbada79bdfb5368bbf46618985cc28ea44e7 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + BUILD START: ['cdbtools-0.99-h077b44d_11.tar.bz2'] + Reloading output folder: ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/cdbtools_1734294223057/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libzlib: 1.3.1-hb9d3cd8_2 conda-forge + zlib: 1.3.1-hb9d3cd8_2 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder: ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder: ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/cdbtools_1734294223057/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.43-h4bf12b8_2 conda-forge + binutils_linux-64: 2.43-h4852527_2 conda-forge + gcc_impl_linux-64: 13.3.0-hfea6d02_1 conda-forge + gcc_linux-64: 13.3.0-hc28eda2_7 conda-forge + gxx_impl_linux-64: 13.3.0-hdbfa832_1 conda-forge + gxx_linux-64: 13.3.0-h6834431_7 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libsanitizer: 13.3.0-heb74ff8_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + make: 4.4.1-hb9d3cd8_2 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: cdbfasta_68767e8b2f.tar.gz + Downloading ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/cdbfasta/cdbfasta.tar.gz + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 103, in download_to_cache + download(url, path) + File "/opt/conda/lib/python3.10/site-packages/conda/common/io.py", line 86, in decorated + return f(*args, **kwds) + File "/opt/conda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 68, in download + download_inner( + File "/opt/conda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 97, in download_inner + resp = session.get( + File "/opt/conda/lib/python3.10/site-packages/requests/sessions.py", line 602, in get + return self.request("GET", url, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/requests/sessions.py", line 589, in request + resp = self.send(prep, **send_kwargs) + File "/opt/conda/lib/python3.10/site-packages/requests/sessions.py", line 703, in send + r = adapter.send(request, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda/gateways/connection/adapters/ftp.py", line 78, in send + self.conn.connect(host, port, timeout) + File "/opt/conda/lib/python3.10/ftplib.py", line 158, in connect + self.sock = socket.create_connection((self.host, self.port), self.timeout, + File "/opt/conda/lib/python3.10/socket.py", line 857, in create_connection + raise err + File "/opt/conda/lib/python3.10/socket.py", line 845, in create_connection + sock.connect(sa) + TimeoutError: timed out +# Last 100 lines of the build log. +category: |- + source download error diff --git a/recipes/cdbtools/build_failure.linux-aarch64.yaml b/recipes/cdbtools/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..aada5b9cc4311 --- /dev/null +++ b/recipes/cdbtools/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 5ef946c139d122b97a7ac5e1df75cbada79bdfb5368bbf46618985cc28ea44e7 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Reloading output folder: ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['cdbtools-0.99-h1e84f2d_11.tar.bz2'] + Reloading output folder: ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/cdbtools_1734270961836/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + + + The following NEW packages will be INSTALLED: + + _openmp_mutex: 4.5-2_gnu conda-forge + libgcc: 14.2.0-he277a41_1 conda-forge + libgomp: 14.2.0-he277a41_1 conda-forge + libstdcxx: 14.2.0-h3f4de04_1 conda-forge + libzlib: 1.3.1-h86ecc28_2 conda-forge + zlib: 1.3.1-h86ecc28_2 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder: ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder: ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/cdbtools_1734270961836/_build_env + + + The following NEW packages will be INSTALLED: + + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-aarch64: 2.43-h4c662bb_2 conda-forge + binutils_linux-aarch64: 2.43-hf1166c9_2 conda-forge + gcc_impl_linux-aarch64: 13.3.0-hcdea9b6_1 conda-forge + gcc_linux-aarch64: 13.3.0-h1cd514b_7 conda-forge + gxx_impl_linux-aarch64: 13.3.0-h1211b58_1 conda-forge + gxx_linux-aarch64: 13.3.0-h2864abd_7 conda-forge + kernel-headers_linux-aarch64: 4.18.0-h05a177a_18 conda-forge + ld_impl_linux-aarch64: 2.43-h80caac9_2 conda-forge + libgcc: 14.2.0-he277a41_1 conda-forge + libgcc-devel_linux-aarch64: 13.3.0-h0c07274_101 conda-forge + libgomp: 14.2.0-he277a41_1 conda-forge + libsanitizer: 13.3.0-ha58e236_1 conda-forge + libstdcxx: 14.2.0-h3f4de04_1 conda-forge + libstdcxx-devel_linux-aarch64: 13.3.0-h0c07274_101 conda-forge + make: 4.4.1-h2a6d0cb_2 conda-forge + sysroot_linux-aarch64: 2.17-h5b4a56d_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: cdbfasta_68767e8b2f.tar.gz + Downloading ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/cdbfasta/cdbfasta.tar.gz + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 103, in download_to_cache + download(url, path) + File "/opt/conda/lib/python3.10/site-packages/conda/common/io.py", line 86, in decorated + return f(*args, **kwds) + File "/opt/conda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 68, in download + download_inner( + File "/opt/conda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 97, in download_inner + resp = session.get( + File "/opt/conda/lib/python3.10/site-packages/requests/sessions.py", line 602, in get + return self.request("GET", url, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/requests/sessions.py", line 589, in request + resp = self.send(prep, **send_kwargs) + File "/opt/conda/lib/python3.10/site-packages/requests/sessions.py", line 703, in send + r = adapter.send(request, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda/gateways/connection/adapters/ftp.py", line 78, in send + self.conn.connect(host, port, timeout) + File "/opt/conda/lib/python3.10/ftplib.py", line 158, in connect + self.sock = socket.create_connection((self.host, self.port), self.timeout, + File "/opt/conda/lib/python3.10/socket.py", line 857, in create_connection + raise err + File "/opt/conda/lib/python3.10/socket.py", line 845, in create_connection + sock.connect(sa) + TimeoutError: timed out +# Last 100 lines of the build log. +category: |- + source download error diff --git a/recipes/cdbtools/build_failure.osx-64.yaml b/recipes/cdbtools/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..4e10d33f6599b --- /dev/null +++ b/recipes/cdbtools/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 5ef946c139d122b97a7ac5e1df75cbada79bdfb5368bbf46618985cc28ea44e7 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/cdbtools_1734295677332/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place + + + The following NEW packages will be INSTALLED: + + libcxx: 19.1.5-hf95d169_0 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + zlib: 1.3.1-hd23fc13_2 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (local): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (local): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/cdbtools_1734295677332/_build_env + + + The following NEW packages will be INSTALLED: + + ca-certificates: 2024.12.14-h8857fd0_0 conda-forge + cctools_osx-64: 1010.6-h00edd4c_2 conda-forge + clang: 18.1.8-default_h179603d_5 conda-forge + clang-18: 18.1.8-default_h0c94c6a_5 conda-forge + clang_impl_osx-64: 18.1.8-h6a44ed1_23 conda-forge + clang_osx-64: 18.1.8-h7e5c614_23 conda-forge + clangxx: 18.1.8-default_h179603d_5 conda-forge + clangxx_impl_osx-64: 18.1.8-h4b7810f_23 conda-forge + clangxx_osx-64: 18.1.8-h7e5c614_23 conda-forge + compiler-rt: 18.1.8-h1020d70_1 conda-forge + compiler-rt_osx-64: 18.1.8-hf2b8a54_1 conda-forge + ld64_osx-64: 951.9-hc8d1a19_2 conda-forge + libclang-cpp18.1: 18.1.8-default_h0c94c6a_5 conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libcxx-devel: 18.1.8-h7c275be_7 conda-forge + libiconv: 1.17-hd75f5a5_2 conda-forge + libllvm18: 18.1.8-h9ce406d_2 conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libxml2: 2.13.5-he8ee3e7_1 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-tools: 18.1.8-h9ce406d_2 conda-forge + llvm-tools-18: 18.1.8-h9ce406d_2 conda-forge + make: 4.4.1-h00291cd_2 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + sigtool: 0.1.3-h88f4db0_0 conda-forge + tapi: 1300.6.5-h390ca13_0 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache + Downloading source to cache: cdbfasta_68767e8b2f.tar.gz + Downloading ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/cdbfasta/cdbfasta.tar.gz + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 103, in download_to_cache + download(url, path) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/common/io.py", line 86, in decorated + return f(*args, **kwds) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 68, in download + download_inner( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 97, in download_inner + resp = session.get( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/requests/sessions.py", line 602, in get + return self.request("GET", url, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/requests/sessions.py", line 589, in request + resp = self.send(prep, **send_kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/requests/sessions.py", line 703, in send + r = adapter.send(request, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/gateways/connection/adapters/ftp.py", line 78, in send + self.conn.connect(host, port, timeout) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/ftplib.py", line 158, in connect + self.sock = socket.create_connection((self.host, self.port), self.timeout, + File "/opt/mambaforge/envs/bioconda/lib/python3.10/socket.py", line 857, in create_connection + raise err + File "/opt/mambaforge/envs/bioconda/lib/python3.10/socket.py", line 845, in create_connection + sock.connect(sa) + TimeoutError: timed out +# Last 100 lines of the build log. +category: |- + source download error diff --git a/recipes/cdbtools/meta.yaml b/recipes/cdbtools/meta.yaml index fd3037deed543..9c584ae3c37bf 100644 --- a/recipes/cdbtools/meta.yaml +++ b/recipes/cdbtools/meta.yaml @@ -10,7 +10,7 @@ source: - zlib.patch build: - number: 10 + number: 11 run_exports: - {{ pin_subpackage('cdbtools', max_pin='x.x') }} diff --git a/recipes/cellsnp-lite/build_failure.linux-64.yaml b/recipes/cellsnp-lite/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0d87e93b6e95d --- /dev/null +++ b/recipes/cellsnp-lite/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 9421e26fff75c6338f86be14b3defa264257dbae5520775c4a1cd0204abdd2e3 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + configure.ac:26: installing './compile' + configure.ac:159: installing './config.guess' + configure.ac:159: installing './config.sub' + checking for a BSD-compatible install... /usr/bin/install -c + checking whether sleep supports fractional seconds... yes + checking filesystem timestamp resolution... 0.01 + checking whether build environment is sane... yes + checking for a race-free mkdir -p... /usr/bin/mkdir -p + checking for gawk... gawk + checking whether make sets $(MAKE)... yes + checking whether make supports nested variables... yes + checking xargs -n works... yes + checking for gawk... (cached) gawk + checking for x86_64-conda-linux-gnu-gcc... $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + checking whether the C compiler works... yes + checking for C compiler default output file name... a.out + checking for suffix of executables... + checking whether we are cross compiling... no + checking for suffix of object files... o + checking whether the compiler supports GNU C... yes + checking whether $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc accepts -g... yes + checking for $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc option to enable C11 features... none needed + checking whether $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc understands -c and -o together... yes + checking whether make supports the include directive... yes (GNU style) + checking dependency style of $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc... gcc3 + checking for math.h... yes + checking for log in -lm... yes + checking for zlib.h... yes + checking for inflate in -lz... yes + checking for bzlib.h... yes + checking for BZ2_bzBuffToBuffCompress in -lbz2... yes + checking for lzma.h... no + checking for lzma_easy_buffer_encode in -llzma... no + configure: error: liblzma development files not found + + The CRAM format may use LZMA2 compression, which is implemented in HTSlib + by using compression routines from liblzma . + Linking HTSlib requires liblzma development files to be installed on the + build machine; you may need to ensure a package such as liblzma-dev (on Debian + or Ubuntu Linux), xz-devel (on RPM-based Linux distributions or Cygwin), or + xz (via Homebrew on macOS) is installed; or build XZ Utils from source. + + FAILED. Please resolve this error to build cellsnp-lite. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cellsnp-lite_1734253150754/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cellsnp-lite_1734253150754/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/cellsnp-lite/build_failure.linux-aarch64.yaml b/recipes/cellsnp-lite/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..288dc3ba2eb4a --- /dev/null +++ b/recipes/cellsnp-lite/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 9421e26fff75c6338f86be14b3defa264257dbae5520775c4a1cd0204abdd2e3 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + configure.ac:26: installing './compile' + configure.ac:159: installing './config.guess' + configure.ac:159: installing './config.sub' + checking for a BSD-compatible install... /usr/bin/install -c + checking whether sleep supports fractional seconds... yes + checking filesystem timestamp resolution... 0.01 + checking whether build environment is sane... yes + checking for a race-free mkdir -p... /usr/bin/mkdir -p + checking for gawk... gawk + checking whether make sets $(MAKE)... yes + checking whether make supports nested variables... yes + checking xargs -n works... yes + checking for gawk... (cached) gawk + checking for aarch64-conda-linux-gnu-gcc... $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc + checking whether the C compiler works... yes + checking for C compiler default output file name... a.out + checking for suffix of executables... + checking whether we are cross compiling... no + checking for suffix of object files... o + checking whether the compiler supports GNU C... yes + checking whether $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc accepts -g... yes + checking for $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc option to enable C11 features... none needed + checking whether $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc understands -c and -o together... yes + checking whether make supports the include directive... yes (GNU style) + checking dependency style of $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc... gcc3 + checking for math.h... yes + checking for log in -lm... yes + checking for zlib.h... yes + checking for inflate in -lz... yes + checking for bzlib.h... yes + checking for BZ2_bzBuffToBuffCompress in -lbz2... yes + checking for lzma.h... no + checking for lzma_easy_buffer_encode in -llzma... no + configure: error: liblzma development files not found + + The CRAM format may use LZMA2 compression, which is implemented in HTSlib + by using compression routines from liblzma . + Linking HTSlib requires liblzma development files to be installed on the + build machine; you may need to ensure a package such as liblzma-dev (on Debian + or Ubuntu Linux), xz-devel (on RPM-based Linux distributions or Cygwin), or + xz (via Homebrew on macOS) is installed; or build XZ Utils from source. + + FAILED. Please resolve this error to build cellsnp-lite. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cellsnp-lite_1734364753710/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cellsnp-lite_1734364753710/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/cellsnp-lite/build_failure.osx-64.yaml b/recipes/cellsnp-lite/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..9cdb12fc1f239 --- /dev/null +++ b/recipes/cellsnp-lite/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 9421e26fff75c6338f86be14b3defa264257dbae5520775c4a1cd0204abdd2e3 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + about: + dev_url: https://github.com/single-cell-genetics/cellsnp-lite + doc_url: https://cellsnp-lite.readthedocs.io/en/latest + home: https://github.com/single-cell-genetics/cellsnp-lite + license: Apache-2.0 + license_family: APACHE + license_file: LICENSE + summary: Efficient genotyping bi-allelic SNPs on single cells. + extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + copy_test_source_files: true + final: true + identifiers: + - doi:10.1093/bioinformatics/btab358 + - biotools:cellsnp-lite + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/cellsnp-lite_1734254241029/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/cellsnp-lite_1734254241029/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/cellsnp-lite_1734254241029/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/cellsnp-lite_1734254241029/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cellsnp-lite-1.2.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cellsnp-lite-1.2.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + checking for a BSD-compatible install... /usr/bin/install -c + checking whether sleep supports fractional seconds... yes + checking filesystem timestamp resolution... 0.01 + checking whether build environment is sane... yes + checking for a race-free mkdir -p... ./install-sh -c -d + checking for gawk... no + checking for mawk... no + checking for nawk... no + checking for awk... awk + checking whether make sets $(MAKE)... yes + checking whether make supports nested variables... yes + checking xargs -n works... yes + checking for gawk... (cached) awk + checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang + checking whether the C compiler works... yes + checking for C compiler default output file name... a.out + checking for suffix of executables... + checking whether we are cross compiling... no + checking for suffix of object files... o + checking whether the compiler supports GNU C... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking for x86_64-apple-darwin13.4.0-clang option to enable C11 features... none needed + checking whether x86_64-apple-darwin13.4.0-clang understands -c and -o together... yes + checking whether make supports the include directive... yes (GNU style) + checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 + checking for math.h... yes + checking for log in -lm... yes + checking for zlib.h... yes + checking for inflate in -lz... yes + checking for bzlib.h... yes + checking for BZ2_bzBuffToBuffCompress in -lbz2... yes + checking for lzma.h... no + checking for lzma_easy_buffer_encode in -llzma... yes +# Last 100 lines of the build log. diff --git a/recipes/cellsnp-lite/build_failure.osx-arm64.yaml b/recipes/cellsnp-lite/build_failure.osx-arm64.yaml new file mode 100644 index 0000000000000..b5658c1698333 --- /dev/null +++ b/recipes/cellsnp-lite/build_failure.osx-arm64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 9421e26fff75c6338f86be14b3defa264257dbae5520775c4a1cd0204abdd2e3 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + license_family: APACHE + license_file: LICENSE + summary: Efficient genotyping bi-allelic SNPs on single cells. + extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + copy_test_source_files: true + final: true + identifiers: + - doi:10.1093/bioinformatics/btab358 + - biotools:cellsnp-lite + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/cellsnp-lite_1733981271627/work + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/cellsnp-lite_1733981271627/work/conda_build.sh']' returned non-zero exit status 1. + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/cellsnp-lite_1733981271627/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/cellsnp-lite_1733981271627/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/cellsnp-lite_1733981271627/work + INFO: activate_clang_osx-arm64.sh made the following environmental changes: + AR=arm64-apple-darwin20.0.0-ar + AS=arm64-apple-darwin20.0.0-as + CC=arm64-apple-darwin20.0.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang + CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cellsnp-lite-1.2.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=arm64-apple-darwin20.0.0-checksyms + CLANG=arm64-apple-darwin20.0.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=11.0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=arm64-apple-darwin20.0.0 + CONDA_TOOLCHAIN_HOST=arm64-apple-darwin20.0.0 + CPP=arm64-apple-darwin20.0.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang-cpp + DEBUG_CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cellsnp-lite-1.2.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=arm64-apple-darwin20.0.0 + INSTALL_NAME_TOOL=arm64-apple-darwin20.0.0-install_name_tool + LD=arm64-apple-darwin20.0.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=arm64-apple-darwin20.0.0-libtool + LIPO=arm64-apple-darwin20.0.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=arm64-apple-darwin20.0.0-nm + NMEDIT=arm64-apple-darwin20.0.0-nmedit + OBJC=arm64-apple-darwin20.0.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang + OTOOL=arm64-apple-darwin20.0.0-otool + PAGESTUFF=arm64-apple-darwin20.0.0-pagestuff + RANLIB=arm64-apple-darwin20.0.0-ranlib + REDO_PREBINDING=arm64-apple-darwin20.0.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk + SEGEDIT=arm64-apple-darwin20.0.0-segedit + SEG_ADDR_TABLE=arm64-apple-darwin20.0.0-seg_addr_table + SEG_HACK=arm64-apple-darwin20.0.0-seg_hack + SIZE=arm64-apple-darwin20.0.0-size + STRINGS=arm64-apple-darwin20.0.0-strings + STRIP=arm64-apple-darwin20.0.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_arm64_apple_darwin20_0_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=arm64-apple-darwin20.0.0 + host_alias=arm64-apple-darwin20.0.0 + checking for a BSD-compatible install... /usr/bin/install -c + checking whether sleep supports fractional seconds... yes + checking filesystem timestamp resolution... 0.01 + checking whether build environment is sane... yes + checking for a race-free mkdir -p... ./install-sh -c -d + checking for gawk... no + checking for mawk... no + checking for nawk... no + checking for awk... awk + checking whether make sets $(MAKE)... yes + checking whether make supports nested variables... yes + checking xargs -n works... yes + checking for gawk... (cached) awk + checking for arm64-apple-darwin20.0.0-gcc... arm64-apple-darwin20.0.0-clang + checking whether the C compiler works... yes + checking for C compiler default output file name... a.out + checking for suffix of executables... + checking whether we are cross compiling... no + checking for suffix of object files... o + checking whether the compiler supports GNU C... yes + checking whether arm64-apple-darwin20.0.0-clang accepts -g... yes + checking for arm64-apple-darwin20.0.0-clang option to enable C11 features... none needed + checking whether arm64-apple-darwin20.0.0-clang understands -c and -o together... yes + checking whether make supports the include directive... yes (GNU style) + checking dependency style of arm64-apple-darwin20.0.0-clang... gcc3 + checking for math.h... yes + checking for log in -lm... yes + checking for zlib.h... yes + checking for inflate in -lz... yes + checking for bzlib.h... yes + checking for BZ2_bzBuffToBuffCompress in -lbz2... yes + checking for lzma.h... no + checking for lzma_easy_buffer_encode in -llzma... yes +# Last 100 lines of the build log. diff --git a/recipes/cellsnp-lite/meta.yaml b/recipes/cellsnp-lite/meta.yaml index f44ac346eecc8..97ff2bc2322d8 100644 --- a/recipes/cellsnp-lite/meta.yaml +++ b/recipes/cellsnp-lite/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage('cellsnp-lite', max_pin="x") }} diff --git a/recipes/centrifuge-core/meta.yaml b/recipes/centrifuge-core/meta.yaml index b9347c7e85535..16f9f0275d751 100644 --- a/recipes/centrifuge-core/meta.yaml +++ b/recipes/centrifuge-core/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 skip: true # [osx] run_exports: - {{ pin_subpackage("centrifuge-core", max_pin="x.x") }} diff --git a/recipes/centrifuge/meta.yaml b/recipes/centrifuge/meta.yaml index e2475be1dea44..add06f4028a8d 100644 --- a/recipes/centrifuge/meta.yaml +++ b/recipes/centrifuge/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: true # [osx] run_exports: - {{ pin_subpackage("centrifuge", max_pin="x.x") }} diff --git a/recipes/centrifuger/meta.yaml b/recipes/centrifuger/meta.yaml index 6f92a7904d167..2af4ccaf2693a 100644 --- a/recipes/centrifuger/meta.yaml +++ b/recipes/centrifuger/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/cesar/meta.yaml b/recipes/cesar/meta.yaml index b8685a944a1c6..a34790c7466f8 100644 --- a/recipes/cesar/meta.yaml +++ b/recipes/cesar/meta.yaml @@ -10,7 +10,7 @@ source: build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/cfm/meta.yaml b/recipes/cfm/meta.yaml index 7ac5e4ae42545..f3935778fbdf3 100644 --- a/recipes/cfm/meta.yaml +++ b/recipes/cfm/meta.yaml @@ -20,7 +20,7 @@ source: folder: train-example build: - number: 6 + number: 7 skip: True # [osx] requirements: diff --git a/recipes/cgmlst-dists/meta.yaml b/recipes/cgmlst-dists/meta.yaml index 22d814e7cc5c0..e4ca6cc0991fc 100644 --- a/recipes/cgmlst-dists/meta.yaml +++ b/recipes/cgmlst-dists/meta.yaml @@ -8,7 +8,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://github.com/{{ user }}/{{ name }}/archive/v{{ version }}.tar.gz diff --git a/recipes/cgpbigwig/build_failure.linux-64.yaml b/recipes/cgpbigwig/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..3e65dcd1b043b --- /dev/null +++ b/recipes/cgpbigwig/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 83abd45a454fe959cb0c80505fc56e453e0bce8ea832e5a04f5f6b5d29d05868 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cgpbigwig-1.7.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + mkdir -p /opt/conda/conda-bld/cgpbigwig_1734248953386/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/bin + make -C c clean + make: Entering directory '$SRC_DIR/c' + clean + rm -f ./*.o *~ ../bin/bam2bedgraph ../bin/bam2bw ../bin/bg2bw ../bin/bam2bwbases ../bin/bwjoin ../bin/detectExtremeDepth ../bin/bwcat ./tests/tests_log ./c_tests/utils_tests ./*.gcda ./*.gcov ./*.gcno *.gcda *.gcov *.gcno ./c_tests/*.gcda ./c_tests/*.gcov ./c_tests/*.gcno + rm -rf ./htslib_tmp ../bin + make: Leaving directory '$SRC_DIR/c' + sed -i.bak s#gcc#/opt/conda/conda-bld/cgpbigwig_1734248953386/_build_env/bin/x86_64-conda-linux-gnu-cc# c/Makefile + export LD_LIBRARY_PATH=/opt/conda/conda-bld/cgpbigwig_1734248953386/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib + LD_LIBRARY_PATH=/opt/conda/conda-bld/cgpbigwig_1734248953386/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib + make -j 4 -C c prefix=/opt/conda/conda-bld/cgpbigwig_1734248953386/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla HTSLOC=/opt/conda/conda-bld/cgpbigwig_1734248953386/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib OPTINC=-I/opt/conda/conda-bld/cgpbigwig_1734248953386/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include LFLAGS=-L/opt/conda/conda-bld/cgpbigwig_1734248953386/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib + make: Entering directory '$SRC_DIR/c' + mkdir ../bin + clean + rm -f ./*.o *~ ../bin/bam2bedgraph ../bin/bam2bw ../bin/bg2bw ../bin/bam2bwbases ../bin/bwjoin ../bin/detectExtremeDepth ../bin/bwcat ./tests/tests_log ./c_tests/utils_tests ./*.gcda ./*.gcov ./*.gcno *.gcda *.gcov *.gcno ./c_tests/*.gcda ./c_tests/*.gcov ./c_tests/*.gcno + mkdir ./htslib_tmp + rm -rf ./htslib_tmp ../bin + #Do some magic to ensure we compile with the static libhts.a rather than libhts.so + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O3 -DVERSION='"1.7.0"' -g -Wall -I$PREFIX/include -I$PREFIX/include -rdynamic -c bam_access.c -o bam_access.o + ln -s $PREFIX/lib/libhts.a ./htslib_tmp/libhts.a + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O3 -DVERSION='"1.7.0"' -g -Wall -I$PREFIX/include -I$PREFIX/include -rdynamic -c utils.c -o utils.o + remove tmp hts location + rm -rf ./htslib_tmp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O3 -DVERSION='"1.7.0"' -g -Wall -I$PREFIX/include -I$PREFIX/include -rdynamic -I./ ./bam_access.o ./utils.o -L$PREFIX/lib -lhts -lpthread -lz -lbz2 -llzma -lm -ldl -ldeflate -L$PREFIX/lib -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib c_tests/utils_tests.c -o c_tests/utils_tests + utils.c: In function 'parse_file_name': + utils.c:53:22: warning: argument to 'sizeof' in 'memset' call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess] + 53 | memset(dir,0,sizeof(dir)); + | ^ + utils.c:54:24: warning: argument to 'sizeof' in 'memset' call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess] + 54 | memset(fname,0,sizeof(fname)); + | ^ + utils.c: In function 'parseRegionString': + utils.c:103:41: warning: pointer targets in passing argument 2 of 'hts_parse_reg' differ in signedness [-Wpointer-sign] + 103 | const char *q = hts_parse_reg(region, start, stop); + | ^~~~~ + | | + | uint32_t * {aka unsigned int *} + In file included from /opt/conda/conda-bld/cgpbigwig_1734248953386/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/htslib/sam.h:33, + from utils.c:36: + /opt/conda/conda-bld/cgpbigwig_1734248953386/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/htslib/hts.h:1190:49: note: expected 'int *' but argument is of type 'uint32_t *' {aka 'unsigned int *'} + 1190 | const char *hts_parse_reg(const char *str, int *beg, int *end); + | ~~~~~^~~ + utils.c:103:48: warning: pointer targets in passing argument 3 of 'hts_parse_reg' differ in signedness [-Wpointer-sign] + 103 | const char *q = hts_parse_reg(region, start, stop); + | ^~~~ + | | + | uint32_t * {aka unsigned int *} + /opt/conda/conda-bld/cgpbigwig_1734248953386/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/htslib/hts.h:1190:59: note: expected 'int *' but argument is of type 'uint32_t *' {aka 'unsigned int *'} + 1190 | const char *hts_parse_reg(const char *str, int *beg, int *end); + | ~~~~~^~~ + bam_access.c: In function 'process_bam_region_bases': + bam_access.c:329:9: warning: unused variable 'contig' [-Wunused-variable] + 329 | char *contig = parseRegionString(region, &start, &stop); + | ^~~~~~ + bam_access.c: In function 'process_bam_region': + bam_access.c:439:9: warning: unused variable 'contig' [-Wunused-variable] + 439 | char *contig = parseRegionString(region, ®_sta, ®_sto); + | ^~~~~~ + /opt/conda/conda-bld/cgpbigwig_1734248953386/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find ./bam_access.o: No such file or directory + collect2: error: ld returned 1 exit status + make: *** [: c_tests/utils_tests] Error 1 + make: *** Waiting for unfinished jobs.... + make: Leaving directory '$SRC_DIR/c' + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cgpbigwig_1734248953386/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cgpbigwig_1734248953386/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/cgpbigwig/build_failure.linux-aarch64.yaml b/recipes/cgpbigwig/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..22c43e242cad9 --- /dev/null +++ b/recipes/cgpbigwig/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 83abd45a454fe959cb0c80505fc56e453e0bce8ea832e5a04f5f6b5d29d05868 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + INFO: activate-binutils_linux-aarch64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strip + INFO: activate-gcc_linux-aarch64.sh made the following environmental changes: + BUILD=aarch64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc + CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cgpbigwig-1.7.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=aarch64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=aarch64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cgpbigwig-1.7.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib + HOST=aarch64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_aarch64_conda_cos7_linux_gnu + build_alias=aarch64-conda-linux-gnu + host_alias=aarch64-conda-linux-gnu + -BUILD=aarch64-conda_cos7-linux-gnu + -CONDA_BUILD_SYSROOT= + mkdir -p /opt/conda/conda-bld/cgpbigwig_1734238011024/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/bin + make -C c clean + make: Entering directory '$SRC_DIR/c' + clean + rm -f ./*.o *~ ../bin/bam2bedgraph ../bin/bam2bw ../bin/bg2bw ../bin/bam2bwbases ../bin/bwjoin ../bin/detectExtremeDepth ../bin/bwcat ./tests/tests_log ./c_tests/utils_tests ./*.gcda ./*.gcov ./*.gcno *.gcda *.gcov *.gcno ./c_tests/*.gcda ./c_tests/*.gcov ./c_tests/*.gcno + rm -rf ./htslib_tmp ../bin + make: Leaving directory '$SRC_DIR/c' + sed -i.bak s#gcc#/opt/conda/conda-bld/cgpbigwig_1734238011024/_build_env/bin/aarch64-conda-linux-gnu-cc# c/Makefile + export LD_LIBRARY_PATH=/opt/conda/conda-bld/cgpbigwig_1734238011024/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib + LD_LIBRARY_PATH=/opt/conda/conda-bld/cgpbigwig_1734238011024/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib + make -j 4 -C c prefix=/opt/conda/conda-bld/cgpbigwig_1734238011024/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla HTSLOC=/opt/conda/conda-bld/cgpbigwig_1734238011024/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib OPTINC=-I/opt/conda/conda-bld/cgpbigwig_1734238011024/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include LFLAGS=-L/opt/conda/conda-bld/cgpbigwig_1734238011024/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib + make: Entering directory '$SRC_DIR/c' + mkdir ../bin + clean + rm -f ./*.o *~ ../bin/bam2bedgraph ../bin/bam2bw ../bin/bg2bw ../bin/bam2bwbases ../bin/bwjoin ../bin/detectExtremeDepth ../bin/bwcat ./tests/tests_log ./c_tests/utils_tests ./*.gcda ./*.gcov ./*.gcno *.gcda *.gcov *.gcno ./c_tests/*.gcda ./c_tests/*.gcov ./c_tests/*.gcno + mkdir ./htslib_tmp + rm -rf ./htslib_tmp ../bin + #Do some magic to ensure we compile with the static libhts.a rather than libhts.so + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O3 -DVERSION='"1.7.0"' -g -Wall -I$PREFIX/include -I$PREFIX/include -rdynamic -c bam_access.c -o bam_access.o + ln -s $PREFIX/lib/libhts.a ./htslib_tmp/libhts.a + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O3 -DVERSION='"1.7.0"' -g -Wall -I$PREFIX/include -I$PREFIX/include -rdynamic -c utils.c -o utils.o + ln: failed to create symbolic link './htslib_tmp/libhts.a': No such file or directory + make: *** [Makefile:151: make_htslib_tmp] Error 1 + make: *** Waiting for unfinished jobs.... + bam_access.c: In function 'process_bam_region_bases': + bam_access.c:329:9: warning: unused variable 'contig' [-Wunused-variable] + 329 | char *contig = parseRegionString(region, &start, &stop); + | ^~~~~~ + bam_access.c: In function 'process_bam_region': + bam_access.c:439:9: warning: unused variable 'contig' [-Wunused-variable] + 439 | char *contig = parseRegionString(region, ®_sta, ®_sto); + | ^~~~~~ + make: Leaving directory '$SRC_DIR/c' + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cgpbigwig_1734238011024/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cgpbigwig_1734238011024/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/cgpbigwig/meta.yaml b/recipes/cgpbigwig/meta.yaml index 6b1022168b253..131d14a93cc98 100644 --- a/recipes/cgpbigwig/meta.yaml +++ b/recipes/cgpbigwig/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('cgpbigwig', max_pin="x") }} diff --git a/recipes/cgranges/meta.yaml b/recipes/cgranges/meta.yaml index cc8be36d7d0a4..61a80da6c11ab 100644 --- a/recipes/cgranges/meta.yaml +++ b/recipes/cgranges/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation -vvv . run_exports: - {{ pin_subpackage('cgranges', max_pin="x") }} diff --git a/recipes/chia-rep/build_failure.linux-64.yaml b/recipes/chia-rep/build_failure.linux-64.yaml index 2da8006503a6b..baf3266bb8a53 100644 --- a/recipes/chia-rep/build_failure.linux-64.yaml +++ b/recipes/chia-rep/build_failure.linux-64.yaml @@ -1,22 +1,12 @@ -recipe_sha: 8ff458bbc184c34e9233f6597ebad2bc7eb9de8afd151614a49ac3ad0787623f # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: dde97bbf8df332b9567520d6fb4d33fdfb6091830ce3d9c5643d48e31bf83e8c # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- - reading manifest file 'ChIA_Rep.egg-info/SOURCES.txt' - reading manifest template 'MANIFEST.in' - adding license file 'LICENSE' - writing manifest file 'ChIA_Rep.egg-info/SOURCES.txt' - copying chia_rep/util.c -> build/lib.linux-x86_64-cpython-312/chia_rep - copying chia_rep/util.pyx -> build/lib.linux-x86_64-cpython-312/chia_rep - running build_ext - building 'chia_rep.util' extension - creating build/temp.linux-x86_64-cpython-312 - creating build/temp.linux-x86_64-cpython-312/chia_rep - /opt/conda/conda-bld/chia-rep_1717892898024/_build_env/bin/x86_64-conda-linux-gnu-cc -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /opt/conda/conda-bld/chia-rep_1717892898024/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fPIC -O2 -isystem /opt/conda/conda-bld/chia-rep_1717892898024/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/conda-bld/chia-rep_1717892898024/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fdebug-prefix-map=/opt/conda/conda-bld/chia-rep_1717892898024/work=/usr/local/src/conda/chia-rep-3.1.1 -fdebug-prefix-map=/opt/conda/conda-bld/chia-rep_1717892898024/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/conda-bld/chia-rep_1717892898024/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fPIC -I/opt/conda/conda-bld/chia-rep_1717892898024/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/python3.12 -c chia_rep/util.c -o build/temp.linux-x86_64-cpython-312/chia_rep/util.o + /opt/conda/conda-bld/chia-rep_1734727917337/_build_env/bin/x86_64-conda-linux-gnu-cc -fno-strict-overflow -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /opt/conda/conda-bld/chia-rep_1734727917337/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fPIC -O2 -isystem /opt/conda/conda-bld/chia-rep_1734727917337/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/conda-bld/chia-rep_1734727917337/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fdebug-prefix-map=/opt/conda/conda-bld/chia-rep_1734727917337/work=/usr/local/src/conda/chia-rep-3.1.1 -fdebug-prefix-map=/opt/conda/conda-bld/chia-rep_1734727917337/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/conda-bld/chia-rep_1734727917337/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fPIC -I/opt/conda/conda-bld/chia-rep_1734727917337/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/python3.12 -c chia_rep/util.c -o build/temp.linux-x86_64-cpython-312/chia_rep/util.o chia_rep/util.c:211:12: fatal error: longintrepr.h: No such file or directory 211 | #include "longintrepr.h" | ^~~~~~~~~~~~~~~ compilation terminated. - error: command '/opt/conda/conda-bld/chia-rep_1717892898024/_build_env/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1 + error: command '/opt/conda/conda-bld/chia-rep_1734727917337/_build_env/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1 [1;31merror[0m: [1msubprocess-exited-with-error[0m [31m[0m [32mpython setup.py bdist_wheel[0m did not run successfully. @@ -24,7 +14,7 @@ log: |2- [31m>[0m See above for output. [1;35mnote[0m: This error originates from a subprocess, and is likely not a problem with pip. - [1;35mfull command[0m: [34m/opt/conda/conda-bld/chia-rep_1717892898024/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python -u -c '[0m + [1;35mfull command[0m: [34m/opt/conda/conda-bld/chia-rep_1734727917337/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python -u -c '[0m [34m exec(compile('"'"''"'"''"'"'[0m [34m # This is -- a caller that pip uses to run setup.py[0m [34m #[0m @@ -59,8 +49,8 @@ log: |2- [34m setup_py_code = "from setuptools import setup; setup()"[0m [34m [0m [34m exec(compile(setup_py_code, filename, "exec"))[0m - [34m '"'"''"'"''"'"' % ('"'"'/opt/conda/conda-bld/chia-rep_1717892898024/work/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-f89o_ox3[0m - [1;35mcwd[0m: /opt/conda/conda-bld/chia-rep_1717892898024/work/ + [34m '"'"''"'"''"'"' % ('"'"'/opt/conda/conda-bld/chia-rep_1734727917337/work/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-deod2l2i[0m + [1;35mcwd[0m: /opt/conda/conda-bld/chia-rep_1734727917337/work/ Building wheel for ChIA-Rep (setup.py): finished with status 'error' [31m ERROR: Failed building wheel for ChIA-Rep[0m[31m [0m Running setup.py clean for ChIA-Rep @@ -72,33 +62,43 @@ log: |2- 'build/scripts-3.12' does not exist -- can't clean it removing 'build' Failed to build ChIA-Rep - [31mERROR: Could not build wheels for ChIA-Rep, which is required to install pyproject.toml-based projects[0m[31m + [31mERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (ChIA-Rep)[0m[31m [0mException information: Traceback (most recent call last): - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + ^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper return func(self, options, args) ^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 429, in run + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 434, in run raise InstallationError( - pip._internal.exceptions.InstallationError: Could not build wheels for ChIA-Rep, which is required to install pyproject.toml-based projects - Removed build tracker: '/tmp/pip-build-tracker-hxy4xhuy' + pip._internal.exceptions.InstallationError: ERROR: Failed to build installable wheels for some pyproject.toml based projects (ChIA-Rep) + Removed build tracker: '/tmp/pip-build-tracker-hq0sfsdp' + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/chia-rep_1734727917337/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + Traceback (most recent call last): File "/opt/conda/bin/conda-build", line 11, in sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/chia-rep_1717892898024/work/conda_build.sh']' returned non-zero exit status 1. + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/chia-rep_1734727917337/work/conda_build.sh']' returned non-zero exit status 1. # Last 100 lines of the build log. diff --git a/recipes/chia-rep/build_failure.osx-64.yaml b/recipes/chia-rep/build_failure.osx-64.yaml index 943283b5e9828..423b65d49a55b 100644 --- a/recipes/chia-rep/build_failure.osx-64.yaml +++ b/recipes/chia-rep/build_failure.osx-64.yaml @@ -1,33 +1,31 @@ -recipe_sha: 8ff458bbc184c34e9233f6597ebad2bc7eb9de8afd151614a49ac3ad0787623f # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: dde97bbf8df332b9567520d6fb4d33fdfb6091830ce3d9c5643d48e31bf83e8c # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/chia-rep_1717683959380/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/chia-rep_1717683959380/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/chia-rep_1717683959380/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/chia-rep_1734756308495/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/chia-rep_1734756308495/work/conda_build.sh']' returned non-zero exit status 1. + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/chia-rep_1734756308495/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/chia-rep_1734756308495/work INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as CC=x86_64-apple-darwin13.4.0-clang CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/chia-rep-3.1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/chia-rep-3.1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool @@ -36,17 +34,16 @@ log: |- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang OTOOL=x86_64-apple-darwin13.4.0-otool - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/chia-rep_1717683959380/work/conda_build.sh']' returned non-zero exit status 1. PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -64,41 +61,44 @@ log: |- CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/chia-rep-3.1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/chia-rep-3.1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - Using pip 24.0 from $PREFIX/lib/python3.11/site-packages/pip (python 3.11) + Using pip 24.3.1 from $PREFIX/lib/python3.12/site-packages/pip (python 3.12) Non-user install because user site-packages disabled Ignoring indexes: https://pypi.org/simple - Created temporary directory: /private/tmp/pip-build-tracker-el8qa0rn - Initialized build tracking at /private/tmp/pip-build-tracker-el8qa0rn - Created build tracker: /private/tmp/pip-build-tracker-el8qa0rn - Entered build tracker: /private/tmp/pip-build-tracker-el8qa0rn - Created temporary directory: /private/tmp/pip-install-19ejc1lj - Created temporary directory: /private/tmp/pip-ephem-wheel-cache-h_bxkjw_ + Created temporary directory: /private/tmp/pip-build-tracker-inbuixg9 + Initialized build tracking at /private/tmp/pip-build-tracker-inbuixg9 + Created build tracker: /private/tmp/pip-build-tracker-inbuixg9 + Entered build tracker: /private/tmp/pip-build-tracker-inbuixg9 + Created temporary directory: /private/tmp/pip-install-6jcga18q + Created temporary directory: /private/tmp/pip-ephem-wheel-cache-va_s5w6w Processing $SRC_DIR - Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-el8qa0rn' + Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-inbuixg9' Running setup.py (path:$SRC_DIR/setup.py) egg_info for package from file://$SRC_DIR - Created temporary directory: /private/tmp/pip-pip-egg-info-wh38j9_a + Created temporary directory: /private/tmp/pip-pip-egg-info-qcuxlo8u Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Source in $SRC_DIR has version 3.1.1, which satisfies requirement ChIA-Rep==3.1.1 from file://$SRC_DIR - Removed ChIA-Rep==3.1.1 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-el8qa0rn' - Created temporary directory: /private/tmp/pip-unpack-6k50nkfr + Removed ChIA-Rep==3.1.1 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-inbuixg9' + Created temporary directory: /private/tmp/pip-unpack-_69_1yml Building wheels for collected packages: ChIA-Rep - Created temporary directory: /private/tmp/pip-wheel-b85llgno + Created temporary directory: /private/tmp/pip-wheel-595rdfsm Building wheel for ChIA-Rep (setup.py): started - Destination directory: /private/tmp/pip-wheel-b85llgno + Destination directory: /private/tmp/pip-wheel-595rdfsm Building wheel for ChIA-Rep (setup.py): finished with status 'error' Running setup.py clean for ChIA-Rep Failed to build ChIA-Rep Exception information: Traceback (most recent call last): - File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + ^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper return func(self, options, args) ^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.11/site-packages/pip/_internal/commands/install.py", line 429, in run + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 434, in run raise InstallationError( - pip._internal.exceptions.InstallationError: Could not build wheels for ChIA-Rep, which is required to install pyproject.toml-based projects - Removed build tracker: '/private/tmp/pip-build-tracker-el8qa0rn' + pip._internal.exceptions.InstallationError: ERROR: Failed to build installable wheels for some pyproject.toml based projects (ChIA-Rep) + Removed build tracker: '/private/tmp/pip-build-tracker-inbuixg9' # Last 100 lines of the build log. diff --git a/recipes/chia-rep/meta.yaml b/recipes/chia-rep/meta.yaml index f9c88f62c885b..4b1fa56755eef 100644 --- a/recipes/chia-rep/meta.yaml +++ b/recipes/chia-rep/meta.yaml @@ -21,6 +21,7 @@ requirements: host: - pip - python + - setuptools run: - numpy >=1.17.0 - pybedgraph >=0.5.40 diff --git a/recipes/chips/build_failure.linux-64.yaml b/recipes/chips/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..3a81efee646cc --- /dev/null +++ b/recipes/chips/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 0d7f248f05d26dd3267b94fea23de94bd77de934f12c372fd5833ffa0b18af2e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + sam.c: In function 'bam_hdr_write': + sam.c:230:5: warning: '__builtin_strncpy' output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] + 230 | strncpy(buf, "BAM\1", 4); + | ^~~~~~~ + cram/cram_io.c: In function 'cram_populate_ref': + cram/cram_io.c:2252:9: warning: '__builtin_strncpy' specified bound 4096 equals destination size [-Wstringop-truncation] + 2252 | strncpy(path, path2, PATH_MAX); + | ^~~~~~~ + cram/cram_io.c:2360:34: warning: '.tmp_' directive writing 5 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] + 2360 | sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t); + | ^~~~~ + cram/cram_io.c:2360:13: note: 'sprintf' output between 11 and 4134 bytes into a destination of size 4096 + 2360 | sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + cram/cram_io.c: In function 'cram_write_SAM_hdr': + cram/cram_io.c:3830:13: warning: '__builtin_strncpy' specified bound 4096 equals destination size [-Wstringop-truncation] + 3830 | strncpy(out, in, PATH_MAX); + | ^~~~~~~ + cram/cram_io.c:3822:9: warning: '__builtin_strncpy' specified bound 4096 equals destination size [-Wstringop-truncation] + 3822 | strncpy(out, in, PATH_MAX); + | ^~~~~~~ + cram/cram_io.c: In function 'cram_dopen': + cram/cram_io.c:4205:9: warning: '__builtin_strncpy' specified bound 20 equals destination size [-Wstringop-truncation] + 4205 | strncpy(def->file_id, filename, 20); + | ^~~~~~~ + hts.c: In function 'hts_idx_init': + hts.c:1201:59: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int' changes value from 'idx->z.last_bin = 4294967295' to '-1' [-Woverflow] + 1201 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; + | ^~~ + sam.c: In function 'bam_hdr_write': + sam.c:230:5: warning: '__builtin_strncpy' output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] + 230 | strncpy(buf, "BAM\1", 4); + | ^~~~~~~ + cram/cram_io.c: In function 'cram_populate_ref': + cram/cram_io.c:2252:9: warning: '__builtin_strncpy' specified bound 4096 equals destination size [-Wstringop-truncation] + 2252 | strncpy(path, path2, PATH_MAX); + | ^~~~~~~ + cram/cram_io.c:2360:34: warning: '.tmp_' directive writing 5 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] + 2360 | sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t); + | ^~~~~ + cram/cram_io.c:2360:13: note: 'sprintf' output between 11 and 4134 bytes into a destination of size 4096 + 2360 | sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + cram/cram_io.c: In function 'cram_write_SAM_hdr': + cram/cram_io.c:3830:13: warning: '__builtin_strncpy' specified bound 4096 equals destination size [-Wstringop-truncation] + 3830 | strncpy(out, in, PATH_MAX); + | ^~~~~~~ + cram/cram_io.c:3822:9: warning: '__builtin_strncpy' specified bound 4096 equals destination size [-Wstringop-truncation] + 3822 | strncpy(out, in, PATH_MAX); + | ^~~~~~~ + cram/cram_io.c: In function 'cram_dopen': + cram/cram_io.c:4205:9: warning: '__builtin_strncpy' specified bound 20 equals destination size [-Wstringop-truncation] + 4205 | strncpy(def->file_id, filename, 20); + | ^~~~~~~ + [ 41%] Performing install step for 'htslib' + [ 44%] Completed 'htslib' + [ 44%] Built target htslib + [ 47%] Building CXX object lib/CMakeFiles/ChIPs.dir/bam_io.cpp.o + In file included from /opt/conda/conda-bld/chips_1734278508007/work/lib/bam_io.h:24, + from /opt/conda/conda-bld/chips_1734278508007/work/lib/bam_io.cpp:5: + /opt/conda/conda-bld/chips_1734278508007/work/lib/common.h:20:72: error: 'std::int32_t' has not been declared + 20 | void RegionParser(const std::string region, std::string& chromID, std::int32_t& start, std::int32_t& end); + | ^~~~~~~ + /opt/conda/conda-bld/chips_1734278508007/work/lib/common.h:20:93: error: 'std::int32_t' has not been declared + 20 | void RegionParser(const std::string region, std::string& chromID, std::int32_t& start, std::int32_t& end); + | ^~~~~~~ + /opt/conda/conda-bld/chips_1734278508007/work/lib/bam_io.h: In member function 'std::string BamHeader::ref_name(int32_t) const': + /opt/conda/conda-bld/chips_1734278508007/work/lib/bam_io.h:416:27: warning: control reaches end of non-void function [-Wreturn-type] + 416 | PrintMessageDieOnError("Invalid reference ID provided to ref_name() function", M_ERROR); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/chips_1734278508007/work/lib/bam_io.h: In member function 'uint32_t BamHeader::ref_length(int32_t) const': + /opt/conda/conda-bld/chips_1734278508007/work/lib/bam_io.h:422:27: warning: control reaches end of non-void function [-Wreturn-type] + 422 | PrintMessageDieOnError("Invalid reference ID provided to ref_length() function", M_ERROR); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + make[2]: *** [lib/CMakeFiles/ChIPs.dir/build.make:79: lib/CMakeFiles/ChIPs.dir/bam_io.cpp.o] Error 1 + make[1]: *** [CMakeFiles/Makefile2:208: lib/CMakeFiles/ChIPs.dir/all] Error 2 + make: *** [Makefile:156: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/chips_1734278508007/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/chips_1734278508007/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/chips/build_failure.osx-64.yaml b/recipes/chips/build_failure.osx-64.yaml index 1ff5dbf4df999..6875136878381 100644 --- a/recipes/chips/build_failure.osx-64.yaml +++ b/recipes/chips/build_failure.osx-64.yaml @@ -1,24 +1,39 @@ -recipe_sha: 650459837761454ad8f1f51856ed5a78655cf6ce77f1b0f17bc480c003baa934 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 0d7f248f05d26dd3267b94fea23de94bd77de934f12c372fd5833ffa0b18af2e # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- +log: |2- + - zlib + - libzlib >=1.3.1,<2.0a0 + test: + commands: + - chips --version + about: + home: https://github.com/gymreklab/chips + license: GNU General Public License v3.0 + summary: ChIPs is a tool for simulating ChIP-sequencing experiments. + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/chips_1734250349300/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/chips_1734250349300/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/chips_1734250349300/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/chips_1734250349300/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/chips-2.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/chips_1717631135898/work/conda_build.sh']' returned non-zero exit status 2. + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/chips-2.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool @@ -27,7 +42,7 @@ log: |- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -36,7 +51,7 @@ log: |- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -54,8 +69,8 @@ log: |- CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/chips-2.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/chips-2.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - -- The C compiler identification is Clang 16.0.6 - -- The CXX compiler identification is Clang 16.0.6 + -- The C compiler identification is Clang 18.1.8 + -- The CXX compiler identification is Clang 18.1.8 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped @@ -66,7 +81,7 @@ log: |- -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done - -- Configuring done (1.4s) + -- Configuring done (2.0s) -- Generating done (0.0s) -- Build files have been written to: $SRC_DIR/build [ 2%] Creating directories for 'zlib' @@ -86,19 +101,4 @@ log: |- Checking for return value of vsnprintf()... Yes. Checking for attribute(visibility) support... No. [ 16%] Performing build step for 'zlib' - [ 19%] Performing install step for 'zlib' - -- zlib install command succeeded. See also $SRC_DIR/build/thirdparty/zlib/src/zlib-stamp/zlib-install-*.log - [ 22%] Completed 'zlib' - [ 22%] Built target zlib - [ 25%] Creating directories for 'htslib' - [ 27%] Performing download step (git clone) for 'htslib' - -- htslib download command succeeded. See also $SRC_DIR/build/thirdparty/htslib/src/htslib-stamp/htslib-download-*.log - [ 30%] No update step for 'htslib' - [ 33%] No patch step for 'htslib' - [ 36%] No configure step for 'htslib' - [ 38%] Performing build step for 'htslib' - [ 41%] Performing install step for 'htslib' - [ 44%] Completed 'htslib' - [ 44%] Built target htslib - [ 47%] Building CXX object lib/CMakeFiles/ChIPs.dir/bam_io.cpp.o # Last 100 lines of the build log. diff --git a/recipes/chips/meta.yaml b/recipes/chips/meta.yaml index 225760c303b73..dc3d0575e32c2 100644 --- a/recipes/chips/meta.yaml +++ b/recipes/chips/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 66577a898cb07986aab27124d748e146cb4c79a01694ce2e073ae45f2ff37ce0 build: - number: 7 + number: 8 requirements: build: diff --git a/recipes/chopper/build_failure.linux-64.yaml b/recipes/chopper/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..8aa241df67959 --- /dev/null +++ b/recipes/chopper/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 33be8f5fc5cb11d07737baeb2158f2e8d9bc8db95983e335d4d49edef523027d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + Running rustc --crate-name clap_derive --edition=2021 /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/clap_derive-4.5.18/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type proc-macro --emit=dep-info,link -C prefer-dynamic -C embed-bitcode=no --warn=rust_2018_idioms '--warn=clippy::zero_sized_map_values' '--warn=clippy::verbose_file_reads' --warn=unused_qualifications --warn=unused_macro_rules --warn=unused_lifetimes --warn=unsafe_op_in_unsafe_fn --warn=unreachable_pub '--warn=clippy::trait_duplication_in_bounds' '--warn=clippy::todo' '--warn=clippy::string_lit_as_bytes' '--warn=clippy::string_add_assign' '--warn=clippy::semicolon_if_nothing_returned' '--warn=clippy::self_named_module_files' '--warn=clippy::same_functions_in_if_condition' '--warn=clippy::rest_pat_in_fully_bound_structs' '--warn=clippy::ref_option_ref' '--warn=clippy::redundant_feature_names' '--warn=clippy::rc_mutex' '--warn=clippy::ptr_as_ptr' '--warn=clippy::path_buf_push_overwrite' '--warn=clippy::negative_feature_names' '--warn=clippy::needless_for_each' '--warn=clippy::needless_continue' '--warn=clippy::mutex_integer' '--allow=clippy::multiple_bound_locations' '--warn=clippy::mem_forget' '--warn=clippy::macro_use_imports' '--warn=clippy::lossy_float_literal' '--warn=clippy::linkedlist' '--allow=clippy::let_and_return' '--warn=clippy::large_types_passed_by_value' '--warn=clippy::large_stack_arrays' '--warn=clippy::large_digit_groups' '--warn=clippy::invalid_upcast_comparisons' '--warn=clippy::infinite_loop' '--warn=clippy::inefficient_to_string' '--warn=clippy::inconsistent_struct_constructor' '--warn=clippy::imprecise_flops' '--warn=clippy::implicit_clone' '--allow=clippy::if_same_then_else' '--warn=clippy::from_iter_instead_of_collect' '--warn=clippy::fn_params_excessive_bools' '--warn=clippy::float_cmp_const' '--warn=clippy::flat_map_option' '--warn=clippy::filter_map_next' '--warn=clippy::fallible_impl_from' '--warn=clippy::explicit_into_iter_loop' '--warn=clippy::explicit_deref_methods' '--warn=clippy::expl_impl_clone_on_copy' '--warn=clippy::enum_glob_use' '--warn=clippy::empty_enum' '--warn=clippy::doc_markdown' '--warn=clippy::debug_assert_with_mut_call' '--warn=clippy::dbg_macro' '--warn=clippy::create_dir' '--allow=clippy::collapsible_else_if' '--warn=clippy::checked_conversions' '--allow=clippy::branches_sharing_code' '--allow=clippy::bool_assert_comparison' '--allow=clippy::blocks_in_conditions' '--allow=clippy::assigning_clones' -C debug-assertions=off --cfg 'feature="default"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("debug", "default", "deprecated", "raw-deprecated", "unstable-v5"))' -C metadata=3c51296092a51781 -C extra-filename=-3c51296092a51781 --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --extern heck=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libheck-979f00b12e8e0081.rlib --extern proc_macro2=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libproc_macro2-e9917080d209ed18.rlib --extern quote=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libquote-fb1f1222afc14bf4.rlib --extern syn=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libsyn-7430f5c12699267b.rlib --extern proc_macro --cap-lints allow + Compiling ndarray v0.15.6 + Running rustc --crate-name ndarray --edition=2018 /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/ndarray-0.15.6/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("approx", "approx-0_5", "blas", "cblas-sys", "default", "docs", "libc", "matrixmultiply-threading", "rayon", "rayon_", "serde", "serde-1", "std", "test"))' -C metadata=5351b9344728f933 -C extra-filename=-5351b9344728f933 --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --extern matrixmultiply=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libmatrixmultiply-1c512f4fb6cda23b.rmeta --extern num_complex=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libnum_complex-46efe7a5a0910605.rmeta --extern num_integer=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libnum_integer-fc9f7b7015fd54df.rmeta --extern num_traits=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libnum_traits-aecc12c36341049b.rmeta --extern rawpointer=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/librawpointer-ea8d03b434d7967d.rmeta --cap-lints allow + Compiling ordered-float v3.9.2 + Running rustc --crate-name ordered_float --edition=2021 /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/ordered-float-3.9.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("arbitrary", "bytemuck", "default", "proptest", "rand", "randtest", "rkyv", "rkyv_16", "rkyv_32", "rkyv_64", "rkyv_ck", "schemars", "serde", "speedy", "std"))' -C metadata=cb78bea52bcfa3a2 -C extra-filename=-cb78bea52bcfa3a2 --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --extern num_traits=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libnum_traits-aecc12c36341049b.rmeta --cap-lints allow + Compiling itertools-num v0.1.3 + Running rustc --crate-name itertools_num --edition=2015 /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/itertools-num-0.1.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=1f8b4515fa815d82 -C extra-filename=-1f8b4515fa815d82 --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --extern num_traits=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libnum_traits-aecc12c36341049b.rmeta --cap-lints allow + Compiling fxhash v0.2.1 + Running rustc --crate-name fxhash --edition=2015 /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/fxhash-0.2.1/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=9cb90fd7e09b01a5 -C extra-filename=-9cb90fd7e09b01a5 --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --extern byteorder=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libbyteorder-b4135b9eba9ebb4c.rmeta --cap-lints allow + Compiling crc32fast v1.4.2 + Running rustc --crate-name crc32fast --edition=2015 /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/crc32fast-1.4.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "nightly", "std"))' -C metadata=3c04bbc78c497618 -C extra-filename=-3c04bbc78c497618 --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --extern cfg_if=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libcfg_if-683714872c84c8c9.rmeta --cap-lints allow + Compiling editdistancek v1.0.2 + Running rustc --crate-name editdistancek --edition=2018 /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/editdistancek-1.0.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=fbcabf80324f8ce3 -C extra-filename=-fbcabf80324f8ce3 --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --cap-lints allow + Compiling strum v0.25.0 + Running rustc --crate-name strum --edition=2018 /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/strum-0.25.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "derive", "phf", "std", "strum_macros"))' -C metadata=443eb9375e87b0d5 -C extra-filename=-443eb9375e87b0d5 --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --cap-lints allow + Compiling custom_derive v0.1.7 + Running rustc --crate-name custom_derive --edition=2015 /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/custom_derive-0.1.7/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "std"))' -C metadata=4d2d6eed4a82340f -C extra-filename=-4d2d6eed4a82340f --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --cap-lints allow + Compiling triple_accel v0.4.0 + Running rustc --crate-name triple_accel --edition=2018 /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/triple_accel-0.4.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="jewel-16bit"' --cfg 'feature="jewel-32bit"' --cfg 'feature="jewel-8bit"' --cfg 'feature="jewel-avx"' --cfg 'feature="jewel-sse"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("debug", "default", "jewel-16bit", "jewel-32bit", "jewel-8bit", "jewel-avx", "jewel-sse"))' -C metadata=3765e75a5345b6e9 -C extra-filename=-3765e75a5345b6e9 --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --cap-lints allow + Compiling clap v4.5.23 + Running rustc --crate-name clap --edition=2021 /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/clap-4.5.23/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --warn=rust_2018_idioms '--warn=clippy::zero_sized_map_values' '--warn=clippy::verbose_file_reads' --warn=unused_qualifications --warn=unused_macro_rules --warn=unused_lifetimes --warn=unsafe_op_in_unsafe_fn --warn=unreachable_pub '--warn=clippy::uninlined_format_args' '--warn=clippy::trait_duplication_in_bounds' '--warn=clippy::todo' '--warn=clippy::string_lit_as_bytes' '--warn=clippy::string_add_assign' '--warn=clippy::semicolon_if_nothing_returned' '--warn=clippy::self_named_module_files' '--warn=clippy::same_functions_in_if_condition' '--warn=clippy::rest_pat_in_fully_bound_structs' '--warn=clippy::ref_option_ref' '--warn=clippy::redundant_feature_names' '--warn=clippy::rc_mutex' '--warn=clippy::ptr_as_ptr' '--warn=clippy::path_buf_push_overwrite' '--warn=clippy::negative_feature_names' '--warn=clippy::needless_for_each' '--warn=clippy::needless_continue' '--warn=clippy::mutex_integer' '--allow=clippy::multiple_bound_locations' '--warn=clippy::mem_forget' '--warn=clippy::macro_use_imports' '--warn=clippy::lossy_float_literal' '--warn=clippy::linkedlist' '--allow=clippy::let_and_return' '--warn=clippy::large_types_passed_by_value' '--warn=clippy::large_stack_arrays' '--warn=clippy::large_digit_groups' '--warn=clippy::invalid_upcast_comparisons' '--warn=clippy::infinite_loop' '--warn=clippy::inefficient_to_string' '--warn=clippy::inconsistent_struct_constructor' '--warn=clippy::imprecise_flops' '--warn=clippy::implicit_clone' '--allow=clippy::if_same_then_else' '--warn=clippy::from_iter_instead_of_collect' '--warn=clippy::fn_params_excessive_bools' '--warn=clippy::float_cmp_const' '--warn=clippy::flat_map_option' '--warn=clippy::filter_map_next' '--warn=clippy::fallible_impl_from' '--warn=clippy::explicit_into_iter_loop' '--warn=clippy::explicit_deref_methods' '--warn=clippy::expl_impl_clone_on_copy' '--warn=clippy::enum_glob_use' '--warn=clippy::empty_enum' '--warn=clippy::doc_markdown' '--warn=clippy::debug_assert_with_mut_call' '--warn=clippy::dbg_macro' '--warn=clippy::create_dir' '--allow=clippy::collapsible_else_if' '--warn=clippy::checked_conversions' '--allow=clippy::branches_sharing_code' '--allow=clippy::bool_assert_comparison' '--allow=clippy::blocks_in_conditions' '--allow=clippy::assigning_clones' --cfg 'feature="color"' --cfg 'feature="default"' --cfg 'feature="derive"' --cfg 'feature="error-context"' --cfg 'feature="help"' --cfg 'feature="std"' --cfg 'feature="suggestions"' --cfg 'feature="usage"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("cargo", "color", "debug", "default", "deprecated", "derive", "env", "error-context", "help", "std", "string", "suggestions", "unicode", "unstable-derive-ui-tests", "unstable-doc", "unstable-ext", "unstable-styles", "unstable-v5", "usage", "wrap_help"))' -C metadata=85ce0993a3b9339d -C extra-filename=-85ce0993a3b9339d --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --extern clap_builder=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libclap_builder-a8077789310e7622.rmeta --extern clap_derive=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libclap_derive-3c51296092a51781.so --cap-lints allow + Compiling bzip2 v0.4.4 + Running rustc --crate-name bzip2 --edition=2015 /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/bzip2-0.4.4/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("futures", "static", "tokio", "tokio-io"))' -C metadata=02b8363a7a85fe31 -C extra-filename=-02b8363a7a85fe31 --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --extern bzip2_sys=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libbzip2_sys-62c8d3759288138f.rmeta --extern libc=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/liblibc-f6fe57662dfc7b71.rmeta --cap-lints allow -L native=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/build/bzip2-sys-fa68d6239c55597b/out/lib + Compiling rayon v1.10.0 + Running rustc --crate-name rayon --edition=2021 /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/rayon-1.10.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("web_spin_lock"))' -C metadata=f976b6e166665c12 -C extra-filename=-f976b6e166665c12 --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --extern either=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libeither-badc83b027c1d302.rmeta --extern rayon_core=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/librayon_core-3c6570c2ea05ef67.rmeta --cap-lints allow + Compiling bio v1.6.0 + Running rustc --crate-name bio --edition=2018 /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/bio-1.6.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("generic-simd", "pest", "pest_derive", "phylogeny", "runtime-dispatch-simd"))' -C metadata=926db6b09a7657d1 -C extra-filename=-926db6b09a7657d1 --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --extern anyhow=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libanyhow-2cb14037eccbaced.rmeta --extern approx=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libapprox-4aba898dd4c68aff.rmeta --extern bio_types=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libbio_types-2d956a0846d80488.rmeta --extern bit_set=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libbit_set-19e680abf55007dc.rmeta --extern bv=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libbv-880a06d48baf80f7.rmeta --extern bytecount=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libbytecount-15c03ca67af35581.rmeta --extern csv=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libcsv-e5e02ca7c1055849.rmeta --extern custom_derive=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libcustom_derive-4d2d6eed4a82340f.rmeta --extern editdistancek=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libeditdistancek-fbcabf80324f8ce3.rmeta --extern enum_map=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libenum_map-4b3a6b3611d6a57c.rmeta --extern fxhash=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libfxhash-9cb90fd7e09b01a5.rmeta --extern itertools=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libitertools-1ef76896f423c2c2.rmeta --extern itertools_num=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libitertools_num-1f8b4515fa815d82.rmeta --extern lazy_static=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/liblazy_static-5690c89ce0b7662a.rmeta --extern multimap=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libmultimap-bcd1edd7a265488c.rmeta --extern ndarray=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libndarray-5351b9344728f933.rmeta --extern newtype_derive=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libnewtype_derive-5d9e9cf2d1b29ac9.rmeta --extern num_integer=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libnum_integer-fc9f7b7015fd54df.rmeta --extern num_traits=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libnum_traits-aecc12c36341049b.rmeta --extern ordered_float=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libordered_float-cb78bea52bcfa3a2.rmeta --extern petgraph=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libpetgraph-99728980c20db1d9.rmeta --extern rand=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/librand-a22306bd3b1bc1c7.rmeta --extern regex=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libregex-8c520ba8846f7e23.rmeta --extern serde=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libserde-34fb06d9d6b84375.rmeta --extern serde_derive=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libserde_derive-45ca93f2c89efa2c.so --extern statrs=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libstatrs-b11802cc84b7aa6a.rmeta --extern strum=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libstrum-443eb9375e87b0d5.rmeta --extern strum_macros=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libstrum_macros-c3411f79c4c99557.so --extern thiserror=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libthiserror-69e9c34a71a684a9.rmeta --extern triple_accel=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libtriple_accel-3765e75a5345b6e9.rmeta --extern vec_map=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libvec_map-0aabd4c879ba795a.rmeta --cap-lints allow + Compiling minimap2 v0.1.22minimap2.2.28 + Running rustc --crate-name minimap2 --edition=2021 /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/minimap2-0.1.22minimap2.2.28/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="map-file"' --cfg 'feature="needletail"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("curl", "default", "htslib", "map-file", "needletail", "rust-htslib", "simde", "sse2only", "static", "zlib-ng"))' -C metadata=0d643049d1b9c0e5 -C extra-filename=-0d643049d1b9c0e5 --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --extern libc=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/liblibc-f6fe57662dfc7b71.rmeta --extern minimap2_sys=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libminimap2_sys-5e2d230906204733.rlib --extern needletail=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libneedletail-d1b29b2845affdbe.rlib --cap-lints allow -L native=/opt/conda/conda-bld/chopper_1734294765053/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/build/minimap2-sys-8437993c0454b95b/out -L native=/opt/conda/conda-bld/chopper_1734294765053/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling xz2 v0.1.7 + Running rustc --crate-name xz2 --edition=2018 /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/xz2-0.1.7/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("futures", "static", "tokio", "tokio-io"))' -C metadata=106b4f6396a89bba -C extra-filename=-106b4f6396a89bba --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --extern lzma_sys=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/liblzma_sys-1761da3f033211b8.rmeta --cap-lints allow -L native=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/build/lzma-sys-255232585765aa46/out + Compiling atty v0.2.14 + Running rustc --crate-name atty --edition=2015 /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/atty-0.2.14/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=29a9a4292baffbe6 -C extra-filename=-29a9a4292baffbe6 --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --extern libc=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/liblibc-f6fe57662dfc7b71.rmeta --cap-lints allow + Running rustc --crate-name libz_ng_sys --edition=2018 /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/libz-ng-sys-1.1.20/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --warn=unexpected_cfgs --check-cfg 'cfg(zng)' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=b50f117159997fef -C extra-filename=-b50f117159997fef --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --extern libc=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/liblibc-f6fe57662dfc7b71.rmeta --cap-lints allow -L native=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/build/libz-ng-sys-194ac4a0836cc10b/out/lib -L native=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/build/libz-ng-sys-194ac4a0836cc10b/out/lib64 -l static=z-ng --cfg zng + Compiling flate2 v1.0.35 + Running rustc --crate-name flate2 --edition=2018 /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/flate2-1.0.35/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="any_impl"' --cfg 'feature="any_zlib"' --cfg 'feature="libz-ng-sys"' --cfg 'feature="zlib-ng"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("any_impl", "any_zlib", "cloudflare-zlib-sys", "cloudflare_zlib", "default", "libz-ng-sys", "libz-rs-sys", "libz-sys", "miniz-sys", "miniz_oxide", "rust_backend", "zlib", "zlib-default", "zlib-ng", "zlib-ng-compat", "zlib-rs"))' -C metadata=68aede372e79f8d5 -C extra-filename=-68aede372e79f8d5 --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --extern crc32fast=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libcrc32fast-3c04bbc78c497618.rmeta --extern libz_ng_sys=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/liblibz_ng_sys-b50f117159997fef.rmeta --cap-lints allow -L native=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/build/libz-ng-sys-194ac4a0836cc10b/out/lib -L native=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/build/libz-ng-sys-194ac4a0836cc10b/out/lib64 + Compiling chopper v0.8.0 (/opt/conda/conda-bld/chopper_1734294765053/work) + Running rustc --crate-name chopper --edition=2021 src/main.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=a8f4db360a65092c -C extra-filename=-a8f4db360a65092c --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --extern approx=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libapprox-4aba898dd4c68aff.rlib --extern atty=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libatty-29a9a4292baffbe6.rlib --extern bio=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libbio-926db6b09a7657d1.rlib --extern bzip2=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libbzip2-02b8363a7a85fe31.rlib --extern clap=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libclap-85ce0993a3b9339d.rlib --extern flate2=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libflate2-68aede372e79f8d5.rlib --extern minimap2=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libminimap2-0d643049d1b9c0e5.rlib --extern rayon=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/librayon-f976b6e166665c12.rlib --extern xz2=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libxz2-106b4f6396a89bba.rlib -L native=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/build/bzip2-sys-fa68d6239c55597b/out/lib -L native=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/build/libz-ng-sys-194ac4a0836cc10b/out/lib -L native=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/build/libz-ng-sys-194ac4a0836cc10b/out/lib64 -L native=/opt/conda/conda-bld/chopper_1734294765053/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/build/minimap2-sys-8437993c0454b95b/out -L native=/opt/conda/conda-bld/chopper_1734294765053/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/build/lzma-sys-255232585765aa46/out + error[E0107]: missing generics for struct minimap2::Aligner + --> src/main.rs:235:71 + | + 235 | fn setup_contamination_filter(contam_fasta: &str, threads: &usize) -> Aligner { + | ^^^^^^^ expected 1 generic argument + | + note: struct defined here, with 1 generic parameter: S + --> /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/minimap2-0.1.22minimap2.2.28/src/lib.rs:300:12 + | + 300 | pub struct Aligner { + | ^^^^^^^ - + help: add missing generic argument + | + 235 | fn setup_contamination_filter(contam_fasta: &str, threads: &usize) -> Aligner { + | + + error[E0107]: missing generics for struct minimap2::Aligner + --> src/main.rs:246:47 + | + 246 | fn is_contamination(readseq: &&[u8], contam: &Aligner) -> bool { + | ^^^^^^^ expected 1 generic argument + | + note: struct defined here, with 1 generic parameter: S + --> /opt/conda/conda-bld/chopper_1734294765053/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/minimap2-0.1.22minimap2.2.28/src/lib.rs:300:12 + | + 300 | pub struct Aligner { + | ^^^^^^^ - + help: add missing generic argument + | + 246 | fn is_contamination(readseq: &&[u8], contam: &Aligner) -> bool { + | + + For more information about this error, try rustc --explain E0107. + error: could not compile chopper (bin "chopper") due to 2 previous errors + + Caused by: + process didn't exit successfully: rustc --crate-name chopper --edition=2021 src/main.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=a8f4db360a65092c -C extra-filename=-a8f4db360a65092c --out-dir /opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps -C linker=/opt/conda/conda-bld/chopper_1734294765053/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps --extern approx=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libapprox-4aba898dd4c68aff.rlib --extern atty=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libatty-29a9a4292baffbe6.rlib --extern bio=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libbio-926db6b09a7657d1.rlib --extern bzip2=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libbzip2-02b8363a7a85fe31.rlib --extern clap=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libclap-85ce0993a3b9339d.rlib --extern flate2=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libflate2-68aede372e79f8d5.rlib --extern minimap2=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libminimap2-0d643049d1b9c0e5.rlib --extern rayon=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/librayon-f976b6e166665c12.rlib --extern xz2=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/deps/libxz2-106b4f6396a89bba.rlib -L native=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/build/bzip2-sys-fa68d6239c55597b/out/lib -L native=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/build/libz-ng-sys-194ac4a0836cc10b/out/lib -L native=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/build/libz-ng-sys-194ac4a0836cc10b/out/lib64 -L native=/opt/conda/conda-bld/chopper_1734294765053/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/build/minimap2-sys-8437993c0454b95b/out -L native=/opt/conda/conda-bld/chopper_1734294765053/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/chopper_1734294765053/work/target/release/build/lzma-sys-255232585765aa46/out (exit status: 1) + error: failed to compile chopper v0.8.0 (/opt/conda/conda-bld/chopper_1734294765053/work), intermediate artifacts can be found at /opt/conda/conda-bld/chopper_1734294765053/work/target. + To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/chopper_1734294765053/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/chopper_1734294765053/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/sherpas/build_failure.osx-64.yaml b/recipes/chopper/build_failure.osx-64.yaml similarity index 54% rename from recipes/sherpas/build_failure.osx-64.yaml rename to recipes/chopper/build_failure.osx-64.yaml index 63f24e877b930..0fb33f87c2106 100644 --- a/recipes/sherpas/build_failure.osx-64.yaml +++ b/recipes/chopper/build_failure.osx-64.yaml @@ -1,48 +1,72 @@ -recipe_sha: 907b6b2ddd7284dea8ef850273c030b75e9184a3f0c59429f0cb37574450168e # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 33be8f5fc5cb11d07737baeb2158f2e8d9bc8db95983e335d4d49edef523027d # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - [[ RA-MD1LOVE ]] - [[ patch ]] - - Key: +log: |2- + - libclang-cpp19.1 19.1.5 default_h3571c67_0 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + - clang-19 19.1.5 default_h3571c67_0 + - clang 19.1.5 default_h576c50e_0 + run: + - zlib + - libzlib >=1.3.1,<2.0a0 + - clang + - libcxx >=18 + run_constrained: + - __osx >=10.13 + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/chopper_1734297738944/work/conda_build.sh']' returned non-zero exit status 101. - R :: Reversible A :: Applicable - Y :: Build-prefix patch in use M :: Minimal, non-amalgamated - D :: Dry-runnable N :: Patch level (1 is preferred) - L :: Patch level not-ambiguous O :: Patch applies without offsets - V :: Patch applies without fuzz E :: Patch applies without emitting to stderr + The above exception was the direct cause of the following exception: - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/sherpas_1717513246162/work + Traceback (most recent call last): + test: + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + commands: + - chopper --help + about: + dev_url: https://github.com/wdecoster/chopper + doc_url: https://github.com/wdecoster/chopper#readme + home: https://github.com/wdecoster/chopper + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + license: MIT + license_file: LICENSE + notes: 'includes native support for Apple Silicon (M1/M2/M3) processors + + ' + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/sherpas_1717513246162/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/sherpas_1717513246162/_build_env - raise subprocess.CalledProcessError(proc.returncode, _args) - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/sherpas_1717513246162/work + summary: A rust command line for filtering and trimming long reads. + extra: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/chopper_1734297738944/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/chopper_1734297738944/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/chopper_1734297738944/work/conda_build.sh']' returned non-zero exit status 101. + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/chopper_1734297738944/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/chopper_1734297738944/work INFO: activate_clang_osx-64.sh made the following environmental changes: - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/sherpas_1717513246162/work/conda_build.sh']' returned non-zero exit status 2. AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as CC=x86_64-apple-darwin13.4.0-clang CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sherpas-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/chopper-0.9.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sherpas-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/chopper-0.9.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool LD=x86_64-apple-darwin13.4.0-ld @@ -50,7 +74,7 @@ log: |- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -59,7 +83,7 @@ log: |- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -74,31 +98,9 @@ log: |- INFO: activate_clangxx_osx-64.sh made the following environmental changes: CLANGXX=x86_64-apple-darwin13.4.0-clang CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sherpas-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/chopper-0.9.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sherpas-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - -- The CXX compiler identification is Clang 16.0.6 - -- Detecting CXX compiler ABI info - -- Detecting CXX compiler ABI info - done - -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped - -- Detecting CXX compile features - -- Detecting CXX compile features - done - -- Hash map option: USE_TSL_HOPSCOTCH_MAP - -- The C compiler identification is Clang 16.0.6 - -- Detecting C compiler ABI info - -- Detecting C compiler ABI info - done - -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped - -- Detecting C compile features - -- Detecting C compile features - done - -- Found Boost: $PREFIX/lib/cmake/Boost-1.85.0/BoostConfig.cmake (found version "1.85.0") found components: serialization iostreams - -- Found Boost: $PREFIX/lib/cmake/Boost-1.85.0/BoostConfig.cmake (found version "1.85.0") found components: filesystem - -- Found Boost: $PREFIX/lib/cmake/Boost-1.85.0/BoostConfig.cmake (found version "1.85.0") found components: filesystem iostreams - -- Found Boost: $PREFIX/lib/cmake/Boost-1.85.0/BoostConfig.cmake (found version "1.85.0") found components: iostreams - -- Found Boost: $PREFIX/lib/cmake/Boost-1.85.0/BoostConfig.cmake (found version "1.85.0") found components: filesystem iostreams - -- Configuring done (2.3s) - -- Generating done (0.3s) - -- Build files have been written to: $SRC_DIR - $SRC_DIR/release-build $SRC_DIR - [ 6%] Building CXX object lib/xpas/utils/CMakeFiles/utils.dir/src/utils/io/file_io.cpp.o - [ 12%] Building CXX object lib/xpas/utils/CMakeFiles/utils.dir/src/utils/io/fasta.cpp.o + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/chopper-0.9.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix # Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/chopper/meta.yaml b/recipes/chopper/meta.yaml index a044b5c8ae375..969d149d29134 100644 --- a/recipes/chopper/meta.yaml +++ b/recipes/chopper/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('chopper', max_pin="x.x") }} diff --git a/recipes/chromap/meta.yaml b/recipes/chromap/meta.yaml index e20cbea5fa14f..36c49d0057f1c 100644 --- a/recipes/chromap/meta.yaml +++ b/recipes/chromap/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('chromap', max_pin="x.x") }} diff --git a/recipes/chromeister/meta.yaml b/recipes/chromeister/meta.yaml index 7f6a5846aa988..5d9bbab21ed0a 100644 --- a/recipes/chromeister/meta.yaml +++ b/recipes/chromeister/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/chromimpute/meta.yaml b/recipes/chromimpute/meta.yaml index 7833648bc3923..0b1faca2aad24 100644 --- a/recipes/chromimpute/meta.yaml +++ b/recipes/chromimpute/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 noarch: generic source: diff --git a/recipes/chromsize/meta.yaml b/recipes/chromsize/meta.yaml index e28195bb187a3..ca2c68a452b0b 100644 --- a/recipes/chromsize/meta.yaml +++ b/recipes/chromsize/meta.yaml @@ -10,7 +10,7 @@ source: sha256: e0358a7a36a74b24b8cbb9034b8060de90d1af867baa66bc093192df9734bd40 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('chromsize', max_pin="x.x") }} diff --git a/recipes/circminer/meta.yaml b/recipes/circminer/meta.yaml index 82ba53093f258..97297efe39e42 100644 --- a/recipes/circminer/meta.yaml +++ b/recipes/circminer/meta.yaml @@ -26,7 +26,7 @@ source: sha256: {{ logger_sha256 }} build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/clair3-illumina/meta.yaml b/recipes/clair3-illumina/meta.yaml index 22db4a4e6d969..7618810608c8c 100644 --- a/recipes/clair3-illumina/meta.yaml +++ b/recipes/clair3-illumina/meta.yaml @@ -10,7 +10,7 @@ source: sha256: e8114dec1ef768d5ecdbf3b0734f41c69c95fee543d999b841bd6bfb8be64ea8 build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/clair3-trio/meta.yaml b/recipes/clair3-trio/meta.yaml index 7ac1658755bff..f5f5052715abb 100644 --- a/recipes/clair3-trio/meta.yaml +++ b/recipes/clair3-trio/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 0ce6c0ebd0db1c7fb9e0a0ecd39d7bdf54ec15de2c1c1a77ec54448141057b63 build: - number: 1 + number: 2 skip: True # [osx] requirements: diff --git a/recipes/clair3/meta.yaml b/recipes/clair3/meta.yaml index 6fe7acdc26c4d..faf5bac1148c1 100644 --- a/recipes/clair3/meta.yaml +++ b/recipes/clair3/meta.yaml @@ -10,7 +10,7 @@ source: sha256: b2de8180d3825f9e1ed4ee1710ce0988dd85eba79ab8bdaf2ad8dae7ac70e228 build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/clan/build_failure.linux-64.yaml b/recipes/clan/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..7a667a4a532e0 --- /dev/null +++ b/recipes/clan/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 9a0e69dfe9c40d658f977343def961792a01054967e333e7c997c3f24becb73a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + | ^~~~~~~~~~ + kmer_unitcoder.cc:26:15: error: expected ';' before 'foo' + 26 | KmerUnitType foo = (KmerUnitType) mer_len_; + | ^~~~ + | ; + kmer_unitcoder.cc:27:29: error: 'foo' was not declared in this scope + 27 | signature_ = signature_ | foo; + | ^~~ + kmer_unitcoder.cc: In member function 'void KmerUnitcoder::CkValid()': + kmer_unitcoder.cc:37:39: error: 'KmerUnitType' was not declared in this scope; did you mean 'KmerUnitcoder'? + 37 | if(num_bit_ * mer_len_ > 8 * sizeof(KmerUnitType)) { + | ^~~~~~~~~~~~ + | KmerUnitcoder + kmer_unitcoder.cc: At global scope: + kmer_unitcoder.cc:44:1: error: 'KmerUnitType' does not name a type; did you mean 'KmerUnitcoder'? + 44 | KmerUnitType KmerUnitcoder::Encode(const char *s) { + | ^~~~~~~~~~~~ + | KmerUnitcoder + kmer_unitcoder.cc:75:13: error: 'std::string KmerUnitcoder::Decode' is not a static data member of 'class KmerUnitcoder' + 75 | std::string KmerUnitcoder::Decode(KmerUnitType ek) { + | ^~~~~~~~~~~~~ + kmer_unitcoder.cc:75:35: error: 'KmerUnitType' was not declared in this scope; did you mean 'KmerUnitcoder'? + 75 | std::string KmerUnitcoder::Decode(KmerUnitType ek) { + | ^~~~~~~~~~~~ + | KmerUnitcoder + kmer_unitcoder.cc:75:53: error: expected ',' or ';' before '{' token + 75 | std::string KmerUnitcoder::Decode(KmerUnitType ek) { + | ^ + kmer_unitcoder.cc:88:1: error: 'KmerUnitType' does not name a type; did you mean 'KmerUnitcoder'? + 88 | KmerUnitType KmerUnitcoder::RightExt(const KmerUnitType ek, const char c) { + | ^~~~~~~~~~~~ + | KmerUnitcoder + kmer_unitcoder.cc:95:1: error: 'KmerUnitType' does not name a type; did you mean 'KmerUnitcoder'? + 95 | KmerUnitType KmerUnitcoder::LeftExt(const KmerUnitType ek, const char c) { + | ^~~~~~~~~~~~ + | KmerUnitcoder + kmer_unitcoder.cc:105:36: error: 'KmerUnitType' does not name a type; did you mean 'KmerUnitcoder'? + 105 | char KmerUnitcoder::HeadChar(const KmerUnitType ek) { + | ^~~~~~~~~~~~ + | KmerUnitcoder + kmer_unitcoder.cc: In member function 'char KmerUnitcoder::HeadChar(int)': + kmer_unitcoder.cc:106:3: error: 'KmerUnitType' was not declared in this scope; did you mean 'KmerUnitcoder'? + 106 | KmerUnitType d = pow(2, num_bit_) - 1; + | ^~~~~~~~~~~~ + | KmerUnitcoder + kmer_unitcoder.cc:107:3: error: 'd' was not declared in this scope + 107 | d = d & (ek >> num_bit_ * (mer_len_ - 1)); + | ^ + kmer_unitcoder.cc: At global scope: + kmer_unitcoder.cc:111:36: error: 'KmerUnitType' does not name a type; did you mean 'KmerUnitcoder'? + 111 | char KmerUnitcoder::TailChar(const KmerUnitType ek) { + | ^~~~~~~~~~~~ + | KmerUnitcoder + kmer_unitcoder.cc: In member function 'char KmerUnitcoder::TailChar(int)': + kmer_unitcoder.cc:112:3: error: 'KmerUnitType' was not declared in this scope; did you mean 'KmerUnitcoder'? + 112 | KmerUnitType d = pow(2, num_bit_) - 1; + | ^~~~~~~~~~~~ + | KmerUnitcoder + kmer_unitcoder.cc:113:3: error: 'd' was not declared in this scope + 113 | d = ek & d; + | ^ + kmer_unitcoder.cc: At global scope: + kmer_unitcoder.cc:117:37: error: 'KmerUnitType' does not name a type; did you mean 'KmerUnitcoder'? + 117 | void KmerUnitcoder::PrintBits(const KmerUnitType ek) { + | ^~~~~~~~~~~~ + | KmerUnitcoder + kmer_unitcoder.cc: In member function 'void KmerUnitcoder::PrintBits(int)': + kmer_unitcoder.cc:118:21: error: 'KmerUnitType' was not declared in this scope; did you mean 'KmerUnitcoder'? + 118 | bitset<8 * sizeof(KmerUnitType)> bek(ek); + | ^~~~~~~~~~~~ + | KmerUnitcoder + kmer_unitcoder.cc:118:34: error: template argument 1 is invalid + 118 | bitset<8 * sizeof(KmerUnitType)> bek(ek); + | ^ + make[1]: *** [Makefile:36: kmer_unitcoder.o] Error 1 + make[1]: Leaving directory '$SRC_DIR/src' + make: *** [Makefile:2: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/clan_1734362526254/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/clan_1734362526254/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/clan/meta.yaml b/recipes/clan/meta.yaml index f60cd65f6e121..189ffb6ef8f65 100644 --- a/recipes/clan/meta.yaml +++ b/recipes/clan/meta.yaml @@ -7,9 +7,11 @@ source: sha256: 302b4734522115daa73665275b514f2290f7efd3d752b94a77cb9254abe3c987 build: - number: 4 + number: 5 skip: True # [osx] - + run_exports: + - {{ pin_subpackage('clan', max_pin="x.x") }} + requirements: build: - make diff --git a/recipes/clark/meta.yaml b/recipes/clark/meta.yaml index 163144f52a7fb..2d476b86de9d3 100644 --- a/recipes/clark/meta.yaml +++ b/recipes/clark/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: http://clark.cs.ucr.edu/Download/CLARKV{{ version }}.tar.gz diff --git a/recipes/classpro/meta.yaml b/recipes/classpro/meta.yaml index fc856a68ba9b6..a1c9f39cd8c85 100644 --- a/recipes/classpro/meta.yaml +++ b/recipes/classpro/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 script: - "mkdir -p $PREFIX/bin" - "cp $SRC_DIR/bin/* $PREFIX/bin/" diff --git a/recipes/clearcut/meta.yaml b/recipes/clearcut/meta.yaml index 3da83e02dcde5..94dcc971aa207 100644 --- a/recipes/clearcut/meta.yaml +++ b/recipes/clearcut/meta.yaml @@ -9,7 +9,7 @@ source: md5: c7c01922d75d5bb6e218d7a9adc72978 build: - number: 6 + number: 7 skip: True # [osx] requirements: diff --git a/recipes/clonalframeml/1.11/build_failure.osx-64.yaml b/recipes/clonalframeml/1.11/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..85c13d3dee20a --- /dev/null +++ b/recipes/clonalframeml/1.11/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 04c71d3fd4df82a2993e0396e1d43d66de1eab9d58f676e02734dcb50dede7a1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/clonalframeml_1733870449011/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + - clangxx_osx-64 18.1.8 h7e5c614_23 + Traceback (most recent call last): + - libcxx-devel 18.1.8 h7c275be_7 + - clang_impl_osx-64 18.1.8 h6a44ed1_23 + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + - openssl 3.4.0 hd471939_0 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + - tapi 1300.6.5 h390ca13_0 + - llvm-tools 18.1.8 h9ce406d_2 + - cctools_osx-64 1010.6 h00edd4c_2 + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/clonalframeml_1733870449011/work/conda_build.sh']' returned non-zero exit status 2. + - clangxx 18.1.8 default_h179603d_5 + - ca-certificates 2024.8.30 h8857fd0_0 + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + host: + - libcxx 19.1.5 hf95d169_0 + run: + - libcxx >=18 + test: + commands: + - ClonalFrameML 2>&1 | grep "ClonalFrameML" + about: + home: https://github.com/xavierdidelot/ClonalFrameML + license: GPLv3 + summary: Efficient inferencing of recombination in bacterial genomes + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/clonalframeml_1733870449011/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/clonalframeml_1733870449011/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/clonalframeml_1733870449011/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/clonalframeml_1733870449011/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/clonalframeml-1.11 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/clonalframeml-1.11 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/clonalframeml-1.11 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/clonalframeml-1.11 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + /bin/echo "#define ClonalFrameML_GITRevision \"git describe --tags\"" > version.h + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/clonalframeml-1.11 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -I./ -I./myutils -I./coalesce -c -o main.o main.cpp +# Last 100 lines of the build log. diff --git a/recipes/clonalframeml/1.11/meta.yaml b/recipes/clonalframeml/1.11/meta.yaml index 47086e5e47ff4..9cbfbfc0c7adf 100644 --- a/recipes/clonalframeml/1.11/meta.yaml +++ b/recipes/clonalframeml/1.11/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.11" build: - number: 6 + number: 7 source: url: https://github.com/xavierdidelot/ClonalFrameML/archive/v1.11.tar.gz diff --git a/recipes/clonalframeml/meta.yaml b/recipes/clonalframeml/meta.yaml index eb47de77ebb1c..aae7201519014 100644 --- a/recipes/clonalframeml/meta.yaml +++ b/recipes/clonalframeml/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('clonalframeml', max_pin="x") }} diff --git a/recipes/cloudspades/meta.yaml b/recipes/cloudspades/meta.yaml index 86a36f47254c5..6179d515777cc 100644 --- a/recipes/cloudspades/meta.yaml +++ b/recipes/cloudspades/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 skip: True # [osx] run_exports: - {{ pin_subpackage('cloudspades', max_pin="x") }} diff --git a/recipes/clustalo/meta.yaml b/recipes/clustalo/meta.yaml index cedb7aded4a1a..a96a062e407b7 100644 --- a/recipes/clustalo/meta.yaml +++ b/recipes/clustalo/meta.yaml @@ -19,7 +19,7 @@ requirements: - argtable2 build: - number: 8 + number: 9 run_exports: - {{ pin_subpackage('clustalo', max_pin="x") }} @@ -34,4 +34,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/clustalw/build_failure.osx-64.yaml b/recipes/clustalw/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..01c731c91660f --- /dev/null +++ b/recipes/clustalw/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 4c2b2e04f384c92f7e9e6f61ff66b80923d2994122fc904248cfecf4d75fccf2 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/clustalw-2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/clustalw-2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + checking build system type... x86_64-apple-darwin13.4.0 + checking host system type... x86_64-apple-darwin13.4.0 + checking target system type... x86_64-apple-darwin13.4.0 + building for darwin13.4.0 + checking for a BSD-compatible install... /usr/bin/install -c + checking whether build environment is sane... yes + checking for a thread-safe mkdir -p... ./install-sh -c -d + checking for gawk... no + checking for mawk... no + checking for nawk... no + checking for awk... awk + checking whether make sets $(MAKE)... yes + checking whether make sets $(MAKE)... (cached) yes + checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang + checking whether the C compiler works... yes + checking for C compiler default output file name... a.out + checking for suffix of executables... + checking whether we are cross compiling... no + checking for suffix of object files... o + checking whether we are using the GNU C compiler... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking for x86_64-apple-darwin13.4.0-clang option to accept ISO C89... none needed + checking for style of include used by make... GNU + checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 + checking whether we are using the GNU C compiler... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 + checking for x86_64-apple-darwin13.4.0-ranlib... x86_64-apple-darwin13.4.0-ranlib + checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang -E + checking for grep that handles long lines and -e... /usr/bin/grep + checking for egrep... /usr/bin/grep -E + checking for ANSI C header files... yes + checking for sys/types.h... yes + checking for sys/stat.h... yes + checking for stdlib.h... yes + checking for string.h... yes + checking for memory.h... yes + checking for strings.h... yes + checking for inttypes.h... yes + checking for stdint.h... yes + checking for unistd.h... yes + checking for stdbool.h that conforms to C99... no + checking for _Bool... no + checking for an ANSI C-conforming const... yes + checking for size_t... yes + checking for stdlib.h... (cached) yes + checking for GNU libc compatible malloc... (cached) yes + configure: creating ./config.status + config.status: creating Makefile + config.status: creating m4/Makefile + config.status: creating src/Makefile + config.status: creating src/clustalw_version.h + config.status: creating src/config.h + config.status: executing depfiles commands + Making install in m4 + make[1]: Entering directory '$SRC_DIR/m4' + make[2]: Entering directory '$SRC_DIR/m4' + make[2]: Nothing to be done for 'install-exec-am'. + test -z "$PREFIX/share/aclocal" || .././install-sh -c -d "$PREFIX/share/aclocal" + make[2]: Leaving directory '$SRC_DIR/m4' + make[1]: Leaving directory '$SRC_DIR/m4' + Making install in src + make[1]: Entering directory '$SRC_DIR/src' + make[2]: Entering directory '$SRC_DIR/src' + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/clustalw-2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT FullPairwiseAlign.o -MD -MP -MF .deps/FullPairwiseAlign.Tpo -c -o FullPairwiseAlign.o test -f './pairwise/FullPairwiseAlign.cpp' || echo './'./pairwise/FullPairwiseAlign.cpp + mv -f .deps/FullPairwiseAlign.Tpo .deps/FullPairwiseAlign.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/clustalw-2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT FastPairwiseAlign.o -MD -MP -MF .deps/FastPairwiseAlign.Tpo -c -o FastPairwiseAlign.o test -f './pairwise/FastPairwiseAlign.cpp' || echo './'./pairwise/FastPairwiseAlign.cpp + mv -f .deps/FastPairwiseAlign.Tpo .deps/FastPairwiseAlign.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/clustalw-2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT MSFFileParser.o -MD -MP -MF .deps/MSFFileParser.Tpo -c -o MSFFileParser.o test -f './fileInput/MSFFileParser.cpp' || echo './'./fileInput/MSFFileParser.cpp + mv -f .deps/MSFFileParser.Tpo .deps/MSFFileParser.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/clustalw-2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT FileReader.o -MD -MP -MF .deps/FileReader.Tpo -c -o FileReader.o test -f './fileInput/FileReader.cpp' || echo './'./fileInput/FileReader.cpp + make[2]: Leaving directory '$SRC_DIR/src' + make[1]: Leaving directory '$SRC_DIR/src' +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/clustalw/meta.yaml b/recipes/clustalw/meta.yaml index 0a24762959d42..bc49e54deddc0 100644 --- a/recipes/clustalw/meta.yaml +++ b/recipes/clustalw/meta.yaml @@ -9,7 +9,7 @@ source: - patch # [osx] build: - number: 10 + number: 11 run_exports: - {{ pin_subpackage('clustalw', max_pin="x.x") }} diff --git a/recipes/cmaple/meta.yaml b/recipes/cmaple/meta.yaml index 9866c9e060621..364a839e3d7d6 100644 --- a/recipes/cmaple/meta.yaml +++ b/recipes/cmaple/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version | replace("-", "_") }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/cmappy/meta.yaml b/recipes/cmappy/meta.yaml index 5c54402bd40e8..0bd41b234d614 100644 --- a/recipes/cmappy/meta.yaml +++ b/recipes/cmappy/meta.yaml @@ -15,7 +15,7 @@ build: - gct2gctx=cmapPy.pandasGEXpress.gct2gctx:main - concat=cmapPy.pandasGEXpress.concat:main - subset=cmapPy.pandasGEXpress.subset:main - number: 7 + number: 8 skip: True # [py<30] script: {{ PYTHON }} -m pip install . --no-deps -vv run_exports: diff --git a/recipes/cmph/meta.yaml b/recipes/cmph/meta.yaml index 49cda688ac31c..fcb826aaec4ca 100644 --- a/recipes/cmph/meta.yaml +++ b/recipes/cmph/meta.yaml @@ -7,7 +7,7 @@ source: url: https://downloads.sourceforge.net/project/cmph/cmph/cmph-2.0.tar.gz build: - number: 6 + number: 7 skip: True # [osx] package: diff --git a/recipes/cnv_facets/build_failure.linux-64.yaml b/recipes/cnv_facets/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..ea7efc85f6187 --- /dev/null +++ b/recipes/cnv_facets/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: d9d8ce6eeff1fd202415b83d7b81c5ed803d967e8f7d07ec06a3f84a816aef2c # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [32mr-base [3.4.1|3.5.1][0m, which can be installed (as previously explained); + [32mr-base [3.5.1|3.6.1|3.6.2][0m would require + [32mgsl >=2.5,<2.6.0a0 [0m, which can be installed; + [32mlibgfortran-ng >=7,<8.0a0 [0m, which can be installed; + [32mr-base 3.5.1[0m would require + [32mgsl >=2.4,<2.5.0a0 [0m, which can be installed; + [32mlibgfortran-ng >=7,<8.0a0 [0m, which can be installed; + [32mr-base 3.5.1[0m would require + [32mkrb5 >=1.16.2,<1.17.0a0 [0m, which can be installed; + [32mlibgfortran-ng >=7,<8.0a0 [0m, which can be installed; + [32mr-base [>=3.4.1,<3.4.2.0a0 |>=3.5.1,<3.5.2.0a0 ][0m with the potential options + [32mr-base 3.4.1[0m, which can be installed; + [32mr-base [3.4.1|3.5.1][0m, which can be installed (as previously explained); + [32mr-base [3.5.1|3.6.1|3.6.2][0m, which can be installed (as previously explained); + [32mr-base 3.5.1[0m, which can be installed (as previously explained); + [32mr-base 3.5.1[0m, which can be installed (as previously explained); + [32mbioconductor-rsamtools 1.34.0[0m would require + [32mbioconductor-biocparallel >=1.16.0,<1.17.0 [0m with the potential options + [32mbioconductor-biocparallel 1.16.2[0m would require + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed (as previously explained); + [32mbioconductor-biocparallel [1.16.2|1.16.6][0m would require + [32mlibgfortran-ng >=7,<8.0a0 [0m, which can be installed; + [32mbioconductor-genomeinfodb >=1.18.0,<1.19.0 [0m, which requires + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed (as previously explained); + [32mbioconductor-rsamtools [2.0.0|2.2.0][0m would require + [32mr-base >=3.6,<3.7.0a0 [0m with the potential options + [32mr-base [3.5.1|3.6.1|3.6.2][0m, which can be installed (as previously explained); + [32mr-base [3.6.2|3.6.3|4.0.0|4.0.1|4.0.2][0m would require + [32mgsl >=2.6,<2.7.0a0 [0m, which can be installed; + [32mlibgfortran-ng >=7,<8.0a0 [0m, which can be installed; + [32mr-base [3.6.3|4.0.3|4.0.5|4.1.0|4.1.1][0m would require + [32mgsl >=2.6,<2.7.0a0 [0m, which can be installed; + [32mbioconductor-rsamtools [2.10.0|2.8.0][0m would require + [32mbioconductor-biocgenerics >=0.40.0,<0.41.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m with the potential options + [32mr-base [3.6.3|4.0.3|4.0.5|4.1.0|4.1.1][0m, which can be installed (as previously explained); + [31mr-base [4.1.1|4.1.2|4.1.3][0m would require + [31mgsl >=2.7,<2.8.0a0 [0m, which conflicts with any installable versions previously reported; + [32mbioconductor-genomeinfodb >=1.28.0,<1.29.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m with the potential options + [32mr-base [3.6.3|4.0.3|4.0.5|4.1.0|4.1.1][0m, which can be installed (as previously explained); + [31mr-base [4.1.1|4.1.2|4.1.3][0m, which cannot be installed (as previously explained); + [32mr-base >=4.1,<4.2.0a0 [0m with the potential options + [32mr-base [3.6.3|4.0.3|4.0.5|4.1.0|4.1.1][0m, which can be installed (as previously explained); + [31mr-base [4.1.1|4.1.2|4.1.3][0m, which cannot be installed (as previously explained); + [32mbioconductor-rsamtools 2.14.0[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-rsamtools [2.16.0|2.18.0][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mbioconductor-rsamtools [2.4.0|2.6.0][0m would require + [32mbioconductor-genomeinfodb >=1.24.0,<1.25.0 [0m, which requires + [32mr-base >=4.0,<4.1.0a0 [0m with the potential options + [32mr-base [3.6.2|3.6.3|4.0.0|4.0.1|4.0.2][0m, which can be installed (as previously explained); + [32mr-base [3.6.3|4.0.3|4.0.5|4.1.0|4.1.1][0m, which can be installed (as previously explained); + [31mr-base 4.0.5[0m would require + [31mgsl >=2.7,<2.8.0a0 [0m, which conflicts with any installable versions previously reported; + [32mkrb5 >=1.19.3,<1.20.0a0 [0m, which can be installed; + [31mr-base 4.0.5[0m would require + [31mgsl >=2.7,<2.8.0a0 [0m, which conflicts with any installable versions previously reported; + [32mkrb5 >=1.19.2,<1.20.0a0 [0m, which can be installed; + [32mr-base >=4.0,<4.1.0a0 [0m with the potential options + [32mr-base [3.6.2|3.6.3|4.0.0|4.0.1|4.0.2][0m, which can be installed (as previously explained); + [32mr-base [3.6.3|4.0.3|4.0.5|4.1.0|4.1.1][0m, which can be installed (as previously explained); + [31mr-base 4.0.5[0m, which cannot be installed (as previously explained); + [31mr-base 4.0.5[0m, which cannot be installed (as previously explained); + [32mlibgfortran[0m is installable with the potential options + [32mlibgfortran 3.0.0[0m, which can be installed; + [31mlibgfortran 12.4.0[0m would require + [31mlibgfortran-ng ==12.4.0 *_1[0m, which conflicts with any installable versions previously reported; + [32mlibgfortran5 12.4.0 h583ef98_1[0m, which can be installed; + [31mlibgfortran 13.3.0[0m would require + [31mlibgfortran-ng ==13.3.0 *_1[0m, which conflicts with any installable versions previously reported; + [31mlibgfortran 14.1.0[0m would require + [31mlibgfortran-ng ==14.1.0 *_1[0m, which conflicts with any installable versions previously reported; + [31mlibgfortran 14.2.0[0m would require + [31mlibgfortran-ng ==14.2.0 *_1[0m, which conflicts with any installable versions previously reported; + [31mlibgfortran5 >=13.3.0 [0m is not installable because there are no viable options + [31mlibgfortran5 13.3.0[0m would require + [31mlibgfortran-ng 13.3.0 [0m, which conflicts with any installable versions previously reported; + [31mlibgfortran5 13.3.0[0m would require + [31mlibgfortran 13.3.0 [0m, which conflicts with any installable versions previously reported; + [31mlibgfortran5 14.1.0[0m would require + [31mlibgfortran-ng 14.1.0 [0m, which conflicts with any installable versions previously reported; + [31mlibgfortran5 14.1.0[0m would require + [31mlibgfortran 14.1.0 [0m, which conflicts with any installable versions previously reported; + [31mlibgfortran5 14.2.0[0m would require + [31mlibgfortran 14.2.0 [0m, which conflicts with any installable versions previously reported; + [31mr-base 4.4.* [0m is not installable because there are no viable options + [31mr-base [4.4.0|4.4.1][0m would require + [31mlibcurl >=8.8.0,<9.0a0 [0m but there are no viable options + [31mlibcurl [8.10.0|8.10.1|...|8.9.1][0m would require + [31mkrb5 >=1.21.3,<1.22.0a0 [0m, which conflicts with any installable versions previously reported; + [31mlibcurl 8.8.0[0m would require + [31mkrb5 >=1.21.2,<1.22.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-base 4.4.1[0m would require + [31mgsl >=2.7,<2.8.0a0 [0m, which conflicts with any installable versions previously reported; + [31mlibcurl >=8.8.0,<9.0a0 [0m, which cannot be installed (as previously explained); + [31mr-base [4.4.1|4.4.2][0m would require + [31mgsl >=2.7,<2.8.0a0 [0m, which conflicts with any installable versions previously reported; + [31mlibcurl [>=8.10.1,<9.0a0 |>=8.11.1,<9.0a0 |>=8.9.0,<9.0a0 |>=8.9.1,<9.0a0 ][0m, which cannot be installed (as previously explained). +# Last 100 lines of the build log. diff --git a/recipes/cnv_facets/build_failure.linux-aarch64.yaml b/recipes/cnv_facets/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..816830209f0d7 --- /dev/null +++ b/recipes/cnv_facets/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: d9d8ce6eeff1fd202415b83d7b81c5ed803d967e8f7d07ec06a3f84a816aef2c # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [31mlibdeflate >=1.20,<1.21.0a0 [0m, which conflicts with any installable versions previously reported; + [31mhtslib 1.21[0m would require + [31mlibdeflate >=1.22,<1.23.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec("htslib[version='>=1.21,<1.22.0a0']"), MatchSpec("snp-pileup==0.6.2=h7021222_7")} + Encountered problems while solving: + - package snp-pileup-0.6.2-h7021222_7 requires htslib >=1.21,<1.22.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-rsamtools[0m is installable and it requires + [32mbioconductor-biocparallel >=1.36.0,<1.37.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m with the potential options + [32mr-base 4.3.0[0m would require + [32mlibtiff >=4.5.0,<4.6.0a0 [0m with the potential options + [32mlibtiff 4.5.0[0m would require + [32mlibdeflate >=1.16,<1.17.0a0 [0m, which can be installed; + [32mlibtiff 4.5.0[0m would require + [32mlibdeflate >=1.17,<1.18.0a0 [0m, which can be installed; + [32mlibtiff [4.5.0|4.5.1][0m would require + [32mlibdeflate >=1.18,<1.19.0a0 [0m, which can be installed; + [32mlibtiff 4.5.0[0m would require + [32mlibdeflate >=1.14,<1.15.0a0 [0m, which can be installed; + [32mr-base [4.3.0|4.3.1][0m would require + [32mlibtiff >=4.5.1,<4.6.0a0 [0m, which can be installed (as previously explained); + [32mr-base [4.3.1|4.3.2|4.3.3][0m, which can be installed; + [32mr-base 4.3.3[0m would require + [32mlibtiff >=4.7.0,<4.8.0a0 [0m with the potential options + [32mlibtiff 4.7.0[0m would require + [32mlibdeflate >=1.21,<1.22.0a0 [0m, which can be installed; + [32mlibtiff 4.7.0[0m would require + [32mlibdeflate >=1.23,<1.24.0a0 [0m, which can be installed; + [31mlibtiff 4.7.0[0m would require + [31mlibdeflate >=1.22,<1.23.0a0 [0m, which conflicts with any installable versions previously reported; + [32mr-base 4.4.* [0m is installable with the potential options + [31mr-base [4.4.0|4.4.1][0m would require + [31mlibdeflate >=1.20,<1.21.0a0 [0m, which conflicts with any installable versions previously reported; + [32mr-base 4.4.1[0m would require + [32mlibdeflate >=1.21,<1.22.0a0 [0m, which can be installed; + [31mr-base 4.4.2[0m would require + [31mlibdeflate >=1.22,<1.23.0a0 [0m, which conflicts with any installable versions previously reported; + [32mr-base 4.4.2[0m would require + [32mlibdeflate >=1.23,<1.24.0a0 [0m, which can be installed; + [31msnp-pileup[0m is not installable because it requires + [31mhtslib >=1.21,<1.22.0a0 [0m but there are no viable options + [31mhtslib 1.21[0m would require + [31mlibdeflate >=1.20,<1.21.0a0 [0m, which conflicts with any installable versions previously reported; + [31mhtslib 1.21[0m would require + [31mlibdeflate >=1.22,<1.23.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/cnv_facets/meta.yaml b/recipes/cnv_facets/meta.yaml index 33bfbf683e95c..aecada7a074ba 100644 --- a/recipes/cnv_facets/meta.yaml +++ b/recipes/cnv_facets/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{sha256}}' build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('cnv_facets', max_pin="x") }} skip: True # [not linux] diff --git a/recipes/cnvnator/meta.yaml b/recipes/cnvnator/meta.yaml index ee720182c3b7c..0318e6a58c640 100644 --- a/recipes/cnvnator/meta.yaml +++ b/recipes/cnvnator/meta.yaml @@ -15,7 +15,7 @@ source: folder: samtools build: - number: 9 + number: 10 skip: True # [osx] requirements: diff --git a/recipes/coatran/meta.yaml b/recipes/coatran/meta.yaml index 73c066d76d605..277356ebafb75 100644 --- a/recipes/coatran/meta.yaml +++ b/recipes/coatran/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('coatran', max_pin="x.x.x") }} diff --git a/recipes/cobs/build_failure.linux-64.yaml b/recipes/cobs/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..20126a4d4ba5f --- /dev/null +++ b/recipes/cobs/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 986dabf2583e232d99c51761eadadbb19ecba80d93aaf533987b7c64743a0ae4 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp: In member function 'virtual void tlx::CmdlineParser::ArgumentBytes64::print_value(std::ostream&) const': + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:364:60: error: 'dest_' was not declared in this scope; did you mean 'desc_'? + 364 | void print_value(std::ostream& os) const final { os << dest_; } + | ^~~~~ + | desc_ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp: At global scope: + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:577:59: error: 'uint32_t' has not been declared + 577 | const std::string& keytype, uint32_t& dest, + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:585:59: error: 'uint64_t' has not been declared + 585 | const std::string& keytype, uint64_t& dest, + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:584:6: error: redefinition of 'void tlx::CmdlineParser::add_bytes(char, const std::string&, const std::string&, int&, const std::string&)' + 584 | void CmdlineParser::add_bytes(char key, const std::string& longkey, + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:576:6: note: 'void tlx::CmdlineParser::add_bytes(char, const std::string&, const std::string&, int&, const std::string&)' previously defined here + 576 | void CmdlineParser::add_bytes(char key, const std::string& longkey, + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:653:31: error: 'uint32_t' has not been declared + 653 | uint32_t& dest, const std::string& desc) { + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:658:31: error: 'uint64_t' has not been declared + 658 | uint64_t& dest, const std::string& desc) { + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:657:6: error: redefinition of 'void tlx::CmdlineParser::add_bytes(char, const std::string&, int&, const std::string&)' + 657 | void CmdlineParser::add_bytes(char key, const std::string& longkey, + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:652:6: note: 'void tlx::CmdlineParser::add_bytes(char, const std::string&, int&, const std::string&)' previously defined here + 652 | void CmdlineParser::add_bytes(char key, const std::string& longkey, + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:716:31: error: 'uint32_t' has not been declared + 716 | uint32_t& dest, const std::string& desc) { + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:721:31: error: 'uint64_t' has not been declared + 721 | uint64_t& dest, const std::string& desc) { + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:720:6: error: redefinition of 'void tlx::CmdlineParser::add_bytes(const std::string&, int&, const std::string&)' + 720 | void CmdlineParser::add_bytes(const std::string& longkey, + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:715:6: note: 'void tlx::CmdlineParser::add_bytes(const std::string&, int&, const std::string&)' previously defined here + 715 | void CmdlineParser::add_bytes(const std::string& longkey, + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:775:30: error: 'uint32_t' has not been declared + 775 | const std::string& name, uint32_t& dest, const std::string& desc) { + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:782:30: error: 'uint64_t' has not been declared + 782 | const std::string& name, uint64_t& dest, const std::string& desc) { + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:781:6: error: redefinition of 'void tlx::CmdlineParser::add_param_bytes(const std::string&, int&, const std::string&)' + 781 | void CmdlineParser::add_param_bytes( + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:774:6: note: 'void tlx::CmdlineParser::add_param_bytes(const std::string&, int&, const std::string&)' previously defined here + 774 | void CmdlineParser::add_param_bytes( + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:842:30: error: 'uint32_t' has not been declared + 842 | const std::string& name, uint32_t& dest, const std::string& desc) { + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:849:30: error: 'uint64_t' has not been declared + 849 | const std::string& name, uint64_t& dest, const std::string& desc) { + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:848:6: error: redefinition of 'void tlx::CmdlineParser::add_opt_param_bytes(const std::string&, int&, const std::string&)' + 848 | void CmdlineParser::add_opt_param_bytes( + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:841:6: note: 'void tlx::CmdlineParser::add_opt_param_bytes(const std::string&, int&, const std::string&)' previously defined here + 841 | void CmdlineParser::add_opt_param_bytes( + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp: In member function 'virtual bool tlx::CmdlineParser::ArgumentBytes64::process(int&, const char* const*&)': + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:362:5: warning: control reaches end of non-void function [-Wreturn-type] + 362 | } + | ^ + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp: In member function 'virtual bool tlx::CmdlineParser::ArgumentBytes32::process(int&, const char* const*&)': + /opt/conda/conda-bld/cobs_1734020599368/work/extlib/tlx/tlx/cmdline_parser.cpp:330:5: warning: control reaches end of non-void function [-Wreturn-type] + 330 | } + | ^ + make[2]: *** [extlib/tlx/tlx/CMakeFiles/tlx.dir/build.make:107: extlib/tlx/tlx/CMakeFiles/tlx.dir/cmdline_parser.cpp.o] Error 1 + make[1]: *** [CMakeFiles/Makefile2:477: extlib/tlx/tlx/CMakeFiles/tlx.dir/all] Error 2 + make: *** [Makefile:146: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cobs_1734020599368/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cobs_1734020599368/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/cobs/build_failure.linux-aarch64.yaml b/recipes/cobs/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..1241d7b1f0a78 --- /dev/null +++ b/recipes/cobs/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 986dabf2583e232d99c51761eadadbb19ecba80d93aaf533987b7c64743a0ae4 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp: In member function 'virtual void tlx::CmdlineParser::ArgumentBytes64::print_value(std::ostream&) const': + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:364:60: error: 'dest_' was not declared in this scope; did you mean 'desc_'? + 364 | void print_value(std::ostream& os) const final { os << dest_; } + | ^~~~~ + | desc_ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp: At global scope: + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:577:59: error: 'uint32_t' has not been declared + 577 | const std::string& keytype, uint32_t& dest, + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:585:59: error: 'uint64_t' has not been declared + 585 | const std::string& keytype, uint64_t& dest, + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:584:6: error: redefinition of 'void tlx::CmdlineParser::add_bytes(char, const std::string&, const std::string&, int&, const std::string&)' + 584 | void CmdlineParser::add_bytes(char key, const std::string& longkey, + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:576:6: note: 'void tlx::CmdlineParser::add_bytes(char, const std::string&, const std::string&, int&, const std::string&)' previously defined here + 576 | void CmdlineParser::add_bytes(char key, const std::string& longkey, + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:653:31: error: 'uint32_t' has not been declared + 653 | uint32_t& dest, const std::string& desc) { + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:658:31: error: 'uint64_t' has not been declared + 658 | uint64_t& dest, const std::string& desc) { + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:657:6: error: redefinition of 'void tlx::CmdlineParser::add_bytes(char, const std::string&, int&, const std::string&)' + 657 | void CmdlineParser::add_bytes(char key, const std::string& longkey, + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:652:6: note: 'void tlx::CmdlineParser::add_bytes(char, const std::string&, int&, const std::string&)' previously defined here + 652 | void CmdlineParser::add_bytes(char key, const std::string& longkey, + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:716:31: error: 'uint32_t' has not been declared + 716 | uint32_t& dest, const std::string& desc) { + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:721:31: error: 'uint64_t' has not been declared + 721 | uint64_t& dest, const std::string& desc) { + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:720:6: error: redefinition of 'void tlx::CmdlineParser::add_bytes(const std::string&, int&, const std::string&)' + 720 | void CmdlineParser::add_bytes(const std::string& longkey, + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:715:6: note: 'void tlx::CmdlineParser::add_bytes(const std::string&, int&, const std::string&)' previously defined here + 715 | void CmdlineParser::add_bytes(const std::string& longkey, + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:775:30: error: 'uint32_t' has not been declared + 775 | const std::string& name, uint32_t& dest, const std::string& desc) { + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:782:30: error: 'uint64_t' has not been declared + 782 | const std::string& name, uint64_t& dest, const std::string& desc) { + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:781:6: error: redefinition of 'void tlx::CmdlineParser::add_param_bytes(const std::string&, int&, const std::string&)' + 781 | void CmdlineParser::add_param_bytes( + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:774:6: note: 'void tlx::CmdlineParser::add_param_bytes(const std::string&, int&, const std::string&)' previously defined here + 774 | void CmdlineParser::add_param_bytes( + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:842:30: error: 'uint32_t' has not been declared + 842 | const std::string& name, uint32_t& dest, const std::string& desc) { + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:849:30: error: 'uint64_t' has not been declared + 849 | const std::string& name, uint64_t& dest, const std::string& desc) { + | ^~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:848:6: error: redefinition of 'void tlx::CmdlineParser::add_opt_param_bytes(const std::string&, int&, const std::string&)' + 848 | void CmdlineParser::add_opt_param_bytes( + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:841:6: note: 'void tlx::CmdlineParser::add_opt_param_bytes(const std::string&, int&, const std::string&)' previously defined here + 841 | void CmdlineParser::add_opt_param_bytes( + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp: In member function 'virtual bool tlx::CmdlineParser::ArgumentBytes64::process(int&, const char* const*&)': + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:362:5: warning: control reaches end of non-void function [-Wreturn-type] + 362 | } + | ^ + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp: In member function 'virtual bool tlx::CmdlineParser::ArgumentBytes32::process(int&, const char* const*&)': + /opt/conda/conda-bld/cobs_1733974359611/work/extlib/tlx/tlx/cmdline_parser.cpp:330:5: warning: control reaches end of non-void function [-Wreturn-type] + 330 | } + | ^ + make[2]: *** [extlib/tlx/tlx/CMakeFiles/tlx.dir/build.make:107: extlib/tlx/tlx/CMakeFiles/tlx.dir/cmdline_parser.cpp.o] Error 1 + make[1]: *** [CMakeFiles/Makefile2:477: extlib/tlx/tlx/CMakeFiles/tlx.dir/all] Error 2 + make: *** [Makefile:146: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cobs_1733974359611/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cobs_1733974359611/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/cobs/build_failure.osx-64.yaml b/recipes/cobs/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..acdc9282e5329 --- /dev/null +++ b/recipes/cobs/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 986dabf2583e232d99c51761eadadbb19ecba80d93aaf533987b7c64743a0ae4 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + -- Installing: $PREFIX/include/tlx/allocator_base.hpp + -- Installing: $PREFIX/include/tlx/string.hpp + -- Installing: $PREFIX/include/tlx/sort.hpp + -- Installing: $PREFIX/include/tlx/simple_vector.hpp + -- Installing: $PREFIX/include/tlx/digest.hpp + -- Installing: $PREFIX/include/tlx/string + -- Installing: $PREFIX/include/tlx/string/join.hpp + -- Installing: $PREFIX/include/tlx/string/index_of.hpp + -- Installing: $PREFIX/include/tlx/string/split_words.hpp + -- Installing: $PREFIX/include/tlx/string/equal_icase.hpp + -- Installing: $PREFIX/include/tlx/string/erase_all.hpp + -- Installing: $PREFIX/include/tlx/string/less_icase.hpp + -- Installing: $PREFIX/include/tlx/string/hash_djb2.hpp + -- Installing: $PREFIX/include/tlx/string/hexdump.hpp + -- Installing: $PREFIX/include/tlx/string/escape_uri.hpp + -- Installing: $PREFIX/include/tlx/string/parse_si_iec_units.hpp + -- Installing: $PREFIX/include/tlx/string/split_view.hpp + -- Installing: $PREFIX/include/tlx/string/to_lower.hpp + -- Installing: $PREFIX/include/tlx/string/ends_with.hpp + -- Installing: $PREFIX/include/tlx/string/parse_uri_form_data.hpp + -- Installing: $PREFIX/include/tlx/string/expand_environment_variables.hpp + -- Installing: $PREFIX/include/tlx/string/format_si_units.hpp + -- Installing: $PREFIX/include/tlx/string/format_iec_units.hpp + -- Installing: $PREFIX/include/tlx/string/to_upper.hpp + -- Installing: $PREFIX/include/tlx/string/compare_icase.hpp + -- Installing: $PREFIX/include/tlx/string/pad.hpp + -- Installing: $PREFIX/include/tlx/string/trim.hpp + -- Installing: $PREFIX/include/tlx/string/ssprintf_generic.hpp + -- Installing: $PREFIX/include/tlx/string/replace.hpp + -- Installing: $PREFIX/include/tlx/string/union_words.hpp + -- Installing: $PREFIX/include/tlx/string/split_quoted.hpp + -- Installing: $PREFIX/include/tlx/string/extract_between.hpp + -- Installing: $PREFIX/include/tlx/string/hash_sdbm.hpp + -- Installing: $PREFIX/include/tlx/string/appendline.hpp + -- Installing: $PREFIX/include/tlx/string/format_si_iec_units.hpp + -- Installing: $PREFIX/include/tlx/string/parse_uri.hpp + -- Installing: $PREFIX/include/tlx/string/word_wrap.hpp + -- Installing: $PREFIX/include/tlx/string/escape_html.hpp + -- Installing: $PREFIX/include/tlx/string/bitdump.hpp + -- Installing: $PREFIX/include/tlx/string/starts_with.hpp + -- Installing: $PREFIX/include/tlx/string/ssprintf.hpp + -- Installing: $PREFIX/include/tlx/string/contains_word.hpp + -- Installing: $PREFIX/include/tlx/string/levenshtein.hpp + -- Installing: $PREFIX/include/tlx/string/join_generic.hpp + -- Installing: $PREFIX/include/tlx/string/join_quoted.hpp + -- Installing: $PREFIX/include/tlx/string/base64.hpp + -- Installing: $PREFIX/include/tlx/string/split.hpp + -- Installing: $PREFIX/include/tlx/string/contains.hpp + -- Installing: $PREFIX/include/tlx/port + -- Installing: $PREFIX/include/tlx/port/setenv.hpp + -- Installing: $PREFIX/include/tlx/vector_free.hpp + -- Installing: $PREFIX/include/tlx/stack_allocator.hpp + -- Installing: $PREFIX/include/tlx/define.hpp + -- Installing: $PREFIX/include/tlx/delegate.hpp + -- Installing: $PREFIX/lib/cmake/tlx/tlx-version.cmake + -- Installing: $PREFIX/lib/cmake/tlx/tlx-config.cmake + -- Installing: $PREFIX/lib/cmake/tlx/tlx-targets.cmake + -- Installing: $PREFIX/lib/cmake/tlx/tlx-targets-release.cmake + -- Installing: $PREFIX/lib/pkgconfig/tlx.pc + -- Installing: $PREFIX/lib/libtlx.a + + Resource usage statistics from building cobs: + Process count: 8 + CPU time: Sys=0:00:20.2, User=0:02:22.5 + Memory: 489.9M + Disk usage: 477.3K + Time elapsed: 0:04:31.8 + + + Packaging cobs + Packaging cobs-0.3.1-he136a0b_2 + number of files: 245 + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2765, in build + newly_built_packages = bundlers[pkg_type]( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1874, in bundle_conda + files = post_process_files(metadata, initial_files) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1653, in post_process_files + post_build(m, new_files, build_python=python) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1759, in post_build + post_process_shared_lib(m, f, prefix_files, host_prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1635, in post_process_shared_lib + mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 477, in mk_relative_osx + names = macho.otool(path, prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 221, in otool + lines = check_output([otool, "-l", path], stderr=STDOUT).decode("utf-8") + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 421, in check_output + return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 526, in run + raise CalledProcessError(retcode, process.args, + subprocess.CalledProcessError: Command '['/opt/mambaforge/envs/bioconda/conda-bld/cobs_1733859619830/_build_env/bin/llvm-otool', '-l', '/opt/mambaforge/envs/bioconda/conda-bld/cobs_1733859619830/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/xxhsum']' died with . +# Last 100 lines of the build log. diff --git a/recipes/cobs/meta.yaml b/recipes/cobs/meta.yaml index ef24ee5f76aac..e43aafc6cad1b 100644 --- a/recipes/cobs/meta.yaml +++ b/recipes/cobs/meta.yaml @@ -12,7 +12,7 @@ source: - cobs-aarch64.patch # [aarch64 or arm64] build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage(name|lower, max_pin="x.x") }} diff --git a/recipes/codingquarry/meta.yaml b/recipes/codingquarry/meta.yaml index c027a2f2b9f6d..312166a7283e1 100644 --- a/recipes/codingquarry/meta.yaml +++ b/recipes/codingquarry/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 9 + number: 10 skip: True # [osx] requirements: diff --git a/recipes/codonw/meta.yaml b/recipes/codonw/meta.yaml index 65a161ef51196..1dae3936603e3 100644 --- a/recipes/codonw/meta.yaml +++ b/recipes/codonw/meta.yaml @@ -7,7 +7,7 @@ source: md5: 1b9c9fe9a759789d035ba6b28787e59d build: - number: 6 + number: 7 skip: true # [osx] requirements: diff --git a/recipes/cofold/meta.yaml b/recipes/cofold/meta.yaml index d8f414ad4c33b..ddcba6819bd97 100644 --- a/recipes/cofold/meta.yaml +++ b/recipes/cofold/meta.yaml @@ -3,7 +3,7 @@ package: version: "2.0.4" build: - number: 7 + number: 8 skip: True # [osx] source: diff --git a/recipes/cogtriangles/meta.yaml b/recipes/cogtriangles/meta.yaml index 81cc6a4c67e9e..f0bfed413c44e 100644 --- a/recipes/cogtriangles/meta.yaml +++ b/recipes/cogtriangles/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 skip: True # [osx] source: diff --git a/recipes/coils/build_failure.osx-64.yaml b/recipes/coils/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..de7b0f8513050 --- /dev/null +++ b/recipes/coils/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 48a6e7d3985953c5044c286d4468e58de7104b3cadac4180a241d4ce779a100f # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - openssl 3.4.0 hd471939_0 + - tapi 1300.6.5 h390ca13_0 + - zstd 1.5.6 h915ae27_0 + - libllvm18 18.1.8 h9ce406d_2 + - sigtool 0.1.3 h88f4db0_0 + - ld64_osx-64 951.9 hc8d1a19_2 + - libclang-cpp18.1 18.1.8 default_h0c94c6a_5 + - llvm-tools-18 18.1.8 h9ce406d_2 + - clang-18 18.1.8 default_h0c94c6a_5 + - llvm-tools 18.1.8 h9ce406d_2 + - cctools_osx-64 1010.6 h00edd4c_2 + raise subprocess.CalledProcessError(proc.returncode, _args) + - clang 18.1.8 default_h179603d_5 + - clangxx 18.1.8 default_h179603d_5 + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + - compiler-rt 18.1.8 h1020d70_1 + - clang_impl_osx-64 18.1.8 h6a44ed1_23 + - clang_osx-64 18.1.8 h7e5c614_23 + run: [] + test: + commands: + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/coils_1734197139905/work/conda_build.sh']' returned non-zero exit status 1. + + - COILSDIR=. ncoils -h 2>&1 | grep -i ncoils + files: + - 1srya.fa + - 1srya_result.txt + about: + home: https://rostlab.org/owiki/index.php/Packages#Package_overview + license: GPL + license_file: LICENSE + summary: A generalized profile syntax for biomolecular sequence motifs and its function + in automatic sequence interpretation. + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/coils_1734197139905/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/coils_1734197139905/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/coils_1734197139905/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/coils_1734197139905/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/coils-2.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/coils_1734197139905/work/conda_build.sh']' returned non-zero exit status 1. + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/coils-2.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 +# Last 100 lines of the build log. diff --git a/recipes/coils/meta.yaml b/recipes/coils/meta.yaml index 235e29e7cd84d..488079d9d47dd 100644 --- a/recipes/coils/meta.yaml +++ b/recipes/coils/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/coinfinder/meta.yaml b/recipes/coinfinder/meta.yaml index ceefbebc62a97..faea1cae41411 100644 --- a/recipes/coinfinder/meta.yaml +++ b/recipes/coinfinder/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 98985910bff4d1845c8d8b11482205b77ef85bbc4f16a2144f5b540945d8548d build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage(name, max_pin="x") }} rpaths: diff --git a/recipes/collect_mgf/build_failure.osx-64.yaml b/recipes/collect_mgf/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..d9a377728b863 --- /dev/null +++ b/recipes/collect_mgf/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 674d8e7cb3bfdea7e10c22f84972660a28ffc04b4be30e22f85eb078ec94c1ea # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - liblzma 5.6.3 hd471939_1 + - ncurses 6.5 hf036a51_1 + - libllvm18 18.1.8 h9ce406d_2 + - libiconv 1.17 hd75f5a5_2 + - libxml2 2.13.5 he8ee3e7_1 + - compiler-rt 18.1.8 h1020d70_1 + - libcxx 19.1.5 hf95d169_0 + - libclang-cpp18.1 18.1.8 default_h0c94c6a_5 + - llvm-tools 18.1.8 h9ce406d_2 + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/collect_mgf_1733964545348/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + - llvm-tools-18 18.1.8 h9ce406d_2 + Traceback (most recent call last): + - clang_impl_osx-64 18.1.8 h6a44ed1_23 + - tapi 1300.6.5 h390ca13_0 + - ca-certificates 2024.8.30 h8857fd0_0 + - clang-18 18.1.8 default_h0c94c6a_5 + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + - clang 18.1.8 default_h179603d_5 + - zstd 1.5.6 h915ae27_0 + - libcxx-devel 18.1.8 h7c275be_7 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + - ld64_osx-64 951.9 hc8d1a19_2 + - clangxx 18.1.8 default_h179603d_5 + host: [] + run: [] + test: + commands: + - collect_mgf + about: + home: http://www.ms-utils.org/collect_mgf.c + license: GPL-3.0 + summary: Collects MGF files and dd_results from an XMass setup_QDD.tcl experiment + to a single MGF file. + extra: + copy_test_source_files: true + final: true + identifiers: + - biotools:collect_mgf + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/collect_mgf_1733964545348/work + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/collect_mgf_1733964545348/work/conda_build.sh']' returned non-zero exit status 1. + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/collect_mgf_1733964545348/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/collect_mgf_1733964545348/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/collect_mgf_1733964545348/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/collect_mgf-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/collect_mgf-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 +# Last 100 lines of the build log. diff --git a/recipes/collect_mgf/meta.yaml b/recipes/collect_mgf/meta.yaml index 2028ea4d88ef9..a926bc8b87de0 100644 --- a/recipes/collect_mgf/meta.yaml +++ b/recipes/collect_mgf/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.0 build: - number: 5 + number: 6 source: url: http://www.ms-utils.org/collect_mgf.c diff --git a/recipes/colorid_bv/meta.yaml b/recipes/colorid_bv/meta.yaml index eb4fbe81ae11a..87133b6525bdb 100644 --- a/recipes/colorid_bv/meta.yaml +++ b/recipes/colorid_bv/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('colorid_bv', max_pin="x.x") }} diff --git a/recipes/comet-ms/2016013/meta.yaml b/recipes/comet-ms/2016013/meta.yaml index 3dd5a6c19b8f4..90bfa51ff4202 100644 --- a/recipes/comet-ms/2016013/meta.yaml +++ b/recipes/comet-ms/2016013/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256_src_bin_bundle }} build: - number: 6 + number: 7 skip: True # [osx] requirements: diff --git a/recipes/comet-ms/build_failure.linux-64.yaml b/recipes/comet-ms/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..46dd1e736aeae --- /dev/null +++ b/recipes/comet-ms/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: c05b821087da6784274f4e511da22bb45bd92f5550fb1f795321da0d0776a5a3 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/comet-ms-2024011 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/comet-ms-2024011 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/comet-ms-2024011 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/comet-ms-2024011 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + export INCLUDE_PATH=/opt/conda/conda-bld/comet-ms_1734293232113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/MSToolkit/include + INCLUDE_PATH=/opt/conda/conda-bld/comet-ms_1734293232113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/MSToolkit/include + export CPPFLAGS=-I/opt/conda/conda-bld/comet-ms_1734293232113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/MSToolkit/include + CPPFLAGS=-I/opt/conda/conda-bld/comet-ms_1734293232113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/MSToolkit/include + sed -i.bak 's#gcc#/opt/conda/conda-bld/comet-ms_1734293232113/_build_env/bin/x86_64-conda-linux-gnu-cc#;s#g#/opt/conda/conda-bld/comet-ms_1734293232113/_build_env/bin/x86_64-conda-linux-gnu-c#' MSToolkit/Makefile + sed -i.bak 's#gcc#/opt/conda/conda-bld/comet-ms_1734293232113/_build_env/bin/x86_64-conda-linux-gnu-cc#;s#g#/opt/conda/conda-bld/comet-ms_1734293232113/_build_env/bin/x86_64-conda-linux-gnu-c#' CometSearch/Makefile + make CXX=/opt/conda/conda-bld/comet-ms_1734293232113/_build_env/bin/x86_64-conda-linux-gnu-c -j 4 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/comet-ms-2024011 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -static -std=c14 -fpermissive -Wall -Wextra -Wno-char-subscripts -DGITHUBSHA='""' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -D_NOSQLITE -IMSToolkit/include -IMSToolkit/src/expat-2.2.9/lib -IMSToolkit/src/zlib-1.2.11 -ICometSearch Comet.cpp -c + In file included from Comet.cpp:19: + CometSearch/CometInterfaces.h:86:23: warning: 'CometInterfaces::_tp' defined but not used [-Wunused-variable] + 86 | static ThreadPool* _tp; + | ^~~ + cd MSToolkit && make all + make[1]: Entering directory '$SRC_DIR/MSToolkit' + mkdir -p $SRC_DIR/MSToolkit/obj + mkdir -p $SRC_DIR/MSToolkit/lic/expat-2.2.9 + mkdir -p $SRC_DIR/MSToolkit/lic + cp $SRC_DIR/MSToolkit/src/expat-2.2.9/COPYING $SRC_DIR/MSToolkit/lic/expat-2.2.9/COPYING + mkdir -p $SRC_DIR/MSToolkit/lic/zlib-1.2.11 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -O3 -static -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H -D_NOSQLITE $SRC_DIR/MSToolkit/src/MSToolkit/MSObject.cpp -c -o $SRC_DIR/MSToolkit/obj/MSObject_lite.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -O3 -static -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H -D_NOSQLITE $SRC_DIR/MSToolkit/src/MSToolkit/MSReader.cpp -c -o $SRC_DIR/MSToolkit/obj/MSReader_lite.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -O3 -static -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H -D_NOSQLITE $SRC_DIR/MSToolkit/src/MSToolkit/Spectrum.cpp -c -o $SRC_DIR/MSToolkit/obj/Spectrum_lite.o + cp $SRC_DIR/MSToolkit/src/zlib-1.2.11/README $SRC_DIR/MSToolkit/lic/zlib-1.2.11/README + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -O3 -static -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H -D_NOSQLITE $SRC_DIR/MSToolkit/src/MSToolkit/mzMLWriter.cpp -c -o $SRC_DIR/MSToolkit/obj/mzMLWriter_lite.o + In file included from ./include/MSReader.h:21, + from /opt/conda/conda-bld/comet-ms_1734293232113/work/MSToolkit/src/MSToolkit/MSReader.cpp:16: + ./include/mzParser.h:32:10: fatal error: expat.h: No such file or directory + 32 | #include "expat.h" + | ^~~~~~~~~ + compilation terminated. + make[1]: *** [Makefile:145: /opt/conda/conda-bld/comet-ms_1734293232113/work/MSToolkit/obj/MSReader_lite.o] Error 1 + make[1]: *** Waiting for unfinished jobs.... + In file included from ./include/MSReader.h:21, + from ./include/mzMLWriter.h:22, + from /opt/conda/conda-bld/comet-ms_1734293232113/work/MSToolkit/src/MSToolkit/mzMLWriter.cpp:16: + ./include/mzParser.h:32:10: fatal error: expat.h: No such file or directory + 32 | #include "expat.h" + | ^~~~~~~~~ + compilation terminated. + make[1]: *** [Makefile:145: /opt/conda/conda-bld/comet-ms_1734293232113/work/MSToolkit/obj/mzMLWriter_lite.o] Error 1 + make[1]: Leaving directory '$SRC_DIR/MSToolkit' + make: *** [Makefile:32: comet.exe] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/comet-ms_1734293232113/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/comet-ms_1734293232113/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/comet-ms/build_failure.linux-aarch64.yaml b/recipes/comet-ms/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..ee7561367982f --- /dev/null +++ b/recipes/comet-ms/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: c05b821087da6784274f4e511da22bb45bd92f5550fb1f795321da0d0776a5a3 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + SIZE=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strip + INFO: activate-gcc_linux-aarch64.sh made the following environmental changes: + BUILD=aarch64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc + CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/comet-ms-2024011 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=aarch64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=aarch64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/comet-ms-2024011 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib + HOST=aarch64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_aarch64_conda_cos7_linux_gnu + build_alias=aarch64-conda-linux-gnu + host_alias=aarch64-conda-linux-gnu + -BUILD=aarch64-conda_cos7-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-aarch64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/comet-ms-2024011 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/comet-ms-2024011 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-g + export INCLUDE_PATH=/opt/conda/conda-bld/comet-ms_1734271211541/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/MSToolkit/include + INCLUDE_PATH=/opt/conda/conda-bld/comet-ms_1734271211541/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/MSToolkit/include + export CPPFLAGS=-I/opt/conda/conda-bld/comet-ms_1734271211541/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/MSToolkit/include + CPPFLAGS=-I/opt/conda/conda-bld/comet-ms_1734271211541/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/MSToolkit/include + sed -i.bak 's#gcc#/opt/conda/conda-bld/comet-ms_1734271211541/_build_env/bin/aarch64-conda-linux-gnu-cc#;s#g#/opt/conda/conda-bld/comet-ms_1734271211541/_build_env/bin/aarch64-conda-linux-gnu-c#' MSToolkit/Makefile + sed -i.bak 's#gcc#/opt/conda/conda-bld/comet-ms_1734271211541/_build_env/bin/aarch64-conda-linux-gnu-cc#;s#g#/opt/conda/conda-bld/comet-ms_1734271211541/_build_env/bin/aarch64-conda-linux-gnu-c#' CometSearch/Makefile + make CXX=/opt/conda/conda-bld/comet-ms_1734271211541/_build_env/bin/aarch64-conda-linux-gnu-c -j 4 + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/comet-ms-2024011 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -static -std=c14 -fpermissive -Wall -Wextra -Wno-char-subscripts -DGITHUBSHA='""' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -D_NOSQLITE -IMSToolkit/include -IMSToolkit/src/expat-2.2.9/lib -IMSToolkit/src/zlib-1.2.11 -ICometSearch Comet.cpp -c + In file included from Comet.cpp:19: + CometSearch/CometInterfaces.h:86:23: warning: 'CometInterfaces::_tp' defined but not used [-Wunused-variable] + 86 | static ThreadPool* _tp; + | ^~~ + cd MSToolkit && make all + make[1]: Entering directory '$SRC_DIR/MSToolkit' + mkdir -p $SRC_DIR/MSToolkit/obj + mkdir -p $SRC_DIR/MSToolkit/lic/expat-2.2.9 + mkdir -p $SRC_DIR/MSToolkit/lic + mkdir -p $SRC_DIR/MSToolkit/lic/zlib-1.2.11 + cp $SRC_DIR/MSToolkit/src/expat-2.2.9/COPYING $SRC_DIR/MSToolkit/lic/expat-2.2.9/COPYING + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -O3 -static -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H -D_NOSQLITE $SRC_DIR/MSToolkit/src/MSToolkit/MSObject.cpp -c -o $SRC_DIR/MSToolkit/obj/MSObject_lite.o + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -O3 -static -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H -D_NOSQLITE $SRC_DIR/MSToolkit/src/MSToolkit/MSReader.cpp -c -o $SRC_DIR/MSToolkit/obj/MSReader_lite.o + cp $SRC_DIR/MSToolkit/src/zlib-1.2.11/README $SRC_DIR/MSToolkit/lic/zlib-1.2.11/README + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -O3 -static -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H -D_NOSQLITE $SRC_DIR/MSToolkit/src/MSToolkit/Spectrum.cpp -c -o $SRC_DIR/MSToolkit/obj/Spectrum_lite.o + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -O3 -static -I. -I./include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -DHAVE_EXPAT_CONFIG_H -D_NOSQLITE $SRC_DIR/MSToolkit/src/MSToolkit/mzMLWriter.cpp -c -o $SRC_DIR/MSToolkit/obj/mzMLWriter_lite.o + In file included from ./include/MSReader.h:21, + from /opt/conda/conda-bld/comet-ms_1734271211541/work/MSToolkit/src/MSToolkit/MSReader.cpp:16: + ./include/mzParser.h:32:10: fatal error: expat.h: No such file or directory + 32 | #include "expat.h" + | ^~~~~~~~~ + In file included from ./include/MSReader.h:21, + from ./include/mzMLWriter.h:22, + from /opt/conda/conda-bld/comet-ms_1734271211541/work/MSToolkit/src/MSToolkit/mzMLWriter.cpp:16: + ./include/mzParser.h:32:10: fatal error: expat.h: No such file or directory + 32 | #include "expat.h" + | ^~~~~~~~~ + compilation terminated. + compilation terminated. + make[1]: *** [Makefile:145: /opt/conda/conda-bld/comet-ms_1734271211541/work/MSToolkit/obj/mzMLWriter_lite.o] Error 1 + make[1]: *** Waiting for unfinished jobs.... + make[1]: *** [Makefile:145: /opt/conda/conda-bld/comet-ms_1734271211541/work/MSToolkit/obj/MSReader_lite.o] Error 1 + make[1]: Leaving directory '$SRC_DIR/MSToolkit' + make: *** [Makefile:32: comet.exe] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/comet-ms_1734271211541/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/comet-ms_1734271211541/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/comet-ms/meta.yaml b/recipes/comet-ms/meta.yaml index addbd48fa6ffe..6ebd719840580 100644 --- a/recipes/comet-ms/meta.yaml +++ b/recipes/comet-ms/meta.yaml @@ -14,7 +14,7 @@ build: run_exports: - {{ pin_subpackage('comet-ms', max_pin=None) }} skip: True # [osx] - number: 0 + number: 1 requirements: build: diff --git a/recipes/commet/build_failure.linux-64.yaml b/recipes/commet/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..96f3f19681261 --- /dev/null +++ b/recipes/commet/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: e6a85ea0103ef6347c521fb77fdb41804c5f6d32ba33ec8d3914087192c2f047 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 14.2.0-h41c2201_101 conda-forge + libgcc-ng: 14.2.0-h69a702a_1 conda-forge + libgfortran: 14.2.0-h69a702a_1 conda-forge + libgfortran-ng: 14.2.0-h69a702a_1 conda-forge + libgfortran5: 14.2.0-hd5240d6_1 conda-forge + libglib: 2.82.2-h2ff4ddf_0 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libiconv: 1.17-hd590300_2 conda-forge + libjpeg-turbo: 3.0.0-hd590300_1 conda-forge + liblapack: 3.9.0-25_linux64_openblas conda-forge + liblzma: 5.6.3-hb9d3cd8_1 conda-forge + liblzma-devel: 5.6.3-hb9d3cd8_1 conda-forge + libmpdec: 4.0.0-h4bc722e_0 conda-forge + libnghttp2: 1.64.0-h161d5f1_0 conda-forge + libopenblas: 0.3.28-pthreads_h94d23a6_1 conda-forge + libpng: 1.6.44-hadc24fc_0 conda-forge + libsanitizer: 14.2.0-h2a3dede_1 conda-forge + libsqlite: 3.47.2-hee588c1_0 conda-forge + libssh2: 1.11.1-hf672d98_0 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-devel_linux-64: 14.2.0-h41c2201_101 conda-forge + libstdcxx-ng: 14.2.0-h4852527_1 conda-forge + libtiff: 4.7.0-hc4654cb_2 conda-forge + libuuid: 2.38.1-h0b41bf4_0 conda-forge + libwebp-base: 1.4.0-hd590300_0 conda-forge + libxcb: 1.17.0-h8a09558_0 conda-forge + libzlib: 1.3.1-hb9d3cd8_2 conda-forge + make: 4.4.1-hb9d3cd8_2 conda-forge + ncurses: 6.5-he02047a_1 conda-forge + openssl: 3.4.0-hb9d3cd8_0 conda-forge + pango: 1.54.0-h3a902e7_3 conda-forge + pcre2: 10.44-hba22ea6_2 conda-forge + pip: 24.3.1-pyh145f28c_0 conda-forge + pixman: 0.44.2-h29eaf8c_0 conda-forge + pthread-stubs: 0.4-hb9d3cd8_1002 conda-forge + python: 3.13.1-ha99a958_102_cp313 conda-forge + python_abi: 3.13-5_cp313 conda-forge + r-base: 4.4.2-h64c9cd0_0 conda-forge + r-bitops: 1.0_9-r44h2b5f3a1_0 conda-forge + r-catools: 1.18.3-r44h93ab643_0 conda-forge + r-gplots: 3.2.0-r44hc72bb7e_0 conda-forge + r-gtools: 3.9.5-r44hb1dbf0f_1 conda-forge + r-kernsmooth: 2.23_24-r44hc2011d3_1 conda-forge + readline: 8.2-h8228510_1 conda-forge + sed: 4.8-he412f7d_0 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tktable: 2.10-h8bc8fbc_6 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + xorg-libice: 1.1.1-hb9d3cd8_1 conda-forge + xorg-libsm: 1.2.4-he73a12e_1 conda-forge + xorg-libx11: 1.8.10-h4f16b4b_1 conda-forge + xorg-libxau: 1.0.11-hb9d3cd8_1 conda-forge + xorg-libxdmcp: 1.1.5-hb9d3cd8_0 conda-forge + xorg-libxext: 1.3.6-hb9d3cd8_0 conda-forge + xorg-libxrender: 0.9.11-hb9d3cd8_2 conda-forge + xorg-libxt: 1.3.1-hb9d3cd8_0 conda-forge + xz: 5.6.3-hbcc6ac9_1 conda-forge + xz-gpl-tools: 5.6.3-hbcc6ac9_1 conda-forge + xz-tools: 5.6.3-hb9d3cd8_1 conda-forge + zlib: 1.3.1-hb9d3cd8_2 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + export PREFIX=/opt/conda/conda-bld/commet_1733950858871/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + export SRC_DIR=/opt/conda/conda-bld/commet_1733950858871/test_tmp + Commet.py -h + Traceback (most recent call last): + File [35m"/opt/conda/conda-bld/commet_1733950858871/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/bin/Commet.py"[0m, line [35m33[0m, in [35m[0m + from distutils.spawn import find_executable + [1;35mModuleNotFoundError[0m: [35mNo module named 'distutils'[0m + WARNING: Tests failed for commet-24.7.14-r44h2555670_12.tar.bz2 - moving package to /opt/conda/conda-bld/broken + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/commet_1733950858871/test_tmp/conda_test_runner.sh']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: commet-24.7.14-r44h2555670_12.tar.bz2 +# Last 100 lines of the build log. diff --git a/recipes/commet/build_failure.osx-64.yaml b/recipes/commet/build_failure.osx-64.yaml index 174b4991df7af..215eea1a7630e 100644 --- a/recipes/commet/build_failure.osx-64.yaml +++ b/recipes/commet/build_failure.osx-64.yaml @@ -1,27 +1,25 @@ -recipe_sha: ea5583246a525ede677c830c075aacd8bbf1f95d5c545f7ba2769d3938b2d79b # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: e6a85ea0103ef6347c521fb77fdb41804c5f6d32ba33ec8d3914087192c2f047 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - Y :: Build-prefix patch in use M :: Minimal, non-amalgamated - D :: Dry-runnable N :: Patch level (1 is preferred) - L :: Patch level not-ambiguous O :: Patch applies without offsets - V :: Patch applies without fuzz E :: Patch applies without emitting to stderr +log: |2- + source path: /opt/mambaforge/envs/bioconda/pkgs/gfortran_impl_osx-64-13.2.0-h2bc304d_3/lib/gcc/x86_64-apple-darwin13.4.0/13.2.0/include/ISO_Fortran_binding.h + target path: /opt/mambaforge/envs/bioconda/conda-bld/commet_1733963221398/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/gcc/x86_64-apple-darwin13.4.0/13.2.0/include/ISO_Fortran_binding.h - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/commet_1717513473652/work - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/commet_1717513473652/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/commet_1717513473652/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/commet_1717513473652/work - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/commet_1717513473652/work/conda_build.sh']' returned non-zero exit status 2. + + + Executing transaction: ...working... done + Commet.py -h + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/conda-bld/commet_1733963221398/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/bin/Commet.py", line 33, in + from distutils.spawn import find_executable + ModuleNotFoundError: No module named 'distutils' + WARNING: Tests failed for commet-24.7.14-r44hef7b531_12.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken + Traceback (most recent call last): + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/commet_1733963221398/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/commet_1733963221398/test_tmp INFO: activate-gfortran_osx-64.sh made the following environmental changes: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/commet-24.7.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/commet-24.7.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran @@ -40,11 +38,34 @@ log: |- CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/commet-24.7.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/commet_1733963221398/test_tmp/conda_test_runner.sh']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=/opt/mambaforge/envs/bioconda/conda-bld/commet_1733963221398/_build_env/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: commet-24.7.14-r44hef7b531_12.tar.bz2 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/commet-24.7.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool @@ -53,7 +74,7 @@ log: |- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -62,7 +83,7 @@ log: |- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -80,25 +101,4 @@ log: |- CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/commet-24.7.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/commet-24.7.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - INFO: activate-gfortran_osx-64.sh made the following environmental changes: - DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/commet-24.7.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/commet-24.7.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - FC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - GFORTRAN=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - -DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/commet-24.7.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments - -DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/commet-24.7.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments - -FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - -GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - INFO: activate_clang_osx-64.sh made the following environmental changes: - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - x86_64-apple-darwin13.4.0-clang -o bin/index_and_search src/index_and_search.cpp -lm -lz -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/commet-24.7.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Iinclude -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - x86_64-apple-darwin13.4.0-clang -o bin/filter_reads src/filter_reads.cpp -lm -lz -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/commet-24.7.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Iinclude -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib # Last 100 lines of the build log. diff --git a/recipes/commet/meta.yaml b/recipes/commet/meta.yaml index 03969732436f1..2d62950d86868 100644 --- a/recipes/commet/meta.yaml +++ b/recipes/commet/meta.yaml @@ -9,7 +9,7 @@ source: - commet.patch build: - number: 11 + number: 12 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/comparems2/meta.yaml b/recipes/comparems2/meta.yaml index d04ab4830688b..e636940336241 100644 --- a/recipes/comparems2/meta.yaml +++ b/recipes/comparems2/meta.yaml @@ -3,7 +3,7 @@ package: version: 1 build: - number: 5 + number: 6 source: url: http://www.ms-utils.org/compareMS2.c diff --git a/recipes/conifer/meta.yaml b/recipes/conifer/meta.yaml index cf42a35cc9875..9a1fd18f36ad7 100644 --- a/recipes/conifer/meta.yaml +++ b/recipes/conifer/meta.yaml @@ -18,7 +18,7 @@ source: folder: third_party/uthash build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/consensify/meta.yaml b/recipes/consensify/meta.yaml index be77f31b16102..d0eb922c96a4d 100644 --- a/recipes/consensify/meta.yaml +++ b/recipes/consensify/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 2b88cda2c6ad44b6fd749d86485d3f16418b189b9c8ff4d20dd19640792dac1e build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('consensify', max_pin="x") }} diff --git a/recipes/consent/meta.yaml b/recipes/consent/meta.yaml index f69a7bed48d99..1fefb07579950 100644 --- a/recipes/consent/meta.yaml +++ b/recipes/consent/meta.yaml @@ -14,7 +14,7 @@ source: build: skip: True # [osx] - number: 3 + number: 4 requirements: build: diff --git a/recipes/contammix/meta.yaml b/recipes/contammix/meta.yaml index 568ab70b4d88b..25d5d5f01ba19 100644 --- a/recipes/contammix/meta.yaml +++ b/recipes/contammix/meta.yaml @@ -8,7 +8,7 @@ source: url: https://github.com/plfjohnson/contamMix/archive/refs/tags/v{{ github_version_str }}.tar.gz sha256: 1bfd53eca5554c957771daa51a2520306e90da17423dded39454ac8f23424a22 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/contatester/meta.yaml b/recipes/contatester/meta.yaml index 47bb63e01796e..858196f70ff7c 100644 --- a/recipes/contatester/meta.yaml +++ b/recipes/contatester/meta.yaml @@ -12,7 +12,7 @@ source: build: script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" skip: true # [py2k] - number: 3 + number: 4 entry_points: - contatester = fr.cea.cnrgh.lbi.contatester.__main__:main diff --git a/recipes/contrafold/meta.yaml b/recipes/contrafold/meta.yaml index 4bd9560480e37..c41569fa0097d 100644 --- a/recipes/contrafold/meta.yaml +++ b/recipes/contrafold/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 skip: True # [osx] source: diff --git a/recipes/control-freec/meta.yaml b/recipes/control-freec/meta.yaml index 806d4014eebe5..5673d86ef4ae5 100644 --- a/recipes/control-freec/meta.yaml +++ b/recipes/control-freec/meta.yaml @@ -14,7 +14,7 @@ source: - perl_shebang.patch build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('control-freec', max_pin="x") }} diff --git a/recipes/conus/build_failure.osx-64.yaml b/recipes/conus/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..4ee75ae296aee --- /dev/null +++ b/recipes/conus/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 79e6b9f624606e4a8b3a151ce5b326fa77d8ba2606cd11fd78dcec1f8ca396dc # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + checking for stdint.h... yes + checking for unistd.h... yes + checking limits.h usability... yes + checking limits.h presence... yes + checking for limits.h... yes + checking for stdlib.h... (cached) yes + checking for string.h... (cached) yes + checking for inline... inline + checking for stdlib.h... (cached) yes + checking for GNU libc compatible malloc... (cached) yes + checking for memset... yes + checking for sqrt... yes + checking for strchr... yes + checking for strerror... yes + configure: creating ./config.status + config.status: creating Makefile + (cd squid; make module;) + make[1]: Entering directory '$SRC_DIR/squid' + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c a2m.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c aligneval.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c alignio.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c clustal.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c cluster.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c dayhoff.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c eps.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c file.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c getopt.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c gki.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c gsi.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c hsregex.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c iupac.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c msa.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c msf.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c phylip.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c revcomp.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c rk.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c selex.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c seqencode.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c shuffle.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c sqerror.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c sqio.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c squidcore.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c sre_ctype.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c sre_math.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c sre_random.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c sre_string.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c ssi.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c stack.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c stockholm.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c stopwatch.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c translate.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c types.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c vectorops.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -DHAVE_CONFIG_H -c weight.c + ar rcv libsquid.a a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o + a - a2m.o + a - aligneval.o + a - alignio.o + a - clustal.o + a - cluster.o + a - dayhoff.o + a - eps.o + a - file.o + a - getopt.o + a - gki.o + a - gsi.o + a - hsregex.o + a - iupac.o + a - msa.o + a - msf.o + a - phylip.o + a - revcomp.o + a - rk.o + a - selex.o + a - seqencode.o + a - shuffle.o + a - sqerror.o + a - sqio.o + a - squidcore.o + a - sre_ctype.o + a - sre_math.o + a - sre_random.o + a - sre_string.o + a - ssi.o + a - stack.o + a - stockholm.o + a - stopwatch.o + a - translate.o + a - types.o + a - vectorops.o + a - weight.o + x86_64-apple-darwin13.4.0-ranlib libsquid.a + chmod 644 libsquid.a + make[1]: Leaving directory '$SRC_DIR/squid' + (cd src; make everything;) + make[1]: Entering directory '$SRC_DIR/src' + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -I../squid -c globals.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -I../squid -c alphabet.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/conus-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -I../squid -c trace.c + make[1]: Leaving directory '$SRC_DIR/src' +# Last 100 lines of the build log. diff --git a/recipes/conus/meta.yaml b/recipes/conus/meta.yaml index 2211bee11b280..8f5e44b926480 100644 --- a/recipes/conus/meta.yaml +++ b/recipes/conus/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.0 build: - number: 5 + number: 6 source: url: http://eddylab.org/software/conus/conus-1.0.tar.gz diff --git a/recipes/cooltools/0.3.2/meta.yaml b/recipes/cooltools/0.3.2/meta.yaml index fc27e32d88250..d608ed062afe8 100644 --- a/recipes/cooltools/0.3.2/meta.yaml +++ b/recipes/cooltools/0.3.2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: fa477e9edee4a4a44e4b0bf051481b95cfc81ca6651744102c7871186ccf72a9 build: - number: 4 + number: 5 skip: True # [py2k or py > 39] entry_points: - cooltools = cooltools.cli:cli diff --git a/recipes/cooltools/meta.yaml b/recipes/cooltools/meta.yaml index cb8b5698bca2c..2df35875170b0 100644 --- a/recipes/cooltools/meta.yaml +++ b/recipes/cooltools/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 1f12494add7b1271b71e418d10d060e1dac906a021fc2bd691e91f5599010051 build: - number: 0 + number: 1 entry_points: - cooltools = cooltools.cli:cli script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" diff --git a/recipes/core-snp-filter/meta.yaml b/recipes/core-snp-filter/meta.yaml index a980cc1dafa02..1bcd472109c67 100644 --- a/recipes/core-snp-filter/meta.yaml +++ b/recipes/core-snp-filter/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 5fa0357c4429e52644a9bdd5dfa4be3a3fc6889073f7678ed5a47f8a7f267c3d build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('core-snp-filter', max_pin="x.x") }} diff --git a/recipes/corset/build_failure.linux-64.yaml b/recipes/corset/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..14a29f7a119ca --- /dev/null +++ b/recipes/corset/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 1bda1159c5a0755ecf6a24a3129a0a13c1dd93c66b51a910feaacafa59357cd1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + ./Cluster.h:46:50: error: template argument 3 is invalid + ./Cluster.h:46:50: error: template argument 4 is invalid + ./Cluster.h:46:50: error: template argument 5 is invalid + ./Cluster.h:46:62: error: expected initializer before 'dist_iterator' + 46 | typedef unordered_map< uint64_t, unsigned char >::iterator dist_iterator; + | ^~~~~~~~~~~~~ + ./Cluster.h:53:3: error: 'uint64_t' does not name a type + 53 | uint64_t ntrans_; + | ^~~~~~~~ + ./Cluster.h:53:3: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + ./Cluster.h:64:13: error: 'uint64_t' has not been declared + 64 | int get_i(uint64_t key){ return(key / ntrans_); }; + | ^~~~~~~~ + ./Cluster.h:65:13: error: 'uint64_t' has not been declared + 65 | int get_j(uint64_t key){ return(key % ntrans_); }; + | ^~~~~~~~ + ./Cluster.h:66:3: error: 'dist_iterator' does not name a type + 66 | dist_iterator begin(){ return(dist_.begin()); }; + | ^~~~~~~~~~~~~ + ./Cluster.h:67:3: error: 'dist_iterator' does not name a type + 67 | dist_iterator end(){ return(dist_.end()); }; + | ^~~~~~~~~~~~~ + ./Cluster.h: In member function 'void DistanceMatrix::set_size(int)': + ./Cluster.h:55:30: error: 'ntrans_' was not declared in this scope; did you mean 'ntrans'? + 55 | void set_size(int ntrans){ ntrans_=ntrans; }; + | ^~~~~~~ + | ntrans + ./Cluster.h: In member function 'unsigned char DistanceMatrix::get(int, int)': + ./Cluster.h:56:49: error: 'ntrans_' was not declared in this scope; did you mean 'wctrans_t'? + 56 | unsigned char get(int i, int j){ return(dist_[ntrans_*ij]); } ; + | ^~~~~~~ + | wctrans_t + ./Cluster.h: In member function 'void DistanceMatrix::set(int, int, int)': + ./Cluster.h:59:13: error: 'ntrans_' was not declared in this scope; did you mean 'wctrans_t'? + 59 | dist_[ntrans_*ij]=value; + | ^~~~~~~ + | wctrans_t + ./Cluster.h: In member function 'bool DistanceMatrix::no_link(int, int)': + ./Cluster.h:63:45: error: request for member 'find' in '((DistanceMatrix*)this)->DistanceMatrix::dist_', which is of non-class type 'dist_map' {aka 'int'} + 63 | bool no_link(int i, int j){ return (dist_.find(ntrans_*ij)==dist_.end());}; + | ^~~~ + ./Cluster.h:63:50: error: 'ntrans_' was not declared in this scope; did you mean 'wctrans_t'? + 63 | bool no_link(int i, int j){ return (dist_.find(ntrans_*ij)==dist_.end());}; + | ^~~~~~~ + | wctrans_t + ./Cluster.h:63:70: error: request for member 'end' in '((DistanceMatrix*)this)->DistanceMatrix::dist_', which is of non-class type 'dist_map' {aka 'int'} + 63 | bool no_link(int i, int j){ return (dist_.find(ntrans_*ij)==dist_.end());}; + | ^~~ + ./Cluster.h: In member function 'int DistanceMatrix::get_i(int)': + ./Cluster.h:64:41: error: 'ntrans_' was not declared in this scope; did you mean 'wctrans_t'? + 64 | int get_i(uint64_t key){ return(key / ntrans_); }; + | ^~~~~~~ + | wctrans_t + ./Cluster.h: In member function 'int DistanceMatrix::get_j(int)': + ./Cluster.h:65:41: error: 'ntrans_' was not declared in this scope; did you mean 'wctrans_t'? + 65 | int get_j(uint64_t key){ return(key % ntrans_); }; + | ^~~~~~~ + | wctrans_t + ./Cluster.h: In member function 'void DistanceMatrix::remove(int, int)': + ./Cluster.h:69:11: error: request for member 'erase' in '((DistanceMatrix*)this)->DistanceMatrix::dist_', which is of non-class type 'dist_map' {aka 'int'} + 69 | dist_.erase(ntrans_*ij); + | ^~~~~ + ./Cluster.h:69:17: error: 'ntrans_' was not declared in this scope; did you mean 'wctrans_t'? + 69 | dist_.erase(ntrans_*ij); + | ^~~~~~~ + | wctrans_t + Cluster.cc: In member function 'unsigned char Cluster::find_next_pair(int&, int&)': + Cluster.cc:206:3: error: 'dist_iterator' was not declared in this scope + 206 | dist_iterator ditr=dist.begin(); + | ^~~~~~~~~~~~~ + Cluster.cc:209:9: error: 'ditr' was not declared in this scope + 209 | for(; ditr!=dist.end(); ditr){ + | ^~~~ + Cluster.cc:209:20: error: 'class DistanceMatrix' has no member named 'end' + 209 | for(; ditr!=dist.end(); ditr){ + | ^~~ + make: *** [Makefile:12: Cluster.o] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/corset_1734288080692/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/corset_1734288080692/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/corset/build_failure.osx-64.yaml b/recipes/corset/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..2247fd2ec9f54 --- /dev/null +++ b/recipes/corset/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 1bda1159c5a0755ecf6a24a3129a0a13c1dd93c66b51a910feaacafa59357cd1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - libclang-cpp18.1 18.1.8 default_h0c94c6a_5 + - cctools_osx-64 1010.6 h00edd4c_2 + - clang-18 18.1.8 default_h0c94c6a_5 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + - clangxx_impl_osx-64 18.1.8 h4b7810f_23 + - liblzma 5.6.3 hd471939_1 + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/corset_1734378985096/work/conda_build.sh']' returned non-zero exit status 1. + - clangxx_osx-64 18.1.8 h7e5c614_23 + - clangxx 18.1.8 default_h179603d_5 + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + - clang_impl_osx-64 18.1.8 h6a44ed1_23 + - llvm-tools-18 18.1.8 h9ce406d_2 + - libcxx-devel 18.1.8 h7c275be_7 + - clang 18.1.8 default_h179603d_5 + - ncurses 6.5 hf036a51_1 + host: + - libcxx 19.1.5 hf95d169_0 + - libzlib 1.2.13 h87427d6_6 + - ncurses 6.5 hf036a51_1 + - zlib 1.2.13 h87427d6_6 + - samtools 0.1.19 hd510865_11 + run: + - libzlib >=1.2.13,<2.0a0 + - libcxx >=18 + test: + commands: + - corset 2>&1 | grep Usage + about: + home: https://github.com/Oshlack/Corset + license: GPLv3 + summary: Software for clustering de novo assembled transcripts and counting overlapping + reads. + extra: + copy_test_source_files: true + final: true + identifiers: + - biotools:corset + - doi:10.1186/s13059-014-0410-6 + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/corset_1734378985096/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/corset_1734378985096/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/corset_1734378985096/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/corset_1734378985096/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/corset-1.09 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/corset-1.09 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/corset-1.09 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/corset-1.09 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + checking whether the C compiler works... yes + checking for C compiler default output file name... a.out + checking for suffix of executables... +# Last 100 lines of the build log. diff --git a/recipes/corset/meta.yaml b/recipes/corset/meta.yaml index c22537b34f644..29878f7bf1e38 100644 --- a/recipes/corset/meta.yaml +++ b/recipes/corset/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://github.com/Oshlack/Corset/archive/version-1.09.tar.gz diff --git a/recipes/coverageanomalyscanner/meta.yaml b/recipes/coverageanomalyscanner/meta.yaml index b9557aaf2c6b3..39448682e640a 100644 --- a/recipes/coverageanomalyscanner/meta.yaml +++ b/recipes/coverageanomalyscanner/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: True # [osx] - number: 3 + number: 4 requirements: build: diff --git a/recipes/coverm/meta.yaml b/recipes/coverm/meta.yaml index d17de6bd0b76c..0dae75d1fe9a8 100644 --- a/recipes/coverm/meta.yaml +++ b/recipes/coverm/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 skip: True # [osx] run_exports: - {{ pin_subpackage('coverm', max_pin="x.x") }} diff --git a/recipes/covtobed/meta.yaml b/recipes/covtobed/meta.yaml index 16e003aa5c4bb..b314eb06bdc4b 100644 --- a/recipes/covtobed/meta.yaml +++ b/recipes/covtobed/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 0d826ad5bc32661806cfa75851e3b70a8a2b6b0b65393908ed954a1aee7c5d6c build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage('covtobed', max_pin="x") }} diff --git a/recipes/cpat/meta.yaml b/recipes/cpat/meta.yaml index b3c44608b4a8c..7ca8e5ab74a80 100644 --- a/recipes/cpat/meta.yaml +++ b/recipes/cpat/meta.yaml @@ -6,7 +6,7 @@ package: version: "{{ version }}" build: - number: 2 + number: 3 skip: True # [py > 39] run_exports: - {{ pin_subpackage('cpat', max_pin="x") }} @@ -47,4 +47,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/cpgeneprofiler/meta.yaml b/recipes/cpgeneprofiler/meta.yaml index 561e876d4d0ab..aa2587fbfcca9 100644 --- a/recipes/cpgeneprofiler/meta.yaml +++ b/recipes/cpgeneprofiler/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 noarch: generic script: R CMD INSTALL --build . rpaths: diff --git a/recipes/crass/meta.yaml b/recipes/crass/meta.yaml index ff8ec2f1fdd17..53957a09dda86 100644 --- a/recipes/crass/meta.yaml +++ b/recipes/crass/meta.yaml @@ -13,7 +13,7 @@ source: - patch build: - number: 5 + number: 6 skip: True # [osx] requirements: diff --git a/recipes/crispresso2/meta.yaml b/recipes/crispresso2/meta.yaml index 5fd4076cdc98a..2fa9e0b8e8081 100644 --- a/recipes/crispresso2/meta.yaml +++ b/recipes/crispresso2/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage('crispresso2', max_pin='x') }} diff --git a/recipes/crispritz/meta.yaml b/recipes/crispritz/meta.yaml index ffc3006edb60b..6e679357f8e06 100644 --- a/recipes/crispritz/meta.yaml +++ b/recipes/crispritz/meta.yaml @@ -9,7 +9,7 @@ source: sha256: a254321a4bb8724023191c3a71697f6e2994c8a0001bc26bbc302fa036bc0807 build: - number: 2 + number: 3 skip: True # [py2k or osx or py > 39] requirements: diff --git a/recipes/crumble/meta.yaml b/recipes/crumble/meta.yaml index ffae1c4ace4a9..064a3e9ba24ad 100644 --- a/recipes/crumble/meta.yaml +++ b/recipes/crumble/meta.yaml @@ -6,7 +6,7 @@ package: version: '{{version}}' build: - number: 3 + number: 4 source: url: https://github.com/jkbonfield/crumble/archive/refs/tags/v{{ version }}.tar.gz diff --git a/recipes/crussmap/build_failure.osx-64.yaml b/recipes/crussmap/build_failure.osx-64.yaml deleted file mode 100644 index d89ee13de013f..0000000000000 --- a/recipes/crussmap/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: b743a1ca09f4f5e5e0d026a3f56eb87696ffa528cf106ca19b2c02c73a4f3277 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - = note: env -u IPHONEOS_DEPLOYMENT_TARGET -u TVOS_DEPLOYMENT_TARGET LC_ALL="C" PATH="/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/bin:/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/bin:/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin:/opt/mambaforge/envs/bioconda/condabin:/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/bin:/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin:/opt/mambaforge/envs/bioconda/bin:/opt/mambaforge/condabin:/opt/mambaforge/bin:/usr/local/lib/ruby/gems/3.0.0/bin:/usr/local/opt/ruby@3.0/bin:/usr/local/opt/pipx_bin:/Users/runner/.cargo/bin:/usr/local/opt/curl/bin:/usr/local/bin:/usr/local/sbin:/Users/runner/bin:/Users/runner/.yarn/bin:/Users/runner/Library/Android/sdk/tools:/Users/runner/Library/Android/sdk/platform-tools:/Library/Frameworks/Python.framework/Versions/Current/bin:/Library/Frameworks/Mono.framework/Versions/Current/Commands:/usr/bin:/bin:/usr/sbin:/sbin:/Users/runner/.dotnet/tools" VSLANG="1033" ZERO_AR_DATE="1" "cc" "-arch" "x86_64" "-m64" "/tmp/rustccHK7kk/symbols.o" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/target/release/build/proc-macro2-acbd332dc98100aa/build_script_build-acbd332dc98100aa.build_script_build.b170873ab59dfdfb-cgu.0.rcgu.o" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/target/release/build/proc-macro2-acbd332dc98100aa/build_script_build-acbd332dc98100aa.build_script_build.b170873ab59dfdfb-cgu.1.rcgu.o" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/target/release/build/proc-macro2-acbd332dc98100aa/build_script_build-acbd332dc98100aa.1cihp38p4lvyzkkj.rcgu.o" "-L" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/target/release/deps" "-L" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libstd-2ad7f97be9e16ca5.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libpanic_unwind-8ce93eee8bf4c86e.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libobject-0e1339b212cc7409.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libmemchr-925e672b3deb429c.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libaddr2line-e92d517a950bccd8.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libgimli-de95e5c2a2ace281.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_demangle-37f4c48e230f618e.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libstd_detect-dfeb4bb0652b6b8e.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libhashbrown-0e3ea0ec18336be2.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_std_workspace_alloc-39dd3003e36d7872.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libminiz_oxide-5ea1513e08ee15e0.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libadler-2967159221f4860d.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libunwind-b70656709e3eca11.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcfg_if-cc5626b2e0399737.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/liblibc-8378684dba6ab463.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/liballoc-0ff05b9b25b786cc.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_std_workspace_core-9a6da74aeab39c54.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcore-1638dc700d175798.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcompiler_builtins-7f42af62722c8f43.rlib" "-lSystem" "-lc" "-lm" "-L" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib" "-o" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/target/release/build/proc-macro2-acbd332dc98100aa/build_script_build-acbd332dc98100aa" "-Wl,-dead_strip" "-nodefaultlibs" - = note: ld: multiple errors: unsupported mach-o filetype (only MH_OBJECT and MH_DYLIB can be linked) in '/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/lib/libSystem.B.dylib'; unsupported mach-o filetype (only MH_OBJECT and MH_DYLIB can be linked) in '/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/lib/libSystem.B.dylib'; unsupported mach-o filetype (only MH_OBJECT and MH_DYLIB can be linked) in '/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/lib/libSystem.B.dylib' - clang: error: linker command failed with exit code 1 (use -v to see invocation) - - - error: linking with cc failed: exit status: 1 - | - = note: env -u IPHONEOS_DEPLOYMENT_TARGET -u TVOS_DEPLOYMENT_TARGET LC_ALL="C" PATH="/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/bin:/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/bin:/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin:/opt/mambaforge/envs/bioconda/condabin:/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/bin:/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin:/opt/mambaforge/envs/bioconda/bin:/opt/mambaforge/condabin:/opt/mambaforge/bin:/usr/local/lib/ruby/gems/3.0.0/bin:/usr/local/opt/ruby@3.0/bin:/usr/local/opt/pipx_bin:/Users/runner/.cargo/bin:/usr/local/opt/curl/bin:/usr/local/bin:/usr/local/sbin:/Users/runner/bin:/Users/runner/.yarn/bin:/Users/runner/Library/Android/sdk/tools:/Users/runner/Library/Android/sdk/platform-tools:/Library/Frameworks/Python.framework/Versions/Current/bin:/Library/Frameworks/Mono.framework/Versions/Current/Commands:/usr/bin:/bin:/usr/sbin:/sbin:/Users/runner/.dotnet/tools" VSLANG="1033" ZERO_AR_DATE="1" "cc" "-arch" "x86_64" "-m64" "/tmp/rustc98NmYZ/symbols.o" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/target/release/build/serde-1e62519906f99e77/build_script_build-1e62519906f99e77.build_script_build.a4f0df5c432a73cf-cgu.0.rcgu.o" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/target/release/build/serde-1e62519906f99e77/build_script_build-1e62519906f99e77.386t7nrmg305mq0l.rcgu.o" "-L" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/target/release/deps" "-L" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libstd-2ad7f97be9e16ca5.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libpanic_unwind-8ce93eee8bf4c86e.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libobject-0e1339b212cc7409.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libmemchr-925e672b3deb429c.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libaddr2line-e92d517a950bccd8.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libgimli-de95e5c2a2ace281.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_demangle-37f4c48e230f618e.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libstd_detect-dfeb4bb0652b6b8e.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libhashbrown-0e3ea0ec18336be2.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_std_workspace_alloc-39dd3003e36d7872.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libminiz_oxide-5ea1513e08ee15e0.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libadler-2967159221f4860d.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libunwind-b70656709e3eca11.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcfg_if-cc5626b2e0399737.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/liblibc-8378684dba6ab463.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/liballoc-0ff05b9b25b786cc.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_std_workspace_core-9a6da74aeab39c54.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcore-1638dc700d175798.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcompiler_builtins-7f42af62722c8f43.rlib" "-lSystem" "-lc" "-lm" "-L" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/lib/rustlib/x86_64-apple-darwin/lib" "-o" "/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/target/release/build/serde-1e62519906f99e77/build_script_build-1e62519906f99e77" "-Wl,-dead_strip" "-nodefaultlibs" - = note: ld: multiple errors: unsupported mach-o filetype (only MH_OBJECT and MH_DYLIB can be linked) in '/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/lib/libSystem.B.dylib'; unsupported mach-o filetype (only MH_OBJECT and MH_DYLIB can be linked) in '/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/lib/libSystem.B.dylib'; unsupported mach-o filetype (only MH_OBJECT and MH_DYLIB can be linked) in '/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/lib/libSystem.B.dylib' - clang: error: linker command failed with exit code 1 (use -v to see invocation) - - - error: could not compile num-traits (build script) due to 1 previous error - - Caused by: - process didn't exit successfully: rustc --crate-name build_script_build --edition=2021 /opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/num-traits-0.2.19/build.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="default"' --cfg 'feature="std"' -C metadata=71100027d0b4f7b1 -C extra-filename=-71100027d0b4f7b1 --out-dir /opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/target/release/build/num-traits-71100027d0b4f7b1 -C strip=debuginfo -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/target/release/deps --extern autocfg=/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/target/release/deps/libautocfg-c5a6e5900b9987d4.rlib --cap-lints allow (exit status: 1) - warning: build failed, waiting for other jobs to finish... - error: could not compile serde (build script) due to 1 previous error - - Caused by: - process didn't exit successfully: rustc --crate-name build_script_build --edition=2018 /opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/serde-1.0.203/build.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="default"' --cfg 'feature="derive"' --cfg 'feature="serde_derive"' --cfg 'feature="std"' -C metadata=1e62519906f99e77 -C extra-filename=-1e62519906f99e77 --out-dir /opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/target/release/build/serde-1e62519906f99e77 -C strip=debuginfo -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/target/release/deps --cap-lints allow (exit status: 1) - error: could not compile proc-macro2 (build script) due to 1 previous error - - Caused by: - process didn't exit successfully: rustc --crate-name build_script_build --edition=2021 /opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/proc-macro2-1.0.85/build.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="default"' --cfg 'feature="proc-macro"' -C metadata=acbd332dc98100aa -C extra-filename=-acbd332dc98100aa --out-dir /opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/target/release/build/proc-macro2-acbd332dc98100aa -C strip=debuginfo -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/target/release/deps --cap-lints allow (exit status: 1) - error: could not compile libc (build script) due to 1 previous error - - Caused by: - process didn't exit successfully: rustc --crate-name build_script_build /opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/libc-0.2.155/build.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="default"' --cfg 'feature="std"' -C metadata=312897ad65048e13 -C extra-filename=-312897ad65048e13 --out-dir /opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/target/release/build/libc-312897ad65048e13 -C strip=debuginfo -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/target/release/deps --cap-lints allow (exit status: 1) - error: failed to compile crussmap v1.0.0 (/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work), intermediate artifacts can be found at /opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/target. - To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. - Extracting download - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/_build_env - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/crussmap-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/crussmap_1717511174373/work/conda_build.sh']' returned non-zero exit status 101. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/crussmap-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/crussmap-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/crussmap-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -# Last 100 lines of the build log. diff --git a/recipes/crussmap/meta.yaml b/recipes/crussmap/meta.yaml index cfa5b52359e23..c49c030859571 100644 --- a/recipes/crussmap/meta.yaml +++ b/recipes/crussmap/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 skip: True # [win] source: diff --git a/recipes/crux-toolkit/meta.yaml b/recipes/crux-toolkit/meta.yaml index cf96b461e5ece..643c451e2d860 100644 --- a/recipes/crux-toolkit/meta.yaml +++ b/recipes/crux-toolkit/meta.yaml @@ -1,49 +1,49 @@ -{% set version = "4.2" %} - -package: - name: crux-toolkit - version: {{ version }} - -source: - - url: https://noble.gs.washington.edu/crux-downloads/crux-{{ version }}/crux-{{ version }}.Linux.x86_64.zip # [linux] - sha256: b5c1a02416f0220beb6106e12a7b330932dec396291ae364af8f2153a1e1655d # [linux] - - url: https://noble.gs.washington.edu/crux-downloads/crux-{{ version }}/crux-{{ version }}.Darwin.x86_64.zip # [osx] - sha256: 5f1fb9124391cec30608740fdce3aea7fcb3f19330531ea90f6ecf81b8583d00 # [osx] - -build: - number: 0 - script: "mkdir -p $PREFIX/bin; chmod a+x bin/*; cp bin/* $PREFIX/bin" - run_exports: - - {{ pin_subpackage('crux-toolkit', max_pin="x")}} - - binary_relocation: False - detect_binary_files_with_prefix: False - missing_dso_whitelist: - - /lib64/libpthread.so.0 - - /lib64/libgomp.so.6 - - /lib64/libstdc.so.6 - - /lib64/libm.so.6 - - /lib64/libgcc_s.so.1 - - /lib64/libc.so.6 - -requirements: - run: -test: - commands: - - export LD_LIBRARY_PATH=/opt/conda/lib64 crux version - - -about: - home: http://crux.ms - summary: A cross-platform suite of analysis tools for interpreting protein mass spectrometry data - license: Apache-2.0 - license_family: Apache - dev_url: https://github.com/crux-toolkit/crux-toolkit - -extra: - recipe-maintainers: - - CharlesEGrant - - wsnoble - - acquayefrank - skip-lints: - - should_be_noarch_generic +{% set version = "4.2" %} + +package: + name: crux-toolkit + version: {{ version }} + +source: + - url: https://noble.gs.washington.edu/crux-downloads/crux-{{ version }}/crux-{{ version }}.Linux.x86_64.zip # [linux] + sha256: b5c1a02416f0220beb6106e12a7b330932dec396291ae364af8f2153a1e1655d # [linux] + - url: https://noble.gs.washington.edu/crux-downloads/crux-{{ version }}/crux-{{ version }}.Darwin.x86_64.zip # [osx] + sha256: 5f1fb9124391cec30608740fdce3aea7fcb3f19330531ea90f6ecf81b8583d00 # [osx] + +build: + number: 0 + script: "mkdir -p $PREFIX/bin; chmod a+x bin/*; cp bin/* $PREFIX/bin" + run_exports: + - {{ pin_subpackage('crux-toolkit', max_pin="x")}} + + binary_relocation: False + detect_binary_files_with_prefix: False + missing_dso_whitelist: + - /lib64/libpthread.so.0 + - /lib64/libgomp.so.6 + - /lib64/libstdc.so.6 + - /lib64/libm.so.6 + - /lib64/libgcc_s.so.1 + - /lib64/libc.so.6 + +requirements: + run: +test: + commands: + - export LD_LIBRARY_PATH=/opt/conda/lib64 crux version + + +about: + home: http://crux.ms + summary: A cross-platform suite of analysis tools for interpreting protein mass spectrometry data + license: Apache-2.0 + license_family: Apache + dev_url: https://github.com/crux-toolkit/crux-toolkit + +extra: + recipe-maintainers: + - CharlesEGrant + - wsnoble + - acquayefrank + skip-lints: + - should_be_noarch_generic diff --git a/recipes/cryfa/meta.yaml b/recipes/cryfa/meta.yaml index 121dbfc8fff27..f36cc7381eab2 100644 --- a/recipes/cryfa/meta.yaml +++ b/recipes/cryfa/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 source: url: https://github.com/cobilab/cryfa/archive/refs/tags/v{{ version }}.tar.gz diff --git a/recipes/csblast/2.2.3/meta.yaml b/recipes/csblast/2.2.3/meta.yaml index 04c90f36b44a1..da27fcf7ad29a 100644 --- a/recipes/csblast/2.2.3/meta.yaml +++ b/recipes/csblast/2.2.3/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 2f4de1e961476f7144e5a17e07a93929aa7c56be587c160fdee449617cf5fc13 # [osx] build: - number: 3 + number: 4 script: - cp -R bin/ "${PREFIX}"/bin/ - cp -R data/ "${PREFIX}"/data/ diff --git a/recipes/curves/build_failure.osx-64.yaml b/recipes/curves/build_failure.osx-64.yaml index 3ec5d235febae..6869b8dd3a62f 100644 --- a/recipes/curves/build_failure.osx-64.yaml +++ b/recipes/curves/build_failure.osx-64.yaml @@ -1,51 +1,48 @@ -recipe_sha: 8ed3ed2a1646f5cf5fa1b3b367f9bc209eb8e2ad2941bb3f9b785ee7baa7b0ad # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: e22cabe3d15a10fd67846e95fbc4b5d57ea8069efbcb511276aac018e3efbb94 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: compiler error -log: |- - Downloading http://curvesplus.bsc.es/static/app/canal.f - Extracting download - Warning: Unrecognized source format. Source file will be copied to the SRC_DIR - Downloading source to cache: canion_81b324d4b4.f - Downloading http://curvesplus.bsc.es/static/app/canion.f - getdate.c:6:11: fatal error: time.h: No such file or directory - 6 | # include - | ^~~~~~~~ - compilation terminated. - make: *** [Makefile:79: getdate.o] Error 1 - Extracting download - Warning: Unrecognized source format. Source file will be copied to the SRC_DIR - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/curves_1718386465597/work - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/curves_1718386465597/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/curves_1718386465597/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/curves_1718386465597/work - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree +log: |2- + - libnetcdf >=4.9.2,<4.9.3.0a0 + - libcxx >=18 + - libgfortran 5.* + test: + files: + - input_files.tar.gz + about: + description: Curves is a revised version of the Curves approach for analysing the + structure of nucleic acids. It respects the international conventions for nucleic + acid analysis, runs much faster and provides new data. + home: http://curvesplus.bsc.es/misc + license: Apache Software License + license_family: APACHE + summary: 'CURVES: Conformational analysis of single nucleic acid structures or + of molecular dynamics trajectories' + extra: + build: + python: + - '3.8' + - '3.9' + - '3.10' + copy_test_source_files: true + final: true + skip: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/curves_1734455067686/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/curves_1734455067686/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/curves_1734455067686/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/curves_1734455067686/work INFO: activate-gfortran_osx-64.sh made the following environmental changes: DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/curves-3.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments - packages_from_this = build( DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/curves-3.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments F77=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran F90=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran F95=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran FC=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran FC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/curves-3.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/curves-3.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix GFORTRAN=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran INFO: activate_clang_osx-64.sh made the following environmental changes: - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/curves_1718386465597/work/conda_build.sh']' returned non-zero exit status 2. AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as CC=x86_64-apple-darwin13.4.0-clang @@ -53,11 +50,13 @@ log: |- CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/curves-3.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/curves-3.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool @@ -66,7 +65,7 @@ log: |- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -75,7 +74,7 @@ log: |- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -103,3 +102,5 @@ log: |- $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran -cpp -w -O2 -I$PREFIX/include/ -DNETCDF -Wno-argument-mismatch -DXTC -fallow-argument-mismatch -c findaxis.f $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran -I/Library/Developer/CommandLineTools/SDKs/MacOSX13.1.sdk/usr/include -Iinclude -dM -c getdate.c # Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/curves/meta.yaml b/recipes/curves/meta.yaml index 9d1499a6c88c0..e0baa3a200d46 100644 --- a/recipes/curves/meta.yaml +++ b/recipes/curves/meta.yaml @@ -17,7 +17,7 @@ source: sha256: 81b324d4b4ff835e56f81a3f7d6a408f511e89a42cac8f390516a9fb3f9026f7 build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage(name, max_pin='x') }} diff --git a/recipes/cuttlefish/build_failure.linux-64.yaml b/recipes/cuttlefish/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..918a2aa3e3f07 --- /dev/null +++ b/recipes/cuttlefish/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: f0decf0fef183264aa515b4255b61dfc06e7c852460672006e6b87b93e7e3c95 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + mv kmc_core/simde-amalgamated-0.7.2 kmc_core/simde + % Total % Received % Xferd Average Speed Time Time Time Current + Dload Upload Total Spent Left Speed + 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 + 100 238k 100 238k 0 0 901k 0 --:--:-- --:--:-- --:--:-- 901k + simde-amalgamated-0.7.2/ + simde-amalgamated-0.7.2/x86/ + simde-amalgamated-0.7.2/x86/avx2.h + simde-amalgamated-0.7.2/x86/avx512.h + simde-amalgamated-0.7.2/x86/avx.h + simde-amalgamated-0.7.2/x86/clmul.h + simde-amalgamated-0.7.2/x86/fma.h + simde-amalgamated-0.7.2/x86/gfni.h + simde-amalgamated-0.7.2/x86/mmx.h + simde-amalgamated-0.7.2/x86/sse2.h + simde-amalgamated-0.7.2/x86/sse3.h + simde-amalgamated-0.7.2/x86/sse4.1.h + simde-amalgamated-0.7.2/x86/sse4.2.h + simde-amalgamated-0.7.2/x86/sse.h + simde-amalgamated-0.7.2/x86/ssse3.h + simde-amalgamated-0.7.2/x86/svml.h + simde-amalgamated-0.7.2/x86/xop.h + simde-amalgamated-0.7.2/arm/ + simde-amalgamated-0.7.2/arm/neon.h + make[3]: Leaving directory '$SRC_DIR/external/KMC-3.2.1' + make[3]: warning: -j4 forced in submake: resetting jobserver mode. + make[3]: Entering directory '$SRC_DIR/external/KMC-3.2.1' + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c14 -fPIC -c kmc_CLI/kmc.cpp -o kmc_CLI/kmc.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c14 -fPIC -c kmc_core/mem_disk_file.cpp -o kmc_core/mem_disk_file.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c14 -fPIC -c kmc_core/rev_byte.cpp -o kmc_core/rev_byte.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c14 -fPIC -c kmc_core/bkb_writer.cpp -o kmc_core/bkb_writer.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c14 -fPIC -c kmc_core/cpu_info.cpp -o kmc_core/cpu_info.o + In file included from kmc_core/mem_disk_file.cpp:12: + kmc_core/critical_error_handler.h: In member function 'void CCriticalErrorHandler::HandleCriticalError(const std::string&)': + kmc_core/critical_error_handler.h:77:28: error: 'runtime_error' is not a member of 'std' + 77 | throw std::runtime_error(msg); + | ^~~~~~~~~~~~~ + kmc_core/critical_error_handler.h:7:1: note: 'std::runtime_error' is defined in header ''; did you forget to '#include '? + 6 | #include + |#include + 7 | + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c14 -fPIC -c kmc_core/bkb_reader.cpp -o kmc_core/bkb_reader.o + In file included from kmc_core/queues.h:25, + from kmc_core/params.h:16, + from kmc_core/bkb_writer.h:14, + from kmc_core/bkb_writer.cpp:11: + kmc_core/critical_error_handler.h: In member function 'void CCriticalErrorHandler::HandleCriticalError(const std::string&)': + kmc_core/critical_error_handler.h:77:28: error: 'runtime_error' is not a member of 'std' + 77 | throw std::runtime_error(msg); + | ^~~~~~~~~~~~~ + kmc_core/critical_error_handler.h:7:1: note: 'std::runtime_error' is defined in header ''; did you forget to '#include '? + 6 | #include + |#include + 7 | + make[3]: *** [Makefile:118: kmc_core/mem_disk_file.o] Error 1 + make[3]: *** Waiting for unfinished jobs.... + In file included from kmc_core/queues.h:25, + from kmc_core/params.h:16, + from kmc_core/bkb_reader.h:15, + from kmc_core/bkb_reader.cpp:11: + kmc_core/critical_error_handler.h: In member function 'void CCriticalErrorHandler::HandleCriticalError(const std::string&)': + kmc_core/critical_error_handler.h:77:28: error: 'runtime_error' is not a member of 'std' + 77 | throw std::runtime_error(msg); + | ^~~~~~~~~~~~~ + kmc_core/critical_error_handler.h:7:1: note: 'std::runtime_error' is defined in header ''; did you forget to '#include '? + 6 | #include + |#include + 7 | + make[3]: *** [Makefile:118: kmc_core/bkb_writer.o] Error 1 + make[3]: *** [Makefile:118: kmc_core/bkb_reader.o] Error 1 + make[3]: Leaving directory '$SRC_DIR/external/KMC-3.2.1' + make[2]: *** [CMakeFiles/prj_kmc.dir/build.make:86: prj_kmc-prefix/src/prj_kmc-stamp/prj_kmc-build] Error 2 + make[2]: Leaving directory '$SRC_DIR/build' + make[1]: *** [CMakeFiles/Makefile2:115: CMakeFiles/prj_kmc.dir/all] Error 2 + make[1]: Leaving directory '$SRC_DIR/build' + make: *** [Makefile:136: all] Error 2 + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cuttlefish_1734294447658/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cuttlefish_1734294447658/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/cuttlefish/build_failure.osx-arm64.yaml b/recipes/cuttlefish/build_failure.osx-arm64.yaml new file mode 100644 index 0000000000000..035e380eaef4f --- /dev/null +++ b/recipes/cuttlefish/build_failure.osx-arm64.yaml @@ -0,0 +1,106 @@ +recipe_sha: f0decf0fef183264aa515b4255b61dfc06e7c852460672006e6b87b93e7e3c95 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + OTOOL=arm64-apple-darwin20.0.0-otool + PAGESTUFF=arm64-apple-darwin20.0.0-pagestuff + RANLIB=arm64-apple-darwin20.0.0-ranlib + REDO_PREBINDING=arm64-apple-darwin20.0.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk + SEGEDIT=arm64-apple-darwin20.0.0-segedit + SEG_ADDR_TABLE=arm64-apple-darwin20.0.0-seg_addr_table + SEG_HACK=arm64-apple-darwin20.0.0-seg_hack + SIZE=arm64-apple-darwin20.0.0-size + STRINGS=arm64-apple-darwin20.0.0-strings + STRIP=arm64-apple-darwin20.0.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_arm64_apple_darwin20_0_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=arm64-apple-darwin20.0.0 + host_alias=arm64-apple-darwin20.0.0 + INFO: activate_clangxx_osx-arm64.sh made the following environmental changes: + CLANGXX=arm64-apple-darwin20.0.0-clang + CXX=arm64-apple-darwin20.0.0-clang + CXXFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cuttlefish-2.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang + DEBUG_CXXFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/cuttlefish-2.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -- The CXX compiler identification is Clang 18.1.8 + -- The C compiler identification is Clang 18.1.8 + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang - skipped + -- Detecting C compile features + -- Detecting C compile features - done + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success + -- Found Threads: TRUE + -- Found ZLIB: $PREFIX/lib/libz.dylib (found version "1.3.1") + -- Found BZip2: $PREFIX/lib/libbz2.dylib (found version "1.0.8") + -- Looking for BZ2_bzCompressInit + -- Looking for BZ2_bzCompressInit - found + -- Found PkgConfig: /opt/homebrew/bin/pkg-config (found version "2.3.0") + -- Found Jemalloc: $PREFIX/lib/libjemalloc.dylib (found suitable version "5.3.0-0-g54eaed1d8b56b1aa528be3bdd1877e59c56fa90c", minimum required is "5.2.1") + -- Configuring done (13.4s) + -- Generating done (0.0s) + -- Build files have been written to: $SRC_DIR/build + Change Dir: '$SRC_DIR/build' + + Run Build Command(s): $BUILD_PREFIX/bin/cmake -E env VERBOSE=1 $BUILD_PREFIX/bin/make -f Makefile -j2 install + $BUILD_PREFIX/bin/cmake -S$SRC_DIR -B$SRC_DIR/build --check-build-system CMakeFiles/Makefile.cmake 0 + $BUILD_PREFIX/bin/cmake -E cmake_progress_start $SRC_DIR/build/CMakeFiles $SRC_DIR/build//CMakeFiles/progress.marks + $BUILD_PREFIX/bin/make -f CMakeFiles/Makefile2 all + make[1]: Entering directory '$SRC_DIR/build' + $BUILD_PREFIX/bin/make -f CMakeFiles/prj_kmc.dir/build.make CMakeFiles/prj_kmc.dir/depend + make[2]: Entering directory '$SRC_DIR/build' + cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR $SRC_DIR/build $SRC_DIR/build $SRC_DIR/build/CMakeFiles/prj_kmc.dir/DependInfo.cmake "--color=" + make[2]: Leaving directory '$SRC_DIR/build' + $BUILD_PREFIX/bin/make -f CMakeFiles/prj_kmc.dir/build.make CMakeFiles/prj_kmc.dir/build + make[2]: Entering directory '$SRC_DIR/build' + [ 1%] Creating directories for 'prj_kmc' + $BUILD_PREFIX/bin/cmake -Dcfgdir= -P $SRC_DIR/build/prj_kmc-prefix/tmp/prj_kmc-mkdirs.cmake + $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/build/prj_kmc-prefix/src/prj_kmc-stamp/prj_kmc-mkdir + [ 3%] Performing download step for 'prj_kmc' + cd $SRC_DIR/external && curl -k -L https://github.com/refresh-bio/KMC/archive/refs/tags/v3.2.1.tar.gz -o KMC-3.2.1.tar.gz && tar -xzf KMC-3.2.1.tar.gz && rm KMC-3.2.1.tar.gz + cd $SRC_DIR/external && $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/build/prj_kmc-prefix/src/prj_kmc-stamp/prj_kmc-download + [ 5%] No update step for 'prj_kmc' + $BUILD_PREFIX/bin/cmake -E echo_append + $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/build/prj_kmc-prefix/src/prj_kmc-stamp/prj_kmc-update + [ 7%] Performing patch step for 'prj_kmc' + cd $SRC_DIR/external/KMC-3.2.1 && patch --strip 1 < $SRC_DIR/patches/kmc_patch.diff + patching file Makefile + patching file kmc_CLI/kmc.cpp + patching file kmc_api/kmer_defs.h + patching file kmc_core/cpu_info.cpp + patching file kmc_core/defs.h + patching file kmc_core/fastq_reader.h + patching file kmc_core/intr_copy.h + patching file kmc_core/queues.h + cd $SRC_DIR/external/KMC-3.2.1 && $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/build/prj_kmc-prefix/src/prj_kmc-stamp/prj_kmc-patch + [ 8%] No configure step for 'prj_kmc' + cd $SRC_DIR/external/KMC-3.2.1 && $BUILD_PREFIX/bin/cmake -E echo_append + cd $SRC_DIR/external/KMC-3.2.1 && $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/build/prj_kmc-prefix/src/prj_kmc-stamp/prj_kmc-configure + [ 10%] Performing build step for 'prj_kmc' + cd $SRC_DIR/external/KMC-3.2.1 && make -j4 CC=clang simde && make -j4 CC=clang kmc + make[3]: Entering directory '$SRC_DIR/external/KMC-3.2.1' + curl -k -L https://github.com/simd-everywhere/simde/releases/download/v0.7.2/simde-amalgamated-0.7.2.tar.xz -o kmc_core/simde-amalgamated-0.7.2.tar.xz && \ + tar -C kmc_core -xvf kmc_core/simde-amalgamated-0.7.2.tar.xz && \ + rm kmc_core/simde-amalgamated-0.7.2.tar.xz && \ + mv kmc_core/simde-amalgamated-0.7.2 kmc_core/simde + make[3]: Leaving directory '$SRC_DIR/external/KMC-3.2.1' + make[3]: Entering directory '$SRC_DIR/external/KMC-3.2.1' + clang -Wall -O3 -m64 -pthread -std=c14 -fPIC -c kmc_CLI/kmc.cpp -o kmc_CLI/kmc.o + clang -Wall -O3 -m64 -pthread -std=c14 -fPIC -c kmc_core/mem_disk_file.cpp -o kmc_core/mem_disk_file.o + clang -Wall -O3 -m64 -pthread -std=c14 -fPIC -c kmc_core/rev_byte.cpp -o kmc_core/rev_byte.o + clang -Wall -O3 -m64 -pthread -std=c14 -fPIC -c kmc_core/bkb_writer.cpp -o kmc_core/bkb_writer.o + clang -Wall -O3 -m64 -pthread -std=c14 -fPIC -c kmc_core/cpu_info.cpp -o kmc_core/cpu_info.o + clang -Wall -O3 -m64 -pthread -std=c14 -fPIC -c kmc_core/bkb_reader.cpp -o kmc_core/bkb_reader.o + make[3]: Leaving directory '$SRC_DIR/external/KMC-3.2.1' + make[2]: Leaving directory '$SRC_DIR/build' + make[1]: Leaving directory '$SRC_DIR/build' +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/cuttlefish/meta.yaml b/recipes/cuttlefish/meta.yaml index f2cef96e5af21..5180e3a12af2c 100644 --- a/recipes/cuttlefish/meta.yaml +++ b/recipes/cuttlefish/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage('cuttlefish', max_pin="x") }} diff --git a/recipes/cvlr/meta.yaml b/recipes/cvlr/meta.yaml index ca135de94ada0..6812b870dcc2a 100644 --- a/recipes/cvlr/meta.yaml +++ b/recipes/cvlr/meta.yaml @@ -10,7 +10,7 @@ source: sha256: eaceaa530925cc42aafdda32d9d6dfb73c26cb6eccc06615947545a6126fb46a build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/cycle_finder/meta.yaml b/recipes/cycle_finder/meta.yaml index fb490d6dacdaf..39db32d383bd5 100644 --- a/recipes/cycle_finder/meta.yaml +++ b/recipes/cycle_finder/meta.yaml @@ -11,7 +11,7 @@ source: url: https://github.com/rkajitani/cycle_finder/archive/refs/tags/v{{ version }}.tar.gz build: - number: 0 + number: 1 skip: True # [osx] requirements: diff --git a/recipes/cyntenator/meta.yaml b/recipes/cyntenator/meta.yaml index c01c17fa3d9ea..e62b1ce65815c 100644 --- a/recipes/cyntenator/meta.yaml +++ b/recipes/cyntenator/meta.yaml @@ -11,7 +11,7 @@ source: - cxx.patch build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/cyrcular/meta.yaml b/recipes/cyrcular/meta.yaml index 26a83c54f2525..fc057df43f11a 100644 --- a/recipes/cyrcular/meta.yaml +++ b/recipes/cyrcular/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage("cyrcular", max_pin="x.x") }} diff --git a/recipes/cyushuffle/meta.yaml b/recipes/cyushuffle/meta.yaml index 501c81c87c1ce..f50123180d16c 100644 --- a/recipes/cyushuffle/meta.yaml +++ b/recipes/cyushuffle/meta.yaml @@ -9,7 +9,7 @@ source: sha256: "bd2c1d038a6d67d5a0c9f3e0b1761dccd9400bde666c82bb8f44732b72d417b6" build: - number: 6 + number: 7 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/cyvcf2/build_failure.linux-64.yaml b/recipes/cyvcf2/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..7d8d5ce53d20c --- /dev/null +++ b/recipes/cyvcf2/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: db56f9435d08d491cd9a2c67a43536f9e2940990ce39b0e1b20b6f3748c8160e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + # cyvcf2: htslib configure options is None + Traceback (most recent call last): + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in + main() + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main + json_out['return_val'] = hook(**hook_input['kwargs']) + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel + return _build_backend().build_wheel(wheel_directory, config_settings, + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/setuptools/build_meta.py", line 438, in build_wheel + return _build(['bdist_wheel', '--dist-info-dir', str(metadata_directory)]) + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/setuptools/build_meta.py", line 426, in _build + return self._build_with_temp_dir( + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/setuptools/build_meta.py", line 407, in _build_with_temp_dir + self.run_setup() + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/setuptools/build_meta.py", line 522, in run_setup + super().run_setup(setup_script=setup_script) + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/setuptools/build_meta.py", line 320, in run_setup + exec(code, locals()) + File "", line 269, in + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/setuptools/__init__.py", line 117, in setup + return distutils.core.setup(**attrs) + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 183, in setup + return run_commands(dist) + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 199, in run_commands + dist.run_commands() + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 954, in run_commands + self.run_command(cmd) + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/setuptools/dist.py", line 995, in run_command + super().run_command(command) + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 973, in run_command + cmd_obj.run() + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/setuptools/command/bdist_wheel.py", line 381, in run + self.run_command("build") + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command + self.distribution.run_command(command) + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/setuptools/dist.py", line 995, in run_command + super().run_command(command) + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 973, in run_command + cmd_obj.run() + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/setuptools/_distutils/command/build.py", line 135, in run + self.run_command(cmd_name) + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command + self.distribution.run_command(command) + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/setuptools/dist.py", line 995, in run_command + super().run_command(command) + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 973, in run_command + cmd_obj.run() + File "", line 116, in run + File "", line 79, in build_htslib + File "/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/subprocess.py", line 526, in run + raise CalledProcessError(retcode, process.args, + subprocess.CalledProcessError: Command '['./configure', 'CFLAGS=-fPIC']' returned non-zero exit status 1. + [1;31merror[0m: [1msubprocess-exited-with-error[0m + + [31m[0m [32mBuilding wheel for cyvcf2 [0m[1;32m([0m[32mpyproject.toml[0m[1;32m)[0m did not run successfully. + [31m[0m exit code: [1;36m1[0m + [31m>[0m See above for output. + + [1;35mnote[0m: This error originates from a subprocess, and is likely not a problem with pip. + [1;35mfull command[0m: [34m/opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/bin/python /opt/conda/conda-bld/cyvcf2_1734294584161/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py build_wheel /tmp/tmpbr40g597[0m + [1;35mcwd[0m: /opt/conda/conda-bld/cyvcf2_1734294584161/work + Building wheel for cyvcf2 (pyproject.toml): finished with status 'error' + [31m ERROR: Failed building wheel for cyvcf2[0m[31m + [0mFailed to build cyvcf2 + [31mERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (cyvcf2)[0m[31m + [0mException information: + Traceback (most recent call last): + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper + return func(self, options, args) + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/commands/install.py", line 434, in run + raise InstallationError( + pip._internal.exceptions.InstallationError: ERROR: Failed to build installable wheels for some pyproject.toml based projects (cyvcf2) + Removed build tracker: '/tmp/pip-build-tracker-vkgcs1f4' + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cyvcf2_1734294584161/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cyvcf2_1734294584161/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + dependency issue diff --git a/recipes/cyvcf2/build_failure.linux-aarch64.yaml b/recipes/cyvcf2/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..1c0538334031e --- /dev/null +++ b/recipes/cyvcf2/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: db56f9435d08d491cd9a2c67a43536f9e2940990ce39b0e1b20b6f3748c8160e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + # cyvcf2: htslib configure options is None + Traceback (most recent call last): + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in + main() + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main + json_out['return_val'] = hook(**hook_input['kwargs']) + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel + return _build_backend().build_wheel(wheel_directory, config_settings, + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/setuptools/build_meta.py", line 438, in build_wheel + return _build(['bdist_wheel', '--dist-info-dir', str(metadata_directory)]) + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/setuptools/build_meta.py", line 426, in _build + return self._build_with_temp_dir( + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/setuptools/build_meta.py", line 407, in _build_with_temp_dir + self.run_setup() + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/setuptools/build_meta.py", line 522, in run_setup + super().run_setup(setup_script=setup_script) + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/setuptools/build_meta.py", line 320, in run_setup + exec(code, locals()) + File "", line 269, in + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/setuptools/__init__.py", line 117, in setup + return distutils.core.setup(**attrs) + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 183, in setup + return run_commands(dist) + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 199, in run_commands + dist.run_commands() + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 954, in run_commands + self.run_command(cmd) + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/setuptools/dist.py", line 995, in run_command + super().run_command(command) + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 973, in run_command + cmd_obj.run() + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/setuptools/command/bdist_wheel.py", line 381, in run + self.run_command("build") + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command + self.distribution.run_command(command) + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/setuptools/dist.py", line 995, in run_command + super().run_command(command) + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 973, in run_command + cmd_obj.run() + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/setuptools/_distutils/command/build.py", line 135, in run + self.run_command(cmd_name) + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command + self.distribution.run_command(command) + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/setuptools/dist.py", line 995, in run_command + super().run_command(command) + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 973, in run_command + cmd_obj.run() + File "", line 116, in run + File "", line 79, in build_htslib + File "/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/subprocess.py", line 528, in run + raise CalledProcessError(retcode, process.args, + subprocess.CalledProcessError: Command '['./configure', 'CFLAGS=-fPIC']' returned non-zero exit status 1. + [1;31merror[0m: [1msubprocess-exited-with-error[0m + + [31m[0m [32mBuilding wheel for cyvcf2 [0m[1;32m([0m[32mpyproject.toml[0m[1;32m)[0m did not run successfully. + [31m[0m exit code: [1;36m1[0m + [31m>[0m See above for output. + + [1;35mnote[0m: This error originates from a subprocess, and is likely not a problem with pip. + [1;35mfull command[0m: [34m/opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/bin/python /opt/conda/conda-bld/cyvcf2_1734536359164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py build_wheel /tmp/tmp90oypfbb[0m + [1;35mcwd[0m: /opt/conda/conda-bld/cyvcf2_1734536359164/work + Building wheel for cyvcf2 (pyproject.toml): finished with status 'error' + [31m ERROR: Failed building wheel for cyvcf2[0m[31m + [0mFailed to build cyvcf2 + [31mERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (cyvcf2)[0m[31m + [0mException information: + Traceback (most recent call last): + File "$PREFIX/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + File "$PREFIX/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + File "$PREFIX/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper + return func(self, options, args) + File "$PREFIX/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 434, in run + raise InstallationError( + pip._internal.exceptions.InstallationError: ERROR: Failed to build installable wheels for some pyproject.toml based projects (cyvcf2) + Removed build tracker: '/tmp/pip-build-tracker-kcgl3fzm' + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cyvcf2_1734536359164/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/cyvcf2_1734536359164/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/cyvcf2/meta.yaml b/recipes/cyvcf2/meta.yaml index a79b51679e3a0..04942c527bb4c 100644 --- a/recipes/cyvcf2/meta.yaml +++ b/recipes/cyvcf2/meta.yaml @@ -14,7 +14,7 @@ source: - patches/setup.py.patch build: - number: 1 + number: 2 skip: True # [py < 37] script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv script_env: diff --git a/recipes/d4binding/build_failure.osx-64.yaml b/recipes/d4binding/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..e59afa59ea862 --- /dev/null +++ b/recipes/d4binding/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: e9292b958d236777884bc20fd58620460cbf53ceefd3275fd2f8c7ce32e8f5fe # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - llvmdev 18.1.8 h9ce406d_2 + - rhash 1.4.5 ha44c9a9_0 + - libedit 3.1.20191231 h0678c8f_2 + - clang-18 18.1.8 default_h0c94c6a_5 + - clang_osx-64 18.1.8 h7e5c614_23 + - rust-std-x86_64-apple-darwin 1.83.0 h38e4360_0 + - clang-format-18 18.1.8 default_h0c94c6a_5 + - make 4.4.1 h00291cd_2 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + - compiler-rt 18.1.8 h1020d70_1 + - cctools_osx-64 1010.6 h00edd4c_2 + host: + - libcxx 19.1.5 hf95d169_0 + run: + - libcxx >=18 + - starcode + run_constrained: + - __osx >=10.13 + test: + commands: + - 'true' + about: + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/d4binding_1734096549901/work/conda_build.sh']' returned non-zero exit status 71. + dev_url: https://github.com/38/d4-format + home: https://github.com/38/d4-format + license: MIT + license_family: MIT + summary: 'The C/C binding for the D4 file format. + + ' + extra: + additional-platforms: + - linux-aarch64 + copy_test_source_files: true + final: true + recipe-maintainers: + - haohou + skip-lints: + - should_use_compilers + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/d4binding_1734096549901/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/d4binding_1734096549901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/d4binding_1734096549901/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/d4binding_1734096549901/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/d4binding-0.3.11 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/d4binding-0.3.11 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/d4binding-0.3.11 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/d4binding-0.3.11 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix +# Last 100 lines of the build log. diff --git a/recipes/d4binding/meta.yaml b/recipes/d4binding/meta.yaml index 3fc0131d181c8..7573a2f4a8a6c 100644 --- a/recipes/d4binding/meta.yaml +++ b/recipes/d4binding/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage("d4binding", max_pin="x.x") }} diff --git a/recipes/d4tools/build_failure.osx-64.yaml b/recipes/d4tools/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..8e67a21ac6d73 --- /dev/null +++ b/recipes/d4tools/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5f8249eb125b6b9da84dea662646c3e20e75d34f79d13288dc8e6ab557e92406 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - libexpat 2.6.4 h240833e_0 + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + - compiler-rt 18.1.8 h1020d70_1 + - cctools_osx-64 1010.6 h00edd4c_2 + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/d4tools_1734096889581/work/conda_build.sh']' returned non-zero exit status 101. + - llvm-tools 18.1.8 h9ce406d_2 + - libxml2 2.13.5 he8ee3e7_1 + - libcxx 19.1.5 hf95d169_0 + - ca-certificates 2024.8.30 h8857fd0_0 + - ncurses 6.5 hf036a51_1 + - llvm-tools-18 18.1.8 h9ce406d_2 + - rhash 1.4.5 ha44c9a9_0 + - make 4.4.1 h00291cd_2 + - bzip2 1.0.8 hfdf4475_7 + host: + - libcxx 19.1.5 hf95d169_0 + run: + - starcode + - libcxx >=18 + run_constrained: + - __osx >=10.13 + test: + commands: + - 'true' + about: + dev_url: https://github.com/38/d4-format + home: https://github.com/38/d4-format + license: MIT + license_family: MIT + summary: 'The D4 command line utility program. + + ' + extra: + additional-platforms: + - linux-aarch64 + copy_test_source_files: true + final: true + recipe-maintainers: + - haohou + skip-lints: + - should_use_compilers + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/d4tools_1734096889581/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/d4tools_1734096889581/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/d4tools_1734096889581/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/d4tools_1734096889581/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/d4tools-0.3.11 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/d4tools-0.3.11 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/d4tools-0.3.11 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/d4tools-0.3.11 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix +# Last 100 lines of the build log. diff --git a/recipes/d4tools/meta.yaml b/recipes/d4tools/meta.yaml index 17f8a4c9838dc..335cb2f53b372 100644 --- a/recipes/d4tools/meta.yaml +++ b/recipes/d4tools/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 376e61c93cfe2efc15f5e74b75214e065e278146555e67b8769818bf49594726 build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('d4tools', max_pin="x.x") }} diff --git a/recipes/dagchainer/meta.yaml b/recipes/dagchainer/meta.yaml index 3b39626f71ca0..f50aeafdb8b69 100644 --- a/recipes/dagchainer/meta.yaml +++ b/recipes/dagchainer/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 ignore_run_exports_from: - perl-data-dumper - perl-storable diff --git a/recipes/daligner/meta.yaml b/recipes/daligner/meta.yaml index 71e9ba8da2f82..49338cfcc4fff 100644 --- a/recipes/daligner/meta.yaml +++ b/recipes/daligner/meta.yaml @@ -15,7 +15,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin=None) }} source: diff --git a/recipes/damasker/meta.yaml b/recipes/damasker/meta.yaml index 72f6140b8fda6..7270a30df7072 100644 --- a/recipes/damasker/meta.yaml +++ b/recipes/damasker/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 6 + number: 7 source: url: https://github.com/thegenemyers/DAMASKER/archive/bf6ccc8918ab99c52d368a780afc0b9e60371a17.tar.gz diff --git a/recipes/dart/build_failure.osx-64.yaml b/recipes/dart/build_failure.osx-64.yaml deleted file mode 100644 index 5b5076b89c23e..0000000000000 --- a/recipes/dart/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: c696aa5e636ef886ff1bcb70bc0fab6e2c5ed7ebb5ab85a6d600d7d890735e02 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - $SRC_DIR/src/BWT_Index $SRC_DIR - x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix utils.c -o utils.o - x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix bwt.c -o bwt.o - x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix bntseq.c -o bntseq.o - x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix QSufSort.c -o QSufSort.o - x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix bwt_gen.c -o bwt_gen.o - x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix bwtindex.c -o bwtindex.o - ar -csru libbwa.a utils.o bwt.o bntseq.o QSufSort.o bwt_gen.o bwtindex.o - x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix main.c -o main.o - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix main.o -o bwt_index -L. -lbwa -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lm -lz - $SRC_DIR - $SRC_DIR/src/htslib $SRC_DIR - echo '/* Default config.h generated by Makefile */' > config.h - echo '#define HAVE_LIBBZ2 1' >> config.h - echo '#define HAVE_LIBLZMA 1' >> config.h - echo '#define HAVE_FSEEKO 1' >> config.h - echo '#define HAVE_DRAND48 1' >> config.h - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o kfunc.o kfunc.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o knetfile.o knetfile.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o kstring.o kstring.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o bcf_sr_sort.o bcf_sr_sort.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o bgzf.o bgzf.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o errmod.o errmod.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o faidx.o faidx.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o hfile.o hfile.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o hfile_net.o hfile_net.c - echo '#define HTS_VERSION "1.5"' > version.h - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o hts.o hts.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o hts_os.o hts_os.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o md5.o md5.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o multipart.o multipart.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o probaln.o probaln.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o realn.o realn.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o regidx.o regidx.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o sam.o sam.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o synced_bcf_reader.o synced_bcf_reader.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o vcf_sweep.o vcf_sweep.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o tbx.o tbx.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o textutils.o textutils.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o thread_pool.o thread_pool.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o vcf.o vcf.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o vcfutils.o vcfutils.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/cram_codecs.o cram/cram_codecs.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/cram_decode.o cram/cram_decode.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/cram_encode.o cram/cram_encode.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/cram_external.o cram/cram_external.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/cram_index.o cram/cram_index.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/cram_io.o cram/cram_io.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/cram_samtools.o cram/cram_samtools.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/cram_stats.o cram/cram_stats.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/files.o cram/files.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/mFILE.o cram/mFILE.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/open_trace_file.o cram/open_trace_file.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/rANS_static.o cram/rANS_static.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/sam_header.o cram/sam_header.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/string_alloc.o cram/string_alloc.c - ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o - ranlib libhts.a - $SRC_DIR - $SRC_DIR/src $SRC_DIR - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dart-1.4.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -D NDEBUG -O3 -m64 -msse4.1 -fPIC -c main.cpp -# Last 100 lines of the build log. diff --git a/recipes/dart/meta.yaml b/recipes/dart/meta.yaml index e0adbdd0c75eb..b7ece04e76de9 100644 --- a/recipes/dart/meta.yaml +++ b/recipes/dart/meta.yaml @@ -9,7 +9,7 @@ source: sha256: '847d5e0a7e10162583fcf7168d31924d38290b5364e08c4a9cdd6653da73c64f' build: - number: 6 + number: 7 run_exports: - {{ pin_subpackage("dart", max_pin='x.x') }} diff --git a/recipes/das_tool/meta.yaml b/recipes/das_tool/meta.yaml index 6aab0c2d4911b..2d8ebb6498984 100644 --- a/recipes/das_tool/meta.yaml +++ b/recipes/das_tool/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/dascrubber/meta.yaml b/recipes/dascrubber/meta.yaml index aef7945150f26..42390990de40a 100644 --- a/recipes/dascrubber/meta.yaml +++ b/recipes/dascrubber/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.0.1a2" build: - number: 6 + number: 7 source: sha256: 2463262ed6caeda97474b868197635824199e7e0008ca65ed8a65ef08bb320ce diff --git a/recipes/dashing/meta.yaml b/recipes/dashing/meta.yaml index ab19927b78739..66d7cd58031ad 100644 --- a/recipes/dashing/meta.yaml +++ b/recipes/dashing/meta.yaml @@ -7,7 +7,7 @@ package: build: skip: True # [osx] - number: 2 + number: 3 source: git_url: https://github.com/dnbaker/dashing diff --git a/recipes/dazz_db/meta.yaml b/recipes/dazz_db/meta.yaml index 9d2ee5064cb31..daf5cd58eebc6 100644 --- a/recipes/dazz_db/meta.yaml +++ b/recipes/dazz_db/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.0p2" build: - number: 7 + number: 8 source: sha256: 3e98d10454b12bf0bcba1cdec226882e8214a3040472cbfaec0f9b589099d730 diff --git a/recipes/dbg2olc/meta.yaml b/recipes/dbg2olc/meta.yaml index 0558f653fc5c4..b05d7bad38604 100644 --- a/recipes/dbg2olc/meta.yaml +++ b/recipes/dbg2olc/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 script: | "${CXX}" ${CPPFLAGS} ${CXXFLAGS} -O3 -o DBG2OLC *.cpp ${LDFLAGS} mkdir -p "${PREFIX}/bin" diff --git a/recipes/dbghaplo/meta.yaml b/recipes/dbghaplo/meta.yaml index f14ef02373001..997c1964bc18d 100644 --- a/recipes/dbghaplo/meta.yaml +++ b/recipes/dbghaplo/meta.yaml @@ -9,7 +9,7 @@ source: sha256: e7e2741afb0c7f12718ec969815d3c8f18ce7ba66517e21c6fcfb3fe4262780b build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('dbghaplo', max_pin="x.x") }} diff --git a/recipes/debwt/meta.yaml b/recipes/debwt/meta.yaml index 8c279f7c5cc3f..a7edcc75d313d 100644 --- a/recipes/debwt/meta.yaml +++ b/recipes/debwt/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.0.1" build: - number: 7 + number: 8 source: # git_rev: 972b5338b2ad027244bb60d185c5a88586affba6 # version 1.0.1 diff --git a/recipes/dechat/build_failure.linux-64.yaml b/recipes/dechat/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..eed9ed44e771e --- /dev/null +++ b/recipes/dechat/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 075530121157793ebc0bb40fef37ca076593c28fb131f9ad82ce44f43271c471 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + 116 | template const _Tp* end(const valarray<_Tp>&) noexcept; + | ^~~ + /opt/conda/conda-bld/dechat_1734218819382/work/gatb-core/gatb-core/thirdparty/kff-cpp-api/merge.cpp:91:91: error: request for member 'find' in 'footer_values', which is of non-class type 'int' + 91 | if (footer_values.find(tuple.first) == footer_values.end()) + | ^~~~ + /opt/conda/conda-bld/dechat_1734218819382/work/gatb-core/gatb-core/thirdparty/kff-cpp-api/merge.cpp:91:126: error: request for member 'end' in 'footer_values', which is of non-class type 'int' + 91 | if (footer_values.find(tuple.first) == footer_values.end()) + | ^~~ + /opt/conda/conda-bld/dechat_1734218819382/work/gatb-core/gatb-core/thirdparty/kff-cpp-api/merge.cpp:100:69: error: 'begin' was not declared in this scope; did you mean 'std::begin'? + 100 | for (auto & p : sgv.vars) + | ^~~~ + | std::begin + /opt/conda/conda-bld/dechat_1734218819382/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/range_access.h:114:37: note: 'std::begin' declared here + 114 | template const _Tp* begin(const valarray<_Tp>&) noexcept; + | ^~~~~ + /opt/conda/conda-bld/dechat_1734218819382/work/gatb-core/gatb-core/thirdparty/kff-cpp-api/merge.cpp:100:69: error: 'end' was not declared in this scope; did you mean 'std::end'? + 100 | for (auto & p : sgv.vars) + | ^~~~ + | std::end + /opt/conda/conda-bld/dechat_1734218819382/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/range_access.h:116:37: note: 'std::end' declared here + 116 | template const _Tp* end(const valarray<_Tp>&) noexcept; + | ^~~ + /opt/conda/conda-bld/dechat_1734218819382/work/gatb-core/gatb-core/thirdparty/kff-cpp-api/merge.cpp:110:57: error: 'begin' was not declared in this scope; did you mean 'std::begin'? + 110 | for (auto & p : variables) { + | ^~~~~~~~~ + | std::begin + /opt/conda/conda-bld/dechat_1734218819382/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/range_access.h:114:37: note: 'std::begin' declared here + 114 | template const _Tp* begin(const valarray<_Tp>&) noexcept; + | ^~~~~ + /opt/conda/conda-bld/dechat_1734218819382/work/gatb-core/gatb-core/thirdparty/kff-cpp-api/merge.cpp:110:57: error: 'end' was not declared in this scope; did you mean 'std::end'? + 110 | for (auto & p : variables) { + | ^~~~~~~~~ + | std::end + /opt/conda/conda-bld/dechat_1734218819382/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/range_access.h:116:37: note: 'std::end' declared here + 116 | template const _Tp* end(const valarray<_Tp>&) noexcept; + | ^~~ + /opt/conda/conda-bld/dechat_1734218819382/work/gatb-core/gatb-core/thirdparty/kff-cpp-api/merge.cpp:111:73: error: request for member 'find' in 'outfile.Kff_file::global_vars', which is of non-class type 'int' + 111 | if (outfile.global_vars.find(p.first) == outfile.global_vars.end() + | ^~~~ + /opt/conda/conda-bld/dechat_1734218819382/work/gatb-core/gatb-core/thirdparty/kff-cpp-api/merge.cpp:111:110: error: request for member 'end' in 'outfile.Kff_file::global_vars', which is of non-class type 'int' + 111 | if (outfile.global_vars.find(p.first) == outfile.global_vars.end() + | ^~~ + /opt/conda/conda-bld/dechat_1734218819382/work/gatb-core/gatb-core/thirdparty/kff-cpp-api/merge.cpp:122:65: error: 'begin' was not declared in this scope; did you mean 'std::begin'? + 122 | for (auto & p : variables) { + | ^~~~~~~~~ + | std::begin + /opt/conda/conda-bld/dechat_1734218819382/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/range_access.h:114:37: note: 'std::begin' declared here + 114 | template const _Tp* begin(const valarray<_Tp>&) noexcept; + | ^~~~~ + /opt/conda/conda-bld/dechat_1734218819382/work/gatb-core/gatb-core/thirdparty/kff-cpp-api/merge.cpp:122:65: error: 'end' was not declared in this scope; did you mean 'std::end'? + 122 | for (auto & p : variables) { + | ^~~~~~~~~ + | std::end + /opt/conda/conda-bld/dechat_1734218819382/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/range_access.h:116:37: note: 'std::end' declared here + 116 | template const _Tp* end(const valarray<_Tp>&) noexcept; + | ^~~ + /opt/conda/conda-bld/dechat_1734218819382/work/gatb-core/gatb-core/thirdparty/kff-cpp-api/merge.cpp:144:54: error: 'buffer' was not declared in this scope; did you mean 'setbuffer'? + 144 | infile->read(buffer, size_to_copy); + | ^~~~~~ + | setbuffer + /opt/conda/conda-bld/dechat_1734218819382/work/gatb-core/gatb-core/thirdparty/kff-cpp-api/merge.cpp:201:43: error: 'begin' was not declared in this scope; did you mean 'std::begin'? + 201 | for (const auto & tuple : footer_values) { + | ^~~~~~~~~~~~~ + | std::begin + /opt/conda/conda-bld/dechat_1734218819382/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/range_access.h:114:37: note: 'std::begin' declared here + 114 | template const _Tp* begin(const valarray<_Tp>&) noexcept; + | ^~~~~ + /opt/conda/conda-bld/dechat_1734218819382/work/gatb-core/gatb-core/thirdparty/kff-cpp-api/merge.cpp:201:43: error: 'end' was not declared in this scope; did you mean 'std::end'? + 201 | for (const auto & tuple : footer_values) { + | ^~~~~~~~~~~~~ + | std::end + /opt/conda/conda-bld/dechat_1734218819382/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/range_access.h:116:37: note: 'std::end' declared here + 116 | template const _Tp* end(const valarray<_Tp>&) noexcept; + | ^~~ + make[2]: *** [ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/build.make:1801: ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/__/thirdparty/kff-cpp-api/merge.cpp.o] Error 1 + make[1]: *** [CMakeFiles/Makefile2:350: ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/all] Error 2 + make: *** [Makefile:156: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/dechat_1734218819382/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/dechat_1734218819382/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/dechat/meta.yaml b/recipes/dechat/meta.yaml index 0eef8c132438d..6a1a0d83355bd 100644 --- a/recipes/dechat/meta.yaml +++ b/recipes/dechat/meta.yaml @@ -10,7 +10,7 @@ source: sha256: e637d985eb4fa3bfa276d6433a5ec3c014471eb8eea6da233720dfe78b16fcda build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('dechat', max_pin="x") }} diff --git a/recipes/decifer/meta.yaml b/recipes/decifer/meta.yaml index c8ff8beddc81c..282450570b6d6 100644 --- a/recipes/decifer/meta.yaml +++ b/recipes/decifer/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 9b67b66cd9dd5c538204c22994b9c61d97f3691d01146bd76500dbd4ed4d3685 build: - number: 2 + number: 3 entry_points: - decifer = decifer.__main__:main run_exports: diff --git a/recipes/deepchopper-cli/build_failure.osx-64.yaml b/recipes/deepchopper-cli/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..27ea0d07057e6 --- /dev/null +++ b/recipes/deepchopper-cli/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 76c98124f05eea36d448f49c438e177113d891c8f10407feabaa46a8a29ebc2d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/deepchopper-cli_1734457592447/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/deepchopper-cli-1.2.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/deepchopper-cli-1.2.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + Warning: Not enforcing strong cipher suites for TLS, this is potentially less secure + Warning: Detected unknown macOS major version: 13.7.1 + Warning TLS capabilities detection may fail + Warning: Not enforcing TLS v1.2, this is potentially less secure + + nightly-x86_64-apple-darwin installed - rustc 1.85.0-nightly (6d9f6ae36 2024-12-16) + + + Rust is installed now. Great! + + To get started you may need to restart your current shell. + This would reload your PATH environment variable to include + Cargo's bin directory + (/opt/mambaforge/envs/bioconda/conda-bld/deepchopper-cli_1734457592447/_ + build_env/.cargo/bin). + + To configure your current shell, you need to source + the corresponding env file under + /opt/mambaforge/envs/bioconda/conda-bld/deepchopper-cli_1734457592447/_ + build_env/.cargo. + + This is usually done by running one of the following (note the leading DOT): + . "/opt/mambaforge/envs/bioconda/conda-bld/deepchopper-cli_1734457592447/_ + build_env/.cargo/env" # For sh/bash/zsh/ash/dash/pdksh + source "/opt/mambaforge/envs/bioconda/conda-bld/deepchopper-cli_1734457592447/_ + build_env/.cargo/env.fish" # For fish + Using pip 24.3.1 from $PREFIX/lib/python3.10/site-packages/pip (python 3.10) + Non-user install because user site-packages disabled + Ignoring indexes: https://pypi.org/simple + Created temporary directory: /private/tmp/pip-build-tracker-3qi6xjqr + Initialized build tracking at /private/tmp/pip-build-tracker-3qi6xjqr + Created build tracker: /private/tmp/pip-build-tracker-3qi6xjqr + Entered build tracker: /private/tmp/pip-build-tracker-3qi6xjqr + Created temporary directory: /private/tmp/pip-install-ua13dsbm + Created temporary directory: /private/tmp/pip-ephem-wheel-cache-l45dej0m + Exception information: + Traceback (most recent call last): + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper + return func(self, options, args) + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/commands/install.py", line 379, in run + requirement_set = resolver.resolve( + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 76, in resolve + collected = self.factory.collect_root_requirements(root_reqs) + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 545, in collect_root_requirements + reqs = list( + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 496, in _make_requirements_from_install_req + self._fail_if_link_is_unsupported_wheel(ireq.link) + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 147, in _fail_if_link_is_unsupported_wheel + raise UnsupportedWheel(msg) + pip._internal.exceptions.UnsupportedWheel: deepchopper_cli-1.2.6-cp310-cp310-macosx_14_0_x86_64.whl is not a supported wheel on this platform. + Removed build tracker: '/private/tmp/pip-build-tracker-3qi6xjqr' +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/deepchopper-cli/meta.yaml b/recipes/deepchopper-cli/meta.yaml index 45fceb4596974..c92d7ee85a1d8 100644 --- a/recipes/deepchopper-cli/meta.yaml +++ b/recipes/deepchopper-cli/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [py < 310] run_exports: - {{ pin_subpackage("deepchopper-cli", max_pin="x") }} diff --git a/recipes/deepchopper/build_failure.linux-64.yaml b/recipes/deepchopper/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..eeaafb7f37a1d --- /dev/null +++ b/recipes/deepchopper/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 076c55355440ff0f5286f51bb4c2900810c80bbf0c4f4a00b77952ae4ee94b6e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + python-dateutil: 2.9.0.post0-pyhff2d567_1 conda-forge + python-dotenv: 1.0.1-pyhd8ed1ab_1 conda-forge + python-multipart: 0.0.12-pyhff2d567_0 conda-forge + python-slugify: 8.0.4-pyhd8ed1ab_1 conda-forge + python-tzdata: 2024.2-pyhd8ed1ab_1 conda-forge + python-xxhash: 3.5.0-py312h66e93f0_1 conda-forge + python_abi: 3.12-5_cp312 conda-forge + pytorch: 2.5.1-cpu_mkl_py312h7bcab40_106 conda-forge + pytorch-lightning: 2.4.0-pyh101cb37_1 conda-forge + pytz: 2024.1-pyhd8ed1ab_0 conda-forge + pyyaml: 6.0.2-py312h66e93f0_1 conda-forge + qhull: 2020.2-h434a139_5 conda-forge + re2: 2024.07.02-h77b4e00_1 conda-forge + readline: 8.2-h8228510_1 conda-forge + regex: 2024.11.6-py312h66e93f0_0 conda-forge + requests: 2.32.3-pyhd8ed1ab_1 conda-forge + responses: 0.18.0-pyhd8ed1ab_0 conda-forge + rich: 13.9.4-pyhd8ed1ab_1 conda-forge + rich-toolkit: 0.11.3-pyh29332c3_0 conda-forge + ruff: 0.8.3-py312h2156523_0 conda-forge + s2n: 1.5.9-h0fd0ee4_0 conda-forge + safetensors: 0.4.5-py312h12e396e_0 conda-forge + scikit-learn: 1.6.0-py312h7a48858_0 conda-forge + scipy: 1.14.1-py312h62794b6_2 conda-forge + semantic_version: 2.10.0-pyhd8ed1ab_0 conda-forge + setuptools: 75.6.0-pyhff2d567_1 conda-forge + shellingham: 1.5.4-pyhd8ed1ab_1 conda-forge + six: 1.17.0-pyhd8ed1ab_0 conda-forge + sleef: 3.7-h1b44611_2 conda-forge + snappy: 1.2.1-h8bd8927_1 conda-forge + sniffio: 1.3.1-pyhd8ed1ab_1 conda-forge + starlette: 0.38.6-pyhd8ed1ab_0 conda-forge + svt-av1: 2.3.0-h5888daf_0 conda-forge + sympy: 1.13.3-pyh2585a3b_104 conda-forge + tbb: 2021.13.0-hceb3a55_1 conda-forge + text-unidecode: 1.3-pyhd8ed1ab_2 conda-forge + threadpoolctl: 3.5.0-pyhc1e730c_0 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tokenizers: 0.21.0-py312h8360d73_0 conda-forge + tomlkit: 0.12.0-pyha770c72_0 conda-forge + torchmetrics: 1.5.2-pyhd8ed1ab_1 conda-forge + tqdm: 4.67.1-pyhd8ed1ab_0 conda-forge + transformers: 4.47.0-pyhd8ed1ab_1 conda-forge + typer: 0.15.1-pyhd8ed1ab_0 conda-forge + typer-slim: 0.15.1-pyhd8ed1ab_0 conda-forge + typer-slim-standard: 0.15.1-hd8ed1ab_0 conda-forge + types-python-dateutil: 2.9.0.20241206-pyhd8ed1ab_0 conda-forge + typing-extensions: 4.12.2-hd8ed1ab_1 conda-forge + typing_extensions: 4.12.2-pyha770c72_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + unicodedata2: 15.1.0-py312h66e93f0_1 conda-forge + urllib3: 2.2.3-pyhd8ed1ab_1 conda-forge + uvicorn: 0.32.1-pyh31011fe_1 conda-forge + uvicorn-standard: 0.32.1-h31011fe_1 conda-forge + uvloop: 0.21.0-py312h66e93f0_1 conda-forge + watchfiles: 1.0.3-py312h12e396e_0 conda-forge + wayland: 1.23.1-h3e06ad9_0 conda-forge + wayland-protocols: 1.37-hd8ed1ab_0 conda-forge + websockets: 12.0-py312h98912ed_0 conda-forge + wheel: 0.45.1-pyhd8ed1ab_1 conda-forge + x264: 1!164.3095-h166bdaf_2 conda-forge + x265: 3.5-h924138e_3 conda-forge + xorg-libice: 1.1.1-hb9d3cd8_1 conda-forge + xorg-libsm: 1.2.4-he73a12e_1 conda-forge + xorg-libx11: 1.8.10-h4f16b4b_1 conda-forge + xorg-libxau: 1.0.11-hb9d3cd8_1 conda-forge + xorg-libxdmcp: 1.1.5-hb9d3cd8_0 conda-forge + xorg-libxext: 1.3.6-hb9d3cd8_0 conda-forge + xorg-libxfixes: 6.0.1-hb9d3cd8_0 conda-forge + xorg-libxrender: 0.9.11-hb9d3cd8_2 conda-forge + xxhash: 0.8.2-hd590300_0 conda-forge + yaml: 0.2.5-h7f98852_2 conda-forge + yarl: 1.18.3-py312h66e93f0_0 conda-forge + zipp: 3.21.0-pyhd8ed1ab_1 conda-forge + zstandard: 0.23.0-py312hef9b889_1 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3462, in test + environ.create_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1050, in create_env + _execute_actions(prefix, precs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1338, in _execute_actions + progressive_fetch_extract.execute() + File "/opt/conda/lib/python3.10/site-packages/conda/core/package_cache_data.py", line 900, in execute + raise CondaMultiError(not_cancelled) + conda.CondaMultiError: Error with archive /opt/conda/pkgs/pillow-10.4.0-py312h56024de_1.conda. You probably need to delete and re-download or re-create this file. Message was: + + failed with error: [Errno 28] No space left on device + Error with archive /opt/conda/pkgs/pytorch-2.5.1-cpu_mkl_py312h7bcab40_106.conda. You probably need to delete and re-download or re-create this file. Message was: + + failed with error: [Errno 28] No space left on device +# Last 100 lines of the build log. diff --git a/recipes/deepchopper/build_failure.osx-64.yaml b/recipes/deepchopper/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..bdfc737c6d188 --- /dev/null +++ b/recipes/deepchopper/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 076c55355440ff0f5286f51bb4c2900810c80bbf0c4f4a00b77952ae4ee94b6e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/deepchopper_1734412367765/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/deepchopper-1.2.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/deepchopper-1.2.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + Warning: Not enforcing strong cipher suites for TLS, this is potentially less secure + Warning: Detected unknown macOS major version: 13.7.1 + Warning TLS capabilities detection may fail + Warning: Not enforcing TLS v1.2, this is potentially less secure + + nightly-x86_64-apple-darwin installed - rustc 1.85.0-nightly (6d9f6ae36 2024-12-16) + + + Rust is installed now. Great! + + To get started you may need to restart your current shell. + This would reload your PATH environment variable to include + Cargo's bin directory + (/opt/mambaforge/envs/bioconda/conda-bld/deepchopper_1734412367765/_ + build_env/.cargo/bin). + + To configure your current shell, you need to source + the corresponding env file under + /opt/mambaforge/envs/bioconda/conda-bld/deepchopper_1734412367765/_ + build_env/.cargo. + + This is usually done by running one of the following (note the leading DOT): + . "/opt/mambaforge/envs/bioconda/conda-bld/deepchopper_1734412367765/_ + build_env/.cargo/env" # For sh/bash/zsh/ash/dash/pdksh + source "/opt/mambaforge/envs/bioconda/conda-bld/deepchopper_1734412367765/_ + build_env/.cargo/env.fish" # For fish + Using pip 24.3.1 from $PREFIX/lib/python3.10/site-packages/pip (python 3.10) + Non-user install because user site-packages disabled + Ignoring indexes: https://pypi.org/simple + Created temporary directory: /private/tmp/pip-build-tracker-3axu8fsw + Initialized build tracking at /private/tmp/pip-build-tracker-3axu8fsw + Created build tracker: /private/tmp/pip-build-tracker-3axu8fsw + Entered build tracker: /private/tmp/pip-build-tracker-3axu8fsw + Created temporary directory: /private/tmp/pip-install-jt7ios6s + Created temporary directory: /private/tmp/pip-ephem-wheel-cache-76hku4g9 + Exception information: + Traceback (most recent call last): + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper + return func(self, options, args) + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/commands/install.py", line 379, in run + requirement_set = resolver.resolve( + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 76, in resolve + collected = self.factory.collect_root_requirements(root_reqs) + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 545, in collect_root_requirements + reqs = list( + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 496, in _make_requirements_from_install_req + self._fail_if_link_is_unsupported_wheel(ireq.link) + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 147, in _fail_if_link_is_unsupported_wheel + raise UnsupportedWheel(msg) + pip._internal.exceptions.UnsupportedWheel: deepchopper-1.2.6-cp310-abi3-macosx_14_0_x86_64.whl is not a supported wheel on this platform. + Removed build tracker: '/private/tmp/pip-build-tracker-3axu8fsw' +# Last 100 lines of the build log. diff --git a/recipes/deepchopper/meta.yaml b/recipes/deepchopper/meta.yaml index a94a5edd37044..3c11b87ec6f41 100644 --- a/recipes/deepchopper/meta.yaml +++ b/recipes/deepchopper/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [py < 310] run_exports: - {{ pin_subpackage("deepchopper", max_pin="x") }} diff --git a/recipes/deeptoolsintervals/meta.yaml b/recipes/deeptoolsintervals/meta.yaml index 82731cf3df9cd..6b5402f422578 100644 --- a/recipes/deeptoolsintervals/meta.yaml +++ b/recipes/deeptoolsintervals/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 7d94c36fd2b6f10d8b99e536d2672e8228971f1fc810497d33527bba2c40d4f6 build: - number: 9 + number: 10 run_exports: - {{ pin_subpackage("deeptoolsintervals", max_pin="x.x") }} diff --git a/recipes/defiant/meta.yaml b/recipes/defiant/meta.yaml index efd992d838edd..f2a16f34e94a7 100644 --- a/recipes/defiant/meta.yaml +++ b/recipes/defiant/meta.yaml @@ -12,7 +12,7 @@ source: - main.patch build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/dehomopolymerate/meta.yaml b/recipes/dehomopolymerate/meta.yaml index 2f49591a2992f..34ba35f113fe5 100644 --- a/recipes/dehomopolymerate/meta.yaml +++ b/recipes/dehomopolymerate/meta.yaml @@ -8,7 +8,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://github.com/{{ user }}/{{ name }}/archive/v{{ version }}.tar.gz diff --git a/recipes/delly/meta.yaml b/recipes/delly/meta.yaml index 7928647fac015..f85a7a03b1afe 100644 --- a/recipes/delly/meta.yaml +++ b/recipes/delly/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("delly", max_pin="x.x") }} diff --git a/recipes/deltapd/build_failure.osx-64.yaml b/recipes/deltapd/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..218f61f5d3ebb --- /dev/null +++ b/recipes/deltapd/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 78afbda98bf59152d83acec789e926327019eee7840f89efa593c62fbb9a720f # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/deltapd-0.1.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/deltapd-0.1.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + Using pip 24.3.1 from $PREFIX/lib/python3.10/site-packages/pip (python 3.10) + Non-user install because user site-packages disabled + Ignoring indexes: https://pypi.org/simple + Created temporary directory: /private/tmp/pip-build-tracker-4ve6g7z3 + Initialized build tracking at /private/tmp/pip-build-tracker-4ve6g7z3 + Created build tracker: /private/tmp/pip-build-tracker-4ve6g7z3 + Entered build tracker: /private/tmp/pip-build-tracker-4ve6g7z3 + Created temporary directory: /private/tmp/pip-install-2lgeldgr + Created temporary directory: /private/tmp/pip-ephem-wheel-cache-xcba89wz + Processing $SRC_DIR + Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-4ve6g7z3' + Running setup.py (path:$SRC_DIR/setup.py) egg_info for package from file://$SRC_DIR + Created temporary directory: /private/tmp/pip-pip-egg-info-6e2aioeu + Preparing metadata (setup.py): started + Preparing metadata (setup.py): finished with status 'done' + Source in $SRC_DIR has version 0.1.5, which satisfies requirement deltapd==0.1.5 from file://$SRC_DIR + Removed deltapd==0.1.5 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-4ve6g7z3' + Created temporary directory: /private/tmp/pip-unpack-w28um_rb + Building wheels for collected packages: deltapd + Created temporary directory: /private/tmp/pip-wheel-uok8r0oj + Building wheel for deltapd (setup.py): started + Destination directory: /private/tmp/pip-wheel-uok8r0oj + Building wheel for deltapd (setup.py): finished with status 'done' + Created wheel for deltapd: filename=deltapd-0.1.5-cp310-cp310-macosx_10_15_x86_64.whl size=1183381 sha256=4dab531906c4eb110a85f15291f59b95c4c0b6f524d8c4a72d6818533f67267c + Stored in directory: /private/tmp/pip-ephem-wheel-cache-xcba89wz/wheels/a1/79/50/713b02c689142d264874df6e2dafc7948319c7361246f5f36e + Successfully built deltapd + Installing collected packages: deltapd + + changing mode of $PREFIX/bin/deltapd to 755 + Successfully installed deltapd-0.1.5 + Removed build tracker: '/private/tmp/pip-build-tracker-4ve6g7z3' + + Resource usage statistics from building deltapd: + Process count: 5 + CPU time: Sys=0:00:01.6, User=0:00:20.3 + Memory: 231.6M + Disk usage: 22.0K + Time elapsed: 0:00:32.7 + + + Packaging deltapd + Packaging deltapd-0.1.5-py310h0087c89_6 + + + + + compiling .pyc files... + number of files: 74 + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2765, in build + newly_built_packages = bundlers[pkg_type]( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1874, in bundle_conda + files = post_process_files(metadata, initial_files) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1653, in post_process_files + post_build(m, new_files, build_python=python) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1759, in post_build + post_process_shared_lib(m, f, prefix_files, host_prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1635, in post_process_shared_lib + mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 512, in mk_relative_osx + assert_relative_osx(path, host_prefix, build_prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 665, in assert_relative_osx + for name in macho.get_dylibs(path, tools_prefix): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 237, in get_dylibs + dylib_loads = otool(path, build_prefix, is_load_dylib) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 221, in otool + lines = check_output([otool, "-l", path], stderr=STDOUT).decode("utf-8") + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 421, in check_output + return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 526, in run + raise CalledProcessError(retcode, process.args, + subprocess.CalledProcessError: Command '['/opt/mambaforge/envs/bioconda/conda-bld/deltapd_1734546949268/_build_env/bin/llvm-otool', '-l', '/opt/mambaforge/envs/bioconda/conda-bld/deltapd_1734546949268/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.10/site-packages/deltapd/util.cpython-310-darwin.so']' died with . +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/deltapd/meta.yaml b/recipes/deltapd/meta.yaml index 31cd6a697ca78..4db83587682ec 100644 --- a/recipes/deltapd/meta.yaml +++ b/recipes/deltapd/meta.yaml @@ -13,7 +13,7 @@ source: - pdm.patch build: - number: 5 + number: 6 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vvv entry_points: - deltapd = deltapd.__main__:main diff --git a/recipes/demuxlet/meta.yaml b/recipes/demuxlet/meta.yaml index acff6f432d287..1582fb6f2b211 100644 --- a/recipes/demuxlet/meta.yaml +++ b/recipes/demuxlet/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 5 + number: 6 skip: True # [osx] source: diff --git a/recipes/deploid/meta.yaml b/recipes/deploid/meta.yaml index 92e296f3dd412..a49107dbff6c5 100644 --- a/recipes/deploid/meta.yaml +++ b/recipes/deploid/meta.yaml @@ -11,7 +11,7 @@ source: - 0001-Pick-up-version-file-rename-in-configure.ac.patch build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/derna/meta.yaml b/recipes/derna/meta.yaml index 193695a14d649..eaa2a3c2a9fbc 100644 --- a/recipes/derna/meta.yaml +++ b/recipes/derna/meta.yaml @@ -9,7 +9,7 @@ source: sha256: eb5fabf0e01d9507ceca3fc687e8c67a9cec91c77e75d2c4f7d310ac926a79cb build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('derna', max_pin="x") }} diff --git a/recipes/desalt/meta.yaml b/recipes/desalt/meta.yaml index 3b9e212663e54..e314b49450d7e 100644 --- a/recipes/desalt/meta.yaml +++ b/recipes/desalt/meta.yaml @@ -9,7 +9,7 @@ source: sha256: ef3396a1bf1ea3c188ee77b90ae50a174c2e50676b8b779698cb6330aa7b34ef build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('desalt', max_pin="x") }} diff --git a/recipes/desman/build_failure.linux-64.yaml b/recipes/desman/build_failure.linux-64.yaml deleted file mode 100644 index 81ddfbc76d586..0000000000000 --- a/recipes/desman/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 589b78385006fb419a020605d6873bd6e3becaf16714268412de6c7c55bc3630 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - [31mpysam [0.15.1|0.15.2|0.15.3][0m would require - [31mlibdeflate >=1.0,<1.1.0a0 [0m, which conflicts with any installable versions previously reported; - [32mpysam [0.15.3|0.15.4|0.9.1][0m would require - [32mpython >=3.7,<3.8.0a0 [0m, which can be installed; - [32mpysam [0.15.4|0.16.0|...|0.9.1][0m would require - [32mpython_abi 3.7.* *_cp37m[0m, which can be installed; - [32mpysam [0.16.0.1|0.17.0|...|0.9.1][0m would require - [32mpython_abi 3.8.* *_cp38[0m, which can be installed; - [32mpysam [0.16.0.1|0.17.0|...|0.9.1][0m would require - [32mpython_abi 3.9.* *_cp39[0m, which can be installed; - [32mpysam [0.19.1|0.20.0|0.21.0|0.22.0|0.22.1][0m would require - [32mpython_abi 3.10.* *_cp310[0m, which can be installed; - [31mpython >=3.11,<3.12.0a0 [0m is not installable because it requires - [31mpython_abi 3.11.* *_cp311[0m, which conflicts with any installable versions previously reported. - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2409, in build - create_build_envs(top_level_pkg, notest) - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2247, in create_build_envs - raise e - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2220, in create_build_envs - environ.get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions - precs = _install_actions(prefix, index, specs)["LINK"] - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions - txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction - unlink_precs, link_precs = self.solve_for_diff( - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff - final_precs = self.solve_final_state( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state - out_state = self._solving_loop(in_state, out_state, index) - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop - solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt - new_conflicts = self._maybe_raise_for_problems( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems - self._maybe_raise_for_conda_build( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build - raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("pysam==0.15.0=py27hdfb72b2_0"), MatchSpec("bcftools=1.9")} - Encountered problems while solving: - - package pysam-0.15.0-py27hdfb72b2_0 requires bcftools 1.9.*, but none of the providers can be installed - - Could not solve for environment specs - The following packages are incompatible - [32mgsl >=2.7,<2.8.0a0 [0m is requested and can be installed; - [32mpysam[0m is installable with the potential options - [32mpysam 0.7.7[0m would require - [32mpython <3.0.0 [0m, which can be installed; - [32mpysam [0.10.0|0.11.0|...|0.9.1.4][0m would require - [32mpython [2.7* |>=2.7,<2.8.0a0 ][0m, which can be installed; - [32mpysam [0.10.0|0.16.0.1|...|0.9.1][0m would require - [32mpython_abi 2.7.* *_cp27mu[0m, which can be installed; - [32mpysam [0.10.0|0.11.0|...|0.9.1.4][0m would require - [32mpython 3.4* [0m, which can be installed; - [32mpysam [0.10.0|0.11.0|...|0.9.1.4][0m would require - [32mpython [3.5* |>=3.5,<3.6.0a0 ][0m, which can be installed; - [32mpysam [0.10.0|0.11.1|...|0.9.1][0m would require - [32mpython 3.6* [0m, which can be installed; - [32mpysam [0.10.0|0.15.4|...|0.9.1][0m would require - [32mpython_abi 3.6.* *_cp36m[0m, which can be installed; - [32mpysam [0.10.0|0.14.1|...|0.9.1][0m would require - [32mpython >=3.6,<3.7.0a0 [0m, which can be installed; - [31mpysam [0.15.0|0.15.0.1|0.15.2][0m would require - [31mbcftools 1.9.* [0m but there are no viable options - [31mbcftools 1.9[0m would require - [31mlibdeflate >=1.0,<1.1.0a0 [0m, which conflicts with any installable versions previously reported; - [31mbcftools 1.9[0m would require - [31mgsl >=2.5,<2.6.0a0 [0m, which conflicts with any installable versions previously reported; - [31mpysam [0.15.1|0.15.2|0.15.3][0m would require - [31mlibdeflate >=1.0,<1.1.0a0 [0m, which conflicts with any installable versions previously reported; - [32mpysam [0.15.3|0.15.4|0.9.1][0m would require - [32mpython >=3.7,<3.8.0a0 [0m, which can be installed; - [32mpysam [0.15.4|0.16.0|...|0.9.1][0m would require - [32mpython_abi 3.7.* *_cp37m[0m, which can be installed; - [32mpysam [0.16.0.1|0.17.0|...|0.9.1][0m would require - [32mpython_abi 3.8.* *_cp38[0m, which can be installed; - [32mpysam [0.16.0.1|0.17.0|...|0.9.1][0m would require - [32mpython_abi 3.9.* *_cp39[0m, which can be installed; - [32mpysam [0.19.1|0.20.0|0.21.0|0.22.0|0.22.1][0m would require - [32mpython_abi 3.10.* *_cp310[0m, which can be installed; - [31mpython >=3.11,<3.12.0a0 [0m is not installable because it requires - [31mpython_abi 3.11.* *_cp311[0m, which conflicts with any installable versions previously reported. -# Last 100 lines of the build log. diff --git a/recipes/desman/meta.yaml b/recipes/desman/meta.yaml index ea2e7f98e1839..5c46782b55cb6 100644 --- a/recipes/desman/meta.yaml +++ b/recipes/desman/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 9 + number: 10 run_exports: - {{ pin_subpackage("desman", max_pin="x") }} script: {{ PYTHON }} -m pip install . --no-deps -vv @@ -24,7 +24,6 @@ requirements: - python - setuptools - cython >=0.19.1 - - numpy - numpy >=1.7.1 - gsl - pandas >=0.11.0 @@ -35,7 +34,7 @@ requirements: - bcbio-gff - biopython - pysam - - cython>=0.19.1 + - cython >=0.19.1 - scipy >=0.12.0 - {{ pin_compatible('numpy') }} - pandas >=0.11.0 diff --git a/recipes/devider/meta.yaml b/recipes/devider/meta.yaml index 90c59b5125124..c78c7a40edaca 100644 --- a/recipes/devider/meta.yaml +++ b/recipes/devider/meta.yaml @@ -11,7 +11,7 @@ source: - devider-aarch64.patch # [aarch64] build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('devider', max_pin="x.x") }} diff --git a/recipes/dextractor/meta.yaml b/recipes/dextractor/meta.yaml index 51e0ad9f023e3..9f4b000b4be0d 100644 --- a/recipes/dextractor/meta.yaml +++ b/recipes/dextractor/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.0p2" build: - number: 8 + number: 9 source: sha256: d5bfe730615d76b29d373b6505421db83f7f1075ef6be331c3ac030e40dcf343 diff --git a/recipes/dfast/meta.yaml b/recipes/dfast/meta.yaml index 1413b87753562..f61078ed70de5 100644 --- a/recipes/dfast/meta.yaml +++ b/recipes/dfast/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 643a6a38129c680809eb378c8ebcf2a4b8822f766922265976d100782ad73794 build: - number: 0 + number: 1 binary_relocation: False # [osx] run_exports: - {{ pin_subpackage("dfast", max_pin="x.x") }} diff --git a/recipes/dialign2/meta.yaml b/recipes/dialign2/meta.yaml index 8b04c81fa41c5..a804033a600fd 100644 --- a/recipes/dialign2/meta.yaml +++ b/recipes/dialign2/meta.yaml @@ -12,7 +12,7 @@ source: - patches/patchdialign.txt build: - number: 7 + number: 8 skip: True # [osx] requirements: diff --git a/recipes/coinfinder/build_failure.osx-64.yaml b/recipes/diamond/0.8.36/build_failure.osx-64.yaml similarity index 55% rename from recipes/coinfinder/build_failure.osx-64.yaml rename to recipes/diamond/0.8.36/build_failure.osx-64.yaml index 0011b4999c3bd..dc94c2428dfc1 100644 --- a/recipes/coinfinder/build_failure.osx-64.yaml +++ b/recipes/diamond/0.8.36/build_failure.osx-64.yaml @@ -1,38 +1,50 @@ -recipe_sha: d0fbf2e0dff1118c517e1a1e01c10fa22029a931c3b5462d0c26754b1f8967f8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: f4aa3231ab1c4e15da5249dbaef728ceb38c17470010c24e709b3d504b746c81 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- - sys.exit(execute()) - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/coinfinder_1717782355556/work - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/coinfinder_1717782355556/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/coinfinder_1717782355556/_build_env - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + - zlib + - libcxx >=18 + test: + commands: + - diamond --help 2>&1 > /dev/null + about: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + home: http://ab.inf.uni-tuebingen.de/software/diamond/ + license: BSD + summary: Accelerated BLAST compatible local sequence aligner + extra: + copy_test_source_files: true + final: true + identifiers: + - biotools:Diamond + - doi:10.1038/nmeth.3176 + + + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree packages_from_this = build( - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/coinfinder_1717782355556/work + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/diamond_1734455678405/work/conda_build.sh']' returned non-zero exit status 2. + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/diamond_1734455678405/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/diamond_1734455678405/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/diamond_1734455678405/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/diamond_1734455678405/work INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as CC=x86_64-apple-darwin13.4.0-clang CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/coinfinder-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/diamond-0.8.36 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ CLANG=x86_64-apple-darwin13.4.0-clang - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/coinfinder_1717782355556/work/conda_build.sh']' returned non-zero exit status 2. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/coinfinder-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/diamond-0.8.36 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool LD=x86_64-apple-darwin13.4.0-ld @@ -40,7 +52,7 @@ log: |2- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -49,7 +61,7 @@ log: |2- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -64,11 +76,11 @@ log: |2- INFO: activate_clangxx_osx-64.sh made the following environmental changes: CLANGXX=x86_64-apple-darwin13.4.0-clang CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/coinfinder-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/diamond-0.8.36 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/coinfinder-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - -- The C compiler identification is Clang 16.0.6 - -- The CXX compiler identification is Clang 16.0.6 + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/diamond-0.8.36 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -- The C compiler identification is Clang 18.1.8 + -- The CXX compiler identification is Clang 18.1.8 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped @@ -79,26 +91,16 @@ log: |2- -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done - -- Found PythonInterp: $PREFIX/bin/python3 (found suitable version "3.9.19", minimum required is "3.6") - -- Found PythonLibs: $PREFIX/lib/libpython3.9.dylib (found suitable version "3.9.19", minimum required is "3.6") - -- Found Boost 1.70.0 at $PREFIX/lib/cmake/Boost-1.70.0 - -- Requested configuration: QUIET REQUIRED COMPONENTS filesystem;system - -- Found boost_headers 1.70.0 at $PREFIX/lib/cmake/boost_headers-1.70.0 - -- Found boost_filesystem 1.70.0 at $PREFIX/lib/cmake/boost_filesystem-1.70.0 - -- libboost_filesystem.a - -- Adding boost_filesystem dependencies: headers - -- Found boost_system 1.70.0 at $PREFIX/lib/cmake/boost_system-1.70.0 - -- libboost_system.a - -- Adding boost_system dependencies: headers - -- Found Boost: $PREFIX/lib/cmake/Boost-1.70.0/BoostConfig.cmake (found version "1.70.0") found components: filesystem system + -- Performing Test COMPILER_SUPPORTS_MARCHNATIVE + -- Performing Test COMPILER_SUPPORTS_MARCHNATIVE - Success + -- Found ZLIB: $PREFIX/lib/libz.dylib (found version "1.3.1") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE - -- Found OpenMP_C: -fopenmp=libomp -Wno-unused-command-line-argument (found version "5.0") - -- Found OpenMP_CXX: -fopenmp=libomp -Wno-unused-command-line-argument (found version "5.0") - -- Found OpenMP: TRUE (found version "5.0") - -- Configuring done (4.1s) - -- Generating done (0.0s) - -- Build files have been written to: $SRC_DIR - [ 6%] Building CXX object CMakeFiles/coinfinder.dir/coinfind-code/main.cpp.o + -- Configuring done (3.3s) + -- Generating done (0.1s) + -- Build files have been written to: $SRC_DIR/build + [ 1%] Building CXX object CMakeFiles/diamond.dir/src/run/main.cpp.o # Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/diamond/0.8.36/meta.yaml b/recipes/diamond/0.8.36/meta.yaml index 578ea77e29237..f0e0c75e41e9c 100644 --- a/recipes/diamond/0.8.36/meta.yaml +++ b/recipes/diamond/0.8.36/meta.yaml @@ -11,7 +11,7 @@ source: md5: {{ md5 }} build: - number: 7 + number: 8 skip: False # We pin on gcc version to avoid gcc-5 dual ABI issues depending on boost. diff --git a/recipes/diamond/meta.yaml b/recipes/diamond/meta.yaml index 355240e301805..8875d00d36761 100644 --- a/recipes/diamond/meta.yaml +++ b/recipes/diamond/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('diamond', max_pin="x") }} diff --git a/recipes/dicey/meta.yaml b/recipes/dicey/meta.yaml index aff17789c7676..50cde649be72c 100644 --- a/recipes/dicey/meta.yaml +++ b/recipes/dicey/meta.yaml @@ -14,7 +14,7 @@ source: build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("dicey", max_pin="x.x") }} diff --git a/recipes/difcover/meta.yaml b/recipes/difcover/meta.yaml index 8c8f384baf7e9..29f354ac538de 100644 --- a/recipes/difcover/meta.yaml +++ b/recipes/difcover/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 skip: True # [osx] run_exports: - {{ pin_subpackage("difcover", max_pin="x") }} diff --git a/recipes/dig2/build_failure.osx-64.yaml b/recipes/dig2/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..578385ed0894e --- /dev/null +++ b/recipes/dig2/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 27055e87003ab665925d171faef1276a7e53cf7b9077c7f56a152a97b00287da # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - clang_osx-64 18.1.8 h7e5c614_23 + - tapi 1300.6.5 h390ca13_0 + - llvm-tools 18.1.8 h9ce406d_2 + - zstd 1.5.6 h915ae27_0 + - sigtool 0.1.3 h88f4db0_0 + - cctools_osx-64 1010.6 h00edd4c_2 + - llvm-tools-18 18.1.8 h9ce406d_2 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + - libclang-cpp18.1 18.1.8 default_h0c94c6a_5 + - ncurses 6.5 hf036a51_1 + - openssl 3.4.0 hd471939_0 + - ld64_osx-64 951.9 hc8d1a19_2 + - libllvm18 18.1.8 h9ce406d_2 + raise subprocess.CalledProcessError(proc.returncode, _args) + - compiler-rt 18.1.8 h1020d70_1 + - libiconv 1.17 hd75f5a5_2 + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/dig2_1733865658420/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + - libcxx-devel 18.1.8 h7c275be_7 + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + host: [] + run: [] + test: + commands: + - dig2 -h + about: + home: http://www.ms-utils.org/dig2/dig2.html + license: GPL3 + summary: dig2 is a simple but flexible in silico digester of protein sequences in + the FASTA format. It allows for almost any enzyme to be simulated, including MS/MS + enzymes to generate CID or ECD/ETD fragments. + extra: + copy_test_source_files: true + final: true + identifiers: + - biotools:dig2 + + + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/dig2_1733865658420/work/conda_build.sh']' returned non-zero exit status 1. + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/dig2_1733865658420/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/dig2_1733865658420/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/dig2_1733865658420/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/dig2_1733865658420/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dig2-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dig2-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 +# Last 100 lines of the build log. diff --git a/recipes/dig2/meta.yaml b/recipes/dig2/meta.yaml index fe6e09d7c87ca..10c61fb895876 100644 --- a/recipes/dig2/meta.yaml +++ b/recipes/dig2/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 6 + number: 7 source: url: http://www.ms-utils.org/dig2/dig2.c diff --git a/recipes/digestiflow-cli/meta.yaml b/recipes/digestiflow-cli/meta.yaml index 558e2226c9305..661dadbc0344f 100644 --- a/recipes/digestiflow-cli/meta.yaml +++ b/recipes/digestiflow-cli/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 6 + number: 7 # TODO wait for CB3 gcc, then try again. skip: true # [osx] run_exports: @@ -36,4 +36,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/dinamo/meta.yaml b/recipes/dinamo/meta.yaml index ebf6efdd07a26..da45885b6c2ec 100644 --- a/recipes/dinamo/meta.yaml +++ b/recipes/dinamo/meta.yaml @@ -14,7 +14,7 @@ source: build: skip: True # [osx] - number: 6 + number: 7 run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} diff --git a/recipes/diphase/build_failure.linux-64.yaml b/recipes/diphase/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..77633b4a3359b --- /dev/null +++ b/recipes/diphase/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 76aafed7a3d7c24d2ff5f740103a41346452be4bca1fd01548d681d7b9f72d8b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [31mpython 3.9.0.* [0m is not installable because it requires + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("python==3.9.0=h2a148a8_4_cpython"), MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']")} + Encountered problems while solving: + - package python-3.9.0-h2a148a8_4_cpython requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mlibzlib >=1.3.1,<2.0a0 [0m is installable with the potential options + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_0[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [31mpython 3.9.0.* [0m is not installable because it requires + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("python==3.9.0=h2a148a8_4_cpython"), MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']")} + Encountered problems while solving: + - package python-3.9.0-h2a148a8_4_cpython requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mlibzlib >=1.3.1,<2.0a0 [0m is installable with the potential options + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_0[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [31mpython 3.9.0.* [0m is not installable because it requires + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/diphase/meta.yaml b/recipes/diphase/meta.yaml index a2c0dfb3380be..bb1779eaf7c9b 100644 --- a/recipes/diphase/meta.yaml +++ b/recipes/diphase/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('diphase', max_pin="x") }} diff --git a/recipes/disco/1.2/build_failure.linux-64.yaml b/recipes/disco/1.2/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..17c1c7939eb0f --- /dev/null +++ b/recipes/disco/1.2/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 928dd1b24eb01b60cdfef9aef1ec448f88831bd674d118093f9e125506588424 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + mpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/disco-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -DINCLUDE_READGZ -fopenmp -o "buildG-MPIRMA" ./src/Dataset.o ./src/Edge.o ./src/HashTable.o ./src/OverlapGraph.o ./src/Read.o ./src/main.o -lz + Finished building target: buildG-MPIRMA + + make[1]: Leaving directory '$SRC_DIR/src/BuildGraphMPIRMA/Release' + make -C src/SimplifyGraph/Release READGZ=1 + make[1]: Entering directory '$SRC_DIR/src/SimplifyGraph/Release' + Building file: ../src/Config.cpp + Invoking: GCC C Compiler + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/disco-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -DINCLUDE_READGZ -O3 -g3 -c -fmessage-length=0 -fopenmp -Wno-sign-compare -lz -lgomp -std=c11 -MMD -MP -MF"src/Config.d" -MT"src/Config.o" -o "src/Config.o" "../src/Config.cpp" + Finished building: ../src/Config.cpp + + Building file: ../src/DataSet.cpp + Invoking: GCC C Compiler + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/disco-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -DINCLUDE_READGZ -O3 -g3 -c -fmessage-length=0 -fopenmp -Wno-sign-compare -lz -lgomp -std=c11 -MMD -MP -MF"src/DataSet.d" -MT"src/DataSet.o" -o "src/DataSet.o" "../src/DataSet.cpp" + Finished building: ../src/DataSet.cpp + + Building file: ../src/Edge.cpp + Invoking: GCC C Compiler + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/disco-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -DINCLUDE_READGZ -O3 -g3 -c -fmessage-length=0 -fopenmp -Wno-sign-compare -lz -lgomp -std=c11 -MMD -MP -MF"src/Edge.d" -MT"src/Edge.o" -o "src/Edge.o" "../src/Edge.cpp" + Finished building: ../src/Edge.cpp + + Building file: ../src/OverlapGraph.cpp + Invoking: GCC C Compiler + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/disco-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -DINCLUDE_READGZ -O3 -g3 -c -fmessage-length=0 -fopenmp -Wno-sign-compare -lz -lgomp -std=c11 -MMD -MP -MF"src/OverlapGraph.d" -MT"src/OverlapGraph.o" -o "src/OverlapGraph.o" "../src/OverlapGraph.cpp" + Finished building: ../src/OverlapGraph.cpp + + Building file: ../src/Read.cpp + Invoking: GCC C Compiler + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/disco-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -DINCLUDE_READGZ -O3 -g3 -c -fmessage-length=0 -fopenmp -Wno-sign-compare -lz -lgomp -std=c11 -MMD -MP -MF"src/Read.d" -MT"src/Read.o" -o "src/Read.o" "../src/Read.cpp" + Finished building: ../src/Read.cpp + + Building file: ../src/Utils.cpp + Invoking: GCC C Compiler + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/disco-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -DINCLUDE_READGZ -O3 -g3 -c -fmessage-length=0 -fopenmp -Wno-sign-compare -lz -lgomp -std=c11 -MMD -MP -MF"src/Utils.d" -MT"src/Utils.o" -o "src/Utils.o" "../src/Utils.cpp" + ../src/Utils.cpp: In function 'std::string Utils::reverseComplement(const std::string&)': + ../src/Utils.cpp:606:9: error: 'uint64_t' was not declared in this scope + 606 | uint64_t sLength = seq.length(); + | ^~~~~~~~ + ../src/Utils.cpp:11:1: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + 10 | #include "Utils.h" + |#include + 11 | #include + ../src/Utils.cpp:607:29: error: 'sLength' was not declared in this scope + 607 | std::string reverse(sLength,'0'); + | ^~~~~~~ + ../src/Utils.cpp:608:21: error: expected ';' before 'i' + 608 | for(uint64_t i = 0;i < sLength; i) + | ^~ + | ; + ../src/Utils.cpp:608:28: error: 'i' was not declared in this scope + 608 | for(uint64_t i = 0;i < sLength; i) + | ^ + ../src/Utils.cpp: In function 'void Utils::ltrim(std::string&)': + ../src/Utils.cpp:633:93: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] + 633 | s.erase(s.begin(), std::find_if(s.begin(), s.end(), std::not1(std::ptr_fun(std::isspace)))); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ + In file included from /opt/conda/conda-bld/disco_1734305300468/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/string:49, + from /opt/conda/conda-bld/disco_1734305300468/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/locale_classes.h:40, + from /opt/conda/conda-bld/disco_1734305300468/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/ios_base.h:41, + from /opt/conda/conda-bld/disco_1734305300468/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/ios:44, + from /opt/conda/conda-bld/disco_1734305300468/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/ostream:40, + from /opt/conda/conda-bld/disco_1734305300468/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/iostream:41, + from ../src/Utils.h:13, + from ../src/Utils.cpp:10: + /opt/conda/conda-bld/disco_1734305300468/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_function.h:1126:5: note: declared here + 1126 | ptr_fun(_Result (*__x)(_Arg)) + | ^~~~~~~ + ../src/Utils.cpp: In function 'void Utils::rtrim(std::string&)': + ../src/Utils.cpp:638:84: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] + 638 | s.erase(std::find_if(s.rbegin(), s.rend(), std::not1(std::ptr_fun(std::isspace))).base(), s.end()); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ + /opt/conda/conda-bld/disco_1734305300468/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_function.h:1126:5: note: declared here + 1126 | ptr_fun(_Result (*__x)(_Arg)) + | ^~~~~~~ + make[1]: *** [src/subdir2.mk:45: src/Utils.o] Error 1 + make[1]: Leaving directory '$SRC_DIR/src/SimplifyGraph/Release' + make: *** [Makefile:43: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/disco_1734305300468/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/disco_1734305300468/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/disco/1.2/meta.yaml b/recipes/disco/1.2/meta.yaml index d743b1568d037..f9c4eeeff44b4 100644 --- a/recipes/disco/1.2/meta.yaml +++ b/recipes/disco/1.2/meta.yaml @@ -13,7 +13,7 @@ source: - sstr.patch build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/discosnp/meta.yaml b/recipes/discosnp/meta.yaml index 67923ba1b5953..923fcbdd40dca 100644 --- a/recipes/discosnp/meta.yaml +++ b/recipes/discosnp/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 skip: True # [osx] run_exports: - {{ pin_subpackage('discosnp', max_pin="x") }} diff --git a/recipes/dist_est/build_failure.osx-64.yaml b/recipes/dist_est/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..71787d7e4e983 --- /dev/null +++ b/recipes/dist_est/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 8846bbd37f39d37aadcca606ef2bf01bd2e964441e4b1914407cabb850c742ba # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - clang_osx-64 18.1.8 h7e5c614_23 + - libclang-cpp18.1 18.1.8 default_h0c94c6a_5 + host: + - libcxx 19.1.5 hf95d169_0 + - llvm-openmp 19.1.5 ha54dae1_0 + - libgfortran5 13.2.0 h2873a65_3 + - libgfortran 5.0.0 13_2_0_h97931a8_3 + run: + - libgfortran5 >=13.2.0 + - libcxx >=18 + - libgfortran 5.* + test: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + commands: + - dist_est -v > /tmp/null + about: + home: https://www.mathstat.dal.ca/~tsusko/doc/ras.pdf + license: GNU General Public v3 or later (GPLv3) + license_family: GPL3 + license_file: LICENSE + summary: Estimation of Rates-Across-Sites Distributions in Phylogenetic Subsititution + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/dist_est_1734454221668/work/conda_build.sh']' returned non-zero exit status 2. + Models + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/dist_est_1734454221668/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/dist_est_1734454221668/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/dist_est_1734454221668/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/dist_est_1734454221668/work + INFO: activate-gfortran_osx-64.sh made the following environmental changes: + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dist_est-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dist_est-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + F77=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F90=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dist_est-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dist_est-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dist_est-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dist_est-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dist_est-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dist_est-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + x86_64-apple-darwin13.4.0-clang -O3 -c dcdflib.c -o dcdflib.o -fcommon + x86_64-apple-darwin13.4.0-clang -O3 -c dist_est.c -o dist_est.o -fcommon +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/dist_est/meta.yaml b/recipes/dist_est/meta.yaml index 06e0f3e4bf685..eb6d595ac10d0 100644 --- a/recipes/dist_est/meta.yaml +++ b/recipes/dist_est/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/distle/meta.yaml b/recipes/distle/meta.yaml index 740d308b1d7e0..b4f7e4527e130 100644 --- a/recipes/distle/meta.yaml +++ b/recipes/distle/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('distle', max_pin="x.x") }} diff --git a/recipes/disty/build_failure.linux-64.yaml b/recipes/disty/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..a30e5e9454758 --- /dev/null +++ b/recipes/disty/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 84c77dcafe5e100284caddf9994769c217b3c3b2bf0e692cfc6d9221488ac467 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/disty-0.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/disty-0.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/disty-0.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/disty-0.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/disty-0.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -std=c11 -Wall -Wextra -Wno-missing-field-initializers -g -O2 -c src/main.cpp -o src/main.cpp.o + src/main.cpp:103:14: error: 'uint8_t' does not name a type + 103 | static const uint8_t acgt_nt256_nt4[] = { + | ^~~~~~~ + src/main.cpp:45:1: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + 44 | #include "kseq.h" + |#include + 45 | + src/main.cpp:141:14: error: 'uint8_t' does not name a type + 141 | static const uint8_t binary_nt256_nt4[] = { + | ^~~~~~~ + src/main.cpp:141:14: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + src/main.cpp: In function 'void pair_matrix_char_acgt(T&, pair_char_t&)': + src/main.cpp:427:21: error: 'acgt_nt256_nt4' was not declared in this scope + 427 | char n1_nt4=acgt_nt256_nt4[i]; + | ^~~~~~~~~~~~~~ + src/main.cpp: In function 'void pair_matrix_char_binary(T&, pair_char_t&)': + src/main.cpp:457:21: error: 'binary_nt256_nt4' was not declared in this scope + 457 | char n1_nt4=binary_nt256_nt4[i]; + | ^~~~~~~~~~~~~~~~ + src/main.cpp: In instantiation of 'void load_sequences(const std::string&, T&, T&) [with T = std::vector >; std::string = std::__cxx11::basic_string]': + src/main.cpp:525:19: required from here + src/main.cpp:257:19: warning: unused variable 'a' [-Wunused-variable] + 257 | for(char &a: s){ + | ^ + src/main.cpp: In instantiation of 'void pair_matrix_char_binary(T&, pair_char_t&) [with T = std::vector >]': + src/main.cpp:594:44: required from here + src/main.cpp:448:33: warning: unused parameter 'pair_matrix' [-Wunused-parameter] + 448 | void pair_matrix_char_binary(T &pair_matrix, pair_char_t &pair_char) { + | ~~~^~~~~~~~~~~ + make: *** [Makefile:22: src/main.cpp.o] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/disty_1733932205897/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/disty_1733932205897/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/disty/meta.yaml b/recipes/disty/meta.yaml index 07846293716a3..93a2d1ec25ecc 100644 --- a/recipes/disty/meta.yaml +++ b/recipes/disty/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 7 + number: 8 requirements: build: diff --git a/recipes/dligand2/meta.yaml b/recipes/dligand2/meta.yaml index 5a92ccd1e656e..1ed12f0bb3b05 100644 --- a/recipes/dligand2/meta.yaml +++ b/recipes/dligand2/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 91c1876c351ce07a5b90d29f12bab6bd8d1234c8f902f2dc92b1c13d49d6e024 build: - number: 4 + number: 5 skip: True # [osx] requirements: diff --git a/recipes/dmtools/build_failure.linux-64.yaml b/recipes/dmtools/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..a58fe5545ba21 --- /dev/null +++ b/recipes/dmtools/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5b102f0821fb930b99398fec8c71d0bb6281c2b20aa9abfca23a33aedc2528f5 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + source tree in: /opt/conda/conda-bld/dmtools_1734277946638/work + export PREFIX=/opt/conda/conda-bld/dmtools_1734277946638/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place + export BUILD_PREFIX=/opt/conda/conda-bld/dmtools_1734277946638/_build_env + export SRC_DIR=/opt/conda/conda-bld/dmtools_1734277946638/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dmtools-0.2.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dmtools-0.2.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -std=c17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dmtools-0.2.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -std=c17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/dmtools-0.2.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + make -C htslib + make[1]: Entering directory '$SRC_DIR/htslib' + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o kfunc.o kfunc.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o kstring.o kstring.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o bgzf.o bgzf.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o errmod.o errmod.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o faidx.o faidx.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o header.o header.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o hfile.o hfile.c + echo '#define HTS_VERSION_TEXT "1.16"' > version.h + echo '#define HTS_CC "$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc"' > config_vars.h + echo '#define HTS_CPPFLAGS ""' >> config_vars.h + echo '#define HTS_CFLAGS "-g -Wall -O2 -fvisibility=hidden"' >> config_vars.h + echo '#define HTS_LDFLAGS "-fvisibility=hidden"' >> config_vars.h + echo '#define HTS_LIBS "-lz -lm -lbz2 -llzma -lcurl"' >> config_vars.h + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o hts.o hts.c + hts.c:46:10: fatal error: lzma.h: No such file or directory + 46 | #include + | ^~~~~~~~ + compilation terminated. + make[1]: *** [Makefile:173: hts.o] Error 1 + make[1]: Leaving directory '$SRC_DIR/htslib' + make: *** [Makefile:150: libs] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/dmtools_1734277946638/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/dmtools_1734277946638/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/dmtools/meta.yaml b/recipes/dmtools/meta.yaml index 478f477f896f6..728483c8d83c8 100644 --- a/recipes/dmtools/meta.yaml +++ b/recipes/dmtools/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('dmtools', max_pin="x.x") }} skip: True # [osx] diff --git a/recipes/dna-nn/build_failure.osx-64.yaml b/recipes/dna-nn/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..dbaffe354213e --- /dev/null +++ b/recipes/dna-nn/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 81bf369a54204e2e54d7501d4c44f7d5d0d97512d08ced66c72bef74c00a2032 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("k8==0.2.5=h7475705_0"), MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']")} + Encountered problems while solving: + - package k8-0.2.5-h7475705_0 requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + k8 is installable with the potential options + k8 0.2.5 would require + zlib >=1.2.11,<1.3.0a0 , which can be installed; + k8 0.2.5 would require + zlib >=1.2.13,<1.3.0a0 , which can be installed; + k8 [0.2.5|1.0|1.1|1.2] would require + libzlib >=1.2.13,<1.3.0a0 , which can be installed; + libzlib >=1.3.1,<2.0a0 is not installable because there are no viable options + libzlib 1.3.1 would require + zlib 1.3.1 *_0, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_1, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_2, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("k8==0.2.5=h7475705_0"), MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']")} + Encountered problems while solving: + - package k8-0.2.5-h7475705_0 requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + k8 is installable with the potential options + k8 0.2.5 would require + zlib >=1.2.11,<1.3.0a0 , which can be installed; + k8 0.2.5 would require + zlib >=1.2.13,<1.3.0a0 , which can be installed; + k8 [0.2.5|1.0|1.1|1.2] would require + libzlib >=1.2.13,<1.3.0a0 , which can be installed; + libzlib >=1.3.1,<2.0a0 is not installable because there are no viable options + libzlib 1.3.1 would require + zlib 1.3.1 *_0, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_1, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_2, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/dna-nn/meta.yaml b/recipes/dna-nn/meta.yaml index 66c70ccaea69a..c0700b1637981 100644 --- a/recipes/dna-nn/meta.yaml +++ b/recipes/dna-nn/meta.yaml @@ -10,7 +10,7 @@ source: sha256: bac26a25ad9e0315351b170bc33ab4e41b7573818fd9527b661f882b96ae0a8a build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage("dna-nn", max_pin="x.x") }} diff --git a/recipes/dnmtools/meta.yaml b/recipes/dnmtools/meta.yaml index d52deda3af845..46025e7f4d208 100644 --- a/recipes/dnmtools/meta.yaml +++ b/recipes/dnmtools/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 56fc62ef1d41cdafa30c98d6cfbcb3707a125921618a1808075eaafb29d22edf build: - number: 0 + number: 1 run_exports: # dnmtools is currently not intended to be stable between minor versions (x.x). - {{ pin_subpackage('dnmtools', max_pin="x.x") }} diff --git a/recipes/dnp-binstrings/meta.yaml b/recipes/dnp-binstrings/meta.yaml index a35a8f7fa8825..7913207434a8d 100644 --- a/recipes/dnp-binstrings/meta.yaml +++ b/recipes/dnp-binstrings/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 19c46d6bc6a1af70e5a2b4a051aab334026dc38c84b367ea9c445da3fdb21cfe build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/dnp-corrprofile/meta.yaml b/recipes/dnp-corrprofile/meta.yaml index faaf536797954..715b05e0f9e68 100644 --- a/recipes/dnp-corrprofile/meta.yaml +++ b/recipes/dnp-corrprofile/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 19c46d6bc6a1af70e5a2b4a051aab334026dc38c84b367ea9c445da3fdb21cfe build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/dnp-diprofile/meta.yaml b/recipes/dnp-diprofile/meta.yaml index a1e16c1236aca..5c4162252b473 100644 --- a/recipes/dnp-diprofile/meta.yaml +++ b/recipes/dnp-diprofile/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 19c46d6bc6a1af70e5a2b4a051aab334026dc38c84b367ea9c445da3fdb21cfe build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/dnp-fourier/meta.yaml b/recipes/dnp-fourier/meta.yaml index 052a0f4274fb2..08df6db921267 100644 --- a/recipes/dnp-fourier/meta.yaml +++ b/recipes/dnp-fourier/meta.yaml @@ -9,7 +9,7 @@ source: - 0001-Use-CXX-and-flags.patch build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/dnp-mapping/meta.yaml b/recipes/dnp-mapping/meta.yaml index dfb600661cad5..6ecc10a1fc4cb 100644 --- a/recipes/dnp-mapping/meta.yaml +++ b/recipes/dnp-mapping/meta.yaml @@ -7,7 +7,7 @@ source: sha256: eec549030dbce176de63e743bf99aa0a6129059f70985b93cec9847abaf797c6 build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/dockq/build_failure.linux-64.yaml b/recipes/dockq/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..9b34e2fded198 --- /dev/null +++ b/recipes/dockq/build_failure.linux-64.yaml @@ -0,0 +1,4 @@ +recipe_sha: 70ba4ad0674758235a967e9c73893cc9234d010b30e90a81432486c8db17c2df # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + exists in conda-forge diff --git a/recipes/dockq/build_failure.osx-64.yaml b/recipes/dockq/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..9b34e2fded198 --- /dev/null +++ b/recipes/dockq/build_failure.osx-64.yaml @@ -0,0 +1,4 @@ +recipe_sha: 70ba4ad0674758235a967e9c73893cc9234d010b30e90a81432486c8db17c2df # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + exists in conda-forge diff --git a/recipes/dockq/meta.yaml b/recipes/dockq/meta.yaml index 9c21a4695b948..b3ec7d10410e8 100644 --- a/recipes/dockq/meta.yaml +++ b/recipes/dockq/meta.yaml @@ -14,7 +14,7 @@ build: entry_points: - DockQ = DockQ.__main__:main script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation - number: 0 + number: 2 run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} diff --git a/recipes/nanovar/build_failure.linux-64.yaml b/recipes/drprg/build_failure.linux-64.yaml similarity index 75% rename from recipes/nanovar/build_failure.linux-64.yaml rename to recipes/drprg/build_failure.linux-64.yaml index 2820ae9473980..eb43ed578214b 100644 --- a/recipes/nanovar/build_failure.linux-64.yaml +++ b/recipes/drprg/build_failure.linux-64.yaml @@ -1,12 +1,20 @@ -recipe_sha: f53195d3afaccd0ad9b558a2fa912d58f556a36c8f21b1a269509d93bddd3b7e # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: ab73189e7b4a85df9b098839fba132a7da9c17f888f73f24f3ffdccbc86e78a8 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: dependency issue -reason: tensorflow-mkl is only available in default channel -log: |2- +log: |- + Encountered problems while solving: + - package mafft-7.505-hec16e2b_0 is excluded by strict repo priority + + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction unlink_precs, link_precs = self.solve_for_diff( - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff final_precs = self.solve_final_state( File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state out_state = self._solving_loop(in_state, out_state, index) @@ -18,24 +26,21 @@ log: |2- self._maybe_raise_for_conda_build( File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("tensorflow-mkl[version='>=2.0.0']")} + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("mafft==7.505=hec16e2b_0")} Encountered problems while solving: - - nothing provides requested tensorflow-mkl >=2.0.0 + - package mafft-7.505-hec16e2b_0 is excluded by strict repo priority - Could not solve for environment specs - The following package could not be installed - [31mtensorflow-mkl >=2.0.0 [0m does not exist (perhaps a typo or a missing channel). During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions - precs = _install_actions(prefix, index, specs)["LINK"] - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction unlink_precs, link_precs = self.solve_for_diff( - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff final_precs = self.solve_final_state( File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state out_state = self._solving_loop(in_state, out_state, index) @@ -47,44 +52,41 @@ log: |2- self._maybe_raise_for_conda_build( File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("tensorflow-mkl[version='>=2.0.0']")} + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("mafft==7.505=hec16e2b_0")} Encountered problems while solving: - - nothing provides requested tensorflow-mkl >=2.0.0 + - package mafft-7.505-hec16e2b_0 is excluded by strict repo priority - Could not solve for environment specs - The following package could not be installed - [31mtensorflow-mkl >=2.0.0 [0m does not exist (perhaps a typo or a missing channel). During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/opt/conda/bin/conda-build", line 11, in sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2409, in build + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build create_build_envs(top_level_pkg, notest) - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2247, in create_build_envs + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs raise e - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2220, in create_build_envs + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs environ.get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions precs = get_package_records( File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions - precs = _install_actions(prefix, index, specs)["LINK"] - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction unlink_precs, link_precs = self.solve_for_diff( - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff final_precs = self.solve_final_state( File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state out_state = self._solving_loop(in_state, out_state, index) @@ -96,11 +98,9 @@ log: |2- self._maybe_raise_for_conda_build( File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("tensorflow-mkl[version='>=2.0.0']")} + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("mafft==7.505=hec16e2b_0")} Encountered problems while solving: - - nothing provides requested tensorflow-mkl >=2.0.0 - - Could not solve for environment specs - The following package could not be installed - [31mtensorflow-mkl >=2.0.0 [0m does not exist (perhaps a typo or a missing channel). + - package mafft-7.505-hec16e2b_0 is excluded by strict repo priority # Last 100 lines of the build log. +category: |- + dependency issue diff --git a/recipes/drprg/meta.yaml b/recipes/drprg/meta.yaml index a7bcfa72cf3aa..bda74edee6f35 100644 --- a/recipes/drprg/meta.yaml +++ b/recipes/drprg/meta.yaml @@ -10,7 +10,7 @@ source: sha256: b5cfba49372867272b40c3e018f12583a0eff98c1e6061c4974fac03986e6b5c build: - number: 1 + number: 2 skip: true # [osx] binary_has_prefix_files: - bin/pandora diff --git a/recipes/dsk/meta.yaml b/recipes/dsk/meta.yaml index d9f31a8beb004..801dc30f1b5f7 100644 --- a/recipes/dsk/meta.yaml +++ b/recipes/dsk/meta.yaml @@ -11,7 +11,7 @@ source: - install_paths.patch build: - number: 5 + number: 6 # Requires clang>=4.5 skip: True # [osx] run_exports: diff --git a/recipes/dsrc/meta.yaml b/recipes/dsrc/meta.yaml index 5841ffe7771a1..caaec8ef2c38f 100644 --- a/recipes/dsrc/meta.yaml +++ b/recipes/dsrc/meta.yaml @@ -7,7 +7,7 @@ source: sha256: a8ddbe986e0477d09ada2b977ae7854e8e8361392b90620192a2cb06b5dc8a58 build: - number: 8 + number: 9 run_exports: - {{ pin_subpackage('dsrc', max_pin=None) }} diff --git a/recipes/dunovo/build_failure.linux-64.yaml b/recipes/dunovo/build_failure.linux-64.yaml deleted file mode 100644 index b162e9f6f4f50..0000000000000 --- a/recipes/dunovo/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 8239adce08ff29c81a856f1c7582399456cd788b75a4c6e44a6b62c896cbabfe # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - INFO:conda_build.utils:shutil.move(work)=/opt/conda/conda-bld/dunovo_1685352493523/work, dest=/opt/conda/conda-bld/dunovo_1685352493523/work_moved_dunovo-3.0.2-h031d066_2_linux-64) - [34mReloading output folder: [0m[34m/opt/conda/[0m[34mconda-bld[0m - [?25l[2K[0G[] 0.0s - [2K[1A[2K[0Gopt/conda/conda-bld/linux-64 825.0 B @ 19.2MB/s 0.0s - opt/conda/conda-bld/noarch 127.0 B @ 5.1MB/s 0.0s - [?25h - ## Package Plan ## - - environment location: /opt/conda/conda-bld/dunovo_1685352493523/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p - - - The following NEW packages will be INSTALLED: - - _libgcc_mutex: 0.1-conda_forge conda-forge - _openmp_mutex: 4.5-2_gnu conda-forge - bash: 5.0.018-h0a1914f_0 conda-forge - biopython: 1.78-py38h497a2fe_2 conda-forge - bowtie: 1.3.1-py38h70e88c0_6 bioconda - bzip2: 1.0.8-h7f98852_4 conda-forge - c-ares: 1.19.1-hd590300_0 conda-forge - ca-certificates: 2023.5.7-hbcca054_0 conda-forge - coreutils: 9.3-h0b41bf4_0 conda-forge - curl: 7.87.0-h6312ad2_0 conda-forge - decorator: 5.1.1-pyhd8ed1ab_0 conda-forge - dunovo: 3.0.2-h031d066_2 local - file: 5.39-h753d276_1 conda-forge - gawk: 5.1.0-h7f98852_0 conda-forge - gzip: 1.12-h166bdaf_0 conda-forge - htslib: 1.9-h244ad75_9 bioconda - icu: 72.1-hcb278e6_0 conda-forge - keyutils: 1.6.1-h166bdaf_0 conda-forge - krb5: 1.20.1-hf9c8cef_0 conda-forge - ld_impl_linux-64: 2.40-h41732ed_0 conda-forge - libblas: 3.9.0-16_linux64_openblas conda-forge - libcblas: 3.9.0-16_linux64_openblas conda-forge - libcurl: 7.87.0-h6312ad2_0 conda-forge - libdeflate: 1.18-h0b41bf4_0 conda-forge - libedit: 3.1.20191231-h46ee950_2 conda-forge - libev: 4.33-h516909a_1 conda-forge - libffi: 3.2.1-he1b5a44_1007 conda-forge - libgcc-ng: 12.2.0-h65d4601_19 conda-forge - libgfortran-ng: 12.2.0-h69a702a_19 conda-forge - libgfortran5: 12.2.0-h337968e_19 conda-forge - libgomp: 12.2.0-h65d4601_19 conda-forge - libhwloc: 2.9.1-hd6dc26d_0 conda-forge - libiconv: 1.17-h166bdaf_0 conda-forge - liblapack: 3.9.0-16_linux64_openblas conda-forge - libmagic: 5.39-h753d276_1 conda-forge - libnghttp2: 1.51.0-hdcd2b5c_0 conda-forge - libnsl: 2.0.0-h7f98852_0 conda-forge - libopenblas: 0.3.21-pthreads_h78a6416_3 conda-forge - libssh2: 1.10.0-haa6b8db_3 conda-forge - libstdcxx-ng: 12.2.0-h46fd767_19 conda-forge - libxml2: 2.10.4-hfdac1af_0 conda-forge - libzlib: 1.2.13-h166bdaf_4 conda-forge - mafft: 7.221-0 bioconda - ncurses: 6.1-hf484d3e_1002 conda-forge - networkx: 2.4-py_1 conda-forge - numpy: 1.24.3-py38h59b608b_0 conda-forge - openssl: 1.1.1t-h0b41bf4_0 conda-forge - perl: 5.32.1-2_h7f98852_perl5 conda-forge - pip: 23.1.2-pyhd8ed1ab_0 conda-forge - python: 3.8.6-h852b56e_0_cpython conda-forge - python_abi: 3.8-3_cp38 conda-forge - readline: 8.0-h46ee950_1 conda-forge - samtools: 1.9-h10a08f8_12 bioconda - setuptools: 67.7.2-pyhd8ed1ab_0 conda-forge - sqlite: 3.40.1-h5082296_0 defaults - tbb: 2021.9.0-hf52228f_0 conda-forge - tk: 8.6.12-h27826a3_0 conda-forge - wheel: 0.40.0-pyhd8ed1ab_0 conda-forge - xz: 5.2.6-h166bdaf_0 conda-forge - zlib: 1.2.13-h166bdaf_4 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - export PREFIX=/opt/conda/conda-bld/dunovo_1685352493523/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p - export SRC_DIR=/opt/conda/conda-bld/dunovo_1685352493523/test_tmp - import: 'networkx' - Traceback (most recent call last): - File "/opt/conda/conda-bld/dunovo_1685352493523/test_tmp/run_test.py", line 2, in - import networkx - File "/opt/conda/conda-bld/dunovo_1685352493523/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.8/site-packages/networkx/__init__.py", line 115, in - import networkx.readwrite - File "/opt/conda/conda-bld/dunovo_1685352493523/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.8/site-packages/networkx/readwrite/__init__.py", line 15, in - from networkx.readwrite.graphml import * - File "/opt/conda/conda-bld/dunovo_1685352493523/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.8/site-packages/networkx/readwrite/graphml.py", line 314, in - class GraphML(object): - File "/opt/conda/conda-bld/dunovo_1685352493523/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.8/site-packages/networkx/readwrite/graphml.py", line 346, in GraphML - (np.int, "int"), (np.int8, "int"), - File "/opt/conda/conda-bld/dunovo_1685352493523/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.8/site-packages/numpy/__init__.py", line 305, in __getattr__ - raise AttributeError(__former_attrs__[attr]) - AttributeError: module 'numpy' has no attribute 'int'. - np.int was a deprecated alias for the builtin int. To avoid this error in existing code, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information. - The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: - https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations - Tests failed for dunovo-3.0.2-h031d066_2.tar.bz2 - moving package to /opt/conda/conda-bld/broken - WARNING:conda_build.build:Tests failed for dunovo-3.0.2-h031d066_2.tar.bz2 - moving package to /opt/conda/conda-bld/broken - TESTS FAILED: dunovo-3.0.2-h031d066_2.tar.bz2 -# Last 100 lines of the build log. diff --git a/recipes/dunovo/meta.yaml b/recipes/dunovo/meta.yaml index 9a4f0613ebc73..c8bf93407f2a9 100644 --- a/recipes/dunovo/meta.yaml +++ b/recipes/dunovo/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 79f6469bdf6752c3a2555feefc26038ae793dac4acb0136355287aed6cb791e0 build: - number: 3 + number: 4 skip: True # [osx] run_exports: - {{ pin_subpackage('dunovo', max_pin="x") }} diff --git a/recipes/duphold/build_failure.linux-64.yaml b/recipes/duphold/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..989bd97a04f3a --- /dev/null +++ b/recipes/duphold/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 7eb6f2104ae709149e772f1e46fb9ffd1064fc011fe525e694ffa1c61b49a42d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/types.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/types.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/names.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/names.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/segmentation.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/segmentation.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/scripts_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/scripts_data.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/widths.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/widths.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/names_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/names_data.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/properties.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/properties.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/casing.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/casing.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/casing_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/casing_data.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/types_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/types_data.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/decompositions_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/decompositions_data.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/collation_mk_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/collation_mk_data.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/decompositions.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/decompositions.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/blocks.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/blocks.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/widths_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/widths_data.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/blocks_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/blocks_data.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/properties_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/properties_data.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/scripts.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/scripts.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/compositions.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/compositions.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/compositions_data.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/compositions_data.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/src/unicodedb/collation.nim to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb/collation.nim + Copying file /tmp/nimble_578/githubcom_nitelynimunicodedb_0.7.2/unicodedb.nimble to /home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a/unicodedb.nimble + Success: unicodedb installed successfully. + Installing regex@0.26.0 + Copying file /tmp/nimble_578/githubcom_nitelynimregex_0.11.1/src/regex.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex.nim + Copying file /tmp/nimble_578/githubcom_nitelynimregex_0.11.1/src/regex/parser.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/parser.nim + Copying file /tmp/nimble_578/githubcom_nitelynimregex_0.11.1/src/regex/nfamacro.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfamacro.nim + Copying file /tmp/nimble_578/githubcom_nitelynimregex_0.11.1/src/regex/types.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/types.nim + Copying file /tmp/nimble_578/githubcom_nitelynimregex_0.11.1/src/regex/exptype.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/exptype.nim + Copying file /tmp/nimble_578/githubcom_nitelynimregex_0.11.1/src/regex/exptransformation.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/exptransformation.nim + Copying file /tmp/nimble_578/githubcom_nitelynimregex_0.11.1/src/regex/nfatype.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfatype.nim + Copying file /tmp/nimble_578/githubcom_nitelynimregex_0.11.1/src/regex/nodematch.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nodematch.nim + Copying file /tmp/nimble_578/githubcom_nitelynimregex_0.11.1/src/regex/nfamatch2.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfamatch2.nim + Copying file /tmp/nimble_578/githubcom_nitelynimregex_0.11.1/src/regex/litopt.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/litopt.nim + Copying file /tmp/nimble_578/githubcom_nitelynimregex_0.11.1/src/regex/nfa.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfa.nim + Copying file /tmp/nimble_578/githubcom_nitelynimregex_0.11.1/src/regex/nfafindall2.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfafindall2.nim + Copying file /tmp/nimble_578/githubcom_nitelynimregex_0.11.1/src/regex/common.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/common.nim + Copying file /tmp/nimble_578/githubcom_nitelynimregex_0.11.1/src/regex/nfafindall.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfafindall.nim + Copying file /tmp/nimble_578/githubcom_nitelynimregex_0.11.1/src/regex/compiler.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/compiler.nim + Copying file /tmp/nimble_578/githubcom_nitelynimregex_0.11.1/src/regex/nfamatch.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/nfamatch.nim + Copying file /tmp/nimble_578/githubcom_nitelynimregex_0.11.1/src/regex/dotgraph.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/dotgraph.nim + Copying file /tmp/nimble_578/githubcom_nitelynimregex_0.11.1/src/regex/scanner.nim to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex/scanner.nim + Copying file /tmp/nimble_578/githubcom_nitelynimregex_0.11.1/regex.nimble to /home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d/regex.nimble + Success: regex installed successfully. + Installing docopt@0.7.1 + Copying file /tmp/nimble_578/githubcom_docoptdocoptnim_0.6.8/src/docopt/util.nim to /home/conda/.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9/docopt/util.nim + Copying file /tmp/nimble_578/githubcom_docoptdocoptnim_0.6.8/src/docopt/value.nim to /home/conda/.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9/docopt/value.nim + Copying file /tmp/nimble_578/githubcom_docoptdocoptnim_0.6.8/src/docopt/dispatch.nim to /home/conda/.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9/docopt/dispatch.nim + Copying file /tmp/nimble_578/githubcom_docoptdocoptnim_0.6.8/src/docopt.nim to /home/conda/.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9/docopt.nim + Copying file /tmp/nimble_578/githubcom_docoptdocoptnim_0.6.8/docopt.nimble to /home/conda/.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9/docopt.nimble + Success: docopt installed successfully. + Reading official package list + Checking for kexpr@any version + Installing kexpr@any version + Reading official package list + Downloading https://github.com/brentp/kexpr-nim using git + Cloning latest tagged version: v0.0.2 + Verifying dependencies for kexpr@0.0.2 + Installing kexpr@0.0.2 + Copying file /tmp/nimble_578/githubcom_brentpkexprnim/kexpr.nim to /home/conda/.nimble/pkgs2/kexpr-0.0.2-43365e83c117f074445c94b28b9ca32e93543385/kexpr.nim + Copying file /tmp/nimble_578/githubcom_brentpkexprnim/kexpr/kexpr-c.h to /home/conda/.nimble/pkgs2/kexpr-0.0.2-43365e83c117f074445c94b28b9ca32e93543385/kexpr/kexpr-c.h + Copying file /tmp/nimble_578/githubcom_brentpkexprnim/kexpr/kexpr-c.c to /home/conda/.nimble/pkgs2/kexpr-0.0.2-43365e83c117f074445c94b28b9ca32e93543385/kexpr/kexpr-c.c + Copying file /tmp/nimble_578/githubcom_brentpkexprnim/kexpr.nimble to /home/conda/.nimble/pkgs2/kexpr-0.0.2-43365e83c117f074445c94b28b9ca32e93543385/kexpr.nimble + Success: kexpr installed successfully. + Installing genoiser@0.2.7 + Building genoiser/genoiser using c backend + Executing $BUILD_PREFIX/nim/bin/nim c --colors:off --noNimblePath -d:release -d:NimblePkgVersion=0.2.7 --path:/home/conda/.nimble/pkgs2/hts-0.2.23-d282c5a3bd0e70cdba01bb5809e8435ba7771ca7 --path:/home/conda/.nimble/pkgs2/docopt-0.7.1-387f1ae17f3b7620c7814cf44a52d3d91b8906e9 --path:/home/conda/.nimble/pkgs2/kexpr-0.0.2-43365e83c117f074445c94b28b9ca32e93543385 --path:/home/conda/.nimble/pkgs2/regex-0.26.0-038733eb4a3fc435afb6b038dca04ebeae7aad7d --path:/home/conda/.nimble/pkgs2/unicodedb-0.13.0-5c5fc0c8a83d270aca74fe41d33158e9042bb91a --colors:off -o:$SRC_DIR/genoiser/genoiser $SRC_DIR/genoiser/src/genoiser.nim + Hint: used config file '/opt/conda/conda-bld/duphold_1734294892511/_build_env/nim/config/nim.cfg' [Conf] + Hint: used config file '/opt/conda/conda-bld/duphold_1734294892511/_build_env/nim/config/config.nims' [Conf] + Hint: used config file '/opt/conda/conda-bld/duphold_1734294892511/work/nim.cfg' [Conf] + Hint: used config file '/opt/conda/conda-bld/duphold_1734294892511/work/genoiser/nim.cfg' [Conf] + ..................................................................... + /opt/conda/conda-bld/duphold_1734294892511/work/genoiser/src/genoiser.nim(75, 20) Error: invalid indentation + nimble.nim(304) buildFromDir + + Error: Build failed for the package: genoiser + Info: Nimble data file "/home/conda/.nimble/nimbledata2.json" has been saved. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/duphold_1734294892511/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/duphold_1734294892511/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + dependency issue diff --git a/recipes/duphold/meta.yaml b/recipes/duphold/meta.yaml index d4fec0d4c66e1..fe9a184326f56 100644 --- a/recipes/duphold/meta.yaml +++ b/recipes/duphold/meta.yaml @@ -20,7 +20,7 @@ source: - 0001-genoiser-dep-restrict-hts-nim-upper-version.patch build: - number: 4 + number: 5 skip: True # [osx] requirements: diff --git a/recipes/duplomap/meta.yaml b/recipes/duplomap/meta.yaml index d5887dae7b27a..8952f3786c5a4 100644 --- a/recipes/duplomap/meta.yaml +++ b/recipes/duplomap/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 847b881788e31ffe77146d5eb1e2a12e7b7f90c42c2c54c44ba8b71db51d1827 build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/dupsifter/meta.yaml b/recipes/dupsifter/meta.yaml index 2e02cdc953848..b79696aca01db 100644 --- a/recipes/dupsifter/meta.yaml +++ b/recipes/dupsifter/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('dupsifter', max_pin='x') }} diff --git a/recipes/dwgsim/meta.yaml b/recipes/dwgsim/meta.yaml index 5f0f3b94548a8..366bd10a22c54 100644 --- a/recipes/dwgsim/meta.yaml +++ b/recipes/dwgsim/meta.yaml @@ -13,7 +13,7 @@ source: folder: samtools build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/easel/meta.yaml b/recipes/easel/meta.yaml index 7dc561b70529f..806d02731fd61 100644 --- a/recipes/easel/meta.yaml +++ b/recipes/easel/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/ecoprimers/meta.yaml b/recipes/ecoprimers/meta.yaml index e66bfe7988781..c9299e2db6685 100644 --- a/recipes/ecoprimers/meta.yaml +++ b/recipes/ecoprimers/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 7 + number: 8 skip: True # [osx] source: diff --git a/recipes/eden/1.1/meta.yaml b/recipes/eden/1.1/meta.yaml index df7a25a31311e..c3971fbccfae5 100644 --- a/recipes/eden/1.1/meta.yaml +++ b/recipes/eden/1.1/meta.yaml @@ -7,8 +7,10 @@ source: sha256: 6709b7dac2dc90f6d914fda33ecc807390a136306e04c63b0ae6f764081db050 build: - number: 4 + number: 5 skip: True # [osx] + run_exports: + - {{ pin_subpackage('eden', max_pin="x") }} requirements: build: diff --git a/recipes/edena/meta.yaml b/recipes/edena/meta.yaml index feb39faad2a23..ff217af5ca856 100644 --- a/recipes/edena/meta.yaml +++ b/recipes/edena/meta.yaml @@ -10,7 +10,7 @@ source: md5: {{ md5 }} build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/egglib/meta.yaml b/recipes/egglib/meta.yaml index 5d52f0a65b5c6..b030200aaf101 100644 --- a/recipes/egglib/meta.yaml +++ b/recipes/egglib/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 685acf514c2b14d3cc4e21e6ca03951599c77b9c0f6530c417cd717d813fafd7 build: - number: 0 + number: 1 skip: True # [osx] script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv entry_points: diff --git a/recipes/eigensoft/meta.yaml b/recipes/eigensoft/meta.yaml index 8f1bc6a86354b..49cd003974dff 100644 --- a/recipes/eigensoft/meta.yaml +++ b/recipes/eigensoft/meta.yaml @@ -14,7 +14,7 @@ source: - 0003-remove-wrong-cflag.patch # [osx] build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('eigensoft', max_pin='x.x') }} diff --git a/recipes/elector/build_failure.linux-64.yaml b/recipes/elector/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..ef4b949f38849 --- /dev/null +++ b/recipes/elector/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c1e459d9a9e46455b50fdbb717e93c3139408e565f05df8b5b13317c3c4a7d79 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/elector-1.0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/elector-1.0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/elector-1.0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + mkdir -p /opt/conda/conda-bld/elector_1734287004874/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin/ + cd src/simulator + make + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -o simulator.o -c simulator.cpp -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/elector-1.0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Ofast -std=c11 -pthread -pipe -Isparsepp + simulator.cpp:15:1: error: 'uint32_t' does not name a type + 15 | uint32_t xs(uint32_t& y){ + | ^~~~~~~~ + simulator.cpp:6:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + 5 | #include + |#include + 6 | + simulator.cpp: In function 'char randNucle(char)': + simulator.cpp:25:17: error: 'xs' was not declared in this scope + 25 | switch (xs(seed)%4){ + | ^~ + simulator.cpp: In function 'int main(int, char**)': + simulator.cpp:131:25: error: 'uint64_t' was not declared in this scope + 131 | uint64_t nucProduced(0); + | ^~~~~~~~ + simulator.cpp:131:25: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + simulator.cpp:132:31: error: 'nucProduced' was not declared in this scope + 132 | while(nucProduced<(uint64_t)(coverage*ref.size())){ + | ^~~~~~~~~~~ + simulator.cpp:137:41: error: expected ';' before 'position' + 137 | uint64_t position=xs(seed)%ref.size(); + | ^~~~~~~~~ + | ; + simulator.cpp:138:36: error: 'position' was not declared in this scope + 138 | if(positionlength<=ref.size()){ + | ^~~~~~~~ + simulator.cpp:140:46: warning: unused variable 'error' [-Wunused-variable] + 140 | uint error(0); + | ^~~~~ + simulator.cpp:165:33: error: expected ';' before 'nucProducedSR' + 165 | uint64_t nucProducedSR(0); + | ^~~~~~~~~~~~~~ + | ; + simulator.cpp:166:31: error: 'nucProducedSR' was not declared in this scope + 166 | while(nucProducedSR<(uint64_t)(coverageSR*ref.size())){ + | ^~~~~~~~~~~~~ + simulator.cpp:170:41: error: expected ';' before 'position' + 170 | uint64_t position=xs(seed)%ref.size(); + | ^~~~~~~~~ + | ; + simulator.cpp:171:36: error: 'position' was not declared in this scope + 171 | if(positionlength<=ref.size()){ + | ^~~~~~~~ + simulator.cpp:177:52: error: 'xs' was not declared in this scope + 177 | if(xs(seed)%10000<=errorRateSR){ + | ^~ + make: *** [makefile:27: simulator.o] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/elector_1734287004874/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/elector_1734287004874/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/elector/meta.yaml b/recipes/elector/meta.yaml index 2f241be4fc74b..b9b8255b1e145 100644 --- a/recipes/elector/meta.yaml +++ b/recipes/elector/meta.yaml @@ -13,7 +13,7 @@ source: - elector_utils.patch build: - number: 5 + number: 6 skip: True # [osx or py<30] requirements: diff --git a/recipes/ema/meta.yaml b/recipes/ema/meta.yaml index caeb9d1858de6..7e6f1b80008b9 100644 --- a/recipes/ema/meta.yaml +++ b/recipes/ema/meta.yaml @@ -13,7 +13,7 @@ source: # - remove_native.patch build: - number: 0 + number: 1 skip: True # [osx] requirements: diff --git a/recipes/emboss/5.0.0/meta.yaml b/recipes/emboss/5.0.0/meta.yaml index b4ce8b6a22524..fb02a9a3c5fe3 100644 --- a/recipes/emboss/5.0.0/meta.yaml +++ b/recipes/emboss/5.0.0/meta.yaml @@ -3,7 +3,7 @@ package: version: "5.0.0" build: - number: 5 + number: 6 source: - url: http://depot.galaxyproject.org/package/linux/x86_64/emboss/emboss-5.0.0-Linux-x86_64.tgz # [linux] diff --git a/recipes/emboss/meta.yaml b/recipes/emboss/meta.yaml index 407d3b8396c8c..d03b4854abf4a 100644 --- a/recipes/emboss/meta.yaml +++ b/recipes/emboss/meta.yaml @@ -3,7 +3,7 @@ package: version: "6.6.0" build: - number: 10 + number: 11 skip: True # [osx] run_exports: - {{ pin_subpackage("emboss", max_pin="x.x") }} diff --git a/recipes/emerald/meta.yaml b/recipes/emerald/meta.yaml index 9e7f883929b5f..a9eabc02650d9 100644 --- a/recipes/emerald/meta.yaml +++ b/recipes/emerald/meta.yaml @@ -12,7 +12,7 @@ source: - no_filesystem.patch build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('emerald', max_pin="x") }} diff --git a/recipes/emvc-2/meta.yaml b/recipes/emvc-2/meta.yaml index 16f43a28dfe34..857613c392347 100644 --- a/recipes/emvc-2/meta.yaml +++ b/recipes/emvc-2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 'edee7e027bb720f625cfc3073798ab39916f1852641cc7f05604ff62b905c7e3' build: - number: 2 + number: 3 # platforms: # - osx-64 diff --git a/recipes/enano/meta.yaml b/recipes/enano/meta.yaml index 49a525d1a8049..7650e0db055cd 100644 --- a/recipes/enano/meta.yaml +++ b/recipes/enano/meta.yaml @@ -6,7 +6,7 @@ package: build: skip: True # [osx] - number: 6 + number: 7 source: url: https://github.com/guilledufort/EnanoFASTQ/archive/v{{ version }}.tar.gz diff --git a/recipes/encode-blacklist/meta.yaml b/recipes/encode-blacklist/meta.yaml index 0104c2736ae6b..b376aaf0231e5 100644 --- a/recipes/encode-blacklist/meta.yaml +++ b/recipes/encode-blacklist/meta.yaml @@ -12,7 +12,7 @@ source: - Makefile.patch build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/epa-ng/meta.yaml b/recipes/epa-ng/meta.yaml index 2d0f4afb9d38d..cf1b75d8bd37f 100644 --- a/recipes/epa-ng/meta.yaml +++ b/recipes/epa-ng/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.3.8" build: - number: 4 + number: 5 source: url: https://github.com/Pbdas/epa-ng/archive/v0.3.8.tar.gz diff --git a/recipes/epic2/meta.yaml b/recipes/epic2/meta.yaml index bafbd7682eb1c..4b3cdc015b899 100644 --- a/recipes/epic2/meta.yaml +++ b/recipes/epic2/meta.yaml @@ -11,7 +11,7 @@ source: sha256: '{{ hash_value }}' build: - number: 8 + number: 9 # Compilation errors on OSX skip: True # [osx or py27] run_exports: diff --git a/recipes/epik/meta.yaml b/recipes/epik/meta.yaml index 2be6f602946ce..bdd2a612663c4 100644 --- a/recipes/epik/meta.yaml +++ b/recipes/epik/meta.yaml @@ -13,7 +13,7 @@ source: - epik-aarch64.patch build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('epik', max_pin="x.x") }} @@ -45,4 +45,4 @@ about: extra: additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 diff --git a/recipes/est-sfs/meta.yaml b/recipes/est-sfs/meta.yaml index e1d3860988113..c8cc8d4aafddf 100644 --- a/recipes/est-sfs/meta.yaml +++ b/recipes/est-sfs/meta.yaml @@ -8,7 +8,7 @@ source: build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/estscan/3.0/meta.yaml b/recipes/estscan/3.0/meta.yaml index 94b9891768eeb..0cb50a1457a72 100644 --- a/recipes/estscan/3.0/meta.yaml +++ b/recipes/estscan/3.0/meta.yaml @@ -7,7 +7,7 @@ source: md5: 1252c862b41b03b59687f5ba148b77cd build: - number: 7 + number: 8 skip: True #[osx] requirements: diff --git a/recipes/eternafold/meta.yaml b/recipes/eternafold/meta.yaml index 1c0d45eeba7a2..e593b29be1d22 100644 --- a/recipes/eternafold/meta.yaml +++ b/recipes/eternafold/meta.yaml @@ -13,7 +13,7 @@ source: sha256: 8aa00b81b6068bff02954ef1621e7aa92f48aadcb3e89b322af46433553691b5 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('eternafold', max_pin="x") }} diff --git a/recipes/evidencemodeler/build_failure.osx-64.yaml b/recipes/evidencemodeler/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..e11e7b4123676 --- /dev/null +++ b/recipes/evidencemodeler/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 1cd38be766096edd817ad8bcb17930d5267bc8d148501093c6a29c2f0ae34ed3 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - cmake 3.31.2 h477996e_1 + - ld64_osx-64 951.9 hc8d1a19_2 + - ncurses 6.5 hf036a51_1 + - libnghttp2 1.64.0 hc7306c3_0 + - libcxx-devel 18.1.8 h7c275be_7 + - clang_osx-64 18.1.8 h7e5c614_23 + - libuv 1.49.2 hd79239c_0 + - make 4.4.1 h00291cd_2 + - tapi 1300.6.5 h390ca13_0 + - clang 18.1.8 default_h179603d_5 + - clang-18 18.1.8 default_h0c94c6a_5 + host: + - libcxx 19.1.5 hf95d169_0 + - llvm-openmp 19.1.5 ha54dae1_0 + run: + - perl + - perl-db_file + - perl-dbi + - perl-carp + - perl-uri + - libcxx >=18 + - llvm-openmp >=18.1.8 + test: + commands: + - EVidenceModeler --version + about: + home: https://github.com/EVidenceModeler/EVidenceModeler + license: BSD 3-Clause + license_family: BSD + license_file: LICENSE.txt + summary: Evidence Modeler combines ab intio gene predictions, protein alignments, + and transcript alignments into weighted consensus gene structures + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/evidencemodeler_1734461397610/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/evidencemodeler_1734461397610/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/evidencemodeler_1734461397610/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/evidencemodeler_1734461397610/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/evidencemodeler-2.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/evidencemodeler-2.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/evidencemodeler-2.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/evidencemodeler-2.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + checking for a BSD-compatible install... /usr/bin/install -c + checking whether build environment is sane... yes + checking for a thread-safe mkdir -p... ./install-sh -c -d + checking for gawk... no + checking for mawk... no + checking for nawk... no + checking for awk... awk + checking whether make sets $(MAKE)... yes + checking for C compiler default output file name... a.out +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/evidencemodeler/meta.yaml b/recipes/evidencemodeler/meta.yaml index d9a8365861794..59d99063b3439 100644 --- a/recipes/evidencemodeler/meta.yaml +++ b/recipes/evidencemodeler/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 3ee69ad822a35204ff02b670fe047d8b0da250cf9f43ebabbe33ce47f498e668 build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage('evidencemodeler', max_pin='x') }} diff --git a/recipes/expansionhunter/build_failure.osx-64.yaml b/recipes/expansionhunter/build_failure.osx-64.yaml deleted file mode 100644 index 2efaf89bccc4d..0000000000000 --- a/recipes/expansionhunter/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: d13c40e2561dd3ae0e0c9525e8725dfcba2bc197aa5ce06a4298b0d59acd0c7c # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/expansionhunter-5.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/expansionhunter-5.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - -- The C compiler identification is Clang 16.0.6 - -- The CXX compiler identification is Clang 16.0.6 - -- Detecting C compiler ABI info - -- Detecting C compiler ABI info - done - -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped - -- Detecting C compile features - -- Detecting C compile features - done - -- Detecting CXX compiler ABI info - -- Detecting CXX compiler ABI info - done - -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped - -- Detecting CXX compile features - -- Detecting CXX compile features - done - -- Found ZLIB: $PREFIX/lib/libz.dylib (found version "1.2.13") - -- Found BZip2: $PREFIX/lib/libbz2.dylib (found version "1.0.8") - -- Looking for BZ2_bzCompressInit - -- Looking for BZ2_bzCompressInit - found - -- Looking for lzma_auto_decoder in $PREFIX/lib/liblzma.dylib - -- Looking for lzma_auto_decoder in $PREFIX/lib/liblzma.dylib - found - -- Looking for lzma_easy_encoder in $PREFIX/lib/liblzma.dylib - -- Looking for lzma_easy_encoder in $PREFIX/lib/liblzma.dylib - found - -- Looking for lzma_lzma_preset in $PREFIX/lib/liblzma.dylib - -- Looking for lzma_lzma_preset in $PREFIX/lib/liblzma.dylib - found - -- Found LibLZMA: $PREFIX/lib/liblzma.dylib (found version "5.2.6") - -- Found CURL: $PREFIX/lib/libcurl.dylib (found version "8.8.0") - -- Configuring done (4.2s) - -- Generating done (0.0s) - -- Build files have been written to: $SRC_DIR/build - [ 11%] Creating directories for 'ehunter' - [ 22%] No download step for 'ehunter' - [ 33%] No update step for 'ehunter' - [ 44%] No patch step for 'ehunter' - [ 55%] Performing configure step for 'ehunter' - -- The C compiler identification is Clang 16.0.6 - -- The CXX compiler identification is Clang 16.0.6 - -- Detecting C compiler ABI info - -- Detecting C compiler ABI info - done - -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped - -- Detecting C compile features - -- Detecting C compile features - done - -- Detecting CXX compiler ABI info - -- Detecting CXX compiler ABI info - done - -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped - -- Detecting CXX compile features - -- Detecting CXX compile features - done - -- BUILD_TYPE: Release - -- Found Boost: $PREFIX/lib/cmake/Boost-1.85.0/BoostConfig.cmake (found suitable version "1.85.0", minimum required is "1.73") found components: program_options filesystem system - -- Found ZLIB: $PREFIX/lib/libz.dylib (found version "1.2.13") - -- Found BZip2: $PREFIX/lib/libbz2.dylib (found version "1.0.8") - -- Looking for BZ2_bzCompressInit - -- Looking for BZ2_bzCompressInit - found - -- Looking for lzma_auto_decoder in $PREFIX/lib/liblzma.dylib - -- Looking for lzma_auto_decoder in $PREFIX/lib/liblzma.dylib - found - -- Looking for lzma_easy_encoder in $PREFIX/lib/liblzma.dylib - -- Looking for lzma_easy_encoder in $PREFIX/lib/liblzma.dylib - found - -- Looking for lzma_lzma_preset in $PREFIX/lib/liblzma.dylib - -- Looking for lzma_lzma_preset in $PREFIX/lib/liblzma.dylib - found - -- Found LibLZMA: $PREFIX/lib/liblzma.dylib (found version "5.2.6") - -- Found CURL: $PREFIX/lib/libcurl.dylib (found version "8.8.0") - -- Found GTest: $PREFIX/lib/cmake/GTest/GTestConfig.cmake (found version "1.14.0") - -- Found Threads: TRUE - -- Found Boost: $PREFIX/lib/cmake/Boost-1.85.0/BoostConfig.cmake (found suitable version "1.85.0", minimum required is "1.5") found components: program_options filesystem system - -- Configuring done (4.4s) - -- Generating done (0.1s) - -- Build files have been written to: $SRC_DIR/build/ehunter-prefix/src/ehunter-build - [ 66%] Performing build step for 'ehunter' - [ 1%] Building CXX object thirdparty/graph-tools-master-f421f4c/CMakeFiles/graphtools.dir/src/graphalign/GappedAligner.cpp.o - [ 2%] Building CXX object thirdparty/graph-tools-master-f421f4c/CMakeFiles/graphtools.dir/src/graphalign/GraphAlignment.cpp.o -# Last 100 lines of the build log. diff --git a/recipes/expansionhunter/meta.yaml b/recipes/expansionhunter/meta.yaml index 67ab975bf2c03..157a13c7426dc 100644 --- a/recipes/expansionhunter/meta.yaml +++ b/recipes/expansionhunter/meta.yaml @@ -15,7 +15,7 @@ source: - 0004-add-fmt-formatters-for-classes.patch - 0005-apply-bioconda-4.0.2-patches.patch # [osx] build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage('expansionhunter', max_pin="x") }} requirements: diff --git a/recipes/expansionhunterdenovo/meta.yaml b/recipes/expansionhunterdenovo/meta.yaml index f21a622b30e9e..6c617662b58bf 100644 --- a/recipes/expansionhunterdenovo/meta.yaml +++ b/recipes/expansionhunterdenovo/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 8 + number: 9 skip: True # [osx] requirements: diff --git a/recipes/exparna/meta.yaml b/recipes/exparna/meta.yaml index bab617c80114e..08d44c3f69e4a 100644 --- a/recipes/exparna/meta.yaml +++ b/recipes/exparna/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.0.1 build: - number: 6 + number: 7 skip: True # [osx] source: diff --git a/recipes/express/build_failure.linux-64.yaml b/recipes/express/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..987114d08bf77 --- /dev/null +++ b/recipes/express/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 1c88011ca1059a412c8ece28305c1adc83d8741fd131e4a545b46a7f47edf803 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/express-1.5.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/express-1.5.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + + Resource usage statistics from building express: + Process count: 2 + CPU time: Sys=-, User=0:00:00.0 + Memory: 11.4M + Disk usage: 10.5K + Time elapsed: 0:00:02.0 + + + Packaging express + Packaging express-1.5.1-h9948957_6 + number of files: 1 + WARNING :: get_rpaths_raw()=[] and patchelf=[''] disagree for /opt/conda/conda-bld/express_1734085701197/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin/express :: + INFO: sysroot: '/opt/conda/conda-bld/express_1734085701197/_build_env/x86_64-conda-linux-gnu/sysroot/' files: '['usr/share/zoneinfo', 'usr/share/locale/zh_TW/LC_MESSAGES/libc.mo', 'usr/share/locale/zh_CN/LC_MESSAGES/libc.mo', 'usr/share/locale/vi/LC_MESSAGES/libc.mo']' + WARNING (express,bin/express): $RPATH/libz.so.1 not found in packages, sysroot(s) nor the missing_dso_whitelist. + .. is this binary repackaging? + INFO (express,bin/express): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libpthread.so.0 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.17=h4a8ded7_18 + INFO (express,bin/express): Needed DSO lib/libstdc.so.6 found in conda-forge/linux-64::libstdcxx==14.2.0=hc0a3c3a_1 + INFO (express,bin/express): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.17=h4a8ded7_18 + INFO (express,bin/express): Needed DSO lib/libgcc_s.so.1 found in conda-forge/linux-64::libgcc==14.2.0=h77fa898_1 + INFO (express,bin/express): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.17=h4a8ded7_18 + Fixing permissions + INFO :: Time taken to mark (prefix) + 0 replacements in 0 files was 0.01 seconds + WARNING: Importing conda-verify failed. Please be sure to test your packages. conda install conda-verify to make this message go away. + TEST START: /opt/conda/conda-bld/linux-64/express-1.5.1-h9948957_6.tar.bz2 + Renaming work directory '/opt/conda/conda-bld/express_1734085701197/work' to '/opt/conda/conda-bld/express_1734085701197/work_moved_express-1.5.1-h9948957_6_linux-64' + shutil.move(work)=/opt/conda/conda-bld/express_1734085701197/work, dest=/opt/conda/conda-bld/express_1734085701197/work_moved_express-1.5.1-h9948957_6_linux-64) + Reloading output folder (local, file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/express_1734085701197/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + express: 1.5.1-h9948957_6 local + libgcc: 14.2.0-h77fa898_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libzlib: 1.3.1-hb9d3cd8_2 conda-forge + zlib: 1.3.1-hb9d3cd8_2 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + export PREFIX=/opt/conda/conda-bld/express_1734085701197/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ + export SRC_DIR=/opt/conda/conda-bld/express_1734085701197/test_tmp + express --help + /opt/conda/conda-bld/express_1734085701197/test_tmp/run_test.sh: line 7: 640 Segmentation fault (core dumped) express --help + [[ 139 == 1 ]] + WARNING: Tests failed for express-1.5.1-h9948957_6.tar.bz2 - moving package to /opt/conda/conda-bld/broken + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/express_1734085701197/test_tmp/conda_test_runner.sh']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: express-1.5.1-h9948957_6.tar.bz2 +# Last 100 lines of the build log. diff --git a/recipes/express/meta.yaml b/recipes/express/meta.yaml index c880015b449eb..b277f5fe2c722 100644 --- a/recipes/express/meta.yaml +++ b/recipes/express/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.5.1" build: - number: 5 + number: 6 skip: True # [osx] source: diff --git a/recipes/expressbetadiversity/meta.yaml b/recipes/expressbetadiversity/meta.yaml index e52e445dc041c..9fb97648bde55 100644 --- a/recipes/expressbetadiversity/meta.yaml +++ b/recipes/expressbetadiversity/meta.yaml @@ -12,7 +12,7 @@ source: - 0001-Fix-hardcoded-g++.patch build: - number: 5 + number: 6 skip: True # [not linux] requirements: diff --git a/recipes/extract_fullseq/meta.yaml b/recipes/extract_fullseq/meta.yaml index e5740131593ad..e970a544b543c 100644 --- a/recipes/extract_fullseq/meta.yaml +++ b/recipes/extract_fullseq/meta.yaml @@ -12,7 +12,7 @@ source: sha256: 1e2c8cd314498bf56ba0291185190d0ed20cbd839098492ab573be2ca6770a66 # [osx] build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('extract_fullseq', max_pin="x") }} diff --git a/recipes/f5c/0.6/build_failure.osx-64.yaml b/recipes/f5c/0.6/build_failure.osx-64.yaml deleted file mode 100644 index bd87afdba999d..0000000000000 --- a/recipes/f5c/0.6/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 0677a29c724faa7f372c921ec6dec6153bf367e08a3f56867d99c1708b0f0a70 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - x86_64-apple-darwin13.4.0-clang -Wall -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/f5c-0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -c -o test/test-vcf-api.o test/test-vcf-api.c - x86_64-apple-darwin13.4.0-clang -Wall -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/f5c-0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c - x86_64-apple-darwin13.4.0-clang -Wall -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/f5c-0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -c -o test/test-bcf-sr.o test/test-bcf-sr.c - x86_64-apple-darwin13.4.0-clang -Wall -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/f5c-0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -c -o test/test-bcf-translate.o test/test-bcf-translate.c - x86_64-apple-darwin13.4.0-clang -Wall -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/f5c-0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -c -o hts.o hts.c - x86_64-apple-darwin13.4.0-clang -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/hts_endian test/hts_endian.o -lz - x86_64-apple-darwin13.4.0-clang -dynamiclib -install_name /usr/local/lib/libhts.2.dylib -current_version 1.9 -compatibility_version 2 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o libhts.dylib kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o -lz - ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o - x86_64-apple-darwin13.4.0-ranlib libhts.a - x86_64-apple-darwin13.4.0-clang -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o bgzip bgzip.o libhts.a -lz -lpthread - x86_64-apple-darwin13.4.0-clang -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o htsfile htsfile.o libhts.a -lz -lpthread - x86_64-apple-darwin13.4.0-clang -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o tabix tabix.o libhts.a -lz -lpthread - x86_64-apple-darwin13.4.0-clang -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/fieldarith test/fieldarith.o libhts.a -lz -lpthread - x86_64-apple-darwin13.4.0-clang -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/hfile test/hfile.o libhts.a -lz -lpthread - x86_64-apple-darwin13.4.0-clang -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/sam test/sam.o libhts.a -lz -lpthread - x86_64-apple-darwin13.4.0-clang -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lpthread - ln -sf libhts.dylib libhts.2.dylib - x86_64-apple-darwin13.4.0-clang -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test_realn test/test_realn.o libhts.a -lz -lpthread - x86_64-apple-darwin13.4.0-clang -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test-regidx test/test-regidx.o libhts.a -lz -lpthread - x86_64-apple-darwin13.4.0-clang -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test_view test/test_view.o libhts.a -lz -lpthread - x86_64-apple-darwin13.4.0-clang -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lpthread - x86_64-apple-darwin13.4.0-clang -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lpthread - x86_64-apple-darwin13.4.0-clang -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lpthread - x86_64-apple-darwin13.4.0-clang -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -lz -lpthread - Successfully installed htslib to ./htslib. - Now run ./configure (again)! - checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang - checking whether the C compiler works... yes - checking for C compiler default output file name... a.out - checking for suffix of executables... - checking whether we are cross compiling... no - checking for suffix of object files... o - checking whether we are using the GNU C compiler... yes - checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes - checking for x86_64-apple-darwin13.4.0-clang option to accept ISO C89... none needed - checking whether we are using the GNU C compiler... yes - checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes - checking for special C compiler options needed for large files... no - checking for _FILE_OFFSET_BITS value needed for large files... no - checking for _LARGEFILE_SOURCE value needed for large files... no - checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang -E - checking for grep that handles long lines and -e... /usr/bin/grep - checking for egrep... /usr/bin/grep -E - checking for ANSI C header files... yes - checking for sys/types.h... yes - checking for sys/stat.h... yes - checking for stdlib.h... yes - checking for string.h... yes - checking for memory.h... yes - checking for strings.h... yes - checking for inttypes.h... yes - checking for stdint.h... yes - checking for unistd.h... yes - checking float.h usability... yes - checking float.h presence... yes - checking for float.h... yes - checking for inttypes.h... (cached) yes - checking for stdint.h... (cached) yes - checking for stdlib.h... (cached) yes - checking for string.h... (cached) yes - checking sys/time.h usability... yes - checking sys/time.h presence... yes - checking for sys/time.h... yes - checking for unistd.h... (cached) yes - checking execinfo.h usability... yes - checking execinfo.h presence... yes - checking for execinfo.h... yes - checking for stdbool.h that conforms to C99... yes - checking for _Bool... yes - checking for inline... inline - checking for int32_t... yes - checking for size_t... yes - checking for ssize_t... yes - checking for uint32_t... yes - checking for uint64_t... yes - checking for uint8_t... yes - checking for stdlib.h... (cached) yes - checking for GNU libc compatible malloc... (cached) yes - checking for gettimeofday... yes - checking for memset... yes - checking for sqrt... yes - checking for strerror... yes - checking for zlib.h... yes - checking for inflate in -lz... yes - checking for ./htslib/htslib/hts.h... yes - checking for ./htslib/libhts.a... yes - checking for library containing H5Fopen... -lhdf5 - checking hdf5.h usability... yes - checking hdf5.h presence... yes - checking for hdf5.h... yes - configure: creating ./config.status - config.status: creating config.mk - config.status: creating src/config.h - x86_64-apple-darwin13.4.0-clang -g -Wall -O2 -std=c11 -D__STDC_FORMAT_MACROS -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I./htslib -x c src/main.c -c -o build/main.o - x86_64-apple-darwin13.4.0-clang -g -Wall -O2 -std=c11 -D__STDC_FORMAT_MACROS -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I./htslib -x c src/meth_main.c -c -o build/meth_main.o - x86_64-apple-darwin13.4.0-clang -g -Wall -O2 -std=c11 -D__STDC_FORMAT_MACROS -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I./htslib -x c src/f5c.c -c -o build/f5c.o - x86_64-apple-darwin13.4.0-clang -g -Wall -O2 -std=c11 -D__STDC_FORMAT_MACROS -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I./htslib -x c src/f5cio.c -c -o build/f5cio.o - x86_64-apple-darwin13.4.0-clang -g -Wall -O2 -std=c11 -D__STDC_FORMAT_MACROS -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I./htslib -x c src/events.c -c -o build/events.o - x86_64-apple-darwin13.4.0-clang -g -Wall -O2 -std=c11 -D__STDC_FORMAT_MACROS -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I./htslib -x c src/nanopolish_read_db.c -c -o build/nanopolish_read_db.o - x86_64-apple-darwin13.4.0-clang -g -Wall -O2 -std=c11 -D__STDC_FORMAT_MACROS -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I./htslib -x c src/index.c -c -o build/index.o -# Last 100 lines of the build log. diff --git a/recipes/f5c/0.6/meta.yaml b/recipes/f5c/0.6/meta.yaml index 13b75019dad77..06ee8d85b3431 100644 --- a/recipes/f5c/0.6/meta.yaml +++ b/recipes/f5c/0.6/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 5ad8ecf16383757645c1757fc886c58437a062f9e1bade8b65ca8a674a75ba3e build: - number: 7 + number: 8 requirements: build: diff --git a/recipes/f5c/1.2/build_failure.osx-64.yaml b/recipes/f5c/1.2/build_failure.osx-64.yaml deleted file mode 100644 index 2c93da7027592..0000000000000 --- a/recipes/f5c/1.2/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 5c997279bceb0404e20ed29e7232a75438a8d4540b856edfef19e3b30ec8b8a7 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - ==> no zlib, building zstd without .gz support - ==> no liblzma, building zstd without .xz/.lzma support - - lz4 support is disabled - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I../lib -I../lib/common -I../lib/compress -I../lib/dictBuilder -DZSTD_NEWAPI -DXXH_NAMESPACE=ZSTD_ -I../lib/legacy -DZSTD_LEGACY_SUPPORT=4 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/f5c-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib ../lib/decompress/huf_decompress.c ../lib/decompress/zstd_decompress.c ../lib/common/entropy_common.c ../lib/common/error_private.c ../lib/common/fse_decompress.c ../lib/common/pool.c ../lib/common/threading.c ../lib/common/xxhash.c ../lib/common/zstd_common.c ../lib/compress/fse_compress.c ../lib/compress/huf_compress.c ../lib/compress/zstd_compress.c ../lib/compress/zstdmt_compress.c ../lib/legacy/zstd_v04.c ../lib/legacy/zstd_v05.c ../lib/legacy/zstd_v06.c ../lib/legacy/zstd_v07.c ../lib/dictBuilder/cover.c ../lib/dictBuilder/divsufsort.c ../lib/dictBuilder/zdict.c zstdcli.o fileio.o bench.o datagen.o dibio.o -o zstd -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - compiling static library - creating versioned links - make[1]: Leaving directory '$SRC_DIR/zstd/lib' - make[1]: Leaving directory '$SRC_DIR/zstd/programs' - cp programs/zstd . - Successfully installed zstd to ./zstd. - checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang - checking whether the C compiler works... yes - checking for C compiler default output file name... a.out - checking for suffix of executables... - checking whether we are cross compiling... no - checking for suffix of object files... o - checking whether we are using the GNU C compiler... yes - checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes - checking for x86_64-apple-darwin13.4.0-clang option to accept ISO C89... none needed - checking whether we are using the GNU C compiler... yes - checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes - checking for special C compiler options needed for large files... no - checking for _FILE_OFFSET_BITS value needed for large files... no - checking for _LARGEFILE_SOURCE value needed for large files... no - checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang -E - checking for grep that handles long lines and -e... /usr/bin/grep - checking for egrep... /usr/bin/grep -E - checking for ANSI C header files... yes - checking for sys/types.h... yes - checking for sys/stat.h... yes - checking for stdlib.h... yes - checking for string.h... yes - checking for memory.h... yes - checking for strings.h... yes - checking for inttypes.h... yes - checking for stdint.h... yes - checking for unistd.h... yes - checking float.h usability... yes - checking float.h presence... yes - checking for float.h... yes - checking for inttypes.h... (cached) yes - checking for stdint.h... (cached) yes - checking for stdlib.h... (cached) yes - checking for string.h... (cached) yes - checking sys/time.h usability... yes - checking sys/time.h presence... yes - checking for sys/time.h... yes - checking for unistd.h... (cached) yes - checking execinfo.h usability... yes - checking execinfo.h presence... yes - checking for execinfo.h... yes - checking for stdbool.h that conforms to C99... yes - checking for _Bool... yes - checking for inline... inline - checking for int32_t... yes - checking for size_t... yes - checking for ssize_t... yes - checking for uint32_t... yes - checking for uint64_t... yes - checking for uint8_t... yes - checking for stdlib.h... (cached) yes - checking for GNU libc compatible malloc... (cached) yes - checking for gettimeofday... yes - checking for memset... yes - checking for sqrt... yes - checking for strerror... yes - checking for zlib.h... yes - checking for inflate in -lz... yes - checking for ./htslib/htslib/hts.h... yes - checking for ./htslib/libhts.a... yes - checking for library containing H5Fopen... -lhdf5 - checking hdf5.h usability... yes - checking hdf5.h presence... yes - checking for hdf5.h... yes - checking for ./zstd/lib/zstd.h... yes - checking for ./zstd/lib/libzstd.a... yes - configure: creating ./config.status - config.status: creating config.mk - config.status: creating src/config.h - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/f5c-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -std=c99 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I include/ -I thirdparty/streamvbyte/include/ src/slow5.c -c -fpic -o lib/slow5.o - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/f5c-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -std=c99 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I include/ -I thirdparty/streamvbyte/include/ src/slow5_idx.c -c -fpic -o lib/slow5_idx.o - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/f5c-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -std=c99 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I include/ -I thirdparty/streamvbyte/include/ src/slow5_misc.c -c -fpic -o lib/slow5_misc.o - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/f5c-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -std=c99 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I include/ -I thirdparty/streamvbyte/include/ src/slow5_press.c -c -fpic -o lib/slow5_press.o - make -C thirdparty/streamvbyte no_simd= libstreamvbyte.a - make[1]: Entering directory '$SRC_DIR/slow5lib/thirdparty/streamvbyte' - x86_64-apple-darwin13.4.0-clang -fPIC -std=c99 -O3 -Wall -Wextra -pedantic -Wshadow -DSTREAMVBYTE_SSSE3=1 -mssse3 -c ./src/streamvbyte_decode.c -Iinclude - x86_64-apple-darwin13.4.0-clang -fPIC -std=c99 -O3 -Wall -Wextra -pedantic -Wshadow -DSTREAMVBYTE_SSSE3=1 -mssse3 -c ./src/streamvbyte_encode.c -Iinclude - x86_64-apple-darwin13.4.0-clang -fPIC -std=c99 -O3 -Wall -Wextra -pedantic -Wshadow -DSTREAMVBYTE_SSSE3=1 -mssse3 -c ./src/streamvbyte_zigzag.c -Iinclude - ar rcs libstreamvbyte.a streamvbyte_decode.o streamvbyte_encode.o streamvbyte_zigzag.o - make[1]: Leaving directory '$SRC_DIR/slow5lib/thirdparty/streamvbyte' - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/f5c-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -std=c99 -shared lib/slow5.o lib/slow5_idx.o lib/slow5_misc.o lib/slow5_press.o thirdparty/streamvbyte/libstreamvbyte.a -o lib/libslow5.so -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lm -lz - cp thirdparty/streamvbyte/libstreamvbyte.a lib/libslow5.a - ar rcs lib/libslow5.a lib/slow5.o lib/slow5_idx.o lib/slow5_misc.o lib/slow5_press.o - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/f5c-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D__STDC_FORMAT_MACROS -g -Wall -O2 -std=c11 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I./htslib -I slow5lib/include/ -x c src/main.c -c -o build/main.o - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/f5c-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D__STDC_FORMAT_MACROS -g -Wall -O2 -std=c11 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I./htslib -I slow5lib/include/ -x c src/meth_main.c -c -o build/meth_main.o - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/f5c-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D__STDC_FORMAT_MACROS -g -Wall -O2 -std=c11 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I./htslib -I slow5lib/include/ -x c src/f5c.c -c -o build/f5c.o - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/f5c-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D__STDC_FORMAT_MACROS -g -Wall -O2 -std=c11 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I./htslib -I slow5lib/include/ -x c src/f5cio.c -c -o build/f5cio.o - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/f5c-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D__STDC_FORMAT_MACROS -g -Wall -O2 -std=c11 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I./htslib -I slow5lib/include/ -x c src/events.c -c -o build/events.o - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/f5c-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D__STDC_FORMAT_MACROS -g -Wall -O2 -std=c11 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I./htslib -I slow5lib/include/ -x c src/nanopolish_read_db.c -c -o build/nanopolish_read_db.o - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/f5c-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D__STDC_FORMAT_MACROS -g -Wall -O2 -std=c11 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I./htslib -I slow5lib/include/ -x c src/index.c -c -o build/index.o -# Last 100 lines of the build log. diff --git a/recipes/f5c/1.2/meta.yaml b/recipes/f5c/1.2/meta.yaml index 05a6a939d6049..5dfdb1809fafa 100644 --- a/recipes/f5c/1.2/meta.yaml +++ b/recipes/f5c/1.2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 1dfec496138fb024623fed2ae5e5fc5759d920d11cbcb570cd9ced001f48687b build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/f5c/meta.yaml b/recipes/f5c/meta.yaml index 307b7c047ae47..eb52ae926c13f 100644 --- a/recipes/f5c/meta.yaml +++ b/recipes/f5c/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 3354813a0523ae3fead68cc3ec5859fa745576b5dc88758a9de172184fac20ab build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('f5c', max_pin="x") }} diff --git a/recipes/fairy/meta.yaml b/recipes/fairy/meta.yaml index 63709b0639e71..d8798aa65b8b3 100644 --- a/recipes/fairy/meta.yaml +++ b/recipes/fairy/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('fairy', max_pin='x.x') }} diff --git a/recipes/falco/meta.yaml b/recipes/falco/meta.yaml index b11966d06a4d1..c68b8d5197234 100644 --- a/recipes/falco/meta.yaml +++ b/recipes/falco/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: # falco is currently not intended to be stable between minor versions (x.x). - {{ pin_subpackage('falco', max_pin="x.x") }} diff --git a/recipes/famsa/meta.yaml b/recipes/famsa/meta.yaml index 57b63bd57adeb..42d296c81421a 100644 --- a/recipes/famsa/meta.yaml +++ b/recipes/famsa/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('famsa', max_pin='x') }} diff --git a/recipes/famseq/meta.yaml b/recipes/famseq/meta.yaml index 27b9a66dca66e..cfaa41c7bcfb3 100644 --- a/recipes/famseq/meta.yaml +++ b/recipes/famseq/meta.yaml @@ -10,7 +10,7 @@ source: md5: 8c0467307967a24ead62d212c8878ef8 build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/fann/meta.yaml b/recipes/fann/meta.yaml index deada89cb78f1..1ca73f5da1f1e 100644 --- a/recipes/fann/meta.yaml +++ b/recipes/fann/meta.yaml @@ -9,7 +9,7 @@ source: md5: 292d914684c9eab1d84eb1f59b0fbf69 build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/faqcs/meta.yaml b/recipes/faqcs/meta.yaml index 33326bdfd34e3..72ad6be45975c 100644 --- a/recipes/faqcs/meta.yaml +++ b/recipes/faqcs/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 7 + number: 8 source: url: https://github.com/LANL-Bioinformatics/FaQCs/archive/{{ version }}.tar.gz diff --git a/recipes/fast-edit-distance/build_failure.linux-64.yaml b/recipes/fast-edit-distance/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..c9a15c7482ff4 --- /dev/null +++ b/recipes/fast-edit-distance/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: f08184ddccb1825107c6164685ef23dafa3b22311d7fcb7a81b3ccac6a010f28 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [1;35mnote[0m: This is an issue with the package mentioned above, not pip. + [1;36mhint[0m: See above for details. + Exception information: + Traceback (most recent call last): + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 35, in generate_metadata + distinfo_dir = backend.prepare_metadata_for_build_wheel(metadata_dir) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/misc.py", line 722, in prepare_metadata_for_build_wheel + return super().prepare_metadata_for_build_wheel( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 186, in prepare_metadata_for_build_wheel + return self._call_hook('prepare_metadata_for_build_wheel', { + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 311, in _call_hook + self._subprocess_runner( + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 237, in runner + call_subprocess( + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 209, in call_subprocess + raise error + pip._internal.exceptions.InstallationSubprocessError: Preparing metadata (pyproject.toml) exited with 1 + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + ^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper + return func(self, options, args) + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 379, in run + requirement_set = resolver.resolve( + ^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 76, in resolve + collected = self.factory.collect_root_requirements(root_reqs) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 545, in collect_root_requirements + reqs = list( + ^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 501, in _make_requirements_from_install_req + cand = self._make_base_candidate_from_link( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 233, in _make_base_candidate_from_link + self._link_candidate_cache[link] = LinkCandidate( + ^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 304, in __init__ + super().__init__( + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 159, in __init__ + self.dist = self._prepare() + ^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 236, in _prepare + dist = self._prepare_distribution() + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 315, in _prepare_distribution + return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 527, in prepare_linked_requirement + return self._prepare_linked_requirement(req, parallel_builds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 642, in _prepare_linked_requirement + dist = _get_prepared_distribution( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 72, in _get_prepared_distribution + abstract_dist.prepare_distribution_metadata( + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/distributions/sdist.py", line 69, in prepare_distribution_metadata + self.req.prepare_metadata() + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/req/req_install.py", line 575, in prepare_metadata + self.metadata_directory = generate_metadata( + ^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 37, in generate_metadata + raise MetadataGenerationFailed(package_details=details) from error + pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed + Removed file://$SRC_DIR from build tracker '/tmp/pip-build-tracker-lyqtcqb7' + Removed build tracker: '/tmp/pip-build-tracker-lyqtcqb7' + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/fast-edit-distance_1734473277457/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/fast-edit-distance_1734473277457/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +reason: |- + pip can't find version from source +category: |- + compiler error diff --git a/recipes/fast-edit-distance/build_failure.linux-aarch64.yaml b/recipes/fast-edit-distance/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..5160346e8a250 --- /dev/null +++ b/recipes/fast-edit-distance/build_failure.linux-aarch64.yaml @@ -0,0 +1,108 @@ +recipe_sha: f08184ddccb1825107c6164685ef23dafa3b22311d7fcb7a81b3ccac6a010f28 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [1;35mnote[0m: This is an issue with the package mentioned above, not pip. + [1;36mhint[0m: See above for details. + Exception information: + Traceback (most recent call last): + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 35, in generate_metadata + distinfo_dir = backend.prepare_metadata_for_build_wheel(metadata_dir) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/misc.py", line 722, in prepare_metadata_for_build_wheel + return super().prepare_metadata_for_build_wheel( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 186, in prepare_metadata_for_build_wheel + return self._call_hook('prepare_metadata_for_build_wheel', { + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 311, in _call_hook + self._subprocess_runner( + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 237, in runner + call_subprocess( + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 209, in call_subprocess + raise error + pip._internal.exceptions.InstallationSubprocessError: Preparing metadata (pyproject.toml) exited with 1 + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + ^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper + return func(self, options, args) + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 379, in run + requirement_set = resolver.resolve( + ^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 76, in resolve + collected = self.factory.collect_root_requirements(root_reqs) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 545, in collect_root_requirements + reqs = list( + ^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 501, in _make_requirements_from_install_req + cand = self._make_base_candidate_from_link( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 233, in _make_base_candidate_from_link + self._link_candidate_cache[link] = LinkCandidate( + ^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 304, in __init__ + super().__init__( + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 159, in __init__ + self.dist = self._prepare() + ^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 236, in _prepare + dist = self._prepare_distribution() + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 315, in _prepare_distribution + return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 527, in prepare_linked_requirement + return self._prepare_linked_requirement(req, parallel_builds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 642, in _prepare_linked_requirement + dist = _get_prepared_distribution( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 72, in _get_prepared_distribution + abstract_dist.prepare_distribution_metadata( + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/distributions/sdist.py", line 69, in prepare_distribution_metadata + self.req.prepare_metadata() + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/req/req_install.py", line 575, in prepare_metadata + self.metadata_directory = generate_metadata( + ^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 37, in generate_metadata + raise MetadataGenerationFailed(package_details=details) from error + pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed + Removed file://$SRC_DIR from build tracker '/tmp/pip-build-tracker-ktu7rk8p' + Removed build tracker: '/tmp/pip-build-tracker-ktu7rk8p' + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/fast-edit-distance_1734473303794/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/fast-edit-distance_1734473303794/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +reason: |- + pip can't find version from source +category: |- + compiler error diff --git a/recipes/fast-edit-distance/build_failure.osx-64.yaml b/recipes/fast-edit-distance/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..0890e8022618d --- /dev/null +++ b/recipes/fast-edit-distance/build_failure.osx-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: f08184ddccb1825107c6164685ef23dafa3b22311d7fcb7a81b3ccac6a010f28 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + Using pip 24.3.1 from $PREFIX/lib/python3.10/site-packages/pip (python 3.10) + Non-user install because user site-packages disabled + Ignoring indexes: https://pypi.org/simple + Created temporary directory: /private/tmp/pip-build-tracker-38zv2w_o + Initialized build tracking at /private/tmp/pip-build-tracker-38zv2w_o + Created build tracker: /private/tmp/pip-build-tracker-38zv2w_o + Entered build tracker: /private/tmp/pip-build-tracker-38zv2w_o + Created temporary directory: /private/tmp/pip-install-m9_r7g8f + Created temporary directory: /private/tmp/pip-ephem-wheel-cache-6h7bgr2f + Processing $SRC_DIR + Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-38zv2w_o' + Created temporary directory: /private/tmp/pip-modern-metadata-0rcpqhhx + Preparing metadata (pyproject.toml): started + Preparing metadata (pyproject.toml): finished with status 'error' + Exception information: + Traceback (most recent call last): + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/operations/build/metadata.py", line 35, in generate_metadata + distinfo_dir = backend.prepare_metadata_for_build_wheel(metadata_dir) + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/utils/misc.py", line 722, in prepare_metadata_for_build_wheel + return super().prepare_metadata_for_build_wheel( + File "$PREFIX/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 186, in prepare_metadata_for_build_wheel + return self._call_hook('prepare_metadata_for_build_wheel', { + File "$PREFIX/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 311, in _call_hook + self._subprocess_runner( + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/utils/subprocess.py", line 237, in runner + call_subprocess( + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/utils/subprocess.py", line 209, in call_subprocess + raise error + pip._internal.exceptions.InstallationSubprocessError: Preparing metadata (pyproject.toml) exited with 1 + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper + return func(self, options, args) + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/commands/install.py", line 379, in run + requirement_set = resolver.resolve( + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 76, in resolve + collected = self.factory.collect_root_requirements(root_reqs) + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 545, in collect_root_requirements + reqs = list( + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 501, in _make_requirements_from_install_req + cand = self._make_base_candidate_from_link( + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 233, in _make_base_candidate_from_link + self._link_candidate_cache[link] = LinkCandidate( + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 304, in __init__ + super().__init__( + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 159, in __init__ + self.dist = self._prepare() + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 236, in _prepare + dist = self._prepare_distribution() + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 315, in _prepare_distribution + return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/operations/prepare.py", line 527, in prepare_linked_requirement + return self._prepare_linked_requirement(req, parallel_builds) + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/operations/prepare.py", line 642, in _prepare_linked_requirement + dist = _get_prepared_distribution( + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/operations/prepare.py", line 72, in _get_prepared_distribution + abstract_dist.prepare_distribution_metadata( + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/distributions/sdist.py", line 69, in prepare_distribution_metadata + self.req.prepare_metadata() + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/req/req_install.py", line 575, in prepare_metadata + self.metadata_directory = generate_metadata( + File "$PREFIX/lib/python3.10/site-packages/pip/_internal/operations/build/metadata.py", line 37, in generate_metadata + raise MetadataGenerationFailed(package_details=details) from error + pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed + Removed file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-38zv2w_o' + Removed build tracker: '/private/tmp/pip-build-tracker-38zv2w_o' +# Last 100 lines of the build log. +reason: |- + pip can't find version from source +category: |- + compiler error diff --git a/recipes/fast-edit-distance/build_failure.osx-arm64.yaml b/recipes/fast-edit-distance/build_failure.osx-arm64.yaml new file mode 100644 index 0000000000000..f8d74c4cb97fa --- /dev/null +++ b/recipes/fast-edit-distance/build_failure.osx-arm64.yaml @@ -0,0 +1,108 @@ +recipe_sha: f08184ddccb1825107c6164685ef23dafa3b22311d7fcb7a81b3ccac6a010f28 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + STRINGS=arm64-apple-darwin20.0.0-strings + STRIP=arm64-apple-darwin20.0.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_arm64_apple_darwin20_0_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=arm64-apple-darwin20.0.0 + host_alias=arm64-apple-darwin20.0.0 + Using pip 24.3.1 from $PREFIX/lib/python3.12/site-packages/pip (python 3.12) + Non-user install because user site-packages disabled + Ignoring indexes: https://pypi.org/simple + Created temporary directory: /private/tmp/pip-build-tracker-_dv6aknf + Initialized build tracking at /private/tmp/pip-build-tracker-_dv6aknf + Created build tracker: /private/tmp/pip-build-tracker-_dv6aknf + Entered build tracker: /private/tmp/pip-build-tracker-_dv6aknf + Created temporary directory: /private/tmp/pip-install-ugxs1u03 + Created temporary directory: /private/tmp/pip-ephem-wheel-cache-0aed7zi8 + Processing $SRC_DIR + Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-_dv6aknf' + Created temporary directory: /private/tmp/pip-modern-metadata-wblgfqh8 + Preparing metadata (pyproject.toml): started + Preparing metadata (pyproject.toml): finished with status 'error' + Exception information: + Traceback (most recent call last): + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 35, in generate_metadata + distinfo_dir = backend.prepare_metadata_for_build_wheel(metadata_dir) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/misc.py", line 722, in prepare_metadata_for_build_wheel + return super().prepare_metadata_for_build_wheel( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 186, in prepare_metadata_for_build_wheel + return self._call_hook('prepare_metadata_for_build_wheel', { + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 311, in _call_hook + self._subprocess_runner( + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 237, in runner + call_subprocess( + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 209, in call_subprocess + raise error + pip._internal.exceptions.InstallationSubprocessError: Preparing metadata (pyproject.toml) exited with 1 + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/fast-edit-distance_1734473158572/work/conda_build.sh']' returned non-zero exit status 1. + ^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper + return func(self, options, args) + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 379, in run + requirement_set = resolver.resolve( + ^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 76, in resolve + collected = self.factory.collect_root_requirements(root_reqs) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 545, in collect_root_requirements + reqs = list( + ^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 501, in _make_requirements_from_install_req + cand = self._make_base_candidate_from_link( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 233, in _make_base_candidate_from_link + self._link_candidate_cache[link] = LinkCandidate( + ^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 304, in __init__ + super().__init__( + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 159, in __init__ + self.dist = self._prepare() + ^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 236, in _prepare + dist = self._prepare_distribution() + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 315, in _prepare_distribution + return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 527, in prepare_linked_requirement + return self._prepare_linked_requirement(req, parallel_builds) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 642, in _prepare_linked_requirement + dist = _get_prepared_distribution( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 72, in _get_prepared_distribution + abstract_dist.prepare_distribution_metadata( + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/distributions/sdist.py", line 69, in prepare_distribution_metadata + self.req.prepare_metadata() + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/req/req_install.py", line 575, in prepare_metadata + self.metadata_directory = generate_metadata( + ^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 37, in generate_metadata + raise MetadataGenerationFailed(package_details=details) from error + pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed + Removed file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-_dv6aknf' + Removed build tracker: '/private/tmp/pip-build-tracker-_dv6aknf' +# Last 100 lines of the build log. +reason: |- + pip can't find version from source +category: |- + compiler error diff --git a/recipes/fast-edit-distance/meta.yaml b/recipes/fast-edit-distance/meta.yaml index a9fa25ffb9240..349d3fddcdf9f 100644 --- a/recipes/fast-edit-distance/meta.yaml +++ b/recipes/fast-edit-distance/meta.yaml @@ -7,10 +7,10 @@ package: source: url: https://github.com/youyupei/fast_edit_distance/archive/v{{ version }}.tar.gz - sha256: 71ead99841435bc2e94be5c8ec89ab5797472b0e7924e0b1a171e5ddf4f7e501 + sha256: 44e8b6a86035965e12170479df1c64290efc3cffab1d43ac2c66f9f8970f30e2 build: - number: 0 + number: 2 script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir run_exports: - {{ pin_subpackage('fast-edit-distance', max_pin="x") }} @@ -22,6 +22,8 @@ requirements: - python - pip - cython + - setuptools + - setuptools_scm run: - python diff --git a/recipes/fasta3/meta.yaml b/recipes/fasta3/meta.yaml index 0ea1ef17edd12..b50d3233c836f 100644 --- a/recipes/fasta3/meta.yaml +++ b/recipes/fasta3/meta.yaml @@ -10,7 +10,7 @@ source: sha256: b4b1c3c9be6beebcbaf4215368e159d69255e34c0bdbc84affa10cdb473ce008 build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -44,4 +44,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/fasta_ushuffle/meta.yaml b/recipes/fasta_ushuffle/meta.yaml index 3edb6037a85ec..e13a604e876f4 100644 --- a/recipes/fasta_ushuffle/meta.yaml +++ b/recipes/fasta_ushuffle/meta.yaml @@ -3,7 +3,7 @@ package: version: 0.2 build: - number: 6 + number: 7 source: url: https://github.com/agordon/fasta_ushuffle/archive/7e4cd85688b5b72f21f26b722167e780c141a49b.zip diff --git a/recipes/fasta_windows/meta.yaml b/recipes/fasta_windows/meta.yaml index cb442c5c1d7d8..1d103a7c503be 100644 --- a/recipes/fasta_windows/meta.yaml +++ b/recipes/fasta_windows/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 source: url: https://github.com/tolkit/fasta_windows/archive/v{{ version }}.tar.gz diff --git a/recipes/fastahack/meta.yaml b/recipes/fastahack/meta.yaml index dfb358e4aad19..62660e7ed239e 100644 --- a/recipes/fastahack/meta.yaml +++ b/recipes/fastahack/meta.yaml @@ -11,7 +11,7 @@ source: sha256: cc1c04729b0c8ba3647cbb7e15e2b490ce701d73773f30f5892d68c36a1dceae build: - number: 1 + number: 2 skip: True # [osx] run_exports: - {{ pin_subpackage("fastahack", max_pin="x") }} diff --git a/recipes/fastani/meta.yaml b/recipes/fastani/meta.yaml index d5463d977a710..b8e772363dd7a 100644 --- a/recipes/fastani/meta.yaml +++ b/recipes/fastani/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage('fastani', max_pin="x") }} diff --git a/recipes/isospecpy/build_failure.osx-64.yaml b/recipes/fastindep/build_failure.osx-64.yaml similarity index 51% rename from recipes/isospecpy/build_failure.osx-64.yaml rename to recipes/fastindep/build_failure.osx-64.yaml index 14a7001284e66..33f08a69ef8ed 100644 --- a/recipes/isospecpy/build_failure.osx-64.yaml +++ b/recipes/fastindep/build_failure.osx-64.yaml @@ -1,37 +1,72 @@ -recipe_sha: e22cb32401e01937fc9b01b36eabc64265850c69f2613a0460aed9a06c4825cd # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: b0ce5d62d01123e1ff9a744c9c1465df016128b2df07be3f3cf5e92fb387ca2b # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + - libzlib 1.3.1 hd23fc13_2 + - llvm-tools 18.1.8 h9ce406d_2 + - zstd 1.5.6 h915ae27_0 + - libcxx 19.1.5 hf95d169_0 + - ca-certificates 2024.8.30 h8857fd0_0 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + - libxml2 2.13.5 he8ee3e7_1 + - openssl 3.4.0 hd471939_0 + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 api.build( - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/isospecpy_1717510144117/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/isospecpy_1717510144117/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/isospecpy_1717510144117/work - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + - clangxx 18.1.8 default_h179603d_5 + - tapi 1300.6.5 h390ca13_0 + - clangxx_osx-64 18.1.8 h7e5c614_23 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + - libclang-cpp18.1 18.1.8 default_h0c94c6a_5 + - clang 18.1.8 default_h179603d_5 + - clang_osx-64 18.1.8 h7e5c614_23 + raise BuildScriptException(str(exc), caused_by=exc) from exc + - cctools_osx-64 1010.6 h00edd4c_2 + host: + - libcxx 19.1.5 hf95d169_0 + run: + - libcxx >=18 + test: + commands: + - fastindep + - fastindep-symmetry + about: + home: https://github.com/endrebak/fastindep + license: MIT + summary: A fast random heuristic algorithm for identifying large sets of unrelated + individuals and unrelated markers + extra: + copy_test_source_files: true + final: true + + + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/fastindep_1733951788267/work/conda_build.sh']' returned non-zero exit status 1. + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/fastindep_1733951788267/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/fastindep_1733951788267/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/fastindep_1733951788267/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/fastindep_1733951788267/work INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as CC=x86_64-apple-darwin13.4.0-clang CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/isospecpy-2.2.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastindep-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/isospecpy_1717510144117/work/conda_build.sh']' returned non-zero exit status 1. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/isospecpy-2.2.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastindep-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool LD=x86_64-apple-darwin13.4.0-ld @@ -39,7 +74,7 @@ log: |2- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -48,7 +83,7 @@ log: |2- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -63,42 +98,7 @@ log: |2- INFO: activate_clangxx_osx-64.sh made the following environmental changes: CLANGXX=x86_64-apple-darwin13.4.0-clang CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/isospecpy-2.2.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastindep-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/isospecpy-2.2.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - Using pip 24.0 from $PREFIX/lib/python3.8/site-packages/pip (python 3.8) - Non-user install because user site-packages disabled - Ignoring indexes: https://pypi.org/simple - Created temporary directory: /private/tmp/pip-build-tracker-jwr7tzd6 - Initialized build tracking at /private/tmp/pip-build-tracker-jwr7tzd6 - Created build tracker: /private/tmp/pip-build-tracker-jwr7tzd6 - Entered build tracker: /private/tmp/pip-build-tracker-jwr7tzd6 - Created temporary directory: /private/tmp/pip-install-v7o3ri7s - Created temporary directory: /private/tmp/pip-ephem-wheel-cache-nmlib6qa - Processing $SRC_DIR - Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-jwr7tzd6' - Running setup.py (path:$SRC_DIR/setup.py) egg_info for package from file://$SRC_DIR - Created temporary directory: /private/tmp/pip-pip-egg-info-hb_xlbm2 - Preparing metadata (setup.py): started - Preparing metadata (setup.py): finished with status 'done' - Source in $SRC_DIR has version 2.2.2, which satisfies requirement IsoSpecPy==2.2.2 from file://$SRC_DIR - Removed IsoSpecPy==2.2.2 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-jwr7tzd6' - Created temporary directory: /private/tmp/pip-unpack-2znkqc52 - Building wheels for collected packages: IsoSpecPy - Created temporary directory: /private/tmp/pip-wheel-4twqti9t - Building wheel for IsoSpecPy (setup.py): started - Destination directory: /private/tmp/pip-wheel-4twqti9t - Building wheel for IsoSpecPy (setup.py): finished with status 'error' - Running setup.py clean for IsoSpecPy - Failed to build IsoSpecPy - Exception information: - Traceback (most recent call last): - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper - return func(self, options, args) - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/commands/install.py", line 429, in run - raise InstallationError( - pip._internal.exceptions.InstallationError: Could not build wheels for IsoSpecPy, which is required to install pyproject.toml-based projects - Removed build tracker: '/private/tmp/pip-build-tracker-jwr7tzd6' + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastindep-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix # Last 100 lines of the build log. diff --git a/recipes/fastindep/meta.yaml b/recipes/fastindep/meta.yaml index 4b62bdc4bb8b9..57d85678ca7e0 100644 --- a/recipes/fastindep/meta.yaml +++ b/recipes/fastindep/meta.yaml @@ -7,7 +7,7 @@ source: url: https://github.com/endrebak/fastindep/archive/1.0.0.tar.gz build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/fastk/meta.yaml b/recipes/fastk/meta.yaml index 72a5ad1be313e..85f5ec2388757 100644 --- a/recipes/fastk/meta.yaml +++ b/recipes/fastk/meta.yaml @@ -13,7 +13,7 @@ source: - patch build: - number: 0 + number: 1 skip: true # [osx] run_exports: - {{ pin_subpackage("fastk", max_pin="x") }} diff --git a/recipes/fastme/meta.yaml b/recipes/fastme/meta.yaml index fa70f80f4d49e..f41226bf52060 100644 --- a/recipes/fastme/meta.yaml +++ b/recipes/fastme/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/fastobo/meta.yaml b/recipes/fastobo/meta.yaml index f07953f5ee29c..30876a638efd1 100644 --- a/recipes/fastobo/meta.yaml +++ b/recipes/fastobo/meta.yaml @@ -10,7 +10,7 @@ source: sha256: "f375932a24b078706797eb9296740f2d2e6987a34309bda7c9f235aba1d74217" build: - number: 2 + number: 3 skip: True # [osx or py27 or py36] run_exports: - {{ pin_subpackage('fastobo', max_pin="x.x") }} diff --git a/recipes/fastool/meta.yaml b/recipes/fastool/meta.yaml index c630514e19130..2cf65a098e0d3 100644 --- a/recipes/fastool/meta.yaml +++ b/recipes/fastool/meta.yaml @@ -7,7 +7,7 @@ source: sha256: f86f02fced9479b77d6d27a442b66e66f0c55d40d5ad2ddd91a752de57024540 build: - number: 9 + number: 10 run_exports: - {{ pin_subpackage("fastool", max_pin="x.x") }} diff --git a/recipes/fastq-and-furious/meta.yaml b/recipes/fastq-and-furious/meta.yaml index 3acff34beb677..f13392c4c0c31 100644 --- a/recipes/fastq-and-furious/meta.yaml +++ b/recipes/fastq-and-furious/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 376bee916d981fd68fbe8a6b3264768059d740d77fdd3227023acddd43d0e0e8 build: - number: 4 + number: 5 # When building, warns "Not tested on OSX. Feedback welcome" and does not compile on OSX and py310. skip: True # [py2k or osx] diff --git a/recipes/fastq-count/meta.yaml b/recipes/fastq-count/meta.yaml index f8a59e3010c89..a171042024b34 100644 --- a/recipes/fastq-count/meta.yaml +++ b/recipes/fastq-count/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 5 + number: 6 source: url: https://github.com/sndrtj/fastq-count/archive/v{{ version }}.tar.gz diff --git a/recipes/fastq-filter/meta.yaml b/recipes/fastq-filter/meta.yaml index c83934cf95b3b..ca7e370add71a 100644 --- a/recipes/fastq-filter/meta.yaml +++ b/recipes/fastq-filter/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 8f28ea8124871b7c2cba2b558b7b64abdcbd4b0fdb7197a82056f7e6202b3e4b build: - number: 2 + number: 3 skip: true # [py < 38] entry_points: - fastq-filter=fastq_filter:main diff --git a/recipes/fastq-join/build_failure.osx-64.yaml b/recipes/fastq-join/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..9b396d7ad8a23 --- /dev/null +++ b/recipes/fastq-join/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: df31d860ac2c9af511ccdec664fd2a172936e493c4e8d907692b16281a73fbfc # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - libllvm18 18.1.8 h9ce406d_2 + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/fastq-join_1733952802348/work/conda_build.sh']' returned non-zero exit status 2. + + - cctools_osx-64 1010.6 h00edd4c_2 + - openssl 3.4.0 hd471939_0 + - clangxx_impl_osx-64 18.1.8 h4b7810f_23 + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + - clang-18 18.1.8 default_h0c94c6a_5 + - llvm-tools-18 18.1.8 h9ce406d_2 + - compiler-rt 18.1.8 h1020d70_1 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + - ca-certificates 2024.8.30 h8857fd0_0 + - libcxx 19.1.5 hf95d169_0 + - ld64_osx-64 951.9 hc8d1a19_2 + - llvm-tools 18.1.8 h9ce406d_2 + host: + - libcxx 19.1.5 hf95d169_0 + run: + - libcxx >=18 + test: + commands: + - fastq-join -h + about: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + home: https://github.com/brwnj/fastq-join + license: MIT + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + summary: Similar to audy's stitch program, but in C, more efficient and supports + some automatic benchmarking and tuning. It uses the same "squared distance for + anchored alignment" as other tools. + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/fastq-join_1733952802348/work + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/fastq-join_1733952802348/work/conda_build.sh']' returned non-zero exit status 2. + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/fastq-join_1733952802348/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/fastq-join_1733952802348/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/fastq-join_1733952802348/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastq-join-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastq-join-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastq-join-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastq-join-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastq-join-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -O3 -I. fastq-join.cpp fastq-lib.cpp -o fastq-join +# Last 100 lines of the build log. diff --git a/recipes/fastq-join/meta.yaml b/recipes/fastq-join/meta.yaml index 46ef0d0778c70..bf3566b4aefb1 100644 --- a/recipes/fastq-join/meta.yaml +++ b/recipes/fastq-join/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.3.1 build: - number: 7 + number: 8 source: url: https://github.com/brwnj/fastq-join/archive/v1.3.1.tar.gz diff --git a/recipes/fastq-multx/build_failure.osx-64.yaml b/recipes/fastq-multx/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..cb2f445f74b93 --- /dev/null +++ b/recipes/fastq-multx/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 8863aa8f2c8b279783ff071a7bea65f1bd5a5c9779d79ddfbc0f4a7aa9e5b8ff # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + - clangxx_impl_osx-64 18.1.8 h4b7810f_23 + - clangxx_osx-64 18.1.8 h7e5c614_23 + - cctools_osx-64 1010.6 h00edd4c_2 + - compiler-rt 18.1.8 h1020d70_1 + - clang_osx-64 18.1.8 h7e5c614_23 + - libclang-cpp18.1 18.1.8 default_h0c94c6a_5 + - ncurses 6.5 hf036a51_1 + - zstd 1.5.6 h915ae27_0 + - libllvm18 18.1.8 h9ce406d_2 + - tapi 1300.6.5 h390ca13_0 + - clang 18.1.8 default_h179603d_5 + - llvm-tools-18 18.1.8 h9ce406d_2 + - ca-certificates 2024.8.30 h8857fd0_0 + - libzlib 1.3.1 hd23fc13_2 + - libxml2 2.13.5 he8ee3e7_1 + - libcxx 19.1.5 hf95d169_0 + - sigtool 0.1.3 h88f4db0_0 + - make 4.4.1 h00291cd_2 + - openssl 3.4.0 hd471939_0 + - llvm-tools 18.1.8 h9ce406d_2 + - libiconv 1.17 hd75f5a5_2 + - clangxx 18.1.8 default_h179603d_5 + - libcxx-devel 18.1.8 h7c275be_7 + - liblzma 5.6.3 hd471939_1 + - clang-18 18.1.8 default_h0c94c6a_5 + - ld64_osx-64 951.9 hc8d1a19_2 + host: + - libcxx 19.1.5 hf95d169_0 + run: + - libcxx >=18 + test: + commands: + - fastq-multx -h + about: + home: https://github.com/brwnj/fastq-multx + license: MIT + summary: Demultiplexes a fastq. Capable of auto-determining barcode id's based on + a master set fields. Keeps multiple reads in-sync during demultiplexing. Can verify + that the reads are in-sync as well, and fail if they're not. + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/fastq-multx_1733868093312/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/fastq-multx_1733868093312/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/fastq-multx_1733868093312/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/fastq-multx_1733868093312/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastq-multx-1.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastq-multx-1.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastq-multx-1.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastq-multx-1.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + x86_64-apple-darwin13.4.0-clang -O3 -I. fastq-multx.cpp fastq-lib.cpp -o fastq-multx +# Last 100 lines of the build log. diff --git a/recipes/fastq-multx/meta.yaml b/recipes/fastq-multx/meta.yaml index 507722971d007..e7c264bc4b623 100644 --- a/recipes/fastq-multx/meta.yaml +++ b/recipes/fastq-multx/meta.yaml @@ -5,7 +5,7 @@ package: version: "{{ version }}" build: - number: 4 + number: 5 source: url: "https://github.com/brwnj/fastq-multx/archive/v{{ version }}.tar.gz" diff --git a/recipes/fastq-pair/meta.yaml b/recipes/fastq-pair/meta.yaml index e48420c80412f..edc777cc2e45d 100644 --- a/recipes/fastq-pair/meta.yaml +++ b/recipes/fastq-pair/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/fastq-scan/meta.yaml b/recipes/fastq-scan/meta.yaml index 5a1e652f87b45..3e3272b80bbce 100644 --- a/recipes/fastq-scan/meta.yaml +++ b/recipes/fastq-scan/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} diff --git a/recipes/fastq-tools/build_failure.osx-64.yaml b/recipes/fastq-tools/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..8d2e68d8e0d99 --- /dev/null +++ b/recipes/fastq-tools/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: a60fcbafd5e542ad35087dea8e550e491504fddf5b11708ca26075c7fbb3b63e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + checking for unistd.h... yes + checking for uint8_t... yes + checking for uint16_t... yes + checking for int32_t... yes + checking for uint32_t... yes + checking for uint64_t... yes + checking for size_t... yes + checking for _Bool... yes + checking for stdbool.h that conforms to C99... yes + checking build system type... x86_64-apple-darwin13.4.0 + checking host system type... x86_64-apple-darwin13.4.0 + checking how to print strings... printf + checking for a sed that does not truncate output... /usr/bin/sed + checking for grep that handles long lines and -e... /usr/bin/grep + checking for egrep... /usr/bin/grep -E + checking for fgrep... /usr/bin/grep -F + checking for ld used by x86_64-apple-darwin13.4.0-clang... x86_64-apple-darwin13.4.0-ld + checking if the linker (x86_64-apple-darwin13.4.0-ld) is GNU ld... no + checking for BSD- or MS-compatible name lister (nm)... x86_64-apple-darwin13.4.0-nm + checking the name lister (x86_64-apple-darwin13.4.0-nm) interface... BSD nm + checking whether ln -s works... yes + checking the maximum length of command line arguments... 786432 + checking how to convert x86_64-apple-darwin13.4.0 file names to x86_64-apple-darwin13.4.0 format... func_convert_file_noop + checking how to convert x86_64-apple-darwin13.4.0 file names to toolchain format... func_convert_file_noop + checking for x86_64-apple-darwin13.4.0-ld option to reload object files... -r + checking for x86_64-apple-darwin13.4.0-file... no + checking for file... file + checking for x86_64-apple-darwin13.4.0-objdump... no + checking for objdump... objdump + checking how to recognize dependent libraries... pass_all + checking for x86_64-apple-darwin13.4.0-dlltool... no + checking for dlltool... no + checking how to associate runtime and link libraries... printf %s\n + checking for x86_64-apple-darwin13.4.0-ar... x86_64-apple-darwin13.4.0-ar + checking for archiver @FILE support... no + checking for x86_64-apple-darwin13.4.0-strip... x86_64-apple-darwin13.4.0-strip + checking for x86_64-apple-darwin13.4.0-ranlib... x86_64-apple-darwin13.4.0-ranlib + checking command to parse x86_64-apple-darwin13.4.0-nm output from x86_64-apple-darwin13.4.0-clang object... ok + checking for sysroot... no + checking for a working dd... /bin/dd + checking how to truncate binary pipes... /bin/dd bs=4096 count=1 + checking for x86_64-apple-darwin13.4.0-mt... no + checking for mt... no + checking if : is a manifest tool... no + checking for x86_64-apple-darwin13.4.0-dsymutil... no + checking for dsymutil... dsymutil + checking for x86_64-apple-darwin13.4.0-nmedit... x86_64-apple-darwin13.4.0-nmedit + checking for x86_64-apple-darwin13.4.0-lipo... x86_64-apple-darwin13.4.0-lipo + checking for x86_64-apple-darwin13.4.0-otool... x86_64-apple-darwin13.4.0-otool + checking for x86_64-apple-darwin13.4.0-otool64... no + checking for otool64... no + checking for -single_module linker flag... yes + checking for -exported_symbols_list linker flag... yes + checking for -force_load linker flag... yes + checking for dlfcn.h... yes + checking for objdir... .libs + checking if x86_64-apple-darwin13.4.0-clang supports -fno-rtti -fno-exceptions... yes + checking for x86_64-apple-darwin13.4.0-clang option to produce PIC... -fno-common -DPIC + checking if x86_64-apple-darwin13.4.0-clang PIC flag -fno-common -DPIC works... yes + checking if x86_64-apple-darwin13.4.0-clang static flag -static works... no + checking if x86_64-apple-darwin13.4.0-clang supports -c -o file.o... yes + checking if x86_64-apple-darwin13.4.0-clang supports -c -o file.o... (cached) yes + checking whether the x86_64-apple-darwin13.4.0-clang linker (x86_64-apple-darwin13.4.0-ld) supports shared libraries... yes + checking dynamic linker characteristics... darwin13.4.0 dyld + checking how to hardcode library paths into programs... immediate + checking whether stripping libraries is possible... yes + checking if libtool supports shared libraries... yes + checking whether to build shared libraries... yes + checking whether to build static libraries... yes + checking for mkstemp... yes + checking for fileno... yes + checking for pcre-config... yes + checking for getopt.h... yes + checking that generated files are newer than configure... done + configure: creating ./config.status + config.status: creating Makefile + config.status: creating src/Makefile + config.status: creating tests/Makefile + config.status: creating doc/Makefile + config.status: creating src/version.h + config.status: executing depfiles commands + config.status: executing libtool commands + Making install in src + make[1]: Entering directory '$SRC_DIR/src' + CC fastq-grep.o + CC common.o + CC parse.o + CCLD fastq-grep + CC fastq-kmers.o + CCLD fastq-kmers + CC fastq-match.o + CC sw.o + CCLD fastq-match + CC fastq-uniq.o + CC hash_table.o + CCLD fastq-uniq + CC fastq-qual.o + CCLD fastq-qual + CC fastq-sample.o + make[1]: Leaving directory '$SRC_DIR/src' +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/fastq-tools/meta.yaml b/recipes/fastq-tools/meta.yaml index 500677adb2a47..00ed0d6e19093 100644 --- a/recipes/fastq-tools/meta.yaml +++ b/recipes/fastq-tools/meta.yaml @@ -8,7 +8,8 @@ source: sha256: 0cd7436e81129090e707f69695682df80623b06448d95df483e572c61ddf538e build: - number: 4 + number: 5 + run_exports: '{{ pin_subpackage("fastq-tools", max_pin="x.x") }}' requirements: build: diff --git a/recipes/fastq_utils/meta.yaml b/recipes/fastq_utils/meta.yaml index a91fe7a2383ed..ae9b913405be6 100644 --- a/recipes/fastq_utils/meta.yaml +++ b/recipes/fastq_utils/meta.yaml @@ -10,7 +10,7 @@ source: build: skip: True # [osx] - number: 1 + number: 2 requirements: build: diff --git a/recipes/fastqc-rs/meta.yaml b/recipes/fastqc-rs/meta.yaml index 3a05e9698633c..58430c8e918c0 100644 --- a/recipes/fastqc-rs/meta.yaml +++ b/recipes/fastqc-rs/meta.yaml @@ -5,7 +5,7 @@ package: version: {{version}} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('fastqc-rs', max_pin="x.x") }} diff --git a/recipes/fastqpuri/meta.yaml b/recipes/fastqpuri/meta.yaml index 30f24bc75706d..44689da70be64 100644 --- a/recipes/fastqpuri/meta.yaml +++ b/recipes/fastqpuri/meta.yaml @@ -7,7 +7,7 @@ source: sha256: af16c1aa0a679a7c921e4ea8532faf83aad2b7790a38717d592fa39680c813d9 build: - number: 8 + number: 9 requirements: build: - cmake diff --git a/recipes/fastqsplitter/meta.yaml b/recipes/fastqsplitter/meta.yaml index e38a75a9d6c7a..0a4153521d6ad 100644 --- a/recipes/fastqsplitter/meta.yaml +++ b/recipes/fastqsplitter/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: True # [py27] - number: 6 + number: 7 entry_points: - fastqsplitter=fastqsplitter:main script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " diff --git a/recipes/fastqtk/meta.yaml b/recipes/fastqtk/meta.yaml index e15173e307a43..f29b62cc00468 100644 --- a/recipes/fastqtk/meta.yaml +++ b/recipes/fastqtk/meta.yaml @@ -13,7 +13,7 @@ source: - makefile.patch build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/fastremap-bio/meta.yaml b/recipes/fastremap-bio/meta.yaml index 5fe4a9054670d..bbb892ba867f5 100644 --- a/recipes/fastremap-bio/meta.yaml +++ b/recipes/fastremap-bio/meta.yaml @@ -9,7 +9,7 @@ source: sha256: ecac10e12c4ce9af73669952fda8c32d07eb307987855fd9fb4a92de14104cd7 build: - number: 1 + number: 2 skip: True # [osx] requirements: diff --git a/recipes/fastsimbac/meta.yaml b/recipes/fastsimbac/meta.yaml index e2bb200b68cfd..e918a3ab50eb5 100644 --- a/recipes/fastsimbac/meta.yaml +++ b/recipes/fastsimbac/meta.yaml @@ -7,7 +7,7 @@ source: md5: "7c183b317bc45606f6b37e27f6ee8357" build: - number: 6 + number: 7 run_exports: - {{ pin_subpackage("fastsimbac", max_pin="x") }} diff --git a/recipes/fastspar/meta.yaml b/recipes/fastspar/meta.yaml index 512728528af2e..498975481bfe1 100644 --- a/recipes/fastspar/meta.yaml +++ b/recipes/fastspar/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{sha256}} build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/fasttree/2.1.3/meta.yaml b/recipes/fasttree/2.1.3/meta.yaml index 71fdaa607c053..17327dc4faafa 100644 --- a/recipes/fasttree/2.1.3/meta.yaml +++ b/recipes/fasttree/2.1.3/meta.yaml @@ -7,7 +7,7 @@ source: md5: "a204fbe70bf9e787509b9433ec371892" build: - number: 6 + number: 7 skip: True # [osx] requirements: diff --git a/recipes/fasttree/2.1.8/meta.yaml b/recipes/fasttree/2.1.8/meta.yaml index ec819d4aeb834..3b04618d4434d 100644 --- a/recipes/fasttree/2.1.8/meta.yaml +++ b/recipes/fasttree/2.1.8/meta.yaml @@ -7,7 +7,7 @@ source: md5: "c7e85689a26cabba241378d4f633c2fa" build: - number: 8 + number: 9 skip: True # [osx] requirements: diff --git a/recipes/fasttree/meta.yaml b/recipes/fasttree/meta.yaml index 63e42529105d4..421fefe4e6426 100644 --- a/recipes/fasttree/meta.yaml +++ b/recipes/fasttree/meta.yaml @@ -10,7 +10,7 @@ source: sha256: "9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f" build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} diff --git a/recipes/fastutils/meta.yaml b/recipes/fastutils/meta.yaml index 200aa6e7b7633..ea8923ed22bfa 100755 --- a/recipes/fastutils/meta.yaml +++ b/recipes/fastutils/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/fastv/meta.yaml b/recipes/fastv/meta.yaml index b7e927e3e3c51..0d6eff8fb8e51 100644 --- a/recipes/fastv/meta.yaml +++ b/recipes/fastv/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('fastv', max_pin="x") }} diff --git a/recipes/fastx_toolkit/build_failure.osx-64.yaml b/recipes/fastx_toolkit/build_failure.osx-64.yaml index 2f7acc0471815..0c41cf70e0d09 100644 --- a/recipes/fastx_toolkit/build_failure.osx-64.yaml +++ b/recipes/fastx_toolkit/build_failure.osx-64.yaml @@ -1,104 +1,106 @@ -recipe_sha: a5de286d625bb6a3095395f164a1957507ec1cc8605d429526b65b7aa38bd266 # The commit at which this recipe failed to build. +recipe_sha: 5e8a4c7c910b810953593f2f8fa55c95e04344cfb040dd50d51e2dd63bf6921f # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- - /bin/sh ../../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastx_trimmer fastx_trimmer.o ../libfastx/libfastx.a - libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastx_trimmer fastx_trimmer.o -L$PREFIX/lib ../libfastx/libfastx.a - ld: warning: Csu support file -lcrt1.10.6.o not found, changing to target macOS 10.8 where it is not needed - ld: warning: object file (fastx_trimmer.o) was built for newer macOS version (10.9) than being linked (10.8) - ld: warning: object file (../libfastx/libfastx.a(fastx_args.o)) was built for newer macOS version (10.9) than being linked (10.8) - ld: warning: object file (../libfastx/libfastx.a(fastx.o)) was built for newer macOS version (10.9) than being linked (10.8) - ld: warning: object file (../libfastx/libfastx.a(chomp.o)) was built for newer macOS version (10.9) than being linked (10.8) + config.status: creating build_scripts/Makefile + config.status: creating config.h + config.status: executing depfiles commands + config.status: executing libtool commands + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + make all-recursive + make[1]: Entering directory '$SRC_DIR' + Making all in m4 + make[2]: Entering directory '$SRC_DIR/m4' + make[2]: Nothing to be done for 'all'. + make[2]: Leaving directory '$SRC_DIR/m4' + Making all in src + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + make[2]: Entering directory '$SRC_DIR/src' + Making all in libfastx + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/fastx_toolkit_1734563654197/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + make[3]: Entering directory '$SRC_DIR/src/libfastx' + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/fastx_toolkit_1734563654197/work/conda_build.sh']' returned non-zero exit status 2. + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT chomp.o -MD -MP -MF .deps/chomp.Tpo -c -o chomp.o chomp.c + mv -f .deps/chomp.Tpo .deps/chomp.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx.o -MD -MP -MF .deps/fastx.Tpo -c -o fastx.o fastx.c + mv -f .deps/fastx.Tpo .deps/fastx.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx_args.o -MD -MP -MF .deps/fastx_args.Tpo -c -o fastx_args.o fastx_args.c + mv -f .deps/fastx_args.Tpo .deps/fastx_args.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -Wall -Wno-implicit-fallthrough -std=c11 -stdlib=libc -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT sequence_alignment.o -MD -MP -MF .deps/sequence_alignment.Tpo -c -o sequence_alignment.o sequence_alignment.cpp + mv -f .deps/sequence_alignment.Tpo .deps/sequence_alignment.Po + rm -f libfastx.a + x86_64-apple-darwin13.4.0-ar cru libfastx.a chomp.o fastx.o fastx_args.o sequence_alignment.o + x86_64-apple-darwin13.4.0-ranlib libfastx.a + make[3]: Leaving directory '$SRC_DIR/src/libfastx' + Making all in fastx_clipper + make[3]: Entering directory '$SRC_DIR/src/fastx_clipper' + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -Wall -Wno-implicit-fallthrough -std=c11 -stdlib=libc -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx_clipper.o -MD -MP -MF .deps/fastx_clipper.Tpo -c -o fastx_clipper.o fastx_clipper.cpp + mv -f .deps/fastx_clipper.Tpo .deps/fastx_clipper.Po + /bin/sh ../../libtool --tag=CXX --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -Wall -Wno-implicit-fallthrough -std=c11 -stdlib=libc -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastx_clipper fastx_clipper.o ../libfastx/libfastx.a + libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -Wall -Wno-implicit-fallthrough -std=c11 -stdlib=libc -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastx_clipper fastx_clipper.o -L$PREFIX/lib ../libfastx/libfastx.a + make[3]: Leaving directory '$SRC_DIR/src/fastx_clipper' + Making all in fastx_trimmer + make[3]: Entering directory '$SRC_DIR/src/fastx_trimmer' + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx_trimmer.o -MD -MP -MF .deps/fastx_trimmer.Tpo -c -o fastx_trimmer.o fastx_trimmer.c + mv -f .deps/fastx_trimmer.Tpo .deps/fastx_trimmer.Po + /bin/sh ../../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastx_trimmer fastx_trimmer.o ../libfastx/libfastx.a + libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastx_trimmer fastx_trimmer.o -L$PREFIX/lib ../libfastx/libfastx.a make[3]: Leaving directory '$SRC_DIR/src/fastx_trimmer' Making all in fastx_quality_stats make[3]: Entering directory '$SRC_DIR/src/fastx_quality_stats' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx_quality_stats.o -MD -MP -MF .deps/fastx_quality_stats.Tpo -c -o fastx_quality_stats.o fastx_quality_stats.c + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx_quality_stats.o -MD -MP -MF .deps/fastx_quality_stats.Tpo -c -o fastx_quality_stats.o fastx_quality_stats.c mv -f .deps/fastx_quality_stats.Tpo .deps/fastx_quality_stats.Po - /bin/sh ../../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastx_quality_stats fastx_quality_stats.o ../libfastx/libfastx.a - libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastx_quality_stats fastx_quality_stats.o -L$PREFIX/lib ../libfastx/libfastx.a - ld: warning: Csu support file -lcrt1.10.6.o not found, changing to target macOS 10.8 where it is not needed - ld: warning: object file (fastx_quality_stats.o) was built for newer macOS version (10.9) than being linked (10.8) - ld: warning: object file (../libfastx/libfastx.a(fastx.o)) was built for newer macOS version (10.9) than being linked (10.8) - ld: warning: object file (../libfastx/libfastx.a(fastx_args.o)) was built for newer macOS version (10.9) than being linked (10.8) - ld: warning: object file (../libfastx/libfastx.a(chomp.o)) was built for newer macOS version (10.9) than being linked (10.8) + /bin/sh ../../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastx_quality_stats fastx_quality_stats.o ../libfastx/libfastx.a + libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastx_quality_stats fastx_quality_stats.o -L$PREFIX/lib ../libfastx/libfastx.a make[3]: Leaving directory '$SRC_DIR/src/fastx_quality_stats' Making all in fastq_quality_converter make[3]: Entering directory '$SRC_DIR/src/fastq_quality_converter' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastq_quality_converter.o -MD -MP -MF .deps/fastq_quality_converter.Tpo -c -o fastq_quality_converter.o fastq_quality_converter.c + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastq_quality_converter.o -MD -MP -MF .deps/fastq_quality_converter.Tpo -c -o fastq_quality_converter.o fastq_quality_converter.c mv -f .deps/fastq_quality_converter.Tpo .deps/fastq_quality_converter.Po - /bin/sh ../../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastq_quality_converter fastq_quality_converter.o ../libfastx/libfastx.a - libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastq_quality_converter fastq_quality_converter.o -L$PREFIX/lib ../libfastx/libfastx.a - ld: warning: Csu support file -lcrt1.10.6.o not found, changing to target macOS 10.8 where it is not needed - ld: warning: object file (fastq_quality_converter.o) was built for newer macOS version (10.9) than being linked (10.8) - ld: warning: object file (../libfastx/libfastx.a(fastx_args.o)) was built for newer macOS version (10.9) than being linked (10.8) - ld: warning: object file (../libfastx/libfastx.a(fastx.o)) was built for newer macOS version (10.9) than being linked (10.8) - ld: warning: object file (../libfastx/libfastx.a(chomp.o)) was built for newer macOS version (10.9) than being linked (10.8) + /bin/sh ../../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastq_quality_converter fastq_quality_converter.o ../libfastx/libfastx.a + libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastq_quality_converter fastq_quality_converter.o -L$PREFIX/lib ../libfastx/libfastx.a make[3]: Leaving directory '$SRC_DIR/src/fastq_quality_converter' Making all in fastq_to_fasta make[3]: Entering directory '$SRC_DIR/src/fastq_to_fasta' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastq_to_fasta.o -MD -MP -MF .deps/fastq_to_fasta.Tpo -c -o fastq_to_fasta.o fastq_to_fasta.c + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastq_to_fasta.o -MD -MP -MF .deps/fastq_to_fasta.Tpo -c -o fastq_to_fasta.o fastq_to_fasta.c mv -f .deps/fastq_to_fasta.Tpo .deps/fastq_to_fasta.Po - /bin/sh ../../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastq_to_fasta fastq_to_fasta.o ../libfastx/libfastx.a - libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastq_to_fasta fastq_to_fasta.o -L$PREFIX/lib ../libfastx/libfastx.a - ld: warning: Csu support file -lcrt1.10.6.o not found, changing to target macOS 10.8 where it is not needed - ld: warning: object file (fastq_to_fasta.o) was built for newer macOS version (10.9) than being linked (10.8) - ld: warning: object file (../libfastx/libfastx.a(fastx_args.o)) was built for newer macOS version (10.9) than being linked (10.8) - ld: warning: object file (../libfastx/libfastx.a(fastx.o)) was built for newer macOS version (10.9) than being linked (10.8) - ld: warning: object file (../libfastx/libfastx.a(chomp.o)) was built for newer macOS version (10.9) than being linked (10.8) + /bin/sh ../../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastq_to_fasta fastq_to_fasta.o ../libfastx/libfastx.a + libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastq_to_fasta fastq_to_fasta.o -L$PREFIX/lib ../libfastx/libfastx.a make[3]: Leaving directory '$SRC_DIR/src/fastq_to_fasta' Making all in fastq_quality_filter make[3]: Entering directory '$SRC_DIR/src/fastq_quality_filter' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastq_quality_filter.o -MD -MP -MF .deps/fastq_quality_filter.Tpo -c -o fastq_quality_filter.o fastq_quality_filter.c + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastq_quality_filter.o -MD -MP -MF .deps/fastq_quality_filter.Tpo -c -o fastq_quality_filter.o fastq_quality_filter.c mv -f .deps/fastq_quality_filter.Tpo .deps/fastq_quality_filter.Po - /bin/sh ../../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastq_quality_filter fastq_quality_filter.o ../libfastx/libfastx.a - libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastq_quality_filter fastq_quality_filter.o -L$PREFIX/lib ../libfastx/libfastx.a - ld: warning: Csu support file -lcrt1.10.6.o not found, changing to target macOS 10.8 where it is not needed - ld: warning: object file (fastq_quality_filter.o) was built for newer macOS version (10.9) than being linked (10.8) - ld: warning: object file (../libfastx/libfastx.a(fastx_args.o)) was built for newer macOS version (10.9) than being linked (10.8) - ld: warning: object file (../libfastx/libfastx.a(fastx.o)) was built for newer macOS version (10.9) than being linked (10.8) - ld: warning: object file (../libfastx/libfastx.a(chomp.o)) was built for newer macOS version (10.9) than being linked (10.8) + /bin/sh ../../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastq_quality_filter fastq_quality_filter.o ../libfastx/libfastx.a + libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastq_quality_filter fastq_quality_filter.o -L$PREFIX/lib ../libfastx/libfastx.a make[3]: Leaving directory '$SRC_DIR/src/fastq_quality_filter' Making all in fastq_quality_trimmer make[3]: Entering directory '$SRC_DIR/src/fastq_quality_trimmer' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastq_quality_trimmer.o -MD -MP -MF .deps/fastq_quality_trimmer.Tpo -c -o fastq_quality_trimmer.o fastq_quality_trimmer.c + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastq_quality_trimmer.o -MD -MP -MF .deps/fastq_quality_trimmer.Tpo -c -o fastq_quality_trimmer.o fastq_quality_trimmer.c mv -f .deps/fastq_quality_trimmer.Tpo .deps/fastq_quality_trimmer.Po - /bin/sh ../../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastq_quality_trimmer fastq_quality_trimmer.o ../libfastx/libfastx.a - libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastq_quality_trimmer fastq_quality_trimmer.o -L$PREFIX/lib ../libfastx/libfastx.a - ld: warning: Csu support file -lcrt1.10.6.o not found, changing to target macOS 10.8 where it is not needed - ld: warning: object file (fastq_quality_trimmer.o) was built for newer macOS version (10.9) than being linked (10.8) - ld: warning: object file (../libfastx/libfastx.a(fastx_args.o)) was built for newer macOS version (10.9) than being linked (10.8) - ld: warning: object file (../libfastx/libfastx.a(fastx.o)) was built for newer macOS version (10.9) than being linked (10.8) - ld: warning: object file (../libfastx/libfastx.a(chomp.o)) was built for newer macOS version (10.9) than being linked (10.8) + /bin/sh ../../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o fastq_quality_trimmer fastq_quality_trimmer.o ../libfastx/libfastx.a + libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath -Wl,$PREFIX/lib -o fastq_quality_trimmer fastq_quality_trimmer.o -L$PREFIX/lib ../libfastx/libfastx.a make[3]: Leaving directory '$SRC_DIR/src/fastq_quality_trimmer' Making all in fastx_artifacts_filter make[3]: Entering directory '$SRC_DIR/src/fastx_artifacts_filter' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx_artifacts_filter.o -MD -MP -MF .deps/fastx_artifacts_filter.Tpo -c -o fastx_artifacts_filter.o fastx_artifacts_filter.c - fastx_artifacts_filter.c:58:6: error: variable 'n_count' set but not used [-Werror,-Wunused-but-set-variable] - int n_count=0; - ^ - 1 error generated. - make[3]: *** [Makefile:405: fastx_artifacts_filter.o] Error 1 + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fastx_toolkit-0.0.14 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx_artifacts_filter.o -MD -MP -MF .deps/fastx_artifacts_filter.Tpo -c -o fastx_artifacts_filter.o fastx_artifacts_filter.c make[3]: Leaving directory '$SRC_DIR/src/fastx_artifacts_filter' - make[2]: *** [Makefile:373: all-recursive] Error 1 make[2]: Leaving directory '$SRC_DIR/src' - make[1]: *** [Makefile:411: all-recursive] Error 1 make[1]: Leaving directory '$SRC_DIR' - make: *** [Makefile:342: all] Error 2 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/fastx_toolkit_1685402222617/work/conda_build.sh']' returned non-zero exit status 2. # Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/fastx_toolkit/meta.yaml b/recipes/fastx_toolkit/meta.yaml index 827887430a03c..a24945a75d1ec 100644 --- a/recipes/fastx_toolkit/meta.yaml +++ b/recipes/fastx_toolkit/meta.yaml @@ -10,7 +10,7 @@ source: build: preserve_egg_dir: True - number: 11 + number: 12 requirements: build: diff --git a/recipes/fec/meta.yaml b/recipes/fec/meta.yaml index 9a6edf21022fc..76e4434f9fc2f 100644 --- a/recipes/fec/meta.yaml +++ b/recipes/fec/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 skip: True # [osx] requirements: diff --git a/recipes/fegenie/meta.yaml b/recipes/fegenie/meta.yaml index 4a7bcb6527205..ecd435e95c72b 100644 --- a/recipes/fegenie/meta.yaml +++ b/recipes/fegenie/meta.yaml @@ -14,7 +14,7 @@ source: build: noarch: generic - number: 4 + number: 5 requirements: host: diff --git a/recipes/fermi-lite/meta.yaml b/recipes/fermi-lite/meta.yaml index d41d999a582ff..607c65626b64c 100644 --- a/recipes/fermi-lite/meta.yaml +++ b/recipes/fermi-lite/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 7 + number: 8 run_exports: - {{ pin_subpackage('fermi-lite', max_pin='x.x') }} diff --git a/recipes/fermi/meta.yaml b/recipes/fermi/meta.yaml index 6b9179c396a55..8f52309d6bcd6 100644 --- a/recipes/fermi/meta.yaml +++ b/recipes/fermi/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.1_r751_beta" build: - number: 8 + number: 9 source: url: https://github.com/lh3/fermi/archive/01cfc0750e654130670846728937076dedfe97b7.tar.gz diff --git a/recipes/fermi2/meta.yaml b/recipes/fermi2/meta.yaml index 6ea3c9f39c9e7..05289623e4a9a 100644 --- a/recipes/fermi2/meta.yaml +++ b/recipes/fermi2/meta.yaml @@ -3,7 +3,7 @@ package: version: "r193" build: - number: 8 + number: 9 run_exports: - {{ pin_subpackage('fermi2', max_pin="x.x.x") }} @@ -37,4 +37,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/fermi2/r170/meta.yaml b/recipes/fermi2/r170/meta.yaml index a0e28c692bd84..bf4a4684fab24 100644 --- a/recipes/fermi2/r170/meta.yaml +++ b/recipes/fermi2/r170/meta.yaml @@ -3,7 +3,7 @@ package: version: "r170" build: - number: 3 + number: 4 source: url: https://github.com/lh3/fermi2/archive/1acdb2ec8fdb7e62bbfd4af5f5cc31469420729d.tar.gz diff --git a/recipes/ffindex/meta.yaml b/recipes/ffindex/meta.yaml index dfabbdef7770c..156e359be9f57 100644 --- a/recipes/ffindex/meta.yaml +++ b/recipes/ffindex/meta.yaml @@ -7,7 +7,7 @@ source: sha256: d1157ad124ae8452eb1028bcc41aa17f1636014972d628dd3e35fac0df2b93f9 build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/fgwas/build_failure.osx-64.yaml b/recipes/fgwas/build_failure.osx-64.yaml deleted file mode 100644 index c5f48d34786a1..0000000000000 --- a/recipes/fgwas/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 8b62cd09c38784d905fc61d00ce481d2b3a6035ab91957aa6f89fd5e77381237 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fgwas-0.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/fgwas_1717522745650/work/conda_build.sh']' returned non-zero exit status 2. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fgwas-0.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fgwas-0.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fgwas-0.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - checking whether the C compiler works... yes - checking for C compiler default output file name... a.out - checking for suffix of executables... - checking whether we are cross compiling... no - checking for suffix of object files... o - checking whether we are using the GNU C compiler... yes - checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes - checking for a BSD-compatible install... /usr/bin/install -c - checking whether build environment is sane... yes - checking for a thread-safe mkdir -p... ./install-sh -c -d - checking for gawk... no - checking for mawk... no - checking for nawk... no - checking for awk... awk - checking whether make sets $(MAKE)... yes - checking for style of include used by make... GNU - checking whether make supports nested variables... yes - checking how to create a pax tar archive... gnutar - checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 - checking for boostlib >= 1.42... yes - checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang - checking whether we are using the GNU C compiler... yes - checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes - checking for x86_64-apple-darwin13.4.0-clang option to accept ISO C89... none needed - checking whether x86_64-apple-darwin13.4.0-clang understands -c and -o together... yes - checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 - checking for gzopen in -lz... yes - checking for cos in -lm... yes - checking for cblas_dgemm in -lgslcblas... yes - checking for gsl_blas_dgemm in -lgsl... yes - checking that generated files are newer than configure... done - configure: creating ./config.status - config.status: creating Makefile - config.status: creating src/Makefile - config.status: creating config.h - config.status: config.h is unchanged - config.status: executing depfiles commands - make all-recursive - make[1]: Entering directory '$SRC_DIR' - Making all in src - make[2]: Entering directory '$SRC_DIR/src' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fgwas-0.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT CmdLine.o -MD -MP -MF .deps/CmdLine.Tpo -c -o CmdLine.o CmdLine.cpp - mv -f .deps/CmdLine.Tpo .deps/CmdLine.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fgwas-0.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT fgwas.o -MD -MP -MF .deps/fgwas.Tpo -c -o fgwas.o fgwas.cpp - mv -f .deps/fgwas.Tpo .deps/fgwas.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fgwas-0.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT gzstream.o -MD -MP -MF .deps/gzstream.Tpo -c -o gzstream.o gzstream.cpp - make[2]: Leaving directory '$SRC_DIR/src' - make[1]: Leaving directory '$SRC_DIR' -# Last 100 lines of the build log. diff --git a/recipes/fgwas/meta.yaml b/recipes/fgwas/meta.yaml index 484d67530cf7b..687957252b5cc 100644 --- a/recipes/fgwas/meta.yaml +++ b/recipes/fgwas/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 40340e7589a4965ad9f216f9f27d6b3ac72aadcc74e585652b1ea2993f580b61 build: - number: 8 + number: 9 requirements: build: diff --git a/recipes/fido/meta.yaml b/recipes/fido/meta.yaml index 98053c0117123..35f31b5123d0c 100644 --- a/recipes/fido/meta.yaml +++ b/recipes/fido/meta.yaml @@ -7,7 +7,7 @@ source: md5: 6ee89316f492105a6fb06729475c37e0 build: - number: 7 + number: 8 skip: True # [osx] run_exports: - {{ pin_subpackage('fido', max_pin='x') }} diff --git a/recipes/filtlong/build_failure.linux-64.yaml b/recipes/filtlong/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..4ab78404356c4 --- /dev/null +++ b/recipes/filtlong/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 112705d33b4bf30cd5f287df1b12ff897fd101f9c01044262a1c7d1e23d0d79d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + 170 | bool Kmers::is_kmer_present(uint32_t kmer) { + | ^~~~~~~~ + src/kmers.cpp:170:29: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + src/kmers.cpp:176:1: error: 'uint32_t' does not name a type + 176 | uint32_t Kmers::base_to_bits_forward(char base) { + | ^~~~~~~~ + src/kmers.cpp:176:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + src/kmers.cpp:199:1: error: 'uint32_t' does not name a type + 199 | uint32_t Kmers::base_to_bits_reverse(char base) { + | ^~~~~~~~ + src/kmers.cpp:199:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + src/kmers.cpp:222:1: error: 'uint32_t' does not name a type + 222 | uint32_t Kmers::starting_kmer_to_bits_forward(char * sequence) { + | ^~~~~~~~ + src/kmers.cpp:222:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + src/kmers.cpp:232:1: error: 'uint32_t' does not name a type + 232 | uint32_t Kmers::starting_kmer_to_bits_reverse(char * sequence) { + | ^~~~~~~~ + src/kmers.cpp:232:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + In file included from src/read.h:25, + from src/main.cpp:27: + src/kmers.h:37:26: error: 'uint32_t' has not been declared + 37 | bool is_kmer_present(uint32_t kmer); + | ^~~~~~~~ + src/kmers.h:39:5: error: 'uint32_t' does not name a type + 39 | uint32_t starting_kmer_to_bits_forward(char * sequence); + | ^~~~~~~~ + src/kmers.h:25:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + 24 | #include "bloom_filter.h" + |#include + 25 | + src/kmers.h:40:5: error: 'uint32_t' does not name a type + 40 | uint32_t starting_kmer_to_bits_reverse(char * sequence); + | ^~~~~~~~ + src/kmers.h:40:5: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + src/kmers.h:42:5: error: 'uint32_t' does not name a type + 42 | uint32_t base_to_bits_forward(char base); + | ^~~~~~~~ + src/kmers.h:42:5: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + src/kmers.h:43:5: error: 'uint32_t' does not name a type + 43 | uint32_t base_to_bits_reverse(char base); + | ^~~~~~~~ + src/kmers.h:43:5: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + src/kmers.h:46:24: error: 'uint32_t' was not declared in this scope + 46 | std::unordered_set m_kmers; + | ^~~~~~~~ + src/kmers.h:46:24: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + src/kmers.h:46:32: error: template argument 1 is invalid + 46 | std::unordered_set m_kmers; + | ^ + src/kmers.h:46:32: error: template argument 2 is invalid + src/kmers.h:46:32: error: template argument 3 is invalid + src/kmers.h:46:32: error: template argument 4 is invalid + src/kmers.h:47:24: error: 'uint32_t' was not declared in this scope + 47 | std::unordered_map m_kmer_counts; + | ^~~~~~~~ + src/kmers.h:47:24: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + src/kmers.h:47:37: error: template argument 1 is invalid + 47 | std::unordered_map m_kmer_counts; + | ^ + src/kmers.h:47:37: error: template argument 3 is invalid + src/kmers.h:47:37: error: template argument 4 is invalid + src/kmers.h:47:37: error: template argument 5 is invalid + src/kmers.h:52:36: error: 'uint32_t' has not been declared + 52 | void add_kmer_require_one_copy(uint32_t kmer); + | ^~~~~~~~ + src/kmers.h:53:43: error: 'uint32_t' has not been declared + 53 | void add_kmer_require_multiple_copies(uint32_t kmer); + | ^~~~~~~~ + src/kmers.h: In member function 'bool Kmers::empty()': + src/kmers.h:33:34: error: request for member 'size' in '((Kmers*)this)->Kmers::m_kmers', which is of non-class type 'int' + 33 | bool empty() {return m_kmers.size() == 0;} + | ^~~~ + make: *** [Makefile:49: src/kmers.o] Error 1 + make: *** Waiting for unfinished jobs.... + make: *** [Makefile:49: src/read.o] Error 1 + make: *** [Makefile:49: src/main.o] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/filtlong_1734129325473/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/filtlong_1734129325473/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/filtlong/build_failure.linux-aarch64.yaml b/recipes/filtlong/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..29f1ddda44647 --- /dev/null +++ b/recipes/filtlong/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 112705d33b4bf30cd5f287df1b12ff897fd101f9c01044262a1c7d1e23d0d79d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + 81 | void (Kmers::*add_kmer)(uint32_t); + | ^ + src/kmers.cpp:83:20: error: cannot convert 'void (Kmers::*)(int)' to 'void Kmers::*' in assignment + 83 | add_kmer = &Kmers::add_kmer_require_multiple_copies; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + src/kmers.cpp:85:20: error: cannot convert 'void (Kmers::*)(int)' to 'void Kmers::*' in assignment + 85 | add_kmer = &Kmers::add_kmer_require_one_copy; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + src/kmers.cpp:106:13: error: 'forward_kmer' was not declared in this scope + 106 | forward_kmer = starting_kmer_to_bits_forward(sequence); + | ^~~~~~~~~~~~ + src/kmers.cpp:106:28: error: 'starting_kmer_to_bits_forward' was not declared in this scope + 106 | forward_kmer = starting_kmer_to_bits_forward(sequence); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + src/kmers.cpp:107:13: error: 'reverse_kmer' was not declared in this scope + 107 | reverse_kmer = starting_kmer_to_bits_reverse(sequence); + | ^~~~~~~~~~~~ + src/kmers.cpp:107:28: error: 'starting_kmer_to_bits_reverse' was not declared in this scope + 107 | reverse_kmer = starting_kmer_to_bits_reverse(sequence); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + src/kmers.cpp:109:21: error: 'void*' is not a pointer-to-object type + 109 | (this->*add_kmer)(forward_kmer); + | ^~~~~~~~ + src/kmers.cpp:110:21: error: 'void*' is not a pointer-to-object type + 110 | (this->*add_kmer)(reverse_kmer); + | ^~~~~~~~ + src/kmers.cpp:114:33: error: 'base_to_bits_forward' was not declared in this scope + 114 | forward_kmer |= base_to_bits_forward(sequence[i]); + | ^~~~~~~~~~~~~~~~~~~~ + src/kmers.cpp:117:33: error: 'base_to_bits_reverse' was not declared in this scope + 117 | reverse_kmer |= base_to_bits_reverse(sequence[i]); + | ^~~~~~~~~~~~~~~~~~~~ + src/kmers.cpp:119:25: error: 'void*' is not a pointer-to-object type + 119 | (this->*add_kmer)(forward_kmer); + | ^~~~~~~~ + src/kmers.cpp:120:25: error: 'void*' is not a pointer-to-object type + 120 | (this->*add_kmer)(reverse_kmer); + | ^~~~~~~~ + src/kmers.cpp: At global scope: + src/kmers.cpp:137:6: error: variable or field 'add_kmer_require_one_copy' declared void + 137 | void Kmers::add_kmer_require_one_copy(uint32_t kmer) { + | ^~~~~ + src/kmers.cpp:137:39: error: 'uint32_t' was not declared in this scope + 137 | void Kmers::add_kmer_require_one_copy(uint32_t kmer) { + | ^~~~~~~~ + src/kmers.cpp:137:39: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + src/kmers.cpp:142:6: error: variable or field 'add_kmer_require_multiple_copies' declared void + 142 | void Kmers::add_kmer_require_multiple_copies(uint32_t kmer) { + | ^~~~~ + src/kmers.cpp:142:46: error: 'uint32_t' was not declared in this scope + 142 | void Kmers::add_kmer_require_multiple_copies(uint32_t kmer) { + | ^~~~~~~~ + src/kmers.cpp:142:46: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + src/kmers.cpp:170:6: error: 'bool Kmers::is_kmer_present' is not a static data member of 'class Kmers' + 170 | bool Kmers::is_kmer_present(uint32_t kmer) { + | ^~~~~ + src/kmers.cpp:170:29: error: 'uint32_t' was not declared in this scope + 170 | bool Kmers::is_kmer_present(uint32_t kmer) { + | ^~~~~~~~ + src/kmers.cpp:170:29: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + src/kmers.cpp:176:1: error: 'uint32_t' does not name a type + 176 | uint32_t Kmers::base_to_bits_forward(char base) { + | ^~~~~~~~ + src/kmers.cpp:176:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + src/kmers.cpp:199:1: error: 'uint32_t' does not name a type + 199 | uint32_t Kmers::base_to_bits_reverse(char base) { + | ^~~~~~~~ + src/kmers.cpp:199:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + src/kmers.cpp:222:1: error: 'uint32_t' does not name a type + 222 | uint32_t Kmers::starting_kmer_to_bits_forward(char * sequence) { + | ^~~~~~~~ + src/kmers.cpp:222:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + src/kmers.cpp:232:1: error: 'uint32_t' does not name a type + 232 | uint32_t Kmers::starting_kmer_to_bits_reverse(char * sequence) { + | ^~~~~~~~ + src/kmers.cpp:232:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + make: *** [Makefile:49: src/kmers.o] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/filtlong_1734016252554/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/filtlong_1734016252554/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/filtlong/meta.yaml b/recipes/filtlong/meta.yaml index d6169fac82ae5..6153064960091 100644 --- a/recipes/filtlong/meta.yaml +++ b/recipes/filtlong/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -36,4 +36,4 @@ about: extra: additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 diff --git a/recipes/finemap/meta.yaml b/recipes/finemap/meta.yaml index 10b7b977ddad4..b2c7e7d8f04a3 100644 --- a/recipes/finemap/meta.yaml +++ b/recipes/finemap/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 3b1fc6eb3c2ccafd647b32e02d0244495cd0ade9ed7d474606c31ebf6e98b0c9 build: - number: 0 + number: 1 # skip osx since binary cannot be relinked b/c it was built without the -headerpad_max_install_names option skip: True # [not linux64] run_exports: diff --git a/recipes/fineradstructure/meta.yaml b/recipes/fineradstructure/meta.yaml index 138f451ef33cd..b8d1ccd8e0809 100644 --- a/recipes/fineradstructure/meta.yaml +++ b/recipes/fineradstructure/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 6 + number: 7 skip: True # [osx] source: diff --git a/recipes/fingerprintscan/build_failure.osx-64.yaml b/recipes/fingerprintscan/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..9c3c9b5b4ebad --- /dev/null +++ b/recipes/fingerprintscan/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: f8a3940778c76666d1a71de115a5854c8d8264caf82b52728025c75bd48f9b05 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fingerprintscan-3_597 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fingerprintscan-3_597 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fingerprintscan-3_597 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + checking for a BSD-compatible install... /usr/bin/install -c + checking whether build environment is sane... yes + checking for gawk... no + checking for mawk... no + checking for nawk... no + checking for awk... awk + checking whether make sets $(MAKE)... yes + checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang + checking for C compiler default output file name... a.out + checking whether the C compiler works... yes + checking whether we are cross compiling... no + checking for suffix of executables... + checking for suffix of object files... o + checking whether we are using the GNU C compiler... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking for x86_64-apple-darwin13.4.0-clang option to accept ISO C89... none needed + checking for style of include used by make... GNU + checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 + checking whether we are using the GNU C compiler... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 + checking whether the compiler implements namespaces... yes + checking whether the compiler supports ISO C standard library... yes + checking whether the compiler supports Standard Template Library... yes + checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang-cpp + checking for grep that handles long lines and -e... /usr/bin/grep + checking for egrep... /usr/bin/grep -E + checking for ANSI C header files... yes + checking for sys/types.h... yes + checking for sys/stat.h... yes + checking for stdlib.h... yes + checking for string.h... yes + checking for memory.h... yes + checking for strings.h... yes + checking for inttypes.h... yes + checking for stdint.h... yes + checking for unistd.h... yes + checking time.h usability... yes + checking time.h presence... yes + checking for time.h... yes + checking for x86_64-apple-darwin13.4.0-strip... x86_64-apple-darwin13.4.0-strip + configure: creating ./config.status + config.status: creating Makefile + config.status: executing depfiles commands + checking dependency style of x86_64-apple-darwin13.4.0-clang... (cached) gcc3 + checking dependency style of x86_64-apple-darwin13.4.0-clang... (cached) gcc3 + checking for x86_64-apple-darwin13.4.0-gcc... (cached) x86_64-apple-darwin13.4.0-clang + checking whether we are using the GNU C compiler... (cached) yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... (cached) yes + checking for x86_64-apple-darwin13.4.0-clang option to accept ISO C89... (cached) none needed + checking dependency style of x86_64-apple-darwin13.4.0-clang... (cached) gcc3 + if x86_64-apple-darwin13.4.0-clang -DPACKAGE_NAME=\"fingerPRINTScan\" -DPACKAGE_TARNAME=\"fingerprintscan\" -DPACKAGE_VERSION=\"3.5.95-r1\ scordis@bioinf.man.ac.uk\" -DPACKAGE_STRING=\"fingerPRINTScan\ 3.5.95-r1\ scordis@bioinf.man.ac.uk\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"fingerprintscan\" -DVERSION=\"3.5.95-r1\ scordis@bioinf.man.ac.uk\" -DHAVE_NAMESPACES= -DHAVE_STD= -DHAVE_STL= -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_TIME_H=1 -I. -I. -I$PREFIX/include -Wno-write-strings -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fingerprintscan-3_597 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT mystring.o -MD -MP -MF ".deps/mystring.Tpo" -c -o mystring.o mystring.cc; \ + then mv -f ".deps/mystring.Tpo" ".deps/mystring.Po"; else rm -f ".deps/mystring.Tpo"; exit 1; fi + if x86_64-apple-darwin13.4.0-clang -DPACKAGE_NAME=\"fingerPRINTScan\" -DPACKAGE_TARNAME=\"fingerprintscan\" -DPACKAGE_VERSION=\"3.5.95-r1\ scordis@bioinf.man.ac.uk\" -DPACKAGE_STRING=\"fingerPRINTScan\ 3.5.95-r1\ scordis@bioinf.man.ac.uk\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"fingerprintscan\" -DVERSION=\"3.5.95-r1\ scordis@bioinf.man.ac.uk\" -DHAVE_NAMESPACES= -DHAVE_STD= -DHAVE_STL= -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_TIME_H=1 -I. -I. -I$PREFIX/include -Wno-write-strings -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fingerprintscan-3_597 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT Score.o -MD -MP -MF ".deps/Score.Tpo" -c -o Score.o Score.cc; \ + then mv -f ".deps/Score.Tpo" ".deps/Score.Po"; else rm -f ".deps/Score.Tpo"; exit 1; fi + if x86_64-apple-darwin13.4.0-clang -DPACKAGE_NAME=\"fingerPRINTScan\" -DPACKAGE_TARNAME=\"fingerprintscan\" -DPACKAGE_VERSION=\"3.5.95-r1\ scordis@bioinf.man.ac.uk\" -DPACKAGE_STRING=\"fingerPRINTScan\ 3.5.95-r1\ scordis@bioinf.man.ac.uk\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"fingerprintscan\" -DVERSION=\"3.5.95-r1\ scordis@bioinf.man.ac.uk\" -DHAVE_NAMESPACES= -DHAVE_STD= -DHAVE_STL= -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_TIME_H=1 -I. -I. -I$PREFIX/include -Wno-write-strings -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fingerprintscan-3_597 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT Sequence_database.o -MD -MP -MF ".deps/Sequence_database.Tpo" -c -o Sequence_database.o Sequence_database.cc; \ + then mv -f ".deps/Sequence_database.Tpo" ".deps/Sequence_database.Po"; else rm -f ".deps/Sequence_database.Tpo"; exit 1; fi +# Last 100 lines of the build log. diff --git a/recipes/fingerprintscan/meta.yaml b/recipes/fingerprintscan/meta.yaml index 2f2727523bcb9..0541d17c3c3c7 100644 --- a/recipes/fingerprintscan/meta.yaml +++ b/recipes/fingerprintscan/meta.yaml @@ -13,7 +13,7 @@ source: - patch1 build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/flash2/meta.yaml b/recipes/flash2/meta.yaml index 9625cc56129a6..9285687d67345 100644 --- a/recipes/flash2/meta.yaml +++ b/recipes/flash2/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 6 + number: 7 source: url: https://github.com/dstreett/FLASH2/archive/{{ version }}.tar.gz diff --git a/recipes/flexbar/meta.yaml b/recipes/flexbar/meta.yaml index 144bc25671b0b..bd5234600a547 100644 --- a/recipes/flexbar/meta.yaml +++ b/recipes/flexbar/meta.yaml @@ -13,7 +13,7 @@ source: - onetbb.patch build: - number: 10 + number: 11 requirements: build: diff --git a/recipes/flexiplex/meta.yaml b/recipes/flexiplex/meta.yaml index 38167cafd3d3e..bfc322419dc2d 100644 --- a/recipes/flexiplex/meta.yaml +++ b/recipes/flexiplex/meta.yaml @@ -9,7 +9,7 @@ source: sha256: a5b3391aded069e15422a0c201d94ca1fdc02e9fec488608b082ff2f43ca3ec7 build: - number: 1 + number: 2 entry_points: - flexiplex-filter = flexiplex_filter.main:cli run_exports: diff --git a/recipes/flexserv/meta.yaml b/recipes/flexserv/meta.yaml index 601e9ae07f37a..16f3e77158037 100644 --- a/recipes/flexserv/meta.yaml +++ b/recipes/flexserv/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 14a1a62b8b0007241975f6964dce2e883b8f86796bc476af07a832413abb7b49 build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/flopp/build_failure.linux-64.yaml b/recipes/flopp/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..fb5029987ff15 --- /dev/null +++ b/recipes/flopp/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: bae31bf67e7e036baac5d5fd4dbf402b9175e4f083083a9fd4640235a68454f8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + cargo:rerun-if-env-changed=AR_x86_64-unknown-linux-gnu + AR_x86_64-unknown-linux-gnu = None + cargo:rerun-if-env-changed=AR_x86_64_unknown_linux_gnu + AR_x86_64_unknown_linux_gnu = None + cargo:rerun-if-env-changed=HOST_AR + HOST_AR = None + cargo:rerun-if-env-changed=AR + AR = Some(/opt/conda/conda-bld/flopp_1733852626676/_build_env/bin/x86_64-conda-linux-gnu-ar) + cargo:rerun-if-env-changed=ARFLAGS_x86_64-unknown-linux-gnu + ARFLAGS_x86_64-unknown-linux-gnu = None + cargo:rerun-if-env-changed=ARFLAGS_x86_64_unknown_linux_gnu + ARFLAGS_x86_64_unknown_linux_gnu = None + cargo:rerun-if-env-changed=HOST_ARFLAGS + HOST_ARFLAGS = None + cargo:rerun-if-env-changed=ARFLAGS + ARFLAGS = None + cargo:rustc-link-lib=static=hts + cargo:rustc-link-search=native=/opt/conda/conda-bld/flopp_1733852626676/work/target/release/build/hts-sys-20b0b0fae09bea42/out + + --- stderr + thread 'main' panicked at /opt/conda/conda-bld/flopp_1733852626676/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/bindgen-0.69.5/lib.rs:622:31: + Unable to find libclang: "couldn't find any valid shared libraries matching: ['libclang.so', 'libclang-*.so', 'libclang.so.*', 'libclang-*.so.*'], set the LIBCLANG_PATH environment variable to a path where one of these files can be found (invalid: [])" + stack backtrace: + 0: rust_begin_unwind + 1: core::panicking::panic_fmt + 2: core::result::unwrap_failed + 3: core::result::Result::expect + 4: core::ops::function::FnOnce::call_once + 5: lazy_static::lazy::Lazy::get::{{closure}} + 6: std::sync::once::Once::call_once::{{closure}} + 7: std::sys::sync::once::futex::Once::call + 8: std::sync::once::Once::call_once + 9: ::deref + 10: bindgen::ensure_libclang_is_loaded + 11: bindgen::Bindings::generate + 12: bindgen::Builder::generate + 13: build_script_build::main + 14: core::ops::function::FnOnce::call_once + note: Some details are omitted, run with RUST_BACKTRACE=full for a verbose backtrace. + error: failed to compile flopp v0.2.0 (/opt/conda/conda-bld/flopp_1733852626676/work), intermediate artifacts can be found at /opt/conda/conda-bld/flopp_1733852626676/work/target. + To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/flopp_1733852626676/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/flopp_1733852626676/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. diff --git a/recipes/flopp/meta.yaml b/recipes/flopp/meta.yaml index 83083d68a75bd..90b43b7972146 100644 --- a/recipes/flopp/meta.yaml +++ b/recipes/flopp/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('flopp', max_pin="x") }} diff --git a/recipes/floria/build_failure.linux-64.yaml b/recipes/floria/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..b84c1690d9a8f --- /dev/null +++ b/recipes/floria/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 9f3a8c493a49d026bc349c30b71c5eccd96a9ada290ba6713c1cad1032ab3229 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + cargo:rerun-if-env-changed=AR_x86_64-unknown-linux-gnu + AR_x86_64-unknown-linux-gnu = None + cargo:rerun-if-env-changed=AR_x86_64_unknown_linux_gnu + AR_x86_64_unknown_linux_gnu = None + cargo:rerun-if-env-changed=HOST_AR + HOST_AR = None + cargo:rerun-if-env-changed=AR + AR = Some(/opt/conda/conda-bld/floria_1734188059116/_build_env/bin/x86_64-conda-linux-gnu-ar) + cargo:rerun-if-env-changed=ARFLAGS_x86_64-unknown-linux-gnu + ARFLAGS_x86_64-unknown-linux-gnu = None + cargo:rerun-if-env-changed=ARFLAGS_x86_64_unknown_linux_gnu + ARFLAGS_x86_64_unknown_linux_gnu = None + cargo:rerun-if-env-changed=HOST_ARFLAGS + HOST_ARFLAGS = None + cargo:rerun-if-env-changed=ARFLAGS + ARFLAGS = None + cargo:rustc-link-lib=static=hts + cargo:rustc-link-search=native=/opt/conda/conda-bld/floria_1734188059116/work/target/release/build/hts-sys-2659d1b3f174ec70/out + + --- stderr + thread 'main' panicked at /opt/conda/conda-bld/floria_1734188059116/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/bindgen-0.69.5/lib.rs:622:31: + Unable to find libclang: "couldn't find any valid shared libraries matching: ['libclang.so', 'libclang-*.so', 'libclang.so.*', 'libclang-*.so.*'], set the LIBCLANG_PATH environment variable to a path where one of these files can be found (invalid: [])" + stack backtrace: + 0: rust_begin_unwind + 1: core::panicking::panic_fmt + 2: core::result::unwrap_failed + 3: core::result::Result::expect + 4: core::ops::function::FnOnce::call_once + 5: lazy_static::lazy::Lazy::get::{{closure}} + 6: std::sync::once::Once::call_once::{{closure}} + 7: std::sys::sync::once::futex::Once::call + 8: std::sync::once::Once::call_once + 9: ::deref + 10: bindgen::ensure_libclang_is_loaded + 11: bindgen::Bindings::generate + 12: bindgen::Builder::generate + 13: build_script_build::main + 14: core::ops::function::FnOnce::call_once + note: Some details are omitted, run with RUST_BACKTRACE=full for a verbose backtrace. + error: failed to compile floria v0.0.1 (/opt/conda/conda-bld/floria_1734188059116/work), intermediate artifacts can be found at /opt/conda/conda-bld/floria_1734188059116/work/target. + To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/floria_1734188059116/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/floria_1734188059116/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. diff --git a/recipes/floria/meta.yaml b/recipes/floria/meta.yaml index ff7c268607c96..95de3c630e015 100644 --- a/recipes/floria/meta.yaml +++ b/recipes/floria/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('floria', max_pin="x") }} diff --git a/recipes/flye/meta.yaml b/recipes/flye/meta.yaml index 74f66f83a7c9b..b610512d2a7bc 100644 --- a/recipes/flye/meta.yaml +++ b/recipes/flye/meta.yaml @@ -13,7 +13,7 @@ source: - 0001-Makefile-aarch64.patch build: - number: 1 + number: 2 entry_points: - flye = flye.main:main run_exports: @@ -29,7 +29,7 @@ requirements: - zlib run: - python - - setuptools # [osx and arm64] + - setuptools # [osx] test: commands: diff --git a/recipes/fmlrc/meta.yaml b/recipes/fmlrc/meta.yaml index 3bba318ded12b..3a11c0b200146 100644 --- a/recipes/fmlrc/meta.yaml +++ b/recipes/fmlrc/meta.yaml @@ -9,7 +9,7 @@ source: sha256: "d8f1a25c8da3f24e9d4c933947283c06cd9764d7c55a35f9e2bca7bdfcb1b30b" build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/fmsi/meta.yaml b/recipes/fmsi/meta.yaml index a8ed730318cfc..526a63bac2c50 100644 --- a/recipes/fmsi/meta.yaml +++ b/recipes/fmsi/meta.yaml @@ -12,7 +12,7 @@ source: - 0001-Makefile.patch build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('fmsi', max_pin="x.x") }} diff --git a/recipes/foldcomp/meta.yaml b/recipes/foldcomp/meta.yaml index 445c78bf0891f..bd7ac646391fe 100644 --- a/recipes/foldcomp/meta.yaml +++ b/recipes/foldcomp/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('foldcomp', max_pin="x.x") }} diff --git a/recipes/foldseek/meta.yaml b/recipes/foldseek/meta.yaml index 1c7ed4957e7f1..95c7b3d86a8cd 100644 --- a/recipes/foldseek/meta.yaml +++ b/recipes/foldseek/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version|replace("-", ".") }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('foldseek', max_pin="x") }} diff --git a/recipes/fpa/meta.yaml b/recipes/fpa/meta.yaml index bfb57239a846b..94532d4996f5d 100644 --- a/recipes/fpa/meta.yaml +++ b/recipes/fpa/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/fpa/v0.4/meta.yaml b/recipes/fpa/v0.4/meta.yaml index 35140cdf92a42..fae48040f5415 100644 --- a/recipes/fpa/v0.4/meta.yaml +++ b/recipes/fpa/v0.4/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 8 + number: 9 requirements: build: diff --git a/recipes/fqgrep/meta.yaml b/recipes/fqgrep/meta.yaml index 013de48317204..b127447e78370 100644 --- a/recipes/fqgrep/meta.yaml +++ b/recipes/fqgrep/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: url: https://github.com/fulcrumgenomics/fqgrep/archive/v{{ version }}.tar.gz diff --git a/recipes/fqtk/meta.yaml b/recipes/fqtk/meta.yaml index 575e3f00fb789..70eed05073afb 100644 --- a/recipes/fqtk/meta.yaml +++ b/recipes/fqtk/meta.yaml @@ -10,7 +10,7 @@ source: sha256: f64598b7493b2c87fe8b17330c137c98eb66e352f3648809e4128ea25f300a2e build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('fqtk', max_pin="x.x") }} diff --git a/recipes/fqtools/meta.yaml b/recipes/fqtools/meta.yaml index 3caa804144dec..163bddbdba8fc 100644 --- a/recipes/fqtools/meta.yaml +++ b/recipes/fqtools/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 13 + number: 14 source: url: https://github.com/alastair-droop/{{ name|lower }}/archive/986e451.tar.gz diff --git a/recipes/fqtrim/build_failure.osx-64.yaml b/recipes/fqtrim/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..a3714baea6ac9 --- /dev/null +++ b/recipes/fqtrim/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: ea91ba426519db9fa0f83fb7bef0bc75fdc1b5d1f0e95760c1c81046dfbe410e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - libxml2 2.13.5 he8ee3e7_1 + - clangxx 18.1.8 default_h179603d_5 + - openssl 3.4.0 hd471939_0 + - clang-18 18.1.8 default_h0c94c6a_5 + host: + - gclib 0.0.1 4 + - libcxx 19.1.5 hf95d169_0 + - libzlib 1.3.1 hd23fc13_2 + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/fqtrim_1733869049413/work/conda_build.sh']' returned non-zero exit status 2. + + - zlib 1.3.1 hd23fc13_2 + run: + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + - libzlib >=1.3.1,<2.0a0 + - libcxx >=18 + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + - gclib + - zlib + test: + commands: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + - fqtrim 2>&1 | grep fqtrim > /dev/null + about: + home: https://ccb.jhu.edu/software/fqtrim/ + license: Artistic License 2.0 + license_file: LICENSE + summary: fqtrim is a versatile stand-alone utility that can be used to trim adapters, + poly-A tails, terminal unknown bases (Ns) and low quality 3' regions in reads + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/fqtrim_1733869049413/work/conda_build.sh']' returned non-zero exit status 2. + from high-throughput next-generation sequencing machines. + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/fqtrim_1733869049413/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/fqtrim_1733869049413/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/fqtrim_1733869049413/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/fqtrim_1733869049413/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fqtrim-0.9.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fqtrim-0.9.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fqtrim-0.9.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fqtrim-0.9.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + x86_64-apple-darwin13.4.0-clang -O2 -DNDEBUG -D_NDEBUG -DNODEBUG -Wall -Wextra -I./gclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fqtrim-0.9.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c gclib/GBase.cpp -o gclib/GBase.o +# Last 100 lines of the build log. diff --git a/recipes/fqtrim/meta.yaml b/recipes/fqtrim/meta.yaml index af20ee08e59df..7ee85f3eed697 100644 --- a/recipes/fqtrim/meta.yaml +++ b/recipes/fqtrim/meta.yaml @@ -7,7 +7,7 @@ source: url: http://ccb.jhu.edu/software/fqtrim/dl/fqtrim-0.9.7.tar.gz build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/fqzcomp/meta.yaml b/recipes/fqzcomp/meta.yaml index f287094194ed9..09141931a865e 100644 --- a/recipes/fqzcomp/meta.yaml +++ b/recipes/fqzcomp/meta.yaml @@ -6,7 +6,7 @@ package: build: skip: True # [osx] - number: 5 + number: 6 source: url: https://sourceforge.net/projects/fqzcomp/files/fqzcomp-{{ version }}.tar.gz diff --git a/recipes/freebayes/build_failure.linux-64.yaml b/recipes/freebayes/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..4167230c2e6db --- /dev/null +++ b/recipes/freebayes/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 9fb71b9bbc73b0b5758470b298cb3c444f136ea63be772fca6fa81cb4d2f0ed0 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + + source tree in: /opt/conda/conda-bld/freebayes_1734577634281/work + export PREFIX=/opt/conda/conda-bld/freebayes_1734577634281/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + export BUILD_PREFIX=/opt/conda/conda-bld/freebayes_1734577634281/_build_env + export SRC_DIR=/opt/conda/conda-bld/freebayes_1734577634281/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + The Meson build system + Version: 1.6.1 + Source dir: $SRC_DIR/freebayes + Build dir: $SRC_DIR/freebayes/build + Build type: native build + Project name: freebayes + Project version: 1.3.8 + C compiler for the host machine: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc (gcc 13.3.0 "x86_64-conda-linux-gnu-cc (conda-forge gcc 13.3.0-1) 13.3.0") + C linker for the host machine: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc ld.bfd 2.43 + C compiler for the host machine: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c (gcc 13.3.0 "x86_64-conda-linux-gnu-c (conda-forge gcc 13.3.0-1) 13.3.0") + C linker for the host machine: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c ld.bfd 2.43 + Host machine cpu family: x86_64 + Host machine cpu: x86_64 + Found pkg-config: YES ($BUILD_PREFIX/bin/pkg-config) 0.29.2 + Did not find CMake 'cmake' + Found CMake: NO + Run-time dependency liblzma found: NO (tried pkgconfig) + + meson.build:26:11: ERROR: Dependency "liblzma" not found, tried pkgconfig + + A full log can be found at $SRC_DIR/freebayes/build/meson-logs/meson-log.txt + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/freebayes_1734577634281/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/freebayes_1734577634281/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/freebayes/build_failure.linux-aarch64.yaml b/recipes/freebayes/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..c71ce44e2770a --- /dev/null +++ b/recipes/freebayes/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 9fb71b9bbc73b0b5758470b298cb3c444f136ea63be772fca6fa81cb4d2f0ed0 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_aarch64_conda_cos7_linux_gnu + build_alias=aarch64-conda-linux-gnu + host_alias=aarch64-conda-linux-gnu + -BUILD=aarch64-conda_cos7-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-aarch64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-g + The Meson build system + Version: 1.6.1 + Source dir: $SRC_DIR/freebayes + Build dir: $SRC_DIR/freebayes/build + Build type: native build + Project name: freebayes + Project version: 1.3.8 + C compiler for the host machine: $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc (gcc 13.3.0 "aarch64-conda-linux-gnu-cc (conda-forge gcc 13.3.0-1) 13.3.0") + C linker for the host machine: $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc ld.bfd 2.43 + C compiler for the host machine: $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c (gcc 13.3.0 "aarch64-conda-linux-gnu-c (conda-forge gcc 13.3.0-1) 13.3.0") + C linker for the host machine: $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c ld.bfd 2.43 + Host machine cpu family: aarch64 + Host machine cpu: aarch64 + Found pkg-config: YES ($BUILD_PREFIX/bin/pkg-config) 0.29.2 + Run-time dependency liblzma found: YES 5.6.3 + Did not find CMake 'cmake' + Found CMake: NO + Run-time dependency libseqlib found: NO (tried pkgconfig and cmake) + Run-time dependency threads found: YES + Run-time dependency zlib found: YES 1.3.1 + Run-time dependency htslib found: YES 1.20 + Compiler for C supports arguments -fpermissive: YES + Compiler for C supports arguments -Wno-reorder: YES + Compiler for C supports arguments -Wno-sign-compare: YES + Compiler for C supports arguments -Wno-unused-variable: YES + Compiler for C supports arguments -Wno-unused-but-set-variable: YES + Program prove found: YES ($PREFIX/bin/prove) + Build targets in project: 4 + + freebayes 1.3.8 + + User defined options + buildtype : release + includedir: $PREFIX/include + libdir : $PREFIX/lib + prefix : $PREFIX + strip : true + + Found ninja-1.12.1 at $BUILD_PREFIX/bin/ninja + [1/47] $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -Ilibcustom_seqlib.a.p -I. -I.. -I$PREFIX/include -I../contrib -I../contrib/SeqLib '-I{PREFIX}/include' -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -std=c17 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -MD -MQ libcustom_seqlib.a.p/contrib_SeqLib_src_ssw_cpp.cpp.o -MF libcustom_seqlib.a.p/contrib_SeqLib_src_ssw_cpp.cpp.o.d -o libcustom_seqlib.a.p/contrib_SeqLib_src_ssw_cpp.cpp.o -c ../contrib/SeqLib/src/ssw_cpp.cpp + [2/47] $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -Ilibcustom_seqlib.a.p -I. -I.. -I$PREFIX/include -I../contrib -I../contrib/SeqLib '-I{PREFIX}/include' -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -std=c17 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -MD -MQ libcustom_seqlib.a.p/contrib_SeqLib_src_BamWriter.cpp.o -MF libcustom_seqlib.a.p/contrib_SeqLib_src_BamWriter.cpp.o.d -o libcustom_seqlib.a.p/contrib_SeqLib_src_BamWriter.cpp.o -c ../contrib/SeqLib/src/BamWriter.cpp + [3/47] $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -Ilibcustom_seqlib.a.p -I. -I.. -I$PREFIX/include -I../contrib -I../contrib/SeqLib '-I{PREFIX}/include' -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -std=c17 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -MD -MQ libcustom_seqlib.a.p/contrib_SeqLib_src_BamHeader.cpp.o -MF libcustom_seqlib.a.p/contrib_SeqLib_src_BamHeader.cpp.o.d -o libcustom_seqlib.a.p/contrib_SeqLib_src_BamHeader.cpp.o -c ../contrib/SeqLib/src/BamHeader.cpp + [4/47] $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Ilibcustom_seqlib.a.p -I. -I.. -I$PREFIX/include -I../contrib -I../contrib/SeqLib -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -O3 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -MD -MQ libcustom_seqlib.a.p/contrib_SeqLib_src_ssw.c.o -MF libcustom_seqlib.a.p/contrib_SeqLib_src_ssw.c.o.d -o libcustom_seqlib.a.p/contrib_SeqLib_src_ssw.c.o -c ../contrib/SeqLib/src/ssw.c + [5/47] $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -Ilibfreebayes_common.a.p -I. -I.. -I../contrib/multichoose -I../contrib/fastahack -I../contrib/smithwaterman -I../src -I../contrib/ttmath -I../contrib -I../contrib/SeqLib -I$PREFIX/include '-I{PREFIX}/include' -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c17 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_AlleleParser.cpp.o -MF libfreebayes_common.a.p/src_AlleleParser.cpp.o.d -o libfreebayes_common.a.p/src_AlleleParser.cpp.o -c ../src/AlleleParser.cpp + FAILED: libfreebayes_common.a.p/src_AlleleParser.cpp.o + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -Ilibfreebayes_common.a.p -I. -I.. -I../contrib/multichoose -I../contrib/fastahack -I../contrib/smithwaterman -I../src -I../contrib/ttmath -I../contrib -I../contrib/SeqLib -I$PREFIX/include '-I{PREFIX}/include' -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c17 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_AlleleParser.cpp.o -MF libfreebayes_common.a.p/src_AlleleParser.cpp.o.d -o libfreebayes_common.a.p/src_AlleleParser.cpp.o -c ../src/AlleleParser.cpp + In file included from ../src/AlleleParser.cpp:1: + ../src/AlleleParser.h:18:10: fatal error: join.h: No such file or directory + 18 | #include "join.h" + | ^~~~~~~~ + compilation terminated. + [6/47] $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -Ilibfreebayes_common.a.p -I. -I.. -I../contrib/multichoose -I../contrib/fastahack -I../contrib/smithwaterman -I../src -I../contrib/ttmath -I../contrib -I../contrib/SeqLib -I$PREFIX/include '-I{PREFIX}/include' -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c17 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_BedReader.cpp.o -MF libfreebayes_common.a.p/src_BedReader.cpp.o.d -o libfreebayes_common.a.p/src_BedReader.cpp.o -c ../src/BedReader.cpp + FAILED: libfreebayes_common.a.p/src_BedReader.cpp.o + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -Ilibfreebayes_common.a.p -I. -I.. -I../contrib/multichoose -I../contrib/fastahack -I../contrib/smithwaterman -I../src -I../contrib/ttmath -I../contrib -I../contrib/SeqLib -I$PREFIX/include '-I{PREFIX}/include' -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c17 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_BedReader.cpp.o -MF libfreebayes_common.a.p/src_BedReader.cpp.o.d -o libfreebayes_common.a.p/src_BedReader.cpp.o -c ../src/BedReader.cpp + In file included from ../src/BedReader.cpp:12: + ../src/BedReader.h:12:10: fatal error: IntervalTree.h: No such file or directory + 12 | #include "IntervalTree.h" + | ^~~~~~~~~~~~~~~~ + compilation terminated. + [7/47] $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -Ilibcustom_seqlib.a.p -I. -I.. -I$PREFIX/include -I../contrib -I../contrib/SeqLib '-I{PREFIX}/include' -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -std=c17 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -MD -MQ libcustom_seqlib.a.p/contrib_SeqLib_src_BamRecord.cpp.o -MF libcustom_seqlib.a.p/contrib_SeqLib_src_BamRecord.cpp.o.d -o libcustom_seqlib.a.p/contrib_SeqLib_src_BamRecord.cpp.o -c ../contrib/SeqLib/src/BamRecord.cpp + [8/47] $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -Ilibcustom_seqlib.a.p -I. -I.. -I$PREFIX/include -I../contrib -I../contrib/SeqLib '-I{PREFIX}/include' -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -std=c17 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -MD -MQ libcustom_seqlib.a.p/contrib_SeqLib_src_BamReader.cpp.o -MF libcustom_seqlib.a.p/contrib_SeqLib_src_BamReader.cpp.o.d -o libcustom_seqlib.a.p/contrib_SeqLib_src_BamReader.cpp.o -c ../contrib/SeqLib/src/BamReader.cpp + [9/47] $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -Ilibfreebayes_common.a.p -I. -I.. -I../contrib/multichoose -I../contrib/fastahack -I../contrib/smithwaterman -I../src -I../contrib/ttmath -I../contrib -I../contrib/SeqLib -I$PREFIX/include '-I{PREFIX}/include' -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c17 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Allele.cpp.o -MF libfreebayes_common.a.p/src_Allele.cpp.o.d -o libfreebayes_common.a.p/src_Allele.cpp.o -c ../src/Allele.cpp + [10/47] $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -Ilibcustom_seqlib.a.p -I. -I.. -I$PREFIX/include -I../contrib -I../contrib/SeqLib '-I{PREFIX}/include' -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -std=c17 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -MD -MQ libcustom_seqlib.a.p/contrib_SeqLib_src_GenomicRegion.cpp.o -MF libcustom_seqlib.a.p/contrib_SeqLib_src_GenomicRegion.cpp.o.d -o libcustom_seqlib.a.p/contrib_SeqLib_src_GenomicRegion.cpp.o -c ../contrib/SeqLib/src/GenomicRegion.cpp + ninja: build stopped: subcommand failed. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/freebayes_1734577658535/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/freebayes_1734577658535/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/freebayes/build_failure.osx-64.yaml b/recipes/freebayes/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..7cd37bebcfaa7 --- /dev/null +++ b/recipes/freebayes/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 9fb71b9bbc73b0b5758470b298cb3c444f136ea63be772fca6fa81cb4d2f0ed0 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - freebayes-parallel + about: + dev_url: https://github.com/freebayes/freebayes + doc_url: https://github.com/freebayes/freebayes/blob/v1.3.8/README.md + home: https://github.com/freebayes/freebayes + license: MIT + license_family: MIT + license_file: freebayes/LICENSE + summary: Bayesian haplotype-based polymorphism discovery and genotyping. + extra: + additional-platforms: + - linux-aarch64 + copy_test_source_files: true + final: true + identifiers: + - biotools:freebayes + - usegalaxy-eu:freebayes + - doi:10.48550/arXiv.1207.3907 + recipe-maintainers: + - jpuritz + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/freebayes_1734608698953/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/freebayes_1734608698953/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/freebayes_1734608698953/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/freebayes_1734608698953/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/freebayes-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + The Meson build system + Version: 1.6.1 + Source dir: $SRC_DIR/freebayes + Build dir: $SRC_DIR/freebayes/build + Build type: native build + Project name: freebayes + Project version: 1.3.8 + C compiler for the host machine: x86_64-apple-darwin13.4.0-clang (clang 18.1.8 "clang version 18.1.8") + C linker for the host machine: x86_64-apple-darwin13.4.0-clang ld64 951.9 + C compiler for the host machine: x86_64-apple-darwin13.4.0-clang (clang 18.1.8 "clang version 18.1.8") + C linker for the host machine: x86_64-apple-darwin13.4.0-clang ld64 951.9 + Host machine cpu family: x86_64 + Host machine cpu: x86_64 + Found pkg-config: YES ($BUILD_PREFIX/bin/pkg-config) 0.29.2 + Found CMake: /usr/local/bin/cmake (3.31.2) + Run-time dependency liblzma found: YES 5.6.3 + Run-time dependency libseqlib found: NO (tried pkgconfig, framework and cmake) + Run-time dependency threads found: YES + Run-time dependency zlib found: YES 1.3.1 + Run-time dependency htslib found: NO (tried pkgconfig, framework and cmake) + + meson.build:69:15: ERROR: Include dir contrib/vcflib/contrib/tabixpp/htslib/ does not exist. + + A full log can be found at $SRC_DIR/freebayes/build/meson-logs/meson-log.txt +# Last 100 lines of the build log. +category: |- + dependency issue diff --git a/recipes/freebayes/meta.yaml b/recipes/freebayes/meta.yaml index 5381e2fb554f3..cc60fcefa48c3 100644 --- a/recipes/freebayes/meta.yaml +++ b/recipes/freebayes/meta.yaml @@ -24,7 +24,7 @@ source: sha256: cc1c04729b0c8ba3647cbb7e15e2b490ce701d73773f30f5892d68c36a1dceae build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage("freebayes", max_pin="x") }} @@ -44,6 +44,7 @@ requirements: - simde - zlib - wfa2-lib + - liblzma run: - parallel - samtools diff --git a/recipes/fsa/meta.yaml b/recipes/fsa/meta.yaml index aa1fa3f79b161..e8e5f9bd26bf1 100644 --- a/recipes/fsa/meta.yaml +++ b/recipes/fsa/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 skip: True # [osx] source: diff --git a/recipes/fsm-lite/meta.yaml b/recipes/fsm-lite/meta.yaml index b76921e017551..e5d4e91fe51fe 100644 --- a/recipes/fsm-lite/meta.yaml +++ b/recipes/fsm-lite/meta.yaml @@ -13,7 +13,7 @@ source: - 0002-CXX-in-Makefile.patch build: - number: 5 + number: 6 skip: true # [win] requirements: diff --git a/recipes/fusioncatcher-seqtk/meta.yaml b/recipes/fusioncatcher-seqtk/meta.yaml index b9547d14bb4fb..a356e9bf69a1d 100644 --- a/recipes/fusioncatcher-seqtk/meta.yaml +++ b/recipes/fusioncatcher-seqtk/meta.yaml @@ -13,7 +13,7 @@ source: - 0001-Makefile-rm-CC-append-CFLGAS-add-CPPFLAGS-add-LDFLAGS.patch build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/fwdpy11/build_failure.osx-64.yaml b/recipes/fwdpy11/build_failure.osx-64.yaml deleted file mode 100644 index 44a2f24f5730e..0000000000000 --- a/recipes/fwdpy11/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 7573cca8e9662cdeecd0bed649c84ff556bc6c8d97e2de79ef5833ea4fc71d50 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - Compiling cbindgen v0.26.0 - Compiling tempfile v3.10.1 - Compiling clap v3.2.25 - Compiling heck v0.4.1 - Compiling log v0.4.21 - error: linking with x86_64-apple-darwin13.4.0-clang failed: exit status: 1 - | - = note: env -u IPHONEOS_DEPLOYMENT_TARGET -u TVOS_DEPLOYMENT_TARGET LC_ALL="C" PATH="/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/bin:/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/.cargo/bin:/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/bin:/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/bin:/opt/mambaforge/envs/bioconda/condabin:/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/bin:/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/bin:/opt/mambaforge/envs/bioconda/bin:/opt/mambaforge/condabin:/opt/mambaforge/bin:/usr/local/lib/ruby/gems/3.0.0/bin:/usr/local/opt/ruby@3.0/bin:/usr/local/opt/pipx_bin:/Users/runner/.cargo/bin:/usr/local/opt/curl/bin:/usr/local/bin:/usr/local/sbin:/Users/runner/bin:/Users/runner/.yarn/bin:/Users/runner/Library/Android/sdk/tools:/Users/runner/Library/Android/sdk/platform-tools:/Library/Frameworks/Python.framework/Versions/Current/bin:/Library/Frameworks/Mono.framework/Versions/Current/Commands:/usr/bin:/bin:/usr/sbin:/sbin:/Users/runner/.dotnet/tools" VSLANG="1033" ZERO_AR_DATE="1" "x86_64-apple-darwin13.4.0-clang" "-Wl,-exported_symbols_list,/tmp/rustcJsKX5w/list" "-arch" "x86_64" "-m64" "/tmp/rustcJsKX5w/symbols.o" "/tmp/cargo-installnrmzCR/release/deps/serde_derive-9f016bff93b5170e.serde_derive.8ad0620eb5003873-cgu.00.rcgu.o" "/tmp/cargo-installnrmzCR/release/deps/serde_derive-9f016bff93b5170e.serde_derive.8ad0620eb5003873-cgu.01.rcgu.o" "/tmp/cargo-installnrmzCR/release/deps/serde_derive-9f016bff93b5170e.serde_derive.8ad0620eb5003873-cgu.02.rcgu.o" "/tmp/cargo-installnrmzCR/release/deps/serde_derive-9f016bff93b5170e.serde_derive.8ad0620eb5003873-cgu.03.rcgu.o" "/tmp/cargo-installnrmzCR/release/deps/serde_derive-9f016bff93b5170e.serde_derive.8ad0620eb5003873-cgu.04.rcgu.o" "/tmp/cargo-installnrmzCR/release/deps/serde_derive-9f016bff93b5170e.serde_derive.8ad0620eb5003873-cgu.05.rcgu.o" "/tmp/cargo-installnrmzCR/release/deps/serde_derive-9f016bff93b5170e.serde_derive.8ad0620eb5003873-cgu.06.rcgu.o" "/tmp/cargo-installnrmzCR/release/deps/serde_derive-9f016bff93b5170e.serde_derive.8ad0620eb5003873-cgu.07.rcgu.o" "/tmp/cargo-installnrmzCR/release/deps/serde_derive-9f016bff93b5170e.serde_derive.8ad0620eb5003873-cgu.08.rcgu.o" "/tmp/cargo-installnrmzCR/release/deps/serde_derive-9f016bff93b5170e.serde_derive.8ad0620eb5003873-cgu.09.rcgu.o" "/tmp/cargo-installnrmzCR/release/deps/serde_derive-9f016bff93b5170e.serde_derive.8ad0620eb5003873-cgu.10.rcgu.o" "/tmp/cargo-installnrmzCR/release/deps/serde_derive-9f016bff93b5170e.serde_derive.8ad0620eb5003873-cgu.11.rcgu.o" "/tmp/cargo-installnrmzCR/release/deps/serde_derive-9f016bff93b5170e.serde_derive.8ad0620eb5003873-cgu.12.rcgu.o" "/tmp/cargo-installnrmzCR/release/deps/serde_derive-9f016bff93b5170e.serde_derive.8ad0620eb5003873-cgu.13.rcgu.o" "/tmp/cargo-installnrmzCR/release/deps/serde_derive-9f016bff93b5170e.serde_derive.8ad0620eb5003873-cgu.14.rcgu.o" "/tmp/cargo-installnrmzCR/release/deps/serde_derive-9f016bff93b5170e.serde_derive.8ad0620eb5003873-cgu.15.rcgu.o" "/tmp/cargo-installnrmzCR/release/deps/serde_derive-9f016bff93b5170e.514q95sj265pstb6.rcgu.rmeta" "/tmp/cargo-installnrmzCR/release/deps/serde_derive-9f016bff93b5170e.o6645hp581cvoef.rcgu.o" "-L" "/tmp/cargo-installnrmzCR/release/deps" "-L" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib" "/private/tmp/cargo-installnrmzCR/release/deps/libsyn-d75fad7b2247b4e5.rlib" "/private/tmp/cargo-installnrmzCR/release/deps/libquote-3ebc22600d494fc7.rlib" "/private/tmp/cargo-installnrmzCR/release/deps/libproc_macro2-443812721a7c3b72.rlib" "/private/tmp/cargo-installnrmzCR/release/deps/libunicode_ident-7eafdde1c7a78df9.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libproc_macro-d9904b6b430ac650.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libstd-2ad7f97be9e16ca5.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libpanic_unwind-8ce93eee8bf4c86e.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libobject-0e1339b212cc7409.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libmemchr-925e672b3deb429c.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libaddr2line-e92d517a950bccd8.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libgimli-de95e5c2a2ace281.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_demangle-37f4c48e230f618e.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libstd_detect-dfeb4bb0652b6b8e.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libhashbrown-0e3ea0ec18336be2.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_std_workspace_alloc-39dd3003e36d7872.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libminiz_oxide-5ea1513e08ee15e0.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libadler-2967159221f4860d.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libunwind-b70656709e3eca11.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcfg_if-cc5626b2e0399737.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/liblibc-8378684dba6ab463.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/liballoc-0ff05b9b25b786cc.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_std_workspace_core-9a6da74aeab39c54.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcore-1638dc700d175798.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcompiler_builtins-7f42af62722c8f43.rlib" "-lSystem" "-lc" "-lm" "-L" "/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib" "-o" "/tmp/cargo-installnrmzCR/release/deps/libserde_derive-9f016bff93b5170e.dylib" "-Wl,-dead_strip" "-dynamiclib" "-Wl,-dylib" "-nodefaultlibs" - = note: ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libproc_macro-d9904b6b430ac650.rlib(proc_macro-d9904b6b430ac650.proc_macro.f7284eae513ccf25-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libstd-2ad7f97be9e16ca5.rlib(std-2ad7f97be9e16ca5.std.73125d0ae810e61b-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcore-1638dc700d175798.rlib(core-1638dc700d175798.core.b1c2fc210f4dfff9-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/liballoc-0ff05b9b25b786cc.rlib(alloc-0ff05b9b25b786cc.alloc.9242d371e396bc4c-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libhashbrown-0e3ea0ec18336be2.rlib(hashbrown-0e3ea0ec18336be2.hashbrown.febebf65344cb99d-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_demangle-37f4c48e230f618e.rlib(rustc_demangle-37f4c48e230f618e.rustc_demangle.9fdffeb2b56169d1-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libgimli-de95e5c2a2ace281.rlib(gimli-de95e5c2a2ace281.gimli.72653df79598dcb2-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libobject-0e1339b212cc7409.rlib(object-0e1339b212cc7409.object.e3756fe3fb577255-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libmemchr-925e672b3deb429c.rlib(memchr-925e672b3deb429c.memchr.4dc4a05d80618598-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libaddr2line-e92d517a950bccd8.rlib(addr2line-e92d517a950bccd8.addr2line.7eb29e6a0a38fefd-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libpanic_unwind-8ce93eee8bf4c86e.rlib(panic_unwind-8ce93eee8bf4c86e.panic_unwind.a3b8ea81b157ee45-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcompiler_builtins-7f42af62722c8f43.rlib(compiler_builtins-7f42af62722c8f43.compiler_builtins.19fed66cffb9e9f5-cgu.089.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - Undefined symbols for architecture x86_64: - "_getentropy", referenced from: - std::sys::pal::unix::rand::hashmap_random_keys::hcc27ed0e9fd421d6 in libstd-2ad7f97be9e16ca5.rlib(std-2ad7f97be9e16ca5.std.73125d0ae810e61b-cgu.0.rcgu.o) - ld: symbol(s) not found for architecture x86_64 - clang-16: error: linker command failed with exit code 1 (use -v to see invocation) - - - error: could not compile serde_derive (lib) due to 1 previous error - warning: build failed, waiting for other jobs to finish... - error: failed to compile cbindgen v0.26.0, intermediate artifacts can be found at /tmp/cargo-installnrmzCR. - To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. - Extracting download - Traceback (most recent call last): - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/work - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fwdpy11-0.22.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fwdpy11-0.22.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fwdpy11-0.22.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/fwdpy11-0.22.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/fwdpy11_1717524874638/work/conda_build.sh']' returned non-zero exit status 101. -# Last 100 lines of the build log. diff --git a/recipes/fwdpy11/meta.yaml b/recipes/fwdpy11/meta.yaml index a08c9d0d69f83..86b3c009e23d2 100644 --- a/recipes/fwdpy11/meta.yaml +++ b/recipes/fwdpy11/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: True # [py < 39 or py > 312] - number: 0 + number: 1 script_env: - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }} entry_points: diff --git a/recipes/fxtract/meta.yaml b/recipes/fxtract/meta.yaml index 0d48cfb32849e..f7d827ead8c33 100644 --- a/recipes/fxtract/meta.yaml +++ b/recipes/fxtract/meta.yaml @@ -14,7 +14,7 @@ source: - Makefile.patch build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/gadem/meta.yaml b/recipes/gadem/meta.yaml index 54b45a700edd1..5fc0558076f53 100644 --- a/recipes/gadem/meta.yaml +++ b/recipes/gadem/meta.yaml @@ -7,7 +7,7 @@ source: sha256: afe89b8d1ecf7d7dc785b9f59ffdfdb511df68c147934eedc0398873fa2640dc build: - number: 7 + number: 8 run_exports: - {{ pin_subpackage('gadem', max_pin="x") }} @@ -28,4 +28,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/galah/meta.yaml b/recipes/galah/meta.yaml index be438161e898a..9e5add19a7746 100644 --- a/recipes/galah/meta.yaml +++ b/recipes/galah/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('galah', max_pin="x.x") }} diff --git a/recipes/galaxy-ml/meta.yaml b/recipes/galaxy-ml/meta.yaml index 9fd6a9564f869..1151d1f393c6f 100644 --- a/recipes/galaxy-ml/meta.yaml +++ b/recipes/galaxy-ml/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 921a7884bfab3a7b40021e33602b13a9a5a2c58a3205c87659423ebd892476f1 build: - number: 2 + number: 3 script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv skip: True # [osx or py<39 or py>39] diff --git a/recipes/gangstr/build_failure.linux-64.yaml b/recipes/gangstr/build_failure.linux-64.yaml index 1bb51b6c4c7d3..25cd3d3e47102 100644 --- a/recipes/gangstr/build_failure.linux-64.yaml +++ b/recipes/gangstr/build_failure.linux-64.yaml @@ -1,20 +1,13 @@ -recipe_sha: 2685a87b6b653fa97093eedb95571af5ed60d2d451580ef9438942d3eacb60e6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 2e2db2a0fecad10ff9412e3979a5e3ec28284b8654fb52e0445dc8bdac7105aa # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- - Y :: Build-prefix patch in use M :: Minimal, non-amalgamated - D :: Dry-runnable N :: Patch level (1 is preferred) - L :: Patch level not-ambiguous O :: Patch applies without offsets - V :: Patch applies without fuzz E :: Patch applies without emitting to stderr - - source tree in: /opt/conda/conda-bld/gangstr_1717785650270/work - export PREFIX=/opt/conda/conda-bld/gangstr_1717785650270/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place - export BUILD_PREFIX=/opt/conda/conda-bld/gangstr_1717785650270/_build_env - export SRC_DIR=/opt/conda/conda-bld/gangstr_1717785650270/work + export SRC_DIR=/opt/conda/conda-bld/gangstr_1734243773656/work INFO: activate-binutils_linux-64.sh made the following environmental changes: ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld @@ -47,7 +40,7 @@ log: |- GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib HOST=x86_64-conda-linux-gnu LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu build_alias=x86_64-conda-linux-gnu host_alias=x86_64-conda-linux-gnu @@ -59,8 +52,8 @@ log: |- CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gangstr-2.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g - -- The C compiler identification is GNU 12.3.0 - -- The CXX compiler identification is GNU 12.3.0 + -- The C compiler identification is GNU 13.3.0 + -- The CXX compiler identification is GNU 13.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - skipped @@ -73,32 +66,39 @@ log: |- -- Detecting CXX compile features - done -- Found PkgConfig: $BUILD_PREFIX/bin/pkg-config (found version "0.29.2") -- Checking for module 'htslib' - -- Package 'zlib', required by 'htslib', not found - CMake Error at /opt/conda/conda-bld/gangstr_1717785650270/_build_env/share/cmake-3.29/Modules/FindPkgConfig.cmake:634 (message): + -- Package 'liblzma', required by 'htslib', not found + CMake Error at /opt/conda/conda-bld/gangstr_1734243773656/_build_env/share/cmake-3.31/Modules/FindPkgConfig.cmake:645 (message): The following required packages were not found: - htslib Call Stack (most recent call first): - /opt/conda/conda-bld/gangstr_1717785650270/_build_env/share/cmake-3.29/Modules/FindPkgConfig.cmake:862 (_pkg_check_modules_internal) + /opt/conda/conda-bld/gangstr_1734243773656/_build_env/share/cmake-3.31/Modules/FindPkgConfig.cmake:873 (_pkg_check_modules_internal) CMakeLists.txt:22 (pkg_check_modules) -- Configuring incomplete, errors occurred! + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/gangstr_1734243773656/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + Traceback (most recent call last): File "/opt/conda/bin/conda-build", line 11, in sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/gangstr_1717785650270/work/conda_build.sh']' returned non-zero exit status 1. + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/gangstr_1734243773656/work/conda_build.sh']' returned non-zero exit status 1. # Last 100 lines of the build log. diff --git a/recipes/gangstr/build_failure.linux-aarch64.yaml b/recipes/gangstr/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..46c1a56166298 --- /dev/null +++ b/recipes/gangstr/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 2e2db2a0fecad10ff9412e3979a5e3ec28284b8654fb52e0445dc8bdac7105aa # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + export SRC_DIR=/opt/conda/conda-bld/gangstr_1734187225675/work + INFO: activate-binutils_linux-aarch64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strip + INFO: activate-gcc_linux-aarch64.sh made the following environmental changes: + BUILD=aarch64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc + CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gangstr-2.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=aarch64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=aarch64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gangstr-2.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib + HOST=aarch64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_aarch64_conda_cos7_linux_gnu + build_alias=aarch64-conda-linux-gnu + host_alias=aarch64-conda-linux-gnu + -BUILD=aarch64-conda_cos7-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-aarch64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gangstr-2.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gangstr-2.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-g + -- The C compiler identification is GNU 13.3.0 + -- The CXX compiler identification is GNU 13.3.0 + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc - skipped + -- Detecting C compile features + -- Detecting C compile features - done + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Found PkgConfig: $BUILD_PREFIX/bin/pkg-config (found version "0.29.2") + -- Checking for module 'htslib' + -- Package 'liblzma', required by 'htslib', not found + CMake Error at /opt/conda/conda-bld/gangstr_1734187225675/_build_env/share/cmake-3.31/Modules/FindPkgConfig.cmake:645 (message): + The following required packages were not found: + + - htslib + + Call Stack (most recent call first): + /opt/conda/conda-bld/gangstr_1734187225675/_build_env/share/cmake-3.31/Modules/FindPkgConfig.cmake:873 (_pkg_check_modules_internal) + CMakeLists.txt:22 (pkg_check_modules) + + + -- Configuring incomplete, errors occurred! + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/gangstr_1734187225675/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/gangstr_1734187225675/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/gangstr/build_failure.osx-64.yaml b/recipes/gangstr/build_failure.osx-64.yaml index 9c735e3675dcb..d5be3d79f2c0d 100644 --- a/recipes/gangstr/build_failure.osx-64.yaml +++ b/recipes/gangstr/build_failure.osx-64.yaml @@ -1,26 +1,40 @@ -recipe_sha: 2685a87b6b653fa97093eedb95571af5ed60d2d451580ef9438942d3eacb60e6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 2e2db2a0fecad10ff9412e3979a5e3ec28284b8654fb52e0445dc8bdac7105aa # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- + - htslib 1.21 h9f635df_1 + - libblas 3.9.0 25_osx64_openblas + - libcblas 3.9.0 25_osx64_openblas + - liblapack 3.9.0 25_osx64_openblas + - gsl 2.7 h93259b0_0 + - numpy 2.2.0 py313h6ae94ac_0 + - nlopt 2.8.0 py313h1f02af7_2 + run: + - libzlib >=1.3.1,<2.0a0 + - htslib >=1.21,<1.22.0a0 + - gsl >=2.7,<2.8.0a0 + - nlopt >=2.8.0,<2.9.0a0 + - libcxx >=18 + test: + commands: + - GangSTR --version 2>&1 | grep -qFx '2.5.0' + about: + home: https://github.com/gymreklab/GangSTR + license: GPL-3.0-or-later + license_file: COPYING + summary: GangSTR is a tool for genome-wide profiling tandem repeats from short reads. + extra: + additional-platforms: + - linux-aarch64 + copy_test_source_files: true + final: true + identifiers: + - doi:10.1093/nar/gkz501 - Extracting download - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/gangstr/0001-Unvendor-dependencies-use-pkg-config-instead.patch - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/gangstr/0001-Unvendor-dependencies-use-pkg-config-instead.patch with args: - ['-Np1', '-i', '/tmp/tmpxexrt89l/0001-Unvendor-dependencies-use-pkg-config-instead.patch.native', '--binary'] - Patch analysis gives: - [[ RA-MD1LOVE ]] - [[ 0001-Unvendor-dependencies-use-pkg-config-instead.patch ]] - Key: - - R :: Reversible A :: Applicable - Y :: Build-prefix patch in use M :: Minimal, non-amalgamated - D :: Dry-runnable N :: Patch level (1 is preferred) - L :: Patch level not-ambiguous O :: Patch applies without offsets - V :: Patch applies without fuzz E :: Patch applies without emitting to stderr - - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/gangstr_1717628038487/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/gangstr_1717628038487/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/gangstr_1717628038487/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/gangstr_1717628038487/work + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/gangstr_1734245639010/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/gangstr_1734245639010/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/gangstr_1734245639010/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/gangstr_1734245639010/work INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as @@ -29,27 +43,22 @@ log: |2- CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gangstr-2.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gangstr-2.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool LD=x86_64-apple-darwin13.4.0-ld LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -58,7 +67,7 @@ log: |2- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -75,18 +84,9 @@ log: |2- CXX=x86_64-apple-darwin13.4.0-clang CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gangstr-2.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/gangstr_1717628038487/work/conda_build.sh']' returned non-zero exit status 1. DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gangstr-2.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - -- The C compiler identification is Clang 16.0.6 - -- The CXX compiler identification is Clang 16.0.6 + -- The C compiler identification is Clang 18.1.8 + -- The CXX compiler identification is Clang 18.1.8 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped @@ -99,6 +99,6 @@ log: |2- -- Detecting CXX compile features - done -- Found PkgConfig: $BUILD_PREFIX/bin/pkg-config (found version "0.29.2") -- Checking for module 'htslib' - -- Package 'zlib', required by 'htslib', not found + -- Package 'bzip2', required by 'htslib', not found -- Configuring incomplete, errors occurred! # Last 100 lines of the build log. diff --git a/recipes/gangstr/meta.yaml b/recipes/gangstr/meta.yaml index b6bb7c7a52853..38aa27f8660a8 100644 --- a/recipes/gangstr/meta.yaml +++ b/recipes/gangstr/meta.yaml @@ -14,7 +14,7 @@ source: - gangstr-aarch64.patch # [linux and aarch64] build: - number: 8 + number: 9 run_exports: - {{ pin_subpackage('gangstr', max_pin="x") }} diff --git a/recipes/ganon/meta.yaml b/recipes/ganon/meta.yaml index b448796cc63d8..b5ad0109d4bcb 100755 --- a/recipes/ganon/meta.yaml +++ b/recipes/ganon/meta.yaml @@ -14,7 +14,7 @@ source: sha256: dcf2b7fa9ef9dd0c67102d94c28e8df3effbe1845e0ed1f31f4772ca5e857fc4 build: - number: 1 + number: 2 skip: True # [py<36 or osx] run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/gap2seq/meta.yaml b/recipes/gap2seq/meta.yaml index 9140cdb128b41..b909259002384 100644 --- a/recipes/gap2seq/meta.yaml +++ b/recipes/gap2seq/meta.yaml @@ -10,7 +10,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 skip: True # [osx or py2k] run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} diff --git a/recipes/gappa/meta.yaml b/recipes/gappa/meta.yaml index 968f366e34297..f3324151fdbf6 100644 --- a/recipes/gappa/meta.yaml +++ b/recipes/gappa/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.8.5" build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('gappa', max_pin='x.x') }} diff --git a/recipes/gargammel-slim/build_failure.osx-64.yaml b/recipes/gargammel-slim/build_failure.osx-64.yaml index 39e8acd9ed637..f6c92d42af453 100644 --- a/recipes/gargammel-slim/build_failure.osx-64.yaml +++ b/recipes/gargammel-slim/build_failure.osx-64.yaml @@ -1,48 +1,46 @@ -recipe_sha: 0e462e5b278dcfaee8a3a55d793270a591c1f9dd1ca05c0e38b2c35b3b3d2fcf # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: db41bb81e8d186569b8de324ac4bc48807a093f30de425a579cdf139191cc54b # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/gargammel-slim/0003-libgab-gzstream-Makefile-use-CXXFLAGS-and-LDFLAGS.patch with args: - ['-Np0', '-i', '/tmp/tmpo55svqht/0003-libgab-gzstream-Makefile-use-CXXFLAGS-and-LDFLAGS.patch.native', '--binary'] - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/gargammel-slim/0004-libgab-Makefile-removed-CXX.patch - Patch level ambiguous, selecting least deep - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/gargammel-slim/0004-libgab-Makefile-removed-CXX.patch with args: - ['-Np0', '-i', '/tmp/tmphkgx4j5e/0004-libgab-Makefile-removed-CXX.patch.native', '--binary'] - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/gargammel-slim/0005-libgab-ReconsReferenceBAM-OSX.patch - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/gargammel-slim/0005-libgab-ReconsReferenceBAM-OSX.patch with args: - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - ['-Np0', '-i', '/tmp/tmp4ng2chds/0005-libgab-ReconsReferenceBAM-OSX.patch.native', '--binary'] - Patch analysis gives: - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/gargammel-slim_1717627393137/work/conda_build.sh']' returned non-zero exit status 2. - [[ RA--D0LOVE ]] - [[ 0001-gargammel-Makefile-keep-basic.patch ]] - [[ RA-MD0-OVE ]] - [[ 0002-gargammel-src-Makefile-change-CXXFLAGS-and-LDFLAGS.patch ]] - [[ RA-MD0-OVE ]] - [[ 0003-libgab-gzstream-Makefile-use-CXXFLAGS-and-LDFLAGS.patch ]] - [[ RA-MD0-OVE ]] - [[ 0004-libgab-Makefile-removed-CXX.patch ]] - [[ RA-MD0LOVE ]] - [[ 0005-libgab-ReconsReferenceBAM-OSX.patch ]] + - libgfortran 5.0.0 13_2_0_h97931a8_3 + - libnghttp2 1.64.0 hc7306c3_0 + - libssh2 1.11.1 h3dc7d44_0 + - libcurl 8.11.1 h5dec5d8_0 + - libopenblas 0.3.28 openmp_hbf64a52_1 + - cmake 3.31.2 h477996e_1 + - libblas 3.9.0 25_osx64_openblas + - libcblas 3.9.0 25_osx64_openblas + - gsl 2.7 h93259b0_0 + run: + - libcxx >=18 + - libzlib >=1.3.1,<2.0a0 + - gsl >=2.7,<2.8.0a0 + - bamtools >=2.5.2,<2.6.0a0 + test: + commands: + - adptSim --help | grep -q 'adptSim' + - deamSim --help | grep -q 'deamSim' + - fragSim --help | grep -q 'fragSim' + about: + description: 'This a stripped version of Gargammel that only builds the programs - Key: + fragSim, deamSim and adptSim. For a full Gargammel installation - R :: Reversible A :: Applicable - Y :: Build-prefix patch in use M :: Minimal, non-amalgamated - D :: Dry-runnable N :: Patch level (1 is preferred) - L :: Patch level not-ambiguous O :: Patch applies without offsets - V :: Patch applies without fuzz E :: Patch applies without emitting to stderr + look at the gargammel package - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/gargammel-slim_1717627393137/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/gargammel-slim_1717627393137/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/gargammel-slim_1717627393137/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/gargammel-slim_1717627393137/work + ' + home: https://github.com/grenaud/gargammel + license: GPL-3.0-only + license_file: gargammel/LICENSE + summary: Tool for simulating ancient DNA datasets + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/gargammel-slim_1734091794185/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/gargammel-slim_1734091794185/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/gargammel-slim_1734091794185/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/gargammel-slim_1734091794185/work INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as @@ -51,11 +49,13 @@ log: |2- CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gargammel-slim-1.1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gargammel-slim-1.1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool @@ -64,7 +64,7 @@ log: |2- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -73,7 +73,7 @@ log: |2- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack diff --git a/recipes/gargammel-slim/meta.yaml b/recipes/gargammel-slim/meta.yaml index 024f9b0ae8770..004f1adfde243 100644 --- a/recipes/gargammel-slim/meta.yaml +++ b/recipes/gargammel-slim/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 5 + number: 6 source: - url: https://github.com/grenaud/libgab/archive/d2bbab7d88fbfdaa0ce57a26dc908d2fc66bf656.tar.gz diff --git a/recipes/gassst/meta.yaml b/recipes/gassst/meta.yaml index ac26800a1bf28..c4531ea1dbf09 100644 --- a/recipes/gassst/meta.yaml +++ b/recipes/gassst/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: true # [osx] - number: 2 + number: 3 requirements: build: diff --git a/recipes/gatb/meta.yaml b/recipes/gatb/meta.yaml index 24333a41f3731..1b9a1020a2890 100644 --- a/recipes/gatb/meta.yaml +++ b/recipes/gatb/meta.yaml @@ -10,7 +10,7 @@ source: - boophf.patch build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/gb-io/meta.yaml b/recipes/gb-io/meta.yaml index 0905a764c28f6..d916ea9f884a1 100644 --- a/recipes/gb-io/meta.yaml +++ b/recipes/gb-io/meta.yaml @@ -6,7 +6,7 @@ package: version: "{{ version }}" build: - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir --use-pep517 run_exports: - {{ pin_subpackage('gb-io', max_pin="x.x") }} diff --git a/recipes/gb_taxonomy_tools/meta.yaml b/recipes/gb_taxonomy_tools/meta.yaml index 7e34a8f17c966..eb687a0a87e3a 100644 --- a/recipes/gb_taxonomy_tools/meta.yaml +++ b/recipes/gb_taxonomy_tools/meta.yaml @@ -7,7 +7,7 @@ source: sha256: d9c0901a66db19fc0f77d02316f663200f739db998746037fcf23e36db9377f4 build: - number: 5 + number: 6 skip: True # [osx] requirements: diff --git a/recipes/gbmunge/meta.yaml b/recipes/gbmunge/meta.yaml index 393c3960600f2..8be335d2bf05a 100644 --- a/recipes/gbmunge/meta.yaml +++ b/recipes/gbmunge/meta.yaml @@ -13,7 +13,7 @@ source: sha256: {{ sha256 }} build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/gctb/meta.yaml b/recipes/gctb/meta.yaml index 2dbc1bb0b4ac4..846e1d4cfd74d 100644 --- a/recipes/gctb/meta.yaml +++ b/recipes/gctb/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: true # [osx] - number: 2 + number: 3 requirements: build: diff --git a/recipes/gdc/build_failure.osx-64.yaml b/recipes/gdc/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..ee8cccaf5f934 --- /dev/null +++ b/recipes/gdc/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 10aa67b550734d250d7d4d3ad907c1e0c9c223712f17e208284c110f649fec92 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - libzlib 1.3.1 hd23fc13_2 + - libcxx 19.1.5 hf95d169_0 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + - libxml2 2.13.5 he8ee3e7_1 + - clang_impl_osx-64 18.1.8 h6a44ed1_23 + - ca-certificates 2024.8.30 h8857fd0_0 + - clang 18.1.8 default_h179603d_5 + - clangxx_impl_osx-64 18.1.8 h4b7810f_23 + - libclang-cpp18.1 18.1.8 default_h0c94c6a_5 + - openssl 3.4.0 hd471939_0 + host: + - libcxx 19.1.5 hf95d169_0 + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/gdc_1734192752038/work/conda_build.sh']' returned non-zero exit status 2. + - libzlib 1.3.1 hd23fc13_2 + - zlib 1.3.1 hd23fc13_2 + run: + - libzlib >=1.3.1,<2.0a0 + - libcxx >=18 + - zlib + test: + commands: + - gdc2 -h + about: + home: http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=gdc&subpage=about + license: GPL2 + summary: Utility designed for compression of genome collections from the same species. + extra: + copy_test_source_files: true + final: true + identifiers: + - biotools:GDC + - doi:10.1038/srep11565 + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/gdc_1734192752038/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/gdc_1734192752038/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/gdc_1734192752038/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/gdc_1734192752038/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gdc-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gdc-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gdc-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gdc-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gdc-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wall -O3 -m64 -std=c11 -stdlib=libc -c c1stage.cpp -o c1stage.o + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gdc-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wall -O3 -m64 -std=c11 -stdlib=libc -c c2stage.cpp -o c2stage.o + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gdc-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wall -O3 -m64 -std=c11 -stdlib=libc -c fasta.cpp -o fasta.o + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gdc-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wall -O3 -m64 -std=c11 -stdlib=libc -c hasher.cpp -o hasher.o + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gdc-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wall -O3 -m64 -std=c11 -stdlib=libc -c main.cpp -o main.o + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gdc-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wall -O3 -m64 -std=c11 -stdlib=libc -c p1stage.cpp -o p1stage.o + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gdc-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wall -O3 -m64 -std=c11 -stdlib=libc -c qsmodel.cpp -o qsmodel.o + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gdc-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wall -O3 -m64 -std=c11 -stdlib=libc -c queue.cpp -o queue.o + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gdc-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wall -O3 -m64 -std=c11 -stdlib=libc -c rangecod.cpp -o rangecod.o + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gdc-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wall -O3 -m64 -std=c11 -stdlib=libc -c timer.cpp -o timer.o + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gdc-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lm -O3 -std=c11 -stdlib=libc ../libs/libamac64.a ../libs/libz.1.2.8.dylib -o gdc2 c1stage.o c2stage.o fasta.o hasher.o main.o p1stage.o qsmodel.o queue.o rangecod.o timer.o +# Last 100 lines of the build log. diff --git a/recipes/gdc/meta.yaml b/recipes/gdc/meta.yaml index 382a7e81ca822..dd2b5d3ab20b3 100644 --- a/recipes/gdc/meta.yaml +++ b/recipes/gdc/meta.yaml @@ -3,7 +3,7 @@ package: version: 2.0 build: - number: 5 + number: 6 source: url: http://sun.aei.polsl.pl/REFRESH/gdc/downloads/2.0/gdc2.tar.gz diff --git a/recipes/gecko/meta.yaml b/recipes/gecko/meta.yaml index 32b4db32d4330..5f3a83cffaa58 100644 --- a/recipes/gecko/meta.yaml +++ b/recipes/gecko/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 skip: true # [osx] requirements: diff --git a/recipes/geco2/meta.yaml b/recipes/geco2/meta.yaml index 6b05b5afff74c..7ce26a0bce6a3 100644 --- a/recipes/geco2/meta.yaml +++ b/recipes/geco2/meta.yaml @@ -7,7 +7,7 @@ package: build: # Passes some invalid flags for clang skip: True # [osx] - number: 4 + number: 5 source: url: https://github.com/cobilab/geco2/archive/v{{ version }}.tar.gz diff --git a/recipes/geco3/meta.yaml b/recipes/geco3/meta.yaml index dacee9732b1d0..d5d46c006a64e 100644 --- a/recipes/geco3/meta.yaml +++ b/recipes/geco3/meta.yaml @@ -7,7 +7,7 @@ package: build: # Passes some invalid flags for clang skip: True # [osx] - number: 4 + number: 5 source: url: https://github.com/cobilab/geco3/archive/v{{ version }}.tar.gz diff --git a/recipes/gecode/5.0.0/meta.yaml b/recipes/gecode/5.0.0/meta.yaml index a911353ee1d9f..4af768df94650 100644 --- a/recipes/gecode/5.0.0/meta.yaml +++ b/recipes/gecode/5.0.0/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 1f1063ff0116cde1a1e0dde47c1328dcf5d92ef0ea8f38d3ad8e7d4c97b4020e build: - number: 6 + number: 7 # OSX build fail due to Clang catching a bug: # examples/photo.cpp:103:10: error: reference member 'spec' binds to a temporary object whose lifetime would be shorter than the lifetime of the constructed object skip: True # [osx] diff --git a/recipes/gecode/meta.yaml b/recipes/gecode/meta.yaml index 6e7f7bf8c3d52..b0b9fbffa1c08 100644 --- a/recipes/gecode/meta.yaml +++ b/recipes/gecode/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: True # [osx] - number: 4 + number: 5 requirements: build: diff --git a/recipes/gefast/build_failure.linux-64.yaml b/recipes/gefast/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..7e8b655aadd17 --- /dev/null +++ b/recipes/gefast/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 6a99c09cdb6d00638b2beff7d2b17cda8a20ae1d01a6f61ed6eb24b83486e4e7 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + -- Installing: $SRC_DIR/libs/stats/include/gcem_incl/abs.hpp + -- Installing: $SRC_DIR/libs/stats/include/gcem_incl/round.hpp + -- Installing: $SRC_DIR/libs/stats/include/gcem_incl/quadrature + -- Installing: $SRC_DIR/libs/stats/include/gcem_incl/quadrature/gauss_legendre_50.hpp + -- Installing: $SRC_DIR/libs/stats/include/gcem_incl/quadrature/gauss_legendre_30.hpp + -- Installing: $SRC_DIR/libs/stats/include/gcem_incl/signbit.hpp + -- Installing: $SRC_DIR/libs/stats/include/gcem_incl/pow_integral.hpp + -- Installing: $SRC_DIR/libs/stats/include/gcem_incl/find_fraction.hpp + -- Installing: $SRC_DIR/libs/stats/include/gcem_incl/incomplete_beta_inv.hpp + -- Installing: $SRC_DIR/libs/stats/include/gcem_incl/is_nan.hpp + -- Installing: $SRC_DIR/libs/stats/include/gcem_incl/expm1.hpp + -- Installing: $SRC_DIR/libs/stats/include/gcem_incl/fmod.hpp + -- Installing: $SRC_DIR/libs/stats/include/gcem_incl/sqrt.hpp + -- Installing: $SRC_DIR/libs/stats/include/gcem.hpp + -- Installing: $SRC_DIR/libs/stats/lib64/cmake/gcem/gcemConfig.cmake + -- Installing: $SRC_DIR/libs/stats/lib64/cmake/gcem/gcemConfigVersion.cmake + -- Installing: $SRC_DIR/libs/stats/lib64/cmake/gcem/gcemTargets.cmake + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=c11 -pthread -O3 -msse4.1 -o build/objects/main.o -c main.cpp + In file included from include/Base.hpp:33, + from include/Factories.hpp:29, + from main.cpp:24: + include/Utility.hpp:480:34: error: 'uint8_t' has not been declared + 480 | static void assign_kmer8(uint8_t* kvec8, const char* seq, int k); + | ^~~~~~~ + include/Utility.hpp:484:33: error: 'uint16_t' has not been declared + 484 | static void assign_kmer(uint16_t* kvec, const char* seq, int k); + | ^~~~~~~~ + include/Utility.hpp:488:39: error: 'uint16_t' has not been declared + 488 | static void assign_kmer_order(uint16_t* kord, const char* seq, int k); + | ^~~~~~~~ + include/Utility.hpp:492:33: error: 'uint16_t' has not been declared + 492 | static double kmer_dist(uint16_t* kv1, int len1, uint16_t* kv2, int len2, int k); + | ^~~~~~~~ + include/Utility.hpp:492:58: error: 'uint16_t' has not been declared + 492 | static double kmer_dist(uint16_t* kv1, int len1, uint16_t* kv2, int len2, int k); + | ^~~~~~~~ + include/Utility.hpp:496:33: error: 'uint16_t' has not been declared + 496 | static double kord_dist(uint16_t* kord1, int len1, uint16_t* kord2, int len2, int k); + | ^~~~~~~~ + include/Utility.hpp:496:60: error: 'uint16_t' has not been declared + 496 | static double kord_dist(uint16_t* kord1, int len1, uint16_t* kord2, int len2, int k); + | ^~~~~~~~ + include/Utility.hpp:537:13: error: 'uint8_t' does not name a type + 537 | uint8_t* qual; // the rounded average qualities at each position for this unique + | ^~~~~~~ + include/Utility.hpp:35:1: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + 34 | #include "Options.hpp" + |#include + 35 | + include/Utility.hpp:539:13: error: 'uint16_t' does not name a type + 539 | uint16_t* kmer; // the 16-bit k-mer vector (counts) of this sequence + | ^~~~~~~~ + include/Utility.hpp:539:13: note: 'uint16_t' is defined in header ''; did you forget to '#include '? + include/Utility.hpp:540:13: error: 'uint8_t' does not name a type + 540 | uint8_t* kmer8; // the 8-bit k-mer vector (counts) of this sequence + | ^~~~~~~ + include/Utility.hpp:540:13: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + include/Utility.hpp:541:13: error: 'uint16_t' does not name a type + 541 | uint16_t* kord; // the k-mers of this sequence in their order of appearance + | ^~~~~~~~ + include/Utility.hpp:541:13: note: 'uint16_t' is defined in header ''; did you forget to '#include '? + include/Utility.hpp:556:67: error: 'uint8_t' has not been declared + 556 | RawSequence(const char* ampl_seq, lenSeqs_t ampl_len, uint8_t* ampl_quals, unsigned int ampl_abundance, bool is_prior); + | ^~~~~~~ + include/Utility.hpp:576:13: error: 'uint16_t' does not name a type + 576 | uint16_t* map; // map of the sequence position in the reference sequence to that in the aligned sequence + | ^~~~~~~~ + include/Utility.hpp:576:13: note: 'uint16_t' is defined in header ''; did you forget to '#include '? + include/Utility.hpp:577:13: error: 'uint16_t' does not name a type + 577 | uint16_t* pos; // sequence position of the substitution: index in the reference sequence + | ^~~~~~~~ + include/Utility.hpp:577:13: note: 'uint16_t' is defined in header ''; did you forget to '#include '? + include/Utility.hpp:598:77: error: 'uint8_t' does not name a type + 598 | static double compute_lambda(const char* seq, size_t seq_len, const uint8_t* qual, Sub* sub, + | ^~~~~~~ + include/Utility.hpp:598:77: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + make: *** [Makefile:16: build/objects/main.o] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/gefast_1734148718942/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/gefast_1734148718942/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/gefast/meta.yaml b/recipes/gefast/meta.yaml index aee9b8a9914a8..b8e09350cac86 100644 --- a/recipes/gefast/meta.yaml +++ b/recipes/gefast/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 source: #The package hasn't been updated in a few years and there was one convenient commit since the 1.0.0 release diff --git a/recipes/gem3-mapper/meta.yaml b/recipes/gem3-mapper/meta.yaml index 9305923a1fcb6..24ecf67c76b1c 100644 --- a/recipes/gem3-mapper/meta.yaml +++ b/recipes/gem3-mapper/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 12 + number: 13 requirements: build: diff --git a/recipes/gembs/build_failure.linux-64.yaml b/recipes/gembs/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..245c80c2f5008 --- /dev/null +++ b/recipes/gembs/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: e5599c16c7d33cf7a0586adbda42598f4e9696d4b8f0f32b080eeb7e620521cd # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + | ^~~~ + bam_tview_curses.c:187:14: note: 'base' was declared here + 187 | tview_t* base=(tview_t*)base; + | ^~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gembs-3.5.5_IHEC -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -I../htslib -I./lz4 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o bam_tview_html.o bam_tview_html.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gembs-3.5.5_IHEC -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -I../htslib -I./lz4 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o bam_lpileup.o bam_lpileup.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gembs-3.5.5_IHEC -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -I../htslib -I./lz4 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o bam_quickcheck.o bam_quickcheck.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gembs-3.5.5_IHEC -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -I../htslib -I./lz4 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o bam_addrprg.o bam_addrprg.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gembs-3.5.5_IHEC -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -I../htslib -I./lz4 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o bam_markdup.o bam_markdup.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gembs-3.5.5_IHEC -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -I../htslib -I./lz4 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o tmp_file.o tmp_file.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gembs-3.5.5_IHEC -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -I../htslib -I./lz4 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o bam_ampliconclip.o bam_ampliconclip.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gembs-3.5.5_IHEC -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -I../htslib -I./lz4 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o amplicon_stats.o amplicon_stats.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gembs-3.5.5_IHEC -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -I../htslib -I./lz4 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o lz4/lz4.o lz4/lz4.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gembs-3.5.5_IHEC -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -I../htslib -I./lz4 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o bam_aux.o bam_aux.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gembs-3.5.5_IHEC -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -I../htslib -I./lz4 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o bam.o bam.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gembs-3.5.5_IHEC -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -I../htslib -I./lz4 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o sam.o sam.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gembs-3.5.5_IHEC -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -I../htslib -I./lz4 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o bam_plbuf.o bam_plbuf.c + ar -csru libbam.a bam_aux.o bam.o sam.o bam_plbuf.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gembs-3.5.5_IHEC -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -I../htslib -I./lz4 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o sam_opts.o sam_opts.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gembs-3.5.5_IHEC -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -I../htslib -I./lz4 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o sam_utils.o sam_utils.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gembs-3.5.5_IHEC -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -I../htslib -I./lz4 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o bedidx.o bedidx.c + ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o + cd ../htslib && make config.h + make[2]: Entering directory '$SRC_DIR/tools/htslib' + echo '/* Default config.h generated by Makefile */' > config.h + echo '#define HAVE_LIBBZ2 1' >> config.h + echo '#define HAVE_LIBLZMA 1' >> config.h + echo '#ifndef __APPLE__' >> config.h + echo '#define HAVE_LZMA_H 1' >> config.h + echo '#endif' >> config.h + echo '#define HAVE_DRAND48 1' >> config.h + echo '#define HAVE_LIBCURL 1' >> config.h + make[2]: Leaving directory '$SRC_DIR/tools/htslib' + cd ../htslib && make hts-object-files + make[2]: Entering directory '$SRC_DIR/tools/htslib' + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o kfunc.o kfunc.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o knetfile.o knetfile.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o kstring.o kstring.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o bcf_sr_sort.o bcf_sr_sort.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o bgzf.o bgzf.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o errmod.o errmod.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o faidx.o faidx.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o header.o header.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o hfile.o hfile.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o hfile_net.o hfile_net.c + echo '#define HTS_VERSION_TEXT "1.11"' > version.h + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o hts.o hts.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o hts_os.o hts_os.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o md5.o md5.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o multipart.o multipart.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o probaln.o probaln.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o realn.o realn.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o regidx.o regidx.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o region.o region.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o sam.o sam.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o synced_bcf_reader.o synced_bcf_reader.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o vcf_sweep.o vcf_sweep.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o tbx.o tbx.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o textutils.o textutils.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o thread_pool.o thread_pool.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o vcf.o vcf.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o vcfutils.o vcfutils.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o cram/cram_codecs.o cram/cram_codecs.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o cram/cram_decode.o cram/cram_decode.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o cram/cram_encode.o cram/cram_encode.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o cram/cram_external.o cram/cram_external.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o cram/cram_index.o cram/cram_index.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -fvisibility=hidden -I. -c -o cram/cram_io.o cram/cram_io.c + cram/cram_io.c:57:10: fatal error: lzma.h: No such file or directory + 57 | #include + | ^~~~~~~~ + compilation terminated. + make[2]: *** [Makefile:136: cram/cram_io.o] Error 1 + make[2]: Leaving directory '$SRC_DIR/tools/htslib' + make[1]: *** [../htslib/htslib.mk:155: ../htslib/hts-object-files] Error 2 + make[1]: Leaving directory '$SRC_DIR/tools/samtools' + make: *** [Makefile:40: _samtools] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/gembs_1734161426919/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/gembs_1734161426919/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/gembs/build_failure.osx-64.yaml b/recipes/gembs/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..e81bfe197d5a0 --- /dev/null +++ b/recipes/gembs/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: e5599c16c7d33cf7a0586adbda42598f4e9696d4b8f0f32b080eeb7e620521cd # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']"), MatchSpec("bs_call==2.02=h477cf5a_0")} + Encountered problems while solving: + - package bs_call-2.02-h477cf5a_0 requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + bs_call is installable with the potential options + bs_call 2.02 would require + zlib >=1.2.11,<1.3.0a0 , which can be installed; + bs_call 2.02 would require + zlib >=1.2.13,<1.3.0a0 , which can be installed; + bs_call 2.02 would require + libzlib >=1.2.13,<1.3.0a0 , which can be installed; + libzlib >=1.3.1,<2.0a0 is not installable because there are no viable options + libzlib 1.3.1 would require + zlib 1.3.1 *_0, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_1, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_2, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']"), MatchSpec("bs_call==2.02=h477cf5a_0")} + Encountered problems while solving: + - package bs_call-2.02-h477cf5a_0 requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + bs_call is installable with the potential options + bs_call 2.02 would require + zlib >=1.2.11,<1.3.0a0 , which can be installed; + bs_call 2.02 would require + zlib >=1.2.13,<1.3.0a0 , which can be installed; + bs_call 2.02 would require + libzlib >=1.2.13,<1.3.0a0 , which can be installed; + libzlib >=1.3.1,<2.0a0 is not installable because there are no viable options + libzlib 1.3.1 would require + zlib 1.3.1 *_0, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_1, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_2, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/gembs/meta.yaml b/recipes/gembs/meta.yaml index 1c116b37d5801..099bf7f2526f5 100644 --- a/recipes/gembs/meta.yaml +++ b/recipes/gembs/meta.yaml @@ -13,7 +13,7 @@ source: - clock.patch build: - number: 8 + number: 9 # This should probably be split into gemBS-tools and a noarch: python gemBS package skip: true # [py < 37] diff --git a/recipes/gemf_favites/meta.yaml b/recipes/gemf_favites/meta.yaml index 12f628887e00f..e22bbd2a18e8d 100644 --- a/recipes/gemf_favites/meta.yaml +++ b/recipes/gemf_favites/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('gemf_favites', max_pin="x.x.x") }} diff --git a/recipes/gemini/build_failure.linux-64.yaml b/recipes/gemini/build_failure.linux-64.yaml index 3896619b45abd..06b9179ac1188 100644 --- a/recipes/gemini/build_failure.linux-64.yaml +++ b/recipes/gemini/build_failure.linux-64.yaml @@ -1,6 +1,5 @@ recipe_sha: 164abbf7c3e0bc8ad245a0a1a02165aa8d1e49c340817b6a97e60bdb6223dd48 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: dependency issue log: |2- [32mnumpy 1.10* [0m, which can be installed; [32mpython 2.7* [0m, which can be installed (as previously explained); @@ -103,3 +102,7 @@ log: |2- [32mopenssl >=1.1.1s,<1.1.2a [0m, which can be installed; [31mpython_abi 3.11.* *_cp311[0m, which conflicts with any installable versions previously reported. # Last 100 lines of the build log. +reason: |- + needs bcolz, which is now unsupported for a year +category: |- + dependency issue diff --git a/recipes/gemini/build_failure.osx-64.yaml b/recipes/gemini/build_failure.osx-64.yaml index 1526ea63e4bf2..d5328ac458d80 100644 --- a/recipes/gemini/build_failure.osx-64.yaml +++ b/recipes/gemini/build_failure.osx-64.yaml @@ -1,6 +1,5 @@ recipe_sha: 164abbf7c3e0bc8ad245a0a1a02165aa8d1e49c340817b6a97e60bdb6223dd48 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: dependency issue log: |2- File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata build_unsat, host_unsat = add_upstream_pins( @@ -103,3 +102,7 @@ log: |2- pandas [2.1.1|2.1.2|...|2.2.2] would require python_abi 3.12.* *_cp312, which conflicts with any installable versions previously reported. # Last 100 lines of the build log. +reason: |- + needs bcolz, which is now unsupported for a year +category: |- + dependency issue diff --git a/recipes/genbank/meta.yaml b/recipes/genbank/meta.yaml index 531460591cbc3..ca39cff303860 100644 --- a/recipes/genbank/meta.yaml +++ b/recipes/genbank/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 37ffb9ecd532aa9bf5faa4006183799ab5cf6990bfe19611efc0957dc47d0b13 build: - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation run_exports: - {{ pin_subpackage('genbank', max_pin="x.x") }} diff --git a/recipes/gencore/meta.yaml b/recipes/gencore/meta.yaml index 8917cac585cc1..8affe8d9b5cca 100644 --- a/recipes/gencore/meta.yaml +++ b/recipes/gencore/meta.yaml @@ -11,7 +11,7 @@ source: - patch build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/genefuse/meta.yaml b/recipes/genefuse/meta.yaml index dc78ff7176cdc..d01c8cea7b1f6 100644 --- a/recipes/genefuse/meta.yaml +++ b/recipes/genefuse/meta.yaml @@ -11,7 +11,7 @@ source: - patch build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/genenotebook/build_failure.linux-64.yaml b/recipes/genenotebook/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..f72d2f116d6e9 --- /dev/null +++ b/recipes/genenotebook/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 4d59725a94ab6afae979a667192473c398a24f5443842778f368b77be1ea53b2 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("nodejs==15.14.0=h92b4a50_0"), MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']")} + Encountered problems while solving: + - package nodejs-15.14.0-h92b4a50_0 requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mblast[0m is installable with the potential options + [32mblast 2.16.0[0m would require + [32mlibzlib >=1.3.1,<2.0a0 [0m with the potential options + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_0[0m, which can be installed; + [31mblast [2.10.1|2.11.0|...|2.9.0][0m conflicts with any installable versions previously reported; + [31mnodejs >=15,<16,>=15.14.0,<16.0a0 [0m is not installable because it requires + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("nodejs==15.14.0=h92b4a50_0"), MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']")} + Encountered problems while solving: + - package nodejs-15.14.0-h92b4a50_0 requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mblast[0m is installable with the potential options + [32mblast 2.16.0[0m would require + [32mlibzlib >=1.3.1,<2.0a0 [0m with the potential options + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_0[0m, which can be installed; + [31mblast [2.10.1|2.11.0|...|2.9.0][0m conflicts with any installable versions previously reported; + [31mnodejs >=15,<16,>=15.14.0,<16.0a0 [0m is not installable because it requires + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/genenotebook/meta.yaml b/recipes/genenotebook/meta.yaml index bac23d5fb3583..c940e4ea61558 100644 --- a/recipes/genenotebook/meta.yaml +++ b/recipes/genenotebook/meta.yaml @@ -24,7 +24,7 @@ requirements: - mongodb >=5.0 build: - number: 2 + number: 3 test: commands: diff --git a/recipes/genepop/meta.yaml b/recipes/genepop/meta.yaml index 0299e1d1d56bc..382df494558f8 100644 --- a/recipes/genepop/meta.yaml +++ b/recipes/genepop/meta.yaml @@ -15,7 +15,7 @@ package: # versions (reproducibility and all). build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("genepop", max_pin="x") }} @@ -41,4 +41,4 @@ test: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/generax/meta.yaml b/recipes/generax/meta.yaml index d3bd3bbf28fd4..fcf8ca11a3ee2 100644 --- a/recipes/generax/meta.yaml +++ b/recipes/generax/meta.yaml @@ -12,7 +12,7 @@ source: sha256: unused build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('generax', max_pin="x") }} requirements: diff --git a/recipes/genericrepeatfinder/meta.yaml b/recipes/genericrepeatfinder/meta.yaml index 9aed78e28fde6..007d896cfd285 100644 --- a/recipes/genericrepeatfinder/meta.yaml +++ b/recipes/genericrepeatfinder/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/genesplicer/meta.yaml b/recipes/genesplicer/meta.yaml index 8a9972d85bc96..f87b540acaae0 100644 --- a/recipes/genesplicer/meta.yaml +++ b/recipes/genesplicer/meta.yaml @@ -3,7 +3,7 @@ package: version: "0_2003.04.03" build: - number: 6 + number: 7 skip: True # [osx] source: diff --git a/recipes/genform/meta.yaml b/recipes/genform/meta.yaml index f149f5a1d7cbb..1b904e928b2ce 100644 --- a/recipes/genform/meta.yaml +++ b/recipes/genform/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 skip: True # [osx] source: diff --git a/recipes/genion/meta.yaml b/recipes/genion/meta.yaml index b783c5d4287b3..9ff2a6854642c 100644 --- a/recipes/genion/meta.yaml +++ b/recipes/genion/meta.yaml @@ -11,7 +11,7 @@ source: build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/genoboo/build_failure.linux-64.yaml b/recipes/genoboo/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..77469aecbfeed --- /dev/null +++ b/recipes/genoboo/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 2f217514012aa00c4fc28e2fa6e7234bd0ff00c3a508f8eda0becb7eca0b3388 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("nodejs==15.14.0=h92b4a50_0"), MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']")} + Encountered problems while solving: + - package nodejs-15.14.0-h92b4a50_0 requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mblast[0m is installable with the potential options + [32mblast 2.16.0[0m would require + [32mlibzlib >=1.3.1,<2.0a0 [0m with the potential options + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_0[0m, which can be installed; + [31mblast [2.10.1|2.11.0|...|2.9.0][0m conflicts with any installable versions previously reported; + [31mnodejs >=15,<16,>=15.14.0,<16.0a0 [0m is not installable because it requires + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("nodejs==15.14.0=h92b4a50_0"), MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']")} + Encountered problems while solving: + - package nodejs-15.14.0-h92b4a50_0 requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mblast[0m is installable with the potential options + [32mblast 2.16.0[0m would require + [32mlibzlib >=1.3.1,<2.0a0 [0m with the potential options + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_0[0m, which can be installed; + [31mblast [2.10.1|2.11.0|...|2.9.0][0m conflicts with any installable versions previously reported; + [31mnodejs >=15,<16,>=15.14.0,<16.0a0 [0m is not installable because it requires + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/genoboo/meta.yaml b/recipes/genoboo/meta.yaml index 5da66b8bdb3c3..3aec5bd8b0932 100644 --- a/recipes/genoboo/meta.yaml +++ b/recipes/genoboo/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('genoboo', max_pin="x") }} diff --git a/recipes/genodsp/meta.yaml b/recipes/genodsp/meta.yaml index ef2eea44d80a4..bd9f0f443016a 100644 --- a/recipes/genodsp/meta.yaml +++ b/recipes/genodsp/meta.yaml @@ -15,7 +15,7 @@ requirements: - make build: - number: 0 + number: 1 skip: True # [not linux] run_exports: - {{ pin_subpackage('genodsp', max_pin="x.x") }} @@ -35,4 +35,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/genomeconstellation/meta.yaml b/recipes/genomeconstellation/meta.yaml index daf405646d6a7..db63ee8746c8b 100644 --- a/recipes/genomeconstellation/meta.yaml +++ b/recipes/genomeconstellation/meta.yaml @@ -11,7 +11,7 @@ source: - makefile.patch build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/genomedata/meta.yaml b/recipes/genomedata/meta.yaml index 12a66928b7dc5..9c25c680948d2 100644 --- a/recipes/genomedata/meta.yaml +++ b/recipes/genomedata/meta.yaml @@ -12,7 +12,7 @@ source: build: skip: True # [osx or py < 39] - number: 1 + number: 2 entry_points: - genomedata-close-data = genomedata._close_data:main - genomedata-erase-data = genomedata._erase_data:main diff --git a/recipes/genomescope2/meta.yaml b/recipes/genomescope2/meta.yaml index b69e08b29ae95..c8864e997c0bd 100644 --- a/recipes/genomescope2/meta.yaml +++ b/recipes/genomescope2/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 55a6dc4006ac3573d011558d5ee49a0f3c85593a5db944a548c0e6f4e5019f75 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('genomescope2', max_pin="x.x") }} diff --git a/recipes/genometester4/meta.yaml b/recipes/genometester4/meta.yaml index 55586cc8ee51e..abb47151f57e8 100644 --- a/recipes/genometester4/meta.yaml +++ b/recipes/genometester4/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 6 + number: 7 skip: True # [osx] source: diff --git a/recipes/genomethreader/meta.yaml b/recipes/genomethreader/meta.yaml index cae1c1bd43666..066c527fad1d3 100644 --- a/recipes/genomethreader/meta.yaml +++ b/recipes/genomethreader/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: True # [not linux] - number: 6 + number: 7 requirements: build: diff --git a/recipes/genometools-genometools/build_failure.linux-64.yaml b/recipes/genometools-genometools/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..902d6c97f3096 --- /dev/null +++ b/recipes/genometools-genometools/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 49fe7f2880ff9dace820764fe0fd87ad172d2eeb475ed8a1d85ee8433b8446b5 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [compile sfx-linlcp.o] + [compile sfx-lwcheck.o] + [compile sfx-mappedstr.o] + [compile sfx-maprange.o] + [compile sfx-opt.o] + [compile sfx-outprj.o] + [compile sfx-partssuf.o] + [compile sfx-radixsort.o] + [compile sfx-run.o] + [compile sfx-sain.o] + [compile sfx-shortreadsort.o] + [compile sfx-suffixer.o] + [compile sfx-suffixgetset.o] + [compile sfx-suftaborder.o] + [compile shu-dfs.o] + [compile shu-divergence.o] + [compile shu-encseq-gc.o] + [compile shu-genomediff.o] + [compile shu_unitfile.o] + [compile spaced-seeds.o] + [compile specialrank.o] + [compile spmsuftab.o] + [compile squarededist.o] + [compile substriter.o] + [compile tagerator.o] + [compile test-mappedstr.o] + [compile test-maxpairs.o] + [compile test-mergeesa.o] + [compile test-mtrieins.o] + [compile test-pairwise.o] + [compile turnwheels.o] + [compile twobits2kmers.o] + [compile tyr-map.o] + [compile tyr-mersplit.o] + [compile tyr-mkindex.o] + [compile tyr-occratio.o] + [compile tyr-search.o] + [compile xdrop.o] + [compile gt_ltrclustering.o] + [compile gt_ltrdigest.o] + [compile gt_ltrharvest.o] + [compile ltr_classify_stream.o] + [compile ltr_cluster_prepare_seq_visitor.o] + [compile ltr_cluster_stream.o] + [compile ltr_four_char_motif.o] + [compile ltr_input_check_visitor.o] + [compile ltr_orf_annotator_stream.o] + [compile ltr_refseq_match_stream.o] + [compile ltrdigest_file_out_stream.o] + [compile ltrdigest_pbs_visitor.o] + [compile ltrdigest_pdom_visitor.o] + [compile ltrdigest_ppt_visitor.o] + [compile ltrdigest_strand_assign_visitor.o] + [compile ltrharvest_fasta_out_stream.o] + [compile ltrharvest_fasta_out_visitor.o] + [compile ltrharvest_stream.o] + [compile ltrharvest_tabout_stream.o] + [compile ltrharvest_tabout_visitor.o] + [compile pdom_model_set.o] + [compile metagenomethreader.o] + [compile mg_codon.o] + [compile mg_combinedscore.o] + [compile mg_compute_gene_prediction.o] + [compile mg_computepath.o] + [compile mg_outputwriter.o] + [compile mg_reverse.o] + [compile mg_xmlparser.o] + [compile block.o] + [compile canvas.o] + [compile canvas_cairo.o] + In file included from src/annotationsketch/canvas_cairo.c:34: + /opt/conda/conda-bld/genometools-genometools_1734292895720/work/src/annotationsketch/graphics_cairo_api.h:21:10: fatal error: cairo.h: No such file or directory + 21 | #include + | ^~~~~~~~~ + compilation terminated. + make: *** [Makefile:839: obj/src/annotationsketch/canvas_cairo.o] Error 1 + make: *** Waiting for unfinished jobs.... + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/genometools-genometools_1734292895720/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/genometools-genometools_1734292895720/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + dependency issue diff --git a/recipes/genometools-genometools/build_failure.linux-aarch64.yaml b/recipes/genometools-genometools/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..80b393942a11d --- /dev/null +++ b/recipes/genometools-genometools/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 49fe7f2880ff9dace820764fe0fd87ad172d2eeb475ed8a1d85ee8433b8446b5 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [compile sfx-radixsort.o] + [compile sfx-run.o] + [compile sfx-sain.o] + [compile sfx-shortreadsort.o] + [compile sfx-suffixer.o] + [compile sfx-suffixgetset.o] + [compile sfx-suftaborder.o] + [compile shu-dfs.o] + [compile shu-divergence.o] + [compile shu-encseq-gc.o] + [compile shu-genomediff.o] + [compile shu_unitfile.o] + [compile spaced-seeds.o] + [compile specialrank.o] + [compile spmsuftab.o] + [compile squarededist.o] + [compile substriter.o] + [compile tagerator.o] + [compile test-mappedstr.o] + [compile test-maxpairs.o] + [compile test-mergeesa.o] + [compile test-mtrieins.o] + [compile test-pairwise.o] + [compile turnwheels.o] + [compile twobits2kmers.o] + [compile tyr-map.o] + [compile tyr-mersplit.o] + [compile tyr-mkindex.o] + [compile tyr-occratio.o] + [compile tyr-search.o] + [compile xdrop.o] + [compile gt_ltrclustering.o] + [compile gt_ltrdigest.o] + [compile gt_ltrharvest.o] + [compile ltr_classify_stream.o] + [compile ltr_cluster_prepare_seq_visitor.o] + [compile ltr_cluster_stream.o] + [compile ltr_four_char_motif.o] + [compile ltr_input_check_visitor.o] + [compile ltr_orf_annotator_stream.o] + [compile ltr_refseq_match_stream.o] + [compile ltrdigest_file_out_stream.o] + [compile ltrdigest_pbs_visitor.o] + [compile ltrdigest_pdom_visitor.o] + [compile ltrdigest_ppt_visitor.o] + [compile ltrdigest_strand_assign_visitor.o] + [compile ltrharvest_fasta_out_stream.o] + [compile ltrharvest_fasta_out_visitor.o] + [compile ltrharvest_stream.o] + [compile ltrharvest_tabout_stream.o] + [compile ltrharvest_tabout_visitor.o] + [compile pdom_model_set.o] + [compile metagenomethreader.o] + [compile mg_codon.o] + [compile mg_combinedscore.o] + [compile mg_compute_gene_prediction.o] + [compile mg_computepath.o] + [compile mg_outputwriter.o] + [compile mg_reverse.o] + [compile mg_xmlparser.o] + [compile block.o] + [compile canvas.o] + [compile canvas_cairo.o] + [compile canvas_cairo_context.o] + In file included from src/annotationsketch/canvas_cairo.c:34: + /opt/conda/conda-bld/genometools-genometools_1734271395265/work/src/annotationsketch/graphics_cairo_api.h:21:10: fatal error: cairo.h: No such file or directory + 21 | #include + | ^~~~~~~~~ + compilation terminated. + make: *** [Makefile:839: obj/src/annotationsketch/canvas_cairo.o] Error 1 + make: *** Waiting for unfinished jobs.... + In file included from src/annotationsketch/canvas_cairo_context.c:30: + /opt/conda/conda-bld/genometools-genometools_1734271395265/work/src/annotationsketch/canvas_cairo_context.h:21:10: fatal error: cairo.h: No such file or directory + 21 | #include + | ^~~~~~~~~ + compilation terminated. + make: *** [Makefile:840: obj/src/annotationsketch/canvas_cairo_context.o] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/genometools-genometools_1734271395265/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/genometools-genometools_1734271395265/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + dependency issue diff --git a/recipes/genometools-genometools/build_failure.osx-64.yaml b/recipes/genometools-genometools/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..84bcdfdb3899e --- /dev/null +++ b/recipes/genometools-genometools/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 49fe7f2880ff9dace820764fe0fd87ad172d2eeb475ed8a1d85ee8433b8446b5 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [compile test-mtrieins.o] + [compile test-pairwise.o] + [compile turnwheels.o] + [compile twobits2kmers.o] + [compile tyr-map.o] + [compile tyr-mersplit.o] + [compile tyr-mkindex.o] + [compile tyr-occratio.o] + [compile tyr-search.o] + [compile xdrop.o] + [compile gt_ltrclustering.o] + [compile gt_ltrdigest.o] + [compile gt_ltrharvest.o] + [compile ltr_classify_stream.o] + [compile ltr_cluster_prepare_seq_visitor.o] + [compile ltr_cluster_stream.o] + [compile ltr_four_char_motif.o] + [compile ltr_input_check_visitor.o] + [compile ltr_orf_annotator_stream.o] + [compile ltr_refseq_match_stream.o] + [compile ltrdigest_file_out_stream.o] + [compile ltrdigest_pbs_visitor.o] + [compile ltrdigest_pdom_visitor.o] + [compile ltrdigest_ppt_visitor.o] + [compile ltrdigest_strand_assign_visitor.o] + [compile ltrharvest_fasta_out_stream.o] + [compile ltrharvest_fasta_out_visitor.o] + [compile ltrharvest_stream.o] + [compile ltrharvest_tabout_stream.o] + [compile ltrharvest_tabout_visitor.o] + [compile pdom_model_set.o] + [compile metagenomethreader.o] + [compile mg_codon.o] + [compile mg_combinedscore.o] + [compile mg_compute_gene_prediction.o] + [compile mg_computepath.o] + [compile mg_outputwriter.o] + [compile mg_reverse.o] + [compile mg_xmlparser.o] + [compile lualib.o] + [compile md5.o] + [compile md5lib.o] + [compile des56.o] + [compile ldes56.o] + [compile compat-5.2.o] + [compile lfs.o] + [compile lpeg.o] + [compile bgzf.o] + [compile kstring.o] + [compile bam_aux.o] + [compile bam.o] + [compile bam_import.o] + [compile sam.o] + [compile bam_index.o] + [compile bam_pileup.o] + [compile bam_lpileup.o] + [compile bam_md.o] + [compile razf.o] + [compile faidx.o] + [compile bedidx.o] + [compile knetfile.o] + [compile bam_sort.o] + [compile sam_header.o] + [compile bam_reheader.o] + [compile kprobaln.o] + [compile bam_cat.o] + [compile xmlparse.o] + [compile xmlrole.o] + [compile xmltok.o] + [compile regcomp.o] + [compile regerror.o] + [compile regexec.o] + [compile tre-ast.o] + [compile tre-compile.o] + [compile tre-filter.o] + [compile tre-match-backtrack.o] + [compile tre-match-parallel.o] + [compile tre-mem.o] + [compile tre-parse.o] + [compile tre-stack.o] + [compile xmalloc.o] + [compile blocksort.o] + [compile huffman.o] + [compile crctable.o] + [compile randtable.o] + [compile compress.o] + [compile decompress.o] + [compile bzlib.o] + [compile adler32.o] + [compile compress.o] + [compile crc32.o] + [compile gzclose.o] + [compile gzlib.o] + [compile gzread.o] + [compile gzwrite.o] + [compile uncompr.o] + [compile deflate.o] + [compile trees.o] + [compile zutil.o] + [compile inflate.o] +# Last 100 lines of the build log. +category: |- + dependency issue diff --git a/recipes/genometools-genometools/meta.yaml b/recipes/genometools-genometools/meta.yaml index 06e8cc51fe99b..ddf70b7375b29 100644 --- a/recipes/genometools-genometools/meta.yaml +++ b/recipes/genometools-genometools/meta.yaml @@ -13,7 +13,7 @@ source: build: # distutils was removed from python 3.12 skip: true # [py == 312 ] - number: 3 + number: 4 run_exports: - {{ pin_subpackage('genometools-genometools', max_pin="x") }} diff --git a/recipes/genrich/meta.yaml b/recipes/genrich/meta.yaml index 9170b66d3c2b0..5c0881551b1e1 100644 --- a/recipes/genrich/meta.yaml +++ b/recipes/genrich/meta.yaml @@ -33,7 +33,7 @@ requirements: build: - number: 4 + number: 5 test: diff --git a/recipes/gentle/build_failure.linux-64.yaml b/recipes/gentle/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..ef8a553fe0574 --- /dev/null +++ b/recipes/gentle/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 93a6112ec302ac24988ab039c82475e1be11fbefacd10c237e74257d38485e96 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - debian:gentle + - biotools:gentle + recipe-maintainers: + - smoe + + + source tree in: /opt/conda/conda-bld/gentle_1733935857623/work + export PREFIX=/opt/conda/conda-bld/gentle_1733935857623/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/conda/conda-bld/gentle_1733935857623/_build_env + export SRC_DIR=/opt/conda/conda-bld/gentle_1733935857623/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gentle-1.9.5.alpha1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gentle-1.9.5.alpha1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gentle-1.9.5.alpha1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gentle-1.9.5.alpha1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + aclocal + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + libtoolize --automake --force --copy + /opt/conda/conda-bld/gentle_1733935857623/work/conda_build.sh: line 7: libtoolize: command not found + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/gentle_1733935857623/work/conda_build.sh']' returned non-zero exit status 127. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/gentle_1733935857623/work/conda_build.sh']' returned non-zero exit status 127. +# Last 100 lines of the build log. diff --git a/recipes/gentle/build_failure.osx-64.yaml b/recipes/gentle/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..cf3b92b1932fd --- /dev/null +++ b/recipes/gentle/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 93a6112ec302ac24988ab039c82475e1be11fbefacd10c237e74257d38485e96 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - libprotobuf 5.28.2 h8b30cf6_0 + - libssh2 1.11.1 h3dc7d44_0 + - mysql-common 9.0.1 h4d37847_3 + - sqlite 3.47.2 h2e4c9dc_0 + - xz 5.6.3 h357f2ed_1 + - libcurl 8.10.1 h58e7537_0 + - libtiff 4.6.0 h603087a_4 + - mysql-client 9.0.1 h2381dc1_3 + - mysql-libs 9.0.1 h2381dc1_3 + - mysql-server 9.0.1 h4f79b90_3 + - mysql-devel 9.0.1 h4d37847_3 + - wxwidgets 3.2.6 h6e2ffcd_0 + - mysql 9.0.1 h88f4db0_3 + run: + - libsqlite >=3.47.2,<4.0a0 + - libcxx >=18 + - wxwidgets >=3.2.6,<3.3.0a0 + - sqlite + - tinyxml + - mysql + test: + commands: + - test -e $PREFIX/bin/GENtle + about: + description: 'GENtle provides a GUI for amino acid editing, plasmid maps, + + restriction and ligation, alignments, sequencer data import, + + calculators, gel image display, PCR, and much more. + + ' + dev_url: https://github.com/GENtle-persons/gentle-m + home: https://github.com/GENtle-persons/gentle-m + license: GPL-2.0-or-later + license_file: COPYING + summary: Software suite for DNA cloning + extra: + copy_test_source_files: true + final: true + identifiers: + - debian:gentle + - biotools:gentle + recipe-maintainers: + - smoe + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/gentle_1733951478465/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/gentle_1733951478465/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/gentle_1733951478465/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/gentle_1733951478465/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gentle-1.9.5.alpha1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gentle-1.9.5.alpha1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gentle-1.9.5.alpha1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gentle-1.9.5.alpha1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix +# Last 100 lines of the build log. diff --git a/recipes/gentle/meta.yaml b/recipes/gentle/meta.yaml index bede2051b03a7..a3402ba1f5b1f 100644 --- a/recipes/gentle/meta.yaml +++ b/recipes/gentle/meta.yaml @@ -10,7 +10,7 @@ source: md5: e14ebb0d99e370584fc8a9fa3e178278 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('gentle', max_pin="x") }} diff --git a/recipes/get_fasta_info/meta.yaml b/recipes/get_fasta_info/meta.yaml index 4798e38f24e42..2c9e7368179fc 100644 --- a/recipes/get_fasta_info/meta.yaml +++ b/recipes/get_fasta_info/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/get_orfs/meta.yaml b/recipes/get_orfs/meta.yaml index c4543774d55d6..bce146214a4be 100644 --- a/recipes/get_orfs/meta.yaml +++ b/recipes/get_orfs/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage('get_orfs', max_pin="x") }} diff --git a/recipes/gfa1/meta.yaml b/recipes/gfa1/meta.yaml index 7a04354468ed6..cd52fb6e008a0 100644 --- a/recipes/gfa1/meta.yaml +++ b/recipes/gfa1/meta.yaml @@ -10,7 +10,7 @@ source: sha256: ignored build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/gfaffix/build_failure.osx-arm64.yaml b/recipes/gfaffix/build_failure.osx-arm64.yaml new file mode 100644 index 0000000000000..aacd9d2dbe901 --- /dev/null +++ b/recipes/gfaffix/build_failure.osx-arm64.yaml @@ -0,0 +1,104 @@ +recipe_sha: f89a731f92d6aacb9cf0b581472f85bc2d9d2b2bf15abfcd20988cc10fd145c1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: false # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - llvm-tools 18.1.8 h5090b49_2 + - cctools_osx-arm64 1010.6 h908b477_2 + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/gfaffix_1736286808328/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + - clang 18.1.8 default_h675cc0c_5 + - clangxx 18.1.8 default_h675cc0c_5 + - compiler-rt_osx-arm64 18.1.8 h832e737_1 + - compiler-rt 18.1.8 h856b3c1_1 + - clang_impl_osx-arm64 18.1.8 h2ae9ea5_23 + - clang_osx-arm64 18.1.8 h07b0088_23 + - rust_osx-arm64 1.83.0 h114d0d1_1 + run: [] + run_constrained: + - __osx >=11.0 + test: + commands: + - gfaffix --help + about: + dev_url: https://github.com/marschall-lab/gfaffix + home: https://github.com/marschall-lab/GFAffix + license: MIT + license_family: MIT + license_file: LICENSE.md + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + summary: GFAffix identifies and collapses walk-preserving shared affixes in variation + graphs + extra: + additional-platforms: + - osx-arm64 + - linux-aarch64 + copy_test_source_files: true + final: true + recipe-maintainers: + - danydoerr + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/gfaffix_1736286808328/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/gfaffix_1736286808328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/gfaffix_1736286808328/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/gfaffix_1736286808328/work + INFO: activate_clang_osx-arm64.sh made the following environmental changes: + AR=arm64-apple-darwin20.0.0-ar + AS=arm64-apple-darwin20.0.0-as + CC=arm64-apple-darwin20.0.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/gfaffix_1736286808328/work/conda_build.sh']' returned non-zero exit status 101. + CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gfaffix-0.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=arm64-apple-darwin20.0.0-checksyms + CLANG=arm64-apple-darwin20.0.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=11.0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=arm64-apple-darwin20.0.0 + CONDA_TOOLCHAIN_HOST=arm64-apple-darwin20.0.0 + CPP=arm64-apple-darwin20.0.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang-cpp + DEBUG_CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/gfaffix-0.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=arm64-apple-darwin20.0.0 + INSTALL_NAME_TOOL=arm64-apple-darwin20.0.0-install_name_tool + LD=arm64-apple-darwin20.0.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=arm64-apple-darwin20.0.0-libtool + LIPO=arm64-apple-darwin20.0.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=arm64-apple-darwin20.0.0-nm + NMEDIT=arm64-apple-darwin20.0.0-nmedit + OBJC=arm64-apple-darwin20.0.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang + OTOOL=arm64-apple-darwin20.0.0-otool + PAGESTUFF=arm64-apple-darwin20.0.0-pagestuff + RANLIB=arm64-apple-darwin20.0.0-ranlib + REDO_PREBINDING=arm64-apple-darwin20.0.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk + SEGEDIT=arm64-apple-darwin20.0.0-segedit + SEG_ADDR_TABLE=arm64-apple-darwin20.0.0-seg_addr_table + SEG_HACK=arm64-apple-darwin20.0.0-seg_hack + SIZE=arm64-apple-darwin20.0.0-size + STRINGS=arm64-apple-darwin20.0.0-strings + STRIP=arm64-apple-darwin20.0.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_arm64_apple_darwin20_0_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=arm64-apple-darwin20.0.0 + host_alias=arm64-apple-darwin20.0.0 +# Last 100 lines of the build log. diff --git a/recipes/gfaffix/meta.yaml b/recipes/gfaffix/meta.yaml index bf9d4be087033..2507fe9c9cf04 100644 --- a/recipes/gfaffix/meta.yaml +++ b/recipes/gfaffix/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x.x", allow_no_other_outputs=True) }} diff --git a/recipes/gfastats/meta.yaml b/recipes/gfastats/meta.yaml index 606f01e6dd06c..42294a4fa2be2 100644 --- a/recipes/gfastats/meta.yaml +++ b/recipes/gfastats/meta.yaml @@ -10,7 +10,7 @@ source: sha256: d98a14559ad3440ead7e6b04302ecaf1c44cffff40d64725d653b7e885a56a98 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('gfastats', max_pin="x") }} diff --git a/recipes/gfatools/meta.yaml b/recipes/gfatools/meta.yaml index c62fae922e304..4d5afbcee74ca 100644 --- a/recipes/gfatools/meta.yaml +++ b/recipes/gfatools/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/gffcompare/meta.yaml b/recipes/gffcompare/meta.yaml index 6204e94d07a36..1edcf778225b7 100644 --- a/recipes/gffcompare/meta.yaml +++ b/recipes/gffcompare/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} diff --git a/recipes/gffread/meta.yaml b/recipes/gffread/meta.yaml index 5ae18c806919d..679f703d7940e 100644 --- a/recipes/gffread/meta.yaml +++ b/recipes/gffread/meta.yaml @@ -12,7 +12,7 @@ source: - Makefile.patch build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage("gffread", max_pin="x.x") }} diff --git a/recipes/gfmix/meta.yaml b/recipes/gfmix/meta.yaml index 4d6587580a8fa..6275759780438 100644 --- a/recipes/gfmix/meta.yaml +++ b/recipes/gfmix/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/ggcat/build_failure.osx-64.yaml b/recipes/ggcat/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..6652cdeb84f8b --- /dev/null +++ b/recipes/ggcat/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 76e781dcdfa0a76b97155733e0370bbc0315f0bee4f7d9c3d71c45a038951d3e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/ggcat_1733978716599/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + - libxml2 2.13.5 he8ee3e7_1 + - llvm-tools 18.1.8 h9ce406d_2 + - cctools_osx-64 1010.6 h00edd4c_2 + - clang 18.1.8 default_h179603d_5 + - rust_osx-64 1.83.0 hca1c201_1 + host: + - libzlib 1.3.1 hd23fc13_2 + - zlib 1.3.1 hd23fc13_2 + run: + - libzlib >=1.3.1,<2.0a0 + run_constrained: + - __osx >=10.13 + test: + commands: + - ggcat --help + about: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + dev_url: https://github.com/algbio/ggcat + home: https://github.com/algbio/ggcat + license: MIT + license_family: MIT + api.build( + license_file: LICENSE + summary: 'Compacted and colored de Bruijn graph construction and querying. + + ' + extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + copy_test_source_files: true + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/ggcat_1733978716599/work/conda_build.sh']' returned non-zero exit status 101. + final: true + identifiers: + - doi:10.1101/gr.277615.122 + recipe-maintainers: + - guilucand + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/ggcat_1733978716599/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/ggcat_1733978716599/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/ggcat_1733978716599/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/ggcat_1733978716599/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ggcat-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ggcat-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 +# Last 100 lines of the build log. diff --git a/recipes/ggcat/build_failure.osx-arm64.yaml b/recipes/ggcat/build_failure.osx-arm64.yaml new file mode 100644 index 0000000000000..f7022acd88956 --- /dev/null +++ b/recipes/ggcat/build_failure.osx-arm64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 76e781dcdfa0a76b97155733e0370bbc0315f0bee4f7d9c3d71c45a038951d3e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + - clang-18 18.1.8 default_h5c12605_5 + - llvm-tools-18 18.1.8 h5090b49_2 + host: + - libzlib 1.3.1 h8359307_2 + - zlib 1.3.1 h8359307_2 + run: + - libzlib >=1.3.1,<2.0a0 + run_constrained: + - __osx >=11.0 + test: + commands: + raise subprocess.CalledProcessError(proc.returncode, _args) + - ggcat --help + about: + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/ggcat_1733861236607/work/conda_build.sh']' returned non-zero exit status 101. + + dev_url: https://github.com/algbio/ggcat + home: https://github.com/algbio/ggcat + license: MIT + license_family: MIT + license_file: LICENSE + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + summary: 'Compacted and colored de Bruijn graph construction and querying. + + ' + extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + copy_test_source_files: true + final: true + identifiers: + - doi:10.1101/gr.277615.122 + recipe-maintainers: + - guilucand + + + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/ggcat_1733861236607/work/conda_build.sh']' returned non-zero exit status 101. + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/ggcat_1733861236607/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/ggcat_1733861236607/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/ggcat_1733861236607/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/ggcat_1733861236607/work + INFO: activate_clang_osx-arm64.sh made the following environmental changes: + AR=arm64-apple-darwin20.0.0-ar + AS=arm64-apple-darwin20.0.0-as + CC=arm64-apple-darwin20.0.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang + CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ggcat-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=arm64-apple-darwin20.0.0-checksyms + CLANG=arm64-apple-darwin20.0.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=11.0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=arm64-apple-darwin20.0.0 + CONDA_TOOLCHAIN_HOST=arm64-apple-darwin20.0.0 + CPP=arm64-apple-darwin20.0.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang-cpp + DEBUG_CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ggcat-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=arm64-apple-darwin20.0.0 + INSTALL_NAME_TOOL=arm64-apple-darwin20.0.0-install_name_tool + LD=arm64-apple-darwin20.0.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=arm64-apple-darwin20.0.0-libtool + LIPO=arm64-apple-darwin20.0.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=arm64-apple-darwin20.0.0-nm + NMEDIT=arm64-apple-darwin20.0.0-nmedit + OBJC=arm64-apple-darwin20.0.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang + OTOOL=arm64-apple-darwin20.0.0-otool + PAGESTUFF=arm64-apple-darwin20.0.0-pagestuff + RANLIB=arm64-apple-darwin20.0.0-ranlib + REDO_PREBINDING=arm64-apple-darwin20.0.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk + SEGEDIT=arm64-apple-darwin20.0.0-segedit + SEG_ADDR_TABLE=arm64-apple-darwin20.0.0-seg_addr_table + SEG_HACK=arm64-apple-darwin20.0.0-seg_hack + SIZE=arm64-apple-darwin20.0.0-size + STRINGS=arm64-apple-darwin20.0.0-strings + STRIP=arm64-apple-darwin20.0.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_arm64_apple_darwin20_0_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=arm64-apple-darwin20.0.0 + host_alias=arm64-apple-darwin20.0.0 +# Last 100 lines of the build log. diff --git a/recipes/ggcat/meta.yaml b/recipes/ggcat/meta.yaml index 6410e45bb271f..fef742937b0cb 100644 --- a/recipes/ggcat/meta.yaml +++ b/recipes/ggcat/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('ggcat', max_pin="x.x") }} diff --git a/recipes/ghostz/meta.yaml b/recipes/ghostz/meta.yaml index 1cf2f79d15768..3a572257eac4c 100644 --- a/recipes/ghostz/meta.yaml +++ b/recipes/ghostz/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: true # [osx] - number: 5 + number: 6 requirements: build: diff --git a/recipes/ginpiper/meta.yaml b/recipes/ginpiper/meta.yaml index 60214638d22c9..1b25ad3da6296 100644 --- a/recipes/ginpiper/meta.yaml +++ b/recipes/ginpiper/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256}} build: - number: 2 + number: 3 noarch: generic requirements: diff --git a/recipes/glimpse-bio/meta.yaml b/recipes/glimpse-bio/meta.yaml index a5023f751e4f5..aac644d989cc7 100644 --- a/recipes/glimpse-bio/meta.yaml +++ b/recipes/glimpse-bio/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 source: url: https://github.com/odelaneau/GLIMPSE/archive/refs/tags/v{{ version }}.tar.gz diff --git a/recipes/glnexus/meta.yaml b/recipes/glnexus/meta.yaml index b52e84f27c388..11a482f01cb48 100644 --- a/recipes/glnexus/meta.yaml +++ b/recipes/glnexus/meta.yaml @@ -9,7 +9,7 @@ source: sha256: e77e4fdb611a7c88eb23a9df96b6d46468c80d0e7153c6f40a0db4b4cadec24c build: - number: 3 + number: 4 skip: True # [osx] requirements: diff --git a/recipes/gloome/build_failure.linux-64.yaml b/recipes/gloome/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..787414a8d83f1 --- /dev/null +++ b/recipes/gloome/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 22df6ab00514307c26fc4617718e2a6dacbd20470e09aca498777b79cf1b8205 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + 2024-12-11T17:07:49 noarch Writing patched repodata + 2024-12-11T17:07:49 noarch Building current_repodata subset + 2024-12-11T17:07:49 noarch Writing current_repodata subset + 2024-12-11T17:07:49 noarch Writing index HTML + /opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (/opt/recipe/meta.yaml). + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml + Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for gloome + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['gloome-VR01.266-h9948957_4.tar.bz2'] + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/gloome_1733936869903/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/gloome_1733936869903/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.43-h4bf12b8_2 conda-forge + binutils_linux-64: 2.43-h4852527_2 conda-forge + gcc_impl_linux-64: 13.3.0-hfea6d02_1 conda-forge + gcc_linux-64: 13.3.0-hc28eda2_7 conda-forge + gxx_impl_linux-64: 13.3.0-hdbfa832_1 conda-forge + gxx_linux-64: 13.3.0-h6834431_7 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libsanitizer: 13.3.0-heb74ff8_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + make: 4.4.1-hb9d3cd8_2 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: gainLoss_6a90c22f84.tar.gz + Downloading https://gloome.tau.ac.il/source/gainLoss.tar.gz + WARNING: Error: HTTP 400 BAD REQUEST for url + Elapsed: 00:00.501704 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download https://gloome.tau.ac.il/source/gainLoss.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/gloome/meta.yaml b/recipes/gloome/meta.yaml index b8a82a7c7e554..98bba857925fc 100644 --- a/recipes/gloome/meta.yaml +++ b/recipes/gloome/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 skip: True # [osx] requirements: diff --git a/recipes/gmap/meta.yaml b/recipes/gmap/meta.yaml index 623703ad60d50..deab8da1453dc 100644 --- a/recipes/gmap/meta.yaml +++ b/recipes/gmap/meta.yaml @@ -13,7 +13,7 @@ source: - single_quote_paths.patch build: - number: 0 + number: 1 skip: True # [osx and x86_64] run_exports: - {{ pin_subpackage('gmap', max_pin=None) }} diff --git a/recipes/gmtk/meta.yaml b/recipes/gmtk/meta.yaml index c2027036abc70..99af28c90e38f 100644 --- a/recipes/gmtk/meta.yaml +++ b/recipes/gmtk/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.4.4" build: - number: 15 + number: 16 skip: True # [osx] source: diff --git a/recipes/gnu-wget/meta.yaml b/recipes/gnu-wget/meta.yaml index 3de5bb94808e1..add357eac8ce7 100644 --- a/recipes/gnu-wget/meta.yaml +++ b/recipes/gnu-wget/meta.yaml @@ -9,7 +9,7 @@ source: url: http://ftp.gnu.org/gnu/wget/wget-{{ version }}.tar.xz build: - number: 9 + number: 10 requirements: build: diff --git a/recipes/goat/meta.yaml b/recipes/goat/meta.yaml index 2058f6236b193..eb4c6c29c097c 100644 --- a/recipes/goat/meta.yaml +++ b/recipes/goat/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 source: url: https://github.com/genomehubs/goat-cli/archive/{{ version }}.tar.gz diff --git a/recipes/gocr/0.50/meta.yaml b/recipes/gocr/0.50/meta.yaml index 87754f8a9a8f1..3ac7271e4716d 100644 --- a/recipes/gocr/0.50/meta.yaml +++ b/recipes/gocr/0.50/meta.yaml @@ -3,7 +3,7 @@ package: version: 0.50 build: - number: 5 + number: 6 #skip: True # [osx] source: diff --git a/recipes/goldrush/build_failure.osx-64.yaml b/recipes/goldrush/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..367f17781bff6 --- /dev/null +++ b/recipes/goldrush/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a6d9b9752a139547f76c02ced782f9bfc1a98ef08c5bc79454b151724dda32fe # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + 441 | AllPathsSearchResult leftResult = allPathsSearch( + | ^ + ../subprojects/goldpolish/subprojects/sealer/Graph/ConstrainedBidiBFSVisitor.h:411:30: note: in instantiation of member function 'ConstrainedBidiBFSVisitor>::buildPaths' requested here + 411 | PathSearchResult result = buildPaths(*i); + | ^ + ../subprojects/goldpolish/subprojects/sealer/Graph/ConstrainedBidiBFSVisitor.h:247:29: note: in instantiation of member function 'ConstrainedBidiBFSVisitor>::buildPaths' requested here + 247 | PathSearchResult result = buildPaths(); + | ^ + ../subprojects/goldpolish/subprojects/sealer/Konnector/konnector.h:323:30: note: in instantiation of member function 'ConstrainedBidiBFSVisitor>::pathsToGoal' requested here + 323 | result.pathResult = visitor.pathsToGoal(paths); + | ^ + ../subprojects/goldpolish/subprojects/sealer/sealer.cpp:434:30: note: in instantiation of function template specialization 'connectPairs>' requested here + 434 | ConnectPairsResult result = connectPairs(k, read1, read2, g, params); + | ^ + ../subprojects/goldpolish/subprojects/sealer/sealer.cpp:624:21: note: in instantiation of function template specialization 'merge>' requested here + 624 | string tempSeq = merge(g, k, read2_it->second, read1, read2, params, g_count); + | ^ + ../subprojects/goldpolish/subprojects/sealer/sealer.cpp:1056:3: note: in instantiation of function template specialization 'kRun>' requested here + 1056 | kRun(params, opt::k, g, allmerged, flanks, gapsclosed); + | ^ + $BUILD_PREFIX/bin/../include/c/v1/__iterator/iterator.h:23:29: note: 'iterator>' has been explicitly marked deprecated here + 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX17 iterator { + | ^ + $BUILD_PREFIX/bin/../include/c/v1/__config:1001:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' + 1001 | # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED + | ^ + $BUILD_PREFIX/bin/../include/c/v1/__config:974:49: note: expanded from macro '_LIBCPP_DEPRECATED' + 974 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) + | ^ + 7 warnings generated. + [57/57] Linking target subprojects/goldpolish/subprojects/sealer/sealer-gr + [0/1] Installing files. + Installing goldrush_path/goldrush-path to $PREFIX/bin + Skipping RPATH fixing + Installing subprojects/goldpolish/src/goldpolish-index to $PREFIX/bin + Skipping RPATH fixing + Installing subprojects/goldpolish/src/goldpolish-targeted-bfs to $PREFIX/bin + Skipping RPATH fixing + Installing subprojects/goldpolish/src/goldpolish-hold to $PREFIX/bin + Skipping RPATH fixing + Installing subprojects/goldpolish/subprojects/ntedit/ntedit-gr to $PREFIX/bin + Skipping RPATH fixing + Installing subprojects/goldpolish/subprojects/sealer/sealer-gr to $PREFIX/bin + Skipping RPATH fixing + Installing $SRC_DIR/bin/goldrush to $PREFIX/bin + Installing $SRC_DIR/bin/goldrush-ulimit to $PREFIX/bin + Installing $SRC_DIR/subprojects/goldpolish/scripts/goldpolish_utils.py to $PREFIX/bin + Installing $SRC_DIR/subprojects/goldpolish/scripts/goldpolish to $PREFIX/bin + Installing $SRC_DIR/subprojects/goldpolish/scripts/goldpolish-autoclean to $PREFIX/bin + Installing $SRC_DIR/subprojects/goldpolish/scripts/goldpolish-make to $PREFIX/bin + Installing $SRC_DIR/subprojects/goldpolish/scripts/goldpolish-mask to $PREFIX/bin + Installing $SRC_DIR/subprojects/goldpolish/scripts/goldpolish-ntedit to $PREFIX/bin + Installing $SRC_DIR/subprojects/goldpolish/scripts/goldpolish-polish-batch to $PREFIX/bin + Installing $SRC_DIR/subprojects/goldpolish/scripts/goldpolish-reaper to $PREFIX/bin + Installing $SRC_DIR/subprojects/goldpolish/scripts/goldpolish-to-upper to $PREFIX/bin + Installing $SRC_DIR/subprojects/goldpolish/scripts/goldpolish-target.py to $PREFIX/bin + Installing $SRC_DIR/subprojects/goldpolish/scripts/goldpolish-target-run-pipeline.smk to $PREFIX/bin + Installing $SRC_DIR/subprojects/goldpolish/scripts/goldpolish-target-extract-seq.py to $PREFIX/bin + Installing $SRC_DIR/subprojects/goldpolish/scripts/goldpolish-target-update-mapping.py to $PREFIX/bin + Installing $SRC_DIR/subprojects/goldpolish/scripts/goldpolish-target-post-processing.py to $PREFIX/bin + + Resource usage statistics from building goldrush: + Process count: 9 + CPU time: Sys=0:00:06.6, User=0:01:35.8 + Memory: 843.4M + Disk usage: 101.4K + Time elapsed: 0:00:48.4 + + + Packaging goldrush + Packaging goldrush-1.2.1-py39ha0dc3d9_3 + number of files: 23 + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2765, in build + newly_built_packages = bundlers[pkg_type]( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1874, in bundle_conda + files = post_process_files(metadata, initial_files) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1653, in post_process_files + post_build(m, new_files, build_python=python) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1759, in post_build + post_process_shared_lib(m, f, prefix_files, host_prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1635, in post_process_shared_lib + mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 477, in mk_relative_osx + names = macho.otool(path, prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 221, in otool + lines = check_output([otool, "-l", path], stderr=STDOUT).decode("utf-8") + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 421, in check_output + return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 526, in run + raise CalledProcessError(retcode, process.args, + subprocess.CalledProcessError: Command '['/opt/mambaforge/envs/bioconda/conda-bld/goldrush_1734283214107/_build_env/bin/llvm-otool', '-l', '/opt/mambaforge/envs/bioconda/conda-bld/goldrush_1734283214107/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin/ntedit-gr']' died with . +# Last 100 lines of the build log. diff --git a/recipes/goldrush/meta.yaml b/recipes/goldrush/meta.yaml index 8f9f9d54b4ba4..72739d9b6a937 100644 --- a/recipes/goldrush/meta.yaml +++ b/recipes/goldrush/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: true # [py < 38 or win or py > 39] - number: 2 + number: 3 run_exports: {{ pin_subpackage("goldrush", max_pin="x") }} requirements: diff --git a/recipes/gopeaks/meta.yaml b/recipes/gopeaks/meta.yaml index 568e7f7d2fbaa..73d4dce6a4a5a 100644 --- a/recipes/gopeaks/meta.yaml +++ b/recipes/gopeaks/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 36e13bf083089accbfef3d463bec16922dd5b5ad0e02db408404d6e5b361a80a build: - number: 2 + number: 3 skip: True # [win] script: - mkdir -p $PREFIX/bin diff --git a/recipes/gotohscan/meta.yaml b/recipes/gotohscan/meta.yaml index af671379efb1d..54563cef7a089 100644 --- a/recipes/gotohscan/meta.yaml +++ b/recipes/gotohscan/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.3" build: - number: 6 + number: 7 skip: True # [osx] source: diff --git a/recipes/grabix/meta.yaml b/recipes/grabix/meta.yaml index c08d290d74b4e..296884052d381 100644 --- a/recipes/grabix/meta.yaml +++ b/recipes/grabix/meta.yaml @@ -4,7 +4,7 @@ package: version: "0.1.8" build: - number: 10 + number: 11 run_exports: - {{ pin_subpackage('grabix', max_pin="x.x") }} @@ -31,4 +31,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/graphembed/build_failure.linux-64.yaml b/recipes/graphembed/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..5ae575ace9504 --- /dev/null +++ b/recipes/graphembed/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: b5dec8063b6c0b33a18a000805b15c0f6a283bcbc287b30a14aaf64b0a9519bf # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + 769 | sprs::MulAcc std::ops::Sub<&ndarray::ArrayBase, ndarray::Dim<[usize; 2]>>>, + | + + error[E0277]: the trait bound &ArrayBase, Dim<[usize; 2]>>: ndarray::impl_ops::ScalarOperand is not satisfied + --> /opt/conda/conda-bld/graphembed_1733953512994/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annembed-0.1.3/src/tools/svdapprox.rs:778:46 + | + 778 | let residue = csr_mat.to_dense() - &(q_mat.dot(&b)); + | ^ the trait ndarray::impl_ops::ScalarOperand is not implemented for &ArrayBase, Dim<[usize; 2]>>, which is required by ndarray::ArrayBase, ndarray::dimension::dim::Dim<[usize; 2]>>: Sub<&ArrayBase, Dim<[usize; 2]>>> + | + help: there are multiple different versions of crate ndarray in the dependency graph + --> /opt/conda/conda-bld/graphembed_1733953512994/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annembed-0.1.3/src/tools/svdapprox.rs:35:5 + | + 35 | use ndarray::{ + | ^^^^^^^ one version of crate ndarray is used here, as a direct dependency of the current crate + ... + 53 | use sprs::{prod, CsMat, CsMatView, TriMat}; + | ^^^^ one version of crate ndarray is used here, as a dependency of crate sprs + = help: you can use cargo tree to explore your dependency tree + = note: required for ndarray::ArrayBase, ndarray::dimension::dim::Dim<[usize; 2]>> to implement Sub<&ArrayBase, Dim<[usize; 2]>>> + + error[E0308]: mismatched types + --> /opt/conda/conda-bld/graphembed_1733953512994/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annembed-0.1.3/src/tools/svdapprox.rs:780:52 + | + 780 | let norm_residue = norm_frobenius_full(&residue.view()); + | ------------------- ^^^^^^^^^^^^^^^ expected &ArrayBase, _>, found &ArrayBase, Dim<...>> + | | + | arguments to this function are incorrect + | + = note: ArrayBase, Dim<...>> and ArrayBase, _> have similar names, but are actually distinct types + note: ArrayBase, Dim<...>> is defined in crate ndarray + --> /opt/conda/conda-bld/graphembed_1733953512994/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/ndarray-0.16.1/src/lib.rs:1280:1 + | + 1280 | pub struct ArrayBase + | ^^^^^^^^^^^^^^^^^^^^^^^^^^ + note: ArrayBase, _> is defined in crate ndarray + --> /opt/conda/conda-bld/graphembed_1733953512994/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/ndarray-0.15.6/src/lib.rs:1268:1 + | + 1268 | pub struct ArrayBase + | ^^^^^^^^^^^^^^^^^^^^^^^^^^ + = note: perhaps two different versions of crate ndarray are being used? + note: function defined here + --> /opt/conda/conda-bld/graphembed_1733953512994/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annembed-0.1.3/src/tools/svdapprox.rs:935:8 + | + 935 | pub fn norm_frobenius_full(v: &ArrayView) -> F { + | ^^^^^^^^^^^^^^^^^^^ ------------------- + + error[E0277]: the trait bound ndarray::ArrayBase, ndarray::dimension::dim::Dim<[usize; 2]>>: ndarray::linalg::impl_linalg::Dot, Dim<[usize; 1]>>> is not satisfied + --> /opt/conda/conda-bld/graphembed_1733953512994/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annembed-0.1.3/src/tools/svdapprox.rs:1001:21 + | + 1001 | v2 = a2.dot(&v1); + | --- ^^^ the trait ndarray::linalg::impl_linalg::Dot, Dim<[usize; 1]>>> is not implemented for ndarray::ArrayBase, ndarray::dimension::dim::Dim<[usize; 2]>> + | | + | required by a bound introduced by this call + | + = help: the following other types implement trait ndarray::linalg::impl_linalg::Dot: + ndarray::ArrayBase> implements ndarray::linalg::impl_linalg::Dot> + ndarray::ArrayBase> implements ndarray::linalg::impl_linalg::Dot>> + ndarray::ArrayBase> implements ndarray::linalg::impl_linalg::Dot>> + ndarray::ArrayBase> implements ndarray::linalg::impl_linalg::Dot>> + ndarray::ArrayBase> implements ndarray::linalg::impl_linalg::Dot>> + note: required by a bound in ndarray::linalg::impl_linalg::>>::dot + --> /opt/conda/conda-bld/graphembed_1733953512994/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/ndarray-0.16.1/src/linalg/impl_linalg.rs:252:17 + | + 251 | pub fn dot(&self, rhs: &Rhs) -> >::Output + | --- required by a bound in this associated function + 252 | where Self: Dot + | ^^^^^^^^ required by this bound in ndarray::linalg::impl_linalg::>>::dot + + Some errors have detailed explanations: E0277, E0308. + For more information about an error, try rustc --explain E0277. + error: could not compile annembed (lib) due to 8 previous errors + + Caused by: + process didn't exit successfully: rustc --crate-name annembed --edition=2021 /opt/conda/conda-bld/graphembed_1733953512994/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annembed-0.1.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="intel-mkl-static"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("blas-src", "default", "intel-mkl-static", "macos-accelerate", "openblas-static", "openblas-system", "simdeez_f", "stdsimd"))' -C metadata=8f1eac33f53e24f9 -C extra-filename=-8f1eac33f53e24f9 --out-dir /opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps -C linker=/opt/conda/conda-bld/graphembed_1733953512994/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps --extern anyhow=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libanyhow-2cb14037eccbaced.rmeta --extern bincode=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libbincode-482e393e0e18fdaa.rmeta --extern bson=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libbson-d5bbcbd7138537aa.rmeta --extern byteorder=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libbyteorder-b4135b9eba9ebb4c.rmeta --extern clap=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libclap-92556b47ba2de303.rmeta --extern cpu_time=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libcpu_time-ea65c8f791473a6d.rmeta --extern csv=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libcsv-825c0d0997d5f831.rmeta --extern env_logger=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libenv_logger-d764e6d126d74489.rmeta --extern hdrhistogram=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libhdrhistogram-e2d8a939df217a95.rmeta --extern hnsw_rs=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libhnsw_rs-dc967f8b64ffcbb5.rmeta --extern indexmap=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libindexmap-28a5b5c9a6c1d4f5.rmeta --extern indxvec=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libindxvec-fae3aa8f90fde38e.rmeta --extern katexit=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libkatexit-9024b258914dd9ea.so --extern lazy_static=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/liblazy_static-5690c89ce0b7662a.rmeta --extern log=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/liblog-054a084181905fb9.rmeta --extern ndarray=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libndarray-53913e88501ada34.rmeta --extern ndarray_linalg=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libndarray_linalg-b3fc3ee6d478eb95.rmeta --extern num_traits=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libnum_traits-aecc12c36341049b.rmeta --extern num_cpus=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libnum_cpus-eac44804cf0ac575.rmeta --extern parking_lot=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libparking_lot-c40253ae1fcc8c36.rmeta --extern quantiles=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libquantiles-2666ecc50ba7153c.rmeta --extern rand=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/librand-e08d048f75edbaf0.rmeta --extern rand_distr=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/librand_distr-378e05c7437d1c1a.rmeta --extern rand_xoshiro=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/librand_xoshiro-719e2c7b858e8d7f.rmeta --extern rayon=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/librayon-780c7a62a46944f8.rmeta --extern serde=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libserde-28c8573a09818418.rmeta --extern sprs=/opt/conda/conda-bld/graphembed_1733953512994/work/target/release/deps/libsprs-7086abe54952007f.rmeta --cap-lints allow -L /home/conda/.local/share/ocipkg/ghcr.io/rust-math/rust-mkl/linux/mkl-static-lp64-seq/__2020.1-3038006115 (exit status: 1) + warning: build failed, waiting for other jobs to finish... + error: failed to compile graphembed v0.0.8 (/opt/conda/conda-bld/graphembed_1733953512994/work), intermediate artifacts can be found at /opt/conda/conda-bld/graphembed_1733953512994/work/target. + To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/graphembed_1733953512994/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/graphembed_1733953512994/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. diff --git a/recipes/graphembed/meta.yaml b/recipes/graphembed/meta.yaml index edbbcb2d2f647..8d08e9164d54c 100644 --- a/recipes/graphembed/meta.yaml +++ b/recipes/graphembed/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('graphembed', max_pin="x.x") }} skip: True # [osx] diff --git a/recipes/graphmap/build_failure.linux-64.yaml b/recipes/graphmap/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0726d1be89fcb --- /dev/null +++ b/recipes/graphmap/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: ffddbcbe271bcb2aca7503cb6a15f5f10c1dc3e858f3dc975aa6a442b372dd1b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + from codebase/argumentparser/src/argparser.cc:11: + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h: In instantiation of 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1859:25: required from 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1950:31: required from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:4894:18: required from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = positional_less_than_key]' + codebase/argumentparser/src/argparser.cc:291:14: required from here + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1822:17: error: no type named 'value_type' in 'struct std::iterator_traits<__gnu_cxx::__normal_iterator > >' + 1822 | __val = _GLIBCXX_MOVE(*__i); + | ^~~~~ + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1824:15: error: no match for 'operator*' (operand type is '__gnu_cxx::__normal_iterator >') + 1824 | *__first = _GLIBCXX_MOVE(__val); + | ^~~~~~~~ + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1822:17: error: no type named 'value_type' in 'struct std::iterator_traits<__gnu_cxx::__normal_iterator > >' + 1822 | __val = _GLIBCXX_MOVE(*__i); + | ^~~~~ + In file included from /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algobase.h:71, + from /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/string:51: + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/predefined_ops.h: In instantiation of 'bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator >; _Iterator2 = __gnu_cxx::__normal_iterator >; _Compare = positional_less_than_key]': + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1819:14: required from 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1859:25: required from 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1950:31: required from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:4894:18: required from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = positional_less_than_key]' + codebase/argumentparser/src/argparser.cc:291:14: required from here + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/predefined_ops.h:158:31: error: no match for 'operator*' (operand type is '__gnu_cxx::__normal_iterator >') + 158 | { return bool(_M_comp(*__it1, *__it2)); } + | ^~~~~~ + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/predefined_ops.h:158:39: error: no match for 'operator*' (operand type is '__gnu_cxx::__normal_iterator >') + 158 | { return bool(_M_comp(*__it1, *__it2)); } + | ^~~~~~ + In file included from /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:61: + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_heap.h: In instantiation of 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1635:23: required from 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1910:25: required from 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1926:27: required from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1947:25: required from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:4894:18: required from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = positional_less_than_key]' + codebase/argumentparser/src/argparser.cc:291:14: required from here + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_heap.h:344:11: error: no type named 'value_type' in 'struct std::iterator_traits<__gnu_cxx::__normal_iterator > >' + 344 | _ValueType; + | ^~~~~~~~~~ + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_heap.h:346:11: error: no type named 'difference_type' in 'struct std::iterator_traits<__gnu_cxx::__normal_iterator > >' + 346 | _DistanceType; + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_heap.h: In instantiation of 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1638:19: required from 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1910:25: required from 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1926:27: required from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1947:25: required from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:4894:18: required from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = positional_less_than_key]' + codebase/argumentparser/src/argparser.cc:291:14: required from here + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_heap.h:258:9: error: no type named 'value_type' in 'struct std::iterator_traits<__gnu_cxx::__normal_iterator > >' + 258 | _ValueType; + | ^~~~~~~~~~ + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_heap.h:260:9: error: no type named 'difference_type' in 'struct std::iterator_traits<__gnu_cxx::__normal_iterator > >' + 260 | _DistanceType; + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_heap.h:263:7: error: no match for 'operator*' (operand type is '__gnu_cxx::__normal_iterator >') + 263 | *__result = _GLIBCXX_MOVE(*__first); + | ^~~~~~~~~ + In file included from /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/new_allocator.h:36: + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_heap.h:263:19: error: no match for 'operator*' (operand type is '__gnu_cxx::__normal_iterator >') + 263 | *__result = _GLIBCXX_MOVE(*__first); + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algobase.h: In instantiation of 'void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]': + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:91:20: required from 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1897:34: required from '_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1931:38: required from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1947:25: required from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:4894:18: required from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = positional_less_than_key]' + codebase/argumentparser/src/argparser.cc:291:14: required from here + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algobase.h:185:12: error: no match for 'operator*' (operand type is '__gnu_cxx::__normal_iterator >') + 185 | swap(*__a, *__b); + | ^~~~ + /opt/conda/conda-bld/graphmap_1734294372418/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algobase.h:185:18: error: no match for 'operator*' (operand type is '__gnu_cxx::__normal_iterator >') + 185 | swap(*__a, *__b); + | ^~~~ + make: *** [Makefile:123: obj_linux/codebase/argumentparser/src/argparser.o] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/graphmap_1734294372418/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/graphmap_1734294372418/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/graphmap/build_failure.linux-aarch64.yaml b/recipes/graphmap/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..dc99db42fb7fb --- /dev/null +++ b/recipes/graphmap/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: ffddbcbe271bcb2aca7503cb6a15f5f10c1dc3e858f3dc975aa6a442b372dd1b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + from codebase/argumentparser/src/argparser.cc:11: + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h: In instantiation of 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1859:25: required from 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1950:31: required from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:4894:18: required from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = positional_less_than_key]' + codebase/argumentparser/src/argparser.cc:291:14: required from here + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1822:17: error: no type named 'value_type' in 'struct std::iterator_traits<__gnu_cxx::__normal_iterator > >' + 1822 | __val = _GLIBCXX_MOVE(*__i); + | ^~~~~ + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1824:15: error: no match for 'operator*' (operand type is '__gnu_cxx::__normal_iterator >') + 1824 | *__first = _GLIBCXX_MOVE(__val); + | ^~~~~~~~ + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1822:17: error: no type named 'value_type' in 'struct std::iterator_traits<__gnu_cxx::__normal_iterator > >' + 1822 | __val = _GLIBCXX_MOVE(*__i); + | ^~~~~ + In file included from /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algobase.h:71, + from /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/string:51: + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/predefined_ops.h: In instantiation of 'bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator >; _Iterator2 = __gnu_cxx::__normal_iterator >; _Compare = positional_less_than_key]': + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1819:14: required from 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1859:25: required from 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1950:31: required from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:4894:18: required from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = positional_less_than_key]' + codebase/argumentparser/src/argparser.cc:291:14: required from here + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/predefined_ops.h:158:31: error: no match for 'operator*' (operand type is '__gnu_cxx::__normal_iterator >') + 158 | { return bool(_M_comp(*__it1, *__it2)); } + | ^~~~~~ + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/predefined_ops.h:158:39: error: no match for 'operator*' (operand type is '__gnu_cxx::__normal_iterator >') + 158 | { return bool(_M_comp(*__it1, *__it2)); } + | ^~~~~~ + In file included from /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:61: + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_heap.h: In instantiation of 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1635:23: required from 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1910:25: required from 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1926:27: required from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1947:25: required from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:4894:18: required from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = positional_less_than_key]' + codebase/argumentparser/src/argparser.cc:291:14: required from here + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_heap.h:344:11: error: no type named 'value_type' in 'struct std::iterator_traits<__gnu_cxx::__normal_iterator > >' + 344 | _ValueType; + | ^~~~~~~~~~ + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_heap.h:346:11: error: no type named 'difference_type' in 'struct std::iterator_traits<__gnu_cxx::__normal_iterator > >' + 346 | _DistanceType; + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_heap.h: In instantiation of 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1638:19: required from 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1910:25: required from 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1926:27: required from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1947:25: required from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:4894:18: required from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = positional_less_than_key]' + codebase/argumentparser/src/argparser.cc:291:14: required from here + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_heap.h:258:9: error: no type named 'value_type' in 'struct std::iterator_traits<__gnu_cxx::__normal_iterator > >' + 258 | _ValueType; + | ^~~~~~~~~~ + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_heap.h:260:9: error: no type named 'difference_type' in 'struct std::iterator_traits<__gnu_cxx::__normal_iterator > >' + 260 | _DistanceType; + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_heap.h:263:7: error: no match for 'operator*' (operand type is '__gnu_cxx::__normal_iterator >') + 263 | *__result = _GLIBCXX_MOVE(*__first); + | ^~~~~~~~~ + In file included from /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/new_allocator.h:36: + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_heap.h:263:19: error: no match for 'operator*' (operand type is '__gnu_cxx::__normal_iterator >') + 263 | *__result = _GLIBCXX_MOVE(*__first); + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algobase.h: In instantiation of 'void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator >; _ForwardIterator2 = __gnu_cxx::__normal_iterator >]': + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:91:20: required from 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1897:34: required from '_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1931:38: required from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:1947:25: required from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algo.h:4894:18: required from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = positional_less_than_key]' + codebase/argumentparser/src/argparser.cc:291:14: required from here + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algobase.h:185:12: error: no match for 'operator*' (operand type is '__gnu_cxx::__normal_iterator >') + 185 | swap(*__a, *__b); + | ^~~~ + /opt/conda/conda-bld/graphmap_1734270840938/_build_env/lib/gcc/aarch64-conda-linux-gnu/13.3.0/include/c/bits/stl_algobase.h:185:18: error: no match for 'operator*' (operand type is '__gnu_cxx::__normal_iterator >') + 185 | swap(*__a, *__b); + | ^~~~ + make: *** [Makefile:123: obj_linux/codebase/argumentparser/src/argparser.o] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/graphmap_1734270840938/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/graphmap_1734270840938/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/graphmap/meta.yaml b/recipes/graphmap/meta.yaml index 9ea30c2ab95d3..fe5b3379e7f94 100644 --- a/recipes/graphmap/meta.yaml +++ b/recipes/graphmap/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/graphtyper/meta.yaml b/recipes/graphtyper/meta.yaml index 4c943b875e2cb..9844b2d8db228 100644 --- a/recipes/graphtyper/meta.yaml +++ b/recipes/graphtyper/meta.yaml @@ -13,7 +13,7 @@ source: - arm_hwcap.patch # [aarch64] build: - number: 0 + number: 1 #binary_relocation: false skip: true # [not linux] run_exports: diff --git a/recipes/greenhill/meta.yaml b/recipes/greenhill/meta.yaml index 117a234afc7c7..29ec8c6962294 100644 --- a/recipes/greenhill/meta.yaml +++ b/recipes/greenhill/meta.yaml @@ -11,7 +11,7 @@ source: url: https://github.com/ShunOuchi/GreenHill/archive/refs/tags/v1.1.0.tar.gz build: - number: 1 + number: 2 skip: True # [osx] requirements: diff --git a/recipes/grenedalf/meta.yaml b/recipes/grenedalf/meta.yaml index 50a33338455c5..a8dfd22dc8fe5 100644 --- a/recipes/grenedalf/meta.yaml +++ b/recipes/grenedalf/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.6.2" build: - number: 0 + number: 1 skip: true # [osx] run_exports: - {{ pin_subpackage('grenedalf', max_pin='x.x') }} diff --git a/recipes/grep/build_failure.linux-64.yaml b/recipes/grep/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..cf674de014d0c --- /dev/null +++ b/recipes/grep/build_failure.linux-64.yaml @@ -0,0 +1,4 @@ +recipe_sha: 9c5993119908d7fbdb3846f98f677e6f028c82c3b46baca186e85593e3ca070a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + new versions in conda-forge; mulled-build reports "package grep-3.4-h93e12ee_5 is excluded by strict repo priority" diff --git a/recipes/grep/build_failure.osx-64.yaml b/recipes/grep/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..cf674de014d0c --- /dev/null +++ b/recipes/grep/build_failure.osx-64.yaml @@ -0,0 +1,4 @@ +recipe_sha: 9c5993119908d7fbdb3846f98f677e6f028c82c3b46baca186e85593e3ca070a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + new versions in conda-forge; mulled-build reports "package grep-3.4-h93e12ee_5 is excluded by strict repo priority" diff --git a/recipes/grep/meta.yaml b/recipes/grep/meta.yaml index 57b6e34327ee7..53468df702a46 100644 --- a/recipes/grep/meta.yaml +++ b/recipes/grep/meta.yaml @@ -3,7 +3,7 @@ package: version: 3.4 build: - number: 4 + number: 5 source: url: http://ftp.gnu.org/gnu/grep/grep-3.4.tar.xz diff --git a/recipes/gretl/meta.yaml b/recipes/gretl/meta.yaml index bca1b21a1bbab..8b134ccc28bee 100644 --- a/recipes/gretl/meta.yaml +++ b/recipes/gretl/meta.yaml @@ -9,7 +9,7 @@ source: sha256: d6d60484031e289b954d930089903086b38b8ce91e20721b476db51ee3456b63 build: - number: 1 + number: 2 run_exports: '{{ pin_subpackage("gretl", max_pin="x") }}' requirements: @@ -51,4 +51,4 @@ about: extra: additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 diff --git a/recipes/gridss/meta.yaml b/recipes/gridss/meta.yaml index 478a47b6b0629..400e543d3d657 100644 --- a/recipes/gridss/meta.yaml +++ b/recipes/gridss/meta.yaml @@ -13,7 +13,7 @@ source: - 0002-set-gridssargs-for-virusbreakend-annotation.patch build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage('gridss', max_pin="x.x.x") }} skip: True # [osx] @@ -28,6 +28,7 @@ requirements: - ncurses - zlib - htslib >=1.14 + - liblzma-devel run: - bc - ncurses diff --git a/recipes/groot/meta.yaml b/recipes/groot/meta.yaml index a7c0072b68075..e97c1792bee92 100644 --- a/recipes/groot/meta.yaml +++ b/recipes/groot/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 46c6f67990397c2230f580be40697e4fdc284fbe7f0a38999a05d81cd6da5928 build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('groot', max_pin='x') }} diff --git a/recipes/gsalign/meta.yaml b/recipes/gsalign/meta.yaml index c15b077b59dee..7394acc95a6ae 100644 --- a/recipes/gsalign/meta.yaml +++ b/recipes/gsalign/meta.yaml @@ -11,7 +11,7 @@ source: - support-linux-aarch64.patch # [linux and aarch64] build: - number: 6 + number: 7 run_exports: - {{ pin_subpackage('gsalign', max_pin='x') }} diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml index 666784f6c44ed..96985a61301a4 100644 --- a/recipes/gseapy/meta.yaml +++ b/recipes/gseapy/meta.yaml @@ -12,7 +12,7 @@ build: run_exports: - {{ pin_subpackage("gseapy", max_pin="x") }} skip: True # [py2k or py == 36 ] - number: 0 + number: 1 requirements: build: diff --git a/recipes/gsearch/build_failure.linux-64.yaml b/recipes/gsearch/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..4aad7fcdbe804 --- /dev/null +++ b/recipes/gsearch/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: 7b578e65902b114db1f8d37b175aeb2d4eaaa6ae2c76b2573468f0e3b9fb36c0 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + Running rustc --crate-name md5 --edition=2015 /opt/conda/conda-bld/gsearch_1736267892313/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/md5-0.7.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "std"))' -C metadata=afdca3483f467e21 -C extra-filename=-afdca3483f467e21 --out-dir /opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/gsearch_1736267892313/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling roots v0.0.8 + Running rustc --crate-name roots --edition=2015 /opt/conda/conda-bld/gsearch_1736267892313/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/roots-0.0.8/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=408c41f538ff1cbd -C extra-filename=-408c41f538ff1cbd --out-dir /opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/gsearch_1736267892313/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling strum v0.21.0 + Running rustc --crate-name strum --edition=2018 /opt/conda/conda-bld/gsearch_1736267892313/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/strum-0.21.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("derive", "strum_macros"))' -C metadata=5bde583deb9818a0 -C extra-filename=-5bde583deb9818a0 --out-dir /opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/gsearch_1736267892313/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling nohash-hasher v0.2.0 + Running rustc --crate-name nohash_hasher --edition=2018 /opt/conda/conda-bld/gsearch_1736267892313/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/nohash-hasher-0.2.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "std"))' -C metadata=e7a8baa1f040a755 -C extra-filename=-e7a8baa1f040a755 --out-dir /opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/gsearch_1736267892313/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling metrohash v1.0.7 + Running rustc --crate-name metrohash --edition=2021 /opt/conda/conda-bld/gsearch_1736267892313/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/metrohash-1.0.7/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=38810b28b4e278bc -C extra-filename=-38810b28b4e278bc --out-dir /opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/gsearch_1736267892313/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling fastrand v1.9.0 + Running rustc --crate-name fastrand --edition=2018 /opt/conda/conda-bld/gsearch_1736267892313/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/fastrand-1.9.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=50579beefca924f0 -C extra-filename=-50579beefca924f0 --out-dir /opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/gsearch_1736267892313/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling indxvec v1.9.6 + Running rustc --crate-name indxvec --edition=2021 /opt/conda/conda-bld/gsearch_1736267892313/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/indxvec-1.9.6/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=cda72b8c4f054576 -C extra-filename=-cda72b8c4f054576 --out-dir /opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/gsearch_1736267892313/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling xxh3 v0.1.1 + Running rustc --crate-name xxh3 --edition=2021 /opt/conda/conda-bld/gsearch_1736267892313/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/xxh3-0.1.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type cdylib --crate-type rlib --emit=dep-info,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("pyo3", "python"))' -C metadata=b91b9f06dcb5b279 -C extra-filename=-b91b9f06dcb5b279 --out-dir /opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/gsearch_1736267892313/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling murmurhash3 v0.0.5 + Running rustc --crate-name murmurhash3 --edition=2015 /opt/conda/conda-bld/gsearch_1736267892313/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/murmurhash3-0.0.5/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("nightly"))' -C metadata=780b6bf4e60e7586 -C extra-filename=-780b6bf4e60e7586 --out-dir /opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/gsearch_1736267892313/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Running rustc --crate-name annembed_gsearch --edition=2021 /opt/conda/conda-bld/gsearch_1736267892313/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annembed_gsearch-0.1.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="intel-mkl-static"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("blas-src", "default", "intel-mkl-static", "macos-accelerate", "openblas-static", "openblas-system", "simdeez_f", "stdsimd"))' -C metadata=ff510b1c84cd9ca8 -C extra-filename=-ff510b1c84cd9ca8 --out-dir /opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/gsearch_1736267892313/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps --extern anyhow=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libanyhow-fb74fdd7b3b79f55.rmeta --extern bincode=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libbincode-2a181ef01d044677.rmeta --extern bson=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libbson-db362a51360d0f21.rmeta --extern byteorder=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libbyteorder-9d499ed7215ae9be.rmeta --extern clap=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libclap-66f69b35abf1b926.rmeta --extern cpu_time=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libcpu_time-b677957ba0cdabcc.rmeta --extern csv=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libcsv-283ea2a93fc71e74.rmeta --extern env_logger=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libenv_logger-be2bb369917203ee.rmeta --extern hdrhistogram=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libhdrhistogram-43469dc4094cd6b7.rmeta --extern hnsw_rs=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libhnsw_rs-37b67dc289836707.rmeta --extern indexmap=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libindexmap-b0fab0fe954af306.rmeta --extern indxvec=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libindxvec-cda72b8c4f054576.rmeta --extern katexit=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps/libkatexit-ddb36ee977e98b9f.so --extern lazy_static=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/liblazy_static-07a083f8437cbd0b.rmeta --extern log=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/liblog-22c5f274688aa5f4.rmeta --extern memory_stats=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libmemory_stats-bb41fc255711c865.rmeta --extern ndarray=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libndarray-9be7b4295ae80307.rmeta --extern ndarray_linalg=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libndarray_linalg-acd0ab337e965dde.rmeta --extern num_traits=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libnum_traits-45cfdbe14cf49886.rmeta --extern num_cpus=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libnum_cpus-128e9aac6f16ba49.rmeta --extern parking_lot=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libparking_lot-44ad0582f585ad02.rmeta --extern quantiles=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libquantiles-7590c523a9176c11.rmeta --extern rand=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/librand-f9537d1a058fa7a0.rmeta --extern rand_distr=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/librand_distr-9c7d1b510402dfa2.rmeta --extern rand_xoshiro=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/librand_xoshiro-0abcb5c8b3b17847.rmeta --extern rayon=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/librayon-6fc56829d0078280.rmeta --extern serde=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libserde-33547977df4dee73.rmeta --extern sprs=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libsprs-b2631533d933764c.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L /home/conda/.local/share/ocipkg/ghcr.io/rust-math/rust-mkl/linux/mkl-static-lp64-seq/__2020.1-3038006115 + Compiling bigsig v0.1.0 + Running rustc --crate-name bigsig --edition=2015 /opt/conda/conda-bld/gsearch_1736267892313/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/bigsig-0.1.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=0b0f43e578bbe590 -C extra-filename=-0b0f43e578bbe590 --out-dir /opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/gsearch_1736267892313/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps --extern bincode=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libbincode-2a181ef01d044677.rmeta --extern bit_vec_serde=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libbit_vec_serde-7da582410135fed7.rmeta --extern clap=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libclap-308c8733dce4b4cf.rmeta --extern env_logger=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libenv_logger-be2bb369917203ee.rmeta --extern flate2=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libflate2-df79d26a49a6ac20.rmeta --extern fnv=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libfnv-62883376e22303b0.rmeta --extern indexmap=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libindexmap-ce0ee00cc54ec05a.rmeta --extern log=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/liblog-22c5f274688aa5f4.rmeta --extern probability=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libprobability-0b75689b08885e84.rmeta --extern rayon=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/librayon-6fc56829d0078280.rmeta --extern serde=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libserde-33547977df4dee73.rmeta --extern serde_derive=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps/libserde_derive-706a76ddadc0d742.so --extern serde_json=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libserde_json-52049f52e6051aea.rmeta --extern systemstat=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libsystemstat-90d0e78ba70c6180.rmeta --extern xxh3=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libxxh3-b91b9f06dcb5b279.rlib --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling skani v0.1.1 + Running rustc --crate-name skani --edition=2021 /opt/conda/conda-bld/gsearch_1736267892313/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/skani-0.1.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="clap"' --cfg 'feature="cli"' --cfg 'feature="default"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("clap", "cli", "default"))' -C metadata=093bafd09dec4190 -C extra-filename=-093bafd09dec4190 --out-dir /opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/gsearch_1736267892313/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps --extern bincode=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libbincode-2a181ef01d044677.rmeta --extern bio=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libbio-3eae0ecb87cc1def.rmeta --extern clap=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libclap-97202111c46230db.rmeta --extern fastrand=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libfastrand-50579beefca924f0.rmeta --extern fxhash=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libfxhash-a7f3791b8c50572a.rmeta --extern gbdt=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libgbdt-86e77f1eaf07725e.rlib --extern gcollections=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libgcollections-2dedf6c177e3bc1c.rmeta --extern interval=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libinterval-77bb9a0234cd81c3.rmeta --extern log=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/liblog-22c5f274688aa5f4.rmeta --extern needletail=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libneedletail-2c31e418517c530a.rlib --extern num_traits=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libnum_traits-45cfdbe14cf49886.rmeta --extern partitions=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libpartitions-16f162ba8e06c643.rmeta --extern rand=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/librand-f9537d1a058fa7a0.rmeta --extern rayon=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/librayon-6fc56829d0078280.rmeta --extern rust_lapper=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/librust_lapper-a5b15f6964ffb2ee.rmeta --extern serde=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libserde-33547977df4dee73.rmeta --extern serde_json=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libserde_json-52049f52e6051aea.rmeta --extern simple_logging=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libsimple_logging-479f5ad7c399fd43.rmeta --extern smallvec=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libsmallvec-084eb8e32bd06b3a.rmeta --extern statrs=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libstatrs-daed28fd32251317.rmeta --extern thiserror=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libthiserror-d8b7b47410edeedb.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/build/bzip2-sys-8d056af817497eb0/out/lib -L native=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/build/lzma-sys-4beac66c687376fb/out + Running rustc --crate-name sourmash --edition=2021 /opt/conda/conda-bld/gsearch_1736267892313/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/sourmash-0.15.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --crate-type staticlib --crate-type cdylib --emit=dep-info,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("branchwater", "default", "from-finch", "maturin", "parallel", "rkyv"))' -C metadata=9bae2ff2c92f5fd6 -C extra-filename=-9bae2ff2c92f5fd6 --out-dir /opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/gsearch_1736267892313/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps --extern az=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libaz-3a643ead20c73b25.rlib --extern byteorder=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libbyteorder-9d499ed7215ae9be.rlib --extern camino=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libcamino-4cdddd24f330278c.rlib --extern cfg_if=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libcfg_if-cc1a207a177f0d2d.rlib --extern counter=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libcounter-1b2740b13525e415.rlib --extern csv=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libcsv-283ea2a93fc71e74.rlib --extern enum_dispatch=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps/libenum_dispatch-26e8546232092fd8.so --extern fixedbitset=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libfixedbitset-7383d8383165ee8b.rlib --extern getset=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps/libgetset-32f186e9b67dcfb9.so --extern histogram=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libhistogram-06058c5624b57e72.rlib --extern itertools=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libitertools-afddb9ba245d247e.rlib --extern log=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/liblog-22c5f274688aa5f4.rlib --extern md5=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libmd5-afdca3483f467e21.rlib --extern memmap2=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libmemmap2-330302ac2ad8c67b.rlib --extern murmurhash3=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libmurmurhash3-780b6bf4e60e7586.rlib --extern needletail=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libneedletail-f49812d3e2a04f75.rlib --extern niffler=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libniffler-284c5c574d9ce5e5.rlib --extern nohash_hasher=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libnohash_hasher-e7a8baa1f040a755.rlib --extern num_iter=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libnum_iter-fee28843c136682e.rlib --extern once_cell=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libonce_cell-14d214d3f0f6a9a9.rlib --extern ouroboros=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libouroboros-770e1dde2b8455d7.rlib --extern piz=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libpiz-fac472e50504032a.rlib --extern primal_check=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libprimal_check-a9f9b8922a249b3c.rlib --extern roaring=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libroaring-e5b9fb7cb34fc95a.rlib --extern roots=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libroots-408c41f538ff1cbd.rlib --extern serde=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libserde-33547977df4dee73.rlib --extern serde_json=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libserde_json-52049f52e6051aea.rlib --extern statrs=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libstatrs-e248cc9c760b407d.rlib --extern stats=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libstats-b4197d12886ba351.rlib --extern thiserror=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libthiserror-d8b7b47410edeedb.rlib --extern twox_hash=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libtwox_hash-fad8d251475ce4ac.rlib --extern typed_builder=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libtyped_builder-2ddfbeb54bad3f4b.rlib --extern vec_collections=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libvec_collections-3b172eb02250df6d.rlib --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/build/bzip2-sys-8d056af817497eb0/out/lib -L native=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/build/lzma-sys-4beac66c687376fb/out + Compiling kmerutils v0.0.11 + Running rustc --crate-name kmerutils --edition=2021 /opt/conda/conda-bld/gsearch_1736267892313/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/kmerutils-0.0.11/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="simdeez_f"' --cfg 'feature="sminhash2"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "simdeez_f", "sminhash2", "withzmq", "zmq"))' -C metadata=ab93b588e7058e3c -C extra-filename=-ab93b588e7058e3c --out-dir /opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/gsearch_1736267892313/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps --extern bloom=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libbloom-2e78b05501c52612.rmeta --extern clap=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libclap-66f69b35abf1b926.rmeta --extern crossbeam=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libcrossbeam-7019e09b661c3cdb.rmeta --extern cuckoofilter=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libcuckoofilter-94b3ed5560f3a787.rmeta --extern env_logger=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libenv_logger-1ab0fd460a6969a1.rmeta --extern fnv=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libfnv-62883376e22303b0.rmeta --extern fxhash=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libfxhash-a7f3791b8c50572a.rmeta --extern hdrhistogram=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libhdrhistogram-43469dc4094cd6b7.rmeta --extern hnsw_rs=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libhnsw_rs-37b67dc289836707.rmeta --extern indexmap=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libindexmap-b0fab0fe954af306.rmeta --extern lazy_static=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/liblazy_static-07a083f8437cbd0b.rmeta --extern log=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/liblog-22c5f274688aa5f4.rmeta --extern memory_stats=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libmemory_stats-bb41fc255711c865.rmeta --extern metrohash=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libmetrohash-38810b28b4e278bc.rmeta --extern multimap=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libmultimap-b350f5615700fe67.rmeta --extern ndarray=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libndarray-9be7b4295ae80307.rmeta --extern needletail=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libneedletail-f49812d3e2a04f75.rlib --extern num=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libnum-079df3888991e763.rmeta --extern num_cpus=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libnum_cpus-128e9aac6f16ba49.rmeta --extern parking_lot=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libparking_lot-44ad0582f585ad02.rmeta --extern probminhash=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libprobminhash-61a454d4e8eb886c.rmeta --extern rand=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/librand-f9537d1a058fa7a0.rmeta --extern rand_distr=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/librand_distr-9c7d1b510402dfa2.rmeta --extern rand_xorshift=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/librand_xorshift-1ed0e8ec036b1e76.rmeta --extern rand_xoshiro=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/librand_xoshiro-0abcb5c8b3b17847.rmeta --extern rayon=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/librayon-6fc56829d0078280.rmeta --extern redis=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libredis-180a06a4c8cf269b.rmeta --extern serde=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libserde-33547977df4dee73.rmeta --extern serde_json=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libserde_json-52049f52e6051aea.rmeta --extern wavelet_matrix=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libwavelet_matrix-e4e5abcb390697f9.rmeta --extern wyhash=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libwyhash-47e76b6482cb1bca.rmeta --extern xdr_codec=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libxdr_codec-0cf34a47138891c9.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/build/bzip2-sys-8d056af817497eb0/out/lib -L native=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/build/lzma-sys-4beac66c687376fb/out + Compiling frag_gene_scan_rs v1.0.1 (https://gitlab.com/Jianshu_Zhao/fraggenescanrs#7bb6708a) + Running rustc --crate-name frag_gene_scan_rs --edition=2018 /opt/conda/conda-bld/gsearch_1736267892313/work/.cargo/git/checkouts/fraggenescanrs-e8d4590477af3c12/7bb6708/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=bc37110f1f0c2ffc -C extra-filename=-bc37110f1f0c2ffc --out-dir /opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/gsearch_1736267892313/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps --extern anyhow=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libanyhow-fb74fdd7b3b79f55.rmeta --extern clap=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libclap-308c8733dce4b4cf.rmeta --extern rayon=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/librayon-6fc56829d0078280.rmeta --extern seq_io=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libseq_io-bb5308f6ede85455.rmeta --extern strum=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libstrum-5bde583deb9818a0.rmeta --extern strum_macros=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps/libstrum_macros-ebcd4e86e2c9fa91.so --extern thiserror=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libthiserror-d8b7b47410edeedb.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling concurrent-queue v2.5.0 + Running rustc --crate-name concurrent_queue --edition=2021 /opt/conda/conda-bld/gsearch_1736267892313/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/concurrent-queue-2.5.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "loom", "portable-atomic", "std"))' -C metadata=b5909475fd74b917 -C extra-filename=-b5909475fd74b917 --out-dir /opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/gsearch_1736267892313/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps --extern crossbeam_utils=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libcrossbeam_utils-572a698404037c80.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling gsearch v0.1.3 (/opt/conda/conda-bld/gsearch_1736267892313/work) + Running rustc --crate-name gsearch --edition=2021 src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="annembed_gsearch"' --cfg 'feature="annembed_intel-mkl"' --cfg 'feature="default"' --cfg 'feature="simdeez_f"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("annembed_gsearch", "annembed_intel-mkl", "annembed_openblas-static", "annembed_openblas-system", "default", "simdeez_f", "withzmq"))' -C metadata=c5abb31d034786bb -C extra-filename=-c5abb31d034786bb --out-dir /opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/gsearch_1736267892313/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps --extern annembed_gsearch=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libannembed_gsearch-ff510b1c84cd9ca8.rmeta --extern anyhow=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libanyhow-fb74fdd7b3b79f55.rmeta --extern bigsig=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libbigsig-0b0f43e578bbe590.rmeta --extern chrono=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libchrono-3ab0222c9b633ab2.rmeta --extern clap=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libclap-66f69b35abf1b926.rmeta --extern concurrent_queue=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libconcurrent_queue-b5909475fd74b917.rmeta --extern cpu_time=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libcpu_time-b677957ba0cdabcc.rmeta --extern crossbeam=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libcrossbeam-7019e09b661c3cdb.rmeta --extern crossbeam_channel=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libcrossbeam_channel-0d1a5eb0abe72f89.rmeta --extern crossbeam_utils=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libcrossbeam_utils-572a698404037c80.rmeta --extern csv=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libcsv-283ea2a93fc71e74.rmeta --extern env_logger=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libenv_logger-be2bb369917203ee.rmeta --extern frag_gene_scan_rs=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libfrag_gene_scan_rs-bc37110f1f0c2ffc.rmeta --extern fxhash=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libfxhash-a7f3791b8c50572a.rmeta --extern hnsw_rs=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libhnsw_rs-37b67dc289836707.rmeta --extern kmerutils=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libkmerutils-ab93b588e7058e3c.rmeta --extern lazy_static=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/liblazy_static-07a083f8437cbd0b.rmeta --extern log=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/liblog-22c5f274688aa5f4.rmeta --extern memory_stats=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libmemory_stats-bb41fc255711c865.rmeta --extern needletail=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libneedletail-f49812d3e2a04f75.rlib --extern num=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libnum-079df3888991e763.rmeta --extern num_cpus=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libnum_cpus-128e9aac6f16ba49.rmeta --extern parking_lot=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libparking_lot-44ad0582f585ad02.rmeta --extern probminhash=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libprobminhash-61a454d4e8eb886c.rmeta --extern rayon=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/librayon-6fc56829d0078280.rmeta --extern seq_io=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libseq_io-bb5308f6ede85455.rmeta --extern serde=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libserde-33547977df4dee73.rmeta --extern serde_json=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libserde_json-52049f52e6051aea.rmeta --extern skani=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libskani-093bafd09dec4190.rmeta --extern sourmash=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libsourmash-9bae2ff2c92f5fd6.rlib --extern strum=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libstrum-5bde583deb9818a0.rmeta --extern strum_macros=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps/libstrum_macros-ebcd4e86e2c9fa91.so --extern thiserror=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libthiserror-d8b7b47410edeedb.rmeta -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L /home/conda/.local/share/ocipkg/ghcr.io/rust-math/rust-mkl/linux/mkl-static-lp64-seq/__2020.1-3038006115 -L native=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/build/bzip2-sys-8d056af817497eb0/out/lib -L native=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/build/lzma-sys-4beac66c687376fb/out + error[E0308]: arguments to this function are incorrect + --> src/utils/reloadhnsw.rs:44:24 + | + 44 | let mut reloader = HnswIo::new(pathb, dumpname); + | ^^^^^^^^^^^ ----- -------- expected &str, found String + | | + | expected &Path, found PathBuf + | + note: associated function defined here + --> /opt/conda/conda-bld/gsearch_1736267892313/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/hnsw_rs-0.3.1/src/hnswio.rs:317:12 + | + 317 | pub fn new(directory: &Path, basename: &str) -> Self { + | ^^^ + help: consider borrowing here + | + 44 | let mut reloader = HnswIo::new(&pathb, dumpname); + | + help: consider borrowing here + | + 44 | let mut reloader = HnswIo::new(pathb, &dumpname); + | + + error[E0061]: this method takes 2 arguments but 1 argument was supplied + --> src/utils/dumpload.rs:30:28 + | + 30 | let resdump = hnsw.file_dump(&hnswdumpname); + | ^^^^^^^^^ ------------- argument #1 of type &Path is missing + | + note: method defined here + --> /opt/conda/conda-bld/gsearch_1736267892313/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/hnsw_rs-0.3.1/src/api.rs:36:8 + | + 36 | fn file_dump(&self, path: &Path, file_basename: &str) -> anyhow::Result; + | ^^^^^^^^^ + help: provide the argument + | + 30 | let resdump = hnsw.file_dump(/* &Path */, &hnswdumpname); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + + Some errors have detailed explanations: E0061, E0308. + For more information about an error, try rustc --explain E0061. + error: could not compile gsearch (lib) due to 2 previous errors + + Caused by: + process didn't exit successfully: rustc --crate-name gsearch --edition=2021 src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="annembed_gsearch"' --cfg 'feature="annembed_intel-mkl"' --cfg 'feature="default"' --cfg 'feature="simdeez_f"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("annembed_gsearch", "annembed_intel-mkl", "annembed_openblas-static", "annembed_openblas-system", "default", "simdeez_f", "withzmq"))' -C metadata=c5abb31d034786bb -C extra-filename=-c5abb31d034786bb --out-dir /opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/gsearch_1736267892313/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps --extern annembed_gsearch=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libannembed_gsearch-ff510b1c84cd9ca8.rmeta --extern anyhow=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libanyhow-fb74fdd7b3b79f55.rmeta --extern bigsig=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libbigsig-0b0f43e578bbe590.rmeta --extern chrono=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libchrono-3ab0222c9b633ab2.rmeta --extern clap=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libclap-66f69b35abf1b926.rmeta --extern concurrent_queue=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libconcurrent_queue-b5909475fd74b917.rmeta --extern cpu_time=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libcpu_time-b677957ba0cdabcc.rmeta --extern crossbeam=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libcrossbeam-7019e09b661c3cdb.rmeta --extern crossbeam_channel=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libcrossbeam_channel-0d1a5eb0abe72f89.rmeta --extern crossbeam_utils=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libcrossbeam_utils-572a698404037c80.rmeta --extern csv=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libcsv-283ea2a93fc71e74.rmeta --extern env_logger=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libenv_logger-be2bb369917203ee.rmeta --extern frag_gene_scan_rs=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libfrag_gene_scan_rs-bc37110f1f0c2ffc.rmeta --extern fxhash=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libfxhash-a7f3791b8c50572a.rmeta --extern hnsw_rs=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libhnsw_rs-37b67dc289836707.rmeta --extern kmerutils=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libkmerutils-ab93b588e7058e3c.rmeta --extern lazy_static=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/liblazy_static-07a083f8437cbd0b.rmeta --extern log=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/liblog-22c5f274688aa5f4.rmeta --extern memory_stats=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libmemory_stats-bb41fc255711c865.rmeta --extern needletail=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libneedletail-f49812d3e2a04f75.rlib --extern num=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libnum-079df3888991e763.rmeta --extern num_cpus=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libnum_cpus-128e9aac6f16ba49.rmeta --extern parking_lot=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libparking_lot-44ad0582f585ad02.rmeta --extern probminhash=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libprobminhash-61a454d4e8eb886c.rmeta --extern rayon=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/librayon-6fc56829d0078280.rmeta --extern seq_io=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libseq_io-bb5308f6ede85455.rmeta --extern serde=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libserde-33547977df4dee73.rmeta --extern serde_json=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libserde_json-52049f52e6051aea.rmeta --extern skani=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libskani-093bafd09dec4190.rmeta --extern sourmash=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libsourmash-9bae2ff2c92f5fd6.rlib --extern strum=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libstrum-5bde583deb9818a0.rmeta --extern strum_macros=/opt/conda/conda-bld/gsearch_1736267892313/work/target/release/deps/libstrum_macros-ebcd4e86e2c9fa91.so --extern thiserror=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/deps/libthiserror-d8b7b47410edeedb.rmeta -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/gsearch_1736267892313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L /home/conda/.local/share/ocipkg/ghcr.io/rust-math/rust-mkl/linux/mkl-static-lp64-seq/__2020.1-3038006115 -L native=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/build/bzip2-sys-8d056af817497eb0/out/lib -L native=/opt/conda/conda-bld/gsearch_1736267892313/work/target/x86_64-unknown-linux-gnu/release/build/lzma-sys-4beac66c687376fb/out (exit status: 1) + error: failed to compile gsearch v0.1.3 (/opt/conda/conda-bld/gsearch_1736267892313/work), intermediate artifacts can be found at /opt/conda/conda-bld/gsearch_1736267892313/work/target. + To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/gsearch_1736267892313/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/gsearch_1736267892313/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. +category: |- + compiler error +reason: |- + hnsw.file_dump this method takes 2 arguments but 1 argument was supplied diff --git a/recipes/gsearch/meta.yaml b/recipes/gsearch/meta.yaml index fe940f49c00c0..bdf8c18b92058 100644 --- a/recipes/gsearch/meta.yaml +++ b/recipes/gsearch/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('gsearch', max_pin="x.x") }} skip: True # [osx] diff --git a/recipes/gtfsort/build_failure.linux-64.yaml b/recipes/gtfsort/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..a59210fddbf21 --- /dev/null +++ b/recipes/gtfsort/build_failure.linux-64.yaml @@ -0,0 +1,90 @@ +recipe_sha: 3910510992edeb84aaef31241bd015d8d65f7ebe152e540570cd81ed0353d5ac # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + 2024-12-13T23:55:30 Subdir: linux-64 Gathering repodata + 2024-12-13T23:55:30 linux-64 Writing pre-patch repodata + 2024-12-13T23:55:30 linux-64 Applying patch instructions + 2024-12-13T23:55:30 linux-64 Writing patched repodata + 2024-12-13T23:55:30 linux-64 Building current_repodata subset + 2024-12-13T23:55:30 linux-64 Writing current_repodata subset + 2024-12-13T23:55:30 linux-64 Writing index HTML + 2024-12-13T23:55:30 Subdir: linux-aarch64 Gathering repodata + 2024-12-13T23:55:30 linux-aarch64 Writing pre-patch repodata + 2024-12-13T23:55:30 linux-aarch64 Applying patch instructions + 2024-12-13T23:55:30 linux-aarch64 Writing patched repodata + 2024-12-13T23:55:30 linux-aarch64 Building current_repodata subset + 2024-12-13T23:55:30 linux-aarch64 Writing current_repodata subset + 2024-12-13T23:55:30 linux-aarch64 Writing index HTML + 2024-12-13T23:55:30 Subdir: noarch Gathering repodata + 2024-12-13T23:55:30 noarch Writing pre-patch repodata + 2024-12-13T23:55:30 noarch Applying patch instructions + 2024-12-13T23:55:30 noarch Writing patched repodata + 2024-12-13T23:55:30 noarch Building current_repodata subset + 2024-12-13T23:55:30 noarch Writing current_repodata subset + 2024-12-13T23:55:30 noarch Writing index HTML + 2024-12-13T23:55:30 Subdir: linux-64 Gathering repodata + 2024-12-13T23:55:30 linux-64 Writing pre-patch repodata + 2024-12-13T23:55:30 linux-64 Applying patch instructions + 2024-12-13T23:55:30 linux-64 Writing patched repodata + 2024-12-13T23:55:30 linux-64 Building current_repodata subset + 2024-12-13T23:55:30 linux-64 Writing current_repodata subset + 2024-12-13T23:55:30 linux-64 Writing index HTML + 2024-12-13T23:55:30 Subdir: linux-aarch64 Gathering repodata + 2024-12-13T23:55:30 linux-aarch64 Writing pre-patch repodata + 2024-12-13T23:55:30 linux-aarch64 Applying patch instructions + 2024-12-13T23:55:30 linux-aarch64 Writing patched repodata + 2024-12-13T23:55:30 linux-aarch64 Building current_repodata subset + 2024-12-13T23:55:30 linux-aarch64 Writing current_repodata subset + 2024-12-13T23:55:30 linux-aarch64 Writing index HTML + 2024-12-13T23:55:30 Subdir: noarch Gathering repodata + 2024-12-13T23:55:30 noarch Writing pre-patch repodata + 2024-12-13T23:55:30 noarch Applying patch instructions + 2024-12-13T23:55:30 noarch Writing patched repodata + 2024-12-13T23:55:30 noarch Building current_repodata subset + 2024-12-13T23:55:30 noarch Writing current_repodata subset + 2024-12-13T23:55:30 noarch Writing index HTML + /opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (/opt/recipe/meta.yaml). + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml + Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for gtfsort + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 465, in add_upstream_pins + build_deps, build_unsat, extra_run_specs_from_build = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 453, in _read_upstream_pin_files + extra_run_specs = get_upstream_pins(m, precs, env) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 425, in get_upstream_pins + loc, dist = execute_download_actions( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 392, in execute_download_actions + pfe.execute() + File "/opt/conda/lib/python3.10/site-packages/conda/core/package_cache_data.py", line 900, in execute + raise CondaMultiError(not_cancelled) + conda.CondaMultiError: Failed to write to /opt/conda/pkgs/rust-1.83.0-h1a8d7c4_0.conda.partial + errno: 28 + Failed to write to /opt/conda/pkgs/rust-1.83.0-h1a8d7c4_0.conda.partial + errno: 28 +# Last 100 lines of the build log. diff --git a/recipes/gtfsort/meta.yaml b/recipes/gtfsort/meta.yaml index b04cc6fac6f30..b9e1ca25da65c 100644 --- a/recipes/gtfsort/meta.yaml +++ b/recipes/gtfsort/meta.yaml @@ -10,7 +10,7 @@ source: sha256: d22a8ef32e30111ad2dd08d1da0e0914ac62a728483b8e39a4ef8ea4e6133b4f build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('gtfsort', max_pin="x.x") }} diff --git a/recipes/guide-counter/meta.yaml b/recipes/guide-counter/meta.yaml index 4c1c2a3947c91..da5f2f52cc781 100644 --- a/recipes/guide-counter/meta.yaml +++ b/recipes/guide-counter/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/guidescan/build_failure.linux-64.yaml b/recipes/guidescan/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..d47624aec2285 --- /dev/null +++ b/recipes/guidescan/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5c919f6b633856f69d99b0780dced89e8f97d57e82ae443694d07e3f4f432fe2 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + /opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/structures.cxx:17:52: error: 'const struct genomics::chromosome' has no member named 'length' + 17 | if (off_target_abs_coords <= (int64_t)(chr.length-1)) { + | ^~~~~~ + /opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/structures.cxx:21:40: error: 'const struct genomics::chromosome' has no member named 'length' + 21 | off_target_abs_coords -= chr.length; + | ^~~~~~ + /opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/structures.cxx:46:62: error: 'struct genomics::chromosome' has no member named 'length' + 46 | if ((start_position < 0) || (end_position > (int64_t)c.length)) { + | ^~~~~~ + /opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/structures.cxx:47:60: error: too many initializers for 'genomics::chromosome' + 47 | return std::make_tuple(coordinates{chromosome{"", 0}, 0}, ""); + | ^ + /opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/structures.cxx:51:46: error: 'uint64_t' was not declared in this scope + 51 | return std::make_tuple(coordinates{c, (uint64_t)start_position}, strand); + | ^~~~~~~~ + /opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/structures.cxx:5:1: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + 4 | #include "genomics/structures.hpp" + |#include + 5 | + /opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/structures.cxx:51:54: error: too many initializers for 'genomics::coordinates' + 51 | return std::make_tuple(coordinates{c, (uint64_t)start_position}, strand); + | ^ + /opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/structures.cxx:51:41: error: expected primary-expression before '{' token + 51 | return std::make_tuple(coordinates{c, (uint64_t)start_position}, strand); + | ^ + make[2]: *** [bin/CMakeFiles/guidescan.dir/build.make:121: bin/CMakeFiles/guidescan.dir/genomics/structures.cxx.o] Error 1 + make[2]: *** Waiting for unfinished jobs.... + /opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/sequences.cxx: In function 'std::string genomics::complement(const std::string&)': + /opt/conda/conda-bld/guidescan_1734201456193/work/src/genomics/sequences.cxx:30:31: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 30 | for (int64_t i = 0; i < kmer.length(); i) { + | ~~^~~~~~~~~~~~~~~ + /opt/conda/conda-bld/guidescan_1734201456193/work/src/guidescan.cxx: In function 'int main(int, char**)': + /opt/conda/conda-bld/guidescan_1734201456193/work/src/guidescan.cxx:335:8: warning: unused variable 'download' [-Wunused-variable] + 335 | auto download = download_cmd(guidescan, download_opts); + | ^~~~~~~~ + [ 91%] Linking CXX executable csa_sada_test + [ 91%] Built target csa_sada_test + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/printer.hpp: In instantiation of 'std::string genomics::get_csv_lines(const genome_index&, const kmer&, bool, int64_t, std::vector > >&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string; int64_t = long int]': + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/process.hpp:118:54: required from 'void genomics::process_kmer_to_stream(const genome_index&, const genome_index&, const enumerate_cmd_options&, const kmer&, std::ostream&, std::mutex&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream]' + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/process.hpp:143:29: required from 'void genomics::process_kmers_to_stream(const genome_index&, const genome_index&, const enumerate_cmd_options&, const std::vector&, std::ostream&, std::mutex&, std::atomic&, uint64_t, const std::chrono::_V2::steady_clock::time_point&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream; uint64_t = long unsigned int; std::chrono::_V2::steady_clock::time_point = std::chrono::time_point > >]' + /opt/conda/conda-bld/guidescan_1734201456193/work/src/guidescan.cxx:245:102: required from here + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/printer.hpp:257:29: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 257 | for (int64_t i = 0; i < off_targets[d].size(); i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~ + In file included from /opt/conda/conda-bld/guidescan_1734201456193/work/src/guidescan.cxx:12: + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/index.hpp: In instantiation of 'void genomics::genome_index::inexact_search(const std::string&, ssize_t, size_t, size_t, std::string, const std::vector >&, size_t, size_t, size_t, size_t, genomics::{anonymous}::affinity, const std::function&, t_data&) const [with t_data = long unsigned int; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string; ssize_t = long int; size_t = long unsigned int]': + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/index.hpp:395:19: required from 'void genomics::genome_index::inexact_search(const std::string&, const std::vector >&, size_t, size_t, size_t, size_t, const std::function&, t_data&) const [with t_data = long unsigned int; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/process.hpp:67:32: required from 'void genomics::process_kmer_to_stream(const genome_index&, const genome_index&, const enumerate_cmd_options&, const kmer&, std::ostream&, std::mutex&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream]' + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/process.hpp:143:29: required from 'void genomics::process_kmers_to_stream(const genome_index&, const genome_index&, const enumerate_cmd_options&, const std::vector&, std::ostream&, std::mutex&, std::atomic&, uint64_t, const std::chrono::_V2::steady_clock::time_point&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream; uint64_t = long unsigned int; std::chrono::_V2::steady_clock::time_point = std::chrono::time_point > >]' + /opt/conda/conda-bld/guidescan_1734201456193/work/src/guidescan.cxx:245:102: required from here + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/index.hpp:276:21: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 276 | && position != query.length() - 1) { + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/index.hpp:369:21: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 369 | && position != query.length() - 1 ) { + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/index.hpp: In instantiation of 'void genomics::genome_index::inexact_search(const std::string&, ssize_t, size_t, size_t, std::string, const std::vector >&, size_t, size_t, size_t, size_t, genomics::{anonymous}::affinity, const std::function&, t_data&) const [with t_data = std::vector >; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string; ssize_t = long int; size_t = long unsigned int]': + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/index.hpp:395:19: required from 'void genomics::genome_index::inexact_search(const std::string&, const std::vector >&, size_t, size_t, size_t, size_t, const std::function&, t_data&) const [with t_data = std::vector >; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/process.hpp:82:32: required from 'void genomics::process_kmer_to_stream(const genome_index&, const genome_index&, const enumerate_cmd_options&, const kmer&, std::ostream&, std::mutex&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream]' + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/process.hpp:143:29: required from 'void genomics::process_kmers_to_stream(const genome_index&, const genome_index&, const enumerate_cmd_options&, const std::vector&, std::ostream&, std::mutex&, std::atomic&, uint64_t, const std::chrono::_V2::steady_clock::time_point&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream; uint64_t = long unsigned int; std::chrono::_V2::steady_clock::time_point = std::chrono::time_point > >]' + /opt/conda/conda-bld/guidescan_1734201456193/work/src/guidescan.cxx:245:102: required from here + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/index.hpp:276:21: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 276 | && position != query.length() - 1) { + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/index.hpp:369:21: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 369 | && position != query.length() - 1 ) { + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/printer.hpp: In instantiation of 'std::string genomics::get_csv_line_nomatch(const genome_index&, const kmer&, bool, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string]': + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/printer.hpp:288:39: required from 'std::string genomics::get_csv_lines(const genome_index&, const kmer&, bool, int64_t, std::vector > >&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string; int64_t = long int]' + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/process.hpp:118:54: required from 'void genomics::process_kmer_to_stream(const genome_index&, const genome_index&, const enumerate_cmd_options&, const kmer&, std::ostream&, std::mutex&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream]' + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/process.hpp:143:29: required from 'void genomics::process_kmers_to_stream(const genome_index&, const genome_index&, const enumerate_cmd_options&, const std::vector&, std::ostream&, std::mutex&, std::atomic&, uint64_t, const std::chrono::_V2::steady_clock::time_point&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream; uint64_t = long unsigned int; std::chrono::_V2::steady_clock::time_point = std::chrono::time_point > >]' + /opt/conda/conda-bld/guidescan_1734201456193/work/src/guidescan.cxx:245:102: required from here + /opt/conda/conda-bld/guidescan_1734201456193/work/include/genomics/printer.hpp:190:84: warning: unused parameter 'gi' [-Wunused-parameter] + 190 | std::string get_csv_line_nomatch(const genome_index& gi, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ + make[1]: *** [CMakeFiles/Makefile2:8238: bin/CMakeFiles/guidescan.dir/all] Error 2 + make: *** [Makefile:156: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/guidescan_1734201456193/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/guidescan_1734201456193/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/guidescan/build_failure.linux-aarch64.yaml b/recipes/guidescan/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..0dedf1c2aa1ca --- /dev/null +++ b/recipes/guidescan/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5c919f6b633856f69d99b0780dced89e8f97d57e82ae443694d07e3f4f432fe2 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + /opt/conda/conda-bld/guidescan_1733853064269/work/src/genomics/structures.cxx:17:52: error: 'const struct genomics::chromosome' has no member named 'length' + 17 | if (off_target_abs_coords <= (int64_t)(chr.length-1)) { + | ^~~~~~ + /opt/conda/conda-bld/guidescan_1733853064269/work/src/genomics/structures.cxx:21:40: error: 'const struct genomics::chromosome' has no member named 'length' + 21 | off_target_abs_coords -= chr.length; + | ^~~~~~ + /opt/conda/conda-bld/guidescan_1733853064269/work/src/genomics/structures.cxx:46:62: error: 'struct genomics::chromosome' has no member named 'length' + 46 | if ((start_position < 0) || (end_position > (int64_t)c.length)) { + | ^~~~~~ + /opt/conda/conda-bld/guidescan_1733853064269/work/src/genomics/structures.cxx:47:60: error: too many initializers for 'genomics::chromosome' + 47 | return std::make_tuple(coordinates{chromosome{"", 0}, 0}, ""); + | ^ + /opt/conda/conda-bld/guidescan_1733853064269/work/src/genomics/structures.cxx:51:46: error: 'uint64_t' was not declared in this scope + 51 | return std::make_tuple(coordinates{c, (uint64_t)start_position}, strand); + | ^~~~~~~~ + /opt/conda/conda-bld/guidescan_1733853064269/work/src/genomics/structures.cxx:5:1: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + 4 | #include "genomics/structures.hpp" + |#include + 5 | + /opt/conda/conda-bld/guidescan_1733853064269/work/src/genomics/structures.cxx:51:54: error: too many initializers for 'genomics::coordinates' + 51 | return std::make_tuple(coordinates{c, (uint64_t)start_position}, strand); + | ^ + /opt/conda/conda-bld/guidescan_1733853064269/work/src/genomics/structures.cxx:51:41: error: expected primary-expression before '{' token + 51 | return std::make_tuple(coordinates{c, (uint64_t)start_position}, strand); + | ^ + /opt/conda/conda-bld/guidescan_1733853064269/work/src/genomics/sequences.cxx: In function 'std::string genomics::complement(const std::string&)': + /opt/conda/conda-bld/guidescan_1733853064269/work/src/genomics/sequences.cxx:30:31: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 30 | for (int64_t i = 0; i < kmer.length(); i) { + | ~~^~~~~~~~~~~~~~~ + make[2]: *** [bin/CMakeFiles/guidescan.dir/build.make:121: bin/CMakeFiles/guidescan.dir/genomics/structures.cxx.o] Error 1 + make[2]: *** Waiting for unfinished jobs.... + /opt/conda/conda-bld/guidescan_1733853064269/work/src/guidescan.cxx: In function 'int main(int, char**)': + /opt/conda/conda-bld/guidescan_1733853064269/work/src/guidescan.cxx:335:8: warning: unused variable 'download' [-Wunused-variable] + 335 | auto download = download_cmd(guidescan, download_opts); + | ^~~~~~~~ + [ 91%] Linking CXX executable csa_sada_test + [ 91%] Built target csa_sada_test + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/printer.hpp: In instantiation of 'std::string genomics::get_csv_lines(const genome_index&, const kmer&, bool, int64_t, std::vector > >&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string; int64_t = long int]': + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/process.hpp:118:54: required from 'void genomics::process_kmer_to_stream(const genome_index&, const genome_index&, const enumerate_cmd_options&, const kmer&, std::ostream&, std::mutex&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream]' + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/process.hpp:143:29: required from 'void genomics::process_kmers_to_stream(const genome_index&, const genome_index&, const enumerate_cmd_options&, const std::vector&, std::ostream&, std::mutex&, std::atomic&, uint64_t, const std::chrono::_V2::steady_clock::time_point&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream; uint64_t = long unsigned int; std::chrono::_V2::steady_clock::time_point = std::chrono::time_point > >]' + /opt/conda/conda-bld/guidescan_1733853064269/work/src/guidescan.cxx:245:102: required from here + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/printer.hpp:257:29: warning: comparison of integer expressions of different signedness: 'int64_t' {aka 'long int'} and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 257 | for (int64_t i = 0; i < off_targets[d].size(); i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~ + In file included from /opt/conda/conda-bld/guidescan_1733853064269/work/src/guidescan.cxx:12: + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/index.hpp: In instantiation of 'void genomics::genome_index::inexact_search(const std::string&, ssize_t, size_t, size_t, std::string, const std::vector >&, size_t, size_t, size_t, size_t, genomics::{anonymous}::affinity, const std::function&, t_data&) const [with t_data = long unsigned int; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string; ssize_t = long int; size_t = long unsigned int]': + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/index.hpp:395:19: required from 'void genomics::genome_index::inexact_search(const std::string&, const std::vector >&, size_t, size_t, size_t, size_t, const std::function&, t_data&) const [with t_data = long unsigned int; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/process.hpp:67:32: required from 'void genomics::process_kmer_to_stream(const genome_index&, const genome_index&, const enumerate_cmd_options&, const kmer&, std::ostream&, std::mutex&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream]' + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/process.hpp:143:29: required from 'void genomics::process_kmers_to_stream(const genome_index&, const genome_index&, const enumerate_cmd_options&, const std::vector&, std::ostream&, std::mutex&, std::atomic&, uint64_t, const std::chrono::_V2::steady_clock::time_point&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream; uint64_t = long unsigned int; std::chrono::_V2::steady_clock::time_point = std::chrono::time_point > >]' + /opt/conda/conda-bld/guidescan_1733853064269/work/src/guidescan.cxx:245:102: required from here + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/index.hpp:276:21: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 276 | && position != query.length() - 1) { + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/index.hpp:369:21: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 369 | && position != query.length() - 1 ) { + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/index.hpp: In instantiation of 'void genomics::genome_index::inexact_search(const std::string&, ssize_t, size_t, size_t, std::string, const std::vector >&, size_t, size_t, size_t, size_t, genomics::{anonymous}::affinity, const std::function&, t_data&) const [with t_data = std::vector >; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string; ssize_t = long int; size_t = long unsigned int]': + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/index.hpp:395:19: required from 'void genomics::genome_index::inexact_search(const std::string&, const std::vector >&, size_t, size_t, size_t, size_t, const std::function&, t_data&) const [with t_data = std::vector >; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/process.hpp:82:32: required from 'void genomics::process_kmer_to_stream(const genome_index&, const genome_index&, const enumerate_cmd_options&, const kmer&, std::ostream&, std::mutex&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream]' + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/process.hpp:143:29: required from 'void genomics::process_kmers_to_stream(const genome_index&, const genome_index&, const enumerate_cmd_options&, const std::vector&, std::ostream&, std::mutex&, std::atomic&, uint64_t, const std::chrono::_V2::steady_clock::time_point&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream; uint64_t = long unsigned int; std::chrono::_V2::steady_clock::time_point = std::chrono::time_point > >]' + /opt/conda/conda-bld/guidescan_1733853064269/work/src/guidescan.cxx:245:102: required from here + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/index.hpp:276:21: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 276 | && position != query.length() - 1) { + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/index.hpp:369:21: warning: comparison of integer expressions of different signedness: 'ssize_t' {aka 'long int'} and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 369 | && position != query.length() - 1 ) { + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/printer.hpp: In instantiation of 'std::string genomics::get_csv_line_nomatch(const genome_index&, const kmer&, bool, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string]': + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/printer.hpp:288:39: required from 'std::string genomics::get_csv_lines(const genome_index&, const kmer&, bool, int64_t, std::vector > >&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::string = std::__cxx11::basic_string; int64_t = long int]' + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/process.hpp:118:54: required from 'void genomics::process_kmer_to_stream(const genome_index&, const genome_index&, const enumerate_cmd_options&, const kmer&, std::ostream&, std::mutex&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream]' + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/process.hpp:143:29: required from 'void genomics::process_kmers_to_stream(const genome_index&, const genome_index&, const enumerate_cmd_options&, const std::vector&, std::ostream&, std::mutex&, std::atomic&, uint64_t, const std::chrono::_V2::steady_clock::time_point&, bool) [with t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >; unsigned int t_dens = 64; unsigned int t_inv_dens = 8192; std::ostream = std::basic_ostream; uint64_t = long unsigned int; std::chrono::_V2::steady_clock::time_point = std::chrono::time_point > >]' + /opt/conda/conda-bld/guidescan_1733853064269/work/src/guidescan.cxx:245:102: required from here + /opt/conda/conda-bld/guidescan_1733853064269/work/include/genomics/printer.hpp:190:84: warning: unused parameter 'gi' [-Wunused-parameter] + 190 | std::string get_csv_line_nomatch(const genome_index& gi, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ + make[1]: *** [CMakeFiles/Makefile2:8238: bin/CMakeFiles/guidescan.dir/all] Error 2 + make: *** [Makefile:156: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/guidescan_1733853064269/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/guidescan_1733853064269/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/guidescan/meta.yaml b/recipes/guidescan/meta.yaml index a77e8729aca56..93bc052bf5eaf 100644 --- a/recipes/guidescan/meta.yaml +++ b/recipes/guidescan/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 24075dc9c391e16af7ac7bf0af4cba0682b420e7ed63ca7c928f16a61adc5ff1 build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/gum/meta.yaml b/recipes/gum/meta.yaml index 80d205fd59d79..8abee1afec29a 100644 --- a/recipes/gum/meta.yaml +++ b/recipes/gum/meta.yaml @@ -27,7 +27,7 @@ source: folder: ext/gfakluge/src/tinyFA/pliib build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/gvcf2coverage/meta.yaml b/recipes/gvcf2coverage/meta.yaml index aeacb09762f55..1d2587c2e3f23 100644 --- a/recipes/gvcf2coverage/meta.yaml +++ b/recipes/gvcf2coverage/meta.yaml @@ -7,7 +7,7 @@ source: git_rev: 4d2c03bcae2f3d2e3f954c4903329c64b3a6a2cd build: - number: 8 + number: 9 requirements: build: diff --git a/recipes/gvcfgenotyper/meta.yaml b/recipes/gvcfgenotyper/meta.yaml index 8e07435e4150f..cfbceac8e9c96 100644 --- a/recipes/gvcfgenotyper/meta.yaml +++ b/recipes/gvcfgenotyper/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ hash }} build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/gw/meta.yaml b/recipes/gw/meta.yaml index 43a534a6e6384..efe2b65beb815 100644 --- a/recipes/gw/meta.yaml +++ b/recipes/gw/meta.yaml @@ -13,7 +13,7 @@ source: - fix-context.patch build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('gw', max_pin="x") }} ignore_run_exports: diff --git a/recipes/gwama/meta.yaml b/recipes/gwama/meta.yaml index 2a34a4b0cccdf..8b183334bfae3 100644 --- a/recipes/gwama/meta.yaml +++ b/recipes/gwama/meta.yaml @@ -9,7 +9,7 @@ source: sha256: f0e1f9d4bb739aa344ee7215c76d79ea22302bc18f7f318598ca95486f89ae8a build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/gxf2chrom/meta.yaml b/recipes/gxf2chrom/meta.yaml index d3925fc4bf0dd..178897b3a4adf 100644 --- a/recipes/gxf2chrom/meta.yaml +++ b/recipes/gxf2chrom/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 453df8aaff017f2ddb0c977de2e5f494feba8fa17d8f8fcddc908642ecb5fb08 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('gxf2chrom', max_pin="x.x") }} diff --git a/recipes/haddock_biobb/build_failure.osx-64.yaml b/recipes/haddock_biobb/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..f032afce05a0a --- /dev/null +++ b/recipes/haddock_biobb/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a539e6f208b010ed0b0754dbaa59baa035b93a5fc73ce48837873921df2f491b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - numpy + - freesasa + - toml + - python_abi 3.11.* *_cp311 + - pandas + - git + - kaleido-core + - plotly + - pdb-tools + test: + commands: + - echo "DONE!" + about: + description: HADDOCK3 is the next generation integrative modelling software in the + long-lasting HADDOCK project. It represents a complete rethinking and rewriting + of the HADDOCK2.X series, implementing a new way to interact with HADDOCK and + offering new features to users who can now define custom workflows. + home: https://github.com/haddocking/haddock3 + license: Apache Software License + license_family: APACHE + summary: HADDOCK3 is the next generation integrative modelling software in the long-lasting + HADDOCK project. + extra: + build: + python: + - '3.8' + - '3.9' + - '3.10' + copy_test_source_files: true + final: true + skip: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/haddock_biobb_1733815142204/work + return build_tree( + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/haddock_biobb_1733815142204/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/haddock_biobb_1733815142204/_build_env + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/haddock_biobb_1733815142204/work/conda_build.sh']' returned non-zero exit status 2. + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/haddock_biobb_1733815142204/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/haddock_biobb-3.0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/haddock_biobb-3.0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/haddock_biobb-3.0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/haddock_biobb-3.0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + make contact_fcc contact_fcc_lig + make[1]: Entering directory '$SRC_DIR/src/fcc/src' + x86_64-apple-darwin13.4.0-clang -O2 -o contact_fcc contact_fcc.cpp + x86_64-apple-darwin13.4.0-clang -O2 -o contact_fcc_lig contact_fcc_lig.cpp + make[1]: Leaving directory '$SRC_DIR/src/fcc/src' + x86_64-apple-darwin13.4.0-clang -Wall -O3 -march=native -std=c99 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o fast-rmsdmatrix.o fast-rmsdmatrix.c + x86_64-apple-darwin13.4.0-clang -Wall -O3 -march=native -std=c99 -o fast-rmsdmatrix fast-rmsdmatrix.o -lm +# Last 100 lines of the build log. diff --git a/recipes/haddock_biobb/meta.yaml b/recipes/haddock_biobb/meta.yaml index ba356bb2e4fe3..49ef43a921065 100644 --- a/recipes/haddock_biobb/meta.yaml +++ b/recipes/haddock_biobb/meta.yaml @@ -10,7 +10,7 @@ source: sha256: e0651a4913fb659a57e897ac68c4f8e8f29b61e00abfcab3f3bbd623e1977f7b build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin='x') }} diff --git a/recipes/hapbin/meta.yaml b/recipes/hapbin/meta.yaml index aceace10fc141..e8fd1950fbee0 100644 --- a/recipes/hapbin/meta.yaml +++ b/recipes/hapbin/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.3.0 build: - number: 5 + number: 6 skip: True # [osx] source: diff --git a/recipes/hapcut2/meta.yaml b/recipes/hapcut2/meta.yaml index e27214ae0c444..47a6478a7623a 100644 --- a/recipes/hapcut2/meta.yaml +++ b/recipes/hapcut2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 33d0a047c4d9b7ef4287be979cc580183acbd09a3ab518b9f5ebc5f41c2bf34e build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('hapcut2', max_pin="x") }} @@ -22,6 +22,7 @@ requirements: host: - zlib - htslib + - liblzma-devel run: - zlib - python >=3.5 diff --git a/recipes/haplink/meta.yaml b/recipes/haplink/meta.yaml index 2c68e6831f118..6ae045e56dd70 100644 --- a/recipes/haplink/meta.yaml +++ b/recipes/haplink/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('haplink', max_pin='x') }} binary_relocation: false diff --git a/recipes/haploflow/meta.yaml b/recipes/haploflow/meta.yaml index 0ac66dc47f5d5..f692c7faf7295 100644 --- a/recipes/haploflow/meta.yaml +++ b/recipes/haploflow/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/haplomap/meta.yaml b/recipes/haplomap/meta.yaml index be1a82bb587b5..5c8570c79fdd2 100644 --- a/recipes/haplomap/meta.yaml +++ b/recipes/haplomap/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{sha256}}' build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('haplomap', max_pin='x.x') }} diff --git a/recipes/hapog/build_failure.linux-64.yaml b/recipes/hapog/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..bba01601641af --- /dev/null +++ b/recipes/hapog/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: f836a66f47ebfd103fc46c75da4bdd28a16f48dc00822d3acd72cf98dda18223 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. + ******************************************************************************** + + !! + self.initialize_options() + running build + running build_py + creating package_build/lib/hapog + copying hapog/pipeline.py -> package_build/lib/hapog + copying hapog/__init__.py -> package_build/lib/hapog + copying hapog/mapping.py -> package_build/lib/hapog + copying hapog/cli.py -> package_build/lib/hapog + running install_lib + creating $PREFIX/lib/python3.10/site-packages/hapog + copying package_build/lib/hapog/pipeline.py -> $PREFIX/lib/python3.10/site-packages/hapog + copying package_build/lib/hapog/__init__.py -> $PREFIX/lib/python3.10/site-packages/hapog + copying package_build/lib/hapog/mapping.py -> $PREFIX/lib/python3.10/site-packages/hapog + copying package_build/lib/hapog/cli.py -> $PREFIX/lib/python3.10/site-packages/hapog + byte-compiling $PREFIX/lib/python3.10/site-packages/hapog/pipeline.py to pipeline.cpython-310.pyc + byte-compiling $PREFIX/lib/python3.10/site-packages/hapog/__init__.py to __init__.cpython-310.pyc + byte-compiling $PREFIX/lib/python3.10/site-packages/hapog/mapping.py to mapping.cpython-310.pyc + byte-compiling $PREFIX/lib/python3.10/site-packages/hapog/cli.py to cli.cpython-310.pyc + running install_egg_info + running egg_info + creating hapog.egg-info + writing hapog.egg-info/PKG-INFO + writing dependency_links to hapog.egg-info/dependency_links.txt + writing entry points to hapog.egg-info/entry_points.txt + writing requirements to hapog.egg-info/requires.txt + writing top-level names to hapog.egg-info/top_level.txt + writing manifest file 'hapog.egg-info/SOURCES.txt' + reading manifest file 'hapog.egg-info/SOURCES.txt' + adding license file 'LICENSE.md' + writing manifest file 'hapog.egg-info/SOURCES.txt' + Copying hapog.egg-info to $PREFIX/lib/python3.10/site-packages/hapog-1.3.8-py3.10.egg-info + running install_scripts + Installing hapog script to $PREFIX/bin + writing list of installed files to 'record.txt' + CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): + Compatibility with CMake < 3.10 will be removed from a future version of + CMake. + + Update the VERSION argument value. Or, use the ... syntax + to tell CMake that the project requires at least but has been updated + to work with policies introduced by or earlier. + + + -- The C compiler identification is GNU 13.3.0 + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - skipped + -- Detecting C compile features + -- Detecting C compile features - done + + Will attempt to find HTSlib at the provided path /opt/conda/conda-bld/hapog_1734204516025/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib + /opt/conda/conda-bld/hapog_1734204516025/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + /opt/conda/conda-bld/hapog_1734204516025/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/libhts.a + htslib_found TRUE + + Found htslib at /opt/conda/conda-bld/hapog_1734204516025/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + -- Configuring done (0.2s) + -- Generating done (0.0s) + -- Build files have been written to: $SRC_DIR/hapog_build + [ 20%] Building C object CMakeFiles/hapog.dir/polish_consensus.c.o + /opt/conda/conda-bld/hapog_1734204516025/work/src/polish_consensus.c: In function 'parse_bam': + /opt/conda/conda-bld/hapog_1734204516025/work/src/polish_consensus.c:111:5: warning: ignoring return value of 'bam_copy1' declared with attribute 'warn_unused_result' [-Wunused-result] + 111 | bam_copy1(aln2, aln); + | ^~~~~~~~~~~~~~~~~~~~ + [ 40%] Building C object CMakeFiles/hapog.dir/alipile.c.o + [ 60%] Building C object CMakeFiles/hapog.dir/hash.c.o + [ 80%] Building C object CMakeFiles/hapog.dir/polished.c.o + [100%] Linking C executable hapog + /opt/conda/conda-bld/hapog_1734204516025/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -llzma: No such file or directory + collect2: error: ld returned 1 exit status + make[2]: *** [CMakeFiles/hapog.dir/build.make:149: hapog] Error 1 + make[1]: *** [CMakeFiles/Makefile2:87: CMakeFiles/hapog.dir/all] Error 2 + make: *** [Makefile:91: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/hapog_1734204516025/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/hapog_1734204516025/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/hapog/build_failure.osx-64.yaml b/recipes/hapog/build_failure.osx-64.yaml index 2d565be3598a8..8a98251eae536 100644 --- a/recipes/hapog/build_failure.osx-64.yaml +++ b/recipes/hapog/build_failure.osx-64.yaml @@ -1,77 +1,77 @@ -recipe_sha: 0b069e46b59bb258fba72fed3373e4f5a5d2b652ef2c18a538ccdc4e411cb4e9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: f836a66f47ebfd103fc46c75da4bdd28a16f48dc00822d3acd72cf98dda18223 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- - ld64_osx-64: 711-ha20a434_0 conda-forge - libclang-cpp16: 16.0.6-default_h4c8afb6_7 conda-forge - libcurl: 8.8.0-hf9fcc65_0 conda-forge - libcxx: 17.0.6-h88467a6_0 conda-forge - libedit: 3.1.20191231-h0678c8f_2 conda-forge - libev: 4.33-h10d778d_2 conda-forge - libexpat: 2.6.2-h73e2aa4_0 conda-forge - libiconv: 1.17-hd75f5a5_2 conda-forge - libllvm16: 16.0.6-hbedff68_3 conda-forge - libnghttp2: 1.58.0-h64cf6d3_1 conda-forge - libssh2: 1.11.0-hd019ec5_0 conda-forge - libuv: 1.48.0-h67532ce_0 conda-forge - libxml2: 2.12.7-h3e169fe_1 conda-forge - libzlib: 1.3.1-h87427d6_1 conda-forge - llvm-tools: 16.0.6-hbedff68_3 conda-forge - make: 4.3-h22f3db7_1 conda-forge - ncurses: 6.5-h5846eda_0 conda-forge - openssl: 3.3.1-h87427d6_0 conda-forge - rhash: 1.4.4-h0dc2134_0 conda-forge - sigtool: 0.1.3-h88f4db0_0 conda-forge - tapi: 1100.0.11-h9ce4665_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - zstd: 1.5.6-h915ae27_0 conda-forge + - liblzma 5.6.3 hd471939_1 + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/hapog_1733817863278/work/conda_build.sh']' returned non-zero exit status 1. + - libzlib 1.3.1 hd23fc13_2 + - ncurses 6.5 hf036a51_1 + - tzdata 2024b hc8b5060_0 + - libedit 3.1.20191231 h0678c8f_2 + - liblzma-devel 5.6.3 hd471939_1 + - libsqlite 3.47.2 hdb6dae5_0 + - openssl 3.4.0 hd471939_0 + - readline 8.2 h9e318b2_1 + - tk 8.6.13 h1abcd95_1 + - xz-gpl-tools 5.6.3 h357f2ed_1 + - xz-tools 5.6.3 hd471939_1 + - zlib 1.3.1 hd23fc13_2 + - zstd 1.5.6 h915ae27_0 + - krb5 1.21.3 h37d8d59_0 + - libnghttp2 1.64.0 hc7306c3_0 + - libssh2 1.11.1 h3dc7d44_0 + - python 3.10.16 h5acdff8_1_cpython + - xz 5.6.3 h357f2ed_1 + - libcurl 8.10.1 h58e7537_0 + - htslib 1.21 hec81eee_0 + run: + - minimap2 + - libzlib >=1.3.1,<2.0a0 + - bwa + - samtools + - biopython + - htslib >=1.21,<1.22.0a0 + - python_abi 3.10.* *_cp310 + - python >=3.10,<3.11.0a0 + test: + commands: + - hapog -h + - hapog_bin -h + imports: + - hapog + about: + dev_url: https://github.com/institut-de-genomique/HAPO-G + doc_url: https://www.genoscope.cns.fr/hapog/ + home: https://github.com/institut-de-genomique/HAPO-G + license: CECILL-2.1 + license_family: OTHER + license_file: LICENSE.md + summary: Haplotype-Aware Polishing of Genomes + extra: + copy_test_source_files: true + final: true + identifiers: + - doi:10.1093/nargab/lqab034 - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - Downloading source to cache: 1.3.8_822f4c7e68.tar.gz - Downloading https://github.com/institut-de-genomique/HAPO-G/archive/refs/tags/1.3.8.tar.gz - Success - /opt/mambaforge/envs/bioconda/conda-bld/hapog_1717692287194/work/setup.py:1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives - import distutils.command.build - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/conda-bld/hapog_1717692287194/work/setup.py", line 3, in - from setuptools import setup - ModuleNotFoundError: No module named 'setuptools' - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/hapog_1717692287194/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/hapog_1717692287194/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol - Traceback (most recent call last): - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/hapog_1717692287194/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/hapog_1717692287194/work + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/hapog_1733817863278/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/hapog_1733817863278/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/hapog_1733817863278/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/hapog_1733817863278/work INFO: activate_clang_osx-64.sh made the following environmental changes: - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as CC=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hapog-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/hapog_1717692287194/work/conda_build.sh']' returned non-zero exit status 1. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hapog-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool @@ -80,7 +80,7 @@ log: |2- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -89,7 +89,7 @@ log: |2- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack diff --git a/recipes/hapog/meta.yaml b/recipes/hapog/meta.yaml index cc373afbe210b..3e4e69be7418d 100644 --- a/recipes/hapog/meta.yaml +++ b/recipes/hapog/meta.yaml @@ -6,7 +6,7 @@ package: build: skip: True # [py < 37] - number: 1 + number: 2 run_exports: - {{ pin_subpackage("hapog", max_pin="x") }} diff --git a/recipes/haproh/meta.yaml b/recipes/haproh/meta.yaml index ced7896ed7ef3..99e961d65e7c5 100644 --- a/recipes/haproh/meta.yaml +++ b/recipes/haproh/meta.yaml @@ -10,7 +10,7 @@ build: entry_points: - hapConX = hapsburg.hapCONX:main script: {{ PYTHON }} -m pip install . -vv - number: 2 + number: 3 source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hapROH-{{ version }}.tar.gz diff --git a/recipes/hardklor/meta.yaml b/recipes/hardklor/meta.yaml index 81ad3215adc89..d8909afcacc32 100644 --- a/recipes/hardklor/meta.yaml +++ b/recipes/hardklor/meta.yaml @@ -11,7 +11,7 @@ source: - patch build: - number: 4 + number: 5 skip: True # [osx] requirements: diff --git a/recipes/harvesttools/meta.yaml b/recipes/harvesttools/meta.yaml index 3ed7d95563bb4..dc3607f19b2a2 100644 --- a/recipes/harvesttools/meta.yaml +++ b/recipes/harvesttools/meta.yaml @@ -14,7 +14,7 @@ source: sha256: '{{sha256osx}}' # [osx] build: - number: 1 + number: 2 requirements: host: diff --git a/recipes/haslr/meta.yaml b/recipes/haslr/meta.yaml index c1a274e3888cf..2e65fb20fae7c 100755 --- a/recipes/haslr/meta.yaml +++ b/recipes/haslr/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 # minia is not available for osx skip: True # [osx or py27] diff --git a/recipes/hatchet/meta.yaml b/recipes/hatchet/meta.yaml index c01d6279a21aa..6b59fdd92fa9c 100755 --- a/recipes/hatchet/meta.yaml +++ b/recipes/hatchet/meta.yaml @@ -17,7 +17,7 @@ source: sha256: 1d58586f9a33ac7035f51f6a04707248218f70bddbec78cb83f11c986ac652cd # [osx] build: - number: 1 + number: 2 skip: True # [py < 37] entry_points: - hatchet = hatchet.__main__:main diff --git a/recipes/hcluster_sg/meta.yaml b/recipes/hcluster_sg/meta.yaml index 412c9f3ef60e0..7294edee0c29b 100644 --- a/recipes/hcluster_sg/meta.yaml +++ b/recipes/hcluster_sg/meta.yaml @@ -7,7 +7,7 @@ source: md5: bdcbc25899be101b421d2e01166876e7 build: - number: 7 + number: 8 requirements: build: diff --git a/recipes/heinz/meta.yaml b/recipes/heinz/meta.yaml index 6cadfe5730804..32d7d0271de53 100644 --- a/recipes/heinz/meta.yaml +++ b/recipes/heinz/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 0cc07f02bb5b6fa02cad316fbccec516302d67597512d37e53ee6f4b3b1e259b build: - number: 4 + number: 5 skip: True # [osx] requirements: diff --git a/recipes/hhsuite/build_failure.linux-64.yaml b/recipes/hhsuite/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..1b0e727ff6b0d --- /dev/null +++ b/recipes/hhsuite/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 8f872c5cb53afb064301593aeeb26eb9061e018d3b0cdc89bfab52a4e6005e6a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + | ^ + /opt/conda/conda-bld/hhsuite_1734292912362/work/src/a3m_compress.cpp:559:58: error: 'void compressed_a3m::readU16(char**, uint16_t&)' should have been declared inside 'compressed_a3m' + 559 | void compressed_a3m::readU16(char** ptr, uint16_t &result) { + | ^ + /opt/conda/conda-bld/hhsuite_1734292912362/work/src/a3m_compress.cpp:570:63: error: 'void compressed_a3m::writeU32(std::ostream&, uint32_t)' should have been declared inside 'compressed_a3m' + 570 | void compressed_a3m::writeU32(std::ostream& file, uint32_t val) { + | ^ + /opt/conda/conda-bld/hhsuite_1734292912362/work/src/a3m_compress.cpp:583:58: error: 'void compressed_a3m::readU32(char**, uint32_t&)' should have been declared inside 'compressed_a3m' + 583 | void compressed_a3m::readU32(char** ptr, uint32_t &result) { + | ^ + [ 13%] Built target ffindex_apply + make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend + make[2]: Entering directory '$SRC_DIR/build' + cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR/lib/ffindex/src $SRC_DIR/build $SRC_DIR/build/lib/ffindex/src $SRC_DIR/build/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" + make[2]: Leaving directory '$SRC_DIR/build' + make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build + make[2]: Entering directory '$SRC_DIR/build' + [ 14%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o + cd $SRC_DIR/build/lib/ffindex/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/lib/ffindex/src/ext -std=c99 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c $SRC_DIR/lib/ffindex/src/ffindex_reduce.c + make[2]: *** [src/CMakeFiles/A3M_COMPRESS.dir/build.make:79: src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o] Error 1 + make[2]: Leaving directory '$SRC_DIR/build' + make[1]: *** [CMakeFiles/Makefile2:1011: src/CMakeFiles/A3M_COMPRESS.dir/all] Error 2 + make[1]: *** Waiting for unfinished jobs.... + [ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o + cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -msse4.1 -mfpmath=sse -fopenmp -fno-strict-aliasing -O3 -DNDEBUG -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c $SRC_DIR/src/cs/as.cc + [ 16%] Linking C executable ffindex_reduce + cd $SRC_DIR/build/lib/ffindex/src && $BUILD_PREFIX/bin/cmake -E cmake_link_script CMakeFiles/ffindex_reduce.dir/link.txt --verbose=1 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -std=c99 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_reduce.dir/link.d CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a + make[2]: Leaving directory '$SRC_DIR/build' + [ 16%] Built target ffindex_reduce + [ 17%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o + cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -msse4.1 -mfpmath=sse -fopenmp -fno-strict-aliasing -O3 -DNDEBUG -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c $SRC_DIR/src/cs/assert_helpers.cc + [ 18%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o + cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -msse4.1 -mfpmath=sse -fopenmp -fno-strict-aliasing -O3 -DNDEBUG -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c $SRC_DIR/src/cs/blosum_matrix.cc + [ 19%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o + cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -msse4.1 -mfpmath=sse -fopenmp -fno-strict-aliasing -O3 -DNDEBUG -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c $SRC_DIR/src/cs/getopt_pp.cc + [ 20%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o + cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -msse4.1 -mfpmath=sse -fopenmp -fno-strict-aliasing -O3 -DNDEBUG -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c $SRC_DIR/src/cs/log.cc + cd $SRC_DIR/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < $SRC_DIR/build/generated/context_data.crf.h > $SRC_DIR/build/generated/context_data.crf.h.tmp + cd $SRC_DIR/data && mv -f $SRC_DIR/build/generated/context_data.crf.h.tmp $SRC_DIR/build/generated/context_data.crf.h + [ 21%] Generating ../generated/context_data.lib.h + cd $SRC_DIR/data && mkdir -p $SRC_DIR/build/generated + cd $SRC_DIR/data && $SRC_DIR/cmake/xxdi.pl context_data.lib > $SRC_DIR/build/generated/context_data.lib.h + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + [ 22%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o + cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -msse4.1 -mfpmath=sse -fopenmp -fno-strict-aliasing -O3 -DNDEBUG -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c $SRC_DIR/src/cs/application.cc + [ 23%] Generating ../generated/cs219.lib.h + cd $SRC_DIR/data && mkdir -p $SRC_DIR/build/generated + cd $SRC_DIR/data && $SRC_DIR/cmake/xxdi.pl cs219.lib > $SRC_DIR/build/generated/cs219.lib.h + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + cd $SRC_DIR/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < $SRC_DIR/build/generated/cs219.lib.h > $SRC_DIR/build/generated/cs219.lib.h.tmp + cd $SRC_DIR/data && mv -f $SRC_DIR/build/generated/cs219.lib.h.tmp $SRC_DIR/build/generated/cs219.lib.h + [ 24%] Linking CXX static library libCS_OBJECTS.a + cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake + cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib libCS_OBJECTS.a + make[2]: Leaving directory '$SRC_DIR/build' + [ 24%] Built target CS_OBJECTS + cd $SRC_DIR/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < $SRC_DIR/build/generated/context_data.lib.h > $SRC_DIR/build/generated/context_data.lib.h.tmp + cd $SRC_DIR/data && mv -f $SRC_DIR/build/generated/context_data.lib.h.tmp $SRC_DIR/build/generated/context_data.lib.h + make[2]: Leaving directory '$SRC_DIR/build' + [ 24%] Built target generated + make[1]: Leaving directory '$SRC_DIR/build' + make: *** [Makefile:156: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/hhsuite_1734292912362/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/hhsuite_1734292912362/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/hhsuite/build_failure.linux-aarch64.yaml b/recipes/hhsuite/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..3ce80d3226efb --- /dev/null +++ b/recipes/hhsuite/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 8f872c5cb53afb064301593aeeb26eb9061e018d3b0cdc89bfab52a4e6005e6a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + | ^ + /opt/conda/conda-bld/hhsuite_1734270873702/work/src/a3m_compress.cpp:570:63: error: 'void compressed_a3m::writeU32(std::ostream&, uint32_t)' should have been declared inside 'compressed_a3m' + 570 | void compressed_a3m::writeU32(std::ostream& file, uint32_t val) { + | ^ + /opt/conda/conda-bld/hhsuite_1734270873702/work/src/a3m_compress.cpp:583:58: error: 'void compressed_a3m::readU32(char**, uint32_t&)' should have been declared inside 'compressed_a3m' + 583 | void compressed_a3m::readU32(char** ptr, uint32_t &result) { + | ^ + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib libhhviterbialgorithm_and_ss.a + make[2]: Leaving directory '$SRC_DIR/build' + [ 11%] Built target hhviterbialgorithm_and_ss + make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend + make[2]: Entering directory '$SRC_DIR/build' + cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR/lib/ffindex/src $SRC_DIR/build $SRC_DIR/build/lib/ffindex/src $SRC_DIR/build/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" + make[2]: Leaving directory '$SRC_DIR/build' + make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build + make[2]: Entering directory '$SRC_DIR/build' + [ 12%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o + cd $SRC_DIR/build/lib/ffindex/src && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/lib/ffindex/src/ext -std=c99 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c $SRC_DIR/lib/ffindex/src/ffindex_apply_mpi.c + make[2]: *** [src/CMakeFiles/A3M_COMPRESS.dir/build.make:79: src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o] Error 1 + make[1]: *** [CMakeFiles/Makefile2:1011: src/CMakeFiles/A3M_COMPRESS.dir/all] Error 2 + make[2]: Leaving directory '$SRC_DIR/build' + make[1]: *** Waiting for unfinished jobs.... + [ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o + cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -march=armv8-asimd -fopenmp -fno-strict-aliasing -O3 -DNDEBUG -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c $SRC_DIR/src/cs/as.cc + [ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o + cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -march=armv8-asimd -fopenmp -fno-strict-aliasing -O3 -DNDEBUG -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c $SRC_DIR/src/cs/assert_helpers.cc + [ 15%] Linking C executable ffindex_apply + cd $SRC_DIR/build/lib/ffindex/src && $BUILD_PREFIX/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -std=c99 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_apply.dir/link.d CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a + make[2]: Leaving directory '$SRC_DIR/build' + [ 15%] Built target ffindex_apply + [ 16%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o + cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -march=armv8-asimd -fopenmp -fno-strict-aliasing -O3 -DNDEBUG -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c $SRC_DIR/src/cs/blosum_matrix.cc + cd $SRC_DIR/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < $SRC_DIR/build/generated/context_data.crf.h > $SRC_DIR/build/generated/context_data.crf.h.tmp + [ 17%] Generating ../generated/context_data.lib.h + cd $SRC_DIR/data && mkdir -p $SRC_DIR/build/generated + cd $SRC_DIR/data && $SRC_DIR/cmake/xxdi.pl context_data.lib > $SRC_DIR/build/generated/context_data.lib.h + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + [ 18%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o + cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -march=armv8-asimd -fopenmp -fno-strict-aliasing -O3 -DNDEBUG -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c $SRC_DIR/src/cs/getopt_pp.cc + cd $SRC_DIR/data && mv -f $SRC_DIR/build/generated/context_data.crf.h.tmp $SRC_DIR/build/generated/context_data.crf.h + [ 19%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o + cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -march=armv8-asimd -fopenmp -fno-strict-aliasing -O3 -DNDEBUG -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c $SRC_DIR/src/cs/log.cc + [ 20%] Generating ../generated/cs219.lib.h + cd $SRC_DIR/data && mkdir -p $SRC_DIR/build/generated + cd $SRC_DIR/data && $SRC_DIR/cmake/xxdi.pl cs219.lib > $SRC_DIR/build/generated/cs219.lib.h + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + cd $SRC_DIR/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < $SRC_DIR/build/generated/cs219.lib.h > $SRC_DIR/build/generated/cs219.lib.h.tmp + cd $SRC_DIR/data && mv -f $SRC_DIR/build/generated/cs219.lib.h.tmp $SRC_DIR/build/generated/cs219.lib.h + [ 21%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o + cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -march=armv8-asimd -fopenmp -fno-strict-aliasing -O3 -DNDEBUG -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c $SRC_DIR/src/cs/application.cc + [ 22%] Linking CXX static library libCS_OBJECTS.a + cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake + cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib libCS_OBJECTS.a + make[2]: Leaving directory '$SRC_DIR/build' + [ 22%] Built target CS_OBJECTS + cd $SRC_DIR/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < $SRC_DIR/build/generated/context_data.lib.h > $SRC_DIR/build/generated/context_data.lib.h.tmp + cd $SRC_DIR/data && mv -f $SRC_DIR/build/generated/context_data.lib.h.tmp $SRC_DIR/build/generated/context_data.lib.h + make[2]: Leaving directory '$SRC_DIR/build' + [ 22%] Built target generated + make[1]: Leaving directory '$SRC_DIR/build' + make: *** [Makefile:156: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/hhsuite_1734270873702/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/hhsuite_1734270873702/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/hhsuite/build_failure.osx-64.yaml b/recipes/hhsuite/build_failure.osx-64.yaml deleted file mode 100644 index 15bda1eff920e..0000000000000 --- a/recipes/hhsuite/build_failure.osx-64.yaml +++ /dev/null @@ -1,106 +0,0 @@ -recipe_sha: a8520adadc6e0abc700caed83e2601f6fa1d3f9b14698f200038c746a58fde55 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - cd $SRC_DIR/build/src && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -I$SRC_DIR/src/cs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -msse4.1 -mfpmath=sse -fopenmp=libomp -fno-strict-aliasing -O3 -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c $SRC_DIR/src/hhviterbialgorithm.cpp - [ 9%] Linking CXX static library libhhviterbialgorithm_with_celloff.a - /opt/mambaforge/envs/bioconda/conda-bld/hhsuite_1717953464012/work/src/a3m_compress.cpp:504:26: error: no member named 'ptr_fun' in namespace 'std' - std::not1(std::ptr_fun(std::isspace))).base(), s.end()); - ~~~~~^ - /opt/mambaforge/envs/bioconda/conda-bld/hhsuite_1717953464012/work/src/a3m_compress.cpp:504:37: error: expected '(' for function-style cast or type construction - std::not1(std::ptr_fun(std::isspace))).base(), s.end()); - ~~~^ - /opt/mambaforge/envs/bioconda/conda-bld/hhsuite_1717953464012/work/src/a3m_compress.cpp:504:42: error: expected '(' for function-style cast or type construction - std::not1(std::ptr_fun(std::isspace))).base(), s.end()); - ~~~^ - /opt/mambaforge/envs/bioconda/conda-bld/hhsuite_1717953464012/work/src/a3m_compress.cpp:504:16: error: no member named 'not1' in namespace 'std' - std::not1(std::ptr_fun(std::isspace))).base(), s.end()); - ~~~~~^ - 4 errors generated. - make[2]: *** [src/CMakeFiles/A3M_COMPRESS.dir/build.make:76: src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o] Error 1 - make[1]: *** [CMakeFiles/Makefile2:840: src/CMakeFiles/A3M_COMPRESS.dir/all] Error 2 - make[1]: *** Waiting for unfinished jobs.... - make: *** [Makefile:156: all] Error 2 - Traceback (most recent call last): - cd $SRC_DIR/build/src && $BUILD_PREFIX/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake - cd $SRC_DIR/build/src && $BUILD_PREFIX/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o - $BUILD_PREFIX/bin/llvm-ranlib libhhviterbialgorithm_with_celloff.a - make[2]: Leaving directory '$SRC_DIR/build' - [ 9%] Built target hhviterbialgorithm_with_celloff - make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend - sys.exit(execute()) - make[2]: Entering directory '$SRC_DIR/build' - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR/src $SRC_DIR/build $SRC_DIR/build/src $SRC_DIR/build/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake "--color=" - make[2]: Leaving directory '$SRC_DIR/build' - make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build - make[2]: Entering directory '$SRC_DIR/build' - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/hhsuite_1717953464012/work/conda_build.sh']' returned non-zero exit status 2. - [ 10%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o - cd $SRC_DIR/build/src && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -I$SRC_DIR/src/cs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -msse4.1 -mfpmath=sse -fopenmp=libomp -fno-strict-aliasing -O3 -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c $SRC_DIR/src/hhviterbialgorithm.cpp - [ 11%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a - cd $SRC_DIR/build/src && $BUILD_PREFIX/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake - cd $SRC_DIR/build/src && $BUILD_PREFIX/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 - $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o - $BUILD_PREFIX/bin/llvm-ranlib libhhviterbialgorithm_with_celloff_and_ss.a - make[2]: Leaving directory '$SRC_DIR/build' - [ 11%] Built target hhviterbialgorithm_with_celloff_and_ss - make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend - make[2]: Entering directory '$SRC_DIR/build' - cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR/src/cs $SRC_DIR/build $SRC_DIR/build/src/cs $SRC_DIR/build/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake "--color=" - make[2]: Leaving directory '$SRC_DIR/build' - make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build - make[2]: Entering directory '$SRC_DIR/build' - [ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o - cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -msse4.1 -mfpmath=sse -fopenmp=libomp -fno-strict-aliasing -O3 -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c $SRC_DIR/src/cs/aa.cc - [ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o - cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -msse4.1 -mfpmath=sse -fopenmp=libomp -fno-strict-aliasing -O3 -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c $SRC_DIR/src/cs/as.cc - [ 14%] Linking CXX static library libhhviterbialgorithm_and_ss.a - cd $SRC_DIR/build/src && $BUILD_PREFIX/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake - cd $SRC_DIR/build/src && $BUILD_PREFIX/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 - $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o - $BUILD_PREFIX/bin/llvm-ranlib libhhviterbialgorithm_and_ss.a - make[2]: Leaving directory '$SRC_DIR/build' - [ 14%] Built target hhviterbialgorithm_and_ss - make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend - make[2]: Entering directory '$SRC_DIR/build' - cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR/src $SRC_DIR/build $SRC_DIR/build/src $SRC_DIR/build/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" - make[2]: Leaving directory '$SRC_DIR/build' - make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build - make[2]: Entering directory '$SRC_DIR/build' - [ 14%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o - cd $SRC_DIR/build/src && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -I$SRC_DIR/src/cs -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -msse4.1 -mfpmath=sse -fopenmp=libomp -fno-strict-aliasing -O3 -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c $SRC_DIR/src/a3m_compress.cpp - [ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o - cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -msse4.1 -mfpmath=sse -fopenmp=libomp -fno-strict-aliasing -O3 -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c $SRC_DIR/src/cs/assert_helpers.cc - make[2]: Leaving directory '$SRC_DIR/build' - [ 16%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o - cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -msse4.1 -mfpmath=sse -fopenmp=libomp -fno-strict-aliasing -O3 -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c $SRC_DIR/src/cs/blosum_matrix.cc - [ 17%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o - cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -msse4.1 -mfpmath=sse -fopenmp=libomp -fno-strict-aliasing -O3 -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c $SRC_DIR/src/cs/getopt_pp.cc - [ 18%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o - cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -msse4.1 -mfpmath=sse -fopenmp=libomp -fno-strict-aliasing -O3 -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c $SRC_DIR/src/cs/log.cc - [ 19%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o - cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DOPENMP -I$SRC_DIR/build/generated -I$SRC_DIR/src -I$SRC_DIR/lib/ffindex/src -I$SRC_DIR/lib/simde -I$SRC_DIR/lib/simd -I$SRC_DIR/build/src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hhsuite-3.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c0x -fsigned-char -msse4.1 -mfpmath=sse -fopenmp=libomp -fno-strict-aliasing -O3 -DNDEBUG -isysroot /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c $SRC_DIR/src/cs/application.cc - [ 20%] Linking CXX static library libCS_OBJECTS.a - cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake - cd $SRC_DIR/build/src/cs && $BUILD_PREFIX/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 - $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o - $BUILD_PREFIX/bin/llvm-ranlib libCS_OBJECTS.a - make[2]: Leaving directory '$SRC_DIR/build' - [ 20%] Built target CS_OBJECTS - make[1]: Leaving directory '$SRC_DIR/build' -# Last 100 lines of the build log. -category: |- - compiler error diff --git a/recipes/hhsuite/meta.yaml b/recipes/hhsuite/meta.yaml index 3c13879216cec..f1d117a0082d6 100644 --- a/recipes/hhsuite/meta.yaml +++ b/recipes/hhsuite/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 13 + number: 14 run_exports: - {{ pin_subpackage('hhsuite', max_pin="x") }} diff --git a/recipes/hi-corrector/build_failure.osx-64.yaml b/recipes/hi-corrector/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..66c4be73f2d7f --- /dev/null +++ b/recipes/hi-corrector/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 88ded6a6293e33ecb908bd0644979ae05c2f8c54143040c040c949d442c36ce5 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + - llvm-tools 18.1.8 h9ce406d_2 + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/hi-corrector_1733854782945/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + - libclang-cpp18.1 18.1.8 default_h0c94c6a_5 + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + - llvm-tools-18 18.1.8 h9ce406d_2 + - ncurses 6.5 hf036a51_1 + - tapi 1300.6.5 h390ca13_0 + sys.exit(execute()) + - zstd 1.5.6 h915ae27_0 + - sigtool 0.1.3 h88f4db0_0 + - clangxx 18.1.8 default_h179603d_5 + - ld64_osx-64 951.9 hc8d1a19_2 + - libcxx 19.1.5 hf95d169_0 + host: + - libcxx 19.1.5 hf95d169_0 + - libzlib 1.3.1 hd23fc13_2 + - llvm-openmp 19.1.5 ha54dae1_0 + - mpi 1.0 openmpi + - libgfortran5 13.2.0 h2873a65_3 + - zlib 1.3.1 hd23fc13_2 + - libgfortran 5.0.0 13_2_0_h97931a8_3 + - openmpi 4.1.6 h7406208_101 + run: + - openmpi >=4.1.6,<5.0a0 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + about: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + home: https://github.com/jasminezhoulab/Hi-Corrector + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + license: BSD-3-Clause + license_family: BSD + license_file: LICENSE + summary: Remove biases from chromatin contact matrices generated by genome-wide + proximity ligation assays, e.g. Hi-C and its variant TCC + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/hi-corrector_1733854782945/work + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/hi-corrector_1733854782945/work/conda_build.sh']' returned non-zero exit status 2. + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/hi-corrector_1733854782945/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/hi-corrector_1733854782945/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/hi-corrector_1733854782945/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hi-corrector-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hi-corrector-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + x86_64-apple-darwin13.4.0-clang -Wall -O3 -c ic.c -o ic.o +# Last 100 lines of the build log. diff --git a/recipes/hi-corrector/meta.yaml b/recipes/hi-corrector/meta.yaml index 7f70cc21a217d..e1f29a8658fa0 100644 --- a/recipes/hi-corrector/meta.yaml +++ b/recipes/hi-corrector/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 source: url: https://github.com/jasminezhoulab/Hi-Corrector/archive/a232fedfdc18f8afe8b4fc502f4d0476091db6f8.tar.gz diff --git a/recipes/hic-straw/meta.yaml b/recipes/hic-straw/meta.yaml index 0585eade01a26..1ba30d87cdb12 100644 --- a/recipes/hic-straw/meta.yaml +++ b/recipes/hic-straw/meta.yaml @@ -12,7 +12,7 @@ source: build: skip: true # [py<36] script: {{ PYTHON }} -m pip install . -vv - number: 4 + number: 5 requirements: build: diff --git a/recipes/hifiasm_meta/build_failure.osx-64.yaml b/recipes/hifiasm_meta/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..53bd4cb168278 --- /dev/null +++ b/recipes/hifiasm_meta/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 8e1418f7b704679d6c873b709616d0960ab6616e15c9914fd761c95d3dbf2032 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/hifiasm_meta_1733858508864/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/hifiasm_meta_1733858508864/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/hifiasm_meta_1733858508864/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/hifiasm_meta_1733858508864/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hifiasm_meta-hamtv0.3.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/hifiasm_meta_1733858508864/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/hifiasm_meta_1733858508864/work/conda_build.sh']' returned non-zero exit status 2. + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hifiasm_meta-hamtv0.3.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hifiasm_meta-hamtv0.3.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hifiasm_meta-hamtv0.3.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include CommandLines.cpp -o CommandLines.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include Process_Read.cpp -o Process_Read.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include Assembly.cpp -o Assembly.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include Hash_Table.cpp -o Hash_Table.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include POA.cpp -o POA.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include Correct.cpp -o Correct.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include Levenshtein_distance.cpp -o Levenshtein_distance.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include Overlaps.cpp -o Overlaps.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include Trio.cpp -o Trio.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include kthread.cpp -o kthread.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include Purge_Dups.cpp -o Purge_Dups.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include htab.cpp -o htab.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include hist.cpp -o hist.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include sketch.cpp -o sketch.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include anchor.cpp -o anchor.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include extract.cpp -o extract.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include sys.cpp -o sys.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include ksw2_extz2_sse.c -o ksw2_extz2_sse.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include meta_util.cpp -o meta_util.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include meta_util_debug.cpp -o meta_util_debug.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include Overlaps_hamt.cpp -o Overlaps_hamt.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include sptree.cpp -o sptree.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include data.c -o data.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include tsne.cpp -o tsne.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include t-sne.cpp -o t-sne.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -I$PREFIX/include main.cpp -o main.o + x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib CommandLines.o Process_Read.o Assembly.o Hash_Table.o POA.o Correct.o Levenshtein_distance.o Overlaps.o Trio.o kthread.o Purge_Dups.o htab.o hist.o sketch.o anchor.o extract.o sys.o ksw2_extz2_sse.o meta_util.o meta_util_debug.o Overlaps_hamt.o sptree.o data.o tsne.o t-sne.o main.o -o hifiasm_meta -lz -lpthread -lm +# Last 100 lines of the build log. diff --git a/recipes/hifiasm_meta/meta.yaml b/recipes/hifiasm_meta/meta.yaml index 9fa17cc01bedc..4f6931cbbfed6 100644 --- a/recipes/hifiasm_meta/meta.yaml +++ b/recipes/hifiasm_meta/meta.yaml @@ -11,7 +11,7 @@ source: - hifiasm_meta-aarch64.patch # [arm64 or aarch64] build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('hifiasm_meta', max_pin="x") }} diff --git a/recipes/hilive2/meta.yaml b/recipes/hilive2/meta.yaml index 2b9c16bcbb58e..7e36f8de4636f 100644 --- a/recipes/hilive2/meta.yaml +++ b/recipes/hilive2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 75532847abedc9041b8710490088a64c2c200fc0652368fb0ac75477ad62bd39 build: - number: 3 + number: 4 skip: True # [osx] requirements: diff --git a/recipes/hisat2/meta.yaml b/recipes/hisat2/meta.yaml index 3b3470ec1fb3d..2cb8a9cac0130 100644 --- a/recipes/hisat2/meta.yaml +++ b/recipes/hisat2/meta.yaml @@ -12,7 +12,7 @@ source: - simde-mr-c.patch build: - number: 7 + number: 8 run_exports: '{{ pin_subpackage(name, max_pin="x") }}' requirements: diff --git a/recipes/hits/meta.yaml b/recipes/hits/meta.yaml index 76845592b805c..09029809f5713 100644 --- a/recipes/hits/meta.yaml +++ b/recipes/hits/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir --use-pep517 run_exports: - {{ pin_subpackage('hits', max_pin="x.x") }} @@ -23,6 +23,7 @@ requirements: - python - cython - pip + - setuptools run: - python - biopython >=1.72 diff --git a/recipes/hla-la/meta.yaml b/recipes/hla-la/meta.yaml index 0297019c8486e..57b4c9b579270 100644 --- a/recipes/hla-la/meta.yaml +++ b/recipes/hla-la/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: true # [osx] run_exports: - {{ pin_subpackage('hla-la', max_pin="x") }} diff --git a/recipes/hmmcopy/meta.yaml b/recipes/hmmcopy/meta.yaml index bf1639367da71..5f9116d03f012 100644 --- a/recipes/hmmcopy/meta.yaml +++ b/recipes/hmmcopy/meta.yaml @@ -7,7 +7,7 @@ source: md5: 205a719e7ac9b9f9ba811cdd7cbdae0a build: - number: 10 + number: 11 run_exports: - {{ pin_subpackage("hmmcopy", max_pin="x.x") }} @@ -36,4 +36,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/hmmer/2.3.2/meta.yaml b/recipes/hmmer/2.3.2/meta.yaml index 37e459353220a..82ef6cf2da481 100644 --- a/recipes/hmmer/2.3.2/meta.yaml +++ b/recipes/hmmer/2.3.2/meta.yaml @@ -7,7 +7,7 @@ source: sha256: d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4 build: - number: 8 + number: 9 requirements: build: diff --git a/recipes/hmmer/3.0/meta.yaml b/recipes/hmmer/3.0/meta.yaml index 83ecd86aa6d15..5acb919470b2e 100644 --- a/recipes/hmmer/3.0/meta.yaml +++ b/recipes/hmmer/3.0/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 6977e6473fcb554b1d5a86dc9edffffa53918c1bd88d7fd20d7499f1ba719e83 build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/hmmer/meta.yaml b/recipes/hmmer/meta.yaml index fdd92c051b30e..954c8073d5999 100644 --- a/recipes/hmmer/meta.yaml +++ b/recipes/hmmer/meta.yaml @@ -7,7 +7,7 @@ source: sha256: ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3 build: - number: 2 + number: 3 run_exports: # commands/options have been removed or replaced between minor versions - {{ pin_subpackage('hmmer', max_pin="x.x") }} diff --git a/recipes/hmmer2/meta.yaml b/recipes/hmmer2/meta.yaml index 449494a380c66..b2748e318c683 100644 --- a/recipes/hmmer2/meta.yaml +++ b/recipes/hmmer2/meta.yaml @@ -9,7 +9,7 @@ source: - Makefile.in.patch build: - number: 9 + number: 10 requirements: build: diff --git a/recipes/hmnillumina/meta.yaml b/recipes/hmnillumina/meta.yaml index 76d81a34a9fdf..7c83a2015c2f8 100644 --- a/recipes/hmnillumina/meta.yaml +++ b/recipes/hmnillumina/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 4ef0913c0f2fe681f2a42102649263c6516dff980dcda6b0af7eee898c49b1ab build: - number: 0 + number: 1 skip: true # [osx] run_exports: - {{ pin_subpackage('hmnillumina', max_pin="x") }} diff --git a/recipes/hmnrandomread/meta.yaml b/recipes/hmnrandomread/meta.yaml index f572333f454e0..19165efb89677 100644 --- a/recipes/hmnrandomread/meta.yaml +++ b/recipes/hmnrandomread/meta.yaml @@ -10,7 +10,7 @@ source: sha256: dc589ef91be1a4c5694aad3e34a4cd0b1818c131b03153e76634f01ed0719854 build: - number: 3 + number: 4 skip: true [osx] requirements: diff --git a/recipes/howdesbt/meta.yaml b/recipes/howdesbt/meta.yaml index c540da7a790e0..ae49fb3901f1b 100644 --- a/recipes/howdesbt/meta.yaml +++ b/recipes/howdesbt/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('howdesbt', max_pin="x") }} diff --git a/recipes/hr2/meta.yaml b/recipes/hr2/meta.yaml index a07ea0fede657..1faa5d88f35b1 100644 --- a/recipes/hr2/meta.yaml +++ b/recipes/hr2/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 0383b88528e49d78113f777d8ac2b82fdc362b58eb6af09912e9e973e020d335 build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/hs-blastn/meta.yaml b/recipes/hs-blastn/meta.yaml index 148670ac80ead..80dc837d36bda 100644 --- a/recipes/hs-blastn/meta.yaml +++ b/recipes/hs-blastn/meta.yaml @@ -13,7 +13,7 @@ source: - 0001-Makefile-append-LDFLAGS.patch build: - number: 5 + number: 6 skip: True # [osx] requirements: diff --git a/recipes/htsbox/meta.yaml b/recipes/htsbox/meta.yaml index 7b1af21cb9476..52828ecc827ac 100644 --- a/recipes/htsbox/meta.yaml +++ b/recipes/htsbox/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage(name, max_pin=None) }} diff --git a/recipes/htsbox/r315/meta.yaml b/recipes/htsbox/r315/meta.yaml index 9052101486f46..4538c72e3a776 100644 --- a/recipes/htsbox/r315/meta.yaml +++ b/recipes/htsbox/r315/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://github.com/lh3/htsbox/archive/570b87feca94bf12ad2be4165aa11c7f0b1bdc96.tar.gz diff --git a/recipes/htseq/meta.yaml b/recipes/htseq/meta.yaml index bd437d80226bc..bda8243e841f9 100644 --- a/recipes/htseq/meta.yaml +++ b/recipes/htseq/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation run_exports: - {{ pin_subpackage('htseq', max_pin="x") }} diff --git a/recipes/htslib/1.1/meta.yaml b/recipes/htslib/1.1/meta.yaml index 445cb04e67b4c..2bb3829529b0f 100644 --- a/recipes/htslib/1.1/meta.yaml +++ b/recipes/htslib/1.1/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.1" build: - number: 5 + number: 6 source: url: https://github.com/samtools/htslib/archive/1.1.tar.gz diff --git a/recipes/htslib/1.3.1/meta.yaml b/recipes/htslib/1.3.1/meta.yaml index 095ed52f6589c..11fdfcad6a2ed 100644 --- a/recipes/htslib/1.3.1/meta.yaml +++ b/recipes/htslib/1.3.1/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.3.1" build: - number: 7 + number: 8 source: url: https://github.com/samtools/htslib/releases/download/1.3.1/htslib-1.3.1.tar.bz2 diff --git a/recipes/htslib/meta.yaml b/recipes/htslib/meta.yaml index cde0c1dcfbca3..9f9eb842a6d64 100644 --- a/recipes/htslib/meta.yaml +++ b/recipes/htslib/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('htslib', max_pin='x.x') }} diff --git a/recipes/htstream/build_failure.osx-64.yaml b/recipes/htstream/build_failure.osx-64.yaml index 400c56a63f8c5..f75189fd273d7 100644 --- a/recipes/htstream/build_failure.osx-64.yaml +++ b/recipes/htstream/build_failure.osx-64.yaml @@ -1,22 +1,21 @@ -recipe_sha: f63c85f1a92190b28ae8a18c503b9179d490949acf6beb8b780ba20b5b2ae2c6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: d1fad5d587980c8952aeda20d2a3143dcca547e80c2887e26f67e0e76e980087 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: compiler error log: |- + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/htstream-1.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/htstream_1718123498186/work/conda_build.sh']' returned non-zero exit status 2. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/htstream-1.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool @@ -25,7 +24,7 @@ log: |- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -34,7 +33,7 @@ log: |- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -52,8 +51,8 @@ log: |- CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/htstream-1.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/htstream-1.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - -- The C compiler identification is Clang 16.0.6 - -- The CXX compiler identification is Clang 16.0.6 + -- The C compiler identification is Clang 18.1.8 + -- The CXX compiler identification is Clang 18.1.8 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped @@ -70,16 +69,16 @@ log: |- -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Found Boost: $PREFIX/lib/cmake/Boost-1.85.0/BoostConfig.cmake (found suitable version "1.85.0", minimum required is "1.56") found components: system program_options iostreams filesystem - -- Configuring done (6.7s) - -- Generating done (0.2s) + -- Configuring done (3.4s) + -- Generating done (0.3s) -- Build files have been written to: $SRC_DIR/build [ 1%] Creating directories for 'googletest' [ 2%] No download step for 'googletest' [ 4%] No update step for 'googletest' [ 5%] No patch step for 'googletest' [ 7%] Performing configure step for 'googletest' - -- The C compiler identification is Clang 16.0.6 - -- The CXX compiler identification is Clang 16.0.6 + -- The C compiler identification is Clang 18.1.8 + -- The CXX compiler identification is Clang 18.1.8 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped @@ -90,11 +89,11 @@ log: |- -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done - -- Found PythonInterp: $PREFIX/bin/python (found version "3.12.3") + -- Found PythonInterp: $PREFIX/bin/python (found version "3.12.8") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE - -- Configuring done (2.0s) + -- Configuring done (2.4s) -- Generating done (0.0s) -- Build files have been written to: $SRC_DIR/build/src/googletest-build [ 8%] Performing build step for 'googletest' @@ -103,3 +102,5 @@ log: |- [ 25%] Built target gtest [ 37%] Building CXX object googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o # Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/htstream/meta.yaml b/recipes/htstream/meta.yaml index 5e55ca6df3bf3..274e1925c2620 100644 --- a/recipes/htstream/meta.yaml +++ b/recipes/htstream/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/humid/build_failure.osx-64.yaml b/recipes/humid/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..acc0e78b1548d --- /dev/null +++ b/recipes/humid/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 40322577f3d72d2ea2a4223d36b360baabd9cf4701086a07d0a19bb8b53953ce # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - make 4.4.1 h00291cd_2 + - ncurses 6.5 hf036a51_1 + - clangxx_impl_osx-64 18.1.8 h4b7810f_23 + - clang-18 18.1.8 default_h0c94c6a_5 + - llvm-tools 18.1.8 h9ce406d_2 + Traceback (most recent call last): + - openssl 3.4.0 hd471939_0 + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + - clangxx 18.1.8 default_h179603d_5 + - libzlib 1.3.1 hd23fc13_2 + - tapi 1300.6.5 h390ca13_0 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + - cctools_osx-64 1010.6 h00edd4c_2 + - isa-l 2.31.0 hfdf4475_2 + host: + - isa-l 2.31.0 hfdf4475_2 + - libcxx 19.1.5 hf95d169_0 + - libdeflate 1.22 h00291cd_0 + run: + - libcxx >=18 + - libdeflate >=1.22,<1.23.0a0 + - isa-l >=2.31.0,<3.0a0 + test: + commands: + - humid > /dev/null + about: + api.build( + doc_url: https://humid.readthedocs.io/en/latest/usage.html + home: https://github.com/jfjlaros/HUMID + license: MIT + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + license_family: MIT + summary: HUMID -- High-performance UMI Deduplicator + extra: + copy_test_source_files: true + final: true + + + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/humid_1733862159785/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/humid_1733862159785/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/humid_1733862159785/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/humid_1733862159785/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/humid-1.0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/humid_1733862159785/work/conda_build.sh']' returned non-zero exit status 2. + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/humid-1.0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/humid-1.0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/humid-1.0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + x86_64-apple-darwin13.4.0-clang -O2 -std=c20 -fcoroutines-ts -D_LIBCPP_DISABLE_AVAILABILITY -o cluster.o -c cluster.cc +# Last 100 lines of the build log. diff --git a/recipes/humid/meta.yaml b/recipes/humid/meta.yaml index 4bb2f60c72a36..78b364d668916 100644 --- a/recipes/humid/meta.yaml +++ b/recipes/humid/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 5da8a2a95514304b7a32a6525bb6047bae16b96e56a9737a57a745470eac7733 build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('humid', max_pin="x") }} diff --git a/recipes/hydra-multi/meta.yaml b/recipes/hydra-multi/meta.yaml index 566b081cedf76..cfb9be15b604b 100644 --- a/recipes/hydra-multi/meta.yaml +++ b/recipes/hydra-multi/meta.yaml @@ -7,7 +7,7 @@ source: sha256: b3d1daea4441091c07b3a7ba419e858b44d7328058a8cd5b297f43a2dc5c9983 build: - number: 3 + number: 4 skip: True # [osx] requirements: diff --git a/recipes/hyphy/meta.yaml b/recipes/hyphy/meta.yaml index 987e35cdb82ae..1c5bcbfbbdda4 100644 --- a/recipes/hyphy/meta.yaml +++ b/recipes/hyphy/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("hyphy", max_pin="x.x") }} requirements: diff --git a/recipes/ibdmix/build_failure.linux-64.yaml b/recipes/ibdmix/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..ae90a3ff4f9f7 --- /dev/null +++ b/recipes/ibdmix/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 816348a3347729e9659a42f9711ab9f297562f7e2230bf0df3da66b0320004ef # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ibdmix-1.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ibdmix-1.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ibdmix-1.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ibdmix-1.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + -- The CXX compiler identification is GNU 13.3.0 + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- No build type selected, default to Release + CMake Deprecation Warning at build_conda/_deps/cli11-src/CMakeLists.txt:1 (cmake_minimum_required): + Compatibility with CMake < 3.10 will be removed from a future version of + CMake. + + Update the VERSION argument value. Or, use the ... syntax + to tell CMake that the project requires at least but has been updated + to work with policies introduced by or earlier. + + + -- Configuring done (1.4s) + -- Generating done (0.0s) + -- Build files have been written to: $SRC_DIR/ibdmix/build_conda + [ 4%] Building CXX object src/CMakeFiles/vcf_file.dir/vcf_file.cc.o + In file included from /opt/conda/conda-bld/ibdmix_1734019496379/work/ibdmix/src/vcf_file.cc:1: + /opt/conda/conda-bld/ibdmix_1734019496379/work/ibdmix/src/../include/IBDmix/vcf_file.h:17:3: error: 'uint64_t' does not name a type + 17 | uint64_t getPosition() const { return position; } + | ^~~~~~~~ + /opt/conda/conda-bld/ibdmix_1734019496379/work/ibdmix/src/../include/IBDmix/vcf_file.h:5:1: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + 4 | #include + |#include + 5 | #include + /opt/conda/conda-bld/ibdmix_1734019496379/work/ibdmix/src/../include/IBDmix/vcf_file.h:32:3: error: 'uint64_t' does not name a type + 32 | uint64_t position; + | ^~~~~~~~ + /opt/conda/conda-bld/ibdmix_1734019496379/work/ibdmix/src/../include/IBDmix/vcf_file.h:32:3: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/ibdmix_1734019496379/work/ibdmix/src/vcf_file.cc: In member function 'bool VCF_File::read_line(bool)': + /opt/conda/conda-bld/ibdmix_1734019496379/work/ibdmix/src/vcf_file.cc:74:37: error: 'position' was not declared in this scope + 74 | if (!(iss >> chromosome && iss >> position)) return false; + | ^~~~~~~~ + make[2]: *** [src/CMakeFiles/vcf_file.dir/build.make:79: src/CMakeFiles/vcf_file.dir/vcf_file.cc.o] Error 1 + make[1]: *** [CMakeFiles/Makefile2:162: src/CMakeFiles/vcf_file.dir/all] Error 2 + make: *** [Makefile:156: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ibdmix_1734019496379/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ibdmix_1734019496379/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/ibdmix/meta.yaml b/recipes/ibdmix/meta.yaml index c6ee9e4728eb3..24f33d107bb3e 100755 --- a/recipes/ibdmix/meta.yaml +++ b/recipes/ibdmix/meta.yaml @@ -11,7 +11,7 @@ source: sha256: ee827a869aa39be4a85baaa748bf950a972ddd903f72b1f22ffb91d8de87a0db build: - number: 2 + number: 3 binary_relocation: true requirements: diff --git a/recipes/ibridges/meta.yml b/recipes/ibridges/meta.yaml similarity index 94% rename from recipes/ibridges/meta.yml rename to recipes/ibridges/meta.yaml index 29df90eb9b8ee..2343f5a0b6540 100644 --- a/recipes/ibridges/meta.yml +++ b/recipes/ibridges/meta.yaml @@ -9,12 +9,13 @@ source: url: https://files.pythonhosted.org/packages/0e/09/dccdec5b2a6a02715d134d623b57a0e41b9459b7e1176452ce857ee6c665/ibridges-1.2.0.tar.gz sha256: ca068d37f147d8ce30a6b676cd6ae3e9c19f7af248bf7af1ef09c582b9d2f9b6 build: - skip: true # [py<38] entry_points: - ibridges = ibridges.__main__:main script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation number: 0 noarch: python + run_exports: + - {{ pin_subpackage('ibridges', max_pin="x") }} requirements: host: diff --git a/recipes/idba/meta.yaml b/recipes/idba/meta.yaml index 86b72dce3069a..5697c3a844ed9 100644 --- a/recipes/idba/meta.yaml +++ b/recipes/idba/meta.yaml @@ -7,7 +7,7 @@ about: summary: 'IDBA is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinformatics.' build: - number: 3 + number: 4 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin='x') }} diff --git a/recipes/idba_subasm/meta.yaml b/recipes/idba_subasm/meta.yaml index a671524be98ff..9d488b1dfe4b3 100644 --- a/recipes/idba_subasm/meta.yaml +++ b/recipes/idba_subasm/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 421d097aaafd27e7b0c8b7bd5ae51b17e2f2a899dfd27fa1e9f5df909168f57e build: - number: 8 + number: 9 skip: True # [osx] requirements: diff --git a/recipes/ideas/1.20/meta.yaml b/recipes/ideas/1.20/meta.yaml index 6274773918f7b..b34d09ba57ce8 100644 --- a/recipes/ideas/1.20/meta.yaml +++ b/recipes/ideas/1.20/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.20" build: - number: 6 + number: 7 skip: True # [osx] source: diff --git a/recipes/idemuxcpp/meta.yaml b/recipes/idemuxcpp/meta.yaml index 683204c9c9c9f..4e5b245eaffa1 100644 --- a/recipes/idemuxcpp/meta.yaml +++ b/recipes/idemuxcpp/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('idemuxcpp', max_pin="x") }} diff --git a/recipes/igphyml/meta.yaml b/recipes/igphyml/meta.yaml index 23c2caae173b0..9feaa44acc52c 100644 --- a/recipes/igphyml/meta.yaml +++ b/recipes/igphyml/meta.yaml @@ -9,7 +9,7 @@ source: url: "https://bitbucket.org/kleinstein/{{ name }}/get/{{ version }}.tar.gz" sha256: 0182d2a46a1449bedd374c8db6659e796aa7297d6821090727c2ffad13f34a26 build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/illumina-interop/meta.yaml b/recipes/illumina-interop/meta.yaml index e2c169cf97e98..38ceb5def6f68 100644 --- a/recipes/illumina-interop/meta.yaml +++ b/recipes/illumina-interop/meta.yaml @@ -6,7 +6,7 @@ package: version: '{{version}}' build: - number: 0 + number: 1 skip: true # [osx] run_exports: - {{ pin_subpackage('illumina-interop', max_pin="x.x") }} diff --git a/recipes/ima3/build_failure.osx-64.yaml b/recipes/ima3/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..7c96e37ed943a --- /dev/null +++ b/recipes/ima3/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 3866b2dfee156c44cb2e2f9abaa068b8c3d775596fded432e537eb641485cb81 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - compiler-rt 18.1.8 h1020d70_1 + host: + - ca-certificates 2024.8.30 h8857fd0_0 + - libcxx 19.1.5 hf95d169_0 + - libfabric 1.22.0 h6e16a3a_2 + - libiconv 1.17 hd75f5a5_2 + - liblzma 5.6.3 hd471939_1 + - libzlib 1.3.1 hd23fc13_2 + - llvm-openmp 19.1.5 ha54dae1_0 + - mpi 1.0 openmpi + - libgfortran5 13.2.0 h2873a65_3 + - libxml2 2.13.5 he8ee3e7_1 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + - openssl 3.4.0 hd471939_0 + - libevent 2.1.12 ha90c15b_1 + - libgfortran 5.0.0 13_2_0_h97931a8_3 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + - libhwloc 2.11.2 default_h4cdd727_1001 + - openmpi 5.0.6 h9f30aec_100 + run: + - openmpi >=1.8 + - openmpi >=5.0.6,<6.0a0 + - libcxx >=18 + test: + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/ima3_1733860574368/work/conda_build.sh']' returned non-zero exit status 2. + commands: + - 'mpirun -mca plm_rsh_agent true --allow-run-as-root IMa3 -h | grep ''IMa3 Release + Version: ''' + about: + home: https://github.com/jodyhey/IMa3 + license: GPL (>= 3) + license_file: LICENSE + summary: IMa3 can be used to solve a fundamental problem in evolutionary genetics, + which is to jointly consider phylogenetic history and pouplation genetic history, + including gene exchange. IMa3 can be used to estimate the rooted phylogenetic + tree for multiple populations, and does so while integrating over all possible + Isolation-with-Migration models + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/ima3_1733860574368/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/ima3_1733860574368/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/ima3_1733860574368/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/ima3_1733860574368/work + setting openmpi environment variables for conda-build + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ima3-1.13 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ima3-1.13 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ima3-1.13 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ima3-1.13 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + mpicxx alltreestrings.cpp autoc.cpp build_gtree.cpp build_poptree.cpp burnphylogenycounts.cpp calc_prob_data.cpp chainprint.cpp freemem.cpp gewekeIM.cpp ginfo.cpp gtint.cpp histograms.cpp ima_main.cpp initialize.cpp jointfind.cpp marglike.cpp mcmcfile.cpp msdirent.cpp multi_t_bins.cpp output.cpp popmig.cpp readata.cpp readpriorfile.cpp surface_call_functions.cpp surface_search_functions.cpp swapchains.cpp treeprint.cpp update_gtree.cpp update_gtree_common.cpp update_hg.cpp update_mc_params.cpp update_poptree.cpp update_priors.cpp update_t_NW.cpp update_t_RY.cpp update_t_RYhg.cpp utilities.cpp -D MPI_ENABLED -D NDEBUG -o IMa3 -O3 -fpermissive +# Last 100 lines of the build log. diff --git a/recipes/ima3/meta.yaml b/recipes/ima3/meta.yaml index 2726a93e83f8d..fbcaa10c8fcbe 100644 --- a/recipes/ima3/meta.yaml +++ b/recipes/ima3/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/imseq/meta.yaml b/recipes/imseq/meta.yaml index 22f1437c161ca..2b6346712bc9c 100644 --- a/recipes/imseq/meta.yaml +++ b/recipes/imseq/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 7 + number: 8 skip: True # [osx] source: diff --git a/recipes/infernal/meta.yaml b/recipes/infernal/meta.yaml index 78a8740143bd8..1bf637724ccf5 100644 --- a/recipes/infernal/meta.yaml +++ b/recipes/infernal/meta.yaml @@ -10,7 +10,7 @@ source: sha256: ad4ddae02f924ca7c85bc8c4a79c9f875af8df96aeb726702fa985cbe752497f build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/inforna/build_failure.linux-64.yaml b/recipes/inforna/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..f4b6f32c34586 --- /dev/null +++ b/recipes/inforna/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 2996f6a3f21040e3e0a937cdd04df560065d7616fde1521c5d27d19d5ba85584 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -O4 -Wall -g -fopenmp -I$PREFIX/include/ViennaRNA -I$PREFIX/include -o inv_folding_const.o inv_folding_const.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -O4 -Wall -g -fopenmp -I$PREFIX/include/ViennaRNA -I$PREFIX/include -o INFO-RNA-2.1.2 basics.o constraints.o struct.o inverse.o energy.o hairpin_energy.o interior_energy.o bulge_energy.o stacking_energy.o multi_energy.o end_energy.o search.o inv_folding_const.o -L$PREFIX/lib -lRNA + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/conda/conda-bld/inforna_1734238157737/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/libRNA.a(boltzmann_sampling.o): in function create_tllr_node': + boltzmann_sampling.c:(.text.create_tllr_node0x82): undefined reference to mpfr_init2' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.create_tllr_node0x88): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.create_tllr_node0x9b): undefined reference to mpfr_set_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.create_tllr_node0xa9): undefined reference to mpfr_init2' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.create_tllr_node0xaf): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.create_tllr_node0xbf): undefined reference to mpfr_set_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/conda/conda-bld/inforna_1734238157737/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/libRNA.a(boltzmann_sampling.o): in function get_weight_type_spec': + boltzmann_sampling.c:(.text.get_weight_type_spec0x2c): undefined reference to mpfr_init2' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.get_weight_type_spec0x32): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.get_weight_type_spec0x41): undefined reference to mpfr_set_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.get_weight_type_spec0x5f): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.get_weight_type_spec0x71): undefined reference to mpfr_add' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.get_weight_type_spec0x82): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.get_weight_type_spec0x8d): undefined reference to mpfr_get_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.get_weight_type_spec0x9c): undefined reference to mpfr_clear' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/conda/conda-bld/inforna_1734238157737/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/libRNA.a(boltzmann_sampling.o): in function update_weight_ll': + boltzmann_sampling.c:(.text.update_weight_ll0x33): undefined reference to mpfr_init2' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.update_weight_ll0x39): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.update_weight_ll0x4c): undefined reference to mpfr_add_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.update_weight_ll0x52): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.update_weight_ll0x64): undefined reference to mpfr_sub' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.update_weight_ll0x75): undefined reference to mpfr_cmp_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.update_weight_ll0x82): undefined reference to mpfr_clear' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.update_weight_ll0x88): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.update_weight_ll0x9b): undefined reference to mpfr_add_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.update_weight_ll0xc2): undefined reference to mpfr_clear' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/conda/conda-bld/inforna_1734238157737/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/libRNA.a(boltzmann_sampling.o): in function backtrack.isra.0': + boltzmann_sampling.c:(.text.backtrack.isra.00x275): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack.isra.00x281): undefined reference to mpfr_get_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack.isra.00xa4a): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack.isra.00xa5e): undefined reference to mpfr_get_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack.isra.00xff2): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack.isra.00x1006): undefined reference to mpfr_get_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack.isra.00x11ba): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack.isra.00x11ce): undefined reference to mpfr_get_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/conda/conda-bld/inforna_1734238157737/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/libRNA.a(boltzmann_sampling.o): in function wrap_pbacktrack': + boltzmann_sampling.c:(.text.wrap_pbacktrack0x414): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.wrap_pbacktrack0x420): undefined reference to mpfr_get_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.wrap_pbacktrack0x44c): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.wrap_pbacktrack0x458): undefined reference to mpfr_get_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.wrap_pbacktrack0xa24): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.wrap_pbacktrack0xa31): undefined reference to mpfr_get_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.wrap_pbacktrack0xbb8): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.wrap_pbacktrack0xbcc): undefined reference to mpfr_get_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/conda/conda-bld/inforna_1734238157737/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/libRNA.a(boltzmann_sampling.o): in function backtrack_qm.isra.0': + boltzmann_sampling.c:(.text.backtrack_qm.isra.00x295): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack_qm.isra.00x2a6): undefined reference to mpfr_get_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack_qm.isra.00x2e3): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack_qm.isra.00x2f4): undefined reference to mpfr_get_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack_qm.isra.00x862): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack_qm.isra.00x86e): undefined reference to mpfr_get_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack_qm.isra.00xc50): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack_qm.isra.00xc61): undefined reference to mpfr_get_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack_qm.isra.00xc9d): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack_qm.isra.00xcae): undefined reference to mpfr_get_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack_qm.isra.00xd36): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack_qm.isra.00xd42): undefined reference to mpfr_get_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/conda/conda-bld/inforna_1734238157737/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/libRNA.a(boltzmann_sampling.o): in function backtrack_qm2.isra.0': + boltzmann_sampling.c:(.text.backtrack_qm2.isra.00x272): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack_qm2.isra.00x282): undefined reference to mpfr_get_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack_qm2.isra.00x2bd): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack_qm2.isra.00x2ce): undefined reference to mpfr_get_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack_qm2.isra.00x6e2): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack_qm2.isra.00x6ee): undefined reference to mpfr_get_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack_qm2.isra.00x99e): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.backtrack_qm2.isra.00x9af): undefined reference to mpfr_get_d' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/conda/conda-bld/inforna_1734238157737/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/libRNA.a(boltzmann_sampling.o): in function vrna_pbacktrack_mem_free': + boltzmann_sampling.c:(.text.vrna_pbacktrack_mem_free0x4c): undefined reference to mpfr_clear' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.vrna_pbacktrack_mem_free0x5a): undefined reference to mpfr_clear' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/conda/conda-bld/inforna_1734238157737/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/libRNA.a(boltzmann_sampling.o): in function vrna_pbacktrack_sub_resume_cb': + boltzmann_sampling.c:(.text.vrna_pbacktrack_sub_resume_cb0x389): undefined reference to mpfr_get_default_rounding_mode' + /opt/conda/conda-bld/inforna_1734238157737/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: boltzmann_sampling.c:(.text.vrna_pbacktrack_sub_resume_cb0x395): undefined reference to mpfr_get_d' + collect2: error: ld returned 1 exit status + make: *** [Makefile:56: INFO-RNA-2.1.2] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/inforna_1734238157737/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/inforna_1734238157737/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/inforna/meta.yaml b/recipes/inforna/meta.yaml index 02a22c6e599b8..d68c1cf4ec397 100644 --- a/recipes/inforna/meta.yaml +++ b/recipes/inforna/meta.yaml @@ -3,7 +3,7 @@ package: version: "2.1.2" build: - number: 6 + number: 7 skip: True # [osx] source: diff --git a/recipes/inmoose/meta.yaml b/recipes/inmoose/meta.yaml index 241dd6ba98d54..abe60d6b4fa74 100644 --- a/recipes/inmoose/meta.yaml +++ b/recipes/inmoose/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [py < 39] run_exports: - {{ pin_subpackage('inmoose', max_pin="x.x") }} diff --git a/recipes/insurveyor/meta.yaml b/recipes/insurveyor/meta.yaml index 8db223d4c12d2..a22ca5c0a1114 100644 --- a/recipes/insurveyor/meta.yaml +++ b/recipes/insurveyor/meta.yaml @@ -12,7 +12,7 @@ source: - INSurVeyor-aarch64.patch # [aarch64 or arm64] build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('insurveyor', max_pin="x") }} diff --git a/recipes/intarna/2.x/build_failure.osx-64.yaml b/recipes/intarna/2.x/build_failure.osx-64.yaml index ba967a602efa2..a2097eb699a36 100644 --- a/recipes/intarna/2.x/build_failure.osx-64.yaml +++ b/recipes/intarna/2.x/build_failure.osx-64.yaml @@ -1,39 +1,106 @@ -recipe_sha: 648983cbd9e4c8e3449ae40f49260473c3a4388187e3f657f43f8d4a76beb773 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 3725cddaa873f43be6f0d120fdc71871bdb13d2f4418ecc442caf7f183a88643 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: compiler error log: |2- - 16:34:09 BIOCONDA INFO (ERR) In file included from runTests.cpp:12: - 16:34:09 BIOCONDA INFO (ERR) In file included from ../src/easylogging++.h:385: - 16:34:09 BIOCONDA INFO (ERR) In file included from /opt/mambaforge/envs/bioconda/conda-bld/intarna_1718123285885/_build_env/bin/../include/c++/v1/string:622: - 16:34:09 BIOCONDA INFO (ERR) In file included from /opt/mambaforge/envs/bioconda/conda-bld/intarna_1718123285885/_build_env/bin/../include/c++/v1/string_view:1059: - 16:34:09 BIOCONDA INFO (ERR) In file included from /opt/mambaforge/envs/bioconda/conda-bld/intarna_1718123285885/_build_env/bin/../include/c++/v1/algorithm:1893: - 16:34:09 BIOCONDA INFO (ERR) In file included from /opt/mambaforge/envs/bioconda/conda-bld/intarna_1718123285885/_build_env/bin/../include/c++/v1/__algorithm/ranges_sample.h:13: - 16:34:09 BIOCONDA INFO (ERR) In file included from /opt/mambaforge/envs/bioconda/conda-bld/intarna_1718123285885/_build_env/bin/../include/c++/v1/__algorithm/sample.h:18: - 16:34:09 BIOCONDA INFO (ERR) /opt/mambaforge/envs/bioconda/conda-bld/intarna_1718123285885/_build_env/bin/../include/c++/v1/__random/uniform_int_distribution.h:237:5: error: static assertion failed due to requirement '__libcpp_random_is_valid_urng::value': - 16:34:09 BIOCONDA INFO (ERR) static_assert(__libcpp_random_is_valid_urng<_URNG>::value, ""); - 16:34:09 BIOCONDA INFO (ERR) ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 16:34:09 BIOCONDA INFO (ERR) /opt/mambaforge/envs/bioconda/conda-bld/intarna_1718123285885/_build_env/bin/../include/c++/v1/__algorithm/shuffle.h:154:35: note: in instantiation of function template specialization 'std::uniform_int_distribution::operator()' requested here - 16:34:09 BIOCONDA INFO (ERR) difference_type __i = __uid(__g, _Pp(0, __d)); - 16:34:09 BIOCONDA INFO (ERR) ^ - 16:34:09 BIOCONDA INFO (ERR) /opt/mambaforge/envs/bioconda/conda-bld/intarna_1718123285885/_build_env/bin/../include/c++/v1/__algorithm/shuffle.h:166:14: note: in instantiation of function template specialization 'std::__shuffle, std::__wrap_iter, Catch::RandomNumberGenerator &>' requested here - 16:34:09 BIOCONDA INFO (ERR) (void)std::__shuffle<_ClassicAlgPolicy>( - 16:34:09 BIOCONDA INFO (ERR) ^ - 16:34:09 BIOCONDA INFO (ERR) ./catch.hpp:6477:18: note: in instantiation of function template specialization 'std::shuffle, Catch::RandomNumberGenerator &>' requested here - 16:34:09 BIOCONDA INFO (ERR) std::shuffle( vector.begin(), vector.end(), rng ); - 16:34:09 BIOCONDA INFO (ERR) ^ - 16:34:09 BIOCONDA INFO (ERR) ./catch.hpp:6495:44: note: in instantiation of function template specialization 'Catch::RandomNumberGenerator::shuffle>' requested here - 16:34:09 BIOCONDA INFO (ERR) RandomNumberGenerator::shuffle( sorted ); - 16:34:09 BIOCONDA INFO (ERR) ^ - 16:34:09 BIOCONDA INFO (ERR) 1 error generated. - 16:34:09 BIOCONDA INFO (ERR) make[2]: *** [Makefile:930: runApiTests-runTests.o] Error 1 - 16:34:09 BIOCONDA INFO (ERR) make[1]: *** [Makefile:1119: check-am] Error 2 - 16:34:09 BIOCONDA INFO (ERR) make: *** [Makefile:878: tests] Error 2 - 16:34:10 BIOCONDA INFO (OUT) Extracting download - 16:34:10 BIOCONDA INFO (ERR) Traceback (most recent call last): - 16:34:10 BIOCONDA INFO (OUT) source tree in: /opt/mambaforge/envs/bioconda/conda-bld/intarna_1718123285885/work - 16:34:10 BIOCONDA INFO (OUT) export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/intarna_1718123285885/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh - 16:34:10 BIOCONDA INFO (OUT) export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/intarna_1718123285885/_build_env - 16:34:10 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - 16:34:10 BIOCONDA INFO (ERR) sys.exit(execute()) - 16:34:10 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - 16:34:10 BIOCONDA INFO (ERR) api.build( \ No newline at end of file + CXX PredictorMfe4dSeed.o + CXX ReverseAccessibility.o + CXX RnaSequence.o + CXX SeedConstraint.o + CXX SeedHandlerExplicit.o + CXX SeedHandlerMfe.o + CXX SeedHandlerNoBulge.o + CXX VrnaHandler.o + AR libIntaRNA.a + make[3]: Leaving directory '$SRC_DIR/src/IntaRNA' + Making all in bin + make[3]: Entering directory '$SRC_DIR/src/bin' + CXX IntaRNA.o + CXX CommandLineParsing.o + CXXLD IntaRNA + make[3]: Leaving directory '$SRC_DIR/src/bin' + make[2]: Leaving directory '$SRC_DIR/src' + make[1]: Leaving directory '$SRC_DIR/src' + Making all in perl + make[1]: Entering directory '$SRC_DIR/perl' + make[1]: Nothing to be done for 'all'. + make[1]: Leaving directory '$SRC_DIR/perl' + Making all in tests + make[1]: Entering directory '$SRC_DIR/tests' + make[1]: Nothing to be done for 'all'. + make[1]: Leaving directory '$SRC_DIR/tests' + Making all in doc + make[1]: Entering directory '$SRC_DIR/doc' + make[1]: Nothing to be done for 'all'. + make[1]: Leaving directory '$SRC_DIR/doc' + Making all in . + make[1]: Entering directory '$SRC_DIR' + make[1]: Nothing to be done for 'all-am'. + make[1]: Leaving directory '$SRC_DIR' + Making all in src + make[1]: Entering directory '$SRC_DIR/src' + make all-recursive + make[2]: Entering directory '$SRC_DIR/src' + Making all in . + make[3]: Entering directory '$SRC_DIR/src' + make[3]: Leaving directory '$SRC_DIR/src' + Making all in IntaRNA + make[3]: Entering directory '$SRC_DIR/src/IntaRNA' + make[3]: Nothing to be done for 'all'. + make[3]: Leaving directory '$SRC_DIR/src/IntaRNA' + Making all in bin + make[3]: Entering directory '$SRC_DIR/src/bin' + make[3]: Nothing to be done for 'all'. + make[3]: Leaving directory '$SRC_DIR/src/bin' + make[2]: Leaving directory '$SRC_DIR/src' + make[1]: Leaving directory '$SRC_DIR/src' + Making all in perl + make[1]: Entering directory '$SRC_DIR/perl' + make[1]: Nothing to be done for 'all'. + make[1]: Leaving directory '$SRC_DIR/perl' + Making all in tests + make[1]: Entering directory '$SRC_DIR/tests' + make[1]: Nothing to be done for 'all'. + make[1]: Leaving directory '$SRC_DIR/tests' + Making all in doc + make[1]: Entering directory '$SRC_DIR/doc' + make[1]: Nothing to be done for 'all'. + make[1]: Leaving directory '$SRC_DIR/doc' + Making all in . + make[1]: Entering directory '$SRC_DIR' + make[1]: Nothing to be done for 'all-am'. + make[1]: Leaving directory '$SRC_DIR' + + => compiling and running tests ... will take a while ... + + CXX runApiTests-AccessibilityConstraint_test.o + CXX runApiTests-AccessibilityFromStream_test.o + CXX runApiTests-AccessibilityBasePair_test.o + CXX runApiTests-HelixConstraint_test.o + CXX runApiTests-HelixHandlerStackingOnly_test.o + CXX runApiTests-HelixHandlerStackingOnlyIdxOffset_test.o + CXX runApiTests-HelixHandlerStackingOnlySeed_test.o + CXX runApiTests-HelixHandlerStackingOnlySeedIdxOffset_test.o + CXX runApiTests-HelixHandlerUnpaired_test.o + CXX runApiTests-HelixHandlerUnpairedIdxOffset_test.o + CXX runApiTests-HelixHandlerUnpairedSeed_test.o + CXX runApiTests-HelixHandlerUnpairedSeedIdxOffset_test.o + CXX runApiTests-IndexRange_test.o + CXX runApiTests-IndexRangeList_test.o + CXX runApiTests-Interaction_test.o + CXX runApiTests-InteractionEnergyBasePair_test.o + CXX runApiTests-InteractionRange_test.o + CXX runApiTests-PredictionTrackerProfileMinE_test.o + CXX runApiTests-PredictorMfe2dHelixHeuristic_test.o + CXX runApiTests-PredictorMfe2dHelixHeuristicSeed_test.o + CXX runApiTests-PredictionTrackerSpotProb_test.o + CXX runApiTests-NussinovHandler_test.o + CXX runApiTests-RnaSequence_test.o + CXX runApiTests-OutputHandlerRangeOnly_test.o + CXX runApiTests-OutputHandlerInteractionList_test.o + CXX runApiTests-SeedHandlerExplicit_test.o + CXX runApiTests-SeedHandlerNoBulge_test.o + CXX runApiTests-SeedHandlerMfe_test.o + CXX runApiTests-SeedHandlerIdxOffset_test.o + CXX runApiTests-runTests.o +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/intarna/2.x/meta.yaml b/recipes/intarna/2.x/meta.yaml index 861d005abb03b..721855c156fa3 100644 --- a/recipes/intarna/2.x/meta.yaml +++ b/recipes/intarna/2.x/meta.yaml @@ -12,7 +12,7 @@ about: summary: Efficient RNA-RNA interaction prediction incorporating seeding and accessibility of interacting sites build: - number: 4 + number: 5 source: url: "https://github.com/BackofenLab/IntaRNA/releases/download/v{{INTARNA_VERSION}}/intaRNA-{{INTARNA_VERSION}}.tar.gz" diff --git a/recipes/intarna/meta.yaml b/recipes/intarna/meta.yaml index 534cc11818644..67f2a0a848e13 100644 --- a/recipes/intarna/meta.yaml +++ b/recipes/intarna/meta.yaml @@ -12,7 +12,7 @@ about: summary: Efficient RNA-RNA interaction prediction incorporating seeding and accessibility of interacting sites build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('intarna', max_pin="x.x") }} diff --git a/recipes/iow/meta.yaml b/recipes/iow/meta.yaml index 4fd7daed8d33f..d96308f6fce65 100644 --- a/recipes/iow/meta.yaml +++ b/recipes/iow/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 6b3ddb08f7ec1dec265de4a0f6025c7a4c81df5aa613f3ead5633073b0fe2271 build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('iow', max_pin='x') }} diff --git a/recipes/ipk/meta.yaml b/recipes/ipk/meta.yaml index 6aa9bfb9e74c2..53f9f2c19cb89 100644 --- a/recipes/ipk/meta.yaml +++ b/recipes/ipk/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('ipk', max_pin="x.x") }} diff --git a/recipes/iqtree/build_failure.osx-64.yaml b/recipes/iqtree/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..79234461d6e9d --- /dev/null +++ b/recipes/iqtree/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 44a07c848d3d71fedcd5f1170969c660b9b0a09370a15205885fb91ca70d810a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CXX=x86_64-apple-darwin13.4.0-clang + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/iqtree_1734461608179/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/iqtree-2.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/iqtree-2.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/iqtree_1734461608179/work/conda_build.sh']' returned non-zero exit status 1. + Not searching for unused variables given on the command line. + -- The C compiler identification is Clang 18.1.8 + -- The CXX compiler identification is Clang 18.1.8 + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped + -- Detecting C compile features + -- Detecting C compile features - done + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Found Boost: $PREFIX/lib/cmake/Boost-1.85.0/BoostConfig.cmake (found version "1.85.0") + -- Looking for gettimeofday + -- Looking for gettimeofday - found + -- Looking for getrusage + -- Looking for getrusage - found + -- Looking for GlobalMemoryStatusEx + -- Looking for GlobalMemoryStatusEx - not found + -- Looking for strndup + -- Looking for strndup - found + -- Looking for strtok_r + -- Looking for strtok_r - found + -- Looking for unistd.h + -- Looking for unistd.h - found + -- Looking for backtrace + -- Looking for backtrace - found + -- backtrace facility detected in default set of libraries + -- Found Backtrace: /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include + -- Found ZLIB: /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/lib/libz.tbd (found version "1.2.11") + -- Looking for unistd.h + -- Looking for unistd.h - found + -- Found Python: /usr/local/Frameworks/Python.framework/Versions/3.13/bin/python3.13 (found version "3.13.1") found components: Interpreter + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success + -- Found Threads: TRUE + -- Performing Test FLAG_WEXTRA + -- Performing Test FLAG_WEXTRA - Success + -- clang-tidy not found. + -- Configuring done (8.5s) + -- Generating done (0.2s) + -- Build files have been written to: $SRC_DIR/build + Change Dir: '$SRC_DIR/build' + + Run Build Command(s): $BUILD_PREFIX/bin/ninja -v -j 2 install + [1/352] $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I$SRC_DIR -I$SRC_DIR/yaml-cpp/include -I$SRC_DIR/after -I$SRC_DIR/system -I/usr/local/include -I$SRC_DIR/build -I$SRC_DIR/build/cmaple -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/iqtree-2.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -w -pthread -O3 -ffunction-sections -fdata-sections -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -I$PREFIX/include/eigen3 -I$PREFIX/include --target=x86_64-apple-macos10.13 -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF sprng/CMakeFiles/sprng.dir/lcg64.c.o.d -o sprng/CMakeFiles/sprng.dir/lcg64.c.o -c $SRC_DIR/sprng/lcg64.c + [2/352] $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I$SRC_DIR -I$SRC_DIR/yaml-cpp/include -I$SRC_DIR/after -I$SRC_DIR/system -I/usr/local/include -I$SRC_DIR/build -I$SRC_DIR/build/cmaple -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/iqtree-2.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -w -pthread -O3 -ffunction-sections -fdata-sections -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -I$PREFIX/include/eigen3 -I$PREFIX/include --target=x86_64-apple-macos10.13 -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF sprng/CMakeFiles/sprng.dir/makeseed.c.o.d -o sprng/CMakeFiles/sprng.dir/makeseed.c.o -c $SRC_DIR/sprng/makeseed.c + [3/352] $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I$SRC_DIR -I$SRC_DIR/yaml-cpp/include -I$SRC_DIR/after -I$SRC_DIR/system -I/usr/local/include -I$SRC_DIR/build -I$SRC_DIR/build/cmaple -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/iqtree-2.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -w -pthread -O3 -ffunction-sections -fdata-sections -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -I$PREFIX/include/eigen3 -I$PREFIX/include --target=x86_64-apple-macos10.13 -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF sprng/CMakeFiles/sprng.dir/memory.c.o.d -o sprng/CMakeFiles/sprng.dir/memory.c.o -c $SRC_DIR/sprng/memory.c + [4/352] $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I$SRC_DIR -I$SRC_DIR/yaml-cpp/include -I$SRC_DIR/after -I$SRC_DIR/system -I/usr/local/include -I$SRC_DIR/build -I$SRC_DIR/build/cmaple -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/iqtree-2.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -w -pthread -O3 -ffunction-sections -fdata-sections -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -I$PREFIX/include/eigen3 -I$PREFIX/include --target=x86_64-apple-macos10.13 -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF sprng/CMakeFiles/sprng.dir/store.c.o.d -o sprng/CMakeFiles/sprng.dir/store.c.o -c $SRC_DIR/sprng/store.c + [5/352] $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I$SRC_DIR -I$SRC_DIR/yaml-cpp/include -I$SRC_DIR/after -I$SRC_DIR/system -I/usr/local/include -I$SRC_DIR/build -I$SRC_DIR/build/cmaple -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/iqtree-2.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -w -pthread -O3 -ffunction-sections -fdata-sections -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -I$PREFIX/include/eigen3 -I$PREFIX/include --target=x86_64-apple-macos10.13 -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -c $SRC_DIR/sprng/primes-lcg64.c + [6/352] $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I$SRC_DIR -I$SRC_DIR/yaml-cpp/include -I$SRC_DIR/after -I$SRC_DIR/system -I/usr/local/include -I$SRC_DIR/build -I$SRC_DIR/build/cmaple -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/iqtree-2.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -w -pthread -O3 -ffunction-sections -fdata-sections -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -I$PREFIX/include/eigen3 -I$PREFIX/include --target=x86_64-apple-macos10.13 -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF sprng/CMakeFiles/sprng.dir/checkid.c.o.d -o sprng/CMakeFiles/sprng.dir/checkid.c.o -c $SRC_DIR/sprng/checkid.c + [7/352] $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I$SRC_DIR -I$SRC_DIR/yaml-cpp/include -I$SRC_DIR/after -I$SRC_DIR/system -I/usr/local/include -I$SRC_DIR/build -I$SRC_DIR/build/cmaple -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/iqtree-2.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -w -mmacosx-version-min=11 -std=c17 -stdlib=libc -std=c17 -Xpreprocessor -fopenmp -pthread -O3 -ffunction-sections -fdata-sections -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -I$PREFIX/include/eigen3 -I$PREFIX/include --target=x86_64-apple-macos10.13 -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c $SRC_DIR/lbfgsb/lbfgsb_new.cpp + [8/352] $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I$SRC_DIR -I$SRC_DIR/yaml-cpp/include -I$SRC_DIR/after -I$SRC_DIR/system -I/usr/local/include -I$SRC_DIR/build -I$SRC_DIR/build/cmaple -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/iqtree-2.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -w -mmacosx-version-min=11 -std=c17 -stdlib=libc -std=c17 -Xpreprocessor -fopenmp -pthread -O3 -ffunction-sections -fdata-sections -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -I$PREFIX/include/eigen3 -I$PREFIX/include --target=x86_64-apple-macos10.13 -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -c $SRC_DIR/utils/eigendecomposition.cpp + [9/352] $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I$SRC_DIR -I$SRC_DIR/yaml-cpp/include -I$SRC_DIR/after -I$SRC_DIR/system -I/usr/local/include -I$SRC_DIR/build -I$SRC_DIR/build/cmaple -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/iqtree-2.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -w -mmacosx-version-min=11 -std=c17 -stdlib=libc -std=c17 -Xpreprocessor -fopenmp -pthread -O3 -ffunction-sections -fdata-sections -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -I$PREFIX/include/eigen3 -I$PREFIX/include --target=x86_64-apple-macos10.13 -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF utils/CMakeFiles/utils.dir/gzstream.cpp.o.d -o utils/CMakeFiles/utils.dir/gzstream.cpp.o -c $SRC_DIR/utils/gzstream.cpp + [10/352] $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I$SRC_DIR -I$SRC_DIR/yaml-cpp/include -I$SRC_DIR/after -I$SRC_DIR/system -I/usr/local/include -I$SRC_DIR/build -I$SRC_DIR/build/cmaple -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/iqtree-2.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -w -mmacosx-version-min=11 -std=c17 -stdlib=libc -std=c17 -Xpreprocessor -fopenmp -pthread -O3 -ffunction-sections -fdata-sections -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -I$PREFIX/include/eigen3 -I$PREFIX/include --target=x86_64-apple-macos10.13 -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF utils/CMakeFiles/utils.dir/optimization.cpp.o.d -o utils/CMakeFiles/utils.dir/optimization.cpp.o -c $SRC_DIR/utils/optimization.cpp + [11/352] $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I$SRC_DIR -I$SRC_DIR/yaml-cpp/include -I$SRC_DIR/after -I$SRC_DIR/system -I/usr/local/include -I$SRC_DIR/build -I$SRC_DIR/build/cmaple -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/iqtree-2.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -w -mmacosx-version-min=11 -std=c17 -stdlib=libc -std=c17 -Xpreprocessor -fopenmp -pthread -O3 -ffunction-sections -fdata-sections -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -I$PREFIX/include/eigen3 -I$PREFIX/include --target=x86_64-apple-macos10.13 -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF utils/CMakeFiles/utils.dir/stoprule.cpp.o.d -o utils/CMakeFiles/utils.dir/stoprule.cpp.o -c $SRC_DIR/utils/stoprule.cpp + [12/352] $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I$SRC_DIR -I$SRC_DIR/yaml-cpp/include -I$SRC_DIR/after -I$SRC_DIR/system -I/usr/local/include -I$SRC_DIR/build -I$SRC_DIR/build/cmaple -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/iqtree-2.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -w -mmacosx-version-min=11 -std=c17 -stdlib=libc -std=c17 -Xpreprocessor -fopenmp -pthread -O3 -ffunction-sections -fdata-sections -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -I$PREFIX/include/eigen3 -I$PREFIX/include --target=x86_64-apple-macos10.13 -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF utils/CMakeFiles/utils.dir/pllnni.cpp.o.d -o utils/CMakeFiles/utils.dir/pllnni.cpp.o -c $SRC_DIR/utils/pllnni.cpp + FAILED: utils/CMakeFiles/utils.dir/pllnni.cpp.o + $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I$SRC_DIR -I$SRC_DIR/yaml-cpp/include -I$SRC_DIR/after -I$SRC_DIR/system -I/usr/local/include -I$SRC_DIR/build -I$SRC_DIR/build/cmaple -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/iqtree-2.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -w -mmacosx-version-min=11 -std=c17 -stdlib=libc -std=c17 -Xpreprocessor -fopenmp -pthread -O3 -ffunction-sections -fdata-sections -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -I$PREFIX/include/eigen3 -I$PREFIX/include --target=x86_64-apple-macos10.13 -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF utils/CMakeFiles/utils.dir/pllnni.cpp.o.d -o utils/CMakeFiles/utils.dir/pllnni.cpp.o -c $SRC_DIR/utils/pllnni.cpp + In file included from $SRC_DIR/utils/pllnni.cpp:34: + $SRC_DIR/tree/phylotree.h:125:15: error: reference to 'aligned_alloc' is ambiguous + 125 | ptr = aligned_alloc(size); + | ^ + $SRC_DIR/tree/phylotree.h:95:11: note: candidate found by name lookup is 'aligned_alloc' + 95 | inline T *aligned_alloc(size_t size) { + | ^ + $BUILD_PREFIX/bin/../include/c/v1/cstdlib:150:9: note: candidate found by name lookup is 'std::aligned_alloc' + 150 | using ::aligned_alloc _LIBCPP_USING_IF_EXISTS; + | ^ + 1 error generated. + [13/352] $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DUSE_CMAPLE -DUSE_LSD2 -D_USE_PTHREADS -I$SRC_DIR -I$SRC_DIR/yaml-cpp/include -I$SRC_DIR/after -I$SRC_DIR/system -I/usr/local/include -I$SRC_DIR/build -I$SRC_DIR/build/cmaple -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/iqtree-2.3.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -w -mmacosx-version-min=11 -std=c17 -stdlib=libc -std=c17 -Xpreprocessor -fopenmp -pthread -O3 -ffunction-sections -fdata-sections -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -I$PREFIX/include/eigen3 -I$PREFIX/include --target=x86_64-apple-macos10.13 -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF utils/CMakeFiles/utils.dir/tools.cpp.o.d -o utils/CMakeFiles/utils.dir/tools.cpp.o -c $SRC_DIR/utils/tools.cpp + ninja: build stopped: subcommand failed. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/iqtree/meta.yaml b/recipes/iqtree/meta.yaml index 875325dc79689..a0b00e7d67e3b 100644 --- a/recipes/iqtree/meta.yaml +++ b/recipes/iqtree/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version | replace("-", "_") }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('iqtree', max_pin="x") }} diff --git a/recipes/ir/build_failure.linux-64.yaml b/recipes/ir/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..5b6a570d43995 --- /dev/null +++ b/recipes/ir/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 360325fe76eb535cd3a13a9615cf42c2c8099a7e3ea327b2507c8050183894f8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + 2024-12-14T03:34:15 noarch Building current_repodata subset + 2024-12-14T03:34:15 noarch Writing current_repodata subset + 2024-12-14T03:34:15 noarch Writing index HTML + /opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (/opt/recipe/meta.yaml). + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml + Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for ir + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['ir-2.8.0-h7b50bb2_7.tar.bz2'] + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/ir_1734147256522/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/ir_1734147256522/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.43-h4bf12b8_2 conda-forge + binutils_linux-64: 2.43-h4852527_2 conda-forge + gcc_impl_linux-64: 13.3.0-hfea6d02_1 conda-forge + gcc_linux-64: 13.3.0-hc28eda2_7 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libsanitizer: 13.3.0-heb74ff8_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + make: 4.4.1-hb9d3cd8_2 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: ir_2.8.0_a642ba254a.tgz + Downloading http://guanine.evolbio.mpg.de/ir/ir_2.8.0.tgz + WARNING:urllib3.connectionpool:Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused')': /ir/ir_2.8.0.tgz + WARNING:urllib3.connectionpool:Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused')': /ir/ir_2.8.0.tgz + WARNING:urllib3.connectionpool:Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused')': /ir/ir_2.8.0.tgz + WARNING: Error: HTTP 000 CONNECTION FAILED for url + Elapsed: - + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download http://guanine.evolbio.mpg.de/ir/ir_2.8.0.tgz +# Last 100 lines of the build log. diff --git a/recipes/ir/meta.yaml b/recipes/ir/meta.yaml index d8c65fa705b32..bbf3fda328d29 100644 --- a/recipes/ir/meta.yaml +++ b/recipes/ir/meta.yaml @@ -12,7 +12,7 @@ source: md5: a642ba254a2c5f6342a2a36c156dae9f build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/irf/build_failure.osx-64.yaml b/recipes/irf/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..990850ae92ba7 --- /dev/null +++ b/recipes/irf/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 1ff5cad15214f9eefe6408b7481e152c590165b7d61c5b61ff01d03dd4d0c8a5 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + - tapi 1300.6.5 h390ca13_0 + - clang-18 18.1.8 default_h0c94c6a_5 + - clangxx 18.1.8 default_h179603d_5 + - llvm-tools-18 18.1.8 h9ce406d_2 + - zstd 1.5.6 h915ae27_0 + - compiler-rt 18.1.8 h1020d70_1 + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/irf_1734474145497/work/conda_build.sh']' returned non-zero exit status 1. + - openssl 3.4.0 hd471939_0 + - libclang-cpp18.1 18.1.8 default_h0c94c6a_5 + - libcxx 19.1.5 hf95d169_0 + - clang 18.1.8 default_h179603d_5 + - cctools_osx-64 1010.6 h00edd4c_2 + - sigtool 0.1.3 h88f4db0_0 + - clangxx_osx-64 18.1.8 h7e5c614_23 + - libcxx-devel 18.1.8 h7c275be_7 + - clang_impl_osx-64 18.1.8 h6a44ed1_23 + - clangxx_impl_osx-64 18.1.8 h4b7810f_23 + - libiconv 1.17 hd75f5a5_2 + - libzlib 1.3.1 hd23fc13_2 + - ncurses 6.5 hf036a51_1 + - ld64_osx-64 951.9 hc8d1a19_2 + - libxml2 2.13.5 he8ee3e7_1 + - llvm-tools 18.1.8 h9ce406d_2 + - liblzma 5.6.3 hd471939_1 + host: + - libcxx 19.1.5 hf95d169_0 + run: + - libcxx >=18 + test: + commands: + - irf + about: + home: https://github.com/Benson-Genomics-Lab/IRF + license: GNU Affero General Public License, Version 3.0 + license_file: COPYING + summary: Inverted Repeats Finder is a program that detects approximate inverted + repeats. + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/irf_1734474145497/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/irf_1734474145497/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/irf_1734474145497/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/irf_1734474145497/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/irf-3.08 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/irf-3.08 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/irf-3.08 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/irf-3.08 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/irf/meta.yaml b/recipes/irf/meta.yaml index c565b0b991f9b..5fafa275b7a6e 100644 --- a/recipes/irf/meta.yaml +++ b/recipes/irf/meta.yaml @@ -7,7 +7,7 @@ source: md5: 9dcda300faaa1af49f12c77ce748f287 build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/irfinder/meta.yaml b/recipes/irfinder/meta.yaml index 7066b218a6a5e..94f8582928cf7 100644 --- a/recipes/irfinder/meta.yaml +++ b/recipes/irfinder/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 94fee8fdac37a5d51ae459d1b06c8d6ed0107752bf2535f207f787e3246ba8b2 build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage("irfinder", max_pin="x") }} diff --git a/recipes/isospecpy/meta.yaml b/recipes/isospecpy/meta.yaml index aacde7c6a4bd8..701ba01068373 100644 --- a/recipes/isospecpy/meta.yaml +++ b/recipes/isospecpy/meta.yaml @@ -11,7 +11,7 @@ source: build: script: {{ PYTHON }} -m pip install . -vv - number: 1 + number: 2 run_exports: - {{ pin_subpackage('isospecpy', max_pin="x.x") }} diff --git a/recipes/ispcr/meta.yaml b/recipes/ispcr/meta.yaml index 8534ed6e507ec..e420670d314d4 100644 --- a/recipes/ispcr/meta.yaml +++ b/recipes/ispcr/meta.yaml @@ -13,7 +13,7 @@ source: - 0001-remove-Werror.patch build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/ivar/build_failure.linux-64.yaml b/recipes/ivar/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..e95af8dcd1d85 --- /dev/null +++ b/recipes/ivar/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 04d4b0898942c89c65df56f2b11b51f4d5c0e67543b5bcde024abb83fabfc2ef # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + | ^~~~~~~ + | set_end + primer_bed.cpp: In function 'void print_primer_info(primer)': + primer_bed.cpp:316:43: error: 'class primer' has no member named 'get_start'; did you mean 'set_start'? + 316 | std::cerr << "Primer start: " << primer.get_start() << std::endl; + | ^~~~~~~~~ + | set_start + primer_bed.cpp:317:41: error: 'class primer' has no member named 'get_end'; did you mean 'set_end'? + 317 | std::cerr << "Primer end: " << primer.get_end() << std::endl; + | ^~~~~~~ + | set_end + depbase=echo allele_functions.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -v -g -std=c11 -Wall -Wextra -Werror -MT allele_functions.o -MD -MP -MF $depbase.Tpo -c -o allele_functions.o allele_functions.cpp &&\ + mv -f $depbase.Tpo $depbase.Po + Reading specs from /opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/specs + could not find specs file conda.specs + COLLECT_GCC=/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/x86_64-conda-linux-gnu-c + Target: x86_64-conda-linux-gnu + Configured with: ../configure --prefix=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho --with-slibdir=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib --libdir=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib --mandir=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/man --build=x86_64-conda-linux-gnu --host=x86_64-conda-linux-gnu --target=x86_64-conda-linux-gnu --enable-languages=c,c,fortran,objc,obj-c --enable-__cxa_atexit --disable-libmudflap --enable-libgomp --disable-libssp --enable-libquadmath --enable-libquadmath-support --enable-lto --enable-target-optspace --enable-plugin --enable-gold --disable-nls --disable-bootstrap --disable-multilib --enable-long-long --with-sysroot=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/x86_64-conda-linux-gnu/sysroot --with-build-sysroot=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/work/cf-compilers/x86_64-conda-linux-gnu/sysroot --with-native-system-header-dir=/usr/include --with-gxx-include-dir=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c --with-pkgversion='conda-forge gcc 13.3.0-1' --with-bugurl=https://github.com/conda-forge/ctng-compilers-feedstock/issues/new/choose --enable-libsanitizer --enable-default-pie --enable-threads=posix + Thread model: posix + Supported LTO compression algorithms: zlib + gcc version 13.3.0 (conda-forge gcc 13.3.0-1) + COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' 'NDEBUG' '-D' '_FORTIFY_SOURCE=2' '-O2' '-isystem' '/opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-I' '/opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-v' '-g' '-std=c11' '-Wall' '-Wextra' '-Werror' '-MT' 'allele_functions.o' '-MD' '-MP' '-MF' '.deps/allele_functions.Tpo' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' + /opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../libexec/gcc/x86_64-conda-linux-gnu/13.3.0/cc1plus -quiet -v -I . -I .. -I /opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include -iprefix /opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/ -isysroot /opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../x86_64-conda-linux-gnu/sysroot -MD allele_functions.d -MF .deps/allele_functions.Tpo -MP -MT allele_functions.o -D_GNU_SOURCE -D HAVE_CONFIG_H -D NDEBUG -D _FORTIFY_SOURCE=2 -isystem /opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include allele_functions.cpp -quiet -dumpbase allele_functions.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -O2 -Wall -Wextra -Werror -std=c11 -version -o /tmp/ccB6jIdU.s + GNU C11 (conda-forge gcc 13.3.0-1) version 13.3.0 (x86_64-conda-linux-gnu) + compiled by GNU C version 14.1.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP + + GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 + ignoring nonexistent directory "/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/include" + ignoring duplicate directory "/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/../../lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c" + ignoring duplicate directory "/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/../../lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/x86_64-conda-linux-gnu" + ignoring duplicate directory "/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/../../lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/backward" + ignoring duplicate directory "/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/../../lib/gcc/x86_64-conda-linux-gnu/13.3.0/include" + ignoring nonexistent directory "/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/local/include" + ignoring duplicate directory "/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/../../lib/gcc/x86_64-conda-linux-gnu/13.3.0/include-fixed" + ignoring nonexistent directory "/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/../../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/include" + ignoring duplicate directory "/opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include" + as it is a non-system directory that duplicates a system directory + ignoring duplicate directory "/opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include" + as it is a non-system directory that duplicates a system directory + #include "..." search starts here: + #include <...> search starts here: + . + .. + /opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include + /opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c + /opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/x86_64-conda-linux-gnu + /opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/backward + /opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/include + /opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/include-fixed + /opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/include + End of search list. + Compiler executable checksum: 039015ee0a9e66f9e392e0a654f3b067 + make[2]: *** [Makefile:397: primer_bed.o] Error 1 + make[2]: *** Waiting for unfinished jobs.... + COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' 'NDEBUG' '-D' '_FORTIFY_SOURCE=2' '-O2' '-isystem' '/opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-I' '/opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-v' '-g' '-std=c11' '-Wall' '-Wextra' '-Werror' '-MT' 'trim_primer_quality.o' '-MD' '-MP' '-MF' '.deps/trim_primer_quality.Tpo' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' + /opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/as -v -I . -I .. -I /opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include --gdwarf-5 --64 -o trim_primer_quality.o /tmp/ccHOa5iL.s + GNU assembler version 2.43 (x86_64-conda-linux-gnu) using BFD version (GNU Binutils) 2.43 + COMPILER_PATH=/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../libexec/gcc/x86_64-conda-linux-gnu/13.3.0/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../libexec/gcc/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ + LIBRARY_PATH=/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib/../lib/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../lib/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/lib/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/ + COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' 'NDEBUG' '-D' '_FORTIFY_SOURCE=2' '-O2' '-isystem' '/opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-I' '/opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-v' '-g' '-std=c11' '-Wall' '-Wextra' '-Werror' '-MT' 'trim_primer_quality.o' '-MD' '-MP' '-MF' '.deps/trim_primer_quality.Tpo' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'trim_primer_quality.' + COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' 'NDEBUG' '-D' '_FORTIFY_SOURCE=2' '-O2' '-isystem' '/opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-I' '/opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-v' '-g' '-std=c11' '-Wall' '-Wextra' '-Werror' '-MT' 'call_variants.o' '-MD' '-MP' '-MF' '.deps/call_variants.Tpo' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' + /opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/as -v -I . -I .. -I /opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include --gdwarf-5 --64 -o call_variants.o /tmp/ccaPZILi.s + GNU assembler version 2.43 (x86_64-conda-linux-gnu) using BFD version (GNU Binutils) 2.43 + COMPILER_PATH=/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../libexec/gcc/x86_64-conda-linux-gnu/13.3.0/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../libexec/gcc/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ + LIBRARY_PATH=/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib/../lib/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../lib/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/lib/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/ + COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' 'NDEBUG' '-D' '_FORTIFY_SOURCE=2' '-O2' '-isystem' '/opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-I' '/opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-v' '-g' '-std=c11' '-Wall' '-Wextra' '-Werror' '-MT' 'call_variants.o' '-MD' '-MP' '-MF' '.deps/call_variants.Tpo' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'call_variants.' + COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' 'NDEBUG' '-D' '_FORTIFY_SOURCE=2' '-O2' '-isystem' '/opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-I' '/opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-v' '-g' '-std=c11' '-Wall' '-Wextra' '-Werror' '-MT' 'allele_functions.o' '-MD' '-MP' '-MF' '.deps/allele_functions.Tpo' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' + /opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/as -v -I . -I .. -I /opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include --gdwarf-5 --64 -o allele_functions.o /tmp/ccB6jIdU.s + GNU assembler version 2.43 (x86_64-conda-linux-gnu) using BFD version (GNU Binutils) 2.43 + COMPILER_PATH=/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../libexec/gcc/x86_64-conda-linux-gnu/13.3.0/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../libexec/gcc/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ + LIBRARY_PATH=/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib/../lib/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../lib/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/lib/:/opt/conda/conda-bld/ivar_1734299628220/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/ + COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' 'NDEBUG' '-D' '_FORTIFY_SOURCE=2' '-O2' '-isystem' '/opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-I' '/opt/conda/conda-bld/ivar_1734299628220/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-v' '-g' '-std=c11' '-Wall' '-Wextra' '-Werror' '-MT' 'allele_functions.o' '-MD' '-MP' '-MF' '.deps/allele_functions.Tpo' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'allele_functions.' + make[2]: Leaving directory '$SRC_DIR/src' + make[1]: *** [Makefile:377: all-recursive] Error 1 + make[1]: Leaving directory '$SRC_DIR' + make: *** [Makefile:318: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ivar_1734299628220/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ivar_1734299628220/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/ivar/build_failure.linux-aarch64.yaml b/recipes/ivar/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..4dc84c9a0df2c --- /dev/null +++ b/recipes/ivar/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 04d4b0898942c89c65df56f2b11b51f4d5c0e67543b5bcde024abb83fabfc2ef # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + primer_bed.cpp:39:29: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + primer_bed.cpp:41:6: error: variable or field 'add_read_count' declared void + 41 | void primer::add_read_count(uint32_t rc) { read_count = rc; } + | ^~~~~~ + primer_bed.cpp:41:29: error: 'uint32_t' was not declared in this scope + 41 | void primer::add_read_count(uint32_t rc) { read_count = rc; } + | ^~~~~~~~ + primer_bed.cpp:41:29: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + primer_bed.cpp: In function 'std::vector get_primers(std::vector, unsigned int)': + primer_bed.cpp:208:13: error: 'class primer' has no member named 'get_start'; did you mean 'set_start'? + 208 | if (it->get_start() <= pos && it->get_end() >= pos) { + | ^~~~~~~~~ + | set_start + primer_bed.cpp:208:39: error: 'class primer' has no member named 'get_end'; did you mean 'set_end'? + 208 | if (it->get_start() <= pos && it->get_end() >= pos) { + | ^~~~~~~ + | set_end + primer_bed.cpp: In lambda function: + primer_bed.cpp:292:47: error: 'class primer' has no member named 'get_start'; did you mean 'set_start'? + 292 | [](primer lhs, primer rhs) { return lhs.get_start() < rhs.get_start(); }); + | ^~~~~~~~~ + | set_start + primer_bed.cpp:292:65: error: 'class primer' has no member named 'get_start'; did you mean 'set_start'? + 292 | [](primer lhs, primer rhs) { return lhs.get_start() < rhs.get_start(); }); + | ^~~~~~~~~ + | set_start + primer_bed.cpp: In lambda function: + primer_bed.cpp:299:47: error: 'class primer' has no member named 'get_end'; did you mean 'set_end'? + 299 | [](primer lhs, primer rhs) { return lhs.get_end() < rhs.get_end(); }); + | ^~~~~~~ + | set_end + primer_bed.cpp:299:63: error: 'class primer' has no member named 'get_end'; did you mean 'set_end'? + 299 | [](primer lhs, primer rhs) { return lhs.get_end() < rhs.get_end(); }); + | ^~~~~~~ + | set_end + primer_bed.cpp: In function 'void print_all_primer_info(std::vector)': + primer_bed.cpp:307:42: error: 'class primer' has no member named 'get_start'; did you mean 'set_start'? + 307 | std::cerr << "Primer start: " << it->get_start() << std::endl; + | ^~~~~~~~~ + | set_start + primer_bed.cpp:308:40: error: 'class primer' has no member named 'get_end'; did you mean 'set_end'? + 308 | std::cerr << "Primer end: " << it->get_end() << std::endl; + | ^~~~~~~ + | set_end + primer_bed.cpp: In function 'void print_primer_info(primer)': + primer_bed.cpp:316:43: error: 'class primer' has no member named 'get_start'; did you mean 'set_start'? + 316 | std::cerr << "Primer start: " << primer.get_start() << std::endl; + | ^~~~~~~~~ + | set_start + primer_bed.cpp:317:41: error: 'class primer' has no member named 'get_end'; did you mean 'set_end'? + 317 | std::cerr << "Primer end: " << primer.get_end() << std::endl; + | ^~~~~~~ + | set_end + make[2]: *** [Makefile:397: primer_bed.o] Error 1 + make[2]: *** Waiting for unfinished jobs.... + COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' 'NDEBUG' '-D' '_FORTIFY_SOURCE=2' '-O2' '-isystem' '/opt/conda/conda-bld/ivar_1734727738481/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-I' '/opt/conda/conda-bld/ivar_1734727738481/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-v' '-g' '-std=c11' '-Wall' '-Wextra' '-Werror' '-MT' 'remove_reads_from_amplicon.o' '-MD' '-MP' '-MF' '.deps/remove_reads_from_amplicon.Tpo' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' + /opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/as -v -I . -I .. -I /opt/conda/conda-bld/ivar_1734727738481/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include --gdwarf-5 -EL -mabi=lp64 -o remove_reads_from_amplicon.o /tmp/cceItFYh.s + GNU assembler version 2.43 (aarch64-conda-linux-gnu) using BFD version (GNU Binutils) 2.43 + COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' 'NDEBUG' '-D' '_FORTIFY_SOURCE=2' '-O2' '-isystem' '/opt/conda/conda-bld/ivar_1734727738481/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-I' '/opt/conda/conda-bld/ivar_1734727738481/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-v' '-g' '-std=c11' '-Wall' '-Wextra' '-Werror' '-MT' 'trim_primer_quality.o' '-MD' '-MP' '-MF' '.deps/trim_primer_quality.Tpo' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' + /opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/as -v -I . -I .. -I /opt/conda/conda-bld/ivar_1734727738481/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include --gdwarf-5 -EL -mabi=lp64 -o trim_primer_quality.o /tmp/ccSK4Gno.s + GNU assembler version 2.43 (aarch64-conda-linux-gnu) using BFD version (GNU Binutils) 2.43 + COMPILER_PATH=/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../libexec/gcc/aarch64-conda-linux-gnu/13.3.0/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../libexec/gcc/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ + LIBRARY_PATH=/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/lib/../lib/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../lib/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../aarch64-conda-linux-gnu/sysroot/lib/../lib/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../aarch64-conda-linux-gnu/sysroot/usr/lib/../lib/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/lib/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../aarch64-conda-linux-gnu/sysroot/lib/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../aarch64-conda-linux-gnu/sysroot/usr/lib/ + COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' 'NDEBUG' '-D' '_FORTIFY_SOURCE=2' '-O2' '-isystem' '/opt/conda/conda-bld/ivar_1734727738481/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-I' '/opt/conda/conda-bld/ivar_1734727738481/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-v' '-g' '-std=c11' '-Wall' '-Wextra' '-Werror' '-MT' 'remove_reads_from_amplicon.o' '-MD' '-MP' '-MF' '.deps/remove_reads_from_amplicon.Tpo' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'remove_reads_from_amplicon.' + COMPILER_PATH=/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../libexec/gcc/aarch64-conda-linux-gnu/13.3.0/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../libexec/gcc/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ + LIBRARY_PATH=/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/lib/../lib/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../lib/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../aarch64-conda-linux-gnu/sysroot/lib/../lib/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../aarch64-conda-linux-gnu/sysroot/usr/lib/../lib/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/lib/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../aarch64-conda-linux-gnu/sysroot/lib/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../aarch64-conda-linux-gnu/sysroot/usr/lib/ + COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' 'NDEBUG' '-D' '_FORTIFY_SOURCE=2' '-O2' '-isystem' '/opt/conda/conda-bld/ivar_1734727738481/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-I' '/opt/conda/conda-bld/ivar_1734727738481/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-v' '-g' '-std=c11' '-Wall' '-Wextra' '-Werror' '-MT' 'trim_primer_quality.o' '-MD' '-MP' '-MF' '.deps/trim_primer_quality.Tpo' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'trim_primer_quality.' + COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' 'NDEBUG' '-D' '_FORTIFY_SOURCE=2' '-O2' '-isystem' '/opt/conda/conda-bld/ivar_1734727738481/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-I' '/opt/conda/conda-bld/ivar_1734727738481/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-v' '-g' '-std=c11' '-Wall' '-Wextra' '-Werror' '-MT' 'call_variants.o' '-MD' '-MP' '-MF' '.deps/call_variants.Tpo' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' + /opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/as -v -I . -I .. -I /opt/conda/conda-bld/ivar_1734727738481/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include --gdwarf-5 -EL -mabi=lp64 -o call_variants.o /tmp/cc2jUCxu.s + GNU assembler version 2.43 (aarch64-conda-linux-gnu) using BFD version (GNU Binutils) 2.43 + COMPILER_PATH=/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../libexec/gcc/aarch64-conda-linux-gnu/13.3.0/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../libexec/gcc/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ + LIBRARY_PATH=/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/lib/../lib/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../lib/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../aarch64-conda-linux-gnu/sysroot/lib/../lib/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../aarch64-conda-linux-gnu/sysroot/usr/lib/../lib/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/lib/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../aarch64-conda-linux-gnu/sysroot/lib/:/opt/conda/conda-bld/ivar_1734727738481/_build_env/bin/../aarch64-conda-linux-gnu/sysroot/usr/lib/ + COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-D' 'NDEBUG' '-D' '_FORTIFY_SOURCE=2' '-O2' '-isystem' '/opt/conda/conda-bld/ivar_1734727738481/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-I' '/opt/conda/conda-bld/ivar_1734727738481/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include' '-v' '-g' '-std=c11' '-Wall' '-Wextra' '-Werror' '-MT' 'call_variants.o' '-MD' '-MP' '-MF' '.deps/call_variants.Tpo' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'call_variants.' + make[2]: Leaving directory '$SRC_DIR/src' + make[1]: *** [Makefile:377: all-recursive] Error 1 + make[1]: Leaving directory '$SRC_DIR' + make: *** [Makefile:318: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ivar_1734727738481/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ivar_1734727738481/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/ivar/meta.yaml b/recipes/ivar/meta.yaml index 1482b668f08ec..5856ff236f173 100644 --- a/recipes/ivar/meta.yaml +++ b/recipes/ivar/meta.yaml @@ -10,7 +10,7 @@ source: sha256: "{{ sha256 }}" build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('ivar', max_pin='x') }} diff --git a/recipes/jarvis/meta.yaml b/recipes/jarvis/meta.yaml index ad31b2aab841a..76a6e63168f97 100644 --- a/recipes/jarvis/meta.yaml +++ b/recipes/jarvis/meta.yaml @@ -7,7 +7,7 @@ package: build: # Passes some invalid flags for clang skip: True # [osx] - number: 4 + number: 5 source: url: https://github.com/cobilab/jarvis/archive/v{{ version }}.tar.gz diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml index bd65c0ad6f2fd..beb88d449212f 100644 --- a/recipes/jbrowse2/meta.yaml +++ b/recipes/jbrowse2/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('jbrowse2', max_pin="x") }} diff --git a/recipes/kaiju/meta.yaml b/recipes/kaiju/meta.yaml index db305614f3c6f..95542b48e3f09 100644 --- a/recipes/kaiju/meta.yaml +++ b/recipes/kaiju/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 3cc05533bf6007ffeff2d755c935354952b09a6b903c5e538dff14285b3c86e8 build: - number: 1 + number: 2 no_link: - bin/kaiju-makedb.sh run_exports: diff --git a/recipes/kakscalculator2/meta.yaml b/recipes/kakscalculator2/meta.yaml index 772df9acc2c07..d2dd5055bdc6a 100644 --- a/recipes/kakscalculator2/meta.yaml +++ b/recipes/kakscalculator2/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://github.com/kullrich/kakscalculator2/archive/v{{ version }}.tar.gz diff --git a/recipes/kalign2/meta.yaml b/recipes/kalign2/meta.yaml index 009cfc0dabbcb..3bac8f488f5c0 100644 --- a/recipes/kalign2/meta.yaml +++ b/recipes/kalign2/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 7 + number: 8 run_exports: - {{ pin_subpackage('kalign2', max_pin='x') }} @@ -34,4 +34,4 @@ extra: - doi:10.1186/1471-2105-6-298 additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 diff --git a/recipes/kalign3/meta.yaml b/recipes/kalign3/meta.yaml index 29793014d4418..d57b17e8d94bb 100644 --- a/recipes/kalign3/meta.yaml +++ b/recipes/kalign3/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin='x') }} diff --git a/recipes/kallisto/build_failure.osx-arm64.yaml b/recipes/kallisto/build_failure.osx-arm64.yaml new file mode 100644 index 0000000000000..7923962e306d7 --- /dev/null +++ b/recipes/kallisto/build_failure.osx-arm64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 43e0970633214f36e707f8e09977f29f61725290b59583f7a93ffb9f4df61227 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o tbx.o tbx.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o textutils.o textutils.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o thread_pool.o thread_pool.c + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/kallisto_1734391155442/work/conda_build.sh']' returned non-zero exit status 2. + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o vcf.o vcf.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o vcfutils.o vcfutils.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o cram/cram_codecs.o cram/cram_codecs.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o cram/cram_decode.o cram/cram_decode.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o cram/cram_encode.o cram/cram_encode.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o cram/cram_external.o cram/cram_external.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o cram/cram_index.o cram/cram_index.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o cram/cram_io.o cram/cram_io.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o cram/cram_samtools.o cram/cram_samtools.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o cram/cram_stats.o cram/cram_stats.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o cram/files.o cram/files.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o cram/mFILE.o cram/mFILE.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o cram/open_trace_file.o cram/open_trace_file.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o cram/pooled_alloc.o cram/pooled_alloc.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o cram/rANS_static.o cram/rANS_static.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o cram/sam_header.o cram/sam_header.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o cram/string_alloc.o cram/string_alloc.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o cram/vlen.o cram/vlen.c + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.51.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -c -o cram/zfio.o cram/zfio.c + ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/vlen.o cram/zfio.o + arm64-apple-darwin20.0.0-ranlib libhts.a + make[3]: Leaving directory '$SRC_DIR/ext/htslib' + cd $SRC_DIR/ext/htslib && $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/ext/htslib/src/htslib-stamp/htslib-build + [ 20%] No install step for 'htslib' + cd $SRC_DIR/ext/htslib && $BUILD_PREFIX/bin/cmake -E echo_append + cd $SRC_DIR/ext/htslib && $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/ext/htslib/src/htslib-stamp/htslib-install + [ 23%] Completed 'htslib' + $BUILD_PREFIX/bin/cmake -E make_directory $SRC_DIR/build/CMakeFiles + $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/build/CMakeFiles/htslib-complete + $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/ext/htslib/src/htslib-stamp/htslib-done + make[2]: Leaving directory '$SRC_DIR/build' + [ 23%] Built target htslib + $BUILD_PREFIX/bin/make -f CMakeFiles/bifrost.dir/build.make CMakeFiles/bifrost.dir/depend + make[2]: Entering directory '$SRC_DIR/build' + cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR $SRC_DIR/build $SRC_DIR/build $SRC_DIR/build/CMakeFiles/bifrost.dir/DependInfo.cmake "--color=" + make[2]: Leaving directory '$SRC_DIR/build' + $BUILD_PREFIX/bin/make -f CMakeFiles/bifrost.dir/build.make CMakeFiles/bifrost.dir/build + make[2]: Entering directory '$SRC_DIR/build' + [ 26%] Creating directories for 'bifrost' + $BUILD_PREFIX/bin/cmake -Dcfgdir= -P $SRC_DIR/ext/bifrost/tmp/bifrost-mkdirs.cmake + $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/ext/bifrost/src/bifrost-stamp/bifrost-mkdir + [ 29%] No download step for 'bifrost' + $BUILD_PREFIX/bin/cmake -E echo_append + $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/ext/bifrost/src/bifrost-stamp/bifrost-download + [ 32%] No update step for 'bifrost' + $BUILD_PREFIX/bin/cmake -E echo_append + $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/ext/bifrost/src/bifrost-stamp/bifrost-update + [ 35%] No patch step for 'bifrost' + $BUILD_PREFIX/bin/cmake -E echo_append + $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/ext/bifrost/src/bifrost-stamp/bifrost-patch + [ 38%] Performing configure step for 'bifrost' + cd $SRC_DIR/ext/bifrost && mkdir -p build && cd build && cmake .. -DMAX_KMER_SIZE=64 -DCMAKE_INSTALL_PREFIX= "-DCMAKE_CXX_FLAGS=-Wno-subobject-linkage -Wno-return-type" -DENABLE_AVX2=OFF + Re-run cmake no build system arguments + -- The C compiler identification is Clang 18.1.8 + -- The CXX compiler identification is Clang 18.1.8 + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang - skipped + -- Detecting C compile features + -- Detecting C compile features - done + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success + -- Found Threads: TRUE + -- Found ZLIB: $PREFIX/lib/libz.dylib (found version "1.3.1") + -- Configuring done (6.9s) + -- Generating done (0.0s) + -- Build files have been written to: $SRC_DIR/ext/bifrost/build + cd $SRC_DIR/ext/bifrost && $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/ext/bifrost/src/bifrost-stamp/bifrost-configure + [ 41%] Performing build step for 'bifrost' + cd $SRC_DIR/ext/bifrost && cd build && make + make[3]: Entering directory '$SRC_DIR/ext/bifrost/build' + $BUILD_PREFIX/bin/cmake -S$SRC_DIR/ext/bifrost -B$SRC_DIR/ext/bifrost/build --check-build-system CMakeFiles/Makefile.cmake 0 + $BUILD_PREFIX/bin/cmake -E cmake_progress_start $SRC_DIR/ext/bifrost/build/CMakeFiles $SRC_DIR/ext/bifrost/build//CMakeFiles/progress.marks + make -f CMakeFiles/Makefile2 all + make[4]: Entering directory '$SRC_DIR/ext/bifrost/build' + make -f src/CMakeFiles/bifrost_static.dir/build.make src/CMakeFiles/bifrost_static.dir/depend + make[5]: Entering directory '$SRC_DIR/ext/bifrost/build' + cd $SRC_DIR/ext/bifrost/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR/ext/bifrost $SRC_DIR/ext/bifrost/src $SRC_DIR/ext/bifrost/build $SRC_DIR/ext/bifrost/build/src $SRC_DIR/ext/bifrost/build/src/CMakeFiles/bifrost_static.dir/DependInfo.cmake "--color=" + make[5]: Leaving directory '$SRC_DIR/ext/bifrost/build' + make -f src/CMakeFiles/bifrost_static.dir/build.make src/CMakeFiles/bifrost_static.dir/build + make[5]: Entering directory '$SRC_DIR/ext/bifrost/build' + [ 3%] Building CXX object src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o + cd $SRC_DIR/ext/bifrost/build/src && $BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang -DMAX_GMER_SIZE=64 -DMAX_KMER_SIZE=64 -I$SRC_DIR/ext/bifrost/src -I$PREFIX/include -Wno-subobject-linkage -Wno-return-type -std=c11 -mno-avx2 -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk -mmacosx-version-min=11.0 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -MF CMakeFiles/bifrost_static.dir/Bifrost.cpp.o.d -o CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -c $SRC_DIR/ext/bifrost/src/Bifrost.cpp + make[5]: Leaving directory '$SRC_DIR/ext/bifrost/build' + make[4]: Leaving directory '$SRC_DIR/ext/bifrost/build' + make[3]: Leaving directory '$SRC_DIR/ext/bifrost/build' + make[2]: Leaving directory '$SRC_DIR/build' + make[1]: Leaving directory '$SRC_DIR/build' +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/kallisto/meta.yaml b/recipes/kallisto/meta.yaml index 49b6ca8115b6e..4d166d78159b3 100644 --- a/recipes/kallisto/meta.yaml +++ b/recipes/kallisto/meta.yaml @@ -10,7 +10,7 @@ source: sha256: a8bcc23bca6ac758f15e30bb77e9e169e628beff2da3be2e34a53e1d42253516 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('kallisto', max_pin="x.x") }} diff --git a/recipes/karect/meta.yaml b/recipes/karect/meta.yaml index 0a6a3e872abb3..292ad672ca671 100644 --- a/recipes/karect/meta.yaml +++ b/recipes/karect/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 47d90bf2e6d4dd26a48bcf9c8041cbe95af0bec48d2488422485378fd8c35681 build: - number: 6 + number: 7 skip: True # [not linux] script: | install -d "${PREFIX}/bin" diff --git a/recipes/kart/build_failure.osx-64.yaml b/recipes/kart/build_failure.osx-64.yaml deleted file mode 100644 index 2b69210bd38f2..0000000000000 --- a/recipes/kart/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 34d5591189ba4b0ec2521b259cd4776a6b46131fe3acb420d156ee4cd35ec170 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - $SRC_DIR/src/BWT_Index $SRC_DIR - x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix utils.c -o utils.o - x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix bwt.c -o bwt.o - x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix bntseq.c -o bntseq.o - x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix QSufSort.c -o QSufSort.o - x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix bwt_gen.c -o bwt_gen.o - x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix bwtindex.c -o bwtindex.o - ar -csru libbwa.a utils.o bwt.o bntseq.o QSufSort.o bwt_gen.o bwtindex.o - x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix main.c -o main.o - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix main.o -o bwt_index -L. -lbwa -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lm -lz - $SRC_DIR - $SRC_DIR/src/htslib $SRC_DIR - echo '/* Default config.h generated by Makefile */' > config.h - echo '#define HAVE_LIBBZ2 1' >> config.h - echo '#define HAVE_LIBLZMA 1' >> config.h - echo '#define HAVE_FSEEKO 1' >> config.h - echo '#define HAVE_DRAND48 1' >> config.h - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o kfunc.o kfunc.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o knetfile.o knetfile.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o kstring.o kstring.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o bcf_sr_sort.o bcf_sr_sort.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o bgzf.o bgzf.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o errmod.o errmod.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o faidx.o faidx.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o hfile.o hfile.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o hfile_net.o hfile_net.c - echo '#define HTS_VERSION "1.5"' > version.h - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o hts.o hts.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o hts_os.o hts_os.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o md5.o md5.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o multipart.o multipart.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o probaln.o probaln.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o realn.o realn.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o regidx.o regidx.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o sam.o sam.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o synced_bcf_reader.o synced_bcf_reader.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o vcf_sweep.o vcf_sweep.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o tbx.o tbx.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o textutils.o textutils.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o thread_pool.o thread_pool.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o vcf.o vcf.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o vcfutils.o vcfutils.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/cram_codecs.o cram/cram_codecs.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/cram_decode.o cram/cram_decode.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/cram_encode.o cram/cram_encode.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/cram_external.o cram/cram_external.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/cram_index.o cram/cram_index.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/cram_io.o cram/cram_io.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/cram_samtools.o cram/cram_samtools.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/cram_stats.o cram/cram_stats.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/files.o cram/files.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/mFILE.o cram/mFILE.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/open_trace_file.o cram/open_trace_file.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/rANS_static.o cram/rANS_static.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/sam_header.o cram/sam_header.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I. -c -o cram/string_alloc.o cram/string_alloc.c - ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o - ranlib libhts.a - $SRC_DIR - $SRC_DIR/src $SRC_DIR - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -D NDEBUG -O3 -m64 -msse4.1 -fPIC -c main.cpp - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kart-2.5.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -D NDEBUG -O3 -m64 -msse4.1 -fPIC -c GetData.cpp -# Last 100 lines of the build log. diff --git a/recipes/kart/meta.yaml b/recipes/kart/meta.yaml index e3a2a13cee4e8..9557f0d49d2b4 100644 --- a/recipes/kart/meta.yaml +++ b/recipes/kart/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 3ec028e0c0bb24e11f1be92b0151e020bcd50b160fdf0f33d120b675f151365a build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/kcounter/build_failure.linux-64.yaml b/recipes/kcounter/build_failure.linux-64.yaml deleted file mode 100644 index ca221592c130a..0000000000000 --- a/recipes/kcounter/build_failure.linux-64.yaml +++ /dev/null @@ -1,106 +0,0 @@ -recipe_sha: c8a36d9ad38f8fbf901cc9e38a52f8856dd4ee9b582a7c12602214de281ea084 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - Downloaded pyo3 v0.13.2 - Downloaded libc v0.2.155 - Downloaded winapi v0.3.9 - Downloaded safemem v0.3.3 - Downloaded pyo3-macros-backend v0.13.2 - Downloaded pyo3-macros v0.13.2 - Downloaded inventory-impl v0.1.11 - Downloaded inventory v0.1.11 - Downloaded indoc v0.3.6 - Downloaded ghost v0.1.17 - Downloaded unindent v0.1.11 - Downloaded winapi-i686-pc-windows-gnu v0.4.0 - Downloaded unicode-ident v1.0.12 - Downloaded winapi-x86_64-pc-windows-gnu v0.4.0 - Downloaded syn v1.0.109 - Downloaded scopeguard v1.2.0 - Downloaded proc-macro2 v1.0.85 - Downloaded pkg-config v0.3.30 - Downloaded paste-impl v0.1.18 - Downloaded paste v0.1.18 - Downloaded parking_lot_core v0.8.6 - Downloaded parking_lot v0.11.2 - Downloaded needletail v0.4.1 - Downloaded miniz_oxide v0.7.3 - Downloaded memchr v2.7.2 - Downloaded lock_api v0.4.12 - Downloaded instant v0.1.13 - Downloaded flate2 v1.0.30 - Downloaded proc-macro-hack v0.5.20deprecated - Downloaded indoc-impl v0.3.6 - Downloaded crc32fast v1.4.2 - Downloaded bzip2-sys v0.1.111.0.8 - Downloaded bytecount v0.6.8 - Downloaded adler v1.0.2 - Downloaded bzip2 v0.4.4 - Downloaded buf_redux v0.8.4 - Downloaded autocfg v1.3.0 - Found pyo3 bindings - Found CPython 3.10 at /opt/conda/conda-bld/kcounter_1717952336381/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python - Compiling proc-macro2 v1.0.85 - Compiling unicode-ident v1.0.12 - Compiling syn v1.0.109 - Compiling libc v0.2.155 - Compiling cc v1.0.99 - error: linking with /opt/conda/conda-bld/kcounter_1717952336381/_build_env/bin/x86_64-conda-linux-gnu-cc failed: exit status: 1 - | - = note: LC_ALL="C" PATH="/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin:/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin/self-contained:/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin:/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin/self-contained:/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin:/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin/self-contained:/home/conda/.cargo/bin:/opt/conda/conda-bld/kcounter_1717952336381/_build_env/bin:/opt/conda/conda-bld/kcounter_1717952336381/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin:/opt/conda/condabin:/opt/conda/conda-bld/kcounter_1717952336381/_build_env/bin:/opt/conda/conda-bld/kcounter_1717952336381/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin:/opt/conda/bin:/opt/conda/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/conda/bin" VSLANG="1033" "/opt/conda/conda-bld/kcounter_1717952336381/_build_env/bin/x86_64-conda-linux-gnu-cc" "-m64" "/tmp/rustcHGtoJS/symbols.o" "/opt/conda/conda-bld/kcounter_1717952336381/work/target/release/build/proc-macro2-f24ef631c5c4453c/build_script_build-f24ef631c5c4453c.build_script_build.ac3926a2cabd960f-cgu.0.rcgu.o" "/opt/conda/conda-bld/kcounter_1717952336381/work/target/release/build/proc-macro2-f24ef631c5c4453c/build_script_build-f24ef631c5c4453c.build_script_build.ac3926a2cabd960f-cgu.1.rcgu.o" "/opt/conda/conda-bld/kcounter_1717952336381/work/target/release/build/proc-macro2-f24ef631c5c4453c/build_script_build-f24ef631c5c4453c.974siq1idrtwlzpe4b7fazd69.rcgu.o" "-Wl,--as-needed" "-L" "/opt/conda/conda-bld/kcounter_1717952336381/work/target/release/deps" "-L" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-Wl,-Bstatic" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-d46578f9a4470f27.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libpanic_unwind-9ff13545d1688b3c.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libobject-98f5e78f871c5595.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libmemchr-f3d3451767410a17.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libaddr2line-16717cdb08dfbef5.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libgimli-58e3f8995df4edb4.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_demangle-2caea079085a58a2.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd_detect-314a4689716cb02e.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libhashbrown-5727477b0a78105a.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_alloc-7e555563aa211118.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libminiz_oxide-d9ed943652059c0d.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libadler-ee5b5774583426df.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunwind-c3e1f40644ffc9b8.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcfg_if-e8bfe52be756260a.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liblibc-7b90a2705bcf265b.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liballoc-b6892f3c52c68f01.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_core-f72b956e24d1de70.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcore-632ae0f28c5e55ff.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcompiler_builtins-e8b7e96e438f08f6.rlib" "-Wl,-Bdynamic" "-lgcc_s" "-lutil" "-lrt" "-lpthread" "-lm" "-ldl" "-lc" "-B/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin/gcc-ld" "-B/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin/gcc-ld" "-B/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin/gcc-ld" "-fuse-ld=lld" "-Wl,--eh-frame-hdr" "-Wl,-z,noexecstack" "-L" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-L" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/self-contained" "-o" "/opt/conda/conda-bld/kcounter_1717952336381/work/target/release/build/proc-macro2-f24ef631c5c4453c/build_script_build-f24ef631c5c4453c" "-Wl,--gc-sections" "-pie" "-Wl,-z,relro,-z,now" "-Wl,--strip-debug" "-nodefaultlibs" - = note: rust-lld: error: undefined symbol: getauxval - >>> referenced by stack_overflow.rs:237 (library/std/src/sys/pal/unix/stack_overflow.rs:237) - >>> std-d46578f9a4470f27.std.a54bcd08e7411830-cgu.0.rcgu.o:(std::sys::pal::unix::stack_overflow::imp::make_handler::h648b6dd35f16ad81) in archive /home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-d46578f9a4470f27.rlib - >>> referenced by stack_overflow.rs:237 (library/std/src/sys/pal/unix/stack_overflow.rs:237) - >>> std-d46578f9a4470f27.std.a54bcd08e7411830-cgu.0.rcgu.o:(std::sys::sync::once::futex::Once::call::h3caf211f3255e91f) in archive /home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-d46578f9a4470f27.rlib - collect2: error: ld returned 1 exit status - - - error: linking with /opt/conda/conda-bld/kcounter_1717952336381/_build_env/bin/x86_64-conda-linux-gnu-cc failed: exit status: 1 - | - = note: LC_ALL="C" PATH="/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin:/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin/self-contained:/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin:/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin/self-contained:/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin:/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin/self-contained:/home/conda/.cargo/bin:/opt/conda/conda-bld/kcounter_1717952336381/_build_env/bin:/opt/conda/conda-bld/kcounter_1717952336381/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin:/opt/conda/condabin:/opt/conda/conda-bld/kcounter_1717952336381/_build_env/bin:/opt/conda/conda-bld/kcounter_1717952336381/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin:/opt/conda/bin:/opt/conda/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/conda/bin" VSLANG="1033" "/opt/conda/conda-bld/kcounter_1717952336381/_build_env/bin/x86_64-conda-linux-gnu-cc" "-m64" "/tmp/rustc9LDuWe/symbols.o" "/opt/conda/conda-bld/kcounter_1717952336381/work/target/release/build/syn-e93e6735c750467a/build_script_build-e93e6735c750467a.build_script_build.5c22b9c1257522dd-cgu.0.rcgu.o" "/opt/conda/conda-bld/kcounter_1717952336381/work/target/release/build/syn-e93e6735c750467a/build_script_build-e93e6735c750467a.build_script_build.5c22b9c1257522dd-cgu.1.rcgu.o" "/opt/conda/conda-bld/kcounter_1717952336381/work/target/release/build/syn-e93e6735c750467a/build_script_build-e93e6735c750467a.build_script_build.5c22b9c1257522dd-cgu.2.rcgu.o" "/opt/conda/conda-bld/kcounter_1717952336381/work/target/release/build/syn-e93e6735c750467a/build_script_build-e93e6735c750467a.5peiopk4mwf6r9hjpzf6gfaed.rcgu.o" "-Wl,--as-needed" "-L" "/opt/conda/conda-bld/kcounter_1717952336381/work/target/release/deps" "-L" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-Wl,-Bstatic" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-d46578f9a4470f27.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libpanic_unwind-9ff13545d1688b3c.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libobject-98f5e78f871c5595.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libmemchr-f3d3451767410a17.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libaddr2line-16717cdb08dfbef5.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libgimli-58e3f8995df4edb4.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_demangle-2caea079085a58a2.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd_detect-314a4689716cb02e.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libhashbrown-5727477b0a78105a.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_alloc-7e555563aa211118.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libminiz_oxide-d9ed943652059c0d.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libadler-ee5b5774583426df.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunwind-c3e1f40644ffc9b8.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcfg_if-e8bfe52be756260a.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liblibc-7b90a2705bcf265b.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liballoc-b6892f3c52c68f01.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_core-f72b956e24d1de70.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcore-632ae0f28c5e55ff.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcompiler_builtins-e8b7e96e438f08f6.rlib" "-Wl,-Bdynamic" "-lgcc_s" "-lutil" "-lrt" "-lpthread" "-lm" "-ldl" "-lc" "-B/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin/gcc-ld" "-B/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin/gcc-ld" "-B/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin/gcc-ld" "-fuse-ld=lld" "-Wl,--eh-frame-hdr" "-Wl,-z,noexecstack" "-L" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-L" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/self-contained" "-o" "/opt/conda/conda-bld/kcounter_1717952336381/work/target/release/build/syn-e93e6735c750467a/build_script_build-e93e6735c750467a" "-Wl,--gc-sections" "-pie" "-Wl,-z,relro,-z,now" "-Wl,--strip-debug" "-nodefaultlibs" - = note: rust-lld: error: undefined symbol: getauxval - >>> referenced by stack_overflow.rs:237 (library/std/src/sys/pal/unix/stack_overflow.rs:237) - >>> std-d46578f9a4470f27.std.a54bcd08e7411830-cgu.0.rcgu.o:(std::sys::pal::unix::stack_overflow::imp::make_handler::h648b6dd35f16ad81) in archive /home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-d46578f9a4470f27.rlib - >>> referenced by stack_overflow.rs:237 (library/std/src/sys/pal/unix/stack_overflow.rs:237) - >>> std-d46578f9a4470f27.std.a54bcd08e7411830-cgu.0.rcgu.o:(std::sys::sync::once::futex::Once::call::h3caf211f3255e91f) in archive /home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-d46578f9a4470f27.rlib - collect2: error: ld returned 1 exit status - - - error: could not compile proc-macro2 (build script) due to 1 previous error - warning: build failed, waiting for other jobs to finish... - error: could not compile syn (build script) due to 1 previous error - error: linking with /opt/conda/conda-bld/kcounter_1717952336381/_build_env/bin/x86_64-conda-linux-gnu-cc failed: exit status: 1 - | - = note: LC_ALL="C" PATH="/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin:/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin/self-contained:/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin:/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin/self-contained:/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin:/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin/self-contained:/home/conda/.cargo/bin:/opt/conda/conda-bld/kcounter_1717952336381/_build_env/bin:/opt/conda/conda-bld/kcounter_1717952336381/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin:/opt/conda/condabin:/opt/conda/conda-bld/kcounter_1717952336381/_build_env/bin:/opt/conda/conda-bld/kcounter_1717952336381/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin:/opt/conda/bin:/opt/conda/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/conda/bin" VSLANG="1033" "/opt/conda/conda-bld/kcounter_1717952336381/_build_env/bin/x86_64-conda-linux-gnu-cc" "-m64" "/tmp/rustcSKCgs9/symbols.o" "/opt/conda/conda-bld/kcounter_1717952336381/work/target/release/build/libc-18a8ba3a588519b1/build_script_build-18a8ba3a588519b1.build_script_build.d1b5672f9cd6361d-cgu.0.rcgu.o" "/opt/conda/conda-bld/kcounter_1717952336381/work/target/release/build/libc-18a8ba3a588519b1/build_script_build-18a8ba3a588519b1.build_script_build.d1b5672f9cd6361d-cgu.1.rcgu.o" "/opt/conda/conda-bld/kcounter_1717952336381/work/target/release/build/libc-18a8ba3a588519b1/build_script_build-18a8ba3a588519b1.build_script_build.d1b5672f9cd6361d-cgu.2.rcgu.o" "/opt/conda/conda-bld/kcounter_1717952336381/work/target/release/build/libc-18a8ba3a588519b1/build_script_build-18a8ba3a588519b1.build_script_build.d1b5672f9cd6361d-cgu.3.rcgu.o" "/opt/conda/conda-bld/kcounter_1717952336381/work/target/release/build/libc-18a8ba3a588519b1/build_script_build-18a8ba3a588519b1.5mkujhylovfp71004z0q46836.rcgu.o" "-Wl,--as-needed" "-L" "/opt/conda/conda-bld/kcounter_1717952336381/work/target/release/deps" "-L" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-Wl,-Bstatic" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-d46578f9a4470f27.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libpanic_unwind-9ff13545d1688b3c.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libobject-98f5e78f871c5595.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libmemchr-f3d3451767410a17.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libaddr2line-16717cdb08dfbef5.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libgimli-58e3f8995df4edb4.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_demangle-2caea079085a58a2.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd_detect-314a4689716cb02e.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libhashbrown-5727477b0a78105a.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_alloc-7e555563aa211118.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libminiz_oxide-d9ed943652059c0d.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libadler-ee5b5774583426df.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunwind-c3e1f40644ffc9b8.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcfg_if-e8bfe52be756260a.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liblibc-7b90a2705bcf265b.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liballoc-b6892f3c52c68f01.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_core-f72b956e24d1de70.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcore-632ae0f28c5e55ff.rlib" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcompiler_builtins-e8b7e96e438f08f6.rlib" "-Wl,-Bdynamic" "-lgcc_s" "-lutil" "-lrt" "-lpthread" "-lm" "-ldl" "-lc" "-B/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin/gcc-ld" "-B/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin/gcc-ld" "-B/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/bin/gcc-ld" "-fuse-ld=lld" "-Wl,--eh-frame-hdr" "-Wl,-z,noexecstack" "-L" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-L" "/home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/self-contained" "-o" "/opt/conda/conda-bld/kcounter_1717952336381/work/target/release/build/libc-18a8ba3a588519b1/build_script_build-18a8ba3a588519b1" "-Wl,--gc-sections" "-pie" "-Wl,-z,relro,-z,now" "-Wl,--strip-debug" "-nodefaultlibs" - = note: rust-lld: error: undefined symbol: getauxval - >>> referenced by stack_overflow.rs:237 (library/std/src/sys/pal/unix/stack_overflow.rs:237) - >>> std-d46578f9a4470f27.std.a54bcd08e7411830-cgu.0.rcgu.o:(std::sys::pal::unix::stack_overflow::imp::make_handler::h648b6dd35f16ad81) in archive /home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-d46578f9a4470f27.rlib - >>> referenced by stack_overflow.rs:237 (library/std/src/sys/pal/unix/stack_overflow.rs:237) - >>> std-d46578f9a4470f27.std.a54bcd08e7411830-cgu.0.rcgu.o:(std::sys::sync::once::futex::Once::call::h3caf211f3255e91f) in archive /home/conda/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-d46578f9a4470f27.rlib - collect2: error: ld returned 1 exit status - - - error: could not compile libc (build script) due to 1 previous error - maturin failed - Caused by: Failed to build a native library through cargo - Caused by: Cargo build finished with "exit status: 101": env -u CARGO PYO3_ENVIRONMENT_SIGNATURE="cpython-3.10-64bit" PYO3_PYTHON="/opt/conda/conda-bld/kcounter_1717952336381/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python" PYTHON_SYS_EXECUTABLE="/opt/conda/conda-bld/kcounter_1717952336381/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python" "cargo" "rustc" "--message-format" "json-render-diagnostics" "--manifest-path" "/opt/conda/conda-bld/kcounter_1717952336381/work/Cargo.toml" "--release" "--lib" - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/kcounter_1717952336381/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. -category: |- - compiler error diff --git a/recipes/kcounter/meta.yaml b/recipes/kcounter/meta.yaml index 4f981cb3b477c..71574a53cbdbb 100644 --- a/recipes/kcounter/meta.yaml +++ b/recipes/kcounter/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 7c837e29d62d1889379a8b6a3ad634a6aa5f0bc0459d5719597c87e046502528 build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/kfoots/meta.yaml b/recipes/kfoots/meta.yaml index 48487b1f245b0..3af12c050ce7b 100644 --- a/recipes/kfoots/meta.yaml +++ b/recipes/kfoots/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 80aabb683626e18239d0294ba534d6f26d9d451fe31c5e7233072fbcd838425a build: - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/khmer/build_failure.linux-64.yaml b/recipes/khmer/build_failure.linux-64.yaml index 9faa1c70a56c4..e5dd5e2e959c2 100644 --- a/recipes/khmer/build_failure.linux-64.yaml +++ b/recipes/khmer/build_failure.linux-64.yaml @@ -1,18 +1,107 @@ -recipe_sha: 27b4bbe98422ab7e905e27f1693fcc531b4fe44fc7ec6d8fd817fe958e90da78 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 9d12f52be335376dd4b7ec581b95d975a87fc19107787c6c9190dc1e14efff63 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- - 01:00:23 BIOCONDA INFO (OUT) /opt/conda/conda-bld/khmer_1721696148356/_build_env/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/conda-bld/khmer_1721696148356/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include -fPIC -O2 -isystem /opt/conda/conda-bld/khmer_1721696148356/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/conda-bld/khmer_1721696148356/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include -fdebug-prefix-map=/opt/conda/conda-bld/khmer_1721696148356/work=/usr/local/src/conda/khmer-3.0.0a3 -fdebug-prefix-map=/opt/conda/conda-bld/khmer_1721696148356/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/conda-bld/khmer_1721696148356/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include -fPIC -DVERSION=3.0.0a3 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -Ithird-party/cqf -Ithird-party/rollinghash -I/opt/conda/conda-bld/khmer_1721696148356/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/python3.11 -c khmer/_oxli/graphs.cpp -o build/temp.linux-x86_64-cpython-311/khmer/_oxli/graphs.o -O3 -std=c++11 -fopenmp - 01:00:23 BIOCONDA INFO (OUT) khmer/_oxli/graphs.cpp:196:12: fatal error: longintrepr.h: No such file or directory - 01:00:23 BIOCONDA INFO (OUT) 196 | #include "longintrepr.h" - 01:00:23 BIOCONDA INFO (OUT) | ^~~~~~~~~~~~~~~ - 01:00:23 BIOCONDA INFO (OUT) compilation terminated. - 01:00:23 BIOCONDA INFO (OUT) error: command '/opt/conda/conda-bld/khmer_1721696148356/_build_env/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1 - 01:00:24 BIOCONDA INFO (OUT) error: subprocess-exited-with-error - 01:00:24 BIOCONDA INFO (OUT) - 01:00:24 BIOCONDA INFO (OUT) python setup.py bdist_wheel did not run successfully. - 01:00:24 BIOCONDA INFO (OUT) │ exit code: 1 - 01:00:24 BIOCONDA INFO (OUT) ╰─> See above for output. -reason: |- - breaks in nightly build + [34m [0m + [34m try:[0m + [34m import setuptools[0m + [34m except ImportError as error:[0m + [34m print([0m + [34m "ERROR: Can not execute setup.py since setuptools is not available in "[0m + [34m "the build environment.",[0m + [34m file=sys.stderr,[0m + [34m )[0m + [34m sys.exit(1)[0m + [34m [0m + [34m __file__ = %r[0m + [34m sys.argv[0] = __file__[0m + [34m [0m + [34m if os.path.exists(__file__):[0m + [34m filename = __file__[0m + [34m with tokenize.open(__file__) as f:[0m + [34m setup_py_code = f.read()[0m + [34m else:[0m + [34m filename = ""[0m + [34m setup_py_code = "from setuptools import setup; setup()"[0m + [34m [0m + [34m exec(compile(setup_py_code, filename, "exec"))[0m + [34m '"'"''"'"''"'"' % ('"'"'/opt/conda/conda-bld/khmer_1736267490703/work/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-mmr4cgqo[0m + [1;35mcwd[0m: /opt/conda/conda-bld/khmer_1736267490703/work/ + Building wheel for khmer (setup.py): finished with status 'error' + [31m ERROR: Failed building wheel for khmer[0m[31m + [0m Running setup.py clean for khmer + Running command python setup.py clean + /opt/conda/conda-bld/khmer_1736267490703/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options + !! + + ******************************************************************************** + Usage of dash-separated 'include-dirs' will not be supported in future + versions. Please use the underscore name 'include_dirs' instead. + + By 2025-Mar-03, you need to update your project and remove deprecated calls + or your builds will no longer be supported. + + See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. + ******************************************************************************** + + !! + opt = self.warn_dash_deprecation(opt, section) + /opt/conda/conda-bld/khmer_1736267490703/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. + !! + + ******************************************************************************** + Requirements should be satisfied by a PEP 517 installer. + If you are using pip, you can try pip install --use-pep517. + ******************************************************************************** + + !! + dist.fetch_build_eggs(dist.setup_requires) + running clean + removing 'build/temp.linux-x86_64-cpython-311' (and everything under it) + removing 'build/lib.linux-x86_64-cpython-311' (and everything under it) + 'build/bdist.linux-x86_64' does not exist -- can't clean it + 'build/scripts-3.11' does not exist -- can't clean it + removing 'build' + Failed to build khmer + [31mERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (khmer)[0m[31m + [0mException information: + Traceback (most recent call last): + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + ^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper + return func(self, options, args) + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/commands/install.py", line 434, in run + raise InstallationError( + pip._internal.exceptions.InstallationError: ERROR: Failed to build installable wheels for some pyproject.toml based projects (khmer) + Removed build tracker: '/tmp/pip-build-tracker-f57x0fyg' + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/khmer_1736267490703/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/khmer_1736267490703/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. category: |- compiler error + diff --git a/recipes/khmer/build_failure.linux-aarch64.yaml b/recipes/khmer/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..2c9d9d86e06d2 --- /dev/null +++ b/recipes/khmer/build_failure.linux-aarch64.yaml @@ -0,0 +1,107 @@ +recipe_sha: 9d12f52be335376dd4b7ec581b95d975a87fc19107787c6c9190dc1e14efff63 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [34m import os, sys, tokenize[0m + [34m [0m + [34m try:[0m + [34m import setuptools[0m + [34m except ImportError as error:[0m + [34m print([0m + [34m "ERROR: Can not execute setup.py since setuptools is not available in "[0m + [34m "the build environment.",[0m + [34m file=sys.stderr,[0m + [34m )[0m + [34m sys.exit(1)[0m + [34m [0m + [34m __file__ = %r[0m + [34m sys.argv[0] = __file__[0m + [34m [0m + [34m if os.path.exists(__file__):[0m + [34m filename = __file__[0m + [34m with tokenize.open(__file__) as f:[0m + [34m setup_py_code = f.read()[0m + [34m else:[0m + [34m filename = ""[0m + [34m setup_py_code = "from setuptools import setup; setup()"[0m + [34m [0m + [34m exec(compile(setup_py_code, filename, "exec"))[0m + [34m '"'"''"'"''"'"' % ('"'"'/opt/conda/conda-bld/khmer_1736268211862/work/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-qbhy3034[0m + [1;35mcwd[0m: /opt/conda/conda-bld/khmer_1736268211862/work/ + Building wheel for khmer (setup.py): finished with status 'error' + [31m ERROR: Failed building wheel for khmer[0m[31m + [0m Running setup.py clean for khmer + Running command python setup.py clean + /opt/conda/conda-bld/khmer_1736268211862/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/setuptools/dist.py:488: SetuptoolsDeprecationWarning: Invalid dash-separated options + !! + + ******************************************************************************** + Usage of dash-separated 'include-dirs' will not be supported in future + versions. Please use the underscore name 'include_dirs' instead. + + By 2025-Mar-03, you need to update your project and remove deprecated calls + or your builds will no longer be supported. + + See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. + ******************************************************************************** + + !! + opt = self.warn_dash_deprecation(opt, section) + /opt/conda/conda-bld/khmer_1736268211862/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. + !! + + ******************************************************************************** + Requirements should be satisfied by a PEP 517 installer. + If you are using pip, you can try pip install --use-pep517. + ******************************************************************************** + + !! + dist.fetch_build_eggs(dist.setup_requires) + running clean + removing 'build/lib.linux-aarch64-cpython-311' (and everything under it) + 'build/bdist.linux-aarch64' does not exist -- can't clean it + 'build/scripts-3.11' does not exist -- can't clean it + removing 'build' + Failed to build khmer + [31mERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (khmer)[0m[31m + [0mException information: + Traceback (most recent call last): + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + ^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper + return func(self, options, args) + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/commands/install.py", line 434, in run + raise InstallationError( + pip._internal.exceptions.InstallationError: ERROR: Failed to build installable wheels for some pyproject.toml based projects (khmer) + Removed build tracker: '/tmp/pip-build-tracker-x1_x2z97' + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/khmer_1736268211862/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/khmer_1736268211862/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + compiler error + diff --git a/recipes/king/meta.yaml b/recipes/king/meta.yaml index 12d3005b91c51..43df16dc92f86 100644 --- a/recipes/king/meta.yaml +++ b/recipes/king/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 486e7e94dde16d427f9d3fc99a33fa3f72f67e2f61b7264b4579111c9fb95be3 build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/kissplice/build_failure.osx-64.yaml b/recipes/kissplice/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..ef261e89f83bd --- /dev/null +++ b/recipes/kissplice/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 8d341739d0a983a3f05ef88e82f8066b6648bb1cbf7a82c4ddd0f485a8338416 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bcalm==2.2.3=hd174df1_1"), MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']")} + Encountered problems while solving: + - package bcalm-2.2.3-hd174df1_1 requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + bcalm >=2.2.3 is installable with the potential options + bcalm 2.2.3 would require + zlib >=1.2.11,<1.3.0a0 , which can be installed; + bcalm 2.2.3 would require + libzlib >=1.2.13,<1.3.0a0 , which can be installed; + bcalm 2.2.3 would require + zlib >=1.2.13,<1.3.0a0 , which can be installed; + libzlib >=1.3.1,<2.0a0 is not installable because there are no viable options + libzlib 1.3.1 would require + zlib 1.3.1 *_0, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_1, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_2, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bcalm==2.2.3=hd174df1_1"), MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']")} + Encountered problems while solving: + - package bcalm-2.2.3-hd174df1_1 requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + bcalm >=2.2.3 is installable with the potential options + bcalm 2.2.3 would require + zlib >=1.2.11,<1.3.0a0 , which can be installed; + bcalm 2.2.3 would require + libzlib >=1.2.13,<1.3.0a0 , which can be installed; + bcalm 2.2.3 would require + zlib >=1.2.13,<1.3.0a0 , which can be installed; + libzlib >=1.3.1,<2.0a0 is not installable because there are no viable options + libzlib 1.3.1 would require + zlib 1.3.1 *_0, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_1, which conflicts with any installable versions previously reported; + libzlib 1.3.1 would require + zlib 1.3.1 *_2, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/kissplice/meta.yaml b/recipes/kissplice/meta.yaml index 68a80f573ed23..624c4f01a8c4e 100644 --- a/recipes/kissplice/meta.yaml +++ b/recipes/kissplice/meta.yaml @@ -10,7 +10,7 @@ source: sha256: "79fa50c8fdd83d5b1235fe5ac9293cd9aa241bb86b7badb3b524edd96b781380" build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} diff --git a/recipes/kma/meta.yaml b/recipes/kma/meta.yaml index 13fd1af05d5f3..6902e4d8fee32 100644 --- a/recipes/kma/meta.yaml +++ b/recipes/kma/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('kma', max_pin="x") }} diff --git a/recipes/kmc/meta.yaml b/recipes/kmc/meta.yaml index bd6b7d6c5e889..32672ab79ec7d 100644 --- a/recipes/kmc/meta.yaml +++ b/recipes/kmc/meta.yaml @@ -18,7 +18,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage("kmc", max_pin="x") }} diff --git a/recipes/kmer-jellyfish/meta.yaml b/recipes/kmer-jellyfish/meta.yaml index d349363ebfb1d..0bddeda8c49c0 100644 --- a/recipes/kmer-jellyfish/meta.yaml +++ b/recipes/kmer-jellyfish/meta.yaml @@ -10,7 +10,7 @@ source: sha256: ee032b57257948ca0f0610883099267572c91a635eecbd88ae5d8974c2430fcd build: - number: 4 + number: 5 skip: True # [py < 38] run_exports: - {{ pin_subpackage("kmer-jellyfish", max_pin="x") }} diff --git a/recipes/kmercamel/meta.yaml b/recipes/kmercamel/meta.yaml index 051d2eae13cd8..2a1b851b1f192 100644 --- a/recipes/kmercamel/meta.yaml +++ b/recipes/kmercamel/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('kmercamel', max_pin="x") }} diff --git a/recipes/kmergenie/meta.yaml b/recipes/kmergenie/meta.yaml index 6726681de11b8..8e9e5de2132dc 100644 --- a/recipes/kmergenie/meta.yaml +++ b/recipes/kmergenie/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 8 + number: 9 skip: True # [osx or py2k] source: diff --git a/recipes/libgtextutils/build_failure.osx-64.yaml b/recipes/kmerstream/build_failure.osx-64.yaml similarity index 56% rename from recipes/libgtextutils/build_failure.osx-64.yaml rename to recipes/kmerstream/build_failure.osx-64.yaml index cc0830e0314a5..8cbf2a83f835d 100644 --- a/recipes/libgtextutils/build_failure.osx-64.yaml +++ b/recipes/kmerstream/build_failure.osx-64.yaml @@ -1,59 +1,71 @@ -recipe_sha: 8b9c4c8d6ccd3d6985a52343529c7bb537f1bf86ed4b7346ceaf38eb39d19990 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 5f7bb1fc3ae0ffb781476cca956b98bab6ff1d1fdc5c18ee2949529980e5843e # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - configure: error: in /opt/mambaforge/envs/bioconda/conda-bld/libgtextutils_1717594491933/work': - configure: error: cannot run C compiled programs. - If you meant to cross compile, use --host'. - See config.log' for more details - Extracting download +log: |2- + - python + - scipy + - libzlib >=1.3.1,<2.0a0 + - zlib + - libcxx >=18 + test: + commands: + - KmerStream 2>&1 | grep "KmerStream 1.1" + - KmerStreamJoin 2>&1 | grep "KmerStreamJoin 1.1" + - KmerStreamEstimate.py 2>&1 | grep "estimate.py TSV-FILE" + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/kmerstream_1733870000728/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + Traceback (most recent call last): - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/libgtextutils/patch - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/libgtextutils/patch with args: File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in sys.exit(execute()) - ['-Np0', '-i', '/tmp/tmpoqzoa0ap/patch.native', '--binary'] - Patch analysis gives: - [[ RA--D0LOVE ]] - [[ patch ]] - - Key: - - R :: Reversible A :: Applicable - Y :: Build-prefix patch in use M :: Minimal, non-amalgamated - D :: Dry-runnable N :: Patch level (1 is preferred) - L :: Patch level not-ambiguous O :: Patch applies without offsets - V :: Patch applies without fuzz E :: Patch applies without emitting to stderr - - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/libgtextutils_1717594491933/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/libgtextutils_1717594491933/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree packages_from_this = build( - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/libgtextutils_1717594491933/_build_env - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/libgtextutils_1717594491933/work/conda_build.sh']' returned non-zero exit status 1. - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/libgtextutils_1717594491933/work + about: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + home: https://github.com/pmelsted/KmerStream + license: free software license + summary: Streaming algorithm for computing kmer statistics for massive genomics + datasets + extra: + copy_test_source_files: true + final: true + identifiers: + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/kmerstream_1733870000728/work/conda_build.sh']' returned non-zero exit status 2. + - biotools:kmerstream + - doi:10.1093/bioinformatics/btu713 + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/kmerstream_1733870000728/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/kmerstream_1733870000728/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/kmerstream_1733870000728/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/kmerstream_1733870000728/work INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as CC=x86_64-apple-darwin13.4.0-clang CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/libgtextutils-0.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kmerstream-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/libgtextutils-0.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kmerstream-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool LD=x86_64-apple-darwin13.4.0-ld @@ -61,7 +73,7 @@ log: |- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -70,7 +82,7 @@ log: |- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -85,20 +97,8 @@ log: |- INFO: activate_clangxx_osx-64.sh made the following environmental changes: CLANGXX=x86_64-apple-darwin13.4.0-clang CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/libgtextutils-0.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kmerstream-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/libgtextutils-0.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - checking for a BSD-compatible install... /usr/bin/install -c - checking whether build environment is sane... yes - checking for a thread-safe mkdir -p... config/install-sh -c -d - checking for gawk... no - checking for mawk... no - checking for nawk... no - checking for awk... awk - checking whether make sets $(MAKE)... yes - checking whether make supports nested variables... yes - checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang - checking whether the C compiler works... yes - checking for C compiler default output file name... a.out - checking for suffix of executables... + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kmerstream-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + x86_64-apple-darwin13.4.0-clang -c -pthread -Wall -Wno-reorder -Wno-header-guard -I. -DMAX_KMER_SIZE=64 -O3 -I$PREFIX/include -c -o KmerStream.o KmerStream.cpp # Last 100 lines of the build log. diff --git a/recipes/kmerstream/meta.yaml b/recipes/kmerstream/meta.yaml index a57162266cb1b..f1ba651acaf6e 100644 --- a/recipes/kmerstream/meta.yaml +++ b/recipes/kmerstream/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 5 + number: 6 source: url: https://github.com/pmelsted/KmerStream/archive/v{{ version }}.tar.gz diff --git a/recipes/knotinframe/meta.yaml b/recipes/knotinframe/meta.yaml index 0a92ed9f51886..1eec69bd6bdaf 100644 --- a/recipes/knotinframe/meta.yaml +++ b/recipes/knotinframe/meta.yaml @@ -10,7 +10,7 @@ source: url: https://github.com/jlab/fold-grammars/archive/{{ version }}.tar.gz build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('knotinframe', max_pin="x") }} diff --git a/recipes/kraken/meta.yaml b/recipes/kraken/meta.yaml index 376a3cbc865cc..bb79ca7799718 100644 --- a/recipes/kraken/meta.yaml +++ b/recipes/kraken/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 9 + number: 10 requirements: build: diff --git a/recipes/kraken2/meta.yaml b/recipes/kraken2/meta.yaml index 3b423e44c971c..f7411b38791fd 100644 --- a/recipes/kraken2/meta.yaml +++ b/recipes/kraken2/meta.yaml @@ -13,7 +13,7 @@ source: - Makefile.patch build: - number: 3 + number: 4 run_exports: - '{{ pin_subpackage(name, max_pin="x.x") }}' diff --git a/recipes/krakenuniq/build_failure.linux-64.yaml b/recipes/krakenuniq/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..5c53ad3583ca8 --- /dev/null +++ b/recipes/krakenuniq/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a3abdbe2f4950b71362539ffb909f6a9eb88afb3cd84c25fa00c888a11d6dae9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("perl-net-ssleay"), MatchSpec("perl-io-socket-ssl==2.075=pl5321hd8ed1ab_0")} + Encountered problems while solving: + - package perl-io-socket-ssl-2.075-pl5321hd8ed1ab_0 requires perl-net-ssleay, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mlibzlib >=1.3.1,<2.0a0 [0m is installable with the potential options + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_0[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [31mperl-libwww-perl[0m is not installable because it requires + [31mperl-net-http [ |>=6.07 |>=6.18 ][0m, which requires + [31mperl-io-socket-ssl[0m but there are no viable options + [31mperl-io-socket-ssl 2.075[0m would require + [31mperl-net-ssleay[0m but there are no viable options + [31mperl-net-ssleay 1.92[0m would require + [31mzlib >=1.2.12,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mperl-net-ssleay [1.72|1.74|...|1.92][0m conflicts with any installable versions previously reported; + [31mperl-io-socket-ssl [2.024|2.056|2.060|2.066|2.074][0m conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("perl-net-ssleay"), MatchSpec("perl-io-socket-ssl==2.075=pl5321hd8ed1ab_0")} + Encountered problems while solving: + - package perl-io-socket-ssl-2.075-pl5321hd8ed1ab_0 requires perl-net-ssleay, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mlibzlib >=1.3.1,<2.0a0 [0m is installable with the potential options + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_0[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [31mperl-libwww-perl[0m is not installable because it requires + [31mperl-net-http [ |>=6.07 |>=6.18 ][0m, which requires + [31mperl-io-socket-ssl[0m but there are no viable options + [31mperl-io-socket-ssl 2.075[0m would require + [31mperl-net-ssleay[0m but there are no viable options + [31mperl-net-ssleay 1.92[0m would require + [31mzlib >=1.2.12,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mperl-net-ssleay [1.72|1.74|...|1.92][0m conflicts with any installable versions previously reported; + [31mperl-io-socket-ssl [2.024|2.056|2.060|2.066|2.074][0m conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/krakenuniq/meta.yaml b/recipes/krakenuniq/meta.yaml index 579f9c222be81..2a1d5576bd904 100644 --- a/recipes/krakenuniq/meta.yaml +++ b/recipes/krakenuniq/meta.yaml @@ -14,7 +14,7 @@ source: build: skip: true # [osx] - number: 2 + number: 3 run_exports: - {{ pin_subpackage('krakenuniq', max_pin="x.x") }} diff --git a/recipes/krbalancing/meta.yaml b/recipes/krbalancing/meta.yaml index d511ecac5eced..ff2d434660fea 100644 --- a/recipes/krbalancing/meta.yaml +++ b/recipes/krbalancing/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 890dee5c98d2037a2d19ba1fc3f700744858e7b22c61b40c714629125e65f464 build: - number: 9 + number: 10 run_exports: - {{ pin_subpackage('krbalancing', max_pin="x.x") }} diff --git a/recipes/kronik/meta.yaml b/recipes/kronik/meta.yaml index 6714d1ed26744..d421de6999a49 100644 --- a/recipes/kronik/meta.yaml +++ b/recipes/kronik/meta.yaml @@ -9,7 +9,7 @@ source: sha256: fb3c7cc92d6c65c76ce61fac2c7bf19c3ac1d4f3af377656122e4db10ca4b5dd build: - number: 6 + number: 7 skipt: True # [osx] requirements: diff --git a/recipes/kseqpp/meta.yaml b/recipes/kseqpp/meta.yaml index 595e642475766..101fd61ff02c6 100644 --- a/recipes/kseqpp/meta.yaml +++ b/recipes/kseqpp/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 80d5da09f725517fe27c13bbc3efea55735ef426ffe086fd0544e18e670190be build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/ksnp/meta.yaml b/recipes/ksnp/meta.yaml index 779b2287a50b2..05fe95d6a0b15 100644 --- a/recipes/ksnp/meta.yaml +++ b/recipes/ksnp/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 78975c007919b12af7a61a27d66347228a43ea223d59e37aad5ce7ae691a0569 build: - number: 1 + number: 2 python: 3.7 run_exports: - {{ pin_subpackage("ksnp", max_pin="x") }} diff --git a/recipes/kssd/meta.yaml b/recipes/kssd/meta.yaml index e7e4517b17806..11b7062d29a0b 100644 --- a/recipes/kssd/meta.yaml +++ b/recipes/kssd/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 2f6217b6e685dbe15c9aa4fa9a7eeb225651eb608f34799efea4ce84e2d0fd86 build: - number: 2 + number: 3 skip: True # [not linux] requirements: diff --git a/recipes/ksw/build_failure.linux-64.yaml b/recipes/ksw/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..b5cbab88fa71d --- /dev/null +++ b/recipes/ksw/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 29b509f619766cba70d3d92ca35c9c20ff12406c9c26f683c05c68b197fa019f # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + -- Looking for stdint.h + -- Looking for stdint.h - found + -- Looking for stddef.h + -- Looking for stddef.h - found + -- Check size of int + -- Check size of int - done + -- Check size of int8_t + -- Check size of int8_t - done + -- Check size of int16_t + -- Check size of int16_t - done + -- Check size of int32_t + -- Check size of int32_t - done + -- Check size of int64_t + -- Check size of int64_t - done + -- Check size of uint8_t + -- Check size of uint8_t - done + -- Check size of uint16_t + -- Check size of uint16_t - done + -- Check size of uint32_t + -- Check size of uint32_t - done + -- Check size of uint64_t + -- Check size of uint64_t - done + -- Performing Test HAVE___BUILTIN_CPU_INIT + -- Performing Test HAVE___BUILTIN_CPU_INIT - Success + -- Performing Test HAVE___BUILTIN_CPU_SUPPORTS + -- Performing Test HAVE___BUILTIN_CPU_SUPPORTS - Success + -- Performing Test HAVE_RESTRICT + -- Performing Test HAVE_RESTRICT - Success + -- Performing Test HAVE_INLINE_NATIVE + -- Performing Test HAVE_INLINE_NATIVE - Success + -- Looking for sys/mman.h + -- Looking for sys/mman.h - found + -- Looking for unistd.h + -- Looking for unistd.h - found + -- Looking for windows.h + -- Looking for windows.h - not found + -- Looking for _aligned_malloc + -- Looking for _aligned_malloc - not found + -- Looking for posix_memalign + -- Looking for posix_memalign - found + -- Looking for aligned_alloc + -- Looking for aligned_alloc - found + -- Looking for memalign + -- Looking for memalign - found + -- Looking for getopt + -- Looking for getopt - found + -- Looking for poll + -- Looking for poll - found + -- Looking for filelength + -- Looking for filelength - not found + -- Looking for GetSystemTimeAsFileTime + -- Looking for GetSystemTimeAsFileTime - not found + -- Looking for SetUnhandledExceptionFilter + -- Looking for SetUnhandledExceptionFilter - not found + -- Looking for clock_get_time + -- Looking for clock_get_time - not found + -- Looking for clock_gettime + -- Looking for clock_gettime - found + -- Looking for clock_gettime in rt + -- Looking for clock_gettime in rt - found + -- Looking for clock_gettime in pthread + -- Looking for clock_gettime in pthread - found + -- Looking for sqrt + -- Looking for sqrt - not found + -- Looking for sqrt in m + -- Looking for sqrt in m - found + -- Performing Test INT64_LITERAL_SUFFIX_I64 + -- Performing Test INT64_LITERAL_SUFFIX_I64 - Failed + -- Performing Test INT64_LITERAL_SUFFIX_LL + -- Performing Test INT64_LITERAL_SUFFIX_LL - Success + -- Performing Test HAVE_CLOCK_GETTIME_MONOTONIC + -- Performing Test HAVE_CLOCK_GETTIME_MONOTONIC - Success + -- Performing Test HAVE_CLOCK_GETTIME_REALTIME + -- Performing Test HAVE_CLOCK_GETTIME_REALTIME - Success + -- Configuring done (11.2s) + -- Generating done (0.3s) + -- Build files have been written to: $SRC_DIR/src/parasail/build + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ksw_1733853905160/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ksw_1733853905160/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/ksw/build_failure.osx-64.yaml b/recipes/ksw/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..0d28386e49bc1 --- /dev/null +++ b/recipes/ksw/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 29b509f619766cba70d3d92ca35c9c20ff12406c9c26f683c05c68b197fa019f # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + -- Try AltiVec C flag = [-maltivec] + -- Performing Test HAVE_ALTIVEC + -- Performing Test HAVE_ALTIVEC - Failed + -- Try AltiVec C flag = [-faltivec] + -- Performing Test HAVE_ALTIVEC + -- Performing Test HAVE_ALTIVEC - Failed + -- Could NOT find ALTIVEC (missing: ALTIVEC_C_FLAGS) + -- Try NEON C flag = [ ] + -- Performing Test HAVE_NEON + -- Performing Test HAVE_NEON - Failed + -- Try NEON C flag = [-mfpu=neon] + -- Performing Test HAVE_NEON + -- Performing Test HAVE_NEON - Failed + -- Try NEON C flag = [-mfpu=neon -mfloat-abi=softfp] + -- Performing Test HAVE_NEON + -- Performing Test HAVE_NEON - Failed + -- Could NOT find NEON (missing: NEON_C_FLAGS) + -- Found ZLIB: $PREFIX/lib/libz.dylib (found version "1.3.1") + -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) + -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) + -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) + -- Looking for sys/types.h + -- Looking for sys/types.h - found + -- Looking for stdint.h + -- Looking for stdint.h - found + -- Looking for stddef.h + -- Looking for stddef.h - found + -- Check size of int + -- Check size of int - done + -- Check size of int8_t + -- Check size of int8_t - done + -- Check size of int16_t + -- Check size of int16_t - done + -- Check size of int32_t + -- Check size of int32_t - done + -- Check size of int64_t + -- Check size of int64_t - done + -- Check size of uint8_t + -- Check size of uint8_t - done + -- Check size of uint16_t + -- Check size of uint16_t - done + -- Check size of uint32_t + -- Check size of uint32_t - done + -- Check size of uint64_t + -- Check size of uint64_t - done + -- Performing Test HAVE___BUILTIN_CPU_INIT + -- Performing Test HAVE___BUILTIN_CPU_INIT - Success + -- Performing Test HAVE___BUILTIN_CPU_SUPPORTS + -- Performing Test HAVE___BUILTIN_CPU_SUPPORTS - Success + -- Performing Test HAVE_RESTRICT + -- Performing Test HAVE_RESTRICT - Success + -- Performing Test HAVE_INLINE_NATIVE + -- Performing Test HAVE_INLINE_NATIVE - Success + -- Looking for sys/mman.h + -- Looking for sys/mman.h - found + -- Looking for unistd.h + -- Looking for unistd.h - found + -- Looking for windows.h + -- Looking for windows.h - not found + -- Looking for _aligned_malloc + -- Looking for _aligned_malloc - not found + -- Looking for posix_memalign + -- Looking for posix_memalign - found + -- Looking for aligned_alloc + -- Looking for aligned_alloc - not found + -- Looking for memalign + -- Looking for memalign - not found + -- Looking for getopt + -- Looking for getopt - found + -- Looking for poll + -- Looking for poll - found + -- Looking for filelength + -- Looking for filelength - not found + -- Looking for GetSystemTimeAsFileTime + -- Looking for GetSystemTimeAsFileTime - not found + -- Looking for SetUnhandledExceptionFilter + -- Looking for SetUnhandledExceptionFilter - not found + -- Looking for clock_get_time + -- Looking for clock_get_time - found + -- Looking for clock_gettime + -- Looking for clock_gettime - found + -- Looking for clock_gettime in rt + -- Looking for clock_gettime in rt - not found + -- Looking for clock_gettime in pthread + -- Looking for clock_gettime in pthread - found + -- Looking for sqrt + -- Looking for sqrt - found + -- Looking for sqrt in m + -- Looking for sqrt in m - found + -- Performing Test INT64_LITERAL_SUFFIX_I64 + -- Performing Test INT64_LITERAL_SUFFIX_I64 - Failed + -- Performing Test INT64_LITERAL_SUFFIX_LL + -- Performing Test INT64_LITERAL_SUFFIX_LL - Success + -- Performing Test HAVE_CLOCK_GETTIME_MONOTONIC + -- Performing Test HAVE_CLOCK_GETTIME_MONOTONIC - Success + -- Performing Test HAVE_CLOCK_GETTIME_REALTIME + -- Performing Test HAVE_CLOCK_GETTIME_REALTIME - Success + -- Configuring done (31.1s) + -- Generating done (0.6s) + -- Build files have been written to: $SRC_DIR/src/parasail/build +# Last 100 lines of the build log. diff --git a/recipes/ksw/meta.yaml b/recipes/ksw/meta.yaml index ef7ffc9504f45..545d5957eddf0 100644 --- a/recipes/ksw/meta.yaml +++ b/recipes/ksw/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('ksw', max_pin="x") }} diff --git a/recipes/kyototycoon/meta.yaml b/recipes/kyototycoon/meta.yaml index 185b95025e675..a1687b4f68738 100755 --- a/recipes/kyototycoon/meta.yaml +++ b/recipes/kyototycoon/meta.yaml @@ -11,7 +11,7 @@ source: - ktulog.patch build: - number: 4 + number: 5 skip: true # [osx] diff --git a/recipes/lambda/1.0.3/build_failure.osx-64.yaml b/recipes/lambda/1.0.3/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..7dc390e0d5036 --- /dev/null +++ b/recipes/lambda/1.0.3/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: b1465c444db93c5d16427e7cb402f933f7421eb8c4c37cbfd06beef445682283 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - clangxx_osx-64 18.1.8 h7e5c614_23 + - libedit 3.1.20191231 h0678c8f_2 + - llvm-openmp 18.1.8 h15ab845_1 + host: + - bzip2 1.0.8 hfdf4475_7 + - libcxx 19.1.5 hf95d169_0 + - llvm-openmp 19.1.5 ha54dae1_0 + - seqan-library 2.4.0 0 + - libzlib 1.3.1 hd23fc13_2 + - zlib 1.3.1 hd23fc13_2 + run: + - llvm-openmp >=19.1.5 + - llvm-openmp >=18.1.8 + - libzlib >=1.3.1,<2.0a0 + - bzip2 >=1.0.8,<2.0a0 + - libcxx >=18 + test: + commands: + - lambda --help + about: + home: http://seqan.github.io/lambda/ + license: GPLv3 + license_file: LICENSE-GPL3.rst + summary: Lambda is a local aligner optimized for many query sequences and searches + in protein space + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/lambda_1734458868802/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/lambda_1734458868802/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/lambda_1734458868802/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/lambda_1734458868802/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/lambda-1.0.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/lambda-1.0.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/lambda-1.0.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/lambda-1.0.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -- The CXX compiler identification is Clang 18.1.8 + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- These dependencies where found: + -- The requirements where met. + -- LAMBDA version is: 1.0.2 + -- The following options are selected for the build: + -- Run 'cmake -LH' to get a comment on each option. + -- Remove CMakeCache.txt and re-run cmake with -DOPTIONNAME=ON|OFF to change an option. + -- Configuring done (4.1s) + -- Generating done (0.1s) + -- Build files have been written to: $SRC_DIR/build + [ 25%] Building CXX object src/CMakeFiles/lambda.dir/lambda.cpp.o +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/lambda/1.0.3/meta.yaml b/recipes/lambda/1.0.3/meta.yaml index 90f3ceac53eb4..f6c728b570e90 100644 --- a/recipes/lambda/1.0.3/meta.yaml +++ b/recipes/lambda/1.0.3/meta.yaml @@ -11,7 +11,7 @@ source: - log2.patch build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/lambda/meta.yaml b/recipes/lambda/meta.yaml index 882b493ea719d..857699a82d3cf 100644 --- a/recipes/lambda/meta.yaml +++ b/recipes/lambda/meta.yaml @@ -9,7 +9,7 @@ source: sha256: fb3388e8b5a9f33f7423699803eaef4e6b9838c11017bd5b0d2b07f66491f191 build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('lambda', max_pin='x') }} diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index 79784544914b0..9e841233562c0 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 6d6b369399445cc7498e35ab518755418200a7d0fc5191a3ae2162057aa2e453 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('last', max_pin=None) }} diff --git a/recipes/lca/meta.yaml b/recipes/lca/meta.yaml index 2eddf97cb5016..b0b01b3b49884 100644 --- a/recipes/lca/meta.yaml +++ b/recipes/lca/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 6aead5585e87821a17c773a22bdba5229c6b7d0f44b06336b929a37c08992ce1 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name|lower, max_pin="x.x") }} diff --git a/recipes/ldblockshow/build_failure.linux-64.yaml b/recipes/ldblockshow/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0d26ac6012e6d --- /dev/null +++ b/recipes/ldblockshow/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 6e1e77c7def0c963e0ffd7d88b0714211c4f778b772ba92cdc198c090cfb9fff # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + 2024-12-14T07:12:41 noarch Writing index HTML + /opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (/opt/recipe/meta.yaml). + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml + Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for ldblockshow + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['ldblockshow-1.40-pl5321h077b44d_4.tar.bz2'] + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/ldblockshow_1734160361913/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-ng: 14.2.0-h69a702a_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libxcrypt: 4.4.36-hd590300_1 conda-forge + libzlib: 1.3.1-hb9d3cd8_2 conda-forge + perl: 5.32.1-7_hd590300_perl5 conda-forge + zlib: 1.3.1-hb9d3cd8_2 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/ldblockshow_1734160361913/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.43-h4bf12b8_2 conda-forge + binutils_linux-64: 2.43-h4852527_2 conda-forge + gcc_impl_linux-64: 13.3.0-hfea6d02_1 conda-forge + gcc_linux-64: 13.3.0-hc28eda2_7 conda-forge + gxx_impl_linux-64: 13.3.0-hdbfa832_1 conda-forge + gxx_linux-64: 13.3.0-h6834431_7 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libsanitizer: 13.3.0-heb74ff8_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + make: 4.4.1-hb9d3cd8_2 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: v1.40_b54395a3e4.tar.gz + Downloading https://github.com/BGI-shenzhen/LDBlockShow/archive/v1.40.tar.gz + Success + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 125, in download_to_cache + raise RuntimeError( + RuntimeError: SHA256 mismatch: '23d13cad65f915bd215e2a24b45b00382fe35e02e4c3cbbe4fd435671a4f0761' != 'b54395a3e494e7d211f8807cbd70a76dc6de826d7e7d8b376a15bf069987d142' +# Last 100 lines of the build log. diff --git a/recipes/ldblockshow/build_failure.osx-64.yaml b/recipes/ldblockshow/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..8e2c8eba76146 --- /dev/null +++ b/recipes/ldblockshow/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 6e1e77c7def0c963e0ffd7d88b0714211c4f778b772ba92cdc198c090cfb9fff # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/mambaforge/envs/bioconda/conda_build_config.yaml + Adding in variants from /opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for ldblockshow + Reloading output folder (local): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (local): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (local): ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['ldblockshow-1.40-pl5321h2ec61ea_4.tar.bz2'] + Reloading output folder (local): ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/ldblockshow_1734146780414/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + + + The following NEW packages will be INSTALLED: + + libcxx: 19.1.5-hf95d169_0 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + perl: 5.32.1-7_h10d778d_perl5 conda-forge + zlib: 1.3.1-hd23fc13_2 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (local): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (local): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/ldblockshow_1734146780414/_build_env + + + The following NEW packages will be INSTALLED: + + ca-certificates: 2024.8.30-h8857fd0_0 conda-forge + cctools_osx-64: 1010.6-h00edd4c_2 conda-forge + clang: 18.1.8-default_h179603d_5 conda-forge + clang-18: 18.1.8-default_h0c94c6a_5 conda-forge + clang_impl_osx-64: 18.1.8-h6a44ed1_23 conda-forge + clang_osx-64: 18.1.8-h7e5c614_23 conda-forge + clangxx: 18.1.8-default_h179603d_5 conda-forge + clangxx_impl_osx-64: 18.1.8-h4b7810f_23 conda-forge + clangxx_osx-64: 18.1.8-h7e5c614_23 conda-forge + compiler-rt: 18.1.8-h1020d70_1 conda-forge + compiler-rt_osx-64: 18.1.8-hf2b8a54_1 conda-forge + ld64_osx-64: 951.9-hc8d1a19_2 conda-forge + libclang-cpp18.1: 18.1.8-default_h0c94c6a_5 conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libcxx-devel: 18.1.8-h7c275be_7 conda-forge + libiconv: 1.17-hd75f5a5_2 conda-forge + libllvm18: 18.1.8-h9ce406d_2 conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libxml2: 2.13.5-he8ee3e7_1 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-tools: 18.1.8-h9ce406d_2 conda-forge + llvm-tools-18: 18.1.8-h9ce406d_2 conda-forge + make: 4.4.1-h00291cd_2 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + sigtool: 0.1.3-h88f4db0_0 conda-forge + tapi: 1300.6.5-h390ca13_0 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache + Downloading source to cache: v1.40_b54395a3e4.tar.gz + Downloading https://github.com/BGI-shenzhen/LDBlockShow/archive/v1.40.tar.gz + Success + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 125, in download_to_cache + raise RuntimeError( + RuntimeError: SHA256 mismatch: '23d13cad65f915bd215e2a24b45b00382fe35e02e4c3cbbe4fd435671a4f0761' != 'b54395a3e494e7d211f8807cbd70a76dc6de826d7e7d8b376a15bf069987d142' +# Last 100 lines of the build log. diff --git a/recipes/ldblockshow/meta.yaml b/recipes/ldblockshow/meta.yaml index 5e173c4d7c2cd..7195395fc3024 100644 --- a/recipes/ldblockshow/meta.yaml +++ b/recipes/ldblockshow/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 source: url: https://github.com/BGI-shenzhen/LDBlockShow/archive/v{{ version }}.tar.gz diff --git a/recipes/ldhelmet/meta.yaml b/recipes/ldhelmet/meta.yaml index 394427b33ca4e..9df98a84642e1 100644 --- a/recipes/ldhelmet/meta.yaml +++ b/recipes/ldhelmet/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.10 build: - number: 7 + number: 8 skip: True # [osx] source: diff --git a/recipes/leviathan/meta.yaml b/recipes/leviathan/meta.yaml index eaee7e17a4d09..9872c0b74c024 100644 --- a/recipes/leviathan/meta.yaml +++ b/recipes/leviathan/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/leviosam/build_failure.linux-64.yaml b/recipes/leviosam/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..20a5b4fc73b27 --- /dev/null +++ b/recipes/leviosam/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 0b68a3318f1f5f300678671a239f1fb07e0e0f13b60aa4222abb3418d69096ea # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/leviosam-5.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/leviosam-5.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + -- The CXX compiler identification is GNU 13.3.0 + -- The C compiler identification is GNU 13.3.0 + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - skipped + -- Detecting C compile features + -- Detecting C compile features - done + type + CMake Warning (dev) at CMakeLists.txt:83 (EXEC_PROGRAM): + Policy CMP0153 is not set: The exec_program command should not be called. + Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy + command to set the policy and suppress this warning. + + Use execute_process() instead. + Call Stack (most recent call first): + CMakeLists.txt:154 (FindSSE) + This warning is for project developers. Use -Wno-dev to suppress it. + + CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): + Compatibility with CMake < 3.10 will be removed from a future version of + CMake. + + Update the VERSION argument value. Or, use the ... syntax + to tell CMake that the project requires at least but has been updated + to work with policies introduced by or earlier. + + + -- Configuring done (0.0s) + -- Generating done (0.0s) + -- Build files have been written to: $SRC_DIR/build/googletest-download + [ 11%] Creating directories for 'googletest' + [ 22%] Performing download step (git clone) for 'googletest' + Cloning into 'googletest-src'... + Already on 'main' + Your branch is up to date with 'origin/main'. + [ 33%] Performing update step for 'googletest' + -- Fetching latest from the remote origin + [ 44%] No patch step for 'googletest' + [ 55%] No configure step for 'googletest' + [ 66%] No build step for 'googletest' + [ 77%] No install step for 'googletest' + [ 88%] No test step for 'googletest' + [100%] Completed 'googletest' + [100%] Built target googletest + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed + -- Looking for pthread_create in pthreads + -- Looking for pthread_create in pthreads - not found + -- Looking for pthread_create in pthread + -- Looking for pthread_create in pthread - found + -- Found Threads: TRUE + -- Configuring done (3.3s) + -- Generating done (0.0s) + -- Build files have been written to: $SRC_DIR/build + [ 4%] Building CXX object CMakeFiles/lvsam.dir/src/aln.cpp.o + [ 8%] Building C object CMakeFiles/lvsam.dir/src/bam_aux.c.o + [ 12%] Building C object CMakeFiles/lvsam.dir/src/bam_md.c.o + [ 16%] Building CXX object CMakeFiles/lvsam.dir/src/bed.cpp.o + In file included from /opt/conda/conda-bld/leviosam_1734241373723/work/src/leviosam_utils.hpp:22, + from /opt/conda/conda-bld/leviosam_1734241373723/work/src/bed.cpp:12: + /opt/conda/conda-bld/leviosam_1734241373723/work/src/gzstream.h:35:10: fatal error: zlib.h: No such file or directory + 35 | #include + | ^~~~~~~~ + compilation terminated. + make[2]: *** [CMakeFiles/lvsam.dir/build.make:121: CMakeFiles/lvsam.dir/src/bed.cpp.o] Error 1 + make[1]: *** [CMakeFiles/Makefile2:163: CMakeFiles/lvsam.dir/all] Error 2 + make: *** [Makefile:146: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/leviosam_1734241373723/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/leviosam_1734241373723/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/leviosam/meta.yaml b/recipes/leviosam/meta.yaml index d710b932f1093..e0ed539471164 100644 --- a/recipes/leviosam/meta.yaml +++ b/recipes/leviosam/meta.yaml @@ -9,7 +9,7 @@ source: sha256: ba57a16da7e32126a950e03b50c12e89d875971c0c9497c8d91053b66aeecb93 build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/leviosam2/meta.yaml b/recipes/leviosam2/meta.yaml index d833f8fd73168..988173dfb8d3d 100644 --- a/recipes/leviosam2/meta.yaml +++ b/recipes/leviosam2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 5829b1565702887aefab78aaba06687724fb229e27e5d7f1244746d9e1744163 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('leviosam2', max_pin="x.x") }} diff --git a/recipes/libbambamc/0.5.00/meta.yaml b/recipes/libbambamc/0.5.00/meta.yaml index 5c72f2f0c54f5..aa1c787cd7210 100644 --- a/recipes/libbambamc/0.5.00/meta.yaml +++ b/recipes/libbambamc/0.5.00/meta.yaml @@ -7,7 +7,7 @@ source: url: https://github.com/gt1/bambamc/archive/0.0.50-release-20140430085950.tar.gz build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('libbambamc', max_pin='x.x') }} diff --git a/recipes/libbigwig/meta.yaml b/recipes/libbigwig/meta.yaml index 1dd557e47859e..b41d1a6d11c9a 100644 --- a/recipes/libbigwig/meta.yaml +++ b/recipes/libbigwig/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 6 + number: 7 run_exports: - {{ pin_subpackage('libbigwig', max_pin='x.x') }} @@ -39,4 +39,4 @@ test: extra: additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 diff --git a/recipes/libcifpp/meta.yaml b/recipes/libcifpp/meta.yaml index c1e89d66c0293..a839278007d75 100644 --- a/recipes/libcifpp/meta.yaml +++ b/recipes/libcifpp/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} diff --git a/recipes/libdivsufsort/meta.yaml b/recipes/libdivsufsort/meta.yaml index 027973b1c178a..13e816f63fafb 100644 --- a/recipes/libdivsufsort/meta.yaml +++ b/recipes/libdivsufsort/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 9 + number: 10 run_exports: - {{ pin_subpackage('libdivsufsort', max_pin='x.x') }} @@ -35,4 +35,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/libgab/meta.yaml b/recipes/libgab/meta.yaml index cda514e4fd3d8..bd22087416a6b 100644 --- a/recipes/libgab/meta.yaml +++ b/recipes/libgab/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 04bd27813e3c001f64d06bee4524502e99f0f80e4a0882ffcead8770b7b2a2da build: - number: 14 + number: 15 skip: True # [osx] run_exports: - {{ pin_subpackage('libgab', max_pin='x.x') }} diff --git a/recipes/libgenome/meta.yaml b/recipes/libgenome/meta.yaml index 99dc1e86f49b1..cb557c6aa6139 100644 --- a/recipes/libgenome/meta.yaml +++ b/recipes/libgenome/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 7 + number: 8 skip: True # [osx] run_exports: - {{ pin_subpackage('libgenome', max_pin='x.x') }} diff --git a/recipes/libgff/build_failure.osx-64.yaml b/recipes/libgff/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..90be7e4dfbdce --- /dev/null +++ b/recipes/libgff/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a1e532785d924b47cb965111e65057a463c3d2643b55bb78b013d6914de1e848 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/libgff-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/libgff-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/libgff-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/libgff-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -- The C compiler identification is Clang 18.1.8 + -- The CXX compiler identification is Clang 18.1.8 + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped + -- Detecting C compile features + -- Detecting C compile features - done + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Install prefix : $PREFIX + -- Configuring done (4.1s) + -- Generating done (0.0s) + -- Build files have been written to: $SRC_DIR/build + Change Dir: '$SRC_DIR/build' + + Run Build Command(s): $BUILD_PREFIX/bin/cmake -E env VERBOSE=1 $BUILD_PREFIX/bin/make -f Makefile -j2 install + $BUILD_PREFIX/bin/cmake -S$SRC_DIR -B$SRC_DIR/build --check-build-system CMakeFiles/Makefile.cmake 0 + $BUILD_PREFIX/bin/cmake -E cmake_progress_start $SRC_DIR/build/CMakeFiles $SRC_DIR/build//CMakeFiles/progress.marks + $BUILD_PREFIX/bin/make -f CMakeFiles/Makefile2 all + make[1]: Entering directory '$SRC_DIR/build' + $BUILD_PREFIX/bin/make -f CMakeFiles/gff.dir/build.make CMakeFiles/gff.dir/depend + make[2]: Entering directory '$SRC_DIR/build' + cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR $SRC_DIR/build $SRC_DIR/build $SRC_DIR/build/CMakeFiles/gff.dir/DependInfo.cmake "--color=" + make[2]: Leaving directory '$SRC_DIR/build' + $BUILD_PREFIX/bin/make -f CMakeFiles/gff.dir/build.make CMakeFiles/gff.dir/build + make[2]: Entering directory '$SRC_DIR/build' + [ 9%] Building CXX object CMakeFiles/gff.dir/src/GArgs.cpp.o + [ 18%] Building CXX object CMakeFiles/gff.dir/src/codons.cpp.o + $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/libgff-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wall -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -std=c14 -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -MD -MT CMakeFiles/gff.dir/src/GArgs.cpp.o -MF CMakeFiles/gff.dir/src/GArgs.cpp.o.d -o CMakeFiles/gff.dir/src/GArgs.cpp.o -c $SRC_DIR/src/GArgs.cpp + $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/libgff-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wall -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -std=c14 -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -MD -MT CMakeFiles/gff.dir/src/codons.cpp.o -MF CMakeFiles/gff.dir/src/codons.cpp.o.d -o CMakeFiles/gff.dir/src/codons.cpp.o -c $SRC_DIR/src/codons.cpp + [ 27%] Building CXX object CMakeFiles/gff.dir/src/GBase.cpp.o + $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/libgff-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wall -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -std=c14 -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -MD -MT CMakeFiles/gff.dir/src/GBase.cpp.o -MF CMakeFiles/gff.dir/src/GBase.cpp.o.d -o CMakeFiles/gff.dir/src/GBase.cpp.o -c $SRC_DIR/src/GBase.cpp + [ 36%] Building CXX object CMakeFiles/gff.dir/src/gdna.cpp.o + $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/libgff-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wall -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -std=c14 -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -MD -MT CMakeFiles/gff.dir/src/gdna.cpp.o -MF CMakeFiles/gff.dir/src/gdna.cpp.o.d -o CMakeFiles/gff.dir/src/gdna.cpp.o -c $SRC_DIR/src/gdna.cpp + [ 45%] Building CXX object CMakeFiles/gff.dir/src/GFaSeqGet.cpp.o + $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/libgff-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wall -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -std=c14 -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -MD -MT CMakeFiles/gff.dir/src/GFaSeqGet.cpp.o -MF CMakeFiles/gff.dir/src/GFaSeqGet.cpp.o.d -o CMakeFiles/gff.dir/src/GFaSeqGet.cpp.o -c $SRC_DIR/src/GFaSeqGet.cpp + [ 54%] Building CXX object CMakeFiles/gff.dir/src/GFastaIndex.cpp.o + $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/libgff-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wall -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -std=c14 -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -MD -MT CMakeFiles/gff.dir/src/GFastaIndex.cpp.o -MF CMakeFiles/gff.dir/src/GFastaIndex.cpp.o.d -o CMakeFiles/gff.dir/src/GFastaIndex.cpp.o -c $SRC_DIR/src/GFastaIndex.cpp + [ 63%] Building CXX object CMakeFiles/gff.dir/src/gff.cpp.o + $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/libgff-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wall -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -std=c14 -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -MD -MT CMakeFiles/gff.dir/src/gff.cpp.o -MF CMakeFiles/gff.dir/src/gff.cpp.o.d -o CMakeFiles/gff.dir/src/gff.cpp.o -c $SRC_DIR/src/gff.cpp + [ 72%] Building CXX object CMakeFiles/gff.dir/src/GStr.cpp.o + $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -I$SRC_DIR/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/libgff-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wall -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -std=c14 -isysroot /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -mmacosx-version-min=10.13 -MD -MT CMakeFiles/gff.dir/src/GStr.cpp.o -MF CMakeFiles/gff.dir/src/GStr.cpp.o.d -o CMakeFiles/gff.dir/src/GStr.cpp.o -c $SRC_DIR/src/GStr.cpp + [ 81%] Linking CXX static library libgff.a + $BUILD_PREFIX/bin/cmake -P CMakeFiles/gff.dir/cmake_clean_target.cmake + $BUILD_PREFIX/bin/cmake -E cmake_link_script CMakeFiles/gff.dir/link.txt --verbose=1 + $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar qc libgff.a CMakeFiles/gff.dir/src/codons.cpp.o CMakeFiles/gff.dir/src/GArgs.cpp.o CMakeFiles/gff.dir/src/GBase.cpp.o CMakeFiles/gff.dir/src/gdna.cpp.o CMakeFiles/gff.dir/src/GFaSeqGet.cpp.o CMakeFiles/gff.dir/src/GFastaIndex.cpp.o CMakeFiles/gff.dir/src/gff.cpp.o CMakeFiles/gff.dir/src/GStr.cpp.o + $BUILD_PREFIX/bin/llvm-ranlib libgff.a + make[2]: Leaving directory '$SRC_DIR/build' + make[1]: Leaving directory '$SRC_DIR/build' +# Last 100 lines of the build log. diff --git a/recipes/libgff/meta.yaml b/recipes/libgff/meta.yaml index aeca79f5a22da..21eee39d493fc 100644 --- a/recipes/libgff/meta.yaml +++ b/recipes/libgff/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('libgff', max_pin='x') }} diff --git a/recipes/libgtextutils/meta.yaml b/recipes/libgtextutils/meta.yaml index 7305f1c72d85c..566659c851efd 100644 --- a/recipes/libgtextutils/meta.yaml +++ b/recipes/libgtextutils/meta.yaml @@ -12,7 +12,7 @@ source: - patch build: - number: 13 + number: 14 run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} @@ -36,4 +36,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/libidn/meta.yaml b/recipes/libidn/meta.yaml index 0d82dc20dd47c..b6dbe8ade615b 100644 --- a/recipes/libidn/meta.yaml +++ b/recipes/libidn/meta.yaml @@ -14,7 +14,7 @@ requirements: - {{ compiler('cxx') }} build: - number: 8 + number: 9 run_exports: - {{ pin_subpackage('libidn', max_pin='x.x') }} diff --git a/recipes/libmaus2/meta.yaml b/recipes/libmaus2/meta.yaml index 7a7a7f2f344b6..e4c8dff1f4364 100644 --- a/recipes/libmaus2/meta.yaml +++ b/recipes/libmaus2/meta.yaml @@ -10,7 +10,7 @@ package: build: # There's some issue with clang skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage('libmaus2', max_pin='x') }} diff --git a/recipes/libsbml/meta.yaml b/recipes/libsbml/meta.yaml index 1f1cc5e0af27c..6644628e82989 100644 --- a/recipes/libsbml/meta.yaml +++ b/recipes/libsbml/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('libsbml', max_pin='x.x') }} diff --git a/recipes/libsequence/build_failure.linux-64.yaml b/recipes/libsequence/build_failure.linux-64.yaml deleted file mode 100644 index b89d9ededc21a..0000000000000 --- a/recipes/libsequence/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 950218319b05117f649a224c4689e3993db070bb73859f2668fead45d8dab9e4 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - ../Sequence/SummStatsDeprecated/Snn.hpp:38:10: note: declared here - 38 | double Snn_statistic( const unsigned individuals[], - | ^~~~~~~~~~~~~ - ../Sequence/bits/Snn.tcc: In function 'std::vector > Sequence::Snn_test_pairwise_details(const PolyTable&, const unsigned int*, const size_t&, shuffler&, const unsigned int&)': - ../Sequence/bits/Snn.tcc:112:50: warning: 'double Sequence::Snn_statistic(const unsigned int*, const std::vector >&, const unsigned int*, const size_t&, const unsigned int&)' is deprecated [-Wdeprecated-declarations] - 112 | const double observed = Snn_statistic( &individuals[0],dkj,_config,2, - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 113 | _config[0]_config[1]); - | ~~~~~~~~~~~~~~~~~~~~~~ - ../Sequence/SummStatsDeprecated/Snn.hpp:38:10: note: declared here - 38 | double Snn_statistic( const unsigned individuals[], - | ^~~~~~~~~~~~~ - ../Sequence/bits/Snn.tcc:119:44: warning: 'double Sequence::Snn_statistic(const unsigned int*, const std::vector >&, const unsigned int*, const size_t&, const unsigned int&)' is deprecated [-Wdeprecated-declarations] - 119 | double perm = Snn_statistic( &individuals[0],dkj,_config,2, - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 120 | _config[0]_config[1]); - | ~~~~~~~~~~~~~~~~~~~~~~ - ../Sequence/SummStatsDeprecated/Snn.hpp:38:10: note: declared here - 38 | double Snn_statistic( const unsigned individuals[], - | ^~~~~~~~~~~~~ - libtool: compile: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT summstats_deprecated/Snn.lo -MD -MP -MF summstats_deprecated/.deps/Snn.Tpo -c summstats_deprecated/Snn.cc -o summstats_deprecated/Snn.o >/dev/null 2>&1 - depbase=echo polySiteVector.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||';\ - /bin/sh ../libtool --tag=CXX --mode=compile $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT polySiteVector.lo -MD -MP -MF $depbase.Tpo -c -o polySiteVector.lo polySiteVector.cc &&\ - mv -f $depbase.Tpo $depbase.Plo - libtool: compile: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT polySiteVector.lo -MD -MP -MF .deps/polySiteVector.Tpo -c polySiteVector.cc -fPIC -DPIC -o .libs/polySiteVector.o - In file included from polySiteVector.cc:24: - ../Sequence/PolyTable.hpp:238:59: warning: 'PolyTable' is deprecated [-Wdeprecated-declarations] - 238 | std::istream &operator>>(std::istream &s, PolyTable &c); - | ^ - ../Sequence/PolyTable.hpp:60:39: note: declared here - 60 | class __attribute__((deprecated)) PolyTable - | ^~~~~~~~~ - libtool: compile: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT polySiteVector.lo -MD -MP -MF .deps/polySiteVector.Tpo -c polySiteVector.cc -o polySiteVector.o >/dev/null 2>&1 - depbase=echo summstats_deprecated/SummStats.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||';\ - /bin/sh ../libtool --tag=CXX --mode=compile $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT summstats_deprecated/SummStats.lo -MD -MP -MF $depbase.Tpo -c -o summstats_deprecated/SummStats.lo summstats_deprecated/SummStats.cc &&\ - mv -f $depbase.Tpo $depbase.Plo - libtool: compile: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT summstats_deprecated/SummStats.lo -MD -MP -MF summstats_deprecated/.deps/SummStats.Tpo -c summstats_deprecated/SummStats.cc -fPIC -DPIC -o summstats_deprecated/.libs/SummStats.o - In file included from ../Sequence/SimData.hpp:65, - from summstats_deprecated/SummStats.cc:2: - ../Sequence/PolyTable.hpp:238:59: warning: 'PolyTable' is deprecated [-Wdeprecated-declarations] - 238 | std::istream &operator>>(std::istream &s, PolyTable &c); - | ^ - ../Sequence/PolyTable.hpp:60:39: note: declared here - 60 | class __attribute__((deprecated)) PolyTable - | ^~~~~~~~~ - ../Sequence/SimData.hpp:81:56: warning: 'PolyTable' is deprecated [-Wdeprecated-declarations] - 81 | const SimData::const_site_iterator &end); - | ^ - ../Sequence/PolyTable.hpp:60:39: note: declared here - 60 | class __attribute__((deprecated)) PolyTable - | ^~~~~~~~~ - ../Sequence/SimData.hpp:81:56: warning: 'PolyTable' is deprecated [-Wdeprecated-declarations] - 81 | const SimData::const_site_iterator &end); - | ^ - ../Sequence/PolyTable.hpp:60:39: note: declared here - 60 | class __attribute__((deprecated)) PolyTable - | ^~~~~~~~~ - ../Sequence/SimData.hpp:81:56: warning: 'PolyTable' is deprecated [-Wdeprecated-declarations] - 81 | const SimData::const_site_iterator &end); - | ^ - ../Sequence/PolyTable.hpp:60:39: note: declared here - 60 | class __attribute__((deprecated)) PolyTable - | ^~~~~~~~~ - ../Sequence/SimData.hpp:81:56: warning: 'PolyTable' is deprecated [-Wdeprecated-declarations] - 81 | const SimData::const_site_iterator &end); - | ^ - ../Sequence/PolyTable.hpp:60:39: note: declared here - 60 | class __attribute__((deprecated)) PolyTable - | ^~~~~~~~~ - summstats_deprecated/SummStats.cc: In function 'double Sequence::Gmin(const polySiteVector&, const std::vector&)': - summstats_deprecated/SummStats.cc:38:21: error: 'numeric_limits' was not declared in this scope - 38 | unsigned mdxy = numeric_limits::max(); - | ^~~~~~~~~~~~~~ - summstats_deprecated/SummStats.cc:38:36: error: expected primary-expression before 'unsigned' - 38 | unsigned mdxy = numeric_limits::max(); - | ^~~~~~~~ - make[2]: *** [Makefile:803: summstats_deprecated/SummStats.lo] Error 1 - make[1]: *** [Makefile:407: all-recursive] Error 1 - make: *** [Makefile:337: all] Error 2 - make[2]: Leaving directory '$SRC_DIR/src' - make[1]: Leaving directory '$SRC_DIR' - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/libsequence_1685480385020/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/libsequence/build_failure.osx-64.yaml b/recipes/libsequence/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..816e04bb8826f --- /dev/null +++ b/recipes/libsequence/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 5f5d9042a99ee15c4d5f5bade849896c1fb2598b587fd3ec9bebf7a68ac843f9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + checking if x86_64-apple-darwin13.4.0-clang supports -c -o file.o... (cached) yes + checking whether the x86_64-apple-darwin13.4.0-clang linker (x86_64-apple-darwin13.4.0-ld) supports shared libraries... yes + checking dynamic linker characteristics... darwin13.4.0 dyld + checking how to hardcode library paths into programs... immediate + checking whether stripping libraries is possible... yes + checking if libtool supports shared libraries... yes + checking whether to build shared libraries... yes + checking whether to build static libraries... yes + checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang -E + checking for ld used by x86_64-apple-darwin13.4.0-clang... x86_64-apple-darwin13.4.0-ld + checking if the linker (x86_64-apple-darwin13.4.0-ld) is GNU ld... no + checking whether the x86_64-apple-darwin13.4.0-clang linker (x86_64-apple-darwin13.4.0-ld) supports shared libraries... yes + checking for x86_64-apple-darwin13.4.0-clang option to produce PIC... -fno-common -DPIC + checking if x86_64-apple-darwin13.4.0-clang PIC flag -fno-common -DPIC works... yes + checking if x86_64-apple-darwin13.4.0-clang static flag -static works... no + checking if x86_64-apple-darwin13.4.0-clang supports -c -o file.o... yes + checking if x86_64-apple-darwin13.4.0-clang supports -c -o file.o... (cached) yes + checking whether the x86_64-apple-darwin13.4.0-clang linker (x86_64-apple-darwin13.4.0-ld) supports shared libraries... yes + checking dynamic linker characteristics... darwin13.4.0 dyld + checking how to hardcode library paths into programs... immediate + checking boost/test/unit_test.hpp usability... no + checking boost/test/unit_test.hpp presence... no + checking for boost/test/unit_test.hpp... no + boost/test/unit_test.hpp not found. Unit tests will not be compiled. + checking that generated files are newer than configure... done + configure: creating ./config.status + config.status: creating Makefile + config.status: creating src/Makefile + config.status: creating Sequence/Makefile + config.status: creating Sequence/bits/Makefile + config.status: creating Sequence/SummStatsDeprecated/Makefile + config.status: creating Sequence/variant_matrix/Makefile + config.status: creating Sequence/summstats/Makefile + config.status: creating test/Makefile + config.status: creating examples/Makefile + config.status: creating doc/libsequence.doxygen + config.status: creating config.h + config.status: executing depfiles commands + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + config.status: executing libtool commands + make all-recursive + make[1]: Entering directory '$SRC_DIR' + Making all in src + make[2]: Entering directory '$SRC_DIR/src' + depbase=echo libsequenceConfig.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT libsequenceConfig.o -MD -MP -MF $depbase.Tpo -c -o libsequenceConfig.o libsequenceConfig.cc &&\ + mv -f $depbase.Tpo $depbase.Po + depbase=echo Grantham.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||';\ + /bin/sh ../libtool --tag=CXX --mode=compile x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT Grantham.lo -MD -MP -MF $depbase.Tpo -c -o Grantham.lo Grantham.cc &&\ + mv -f $depbase.Tpo $depbase.Plo + libtool: compile: x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT Grantham.lo -MD -MP -MF .deps/Grantham.Tpo -c Grantham.cc -fno-common -DPIC -o .libs/Grantham.o + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + libtool: compile: x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT Grantham.lo -MD -MP -MF .deps/Grantham.Tpo -c Grantham.cc -o Grantham.o >/dev/null 2>&1 + depbase=echo PathwayHelper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||';\ + /bin/sh ../libtool --tag=CXX --mode=compile x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT PathwayHelper.lo -MD -MP -MF $depbase.Tpo -c -o PathwayHelper.lo PathwayHelper.cc &&\ + mv -f $depbase.Tpo $depbase.Plo + libtool: compile: x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT PathwayHelper.lo -MD -MP -MF .deps/PathwayHelper.Tpo -c PathwayHelper.cc -fno-common -DPIC -o .libs/PathwayHelper.o + depbase=echo SimParams.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||';\ + /bin/sh ../libtool --tag=CXX --mode=compile x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT SimParams.lo -MD -MP -MF $depbase.Tpo -c -o SimParams.lo SimParams.cc &&\ + mv -f $depbase.Tpo $depbase.Plo + libtool: compile: x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT PathwayHelper.lo -MD -MP -MF .deps/PathwayHelper.Tpo -c PathwayHelper.cc -o PathwayHelper.o >/dev/null 2>&1 + libtool: compile: x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT SimParams.lo -MD -MP -MF .deps/SimParams.Tpo -c SimParams.cc -fno-common -DPIC -o .libs/SimParams.o + depbase=echo Translate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||';\ + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/libsequence_1734535759508/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + /bin/sh ../libtool --tag=CXX --mode=compile x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT Translate.lo -MD -MP -MF $depbase.Tpo -c -o Translate.lo Translate.cc &&\ + mv -f $depbase.Tpo $depbase.Plo + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/libsequence_1734535759508/work/conda_build.sh']' returned non-zero exit status 2. + libtool: compile: x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT Translate.lo -MD -MP -MF .deps/Translate.Tpo -c Translate.cc -fno-common -DPIC -o .libs/Translate.o + libtool: compile: x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT SimParams.lo -MD -MP -MF .deps/SimParams.Tpo -c SimParams.cc -o SimParams.o >/dev/null 2>&1 + libtool: compile: x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT Translate.lo -MD -MP -MF .deps/Translate.Tpo -c Translate.cc -o Translate.o >/dev/null 2>&1 + depbase=echo Comeron95.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||';\ + /bin/sh ../libtool --tag=CXX --mode=compile x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT Comeron95.lo -MD -MP -MF $depbase.Tpo -c -o Comeron95.lo Comeron95.cc &&\ + mv -f $depbase.Tpo $depbase.Plo + depbase=echo GranthamWeights.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||';\ + /bin/sh ../libtool --tag=CXX --mode=compile x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT GranthamWeights.lo -MD -MP -MF $depbase.Tpo -c -o GranthamWeights.lo GranthamWeights.cc &&\ + mv -f $depbase.Tpo $depbase.Plo + libtool: compile: x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT Comeron95.lo -MD -MP -MF .deps/Comeron95.Tpo -c Comeron95.cc -fno-common -DPIC -o .libs/Comeron95.o + libtool: compile: x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT GranthamWeights.lo -MD -MP -MF .deps/GranthamWeights.Tpo -c GranthamWeights.cc -fno-common -DPIC -o .libs/GranthamWeights.o + libtool: compile: x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT GranthamWeights.lo -MD -MP -MF .deps/GranthamWeights.Tpo -c GranthamWeights.cc -o GranthamWeights.o >/dev/null 2>&1 + make[2]: Leaving directory '$SRC_DIR/src' + make[1]: Leaving directory '$SRC_DIR' +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/libsequence/meta.yaml b/recipes/libsequence/meta.yaml index 8237c0cdd1ce6..55d62cb63b046 100644 --- a/recipes/libsequence/meta.yaml +++ b/recipes/libsequence/meta.yaml @@ -13,7 +13,7 @@ source: - fix-build.patch build: - number: 6 + number: 7 run_exports: - {{ pin_subpackage('libsequence', max_pin='x.x') }} @@ -35,4 +35,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/libstatgen/meta.yaml b/recipes/libstatgen/meta.yaml index 4e56edc480495..4bf8f6b5e0885 100644 --- a/recipes/libstatgen/meta.yaml +++ b/recipes/libstatgen/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('libstatgen', max_pin='x.x') }} diff --git a/recipes/lightassembler/meta.yaml b/recipes/lightassembler/meta.yaml index 9bd4372236808..cf7a4386ab024 100644 --- a/recipes/lightassembler/meta.yaml +++ b/recipes/lightassembler/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.0 build: - number: 5 + number: 6 source: url: https://github.com/SaraEl-Metwally/LightAssembler/archive/v1.0.0.tar.gz diff --git a/recipes/lighter/meta.yaml b/recipes/lighter/meta.yaml index d53e24e3298d2..a2aa782c7279f 100644 --- a/recipes/lighter/meta.yaml +++ b/recipes/lighter/meta.yaml @@ -13,7 +13,7 @@ source: - 0001-makefile.patch build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('lighter', max_pin="x") }} diff --git a/recipes/lightstringgraph/meta.yaml b/recipes/lightstringgraph/meta.yaml index 09a8d1446e09d..1ba14789ba0f6 100644 --- a/recipes/lightstringgraph/meta.yaml +++ b/recipes/lightstringgraph/meta.yaml @@ -3,7 +3,7 @@ package: version: 0.4.0 build: - number: 6 + number: 7 skip: True # [osx] source: diff --git a/recipes/linearfold/meta.yaml b/recipes/linearfold/meta.yaml index 62e614174d93e..bb150a979f32c 100644 --- a/recipes/linearfold/meta.yaml +++ b/recipes/linearfold/meta.yaml @@ -8,7 +8,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage(name | lower, max_pin="x.x.x") }} diff --git a/recipes/linearpartition/meta.yaml b/recipes/linearpartition/meta.yaml index 7a42168cc778e..6507b4d785537 100644 --- a/recipes/linearpartition/meta.yaml +++ b/recipes/linearpartition/meta.yaml @@ -8,7 +8,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage(name | lower, max_pin="x.x.x") }} diff --git a/recipes/links/build_failure.linux-64.yaml b/recipes/links/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..3803868daa2f4 --- /dev/null +++ b/recipes/links/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 4372c269a67409b2563f3dc86d6c54701e5e6bd6d2a7234a55a1cb5bd12da860 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + InputParser.hpp: In constructor 'InputParser::InputParser(int&, char**)': + InputParser.hpp:170:9: error: 'k' was not declared in this scope + 170 | k = strtoul(optarg, &end, BASE_TEN); + | ^ + InputParser.hpp:180:9: error: 'offset' was not declared in this scope; did you mean 'off_t'? + 180 | offset = strtoul(optarg, &end, BASE_TEN); + | ^~~~~~ + | off_t + InputParser.hpp:186:9: error: 'min_links' was not declared in this scope + 186 | min_links = strtoul(optarg, &end, BASE_TEN); + | ^~~~~~~~~ + InputParser.hpp:192:9: error: 'min_size' was not declared in this scope + 192 | min_size = strtoul(optarg, &end, BASE_TEN); + | ^~~~~~~~ + InputParser.hpp:217:19: error: request for member 'size' in '((InputParser*)this)->InputParser::distances', which is of non-class type 'int' + 217 | if (distances.size() > step_sizes.size()) { + | ^~~~ + InputParser.hpp:217:39: error: request for member 'size' in '((InputParser*)this)->InputParser::step_sizes', which is of non-class type 'int' + 217 | if (distances.size() > step_sizes.size()) { + | ^~~~ + InputParser.hpp:218:35: error: request for member 'back' in '((InputParser*)this)->InputParser::step_sizes', which is of non-class type 'int' + 218 | uint last_step = step_sizes.back(); + | ^~~~ + InputParser.hpp:219:31: error: request for member 'size' in '((InputParser*)this)->InputParser::step_sizes', which is of non-class type 'int' + 219 | for (int i = step_sizes.size(); i < distances.size(); i) { + | ^~~~ + InputParser.hpp:219:53: error: request for member 'size' in '((InputParser*)this)->InputParser::distances', which is of non-class type 'int' + 219 | for (int i = step_sizes.size(); i < distances.size(); i) { + | ^~~~ + InputParser.hpp:220:20: error: request for member 'push_back' in '((InputParser*)this)->InputParser::step_sizes', which is of non-class type 'int' + 220 | step_sizes.push_back(last_step); + | ^~~~~~~~~ + InputParser.hpp:229:19: error: request for member 'size' in '((InputParser*)this)->InputParser::distances', which is of non-class type 'int' + 229 | if (distances.size() < step_sizes.size()) { + | ^~~~ + InputParser.hpp:229:39: error: request for member 'size' in '((InputParser*)this)->InputParser::step_sizes', which is of non-class type 'int' + 229 | if (distances.size() < step_sizes.size()) { + | ^~~~ + InputParser.hpp:238:26: error: 'k' was not declared in this scope + 238 | std::to_string(k) "_e" std::to_string(insert_stdev) "_l" + | ^ + InputParser.hpp:239:26: error: 'min_links' was not declared in this scope + 239 | std::to_string(min_links) "_a" std::to_string(max_link_ratio) + | ^~~~~~~~~ + InputParser.hpp:240:33: error: 'min_size' was not declared in this scope + 240 | "_z" std::to_string(min_size) "_t" step_sizes_text "_o" + | ^~~~~~~~ + InputParser.hpp:241:26: error: 'offset' was not declared in this scope; did you mean 'off_t'? + 241 | std::to_string(offset) "_r-" (bf_off ? "-" : bf_file) "_p" + | ^~~~~~ + | off_t + In file included from main.cpp:2: + LINKS.hpp: In member function 'btllib::KmerBloomFilter* LINKS::make_bf(uint64_t, InputParser)': + LINKS.hpp:312:53: error: 'class InputParser' has no member named 'k' + 312 | << "- kmersize: " << links_arg_parser.k << "\n" + | ^ + LINKS.hpp:321:64: error: 'class InputParser' has no member named 'k' + 321 | std::cout << "- Filter output file : " << links_arg_parser.k << "\n"; + | ^ + LINKS.hpp:323:71: error: 'class InputParser' has no member named 'k' + 323 | new btllib::KmerBloomFilter(m / 8, hash_fct, links_arg_parser.k); + | ^ + LINKS.hpp: In constructor 'LINKS::LINKS(InputParser)': + LINKS.hpp:343:22: error: 'class InputParser' has no member named 'k' + 343 | k(input_parser.k), verbose(input_parser.verbose), + | ^ + LINKS.hpp:344:29: error: 'class InputParser' has no member named 'min_size' + 344 | min_size(input_parser.min_size), step_sizes(input_parser.step_sizes), + | ^~~~~~~~ + LINKS.hpp:346:62: error: 'class InputParser' has no member named 'offset' + 346 | base_name(input_parser.base_name), offset(input_parser.offset), + | ^~~~~~ + make[2]: *** [Makefile:373: LINKS_CPP-main.o] Error 1 + make[2]: Leaving directory '$SRC_DIR/src' + make[1]: *** [Makefile:443: all-recursive] Error 1 + make[1]: Leaving directory '$SRC_DIR' + make: *** [Makefile:327: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/links_1734293262817/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/links_1734293262817/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/links/build_failure.linux-aarch64.yaml b/recipes/links/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..abff5fd7f2ecf --- /dev/null +++ b/recipes/links/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 4372c269a67409b2563f3dc86d6c54701e5e6bd6d2a7234a55a1cb5bd12da860 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + InputParser.hpp: In constructor 'InputParser::InputParser(int&, char**)': + InputParser.hpp:170:9: error: 'k' was not declared in this scope + 170 | k = strtoul(optarg, &end, BASE_TEN); + | ^ + InputParser.hpp:180:9: error: 'offset' was not declared in this scope; did you mean 'off_t'? + 180 | offset = strtoul(optarg, &end, BASE_TEN); + | ^~~~~~ + | off_t + InputParser.hpp:186:9: error: 'min_links' was not declared in this scope + 186 | min_links = strtoul(optarg, &end, BASE_TEN); + | ^~~~~~~~~ + InputParser.hpp:192:9: error: 'min_size' was not declared in this scope + 192 | min_size = strtoul(optarg, &end, BASE_TEN); + | ^~~~~~~~ + InputParser.hpp:217:19: error: request for member 'size' in '((InputParser*)this)->InputParser::distances', which is of non-class type 'int' + 217 | if (distances.size() > step_sizes.size()) { + | ^~~~ + InputParser.hpp:217:39: error: request for member 'size' in '((InputParser*)this)->InputParser::step_sizes', which is of non-class type 'int' + 217 | if (distances.size() > step_sizes.size()) { + | ^~~~ + InputParser.hpp:218:35: error: request for member 'back' in '((InputParser*)this)->InputParser::step_sizes', which is of non-class type 'int' + 218 | uint last_step = step_sizes.back(); + | ^~~~ + InputParser.hpp:219:31: error: request for member 'size' in '((InputParser*)this)->InputParser::step_sizes', which is of non-class type 'int' + 219 | for (int i = step_sizes.size(); i < distances.size(); i) { + | ^~~~ + InputParser.hpp:219:53: error: request for member 'size' in '((InputParser*)this)->InputParser::distances', which is of non-class type 'int' + 219 | for (int i = step_sizes.size(); i < distances.size(); i) { + | ^~~~ + InputParser.hpp:220:20: error: request for member 'push_back' in '((InputParser*)this)->InputParser::step_sizes', which is of non-class type 'int' + 220 | step_sizes.push_back(last_step); + | ^~~~~~~~~ + InputParser.hpp:229:19: error: request for member 'size' in '((InputParser*)this)->InputParser::distances', which is of non-class type 'int' + 229 | if (distances.size() < step_sizes.size()) { + | ^~~~ + InputParser.hpp:229:39: error: request for member 'size' in '((InputParser*)this)->InputParser::step_sizes', which is of non-class type 'int' + 229 | if (distances.size() < step_sizes.size()) { + | ^~~~ + InputParser.hpp:238:26: error: 'k' was not declared in this scope + 238 | std::to_string(k) "_e" std::to_string(insert_stdev) "_l" + | ^ + InputParser.hpp:239:26: error: 'min_links' was not declared in this scope + 239 | std::to_string(min_links) "_a" std::to_string(max_link_ratio) + | ^~~~~~~~~ + InputParser.hpp:240:33: error: 'min_size' was not declared in this scope + 240 | "_z" std::to_string(min_size) "_t" step_sizes_text "_o" + | ^~~~~~~~ + InputParser.hpp:241:26: error: 'offset' was not declared in this scope; did you mean 'off_t'? + 241 | std::to_string(offset) "_r-" (bf_off ? "-" : bf_file) "_p" + | ^~~~~~ + | off_t + In file included from main.cpp:2: + LINKS.hpp: In member function 'btllib::KmerBloomFilter* LINKS::make_bf(uint64_t, InputParser)': + LINKS.hpp:312:53: error: 'class InputParser' has no member named 'k' + 312 | << "- kmersize: " << links_arg_parser.k << "\n" + | ^ + LINKS.hpp:321:64: error: 'class InputParser' has no member named 'k' + 321 | std::cout << "- Filter output file : " << links_arg_parser.k << "\n"; + | ^ + LINKS.hpp:323:71: error: 'class InputParser' has no member named 'k' + 323 | new btllib::KmerBloomFilter(m / 8, hash_fct, links_arg_parser.k); + | ^ + LINKS.hpp: In constructor 'LINKS::LINKS(InputParser)': + LINKS.hpp:343:22: error: 'class InputParser' has no member named 'k' + 343 | k(input_parser.k), verbose(input_parser.verbose), + | ^ + LINKS.hpp:344:29: error: 'class InputParser' has no member named 'min_size' + 344 | min_size(input_parser.min_size), step_sizes(input_parser.step_sizes), + | ^~~~~~~~ + LINKS.hpp:346:62: error: 'class InputParser' has no member named 'offset' + 346 | base_name(input_parser.base_name), offset(input_parser.offset), + | ^~~~~~ + make[2]: *** [Makefile:373: LINKS_CPP-main.o] Error 1 + make[2]: Leaving directory '$SRC_DIR/src' + make[1]: *** [Makefile:443: all-recursive] Error 1 + make[1]: Leaving directory '$SRC_DIR' + make: *** [Makefile:327: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/links_1734271122316/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/links_1734271122316/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/links/meta.yaml b/recipes/links/meta.yaml index 4401e28541db5..85a16d6fa811c 100644 --- a/recipes/links/meta.yaml +++ b/recipes/links/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage("links", max_pin="x") }} @@ -34,4 +34,4 @@ about: extra: additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 diff --git a/recipes/livekraken/meta.yaml b/recipes/livekraken/meta.yaml index c51290ce4328f..2dc1a60c8578a 100644 --- a/recipes/livekraken/meta.yaml +++ b/recipes/livekraken/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 10 + number: 11 skip: True # [osx] has_prefix_files: - libexec/livekraken diff --git a/recipes/lja/build_failure.linux-64.yaml b/recipes/lja/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..a37805f39d612 --- /dev/null +++ b/recipes/lja/build_failure.linux-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: de282e6329950b5cc145ff1bb79c1848c565453d897fec1b20b2742f4a557ef9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("cmake=3.22.1")} + Encountered problems while solving: + - nothing provides requested cmake 3.22.1.* + + Could not solve for environment specs + The following package could not be installed + [31mcmake 3.22.1.* [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("cmake=3.22.1")} + Encountered problems while solving: + - nothing provides requested cmake 3.22.1.* + + Could not solve for environment specs + The following package could not be installed + [31mcmake 3.22.1.* [0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 465, in add_upstream_pins + build_deps, build_unsat, extra_run_specs_from_build = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("cmake=3.22.1")} + Encountered problems while solving: + - nothing provides requested cmake 3.22.1.* + + Could not solve for environment specs + The following package could not be installed + [31mcmake 3.22.1.* [0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. +reason: |- + specifies a cmake version unavailable in conda-forge +category: |- + dependency issue diff --git a/recipes/lja/build_failure.osx-64.yaml b/recipes/lja/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..a47c8a2ee1a6f --- /dev/null +++ b/recipes/lja/build_failure.osx-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: de282e6329950b5cc145ff1bb79c1848c565453d897fec1b20b2742f4a557ef9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + specifies a cmake version unavailable in conda-forge +category: |- + dependency issue diff --git a/recipes/lja/meta.yaml b/recipes/lja/meta.yaml index e7cfc53833730..25ad4cc2aeda0 100644 --- a/recipes/lja/meta.yaml +++ b/recipes/lja/meta.yaml @@ -11,7 +11,7 @@ source: sha256: '{{ sha256 }}' build: - number: 2 + number: 3 skip: True # [osx] requirements: diff --git a/recipes/localhgt/meta.yaml b/recipes/localhgt/meta.yaml index 94f06028c03df..0c753a75dacbf 100644 --- a/recipes/localhgt/meta.yaml +++ b/recipes/localhgt/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage("localhgt", max_pin="x") }} entry_points: diff --git a/recipes/locarna/meta.yaml b/recipes/locarna/meta.yaml index 68b1253eb8c61..9952c6e72c554 100644 --- a/recipes/locarna/meta.yaml +++ b/recipes/locarna/meta.yaml @@ -13,7 +13,7 @@ about: summary: Multiple alignment of RNAs build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('locarna', max_pin="x.x") }} diff --git a/recipes/lofreq/meta.yaml b/recipes/lofreq/meta.yaml index a4e8fbd6e32c5..c5f31cd515b9a 100644 --- a/recipes/lofreq/meta.yaml +++ b/recipes/lofreq/meta.yaml @@ -11,7 +11,7 @@ source: - 0001-patches build: - number: 14 + number: 15 run_exports: - {{ pin_subpackage('lofreq', max_pin='x') }} diff --git a/recipes/logomaker/build_failure.linux-64.yaml b/recipes/logomaker/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..faf75f53c0cc0 --- /dev/null +++ b/recipes/logomaker/build_failure.linux-64.yaml @@ -0,0 +1,4 @@ +recipe_sha: 7e14c26aa1a7f80f22a62ee46e53e4c69b0c83e3c9dc897122799de48c737d54 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + also on conda-forge diff --git a/recipes/logomaker/build_failure.osx-64.yaml b/recipes/logomaker/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..faf75f53c0cc0 --- /dev/null +++ b/recipes/logomaker/build_failure.osx-64.yaml @@ -0,0 +1,4 @@ +recipe_sha: 7e14c26aa1a7f80f22a62ee46e53e4c69b0c83e3c9dc897122799de48c737d54 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + also on conda-forge diff --git a/recipes/logomaker/meta.yaml b/recipes/logomaker/meta.yaml index 0be1cfd2c9383..75eb914f041ce 100644 --- a/recipes/logomaker/meta.yaml +++ b/recipes/logomaker/meta.yaml @@ -10,7 +10,7 @@ source: sha256: d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d build: - number: 1 + number: 2 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " diff --git a/recipes/longgf/meta.yaml b/recipes/longgf/meta.yaml index d8071e50f73fd..d3ad79d226a28 100644 --- a/recipes/longgf/meta.yaml +++ b/recipes/longgf/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 4790421de904e809c2ec1b1d3804493b1cd178ccb834066d2485db01b8c466e6 build: - number: 7 + number: 8 requirements: build: diff --git a/recipes/longphase/build_failure.linux-64.yaml b/recipes/longphase/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..e856dceab28ce --- /dev/null +++ b/recipes/longphase/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 88edba1ca550a5099a79cc429851eb654a80470a0bfc45d1edd4802429891b45 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/sam.o test/sam.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_bgzf.o test/test_bgzf.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_expr.o test/test_expr.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_kfunc.o test/test_kfunc.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_kstring.o test/test_kstring.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_mod.o test/test_mod.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_realn.o test/test_realn.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-regidx.o test/test-regidx.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_str2int.o test/test_str2int.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_time_funcs.o test/test_time_funcs.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_view.o test/test_view.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_index.o test/test_index.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-vcf-api.o test/test-vcf-api.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-bcf-sr.o test/test-bcf-sr.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-bcf-translate.o test/test-bcf-translate.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-parse-reg.o test/test-parse-reg.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_introspection.o test/test_introspection.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c + sed -e 's#@-includedir@#'pwd'#g;s#@-libdir@#'pwd'#g' htslib.pc.tmp > htslib-uninstalled.pc + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o hts.o hts.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -shared -Wl,-soname,libhts.so.3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/utils.pico -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/plugins-dlhts test/plugins-dlhts.o -llzma -lbz2 -lz -lm + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_time_funcs test/test_time_funcs.o + ln -sf libhts.so libhts.so.3 + ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib libhts.a + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/pileup_mod test/pileup_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_expr test/test_expr.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_kfunc test/test_kfunc.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_kstring test/test_kstring.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_mod test/test_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_str2int test/test_str2int.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_introspection test/test_introspection.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -llzma -lbz2 -lz -lm -lpthread + make[1]: Leaving directory '$SRC_DIR/htslib' + make longphase + make[1]: Entering directory '$SRC_DIR' + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o Haplotag.o -c Haplotag.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o ParsingBam.o -c ParsingBam.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o Util.o -c Util.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o HaplotagProcess.o -c HaplotagProcess.cpp + ParsingBam.cpp:28: warning: ignoring '#pragma omp parallfel' [-Wunknown-pragmas] + 28 | #pragma omp parallfel for schedule(dynamic) num_threads(numThreads) + | + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o PhasingProcess.o -c PhasingProcess.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o Phasing.o -c Phasing.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o PhasingGraph.o -c PhasingGraph.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o ModCall.o -c ModCall.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o ModCallParsingBam.o -c ModCallParsingBam.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o ModCallProcess.o -c ModCallProcess.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o main.o -c main.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -Lhtslib/htslib -Ljemalloc/lib -o longphase Haplotag.o ParsingBam.o Util.o HaplotagProcess.o PhasingProcess.o Phasing.o PhasingGraph.o ModCall.o ModCallParsingBam.o ModCallProcess.o main.o htslib/libhts.a -lpthread -lz -lm -lbz2 -llzma jemalloc/lib/libjemalloc.a -ldl + /opt/conda/conda-bld/longphase_1734150120234/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -llzma: No such file or directory + collect2: error: ld returned 1 exit status + make[1]: *** [Makefile:40: longphase] Error 1 + make[1]: Leaving directory '$SRC_DIR' + make: *** [Makefile:19: subprojects] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/longphase_1734150120234/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/longphase_1734150120234/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/longphase/build_failure.linux-aarch64.yaml b/recipes/longphase/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..47b77fde52649 --- /dev/null +++ b/recipes/longphase/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 88edba1ca550a5099a79cc429851eb654a80470a0bfc45d1edd4802429891b45 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/sam.o test/sam.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_bgzf.o test/test_bgzf.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_expr.o test/test_expr.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_kfunc.o test/test_kfunc.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_kstring.o test/test_kstring.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_mod.o test/test_mod.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_realn.o test/test_realn.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-regidx.o test/test-regidx.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_str2int.o test/test_str2int.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_time_funcs.o test/test_time_funcs.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_view.o test/test_view.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_index.o test/test_index.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-vcf-api.o test/test-vcf-api.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-bcf-sr.o test/test-bcf-sr.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-bcf-translate.o test/test-bcf-translate.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-parse-reg.o test/test-parse-reg.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_introspection.o test/test_introspection.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c + sed -e 's#@-includedir@#'pwd'#g;s#@-libdir@#'pwd'#g' htslib.pc.tmp > htslib-uninstalled.pc + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wall -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longphase-1.7.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o hts.o hts.c + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -shared -Wl,-soname,libhts.so.3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/utils.pico -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/plugins-dlhts test/plugins-dlhts.o -llzma -lbz2 -lz -lm + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_time_funcs test/test_time_funcs.o + ln -sf libhts.so libhts.so.3 + ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib libhts.a + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/pileup_mod test/pileup_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_expr test/test_expr.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_kfunc test/test_kfunc.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_kstring test/test_kstring.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_mod test/test_mod.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_str2int test/test_str2int.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test_introspection test/test_introspection.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fvisibility=hidden -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -llzma -lbz2 -lz -lm -lpthread + make[1]: Leaving directory '$SRC_DIR/htslib' + make longphase + make[1]: Entering directory '$SRC_DIR' + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o Haplotag.o -c Haplotag.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o ParsingBam.o -c ParsingBam.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o Util.o -c Util.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o HaplotagProcess.o -c HaplotagProcess.cpp + ParsingBam.cpp:28: warning: ignoring '#pragma omp parallfel' [-Wunknown-pragmas] + 28 | #pragma omp parallfel for schedule(dynamic) num_threads(numThreads) + | + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o PhasingProcess.o -c PhasingProcess.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o Phasing.o -c Phasing.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o PhasingGraph.o -c PhasingGraph.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o ModCall.o -c ModCall.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o ModCallParsingBam.o -c ModCallParsingBam.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o ModCallProcess.o -c ModCallProcess.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -o main.o -c main.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -I. -std=c11 -g -Wall -O3 -fopenmp -Ihtslib -Ijemalloc -Lhtslib/htslib -Ljemalloc/lib -o longphase Haplotag.o ParsingBam.o Util.o HaplotagProcess.o PhasingProcess.o Phasing.o PhasingGraph.o ModCall.o ModCallParsingBam.o ModCallProcess.o main.o htslib/libhts.a -lpthread -lz -lm -lbz2 -llzma jemalloc/lib/libjemalloc.a -ldl + /opt/conda/conda-bld/longphase_1733932058240/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: cannot find -llzma: No such file or directory + collect2: error: ld returned 1 exit status + make[1]: *** [Makefile:40: longphase] Error 1 + make[1]: Leaving directory '$SRC_DIR' + make: *** [Makefile:19: subprojects] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/longphase_1733932058240/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/longphase_1733932058240/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/longphase/meta.yaml b/recipes/longphase/meta.yaml index cf8b762b52c4a..b7ee75ce69b32 100644 --- a/recipes/longphase/meta.yaml +++ b/recipes/longphase/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('longphase', max_pin="x") }} diff --git a/recipes/longreadsum/meta.yaml b/recipes/longreadsum/meta.yaml index b8059e7edc4e3..4acaece35a52c 100644 --- a/recipes/longreadsum/meta.yaml +++ b/recipes/longreadsum/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 2 + number: 3 entry_points: - longreadsum = entry_point:main run_exports: diff --git a/recipes/longshot/build_failure.osx-64.yaml b/recipes/longshot/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..2548799bce171 --- /dev/null +++ b/recipes/longshot/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c22197e2f3e91398e2a34bed3b70a9d15baa610cd08503c8a80aa405f0e07ef8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - zstd 1.5.6 h915ae27_0 + - libllvm19 19.1.5 hc29ff6c_0 + - xz 5.6.3 h357f2ed_1 + - libclang-cpp19.1 19.1.5 default_h3571c67_0 + - libclang13 19.1.5 default_hf2b7afa_0 + - llvm-tools-19 19.1.5 he90a8e3_0 + - clang-19 19.1.5 default_h3571c67_0 + - clang-format-19 19.1.5 default_h3571c67_0 + - libclang 19.1.5 default_h3571c67_0 + - libclang-cpp 19.1.5 default_h3571c67_0 + - llvm-tools 19.1.5 h3fe3016_0 + - clang 19.1.5 default_h576c50e_0 + - clang-format 19.1.5 default_h3571c67_0 + - llvmdev 19.1.5 he90a8e3_0 + - clang-tools 19.1.5 default_h3571c67_0 + - clangxx 19.1.5 default_heb2e8d1_0 + - clangdev 19.1.5 default_h3571c67_0 + run: + - libzlib >=1.3.1,<2.0a0 + - liblzma >=5.6.3,<6.0a0 + - libcxx >=18 + run_constrained: + - __osx >=10.13 + test: + commands: + - longshot --help + - longshot --version + about: + dev_url: https://github.com/pjedge/longshot + doc_url: https://github.com/pjedge/longshot/blob/v(( version }}/README.md + home: https://github.com/pjedge/longshot + license: MIT + license_family: MIT + license_file: LICENSE + summary: Diploid SNV caller for error-prone reads. + extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + copy_test_source_files: true + final: true + identifiers: + - doi:10.1038/s41467-019-12493-y + - biotools:longshot + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/longshot_1733989742517/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/longshot_1733989742517/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/longshot_1733989742517/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/longshot_1733989742517/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longshot-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longshot-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longshot-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/longshot-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix +# Last 100 lines of the build log. diff --git a/recipes/longshot/meta.yaml b/recipes/longshot/meta.yaml index b02c830a4eddd..bb68aa6f62af2 100644 --- a/recipes/longshot/meta.yaml +++ b/recipes/longshot/meta.yaml @@ -12,7 +12,7 @@ source: - update-rust-htslib.patch build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('longshot', max_pin="x") }} diff --git a/recipes/lordfast/meta.yaml b/recipes/lordfast/meta.yaml index fb49fd65ba241..c1c24f8bd2b03 100644 --- a/recipes/lordfast/meta.yaml +++ b/recipes/lordfast/meta.yaml @@ -12,7 +12,7 @@ source: - 0001-Append-flags-in-Makefile.patch build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/lorikeet-genome/build_failure.linux-64.yaml b/recipes/lorikeet-genome/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..7c1da1382765e --- /dev/null +++ b/recipes/lorikeet-genome/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 66381714068816f0940b865f892d81c055dc6dbe1e63f03b09b118999f1efb9a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("k8==1.2=h6618dc6_1"), MatchSpec("python_abi=3.8[build=*_cp38]")} + Encountered problems while solving: + - package k8-1.2-h6618dc6_1 requires python_abi 3.8.* *_cp38, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mlibzlib >=1.3.1,<2.0a0 [0m is installable with the potential options + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_0[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [32mminimap2 >=2.24 [0m is installable with the potential options + [32mminimap2 2.28[0m would require + [32mk8[0m with the potential options + [32mk8 1.2[0m would require + [32mpython_abi 3.8.* *_cp38[0m with the potential options + [32mpython_abi 3.8[0m would require + [32mpython 3.8.* [0m with the potential options + [32mpython [3.8.0|3.8.1][0m would require + [32mopenssl >=1.1.1a,<1.1.2a [0m, which can be installed; + [32mpython 3.8.10[0m would require + [32mopenssl >=1.1.1k,<1.1.2a [0m, which can be installed; + [32mpython [3.10.0|3.10.1|3.10.2|3.8.10|3.8.12][0m would require + [32mopenssl >=1.1.1l,<1.1.2a [0m, which can be installed; + [32mpython 3.8.12[0m would require + [32mpypy3.8 7.3.8.* [0m with the potential options + [32mpypy3.8 7.3.8[0m would require + [32mopenssl >=1.1.1n,<1.1.2a [0m, which can be installed; + [31mpypy3.8 7.3.8[0m would require + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [32mpython [3.8.12|3.8.13|...|3.8.5][0m, which can be installed; + [31mpython 3.8.12[0m would require + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [32mpython [3.10.4|3.8.13][0m would require + [32mopenssl >=1.1.1n,<1.1.2a [0m, which can be installed; + [32mpython 3.8.2[0m would require + [32mopenssl >=1.1.1e,<1.1.2a [0m, which can be installed; + [32mpython 3.8.2[0m would require + [32mopenssl >=1.1.1f,<1.1.2a [0m, which can be installed; + [32mpython [3.8.2|3.8.3|3.8.4|3.8.5][0m would require + [32mopenssl >=1.1.1g,<1.1.2a [0m, which can be installed; + [32mpython 3.8.2[0m would require + [32mopenssl >=1.1.1d,<1.1.2a [0m, which can be installed; + [32mpython [3.8.5|3.8.6][0m would require + [32mopenssl >=1.1.1h,<1.1.2a [0m, which can be installed; + [32mpython 3.8.6[0m would require + [32mopenssl >=1.1.1i,<1.1.2a [0m, which can be installed; + [32mpython 3.8.8[0m would require + [32mopenssl >=1.1.1j,<1.1.2a [0m, which can be installed; + [32mpython [3.10.7|3.10.8|3.8.14|3.8.15][0m would require + [32mopenssl >=1.1.1s,<1.1.2a [0m, which can be installed; + [32mpython_abi 3.8[0m, which can be installed; + [31mk8 0.2.5[0m would require + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mk8 0.2.5[0m would require + [31mzlib >=1.2.13,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mk8 [0.2.5|1.0|1.2][0m would require + [31mlibzlib >=1.2.13,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [32mk8 1.2[0m would require + [32mpython_abi 3.12.* *_cp312[0m, which can be installed; + [32mk8 1.2[0m would require + [32mpython_abi 3.13.* *_cp313[0m, which can be installed; + [31mminimap2 2.24[0m would require + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mminimap2 [2.25|2.26][0m would require + [31mzlib >=1.2.13,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mminimap2 [2.26|2.27|2.28][0m would require + [31mlibzlib >=1.2.13,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mopenssl >=3.4.0,<4.0a0 [0m is not installable because it conflicts with any installable versions previously reported; + [32mpython 3.10.* [0m is installable with the potential options + [32mpython [3.10.0|3.10.1|3.10.2|3.8.10|3.8.12][0m, which can be installed (as previously explained); + [32mpython [3.10.4|3.8.13][0m, which can be installed (as previously explained); + [32mpython [3.10.7|3.10.8|3.8.14|3.8.15][0m, which can be installed (as previously explained); + [31mpython 3.10.8[0m conflicts with any installable versions previously reported; + [31mpython [3.10.0|3.10.1|...|3.10.9][0m would require + [31mpython_abi 3.10.* *_cp310[0m, which conflicts with any installable versions previously reported; + [32mpython 3.10.5[0m would require + [32mopenssl >=1.1.1o,<1.1.2a [0m, which can be installed; + [32mpython 3.10.6[0m would require + [32mopenssl >=1.1.1q,<1.1.2a [0m, which can be installed. +# Last 100 lines of the build log. diff --git a/recipes/lorikeet-genome/meta.yaml b/recipes/lorikeet-genome/meta.yaml index 74cd2f2cb9905..415dc8d83501e 100644 --- a/recipes/lorikeet-genome/meta.yaml +++ b/recipes/lorikeet-genome/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/lra/meta.yaml b/recipes/lra/meta.yaml index f683cad878878..4b7db7b4970d9 100644 --- a/recipes/lra/meta.yaml +++ b/recipes/lra/meta.yaml @@ -9,7 +9,7 @@ source: sha256: aedf99e7488ddbc679c3e5015704ffab31d3c6e914f23a0b196304f962492ff6 build: - number: 2 + number: 3 skip: True # [osx] requirements: diff --git a/recipes/lrge/meta.yaml b/recipes/lrge/meta.yaml index 1e656849d4fed..b12c67e26d43f 100644 --- a/recipes/lrge/meta.yaml +++ b/recipes/lrge/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 7cb7f6308169b2fff9b072d5f578d7d2f821ca7506c52ef3a4ed15990cea0fce build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('lrge', max_pin="x.x") }} diff --git a/recipes/lrsim/build_failure.linux-64.yaml b/recipes/lrsim/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..c907512236b1f --- /dev/null +++ b/recipes/lrsim/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 577821885c63b3f5f88aada59a8e6b8bc12cf5a7f29d8c80385a1675bfe5d895 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("perl-inline-c==0.81=pl5321hec16e2b_1"), MatchSpec("gcc_linux-64=10")} + Encountered problems while solving: + - package perl-inline-c-0.81-pl5321hec16e2b_1 requires gcc_linux-64 10.*, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mgcc_linux-64 13.* [0m is installable with the potential options + [32mgcc_linux-64 13.1.0[0m, which can be installed; + [32mgcc_linux-64 13.1.0[0m, which can be installed; + [32mgcc_linux-64 13.2.0[0m, which can be installed; + [32mgcc_linux-64 13.2.0[0m, which can be installed; + [32mgcc_linux-64 13.2.0[0m, which can be installed; + [32mgcc_linux-64 13.2.0[0m, which can be installed; + [32mgcc_linux-64 13.2.0[0m, which can be installed; + [32mgcc_linux-64 13.2.0[0m, which can be installed; + [32mgcc_linux-64 13.2.0[0m, which can be installed; + [31mgcc_linux-64 13.2.0[0m conflicts with any installable versions previously reported; + [32mgcc_linux-64 13.2.0[0m, which can be installed; + [32mgcc_linux-64 13.2.0[0m, which can be installed; + [32mgcc_linux-64 13.3.0[0m, which can be installed; + [32mgcc_linux-64 13.3.0[0m, which can be installed; + [32mgcc_linux-64 13.3.0[0m, which can be installed; + [32mgcc_linux-64 13.3.0[0m, which can be installed; + [32mgcc_linux-64 13.3.0[0m, which can be installed; + [32mgcc_linux-64 13.3.0[0m, which can be installed; + [32mgcc_linux-64 13.3.0[0m, which can be installed; + [32mgcc_linux-64 13.3.0[0m, which can be installed; + [32mgxx_linux-64 13.* [0m is installable with the potential options + [32mgxx_linux-64 13.1.0[0m would require + [32mgcc_linux-64 13.1.0 hd2d1137_0[0m, which can be installed; + [32mgxx_linux-64 13.1.0[0m would require + [32mgcc_linux-64 13.1.0 hd2d1137_1[0m, which can be installed; + [32mgxx_linux-64 13.2.0[0m would require + [32mgcc_linux-64 13.2.0 h3668938_3[0m, which can be installed; + [32mgxx_linux-64 13.2.0[0m would require + [32mgcc_linux-64 13.2.0 h3668938_4[0m, which can be installed; + [32mgxx_linux-64 13.2.0[0m would require + [32mgcc_linux-64 13.2.0 h3668938_5[0m, which can be installed; + [32mgxx_linux-64 13.2.0[0m would require + [32mgcc_linux-64 13.2.0 h3668938_6[0m, which can be installed; + [32mgxx_linux-64 13.2.0[0m would require + [32mgcc_linux-64 13.2.0 h3668938_7[0m, which can be installed; + [32mgxx_linux-64 13.2.0[0m would require + [32mgcc_linux-64 13.2.0 h50dba11_8[0m, which can be installed; + [32mgxx_linux-64 13.2.0[0m would require + [32mgcc_linux-64 13.2.0 h50dba11_9[0m, which can be installed; + [32mgxx_linux-64 13.2.0[0m would require + [32mgcc_linux-64 13.2.0 h112eaf3_2[0m, which can be installed; + [32mgxx_linux-64 13.2.0[0m would require + [32mgcc_linux-64 13.2.0 h1ed452b_3[0m, which can be installed; + [32mgxx_linux-64 13.3.0[0m would require + [32mgcc_linux-64 13.3.0 hc28eda2_0[0m, which can be installed; + [32mgxx_linux-64 13.3.0[0m would require + [32mgcc_linux-64 13.3.0 hc28eda2_1[0m, which can be installed; + [32mgxx_linux-64 13.3.0[0m would require + [32mgcc_linux-64 13.3.0 hc28eda2_2[0m, which can be installed; + [32mgxx_linux-64 13.3.0[0m would require + [32mgcc_linux-64 13.3.0 hc28eda2_3[0m, which can be installed; + [32mgxx_linux-64 13.3.0[0m would require + [32mgcc_linux-64 13.3.0 hc28eda2_4[0m, which can be installed; + [32mgxx_linux-64 13.3.0[0m would require + [32mgcc_linux-64 13.3.0 hc28eda2_5[0m, which can be installed; + [32mgxx_linux-64 13.3.0[0m would require + [32mgcc_linux-64 13.3.0 hc28eda2_6[0m, which can be installed; + [32mgxx_linux-64 13.3.0[0m would require + [32mgcc_linux-64 13.3.0 hc28eda2_7[0m, which can be installed; + [32mperl-inline-c[0m is installable with the potential options + [32mperl-inline-c 0.76[0m would require + [32mperl >=5.22.0,<5.23.0 [0m, which can be installed; + [32mperl-inline-c [0.76|0.78][0m would require + [32mperl [>=5.26.2,<5.26.3.0a0 |>=5.26.2,<5.27.0a0 ][0m, which can be installed; + [31mperl-inline-c 0.81[0m would require + [31mgcc_linux-64 12.* [0m, which conflicts with any installable versions previously reported; + [31mperl-inline-c 0.81[0m would require + [31mgcc_linux-64 9.* [0m, which conflicts with any installable versions previously reported; + [31mperl-inline-c 0.81[0m would require + [31mgcc_linux-64 10.* [0m, which conflicts with any installable versions previously reported; + [31mperl 5.32.1.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/lrsim/meta.yaml b/recipes/lrsim/meta.yaml index eb97739dad760..5a9e28872e557 100644 --- a/recipes/lrsim/meta.yaml +++ b/recipes/lrsim/meta.yaml @@ -16,7 +16,7 @@ source: - 0005-fix-perl-loc.patch build: - number: 0 + number: 1 skip: True # [not linux] run_exports: - {{ pin_subpackage(name | lower, max_pin="x") }} diff --git a/recipes/lrzip/meta.yaml b/recipes/lrzip/meta.yaml index df073ed1df8c8..d90699feea517 100644 --- a/recipes/lrzip/meta.yaml +++ b/recipes/lrzip/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 48bd8decb097c1596c9b3777959cd3e332819434ed77a2823e65aa436f1602f9 build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('lrzip', max_pin="x.x") }} @@ -50,4 +50,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ltr_finder/build_failure.osx-64.yaml b/recipes/ltr_finder/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..1fd3e1152f880 --- /dev/null +++ b/recipes/ltr_finder/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 9234a2d557380307feacc6a8c3fc91e144f4958b559e5b7ccfe613e39208aa9a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + - clang_impl_osx-64 18.1.8 h6a44ed1_23 + - liblzma 5.6.3 hd471939_1 + - libiconv 1.17 hd75f5a5_2 + - libxml2 2.13.5 he8ee3e7_1 + - ca-certificates 2024.12.14 h8857fd0_0 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + - openssl 3.4.0 hd471939_0 + - clang_osx-64 18.1.8 h7e5c614_23 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + host: + - libcxx 19.1.5 hf95d169_0 + - llvm-openmp 19.1.5 ha54dae1_0 + run: + - llvm-openmp >=18.1.8 + - perl + - perl-gd + - libcxx >=18 + test: + commands: + - ltr_finder 2>&1 | grep -i usage + about: + dev_url: https://github.com/NBISweden/LTR_Finder/ + home: https://github.com/NBISweden/LTR_Finder/ + license: MIT + license_file: LICENSE + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + summary: LTR_Finder is an efficient program for finding full-length LTR retrotranspsons + in genome sequences. + extra: + copy_test_source_files: true + final: true + + + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/ltr_finder_1734475375021/work/conda_build.sh']' returned non-zero exit status 2. + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/ltr_finder_1734475375021/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/ltr_finder_1734475375021/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/ltr_finder_1734475375021/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/ltr_finder_1734475375021/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ltr_finder-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ltr_finder-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ltr_finder-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ltr_finder-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + x86_64-apple-darwin13.4.0-clang -c regex.c -fomit-frame-pointer -DNDBUG -O3 + x86_64-apple-darwin13.4.0-clang -c Timing.C -fomit-frame-pointer -DNDBUG -O3 + x86_64-apple-darwin13.4.0-clang -c BooleanString.C -fomit-frame-pointer -DNDBUG -O3 + x86_64-apple-darwin13.4.0-clang -c LinearSuffixSort.cpp -fomit-frame-pointer -DNDBUG -O3 + x86_64-apple-darwin13.4.0-clang -c lcp.c -fomit-frame-pointer -DNDBUG -O3 + x86_64-apple-darwin13.4.0-clang -c stdaln.c -fomit-frame-pointer -DNDBUG -O3 +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/ltr_finder/meta.yaml b/recipes/ltr_finder/meta.yaml index 24fd161268de4..175eec896adf1 100644 --- a/recipes/ltr_finder/meta.yaml +++ b/recipes/ltr_finder/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/lumpy-sv-minimal/meta.yaml b/recipes/lumpy-sv-minimal/meta.yaml index e70146c118590..86fe999a7ef0e 100644 --- a/recipes/lumpy-sv-minimal/meta.yaml +++ b/recipes/lumpy-sv-minimal/meta.yaml @@ -12,7 +12,7 @@ source: - const.patch build: - number: 4 + number: 5 # The packaged bamtools has issues with compilation on OSX skip: True # [osx] diff --git a/recipes/lz4-bin/meta.yaml b/recipes/lz4-bin/meta.yaml index e3c93509cf160..016c4ebc789a3 100644 --- a/recipes/lz4-bin/meta.yaml +++ b/recipes/lz4-bin/meta.yaml @@ -11,7 +11,7 @@ extra: notes: "This package is for the lz4 C binary, while the package in the default channel is (as of 9/9/16) for the lz4 Python bindings (hence the '-bin' suffix of this package)" build: - number: 7 + number: 8 source: url: https://github.com/Cyan4973/lz4/archive/r131.zip diff --git a/recipes/maast/meta.yaml b/recipes/maast/meta.yaml index e031ece0da1ce..c6503cf8cecad 100644 --- a/recipes/maast/meta.yaml +++ b/recipes/maast/meta.yaml @@ -13,7 +13,7 @@ source: - maast.patch build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/macs2/meta.yaml b/recipes/macs2/meta.yaml index 3f6bf8c66c9dc..b337d44d8df77 100644 --- a/recipes/macs2/meta.yaml +++ b/recipes/macs2/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . --use-pep517 --no-deps --no-cache-dir -vvv skip: True # [py == 312] run_exports: diff --git a/recipes/macs3/meta.yaml b/recipes/macs3/meta.yaml index 7fcee4f154187..0f358afe355f9 100644 --- a/recipes/macs3/meta.yaml +++ b/recipes/macs3/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 skip: True # [py < 39] script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv run_exports: diff --git a/recipes/maelstrom-core/meta.yaml b/recipes/maelstrom-core/meta.yaml index e47917996ca90..58f6bc4694a7a 100644 --- a/recipes/maelstrom-core/meta.yaml +++ b/recipes/maelstrom-core/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 skip: True # [osx] source: diff --git a/recipes/maf2synteny/meta.yaml b/recipes/maf2synteny/meta.yaml index 4b2f5e7bd6cc2..f5ac9a0f42728 100644 --- a/recipes/maf2synteny/meta.yaml +++ b/recipes/maf2synteny/meta.yaml @@ -12,7 +12,7 @@ source: - Makefile.patch build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/mageck/meta.yaml b/recipes/mageck/meta.yaml index 9ec3288ccc08a..05c954790d018 100644 --- a/recipes/mageck/meta.yaml +++ b/recipes/mageck/meta.yaml @@ -7,7 +7,7 @@ source: sha256: b06a18036da63959cd7751911a46727aefe2fb1d8dd79d95043c3e3bdaf1d93a build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('mageck', max_pin="x.x") }} diff --git a/recipes/malder/meta.yaml b/recipes/malder/meta.yaml index 462ddfa884b55..d40766fae7c6b 100644 --- a/recipes/malder/meta.yaml +++ b/recipes/malder/meta.yaml @@ -5,7 +5,9 @@ package: version: "1.0.1e83d4e" build: - number: 7 + number: 8 + run_exports: + - {{ pin_subpackage('malder', max_pin="x") }} source: url: https://github.com/joepickrell/malder/archive/1e83d4ef3683de56e0d1c66cc0e55ee01ba16967.tar.gz diff --git a/recipes/malva/build_failure.linux-64.yaml b/recipes/malva/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..9b1e2272c0099 --- /dev/null +++ b/recipes/malva/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 7e8c24b034eccda8e62497b64fb8526b2e59f195d3bf5807ee7e76a4c934b548 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + identifiers: + - biotools:malva + + + source tree in: /opt/conda/conda-bld/malva_1734273381501/work + export PREFIX=/opt/conda/conda-bld/malva_1734273381501/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/conda/conda-bld/malva_1734273381501/_build_env + export SRC_DIR=/opt/conda/conda-bld/malva_1734273381501/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/malva-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/malva-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/malva-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/malva-2.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + -- The C compiler identification is GNU 13.3.0 + -- The CXX compiler identification is GNU 13.3.0 + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - skipped + -- Detecting C compile features + -- Detecting C compile features - done + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- SDSL found $BUILD_PREFIX/lib/libsdsl.a + -- SDSL includes found $BUILD_PREFIX/include + CMake Error at CMakeLists.txt:30 (message): + kmc_file.h (part of libkmc-dev) required + + + -- Configuring incomplete, errors occurred! + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/malva_1734273381501/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/malva_1734273381501/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/malva/meta.yaml b/recipes/malva/meta.yaml index 72c392b21a442..33ff45a3dfd13 100644 --- a/recipes/malva/meta.yaml +++ b/recipes/malva/meta.yaml @@ -13,7 +13,7 @@ source: - malva.CMakeList.patch build: - number: 4 + number: 5 skip: True # [osx] run_exports: - {{ pin_subpackage('malva', max_pin="x") }} diff --git a/recipes/mammal/meta.yaml b/recipes/mammal/meta.yaml index c92e04b1e0747..c8caac17df023 100644 --- a/recipes/mammal/meta.yaml +++ b/recipes/mammal/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/mantis-msi/build_failure.linux-64.yaml b/recipes/mantis-msi/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..4e262e7980f66 --- /dev/null +++ b/recipes/mantis-msi/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: b59583e0eddb8057c170e9dcffc245ec6114a8ea22e050c08697d3db06ffba70 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + INFO (mantis-msi,bin/RepeatFinder): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.17=h4a8ded7_18 + Fixing permissions + INFO :: Time taken to mark (prefix) + 0 replacements in 0 files was 0.01 seconds + WARNING: Importing conda-verify failed. Please be sure to test your packages. conda install conda-verify to make this message go away. + TEST START: /opt/conda/conda-bld/linux-64/mantis-msi-1.0.5-h9948957_3.tar.bz2 + Renaming work directory '/opt/conda/conda-bld/mantis-msi_1734382792777/work' to '/opt/conda/conda-bld/mantis-msi_1734382792777/work_moved_mantis-msi-1.0.5-h9948957_3_linux-64' + shutil.move(work)=/opt/conda/conda-bld/mantis-msi_1734382792777/work, dest=/opt/conda/conda-bld/mantis-msi_1734382792777/work_moved_mantis-msi-1.0.5-h9948957_3_linux-64) + Reloading output folder (local, file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/mantis-msi_1734382792777/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + bzip2: 1.0.8-h4bc722e_7 conda-forge + c-ares: 1.34.4-hb9d3cd8_0 conda-forge + ca-certificates: 2024.12.14-hbcca054_0 conda-forge + keyutils: 1.6.1-h166bdaf_0 conda-forge + krb5: 1.21.3-h659f571_0 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libblas: 3.9.0-25_linux64_openblas conda-forge + libcblas: 3.9.0-25_linux64_openblas conda-forge + libcurl: 8.11.1-h332b0f4_0 conda-forge + libdeflate: 1.22-hb9d3cd8_0 conda-forge + libedit: 3.1.20191231-he28a2e2_2 conda-forge + libev: 4.33-hd590300_2 conda-forge + libexpat: 2.6.4-h5888daf_0 conda-forge + libffi: 3.4.2-h7f98852_5 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-ng: 14.2.0-h69a702a_1 conda-forge + libgfortran: 14.2.0-h69a702a_1 conda-forge + libgfortran5: 14.2.0-hd5240d6_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + liblapack: 3.9.0-25_linux64_openblas conda-forge + liblzma: 5.6.3-hb9d3cd8_1 conda-forge + libnghttp2: 1.64.0-h161d5f1_0 conda-forge + libnsl: 2.0.1-hd590300_0 conda-forge + libopenblas: 0.3.28-pthreads_h94d23a6_1 conda-forge + libsqlite: 3.47.2-hee588c1_0 conda-forge + libssh2: 1.11.1-hf672d98_0 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-ng: 14.2.0-h4852527_1 conda-forge + libuuid: 2.38.1-h0b41bf4_0 conda-forge + libxcrypt: 4.4.36-hd590300_1 conda-forge + libzlib: 1.3.1-hb9d3cd8_2 conda-forge + mantis-msi: 1.0.5-h9948957_3 local + ncurses: 6.5-he02047a_1 conda-forge + numpy: 2.2.0-py312h7e784f5_0 conda-forge + openssl: 3.4.0-hb9d3cd8_0 conda-forge + pip: 24.3.1-pyh145f28c_1 conda-forge + pysam: 0.22.1-py312h47d5410_3 bioconda + python: 3.12.8-h9e4cc4f_1_cpython conda-forge + python_abi: 3.12-5_cp312 conda-forge + readline: 8.2-h8228510_1 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + export PREFIX=/opt/conda/conda-bld/mantis-msi_1734382792777/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export SRC_DIR=/opt/conda/conda-bld/mantis-msi_1734382792777/test_tmp + mantis-msi.py --help + Microsatellite Analysis for Normal-Tumor InStability (v1.0.4) + Error: You must have Pysam available in your environment! + Error: You must have NumPy available in your environment! + Please check your $PYTHONPATH to make sure you have properly included required moudles/libraries in it. + WARNING: Tests failed for mantis-msi-1.0.5-h9948957_3.tar.bz2 - moving package to /opt/conda/conda-bld/broken + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/mantis-msi_1734382792777/test_tmp/conda_test_runner.sh']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: mantis-msi-1.0.5-h9948957_3.tar.bz2 +# Last 100 lines of the build log. +category: |- + test failure diff --git a/recipes/mantis-msi/build_failure.osx-64.yaml b/recipes/mantis-msi/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..2b65e689aacff --- /dev/null +++ b/recipes/mantis-msi/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: b59583e0eddb8057c170e9dcffc245ec6114a8ea22e050c08697d3db06ffba70 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + + Packaging mantis-msi + Packaging mantis-msi-1.0.5-h5fa12a8_3 + + WARNING: Importing conda-verify failed. Please be sure to test your packages. conda install conda-verify to make this message go away. + number of files: 9 + INFO: sysroot: '/System/Library/Frameworks/' files: '['vmnet.framework/Versions/Current', 'vmnet.framework/Versions/A/_CodeSignature/CodeResources', 'vmnet.framework/Versions/A/Resources/version.plist', 'vmnet.framework/Versions/A/Resources/InfoPlist.loctable']' + INFO: sysroot: '/usr/lib/' files: '['zsh/5.9/zsh/zselect.so', 'zsh/5.9/zsh/zpty.so', 'zsh/5.9/zsh/zprof.so', 'zsh/5.9/zsh/zleparameter.so']' + INFO: sysroot: '/opt/X11/' files: '[]' + INFO (mantis-msi,bin/RepeatFinder): Needed DSO /System/Library/Frameworks/libc.1.dylib found in $SYSROOT + INFO (mantis-msi,bin/RepeatFinder): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT + WARNING (mantis-msi): dso library package conda-forge/osx-64::libcxx==19.1.6=hf95d169_1 in requirements/run but it is not used (i.e. it is overdepending or perhaps statically linked? If that is what you want then add it to build/ignore_run_exports) + Fixing permissions + INFO :: Time taken to mark (prefix) + 0 replacements in 0 files was 0.04 seconds + TEST START: /opt/mambaforge/envs/bioconda/conda-bld/osx-64/mantis-msi-1.0.5-h5fa12a8_3.tar.bz2 + Renaming work directory '/opt/mambaforge/envs/bioconda/conda-bld/mantis-msi_1734565582638/work' to '/opt/mambaforge/envs/bioconda/conda-bld/mantis-msi_1734565582638/work_moved_mantis-msi-1.0.5-h5fa12a8_3_osx-64' + shutil.move(work)=/opt/mambaforge/envs/bioconda/conda-bld/mantis-msi_1734565582638/work, dest=/opt/mambaforge/envs/bioconda/conda-bld/mantis-msi_1734565582638/work_moved_mantis-msi-1.0.5-h5fa12a8_3_osx-64) + Reloading output folder (local): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/mantis-msi_1734565582638/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + + + The following NEW packages will be INSTALLED: + + bzip2: 1.0.8-hfdf4475_7 conda-forge + c-ares: 1.34.4-hf13058a_0 conda-forge + ca-certificates: 2024.12.14-h8857fd0_0 conda-forge + krb5: 1.21.3-h37d8d59_0 conda-forge + libblas: 3.9.0-26_osx64_openblas conda-forge + libcblas: 3.9.0-26_osx64_openblas conda-forge + libcurl: 8.11.1-h5dec5d8_0 conda-forge + libcxx: 19.1.6-hf95d169_1 conda-forge + libdeflate: 1.22-h00291cd_0 conda-forge + libedit: 3.1.20191231-h0678c8f_2 conda-forge + libev: 4.33-h10d778d_2 conda-forge + libexpat: 2.6.4-h240833e_0 conda-forge + libffi: 3.4.2-h0d85af4_5 conda-forge + libgfortran: 5.0.0-13_2_0_h97931a8_3 conda-forge + libgfortran5: 13.2.0-h2873a65_3 conda-forge + liblapack: 3.9.0-26_osx64_openblas conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libnghttp2: 1.64.0-hc7306c3_0 conda-forge + libopenblas: 0.3.28-openmp_hbf64a52_1 conda-forge + libsqlite: 3.47.2-hdb6dae5_0 conda-forge + libssh2: 1.11.1-h3dc7d44_0 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-openmp: 19.1.6-ha54dae1_0 conda-forge + mantis-msi: 1.0.5-h5fa12a8_3 local + ncurses: 6.5-hf036a51_1 conda-forge + numpy: 2.2.0-py312h22eab8f_0 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + pysam: 0.22.1-py312hc68ed8a_3 bioconda + python: 3.12.8-h9ccd52b_1_cpython conda-forge + python_abi: 3.12-5_cp312 conda-forge + readline: 8.2-h9e318b2_1 conda-forge + tk: 8.6.13-h1abcd95_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + mantis-msi.py --help + WARNING: Tests failed for mantis-msi-1.0.5-h5fa12a8_3.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/mantis-msi_1734565582638/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/mantis-msi_1734565582638/test_tmp + Microsatellite Analysis for Normal-Tumor InStability (v1.0.4) + Error: You must have Pysam available in your environment! + Error: You must have NumPy available in your environment! + Please check your $PYTHONPATH to make sure you have properly included required moudles/libraries in it. + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/mantis-msi_1734565582638/test_tmp/conda_test_runner.sh']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: mantis-msi-1.0.5-h5fa12a8_3.tar.bz2 +# Last 100 lines of the build log. +category: |- + test failure diff --git a/recipes/mantis-msi/meta.yaml b/recipes/mantis-msi/meta.yaml index 15629133004f8..ee4b442943bc4 100644 --- a/recipes/mantis-msi/meta.yaml +++ b/recipes/mantis-msi/meta.yaml @@ -13,7 +13,7 @@ source: - Makefile.patch build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/mantis-msi2/build_failure.linux-64.yaml b/recipes/mantis-msi2/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..18fd5122f7268 --- /dev/null +++ b/recipes/mantis-msi2/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 252f48999d534b2dc22a8cf8bcfa0750e0a444d2c0523584a557eacccc8961fb # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + INFO (mantis-msi2,bin/mantis-msi2-repeat-finder): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.17=h4a8ded7_18 + Fixing permissions + INFO :: Time taken to mark (prefix) + 0 replacements in 0 files was 0.02 seconds + WARNING: Importing conda-verify failed. Please be sure to test your packages. conda install conda-verify to make this message go away. + TEST START: /opt/conda/conda-bld/linux-64/mantis-msi2-2.0.0-h9948957_2.tar.bz2 + Renaming work directory '/opt/conda/conda-bld/mantis-msi2_1734381494991/work' to '/opt/conda/conda-bld/mantis-msi2_1734381494991/work_moved_mantis-msi2-2.0.0-h9948957_2_linux-64' + shutil.move(work)=/opt/conda/conda-bld/mantis-msi2_1734381494991/work, dest=/opt/conda/conda-bld/mantis-msi2_1734381494991/work_moved_mantis-msi2-2.0.0-h9948957_2_linux-64) + Reloading output folder (local, file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/mantis-msi2_1734381494991/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + bzip2: 1.0.8-h4bc722e_7 conda-forge + c-ares: 1.34.4-hb9d3cd8_0 conda-forge + ca-certificates: 2024.12.14-hbcca054_0 conda-forge + keyutils: 1.6.1-h166bdaf_0 conda-forge + krb5: 1.21.3-h659f571_0 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libblas: 3.9.0-25_linux64_openblas conda-forge + libcblas: 3.9.0-25_linux64_openblas conda-forge + libcurl: 8.11.1-h332b0f4_0 conda-forge + libdeflate: 1.22-hb9d3cd8_0 conda-forge + libedit: 3.1.20191231-he28a2e2_2 conda-forge + libev: 4.33-hd590300_2 conda-forge + libexpat: 2.6.4-h5888daf_0 conda-forge + libffi: 3.4.2-h7f98852_5 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-ng: 14.2.0-h69a702a_1 conda-forge + libgfortran: 14.2.0-h69a702a_1 conda-forge + libgfortran5: 14.2.0-hd5240d6_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + liblapack: 3.9.0-25_linux64_openblas conda-forge + liblzma: 5.6.3-hb9d3cd8_1 conda-forge + libnghttp2: 1.64.0-h161d5f1_0 conda-forge + libnsl: 2.0.1-hd590300_0 conda-forge + libopenblas: 0.3.28-pthreads_h94d23a6_1 conda-forge + libsqlite: 3.47.2-hee588c1_0 conda-forge + libssh2: 1.11.1-hf672d98_0 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-ng: 14.2.0-h4852527_1 conda-forge + libuuid: 2.38.1-h0b41bf4_0 conda-forge + libxcrypt: 4.4.36-hd590300_1 conda-forge + libzlib: 1.3.1-hb9d3cd8_2 conda-forge + mantis-msi2: 2.0.0-h9948957_2 local + ncurses: 6.5-he02047a_1 conda-forge + numpy: 2.2.0-py312h7e784f5_0 conda-forge + openssl: 3.4.0-hb9d3cd8_0 conda-forge + pip: 24.3.1-pyh145f28c_1 conda-forge + pysam: 0.22.1-py312h47d5410_3 bioconda + python: 3.12.8-h9e4cc4f_1_cpython conda-forge + python_abi: 3.12-5_cp312 conda-forge + readline: 8.2-h8228510_1 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + export PREFIX=/opt/conda/conda-bld/mantis-msi2_1734381494991/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export SRC_DIR=/opt/conda/conda-bld/mantis-msi2_1734381494991/test_tmp + mantis-msi2 --help + Microsatellite Analysis for Normal-Tumor InStability (v2.0.0) + Error: You must have Pysam available in your environment! + Error: You must have NumPy available in your environment! + Please check your $PYTHONPATH to make sure you have properly included required moudles/libraries in it. + WARNING: Tests failed for mantis-msi2-2.0.0-h9948957_2.tar.bz2 - moving package to /opt/conda/conda-bld/broken + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/mantis-msi2_1734381494991/test_tmp/conda_test_runner.sh']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: mantis-msi2-2.0.0-h9948957_2.tar.bz2 +# Last 100 lines of the build log. +category: |- + test failure diff --git a/recipes/mantis-msi2/build_failure.osx-64.yaml b/recipes/mantis-msi2/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..13491491b7649 --- /dev/null +++ b/recipes/mantis-msi2/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 252f48999d534b2dc22a8cf8bcfa0750e0a444d2c0523584a557eacccc8961fb # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + + Packaging mantis-msi2 + Packaging mantis-msi2-2.0.0-h5fa12a8_2 + + WARNING: Importing conda-verify failed. Please be sure to test your packages. conda install conda-verify to make this message go away. + number of files: 9 + INFO: sysroot: '/System/Library/Frameworks/' files: '['vmnet.framework/Versions/Current', 'vmnet.framework/Versions/A/_CodeSignature/CodeResources', 'vmnet.framework/Versions/A/Resources/version.plist', 'vmnet.framework/Versions/A/Resources/InfoPlist.loctable']' + INFO: sysroot: '/usr/lib/' files: '['zsh/5.9/zsh/zselect.so', 'zsh/5.9/zsh/zpty.so', 'zsh/5.9/zsh/zprof.so', 'zsh/5.9/zsh/zleparameter.so']' + INFO: sysroot: '/opt/X11/' files: '[]' + INFO (mantis-msi2,bin/mantis-msi2-repeat-finder): Needed DSO /System/Library/Frameworks/libc.1.dylib found in $SYSROOT + INFO (mantis-msi2,bin/mantis-msi2-repeat-finder): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT + WARNING (mantis-msi2): dso library package conda-forge/osx-64::libcxx==19.1.6=hf95d169_1 in requirements/run but it is not used (i.e. it is overdepending or perhaps statically linked? If that is what you want then add it to build/ignore_run_exports) + Fixing permissions + INFO :: Time taken to mark (prefix) + 0 replacements in 0 files was 0.06 seconds + TEST START: /opt/mambaforge/envs/bioconda/conda-bld/osx-64/mantis-msi2-2.0.0-h5fa12a8_2.tar.bz2 + Renaming work directory '/opt/mambaforge/envs/bioconda/conda-bld/mantis-msi2_1734565397616/work' to '/opt/mambaforge/envs/bioconda/conda-bld/mantis-msi2_1734565397616/work_moved_mantis-msi2-2.0.0-h5fa12a8_2_osx-64' + shutil.move(work)=/opt/mambaforge/envs/bioconda/conda-bld/mantis-msi2_1734565397616/work, dest=/opt/mambaforge/envs/bioconda/conda-bld/mantis-msi2_1734565397616/work_moved_mantis-msi2-2.0.0-h5fa12a8_2_osx-64) + Reloading output folder (local): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/mantis-msi2_1734565397616/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + + + The following NEW packages will be INSTALLED: + + bzip2: 1.0.8-hfdf4475_7 conda-forge + c-ares: 1.34.4-hf13058a_0 conda-forge + ca-certificates: 2024.12.14-h8857fd0_0 conda-forge + krb5: 1.21.3-h37d8d59_0 conda-forge + libblas: 3.9.0-26_osx64_openblas conda-forge + libcblas: 3.9.0-26_osx64_openblas conda-forge + libcurl: 8.11.1-h5dec5d8_0 conda-forge + libcxx: 19.1.6-hf95d169_1 conda-forge + libdeflate: 1.22-h00291cd_0 conda-forge + libedit: 3.1.20191231-h0678c8f_2 conda-forge + libev: 4.33-h10d778d_2 conda-forge + libexpat: 2.6.4-h240833e_0 conda-forge + libffi: 3.4.2-h0d85af4_5 conda-forge + libgfortran: 5.0.0-13_2_0_h97931a8_3 conda-forge + libgfortran5: 13.2.0-h2873a65_3 conda-forge + liblapack: 3.9.0-26_osx64_openblas conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libnghttp2: 1.64.0-hc7306c3_0 conda-forge + libopenblas: 0.3.28-openmp_hbf64a52_1 conda-forge + libsqlite: 3.47.2-hdb6dae5_0 conda-forge + libssh2: 1.11.1-h3dc7d44_0 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-openmp: 19.1.6-ha54dae1_0 conda-forge + mantis-msi2: 2.0.0-h5fa12a8_2 local + ncurses: 6.5-hf036a51_1 conda-forge + numpy: 2.2.0-py312h22eab8f_0 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + pysam: 0.22.1-py312hc68ed8a_3 bioconda + python: 3.12.8-h9ccd52b_1_cpython conda-forge + python_abi: 3.12-5_cp312 conda-forge + readline: 8.2-h9e318b2_1 conda-forge + tk: 8.6.13-h1abcd95_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + mantis-msi2 --help + WARNING: Tests failed for mantis-msi2-2.0.0-h5fa12a8_2.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/mantis-msi2_1734565397616/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/mantis-msi2_1734565397616/test_tmp + Microsatellite Analysis for Normal-Tumor InStability (v2.0.0) + Error: You must have Pysam available in your environment! + Error: You must have NumPy available in your environment! + Please check your $PYTHONPATH to make sure you have properly included required moudles/libraries in it. + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/mantis-msi2_1734565397616/test_tmp/conda_test_runner.sh']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: mantis-msi2-2.0.0-h5fa12a8_2.tar.bz2 +# Last 100 lines of the build log. +category: |- + test failure diff --git a/recipes/mantis-msi2/meta.yaml b/recipes/mantis-msi2/meta.yaml index 66a6f00e23c63..cf930d74bdb7d 100644 --- a/recipes/mantis-msi2/meta.yaml +++ b/recipes/mantis-msi2/meta.yaml @@ -13,7 +13,7 @@ source: - Makefile.patch build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/mantis_pfa/meta.yaml b/recipes/mantis_pfa/meta.yaml index b1325154537ba..b85877820137c 100644 --- a/recipes/mantis_pfa/meta.yaml +++ b/recipes/mantis_pfa/meta.yaml @@ -12,7 +12,7 @@ source: sha256: a530c281c22221f54aeffa2a6e495a8c20c79c86a7d16c640bec2dd9f5d5e26b build: - number: 3 + number: 4 script: {{ PYTHON }} -m pip install . -vv skip: True # [ py < 37 ] entry_points: diff --git a/recipes/mapad/meta.yaml b/recipes/mapad/meta.yaml index 20fdd3b931c85..383c05f0fa8ee 100644 --- a/recipes/mapad/meta.yaml +++ b/recipes/mapad/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('mapad', max_pin="x.x") }} diff --git a/recipes/mapcaller/meta.yaml b/recipes/mapcaller/meta.yaml index 1aaacd6caf71b..4ad2a9b92dcb6 100644 --- a/recipes/mapcaller/meta.yaml +++ b/recipes/mapcaller/meta.yaml @@ -9,7 +9,7 @@ source: sha256: f1630d7c9243e70e33b244e3dfdb3ffa2a9836cea37fd2f8b49044dea029b12f build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/mapdia/meta.yaml b/recipes/mapdia/meta.yaml index 4fd263966a3f2..392a009dab9b9 100644 --- a/recipes/mapdia/meta.yaml +++ b/recipes/mapdia/meta.yaml @@ -3,7 +3,7 @@ package: version: 3.1.0 build: - number: 5 + number: 6 skip: True # [osx] source: diff --git a/recipes/mapping-iterative-assembler/meta.yaml b/recipes/mapping-iterative-assembler/meta.yaml index 75b613b94f13a..1393c9896a268 100644 --- a/recipes/mapping-iterative-assembler/meta.yaml +++ b/recipes/mapping-iterative-assembler/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/mappy/meta.yaml b/recipes/mappy/meta.yaml index 87e127733581f..cfb6bc658af57 100644 --- a/recipes/mappy/meta.yaml +++ b/recipes/mappy/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 0ebf7a5d62bd668f5456028215e26176e180ca68161ac18d4f7b48045484cebb build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('mappy', max_pin="x") }} diff --git a/recipes/mapseq/meta.yaml b/recipes/mapseq/meta.yaml index 46a663ed8d742..89892dedc67bb 100644 --- a/recipes/mapseq/meta.yaml +++ b/recipes/mapseq/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage('mapseq', max_pin="x") }} diff --git a/recipes/mash/meta.yaml b/recipes/mash/meta.yaml index a81dfe7d69293..ef59f1b60e831 100644 --- a/recipes/mash/meta.yaml +++ b/recipes/mash/meta.yaml @@ -12,7 +12,7 @@ source: build: skip: True # [osx] - number: 7 + number: 8 requirements: build: diff --git a/recipes/mason/meta.yaml b/recipes/mason/meta.yaml index af35dcb259990..36669b004b468 100644 --- a/recipes/mason/meta.yaml +++ b/recipes/mason/meta.yaml @@ -11,7 +11,7 @@ source: sha256: d7084d17729214003e84818e0280a16f223c8f1c6a30eeef040c27e0c0047bd7 build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage("mason", max_pin="x.y") }} diff --git a/recipes/masurca/build_failure.linux-64.yaml b/recipes/masurca/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..004df1695a2e1 --- /dev/null +++ b/recipes/masurca/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 0508bca579c70b25d563e294cb2493d3a64bd8ea0e5184b4bb06c8a19d92ac36 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + 103 | self->p1 = n; + | ~~~~~~^~ + ./include/mummer/48bit_iterator.hpp:104:11: error: 'class fortyeight_iterator' has no member named 'p2' + 104 | self->p2 = n; + | ~~~~~~^~ + ./include/mummer/48bit_iterator.hpp: In instantiation of 'Derived& fortyeight_iterator_imp::common::operator-=(difference_type) [with Derived = fortyeight_iterator; IDX = long int; difference_type = long int]': + ./include/mummer/48bit_iterator.hpp:117:56: required from 'Derived fortyeight_iterator_imp::common::operator-(difference_type) const [with Derived = fortyeight_iterator; IDX = long int; difference_type = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:99:20: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' + ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' + src/essaMEM/sparseSA.cpp:496:31: required from here + ./include/mummer/48bit_iterator.hpp:112:11: error: 'class fortyeight_iterator' has no member named 'p1' + 112 | self->p1 -= n; + | ~~~~~~^~ + ./include/mummer/48bit_iterator.hpp:113:11: error: 'class fortyeight_iterator' has no member named 'p2' + 113 | self->p2 -= n; + | ~~~~~~^~ + ./include/mummer/48bit_iterator.hpp: In instantiation of 'bool fortyeight_iterator_imp::common::operator==(const Derived&) const [with Derived = fortyeight_iterator; IDX = long int]': + ./include/compactsufsort/sssort_imp.hpp:595:31: required from 'static void compactsufsort_imp::ss::swapmerge(CHARPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/sssort_imp.hpp:654:18: required from 'static void compactsufsort_imp::ss::sort(CHARPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDX, SAIDX, SAIDX, saint_t) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator; SAIDX = long int; saint_t = int]' + ./include/compactsufsort/compactsufsort_imp.hpp:145:39: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' + ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' + src/essaMEM/sparseSA.cpp:496:31: required from here + ./include/mummer/48bit_iterator.hpp:56:47: error: 'const class fortyeight_iterator' has no member named 'p1' + 56 | return static_cast(this)->p1 == rhs.p1; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ + ./include/mummer/48bit_iterator.hpp:56:57: error: 'const class fortyeight_iterator' has no member named 'p1' + 56 | return static_cast(this)->p1 == rhs.p1; + | ~~~~^~ + ./include/mummer/48bit_iterator.hpp: In instantiation of 'fortyeight_iterator_imp::common::difference_type fortyeight_iterator_imp::common::operator-(const fortyeight_iterator_imp::common&) const [with DD = fortyeight_iterator; II = long int; Derived = const_fortyeight_iterator; IDX = long int; difference_type = long int]': + ./include/compactsufsort/trsort_imp.hpp:254:29: required from 'static void compactsufsort_imp::tr::introsort(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, trbudget_t*) [with SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator]' + ./include/compactsufsort/trsort_imp.hpp:511:22: required from 'static void compactsufsort_imp::tr::sort(SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:170:24: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' + ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' + src/essaMEM/sparseSA.cpp:496:31: required from here + ./include/mummer/48bit_iterator.hpp:121:47: error: 'const class const_fortyeight_iterator' has no member named 'p1' + 121 | return static_cast(this)->p1 - static_cast(&rhs)->p1; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ + ./include/mummer/48bit_iterator.hpp:121:82: error: 'const class fortyeight_iterator' has no member named 'p1' + 121 | return static_cast(this)->p1 - static_cast(&rhs)->p1; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ + ./include/mummer/48bit_iterator.hpp: In instantiation of 'Derived& fortyeight_iterator_imp::common::operator-=(difference_type) [with Derived = const_fortyeight_iterator; IDX = long int; difference_type = long int]': + ./include/mummer/48bit_iterator.hpp:117:56: required from 'Derived fortyeight_iterator_imp::common::operator-(difference_type) const [with Derived = const_fortyeight_iterator; IDX = long int; difference_type = long int]' + ./include/compactsufsort/trsort_imp.hpp:264:26: required from 'static void compactsufsort_imp::tr::introsort(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, trbudget_t*) [with SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator]' + ./include/compactsufsort/trsort_imp.hpp:511:22: required from 'static void compactsufsort_imp::tr::sort(SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:170:24: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' + ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' + src/essaMEM/sparseSA.cpp:496:31: required from here + ./include/mummer/48bit_iterator.hpp:112:11: error: 'class const_fortyeight_iterator' has no member named 'p1' + 112 | self->p1 -= n; + | ~~~~~~^~ + ./include/mummer/48bit_iterator.hpp:113:11: error: 'class const_fortyeight_iterator' has no member named 'p2' + 113 | self->p2 -= n; + | ~~~~~~^~ + ./include/mummer/48bit_iterator.hpp: In instantiation of 'fortyeight_iterator_imp::common::difference_type fortyeight_iterator_imp::common::operator-(const fortyeight_iterator_imp::common&) const [with DD = const_fortyeight_iterator; II = long int; Derived = fortyeight_iterator; IDX = long int; difference_type = long int]': + ./include/compactsufsort/trsort_imp.hpp:196:11: required from 'static void compactsufsort_imp::tr::copy(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDX) [with SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/trsort_imp.hpp:307:17: required from 'static void compactsufsort_imp::tr::introsort(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, trbudget_t*) [with SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator]' + ./include/compactsufsort/trsort_imp.hpp:511:22: required from 'static void compactsufsort_imp::tr::sort(SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:170:24: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' + ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' + src/essaMEM/sparseSA.cpp:496:31: required from here + ./include/mummer/48bit_iterator.hpp:121:47: error: 'const class fortyeight_iterator' has no member named 'p1' + 121 | return static_cast(this)->p1 - static_cast(&rhs)->p1; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ + ./include/mummer/48bit_iterator.hpp:121:82: error: 'const class const_fortyeight_iterator' has no member named 'p1' + 121 | return static_cast(this)->p1 - static_cast(&rhs)->p1; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ + make[2]: *** [Makefile:2073: src/essaMEM/sparseSA.lo] Error 1 + make[2]: *** Waiting for unfinished jobs.... + make[2]: Leaving directory '$SRC_DIR/global-1/MUMmer' + make[1]: *** [Makefile:2481: install] Error 2 + make[1]: Leaving directory '$SRC_DIR/global-1/MUMmer' + make: *** [Makefile:860: install-special] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/masurca_1734220589219/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/masurca_1734220589219/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/masurca/meta.yaml b/recipes/masurca/meta.yaml index 3f00ac29f5fe2..93293c867c29e 100644 --- a/recipes/masurca/meta.yaml +++ b/recipes/masurca/meta.yaml @@ -12,7 +12,7 @@ source: - 0001-install.sh.patch build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin='x') }} diff --git a/recipes/matam/meta.yaml b/recipes/matam/meta.yaml index 376f818617052..815a80bbd4991 100644 --- a/recipes/matam/meta.yaml +++ b/recipes/matam/meta.yaml @@ -14,7 +14,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 skip: True # [osx] requirements: diff --git a/recipes/matchtigs/meta.yaml b/recipes/matchtigs/meta.yaml index c27476b2c0647..e962915e9769d 100644 --- a/recipes/matchtigs/meta.yaml +++ b/recipes/matchtigs/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('matchtigs', max_pin="x") }} diff --git a/recipes/matlock/build_failure.osx-64.yaml b/recipes/matlock/build_failure.osx-64.yaml index 98b1480d66efb..c11f427a0bb29 100644 --- a/recipes/matlock/build_failure.osx-64.yaml +++ b/recipes/matlock/build_failure.osx-64.yaml @@ -1,104 +1,104 @@ -recipe_sha: 394c271b49e70fa1c1d5c758ee5a4ea9646bfa48f99d9ff5c0e9e2aeb1817c55 # The commit at which this recipe failed to build. +recipe_sha: 6e4bd85d398ce3740b151468a45ac5b4801e61c78605a2280722b75edc880ca6 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/hfile test/hfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread - x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o test/sam.o test/sam.c - clang-15: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/sam test/sam.o libhts.a -lz -lm -lbz2 -llzma -lpthread - x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o test/test_bgzf.o test/test_bgzf.c - clang-15: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread - x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o test/test-regidx.o test/test-regidx.c - clang-15: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lbz2 -llzma -lpthread - x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o test/test_view.o test/test_view.c - clang-15: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test_view test/test_view.o libhts.a -lz -lm -lbz2 -llzma -lpthread - x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o test/test-vcf-api.o test/test-vcf-api.c - clang-15: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lbz2 -llzma -lpthread - x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c - clang-15: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lbz2 -llzma -lpthread - x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c - clang-15: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread - x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c - clang-15: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread - make[1]: Leaving directory '$SRC_DIR/htslib' - x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wall -O3 -Ihtslib -Isrc -c src/matrix.c -o src/matrix.o - clang-15: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wall -O3 -Ihtslib -Isrc -c src/bam_filt.c -o src/bam_filt.o - clang-15: warning: -Wl,-pie: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o cram/files.o cram/files.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o cram/mFILE.o cram/mFILE.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o cram/sam_header.o cram/sam_header.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c + ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o + ranlib libhts.a + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -dynamiclib -install_name /usr/local/lib/libhts.2.dylib -current_version 1.7 -compatibility_version 2 -o libhts.dylib kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o -lz -lm -lbz2 -llzma + ln -sf libhts.dylib libhts.2.dylib + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o bgzip.o bgzip.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lpthread + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o htsfile.o htsfile.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o tabix.o tabix.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lpthread + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o test/hts_endian.o test/hts_endian.c + x86_64-apple-darwin13.4: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/matlock_1733852761464/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/matlock_1733852761464/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/matlock_1733852761464/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/matlock_1733852761464/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/matlock_1733852761464/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/matlock_1733852761464/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/matlock_1733852761464/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/matlock_1733852761464/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] src/bam_filt.c:187:11: error: incompatible pointer to integer conversion passing 'FILE *' (aka 'struct __sFILE *') to parameter of type 'int' [-Wint-conversion] - close(exclude_fn); - ^~~~~~~~~~ - /Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/unistd.h:431:15: note: passing argument to parameter here - int close(int) __DARWIN_ALIAS_C(close); - ^ + 187 | close(exclude_fn); + | ^~~~~~~~~~ + /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/unistd.h:436:15: note: passing argument to parameter here + 436 | int close(int) __DARWIN_ALIAS_C(close); + | ^ src/bam_filt.c:340:6: warning: variable 'okay' set but not used [-Wunused-but-set-variable] - int okay; - ^ + 340 | int okay; + | ^ 1 warning and 1 error generated. make: *** [Makefile:19: src/bam_filt.o] Error 1 Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/hts_endian test/hts_endian.o -lz -lm -lbz2 -llzma + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/matlock_1685351117927/work/conda_build.sh']' returned non-zero exit status 2. + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o test/fieldarith.o test/fieldarith.c + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/matlock_1733852761464/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lbz2 -llzma -lpthread + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/matlock_1733852761464/work/conda_build.sh']' returned non-zero exit status 2. + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o test/hfile.o test/hfile.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/hfile test/hfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o test/sam.o test/sam.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/sam test/sam.o libhts.a -lz -lm -lbz2 -llzma -lpthread + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o test/test_bgzf.o test/test_bgzf.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o test/test-regidx.o test/test-regidx.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lbz2 -llzma -lpthread + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o test/test_view.o test/test_view.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test_view test/test_view.o libhts.a -lz -lm -lbz2 -llzma -lpthread + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o test/test-vcf-api.o test/test-vcf-api.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lbz2 -llzma -lpthread + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lbz2 -llzma -lpthread + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -g -Wall -O2 -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread + make[1]: Leaving directory '$SRC_DIR/htslib' + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wall -O3 -Ihtslib -Isrc -c src/matrix.c -o src/matrix.o + x86_64-apple-darwin13.4.0-clang -fcommon -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/matlock-20181227 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wall -O3 -Ihtslib -Isrc -c src/bam_filt.c -o src/bam_filt.o # Last 100 lines of the build log. diff --git a/recipes/matlock/meta.yaml b/recipes/matlock/meta.yaml index fa4f347100d12..e95a86d050590 100644 --- a/recipes/matlock/meta.yaml +++ b/recipes/matlock/meta.yaml @@ -3,7 +3,7 @@ package: version: 20181227 build: - number: 7 + number: 8 source: - url: https://github.com/phasegenomics/matlock/archive/9fe3fdd30ca792a4e43324137d84793689893e4d.tar.gz diff --git a/recipes/mawk/meta.yaml b/recipes/mawk/meta.yaml index 4ee5d4cf677b2..873def0df7df8 100644 --- a/recipes/mawk/meta.yaml +++ b/recipes/mawk/meta.yaml @@ -10,7 +10,7 @@ source: sha256: db17115d1ed18ed1607c8b93291db9ccd4fe5e0f30d2928c3c5d127b23ec9e5b build: - number: 9 + number: 10 run_exports: - {{ pin_subpackage('mawk', max_pin="x") }} @@ -31,4 +31,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/maxbin2/meta.yaml b/recipes/maxbin2/meta.yaml index be3678a5ae378..e4648c0c5aa66 100644 --- a/recipes/maxbin2/meta.yaml +++ b/recipes/maxbin2/meta.yaml @@ -3,7 +3,7 @@ {% set sha256 = "cb6429e857280c2b75823c8cd55058ed169c93bc707a46bde0c4383f2bffe09e" %} build: - number: 5 + number: 6 skip: true # [osx] package: diff --git a/recipes/maxit/meta.yaml b/recipes/maxit/meta.yaml index 02ddd83cbf6c9..943952ff9e29a 100644 --- a/recipes/maxit/meta.yaml +++ b/recipes/maxit/meta.yaml @@ -21,7 +21,7 @@ source: sha256: b28f04dedc5fe46052a160b8124e92e94b8194ce57a463af76b37a0ca1d6f4ec # [linux and x86_64] build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} diff --git a/recipes/mbg/build_failure.linux-64.yaml b/recipes/mbg/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..7bef5df1cb4c2 --- /dev/null +++ b/recipes/mbg/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: c3225b7c93a12eda94539d2841bdb50fa341dc0b84bf5425e4b0a7872bacbfc7 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + src/VectorView.h:42:50: error: 'uint16_t' was not declared in this scope + 42 | friend unsigned __int128 hash(VectorView sequence, VectorView reverseSequence); + | ^~~~~~~~ + src/VectorView.h:42:50: note: 'uint16_t' is defined in header ''; did you forget to '#include '? + src/VectorView.h:42:58: error: template argument 1 is invalid + 42 | friend unsigned __int128 hash(VectorView sequence, VectorView reverseSequence); + | ^ + src/VectorView.h:42:81: error: 'uint16_t' was not declared in this scope + 42 | friend unsigned __int128 hash(VectorView sequence, VectorView reverseSequence); + | ^~~~~~~~ + src/VectorView.h:42:81: note: 'uint16_t' is defined in header ''; did you forget to '#include '? + src/VectorView.h:42:89: error: template argument 1 is invalid + 42 | friend unsigned __int128 hash(VectorView sequence, VectorView reverseSequence); + | ^ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -o obj/FastHasher.o src/FastHasher.cpp -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mbg-1.0.16 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -std=c17 -O3 -g -Izstr/src -Iparallel-hashmap/parallel_hashmap/ -Wno-unused-parameter -Icxxopts/include -Iconcurrentqueue pkg-config --cflags zlib + src/MBGCommon.cpp: In function 'HashType hash(VectorView)': + src/MBGCommon.cpp:13:51: error: 'const std::vector& VectorView::data' is private within this context + 13 | VectorView firstHalf { sequence.data, sequence.startpos, sequence.startpos half }; + | ^~~~ + src/VectorView.h:38:31: note: declared private here + 38 | const std::vector& data; + | ^~~~ + src/MBGCommon.cpp:13:66: error: 'size_t VectorView::startpos' is private within this context + 13 | VectorView firstHalf { sequence.data, sequence.startpos, sequence.startpos half }; + | ^~~~~~~~ + src/VectorView.h:39:16: note: declared private here + 39 | size_t startpos; + | ^~~~~~~~ + src/MBGCommon.cpp:13:85: error: 'size_t VectorView::startpos' is private within this context + 13 | VectorView firstHalf { sequence.data, sequence.startpos, sequence.startpos half }; + | ^~~~~~~~ + src/VectorView.h:39:16: note: declared private here + 39 | size_t startpos; + | ^~~~~~~~ + src/MBGCommon.cpp: In function 'HashType hash(VectorView, VectorView)': + src/MBGCommon.cpp:30:51: error: 'const std::vector& VectorView::data' is private within this context + 30 | VectorView firstHalf { sequence.data, sequence.startpos, sequence.startpos half }; + | ^~~~ + src/VectorView.h:38:31: note: declared private here + 38 | const std::vector& data; + | ^~~~ + src/MBGCommon.cpp:30:66: error: 'size_t VectorView::startpos' is private within this context + 30 | VectorView firstHalf { sequence.data, sequence.startpos, sequence.startpos half }; + | ^~~~~~~~ + src/VectorView.h:39:16: note: declared private here + 39 | size_t startpos; + | ^~~~~~~~ + src/MBGCommon.cpp:30:85: error: 'size_t VectorView::startpos' is private within this context + 30 | VectorView firstHalf { sequence.data, sequence.startpos, sequence.startpos half }; + | ^~~~~~~~ + src/VectorView.h:39:16: note: declared private here + 39 | size_t startpos; + | ^~~~~~~~ + src/MBGCommon.cpp:31:59: error: 'const std::vector& VectorView::data' is private within this context + 31 | VectorView secondHalf { reverseSequence.data, reverseSequence.startpos, reverseSequence.startpos half }; + | ^~~~ + src/VectorView.h:38:31: note: declared private here + 38 | const std::vector& data; + | ^~~~ + src/MBGCommon.cpp:31:81: error: 'size_t VectorView::startpos' is private within this context + 31 | VectorView secondHalf { reverseSequence.data, reverseSequence.startpos, reverseSequence.startpos half }; + | ^~~~~~~~ + src/VectorView.h:39:16: note: declared private here + 39 | size_t startpos; + | ^~~~~~~~ + src/MBGCommon.cpp:31:107: error: 'size_t VectorView::startpos' is private within this context + 31 | VectorView secondHalf { reverseSequence.data, reverseSequence.startpos, reverseSequence.startpos half }; + | ^~~~~~~~ + src/VectorView.h:39:16: note: declared private here + 39 | size_t startpos; + | ^~~~~~~~ + make: *** [makefile:45: obj/MBGCommon.o] Error 1 + make: *** Waiting for unfinished jobs.... + src/MBG.cpp: In function 'void runMBG(const std::vector >&, const std::string&, size_t, size_t, size_t, double, ErrorMasking, size_t, bool, const std::string&, size_t, bool, size_t, const std::string&, const std::string&, bool, double, bool, bool, bool, const std::string&, bool, bool)': + src/MBG.cpp:1540:14: warning: variable 'beforeReading' set but not used [-Wunused-but-set-variable] + 1540 | auto beforeReading = getTime(); + | ^~~~~~~~~~~~~ + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/mbg_1734293909709/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/mbg_1734293909709/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/mbg/build_failure.linux-aarch64.yaml b/recipes/mbg/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..aeb1b41a2f039 --- /dev/null +++ b/recipes/mbg/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: c3225b7c93a12eda94539d2841bdb50fa341dc0b84bf5425e4b0a7872bacbfc7 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + src/VectorView.h:42:50: error: 'uint16_t' was not declared in this scope + 42 | friend unsigned __int128 hash(VectorView sequence, VectorView reverseSequence); + | ^~~~~~~~ + src/VectorView.h:42:50: note: 'uint16_t' is defined in header ''; did you forget to '#include '? + src/VectorView.h:42:58: error: template argument 1 is invalid + 42 | friend unsigned __int128 hash(VectorView sequence, VectorView reverseSequence); + | ^ + src/VectorView.h:42:81: error: 'uint16_t' was not declared in this scope + 42 | friend unsigned __int128 hash(VectorView sequence, VectorView reverseSequence); + | ^~~~~~~~ + src/VectorView.h:42:81: note: 'uint16_t' is defined in header ''; did you forget to '#include '? + src/VectorView.h:42:89: error: template argument 1 is invalid + 42 | friend unsigned __int128 hash(VectorView sequence, VectorView reverseSequence); + | ^ + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -c -o obj/FastHasher.o src/FastHasher.cpp -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mbg-1.0.16 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -std=c17 -O3 -g -Izstr/src -Iparallel-hashmap/parallel_hashmap/ -Wno-unused-parameter -Icxxopts/include -Iconcurrentqueue pkg-config --cflags zlib + src/MBGCommon.cpp: In function 'HashType hash(VectorView)': + src/MBGCommon.cpp:13:51: error: 'const std::vector& VectorView::data' is private within this context + 13 | VectorView firstHalf { sequence.data, sequence.startpos, sequence.startpos half }; + | ^~~~ + src/VectorView.h:38:31: note: declared private here + 38 | const std::vector& data; + | ^~~~ + src/MBGCommon.cpp:13:66: error: 'size_t VectorView::startpos' is private within this context + 13 | VectorView firstHalf { sequence.data, sequence.startpos, sequence.startpos half }; + | ^~~~~~~~ + src/VectorView.h:39:16: note: declared private here + 39 | size_t startpos; + | ^~~~~~~~ + src/MBGCommon.cpp:13:85: error: 'size_t VectorView::startpos' is private within this context + 13 | VectorView firstHalf { sequence.data, sequence.startpos, sequence.startpos half }; + | ^~~~~~~~ + src/VectorView.h:39:16: note: declared private here + 39 | size_t startpos; + | ^~~~~~~~ + src/MBGCommon.cpp: In function 'HashType hash(VectorView, VectorView)': + src/MBGCommon.cpp:30:51: error: 'const std::vector& VectorView::data' is private within this context + 30 | VectorView firstHalf { sequence.data, sequence.startpos, sequence.startpos half }; + | ^~~~ + src/VectorView.h:38:31: note: declared private here + 38 | const std::vector& data; + | ^~~~ + src/MBGCommon.cpp:30:66: error: 'size_t VectorView::startpos' is private within this context + 30 | VectorView firstHalf { sequence.data, sequence.startpos, sequence.startpos half }; + | ^~~~~~~~ + src/VectorView.h:39:16: note: declared private here + 39 | size_t startpos; + | ^~~~~~~~ + src/MBGCommon.cpp:30:85: error: 'size_t VectorView::startpos' is private within this context + 30 | VectorView firstHalf { sequence.data, sequence.startpos, sequence.startpos half }; + | ^~~~~~~~ + src/VectorView.h:39:16: note: declared private here + 39 | size_t startpos; + | ^~~~~~~~ + src/MBGCommon.cpp:31:59: error: 'const std::vector& VectorView::data' is private within this context + 31 | VectorView secondHalf { reverseSequence.data, reverseSequence.startpos, reverseSequence.startpos half }; + | ^~~~ + src/VectorView.h:38:31: note: declared private here + 38 | const std::vector& data; + | ^~~~ + src/MBGCommon.cpp:31:81: error: 'size_t VectorView::startpos' is private within this context + 31 | VectorView secondHalf { reverseSequence.data, reverseSequence.startpos, reverseSequence.startpos half }; + | ^~~~~~~~ + src/VectorView.h:39:16: note: declared private here + 39 | size_t startpos; + | ^~~~~~~~ + src/MBGCommon.cpp:31:107: error: 'size_t VectorView::startpos' is private within this context + 31 | VectorView secondHalf { reverseSequence.data, reverseSequence.startpos, reverseSequence.startpos half }; + | ^~~~~~~~ + src/VectorView.h:39:16: note: declared private here + 39 | size_t startpos; + | ^~~~~~~~ + make: *** [makefile:45: obj/MBGCommon.o] Error 1 + make: *** Waiting for unfinished jobs.... + src/MBG.cpp: In function 'void runMBG(const std::vector >&, const std::string&, size_t, size_t, size_t, double, ErrorMasking, size_t, bool, const std::string&, size_t, bool, size_t, const std::string&, const std::string&, bool, double, bool, bool, bool, const std::string&, bool, bool)': + src/MBG.cpp:1540:14: warning: variable 'beforeReading' set but not used [-Wunused-but-set-variable] + 1540 | auto beforeReading = getTime(); + | ^~~~~~~~~~~~~ + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/mbg_1734270837794/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/mbg_1734270837794/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/mbg/build_failure.osx-64.yaml b/recipes/mbg/build_failure.osx-64.yaml deleted file mode 100644 index 59835935b63cd..0000000000000 --- a/recipes/mbg/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: a7e0ef3800e530d0039f90535f17f2d4a16eeaaeeeadbee534525ea1d2381a5c # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - BUILD START: ['mbg-1.0.14-hdf58011_2.tar.bz2'] - Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld - - ## Package Plan ## - - environment location: /opt/mambaforge/envs/bioconda/conda-bld/mbg_1685384925071/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ - - - The following NEW packages will be INSTALLED: - - libcxx: 16.0.4-hd57cbcb_0 conda-forge - libzlib: 1.2.13-hfd90126_4 conda-forge - zlib: 1.2.13-hfd90126_4 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld - Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld - - ## Package Plan ## - - environment location: /opt/mambaforge/envs/bioconda/conda-bld/mbg_1685384925071/_build_env - - - The following NEW packages will be INSTALLED: - - ca-certificates: 2023.5.7-h8857fd0_0 conda-forge - cctools_osx-64: 973.0.1-h48a5a9d_13 conda-forge - clang: 15.0.7-h694c41f_2 conda-forge - clang-15: 15.0.7-default_hdb78580_2 conda-forge - clang_osx-64: 15.0.7-h03d6864_3 conda-forge - clangxx: 15.0.7-default_hdb78580_2 conda-forge - clangxx_osx-64: 15.0.7-h2133e9c_3 conda-forge - compiler-rt: 15.0.7-he1888fc_1 conda-forge - compiler-rt_osx-64: 15.0.7-he1888fc_1 conda-forge - icu: 72.1-h7336db1_0 conda-forge - ld64_osx-64: 609-h8ce0179_13 conda-forge - libclang-cpp15: 15.0.7-default_hdb78580_2 conda-forge - libcxx: 16.0.4-hd57cbcb_0 conda-forge - libiconv: 1.17-hac89ed1_0 conda-forge - libllvm15: 15.0.7-he4b1e75_2 conda-forge - libxml2: 2.11.4-hd95e348_0 conda-forge - libzlib: 1.2.13-hfd90126_4 conda-forge - llvm-tools: 15.0.7-he4b1e75_2 conda-forge - make: 4.3-h22f3db7_1 conda-forge - openssl: 3.1.0-h8a1eda9_3 conda-forge - sigtool: 0.1.3-h88f4db0_0 conda-forge - tapi: 1100.0.11-h9ce4665_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - zstd: 1.5.2-hbc0c0cd_6 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - INFO:conda_build.source:Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - INFO:conda_build.source:Downloading source to cache: MBG_457d4540af.tar.gz - INFO:conda_build.source:Downloading https://github.com/maickrau/MBG/files/10847732/MBG.tar.gz - Downloading source to cache: MBG_457d4540af.tar.gz - Downloading https://github.com/maickrau/MBG/files/10847732/MBG.tar.gz - Success - INFO:conda_build.source:Success - Extracting download - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/mbg/version.patch - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/mbg/version.patch with args: - ['-Np1', '-i', '/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpaez38ful/version.patch.native', '--binary'] - checking file makefile - Hunk #1 succeeded at 22 with fuzz 2 (offset 7 lines). - patch unexpectedly ends in middle of line - patch unexpectedly ends in middle of line - patching file makefile - Hunk #1 succeeded at 22 with fuzz 2 (offset 7 lines). - patch unexpectedly ends in middle of line - patch unexpectedly ends in middle of line - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/mbg/osx_availability.patch - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/mbg/osx_availability.patch with args: - ['-Np1', '-i', '/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpf8lus_a3/osx_availability.patch.native', '--binary'] - checking file makefile - /opt/mambaforge/envs/bioconda/bin/patch: **** malformed patch at line 7: - - Warning: failed to download source. If building, will try again after downloading recipe dependencies. - Error was: - Command '['/opt/mambaforge/envs/bioconda/bin/patch', '--no-backup-if-mismatch', '--batch', '-Np1', '-i', '/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmpf8lus_a3/osx_availability.patch.native', '--binary', '--dry-run']' returned non-zero exit status 2. - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2125, in build - try_download(m, no_download_source=False, raise_error=True) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 663, in try_download - raise RuntimeError("Failed to download or patch source. Please see build log for info.") - RuntimeError: Failed to download or patch source. Please see build log for info. -# Last 100 lines of the build log. diff --git a/recipes/mbg/meta.yaml b/recipes/mbg/meta.yaml index 8b8037f18df43..41290b1aceba5 100644 --- a/recipes/mbg/meta.yaml +++ b/recipes/mbg/meta.yaml @@ -15,7 +15,7 @@ source: - mbg-aarch64.patch # [aarch64 or arm64] build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('mbg', max_pin="x.x") }} @@ -39,4 +39,4 @@ about: extra: additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 diff --git a/recipes/mbgc/meta.yaml b/recipes/mbgc/meta.yaml index a84733a119b9f..51c055cc557fb 100644 --- a/recipes/mbgc/meta.yaml +++ b/recipes/mbgc/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('mbgc', max_pin="x") }} diff --git a/recipes/mbuffer/meta.yaml b/recipes/mbuffer/meta.yaml index 6c9070f040956..9c0a3db7d6ede 100644 --- a/recipes/mbuffer/meta.yaml +++ b/recipes/mbuffer/meta.yaml @@ -7,7 +7,7 @@ source: sha256: f7769f729e9b26a22a5d91922a740a0d1df6004dbe2b7a1febb0d7e4c3ef9e62 build: - number: 6 + number: 7 skip: True # [osx] requirements: diff --git a/recipes/mcl/meta.yaml b/recipes/mcl/meta.yaml index 34eb97e7fe060..dfbbaaadbb8d2 100644 --- a/recipes/mcl/meta.yaml +++ b/recipes/mcl/meta.yaml @@ -14,7 +14,7 @@ source: folder: cimfomfa build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('mcl', max_pin=None) }} diff --git a/recipes/mdasim/meta.yaml b/recipes/mdasim/meta.yaml index feeb0fea4e740..144f573f076f1 100644 --- a/recipes/mdasim/meta.yaml +++ b/recipes/mdasim/meta.yaml @@ -12,7 +12,7 @@ source: build: # omitting OSX as the Makefile wasn't made for this (tried debugging, never ends) skip: true # [not linux64] - number: 5 + number: 6 script: make prefix=$PREFIX CPP="${CXX} ${CXXFLAGS} ${CPPFLAGS} ${LDFLAGS}" requirements: diff --git a/recipes/me-pcr/meta.yaml b/recipes/me-pcr/meta.yaml index 76450d25ec72c..8202b9a554b17 100644 --- a/recipes/me-pcr/meta.yaml +++ b/recipes/me-pcr/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/mea/meta.yaml b/recipes/mea/meta.yaml index 168e6a3500602..2577534dbbfdb 100644 --- a/recipes/mea/meta.yaml +++ b/recipes/mea/meta.yaml @@ -3,7 +3,7 @@ package: version: 0.6.4 build: - number: 8 + number: 9 skip: True # [osx] source: diff --git a/recipes/medaka/build_failure.linux-64.yaml b/recipes/medaka/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..8a8b4f19ae6c9 --- /dev/null +++ b/recipes/medaka/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 658a7dad739290a6a390f07dc587f48526cf23e7f2e2f13a8f6490bba1c30739 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [31mpython 3.10.* *_cpython[0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("libssh2[version='>=1.11.1,<2.0a0']"), MatchSpec("libcurl==8.11.1=h332b0f4_0")} + Encountered problems while solving: + - package libcurl-8.11.1-h332b0f4_0 requires libssh2 >=1.11.1,<2.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mlibcurl >=8.11.1,<9.0a0 [0m is installable and it requires + [32mlibssh2 >=1.11.1,<2.0a0 [0m, which requires + [32mlibzlib >=1.3.1,<2.0a0 [0m with the potential options + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_0[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [32mminimap2 >=2.17 [0m is installable with the potential options + [32mminimap2 2.28[0m would require + [32mk8[0m with the potential options + [31mk8 0.2.5[0m would require + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mk8 0.2.5[0m would require + [31mzlib >=1.2.13,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mk8 [0.2.5|1.0|1.2][0m would require + [31mlibzlib >=1.2.13,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [32mk8 1.2[0m would require + [32mpython_abi 3.8.* *_cp38[0m, which can be installed; + [32mk8 1.2[0m would require + [32mpython_abi 3.12.* *_cp312[0m, which can be installed; + [32mk8 1.2[0m would require + [32mpython_abi 3.13.* *_cp313[0m, which can be installed; + [31mminimap2 [2.17|2.18|...|2.24][0m would require + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mminimap2 [2.25|2.26][0m would require + [31mzlib >=1.2.13,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mminimap2 [2.26|2.27|2.28][0m would require + [31mlibzlib >=1.2.13,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [32mopenssl >=3.4.0,<4.0a0 [0m is requested and can be installed; + [32mpython >=3.10,<3.11.0a0 [0m is installable with the potential options + [31mpython [3.10.0|3.10.1|...|3.10.9][0m would require + [31mpython_abi 3.10.* *_cp310[0m, which conflicts with any installable versions previously reported; + [31mpython [3.10.0|3.10.1|3.10.2][0m would require + [31mopenssl >=1.1.1l,<1.1.2a [0m, which conflicts with any installable versions previously reported; + [31mpython 3.10.4[0m would require + [31mopenssl >=1.1.1n,<1.1.2a [0m, which conflicts with any installable versions previously reported; + [31mpython 3.10.5[0m would require + [31mopenssl >=1.1.1o,<1.1.2a [0m, which conflicts with any installable versions previously reported; + [31mpython 3.10.6[0m would require + [31mopenssl >=1.1.1q,<1.1.2a [0m, which conflicts with any installable versions previously reported; + [31mpython [3.10.7|3.10.8][0m would require + [31mopenssl >=1.1.1s,<1.1.2a [0m, which conflicts with any installable versions previously reported; + [32mpython 3.10.8[0m would require + [32mgraalpy >=23.0.0,<23.0.1.0a0 [0m, which requires + [32mpython_abi 3.10.* *_graalpy230_310_native[0m, which can be installed; + [31mpython_abi 3.10.* *_cp310[0m is not installable because there are no viable options + [31mpython_abi 3.10[0m conflicts with any installable versions previously reported; + [31mpython_abi 3.10[0m would require + [31mpython 3.10.* *_cpython[0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. +category: |- + dependency issue diff --git a/recipes/medaka/meta.yaml b/recipes/medaka/meta.yaml index 9f2a28e5e98ac..a37116b2af228 100644 --- a/recipes/medaka/meta.yaml +++ b/recipes/medaka/meta.yaml @@ -14,7 +14,7 @@ source: - patch build: - number: 0 + number: 1 skip: True # [osx or py < 38 or py > 311] entry_points: - medaka = medaka.medaka:main diff --git a/recipes/medicc2/meta.yaml b/recipes/medicc2/meta.yaml index a994a9c9b558f..3012f1cacbb90 100644 --- a/recipes/medicc2/meta.yaml +++ b/recipes/medicc2/meta.yaml @@ -12,7 +12,7 @@ source: sha256: {{ hash }} build: - number: 0 + number: 1 skip: True # [py < 38 or py >= 311] run_exports: - {{ pin_subpackage("medicc2", max_pin="x") }} diff --git a/recipes/megadepth/meta.yaml b/recipes/megadepth/meta.yaml index 44bdcbe3ea800..2b1369a96e40d 100644 --- a/recipes/megadepth/meta.yaml +++ b/recipes/megadepth/meta.yaml @@ -8,7 +8,7 @@ package: version: {{ version }} build: - number: 6 + number: 7 source: url: https://github.com/ChristopherWilks/megadepth/archive/{{ version }}.tar.gz diff --git a/recipes/megahit/build_failure.linux-64.yaml b/recipes/megahit/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..879a2344a6e7b --- /dev/null +++ b/recipes/megahit/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: faa6d80ad78999c4217cfcde4184d22d89a823a90fc880946ae638894a10a776 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + /opt/conda/conda-bld/megahit_1734292857393/work/src/localasm/local_assemble.h:1:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + |#include + 1 | /* + /opt/conda/conda-bld/megahit_1734292857393/work/src/localasm/local_assemble.h:32:3: error: 'uint32_t' does not name a type + 32 | uint32_t kmax{41}; + | ^~~~~~~~ + /opt/conda/conda-bld/megahit_1734292857393/work/src/localasm/local_assemble.h:32:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/megahit_1734292857393/work/src/localasm/local_assemble.h:33:3: error: 'uint32_t' does not name a type + 33 | uint32_t step{6}; + | ^~~~~~~~ + /opt/conda/conda-bld/megahit_1734292857393/work/src/localasm/local_assemble.h:33:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/megahit_1734292857393/work/src/localasm/local_assemble.h:34:3: error: 'uint32_t' does not name a type + 34 | uint32_t seed_kmer{31}; + | ^~~~~~~~ + /opt/conda/conda-bld/megahit_1734292857393/work/src/localasm/local_assemble.h:34:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/megahit_1734292857393/work/src/localasm/local_assemble.h:36:3: error: 'uint32_t' does not name a type + 36 | uint32_t min_contig_len{200}; + | ^~~~~~~~ + /opt/conda/conda-bld/megahit_1734292857393/work/src/localasm/local_assemble.h:36:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/megahit_1734292857393/work/src/localasm/local_assemble.h:37:3: error: 'uint32_t' does not name a type + 37 | uint32_t sparsity{8}; + | ^~~~~~~~ + /opt/conda/conda-bld/megahit_1734292857393/work/src/localasm/local_assemble.h:37:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/megahit_1734292857393/work/src/localasm/local_assemble.h:39:3: error: 'uint32_t' does not name a type + 39 | uint32_t min_mapping_len{75}; + | ^~~~~~~~ + /opt/conda/conda-bld/megahit_1734292857393/work/src/localasm/local_assemble.h:39:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/megahit_1734292857393/work/src/localasm/local_assemble.h:41:3: error: 'uint32_t' does not name a type + 41 | uint32_t num_threads{0}; + | ^~~~~~~~ + /opt/conda/conda-bld/megahit_1734292857393/work/src/localasm/local_assemble.h:41:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/megahit_1734292857393/work/src/main_local_assemble.cpp: In function 'LocalAsmOption {anonymous}::ParseLocalAsmOptions(int, char**)': + /opt/conda/conda-bld/megahit_1734292857393/work/src/main_local_assemble.cpp:40:34: error: 'struct LocalAsmOption' has no member named 'kmin' + 40 | desc.AddOption("kmin", "", opt.kmin, ""); + | ^~~~ + /opt/conda/conda-bld/megahit_1734292857393/work/src/main_local_assemble.cpp:41:34: error: 'struct LocalAsmOption' has no member named 'kmax' + 41 | desc.AddOption("kmax", "", opt.kmax, ""); + | ^~~~ + /opt/conda/conda-bld/megahit_1734292857393/work/src/main_local_assemble.cpp:42:34: error: 'struct LocalAsmOption' has no member named 'step' + 42 | desc.AddOption("step", "", opt.step, ""); + | ^~~~ + /opt/conda/conda-bld/megahit_1734292857393/work/src/main_local_assemble.cpp:43:39: error: 'struct LocalAsmOption' has no member named 'seed_kmer' + 43 | desc.AddOption("seed_kmer", "", opt.seed_kmer, + | ^~~~~~~~~ + /opt/conda/conda-bld/megahit_1734292857393/work/src/main_local_assemble.cpp:45:44: error: 'struct LocalAsmOption' has no member named 'min_contig_len' + 45 | desc.AddOption("min_contig_len", "", opt.min_contig_len, ""); + | ^~~~~~~~~~~~~~ + /opt/conda/conda-bld/megahit_1734292857393/work/src/main_local_assemble.cpp:46:45: error: 'struct LocalAsmOption' has no member named 'min_mapping_len' + 46 | desc.AddOption("min_mapping_len", "", opt.min_mapping_len, ""); + | ^~~~~~~~~~~~~~~ + /opt/conda/conda-bld/megahit_1734292857393/work/src/main_local_assemble.cpp:47:38: error: 'struct LocalAsmOption' has no member named 'sparsity' + 47 | desc.AddOption("sparsity", "", opt.sparsity, "sparsity of hash mapper"); + | ^~~~~~~~ + /opt/conda/conda-bld/megahit_1734292857393/work/src/main_local_assemble.cpp:50:42: error: 'struct LocalAsmOption' has no member named 'num_threads' + 50 | desc.AddOption("num_threads", "t", opt.num_threads, ""); + | ^~~~~~~~~~~ + /opt/conda/conda-bld/megahit_1734292857393/work/src/main_local_assemble.cpp:64:13: error: 'struct LocalAsmOption' has no member named 'num_threads' + 64 | if (opt.num_threads == 0) { + | ^~~~~~~~~~~ + /opt/conda/conda-bld/megahit_1734292857393/work/src/main_local_assemble.cpp:65:11: error: 'struct LocalAsmOption' has no member named 'num_threads' + 65 | opt.num_threads = omp_get_max_threads(); + | ^~~~~~~~~~~ + /opt/conda/conda-bld/megahit_1734292857393/work/src/main_local_assemble.cpp: In function 'int main_local(int, char**)': + /opt/conda/conda-bld/megahit_1734292857393/work/src/main_local_assemble.cpp:83:27: error: 'struct LocalAsmOption' has no member named 'num_threads' + 83 | omp_set_num_threads(opt.num_threads); + | ^~~~~~~~~~~ + make[2]: *** [CMakeFiles/megahit_core.dir/build.make:138: CMakeFiles/megahit_core.dir/src/main_local_assemble.cpp.o] Error 1 + make[2]: *** Waiting for unfinished jobs.... + make[1]: *** [CMakeFiles/Makefile2:134: CMakeFiles/megahit_core_popcnt.dir/all] Error 2 + make[1]: *** Waiting for unfinished jobs.... + make[2]: Leaving directory '$SRC_DIR/build' + make[2]: Leaving directory '$SRC_DIR/build' + make[1]: *** [CMakeFiles/Makefile2:165: CMakeFiles/megahit_core_no_hw_accel.dir/all] Error 2 + make[2]: Leaving directory '$SRC_DIR/build' + make[1]: *** [CMakeFiles/Makefile2:103: CMakeFiles/megahit_core.dir/all] Error 2 + make[1]: Leaving directory '$SRC_DIR/build' + make: *** [Makefile:139: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/megahit_1734292857393/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/megahit_1734292857393/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/megahit/build_failure.linux-aarch64.yaml b/recipes/megahit/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..c590376ef967f --- /dev/null +++ b/recipes/megahit/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: faa6d80ad78999c4217cfcde4184d22d89a823a90fc880946ae638894a10a776 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + /opt/conda/conda-bld/megahit_1734271126154/work/src/localasm/local_assemble.h:1:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + |#include + 1 | /* + /opt/conda/conda-bld/megahit_1734271126154/work/src/localasm/local_assemble.h:32:3: error: 'uint32_t' does not name a type + 32 | uint32_t kmax{41}; + | ^~~~~~~~ + /opt/conda/conda-bld/megahit_1734271126154/work/src/localasm/local_assemble.h:32:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/megahit_1734271126154/work/src/localasm/local_assemble.h:33:3: error: 'uint32_t' does not name a type + 33 | uint32_t step{6}; + | ^~~~~~~~ + /opt/conda/conda-bld/megahit_1734271126154/work/src/localasm/local_assemble.h:33:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/megahit_1734271126154/work/src/localasm/local_assemble.h:34:3: error: 'uint32_t' does not name a type + 34 | uint32_t seed_kmer{31}; + | ^~~~~~~~ + /opt/conda/conda-bld/megahit_1734271126154/work/src/localasm/local_assemble.h:34:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/megahit_1734271126154/work/src/localasm/local_assemble.h:36:3: error: 'uint32_t' does not name a type + 36 | uint32_t min_contig_len{200}; + | ^~~~~~~~ + /opt/conda/conda-bld/megahit_1734271126154/work/src/localasm/local_assemble.h:36:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/megahit_1734271126154/work/src/localasm/local_assemble.h:37:3: error: 'uint32_t' does not name a type + 37 | uint32_t sparsity{8}; + | ^~~~~~~~ + /opt/conda/conda-bld/megahit_1734271126154/work/src/localasm/local_assemble.h:37:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/megahit_1734271126154/work/src/localasm/local_assemble.h:39:3: error: 'uint32_t' does not name a type + 39 | uint32_t min_mapping_len{75}; + | ^~~~~~~~ + /opt/conda/conda-bld/megahit_1734271126154/work/src/localasm/local_assemble.h:39:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/megahit_1734271126154/work/src/localasm/local_assemble.h:41:3: error: 'uint32_t' does not name a type + 41 | uint32_t num_threads{0}; + | ^~~~~~~~ + /opt/conda/conda-bld/megahit_1734271126154/work/src/localasm/local_assemble.h:41:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/megahit_1734271126154/work/src/main_local_assemble.cpp: In function 'LocalAsmOption {anonymous}::ParseLocalAsmOptions(int, char**)': + /opt/conda/conda-bld/megahit_1734271126154/work/src/main_local_assemble.cpp:40:34: error: 'struct LocalAsmOption' has no member named 'kmin' + 40 | desc.AddOption("kmin", "", opt.kmin, ""); + | ^~~~ + /opt/conda/conda-bld/megahit_1734271126154/work/src/main_local_assemble.cpp:41:34: error: 'struct LocalAsmOption' has no member named 'kmax' + 41 | desc.AddOption("kmax", "", opt.kmax, ""); + | ^~~~ + /opt/conda/conda-bld/megahit_1734271126154/work/src/main_local_assemble.cpp:42:34: error: 'struct LocalAsmOption' has no member named 'step' + 42 | desc.AddOption("step", "", opt.step, ""); + | ^~~~ + /opt/conda/conda-bld/megahit_1734271126154/work/src/main_local_assemble.cpp:43:39: error: 'struct LocalAsmOption' has no member named 'seed_kmer' + 43 | desc.AddOption("seed_kmer", "", opt.seed_kmer, + | ^~~~~~~~~ + /opt/conda/conda-bld/megahit_1734271126154/work/src/main_local_assemble.cpp:45:44: error: 'struct LocalAsmOption' has no member named 'min_contig_len' + 45 | desc.AddOption("min_contig_len", "", opt.min_contig_len, ""); + | ^~~~~~~~~~~~~~ + /opt/conda/conda-bld/megahit_1734271126154/work/src/main_local_assemble.cpp:46:45: error: 'struct LocalAsmOption' has no member named 'min_mapping_len' + 46 | desc.AddOption("min_mapping_len", "", opt.min_mapping_len, ""); + | ^~~~~~~~~~~~~~~ + /opt/conda/conda-bld/megahit_1734271126154/work/src/main_local_assemble.cpp:47:38: error: 'struct LocalAsmOption' has no member named 'sparsity' + 47 | desc.AddOption("sparsity", "", opt.sparsity, "sparsity of hash mapper"); + | ^~~~~~~~ + /opt/conda/conda-bld/megahit_1734271126154/work/src/main_local_assemble.cpp:50:42: error: 'struct LocalAsmOption' has no member named 'num_threads' + 50 | desc.AddOption("num_threads", "t", opt.num_threads, ""); + | ^~~~~~~~~~~ + /opt/conda/conda-bld/megahit_1734271126154/work/src/main_local_assemble.cpp:64:13: error: 'struct LocalAsmOption' has no member named 'num_threads' + 64 | if (opt.num_threads == 0) { + | ^~~~~~~~~~~ + /opt/conda/conda-bld/megahit_1734271126154/work/src/main_local_assemble.cpp:65:11: error: 'struct LocalAsmOption' has no member named 'num_threads' + 65 | opt.num_threads = omp_get_max_threads(); + | ^~~~~~~~~~~ + /opt/conda/conda-bld/megahit_1734271126154/work/src/main_local_assemble.cpp: In function 'int main_local(int, char**)': + /opt/conda/conda-bld/megahit_1734271126154/work/src/main_local_assemble.cpp:83:27: error: 'struct LocalAsmOption' has no member named 'num_threads' + 83 | omp_set_num_threads(opt.num_threads); + | ^~~~~~~~~~~ + make[2]: *** [CMakeFiles/megahit_core_no_hw_accel.dir/build.make:138: CMakeFiles/megahit_core_no_hw_accel.dir/src/main_local_assemble.cpp.o] Error 1 + make[2]: *** Waiting for unfinished jobs.... + make[2]: Leaving directory '$SRC_DIR/build' + make[1]: *** [CMakeFiles/Makefile2:103: CMakeFiles/megahit_core.dir/all] Error 2 + make[1]: *** Waiting for unfinished jobs.... + make[2]: Leaving directory '$SRC_DIR/build' + make[1]: *** [CMakeFiles/Makefile2:165: CMakeFiles/megahit_core_no_hw_accel.dir/all] Error 2 + make[2]: Leaving directory '$SRC_DIR/build' + make[1]: *** [CMakeFiles/Makefile2:134: CMakeFiles/megahit_core_popcnt.dir/all] Error 2 + make: *** [Makefile:139: all] Error 2 + make[1]: Leaving directory '$SRC_DIR/build' + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/megahit_1734271126154/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/megahit_1734271126154/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/megalodon/build_failure.linux-64.yaml b/recipes/megalodon/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..b1562cc32d5ca --- /dev/null +++ b/recipes/megalodon/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: a097c604b06c83d212f1ff4e664539f534d3191b6db3a990ca01b989fc39a76b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + libpng: 1.6.44-hadc24fc_0 conda-forge + libsqlite: 3.47.2-hee588c1_0 conda-forge + libssh2: 1.11.1-hf672d98_0 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-ng: 14.2.0-h4852527_1 conda-forge + libtiff: 4.7.0-hc4654cb_2 conda-forge + libuuid: 2.38.1-h0b41bf4_0 conda-forge + libwebp-base: 1.4.0-hd590300_0 conda-forge + libxcb: 1.17.0-h8a09558_0 conda-forge + libxcrypt: 4.4.36-hd590300_1 conda-forge + libzlib: 1.3.1-hb9d3cd8_2 conda-forge + mappy: 2.28-py310h397c9d8_3 bioconda + matplotlib-base: 3.9.4-py310h68603db_0 conda-forge + megalodon: 2.5.0-py310h1fe012e_3 local + munkres: 1.1.4-pyh9f0ad1d_0 conda-forge + ncurses: 6.5-he02047a_1 conda-forge + numpy: 2.2.0-py310h5851e9f_0 conda-forge + ont-fast5-api: 4.1.3-pyhdfd78af_0 bioconda + openjpeg: 2.5.3-h5fbd93e_0 conda-forge + openssl: 3.4.0-hb9d3cd8_0 conda-forge + packaging: 24.2-pyhd8ed1ab_2 conda-forge + pandas: 2.2.3-py310h5eaa309_1 conda-forge + patsy: 1.0.1-pyhd8ed1ab_1 conda-forge + pillow: 11.0.0-py310hfeaa1f3_0 conda-forge + pip: 24.3.1-pyh8b19718_0 conda-forge + progressbar33: 2.4-py_0 conda-forge + pthread-stubs: 0.4-hb9d3cd8_1002 conda-forge + pyparsing: 3.2.0-pyhd8ed1ab_2 conda-forge + pysam: 0.22.1-py310h64e62c9_3 file:///opt/host-conda-bld + python: 3.10.16-he725a3c_1_cpython conda-forge + python-dateutil: 2.9.0.post0-pyhff2d567_1 conda-forge + python-tzdata: 2024.2-pyhd8ed1ab_1 conda-forge + python_abi: 3.10-5_cp310 conda-forge + pytz: 2024.1-pyhd8ed1ab_0 conda-forge + qhull: 2020.2-h434a139_5 conda-forge + readline: 8.2-h8228510_1 conda-forge + scikit-learn: 1.6.0-py310h27f47ee_0 conda-forge + scipy: 1.14.1-py310hfcf56fc_2 conda-forge + seaborn: 0.13.2-hd8ed1ab_3 conda-forge + seaborn-base: 0.13.2-pyhd8ed1ab_3 conda-forge + setuptools: 75.6.0-pyhff2d567_1 conda-forge + six: 1.17.0-pyhd8ed1ab_0 conda-forge + statsmodels: 0.14.4-py310hf462985_0 conda-forge + tar: 1.34-hb2e2bae_1 conda-forge + threadpoolctl: 3.5.0-pyhc1e730c_0 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tqdm: 4.67.1-pyhd8ed1ab_0 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + unicodedata2: 15.1.0-py310ha75aee5_1 conda-forge + wheel: 0.45.1-pyhd8ed1ab_1 conda-forge + xorg-libxau: 1.0.12-hb9d3cd8_0 conda-forge + xorg-libxdmcp: 1.1.5-hb9d3cd8_0 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + export PREFIX=/opt/conda/conda-bld/megalodon_1734308078821/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export SRC_DIR=/opt/conda/conda-bld/megalodon_1734308078821/test_tmp + import: 'megalodon' + import: 'megalodon_extras' + import: 'megalodon' + import: 'megalodon_extras' + megalodon --help + Traceback (most recent call last): + File "/opt/conda/conda-bld/megalodon_1734308078821/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/megalodon", line 7, in + from megalodon.__main__ import _main + File "/opt/conda/conda-bld/megalodon_1734308078821/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/python3.10/site-packages/megalodon/__main__.py", line 4, in + from megalodon import megalodon_helper as mh, __version__ + File "/opt/conda/conda-bld/megalodon_1734308078821/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/python3.10/site-packages/megalodon/megalodon_helper.py", line 63, in + SEQ_TO_INT_ARR = np.full(26, -1, dtype=np.uintp) + File "/opt/conda/conda-bld/megalodon_1734308078821/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/python3.10/site-packages/numpy/_core/numeric.py", line 353, in full + multiarray.copyto(a, fill_value, casting='unsafe') + OverflowError: Python integer -1 out of bounds for uint64 + WARNING: Tests failed for megalodon-2.5.0-py310h1fe012e_3.tar.bz2 - moving package to /opt/conda/conda-bld/broken + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/megalodon_1734308078821/test_tmp/conda_test_runner.sh']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: megalodon-2.5.0-py310h1fe012e_3.tar.bz2 +# Last 100 lines of the build log. +category: |- + test failure diff --git a/recipes/megalodon/build_failure.linux-aarch64.yaml b/recipes/megalodon/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..6ffd82e48338d --- /dev/null +++ b/recipes/megalodon/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: a097c604b06c83d212f1ff4e664539f534d3191b6db3a990ca01b989fc39a76b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + libsqlite: 3.47.2-h5eb1b54_0 conda-forge + libssh2: 1.11.1-ha41c0db_0 conda-forge + libstdcxx: 14.2.0-h3f4de04_1 conda-forge + libstdcxx-ng: 14.2.0-hf1166c9_1 conda-forge + libtiff: 4.7.0-hca96517_2 conda-forge + libuuid: 2.38.1-hb4cce97_0 conda-forge + libwebp-base: 1.4.0-h31becfc_0 conda-forge + libxcb: 1.17.0-h262b8f6_0 conda-forge + libxcrypt: 4.4.36-h31becfc_1 conda-forge + libzlib: 1.3.1-h86ecc28_2 conda-forge + mappy: 2.28-py311hb8445d5_3 bioconda + matplotlib-base: 3.10.0-py311h0385ec1_0 conda-forge + megalodon: 2.5.0-py311he810f1b_3 local + munkres: 1.1.4-pyh9f0ad1d_0 conda-forge + ncurses: 6.5-hcccb83c_1 conda-forge + numpy: 2.2.0-py311h9fc3674_0 conda-forge + ont-fast5-api: 4.1.3-pyhdfd78af_0 bioconda + openjpeg: 2.5.3-h3f56577_0 conda-forge + openssl: 3.4.0-h86ecc28_0 conda-forge + packaging: 24.2-pyhd8ed1ab_2 conda-forge + pandas: 2.2.3-py311h848c333_1 conda-forge + patsy: 1.0.1-pyhd8ed1ab_1 conda-forge + pillow: 11.0.0-py311hb2a0dd2_0 conda-forge + pip: 24.3.1-pyh8b19718_2 conda-forge + progressbar33: 2.4-py_0 conda-forge + pthread-stubs: 0.4-h86ecc28_1002 conda-forge + pyparsing: 3.2.0-pyhd8ed1ab_2 conda-forge + pysam: 0.22.1-py311h3a7b516_3 bioconda + python: 3.11.11-h1683364_1_cpython conda-forge + python-dateutil: 2.9.0.post0-pyhff2d567_1 conda-forge + python-tzdata: 2024.2-pyhd8ed1ab_1 conda-forge + python_abi: 3.11-5_cp311 conda-forge + pytz: 2024.1-pyhd8ed1ab_0 conda-forge + qhull: 2020.2-h70be974_5 conda-forge + readline: 8.2-h8fc344f_1 conda-forge + scikit-learn: 1.6.0-py311hd29cff0_0 conda-forge + scipy: 1.14.1-py311h5912639_2 conda-forge + seaborn: 0.13.2-hd8ed1ab_3 conda-forge + seaborn-base: 0.13.2-pyhd8ed1ab_3 conda-forge + setuptools: 75.6.0-pyhff2d567_1 conda-forge + six: 1.17.0-pyhd8ed1ab_0 conda-forge + statsmodels: 0.14.4-py311hec9beba_0 conda-forge + tar: 1.34-h048efde_0 conda-forge + threadpoolctl: 3.5.0-pyhc1e730c_0 conda-forge + tk: 8.6.13-h194ca79_0 conda-forge + tqdm: 4.67.1-pyhd8ed1ab_0 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + unicodedata2: 15.1.0-py311ha879c10_1 conda-forge + wheel: 0.45.1-pyhd8ed1ab_1 conda-forge + xorg-libxau: 1.0.12-h86ecc28_0 conda-forge + xorg-libxdmcp: 1.1.5-h57736b2_0 conda-forge + zstd: 1.5.6-h02f22dd_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + export PREFIX=/opt/conda/conda-bld/megalodon_1734553995965/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export SRC_DIR=/opt/conda/conda-bld/megalodon_1734553995965/test_tmp + import: 'megalodon' + import: 'megalodon_extras' + import: 'megalodon' + import: 'megalodon_extras' + megalodon --help + Traceback (most recent call last): + File "/opt/conda/conda-bld/megalodon_1734553995965/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/megalodon", line 7, in + from megalodon.__main__ import _main + File "/opt/conda/conda-bld/megalodon_1734553995965/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/python3.11/site-packages/megalodon/__main__.py", line 4, in + from megalodon import megalodon_helper as mh, __version__ + File "/opt/conda/conda-bld/megalodon_1734553995965/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/python3.11/site-packages/megalodon/megalodon_helper.py", line 63, in + SEQ_TO_INT_ARR = np.full(26, -1, dtype=np.uintp) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/conda/conda-bld/megalodon_1734553995965/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/python3.11/site-packages/numpy/_core/numeric.py", line 353, in full + multiarray.copyto(a, fill_value, casting='unsafe') + OverflowError: Python integer -1 out of bounds for uint64 + WARNING: Tests failed for megalodon-2.5.0-py311he810f1b_3.tar.bz2 - moving package to /opt/conda/conda-bld/broken + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/megalodon_1734553995965/test_tmp/conda_test_runner.sh']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: megalodon-2.5.0-py311he810f1b_3.tar.bz2 +# Last 100 lines of the build log. +category: |- + test failure diff --git a/recipes/megalodon/build_failure.osx-64.yaml b/recipes/megalodon/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..83e2b55aebe35 --- /dev/null +++ b/recipes/megalodon/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: a097c604b06c83d212f1ff4e664539f534d3191b6db3a990ca01b989fc39a76b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + liblapack: 3.9.0-26_osx64_openblas conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libnghttp2: 1.64.0-hc7306c3_0 conda-forge + libopenblas: 0.3.28-openmp_hbf64a52_1 conda-forge + libpng: 1.6.44-h4b8f8c9_0 conda-forge + libsqlite: 3.47.2-hdb6dae5_0 conda-forge + libssh2: 1.11.1-h3dc7d44_0 conda-forge + libtiff: 4.7.0-hf4bdac2_2 conda-forge + libwebp-base: 1.4.0-h10d778d_0 conda-forge + libxcb: 1.17.0-hf1f96e2_0 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-openmp: 19.1.6-ha54dae1_0 conda-forge + mappy: 2.28-py312h3f31e45_3 bioconda + matplotlib-base: 3.10.0-py312h535dea3_0 conda-forge + megalodon: 2.5.0-py312h73b7c68_3 local + munkres: 1.1.4-pyh9f0ad1d_0 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + numpy: 2.2.0-py312h22eab8f_0 conda-forge + ont-fast5-api: 4.1.3-pyhdfd78af_0 bioconda + openjpeg: 2.5.3-h7fd6d84_0 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + packaging: 24.2-pyhd8ed1ab_2 conda-forge + pandas: 2.2.3-py312h98e817e_1 conda-forge + patsy: 1.0.1-pyhd8ed1ab_1 conda-forge + pillow: 11.0.0-py312h66fe14f_0 conda-forge + progressbar33: 2.4-py_0 conda-forge + pthread-stubs: 0.4-h00291cd_1002 conda-forge + pyparsing: 3.2.0-pyhd8ed1ab_2 conda-forge + pysam: 0.22.1-py312hc68ed8a_3 bioconda + python: 3.12.8-h9ccd52b_1_cpython conda-forge + python-dateutil: 2.9.0.post0-pyhff2d567_1 conda-forge + python-tzdata: 2024.2-pyhd8ed1ab_1 conda-forge + python_abi: 3.12-5_cp312 conda-forge + pytz: 2024.1-pyhd8ed1ab_0 conda-forge + qhull: 2020.2-h3c5361c_5 conda-forge + readline: 8.2-h9e318b2_1 conda-forge + scikit-learn: 1.6.0-py312he1a5313_0 conda-forge + scipy: 1.14.1-py312h3b0f538_2 conda-forge + seaborn: 0.13.2-hd8ed1ab_3 conda-forge + seaborn-base: 0.13.2-pyhd8ed1ab_3 conda-forge + setuptools: 75.6.0-pyhff2d567_1 conda-forge + six: 1.17.0-pyhd8ed1ab_0 conda-forge + statsmodels: 0.14.4-py312h3a11e2b_0 conda-forge + tar: 1.34-hcb2f6ea_1 conda-forge + threadpoolctl: 3.5.0-pyhc1e730c_0 conda-forge + tk: 8.6.13-h1abcd95_1 conda-forge + tqdm: 4.67.1-pyhd8ed1ab_0 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + unicodedata2: 15.1.0-py312h3d0f464_1 conda-forge + xorg-libxau: 1.0.12-h6e16a3a_0 conda-forge + xorg-libxdmcp: 1.1.5-h00291cd_0 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + megalodon --help + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/conda-bld/megalodon_1734562430956/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/megalodon", line 7, in + from megalodon.__main__ import _main + File "/opt/mambaforge/envs/bioconda/conda-bld/megalodon_1734562430956/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/python3.12/site-packages/megalodon/__main__.py", line 4, in + from megalodon import megalodon_helper as mh, __version__ + File "/opt/mambaforge/envs/bioconda/conda-bld/megalodon_1734562430956/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/python3.12/site-packages/megalodon/megalodon_helper.py", line 63, in + SEQ_TO_INT_ARR = np.full(26, -1, dtype=np.uintp) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "/opt/mambaforge/envs/bioconda/conda-bld/megalodon_1734562430956/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/python3.12/site-packages/numpy/_core/numeric.py", line 353, in full + multiarray.copyto(a, fill_value, casting='unsafe') + OverflowError: Python integer -1 out of bounds for uint64 + WARNING: Tests failed for megalodon-2.5.0-py312h73b7c68_3.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/megalodon_1734562430956/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/megalodon_1734562430956/test_tmp + import: 'megalodon' + import: 'megalodon_extras' + import: 'megalodon' + import: 'megalodon_extras' + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/megalodon_1734562430956/test_tmp/conda_test_runner.sh']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: megalodon-2.5.0-py312h73b7c68_3.tar.bz2 +# Last 100 lines of the build log. +category: |- + test failure diff --git a/recipes/megalodon/meta.yaml b/recipes/megalodon/meta.yaml index a6b6ad8d40cfb..a42ce86932c8c 100644 --- a/recipes/megalodon/meta.yaml +++ b/recipes/megalodon/meta.yaml @@ -16,7 +16,7 @@ build: - megalodon = megalodon.__main__:_main - megalodon_extras = megalodon_extras.__main__:_main script: {{ PYTHON }} -m pip install . --no-deps -vv - number: 2 + number: 3 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/parascopy/build_failure.linux-64.yaml b/recipes/megapath/build_failure.linux-64.yaml similarity index 58% rename from recipes/parascopy/build_failure.linux-64.yaml rename to recipes/megapath/build_failure.linux-64.yaml index 1d06571c199a5..15700464c39b6 100644 --- a/recipes/parascopy/build_failure.linux-64.yaml +++ b/recipes/megapath/build_failure.linux-64.yaml @@ -1,13 +1,23 @@ -recipe_sha: 8e3479136cbb5821860a11749a2a429e5538586bdb8a323823d8dabca6a4807f # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: d52ee7b1add0ea13903e43a9e0c52ac23bad38e1f9569fb1ba54e57165ecb090 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [31msamtools 1.10.* [0m is not installable because it requires + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions - precs = _install_actions(prefix, index, specs)["LINK"] - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction unlink_precs, link_precs = self.solve_for_diff( - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff final_precs = self.solve_final_state( File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state out_state = self._solving_loop(in_state, out_state, index) @@ -19,57 +29,52 @@ log: |2- self._maybe_raise_for_conda_build( File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("python_abi=2.7[build=*_cp27mu]"), MatchSpec("pysam==0.17.0=py27h2b63b3a_1")} + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']"), MatchSpec("samtools==1.10=h2e538c0_3")} Encountered problems while solving: - - package pysam-0.17.0-py27h2b63b3a_1 requires python_abi 2.7.* *_cp27mu, but none of the providers can be installed + - package samtools-1.10-h2e538c0_3 requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed Could not solve for environment specs The following packages are incompatible - [32mpysam >=0.17 [0m is installable with the potential options - [32mpysam [0.17.0|0.18.0|0.19.0|0.19.1|0.20.0][0m would require - [32mpython_abi 2.7.* *_cp27mu[0m, which can be installed; - [32mpysam [0.17.0|0.18.0|...|0.21.0][0m would require - [32mpython_abi 3.6.* *_cp36m[0m, which can be installed; - [32mpysam [0.17.0|0.18.0|...|0.21.0][0m would require - [32mpython_abi 3.7.* *_cp37m[0m, which can be installed; - [32mpysam [0.17.0|0.18.0|...|0.22.1][0m would require - [32mpython_abi 3.8.* *_cp38[0m, which can be installed; - [32mpysam [0.17.0|0.18.0|...|0.22.1][0m would require - [32mpython_abi 3.9.* *_cp39[0m, which can be installed; - [32mpysam [0.19.1|0.20.0|0.21.0|0.22.0|0.22.1][0m would require - [32mpython_abi 3.10.* *_cp310[0m, which can be installed; - [31mpython_abi 3.12.* *_cp312[0m is not installable because it conflicts with any installable versions previously reported. + [32mlibzlib >=1.3.1,<2.0a0 [0m is installable with the potential options + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_0[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [31msamtools 1.10.* [0m is not installable because it requires + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/opt/conda/bin/conda-build", line 11, in sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2409, in build + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build create_build_envs(top_level_pkg, notest) - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2247, in create_build_envs + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs raise e - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2220, in create_build_envs + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs environ.get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions precs = get_package_records( File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions - precs = _install_actions(prefix, index, specs)["LINK"] - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction unlink_precs, link_precs = self.solve_for_diff( - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff final_precs = self.solve_final_state( File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state out_state = self._solving_loop(in_state, out_state, index) @@ -81,24 +86,19 @@ log: |2- self._maybe_raise_for_conda_build( File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("python_abi=2.7[build=*_cp27mu]"), MatchSpec("pysam==0.17.0=py27h2b63b3a_1")} + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']"), MatchSpec("samtools==1.10=h2e538c0_3")} Encountered problems while solving: - - package pysam-0.17.0-py27h2b63b3a_1 requires python_abi 2.7.* *_cp27mu, but none of the providers can be installed + - package samtools-1.10-h2e538c0_3 requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed Could not solve for environment specs The following packages are incompatible - [32mpysam >=0.17 [0m is installable with the potential options - [32mpysam [0.17.0|0.18.0|0.19.0|0.19.1|0.20.0][0m would require - [32mpython_abi 2.7.* *_cp27mu[0m, which can be installed; - [32mpysam [0.17.0|0.18.0|...|0.21.0][0m would require - [32mpython_abi 3.6.* *_cp36m[0m, which can be installed; - [32mpysam [0.17.0|0.18.0|...|0.21.0][0m would require - [32mpython_abi 3.7.* *_cp37m[0m, which can be installed; - [32mpysam [0.17.0|0.18.0|...|0.22.1][0m would require - [32mpython_abi 3.8.* *_cp38[0m, which can be installed; - [32mpysam [0.17.0|0.18.0|...|0.22.1][0m would require - [32mpython_abi 3.9.* *_cp39[0m, which can be installed; - [32mpysam [0.19.1|0.20.0|0.21.0|0.22.0|0.22.1][0m would require - [32mpython_abi 3.10.* *_cp310[0m, which can be installed; - [31mpython_abi 3.12.* *_cp312[0m is not installable because it conflicts with any installable versions previously reported. + [32mlibzlib >=1.3.1,<2.0a0 [0m is installable with the potential options + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_0[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [31msamtools 1.10.* [0m is not installable because it requires + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported. # Last 100 lines of the build log. diff --git a/recipes/megapath/meta.yaml b/recipes/megapath/meta.yaml index ef298cec6be58..7921ac1eddbd7 100644 --- a/recipes/megapath/meta.yaml +++ b/recipes/megapath/meta.yaml @@ -12,7 +12,7 @@ source: build: skip: True # [not linux] - number: 4 + number: 5 requirements: build: diff --git a/recipes/mehari/build_failure.linux-64.yaml b/recipes/mehari/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..eb1a35144cfba --- /dev/null +++ b/recipes/mehari/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 6791a3edec1b5d14f9faf7c8e9788b1306d9776fece9e216b4c9e6e7048a3302 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + Compiling actix-web-codegen v4.3.0 + Compiling actix-server v2.5.0 + Compiling serde_urlencoded v0.7.1 + Compiling biocommons-bioutils v0.1.4 + Compiling noodles-gff v0.34.0 + Compiling annonars v0.40.0 + Compiling noodles-fasta v0.40.0 + Compiling env_filter v0.1.2 + Compiling serde_with_macros v3.9.0 + Compiling cached_proc_macro v0.23.0 + Compiling derive_builder_core v0.20.0 + Compiling sharded-slab v0.1.7 + Compiling tracing-log v0.2.0 + Compiling noodles-bed v0.15.0 + Compiling actix-macros v0.2.4 + Compiling thread_local v1.1.8 + Compiling object v0.36.3 + Compiling web-time v1.1.0 + Compiling hex v0.4.3 + Compiling typeid v1.0.0 + Compiling procfs v0.16.0 + Compiling impl-more v0.1.6 + Compiling cached_proc_macro_types v0.1.1 + Compiling urlencoding v2.1.3 + Compiling number_prefix v0.4.0 + Compiling rustc-hash v2.0.0 + Compiling humantime v2.1.0 + Compiling arrayvec v0.7.4 + Compiling rustc-demangle v0.1.24 + Compiling env_logger v0.11.5 + Compiling nutype_macros v0.4.3 + Compiling indicatif v0.17.8 + Compiling cached v0.53.1 + Compiling actix-web v4.9.0 + Compiling erased-serde v0.4.5 + Compiling procfs-core v0.16.0 + Compiling noodles v0.77.0 + Compiling tracing-subscriber v0.3.18 + Compiling derive_builder_macro v0.20.0 + Compiling serde_with v3.9.0 + error: failed to run custom build command for annonars v0.40.0 + + Caused by: + process didn't exit successfully: /opt/conda/conda-bld/mehari_1734154596961/work/target/release/build/annonars-be8d8e77076395a1/build-script-build (exit status: 1) + --- stdout + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/class_by_freq.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/clinvar_public.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/extracted_vars.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/gene_impact.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/phenotype_link.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar/minimal.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar/per_gene.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar/sv.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/cons/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/dbsnp/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/functional/refseq.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/genes/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/exac_cnv.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad2.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad3.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad_cnv4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad_sv2.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad_sv4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/mtdna.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/vep_common.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/vep_gnomad2.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/vep_gnomad3.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/vep_gnomad4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/helixmtdb/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734154596961/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/regions/clingen.proto + + --- stderr + Error: Could not find protoc. If protoc is installed, try setting the PROTOC environment variable to the path of the protoc binary. To install it on Debian, run apt-get install protobuf-compiler. It is also available at https://github.com/protocolbuffers/protobuf/releases For more information: https://docs.rs/prost-build/#sourcing-protoc + warning: build failed, waiting for other jobs to finish... + error: failed to compile mehari v0.28.1 (/opt/conda/conda-bld/mehari_1734154596961/work), intermediate artifacts can be found at /opt/conda/conda-bld/mehari_1734154596961/work/target. + To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/mehari_1734154596961/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/mehari_1734154596961/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. diff --git a/recipes/mehari/build_failure.linux-aarch64.yaml b/recipes/mehari/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..ada2e611c17df --- /dev/null +++ b/recipes/mehari/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 6791a3edec1b5d14f9faf7c8e9788b1306d9776fece9e216b4c9e6e7048a3302 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + Compiling actix-web-codegen v4.3.0 + Compiling actix-server v2.5.0 + Compiling serde_urlencoded v0.7.1 + Compiling biocommons-bioutils v0.1.4 + Compiling noodles-gff v0.34.0 + Compiling annonars v0.40.0 + Compiling noodles-fasta v0.40.0 + Compiling env_filter v0.1.2 + Compiling cached_proc_macro v0.23.0 + Compiling serde_with_macros v3.9.0 + Compiling derive_builder_core v0.20.0 + Compiling sharded-slab v0.1.7 + Compiling tracing-log v0.2.0 + Compiling noodles-bed v0.15.0 + Compiling actix-macros v0.2.4 + Compiling thread_local v1.1.8 + Compiling object v0.36.3 + Compiling rustc-hash v2.0.0 + Compiling humantime v2.1.0 + Compiling cached_proc_macro_types v0.1.1 + Compiling typeid v1.0.0 + Compiling rustc-demangle v0.1.24 + Compiling web-time v1.1.0 + Compiling number_prefix v0.4.0 + Compiling hex v0.4.3 + Compiling impl-more v0.1.6 + Compiling arrayvec v0.7.4 + Compiling procfs v0.16.0 + Compiling urlencoding v2.1.3 + Compiling nutype_macros v0.4.3 + Compiling actix-web v4.9.0 + Compiling procfs-core v0.16.0 + Compiling indicatif v0.17.8 + Compiling cached v0.53.1 + Compiling env_logger v0.11.5 + Compiling erased-serde v0.4.5 + Compiling noodles v0.77.0 + Compiling tracing-subscriber v0.3.18 + Compiling derive_builder_macro v0.20.0 + Compiling serde_with v3.9.0 + error: failed to run custom build command for annonars v0.40.0 + + Caused by: + process didn't exit successfully: /opt/conda/conda-bld/mehari_1734060148711/work/target/release/build/annonars-4288d3a22ffdacb9/build-script-build (exit status: 1) + --- stdout + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/class_by_freq.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/clinvar_public.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/extracted_vars.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/gene_impact.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/phenotype_link.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar/minimal.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar/per_gene.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar/sv.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/cons/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/dbsnp/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/functional/refseq.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/genes/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/exac_cnv.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad2.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad3.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad_cnv4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad_sv2.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad_sv4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/mtdna.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/vep_common.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/vep_gnomad2.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/vep_gnomad3.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/vep_gnomad4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/helixmtdb/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/mehari_1734060148711/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/regions/clingen.proto + + --- stderr + Error: Could not find protoc. If protoc is installed, try setting the PROTOC environment variable to the path of the protoc binary. To install it on Debian, run apt-get install protobuf-compiler. It is also available at https://github.com/protocolbuffers/protobuf/releases For more information: https://docs.rs/prost-build/#sourcing-protoc + warning: build failed, waiting for other jobs to finish... + error: failed to compile mehari v0.28.1 (/opt/conda/conda-bld/mehari_1734060148711/work), intermediate artifacts can be found at /opt/conda/conda-bld/mehari_1734060148711/work/target. + To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/mehari_1734060148711/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/mehari_1734060148711/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 6584018563bc8..c076046783e44 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -13,7 +13,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage("mehari", max_pin="x.x") }} diff --git a/recipes/meme/meta.yaml b/recipes/meme/meta.yaml index b44bef89008de..d7480a8151b15 100644 --- a/recipes/meme/meta.yaml +++ b/recipes/meme/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("meme", max_pin="x") }} diff --git a/recipes/mentalist/meta.yaml b/recipes/mentalist/meta.yaml index 4108bbcb279ca..7874fa8e2a90c 100644 --- a/recipes/mentalist/meta.yaml +++ b/recipes/mentalist/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 408a1080bef46b88f21132d20c8b8d287f081f5aae47af25a379177a32e8abc5 build: - number: 7 + number: 8 skip: True # [osx] requirements: diff --git a/recipes/meraculous/meta.yaml b/recipes/meraculous/meta.yaml index a7e62c92d6225..9ae889be4ff0b 100644 --- a/recipes/meraculous/meta.yaml +++ b/recipes/meraculous/meta.yaml @@ -14,7 +14,7 @@ source: build: skip: True # [osx] - number: 8 + number: 9 run_exports: - {{ pin_subpackage("meraculous", max_pin="x") }} diff --git a/recipes/merfin/build_failure.osx-64.yaml b/recipes/merfin/build_failure.osx-64.yaml deleted file mode 100644 index 73a1f9aa3b3fa..0000000000000 --- a/recipes/merfin/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 98a917141e0418a0fb8319331b3e5faaff4d461d6525e21411e1361b7eab089b # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - - R :: Reversible A :: Applicable - Y :: Build-prefix patch in use M :: Minimal, non-amalgamated - D :: Dry-runnable N :: Patch level (1 is preferred) - L :: Patch level not-ambiguous O :: Patch applies without offsets - V :: Patch applies without fuzz E :: Patch applies without emitting to stderr - - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/merfin_1685523836626/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/merfin_1685523836626/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/merfin_1685523836626/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/merfin_1685523836626/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - Building release v1.0 - For 'Darwin' '21.6.0' as 'amd64' into '$SRC_DIR/build/{bin,obj}'. - Using '$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang' version '15.0.7'. - Using user-supplied CXXFLAGS '-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix'. - - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/obj/lib/libmerfin.a/utility/src/utility/edlib.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Iutility/src/utility utility/src/utility/edlib.C - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/obj/lib/libmerfin.a/utility/src/utility/files.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Iutility/src/utility utility/src/utility/files.C - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/obj/lib/libmerfin.a/utility/src/utility/files-buffered.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Iutility/src/utility utility/src/utility/files-buffered.C - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/obj/lib/libmerfin.a/utility/src/utility/files-compressed.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Iutility/src/utility utility/src/utility/files-compressed.C - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/obj/lib/libmerfin.a/utility/src/utility/files-fasta-fastq.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Iutility/src/utility utility/src/utility/files-fasta-fastq.C - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/obj/lib/libmerfin.a/utility/src/utility/files-memoryMapped.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Iutility/src/utility utility/src/utility/files-memoryMapped.C - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/obj/lib/libmerfin.a/utility/src/utility/logging.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Iutility/src/utility utility/src/utility/logging.C - utility/src/utility/logging.C:170:7: warning: 'snprintf' size argument is too large; destination buffer has size 256, but size argument is 1024 [-Wfortify-source] - snprintf(rotmes, 1024, "logFile()-- next message will exceed file size limit of " F_U64 "; rotate to new file.\n", - ^ - 1 warning generated. - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/obj/lib/libmerfin.a/utility/src/utility/strings.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Iutility/src/utility utility/src/utility/strings.C - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/obj/lib/libmerfin.a/utility/src/utility/system.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Iutility/src/utility utility/src/utility/system.C - utility/src/utility/system.C:167:32: error: use of undeclared identifier '_SC_PHYS_PAGES' - uint64 physPages = sysconf(_SC_PHYS_PAGES); - ^ - 1 error generated. - make: *** [Makefile:667: /opt/mambaforge/envs/bioconda/conda-bld/merfin_1685523836626/work/build/obj/lib/libmerfin.a/utility/src/utility/system.o] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/merfin_1685523836626/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/merfin/meta.yaml b/recipes/merfin/meta.yaml index 5a23253ed9145..3812a4f5cc6fe 100644 --- a/recipes/merfin/meta.yaml +++ b/recipes/merfin/meta.yaml @@ -13,7 +13,7 @@ source: - macos.patch # [osx] build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/merfishtools/meta.yaml b/recipes/merfishtools/meta.yaml index 414515d22a58b..95b671d9cb16d 100644 --- a/recipes/merfishtools/meta.yaml +++ b/recipes/merfishtools/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('merfishtools', max_pin="x") }} skip: True # [not py3k or osx] diff --git a/recipes/mergenotcombined/meta.yaml b/recipes/mergenotcombined/meta.yaml index 8e0c8ee1c7adb..13bde89d9c523 100644 --- a/recipes/mergenotcombined/meta.yaml +++ b/recipes/mergenotcombined/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 0965866c580bbe8e5432f7716534062190cc4fb8c3a8ab34b2e845331cddfc05 build: - number: 3 + number: 4 skip: True # [osx] requirements: diff --git a/recipes/merlin/meta.yaml b/recipes/merlin/meta.yaml index 7675badc0d725..770f960dd7967 100644 --- a/recipes/merlin/meta.yaml +++ b/recipes/merlin/meta.yaml @@ -10,7 +10,7 @@ source: - 0002-Use-same-owner-for-tar-extract.patch build: - number: 7 + number: 8 requirements: build: diff --git a/recipes/merquryfk/meta.yaml b/recipes/merquryfk/meta.yaml index a6825bf9b88ef..e3d934837ced8 100644 --- a/recipes/merquryfk/meta.yaml +++ b/recipes/merquryfk/meta.yaml @@ -13,7 +13,7 @@ source: - patch build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage("merquryfk", max_pin="x") }} diff --git a/recipes/meryl/meta.yaml b/recipes/meryl/meta.yaml index 1eb2454b22499..19c216c461d4a 100644 --- a/recipes/meryl/meta.yaml +++ b/recipes/meryl/meta.yaml @@ -16,7 +16,7 @@ source: - meryl-utility-aarch64.patch # [aarch64 or arm64] build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('meryl', max_pin="x") }} diff --git a/recipes/meta-apo/meta.yaml b/recipes/meta-apo/meta.yaml index d8b40ed36b1eb..43a4e9723c396 100644 --- a/recipes/meta-apo/meta.yaml +++ b/recipes/meta-apo/meta.yaml @@ -14,7 +14,7 @@ source: sha256: 4ab5753da65b5a31c9808f8301d26c3f9629fd710ea3e931a71c8bcb37708339 build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/meta-neuro/meta.yaml b/recipes/meta-neuro/meta.yaml index dfcd922cb0f7c..4bac292acfcd1 100644 --- a/recipes/meta-neuro/meta.yaml +++ b/recipes/meta-neuro/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: true # [win ] run_exports: - {{ pin_subpackage('meta-neuro', max_pin="x.x.x") }} diff --git a/recipes/metabat2/meta.yaml b/recipes/metabat2/meta.yaml index 1644f7f07c36d..d4dd1dc028de6 100644 --- a/recipes/metabat2/meta.yaml +++ b/recipes/metabat2/meta.yaml @@ -13,7 +13,7 @@ source: - cmake-htslib.patch # [linux and aarch64] build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -53,4 +53,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/metabinkit/meta.yaml b/recipes/metabinkit/meta.yaml index 8b2c2437ad70d..a00aab7311d8f 100644 --- a/recipes/metabinkit/meta.yaml +++ b/recipes/metabinkit/meta.yaml @@ -10,7 +10,7 @@ source: sha256: fba5623f9d769ef672e2663964dd4ea8397759f5b1a17dbd86290874fc8ef9e2 build: - number: 2 + number: 3 skip: true # [osx] requirements: diff --git a/recipes/metabuli/meta.yaml b/recipes/metabuli/meta.yaml index f1b9ef9368ef7..c3480078c2b05 100644 --- a/recipes/metabuli/meta.yaml +++ b/recipes/metabuli/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('metabuli', max_pin="x") }} diff --git a/recipes/metacache/meta.yaml b/recipes/metacache/meta.yaml index c2067924f2f8b..797ca30420b26 100644 --- a/recipes/metacache/meta.yaml +++ b/recipes/metacache/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 2b43aa1ac051d6cbaa4d29c3ed7d9593e226e7e2b35cdd0b2e513e465456a7b2 build: - number: 1 + number: 2 skip: True # [osx] run_exports: - {{ pin_subpackage('metacache', max_pin="x") }} diff --git a/recipes/metacluster/meta.yaml b/recipes/metacluster/meta.yaml index 0d45311da25ed..b2777c8be86c3 100644 --- a/recipes/metacluster/meta.yaml +++ b/recipes/metacluster/meta.yaml @@ -8,7 +8,7 @@ package: version: {{ version }} build: - number: 6 + number: 7 skip: True # [osx] source: diff --git a/recipes/metacortex/meta.yaml b/recipes/metacortex/meta.yaml index 2aaee7c446eb5..d874ec824e85c 100644 --- a/recipes/metacortex/meta.yaml +++ b/recipes/metacortex/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 32cf14e00bc9db95aafcdd7ae7bbcd3e6fd606ee7003572cc00f18431fa1df68 build: - number: 2 + number: 3 skip: True # [osx] requirements: diff --git a/recipes/metadmg/build_failure.osx-64.yaml b/recipes/metadmg/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..81d44eccc949d --- /dev/null +++ b/recipes/metadmg/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 6214e6be8a42a193448014e6a7bc39c1d9a71ac9dce32bb5866b515f6eb9680e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + x86_64-apple-darwin13.4: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/metadmg_1734250835902/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/metadmg_1734250835902/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/metadmg_1734250835902/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/metadmg_1734250835902/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/metadmg_1734250835902/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/metadmg_1734250835902/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/metadmg_1734250835902/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/metadmg_1734250835902/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/metadmg_1734250835902/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/metadmg_1734250835902/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/metadmg_1734250835902/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/metadmg_1734250835902/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -lbz2: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -llzma: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-headerpad_max_install_names: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-dead_strip_dylibs: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/metadmg_1734250835902/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib: 'linker' input unused [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/metadmg_1734250835902/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/metadmg_1734250835902/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] + x86_64-apple-darwin13.4: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/metadmg_1734250835902/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib' [-Wunused-command-line-argument] + x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -MM -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lbz2 -llzma -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metadmg-0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix metaDMG.cpp >metaDMG.d + x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -c -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lbz2 -llzma -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metadmg-0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix ngsLCA.cpp + x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -MM -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lbz2 -llzma -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metadmg-0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix ngsLCA.cpp >ngsLCA.d + x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -c -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lbz2 -llzma -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metadmg-0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix ngsLCA_cli.cpp + x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -MM -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lbz2 -llzma -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metadmg-0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix ngsLCA_cli.cpp >ngsLCA_cli.d + x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -c -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lbz2 -llzma -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metadmg-0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix profile.cpp + x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -MM -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lbz2 -llzma -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metadmg-0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix profile.cpp >profile.d + x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -c -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lbz2 -llzma -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metadmg-0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix pval.cpp + x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -MM -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lbz2 -llzma -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metadmg-0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix pval.cpp >pval.d + x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -c -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lbz2 -llzma -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metadmg-0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix regression.cpp + x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -MM -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lbz2 -llzma -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metadmg-0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix regression.cpp >regression.d + x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -c -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lbz2 -llzma -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metadmg-0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix shared.cpp + x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -MM -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lbz2 -llzma -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metadmg-0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix shared.cpp >shared.d + x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -O3 -o metaDMG-cpp *.o -lz -lm -lbz2 -llzma -lpthread -lcurl -lgsl -lgslcblas -lcrypto -lhts + make -C misc HTSSRC="" + make[1]: Entering directory '$SRC_DIR/misc' + Crypto library is not available to link; will not use -lcrypto + HTSSRC not defined, assuming systemwide installation + x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lbz2 -llzma -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib compressbam.cpp -o compressbam -lz -lm -lbz2 -llzma -lpthread -lcurl -lhts + x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lbz2 -llzma -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -c M3Load.cpp + x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lbz2 -llzma -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metadmg-0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o bfgs.o bfgs.cpp + x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lbz2 -llzma -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -c Likelihood.cpp + x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lbz2 -llzma -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -std=c11 MAP.cpp M3Load.o bfgs.o Likelihood.o -o MAP -lz -lm -lbz2 -llzma -lpthread -lcurl -lhts -D__WITH_MAIN__ + x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lbz2 -llzma -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib dfit_optim.cpp bfgs.o -o dfit_optim -lz -lm -lbz2 -llzma -lpthread -lcurl -lhts -D__WITH_MAIN__ + make[1]: Leaving directory '$SRC_DIR/misc' + + Resource usage statistics from building metadmg: + Process count: 7 + CPU time: Sys=0:00:01.6, User=0:00:33.8 + Memory: 583.7M + Disk usage: 140.2K + Time elapsed: 0:01:04.3 + + + Packaging metadmg + Packaging metadmg-0.4-hd84cb12_1 + number of files: 2 + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2765, in build + newly_built_packages = bundlers[pkg_type]( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1874, in bundle_conda + files = post_process_files(metadata, initial_files) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1653, in post_process_files + post_build(m, new_files, build_python=python) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1759, in post_build + post_process_shared_lib(m, f, prefix_files, host_prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1635, in post_process_shared_lib + mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 477, in mk_relative_osx + names = macho.otool(path, prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 221, in otool + lines = check_output([otool, "-l", path], stderr=STDOUT).decode("utf-8") + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 421, in check_output + return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 526, in run + raise CalledProcessError(retcode, process.args, + subprocess.CalledProcessError: Command '['/opt/mambaforge/envs/bioconda/conda-bld/metadmg_1734250835902/_build_env/bin/llvm-otool', '-l', '/opt/mambaforge/envs/bioconda/conda-bld/metadmg_1734250835902/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/bin/compressbam']' died with . +# Last 100 lines of the build log. diff --git a/recipes/metadmg/meta.yaml b/recipes/metadmg/meta.yaml index 599061d0629ce..bdac95a299fcb 100644 --- a/recipes/metadmg/meta.yaml +++ b/recipes/metadmg/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: false run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/metaeuk/meta.yaml b/recipes/metaeuk/meta.yaml index d4880f6922390..8744b3505bfb2 100644 --- a/recipes/metaeuk/meta.yaml +++ b/recipes/metaeuk/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version|replace("-", ".") }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('metaeuk', max_pin="x") }} @@ -54,4 +54,4 @@ extra: - elileka additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 diff --git a/recipes/metamdbg/0.3/build_failure.linux-64.yaml b/recipes/metamdbg/0.3/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..d133ea54f7d2a --- /dev/null +++ b/recipes/metamdbg/0.3/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c0b8d9da006f88dcc9896b6321890cbeda825c3b47b387932cf75a00d707b414 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("libzlib[version='>=1.2.11,<1.3.0a0']"), MatchSpec("wfmash==0.8.2=h144baf3_0")} + Encountered problems while solving: + - package wfmash-0.8.2-h144baf3_0 requires libzlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mlibzlib >=1.3.1,<2.0a0 [0m is requested and can be installed; + [31mwfmash 0.8.2.* [0m is not installable because it requires + [31mlibzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("libzlib[version='>=1.2.11,<1.3.0a0']"), MatchSpec("wfmash==0.8.2=h144baf3_0")} + Encountered problems while solving: + - package wfmash-0.8.2-h144baf3_0 requires libzlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mlibzlib >=1.3.1,<2.0a0 [0m is requested and can be installed; + [31mwfmash 0.8.2.* [0m is not installable because it requires + [31mlibzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("libzlib[version='>=1.2.11,<1.3.0a0']"), MatchSpec("wfmash==0.8.2=h144baf3_0")} + Encountered problems while solving: + - package wfmash-0.8.2-h144baf3_0 requires libzlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mlibzlib >=1.3.1,<2.0a0 [0m is requested and can be installed; + [31mwfmash 0.8.2.* [0m is not installable because it requires + [31mlibzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/metamdbg/0.3/meta.yaml b/recipes/metamdbg/0.3/meta.yaml index 7316c6c86c897..386dbc2e99304 100644 --- a/recipes/metamdbg/0.3/meta.yaml +++ b/recipes/metamdbg/0.3/meta.yaml @@ -10,7 +10,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage('metamdbg', max_pin="x.x") }} diff --git a/recipes/metamdbg/1.0/meta.yaml b/recipes/metamdbg/1.0/meta.yaml index 1465c0636bde5..15d7863b13965 100644 --- a/recipes/metamdbg/1.0/meta.yaml +++ b/recipes/metamdbg/1.0/meta.yaml @@ -10,7 +10,7 @@ source: build: skip: True # [osx] - number: 1 + number: 2 run_exports: - {{ pin_subpackage('metamdbg', max_pin="x.x") }} diff --git a/recipes/metaphyler/meta.yaml b/recipes/metaphyler/meta.yaml index ce2e6566ed2b8..c941e5c3cedae 100644 --- a/recipes/metaphyler/meta.yaml +++ b/recipes/metaphyler/meta.yaml @@ -7,7 +7,7 @@ source: url: http://metaphyler.cbcb.umd.edu/MetaPhylerV1.25.tar.gz build: - number: 7 + number: 8 skip: True # [osx] package: diff --git a/recipes/metaplatanus/build_failure.linux-64.yaml b/recipes/metaplatanus/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..08e1c3028011c --- /dev/null +++ b/recipes/metaplatanus/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 034e7a4095d8a8ab6d2a997f249c310ac5af10fe2f3210f624f41173b71ceef2 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("libzlib[version='>=1.2.13,<1.3.0a0']"), MatchSpec("tgsgapcloser==1.2.1=h5b5514e_1")} + Encountered problems while solving: + - package tgsgapcloser-1.2.1-h5b5514e_1 requires libzlib >=1.2.13,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mlibzlib >=1.3.1,<2.0a0 [0m is installable with the potential options + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_0[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [31mtgsgapcloser >=1.0.3 [0m is not installable because there are no viable options + [31mtgsgapcloser 1.0.3[0m would require + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mtgsgapcloser 1.2.1[0m would require + [31mzlib >=1.2.13,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mtgsgapcloser 1.2.1[0m would require + [31mlibzlib >=1.2.13,<1.3.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("libzlib[version='>=1.2.13,<1.3.0a0']"), MatchSpec("tgsgapcloser==1.2.1=h5b5514e_1")} + Encountered problems while solving: + - package tgsgapcloser-1.2.1-h5b5514e_1 requires libzlib >=1.2.13,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mlibzlib >=1.3.1,<2.0a0 [0m is installable with the potential options + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_0[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_1[0m, which can be installed; + [32mlibzlib 1.3.1[0m would require + [32mzlib 1.3.1 *_2[0m, which can be installed; + [31mtgsgapcloser >=1.0.3 [0m is not installable because there are no viable options + [31mtgsgapcloser 1.0.3[0m would require + [31mzlib >=1.2.11,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mtgsgapcloser 1.2.1[0m would require + [31mzlib >=1.2.13,<1.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mtgsgapcloser 1.2.1[0m would require + [31mlibzlib >=1.2.13,<1.3.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/metaplatanus/meta.yaml b/recipes/metaplatanus/meta.yaml index cc1c2ef32952a..e337f9e434f41 100644 --- a/recipes/metaplatanus/meta.yaml +++ b/recipes/metaplatanus/meta.yaml @@ -10,7 +10,7 @@ source: url: https://github.com/rkajitani/metaplatanus/archive/v{{version}}.tar.gz build: - number: 1 + number: 2 skip: True # [osx] requirements: diff --git a/recipes/metasnv/meta.yaml b/recipes/metasnv/meta.yaml index 4e0732276cf00..f852c3ecdc840 100644 --- a/recipes/metasnv/meta.yaml +++ b/recipes/metasnv/meta.yaml @@ -12,7 +12,7 @@ source: build: # on macOS, build error from rpath complaining of a too-long path skip: True # [py2k or py36 or osx] - number: 8 + number: 9 run_exports: - {{ pin_subpackage( "metasnv", max_pin="x") }} diff --git a/recipes/methpipe/build_failure.linux-64.yaml b/recipes/methpipe/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..b5bedc1249bf0 --- /dev/null +++ b/recipes/methpipe/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 7027d30551f2c13e51d12b85a7819c9a9db7868e6f717edd5b9727bafaa2c00d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + 46 | << check(the_flags, samflags::read_pair_mapped) << '\n' + | ^~~~~~~~~~~~~~~~ + ../../../src/smithlab_cpp/sam_record.cpp:47:58: error: 'read_unmapped' is not a member of 'samflags' + 47 | << "read_unmapped: " << check(the_flags, samflags::read_unmapped) << '\n' + | ^~~~~~~~~~~~~ + ../../../src/smithlab_cpp/sam_record.cpp:48:58: error: 'mate_unmapped' is not a member of 'samflags' + 48 | << "mate_unmapped: " << check(the_flags, samflags::mate_unmapped) << '\n' + | ^~~~~~~~~~~~~ + ../../../src/smithlab_cpp/sam_record.cpp:49:52: error: 'read_rc' is not a member of 'samflags' + 49 | << "read_rc: " << check(the_flags, samflags::read_rc) << '\n' + | ^~~~~~~ + ../../../src/smithlab_cpp/sam_record.cpp:50:52: error: 'mate_rc' is not a member of 'samflags' + 50 | << "mate_rc: " << check(the_flags, samflags::mate_rc) << '\n' + | ^~~~~~~ + ../../../src/smithlab_cpp/sam_record.cpp:52:37: error: 'template_first' is not a member of 'samflags' + 52 | << check(the_flags, samflags::template_first) << '\n' + | ^~~~~~~~~~~~~~ + ../../../src/smithlab_cpp/sam_record.cpp:53:58: error: 'template_last' is not a member of 'samflags' + 53 | << "template_last: " << check(the_flags, samflags::template_last) << '\n' + | ^~~~~~~~~~~~~ + ../../../src/smithlab_cpp/sam_record.cpp:54:58: error: 'secondary_aln' is not a member of 'samflags' + 54 | << "secondary_aln: " << check(the_flags, samflags::secondary_aln) << '\n' + | ^~~~~~~~~~~~~ + ../../../src/smithlab_cpp/sam_record.cpp:55:58: error: 'below_quality' is not a member of 'samflags' + 55 | << "below_quality: " << check(the_flags, samflags::below_quality) << '\n' + | ^~~~~~~~~~~~~ + ../../../src/smithlab_cpp/sam_record.cpp:56:58: error: 'pcr_duplicate' is not a member of 'samflags' + 56 | << "pcr_duplicate: " << check(the_flags, samflags::pcr_duplicate) << '\n' + | ^~~~~~~~~~~~~ + ../../../src/smithlab_cpp/sam_record.cpp:58:37: error: 'supplementary_aln' is not a member of 'samflags' + 58 | << check(the_flags, samflags::supplementary_aln); + | ^~~~~~~~~~~~~~~~~ + ../../../src/smithlab_cpp/sam_record.cpp: In member function 'std::string sam_rec::tostring() const': + ../../../src/smithlab_cpp/sam_record.cpp:88:26: error: 'flags' was not declared in this scope + 88 | to_string(flags) "\t" + | ^~~~~ + ../../../src/smithlab_cpp/sam_record.cpp:90:26: error: 'pos' was not declared in this scope; did you mean 'pow'? + 90 | to_string(pos) "\t" + | ^~~ + | pow + ../../../src/smithlab_cpp/sam_record.cpp:91:48: error: 'mapq' was not declared in this scope + 91 | to_string(static_cast(mapq)) "\t" + | ^~~~ + ../../../src/smithlab_cpp/sam_record.cpp:94:26: error: 'pnext' was not declared in this scope; did you mean 'rnext'? + 94 | to_string(pnext) "\t" + | ^~~~~ + | rnext + ../../../src/smithlab_cpp/sam_record.cpp: In constructor 'sam_rec::sam_rec(const std::string&)': + ../../../src/smithlab_cpp/sam_record.cpp:118:18: error: 'flags' was not declared in this scope + 118 | qname >> flags >> rname >> pos >> will_become_mapq >> + | ^~~~~ + ../../../src/smithlab_cpp/sam_record.cpp:118:36: error: 'pos' was not declared in this scope; did you mean 'pow'? + 118 | qname >> flags >> rname >> pos >> will_become_mapq >> + | ^~~ + | pow + ../../../src/smithlab_cpp/sam_record.cpp:119:27: error: 'pnext' was not declared in this scope; did you mean 'rnext'? + 119 | cigar >> rnext >> pnext >> tlen >> seq >> qual)) + | ^~~~~ + | rnext + ../../../src/smithlab_cpp/sam_record.cpp:121:7: error: 'mapq' was not declared in this scope + 121 | if (mapq > 255) + | ^~~~ + ../../../src/smithlab_cpp/sam_record.cpp:123:3: error: 'mapq' was not declared in this scope + 123 | mapq = static_cast(will_become_mapq); + | ^~~~ + ../../../src/smithlab_cpp/sam_record.cpp: In member function 'bool sam_rec::empty() const': + ../../../src/smithlab_cpp/sam_record.cpp:132:10: error: 'pos' was not declared in this scope; did you mean 'pow'? + 132 | return pos == 0; + | ^~~ + | pow + make[3]: *** [Makefile:491: sam_record.o] Error 1 + make[3]: Leaving directory '$SRC_DIR/build/src/smithlab_cpp' + make[2]: *** [Makefile:374: all] Error 2 + make[2]: Leaving directory '$SRC_DIR/build/src/smithlab_cpp' + make[1]: *** [Makefile:1066: all-recursive] Error 1 + make[1]: Leaving directory '$SRC_DIR/build' + make: *** [Makefile:637: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/methpipe_1734247951628/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/methpipe_1734247951628/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/methpipe/build_failure.osx-64.yaml b/recipes/methpipe/build_failure.osx-64.yaml deleted file mode 100644 index 30a95509a271c..0000000000000 --- a/recipes/methpipe/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 75ceaf6e80509d4e1b7cfa64e61685e0361dc4103d557386ae8a26816f31990e # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/analysis/methcounts.o -MD -MP -MF $depbase.Tpo -c -o src/analysis/methcounts.o ../src/analysis/methcounts.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o methcounts src/analysis/methcounts.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/analysis/bsrate.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/analysis/bsrate.o -MD -MP -MF $depbase.Tpo -c -o src/analysis/bsrate.o ../src/analysis/bsrate.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o bsrate src/analysis/bsrate.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/analysis/hmr.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/analysis/hmr.o -MD -MP -MF $depbase.Tpo -c -o src/analysis/hmr.o ../src/analysis/hmr.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o hmr src/analysis/hmr.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/analysis/hypermr.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/analysis/hypermr.o -MD -MP -MF $depbase.Tpo -c -o src/analysis/hypermr.o ../src/analysis/hypermr.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o hypermr src/analysis/hypermr.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/analysis/levels.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/analysis/levels.o -MD -MP -MF $depbase.Tpo -c -o src/analysis/levels.o ../src/analysis/levels.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o levels src/analysis/levels.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/analysis/roimethstat.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/analysis/roimethstat.o -MD -MP -MF $depbase.Tpo -c -o src/analysis/roimethstat.o ../src/analysis/roimethstat.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o roimethstat src/analysis/roimethstat.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/analysis/methstates.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/analysis/methstates.o -MD -MP -MF $depbase.Tpo -c -o src/analysis/methstates.o ../src/analysis/methstates.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o methstates src/analysis/methstates.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/analysis/methentropy.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/analysis/methentropy.o -MD -MP -MF $depbase.Tpo -c -o src/analysis/methentropy.o ../src/analysis/methentropy.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o methentropy src/analysis/methentropy.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/analysis/hmr_rep.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/analysis/hmr_rep.o -MD -MP -MF $depbase.Tpo -c -o src/analysis/hmr_rep.o ../src/analysis/hmr_rep.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o hmr_rep src/analysis/hmr_rep.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/analysis/multimethstat.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/analysis/multimethstat.o -MD -MP -MF $depbase.Tpo -c -o src/analysis/multimethstat.o ../src/analysis/multimethstat.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o multimethstat src/analysis/multimethstat.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/utils/lc_approx.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/utils/lc_approx.o -MD -MP -MF $depbase.Tpo -c -o src/utils/lc_approx.o ../src/utils/lc_approx.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o lc_approx src/utils/lc_approx.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/utils/fast-liftover.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/utils/fast-liftover.o -MD -MP -MF $depbase.Tpo -c -o src/utils/fast-liftover.o ../src/utils/fast-liftover.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o fast-liftover src/utils/fast-liftover.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/utils/lift-filter.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/utils/lift-filter.o -MD -MP -MF $depbase.Tpo -c -o src/utils/lift-filter.o ../src/utils/lift-filter.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o lift-filter src/utils/lift-filter.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/utils/merge-bsrate.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/utils/merge-bsrate.o -MD -MP -MF $depbase.Tpo -c -o src/utils/merge-bsrate.o ../src/utils/merge-bsrate.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o merge-bsrate src/utils/merge-bsrate.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/utils/merge-methcounts.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/utils/merge-methcounts.o -MD -MP -MF $depbase.Tpo -c -o src/utils/merge-methcounts.o ../src/utils/merge-methcounts.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o merge-methcounts src/utils/merge-methcounts.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/utils/duplicate-remover.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/utils/duplicate-remover.o -MD -MP -MF $depbase.Tpo -c -o src/utils/duplicate-remover.o ../src/utils/duplicate-remover.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o duplicate-remover src/utils/duplicate-remover.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/utils/symmetric-cpgs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/utils/symmetric-cpgs.o -MD -MP -MF $depbase.Tpo -c -o src/utils/symmetric-cpgs.o ../src/utils/symmetric-cpgs.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o symmetric-cpgs src/utils/symmetric-cpgs.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/utils/clean-hairpins.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/utils/clean-hairpins.o -MD -MP -MF $depbase.Tpo -c -o src/utils/clean-hairpins.o ../src/utils/clean-hairpins.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o clean-hairpins src/utils/clean-hairpins.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/utils/selectsites.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/utils/selectsites.o -MD -MP -MF $depbase.Tpo -c -o src/utils/selectsites.o ../src/utils/selectsites.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o selectsites src/utils/selectsites.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/utils/guessprotocol.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/utils/guessprotocol.o -MD -MP -MF $depbase.Tpo -c -o src/utils/guessprotocol.o ../src/utils/guessprotocol.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o guessprotocol src/utils/guessprotocol.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/utils/format_reads.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/utils/format_reads.o -MD -MP -MF $depbase.Tpo -c -o src/utils/format_reads.o ../src/utils/format_reads.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o format_reads src/utils/format_reads.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/amrfinder/allelicmeth.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/amrfinder/allelicmeth.o -MD -MP -MF $depbase.Tpo -c -o src/amrfinder/allelicmeth.o ../src/amrfinder/allelicmeth.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o allelicmeth src/amrfinder/allelicmeth.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/amrfinder/amrfinder.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/amrfinder/amrfinder.o -MD -MP -MF $depbase.Tpo -c -o src/amrfinder/amrfinder.o ../src/amrfinder/amrfinder.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o amrfinder src/amrfinder/amrfinder.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/amrfinder/amrtester.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/amrfinder/amrtester.o -MD -MP -MF $depbase.Tpo -c -o src/amrfinder/amrtester.o ../src/amrfinder/amrtester.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o amrtester src/amrfinder/amrtester.o libmethpipe.a src/smithlab_cpp/libsmithlab_cpp.a -lgsl -lgslcblas -lz -lhts - depbase=echo src/radmeth/radmeth.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -std=c11 -DHAVE_CONFIG_H -I. -I.. -I ../src/common -I ../src/smithlab_cpp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -MT src/radmeth/radmeth.o -MD -MP -MF $depbase.Tpo -c -o src/radmeth/radmeth.o ../src/radmeth/radmeth.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - make[2]: Leaving directory '$SRC_DIR/build' - make[1]: Leaving directory '$SRC_DIR/build' -# Last 100 lines of the build log. diff --git a/recipes/methpipe/meta.yaml b/recipes/methpipe/meta.yaml index 2e533a09822e8..16dd7d9cbbd17 100644 --- a/recipes/methpipe/meta.yaml +++ b/recipes/methpipe/meta.yaml @@ -9,7 +9,7 @@ source: md5: 735bdafc5b25ae6df30e43442127571e build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/methyldackel/meta.yaml b/recipes/methyldackel/meta.yaml index 190ff19e602b1..d2548b5c6c0bb 100644 --- a/recipes/methyldackel/meta.yaml +++ b/recipes/methyldackel/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 7 + number: 8 run_exports: - {{ pin_subpackage("methyldackel", max_pin="x.x") }} @@ -34,4 +34,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/metilene/build_failure.osx-64.yaml b/recipes/metilene/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..f1034ea865d73 --- /dev/null +++ b/recipes/metilene/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 23159488f633d13bea22ed9f946825b77e3187c7121c830ef389d072f9e17b50 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/metilene_1734100584503/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/metilene_1734100584503/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/metilene_1734100584503/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metilene-0.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metilene-0.2.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + x86_64-apple-darwin13.4.0-clang -Wall -pedantic -std=c99 -O3 -D_GNU_SOURCE_ -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGLEVEL=0 -DPROGNFO -I -Lsrc -DPCGRNG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o src/manopt.o src/manopt.c + x86_64-apple-darwin13.4.0-clang -Wall -pedantic -std=c99 -O3 -D_GNU_SOURCE_ -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGLEVEL=0 -DPROGNFO -I -Lsrc -DPCGRNG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o src/memory.o src/memory.c + x86_64-apple-darwin13.4.0-clang -Wall -pedantic -std=c99 -O3 -D_GNU_SOURCE_ -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGLEVEL=0 -DPROGNFO -I -Lsrc -DPCGRNG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o src/debug.o src/debug.c + x86_64-apple-darwin13.4.0-clang -Wall -pedantic -std=c99 -O3 -D_GNU_SOURCE_ -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGLEVEL=0 -DPROGNFO -I -Lsrc -DPCGRNG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o src/info.o src/info.c + x86_64-apple-darwin13.4.0-clang -Wall -pedantic -std=c99 -O3 -D_GNU_SOURCE_ -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGLEVEL=0 -DPROGNFO -I -Lsrc -DPCGRNG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o src/stringutils.o src/stringutils.c + x86_64-apple-darwin13.4.0-clang -Wall -pedantic -std=c99 -O3 -D_GNU_SOURCE_ -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGLEVEL=0 -DPROGNFO -I -Lsrc -DPCGRNG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o src/fileio.o src/fileio.c + x86_64-apple-darwin13.4.0-clang -Wall -pedantic -std=c99 -O3 -D_GNU_SOURCE_ -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGLEVEL=0 -DPROGNFO -I -Lsrc -DPCGRNG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o src/mathematics.o src/mathematics.c + x86_64-apple-darwin13.4.0-clang -Wall -pedantic -std=c99 -O3 -D_GNU_SOURCE_ -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGLEVEL=0 -DPROGNFO -I -Lsrc -DPCGRNG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o src/sort.o src/sort.c + x86_64-apple-darwin13.4.0-clang -Wall -pedantic -std=c99 -O3 -D_GNU_SOURCE_ -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGLEVEL=0 -DPROGNFO -I -Lsrc -DPCGRNG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o src/vstack.o src/vstack.c + x86_64-apple-darwin13.4.0-clang -Wall -pedantic -std=c99 -O3 -D_GNU_SOURCE_ -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGLEVEL=0 -DPROGNFO -I -Lsrc -DPCGRNG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o src/segmentstack.o src/segmentstack.c + x86_64-apple-darwin13.4.0-clang -Wall -pedantic -std=c99 -O3 -D_GNU_SOURCE_ -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGLEVEL=0 -DPROGNFO -I -Lsrc -DPCGRNG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o src/mtc.o src/mtc.c + x86_64-apple-darwin13.4.0-clang -Wall -pedantic -std=c99 -O3 -D_GNU_SOURCE_ -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGLEVEL=0 -DPROGNFO -I -Lsrc -DPCGRNG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o src/metseg.o src/metseg.c + x86_64-apple-darwin13.4.0-clang -Wall -pedantic -std=c99 -O3 -D_GNU_SOURCE_ -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGLEVEL=0 -DPROGNFO -I -Lsrc -DPCGRNG src/manopt.o src/memory.o src/debug.o src/info.o src/stringutils.o src/fileio.o src/mathematics.o src/sort.o src/vstack.o src/segmentstack.o src/mtc.o src/metseg.o -o metilene -lm -lpthread + + Resource usage statistics from building metilene: + Process count: 4 + CPU time: Sys=0:00:00.0, User=0:00:00.1 + Memory: 19.3M + Disk usage: 6.0K + Time elapsed: 0:00:04.2 + + + Packaging metilene + Packaging metilene-0.2.8-h18d8cf3_4 + number of files: 6 + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2765, in build + newly_built_packages = bundlers[pkg_type]( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1874, in bundle_conda + files = post_process_files(metadata, initial_files) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1653, in post_process_files + post_build(m, new_files, build_python=python) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1759, in post_build + post_process_shared_lib(m, f, prefix_files, host_prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1635, in post_process_shared_lib + mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 477, in mk_relative_osx + names = macho.otool(path, prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 221, in otool + lines = check_output([otool, "-l", path], stderr=STDOUT).decode("utf-8") + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 421, in check_output + return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 526, in run + raise CalledProcessError(retcode, process.args, + subprocess.CalledProcessError: Command '['/opt/mambaforge/envs/bioconda/conda-bld/metilene_1734100584503/_build_env/bin/llvm-otool', '-l', '/opt/mambaforge/envs/bioconda/conda-bld/metilene_1734100584503/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin/metilene']' died with . +# Last 100 lines of the build log. diff --git a/recipes/metilene/meta.yaml b/recipes/metilene/meta.yaml index 180f399d3e146..d3a4767902889 100644 --- a/recipes/metilene/meta.yaml +++ b/recipes/metilene/meta.yaml @@ -9,7 +9,7 @@ about: summary: Fast and sensitive detection of differential DNA methylation build: - number: 3 + number: 4 source: url: "http://www.bioinf.uni-leipzig.de/Software/metilene/metilene_v02-8.tar.gz" diff --git a/recipes/mfold/build_failure.linux-64.yaml b/recipes/mfold/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..4d60ac3fb0356 --- /dev/null +++ b/recipes/mfold/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 74ef5c947812f2a2e6c0f5ce9bb05fb35f575c8636313d2e2921fa70756a6942 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml + Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for mfold + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['mfold-3.6-hb2a3317_4.tar.bz2'] + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/mfold_1734061548395/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgfortran: 14.2.0-h69a702a_1 conda-forge + libgfortran5: 14.2.0-hd5240d6_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/mfold_1734061548395/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.43-h4bf12b8_2 conda-forge + binutils_linux-64: 2.43-h4852527_2 conda-forge + gcc_impl_linux-64: 13.3.0-hfea6d02_1 conda-forge + gcc_linux-64: 13.3.0-hc28eda2_7 conda-forge + gfortran_impl_linux-64: 13.3.0-h10434e7_1 conda-forge + gfortran_linux-64: 13.3.0-hb919d3a_7 conda-forge + gxx_impl_linux-64: 13.3.0-hdbfa832_1 conda-forge + gxx_linux-64: 13.3.0-h6834431_7 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libgfortran5: 14.2.0-hd5240d6_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libsanitizer: 13.3.0-heb74ff8_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + make: 4.4.1-hb9d3cd8_2 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: mfold-3.6_04c317bca2.tar.gz + Downloading http://www.unafold.org/download/mfold-3.6.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(, 'Connection to www.unafold.org timed out. (connect timeout=9.15)')': /download/mfold-3.6.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(, 'Connection to www.unafold.org timed out. (connect timeout=9.15)')': /download/mfold-3.6.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(, 'Connection to www.unafold.org timed out. (connect timeout=9.15)')': /download/mfold-3.6.tar.gz + WARNING: Error: HTTP 000 CONNECTION FAILED for url + Elapsed: - + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download http://www.unafold.org/download/mfold-3.6.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/mfold/build_failure.osx-64.yaml b/recipes/mfold/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..f8c8057f2d263 --- /dev/null +++ b/recipes/mfold/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 74ef5c947812f2a2e6c0f5ce9bb05fb35f575c8636313d2e2921fa70756a6942 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/mfold_1734235901262/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + + + The following NEW packages will be INSTALLED: + + libcxx: 19.1.5-hf95d169_0 conda-forge + libgfortran: 5.0.0-13_2_0_h97931a8_3 conda-forge + libgfortran5: 13.2.0-h2873a65_3 conda-forge + llvm-openmp: 19.1.5-ha54dae1_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (local): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (local): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/mfold_1734235901262/_build_env + + + The following NEW packages will be INSTALLED: + + ca-certificates: 2024.12.14-h8857fd0_0 conda-forge + cctools_osx-64: 1010.6-h00edd4c_2 conda-forge + clang: 18.1.8-default_h179603d_5 conda-forge + clang-18: 18.1.8-default_h0c94c6a_5 conda-forge + clang_impl_osx-64: 18.1.8-h6a44ed1_23 conda-forge + clang_osx-64: 18.1.8-h7e5c614_23 conda-forge + clangxx: 18.1.8-default_h179603d_5 conda-forge + clangxx_impl_osx-64: 18.1.8-h4b7810f_23 conda-forge + clangxx_osx-64: 18.1.8-h7e5c614_23 conda-forge + compiler-rt: 18.1.8-h1020d70_1 conda-forge + compiler-rt_osx-64: 18.1.8-hf2b8a54_1 conda-forge + gfortran_impl_osx-64: 13.2.0-h2bc304d_3 conda-forge + gfortran_osx-64: 13.2.0-h18f7dce_1 conda-forge + gmp: 6.3.0-hf036a51_2 conda-forge + isl: 0.26-imath32_h2e86a7b_101 conda-forge + ld64_osx-64: 951.9-hc8d1a19_2 conda-forge + libclang-cpp18.1: 18.1.8-default_h0c94c6a_5 conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libcxx-devel: 18.1.8-h7c275be_7 conda-forge + libgfortran: 5.0.0-13_2_0_h97931a8_3 conda-forge + libgfortran-devel_osx-64: 13.2.0-h80d4556_3 conda-forge + libgfortran5: 13.2.0-h2873a65_3 conda-forge + libiconv: 1.17-hd75f5a5_2 conda-forge + libllvm18: 18.1.8-h9ce406d_2 conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libxml2: 2.13.5-he8ee3e7_1 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-openmp: 19.1.5-ha54dae1_0 conda-forge + llvm-tools: 18.1.8-h9ce406d_2 conda-forge + llvm-tools-18: 18.1.8-h9ce406d_2 conda-forge + make: 4.4.1-h00291cd_2 conda-forge + mpc: 1.3.1-h9d8efa1_1 conda-forge + mpfr: 4.2.1-haed47dc_3 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + sigtool: 0.1.3-h88f4db0_0 conda-forge + tapi: 1300.6.5-h390ca13_0 conda-forge + zlib: 1.3.1-hd23fc13_2 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache + Downloading source to cache: mfold-3.6_04c317bca2.tar.gz + Downloading http://www.unafold.org/download/mfold-3.6.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(, 'Connection to www.unafold.org timed out. (connect timeout=9.15)')': /download/mfold-3.6.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(, 'Connection to www.unafold.org timed out. (connect timeout=9.15)')': /download/mfold-3.6.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(, 'Connection to www.unafold.org timed out. (connect timeout=9.15)')': /download/mfold-3.6.tar.gz + WARNING: Error: HTTP 000 CONNECTION FAILED for url + Elapsed: - + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download http://www.unafold.org/download/mfold-3.6.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/mfold/meta.yaml b/recipes/mfold/meta.yaml index 360c72f18f5fc..6b9dcb987c6b4 100644 --- a/recipes/mfold/meta.yaml +++ b/recipes/mfold/meta.yaml @@ -11,7 +11,9 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 + run_exports: + - {{ pin_subpackage('mfold', max_pin="x") }} requirements: build: diff --git a/recipes/mfqe/meta.yaml b/recipes/mfqe/meta.yaml index 515cda0b8f256..e9c2ef08af153 100644 --- a/recipes/mfqe/meta.yaml +++ b/recipes/mfqe/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 skip: True # [osx] source: diff --git a/recipes/mgems/meta.yaml b/recipes/mgems/meta.yaml index be00e71ac1a41..8c1e1bc2a237c 100644 --- a/recipes/mgems/meta.yaml +++ b/recipes/mgems/meta.yaml @@ -10,7 +10,7 @@ source: sha256: c16db45f575d039ca5219b9bc7b7a4dc4bc3ceb3239b2a61085106d3d666b57a build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('mgems', max_pin="x") }} diff --git a/recipes/mgikit/build_failure.osx-64.yaml b/recipes/mgikit/build_failure.osx-64.yaml deleted file mode 100644 index adb0e9a3f949a..0000000000000 --- a/recipes/mgikit/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: bffa7226da5ba47a6baeeba197aed986c9e517280d39bdfbba65337d2fb1e621 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - Running rustc --crate-name syn --edition=2021 /opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/syn-2.0.66/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="clone-impls"' --cfg 'feature="default"' --cfg 'feature="derive"' --cfg 'feature="parsing"' --cfg 'feature="printing"' --cfg 'feature="proc-macro"' -C metadata=9458422a6b6a27ee -C extra-filename=-9458422a6b6a27ee --out-dir /opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/deps -C linker=x86_64-apple-darwin13.4.0-clang -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/deps --extern proc_macro2=/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/deps/libproc_macro2-4a4f23b2b4b41ec2.rmeta --extern quote=/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/deps/libquote-6ad0329045fa9111.rmeta --extern unicode_ident=/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/deps/libunicode_ident-0f8c807562e934ee.rmeta --cap-lints allow - Compiling crossbeam-deque v0.8.5 - Running rustc --crate-name crossbeam_deque --edition=2021 /opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/crossbeam-deque-0.8.5/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C panic=abort -C codegen-units=1 --cfg 'feature="default"' --cfg 'feature="std"' -C metadata=3f194d1e9b95e04b -C extra-filename=-3f194d1e9b95e04b --out-dir /opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/x86_64-apple-darwin/release/deps --target x86_64-apple-darwin -C linker=x86_64-apple-darwin13.4.0-clang -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/x86_64-apple-darwin/release/deps -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/deps --extern crossbeam_epoch=/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/x86_64-apple-darwin/release/deps/libcrossbeam_epoch-7b8ad32966f9f2ef.rmeta --extern crossbeam_utils=/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/x86_64-apple-darwin/release/deps/libcrossbeam_utils-242b3d56cf579aaa.rmeta --cap-lints allow -C link-arg=-Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib -C link-arg=-Wl,-headerpad_max_install_names -C link-arg=-Wl,-dead_strip_dylibs - error: linking with x86_64-apple-darwin13.4.0-clang failed: exit status: 1 - | - = note: env -u IPHONEOS_DEPLOYMENT_TARGET -u TVOS_DEPLOYMENT_TARGET LC_ALL="C" PATH="/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/bin:/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/.cargo/bin:/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/bin:/opt/mambaforge/envs/bioconda/condabin:/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/bin:/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin:/opt/mambaforge/envs/bioconda/bin:/opt/mambaforge/condabin:/opt/mambaforge/bin:/usr/local/lib/ruby/gems/3.0.0/bin:/usr/local/opt/ruby@3.0/bin:/usr/local/opt/pipx_bin:/Users/runner/.cargo/bin:/usr/local/opt/curl/bin:/usr/local/bin:/usr/local/sbin:/Users/runner/bin:/Users/runner/.yarn/bin:/Users/runner/Library/Android/sdk/tools:/Users/runner/Library/Android/sdk/platform-tools:/Library/Frameworks/Python.framework/Versions/Current/bin:/Library/Frameworks/Mono.framework/Versions/Current/Commands:/usr/bin:/bin:/usr/sbin:/sbin:/Users/runner/.dotnet/tools" VSLANG="1033" ZERO_AR_DATE="1" "x86_64-apple-darwin13.4.0-clang" "-arch" "x86_64" "-m64" "/tmp/rustcSPtvLo/symbols.o" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/build/libz-sys-02ae29bc08faf3d8/build_script_build-02ae29bc08faf3d8.build_script_build.de5941c10eba5054-cgu.0.rcgu.o" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/build/libz-sys-02ae29bc08faf3d8/build_script_build-02ae29bc08faf3d8.4b1epf52pjihq6yx.rcgu.o" "-L" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/deps" "-L" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/deps/libvcpkg-ddd7867e4658c133.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/deps/libcmake-818d25fd5a22877c.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/deps/libcc-6d393b2df27c1f92.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/deps/libpkg_config-b8a6842b1b583327.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libstd-2ad7f97be9e16ca5.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libpanic_unwind-8ce93eee8bf4c86e.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libobject-0e1339b212cc7409.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libmemchr-925e672b3deb429c.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libaddr2line-e92d517a950bccd8.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libgimli-de95e5c2a2ace281.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_demangle-37f4c48e230f618e.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libstd_detect-dfeb4bb0652b6b8e.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libhashbrown-0e3ea0ec18336be2.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_std_workspace_alloc-39dd3003e36d7872.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libminiz_oxide-5ea1513e08ee15e0.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libadler-2967159221f4860d.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libunwind-b70656709e3eca11.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcfg_if-cc5626b2e0399737.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/liblibc-8378684dba6ab463.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/liballoc-0ff05b9b25b786cc.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_std_workspace_core-9a6da74aeab39c54.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcore-1638dc700d175798.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcompiler_builtins-7f42af62722c8f43.rlib" "-lSystem" "-lc" "-lm" "-L" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib" "-o" "/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/build/libz-sys-02ae29bc08faf3d8/build_script_build-02ae29bc08faf3d8" "-Wl,-dead_strip" "-nodefaultlibs" - = note: ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libstd-2ad7f97be9e16ca5.rlib(std-2ad7f97be9e16ca5.std.73125d0ae810e61b-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcore-1638dc700d175798.rlib(core-1638dc700d175798.core.b1c2fc210f4dfff9-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/liballoc-0ff05b9b25b786cc.rlib(alloc-0ff05b9b25b786cc.alloc.9242d371e396bc4c-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_demangle-37f4c48e230f618e.rlib(rustc_demangle-37f4c48e230f618e.rustc_demangle.9fdffeb2b56169d1-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libgimli-de95e5c2a2ace281.rlib(gimli-de95e5c2a2ace281.gimli.72653df79598dcb2-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libobject-0e1339b212cc7409.rlib(object-0e1339b212cc7409.object.e3756fe3fb577255-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libmemchr-925e672b3deb429c.rlib(memchr-925e672b3deb429c.memchr.4dc4a05d80618598-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libaddr2line-e92d517a950bccd8.rlib(addr2line-e92d517a950bccd8.addr2line.7eb29e6a0a38fefd-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libhashbrown-0e3ea0ec18336be2.rlib(hashbrown-0e3ea0ec18336be2.hashbrown.febebf65344cb99d-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libpanic_unwind-8ce93eee8bf4c86e.rlib(panic_unwind-8ce93eee8bf4c86e.panic_unwind.a3b8ea81b157ee45-cgu.0.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - ld: warning: object file (/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcompiler_builtins-7f42af62722c8f43.rlib(compiler_builtins-7f42af62722c8f43.compiler_builtins.19fed66cffb9e9f5-cgu.089.rcgu.o)) was built for newer macOS version (10.12) than being linked (10.9) - Undefined symbols for architecture x86_64: - "_getentropy", referenced from: - std::sys::pal::unix::rand::hashmap_random_keys::hcc27ed0e9fd421d6 in libstd-2ad7f97be9e16ca5.rlib(std-2ad7f97be9e16ca5.std.73125d0ae810e61b-cgu.0.rcgu.o) - ld: symbol(s) not found for architecture x86_64 - clang-16: error: linker command failed with exit code 1 (use -v to see invocation) - - - error: could not compile libz-sys (build script) due to 1 previous error - - Caused by: - process didn't exit successfully: rustc --crate-name build_script_build --edition=2018 /opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/libz-sys-1.1.18/build.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="cmake"' --cfg 'feature="libc"' --cfg 'feature="zlib-ng"' -C metadata=02ae29bc08faf3d8 -C extra-filename=-02ae29bc08faf3d8 --out-dir /opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/build/libz-sys-02ae29bc08faf3d8 -C linker=x86_64-apple-darwin13.4.0-clang -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/deps --extern cc=/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/deps/libcc-6d393b2df27c1f92.rlib --extern cmake=/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/deps/libcmake-818d25fd5a22877c.rlib --extern pkg_config=/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/deps/libpkg_config-b8a6842b1b583327.rlib --extern vcpkg=/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target/release/deps/libvcpkg-ddd7867e4658c133.rlib --cap-lints allow (exit status: 1) - warning: build failed, waiting for other jobs to finish... - error: failed to compile mgikit v0.1.5 (/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work), intermediate artifacts can be found at /opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/target. - To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. - Extracting download - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mgikit-0.1.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/mgikit_1717595220511/work/conda_build.sh']' returned non-zero exit status 101. - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mgikit-0.1.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mgikit-0.1.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mgikit-0.1.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -# Last 100 lines of the build log. diff --git a/recipes/mgikit/meta.yaml b/recipes/mgikit/meta.yaml index e8ec1141a2616..253b182cd9707 100644 --- a/recipes/mgikit/meta.yaml +++ b/recipes/mgikit/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('mgikit', max_pin="x.x") }} diff --git a/recipes/mgkit/meta.yaml b/recipes/mgkit/meta.yaml index a3645fbd2bf88..df16be173b7d5 100644 --- a/recipes/mgkit/meta.yaml +++ b/recipes/mgkit/meta.yaml @@ -9,7 +9,7 @@ source: sha256: d19b26b20ec628a8d208a28b7df3956ba17799d11ea0b1d1ced8a6c1bded1343 build: - number: 3 + number: 4 skip: True # [py<37 or py > 39] script: rm mgkit/utils/*.c && USE_CYTHON=True {{ PYTHON }} -m pip install . --no-deps -vv entry_points: diff --git a/recipes/mgs-canopy/meta.yaml b/recipes/mgs-canopy/meta.yaml index 065bce4da6dbd..39c5a56258de8 100644 --- a/recipes/mgs-canopy/meta.yaml +++ b/recipes/mgs-canopy/meta.yaml @@ -12,7 +12,7 @@ source: md5: {{ md5 }} build: - number: 8 + number: 9 skip: True # [osx] requirements: diff --git a/recipes/micall-lite/meta.yaml b/recipes/micall-lite/meta.yaml index 217ffee25e745..c07ec44b11b4d 100644 --- a/recipes/micall-lite/meta.yaml +++ b/recipes/micall-lite/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv skip: True # [py2k or osx] diff --git a/recipes/micro_razers/meta.yaml b/recipes/micro_razers/meta.yaml index bd70af9020214..fab909fd09ce1 100644 --- a/recipes/micro_razers/meta.yaml +++ b/recipes/micro_razers/meta.yaml @@ -7,7 +7,7 @@ source: sha256: df083d5939d7e73fd00bbc6bb291ac7ea7b8d446cf89a9758fdffdc0eca9ec1c build: - number: 7 + number: 8 skip: True # [osx] requirements: diff --git a/recipes/microphaser/build_failure.linux-64.yaml b/recipes/microphaser/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..51279122447ef --- /dev/null +++ b/recipes/microphaser/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 950043fd9bcf60a3c882fefdfed1520d53fd38d8828fc3b8d66a28f748d0722c # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + --> src/microphasing.rs:2100:48 + | + 2100 | if record.strand() == Some(Strand::Forward) { + | ---- ^^^^^^^^^^^^^^^ expected bio_types::strand::Strand, found Strand + | | + | arguments to this enum variant are incorrect + | + = note: Strand and bio_types::strand::Strand have similar names, but are actually distinct types + note: Strand is defined in crate bio_types + --> /opt/conda/conda-bld/microphaser_1734019631252/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/bio-types-0.13.0/src/strand.rs:18:1 + | + 18 | pub enum Strand { + | ^^^^^^^^^^^^^^^ + note: bio_types::strand::Strand is defined in crate bio_types + --> /opt/conda/conda-bld/microphaser_1734019631252/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/bio-types-1.0.4/src/strand.rs:18:1 + | + 18 | pub enum Strand { + | ^^^^^^^^^^^^^^^ + = note: perhaps two different versions of crate bio_types are being used? + help: the type constructed contains Strand due to the type of the argument passed + --> src/microphasing.rs:2100:43 + | + 2100 | if record.strand() == Some(Strand::Forward) { + | ^^^^^---------------^ + | | + | this argument influences the type of Some + note: tuple variant defined here + --> /rustc/90b35a6239c3d8bdabc530a6a0816f7ff89a0aaf/library/core/src/option.rs:579:5 + + error[E0277]: the trait bound PhasingStrand: From is not satisfied + --> src/normal_microphasing.rs:1369:25 + | + 1369 | PhasingStrand::from( + | ^^^^^^^^^^^^^ the trait From is not implemented for PhasingStrand + | + = help: the trait From is implemented for PhasingStrand + = help: for that trait implementation, expected Strand, found bio_types::strand::Strand + + error[E0308]: mismatched types + --> src/normal_microphasing.rs:1410:44 + | + 1410 | if record.strand() == Some(Strand::Forward) { + | ---- ^^^^^^^^^^^^^^^ expected bio_types::strand::Strand, found Strand + | | + | arguments to this enum variant are incorrect + | + = note: Strand and bio_types::strand::Strand have similar names, but are actually distinct types + note: Strand is defined in crate bio_types + --> /opt/conda/conda-bld/microphaser_1734019631252/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/bio-types-0.13.0/src/strand.rs:18:1 + | + 18 | pub enum Strand { + | ^^^^^^^^^^^^^^^ + note: bio_types::strand::Strand is defined in crate bio_types + --> /opt/conda/conda-bld/microphaser_1734019631252/work/.cargo/registry/src/index.crates.io-6f17d22bba15001f/bio-types-1.0.4/src/strand.rs:18:1 + | + 18 | pub enum Strand { + | ^^^^^^^^^^^^^^^ + = note: perhaps two different versions of crate bio_types are being used? + help: the type constructed contains Strand due to the type of the argument passed + --> src/normal_microphasing.rs:1410:39 + | + 1410 | if record.strand() == Some(Strand::Forward) { + | ^^^^^---------------^ + | | + | this argument influences the type of Some + note: tuple variant defined here + --> /rustc/90b35a6239c3d8bdabc530a6a0816f7ff89a0aaf/library/core/src/option.rs:579:5 + + Some errors have detailed explanations: E0277, E0308. + For more information about an error, try rustc --explain E0277. + warning: microphaser (bin "microphaser") generated 2 warnings + error: could not compile microphaser (bin "microphaser") due to 5 previous errors; 2 warnings emitted + + Caused by: + process didn't exit successfully: rustc --crate-name microphaser --edition=2018 src/main.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=ef863b1be0678ba2 -C extra-filename=-ef863b1be0678ba2 --out-dir /opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps -C linker=/opt/conda/conda-bld/microphaser_1734019631252/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps --extern bincode=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps/libbincode-c18a82c0361c31fc.rlib --extern bio=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps/libbio-469a81732bb7e935.rlib --extern bio_types=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps/libbio_types-358d14efe18f1826.rlib --extern clap=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps/libclap-b5adde01c3d7f293.rlib --extern csv=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps/libcsv-2b2e3022338714d6.rlib --extern fern=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps/libfern-095327e78a18b7ae.rlib --extern flate2=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps/libflate2-a0eb9162ad37aaa3.rlib --extern http=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps/libhttp-42de3eabbcfaac9f.rlib --extern hyper=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps/libhyper-ddb81c7254a29bc6.rlib --extern itertools=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps/libitertools-e9e9cc03f1327ba5.rlib --extern log=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps/liblog-054a084181905fb9.rlib --extern rust_htslib=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps/librust_htslib-ffec952acdfe2828.rlib --extern serde=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps/libserde-080f39e3ff02ebc4.rlib --extern serde_derive=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps/libserde_derive-c5359619a68902d0.so --extern sha1=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps/libsha1-d35bed011a525ecf.rlib --extern statrs=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps/libstatrs-a8801d3760a73983.rlib --extern struct_field_names_as_array=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps/libstruct_field_names_as_array-e3b1d72d0756f432.so --extern vec_map=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/deps/libvec_map-44acbff0af859d1b.rlib -L native=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/build/miniz-sys-8566d628f30b51d3/out -L native=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/build/hts-sys-4d9cfed115ebe0e9/out -L native=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/build/bzip2-sys-f052b245a2eefc4e/out/lib -L native=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/build/curl-sys-9e46da162a05378e/out/build -L native=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/build/libz-sys-273aa2af71d66ef7/out/lib -L native=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/build/libz-sys-273aa2af71d66ef7/out/lib -L native=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/build/openssl-sys-7f1bbcc825040199/out/openssl-build/install/lib -L native=/opt/conda/conda-bld/microphaser_1734019631252/work/target/release/build/lzma-sys-acf89db7aa15278c/out (exit status: 1) + error: failed to compile microphaser v0.8.0 (/opt/conda/conda-bld/microphaser_1734019631252/work), intermediate artifacts can be found at /opt/conda/conda-bld/microphaser_1734019631252/work/target. + To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/microphaser_1734019631252/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/microphaser_1734019631252/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. diff --git a/recipes/microphaser/meta.yaml b/recipes/microphaser/meta.yaml index 1c1ee135d27cd..d339304f685e2 100644 --- a/recipes/microphaser/meta.yaml +++ b/recipes/microphaser/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 # Skipping macOS builds due to unresolved linking error: # Undefined symbols for architecture x86_64: # "_SSLCopyALPNProtocols", referenced from: diff --git a/recipes/migraine/meta.yaml b/recipes/migraine/meta.yaml index 7e1f433a0622a..90e77727eb224 100644 --- a/recipes/migraine/meta.yaml +++ b/recipes/migraine/meta.yaml @@ -3,7 +3,7 @@ package: version: 0.6.0 build: - number: 3 + number: 4 skip: True # [osx] source: diff --git a/recipes/migrate-n/meta.yaml b/recipes/migrate-n/meta.yaml index 8e41eb417c853..119689a868f6d 100644 --- a/recipes/migrate-n/meta.yaml +++ b/recipes/migrate-n/meta.yaml @@ -14,7 +14,7 @@ source: - 0003-Makefile.patch build: - number: 6 + number: 7 skip: True # [not linux] requirements: diff --git a/recipes/mindthegap/build_failure.osx-64.yaml b/recipes/mindthegap/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c9a51e7ea8a47 --- /dev/null +++ b/recipes/mindthegap/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: c5ee3d34d02878cbb9d193815f360928cfe13931540b4eda6cfc3b678a651b08 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [ 27%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FO.c.o + [ 27%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FS.c.o + [ 27%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FScache.c.o + [ 28%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FSdbg.c.o + [ 28%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FSint.c.o + [ 28%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FSsection.c.o + [ 28%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FSstat.c.o + [ 28%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FStest.c.o + [ 29%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5G.c.o + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/mindthegap_1734454651113/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + [ 29%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gbtree2.c.o + [ 29%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gcache.c.o + [ 29%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gcompact.c.o + [ 30%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gdense.c.o + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + [ 30%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gdeprec.c.o + [ 30%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gent.c.o + [ 30%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gint.c.o + [ 30%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Glink.c.o + [ 31%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gloc.c.o + [ 31%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gname.c.o + [ 31%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gnode.c.o + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + [ 31%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gobj.c.o + [ 32%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Goh.c.o + [ 32%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Groot.c.o + [ 32%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gstab.c.o + [ 32%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gtest.c.o + [ 32%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gtraverse.c.o + [ 33%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HF.c.o + [ 33%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFbtree2.c.o + [ 33%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFcache.c.o + [ 33%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFdbg.c.o + [ 34%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFdblock.c.o + [ 34%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFdtable.c.o + [ 34%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFhdr.c.o + [ 34%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFhuge.c.o + [ 34%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFiblock.c.o + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + [ 35%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFiter.c.o + [ 35%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFman.c.o + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + [ 35%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFsection.c.o + [ 35%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFspace.c.o + [ 36%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFstat.c.o + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/mindthegap_1734454651113/work/conda_build.sh']' returned non-zero exit status 2. + [ 36%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFtest.c.o + [ 36%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFtiny.c.o + [ 36%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HG.c.o + [ 36%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HGcache.c.o + [ 37%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HGdbg.c.o + [ 37%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HGquery.c.o + [ 37%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HL.c.o + [ 37%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HLcache.c.o + [ 38%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HLdbg.c.o + [ 38%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HLdblk.c.o + [ 38%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HLint.c.o + [ 38%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HLprfx.c.o + [ 38%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HP.c.o + [ 39%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5I.c.o + [ 39%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Itest.c.o + [ 39%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5L.c.o + [ 39%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Lexternal.c.o + [ 40%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MF.c.o + [ 40%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MFaggr.c.o + [ 40%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MFdbg.c.o + [ 40%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MFsection.c.o + [ 40%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MM.c.o + [ 41%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MP.c.o + [ 41%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MPtest.c.o + [ 41%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5O.c.o + [ 41%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Oainfo.c.o + [ 42%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Oalloc.c.o + [ 42%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Oattr.c.o + [ 42%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Oattribute.c.o + [ 42%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Obogus.c.o + [ 42%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Obtreek.c.o + [ 43%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Ocache.c.o + [ 43%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Ocache_image.c.o + [ 43%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Ochunk.c.o + [ 43%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Ocont.c.o + [ 44%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Odbg.c.o + [ 44%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Ocopy.c.o + [ 44%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Odeprec.c.o + [ 44%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Odrvinfo.c.o +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/mindthegap/meta.yaml b/recipes/mindthegap/meta.yaml index a5bcd84f938e9..3d0517bb1234e 100644 --- a/recipes/mindthegap/meta.yaml +++ b/recipes/mindthegap/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 source: url: https://github.com/GATB/mindthegap/releases/download/v{{ version }}/mindthegap-v{{ version }}-Source.tar.gz diff --git a/recipes/minia/build_failure.linux-64.yaml b/recipes/minia/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..dfe2e98f9685f --- /dev/null +++ b/recipes/minia/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 3e6544a08c4a9fffbd4f96990ee6921dd8de2b0b0a7d35f53e8785dce2482c3b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + 912 | remaining_blocks = current_section->nb_blocks; + | ^~~~~~~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp: In member function 'void Kff_reader::read_next_block()': + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:920:9: error: 'current_seq_kmers' was not declared in this scope + 920 | current_seq_kmers = remaining_kmers = current_section->read_compacted_sequence(current_sequence, current_data); + | ^~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:920:29: error: 'remaining_kmers' was not declared in this scope + 920 | current_seq_kmers = remaining_kmers = current_section->read_compacted_sequence(current_sequence, current_data); + | ^~~~~~~~~~~~~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:920:64: error: 'class Block_section_reader' has no member named 'read_compacted_sequence' + 920 | current_seq_kmers = remaining_kmers = current_section->read_compacted_sequence(current_sequence, current_data); + | ^~~~~~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:920:88: error: 'current_sequence' was not declared in this scope + 920 | current_seq_kmers = remaining_kmers = current_section->read_compacted_sequence(current_sequence, current_data); + | ^~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:920:106: error: 'current_data' was not declared in this scope + 920 | current_seq_kmers = remaining_kmers = current_section->read_compacted_sequence(current_sequence, current_data); + | ^~~~~~~~~~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:921:9: error: 'current_seq_nucleotides' was not declared in this scope + 921 | current_seq_nucleotides = remaining_kmers current_section->k - 1; + | ^~~~~~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:921:70: error: 'class Block_section_reader' has no member named 'k' + 921 | current_seq_nucleotides = remaining_kmers current_section->k - 1; + | ^ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:922:9: error: 'current_seq_bytes' was not declared in this scope + 922 | current_seq_bytes = bytes_from_bit_array(2, current_seq_nucleotides); + | ^~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:922:29: error: 'bytes_from_bit_array' was not declared in this scope + 922 | current_seq_bytes = bytes_from_bit_array(2, current_seq_nucleotides); + | ^~~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:925:14: error: 'uint8_t' was not declared in this scope + 925 | for (uint8_t i=1 ; i<4 ; i) { + | ^~~~~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:925:14: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:925:28: error: 'i' was not declared in this scope + 925 | for (uint8_t i=1 ; i<4 ; i) { + | ^ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:927:24: error: 'current_shifts' was not declared in this scope + 927 | memcpy(current_shifts[i], current_sequence, current_seq_bytes); + | ^~~~~~~~~~~~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:929:17: error: 'rightshift8' was not declared in this scope + 929 | rightshift8(current_shifts[i], current_seq_bytes, 2 * i); + | ^~~~~~~~~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp: At global scope: + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:939:1: error: 'uint64_t' does not name a type + 939 | uint64_t Kff_reader::next_block(uint8_t* & sequence, uint8_t* & data) { + | ^~~~~~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:939:1: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:963:6: error: variable or field 'next_kmer' declared void + 963 | void Kff_reader::next_kmer(uint8_t* & kmer, uint8_t* & data) { + | ^~~~~~~~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:963:28: error: 'uint8_t' was not declared in this scope + 963 | void Kff_reader::next_kmer(uint8_t* & kmer, uint8_t* & data) { + | ^~~~~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:963:28: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:963:39: error: 'kmer' was not declared in this scope + 963 | void Kff_reader::next_kmer(uint8_t* & kmer, uint8_t* & data) { + | ^~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:963:45: error: 'uint8_t' was not declared in this scope + 963 | void Kff_reader::next_kmer(uint8_t* & kmer, uint8_t* & data) { + | ^~~~~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:963:45: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:963:56: error: 'data' was not declared in this scope + 963 | void Kff_reader::next_kmer(uint8_t* & kmer, uint8_t* & data) { + | ^~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:1001:1: error: 'uint64_t' does not name a type + 1001 | uint64_t Kff_reader::get_var(string name) { + | ^~~~~~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:1001:1: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:1012:1: error: 'uint8_t' does not name a type + 1012 | uint8_t * Kff_reader::get_encoding() { + | ^~~~~~~ + /opt/conda/conda-bld/minia_1734293897416/work/thirdparty/gatb-core/gatb-core/thirdparty/kff-cpp-api/kff_io.cpp:1012:1: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + make[2]: *** [ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/build.make:1507: ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/__/thirdparty/kff-cpp-api/kff_io.cpp.o] Error 1 + make[2]: *** Waiting for unfinished jobs.... + make[1]: *** [CMakeFiles/Makefile2:385: ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/all] Error 2 + make: *** [Makefile:156: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/minia_1734293897416/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/minia_1734293897416/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/minia/meta.yaml b/recipes/minia/meta.yaml index 67531ed633a1b..80dbd5e3c543c 100644 --- a/recipes/minia/meta.yaml +++ b/recipes/minia/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 skip: True # [osx] source: diff --git a/recipes/miniasm/meta.yaml b/recipes/miniasm/meta.yaml index 1d5f46060d2d0..3e283f31581e0 100644 --- a/recipes/miniasm/meta.yaml +++ b/recipes/miniasm/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage('miniasm', max_pin='x.x') }} @@ -34,4 +34,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/minigraph/meta.yaml b/recipes/minigraph/meta.yaml index 456963ae6b205..0f413bd1c42bb 100644 --- a/recipes/minigraph/meta.yaml +++ b/recipes/minigraph/meta.yaml @@ -12,7 +12,7 @@ source: - minigraph-aarch64.patch # [aarch64 or arm64] build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('minigraph', max_pin="x.x") }} diff --git a/recipes/minimac4/build_failure.osx-64.yaml b/recipes/minimac4/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..e1c5f637b6ce9 --- /dev/null +++ b/recipes/minimac4/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 59c01f90c3218dc437acd970e250fa49aef8f805d988b0f3047fd5cb209e80f3 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + -- Build files have been written to: $SRC_DIR/cget/cget/build/tmp-4ed80092c8f7419aa5a9b20212ede1c6/build + [ 3%] Creating pkg-config file + [ 15%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/entropy_common.c.o + [ 15%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/fse_decompress.c.o + [ 15%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/threading.c.o + [ 15%] Built target libzstd.pc + [ 19%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/pool.c.o + [ 23%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/zstd_common.c.o + [ 26%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/error_private.c.o + [ 30%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/common/xxhash.c.o + [ 34%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/fse_compress.c.o + [ 38%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/huf_compress.c.o + [ 42%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_compress.c.o + [ 46%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstdmt_compress.c.o + [ 50%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_fast.c.o + [ 53%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_double_fast.c.o + [ 57%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_lazy.c.o + [ 61%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_opt.c.o + [ 65%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_ldm.c.o + [ 69%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/huf_decompress.c.o + [ 73%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress.c.o + [ 76%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o + [ 80%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o + [ 84%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o + [ 88%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o + [ 92%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o + [ 96%] Building C object build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o + [100%] Linking C static library libzstd.a + [100%] Built target libzstd_static + [ 3%] Creating pkg-config file + [100%] Built target libzstd_static + [100%] Built target libzstd.pc + Install the project... + -- Install configuration: "Release" + -- Installing: $SRC_DIR/cget/cget/pkg/zstd/install/share/pkgconfig/libzstd.pc + -- Installing: $SRC_DIR/cget/cget/pkg/zstd/install/include/zstd.h + -- Installing: $SRC_DIR/cget/cget/pkg/zstd/install/include/zbuff.h + -- Installing: $SRC_DIR/cget/cget/pkg/zstd/install/include/zdict.h + -- Installing: $SRC_DIR/cget/cget/pkg/zstd/install/include/zstd_errors.h + -- Installing: $SRC_DIR/cget/cget/pkg/zstd/install/lib/libzstd.a + Downloading http://zlib.net/fossils/zlib-1.2.11.tar.gz + + Extracting archive $SRC_DIR/cget/cget/build/tmp-322a4a3a1280414982261077138abb84/zlib-1.2.11.tar.gz ... + -- The C compiler identification is Clang 18.1.8 + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped + -- Detecting C compile features + -- Detecting C compile features - done + -- Looking for sys/types.h + -- Looking for sys/types.h - found + -- Looking for stdint.h + -- Looking for stdint.h - found + -- Looking for stddef.h + -- Looking for stddef.h - found + -- Check size of off64_t + -- Check size of off64_t - failed + -- Looking for fseeko + -- Looking for fseeko - found + -- Looking for unistd.h + -- Looking for unistd.h - found + -- Renaming + -- $SRC_DIR/cget/cget/build/tmp-322a4a3a1280414982261077138abb84/zlib-1.2.11/zconf.h + -- to 'zconf.h.included' because this file is included with zlib + -- but CMake generates it automatically in the build directory. + -- Configuring done (2.9s) + -- Generating done (0.0s) + -- Build files have been written to: $SRC_DIR/cget/cget/build/tmp-322a4a3a1280414982261077138abb84/build + [ 5%] Building C object CMakeFiles/zlibstatic.dir/adler32.o + [ 8%] Building C object CMakeFiles/zlibstatic.dir/compress.o + [ 11%] Building C object CMakeFiles/zlibstatic.dir/crc32.o + [ 11%] Building C object CMakeFiles/zlib.dir/adler32.o + [ 13%] Building C object CMakeFiles/zlibstatic.dir/deflate.o + [ 19%] Building C object CMakeFiles/zlibstatic.dir/gzclose.o + [ 19%] Building C object CMakeFiles/zlib.dir/compress.o + [ 22%] Building C object CMakeFiles/zlibstatic.dir/gzlib.o + [ 25%] Building C object CMakeFiles/zlib.dir/crc32.o + [ 27%] Building C object CMakeFiles/zlib.dir/deflate.o + [ 30%] Building C object CMakeFiles/zlibstatic.dir/gzread.o + [ 33%] Building C object CMakeFiles/zlib.dir/gzclose.o + [ 36%] Building C object CMakeFiles/zlibstatic.dir/gzwrite.o + [ 38%] Building C object CMakeFiles/zlib.dir/gzlib.o + [ 41%] Building C object CMakeFiles/zlibstatic.dir/inflate.o + [ 44%] Building C object CMakeFiles/zlib.dir/gzread.o + [ 47%] Building C object CMakeFiles/zlib.dir/gzwrite.o + [ 50%] Building C object CMakeFiles/zlib.dir/inflate.o + [ 52%] Building C object CMakeFiles/zlib.dir/infback.o + [ 55%] Building C object CMakeFiles/zlib.dir/inftrees.o + [ 58%] Building C object CMakeFiles/zlibstatic.dir/infback.o + [ 61%] Building C object CMakeFiles/zlib.dir/inffast.o + [ 63%] Building C object CMakeFiles/zlib.dir/trees.o + [ 66%] Building C object CMakeFiles/zlibstatic.dir/inftrees.o + [ 69%] Building C object CMakeFiles/zlib.dir/uncompr.o + [ 72%] Building C object CMakeFiles/zlib.dir/zutil.o + [ 75%] Building C object CMakeFiles/zlibstatic.dir/inffast.o + [ 77%] Building C object CMakeFiles/zlibstatic.dir/trees.o + [ 80%] Building C object CMakeFiles/zlibstatic.dir/uncompr.o + [ 83%] Building C object CMakeFiles/zlibstatic.dir/zutil.o + Command failed: ['$BUILD_PREFIX/bin/cmake', '--build', '$SRC_DIR/cget/cget/build/tmp-322a4a3a1280414982261077138abb84/build', '--config', 'Release', '--', '-j', '4'] + Failed to build package statgen/savvy +# Last 100 lines of the build log. diff --git a/recipes/minimac4/meta.yaml b/recipes/minimac4/meta.yaml index 889e9cbc3f5d8..dc60285c3145c 100644 --- a/recipes/minimac4/meta.yaml +++ b/recipes/minimac4/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('minimac4', max_pin='x.x.x') }} diff --git a/recipes/minimap/meta.yaml b/recipes/minimap/meta.yaml index 91ac3c52d8187..ef8b322533f5d 100644 --- a/recipes/minimap/meta.yaml +++ b/recipes/minimap/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.2_r124" build: - number: 7 + number: 8 source: url: https://github.com/lh3/minimap/archive/1cd6ae3bc7c7a6f9e7c03c0b7a93a12647bba244.tar.gz diff --git a/recipes/minimap2-coverage/meta.yaml b/recipes/minimap2-coverage/meta.yaml index 636e196a5b71c..8d0d8e1240b09 100644 --- a/recipes/minimap2-coverage/meta.yaml +++ b/recipes/minimap2-coverage/meta.yaml @@ -11,7 +11,7 @@ source: build: # uses argp, which is glib-only skip: true # [osx] - number: 3 + number: 4 requirements: build: diff --git a/recipes/minimap2/meta.yaml b/recipes/minimap2/meta.yaml index bcfd16f66dfac..472f80dc3e1df 100644 --- a/recipes/minimap2/meta.yaml +++ b/recipes/minimap2/meta.yaml @@ -12,7 +12,7 @@ source: - override-makefile.patch build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/miniprot-boundary-scorer/meta.yaml b/recipes/miniprot-boundary-scorer/meta.yaml index cb7ef5acd15e7..d95b3c903e02c 100644 --- a/recipes/miniprot-boundary-scorer/meta.yaml +++ b/recipes/miniprot-boundary-scorer/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 9a5f3babd6db07b673589f2bb8de9436fd9a9c844483ce893d27de0d79ed79e8 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/miniprot/meta.yaml b/recipes/miniprot/meta.yaml index 203fcc669f373..a634b507be474 100644 --- a/recipes/miniprot/meta.yaml +++ b/recipes/miniprot/meta.yaml @@ -7,7 +7,7 @@ package: version: "{{ version }}" build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -39,4 +39,4 @@ about: extra: additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 diff --git a/recipes/minirmd/build_failure.osx-64.yaml b/recipes/minirmd/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..d9e53d7402572 --- /dev/null +++ b/recipes/minirmd/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 0dd6bbb7d32b3d6791aae3261da707706ac2dcbdf2572af45d460d6656ba51d0 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + Traceback (most recent call last): + - ncurses 6.5 hf036a51_1 + - openssl 3.4.0 hd471939_0 + - ld64_osx-64 951.9 hc8d1a19_2 + - clang_impl_osx-64 18.1.8 h6a44ed1_23 + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + - clangxx_osx-64 18.1.8 h7e5c614_23 + - make 4.4.1 h00291cd_2 + - clang 18.1.8 default_h179603d_5 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + - ca-certificates 2024.8.30 h8857fd0_0 + - libclang-cpp18.1 18.1.8 default_h0c94c6a_5 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + - sigtool 0.1.3 h88f4db0_0 + - clangxx 18.1.8 default_h179603d_5 + host: + - libcxx 19.1.5 hf95d169_0 + - libzlib 1.3.1 hd23fc13_2 + - zlib 1.3.1 hd23fc13_2 + run: + - zlib + - libzlib >=1.3.1,<2.0a0 + - libcxx >=18 + test: + commands: + - minirmd -h + about: + home: https://github.com/yuansliu/minirmd + license: GPL-3.0-only + license_file: LICENSE + summary: Remove duplicate and near-duplicate reads + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/minirmd_1733956525528/work + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/minirmd_1733956525528/work/conda_build.sh']' returned non-zero exit status 2. + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/minirmd_1733956525528/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/minirmd_1733956525528/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/minirmd_1733956525528/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/minirmd-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/minirmd-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/minirmd-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/minirmd-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 src/minirmd.cpp src/bseq.c -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lm -lz -lpthread -o minirmd +# Last 100 lines of the build log. diff --git a/recipes/minirmd/meta.yaml b/recipes/minirmd/meta.yaml index d6c07aa4d2a83..0c17907fcdd6c 100644 --- a/recipes/minirmd/meta.yaml +++ b/recipes/minirmd/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://github.com/yuansliu/minirmd/archive/v{{ version }}.tar.gz diff --git a/recipes/anise_basil/build_failure.osx-64.yaml b/recipes/minys/build_failure.osx-64.yaml similarity index 57% rename from recipes/anise_basil/build_failure.osx-64.yaml rename to recipes/minys/build_failure.osx-64.yaml index cf492bee68734..df212f9d4f4c2 100644 --- a/recipes/anise_basil/build_failure.osx-64.yaml +++ b/recipes/minys/build_failure.osx-64.yaml @@ -1,104 +1,104 @@ -recipe_sha: a4f527f34f72188524afb48002a4a66249e87016763e6bfaa429a82684283696 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: d19d6ebb5aff69b98186c8ac629bcbbc1e3ebeaa6c7cec05d8cfde0b8da4fa82 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - CMake Error at ext/seqan/util/cmake/FindSeqAn.cmake:404 (string): - string sub-command REGEX, mode REPLACE needs at least 6 arguments total to - command. - Call Stack (most recent call first): - src/CMakeLists.txt:15 (find_package) +log: |2- + - minia + - libcxx >=18 + - mindthegap + - bwa + - python>=3 + - samtools + - numpy + - pyani + test: + commands: + - MinYS.py -h + about: + home: https://github.com/cguyomar/MinYS + license: file + license_file: LICENSE + summary: MinYS allows targeted assembly of bacterial genomes using a reference-guided + pipeline. + extra: + copy_test_source_files: true + final: true - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/anise_basil_1717515166943/work - Traceback (most recent call last): - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/anise_basil_1717515166943/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/anise_basil_1717515166943/_build_env - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/anise_basil_1717515166943/work + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/minys_1734757722014/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/minys_1734757722014/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/minys_1734757722014/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/minys_1734757722014/work INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as CC=x86_64-apple-darwin13.4.0-clang CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/anise_basil-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/minys-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/anise_basil-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/minys-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool LD=x86_64-apple-darwin13.4.0-ld + raise subprocess.CalledProcessError(proc.returncode, _args) LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/anise_basil_1717515166943/work/conda_build.sh']' returned non-zero exit status 1. LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/minys_1734757722014/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang OTOOL=x86_64-apple-darwin13.4.0-otool PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack SIZE=x86_64-apple-darwin13.4.0-size STRINGS=x86_64-apple-darwin13.4.0-strings STRIP=x86_64-apple-darwin13.4.0-strip + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 ac_cv_func_malloc_0_nonnull=yes + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc ac_cv_func_realloc_0_nonnull=yes build_alias=x86_64-apple-darwin13.4.0 host_alias=x86_64-apple-darwin13.4.0 INFO: activate_clangxx_osx-64.sh made the following environmental changes: CLANGXX=x86_64-apple-darwin13.4.0-clang CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/anise_basil-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/minys_1734757722014/work/conda_build.sh']' returned non-zero exit status 2. + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/minys-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/anise_basil-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - -- The C compiler identification is Clang 16.0.6 - -- The CXX compiler identification is Clang 16.0.6 - -- Detecting C compiler ABI info - -- Detecting C compiler ABI info - done - -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped - -- Detecting C compile features - -- Detecting C compile features - done - -- Detecting CXX compiler ABI info - -- Detecting CXX compiler ABI info - done - -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped - -- Detecting CXX compile features - -- Detecting CXX compile features - done - -- Performing Test CXX11_FOUND - -- Performing Test CXX11_FOUND - Success - -- Looking for include file execinfo.h - -- Looking for include file execinfo.h - found - -- Determined version is .. - -- Found LEMON: $SRC_DIR/ext/lemon - -- Found Boost 1.85.0 at $PREFIX/lib/cmake/Boost-1.85.0 - -- Requested configuration: QUIET REQUIRED - -- BoostConfig: find_package(boost_headers 1.85.0 EXACT CONFIG REQUIRED QUIET HINTS $PREFIX/lib/cmake) - -- Found boost_headers 1.85.0 at $PREFIX/lib/cmake/boost_headers-1.85.0 - -- Found Boost: $PREFIX/lib/cmake/Boost-1.85.0/BoostConfig.cmake - -- Configuring incomplete, errors occurred! + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/minys-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + make: Entering directory '$PREFIX/share/minys-1.1-6/graph_simplification/nwalign' + g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/minys-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -c -o nwalign.o nwalign.cpp + make: Leaving directory '$PREFIX/share/minys-1.1-6/graph_simplification/nwalign' # Last 100 lines of the build log. diff --git a/recipes/minys/meta.yaml b/recipes/minys/meta.yaml index 27ba6e4943b05..79ff273c5deed 100644 --- a/recipes/minys/meta.yaml +++ b/recipes/minys/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 5 + number: 6 source: url: https://github.com/cguyomar/MinYS/releases/download/v{{ version }}/MinYS-v{{ version }}-Source.tar.gz diff --git a/recipes/mira-moods/build_failure.osx-64.yaml b/recipes/mira-moods/build_failure.osx-64.yaml deleted file mode 100644 index 1975dce4291ce..0000000000000 --- a/recipes/mira-moods/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: b57dc98d2f651f1b95d8803759b80ca2c83183448f724cf4c4222a785f97d5dd # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mira-moods-1.9.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2711, in build - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - newly_built_packages = bundlers[pkg_type](output_d, m, env, stats) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1850, in bundle_conda - files = post_process_files(metadata, initial_files) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1664, in post_process_files - post_build(m, new_files, build_python=python) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1727, in post_build - post_process_shared_lib(m, f, prefix_files, host_prefix) - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mira-moods-1.9.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1603, in post_process_shared_lib - mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 470, in mk_relative_osx - names = macho.otool(path, prefix) - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 221, in otool - lines = check_output([otool, "-l", path], stderr=STDOUT).decode("utf-8") - File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 421, in check_output - return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, - File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 526, in run - raise CalledProcessError(retcode, process.args, - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mira-moods-1.9.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - Using pip 24.0 from $PREFIX/lib/python3.12/site-packages/pip (python 3.12) - subprocess.CalledProcessError: Command '['/opt/mambaforge/envs/bioconda/conda-bld/mira-moods_1717611232909/_build_env/bin/llvm-otool', '-l', '/opt/mambaforge/envs/bioconda/conda-bld/mira-moods_1717611232909/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/python3.12/site-packages/MOODS/_tools.cpython-312-darwin.so']' died with . - Non-user install because user site-packages disabled - Ignoring indexes: https://pypi.org/simple - Created temporary directory: /private/tmp/pip-build-tracker-cz6pu1q3 - Initialized build tracking at /private/tmp/pip-build-tracker-cz6pu1q3 - Created build tracker: /private/tmp/pip-build-tracker-cz6pu1q3 - Entered build tracker: /private/tmp/pip-build-tracker-cz6pu1q3 - Created temporary directory: /private/tmp/pip-install-alwg1khm - Created temporary directory: /private/tmp/pip-ephem-wheel-cache-tfvawc9t - Processing $SRC_DIR - Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-cz6pu1q3' - Running setup.py (path:$SRC_DIR/setup.py) egg_info for package from file://$SRC_DIR - Created temporary directory: /private/tmp/pip-pip-egg-info-_04ai9g1 - Preparing metadata (setup.py): started - Preparing metadata (setup.py): finished with status 'done' - Source in $SRC_DIR has version 1.9.4.2, which satisfies requirement mira-moods==1.9.4.2 from file://$SRC_DIR - Removed mira-moods==1.9.4.2 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-cz6pu1q3' - Created temporary directory: /private/tmp/pip-unpack-y11ehv9b - Building wheels for collected packages: mira-moods - Created temporary directory: /private/tmp/pip-wheel-k72_4yxq - Building wheel for mira-moods (setup.py): started - Destination directory: /private/tmp/pip-wheel-k72_4yxq - Building wheel for mira-moods (setup.py): finished with status 'done' - Created wheel for mira-moods: filename=mira_moods-1.9.4.2-cp312-cp312-macosx_10_9_x86_64.whl size=589618 sha256=1772a60ee896c5b0bf889724d91b8f0c28bcf945f0616fccd849478dd684143f - Stored in directory: /private/tmp/pip-ephem-wheel-cache-tfvawc9t/wheels/a4/ff/16/f51d120cb8b53c8435cb7c2553b2f3fc693287daaceeb58516 - Successfully built mira-moods - Installing collected packages: mira-moods - - Successfully installed mira-moods-1.9.4.2 - Removed build tracker: '/private/tmp/pip-build-tracker-cz6pu1q3' - - Resource usage statistics from building mira-moods: - Process count: 5 - CPU time: Sys=0:00:03.2, User=0:00:38.8 - Memory: 257.0M - Disk usage: 15.6K - Time elapsed: 0:01:05.9 - - - compiling .pyc files... - number of files: 23 -# Last 100 lines of the build log. diff --git a/recipes/mira-moods/meta.yaml b/recipes/mira-moods/meta.yaml index 305aac0447f80..48a3076b74b65 100644 --- a/recipes/mira-moods/meta.yaml +++ b/recipes/mira-moods/meta.yaml @@ -11,7 +11,7 @@ source: build: script: {{ PYTHON }} -m pip install . -vv - number: 1 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -22,7 +22,8 @@ requirements: - {{ compiler('cxx') }} host: - pip - - python >=3.5 + - python + - setuptools - swig run: - python @@ -51,4 +52,4 @@ extra: - AllenWLynch identifiers: - biotools:MOODS - - doi:10.1109/TCBB.2009.35 \ No newline at end of file + - doi:10.1109/TCBB.2009.35 diff --git a/recipes/miranda/build_failure.linux-64.yaml b/recipes/miranda/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..db12c53f480ad --- /dev/null +++ b/recipes/miranda/build_failure.linux-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: e06b8b844d480c951bf46535dbfb41c7e802b26d37ce8e087dfd630092bec8b6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + lint fails due to license; source (presumably with license) unavailable +category: |- + source download error diff --git a/recipes/miranda/build_failure.osx-64.yaml b/recipes/miranda/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..39d3c602b1d32 --- /dev/null +++ b/recipes/miranda/build_failure.osx-64.yaml @@ -0,0 +1,86 @@ +recipe_sha: e06b8b844d480c951bf46535dbfb41c7e802b26d37ce8e087dfd630092bec8b6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + /opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (recipes/miranda/meta.yaml). + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/mambaforge/envs/bioconda/conda_build_config.yaml + Adding in variants from /opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for miranda + Reloading output folder: ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder: ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['miranda-3.3a-h18d8cf3_7.tar.bz2'] + Reloading output folder: ...working... done + Solving environment (_build_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/miranda_1734125343654/_build_env + + + The following NEW packages will be INSTALLED: + + ca-certificates: 2024.8.30-h8857fd0_0 conda-forge + cctools_osx-64: 1010.6-h00edd4c_2 conda-forge + clang: 18.1.8-default_h179603d_5 conda-forge + clang-18: 18.1.8-default_h0c94c6a_5 conda-forge + clang_impl_osx-64: 18.1.8-h6a44ed1_23 conda-forge + clang_osx-64: 18.1.8-h7e5c614_23 conda-forge + clangxx: 18.1.8-default_h179603d_5 conda-forge + compiler-rt: 18.1.8-h1020d70_1 conda-forge + compiler-rt_osx-64: 18.1.8-hf2b8a54_1 conda-forge + ld64_osx-64: 951.9-hc8d1a19_2 conda-forge + libclang-cpp18.1: 18.1.8-default_h0c94c6a_5 conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libcxx-devel: 18.1.8-h7c275be_7 conda-forge + libiconv: 1.17-hd75f5a5_2 conda-forge + libllvm18: 18.1.8-h9ce406d_2 conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libxml2: 2.13.5-he8ee3e7_1 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-tools: 18.1.8-h9ce406d_2 conda-forge + llvm-tools-18: 18.1.8-h9ce406d_2 conda-forge + make: 4.4.1-h00291cd_2 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + sigtool: 0.1.3-h88f4db0_0 conda-forge + tapi: 1300.6.5-h390ca13_0 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache + Downloading source to cache: miRanda-aug2010_a671da562c.tar.gz + Downloading http://cbio.mskcc.org/microrna_data/miRanda-aug2010.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.198234 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download http://cbio.mskcc.org/microrna_data/miRanda-aug2010.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/miranda/meta.yaml b/recipes/miranda/meta.yaml index 60f303aabe23d..5f4582378947c 100644 --- a/recipes/miranda/meta.yaml +++ b/recipes/miranda/meta.yaml @@ -7,7 +7,7 @@ source: sha256: a671da562cf4636ef5085b27349df2df2f335774663fd423deb08f31212ec778 build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/mlrho/meta.yaml b/recipes/mlrho/meta.yaml index ffb15aa8ec06a..f19e80cf0eea7 100644 --- a/recipes/mlrho/meta.yaml +++ b/recipes/mlrho/meta.yaml @@ -13,7 +13,7 @@ source: - 0001-Makefile.patch build: - number: 8 + number: 9 requirements: build: diff --git a/recipes/mlst/2.9/meta.yaml b/recipes/mlst/2.9/meta.yaml index 0099eeba469b0..2cdeb8724e8d1 100644 --- a/recipes/mlst/2.9/meta.yaml +++ b/recipes/mlst/2.9/meta.yaml @@ -3,7 +3,7 @@ package: version: "2.9" build: - number: 5 + number: 6 source: url: https://github.com/tseemann/mlst/archive/2.9.tar.gz diff --git a/recipes/mmannot/meta.yaml b/recipes/mmannot/meta.yaml index 5a793146b9bb9..1725be17bdf86 100644 --- a/recipes/mmannot/meta.yaml +++ b/recipes/mmannot/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 source: url: https://github.com/mzytnicki/mmannot/archive/refs/tags/v{{ version }}.tar.gz diff --git a/recipes/mmquant/build_failure.osx-64.yaml b/recipes/mmquant/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..07978a7046512 --- /dev/null +++ b/recipes/mmquant/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: f80459ace5c9f1ac1c367d95eff4df467095cbf55568eabfadc50a23e7b43cd9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - zstd 1.5.6 h915ae27_0 + - clang-18 18.1.8 default_h0c94c6a_5 + - libcxx-devel 18.1.8 h7c275be_7 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + - libiconv 1.17 hd75f5a5_2 + - libclang-cpp18.1 18.1.8 default_h0c94c6a_5 + - libllvm18 18.1.8 h9ce406d_2 + - tapi 1300.6.5 h390ca13_0 + - clang 18.1.8 default_h179603d_5 + - make 4.4.1 h00291cd_2 + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + - clang_osx-64 18.1.8 h7e5c614_23 + - openssl 3.4.0 hd471939_0 + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/mmquant_1733955442065/work/conda_build.sh']' returned non-zero exit status 2. + - clangxx 18.1.8 default_h179603d_5 + - cctools_osx-64 1010.6 h00edd4c_2 + - ld64_osx-64 951.9 hc8d1a19_2 + host: + - libcxx 19.1.5 hf95d169_0 + - libzlib 1.3.1 hd23fc13_2 + - zlib 1.3.1 hd23fc13_2 + run: + - libcxx >=18 + - zlib + - libzlib >=1.3.1,<2.0a0 + - make + test: + commands: + - mmquant -h + about: + home: https://bitbucket.org/mzytnicki/multi-mapping-counter/ + license: GPL3/LGPL3 + license_file: gpl-3.0.txt + summary: RNA-Seq quantification tool, with special handling on multi-mapping reads. + extra: + copy_test_source_files: true + final: true + recipe-maintainers: + - mzytnicki + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/mmquant_1733955442065/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/mmquant_1733955442065/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/mmquant_1733955442065/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/mmquant_1733955442065/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mmquant-1.0.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mmquant-1.0.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mmquant-1.0.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mmquant-1.0.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + x86_64-apple-darwin13.4.0-clang mmquant.cpp -DMMSTANDALONE -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mmquant-1.0.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -o mmquant -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -pthread -lz +# Last 100 lines of the build log. diff --git a/recipes/mmquant/meta.yaml b/recipes/mmquant/meta.yaml index 9e281487b471e..930a80e2e1bdb 100644 --- a/recipes/mmquant/meta.yaml +++ b/recipes/mmquant/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/mmseqs2/meta.yaml b/recipes/mmseqs2/meta.yaml index e13ce6f50a2a0..4e2b65aae6a07 100644 --- a/recipes/mmseqs2/meta.yaml +++ b/recipes/mmseqs2/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version|replace("-", ".") }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('mmseqs2', max_pin=None) }} diff --git a/recipes/modeltest-ng/build_failure.osx-64.yaml b/recipes/modeltest-ng/build_failure.osx-64.yaml deleted file mode 100644 index 6caac540bb633..0000000000000 --- a/recipes/modeltest-ng/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: ead9f20290840b76f8debd8ec990605d4baefb8e6c9089d0f0592ddcb807e951 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - /opt/mambaforge/envs/bioconda/conda-bld/modeltest-ng_1685393044934/work/libs/pll-modules/src/tree/tbe_functions.c:400:32: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare] - if (abs(bs_light[j] - p) > min_hdist && - ~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~ - 4 warnings generated. - [ 66%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/utree_operations.c.o - [ 67%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/split_utree.c.o - [ 68%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/lex_split.c.o - [ 68%] Built target pllmodtree_obj - [ 69%] Linking C static library libpllmodtree.a - [ 69%] Built target pllmodtree_static - [ 70%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/__/pllmod_common.c.o - [ 70%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models.c.o - /opt/mambaforge/envs/bioconda/conda-bld/modeltest-ng_1685393044934/work/libs/pll-modules/src/util/models.c:396:37: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare] - assert(PLL_STATE_POPCNT(gapstate) == states); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ - /Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/assert.h:93:25: note: expanded from macro 'assert' - (__builtin_expect(!(e), 0) ? __assert_rtn(__func__, __FILE__, __LINE__, #e) : (void)0) - ^ - 1 warning generated. - [ 71%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models_aa.c.o - [ 72%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models_dna.c.o - [ 73%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models_gt.c.o - [ 74%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models_mult.c.o - [ 74%] Built target pllmodutil_obj - [ 75%] Linking C static library libpllmodutil.a - [ 75%] Built target pllmodutil_static - [ 75%] Building CXX object src/CMakeFiles/modeltest_module.dir/genesis/date_time.cpp.o - [ 76%] Building CXX object src/CMakeFiles/modeltest_module.dir/genesis/logging.cpp.o - [ 77%] Building CXX object src/CMakeFiles/modeltest_module.dir/genesis/string.cpp.o - [ 78%] Building CXX object src/CMakeFiles/modeltest_module.dir/main.cpp.o - [ 79%] Building CXX object src/CMakeFiles/modeltest_module.dir/meta.cpp.o - [ 79%] Building CXX object src/CMakeFiles/modeltest_module.dir/model/abstract_parameter.cpp.o - [ 80%] Building CXX object src/CMakeFiles/modeltest_module.dir/model/dnamodel.cpp.o - /opt/mambaforge/envs/bioconda/conda-bld/modeltest-ng_1685393044934/work/src/model/dnamodel.cpp:204:52: warning: operator '?:' has lower precedence than '|'; '|' will be evaluated first [-Wbitwise-conditional-parentheses] - optimize_gamma | optimize_ratecats ? n_categories : 1, /* rate cats */ - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ - /opt/mambaforge/envs/bioconda/conda-bld/modeltest-ng_1685393044934/work/src/model/dnamodel.cpp:204:52: note: place parentheses around the '|' expression to silence this warning - optimize_gamma | optimize_ratecats ? n_categories : 1, /* rate cats */ - ^ - ( ) - /opt/mambaforge/envs/bioconda/conda-bld/modeltest-ng_1685393044934/work/src/model/dnamodel.cpp:204:52: note: place parentheses around the '?:' expression to evaluate it first - optimize_gamma | optimize_ratecats ? n_categories : 1, /* rate cats */ - ^ - ( ) - 1 warning generated. - [ 81%] Building CXX object src/CMakeFiles/modeltest_module.dir/model/model.cpp.o - [ 82%] Building CXX object src/CMakeFiles/modeltest_module.dir/model/parameter_branches.cpp.o - [ 83%] Building CXX object src/CMakeFiles/modeltest_module.dir/model/parameter_frequencies.cpp.o - [ 84%] Building CXX object src/CMakeFiles/modeltest_module.dir/model/parameter_gamma.cpp.o - [ 84%] Building CXX object src/CMakeFiles/modeltest_module.dir/model/parameter_pinv.cpp.o - [ 85%] Building CXX object src/CMakeFiles/modeltest_module.dir/model/parameter_ratecats.cpp.o - [ 86%] Building CXX object src/CMakeFiles/modeltest_module.dir/model/parameter_substrates.cpp.o - [ 87%] Building CXX object src/CMakeFiles/modeltest_module.dir/model/protmodel.cpp.o - [ 88%] Building CXX object src/CMakeFiles/modeltest_module.dir/model_selection.cpp.o - [ 88%] Building CXX object src/CMakeFiles/modeltest_module.dir/modeltest.cpp.o - [ 89%] Building CXX object src/CMakeFiles/modeltest_module.dir/msapll.cpp.o - [ 90%] Building CXX object src/CMakeFiles/modeltest_module.dir/optimize/model_optimizer_pll.cpp.o - [ 91%] Building CXX object src/CMakeFiles/modeltest_module.dir/optimize/partition_optimizer.cpp.o - /opt/mambaforge/envs/bioconda/conda-bld/modeltest-ng_1685393044934/work/src/optimize/partition_optimizer.cpp:251:15: warning: variable 'opt_models_count' set but not used [-Wunused-but-set-variable] - mt_size_t opt_models_count = 0; - ^ - 1 warning generated. - [ 92%] Building CXX object src/CMakeFiles/modeltest_module.dir/partition.cpp.o - [ 93%] Building CXX object src/CMakeFiles/modeltest_module.dir/partition_selection.cpp.o - [ 93%] Building CXX object src/CMakeFiles/modeltest_module.dir/partitioning_scheme.cpp.o - [ 94%] Building CXX object src/CMakeFiles/modeltest_module.dir/service/checkpoint.cpp.o - [ 95%] Building CXX object src/CMakeFiles/modeltest_module.dir/service/modeltestservice.cpp.o - [ 96%] Building CXX object src/CMakeFiles/modeltest_module.dir/static_analyzer.cpp.o - [ 97%] Building CXX object src/CMakeFiles/modeltest_module.dir/thread/observer.cpp.o - [ 97%] Building CXX object src/CMakeFiles/modeltest_module.dir/thread/parallel_context.cpp.o - [ 98%] Building CXX object src/CMakeFiles/modeltest_module.dir/treepll.cpp.o - [ 99%] Building CXX object src/CMakeFiles/modeltest_module.dir/utils.cpp.o - /opt/mambaforge/envs/bioconda/conda-bld/modeltest-ng_1685393044934/work/src/utils.cpp:949:44: error: expected ')' in preprocessor expression - #if defined(CTL_HW) && (defined(HW_MEMSIZE) - ~~~~~~~~~~~~~~~~~~~^ - /opt/mambaforge/envs/bioconda/conda-bld/modeltest-ng_1685393044934/work/src/utils.cpp:949:24: note: to match this '(' - #if defined(CTL_HW) && (defined(HW_MEMSIZE) - ^ - 1 error generated. - make[2]: *** [src/CMakeFiles/modeltest_module.dir/build.make:482: src/CMakeFiles/modeltest_module.dir/utils.cpp.o] Error 1 - make[1]: *** [CMakeFiles/Makefile2:674: src/CMakeFiles/modeltest_module.dir/all] Error 2 - make: *** [Makefile:91: all] Error 2 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/modeltest-ng_1685393044934/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/modeltest-ng/meta.yaml b/recipes/modeltest-ng/meta.yaml index e342b34a3e3e3..c5ee2b13cc379 100644 --- a/recipes/modeltest-ng/meta.yaml +++ b/recipes/modeltest-ng/meta.yaml @@ -11,7 +11,7 @@ source: git_rev: v{{ version }} build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/modle/build_failure.linux-64.yaml b/recipes/modle/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..9e496f8376eb7 --- /dev/null +++ b/recipes/modle/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: ec6c22b4e7b057f3adac99bafd3d7f00bad1d8865a520c42d4472d9738fafecf # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/modle-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/modle-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + [1m[35m + ======== Input profiles ========[0m + [1m[36mProfile host:[0m + [settings] + arch=x86_64 + build_type=Release + compiler=gcc + compiler.cppstd=17 + compiler.libcxx=libstdc11 + compiler.version=13 + os=Linux + [0m + [1m[36mProfile build:[0m + [settings] + arch=x86_64 + build_type=Release + compiler=gcc + compiler.cppstd=17 + compiler.libcxx=libstdc11 + compiler.version=13 + os=Linux + [0m + [1m[35m + ======== Computing dependency graph ========[0m + abseil/20230125.3:[0m Not found in local cache, looking in remotes...[0m + abseil/20230125.3:[0m Checking remote: conancenter[0m + abseil/20230125.3:[0m Downloaded recipe revision 5431a4c609f5fb48bb8d8567e953243f[0m + bitflags/1.5.0:[0m Not found in local cache, looking in remotes...[0m + bitflags/1.5.0:[0m Checking remote: conancenter[0m + bitflags/1.5.0:[0m Downloaded recipe revision 626da9d1913161321841f30caf9b994e[0m + boost/1.82.0:[0m Not found in local cache, looking in remotes...[0m + boost/1.82.0:[0m Checking remote: conancenter[0m + boost/1.82.0:[0m Downloaded recipe revision 902463606663219fc8c6d2102f1b8c6a[0m + zlib/1.2.13:[0m Not found in local cache, looking in remotes...[0m + zlib/1.2.13:[0m Checking remote: conancenter[0m + zlib/1.2.13:[0m Downloaded recipe revision fb5cf5f28601b7e4391fdac28352ab0f[0m + bzip2/1.0.8:[0m Not found in local cache, looking in remotes...[0m + bzip2/1.0.8:[0m Checking remote: conancenter[0m + bzip2/1.0.8:[0m Downloaded recipe revision d00dac990f08d991998d624be81a9526[0m + xz_utils/5.4.2:[0m Not found in local cache, looking in remotes...[0m + xz_utils/5.4.2:[0m Checking remote: conancenter[0m + xz_utils/5.4.2:[0m Downloaded recipe revision 2711f2576a1c71ec9e01ef7f24080055[0m + zstd/1.5.5:[0m Not found in local cache, looking in remotes...[0m + zstd/1.5.5:[0m Checking remote: conancenter[0m + zstd/1.5.5:[0m Downloaded recipe revision 1f239731dc45147c7fc2f54bfbde73df[0m + b2/4.9.6:[0m Not found in local cache, looking in remotes...[0m + b2/4.9.6:[0m Checking remote: conancenter[0m + b2/4.9.6:[0m Downloaded recipe revision 3a760bc91df89901478565a554b15a19[0m + bshoshany-thread-pool/3.5.0:[0m Not found in local cache, looking in remotes...[0m + bshoshany-thread-pool/3.5.0:[0m Checking remote: conancenter[0m + bshoshany-thread-pool/3.5.0:[0m Downloaded recipe revision 3c9fd1e21a688432b7f31b40d2d168ee[0m + [1m[33mGraph root[0m + [1m[36m conanfile.txt: /opt/conda/conda-bld/modle_1734061823461/work/conanfile.txt[0m + [1m[33mRequirements[0m + [1m[36m abseil/20230125.3#5431a4c609f5fb48bb8d8567e953243f - Downloaded (conancenter)[0m + [1m[36m bitflags/1.5.0#626da9d1913161321841f30caf9b994e - Downloaded (conancenter)[0m + [1m[36m boost/1.82.0#902463606663219fc8c6d2102f1b8c6a - Downloaded (conancenter)[0m + [1m[36m bshoshany-thread-pool/3.5.0#3c9fd1e21a688432b7f31b40d2d168ee - Downloaded (conancenter)[0m + [1m[36m bzip2/1.0.8#d00dac990f08d991998d624be81a9526 - Downloaded (conancenter)[0m + [1m[36m xz_utils/5.4.2#2711f2576a1c71ec9e01ef7f24080055 - Downloaded (conancenter)[0m + [1m[36m zlib/1.2.13#fb5cf5f28601b7e4391fdac28352ab0f - Downloaded (conancenter)[0m + [1m[36m zstd/1.5.5#1f239731dc45147c7fc2f54bfbde73df - Downloaded (conancenter)[0m + [1m[33mBuild requirements[0m + [1m[36m b2/4.9.6#3a760bc91df89901478565a554b15a19 - Downloaded (conancenter)[0m + [31mERROR: Version conflict: Conflict between bzip2/1.0.8 and bzip2/1.0.8 in the graph. + Run 'conan graph info ... --format=html > graph.html' and open 'graph.html' to inspect the conflict graphically.[0m + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/modle_1734061823461/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/modle_1734061823461/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/modle/build_failure.osx-64.yaml b/recipes/modle/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..8a2ec320c3994 --- /dev/null +++ b/recipes/modle/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: ec6c22b4e7b057f3adac99bafd3d7f00bad1d8865a520c42d4472d9738fafecf # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - libcxx 19.1.5 hf95d169_0 + - make 4.4.1 h00291cd_2 + - ncurses 6.5 hf036a51_1 + host: + - libcxx 19.1.5 hf95d169_0 + run: + - libcxx >=18 + test: + commands: + - modle --help + - modle_tools --help + - modle --version + - modle_tools --version + requires: + - xz + - perl-digest-sha1 + - pyBigWig>=0.3.22 + - cooler>=0.9 + - curl + source_files: + - cmake/FetchTestDataset.cmake + - test/scripts/compare_bwigs.py + - test/scripts/modle_integration_test.sh + - test/scripts/modle_tools_annotate_barriers_integration_test.sh + - test/scripts/modle_tools_eval_integration_test.sh + - test/scripts/modle_tools_transform_integration_test.sh + about: + dev_url: https://github.com/paulsengroup/MoDLE + doc_url: https://github.com/paulsengroup/MoDLE#readme + home: https://github.com/paulsengroup/MoDLE + license: MIT + license_file: LICENSE + summary: High-performance stochastic modeling of DNA loop extrusion interactions + extra: + copy_test_source_files: true + final: true + identifiers: + - biotools:modle + - biotools:modle_tools + - doi:10.1186/s13059-022-02815-7 + - doi:10.5281/zenodo.6992533 + recipe-maintainers: + - robomics + - jonnings + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/modle_1733990998204/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/modle_1733990998204/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/modle_1733990998204/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/modle_1733990998204/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/modle-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/modle-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/modle-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/modle-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix +# Last 100 lines of the build log. diff --git a/recipes/modle/meta.yaml b/recipes/modle/meta.yaml index 602ba4b530f81..cd005ff76725d 100644 --- a/recipes/modle/meta.yaml +++ b/recipes/modle/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: url: https://github.com/paulsengroup/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz diff --git a/recipes/molpopgen-analysis/meta.yaml b/recipes/molpopgen-analysis/meta.yaml index 43b9f481105a3..be4ae92cd570b 100644 --- a/recipes/molpopgen-analysis/meta.yaml +++ b/recipes/molpopgen-analysis/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ hash }} build: - number: 9 + number: 10 requirements: build: diff --git a/recipes/moments/build_failure.linux-64.yaml b/recipes/moments/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..d0117f1b42e71 --- /dev/null +++ b/recipes/moments/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 3a6027d4be009d98bca888c956049039d96498f347452892c395863daab87ea8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + bzip2: 1.0.8-h4bc722e_7 conda-forge + ca-certificates: 2024.12.14-hbcca054_0 conda-forge + cython: 3.0.11-py312h8fd2918_3 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libblas: 3.9.0-25_linux64_openblas conda-forge + libcblas: 3.9.0-25_linux64_openblas conda-forge + libexpat: 2.6.4-h5888daf_0 conda-forge + libffi: 3.4.2-h7f98852_5 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-ng: 14.2.0-h69a702a_1 conda-forge + libgfortran: 14.2.0-h69a702a_1 conda-forge + libgfortran5: 14.2.0-hd5240d6_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + liblapack: 3.9.0-25_linux64_openblas conda-forge + liblzma: 5.6.3-hb9d3cd8_1 conda-forge + libnsl: 2.0.1-hd590300_0 conda-forge + libopenblas: 0.3.28-pthreads_h94d23a6_1 conda-forge + libsqlite: 3.47.2-hee588c1_0 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-ng: 14.2.0-h4852527_1 conda-forge + libuuid: 2.38.1-h0b41bf4_0 conda-forge + libxcrypt: 4.4.36-hd590300_1 conda-forge + libzlib: 1.3.1-hb9d3cd8_2 conda-forge + ncurses: 6.5-he02047a_1 conda-forge + numpy: 1.26.4-py312heda63a1_0 conda-forge + openssl: 3.4.0-hb9d3cd8_0 conda-forge + pip: 24.3.1-pyh145f28c_1 conda-forge + pkg-config: 0.29.2-h4bc722e_1009 conda-forge + pkgconfig: 1.5.5-pyhd8ed1ab_5 conda-forge + python: 3.12.8-h9e4cc4f_1_cpython conda-forge + python_abi: 3.12-5_cp312 conda-forge + readline: 8.2-h8228510_1 conda-forge + scipy: 1.14.1-py312h62794b6_2 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder: ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder: ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/moments_1734390874887/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.43-h4bf12b8_2 conda-forge + binutils_linux-64: 2.43-h4852527_2 conda-forge + gcc_impl_linux-64: 13.3.0-hfea6d02_1 conda-forge + gcc_linux-64: 13.3.0-hc28eda2_7 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libsanitizer: 13.3.0-heb74ff8_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: v1.1.16_e3b0c44298.tar.gz + Downloading https://github.com/MomentsLD/moments/archive/refs/tags/v1.1.16.tar.gz + Success + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 125, in download_to_cache + raise RuntimeError( + RuntimeError: SHA256 mismatch: '3a6816f9eef9d0754ffbf9015c4f8d7d9e42cbcd1f646193a11d8b6c70843749' != 'e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855' +# Last 100 lines of the build log. +category: |- + checksum mismatch diff --git a/recipes/moments/build_failure.linux-aarch64.yaml b/recipes/moments/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..132cbcb64e628 --- /dev/null +++ b/recipes/moments/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 3a6027d4be009d98bca888c956049039d96498f347452892c395863daab87ea8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + _openmp_mutex: 4.5-2_gnu conda-forge + bzip2: 1.0.8-h68df207_7 conda-forge + ca-certificates: 2024.12.14-hcefe29a_0 conda-forge + cython: 3.0.11-py310he223470_3 conda-forge + ld_impl_linux-aarch64: 2.43-h80caac9_2 conda-forge + libblas: 3.9.0-26_linuxaarch64_openblas conda-forge + libcblas: 3.9.0-26_linuxaarch64_openblas conda-forge + libffi: 3.4.2-h3557bc0_5 conda-forge + libgcc: 14.2.0-he277a41_1 conda-forge + libgcc-ng: 14.2.0-he9431aa_1 conda-forge + libgfortran: 14.2.0-he9431aa_1 conda-forge + libgfortran-ng: 14.2.0-he9431aa_1 conda-forge + libgfortran5: 14.2.0-hb6113d0_1 conda-forge + libglib: 2.82.2-hc486b8e_0 conda-forge + libgomp: 14.2.0-he277a41_1 conda-forge + libiconv: 1.17-h31becfc_2 conda-forge + liblapack: 3.9.0-26_linuxaarch64_openblas conda-forge + liblzma: 5.6.3-h86ecc28_1 conda-forge + libnsl: 2.0.1-h31becfc_0 conda-forge + libopenblas: 0.3.28-pthreads_h9d3fd7e_1 conda-forge + libsqlite: 3.47.2-h5eb1b54_0 conda-forge + libstdcxx: 14.2.0-h3f4de04_1 conda-forge + libstdcxx-ng: 14.2.0-hf1166c9_1 conda-forge + libuuid: 2.38.1-hb4cce97_0 conda-forge + libxcrypt: 4.4.36-h31becfc_1 conda-forge + libzlib: 1.3.1-h86ecc28_2 conda-forge + ncurses: 6.5-hcccb83c_1 conda-forge + numpy: 1.22.4-py310h7f880a9_0 conda-forge + openssl: 3.4.0-h86ecc28_0 conda-forge + pcre2: 10.44-h070dd5b_2 conda-forge + pip: 24.3.1-pyh8b19718_2 conda-forge + pkg-config: 0.29.2-hce167ba_1009 conda-forge + pkgconfig: 1.5.5-pyhd8ed1ab_5 conda-forge + python: 3.10.16-h57b00e1_1_cpython conda-forge + python_abi: 3.10-5_cp310 conda-forge + readline: 8.2-h8fc344f_1 conda-forge + scipy: 1.13.1-py310h70fbbe5_0 conda-forge + setuptools: 75.6.0-pyhff2d567_1 conda-forge + tk: 8.6.13-h194ca79_0 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + wheel: 0.45.1-pyhd8ed1ab_1 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder: ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder: ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/moments_1734538908037/_build_env + + + The following NEW packages will be INSTALLED: + + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-aarch64: 2.43-h4c662bb_2 conda-forge + binutils_linux-aarch64: 2.43-hf1166c9_2 conda-forge + gcc_impl_linux-aarch64: 13.3.0-hcdea9b6_1 conda-forge + gcc_linux-aarch64: 13.3.0-h1cd514b_7 conda-forge + kernel-headers_linux-aarch64: 4.18.0-h05a177a_18 conda-forge + ld_impl_linux-aarch64: 2.43-h80caac9_2 conda-forge + libgcc: 14.2.0-he277a41_1 conda-forge + libgcc-devel_linux-aarch64: 13.3.0-h0c07274_101 conda-forge + libgomp: 14.2.0-he277a41_1 conda-forge + libsanitizer: 13.3.0-ha58e236_1 conda-forge + libstdcxx: 14.2.0-h3f4de04_1 conda-forge + sysroot_linux-aarch64: 2.17-h5b4a56d_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: v1.1.16_e3b0c44298.tar.gz + Downloading https://github.com/MomentsLD/moments/archive/refs/tags/v1.1.16.tar.gz + Success + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 125, in download_to_cache + raise RuntimeError( + RuntimeError: SHA256 mismatch: '3a6816f9eef9d0754ffbf9015c4f8d7d9e42cbcd1f646193a11d8b6c70843749' != 'e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855' +# Last 100 lines of the build log. +category: |- + checksum mismatch diff --git a/recipes/moments/build_failure.osx-64.yaml b/recipes/moments/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..95f35f9d415fd --- /dev/null +++ b/recipes/moments/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 3a6027d4be009d98bca888c956049039d96498f347452892c395863daab87ea8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + The following NEW packages will be INSTALLED: + + bzip2: 1.0.8-hfdf4475_7 conda-forge + ca-certificates: 2024.12.14-h8857fd0_0 conda-forge + cython: 3.0.11-py310h62447e2_3 conda-forge + libblas: 3.9.0-26_osx64_openblas conda-forge + libcblas: 3.9.0-26_osx64_openblas conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libffi: 3.4.2-h0d85af4_5 conda-forge + libgfortran: 5.0.0-13_2_0_h97931a8_3 conda-forge + libgfortran5: 13.2.0-h2873a65_3 conda-forge + libiconv: 1.17-hd75f5a5_2 conda-forge + liblapack: 3.9.0-26_osx64_openblas conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libopenblas: 0.3.28-openmp_hbf64a52_1 conda-forge + libsqlite: 3.47.2-hdb6dae5_0 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-openmp: 19.1.5-ha54dae1_0 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + numpy: 1.22.4-py310hed37afb_0 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + pip: 24.3.1-pyh145f28c_1 conda-forge + pkg-config: 0.29.2-hf7e621a_1009 conda-forge + pkgconfig: 1.5.5-pyhd8ed1ab_5 conda-forge + python: 3.10.16-h5acdff8_1_cpython conda-forge + python_abi: 3.10-5_cp310 conda-forge + readline: 8.2-h9e318b2_1 conda-forge + scipy: 1.13.1-py310h35d8cac_0 conda-forge + tk: 8.6.13-h1abcd95_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (local): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (local): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/moments_1734456350210/_build_env + + + The following NEW packages will be INSTALLED: + + ca-certificates: 2024.12.14-h8857fd0_0 conda-forge + cctools_osx-64: 1010.6-h00edd4c_2 conda-forge + clang: 18.1.8-default_h179603d_5 conda-forge + clang-18: 18.1.8-default_h0c94c6a_5 conda-forge + clang_impl_osx-64: 18.1.8-h6a44ed1_23 conda-forge + clang_osx-64: 18.1.8-h7e5c614_23 conda-forge + clangxx: 18.1.8-default_h179603d_5 conda-forge + compiler-rt: 18.1.8-h1020d70_1 conda-forge + compiler-rt_osx-64: 18.1.8-hf2b8a54_1 conda-forge + ld64_osx-64: 951.9-hc8d1a19_2 conda-forge + libclang-cpp18.1: 18.1.8-default_h0c94c6a_5 conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libcxx-devel: 18.1.8-h7c275be_7 conda-forge + libiconv: 1.17-hd75f5a5_2 conda-forge + libllvm18: 18.1.8-h9ce406d_2 conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libxml2: 2.13.5-he8ee3e7_1 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-tools: 18.1.8-h9ce406d_2 conda-forge + llvm-tools-18: 18.1.8-h9ce406d_2 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + sigtool: 0.1.3-h88f4db0_0 conda-forge + tapi: 1300.6.5-h390ca13_0 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache + Downloading source to cache: v1.1.16_e3b0c44298.tar.gz + Downloading https://github.com/MomentsLD/moments/archive/refs/tags/v1.1.16.tar.gz + Success + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 125, in download_to_cache + raise RuntimeError( + RuntimeError: SHA256 mismatch: '3a6816f9eef9d0754ffbf9015c4f8d7d9e42cbcd1f646193a11d8b6c70843749' != 'e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855' +# Last 100 lines of the build log. +category: |- + checksum mismatch diff --git a/recipes/moments/meta.yaml b/recipes/moments/meta.yaml index e35d11ad6c976..9118cc32c00ce 100644 --- a/recipes/moments/meta.yaml +++ b/recipes/moments/meta.yaml @@ -6,11 +6,11 @@ package: version: '{{ version }}' source: - url: https://github.com/MomentsLD/moments/archive/refs/tags/{{ name }}-{{ version }}.tar.gz - sha256: 3a131126af9eaf606da123448b6b62a83d2308f052deb3fdcbdf0255fcc9b7fe + url: https://github.com/MomentsLD/moments/archive/refs/tags/v{{ version }}.tar.gz + sha256: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/moni/meta.yaml b/recipes/moni/meta.yaml index b5da94ad049f8..ee721628d3274 100644 --- a/recipes/moni/meta.yaml +++ b/recipes/moni/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} @@ -51,4 +51,4 @@ about: extra: recipe-maintainers: - AndreaGuarracino - - maxrossi91 \ No newline at end of file + - maxrossi91 diff --git a/recipes/moods/meta.yaml b/recipes/moods/meta.yaml index 36ffbea571da0..c8cd4f14980bb 100644 --- a/recipes/moods/meta.yaml +++ b/recipes/moods/meta.yaml @@ -10,7 +10,7 @@ source: sha256: e694e37c7487286801bffcda3e0576157960007919dd5ceb8b5a1626dc2968e1 build: - number: 2 + number: 3 skip: True # [py < 36] run_exports: - {{ pin_subpackage('moods', max_pin="x") }} diff --git a/recipes/motifscan/meta.yaml b/recipes/motifscan/meta.yaml index 65a0282043641..b126068d22d84 100644 --- a/recipes/motifscan/meta.yaml +++ b/recipes/motifscan/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 8059ab3232dfe7580835c5e953a8edd3f843676d57a6afbc41c5518a8a4dfde2 build: - number: 4 + number: 5 skip: True # [py<36] entry_points: - motifscan=motifscan.cli.main:main @@ -22,6 +22,7 @@ requirements: host: - python - pip + - setuptools run: - python - numpy >=1.15 diff --git a/recipes/mp-est/meta.yaml b/recipes/mp-est/meta.yaml index 86211692cfb7f..2cde3ac00bba4 100644 --- a/recipes/mp-est/meta.yaml +++ b/recipes/mp-est/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/mrbayes/build_failure.osx-64.yaml b/recipes/mrbayes/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..a210184f8ff27 --- /dev/null +++ b/recipes/mrbayes/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 1841254413f548ecd8ab882f56238eabae8c6b1bff0846e45bcc8c7f48661264 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("beagle-lib==3.1.2=hcd10b59_4")} + Encountered problems while solving: + - package beagle-lib-3.1.2-hcd10b59_4 is excluded by strict repo priority + + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("beagle-lib==3.1.2=hcd10b59_4")} + Encountered problems while solving: + - package beagle-lib-3.1.2-hcd10b59_4 is excluded by strict repo priority + + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("beagle-lib==3.1.2=hcd10b59_4")} + Encountered problems while solving: + - package beagle-lib-3.1.2-hcd10b59_4 is excluded by strict repo priority +# Last 100 lines of the build log. diff --git a/recipes/mreps/meta.yaml b/recipes/mreps/meta.yaml index 143b1eb0b7be6..4f35d262c86b1 100644 --- a/recipes/mreps/meta.yaml +++ b/recipes/mreps/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://github.com/gregorykucherov/{{ name }}/archive/{{ version }}.tar.gz diff --git a/recipes/mrsfast/meta.yaml b/recipes/mrsfast/meta.yaml index 516918dff8c19..dc69591bbef08 100644 --- a/recipes/mrsfast/meta.yaml +++ b/recipes/mrsfast/meta.yaml @@ -11,7 +11,7 @@ source: patches: Makefile.patch build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/ms2rescore-rs/build_failure.osx-64.yaml b/recipes/ms2rescore-rs/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c02cbff849679 --- /dev/null +++ b/recipes/ms2rescore-rs/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: a6b7f899ce0b4ea187a2362423df198c38082e7310e03f8b90a3d6b04384242d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + imports: + - ms2rescore_rs + requires: + - pip + about: + home: https://github.com/compomics/ms2rescore-rs + license: Apache-2.0 + license_file: LICENSE + summary: "Rust functionality for the MS\xB2Rescore package" + extra: + copy_test_source_files: true + final: true + recipe-maintainers: + - CompOmics + - RalfG + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/ms2rescore-rs_1734475608622/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/ms2rescore-rs_1734475608622/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/ms2rescore-rs_1734475608622/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/ms2rescore-rs_1734475608622/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ms2rescore-rs-0.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ms2rescore-rs-0.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + Using pip 24.3.1 from $PREFIX/lib/python3.12/site-packages/pip (python 3.12) + Non-user install because user site-packages disabled + Ignoring indexes: https://pypi.org/simple + Created temporary directory: /private/tmp/pip-build-tracker-o9l18q51 + Initialized build tracking at /private/tmp/pip-build-tracker-o9l18q51 + Created build tracker: /private/tmp/pip-build-tracker-o9l18q51 + Entered build tracker: /private/tmp/pip-build-tracker-o9l18q51 + Created temporary directory: /private/tmp/pip-install-kkbkkpjc + Created temporary directory: /private/tmp/pip-ephem-wheel-cache-lo_2tblv + Exception information: + Traceback (most recent call last): + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + ^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper + return func(self, options, args) + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 379, in run + requirement_set = resolver.resolve( + ^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 76, in resolve + collected = self.factory.collect_root_requirements(root_reqs) + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 545, in collect_root_requirements + reqs = list( + ^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 496, in _make_requirements_from_install_req + self._fail_if_link_is_unsupported_wheel(ireq.link) + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 147, in _fail_if_link_is_unsupported_wheel + raise UnsupportedWheel(msg) + pip._internal.exceptions.UnsupportedWheel: ms2rescore_rs-0.2.0-cp312-cp312-macosx_14_0_x86_64.whl is not a supported wheel on this platform. + Removed build tracker: '/private/tmp/pip-build-tracker-o9l18q51' +# Last 100 lines of the build log. +reason: |- + unsupported wheel on this platform diff --git a/recipes/ms2rescore-rs/meta.yaml b/recipes/ms2rescore-rs/meta.yaml index 1a0a2afa568f4..86ae6e083ea74 100644 --- a/recipes/ms2rescore-rs/meta.yaml +++ b/recipes/ms2rescore-rs/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 skip: True # [py < 37] run_exports: - {{ pin_subpackage(name|lower, max_pin="x.x") }} diff --git a/recipes/msalign2/meta.yaml b/recipes/msalign2/meta.yaml index 713087295dba8..e4d6b433ebf4f 100644 --- a/recipes/msalign2/meta.yaml +++ b/recipes/msalign2/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.0 build: - number: 5 + number: 6 skip: True # [osx] source: diff --git a/recipes/msamtools/meta.yaml b/recipes/msamtools/meta.yaml index 2b8872e292078..0f39a93514db3 100644 --- a/recipes/msamtools/meta.yaml +++ b/recipes/msamtools/meta.yaml @@ -9,7 +9,7 @@ source: sha256: f5a634105704f6da151f52eff7b7087231b8cce70a15d2a3fc76bfe4700109c1 build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/msaprobs/meta.yaml b/recipes/msaprobs/meta.yaml index 073b912125f02..019a3b809b37e 100644 --- a/recipes/msaprobs/meta.yaml +++ b/recipes/msaprobs/meta.yaml @@ -11,7 +11,7 @@ source: - Makefile.patch build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/mseqtools/build_failure.osx-64.yaml b/recipes/mseqtools/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c310f3a7e6e9f --- /dev/null +++ b/recipes/mseqtools/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a692a74f2ee2ad523af5e2e351795fc8e200d8e505e332c49ca84113a69f73d3 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mseqtools-0.9.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + checking for a BSD-compatible install... /usr/bin/install -c + checking whether sleep supports fractional seconds... yes + checking filesystem timestamp resolution... 0.01 + checking whether build environment is sane... yes + checking for a race-free mkdir -p... ./build-aux/install-sh -c -d + checking for gawk... no + checking for mawk... no + checking for nawk... no + checking for awk... awk + checking whether make sets $(MAKE)... yes + checking whether make supports nested variables... yes + checking xargs -n works... yes + checking how to create a pax tar archive... gnutar + checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang + checking whether the C compiler works... yes + checking for C compiler default output file name... a.out + checking for suffix of executables... + checking whether we are cross compiling... no + checking for suffix of object files... o + checking whether the compiler supports GNU C... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking for x86_64-apple-darwin13.4.0-clang option to enable C11 features... none needed + checking whether x86_64-apple-darwin13.4.0-clang understands -c and -o together... yes + checking whether make supports the include directive... yes (GNU style) + checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 + checking for x86_64-apple-darwin13.4.0-ranlib... x86_64-apple-darwin13.4.0-ranlib + checking for x86_64-apple-darwin13.4.0-ar... x86_64-apple-darwin13.4.0-ar + checking the archiver (x86_64-apple-darwin13.4.0-ar) interface... ar + checking for gzip... found + checking for wget... wget + checking for a sed that does not truncate output... /usr/bin/sed + checking for grep that handles long lines and -e... /usr/bin/grep + checking for arg_parse in -largtable2... yes + checking for inflate in -lz... yes + checking for library containing log... none required + checking build system type... x86_64-apple-darwin13.4.0 + checking host system type... x86_64-apple-darwin13.4.0 + checking that generated files are newer than configure... done + configure: creating ./config.status + config.status: creating Makefile + config.status: executing depfiles commands + + ------------------------------------------------------------------------------- + mseqtools was successfully configured with the following options: + + Host type : x86_64-apple-darwin13.4.0 + Install directory : $PREFIX + + You can build mseqtools executables by typing: + + make + + You can install mseqtools now by typing: + + make install + + This will install the executables in $PREFIX/bin + ------------------------------------------------------------------------------- + + -e [1;31mDownloading kseq.h from Heng Li's seqtk github repository:[0m + wget --quiet -O - "https://raw.githubusercontent.com/lh3/seqtk/7c04ce7898ad5909bd309c6ba3cd9c3bd0651f0e/kseq.h" > kseq.h + x86_64-apple-darwin13.4.0-clang -DPACKAGE_NAME=\"mseqtools\" -DPACKAGE_TARNAME=\"mseqtools\" -DPACKAGE_VERSION=\"0.9.1\" -DPACKAGE_STRING=\"mseqtools\ 0.9.1\" -DPACKAGE_BUGREPORT=\"http://www.arumugamlab.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mseqtools\" -DVERSION=\"0.9.1\" -DHAVE_LIBARGTABLE2=1 -DHAVE_LIBZ=1 -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -W -Wall -Wwrite-strings -std=gnu99 -pedantic -DBUILD=\"@BUILD@\" -DPROGRAM=\"mseqtools\" -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mseqtools-0.9.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT mseqtools.o -MD -MP -MF .deps/mseqtools.Tpo -c -o mseqtools.o mseqtools.c + x86_64-apple-darwin13.4.0-clang -DPACKAGE_NAME=\"mseqtools\" -DPACKAGE_TARNAME=\"mseqtools\" -DPACKAGE_VERSION=\"0.9.1\" -DPACKAGE_STRING=\"mseqtools\ 0.9.1\" -DPACKAGE_BUGREPORT=\"http://www.arumugamlab.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mseqtools\" -DVERSION=\"0.9.1\" -DHAVE_LIBARGTABLE2=1 -DHAVE_LIBZ=1 -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -W -Wall -Wwrite-strings -std=gnu99 -pedantic -DBUILD=\"@BUILD@\" -DPROGRAM=\"mseqtools\" -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mseqtools-0.9.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT mCommon.o -MD -MP -MF .deps/mCommon.Tpo -c -o mCommon.o mCommon.c + x86_64-apple-darwin13.4.0-clang -DPACKAGE_NAME=\"mseqtools\" -DPACKAGE_TARNAME=\"mseqtools\" -DPACKAGE_VERSION=\"0.9.1\" -DPACKAGE_STRING=\"mseqtools\ 0.9.1\" -DPACKAGE_BUGREPORT=\"http://www.arumugamlab.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mseqtools\" -DVERSION=\"0.9.1\" -DHAVE_LIBARGTABLE2=1 -DHAVE_LIBZ=1 -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -W -Wall -Wwrite-strings -std=gnu99 -pedantic -DBUILD=\"@BUILD@\" -DPROGRAM=\"mseqtools\" -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mseqtools-0.9.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT mSequence.o -MD -MP -MF .deps/mSequence.Tpo -c -o mSequence.o mSequence.c + x86_64-apple-darwin13.4.0-clang -DPACKAGE_NAME=\"mseqtools\" -DPACKAGE_TARNAME=\"mseqtools\" -DPACKAGE_VERSION=\"0.9.1\" -DPACKAGE_STRING=\"mseqtools\ 0.9.1\" -DPACKAGE_BUGREPORT=\"http://www.arumugamlab.org\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mseqtools\" -DVERSION=\"0.9.1\" -DHAVE_LIBARGTABLE2=1 -DHAVE_LIBZ=1 -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -W -Wall -Wwrite-strings -std=gnu99 -pedantic -DBUILD=\"@BUILD@\" -DPROGRAM=\"mseqtools\" -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/mseqtools-0.9.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT zoeTools.o -MD -MP -MF .deps/zoeTools.Tpo -c -o zoeTools.o zoeTools.c + mv -f .deps/mSequence.Tpo .deps/mSequence.Po + mv -f .deps/zoeTools.Tpo .deps/zoeTools.Po + mv -f .deps/mCommon.Tpo .deps/mCommon.Po +# Last 100 lines of the build log. diff --git a/recipes/mseqtools/meta.yaml b/recipes/mseqtools/meta.yaml index 4c205d2b1186a..dac2815b22aa9 100644 --- a/recipes/mseqtools/meta.yaml +++ b/recipes/mseqtools/meta.yaml @@ -9,7 +9,7 @@ source: sha256: f99647334c6e9fbe694c12c227e82348c223c1b5282da9f9fbde008412cece15 build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/msisensor-pro/meta.yaml b/recipes/msisensor-pro/meta.yaml index fd05528df5614..798cf3fc9283d 100644 --- a/recipes/msisensor-pro/meta.yaml +++ b/recipes/msisensor-pro/meta.yaml @@ -12,7 +12,7 @@ source: - buildfixes.patch build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('msisensor-pro', max_pin="x") }} diff --git a/recipes/msisensor2/meta.yaml b/recipes/msisensor2/meta.yaml index 55018fc1cb2f5..0a226a9d3cfe9 100644 --- a/recipes/msisensor2/meta.yaml +++ b/recipes/msisensor2/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 skip: True # [osx] source: diff --git a/recipes/mstmap/build_failure.linux-64.yaml b/recipes/mstmap/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..d574b8d2ad96a --- /dev/null +++ b/recipes/mstmap/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: e4ccd9283635876a7e5f2b7ab2cc723afa8e808bdbcf262fea08a012f93c9890 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + 2024-12-10T18:10:45 noarch Writing patched repodata + 2024-12-10T18:10:45 noarch Building current_repodata subset + 2024-12-10T18:10:45 noarch Writing current_repodata subset + 2024-12-10T18:10:45 noarch Writing index HTML + /opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (/opt/recipe/meta.yaml). + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml + Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for mstmap + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['mstmap-1-h9948957_4.tar.bz2'] + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/mstmap_1733854246453/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/mstmap_1733854246453/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.43-h4bf12b8_2 conda-forge + binutils_linux-64: 2.43-h4852527_2 conda-forge + gcc_impl_linux-64: 13.3.0-hfea6d02_1 conda-forge + gcc_linux-64: 13.3.0-hc28eda2_7 conda-forge + gxx_impl_linux-64: 13.3.0-hdbfa832_1 conda-forge + gxx_linux-64: 13.3.0-h6834431_7 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libsanitizer: 13.3.0-heb74ff8_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + make: 4.4.1-hb9d3cd8_2 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: mstmap_v1_8a84c4607e.tar.gz + Downloading http://www.cs.ucr.edu/~stelo/pub/mstmap_v1.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.394634 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download http://www.cs.ucr.edu/~stelo/pub/mstmap_v1.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/mstmap/build_failure.osx-64.yaml b/recipes/mstmap/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..2bb55ed749c81 --- /dev/null +++ b/recipes/mstmap/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: e4ccd9283635876a7e5f2b7ab2cc723afa8e808bdbcf262fea08a012f93c9890 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/mambaforge/envs/bioconda/conda_build_config.yaml + Adding in variants from /opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for mstmap + Reloading output folder (local): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (local): ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['mstmap-1-h5fa12a8_4.tar.bz2'] + Reloading output folder (local): ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/mstmap_1733855250391/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + + + The following NEW packages will be INSTALLED: + + libcxx: 19.1.5-hf95d169_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (local): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (local): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/mstmap_1733855250391/_build_env + + + The following NEW packages will be INSTALLED: + + ca-certificates: 2024.8.30-h8857fd0_0 conda-forge + cctools_osx-64: 1010.6-h00edd4c_2 conda-forge + clang: 18.1.8-default_h179603d_5 conda-forge + clang-18: 18.1.8-default_h0c94c6a_5 conda-forge + clang_impl_osx-64: 18.1.8-h6a44ed1_23 conda-forge + clang_osx-64: 18.1.8-h7e5c614_23 conda-forge + clangxx: 18.1.8-default_h179603d_5 conda-forge + clangxx_impl_osx-64: 18.1.8-h4b7810f_23 conda-forge + clangxx_osx-64: 18.1.8-h7e5c614_23 conda-forge + compiler-rt: 18.1.8-h1020d70_1 conda-forge + compiler-rt_osx-64: 18.1.8-hf2b8a54_1 conda-forge + ld64_osx-64: 951.9-hc8d1a19_2 conda-forge + libclang-cpp18.1: 18.1.8-default_h0c94c6a_5 conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libcxx-devel: 18.1.8-h7c275be_7 conda-forge + libiconv: 1.17-hd75f5a5_2 conda-forge + libllvm18: 18.1.8-h9ce406d_2 conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libxml2: 2.13.5-he8ee3e7_1 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-tools: 18.1.8-h9ce406d_2 conda-forge + llvm-tools-18: 18.1.8-h9ce406d_2 conda-forge + make: 4.4.1-h00291cd_2 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + sigtool: 0.1.3-h88f4db0_0 conda-forge + tapi: 1300.6.5-h390ca13_0 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache + Downloading source to cache: mstmap_v1_8a84c4607e.tar.gz + Downloading http://www.cs.ucr.edu/~stelo/pub/mstmap_v1.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.042976 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download http://www.cs.ucr.edu/~stelo/pub/mstmap_v1.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/mstmap/meta.yaml b/recipes/mstmap/meta.yaml index 8812acb5c2312..232dbfa02ba73 100644 --- a/recipes/mstmap/meta.yaml +++ b/recipes/mstmap/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 source: url: http://www.cs.ucr.edu/~stelo/pub/mstmap_v{{ version }}.tar.gz diff --git a/recipes/msweep/meta.yaml b/recipes/msweep/meta.yaml index 64708742989df..190a65a022af1 100644 --- a/recipes/msweep/meta.yaml +++ b/recipes/msweep/meta.yaml @@ -12,7 +12,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: true # [osx] run_exports: - {{ pin_subpackage('msweep', max_pin='x') }} diff --git a/recipes/mtm-align/build_failure.linux-64.yaml b/recipes/mtm-align/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..b7b895ae7f7b5 --- /dev/null +++ b/recipes/mtm-align/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 7f56f103d3143323f94ba52dfe8ac685870bfac8ca968a5eab9911409197d62a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + 2024-12-12T03:42:29 noarch Writing index HTML + /opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (/opt/recipe/meta.yaml). + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml + Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for mtm-align + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['mtm-align-20220104-h9948957_1.tar.bz2'] + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/mtm-align_1733974950089/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/mtm-align_1733974950089/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.43-h4bf12b8_2 conda-forge + binutils_linux-64: 2.43-h4852527_2 conda-forge + gcc_impl_linux-64: 13.3.0-hfea6d02_1 conda-forge + gcc_linux-64: 13.3.0-hc28eda2_7 conda-forge + gxx_impl_linux-64: 13.3.0-hdbfa832_1 conda-forge + gxx_linux-64: 13.3.0-h6834431_7 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libsanitizer: 13.3.0-heb74ff8_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + make: 4.4.1-hb9d3cd8_2 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: mTM-align_f7ed827ff2.tar.bz2 + Downloading http://yanglab.nankai.edu.cn/mTM-align/version/mTM-align.tar.bz2 + WARNING:urllib3.connectionpool:Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(, 'Connection to yanglab.nankai.edu.cn timed out. (connect timeout=9.15)')': /mTM-align/version/mTM-align.tar.bz2 + WARNING:urllib3.connectionpool:Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(, 'Connection to yanglab.nankai.edu.cn timed out. (connect timeout=9.15)')': /mTM-align/version/mTM-align.tar.bz2 + WARNING:urllib3.connectionpool:Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(, 'Connection to yanglab.nankai.edu.cn timed out. (connect timeout=9.15)')': /mTM-align/version/mTM-align.tar.bz2 + WARNING: Error: HTTP 000 CONNECTION FAILED for url + Elapsed: - + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download http://yanglab.nankai.edu.cn/mTM-align/version/mTM-align.tar.bz2 +# Last 100 lines of the build log. diff --git a/recipes/mtm-align/meta.yaml b/recipes/mtm-align/meta.yaml index 4e78d94b7ce57..99ce073813e2f 100644 --- a/recipes/mtm-align/meta.yaml +++ b/recipes/mtm-align/meta.yaml @@ -10,7 +10,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage('mtm-align', max_pin="x") }} diff --git a/recipes/mtsv-tools/meta.yaml b/recipes/mtsv-tools/meta.yaml index 0374bdf948683..29f190553d0a1 100644 --- a/recipes/mtsv-tools/meta.yaml +++ b/recipes/mtsv-tools/meta.yaml @@ -12,7 +12,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 skip: True # [osx] requirements: diff --git a/recipes/multirnafold/meta.yaml b/recipes/multirnafold/meta.yaml index ad45a1c49cb85..d2a71d646cc27 100644 --- a/recipes/multirnafold/meta.yaml +++ b/recipes/multirnafold/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name | lower, max_pin="x.x") }} diff --git a/recipes/multiz/meta.yaml b/recipes/multiz/meta.yaml index f25d645cec7aa..29df2dd13d723 100644 --- a/recipes/multiz/meta.yaml +++ b/recipes/multiz/meta.yaml @@ -3,7 +3,7 @@ package: version: "11.2" build: - number: 5 + number: 6 source: url: https://github.com/multiz/multiz/archive/20190527.tar.gz diff --git a/recipes/mummer/meta.yaml b/recipes/mummer/meta.yaml index 231fd29aec1a8..67f71dcb67300 100644 --- a/recipes/mummer/meta.yaml +++ b/recipes/mummer/meta.yaml @@ -18,7 +18,7 @@ source: - patches/procmaxmat_explicit.patch build: - number: 20 + number: 21 run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} diff --git a/recipes/mummer4/build_failure.linux-64.yaml b/recipes/mummer4/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..54420714092c6 --- /dev/null +++ b/recipes/mummer4/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 60764d0f0868927f30b538c6924f75777f4b2da549e504f7e284c2773841769c # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + ./include/mummer/48bit_iterator.hpp:103:11: error: 'class fortyeight_iterator' has no member named 'p1' + 103 | self->p1 = n; + | ~~~~~~^~ + ./include/mummer/48bit_iterator.hpp:104:11: error: 'class fortyeight_iterator' has no member named 'p2' + 104 | self->p2 = n; + | ~~~~~~^~ + ./include/mummer/48bit_iterator.hpp: In instantiation of 'Derived& fortyeight_iterator_imp::common::operator-=(difference_type) [with Derived = fortyeight_iterator; IDX = long int; difference_type = long int]': + ./include/mummer/48bit_iterator.hpp:117:56: required from 'Derived fortyeight_iterator_imp::common::operator-(difference_type) const [with Derived = fortyeight_iterator; IDX = long int; difference_type = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:99:20: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' + ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' + src/essaMEM/sparseSA.cpp:496:31: required from here + ./include/mummer/48bit_iterator.hpp:112:11: error: 'class fortyeight_iterator' has no member named 'p1' + 112 | self->p1 -= n; + | ~~~~~~^~ + ./include/mummer/48bit_iterator.hpp:113:11: error: 'class fortyeight_iterator' has no member named 'p2' + 113 | self->p2 -= n; + | ~~~~~~^~ + CXX src/tigr/mgaps.lo + ./include/mummer/48bit_iterator.hpp: In instantiation of 'bool fortyeight_iterator_imp::common::operator==(const Derived&) const [with Derived = fortyeight_iterator; IDX = long int]': + ./include/compactsufsort/sssort_imp.hpp:595:31: required from 'static void compactsufsort_imp::ss::swapmerge(CHARPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/sssort_imp.hpp:654:18: required from 'static void compactsufsort_imp::ss::sort(CHARPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDX, SAIDX, SAIDX, saint_t) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator; SAIDX = long int; saint_t = int]' + ./include/compactsufsort/compactsufsort_imp.hpp:145:39: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' + ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' + src/essaMEM/sparseSA.cpp:496:31: required from here + ./include/mummer/48bit_iterator.hpp:56:47: error: 'const class fortyeight_iterator' has no member named 'p1' + 56 | return static_cast(this)->p1 == rhs.p1; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ + ./include/mummer/48bit_iterator.hpp:56:57: error: 'const class fortyeight_iterator' has no member named 'p1' + 56 | return static_cast(this)->p1 == rhs.p1; + | ~~~~^~ + ./include/mummer/48bit_iterator.hpp: In instantiation of 'fortyeight_iterator_imp::common::difference_type fortyeight_iterator_imp::common::operator-(const fortyeight_iterator_imp::common&) const [with DD = fortyeight_iterator; II = long int; Derived = const_fortyeight_iterator; IDX = long int; difference_type = long int]': + ./include/compactsufsort/trsort_imp.hpp:254:29: required from 'static void compactsufsort_imp::tr::introsort(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, trbudget_t*) [with SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator]' + ./include/compactsufsort/trsort_imp.hpp:511:22: required from 'static void compactsufsort_imp::tr::sort(SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:170:24: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' + ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' + src/essaMEM/sparseSA.cpp:496:31: required from here + ./include/mummer/48bit_iterator.hpp:121:47: error: 'const class const_fortyeight_iterator' has no member named 'p1' + 121 | return static_cast(this)->p1 - static_cast(&rhs)->p1; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ + ./include/mummer/48bit_iterator.hpp:121:82: error: 'const class fortyeight_iterator' has no member named 'p1' + 121 | return static_cast(this)->p1 - static_cast(&rhs)->p1; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ + ./include/mummer/48bit_iterator.hpp: In instantiation of 'Derived& fortyeight_iterator_imp::common::operator-=(difference_type) [with Derived = const_fortyeight_iterator; IDX = long int; difference_type = long int]': + ./include/mummer/48bit_iterator.hpp:117:56: required from 'Derived fortyeight_iterator_imp::common::operator-(difference_type) const [with Derived = const_fortyeight_iterator; IDX = long int; difference_type = long int]' + ./include/compactsufsort/trsort_imp.hpp:264:26: required from 'static void compactsufsort_imp::tr::introsort(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, trbudget_t*) [with SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator]' + ./include/compactsufsort/trsort_imp.hpp:511:22: required from 'static void compactsufsort_imp::tr::sort(SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:170:24: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' + ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' + src/essaMEM/sparseSA.cpp:496:31: required from here + ./include/mummer/48bit_iterator.hpp:112:11: error: 'class const_fortyeight_iterator' has no member named 'p1' + 112 | self->p1 -= n; + | ~~~~~~^~ + ./include/mummer/48bit_iterator.hpp:113:11: error: 'class const_fortyeight_iterator' has no member named 'p2' + 113 | self->p2 -= n; + | ~~~~~~^~ + ./include/mummer/48bit_iterator.hpp: In instantiation of 'fortyeight_iterator_imp::common::difference_type fortyeight_iterator_imp::common::operator-(const fortyeight_iterator_imp::common&) const [with DD = const_fortyeight_iterator; II = long int; Derived = fortyeight_iterator; IDX = long int; difference_type = long int]': + ./include/compactsufsort/trsort_imp.hpp:196:11: required from 'static void compactsufsort_imp::tr::copy(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDX) [with SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/trsort_imp.hpp:307:17: required from 'static void compactsufsort_imp::tr::introsort(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, trbudget_t*) [with SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator]' + ./include/compactsufsort/trsort_imp.hpp:511:22: required from 'static void compactsufsort_imp::tr::sort(SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:170:24: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' + ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' + src/essaMEM/sparseSA.cpp:496:31: required from here + ./include/mummer/48bit_iterator.hpp:121:47: error: 'const class fortyeight_iterator' has no member named 'p1' + 121 | return static_cast(this)->p1 - static_cast(&rhs)->p1; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ + ./include/mummer/48bit_iterator.hpp:121:82: error: 'const class const_fortyeight_iterator' has no member named 'p1' + 121 | return static_cast(this)->p1 - static_cast(&rhs)->p1; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ + make[1]: *** [Makefile:2087: src/essaMEM/sparseSA.lo] Error 1 + make[1]: *** Waiting for unfinished jobs.... + make[1]: Leaving directory '$SRC_DIR' + make: *** [Makefile:1073: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/mummer4_1734293289048/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/mummer4_1734293289048/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/mummer4/build_failure.linux-aarch64.yaml b/recipes/mummer4/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..bff40fe6897ea --- /dev/null +++ b/recipes/mummer4/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 60764d0f0868927f30b538c6924f75777f4b2da549e504f7e284c2773841769c # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + src/essaMEM/sparseSA.cpp:498:59: required from here + ./include/mummer/48bit_iterator.hpp:103:11: error: 'class fortyeight_iterator' has no member named 'p1' + 103 | self->p1 = n; + | ~~~~~~^~ + ./include/mummer/48bit_iterator.hpp:104:11: error: 'class fortyeight_iterator' has no member named 'p2' + 104 | self->p2 = n; + | ~~~~~~^~ + ./include/mummer/48bit_iterator.hpp: In instantiation of 'Derived& fortyeight_iterator_imp::common::operator-=(difference_type) [with Derived = fortyeight_iterator; IDX = long int; difference_type = long int]': + ./include/mummer/48bit_iterator.hpp:117:56: required from 'Derived fortyeight_iterator_imp::common::operator-(difference_type) const [with Derived = fortyeight_iterator; IDX = long int; difference_type = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:99:20: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' + ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' + src/essaMEM/sparseSA.cpp:496:31: required from here + ./include/mummer/48bit_iterator.hpp:112:11: error: 'class fortyeight_iterator' has no member named 'p1' + 112 | self->p1 -= n; + | ~~~~~~^~ + ./include/mummer/48bit_iterator.hpp:113:11: error: 'class fortyeight_iterator' has no member named 'p2' + 113 | self->p2 -= n; + | ~~~~~~^~ + ./include/mummer/48bit_iterator.hpp: In instantiation of 'bool fortyeight_iterator_imp::common::operator==(const Derived&) const [with Derived = fortyeight_iterator; IDX = long int]': + ./include/compactsufsort/sssort_imp.hpp:595:31: required from 'static void compactsufsort_imp::ss::swapmerge(CHARPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/sssort_imp.hpp:654:18: required from 'static void compactsufsort_imp::ss::sort(CHARPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDX, SAIDX, SAIDX, saint_t) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator; SAIDX = long int; saint_t = int]' + ./include/compactsufsort/compactsufsort_imp.hpp:145:39: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' + ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' + src/essaMEM/sparseSA.cpp:496:31: required from here + ./include/mummer/48bit_iterator.hpp:56:47: error: 'const class fortyeight_iterator' has no member named 'p1' + 56 | return static_cast(this)->p1 == rhs.p1; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ + ./include/mummer/48bit_iterator.hpp:56:57: error: 'const class fortyeight_iterator' has no member named 'p1' + 56 | return static_cast(this)->p1 == rhs.p1; + | ~~~~^~ + ./include/mummer/48bit_iterator.hpp: In instantiation of 'fortyeight_iterator_imp::common::difference_type fortyeight_iterator_imp::common::operator-(const fortyeight_iterator_imp::common&) const [with DD = fortyeight_iterator; II = long int; Derived = const_fortyeight_iterator; IDX = long int; difference_type = long int]': + ./include/compactsufsort/trsort_imp.hpp:254:29: required from 'static void compactsufsort_imp::tr::introsort(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, trbudget_t*) [with SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator]' + ./include/compactsufsort/trsort_imp.hpp:511:22: required from 'static void compactsufsort_imp::tr::sort(SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:170:24: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' + ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' + src/essaMEM/sparseSA.cpp:496:31: required from here + ./include/mummer/48bit_iterator.hpp:121:47: error: 'const class const_fortyeight_iterator' has no member named 'p1' + 121 | return static_cast(this)->p1 - static_cast(&rhs)->p1; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ + ./include/mummer/48bit_iterator.hpp:121:82: error: 'const class fortyeight_iterator' has no member named 'p1' + 121 | return static_cast(this)->p1 - static_cast(&rhs)->p1; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ + ./include/mummer/48bit_iterator.hpp: In instantiation of 'Derived& fortyeight_iterator_imp::common::operator-=(difference_type) [with Derived = const_fortyeight_iterator; IDX = long int; difference_type = long int]': + ./include/mummer/48bit_iterator.hpp:117:56: required from 'Derived fortyeight_iterator_imp::common::operator-(difference_type) const [with Derived = const_fortyeight_iterator; IDX = long int; difference_type = long int]' + ./include/compactsufsort/trsort_imp.hpp:264:26: required from 'static void compactsufsort_imp::tr::introsort(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, trbudget_t*) [with SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator]' + ./include/compactsufsort/trsort_imp.hpp:511:22: required from 'static void compactsufsort_imp::tr::sort(SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:170:24: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' + ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' + src/essaMEM/sparseSA.cpp:496:31: required from here + ./include/mummer/48bit_iterator.hpp:112:11: error: 'class const_fortyeight_iterator' has no member named 'p1' + 112 | self->p1 -= n; + | ~~~~~~^~ + ./include/mummer/48bit_iterator.hpp:113:11: error: 'class const_fortyeight_iterator' has no member named 'p2' + 113 | self->p2 -= n; + | ~~~~~~^~ + ./include/mummer/48bit_iterator.hpp: In instantiation of 'fortyeight_iterator_imp::common::difference_type fortyeight_iterator_imp::common::operator-(const fortyeight_iterator_imp::common&) const [with DD = const_fortyeight_iterator; II = long int; Derived = fortyeight_iterator; IDX = long int; difference_type = long int]': + ./include/compactsufsort/trsort_imp.hpp:196:11: required from 'static void compactsufsort_imp::tr::copy(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, SAIDX) [with SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/trsort_imp.hpp:307:17: required from 'static void compactsufsort_imp::tr::introsort(SAIDPTR, CSAIDPTR, SAIDPTR, SAIDPTR, SAIDPTR, trbudget_t*) [with SAIDPTR = fortyeight_iterator; CSAIDPTR = const_fortyeight_iterator]' + ./include/compactsufsort/trsort_imp.hpp:511:22: required from 'static void compactsufsort_imp::tr::sort(SAIDPTR, SAIDPTR, SAIDX, SAIDX) [with SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:170:24: required from 'static compactsufsort_imp::SA::SAIDX compactsufsort_imp::SA::sort_typeBstar(CHARPTR, SAIDPTR, SAIDX*, SAIDX*, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int]' + ./include/compactsufsort/compactsufsort_imp.hpp:287:25: required from 'static saint_t compactsufsort_imp::SA::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; saint_t = int; SAIDX = long int]' + ./include/compactsufsort/compactsufsort.hpp:26:97: required from 'saint_t compactsufsort::create(CHARPTR, SAIDPTR, SAIDX) [with CHARPTR = const unsigned char*; SAIDPTR = fortyeight_iterator; SAIDX = long int; saint_t = int]' + src/essaMEM/sparseSA.cpp:496:31: required from here + ./include/mummer/48bit_iterator.hpp:121:47: error: 'const class fortyeight_iterator' has no member named 'p1' + 121 | return static_cast(this)->p1 - static_cast(&rhs)->p1; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ + ./include/mummer/48bit_iterator.hpp:121:82: error: 'const class const_fortyeight_iterator' has no member named 'p1' + 121 | return static_cast(this)->p1 - static_cast(&rhs)->p1; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ + make[1]: *** [Makefile:2087: src/essaMEM/sparseSA.lo] Error 1 + make[1]: *** Waiting for unfinished jobs.... + make[1]: Leaving directory '$SRC_DIR' + make: *** [Makefile:1073: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/mummer4_1734270837562/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/mummer4_1734270837562/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/mummer4/meta.yaml b/recipes/mummer4/meta.yaml index fdfe98e2ce29b..34059a8409b58 100644 --- a/recipes/mummer4/meta.yaml +++ b/recipes/mummer4/meta.yaml @@ -14,7 +14,7 @@ source: - 0001-sort-mgaps-file-before-postpro.-on-behalf-of-jervied.patch # fixes https://github.com/mummer4/mummer/issues/55 build: - number: 7 + number: 8 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/mupbwt/meta.yaml b/recipes/mupbwt/meta.yaml index 06d835069998b..2df364f5fe865 100644 --- a/recipes/mupbwt/meta.yaml +++ b/recipes/mupbwt/meta.yaml @@ -12,7 +12,7 @@ source: - cmake.patch build: - number: 3 + number: 4 skip: True # [osx] requirements: diff --git a/recipes/muscle/build_failure.linux-64.yaml b/recipes/muscle/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..feae972e2cfad --- /dev/null +++ b/recipes/muscle/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: d38a2fc1a49f21bddae0215bab20f7b1a5e50c38781cef4a8c9ec1c2ddb97639 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/seqinfo.o seqinfo.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/showseqstats.o showseqstats.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/shrub.o shrub.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/simplecluster.o simplecluster.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/spatter.o spatter.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/stripgappy.o stripgappy.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/stripgappyrows.o stripgappyrows.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/strip_anchors.o strip_anchors.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/substmxfromfile.o substmxfromfile.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/super6.o super6.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/super7.o super7.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/super7_mega.o super7_mega.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/sw.o sw.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/swdistmx.o swdistmx.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/sweep.o sweep.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/sweeper.o sweeper.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/swmasm.o swmasm.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/swmasm_seq.o swmasm_seq.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/test.o test.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/test_malloc.o test_malloc.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/test_mega.o test_mega.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/tracebackbitmem.o tracebackbitmem.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/transalnref.o transalnref.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/tree.o tree.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/tree2.o tree2.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/tree4.o tree4.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/treefromfile.o treefromfile.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/treetofile.o treetofile.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/pairhmm.o pairhmm.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/progalnflat.o progalnflat.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/project.o project.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/qscore_oldcode.o qscore_oldcode.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/qscore2.o qscore2.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/qscorer.o qscorer.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/quarts.o quarts.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/refineflat.o refineflat.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/relaxflat.o relaxflat.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/seb8.o seb8.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/sequence.o sequence.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/setprobconsparams.o setprobconsparams.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/seq.o seq.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/stripgappycols.o stripgappycols.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/super4.o super4.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/super5.o super5.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/testfb.o testfb.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/testlog.o testlog.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/testscoretype.o testscoretype.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/textfile.o textfile.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/totalprobflat.o totalprobflat.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/tracebackflat.o tracebackflat.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/transaln.o transaln.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/transq.o transq.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/treeperm.o treeperm.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/treesplitter.o treesplitter.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/treesubsetnodes.o treesubsetnodes.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/trimtoref.o trimtoref.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/trimtorefefa.o trimtorefefa.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/uclust.o uclust.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/uclustpd.o uclustpd.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/uclustpd2.o uclustpd2.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/upgma5.o upgma5.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/upgma5_msa.o upgma5_msa.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/usage.o usage.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/usorter.o usorter.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/viterbifastmem.o viterbifastmem.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -ffast-math -march=native -O3 -fopenmp -static o/addconfseq.o o/align.o o/alignmsasbycols.o o/alnmsasflat_mega.o o/blosumsmx.o o/bwdflat_mega.o o/calcpost.o o/cmd_cmp_msa.o o/cmd_m3ensemble.o o/cmd_mustang_core.o o/cmd_newbench_pfamgroups.o o/cmd_newbench_selectpfams.o o/cmd_squeeze_inserts.o o/cmp_ref_msas.o o/enumpaths.o o/fwdflat_mega.o o/getpostpairsalignedflat_mega.o o/hscore.o o/loadinput.o o/logaln_masm.o o/pathscorer.o o/swenumdp.o o/swer.o o/swmasm_megaprof.o o/swps.o o/swsimple.o o/swsimple2.o o/swtest.o o/swtester.o o/swtestmm.o o/test_sw_aa.o o/test_sw_mm.o o/viterbimega.o o/writelocalaln.o o/m3alnparams.o o/alignpairflat.o o/allocflat.o o/alnalnsflat.o o/alnmsasbypath.o o/alnmsasflat.o o/alnmsasflat3.o o/alnprof3sbypath.o o/alpha2.o o/alpha3.o o/alpha6.o o/assertsameseqs.o o/bench.o o/cmd_bench.o o/bittraceback.o o/blosum.o o/clustalweights.o o/cmd_batch.o o/cmd_muscle3.o o/enumgrid.o o/estring.o o/build_guide_tree.o o/calcalnscoresparse.o o/eesort.o o/gtbnode.o o/heatmapcolors.o o/jalview.o o/kimuradist.o o/kmerdist33.o o/kmerdist66.o o/letterconf.o o/diagbox.o o/buildposterior3flat.o o/buildpostflat.o o/bwdflat3.o o/calcalnflat.o o/calcalnscoreflat.o o/calcposteriorflat.o o/conspairflat.o o/consflat.o o/defaulthmmparams.o o/derep.o o/disperse.o o/dividetree.o o/eacluster.o o/efabestcols.o o/efabestconf.o o/efaexplode.o o/efastats.o o/ensemble.o o/fa2efa.o o/fwdflat3.o o/getpairs.o o/getpostpairsalignedflat.o o/letterconfhtml.o o/logdistmx.o o/logmx.o o/m3refine.o o/m3select.o o/make_a2m.o o/make_a2m_refseq.o o/make_substmx.o o/masm.o o/masm_train.o o/maxcc.o o/mega_msas.o o/mpcflat.o o/eadistmx.o o/eadistmxmsas.o o/fasta.o o/fasta2.o o/mpcflat_mega.o o/msaselfscore3.o o/muscle3.o o/mx.o o/myalloc.o o/mysparsemx.o o/nwsmall3.o o/objmgr.o o/pathinfo.o o/perturbhmm.o o/getconsseq.o o/globalinputms.o o/guidetreejoinorder.o o/hmmdump.o o/hmmparams.o o/jointrees.o o/logaln.o o/main.o o/msastats.o o/multisequence.o o/permutetree.o o/pprog.o o/pprog2.o o/pprog3.o o/pprogt.o o/pprog_mega.o o/pprog_tree.o o/probcons.o o/msa.o o/msa2.o o/myutils.o o/colscoreefa.o o/profalign.o o/profile3.o o/masmcol.o o/mega.o o/profpos3.o o/profprof3.o o/profseq.o o/protdist.o o/protdistpair.o o/protdists.o o/qscore.o o/qscoreefa.o o/qscorer2.o o/randomchaintree.o o/randomdistmx.o o/relabel.o o/repredict.o o/resample.o o/runthreads.o o/scoretest.o o/searchpd.o o/seqinfo.o o/showseqstats.o o/shrub.o o/simplecluster.o o/spatter.o o/stripgappy.o o/stripgappyrows.o o/strip_anchors.o o/substmxfromfile.o o/super6.o o/super7.o o/super7_mega.o o/sw.o o/swdistmx.o o/sweep.o o/sweeper.o o/swmasm.o o/swmasm_seq.o o/test.o o/test_malloc.o o/test_mega.o o/tracebackbitmem.o o/transalnref.o o/tree.o o/tree2.o o/tree4.o o/treefromfile.o o/treetofile.o o/pairhmm.o o/progalnflat.o o/project.o o/qscore_oldcode.o o/qscore2.o o/qscorer.o o/quarts.o o/refineflat.o o/relaxflat.o o/seb8.o o/sequence.o o/setprobconsparams.o o/seq.o o/stripgappycols.o o/super4.o o/super5.o o/testfb.o o/testlog.o o/testscoretype.o o/textfile.o o/totalprobflat.o o/tracebackflat.o o/transaln.o o/transq.o o/treeperm.o o/treesplitter.o o/treesubsetnodes.o o/trimtoref.o o/trimtorefefa.o o/uclust.o o/uclustpd.o o/uclustpd2.o o/upgma5.o o/upgma5_msa.o o/usage.o o/usorter.o o/viterbifastmem.o -o ../bin/muscle + /opt/conda/conda-bld/muscle_1734292847458/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/conda/conda-bld/muscle_1734292847458/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/libgomp.a(oacc-profiling.o): in function goacc_profiling_initialize': + /home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/work/build/x86_64-conda-linux-gnu/libgomp/../../../libgomp/oacc-profiling.c:137:(.text0x60f): undefined reference to dlopen' + /opt/conda/conda-bld/muscle_1734292847458/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/work/build/x86_64-conda-linux-gnu/libgomp/../../../libgomp/oacc-profiling.c:141:(.text0x62b): undefined reference to dlsym' + /opt/conda/conda-bld/muscle_1734292847458/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/work/build/x86_64-conda-linux-gnu/libgomp/../../../libgomp/oacc-profiling.c:156:(.text0x67b): undefined reference to dlclose' + /opt/conda/conda-bld/muscle_1734292847458/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/work/build/x86_64-conda-linux-gnu/libgomp/../../../libgomp/oacc-profiling.c:152:(.text0x684): undefined reference to dlerror' + collect2: error: ld returned 1 exit status + make: *** [Makefile:343: ../bin/muscle] Error 1 + + + ERROR -- make failed + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/muscle_1734292847458/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/muscle_1734292847458/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/muscle/build_failure.linux-aarch64.yaml b/recipes/muscle/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..23fd3abeb328b --- /dev/null +++ b/recipes/muscle/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: d38a2fc1a49f21bddae0215bab20f7b1a5e50c38781cef4a8c9ec1c2ddb97639 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/seqinfo.o seqinfo.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/showseqstats.o showseqstats.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/shrub.o shrub.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/simplecluster.o simplecluster.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/spatter.o spatter.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/stripgappy.o stripgappy.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/stripgappyrows.o stripgappyrows.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/strip_anchors.o strip_anchors.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/substmxfromfile.o substmxfromfile.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/super6.o super6.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/super7.o super7.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/super7_mega.o super7_mega.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/sw.o sw.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/swdistmx.o swdistmx.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/sweep.o sweep.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/sweeper.o sweeper.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/swmasm.o swmasm.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/swmasm_seq.o swmasm_seq.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/test.o test.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/test_malloc.o test_malloc.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/test_mega.o test_mega.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/tracebackbitmem.o tracebackbitmem.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/transalnref.o transalnref.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/tree.o tree.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/tree2.o tree2.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/tree4.o tree4.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/treefromfile.o treefromfile.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/treetofile.o treetofile.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/pairhmm.o pairhmm.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/progalnflat.o progalnflat.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/project.o project.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/qscore_oldcode.o qscore_oldcode.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/qscore2.o qscore2.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/qscorer.o qscorer.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/quarts.o quarts.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/refineflat.o refineflat.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/relaxflat.o relaxflat.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/seb8.o seb8.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/sequence.o sequence.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/setprobconsparams.o setprobconsparams.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/seq.o seq.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/stripgappycols.o stripgappycols.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/super4.o super4.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/super5.o super5.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/testfb.o testfb.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/testlog.o testlog.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/testscoretype.o testscoretype.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/textfile.o textfile.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/totalprobflat.o totalprobflat.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/tracebackflat.o tracebackflat.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/transaln.o transaln.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/transq.o transq.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/treeperm.o treeperm.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/treesplitter.o treesplitter.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/treesubsetnodes.o treesubsetnodes.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/trimtoref.o trimtoref.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/trimtorefefa.o trimtorefefa.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/uclust.o uclust.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/uclustpd.o uclustpd.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/uclustpd2.o uclustpd2.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/upgma5.o upgma5.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/upgma5_msa.o upgma5_msa.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/usage.o usage.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/usorter.o usorter.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/muscle-5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/viterbifastmem.o viterbifastmem.cpp + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -ffast-math -march=native -O3 -fopenmp -static o/addconfseq.o o/align.o o/alignmsasbycols.o o/alnmsasflat_mega.o o/blosumsmx.o o/bwdflat_mega.o o/calcpost.o o/cmd_cmp_msa.o o/cmd_m3ensemble.o o/cmd_mustang_core.o o/cmd_newbench_pfamgroups.o o/cmd_newbench_selectpfams.o o/cmd_squeeze_inserts.o o/cmp_ref_msas.o o/enumpaths.o o/fwdflat_mega.o o/getpostpairsalignedflat_mega.o o/hscore.o o/loadinput.o o/logaln_masm.o o/pathscorer.o o/swenumdp.o o/swer.o o/swmasm_megaprof.o o/swps.o o/swsimple.o o/swsimple2.o o/swtest.o o/swtester.o o/swtestmm.o o/test_sw_aa.o o/test_sw_mm.o o/viterbimega.o o/writelocalaln.o o/m3alnparams.o o/alignpairflat.o o/allocflat.o o/alnalnsflat.o o/alnmsasbypath.o o/alnmsasflat.o o/alnmsasflat3.o o/alnprof3sbypath.o o/alpha2.o o/alpha3.o o/alpha6.o o/assertsameseqs.o o/bench.o o/cmd_bench.o o/bittraceback.o o/blosum.o o/clustalweights.o o/cmd_batch.o o/cmd_muscle3.o o/enumgrid.o o/estring.o o/build_guide_tree.o o/calcalnscoresparse.o o/eesort.o o/gtbnode.o o/heatmapcolors.o o/jalview.o o/kimuradist.o o/kmerdist33.o o/kmerdist66.o o/letterconf.o o/diagbox.o o/buildposterior3flat.o o/buildpostflat.o o/bwdflat3.o o/calcalnflat.o o/calcalnscoreflat.o o/calcposteriorflat.o o/conspairflat.o o/consflat.o o/defaulthmmparams.o o/derep.o o/disperse.o o/dividetree.o o/eacluster.o o/efabestcols.o o/efabestconf.o o/efaexplode.o o/efastats.o o/ensemble.o o/fa2efa.o o/fwdflat3.o o/getpairs.o o/getpostpairsalignedflat.o o/letterconfhtml.o o/logdistmx.o o/logmx.o o/m3refine.o o/m3select.o o/make_a2m.o o/make_a2m_refseq.o o/make_substmx.o o/masm.o o/masm_train.o o/maxcc.o o/mega_msas.o o/mpcflat.o o/eadistmx.o o/eadistmxmsas.o o/fasta.o o/fasta2.o o/mpcflat_mega.o o/msaselfscore3.o o/muscle3.o o/mx.o o/myalloc.o o/mysparsemx.o o/nwsmall3.o o/objmgr.o o/pathinfo.o o/perturbhmm.o o/getconsseq.o o/globalinputms.o o/guidetreejoinorder.o o/hmmdump.o o/hmmparams.o o/jointrees.o o/logaln.o o/main.o o/msastats.o o/multisequence.o o/permutetree.o o/pprog.o o/pprog2.o o/pprog3.o o/pprogt.o o/pprog_mega.o o/pprog_tree.o o/probcons.o o/msa.o o/msa2.o o/myutils.o o/colscoreefa.o o/profalign.o o/profile3.o o/masmcol.o o/mega.o o/profpos3.o o/profprof3.o o/profseq.o o/protdist.o o/protdistpair.o o/protdists.o o/qscore.o o/qscoreefa.o o/qscorer2.o o/randomchaintree.o o/randomdistmx.o o/relabel.o o/repredict.o o/resample.o o/runthreads.o o/scoretest.o o/searchpd.o o/seqinfo.o o/showseqstats.o o/shrub.o o/simplecluster.o o/spatter.o o/stripgappy.o o/stripgappyrows.o o/strip_anchors.o o/substmxfromfile.o o/super6.o o/super7.o o/super7_mega.o o/sw.o o/swdistmx.o o/sweep.o o/sweeper.o o/swmasm.o o/swmasm_seq.o o/test.o o/test_malloc.o o/test_mega.o o/tracebackbitmem.o o/transalnref.o o/tree.o o/tree2.o o/tree4.o o/treefromfile.o o/treetofile.o o/pairhmm.o o/progalnflat.o o/project.o o/qscore_oldcode.o o/qscore2.o o/qscorer.o o/quarts.o o/refineflat.o o/relaxflat.o o/seb8.o o/sequence.o o/setprobconsparams.o o/seq.o o/stripgappycols.o o/super4.o o/super5.o o/testfb.o o/testlog.o o/testscoretype.o o/textfile.o o/totalprobflat.o o/tracebackflat.o o/transaln.o o/transq.o o/treeperm.o o/treesplitter.o o/treesubsetnodes.o o/trimtoref.o o/trimtorefefa.o o/uclust.o o/uclustpd.o o/uclustpd2.o o/upgma5.o o/upgma5_msa.o o/usage.o o/usorter.o o/viterbifastmem.o -o ../bin/muscle + /opt/conda/conda-bld/muscle_1734271562715/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: /opt/conda/conda-bld/muscle_1734271562715/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/libgomp.a(oacc-profiling.o): in function goacc_profiling_initialize': + /home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798803082/work/build/aarch64-conda-linux-gnu/libgomp/../../../libgomp/oacc-profiling.c:137:(.text0x6f4): undefined reference to dlopen' + /opt/conda/conda-bld/muscle_1734271562715/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: /home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798803082/work/build/aarch64-conda-linux-gnu/libgomp/../../../libgomp/oacc-profiling.c:152:(.text0x708): undefined reference to dlerror' + /opt/conda/conda-bld/muscle_1734271562715/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: /home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798803082/work/build/aarch64-conda-linux-gnu/libgomp/../../../libgomp/oacc-profiling.c:156:(.text0x728): undefined reference to dlclose' + /opt/conda/conda-bld/muscle_1734271562715/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: /home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798803082/work/build/aarch64-conda-linux-gnu/libgomp/../../../libgomp/oacc-profiling.c:141:(.text0x740): undefined reference to dlsym' + collect2: error: ld returned 1 exit status + make: *** [Makefile:343: ../bin/muscle] Error 1 + + + ERROR -- make failed + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/muscle_1734271562715/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/muscle_1734271562715/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/muscle/meta.yaml b/recipes/muscle/meta.yaml index 1bd528fba686b..0c054561524b0 100644 --- a/recipes/muscle/meta.yaml +++ b/recipes/muscle/meta.yaml @@ -12,7 +12,7 @@ source: - support-linux-aarch64.patch build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/muse/meta.yaml b/recipes/muse/meta.yaml index 2ebcef1e3f1a7..5631744523c4b 100644 --- a/recipes/muse/meta.yaml +++ b/recipes/muse/meta.yaml @@ -18,7 +18,7 @@ source: folder: boost-1.87.0.beta1 build: - number: 2 + number: 3 skip: True # [osx] run_exports: - {{ pin_subpackage('muse', max_pin="x") }} diff --git a/recipes/mutscan/meta.yaml b/recipes/mutscan/meta.yaml index d8b58ec756fec..4b0bc53883236 100644 --- a/recipes/mutscan/meta.yaml +++ b/recipes/mutscan/meta.yaml @@ -11,7 +11,7 @@ source: - patch build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/mutyper/meta.yaml b/recipes/mutyper/meta.yaml index 0dd97d2454a96..6f864086168de 100644 --- a/recipes/mutyper/meta.yaml +++ b/recipes/mutyper/meta.yaml @@ -12,7 +12,7 @@ source: build: run_exports: - {{ pin_subpackage('mutyper', max_pin="x") }} - number: 1 + number: 2 skip: True # [py < 38 or py > 311] script_env: - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }} @@ -57,4 +57,4 @@ about: extra: additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 diff --git a/recipes/mvicuna/meta.yaml b/recipes/mvicuna/meta.yaml index 89067e80729d5..71078ded8d7a6 100644 --- a/recipes/mvicuna/meta.yaml +++ b/recipes/mvicuna/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 83bc56848a000e0fbaa3e934205d9b888ecf8c32612a98b54159efd11e284933 build: - number: 10 + number: 11 requirements: build: diff --git a/recipes/mwga-utils/meta.yaml b/recipes/mwga-utils/meta.yaml index 2dec103612f71..016057d63933b 100644 --- a/recipes/mwga-utils/meta.yaml +++ b/recipes/mwga-utils/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 source: url: https://github.com/RomainFeron/mgwa_utils/archive/{{ version }}.tar.gz diff --git a/recipes/mykatlas/meta.yaml b/recipes/mykatlas/meta.yaml index be460fd03c13f..5df0f4cf2c9a8 100644 --- a/recipes/mykatlas/meta.yaml +++ b/recipes/mykatlas/meta.yaml @@ -13,7 +13,7 @@ build: # includes precompiled Linux binary `mccortex31` # needs pyvcf rebuild for python 3.10 on conda-forge skip: True # [osx or py > 39] - number: 7 + number: 8 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv entry_points: - atlas = mykatlas.atlas_main:main diff --git a/recipes/mykrobe/build_failure.linux-aarch64.yaml b/recipes/mykrobe/build_failure.linux-aarch64.yaml deleted file mode 100644 index c55bb7d055e77..0000000000000 --- a/recipes/mykrobe/build_failure.linux-aarch64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: e7d1ddad4763fea69155d4b1c3da4714c660d3f0706e622663a47bfd0130844b # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - 301 | struct cram_codec *codecs[DS_END]; - | ^~~~~~ - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -fpic -c -o cram/files.pico cram/files.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c - cram/cram_io.c: In function 'cram_populate_ref': - cram/cram_io.c:2234:9: warning: '__builtin_strncpy' specified bound 4096 equals destination size [-Wstringop-truncation] - 2234 | strncpy(path, path2, PATH_MAX); - | ^~~~~~~ - cram/cram_io.c:2332:34: warning: '.tmp_' directive writing 5 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] - 2332 | sprintf(path_tmp, "%s.tmp_%d", path, /*getpid(),*/ i); - | ^~~~~ - cram/cram_io.c:2332:31: note: directive argument in the range [0, 2147483647] - 2332 | sprintf(path_tmp, "%s.tmp_%d", path, /*getpid(),*/ i); - | ^~~~~~~~~~~ - cram/cram_io.c:2332:13: note: 'sprintf' output between 7 and 4111 bytes into a destination of size 4096 - 2332 | sprintf(path_tmp, "%s.tmp_%d", path, /*getpid(),*/ i); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -fpic -c -o cram/rANS_static.pico cram/rANS_static.c - cram/cram_io.c: In function 'cram_write_SAM_hdr': - cram/cram_io.c:3781:13: warning: '__builtin_strncpy' specified bound 4096 equals destination size [-Wstringop-truncation] - 3781 | strncpy(out, in, PATH_MAX); - | ^~~~~~~ - cram/cram_io.c:3773:9: warning: '__builtin_strncpy' specified bound 4096 equals destination size [-Wstringop-truncation] - 3773 | strncpy(out, in, PATH_MAX); - | ^~~~~~~ - cram/cram_io.c: In function 'cram_dopen': - cram/cram_io.c:4156:9: warning: '__builtin_strncpy' specified bound 20 equals destination size [-Wstringop-truncation] - 4156 | strncpy(def->file_id, filename, 20); - | ^~~~~~~ - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -fpic -c -o cram/sam_header.pico cram/sam_header.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -fpic -c -o cram/thread_pool.pico cram/thread_pool.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -fpic -c -o cram/vlen.pico cram/vlen.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -fpic -c -o cram/zfio.pico cram/zfio.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -c -o bgzip.o bgzip.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -c -o htsfile.o htsfile.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -c -o tabix.o tabix.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -c -o test/fieldarith.o test/fieldarith.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -c -o test/hfile.o test/hfile.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -c -o test/sam.o test/sam.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -c -o test/test-regidx.o test/test-regidx.c - test/sam.c: In function 'faidx1': - test/sam.c:186:5: warning: 'faidx_fetch_nseq' is deprecated: Please use faidx_nseq instead [-Wdeprecated-declarations] - 186 | n = faidx_fetch_nseq(fai); - | ^ - In file included from test/sam.c:32: - ./htslib/faidx.h:94:9: note: declared here - 94 | int faidx_fetch_nseq(const faidx_t *fai) HTS_DEPRECATED("Please use faidx_nseq instead"); - | ^~~~~~~~~~~~~~~~ - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -c -o test/test_view.o test/test_view.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -c -o test/test-vcf-api.o test/test-vcf-api.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -c -o bgzf.o bgzf.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -c -o faidx.o faidx.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -c -o hfile.o hfile.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -g -Wall -O2 -I. -c -o hts.o hts.c - hts.c: In function 'hts_idx_init': - hts.c:1180:59: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int' changes value from 'idx->z.last_bin = 4294967295' to '-1' [-Woverflow] - 1180 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; - | ^~~ - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -shared -Wl,-soname,libhts.so.1 -pthread -L$PREFIX/lib -o libhts.so kfunc.pico knetfile.pico kstring.pico bgzf.pico faidx.pico hfile.pico hfile_net.pico hts.pico md5.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico cram/thread_pool.pico cram/vlen.pico cram/zfio.pico -lz -lm - ln -sf libhts.so libhts.so.1 - ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o - ranlib libhts.a - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -pthread -L$PREFIX/lib -o bgzip bgzip.o libhts.a -lz - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -pthread -L$PREFIX/lib -o htsfile htsfile.o libhts.a -lz - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -pthread -L$PREFIX/lib -o tabix tabix.o libhts.a -lz - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -pthread -L$PREFIX/lib -o test/fieldarith test/fieldarith.o libhts.a -lz - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -pthread -L$PREFIX/lib -o test/hfile test/hfile.o libhts.a -lz - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -pthread -L$PREFIX/lib -o test/sam test/sam.o libhts.a -lz - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -pthread -L$PREFIX/lib -o test/test-regidx test/test-regidx.o libhts.a -lz - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -pthread -L$PREFIX/lib -o test/test_view test/test_view.o libhts.a -lz - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -pthread -L$PREFIX/lib -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -fcommon -lstdc -pthread -L$PREFIX/lib -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz - make[2]: Leaving directory '$SRC_DIR/mccortex/libs/htslib' - make[1]: Leaving directory '$SRC_DIR/mccortex/libs' - make: *** [Makefile:237: libs-core] Error 2 - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/mykrobe_1718310118031/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/mykrobe/meta.yaml b/recipes/mykrobe/meta.yaml index 35c9b0475bbb2..e345aec81dffd 100644 --- a/recipes/mykrobe/meta.yaml +++ b/recipes/mykrobe/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 49662937378a4ff10ffcb3876efcc069be58f0dc183615e9cffb57f51348a45e build: - number: 3 + number: 4 entry_points: - mykrobe = mykrobe.cli:main run_exports: diff --git a/recipes/naf/build_failure.osx-64.yaml b/recipes/naf/build_failure.osx-64.yaml deleted file mode 100644 index 429c9f7e31b5b..0000000000000 --- a/recipes/naf/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 4eac1eaf693fe046dc4bb8a41a748a46f982246edd2ee4d7de1e1b400b0f2e49 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/naf-1.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - make -C zstd/lib ZSTD_LEGACY_SUPPORT=0 ZSTD_LIB_DEPRECATED=0 ZSTD_LIB_DICTBUILDER=0 libzstd.a - make[1]: Entering directory '$SRC_DIR/zstd/lib' - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/debug.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/entropy_common.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/error_private.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/fse_decompress.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/pool.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/threading.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/xxhash.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/zstd_common.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/fse_compress.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/hist.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/huf_compress.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/zstd_compress.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/zstd_compress_literals.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/zstd_compress_sequences.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/zstd_compress_superblock.o - compress/zstd_compress_superblock.c:134:12: warning: variable 'litLengthSum' set but not used [-Wunused-but-set-variable] - size_t litLengthSum = 0; - ^ - 1 warning generated. - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/zstd_double_fast.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/zstd_fast.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/zstd_lazy.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/zstd_ldm.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/zstd_opt.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/zstdmt_compress.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/huf_decompress.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/zstd_ddict.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/zstd_decompress.o - CC obj/conf_24dbbb325131eb57d2791374f9058f2e/static/zstd_decompress_block.o - compiling single-threaded static library 1.5.0 - make[1]: Leaving directory '$SRC_DIR/zstd/lib' - make -C ennaf - make[1]: Entering directory '$SRC_DIR/ennaf' - x86_64-apple-darwin13.4.0-clang -std=gnu99 -Wall -Wextra -O3 -march=native -ffast-math -s -I../zstd/lib -o ennaf src/ennaf.c ../zstd/lib/libzstd.a - In file included from src/ennaf.c:121: - src/files.c:131:9: warning: call to undeclared function 'futimens'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] - if (futimens(fileno(OUT), input_timestamp) != 0) { err("can't transfer timestamp from input to output file\n"); } - ^ - 1 warning generated. - ld: warning: option -s is obsolete and being ignored - Undefined symbols for architecture x86_64: - "_futimens", referenced from: - _main in ennaf-9063c5.o - ld: symbol(s) not found for architecture x86_64 - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make[1]: *** [Makefile:17: ennaf] Error 1 - make: *** [Makefile:10: default] Error 2 - make[1]: Leaving directory '$SRC_DIR/ennaf' - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/naf_1685355227243/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/naf/meta.yaml b/recipes/naf/meta.yaml index 7eb2131cc4ec9..b9a7622dc24e0 100644 --- a/recipes/naf/meta.yaml +++ b/recipes/naf/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://github.com/KirillKryukov/{{ name }}/releases/download/v{{ version }}/{{ name }}-{{ version }}-with-deps.tar.gz diff --git a/recipes/namfinder/meta.yaml b/recipes/namfinder/meta.yaml index 3f122eefbc948..a0c86607fa520 100644 --- a/recipes/namfinder/meta.yaml +++ b/recipes/namfinder/meta.yaml @@ -8,14 +8,14 @@ package: version: {{ version }} build: - number: 0 + number: 1 requirements: build: - {{ compiler('cxx') }} - make - cmake - run: + host: - zlib source: diff --git a/recipes/nanoblaster/meta.yaml b/recipes/nanoblaster/meta.yaml index bca13a8c8b26e..c6f06eeadc0fa 100644 --- a/recipes/nanoblaster/meta.yaml +++ b/recipes/nanoblaster/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.16" build: - number: 6 + number: 7 source: url: https://github.com/ruhulsbu/NanoBLASTer/archive/417c48c8ae8d824ba591922c20b0e4ec09b738cb.tar.gz diff --git a/recipes/nanocaller/meta.yaml b/recipes/nanocaller/meta.yaml index 0b20c2fbc6e46..2df0c18750274 100644 --- a/recipes/nanocaller/meta.yaml +++ b/recipes/nanocaller/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 63acb2fd97bef760f9fd8a06021dd1a0865e6b9d22b461d3bd58acc4028d9c31 build: - number: 1 + number: 2 noarch: generic run_exports: - {{ pin_subpackage('nanocaller', max_pin="x") }} diff --git a/recipes/nanoplexer/meta.yaml b/recipes/nanoplexer/meta.yaml index 9c66c73af153e..6705f9685333c 100644 --- a/recipes/nanoplexer/meta.yaml +++ b/recipes/nanoplexer/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 skip: True # [osx] source: diff --git a/recipes/nanopolish/meta.yaml b/recipes/nanopolish/meta.yaml index 8480616316753..d8a5227b12791 100644 --- a/recipes/nanopolish/meta.yaml +++ b/recipes/nanopolish/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: git_url: https://github.com/jts/nanopolish diff --git a/recipes/nanoq/meta.yaml b/recipes/nanoq/meta.yaml index 86b5c43fd1e13..adcf2c9051f52 100644 --- a/recipes/nanoq/meta.yaml +++ b/recipes/nanoq/meta.yaml @@ -10,7 +10,7 @@ source: sha256: c6ab28a5c738be950bfbf36ddf9e0e46216a9a1aa040d6745fcb9d87cc32534a build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/nanospring/build_failure.linux-64.yaml b/recipes/nanospring/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..ea20bfc83488e --- /dev/null +++ b/recipes/nanospring/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: b2e8d66ee11766a080316d13c310ee071c9517d761ba3863873cdfd7d4f67326 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + -- Looking for _WIN32 - not found + -- Looking for __APPLE__ + -- Looking for __APPLE__ - not found + -- Looking for __ANDROID__ + -- Looking for __ANDROID__ - not found + -- Looking for __FreeBSD__ + -- Looking for __FreeBSD__ - not found + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed + -- Looking for pthread_create in pthreads + -- Looking for pthread_create in pthreads - not found + -- Looking for pthread_create in pthread + -- Looking for pthread_create in pthread - found + -- Found Threads: TRUE + -- The ASM compiler identification is GNU + -- Found assembler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + -- Found BZip2: $BUILD_PREFIX/lib/libbz2.so (found version "1.0.8") + -- Looking for BZ2_bzCompressInit + -- Looking for BZ2_bzCompressInit - found + -- Found ZLIB: $PREFIX/lib/libz.so (found version "1.3.1") + -- Failed to find all ICU components (missing: ICU_INCLUDE_DIR ICU_LIBRARY uc dt i18n) + -- Looking for iconv + -- Looking for iconv - found + -- Boost locale unsupported on platform: need either iconv or ICU. + -- Checking for module 'mpi-c' + -- No package 'mpi-c' found + -- Checking for module 'mpi-cxx' + -- No package 'mpi-cxx' found + -- Configuring done (24.4s) + -- Generating done (0.2s) + -- Build files have been written to: $SRC_DIR/build + [ 0%] Building CXX object CMakeFiles/libbsc.dir/libbsc/adler32/adler32.cpp.o + [ 5%] Building C object CMakeFiles/libbsc.dir/libbsc/bwt/libsais/libsais.c.o + [ 5%] Building CXX object CMakeFiles/libbsc.dir/libbsc/bwt/bwt.cpp.o + [ 5%] Building CXX object CMakeFiles/libbsc.dir/libbsc/coder/coder.cpp.o + [ 5%] Building CXX object CMakeFiles/libbsc.dir/libbsc/coder/qlfc/qlfc.cpp.o + [ 11%] Building CXX object CMakeFiles/libbsc.dir/libbsc/coder/qlfc/qlfc_model.cpp.o + [ 11%] Building CXX object CMakeFiles/libbsc.dir/libbsc/filters/detectors.cpp.o + [ 11%] Building CXX object CMakeFiles/libbsc.dir/libbsc/filters/preprocessing.cpp.o + [ 16%] Building CXX object CMakeFiles/libbsc.dir/libbsc/libbsc/libbsc.cpp.o + [ 16%] Building CXX object CMakeFiles/libbsc.dir/libbsc/lzp/lzp.cpp.o + [ 16%] Building CXX object CMakeFiles/libbsc.dir/libbsc/platform/platform.cpp.o + [ 22%] Building CXX object CMakeFiles/libbsc.dir/libbsc/st/st.cpp.o + [ 22%] Linking CXX static library liblibbsc.a + [ 22%] Built target libbsc + [ 27%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/__/_deps/boost-src/libs/program_options/src/cmdline.cpp.o + [ 27%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/__/_deps/boost-src/libs/program_options/src/config_file.cpp.o + [ 27%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/__/_deps/boost-src/libs/program_options/src/options_description.cpp.o + [ 33%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/__/_deps/boost-src/libs/program_options/src/parsers.cpp.o + [ 33%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/__/_deps/boost-src/libs/program_options/src/variables_map.cpp.o + [ 33%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/__/_deps/boost-src/libs/program_options/src/value_semantic.cpp.o + [ 38%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/__/_deps/boost-src/libs/program_options/src/positional_options.cpp.o + [ 38%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/__/_deps/boost-src/libs/program_options/src/utf8_codecvt_facet.cpp.o + [ 38%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/__/_deps/boost-src/libs/program_options/src/convert.cpp.o + [ 38%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/__/_deps/boost-src/libs/program_options/src/winmain.cpp.o + [ 44%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/__/_deps/boost-src/libs/program_options/src/split.cpp.o + [ 44%] Linking CXX static library libboost_program_options.a + [ 44%] Built target Boost_program_options + Build static & dynamic library. + /opt/conda/conda-bld/nanospring_1734146587908/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: warning: lzma_dec_x86_64.o: missing .note.GNU-stack section implies executable stack + /opt/conda/conda-bld/nanospring_1734146587908/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: NOTE: This behaviour is deprecated and will be removed in a future version of the linker + Library build SUCCESS. + [ 44%] Built target FASTLZMA2 + chain.c: In function 'mm_chain_dp': + chain.c:90:9: warning: 'memset' specified bound between 9223372036854775808 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] + 90 | memset(t, 0, n * 4); + | ^~~~~~~~~~~~~~~~~~~ + format.c: In function 'mm_write_sam3': + format.c:395:43: warning: variable 'this_rev' set but not used [-Wunused-but-set-variable] + 395 | int this_rid = -1, this_pos = -1, this_rev = 0; + | ^~~~~~~~ + /opt/conda/conda-bld/nanospring_1734146587908/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lz: No such file or directory + collect2: error: ld returned 1 exit status + make[3]: *** [Makefile:46: minimap2] Error 1 + make[2]: *** [CMakeFiles/MINIMAP2.dir/build.make:70: CMakeFiles/MINIMAP2] Error 2 + make[1]: *** [CMakeFiles/Makefile2:174: CMakeFiles/MINIMAP2.dir/all] Error 2 + make: *** [Makefile:91: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/nanospring_1734146587908/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/nanospring_1734146587908/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/nanospring/meta.yaml b/recipes/nanospring/meta.yaml index 4f05760a01740..18525ffe28066 100644 --- a/recipes/nanospring/meta.yaml +++ b/recipes/nanospring/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 skip: True # [osx] source: diff --git a/recipes/narfmap/meta.yaml b/recipes/narfmap/meta.yaml index 5db049e65b13a..04b6e98e5304c 100644 --- a/recipes/narfmap/meta.yaml +++ b/recipes/narfmap/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 skip: True # [osx] run_exports: - {{ pin_subpackage("narfmap", max_pin="x") }} diff --git a/recipes/ncbi-ngs-sdk/meta.yaml b/recipes/ncbi-ngs-sdk/meta.yaml index 5949626193ffd..87e076ce02059 100644 --- a/recipes/ncbi-ngs-sdk/meta.yaml +++ b/recipes/ncbi-ngs-sdk/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage('ncbi-ngs-sdk', max_pin="x") }} diff --git a/recipes/ncbi-vdb/build.sh b/recipes/ncbi-vdb/build.sh index f1b45b55eedd6..726192d356ac1 100644 --- a/recipes/ncbi-vdb/build.sh +++ b/recipes/ncbi-vdb/build.sh @@ -24,6 +24,7 @@ end-of-patch if [[ "$(uname)" == "Darwin" ]]; then export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" + export CFLAGS="${CFLAGS} -fno-define-target-os-macros" else export CONFIG_ARGS="" fi diff --git a/recipes/ncbi-vdb/meta.yaml b/recipes/ncbi-vdb/meta.yaml index 68b395345f2bf..0d472e0a087f9 100644 --- a/recipes/ncbi-vdb/meta.yaml +++ b/recipes/ncbi-vdb/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('ncbi-vdb', max_pin='x') }} diff --git a/recipes/ncls/meta.yaml b/recipes/ncls/meta.yaml index ec199e0d08771..e7f2ef33ff7d6 100644 --- a/recipes/ncls/meta.yaml +++ b/recipes/ncls/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93 build: - number: 4 + number: 5 script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv run_exports: - {{ pin_subpackage(name, max_pin="x.x.x") }} diff --git a/recipes/ncrf/meta.yaml b/recipes/ncrf/meta.yaml index 85e1925281c58..b10d02d811712 100644 --- a/recipes/ncrf/meta.yaml +++ b/recipes/ncrf/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 5 + number: 6 source: url: https://github.com/makovalab-psu/NoiseCancellingRepeatFinder/archive/v{{ version }}.tar.gz diff --git a/recipes/necat/build_failure.linux-64.yaml b/recipes/necat/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..2ec5cac05ad49 --- /dev/null +++ b/recipes/necat/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5ec25115b5782e731eb64f62056f930553e92d3cb1a53699758ba3adaf4f5435 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + | ^~~~ + fsa/simple_align.hpp:32:31: error: request for member 'end' in '((const fsa::SimpleAlign::KmerList*)this)->fsa::SimpleAlign::KmerList::list', which is of non-class type 'const int' + 32 | return it != list.end() ? it->second.count : 0; + | ^~~ + fsa/simple_align.cpp: At global scope: + fsa/simple_align.cpp:21:1: error: no declaration matches 'fsa::SimpleAlign::KmerList::KmerList(const std::string&, uint8_t)' + 21 | SimpleAlign::KmerList::KmerList(const std::string &target, uint8_t k) { + | ^~~~~~~~~~~ + fsa/simple_align.hpp:13:12: note: candidates are: 'fsa::SimpleAlign::KmerList::KmerList(fsa::SimpleAlign::KmerList&&)' + 13 | struct KmerList { + | ^~~~~~~~ + fsa/simple_align.hpp:13:12: note: 'fsa::SimpleAlign::KmerList::KmerList(const fsa::SimpleAlign::KmerList&)' + fsa/simple_align.hpp:14:9: note: 'fsa::SimpleAlign::KmerList::KmerList(const std::string&, int)' + 14 | KmerList(const std::string& target, uint8_t k); + | ^~~~~~~~ + fsa/simple_align.hpp:13:12: note: 'struct fsa::SimpleAlign::KmerList' defined here + 13 | struct KmerList { + | ^~~~~~~~ + fsa/simple_align.cpp:56:1: error: no declaration matches 'fsa::SimpleAlign::SimpleAlign(const std::string&, uint8_t)' + 56 | SimpleAlign::SimpleAlign(const std::string &target, uint8_t k) + | ^~~~~~~~~~~ + fsa/simple_align.hpp:11:7: note: candidates are: 'fsa::SimpleAlign::SimpleAlign(fsa::SimpleAlign&&)' + 11 | class SimpleAlign { + | ^~~~~~~~~~~ + fsa/simple_align.hpp:11:7: note: 'fsa::SimpleAlign::SimpleAlign(const fsa::SimpleAlign&)' + fsa/simple_align.hpp:76:5: note: 'fsa::SimpleAlign::SimpleAlign(const std::string&, int)' + 76 | SimpleAlign(const std::string &target, uint8_t k); + | ^~~~~~~~~~~ + fsa/simple_align.hpp:11:7: note: 'class fsa::SimpleAlign' defined here + 11 | class SimpleAlign { + | ^~~~~~~~~~~ + fsa/simple_align.cpp: In member function 'fsa::SimpleAlign::KmerMatch fsa::SimpleAlign::FindKmerMatch(const std::string&, size_t)': + fsa/simple_align.cpp:66:39: error: 'k_' was not declared in this scope + 66 | for (size_t i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 154 | if ( node.x node.len >= query.size() || node.y node.len >= target_.size()) { + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ + fsa/simple_align.cpp:154:75: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 154 | if ( node.x node.len >= query.size() || node.y node.len >= target_.size()) { + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + fsa/simple_align.cpp: At global scope: + fsa/simple_align.cpp:298:10: error: no declaration matches 'uint32_t fsa::SimpleAlign::KmerMask(uint8_t)' + 298 | uint32_t SimpleAlign::KmerMask(uint8_t k) { + | ^~~~~~~~~~~ + fsa/simple_align.cpp:298:10: note: no functions named 'uint32_t fsa::SimpleAlign::KmerMask(uint8_t)' + fsa/simple_align.hpp:11:7: note: 'class fsa::SimpleAlign' defined here + 11 | class SimpleAlign { + | ^~~~~~~~~~~ + fsa/simple_align.cpp:309:10: error: no declaration matches 'uint32_t fsa::SimpleAlign::CalcKmer(const char*, size_t)' + 309 | uint32_t SimpleAlign::CalcKmer(const char* seq, size_t k) { + | ^~~~~~~~~~~ + fsa/simple_align.cpp:309:10: note: no functions named 'uint32_t fsa::SimpleAlign::CalcKmer(const char*, size_t)' + fsa/simple_align.hpp:11:7: note: 'class fsa::SimpleAlign' defined here + 11 | class SimpleAlign { + | ^~~~~~~~~~~ + fsa/simple_align.cpp:322:10: error: no declaration matches 'uint32_t fsa::SimpleAlign::MoveKmer(uint32_t, size_t, char)' + 322 | uint32_t SimpleAlign::MoveKmer(uint32_t bkmer, size_t k, char e) { + | ^~~~~~~~~~~ + fsa/simple_align.cpp:322:10: note: no functions named 'uint32_t fsa::SimpleAlign::MoveKmer(uint32_t, size_t, char)' + fsa/simple_align.hpp:11:7: note: 'class fsa::SimpleAlign' defined here + 11 | class SimpleAlign { + | ^~~~~~~~~~~ + make: *** [Makefile:414: ../Linux-amd64/obj/libfsa.a/fsa/simple_align.o] Error 1 + make: *** Waiting for unfinished jobs.... + make: Leaving directory '$SRC_DIR/src' + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/necat_1734148578463/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/necat_1734148578463/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/necat/build_failure.linux-aarch64.yaml b/recipes/necat/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..d6ca5bad6088a --- /dev/null +++ b/recipes/necat/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5ec25115b5782e731eb64f62056f930553e92d3cb1a53699758ba3adaf4f5435 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + | ^~~~ + fsa/simple_align.hpp:32:31: error: request for member 'end' in '((const fsa::SimpleAlign::KmerList*)this)->fsa::SimpleAlign::KmerList::list', which is of non-class type 'const int' + 32 | return it != list.end() ? it->second.count : 0; + | ^~~ + fsa/simple_align.cpp: At global scope: + fsa/simple_align.cpp:21:1: error: no declaration matches 'fsa::SimpleAlign::KmerList::KmerList(const std::string&, uint8_t)' + 21 | SimpleAlign::KmerList::KmerList(const std::string &target, uint8_t k) { + | ^~~~~~~~~~~ + fsa/simple_align.hpp:13:12: note: candidates are: 'fsa::SimpleAlign::KmerList::KmerList(fsa::SimpleAlign::KmerList&&)' + 13 | struct KmerList { + | ^~~~~~~~ + fsa/simple_align.hpp:13:12: note: 'fsa::SimpleAlign::KmerList::KmerList(const fsa::SimpleAlign::KmerList&)' + fsa/simple_align.hpp:14:9: note: 'fsa::SimpleAlign::KmerList::KmerList(const std::string&, int)' + 14 | KmerList(const std::string& target, uint8_t k); + | ^~~~~~~~ + fsa/simple_align.hpp:13:12: note: 'struct fsa::SimpleAlign::KmerList' defined here + 13 | struct KmerList { + | ^~~~~~~~ + fsa/simple_align.cpp:56:1: error: no declaration matches 'fsa::SimpleAlign::SimpleAlign(const std::string&, uint8_t)' + 56 | SimpleAlign::SimpleAlign(const std::string &target, uint8_t k) + | ^~~~~~~~~~~ + fsa/simple_align.hpp:11:7: note: candidates are: 'fsa::SimpleAlign::SimpleAlign(fsa::SimpleAlign&&)' + 11 | class SimpleAlign { + | ^~~~~~~~~~~ + fsa/simple_align.hpp:11:7: note: 'fsa::SimpleAlign::SimpleAlign(const fsa::SimpleAlign&)' + fsa/simple_align.hpp:76:5: note: 'fsa::SimpleAlign::SimpleAlign(const std::string&, int)' + 76 | SimpleAlign(const std::string &target, uint8_t k); + | ^~~~~~~~~~~ + fsa/simple_align.hpp:11:7: note: 'class fsa::SimpleAlign' defined here + 11 | class SimpleAlign { + | ^~~~~~~~~~~ + fsa/simple_align.cpp: In member function 'fsa::SimpleAlign::KmerMatch fsa::SimpleAlign::FindKmerMatch(const std::string&, size_t)': + fsa/simple_align.cpp:66:39: error: 'k_' was not declared in this scope + 66 | for (size_t i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 154 | if ( node.x node.len >= query.size() || node.y node.len >= target_.size()) { + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ + fsa/simple_align.cpp:154:75: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 154 | if ( node.x node.len >= query.size() || node.y node.len >= target_.size()) { + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + fsa/simple_align.cpp: At global scope: + fsa/simple_align.cpp:298:10: error: no declaration matches 'uint32_t fsa::SimpleAlign::KmerMask(uint8_t)' + 298 | uint32_t SimpleAlign::KmerMask(uint8_t k) { + | ^~~~~~~~~~~ + fsa/simple_align.cpp:298:10: note: no functions named 'uint32_t fsa::SimpleAlign::KmerMask(uint8_t)' + fsa/simple_align.hpp:11:7: note: 'class fsa::SimpleAlign' defined here + 11 | class SimpleAlign { + | ^~~~~~~~~~~ + fsa/simple_align.cpp:309:10: error: no declaration matches 'uint32_t fsa::SimpleAlign::CalcKmer(const char*, size_t)' + 309 | uint32_t SimpleAlign::CalcKmer(const char* seq, size_t k) { + | ^~~~~~~~~~~ + fsa/simple_align.cpp:309:10: note: no functions named 'uint32_t fsa::SimpleAlign::CalcKmer(const char*, size_t)' + fsa/simple_align.hpp:11:7: note: 'class fsa::SimpleAlign' defined here + 11 | class SimpleAlign { + | ^~~~~~~~~~~ + fsa/simple_align.cpp:322:10: error: no declaration matches 'uint32_t fsa::SimpleAlign::MoveKmer(uint32_t, size_t, char)' + 322 | uint32_t SimpleAlign::MoveKmer(uint32_t bkmer, size_t k, char e) { + | ^~~~~~~~~~~ + fsa/simple_align.cpp:322:10: note: no functions named 'uint32_t fsa::SimpleAlign::MoveKmer(uint32_t, size_t, char)' + fsa/simple_align.hpp:11:7: note: 'class fsa::SimpleAlign' defined here + 11 | class SimpleAlign { + | ^~~~~~~~~~~ + make: *** [Makefile:414: ../Linux-aarch64/obj/libfsa.a/fsa/simple_align.o] Error 1 + make: *** Waiting for unfinished jobs.... + make: Leaving directory '$SRC_DIR/src' + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/necat_1733977159712/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/necat_1733977159712/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/nedbit-features-calculator/meta.yaml b/recipes/nedbit-features-calculator/meta.yaml index 390e2826acadf..ec52bd6b6ae36 100644 --- a/recipes/nedbit-features-calculator/meta.yaml +++ b/recipes/nedbit-features-calculator/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 50424bf7df99b51dc71a4121beae89ef69b2bb4eaba559c99643baecb8544806 build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('nedbit-features-calculator', max_pin="x.x") }} diff --git a/recipes/needle/build_failure.linux-64.yaml b/recipes/needle/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..e0652ef286a6b --- /dev/null +++ b/recipes/needle/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: be66a8a83187659942463276c68f3f0b883abcff142c2ebb75d4261f0570e3e9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/needle-1.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/needle-1.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/needle-1.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/needle-1.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): + Compatibility with CMake < 3.10 will be removed from a future version of + CMake. + + Update the VERSION argument value. Or, use the ... syntax + to tell CMake that the project requires at least but has been updated + to work with policies introduced by or earlier. + + + -- The C compiler identification is GNU 13.3.0 + -- The CXX compiler identification is GNU 13.3.0 + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - skipped + -- Detecting C compile features + -- Detecting C compile features - done + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Check if compiler accepts -pthread + -- Check if compiler accepts -pthread - yes + CMake Error at lib/seqan3/build_system/seqan3-config.cmake:114 (message): + The SDSL library is required, but wasn't found. Get it from + https://github.com/xxsds/sdsl-lite + Call Stack (most recent call first): + lib/seqan3/build_system/seqan3-config.cmake:379 (seqan3_config_error) + CMakeLists.txt:28 (find_package) + + + -- Configuring incomplete, errors occurred! + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/needle_1734128369283/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/needle_1734128369283/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/needle/meta.yaml b/recipes/needle/meta.yaml index e25d49c5cd6ba..0c681fe18a7d1 100644 --- a/recipes/needle/meta.yaml +++ b/recipes/needle/meta.yaml @@ -10,7 +10,7 @@ source: git_rev: needle-v{{ version }} build: - number: 3 + number: 4 skip: True # [osx] requirements: diff --git a/recipes/nemo-age/build_failure.osx-64.yaml b/recipes/nemo-age/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..d8b15ebfc7e25 --- /dev/null +++ b/recipes/nemo-age/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 7c34922703e71f60090ec7bf7e95f892013094f04d49510ba17fc9663337ec28 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + - sed 4.7 h3efe00b_1000 + - clang-18 18.1.8 default_h0c94c6a_5 + raise BuildScriptException(str(exc), caused_by=exc) from exc + - clang 18.1.8 default_h179603d_5 + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/nemo-age_1733981466164/work/conda_build.sh']' returned non-zero exit status 2. + - ld64_osx-64 951.9 hc8d1a19_2 + - libcxx-devel 18.1.8 h7c275be_7 + - openssl 3.4.0 hd471939_0 + - libintl-devel 0.22.5 hdfe23c8_3 + - compiler-rt 18.1.8 h1020d70_1 + - cctools_osx-64 1010.6 h00edd4c_2 + - gettext-tools 0.22.5 hdfe23c8_3 + - ncurses 6.5 hf036a51_1 + - clangxx 18.1.8 default_h179603d_5 + - libgettextpo 0.22.5 hdfe23c8_3 + host: + - libcxx 19.1.5 hf95d169_0 + - llvm-openmp 19.1.5 ha54dae1_0 + - libgfortran5 13.2.0 h2873a65_3 + - libgfortran 5.0.0 13_2_0_h97931a8_3 + - libopenblas 0.3.28 openmp_hbf64a52_1 + - libblas 3.9.0 25_osx64_openblas + - libcblas 3.9.0 25_osx64_openblas + - gsl 2.7 h93259b0_0 + run: + - gsl >=2.7,<2.8.0a0 + - libcxx >=18 + test: + commands: + - nemoage 2>&1 | grep "N E M O A G E" + about: + home: https://bitbucket.org/ecoevo/nemo-age-release + license: GPL-3 + license_family: GPL3 + license_file: readme.txt + summary: In Nemo-age, it is possible to model genetic and phenotypic evolution in + populations with, for instance, overlapping generations, a seed bank, and multiple + age classes with stage-specific transition rates, fecundities, selection pressures, + and dispersal rates, among other things. + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/nemo-age_1733981466164/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/nemo-age_1733981466164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/nemo-age_1733981466164/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/nemo-age_1733981466164/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/nemo-age-0.30.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/nemo-age-0.30.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/nemo-age-0.30.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/nemo-age-0.30.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/nemo-age-0.30.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DHAS_GSL -w -O3 -funroll-loops -ffast-math -c src/LCEbreed.cc -o src/LCEbreed.o -I$PREFIX/include +# Last 100 lines of the build log. diff --git a/recipes/nemo-age/meta.yaml b/recipes/nemo-age/meta.yaml index aec850f4aab67..ec1bee382ff4f 100644 --- a/recipes/nemo-age/meta.yaml +++ b/recipes/nemo-age/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://bitbucket.org/ecoevo/nemo-age-release/get/v{{ version }}.tar.gz diff --git a/recipes/netcdf-metadata-info/meta.yaml b/recipes/netcdf-metadata-info/meta.yaml index 981be653c617f..b459ec4b9adb0 100644 --- a/recipes/netcdf-metadata-info/meta.yaml +++ b/recipes/netcdf-metadata-info/meta.yaml @@ -10,7 +10,7 @@ source: md5: {{ md5 }} build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/newick_utils/meta.yaml b/recipes/newick_utils/meta.yaml index 762c33482c161..dc8a120335232 100644 --- a/recipes/newick_utils/meta.yaml +++ b/recipes/newick_utils/meta.yaml @@ -8,7 +8,7 @@ package: version: {{ version }} build: - number: 8 + number: 9 source: url: https://github.com/tjunier/newick_utils/archive/{{ revision }}.tar.gz diff --git a/recipes/nextdenovo/meta.yaml b/recipes/nextdenovo/meta.yaml index 9cd2862116599..8f2f26c555feb 100644 --- a/recipes/nextdenovo/meta.yaml +++ b/recipes/nextdenovo/meta.yaml @@ -12,7 +12,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 binary_has_prefix_files: - nextDenovo run_exports: diff --git a/recipes/nextpolish/build_failure.osx-64.yaml b/recipes/nextpolish/build_failure.osx-64.yaml index 71e48079f203a..23477f682d3ff 100644 --- a/recipes/nextpolish/build_failure.osx-64.yaml +++ b/recipes/nextpolish/build_failure.osx-64.yaml @@ -1,45 +1,56 @@ -recipe_sha: 00446774e10e402207b5471dce316d7b6277689c33e12899d656bf1895f730fa # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: a371034e03e43b05e9b7562bec6dbb3e05217f80d3727b719266e217d470a0e7 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: compiler error log: |2- - fprintf(stderr, "[STAT] Total used bases:%lu reads count(with N Base):%lu(%lu)\n",total_base, total_read, total_nread); - ~~~ ^~~~~~~~~~ - %llu - seq_split.c:345:108: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat] - fprintf(stderr, "[STAT] Total used bases:%lu reads count(with N Base):%lu(%lu)\n",total_base, total_read, total_nread); - ~~~ ^~~~~~~~~~~ - %llu - 3 warnings generated. - thpool.c:329:2: error: call to undeclared function 'pthread_setname_np'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] - pthread_setname_np(thread_name); - ^ - 1 error generated. - make[1]: *** [Makefile:13: seq_split] Error 1 - make: *** [Makefile:18: all] Error 2 - Extracting download - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/nextpolish/fix_nextpolish_paths.patch - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/nextpolish/fix_nextpolish_paths.patch with args: - ['-Np1', '-i', '/tmp/tmp8zk8i4n4/fix_nextpolish_paths.patch.native', '--binary'] - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/nextpolish/fix_get_version.patch - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/nextpolish/fix_get_version.patch with args: - ['-Np1', '-i', '/tmp/tmp1g2fvfsm/fix_get_version.patch.native', '--binary'] - Patch analysis gives: - [[ RA-MD1LOVE ]] - [[ fix_nextpolish_paths.patch ]] - Traceback (most recent call last): - [[ RA-MD1LOVE ]] - [[ fix_get_version.patch ]] - - Key: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + - openssl 3.4.0 hd471939_0 + raise BuildScriptException(str(exc), caused_by=exc) from exc + - readline 8.2 h9e318b2_1 + - tk 8.6.13 h1abcd95_1 + - zlib 1.3.1 hd23fc13_2 + - python 3.11.11 h9ccd52b_1_cpython + - psutil 6.1.0 py311h1314207_0 + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/nextpolish_1734795292397/work/conda_build.sh']' returned non-zero exit status 2. + - setuptools 75.6.0 pyhff2d567_1 + - wheel 0.45.1 pyhd8ed1ab_1 + - paralleltask 0.1.1 pyhd8ed1ab_0 + - pip 24.3.1 pyh8b19718_2 + run: + - bzip2 >=1.0.8,<2.0a0 + - python >=3.11,<3.12.0a0 + - paralleltask + - libzlib >=1.3.1,<2.0a0 + - samtools + - bwa + - python_abi 3.11.* *_cp311 + - minimap2 + test: + commands: + - nextPolish --help + - nextPolish --version + about: + dev_url: https://github.com/Nextomics/NextPolish + doc_url: https://nextpolish.readthedocs.io/en/latest + home: https://github.com/Nextomics/NextPolish + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + summary: Fast and accurately polish the genome generated by noisy long reads + extra: + copy_test_source_files: true + final: true + identifiers: + - biotools:NextPolish + - doi:10.1093/bioinformatics/btz891 + recipe-maintainers: + - rpetit3 - R :: Reversible A :: Applicable - Y :: Build-prefix patch in use M :: Minimal, non-amalgamated - D :: Dry-runnable N :: Patch level (1 is preferred) - L :: Patch level not-ambiguous O :: Patch applies without offsets - V :: Patch applies without fuzz E :: Patch applies without emitting to stderr - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/nextpolish_1718144212493/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/nextpolish_1718144212493/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/nextpolish_1718144212493/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/nextpolish_1718144212493/work + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/nextpolish_1734795292397/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/nextpolish_1734795292397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/nextpolish_1734795292397/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/nextpolish_1734795292397/work INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as @@ -48,11 +59,13 @@ log: |2- CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/nextpolish-1.4.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/nextpolish-1.4.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool @@ -61,7 +74,7 @@ log: |2- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -70,7 +83,7 @@ log: |2- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -86,20 +99,8 @@ log: |2- make -C util; make[1]: Entering directory '$SRC_DIR/util' x86_64-apple-darwin13.4.0-clang -O3 -pthread -o seq_split seq_split.c thpool.c -lz -isystem $PREFIX/include + x86_64-apple-darwin13.4.0-clang -O3 -std=c99 -o seq_count seq_count.c -lz -isystem $PREFIX/include make[1]: Leaving directory '$SRC_DIR/util' - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/nextpolish_1718144212493/work/conda_build.sh']' returned non-zero exit status 2. # Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/nextpolish/meta.yaml b/recipes/nextpolish/meta.yaml index 2b2cd7b3873ea..f5a54db4b2958 100644 --- a/recipes/nextpolish/meta.yaml +++ b/recipes/nextpolish/meta.yaml @@ -13,7 +13,7 @@ source: - fix_get_version.patch build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage('nextpolish', max_pin="x") }} diff --git a/recipes/nextpolish2/build_failure.osx-64.yaml b/recipes/nextpolish2/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c4c08da35a5ef --- /dev/null +++ b/recipes/nextpolish2/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a7f2d4497f5df3c87491b09ae25905f5cba990d03f30191af8bb169d23c8e224 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - libclang-cpp18.1 18.1.8 default_h0c94c6a_5 + - krb5 1.21.3 h37d8d59_0 + - clang_osx-64 18.1.8 h7e5c614_23 + - libnghttp2 1.64.0 hc7306c3_0 + - rust-std-x86_64-apple-darwin 1.83.0 h38e4360_0 + - cctools_osx-64 1010.6 h00edd4c_2 + - libzlib 1.3.1 hd23fc13_2 + packages_from_this = build( + - ncurses 6.5 hf036a51_1 + host: + - libcxx 19.1.5 hf95d169_0 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + - libzlib 1.3.1 hd23fc13_2 + - zlib 1.3.1 hd23fc13_2 + run: + - libcxx >=18 + - yak >=0.1 + - libzlib >=1.3.1,<2.0a0 + run_constrained: + - __osx >=10.13 + test: + commands: + - nextPolish2 --help + source_files: + - test + about: + dev_url: https://github.com/Nextomics/NextPolish2 + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/nextpolish2_1734097804296/work/conda_build.sh']' returned non-zero exit status 101. + doc_url: https://github.com/Nextomics/NextPolish2/blob/0.2.1/README.md + home: https://github.com/Nextomics/NextPolish2 + license: GBPL + license_file: LICENSE + summary: Repeat-aware polishing genomes assembled using HiFi long reads. + extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + copy_test_source_files: true + final: true + identifiers: + - doi:10.1093/gpbjnl/qzad009 + recipe-maintainers: + - moold + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/nextpolish2_1734097804296/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/nextpolish2_1734097804296/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/nextpolish2_1734097804296/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/nextpolish2_1734097804296/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/nextpolish2-0.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/nextpolish2-0.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/nextpolish2-0.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/nextpolish2-0.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix +# Last 100 lines of the build log. diff --git a/recipes/nextpolish2/meta.yaml b/recipes/nextpolish2/meta.yaml index 714e5aab5d652..a98453ac2eb91 100644 --- a/recipes/nextpolish2/meta.yaml +++ b/recipes/nextpolish2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 5f94cfabae5d38397a33c118f572246070707aa23f7b2ab831fd255710f50280 build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('nextpolish2', max_pin="x.x") }} diff --git a/recipes/ngmlr/meta.yaml b/recipes/ngmlr/meta.yaml index b6c6f43f7c46c..6cd55eaa9989a 100644 --- a/recipes/ngmlr/meta.yaml +++ b/recipes/ngmlr/meta.yaml @@ -12,7 +12,7 @@ source: - ngmlr-aarch64.patch # [linux and aarch64] build: - number: 7 + number: 8 run_exports: - {{ pin_subpackage('ngmlr', max_pin="x") }} @@ -37,4 +37,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ngs-bits/meta.yaml b/recipes/ngs-bits/meta.yaml index c805ca599d4f7..505221bdeb060 100644 --- a/recipes/ngs-bits/meta.yaml +++ b/recipes/ngs-bits/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("ngs-bits", max_pin=None) }} diff --git a/recipes/ngs-disambiguate/meta.yaml b/recipes/ngs-disambiguate/meta.yaml index 707528f6bf094..64fb95b1193f0 100644 --- a/recipes/ngs-disambiguate/meta.yaml +++ b/recipes/ngs-disambiguate/meta.yaml @@ -10,7 +10,7 @@ source: sha256: d5b05caec68db7596fc31564f44afdce27c4d5215785f9c97581d58e87d9cc94 build: - number: 9 + number: 10 skip: true # [osx] run_exports: - {{ pin_subpackage('ngs-disambiguate', max_pin=None) }} @@ -36,4 +36,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ngslca/meta.yaml b/recipes/ngslca/meta.yaml index 289201d453874..a0f47b2f1efc5 100644 --- a/recipes/ngslca/meta.yaml +++ b/recipes/ngslca/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/ngsngs/meta.yaml b/recipes/ngsngs/meta.yaml index 2a6dccd5bee55..a246dd573648b 100644 --- a/recipes/ngsngs/meta.yaml +++ b/recipes/ngsngs/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 skip: false run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/niemagraphgen/meta.yaml b/recipes/niemagraphgen/meta.yaml index 12c498054c879..2a93dbabb845d 100644 --- a/recipes/niemagraphgen/meta.yaml +++ b/recipes/niemagraphgen/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('niemagraphgen', max_pin="x.x.x") }} diff --git a/recipes/nim-falcon/meta.yaml b/recipes/nim-falcon/meta.yaml index 17539af17cfa4..a972409d4db95 100644 --- a/recipes/nim-falcon/meta.yaml +++ b/recipes/nim-falcon/meta.yaml @@ -17,7 +17,7 @@ source: build: skip: True # [osx] - number: 1 + number: 2 requirements: host: diff --git a/recipes/nimnexus/build_failure.linux-64.yaml b/recipes/nimnexus/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..e2fa12c93bbc5 --- /dev/null +++ b/recipes/nimnexus/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: d1fb58e91e161c141b6c2d8022fd77ade1c921583b483951b520a2758a73d54b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + source tree in: /opt/conda/conda-bld/nimnexus_1734241733948/work + export PREFIX=/opt/conda/conda-bld/nimnexus_1734241733948/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + export BUILD_PREFIX=/opt/conda/conda-bld/nimnexus_1734241733948/_build_env + export SRC_DIR=/opt/conda/conda-bld/nimnexus_1734241733948/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/nimnexus-0.1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/nimnexus-0.1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/nimnexus-0.1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/nimnexus-0.1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + $SRC_DIR/hts-nim $SRC_DIR + Verifying dependencies for hts@0.2.23 + Installing hts@0.2.23 + Success: hts installed successfully. + $SRC_DIR + Verifying dependencies for nimnexus@0.1.1 + Prompt: No local packages.json found, download it from internet? -> [forced yes] + Downloading Official package list + Success Package list downloaded. + Info: Dependency on hts@>= 0.2.7 & < 0.3 already satisfied + Verifying dependencies for hts@0.2.23 + Installing docopt@#0abba63 + Downloading https://github.com/docopt/docopt.nim using git + Verifying dependencies for docopt@0.6.6 + Installing docopt@0.6.6 + Success: docopt installed successfully. + Installing nimnexus@0.1.1 + Building nimnexus/nimnexus using c backend + /home/conda/.nimble/pkgs2/docopt-0.6.6-a56c015b9d36d9ca57708ed6d9c0c915d2a1c5e8/docopt.nim(604, 6) Error: 'docopt' is not GC-safe as it calls 'docopt_exc' + Tip: 15 messages have been suppressed, use --verbose to show them. + nimble.nim(304) buildFromDir + + Error: Build failed for the package: nimnexus + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/nimnexus_1734241733948/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/nimnexus_1734241733948/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/nimnexus/meta.yaml b/recipes/nimnexus/meta.yaml index 1cf226fe6d430..cf88adc836abe 100644 --- a/recipes/nimnexus/meta.yaml +++ b/recipes/nimnexus/meta.yaml @@ -18,7 +18,7 @@ source: folder: genoiser build: - number: 4 + number: 5 skip: True # [osx] requirements: diff --git a/recipes/ninja-nj/meta.yaml b/recipes/ninja-nj/meta.yaml index 2559d602650ff..9499381db78cc 100644 --- a/recipes/ninja-nj/meta.yaml +++ b/recipes/ninja-nj/meta.yaml @@ -13,7 +13,7 @@ source: - 0001-Makefile.patch build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("ninja-nj", max_pin="x") }} diff --git a/recipes/nmrglue/meta.yaml b/recipes/nmrglue/meta.yaml index 0dda4c54cb9f6..b883f01bdedd2 100644 --- a/recipes/nmrglue/meta.yaml +++ b/recipes/nmrglue/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 skip: True # [py2k] script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv diff --git a/recipes/nohuman/build_failure.osx-64.yaml b/recipes/nohuman/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..66354b8aa12d8 --- /dev/null +++ b/recipes/nohuman/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: d9f8bcdaed5cf95f98db9e13d464257c510b86486da1bc2814c38976529c4617 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + - cargo-bundle-licenses 2.0.0 he829971_1 + - clang-18 18.1.8 default_h0c94c6a_5 + - llvm-tools 18.1.8 h9ce406d_2 + - cctools_osx-64 1010.6 h00edd4c_2 + - clang 18.1.8 default_h179603d_5 + - clangxx 18.1.8 default_h179603d_5 + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + - compiler-rt 18.1.8 h1020d70_1 + - clang_impl_osx-64 18.1.8 h6a44ed1_23 + - clang_osx-64 18.1.8 h7e5c614_23 + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/nohuman_1734758102814/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + - rust_osx-64 1.83.0 hca1c201_1 + run: + - kraken2 =2.1 + run_constrained: + - __osx >=10.13 + test: + commands: + - nohuman --help + - nohuman --check + about: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + home: https://github.com/mbhall88/nohuman + license: MIT + license_file: + - LICENSE + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + - THIRDPARTY.yml + summary: Remove human reads from a sequencing run + extra: + copy_test_source_files: true + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + final: true + recipe-maintainers: + - mbhall88 + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/nohuman_1734758102814/work + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/nohuman_1734758102814/work/conda_build.sh']' returned non-zero exit status 101. + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/nohuman_1734758102814/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/nohuman_1734758102814/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/nohuman_1734758102814/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/nohuman-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/nohuman-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 +# Last 100 lines of the build log. diff --git a/recipes/nohuman/meta.yaml b/recipes/nohuman/meta.yaml index faca6ca3f3f18..6ffdfa183119c 100644 --- a/recipes/nohuman/meta.yaml +++ b/recipes/nohuman/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 3503a0e8b6fcbf92832fe4bfcfb3d5a071536a8ebe3230cac1ee4e053de3cf6a build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('nohuman', max_pin="x.x") }} diff --git a/recipes/nonpareil/meta.yaml b/recipes/nonpareil/meta.yaml index b9efb68dcc775..56ef5d176fe33 100644 --- a/recipes/nonpareil/meta.yaml +++ b/recipes/nonpareil/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('nonpareil', max_pin="x.x") }} script: | diff --git a/recipes/novoalign/3.09.04/meta.yaml b/recipes/novoalign/3.09.04/meta.yaml index 173b77d9d444e..c92e99dafd85c 100644 --- a/recipes/novoalign/3.09.04/meta.yaml +++ b/recipes/novoalign/3.09.04/meta.yaml @@ -13,7 +13,7 @@ source: sha256: {{ sha256 }} build: - number: 6 + number: 7 skip: True # [not linux] requirements: diff --git a/recipes/novoalign/meta.yaml b/recipes/novoalign/meta.yaml index 41f4b92cc3192..ea495547390c8 100644 --- a/recipes/novoalign/meta.yaml +++ b/recipes/novoalign/meta.yaml @@ -13,7 +13,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 skip: True # [not linux] requirements: diff --git a/recipes/novobreak/build_failure.osx-64.yaml b/recipes/novobreak/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..6c5768f7a387c --- /dev/null +++ b/recipes/novobreak/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 61844d7df72fa23cddddd63b35bb2bb97b0e491a7062bdb3ed07fcc3b65783b3 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + libedit: 3.1.20191231-h0678c8f_2 conda-forge + libev: 4.33-h10d778d_2 conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libnghttp2: 1.64.0-hc7306c3_0 conda-forge + libssh2: 1.11.1-h3dc7d44_0 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + novobreak: 1.1.3rc-h7f84b70_10 local + openssl: 3.4.0-hd471939_0 conda-forge + perl: 5.32.1-7_h10d778d_perl5 conda-forge + perl-exporter-tiny: 1.002002-pl5321hd8ed1ab_0 conda-forge + perl-list-moreutils: 0.430-pl5321hdfd78af_0 bioconda + perl-list-moreutils-xs: 0.430-pl5321h8af04d4_3 bioconda + perl-statistics-descriptive: 3.0801-pl5321hdfd78af_0 bioconda + python: 2.0-0 conda-forge + samtools: 1.21-h94387ee_0 bioconda + ssake: 4.0-hdfd78af_5 bioconda + zlib: 1.3.1-hd23fc13_2 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... failed + WARNING: Build prefix failed with prefix length 255 + WARNING: Error was: + WARNING: Placeholder of length '80' too short in package /opt/mambaforge/envs/bioconda/conda-bld/novobreak_1734094563551/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/python. + The package must be rebuilt with conda-build > 2.0. + WARNING: One or more of your package dependencies needs to be rebuilt with a longer prefix length. + WARNING: Falling back to legacy prefix length of 80 characters. + WARNING: Your package will not install into prefixes > 80 characters. + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/novobreak_1734094563551/_build_env + + + The following NEW packages will be INSTALLED: + + bwa: 0.7.18-h7f84b70_2 bioconda + bzip2: 1.0.8-hfdf4475_7 conda-forge + c-ares: 1.34.3-hf13058a_1 conda-forge + ca-certificates: 2024.8.30-h8857fd0_0 conda-forge + htslib: 1.21-h9f635df_1 bioconda + krb5: 1.21.3-h37d8d59_0 conda-forge + libcurl: 8.11.1-h5dec5d8_0 conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libdeflate: 1.22-h00291cd_0 conda-forge + libedit: 3.1.20191231-h0678c8f_2 conda-forge + libev: 4.33-h10d778d_2 conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libnghttp2: 1.64.0-hc7306c3_0 conda-forge + libssh2: 1.11.1-h3dc7d44_0 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + novobreak: 1.1.3rc-h7f84b70_10 local + openssl: 3.4.0-hd471939_0 conda-forge + perl: 5.32.1-7_h10d778d_perl5 conda-forge + perl-exporter-tiny: 1.002002-pl5321hd8ed1ab_0 conda-forge + perl-list-moreutils: 0.430-pl5321hdfd78af_0 bioconda + perl-list-moreutils-xs: 0.430-pl5321h8af04d4_3 bioconda + perl-statistics-descriptive: 3.0801-pl5321hdfd78af_0 bioconda + python: 2.0-0 conda-forge + samtools: 1.21-h94387ee_0 bioconda + ssake: 4.0-hdfd78af_5 bioconda + zlib: 1.3.1-hd23fc13_2 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + + EnvironmentLocationNotFound: Not a conda environment: /opt/mambaforge/envs/bioconda/conda-bld/novobreak_1734094563551/_test_env_plac + + WARNING: Tests failed for novobreak-1.1.3rc-h7f84b70_10.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/novobreak_1734094563551/_test_env_plac + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/novobreak_1734094563551/test_tmp + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/novobreak_1734094563551/test_tmp/conda_test_runner.sh']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: novobreak-1.1.3rc-h7f84b70_10.tar.bz2 +# Last 100 lines of the build log. diff --git a/recipes/novobreak/meta.yaml b/recipes/novobreak/meta.yaml index 9cfee5e4d52c4..cb34b167edf69 100644 --- a/recipes/novobreak/meta.yaml +++ b/recipes/novobreak/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 9 + number: 10 source: url: https://github.com/czc/novobreak_src/archive/7435b2758c1c861eadce90cf1d4e199fbbaa981a.zip diff --git a/recipes/nseg/meta.yaml b/recipes/nseg/meta.yaml index 5ee0b693ffaaa..1022a5faa37b0 100644 --- a/recipes/nseg/meta.yaml +++ b/recipes/nseg/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage("nseg", max_pin="x") }} diff --git a/recipes/ntcard/build_failure.osx-64.yaml b/recipes/ntcard/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..61eb0d9e0e024 --- /dev/null +++ b/recipes/ntcard/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: c6e6f7385e423ad2495da5c45880c3c08072ad8a998908befed719627d39991e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking for x86_64-apple-darwin13.4.0-clang option to enable C11 features... none needed + checking whether x86_64-apple-darwin13.4.0-clang understands -c and -o together... yes + checking whether make supports the include directive... yes (GNU style) + checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 + checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang-cpp + checking whether the compiler supports GNU C... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking for x86_64-apple-darwin13.4.0-clang option to enable C11 features... none needed + checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 + checking for x86_64-apple-darwin13.4.0-ranlib... x86_64-apple-darwin13.4.0-ranlib + checking for stdio.h... yes + checking for stdlib.h... yes + checking for string.h... yes + checking for inttypes.h... yes + checking for stdint.h... yes + checking for strings.h... yes + checking for sys/stat.h... yes + checking for sys/types.h... yes + checking for unistd.h... yes + checking for vfork.h... no + checking for dlfcn.h... yes + checking for fcntl.h... yes + checking for float.h... yes + checking for limits.h... yes + checking for stddef.h... yes + checking for stdint.h... (cached) yes + checking for stdlib.h... (cached) yes + checking for sys/param.h... yes + checking for zlib.h... yes + checking for _Bool... yes + checking for stdbool.h that conforms to C99... yes + checking for grep that handles long lines and -e... /usr/bin/grep + checking for egrep... /usr/bin/grep -E + checking for dup2... yes + checking for gethostname... yes + checking for getopt_long... yes + checking for getpagesize... yes + checking for memset... yes + checking for strdup... yes + checking for strerror... yes + checking for strtoul... yes + checking for pid_t... yes + checking for fork... yes + checking for vfork... yes + checking for vprintf... yes + checking for working fork... yes + checking for working vfork... (cached) yes + checking build system type... x86_64-apple-darwin13.4.0 + checking host system type... x86_64-apple-darwin13.4.0 + checking for GNU libc compatible malloc... (cached) yes + checking for working memcmp... yes + checking for GNU libc compatible realloc... (cached) yes + checking whether byte ordering is bigendian... no + checking for an ANSI C-conforming const... yes + checking for inline... inline + checking for ptrdiff_t... yes + checking for mode_t... yes + checking for pid_t... (cached) yes + checking for size_t... yes + checking for ssize_t... yes + checking for int64_t... yes + checking for uint8_t... yes + checking for uint16_t... yes + checking for uint32_t... yes + checking for uint64_t... yes + checking for sqrt in -lm... yes + checking for pow... yes + checking for sqrt... yes + checking for ceilf... yes + checking for dlsym in -ldl... yes + checking for gzwrite in -lz... yes + checking for x86_64-apple-darwin13.4.0-clang option to support OpenMP... -fopenmp + checking that generated files are newer than configure... done + configure: creating ./config.status + config.status: creating Makefile + config.status: creating vendor/Makefile + config.status: creating data/Makefile + config.status: creating config.h + config.status: executing depfiles commands + make all-recursive + make[1]: Entering directory '$SRC_DIR' + Making all in vendor + make[2]: Entering directory '$SRC_DIR/vendor' + make[2]: Nothing to be done for 'all'. + make[2]: Leaving directory '$SRC_DIR/vendor' + Making all in data + make[2]: Entering directory '$SRC_DIR/data' + make[2]: Nothing to be done for 'all'. + make[2]: Leaving directory '$SRC_DIR/data' + make[2]: Entering directory '$SRC_DIR' + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I./Common -I$SRC_DIR -fopenmp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wall -Wextra -Werror -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntcard-1.2.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-array-bounds -MT Common/ntcard-Uncompress.o -MD -MP -MF Common/.deps/ntcard-Uncompress.Tpo -c -o Common/ntcard-Uncompress.o test -f 'Common/Uncompress.cpp' || echo './'Common/Uncompress.cpp + mv -f Common/.deps/ntcard-Uncompress.Tpo Common/.deps/ntcard-Uncompress.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I./Common -I$SRC_DIR -fopenmp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wall -Wextra -Werror -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntcard-1.2.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-array-bounds -MT Common/ntcard-SignalHandler.o -MD -MP -MF Common/.deps/ntcard-SignalHandler.Tpo -c -o Common/ntcard-SignalHandler.o test -f 'Common/SignalHandler.cpp' || echo './'Common/SignalHandler.cpp + mv -f Common/.deps/ntcard-SignalHandler.Tpo Common/.deps/ntcard-SignalHandler.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I./Common -I$SRC_DIR -fopenmp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wall -Wextra -Werror -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntcard-1.2.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-array-bounds -MT Common/ntcard-Fcontrol.o -MD -MP -MF Common/.deps/ntcard-Fcontrol.Tpo -c -o Common/ntcard-Fcontrol.o test -f 'Common/Fcontrol.cpp' || echo './'Common/Fcontrol.cpp + mv -f Common/.deps/ntcard-Fcontrol.Tpo Common/.deps/ntcard-Fcontrol.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I./Common -I$SRC_DIR -fopenmp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wall -Wextra -Werror -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntcard-1.2.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-array-bounds -MT ntcard-ntcard.o -MD -MP -MF .deps/ntcard-ntcard.Tpo -c -o ntcard-ntcard.o test -f 'ntcard.cpp' || echo './'ntcard.cpp + make[2]: Leaving directory '$SRC_DIR' + make[1]: Leaving directory '$SRC_DIR' +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/ntcard/build_failure.osx-arm64.yaml b/recipes/ntcard/build_failure.osx-arm64.yaml new file mode 100644 index 0000000000000..aee5e0e12a007 --- /dev/null +++ b/recipes/ntcard/build_failure.osx-arm64.yaml @@ -0,0 +1,106 @@ +recipe_sha: c6e6f7385e423ad2495da5c45880c3c08072ad8a998908befed719627d39991e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + checking for arm64-apple-darwin20.0.0-clang option to enable C11 features... none needed + checking whether arm64-apple-darwin20.0.0-clang understands -c and -o together... yes + checking whether make supports the include directive... yes (GNU style) + checking dependency style of arm64-apple-darwin20.0.0-clang... gcc3 + checking how to run the C preprocessor... arm64-apple-darwin20.0.0-clang-cpp + checking whether the compiler supports GNU C... yes + checking whether arm64-apple-darwin20.0.0-clang accepts -g... yes + checking for arm64-apple-darwin20.0.0-clang option to enable C11 features... none needed + checking dependency style of arm64-apple-darwin20.0.0-clang... gcc3 + checking for arm64-apple-darwin20.0.0-ranlib... arm64-apple-darwin20.0.0-ranlib + checking for stdio.h... yes + checking for stdlib.h... yes + checking for string.h... yes + checking for inttypes.h... yes + checking for stdint.h... yes + checking for strings.h... yes + checking for sys/stat.h... yes + checking for sys/types.h... yes + checking for unistd.h... yes + checking for vfork.h... no + checking for dlfcn.h... yes + checking for fcntl.h... yes + checking for float.h... yes + checking for limits.h... yes + checking for stddef.h... yes + checking for stdint.h... (cached) yes + checking for stdlib.h... (cached) yes + checking for sys/param.h... yes + checking for zlib.h... yes + checking for _Bool... yes + checking for stdbool.h that conforms to C99... yes + checking for grep that handles long lines and -e... /usr/bin/grep + checking for egrep... /usr/bin/grep -E + checking for dup2... yes + checking for gethostname... yes + checking for getopt_long... yes + checking for getpagesize... yes + checking for memset... yes + checking for strdup... yes + checking for strerror... yes + checking for strtoul... yes + checking for pid_t... yes + checking for fork... yes + checking for vfork... yes + checking for vprintf... yes + checking for working fork... yes + checking for working vfork... (cached) yes + checking build system type... aarch64-apple-darwin20.0.0 + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/ntcard_1734454481817/work/conda_build.sh']' returned non-zero exit status 2. + checking host system type... aarch64-apple-darwin20.0.0 + checking for GNU libc compatible malloc... (cached) yes + checking for working memcmp... yes + checking for GNU libc compatible realloc... (cached) yes + checking whether byte ordering is bigendian... no + checking for an ANSI C-conforming const... yes + checking for inline... inline + checking for ptrdiff_t... yes + checking for mode_t... yes + checking for pid_t... (cached) yes + checking for size_t... yes + checking for ssize_t... yes + checking for int64_t... yes + checking for uint8_t... yes + checking for uint16_t... yes + checking for uint32_t... yes + checking for uint64_t... yes + checking for sqrt in -lm... yes + checking for pow... yes + checking for sqrt... yes + checking for ceilf... yes + checking for dlsym in -ldl... yes + checking for gzwrite in -lz... yes + checking for arm64-apple-darwin20.0.0-clang option to support OpenMP... -fopenmp + checking that generated files are newer than configure... done + configure: creating ./config.status + config.status: creating Makefile + config.status: creating vendor/Makefile + config.status: creating data/Makefile + config.status: creating config.h + config.status: executing depfiles commands + make all-recursive + make[1]: Entering directory '$SRC_DIR' + Making all in vendor + make[2]: Entering directory '$SRC_DIR/vendor' + make[2]: Nothing to be done for 'all'. + make[2]: Leaving directory '$SRC_DIR/vendor' + Making all in data + make[2]: Entering directory '$SRC_DIR/data' + make[2]: Nothing to be done for 'all'. + make[2]: Leaving directory '$SRC_DIR/data' + make[2]: Entering directory '$SRC_DIR' + arm64-apple-darwin20.0.0-clang -DHAVE_CONFIG_H -I. -I./Common -I$SRC_DIR -fopenmp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -Wall -Wextra -Werror -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntcard-1.2.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-array-bounds -MT Common/ntcard-Uncompress.o -MD -MP -MF Common/.deps/ntcard-Uncompress.Tpo -c -o Common/ntcard-Uncompress.o test -f 'Common/Uncompress.cpp' || echo './'Common/Uncompress.cpp + mv -f Common/.deps/ntcard-Uncompress.Tpo Common/.deps/ntcard-Uncompress.Po + arm64-apple-darwin20.0.0-clang -DHAVE_CONFIG_H -I. -I./Common -I$SRC_DIR -fopenmp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -Wall -Wextra -Werror -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntcard-1.2.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-array-bounds -MT Common/ntcard-SignalHandler.o -MD -MP -MF Common/.deps/ntcard-SignalHandler.Tpo -c -o Common/ntcard-SignalHandler.o test -f 'Common/SignalHandler.cpp' || echo './'Common/SignalHandler.cpp + mv -f Common/.deps/ntcard-SignalHandler.Tpo Common/.deps/ntcard-SignalHandler.Po + arm64-apple-darwin20.0.0-clang -DHAVE_CONFIG_H -I. -I./Common -I$SRC_DIR -fopenmp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -Wall -Wextra -Werror -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntcard-1.2.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-array-bounds -MT Common/ntcard-Fcontrol.o -MD -MP -MF Common/.deps/ntcard-Fcontrol.Tpo -c -o Common/ntcard-Fcontrol.o test -f 'Common/Fcontrol.cpp' || echo './'Common/Fcontrol.cpp + mv -f Common/.deps/ntcard-Fcontrol.Tpo Common/.deps/ntcard-Fcontrol.Po + arm64-apple-darwin20.0.0-clang -DHAVE_CONFIG_H -I. -I./Common -I$SRC_DIR -fopenmp -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -Wall -Wextra -Werror -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntcard-1.2.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wno-array-bounds -MT ntcard-ntcard.o -MD -MP -MF .deps/ntcard-ntcard.Tpo -c -o ntcard-ntcard.o test -f 'ntcard.cpp' || echo './'ntcard.cpp + make[2]: Leaving directory '$SRC_DIR' + make[1]: Leaving directory '$SRC_DIR' +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/ntcard/meta.yaml b/recipes/ntcard/meta.yaml index 06daf06500ea3..9991403095166 100644 --- a/recipes/ntcard/meta.yaml +++ b/recipes/ntcard/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('ntcard', max_pin="x") }} @@ -42,4 +42,4 @@ about: extra: additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 diff --git a/recipes/nthits/meta.yaml b/recipes/nthits/meta.yaml index 2e1d256d54b0a..61fe3017fe4ab 100644 --- a/recipes/nthits/meta.yaml +++ b/recipes/nthits/meta.yaml @@ -10,7 +10,7 @@ source: sha256: ee50e825f2c99f859031fa7e5bfe4cbbc71357108c32863e31b40b950cc077b2 build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('nthits', max_pin="x") }} @@ -42,4 +42,4 @@ about: extra: additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 diff --git a/recipes/ntjoin/meta.yaml b/recipes/ntjoin/meta.yaml index bd29bd4215cb8..9a9cf845771aa 100644 --- a/recipes/ntjoin/meta.yaml +++ b/recipes/ntjoin/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 808260e3e8c25121f4b7b88a0dd1766c9da0b59d5ebf843a5ec84efb13944009 build: - number: 1 + number: 2 noarch: generic run_exports: - {{ pin_subpackage("ntjoin", max_pin="x") }} diff --git a/recipes/ntlink/meta.yaml b/recipes/ntlink/meta.yaml index 65015d97b04aa..f4616f0bcce0b 100644 --- a/recipes/ntlink/meta.yaml +++ b/recipes/ntlink/meta.yaml @@ -9,7 +9,7 @@ source: sha256: ca92bd4eb4cd6f2f81db54faaeaaf4686236f42db4b6f274f552a52a8460b869 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('ntlink', max_pin="x") }} diff --git a/recipes/ntsm/build_failure.osx-64.yaml b/recipes/ntsm/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..815dd3eabf7e7 --- /dev/null +++ b/recipes/ntsm/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c6ec16ab5e823f38b7fc7055705ceadb5971f79f65a2aa18405cd8fe2c1b4bef # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsm-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsm-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsm-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + checking for a BSD-compatible install... /usr/bin/install -c + checking whether sleep supports fractional seconds... yes + checking filesystem timestamp resolution... 0.01 + checking whether build environment is sane... yes + checking for x86_64-strip... x86_64-apple-darwin13.4.0-strip + checking for a race-free mkdir -p... ./install-sh -c -d + checking for gawk... no + checking for mawk... no + checking for nawk... no + checking for awk... awk + checking whether make sets $(MAKE)... yes + checking whether make supports nested variables... yes + checking xargs -n works... yes + checking for x86_64-ranlib... x86_64-apple-darwin13.4.0-ranlib + checking whether the C compiler works... yes + checking for C compiler default output file name... a.out + checking for suffix of executables... + checking whether we are cross compiling... yes + checking for suffix of object files... o + checking whether the compiler supports GNU C... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking for x86_64-apple-darwin13.4.0-clang option to enable C11 features... none needed + checking whether make supports the include directive... yes (GNU style) + checking dependency style of x86_64-apple-darwin13.4.0-clang... none + checking for x86_64-gcc... x86_64-apple-darwin13.4.0-clang + checking whether the compiler supports GNU C... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking for x86_64-apple-darwin13.4.0-clang option to enable C11 features... none needed + checking whether x86_64-apple-darwin13.4.0-clang understands -c and -o together... yes + checking dependency style of x86_64-apple-darwin13.4.0-clang... none + checking for dlopen in -ldl... yes + checking for stdio.h... yes + checking for stdlib.h... yes + checking for string.h... yes + checking for inttypes.h... yes + checking for stdint.h... yes + checking for strings.h... yes + checking for sys/stat.h... yes + checking for sys/types.h... yes + checking for unistd.h... yes + checking for size_t... yes + checking for x86_64-apple-darwin13.4.0-clang option to support OpenMP... -fopenmp + checking that generated files are newer than configure... done + configure: creating ./config.status + config.status: creating Makefile + config.status: creating src/Makefile + config.status: creating config.h + config.status: executing depfiles commands + make all-recursive + make[1]: Entering directory '$SRC_DIR' + Making all in src + make[2]: Entering directory '$SRC_DIR/src' + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR/src -I$SRC_DIR/vendor -I$SRC_DIR -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -Wall -Wextra -Werror -fopenmp -O3 -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsm-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -O3 -std=c17 -Wno-braced-scalar-init -c -o ntsmCount-ntSeqMatchCount.o test -f 'ntSeqMatchCount.cpp' || echo '$SRC_DIR/src/'ntSeqMatchCount.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR/src -I$SRC_DIR/vendor -I$SRC_DIR -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -Wall -Wextra -Werror -fopenmp -O3 -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsm-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -O3 -std=c17 -Wno-braced-scalar-init -c -o ntsmCount-Options.o test -f 'Options.cpp' || echo '$SRC_DIR/src/'Options.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR/src -I$SRC_DIR/vendor -I$SRC_DIR -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -Wall -Wextra -Werror -fopenmp -O3 -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsm-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -O3 -std=c17 -Wno-braced-scalar-init -c -o ntsmEval-ntSeqMatchEval.o test -f 'ntSeqMatchEval.cpp' || echo '$SRC_DIR/src/'ntSeqMatchEval.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR/src -I$SRC_DIR/vendor -I$SRC_DIR -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -Wall -Wextra -Werror -fopenmp -O3 -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsm-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -O3 -std=c17 -Wno-braced-scalar-init -c -o ntsmEval-Options.o test -f 'Options.cpp' || echo '$SRC_DIR/src/'Options.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR/src -I$SRC_DIR/vendor -I$SRC_DIR -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -Wall -Wextra -Werror -fopenmp -O3 -std=c11 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsm-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -O3 -std=c17 -Wno-braced-scalar-init -c -o ntsmVCF-ntSeqMatchVCF.o test -f 'ntSeqMatchVCF.cpp' || echo '$SRC_DIR/src/'ntSeqMatchVCF.cpp + make[2]: Leaving directory '$SRC_DIR/src' + make[1]: Leaving directory '$SRC_DIR' +# Last 100 lines of the build log. diff --git a/recipes/ntsm/build_failure.osx-arm64.yaml b/recipes/ntsm/build_failure.osx-arm64.yaml new file mode 100644 index 0000000000000..b5eea8613465e --- /dev/null +++ b/recipes/ntsm/build_failure.osx-arm64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c6ec16ab5e823f38b7fc7055705ceadb5971f79f65a2aa18405cd8fe2c1b4bef # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=arm64-apple-darwin20.0.0 + CONDA_TOOLCHAIN_HOST=arm64-apple-darwin20.0.0 + CPP=arm64-apple-darwin20.0.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang-cpp + DEBUG_CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsm-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=arm64-apple-darwin20.0.0 + INSTALL_NAME_TOOL=arm64-apple-darwin20.0.0-install_name_tool + LD=arm64-apple-darwin20.0.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=arm64-apple-darwin20.0.0-libtool + LIPO=arm64-apple-darwin20.0.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=arm64-apple-darwin20.0.0-nm + NMEDIT=arm64-apple-darwin20.0.0-nmedit + OBJC=arm64-apple-darwin20.0.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang + OTOOL=arm64-apple-darwin20.0.0-otool + PAGESTUFF=arm64-apple-darwin20.0.0-pagestuff + RANLIB=arm64-apple-darwin20.0.0-ranlib + REDO_PREBINDING=arm64-apple-darwin20.0.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk + SEGEDIT=arm64-apple-darwin20.0.0-segedit + SEG_ADDR_TABLE=arm64-apple-darwin20.0.0-seg_addr_table + SEG_HACK=arm64-apple-darwin20.0.0-seg_hack + SIZE=arm64-apple-darwin20.0.0-size + STRINGS=arm64-apple-darwin20.0.0-strings + STRIP=arm64-apple-darwin20.0.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_arm64_apple_darwin20_0_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=arm64-apple-darwin20.0.0 + host_alias=arm64-apple-darwin20.0.0 + INFO: activate_clangxx_osx-arm64.sh made the following environmental changes: + CLANGXX=arm64-apple-darwin20.0.0-clang + CXX=arm64-apple-darwin20.0.0-clang + CXXFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsm-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang + DEBUG_CXXFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsm-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + checking for a BSD-compatible install... /usr/bin/install -c + checking whether sleep supports fractional seconds... yes + checking filesystem timestamp resolution... 0.01 + checking whether build environment is sane... yes + checking for arm64-strip... arm64-apple-darwin20.0.0-strip + checking for a race-free mkdir -p... ./install-sh -c -d + checking for gawk... no + checking for mawk... no + checking for nawk... no + checking for awk... awk + checking whether make sets $(MAKE)... yes + checking whether make supports nested variables... yes + checking xargs -n works... yes + checking for arm64-ranlib... arm64-apple-darwin20.0.0-ranlib + checking whether the C compiler works... yes + checking for C compiler default output file name... a.out + checking for suffix of executables... + checking whether we are cross compiling... yes + checking for suffix of object files... o + checking whether the compiler supports GNU C... yes + checking whether arm64-apple-darwin20.0.0-clang accepts -g... yes + checking for arm64-apple-darwin20.0.0-clang option to enable C11 features... none needed + checking whether make supports the include directive... yes (GNU style) + checking dependency style of arm64-apple-darwin20.0.0-clang... none + checking for arm64-gcc... arm64-apple-darwin20.0.0-clang + checking whether the compiler supports GNU C... yes + checking whether arm64-apple-darwin20.0.0-clang accepts -g... yes + checking for arm64-apple-darwin20.0.0-clang option to enable C11 features... none needed + checking whether arm64-apple-darwin20.0.0-clang understands -c and -o together... yes + checking dependency style of arm64-apple-darwin20.0.0-clang... none + checking for dlopen in -ldl... yes + checking for stdio.h... yes + checking for stdlib.h... yes + checking for string.h... yes + checking for inttypes.h... yes + checking for stdint.h... yes + checking for strings.h... yes + checking for sys/stat.h... yes + checking for sys/types.h... yes + checking for unistd.h... yes + checking for size_t... yes + checking for arm64-apple-darwin20.0.0-clang option to support OpenMP... -fopenmp + checking that generated files are newer than configure... done + configure: creating ./config.status + config.status: creating Makefile + config.status: creating src/Makefile + config.status: creating config.h + config.status: executing depfiles commands + make all-recursive + make[1]: Entering directory '$SRC_DIR' + Making all in src + make[2]: Entering directory '$SRC_DIR/src' + arm64-apple-darwin20.0.0-clang -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR/src -I$SRC_DIR/vendor -I$SRC_DIR -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -I$PREFIX/include -Wall -Wextra -Werror -fopenmp -O3 -std=c11 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsm-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -O3 -std=c17 -Wno-braced-scalar-init -c -o ntsmCount-ntSeqMatchCount.o test -f 'ntSeqMatchCount.cpp' || echo '$SRC_DIR/src/'ntSeqMatchCount.cpp + arm64-apple-darwin20.0.0-clang -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR/src -I$SRC_DIR/vendor -I$SRC_DIR -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -I$PREFIX/include -Wall -Wextra -Werror -fopenmp -O3 -std=c11 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsm-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -O3 -std=c17 -Wno-braced-scalar-init -c -o ntsmCount-Options.o test -f 'Options.cpp' || echo '$SRC_DIR/src/'Options.cpp + arm64-apple-darwin20.0.0-clang -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR/src -I$SRC_DIR/vendor -I$SRC_DIR -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -I$PREFIX/include -Wall -Wextra -Werror -fopenmp -O3 -std=c11 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsm-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -O3 -std=c17 -Wno-braced-scalar-init -c -o ntsmEval-ntSeqMatchEval.o test -f 'ntSeqMatchEval.cpp' || echo '$SRC_DIR/src/'ntSeqMatchEval.cpp + arm64-apple-darwin20.0.0-clang -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR/src -I$SRC_DIR/vendor -I$SRC_DIR -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -I$PREFIX/include -Wall -Wextra -Werror -fopenmp -O3 -std=c11 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsm-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -O3 -std=c17 -Wno-braced-scalar-init -c -o ntsmEval-Options.o test -f 'Options.cpp' || echo '$SRC_DIR/src/'Options.cpp + arm64-apple-darwin20.0.0-clang -DHAVE_CONFIG_H -I. -I.. -I$SRC_DIR/src -I$SRC_DIR/vendor -I$SRC_DIR -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -I$PREFIX/include -Wall -Wextra -Werror -fopenmp -O3 -std=c11 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsm-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I$PREFIX/include -O3 -std=c17 -Wno-braced-scalar-init -c -o ntsmVCF-ntSeqMatchVCF.o test -f 'ntSeqMatchVCF.cpp' || echo '$SRC_DIR/src/'ntSeqMatchVCF.cpp + make[2]: Leaving directory '$SRC_DIR/src' + make[1]: Leaving directory '$SRC_DIR' +# Last 100 lines of the build log. diff --git a/recipes/ntsm/meta.yaml b/recipes/ntsm/meta.yaml index 1a2baad87299c..7cdef89c45b65 100644 --- a/recipes/ntsm/meta.yaml +++ b/recipes/ntsm/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: True # [win] - number: 0 + number: 1 run_exports: - {{ pin_subpackage('ntsm', max_pin="x") }} diff --git a/recipes/ntstat/meta.yaml b/recipes/ntstat/meta.yaml index e09a889ebcb3c..9485ad61e2fce 100644 --- a/recipes/ntstat/meta.yaml +++ b/recipes/ntstat/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 4cf215c15c2b1035c40a453372e39c3a87c37c4b09b5716ef5a07bba96f9cb99 build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('ntstat', max_pin="x") }} diff --git a/recipes/ntsynt/build_failure.osx-64.yaml b/recipes/ntsynt/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c18350d4ef82f --- /dev/null +++ b/recipes/ntsynt/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 481fa36509229eecd00fc95bcfc9ee9a878e68a9dead043b990bc2e4f9e920ed # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - btllib >=1.7.3,<2.0a0 + - btllib >=1.7.1 + - snakemake + - python >=3.12,<3.13.0a0 + - ncls + - python-igraph + - libcxx >=18 + - llvm-openmp >=18.1.8 + - python_abi 3.12.* *_cp312 + - samtools + - pybedtools + - intervaltree + test: + commands: + - ntSynt -h + imports: + - btllib + about: + home: https://github.com/bcgsc/ntsynt + license: GPL-3.0 + license_file: LICENSE + summary: Detecting multi-genome synteny blocks using minimizer graph mapping + extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/ntsynt_1734150589487/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/ntsynt_1734150589487/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/ntsynt_1734150589487/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/ntsynt_1734150589487/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsynt-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsynt-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsynt-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsynt-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + The Meson build system + Version: 1.6.0 + Source dir: $SRC_DIR + Build dir: $SRC_DIR/build + Build type: native build + Project name: ntSynt + Project version: 1.0.2 + + meson.build:1:0: ERROR: Unable to detect linker for compiler x86_64-apple-darwin13.4.0-clang -Wl,--version -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ntsynt-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_LIBCPP_DISABLE_AVAILABILITY -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + stdout: + stderr: dyld[9816]: Library not loaded: @rpath/libclang-cpp.18.1.dylib + Referenced from: /opt/mambaforge/envs/bioconda/pkgs/clang-18-18.1.8-default_h0c94c6a_5/bin/clang-18 + Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/clang-18-18.1.8-default_h0c94c6a_5/bin/../lib/libclang-cpp.18.1.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-18-18.1.8-default_h0c94c6a_5/bin/../lib/libclang-cpp.18.1.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-18-18.1.8-default_h0c94c6a_5/bin/../lib/libclang-cpp.18.1.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/clang-18-18.1.8-default_h0c94c6a_5/bin/../lib/libclang-cpp.18.1.dylib' (no such file), '/usr/local/lib/libclang-cpp.18.1.dylib' (no such file), '/usr/lib/libclang-cpp.18.1.dylib' (no such file, not in dyld cache) + + + A full log can be found at $SRC_DIR/build/meson-logs/meson-log.txt +# Last 100 lines of the build log. diff --git a/recipes/ntsynt/meta.yaml b/recipes/ntsynt/meta.yaml index 96b331202d4a4..6582fa58828c1 100644 --- a/recipes/ntsynt/meta.yaml +++ b/recipes/ntsynt/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 6ada92dfe51dec8cd47900a5c41ee3c649cc95777eb81fe860e10748ce04e133 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("ntsynt", max_pin="x") }} diff --git a/recipes/nucleosome_prediction/meta.yaml b/recipes/nucleosome_prediction/meta.yaml index 73b807d4bdfc2..bb9ba3c92915a 100644 --- a/recipes/nucleosome_prediction/meta.yaml +++ b/recipes/nucleosome_prediction/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 9d175f00c201b8adc8f65b211b576517f94750e4150c59b8f1803e5a755a0b17 build: - number: 6 + number: 7 skip: True # [osx] requirements: diff --git a/recipes/nwalign3/build_failure.linux-64.yaml b/recipes/nwalign3/build_failure.linux-64.yaml index 61c30299dbffa..4883b0f200040 100644 --- a/recipes/nwalign3/build_failure.linux-64.yaml +++ b/recipes/nwalign3/build_failure.linux-64.yaml @@ -1,22 +1,10 @@ -recipe_sha: dbf9df6c34d006d9f1dd02bf9957d314595c9c369729e51601d1310bcde9c051 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 04b0f169ca262943b2607ed21913ab873a6734264f88c0e10e7aff6d18f85aa0 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- - | ^~~~~~~~~~ - nwalign3/cnwalign.c:8651:13: error: invalid use of incomplete typedef 'PyFrameObject' {aka 'struct _frame'} - 8651 | py_frame->f_lineno = __pyx_lineno; - | ^~ - nwalign3/cnwalign.c: At top level: - nwalign3/cnwalign.c:5716:13: warning: '__pyx_pf_5numpy_7ndarray___releasebuffer__' defined but not used [-Wunused-function] - 5716 | static void __pyx_pf_5numpy_7ndarray___releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - nwalign3/cnwalign.c:4911:12: warning: '__pyx_pf_5numpy_7ndarray___getbuffer__' defined but not used [-Wunused-function] - 4911 | static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - In file included from /opt/conda/conda-bld/nwalign3_1717531771200/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:21: - /opt/conda/conda-bld/nwalign3_1717531771200/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.11/site-packages/numpy/core/include/numpy/__multiarray_api.h:1477:1: warning: '_import_array' defined but not used [-Wunused-function] - 1477 | _import_array(void) + /opt/conda/conda-bld/nwalign3_1734733372616/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.12/site-packages/numpy/core/include/numpy/__multiarray_api.h:1483:1: warning: '_import_array' defined but not used [-Wunused-function] + 1483 | _import_array(void) | ^~~~~~~~~~~~~ - error: command '/opt/conda/conda-bld/nwalign3_1717531771200/_build_env/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1 + error: command '/opt/conda/conda-bld/nwalign3_1734733372616/_build_env/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1 [1;31merror[0m: [1msubprocess-exited-with-error[0m [31m[0m [32mpython setup.py bdist_wheel[0m did not run successfully. @@ -24,7 +12,7 @@ log: |2- [31m>[0m See above for output. [1;35mnote[0m: This error originates from a subprocess, and is likely not a problem with pip. - [1;35mfull command[0m: [34m/opt/conda/conda-bld/nwalign3_1717531771200/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python -u -c '[0m + [1;35mfull command[0m: [34m/opt/conda/conda-bld/nwalign3_1734733372616/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python -u -c '[0m [34m exec(compile('"'"''"'"''"'"'[0m [34m # This is -- a caller that pip uses to run setup.py[0m [34m #[0m @@ -59,46 +47,60 @@ log: |2- [34m setup_py_code = "from setuptools import setup; setup()"[0m [34m [0m [34m exec(compile(setup_py_code, filename, "exec"))[0m - [34m '"'"''"'"''"'"' % ('"'"'/opt/conda/conda-bld/nwalign3_1717531771200/work/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-_0o4tfsq[0m - [1;35mcwd[0m: /opt/conda/conda-bld/nwalign3_1717531771200/work/ + [34m '"'"''"'"''"'"' % ('"'"'/opt/conda/conda-bld/nwalign3_1734733372616/work/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-63ddgief[0m + [1;35mcwd[0m: /opt/conda/conda-bld/nwalign3_1734733372616/work/ Building wheel for nwalign3 (setup.py): finished with status 'error' [31m ERROR: Failed building wheel for nwalign3[0m[31m [0m Running setup.py clean for nwalign3 Running command python setup.py clean + /opt/conda/conda-bld/nwalign3_1734733372616/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.12/site-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' + warnings.warn(msg) running clean - removing 'build/temp.linux-x86_64-cpython-311' (and everything under it) - removing 'build/lib.linux-x86_64-cpython-311' (and everything under it) + removing 'build/temp.linux-x86_64-cpython-312' (and everything under it) + removing 'build/lib.linux-x86_64-cpython-312' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it - 'build/scripts-3.11' does not exist -- can't clean it + 'build/scripts-3.12' does not exist -- can't clean it removing 'build' Failed to build nwalign3 - [31mERROR: Could not build wheels for nwalign3, which is required to install pyproject.toml-based projects[0m[31m + [31mERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (nwalign3)[0m[31m [0mException information: Traceback (most recent call last): - File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + ^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper return func(self, options, args) ^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.11/site-packages/pip/_internal/commands/install.py", line 429, in run + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 434, in run raise InstallationError( - pip._internal.exceptions.InstallationError: Could not build wheels for nwalign3, which is required to install pyproject.toml-based projects - Removed build tracker: '/tmp/pip-build-tracker-aq9xmljq' + pip._internal.exceptions.InstallationError: ERROR: Failed to build installable wheels for some pyproject.toml based projects (nwalign3) + Removed build tracker: '/tmp/pip-build-tracker-1n4uwr1p' + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/nwalign3_1734733372616/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + Traceback (most recent call last): File "/opt/conda/bin/conda-build", line 11, in sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/nwalign3_1717531771200/work/conda_build.sh']' returned non-zero exit status 1. + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/nwalign3_1734733372616/work/conda_build.sh']' returned non-zero exit status 1. # Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/nwalign3/build_failure.osx-64.yaml b/recipes/nwalign3/build_failure.osx-64.yaml index 7bac99b95b646..bb169bf06b979 100644 --- a/recipes/nwalign3/build_failure.osx-64.yaml +++ b/recipes/nwalign3/build_failure.osx-64.yaml @@ -1,40 +1,37 @@ -recipe_sha: dbf9df6c34d006d9f1dd02bf9957d314595c9c369729e51601d1310bcde9c051 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 04b0f169ca262943b2607ed21913ab873a6734264f88c0e10e7aff6d18f85aa0 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/nwalign3_1717520451013/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/nwalign3_1717520451013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/nwalign3_1717520451013/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/nwalign3_1717520451013/work +log: |2- + home: https://github.com/briney/nwalign3 + license: BSD + summary: Updated version of nwalign with Python 3.x compatibility. + extra: + copy_test_source_files: true + final: true + identifiers: + - biotools:nwalign3 + recipe-maintainers: + - alienzj + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/nwalign3_1734714426033/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/nwalign3_1734714426033/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/nwalign3_1734714426033/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/nwalign3_1734714426033/work INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as CC=x86_64-apple-darwin13.4.0-clang CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/nwalign3-0.1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/nwalign3_1717520451013/work/conda_build.sh']' returned non-zero exit status 1. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/nwalign3-0.1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool @@ -43,7 +40,7 @@ log: |- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -52,7 +49,7 @@ log: |- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -64,41 +61,46 @@ log: |- ac_cv_func_realloc_0_nonnull=yes build_alias=x86_64-apple-darwin13.4.0 host_alias=x86_64-apple-darwin13.4.0 - Using pip 24.0 from $PREFIX/lib/python3.12/site-packages/pip (python 3.12) + Using pip 24.3.1 from $PREFIX/lib/python3.12/site-packages/pip (python 3.12) Non-user install because user site-packages disabled Ignoring indexes: https://pypi.org/simple - Created temporary directory: /private/tmp/pip-build-tracker-0tezvuvu - Initialized build tracking at /private/tmp/pip-build-tracker-0tezvuvu - Created build tracker: /private/tmp/pip-build-tracker-0tezvuvu - Entered build tracker: /private/tmp/pip-build-tracker-0tezvuvu - Created temporary directory: /private/tmp/pip-install-6vpcfiwl - Created temporary directory: /private/tmp/pip-ephem-wheel-cache-w5jx5jvm + Created temporary directory: /private/tmp/pip-build-tracker-n6at_uy5 + Initialized build tracking at /private/tmp/pip-build-tracker-n6at_uy5 + Created build tracker: /private/tmp/pip-build-tracker-n6at_uy5 + Entered build tracker: /private/tmp/pip-build-tracker-n6at_uy5 + Created temporary directory: /private/tmp/pip-install-4pfrt_hu + Created temporary directory: /private/tmp/pip-ephem-wheel-cache-wyo50zkg Processing $SRC_DIR - Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-0tezvuvu' + Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-n6at_uy5' Running setup.py (path:$SRC_DIR/setup.py) egg_info for package from file://$SRC_DIR - Created temporary directory: /private/tmp/pip-pip-egg-info-b0asuy5a + Created temporary directory: /private/tmp/pip-pip-egg-info-nfudaq_6 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Source in $SRC_DIR has version 0.1.2, which satisfies requirement nwalign3==0.1.2 from file://$SRC_DIR - Removed nwalign3==0.1.2 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-0tezvuvu' - Created temporary directory: /private/tmp/pip-unpack-hj1h28km + Removed nwalign3==0.1.2 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-n6at_uy5' + Created temporary directory: /private/tmp/pip-unpack-g2qfpe9u Building wheels for collected packages: nwalign3 - Created temporary directory: /private/tmp/pip-wheel-tivhluca + Created temporary directory: /private/tmp/pip-wheel-mhzmz5b4 Building wheel for nwalign3 (setup.py): started - Destination directory: /private/tmp/pip-wheel-tivhluca + Destination directory: /private/tmp/pip-wheel-mhzmz5b4 Building wheel for nwalign3 (setup.py): finished with status 'error' Running setup.py clean for nwalign3 Failed to build nwalign3 Exception information: Traceback (most recent call last): - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + ^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper return func(self, options, args) ^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 429, in run + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 434, in run raise InstallationError( - pip._internal.exceptions.InstallationError: Could not build wheels for nwalign3, which is required to install pyproject.toml-based projects - Removed build tracker: '/private/tmp/pip-build-tracker-0tezvuvu' + pip._internal.exceptions.InstallationError: ERROR: Failed to build installable wheels for some pyproject.toml based projects (nwalign3) + Removed build tracker: '/private/tmp/pip-build-tracker-n6at_uy5' # Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/nwalign3/meta.yaml b/recipes/nwalign3/meta.yaml index 753b97b146095..4bb7694932c7a 100644 --- a/recipes/nwalign3/meta.yaml +++ b/recipes/nwalign3/meta.yaml @@ -19,6 +19,7 @@ requirements: host: - pip - python + - setuptools - cython - numpy run: diff --git a/recipes/nxtrim/meta.yaml b/recipes/nxtrim/meta.yaml index fa421b6f49534..01e2a89780e7f 100644 --- a/recipes/nxtrim/meta.yaml +++ b/recipes/nxtrim/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://github.com/sequencing/{{ name }}/archive/v{{ version }}.tar.gz diff --git a/recipes/oarfish/meta.yaml b/recipes/oarfish/meta.yaml index 0deb4d8fac6fc..4cabd57108d39 100644 --- a/recipes/oarfish/meta.yaml +++ b/recipes/oarfish/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("oarfish", max_pin="x.x") }} diff --git a/recipes/oatk/meta.yaml b/recipes/oatk/meta.yaml index d3b3d028c7c8e..cb1d7ecacee33 100644 --- a/recipes/oatk/meta.yaml +++ b/recipes/oatk/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 5d1a1f44750dac04b436b99f6877b531b19e2e87a3eab956627fbb5e70af463c build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('oatk', max_pin="x") }} diff --git a/recipes/occultercut/meta.yaml b/recipes/occultercut/meta.yaml index 9cee221adf90c..b0fb21cc6cbb4 100644 --- a/recipes/occultercut/meta.yaml +++ b/recipes/occultercut/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 34aa8c3ef4c216435b4f722ea25f9dc431ef6937e47cfeb5afa323d451cc06ae build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('occultercut', max_pin="x") }} diff --git a/recipes/ococo/meta.yaml b/recipes/ococo/meta.yaml index 833d6bc60930d..30ad6646523f2 100644 --- a/recipes/ococo/meta.yaml +++ b/recipes/ococo/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 9 + number: 10 source: - url: https://github.com/karel-brinda/ococo/archive/{{ version }}.tar.gz diff --git a/recipes/odgi/meta.yaml b/recipes/odgi/meta.yaml index 4de1264118239..bffb04375d306 100644 --- a/recipes/odgi/meta.yaml +++ b/recipes/odgi/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/oligomap/meta.yaml b/recipes/oligomap/meta.yaml index 8219cb0ada660..b277e06b85d8d 100644 --- a/recipes/oligomap/meta.yaml +++ b/recipes/oligomap/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 0dba5ca4a4ed098c129a7558115d6d48bbb9ce2f0fe508e46181b017ef51eb85 build: - number: 0 + number: 1 binary_relocation: true script: - cmake -H. -Bbuild_conda -G "${CMAKE_GENERATOR}" -DCMAKE_INSTALL_PREFIX=${PREFIX} diff --git a/recipes/oncocnv/meta.yaml b/recipes/oncocnv/meta.yaml index 24e9277704806..2aed573fadb95 100644 --- a/recipes/oncocnv/meta.yaml +++ b/recipes/oncocnv/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/ont-modkit/build_failure.osx-64.yaml b/recipes/ont-modkit/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c0a5e28b8ce0e --- /dev/null +++ b/recipes/ont-modkit/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: e8dd7fcd136254fce3db3c90b0805da3a984d5800fe2a97829064054b6fa5ae4 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - autoconf 2.71 pl5321hed12c24_1 + - ncurses 6.5 hf036a51_1 + - m4 1.4.18 haf1e3a3_1001 + - clang-18 18.1.8 default_h0c94c6a_5 + - libcurl 8.11.1 h5dec5d8_0 + - make 4.4.1 h00291cd_2 + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + - clang_osx-64 18.1.8 h7e5c614_23 + - macosx_deployment_target_osx-64 14.5 h5d9aa64_2 + - llvm-tools 18.1.8 h9ce406d_2 + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/ont-modkit_1734473548296/work/conda_build.sh']' returned non-zero exit status 101. + - krb5 1.21.3 h37d8d59_0 + - clangxx 18.1.8 default_h179603d_5 + - pkg-config 0.29.2 hf7e621a_1009 + - c-ares 1.34.4 hf13058a_0 + - zstd 1.5.6 h915ae27_0 + host: + - libcxx 19.1.5 hf95d169_0 + - libzlib 1.3.1 hd23fc13_2 + - zlib 1.3.1 hd23fc13_2 + run: + - libcxx >=18 + - libzlib >=1.3.1,<2.0a0 + run_constrained: + - __osx >=10.13 + test: + commands: + - modkit --version + about: + dev_url: https://github.com/nanoporetech/modkit + doc_url: https://nanoporetech.github.io/modkit/ + home: https://github.com/nanoporetech/modkit + license: Oxford Nanopore Technologies PLC. Public License Version 1.0 + license_family: PROPRIETARY + license_file: LICENCE.txt + summary: A bioinformatics tool for working with modified bases in Oxford Nanopore + sequencing data. + extra: + additional-platforms: + - linux-aarch64 + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/ont-modkit_1734473548296/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/ont-modkit_1734473548296/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/ont-modkit_1734473548296/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/ont-modkit_1734473548296/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ont-modkit-0.4.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ont-modkit-0.4.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ont-modkit-0.4.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ont-modkit-0.4.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/ont-modkit/meta.yaml b/recipes/ont-modkit/meta.yaml index f6a36fb5d4699..f20790e60fe66 100644 --- a/recipes/ont-modkit/meta.yaml +++ b/recipes/ont-modkit/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("ont-modkit", max_pin="x.x") }} diff --git a/recipes/ont_vbz_hdf_plugin/build_failure.linux-64.yaml b/recipes/ont_vbz_hdf_plugin/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..dd7dfcf1096f9 --- /dev/null +++ b/recipes/ont_vbz_hdf_plugin/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 6336155997d8a8d281d61a092ce29176e5fda3b6ee5fff392a1d2248c2118f7f # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + LIBRARY_PATH=/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib/../lib/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../lib/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/lib/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/ + COLLECT_GCC_OPTIONS='-std=c99' '-O3' '-D' 'NDEBUG' '-L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/lib' '-v' '-rdynamic' '-o' 'writeseq' '-std=c99' '-fPIC' '-Wextra' '-Wpedantic' '-Wshadow' '-O3' '-g' '-mtune=generic' '-march=x86-64' '-dumpdir' 'writeseq.' + /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../libexec/gcc/x86_64-conda-linux-gnu/13.3.0/collect2 -plugin /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../libexec/gcc/x86_64-conda-linux-gnu/13.3.0/liblto_plugin.so -plugin-opt=/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../libexec/gcc/x86_64-conda-linux-gnu/13.3.0/lto-wrapper -plugin-opt=-fresolution=/tmp/ccOQbyVK.res -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s --sysroot=/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot --eh-frame-hdr -m elf_x86_64 -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -o writeseq /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/Scrt1.o /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/crti.o /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/crtbeginS.o -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0 -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib/../lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../.. -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib --dependency-file=CMakeFiles/writeseq.dir/link.d CMakeFiles/writeseq.dir/tests/writeseq.c.o libstreamvbyte_static.a -lgcc --push-state --as-needed -lgcc_s --pop-state -lc -lgcc --push-state --as-needed -lgcc_s --pop-state /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/crtendS.o /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/crtn.o -rpath /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/lib + COLLECT_GCC_OPTIONS='-std=c99' '-O3' '-D' 'NDEBUG' '-L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/lib' '-v' '-rdynamic' '-o' 'example' '-std=c99' '-fPIC' '-Wextra' '-Wpedantic' '-Wshadow' '-O3' '-g' '-mtune=generic' '-march=x86-64' '-dumpdir' 'example.' + [ 95%] Linking C executable perf + Reading specs from /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/specs + could not find specs file conda.specs + COLLECT_GCC=/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/x86_64-conda-linux-gnu-cc + COLLECT_LTO_WRAPPER=/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../libexec/gcc/x86_64-conda-linux-gnu/13.3.0/lto-wrapper + Target: x86_64-conda-linux-gnu + Configured with: ../configure --prefix=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho --with-slibdir=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib --libdir=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib --mandir=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/man --build=x86_64-conda-linux-gnu --host=x86_64-conda-linux-gnu --target=x86_64-conda-linux-gnu --enable-languages=c,c,fortran,objc,obj-c --enable-__cxa_atexit --disable-libmudflap --enable-libgomp --disable-libssp --enable-libquadmath --enable-libquadmath-support --enable-lto --enable-target-optspace --enable-plugin --enable-gold --disable-nls --disable-bootstrap --disable-multilib --enable-long-long --with-sysroot=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/x86_64-conda-linux-gnu/sysroot --with-build-sysroot=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/work/cf-compilers/x86_64-conda-linux-gnu/sysroot --with-native-system-header-dir=/usr/include --with-gxx-include-dir=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c --with-pkgversion='conda-forge gcc 13.3.0-1' --with-bugurl=https://github.com/conda-forge/ctng-compilers-feedstock/issues/new/choose --enable-libsanitizer --enable-default-pie --enable-threads=posix + Thread model: posix + Supported LTO compression algorithms: zlib + gcc version 13.3.0 (conda-forge gcc 13.3.0-1) + COMPILER_PATH=/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../libexec/gcc/x86_64-conda-linux-gnu/13.3.0/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../libexec/gcc/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ + LIBRARY_PATH=/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib/../lib/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../lib/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/lib/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/ + COLLECT_GCC_OPTIONS='-std=c99' '-O3' '-D' 'NDEBUG' '-L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/lib' '-v' '-rdynamic' '-o' 'perf' '-std=c99' '-fPIC' '-Wextra' '-Wpedantic' '-Wshadow' '-O3' '-g' '-mtune=generic' '-march=x86-64' '-dumpdir' 'perf.' + /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../libexec/gcc/x86_64-conda-linux-gnu/13.3.0/collect2 -plugin /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../libexec/gcc/x86_64-conda-linux-gnu/13.3.0/liblto_plugin.so -plugin-opt=/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../libexec/gcc/x86_64-conda-linux-gnu/13.3.0/lto-wrapper -plugin-opt=-fresolution=/tmp/ccmLdqoN.res -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s --sysroot=/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot --eh-frame-hdr -m elf_x86_64 -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -o perf /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/Scrt1.o /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/crti.o /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/crtbeginS.o -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0 -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib/../lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../.. -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib --dependency-file=CMakeFiles/perf.dir/link.d CMakeFiles/perf.dir/tests/perf.c.o libstreamvbyte_static.a -lm -lgcc --push-state --as-needed -lgcc_s --pop-state -lc -lgcc --push-state --as-needed -lgcc_s --pop-state /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/crtendS.o /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/crtn.o -rpath /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/lib + [ 95%] Built target example + COLLECT_GCC_OPTIONS='-std=c99' '-O3' '-D' 'NDEBUG' '-L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/lib' '-v' '-rdynamic' '-o' 'writeseq' '-std=c99' '-fPIC' '-Wextra' '-Wpedantic' '-Wshadow' '-O3' '-g' '-mtune=generic' '-march=x86-64' '-dumpdir' 'writeseq.' + [ 95%] Built target writeseq + COLLECT_GCC_OPTIONS='-std=c99' '-O3' '-D' 'NDEBUG' '-L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/lib' '-v' '-rdynamic' '-o' 'perf' '-std=c99' '-fPIC' '-Wextra' '-Wpedantic' '-Wshadow' '-O3' '-g' '-mtune=generic' '-march=x86-64' '-dumpdir' 'perf.' + [ 95%] Built target perf + [100%] Linking C executable unit + Reading specs from /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/specs + could not find specs file conda.specs + COLLECT_GCC=/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/x86_64-conda-linux-gnu-cc + COLLECT_LTO_WRAPPER=/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../libexec/gcc/x86_64-conda-linux-gnu/13.3.0/lto-wrapper + Target: x86_64-conda-linux-gnu + Configured with: ../configure --prefix=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho --with-slibdir=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib --libdir=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib --mandir=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/man --build=x86_64-conda-linux-gnu --host=x86_64-conda-linux-gnu --target=x86_64-conda-linux-gnu --enable-languages=c,c,fortran,objc,obj-c --enable-__cxa_atexit --disable-libmudflap --enable-libgomp --disable-libssp --enable-libquadmath --enable-libquadmath-support --enable-lto --enable-target-optspace --enable-plugin --enable-gold --disable-nls --disable-bootstrap --disable-multilib --enable-long-long --with-sysroot=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/x86_64-conda-linux-gnu/sysroot --with-build-sysroot=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/work/cf-compilers/x86_64-conda-linux-gnu/sysroot --with-native-system-header-dir=/usr/include --with-gxx-include-dir=/home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c --with-pkgversion='conda-forge gcc 13.3.0-1' --with-bugurl=https://github.com/conda-forge/ctng-compilers-feedstock/issues/new/choose --enable-libsanitizer --enable-default-pie --enable-threads=posix + Thread model: posix + Supported LTO compression algorithms: zlib + gcc version 13.3.0 (conda-forge gcc 13.3.0-1) + COMPILER_PATH=/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../libexec/gcc/x86_64-conda-linux-gnu/13.3.0/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../libexec/gcc/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ + LIBRARY_PATH=/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib/../lib/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../lib/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/lib/:/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/ + COLLECT_GCC_OPTIONS='-std=c99' '-O3' '-D' 'NDEBUG' '-L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/lib' '-v' '-rdynamic' '-o' 'unit' '-std=c99' '-fPIC' '-Wextra' '-Wpedantic' '-Wshadow' '-O3' '-g' '-mtune=generic' '-march=x86-64' '-dumpdir' 'unit.' + /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../libexec/gcc/x86_64-conda-linux-gnu/13.3.0/collect2 -plugin /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../libexec/gcc/x86_64-conda-linux-gnu/13.3.0/liblto_plugin.so -plugin-opt=/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../libexec/gcc/x86_64-conda-linux-gnu/13.3.0/lto-wrapper -plugin-opt=-fresolution=/tmp/ccQqJBJR.res -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s --sysroot=/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot --eh-frame-hdr -m elf_x86_64 -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -o unit /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/Scrt1.o /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/crti.o /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/crtbeginS.o -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0 -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib/../lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/lib/../lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../.. -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/lib -L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib --dependency-file=CMakeFiles/unit.dir/link.d CMakeFiles/unit.dir/tests/unit.c.o libstreamvbyte_static.a -lgcc --push-state --as-needed -lgcc_s --pop-state -lc -lgcc --push-state --as-needed -lgcc_s --pop-state /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/crtendS.o /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/bin/../x86_64-conda-linux-gnu/sysroot/usr/lib/../lib/crtn.o -rpath /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/lib + COLLECT_GCC_OPTIONS='-std=c99' '-O3' '-D' 'NDEBUG' '-L/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/_build_env/lib' '-v' '-rdynamic' '-o' 'unit' '-std=c99' '-fPIC' '-Wextra' '-Wpedantic' '-Wshadow' '-O3' '-g' '-mtune=generic' '-march=x86-64' '-dumpdir' 'unit.' + [100%] Built target unit + [ 39%] Performing install step for 'streamvbyte' + [ 66%] Built target streamvbyte + [ 66%] Built target streamvbyte_static + [ 95%] Built target writeseq + [ 95%] Built target perf + [100%] Built target example + [100%] Built target unit + Install the project... + -- Install configuration: "Release" + -- Installing: $SRC_DIR/build/streamvbyte_lib/include/streamvbyte.h + -- Installing: $SRC_DIR/build/streamvbyte_lib/include/streamvbytedelta.h + -- Installing: $SRC_DIR/build/streamvbyte_lib/include/streamvbyte_zigzag.h + -- Installing: $SRC_DIR/build/streamvbyte_lib/lib/libstreamvbyte.so + -- Installing: $SRC_DIR/build/streamvbyte_lib/lib/libstreamvbyte_static.a + [ 43%] Completed 'streamvbyte' + [ 43%] Built target streamvbyte + [ 47%] Building CXX object vbz/CMakeFiles/vbz.dir/v1/vbz_streamvbyte.cpp.o + [ 52%] Building CXX object vbz/CMakeFiles/vbz.dir/v0/vbz_streamvbyte.cpp.o + [ 56%] Building CXX object vbz/CMakeFiles/vbz.dir/vbz.cpp.o + /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/work/vbz/vbz.cpp: In function 'vbz_size_t vbz_decompress_sized(const void*, vbz_size_t, void*, vbz_size_t, const CompressionOptions*)': + /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/work/vbz/vbz.cpp:314:17: error: possibly dangling reference to a temporary [-Werror=dangling-reference] + 314 | auto const& source_header = source_buffer.subspan(0, sizeof(VbzSizedHeader)).as_span()[0]; + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/work/vbz/vbz.cpp:314:115: note: the temporary was destroyed at the end of the full expression 'source_buffer.gsl::span::subspan(0, sizeof ({anonymous}::VbzSizedHeader)).gsl::span::as_span().gsl::span::operator[](0)' + 314 | auto const& source_header = source_buffer.subspan(0, sizeof(VbzSizedHeader)).as_span()[0]; + | ^ + /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/work/vbz/vbz.cpp: In function 'vbz_size_t vbz_decompressed_size(const void*, vbz_size_t, const CompressionOptions*)': + /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/work/vbz/vbz.cpp:338:17: error: possibly dangling reference to a temporary [-Werror=dangling-reference] + 338 | auto const& source_header = source_buffer.subspan(0, sizeof(VbzSizedHeader)).as_span()[0]; + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/work/vbz/vbz.cpp:338:115: note: the temporary was destroyed at the end of the full expression 'source_buffer.gsl::span::subspan(0, sizeof ({anonymous}::VbzSizedHeader)).gsl::span::as_span().gsl::span::operator[](0)' + 338 | auto const& source_header = source_buffer.subspan(0, sizeof(VbzSizedHeader)).as_span()[0]; + | ^ + cc1plus: all warnings being treated as errors + make[2]: *** [vbz/CMakeFiles/vbz.dir/build.make:107: vbz/CMakeFiles/vbz.dir/vbz.cpp.o] Error 1 + make[2]: *** Waiting for unfinished jobs.... + make[1]: *** [CMakeFiles/Makefile2:1149: vbz/CMakeFiles/vbz.dir/all] Error 2 + make: *** [Makefile:166: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ont_vbz_hdf_plugin_1734293740924/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/ont_vbz_hdf_plugin/meta.yaml b/recipes/ont_vbz_hdf_plugin/meta.yaml index 6bd574d7be07a..b2ae8f0457fd1 100644 --- a/recipes/ont_vbz_hdf_plugin/meta.yaml +++ b/recipes/ont_vbz_hdf_plugin/meta.yaml @@ -9,7 +9,9 @@ source: git_rev: v{{ version }} build: - number: 6 + number: 7 + run_exports: + - {{ pin_subpackage("ont_vbz_hdf_plugin", max_pin="x") }} extra: skip-lints: diff --git a/recipes/ontime/build_failure.linux-64.yaml b/recipes/ontime/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..e516d6e007e4a --- /dev/null +++ b/recipes/ontime/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5bba5fe576c6ca64bd31bd54f2c1c9c110644b0353379103f2a026d462dc1c0f # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + Compiling linux-raw-sys v0.4.10 + Running rustc --crate-name linux_raw_sys --edition=2021 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/linux-raw-sys-0.4.10/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="elf"' --cfg 'feature="errno"' --cfg 'feature="general"' --cfg 'feature="ioctl"' --cfg 'feature="no_std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("compiler_builtins", "core", "default", "elf", "errno", "general", "if_ether", "io_uring", "ioctl", "net", "netlink", "no_std", "prctl", "rustc-dep-of-std", "std", "system"))' -C metadata=1f17b63a56a4304e -C extra-filename=-1f17b63a56a4304e --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --cap-lints allow + Compiling powerfmt v0.2.0 + Running rustc --crate-name powerfmt --edition=2021 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/powerfmt-0.2.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "default", "macros", "std"))' -C metadata=daf7a29ee259131c -C extra-filename=-daf7a29ee259131c --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --cap-lints allow + Compiling colorchoice v1.0.0 + Running rustc --crate-name colorchoice --edition=2021 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/colorchoice-1.0.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=275a79b5fdba1d33 -C extra-filename=-275a79b5fdba1d33 --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --cap-lints allow + Compiling serde v1.0.190 + Running rustc --crate-name build_script_build --edition=2018 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/serde-1.0.190/build.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="default"' --cfg 'feature="derive"' --cfg 'feature="serde_derive"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "default", "derive", "rc", "serde_derive", "std", "unstable"))' -C metadata=418ebe33af5b0ef7 -C extra-filename=-418ebe33af5b0ef7 --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/build/serde-418ebe33af5b0ef7 -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --cap-lints allow + Compiling anstyle-query v1.0.0 + Running rustc --crate-name anstyle_query --edition=2021 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/anstyle-query-1.0.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=dfbfa71bd7176bc1 -C extra-filename=-dfbfa71bd7176bc1 --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --cap-lints allow + Compiling anstream v0.6.4 + Running rustc --crate-name anstream --edition=2021 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/anstream-0.6.4/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="auto"' --cfg 'feature="default"' --cfg 'feature="wincon"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("auto", "default", "test", "wincon"))' -C metadata=c9697c141f433110 -C extra-filename=-c9697c141f433110 --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --extern anstyle=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libanstyle-7f233d31cb3f22b9.rmeta --extern anstyle_parse=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libanstyle_parse-7f4ef08a6f3e57fb.rmeta --extern anstyle_query=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libanstyle_query-dfbfa71bd7176bc1.rmeta --extern colorchoice=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libcolorchoice-275a79b5fdba1d33.rmeta --extern utf8parse=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libutf8parse-4ed97df3ab5e3e41.rmeta --cap-lints allow + Running rustc --crate-name rustix --edition=2021 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/rustix-0.38.21/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="alloc"' --cfg 'feature="default"' --cfg 'feature="std"' --cfg 'feature="termios"' --cfg 'feature="use-libc-auxv"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("all-apis", "alloc", "cc", "default", "event", "fs", "io_uring", "itoa", "libc", "libc_errno", "linux_4_11", "linux_latest", "mm", "mount", "net", "once_cell", "param", "pipe", "process", "procfs", "pty", "rand", "runtime", "rustc-dep-of-std", "shm", "std", "stdio", "system", "termios", "thread", "time", "use-explicitly-provided-auxv", "use-libc", "use-libc-auxv"))' -C metadata=0cd66999510e5787 -C extra-filename=-0cd66999510e5787 --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --extern bitflags=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libbitflags-7948688fab9c192b.rmeta --extern linux_raw_sys=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/liblinux_raw_sys-1f17b63a56a4304e.rmeta --cap-lints allow --cfg static_assertions --cfg linux_raw --cfg linux_like --cfg linux_kernel + Running /opt/conda/conda-bld/ontime_1734064215434/work/target/release/build/serde-418ebe33af5b0ef7/build-script-build + Compiling deranged v0.3.9 + Running rustc --crate-name deranged --edition=2021 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/deranged-0.3.9/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="alloc"' --cfg 'feature="powerfmt"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "default", "num", "powerfmt", "quickcheck", "rand", "serde", "std"))' -C metadata=f605c6323e040482 -C extra-filename=-f605c6323e040482 --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --extern powerfmt=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libpowerfmt-daf7a29ee259131c.rmeta --cap-lints allow + Running /opt/conda/conda-bld/ontime_1734064215434/work/target/release/build/rust_decimal-7e6f4cc22bad2534/build-script-build + Compiling time-macros v0.2.15 + Running rustc --crate-name time_macros --edition=2021 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/time-macros-0.2.15/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type proc-macro --emit=dep-info,link -C prefer-dynamic -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="formatting"' --cfg 'feature="parsing"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("formatting", "large-dates", "parsing", "serde"))' -C metadata=c2a9c14a49ad16b2 -C extra-filename=-c2a9c14a49ad16b2 --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --extern time_core=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libtime_core-732a055c3adb964d.rlib --extern proc_macro --cap-lints allow + Compiling noodles-bam v0.54.1 + Running rustc --crate-name noodles_bam --edition=2021 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-bam-0.54.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("async"))' -C metadata=2657fe1156d1ff96 -C extra-filename=-2657fe1156d1ff96 --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --extern bit_vec=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libbit_vec-1b3c04d97e80c1e1.rmeta --extern bstr=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libbstr-3b13068467058a99.rmeta --extern byteorder=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libbyteorder-b4135b9eba9ebb4c.rmeta --extern bytes=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libbytes-981dc1c1ac88ce0d.rmeta --extern indexmap=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libindexmap-6f1640655a184f80.rmeta --extern noodles_bgzf=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libnoodles_bgzf-7b0e49d82f121243.rmeta --extern noodles_core=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libnoodles_core-11e4020d7d500181.rmeta --extern noodles_csi=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libnoodles_csi-bf658c53d0b64834.rmeta --extern noodles_sam=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libnoodles_sam-ca51520a111c1739.rmeta --cap-lints allow + Compiling md-5 v0.10.6 + Running rustc --crate-name md5 --edition=2018 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/md-5-0.10.6/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("asm", "default", "force-soft", "loongarch64_asm", "md5-asm", "oid", "std"))' -C metadata=e25e3cdccafdd66e -C extra-filename=-e25e3cdccafdd66e --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --extern cfg_if=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libcfg_if-683714872c84c8c9.rmeta --extern digest=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libdigest-37f0ab0e0facc9d5.rmeta --cap-lints allow + Compiling noodles-fasta v0.32.0 + Running rustc --crate-name noodles_fasta --edition=2021 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-fasta-0.32.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("async"))' -C metadata=2f16a17cda9ced00 -C extra-filename=-2f16a17cda9ced00 --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --extern bytes=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libbytes-981dc1c1ac88ce0d.rmeta --extern memchr=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libmemchr-ca403b68c998ac03.rmeta --extern noodles_bgzf=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libnoodles_bgzf-7b0e49d82f121243.rmeta --extern noodles_core=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libnoodles_core-11e4020d7d500181.rmeta --cap-lints allow + Compiling serde_derive v1.0.190 + Running rustc --crate-name serde_derive --edition=2015 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/serde_derive-1.0.190/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type proc-macro --emit=dep-info,link -C prefer-dynamic -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="default"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "deserialize_in_place"))' -C metadata=7eb5d72c65148762 -C extra-filename=-7eb5d72c65148762 --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --extern proc_macro2=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libproc_macro2-698514f2d758bda1.rlib --extern quote=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libquote-19d88228c8726619.rlib --extern syn=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libsyn-270af3d60ef09606.rlib --extern proc_macro --cap-lints allow + Compiling clap_lex v0.6.0 + Running rustc --crate-name clap_lex --edition=2021 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/clap_lex-0.6.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=509227286a1a98f7 -C extra-filename=-509227286a1a98f7 --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --cap-lints allow + Running rustc --crate-name time_core --edition=2021 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/time-core-0.1.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=bcb38a3679361ff7 -C extra-filename=-bcb38a3679361ff7 --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --cap-lints allow + Compiling minimal-lexical v0.2.1 + Running rustc --crate-name minimal_lexical --edition=2018 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/minimal-lexical-0.2.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "compact", "default", "lint", "nightly", "std"))' -C metadata=8a483958edd4d131 -C extra-filename=-8a483958edd4d131 --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --cap-lints allow + Compiling arrayvec v0.7.4 + Running rustc --crate-name arrayvec --edition=2018 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/arrayvec-0.7.4/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "serde", "std", "zeroize"))' -C metadata=5cd38e7e8da9347a -C extra-filename=-5cd38e7e8da9347a --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --cap-lints allow + Compiling itoa v1.0.9 + Running rustc --crate-name itoa --edition=2018 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/itoa-1.0.9/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("no-panic"))' -C metadata=0865bc89f37cb38b -C extra-filename=-0865bc89f37cb38b --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --cap-lints allow + Compiling safemem v0.3.3 + Running rustc --crate-name safemem --edition=2015 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/safemem-0.3.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "std"))' -C metadata=83135c0035ebeae5 -C extra-filename=-83135c0035ebeae5 --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --cap-lints allow + Compiling iana-time-zone v0.1.58 + Running rustc --crate-name iana_time_zone --edition=2018 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/iana-time-zone-0.1.58/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="fallback"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("fallback"))' -C metadata=b8251a853cdee8ac -C extra-filename=-b8251a853cdee8ac --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --cap-lints allow + Compiling strsim v0.10.0 + Running rustc --crate-name strsim --edition=2015 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/strsim-0.10.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=d4476eda60dce166 -C extra-filename=-d4476eda60dce166 --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --cap-lints allow + Compiling heck v0.4.1 + Running rustc --crate-name heck --edition=2018 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/heck-0.4.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="default"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "unicode", "unicode-segmentation"))' -C metadata=adc8b52c5fa99759 -C extra-filename=-adc8b52c5fa99759 --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --cap-lints allow + Compiling anyhow v1.0.75 + Running rustc --crate-name build_script_build --edition=2018 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/anyhow-1.0.75/build.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("backtrace", "default", "std"))' -C metadata=a5f76368bb9811e7 -C extra-filename=-a5f76368bb9811e7 --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/build/anyhow-a5f76368bb9811e7 -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --cap-lints allow + Running /opt/conda/conda-bld/ontime_1734064215434/work/target/release/build/anyhow-a5f76368bb9811e7/build-script-build + Compiling clap_derive v4.4.7 + Running rustc --crate-name clap_derive --edition=2021 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/clap_derive-4.4.7/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type proc-macro --emit=dep-info,link -C prefer-dynamic -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="default"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("debug", "default", "deprecated", "raw-deprecated", "unstable-v5"))' -C metadata=af6703345b7e02f3 -C extra-filename=-af6703345b7e02f3 --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --extern heck=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libheck-adc8b52c5fa99759.rlib --extern proc_macro2=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libproc_macro2-698514f2d758bda1.rlib --extern quote=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libquote-19d88228c8726619.rlib --extern syn=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libsyn-270af3d60ef09606.rlib --extern proc_macro --cap-lints allow + Compiling clap_builder v4.4.7 + Running rustc --crate-name clap_builder --edition=2021 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/clap_builder-4.4.7/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="color"' --cfg 'feature="error-context"' --cfg 'feature="help"' --cfg 'feature="std"' --cfg 'feature="suggestions"' --cfg 'feature="usage"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("cargo", "color", "debug", "default", "deprecated", "env", "error-context", "help", "std", "string", "suggestions", "unicode", "unstable-doc", "unstable-styles", "unstable-v5", "usage", "wrap_help"))' -C metadata=3bbf954755057f8d -C extra-filename=-3bbf954755057f8d --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --extern anstream=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libanstream-c9697c141f433110.rmeta --extern anstyle=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libanstyle-7f233d31cb3f22b9.rmeta --extern clap_lex=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libclap_lex-509227286a1a98f7.rmeta --extern strsim=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libstrsim-d4476eda60dce166.rmeta --cap-lints allow + Compiling chrono v0.4.31 + Running rustc --crate-name chrono --edition=2021 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/chrono-0.4.31/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="android-tzdata"' --cfg 'feature="clock"' --cfg 'feature="default"' --cfg 'feature="iana-time-zone"' --cfg 'feature="js-sys"' --cfg 'feature="oldtime"' --cfg 'feature="std"' --cfg 'feature="wasm-bindgen"' --cfg 'feature="wasmbind"' --cfg 'feature="winapi"' --cfg 'feature="windows-targets"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("__internal_bench", "alloc", "android-tzdata", "arbitrary", "clock", "default", "iana-time-zone", "js-sys", "libc", "oldtime", "pure-rust-locales", "rkyv", "rustc-serialize", "serde", "std", "unstable-locales", "wasm-bindgen", "wasmbind", "winapi", "windows-targets"))' -C metadata=e51feb06cf2cb31e -C extra-filename=-e51feb06cf2cb31e --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --extern iana_time_zone=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libiana_time_zone-b8251a853cdee8ac.rmeta --extern num_traits=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libnum_traits-500558dcd80592f9.rmeta --cap-lints allow + Running rustc --crate-name serde --edition=2018 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/serde-1.0.190/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="derive"' --cfg 'feature="serde_derive"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "default", "derive", "rc", "serde_derive", "std", "unstable"))' -C metadata=38edc700bd06876a -C extra-filename=-38edc700bd06876a --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --extern serde_derive=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libserde_derive-7eb5d72c65148762.so --cap-lints allow + Compiling buffer-redux v1.0.0 + Running rustc --crate-name buffer_redux --edition=2021 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/buffer-redux-1.0.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "slice-deque"))' -C metadata=de5bdfd52d5d72c6 -C extra-filename=-de5bdfd52d5d72c6 --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --extern memchr=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libmemchr-ca403b68c998ac03.rmeta --extern safemem=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libsafemem-83135c0035ebeae5.rmeta --cap-lints allow + Compiling time v0.3.30 + Running rustc --crate-name time --edition=2021 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/time-0.3.30/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="alloc"' --cfg 'feature="default"' --cfg 'feature="formatting"' --cfg 'feature="macros"' --cfg 'feature="parsing"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "default", "formatting", "large-dates", "local-offset", "macros", "parsing", "quickcheck", "rand", "serde", "serde-human-readable", "serde-well-known", "std", "wasm-bindgen"))' -C metadata=97a55092693d42bd -C extra-filename=-97a55092693d42bd --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --extern deranged=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libderanged-f605c6323e040482.rmeta --extern itoa=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libitoa-0865bc89f37cb38b.rmeta --extern powerfmt=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libpowerfmt-daf7a29ee259131c.rmeta --extern time_core=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libtime_core-bcb38a3679361ff7.rmeta --extern time_macros=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libtime_macros-c2a9c14a49ad16b2.so --cap-lints allow + error[E0282]: type annotations needed for Box<_> + --> /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/time-0.3.30/src/format_description/parse/mod.rs:83:9 + | + 83 | let items = format_items + | ^^^^^ + ... + 86 | Ok(items.into()) + | ---- type must be known at this point + | + = note: this is an inference error on crate time caused by an API change in Rust 1.80.0; update time to version >=0.3.35 by calling cargo update + + For more information about this error, try rustc --explain E0282. + error: could not compile time (lib) due to 1 previous error + + Caused by: + process didn't exit successfully: rustc --crate-name time --edition=2021 /home/conda/.cargo/registry/src/index.crates.io-6f17d22bba15001f/time-0.3.30/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="alloc"' --cfg 'feature="default"' --cfg 'feature="formatting"' --cfg 'feature="macros"' --cfg 'feature="parsing"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "default", "formatting", "large-dates", "local-offset", "macros", "parsing", "quickcheck", "rand", "serde", "serde-human-readable", "serde-well-known", "std", "wasm-bindgen"))' -C metadata=97a55092693d42bd -C extra-filename=-97a55092693d42bd --out-dir /opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps -C linker=/opt/conda/conda-bld/ontime_1734064215434/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps --extern deranged=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libderanged-f605c6323e040482.rmeta --extern itoa=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libitoa-0865bc89f37cb38b.rmeta --extern powerfmt=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libpowerfmt-daf7a29ee259131c.rmeta --extern time_core=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libtime_core-bcb38a3679361ff7.rmeta --extern time_macros=/opt/conda/conda-bld/ontime_1734064215434/work/target/release/deps/libtime_macros-c2a9c14a49ad16b2.so --cap-lints allow (exit status: 1) + warning: build failed, waiting for other jobs to finish... + error: failed to compile ontime v0.3.1 (/opt/conda/conda-bld/ontime_1734064215434/work), intermediate artifacts can be found at /opt/conda/conda-bld/ontime_1734064215434/work/target. + To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ontime_1734064215434/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ontime_1734064215434/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. diff --git a/recipes/ontime/build_failure.osx-64.yaml b/recipes/ontime/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..e1b3173170414 --- /dev/null +++ b/recipes/ontime/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5bba5fe576c6ca64bd31bd54f2c1c9c110644b0353379103f2a026d462dc1c0f # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - libllvm18 18.1.8 h9ce406d_2 + - sigtool 0.1.3 h88f4db0_0 + - ld64_osx-64 951.9 hc8d1a19_2 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + - libclang-cpp18.1 18.1.8 default_h0c94c6a_5 + - llvm-tools-18 18.1.8 h9ce406d_2 + - clang-18 18.1.8 default_h0c94c6a_5 + - llvm-tools 18.1.8 h9ce406d_2 + - cctools_osx-64 1010.6 h00edd4c_2 + - clang 18.1.8 default_h179603d_5 + - clangxx 18.1.8 default_h179603d_5 + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + - compiler-rt 18.1.8 h1020d70_1 + - clang_impl_osx-64 18.1.8 h6a44ed1_23 + - clang_osx-64 18.1.8 h7e5c614_23 + run: [] + run_constrained: + - __osx >=10.13 + test: + commands: + - ontime --help + about: + home: https://github.com/mbhall88/ontime + license: MIT + license_family: MIT + license_file: LICENSE + summary: Extract subsets of ONT (Nanopore) reads based on time + extra: + copy_test_source_files: true + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/ontime_1733853117352/work/conda_build.sh']' returned non-zero exit status 101. + + final: true + recipe-maintainers: + - mbhall88 + + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/ontime_1733853117352/work + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/ontime_1733853117352/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/ontime_1733853117352/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/ontime_1733853117352/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + CC=x86_64-apple-darwin13.4.0-clang + api.build( + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ontime-0.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/ontime_1733853117352/work/conda_build.sh']' returned non-zero exit status 101. + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ontime-0.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + HOME is $SRC_DIR +# Last 100 lines of the build log. diff --git a/recipes/ontime/meta.yaml b/recipes/ontime/meta.yaml index b0764d525b178..f33997fe54ff3 100644 --- a/recipes/ontime/meta.yaml +++ b/recipes/ontime/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 1caee3197d1032da38c55a47c3b626fe00b07831362e734fb2174747fca17fc4 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('ontime', max_pin="x.x") }} diff --git a/recipes/orfanage/meta.yaml b/recipes/orfanage/meta.yaml index 69e4c32edb1ae..566cc6fe9d9a6 100644 --- a/recipes/orfanage/meta.yaml +++ b/recipes/orfanage/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('orfanage', max_pin="x") }} diff --git a/recipes/orfipy/build_failure.osx-64.yaml b/recipes/orfipy/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..63f08c25b34d3 --- /dev/null +++ b/recipes/orfipy/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: b294277162231f1723ec5421b2fdd80cc19693fd4cc44534273d1fa35b361da4 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - psutil 6.1.0 py310hb9d19b6_0 + - pyahocorasick 2.1.0 py310hb372a2b_0 + - pyfastx 2.1.0 py310h80ca7e9_3 + run: + - colorama + - libcxx >=18 + - psutil + - python_abi 3.10.* *_cp310 + - pyfastx >=2.1.0,<3.0a0 + - pyahocorasick + - python >=3.10,<3.11.0a0 + test: + commands: + - orfipy --help + imports: + - orfipy + requires: + - pytest + about: + home: https://github.com/urmi-21/orfipy + license: MIT + license_family: MIT + summary: 'orfipy: fast and flexible search for open reading frames in fasta sequences' + extra: + copy_test_source_files: true + final: true + recipe-maintainers: + - urmi-21 + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/orfipy_1734411264706/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/orfipy_1734411264706/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/orfipy_1734411264706/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/orfipy_1734411264706/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/orfipy-0.0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/orfipy-0.0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/orfipy-0.0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/orfipy-0.0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + Using pip 24.3.1 from $PREFIX/lib/python3.10/site-packages/pip (python 3.10) + Non-user install because user site-packages disabled + Ignoring indexes: https://pypi.org/simple + Created temporary directory: /private/tmp/pip-build-tracker-yf__0tnw + Initialized build tracking at /private/tmp/pip-build-tracker-yf__0tnw + Created build tracker: /private/tmp/pip-build-tracker-yf__0tnw + Entered build tracker: /private/tmp/pip-build-tracker-yf__0tnw + Created temporary directory: /private/tmp/pip-install-y4h4qmqd + Created temporary directory: /private/tmp/pip-ephem-wheel-cache-lhtjl126 + Processing $SRC_DIR + Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-yf__0tnw' + Created temporary directory: /private/tmp/pip-modern-metadata-1yz0dpv_ + Preparing metadata (pyproject.toml): started + Preparing metadata (pyproject.toml): finished with status 'done' + Removed file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-yf__0tnw' + Removed build tracker: '/private/tmp/pip-build-tracker-yf__0tnw' +# Last 100 lines of the build log. diff --git a/recipes/orfipy/meta.yaml b/recipes/orfipy/meta.yaml index 233aae1aa59db..b98a0ecdfc126 100644 --- a/recipes/orfipy/meta.yaml +++ b/recipes/orfipy/meta.yaml @@ -10,7 +10,7 @@ source: sha256: b8736e1ab275a7a611d62a9718162988c6393e46f9a9074c690a75254fdcf760 build: - number: 3 + number: 4 skip: True # [py2k] entry_points: - orfipy = orfipy.__main__:main diff --git a/recipes/orfquant/meta.yaml b/recipes/orfquant/meta.yaml index 0023474d85125..e309134fe6dbe 100644 --- a/recipes/orfquant/meta.yaml +++ b/recipes/orfquant/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/orientagraph/build_failure.osx-64.yaml b/recipes/orientagraph/build_failure.osx-64.yaml index 43e5e41c13ad2..89386ac2126c0 100644 --- a/recipes/orientagraph/build_failure.osx-64.yaml +++ b/recipes/orientagraph/build_failure.osx-64.yaml @@ -1,48 +1,18 @@ -recipe_sha: d446dcef765ca05d16a950ff7bea343ccc3c718556126b490882b4d306474d38 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 72cf45072e1f7bb6d60ab8e8d6976320649274ae846f07f5a5683299819903f3 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - Downloading source to cache: 0f81b2604993285a56fbf83384481274f7c89883_d51e21d9e4.zip - Downloading https://github.com/sriramlab/OrientAGraph/archive/0f81b2604993285a56fbf83384481274f7c89883.zip - Success - configure: error: could not find zlib - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/orientagraph_1717521672230/work - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/orientagraph_1717521672230/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/orientagraph_1717521672230/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/orientagraph_1717521672230/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as CC=x86_64-apple-darwin13.4.0-clang CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/orientagraph-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/orientagraph_1717521672230/work/conda_build.sh']' returned non-zero exit status 1. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/orientagraph-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool @@ -51,7 +21,7 @@ log: |- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -60,7 +30,7 @@ log: |- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -100,5 +70,35 @@ log: |- checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes checking for x86_64-apple-darwin13.4.0-clang option to accept ISO C89... none needed checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 - checking for gzopen in -lz... no + checking for gzopen in -lz... yes + checking for cos in -lm... yes + checking for cblas_dgemm in -lgslcblas... yes + checking for gsl_blas_dgemm in -lgsl... yes + checking for boostlib >= 1.42... yes + configure: creating ./config.status + config.status: creating Makefile + config.status: creating src/Makefile + config.status: creating config.h + config.status: executing depfiles commands + make all-recursive + make[1]: Entering directory '$SRC_DIR' + Making all in src + make[2]: Entering directory '$SRC_DIR/src' + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/orientagraph-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT TreeMix.o -MD -MP -MF .deps/TreeMix.Tpo -c -o TreeMix.o TreeMix.cpp + mv -f .deps/TreeMix.Tpo .deps/TreeMix.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/orientagraph-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT gzstream.o -MD -MP -MF .deps/gzstream.Tpo -c -o gzstream.o gzstream.cpp + mv -f .deps/gzstream.Tpo .deps/gzstream.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/orientagraph-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT PopGraph.o -MD -MP -MF .deps/PopGraph.Tpo -c -o PopGraph.o PopGraph.cpp + mv -f .deps/PopGraph.Tpo .deps/PopGraph.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/orientagraph-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT nnls.o -MD -MP -MF .deps/nnls.Tpo -c -o nnls.o nnls.cpp + mv -f .deps/nnls.Tpo .deps/nnls.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/orientagraph-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT PhyloPop_params.o -MD -MP -MF .deps/PhyloPop_params.Tpo -c -o PhyloPop_params.o PhyloPop_params.cpp + mv -f .deps/PhyloPop_params.Tpo .deps/PhyloPop_params.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/orientagraph-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT CountData.o -MD -MP -MF .deps/CountData.Tpo -c -o CountData.o CountData.cpp + mv -f .deps/CountData.Tpo .deps/CountData.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/orientagraph-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT CmdLine.o -MD -MP -MF .deps/CmdLine.Tpo -c -o CmdLine.o CmdLine.cpp + mv -f .deps/CmdLine.Tpo .deps/CmdLine.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/orientagraph-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT GraphState2.o -MD -MP -MF .deps/GraphState2.Tpo -c -o GraphState2.o GraphState2.cpp + make[2]: Leaving directory '$SRC_DIR/src' + make[1]: Leaving directory '$SRC_DIR' # Last 100 lines of the build log. diff --git a/recipes/orientagraph/meta.yaml b/recipes/orientagraph/meta.yaml index 0d0e032a32a5e..44a8fec6f480d 100644 --- a/recipes/orientagraph/meta.yaml +++ b/recipes/orientagraph/meta.yaml @@ -7,7 +7,7 @@ source: sha256: d51e21d9e46c8d60bedf83a7a956032f8757bb69947b37b181e867452bb09aac build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/orna/build_failure.osx-64.yaml b/recipes/orna/build_failure.osx-64.yaml index 413245ac90f9b..6c5df02eb9394 100644 --- a/recipes/orna/build_failure.osx-64.yaml +++ b/recipes/orna/build_failure.osx-64.yaml @@ -1,4 +1,4 @@ -recipe_sha: 89e935cbf0962078a096807e0c214a01be355ad16c3cc5d1e3c82671f3f3efe4 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 5016859557815e2076766771d2ca0e22b899a236a2539c1d3f8a4f5932c1ac61 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- [ 23%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FAdbg.c.o diff --git a/recipes/orna/meta.yaml b/recipes/orna/meta.yaml index ad2481b35fa4a..3ba76e0162857 100644 --- a/recipes/orna/meta.yaml +++ b/recipes/orna/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 4be912455a467e89a49ce1e7643b6101f2565a3dc6873d971fad2062566652eb build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/orthanq/meta.yaml b/recipes/orthanq/meta.yaml index bf9c98d9a23da..7998966147049 100644 --- a/recipes/orthanq/meta.yaml +++ b/recipes/orthanq/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage("orthanq", max_pin="x") }} diff --git a/recipes/orthologer/meta.yaml b/recipes/orthologer/meta.yaml index 8279dbe399fc0..40061710d6f26 100644 --- a/recipes/orthologer/meta.yaml +++ b/recipes/orthologer/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('orthologer', max_pin="x") }} diff --git a/recipes/pairix/meta.yaml b/recipes/pairix/meta.yaml index 873aa8e04a725..c9dfde7ec27ba 100644 --- a/recipes/pairix/meta.yaml +++ b/recipes/pairix/meta.yaml @@ -11,7 +11,7 @@ source: - src_Makefile.patch build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage('pairix', max_pin="x.x") }} diff --git a/recipes/pairsnp/meta.yaml b/recipes/pairsnp/meta.yaml index 91d9c1c101247..720948670ff72 100644 --- a/recipes/pairsnp/meta.yaml +++ b/recipes/pairsnp/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 5d3be3fe446cbd0861ea601e48641e13e8039de1e02c469f73cdce61e099fbc4 build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/paladin/meta.yaml b/recipes/paladin/meta.yaml index bb0c5a829acf2..7fde4dcc35433 100644 --- a/recipes/paladin/meta.yaml +++ b/recipes/paladin/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/palikiss/build_failure.osx-64.yaml b/recipes/palikiss/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..8b0e990ed00d7 --- /dev/null +++ b/recipes/palikiss/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: b0187d9fc9d38a3db7f03dc050ab9c3ac02489d087c96e8d2a8aa172586eebe9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/palikiss-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/palikiss-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/palikiss-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/palikiss-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + make: Entering directory '$SRC_DIR/Misc/Applications/pAliKiss' + make all_normal + make[1]: Entering directory '$SRC_DIR/Misc/Applications/pAliKiss' + make compile \ + gapc_product="alg_ali_pknot_mfe * alg_ali_pknot_dotBracket" \ + gapc_options="--kbacktrace --no-coopt --tab-all " \ + gapc_file="ali_pKiss.gap" \ + gapc_binaryname="mfe"; + make compile \ + gapc_product="alg_ali_pknot_mfe_subopt * alg_ali_pknot_dotBracket" \ + gapc_options="--kbacktrace --tab-all " \ + gapc_file="ali_pKiss.gap" \ + gapc_binaryname="subopt"; + make[2]: Entering directory '$SRC_DIR/Misc/Applications/pAliKiss' + make[2]: Entering directory '$SRC_DIR/Misc/Applications/pAliKiss' + if [ ! -f "x86_64-apple-darwin13.4.0/pAliKiss_subopt" ]; then \ + cd /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.Z2XeBvy7 && gapc -I $SRC_DIR/Misc/Applications/pAliKiss/../../../ -p "alg_ali_pknot_mfe_subopt * alg_ali_pknot_dotBracket" --kbacktrace --tab-all $SRC_DIR/Misc/Applications/pAliKiss/../../..//ali_pKiss.gap; \ + perl $SRC_DIR/Misc/Applications/pAliKiss/../../..///Misc/Applications/addRNAoptions.pl /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.Z2XeBvy7/out.mf 0 'subopt' 'alg_ali_pknot_mfe_subopt * alg_ali_pknot_dotBracket'; \ + cd /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.Z2XeBvy7 && make -f out.mf CPPFLAGS_EXTRA="-I $SRC_DIR/Misc/Applications/pAliKiss/../../../ -I ./" CXXFLAGS_EXTRA="-O3 -DNDEBUG" LDFLAGS_EXTRA=""; \ + install -d $SRC_DIR/Misc/Applications/pAliKiss/x86_64-apple-darwin13.4.0; \ + install /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.Z2XeBvy7/out $SRC_DIR/Misc/Applications/pAliKiss/x86_64-apple-darwin13.4.0/pAliKiss_subopt; \ + fi; + if [ ! -f "x86_64-apple-darwin13.4.0/pAliKiss_mfe" ]; then \ + cd /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.muO27tWX && gapc -I $SRC_DIR/Misc/Applications/pAliKiss/../../../ -p "alg_ali_pknot_mfe * alg_ali_pknot_dotBracket" --kbacktrace --no-coopt --tab-all $SRC_DIR/Misc/Applications/pAliKiss/../../..//ali_pKiss.gap; \ + perl $SRC_DIR/Misc/Applications/pAliKiss/../../..///Misc/Applications/addRNAoptions.pl /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.muO27tWX/out.mf 0 'mfe' 'alg_ali_pknot_mfe * alg_ali_pknot_dotBracket'; \ + cd /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.muO27tWX && make -f out.mf CPPFLAGS_EXTRA="-I $SRC_DIR/Misc/Applications/pAliKiss/../../../ -I ./" CXXFLAGS_EXTRA="-O3 -DNDEBUG" LDFLAGS_EXTRA=""; \ + install -d $SRC_DIR/Misc/Applications/pAliKiss/x86_64-apple-darwin13.4.0; \ + install /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.muO27tWX/out $SRC_DIR/Misc/Applications/pAliKiss/x86_64-apple-darwin13.4.0/pAliKiss_mfe; \ + fi; + make[3]: Entering directory '/private/var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.muO27tWX' + make[3]: Entering directory '/private/var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.Z2XeBvy7' + Including global makefile $PREFIX/share/gapc/config_darwin13.4.0.mf + Including global makefile $PREFIX/share/gapc/config_darwin13.4.0.mf + echo '#include "out.hh"' > out_main.cc + echo '#include "out.hh"' > out_main.cc + cat $PREFIX/include/rtlib/generic_main.cc >> out_main.cc + cat $PREFIX/include/rtlib/generic_main.cc >> out_main.cc + $PREFIX/bin/sed -i 's|gapc::Opts opts;||' out_main.cc + $PREFIX/bin/sed -i 's|gapc::Opts opts;||' out_main.cc + $PREFIX/bin/sed -i 's|\([^_]\)opts\.|\1gapc::Opts::getOpts()->|g' out_main.cc + $PREFIX/bin/sed -i 's|\([^_]\)opts\.|\1gapc::Opts::getOpts()->|g' out_main.cc + $PREFIX/bin/sed -i 's|obj.init(opts);|obj.init(\*gapc::Opts::getOpts());|g' out_main.cc + $PREFIX/bin/sed -i 's|obj.init(opts);|obj.init(\*gapc::Opts::getOpts());|g' out_main.cc + $PREFIX/bin/sed -i 's|#include .rtlib/generic_opts.hh.|#include "Extensions/rnaoptions.hh"|' out_main.cc + $PREFIX/bin/sed -i 's|#include .rtlib/generic_opts.hh.|#include "Extensions/rnaoptions.hh"|' out_main.cc + $PREFIX/bin/sed -i 's%#include .rtlib/generic_opts.hh.%#include "Extensions/rnaoptions.hh"%' out.hh out.cc + $PREFIX/bin/sed -i 's%#include .rtlib/generic_opts.hh.%#include "Extensions/rnaoptions.hh"%' out.hh out.cc + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bellmans-gapc_1721071508431/work=/usr/local/src/conda/bellmans-gapc-2024.01.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -MMD -MP -Wall -Wnon-virtual-dtor -Wno-unused-variable -Wno-parentheses -DNDEBUG -DBISONNEW -O3 -DNDEBUG -DWITH_RNAOPTIONS -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I $SRC_DIR/Misc/Applications/pAliKiss/../../../ -I ./ -I$PREFIX/include -I$PREFIX/include/ -I$PREFIX/include/rtlib -I$PREFIX/include/librna -c -o out.o out.cc + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bellmans-gapc_1721071508431/work=/usr/local/src/conda/bellmans-gapc-2024.01.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -MMD -MP -Wall -Wnon-virtual-dtor -Wno-unused-variable -Wno-parentheses -DNDEBUG -DBISONNEW -O3 -DNDEBUG -DWITH_RNAOPTIONS -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I $SRC_DIR/Misc/Applications/pAliKiss/../../../ -I ./ -I$PREFIX/include -I$PREFIX/include/ -I$PREFIX/include/rtlib -I$PREFIX/include/librna -c -o out.o out.cc + make[3]: Leaving directory '/private/var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.Z2XeBvy7' + make[3]: Leaving directory '/private/var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.muO27tWX' + make[2]: Leaving directory '$SRC_DIR/Misc/Applications/pAliKiss' + make[2]: Leaving directory '$SRC_DIR/Misc/Applications/pAliKiss' + make[1]: Leaving directory '$SRC_DIR/Misc/Applications/pAliKiss' + make: Leaving directory '$SRC_DIR/Misc/Applications/pAliKiss' +# Last 100 lines of the build log. diff --git a/recipes/palikiss/meta.yaml b/recipes/palikiss/meta.yaml index 556c317057398..0aee7e12ad783 100644 --- a/recipes/palikiss/meta.yaml +++ b/recipes/palikiss/meta.yaml @@ -14,7 +14,7 @@ source: url: https://github.com/jlab/fold-grammars/archive/{{ fold_grammars_version }}.tar.gz build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('palikiss', max_pin="x") }} diff --git a/recipes/paml/build_failure.osx-64.yaml b/recipes/paml/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c24dc723ee40e --- /dev/null +++ b/recipes/paml/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: ae7cc302b66fe1048a29ec33d0bb0e255da4c12e9c42e97fdd316b10b2d33690 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - llvm-tools-18 18.1.8 h9ce406d_2 + - clang-18 18.1.8 default_h0c94c6a_5 + - llvm-tools 18.1.8 h9ce406d_2 + - cctools_osx-64 1010.6 h00edd4c_2 + - clang 18.1.8 default_h179603d_5 + - clangxx 18.1.8 default_h179603d_5 + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + - compiler-rt 18.1.8 h1020d70_1 + - clang_impl_osx-64 18.1.8 h6a44ed1_23 + - clang_osx-64 18.1.8 h7e5c614_23 + run: [] + test: + commands: + - chi2 1 .1 + - evolver 1 | grep EVOLVER + - codeml /dev/null 2>&1 | grep paml + about: + home: http://abacus.gene.ucl.ac.uk/software/paml.html + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/paml_1734456940428/work/conda_build.sh']' returned non-zero exit status 2. + + license: GNU General Public License v3 (GPLv3) + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + license_file: LICENSE + summary: A package of programs for phylogenetic analyses of DNA or protein sequences + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + using maximum likelihood. + extra: + additional-platforms: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + - linux-aarch64 + copy_test_source_files: true + final: true + identifiers: + - biotools:paml + raise BuildScriptException(str(exc), caused_by=exc) from exc + - doi:10.1093/bioinformatics/13.5.555 + + + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/paml_1734456940428/work/conda_build.sh']' returned non-zero exit status 2. + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/paml_1734456940428/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/paml_1734456940428/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/paml_1734456940428/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/paml_1734456940428/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/paml-4.10.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/paml-4.10.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/paml-4.10.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -c baseml.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/paml-4.10.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -c tools.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/paml-4.10.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -c codeml.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/paml-4.10.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -c basemlg.c +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/paml/meta.yaml b/recipes/paml/meta.yaml index e2eeb810e8291..b1da351a551dc 100644 --- a/recipes/paml/meta.yaml +++ b/recipes/paml/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('paml', max_pin="x.x") }} diff --git a/recipes/panacus/meta.yaml b/recipes/panacus/meta.yaml index fa4b81e48bfac..4cd45d580f27a 100644 --- a/recipes/panacus/meta.yaml +++ b/recipes/panacus/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 7b4e4aee52528c569ad663d0fcd00bd42f221f29f93f0768f18c2ac2d3f0d769 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/pandaseq/2.8.1/build_failure.osx-64.yaml b/recipes/pandaseq/2.8.1/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c9dc958c0a89f --- /dev/null +++ b/recipes/pandaseq/2.8.1/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c805945d23466197c5f67f4ce625e0c488306c048e70c83e75e46bf17ce2f1f1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + checking for a working dd... /bin/dd + checking how to truncate binary pipes... /bin/dd bs=4096 count=1 + checking for x86_64-apple-darwin13.4.0-mt... no + checking for mt... no + checking if : is a manifest tool... no + checking for x86_64-apple-darwin13.4.0-dsymutil... no + checking for dsymutil... dsymutil + checking for x86_64-apple-darwin13.4.0-nmedit... x86_64-apple-darwin13.4.0-nmedit + checking for x86_64-apple-darwin13.4.0-lipo... x86_64-apple-darwin13.4.0-lipo + checking for x86_64-apple-darwin13.4.0-otool... x86_64-apple-darwin13.4.0-otool + checking for x86_64-apple-darwin13.4.0-otool64... no + checking for otool64... no + checking for -single_module linker flag... yes + checking for -exported_symbols_list linker flag... yes + checking for -force_load linker flag... yes + checking for stdio.h... yes + checking for stdlib.h... yes + checking for string.h... yes + checking for inttypes.h... yes + checking for stdint.h... yes + checking for strings.h... yes + checking for sys/stat.h... yes + checking for sys/types.h... yes + checking for unistd.h... yes + checking for sys/param.h... yes + checking for dlfcn.h... yes + checking for objdir... .libs + checking if x86_64-apple-darwin13.4.0-clang supports -fno-rtti -fno-exceptions... yes + checking for x86_64-apple-darwin13.4.0-clang option to produce PIC... -fno-common -DPIC + checking if x86_64-apple-darwin13.4.0-clang PIC flag -fno-common -DPIC works... yes + checking if x86_64-apple-darwin13.4.0-clang static flag -static works... no + checking if x86_64-apple-darwin13.4.0-clang supports -c -o file.o... yes + checking if x86_64-apple-darwin13.4.0-clang supports -c -o file.o... (cached) yes + checking whether the x86_64-apple-darwin13.4.0-clang linker (x86_64-apple-darwin13.4.0-ld) supports shared libraries... yes + checking dynamic linker characteristics... darwin13.4.0 dyld + checking how to hardcode library paths into programs... immediate + checking whether stripping libraries is possible... yes + checking if libtool supports shared libraries... yes + checking whether to build shared libraries... yes + checking whether to build static libraries... yes + checking for x86_64-apple-darwin13.4.0-windres... no + checking for windres... no + checking whether compiler accepts "-pedantic"... yes + checking for egrep... (cached) /usr/bin/grep -E + checking (non-cross) C compiler for building tools... $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + checking for module flags... -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -no-undefined -avoid-version -shared -flat_namespace + checking for the pthreads library -lpthreads... no + checking whether pthreads work without any flags... yes + checking whether pthreads work with -Kthread... no + checking whether pthreads work with -kthread... no + checking for the pthreads library -llthread... no + checking whether pthreads work with -pthread... yes + checking whether pthreads work with -pthreads... no + checking whether pthreads work with -mthreads... no + checking for the pthreads library -lpthread... yes + checking whether pthreads work with --thread-safe... no + checking whether pthreads work with -mt... no + checking for the pthreads library -lpthreadGC2... no + checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE + checking if more special flags are required for pthreads... no + checking for cc_r... x86_64-apple-darwin13.4.0-clang + checking whether uname(2) is POSIX... yes + checking for sys/sysctl.h... yes + checking for x86_64-apple-darwin13.4.0-pkg-config... $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-pkg-config + checking pkg-config is at least version 0.9.0... yes + checking for zlib ... yes + checking for libcurl ... no + checking for bzlib.h... yes + checking for BZ2_bzDecompressInit in -lbz2... yes + checking for ltdl.h... yes + checking for lt_dlinit in -lltdl... yes + checking that generated files are newer than configure... done + configure: creating ./config.status + config.status: creating Makefile + config.status: creating pandaseq.spec + config.status: creating pandaseq-2.pc + config.status: creating pandaseq-2.vapi + config.status: creating pandaseq-2-url.deps + config.status: creating pandaseq-2-url.pc + config.status: creating pandaseq-2-url.vapi + config.status: creating pandaxs + config.status: creating build-macos-pkg + config.status: creating config.h + config.status: executing depfiles commands + config.status: executing libtool commands + $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -std=c99 -g -Wall -Wextra -Wformat -o mktable mktable.c tablebuilder.c -lm + ./mktable + make all-am + make[1]: Entering directory '$SRC_DIR' + CC pandaseq-main.o + CC libpandaseq_la-algo.lo + CC libpandaseq_la-algo_ea_util.lo + CC libpandaseq_la-algo_flash.lo + CC libpandaseq_la-algo_pear.lo + CC libpandaseq_la-algo_rdp_mle.lo + CC libpandaseq_la-algo_simple_bayes.lo + CC libpandaseq_la-algo_stitch.lo + CC libpandaseq_la-algo_uparse.lo + CC libpandaseq_la-args.lo + make[1]: Leaving directory '$SRC_DIR' +# Last 100 lines of the build log. diff --git a/recipes/pandaseq/2.8.1/meta.yaml b/recipes/pandaseq/2.8.1/meta.yaml index b9193bc6ee379..9cf986217c7e2 100644 --- a/recipes/pandaseq/2.8.1/meta.yaml +++ b/recipes/pandaseq/2.8.1/meta.yaml @@ -3,7 +3,7 @@ package: version: "2.8.1" build: - number: 7 + number: 8 skip: False source: diff --git a/recipes/pandaseq/build_failure.osx-64.yaml b/recipes/pandaseq/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..4e909d024a618 --- /dev/null +++ b/recipes/pandaseq/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 44597bd728a837b2af82c649483f984a83cd615287f1a4bf8e2b06d1886d29cc # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + checking for a working dd... /bin/dd + checking how to truncate binary pipes... /bin/dd bs=4096 count=1 + checking for x86_64-apple-darwin13.4.0-mt... no + checking for mt... no + checking if : is a manifest tool... no + checking for x86_64-apple-darwin13.4.0-dsymutil... no + checking for dsymutil... dsymutil + checking for x86_64-apple-darwin13.4.0-nmedit... x86_64-apple-darwin13.4.0-nmedit + checking for x86_64-apple-darwin13.4.0-lipo... x86_64-apple-darwin13.4.0-lipo + checking for x86_64-apple-darwin13.4.0-otool... x86_64-apple-darwin13.4.0-otool + checking for x86_64-apple-darwin13.4.0-otool64... no + checking for otool64... no + checking for -single_module linker flag... yes + checking for -exported_symbols_list linker flag... yes + checking for -force_load linker flag... yes + checking for stdio.h... yes + checking for stdlib.h... yes + checking for string.h... yes + checking for inttypes.h... yes + checking for stdint.h... yes + checking for strings.h... yes + checking for sys/stat.h... yes + checking for sys/types.h... yes + checking for unistd.h... yes + checking for sys/param.h... yes + checking for dlfcn.h... yes + checking for objdir... .libs + checking if x86_64-apple-darwin13.4.0-clang supports -fno-rtti -fno-exceptions... yes + checking for x86_64-apple-darwin13.4.0-clang option to produce PIC... -fno-common -DPIC + checking if x86_64-apple-darwin13.4.0-clang PIC flag -fno-common -DPIC works... yes + checking if x86_64-apple-darwin13.4.0-clang static flag -static works... no + checking if x86_64-apple-darwin13.4.0-clang supports -c -o file.o... yes + checking if x86_64-apple-darwin13.4.0-clang supports -c -o file.o... (cached) yes + checking whether the x86_64-apple-darwin13.4.0-clang linker (x86_64-apple-darwin13.4.0-ld) supports shared libraries... yes + checking dynamic linker characteristics... darwin13.4.0 dyld + checking how to hardcode library paths into programs... immediate + checking whether stripping libraries is possible... yes + checking if libtool supports shared libraries... yes + checking whether to build shared libraries... yes + checking whether to build static libraries... yes + checking for x86_64-apple-darwin13.4.0-windres... no + checking for windres... no + checking whether compiler accepts "-pedantic"... yes + checking for egrep... (cached) /usr/bin/grep -E + checking (non-cross) C compiler for building tools... $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + checking for module flags... -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -no-undefined -avoid-version -shared -flat_namespace + checking for the pthreads library -lpthreads... no + checking whether pthreads work without any flags... yes + checking whether pthreads work with -Kthread... no + checking whether pthreads work with -kthread... no + checking for the pthreads library -llthread... no + checking whether pthreads work with -pthread... yes + checking whether pthreads work with -pthreads... no + checking whether pthreads work with -mthreads... no + checking for the pthreads library -lpthread... yes + checking whether pthreads work with --thread-safe... no + checking whether pthreads work with -mt... no + checking for the pthreads library -lpthreadGC2... no + checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE + checking if more special flags are required for pthreads... no + checking for cc_r... x86_64-apple-darwin13.4.0-clang + checking whether uname(2) is POSIX... yes + checking for sys/sysctl.h... yes + checking for x86_64-apple-darwin13.4.0-pkg-config... $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-pkg-config + checking pkg-config is at least version 0.9.0... yes + checking for zlib ... yes + checking for libcurl ... no + checking for bzlib.h... yes + checking for BZ2_bzDecompressInit in -lbz2... yes + checking for ltdl.h... yes + checking for lt_dlinit in -lltdl... yes + checking that generated files are newer than configure... done + configure: creating ./config.status + config.status: creating Makefile + config.status: creating pandaseq.spec + config.status: creating pandaseq-2.pc + config.status: creating pandaseq-2.vapi + config.status: creating pandaseq-2-url.deps + config.status: creating pandaseq-2-url.pc + config.status: creating pandaseq-2-url.vapi + config.status: creating pandaxs + config.status: creating build-macos-pkg + config.status: creating config.h + config.status: executing depfiles commands + config.status: executing libtool commands + $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang -std=c99 -g -Wall -Wextra -Wformat -o mktable mktable.c tablebuilder.c -lm + ./mktable + make all-am + make[1]: Entering directory '$SRC_DIR' + CC pandaseq-main.o + CC libpandaseq_la-algo.lo + CC libpandaseq_la-algo_ea_util.lo + CC libpandaseq_la-algo_flash.lo + CC libpandaseq_la-algo_pear.lo + CC libpandaseq_la-algo_rdp_mle.lo + CC libpandaseq_la-algo_simple_bayes.lo + CC libpandaseq_la-algo_stitch.lo + CC libpandaseq_la-algo_uparse.lo + CC libpandaseq_la-args.lo + make[1]: Leaving directory '$SRC_DIR' +# Last 100 lines of the build log. diff --git a/recipes/pandaseq/meta.yaml b/recipes/pandaseq/meta.yaml index c405d170eb1b4..4dbcd3cf71ca9 100644 --- a/recipes/pandaseq/meta.yaml +++ b/recipes/pandaseq/meta.yaml @@ -3,7 +3,7 @@ package: version: "2.11" build: - number: 8 + number: 9 skip: False source: diff --git a/recipes/pandora/meta.yaml b/recipes/pandora/meta.yaml index 32af134587696..9c90ac192773d 100644 --- a/recipes/pandora/meta.yaml +++ b/recipes/pandora/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 0e6189990dcf51eb28d175e0be76154a3ede1b602e5197f1a86ce8ba2839ba4e build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('pandora', max_pin="x") }} diff --git a/recipes/pangwes/meta.yaml b/recipes/pangwes/meta.yaml index 44874495eafd5..7b1bd2f017c55 100644 --- a/recipes/pangwes/meta.yaml +++ b/recipes/pangwes/meta.yaml @@ -10,7 +10,7 @@ source: sha256: d91f01f2a098cb8f7492c2208d0ae143d2b66f0d58b89b9c96dfb17ebca07c8e build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/paraclu/meta.yaml b/recipes/paraclu/meta.yaml index 9be95d9c83741..0fceeb53225b6 100644 --- a/recipes/paraclu/meta.yaml +++ b/recipes/paraclu/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://gitlab.com/mcfrith/paraclu/-/archive/{{ version }}/paraclu-{{ version }}.tar.gz diff --git a/recipes/parafly/meta.yaml b/recipes/parafly/meta.yaml index bb7fa4c6d6d1b..469434c8accff 100644 --- a/recipes/parafly/meta.yaml +++ b/recipes/parafly/meta.yaml @@ -10,7 +10,7 @@ source: build: skip: True # [osx] - number: 3 + number: 4 run_exports: - {{ pin_subpackage("parafly", max_pin=None) }} diff --git a/recipes/parallel-meta-suite/meta.yaml b/recipes/parallel-meta-suite/meta.yaml index c309a59872b62..500c3edf39dca 100644 --- a/recipes/parallel-meta-suite/meta.yaml +++ b/recipes/parallel-meta-suite/meta.yaml @@ -12,7 +12,7 @@ source: sha256: 5bd54b2e07e14ea16fe9bb49e5a138edbf233012f561c9199425070f30cdfb7d build: - number: 4 + number: 5 skip: True # [osx] requirements: diff --git a/recipes/parasail-python/meta.yaml b/recipes/parasail-python/meta.yaml index b43bb6bfb09cf..7071f2eabde28 100644 --- a/recipes/parasail-python/meta.yaml +++ b/recipes/parasail-python/meta.yaml @@ -13,7 +13,7 @@ source: - darwin-libtool-name.patch build: - number: 2 + number: 3 skip: True # [py < 37] script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv run_exports: diff --git a/recipes/parascopy/meta.yaml b/recipes/parascopy/meta.yaml index b67f955198f05..b0dd879dd9c45 100644 --- a/recipes/parascopy/meta.yaml +++ b/recipes/parascopy/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 entry_points: - parascopy=parascopy.entry_point:main run_exports: diff --git a/recipes/pardre/meta.yaml b/recipes/pardre/meta.yaml index 281a82ff0a24b..380ff36030153 100644 --- a/recipes/pardre/meta.yaml +++ b/recipes/pardre/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256sum }} build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/parsnp/build_failure.osx-64.yaml b/recipes/parsnp/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..49d10c882daf9 --- /dev/null +++ b/recipes/parsnp/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: b287ce58da1df7ae69fe34364641490bf5d3f3c1c7584dd49b2d9642ce30c278 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + |-OS: Darwin + |-threads: 2 + ************************** + + 15:29:48 - [1;37mINFO[0m - <> + 15:29:48 - [1;37mINFO[0m - No genbank file provided for reference annotations, skipping.. + 15:29:48 - [1;31mERROR[0m - Genome sequence mers_virus/genomes/Jeddah_2014_C7149.fna seems to be aligned! Skip! + 15:29:48 - [1;31mERROR[0m - Genome sequence mers_virus/genomes/Jeddah_2014_C7569.fna seems to be aligned! Skip! + 15:29:48 - [1;31mERROR[0m - Genome sequence mers_virus/genomes/Jeddah_2014_C7770.fna seems to be aligned! Skip! + 15:29:48 - [1;34mDEBUG[0m - Writing .ini file + 15:29:48 - [1;37mINFO[0m - Filtering genomes... + 15:29:48 - [1;33mWARNING[0m - You are using a randomly selected genome to filter genomes from your input with Mash. If input genomes vary greatly in size, results could be suboptimal. It is advised to select a reference genome for filter... + 15:29:48 - [1;34mDEBUG[0m - time mash dist -t -d 0.1 -p 2 test-mash/Riyadh_14_2013.fna.ref -l test-mash/tmp/genomes.lst + 15:29:48 - [1;34mDEBUG[0m - STDOUT was piped... please see output file: test-mash/log/mash.out + 15:29:48 - [1;34mDEBUG[0m - STDERR was piped... please see output file: test-mash/log/mash.err + 15:29:48 - [1;34mDEBUG[0m - + 15:29:48 - [1;37mINFO[0m - Too few genomes to run partitions of size >50. Running all genomes at once. + 15:29:48 - [1;37mINFO[0m - Running Parsnp multi-MUM search and libMUSCLE aligner... + 15:29:48 - [1;34mDEBUG[0m - time /opt/mambaforge/envs/bioconda/conda-bld/parsnp_1734535473104/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/bin/bin/parsnp_core test-mash/parsnpAligner.ini + 15:29:48 - [1;34mDEBUG[0m - STDOUT was piped... please see output file: test-mash/log/parsnp-aligner.out + 15:29:48 - [1;34mDEBUG[0m - STDERR was piped... please see output file: test-mash/log/parsnp-aligner.err + 15:29:48 - [1;34mDEBUG[0m - + 15:29:48 - [1;34mDEBUG[0m - Writing MAF file to test-mash/parsnp.maf + 15:29:48 - [1;34mDEBUG[0m - harvesttools -q -o test-mash/parsnp.ggr -f test-mash/Riyadh_14_2013.fna.ref -x test-mash/parsnp.xmfa + 15:29:48 - [1;34mDEBUG[0m - + 15:29:48 - [1;34mDEBUG[0m - + 15:29:48 - [1;34mDEBUG[0m - + 15:29:48 - [1;34mDEBUG[0m - time harvesttools -i test-mash/parsnp.ggr -S test-mash/parsnp.snps.mblocks + 15:29:48 - [1;34mDEBUG[0m - STDOUT was piped... please see output file: test-mash/log/harvest-mblocks.out + 15:29:48 - [1;34mDEBUG[0m - STDERR was piped... please see output file: test-mash/log/harvest-mblocks.err + 15:29:48 - [1;34mDEBUG[0m - + 15:29:48 - [1;37mINFO[0m - Aligned 47 genomes in 0.82 seconds + 15:29:48 - [1;37mINFO[0m - Parsnp finished! All output available in test-mash + 15:29:48 - [1;34mDEBUG[0m - Validating output directory contents + 15:29:49 - [1;37mINFO[0m - |--Parsnp 2.1.1--| + + 15:29:49 - [1;37mINFO[0m - + ***************************** + SETTINGS: + |-refgenome: autopick + |-genomes: + mers_virus/genomes/Al-Hasa_12_2013.fna + mers_virus/genomes/Al-Hasa_15_2013.fna + ...45 more file(s)... + mers_virus/genomes/Taif_1_2013.fna + mers_virus/genomes/Wadi-Ad-Dawasir_1_2013.fna + |-aligner: muscle + |-outdir: test-fastani + |-OS: Darwin + |-threads: 2 + ***************************** + + 15:29:49 - [1;37mINFO[0m - <> + 15:29:49 - [1;37mINFO[0m - No genbank file provided for reference annotations, skipping.. + 15:29:49 - [1;31mERROR[0m - Genome sequence mers_virus/genomes/Jeddah_2014_C7149.fna seems to be aligned! Skip! + 15:29:49 - [1;31mERROR[0m - Genome sequence mers_virus/genomes/Jeddah_2014_C7569.fna seems to be aligned! Skip! + 15:29:49 - [1;31mERROR[0m - Genome sequence mers_virus/genomes/Jeddah_2014_C7770.fna seems to be aligned! Skip! + 15:29:49 - [1;34mDEBUG[0m - Writing .ini file + 15:29:49 - [1;37mINFO[0m - Filtering genomes... + 15:29:49 - [1;33mWARNING[0m - You have not selected a reference and are using ANI filter. All-to-all FastANI will be performed in order to obtain the best reference. As this is O(N^2), it is advised to select a reference genome if you have many query sequences. + 15:29:49 - [1;34mDEBUG[0m - time fastANI --rl test-fastani/tmp/genomes.lst --ql test-fastani/tmp/genomes.lst --fragLen 500 -t 2 -o test-fastani/fastANI.tsv + 15:29:49 - [1;31mCRITICAL[0m - The following command failed: + >>$ time fastANI --rl test-fastani/tmp/genomes.lst --ql test-fastani/tmp/genomes.lst --fragLen 500 -t 2 -o test-fastani/fastANI.tsv + Please veryify input data and restart Parsnp. + If the problem persists please contact the Parsnp development team. + + STDOUT: + STDOUT was piped... please see output file: test-fastani/log/fastANI.out + + STDERR: + STDERR was piped... please see output file: test-fastani/log/fastANI.err + WARNING: Tests failed for parsnp-2.1.1-he136a0b_1.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/parsnp_1734535473104/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/parsnp_1734535473104/test_tmp + parsnp 2.1.1 + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/parsnp_1734535473104/test_tmp/conda_test_runner.sh']' returned non-zero exit status 250. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: parsnp-2.1.1-he136a0b_1.tar.bz2 +# Last 100 lines of the build log. +category: |- + test failure diff --git a/recipes/parsnp/meta.yaml b/recipes/parsnp/meta.yaml index 0a3982f7469da..e95d342b33169 100644 --- a/recipes/parsnp/meta.yaml +++ b/recipes/parsnp/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 7887ee4030dad6f30a4b735f1ee463024204030adbdcb0fa96562e6e8664474e build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('parsnp', max_pin="x") }} diff --git a/recipes/pasa/build_failure.osx-64.yaml b/recipes/pasa/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..0b946bd4bdece --- /dev/null +++ b/recipes/pasa/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: e36fc004df4bd34c0a06e946a0d4cbf455f7e56ba263084d1530037aa42daea0 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + doc_url: https://github.com/PASApipeline/PASApipeline/wiki + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/pasa_1734565090508/work/conda_build.sh']' returned non-zero exit status 2. + home: https://github.com/PASApipeline/PASApipeline + license: BSD-3-Clause + license_family: BSD + license_file: LICENSE + summary: PASA, acronym for Program to Assemble Spliced Alignments (and pronounced + 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments + of expressed transcript sequences to automatically model gene structures, and + to maintain gene structure annotation consistent with the most recently available + experimental sequence data. PASA also identifies and classifies all splicing variations + supported by the transcript alignments. + extra: + copy_test_source_files: true + final: true + identifiers: + - biotools:PASA + - doi:10.1093/nar/gkg770 + - doi:10.1186/gb-2008-9-1-r7 + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/pasa_1734565090508/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/pasa_1734565090508/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/pasa_1734565090508/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/pasa_1734565090508/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pasa-2.5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pasa-2.5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pasa-2.5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pasa-2.5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + if [ ! -d bin ]; then mkdir bin; fi + cd pasa_cpp && make && cp pasa ../bin/. + make[1]: Entering directory '$SRC_DIR/pasa_cpp' + x86_64-apple-darwin13.4.0-clang -O3 -c alignment_segment.cpp -o alignment_segment.o + x86_64-apple-darwin13.4.0-clang -O3 -c cdna_alignment.cpp -o cdna_alignment.o + x86_64-apple-darwin13.4.0-clang -O3 -c common_subs.cpp -o common_subs.o + x86_64-apple-darwin13.4.0-clang -O3 -c cdna_alignment_assembler.cpp -o cdna_alignment_assembler.o + x86_64-apple-darwin13.4.0-clang -O3 -c Lobject.cpp -o Lobject.o + x86_64-apple-darwin13.4.0-clang -O3 -c stringFuncts.cpp -o stringFuncts.o + x86_64-apple-darwin13.4.0-clang -O3 -c pasa.cpp -o pasa.o + x86_64-apple-darwin13.4.0-clang -O3 -c argProcessor.cpp -o argProcessor.o + x86_64-apple-darwin13.4.0-clang -o ./pasa alignment_segment.o cdna_alignment.o common_subs.o cdna_alignment_assembler.o Lobject.o stringFuncts.o pasa.o argProcessor.o -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + make[1]: Leaving directory '$SRC_DIR/pasa_cpp' + cd pasa-plugins/seqclean/mdust && make && cp mdust ../../../bin + make[1]: Entering directory '$SRC_DIR/pasa-plugins/seqclean/mdust' + x86_64-apple-darwin13.4.0-clang -O2 -Wall -c mdust.c -o mdust.o + x86_64-apple-darwin13.4.0-clang -O2 -Wall -c dust.c -o dust.o + x86_64-apple-darwin13.4.0-clang -O2 -Wall -c fastafile.c -o fastafile.o + x86_64-apple-darwin13.4.0-clang -o mdust mdust.o dust.o fastafile.o + make[1]: Leaving directory '$SRC_DIR/pasa-plugins/seqclean/mdust' + cd pasa-plugins/seqclean/psx && make && cp psx ../../../bin + make[1]: Entering directory '$SRC_DIR/pasa-plugins/seqclean/psx' + x86_64-apple-darwin13.4.0-clang -O2 -c psx.c -o psx.o + x86_64-apple-darwin13.4.0-clang -O2 -c child_dir.c -o child_dir.o + make[1]: Leaving directory '$SRC_DIR/pasa-plugins/seqclean/psx' +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/pasa/meta.yaml b/recipes/pasa/meta.yaml index b86f75dd4dd78..a9fc6e4096ae5 100644 --- a/recipes/pasa/meta.yaml +++ b/recipes/pasa/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('pasa', max_pin="x") }} diff --git a/recipes/pasta/build_failure.linux-64.yaml b/recipes/pasta/build_failure.linux-64.yaml deleted file mode 100644 index 3227c0b4386f7..0000000000000 --- a/recipes/pasta/build_failure.linux-64.yaml +++ /dev/null @@ -1,105 +0,0 @@ -recipe_sha: 65e7d2e1e37f5d09b369b83c2b28d55d132f52dfa10e858233a874f106158aa3 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: test failure -log: |2- - xorg-inputproto: 2.3.2-h7f98852_1002 conda-forge - xorg-kbproto: 1.0.7-h7f98852_1002 conda-forge - xorg-libice: 1.1.1-hd590300_0 conda-forge - xorg-libsm: 1.2.4-h7391055_0 conda-forge - xorg-libx11: 1.8.9-h8ee46fc_0 conda-forge - xorg-libxau: 1.0.11-hd590300_0 conda-forge - xorg-libxdmcp: 1.1.3-h7f98852_0 conda-forge - xorg-libxext: 1.3.4-h0b41bf4_2 conda-forge - xorg-libxfixes: 5.0.3-h7f98852_1004 conda-forge - xorg-libxi: 1.7.10-h7f98852_0 conda-forge - xorg-libxrender: 0.9.11-hd590300_0 conda-forge - xorg-libxt: 1.3.0-hd590300_1 conda-forge - xorg-libxtst: 1.2.3-h7f98852_1002 conda-forge - xorg-recordproto: 1.14.2-h7f98852_1002 conda-forge - xorg-renderproto: 0.11.1-h7f98852_1002 conda-forge - xorg-xextproto: 7.3.0-h0b41bf4_1003 conda-forge - xorg-xproto: 7.0.31-h7f98852_1007 conda-forge - xz: 5.2.6-h166bdaf_0 conda-forge - zlib: 1.3.1-h4ab18f5_1 conda-forge - zstd: 1.5.6-ha6fb4c9_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - export PREFIX=/opt/conda/conda-bld/pasta_1718122849359/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl - export SRC_DIR=/opt/conda/conda-bld/pasta_1718122849359/test_tmp - import: 'pasta' - import: 'pasta' - clustalw2 -help - grep OPTIONS - -OPTIONS :list the command line parameters - hmmalign -h - grep HMMER - # HMMER 3.1b2 (February 2015); http://hmmer.org/ - hmmbuild -h - grep HMMER - # HMMER 3.1b2 (February 2015); http://hmmer.org/ - muscle -version - grep -i MUSCLE - MUSCLE v3.8.1551 by Robert C. Edgar - prank -help - grep prank - prank v.170427. Minimal usage: 'prank sequence_file' - Advanced usage: 'prank [optional parameters] -d=sequence_file [optional parameters]' - raxml -h - grep -i raxml - This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018. - Please also consult the RAxML-manual - Please report bugs via the RAxML google group! - raxmlHPC[-SSE3|-AVX|-PTHREADS|-PTHREADS-SSE3|-PTHREADS-AVX|-HYBRID|-HYBRID-SSE3|HYBRID-AVX] - -A Specify one of the secondary structure substitution models implemented in RAxML. - -c Specify number of distinct rate catgories for RAxML when model of rate heterogeneity - "-f c": check if the alignment can be properly read by RAxML - in the two tree files. A file called RAxML_bipartitionFrequencies.outpuFileName - you will need to start RAxML with a non-comprehensive reference tree and an alignment containing all sequences (reference query) - you will need to start RAxML with a non-comprehensive reference tree and an alignment containing all sequences (reference query) - you will need to start RAxML with a non-comprehensive reference tree and an alignment containing all sequences (reference query) - -K Specify one of the multi-state substitution models (max 32 states) implemented in RAxML. - with RAxML using the -f e tree evaluation option. The file name should be: - RAxML_binaryModelParameters.runID - -w FULL (!) path to the directory into which RAxML shall write its output files - CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under - RAxML will only do a randomized stepwise addition order parsimony tree reconstruction - -y If you want to only compute a parsimony starting tree with RAxML specify "-y", - --flag-check When using this option, RAxML will only check if all command line flags specifed are available and then exit - RAxML will test all available prot subst. models except for LG4M, LG4X and GTR-based models, with and without empirical base frequencies. - --print-identical-sequences specify that RAxML shall automatically generate a .reduced alignment with all - grep -i raxml - raxmlp -h - This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018. - Please also consult the RAxML-manual - Please report bugs via the RAxML google group! - raxmlHPC[-SSE3|-AVX|-PTHREADS|-PTHREADS-SSE3|-PTHREADS-AVX|-HYBRID|-HYBRID-SSE3|HYBRID-AVX] - -A Specify one of the secondary structure substitution models implemented in RAxML. - -c Specify number of distinct rate catgories for RAxML when model of rate heterogeneity - "-f c": check if the alignment can be properly read by RAxML - in the two tree files. A file called RAxML_bipartitionFrequencies.outpuFileName - you will need to start RAxML with a non-comprehensive reference tree and an alignment containing all sequences (reference query) - you will need to start RAxML with a non-comprehensive reference tree and an alignment containing all sequences (reference query) - export PASTA_LOGGING_LEVEL=DEBUG - PASTA_LOGGING_LEVEL=DEBUG - you will need to start RAxML with a non-comprehensive reference tree and an alignment containing all sequences (reference query) - -K Specify one of the multi-state substitution models (max 32 states) implemented in RAxML. - export PASTA_LOGGING_FORMAT=RICH - with RAxML using the -f e tree evaluation option. The file name should be: - PASTA_LOGGING_FORMAT=RICH - RAxML_binaryModelParameters.runID - -w FULL (!) path to the directory into which RAxML shall write its output files - CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under - RAxML will only do a randomized stepwise addition order parsimony tree reconstruction - run_pasta.py -i /opt/conda/conda-bld/pasta_1718122849359/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/share/pasta/data/small.fasta - -y If you want to only compute a parsimony starting tree with RAxML specify "-y", - --flag-check When using this option, RAxML will only check if all command line flags specifed are available and then exit - RAxML will test all available prot subst. models except for LG4M, LG4X and GTR-based models, with and without empirical base frequencies. - --print-identical-sequences specify that RAxML shall automatically generate a .reduced alignment with all - PASTA ERROR: PASTA is exiting because of an error: - invalid mode: 'rU' - PASTA INFO: Reading input sequences from '$PREFIX/share/pasta/data/small.fasta'... - WARNING: Tests failed for pasta-1.9.0-py311hfad2c56_1.tar.bz2 - moving package to /opt/conda/conda-bld/broken - TESTS FAILED: pasta-1.9.0-py311hfad2c56_1.tar.bz2 -# Last 100 lines of the build log. diff --git a/recipes/pasta/build_failure.osx-64.yaml b/recipes/pasta/build_failure.osx-64.yaml deleted file mode 100644 index 9f49c41e872cc..0000000000000 --- a/recipes/pasta/build_failure.osx-64.yaml +++ /dev/null @@ -1,105 +0,0 @@ -recipe_sha: 65e7d2e1e37f5d09b369b83c2b28d55d132f52dfa10e858233a874f106158aa3 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: test failure -log: |2- - libzlib: 1.3.1-h87427d6_1 conda-forge - llvm-openmp: 18.1.7-h15ab845_0 conda-forge - mafft: 7.526-hec52a4b_0 conda-forge - mpfr: 4.2.1-h4f6b447_1 conda-forge - muscle: 3.8.1551-hb280591_6 bioconda - ncurses: 6.5-h5846eda_0 conda-forge - openjdk: 22.0.1-h2d185b6_0 conda-forge - openssl: 3.3.1-h87427d6_0 conda-forge - pasta: 1.9.0-py311h29d3010_1 local - pcre: 8.45-he49afe7_0 conda-forge - prank: 170427-h85dcccf_0 bioconda - pymongo: 4.7.3-py311hbafa61a_0 conda-forge - python: 3.11.9-h657bba9_0_cpython conda-forge - python_abi: 3.11-4_cp311 conda-forge - raxml: 8.2.13-h2413b67_1 bioconda - readline: 8.2-h9e318b2_1 conda-forge - sniffio: 1.3.1-pyhd8ed1ab_0 conda-forge - tk: 8.6.13-h1abcd95_1 conda-forge - tzdata: 2024a-h0c530f3_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - clustalw2 -help - grep OPTIONS - hmmalign -h - grep HMMER - hmmbuild -h - grep HMMER - muscle -version - grep -i MUSCLE - prank -help - grep prank - raxml -h - grep -i raxml - raxmlp -h - grep -i raxml - export PASTA_LOGGING_LEVEL=DEBUG - PASTA_LOGGING_LEVEL=DEBUG - export PASTA_LOGGING_FORMAT=RICH - PASTA_LOGGING_FORMAT=RICH - run_pasta.py -i /opt/mambaforge/envs/bioconda/conda-bld/pasta_1718123761694/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/share/pasta/data/small.fasta - PASTA ERROR: PASTA is exiting because of an error: - invalid mode: 'rU' - WARNING: Tests failed for pasta-1.9.0-py311h29d3010_1.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken - TESTS FAILED: pasta-1.9.0-py311h29d3010_1.tar.bz2 - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/pasta_1718123761694/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/pasta_1718123761694/test_tmp - import: 'pasta' - import: 'pasta' - -OPTIONS :list the command line parameters - # HMMER 3.1b2 (February 2015); http://hmmer.org/ - # HMMER 3.1b2 (February 2015); http://hmmer.org/ - MUSCLE v3.8.1551 by Robert C. Edgar - prank v.170427. Minimal usage: 'prank sequence_file' - Advanced usage: 'prank [optional parameters] -d=sequence_file [optional parameters]' - This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018. - Please also consult the RAxML-manual - Please report bugs via the RAxML google group! - raxmlHPC[-SSE3|-AVX|-PTHREADS|-PTHREADS-SSE3|-PTHREADS-AVX|-HYBRID|-HYBRID-SSE3|HYBRID-AVX] - -A Specify one of the secondary structure substitution models implemented in RAxML. - -c Specify number of distinct rate catgories for RAxML when model of rate heterogeneity - "-f c": check if the alignment can be properly read by RAxML - in the two tree files. A file called RAxML_bipartitionFrequencies.outpuFileName - you will need to start RAxML with a non-comprehensive reference tree and an alignment containing all sequences (reference query) - you will need to start RAxML with a non-comprehensive reference tree and an alignment containing all sequences (reference query) - you will need to start RAxML with a non-comprehensive reference tree and an alignment containing all sequences (reference query) - -K Specify one of the multi-state substitution models (max 32 states) implemented in RAxML. - with RAxML using the -f e tree evaluation option. The file name should be: - RAxML_binaryModelParameters.runID - -w FULL (!) path to the directory into which RAxML shall write its output files - CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under - RAxML will only do a randomized stepwise addition order parsimony tree reconstruction - -y If you want to only compute a parsimony starting tree with RAxML specify "-y", - --flag-check When using this option, RAxML will only check if all command line flags specifed are available and then exit - RAxML will test all available prot subst. models except for LG4M, LG4X and GTR-based models, with and without empirical base frequencies. - --print-identical-sequences specify that RAxML shall automatically generate a .reduced alignment with all - This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018. - Please also consult the RAxML-manual - Please report bugs via the RAxML google group! - raxmlHPC[-SSE3|-AVX|-PTHREADS|-PTHREADS-SSE3|-PTHREADS-AVX|-HYBRID|-HYBRID-SSE3|HYBRID-AVX] - -A Specify one of the secondary structure substitution models implemented in RAxML. - -c Specify number of distinct rate catgories for RAxML when model of rate heterogeneity - "-f c": check if the alignment can be properly read by RAxML - in the two tree files. A file called RAxML_bipartitionFrequencies.outpuFileName - you will need to start RAxML with a non-comprehensive reference tree and an alignment containing all sequences (reference query) - you will need to start RAxML with a non-comprehensive reference tree and an alignment containing all sequences (reference query) - you will need to start RAxML with a non-comprehensive reference tree and an alignment containing all sequences (reference query) - -K Specify one of the multi-state substitution models (max 32 states) implemented in RAxML. - with RAxML using the -f e tree evaluation option. The file name should be: - RAxML_binaryModelParameters.runID - -w FULL (!) path to the directory into which RAxML shall write its output files - CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under - RAxML will only do a randomized stepwise addition order parsimony tree reconstruction - -y If you want to only compute a parsimony starting tree with RAxML specify "-y", - --flag-check When using this option, RAxML will only check if all command line flags specifed are available and then exit - RAxML will test all available prot subst. models except for LG4M, LG4X and GTR-based models, with and without empirical base frequencies. - --print-identical-sequences specify that RAxML shall automatically generate a .reduced alignment with all - PASTA INFO: Reading input sequences from '$PREFIX/share/pasta/data/small.fasta'... -# Last 100 lines of the build log. diff --git a/recipes/pasta/meta.yaml b/recipes/pasta/meta.yaml index 03ae3152eaa67..7115e94c09680 100644 --- a/recipes/pasta/meta.yaml +++ b/recipes/pasta/meta.yaml @@ -13,7 +13,7 @@ source: - mpstart.patch # issue in OSX py38 (not in Linux nor OSX py37): RuntimeError: An attempt has been made to start a new process before the current process has finished its bootstrapping phase. build: - number: 1 + number: 2 skip: true # [py == 312] run_exports: - {{ pin_subpackage('pasta', max_pin="x") }} diff --git a/recipes/pathracer/build_failure.linux-64.yaml b/recipes/pathracer/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..a5ce6e62205f5 --- /dev/null +++ b/recipes/pathracer/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 94d8ba445828f69d966fcc16252e5537bd717701e9ddf8922b6342ee744ab170 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + libzlib: 1.3.1-hb9d3cd8_2 conda-forge + llvm-openmp: 8.0.1-hc9558a2_0 conda-forge + openmp: 8.0.1-0 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + zlib: 1.3.1-hb9d3cd8_2 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/pathracer_1734019783838/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.39-he00db2b_1 conda-forge + binutils_linux-64: 2.39-h5fc0e48_13 conda-forge + bzip2: 1.0.8-h4bc722e_7 conda-forge + c-ares: 1.34.3-hb9d3cd8_1 conda-forge + ca-certificates: 2024.8.30-hbcca054_0 conda-forge + cmake: 3.31.2-h74e3db0_1 conda-forge + gcc_impl_linux-64: 9.5.0-h99780fb_19 conda-forge + gcc_linux-64: 9.5.0-h4258300_13 conda-forge + gxx_impl_linux-64: 9.5.0-h99780fb_19 conda-forge + gxx_linux-64: 9.5.0-h43f449f_13 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + keyutils: 1.6.1-h166bdaf_0 conda-forge + krb5: 1.21.3-h659f571_0 conda-forge + ld_impl_linux-64: 2.39-hcc3a1bd_1 conda-forge + libcurl: 8.11.1-h332b0f4_0 conda-forge + libedit: 3.1.20191231-he28a2e2_2 conda-forge + libev: 4.33-hd590300_2 conda-forge + libexpat: 2.6.4-h5888daf_0 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 9.5.0-h0a57e50_19 conda-forge + libgcc-ng: 14.2.0-h69a702a_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + liblzma: 5.6.3-hb9d3cd8_1 conda-forge + libnghttp2: 1.64.0-h161d5f1_0 conda-forge + libsanitizer: 9.5.0-h2f262e1_19 conda-forge + libssh2: 1.11.1-hf672d98_0 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-devel_linux-64: 9.5.0-h0a57e50_19 conda-forge + libstdcxx-ng: 14.2.0-h4852527_1 conda-forge + libuv: 1.49.2-hb9d3cd8_0 conda-forge + libzlib: 1.3.1-hb9d3cd8_2 conda-forge + llvm-openmp: 8.0.1-hc9558a2_0 conda-forge + make: 4.4.1-hb9d3cd8_2 conda-forge + ncurses: 6.5-he02047a_1 conda-forge + openmp: 8.0.1-0 conda-forge + openssl: 3.4.0-hb9d3cd8_0 conda-forge + pkg-config: 0.29.2-h4bc722e_1009 conda-forge + rhash: 1.4.5-hb9d3cd8_0 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: SPAdes-3.16.0-pathracer-dev_21aeefb2b2.tar.gz + Downloading http://cab.spbu.ru/files/pathracer/SPAdes-3.16.0-pathracer-dev.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NameResolutionError(": Failed to resolve 'cab.spbu.ru' ([Errno -2] Name or service not known)")': /files/pathracer/SPAdes-3.16.0-pathracer-dev.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NameResolutionError(": Failed to resolve 'cab.spbu.ru' ([Errno -2] Name or service not known)")': /files/pathracer/SPAdes-3.16.0-pathracer-dev.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NameResolutionError(": Failed to resolve 'cab.spbu.ru' ([Errno -2] Name or service not known)")': /files/pathracer/SPAdes-3.16.0-pathracer-dev.tar.gz + WARNING: Error: HTTP 000 CONNECTION FAILED for url + Elapsed: - + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download http://cab.spbu.ru/files/pathracer/SPAdes-3.16.0-pathracer-dev.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/pathracer/build_failure.osx-64.yaml b/recipes/pathracer/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..99a7a8bb3feb2 --- /dev/null +++ b/recipes/pathracer/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 94d8ba445828f69d966fcc16252e5537bd717701e9ddf8922b6342ee744ab170 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (local): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (local): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/pathracer_1733953408929/_build_env + + + The following NEW packages will be INSTALLED: + + bzip2: 1.0.8-hfdf4475_7 conda-forge + c-ares: 1.34.3-hf13058a_1 conda-forge + ca-certificates: 2024.8.30-h8857fd0_0 conda-forge + cctools_osx-64: 1010.6-h00edd4c_2 conda-forge + clang: 18.1.8-default_h179603d_5 conda-forge + clang-18: 18.1.8-default_h0c94c6a_5 conda-forge + clang-format: 18.1.8-default_h0c94c6a_5 conda-forge + clang-format-18: 18.1.8-default_h0c94c6a_5 conda-forge + clang-tools: 18.1.8-default_h0c94c6a_5 conda-forge + clang_impl_osx-64: 18.1.8-h6a44ed1_23 conda-forge + clang_osx-64: 18.1.8-h7e5c614_23 conda-forge + clangdev: 18.1.8-default_h0c94c6a_5 conda-forge + clangxx: 18.1.8-default_h179603d_5 conda-forge + clangxx_impl_osx-64: 18.1.8-h4b7810f_23 conda-forge + clangxx_osx-64: 18.1.8-h7e5c614_23 conda-forge + cmake: 3.31.2-h477996e_1 conda-forge + compiler-rt: 18.1.8-h1020d70_1 conda-forge + compiler-rt_osx-64: 18.1.8-hf2b8a54_1 conda-forge + krb5: 1.21.3-h37d8d59_0 conda-forge + ld64_osx-64: 951.9-hc8d1a19_2 conda-forge + libclang: 18.1.8-default_h0c94c6a_5 conda-forge + libclang-cpp: 18.1.8-default_h0c94c6a_5 conda-forge + libclang-cpp18.1: 18.1.8-default_h0c94c6a_5 conda-forge + libclang13: 18.1.8-default_h9ff962c_5 conda-forge + libcurl: 8.10.1-h58e7537_0 conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libcxx-devel: 18.1.8-h7c275be_7 conda-forge + libedit: 3.1.20191231-h0678c8f_2 conda-forge + libev: 4.33-h10d778d_2 conda-forge + libexpat: 2.6.4-h240833e_0 conda-forge + libiconv: 1.17-hd75f5a5_2 conda-forge + libllvm18: 18.1.8-h9ce406d_2 conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libnghttp2: 1.64.0-hc7306c3_0 conda-forge + libssh2: 1.11.1-h3dc7d44_0 conda-forge + libuv: 1.49.2-hd79239c_0 conda-forge + libxml2: 2.13.5-he8ee3e7_1 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-openmp: 18.1.8-h15ab845_1 conda-forge + llvm-tools: 18.1.8-h9ce406d_2 conda-forge + llvm-tools-18: 18.1.8-h9ce406d_2 conda-forge + llvmdev: 18.1.8-h9ce406d_2 conda-forge + make: 4.4.1-h00291cd_2 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + pkg-config: 0.29.2-hf7e621a_1009 conda-forge + rhash: 1.4.5-ha44c9a9_0 conda-forge + sigtool: 0.1.3-h88f4db0_0 conda-forge + tapi: 1300.6.5-h390ca13_0 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache + Downloading source to cache: SPAdes-3.16.0-pathracer-dev_21aeefb2b2.tar.gz + Downloading http://cab.spbu.ru/files/pathracer/SPAdes-3.16.0-pathracer-dev.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NameResolutionError(": Failed to resolve 'cab.spbu.ru' ([Errno 8] nodename nor servname provided, or not known)")': /files/pathracer/SPAdes-3.16.0-pathracer-dev.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NameResolutionError(": Failed to resolve 'cab.spbu.ru' ([Errno 8] nodename nor servname provided, or not known)")': /files/pathracer/SPAdes-3.16.0-pathracer-dev.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NameResolutionError(": Failed to resolve 'cab.spbu.ru' ([Errno 8] nodename nor servname provided, or not known)")': /files/pathracer/SPAdes-3.16.0-pathracer-dev.tar.gz + WARNING: Error: HTTP 000 CONNECTION FAILED for url + Elapsed: - + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download http://cab.spbu.ru/files/pathracer/SPAdes-3.16.0-pathracer-dev.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/pathracer/meta.yaml b/recipes/pathracer/meta.yaml index 5298fc0f223f3..c81d68a37f9bf 100644 --- a/recipes/pathracer/meta.yaml +++ b/recipes/pathracer/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/pb-dazzler/meta.yaml b/recipes/pb-dazzler/meta.yaml index 40739d961b9b1..83ecb1b6d5650 100644 --- a/recipes/pb-dazzler/meta.yaml +++ b/recipes/pb-dazzler/meta.yaml @@ -2,7 +2,7 @@ package: name: pb-dazzler version: "0.0.1" build: - number: 4 + number: 5 source: - url: https://github.com/PacificBiosciences/DAZZ_DB/archive/b1c0f9c5beecf39ec316699d1e782814d45342c7.tar.gz folder: DAZZ_DB/ diff --git a/recipes/pb-falcon/meta.yaml b/recipes/pb-falcon/meta.yaml index 9963caac76c4d..60fd5a2398a99 100644 --- a/recipes/pb-falcon/meta.yaml +++ b/recipes/pb-falcon/meta.yaml @@ -12,7 +12,7 @@ source: folder: pb-falcon build: - number: 6 + number: 7 skip: True # [py27 or py36 or osx] run_exports: - {{ pin_subpackage(name, max_pin='x') }} diff --git a/recipes/pb-falconc/meta.yaml b/recipes/pb-falconc/meta.yaml index f4b77804ef6d7..0009d595d40ea 100644 --- a/recipes/pb-falconc/meta.yaml +++ b/recipes/pb-falconc/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 skip: True # [osx] requirements: diff --git a/recipes/pbbam/meta.yaml b/recipes/pbbam/meta.yaml index 62c86b7cd19b4..8c9afd195655c 100644 --- a/recipes/pbbam/meta.yaml +++ b/recipes/pbbam/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 skip: True # [osx] run_exports: - {{ pin_subpackage('pbbam', max_pin='x.x') }} diff --git a/recipes/pbcopper/build_failure.linux-64.yaml b/recipes/pbcopper/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..2b4e0f13e36fa --- /dev/null +++ b/recipes/pbcopper/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: a699b14e900de633e1d6327d9aa14636d45f982e79da491d1f4f54b3c3cc07de # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + ../include/pbcopper/align/LocalAlignment.h:19:5: note: 'PacBio::Align::LocalAlignment::LocalAlignment(int32_t, int32_t, int32_t, int32_t, int32_t, int, int, std::string)' + 19 | LocalAlignment(int32_t targetBegin, int32_t targetEnd, int32_t queryBegin, int32_t queryEnd, + | ^~~~~~~~~~~~~~ + ../include/pbcopper/align/LocalAlignment.h:16:7: note: 'class PacBio::Align::LocalAlignment' defined here + 16 | class LocalAlignment + | ^~~~~~~~~~~~~~ + ../src/align/LocalAlignment.cpp: In function 'PacBio::Align::LocalAlignment PacBio::Align::LocalAlign(const std::string&, const std::string&, const LocalAlignConfig&)': + ../src/align/LocalAlignment.cpp:40:50: error: 'const struct PacBio::Align::LocalAlignConfig' has no member named 'MatchScore' + 40 | StripedSmithWaterman::Aligner aligner{config.MatchScore, config.MismatchPenalty, + | ^~~~~~~~~~ + ../src/align/LocalAlignment.cpp:40:69: error: 'const struct PacBio::Align::LocalAlignConfig' has no member named 'MismatchPenalty' + 40 | StripedSmithWaterman::Aligner aligner{config.MatchScore, config.MismatchPenalty, + | ^~~~~~~~~~~~~~~ + ../src/align/LocalAlignment.cpp:41:50: error: 'const struct PacBio::Align::LocalAlignConfig' has no member named 'GapOpenPenalty' + 41 | config.GapOpenPenalty, config.GapExtendPenalty}; + | ^~~~~~~~~~~~~~ + ../src/align/LocalAlignment.cpp:41:73: error: 'const struct PacBio::Align::LocalAlignConfig' has no member named 'GapExtendPenalty' + 41 | config.GapOpenPenalty, config.GapExtendPenalty}; + | ^~~~~~~~~~~~~~~~ + ../src/align/LocalAlignment.cpp:41:89: error: no matching function for call to 'StripedSmithWaterman::Aligner::Aligner()' + 41 | config.GapOpenPenalty, config.GapExtendPenalty}; + | ^ + In file included from ../src/align/LocalAlignment.cpp:9: + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:194:5: note: candidate: 'StripedSmithWaterman::Aligner::Aligner(const StripedSmithWaterman::Aligner&)' + 194 | Aligner(const Aligner&); + | ^~~~~~~ + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:194:5: note: candidate expects 1 argument, 4 provided + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:93:5: note: candidate: 'StripedSmithWaterman::Aligner::Aligner(const int8_t*, const int&, const int8_t*, const int&)' + 93 | Aligner(const int8_t* score_matrix, const int& score_matrix_size, + | ^~~~~~~ + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:93:5: note: conversion of argument 1 would be ill-formed: + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:87:5: note: candidate: 'StripedSmithWaterman::Aligner::Aligner(const uint8_t&, const uint8_t&, const uint8_t&, const uint8_t&)' + 87 | Aligner(const uint8_t& match_score, const uint8_t& mismatch_penalty, + | ^~~~~~~ + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:87:5: note: conversion of argument 1 would be ill-formed: + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:79:5: note: candidate: 'StripedSmithWaterman::Aligner::Aligner()' + 79 | Aligner(void); + | ^~~~~~~ + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:79:5: note: candidate expects 0 arguments, 4 provided + ../src/align/LocalAlignment.cpp: In function 'std::vector PacBio::Align::LocalAlign(const std::string&, const std::vector >&, const LocalAlignConfig&)': + ../src/align/LocalAlignment.cpp:53:50: error: 'const struct PacBio::Align::LocalAlignConfig' has no member named 'MatchScore' + 53 | StripedSmithWaterman::Aligner aligner{config.MatchScore, config.MismatchPenalty, + | ^~~~~~~~~~ + ../src/align/LocalAlignment.cpp:53:69: error: 'const struct PacBio::Align::LocalAlignConfig' has no member named 'MismatchPenalty' + 53 | StripedSmithWaterman::Aligner aligner{config.MatchScore, config.MismatchPenalty, + | ^~~~~~~~~~~~~~~ + ../src/align/LocalAlignment.cpp:54:50: error: 'const struct PacBio::Align::LocalAlignConfig' has no member named 'GapOpenPenalty' + 54 | config.GapOpenPenalty, config.GapExtendPenalty}; + | ^~~~~~~~~~~~~~ + ../src/align/LocalAlignment.cpp:54:73: error: 'const struct PacBio::Align::LocalAlignConfig' has no member named 'GapExtendPenalty' + 54 | config.GapOpenPenalty, config.GapExtendPenalty}; + | ^~~~~~~~~~~~~~~~ + ../src/align/LocalAlignment.cpp:54:89: error: no matching function for call to 'StripedSmithWaterman::Aligner::Aligner()' + 54 | config.GapOpenPenalty, config.GapExtendPenalty}; + | ^ + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:194:5: note: candidate: 'StripedSmithWaterman::Aligner::Aligner(const StripedSmithWaterman::Aligner&)' + 194 | Aligner(const Aligner&); + | ^~~~~~~ + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:194:5: note: candidate expects 1 argument, 4 provided + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:93:5: note: candidate: 'StripedSmithWaterman::Aligner::Aligner(const int8_t*, const int&, const int8_t*, const int&)' + 93 | Aligner(const int8_t* score_matrix, const int& score_matrix_size, + | ^~~~~~~ + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:93:5: note: conversion of argument 1 would be ill-formed: + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:87:5: note: candidate: 'StripedSmithWaterman::Aligner::Aligner(const uint8_t&, const uint8_t&, const uint8_t&, const uint8_t&)' + 87 | Aligner(const uint8_t& match_score, const uint8_t& mismatch_penalty, + | ^~~~~~~ + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:87:5: note: conversion of argument 1 would be ill-formed: + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:79:5: note: candidate: 'StripedSmithWaterman::Aligner::Aligner()' + 79 | Aligner(void); + | ^~~~~~~ + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:79:5: note: candidate expects 0 arguments, 4 provided + [15/100] $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -Isrc/libpbcopper.a.p -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c20 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pbcopper-2.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -isystem$PREFIX/include -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbcopper.a.p/align_Seed.cpp.o -MF src/libpbcopper.a.p/align_Seed.cpp.o.d -o src/libpbcopper.a.p/align_Seed.cpp.o -c ../src/align/Seed.cpp + [16/100] $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -Isrc/libpbcopper.a.p -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c20 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pbcopper-2.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -isystem$PREFIX/include -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbcopper.a.p/align_Seeds.cpp.o -MF src/libpbcopper.a.p/align_Seeds.cpp.o.d -o src/libpbcopper.a.p/align_Seeds.cpp.o -c ../src/align/Seeds.cpp + [17/100] $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -Isrc/libpbcopper.a.p -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c20 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pbcopper-2.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -isystem$PREFIX/include -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbcopper.a.p/align_FindSeeds.cpp.o -MF src/libpbcopper.a.p/align_FindSeeds.cpp.o.d -o src/libpbcopper.a.p/align_FindSeeds.cpp.o -c ../src/align/FindSeeds.cpp + [18/100] $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -Isrc/libpbcopper.a.p -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c20 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pbcopper-2.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -isystem$PREFIX/include -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbcopper.a.p/align_LinearAlignment.cpp.o -MF src/libpbcopper.a.p/align_LinearAlignment.cpp.o.d -o src/libpbcopper.a.p/align_LinearAlignment.cpp.o -c ../src/align/LinearAlignment.cpp + [19/100] $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -Isrc/libpbcopper.a.p -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c20 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pbcopper-2.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -isystem$PREFIX/include -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbcopper.a.p/align_PairwiseAlignment.cpp.o -MF src/libpbcopper.a.p/align_PairwiseAlignment.cpp.o.d -o src/libpbcopper.a.p/align_PairwiseAlignment.cpp.o -c ../src/align/PairwiseAlignment.cpp + ninja: build stopped: subcommand failed. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/pbcopper_1734293730106/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/pbcopper_1734293730106/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/pbcopper/build_failure.linux-aarch64.yaml b/recipes/pbcopper/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..1336b0950020e --- /dev/null +++ b/recipes/pbcopper/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: a699b14e900de633e1d6327d9aa14636d45f982e79da491d1f4f54b3c3cc07de # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + ../include/pbcopper/align/LocalAlignment.h:19:5: note: 'PacBio::Align::LocalAlignment::LocalAlignment(int32_t, int32_t, int32_t, int32_t, int32_t, int, int, std::string)' + 19 | LocalAlignment(int32_t targetBegin, int32_t targetEnd, int32_t queryBegin, int32_t queryEnd, + | ^~~~~~~~~~~~~~ + ../include/pbcopper/align/LocalAlignment.h:16:7: note: 'class PacBio::Align::LocalAlignment' defined here + 16 | class LocalAlignment + | ^~~~~~~~~~~~~~ + ../src/align/LocalAlignment.cpp: In function 'PacBio::Align::LocalAlignment PacBio::Align::LocalAlign(const std::string&, const std::string&, const LocalAlignConfig&)': + ../src/align/LocalAlignment.cpp:40:50: error: 'const struct PacBio::Align::LocalAlignConfig' has no member named 'MatchScore' + 40 | StripedSmithWaterman::Aligner aligner{config.MatchScore, config.MismatchPenalty, + | ^~~~~~~~~~ + ../src/align/LocalAlignment.cpp:40:69: error: 'const struct PacBio::Align::LocalAlignConfig' has no member named 'MismatchPenalty' + 40 | StripedSmithWaterman::Aligner aligner{config.MatchScore, config.MismatchPenalty, + | ^~~~~~~~~~~~~~~ + ../src/align/LocalAlignment.cpp:41:50: error: 'const struct PacBio::Align::LocalAlignConfig' has no member named 'GapOpenPenalty' + 41 | config.GapOpenPenalty, config.GapExtendPenalty}; + | ^~~~~~~~~~~~~~ + ../src/align/LocalAlignment.cpp:41:73: error: 'const struct PacBio::Align::LocalAlignConfig' has no member named 'GapExtendPenalty' + 41 | config.GapOpenPenalty, config.GapExtendPenalty}; + | ^~~~~~~~~~~~~~~~ + ../src/align/LocalAlignment.cpp:41:89: error: no matching function for call to 'StripedSmithWaterman::Aligner::Aligner()' + 41 | config.GapOpenPenalty, config.GapExtendPenalty}; + | ^ + In file included from ../src/align/LocalAlignment.cpp:9: + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:194:5: note: candidate: 'StripedSmithWaterman::Aligner::Aligner(const StripedSmithWaterman::Aligner&)' + 194 | Aligner(const Aligner&); + | ^~~~~~~ + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:194:5: note: candidate expects 1 argument, 4 provided + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:93:5: note: candidate: 'StripedSmithWaterman::Aligner::Aligner(const int8_t*, const int&, const int8_t*, const int&)' + 93 | Aligner(const int8_t* score_matrix, const int& score_matrix_size, + | ^~~~~~~ + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:93:5: note: conversion of argument 1 would be ill-formed: + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:87:5: note: candidate: 'StripedSmithWaterman::Aligner::Aligner(const uint8_t&, const uint8_t&, const uint8_t&, const uint8_t&)' + 87 | Aligner(const uint8_t& match_score, const uint8_t& mismatch_penalty, + | ^~~~~~~ + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:87:5: note: conversion of argument 1 would be ill-formed: + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:79:5: note: candidate: 'StripedSmithWaterman::Aligner::Aligner()' + 79 | Aligner(void); + | ^~~~~~~ + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:79:5: note: candidate expects 0 arguments, 4 provided + ../src/align/LocalAlignment.cpp: In function 'std::vector PacBio::Align::LocalAlign(const std::string&, const std::vector >&, const LocalAlignConfig&)': + ../src/align/LocalAlignment.cpp:53:50: error: 'const struct PacBio::Align::LocalAlignConfig' has no member named 'MatchScore' + 53 | StripedSmithWaterman::Aligner aligner{config.MatchScore, config.MismatchPenalty, + | ^~~~~~~~~~ + ../src/align/LocalAlignment.cpp:53:69: error: 'const struct PacBio::Align::LocalAlignConfig' has no member named 'MismatchPenalty' + 53 | StripedSmithWaterman::Aligner aligner{config.MatchScore, config.MismatchPenalty, + | ^~~~~~~~~~~~~~~ + ../src/align/LocalAlignment.cpp:54:50: error: 'const struct PacBio::Align::LocalAlignConfig' has no member named 'GapOpenPenalty' + 54 | config.GapOpenPenalty, config.GapExtendPenalty}; + | ^~~~~~~~~~~~~~ + ../src/align/LocalAlignment.cpp:54:73: error: 'const struct PacBio::Align::LocalAlignConfig' has no member named 'GapExtendPenalty' + 54 | config.GapOpenPenalty, config.GapExtendPenalty}; + | ^~~~~~~~~~~~~~~~ + ../src/align/LocalAlignment.cpp:54:89: error: no matching function for call to 'StripedSmithWaterman::Aligner::Aligner()' + 54 | config.GapOpenPenalty, config.GapExtendPenalty}; + | ^ + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:194:5: note: candidate: 'StripedSmithWaterman::Aligner::Aligner(const StripedSmithWaterman::Aligner&)' + 194 | Aligner(const Aligner&); + | ^~~~~~~ + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:194:5: note: candidate expects 1 argument, 4 provided + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:93:5: note: candidate: 'StripedSmithWaterman::Aligner::Aligner(const int8_t*, const int&, const int8_t*, const int&)' + 93 | Aligner(const int8_t* score_matrix, const int& score_matrix_size, + | ^~~~~~~ + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:93:5: note: conversion of argument 1 would be ill-formed: + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:87:5: note: candidate: 'StripedSmithWaterman::Aligner::Aligner(const uint8_t&, const uint8_t&, const uint8_t&, const uint8_t&)' + 87 | Aligner(const uint8_t& match_score, const uint8_t& mismatch_penalty, + | ^~~~~~~ + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:87:5: note: conversion of argument 1 would be ill-formed: + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:79:5: note: candidate: 'StripedSmithWaterman::Aligner::Aligner()' + 79 | Aligner(void); + | ^~~~~~~ + ../src/align/../../include/pbcopper/align/cssw/ssw_cpp.h:79:5: note: candidate expects 0 arguments, 4 provided + [15/100] $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -Isrc/libpbcopper.a.p -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c20 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pbcopper-2.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -isystem$PREFIX/include -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbcopper.a.p/align_Seed.cpp.o -MF src/libpbcopper.a.p/align_Seed.cpp.o.d -o src/libpbcopper.a.p/align_Seed.cpp.o -c ../src/align/Seed.cpp + [16/100] $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -Isrc/libpbcopper.a.p -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c20 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pbcopper-2.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -isystem$PREFIX/include -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbcopper.a.p/align_Seeds.cpp.o -MF src/libpbcopper.a.p/align_Seeds.cpp.o.d -o src/libpbcopper.a.p/align_Seeds.cpp.o -c ../src/align/Seeds.cpp + [17/100] $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -Isrc/libpbcopper.a.p -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c20 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pbcopper-2.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -isystem$PREFIX/include -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbcopper.a.p/align_FindSeeds.cpp.o -MF src/libpbcopper.a.p/align_FindSeeds.cpp.o.d -o src/libpbcopper.a.p/align_FindSeeds.cpp.o -c ../src/align/FindSeeds.cpp + [18/100] $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -Isrc/libpbcopper.a.p -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c20 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pbcopper-2.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -isystem$PREFIX/include -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbcopper.a.p/align_LinearAlignment.cpp.o -MF src/libpbcopper.a.p/align_LinearAlignment.cpp.o.d -o src/libpbcopper.a.p/align_LinearAlignment.cpp.o -c ../src/align/LinearAlignment.cpp + [19/100] $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -Isrc/libpbcopper.a.p -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c20 -O3 -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pbcopper-2.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -isystem$PREFIX/include -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbcopper.a.p/align_PairwiseAlignment.cpp.o -MF src/libpbcopper.a.p/align_PairwiseAlignment.cpp.o.d -o src/libpbcopper.a.p/align_PairwiseAlignment.cpp.o -c ../src/align/PairwiseAlignment.cpp + ninja: build stopped: subcommand failed. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/pbcopper_1734270977997/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/pbcopper_1734270977997/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/pbcopper/meta.yaml b/recipes/pbcopper/meta.yaml index 88e34ecffcf75..12dfbbcb3efa3 100644 --- a/recipes/pbcopper/meta.yaml +++ b/recipes/pbcopper/meta.yaml @@ -24,7 +24,7 @@ extra: - armintoepfer build: - number: 3 + number: 4 skip: True # [osx] run_exports: - {{ pin_subpackage('pbcopper', max_pin='x.x') }} diff --git a/recipes/pbgzip/meta.yaml b/recipes/pbgzip/meta.yaml index dc3cfeeb5b6d3..cb219e6ceff2e 100644 --- a/recipes/pbgzip/meta.yaml +++ b/recipes/pbgzip/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 544820be0da38f6af7be18792d00d6d3dd2fe3f7f3b08a67c3aa35fb1bbeaeb1 build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('pbgzip', max_pin=None) }} @@ -35,4 +35,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/pbipa/meta.yaml b/recipes/pbipa/meta.yaml index 2132f8fc999f9..fa0ce722736b1 100644 --- a/recipes/pbipa/meta.yaml +++ b/recipes/pbipa/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 skip: True # [osx] extra: diff --git a/recipes/pbjasmine/meta.yaml b/recipes/pbjasmine/meta.yaml index e73d1f40afbb0..bfd68790e21f4 100644 --- a/recipes/pbjasmine/meta.yaml +++ b/recipes/pbjasmine/meta.yaml @@ -24,7 +24,7 @@ extra: - should_be_noarch_generic build: - number: 0 + number: 1 skip: True # [osx] binary_relocation: False run_exports: diff --git a/recipes/pblat/meta.yaml b/recipes/pblat/meta.yaml index 6a444d26da303..46ad73168b02d 100644 --- a/recipes/pblat/meta.yaml +++ b/recipes/pblat/meta.yaml @@ -11,7 +11,7 @@ source: - pblat-aarch64.patch # [aarch64] build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage("pblat", max_pin="x.x") }} diff --git a/recipes/pbpigeon/meta.yaml b/recipes/pbpigeon/meta.yaml index 1f109235cc705..d815c1384c241 100644 --- a/recipes/pbpigeon/meta.yaml +++ b/recipes/pbpigeon/meta.yaml @@ -12,7 +12,7 @@ source: build: # repackaged binaries skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage('pbpigeon', max_pin='x.x') }} requirements: diff --git a/recipes/pbsim/meta.yaml b/recipes/pbsim/meta.yaml index 24c441d99f778..474c52adb5abc 100644 --- a/recipes/pbsim/meta.yaml +++ b/recipes/pbsim/meta.yaml @@ -9,7 +9,7 @@ source: - 0001-Fix-nullptr-char-comparision.patch build: - number: 7 + number: 8 requirements: build: diff --git a/recipes/pbsim2/meta.yaml b/recipes/pbsim2/meta.yaml index 1317c9d393da9..9e0706ef7f2fb 100644 --- a/recipes/pbsim2/meta.yaml +++ b/recipes/pbsim2/meta.yaml @@ -10,7 +10,7 @@ source: - recursive-include data * build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/pbsim3/meta.yaml b/recipes/pbsim3/meta.yaml index c9902c70eb6ef..71996a3a266ef 100644 --- a/recipes/pbsim3/meta.yaml +++ b/recipes/pbsim3/meta.yaml @@ -14,7 +14,7 @@ source: - recursive-include data * build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/pbwt/build_failure.linux-64.yaml b/recipes/pbwt/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..cb250d58f5bc6 --- /dev/null +++ b/recipes/pbwt/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: dc29f31f36cfd9aa02a6558a8e72ba1e82ba2d41ecff4400d2aef7a2fe9c972b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pbwt-3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pbwt-3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + Makefile + README.md + array.c + array.h + build_env_setup.sh + conda_build.sh + dict.c + dict.h + hash.c + hash.h + metadata_conda_debug.yaml + pbwt.h + pbwtCore.c + pbwtGeneticMap.c + pbwtHtslib.c + pbwtIO.c + pbwtImpute.c + pbwtLikelihood.c + pbwtMain.c + pbwtMatch.c + pbwtMerge.c + pbwtPaint.c + pbwtSample.c + test + utils.c + utils.h + echo '#define PBWT_COMMIT_HASH """"' > version.h + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -O3 -I../htslib -c -o pbwtMain.o pbwtMain.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -O3 -I../htslib -c -o pbwtCore.o pbwtCore.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -O3 -I../htslib -c -o pbwtSample.o pbwtSample.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -O3 -I../htslib -c -o pbwtIO.o pbwtIO.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -O3 -I../htslib -c -o pbwtMatch.o pbwtMatch.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -O3 -I../htslib -c -o pbwtImpute.o pbwtImpute.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -O3 -I../htslib -c -o pbwtPaint.o pbwtPaint.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -O3 -I../htslib -c -o pbwtLikelihood.o pbwtLikelihood.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -O3 -I../htslib -c -o pbwtMerge.o pbwtMerge.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -O3 -I../htslib -c -o pbwtGeneticMap.o pbwtGeneticMap.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -O3 -I../htslib -c -o pbwtHtslib.o pbwtHtslib.c + pbwtHtslib.c: In function 'pbwtWriteVcf': + pbwtHtslib.c:296:3: warning: ignoring return value of 'bcf_hdr_write' declared with attribute 'warn_unused_result' [-Wunused-result] + 296 | bcf_hdr_write(fp, bcfHeader) ; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ + pbwtHtslib.c:380:7: warning: ignoring return value of 'bcf_write' declared with attribute 'warn_unused_result' [-Wunused-result] + 380 | bcf_write(fp, bcfHeader, bcfRecord) ; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -O3 -I../htslib -c -o hash.o hash.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -O3 -I../htslib -c -o dict.o dict.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -O3 -I../htslib -c -o array.o array.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -O3 -I../htslib -c -o utils.o utils.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -O3 -I../htslib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib pbwtMain.o pbwtCore.o pbwtSample.o pbwtIO.o pbwtMatch.o pbwtImpute.o pbwtPaint.o pbwtLikelihood.o pbwtMerge.o pbwtGeneticMap.o pbwtHtslib.o hash.o dict.o array.o utils.o -lpthread -lhts -lz -lm -lbz2 -llzma -o pbwt + /opt/conda/conda-bld/pbwt_1734240823040/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -llzma: No such file or directory + collect2: error: ld returned 1 exit status + make: *** [Makefile:30: pbwt] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/pbwt_1734240823040/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/pbwt_1734240823040/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/pbwt/meta.yaml b/recipes/pbwt/meta.yaml index b92f7636c810a..52f114c197d00 100644 --- a/recipes/pbwt/meta.yaml +++ b/recipes/pbwt/meta.yaml @@ -8,7 +8,7 @@ source: sha256: 57b02f4ec56d236a3f4e6e9789dbefbc505a3157840edcbee2201a831806003e build: - number: 10 + number: 11 requirements: build: diff --git a/recipes/pcaone/build_failure.linux-64.yaml b/recipes/pcaone/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..b0feaafa1a074 --- /dev/null +++ b/recipes/pcaone/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 278122194efa470dc28874f43a1db09e7e32808ffe5f3442ade3ca0d8615b7e0 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + 10 | class CppBgenWriter { + | ^~~~~~~~~~~~~ + writer.cpp:463:15: error: no declaration matches 'uint64_t bgen::CppBgenWriter::add_genotype_data(uint16_t, float*, uint32_t, uint8_t, bool, uint8_t)' + 463 | std::uint64_t CppBgenWriter::add_genotype_data(std::uint16_t n_alleles, + | ^~~~~~~~~~~~~ + writer.cpp:463:15: note: no functions named 'uint64_t bgen::CppBgenWriter::add_genotype_data(uint16_t, float*, uint32_t, uint8_t, bool, uint8_t)' + writer.h:10:7: note: 'class bgen::CppBgenWriter' defined here + 10 | class CppBgenWriter { + | ^~~~~~~~~~~~~ + writer.cpp:474:15: error: no declaration matches 'uint64_t bgen::CppBgenWriter::add_genotype_data(uint16_t, float*, uint32_t, uint8_t*, uint8_t, uint8_t, bool, uint8_t)' + 474 | std::uint64_t CppBgenWriter::add_genotype_data(std::uint16_t n_alleles, + | ^~~~~~~~~~~~~ + writer.cpp:474:15: note: no functions named 'uint64_t bgen::CppBgenWriter::add_genotype_data(uint16_t, float*, uint32_t, uint8_t*, uint8_t, uint8_t, bool, uint8_t)' + writer.h:10:7: note: 'class bgen::CppBgenWriter' defined here + 10 | class CppBgenWriter { + | ^~~~~~~~~~~~~ + make[1]: *** [Makefile:20: writer.o] Error 1 + make[1]: Leaving directory '$SRC_DIR/external/bgen' + make: *** [Makefile:171: bgenlib] Error 2 + + Resource usage statistics from building pcaone: + Process count: 9 + CPU time: Sys=0:00:01.2, User=0:00:36.3 + Memory: 176.0M + Disk usage: 17.7K + Time elapsed: 0:01:42.5 + + + Packaging pcaone + Packaging pcaone-0.4.8-h346a427_1 + number of files: 1 + Fixing permissions + Packaged license file/s. + INFO :: Time taken to mark (prefix) + 0 replacements in 0 files was 0.01 seconds + Files containing CONDA_PREFIX + ----------------------------- + bin/PCAone (text): Patching + WARNING: Importing conda-verify failed. Please be sure to test your packages. conda install conda-verify to make this message go away. + TEST START: /opt/conda/conda-bld/linux-64/pcaone-0.4.8-h346a427_1.tar.bz2 + Renaming work directory '/opt/conda/conda-bld/pcaone_1733855445241/work' to '/opt/conda/conda-bld/pcaone_1733855445241/work_moved_pcaone-0.4.8-h346a427_1_linux-64' + shutil.move(work)=/opt/conda/conda-bld/pcaone_1733855445241/work, dest=/opt/conda/conda-bld/pcaone_1733855445241/work_moved_pcaone-0.4.8-h346a427_1_linux-64) + Reloading output folder (local, file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/pcaone_1733855445241/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_kmp_llvm conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-ng: 14.2.0-h69a702a_1 conda-forge + libhwloc: 2.11.2-default_h0d58e46_1001 conda-forge + libiconv: 1.17-hd590300_2 conda-forge + liblzma: 5.6.3-hb9d3cd8_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libxml2: 2.13.5-h0d44e9d_1 conda-forge + libzlib: 1.3.1-hb9d3cd8_2 conda-forge + llvm-openmp: 19.1.5-h024ca30_0 conda-forge + mkl: 2025.0.0-h901ac74_941 conda-forge + pcaone: 0.4.8-h346a427_1 local + tbb: 2022.0.0-hceb3a55_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + export PREFIX=/opt/conda/conda-bld/pcaone_1733855445241/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + export SRC_DIR=/opt/conda/conda-bld/pcaone_1733855445241/test_tmp + PCAone --help + /opt/conda/conda-bld/pcaone_1733855445241/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/bin/PCAone: line 5: /opt/conda/conda-bld/pcaone_1733855445241/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/bin/PCAone.avx2: No such file or directory + WARNING: Tests failed for pcaone-0.4.8-h346a427_1.tar.bz2 - moving package to /opt/conda/conda-bld/broken + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/pcaone_1733855445241/test_tmp/conda_test_runner.sh']' returned non-zero exit status 127. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: pcaone-0.4.8-h346a427_1.tar.bz2 +# Last 100 lines of the build log. diff --git a/recipes/pcaone/meta.yaml b/recipes/pcaone/meta.yaml index 6cf82d11d8f79..e78452ab26610 100644 --- a/recipes/pcaone/meta.yaml +++ b/recipes/pcaone/meta.yaml @@ -11,7 +11,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('pcaone', max_pin="x") }} diff --git a/recipes/pcasuite/meta.yaml b/recipes/pcasuite/meta.yaml index 19dd174a2397b..e68fde3d5d9cf 100644 --- a/recipes/pcasuite/meta.yaml +++ b/recipes/pcasuite/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 79d0d94d9e483d516b903970f8d5a9f69bc793fe4e8d81ed25b74af2b1d115e4 build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/peakranger/build_failure.linux-64.yaml b/recipes/peakranger/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..ae561857f04b8 --- /dev/null +++ b/recipes/peakranger/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: d495f989077131e55609dc8b9ac26034fc136c8b6826497fafa784a97d71148f # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + from /opt/conda/conda-bld/peakranger_1733963156572/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include/boost/smart_ptr/make_shared.hpp:14, + from /opt/conda/conda-bld/peakranger_1733963156572/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include/boost/make_shared.hpp:14, + from ./common/boost_header.h:11, + from short_reads/BlockedRead.h:12, + from short_reads/BlockedRead.cpp:8: + /opt/conda/conda-bld/peakranger_1733963156572/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ + In file included from /opt/conda/conda-bld/peakranger_1733963156572/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, + from /opt/conda/conda-bld/peakranger_1733963156572/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include/boost/smart_ptr/make_shared.hpp:14, + from /opt/conda/conda-bld/peakranger_1733963156572/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include/boost/make_shared.hpp:14, + from ./common/boost_header.h:11, + from short_reads/PairEndedReads.h:12, + from short_reads/PairEndedReadsAux.h:11, + from short_reads/PairEndedReadsAux.cpp:9: + /opt/conda/conda-bld/peakranger_1733963156572/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ + In file included from /opt/conda/conda-bld/peakranger_1733963156572/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, + from /opt/conda/conda-bld/peakranger_1733963156572/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include/boost/smart_ptr/make_shared.hpp:14, + from /opt/conda/conda-bld/peakranger_1733963156572/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include/boost/make_shared.hpp:14, + from ./common/boost_header.h:11, + from ./short_reads/BlockedRead.h:12, + from short_reads/ReadPairAux.h:13, + from short_reads/ReadPairAux.cpp:8: + /opt/conda/conda-bld/peakranger_1733963156572/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ + short_reads/point_reads.cpp: In member function 'void point_reads::set_reads(uint32_t, uint32_t, uint32_t, uint32_t, std::vector::iterator, std::vector::iterator, std::vector::iterator, std::vector::iterator, std::vector >&)': + short_reads/point_reads.cpp:56:14: warning: variable 'arrayStart' set but not used [-Wunused-but-set-variable] + 56 | uint32_t arrayStart; + | ^~~~~~~~~~ + short_reads/point_reads.cpp:57:14: warning: variable 'arrayEnd' set but not used [-Wunused-but-set-variable] + 57 | uint32_t arrayEnd; + | ^~~~~~~~ + wiggle/JTwigglefile.cpp: In member function 'virtual void JT_wiggle_file::_process(uint32_t, uint32_t, uint32_t, uint32_t, std::vector::iterator, std::vector::iterator, std::vector::iterator, std::vector::iterator, std::ostream&)': + wiggle/JTwigglefile.cpp:53:18: warning: variable 'arrayStart' set but not used [-Wunused-but-set-variable] + 53 | uint32_t arrayStart; + | ^~~~~~~~~~ + wiggle/JTwigglefile.cpp:54:18: warning: variable 'arrayEnd' set but not used [-Wunused-but-set-variable] + 54 | uint32_t arrayEnd; + | ^~~~~~~~ + wiggle/strandedjtwiggle.cpp: In member function 'virtual void stranded_jtwiggle::_process_neg(uint32_t, uint32_t, uint32_t, uint32_t, std::vector::iterator, std::vector::iterator, std::ostream&)': + wiggle/strandedjtwiggle.cpp:655:14: warning: variable 'arrayStart' set but not used [-Wunused-but-set-variable] + 655 | uint32_t arrayStart; + | ^~~~~~~~~~ + wiggle/strandedjtwiggle.cpp:656:14: warning: variable 'arrayEnd' set but not used [-Wunused-but-set-variable] + 656 | uint32_t arrayEnd; + | ^~~~~~~~ + In file included from wiggle/testwig.h:14, + from wiggle/testwig.cpp:8: + ./wiggle/wigbuilder.h: In instantiation of 'void wig_builder::_process(uint32_t, uint32_t, uint32_t, uint32_t, std::vector::iterator, std::vector::iterator, wigs&, _T) [with _T = void (*)(unsigned int, unsigned int, unsigned int, unsigned int&, unsigned int&); uint32_t = unsigned int; std::vector::iterator = std::vector::iterator; wigs = std::vector]': + ./wiggle/wigbuilder.h:208:25: required from 'void wig_builder::_binned_wig_compiler(uint32_t, uint32_t, uint32_t, std::vector::iterator, std::vector::iterator, std::ostream&, const char*, _T) [with _T = void (*)(unsigned int, unsigned int, unsigned int, unsigned int&, unsigned int&); uint32_t = unsigned int; std::vector::iterator = std::vector::iterator; std::ostream = std::basic_ostream]' + wiggle/testwig.cpp:134:28: required from here + ./wiggle/wigbuilder.h:98:18: warning: variable 'arrayStart' set but not used [-Wunused-but-set-variable] + 98 | uint32_t arrayStart; + | ^~~~~~~~~~ + ./wiggle/wigbuilder.h:99:18: warning: variable 'arrayEnd' set but not used [-Wunused-but-set-variable] + 99 | uint32_t arrayEnd; + | ^~~~~~~~ + In file included from wiggle/wigbuilder.cpp:8: + wiggle/wigbuilder.h: In instantiation of 'void wig_builder::_process(uint32_t, uint32_t, uint32_t, uint32_t, std::vector::iterator, std::vector::iterator, wigs&, _T) [with _T = void (*)(unsigned int, unsigned int, unsigned int, unsigned int&, unsigned int&); uint32_t = unsigned int; std::vector::iterator = std::vector::iterator; wigs = std::vector]': + wiggle/wigbuilder.cpp:45:13: required from here + wiggle/wigbuilder.h:98:18: warning: variable 'arrayStart' set but not used [-Wunused-but-set-variable] + 98 | uint32_t arrayStart; + | ^~~~~~~~~~ + wiggle/wigbuilder.h:99:18: warning: variable 'arrayEnd' set but not used [-Wunused-but-set-variable] + 99 | uint32_t arrayEnd; + | ^~~~~~~~ + wiggle/wiggle_reporter.cpp: In member function 'virtual void wiggle_reporter::_process(uint32_t, uint32_t, uint32_t, uint32_t, std::vector::iterator, std::vector::iterator, std::vector::iterator, std::vector::iterator, std::ostream&)': + wiggle/wiggle_reporter.cpp:185:14: warning: variable 'arrayStart' set but not used [-Wunused-but-set-variable] + 185 | uint32_t arrayStart; + | ^~~~~~~~~~ + wiggle/wiggle_reporter.cpp:186:14: warning: variable 'arrayEnd' set but not used [-Wunused-but-set-variable] + 186 | uint32_t arrayEnd; + | ^~~~~~~~ + make: *** [Makefile:18: peakranger] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/peakranger_1733963156572/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/peakranger_1733963156572/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/peakranger/meta.yaml b/recipes/peakranger/meta.yaml index 316991275986f..e4264106268c3 100644 --- a/recipes/peakranger/meta.yaml +++ b/recipes/peakranger/meta.yaml @@ -9,7 +9,7 @@ source: - makefile.patch build: - number: 9 + number: 10 skip: True # [osx] requirements: diff --git a/recipes/pear/meta.yaml b/recipes/pear/meta.yaml index 1deddbffdcd79..10b43ac754809 100644 --- a/recipes/pear/meta.yaml +++ b/recipes/pear/meta.yaml @@ -12,7 +12,7 @@ source: url: https://depot.galaxyproject.org/software/pear/pear_0.9.6_src_all.tar.gz build: - number: 10 + number: 11 skip: True # [osx] requirements: diff --git a/recipes/pecat/meta.yaml b/recipes/pecat/meta.yaml index 1f11b5bf2cede..ebc7bcf1db1d7 100644 --- a/recipes/pecat/meta.yaml +++ b/recipes/pecat/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('pecat', max_pin="x") }} diff --git a/recipes/peer/build_failure.osx-64.yaml b/recipes/peer/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..4210be0039b3c --- /dev/null +++ b/recipes/peer/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 46e7ae8ca2a6572da2cab51d60b4cf47368a4796022c082dd62ee55f228b310d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + license: GPL-2.0-or-later + license_file: + - LICENSE + - External/yaml-cpp/license.txt + packages_from_this = build( + summary: A collection of Bayesian approaches to infer hidden determinants and their + effects from gene expression profiles using factor analysis methods + extra: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + copy_test_source_files: true + final: true + + + raise BuildScriptException(str(exc), caused_by=exc) from exc + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/peer_1733863051246/work + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/peer_1733863051246/work/conda_build.sh']' returned non-zero exit status 2. + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/peer_1733863051246/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/peer_1733863051246/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/peer_1733863051246/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/peer-1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/peer-1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/peer-1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/peer-1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -- The C compiler identification is Clang 18.1.8 + -- The CXX compiler identification is Clang 18.1.8 + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped + -- Detecting C compile features + -- Detecting C compile features - done + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Configuring done (2.7s) + -- Generating done (0.1s) + -- Build files have been written to: $SRC_DIR/build + [ 2%] Building CXX object External/alglib/src/CMakeFiles/alglib.dir/ap.cpp.o + [ 4%] Building CXX object External/csv_parser/CMakeFiles/csv_parser.dir/csv_parser.cpp.o + [ 6%] Building CXX object External/alglib/src/CMakeFiles/alglib.dir/fasttransforms.cpp.o + [ 8%] Building CXX object External/alglib/src/CMakeFiles/alglib.dir/solvers.cpp.o + [ 10%] Building CXX object External/alglib/src/CMakeFiles/alglib.dir/dataanalysis.cpp.o + [ 12%] Building CXX object External/alglib/src/CMakeFiles/alglib.dir/linalg.cpp.o + [ 14%] Building CXX object External/alglib/src/CMakeFiles/alglib.dir/alglibmisc.cpp.o + [ 16%] Building CXX object External/alglib/src/CMakeFiles/alglib.dir/integration.cpp.o + [ 18%] Building CXX object External/alglib/src/CMakeFiles/alglib.dir/specialfunctions.cpp.o + [ 20%] Building CXX object External/alglib/src/CMakeFiles/alglib.dir/diffequations.cpp.o + [ 22%] Building CXX object External/alglib/src/CMakeFiles/alglib.dir/optimization.cpp.o + [ 24%] Building CXX object External/alglib/src/CMakeFiles/alglib.dir/interpolation.cpp.o + [ 26%] Building CXX object External/alglib/src/CMakeFiles/alglib.dir/statistics.cpp.o + [ 28%] Building CXX object External/alglib/src/CMakeFiles/alglib.dir/alglibinternal.cpp.o + [ 30%] Linking CXX static library libalglib.a + [ 30%] Built target alglib +# Last 100 lines of the build log. diff --git a/recipes/peer/meta.yaml b/recipes/peer/meta.yaml index b24994dc6127a..1d86cf04189c6 100644 --- a/recipes/peer/meta.yaml +++ b/recipes/peer/meta.yaml @@ -14,7 +14,7 @@ source: - patches/0001-Comment-out-SWIG-package-search.patch build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/pegasusio/meta.yaml b/recipes/pegasusio/meta.yaml index 2160e3d1d318a..7dda20480503c 100644 --- a/recipes/pegasusio/meta.yaml +++ b/recipes/pegasusio/meta.yaml @@ -10,7 +10,7 @@ source: sha256: "bdbcad3652e31cb128d0d4526ae3f50706f75ba05a2efa9f3ed77e2acf37b1ef" build: - number: 1 + number: 2 entry_points: - pegasusio = pegasusio.__main__:main script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" diff --git a/recipes/pepnovo/meta.yaml b/recipes/pepnovo/meta.yaml index 63618acce1669..b8aa10e18a832 100644 --- a/recipes/pepnovo/meta.yaml +++ b/recipes/pepnovo/meta.yaml @@ -10,7 +10,7 @@ source: - 0002-fix-float-positive-infinity.patch build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage('pepnovo', max_pin=None) }} diff --git a/recipes/percolator/build_failure.linux-64.yaml b/recipes/percolator/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..5e842071f249e --- /dev/null +++ b/recipes/percolator/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 40e473305bea8a805f034a53916ceb8647178fbbfa7fc56834513492033ccb98 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + /opt/conda/conda-bld/percolator_1734018227004/work/converterbuild/percolator_out.cxx:11123:9: error: expected initializer at end of input + 11123 | ::xml_schema::dom::unique_ptr< ::xercesc::DOMDocument > d ( + | ^ + /opt/conda/conda-bld/percolator_1734018227004/work/converterbuild/percolator_out.cxx:11123:9: error: expected '}' at end of input + /opt/conda/conda-bld/percolator_1734018227004/work/converterbuild/percolator_out.hxx:4069:1: note: to match this '{' + 4069 | { + | ^ + make[2]: *** [CMakeFiles/perclibrary_part.dir/build.make:107: CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o] Error 1 + make[2]: *** Waiting for unfinished jobs.... + [ 26%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o + cd $SRC_DIR/converterbuild/MSToolkit && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o -MF CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o -c $SRC_DIR/src/converters/MSToolkit/MSConvertFile.cpp + [ 28%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSObject.cpp.o + cd $SRC_DIR/converterbuild/MSToolkit && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSObject.cpp.o -MF CMakeFiles/MSToolkit.dir/MSObject.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSObject.cpp.o -c $SRC_DIR/src/converters/MSToolkit/MSObject.cpp + [ 30%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSReader.cpp.o + cd $SRC_DIR/converterbuild/MSToolkit && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSReader.cpp.o -MF CMakeFiles/MSToolkit.dir/MSReader.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSReader.cpp.o -c $SRC_DIR/src/converters/MSToolkit/MSReader.cpp + [ 32%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o + cd $SRC_DIR/converterbuild/MSToolkit && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o -MF CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o -c $SRC_DIR/src/converters/MSToolkit/MSSingleScan.cpp + [ 33%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o + cd $SRC_DIR/converterbuild/MSToolkit && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o -MF CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o -c $SRC_DIR/src/converters/MSToolkit/MSTAllRT.cpp + [ 35%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o + cd $SRC_DIR/converterbuild/MSToolkit && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o -MF CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o -c $SRC_DIR/src/converters/MSToolkit/MSTDemo.cpp + [ 37%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSWarper.cpp.o + cd $SRC_DIR/converterbuild/MSToolkit && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSWarper.cpp.o -MF CMakeFiles/MSToolkit.dir/MSWarper.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSWarper.cpp.o -c $SRC_DIR/src/converters/MSToolkit/MSWarper.cpp + [ 39%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/Spectrum.cpp.o + cd $SRC_DIR/converterbuild/MSToolkit && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/Spectrum.cpp.o -MF CMakeFiles/MSToolkit.dir/Spectrum.cpp.o.d -o CMakeFiles/MSToolkit.dir/Spectrum.cpp.o -c $SRC_DIR/src/converters/MSToolkit/Spectrum.cpp + [ 41%] Building CXX object CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DBOOST_ALL_NO_LIB -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -I$SRC_DIR/src/converters/MSToolkit -I$SRC_DIR/src/converters/../../src -I$SRC_DIR/converterbuild -I$SRC_DIR/src/converters -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o -MF CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o.d -o CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o -c $SRC_DIR/converterbuild/gaml_tandem1.0.cxx + [ 42%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/crawutils.cpp.o + cd $SRC_DIR/converterbuild/MSToolkit && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/crawutils.cpp.o -MF CMakeFiles/MSToolkit.dir/crawutils.cpp.o.d -o CMakeFiles/MSToolkit.dir/crawutils.cpp.o -c $SRC_DIR/src/converters/MSToolkit/crawutils.cpp + make[2]: Leaving directory '$SRC_DIR/converterbuild' + make[1]: *** [CMakeFiles/Makefile2:198: CMakeFiles/perclibrary_part.dir/all] Error 2 + make[1]: *** Waiting for unfinished jobs.... + [ 44%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat.cpp.o + cd $SRC_DIR/converterbuild/MSToolkit && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat.cpp.o -c $SRC_DIR/src/converters/MSToolkit/msmat.cpp + [ 46%] Building CXX object CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DBOOST_ALL_NO_LIB -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -I$SRC_DIR/src/converters/MSToolkit -I$SRC_DIR/src/converters/../../src -I$SRC_DIR/converterbuild -I$SRC_DIR/src/converters -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o -MF CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o.d -o CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o -c $SRC_DIR/converterbuild/tandem2011.12.01.1.cxx + [ 48%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_base.cpp.o + cd $SRC_DIR/converterbuild/MSToolkit && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat_base.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat_base.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat_base.cpp.o -c $SRC_DIR/src/converters/MSToolkit/msmat_base.cpp + [ 50%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o + cd $SRC_DIR/converterbuild/MSToolkit && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o -c $SRC_DIR/src/converters/MSToolkit/msmat_header_parser.cpp + [ 51%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_test.cpp.o + cd $SRC_DIR/converterbuild/MSToolkit && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat_test.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat_test.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat_test.cpp.o -c $SRC_DIR/src/converters/MSToolkit/msmat_test.cpp + [ 53%] Building CXX object CMakeFiles/converters.dir/Reader.cpp.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DBOOST_ALL_NO_LIB -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -I$SRC_DIR/src/converters/MSToolkit -I$SRC_DIR/src/converters/../../src -I$SRC_DIR/converterbuild -I$SRC_DIR/src/converters -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT CMakeFiles/converters.dir/Reader.cpp.o -MF CMakeFiles/converters.dir/Reader.cpp.o.d -o CMakeFiles/converters.dir/Reader.cpp.o -c $SRC_DIR/src/converters/Reader.cpp + [ 55%] Linking CXX static library libMSToolkit.a + cd $SRC_DIR/converterbuild/MSToolkit && $BUILD_PREFIX/bin/cmake -P CMakeFiles/MSToolkit.dir/cmake_clean_target.cmake + cd $SRC_DIR/converterbuild/MSToolkit && $BUILD_PREFIX/bin/cmake -E cmake_link_script CMakeFiles/MSToolkit.dir/link.txt --verbose=1 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar qc libMSToolkit.a CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o CMakeFiles/MSToolkit.dir/MSObject.cpp.o CMakeFiles/MSToolkit.dir/MSReader.cpp.o CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o CMakeFiles/MSToolkit.dir/MSWarper.cpp.o CMakeFiles/MSToolkit.dir/Spectrum.cpp.o CMakeFiles/MSToolkit.dir/crawutils.cpp.o CMakeFiles/MSToolkit.dir/msmat.cpp.o CMakeFiles/MSToolkit.dir/msmat_base.cpp.o CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o CMakeFiles/MSToolkit.dir/msmat_test.cpp.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib libMSToolkit.a + make[2]: Leaving directory '$SRC_DIR/converterbuild' + [ 55%] Built target MSToolkit + [ 57%] Building CXX object CMakeFiles/converters.dir/SqtReader.cpp.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DBOOST_ALL_NO_LIB -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -I$SRC_DIR/src/converters/MSToolkit -I$SRC_DIR/src/converters/../../src -I$SRC_DIR/converterbuild -I$SRC_DIR/src/converters -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT CMakeFiles/converters.dir/SqtReader.cpp.o -MF CMakeFiles/converters.dir/SqtReader.cpp.o.d -o CMakeFiles/converters.dir/SqtReader.cpp.o -c $SRC_DIR/src/converters/SqtReader.cpp + [ 58%] Building CXX object CMakeFiles/converters.dir/MzidentmlReader.cpp.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DBOOST_ALL_NO_LIB -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -I$SRC_DIR/src/converters/MSToolkit -I$SRC_DIR/src/converters/../../src -I$SRC_DIR/converterbuild -I$SRC_DIR/src/converters -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT CMakeFiles/converters.dir/MzidentmlReader.cpp.o -MF CMakeFiles/converters.dir/MzidentmlReader.cpp.o.d -o CMakeFiles/converters.dir/MzidentmlReader.cpp.o -c $SRC_DIR/src/converters/MzidentmlReader.cpp + [ 60%] Building CXX object CMakeFiles/converters.dir/SequestReader.cpp.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DBOOST_ALL_NO_LIB -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -I$SRC_DIR/src/converters/MSToolkit -I$SRC_DIR/src/converters/../../src -I$SRC_DIR/converterbuild -I$SRC_DIR/src/converters -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT CMakeFiles/converters.dir/SequestReader.cpp.o -MF CMakeFiles/converters.dir/SequestReader.cpp.o.d -o CMakeFiles/converters.dir/SequestReader.cpp.o -c $SRC_DIR/src/converters/SequestReader.cpp + [ 62%] Building CXX object CMakeFiles/converters.dir/MsgfplusReader.cpp.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DBOOST_ALL_NO_LIB -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -I$SRC_DIR/src/converters/MSToolkit -I$SRC_DIR/src/converters/../../src -I$SRC_DIR/converterbuild -I$SRC_DIR/src/converters -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT CMakeFiles/converters.dir/MsgfplusReader.cpp.o -MF CMakeFiles/converters.dir/MsgfplusReader.cpp.o.d -o CMakeFiles/converters.dir/MsgfplusReader.cpp.o -c $SRC_DIR/src/converters/MsgfplusReader.cpp + [ 64%] Building CXX object CMakeFiles/converters.dir/TandemReader.cpp.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DBOOST_ALL_NO_LIB -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -I$SRC_DIR/src/converters/MSToolkit -I$SRC_DIR/src/converters/../../src -I$SRC_DIR/converterbuild -I$SRC_DIR/src/converters -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT CMakeFiles/converters.dir/TandemReader.cpp.o -MF CMakeFiles/converters.dir/TandemReader.cpp.o.d -o CMakeFiles/converters.dir/TandemReader.cpp.o -c $SRC_DIR/src/converters/TandemReader.cpp + [ 66%] Building CXX object CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DBOOST_ALL_NO_LIB -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -I$SRC_DIR/src/converters/MSToolkit -I$SRC_DIR/src/converters/../../src -I$SRC_DIR/converterbuild -I$SRC_DIR/src/converters -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o -MF CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o.d -o CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o -c $SRC_DIR/src/converters/FragSpectrumScanDatabase.cpp + [ 67%] Building CXX object CMakeFiles/converters.dir/Interface.cpp.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DBOOST_ALL_NO_LIB -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -I$SRC_DIR/src/converters/MSToolkit -I$SRC_DIR/src/converters/../../src -I$SRC_DIR/converterbuild -I$SRC_DIR/src/converters -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT CMakeFiles/converters.dir/Interface.cpp.o -MF CMakeFiles/converters.dir/Interface.cpp.o.d -o CMakeFiles/converters.dir/Interface.cpp.o -c $SRC_DIR/src/converters/Interface.cpp + [ 69%] Building CXX object CMakeFiles/converters.dir/FragSpectrumScanDatabaseBoostdb.cpp.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DBOOST_ALL_NO_LIB -DXML_SUPPORT -DXSD_CXX11 -D__BOOSTDB__ -I$SRC_DIR/src/converters/MSToolkit/RAMP -I$SRC_DIR/src/converters/MSToolkit -I$SRC_DIR/src/converters/../../src -I$SRC_DIR/converterbuild -I$SRC_DIR/src/converters -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/percolator-3.7.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c14 -O3 -I{PREFIX}/include -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -DNDEBUG -O3 -DNDEBUG -std=c14 -MD -MT CMakeFiles/converters.dir/FragSpectrumScanDatabaseBoostdb.cpp.o -MF CMakeFiles/converters.dir/FragSpectrumScanDatabaseBoostdb.cpp.o.d -o CMakeFiles/converters.dir/FragSpectrumScanDatabaseBoostdb.cpp.o -c $SRC_DIR/src/converters/FragSpectrumScanDatabaseBoostdb.cpp + [ 71%] Linking CXX static library libconverters.a + $BUILD_PREFIX/bin/cmake -P CMakeFiles/converters.dir/cmake_clean_target.cmake + $BUILD_PREFIX/bin/cmake -E cmake_link_script CMakeFiles/converters.dir/link.txt --verbose=1 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar qc libconverters.a CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o CMakeFiles/converters.dir/Reader.cpp.o CMakeFiles/converters.dir/SqtReader.cpp.o CMakeFiles/converters.dir/MzidentmlReader.cpp.o CMakeFiles/converters.dir/SequestReader.cpp.o CMakeFiles/converters.dir/MsgfplusReader.cpp.o CMakeFiles/converters.dir/TandemReader.cpp.o CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o CMakeFiles/converters.dir/Interface.cpp.o CMakeFiles/converters.dir/FragSpectrumScanDatabaseBoostdb.cpp.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib libconverters.a + make[2]: Leaving directory '$SRC_DIR/converterbuild' + [ 71%] Built target converters + make[1]: Leaving directory '$SRC_DIR/converterbuild' + make: *** [Makefile:166: all] Error 2 + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/percolator_1734018227004/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/percolator_1734018227004/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/percolator/meta.yaml b/recipes/percolator/meta.yaml index 263639be02075..4e9f35939f0ae 100644 --- a/recipes/percolator/meta.yaml +++ b/recipes/percolator/meta.yaml @@ -10,7 +10,7 @@ source: sha256: f1c9833063cb4e99c51a632efc3f80c6b8f48a43fd440ea3eb0968af5c84b97a build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('percolator', max_pin="x") }} diff --git a/recipes/peregrine-2021/meta.yaml b/recipes/peregrine-2021/meta.yaml index 0fde3c8097ef9..b1627c18ebb58 100644 --- a/recipes/peregrine-2021/meta.yaml +++ b/recipes/peregrine-2021/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 source: url: https://github.com/cschin/peregrine-2021/archive/refs/tags/v{{version}}.tar.gz diff --git a/recipes/perl-aceperl/build_failure.osx-64.yaml b/recipes/perl-aceperl/build_failure.osx-64.yaml deleted file mode 100644 index 52c1ba19b69d8..0000000000000 --- a/recipes/perl-aceperl/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: dc19b25fa2da363df4e6bbaddd1c664388f934f77843ddcdfa3fc60d2a732975 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-aceperl_1685358473248/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - Freesubs.xs:120:4: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XPUSHs(sv_2mortal(newSVpv(timestamp,timestamp_size))); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-aceperl_1685358473248/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:462:19: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-aceperl_1685358473248/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:666:29: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports "({ STATEMENTS; })" */ - ^ - Freesubs.xs:120:4: note: '{' token is here - XPUSHs(sv_2mortal(newSVpv(timestamp,timestamp_size))); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-aceperl_1685358473248/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:462:30: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^ - Freesubs.xs:120:4: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XPUSHs(sv_2mortal(newSVpv(timestamp,timestamp_size))); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-aceperl_1685358473248/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:462:32: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-aceperl_1685358473248/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:371:25: note: expanded from macro 'EXTEND' - # define EXTEND(p,n) STMT_START { \ - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-aceperl_1685358473248/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:666:29: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports "({ STATEMENTS; })" */ - ^ - Freesubs.xs:120:4: note: '{' token is here - XPUSHs(sv_2mortal(newSVpv(timestamp,timestamp_size))); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-aceperl_1685358473248/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:462:32: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-aceperl_1685358473248/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:371:36: note: expanded from macro 'EXTEND' - # define EXTEND(p,n) STMT_START { \ - ^ - Freesubs.xs:120:4: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XPUSHs(sv_2mortal(newSVpv(timestamp,timestamp_size))); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-aceperl_1685358473248/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:462:32: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-aceperl_1685358473248/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:376:28: note: expanded from macro 'EXTEND' - } } STMT_END - ^ - Freesubs.xs:120:4: note: ')' token is here - XPUSHs(sv_2mortal(newSVpv(timestamp,timestamp_size))); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-aceperl_1685358473248/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:462:32: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-aceperl_1685358473248/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:376:30: note: expanded from macro 'EXTEND' - } } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-aceperl_1685358473248/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - Freesubs.xs:120:4: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XPUSHs(sv_2mortal(newSVpv(timestamp,timestamp_size))); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-aceperl_1685358473248/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:462:59: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^ - Freesubs.xs:120:4: note: ')' token is here - XPUSHs(sv_2mortal(newSVpv(timestamp,timestamp_size))); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-aceperl_1685358473248/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:462:61: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-aceperl_1685358473248/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - 128 warnings generated. - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make[1]: *** [Makefile:460: ../blib/arch/auto/Ace/Freesubs/Freesubs.bundle] Error 1 - make[1]: Leaving directory '$SRC_DIR/Freesubs' - make: *** [Makefile:679: subdirs] Error 2 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-aceperl_1685358473248/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-aceperl/meta.yaml b/recipes/perl-aceperl/meta.yaml index 2638b8cd23eb8..a36d94373b49e 100644 --- a/recipes/perl-aceperl/meta.yaml +++ b/recipes/perl-aceperl/meta.yaml @@ -13,7 +13,7 @@ source: - makefile-options.patch build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/perl-acme-damn/meta.yaml b/recipes/perl-acme-damn/meta.yaml index c7e270f00201a..75832937d32c5 100644 --- a/recipes/perl-acme-damn/meta.yaml +++ b/recipes/perl-acme-damn/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 7 + number: 8 requirements: build: diff --git a/recipes/perl-algorithm-cluster/meta.yaml b/recipes/perl-algorithm-cluster/meta.yaml index b774eb2cfaf6f..93d040300f0ba 100644 --- a/recipes/perl-algorithm-cluster/meta.yaml +++ b/recipes/perl-algorithm-cluster/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage('perl-algorithm-cluster', max_pin="x") }} @@ -38,4 +38,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/perl-bio-bigfile/build_failure.osx-64.yaml b/recipes/perl-bio-bigfile/build_failure.osx-64.yaml deleted file mode 100644 index 71c7c3958ec15..0000000000000 --- a/recipes/perl-bio-bigfile/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: a91240c97d13ef07dbbcea68c57c8e871e81fc679fc71a3abc532d40ce3b7176 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o spacedSeed.o -c spacedSeed.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o splatAli.o -c splatAli.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o sqlList.o -c sqlList.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o sqlNum.o -c sqlNum.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o subText.o -c subText.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o sufa.o -c sufa.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o sufx.o -c sufx.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o synQueue.o -c synQueue.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o tabRow.o -c tabRow.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o tagStorm.o -c tagStorm.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - tagStorm.c:163:5: warning: variable 'stanzaCount' set but not used [-Wunused-but-set-variable] - int stanzaCount = 0; - ^ - tagStorm.c:164:5: warning: variable 'tagCount' set but not used [-Wunused-but-set-variable] - int tagCount = 0; - ^ - 2 warnings generated. - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o textOut.o -c textOut.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o tokenizer.o -c tokenizer.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o trix.o -c trix.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o twoBit.o -c twoBit.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o udc.o -c udc.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o vcf.o -c vcf.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o vcfBits.o -c vcfBits.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o vGfx.o -c vGfx.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o vPng.o -c vPng.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o verbose.o -c verbose.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o wildcmp.o -c wildcmp.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o wormdna.o -c wormdna.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - wormdna.c:625:5: warning: variable 'lineCount' set but not used [-Wunused-but-set-variable] - int lineCount = 0; - ^ - 1 warning generated. - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o xAli.o -c xAli.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o xa.o -c xa.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o xap.o -c xap.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o xenshow.o -c xenshow.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o xmlEscape.o -c xmlEscape.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o xp.o -c xp.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - x86_64-apple-darwin13.4.0-clang -O -g -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-bio-bigfile-1.07 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -L$PREFIX/lib -I$PREFIX/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wno-unused-variable -Wno-deprecated-declarations -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$PREFIX/include/libpng16 -o zlibFace.o -c zlibFace.c - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - ar rcus x86_64/jkweb.a aliType.o annoAssembly.o annoFilter.o annoFormatter.o annoFormatTab.o annoGrator.o annoGrateWig.o annoGratorQuery.o annoOption.o annoRow.o annoStreamer.o annoStreamBigBed.o annoStreamBigWig.o annoStreamTab.o annoStreamTabix.o annoStreamVcf.o apacheLog.o asParse.o aveStats.o axt.o axtAffine.o bamFile.o base64.o basicBed.o bbiRead.o bbiWrite.o bedTabix.o bigBed.o binRange.o bits.o blastOut.o blastParse.o boxClump.o boxLump.o bPlusTree.o bwgCreate.o bwgQuery.o bwgValsOnChrom.o cda.o chain.o chainBlock.o chainConnect.o chainToAxt.o chainToPsl.o cheapcgi.o cirTree.o codebias.o colHash.o common.o correlate.o crTree.o dgRange.o diGraph.o dlist.o dnaLoad.o dnaMarkov.o dnaMotif.o dnaseq.o dnautil.o dtdParse.o dyOut.o dystring.o elmTree.o emblParse.o errCatch.o errAbort.o fa.o ffAli.o ffScore.o fieldedTable.o filePath.o fixColor.o flydna.o fof.o font/mgCourier10.o font/mgCourier12.o font/mgCourier14.o font/mgCourier18.o font/mgCourier24.o font/mgCourier34.o font/mgCourier8.o font/mgHelvetica10.o font/mgHelvetica12.o font/mgHelvetica14.o font/mgHelvetica18.o font/mgHelvetica24.o font/mgHelvetica34.o font/mgHelvetica8.o font/mgHelveticaBold10.o font/mgHelveticaBold12.o font/mgHelveticaBold14.o font/mgHelveticaBold18.o font/mgHelveticaBold24.o font/mgHelveticaBold34.o font/mgHelveticaBold8.o font/mgSixhi6.o font/mgSail8.o font/mgTimes10.o font/mgTimes12.o font/mgTimes14.o font/mgTimes18.o font/mgTimes24.o font/mgTimes34.o font/mgTimes8.o font/mgMenlo12.o fq.o fuzzyShow.o gapCalc.o gdf.o gemfont.o genomeRangeTree.o gfNet.o gff.o gff3.o gfxPoly.o gifLabel.o hacTree.o hash.o hex.o histogram.o hmmPfamParse.o hmmstats.o htmlPage.o htmshell.o hmac.o https.o intExp.o intValTree.o internet.o itsa.o iupac.o jointalign.o jpegSize.o jsonParse.o jsonWrite.o keys.o knetUdc.o kxTok.o linefile.o lineFileOnBigBed.o localmem.o log.o longToList.o maf.o mafFromAxt.o mafScore.o mailViaPipe.o md5.o memalloc.o memgfx.o meta.o metaWig.o mgCircle.o mgPolygon.o mime.o net.o nib.o nibTwo.o nt4.o numObscure.o obscure.o oldGff.o oligoTm.o options.o osunix.o pairHmm.o pairDistance.o paraFetch.o peakCluster.o phyloTree.o pipeline.o portimpl.o pngwrite.o psGfx.o psPoly.o pscmGfx.o psl.o pslGenoShow.o pslShow.o pslTbl.o pslTransMap.o pthreadDoList.o pthreadWrap.o qa.o quickHeap.o quotedP.o ra.o rainbow.o raToStruct.o rbTree.o rangeTree.o regexHelper.o repMask.o rle.o rnautil.o rqlEval.o rqlParse.o rudp.o scoreWindow.o seg.o seqOut.o seqStats.o servBrcMcw.o servCrunx.o servcis.o servcl.o servmsII.o servpws.o shaRes.o slog.o snof.o snofmake.o snofsig.o spaceSaver.o spacedColumn.o spacedSeed.o splatAli.o sqlList.o sqlNum.o subText.o sufa.o sufx.o synQueue.o tabRow.o tagStorm.o textOut.o tokenizer.o trix.o twoBit.o udc.o vcf.o vcfBits.o vGfx.o vPng.o verbose.o wildcmp.o wormdna.o xAli.o xa.o xap.o xenshow.o xmlEscape.o xp.o zlibFace.o - make: Leaving directory '$SRC_DIR/kent-335_base/src/lib' - clang-15: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - Warning: ExtUtils::CBuilder not installed or no compiler detected - Proceeding with configuration, but compilation may fail during Build - - Created MYMETA.yml and MYMETA.json - Creating new 'Build' script for 'Bio-BigFile' version '1.07' - Building Bio-BigFile - Error: no compiler detected to compile 'lib/Bio/DB/BigFile.c'. Aborting - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-bio-bigfile_1685531699280/work/conda_build.sh']' returned non-zero exit status 255. -# Last 100 lines of the build log. diff --git a/recipes/perl-bio-bigfile/meta.yaml b/recipes/perl-bio-bigfile/meta.yaml index d7d6e2e69e884..779aabe019222 100644 --- a/recipes/perl-bio-bigfile/meta.yaml +++ b/recipes/perl-bio-bigfile/meta.yaml @@ -12,7 +12,9 @@ source: folder: kent-335_base build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage("perl-bio-bigfile", max_pin="x") }} requirements: build: diff --git a/recipes/perl-bio-db-hts/meta.yaml b/recipes/perl-bio-db-hts/meta.yaml index c6b1db9d44812..24cc4d9bf46d2 100644 --- a/recipes/perl-bio-db-hts/meta.yaml +++ b/recipes/perl-bio-db-hts/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 12a6bc1f579513cac8b9167cce4e363655cc8eba26b7d9fe1170dfe95e044f42 build: - number: 9 + number: 10 run_exports: - {{ pin_subpackage("perl-bio-db-hts", max_pin="x") }} diff --git a/recipes/perl-bio-easel/meta.yaml b/recipes/perl-bio-easel/meta.yaml index d7e9036ac09e7..5730aa41a4326 100644 --- a/recipes/perl-bio-easel/meta.yaml +++ b/recipes/perl-bio-easel/meta.yaml @@ -18,7 +18,7 @@ source: folder: src/easel build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/perl-bloom-faster/meta.yaml b/recipes/perl-bloom-faster/meta.yaml index 29341c0aa36d2..06d80618b96f0 100644 --- a/recipes/perl-bloom-faster/meta.yaml +++ b/recipes/perl-bloom-faster/meta.yaml @@ -13,7 +13,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x") }} - number: 7 + number: 8 requirements: build: diff --git a/recipes/perl-cairo/build_failure.linux-64.yaml b/recipes/perl-cairo/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..bc5934234d361 --- /dev/null +++ b/recipes/perl-cairo/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: fa3620ab4b79ce7451222ba0ee23b341149b0ef4efb61859b93c4b6cc730d5fe # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - xorg-libxrender + test: + commands: + - perl -e "use Cairo" + about: + home: http://gtk2-perl.sourceforge.net + license: lgpl_2_1 + summary: Perl interface to the cairo 2d vector graphics library + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/conda/conda-bld/perl-cairo_1734214301783/work + export PREFIX=/opt/conda/conda-bld/perl-cairo_1734214301783/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl + export BUILD_PREFIX=/opt/conda/conda-bld/perl-cairo_1734214301783/_build_env + export SRC_DIR=/opt/conda/conda-bld/perl-cairo_1734214301783/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-cairo-1.109 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-cairo-1.109 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + Package zlib was not found in the pkg-config search path. + Perhaps you should add the directory containing zlib.pc' + to the PKG_CONFIG_PATH environment variable + Package 'zlib', required by 'cairo', not found + at Makefile.PL line 99. + *** can not find package cairo >= 1.0.0 + *** check that it is properly installed and available in PKG_CONFIG_PATH + at Makefile.PL line 99. + make: *** No targets specified and no makefile found. Stop. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/perl-cairo_1734214301783/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/perl-cairo_1734214301783/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/perl-cairo/build_failure.osx-64.yaml b/recipes/perl-cairo/build_failure.osx-64.yaml index 43f625a15ef4d..75f82d7871b5f 100644 --- a/recipes/perl-cairo/build_failure.osx-64.yaml +++ b/recipes/perl-cairo/build_failure.osx-64.yaml @@ -1,104 +1,104 @@ -recipe_sha: bad751686d858366f05c2b116c8009fa9a67aef0346f1584763ba3c907dc7d6d # The commit at which this recipe failed to build. +recipe_sha: fa3620ab4b79ce7451222ba0ee23b341149b0ef4efb61859b93c4b6cc730d5fe # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- - STMT_START { \ - ^ - In file included from cairo-perl-flags.c:5: - In file included from ./cairo-perl.h:14: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:6161: - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/inline.h:2619:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - ENV_LOCK; - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:2924:31: note: expanded from macro 'ENV_LOCK' - # define ENV_LOCK MUTEX_LOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/thread.h:219:5: note: expanded from macro 'MUTEX_LOCK' - } STMT_END - ^ - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/inline.h:2619:5: note: ')' token is here - ENV_LOCK; - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:2924:31: note: expanded from macro 'ENV_LOCK' - # define ENV_LOCK MUTEX_LOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/thread.h:219:7: note: expanded from macro 'MUTEX_LOCK' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - In file included from cairo-perl-flags.c:5: - In file included from ./cairo-perl.h:14: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:6161: - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/inline.h:2627:5: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - ENV_UNLOCK; - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:2925:31: note: expanded from macro 'ENV_UNLOCK' - # define ENV_UNLOCK MUTEX_UNLOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/thread.h:222:5: note: expanded from macro 'MUTEX_UNLOCK' - STMT_START { \ - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:666:29: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports "({ STATEMENTS; })" */ - ^ - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/inline.h:2627:5: note: '{' token is here - ENV_UNLOCK; - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:2925:31: note: expanded from macro 'ENV_UNLOCK' - # define ENV_UNLOCK MUTEX_UNLOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/thread.h:222:16: note: expanded from macro 'MUTEX_UNLOCK' - STMT_START { \ - ^ - In file included from cairo-perl-flags.c:5: - In file included from ./cairo-perl.h:14: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:6161: - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/inline.h:2627:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - ENV_UNLOCK; - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:2925:31: note: expanded from macro 'ENV_UNLOCK' - # define ENV_UNLOCK MUTEX_UNLOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/thread.h:227:5: note: expanded from macro 'MUTEX_UNLOCK' - } STMT_END - ^ - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/inline.h:2627:5: note: ')' token is here - ENV_UNLOCK; - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:2925:31: note: expanded from macro 'ENV_UNLOCK' - # define ENV_UNLOCK MUTEX_UNLOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/thread.h:227:7: note: expanded from macro 'MUTEX_UNLOCK' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - 98 warnings generated. - rm -f blib/arch/auto/Cairo/Cairo.bundle - LD_RUN_PATH="$PREFIX/lib" x86_64-apple-darwin13.4.0-clang -Wl,-rpath,"$PREFIX/lib" -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fstack-protector-strong Cairo.o CairoFont.o CairoMatrix.o CairoPath.o CairoPattern.o CairoSurface.o CairoRegion.o CairoFt.o cairo-perl-enums.o cairo-perl-flags.o -o blib/arch/auto/Cairo/Cairo.bundle \ - -L$PREFIX/lib -lcairo -lfreetype \ + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + - font-ttf-source-code-pro 2.038 h77eed37_0 + - font-ttf-ubuntu 0.83 h77eed37_3 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + - icu 75.1 h120a0e1_0 + - libcxx 19.1.5 hf95d169_0 + - libexpat 2.6.4 h240833e_0 + - libffi 3.4.2 h0d85af4_5 + - libiconv 1.17 hd75f5a5_2 + - libzlib 1.3.1 hd23fc13_2 + raise BuildScriptException(str(exc), caused_by=exc) from exc + - perl 5.32.1 7_h10d778d_perl5 + - fonts-conda-forge 1 0 + - libintl 0.22.5 hdfe23c8_3 + - libpng 1.6.44 h4b8f8c9_0 + - pcre2 10.44 h7634a1b_2 + - perl-data-dumper 2.183 pl5321h10d778d_0 + - perl-exporter 5.74 pl5321hd8ed1ab_0 + - perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 + - perl-extutils-pkgconfig 1.16 pl5321hdfd78af_2 + - pixman 0.44.2 h1fd1274_0 + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1734244947873/work/conda_build.sh']' returned non-zero exit status 2. + - pkg-config 0.29.2 hf7e621a_1009 + - fonts-conda-ecosystem 1 0 + - freetype 2.12.1 h60636b9_2 + - libglib 2.82.2 hb6ef654_0 + - perl-carp 1.50 pl5321hd8ed1ab_0 + - fontconfig 2.15.0 h37eeddb_1 + - perl-pathtools 3.75 pl5321h6e16a3a_1 + - cairo 1.18.2 h950ec3b_1 + - perl-extutils-depends 0.8001 pl5321hdfd78af_0 + run: + - cairo >=1.18.2,<2.0a0 + - xorg-libxrender + - perl >=5.32.1,<5.33.0a0 *_perl5 + - xorg-libxext + - xorg-libsm + - perl-extutils-depends + - perl-extutils-pkgconfig + test: + commands: + - perl -e "use Cairo" + about: + home: http://gtk2-perl.sourceforge.net + license: lgpl_2_1 + summary: Perl interface to the cairo 2d vector graphics library + extra: + copy_test_source_files: true + final: true - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make: *** [Makefile:521: blib/arch/auto/Cairo/Cairo.bundle] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1685385263397/work/conda_build.sh']' returned non-zero exit status 2. + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1734244947873/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1734244947873/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1734244947873/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/perl-cairo_1734244947873/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-cairo-1.109 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-cairo-1.109 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 # Last 100 lines of the build log. diff --git a/recipes/perl-cairo/meta.yaml b/recipes/perl-cairo/meta.yaml index c7ceaa13d41d9..ec0fe9a07752c 100644 --- a/recipes/perl-cairo/meta.yaml +++ b/recipes/perl-cairo/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 8219736e401c2311da5f515775de43fd87e6384b504da36a192f2b217643077f build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/perl-cgi/meta.yaml b/recipes/perl-cgi/meta.yaml index b2247d77e4deb..ea97481b54172 100644 --- a/recipes/perl-cgi/meta.yaml +++ b/recipes/perl-cgi/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 2d36d930b89ecdfbcc7d6d4740821bd466a0218abf1bd413568640b2f43799b7 build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/perl-class-methodmaker/build_failure.osx-64.yaml b/recipes/perl-class-methodmaker/build_failure.osx-64.yaml deleted file mode 100644 index d99d31f5ec9a9..0000000000000 --- a/recipes/perl-class-methodmaker/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: aaac3cebb57bd6fbe2f018e81cb9c3015220ee8e059776980ec78f9e70579d04 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - XSprePUSH; PUSHi((IV)RETVAL); - ^~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-class-methodmaker_1685358267518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:459:31: note: expanded from macro 'PUSHi' - #define PUSHi(i) STMT_START { TARGi(i,1); PUSHs(TARG); } STMT_END - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-class-methodmaker_1685358267518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:392:16: note: expanded from macro 'TARGi' - STMT_START { \ - ^ - MethodMaker.c:197:13: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSprePUSH; PUSHi((IV)RETVAL); - ^~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-class-methodmaker_1685358267518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:459:31: note: expanded from macro 'PUSHi' - #define PUSHi(i) STMT_START { TARGi(i,1); PUSHs(TARG); } STMT_END - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-class-methodmaker_1685358267518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:409:5: note: expanded from macro 'TARGi' - } STMT_END - ^ - MethodMaker.c:197:13: note: ')' token is here - XSprePUSH; PUSHi((IV)RETVAL); - ^~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-class-methodmaker_1685358267518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:459:31: note: expanded from macro 'PUSHi' - #define PUSHi(i) STMT_START { TARGi(i,1); PUSHs(TARG); } STMT_END - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-class-methodmaker_1685358267518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:409:7: note: expanded from macro 'TARGi' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-class-methodmaker_1685358267518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - MethodMaker.c:197:13: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSprePUSH; PUSHi((IV)RETVAL); - ^~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-class-methodmaker_1685358267518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:459:56: note: expanded from macro 'PUSHi' - #define PUSHi(i) STMT_START { TARGi(i,1); PUSHs(TARG); } STMT_END - ^ - MethodMaker.c:197:13: note: ')' token is here - XSprePUSH; PUSHi((IV)RETVAL); - ^~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-class-methodmaker_1685358267518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:459:58: note: expanded from macro 'PUSHi' - #define PUSHi(i) STMT_START { TARGi(i,1); PUSHs(TARG); } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-class-methodmaker_1685358267518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - MethodMaker.c:199:5: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-class-methodmaker_1685358267518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:5: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-class-methodmaker_1685358267518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:666:29: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports "({ STATEMENTS; })" */ - ^ - MethodMaker.c:199:5: note: '{' token is here - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-class-methodmaker_1685358267518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:16: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^ - MethodMaker.c:199:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-class-methodmaker_1685358267518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:5: note: expanded from macro 'XSRETURN' - } STMT_END - ^ - MethodMaker.c:199:5: note: ')' token is here - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-class-methodmaker_1685358267518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:7: note: expanded from macro 'XSRETURN' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-class-methodmaker_1685358267518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - 108 warnings generated. - rm -f blib/arch/auto/Class/MethodMaker/MethodMaker.bundle - x86_64-apple-darwin13.4.0-clang -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fstack-protector-strong MethodMaker.o -o blib/arch/auto/Class/MethodMaker/MethodMaker.bundle \ - \ - - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make: *** [Makefile:500: blib/arch/auto/Class/MethodMaker/MethodMaker.bundle] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-class-methodmaker_1685358267518/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-class-methodmaker/meta.yaml b/recipes/perl-class-methodmaker/meta.yaml index 008ce2d081dce..352eb950f9b37 100644 --- a/recipes/perl-class-methodmaker/meta.yaml +++ b/recipes/perl-class-methodmaker/meta.yaml @@ -14,7 +14,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x") }} - number: 0 + number: 1 requirements: build: diff --git a/recipes/perl-class-xsaccessor/meta.yaml b/recipes/perl-class-xsaccessor/meta.yaml index 40daa3938c895..c6062fc88d504 100644 --- a/recipes/perl-class-xsaccessor/meta.yaml +++ b/recipes/perl-class-xsaccessor/meta.yaml @@ -13,7 +13,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x") }} - number: 7 + number: 8 requirements: build: diff --git a/recipes/perl-config-any/meta.yaml b/recipes/perl-config-any/meta.yaml index cbc8b71ec8028..ee3e8cdbf8e98 100644 --- a/recipes/perl-config-any/meta.yaml +++ b/recipes/perl-config-any/meta.yaml @@ -12,7 +12,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - number: 3 + number: 4 requirements: build: diff --git a/recipes/perl-config-autoconf/build_failure.osx-64.yaml b/recipes/perl-config-autoconf/build_failure.osx-64.yaml deleted file mode 100644 index b7bdefa59c436..0000000000000 --- a/recipes/perl-config-autoconf/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: dcd887631f97f5d035a0acf4f40151b3c3e27e29b89608c94f69528c31a51121 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-config-autoconf-0.320 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - Checking if your kit is complete... - Looks good - Generating a Unix-style Makefile - Writing Makefile for Config::AutoConf - Writing MYMETA.yml and MYMETA.json - cp lib/Config/AutoConf.pm blib/lib/Config/AutoConf.pm - Manifying 1 pod document - PERL_DL_NONLAZY=1 "$PREFIX/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t xt/*.t - t/00.load.t ....... ok - # Check for some progs to get an overview about world outside - # Found AWK as /usr/bin/awk - # Found SED as /usr/bin/sed - # Found EGREP as /usr/bin/egrep - # Found YACC as /usr/bin/bison -y - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - Unsupported compile language "C" at t/01.checkprog.t line 105. - # Looks like your test exited with 2 just after 16. - t/01.checkprog.t .. - Dubious, test returned 2 (wstat 512, 0x200) - Failed 2/18 subtests - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - Unsupported compile language "C" at t/02.compile.t line 19. - t/02.compile.t .... - Dubious, test returned 2 (wstat 512, 0x200) - No subtests run - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - Unsupported compile language "C" at t/03.link.t line 17. - t/03.link.t ....... - Dubious, test returned 2 (wstat 512, 0x200) - No subtests run - - Test Summary Report - ------------------- - t/01.checkprog.t (Wstat: 512 Tests: 16 Failed: 0) - Non-zero exit status: 2 - Parse errors: Bad plan. You planned 18 tests but ran 16. - t/02.compile.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Failed 3/4 test programs. 0/17 subtests failed. - Parse errors: No plan found in TAP output - t/03.link.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - Files=4, Tests=17, 10 wallclock secs ( 0.03 usr 0.01 sys 2.93 cusr 1.96 csys = 4.93 CPU) - Result: FAIL - make: *** [Makefile:921: test_dynamic] Error 2 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-config-autoconf_1685403991662/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-config-autoconf/meta.yaml b/recipes/perl-config-autoconf/meta.yaml index 0be34741d1a93..5ddf0ad3877b3 100644 --- a/recipes/perl-config-autoconf/meta.yaml +++ b/recipes/perl-config-autoconf/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/perl-convert-binary-c/meta.yaml b/recipes/perl-convert-binary-c/meta.yaml index 94f4002d4df60..d6fb2d0eba6be 100644 --- a/recipes/perl-convert-binary-c/meta.yaml +++ b/recipes/perl-convert-binary-c/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('perl-convert-binary-c', max_pin="x.x") }} diff --git a/recipes/perl-crypt-openssl-random/0.11/meta.yaml b/recipes/perl-crypt-openssl-random/0.11/meta.yaml index 93c01b767e90c..4fd80134f238a 100644 --- a/recipes/perl-crypt-openssl-random/0.11/meta.yaml +++ b/recipes/perl-crypt-openssl-random/0.11/meta.yaml @@ -15,7 +15,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - number: 6 + number: 7 requirements: build: diff --git a/recipes/perl-crypt-openssl-rsa/build_failure.osx-64.yaml b/recipes/perl-crypt-openssl-rsa/build_failure.osx-64.yaml deleted file mode 100644 index e85343f8a6f2f..0000000000000 --- a/recipes/perl-crypt-openssl-rsa/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 51fc420ce22a581ea4c4446eb2e36cd2877908754518c7e2e622b7748637b981 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - XSprePUSH; PUSHi((IV)RETVAL); - ^~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-crypt-openssl-rsa_1685355984785/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:459:31: note: expanded from macro 'PUSHi' - #define PUSHi(i) STMT_START { TARGi(i,1); PUSHs(TARG); } STMT_END - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-crypt-openssl-rsa_1685355984785/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:392:16: note: expanded from macro 'TARGi' - STMT_START { \ - ^ - RSA.c:1493:13: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSprePUSH; PUSHi((IV)RETVAL); - ^~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-crypt-openssl-rsa_1685355984785/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:459:31: note: expanded from macro 'PUSHi' - #define PUSHi(i) STMT_START { TARGi(i,1); PUSHs(TARG); } STMT_END - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-crypt-openssl-rsa_1685355984785/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:409:5: note: expanded from macro 'TARGi' - } STMT_END - ^ - RSA.c:1493:13: note: ')' token is here - XSprePUSH; PUSHi((IV)RETVAL); - ^~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-crypt-openssl-rsa_1685355984785/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:459:31: note: expanded from macro 'PUSHi' - #define PUSHi(i) STMT_START { TARGi(i,1); PUSHs(TARG); } STMT_END - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-crypt-openssl-rsa_1685355984785/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:409:7: note: expanded from macro 'TARGi' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-crypt-openssl-rsa_1685355984785/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - RSA.c:1493:13: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSprePUSH; PUSHi((IV)RETVAL); - ^~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-crypt-openssl-rsa_1685355984785/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:459:56: note: expanded from macro 'PUSHi' - #define PUSHi(i) STMT_START { TARGi(i,1); PUSHs(TARG); } STMT_END - ^ - RSA.c:1493:13: note: ')' token is here - XSprePUSH; PUSHi((IV)RETVAL); - ^~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-crypt-openssl-rsa_1685355984785/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:459:58: note: expanded from macro 'PUSHi' - #define PUSHi(i) STMT_START { TARGi(i,1); PUSHs(TARG); } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-crypt-openssl-rsa_1685355984785/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - RSA.c:1495:5: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-crypt-openssl-rsa_1685355984785/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:5: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-crypt-openssl-rsa_1685355984785/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:666:29: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports "({ STATEMENTS; })" */ - ^ - RSA.c:1495:5: note: '{' token is here - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-crypt-openssl-rsa_1685355984785/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:16: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^ - RSA.c:1495:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-crypt-openssl-rsa_1685355984785/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:5: note: expanded from macro 'XSRETURN' - } STMT_END - ^ - RSA.c:1495:5: note: ')' token is here - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-crypt-openssl-rsa_1685355984785/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:7: note: expanded from macro 'XSRETURN' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-crypt-openssl-rsa_1685355984785/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - 282 warnings generated. - rm -f blib/arch/auto/Crypt/OpenSSL/RSA/RSA.bundle - LD_RUN_PATH="/usr/local/opt/openssl@3/lib" x86_64-apple-darwin13.4.0-clang -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fstack-protector-strong RSA.o -o blib/arch/auto/Crypt/OpenSSL/RSA/RSA.bundle \ - -L$PREFIX/lib -lssl -lcrypto \ - - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make: *** [Makefile:490: blib/arch/auto/Crypt/OpenSSL/RSA/RSA.bundle] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-crypt-openssl-rsa_1685355984785/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-crypt-openssl-rsa/meta.yaml b/recipes/perl-crypt-openssl-rsa/meta.yaml index 53b6430a88360..83a7f627d617c 100644 --- a/recipes/perl-crypt-openssl-rsa/meta.yaml +++ b/recipes/perl-crypt-openssl-rsa/meta.yaml @@ -13,7 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: - number: 3 + number: 4 run_exports: weak: - {{ name }} ={{ version }} diff --git a/recipes/perl-data-uuid/build_failure.osx-64.yaml b/recipes/perl-data-uuid/build_failure.osx-64.yaml deleted file mode 100644 index ab74df17e7da9..0000000000000 --- a/recipes/perl-data-uuid/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 8a6aa566ee0f9904c1d66ca32464dbd5ed69920de4ec335ea8367eaf05be557d # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-data-uuid_1685394187309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:52: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-data-uuid_1685394187309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:16: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^ - UUID.c:894:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-data-uuid_1685394187309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:52: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-data-uuid_1685394187309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:5: note: expanded from macro 'XSRETURN' - } STMT_END - ^ - UUID.c:894:5: note: ')' token is here - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-data-uuid_1685394187309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:52: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-data-uuid_1685394187309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:7: note: expanded from macro 'XSRETURN' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-data-uuid_1685394187309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - UUID.c:894:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-data-uuid_1685394187309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:65: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^ - UUID.c:894:5: note: ')' token is here - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-data-uuid_1685394187309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:67: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-data-uuid_1685394187309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - UUID.xs:607:3: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - MUTEX_INIT(&instances_mutex); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-data-uuid_1685394187309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/thread.h:197:5: note: expanded from macro 'MUTEX_INIT' - STMT_START { \ - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-data-uuid_1685394187309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/perl.h:666:29: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports "({ STATEMENTS; })" */ - ^ - UUID.xs:607:3: note: '{' token is here - MUTEX_INIT(&instances_mutex); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-data-uuid_1685394187309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/thread.h:197:16: note: expanded from macro 'MUTEX_INIT' - STMT_START { \ - ^ - UUID.xs:607:3: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - MUTEX_INIT(&instances_mutex); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-data-uuid_1685394187309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/thread.h:202:5: note: expanded from macro 'MUTEX_INIT' - } STMT_END - ^ - UUID.xs:607:3: note: ')' token is here - MUTEX_INIT(&instances_mutex); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-data-uuid_1685394187309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/thread.h:202:7: note: expanded from macro 'MUTEX_INIT' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-data-uuid_1685394187309/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - 158 warnings generated. - rm -f blib/arch/auto/Data/UUID/UUID.bundle - x86_64-apple-darwin13.4.0-clang -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fstack-protector-strong UUID.o -o blib/arch/auto/Data/UUID/UUID.bundle \ - \ - - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make: *** [Makefile:487: blib/arch/auto/Data/UUID/UUID.bundle] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-data-uuid_1685394187309/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-data-uuid/meta.yaml b/recipes/perl-data-uuid/meta.yaml index cd592500da578..e26358db86fc3 100644 --- a/recipes/perl-data-uuid/meta.yaml +++ b/recipes/perl-data-uuid/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/perl-datetime-locale/meta.yaml b/recipes/perl-datetime-locale/meta.yaml index 40db36081f33a..38a2ed7dc3ca3 100644 --- a/recipes/perl-datetime-locale/meta.yaml +++ b/recipes/perl-datetime-locale/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("perl-datetime-locale", max_pin="x") }} diff --git a/recipes/perl-datetime/build_failure.osx-64.yaml b/recipes/perl-datetime/build_failure.osx-64.yaml deleted file mode 100644 index 1c5df53d7379c..0000000000000 --- a/recipes/perl-datetime/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 450347829df10f415d16138a7ab053a2014c4c7090210c80095737768043b6cf # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - # define ENV_LOCK MUTEX_LOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/thread.h:214:16: note: expanded from macro 'MUTEX_LOCK' - STMT_START { \ - ^ - In file included from DateTime.xs:2: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/perl.h:6161: - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/inline.h:2619:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - ENV_LOCK; - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/perl.h:2924:31: note: expanded from macro 'ENV_LOCK' - # define ENV_LOCK MUTEX_LOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/thread.h:219:5: note: expanded from macro 'MUTEX_LOCK' - } STMT_END - ^ - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/inline.h:2619:5: note: ')' token is here - ENV_LOCK; - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/perl.h:2924:31: note: expanded from macro 'ENV_LOCK' - # define ENV_LOCK MUTEX_LOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/thread.h:219:7: note: expanded from macro 'MUTEX_LOCK' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - In file included from DateTime.xs:2: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/perl.h:6161: - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/inline.h:2627:5: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - ENV_UNLOCK; - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/perl.h:2925:31: note: expanded from macro 'ENV_UNLOCK' - # define ENV_UNLOCK MUTEX_UNLOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/thread.h:222:5: note: expanded from macro 'MUTEX_UNLOCK' - STMT_START { \ - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/perl.h:666:29: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports "({ STATEMENTS; })" */ - ^ - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/inline.h:2627:5: note: '{' token is here - ENV_UNLOCK; - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/perl.h:2925:31: note: expanded from macro 'ENV_UNLOCK' - # define ENV_UNLOCK MUTEX_UNLOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/thread.h:222:16: note: expanded from macro 'MUTEX_UNLOCK' - STMT_START { \ - ^ - In file included from DateTime.xs:2: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/perl.h:6161: - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/inline.h:2627:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - ENV_UNLOCK; - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/perl.h:2925:31: note: expanded from macro 'ENV_UNLOCK' - # define ENV_UNLOCK MUTEX_UNLOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/thread.h:227:5: note: expanded from macro 'MUTEX_UNLOCK' - } STMT_END - ^ - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/inline.h:2627:5: note: ')' token is here - ENV_UNLOCK; - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/perl.h:2925:31: note: expanded from macro 'ENV_UNLOCK' - # define ENV_UNLOCK MUTEX_UNLOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/thread.h:227:7: note: expanded from macro 'MUTEX_UNLOCK' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - 98 warnings generated. - rm -f blib/arch/auto/DateTime/DateTime.bundle - x86_64-apple-darwin13.4.0-clang -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk DateTime.o -o blib/arch/auto/DateTime/DateTime.bundle \ - \ - - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make: *** [Makefile:492: blib/arch/auto/DateTime/DateTime.bundle] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-datetime_1685394780013/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-datetime/meta.yaml b/recipes/perl-datetime/meta.yaml index d2a1bbedc3056..2ef4e5e17002f 100644 --- a/recipes/perl-datetime/meta.yaml +++ b/recipes/perl-datetime/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/perl-dbd-mysql/meta.yaml b/recipes/perl-dbd-mysql/meta.yaml index 363646c827487..9afdc6b063010 100644 --- a/recipes/perl-dbd-mysql/meta.yaml +++ b/recipes/perl-dbd-mysql/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 run_exports: '{{ pin_subpackage(name, max_pin="x") }}' requirements: diff --git a/recipes/perl-dbd-pg/meta.yaml b/recipes/perl-dbd-pg/meta.yaml index f56c4c929513b..d04ab61be743d 100644 --- a/recipes/perl-dbd-pg/meta.yaml +++ b/recipes/perl-dbd-pg/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: weak: - {{ name }} ={{ version }} diff --git a/recipes/perl-dbd-sqlite/meta.yaml b/recipes/perl-dbd-sqlite/meta.yaml index 5b17948a07582..8b99f2309bc44 100644 --- a/recipes/perl-dbd-sqlite/meta.yaml +++ b/recipes/perl-dbd-sqlite/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 0a33a7a935be63371071dbe600cfaefa67cd971b67580a917bbf6ebaf723c584 build: - number: 0 + number: 1 run_exports: '{{ pin_subpackage(name, max_pin="x") }}' requirements: diff --git a/recipes/perl-devel-size/meta.yaml b/recipes/perl-devel-size/meta.yaml index c1eb19414e9e9..92dbd810adf79 100644 --- a/recipes/perl-devel-size/meta.yaml +++ b/recipes/perl-devel-size/meta.yaml @@ -12,7 +12,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - number: 0 + number: 1 requirements: build: diff --git a/recipes/perl-digest-crc/0.23/meta.yaml b/recipes/perl-digest-crc/0.23/meta.yaml index d12c9a9d85ff4..c4de65885347c 100644 --- a/recipes/perl-digest-crc/0.23/meta.yaml +++ b/recipes/perl-digest-crc/0.23/meta.yaml @@ -13,7 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: - number: 4 + number: 5 run_exports: weak: - {{ name }} ={{ version }} diff --git a/recipes/perl-digest-sha1/meta.yaml b/recipes/perl-digest-sha1/meta.yaml index bdf801fadae07..52c31260de877 100644 --- a/recipes/perl-digest-sha1/meta.yaml +++ b/recipes/perl-digest-sha1/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 7 + number: 8 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/perl-escape-houdini/0.3.0/build_failure.osx-64.yaml b/recipes/perl-escape-houdini/0.3.0/build_failure.osx-64.yaml index 16505ef426087..e03de0624cc5d 100644 --- a/recipes/perl-escape-houdini/0.3.0/build_failure.osx-64.yaml +++ b/recipes/perl-escape-houdini/0.3.0/build_failure.osx-64.yaml @@ -1,51 +1,65 @@ -recipe_sha: b1f4c50712a1d7be0e5fa3096262aa91a034a73dc5ecc144024f0843847ae078 # The commit at which this recipe failed to build. +recipe_sha: d11c48c154522e8c615e52cfc4b1a4cb4f862c6208bf0e5f419e65a1c7c1d550 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- - make: 4.3-h22f3db7_1 conda-forge - openssl: 3.1.0-h8a1eda9_3 conda-forge - sigtool: 0.1.3-h88f4db0_0 conda-forge - tapi: 1100.0.11-h9ce4665_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - zstd: 1.5.2-hbc0c0cd_6 conda-forge + - perl-version 0.9933 pl5321h6e16a3a_0 + - perl-carp 1.50 pl5321hd8ed1ab_0 + - perl-encode 3.21 pl5321h00291cd_1 + - perl-file-path 2.18 pl5321hd8ed1ab_0 + - perl-module-build 0.4234 pl5321h694c41f_0 + - perl-module-corelist 5.20220620 pl5321hdfd78af_0 + - perl-perl-ostype 1.010 pl5321hd8ed1ab_0 + - perl-test-exception 0.43 pl5321hd8ed1ab_0 + - perl-text-parsewords 3.31 pl5321hd8ed1ab_0 + - perl-file-temp 0.2304 pl5321hd8ed1ab_0 + - perl-module-metadata 1.000038 pl5321hdfd78af_0 + - perl-module-load-conditional 0.68 pl5321hdfd78af_3 + - perl-ipc-cmd 1.04 pl5321hdfd78af_0 + - perl-extutils-cbuilder 0.280230 pl5321hdfd78af_2 + run: + - perl-module-build =0.4234 + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-parent + - perl-exporter + test: + imports: + - Escape::Houdini + about: + home: https://github.com/yanick/Escape-Houdini + license: perl_5 + summary: Perl API to Houdini, a zero-dependency C web escaping library + extra: + copy_test_source_files: true + final: true - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - INFO:conda_build.source:Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - Downloading source to cache: Escape-Houdini-0.3.0_c78074a9a8.tar.gz - Downloading https://cpan.metacpan.org/authors/id/Y/YA/YANICK/Escape-Houdini-0.3.0.tar.gz - INFO:conda_build.source:Downloading source to cache: Escape-Houdini-0.3.0_c78074a9a8.tar.gz - INFO:conda_build.source:Downloading https://cpan.metacpan.org/authors/id/Y/YA/YANICK/Escape-Houdini-0.3.0.tar.gz - Success - INFO:conda_build.source:Success - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/perl-escape-houdini_1685404403324/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/perl-escape-houdini_1685404403324/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/perl-escape-houdini_1685404403324/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/perl-escape-houdini_1685404403324/work + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/perl-escape-houdini_1734134816363/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/perl-escape-houdini_1734134816363/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/perl-escape-houdini_1734134816363/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/perl-escape-houdini_1734134816363/work INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as CC=x86_64-apple-darwin13.4.0-clang CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-escape-houdini-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-escape-houdini-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-escape-houdini-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-escape-houdini-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -54,7 +68,7 @@ log: |2- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -70,35 +84,21 @@ log: |2- Looks good Adding to build_requires: ExtUtils::CBuilder => 0 - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - Warning: ExtUtils::CBuilder not installed or no compiler detected - Proceeding with configuration, but compilation may fail during Build - - Checking if compiler tools configured... failed. + Checking if compiler tools configured... ok. Checking prerequisites... Looks good Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Escape-Houdini' version '0.3.0' - Error: no compiler detected to compile 'houdini/buffer.c'. Aborting Building Escape-Houdini - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-escape-houdini_1685404403324/work/conda_build.sh']' returned non-zero exit status 2. + x86_64-apple-darwin13.4.0-clang -Ihoudini -I$PREFIX/lib/perl5/5.32/core_perl/CORE -fPIC -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/perl_1703310145184/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-common -DPERL_DARWIN -no-cpp-precomp -Werror=partial-availability -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-strict-aliasing -pipe -fstack-protector-strong -DPERL_USE_SAFE_PUTENV -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-escape-houdini-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -o houdini/buffer.o houdini/buffer.c + x86_64-apple-darwin13.4.0-clang -Ihoudini -I$PREFIX/lib/perl5/5.32/core_perl/CORE -fPIC -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/perl_1703310145184/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-common -DPERL_DARWIN -no-cpp-precomp -Werror=partial-availability -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-strict-aliasing -pipe -fstack-protector-strong -DPERL_USE_SAFE_PUTENV -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-escape-houdini-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -o houdini/houdini_href_e.o houdini/houdini_href_e.c + x86_64-apple-darwin13.4.0-clang -Ihoudini -I$PREFIX/lib/perl5/5.32/core_perl/CORE -fPIC -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/perl_1703310145184/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-common -DPERL_DARWIN -no-cpp-precomp -Werror=partial-availability -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-strict-aliasing -pipe -fstack-protector-strong -DPERL_USE_SAFE_PUTENV -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-escape-houdini-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -o houdini/houdini_html_e.o houdini/houdini_html_e.c + x86_64-apple-darwin13.4.0-clang -Ihoudini -I$PREFIX/lib/perl5/5.32/core_perl/CORE -fPIC -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/perl_1703310145184/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-common -DPERL_DARWIN -no-cpp-precomp -Werror=partial-availability -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-strict-aliasing -pipe -fstack-protector-strong -DPERL_USE_SAFE_PUTENV -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-escape-houdini-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -o houdini/houdini_html_u.o houdini/houdini_html_u.c + x86_64-apple-darwin13.4.0-clang -Ihoudini -I$PREFIX/lib/perl5/5.32/core_perl/CORE -fPIC -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/perl_1703310145184/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-common -DPERL_DARWIN -no-cpp-precomp -Werror=partial-availability -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-strict-aliasing -pipe -fstack-protector-strong -DPERL_USE_SAFE_PUTENV -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-escape-houdini-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -o houdini/houdini_js_e.o houdini/houdini_js_e.c + x86_64-apple-darwin13.4.0-clang -Ihoudini -I$PREFIX/lib/perl5/5.32/core_perl/CORE -fPIC -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/perl_1703310145184/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-common -DPERL_DARWIN -no-cpp-precomp -Werror=partial-availability -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-strict-aliasing -pipe -fstack-protector-strong -DPERL_USE_SAFE_PUTENV -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-escape-houdini-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -o houdini/houdini_js_u.o houdini/houdini_js_u.c + x86_64-apple-darwin13.4.0-clang -Ihoudini -I$PREFIX/lib/perl5/5.32/core_perl/CORE -fPIC -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/perl_1703310145184/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-common -DPERL_DARWIN -no-cpp-precomp -Werror=partial-availability -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-strict-aliasing -pipe -fstack-protector-strong -DPERL_USE_SAFE_PUTENV -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-escape-houdini-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -o houdini/houdini_uri_e.o houdini/houdini_uri_e.c + x86_64-apple-darwin13.4.0-clang -Ihoudini -I$PREFIX/lib/perl5/5.32/core_perl/CORE -fPIC -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/perl_1703310145184/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-common -DPERL_DARWIN -no-cpp-precomp -Werror=partial-availability -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-strict-aliasing -pipe -fstack-protector-strong -DPERL_USE_SAFE_PUTENV -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-escape-houdini-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -o houdini/houdini_uri_u.o houdini/houdini_uri_u.c + x86_64-apple-darwin13.4.0-clang -Ihoudini -I$PREFIX/lib/perl5/5.32/core_perl/CORE -fPIC -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/perl_1703310145184/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-common -DPERL_DARWIN -no-cpp-precomp -Werror=partial-availability -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-strict-aliasing -pipe -fstack-protector-strong -DPERL_USE_SAFE_PUTENV -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-escape-houdini-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -o houdini/houdini_xml_e.o houdini/houdini_xml_e.c + x86_64-apple-darwin13.4.0-clang -Ihoudini -I$PREFIX/lib/perl5/5.32/core_perl/CORE -fPIC -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/perl_1703310145184/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-common -DPERL_DARWIN -no-cpp-precomp -Werror=partial-availability -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-strict-aliasing -pipe -fstack-protector-strong -DPERL_USE_SAFE_PUTENV -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-escape-houdini-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -o houdini/tools/build_tables.o houdini/tools/build_tables.c # Last 100 lines of the build log. diff --git a/recipes/perl-escape-houdini/0.3.0/meta.yaml b/recipes/perl-escape-houdini/0.3.0/meta.yaml index abc09b1b334e1..1094713c41444 100644 --- a/recipes/perl-escape-houdini/0.3.0/meta.yaml +++ b/recipes/perl-escape-houdini/0.3.0/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/perl-extutils-cppguess/build_failure.osx-64.yaml b/recipes/perl-extutils-cppguess/build_failure.osx-64.yaml deleted file mode 100644 index 749437a101392..0000000000000 --- a/recipes/perl-extutils-cppguess/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: e0e86fee1ed06991ab987402f63cc9b2fa47edfed04c3501e18c74cfdedc6827 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - # 'OTHERLDFLAGS' => ' -lstdc' - # } - # } - t/004_env.t ............ ok - # Module::Build version: 0.4234 - # ExtUtils::CBuilder version: 0.280234 - - # Failed test 'build with Module::Build' - # at t/010_module_build.t line 19. - # Build.PL output - # ======================================== - # ld: library not found for -lSystem - # clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - # Warning: ExtUtils::CBuilder not installed or no compiler detected - # Proceeding with configuration, but compilation may fail during Build - # - # Created MYMETA.yml and MYMETA.json - # Creating new 'Build' script for 'CppGuessTest' version '0.01' - # ======================================== - # Build output - # ======================================== - # Building CppGuessTest - # Error: no compiler detected to compile 'lib/CppGuessTest.c'. Aborting - # ======================================== - # Looks like you failed 1 test of 1. - t/010_module_build.t ... - Dubious, test returned 1 (wstat 256, 0x100) - Failed 1/1 subtests - - # Failed test 'build with ExtUtils::MakeMaker' - # at t/011_makemaker.t line 11. - # Makefile.PL output - # ======================================== - # Checking if your kit is complete... - # Looks good - # Generating a Unix-style Makefile - # Writing Makefile for CppGuessTest - # Writing MYMETA.yml and MYMETA.json - # ======================================== - # make output - # ======================================== - # make[1]: Entering directory '/opt/mambaforge/envs/bioconda/conda-bld/perl-extutils-cppguess_1685396755414/work/t/makemaker' - # cp lib/CppGuessTest.pm blib/lib/CppGuessTest.pm - # Running Mkbootstrap for CppGuessTest () - # chmod 644 "CppGuessTest.bs" - # "/opt/mambaforge/envs/bioconda/conda-bld/perl-extutils-cppguess_1685396755414/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- CppGuessTest.bs blib/arch/auto/CppGuessTest/CppGuessTest.bs 644 - # "/opt/mambaforge/envs/bioconda/conda-bld/perl-extutils-cppguess_1685396755414/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/bin/perl" "/opt/mambaforge/envs/bioconda/conda-bld/perl-extutils-cppguess_1685396755414/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/core_perl/ExtUtils/xsubpp" -typemap '/opt/mambaforge/envs/bioconda/conda-bld/perl-extutils-cppguess_1685396755414/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/core_perl/ExtUtils/typemap' -typemap '/opt/mambaforge/envs/bioconda/conda-bld/perl-extutils-cppguess_1685396755414/work/t/makemaker/typemap' CppGuessTest.xs > CppGuessTest.xsc - # mv CppGuessTest.xsc CppGuessTest.c - # x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /opt/mambaforge/envs/bioconda/conda-bld/perl-extutils-cppguess_1685396755414/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/perl_1645063215412/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/perl-extutils-cppguess_1685396755414/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p=/usr/local/src/conda-prefix -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-common -DPERL_DARWIN -no-cpp-precomp -Werror=partial-availability -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-strict-aliasing -pipe -fstack-protector-strong -DPERL_USE_SAFE_PUTENV -D_FORTIFY_SOURCE=2 -isystem /opt/mambaforge/envs/bioconda/conda-bld/perl-extutils-cppguess_1685396755414/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/include -mmacosx-version-min=10.9 -xc -DINCLUDE_DOT=0 -Wno-reserved-user-defined-literal -Wno-error=implicit-function-declaration -O3 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk "-I/opt/mambaforge/envs/bioconda/conda-bld/perl-extutils-cppguess_1685396755414/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE" CppGuessTest.c - # CppGuessTest.c:290:1: warning: duplicate 'extern' declaration specifier [-Wduplicate-decl-specifier] - # XS_EXTERNAL(boot_CppGuessTest); /* prototype to pass -Wmissing-prototypes */ - # ^ - # /opt/mambaforge/envs/bioconda/conda-bld/perl-extutils-cppguess_1685396755414/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:134:29: note: expanded from macro 'XS_EXTERNAL' - # # define XS_EXTERNAL(name) extern "C" XSPROTO(name) - # ^ - # 1 warning generated. - # rm -f blib/arch/auto/CppGuessTest/CppGuessTest.bundle - # x86_64-apple-darwin13.4.0-clang -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/opt/mambaforge/envs/bioconda/conda-bld/perl-extutils-cppguess_1685396755414/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -L/opt/mambaforge/envs/bioconda/conda-bld/perl-extutils-cppguess_1685396755414/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fstack-protector-strong CppGuessTest.o -lstdc -o blib/arch/auto/CppGuessTest/CppGuessTest.bundle \ - # \ - # - # ld: library not found for -lSystem - # clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - # make[1]: *** [Makefile:473: blib/arch/auto/CppGuessTest/CppGuessTest.bundle] Error 1 - # make[1]: Leaving directory '/opt/mambaforge/envs/bioconda/conda-bld/perl-extutils-cppguess_1685396755414/work/t/makemaker' - # ======================================== - # Looks like you failed 1 test of 1. - Failed 2/7 test programs. 2/20 subtests failed. - t/011_makemaker.t ...... - Dubious, test returned 1 (wstat 256, 0x100) - Failed 1/1 subtests - - Test Summary Report - ------------------- - t/010_module_build.t (Wstat: 256 Tests: 1 Failed: 1) - Failed test: 1 - Non-zero exit status: 1 - t/011_makemaker.t (Wstat: 256 Tests: 1 Failed: 1) - Failed test: 1 - Non-zero exit status: 1 - Files=7, Tests=20, 16 wallclock secs ( 0.04 usr 0.02 sys 10.08 cusr 2.32 csys = 12.46 CPU) - Result: FAIL - make: *** [Makefile:884: test_dynamic] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-extutils-cppguess_1685396755414/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-extutils-cppguess/meta.yaml b/recipes/perl-extutils-cppguess/meta.yaml index 665bf7124eefa..2de27ccdb176b 100644 --- a/recipes/perl-extutils-cppguess/meta.yaml +++ b/recipes/perl-extutils-cppguess/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 run_exports: '{{ pin_subpackage(name, max_pin="x.x") }}' requirements: diff --git a/recipes/perl-file-copy-link/meta.yaml b/recipes/perl-file-copy-link/meta.yaml index d4db82618124f..88b65856deab0 100644 --- a/recipes/perl-file-copy-link/meta.yaml +++ b/recipes/perl-file-copy-link/meta.yaml @@ -12,7 +12,7 @@ source: - version.patch build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/perl-file-copy-recursive/meta.yaml b/recipes/perl-file-copy-recursive/meta.yaml index f3c7e267bfb2c..70763644f2e02 100644 --- a/recipes/perl-file-copy-recursive/meta.yaml +++ b/recipes/perl-file-copy-recursive/meta.yaml @@ -13,7 +13,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - number: 4 + number: 5 requirements: build: diff --git a/recipes/perl-filesys-df/meta.yaml b/recipes/perl-filesys-df/meta.yaml index e489baf31724f..4b4dde0f51aba 100644 --- a/recipes/perl-filesys-df/meta.yaml +++ b/recipes/perl-filesys-df/meta.yaml @@ -13,7 +13,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - number: 8 + number: 9 requirements: build: diff --git a/recipes/perl-findbin-real/meta.yaml b/recipes/perl-findbin-real/meta.yaml index 28595fb8668ad..aed494190461c 100644 --- a/recipes/perl-findbin-real/meta.yaml +++ b/recipes/perl-findbin-real/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 1 + number: 2 requirements: build: diff --git a/recipes/perl-forks/build_failure.osx-64.yaml b/recipes/perl-forks/build_failure.osx-64.yaml deleted file mode 100644 index 231b45b97173b..0000000000000 --- a/recipes/perl-forks/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: e4edcb084b84d8b07d32c262ba17ee6e8f26bcbe86c535702c8fb99737d3ddbf # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - XSprePUSH; PUSHu((UV)RETVAL); - ^~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-forks_1685357146585/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/pp.h:460:31: note: expanded from macro 'PUSHu' - #define PUSHu(u) STMT_START { TARGu(u,1); PUSHs(TARG); } STMT_END - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-forks_1685357146585/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/pp.h:414:16: note: expanded from macro 'TARGu' - STMT_START { \ - ^ - forks.c:679:13: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSprePUSH; PUSHu((UV)RETVAL); - ^~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-forks_1685357146585/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/pp.h:460:31: note: expanded from macro 'PUSHu' - #define PUSHu(u) STMT_START { TARGu(u,1); PUSHs(TARG); } STMT_END - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-forks_1685357146585/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/pp.h:432:5: note: expanded from macro 'TARGu' - } STMT_END - ^ - forks.c:679:13: note: ')' token is here - XSprePUSH; PUSHu((UV)RETVAL); - ^~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-forks_1685357146585/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/pp.h:460:31: note: expanded from macro 'PUSHu' - #define PUSHu(u) STMT_START { TARGu(u,1); PUSHs(TARG); } STMT_END - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-forks_1685357146585/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/pp.h:432:7: note: expanded from macro 'TARGu' - } STMT_END - ^~~~~~~~ - ./ppport.h:597:18: note: expanded from macro 'STMT_END' - #define STMT_END ) - ^ - forks.c:679:13: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSprePUSH; PUSHu((UV)RETVAL); - ^~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-forks_1685357146585/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/pp.h:460:56: note: expanded from macro 'PUSHu' - #define PUSHu(u) STMT_START { TARGu(u,1); PUSHs(TARG); } STMT_END - ^ - forks.c:679:13: note: ')' token is here - XSprePUSH; PUSHu((UV)RETVAL); - ^~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-forks_1685357146585/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/pp.h:460:58: note: expanded from macro 'PUSHu' - #define PUSHu(u) STMT_START { TARGu(u,1); PUSHs(TARG); } STMT_END - ^~~~~~~~ - ./ppport.h:597:18: note: expanded from macro 'STMT_END' - #define STMT_END ) - ^ - forks.c:681:5: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-forks_1685357146585/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:5: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^~~~~~~~~~ - ./ppport.h:596:26: note: expanded from macro 'STMT_START' - #define STMT_START (void)( - ^ - forks.c:681:5: note: '{' token is here - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-forks_1685357146585/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:16: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^ - forks.c:681:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-forks_1685357146585/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:5: note: expanded from macro 'XSRETURN' - } STMT_END - ^ - forks.c:681:5: note: ')' token is here - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-forks_1685357146585/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:7: note: expanded from macro 'XSRETURN' - } STMT_END - ^~~~~~~~ - ./ppport.h:597:18: note: expanded from macro 'STMT_END' - #define STMT_END ) - ^ - 224 warnings generated. - rm -f blib/arch/auto/forks/forks.bundle - x86_64-apple-darwin13.4.0-clang -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fstack-protector-strong forks.o -o blib/arch/auto/forks/forks.bundle \ - \ - - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make: *** [Makefile:491: blib/arch/auto/forks/forks.bundle] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-forks_1685357146585/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-forks/meta.yaml b/recipes/perl-forks/meta.yaml index 3252baeb0dc44..d86bde9fda96d 100644 --- a/recipes/perl-forks/meta.yaml +++ b/recipes/perl-forks/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 8 + number: 9 requirements: build: diff --git a/recipes/perl-gdtextutil/meta.yaml b/recipes/perl-gdtextutil/meta.yaml index 51f9bef314765..7e4277d5c9bdd 100644 --- a/recipes/perl-gdtextutil/meta.yaml +++ b/recipes/perl-gdtextutil/meta.yaml @@ -7,7 +7,7 @@ source: md5: 941ad06eadc86b47f3a32da405665c41 build: - number: 8 + number: 9 requirements: build: diff --git a/recipes/perl-heap-simple-xs/meta.yaml b/recipes/perl-heap-simple-xs/meta.yaml index f71773be3e19d..2907dfac981da 100644 --- a/recipes/perl-heap-simple-xs/meta.yaml +++ b/recipes/perl-heap-simple-xs/meta.yaml @@ -12,7 +12,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - number: 7 + number: 8 requirements: build: diff --git a/recipes/perl-html-parser/build_failure.osx-64.yaml b/recipes/perl-html-parser/build_failure.osx-64.yaml deleted file mode 100644 index a7385f1a70a9b..0000000000000 --- a/recipes/perl-html-parser/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: fd641a8957b3374f21470ede1b08c2a7377fbec6961bc27c333c52dce38c3dfc # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - # define ENV_LOCK MUTEX_LOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/thread.h:214:16: note: expanded from macro 'MUTEX_LOCK' - STMT_START { \ - ^ - In file included from Parser.xs:11: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/perl.h:6161: - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/inline.h:2619:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - ENV_LOCK; - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/perl.h:2924:31: note: expanded from macro 'ENV_LOCK' - # define ENV_LOCK MUTEX_LOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/thread.h:219:5: note: expanded from macro 'MUTEX_LOCK' - } STMT_END - ^ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/inline.h:2619:5: note: ')' token is here - ENV_LOCK; - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/perl.h:2924:31: note: expanded from macro 'ENV_LOCK' - # define ENV_LOCK MUTEX_LOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/thread.h:219:7: note: expanded from macro 'MUTEX_LOCK' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - In file included from Parser.xs:11: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/perl.h:6161: - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/inline.h:2627:5: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - ENV_UNLOCK; - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/perl.h:2925:31: note: expanded from macro 'ENV_UNLOCK' - # define ENV_UNLOCK MUTEX_UNLOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/thread.h:222:5: note: expanded from macro 'MUTEX_UNLOCK' - STMT_START { \ - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/perl.h:666:29: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports "({ STATEMENTS; })" */ - ^ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/inline.h:2627:5: note: '{' token is here - ENV_UNLOCK; - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/perl.h:2925:31: note: expanded from macro 'ENV_UNLOCK' - # define ENV_UNLOCK MUTEX_UNLOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/thread.h:222:16: note: expanded from macro 'MUTEX_UNLOCK' - STMT_START { \ - ^ - In file included from Parser.xs:11: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/perl.h:6161: - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/inline.h:2627:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - ENV_UNLOCK; - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/perl.h:2925:31: note: expanded from macro 'ENV_UNLOCK' - # define ENV_UNLOCK MUTEX_UNLOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/thread.h:227:5: note: expanded from macro 'MUTEX_UNLOCK' - } STMT_END - ^ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/inline.h:2627:5: note: ')' token is here - ENV_UNLOCK; - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/perl.h:2925:31: note: expanded from macro 'ENV_UNLOCK' - # define ENV_UNLOCK MUTEX_UNLOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/thread.h:227:7: note: expanded from macro 'MUTEX_UNLOCK' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - 98 warnings generated. - rm -f blib/arch/auto/HTML/Parser/Parser.bundle - x86_64-apple-darwin13.4.0-clang -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fstack-protector-strong Parser.o -o blib/arch/auto/HTML/Parser/Parser.bundle \ - \ - - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make: *** [Makefile:500: blib/arch/auto/HTML/Parser/Parser.bundle] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-html-parser_1685386432331/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-html-parser/meta.yaml b/recipes/perl-html-parser/meta.yaml index a1caf7a76709c..110e68b48cc05 100644 --- a/recipes/perl-html-parser/meta.yaml +++ b/recipes/perl-html-parser/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/perl-html-tidy/build_failure.linux-64.yaml b/recipes/perl-html-tidy/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..7215c67f6b80e --- /dev/null +++ b/recipes/perl-html-tidy/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c262570db2e39f214a4f3906aa464e8b03fc1265e4ee958a3e821c50723ac168 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + perl: warning: Falling back to the standard locale ("C"). + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + cp lib/HTML/Tidy.pm blib/lib/HTML/Tidy.pm + cp lib/HTML/Tidy/Message.pm blib/lib/HTML/Tidy/Message.pm + Running Mkbootstrap for Tidy () + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + chmod 644 "Tidy.bs" + "$PREFIX/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- Tidy.bs blib/arch/auto/HTML/Tidy/Tidy.bs 644 + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + "$PREFIX/bin/perl" "$PREFIX/lib/perl5/core_perl/ExtUtils/xsubpp" -typemap '$PREFIX/lib/perl5/core_perl/ExtUtils/typemap' Tidy.xs > Tidy.xsc + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + mv Tidy.xsc Tidy.c + $BUILD_PREFIX/bin/..//bin/x86_64-conda-linux-gnu-gcc -c -I$PREFIX/include/tidyp -D_REENTRANT -D_GNU_SOURCE -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/perl_1703310062586/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -DVERSION=\"1.60\" -DXS_VERSION=\"1.60\" -fPIC --sysroot=$BUILD_PREFIX/bin/..//x86_64-conda-linux-gnu/sysroot "-I$PREFIX/lib/perl5/5.32/core_perl/CORE" Tidy.c + Tidy.xs:5:10: fatal error: tidyp.h: No such file or directory + 5 | #include + | ^~~~~~~~~ + compilation terminated. + make: *** [Makefile:345: Tidy.o] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/perl-html-tidy_1734212063722/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/perl-html-tidy_1734212063722/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/perl-html-tidy/build_failure.osx-64.yaml b/recipes/perl-html-tidy/build_failure.osx-64.yaml index fa2d76ac0da0b..2975b82619b52 100644 --- a/recipes/perl-html-tidy/build_failure.osx-64.yaml +++ b/recipes/perl-html-tidy/build_failure.osx-64.yaml @@ -1,104 +1,104 @@ -recipe_sha: edb10f16fc7ac1f16b3294cfdaa6b34ae7649e981f235812cf09f4b69933009d # The commit at which this recipe failed to build. +recipe_sha: c262570db2e39f214a4f3906aa464e8b03fc1265e4ee958a3e821c50723ac168 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1685357997432/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/perl.h:666:29: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports "({ STATEMENTS; })" */ - ^ - Tidy.xs:190:13: note: '{' token is here - XSRETURN_UNDEF; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1685357997432/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:329:52: note: expanded from macro 'XSRETURN_UNDEF' - #define XSRETURN_UNDEF STMT_START { XST_mUNDEF(0); XSRETURN(1); } STMT_END - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1685357997432/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:16: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^ - Tidy.xs:190:13: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN_UNDEF; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1685357997432/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:329:52: note: expanded from macro 'XSRETURN_UNDEF' - #define XSRETURN_UNDEF STMT_START { XST_mUNDEF(0); XSRETURN(1); } STMT_END - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1685357997432/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:5: note: expanded from macro 'XSRETURN' - } STMT_END - ^ - Tidy.xs:190:13: note: ')' token is here - XSRETURN_UNDEF; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1685357997432/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:329:52: note: expanded from macro 'XSRETURN_UNDEF' - #define XSRETURN_UNDEF STMT_START { XST_mUNDEF(0); XSRETURN(1); } STMT_END - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1685357997432/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:7: note: expanded from macro 'XSRETURN' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1685357997432/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - Tidy.xs:190:13: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN_UNDEF; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1685357997432/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:329:65: note: expanded from macro 'XSRETURN_UNDEF' - #define XSRETURN_UNDEF STMT_START { XST_mUNDEF(0); XSRETURN(1); } STMT_END - ^ - Tidy.xs:190:13: note: ')' token is here - XSRETURN_UNDEF; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1685357997432/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:329:67: note: expanded from macro 'XSRETURN_UNDEF' - #define XSRETURN_UNDEF STMT_START { XST_mUNDEF(0); XSRETURN(1); } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1685357997432/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - Tidy.c:419:5: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1685357997432/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:5: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1685357997432/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/perl.h:666:29: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports "({ STATEMENTS; })" */ - ^ - Tidy.c:419:5: note: '{' token is here - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1685357997432/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:16: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^ - Tidy.c:419:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1685357997432/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:5: note: expanded from macro 'XSRETURN' - } STMT_END - ^ - Tidy.c:419:5: note: ')' token is here - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1685357997432/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:7: note: expanded from macro 'XSRETURN' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1685357997432/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - 133 warnings generated. - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make: *** [Makefile:486: blib/arch/auto/HTML/Tidy/Tidy.bundle] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1685357997432/work/conda_build.sh']' returned non-zero exit status 2. +log: |2- + - perl >=5.32.1,<5.33.0a0 *_perl5 + - perl-getopt-long >=2.58,<3.0a0 + - perl-constant + - tidyp >=1.4,<2.0a0 + - perl-encode + - perl-carp + - perl-exporter + test: + imports: + - HTML::Tidy + - HTML::Tidy::Message + about: + home: http://github.com/petdance/html-tidy + license: artistic_2 + summary: (X)HTML validation in a Perl object + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1734093406963/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1734093406963/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1734093406963/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/perl-html-tidy_1734093406963/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-html-tidy-1.60 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-html-tidy-1.60 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + Alien::Tidyp not found. Looking for for tidyp on your system. + + It seems that you don't have tidyp installed. HTML::Tidy does no + real work on its own. It's just a wrapper around tidyp. + + Please read the README.markdown file for details on how to install tidyp. + + If you do have tidyp installed, but Makefile.PL can't detect it, + go ahead and try building. If HTML::Tidy builds and tests correctly, + please file a ticket at Github at + http://github.com/petdance/html-tidy/issues, so we can fix the + library detection code. + + + NOTE: It seems that you don't have LWP::Simple installed. + The webtidy program will not be able to retrieve web pages. + + *** inc = -I$PREFIX/include/tidyp + *** libs = -ltidyp + Checking if your kit is complete... + Looks good + Generating a Unix-style Makefile + Writing Makefile for HTML::Tidy + Writing MYMETA.yml and MYMETA.json + cp lib/HTML/Tidy.pm blib/lib/HTML/Tidy.pm + cp lib/HTML/Tidy/Message.pm blib/lib/HTML/Tidy/Message.pm + Running Mkbootstrap for Tidy () + chmod 644 "Tidy.bs" + "$PREFIX/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- Tidy.bs blib/arch/auto/HTML/Tidy/Tidy.bs 644 + "$PREFIX/bin/perl" "$PREFIX/lib/perl5/core_perl/ExtUtils/xsubpp" -typemap '$PREFIX/lib/perl5/core_perl/ExtUtils/typemap' Tidy.xs > Tidy.xsc + mv Tidy.xsc Tidy.c + x86_64-apple-darwin13.4.0-clang -c -I$PREFIX/include/tidyp -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/perl_1703310145184/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-common -DPERL_DARWIN -no-cpp-precomp -Werror=partial-availability -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-strict-aliasing -pipe -fstack-protector-strong -DPERL_USE_SAFE_PUTENV -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wno-error=implicit-function-declaration -O3 -DVERSION=\"1.60\" -DXS_VERSION=\"1.60\" -fPIC "-I$PREFIX/lib/perl5/5.32/core_perl/CORE" Tidy.c # Last 100 lines of the build log. diff --git a/recipes/perl-html-tidy/meta.yaml b/recipes/perl-html-tidy/meta.yaml index fa4c62a83ce32..38b2c303ef164 100644 --- a/recipes/perl-html-tidy/meta.yaml +++ b/recipes/perl-html-tidy/meta.yaml @@ -9,7 +9,7 @@ source: - makefile-pl.patch build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/perl-indirect/build_failure.osx-64.yaml b/recipes/perl-indirect/build_failure.osx-64.yaml deleted file mode 100644 index 2f8933e997a06..0000000000000 --- a/recipes/perl-indirect/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: b8fcfce4937f464f50693447f1bb5a429c4d60d902941c536817168999fef3b9 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - XSRETURN(0); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-indirect_1685356316591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:5: note: expanded from macro 'XSRETURN' - } STMT_END - ^ - indirect.xs:737:2: note: ')' token is here - XSRETURN(0); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-indirect_1685356316591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:7: note: expanded from macro 'XSRETURN' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-indirect_1685356316591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - indirect.c:919:5: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-indirect_1685356316591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:5: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-indirect_1685356316591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/perl.h:666:29: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports "({ STATEMENTS; })" */ - ^ - indirect.c:919:5: note: '{' token is here - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-indirect_1685356316591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:16: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^ - indirect.c:919:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-indirect_1685356316591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:5: note: expanded from macro 'XSRETURN' - } STMT_END - ^ - indirect.c:919:5: note: ')' token is here - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-indirect_1685356316591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:7: note: expanded from macro 'XSRETURN' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-indirect_1685356316591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - indirect.xs:766:2: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN(0); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-indirect_1685356316591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:5: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-indirect_1685356316591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/perl.h:666:29: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports "({ STATEMENTS; })" */ - ^ - indirect.xs:766:2: note: '{' token is here - XSRETURN(0); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-indirect_1685356316591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:16: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^ - indirect.xs:766:2: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN(0); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-indirect_1685356316591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:5: note: expanded from macro 'XSRETURN' - } STMT_END - ^ - indirect.xs:766:2: note: ')' token is here - XSRETURN(0); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-indirect_1685356316591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:7: note: expanded from macro 'XSRETURN' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-indirect_1685356316591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - 136 warnings generated. - rm -f blib/arch/auto/indirect/indirect.bundle - x86_64-apple-darwin13.4.0-clang -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fstack-protector-strong indirect.o -o blib/arch/auto/indirect/indirect.bundle \ - \ - - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make: *** [Makefile:477: blib/arch/auto/indirect/indirect.bundle] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-indirect_1685356316591/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-indirect/meta.yaml b/recipes/perl-indirect/meta.yaml index 67179c8f741d1..b3eabddcdc754 100644 --- a/recipes/perl-indirect/meta.yaml +++ b/recipes/perl-indirect/meta.yaml @@ -13,7 +13,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - number: 4 + number: 5 requirements: build: diff --git a/recipes/perl-inline-c/build_failure.osx-64.yaml b/recipes/perl-inline-c/build_failure.osx-64.yaml deleted file mode 100644 index ca2ed8b7219e4..0000000000000 --- a/recipes/perl-inline-c/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: cce4729b332a0f15e5648fd76ea0e225e1dc662129a387d23da58d0943fadb1b # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - t/04perlapi.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - Failed 29/35 test programs. 12/69 subtests failed. - t/05xsmode.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - t/06parseregexp.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - t/07typemap_multi.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - t/09parser.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - t/10callback.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - t/11default_readonly.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: Bad plan. You planned 1 tests but ran 0. - make: *** [Makefile:899: test_dynamic] Error 255 - t/14void_arg.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - t/14void_arg_PRD.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - t/15ccflags.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - t/16ccflagsex.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - t/17prehead.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - t/19INC.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - t/20eval.t (Wstat: 0 Tests: 5 Failed: 1) - Failed test: 1 - t/21read_DATA.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - t/22read_DATA_2.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - t/24prefix.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - t/25proto.t (Wstat: 0 Tests: 6 Failed: 4) - Failed tests: 1-4 - t/26fork.t (Wstat: 768 Tests: 4 Failed: 3) - Failed tests: 2-4 - Non-zero exit status: 3 - t/27inline_maker.t (Wstat: 1024 Tests: 8 Failed: 4) - Failed tests: 2-3, 6-7 - Non-zero exit status: 4 - t/28autowrap.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - t/29refargs.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - t/30cppflags.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - t/31include_dirs_angle_brackets.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: Bad plan. You planned 1 tests but ran 0. - t/32include_dirs_double_quotes.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - t/33intended_double_quotes.t (Wstat: 512 Tests: 0 Failed: 0) - Non-zero exit status: 2 - Parse errors: No plan found in TAP output - t/parse-pegex.t (Wstat: 0 Tests: 24 Failed: 0) - TODO passed: 4, 7-9 - Files=35, Tests=69, 110 wallclock secs ( 0.13 usr 2.41 sys 66.02 cusr 17.81 csys = 86.37 CPU) - Result: FAIL - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-inline-c_1685526906115/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-inline-c/meta.yaml b/recipes/perl-inline-c/meta.yaml index fd4b56ba1bda0..c8258784c0c36 100644 --- a/recipes/perl-inline-c/meta.yaml +++ b/recipes/perl-inline-c/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/perl-io-compress/meta.yaml b/recipes/perl-io-compress/meta.yaml index ec9551d86e261..ddeabc37dbedb 100644 --- a/recipes/perl-io-compress/meta.yaml +++ b/recipes/perl-io-compress/meta.yaml @@ -8,7 +8,7 @@ source: sha256: f6c55c4e39cfaa3219965dd3b36c9de1edee9a82a10a9cadeb3b74a9ceeeaaad build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/perl-ipc-sharelite/meta.yaml b/recipes/perl-ipc-sharelite/meta.yaml index c0b03629528c8..850328a9057d3 100644 --- a/recipes/perl-ipc-sharelite/meta.yaml +++ b/recipes/perl-ipc-sharelite/meta.yaml @@ -13,7 +13,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - number: 6 + number: 7 requirements: build: diff --git a/recipes/perl-json-create/build_failure.osx-64.yaml b/recipes/perl-json-create/build_failure.osx-64.yaml deleted file mode 100644 index 33553625a1b1a..0000000000000 --- a/recipes/perl-json-create/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: d4705207628e21447d9fccc6de67d7207c5716e93a7adf17fe10cf001b0fa4f3 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - ^ - Create.c:913:5: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-create_1685358114433/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:24: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~~~ - ./ppport.h:11657:31: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports ({ STATEMENTS; })'' */ - ^ - Create.c:913:5: note: '{' token is here - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-create_1685358114433/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:35: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^ - Create.c:913:5: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-create_1685358114433/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:52: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-create_1685358114433/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:5: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^~~~~~~~~~ - ./ppport.h:11657:31: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports ({ STATEMENTS; })'' */ - ^ - Create.c:913:5: note: '{' token is here - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-create_1685358114433/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:52: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-create_1685358114433/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:16: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^ - Create.c:913:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-create_1685358114433/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:52: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-create_1685358114433/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:5: note: expanded from macro 'XSRETURN' - } STMT_END - ^ - Create.c:913:5: note: ')' token is here - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-create_1685358114433/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:52: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-create_1685358114433/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:7: note: expanded from macro 'XSRETURN' - } STMT_END - ^~~~~~~~ - ./ppport.h:11658:25: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - Create.c:913:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-create_1685358114433/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:65: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^ - Create.c:913:5: note: ')' token is here - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-create_1685358114433/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:67: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~ - ./ppport.h:11658:25: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - 210 warnings generated. - x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/perl_1645063215412/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-common -DPERL_DARWIN -no-cpp-precomp -Werror=partial-availability -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-strict-aliasing -pipe -fstack-protector-strong -DPERL_USE_SAFE_PUTENV -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -Wno-error=implicit-function-declaration -O3 -DVERSION=\"0.35\" -DXS_VERSION=\"0.35\" -fPIC --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk "-I$PREFIX/lib/perl5/5.32/core_perl/CORE" unicode.c - rm -f blib/arch/auto/JSON/Create/Create.bundle - x86_64-apple-darwin13.4.0-clang -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fstack-protector-strong Create.o unicode.o -o blib/arch/auto/JSON/Create/Create.bundle \ - \ - - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make: *** [Makefile:489: blib/arch/auto/JSON/Create/Create.bundle] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-json-create_1685358114433/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-json-create/meta.yaml b/recipes/perl-json-create/meta.yaml index 8ce75d9a58407..91760c34156a3 100644 --- a/recipes/perl-json-create/meta.yaml +++ b/recipes/perl-json-create/meta.yaml @@ -13,7 +13,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - number: 3 + number: 4 requirements: build: diff --git a/recipes/perl-json-parse/meta.yaml b/recipes/perl-json-parse/meta.yaml index 23d23915f13fd..8e95f037d3f07 100644 --- a/recipes/perl-json-parse/meta.yaml +++ b/recipes/perl-json-parse/meta.yaml @@ -13,7 +13,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - number: 4 + number: 5 requirements: build: diff --git a/recipes/perl-json-xs/2.34/build_failure.osx-64.yaml b/recipes/perl-json-xs/2.34/build_failure.osx-64.yaml deleted file mode 100644 index 64da9dcb6a083..0000000000000 --- a/recipes/perl-json-xs/2.34/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 1831a34ec32ff8b7141fb43f1851516c5a2d9c8545d5fd66bfe7b8575b6e2ebf # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - # define STMT_END ) - ^ - XS.xs:2098:9: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XPUSHs (jsonstr); - ^~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-xs_1685395614862/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:462:19: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-xs_1685395614862/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:666:29: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports "({ STATEMENTS; })" */ - ^ - XS.xs:2098:9: note: '{' token is here - XPUSHs (jsonstr); - ^~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-xs_1685395614862/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:462:30: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^ - XS.xs:2098:9: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XPUSHs (jsonstr); - ^~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-xs_1685395614862/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:462:32: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-xs_1685395614862/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:371:25: note: expanded from macro 'EXTEND' - # define EXTEND(p,n) STMT_START { \ - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-xs_1685395614862/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:666:29: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports "({ STATEMENTS; })" */ - ^ - XS.xs:2098:9: note: '{' token is here - XPUSHs (jsonstr); - ^~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-xs_1685395614862/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:462:32: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-xs_1685395614862/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:371:36: note: expanded from macro 'EXTEND' - # define EXTEND(p,n) STMT_START { \ - ^ - XS.xs:2098:9: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XPUSHs (jsonstr); - ^~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-xs_1685395614862/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:462:32: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-xs_1685395614862/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:376:28: note: expanded from macro 'EXTEND' - } } STMT_END - ^ - XS.xs:2098:9: note: ')' token is here - XPUSHs (jsonstr); - ^~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-xs_1685395614862/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:462:32: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-xs_1685395614862/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:376:30: note: expanded from macro 'EXTEND' - } } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-xs_1685395614862/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - XS.xs:2098:9: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XPUSHs (jsonstr); - ^~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-xs_1685395614862/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:462:59: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^ - XS.xs:2098:9: note: ')' token is here - XPUSHs (jsonstr); - ^~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-xs_1685395614862/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/pp.h:462:61: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-json-xs_1685395614862/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - 227 warnings generated. - rm -f blib/arch/auto/JSON/XS/XS.bundle - x86_64-apple-darwin13.4.0-clang -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fstack-protector-strong XS.o -o blib/arch/auto/JSON/XS/XS.bundle \ - \ - - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make: *** [Makefile:473: blib/arch/auto/JSON/XS/XS.bundle] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-json-xs_1685395614862/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-json-xs/2.34/meta.yaml b/recipes/perl-json-xs/2.34/meta.yaml index d48244ef7de5a..915fc55386802 100644 --- a/recipes/perl-json-xs/2.34/meta.yaml +++ b/recipes/perl-json-xs/2.34/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/perl-json-xs/meta.yaml b/recipes/perl-json-xs/meta.yaml index 871c1c95fef43..b73e404cef4a0 100644 --- a/recipes/perl-json-xs/meta.yaml +++ b/recipes/perl-json-xs/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/perl-list-moreutils-xs/build_failure.osx-64.yaml b/recipes/perl-list-moreutils-xs/build_failure.osx-64.yaml deleted file mode 100644 index 699ac3fb6c3bf..0000000000000 --- a/recipes/perl-list-moreutils-xs/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 4d8bd4d1b644879f46cfe4ab7a87be61ddd682d24979725ef33f83e0712d5e9c # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - intsize=4 - longsize=8 - ptrsize=8 - doublesize=8 - byteorder=12345678 - doublekind=3 - d_longlong=define - longlongsize=8 - d_longdbl=define - longdblsize=16 - longdblkind=3 - ivtype='long' - ivsize=8 - nvtype='double' - nvsize=8 - Off_t='off_t' - lseeksize=8 - alignbytes=8 - prototype=define - Linker and Libraries: - ld='x86_64-apple-darwin13.4.0-clang' - ldflags ='-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -fstack-protector-strong' - libpth=./..//lib/clang/11.1.0/lib /Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/lib - libs=-lpthread -ldbm -ldl -lm -lutil -lc - perllibs=-lpthread -ldl -lm -lutil -lc - libc= - so=dylib - useshrplib=true - libperl=libperl.dylib - gnulibc_version='' - Dynamic Linking: - dlsrc=dl_dlopen.xs - dlext=bundle - d_dlsymun=undef - ccdlflags=' ' - cccdlflags='-fPIC --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk' - lddlflags='-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fstack-protector-strong' - - - Characteristics of this binary (from libperl): - Compile-time options: - HAS_TIMES - MULTIPLICITY - PERLIO_LAYERS - PERL_COPY_ON_WRITE - PERL_DONT_CREATE_GVSV - PERL_IMPLICIT_CONTEXT - PERL_MALLOC_WRAP - PERL_OP_PARENT - PERL_PRESERVE_IVUV - PERL_USE_SAFE_PUTENV - USE_64_BIT_ALL - USE_64_BIT_INT - USE_ITHREADS - USE_LARGE_FILES - USE_LOCALE - USE_LOCALE_COLLATE - USE_LOCALE_CTYPE - USE_LOCALE_NUMERIC - USE_LOCALE_TIME - USE_PERLIO - USE_PERL_ATOF - USE_REENTRANT_API - USE_THREAD_SAFE_LOCALE - Built under darwin - Compiled at Feb 17 2022 02:07:16 - %ENV: - PERL="$PREFIX/bin/perl" - PERL_VER="5.32" - @INC: - $PREFIX/lib/perl5/5.32/site_perl - $PREFIX/lib/perl5/site_perl - $PREFIX/lib/perl5/5.32/vendor_perl - $PREFIX/lib/perl5/vendor_perl - $PREFIX/lib/perl5/5.32/core_perl - $PREFIX/lib/perl5/core_perl - . - Checking whether pureperl is required... no - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - Can't produce loadable XS module at inc/Config/AutoConf/LMU.pm line 73. - Checking for cc... - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-list-moreutils-xs_1685403740954/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-list-moreutils-xs/meta.yaml b/recipes/perl-list-moreutils-xs/meta.yaml index 4f65724892370..4791a3efdd1a3 100644 --- a/recipes/perl-list-moreutils-xs/meta.yaml +++ b/recipes/perl-list-moreutils-xs/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 run_exports: '{{ pin_subpackage(name, max_pin="x.x") }}' requirements: diff --git a/recipes/perl-list-someutils/meta.yaml b/recipes/perl-list-someutils/meta.yaml index c281f0b4900db..f800d99b3bc29 100644 --- a/recipes/perl-list-someutils/meta.yaml +++ b/recipes/perl-list-someutils/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/perl-math-cdf/meta.yaml b/recipes/perl-math-cdf/meta.yaml index aa9058106d27c..1149ff1ff35c0 100644 --- a/recipes/perl-math-cdf/meta.yaml +++ b/recipes/perl-math-cdf/meta.yaml @@ -12,7 +12,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - number: 10 + number: 11 requirements: build: diff --git a/recipes/perl-math-random/meta.yaml b/recipes/perl-math-random/meta.yaml index 3b45dcebed81a..280fa999aec1f 100644 --- a/recipes/perl-math-random/meta.yaml +++ b/recipes/perl-math-random/meta.yaml @@ -12,7 +12,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - number: 7 + number: 8 # skip osx on x86 - builds fail in CI skip: True # [osx] diff --git a/recipes/perl-moosex-role-withoverloading/build_failure.osx-64.yaml b/recipes/perl-moosex-role-withoverloading/build_failure.osx-64.yaml deleted file mode 100644 index 9aef33f4fd99c..0000000000000 --- a/recipes/perl-moosex-role-withoverloading/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 95f99bf4336849eb4226ed997becbebb2b3e8c12579f977a17b601bfe69b6291 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - # define STMT_END ) - ^ - WithOverloading.c:223:5: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-moosex-role-withoverloading_1685357471552/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:24: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-moosex-role-withoverloading_1685357471552/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:666:29: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports "({ STATEMENTS; })" */ - ^ - WithOverloading.c:223:5: note: '{' token is here - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-moosex-role-withoverloading_1685357471552/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:35: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^ - WithOverloading.c:223:5: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-moosex-role-withoverloading_1685357471552/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:52: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-moosex-role-withoverloading_1685357471552/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:5: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-moosex-role-withoverloading_1685357471552/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:666:29: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports "({ STATEMENTS; })" */ - ^ - WithOverloading.c:223:5: note: '{' token is here - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-moosex-role-withoverloading_1685357471552/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:52: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-moosex-role-withoverloading_1685357471552/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:16: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^ - WithOverloading.c:223:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-moosex-role-withoverloading_1685357471552/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:52: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-moosex-role-withoverloading_1685357471552/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:5: note: expanded from macro 'XSRETURN' - } STMT_END - ^ - WithOverloading.c:223:5: note: ')' token is here - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-moosex-role-withoverloading_1685357471552/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:52: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-moosex-role-withoverloading_1685357471552/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:7: note: expanded from macro 'XSRETURN' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-moosex-role-withoverloading_1685357471552/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - WithOverloading.c:223:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-moosex-role-withoverloading_1685357471552/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:65: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^ - WithOverloading.c:223:5: note: ')' token is here - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-moosex-role-withoverloading_1685357471552/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:67: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-moosex-role-withoverloading_1685357471552/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - 102 warnings generated. - rm -f blib/arch/auto/MooseX/Role/WithOverloading/WithOverloading.bundle - x86_64-apple-darwin13.4.0-clang -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fstack-protector-strong WithOverloading.o -o blib/arch/auto/MooseX/Role/WithOverloading/WithOverloading.bundle \ - \ - - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make: *** [Makefile:487: blib/arch/auto/MooseX/Role/WithOverloading/WithOverloading.bundle] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-moosex-role-withoverloading_1685357471552/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-moosex-role-withoverloading/meta.yaml b/recipes/perl-moosex-role-withoverloading/meta.yaml index 47f517800e7aa..6e880f2eeb52c 100644 --- a/recipes/perl-moosex-role-withoverloading/meta.yaml +++ b/recipes/perl-moosex-role-withoverloading/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/perl-namespace-autoclean/meta.yaml b/recipes/perl-namespace-autoclean/meta.yaml index 4cc0492a1364e..a4a3c28e700b0 100644 --- a/recipes/perl-namespace-autoclean/meta.yaml +++ b/recipes/perl-namespace-autoclean/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/perl-padwalker/meta.yaml b/recipes/perl-padwalker/meta.yaml index 1099d70539734..294983cb91364 100644 --- a/recipes/perl-padwalker/meta.yaml +++ b/recipes/perl-padwalker/meta.yaml @@ -13,7 +13,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x") }} - number: 4 + number: 5 requirements: build: diff --git a/recipes/perl-par-packer/1.036/meta.yaml b/recipes/perl-par-packer/1.036/meta.yaml index 76486b40476d3..245f7b0f52929 100644 --- a/recipes/perl-par-packer/1.036/meta.yaml +++ b/recipes/perl-par-packer/1.036/meta.yaml @@ -13,7 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: - number: 5 + number: 6 skip: True # [osx] requirements: diff --git a/recipes/perl-params-validate/meta.yaml b/recipes/perl-params-validate/meta.yaml index 5fa61a588766a..1c11329ed3692 100644 --- a/recipes/perl-params-validate/meta.yaml +++ b/recipes/perl-params-validate/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 1bf2518ef2c4869f91590e219f545c8ef12ed53cf313e0eb5704adf7f1b2961e build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/perl-perl-unsafe-signals/meta.yaml b/recipes/perl-perl-unsafe-signals/meta.yaml index 14ece03872921..9f7f59635a338 100644 --- a/recipes/perl-perl-unsafe-signals/meta.yaml +++ b/recipes/perl-perl-unsafe-signals/meta.yaml @@ -13,7 +13,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - number: 8 + number: 9 requirements: build: diff --git a/recipes/perl-perlio-gzip/meta.yaml b/recipes/perl-perlio-gzip/meta.yaml index bf37a23f9a7f4..84eb9beaf365b 100644 --- a/recipes/perl-perlio-gzip/meta.yaml +++ b/recipes/perl-perlio-gzip/meta.yaml @@ -12,7 +12,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - number: 6 + number: 7 requirements: build: diff --git a/recipes/perl-pod-elemental/meta.yaml b/recipes/perl-pod-elemental/meta.yaml index de4641f6368e8..b687ac32a8f17 100644 --- a/recipes/perl-pod-elemental/meta.yaml +++ b/recipes/perl-pod-elemental/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 750c3a79d8e1824758a6ef7d2dd077dcddca503542b8c34eccd5acbb779dc423 build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/perl-retroseq/meta.yaml b/recipes/perl-retroseq/meta.yaml index 12628a099a06f..ee9866d093224 100644 --- a/recipes/perl-retroseq/meta.yaml +++ b/recipes/perl-retroseq/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 2 + number: 3 run_exports: {{ pin_subpackage("perl-retroseq", max_pin="x") }} requirements: @@ -45,4 +45,4 @@ test: about: home: https://github.com/tk2/RetroSeq license: GPL - summary: 'RetroSeq: discovery and genotyping of TEVs from reads in BAM format.' \ No newline at end of file + summary: 'RetroSeq: discovery and genotyping of TEVs from reads in BAM format.' diff --git a/recipes/perl-sanger-cgp-allelecount/meta.yaml b/recipes/perl-sanger-cgp-allelecount/meta.yaml index 5070213e4410c..68ccd381e5791 100644 --- a/recipes/perl-sanger-cgp-allelecount/meta.yaml +++ b/recipes/perl-sanger-cgp-allelecount/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 5363ae12c2385c962728336a4498b1a29c9eaa3d4a24492d0debf897771cfd3c build: - number: 1 + number: 2 skip: True # [osx] requirements: diff --git a/recipes/perl-sanger-cgp-battenberg/build_failure.linux-64.yaml b/recipes/perl-sanger-cgp-battenberg/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..95f8a5d475141 --- /dev/null +++ b/recipes/perl-sanger-cgp-battenberg/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 3deaac6675689a157c29e9108000787670a44bbf65e6e44f9041a909de42cc55 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [32mperl-pcap[0m is installable with the potential options + [31mperl-pcap 1.11.1[0m would require + [32mperl 5.22.0* [0m, which can be installed; + [31mperl-ipc-system-simple[0m but there are no viable options + [31mperl-ipc-system-simple 1.30[0m would require + [31mperl >=5.32.1,<5.33.0a0 *_perl5[0m, which conflicts with any installable versions previously reported; + [31mperl-ipc-system-simple [1.25|1.30][0m conflicts with any installable versions previously reported; + [31mperl-pcap 1.11.1[0m would require + [32mperl >=5.22.0,<5.23.0 [0m, which can be installed; + [31mperl-ipc-system-simple[0m but there are no viable options + [31mperl-ipc-system-simple 1.30[0m, which cannot be installed (as previously explained); + [31mperl-ipc-system-simple [1.25|1.30][0m conflicts with any installable versions previously reported; + [32mperl-pcap 3.5.2[0m would require + [32mperl-bio-db-hts[0m with the potential options + [31mperl-bio-db-hts [2.4|2.7|3.01][0m conflicts with any installable versions previously reported; + [32mperl-bio-db-hts 3.01[0m would require + [32mperl-module-build 0.4234.* [0m, which can be installed; + [31mperl-sanger-cgp-allelecount[0m is not installable because there are no viable options + [31mperl-sanger-cgp-allelecount 4.3.0[0m would require + [31mperl-module-build 0.4232.* [0m, which conflicts with any installable versions previously reported; + [31mperl-sanger-cgp-allelecount [2.1.2|4.0.0|4.1.0|4.2.1|4.3.0][0m conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("perl-ipc-system-simple==1.30=pl5321ha770c72_0"), MatchSpec("perl[version='>=5.32.1,<5.33.0a0',build=*_perl5]")} + Encountered problems while solving: + - package perl-ipc-system-simple-1.30-pl5321ha770c72_0 requires perl >=5.32.1,<5.33.0a0 *_perl5, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mperl-pcap[0m is installable with the potential options + [31mperl-pcap 1.11.1[0m would require + [32mperl 5.22.0* [0m, which can be installed; + [31mperl-ipc-system-simple[0m but there are no viable options + [31mperl-ipc-system-simple 1.30[0m would require + [31mperl >=5.32.1,<5.33.0a0 *_perl5[0m, which conflicts with any installable versions previously reported; + [31mperl-ipc-system-simple [1.25|1.30][0m conflicts with any installable versions previously reported; + [31mperl-pcap 1.11.1[0m would require + [32mperl >=5.22.0,<5.23.0 [0m, which can be installed; + [31mperl-ipc-system-simple[0m but there are no viable options + [31mperl-ipc-system-simple 1.30[0m, which cannot be installed (as previously explained); + [31mperl-ipc-system-simple [1.25|1.30][0m conflicts with any installable versions previously reported; + [32mperl-pcap 3.5.2[0m would require + [32mperl-bio-db-hts[0m with the potential options + [31mperl-bio-db-hts [2.4|2.7|3.01][0m conflicts with any installable versions previously reported; + [32mperl-bio-db-hts 3.01[0m would require + [32mperl-module-build 0.4234.* [0m, which can be installed; + [31mperl-sanger-cgp-allelecount[0m is not installable because there are no viable options + [31mperl-sanger-cgp-allelecount 4.3.0[0m would require + [31mperl-module-build 0.4232.* [0m, which conflicts with any installable versions previously reported; + [31mperl-sanger-cgp-allelecount [2.1.2|4.0.0|4.1.0|4.2.1|4.3.0][0m conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/perl-sanger-cgp-battenberg/meta.yaml b/recipes/perl-sanger-cgp-battenberg/meta.yaml index 09b177258fcb4..629f2fa1e28e6 100644 --- a/recipes/perl-sanger-cgp-battenberg/meta.yaml +++ b/recipes/perl-sanger-cgp-battenberg/meta.yaml @@ -8,7 +8,7 @@ source: #url: https://github.com/cancerit/cgpBattenberg/archive/ef74823.tar.gz build: - number: 9 + number: 10 skip: True # [osx] requirements: diff --git a/recipes/perl-sanger-cgp-vagrent/meta.yaml b/recipes/perl-sanger-cgp-vagrent/meta.yaml index 820b552da08fe..4ceefc26cc82b 100644 --- a/recipes/perl-sanger-cgp-vagrent/meta.yaml +++ b/recipes/perl-sanger-cgp-vagrent/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 skip: True # [osx] requirements: diff --git a/recipes/perl-sanger-cgp-vcf/meta.yaml b/recipes/perl-sanger-cgp-vcf/meta.yaml index e3a9937437a99..bb46ed530a8e0 100644 --- a/recipes/perl-sanger-cgp-vcf/meta.yaml +++ b/recipes/perl-sanger-cgp-vcf/meta.yaml @@ -7,7 +7,7 @@ source: sha256: b93ae878eac4b111966c1e9845b63a89fb79882d242e8e3cd0bae6e9573d6d75 build: - number: 9 + number: 10 requirements: build: diff --git a/recipes/perl-scalar-util-numeric/build_failure.osx-64.yaml b/recipes/perl-scalar-util-numeric/build_failure.osx-64.yaml deleted file mode 100644 index 0e54e71d413b9..0000000000000 --- a/recipes/perl-scalar-util-numeric/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: e1e0a50e6767dc8e23fe41f9b250ef98ca18c394b3b505482bd241b1f889a8e8 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - /opt/mambaforge/envs/bioconda/conda-bld/perl-scalar-util-numeric_1685394748148/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:322:67: note: expanded from macro 'XSRETURN_IV' - #define XSRETURN_IV(v) STMT_START { XST_mIV(0,v); XSRETURN(1); } STMT_END - ^~~~~~~~ - ./ppport.h:4189:25: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - Numeric.c:427:5: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-scalar-util-numeric_1685394748148/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:24: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~~~ - ./ppport.h:4188:31: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports ({ STATEMENTS; })'' */ - ^ - Numeric.c:427:5: note: '{' token is here - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-scalar-util-numeric_1685394748148/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:35: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^ - Numeric.c:427:5: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-scalar-util-numeric_1685394748148/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:52: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-scalar-util-numeric_1685394748148/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:5: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^~~~~~~~~~ - ./ppport.h:4188:31: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports ({ STATEMENTS; })'' */ - ^ - Numeric.c:427:5: note: '{' token is here - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-scalar-util-numeric_1685394748148/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:52: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-scalar-util-numeric_1685394748148/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:16: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^ - Numeric.c:427:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-scalar-util-numeric_1685394748148/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:52: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-scalar-util-numeric_1685394748148/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:5: note: expanded from macro 'XSRETURN' - } STMT_END - ^ - Numeric.c:427:5: note: ')' token is here - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-scalar-util-numeric_1685394748148/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:52: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-scalar-util-numeric_1685394748148/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:7: note: expanded from macro 'XSRETURN' - } STMT_END - ^~~~~~~~ - ./ppport.h:4189:25: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - Numeric.c:427:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-scalar-util-numeric_1685394748148/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:65: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^ - Numeric.c:427:5: note: ')' token is here - XSRETURN_EMPTY; - ^~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-scalar-util-numeric_1685394748148/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/perl5/5.32/core_perl/CORE/XSUB.h:330:67: note: expanded from macro 'XSRETURN_EMPTY' - #define XSRETURN_EMPTY STMT_START { XSRETURN(0); } STMT_END - ^~~~~~~~ - ./ppport.h:4189:25: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - 171 warnings generated. - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make: *** [Makefile:482: blib/arch/auto/Scalar/Util/Numeric/Numeric.bundle] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-scalar-util-numeric_1685394748148/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-scalar-util-numeric/meta.yaml b/recipes/perl-scalar-util-numeric/meta.yaml index a5eed6627236f..7ee7ad0a5e8df 100644 --- a/recipes/perl-scalar-util-numeric/meta.yaml +++ b/recipes/perl-scalar-util-numeric/meta.yaml @@ -12,7 +12,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - number: 6 + number: 7 requirements: build: diff --git a/recipes/perl-set-intervaltree/build_failure.osx-64.yaml b/recipes/perl-set-intervaltree/build_failure.osx-64.yaml deleted file mode 100644 index d77adaebf0bb2..0000000000000 --- a/recipes/perl-set-intervaltree/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 6bd282f07b47e1bdb160e3080c3254cf3a16aabc00afa2f43af90b294cdae8e1 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - Success - INFO:conda_build.source:Success - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/perl-set-intervaltree_1685523105591/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/perl-set-intervaltree_1685523105591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/perl-set-intervaltree_1685523105591/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/perl-set-intervaltree_1685523105591/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-set-intervaltree-0.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-set-intervaltree-0.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-set-intervaltree-0.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/perl-set-intervaltree-0.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - Checking if your kit is complete... - Looks good - Generating a Unix-style Makefile - Writing Makefile for Set::IntervalTree - Writing MYMETA.yml and MYMETA.json - cp lib/Set/IntervalTree.pm blib/lib/Set/IntervalTree.pm - AutoSplitting blib/lib/Set/IntervalTree.pm (blib/lib/auto/Set/IntervalTree) - Running Mkbootstrap for IntervalTree () - chmod 644 "IntervalTree.bs" - "$PREFIX/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- IntervalTree.bs blib/arch/auto/Set/IntervalTree/IntervalTree.bs 644 - "$PREFIX/bin/perl" "$PREFIX/lib/perl5/core_perl/ExtUtils/xsubpp" -C -typemap '$PREFIX/lib/perl5/core_perl/ExtUtils/typemap' -typemap '$SRC_DIR/perlobject.map' -typemap '$SRC_DIR/typemap' IntervalTree.xs > IntervalTree.xsc - mv IntervalTree.xsc IntervalTree.c - x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/perl_1645063215412/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-common -DPERL_DARWIN -no-cpp-precomp -Werror=partial-availability -D_DARWIN_FEATURE_CLOCK_GETTIME=0 -fno-strict-aliasing -pipe -fstack-protector-strong -DPERL_USE_SAFE_PUTENV -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -xc -Wno-reserved-user-defined-literal -O3 -DVERSION=\"0.12\" -DXS_VERSION=\"0.12\" -fPIC --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk "-I$PREFIX/lib/perl5/5.32/core_perl/CORE" -DNOMINMAX IntervalTree.c - IntervalTree.c:773:1: warning: duplicate 'extern' declaration specifier [-Wduplicate-decl-specifier] - XS_EXTERNAL(boot_Set__IntervalTree); /* prototype to pass -Wmissing-prototypes */ - ^ - /opt/mambaforge/envs/bioconda/conda-bld/perl-set-intervaltree_1685523105591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/XSUB.h:134:29: note: expanded from macro 'XS_EXTERNAL' - # define XS_EXTERNAL(name) extern "C" XSPROTO(name) - ^ - 1 warning generated. - rm -f blib/arch/auto/Set/IntervalTree/IntervalTree.bundle - x86_64-apple-darwin13.4.0-clang -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fstack-protector-strong IntervalTree.o -lstdc -o blib/arch/auto/Set/IntervalTree/IntervalTree.bundle \ - \ - - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make: *** [Makefile:487: blib/arch/auto/Set/IntervalTree/IntervalTree.bundle] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-set-intervaltree_1685523105591/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-set-intervaltree/meta.yaml b/recipes/perl-set-intervaltree/meta.yaml index bd570c754ed91..5c4b095349c49 100644 --- a/recipes/perl-set-intervaltree/meta.yaml +++ b/recipes/perl-set-intervaltree/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349 build: - number: 4 + number: 5 run_exports: '{{ pin_subpackage(name, max_pin="x.x") }}' requirements: diff --git a/recipes/perl-set-object/meta.yaml b/recipes/perl-set-object/meta.yaml index 7fb3c667489ca..0da9a819d4867 100644 --- a/recipes/perl-set-object/meta.yaml +++ b/recipes/perl-set-object/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 run_exports: weak: - {{ name }} ={{ version }} diff --git a/recipes/perl-socket/2.027/build_failure.osx-64.yaml b/recipes/perl-socket/2.027/build_failure.osx-64.yaml deleted file mode 100644 index c6545aa8b5351..0000000000000 --- a/recipes/perl-socket/2.027/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: b94f3001ca84aa35d2d229f38b51338b75d9fe41107814e57dbf44fff5c0bbb5 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - EXTEND(SP, 3); - ^~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-socket_1685404211652/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/pp.h:376:28: note: expanded from macro 'EXTEND' - } } STMT_END - ^ - Socket.xs:1338:2: note: ')' token is here - EXTEND(SP, 3); - ^~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-socket_1685404211652/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/pp.h:376:30: note: expanded from macro 'EXTEND' - } } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-socket_1685404211652/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - Socket.c:1786:5: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-socket_1685404211652/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:5: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-socket_1685404211652/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/perl.h:666:29: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports "({ STATEMENTS; })" */ - ^ - Socket.c:1786:5: note: '{' token is here - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-socket_1685404211652/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:16: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^ - Socket.c:1786:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-socket_1685404211652/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:5: note: expanded from macro 'XSRETURN' - } STMT_END - ^ - Socket.c:1786:5: note: ')' token is here - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-socket_1685404211652/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:7: note: expanded from macro 'XSRETURN' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-socket_1685404211652/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - Socket.xs:1390:2: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - EXTEND(SP, 2); - ^~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-socket_1685404211652/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/pp.h:371:25: note: expanded from macro 'EXTEND' - # define EXTEND(p,n) STMT_START { \ - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-socket_1685404211652/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/perl.h:666:29: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports "({ STATEMENTS; })" */ - ^ - Socket.xs:1390:2: note: '{' token is here - EXTEND(SP, 2); - ^~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-socket_1685404211652/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/pp.h:371:36: note: expanded from macro 'EXTEND' - # define EXTEND(p,n) STMT_START { \ - ^ - Socket.xs:1390:2: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - EXTEND(SP, 2); - ^~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-socket_1685404211652/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/pp.h:376:28: note: expanded from macro 'EXTEND' - } } STMT_END - ^ - Socket.xs:1390:2: note: ')' token is here - EXTEND(SP, 2); - ^~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-socket_1685404211652/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/pp.h:376:30: note: expanded from macro 'EXTEND' - } } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-socket_1685404211652/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - 174 warnings generated. - rm -f blib/arch/auto/Socket/Socket.bundle - x86_64-apple-darwin13.4.0-clang -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fstack-protector-strong Socket.o -o blib/arch/auto/Socket/Socket.bundle \ - \ - - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make: *** [Makefile:476: blib/arch/auto/Socket/Socket.bundle] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-socket_1685404211652/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-socket/2.027/meta.yaml b/recipes/perl-socket/2.027/meta.yaml index 4e7e3dd618d80..d30e4ac15535a 100644 --- a/recipes/perl-socket/2.027/meta.yaml +++ b/recipes/perl-socket/2.027/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/perl-socket6/meta.yaml b/recipes/perl-socket6/meta.yaml index bbb6526df15eb..978674ccd5175 100644 --- a/recipes/perl-socket6/meta.yaml +++ b/recipes/perl-socket6/meta.yaml @@ -12,7 +12,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - number: 5 + number: 6 requirements: build: diff --git a/recipes/perl-statistics-caseresampling/0.15/build_failure.osx-64.yaml b/recipes/perl-statistics-caseresampling/0.15/build_failure.osx-64.yaml deleted file mode 100644 index 7453bca60e2e5..0000000000000 --- a/recipes/perl-statistics-caseresampling/0.15/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: fb76f8bc077db99b5ac327f496146fa828534861ceef6e75b151c4c898006cbe # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - STMT_START { \ - ^ - In file included from _stats.c:1: - In file included from ./stats.h:8: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:6161: - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/inline.h:2619:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - ENV_LOCK; - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:2924:31: note: expanded from macro 'ENV_LOCK' - # define ENV_LOCK MUTEX_LOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/thread.h:219:5: note: expanded from macro 'MUTEX_LOCK' - } STMT_END - ^ - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/inline.h:2619:5: note: ')' token is here - ENV_LOCK; - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:2924:31: note: expanded from macro 'ENV_LOCK' - # define ENV_LOCK MUTEX_LOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/thread.h:219:7: note: expanded from macro 'MUTEX_LOCK' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - In file included from _stats.c:1: - In file included from ./stats.h:8: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:6161: - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/inline.h:2627:5: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - ENV_UNLOCK; - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:2925:31: note: expanded from macro 'ENV_UNLOCK' - # define ENV_UNLOCK MUTEX_UNLOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/thread.h:222:5: note: expanded from macro 'MUTEX_UNLOCK' - STMT_START { \ - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:666:29: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports "({ STATEMENTS; })" */ - ^ - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/inline.h:2627:5: note: '{' token is here - ENV_UNLOCK; - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:2925:31: note: expanded from macro 'ENV_UNLOCK' - # define ENV_UNLOCK MUTEX_UNLOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/thread.h:222:16: note: expanded from macro 'MUTEX_UNLOCK' - STMT_START { \ - ^ - In file included from _stats.c:1: - In file included from ./stats.h:8: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:6161: - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/inline.h:2627:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - ENV_UNLOCK; - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:2925:31: note: expanded from macro 'ENV_UNLOCK' - # define ENV_UNLOCK MUTEX_UNLOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/thread.h:227:5: note: expanded from macro 'MUTEX_UNLOCK' - } STMT_END - ^ - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/inline.h:2627:5: note: ')' token is here - ENV_UNLOCK; - ^~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:2925:31: note: expanded from macro 'ENV_UNLOCK' - # define ENV_UNLOCK MUTEX_UNLOCK(&PL_env_mutex) - ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/thread.h:227:7: note: expanded from macro 'MUTEX_UNLOCK' - } STMT_END - ^~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/perl5/5.32/core_perl/CORE/perl.h:667:21: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - 98 warnings generated. - rm -f blib/arch/auto/Statistics/CaseResampling/CaseResampling.bundle - x86_64-apple-darwin13.4.0-clang -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fstack-protector-strong CaseResampling.o _mt.o _stats.o -o blib/arch/auto/Statistics/CaseResampling/CaseResampling.bundle \ - \ - - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make: *** [Makefile:483: blib/arch/auto/Statistics/CaseResampling/CaseResampling.bundle] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-statistics-caseresampling_1685382879901/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-statistics-caseresampling/0.15/meta.yaml b/recipes/perl-statistics-caseresampling/0.15/meta.yaml index a8d21764faa77..899183c842d32 100644 --- a/recipes/perl-statistics-caseresampling/0.15/meta.yaml +++ b/recipes/perl-statistics-caseresampling/0.15/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/perl-statistics-r/meta.yaml b/recipes/perl-statistics-r/meta.yaml index 379b358df0bf1..dc07ae0f81ff0 100644 --- a/recipes/perl-statistics-r/meta.yaml +++ b/recipes/perl-statistics-r/meta.yaml @@ -9,7 +9,7 @@ about: build: noarch: generic - number: 6 + number: 7 source: url: "http://search.cpan.org/CPAN/authors/id/F/FA/FANGLY/Statistics-R-0.34.tar.gz" diff --git a/recipes/perl-string-approx/3.27/meta.yaml b/recipes/perl-string-approx/3.27/meta.yaml index 768541c645f7e..5c3ee5be5b12f 100644 --- a/recipes/perl-string-approx/3.27/meta.yaml +++ b/recipes/perl-string-approx/3.27/meta.yaml @@ -13,7 +13,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/perl-sub-attribute/build_failure.osx-64.yaml b/recipes/perl-sub-attribute/build_failure.osx-64.yaml deleted file mode 100644 index 3efd1ae378ed7..0000000000000 --- a/recipes/perl-sub-attribute/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: b9dbb0ac444c16b1ebe0020e4e9259d27c45dd8228f91e1601930c526d84935b # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - # define STMT_END ) - ^ - Attribute.xs:248:13: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XPUSHs(ST(i)); - ^~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-sub-attribute_1685404599742/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/perl5/5.32/core_perl/CORE/pp.h:462:19: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^~~~~~~~~~ - ./ppport.h:4392:31: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports ({ STATEMENTS; })'' */ - ^ - Attribute.xs:248:13: note: '{' token is here - XPUSHs(ST(i)); - ^~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-sub-attribute_1685404599742/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/perl5/5.32/core_perl/CORE/pp.h:462:30: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^ - Attribute.xs:248:13: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XPUSHs(ST(i)); - ^~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-sub-attribute_1685404599742/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/perl5/5.32/core_perl/CORE/pp.h:462:32: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-sub-attribute_1685404599742/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/perl5/5.32/core_perl/CORE/pp.h:371:25: note: expanded from macro 'EXTEND' - # define EXTEND(p,n) STMT_START { \ - ^~~~~~~~~~ - ./ppport.h:4392:31: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports ({ STATEMENTS; })'' */ - ^ - Attribute.xs:248:13: note: '{' token is here - XPUSHs(ST(i)); - ^~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-sub-attribute_1685404599742/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/perl5/5.32/core_perl/CORE/pp.h:462:32: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-sub-attribute_1685404599742/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/perl5/5.32/core_perl/CORE/pp.h:371:36: note: expanded from macro 'EXTEND' - # define EXTEND(p,n) STMT_START { \ - ^ - Attribute.xs:248:13: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XPUSHs(ST(i)); - ^~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-sub-attribute_1685404599742/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/perl5/5.32/core_perl/CORE/pp.h:462:32: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-sub-attribute_1685404599742/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/perl5/5.32/core_perl/CORE/pp.h:376:28: note: expanded from macro 'EXTEND' - } } STMT_END - ^ - Attribute.xs:248:13: note: ')' token is here - XPUSHs(ST(i)); - ^~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-sub-attribute_1685404599742/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/perl5/5.32/core_perl/CORE/pp.h:462:32: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-sub-attribute_1685404599742/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/perl5/5.32/core_perl/CORE/pp.h:376:30: note: expanded from macro 'EXTEND' - } } STMT_END - ^~~~~~~~ - ./ppport.h:4393:25: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - Attribute.xs:248:13: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XPUSHs(ST(i)); - ^~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-sub-attribute_1685404599742/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/perl5/5.32/core_perl/CORE/pp.h:462:59: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^ - Attribute.xs:248:13: note: ')' token is here - XPUSHs(ST(i)); - ^~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-sub-attribute_1685404599742/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/perl5/5.32/core_perl/CORE/pp.h:462:61: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^~~~~~~~ - ./ppport.h:4393:25: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - 113 warnings generated. - rm -f blib/arch/auto/Sub/Attribute/Attribute.bundle - x86_64-apple-darwin13.4.0-clang -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk Attribute.o -o blib/arch/auto/Sub/Attribute/Attribute.bundle \ - \ - - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make: *** [Makefile:477: blib/arch/auto/Sub/Attribute/Attribute.bundle] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-sub-attribute_1685404599742/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-sub-attribute/meta.yaml b/recipes/perl-sub-attribute/meta.yaml index b80a1155fafc8..36d1e0dc25ee5 100644 --- a/recipes/perl-sub-attribute/meta.yaml +++ b/recipes/perl-sub-attribute/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/perl-template-toolkit/build_failure.osx-64.yaml b/recipes/perl-template-toolkit/build_failure.osx-64.yaml deleted file mode 100644 index ca56b45742199..0000000000000 --- a/recipes/perl-template-toolkit/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 3a2dcf2c467b145364571d48c1ed4e8e87adfcddf5d39c3472cab28404d6b64d # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - /opt/mambaforge/envs/bioconda/conda-bld/perl-template-toolkit_1685394414995/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/pp.h:462:59: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^ - Stash.xs:1230:9: note: ')' token is here - XPUSHs(ident); - ^~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-template-toolkit_1685394414995/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/pp.h:462:61: note: expanded from macro 'XPUSHs' - #define XPUSHs(s) STMT_START { EXTEND(sp,1); *sp = (s); } STMT_END - ^~~~~~~~ - ./ppport.h:4002:20: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - Stash.c:1403:5: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-template-toolkit_1685394414995/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:5: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^~~~~~~~~~ - ./ppport.h:4001:28: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports ({ STATEMENTS; })'' */ - ^ - Stash.c:1403:5: note: '{' token is here - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-template-toolkit_1685394414995/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:16: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^ - Stash.c:1403:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-template-toolkit_1685394414995/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:5: note: expanded from macro 'XSRETURN' - } STMT_END - ^ - Stash.c:1403:5: note: ')' token is here - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-template-toolkit_1685394414995/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:7: note: expanded from macro 'XSRETURN' - } STMT_END - ^~~~~~~~ - ./ppport.h:4002:20: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - Stash.c:1457:5: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-template-toolkit_1685394414995/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:5: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^~~~~~~~~~ - ./ppport.h:4001:28: note: expanded from macro 'STMT_START' - # define STMT_START (void)( /* gcc supports ({ STATEMENTS; })'' */ - ^ - Stash.c:1457:5: note: '{' token is here - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-template-toolkit_1685394414995/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/XSUB.h:315:16: note: expanded from macro 'XSRETURN' - STMT_START { \ - ^ - Stash.c:1457:5: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-template-toolkit_1685394414995/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:5: note: expanded from macro 'XSRETURN' - } STMT_END - ^ - Stash.c:1457:5: note: ')' token is here - XSRETURN(1); - ^~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/perl-template-toolkit_1685394414995/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/perl5/5.32/core_perl/CORE/XSUB.h:320:7: note: expanded from macro 'XSRETURN' - } STMT_END - ^~~~~~~~ - ./ppport.h:4002:20: note: expanded from macro 'STMT_END' - # define STMT_END ) - ^ - 148 warnings generated. - rm -f ../blib/arch/auto/Template/Stash/XS/XS.bundle - x86_64-apple-darwin13.4.0-clang -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup --sysroot=/Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -fstack-protector-strong Stash.o -o ../blib/arch/auto/Template/Stash/XS/XS.bundle \ - \ - - ld: library not found for -lSystem - clang-15: error: linker command failed with exit code 1 (use -v to see invocation) - make[1]: *** [Makefile:458: ../blib/arch/auto/Template/Stash/XS/XS.bundle] Error 1 - make[1]: Leaving directory '$SRC_DIR/xs' - make: *** [Makefile:778: subdirs] Error 2 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/perl-template-toolkit_1685394414995/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/perl-template-toolkit/meta.yaml b/recipes/perl-template-toolkit/meta.yaml index eb8b12f62842e..3e20b09fde8f4 100644 --- a/recipes/perl-template-toolkit/meta.yaml +++ b/recipes/perl-template-toolkit/meta.yaml @@ -10,7 +10,7 @@ source: sha256: cec7c20af57ed4b0d8131599a41027f56e22b544c8083704afad6a13cd483ffc build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/perl-tie-hash-indexed/meta.yaml b/recipes/perl-tie-hash-indexed/meta.yaml index 73b68ddc2dc19..522ffe160cd73 100644 --- a/recipes/perl-tie-hash-indexed/meta.yaml +++ b/recipes/perl-tie-hash-indexed/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 37bc62815f5a848ac77912b9bf4788a9f272884e83a52e2093dab4a83a4a7b10 build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/perl-time-hires/meta.yaml b/recipes/perl-time-hires/meta.yaml index 29a2702b32606..58bcd847e6842 100644 --- a/recipes/perl-time-hires/meta.yaml +++ b/recipes/perl-time-hires/meta.yaml @@ -13,7 +13,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x") }} - number: 5 + number: 6 requirements: build: diff --git a/recipes/perl-unicode-map/meta.yaml b/recipes/perl-unicode-map/meta.yaml index 2628f73f65d49..04843620aad81 100644 --- a/recipes/perl-unicode-map/meta.yaml +++ b/recipes/perl-unicode-map/meta.yaml @@ -13,7 +13,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - number: 8 + number: 9 requirements: build: diff --git a/recipes/perl-unicode-normalize/meta.yaml b/recipes/perl-unicode-normalize/meta.yaml index 96a87f3761326..0360cea613b61 100644 --- a/recipes/perl-unicode-normalize/meta.yaml +++ b/recipes/perl-unicode-normalize/meta.yaml @@ -13,7 +13,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x") }} - number: 6 + number: 7 requirements: build: diff --git a/recipes/perl-unicode-utf8/meta.yaml b/recipes/perl-unicode-utf8/meta.yaml index 311d5ce748c39..0a7e3c1b4bfc3 100644 --- a/recipes/perl-unicode-utf8/meta.yaml +++ b/recipes/perl-unicode-utf8/meta.yaml @@ -13,7 +13,7 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - number: 7 + number: 8 requirements: build: diff --git a/recipes/perl-want/meta.yaml b/recipes/perl-want/meta.yaml index 733f0865ad983..a4bf351031eea 100644 --- a/recipes/perl-want/meta.yaml +++ b/recipes/perl-want/meta.yaml @@ -10,7 +10,7 @@ source: md5: 33b2dae5db59781b9a0434fa1db04aab build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/perl-xml-libxslt/meta.yaml b/recipes/perl-xml-libxslt/meta.yaml index 2fa206a0fe02e..f0b5f16c2edba 100644 --- a/recipes/perl-xml-libxslt/meta.yaml +++ b/recipes/perl-xml-libxslt/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 7caa5aee72f53be59d8b84eecb6864a07c612a12ea6b27d5c706960edcd54587 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/pfp/build_failure.linux-64.yaml b/recipes/pfp/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..de690a6c7478f --- /dev/null +++ b/recipes/pfp/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 505d2867d60861e94fef4a31d679b550392177d80ab8e610a08534c263c58749 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CMake Warning (dev) at /opt/conda/conda-bld/pfp_1734240947028/_build_env/share/cmake-3.31/Modules/FetchContent.cmake:1953 (message): + Calling FetchContent_Populate(smhasher) is deprecated, call + FetchContent_MakeAvailable(smhasher) instead. Policy CMP0169 can be set to + OLD to allow FetchContent_Populate(smhasher) to be called directly for now, + but the ability to call it with declared details will be removed completely + in a future version. + Call Stack (most recent call first): + CMakeLists.txt:110 (FetchContent_Populate) + This warning is for project developers. Use -Wno-dev to suppress it. + + CMake Warning (dev) at /opt/conda/conda-bld/pfp_1734240947028/_build_env/share/cmake-3.31/Modules/FetchContent.cmake:1953 (message): + Calling FetchContent_Populate(cli11) is deprecated, call + FetchContent_MakeAvailable(cli11) instead. Policy CMP0169 can be set to + OLD to allow FetchContent_Populate(cli11) to be called directly for now, + but the ability to call it with declared details will be removed completely + in a future version. + Call Stack (most recent call first): + CMakeLists.txt:122 (FetchContent_Populate) + This warning is for project developers. Use -Wno-dev to suppress it. + + CMake Warning (dev) at /opt/conda/conda-bld/pfp_1734240947028/_build_env/share/cmake-3.31/Modules/FetchContent.cmake:1953 (message): + Calling FetchContent_Populate(spdlog) is deprecated, call + FetchContent_MakeAvailable(spdlog) instead. Policy CMP0169 can be set to + OLD to allow FetchContent_Populate(spdlog) to be called directly for now, + but the ability to call it with declared details will be removed completely + in a future version. + Call Stack (most recent call first): + CMakeLists.txt:133 (FetchContent_Populate) + This warning is for project developers. Use -Wno-dev to suppress it. + + CMake Warning (dev) at /opt/conda/conda-bld/pfp_1734240947028/_build_env/share/cmake-3.31/Modules/FetchContent.cmake:1953 (message): + Calling FetchContent_Populate(zstr) is deprecated, call + FetchContent_MakeAvailable(zstr) instead. Policy CMP0169 can be set to OLD + to allow FetchContent_Populate(zstr) to be called directly for now, but the + ability to call it with declared details will be removed completely in a + future version. + Call Stack (most recent call first): + CMakeLists.txt:144 (FetchContent_Populate) + This warning is for project developers. Use -Wno-dev to suppress it. + + CMake Warning (dev) at /opt/conda/conda-bld/pfp_1734240947028/_build_env/share/cmake-3.31/Modules/FetchContent.cmake:1953 (message): + Calling FetchContent_Populate(malloc_count) is deprecated, call + FetchContent_MakeAvailable(malloc_count) instead. Policy CMP0169 can be + set to OLD to allow FetchContent_Populate(malloc_count) to be called + directly for now, but the ability to call it with declared details will be + removed completely in a future version. + Call Stack (most recent call first): + CMakeLists.txt:155 (FetchContent_Populate) + This warning is for project developers. Use -Wno-dev to suppress it. + + CMake Warning (dev) at /opt/conda/conda-bld/pfp_1734240947028/_build_env/share/cmake-3.31/Modules/FetchContent.cmake:1953 (message): + Calling FetchContent_Populate(kseq) is deprecated, call + FetchContent_MakeAvailable(kseq) instead. Policy CMP0169 can be set to OLD + to allow FetchContent_Populate(kseq) to be called directly for now, but the + ability to call it with declared details will be removed completely in a + future version. + Call Stack (most recent call first): + CMakeLists.txt:169 (FetchContent_Populate) + This warning is for project developers. Use -Wno-dev to suppress it. + + -- Found OpenMP_C: -fopenmp (found version "4.5") + -- Found OpenMP_CXX: -fopenmp (found version "4.5") + -- Found OpenMP: TRUE (found version "4.5") + -- HAVE_OPENMP: OpenMP + -- Found ZLIB: $PREFIX/lib/libz.so (found version "1.3.1") + CMake Error at /opt/conda/conda-bld/pfp_1734240947028/_build_env/share/cmake-3.31/Modules/FindPackageHandleStandardArgs.cmake:233 (message): + Could NOT find LibLZMA (missing: LIBLZMA_LIBRARY LIBLZMA_INCLUDE_DIR + LIBLZMA_HAS_AUTO_DECODER LIBLZMA_HAS_EASY_ENCODER LIBLZMA_HAS_LZMA_PRESET) + Call Stack (most recent call first): + /opt/conda/conda-bld/pfp_1734240947028/_build_env/share/cmake-3.31/Modules/FindPackageHandleStandardArgs.cmake:603 (_FPHSA_FAILURE_MESSAGE) + /opt/conda/conda-bld/pfp_1734240947028/_build_env/share/cmake-3.31/Modules/FindLibLZMA.cmake:108 (find_package_handle_standard_args) + cmake/LibFindMacros.cmake:14 (find_package) + cmake/FindHTSlib.cmake:12 (libfind_package) + CMakeLists.txt:238 (find_package) + + + -- Configuring incomplete, errors occurred! + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/pfp_1734240947028/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/pfp_1734240947028/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/pfp/meta.yaml b/recipes/pfp/meta.yaml index f9f7408bd65bb..adc4590729950 100644 --- a/recipes/pfp/meta.yaml +++ b/recipes/pfp/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 66fc33d79f30d123a0465020e2c9d81b873c95ef8a7fefefc36791f04f82aa08 build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/pftools/meta.yaml b/recipes/pftools/meta.yaml index 74d61b9b819a1..cba90dd264eaf 100644 --- a/recipes/pftools/meta.yaml +++ b/recipes/pftools/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 skip: True # [osx] requirements: diff --git a/recipes/pgenlib/meta.yaml b/recipes/pgenlib/meta.yaml index a5786127871dc..359bcb678d620 100644 --- a/recipes/pgenlib/meta.yaml +++ b/recipes/pgenlib/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 32992274214d2e6735b721544abfd0ae0c76906c4193120f7091065b88f68dfa build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation" run_exports: - {{ pin_subpackage('pgenlib', max_pin="x.x") }} diff --git a/recipes/pgma-simple/meta.yaml b/recipes/pgma-simple/meta.yaml index 6fe7a1d4f8636..79410d6454035 100644 --- a/recipes/pgma-simple/meta.yaml +++ b/recipes/pgma-simple/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 785c86b3e57461ffd6c4b8d1002c24d69fc33552b2e81bcd0a9da589330d2b70 build: - number: 6 + number: 7 requirements: diff --git a/recipes/pgrc/meta.yaml b/recipes/pgrc/meta.yaml index 23429e64db634..a93e199e1df6b 100644 --- a/recipes/pgrc/meta.yaml +++ b/recipes/pgrc/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('pgrc', max_pin="x") }} diff --git a/recipes/pgsa/build_failure.linux-64.yaml b/recipes/pgsa/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..189eb2f1a844c --- /dev/null +++ b/recipes/pgsa/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 02f8e94a24d389cd7746d06954e4907e9452938d7bb19a1dbd65b545084d3aba # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pgsa-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pgsa-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pgsa-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pgsa-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + "make" -f nbproject/Makefile-pgsagen.mk QMAKE= SUBPROJECTS= .build-conf + make[1]: Entering directory '$SRC_DIR' + "make" -f nbproject/Makefile-pgsagen.mk dist/pgsagen/GNU-Linux-x86/PgSAgen + make[2]: Entering directory '$SRC_DIR' + mkdir -p build/pgsagen/GNU-Linux-x86/src + rm -f "build/pgsagen/GNU-Linux-x86/src/PgSAgen.o.d" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -O3 -Wall -s -I. -std=c11 -MMD -MP -MF "build/pgsagen/GNU-Linux-x86/src/PgSAgen.o.d" -o build/pgsagen/GNU-Linux-x86/src/PgSAgen.o src/PgSAgen.cpp + mkdir -p build/pgsagen/GNU-Linux-x86/src + rm -f "build/pgsagen/GNU-Linux-x86/src/helper.o.d" + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -O3 -Wall -s -I. -std=c11 -MMD -MP -MF "build/pgsagen/GNU-Linux-x86/src/helper.o.d" -o build/pgsagen/GNU-Linux-x86/src/helper.o src/helper.cpp + src/helper.cpp: In function 'int PgSAHelpers::strcmplcp(const char*, const char*, int)': + src/helper.cpp:184:30: error: 'uint32_t' was not declared in this scope + 184 | int cmp = bswap_32(*(uint32_t*) lStrPtr) - bswap_32(*(uint32_t*) rStrPtr); + | ^~~~~~~~ + src/helper.cpp:4:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + 3 | #include "byteswap.h" + |#include + 4 | + src/helper.cpp:184:39: error: expected primary-expression before ')' token + 184 | int cmp = bswap_32(*(uint32_t*) lStrPtr) - bswap_32(*(uint32_t*) rStrPtr); + | ^ + src/helper.cpp:184:72: error: expected primary-expression before ')' token + 184 | int cmp = bswap_32(*(uint32_t*) lStrPtr) - bswap_32(*(uint32_t*) rStrPtr); + | ^ + make[2]: *** [nbproject/Makefile-pgsagen.mk:101: build/pgsagen/GNU-Linux-x86/src/helper.o] Error 1 + make[2]: Leaving directory '$SRC_DIR' + make[1]: *** [nbproject/Makefile-pgsagen.mk:87: .build-conf] Error 2 + make[1]: Leaving directory '$SRC_DIR' + make: *** [nbproject/Makefile-impl.mk:40: .build-impl] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/pgsa_1733855165277/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/pgsa_1733855165277/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/pgsa/meta.yaml b/recipes/pgsa/meta.yaml index 43539c012e67b..7d3333062fdce 100644 --- a/recipes/pgsa/meta.yaml +++ b/recipes/pgsa/meta.yaml @@ -7,7 +7,7 @@ source: md5: e69596048ed3831a6c92580814d48f19 build: - number: 6 + number: 7 skip: True # [osx] patches: - patch diff --git a/recipes/phast/meta.yaml b/recipes/phast/meta.yaml index f40cf1da8f5c0..79bdce761fbdd 100644 --- a/recipes/phast/meta.yaml +++ b/recipes/phast/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 6 + number: 7 source: url: http://compgen.cshl.edu/phast/downloads/phast.v1_5.tgz diff --git a/recipes/phcue-ck/meta.yaml b/recipes/phcue-ck/meta.yaml index 2ad7201ffedc5..e7dccc9f0f691 100644 --- a/recipes/phcue-ck/meta.yaml +++ b/recipes/phcue-ck/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 source: url: https://github.com/lgi-onehealth/phcue-ck/archive/refs/tags/v{{ version }}.tar.gz diff --git a/recipes/phipack/build_failure.osx-64.yaml b/recipes/phipack/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c068212d1e7c2 --- /dev/null +++ b/recipes/phipack/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 0a9252d55a4a2699074dc3531589103882f72ead94678082f5f70f87276db51e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phipack-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix stats.c -o stats.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phipack-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix maxChi.c -o maxChi.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phipack-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix main.c -o main.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phipack-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix queue.c -o queue.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phipack-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix graphCode.c -o graphCode.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phipack-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix fasta.c -o fasta.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phipack-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix phylip.c -o phylip.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phipack-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix mem.c -o mem.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phipack-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix misc.c -o misc.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phipack-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix pairScore.c -o pairScore.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phipack-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix seqManip.c -o seqManip.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phipack-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix global.c -o global.o + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phipack-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o Phi normal.o stats.o maxChi.o main.o queue.o graphCode.o fasta.o phylip.o mem.o misc.o pairScore.o seqManip.o global.o -lm + cp Phi ../ + cd ppma_2_bmp && make + make[1]: Entering directory '$SRC_DIR/src/ppma_2_bmp' + make[1]: Nothing to be done for 'default'. + make[1]: Leaving directory '$SRC_DIR/src/ppma_2_bmp' + cp ppma_2_bmp/ppma_2_bmp ../ + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phipack-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix profile.c -o profile.o + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phipack-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o Profile normal.o stats.o fasta.o phylip.o mem.o misc.o pairScore.o seqManip.o global.o profile.o -lm + cp Profile ../ + + Resource usage statistics from building phipack: + Process count: 4 + CPU time: Sys=0:00:00.2, User=0:00:00.2 + Memory: 19.0M + Disk usage: 1.8K + Time elapsed: 0:00:06.3 + + + Packaging phipack + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/phipack_1734475547466/_build_env + + + The following NEW packages will be INSTALLED: + + ca-certificates: 2024.12.14-h8857fd0_0 conda-forge + cctools_osx-64: 1010.6-h00edd4c_2 conda-forge + clang: 18.1.8-default_h179603d_5 conda-forge + clang-18: 18.1.8-default_h0c94c6a_5 conda-forge + clang_impl_osx-64: 18.1.8-h6a44ed1_23 conda-forge + clang_osx-64: 18.1.8-h7e5c614_23 conda-forge + clangxx: 18.1.8-default_h179603d_5 conda-forge + compiler-rt: 18.1.8-h1020d70_1 conda-forge + compiler-rt_osx-64: 18.1.8-hf2b8a54_1 conda-forge + ld64_osx-64: 951.9-hc8d1a19_2 conda-forge + libclang-cpp18.1: 18.1.8-default_h0c94c6a_5 conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libcxx-devel: 18.1.8-h7c275be_7 conda-forge + libiconv: 1.17-hd75f5a5_2 conda-forge + libllvm18: 18.1.8-h9ce406d_2 conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libxml2: 2.13.5-he8ee3e7_1 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-tools: 18.1.8-h9ce406d_2 conda-forge + llvm-tools-18: 18.1.8-h9ce406d_2 conda-forge + make: 4.4.1-h00291cd_2 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + sigtool: 0.1.3-h88f4db0_0 conda-forge + tapi: 1300.6.5-h390ca13_0 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Packaging phipack-1.1-h18d8cf3_5 + + error: /opt/mambaforge/envs/bioconda/conda-bld/phipack_1734475547466/_build_env/bin/x86_64-apple-darwin13.4.0-install_name_tool: in swap_object_headers(): malformed load command 0 (cmdsize is zero) + fatal error: /opt/mambaforge/envs/bioconda/conda-bld/phipack_1734475547466/_build_env/bin/x86_64-apple-darwin13.4.0-install_name_tool: internal error: swap_object_headers() failed + + number of files: 10 + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2765, in build + newly_built_packages = bundlers[pkg_type]( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1874, in bundle_conda + files = post_process_files(metadata, initial_files) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1653, in post_process_files + post_build(m, new_files, build_python=python) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1759, in post_build + post_process_shared_lib(m, f, prefix_files, host_prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1635, in post_process_shared_lib + mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 498, in mk_relative_osx + macho.add_rpath(path, rpath_new, build_prefix=prefix, verbose=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 297, in add_rpath + raise RuntimeError("install_name_tool failed with exit status %d" % code) + RuntimeError: install_name_tool failed with exit status 1 +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/phipack/meta.yaml b/recipes/phipack/meta.yaml index 8eec2c2e15298..daaa7443d0cc8 100644 --- a/recipes/phipack/meta.yaml +++ b/recipes/phipack/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.1" build: - number: 4 + number: 5 source: url: http://www.maths.otago.ac.nz/~dbryant/software/PhiPack.tar.gz diff --git a/recipes/phispy/build_failure.osx-64.yaml b/recipes/phispy/build_failure.osx-64.yaml deleted file mode 100644 index d88b6d5ee1ba6..0000000000000 --- a/recipes/phispy/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: c9c71853172ce7a3e354a56c027483c811957efef56eef911e4b94cbb044a44f # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1850, in bundle_conda - files = post_process_files(metadata, initial_files) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1664, in post_process_files - post_build(m, new_files, build_python=python) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1727, in post_build - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phispy-4.2.21 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - post_process_shared_lib(m, f, prefix_files, host_prefix) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1603, in post_process_shared_lib - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 470, in mk_relative_osx - names = macho.otool(path, prefix) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 221, in otool - lines = check_output([otool, "-l", path], stderr=STDOUT).decode("utf-8") - File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 421, in check_output - return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, - File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 526, in run - raise CalledProcessError(retcode, process.args, - subprocess.CalledProcessError: Command '['/opt/mambaforge/envs/bioconda/conda-bld/phispy_1718318993033/_build_env/bin/llvm-otool', '-l', '/opt/mambaforge/envs/bioconda/conda-bld/phispy_1718318993033/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.11/site-packages/PhiSpyRepeatFinder.cpython-311-darwin.so']' died with . - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phispy-4.2.21 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phispy-4.2.21 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - Using pip 24.0 from $PREFIX/lib/python3.11/site-packages/pip (python 3.11) - Non-user install because user site-packages disabled - Ignoring indexes: https://pypi.org/simple - Created temporary directory: /private/tmp/pip-build-tracker-k4rcmtb3 - Initialized build tracking at /private/tmp/pip-build-tracker-k4rcmtb3 - Created build tracker: /private/tmp/pip-build-tracker-k4rcmtb3 - Entered build tracker: /private/tmp/pip-build-tracker-k4rcmtb3 - Created temporary directory: /private/tmp/pip-install-sabiqxhb - Created temporary directory: /private/tmp/pip-ephem-wheel-cache-c27hxbct - Processing $SRC_DIR - Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-k4rcmtb3' - Running setup.py (path:$SRC_DIR/setup.py) egg_info for package from file://$SRC_DIR - Created temporary directory: /private/tmp/pip-pip-egg-info-0406583g - Preparing metadata (setup.py): started - Preparing metadata (setup.py): finished with status 'done' - Source in $SRC_DIR has version 4.2.21, which satisfies requirement PhiSpy==4.2.21 from file://$SRC_DIR - Removed PhiSpy==4.2.21 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-k4rcmtb3' - Created temporary directory: /private/tmp/pip-unpack-ftp04rd6 - Building wheels for collected packages: PhiSpy - Created temporary directory: /private/tmp/pip-wheel-eyso9vyq - Building wheel for PhiSpy (setup.py): started - Destination directory: /private/tmp/pip-wheel-eyso9vyq - Building wheel for PhiSpy (setup.py): finished with status 'done' - Created wheel for PhiSpy: filename=PhiSpy-4.2.21-cp311-cp311-macosx_10_13_x86_64.whl size=19193361 sha256=2fd6b7c4708d36120a5a1c24c6e7cf4e0cb826c1bbdfa08be4f396c13a6b33b3 - Stored in directory: /private/tmp/pip-ephem-wheel-cache-c27hxbct/wheels/2a/82/cf/c866a05b78178153fa1ace983db9616900e7be463b1da03fca - Successfully built PhiSpy - Installing collected packages: PhiSpy - - changing mode of $PREFIX/bin/PhiSpy.py to 755 - changing mode of $PREFIX/bin/phispy to 755 - Successfully installed PhiSpy-4.2.21 - Removed build tracker: '/private/tmp/pip-build-tracker-k4rcmtb3' - - Resource usage statistics from building phispy: - Process count: 5 - CPU time: Sys=0:00:00.7, User=0:00:43.2 - Memory: 190.3M - Disk usage: 304.2K - Time elapsed: 0:00:48.4 - - - compiling .pyc files... - number of files: 120 -# Last 100 lines of the build log. diff --git a/recipes/phispy/meta.yaml b/recipes/phispy/meta.yaml index a7d707cd0a82f..8de1ca18c3691 100644 --- a/recipes/phispy/meta.yaml +++ b/recipes/phispy/meta.yaml @@ -11,7 +11,7 @@ source: sha256: "1dc3ec45c15328577557908517254d8e4ba152416f0e6bbad39e965b86730e28" build: - number: 6 + number: 7 script: "{{ PYTHON }} -m pip install . --no-deps -vv " run_exports: - {{ pin_subpackage('phispy', max_pin="x") }} diff --git a/recipes/phyloacc/build_failure.osx-64.yaml b/recipes/phyloacc/build_failure.osx-64.yaml deleted file mode 100644 index 87d350a41d6d6..0000000000000 --- a/recipes/phyloacc/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: e081ddfcb312d17f3886fad07d2492cab6b0e0716c61e66c83e271766d9ebfdf # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - In file included from src/PhyloAcc-GT/bpp_c.hpp:27: - /opt/mambaforge/envs/bioconda/conda-bld/phyloacc_1718294848149/_build_env/bin/../include/c/v1/set:741:30: warning: the specified comparator type does not provide a viable const call operator [-Wuser-defined-warnings] - static_assert(sizeof(__diagnose_non_const_comparator<_Key, _Compare>()), ""); - ^ - src/PhyloAcc-GT//genetree.cpp:316:37: note: in instantiation of member function 'std::set, Cmp>::~set' requested here - set, Cmp> tocoal; - ^ - /opt/mambaforge/envs/bioconda/conda-bld/phyloacc_1718294848149/_build_env/bin/../include/c/v1/__tree:994:5: note: from 'diagnose_if' attribute on '__diagnose_non_const_comparator, Cmp>': - _LIBCPP_DIAGNOSE_WARNING(!__invokable<_Compare const&, _Tp const&, _Tp const&>::value, - ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - /opt/mambaforge/envs/bioconda/conda-bld/phyloacc_1718294848149/_build_env/bin/../include/c/v1/__config:1322:58: note: expanded from macro '_LIBCPP_DIAGNOSE_WARNING' - # define _LIBCPP_DIAGNOSE_WARNING(...) __attribute__((__diagnose_if__(__VA_ARGS__, "warning"))) - ^ ~~~~~~~~~~~ - 7 warnings generated. - In file included from src/PhyloAcc-GT//main.cpp:26: - src/PhyloAcc-GT/bpp_c.hpp:223:13: warning: unused variable 'tot' [-Wunused-variable] - int tot = ceil((double)(GG - 15)/GG_block); - ^ - 1 warning generated. - dyld[53487]: Library not loaded: @rpath/libLLVM-16.dylib - Referenced from: <7C18778E-BF33-3AEA-A118-E46B35B5996F> /opt/mambaforge/envs/bioconda/pkgs/llvm-tools-16.0.6-hbedff68_3/bin/dsymutil - Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/llvm-tools-16.0.6-hbedff68_3/bin/../lib/libLLVM-16.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/llvm-tools-16.0.6-hbedff68_3/bin/../lib/libLLVM-16.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/llvm-tools-16.0.6-hbedff68_3/bin/../lib/libLLVM-16.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/llvm-tools-16.0.6-hbedff68_3/bin/../lib/libLLVM-16.dylib' (no such file), '/usr/local/lib/libLLVM-16.dylib' (no such file), '/usr/lib/libLLVM-16.dylib' (no such file, not in dyld cache) - clang-16: error: unable to execute command: Abort trap: 6 - clang-16: error: dsymutil command failed due to signal (use -v to see invocation) - make: *** [Makefile:49: PhyloAcc-GT] Error 1 - Extracting download - Traceback (most recent call last): - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/phyloacc_1718294848149/work - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/phyloacc_1718294848149/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/phyloacc_1718294848149/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/phyloacc_1718294848149/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phyloacc-2.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - CLANG=x86_64-apple-darwin13.4.0-clang - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phyloacc-2.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - packages_from_this = build( - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/phyloacc_1718294848149/work/conda_build.sh']' returned non-zero exit status 2. - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phyloacc-2.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phyloacc-2.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - $CXX is [x86_64-apple-darwin13.4.0-clang] - $PREFIX is [$PREFIX] - $GSL_INCLUDE is [$PREFIX/include/] - $GSL_LIB is [$PREFIX/lib/] - x86_64-apple-darwin13.4.0-clang -Wall -g -O2 -std=c11 -I$PREFIX/include/ -L$PREFIX/lib/ src/PhyloAcc-ST//*.cpp -o PhyloAcc-ST -lgsl -lm -lgslcblas -larmadillo -fopenmp - x86_64-apple-darwin13.4.0-clang -Wall -g -O2 -std=c11 -I$PREFIX/include/ -L$PREFIX/lib/ src/PhyloAcc-GT//*.cpp -o PhyloAcc-GT -lgsl -lm -lgslcblas -larmadillo -fopenmp -# Last 100 lines of the build log. diff --git a/recipes/phyloacc/meta.yaml b/recipes/phyloacc/meta.yaml index 945e20339b3fb..5778ee7929a42 100644 --- a/recipes/phyloacc/meta.yaml +++ b/recipes/phyloacc/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [py < 311] run_exports: - {{ pin_subpackage('phyloacc', max_pin="x") }} diff --git a/recipes/phylobayes-mpi/meta.yaml b/recipes/phylobayes-mpi/meta.yaml index f7e1222486eef..d6a18c3d15d00 100644 --- a/recipes/phylobayes-mpi/meta.yaml +++ b/recipes/phylobayes-mpi/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 567d8db995f23b2b0109c1e6088a7e5621e38fec91d6b2f27abd886b90ea31ce build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/phylocsfpp/meta.yaml b/recipes/phylocsfpp/meta.yaml index ec508fe46773e..6501b2c334e54 100644 --- a/recipes/phylocsfpp/meta.yaml +++ b/recipes/phylocsfpp/meta.yaml @@ -10,7 +10,7 @@ source: git_rev: {{ commit_id }} build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/phylodm/meta.yaml b/recipes/phylodm/meta.yaml index 1bfd5232396a0..c5e89e744a172 100644 --- a/recipes/phylodm/meta.yaml +++ b/recipes/phylodm/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [py < 38] run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/phylommand/build_failure.osx-64.yaml b/recipes/phylommand/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..0385b5fa1787d --- /dev/null +++ b/recipes/phylommand/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: a5a5009dfb0df231486148d0a60573a001823a142a2804a004fa2b0b38265332 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - libcxx >=18 + - nlopt >=2.8.0,<2.9.0a0 + test: + commands: + - contree --help + - pairalign --help + - treebender --help + about: + description: Command-line tools to create, manipulate, and/or analyze phylogenetic + trees or pairwise alignments. Does not include "rudisvg" svg viewer. + home: https://github.com/mr-y/phylommand + license: GPLv3 + license_file: LICENSE + summary: Command-line phylogenetics tools. + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/phylommand_1734463917799/work + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/phylommand_1734463917799/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/phylommand_1734463917799/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/phylommand_1734463917799/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/phylommand_1734463917799/work/conda_build.sh']' returned non-zero exit status 2. + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c tree.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c treebender.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c string_tree.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c file_parser.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c argv_parser.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c matrix_parser.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c clustertree.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o treebender tree.o treebender.o string_tree.o file_parser.o argv_parser.o matrix_parser.o clustertree.o + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c seqpair.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DPTHREAD -c pairalign.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c align_group.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c seqdatabase.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c indexedfasta.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o pairalign seqpair.o pairalign.o align_group.o seqdatabase.o argv_parser.o indexedfasta.o -ldl -lpthread + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c contree.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c decisiveness.cpp + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o contree contree.o tree.o decisiveness.o string_tree.o matrix_parser.o file_parser.o + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/phylommand-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c treeator.cpp -DNLOPT +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/phylommand/meta.yaml b/recipes/phylommand/meta.yaml index 867ce98e3e5d8..09e7b60ae563c 100644 --- a/recipes/phylommand/meta.yaml +++ b/recipes/phylommand/meta.yaml @@ -9,7 +9,7 @@ source: md5: 14ae8509ff838530dcb50e7fb3ca48c1 build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/phyml/meta.yaml b/recipes/phyml/meta.yaml index e09590285ebc7..76dfa47845946 100644 --- a/recipes/phyml/meta.yaml +++ b/recipes/phyml/meta.yaml @@ -15,7 +15,7 @@ source: - phyml-aarch64.patch # [linux and aarch64] build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} diff --git a/recipes/phynder/meta.yaml b/recipes/phynder/meta.yaml index a422be287ac0f..763eba8af0404 100644 --- a/recipes/phynder/meta.yaml +++ b/recipes/phynder/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 94d629d0c2e9085bfe9dbbe2c6302021ad81a00b3696696e103aa31db51d849f build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage('phynder', max_pin="x") }} diff --git a/recipes/physher/build_failure.linux-64.yaml b/recipes/physher/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..3650cde0ade75 --- /dev/null +++ b/recipes/physher/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5def322f64605e2e85bf64677d889e87624b61b98f4f9f9d498ba5df0f1636bd # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + gsl: 2.7-he838d99_0 conda-forge + libblas: 3.9.0-25_linux64_openblas conda-forge + libcblas: 3.9.0-25_linux64_openblas conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-ng: 14.2.0-h69a702a_1 conda-forge + libgfortran: 14.2.0-h69a702a_1 conda-forge + libgfortran5: 14.2.0-hd5240d6_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libopenblas: 0.3.28-pthreads_h94d23a6_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/physher_1733980574674/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.43-h4bf12b8_2 conda-forge + binutils_linux-64: 2.43-h4852527_2 conda-forge + bzip2: 1.0.8-h4bc722e_7 conda-forge + c-ares: 1.34.3-hb9d3cd8_1 conda-forge + ca-certificates: 2024.8.30-hbcca054_0 conda-forge + cmake: 3.31.2-h74e3db0_1 conda-forge + gcc_impl_linux-64: 13.3.0-hfea6d02_1 conda-forge + gcc_linux-64: 13.3.0-hc28eda2_7 conda-forge + gxx_impl_linux-64: 13.3.0-hdbfa832_1 conda-forge + gxx_linux-64: 13.3.0-h6834431_7 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + keyutils: 1.6.1-h166bdaf_0 conda-forge + krb5: 1.21.3-h659f571_0 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libcurl: 8.10.1-hbbe4b11_0 conda-forge + libedit: 3.1.20191231-he28a2e2_2 conda-forge + libev: 4.33-hd590300_2 conda-forge + libexpat: 2.6.4-h5888daf_0 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libgcc-ng: 14.2.0-h69a702a_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + liblzma: 5.6.3-hb9d3cd8_1 conda-forge + libnghttp2: 1.64.0-h161d5f1_0 conda-forge + libsanitizer: 13.3.0-heb74ff8_1 conda-forge + libssh2: 1.11.1-hf672d98_0 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libstdcxx-ng: 14.2.0-h4852527_1 conda-forge + libuv: 1.49.2-hb9d3cd8_0 conda-forge + libzlib: 1.3.1-hb9d3cd8_2 conda-forge + make: 4.4.1-hb9d3cd8_2 conda-forge + ncurses: 6.5-he02047a_1 conda-forge + openssl: 3.4.0-hb9d3cd8_0 conda-forge + rhash: 1.4.5-hb9d3cd8_0 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: v2.0.1_b87a69f49a.tar.gz + Downloading https://github.com/4ment/physher/archive/refs/tags/v2.0.1.tar.gz + Success + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 125, in download_to_cache + raise RuntimeError( + RuntimeError: SHA256 mismatch: '0e90418f0a2d4b57295917925b7293f953c3a532a30c5e4601b8ff7474b9a4a8' != 'b87a69f49a81401e02cde0c99331f6ddbb10b53c8b4e671419510fb3093796d4' +# Last 100 lines of the build log. diff --git a/recipes/physher/build_failure.linux-aarch64.yaml b/recipes/physher/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..f0f0358bcf753 --- /dev/null +++ b/recipes/physher/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5def322f64605e2e85bf64677d889e87624b61b98f4f9f9d498ba5df0f1636bd # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + environment location: /opt/conda/conda-bld/physher_1734125235842/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place + + + The following NEW packages will be INSTALLED: + + _openmp_mutex: 4.5-2_gnu conda-forge + gsl: 2.7-h294027d_0 conda-forge + libblas: 3.9.0-25_linuxaarch64_openblas conda-forge + libcblas: 3.9.0-25_linuxaarch64_openblas conda-forge + libgcc: 14.2.0-he277a41_1 conda-forge + libgcc-ng: 14.2.0-he9431aa_1 conda-forge + libgfortran: 14.2.0-he9431aa_1 conda-forge + libgfortran5: 14.2.0-hb6113d0_1 conda-forge + libgomp: 14.2.0-he277a41_1 conda-forge + libopenblas: 0.3.28-pthreads_h9d3fd7e_1 conda-forge + libstdcxx: 14.2.0-h3f4de04_1 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/physher_1734125235842/_build_env + + + The following NEW packages will be INSTALLED: + + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-aarch64: 2.43-h4c662bb_2 conda-forge + binutils_linux-aarch64: 2.43-hf1166c9_2 conda-forge + bzip2: 1.0.8-h68df207_7 conda-forge + c-ares: 1.34.3-h86ecc28_1 conda-forge + ca-certificates: 2024.8.30-hcefe29a_0 conda-forge + cmake: 3.31.2-h0efca9c_1 conda-forge + gcc_impl_linux-aarch64: 13.3.0-hcdea9b6_1 conda-forge + gcc_linux-aarch64: 13.3.0-h1cd514b_7 conda-forge + gxx_impl_linux-aarch64: 13.3.0-h1211b58_1 conda-forge + gxx_linux-aarch64: 13.3.0-h2864abd_7 conda-forge + kernel-headers_linux-aarch64: 4.18.0-h05a177a_18 conda-forge + keyutils: 1.6.1-h4e544f5_0 conda-forge + krb5: 1.21.3-h50a48e9_0 conda-forge + ld_impl_linux-aarch64: 2.43-h80caac9_2 conda-forge + libcurl: 8.11.1-h6702fde_0 conda-forge + libedit: 3.1.20191231-he28a2e2_2 conda-forge + libev: 4.33-h31becfc_2 conda-forge + libexpat: 2.6.4-h5ad3122_0 conda-forge + libgcc: 14.2.0-he277a41_1 conda-forge + libgcc-devel_linux-aarch64: 13.3.0-h0c07274_101 conda-forge + libgcc-ng: 14.2.0-he9431aa_1 conda-forge + libgomp: 14.2.0-he277a41_1 conda-forge + liblzma: 5.6.3-h86ecc28_1 conda-forge + libnghttp2: 1.64.0-hc8609a4_0 conda-forge + libsanitizer: 13.3.0-ha58e236_1 conda-forge + libssh2: 1.11.1-ha41c0db_0 conda-forge + libstdcxx: 14.2.0-h3f4de04_1 conda-forge + libstdcxx-devel_linux-aarch64: 13.3.0-h0c07274_101 conda-forge + libstdcxx-ng: 14.2.0-hf1166c9_1 conda-forge + libuv: 1.49.2-h86ecc28_0 conda-forge + libzlib: 1.3.1-h86ecc28_2 conda-forge + make: 4.4.1-h2a6d0cb_2 conda-forge + ncurses: 6.5-hcccb83c_1 conda-forge + openssl: 3.4.0-h86ecc28_0 conda-forge + rhash: 1.4.5-h86ecc28_0 conda-forge + sysroot_linux-aarch64: 2.17-h5b4a56d_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + zstd: 1.5.6-h02f22dd_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: v2.0.1_b87a69f49a.tar.gz + Downloading https://github.com/4ment/physher/archive/refs/tags/v2.0.1.tar.gz + Success + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 125, in download_to_cache + raise RuntimeError( + RuntimeError: SHA256 mismatch: '0e90418f0a2d4b57295917925b7293f953c3a532a30c5e4601b8ff7474b9a4a8' != 'b87a69f49a81401e02cde0c99331f6ddbb10b53c8b4e671419510fb3093796d4' +# Last 100 lines of the build log. diff --git a/recipes/physher/build_failure.osx-64.yaml b/recipes/physher/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..eb9231a899557 --- /dev/null +++ b/recipes/physher/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5def322f64605e2e85bf64677d889e87624b61b98f4f9f9d498ba5df0f1636bd # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/physher_1733962990768/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + + + The following NEW packages will be INSTALLED: + + gsl: 2.7-h93259b0_0 conda-forge + libblas: 3.9.0-25_osx64_openblas conda-forge + libcblas: 3.9.0-25_osx64_openblas conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libgfortran: 5.0.0-13_2_0_h97931a8_3 conda-forge + libgfortran5: 13.2.0-h2873a65_3 conda-forge + libopenblas: 0.3.28-openmp_hbf64a52_1 conda-forge + llvm-openmp: 19.1.5-ha54dae1_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (local): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (local): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/physher_1733962990768/_build_env + + + The following NEW packages will be INSTALLED: + + bzip2: 1.0.8-hfdf4475_7 conda-forge + c-ares: 1.34.3-hf13058a_1 conda-forge + ca-certificates: 2024.8.30-h8857fd0_0 conda-forge + cctools_osx-64: 1010.6-h00edd4c_2 conda-forge + clang: 18.1.8-default_h179603d_5 conda-forge + clang-18: 18.1.8-default_h0c94c6a_5 conda-forge + clang_impl_osx-64: 18.1.8-h6a44ed1_23 conda-forge + clang_osx-64: 18.1.8-h7e5c614_23 conda-forge + clangxx: 18.1.8-default_h179603d_5 conda-forge + clangxx_impl_osx-64: 18.1.8-h4b7810f_23 conda-forge + clangxx_osx-64: 18.1.8-h7e5c614_23 conda-forge + cmake: 3.31.2-h477996e_1 conda-forge + compiler-rt: 18.1.8-h1020d70_1 conda-forge + compiler-rt_osx-64: 18.1.8-hf2b8a54_1 conda-forge + krb5: 1.21.3-h37d8d59_0 conda-forge + ld64_osx-64: 951.9-hc8d1a19_2 conda-forge + libclang-cpp18.1: 18.1.8-default_h0c94c6a_5 conda-forge + libcurl: 8.10.1-h58e7537_0 conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libcxx-devel: 18.1.8-h7c275be_7 conda-forge + libedit: 3.1.20191231-h0678c8f_2 conda-forge + libev: 4.33-h10d778d_2 conda-forge + libexpat: 2.6.4-h240833e_0 conda-forge + libiconv: 1.17-hd75f5a5_2 conda-forge + libllvm18: 18.1.8-h9ce406d_2 conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libnghttp2: 1.64.0-hc7306c3_0 conda-forge + libssh2: 1.11.1-h3dc7d44_0 conda-forge + libuv: 1.49.2-hd79239c_0 conda-forge + libxml2: 2.13.5-he8ee3e7_1 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-tools: 18.1.8-h9ce406d_2 conda-forge + llvm-tools-18: 18.1.8-h9ce406d_2 conda-forge + make: 4.4.1-h00291cd_2 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + rhash: 1.4.5-ha44c9a9_0 conda-forge + sigtool: 0.1.3-h88f4db0_0 conda-forge + tapi: 1300.6.5-h390ca13_0 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache + Downloading source to cache: v2.0.1_b87a69f49a.tar.gz + Downloading https://github.com/4ment/physher/archive/refs/tags/v2.0.1.tar.gz + Success + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 125, in download_to_cache + raise RuntimeError( + RuntimeError: SHA256 mismatch: '0e90418f0a2d4b57295917925b7293f953c3a532a30c5e4601b8ff7474b9a4a8' != 'b87a69f49a81401e02cde0c99331f6ddbb10b53c8b4e671419510fb3093796d4' +# Last 100 lines of the build log. diff --git a/recipes/physher/meta.yaml b/recipes/physher/meta.yaml index d049c02266827..ff29dd9dc7ec6 100644 --- a/recipes/physher/meta.yaml +++ b/recipes/physher/meta.yaml @@ -6,7 +6,7 @@ package: version: "{{ version }}" build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('physher', max_pin="x") }} diff --git a/recipes/physlr/meta.yaml b/recipes/physlr/meta.yaml index 0e895a6db9285..dfde8c5af4402 100644 --- a/recipes/physlr/meta.yaml +++ b/recipes/physlr/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 6 + number: 7 source: url: https://github.com/bcgsc/{{ name|lower }}/releases/download/v{{ version }}/{{ name|lower }}-{{ version }}.tar.gz diff --git a/recipes/phyx/meta.yaml b/recipes/phyx/meta.yaml index 97b0118b7a437..281ab7c36595f 100644 --- a/recipes/phyx/meta.yaml +++ b/recipes/phyx/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ hash }} build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/piler-cr/build_failure.osx-64.yaml b/recipes/piler-cr/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..aed3001c80570 --- /dev/null +++ b/recipes/piler-cr/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 425541fa30d4e6c8225c67f1b462fd9cdbd9162cda6304780f544ad5f77e0ba0 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + - clang_impl_osx-64 18.1.8 h6a44ed1_23 + - libxml2 2.13.5 he8ee3e7_1 + - sigtool 0.1.3 h88f4db0_0 + - libcxx 19.1.5 hf95d169_0 + - libllvm18 18.1.8 h9ce406d_2 + - llvm-tools-18 18.1.8 h9ce406d_2 + - ca-certificates 2024.12.14 h8857fd0_0 + - zstd 1.5.6 h915ae27_0 + host: + - libcxx 19.1.5 hf95d169_0 + run: + - libcxx >=18 + test: + commands: + - pilercr -options + about: + home: http://www.drive5.com/pilercr/ + license: Public Domain + summary: Identification and analysis of CRISPR repeats. + extra: + copy_test_source_files: true + final: true + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/piler-cr_1734460671336/work/conda_build.sh']' returned non-zero exit status 2. + maintainers: Edgar, R.C. + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/piler-cr_1734460671336/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/piler-cr_1734460671336/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/piler-cr_1734460671336/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/piler-cr_1734460671336/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/piler-cr-1.06 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/piler-cr-1.06 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/piler-cr-1.06 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/piler-cr-1.06 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/piler-cr-1.06 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix acceptaa.cpp -o acceptaa.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/piler-cr-1.06 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix accepthit.cpp -o accepthit.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/piler-cr-1.06 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix alignarrays.cpp -o alignarrays.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/piler-cr-1.06 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix alignclust.cpp -o alignclust.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/piler-cr-1.06 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix alignprofs.cpp -o alignprofs.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/piler-cr-1.06 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix aligntraps.cpp -o aligntraps.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/piler-cr-1.06 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix alnarray.cpp -o alnarray.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/piler-cr-1.06 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix alngivenpath.cpp -o alngivenpath.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/piler-cr-1.06 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix alpha.cpp -o alpha.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/piler-cr-1.06 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix assert.cpp -o assert.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/piler-cr-1.06 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix bittb.cpp -o bittb.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/piler-cr-1.06 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix clustcons.cpp -o clustcons.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/piler-cr-1.06 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix clustconsr.cpp -o clustconsr.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/piler-cr-1.06 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix cmp.cpp -o cmp.o + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/piler-cr-1.06 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix comp.cpp -o comp.o +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/piler-cr/meta.yaml b/recipes/piler-cr/meta.yaml index 489ea70a44b7e..009012878fd77 100644 --- a/recipes/piler-cr/meta.yaml +++ b/recipes/piler-cr/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 50175f7aa171674cda5ba255631f340f9cc7f80e8cc25135a4cb857147d91068 build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/pin_hic/meta.yaml b/recipes/pin_hic/meta.yaml index 8c3c542cf4dae..37b79b8391a23 100644 --- a/recipes/pin_hic/meta.yaml +++ b/recipes/pin_hic/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 source: url: https://github.com/dfguan/pin_hic/archive/refs/tags/v{{ version }}.tar.gz diff --git a/recipes/pindel/meta.yaml b/recipes/pindel/meta.yaml index fc5a2aae1e96c..e79e2f26a3a81 100644 --- a/recipes/pindel/meta.yaml +++ b/recipes/pindel/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 11 + number: 12 skip: True # [osx] run_exports: - {{ pin_subpackage('pindel', max_pin='x.x') }} diff --git a/recipes/piscem/build.sh b/recipes/piscem/build.sh index b2d78efc2f3e2..fa526e2c224a2 100644 --- a/recipes/piscem/build.sh +++ b/recipes/piscem/build.sh @@ -11,7 +11,7 @@ then fi export MACOSX_DEPLOYMENT_TARGET=10.15 export MACOSX_SDK_VERSION=10.15 - export CFLAGS="${CFLAGS} -fcommon -D_LIBCPP_DISABLE_AVAILABILITY" + export CFLAGS="${CFLAGS} -fcommon -D_LIBCPP_DISABLE_AVAILABILITY -fno-define-target-os-macros" export CXXFLAGS="${CXXFLAGS} -fcommon -D_LIBCPP_DISABLE_AVAILABILITY" else export CFLAGS="${CFLAGS} -fcommon" diff --git a/recipes/piscem/meta.yaml b/recipes/piscem/meta.yaml index aef5a093ad42f..19890a41b46e4 100644 --- a/recipes/piscem/meta.yaml +++ b/recipes/piscem/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("piscem", max_pin="x.x") }} diff --git a/recipes/pizzly/0.37.1/meta.yaml b/recipes/pizzly/0.37.1/meta.yaml index f687ddd2143cd..f4f90f5988955 100644 --- a/recipes/pizzly/0.37.1/meta.yaml +++ b/recipes/pizzly/0.37.1/meta.yaml @@ -9,7 +9,7 @@ source: sha256: d8a922b76445bae79acb41d818dedba51567e7c041e8bb14360fd4cc0f674778 # [osx] build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/pkiss/build_failure.osx-64.yaml b/recipes/pkiss/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..9378d2ed6ba3d --- /dev/null +++ b/recipes/pkiss/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 699441bd3d653cac087a1782d22a33724dab0ba6a8ba84b7387532e540cd5772 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pkiss-2.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pkiss-2.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pkiss-2.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pkiss-2.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + make: Entering directory '$SRC_DIR/Misc/Applications/pKiss' + make all_normal + make[1]: Entering directory '$SRC_DIR/Misc/Applications/pKiss' + make compile \ + gapc_product="alg_pknot_mfe * alg_pknot_dotBracket" \ + gapc_options="--kbacktrace --no-coopt --tab-all " \ + gapc_file="pKiss.gap" \ + gapc_binaryname="mfe"; + make compile \ + gapc_product="alg_pknot_mfe_subopt * alg_pknot_dotBracket" \ + gapc_options="--kbacktrace --tab-all " \ + gapc_file="pKiss.gap" \ + gapc_binaryname="subopt"; + make[2]: Entering directory '$SRC_DIR/Misc/Applications/pKiss' + make[2]: Entering directory '$SRC_DIR/Misc/Applications/pKiss' + if [ ! -f "x86_64-apple-darwin13.4.0/pKiss_subopt" ]; then \ + cd /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.c4zErUTJ && gapc -I $SRC_DIR/Misc/Applications/pKiss/../../../ -p "alg_pknot_mfe_subopt * alg_pknot_dotBracket" --kbacktrace --tab-all $SRC_DIR/Misc/Applications/pKiss/../../..//pKiss.gap; \ + perl $SRC_DIR/Misc/Applications/pKiss/../../..///Misc/Applications/addRNAoptions.pl /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.c4zErUTJ/out.mf 0 'subopt' 'alg_pknot_mfe_subopt * alg_pknot_dotBracket'; \ + cd /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.c4zErUTJ && make -f out.mf CPPFLAGS_EXTRA="-I $SRC_DIR/Misc/Applications/pKiss/../../../ -I ./" CXXFLAGS_EXTRA="-O3 -DNDEBUG" LDFLAGS_EXTRA=""; \ + install -d $SRC_DIR/Misc/Applications/pKiss/x86_64-apple-darwin13.4.0; \ + install /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.c4zErUTJ/out $SRC_DIR/Misc/Applications/pKiss/x86_64-apple-darwin13.4.0/pKiss_subopt; \ + fi; + if [ ! -f "x86_64-apple-darwin13.4.0/pKiss_mfe" ]; then \ + cd /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.ZbwYmEds && gapc -I $SRC_DIR/Misc/Applications/pKiss/../../../ -p "alg_pknot_mfe * alg_pknot_dotBracket" --kbacktrace --no-coopt --tab-all $SRC_DIR/Misc/Applications/pKiss/../../..//pKiss.gap; \ + perl $SRC_DIR/Misc/Applications/pKiss/../../..///Misc/Applications/addRNAoptions.pl /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.ZbwYmEds/out.mf 0 'mfe' 'alg_pknot_mfe * alg_pknot_dotBracket'; \ + cd /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.ZbwYmEds && make -f out.mf CPPFLAGS_EXTRA="-I $SRC_DIR/Misc/Applications/pKiss/../../../ -I ./" CXXFLAGS_EXTRA="-O3 -DNDEBUG" LDFLAGS_EXTRA=""; \ + install -d $SRC_DIR/Misc/Applications/pKiss/x86_64-apple-darwin13.4.0; \ + install /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.ZbwYmEds/out $SRC_DIR/Misc/Applications/pKiss/x86_64-apple-darwin13.4.0/pKiss_mfe; \ + fi; + make[3]: Entering directory '/private/var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.ZbwYmEds' + Including global makefile $PREFIX/share/gapc/config_darwin13.4.0.mf + make[3]: Entering directory '/private/var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.c4zErUTJ' + Including global makefile $PREFIX/share/gapc/config_darwin13.4.0.mf + echo '#include "out.hh"' > out_main.cc + echo '#include "out.hh"' > out_main.cc + cat $PREFIX/include/rtlib/generic_main.cc >> out_main.cc + cat $PREFIX/include/rtlib/generic_main.cc >> out_main.cc + $PREFIX/bin/sed -i 's|gapc::Opts opts;||' out_main.cc + $PREFIX/bin/sed -i 's|gapc::Opts opts;||' out_main.cc + $PREFIX/bin/sed -i 's|\([^_]\)opts\.|\1gapc::Opts::getOpts()->|g' out_main.cc + $PREFIX/bin/sed -i 's|\([^_]\)opts\.|\1gapc::Opts::getOpts()->|g' out_main.cc + $PREFIX/bin/sed -i 's|obj.init(opts);|obj.init(\*gapc::Opts::getOpts());|g' out_main.cc + $PREFIX/bin/sed -i 's|obj.init(opts);|obj.init(\*gapc::Opts::getOpts());|g' out_main.cc + $PREFIX/bin/sed -i 's|#include .rtlib/generic_opts.hh.|#include "Extensions/rnaoptions.hh"|' out_main.cc + $PREFIX/bin/sed -i 's|#include .rtlib/generic_opts.hh.|#include "Extensions/rnaoptions.hh"|' out_main.cc + $PREFIX/bin/sed -i 's%#include .rtlib/generic_opts.hh.%#include "Extensions/rnaoptions.hh"%' out.hh out.cc + $PREFIX/bin/sed -i 's%#include .rtlib/generic_opts.hh.%#include "Extensions/rnaoptions.hh"%' out.hh out.cc + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bellmans-gapc_1721071508431/work=/usr/local/src/conda/bellmans-gapc-2024.01.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -MMD -MP -Wall -Wnon-virtual-dtor -Wno-unused-variable -Wno-parentheses -DNDEBUG -DBISONNEW -O3 -DNDEBUG -DWITH_RNAOPTIONS -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I $SRC_DIR/Misc/Applications/pKiss/../../../ -I ./ -I$PREFIX/include -I$PREFIX/include/ -I$PREFIX/include/rtlib -I$PREFIX/include/librna -c -o out.o out.cc + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bellmans-gapc_1721071508431/work=/usr/local/src/conda/bellmans-gapc-2024.01.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -MMD -MP -Wall -Wnon-virtual-dtor -Wno-unused-variable -Wno-parentheses -DNDEBUG -DBISONNEW -O3 -DNDEBUG -DWITH_RNAOPTIONS -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I $SRC_DIR/Misc/Applications/pKiss/../../../ -I ./ -I$PREFIX/include -I$PREFIX/include/ -I$PREFIX/include/rtlib -I$PREFIX/include/librna -c -o out.o out.cc + make[3]: Leaving directory '/private/var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.c4zErUTJ' + make[2]: Leaving directory '$SRC_DIR/Misc/Applications/pKiss' + x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I $SRC_DIR/Misc/Applications/pKiss/../../../ -I ./ -I$PREFIX/include -I$PREFIX/include/ -I$PREFIX/include/rtlib -I$PREFIX/include/librna -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bellmans-gapc_1721071508431/work=/usr/local/src/conda/bellmans-gapc-2024.01.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -MMD -MP -Wall -Wnon-virtual-dtor -Wno-unused-variable -Wno-parentheses -DNDEBUG -DBISONNEW -O3 -DNDEBUG -DWITH_RNAOPTIONS -c $PREFIX/include/rtlib/string.cc -o string.o + make[3]: Leaving directory '/private/var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.ZbwYmEds' + make[2]: Leaving directory '$SRC_DIR/Misc/Applications/pKiss' + make[1]: Leaving directory '$SRC_DIR/Misc/Applications/pKiss' + make: Leaving directory '$SRC_DIR/Misc/Applications/pKiss' +# Last 100 lines of the build log. diff --git a/recipes/pkiss/meta.yaml b/recipes/pkiss/meta.yaml index 5bef440d7e10c..1e75934a9b4ef 100644 --- a/recipes/pkiss/meta.yaml +++ b/recipes/pkiss/meta.yaml @@ -14,7 +14,7 @@ source: url: https://github.com/jlab/fold-grammars/archive/{{ fold_grammars_version }}.tar.gz build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('pkiss', max_pin="x") }} diff --git a/recipes/plass/build_failure.linux-64.yaml b/recipes/plass/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..4e22c467f7246 --- /dev/null +++ b/recipes/plass/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: eddf2e3c47eaf14497f3f4c2362bd2befb0892fdec84af68c258090805207968 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [ 34%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/cover.c + [ 34%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/fastcover.c + [ 35%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/divsufsort.c + [ 35%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/zdict.c + [ 35%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/deprecated/zbuff_common.c + [ 36%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/deprecated/zbuff_compress.c + [ 36%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/deprecated/zbuff_decompress.c + [ 36%] Linking C static library libzstd.a + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/cmake -P CMakeFiles/libzstd_static.dir/cmake_clean_target.cmake + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/cmake -E cmake_link_script CMakeFiles/libzstd_static.dir/link.txt --verbose=1 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar qc libzstd.a CMakeFiles/libzstd_static.dir/__/__/__/lib/common/entropy_common.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/fse_decompress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/threading.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/pool.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/zstd_common.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/error_private.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/xxhash.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/hist.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/fse_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/huf_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstdmt_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_fast.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_double_fast.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_lazy.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_opt.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_ldm.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/huf_decompress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress_block.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_ddict.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib libzstd.a + make[2]: Leaving directory '$SRC_DIR/build' + [ 36%] Built target libzstd_static + make -f lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build.make lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/depend + make[2]: Entering directory '$SRC_DIR/build' + cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR/lib/mmseqs/src $SRC_DIR/build $SRC_DIR/build/lib/mmseqs/src $SRC_DIR/build/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/DependInfo.cmake "--color=" + make[2]: Leaving directory '$SRC_DIR/build' + make -f lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build.make lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build + make[2]: Entering directory '$SRC_DIR/build' + [ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o + [ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o + [ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/Alignment.cpp + [ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/CompressedA3M.cpp + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/Main.cpp + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/Matcher.cpp + [ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/MsaFilter.cpp + [ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/MultipleAlignment.cpp + [ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/PSSMCalculator.cpp + In file included from /opt/conda/conda-bld/plass_1734188689892/work/lib/mmseqs/src/commons/Debug.h:5, + from /opt/conda/conda-bld/plass_1734188689892/work/lib/mmseqs/src/alignment/MsaFilter.cpp:5: + /opt/conda/conda-bld/plass_1734188689892/work/lib/mmseqs/src/commons/Util.h:89:12: error: 'uint64_t' does not name a type + 89 | static uint64_t getL2CacheSize(); + | ^~~~~~~~ + /opt/conda/conda-bld/plass_1734188689892/work/lib/mmseqs/src/commons/Util.h:11:1: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + 10 | #include "MMseqsMPI.h" + |#include + 11 | + /opt/conda/conda-bld/plass_1734188689892/work/lib/mmseqs/src/commons/Util.h:362:12: error: 'uint64_t' does not name a type + 362 | static uint64_t revComplement(const uint64_t kmer, const int k); + | ^~~~~~~~ + /opt/conda/conda-bld/plass_1734188689892/work/lib/mmseqs/src/commons/Util.h:362:12: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/plass_1734188689892/work/lib/mmseqs/src/commons/Debug.h: In constructor 'Debug::Progress::Progress()': + /opt/conda/conda-bld/plass_1734188689892/work/lib/mmseqs/src/commons/Debug.h:169:69: error: 'SIZE_MAX' was not declared in this scope + 169 | Progress() : currentPos(0), prevPrintedId(0), totalEntries(SIZE_MAX){ + | ^~~~~~~~ + /opt/conda/conda-bld/plass_1734188689892/work/lib/mmseqs/src/commons/Debug.h:12:1: note: 'SIZE_MAX' is defined in header ''; did you forget to '#include '? + 11 | #include + |#include + 12 | + /opt/conda/conda-bld/plass_1734188689892/work/lib/mmseqs/src/commons/Debug.h: In member function 'void Debug::Progress::updateProgress()': + /opt/conda/conda-bld/plass_1734188689892/work/lib/mmseqs/src/commons/Debug.h:184:34: error: 'SIZE_MAX' was not declared in this scope + 184 | if(totalEntries==SIZE_MAX) { + | ^~~~~~~~ + /opt/conda/conda-bld/plass_1734188689892/work/lib/mmseqs/src/commons/Debug.h:184:34: note: 'SIZE_MAX' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/plass_1734188689892/work/lib/mmseqs/src/commons/Debug.h:218:34: error: 'SIZE_MAX' was not declared in this scope + 218 | if(totalEntries==SIZE_MAX){ + | ^~~~~~~~ + /opt/conda/conda-bld/plass_1734188689892/work/lib/mmseqs/src/commons/Debug.h:218:34: note: 'SIZE_MAX' is defined in header ''; did you forget to '#include '? + make[2]: *** [lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build.make:135: lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o] Error 1 + make[2]: *** Waiting for unfinished jobs.... + make[2]: Leaving directory '$SRC_DIR/build' + make[1]: *** [CMakeFiles/Makefile2:1029: lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/all] Error 2 + make[1]: Leaving directory '$SRC_DIR/build' + make: *** [Makefile:136: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/plass_1734188689892/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/plass_1734188689892/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/plass/build_failure.linux-aarch64.yaml b/recipes/plass/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..9be6dcac78f90 --- /dev/null +++ b/recipes/plass/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: eddf2e3c47eaf14497f3f4c2362bd2befb0892fdec84af68c258090805207968 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [ 34%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/cover.c + [ 34%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/fastcover.c + [ 35%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/divsufsort.c + [ 35%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/zdict.c + [ 35%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/deprecated/zbuff_common.c + [ 36%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/deprecated/zbuff_compress.c + [ 36%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/deprecated/zbuff_decompress.c + [ 36%] Linking C static library libzstd.a + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/cmake -P CMakeFiles/libzstd_static.dir/cmake_clean_target.cmake + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/cmake -E cmake_link_script CMakeFiles/libzstd_static.dir/link.txt --verbose=1 + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ar qc libzstd.a CMakeFiles/libzstd_static.dir/__/__/__/lib/common/entropy_common.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/fse_decompress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/threading.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/pool.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/zstd_common.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/error_private.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/xxhash.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/hist.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/fse_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/huf_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstdmt_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_fast.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_double_fast.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_lazy.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_opt.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_ldm.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/huf_decompress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress_block.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_ddict.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib libzstd.a + make[2]: Leaving directory '$SRC_DIR/build' + [ 36%] Built target libzstd_static + make -f lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build.make lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/depend + make[2]: Entering directory '$SRC_DIR/build' + cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR/lib/mmseqs/src $SRC_DIR/build $SRC_DIR/build/lib/mmseqs/src $SRC_DIR/build/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/DependInfo.cmake "--color=" + make[2]: Leaving directory '$SRC_DIR/build' + make -f lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build.make lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build + make[2]: Entering directory '$SRC_DIR/build' + [ 36%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o + [ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/Alignment.cpp + [ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/CompressedA3M.cpp + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/Main.cpp + [ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/Matcher.cpp + [ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/MsaFilter.cpp + [ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/MultipleAlignment.cpp + [ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/plass-5.cf8933 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/PSSMCalculator.cpp + In file included from /opt/conda/conda-bld/plass_1734126202679/work/lib/mmseqs/src/commons/Debug.h:5, + from /opt/conda/conda-bld/plass_1734126202679/work/lib/mmseqs/src/alignment/MsaFilter.cpp:5: + /opt/conda/conda-bld/plass_1734126202679/work/lib/mmseqs/src/commons/Util.h:89:12: error: 'uint64_t' does not name a type + 89 | static uint64_t getL2CacheSize(); + | ^~~~~~~~ + /opt/conda/conda-bld/plass_1734126202679/work/lib/mmseqs/src/commons/Util.h:11:1: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + 10 | #include "MMseqsMPI.h" + |#include + 11 | + /opt/conda/conda-bld/plass_1734126202679/work/lib/mmseqs/src/commons/Util.h:362:12: error: 'uint64_t' does not name a type + 362 | static uint64_t revComplement(const uint64_t kmer, const int k); + | ^~~~~~~~ + /opt/conda/conda-bld/plass_1734126202679/work/lib/mmseqs/src/commons/Util.h:362:12: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/plass_1734126202679/work/lib/mmseqs/src/commons/Debug.h: In constructor 'Debug::Progress::Progress()': + /opt/conda/conda-bld/plass_1734126202679/work/lib/mmseqs/src/commons/Debug.h:169:69: error: 'SIZE_MAX' was not declared in this scope + 169 | Progress() : currentPos(0), prevPrintedId(0), totalEntries(SIZE_MAX){ + | ^~~~~~~~ + /opt/conda/conda-bld/plass_1734126202679/work/lib/mmseqs/src/commons/Debug.h:12:1: note: 'SIZE_MAX' is defined in header ''; did you forget to '#include '? + 11 | #include + |#include + 12 | + /opt/conda/conda-bld/plass_1734126202679/work/lib/mmseqs/src/commons/Debug.h: In member function 'void Debug::Progress::updateProgress()': + /opt/conda/conda-bld/plass_1734126202679/work/lib/mmseqs/src/commons/Debug.h:184:34: error: 'SIZE_MAX' was not declared in this scope + 184 | if(totalEntries==SIZE_MAX) { + | ^~~~~~~~ + /opt/conda/conda-bld/plass_1734126202679/work/lib/mmseqs/src/commons/Debug.h:184:34: note: 'SIZE_MAX' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/plass_1734126202679/work/lib/mmseqs/src/commons/Debug.h:218:34: error: 'SIZE_MAX' was not declared in this scope + 218 | if(totalEntries==SIZE_MAX){ + | ^~~~~~~~ + /opt/conda/conda-bld/plass_1734126202679/work/lib/mmseqs/src/commons/Debug.h:218:34: note: 'SIZE_MAX' is defined in header ''; did you forget to '#include '? + make[2]: *** [lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build.make:135: lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o] Error 1 + make[2]: *** Waiting for unfinished jobs.... + make[2]: Leaving directory '$SRC_DIR/build' + make[1]: *** [CMakeFiles/Makefile2:1029: lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/all] Error 2 + make[1]: Leaving directory '$SRC_DIR/build' + make: *** [Makefile:136: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/plass_1734126202679/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/plass_1734126202679/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/plass/meta.yaml b/recipes/plass/meta.yaml index 99a820fb0e6d5..236b2424a661f 100644 --- a/recipes/plass/meta.yaml +++ b/recipes/plass/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version|replace("-", ".") }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('plass', max_pin=None) }} @@ -52,4 +52,4 @@ extra: - martin-steinegger additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 diff --git a/recipes/plastid/build_failure.linux-64.yaml b/recipes/plastid/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..8a88fa6bc7cb9 --- /dev/null +++ b/recipes/plastid/build_failure.linux-64.yaml @@ -0,0 +1,4 @@ +recipe_sha: 0b8f4f229432444fe063cced79c43374038dbe78fa551e1091a8e0288494d89a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + dependency issue diff --git a/recipes/plek/meta.yaml b/recipes/plek/meta.yaml index 7968a36bb11c0..4b890ecd81e5d 100644 --- a/recipes/plek/meta.yaml +++ b/recipes/plek/meta.yaml @@ -13,7 +13,7 @@ source: - dos2unix.patch build: - number: 8 + number: 9 skip: True # [osx] requirements: diff --git a/recipes/plink/meta.yaml b/recipes/plink/meta.yaml index d243f2d3d98b2..35575094d4f71 100644 --- a/recipes/plink/meta.yaml +++ b/recipes/plink/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.90b6.21" build: - number: 5 + number: 6 source: url: http://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20201019.zip # [linux] diff --git a/recipes/plink2/meta.yaml b/recipes/plink2/meta.yaml index 7ea74ac5f31fc..29bf722752d2c 100644 --- a/recipes/plink2/meta.yaml +++ b/recipes/plink2/meta.yaml @@ -3,7 +3,7 @@ package: version: "2.00a5.12" build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('plink2', max_pin=None) }} diff --git a/recipes/plinkio/meta.yaml b/recipes/plinkio/meta.yaml index c5dc1227beb95..f66ae146600b7 100644 --- a/recipes/plinkio/meta.yaml +++ b/recipes/plinkio/meta.yaml @@ -11,7 +11,7 @@ source: build: script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation - number: 1 + number: 2 run_exports: {{ pin_subpackage('plinkio', max_pin="x.x") }} diff --git a/recipes/plncpro/meta.yaml b/recipes/plncpro/meta.yaml index 8b2fbd0d87f53..082d5169cba56 100644 --- a/recipes/plncpro/meta.yaml +++ b/recipes/plncpro/meta.yaml @@ -10,7 +10,7 @@ source: sha256: "78537a49a5b7ec082af8a3c043d9429f063c6197b32903d7f503c6ee3b289400" build: - number: 6 + number: 7 skip: True # [py2k] entry_points: - plncpro = plncpro.__main__:main diff --git a/recipes/polypolish/meta.yaml b/recipes/polypolish/meta.yaml index 45fd078a4a41d..a9661d3389450 100644 --- a/recipes/polypolish/meta.yaml +++ b/recipes/polypolish/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 99ea799352cecf6723b73fb4c5c64dd2091ff1cdab6eef10309e06c642e56855 build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('polypolish', max_pin="x.x") }} diff --git a/recipes/popdel/meta.yaml b/recipes/popdel/meta.yaml index b73c3594094cf..d20c7191b57b4 100644 --- a/recipes/popdel/meta.yaml +++ b/recipes/popdel/meta.yaml @@ -7,7 +7,7 @@ source: sha256: c4f9dd1838379a9bcb3545da3a8d2d779f85212528a523215df9d2dc505fe515 build: - number: 7 + number: 8 run_exports: - {{ pin_subpackage('popdel', max_pin='x') }} @@ -33,4 +33,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/popgen-entropy/build_failure.osx-64.yaml b/recipes/popgen-entropy/build_failure.osx-64.yaml deleted file mode 100644 index 8809fe81648ed..0000000000000 --- a/recipes/popgen-entropy/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: de4fe897707e7ddcc2b1ec439b277e821fd895de2934641bb5fd2adb8b315794 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/popgen-entropy-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/popgen-entropy-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - checking for a BSD-compatible install... /usr/bin/install -c - checking whether build environment is sane... yes - checking for a race-free mkdir -p... ./install-sh -c -d - checking for gawk... no - checking for mawk... no - checking for nawk... no - checking for awk... awk - checking whether make sets $(MAKE)... yes - checking whether make supports nested variables... yes - Testing for gsl - checking whether make supports the include directive... yes (GNU style) - checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang - checking whether the C compiler works... yes - checking for C compiler default output file name... a.out - checking for suffix of executables... - checking whether we are cross compiling... no - checking for suffix of object files... o - checking whether the compiler supports GNU C... yes - checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes - checking for x86_64-apple-darwin13.4.0-clang option to enable C11 features... none needed - checking whether x86_64-apple-darwin13.4.0-clang understands -c and -o together... yes - checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 - checking for cos in -lm... yes - checking for cblas_dgemm in -lgslcblas... yes - checking for gsl_blas_dgemm in -lgsl... yes - Testing for a C compiler - checking whether the compiler supports GNU C... yes - checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes - checking for x86_64-apple-darwin13.4.0-clang option to enable C11 features... none needed - checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 - checking whether x86_64-apple-darwin13.4.0-clang understands -c and -o together... yes - checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang -E - Setting language to C - Setting CXXFLAGS -DGSL_RANGE_CHECK=0 - Testing for iostream - checking for stdio.h... yes - checking for stdlib.h... yes - checking for string.h... yes - checking for inttypes.h... yes - checking for stdint.h... yes - checking for strings.h... yes - checking for sys/stat.h... yes - checking for sys/types.h... yes - checking for unistd.h... yes - checking for iostream... yes - Testing for iomanip - checking for iomanip... yes - Testing for cmath - checking for cmath... yes - Testing for fstream - checking for fstream... yes - Testing for sstream - checking for sstream... yes - Testing for functions - checking for pow... yes - checking for sqrt... yes - Testing for float.h, sting.h, & unistd.hrm - checking for float.h... yes - checking for string.h... (cached) yes - checking for unistd.h... (cached) yes - Testing for STDBOOL - checking for _Bool... no - checking for stdbool.h that conforms to C99... yes - Testing for TYPE_SIZE_T - checking for size_t... yes - Creating Makefile - Creating config.h, config.h.in, and config.status - checking that generated files are newer than configure... done - configure: creating ./config.status - config.status: creating Makefile - config.status: creating config.h - config.status: executing depfiles commands - make all-am - make[1]: Entering directory '$SRC_DIR' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/popgen-entropy-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DGSL_RANGE_CHECK=0 -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.C - mv -f .deps/main.Tpo .deps/main.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/popgen-entropy-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DGSL_RANGE_CHECK=0 -MT func.o -MD -MP -MF .deps/func.Tpo -c -o func.o func.C - make[1]: Leaving directory '$SRC_DIR' -# Last 100 lines of the build log. diff --git a/recipes/popgen-entropy/meta.yaml b/recipes/popgen-entropy/meta.yaml index 45d462a230b86..bb3eed9fa0e4a 100755 --- a/recipes/popgen-entropy/meta.yaml +++ b/recipes/popgen-entropy/meta.yaml @@ -9,7 +9,7 @@ source: sha1: d4e4227e5ca89223b3ea09744bd15ffa884906e8 build: - number: 9 + number: 10 requirements: build: diff --git a/recipes/poplddecay/meta.yaml b/recipes/poplddecay/meta.yaml index 6c2d6e9728491..54df64791f41e 100644 --- a/recipes/poplddecay/meta.yaml +++ b/recipes/poplddecay/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('poplddecay', max_pin="x") }} diff --git a/recipes/poppunk/build_failure.osx-64.yaml b/recipes/poppunk/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..993cc57a5c6a2 --- /dev/null +++ b/recipes/poppunk/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 9ab58c61e51a490960153c6927593c44a70420c51f3b2ebd5577b3a4bb75a4f5 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/poppunk_1734243825529/work + INFO: activate-gfortran_osx-64.sh made the following environmental changes: + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/poppunk-2.7.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/poppunk-2.7.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + F77=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F90=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/poppunk-2.7.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/poppunk-2.7.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/poppunk-2.7.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/poppunk-2.7.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/poppunk-2.7.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/poppunk-2.7.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + Using pip 24.3.1 from $PREFIX/lib/python3.12/site-packages/pip (python 3.12) + Non-user install because user site-packages disabled + Ignoring indexes: https://pypi.org/simple + Created temporary directory: /private/tmp/pip-build-tracker-obdp_86c + Initialized build tracking at /private/tmp/pip-build-tracker-obdp_86c + Created build tracker: /private/tmp/pip-build-tracker-obdp_86c + Entered build tracker: /private/tmp/pip-build-tracker-obdp_86c + Created temporary directory: /private/tmp/pip-install-4rexwh7s + Created temporary directory: /private/tmp/pip-ephem-wheel-cache-ubse99fq + Processing $SRC_DIR + Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-obdp_86c' + Created temporary directory: /private/tmp/pip-modern-metadata-3y53wskv + Preparing metadata (pyproject.toml): started + Preparing metadata (pyproject.toml): finished with status 'done' + Source in $SRC_DIR has version 2.7.2, which satisfies requirement poppunk==2.7.2 from file://$SRC_DIR + Removed poppunk==2.7.2 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-obdp_86c' + Created temporary directory: /private/tmp/pip-unpack-wjzc8hng + Building wheels for collected packages: poppunk + Created temporary directory: /private/tmp/pip-wheel-kln674g9 + Destination directory: /private/tmp/pip-wheel-kln674g9 + Building wheel for poppunk (pyproject.toml): started + Building wheel for poppunk (pyproject.toml): finished with status 'error' + Failed to build poppunk + Exception information: + Traceback (most recent call last): + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + ^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper + return func(self, options, args) + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 434, in run + raise InstallationError( + pip._internal.exceptions.InstallationError: ERROR: Failed to build installable wheels for some pyproject.toml based projects (poppunk) + Removed build tracker: '/private/tmp/pip-build-tracker-obdp_86c' +# Last 100 lines of the build log. diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml index da399ad941f42..1545c56267f92 100644 --- a/recipes/poppunk/meta.yaml +++ b/recipes/poppunk/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 1ea36fd3dee28b47c7e629eacd5ae5bf6dda3e464c23cfa5f51e63dc3d06e371 build: - number: 0 + number: 1 skip: True # [py < 39] script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" entry_points: diff --git a/recipes/porechop/meta.yaml b/recipes/porechop/meta.yaml index 09a59721d8130..246640641a21d 100644 --- a/recipes/porechop/meta.yaml +++ b/recipes/porechop/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299 build: - number: 8 + number: 9 run_exports: - {{ pin_subpackage("porechop", max_pin="x.x") }} entry_points: @@ -40,4 +40,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/porechop_abi/build_failure.osx-64.yaml b/recipes/porechop_abi/build_failure.osx-64.yaml index 4fde06acbf4ed..6d41557c5b099 100644 --- a/recipes/porechop_abi/build_failure.osx-64.yaml +++ b/recipes/porechop_abi/build_failure.osx-64.yaml @@ -1,34 +1,31 @@ -recipe_sha: 073726cff6842c0b9a5f40952bce9a0c41e3b02572a0e9910866971a5cd36abe # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 6c77ca0814bafca81086c6cc957dc36ec8690528a6f5b602ad962fc07cf1519d # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/porechop_abi_1717520240785/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/porechop_abi_1717520240785/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/porechop_abi_1717520240785/work + summary: Adapter inferrence and removal of Oxford Nanopore reads + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/porechop_abi_1733953747935/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/porechop_abi_1733953747935/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/porechop_abi_1733953747935/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/porechop_abi_1733953747935/work INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as CC=x86_64-apple-darwin13.4.0-clang CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/porechop_abi-0.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/porechop_abi_1717520240785/work/conda_build.sh']' returned non-zero exit status 1. - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/porechop_abi-0.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool @@ -37,7 +34,7 @@ log: |2- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -46,7 +43,7 @@ log: |2- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -64,41 +61,44 @@ log: |2- CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/porechop_abi-0.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/porechop_abi-0.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - Using pip 24.0 from $PREFIX/lib/python3.11/site-packages/pip (python 3.11) + Using pip 24.3.1 from $PREFIX/lib/python3.11/site-packages/pip (python 3.11) Non-user install because user site-packages disabled Ignoring indexes: https://pypi.org/simple - Created temporary directory: /private/tmp/pip-build-tracker-1pl8dy66 - Initialized build tracking at /private/tmp/pip-build-tracker-1pl8dy66 - Created build tracker: /private/tmp/pip-build-tracker-1pl8dy66 - Entered build tracker: /private/tmp/pip-build-tracker-1pl8dy66 - Created temporary directory: /private/tmp/pip-install-qlg4jful - Created temporary directory: /private/tmp/pip-ephem-wheel-cache-2judixeb + Created temporary directory: /private/tmp/pip-build-tracker-or5z80cg + Initialized build tracking at /private/tmp/pip-build-tracker-or5z80cg + Created build tracker: /private/tmp/pip-build-tracker-or5z80cg + Entered build tracker: /private/tmp/pip-build-tracker-or5z80cg + Created temporary directory: /private/tmp/pip-install-nqldcdar + Created temporary directory: /private/tmp/pip-ephem-wheel-cache-k0hdgvek Processing $SRC_DIR - Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-1pl8dy66' + Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-or5z80cg' Running setup.py (path:$SRC_DIR/setup.py) egg_info for package from file://$SRC_DIR - Created temporary directory: /private/tmp/pip-pip-egg-info-vx9saxas + Created temporary directory: /private/tmp/pip-pip-egg-info-czw1rcys Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Source in $SRC_DIR has version 0.5.0, which satisfies requirement Porechop_ABI==0.5.0 from file://$SRC_DIR - Removed Porechop_ABI==0.5.0 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-1pl8dy66' - Created temporary directory: /private/tmp/pip-unpack-04191cw_ + Removed Porechop_ABI==0.5.0 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-or5z80cg' + Created temporary directory: /private/tmp/pip-unpack-lwpwdvhn Building wheels for collected packages: Porechop_ABI - Created temporary directory: /private/tmp/pip-wheel-vn1qtfkb + Created temporary directory: /private/tmp/pip-wheel-fe92wrjr Building wheel for Porechop_ABI (setup.py): started - Destination directory: /private/tmp/pip-wheel-vn1qtfkb + Destination directory: /private/tmp/pip-wheel-fe92wrjr Building wheel for Porechop_ABI (setup.py): finished with status 'error' Running setup.py clean for Porechop_ABI Failed to build Porechop_ABI Exception information: Traceback (most recent call last): - File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + ^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper return func(self, options, args) ^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.11/site-packages/pip/_internal/commands/install.py", line 429, in run + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/commands/install.py", line 434, in run raise InstallationError( - pip._internal.exceptions.InstallationError: Could not build wheels for Porechop_ABI, which is required to install pyproject.toml-based projects - Removed build tracker: '/private/tmp/pip-build-tracker-1pl8dy66' + pip._internal.exceptions.InstallationError: ERROR: Failed to build installable wheels for some pyproject.toml based projects (Porechop_ABI) + Removed build tracker: '/private/tmp/pip-build-tracker-or5z80cg' # Last 100 lines of the build log. diff --git a/recipes/poseidon-trident/meta.yaml b/recipes/poseidon-trident/meta.yaml index abb6356acd5b8..583edb563a9f5 100644 --- a/recipes/poseidon-trident/meta.yaml +++ b/recipes/poseidon-trident/meta.yaml @@ -14,7 +14,7 @@ source: md5: 949200977a85883a078f1ee8ed0292a9 # [osx and arm64] build: - number: 0 + number: 1 script: - "mkdir -p $PREFIX/bin" - "mv trident* $PREFIX/bin/trident" diff --git a/recipes/poseidon-xerxes/meta.yaml b/recipes/poseidon-xerxes/meta.yaml index efb89c986c028..ee8d86af5150a 100644 --- a/recipes/poseidon-xerxes/meta.yaml +++ b/recipes/poseidon-xerxes/meta.yaml @@ -10,7 +10,7 @@ source: md5: f101c7d0448b486b86edc259c7838a92 # [osx] build: - number: 0 + number: 1 script: - "mkdir -p $PREFIX/bin" - "mv xerxes* $PREFIX/bin/xerxes" diff --git a/recipes/potrace/1.11/meta.yaml b/recipes/potrace/1.11/meta.yaml index 0ccf5368a07dc..92480ce8ad417 100644 --- a/recipes/potrace/1.11/meta.yaml +++ b/recipes/potrace/1.11/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.11 build: - number: 6 + number: 7 skip: True # [osx] source: diff --git a/recipes/pourrna/build_failure.linux-64.yaml b/recipes/pourrna/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..bd0f2634bf334 --- /dev/null +++ b/recipes/pourrna/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 207b0fa560d3d451aaba156a368760bfbe2f8da1f7781b971261bda121c8984d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + checking dependency style of $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc... gcc3 + checking dependency style of $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c... gcc3 + checking whether $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c supports C11 features by default... yes + checking whether to build with debug information... no + checking how to run the C preprocessor... $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -E + checking for grep that handles long lines and -e... /usr/bin/grep + checking for egrep... /usr/bin/grep -E + checking for ANSI C header files... yes + checking for sys/types.h... yes + checking for sys/stat.h... yes + checking for stdlib.h... yes + checking for string.h... yes + checking for memory.h... yes + checking for strings.h... yes + checking for inttypes.h... yes + checking for stdint.h... yes + checking for unistd.h... yes + checking for size_t... yes + checking for ANSI C header files... (cached) yes + checking for the Vienna RNA package >=2.4.11 headers... yes + checking for vrna_neighbors in -lRNA... yes + checking for help2man... false + checking that generated files are newer than configure... done + configure: creating ./config.status + config.status: creating Makefile + config.status: creating src/Makefile + config.status: creating misc/Makefile + config.status: creating doc/Makefile + config.status: creating packaging/pourRNA.spec + config.status: creating packaging/PKGBUILD + config.status: creating src/config.h + config.status: executing depfiles commands + Making all in src + make[1]: Entering directory '$SRC_DIR/src' + make all-am + make[2]: Entering directory '$SRC_DIR/src' + depbase=echo pourRNA_cmdl.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -DHAVE_CONFIG_H -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT pourRNA_cmdl.o -MD -MP -MF $depbase.Tpo -c -o pourRNA_cmdl.o pourRNA_cmdl.c &&\ + mv -f $depbase.Tpo $depbase.Po + In file included from pourRNA_cmdl.c:13: + config.h:38: warning: "NDEBUG" redefined + 38 | #define NDEBUG /**/ + | + : note: this is the location of the previous definition + depbase=echo SpookyHash/SpookyV2.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -O3 -fno-strict-aliasing -Wno-uninitialized -Wno-deprecated -pthread -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT SpookyHash/SpookyV2.o -MD -MP -MF $depbase.Tpo -c -o SpookyHash/SpookyV2.o SpookyHash/SpookyV2.cpp &&\ + mv -f $depbase.Tpo $depbase.Po + depbase=echo RNAkinetics/RateMatrixUtil.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -O3 -fno-strict-aliasing -Wno-uninitialized -Wno-deprecated -pthread -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT RNAkinetics/RateMatrixUtil.o -MD -MP -MF $depbase.Tpo -c -o RNAkinetics/RateMatrixUtil.o RNAkinetics/RateMatrixUtil.cpp &&\ + mv -f $depbase.Tpo $depbase.Po + In file included from RNAkinetics/RateMatrixUtil.h:22, + from RNAkinetics/RateMatrixUtil.cpp:8: + RNAkinetics/../SC_PartitionFunction.h:101:8: error: 'uint64_t' in namespace 'std' does not name a type; did you mean 'wint_t'? + 101 | std::uint64_t + | ^~~~~~~~ + | wint_t + In file included from /opt/conda/conda-bld/pourrna_1734238012098/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/hashtable.h:35, + from /opt/conda/conda-bld/pourrna_1734238012098/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/unordered_map.h:33, + from /opt/conda/conda-bld/pourrna_1734238012098/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/unordered_map:41, + from RNAkinetics/../BIUlibPart/MatrixSparse.hh:5, + from RNAkinetics/RateMatrixUtil.h:14: + /opt/conda/conda-bld/pourrna_1734238012098/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/hashtable_policy.h: In instantiation of 'std::__detail::_Hash_code_base<_Key, _Value, _ExtractKey, _Hash, _RangeHash, _Unused, __cache_hash_code>::__hash_code std::__detail::_Hash_code_base<_Key, _Value, _ExtractKey, _Hash, _RangeHash, _Unused, __cache_hash_code>::_M_hash_code(const _Key&) const [with _Key = std::pair; _Value = std::pair, SC_PartitionFunction>; _ExtractKey = std::__detail::_Select1st; _Hash = SC_PartitionFunction::UInt_Pair_Hash; _RangeHash = std::__detail::_Mod_range_hashing; _Unused = std::__detail::_Default_ranged_hash; bool __cache_hash_code = true; __hash_code = long unsigned int]': + /opt/conda/conda-bld/pourrna_1734238012098/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/hashtable.h:1700:46: required from 'std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _Hash, _RangeHash, _Unused, _RehashPolicy, _Traits>::const_iterator std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _Hash, _RangeHash, _Unused, _RehashPolicy, _Traits>::find(const key_type&) const [with _Key = std::pair; _Value = std::pair, SC_PartitionFunction>; _Alloc = std::allocator, SC_PartitionFunction> >; _ExtractKey = std::__detail::_Select1st; _Equal = std::equal_to >; _Hash = SC_PartitionFunction::UInt_Pair_Hash; _RangeHash = std::__detail::_Mod_range_hashing; _Unused = std::__detail::_Default_ranged_hash; _RehashPolicy = std::__detail::_Prime_rehash_policy; _Traits = std::__detail::_Hashtable_traits; const_iterator = std::__detail::_Insert_base, std::pair, SC_PartitionFunction>, std::allocator, SC_PartitionFunction> >, std::__detail::_Select1st, std::equal_to >, SC_PartitionFunction::UInt_Pair_Hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator; key_type = std::pair]' + /opt/conda/conda-bld/pourrna_1734238012098/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/unordered_map.h:887:25: required from 'std::unordered_map<_Key, _Tp, _Hash, _Pred, _Alloc>::const_iterator std::unordered_map<_Key, _Tp, _Hash, _Pred, _Alloc>::find(const key_type&) const [with _Key = std::pair; _Tp = SC_PartitionFunction; _Hash = SC_PartitionFunction::UInt_Pair_Hash; _Pred = std::equal_to >; _Alloc = std::allocator, SC_PartitionFunction> >; const_iterator = std::__detail::_Insert_base, std::pair, SC_PartitionFunction>, std::allocator, SC_PartitionFunction> >, std::__detail::_Select1st, std::equal_to >, SC_PartitionFunction::UInt_Pair_Hash, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits >::const_iterator; key_type = std::pair]' + RNAkinetics/RateMatrixUtil.cpp:317:65: required from here + /opt/conda/conda-bld/pourrna_1734238012098/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/hashtable_policy.h:1308:23: error: static assertion failed: hash function must be invocable with an argument of key type + 1308 | static_assert(__is_invocable{}, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/pourrna_1734238012098/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/hashtable_policy.h:1308:23: note: 'std::__is_invocable&>()' evaluates to false + /opt/conda/conda-bld/pourrna_1734238012098/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/hashtable_policy.h:1310:25: error: no match for call to '(const SC_PartitionFunction::UInt_Pair_Hash) (const std::pair&)' + 1310 | return _M_hash()(__k); + | ~~~~~~~~~^~~~~ + make[2]: *** [Makefile:486: RNAkinetics/RateMatrixUtil.o] Error 1 + make[2]: Leaving directory '$SRC_DIR/src' + make[1]: *** [Makefile:332: all] Error 2 + make[1]: Leaving directory '$SRC_DIR/src' + make: *** [Makefile:361: all-recursive] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/pourrna_1734238012098/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/pourrna_1734238012098/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/pourrna/build_failure.osx-64.yaml b/recipes/pourrna/build_failure.osx-64.yaml index 455445002af3e..97ea3f40cb005 100644 --- a/recipes/pourrna/build_failure.osx-64.yaml +++ b/recipes/pourrna/build_failure.osx-64.yaml @@ -1,104 +1,104 @@ -recipe_sha: b4bde0494de3b385d34b31a234c5644469e77bbceaa94ca991f8befd6b6d4583 # The commit at which this recipe failed to build. +recipe_sha: 207b0fa560d3d451aaba156a368760bfbe2f8da1f7781b971261bda121c8984d # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - checking for sys/stat.h... yes - checking for stdlib.h... yes - checking for string.h... yes - checking for memory.h... yes - checking for strings.h... yes - checking for inttypes.h... yes - checking for stdint.h... yes - checking for unistd.h... yes - checking for size_t... yes - checking for ANSI C header files... (cached) yes - checking for the Vienna RNA package >=2.4.11 headers... yes - checking for vrna_neighbors in -lRNA... yes - checking for help2man... false - checking that generated files are newer than configure... done - configure: creating ./config.status - config.status: creating Makefile - config.status: creating src/Makefile - config.status: creating misc/Makefile - config.status: creating doc/Makefile - config.status: creating packaging/pourRNA.spec - config.status: creating packaging/PKGBUILD - config.status: creating src/config.h - config.status: executing depfiles commands - Making all in src - make[1]: Entering directory '$SRC_DIR/src' - make all-am - make[2]: Entering directory '$SRC_DIR/src' - depbase=echo pourRNA_cmdl.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT pourRNA_cmdl.o -MD -MP -MF $depbase.Tpo -c -o pourRNA_cmdl.o pourRNA_cmdl.c &&\ - mv -f $depbase.Tpo $depbase.Po - depbase=echo SpookyHash/SpookyV2.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -fno-strict-aliasing -Wno-uninitialized -Wno-deprecated -pthread -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT SpookyHash/SpookyV2.o -MD -MP -MF $depbase.Tpo -c -o SpookyHash/SpookyV2.o SpookyHash/SpookyV2.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - depbase=echo RNAkinetics/RateMatrixUtil.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -fno-strict-aliasing -Wno-uninitialized -Wno-deprecated -pthread -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT RNAkinetics/RateMatrixUtil.o -MD -MP -MF $depbase.Tpo -c -o RNAkinetics/RateMatrixUtil.o RNAkinetics/RateMatrixUtil.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - depbase=echo RNAkinetics/RNA_NeighMinFilter.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -fno-strict-aliasing -Wno-uninitialized -Wno-deprecated -pthread -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT RNAkinetics/RNA_NeighMinFilter.o -MD -MP -MF $depbase.Tpo -c -o RNAkinetics/RNA_NeighMinFilter.o RNAkinetics/RNA_NeighMinFilter.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - depbase=echo TypeID.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -fno-strict-aliasing -Wno-uninitialized -Wno-deprecated -pthread -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT TypeID.o -MD -MP -MF $depbase.Tpo -c -o TypeID.o TypeID.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - depbase=echo MyState.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -fno-strict-aliasing -Wno-uninitialized -Wno-deprecated -pthread -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT MyState.o -MD -MP -MF $depbase.Tpo -c -o MyState.o MyState.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - depbase=echo Flooder.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -fno-strict-aliasing -Wno-uninitialized -Wno-deprecated -pthread -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT Flooder.o -MD -MP -MF $depbase.Tpo -c -o Flooder.o Flooder.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - depbase=echo WalkGradientHashed.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -fno-strict-aliasing -Wno-uninitialized -Wno-deprecated -pthread -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT WalkGradientHashed.o -MD -MP -MF $depbase.Tpo -c -o WalkGradientHashed.o WalkGradientHashed.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - depbase=echo StructureUtils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -fno-strict-aliasing -Wno-uninitialized -Wno-deprecated -pthread -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT StructureUtils.o -MD -MP -MF $depbase.Tpo -c -o StructureUtils.o StructureUtils.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - depbase=echo SC_PartitionFunction.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -fno-strict-aliasing -Wno-uninitialized -Wno-deprecated -pthread -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT SC_PartitionFunction.o -MD -MP -MF $depbase.Tpo -c -o SC_PartitionFunction.o SC_PartitionFunction.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - depbase=echo SC_DotPlot.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -fno-strict-aliasing -Wno-uninitialized -Wno-deprecated -pthread -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT SC_DotPlot.o -MD -MP -MF $depbase.Tpo -c -o SC_DotPlot.o SC_DotPlot.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - SC_DotPlot.cpp:140:33: warning: object backing the pointer will be destroyed at the end of the full-expression [-Wdangling-gsl] - char *emptyChar = (char *)std::string().c_str(); - ^~~~~~~~~~~~~ - 1 warning generated. - depbase=echo StateCollector.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -fno-strict-aliasing -Wno-uninitialized -Wno-deprecated -pthread -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT StateCollector.o -MD -MP -MF $depbase.Tpo -c -o StateCollector.o StateCollector.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - depbase=echo StatePairCollector.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -fno-strict-aliasing -Wno-uninitialized -Wno-deprecated -pthread -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT StatePairCollector.o -MD -MP -MF $depbase.Tpo -c -o StatePairCollector.o StatePairCollector.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - depbase=echo pourRNA.o | sed 's|[^/]*$|.deps/&|;s|\.o$||';\ - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -O3 -fno-strict-aliasing -Wno-uninitialized -Wno-deprecated -pthread -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT pourRNA.o -MD -MP -MF $depbase.Tpo -c -o pourRNA.o pourRNA.cpp &&\ - mv -f $depbase.Tpo $depbase.Po - pourRNA.cpp:374:29: error: use of undeclared identifier '_SC_PHYS_PAGES' - long pages = sysconf(_SC_PHYS_PAGES); - ^ - 1 error generated. - make[2]: *** [Makefile:486: pourRNA.o] Error 1 - make[1]: *** [Makefile:332: all] Error 2 - make[2]: Leaving directory '$SRC_DIR/src' - make[1]: Leaving directory '$SRC_DIR/src' - make: *** [Makefile:361: all-recursive] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/pourrna_1685396441406/work/conda_build.sh']' returned non-zero exit status 2. +log: |2- + - ca-certificates 2024.12.14 h8857fd0_0 + host: + - bzip2 1.0.8 hfdf4475_7 + - ca-certificates 2024.12.14 h8857fd0_0 + - libcxx 19.1.5 hf95d169_0 + - libexpat 2.6.4 h240833e_0 + - libffi 3.4.2 h0d85af4_5 + - liblzma 5.6.3 hd471939_1 + - libzlib 1.3.1 hd23fc13_2 + - llvm-openmp 19.1.5 ha54dae1_0 + - ncurses 6.5 hf036a51_1 + - perl 5.32.1 7_h10d778d_perl5 + - python_abi 3.12 5_cp312 + - tzdata 2024b hc8b5060_0 + - gengetopt 2.23 he49afe7_0 + - libsqlite 3.47.2 hdb6dae5_0 + - openssl 3.4.0 hd471939_0 + - readline 8.2 h9e318b2_1 + - tk 8.6.13 h1abcd95_1 + - python 3.12.8 h9ccd52b_1_cpython + - viennarna 2.7.0 py312pl5321h2c65b86_1 + run: + - viennarna >=2.4.14,<3.0.0 + - viennarna >=2.7.0,<2.8.0a0 + - libcxx >=18 + test: + commands: + - pourRNA --version + about: + home: https://github.com/ViennaRNA/pourRNA/ + license: GPLv2 + license_file: COPYING + summary: Compute local minima and respective transition rates of an RNA energy landscape. + extra: + copy_test_source_files: true + final: true + identifiers: + - doi:10.1093/bioinformatics/btz583 + recipe-maintainers: + - entzian + - martin-raden + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/pourrna_1734227810589/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/pourrna_1734227810589/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/pourrna_1734227810589/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/pourrna_1734227810589/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pourrna-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + checking build system type... x86_64-apple-darwin13.4.0 + checking host system type... x86_64-apple-darwin13.4.0 + checking whether the C compiler works... no # Last 100 lines of the build log. diff --git a/recipes/pourrna/meta.yaml b/recipes/pourrna/meta.yaml index 4313accff6e9c..bede6a0eacd5d 100644 --- a/recipes/pourrna/meta.yaml +++ b/recipes/pourrna/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage( name, max_pin="x.x") }} diff --git a/recipes/prefersim/meta.yaml b/recipes/prefersim/meta.yaml index 521d6249da162..e54e3ad5c56f8 100644 --- a/recipes/prefersim/meta.yaml +++ b/recipes/prefersim/meta.yaml @@ -10,7 +10,7 @@ source: sha256: cc4f3f2e56c012968660b7034274555836c300b0e0f364ee9a7a9ec65b3e83d2 build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/prequal/meta.yaml b/recipes/prequal/meta.yaml index e9fc9dfc88731..cb6fce7132f38 100644 --- a/recipes/prequal/meta.yaml +++ b/recipes/prequal/meta.yaml @@ -9,7 +9,7 @@ source: sha256: a46bb03fe6831ac8435e32cbfd108b6f5761357a555b44ca91266f0d4f5422f3 build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/preseq/build_failure.linux-64.yaml b/recipes/preseq/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..fa0909c1b1512 --- /dev/null +++ b/recipes/preseq/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 849663d3d24092a6e1a9138c19394056f5b5ed60c2673d60ed8d7cc4fd7cc607 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + | ^~~~~ + sam_record.cpp: In function 'std::string format_sam_flags(uint16_t)': + sam_record.cpp:42:56: error: 'read_paired' is not a member of 'samflags' + 42 | oss << "read_paired: " << check(the_flags, samflags::read_paired) << '\n' + | ^~~~~~~~~~~ + sam_record.cpp:44:37: error: 'read_pair_mapped' is not a member of 'samflags' + 44 | << check(the_flags, samflags::read_pair_mapped) << '\n' + | ^~~~~~~~~~~~~~~~ + sam_record.cpp:45:58: error: 'read_unmapped' is not a member of 'samflags' + 45 | << "read_unmapped: " << check(the_flags, samflags::read_unmapped) << '\n' + | ^~~~~~~~~~~~~ + sam_record.cpp:46:58: error: 'mate_unmapped' is not a member of 'samflags' + 46 | << "mate_unmapped: " << check(the_flags, samflags::mate_unmapped) << '\n' + | ^~~~~~~~~~~~~ + sam_record.cpp:47:52: error: 'read_rc' is not a member of 'samflags' + 47 | << "read_rc: " << check(the_flags, samflags::read_rc) << '\n' + | ^~~~~~~ + sam_record.cpp:48:52: error: 'mate_rc' is not a member of 'samflags' + 48 | << "mate_rc: " << check(the_flags, samflags::mate_rc) << '\n' + | ^~~~~~~ + sam_record.cpp:50:37: error: 'template_first' is not a member of 'samflags' + 50 | << check(the_flags, samflags::template_first) << '\n' + | ^~~~~~~~~~~~~~ + sam_record.cpp:51:58: error: 'template_last' is not a member of 'samflags' + 51 | << "template_last: " << check(the_flags, samflags::template_last) << '\n' + | ^~~~~~~~~~~~~ + sam_record.cpp:52:58: error: 'secondary_aln' is not a member of 'samflags' + 52 | << "secondary_aln: " << check(the_flags, samflags::secondary_aln) << '\n' + | ^~~~~~~~~~~~~ + sam_record.cpp:53:58: error: 'below_quality' is not a member of 'samflags' + 53 | << "below_quality: " << check(the_flags, samflags::below_quality) << '\n' + | ^~~~~~~~~~~~~ + sam_record.cpp:54:58: error: 'pcr_duplicate' is not a member of 'samflags' + 54 | << "pcr_duplicate: " << check(the_flags, samflags::pcr_duplicate) << '\n' + | ^~~~~~~~~~~~~ + sam_record.cpp:56:37: error: 'supplementary_aln' is not a member of 'samflags' + 56 | << check(the_flags, samflags::supplementary_aln); + | ^~~~~~~~~~~~~~~~~ + sam_record.cpp: In function 'std::ostream& operator<<(std::ostream&, const sam_rec&)': + sam_record.cpp:79:19: error: 'const class sam_rec' has no member named 'flags' + 79 | << r.flags << '\t' + | ^~~~~ + sam_record.cpp:81:19: error: 'const class sam_rec' has no member named 'pos' + 81 | << r.pos << '\t' + | ^~~ + sam_record.cpp:82:41: error: 'const class sam_rec' has no member named 'mapq' + 82 | << static_cast(r.mapq) << '\t' + | ^~~~ + sam_record.cpp:85:19: error: 'const class sam_rec' has no member named 'pnext'; did you mean 'rnext'? + 85 | << r.pnext << '\t' + | ^~~~~ + | rnext + sam_record.cpp: In constructor 'sam_rec::sam_rec(const std::string&)': + sam_record.cpp:102:18: error: 'flags' was not declared in this scope + 102 | qname >> flags >> rname >> pos >> will_become_mapq >> + | ^~~~~ + sam_record.cpp:102:36: error: 'pos' was not declared in this scope; did you mean 'pow'? + 102 | qname >> flags >> rname >> pos >> will_become_mapq >> + | ^~~ + | pow + sam_record.cpp:103:27: error: 'pnext' was not declared in this scope; did you mean 'rnext'? + 103 | cigar >> rnext >> pnext >> tlen >> seq >> qual)) + | ^~~~~ + | rnext + sam_record.cpp:105:7: error: 'mapq' was not declared in this scope + 105 | if (mapq > 255) + | ^~~~ + sam_record.cpp:107:3: error: 'mapq' was not declared in this scope + 107 | mapq = static_cast(will_become_mapq); + | ^~~~ + make[3]: *** [Makefile:487: sam_record.o] Error 1 + make[3]: Leaving directory '$SRC_DIR/src/smithlab_cpp' + make[2]: *** [Makefile:370: all] Error 2 + make[2]: Leaving directory '$SRC_DIR/src/smithlab_cpp' + make[1]: *** [Makefile:540: all-recursive] Error 1 + make[1]: Leaving directory '$SRC_DIR' + make: *** [Makefile:380: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/preseq_1734244836153/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/preseq_1734244836153/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/preseq/build_failure.linux-aarch64.yaml b/recipes/preseq/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..4245bc9f9e251 --- /dev/null +++ b/recipes/preseq/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 849663d3d24092a6e1a9138c19394056f5b5ed60c2673d60ed8d7cc4fd7cc607 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + | ^~~~~ + sam_record.cpp: In function 'std::string format_sam_flags(uint16_t)': + sam_record.cpp:42:56: error: 'read_paired' is not a member of 'samflags' + 42 | oss << "read_paired: " << check(the_flags, samflags::read_paired) << '\n' + | ^~~~~~~~~~~ + sam_record.cpp:44:37: error: 'read_pair_mapped' is not a member of 'samflags' + 44 | << check(the_flags, samflags::read_pair_mapped) << '\n' + | ^~~~~~~~~~~~~~~~ + sam_record.cpp:45:58: error: 'read_unmapped' is not a member of 'samflags' + 45 | << "read_unmapped: " << check(the_flags, samflags::read_unmapped) << '\n' + | ^~~~~~~~~~~~~ + sam_record.cpp:46:58: error: 'mate_unmapped' is not a member of 'samflags' + 46 | << "mate_unmapped: " << check(the_flags, samflags::mate_unmapped) << '\n' + | ^~~~~~~~~~~~~ + sam_record.cpp:47:52: error: 'read_rc' is not a member of 'samflags' + 47 | << "read_rc: " << check(the_flags, samflags::read_rc) << '\n' + | ^~~~~~~ + sam_record.cpp:48:52: error: 'mate_rc' is not a member of 'samflags' + 48 | << "mate_rc: " << check(the_flags, samflags::mate_rc) << '\n' + | ^~~~~~~ + sam_record.cpp:50:37: error: 'template_first' is not a member of 'samflags' + 50 | << check(the_flags, samflags::template_first) << '\n' + | ^~~~~~~~~~~~~~ + sam_record.cpp:51:58: error: 'template_last' is not a member of 'samflags' + 51 | << "template_last: " << check(the_flags, samflags::template_last) << '\n' + | ^~~~~~~~~~~~~ + sam_record.cpp:52:58: error: 'secondary_aln' is not a member of 'samflags' + 52 | << "secondary_aln: " << check(the_flags, samflags::secondary_aln) << '\n' + | ^~~~~~~~~~~~~ + sam_record.cpp:53:58: error: 'below_quality' is not a member of 'samflags' + 53 | << "below_quality: " << check(the_flags, samflags::below_quality) << '\n' + | ^~~~~~~~~~~~~ + sam_record.cpp:54:58: error: 'pcr_duplicate' is not a member of 'samflags' + 54 | << "pcr_duplicate: " << check(the_flags, samflags::pcr_duplicate) << '\n' + | ^~~~~~~~~~~~~ + sam_record.cpp:56:37: error: 'supplementary_aln' is not a member of 'samflags' + 56 | << check(the_flags, samflags::supplementary_aln); + | ^~~~~~~~~~~~~~~~~ + sam_record.cpp: In function 'std::ostream& operator<<(std::ostream&, const sam_rec&)': + sam_record.cpp:79:19: error: 'const class sam_rec' has no member named 'flags' + 79 | << r.flags << '\t' + | ^~~~~ + sam_record.cpp:81:19: error: 'const class sam_rec' has no member named 'pos' + 81 | << r.pos << '\t' + | ^~~ + sam_record.cpp:82:41: error: 'const class sam_rec' has no member named 'mapq' + 82 | << static_cast(r.mapq) << '\t' + | ^~~~ + sam_record.cpp:85:19: error: 'const class sam_rec' has no member named 'pnext'; did you mean 'rnext'? + 85 | << r.pnext << '\t' + | ^~~~~ + | rnext + sam_record.cpp: In constructor 'sam_rec::sam_rec(const std::string&)': + sam_record.cpp:102:18: error: 'flags' was not declared in this scope + 102 | qname >> flags >> rname >> pos >> will_become_mapq >> + | ^~~~~ + sam_record.cpp:102:36: error: 'pos' was not declared in this scope; did you mean 'pow'? + 102 | qname >> flags >> rname >> pos >> will_become_mapq >> + | ^~~ + | pow + sam_record.cpp:103:27: error: 'pnext' was not declared in this scope; did you mean 'rnext'? + 103 | cigar >> rnext >> pnext >> tlen >> seq >> qual)) + | ^~~~~ + | rnext + sam_record.cpp:105:7: error: 'mapq' was not declared in this scope + 105 | if (mapq > 255) + | ^~~~ + sam_record.cpp:107:3: error: 'mapq' was not declared in this scope + 107 | mapq = static_cast(will_become_mapq); + | ^~~~ + make[3]: *** [Makefile:487: sam_record.o] Error 1 + make[3]: Leaving directory '$SRC_DIR/src/smithlab_cpp' + make[2]: *** [Makefile:370: all] Error 2 + make[2]: Leaving directory '$SRC_DIR/src/smithlab_cpp' + make[1]: *** [Makefile:540: all-recursive] Error 1 + make[1]: Leaving directory '$SRC_DIR' + make: *** [Makefile:380: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/preseq_1734187088099/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/preseq_1734187088099/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/preseq/meta.yaml b/recipes/preseq/meta.yaml index 462b966c1500e..a07ccc454358e 100644 --- a/recipes/preseq/meta.yaml +++ b/recipes/preseq/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 6 + number: 7 run_exports: - {{ pin_subpackage("preseq", max_pin="x.x") }} diff --git a/recipes/pretextgraph/meta.yaml b/recipes/pretextgraph/meta.yaml index e93bc950bbaac..410b747e80f19 100644 --- a/recipes/pretextgraph/meta.yaml +++ b/recipes/pretextgraph/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 # the build number should be incremented if the same version of the package is built with different build settings + number: 1 # the build number should be incremented if the same version of the package is built with different build settings run_exports: - {{ pin_subpackage('pretextgraph', max_pin="x.x") }} diff --git a/recipes/pretextmap/meta.yaml b/recipes/pretextmap/meta.yaml index 48ad7afae6d7c..610a7f1e5c098 100644 --- a/recipes/pretextmap/meta.yaml +++ b/recipes/pretextmap/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/pretextsnapshot/meta.yaml b/recipes/pretextsnapshot/meta.yaml index f7aafcbda5522..386116309a216 100644 --- a/recipes/pretextsnapshot/meta.yaml +++ b/recipes/pretextsnapshot/meta.yaml @@ -14,7 +14,7 @@ source: # - 0001-disable-auto-vectorisation-for-conda-libm.patch # [linux] build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/primer3-py/meta.yaml b/recipes/primer3-py/meta.yaml index 6e59d2ae15ff7..bef64c8b3a8db 100644 --- a/recipes/primer3-py/meta.yaml +++ b/recipes/primer3-py/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 1ec6ce99ea149b1c82361c654a0eab824e698ce32d5f9ed2dd8f8f37564b3f5f build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage('primer3-py', max_pin="x") }} diff --git a/recipes/primer3/1.1.4/build_failure.osx-64.yaml b/recipes/primer3/1.1.4/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..49810e2cea522 --- /dev/null +++ b/recipes/primer3/1.1.4/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: eaf9d4523d645136c03e982cab06b7cdfd2b22f60c0904529a1481b40ff43aba # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - libllvm18 18.1.8 h9ce406d_2 + - sigtool 0.1.3 h88f4db0_0 + - ld64_osx-64 951.9 hc8d1a19_2 + - libclang-cpp18.1 18.1.8 default_h0c94c6a_5 + - llvm-tools-18 18.1.8 h9ce406d_2 + - clang-18 18.1.8 default_h0c94c6a_5 + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + - llvm-tools 18.1.8 h9ce406d_2 + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + - cctools_osx-64 1010.6 h00edd4c_2 + return build_tree( + - clang 18.1.8 default_h179603d_5 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + - clangxx 18.1.8 default_h179603d_5 + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/primer3_1734455056038/work/conda_build.sh']' returned non-zero exit status 2. + - compiler-rt 18.1.8 h1020d70_1 + - clang_impl_osx-64 18.1.8 h6a44ed1_23 + - clang_osx-64 18.1.8 h7e5c614_23 + run: + - perl + test: + commands: + - primer3_core --help 2>&1 | grep -F 'This is primer3' + - test -x "${PREFIX}/bin/long_seq_tm_test" + - test -x "${PREFIX}/bin/ntdpal" + - test -x "${PREFIX}/bin/oligotm" + about: + home: http://primer3.sourceforge.net/ + license: GPLv2 + license_file: COPYING.txt + summary: Design PCR primers from DNA sequence. From mispriming libraries to sequence + quality data to the generation of internal oligos, primer3 does it. + extra: + copy_test_source_files: true + final: true + identifiers: + - biotools:primer3 + - doi:10.1093/nar/gks596 + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/primer3_1734455056038/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/primer3_1734455056038/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/primer3_1734455056038/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/primer3_1734455056038/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/primer3-1.1.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/primer3-1.1.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + $SRC_DIR/src $SRC_DIR + x86_64-apple-darwin13.4.0-clang -c -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/primer3-1.1.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O2 -g -Wall -D__USE_FIXED_PROTOTYPES__ -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 primer3_main.c +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/primer3/1.1.4/meta.yaml b/recipes/primer3/1.1.4/meta.yaml index 4e2ccf3549e14..99ad7ab302f6c 100644 --- a/recipes/primer3/1.1.4/meta.yaml +++ b/recipes/primer3/1.1.4/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 6 + number: 7 source: url: http://downloads.sourceforge.net/project/primer3/primer3/1.1.4/primer3-1.1.4.tar.gz diff --git a/recipes/primer3/2.0.0a/meta.yaml b/recipes/primer3/2.0.0a/meta.yaml index ea003cbca0e1b..00e537e7dda7d 100644 --- a/recipes/primer3/2.0.0a/meta.yaml +++ b/recipes/primer3/2.0.0a/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 7 + number: 8 skip: True # [osx] source: diff --git a/recipes/primer3/meta.yaml b/recipes/primer3/meta.yaml index fab1baf1e1cce..5943daf005f9c 100644 --- a/recipes/primer3/meta.yaml +++ b/recipes/primer3/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/prinseq-plus-plus/build_failure.osx-64.yaml b/recipes/prinseq-plus-plus/build_failure.osx-64.yaml deleted file mode 100644 index b97154672bd28..0000000000000 --- a/recipes/prinseq-plus-plus/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 2090336535d2a66c3424d552d85f258d260d4d60b64855f38ee4238515d91532 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/prinseq-plus-plus-1.2.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/prinseq-plus-plus-1.2.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - checking whether the C compiler works... yes - checking for C compiler default output file name... a.out - checking for suffix of executables... - checking whether we are cross compiling... no - checking for suffix of object files... o - checking whether the compiler supports GNU C... yes - checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes - checking for x86_64-apple-darwin13.4.0-clang option to enable C11 features... none needed - checking whether x86_64-apple-darwin13.4.0-clang supports C11 features by default... yes - checking whether the compiler supports GNU C... (cached) yes - checking whether x86_64-apple-darwin13.4.0-clang accepts -g... (cached) yes - checking for x86_64-apple-darwin13.4.0-clang option to enable C11 features... (cached) none needed - checking for a BSD-compatible install... /usr/bin/install -c - checking build system type... x86_64-apple-darwin13.4.0 - checking host system type... x86_64-apple-darwin13.4.0 - checking for boostlib >= 1.41 (104100) includes in "$PREFIX/include"... yes - checking for boostlib >= 1.41 (104100) lib path in "$PREFIX/lib/x86_64-darwin13.4.0"... no - checking for boostlib >= 1.41 (104100) lib path in "$PREFIX/lib64"... no - checking for boostlib >= 1.41 (104100) lib path in "$PREFIX/libx32"... no - checking for boostlib >= 1.41 (104100) lib path in "$PREFIX/lib"... yes - checking for boostlib >= 1.41 (104100)... yes - checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang - checking whether the compiler supports GNU C... yes - checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes - checking for x86_64-apple-darwin13.4.0-clang option to enable C11 features... none needed - checking whether the Boost::System library is available... yes - checking for exit in -lboost_system... yes - checking whether the Boost::Filesystem library is available... yes - checking for exit in -lboost_filesystem... yes - checking whether the Boost::IOStreams library is available... yes - checking for exit in -lboost_iostreams... yes - checking for stdio.h... yes - checking for stdlib.h... yes - checking for string.h... yes - checking for inttypes.h... yes - checking for stdint.h... yes - checking for strings.h... yes - checking for sys/stat.h... yes - checking for sys/types.h... yes - checking for unistd.h... yes - checking if zlib is wanted... yes - checking for inflateEnd in -lz... yes - checking for zlib.h... yes - checking for a sed that does not truncate output... /usr/bin/sed - checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang -E - checking for grep that handles long lines and -e... /usr/bin/grep - checking for egrep... /usr/bin/grep -E - checking whether x86_64-apple-darwin13.4.0-clang is Clang... yes - checking whether Clang needs flag to prevent "argument unused" warning when linking with -pthread... no - checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE - checking whether more special flags are required for pthreads... no - checking for PTHREAD_PRIO_INHERIT... yes - checking for stdlib.h... (cached) yes - checking for unistd.h... (cached) yes - checking for _Bool... no - checking for stdbool.h that conforms to C99... yes - configure: creating ./config.status - config.status: creating Makefile - config.status: creating src/Makefile - config.status: creating README.md - config.status: creating config.h - cd src && make all - make[1]: Entering directory '$SRC_DIR/src' - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/prinseq-plus-plus-1.2.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -c -o main.o main.cpp - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/prinseq-plus-plus-1.2.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -c -o reads.o reads.cpp - make[1]: Leaving directory '$SRC_DIR/src' - cd src && make install - make[1]: Entering directory '$SRC_DIR/src' - install -d $PREFIX/bin - install -m 0775 prinseq $PREFIX/bin - make[1]: Leaving directory '$SRC_DIR/src' -# Last 100 lines of the build log. diff --git a/recipes/prinseq-plus-plus/meta.yaml b/recipes/prinseq-plus-plus/meta.yaml index 00785a0089dcb..a879158fba8a0 100644 --- a/recipes/prinseq-plus-plus/meta.yaml +++ b/recipes/prinseq-plus-plus/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/probeit/meta.yaml b/recipes/probeit/meta.yaml index d58fd58c535d6..baa33fe9e4e0e 100644 --- a/recipes/probeit/meta.yaml +++ b/recipes/probeit/meta.yaml @@ -7,7 +7,7 @@ package: build: skip: true # [py2k] - number: 3 + number: 4 source: url: "https://github.com/steineggerlab/probeit/archive/refs/tags/v{{ version }}.tar.gz" diff --git a/recipes/proda/meta.yaml b/recipes/proda/meta.yaml index a0ff402f3f205..261de23dbbfde 100644 --- a/recipes/proda/meta.yaml +++ b/recipes/proda/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 5 + number: 6 source: url: http://proda.stanford.edu/proda_1_0.tar.gz diff --git a/recipes/prodigal-gv/meta.yaml b/recipes/prodigal-gv/meta.yaml index 1221209bd1622..48fc6460f77cf 100644 --- a/recipes/prodigal-gv/meta.yaml +++ b/recipes/prodigal-gv/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 1fb40a8ae204ce2f41a413edb1edf5b8f22c28c2812320e2807ab48f8e8ce795 build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage('prodigal-gv', max_pin="x") }} @@ -35,4 +35,4 @@ about: extra: additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 diff --git a/recipes/prodigal/meta.yaml b/recipes/prodigal/meta.yaml index 054aa0a7d3ba8..2c47dc46fcf55 100644 --- a/recipes/prodigal/meta.yaml +++ b/recipes/prodigal/meta.yaml @@ -13,7 +13,7 @@ source: - sd_motif_B.patch build: - number: 9 + number: 10 run_exports: - {{ pin_subpackage('prodigal', max_pin=None) }} @@ -35,4 +35,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/prophasm/meta.yaml b/recipes/prophasm/meta.yaml index 34bad6cc121ed..59a95d8e66be3 100644 --- a/recipes/prophasm/meta.yaml +++ b/recipes/prophasm/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/prophex/meta.yaml b/recipes/prophex/meta.yaml index 0538ce344c326..2c0f8da6e72c2 100644 --- a/recipes/prophex/meta.yaml +++ b/recipes/prophex/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/prophyle/meta.yaml b/recipes/prophyle/meta.yaml index 1a06445a421e8..2e9846cbf211c 100644 --- a/recipes/prophyle/meta.yaml +++ b/recipes/prophyle/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 skip: True # [py27] run_exports: - {{ pin_subpackage("prophyle", max_pin="x.x") }} diff --git a/recipes/prosampler/meta.yaml b/recipes/prosampler/meta.yaml index 4433e38f225ef..26c9c1e972450 100644 --- a/recipes/prosampler/meta.yaml +++ b/recipes/prosampler/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('prosampler', max_pin=None) }} diff --git a/recipes/prot-scriber/meta.yaml b/recipes/prot-scriber/meta.yaml index b32921251aa5a..38e7a8e8d16bf 100644 --- a/recipes/prot-scriber/meta.yaml +++ b/recipes/prot-scriber/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage("prot-scriber", max_pin="x") }} diff --git a/recipes/proteinortho/build_failure.osx-64.yaml b/recipes/proteinortho/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..eb7023eec6659 --- /dev/null +++ b/recipes/proteinortho/build_failure.osx-64.yaml @@ -0,0 +1,107 @@ +recipe_sha: a98dfbbf64c259cca30746c9221d5af13905f66e1c07c42a1dbe80a9d6eade32 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/proteinortho-6.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/proteinortho-6.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + F77=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F90=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/proteinortho-6.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/proteinortho-6.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/proteinortho-6.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/proteinortho-6.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/proteinortho-6.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/proteinortho-6.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + rm -rf src/BUILD test/C*.faa.* test/E.faa.* test/C2.faa.* test/L.faa.* test/M.faa.* + rm -rf src/lapack-3.8.0/ + -n CC = + x86_64-apple-darwin13.4.0-clang + Creating build directory ... + -n CCFLAGS = + + -n CXX = + x86_64-apple-darwin13.4.0-clang + -n CXXFLAGS = + -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/proteinortho-6.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -I$PREFIX/include + -n MTUNEARCHFLAGS = + + -n LDFLAGS = + -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names + -n LDLIBS = + + -n STATIC = + FALSE + [ 10%] Prepare proteinortho_clustering ... + [ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking) + [ 25%] Building **graphMinusRemovegraph** + x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -funroll-loops -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/proteinortho-6.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -I$PREFIX/include -fopenmp -o src/BUILD/Darwin_x86_64/proteinortho_clustering src/proteinortho_clustering.cpp -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/proteinortho_1736281930262/work/conda_build.sh']' returned non-zero exit status 2. + x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/proteinortho-6.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -I$PREFIX/include -o src/BUILD/Darwin_x86_64/proteinortho_graphMinusRemovegraph src/graphMinusRemovegraph.cpp -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names + ......dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive (this should now work for OSX). + x86_64-apple-darwin13.4.0-clang -std=c11 -O3 -funroll-loops -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/proteinortho-6.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -I$PREFIX/include -fopenmp -o src/BUILD/Darwin_x86_64/proteinortho_clustering src/proteinortho_clustering.cpp -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -llapack -lblas -pthread -lpthread + ......OK dynamic linking was successful for proteinortho_clustering! +# Last 100 lines of the build log. +category: |- + compiler error + diff --git a/recipes/proteinortho/meta.yaml b/recipes/proteinortho/meta.yaml index 1e713103abcbe..925175f902b2a 100755 --- a/recipes/proteinortho/meta.yaml +++ b/recipes/proteinortho/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('proteinortho', max_pin="x") }} diff --git a/recipes/provean/meta.yaml b/recipes/provean/meta.yaml index 892a1639a11b6..80229c14688e2 100644 --- a/recipes/provean/meta.yaml +++ b/recipes/provean/meta.yaml @@ -14,7 +14,7 @@ source: - blast_db.patch build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/psascan/meta.yaml b/recipes/psascan/meta.yaml index 1112b084b3284..f173da49d1323 100644 --- a/recipes/psascan/meta.yaml +++ b/recipes/psascan/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 skip: True # [osx] source: diff --git a/recipes/psass/build_failure.linux-64.yaml b/recipes/psass/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..2199bf50315df --- /dev/null +++ b/recipes/psass/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 6e12a8a4f61d461e88882f17422eddc69635e7ffdacf829381e56b25768f8c27 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fpic -c -o cram/cram_external.pico cram/cram_external.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fpic -c -o cram/cram_index.pico cram/cram_index.c + cram/cram_index.c: In function 'cram_index_build': + cram/cram_index.c:690:17: warning: variable 'hpos' set but not used [-Wunused-but-set-variable] + 690 | off_t cpos, hpos; + | ^~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fpic -c -o cram/cram_io.pico cram/cram_io.c + cram/cram_io.c: In function 'cram_dopen': + cram/cram_io.c:4304:9: warning: '__builtin_strncpy' specified bound 20 equals destination size [-Wstringop-truncation] + 4304 | strncpy(def->file_id, filename, 20); + | ^ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fpic -c -o cram/cram_stats.pico cram/cram_stats.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fpic -c -o cram/mFILE.pico cram/mFILE.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fpic -c -o cram/rANS_static.pico cram/rANS_static.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fpic -c -o cram/string_alloc.pico cram/string_alloc.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -shared -Wl,-soname,libhts.so.3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/string_alloc.pico -llzma -lbz2 -lz -lm -lpthread + ln -sf libhts.so libhts.so.3 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o bgzip.o bgzip.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o bgzip bgzip.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o htsfile.o htsfile.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o htsfile htsfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o tabix.o tabix.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o tabix tabix.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/hts_endian.o test/hts_endian.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o test/hts_endian test/hts_endian.o -llzma -lbz2 -lz -lm + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/fieldarith.o test/fieldarith.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o test/fieldarith test/fieldarith.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/hfile.o test/hfile.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o test/hfile test/hfile.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/pileup.o test/pileup.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o test/pileup test/pileup.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/sam.o test/sam.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o test/sam test/sam.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_bgzf.o test/test_bgzf.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o test/test_bgzf test/test_bgzf.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_kstring.o test/test_kstring.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o test/test_kstring test/test_kstring.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_realn.o test/test_realn.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o test/test_realn test/test_realn.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-regidx.o test/test-regidx.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o test/test-regidx test/test-regidx.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_str2int.o test/test_str2int.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o test/test_str2int test/test_str2int.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_view.o test/test_view.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o test/test_view test/test_view.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test_index.o test/test_index.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o test/test_index test/test_index.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-vcf-api.o test/test-vcf-api.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o test/test-vcf-api test/test-vcf-api.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-bcf-sr.o test/test-bcf-sr.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-bcf-translate.o test/test-bcf-translate.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -llzma -lbz2 -lz -lm -lpthread + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fvisibility=hidden -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o test/test-parse-reg.o test/test-parse-reg.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -pthread -lstdc -lz -llzma -lbz2 -fvisibility=hidden -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm -lpthread + make[1]: Leaving directory '$SRC_DIR/include/htslib' + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -std=c11 -I ./include -c -o build/analyze.o src/analyze.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psass-3.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -std=c11 -I ./include -c -o build/gff_file.o src/gff_file.cpp + In file included from src/gff_file.h:6, + from src/gff_file.cpp:1: + src/input_data.h:22:9: error: 'uint32_t' does not name a type + 22 | uint32_t position = 0; + | ^~~~~~~~ + src/input_data.h:1:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + |#include + 1 | #pragma once + src/input_data.h:23:9: error: 'uint32_t' does not name a type + 23 | uint32_t last_position = 0; + | ^~~~~~~~ + src/input_data.h:23:9: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + make: *** [makefile:66: build/gff_file.o] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/psass_1734019952274/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/psass_1734019952274/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/psass/meta.yaml b/recipes/psass/meta.yaml index f46e29eb335e3..83fdb21527edc 100644 --- a/recipes/psass/meta.yaml +++ b/recipes/psass/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://github.com/SexGenomicsToolkit/PSASS/archive/{{ version }}.tar.gz diff --git a/recipes/psdm/meta.yaml b/recipes/psdm/meta.yaml index 96753b338e84b..aa22771abbd51 100644 --- a/recipes/psdm/meta.yaml +++ b/recipes/psdm/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 0414b2fde2e6c43a7d9bfd7a53da67f8e084cc4ec350ad7c498cc1937b9a15cc build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} diff --git a/recipes/psiclass/build_failure.osx-64.yaml b/recipes/psiclass/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..70035a7afcdd3 --- /dev/null +++ b/recipes/psiclass/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 6b903cc18850f01a006e9084c345be814de43983452a498dc9081e0a5d71734e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - libclang-cpp18.1 18.1.8 default_h0c94c6a_5 + - cctools_osx-64 1010.6 h00edd4c_2 + - clangxx_impl_osx-64 18.1.8 h4b7810f_23 + - clang 18.1.8 default_h179603d_5 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + - libcxx-devel 18.1.8 h7c275be_7 + - make 4.4.1 h00291cd_2 + raise BuildScriptException(str(exc), caused_by=exc) from exc + - ncurses 6.5 hf036a51_1 + - libiconv 1.17 hd75f5a5_2 + - compiler-rt 18.1.8 h1020d70_1 + host: + - libcxx 19.1.5 hf95d169_0 + - libzlib 1.2.13 h87427d6_6 + - ncurses 6.5 hf036a51_1 + - zlib 1.2.13 h87427d6_6 + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/psiclass_1734377967110/work/conda_build.sh']' returned non-zero exit status 2. + - samtools 0.1.19 hd510865_11 + run: + - perl + - libcxx >=18 + - libzlib >=1.2.13,<2.0a0 + - samtools 0.1.19.* + test: + commands: + - classes 2>&1 | cat > /dev/null + - junc 2>&1 | cat > /dev/null + - trust-splice 2>&1 | cat > /dev/null + - subexon-info 2>&1 | cat > /dev/null + - combine-subexons 2>&1 | cat > /dev/null + - vote-transcripts 2>&1 | cat > /dev/null + - add-genename 2>&1 | cat > /dev/null + - which FilterSplice.pl + - which psiclass + about: + home: https://github.com/splicebox/PsiCLASS + license: GPL-3.0-only + license_file: LICENSE + summary: Simultaneous multi-sample transcript assembler for RNA-seq data + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/psiclass_1734377967110/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/psiclass_1734377967110/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/psiclass_1734377967110/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/psiclass_1734377967110/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psiclass-1.0.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psiclass-1.0.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psiclass-1.0.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psiclass-1.0.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + x86_64-apple-darwin13.4.0-clang -c -o subexon-info.o -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -I./samtools-0.1.19 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psiclass-1.0.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wformat -O3 SubexonInfo.cpp -lbam -lz -lm -lpthread + x86_64-apple-darwin13.4.0-clang -c -o stats.o -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -I./samtools-0.1.19 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/psiclass-1.0.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wformat -O3 stats.cpp -lbam -lz -lm -lpthread +# Last 100 lines of the build log. diff --git a/recipes/psiclass/meta.yaml b/recipes/psiclass/meta.yaml index 9915fbfda7c20..c582411ff951d 100644 --- a/recipes/psiclass/meta.yaml +++ b/recipes/psiclass/meta.yaml @@ -8,7 +8,7 @@ source: sha256: c60c0f33f9a076b97ccdba68b9140a5fb6936a5c5e309d70b3d0cf558828f73d build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage("psiclass", max_pin="x.x") }} diff --git a/recipes/psirc/meta.yaml b/recipes/psirc/meta.yaml index cd19440ace3ce..ff21334d412c5 100644 --- a/recipes/psirc/meta.yaml +++ b/recipes/psirc/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 7acff956ceb8e24b43aa14ad35bbce8f2e646884d83aec45e9e6326d9a1a5a26 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('psirc', max_pin="x") }} diff --git a/recipes/psmc/meta.yaml b/recipes/psmc/meta.yaml index 2df48c2012c23..f6cd38f3b498b 100644 --- a/recipes/psmc/meta.yaml +++ b/recipes/psmc/meta.yaml @@ -11,7 +11,7 @@ source: build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -40,4 +40,4 @@ test: extra: additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 diff --git a/recipes/pstools/meta.yaml b/recipes/pstools/meta.yaml index b2d313d78b8db..b79c626272f16 100644 --- a/recipes/pstools/meta.yaml +++ b/recipes/pstools/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 84d3cb7c1a62efb9d89c921b7dbf818e00f1a8374a1eef388bca608bfc269165 build: - number: 3 + number: 4 skip: True # [osx] requirements: diff --git a/recipes/ptrimmer/meta.yaml b/recipes/ptrimmer/meta.yaml index 113702231d46c..8478673e1da73 100644 --- a/recipes/ptrimmer/meta.yaml +++ b/recipes/ptrimmer/meta.yaml @@ -10,7 +10,7 @@ source: sha256: dbc332ec8a3b8aba529eca6fcd29008ede28a52e7f84dd2a9f397b2870e8c5fe build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('ptrimmer', max_pin="x") }} diff --git a/recipes/pulchra/build_failure.linux-64.yaml b/recipes/pulchra/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..9419cd9bc6440 --- /dev/null +++ b/recipes/pulchra/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: f63d275b5587dfaab09b6093d8eeffb8d365dea790449c860a0636d581f6e787 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + 2024-12-15T20:11:54 linux-aarch64 Writing index HTML + 2024-12-15T20:11:54 Subdir: noarch Gathering repodata + 2024-12-15T20:11:54 noarch Writing pre-patch repodata + 2024-12-15T20:11:54 noarch Applying patch instructions + 2024-12-15T20:11:54 noarch Writing patched repodata + 2024-12-15T20:11:54 noarch Building current_repodata subset + 2024-12-15T20:11:54 noarch Writing current_repodata subset + 2024-12-15T20:11:54 noarch Writing index HTML + /opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (/opt/recipe/meta.yaml). + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml + Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for pulchra + Reloading output folder: ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder: ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['pulchra-3.06-h7b50bb2_5.tar.bz2'] + Reloading output folder: ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/pulchra_1734293514964/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder: ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder: ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/pulchra_1734293514964/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.43-h4bf12b8_2 conda-forge + binutils_linux-64: 2.43-h4852527_2 conda-forge + gcc_impl_linux-64: 13.3.0-hfea6d02_1 conda-forge + gcc_linux-64: 13.3.0-hc28eda2_7 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libsanitizer: 13.3.0-heb74ff8_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: download.cgi?pulchra_306_7b3deb43d3.tgz + Downloading http://www.pirx.com/cgi-bin/download.cgi?pulchra_306.tgz + WARNING: Error: HTTP 403 FORBIDDEN for url + Elapsed: 00:00.042521 + CF-RAY: 8f291807ae696212-ORD + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download http://www.pirx.com/cgi-bin/download.cgi?pulchra_306.tgz +# Last 100 lines of the build log. +category: |- + source download error diff --git a/recipes/pulchra/meta.yaml b/recipes/pulchra/meta.yaml index ceab582a45483..e22b16662ccee 100644 --- a/recipes/pulchra/meta.yaml +++ b/recipes/pulchra/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 skip: true # [osx] source: diff --git a/recipes/pullseq/build_failure.osx-64.yaml b/recipes/pullseq/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..764f1ab3264b9 --- /dev/null +++ b/recipes/pullseq/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 20178f7a04cb06f99848d7d4184e953604e96959cd1b15f3e72e267d258f1ef9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + Usable autoreconf found, running + checking for a BSD-compatible install... /usr/bin/install -c + checking whether sleep supports fractional seconds... yes + checking filesystem timestamp resolution... 0.01 + checking whether build environment is sane... yes + checking for a race-free mkdir -p... ./install-sh -c -d + checking for gawk... no + checking for mawk... no + checking for nawk... no + checking for awk... awk + checking whether make sets $(MAKE)... yes + checking whether make supports nested variables... yes + checking xargs -n works... yes + checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang + checking whether the C compiler works... yes + checking for C compiler default output file name... a.out + checking for suffix of executables... + checking whether we are cross compiling... no + checking for suffix of object files... o + checking whether the compiler supports GNU C... yes + checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes + checking for x86_64-apple-darwin13.4.0-clang option to enable C11 features... none needed + checking whether x86_64-apple-darwin13.4.0-clang understands -c and -o together... yes + checking whether make supports the include directive... yes (GNU style) + checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 + checking for gzopen in -lz... yes + checking for pcre_compile in -lpcre... yes + checking for stdio.h... yes + checking for stdlib.h... yes + checking for string.h... yes + checking for inttypes.h... yes + checking for stdint.h... yes + checking for strings.h... yes + checking for sys/stat.h... yes + checking for sys/types.h... yes + checking for unistd.h... yes + checking for inttypes.h... (cached) yes + checking for limits.h... yes + checking for stddef.h... yes + checking for stdlib.h... (cached) yes + checking for string.h... (cached) yes + checking for pcre.h... yes + checking for inline... inline + checking for size_t... yes + checking for ssize_t... yes + checking for uint16_t... yes + checking for uint32_t... yes + checking for uint8_t... yes + checking for ptrdiff_t... yes + checking build system type... x86_64-apple-darwin13.4.0 + checking host system type... x86_64-apple-darwin13.4.0 + checking for GNU libc compatible malloc... (cached) yes + checking for GNU libc compatible realloc... (cached) yes + checking for strlen... yes + checking for memset... yes + checking for strchr... yes + checking for strerror... yes + checking for strtol... yes + checking that generated files are newer than configure... done + configure: creating ./config.status + config.status: creating Makefile + config.status: creating src/Makefile + config.status: creating src/config.h + config.status: executing depfiles commands + Making all in src + make[1]: Entering directory '$SRC_DIR/src' + make all-am + make[2]: Entering directory '$SRC_DIR/src' + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pullseq-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT hash.o -MD -MP -MF .deps/hash.Tpo -c -o hash.o hash.c + mv -f .deps/hash.Tpo .deps/hash.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pullseq-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT output.o -MD -MP -MF .deps/output.Tpo -c -o output.o output.c + mv -f .deps/output.Tpo .deps/output.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pullseq-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT size_filter.o -MD -MP -MF .deps/size_filter.Tpo -c -o size_filter.o size_filter.c + mv -f .deps/size_filter.Tpo .deps/size_filter.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pullseq-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT search_header.o -MD -MP -MF .deps/search_header.Tpo -c -o search_header.o search_header.c + mv -f .deps/search_header.Tpo .deps/search_header.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pullseq-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT file_read.o -MD -MP -MF .deps/file_read.Tpo -c -o file_read.o file_read.c + mv -f .deps/file_read.Tpo .deps/file_read.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/pullseq-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT pull_by_re.o -MD -MP -MF .deps/pull_by_re.Tpo -c -o pull_by_re.o pull_by_re.c + make[2]: Leaving directory '$SRC_DIR/src' + make[1]: Leaving directory '$SRC_DIR/src' +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/pullseq/meta.yaml b/recipes/pullseq/meta.yaml index 0f9e16f0eb3ab..235bb6376669b 100644 --- a/recipes/pullseq/meta.yaml +++ b/recipes/pullseq/meta.yaml @@ -7,7 +7,7 @@ source: md5: a4ef6e5b4b5c77be2ef5d444c44fb6c0 build: - number: 9 + number: 10 requirements: build: diff --git a/recipes/py2bit/meta.yaml b/recipes/py2bit/meta.yaml index 810b068f6474a..b123f70220a53 100644 --- a/recipes/py2bit/meta.yaml +++ b/recipes/py2bit/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.3.0" build: - number: 10 + number: 11 run_exports: - {{ pin_subpackage('py2bit', max_pin='x.x') }} diff --git a/recipes/py_fasta_validator/meta.yaml b/recipes/py_fasta_validator/meta.yaml index d5cea65e8a4c2..dfef902736541 100644 --- a/recipes/py_fasta_validator/meta.yaml +++ b/recipes/py_fasta_validator/meta.yaml @@ -10,7 +10,7 @@ source: sha256: "ca29c20e1be31ef190f923b62ddb7fccda8c1c3ba9cf699a6ccaccce10ea011a" build: - number: 4 + number: 5 skip: True # [py < 37] script: "{{ PYTHON }} -m pip install --ignore-installed --no-cache-dir -vvv ." diff --git a/recipes/pyabpoa/meta.yaml b/recipes/pyabpoa/meta.yaml index 78b8f0a130346..4a18349d67261 100644 --- a/recipes/pyabpoa/meta.yaml +++ b/recipes/pyabpoa/meta.yaml @@ -10,7 +10,7 @@ source: sha256: bb97de2dbdec014f2fb24beb0c85fa0b2073f717f3b68639e1edd89239729e6c build: - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/pybbi/meta.yaml b/recipes/pybbi/meta.yaml index 6bbaf82e9fbe0..e9cb372643159 100644 --- a/recipes/pybbi/meta.yaml +++ b/recipes/pybbi/meta.yaml @@ -10,7 +10,7 @@ source: sha256: "6a193dcd0d4d4575c258d6cd5d2d7c5368a5cf58e939d8faae9f8fe192373a5c" build: - number: 1 + number: 2 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} diff --git a/recipes/pybedgraph/meta.yaml b/recipes/pybedgraph/meta.yaml index 8fb405cf00569..61c4a48e84620 100644 --- a/recipes/pybedgraph/meta.yaml +++ b/recipes/pybedgraph/meta.yaml @@ -10,7 +10,7 @@ source: sha256: b3064790c4b47439846ad2d121ba6f9b1b0c2b4810f5aaa7fff8138fe13c86a9 build: - number: 5 + number: 6 skip: True # [py27] script: "rm pyBedGraph/*.c; {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" diff --git a/recipes/pybedlite/meta.yaml b/recipes/pybedlite/meta.yaml index 711845645471b..b729025260cd0 100644 --- a/recipes/pybedlite/meta.yaml +++ b/recipes/pybedlite/meta.yaml @@ -10,7 +10,7 @@ source: sha256: c87a246a673f69b929103176b744b6ad6978b63fae45f1ca6becc315a72d671c build: - number: 1 + number: 2 script: {{ PYTHON }} -m pip install . -vvv --no-deps run_exports: - {{ pin_subpackage('pybedlite', max_pin="x") }} diff --git a/recipes/pybigtools/meta.yaml b/recipes/pybigtools/meta.yaml index 2e0ee831f8c85..f1c8fbe4b4a95 100644 --- a/recipes/pybigtools/meta.yaml +++ b/recipes/pybigtools/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('pybigtools', max_pin="x.x") }} diff --git a/recipes/pycluster/meta.yaml b/recipes/pycluster/meta.yaml index 13b39a816cc9f..31155d7887482 100644 --- a/recipes/pycluster/meta.yaml +++ b/recipes/pycluster/meta.yaml @@ -7,7 +7,7 @@ source: md5: 9ae5425af709724e289546619d1838c8 build: - number: 8 + number: 9 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: diff --git a/recipes/pydna_repeatfinder/meta.yaml b/recipes/pydna_repeatfinder/meta.yaml index 23c9b137b3fbf..72300a9e7b9e6 100644 --- a/recipes/pydna_repeatfinder/meta.yaml +++ b/recipes/pydna_repeatfinder/meta.yaml @@ -12,7 +12,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 script: "{{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv" entry_points: - pydna_repeatfinder = pydna_repeatfinder.cli:run diff --git a/recipes/pydustmasker/meta.yaml b/recipes/pydustmasker/meta.yaml index 9ba1605e6cfb3..f6d27953a6f4c 100644 --- a/recipes/pydustmasker/meta.yaml +++ b/recipes/pydustmasker/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 03f875b3cdb595394eabed823d80d4da50d687f3ade4a017ff0159ce277ae331 build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/pyfamsa/meta.yaml b/recipes/pyfamsa/meta.yaml index a08d3a6682906..2a612275b5daa 100644 --- a/recipes/pyfamsa/meta.yaml +++ b/recipes/pyfamsa/meta.yaml @@ -10,7 +10,7 @@ source: sha256: d5492e885c71dedfd3ddb1fc16b02981388f7fcb7dbb152c37b8bffa5f760ce5 build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv" run_exports: - {{ pin_subpackage('pyfamsa', max_pin="x.x") }} diff --git a/recipes/pyfastani/meta.yaml b/recipes/pyfastani/meta.yaml index 6449236f384f7..8f43db85d55a7 100644 --- a/recipes/pyfastani/meta.yaml +++ b/recipes/pyfastani/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 255e890d3ee6bbd051bb94d71a5245703b254be1ff2b5dc6789d28b715ec5fa9 build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/pyfastx/build.sh b/recipes/pyfastx/build.sh new file mode 100644 index 0000000000000..2e3864f7708c5 --- /dev/null +++ b/recipes/pyfastx/build.sh @@ -0,0 +1,5 @@ +#!/bin/bash +if [[ "$(uname)" == "Darwin" ]]; then + export CFLAGS="${CFLAGS} -fno-define-target-os-macros" +fi +$PYTHON -m pip install . --no-deps -vvv \ No newline at end of file diff --git a/recipes/pyfastx/meta.yaml b/recipes/pyfastx/meta.yaml index 2260142b39ee1..d933f65a256f6 100644 --- a/recipes/pyfastx/meta.yaml +++ b/recipes/pyfastx/meta.yaml @@ -12,8 +12,6 @@ source: build: number: 0 - script: {{ PYTHON }} -m pip install . --no-deps -vvv - skip: True # [py < 36] entry_points: - pyfastx = pyfastxcli:main run_exports: @@ -26,6 +24,7 @@ requirements: - python - zlib - pip + - setuptools run: - python diff --git a/recipes/pygtftk/meta.yaml b/recipes/pygtftk/meta.yaml index c471dc44301ef..5030a06fa5c2c 100644 --- a/recipes/pygtftk/meta.yaml +++ b/recipes/pygtftk/meta.yaml @@ -9,7 +9,7 @@ source: sha256: e31b1db156a2d20427c03b6ad868ef2e90a9a834a8842feb7fa284c9eb0690b7 build: - number: 3 + number: 4 skip: True # [py != 39] script: {{ PYTHON }} -m pip install . --no-deps -vv run_exports: diff --git a/recipes/pyhmmer/meta.yaml b/recipes/pyhmmer/meta.yaml index 16152427e6b13..ef5da8909981d 100644 --- a/recipes/pyhmmer/meta.yaml +++ b/recipes/pyhmmer/meta.yaml @@ -10,7 +10,7 @@ source: sha256: bf8e97ce8da6fb5850298f3074640f3e998d5a655877f865c1592eb057dc7921 build: - number: 0 + number: 1 skip: True # [py2k or win] script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv" run_exports: diff --git a/recipes/pyjess/meta.yaml b/recipes/pyjess/meta.yaml index 97fee422bb2a0..d2bd512e6baf9 100644 --- a/recipes/pyjess/meta.yaml +++ b/recipes/pyjess/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 93777c121892e86ef33e266feb057850309d4423edbfbdcab13a97c081ba27ea build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv" run_exports: - {{ pin_subpackage("pyjess", max_pin="x.x") }} diff --git a/recipes/pyopal/meta.yaml b/recipes/pyopal/meta.yaml index f0cb6488709ba..0160db7968e7a 100644 --- a/recipes/pyopal/meta.yaml +++ b/recipes/pyopal/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 690b46fb158f10c663e14cf51a50060a27adb51e113ed1cdfbe50b4b9b1d7689 build: - number: 0 + number: 1 skip: True #[py2k] run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/pyprophet/meta.yaml b/recipes/pyprophet/meta.yaml index 530f132015959..4e2e3d37077dd 100644 --- a/recipes/pyprophet/meta.yaml +++ b/recipes/pyprophet/meta.yaml @@ -12,7 +12,7 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage(name, max_pin="x") }} entry_points: diff --git a/recipes/pyrle/meta.yaml b/recipes/pyrle/meta.yaml index e8ddb549361da..e8dafe7457e7d 100644 --- a/recipes/pyrle/meta.yaml +++ b/recipes/pyrle/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 32ccdbbe594377c7b6a2e04b11fedd7886b330468f6fa378a5e06e070763f4ba build: - number: 1 + number: 2 skip: True # [py2k] script: python setup.py install --single-version-externally-managed --record=record.txt run_exports: diff --git a/recipes/pyrodigal/meta.yaml b/recipes/pyrodigal/meta.yaml index bf4a900db8352..3d7c589c849a6 100644 --- a/recipes/pyrodigal/meta.yaml +++ b/recipes/pyrodigal/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 3e226f743c960d4d30c46ae6868aff7e2a6b98f8d837cfbd2637568569b21f78 build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv" entry_points: - pyrodigal = pyrodigal.cli:main diff --git a/recipes/pysais/meta.yaml b/recipes/pysais/meta.yaml index 08fa728a516a3..19c30d47bb7dd 100644 --- a/recipes/pysais/meta.yaml +++ b/recipes/pysais/meta.yaml @@ -11,7 +11,7 @@ source: build: script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation - number: 1 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/pysam/meta.yaml b/recipes/pysam/meta.yaml index 3240440cf1aab..b17df5cfbf93e 100644 --- a/recipes/pysam/meta.yaml +++ b/recipes/pysam/meta.yaml @@ -11,7 +11,7 @@ source: - arm_hwcap.patch build: - number: 2 + number: 3 skip: True # [py2k] binary_relocation: False # [linux] run_exports: diff --git a/recipes/pysamstats/meta.yaml b/recipes/pysamstats/meta.yaml index 632958c1c7358..561abd4dcb364 100644 --- a/recipes/pysamstats/meta.yaml +++ b/recipes/pysamstats/meta.yaml @@ -7,7 +7,7 @@ source: md5: 050294fe9fe99aae3b07ea28f6cbe449 build: - number: 12 + number: 13 run_exports: - {{ pin_subpackage('pysamstats', max_pin="x") }} diff --git a/recipes/pyseq-align/meta.yaml b/recipes/pyseq-align/meta.yaml index e5e77e8dde581..83236e831b89c 100644 --- a/recipes/pyseq-align/meta.yaml +++ b/recipes/pyseq-align/meta.yaml @@ -10,7 +10,7 @@ source: sha256: "d9d450269d492c9a83ea9b795b14347140f12153ea93e2e5ed409606c5ac9e4d" build: - number: 4 + number: 5 skip: True # [py2k] script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " diff --git a/recipes/pyslow5/meta.yaml b/recipes/pyslow5/meta.yaml index 087931ecc29c0..994acfff8422e 100644 --- a/recipes/pyslow5/meta.yaml +++ b/recipes/pyslow5/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('pyslow5', max_pin="x") }} diff --git a/recipes/pyspoa/meta.yaml b/recipes/pyspoa/meta.yaml index a8d2bdcf48d67..3e42d59d03eb7 100644 --- a/recipes/pyspoa/meta.yaml +++ b/recipes/pyspoa/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 skip: True # [py < 38] script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir run_exports: diff --git a/recipes/pytabix/meta.yaml b/recipes/pytabix/meta.yaml index 827d74ce191af..6ecb20c2a2603 100644 --- a/recipes/pytabix/meta.yaml +++ b/recipes/pytabix/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 6 + number: 7 script: '{{ PYTHON }} -m pip install . --no-deps -vv' run_exports: - {{ pin_subpackage('pytabix', max_pin='x.x') }} diff --git a/recipes/python-bioext/build_failure.osx-arm64.yaml b/recipes/python-bioext/build_failure.osx-arm64.yaml new file mode 100644 index 0000000000000..b2eeeb53df15d --- /dev/null +++ b/recipes/python-bioext/build_failure.osx-arm64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 314a635304d8b1330f03e5537af612850d3e40249afbe97bc51d8bbb1b84f7ab # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + copying BioExt/data/fonts/ttf/Roboto-Regular.ttf -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/fonts/ttf + copying BioExt/data/fonts/ttf/Roboto-MediumItalic.ttf -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/fonts/ttf + copying BioExt/data/fonts/ttf/Roboto-BoldCondensed.ttf -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/fonts/ttf + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + copying BioExt/data/fonts/ttf/Roboto-BoldCondensedItalic.ttf -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/fonts/ttf + copying BioExt/data/fonts/ttf/Roboto-Condensed.ttf -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/fonts/ttf + copying BioExt/data/fonts/ttf/Roboto-ThinItalic.ttf -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/fonts/ttf + copying BioExt/data/fonts/ttf/Roboto-BoldItalic.ttf -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/fonts/ttf + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/python-bioext_1734473453914/work/conda_build.sh']' returned non-zero exit status 1. + copying BioExt/data/fonts/ttf/Roboto-LightItalic.ttf -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/fonts/ttf + copying BioExt/data/fonts/ttf/Roboto-CondensedItalic.ttf -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/fonts/ttf + copying BioExt/data/fonts/ttf/Roboto-Italic.ttf -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/fonts/ttf + copying BioExt/data/fonts/ttf/Roboto-BlackItalic.ttf -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/fonts/ttf + copying BioExt/data/fonts/ttf/Roboto-Bold.ttf -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/fonts/ttf + copying BioExt/data/fonts/ttf/Roboto-Thin.ttf -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/fonts/ttf + copying BioExt/data/fonts/ttf/Roboto-Black.ttf -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/fonts/ttf + creating build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/scorematrices + copying BioExt/data/scorematrices/PAM200.txt -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/scorematrices + copying BioExt/data/scorematrices/BLOSUM62.txt -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/scorematrices + copying BioExt/data/scorematrices/HIV_BETWEEN_F.txt -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/scorematrices + copying BioExt/data/scorematrices/PAM250.txt -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/scorematrices + creating build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-methyltransferase.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-ORF5.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-M.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-nsp4.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-ORF1a.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-exonuclease.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-ORF3a.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-ORF7a.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-ORF10.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-endornase.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-nsp2.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-ORF7b.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-RdRp.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-nsp6.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-nsp7.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-ORF8.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-ORF1b.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-E.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-nsp10.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-nsp3.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-helicase.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-threeC.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-nsp8.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-leader.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-N.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-S.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-ORF6.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + copying BioExt/data/references/cov2/CoV2-nsp9.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/cov2 + creating build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/hxb2 + copying BioExt/data/references/hxb2/HXB2_vpu.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/hxb2 + copying BioExt/data/references/hxb2/HXB2_env.gb -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/hxb2 + copying BioExt/data/references/hxb2/HXB2_pr.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/hxb2 + copying BioExt/data/references/hxb2/HXB2_rev.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/hxb2 + copying BioExt/data/references/hxb2/HXB2_prrt.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/hxb2 + copying BioExt/data/references/hxb2/HXB2_nef.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/hxb2 + copying BioExt/data/references/hxb2/HXB2_int.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/hxb2 + copying BioExt/data/references/hxb2/HXB2_pol.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/hxb2 + copying BioExt/data/references/hxb2/HXB2_vif.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/hxb2 + copying BioExt/data/references/hxb2/HXB2_vpr.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/hxb2 + copying BioExt/data/references/hxb2/HXB2_gag.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/hxb2 + copying BioExt/data/references/hxb2/HXB2_rt.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/hxb2 + copying BioExt/data/references/hxb2/HXB2_tat.fa -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/hxb2 + creating build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/nl4-3 + copying BioExt/data/references/nl4-3/NL4_3_gag.fna -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/nl4-3 + copying BioExt/data/references/nl4-3/NL4_3_nef.fna -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/nl4-3 + copying BioExt/data/references/nl4-3/NL4_3_vpr.fna -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/nl4-3 + copying BioExt/data/references/nl4-3/NL4_3_vif.fna -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/nl4-3 + copying BioExt/data/references/nl4-3/NL4_3_rev.fna -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/nl4-3 + copying BioExt/data/references/nl4-3/NL4_3_vpu.fna -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/nl4-3 + copying BioExt/data/references/nl4-3/NL4_3_prrt.fna -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/nl4-3 + copying BioExt/data/references/nl4-3/NL4_3_env.fna -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/nl4-3 + copying BioExt/data/references/nl4-3/NL4_3_tat.fna -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/nl4-3 + copying BioExt/data/references/nl4-3/NL4_3_pol.fna -> build/lib.macosx-11.0-arm64-cpython-39/BioExt/data/references/nl4-3 + running build_ext + building 'BioExt.align._align' extension + creating build/temp.macosx-11.0-arm64-cpython-39/BioExt/align + arm64-apple-darwin20.0.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -arch arm64 -fPIC -O2 -isystem $PREFIX/include -arch arm64 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/python-bioext-0.21.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -IBioExt/align -I$PREFIX/lib/python3.9/site-packages/numpy/core/include -I$PREFIX/include/python3.9 -c BioExt/align/_align.c -o build/temp.macosx-11.0-arm64-cpython-39/BioExt/align/_align.o -O3 -I. + arm64-apple-darwin20.0.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -arch arm64 -fPIC -O2 -isystem $PREFIX/include -arch arm64 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/python-bioext-0.21.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -IBioExt/align -I$PREFIX/lib/python3.9/site-packages/numpy/core/include -I$PREFIX/include/python3.9 -c BioExt/align/alignment.c -o build/temp.macosx-11.0-arm64-cpython-39/BioExt/align/alignment.o -O3 -I. + arm64-apple-darwin20.0.0-clang -bundle -undefined dynamic_lookup -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/python-bioext-0.21.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 build/temp.macosx-11.0-arm64-cpython-39/BioExt/align/_align.o build/temp.macosx-11.0-arm64-cpython-39/BioExt/align/alignment.o -lm -o build/lib.macosx-11.0-arm64-cpython-39/BioExt/align/_align.cpython-39-darwin.so + building 'BioExt.merge._merge' extension + creating build/temp.macosx-11.0-arm64-cpython-39/BioExt/merge + arm64-apple-darwin20.0.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -arch arm64 -fPIC -O2 -isystem $PREFIX/include -arch arm64 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/python-bioext-0.21.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -IBioExt/merge -I$PREFIX/include/python3.9 -c BioExt/merge/_merge.c -o build/temp.macosx-11.0-arm64-cpython-39/BioExt/merge/_merge.o -O3 -I. + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/python-bioext-0.21.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -IBioExt/merge -I$PREFIX/include/python3.9 -c BioExt/merge/merge.cpp -o build/temp.macosx-11.0-arm64-cpython-39/BioExt/merge/merge.o -O3 -I. + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/python-bioext-0.21.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -bundle -undefined dynamic_lookup -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/python-bioext-0.21.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 build/temp.macosx-11.0-arm64-cpython-39/BioExt/merge/_merge.o build/temp.macosx-11.0-arm64-cpython-39/BioExt/merge/merge.o -o build/lib.macosx-11.0-arm64-cpython-39/BioExt/merge/_merge.cpython-39-darwin.so + building 'BioExt.rateclass._rateclass' extension + creating build/temp.macosx-11.0-arm64-cpython-39/BioExt/rateclass + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/python-bioext-0.21.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -IBioExt/rateclass -I$PREFIX/include/python3.9 -c BioExt/rateclass/_rateclass.cpp -o build/temp.macosx-11.0-arm64-cpython-39/BioExt/rateclass/_rateclass.o -O3 -I. + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/python-bioext-0.21.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -IBioExt/rateclass -I$PREFIX/include/python3.9 -c BioExt/rateclass/rateclass.cpp -o build/temp.macosx-11.0-arm64-cpython-39/BioExt/rateclass/rateclass.o -O3 -I. + arm64-apple-darwin20.0.0-clang -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/python-bioext-0.21.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 -bundle -undefined dynamic_lookup -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/python-bioext-0.21.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 build/temp.macosx-11.0-arm64-cpython-39/BioExt/rateclass/_rateclass.o build/temp.macosx-11.0-arm64-cpython-39/BioExt/rateclass/rateclass.o -o build/lib.macosx-11.0-arm64-cpython-39/BioExt/rateclass/_rateclass.cpython-39-darwin.so +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/python-bioext/meta.yaml b/recipes/python-bioext/meta.yaml index 0ea3844b07ae1..6452b68bdf6a5 100644 --- a/recipes/python-bioext/meta.yaml +++ b/recipes/python-bioext/meta.yaml @@ -14,7 +14,7 @@ source: - osx-freetype.patch # [osx] build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("python-bioext", max_pin="x.x") }} @@ -27,6 +27,7 @@ requirements: - pip - cython - numpy + - setuptools run: - freetype - python diff --git a/recipes/python-edlib/meta.yaml b/recipes/python-edlib/meta.yaml index 468f2b9a27044..97ed43065634c 100644 --- a/recipes/python-edlib/meta.yaml +++ b/recipes/python-edlib/meta.yaml @@ -9,7 +9,7 @@ source: sha256: b0fb6e85882cab02208ccd6daa46f80cb9ff1d05764e91bf22920a01d7a6fbfa build: - number: 0 + number: 1 script: "EDLIB_USE_CYTHON=1 {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" run_exports: - {{ pin_subpackage("python-edlib", max_pin="x") }} diff --git a/recipes/python-hppy/build_failure.osx-64.yaml b/recipes/python-hppy/build_failure.osx-64.yaml deleted file mode 100644 index 2206f06c5a1d3..0000000000000 --- a/recipes/python-hppy/build_failure.osx-64.yaml +++ /dev/null @@ -1,105 +0,0 @@ -recipe_sha: e93d9813de6c2fbff2b946a68f91bba2c6d0684a3eeaecaf363fba1deaa7d198 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: dependency issue -log: |- - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("python-hyphy-python==0.1.9=py27h8c18e5c_0"), MatchSpec("python[version='>=2.7,<2.8.0a0']")} - Encountered problems while solving: - - package python-hyphy-python-0.1.9-py27h8c18e5c_0 requires python >=2.7,<2.8.0a0, but none of the providers can be installed - - Could not solve for environment specs - The following packages are incompatible - python-hyphy-python >=0.1.8 is installable with the potential options - python-hyphy-python 0.1.9 would require - python >=2.7,<2.8.0a0 , which can be installed; - python-hyphy-python [0.1.10|0.1.9] would require - python_abi 2.7.* *_cp27m, which can be installed; - python-hyphy-python [0.1.10|0.1.11|0.1.12] would require - python_abi 3.10.* *_cp310, which can be installed; - python-hyphy-python [0.1.10|0.1.11|0.1.9] would require - python_abi 3.6.* *_cp36m, which can be installed; - python-hyphy-python [0.1.10|0.1.11|0.1.9] would require - python_abi 3.7.* *_cp37m, which can be installed; - python-hyphy-python [0.1.10|0.1.11|0.1.12|0.1.9] would require - python_abi 3.8.* *_cp38, which can be installed; - python-hyphy-python [0.1.10|0.1.11|0.1.12] would require - python_abi 3.9.* *_cp39, which can be installed; - python-hyphy-python 0.1.9 would require - python >=3.5,<3.6.0a0 , which can be installed; - python-hyphy-python 0.1.9 would require - python >=3.6,<3.7.0a0 , which can be installed; - python-hyphy-python 0.1.9 would require - python >=3.7,<3.8.0a0 , which can be installed; - python >=3.11,<3.12.0a0 is not installable because it requires - python_abi 3.11.* *_cp311, which conflicts with any installable versions previously reported. - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2409, in build - create_build_envs(top_level_pkg, notest) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2247, in create_build_envs - raise e - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2220, in create_build_envs - environ.get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions - precs = _install_actions(prefix, index, specs)["LINK"] - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions - txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction - unlink_precs, link_precs = self.solve_for_diff( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff - final_precs = self.solve_final_state( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state - out_state = self._solving_loop(in_state, out_state, index) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop - solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt - new_conflicts = self._maybe_raise_for_problems( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems - self._maybe_raise_for_conda_build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build - raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("python-hyphy-python==0.1.9=py27h8c18e5c_0"), MatchSpec("python[version='>=2.7,<2.8.0a0']")} - Encountered problems while solving: - - package python-hyphy-python-0.1.9-py27h8c18e5c_0 requires python >=2.7,<2.8.0a0, but none of the providers can be installed - - Could not solve for environment specs - The following packages are incompatible - python-hyphy-python >=0.1.8 is installable with the potential options - python-hyphy-python 0.1.9 would require - python >=2.7,<2.8.0a0 , which can be installed; - python-hyphy-python [0.1.10|0.1.9] would require - python_abi 2.7.* *_cp27m, which can be installed; - python-hyphy-python [0.1.10|0.1.11|0.1.12] would require - python_abi 3.10.* *_cp310, which can be installed; - python-hyphy-python [0.1.10|0.1.11|0.1.9] would require - python_abi 3.6.* *_cp36m, which can be installed; - python-hyphy-python [0.1.10|0.1.11|0.1.9] would require - python_abi 3.7.* *_cp37m, which can be installed; - python-hyphy-python [0.1.10|0.1.11|0.1.12|0.1.9] would require - python_abi 3.8.* *_cp38, which can be installed; - python-hyphy-python [0.1.10|0.1.11|0.1.12] would require - python_abi 3.9.* *_cp39, which can be installed; - python-hyphy-python 0.1.9 would require - python >=3.5,<3.6.0a0 , which can be installed; - python-hyphy-python 0.1.9 would require - python >=3.6,<3.7.0a0 , which can be installed; - python-hyphy-python 0.1.9 would require - python >=3.7,<3.8.0a0 , which can be installed; - python >=3.11,<3.12.0a0 is not installable because it requires - python_abi 3.11.* *_cp311, which conflicts with any installable versions previously reported. -# Last 100 lines of the build log. diff --git a/recipes/python-hppy/meta.yaml b/recipes/python-hppy/meta.yaml index 25d0459cfe20c..b901783eee9e8 100644 --- a/recipes/python-hppy/meta.yaml +++ b/recipes/python-hppy/meta.yaml @@ -11,7 +11,7 @@ source: build: script: {{ PYTHON }} -m pip install . -vv - number: 1 + number: 2 requirements: build: diff --git a/recipes/python-hyphy-python/meta.yaml b/recipes/python-hyphy-python/meta.yaml index 6d17c7fcfe6e9..aef47d96527b2 100644 --- a/recipes/python-hyphy-python/meta.yaml +++ b/recipes/python-hyphy-python/meta.yaml @@ -12,7 +12,7 @@ source: - 0001-importlib.patch build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('python-hyphy-python', max_pin="x.x") }} diff --git a/recipes/python-msgpack/meta.yaml b/recipes/python-msgpack/meta.yaml index ed09391704528..0e938da70aff2 100644 --- a/recipes/python-msgpack/meta.yaml +++ b/recipes/python-msgpack/meta.yaml @@ -7,7 +7,7 @@ source: url: https://files.pythonhosted.org/packages/81/9c/0036c66234482044070836cc622266839e2412f8108849ab0bfdeaab8578/msgpack-{{ version }}.tar.gz sha256: 4008c72f5ef2b7936447dcb83db41d97e9791c83221be13d5e19db0796df1972 build: - number: 10 + number: 11 run_exports: - {{ pin_subpackage('python-msgpack', max_pin='x.x') }} requirements: diff --git a/recipes/pytriangle/meta.yaml b/recipes/pytriangle/meta.yaml index 97e7e6f92071c..5f12c1230de6c 100644 --- a/recipes/pytriangle/meta.yaml +++ b/recipes/pytriangle/meta.yaml @@ -7,7 +7,7 @@ source: git_rev: f87b411 build: - number: 9 + number: 10 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv test: diff --git a/recipes/pytrimal/meta.yaml b/recipes/pytrimal/meta.yaml index a1d08ae93515a..a835961d9facf 100644 --- a/recipes/pytrimal/meta.yaml +++ b/recipes/pytrimal/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 2331e67a74f3144d82373b6a79f42198f6632bd1b5025ab01cdd3eb527ef88cf build: - number: 1 + number: 2 script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv" run_exports: - {{ pin_subpackage('pytrimal', max_pin="x.x") }} diff --git a/recipes/pywgsim/build_failure.linux-64.yaml b/recipes/pywgsim/build_failure.linux-64.yaml deleted file mode 100644 index 2db726c5cbc65..0000000000000 --- a/recipes/pywgsim/build_failure.linux-64.yaml +++ /dev/null @@ -1,105 +0,0 @@ -recipe_sha: 8d9e5e59c6ea28dd0859351ab4bad2461cbb730265c8d7c93e8d94a561080586 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: compiler error -log: |2- - reading manifest template 'MANIFEST.in' - writing manifest file 'pywgsim.egg-info/SOURCES.txt' - copying pywgsim/wgsim_lib.c -> build/lib.linux-x86_64-cpython-38/pywgsim - copying pywgsim/wgsim_lib.pyx -> build/lib.linux-x86_64-cpython-38/pywgsim - creating build/lib.linux-x86_64-cpython-38/pywgsim/src - copying pywgsim/src/Makefile -> build/lib.linux-x86_64-cpython-38/pywgsim/src - copying pywgsim/src/kseq.h -> build/lib.linux-x86_64-cpython-38/pywgsim/src - copying pywgsim/src/wgsim_mod.c -> build/lib.linux-x86_64-cpython-38/pywgsim/src - copying pywgsim/src/wgsim_mod.h -> build/lib.linux-x86_64-cpython-38/pywgsim/src - running build_ext - building 'pywgsim.wgsim' extension - creating build/temp.linux-x86_64-cpython-38 - creating build/temp.linux-x86_64-cpython-38/pywgsim - creating build/temp.linux-x86_64-cpython-38/pywgsim/src - /opt/conda/conda-bld/pywgsim_1718134883721/_build_env/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/conda/conda-bld/pywgsim_1718134883721/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fPIC -O2 -isystem /opt/conda/conda-bld/pywgsim_1718134883721/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/conda-bld/pywgsim_1718134883721/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fdebug-prefix-map=/opt/conda/conda-bld/pywgsim_1718134883721/work=/usr/local/src/conda/pywgsim-0.5.2 -fdebug-prefix-map=/opt/conda/conda-bld/pywgsim_1718134883721/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/conda-bld/pywgsim_1718134883721/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include -fPIC -Ipywgsim/src -I/opt/conda/conda-bld/pywgsim_1718134883721/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include/python3.8 -c pywgsim/src/wgsim_mod.c -o build/temp.linux-x86_64-cpython-38/pywgsim/src/wgsim_mod.o - pywgsim/src/wgsim_mod.c:39:10: fatal error: zlib.h: No such file or directory - 39 | #include - | ^~~~~~~~ - compilation terminated. - /opt/conda/conda-bld/pywgsim_1718134883721/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.8/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'pywgsim.src' is absent from the packages configuration. - !! - - ******************************************************************************** - ############################ - # Package would be ignored # - ############################ - Python recognizes 'pywgsim.src' as an importable package[^1], - but it is absent from setuptools' packages configuration. - - This leads to an ambiguous overall configuration. If you want to distribute this - package, please make sure that 'pywgsim.src' is explicitly added - to the packages configuration field. - - Alternatively, you can also rely on setuptools' discovery methods - (for example by using find_namespace_packages(...)/find_namespace: - instead of find_packages(...)/find:). - - You can read more about "package discovery" on setuptools documentation page: - - - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html - - If you don't want 'pywgsim.src' to be distributed and are - already explicitly excluding 'pywgsim.src' via - find_namespace_packages(...)/find_namespace or find_packages(...)/find, - you can try to use exclude_package_data, or include-package-data=False in - combination with a more fine grained package-data configuration. - - You can read more about "package data files" on setuptools documentation page: - - - https://setuptools.pypa.io/en/latest/userguide/datafiles.html - - - [^1]: For Python, any directory (with suitable naming) can be imported, - even if it does not contain any .py files. - On the other hand, currently there is no concept of package data - directory, all directories are treated like packages. - ******************************************************************************** - - !! - check.warn(importable) - error: command '/opt/conda/conda-bld/pywgsim_1718134883721/_build_env/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1 - [1;31merror[0m: [1msubprocess-exited-with-error[0m - - [31m[0m [32mBuilding wheel for pywgsim [0m[1;32m([0m[32mpyproject.toml[0m[1;32m)[0m did not run successfully. - [31m[0m exit code: [1;36m1[0m - [31m>[0m See above for output. - - [1;35mnote[0m: This error originates from a subprocess, and is likely not a problem with pip. - [1;35mfull command[0m: [34m/opt/conda/conda-bld/pywgsim_1718134883721/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin/python /opt/conda/conda-bld/pywgsim_1718134883721/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/python3.8/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py build_wheel /tmp/tmpdpqqbkrp[0m - [1;35mcwd[0m: /opt/conda/conda-bld/pywgsim_1718134883721/work - Building wheel for pywgsim (pyproject.toml): finished with status 'error' - [31m ERROR: Failed building wheel for pywgsim[0m[31m - [0mFailed to build pywgsim - [31mERROR: Could not build wheels for pywgsim, which is required to install pyproject.toml-based projects[0m[31m - [0mException information: - Traceback (most recent call last): - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper - return func(self, options, args) - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/commands/install.py", line 429, in run - raise InstallationError( - pip._internal.exceptions.InstallationError: Could not build wheels for pywgsim, which is required to install pyproject.toml-based projects - Removed build tracker: '/tmp/pip-build-tracker-nmdku6cp' - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/pywgsim_1718134883721/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/pywgsim/meta.yaml b/recipes/pywgsim/meta.yaml index 423f649062f80..d109384ecef99 100644 --- a/recipes/pywgsim/meta.yaml +++ b/recipes/pywgsim/meta.yaml @@ -9,7 +9,9 @@ build: entry_points: - pywgsim=pywgsim.main:run script: {{ PYTHON }} -m pip install . -vv - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage('pywgsim', max_pin="x.x") }} source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pywgsim-{{ version }}.tar.gz @@ -22,6 +24,8 @@ requirements: - cython - pip - python + - zlib + - setuptools run: - plac - python diff --git a/recipes/qax/build_failure.linux-64.yaml b/recipes/qax/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..c7d77fbc5a577 --- /dev/null +++ b/recipes/qax/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: c756f8509e05f3cd8961f706cae2f23442d70e4bff68ccc53ad8a2f9fd56e607 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/qax-0.9.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/qax-0.9.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/qax-0.9.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + [[ linux-gnu == \d\a\r\w\i\n* ]] + mkdir -p /opt/conda/conda-bld/qax_1734293495993/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin + nimble build -y + Verifying dependencies for qax@0.9.6 + Prompt: No local packages.json found, download it from internet? -> [forced yes] + Downloading Official package list + Success Package list downloaded. + Installing docopt@any version + Downloading https://github.com/docopt/docopt.nim using git + Verifying dependencies for docopt@0.7.1 + Installing regex@>= 0.11.1 + Downloading https://github.com/nitely/nim-regex using git + Verifying dependencies for regex@0.26.0 + Installing unicodedb@>= 0.7.2 + Downloading https://github.com/nitely/nim-unicodedb using git + Verifying dependencies for unicodedb@0.13.0 + Installing unicodedb@0.13.0 + Success: unicodedb installed successfully. + Installing regex@0.26.0 + Success: regex installed successfully. + Installing docopt@0.7.1 + Success: docopt installed successfully. + Installing terminaltables@any version + Downloading https://github.com/xmonader/nim-terminaltables using git + Warning: The package has no tagged releases, downloading HEAD instead. + Verifying dependencies for terminaltables@0.1.1 + Installing terminaltables@0.1.1 + Success: terminaltables installed successfully. + Installing zip@any version + Downloading https://github.com/nim-lang/zip using git + Verifying dependencies for zip@0.3.1 + Installing zip@0.3.1 + Success: zip installed successfully. + Installing uuids@any version + Downloading https://github.com/pragmagic/uuids using git + Verifying dependencies for uuids@0.1.12 + Installing isaac@>= 0.1.3 + Downloading https://github.com/pragmagic/isaac using git + Verifying dependencies for isaac@0.1.3 + Installing isaac@0.1.3 + Success: isaac installed successfully. + Installing uuids@0.1.12 + Success: uuids installed successfully. + Building qax/bin/qax using c backend + /opt/conda/conda-bld/qax_1734293495993/work/lib/yaml/yaml/stream.nim(115, 3) Error: undeclared identifier: 'shallowCopy' + candidates (edit distance, scope distance); see '--spellSuggest': + (6, 4): 'alloc' + (6, 4): 'alloc0' + (6, 4): 'allocImpl' + Tip: 103 messages have been suppressed, use --verbose to show them. + nimble.nim(304) buildFromDir + + Error: Build failed for the package: qax + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/qax_1734293495993/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/qax_1734293495993/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/qax/build_failure.osx-64.yaml b/recipes/qax/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..d56a002a45dda --- /dev/null +++ b/recipes/qax/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: c756f8509e05f3cd8961f706cae2f23442d70e4bff68ccc53ad8a2f9fd56e607 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/qax_1734210735720/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/qax_1734210735720/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/qax_1734210735720/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/qax_1734210735720/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/qax-0.9.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/qax-0.9.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/qax-0.9.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/qax-0.9.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + Verifying dependencies for qax@0.9.6 + Prompt: No local packages.json found, download it from internet? -> [forced yes] + Downloading Official package list + Success Package list downloaded. + Installing docopt@any version + Downloading https://github.com/docopt/docopt.nim using git + Verifying dependencies for docopt@0.7.1 + Installing regex@>= 0.11.1 + Downloading https://github.com/nitely/nim-regex using git + Verifying dependencies for regex@0.26.0 + Installing unicodedb@>= 0.7.2 + Downloading https://github.com/nitely/nim-unicodedb using git + Verifying dependencies for unicodedb@0.13.0 + Installing unicodedb@0.13.0 + Success: unicodedb installed successfully. + Installing regex@0.26.0 + Success: regex installed successfully. + Installing docopt@0.7.1 + Success: docopt installed successfully. + Installing terminaltables@any version + Downloading https://github.com/xmonader/nim-terminaltables using git + Warning: The package has no tagged releases, downloading HEAD instead. + Verifying dependencies for terminaltables@0.1.1 + Installing terminaltables@0.1.1 + Success: terminaltables installed successfully. + Installing zip@any version + Downloading https://github.com/nim-lang/zip using git + Verifying dependencies for zip@0.3.1 + Installing zip@0.3.1 + Success: zip installed successfully. + Installing uuids@any version + Downloading https://github.com/pragmagic/uuids using git + Verifying dependencies for uuids@0.1.12 + Installing isaac@>= 0.1.3 + Downloading https://github.com/pragmagic/isaac using git + Verifying dependencies for isaac@0.1.3 + Installing isaac@0.1.3 + Success: isaac installed successfully. + Installing uuids@0.1.12 + Success: uuids installed successfully. + Building qax/bin/qax using c backend + Tip: 108 messages have been suppressed, use --verbose to show them. + nimble.nim(304) buildFromDir + + Error: Build failed for the package: qax +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/qax/meta.yaml b/recipes/qax/meta.yaml index 7bd3ad663543e..c73de8cdaead1 100644 --- a/recipes/qax/meta.yaml +++ b/recipes/qax/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256hash }} build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/qfilt/meta.yaml b/recipes/qfilt/meta.yaml index e8c0d44a3bb4e..681bbbb6c0d0f 100644 --- a/recipes/qfilt/meta.yaml +++ b/recipes/qfilt/meta.yaml @@ -1,7 +1,7 @@ {% set version = "0.0.1" %} build: - number: 6 + number: 7 package: name: qfilt diff --git a/recipes/qgrs-cpp/meta.yaml b/recipes/qgrs-cpp/meta.yaml index a5c1fe0bcc709..0e4762cad5c34 100644 --- a/recipes/qgrs-cpp/meta.yaml +++ b/recipes/qgrs-cpp/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/quast/meta.yaml b/recipes/quast/meta.yaml index bbe2024660d3b..cd5a107d204ee 100644 --- a/recipes/quast/meta.yaml +++ b/recipes/quast/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("quast", max_pin="x.x") }} diff --git a/recipes/quatradis/meta.yaml b/recipes/quatradis/meta.yaml index d66e518293ca6..8293cc5492d69 100644 --- a/recipes/quatradis/meta.yaml +++ b/recipes/quatradis/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 2f37287a97e7721a2f127373ea5ae67e147215aa91e73729133c3746fde2a0fa build: - number: 0 + number: 1 script: {{ PYTHON }} -m pip install -vvv --no-deps --no-build-isolation --no-cache-dir . run_exports: - {{ pin_subpackage('quatradis', max_pin="x") }} diff --git a/recipes/quickmerge/meta.yaml b/recipes/quickmerge/meta.yaml index 84c0712aa972b..35073927ba96e 100644 --- a/recipes/quickmerge/meta.yaml +++ b/recipes/quickmerge/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/quicksect/meta.yaml b/recipes/quicksect/meta.yaml index d697f65359be5..523f6334ba68c 100644 --- a/recipes/quicksect/meta.yaml +++ b/recipes/quicksect/meta.yaml @@ -10,7 +10,7 @@ source: sha256: "d3e65b55b7f48e6105b11b1e1d6f37ccbf8caecfc7d7db7aba73dfaf6d732a9c" build: - number: 10 + number: 11 script: rm -f src/*.c ; {{ PYTHON }} -m pip install --no-deps --ignore-installed . run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -40,4 +40,4 @@ about: extra: additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 diff --git a/recipes/quicktree/meta.yaml b/recipes/quicktree/meta.yaml index 8e9fe92a91c7a..3cf87a33da933 100644 --- a/recipes/quicktree/meta.yaml +++ b/recipes/quicktree/meta.yaml @@ -13,7 +13,7 @@ source: - patches/0002-Fix-segfault-in-sonLib-phylogeny-tests.patch build: - number: 6 + number: 7 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/r-DGEclustering/build_failure.linux-64.yaml b/recipes/r-DGEclustering/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..c99c1f9e135a6 --- /dev/null +++ b/recipes/r-DGEclustering/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 74f580c997a9e4e5a3c1a99417be3cbf1cd20dc4e959f1e35504a88f06a8e800 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - bioconductor-summarizedexperiment 1.36.0 r44hdfd78af_0 + - r-broom 1.0.7 r44hc72bb7e_0 + - r-dt 0.33 r44hc72bb7e_1 + - r-recipes 1.1.0 r44hc72bb7e_1 + - bioconductor-annotationdbi 1.68.0 r44hdfd78af_0 + - bioconductor-genomicalignments 1.42.0 r44h3df3fcb_0 + - r-caret 6.0_94 r44hdb488b9_2 + - r-modelr 0.1.11 r44hc72bb7e_2 + - bioconductor-annotate 1.84.0 r44hdfd78af_0 + - bioconductor-go.db 3.20.0 r44hdfd78af_0 + - bioconductor-rtracklayer 1.66.0 r44h15a9599_0 + - r-conquer 1.3.3 r44hb424bfc_4 + - r-doby 4.6.24 r44hc72bb7e_0 + - bioconductor-genomicfeatures 1.58.0 r44hdfd78af_0 + - bioconductor-gosemsim 2.32.0 r44he5774e6_0 + - bioconductor-gseabase 1.68.0 r44hdfd78af_0 + - bioconductor-topgo 2.58.0 r44hdfd78af_0 + - r-pbkrtest 0.5.3 r44hc72bb7e_0 + - r-quantreg 5.99.1 r44h9ad1c49_0 + - bioconductor-dose 4.0.0 r44hdfd78af_0 + - r-car 3.1_3 r44hc72bb7e_0 + - bioconductor-clusterprofiler 3.0.4 1 + - r-factominer 2.11 r44hdb488b9_0 + - r-intego 2.0 r44h9ee0642_6 + run: + - r-intego + - bioconductor-annotationdbi >=1.68.0,<1.69.0a0 + - r-reshape2 + - r-ggplot2 + - r-rlist + - bioconductor-gosemsim >=2.32.0,<2.33.0a0 + - bioconductor-clusterprofiler + - bioconductor-genomicfeatures >=1.58.0,<1.59.0a0 + - r-factominer + - r-base >=4.4,<4.5.0a0 + - r-base >=4.4,<4.5.0a0 + - r-cluster + test: + commands: + - $R -e "library('DGEclustering')" + about: + home: https://github.com/reneechou123/DGEclustering + license: MIT + summary: DGEclustering is an R package for multidimensional clustering of differential + gene expression datasets, and it integrates GO annotations to improve the clustering + result. + extra: + copy_test_source_files: true + final: true + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak + + + source tree in: /opt/conda/conda-bld/r-dgeclustering_1735779178685/work + export PREFIX=/opt/conda/conda-bld/r-dgeclustering_1735779178685/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/conda/conda-bld/r-dgeclustering_1735779178685/_build_env + export SRC_DIR=/opt/conda/conda-bld/r-dgeclustering_1735779178685/work + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/r-dgeclustering_1735779178685/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/R/library + * installing *source* package DGEclustering ... + ** using staged installation + ** R + ** inst + ** byte-compile and prepare package for lazy loading + During startup - Warning message: + Setting LC_TIME failed, using "C" + Error: package clusterProfiler was installed before R 4.0.0: please re-install it + Execution halted + ERROR: lazy loading failed for package DGEclustering + * removing /opt/conda/conda-bld/r-dgeclustering_1735779178685/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/R/library/DGEclustering + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/r-dgeclustering_1735779178685/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/r-dgeclustering_1735779178685/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/r-DGEclustering/build_failure.osx-64.yaml b/recipes/r-DGEclustering/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..dfc245bec0c5d --- /dev/null +++ b/recipes/r-DGEclustering/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 74f580c997a9e4e5a3c1a99417be3cbf1cd20dc4e959f1e35504a88f06a8e800 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Could not solve for environment specs + The following packages are incompatible + bioconductor-genomicfeatures is installable with the potential options + bioconductor-genomicfeatures [1.22.13|1.22.6] would require + r 3.2.2* , which does not exist (perhaps a missing channel); + bioconductor-genomicfeatures [1.24.5|1.26.0] would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-genomicfeatures 1.26.4 would require + r-base 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-genomicfeatures 1.26.4 would require + r-base 3.3.2* , which can be installed; + bioconductor-genomicfeatures [1.26.4|1.28.5|1.30.0|1.30.3] would require + r-base 3.4.1* , which can be installed; + bioconductor-genomicfeatures 1.32.3 would require + bioconductor-annotationdbi >=1.42.1,<1.44.0 with the potential options + bioconductor-annotationdbi 1.42.1 would require + r-base >=3.4.1,<3.4.2.0a0 , which can be installed; + bioconductor-annotationdbi 1.42.1 would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed; + bioconductor-genomicfeatures 1.34.1 would require + bioconductor-annotationdbi >=1.44.0,<1.45.0 , which can be installed; + bioconductor-xvector >=0.22.0,<0.23.0 , which requires + bioconductor-zlibbioc >=1.28.0,<1.29.0 , which requires + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed; + bioconductor-genomicfeatures [1.36.0|1.36.4] would require + bioconductor-annotationdbi >=1.46.0,<1.47.0 , which can be installed; + bioconductor-genomeinfodb >=1.20.0,<1.21.0 , which requires + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-genomicfeatures 1.38.0 would require + bioconductor-annotationdbi >=1.48.0,<1.49.0 , which can be installed; + bioconductor-rtracklayer >=1.46.0,<1.47.0 , which requires + bioconductor-genomicalignments >=1.22.0,<1.23.0 , which requires + bioconductor-summarizedexperiment >=1.16.0,<1.17.0 , which requires + bioconductor-delayedarray >=0.12.0,<0.13.0 , which requires + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-genomicfeatures 1.40.0 would require + bioconductor-annotationdbi >=1.50.0,<1.51.0 , which can be installed; + bioconductor-rtracklayer >=1.48.0,<1.49.0 , which requires + bioconductor-genomicalignments >=1.24.0,<1.25.0 , which requires + bioconductor-summarizedexperiment >=1.18.0,<1.19.0 , which requires + bioconductor-delayedarray >=0.14.0,<0.15.0 , which requires + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-genomicfeatures [1.42.0|1.42.2] would require + bioconductor-annotationdbi >=1.52.0,<1.53.0 , which requires + r-base >=4.0,<4.1.0a0 , which can be installed; + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-genomicfeatures 1.44.0 would require + bioconductor-annotationdbi >=1.54.0,<1.55.0 , which can be installed; + bioconductor-rtracklayer >=1.52.0,<1.53.0 , which requires + bioconductor-genomicalignments >=1.28.0,<1.29.0 , which requires + bioconductor-summarizedexperiment >=1.22.0,<1.23.0 , which requires + bioconductor-matrixgenerics >=1.4.0,<1.5.0 , which requires + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-genomicfeatures 1.46.1 would require + bioconductor-annotationdbi >=1.56.0,<1.57.0 , which requires + bioconductor-keggrest >=1.34.0,<1.35.0 , which requires + r-base >=4.1,<4.2.0a0 , which can be installed; + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-biomart >=2.50.0,<2.51.0 , which requires + bioconductor-biocfilecache >=2.2.0,<2.3.0 , which requires + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-genomicfeatures 1.50.2 would require + bioconductor-annotationdbi >=1.60.0,<1.61.0 , which requires + bioconductor-keggrest >=1.38.0,<1.39.0 , which requires + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-biomart >=2.54.0,<2.55.0 , which requires + bioconductor-biocfilecache >=2.6.0,<2.7.0 , which requires + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-genomicfeatures 1.52.1 would require + bioconductor-annotationdbi >=1.62.0,<1.63.0 , which can be installed; + bioconductor-rtracklayer >=1.60.0,<1.61.0 , which requires + bioconductor-genomicalignments >=1.36.0,<1.37.0 , which requires + bioconductor-summarizedexperiment >=1.30.0,<1.31.0 , which requires + bioconductor-matrixgenerics >=1.12.0,<1.13.0 , which requires + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-genomicfeatures 1.54.1 would require + bioconductor-annotationdbi >=1.64.0,<1.65.0 , which requires + bioconductor-keggrest >=1.42.0,<1.43.0 , which requires + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-biomart >=2.58.0,<2.59.0 , which requires + bioconductor-biocfilecache >=2.10.0,<2.11.0 , which requires + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-DGEclustering/meta.yaml b/recipes/r-DGEclustering/meta.yaml index 8c47cbbcd9e83..b8aa9155553ea 100644 --- a/recipes/r-DGEclustering/meta.yaml +++ b/recipes/r-DGEclustering/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{sha256}} build: - number: 5 + number: 6 skip: true # [win32] rpaths: - lib/R/lib/ diff --git a/recipes/r-abdiv/meta.yaml b/recipes/r-abdiv/meta.yaml index c1194981e822d..101eb07569b42 100644 --- a/recipes/r-abdiv/meta.yaml +++ b/recipes/r-abdiv/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 49484975fda33200175fd58b5387ea6dff120b66566b740018be699417497414 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-acidbase/meta.yaml b/recipes/r-acidbase/meta.yaml index bd6a6b423c173..aeb9cc9f4555f 100644 --- a/recipes/r-acidbase/meta.yaml +++ b/recipes/r-acidbase/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 104b8c7907375ef5943217aa1565ef8fd01ac8bed4e4d9addc2aa489195b172d build: - number: 1 + number: 2 noarch: generic run_exports: - {{ pin_subpackage('r-acidbase', max_pin="x.x") }} diff --git a/recipes/r-acidcli/meta.yaml b/recipes/r-acidcli/meta.yaml index 3b96b51a9342c..450e12c4db17c 100644 --- a/recipes/r-acidcli/meta.yaml +++ b/recipes/r-acidcli/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 451c595aefad37abede3f37ba0b64f20d41eb3513146dc80124adf92414e9546 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-acidcli', max_pin="x.x") }} diff --git a/recipes/r-acidexperiment/meta.yaml b/recipes/r-acidexperiment/meta.yaml index 7b252486f45e8..8268f62f9e683 100644 --- a/recipes/r-acidexperiment/meta.yaml +++ b/recipes/r-acidexperiment/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 4b8d093269e15d11a7565e4144d17caeac59e0491043bb3639713a9b769b5918 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-acidexperiment', max_pin="x.x") }} diff --git a/recipes/r-acidgenerics/meta.yaml b/recipes/r-acidgenerics/meta.yaml index e3a427c3792d3..b9ef8365541a3 100644 --- a/recipes/r-acidgenerics/meta.yaml +++ b/recipes/r-acidgenerics/meta.yaml @@ -10,7 +10,7 @@ source: sha256: baa0346b8cd0ebcdbef2d15028eb2d0c425731acfea718f057c6faef1606ff3b build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-acidgenerics', max_pin="x.x") }} diff --git a/recipes/r-acidgenomes/meta.yaml b/recipes/r-acidgenomes/meta.yaml index ef00b8d102371..09940aeffa6a0 100644 --- a/recipes/r-acidgenomes/meta.yaml +++ b/recipes/r-acidgenomes/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 7305aeaadbb0507c49b59f3b12971fd6d0f3504473f196f68ac20f59e751d131 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-acidgenomes', max_pin="x.x") }} diff --git a/recipes/r-acidgsea/meta.yaml b/recipes/r-acidgsea/meta.yaml index 557872f114317..9c0a1684971c2 100644 --- a/recipes/r-acidgsea/meta.yaml +++ b/recipes/r-acidgsea/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 7ebe40096263d7d8ae4fd2c0ec49b2a3afcb45fb26d7ba1816d99fd16b3ff73e build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-acidgsea', max_pin="x.x") }} diff --git a/recipes/r-acidmarkdown/meta.yaml b/recipes/r-acidmarkdown/meta.yaml index 0599b28ba64c8..106f6341f63a3 100644 --- a/recipes/r-acidmarkdown/meta.yaml +++ b/recipes/r-acidmarkdown/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 159dfee3894b5e95f8316e5ac82a812dd976b3e07d78ace9261570d0f115fe06 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-acidmarkdown', max_pin="x.x") }} diff --git a/recipes/r-acidplots/meta.yaml b/recipes/r-acidplots/meta.yaml index 491f5b79bb3d1..fc40ce91ccbeb 100644 --- a/recipes/r-acidplots/meta.yaml +++ b/recipes/r-acidplots/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('r-acidplots', max_pin="x.x") }} diff --git a/recipes/r-acidplyr/meta.yaml b/recipes/r-acidplyr/meta.yaml index e3ef97b68da93..f4f75d6f352f5 100644 --- a/recipes/r-acidplyr/meta.yaml +++ b/recipes/r-acidplyr/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 6fd487f33b1ed9ccc1c2580003c8ea9907efd0fcf2b3875f27efa3ccf7d62e45 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-acidplyr', max_pin="x.x") }} diff --git a/recipes/r-acidsinglecell/meta.yaml b/recipes/r-acidsinglecell/meta.yaml index 962ac75f917b7..5ba7bf74b0c9d 100644 --- a/recipes/r-acidsinglecell/meta.yaml +++ b/recipes/r-acidsinglecell/meta.yaml @@ -10,7 +10,7 @@ source: sha256: cc3068a1653e99a218607a9a994d8ee13490ebe162c403a6a7805ba10bfc50b0 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-acidsinglecell', max_pin="x.x") }} diff --git a/recipes/r-alakazam/build_failure.linux-64.yaml b/recipes/r-alakazam/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..7f6eb929e4fc8 --- /dev/null +++ b/recipes/r-alakazam/build_failure.linux-64.yaml @@ -0,0 +1,6 @@ +recipe_sha: c45b510257f1ae0780eb007311631856bb20ede26af533b37bf32190b87f576c # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + r-alakazam wanted to move from conda-forge but strict priority blocks it +category: |- + conda/mamba bug diff --git a/recipes/r-alakazam/build_failure.osx-64.yaml b/recipes/r-alakazam/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..31f56523eebfa --- /dev/null +++ b/recipes/r-alakazam/build_failure.osx-64.yaml @@ -0,0 +1,4 @@ +recipe_sha: c45b510257f1ae0780eb007311631856bb20ede26af533b37bf32190b87f576c # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + test failure diff --git a/recipes/r-alakazam/meta.yaml b/recipes/r-alakazam/meta.yaml index e33bf7fd4e3d3..adae54f5fd560 100644 --- a/recipes/r-alakazam/meta.yaml +++ b/recipes/r-alakazam/meta.yaml @@ -13,10 +13,12 @@ source: sha256: 161c87a946857da2b876f679abc4ae8d265835c92c0d56e0ecacf0aea04084d4 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-alakazam', max_pin="x") }} requirements: build: diff --git a/recipes/r-ampvis/build_failure.osx-64.yaml b/recipes/r-ampvis/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..49e45973c3f28 --- /dev/null +++ b/recipes/r-ampvis/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: ae5c4814ec850126e94327be093dd30c536a50f0919dc9c272437b7808d7b268 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-deseq2==1.10.0=r3.2.2_1"), MatchSpec("3.2.2*")} + Encountered problems while solving: + - nothing provides r 3.2.2* needed by bioconductor-deseq2-1.10.0-r3.2.2_1 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-deseq2 is installable with the potential options + bioconductor-deseq2 [1.14.1|1.16.1] would require + r-base 3.3.2* , which can be installed; + bioconductor-deseq2 [1.10.0|1.10.1] would require + r 3.2.2* , which does not exist (perhaps a missing channel); + bioconductor-deseq2 1.12.4 would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-deseq2 1.14.1 would require + r-base 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-deseq2 [1.16.1|1.18.0|1.18.1|1.20.0] would require + r-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ], which can be installed; + bioconductor-deseq2 [1.20.0|1.22.1] would require + bioconductor-summarizedexperiment >=1.12.0,<1.13.0 , which requires + bioconductor-delayedarray >=0.8.0,<0.9.0 , which requires + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed; + bioconductor-deseq2 [1.24.0|1.26.0] would require + bioconductor-summarizedexperiment [>=1.14.0,<1.15.0 |>=1.16.0,<1.17.0 ], which requires + bioconductor-delayedarray [>=0.10.0,<0.11.0 |>=0.12.0,<0.13.0 ], which requires + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-deseq2 [1.28.0|1.30.0|1.30.1] would require + bioconductor-summarizedexperiment >=1.18.0,<1.19.0 , which requires + bioconductor-delayedarray >=0.14.0,<0.15.0 , which requires + r-base >=4.0,<4.1.0a0 , which can be installed; + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-deseq2 [1.32.0|1.34.0] would require + bioconductor-geneplotter >=1.70.0,<1.71.0 , which requires + bioconductor-annotationdbi >=1.54.0,<1.55.0 , which requires + bioconductor-keggrest >=1.32.0,<1.33.0 , which requires + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-summarizedexperiment >=1.24.0,<1.25.0 , which requires + bioconductor-matrixgenerics >=1.6.0,<1.7.0 , which requires + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-deseq2 1.38.0 would require + bioconductor-geneplotter >=1.76.0,<1.77.0 , which requires + bioconductor-annotationdbi >=1.60.0,<1.61.0 , which requires + bioconductor-keggrest >=1.38.0,<1.39.0 , which requires + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-deseq2 [1.40.2|1.42.0] would require + bioconductor-summarizedexperiment [>=1.30.0,<1.31.0 |>=1.32.0,<1.33.0 ], which requires + bioconductor-matrixgenerics >=1.12.0,<1.13.0 , which requires + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-ampvis/meta.yaml b/recipes/r-ampvis/meta.yaml index 7caf7dd87a020..f70c48193dca0 100644 --- a/recipes/r-ampvis/meta.yaml +++ b/recipes/r-ampvis/meta.yaml @@ -10,7 +10,7 @@ source: md5: e898bf83d56eb7bfc17535b563932690 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ diff --git a/recipes/r-ampvis2/meta.yaml b/recipes/r-ampvis2/meta.yaml index cb179f12c271e..51eea302bd916 100644 --- a/recipes/r-ampvis2/meta.yaml +++ b/recipes/r-ampvis2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 0e94062ab2a366ed7a0dec0881fdfbaf7d650e153e3249bb73992766352a5a80 build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-anndata/meta.yaml b/recipes/r-anndata/meta.yaml index 0d2095fcfb869..f5d47489f41da 100644 --- a/recipes/r-anndata/meta.yaml +++ b/recipes/r-anndata/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 1a4dc28c5a99a1d816d0b6cf7eabc6388a61af03b53b38297cfce304ae6c8bcb build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-annotables/meta.yaml b/recipes/r-annotables/meta.yaml index c5da1affd1ed6..a8ea21d2c61fe 100644 --- a/recipes/r-annotables/meta.yaml +++ b/recipes/r-annotables/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 779d888f641544d85f2e072cd3b6f144b34bbc69989ba37c4310b888a74af805 build: - number: 1 + number: 2 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-archr/build_failure.linux-64.yaml b/recipes/r-archr/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..2ea4e913635b8 --- /dev/null +++ b/recipes/r-archr/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: ccdd1c84c90177087b1a6ad34f57515b7f4f64728df75fb732c607d9f4ac818e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - package r-chromvarmotifs-0.2.0-r41hdfd78af_0 requires r-base >=4.1,<4.2.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is installable with the potential options + [32mr-base [4.4.0|4.4.1][0m, which can be installed; + [32mr-base [4.4.1|4.4.2][0m would require + [32mgsl >=2.7,<2.8.0a0 [0m, which can be installed; + [31mr-chromvarmotifs[0m is not installable because there are no viable options + [31mr-chromvarmotifs 0.2.0[0m would require + [31mr-base >=4.1,<4.2.0a0 [0m but there are no viable options + [31mr-base [4.1.0|4.1.1][0m would require + [31mgsl >=2.6,<2.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-base [4.1.1|4.1.2|...|4.3.3][0m would require + [32mgsl >=2.7,<2.8.0a0 [0m, which can be installed; + [31mr-chromvarmotifs 0.2.0[0m would require + [31mr-base >=4.2,<4.3.0a0 [0m but there are no viable options + [31mr-base [4.1.1|4.1.2|...|4.3.3][0m, which cannot be installed (as previously explained); + [31mr-base 4.2.3[0m conflicts with any installable versions previously reported; + [31mr-chromvarmotifs 0.2.0[0m would require + [31mr-base >=4.3,<4.4.0a0 [0m but there are no viable options + [31mr-base [4.1.1|4.1.2|...|4.3.3][0m, which cannot be installed (as previously explained); + [31mr-base [4.3.1|4.3.2|4.3.3][0m conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-base[version='>=4.1,<4.2.0a0']"), MatchSpec("r-chromvarmotifs==0.2.0=r41hdfd78af_0")} + Encountered problems while solving: + - package r-chromvarmotifs-0.2.0-r41hdfd78af_0 requires r-base >=4.1,<4.2.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is installable with the potential options + [32mr-base [4.4.0|4.4.1][0m, which can be installed; + [32mr-base [4.4.1|4.4.2][0m would require + [32mgsl >=2.7,<2.8.0a0 [0m, which can be installed; + [31mr-chromvarmotifs[0m is not installable because there are no viable options + [31mr-chromvarmotifs 0.2.0[0m would require + [31mr-base >=4.1,<4.2.0a0 [0m but there are no viable options + [31mr-base [4.1.0|4.1.1][0m would require + [31mgsl >=2.6,<2.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-base [4.1.1|4.1.2|...|4.3.3][0m would require + [32mgsl >=2.7,<2.8.0a0 [0m, which can be installed; + [31mr-chromvarmotifs 0.2.0[0m would require + [31mr-base >=4.2,<4.3.0a0 [0m but there are no viable options + [31mr-base [4.1.1|4.1.2|...|4.3.3][0m, which cannot be installed (as previously explained); + [31mr-base 4.2.3[0m conflicts with any installable versions previously reported; + [31mr-chromvarmotifs 0.2.0[0m would require + [31mr-base >=4.3,<4.4.0a0 [0m but there are no viable options + [31mr-base [4.1.1|4.1.2|...|4.3.3][0m, which cannot be installed (as previously explained); + [31mr-base [4.3.1|4.3.2|4.3.3][0m conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-archr/build_failure.osx-64.yaml b/recipes/r-archr/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..4efd6227b856c --- /dev/null +++ b/recipes/r-archr/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: ccdd1c84c90177087b1a6ad34f57515b7f4f64728df75fb732c607d9f4ac818e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-bsgenome 1.74.0 would require + bioconductor-biocgenerics >=0.52.0,<0.53.0 , which conflicts with any installable versions previously reported; + bioconductor-rtracklayer >=1.66.0,<1.67.0 , which requires + bioconductor-genomicalignments >=1.42.0,<1.43.0 , which requires + bioconductor-summarizedexperiment >=1.36.0,<1.37.0 , which requires + bioconductor-matrixgenerics >=1.18.0,<1.19.0 , which conflicts with any installable versions previously reported; + r-base >=3.4.1,<3.4.2.0a0 , which can be installed; + bioconductor-chromvar [1.2.0|1.4.0] would require + bioconductor-bsgenome with the potential options + bioconductor-bsgenome 1.70.1, which can be installed (as previously explained); + bioconductor-bsgenome 1.68.0, which cannot be installed (as previously explained); + bioconductor-bsgenome [1.66.1|1.66.3], which can be installed (as previously explained); + bioconductor-bsgenome 1.62.0, which cannot be installed (as previously explained); + bioconductor-bsgenome 1.60.0, which can be installed (as previously explained); + bioconductor-bsgenome 1.58.0, which can be installed (as previously explained); + bioconductor-bsgenome 1.56.0, which can be installed (as previously explained); + bioconductor-bsgenome 1.54.0, which cannot be installed (as previously explained); + bioconductor-bsgenome 1.52.0, which cannot be installed (as previously explained); + bioconductor-bsgenome 1.50.0, which cannot be installed (as previously explained); + bioconductor-bsgenome [1.38.0|1.42.0|1.44.2|1.46.0|1.48.0] conflicts with any installable versions previously reported; + bioconductor-bsgenome [1.40.1|1.42.0], which cannot be installed (as previously explained); + bioconductor-bsgenome 1.74.0, which cannot be installed (as previously explained); + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed; + bioconductor-chromvar 1.20.0 would require + bioconductor-biocgenerics >=0.44.0,<0.45.0 , which can be installed; + bioconductor-s4vectors >=0.36.0,<0.37.0 , which can be installed (as previously explained); + bioconductor-chromvar 1.22.1 would require + bioconductor-biocgenerics >=0.46.0,<0.47.0 , which can be installed; + bioconductor-summarizedexperiment >=1.30.0,<1.31.0 , which cannot be installed (as previously explained); + bioconductor-chromvar 1.24.0 would require + bioconductor-biocgenerics >=0.48.0,<0.49.0 , which can be installed; + bioconductor-s4vectors >=0.40.0,<0.41.0 , which can be installed (as previously explained); + bioconductor-chromvar 1.28.0 would require + bioconductor-tfbstools >=1.44.0,<1.45.0 , which requires + bioconductor-cner >=1.42.0,<1.43.0 , which requires + bioconductor-annotate >=1.84.0,<1.85.0 , which does not exist (perhaps a missing channel); + bioconductor-chromvar [1.4.0|1.4.1] would require + bioconductor-biocgenerics >=0.28.0,<0.29.0 , which conflicts with any installable versions previously reported; + bioconductor-summarizedexperiment >=1.12.0,<1.13.0 , which can be installed (as previously explained); + bioconductor-chromvar 1.6.0 would require + bioconductor-biocgenerics >=0.30.0,<0.31.0 , which cannot be installed (as previously explained); + bioconductor-tfbstools >=1.22.0,<1.23.0 , which requires + bioconductor-cner [>=1.20.0,<1.21.0 |>=1.22.0,<1.23.0 ], which requires + bioconductor-go.db [>=3.10.0,<3.11.0 |>=3.8.0,<3.9.0 ], which requires + bioconductor-annotationdbi [>=1.46.0,<1.47.0 |>=1.48.0,<1.49.0 ], which requires + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-chromvar 1.8.0 would require + bioconductor-biocgenerics >=0.32.0,<0.33.0 , which conflicts with any installable versions previously reported; + bioconductor-tfbstools >=1.24.0,<1.25.0 , which can be installed (as previously explained); + bioconductor-motifmatchr is installable with the potential options + bioconductor-motifmatchr 1.10.0 would require + bioconductor-bsgenome >=1.56.0,<1.57.0 , which can be installed (as previously explained); + bioconductor-motifmatchr 1.12.0 would require + bioconductor-bsgenome >=1.58.0,<1.59.0 , which can be installed (as previously explained); + bioconductor-motifmatchr 1.14.0 would require + bioconductor-bsgenome >=1.60.0,<1.61.0 , which can be installed (as previously explained); + bioconductor-motifmatchr 1.16.0 would require + bioconductor-bsgenome >=1.62.0,<1.63.0 , which cannot be installed (as previously explained); + bioconductor-motifmatchr 1.20.0 would require + bioconductor-bsgenome >=1.66.0,<1.67.0 , which can be installed (as previously explained); + bioconductor-motifmatchr 1.22.0 would require + bioconductor-bsgenome >=1.68.0,<1.69.0 , which cannot be installed (as previously explained); + bioconductor-motifmatchr 1.24.0 would require + bioconductor-bsgenome >=1.70.0,<1.71.0 , which can be installed (as previously explained); + bioconductor-motifmatchr 1.28.0 would require + bioconductor-tfbstools >=1.44.0,<1.45.0 , which cannot be installed (as previously explained); + bioconductor-motifmatchr 1.4.0 would require + bioconductor-bsgenome >=1.50.0,<1.51.0 , which cannot be installed (as previously explained); + bioconductor-motifmatchr 1.6.0 would require + bioconductor-bsgenome >=1.52.0,<1.53.0 , which cannot be installed (as previously explained); + bioconductor-motifmatchr 1.8.0 would require + bioconductor-bsgenome >=1.54.0,<1.55.0 , which cannot be installed (as previously explained); + bioconductor-sparsematrixstats is installable with the potential options + bioconductor-sparsematrixstats 1.0.0 would require + bioconductor-matrixgenerics >=1.0.0,<1.1.0 , which conflicts with any installable versions previously reported; + bioconductor-sparsematrixstats 1.10.0 would require + bioconductor-matrixgenerics >=1.10.0,<1.11.0 , which conflicts with any installable versions previously reported; + bioconductor-sparsematrixstats 1.12.2 would require + bioconductor-matrixgenerics >=1.12.0,<1.13.0 , which conflicts with any installable versions previously reported; + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-sparsematrixstats 1.14.0 would require + bioconductor-matrixgenerics >=1.14.0,<1.15.0 , which can be installed; + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-sparsematrixstats 1.18.0 would require + bioconductor-matrixgenerics >=1.18.0,<1.19.0 , which conflicts with any installable versions previously reported; + r-base >=4.4,<4.5.0a0 , which conflicts with any installable versions previously reported; + bioconductor-sparsematrixstats [1.2.0|1.2.1] would require + bioconductor-matrixgenerics >=1.2.0,<1.3.0 , which conflicts with any installable versions previously reported; + bioconductor-sparsematrixstats 1.4.0 would require + bioconductor-matrixgenerics >=1.4.0,<1.5.0 , which can be installed; + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-sparsematrixstats 1.6.0 would require + bioconductor-matrixgenerics >=1.6.0,<1.7.0 , which conflicts with any installable versions previously reported; + r-base >=4.1,<4.2.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-archr/meta.yaml b/recipes/r-archr/meta.yaml index 4051558d4a6df..4bc16612f3f44 100644 --- a/recipes/r-archr/meta.yaml +++ b/recipes/r-archr/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 9c07c785a095062a998ed94c65df17a58f273d0d64062c14210f0a2c491304cf build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-aroma.affymetrix/meta.yaml b/recipes/r-aroma.affymetrix/meta.yaml index c8237d9eb4f99..ff9f84b503bc0 100644 --- a/recipes/r-aroma.affymetrix/meta.yaml +++ b/recipes/r-aroma.affymetrix/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-aroma.core/meta.yaml b/recipes/r-aroma.core/meta.yaml index 5d9c36cd653b2..ec079c9a8cebe 100644 --- a/recipes/r-aroma.core/meta.yaml +++ b/recipes/r-aroma.core/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-autospill/meta.yaml b/recipes/r-autospill/meta.yaml index 34034f7388346..33e1b403d9ffb 100644 --- a/recipes/r-autospill/meta.yaml +++ b/recipes/r-autospill/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 902d87a7b5dec2fe20b024b39f13c80e24e29d1b69e899dff69546b98fd26599 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-azimuth/build_failure.linux-64.yaml b/recipes/r-azimuth/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..dcf2618ec1884 --- /dev/null +++ b/recipes/r-azimuth/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c8c0f2f2410f4fd6f4ec03e77ad2a430db43ad9f317a056a725fe08c034cf9bb # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [32mbioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.1[0m would require + [32mbioconductor-bsgenome >=1.54.0,<1.55.0 [0m, which requires + [32mbioconductor-genomicranges >=1.38.0,<1.39.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.3[0m would require + [32mbioconductor-bsgenome >=1.56.0,<1.57.0 [0m, which requires + [32mbioconductor-genomicranges >=1.40.0,<1.41.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.3[0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.3[0m would require + [32mbioconductor-bsgenome >=1.60.0,<1.61.0 [0m, which requires + [32mbioconductor-genomicranges >=1.44.0,<1.45.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.4[0m would require + [32mbioconductor-bsgenome >=1.62.0,<1.63.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.40.0,<0.41.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.4[0m would require + [32mbioconductor-bsgenome >=1.66.0,<1.67.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.44.0,<0.45.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.5[0m would require + [32mbioconductor-genomeinfodb >=1.34.9,<1.35.0 [0m, which can be installed; + [32mbioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.5[0m would require + [32mbioconductor-bsgenome [>=1.68.0,<1.69.0 |>=1.70.0,<1.71.0 ][0m, which requires + [32mbioconductor-biocio >=1.12.0,<1.13.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mbioconductor-rtracklayer >=1.60.0,<1.61.0 [0m, which requires + [32mbioconductor-genomicalignments >=1.36.0,<1.37.0 [0m, which requires + [32mbioconductor-summarizedexperiment >=1.30.0,<1.31.0 [0m, which requires + [32mbioconductor-matrixgenerics >=1.12.0,<1.13.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v86[0m is installable with the potential options + [32mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.6.0,<2.7.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.28.0,<0.29.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.8.0,<2.9.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.30.0,<0.31.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.10.0,<2.11.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.32.0,<0.33.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.12.0,<2.13.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.34.0,<0.35.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.14.0,<2.15.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.36.0,<0.37.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.16.0,<2.17.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.38.0,<0.39.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.18.0,<2.19.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.40.0,<0.41.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.22.0,<2.23.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.44.0,<0.45.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.24.0,<2.25.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.46.0,<0.47.0 [0m, which can be installed; + [31mbioconductor-ensdb.hsapiens.v86 2.99.0[0m would require + [31mbioconductor-ensembldb >=2.26.0,<2.27.0 [0m, which requires + [31mbioconductor-biocgenerics >=0.48.0,<0.49.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-glmgampoi >=1.0.0 [0m is not installable because there are no viable options + [31mbioconductor-glmgampoi 1.18.0[0m would require + [31mbioconductor-biocgenerics >=0.52.0,<0.53.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-glmgampoi [1.0.0|1.10.0|...|1.6.0][0m conflicts with any installable versions previously reported; + [32mbioconductor-tfbstools[0m is installable with the potential options + [32mbioconductor-tfbstools [1.12.2|1.14.2|1.15.7|1.16.0|1.18.0][0m would require + [32mr-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ][0m, which can be installed; + [32mbioconductor-tfbstools 1.18.0[0m would require + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-tfbstools 1.20.0[0m would require + [32mbioconductor-genomicranges >=1.34.0,<1.35.0 [0m, which can be installed; + [32mbioconductor-tfbstools 1.22.0[0m would require + [32mbioconductor-genomicranges >=1.36.0,<1.37.0 [0m, which can be installed; + [32mbioconductor-tfbstools 1.24.0[0m would require + [32mbioconductor-genomicranges >=1.38.0,<1.39.0 [0m, which can be installed; + [32mbioconductor-tfbstools 1.26.0[0m would require + [32mbioconductor-genomicranges >=1.40.0,<1.41.0 [0m, which can be installed; + [32mbioconductor-tfbstools 1.28.0[0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-tfbstools 1.30.0[0m would require + [32mbioconductor-genomicranges >=1.44.0,<1.45.0 [0m, which can be installed; + [32mbioconductor-tfbstools 1.32.0[0m would require + [32mbioconductor-biocgenerics >=0.40.0,<0.41.0 [0m, which can be installed; + [32mbioconductor-tfbstools 1.36.0[0m would require + [32mbioconductor-biocgenerics >=0.44.0,<0.45.0 [0m, which can be installed; + [32mbioconductor-tfbstools [1.38.0|1.40.0][0m would require + [32mbioconductor-rtracklayer >=1.60.0,<1.61.0 [0m, which can be installed (as previously explained); + [32mbioconductor-seqlogo >=1.68.0,<1.69.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported; + [32mr-signac >=1.12.0 [0m is installable with the potential options + [32mr-signac 1.12.0[0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-signac [1.13.0|1.14.0][0m would require + [31mbioconductor-biocgenerics >=0.48.1,<0.49.0a0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-genomeinfodb >=1.38.1,<1.39.0a0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-genomicranges >=1.54.1,<1.55.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-signac 1.14.0[0m would require + [31mbioconductor-biocgenerics >=0.52.0,<0.53.0a0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-genomeinfodb >=1.42.0,<1.43.0a0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-genomicranges >=1.58.0,<1.59.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-azimuth/build_failure.osx-64.yaml b/recipes/r-azimuth/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..5272a3ba29e47 --- /dev/null +++ b/recipes/r-azimuth/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c8c0f2f2410f4fd6f4ec03e77ad2a430db43ad9f317a056a725fe08c034cf9bb # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + bioconductor-bsgenome 1.62.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.60.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.58.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.56.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.54.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.52.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.50.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.48.0 conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.74.0, which can be installed (as previously explained); + bioconductor-bsgenome [1.38.0|1.42.0|1.44.2|1.46.0] conflicts with any installable versions previously reported; + bioconductor-bsgenome [1.40.1|1.42.0], which cannot be installed (as previously explained); + r-base 3.4.1* , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.1 would require + bioconductor-bsgenome >=1.48.0,<1.50.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.1 would require + bioconductor-bsgenome >=1.50.0,<1.51.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.1 would require + bioconductor-bsgenome >=1.52.0,<1.53.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.1 would require + bioconductor-bsgenome >=1.54.0,<1.55.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.3 would require + bioconductor-bsgenome >=1.56.0,<1.57.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.3 would require + bioconductor-bsgenome >=1.58.0,<1.59.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.3 would require + bioconductor-bsgenome >=1.60.0,<1.61.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.4 would require + bioconductor-bsgenome >=1.62.0,<1.63.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.4 would require + bioconductor-bsgenome >=1.66.0,<1.67.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.5 would require + bioconductor-bsgenome >=1.66.2,<1.67.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.5 would require + bioconductor-bsgenome >=1.68.0,<1.69.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome.hsapiens.ucsc.hg38 1.4.5 would require + bioconductor-bsgenome >=1.70.0,<1.71.0 , which conflicts with any installable versions previously reported; + bioconductor-ensdb.hsapiens.v86 is not installable because there are no viable options + bioconductor-ensdb.hsapiens.v86 2.99.0 would require + bioconductor-ensembldb >=2.6.0,<2.7.0 , which requires + bioconductor-rtracklayer >=1.42.0,<1.43.0 , which conflicts with any installable versions previously reported; + bioconductor-ensdb.hsapiens.v86 2.99.0 would require + bioconductor-ensembldb >=2.8.0,<2.9.0 , which requires + bioconductor-rtracklayer >=1.44.0,<1.45.0 , which conflicts with any installable versions previously reported; + bioconductor-ensdb.hsapiens.v86 2.99.0 would require + bioconductor-ensembldb >=2.10.0,<2.11.0 , which requires + bioconductor-rtracklayer >=1.46.0,<1.47.0 , which conflicts with any installable versions previously reported; + bioconductor-ensdb.hsapiens.v86 2.99.0 would require + bioconductor-ensembldb >=2.12.0,<2.13.0 , which requires + bioconductor-rtracklayer >=1.48.0,<1.49.0 , which conflicts with any installable versions previously reported; + bioconductor-ensdb.hsapiens.v86 2.99.0 would require + bioconductor-ensembldb >=2.14.0,<2.15.0 , which requires + bioconductor-rtracklayer >=1.50.0,<1.51.0 , which conflicts with any installable versions previously reported; + bioconductor-ensdb.hsapiens.v86 2.99.0 would require + bioconductor-ensembldb >=2.16.0,<2.17.0 , which requires + bioconductor-rtracklayer >=1.52.0,<1.53.0 , which conflicts with any installable versions previously reported; + bioconductor-ensdb.hsapiens.v86 2.99.0 would require + bioconductor-ensembldb >=2.18.0,<2.19.0 , which requires + bioconductor-rtracklayer >=1.54.0,<1.55.0 , which conflicts with any installable versions previously reported; + bioconductor-ensdb.hsapiens.v86 2.99.0 would require + bioconductor-ensembldb >=2.22.0,<2.23.0 , which requires + bioconductor-rtracklayer >=1.58.0,<1.59.0 , which conflicts with any installable versions previously reported; + bioconductor-ensdb.hsapiens.v86 2.99.0 would require + bioconductor-ensembldb >=2.24.0,<2.25.0 , which requires + bioconductor-rtracklayer >=1.60.0,<1.61.0 , which conflicts with any installable versions previously reported; + bioconductor-ensdb.hsapiens.v86 2.99.0 would require + bioconductor-ensembldb >=2.26.0,<2.27.0 , which requires + bioconductor-rtracklayer >=1.62.0,<1.63.0 , which conflicts with any installable versions previously reported; + bioconductor-tfbstools is not installable because there are no viable options + bioconductor-tfbstools [1.12.2|1.14.2|1.15.7|1.16.0] would require + r-base 3.4.1* , which conflicts with any installable versions previously reported; + bioconductor-tfbstools 1.18.0 would require + bioconductor-bsgenome >=1.48.0,<1.50.0 , which conflicts with any installable versions previously reported; + bioconductor-tfbstools 1.20.0 would require + bioconductor-bsgenome >=1.50.0,<1.51.0 , which conflicts with any installable versions previously reported; + bioconductor-tfbstools 1.22.0 would require + bioconductor-bsgenome >=1.52.0,<1.53.0 , which conflicts with any installable versions previously reported; + bioconductor-tfbstools 1.24.0 would require + bioconductor-bsgenome >=1.54.0,<1.55.0 , which conflicts with any installable versions previously reported; + bioconductor-tfbstools 1.26.0 would require + bioconductor-bsgenome >=1.56.0,<1.57.0 , which conflicts with any installable versions previously reported; + bioconductor-tfbstools 1.28.0 would require + bioconductor-bsgenome >=1.58.0,<1.59.0 , which conflicts with any installable versions previously reported; + bioconductor-tfbstools 1.30.0 would require + bioconductor-bsgenome >=1.60.0,<1.61.0 , which conflicts with any installable versions previously reported; + bioconductor-tfbstools 1.32.0 would require + bioconductor-bsgenome >=1.62.0,<1.63.0 , which conflicts with any installable versions previously reported; + bioconductor-tfbstools 1.36.0 would require + bioconductor-bsgenome >=1.66.0,<1.67.0 , which conflicts with any installable versions previously reported; + bioconductor-tfbstools 1.38.0 would require + bioconductor-bsgenome >=1.68.0,<1.69.0 , which conflicts with any installable versions previously reported; + bioconductor-tfbstools 1.40.0 would require + bioconductor-bsgenome >=1.70.0,<1.71.0 , which conflicts with any installable versions previously reported; + r-base 4.4.* is requested and can be installed; + r-presto 1.0.0.* is not installable because there are no viable options + r-presto 1.0.0 would require + r-base >=4.1,<4.2.0a0 , which conflicts with any installable versions previously reported; + r-presto 1.0.0 would require + r-base >=4.2,<4.3.0a0 , which conflicts with any installable versions previously reported; + r-presto 1.0.0 would require + r-base >=4.3,<4.4.0a0 , which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-azimuth/meta.yaml b/recipes/r-azimuth/meta.yaml index ece8b017733ac..20673690990fd 100644 --- a/recipes/r-azimuth/meta.yaml +++ b/recipes/r-azimuth/meta.yaml @@ -12,7 +12,7 @@ build: script: $R CMD INSTALL --build . run_exports: - {{ pin_subpackage("r-azimuth", max_pin="x.x.x") }} - number: 0 + number: 1 rpaths: - lib/R/lib/ diff --git a/recipes/r-basejump/meta.yaml b/recipes/r-basejump/meta.yaml index 6fe0a1493ed18..b172bc71b9b4b 100644 --- a/recipes/r-basejump/meta.yaml +++ b/recipes/r-basejump/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 06b216c539d112468172d021ba9445b8d98918609319fb34c200093fa052cbb9 build: - number: 1 + number: 2 noarch: generic run_exports: - {{ pin_subpackage('r-basejump', max_pin="x.x") }} diff --git a/recipes/r-bcbiobase/meta.yaml b/recipes/r-bcbiobase/meta.yaml index 2fbc32b4e4ad2..969be5d3c187a 100644 --- a/recipes/r-bcbiobase/meta.yaml +++ b/recipes/r-bcbiobase/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('r-bcbiobase', max_pin="x.x") }} diff --git a/recipes/r-bcbiornaseq/build_failure.linux-64.yaml b/recipes/r-bcbiornaseq/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..513e9feabc60a --- /dev/null +++ b/recipes/r-bcbiornaseq/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 266c6c0bea2bb18caca960e65d154239916cd42324186e951171254724064c6b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [32mbioconductor-enrichplot >=1.20.0,<1.21.0 [0m, which requires + [32mbioconductor-ggtree >=3.8.0,<3.9.0 [0m, which requires + [32mbioconductor-treeio >=1.24.0,<1.25.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mbioconductor-dose >=3.26.0 [0m is installable with the potential options + [31mbioconductor-dose 3.26.1[0m would require + [31mbioconductor-annotationdbi >=1.62.0,<1.63.0 [0m, which cannot be installed (as previously explained); + [32mbioconductor-dose 3.28.1[0m would require + [32mbioconductor-annotationdbi >=1.64.0,<1.65.0 [0m, which can be installed (as previously explained); + [32mbioconductor-enrichplot >=1.20.0 [0m is installable with the potential options + [32mbioconductor-enrichplot 1.20.0[0m, which can be installed (as previously explained); + [32mbioconductor-enrichplot 1.22.0[0m would require + [32mbioconductor-dose >=3.28.0,<3.29.0 [0m, which can be installed (as previously explained); + [32mbioconductor-ensdb.hsapiens.v75 >=2.99.0 [0m is installable with the potential options + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mr-base 3.4.1* [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.4.1,<2.6.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.26.0,<0.28.0 [0m, which can be installed; + [32mbioconductor-s4vectors >=0.18.3,<0.20.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.6.0,<2.7.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.28.0,<0.29.0 [0m, which can be installed; + [32mbioconductor-s4vectors >=0.20.0,<0.21.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.8.0,<2.9.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.30.0,<0.31.0 [0m, which can be installed; + [32mbioconductor-s4vectors >=0.22.0,<0.23.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.10.0,<2.11.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.32.0,<0.33.0 [0m, which can be installed; + [32mbioconductor-s4vectors >=0.24.0,<0.25.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.12.0,<2.13.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.34.0,<0.35.0 [0m, which can be installed; + [32mbioconductor-s4vectors >=0.26.0,<0.27.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.14.0,<2.15.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.36.0,<0.37.0 [0m, which can be installed; + [32mbioconductor-s4vectors >=0.28.0,<0.29.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.16.0,<2.17.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.38.0,<0.39.0 [0m, which can be installed; + [32mbioconductor-s4vectors >=0.30.0,<0.31.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.18.0,<2.19.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.40.0,<0.41.0 [0m, which can be installed; + [32mbioconductor-s4vectors >=0.32.0,<0.33.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.22.0,<2.23.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.44.0,<0.45.0 [0m, which can be installed; + [32mbioconductor-s4vectors >=0.36.0,<0.37.0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.24.0,<2.25.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.46.0,<0.47.0 [0m, which can be installed; + [32mbioconductor-genomicfeatures >=1.52.0,<1.53.0 [0m, which requires + [32mbioconductor-biomart >=2.56.0,<2.57.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mbioconductor-ensdb.hsapiens.v75 2.99.0[0m would require + [32mbioconductor-ensembldb >=2.26.0,<2.27.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.48.0,<0.49.0 [0m, which can be installed; + [32mbioconductor-s4vectors >=0.40.0,<0.41.0 [0m, which can be installed; + [32mr-acidbase >=0.7.0 [0m is installable with the potential options + [32mr-acidbase [0.7.0|0.7.1|0.7.2][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mr-acidbase 0.7.3[0m would require + [32mbioconductor-s4vectors >=0.40.0 [0m with the potential options + [32mbioconductor-s4vectors 0.40.2[0m, which can be installed; + [31mbioconductor-s4vectors 0.44.0[0m would require + [31mbioconductor-biocgenerics >=0.52.0,<0.53.0 [0m, which conflicts with any installable versions previously reported; + [32mr-acidgenomes >=0.6.0 [0m is installable and it requires + [32mbioconductor-annotationhub >=3.8.0 [0m with the potential options + [31mbioconductor-annotationhub 3.8.0[0m would require + [31mbioconductor-annotationdbi >=1.62.0,<1.63.0 [0m, which cannot be installed (as previously explained); + [31mbioconductor-s4vectors >=0.38.0,<0.39.0 [0m, which conflicts with any installable versions previously reported; + [32mbioconductor-annotationhub 3.10.0[0m would require + [32mbioconductor-interactivedisplaybase >=1.40.0,<1.41.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mbioconductor-annotationhub 3.14.0[0m would require + [31mbioconductor-biocgenerics >=0.52.0,<0.53.0 [0m, which conflicts with any installable versions previously reported; + [31mr-acidgsea >=0.9.0 [0m is not installable because there are no viable options + [31mr-acidgsea 0.9.0[0m would require + [32mr-acidbase >=0.7.0 [0m, which can be installed (as previously explained); + [31mr-base >=4.4,<4.5.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-acidgsea 0.9.0[0m conflicts with any installable versions previously reported; + [31mr-acidplots >=0.7.1 [0m is not installable because there are no viable options + [31mr-acidplots 0.7.3[0m would require + [32mr-acidbase >=0.7.0 [0m, which can be installed (as previously explained); + [31mr-base >=4.4,<4.5.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-acidplots [0.7.1|0.7.2|0.7.3][0m conflicts with any installable versions previously reported; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported; + [31mr-basejump >=0.18.0 [0m is not installable because there are no viable options + [31mr-basejump 0.18.0[0m would require + [32mr-acidgenomes >=0.6.0 [0m, which can be installed (as previously explained); + [31mr-base >=4.4,<4.5.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-basejump 0.18.0[0m conflicts with any installable versions previously reported; + [32mr-deseqanalysis >=0.7.0 [0m is installable with the potential options + [32mr-deseqanalysis 0.7.1[0m would require + [32mr-acidgenomes >=0.5.2 [0m, which can be installed (as previously explained); + [31mr-deseqanalysis [0.7.0|0.7.1][0m conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-bcbiornaseq/meta.yaml b/recipes/r-bcbiornaseq/meta.yaml index 5438c656df52d..19a411ba33715 100644 --- a/recipes/r-bcbiornaseq/meta.yaml +++ b/recipes/r-bcbiornaseq/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 01c7848a13e5eb5bb043725fbdcec2de9e545dd37c2995bcbbfde73a8632ede8 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-bcbiornaseq', max_pin="x.x") }} diff --git a/recipes/r-bcbiosinglecell/meta.yaml b/recipes/r-bcbiosinglecell/meta.yaml index f0d67d0cfeb51..38ed77ac3f890 100644 --- a/recipes/r-bcbiosinglecell/meta.yaml +++ b/recipes/r-bcbiosinglecell/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 42a7272709a65cda9b45b79aa172226839342578049a9841b73ee92a5e76e3f5 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-bcbiosinglecell', max_pin="x.x") }} diff --git a/recipes/r-bedtoolsr/meta.yaml b/recipes/r-bedtoolsr/meta.yaml index 539026ce47504..4bb13b3f48de1 100644 --- a/recipes/r-bedtoolsr/meta.yaml +++ b/recipes/r-bedtoolsr/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 2 + number: 3 requirements: host: diff --git a/recipes/r-biodb/build_failure.linux-64.yaml b/recipes/r-biodb/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..f91f49a1ad85d --- /dev/null +++ b/recipes/r-biodb/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: d10cb8fa37b5a376f5cd341b23653d737c3ef5d77ef7f5efcb02fd700b875dde # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-purrr: 1.0.2-r44hdb488b9_1 conda-forge + r-r.methodss3: 1.8.2-r44hc72bb7e_3 conda-forge + r-r.oo: 1.27.0-r44hc72bb7e_0 conda-forge + r-r.utils: 2.12.3-r44hc72bb7e_1 conda-forge + r-r6: 2.5.1-r44hc72bb7e_3 conda-forge + r-ragg: 1.3.3-r44h9aa3752_0 conda-forge + r-rappdirs: 0.3.3-r44hb1dbf0f_3 conda-forge + r-rcmdcheck: 1.4.0-r44h785f33e_3 conda-forge + r-rcpp: 1.0.13_1-r44h93ab643_0 conda-forge + r-rcurl: 1.98_1.16-r44he8228da_1 conda-forge + r-rematch2: 2.1.2-r44hc72bb7e_4 conda-forge + r-remotes: 2.5.0-r44hc72bb7e_1 conda-forge + r-rlang: 1.1.4-r44ha18555a_1 conda-forge + r-rmarkdown: 2.29-r44hc72bb7e_0 conda-forge + r-roxygen2: 7.3.2-r44h0d4f4ea_1 conda-forge + r-rprojroot: 2.0.4-r44hc72bb7e_1 conda-forge + r-rstudioapi: 0.17.1-r44hc72bb7e_0 conda-forge + r-rversions: 2.1.2-r44hc72bb7e_3 conda-forge + r-sass: 0.4.9-r44ha18555a_1 conda-forge + r-sessioninfo: 1.2.2-r44hc72bb7e_3 conda-forge + r-shiny: 1.9.1-r44h785f33e_0 conda-forge + r-sourcetools: 0.1.7_1-r44ha18555a_2 conda-forge + r-stringi: 1.8.4-r44h33cde33_3 conda-forge + r-stringr: 1.5.1-r44h785f33e_1 conda-forge + r-sys: 3.4.3-r44h2b5f3a1_0 conda-forge + r-systemfonts: 1.1.0-r44h38d38ca_1 conda-forge + r-testthat: 3.2.1.1-r44h0d4f4ea_1 conda-forge + r-textshaping: 0.4.0-r44ha47bcaa_2 conda-forge + r-tibble: 3.2.1-r44hdb488b9_3 conda-forge + r-tinytex: 0.54-r44hc72bb7e_0 conda-forge + r-urlchecker: 1.0.1-r44hc72bb7e_3 conda-forge + r-usethis: 3.1.0-r44hc72bb7e_0 conda-forge + r-utf8: 1.2.4-r44hb1dbf0f_1 conda-forge + r-vctrs: 0.6.5-r44h0d4f4ea_1 conda-forge + r-waldo: 0.6.1-r44hc72bb7e_0 conda-forge + r-whisker: 0.4.1-r44hc72bb7e_2 conda-forge + r-withr: 3.0.2-r44hc72bb7e_0 conda-forge + r-xfun: 0.49-r44h93ab643_0 conda-forge + r-xml: 3.99_0.17-r44h5bae778_2 conda-forge + r-xml2: 1.3.6-r44h8194278_2 conda-forge + r-xopen: 1.0.1-r44hc72bb7e_1 conda-forge + r-xtable: 1.8_4-r44hc72bb7e_6 conda-forge + r-yaml: 2.3.10-r44hdb488b9_0 conda-forge + r-zip: 2.3.1-r44hb1dbf0f_1 conda-forge + readline: 8.2-h8228510_1 conda-forge + sed: 4.8-he412f7d_0 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tktable: 2.10-h8bc8fbc_6 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + xorg-libice: 1.1.1-hb9d3cd8_1 conda-forge + xorg-libsm: 1.2.4-he73a12e_1 conda-forge + xorg-libx11: 1.8.10-h4f16b4b_1 conda-forge + xorg-libxau: 1.0.11-hb9d3cd8_1 conda-forge + xorg-libxdmcp: 1.1.5-hb9d3cd8_0 conda-forge + xorg-libxext: 1.3.6-hb9d3cd8_0 conda-forge + xorg-libxrender: 0.9.11-hb9d3cd8_2 conda-forge + xorg-libxt: 1.3.1-hb9d3cd8_0 conda-forge + xz: 5.6.3-hbcc6ac9_1 conda-forge + xz-gpl-tools: 5.6.3-hbcc6ac9_1 conda-forge + xz-tools: 5.6.3-hb9d3cd8_1 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2213, in create_build_envs + environ.create_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1050, in create_env + _execute_actions(prefix, precs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1338, in _execute_actions + progressive_fetch_extract.execute() + File "/opt/conda/lib/python3.10/site-packages/conda/core/package_cache_data.py", line 900, in execute + raise CondaMultiError(not_cancelled) + conda.CondaMultiError: Failed to write to /opt/conda/pkgs/gcc_impl_linux-64-14.2.0-h6b349bd_1.conda.partial + errno: 28 + Failed to write to /opt/conda/pkgs/pandoc-3.6-ha770c72_0.conda.partial + errno: 28 + Failed to write to /opt/conda/pkgs/sysroot_linux-64-2.17-h4a8ded7_18.conda.partial + errno: 28 + Failed to write to /opt/conda/pkgs/gcc_impl_linux-64-14.2.0-h6b349bd_1.conda.partial + errno: 28 + Failed to write to /opt/conda/pkgs/gfortran_impl_linux-64-14.2.0-hc73f493_1.conda.partial + errno: 28 + Failed to write to /opt/conda/pkgs/gxx_impl_linux-64-14.2.0-h2c03514_1.conda.partial + errno: 28 + Failed to write to /opt/conda/pkgs/libglib-2.82.2-h2ff4ddf_0.conda.partial + errno: 28 + Failed to write to /opt/conda/pkgs/libstdcxx-devel_linux-64-14.2.0-h41c2201_101.conda.partial + errno: 28 + Failed to write to /opt/conda/pkgs/binutils_impl_linux-64-2.43-h4bf12b8_2.conda.partial + errno: 28 +# Last 100 lines of the build log. diff --git a/recipes/r-biodb/meta.yaml b/recipes/r-biodb/meta.yaml index 1f5bd0438fbb8..e4ea77cd663d2 100644 --- a/recipes/r-biodb/meta.yaml +++ b/recipes/r-biodb/meta.yaml @@ -9,7 +9,7 @@ source: sha256: abc4c533a2824e98bb6b4e94b5288bf89c6cf2ba5e62804d0e8dc75147eecb88 build: - number: 9 + number: 10 run_exports: - {{ pin_subpackage('r-biodb', max_pin="x") }} rpaths: diff --git a/recipes/r-biomartr/meta.yaml b/recipes/r-biomartr/meta.yaml index a4fbd52da4fc5..340e7bf115f6b 100644 --- a/recipes/r-biomartr/meta.yaml +++ b/recipes/r-biomartr/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-bisquerna/meta.yaml b/recipes/r-bisquerna/meta.yaml index 8e6652ec6dcdc..58deb73607adc 100644 --- a/recipes/r-bisquerna/meta.yaml +++ b/recipes/r-bisquerna/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 76886871c497a71427929654ca0e257ae949f23af53a6cf43e31bf642e2d775c build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-boutroslabplottinggeneral/build_failure.osx-64.yaml b/recipes/r-boutroslabplottinggeneral/build_failure.osx-64.yaml deleted file mode 100644 index 1d7d16a9230e1..0000000000000 --- a/recipes/r-boutroslabplottinggeneral/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 164bf07bd6c5696217fee0fdf178ae6a5c12a6cd9c244ee4117f7d357b9a8d64 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/boutroslabplottinggeneral-5.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/boutroslabplottinggeneral-5.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/boutroslabplottinggeneral-5.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/boutroslabplottinggeneral-5.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/boutroslabplottinggeneral-5.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/boutroslabplottinggeneral-5.3.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - * installing to library /opt/mambaforge/envs/bioconda/conda-bld/boutroslabplottinggeneral_1689801727335/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/R/library - * installing *source* package BoutrosLab.plotting.general ... - ** using staged installation - ** libs - x86_64-apple-darwin13.4.0-clang -I"$PREFIX/lib/R/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1689263077211/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c distance.c -o distance.o - x86_64-apple-darwin13.4.0-clang -I"$PREFIX/lib/R/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1689263077211/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c ks.c -o ks.o - R CMD SHLIB -o BoutrosLab.plotting.general.so distance.o ks.o - make[1]: Entering directory '$SRC_DIR/src' - x86_64-apple-darwin13.4.0-clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L$PREFIX/lib/R/lib -Wl,-dead_strip_dylibs -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o BoutrosLab.plotting.general.so distance.o ks.o -L$PREFIX/lib/R/lib -lR -Wl,-framework -Wl,CoreFoundation - ld: warning: -pie being ignored. It is only used when linking a main executable - make[1]: Leaving directory '$SRC_DIR/src' - ** R - ** data - *** moving datasets to lazyload DB - ** inst - ** byte-compile and prepare package for lazy loading - ** help - *** installing help indices - ** building package indices - ** installing vignettes - ** testing if installed package can be loaded from temporary location - ERROR: loading failed - Error: package or namespace load failed for BoutrosLab.plotting.general in library.dynam(lib, package, package.lib): - shared object BoutrosLab.plotting.general.dylib not found - Error: loading failed - Execution halted - * removing /opt/mambaforge/envs/bioconda/conda-bld/boutroslabplottinggeneral_1689801727335/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/R/library/BoutrosLab.plotting.general - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/boutroslabplottinggeneral_1689801727335/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/r-boutroslabplottinggeneral/meta.yaml b/recipes/r-boutroslabplottinggeneral/meta.yaml index 962520b5a1b61..1ac603a047ed4 100644 --- a/recipes/r-boutroslabplottinggeneral/meta.yaml +++ b/recipes/r-boutroslabplottinggeneral/meta.yaml @@ -3,7 +3,7 @@ package: version: "5.3.4" build: - number: 5 + number: 6 source: url: https://depot.galaxyproject.org/software/boutroslabplottinggeneral/boutroslabplottinggeneral_5.3.4_src_all.tar.gz diff --git a/recipes/r-breakaway/build_failure.linux-64.yaml b/recipes/r-breakaway/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..2e4e8dae0fa4f --- /dev/null +++ b/recipes/r-breakaway/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 08a968ecc0c8aa3cd0f628c8af708d8fff1bb285703981011476a2a0a91c29b3 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-phyloseq==1.16.2=r3.3.1_1"), MatchSpec("3.3.1*")} + Encountered problems while solving: + - nothing provides r 3.3.1* needed by bioconductor-phyloseq-1.16.2-r3.3.1_1 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-phyloseq[0m is installable with the potential options + [32mbioconductor-phyloseq 1.14.0[0m would require + [32mr-biom >=0.3.9 [0m with the potential options + [31mr-biom 0.3.12[0m would require + [31mr 3.2.2* [0m, which does not exist (perhaps a missing channel); + [31mr-biom 0.3.12[0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [32mr-biom 0.3.12[0m would require + [32mr-base 3.3.2* [0m, which can be installed; + [32mr-biom 0.3.12[0m would require + [32mr-base 3.4.1* [0m, which can be installed; + [32mbioconductor-phyloseq 1.16.2[0m would require + [32mbioconductor-biomformat >=1.0.2 [0m with the potential options + [32mbioconductor-biomformat 1.0.2[0m would require + [32mbioconductor-rhdf5 >=2.16.0 [0m with the potential options + [31mbioconductor-rhdf5 2.16.0[0m would require + [31mr 3.2.2* [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-rhdf5 2.16.0[0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [32mbioconductor-rhdf5 2.16.0[0m would require + [32mr-base 3.3.2* [0m, which can be installed; + [32mbioconductor-rhdf5 [2.16.0|2.20.0|2.22.0|2.24.0][0m would require + [32mr-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ][0m, which can be installed; + [32mbioconductor-rhdf5 [2.24.0|2.26.0|2.26.1|2.26.2|2.28.0][0m would require + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.28.0|2.30.0][0m would require + [32mbioconductor-rhdf5lib >=1.8.0,<1.9.0 [0m, which requires + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.32.0|2.34.0][0m would require + [32mbioconductor-rhdf5lib >=1.10.0,<1.11.0 [0m, which requires + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.36.0|2.38.0|2.38.1][0m would require + [32mbioconductor-rhdf5lib >=1.14.0,<1.15.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 2.42.0[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.44.0|2.46.1][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mbioconductor-biomformat [1.0.2|1.2.0][0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [32mbioconductor-biomformat 1.2.0[0m would require + [32mr-base 3.3.2* [0m, which can be installed; + [32mbioconductor-biomformat [1.2.0|1.4.0|1.6.0|1.8.0][0m would require + [32mr-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ][0m, which can be installed; + [32mbioconductor-biomformat [1.10.0|1.10.1|1.12.0|1.8.0][0m would require + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-biomformat [1.12.0|1.14.0][0m would require + [32mbioconductor-rhdf5 >=2.30.0,<2.31.0 [0m, which can be installed (as previously explained); + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-biomformat [1.16.0|1.18.0][0m would require + [32mbioconductor-rhdf5 >=2.32.0,<2.33.0 [0m, which can be installed (as previously explained); + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-biomformat [1.20.0|1.22.0][0m would require + [32mbioconductor-rhdf5 >=2.36.0,<2.37.0 [0m, which can be installed (as previously explained); + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-biomformat 1.26.0[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-biomformat [1.28.0|1.30.0][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mbioconductor-phyloseq [1.16.2|1.19.1][0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [32mbioconductor-phyloseq [1.19.1|1.20.0][0m would require + [32mr-base [3.3.2* |>=3.3,<3.4 ][0m, which can be installed; + [32mbioconductor-phyloseq [1.19.1|1.20.0|1.22.3|1.24.2][0m would require + [32mr-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ][0m, which can be installed; + [32mbioconductor-phyloseq [1.24.2|1.26.0|1.26.1][0m would require + [32mbioconductor-multtest >=2.38.0,<2.39.0 [0m, which requires + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-phyloseq [1.28.0|1.30.0][0m would require + [32mbioconductor-biomformat >=1.14.0,<1.15.0 [0m, which can be installed (as previously explained); + [32mbioconductor-biostrings >=2.52.0,<2.53.0 [0m, which requires + [32mbioconductor-xvector >=0.24.0,<0.25.0 [0m, which requires + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-phyloseq [1.32.0|1.34.0][0m would require + [32mbioconductor-biomformat >=1.16.0,<1.17.0 [0m, which can be installed (as previously explained); + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-phyloseq [1.36.0|1.38.0][0m would require + [32mbioconductor-biomformat [>=1.20.0,<1.21.0 |>=1.22.0,<1.23.0 ][0m, which can be installed (as previously explained); + [32mbioconductor-phyloseq 1.42.0[0m would require + [32mbioconductor-biomformat >=1.26.0,<1.27.0 [0m, which can be installed (as previously explained); + [32mbioconductor-phyloseq [1.44.0|1.46.0][0m would require + [32mbioconductor-biomformat >=1.30.0,<1.31.0 [0m, which can be installed (as previously explained); + [32mbioconductor-biostrings >=2.68.0,<2.69.0 [0m, which requires + [32mbioconductor-xvector >=0.40.0,<0.41.0 [0m, which requires + [32mbioconductor-zlibbioc >=1.46.0,<1.47.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-breakaway/meta.yaml b/recipes/r-breakaway/meta.yaml index 34b060b5c1cdf..79db42547db37 100644 --- a/recipes/r-breakaway/meta.yaml +++ b/recipes/r-breakaway/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 11019e462415619fa56af60c92d574e2d29e57cfcaf554afc209fad929183691 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-bseqsc/build_failure.linux-64.yaml b/recipes/r-bseqsc/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..880afebaefff3 --- /dev/null +++ b/recipes/r-bseqsc/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 2aec1ea27babbb207e51e477ea92eda8ed2718b8b6ea52c063c374113572366d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Encountered problems while solving: + - package r-cssam-1.4-r40h7d875b9_0 requires r-base >=4.0,<4.1, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-cssam >=1.4 [0m is not installable because it requires + [31mr-base >=4.0,<4.1 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-base[version='>=4.0,<4.1']"), MatchSpec("r-cssam==1.4=r40h7d875b9_0")} + Encountered problems while solving: + - package r-cssam-1.4-r40h7d875b9_0 requires r-base >=4.0,<4.1, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-cssam >=1.4 [0m is not installable because it requires + [31mr-base >=4.0,<4.1 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-base[version='>=4.0,<4.1']"), MatchSpec("r-cssam==1.4=r40h7d875b9_0")} + Encountered problems while solving: + - package r-cssam-1.4-r40h7d875b9_0 requires r-base >=4.0,<4.1, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-cssam >=1.4 [0m is not installable because it requires + [31mr-base >=4.0,<4.1 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-bseqsc/meta.yaml b/recipes/r-bseqsc/meta.yaml index cddcb3a531506..9c314ba1ff5d2 100644 --- a/recipes/r-bseqsc/meta.yaml +++ b/recipes/r-bseqsc/meta.yaml @@ -10,7 +10,7 @@ source: sha256: c7fc7be6131fc4b55bec069beb9192a221f7de323a93d2b6a6d1ef04b1c19ac7 build: - number: 3 + number: 4 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-buencolors/meta.yaml b/recipes/r-buencolors/meta.yaml index 51fca6e5f9c0a..77a74a6c26748 100644 --- a/recipes/r-buencolors/meta.yaml +++ b/recipes/r-buencolors/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-bulkanalyser/meta.yaml b/recipes/r-bulkanalyser/meta.yaml index de2c1fe87d5c5..6171027d85d2a 100644 --- a/recipes/r-bulkanalyser/meta.yaml +++ b/recipes/r-bulkanalyser/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 7f30a27c9f12d41d30e5a2176d422ffd9ecc564d8486088441cd08a5d8b41b01 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-calder2/build_failure.linux-64.yaml b/recipes/r-calder2/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..8bd1addc2b82e --- /dev/null +++ b/recipes/r-calder2/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 050299fb596cf4254c7e709fc51356348b37fa74f7c12122f1153a79d329cc44 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-rhdf5 >=2.28.0 [0m is installable with the potential options + [32mbioconductor-rhdf5 2.28.0[0m would require + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.28.0|2.30.0][0m would require + [32mbioconductor-rhdf5lib >=1.8.0,<1.9.0 [0m, which requires + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.32.0|2.34.0][0m would require + [32mbioconductor-rhdf5lib >=1.10.0,<1.11.0 [0m, which requires + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.36.0|2.38.0|2.38.1][0m would require + [32mbioconductor-rhdf5lib >=1.14.0,<1.15.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 2.42.0[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.44.0|2.46.1][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-base[version='>=3.5.1,<3.5.2.0a0']"), MatchSpec("bioconductor-rhdf5==2.28.0=r351hf484d3e_0")} + Encountered problems while solving: + - package bioconductor-rhdf5-2.28.0-r351hf484d3e_0 requires r-base >=3.5.1,<3.5.2.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-rhdf5 >=2.28.0 [0m is installable with the potential options + [32mbioconductor-rhdf5 2.28.0[0m would require + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.28.0|2.30.0][0m would require + [32mbioconductor-rhdf5lib >=1.8.0,<1.9.0 [0m, which requires + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.32.0|2.34.0][0m would require + [32mbioconductor-rhdf5lib >=1.10.0,<1.11.0 [0m, which requires + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.36.0|2.38.0|2.38.1][0m would require + [32mbioconductor-rhdf5lib >=1.14.0,<1.15.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 2.42.0[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.44.0|2.46.1][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-calder2/meta.yaml b/recipes/r-calder2/meta.yaml index 5fc3a52815544..7a946fd80346b 100644 --- a/recipes/r-calder2/meta.yaml +++ b/recipes/r-calder2/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-cate/meta.yaml b/recipes/r-cate/meta.yaml index b24160a34b998..ec589d1f26203 100644 --- a/recipes/r-cate/meta.yaml +++ b/recipes/r-cate/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 85351ed4dce99c6703350659d9561ddc9efd05a765db752d4f5de6933d5d0e73 build: - number: 5 + number: 6 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-ccube/meta.yaml b/recipes/r-ccube/meta.yaml index cc55304fb863c..2e913daac1124 100644 --- a/recipes/r-ccube/meta.yaml +++ b/recipes/r-ccube/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 6 + number: 7 script: R CMD INSTALL --build . rpaths: - lib/R/lib/ diff --git a/recipes/r-cdseq/meta.yaml b/recipes/r-cdseq/meta.yaml index 0bcaea4c98fab..08e94b525ca19 100644 --- a/recipes/r-cdseq/meta.yaml +++ b/recipes/r-cdseq/meta.yaml @@ -12,7 +12,7 @@ source: build: # no r-harmony on OSX skip: True # [osx] - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-cellassign/meta.yaml b/recipes/r-cellassign/meta.yaml index 6590a04e26ea7..5da980f189771 100644 --- a/recipes/r-cellassign/meta.yaml +++ b/recipes/r-cellassign/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-cellosaurus/meta.yaml b/recipes/r-cellosaurus/meta.yaml index 303e14d510275..6be0c70a6618e 100644 --- a/recipes/r-cellosaurus/meta.yaml +++ b/recipes/r-cellosaurus/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('r-cellosaurus', max_pin="x.x") }} diff --git a/recipes/r-chbutils/meta.yaml b/recipes/r-chbutils/meta.yaml index 0291d124ad499..6252abc6c13d1 100644 --- a/recipes/r-chbutils/meta.yaml +++ b/recipes/r-chbutils/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-chord/build_failure.linux-64.yaml b/recipes/r-chord/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..3ea72145c8225 --- /dev/null +++ b/recipes/r-chord/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 12290268f049d96048925f3c2f65a1ba13d1320b4406ca974401a3614c666420 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Encountered problems while solving: + - package r-mutsigextractor-1.14-r43hdfd78af_0 requires r-base >=4.3,<4.4.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-mutsigextractor 1.14.* [0m is not installable because it requires + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-mutsigextractor==1.14=r43hdfd78af_0"), MatchSpec("r-base[version='>=4.3,<4.4.0a0']")} + Encountered problems while solving: + - package r-mutsigextractor-1.14-r43hdfd78af_0 requires r-base >=4.3,<4.4.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-mutsigextractor 1.14.* [0m is not installable because it requires + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-mutsigextractor==1.14=r43hdfd78af_0"), MatchSpec("r-base[version='>=4.3,<4.4.0a0']")} + Encountered problems while solving: + - package r-mutsigextractor-1.14-r43hdfd78af_0 requires r-base >=4.3,<4.4.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-mutsigextractor 1.14.* [0m is not installable because it requires + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-chord/meta.yaml b/recipes/r-chord/meta.yaml index 112ef12290bf6..f5307c08f4a4d 100644 --- a/recipes/r-chord/meta.yaml +++ b/recipes/r-chord/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage("r-chord", max_pin="x.x") }} diff --git a/recipes/r-chromium/meta.yaml b/recipes/r-chromium/meta.yaml index 0c8141d3d61c6..7b182a5506d4a 100644 --- a/recipes/r-chromium/meta.yaml +++ b/recipes/r-chromium/meta.yaml @@ -10,7 +10,7 @@ source: sha256: e2f58a6141ce55b73d631323360d86d3713bf7870476c2505f457c61f41a3d0b build: - number: 1 + number: 2 noarch: generic run_exports: - {{ pin_subpackage('r-chromium', max_pin="x.x") }} diff --git a/recipes/r-cimpl/build_failure.osx-64.yaml b/recipes/r-cimpl/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..59f0863ae6fa8 --- /dev/null +++ b/recipes/r-cimpl/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 4c21989c0dbfd83fa04078f8e4798f6c134e42bc1b971f5ab72b28c825337245 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("3.2.2*"), MatchSpec("bioconductor-biomart==2.26.1=r3.2.2_0")} + Encountered problems while solving: + - nothing provides r 3.2.2* needed by bioconductor-biomart-2.26.1-r3.2.2_0 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-biomart is installable with the potential options + bioconductor-biomart [2.28.0|2.30.0] would require + r-base 3.3.2* , which can be installed; + bioconductor-biomart [2.26.1|2.28.0] would require + r 3.2.2* , which does not exist (perhaps a missing channel); + bioconductor-biomart [2.27.0|2.28.0] would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-biomart [2.30.0|2.32.1|2.34.0|2.34.2] would require + r-base 3.4.1* , which can be installed; + bioconductor-biomart 2.36.1 would require + bioconductor-annotationdbi >=1.42.1,<1.44.0 , which requires + bioconductor-iranges >=2.14.12,<2.16.0 , which conflicts with any installable versions previously reported; + bioconductor-biomart 2.38.0 would require + bioconductor-annotationdbi >=1.44.0,<1.45.0 , which requires + bioconductor-iranges >=2.16.0,<2.17.0 , which conflicts with any installable versions previously reported; + bioconductor-biomart 2.40.3 would require + bioconductor-annotationdbi >=1.46.0,<1.47.0 , which requires + bioconductor-iranges >=2.18.0,<2.19.0 , which conflicts with any installable versions previously reported; + bioconductor-biomart 2.42.0 would require + bioconductor-annotationdbi >=1.48.0,<1.49.0 , which requires + bioconductor-iranges >=2.20.0,<2.21.0 , which conflicts with any installable versions previously reported; + bioconductor-biomart 2.44.0 would require + bioconductor-annotationdbi >=1.50.0,<1.51.0 , which requires + bioconductor-iranges >=2.22.0,<2.23.0 , which conflicts with any installable versions previously reported; + bioconductor-biomart [2.46.0|2.46.3] would require + bioconductor-annotationdbi >=1.52.0,<1.53.0 , which requires + bioconductor-iranges >=2.24.0,<2.25.0 , which conflicts with any installable versions previously reported; + bioconductor-biomart 2.48.0 would require + bioconductor-annotationdbi >=1.54.0,<1.55.0 , which requires + bioconductor-iranges >=2.26.0,<2.27.0 , which conflicts with any installable versions previously reported; + bioconductor-biomart 2.50.0 would require + bioconductor-annotationdbi >=1.56.0,<1.57.0 , which requires + bioconductor-iranges >=2.28.0,<2.29.0 , which conflicts with any installable versions previously reported; + bioconductor-biomart 2.54.0 would require + bioconductor-annotationdbi >=1.60.0,<1.61.0 , which requires + bioconductor-iranges >=2.32.0,<2.33.0 , which conflicts with any installable versions previously reported; + bioconductor-biomart 2.56.1 would require + bioconductor-annotationdbi >=1.62.0,<1.63.0 , which requires + bioconductor-iranges >=2.34.0,<2.35.0 , which conflicts with any installable versions previously reported; + bioconductor-biomart 2.58.0 would require + bioconductor-annotationdbi >=1.64.0,<1.65.0 , which requires + bioconductor-iranges >=2.36.0,<2.37.0 , which conflicts with any installable versions previously reported; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-cimpl/meta.yaml b/recipes/r-cimpl/meta.yaml index 6ee69e0f3d733..2a87576df24cf 100644 --- a/recipes/r-cimpl/meta.yaml +++ b/recipes/r-cimpl/meta.yaml @@ -5,7 +5,7 @@ source: url: https://github.com/NKI-CCB/cimpl/archive/v1.1.tar.gz sha256: 4895f221e8d12efc65d892684efbd151e909b32d5c5041d4bcefea9e832995f5 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-classdiscovery/meta.yaml b/recipes/r-classdiscovery/meta.yaml index 031a2df080c26..f2264c4b03f8d 100644 --- a/recipes/r-classdiscovery/meta.yaml +++ b/recipes/r-classdiscovery/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-cleangeostreamr/meta.yaml b/recipes/r-cleangeostreamr/meta.yaml index 397cf3281f8cd..f90905d53a75b 100644 --- a/recipes/r-cleangeostreamr/meta.yaml +++ b/recipes/r-cleangeostreamr/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 8d9b345d47e0739d9664119162c5aff1e3ca91c99c76be2a09baf7bd82c63258 build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-cobrar/meta.yaml b/recipes/r-cobrar/meta.yaml index 78121f95e2bfa..74cf6c5423d7a 100644 --- a/recipes/r-cobrar/meta.yaml +++ b/recipes/r-cobrar/meta.yaml @@ -13,7 +13,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 script: R CMD INSTALL --build . rpaths: - lib/R/lib/ diff --git a/recipes/r-codedepends/meta.yaml b/recipes/r-codedepends/meta.yaml index 321e8713df784..e0177abf8676c 100644 --- a/recipes/r-codedepends/meta.yaml +++ b/recipes/r-codedepends/meta.yaml @@ -14,7 +14,7 @@ source: build: merge_build_host: True # [win] - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-conos/build_failure.osx-64.yaml b/recipes/r-conos/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..a4370fde2c984 --- /dev/null +++ b/recipes/r-conos/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 8c534664fd65b27f1b2ac21356b0c5e90854eb3e7c74efdbe38d7b7a03988d75 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-conos-1.5.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-conos-1.5.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-conos-1.5.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-conos-1.5.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-conos-1.5.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-conos-1.5.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-conos-1.5.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-conos-1.5.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -I'$PREFIX/lib/R/library/RcppProgress/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -I"./include" -fopenmp -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -I'$PREFIX/lib/R/library/RcppProgress/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -I"./include" -fopenmp -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c Rjnmf.cpp -o Rjnmf.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -I'$PREFIX/lib/R/library/RcppProgress/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -I"./include" -fopenmp -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c adjustedRand.cpp -o adjustedRand.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -I'$PREFIX/lib/R/library/RcppProgress/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -I"./include" -fopenmp -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c checkfunctions.cpp -o checkfunctions.o + ld: warning: directory not found for option '-L/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/_build_env/lib' + installing to /opt/mambaforge/envs/bioconda/conda-bld/r-conos_1734133711283/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/R/library/00LOCK-work/00new/conos/libs + ** R + ** data + *** moving datasets to lazyload DB + Warning: namespace pagoda2 is not available and has been replaced + by .GlobalEnv when processing object small_panel.preprocessed + Warning: namespace pagoda2 is not available and has been replaced + by .GlobalEnv when processing object small_panel.preprocessed + ** inst + ** byte-compile and prepare package for lazy loading + ERROR: lazy loading failed for package conos + * removing /opt/mambaforge/envs/bioconda/conda-bld/r-conos_1734133711283/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/R/library/conos + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -I'$PREFIX/lib/R/library/RcppProgress/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -I"./include" -fopenmp -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c cpca.cpp -o cpca.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -I'$PREFIX/lib/R/library/RcppProgress/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -I"./include" -fopenmp -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c deltacut.cpp -o deltacut.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -I'$PREFIX/lib/R/library/RcppProgress/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -I"./include" -fopenmp -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c edgeFilter.cpp -o edgeFilter.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -I'$PREFIX/lib/R/library/RcppProgress/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -I"./include" -fopenmp -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c edge_rebalancing.cpp -o edge_rebalancing.o + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -I'$PREFIX/lib/R/library/RcppProgress/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -I"./include" -fopenmp -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c edgeweights.cpp -o edgeweights.o + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -I'$PREFIX/lib/R/library/RcppProgress/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -I"./include" -fopenmp -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c gradients.cpp -o gradients.o + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/r-conos_1734133711283/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -I'$PREFIX/lib/R/library/RcppProgress/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -I"./include" -fopenmp -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c graph_embedding.cpp -o graph_embedding.o + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/r-conos_1734133711283/work/conda_build.sh']' returned non-zero exit status 1. + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -I'$PREFIX/lib/R/library/RcppProgress/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -I"./include" -fopenmp -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c largeVis.cpp -o largeVis.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -I'$PREFIX/lib/R/library/RcppProgress/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -I"./include" -fopenmp -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c propagate_labels.cpp -o propagate_labels.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/RcppEigen/include' -I'$PREFIX/lib/R/library/RcppProgress/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -I"./include" -fopenmp -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c spcov.cpp -o spcov.o + x86_64-apple-darwin13.4.0-clang -std=gnu17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L$PREFIX/lib/R/lib -Wl,-dead_strip_dylibs -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -o conos.so RcppExports.o Rjnmf.o adjustedRand.o checkfunctions.o cpca.o deltacut.o edgeFilter.o edge_rebalancing.o edgeweights.o gradients.o graph_embedding.o largeVis.o propagate_labels.o spcov.o -L. -lpthread -lm -llapack -lblas -L$PREFIX/lib/gcc/x86_64-apple-darwin13.4.0/13.2.0 -L/Users/runner/miniforge3/conda-bld/r-base-split_1732138555983/_build_env/lib -lgfortran -lquadmath -lm -fopenmp -L$PREFIX/lib/R/lib -lR -Wl,-framework -Wl,CoreFoundation + Error: package ComplexHeatmap was installed before R 4.0.0: please re-install it + Execution halted +# Last 100 lines of the build log. diff --git a/recipes/r-conos/meta.yaml b/recipes/r-conos/meta.yaml index 764a6f992dd1a..0112f07be4539 100644 --- a/recipes/r-conos/meta.yaml +++ b/recipes/r-conos/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 736a00a2574fd39d063d70038ae1ff738cfcb6de61827aaf765f7004c67ac65c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-consensustme/meta.yaml b/recipes/r-consensustme/meta.yaml index df9cd107895c2..ef1e313ac864c 100644 --- a/recipes/r-consensustme/meta.yaml +++ b/recipes/r-consensustme/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 336d47a83a2be0a1d37147fdda71cfd6f8b198100a6a828c3987ce8ba776cea4 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-corncob/meta.yaml b/recipes/r-corncob/meta.yaml index 59804c6fc189d..9a1ef5e826935 100644 --- a/recipes/r-corncob/meta.yaml +++ b/recipes/r-corncob/meta.yaml @@ -14,7 +14,7 @@ source: build: merge_build_host: True # [win] - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-cp4p/meta.yaml b/recipes/r-cp4p/meta.yaml index 5f48d30d5c83b..5f8f6bbb022c0 100644 --- a/recipes/r-cp4p/meta.yaml +++ b/recipes/r-cp4p/meta.yaml @@ -14,7 +14,7 @@ source: build: merge_build_host: True # [win] - number: 6 + number: 7 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-crbhits/build_failure.linux-64.yaml b/recipes/r-crbhits/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..93258c47fd3dc --- /dev/null +++ b/recipes/r-crbhits/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5e5bbaa918ff5142818498b392a69997dfb1f79717a71e0483adcf803394b0e0 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + copy_test_source_files: true + final: true + identifiers: + - doi:10.21105/joss.02424 + + + source tree in: /opt/conda/conda-bld/r-crbhits_1734896932795/work + export PREFIX=/opt/conda/conda-bld/r-crbhits_1734896932795/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + export BUILD_PREFIX=/opt/conda/conda-bld/r-crbhits_1734896932795/_build_env + export SRC_DIR=/opt/conda/conda-bld/r-crbhits_1734896932795/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-crbhits-0.0.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-crbhits-0.0.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-crbhits-0.0.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-crbhits-0.0.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/r-crbhits_1734896932795/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library + * installing *source* package CRBHits ... + ** using staged installation + ** R + ** data + ** inst + ** byte-compile and prepare package for lazy loading + During startup - Warning message: + Setting LC_TIME failed, using "C" + Error in get(".makePostalignedSeqs", envir = asNamespace("Biostrings"), : + object '.makePostalignedSeqs' not found + Error: unable to load R code in package CRBHits + Execution halted + ERROR: lazy loading failed for package CRBHits + * removing /opt/conda/conda-bld/r-crbhits_1734896932795/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/library/CRBHits + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/r-crbhits_1734896932795/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/r-crbhits_1734896932795/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/r-crbhits/build_failure.osx-64.yaml b/recipes/r-crbhits/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..31ccd3488616b --- /dev/null +++ b/recipes/r-crbhits/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5e5bbaa918ff5142818498b392a69997dfb1f79717a71e0483adcf803394b0e0 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("r-base[version='>=4.2,<4.3.0a0']"), MatchSpec("bioconductor-msa2dist==1.2.0=r42hb890f52_0")} + Encountered problems while solving: + - package bioconductor-msa2dist-1.2.0-r42hb890f52_0 requires r-base >=4.2,<4.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + bioconductor-msa2dist is installable with the potential options + bioconductor-msa2dist 1.2.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-msa2dist [1.4.0|1.6.0] would require + bioconductor-genomicranges >=1.52.0,<1.53.0 , which requires + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("r-base[version='>=4.2,<4.3.0a0']"), MatchSpec("bioconductor-msa2dist==1.2.0=r42hb890f52_0")} + Encountered problems while solving: + - package bioconductor-msa2dist-1.2.0-r42hb890f52_0 requires r-base >=4.2,<4.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + bioconductor-msa2dist is installable with the potential options + bioconductor-msa2dist 1.2.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-msa2dist [1.4.0|1.6.0] would require + bioconductor-genomicranges >=1.52.0,<1.53.0 , which requires + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-crbhits/meta.yaml b/recipes/r-crbhits/meta.yaml index 290bc8fe95bf1..c24914e7f970a 100644 --- a/recipes/r-crbhits/meta.yaml +++ b/recipes/r-crbhits/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 2b16cebb11acb1460c7c99c3455f7570cd2b1e485e986bb02a609a956849a43f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-crisprcleanr/meta.yaml b/recipes/r-crisprcleanr/meta.yaml index 6f09d783546e8..454ee275c1e03 100644 --- a/recipes/r-crisprcleanr/meta.yaml +++ b/recipes/r-crisprcleanr/meta.yaml @@ -10,7 +10,7 @@ source: sha256: d14088fdba4d8f3c51418804458eb6d430de1016f75d91097e13abe10e187faa build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-crmn/meta.yaml b/recipes/r-crmn/meta.yaml index 20c205201302a..8b68c1c495716 100644 --- a/recipes/r-crmn/meta.yaml +++ b/recipes/r-crmn/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 659eb2ba41111ef7a17e1ffe75750735ec9cf2394e881eee4b05f9c3b54be972 build: - number: 4 + number: 5 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-cssam/meta.yaml b/recipes/r-cssam/meta.yaml index 304039fe27b53..d3ac29398886b 100644 --- a/recipes/r-cssam/meta.yaml +++ b/recipes/r-cssam/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 722838845a8d3637b4c45b6a9316e70aaeccec0f68fa764ec311c24aaf915fc9 build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-dartr/build_failure.linux-64.yaml b/recipes/r-dartr/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..655505bd74061 --- /dev/null +++ b/recipes/r-dartr/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 4ca3e5e4270ab73127103783bc05250fff483f3d0fa8c3211ecaaa1e1a177f1b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-base[version='>=4.0,<4.1.0a0']"), MatchSpec("r-popgenreport==3.0.7=r40hc72bb7e_0")} + Encountered problems while solving: + - package r-popgenreport-3.0.7-r40hc72bb7e_0 requires r-base >=4.0,<4.1.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-popgenreport[0m is not installable because there are no viable options + [31mr-popgenreport 3.0.7[0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-popgenreport 3.0.7[0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-popgenreport [3.0.7|3.1][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-popgenreport [3.0.7|3.1][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-popgenreport 3.0.4[0m conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-base[version='>=4.0,<4.1.0a0']"), MatchSpec("r-popgenreport==3.0.7=r40hc72bb7e_0")} + Encountered problems while solving: + - package r-popgenreport-3.0.7-r40hc72bb7e_0 requires r-base >=4.0,<4.1.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mr-base 4.4.* [0m is requested and can be installed; + [31mr-popgenreport[0m is not installable because there are no viable options + [31mr-popgenreport 3.0.7[0m would require + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-popgenreport 3.0.7[0m would require + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-popgenreport [3.0.7|3.1][0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-popgenreport [3.0.7|3.1][0m would require + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-popgenreport 3.0.4[0m conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-dartr/meta.yaml b/recipes/r-dartr/meta.yaml index 1140388165d1c..bc74840d016f9 100644 --- a/recipes/r-dartr/meta.yaml +++ b/recipes/r-dartr/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 7d8f7467f6d7c5514531bb0fb7917ae0e28eedec4fc3a0b404890e72f01395f3 build: - number: 1 + number: 2 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-ddir/meta.yaml b/recipes/r-ddir/meta.yaml index c7e84843cb0d7..d82a7673cc5cc 100644 --- a/recipes/r-ddir/meta.yaml +++ b/recipes/r-ddir/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 4a58d5c81b467eaff60bb62a3a592a39ef13eed64e641d41840dffdf69aa14cd build: - number: 5 + number: 6 noarch: generic script: R CMD INSTALL --build . diff --git a/recipes/r-deconcell/meta.yaml b/recipes/r-deconcell/meta.yaml index 211669e1ffeda..098d10cdc904a 100644 --- a/recipes/r-deconcell/meta.yaml +++ b/recipes/r-deconcell/meta.yaml @@ -12,7 +12,7 @@ source: build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-deconstructsigs/meta.yaml b/recipes/r-deconstructsigs/meta.yaml index 4aadfbcbfd26a..23f433a817a3f 100644 --- a/recipes/r-deconstructsigs/meta.yaml +++ b/recipes/r-deconstructsigs/meta.yaml @@ -17,7 +17,7 @@ source: build: noarch: generic - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-deseqanalysis/meta.yaml b/recipes/r-deseqanalysis/meta.yaml index c946b43612c5b..3f669b38875a4 100644 --- a/recipes/r-deseqanalysis/meta.yaml +++ b/recipes/r-deseqanalysis/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('r-deseqanalysis', max_pin="x.x") }} diff --git a/recipes/r-diffcorr/meta.yaml b/recipes/r-diffcorr/meta.yaml index 71a4ef28bc8e3..dd97423f56a13 100644 --- a/recipes/r-diffcorr/meta.yaml +++ b/recipes/r-diffcorr/meta.yaml @@ -11,7 +11,7 @@ source: sha256: c729fe399aceaf3afb975777ff3483e5d557d9b55b33fe5803bdb8949ff33b17 build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-dimsum/meta.yaml b/recipes/r-dimsum/meta.yaml index e9fa3a19d4f22..827a16afc104b 100644 --- a/recipes/r-dimsum/meta.yaml +++ b/recipes/r-dimsum/meta.yaml @@ -22,10 +22,10 @@ requirements: build: - r-base host: - - r-base =4.0 + - r-base ==4.0 - pandoc >=1.17.2 - fastqc =0.11 - - cutadapt =2.4 + - cutadapt ==2.4 - vsearch >=2.17 - starcode >=1.3 - bioconductor-biostrings @@ -45,10 +45,10 @@ requirements: - r-seqinr - r-stringr run: - - r-base =4.0 + - r-base ==4.0 - pandoc >=1.17.2 - - fastqc =0.11 - - cutadapt =2.4 + - fastqc ==0.11 + - cutadapt ==2.4 - vsearch >=2.17 - starcode >=1.3 - bioconductor-biostrings diff --git a/recipes/r-dinamic.duo/meta.yaml b/recipes/r-dinamic.duo/meta.yaml index 4c931d631e648..0c063ddc3794b 100644 --- a/recipes/r-dinamic.duo/meta.yaml +++ b/recipes/r-dinamic.duo/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 173dedb65cb9e6c3f5af6b48adb580fed90dcab7f6acbe7c7ae5cde618608f19 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-disprose/meta.yaml b/recipes/r-disprose/meta.yaml index 823ce9251552f..d15b1f8f3425a 100644 --- a/recipes/r-disprose/meta.yaml +++ b/recipes/r-disprose/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 65a4abf261063171e23b29bf5ad2b437617afe44988e5e75866d64c76547b64a build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-dnet/build_failure.linux-64.yaml b/recipes/r-dnet/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..dbd29c7c29d26 --- /dev/null +++ b/recipes/r-dnet/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 3296b213ecadfa4b7dec2166cda390891c3d3faf95c6256dc1293af0602833cd # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Encountered problems while solving: + - package bioconductor-suprahex-1.40.0-r43hdfd78af_0 requires r-base >=4.3,<4.4.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-suprahex >=1.40.0 [0m is installable and it requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-suprahex==1.40.0=r43hdfd78af_0"), MatchSpec("r-base[version='>=4.3,<4.4.0a0']")} + Encountered problems while solving: + - package bioconductor-suprahex-1.40.0-r43hdfd78af_0 requires r-base >=4.3,<4.4.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-suprahex >=1.40.0 [0m is installable and it requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-suprahex==1.40.0=r43hdfd78af_0"), MatchSpec("r-base[version='>=4.3,<4.4.0a0']")} + Encountered problems while solving: + - package bioconductor-suprahex-1.40.0-r43hdfd78af_0 requires r-base >=4.3,<4.4.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-suprahex >=1.40.0 [0m is installable and it requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. +category: |- + dependency issue diff --git a/recipes/r-dnet/meta.yaml b/recipes/r-dnet/meta.yaml index 6a7abcfdddfa8..10e05ad93a8dc 100644 --- a/recipes/r-dnet/meta.yaml +++ b/recipes/r-dnet/meta.yaml @@ -13,11 +13,13 @@ source: sha256: ac2be6d2b64dd6f63002c80b4646506fadf3ec9dc690249193db40d1d17db816 build: - number: 5 + number: 6 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-dnet', max_pin="x") }} requirements: build: @@ -28,14 +30,14 @@ requirements: - bioconductor-rgraphviz - bioconductor-graph - r-igraph - - bioconductor-suprahex + - bioconductor-suprahex >=1.40.0 run: - r-base - r-matrix - bioconductor-rgraphviz - bioconductor-graph - r-igraph - - bioconductor-suprahex + - bioconductor-suprahex >=1.40.0 test: commands: diff --git a/recipes/r-dpeak/meta.yaml b/recipes/r-dpeak/meta.yaml index 0c69036171997..22b5fcdaeb68f 100644 --- a/recipes/r-dpeak/meta.yaml +++ b/recipes/r-dpeak/meta.yaml @@ -8,7 +8,7 @@ source: git_rev: b4627c94ef87b3dbd0821230821df4ab7e85be8f build: - number: 9 + number: 10 rpaths: - lib/R/lib/ diff --git a/recipes/r-dsb/build_failure.linux-64.yaml b/recipes/r-dsb/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..4a0a086d5db23 --- /dev/null +++ b/recipes/r-dsb/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 71e9e28496f6c948b4ec3d97b2d9796a82693a40237c5ab8de8cfd9cd7847be6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - r-foreign 0.8_87 r44hb1dbf0f_1 + - r-kernsmooth 2.23_24 r44hc2011d3_1 + - r-lattice 0.22_6 r44hb1dbf0f_1 + - r-magrittr 2.0.3 r44hb1dbf0f_3 + - r-mass 7.3_60.0.1 r44hb1dbf0f_1 + - r-mclust 6.1.1 r44hc29710b_0 + - r-rpart 4.1.23 r44hb1dbf0f_1 + - r-spatial 7.3_17 r44hb1dbf0f_1 + - r-class 7.3_22 r44hb1dbf0f_2 + - r-matrix 1.6_5 r44he966344_1 + - r-nlme 3.1_165 r44hbcb9c34_1 + - r-nnet 7.3_19 r44hb1dbf0f_2 + - r-mgcv 1.9_1 r44h0d28552_1 + - r-survival 3.7_0 r44hdb488b9_1 + - r-recommended 4.4 r44hd8ed1ab_1007 + - r 4.4 r44hd8ed1ab_1008 + - bioconductor-limma 3.28.10 0 + run: + - r-base >=4.4,<4.5.0a0 + - r-base >=4.4,<4.5.0a0 + - bioconductor-limma + - r-mclust + - r-magrittr + test: + commands: + - $R -e "library('dsb')" + about: + description: "This lightweight R package provides a method for normalizing and denoising\ + \ protein expression data from droplet based single cell experiments. Raw protein\ + \ Unique Molecular Index (UMI) counts from sequencing DNA-conjugated antibody\ + \ derived tags (ADT) in droplets (e.g. 'CITE-seq') have substantial measurement\ + \ noise. Our experiments and computational modeling revealed two major components\ + \ of this noise: 1) protein-specific noise originating from ambient, unbound antibody\ + \ encapsulated in droplets that can be accurately inferred via the expected protein\ + \ counts detected in empty droplets, and 2) droplet/cell-specific noise revealed\ + \ via the shared variance component associated with isotype antibody controls\ + \ and background protein counts in each cell. This package normalizes and removes\ + \ both of these sources of noise from raw protein data derived from methods such\ + \ as 'CITE-seq', 'REAP-seq', 'ASAP-seq', 'TEA-seq', 'proteogenomic' data from\ + \ the Mission Bio platform, etc. See the vignette for tutorials on how to integrate\ + \ dsb with 'Seurat' and 'Bioconductor' and how to use dsb in 'Python'. Please\ + \ see our paper Mul\xE8 M.P., Martins A.J., and Tsang J.S. Nature Communications\ + \ 2022 for more details on\ + \ the method." + home: https://github.com/niaid/dsb + license: CC0 | file LICENSE + license_family: CC + license_file: + - LICENSE + summary: Normalizing and denoising protein expression data from droplet-based single + cell profiling + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/conda/conda-bld/r-dsb_1734164131560/work + export PREFIX=/opt/conda/conda-bld/r-dsb_1734164131560/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/conda/conda-bld/r-dsb_1734164131560/_build_env + export SRC_DIR=/opt/conda/conda-bld/r-dsb_1734164131560/work + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/r-dsb_1734164131560/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/R/library + * installing *source* package dsb ... + ** package dsb successfully unpacked and MD5 sums checked + ** using staged installation + ** R + ** data + *** moving datasets to lazyload DB + ** inst + ** byte-compile and prepare package for lazy loading + During startup - Warning message: + Setting LC_TIME failed, using "C" + Error: package limma was installed before R 4.0.0: please re-install it + Execution halted + ERROR: lazy loading failed for package dsb + * removing /opt/conda/conda-bld/r-dsb_1734164131560/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/R/library/dsb + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/r-dsb_1734164131560/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/r-dsb_1734164131560/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/r-dsb/meta.yaml b/recipes/r-dsb/meta.yaml index de253ca893b77..b859c97f9219b 100644 --- a/recipes/r-dsb/meta.yaml +++ b/recipes/r-dsb/meta.yaml @@ -16,7 +16,7 @@ source: build: merge_build_host: True # [win] # If this is a new build for the same version, increment the build number. - number: 0 + number: 1 # no skip noarch: generic # This is required to make R link correctly on Linux. diff --git a/recipes/r-dwls/meta.yaml b/recipes/r-dwls/meta.yaml index ec69650af3908..bd04f9ad10843 100644 --- a/recipes/r-dwls/meta.yaml +++ b/recipes/r-dwls/meta.yaml @@ -10,7 +10,7 @@ source: sha256: dbb4a4b384c4d804286785bb8d85b4f601dde95ac4fc256353dbec6c27b44f9f build: - number: 4 + number: 5 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-easydifferentialgenecoexpression/meta.yaml b/recipes/r-easydifferentialgenecoexpression/meta.yaml index da710a321155f..324c5197e636d 100644 --- a/recipes/r-easydifferentialgenecoexpression/meta.yaml +++ b/recipes/r-easydifferentialgenecoexpression/meta.yaml @@ -11,7 +11,7 @@ source: sha256: d0e1653a311d5e5834ef4b9c333ae3fe5aee8333c1201517ee5f6cb556b054c7 build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-easylift/meta.yaml b/recipes/r-easylift/meta.yaml index 266299908bd36..a290937a977fe 100644 --- a/recipes/r-easylift/meta.yaml +++ b/recipes/r-easylift/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-eggnog/meta.yaml b/recipes/r-eggnog/meta.yaml index 97de17d22f778..aa3eb21293bba 100644 --- a/recipes/r-eggnog/meta.yaml +++ b/recipes/r-eggnog/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 8c003ee0b7dd03b44b7d110eb5d45e46a98822950a8f7e75f70798d2c680cb2c build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-eggnog', max_pin="x.x") }} diff --git a/recipes/r-empiricalfdr.deseq2/meta.yaml b/recipes/r-empiricalfdr.deseq2/meta.yaml index 96a15bd5c5d6f..5c0a8335411f8 100644 --- a/recipes/r-empiricalfdr.deseq2/meta.yaml +++ b/recipes/r-empiricalfdr.deseq2/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-epic/meta.yaml b/recipes/r-epic/meta.yaml index 67c8f05253138..03f0c285bfa43 100755 --- a/recipes/r-epic/meta.yaml +++ b/recipes/r-epic/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 795150b042606a9ab6efbf3b50145c4ee6b626ede5f344b3dd83045238b1f625 build: - number: 1 + number: 2 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-erah/meta.yaml b/recipes/r-erah/meta.yaml index 78d36cf3c8adc..5c78a99978baf 100644 --- a/recipes/r-erah/meta.yaml +++ b/recipes/r-erah/meta.yaml @@ -12,7 +12,7 @@ source: sha256: bd7f89d671ff90f70228ed59c8c1554ca6b3ffab721d50e4ac873daf1e80dc8c build: - number: 0 + number: 1 merge_build_host: false script: R CMD INSTALL --build . run_exports: diff --git a/recipes/r-exomedepth/build_failure.osx-64.yaml b/recipes/r-exomedepth/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..96e185a8961b6 --- /dev/null +++ b/recipes/r-exomedepth/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: b4fecd1c8dd77a25c69f425c4d7db47f111da22e187d618f65795bb04fb23d94 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1 would require + libgfortran >=3.0,<4.0.0.a0 , which can be installed; + r-base [3.5.1|3.6.1|...|4.0.2] would require + libgfortran [4.* |>=4.0.0,<5.0.0.a0 ], which can be installed; + r-base 3.5.1 would require + libgfortran >=3.0.1,<4.0.0.a0 , which can be installed; + bioconductor-iranges [2.14.12|2.16.0] would require + bioconductor-s4vectors >=0.20.0,<0.21.0 , which can be installed (as previously explained); + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed (as previously explained); + r-base [3.5.1|3.6.1|...|4.0.2], which can be installed (as previously explained); + r-base 3.5.1, which can be installed (as previously explained); + bioconductor-iranges [2.18.1|2.18.2|2.20.0] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.5.1|3.6.1|...|4.0.2], which can be installed (as previously explained); + r-base 3.6.3, which can be installed; + bioconductor-iranges [2.22.1|2.24.0|2.24.1] would require + r-base >=4.0,<4.1.0a0 with the potential options + r-base [3.5.1|3.6.1|...|4.0.2], which can be installed (as previously explained); + r-base [4.0.3|4.0.5], which can be installed; + bioconductor-iranges [2.26.0|2.28.0] would require + bioconductor-biocgenerics >=0.38.0,<0.39.0 , which requires + r-base >=4.1,<4.2.0a0 , which can be installed; + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-iranges 2.32.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-iranges [2.34.1|2.36.0] would require + bioconductor-biocgenerics >=0.46.0,<0.47.0 , which requires + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-genomicranges 1.32.7 would require + bioconductor-xvector >=0.20.0,<0.22.0 with the potential options + bioconductor-xvector 0.20.0 would require + bioconductor-zlibbioc >=1.26.0,<1.28.0 with the potential options + bioconductor-zlibbioc 1.26.0 would require + r-base >=3.4.1,<3.4.2.0a0 , which can be installed; + bioconductor-zlibbioc [1.26.0|1.30.0] would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed (as previously explained); + r-base [3.5.1|3.6.1|...|4.0.2], which can be installed (as previously explained); + r-base 3.5.1, which can be installed (as previously explained); + bioconductor-xvector 0.20.0 would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed (as previously explained); + r-base [3.5.1|3.6.1|...|4.0.2], which can be installed (as previously explained); + r-base 3.5.1, which can be installed (as previously explained); + bioconductor-genomicranges [1.32.7|1.34.0] would require + bioconductor-genomeinfodb >=1.18.0,<1.19.0 , which requires + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed (as previously explained); + r-base [3.5.1|3.6.1|...|4.0.2], which can be installed (as previously explained); + r-base 3.5.1, which can be installed (as previously explained); + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed (as previously explained); + r-base [3.5.1|3.6.1|...|4.0.2], which can be installed (as previously explained); + r-base 3.5.1, which can be installed (as previously explained); + bioconductor-genomicranges 1.36.0 would require + bioconductor-xvector >=0.24.0,<0.25.0 , which requires + bioconductor-zlibbioc >=1.30.0,<1.31.0 with the potential options + bioconductor-zlibbioc [1.26.0|1.30.0], which can be installed (as previously explained); + bioconductor-zlibbioc 1.30.0 would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.5.1|3.6.1|...|4.0.2], which can be installed (as previously explained); + r-base 3.6.3, which can be installed; + bioconductor-genomicranges 1.38.0 would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.5.1|3.6.1|...|4.0.2], which can be installed (as previously explained); + r-base 3.6.3, which can be installed; + bioconductor-genomicranges [1.40.0|1.42.0] would require + r-base >=4.0,<4.1.0a0 with the potential options + r-base [3.5.1|3.6.1|...|4.0.2], which can be installed (as previously explained); + r-base [4.0.3|4.0.5], which can be installed; + bioconductor-genomicranges [1.44.0|1.46.0|1.46.1] would require + bioconductor-iranges >=2.28.0,<2.29.0 , which can be installed (as previously explained); + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-genomicranges 1.50.0 would require + bioconductor-iranges >=2.32.0,<2.33.0 , which can be installed (as previously explained); + bioconductor-genomicranges [1.52.0|1.54.1] would require + bioconductor-iranges >=2.36.0,<2.37.0 , which can be installed (as previously explained); + r-base >=4.3,<4.4.0a0 , which can be installed; + libgfortran5 >=13.2.0 is not installable because there are no viable options + libgfortran5 13.2.0 would require + libgfortran 5.0.0 13_2_0_*_1, which conflicts with any installable versions previously reported; + libgfortran5 13.2.0 would require + libgfortran 5.0.0 13_2_0_*_2, which conflicts with any installable versions previously reported; + libgfortran5 13.2.0 would require + libgfortran 5.0.0 13_2_0_*_3, which conflicts with any installable versions previously reported; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-exomedepth/meta.yaml b/recipes/r-exomedepth/meta.yaml index 84312dcf3d294..0238a90ece115 100644 --- a/recipes/r-exomedepth/meta.yaml +++ b/recipes/r-exomedepth/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 7ba6b51e7ea435a2799b25d99bb9f48e2b1e99e15e47f88e514e98120b4cebe4 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-eztune/meta.yaml b/recipes/r-eztune/meta.yaml index 883a4390bbadc..c81acdc97b9e4 100644 --- a/recipes/r-eztune/meta.yaml +++ b/recipes/r-eztune/meta.yaml @@ -11,7 +11,7 @@ source: sha256: d3d57b42cb436b805fc066ea7e0eb25c164f51795c250eb23eaaf2b5dea29a69 build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-facets/meta.yaml b/recipes/r-facets/meta.yaml index f0ea43f0f9c9d..2bcf982889974 100644 --- a/recipes/r-facets/meta.yaml +++ b/recipes/r-facets/meta.yaml @@ -7,7 +7,7 @@ source: sha256: aa671d4fc66e10ce2fe4c8b2cbac4946da8a1564627240ea916db6cd8ec2a6c5 build: - number: 6 + number: 7 run_exports: - {{ pin_subpackage("r-facets", max_pin="x") }} rpaths: diff --git a/recipes/r-fastbaps/build_failure.osx-64.yaml b/recipes/r-fastbaps/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..cb37d224773be --- /dev/null +++ b/recipes/r-fastbaps/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 92623b068175015a7edbbf503f4635e4809e3a049b996c6f29cc866f8bff4c7f # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("clang==4.0.1=1"), MatchSpec("4.0.1==hcfea43d_1")} + Encountered problems while solving: + - nothing provides compiler-rt 4.0.1 hcfea43d_1 needed by clang-4.0.1-1 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-ggtree is installable with the potential options + bioconductor-ggtree 1.2.12 would require + bioconductor-biostrings with the potential options + bioconductor-biostrings [2.38.3|2.38.4] would require + bioconductor-biocgenerics >=0.15.6 with the potential options + bioconductor-biocgenerics [0.16.1|0.18.0] would require + r 3.2.2* , which does not exist (perhaps a missing channel); + bioconductor-biocgenerics [0.16.1|0.18.0|0.20.0] would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-biocgenerics [0.20.0|0.22.0] would require + r-base 3.3.2* , which can be installed; + bioconductor-biocgenerics [0.22.0|0.22.1|0.24.0|0.26.0] would require + r-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ], which can be installed; + bioconductor-biocgenerics [0.24.0|0.26.0|0.28.0] would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-biocgenerics [0.30.0|0.32.0] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-biocgenerics [0.34.0|0.36.0] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-biocgenerics [0.38.0|0.40.0] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-biocgenerics 0.44.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-biocgenerics [0.46.0|0.48.1] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-biostrings [2.40.0|2.40.2] would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-biostrings 2.42.1 would require + r-base 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-biostrings 2.42.1 would require + r-base 3.3.2* , which can be installed; + bioconductor-biostrings [2.42.1|2.44.2|2.46.0|2.48.0] would require + r-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ], which can be installed; + bioconductor-biostrings [2.48.0|2.50.1|2.50.2] would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed; + bioconductor-biostrings [2.52.0|2.54.0] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-biostrings [2.56.0|2.58.0] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-biostrings [2.60.0|2.62.0] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-biostrings 2.66.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-biostrings [2.68.1|2.70.1] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-ggtree [1.10.0|1.12.7|1.4.20] would require + r-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ], which can be installed; + bioconductor-ggtree [1.12.7|1.14.4|1.14.6|1.16.0] would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed; + bioconductor-ggtree 1.4.20 would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-ggtree [1.4.20|1.8.2] would require + r-base [3.3.2* |>=3.3,<3.4 ], which can be installed; + bioconductor-ggtree [1.16.3|2.0.0] would require + bioconductor-treeio >=1.10.0,<1.11.0 , which requires + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-ggtree [2.2.1|2.4.0|2.4.1] would require + bioconductor-treeio >=1.12.0,<1.13.0 , which requires + r-base >=4.0,<4.1.0a0 , which can be installed; + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-ggtree [3.0.1|3.2.0] would require + bioconductor-treeio [>=1.16.0,<1.17.0 |>=1.18.0,<1.19.0 ], which requires + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-ggtree [3.10.0|3.8.0] would require + bioconductor-treeio >=1.24.0,<1.25.0 , which requires + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-ggtree 3.6.0 would require + bioconductor-treeio >=1.22.0,<1.23.0 , which requires + r-base >=4.2,<4.3.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-fastbaps/meta.yaml b/recipes/r-fastbaps/meta.yaml index b6e6b2712c33d..3f4b2f656f2d2 100644 --- a/recipes/r-fastbaps/meta.yaml +++ b/recipes/r-fastbaps/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ diff --git a/recipes/r-fgwas/build_failure.linux-64.yaml b/recipes/r-fgwas/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..eeedd412c8910 --- /dev/null +++ b/recipes/r-fgwas/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 029a45489092eab2c781f6286a6fce037bc40e88cbbad24b188767b89f1ddb14 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [32mbioconductor-snpstats [1.38.0|1.40.0][0m would require + [32mbioconductor-biocgenerics >=0.34.0,<0.35.0 [0m, which requires + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-snpstats [1.42.0|1.44.0][0m would require + [32mbioconductor-biocgenerics [>=0.38.0,<0.39.0 |>=0.40.0,<0.41.0 ][0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-snpstats 1.48.0[0m would require + [32mbioconductor-biocgenerics >=0.44.0,<0.45.0 [0m, which requires + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-snpstats [1.50.0|1.52.0][0m would require + [32mbioconductor-biocgenerics >=0.46.0,<0.47.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-base=3.3.2"), MatchSpec("bioconductor-snpstats==1.26.0=r3.3.2_0")} + Encountered problems while solving: + - package bioconductor-snpstats-1.26.0-r3.3.2_0 requires r-base 3.3.2*, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-snpstats[0m is installable with the potential options + [32mbioconductor-snpstats 1.26.0[0m would require + [32mr-base 3.3.2* [0m, which can be installed; + [32mbioconductor-snpstats [1.26.0|1.28.0|1.30.0][0m would require + [32mr-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ][0m, which can be installed; + [32mbioconductor-snpstats [1.28.0|1.30.0|1.32.0][0m would require + [32mbioconductor-zlibbioc >=1.28.0,<1.29.0 [0m, which requires + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-snpstats [1.34.0|1.36.0][0m would require + [32mbioconductor-biocgenerics [>=0.30.0,<0.31.0 |>=0.32.0,<0.33.0 ][0m, which requires + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-snpstats [1.38.0|1.40.0][0m would require + [32mbioconductor-biocgenerics >=0.34.0,<0.35.0 [0m, which requires + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-snpstats [1.42.0|1.44.0][0m would require + [32mbioconductor-biocgenerics [>=0.38.0,<0.39.0 |>=0.40.0,<0.41.0 ][0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-snpstats 1.48.0[0m would require + [32mbioconductor-biocgenerics >=0.44.0,<0.45.0 [0m, which requires + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-snpstats [1.50.0|1.52.0][0m would require + [32mbioconductor-biocgenerics >=0.46.0,<0.47.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-fgwas/meta.yaml b/recipes/r-fgwas/meta.yaml index 6fe99c1c43515..a7688c021d485 100644 --- a/recipes/r-fgwas/meta.yaml +++ b/recipes/r-fgwas/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 7 + number: 8 # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ diff --git a/recipes/r-firebrowser/meta.yaml b/recipes/r-firebrowser/meta.yaml index 3945642b7d225..fb8336491acb7 100644 --- a/recipes/r-firebrowser/meta.yaml +++ b/recipes/r-firebrowser/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 5 + number: 6 rpaths: - lib/R/lib/ diff --git a/recipes/r-garnett/meta.yaml b/recipes/r-garnett/meta.yaml index 78f50a85b9832..baee079aea23f 100644 --- a/recipes/r-garnett/meta.yaml +++ b/recipes/r-garnett/meta.yaml @@ -9,7 +9,7 @@ source: sha256: b96c659b83d298786be00655b56424c0d1bcaae5fbcbf38e15545c462308323d build: - number: 5 + number: 6 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-gchromvar/meta.yaml b/recipes/r-gchromvar/meta.yaml index 5d3b2466a581a..4cab6d09b52f7 100644 --- a/recipes/r-gchromvar/meta.yaml +++ b/recipes/r-gchromvar/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-geneexpressionfromgeo/meta.yaml b/recipes/r-geneexpressionfromgeo/meta.yaml index 23c95d62dec9b..710f624f14ee4 100644 --- a/recipes/r-geneexpressionfromgeo/meta.yaml +++ b/recipes/r-geneexpressionfromgeo/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 77212160725f2e866d8364f5414073650cd4ad638d5d275f0dbc6a4b9ce8bb95 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-genomictools.filehandler/meta.yaml b/recipes/r-genomictools.filehandler/meta.yaml index 37dbf40acd32b..58c053f6c4c59 100644 --- a/recipes/r-genomictools.filehandler/meta.yaml +++ b/recipes/r-genomictools.filehandler/meta.yaml @@ -14,7 +14,7 @@ source: build: merge_build_host: True # [win] - number: 4 + number: 5 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-genomictools/build_failure.osx-64.yaml b/recipes/r-genomictools/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..aa07c0412362e --- /dev/null +++ b/recipes/r-genomictools/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: afd5e7719de0e2fabfe04149a5cfe0ae467f2d832198bed604fcaa21fd13481d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("r-base=3.3.2"), MatchSpec("bioconductor-snpstats==1.26.0=r3.3.2_0")} + Encountered problems while solving: + - package bioconductor-snpstats-1.26.0-r3.3.2_0 requires r-base 3.3.2*, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + bioconductor-snpstats is installable with the potential options + bioconductor-snpstats 1.26.0 would require + r-base 3.3.2* , which can be installed; + bioconductor-snpstats [1.26.0|1.28.0|1.30.0] would require + r-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ], which can be installed; + bioconductor-snpstats [1.28.0|1.30.0|1.32.0] would require + bioconductor-zlibbioc >=1.28.0,<1.29.0 , which requires + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed; + bioconductor-snpstats [1.34.0|1.36.0] would require + bioconductor-biocgenerics [>=0.30.0,<0.31.0 |>=0.32.0,<0.33.0 ], which requires + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-snpstats [1.38.0|1.40.0] would require + bioconductor-biocgenerics >=0.34.0,<0.35.0 , which requires + r-base >=4.0,<4.1.0a0 , which can be installed; + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-snpstats [1.42.0|1.44.0] would require + bioconductor-biocgenerics [>=0.38.0,<0.39.0 |>=0.40.0,<0.41.0 ], which requires + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-snpstats 1.48.0 would require + bioconductor-biocgenerics >=0.44.0,<0.45.0 , which requires + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-snpstats [1.50.0|1.52.0] would require + bioconductor-biocgenerics >=0.46.0,<0.47.0 , which requires + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-genomictools/meta.yaml b/recipes/r-genomictools/meta.yaml index c34c5fd65a00c..40ee72a8d2b7a 100644 --- a/recipes/r-genomictools/meta.yaml +++ b/recipes/r-genomictools/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 15fcf653177f3b9cb822c4da08d7cc5507b9f48d4a6ca58e523c3e965787daa4 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-george/meta.yaml b/recipes/r-george/meta.yaml index 414a2eab19d09..ca6fdcb8be08b 100644 --- a/recipes/r-george/meta.yaml +++ b/recipes/r-george/meta.yaml @@ -5,7 +5,7 @@ source: url: https://github.com/jcapelladesto/geoRge/archive/v1.0.1.zip md5: 0c30595306dcea334d054b7733bba375 build: - number: 6 + number: 7 skip: True # [osx] rpaths: - lib/R/lib/ diff --git a/recipes/r-gganatogram/meta.yaml b/recipes/r-gganatogram/meta.yaml index a3a482e47fffb..4fc91f8f53602 100644 --- a/recipes/r-gganatogram/meta.yaml +++ b/recipes/r-gganatogram/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 55154029f5cd042b4c1caeda5ed780d703e3ed129e6f100c4f5121721c92c9e2 build: - number: 2 + number: 3 noarch: generic requirements: diff --git a/recipes/r-ggbiplot/meta.yaml b/recipes/r-ggbiplot/meta.yaml index dad5c7cebb6e3..0200c22cd5d83 100644 --- a/recipes/r-ggbiplot/meta.yaml +++ b/recipes/r-ggbiplot/meta.yaml @@ -6,7 +6,7 @@ source: - 'https://github.com/likelet/ggbiplot/archive/v0.55.tar.gz' sha256: f4be01b2ddbe05846efe67f7182905489de356af017b9e2a09f96625c2d648f2 build: - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-ggcoverage/meta.yaml b/recipes/r-ggcoverage/meta.yaml index 53a9123c5c8e3..0d88cc09a523a 100644 --- a/recipes/r-ggcoverage/meta.yaml +++ b/recipes/r-ggcoverage/meta.yaml @@ -11,7 +11,7 @@ source: sha256: d1c3eb86a4da83484910369b49b0f7d96fcb0089e5dd3147efa891020cf30f21 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-ggmsa/meta.yaml b/recipes/r-ggmsa/meta.yaml index 722bea2d6cbc1..5a00739cb1c95 100644 --- a/recipes/r-ggmsa/meta.yaml +++ b/recipes/r-ggmsa/meta.yaml @@ -17,7 +17,7 @@ build: noarch: generic merge_build_host: True # [win] # If this is a new build for the same version, increment the build number. - number: 3 + number: 4 # no skip # This is required to make R link correctly on Linux. diff --git a/recipes/r-gkmsvm/meta.yaml b/recipes/r-gkmsvm/meta.yaml index 8a6e9c9e03482..1c48a780b0cf0 100644 --- a/recipes/r-gkmsvm/meta.yaml +++ b/recipes/r-gkmsvm/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 65825a0a3dc8bcb383331606199b132565da452d17e449c508d21c950997e9ad build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-goalie/meta.yaml b/recipes/r-goalie/meta.yaml index 166ff214cc367..6556a7a5efe1a 100644 --- a/recipes/r-goalie/meta.yaml +++ b/recipes/r-goalie/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 58e751134e5b0431a3a8fee58eefdef2b169e782f1a6eea623c6c9e7fadcd937 build: - number: 1 + number: 2 noarch: generic run_exports: - {{ pin_subpackage('r-goalie', max_pin="x.x") }} diff --git a/recipes/r-grain/build_failure.osx-64.yaml b/recipes/r-grain/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..efcae8659ea09 --- /dev/null +++ b/recipes/r-grain/build_failure.osx-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: f44e1a33601a1ce491d82e262549c72d59bbdd15cd4b0007ed9b7886887ace27 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-rgraphviz [2.32.0|2.34.0] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-rgraphviz [2.36.0|2.38.0] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-rgraphviz 2.42.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-rgraphviz [2.44.0|2.46.0] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("3.3.1*"), MatchSpec("bioconductor-rgraphviz==2.16.0=r3.3.1_1")} + Encountered problems while solving: + - nothing provides r 3.3.1* needed by bioconductor-rgraphviz-2.16.0-r3.3.1_1 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-rgraphviz is installable with the potential options + bioconductor-rgraphviz 2.16.0 would require + r-base 3.3.2* , which can be installed; + bioconductor-rgraphviz 2.16.0 would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-rgraphviz [2.16.0|2.20.0|2.22.0] would require + r-base 3.4.1* , which can be installed; + bioconductor-rgraphviz 2.26.0 would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-rgraphviz [2.28.0|2.30.0] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-rgraphviz [2.32.0|2.34.0] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-rgraphviz [2.36.0|2.38.0] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-rgraphviz 2.42.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-rgraphviz [2.44.0|2.46.0] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. +category: |- + dependency issue +reason: |- + dependency bioconductor-rgraphviz is also skipped for osx-64 diff --git a/recipes/r-grain/meta.yaml b/recipes/r-grain/meta.yaml index c08984074b2f0..1f1ad89a15bae 100644 --- a/recipes/r-grain/meta.yaml +++ b/recipes/r-grain/meta.yaml @@ -11,7 +11,7 @@ source: sha256: b31b46dab12ca071d67c480ec70106ef05afdc7142f68c0af5c8cff3384d900b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-grbase/meta.yaml b/recipes/r-grbase/meta.yaml index d7d5dc795c461..abed8657320e9 100644 --- a/recipes/r-grbase/meta.yaml +++ b/recipes/r-grbase/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 2ac60cbf683f1bebd3fbc50f3e71d76ff9e0b1daa441c397b0b7c43b326f1ba2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-gwpcr/meta.yaml b/recipes/r-gwpcr/meta.yaml index 6eabff333edf9..d948e71d2ebe1 100644 --- a/recipes/r-gwpcr/meta.yaml +++ b/recipes/r-gwpcr/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 094f17ceea8efddc993183269754c991953aac122e508dfea71985fbcb626860 build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-hemdag/build_failure.osx-64.yaml b/recipes/r-hemdag/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..80d129c5b3cfb --- /dev/null +++ b/recipes/r-hemdag/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 985515e858942055b6db147f2a2ba9f6468803e9bff986f6399179c4239c8f4b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-rbgl [1.64.0|1.66.0] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-rbgl [1.68.0|1.70.0] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-rbgl 1.74.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-rbgl [1.76.0|1.78.0] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("3.2.2*"), MatchSpec("bioconductor-rbgl==1.46.0=r3.2.2_0")} + Encountered problems while solving: + - nothing provides r 3.2.2* needed by bioconductor-rbgl-1.46.0-r3.2.2_0 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-rbgl is installable with the potential options + bioconductor-rbgl 1.48.1 would require + r-base 3.3.2* , which can be installed; + bioconductor-rbgl 1.46.0 would require + r 3.2.2* , which does not exist (perhaps a missing channel); + bioconductor-rbgl [1.46.0|1.48.1] would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-rbgl [1.48.1|1.52.0|1.54.0] would require + r-base 3.4.1* , which can be installed; + bioconductor-rbgl [1.58.1|1.58.2] would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-rbgl [1.60.0|1.62.1] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-rbgl [1.64.0|1.66.0] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-rbgl [1.68.0|1.70.0] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-rbgl 1.74.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-rbgl [1.76.0|1.78.0] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-hemdag/meta.yaml b/recipes/r-hemdag/meta.yaml index 7981395d2be28..411f853919ed0 100644 --- a/recipes/r-hemdag/meta.yaml +++ b/recipes/r-hemdag/meta.yaml @@ -11,7 +11,7 @@ source: sha256: bb51b308659f431482211c1ae914cfec6e983e1a110c721a59b24abb56f1aeb6 build: - number: 7 + number: 8 run_exports: - {{ pin_subpackage('r-hemdag', max_pin="x") }} rpaths: diff --git a/recipes/r-hgvsparser/meta.yaml b/recipes/r-hgvsparser/meta.yaml index 2486c3ba91064..f507619e84c95 100644 --- a/recipes/r-hgvsparser/meta.yaml +++ b/recipes/r-hgvsparser/meta.yaml @@ -11,7 +11,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 noarch: generic script: '$R CMD INSTALL --build .' run_exports: @@ -37,4 +37,4 @@ about: license_file: COPYING summary: {{ name }} doc_url: https://github.com/VariantEffect/hgvsParseR - dev_url: https://github.com/VariantEffect/hgvsParseR \ No newline at end of file + dev_url: https://github.com/VariantEffect/hgvsParseR diff --git a/recipes/r-htscluster/meta.yaml b/recipes/r-htscluster/meta.yaml index f931d828be854..607d9e23326db 100644 --- a/recipes/r-htscluster/meta.yaml +++ b/recipes/r-htscluster/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 77dd865197c859a3f47f68f5786fa0e24ce06a73ef9801e76c7425453d843a75 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage("r-htscluster", max_pin="x") }} diff --git a/recipes/r-htssip/meta.yaml b/recipes/r-htssip/meta.yaml index 5bad9a7b7f4a3..aeb73883b41f2 100644 --- a/recipes/r-htssip/meta.yaml +++ b/recipes/r-htssip/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 636de0bf5e25da77f910d6419545a385bcac2cf8fd1132f55e24361287334ec8 build: - number: 5 + number: 6 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-ic10/meta.yaml b/recipes/r-ic10/meta.yaml index 82853f886728a..6775fc111746f 100644 --- a/recipes/r-ic10/meta.yaml +++ b/recipes/r-ic10/meta.yaml @@ -12,7 +12,7 @@ source: sha256: 8c417097765b74576aad6a4dfa30917910dc06a05e858f6a6080574c109c1b32 build: - number: 0 + number: 1 noarch: generic script: ${R} CMD INSTALL --build . ${R_ARGS} rpaths: diff --git a/recipes/r-immucellaimouse/meta.yaml b/recipes/r-immucellaimouse/meta.yaml index 26e04ad0e5e3d..4b748b308f079 100644 --- a/recipes/r-immucellaimouse/meta.yaml +++ b/recipes/r-immucellaimouse/meta.yaml @@ -12,7 +12,7 @@ source: build: run_exports: - {{ pin_subpackage('r-immucellaimouse', max_pin="2") }} - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-immunedeconv/meta.yaml b/recipes/r-immunedeconv/meta.yaml index 3e29f8b12206b..ff3b42a71fbf7 100755 --- a/recipes/r-immunedeconv/meta.yaml +++ b/recipes/r-immunedeconv/meta.yaml @@ -13,7 +13,7 @@ source: build: script: $R CMD INSTALL --build . - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-imputelcmd/meta.yaml b/recipes/r-imputelcmd/meta.yaml index c92fc50136b31..cc9ed579d3b11 100644 --- a/recipes/r-imputelcmd/meta.yaml +++ b/recipes/r-imputelcmd/meta.yaml @@ -14,7 +14,7 @@ source: build: merge_build_host: True # [win] - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-intego/meta.yaml b/recipes/r-intego/meta.yaml index 40078132ae216..c8d79b880b572 100644 --- a/recipes/r-intego/meta.yaml +++ b/recipes/r-intego/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{sha256}} build: - number: 5 + number: 6 skip: true # [win32] rpaths: - lib/R/lib/ diff --git a/recipes/r-intlim/meta.yaml b/recipes/r-intlim/meta.yaml index b2484dd9369bc..45252a827af99 100644 --- a/recipes/r-intlim/meta.yaml +++ b/recipes/r-intlim/meta.yaml @@ -9,7 +9,7 @@ source: sha256: b0ea63ec73a045037e1bfec035eda1f085f617fdfd339c69e9b4522e841ffe7d build: - number: 5 + number: 6 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-isogene/meta.yaml b/recipes/r-isogene/meta.yaml index 0ec8786f33a25..8fb9a783035b8 100644 --- a/recipes/r-isogene/meta.yaml +++ b/recipes/r-isogene/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 19049382c45c870cd8e51e47ec1ec9b38bbfa1ff4af31fd5a07b5af57505953a build: - number: 7 + number: 8 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-isva/meta.yaml b/recipes/r-isva/meta.yaml index cb7d01fdf2675..6faee2c983bec 100644 --- a/recipes/r-isva/meta.yaml +++ b/recipes/r-isva/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 9fd016e0b34034d271d45f8a0d0db62780bf0187112e45f610aa9237014e1d17 build: - number: 6 + number: 7 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-jackstraw/meta.yaml b/recipes/r-jackstraw/meta.yaml index 87c8d069725c3..1ef28586229e1 100644 --- a/recipes/r-jackstraw/meta.yaml +++ b/recipes/r-jackstraw/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 6a599ec3803c64884973eeab44aaf5a78ec44406ef4f536993406e4b6c90f871 build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-jetset/meta.yaml b/recipes/r-jetset/meta.yaml index 2a70a3dfd8a20..1f6ca5677d73b 100644 --- a/recipes/r-jetset/meta.yaml +++ b/recipes/r-jetset/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 1776e30d76d7c2cf8998d3b37c87e20bca8ad58498e8545a714f6c7d6d812931 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-leapp/meta.yaml b/recipes/r-leapp/meta.yaml index 007b84ff2377e..03734387c81b3 100644 --- a/recipes/r-leapp/meta.yaml +++ b/recipes/r-leapp/meta.yaml @@ -11,7 +11,7 @@ source: sha256: b9973cf53cafef5ceede0154aaa3f7f835f7cdd51872fa4179d1117d4489d770 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-leidenbase/meta.yaml b/recipes/r-leidenbase/meta.yaml index c98059bb3464d..7c5f51ef72e07 100644 --- a/recipes/r-leidenbase/meta.yaml +++ b/recipes/r-leidenbase/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.27" %} +{% set version = "0.1.31" %} package: name: r-leidenbase @@ -6,13 +6,15 @@ package: source: url: https://cran.rstudio.com/src/contrib/leidenbase_{{ version }}.tar.gz - sha256: c3168a68828aacfcf78c6c39415b4771f084c5b5c3c9b2e226dcb8cf909d7b27 + sha256: cd0a825fa44485e957847321c02b32ac5205675e56df00cd883ea50b9aab23e1 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-leidenbase', max_pin="x.x") }} requirements: build: @@ -27,6 +29,8 @@ requirements: - glpk - libblas - liblapack + - zlib + - liblzma-devel run: - r-base - r-igraph >=1.3.4 @@ -40,6 +44,7 @@ about: home: https://cole-trapnell-lab.github.io/leidenbase/ license: GPL-2.0-only, GPL-3.0-only, BSD summary: An R to C interface that runs the Leiden community detection algorithm to find a basic partition + license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: additional-platforms: diff --git a/recipes/r-lipidomer/build_failure.linux-64.yaml b/recipes/r-lipidomer/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..5d47cbf7192da --- /dev/null +++ b/recipes/r-lipidomer/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c1c73b940001861461384999547ece612213a03f364f7d7774bdaeeafff55870 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - r-stringr 1.5.1 r44h785f33e_1 + - r-survey 4.4_2 r44h0d4f4ea_1 + - r-tidyselect 1.2.1 r44hc72bb7e_1 + - r 4.4 r44hd8ed1ab_1008 + - r-progress 1.2.3 r44hc72bb7e_1 + - r-reshape2 1.4.4 r44h0d4f4ea_4 + - r-tibble 3.2.1 r44hdb488b9_3 + - bioconductor-limma 3.28.10 0 + - r-dplyr 1.1.4 r44h0d4f4ea_1 + - r-forcats 1.0.0 r44hc72bb7e_2 + - r-ggplot2 3.5.1 r44hc72bb7e_1 + - r-vroom 1.6.5 r44h0d4f4ea_1 + - r-readr 2.1.5 r44h0d4f4ea_1 + - r-shadowtext 0.1.4 r44hc72bb7e_1 + - r-tidyr 1.3.1 r44h0d4f4ea_1 + - r-haven 2.5.4 r44h0d4f4ea_1 + - r-labelled 2.13.0 r44hc72bb7e_1 + - r-tableone 0.13.2 r44hc72bb7e_3 + run: + - bioconductor-limma + - r-reshape2 + - r-stringr + - r-ggplot2 + - r-base >=4.4,<4.5.0a0 + - r-base >=4.4,<4.5.0a0 + - r-tableone + - r-tidyr + - r-dplyr + - r-biocmanager + - r-shadowtext + - r-knitr + test: + commands: + - $R -e "library('lipidomeR')" + about: + home: https://tommi-s.github.io/ + license: GPL-3.0-only + license_family: GPL3 + license_file: + - /opt/conda/conda-bld/r-lipidomer_1734164428537/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/share/licenses/GPL-3 + summary: Create lipidome-wide heatmaps of statistics with the 'lipidomeR'. The 'lipidomeR' + provides a streamlined pipeline for the systematic interpretation of the lipidome + through publication-ready visualizations of regression models fitted on lipidomics + data. With 'lipidomeR', associations between covariates and the lipidome can be + interpreted systematically and intuitively through heatmaps, where lipids are + categorized by the lipid class and are presented on two-dimensional maps organized + by the lipid size and level of saturation. This way, the 'lipidomeR' helps you + gain an immediate understanding of the multivariate patterns in the lipidome already + at first glance. You can create lipidome-wide heatmaps of statistical associations, + changes, differences, variation, or other lipid-specific values. The heatmaps + are provided with publication-ready quality and the results behind the visualizations + are based on rigorous statistical models. + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/conda/conda-bld/r-lipidomer_1734164428537/work + export PREFIX=/opt/conda/conda-bld/r-lipidomer_1734164428537/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + export BUILD_PREFIX=/opt/conda/conda-bld/r-lipidomer_1734164428537/_build_env + export SRC_DIR=/opt/conda/conda-bld/r-lipidomer_1734164428537/work + During startup - Warning message: + Setting LC_TIME failed, using "C" + * installing to library /opt/conda/conda-bld/r-lipidomer_1734164428537/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library + * installing *source* package lipidomeR ... + ** package lipidomeR successfully unpacked and MD5 sums checked + ** using staged installation + ** R + ** data + *** moving datasets to lazyload DB + ** byte-compile and prepare package for lazy loading + During startup - Warning message: + Setting LC_TIME failed, using "C" + Error: package limma was installed before R 4.0.0: please re-install it + Execution halted + ERROR: lazy loading failed for package lipidomeR + * removing /opt/conda/conda-bld/r-lipidomer_1734164428537/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/lipidomeR + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/r-lipidomer_1734164428537/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/r-lipidomer_1734164428537/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/r-lipidomer/meta.yaml b/recipes/r-lipidomer/meta.yaml index 8604f154d24da..bc4285d689c9d 100644 --- a/recipes/r-lipidomer/meta.yaml +++ b/recipes/r-lipidomer/meta.yaml @@ -11,7 +11,7 @@ source: sha256: cd4d078c73b2f00c8213aa3dccb7d5858df8d44a4cdff3280afcd81a048a3fa9 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-lisi/meta.yaml b/recipes/r-lisi/meta.yaml index 3c0014542fe0e..7dec96174bf9e 100644 --- a/recipes/r-lisi/meta.yaml +++ b/recipes/r-lisi/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-lme4qtl/meta.yaml b/recipes/r-lme4qtl/meta.yaml index cff49ff8d98c8..3b117f392226b 100644 --- a/recipes/r-lme4qtl/meta.yaml +++ b/recipes/r-lme4qtl/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 59ae1e4aac83b55794cebdcda5529bdabab53a716213b964e6728468d8d594e8 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-lncpipereporter/build_failure.osx-64.yaml b/recipes/r-lncpipereporter/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..938161dffa509 --- /dev/null +++ b/recipes/r-lncpipereporter/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 3f6c59f6ebdcb8b763e5992b8ce8a11d3bd707ea8d718235486be6ce487d0a67 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-noiseq [2.36.0|2.38.0] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-noiseq 2.42.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-noiseq [2.44.0|2.46.0] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-noiseq==2.18.0=r3.3.1_0"), MatchSpec("3.3.1*")} + Encountered problems while solving: + - nothing provides r 3.3.1* needed by bioconductor-noiseq-2.18.0-r3.3.1_0 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-noiseq is installable with the potential options + bioconductor-noiseq 2.18.0 would require + r-base 3.3.2* , which can be installed; + bioconductor-noiseq 2.18.0 would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-noiseq [2.18.0|2.20.0|2.22.0|2.24.0] would require + r-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ], which can be installed; + bioconductor-noiseq 2.20.0 would require + r-base >=2.13,<2.14 , which does not exist (perhaps a missing channel); + bioconductor-noiseq [2.24.0|2.26.0|2.26.1] would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-noiseq [2.28.0|2.30.0] would require + bioconductor-biobase [>=2.44.0,<2.45.0 |>=2.46.0,<2.47.0 ], which requires + bioconductor-biocgenerics [>=0.30.0,<0.31.0 |>=0.32.0,<0.33.0 ], which requires + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-noiseq [2.31.0|2.34.0] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-noiseq [2.36.0|2.38.0] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-noiseq 2.42.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-noiseq [2.44.0|2.46.0] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-lncpipereporter/meta.yaml b/recipes/r-lncpipereporter/meta.yaml index 35cb57aa65467..ae641615e86e7 100644 --- a/recipes/r-lncpipereporter/meta.yaml +++ b/recipes/r-lncpipereporter/meta.yaml @@ -6,7 +6,7 @@ source: - 'https://github.com/bioinformatist/LncPipeReporter/archive/v0.1.1.tar.gz' sha256: e7c6fc1865b323cfad0f23bec8ee5ead7692b4a30287cf7fd51c0d44d44e1257 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-locuszoomr/meta.yaml b/recipes/r-locuszoomr/meta.yaml index 10a955fc63a37..1c65660143f85 100644 --- a/recipes/r-locuszoomr/meta.yaml +++ b/recipes/r-locuszoomr/meta.yaml @@ -15,7 +15,7 @@ build: - {{ pin_subpackage("r-locuszoomr", max_pin="x.x") }} noarch: generic merge_build_host: True # [win] - number: 0 + number: 1 rpaths: - lib/R/lib/ diff --git a/recipes/r-loom/meta.yaml b/recipes/r-loom/meta.yaml index c8158f8c61aac..f44bda5602a0e 100644 --- a/recipes/r-loom/meta.yaml +++ b/recipes/r-loom/meta.yaml @@ -8,7 +8,7 @@ source: sha256: 7ad37bee3f91cc7d0cfb7e31b2de33e4bf7dd03ed2205732c34f150c97faa652 build: - number: 6 + number: 7 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-loomr/meta.yaml b/recipes/r-loomr/meta.yaml index 901fb2f9b72ac..ddb36a5286b10 100644 --- a/recipes/r-loomr/meta.yaml +++ b/recipes/r-loomr/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 script: R CMD INSTALL --build . noarch: generic rpaths: diff --git a/recipes/r-lymphclon/meta.yaml b/recipes/r-lymphclon/meta.yaml index 0775d8645cff9..ff0de48872cff 100644 --- a/recipes/r-lymphclon/meta.yaml +++ b/recipes/r-lymphclon/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 80ba1dc0413e6c5fdd21dad8b9a0bb0f8c4906f1bf19f0ea90a167317520daca build: - number: 3 + number: 4 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-mams/meta.yaml b/recipes/r-mams/meta.yaml index 673fe63a605e3..da227c16d1072 100644 --- a/recipes/r-mams/meta.yaml +++ b/recipes/r-mams/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 script: ${R} CMD INSTALL --build . ${R_ARGS} rpaths: - lib/R/lib/ diff --git a/recipes/r-mcpcounter/meta.yaml b/recipes/r-mcpcounter/meta.yaml index a639770cdbd81..d37e24c371c00 100755 --- a/recipes/r-mcpcounter/meta.yaml +++ b/recipes/r-mcpcounter/meta.yaml @@ -8,7 +8,7 @@ source: sha256: 24fb58ed60cfff07d056aeb066db80bcd41e48bfa430a0989d80d8795157693f build: - number: 5 + number: 6 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-metacoder/meta.yaml b/recipes/r-metacoder/meta.yaml index 82b9450e80aaf..5fc49a94691e9 100644 --- a/recipes/r-metacoder/meta.yaml +++ b/recipes/r-metacoder/meta.yaml @@ -11,7 +11,7 @@ source: sha256: a48bf05b526cc3125605fcb221e96f55c74fd18d535c1a0e55982e3cbf3ffe38 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('r-metacoder', max_pin="x.x") }} rpaths: diff --git a/recipes/r-metadig/meta.yaml b/recipes/r-metadig/meta.yaml index a618296b8facd..8d6f3e63f73a6 100644 --- a/recipes/r-metadig/meta.yaml +++ b/recipes/r-metadig/meta.yaml @@ -12,7 +12,7 @@ source: build: merge_build_host: True # [win] noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-metalonda/build_failure.linux-64.yaml b/recipes/r-metalonda/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..85b19302f1cf0 --- /dev/null +++ b/recipes/r-metalonda/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: da1d78511f7efcd36b4cd471a0e3af8af9a145685b59a7078fe3dc80781ecdf9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("3.3.1*"), MatchSpec("bioconductor-metagenomeseq==1.16.0=r3.3.1_0")} + Encountered problems while solving: + - nothing provides r 3.3.1* needed by bioconductor-metagenomeseq-1.16.0-r3.3.1_0 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-metagenomeseq[0m is installable with the potential options + [31mbioconductor-metagenomeseq 1.16.0[0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [32mbioconductor-metagenomeseq 1.16.0[0m would require + [32mr-base 3.3.2* [0m, which can be installed; + [32mbioconductor-metagenomeseq [1.16.0|1.18.0|1.20.0][0m would require + [32mr-base 3.4.1* [0m, which can be installed; + [32mbioconductor-metagenomeseq 1.22.0[0m would require + [32mbioconductor-limma >=3.36.5,<3.38.0 [0m, which can be installed; + [32mr-base >=3.4.1,<3.4.2.0a0 [0m, which can be installed; + [32mbioconductor-metagenomeseq 1.22.0[0m would require + [32mbioconductor-limma >=3.36.5,<3.38.0 [0m, which can be installed; + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-metagenomeseq [1.24.0|1.24.1][0m would require + [32mbioconductor-limma >=3.38.0,<3.39.0 [0m, which requires + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-metagenomeseq 1.26.2[0m would require + [32mbioconductor-ihw >=1.12.0,<1.13.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.30.0,<0.31.0 [0m, which requires + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-lpsymphony >=1.14.0,<1.15.0 [0m, which requires + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-limma >=3.40.0,<3.41.0 [0m, which can be installed; + [32mbioconductor-metagenomeseq 1.28.0[0m would require + [32mbioconductor-ihw >=1.14.0,<1.15.0 [0m, which can be installed (as previously explained); + [32mbioconductor-limma >=3.42.0,<3.43.0 [0m, which can be installed; + [32mbioconductor-metagenomeseq 1.30.0[0m would require + [32mbioconductor-biobase >=2.48.0,<2.49.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.34.0,<0.35.0 [0m, which requires + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-limma >=3.44.0,<3.45.0 [0m, which can be installed; + [32mbioconductor-wrench >=1.6.0,<1.7.0 [0m, which requires + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-metagenomeseq 1.32.0[0m would require + [32mbioconductor-limma >=3.46.0,<3.47.0 [0m, which can be installed; + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [31mbioconductor-metagenomeseq 1.34.0[0m would require + [31mbioconductor-limma >=3.48.0,<3.49.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-wrench >=1.10.0,<1.11.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-metagenomeseq 1.36.0[0m would require + [32mbioconductor-limma >=3.50.0,<3.51.0 [0m, which can be installed; + [32mbioconductor-wrench >=1.12.0,<1.13.0 [0m, which can be installed (as previously explained); + [32mbioconductor-metagenomeseq 1.40.0[0m would require + [32mbioconductor-limma >=3.54.0,<3.55.0 [0m, which can be installed; + [32mbioconductor-wrench >=1.16.0,<1.17.0 [0m, which requires + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [31mbioconductor-metagenomeseq [1.42.0|1.43.0][0m would require + [31mbioconductor-limma >=3.56.0,<3.57.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mbioconductor-wrench [>=1.18.0,<1.19.0 |>=1.20.0,<1.21.0 ][0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-metalonda/meta.yaml b/recipes/r-metalonda/meta.yaml index 615679fcc6ad6..c6ed0d7799f1c 100644 --- a/recipes/r-metalonda/meta.yaml +++ b/recipes/r-metalonda/meta.yaml @@ -12,7 +12,7 @@ source: sha256: 4ff0715d83fb3d7b18af21bbfbe0413480e5d4bbec9b900fe0568918759d5459 build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-metama/meta.yaml b/recipes/r-metama/meta.yaml index 1813002288080..ebb56c0ff24e2 100644 --- a/recipes/r-metama/meta.yaml +++ b/recipes/r-metama/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-metap/build.sh b/recipes/r-metap/build.sh deleted file mode 100644 index d0490408a7c59..0000000000000 --- a/recipes/r-metap/build.sh +++ /dev/null @@ -1,17 +0,0 @@ -#!/bin/bash - -# 'Autobrew' is being used by more and more packages these days -# to grab static libraries from Homebrew bottles. These bottles -# are fetched via Homebrew's --force-bottle option which grabs -# a bottle for the build machine which may not be macOS 10.9. -# Also, we want to use conda packages (and shared libraries) for -# these 'system' dependencies. See: -# https://github.com/jeroen/autobrew/issues/3 -export DISABLE_AUTOBREW=1 - -# R refuses to build packages that mark themselves as Priority: Recommended -mv DESCRIPTION DESCRIPTION.old -grep -va '^Priority: ' DESCRIPTION.old > DESCRIPTION -# shellcheck disable=SC2086 -${R} CMD INSTALL --build . ${R_ARGS} - diff --git a/recipes/r-metap/meta.yaml b/recipes/r-metap/meta.yaml deleted file mode 100644 index c486e6c3c7da4..0000000000000 --- a/recipes/r-metap/meta.yaml +++ /dev/null @@ -1,60 +0,0 @@ -{% set version = '1.4' %} - -package: - name: r-metap - version: {{ version|replace("-", "_") }} - -source: - url: - - {{ cran_mirror }}/src/contrib/metap_{{ version }}.tar.gz - - {{ cran_mirror }}/src/contrib/Archive/metap/metap_{{ version }}.tar.gz - sha256: 5fac23d823d0ad4eebc3f97620364e25f7b41f8d0c3579f6c09ec059940b85a5 - -build: - noarch: generic - number: 3 - # no skip - - # This is required to make R link correctly on Linux. - rpaths: - - lib/R/lib/ - - lib/ - -requirements: - host: - - r-base - - r-rdpack >=0.7 - - r-tfisher - - r-lattice - - r-mathjaxr >=0.8_3 - - r-mutoss - - run: - - r-base - - r-rdpack >=0.7 - - r-tfisher - - r-lattice - - r-mathjaxr >=0.8_3 - - r-mutoss - -test: - commands: - - $R -e "library('metap')" - -about: - home: http://www.dewey.myzen.co.uk/meta/meta.html - - license: GPL-2 - summary: The canonical way to perform meta-analysis involves using effect sizes. When they - are not available this package provides a number of methods for meta-analysis of - significance values including the methods of Edgington, Fisher, Lancaster, Stouffer, - Tippett, and Wilkinson; a number of data-sets to replicate published results; and - a routine for graphical display. - - license_family: GPL2 - license_file: - - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' - -extra: - skip-lints: - - in_other_channels diff --git a/recipes/r-mgsz/meta.yaml b/recipes/r-mgsz/meta.yaml index 6ea3ffc4916e5..46c6be7270ed1 100644 --- a/recipes/r-mgsz/meta.yaml +++ b/recipes/r-mgsz/meta.yaml @@ -11,7 +11,7 @@ source: sha256: f0978d2c6468c26399432f1f49aca1c04189322ef76f3d539f080a584e448922 build: - number: 5 + number: 6 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-millefy/build_failure.linux-64.yaml b/recipes/r-millefy/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..7ffc302dfad59 --- /dev/null +++ b/recipes/r-millefy/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 0a88dab220eccd7d3a1603b6cdd5718632025459cf6d542c5c783625c0f20df5 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [32mbioconductor-destiny 3.8.1[0m would require + [32mbioconductor-summarizedexperiment >=1.24.0,<1.25.0 [0m, which requires + [32mbioconductor-genomicranges >=1.46.0,<1.47.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-base[version='>=3.5.1,<3.5.2.0a0']"), MatchSpec("bioconductor-zlibbioc==1.28.0=r351h14c3975_0")} + Encountered problems while solving: + - package bioconductor-zlibbioc-1.28.0-r351h14c3975_0 requires r-base >=3.5.1,<3.5.2.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-destiny[0m is installable with the potential options + [32mbioconductor-destiny 2.12.0[0m would require + [32mbioconductor-summarizedexperiment >=1.12.0,<1.13.0 [0m, which requires + [32mbioconductor-genomicranges >=1.34.0,<1.35.0 [0m, which requires + [32mbioconductor-xvector >=0.22.0,<0.23.0 [0m, which requires + [32mbioconductor-zlibbioc >=1.28.0,<1.29.0 [0m, which requires + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-destiny [2.14.0|2.15.0][0m would require + [32mbioconductor-summarizedexperiment [>=1.14.0,<1.15.0 |>=1.16.0,<1.17.0 ][0m, which requires + [32mbioconductor-genomicranges [>=1.36.0,<1.37.0 |>=1.38.0,<1.39.0 ][0m, which requires + [32mbioconductor-xvector [>=0.24.0,<0.25.0 |>=0.26.0,<0.27.0 ][0m, which requires + [32mbioconductor-zlibbioc >=1.32.0,<1.33.0 [0m, which requires + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-destiny 3.12.0[0m would require + [32mbioconductor-summarizedexperiment >=1.28.0,<1.29.0 [0m, which requires + [32mbioconductor-genomicranges >=1.50.0,<1.51.0 [0m, which requires + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-destiny [3.14.0|3.16.0][0m would require + [32mbioconductor-summarizedexperiment [>=1.30.0,<1.31.0 |>=1.32.0,<1.33.0 ][0m, which requires + [32mbioconductor-genomicranges [>=1.52.0,<1.53.0 |>=1.54.0,<1.55.0 ][0m, which requires + [32mbioconductor-xvector >=0.40.0,<0.41.0 [0m, which requires + [32mbioconductor-zlibbioc >=1.46.0,<1.47.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mbioconductor-destiny [3.2.0|3.4.0][0m would require + [32mbioconductor-summarizedexperiment [>=1.18.0,<1.19.0 |>=1.20.0,<1.21.0 ][0m, which requires + [32mbioconductor-genomicranges [>=1.40.0,<1.41.0 |>=1.42.0,<1.43.0 ][0m, which requires + [32mbioconductor-xvector >=0.28.0,<0.29.0 [0m, which requires + [32mbioconductor-zlibbioc >=1.34.0,<1.35.0 [0m, which requires + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-destiny 3.8.1[0m would require + [32mbioconductor-summarizedexperiment >=1.24.0,<1.25.0 [0m, which requires + [32mbioconductor-genomicranges >=1.46.0,<1.47.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-millefy/meta.yaml b/recipes/r-millefy/meta.yaml index b3fe4fecac221..19e095e7b1b10 100644 --- a/recipes/r-millefy/meta.yaml +++ b/recipes/r-millefy/meta.yaml @@ -13,7 +13,7 @@ source: build: noarch: generic - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-minems2/build_failure.osx-64.yaml b/recipes/r-minems2/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..85b6ac2867db4 --- /dev/null +++ b/recipes/r-minems2/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a2c7489dbd0338504ae08a1e7f3bdde4a03c147faa8e9b0d299a56982bf40619 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-msnbase==2.2.0=r3.4.1_0"), MatchSpec("r-base=3.4.1")} + Encountered problems while solving: + - package bioconductor-msnbase-2.2.0-r3.4.1_0 requires r-base 3.4.1*, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + bioconductor-msnbase is installable with the potential options + bioconductor-msnbase [2.2.0|2.4.0] would require + r-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ], which can be installed; + bioconductor-msnbase [2.10.1|2.12.0] would require + bioconductor-biocgenerics >=0.30.0,<0.31.0 , which requires + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-vsn >=3.54.0,<3.55.0 , which requires + bioconductor-limma >=3.42.0,<3.43.0 , which requires + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-msnbase [2.14.1|2.16.0|2.16.1] would require + bioconductor-mzr >=2.24.0,<2.25.0 , which requires + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-vsn >=3.56.0,<3.57.0 , which requires + bioconductor-limma >=3.44.0,<3.45.0 , which requires + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-msnbase [2.18.0|2.20.0|2.20.4] would require + bioconductor-protgenerics >=1.26.0,<1.27.0 , which requires + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-vsn >=3.60.0,<3.61.0 , which requires + bioconductor-limma >=3.48.0,<3.49.0 , which requires + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-msnbase 2.24.0 would require + bioconductor-protgenerics >=1.30.0,<1.31.0 , which requires + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-msnbase [2.26.0|2.28.1] would require + bioconductor-protgenerics >=1.34.0,<1.35.0 , which requires + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-vsn >=3.68.0,<3.69.0 , which requires + bioconductor-limma >=3.56.0,<3.57.0 , which requires + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-msnbase [2.8.2|2.8.3] would require + bioconductor-vsn >=3.50.0,<3.51.0 , which requires + bioconductor-limma >=3.38.0,<3.39.0 , which requires + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-minems2/meta.yaml b/recipes/r-minems2/meta.yaml index 7061bf54be5b2..173a83ee760dc 100644 --- a/recipes/r-minems2/meta.yaml +++ b/recipes/r-minems2/meta.yaml @@ -9,7 +9,7 @@ source: sha256: fba9a32d1f196361854bbe4803c0c5419a20bf4bdb2437bf4e8112ceda805c0e build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-minionqc/meta.yaml b/recipes/r-minionqc/meta.yaml index 31733da325cf7..a6f3b191ff57b 100644 --- a/recipes/r-minionqc/meta.yaml +++ b/recipes/r-minionqc/meta.yaml @@ -8,7 +8,7 @@ source: build: noarch: generic - number: 4 + number: 5 requirements: host: diff --git a/recipes/r-misha/3.7.0/meta.yaml b/recipes/r-misha/3.7.0/meta.yaml index 29c2d9b973b1c..3f04950922ccc 100644 --- a/recipes/r-misha/3.7.0/meta.yaml +++ b/recipes/r-misha/3.7.0/meta.yaml @@ -13,7 +13,7 @@ source: build: # https://github.com/tanaylab/misha/issues/9 skip: True # [osx] - number: 0 + number: 1 rpaths: - lib/R/lib - lib/ diff --git a/recipes/r-misha/3.7.1/meta.yaml b/recipes/r-misha/3.7.1/meta.yaml index 1a4b49c1cc2ec..e5e70d2e769e5 100644 --- a/recipes/r-misha/3.7.1/meta.yaml +++ b/recipes/r-misha/3.7.1/meta.yaml @@ -13,7 +13,7 @@ source: build: # https://github.com/tanaylab/misha/issues/9 skip: True # [osx] - number: 0 + number: 1 rpaths: - lib/R/lib - lib/ diff --git a/recipes/r-misha/meta.yaml b/recipes/r-misha/meta.yaml index 199891473173f..b3fc27ba26240 100644 --- a/recipes/r-misha/meta.yaml +++ b/recipes/r-misha/meta.yaml @@ -11,7 +11,7 @@ source: build: # https://github.com/tanaylab/misha/issues/9 skip: True # [osx] - number: 7 + number: 8 rpaths: - lib/R/lib - lib/ diff --git a/recipes/r-mixkernel/build_failure.linux-64.yaml b/recipes/r-mixkernel/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..561b20fbec95a --- /dev/null +++ b/recipes/r-mixkernel/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 44a9676ffd16bf8b1f9bc32839fd565552d7b15c3474c1e8388cd7edc319df71 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [32mbioconductor-mixomics 6.22.0[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-mixomics [6.24.0|6.26.0][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mbioconductor-mixomics 6.30.0[0m would require + [31mbioconductor-biocparallel >=1.40.0,<1.41.0 [0m, which requires + [31mr-base >=4.4,<4.5.0a0 [0m, which conflicts with any installable versions previously reported; + [32mbioconductor-mixomics [6.6.0|6.6.2|6.8.0][0m would require + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-phyloseq[0m is installable with the potential options + [32mbioconductor-phyloseq 1.14.0[0m would require + [32mr-biom >=0.3.9 [0m with the potential options + [31mr-biom 0.3.12[0m would require + [31mr 3.2.2* [0m, which does not exist (perhaps a missing channel); + [31mr-biom 0.3.12[0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [32mr-biom 0.3.12[0m would require + [32mr-base 3.3.2* [0m, which can be installed; + [32mr-biom 0.3.12[0m would require + [32mr-base 3.4.1* [0m, which can be installed; + [32mbioconductor-phyloseq 1.16.2[0m would require + [32mbioconductor-biomformat >=1.0.2 [0m with the potential options + [32mbioconductor-biomformat [1.16.0|1.18.0][0m would require + [32mbioconductor-rhdf5 >=2.32.0,<2.33.0 [0m, which requires + [32mbioconductor-rhdf5lib >=1.10.0,<1.11.0 [0m, which requires + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-biomformat 1.0.2[0m would require + [32mbioconductor-rhdf5 >=2.16.0 [0m with the potential options + [31mbioconductor-rhdf5 2.16.0[0m would require + [31mr 3.2.2* [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-rhdf5 2.16.0[0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [32mbioconductor-rhdf5 2.16.0[0m would require + [32mr-base 3.3.2* [0m, which can be installed; + [32mbioconductor-rhdf5 [2.16.0|2.20.0|2.22.0|2.24.0][0m would require + [32mr-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ][0m, which can be installed; + [32mbioconductor-rhdf5 [2.24.0|2.26.0|2.26.1|2.26.2|2.28.0][0m would require + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.28.0|2.30.0][0m would require + [32mbioconductor-rhdf5lib >=1.8.0,<1.9.0 [0m, which requires + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.32.0|2.34.0][0m, which can be installed (as previously explained); + [32mbioconductor-rhdf5 [2.36.0|2.38.0|2.38.1][0m would require + [32mbioconductor-rhdf5lib >=1.14.0,<1.15.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 2.42.0[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.44.0|2.46.1][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mbioconductor-biomformat [1.0.2|1.2.0][0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [32mbioconductor-biomformat 1.2.0[0m would require + [32mr-base 3.3.2* [0m, which can be installed; + [32mbioconductor-biomformat [1.2.0|1.4.0|1.6.0|1.8.0][0m would require + [32mr-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ][0m, which can be installed; + [32mbioconductor-biomformat [1.10.0|1.10.1|1.12.0|1.8.0][0m would require + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-biomformat [1.12.0|1.14.0][0m would require + [32mbioconductor-rhdf5 >=2.30.0,<2.31.0 [0m, which can be installed (as previously explained); + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-biomformat [1.20.0|1.22.0][0m would require + [32mbioconductor-rhdf5 >=2.36.0,<2.37.0 [0m, which can be installed (as previously explained); + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-biomformat 1.26.0[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-biomformat [1.28.0|1.30.0][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mbioconductor-phyloseq [1.16.2|1.19.1][0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [32mbioconductor-phyloseq [1.19.1|1.20.0][0m would require + [32mr-base [3.3.2* |>=3.3,<3.4 ][0m, which can be installed; + [32mbioconductor-phyloseq [1.19.1|1.20.0|1.22.3|1.24.2][0m would require + [32mr-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ][0m, which can be installed; + [32mbioconductor-phyloseq [1.24.2|1.26.0|1.26.1][0m would require + [32mbioconductor-multtest >=2.38.0,<2.39.0 [0m, which requires + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-phyloseq [1.28.0|1.30.0][0m would require + [32mbioconductor-biomformat >=1.14.0,<1.15.0 [0m, which can be installed (as previously explained); + [32mbioconductor-biostrings >=2.52.0,<2.53.0 [0m, which requires + [32mbioconductor-xvector >=0.24.0,<0.25.0 [0m, which requires + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-phyloseq [1.32.0|1.34.0][0m would require + [32mbioconductor-biomformat >=1.16.0,<1.17.0 [0m, which can be installed (as previously explained); + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-phyloseq [1.36.0|1.38.0][0m would require + [32mbioconductor-biomformat [>=1.20.0,<1.21.0 |>=1.22.0,<1.23.0 ][0m, which can be installed (as previously explained); + [32mbioconductor-phyloseq 1.42.0[0m would require + [32mbioconductor-biomformat >=1.26.0,<1.27.0 [0m, which can be installed (as previously explained); + [32mbioconductor-phyloseq [1.44.0|1.46.0][0m would require + [32mbioconductor-biomformat >=1.30.0,<1.31.0 [0m, which can be installed (as previously explained); + [32mbioconductor-biostrings >=2.68.0,<2.69.0 [0m, which requires + [32mbioconductor-xvector >=0.40.0,<0.41.0 [0m, which requires + [32mbioconductor-zlibbioc >=1.46.0,<1.47.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-mixkernel/meta.yaml b/recipes/r-mixkernel/meta.yaml index 3d36221f9ce5b..a3d54c93209d2 100644 --- a/recipes/r-mixkernel/meta.yaml +++ b/recipes/r-mixkernel/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-mkmisc/meta.yaml b/recipes/r-mkmisc/meta.yaml index 054d0b8d69491..e246b15bc4f01 100644 --- a/recipes/r-mkmisc/meta.yaml +++ b/recipes/r-mkmisc/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 23f97ab7f80142f870b15d610c2f842e75ffd7ef6a75bb244278f0d29de66d26 build: - number: 1 + number: 2 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-mmcpcounter/meta.yaml b/recipes/r-mmcpcounter/meta.yaml index 20e67d441a0f7..6a80522ed1cfc 100644 --- a/recipes/r-mmcpcounter/meta.yaml +++ b/recipes/r-mmcpcounter/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 3f2cfdc07ed8414d67c035b9b7e44c63d0fb67f06bcc76c13d9bd45f7f2bdeb4 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-mmgenome/build_failure.osx-64.yaml b/recipes/r-mmgenome/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..90288b1cd4a2f --- /dev/null +++ b/recipes/r-mmgenome/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: b9ae75b3c69f8ca5539aa966ba6cdc54471e5632703780b040245a9f90134be8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Encountered problems while solving: + - nothing provides compiler-rt 4.0.1 hcfea43d_1 needed by clang-4.0.1-1 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-biostrings >=2.32.0 is installable with the potential options + bioconductor-biostrings [2.38.3|2.38.4] would require + bioconductor-xvector >=0.9.3 with the potential options + bioconductor-xvector 0.10.0 would require + bioconductor-zlibbioc with the potential options + bioconductor-zlibbioc 1.16.0 would require + r 3.2.2* , which does not exist (perhaps a missing channel); + bioconductor-zlibbioc [1.16.0|1.18.0|1.20.0] would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-zlibbioc 1.20.0 would require + r-base 3.3.2* , which can be installed; + bioconductor-zlibbioc [1.20.0|1.22.0|1.24.0|1.26.0] would require + r-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ], which can be installed; + bioconductor-zlibbioc [1.26.0|1.28.0|1.30.0] would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-zlibbioc [1.30.0|1.32.0] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-zlibbioc [1.34.0|1.36.0] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-zlibbioc [1.38.0|1.40.0] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-zlibbioc 1.44.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-zlibbioc [1.46.0|1.48.0] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-xvector 0.12.1 would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-xvector 0.14.1 would require + r-base 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-xvector 0.14.1 would require + r-base 3.3.2* , which can be installed; + bioconductor-xvector [0.14.1|0.16.0|0.18.0|0.20.0] would require + r-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ], which can be installed; + bioconductor-xvector [0.20.0|0.22.0] would require + bioconductor-zlibbioc >=1.28.0,<1.29.0 , which can be installed (as previously explained); + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed; + bioconductor-xvector [0.24.0|0.26.0] would require + bioconductor-biocgenerics >=0.30.0,<0.31.0 , which requires + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-zlibbioc >=1.32.0,<1.33.0 , which can be installed (as previously explained); + bioconductor-xvector [0.28.0|0.30.0] would require + bioconductor-zlibbioc >=1.34.0,<1.35.0 , which can be installed (as previously explained); + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-xvector [0.32.0|0.34.0] would require + bioconductor-biocgenerics >=0.40.0,<0.41.0 , which requires + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-zlibbioc >=1.38.0,<1.39.0 , which can be installed (as previously explained); + bioconductor-xvector 0.38.0 would require + bioconductor-biocgenerics >=0.44.0,<0.45.0 , which requires + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-xvector [0.40.0|0.42.0] would require + bioconductor-zlibbioc >=1.46.0,<1.47.0 , which can be installed (as previously explained); + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-biostrings [2.40.0|2.40.2] would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-biostrings 2.42.1 would require + r-base 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-biostrings 2.42.1 would require + r-base 3.3.2* , which can be installed; + bioconductor-biostrings [2.42.1|2.44.2|2.46.0|2.48.0] would require + r-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ], which can be installed; + bioconductor-biostrings [2.48.0|2.50.1|2.50.2] would require + bioconductor-xvector >=0.22.0,<0.23.0 , which can be installed (as previously explained); + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed; + bioconductor-biostrings [2.52.0|2.54.0] would require + bioconductor-biocgenerics >=0.30.0,<0.31.0 , which can be installed (as previously explained); + bioconductor-xvector >=0.26.0,<0.27.0 , which can be installed (as previously explained); + bioconductor-biostrings [2.56.0|2.58.0] would require + bioconductor-xvector >=0.28.0,<0.29.0 , which can be installed (as previously explained); + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-biostrings [2.60.0|2.62.0] would require + bioconductor-biocgenerics >=0.40.0,<0.41.0 , which can be installed (as previously explained); + bioconductor-xvector >=0.32.0,<0.33.0 , which can be installed (as previously explained); + bioconductor-biostrings 2.66.0 would require + bioconductor-biocgenerics >=0.44.0,<0.45.0 , which can be installed (as previously explained); + bioconductor-biostrings [2.68.1|2.70.1] would require + bioconductor-xvector >=0.40.0,<0.41.0 , which can be installed (as previously explained); + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-mmgenome/meta.yaml b/recipes/r-mmgenome/meta.yaml index 01c128d2765b3..b68105b5e000d 100644 --- a/recipes/r-mmgenome/meta.yaml +++ b/recipes/r-mmgenome/meta.yaml @@ -10,7 +10,7 @@ source: md5: ae6d9430b08bb7e4a6448d24e19c5d19 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-momf/meta.yaml b/recipes/r-momf/meta.yaml index 1fd733b8c87f2..81de826e60053 100644 --- a/recipes/r-momf/meta.yaml +++ b/recipes/r-momf/meta.yaml @@ -10,7 +10,7 @@ source: sha256: ad1e0207b049d34a4fa7709a7835c96adae033cce01c21d9a30b407c3893caac build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-monocle3/meta.yaml b/recipes/r-monocle3/meta.yaml index f2d836c191569..8f97037a7725f 100644 --- a/recipes/r-monocle3/meta.yaml +++ b/recipes/r-monocle3/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 30e86d5323ea22b302614813ecf102f26774b42710589671a1f1d51ef9ad183d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -61,6 +61,7 @@ requirements: - r-rann >=2.6.1 - r-rcolorbrewer - r-rcpp >=1.0.1 + - r-rcpphnsw - r-rcppparallel - r-reshape2 >=1.4.3mass - r-reticulate >=1.11.1 @@ -72,6 +73,7 @@ requirements: - r-spdep >=1.1_2 - r-speedglm >=0.3_2 - r-stringr >=1.4 + - r-terra - r-tibble >=2.1.1 - r-tidyr >=0.8.3 - r-uwot >=0.1.3 @@ -122,6 +124,7 @@ requirements: - r-purrr >=0.3.2 - r-rann >=2.6.1 - r-rcpp >=1.0.1 + - r-rcpphnsw - r-rcppparallel - r-reshape2 >=1.4.3 - r-reticulate >=1.11.1 @@ -133,6 +136,7 @@ requirements: - r-spdep >=1.1_2 - r-speedglm >=0.3_2 - r-stringr >=1.4 + - r-terra - r-tibble >=2.1.1 - r-tidyr >=0.8.3 - r-uwot >=0.1.3 diff --git a/recipes/r-motifbinner/build_failure.osx-64.yaml b/recipes/r-motifbinner/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..1c72292a3ef3d --- /dev/null +++ b/recipes/r-motifbinner/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: e000065477090fd73909627bfe8593a06feac1389f5e168d4de90707106e6ec2 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-biocgenerics [0.34.0|0.36.0] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-biocgenerics [0.38.0|0.40.0] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-biocgenerics 0.44.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-biocgenerics [0.46.0|0.48.1] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-biocgenerics==0.16.1=r3.2.2_0"), MatchSpec("3.2.2*")} + Encountered problems while solving: + - nothing provides r 3.2.2* needed by bioconductor-biocgenerics-0.16.1-r3.2.2_0 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-biocgenerics is installable with the potential options + bioconductor-biocgenerics [0.20.0|0.22.0] would require + r-base 3.3.2* , which can be installed; + bioconductor-biocgenerics [0.16.1|0.18.0] would require + r 3.2.2* , which does not exist (perhaps a missing channel); + bioconductor-biocgenerics [0.16.1|0.18.0|0.20.0] would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-biocgenerics [0.22.0|0.22.1|0.24.0|0.26.0] would require + r-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ], which can be installed; + bioconductor-biocgenerics [0.24.0|0.26.0|0.28.0] would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-biocgenerics [0.30.0|0.32.0] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-biocgenerics [0.34.0|0.36.0] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-biocgenerics [0.38.0|0.40.0] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-biocgenerics 0.44.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-biocgenerics [0.46.0|0.48.1] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-motifbinner/meta.yaml b/recipes/r-motifbinner/meta.yaml index 4dfbb3d4509d6..eadfde56b8a47 100644 --- a/recipes/r-motifbinner/meta.yaml +++ b/recipes/r-motifbinner/meta.yaml @@ -12,7 +12,7 @@ source: sha256: 6337bf7a7c84c4d3dbdf784b1acc6ad92f05b97fe4068b58ef19630da0c5590d build: - number: 7 + number: 8 script: "$R CMD INSTALL --build ." rpaths: - lib/R/lib/ diff --git a/recipes/r-mspbwt/meta.yaml b/recipes/r-mspbwt/meta.yaml index c4e12068526ed..b4a3eb54a7b0d 100644 --- a/recipes/r-mspbwt/meta.yaml +++ b/recipes/r-mspbwt/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('r-mspbwt', max_pin="x.x") }} diff --git a/recipes/r-msqrob/meta.yaml b/recipes/r-msqrob/meta.yaml index ef4a0f666ef26..fc4534b95b609 100644 --- a/recipes/r-msqrob/meta.yaml +++ b/recipes/r-msqrob/meta.yaml @@ -6,7 +6,7 @@ source: sha256: 7d6a1fd0e08653d4b0fe3999872c30c6b84b7dc9f06228554f78aa0ca9a933a4 build: noarch: generic - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-music/meta.yaml b/recipes/r-music/meta.yaml index 2905466a68b6f..ecd0451ed1c32 100644 --- a/recipes/r-music/meta.yaml +++ b/recipes/r-music/meta.yaml @@ -9,7 +9,7 @@ source: sha256: cd34955e46e10bb52d7348dc4771702bb23104b1c54989f40a36f542ef4b9f34 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-mutoss/meta.yaml b/recipes/r-mutoss/meta.yaml index 06e0cb9c6e7e3..6e8bfc0a79e0a 100644 --- a/recipes/r-mutoss/meta.yaml +++ b/recipes/r-mutoss/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-mutsigextractor/meta.yaml b/recipes/r-mutsigextractor/meta.yaml index f37f235e466e4..2da78e6ad199e 100644 --- a/recipes/r-mutsigextractor/meta.yaml +++ b/recipes/r-mutsigextractor/meta.yaml @@ -1,5 +1,5 @@ {% set version = "1.29" %} -{% set sha256 = "7edea78713d59166c8a03c374288e3f72ddcb9b69b0ce06def7c76f27ce49f45" %} +{% set sha256 = "4c3ce87942907443be5c9cabb7fef1d75085ce59dc7c3943d51b37bc56fb8b7f" %} package: name: r-mutsigextractor @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage("r-mutsigextractor", max_pin="x.x") }} diff --git a/recipes/r-nanopore/build_failure.linux-64.yaml b/recipes/r-nanopore/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..08de65826bcd3 --- /dev/null +++ b/recipes/r-nanopore/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: ec276c9e38223109a41027d95a01dc84ad12c8f53e4b3cbe676264cea48fbc79 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-vctrs: 0.6.5-r44h0d4f4ea_1 conda-forge + r-vegan: 2.6_8-r44h9ad1c49_0 conda-forge + r-viridis: 0.6.5-r44hc72bb7e_1 conda-forge + r-viridislite: 0.4.2-r44hc72bb7e_2 conda-forge + r-vroom: 1.6.5-r44h0d4f4ea_1 conda-forge + r-webshot: 0.5.5-r44hc72bb7e_1 conda-forge + r-withr: 3.0.2-r44hc72bb7e_0 conda-forge + r-writexl: 1.5.1-r44h2b5f3a1_0 conda-forge + r-xfun: 0.49-r44h93ab643_0 conda-forge + r-xml: 3.99_0.17-r44h5bae778_2 conda-forge + r-xml2: 1.3.6-r44h8194278_2 conda-forge + r-yaml: 2.3.10-r44hdb488b9_0 conda-forge + readline: 8.2-h8228510_1 conda-forge + sed: 4.8-he412f7d_0 conda-forge + setuptools: 75.6.0-pyhff2d567_1 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tktable: 2.10-h8bc8fbc_6 conda-forge + toml: 0.10.2-pyhd8ed1ab_1 conda-forge + tomlkit: 0.13.2-pyha770c72_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + xmltodict: 0.14.2-pyhd8ed1ab_1 conda-forge + xorg-libice: 1.1.2-hb9d3cd8_0 conda-forge + xorg-libsm: 1.2.5-he73a12e_0 conda-forge + xorg-libx11: 1.8.10-h4f16b4b_1 conda-forge + xorg-libxau: 1.0.12-hb9d3cd8_0 conda-forge + xorg-libxdmcp: 1.1.5-hb9d3cd8_0 conda-forge + xorg-libxext: 1.3.6-hb9d3cd8_0 conda-forge + xorg-libxrender: 0.9.12-hb9d3cd8_0 conda-forge + xorg-libxt: 1.3.1-hb9d3cd8_0 conda-forge + yaml: 0.2.5-h7f98852_2 conda-forge + yq: 3.4.3-pyhd8ed1ab_1 conda-forge + zlib: 1.3.1-hb9d3cd8_2 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/r-nanopore_1735203061416/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.43-h4bf12b8_2 conda-forge + binutils_linux-64: 2.43-h4852527_2 conda-forge + gcc_impl_linux-64: 13.3.0-hfea6d02_1 conda-forge + gcc_linux-64: 13.3.0-hc28eda2_7 conda-forge + gxx_impl_linux-64: 13.3.0-hdbfa832_1 conda-forge + gxx_linux-64: 13.3.0-h6834431_7 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libsanitizer: 13.3.0-heb74ff8_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: 0.2.9_c0d4ab2096.tar.gz + Downloading https://github.com/sagrudd/nanopoRe/archive/0.2.9.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.122599 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download https://github.com/sagrudd/nanopoRe/archive/0.2.9.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/r-nanopore/build_failure.osx-64.yaml b/recipes/r-nanopore/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..f1208babfce86 --- /dev/null +++ b/recipes/r-nanopore/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: ec276c9e38223109a41027d95a01dc84ad12c8f53e4b3cbe676264cea48fbc79 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + bioconductor-s4vectors 0.44.0 would require + bioconductor-biocgenerics >=0.52.0,<0.53.0 , which requires + r-base >=4.4,<4.5.0a0 , which can be installed; + bioconductor-s4vectors [0.10.3|0.12.0|0.8.11|0.9.0] would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-s4vectors 0.12.2 would require + r-base 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-s4vectors [0.12.2|0.14.7|...|0.8.7] conflicts with any installable versions previously reported; + bioconductor-s4vectors 0.18.3 conflicts with any installable versions previously reported; + bioconductor-s4vectors 0.20.1 conflicts with any installable versions previously reported; + bioconductor-s4vectors 0.22.0 conflicts with any installable versions previously reported; + bioconductor-s4vectors 0.24.0 conflicts with any installable versions previously reported; + bioconductor-s4vectors 0.26.0 conflicts with any installable versions previously reported; + bioconductor-s4vectors [0.28.0|0.28.1] conflicts with any installable versions previously reported; + bioconductor-s4vectors 0.30.0 conflicts with any installable versions previously reported; + bioconductor-s4vectors [0.32.0|0.32.3|0.32.4] conflicts with any installable versions previously reported; + bioconductor-s4vectors 0.36.0 conflicts with any installable versions previously reported; + bioconductor-s4vectors 0.38.1 conflicts with any installable versions previously reported; + bioconductor-s4vectors 0.40.2 conflicts with any installable versions previously reported; + bioconductor-variantannotation is not installable because there are no viable options + bioconductor-variantannotation 1.16.4 would require + bioconductor-bsgenome >=1.37.6 but there are no viable options + bioconductor-bsgenome 1.38.0 would require + bioconductor-rsamtools, which cannot be installed (as previously explained); + bioconductor-bsgenome [1.40.1|1.42.0] would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-bsgenome 1.42.0 would require + bioconductor-genomicranges >=1.23.15 , which cannot be installed (as previously explained); + bioconductor-bsgenome [1.44.2|1.46.0] would require + bioconductor-genomeinfodb [>=1.11.4 |>=1.13.1 ], which cannot be installed (as previously explained); + bioconductor-bsgenome 1.48.0 would require + bioconductor-s4vectors >=0.18.3,<0.20.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.50.0 would require + bioconductor-s4vectors >=0.20.0,<0.21.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.52.0 would require + bioconductor-s4vectors >=0.22.0,<0.23.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.54.0 would require + bioconductor-s4vectors >=0.24.0,<0.25.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.56.0 would require + bioconductor-s4vectors >=0.26.0,<0.27.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.58.0 would require + bioconductor-s4vectors >=0.28.0,<0.29.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.60.0 would require + bioconductor-s4vectors >=0.30.0,<0.31.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.62.0 would require + bioconductor-s4vectors >=0.32.0,<0.33.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome [1.66.1|1.66.3] would require + bioconductor-s4vectors >=0.36.0,<0.37.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.68.0 would require + bioconductor-s4vectors >=0.38.0,<0.39.0 , which conflicts with any installable versions previously reported; + bioconductor-bsgenome 1.70.1 would require + bioconductor-s4vectors >=0.40.0,<0.41.0 , which conflicts with any installable versions previously reported; + bioconductor-variantannotation [1.18.7|1.20.3] would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-variantannotation 1.20.3 would require + bioconductor-genomeinfodb >=1.7.1 but there are no viable options + bioconductor-genomeinfodb 1.10.3 would require + r-base 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-genomeinfodb 1.10.3 would require + r-base 3.3.2* , which conflicts with any installable versions previously reported; + bioconductor-genomeinfodb [1.10.3|1.12.3|1.14.0], which cannot be installed (as previously explained); + bioconductor-genomeinfodb 1.16.0, which cannot be installed (as previously explained); + bioconductor-genomeinfodb 1.16.0, which cannot be installed (as previously explained); + bioconductor-genomeinfodb 1.8.7 would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-genomeinfodb 1.18.1, which cannot be installed (as previously explained); + bioconductor-genomeinfodb 1.20.0, which cannot be installed (as previously explained); + bioconductor-genomeinfodb 1.22.0, which cannot be installed (as previously explained); + bioconductor-genomeinfodb 1.24.0, which cannot be installed (as previously explained); + bioconductor-genomeinfodb [1.26.0|1.26.4], which cannot be installed (as previously explained); + bioconductor-genomeinfodb 1.28.0, which cannot be installed (as previously explained); + bioconductor-genomeinfodb [1.30.0|1.30.1], which cannot be installed (as previously explained); + bioconductor-genomeinfodb [1.34.1|1.34.8|1.34.9], which cannot be installed (as previously explained); + bioconductor-genomeinfodb 1.36.1, which cannot be installed (as previously explained); + bioconductor-genomeinfodb 1.38.1, which cannot be installed (as previously explained); + bioconductor-variantannotation [1.22.3|1.24.1] would require + bioconductor-genomeinfodb >=1.11.4 , which cannot be installed (as previously explained); + bioconductor-variantannotation 1.26.1 would require + bioconductor-s4vectors >=0.18.3,<0.20.0 , which conflicts with any installable versions previously reported; + bioconductor-variantannotation 1.28.3 would require + bioconductor-s4vectors >=0.20.0,<0.21.0 , which conflicts with any installable versions previously reported; + bioconductor-variantannotation [1.30.0|1.30.1] would require + bioconductor-s4vectors >=0.22.0,<0.23.0 , which conflicts with any installable versions previously reported; + bioconductor-variantannotation 1.32.0 would require + bioconductor-s4vectors >=0.24.0,<0.25.0 , which conflicts with any installable versions previously reported; + bioconductor-variantannotation 1.34.0 would require + bioconductor-s4vectors >=0.26.0,<0.27.0 , which conflicts with any installable versions previously reported; + bioconductor-variantannotation 1.36.0 would require + bioconductor-s4vectors >=0.28.0,<0.29.0 , which conflicts with any installable versions previously reported; + bioconductor-variantannotation 1.38.0 would require + bioconductor-s4vectors >=0.30.0,<0.31.0 , which conflicts with any installable versions previously reported; + bioconductor-variantannotation 1.40.0 would require + bioconductor-s4vectors >=0.32.0,<0.33.0 , which conflicts with any installable versions previously reported; + bioconductor-variantannotation 1.44.0 would require + bioconductor-s4vectors >=0.36.0,<0.37.0 , which conflicts with any installable versions previously reported; + bioconductor-variantannotation 1.46.0 would require + bioconductor-s4vectors >=0.38.0,<0.39.0 , which conflicts with any installable versions previously reported; + bioconductor-variantannotation 1.48.1 would require + bioconductor-s4vectors >=0.40.0,<0.41.0 , which conflicts with any installable versions previously reported; + r-base 4.4.* is requested and can be installed. +# Last 100 lines of the build log. diff --git a/recipes/r-nanopore/meta.yaml b/recipes/r-nanopore/meta.yaml index 668b575fb370c..7eb2d088c17c0 100644 --- a/recipes/r-nanopore/meta.yaml +++ b/recipes/r-nanopore/meta.yaml @@ -11,7 +11,7 @@ source: sha256: c0d4ab2096ab7e5f0be7b2583bf41f6f5182932b4932b57227963e02bda2ae00 build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-nanostringnorm/meta.yaml b/recipes/r-nanostringnorm/meta.yaml index 7938ebf38b6ce..adb4983370644 100644 --- a/recipes/r-nanostringnorm/meta.yaml +++ b/recipes/r-nanostringnorm/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-nbpseq/meta.yaml b/recipes/r-nbpseq/meta.yaml index d990b86f5fbd6..58a7f0e6070c0 100644 --- a/recipes/r-nbpseq/meta.yaml +++ b/recipes/r-nbpseq/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 2454246b639e6bde46438b8fe7749fc2e898cc30de0c5ec3d5d33360c9b4b61e build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-noisyr/meta.yaml b/recipes/r-noisyr/meta.yaml index 94f3ce4a58d90..ce8c19b90cb8a 100644 --- a/recipes/r-noisyr/meta.yaml +++ b/recipes/r-noisyr/meta.yaml @@ -11,7 +11,7 @@ source: sha256: b98de24f1963c676b0b6457644a7648a5a642ac19e1cb585899a1285cbefdb16 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-oncopharmadb/meta.yaml b/recipes/r-oncopharmadb/meta.yaml index f0ed715fff932..e0fcc1fae69e3 100644 --- a/recipes/r-oncopharmadb/meta.yaml +++ b/recipes/r-oncopharmadb/meta.yaml @@ -11,7 +11,7 @@ source: sha256: ead1e1b20623ec6a707b983a32c9da89eecd5d498e43cdb0edbc011a18ffd6d1 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/r-ontologyplot/meta.yaml b/recipes/r-ontologyplot/meta.yaml index 94c88333bac20..2599022b6d91f 100644 --- a/recipes/r-ontologyplot/meta.yaml +++ b/recipes/r-ontologyplot/meta.yaml @@ -11,7 +11,7 @@ source: sha256: d508b861cfd596555f1b7bea681de71c9674fa7b708bb00b7a55744fb2cfd61b build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-orqa/build_failure.osx-64.yaml b/recipes/r-orqa/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..a4da8ae8e353d --- /dev/null +++ b/recipes/r-orqa/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 169282a80d390f5d59b8a1315aa467aaa732cbfaac3cdf6ee8534643174d51d1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("3.2.2*"), MatchSpec("bioconductor-genefilter==1.51.0=r3.2.2_0")} + Encountered problems while solving: + - nothing provides r 3.2.2* needed by bioconductor-genefilter-1.51.0-r3.2.2_0 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-genefilter >=1.24.3 is installable with the potential options + bioconductor-genefilter 1.58.1 would require + r-base 3.3.2* , which can be installed; + bioconductor-genefilter [1.51.0|1.52.1] would require + r 3.2.2* , which does not exist (perhaps a missing channel); + bioconductor-genefilter [1.54.2|1.56.0] would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-genefilter [1.58.1|1.60.0|1.62.0] would require + r-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ], which can be installed; + bioconductor-genefilter [1.62.0|1.64.0] would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + r-base 3.5.1 would require + libgfortran >=3.0.1,<4.0.0.a0 , which can be installed; + bioconductor-genefilter 1.64.0 would require + libgfortran >=3.0.1,<4.0.0.a0 , which can be installed; + bioconductor-genefilter [1.66.0|1.68.0] would require + bioconductor-annotationdbi [>=1.46.0,<1.47.0 |>=1.48.0,<1.49.0 ], which requires + bioconductor-biocgenerics >=0.30.0,<0.31.0 , which requires + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-s4vectors >=0.24.0,<0.25.0 , which requires + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-genefilter [1.70.0|1.72.0|1.72.1] would require + bioconductor-annotationdbi >=1.50.0,<1.51.0 , which requires + bioconductor-s4vectors >=0.26.0,<0.27.0 , which requires + r-base >=4.0,<4.1.0a0 , which can be installed; + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-genefilter [1.74.0|1.76.0] would require + bioconductor-annotationdbi >=1.54.0,<1.55.0 , which requires + bioconductor-keggrest >=1.32.0,<1.33.0 , which requires + bioconductor-biostrings >=2.60.0,<2.61.0 , which requires + bioconductor-xvector >=0.32.0,<0.33.0 , which requires + bioconductor-zlibbioc >=1.38.0,<1.39.0 , which requires + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-biocgenerics >=0.40.0,<0.41.0 , which requires + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-genefilter 1.80.0 would require + bioconductor-annotationdbi >=1.60.0,<1.61.0 , which requires + bioconductor-keggrest >=1.38.0,<1.39.0 , which requires + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-genefilter [1.82.1|1.84.0] would require + bioconductor-annotationdbi [>=1.62.0,<1.63.0 |>=1.64.0,<1.65.0 ], which requires + bioconductor-keggrest [>=1.40.0,<1.41.0 |>=1.42.0,<1.43.0 ], which requires + bioconductor-biostrings >=2.68.0,<2.69.0 , which requires + bioconductor-xvector >=0.40.0,<0.41.0 , which requires + bioconductor-zlibbioc >=1.46.0,<1.47.0 , which requires + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it requires + libgfortran5 >=13.2.0 but there are no viable options + libgfortran5 13.2.0 would require + libgfortran 5.0.0 13_2_0_*_1, which conflicts with any installable versions previously reported; + libgfortran5 13.2.0 would require + libgfortran 5.0.0 13_2_0_*_2, which conflicts with any installable versions previously reported; + libgfortran5 13.2.0 would require + libgfortran 5.0.0 13_2_0_*_3, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-orqa/meta.yaml b/recipes/r-orqa/meta.yaml index 5b56fd053409b..0437031f7cf0e 100644 --- a/recipes/r-orqa/meta.yaml +++ b/recipes/r-orqa/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 18378f62fbfc7f751dda71ca21e438fb3677dd0c293e74801784e2c56e963b6e build: - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-panther/meta.yaml b/recipes/r-panther/meta.yaml index 2e919526cef60..7fcf9fcc53e9a 100644 --- a/recipes/r-panther/meta.yaml +++ b/recipes/r-panther/meta.yaml @@ -10,7 +10,7 @@ source: sha256: e636e0e6ec3bbaf382609f93f2b02311db3b9138a4819e777176cabd07e7a05c build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-panther', max_pin="x.x") }} diff --git a/recipes/r-pathfindr/build_failure.linux-64.yaml b/recipes/r-pathfindr/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..cb649fedcc6e9 --- /dev/null +++ b/recipes/r-pathfindr/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: f8784dfbaf6cbec6cf0812a199842e987caa03a2be733322ae788b5464cebb83 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported; + [32mr-base 4.4.* [0m is requested and can be installed. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("3.2.2*"), MatchSpec("bioconductor-kegggraph==1.28.0=r3.2.2_0")} + Encountered problems while solving: + - nothing provides r 3.2.2* needed by bioconductor-kegggraph-1.28.0-r3.2.2_0 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-ggkegg[0m is installable with the potential options + [32mbioconductor-ggkegg 1.4.0[0m would require + [32mbioconductor-biocfilecache >=2.14.0,<2.15.0 [0m, which requires + [32mr-base >=4.4,<4.5.0a0 [0m, which can be installed; + [31mbioconductor-ggkegg 1.0.2[0m would require + [31mbioconductor-org.hs.eg.db >=3.18.0,<3.19.0 [0m, which requires + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-kegggraph[0m is not installable because there are no viable options + [31mbioconductor-kegggraph 1.30.0[0m would require + [31mr-base 3.3.2* [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-kegggraph 1.28.0[0m would require + [31mr 3.2.2* [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-kegggraph [1.28.0|1.30.0][0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-kegggraph [1.30.0|1.38.0|1.38.1|1.40.0][0m would require + [31mr-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ][0m, which conflicts with any installable versions previously reported; + [31mbioconductor-kegggraph [1.40.0|1.42.0][0m would require + [31mbioconductor-graph >=1.60.0,<1.61.0 [0m, which requires + [31mr-base >=3.5.1,<3.5.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-base >=3.5.1,<3.5.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-kegggraph [1.44.0|1.46.0][0m would require + [31mbioconductor-graph [>=1.62.0,<1.63.0 |>=1.64.0,<1.65.0 ][0m, which requires + [31mbioconductor-biocgenerics [>=0.30.0,<0.31.0 |>=0.32.0,<0.33.0 ][0m, which requires + [31mr-base >=3.6,<3.7.0a0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-kegggraph [1.48.0|1.50.0][0m would require + [31mbioconductor-graph >=1.66.0,<1.67.0 [0m, which requires + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-base >=4.0,<4.1.0a0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-kegggraph [1.52.0|1.54.0][0m would require + [31mbioconductor-rgraphviz >=2.36.0,<2.37.0 [0m, which requires + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-base >=4.1,<4.2.0a0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-kegggraph 1.58.0[0m would require + [31mr-base >=4.2,<4.3.0a0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-kegggraph [1.60.0|1.62.0][0m would require + [31mbioconductor-rgraphviz >=2.44.0,<2.45.0 [0m, which requires + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported; + [31mr-base >=4.3,<4.4.0a0 [0m, which conflicts with any installable versions previously reported; + [32mr-base 4.4.* [0m is requested and can be installed. +# Last 100 lines of the build log. diff --git a/recipes/r-pathfindr/meta.yaml b/recipes/r-pathfindr/meta.yaml index bb794fe4d84d6..f9e41ed653928 100644 --- a/recipes/r-pathfindr/meta.yaml +++ b/recipes/r-pathfindr/meta.yaml @@ -12,7 +12,7 @@ source: sha256: 031f5dad32ba32bc3084bd63d0c8326c04e82ffb07689546f4e2e33c0db79253 build: - number: 0 + number: 1 noarch: generic merge_build_host: True # [win] rpaths: diff --git a/recipes/r-pathwaytmb/meta.yaml b/recipes/r-pathwaytmb/meta.yaml index 9e9e898dddea7..bac5341cee4d6 100644 --- a/recipes/r-pathwaytmb/meta.yaml +++ b/recipes/r-pathwaytmb/meta.yaml @@ -11,11 +11,13 @@ source: sha256: 1565b09cf04bad988f1e23c93ae8604d4da48dee165c20668f3abbb8133d3aff build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-pathwaytmb', max_pin="x.x") }} requirements: host: diff --git a/recipes/r-pcalg/build_failure.osx-64.yaml b/recipes/r-pcalg/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..794503c0cb171 --- /dev/null +++ b/recipes/r-pcalg/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 95859f676a32b13f8e568040e445786fa2b390a5fd474ec143cc3c843cd868a5 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + summary: Functions for causal structure learning and causal inference using graphical + models. The main algorithms for causal structure learning are PC (for observational + data without hidden variables), FCI and RFCI (for observational data with hidden + variables), and GIES (for a mix of data from observational studies (i.e. observational + data) and data from experiments involving interventions (i.e. interventional data) + without hidden variables). For causal inference the IDA algorithm, the Generalized + Backdoor Criterion (GBC), the Generalized Adjustment Criterion (GAC) and some + related functions are implemented. Functions for incorporating background knowledge + are provided. + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/r-pcalg_1735582115583/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/r-pcalg_1735582115583/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/r-pcalg_1735582115583/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/r-pcalg_1735582115583/work + INFO: activate-gfortran_osx-64.sh made the following environmental changes: + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-pcalg-2.6_12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-pcalg-2.6_12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-pcalg-2.6_12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-pcalg-2.6_12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-pcalg-2.6_12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-pcalg-2.6_12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-pcalg-2.6_12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-pcalg-2.6_12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-pcalg-2.6_12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-pcalg-2.6_12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-pcalg-2.6_12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-pcalg-2.6_12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-pcalg-2.6_12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-pcalg-2.6_12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -I'$PREFIX/lib/R/library/BH/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -I"../inst/include" -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1720307552622/work=/usr/local/src/conda/r-base-4.4.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c constraint.cpp -o constraint.o +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/r-pcalg/meta.yaml b/recipes/r-pcalg/meta.yaml index 3a46900fcb68a..732679d2c7640 100644 --- a/recipes/r-pcalg/meta.yaml +++ b/recipes/r-pcalg/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 4c18c96dbe38d672666c11bd0dc9d4e93fa29497a1c4b905440f52593c10674a build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-pctgcdata/meta.yaml b/recipes/r-pctgcdata/meta.yaml index 9db796dd1f819..09439d527a14a 100644 --- a/recipes/r-pctgcdata/meta.yaml +++ b/recipes/r-pctgcdata/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 9397b5a88b3262c4eaeb1737e30c2eac319f0418c499d003763d5cceef1f77bc build: - number: 4 + number: 5 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-perfmeas/build_failure.osx-64.yaml b/recipes/r-perfmeas/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..79f16384d0dac --- /dev/null +++ b/recipes/r-perfmeas/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 115e04e5d260365acf82b334abd627e540494b1940c2d4f1e88849b3d5da86d9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-rbgl [1.64.0|1.66.0] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-rbgl [1.68.0|1.70.0] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-rbgl 1.74.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-rbgl [1.76.0|1.78.0] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("3.2.2*"), MatchSpec("bioconductor-rbgl==1.46.0=r3.2.2_0")} + Encountered problems while solving: + - nothing provides r 3.2.2* needed by bioconductor-rbgl-1.46.0-r3.2.2_0 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-rbgl is installable with the potential options + bioconductor-rbgl 1.48.1 would require + r-base 3.3.2* , which can be installed; + bioconductor-rbgl 1.46.0 would require + r 3.2.2* , which does not exist (perhaps a missing channel); + bioconductor-rbgl [1.46.0|1.48.1] would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-rbgl [1.48.1|1.52.0|1.54.0] would require + r-base 3.4.1* , which can be installed; + bioconductor-rbgl [1.58.1|1.58.2] would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-rbgl [1.60.0|1.62.1] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-rbgl [1.64.0|1.66.0] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-rbgl [1.68.0|1.70.0] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-rbgl 1.74.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-rbgl [1.76.0|1.78.0] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-perfmeas/meta.yaml b/recipes/r-perfmeas/meta.yaml index 431c875eb46dc..e9f55acdb6554 100644 --- a/recipes/r-perfmeas/meta.yaml +++ b/recipes/r-perfmeas/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 4b4212182203d7ee1ae4c132ac1c9935e425e407ee435300e558afcb2798d28f build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-phewas/meta.yaml b/recipes/r-phewas/meta.yaml index 20299cbc1494c..432063b3bb17f 100644 --- a/recipes/r-phewas/meta.yaml +++ b/recipes/r-phewas/meta.yaml @@ -11,7 +11,7 @@ source: sha256: '{{ hash }}' build: - number: 0 + number: 1 skip: true # [win32] run_exports: - {{ pin_subpackage("r-phewas", max_pin="x.x") }} diff --git a/recipes/r-phyext2/LICENSE.txt b/recipes/r-phyext2/LICENSE.txt new file mode 100644 index 0000000000000..10926e87f113f --- /dev/null +++ b/recipes/r-phyext2/LICENSE.txt @@ -0,0 +1,675 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. We, the Free Software Foundation, use the +GNU General Public License for most of our software; it applies also to +any other work released this way by its authors. You can apply it to +your programs, too. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + + To protect your rights, we need to prevent others from denying you +these rights or asking you to surrender the rights. Therefore, you have +certain responsibilities if you distribute copies of the software, or if +you modify it: responsibilities to respect the freedom of others. + + For example, if you distribute copies of such a program, whether +gratis or for a fee, you must pass on to the recipients the same +freedoms that you received. You must make sure that they, too, receive +or can get the source code. And you must show them these terms so they +know their rights. + + Developers that use the GNU GPL protect your rights with two steps: +(1) assert copyright on the software, and (2) offer you this License +giving you legal permission to copy, distribute and/or modify it. + + For the developers' and authors' protection, the GPL clearly explains +that there is no warranty for this free software. For both users' and +authors' sake, the GPL requires that modified versions be marked as +changed, so that their problems will not be attributed erroneously to +authors of previous versions. + + Some devices are designed to deny users access to install or run +modified versions of the software inside them, although the manufacturer +can do so. This is fundamentally incompatible with the aim of +protecting users' freedom to change the software. The systematic +pattern of such abuse occurs in the area of products for individuals to +use, which is precisely where it is most unacceptable. Therefore, we +have designed this version of the GPL to prohibit the practice for those +products. If such problems arise substantially in other domains, we +stand ready to extend this provision to those domains in future versions +of the GPL, as needed to protect the freedom of users. + + Finally, every program is threatened constantly by software patents. +States should not allow patents to restrict development and use of +software on general-purpose computers, but in those that do, we wish to +avoid the special danger that patents applied to a free program could +make it effectively proprietary. To prevent this, the GPL assures that +patents cannot be used to render the program non-free. + + The precise terms and conditions for copying, distribution and +modification follow. + + TERMS AND CONDITIONS + + 0. Definitions. + + "This License" refers to version 3 of the GNU General Public License. + + "Copyright" also means copyright-like laws that apply to other kinds of +works, such as semiconductor masks. + + "The Program" refers to any copyrightable work licensed under this +License. Each licensee is addressed as "you". "Licensees" and +"recipients" may be individuals or organizations. + + To "modify" a work means to copy from or adapt all or part of the work +in a fashion requiring copyright permission, other than the making of an +exact copy. The resulting work is called a "modified version" of the +earlier work or a work "based on" the earlier work. + + A "covered work" means either the unmodified Program or a work based +on the Program. + + To "propagate" a work means to do anything with it that, without +permission, would make you directly or secondarily liable for +infringement under applicable copyright law, except executing it on a +computer or modifying a private copy. Propagation includes copying, +distribution (with or without modification), making available to the +public, and in some countries other activities as well. + + To "convey" a work means any kind of propagation that enables other +parties to make or receive copies. Mere interaction with a user through +a computer network, with no transfer of a copy, is not conveying. + + An interactive user interface displays "Appropriate Legal Notices" +to the extent that it includes a convenient and prominently visible +feature that (1) displays an appropriate copyright notice, and (2) +tells the user that there is no warranty for the work (except to the +extent that warranties are provided), that licensees may convey the +work under this License, and how to view a copy of this License. If +the interface presents a list of user commands or options, such as a +menu, a prominent item in the list meets this criterion. + + 1. Source Code. + + The "source code" for a work means the preferred form of the work +for making modifications to it. "Object code" means any non-source +form of a work. + + A "Standard Interface" means an interface that either is an official +standard defined by a recognized standards body, or, in the case of +interfaces specified for a particular programming language, one that +is widely used among developers working in that language. + + The "System Libraries" of an executable work include anything, other +than the work as a whole, that (a) is included in the normal form of +packaging a Major Component, but which is not part of that Major +Component, and (b) serves only to enable use of the work with that +Major Component, or to implement a Standard Interface for which an +implementation is available to the public in source code form. A +"Major Component", in this context, means a major essential component +(kernel, window system, and so on) of the specific operating system +(if any) on which the executable work runs, or a compiler used to +produce the work, or an object code interpreter used to run it. + + The "Corresponding Source" for a work in object code form means all +the source code needed to generate, install, and (for an executable +work) run the object code and to modify the work, including scripts to +control those activities. However, it does not include the work's +System Libraries, or general-purpose tools or generally available free +programs which are used unmodified in performing those activities but +which are not part of the work. For example, Corresponding Source +includes interface definition files associated with source files for +the work, and the source code for shared libraries and dynamically +linked subprograms that the work is specifically designed to require, +such as by intimate data communication or control flow between those +subprograms and other parts of the work. + + The Corresponding Source need not include anything that users +can regenerate automatically from other parts of the Corresponding +Source. + + The Corresponding Source for a work in source code form is that +same work. + + 2. Basic Permissions. + + All rights granted under this License are granted for the term of +copyright on the Program, and are irrevocable provided the stated +conditions are met. This License explicitly affirms your unlimited +permission to run the unmodified Program. The output from running a +covered work is covered by this License only if the output, given its +content, constitutes a covered work. This License acknowledges your +rights of fair use or other equivalent, as provided by copyright law. + + You may make, run and propagate covered works that you do not +convey, without conditions so long as your license otherwise remains +in force. You may convey covered works to others for the sole purpose +of having them make modifications exclusively for you, or provide you +with facilities for running those works, provided that you comply with +the terms of this License in conveying all material for which you do +not control copyright. Those thus making or running the covered works +for you must do so exclusively on your behalf, under your direction +and control, on terms that prohibit them from making any copies of +your copyrighted material outside their relationship with you. + + Conveying under any other circumstances is permitted solely under +the conditions stated below. Sublicensing is not allowed; section 10 +makes it unnecessary. + + 3. Protecting Users' Legal Rights From Anti-Circumvention Law. + + No covered work shall be deemed part of an effective technological +measure under any applicable law fulfilling obligations under article +11 of the WIPO copyright treaty adopted on 20 December 1996, or +similar laws prohibiting or restricting circumvention of such +measures. + + When you convey a covered work, you waive any legal power to forbid +circumvention of technological measures to the extent such circumvention +is effected by exercising rights under this License with respect to +the covered work, and you disclaim any intention to limit operation or +modification of the work as a means of enforcing, against the work's +users, your or third parties' legal rights to forbid circumvention of +technological measures. + + 4. Conveying Verbatim Copies. + + You may convey verbatim copies of the Program's source code as you +receive it, in any medium, provided that you conspicuously and +appropriately publish on each copy an appropriate copyright notice; +keep intact all notices stating that this License and any +non-permissive terms added in accord with section 7 apply to the code; +keep intact all notices of the absence of any warranty; and give all +recipients a copy of this License along with the Program. + + You may charge any price or no price for each copy that you convey, +and you may offer support or warranty protection for a fee. + + 5. Conveying Modified Source Versions. + + You may convey a work based on the Program, or the modifications to +produce it from the Program, in the form of source code under the +terms of section 4, provided that you also meet all of these conditions: + + a) The work must carry prominent notices stating that you modified + it, and giving a relevant date. + + b) The work must carry prominent notices stating that it is + released under this License and any conditions added under section + 7. This requirement modifies the requirement in section 4 to + "keep intact all notices". + + c) You must license the entire work, as a whole, under this + License to anyone who comes into possession of a copy. This + License will therefore apply, along with any applicable section 7 + additional terms, to the whole of the work, and all its parts, + regardless of how they are packaged. This License gives no + permission to license the work in any other way, but it does not + invalidate such permission if you have separately received it. + + d) If the work has interactive user interfaces, each must display + Appropriate Legal Notices; however, if the Program has interactive + interfaces that do not display Appropriate Legal Notices, your + work need not make them do so. + + A compilation of a covered work with other separate and independent +works, which are not by their nature extensions of the covered work, +and which are not combined with it such as to form a larger program, +in or on a volume of a storage or distribution medium, is called an +"aggregate" if the compilation and its resulting copyright are not +used to limit the access or legal rights of the compilation's users +beyond what the individual works permit. Inclusion of a covered work +in an aggregate does not cause this License to apply to the other +parts of the aggregate. + + 6. Conveying Non-Source Forms. + + You may convey a covered work in object code form under the terms +of sections 4 and 5, provided that you also convey the +machine-readable Corresponding Source under the terms of this License, +in one of these ways: + + a) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by the + Corresponding Source fixed on a durable physical medium + customarily used for software interchange. + + b) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by a + written offer, valid for at least three years and valid for as + long as you offer spare parts or customer support for that product + model, to give anyone who possesses the object code either (1) a + copy of the Corresponding Source for all the software in the + product that is covered by this License, on a durable physical + medium customarily used for software interchange, for a price no + more than your reasonable cost of physically performing this + conveying of source, or (2) access to copy the + Corresponding Source from a network server at no charge. + + c) Convey individual copies of the object code with a copy of the + written offer to provide the Corresponding Source. This + alternative is allowed only occasionally and noncommercially, and + only if you received the object code with such an offer, in accord + with subsection 6b. + + d) Convey the object code by offering access from a designated + place (gratis or for a charge), and offer equivalent access to the + Corresponding Source in the same way through the same place at no + further charge. You need not require recipients to copy the + Corresponding Source along with the object code. If the place to + copy the object code is a network server, the Corresponding Source + may be on a different server (operated by you or a third party) + that supports equivalent copying facilities, provided you maintain + clear directions next to the object code saying where to find the + Corresponding Source. Regardless of what server hosts the + Corresponding Source, you remain obligated to ensure that it is + available for as long as needed to satisfy these requirements. + + e) Convey the object code using peer-to-peer transmission, provided + you inform other peers where the object code and Corresponding + Source of the work are being offered to the general public at no + charge under subsection 6d. + + A separable portion of the object code, whose source code is excluded +from the Corresponding Source as a System Library, need not be +included in conveying the object code work. + + A "User Product" is either (1) a "consumer product", which means any +tangible personal property which is normally used for personal, family, +or household purposes, or (2) anything designed or sold for incorporation +into a dwelling. In determining whether a product is a consumer product, +doubtful cases shall be resolved in favor of coverage. For a particular +product received by a particular user, "normally used" refers to a +typical or common use of that class of product, regardless of the status +of the particular user or of the way in which the particular user +actually uses, or expects or is expected to use, the product. A product +is a consumer product regardless of whether the product has substantial +commercial, industrial or non-consumer uses, unless such uses represent +the only significant mode of use of the product. + + "Installation Information" for a User Product means any methods, +procedures, authorization keys, or other information required to install +and execute modified versions of a covered work in that User Product from +a modified version of its Corresponding Source. The information must +suffice to ensure that the continued functioning of the modified object +code is in no case prevented or interfered with solely because +modification has been made. + + If you convey an object code work under this section in, or with, or +specifically for use in, a User Product, and the conveying occurs as +part of a transaction in which the right of possession and use of the +User Product is transferred to the recipient in perpetuity or for a +fixed term (regardless of how the transaction is characterized), the +Corresponding Source conveyed under this section must be accompanied +by the Installation Information. But this requirement does not apply +if neither you nor any third party retains the ability to install +modified object code on the User Product (for example, the work has +been installed in ROM). + + The requirement to provide Installation Information does not include a +requirement to continue to provide support service, warranty, or updates +for a work that has been modified or installed by the recipient, or for +the User Product in which it has been modified or installed. Access to a +network may be denied when the modification itself materially and +adversely affects the operation of the network or violates the rules and +protocols for communication across the network. + + Corresponding Source conveyed, and Installation Information provided, +in accord with this section must be in a format that is publicly +documented (and with an implementation available to the public in +source code form), and must require no special password or key for +unpacking, reading or copying. + + 7. Additional Terms. + + "Additional permissions" are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. +Additional permissions that are applicable to the entire Program shall +be treated as though they were included in this License, to the extent +that they are valid under applicable law. If additional permissions +apply only to part of the Program, that part may be used separately +under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + + When you convey a copy of a covered work, you may at your option +remove any additional permissions from that copy, or from any part of +it. (Additional permissions may be written to require their own +removal in certain cases when you modify the work.) You may place +additional permissions on material, added by you to a covered work, +for which you have or can give appropriate copyright permission. + + Notwithstanding any other provision of this License, for material you +add to a covered work, you may (if authorized by the copyright holders of +that material) supplement the terms of this License with terms: + + a) Disclaiming warranty or limiting liability differently from the + terms of sections 15 and 16 of this License; or + + b) Requiring preservation of specified reasonable legal notices or + author attributions in that material or in the Appropriate Legal + Notices displayed by works containing it; or + + c) Prohibiting misrepresentation of the origin of that material, or + requiring that modified versions of such material be marked in + reasonable ways as different from the original version; or + + d) Limiting the use for publicity purposes of names of licensors or + authors of the material; or + + e) Declining to grant rights under trademark law for use of some + trade names, trademarks, or service marks; or + + f) Requiring indemnification of licensors and authors of that + material by anyone who conveys the material (or modified versions of + it) with contractual assumptions of liability to the recipient, for + any liability that these contractual assumptions directly impose on + those licensors and authors. + + All other non-permissive additional terms are considered "further +restrictions" within the meaning of section 10. If the Program as you +received it, or any part of it, contains a notice stating that it is +governed by this License along with a term that is a further +restriction, you may remove that term. If a license document contains +a further restriction but permits relicensing or conveying under this +License, you may add to a covered work material governed by the terms +of that license document, provided that the further restriction does +not survive such relicensing or conveying. + + If you add terms to a covered work in accord with this section, you +must place, in the relevant source files, a statement of the +additional terms that apply to those files, or a notice indicating +where to find the applicable terms. + + Additional terms, permissive or non-permissive, may be stated in the +form of a separately written license, or stated as exceptions; +the above requirements apply either way. + + 8. Termination. + + You may not propagate or modify a covered work except as expressly +provided under this License. Any attempt otherwise to propagate or +modify it is void, and will automatically terminate your rights under +this License (including any patent licenses granted under the third +paragraph of section 11). + + However, if you cease all violation of this License, then your +license from a particular copyright holder is reinstated (a) +provisionally, unless and until the copyright holder explicitly and +finally terminates your license, and (b) permanently, if the copyright +holder fails to notify you of the violation by some reasonable means +prior to 60 days after the cessation. + + Moreover, your license from a particular copyright holder is +reinstated permanently if the copyright holder notifies you of the +violation by some reasonable means, this is the first time you have +received notice of violation of this License (for any work) from that +copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + + Termination of your rights under this section does not terminate the +licenses of parties who have received copies or rights from you under +this License. If your rights have been terminated and not permanently +reinstated, you do not qualify to receive new licenses for the same +material under section 10. + + 9. Acceptance Not Required for Having Copies. + + You are not required to accept this License in order to receive or +run a copy of the Program. Ancillary propagation of a covered work +occurring solely as a consequence of using peer-to-peer transmission +to receive a copy likewise does not require acceptance. However, +nothing other than this License grants you permission to propagate or +modify any covered work. These actions infringe copyright if you do +not accept this License. Therefore, by modifying or propagating a +covered work, you indicate your acceptance of this License to do so. + + 10. Automatic Licensing of Downstream Recipients. + + Each time you convey a covered work, the recipient automatically +receives a license from the original licensors, to run, modify and +propagate that work, subject to this License. You are not responsible +for enforcing compliance by third parties with this License. + + An "entity transaction" is a transaction transferring control of an +organization, or substantially all assets of one, or subdividing an +organization, or merging organizations. If propagation of a covered +work results from an entity transaction, each party to that +transaction who receives a copy of the work also receives whatever +licenses to the work the party's predecessor in interest had or could +give under the previous paragraph, plus a right to possession of the +Corresponding Source of the work from the predecessor in interest, if +the predecessor has it or can get it with reasonable efforts. + + You may not impose any further restrictions on the exercise of the +rights granted or affirmed under this License. For example, you may +not impose a license fee, royalty, or other charge for exercise of +rights granted under this License, and you may not initiate litigation +(including a cross-claim or counterclaim in a lawsuit) alleging that +any patent claim is infringed by making, using, selling, offering for +sale, or importing the Program or any portion of it. + + 11. Patents. + + A "contributor" is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The +work thus licensed is called the contributor's "contributor version". + + A contributor's "essential patent claims" are all patent claims +owned or controlled by the contributor, whether already acquired or +hereafter acquired, that would be infringed by some manner, permitted +by this License, of making, using, or selling its contributor version, +but do not include claims that would be infringed only as a +consequence of further modification of the contributor version. For +purposes of this definition, "control" includes the right to grant +patent sublicenses in a manner consistent with the requirements of +this License. + + Each contributor grants you a non-exclusive, worldwide, royalty-free +patent license under the contributor's essential patent claims, to +make, use, sell, offer for sale, import and otherwise run, modify and +propagate the contents of its contributor version. + + In the following three paragraphs, a "patent license" is any express +agreement or commitment, however denominated, not to enforce a patent +(such as an express permission to practice a patent or covenant not to +sue for patent infringement). To "grant" such a patent license to a +party means to make such an agreement or commitment not to enforce a +patent against the party. + + If you convey a covered work, knowingly relying on a patent license, +and the Corresponding Source of the work is not available for anyone +to copy, free of charge and under the terms of this License, through a +publicly available network server or other readily accessible means, +then you must either (1) cause the Corresponding Source to be so +available, or (2) arrange to deprive yourself of the benefit of the +patent license for this particular work, or (3) arrange, in a manner +consistent with the requirements of this License, to extend the patent +license to downstream recipients. "Knowingly relying" means you have +actual knowledge that, but for the patent license, your conveying the +covered work in a country, or your recipient's use of the covered work +in a country, would infringe one or more identifiable patents in that +country that you have reason to believe are valid. + + If, pursuant to or in connection with a single transaction or +arrangement, you convey, or propagate by procuring conveyance of, a +covered work, and grant a patent license to some of the parties +receiving the covered work authorizing them to use, propagate, modify +or convey a specific copy of the covered work, then the patent license +you grant is automatically extended to all recipients of the covered +work and works based on it. + + A patent license is "discriminatory" if it does not include within +the scope of its coverage, prohibits the exercise of, or is +conditioned on the non-exercise of one or more of the rights that are +specifically granted under this License. You may not convey a covered +work if you are a party to an arrangement with a third party that is +in the business of distributing software, under which you make payment +to the third party based on the extent of your activity of conveying +the work, and under which the third party grants, to any of the +parties who would receive the covered work from you, a discriminatory +patent license (a) in connection with copies of the covered work +conveyed by you (or copies made from those copies), or (b) primarily +for and in connection with specific products or compilations that +contain the covered work, unless you entered into that arrangement, +or that patent license was granted, prior to 28 March 2007. + + Nothing in this License shall be construed as excluding or limiting +any implied license or other defenses to infringement that may +otherwise be available to you under applicable patent law. + + 12. No Surrender of Others' Freedom. + + If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you may +not convey it at all. For example, if you agree to terms that obligate you +to collect a royalty for further conveying from those to whom you convey +the Program, the only way you could satisfy both those terms and this +License would be to refrain entirely from conveying the Program. + + 13. Use with the GNU Affero General Public License. + + Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU Affero General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the special requirements of the GNU Affero General Public License, +section 13, concerning interaction through a network will apply to the +combination as such. + + 14. Revised Versions of this License. + + The Free Software Foundation may publish revised and/or new versions of +the GNU General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + + Each version is given a distinguishing version number. If the +Program specifies that a certain numbered version of the GNU General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. + diff --git a/recipes/r-phyext2/meta.yaml b/recipes/r-phyext2/meta.yaml index f4572c8f4f379..5cf7f274f56f3 100644 --- a/recipes/r-phyext2/meta.yaml +++ b/recipes/r-phyext2/meta.yaml @@ -1,8 +1,5 @@ {% set version = '0.0.4' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - package: name: r-phyext2 version: {{ version|replace("-", "_") }} @@ -16,10 +13,12 @@ source: build: noarch: generic merge_build_host: True # [win] - number: 9 + number: 10 rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-phyext2', max_pin="x") }} requirements: build: @@ -35,12 +34,12 @@ requirements: test: commands: - - $R -e "library('phyext2')" # [not win] - - "\"%R%\" -e \"library('phyext2')\"" # [win] + - $R -e "library('phyext2')" about: home: https://CRAN.R-project.org/package=phyext2 license: GPL-3 + license_file: LICENSE.txt summary: Based on (but not identical to) the no-longer-maintained package 'phyext', provides enhancements to 'phylobase' classes, specifically for use by package 'SigTree'; provides classes and methods which help users manipulate branch-annotated trees diff --git a/recipes/r-phylomeasures/meta.yaml b/recipes/r-phylomeasures/meta.yaml index 27e8b9c08b02e..7f2d93ccb96fe 100644 --- a/recipes/r-phylomeasures/meta.yaml +++ b/recipes/r-phylomeasures/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 1982f47cb5bfa61e56f47cae78e199f13778edde49af86fa5cc183a0d1d15d05 build: - number: 9 + number: 10 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-pipette/meta.yaml b/recipes/r-pipette/meta.yaml index 3c673788c57bd..a84149c97a964 100644 --- a/recipes/r-pipette/meta.yaml +++ b/recipes/r-pipette/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 80298775063372e1275191ff800ec00b7feb9cc33fdb9afb453826499e3b54c0 build: - number: 1 + number: 2 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-pophelper/meta.yaml b/recipes/r-pophelper/meta.yaml index 283e72455e841..ff24907cf3be4 100644 --- a/recipes/r-pophelper/meta.yaml +++ b/recipes/r-pophelper/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-pore/build_failure.osx-64.yaml b/recipes/r-pore/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..34a169b9e24e8 --- /dev/null +++ b/recipes/r-pore/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 8d723b5c52e5c5e12483da404dbe0d90f0c7490baaa5aa99628d3ef1bf5a3fdb # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-rhdf5==2.16.0=r3.3.1_1"), MatchSpec("3.3.1*")} + Encountered problems while solving: + - nothing provides r 3.3.1* needed by bioconductor-rhdf5-2.16.0-r3.3.1_1 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-rhdf5 is installable with the potential options + bioconductor-rhdf5 2.16.0 would require + r-base 3.3.2* , which can be installed; + bioconductor-rhdf5 2.16.0 would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-rhdf5 [2.16.0|2.20.0|2.24.0] would require + r-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ], which can be installed; + bioconductor-rhdf5 [2.24.0|2.26.0|2.26.1|2.26.2|2.28.0] would require + bioconductor-rhdf5lib >=1.4.0,<1.5.0 with the potential options + bioconductor-rhdf5lib [1.4.2|1.4.3] would require + libgfortran >=3.0.1,<4.0.0.a0 , which can be installed; + bioconductor-rhdf5lib 1.4.2 would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + r-base 3.5.1 would require + libgfortran >=3.0.1,<4.0.0.a0 , which can be installed; + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed; + r-base 3.5.1, which can be installed (as previously explained); + bioconductor-rhdf5 2.26.2 would require + bioconductor-rhdf5lib >=1.4.3,<1.5.0 , which can be installed (as previously explained); + bioconductor-rhdf5 [2.28.0|2.30.0] would require + bioconductor-rhdf5lib >=1.8.0,<1.9.0 , which requires + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-rhdf5 [2.32.0|2.34.0] would require + bioconductor-rhdf5filters >=1.2.0,<1.3.0 , which requires + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-rhdf5lib >=1.10.0,<1.11.0 , which requires + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-rhdf5 [2.36.0|2.38.0|2.38.1] would require + bioconductor-rhdf5lib >=1.14.0,<1.15.0 , which requires + r-base >=4.1,<4.2.0a0 , which can be installed; + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-rhdf5 2.42.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-rhdf5 [2.44.0|2.46.1] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it requires + libgfortran5 >=13.2.0 but there are no viable options + libgfortran5 13.2.0 would require + libgfortran 5.0.0 13_2_0_*_1, which conflicts with any installable versions previously reported; + libgfortran5 13.2.0 would require + libgfortran 5.0.0 13_2_0_*_2, which conflicts with any installable versions previously reported; + libgfortran5 13.2.0 would require + libgfortran 5.0.0 13_2_0_*_3, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-pore/meta.yaml b/recipes/r-pore/meta.yaml index d6d82bff11fa7..ee8925dd7ed35 100644 --- a/recipes/r-pore/meta.yaml +++ b/recipes/r-pore/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 5bcf5a2dfe3e714baef545972cd05901198cd58949cc9951270fed25a94d305e build: - number: 6 + number: 7 rpaths: - lib/R/lib/ diff --git a/recipes/r-presto/meta.yaml b/recipes/r-presto/meta.yaml index 1f91ce9cadbf2..a0469c5a74a90 100644 --- a/recipes/r-presto/meta.yaml +++ b/recipes/r-presto/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 96e1b3a2fec84bbd0781d4d3235e33003cd4eb28944a433868ba446b956abcdb build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-proteus-bartongroup/meta.yaml b/recipes/r-proteus-bartongroup/meta.yaml index 929156bc46190..cdee1c76844cf 100644 --- a/recipes/r-proteus-bartongroup/meta.yaml +++ b/recipes/r-proteus-bartongroup/meta.yaml @@ -10,7 +10,7 @@ source: sha256: befd66aeb5c29ea10d1c457aad9e47f3f757347e8c60734a8f01161222718137 build: - number: 1 + number: 2 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-pscbs/meta.yaml b/recipes/r-pscbs/meta.yaml index 6b9486d7121bf..1fd0e342e771c 100644 --- a/recipes/r-pscbs/meta.yaml +++ b/recipes/r-pscbs/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-qiime2r/build_failure.linux-64.yaml b/recipes/r-qiime2r/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..6d7f7a3c06d2c --- /dev/null +++ b/recipes/r-qiime2r/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 473da121cee17c067de5c3d9d7b3ded979c3304b3dca29efaa472c657a35d873 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [32mbioconductor-rhdf5lib >=1.4.3,<1.5.0 [0m, which requires + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.28.0|2.30.0][0m would require + [32mbioconductor-rhdf5lib >=1.8.0,<1.9.0 [0m, which requires + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.32.0|2.34.0][0m would require + [32mbioconductor-rhdf5lib >=1.10.0,<1.11.0 [0m, which requires + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.36.0|2.38.0|2.38.1][0m would require + [32mbioconductor-rhdf5lib >=1.14.0,<1.15.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 2.42.0[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.44.0|2.46.1][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-rhdf5==2.26.2=r351hdbcaa40_1"), MatchSpec("r-base[version='>=3.5.1,<3.5.2.0a0']")} + Encountered problems while solving: + - package bioconductor-rhdf5-2.26.2-r351hdbcaa40_1 requires r-base >=3.5.1,<3.5.2.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-rhdf5 >=2.26.2 [0m is installable with the potential options + [32mbioconductor-rhdf5 [2.26.2|2.28.0][0m would require + [32mbioconductor-rhdf5lib >=1.4.3,<1.5.0 [0m, which requires + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.28.0|2.30.0][0m would require + [32mbioconductor-rhdf5lib >=1.8.0,<1.9.0 [0m, which requires + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.32.0|2.34.0][0m would require + [32mbioconductor-rhdf5lib >=1.10.0,<1.11.0 [0m, which requires + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.36.0|2.38.0|2.38.1][0m would require + [32mbioconductor-rhdf5lib >=1.14.0,<1.15.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 2.42.0[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.44.0|2.46.1][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-qiime2r/meta.yaml b/recipes/r-qiime2r/meta.yaml index b87c1d8ed9196..6f06b4f1bbb08 100644 --- a/recipes/r-qiime2r/meta.yaml +++ b/recipes/r-qiime2r/meta.yaml @@ -12,7 +12,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 noarch: generic # This is required to make R link correctly on Linux. rpaths: diff --git a/recipes/r-qorts/meta.yaml b/recipes/r-qorts/meta.yaml index e9bc406748bfa..0b37750fa4e99 100644 --- a/recipes/r-qorts/meta.yaml +++ b/recipes/r-qorts/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 51095994e1bd8fe5403d27eada8ceca97be0cecbee8eed802b6dc3fc6ce372af build: - number: 5 + number: 6 noarch: generic script: R CMD INSTALL --build QoRTs_1.3.6.tar.gz rpaths: diff --git a/recipes/r-qtlseqr/meta.yaml b/recipes/r-qtlseqr/meta.yaml index 625894675784e..f858a9c152bab 100644 --- a/recipes/r-qtlseqr/meta.yaml +++ b/recipes/r-qtlseqr/meta.yaml @@ -9,7 +9,7 @@ source: sha256: unused build: - number: 6 + number: 7 rpaths: - lib/R/lib/ diff --git a/recipes/r-quilt/build_failure.osx-64.yaml b/recipes/r-quilt/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..6f976a35b4ba8 --- /dev/null +++ b/recipes/r-quilt/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: f043f01b0a816869b396fbfa1d43a0a433f35cb682caf384cd0e1a5068dcd694 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-quilt-2.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/r-quilt_1734623925881/test_tmp/conda_test_runner.sh']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: r-quilt-2.0.1-r44h5eaf441_1.tar.bz2 + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=/opt/mambaforge/envs/bioconda/conda-bld/r-quilt_1734623925881/_build_env/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-quilt-2.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-quilt-2.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-quilt-2.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + + R version 4.4.2 (2024-10-31) -- "Pile of Leaves" + Copyright (C) 2024 The R Foundation for Statistical Computing + Platform: x86_64-apple-darwin13.4.0 + + R is free software and comes with ABSOLUTELY NO WARRANTY. + You are welcome to redistribute it under certain conditions. + Type 'license()' or 'licence()' for distribution details. + + Natural language support but running in an English locale + + R is a collaborative project with many contributors. + Type 'contributors()' for more information and + 'citation()' on how to cite R or R packages in publications. + + Type 'demo()' for some demos, 'help()' for on-line help, or + 'help.start()' for an HTML browser interface to help. + Type 'q()' to quit R. + + > library('QUILT'); testthat::test_package('QUILT', stop_on_failure = TRUE, stop_on_warning = TRUE, filter = 'acceptance-one', reporter = 'summary') + acceptance-one: .W1 + + Warnings + 1. QUILT can impute a few samples in a standard way, using a large panel ('test-acceptance-one.R:100:9') - cannot open file '/tmp/RtmptSgHLZ/folderac44746c0020wer wer2/quilt.10.11.40.vcf.gz': No such file or directory + + Failed + 1. Error ('test-acceptance-one.R:100:9'): QUILT can impute a few samples in a + Error in file(file, "rt"): cannot open the connection + Backtrace: + + 1. QUILT:::check_quilt_output(...) at test-acceptance-one.R:100:9 + 2. utils::read.table(file, header = FALSE, stringsAsFactors = FALSE) + 3. base::file(file, "rt") + + DONE +# Last 100 lines of the build log. +category: |- + dependency issue diff --git a/recipes/r-quilt/meta.yaml b/recipes/r-quilt/meta.yaml index 6e6ef9613842c..6031b3f1c1eea 100644 --- a/recipes/r-quilt/meta.yaml +++ b/recipes/r-quilt/meta.yaml @@ -11,7 +11,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('r-quilt', max_pin="x") }} diff --git a/recipes/r-r0/meta.yaml b/recipes/r-r0/meta.yaml index aa51a5a6ef75d..5e34dae8ef039 100644 --- a/recipes/r-r0/meta.yaml +++ b/recipes/r-r0/meta.yaml @@ -13,7 +13,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-r4cker/meta.yaml b/recipes/r-r4cker/meta.yaml index cc49fae7a7f4b..ac5a04816a47e 100644 --- a/recipes/r-r4cker/meta.yaml +++ b/recipes/r-r4cker/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 9f5f6276ce013ee0bb13420cf12f31ddc22af89bf6c0f315580807616c6ee362 build: - number: 5 + number: 6 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-rBLAST/meta.yaml b/recipes/r-rBLAST/meta.yaml index a2b3da2919be5..1922859025ad6 100644 --- a/recipes/r-rBLAST/meta.yaml +++ b/recipes/r-rBLAST/meta.yaml @@ -6,7 +6,7 @@ source: - https://github.com/mhahsler/rBLAST/archive/5cbc5039705e45c83d88c324c4f2a64dfc63e4e1.tar.gz md5: 5773ffb34b208af1d7999518c645728a build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-rapidr/meta.yaml b/recipes/r-rapidr/meta.yaml index 675137865c84f..0da2b5b3d0aa2 100644 --- a/recipes/r-rapidr/meta.yaml +++ b/recipes/r-rapidr/meta.yaml @@ -16,7 +16,7 @@ source: build: noarch: generic merge_build_host: True # [win] - number: 9 + number: 10 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-recetox-aplcms/build_failure.linux-64.yaml b/recipes/r-recetox-aplcms/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..4e9b63cba3fa2 --- /dev/null +++ b/recipes/r-recetox-aplcms/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 94f10ea4f72e03c6d45c7f8b83912658a1a2e1d32232c5689b1a208b2bffe479 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-mzr 2.36.0.* [0m is installable and it requires + [32mbioconductor-protgenerics >=1.34.0,<1.35.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-protgenerics[version='>=1.34.0,<1.35.0']"), MatchSpec("bioconductor-mzr==2.36.0=r43hf17093f_0")} + Encountered problems while solving: + - package bioconductor-mzr-2.36.0-r43hf17093f_0 requires bioconductor-protgenerics >=1.34.0,<1.35.0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-mzr 2.36.0.* [0m is installable and it requires + [32mbioconductor-protgenerics >=1.34.0,<1.35.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-protgenerics[version='>=1.34.0,<1.35.0']"), MatchSpec("bioconductor-mzr==2.36.0=r43hf17093f_0")} + Encountered problems while solving: + - package bioconductor-mzr-2.36.0-r43hf17093f_0 requires bioconductor-protgenerics >=1.34.0,<1.35.0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-mzr 2.36.0.* [0m is installable and it requires + [32mbioconductor-protgenerics >=1.34.0,<1.35.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. +category: |- + dependency issue diff --git a/recipes/r-recetox-aplcms/meta.yaml b/recipes/r-recetox-aplcms/meta.yaml index 81fdcd3fa1705..bbcc25e5a5fdb 100644 --- a/recipes/r-recetox-aplcms/meta.yaml +++ b/recipes/r-recetox-aplcms/meta.yaml @@ -11,7 +11,7 @@ source: sha256: c6c08d7e0def2b4df9f5ae366e0f69bf982d271bb8a4aec165e66c373d45c791 build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-recetox-waveica/meta.yaml b/recipes/r-recetox-waveica/meta.yaml index acb77fa0d4057..69b323c058505 100644 --- a/recipes/r-recetox-waveica/meta.yaml +++ b/recipes/r-recetox-waveica/meta.yaml @@ -11,7 +11,7 @@ source: sha256: dd6e7ea73e908aebfface2e7f991ce6adbeae6ab6027661561e2392ffe0e15f8 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/ diff --git a/recipes/r-redeemr/build_failure.osx-64.yaml b/recipes/r-redeemr/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c7eac4361c954 --- /dev/null +++ b/recipes/r-redeemr/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: f1932d4f20593d945d553ba1183eb80a9a7bb972197a21934b55a3944412e3bd # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Could not solve for environment specs + The following packages are incompatible + r-base 4.4.* is requested and can be installed; + r-scavenge is not installable because it requires + r-gchromvar, which requires + r-base >=4.3,<4.4.0a0 , which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("r-gchromvar"), MatchSpec("r-scavenge==1.0.2=r43hdfd78af_0")} + Encountered problems while solving: + - package r-scavenge-1.0.2-r43hdfd78af_0 requires r-gchromvar, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + r-base 4.4.* is requested and can be installed; + r-scavenge is not installable because it requires + r-gchromvar, which requires + r-base >=4.3,<4.4.0a0 , which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("r-gchromvar"), MatchSpec("r-scavenge==1.0.2=r43hdfd78af_0")} + Encountered problems while solving: + - package r-scavenge-1.0.2-r43hdfd78af_0 requires r-gchromvar, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + r-base 4.4.* is requested and can be installed; + r-scavenge is not installable because it requires + r-gchromvar, which requires + r-base >=4.3,<4.4.0a0 , which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-redeemr/meta.yaml b/recipes/r-redeemr/meta.yaml index d9ac70e68cddc..2aadf92030ab3 100644 --- a/recipes/r-redeemr/meta.yaml +++ b/recipes/r-redeemr/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 2837bee4a5a6130de08e31f543b11bfbd19eef30d351868b74c42681f45bb6e9 build: - number: 0 + number: 1 script: ${R} CMD INSTALL --build . ${R_ARGS} rpaths: - lib/R/lib/ diff --git a/recipes/r-restfulr/meta.yaml b/recipes/r-restfulr/meta.yaml index 8ff3b6baf8689..86ad51abd16ba 100644 --- a/recipes/r-restfulr/meta.yaml +++ b/recipes/r-restfulr/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 40ff8f1fb2987af2223e1a855bb1680c5ce2143fbce7ebc42f1edb291f80e692 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-riborex/meta.yaml b/recipes/r-riborex/meta.yaml index f14677c1406bd..7e5ed730d9d0a 100644 --- a/recipes/r-riborex/meta.yaml +++ b/recipes/r-riborex/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-rrbgen/meta.yaml b/recipes/r-rrbgen/meta.yaml index ca175e16d940b..d56ba217754d3 100644 --- a/recipes/r-rrbgen/meta.yaml +++ b/recipes/r-rrbgen/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 11 + number: 12 script: '$R CMD INSTALL --build --install-tests .' run_exports: - {{ pin_subpackage('r-rrbgen', max_pin="x.x") }} diff --git a/recipes/r-rspectral/meta.yaml b/recipes/r-rspectral/meta.yaml index 045d3adb71035..1c16316a2decb 100644 --- a/recipes/r-rspectral/meta.yaml +++ b/recipes/r-rspectral/meta.yaml @@ -14,10 +14,12 @@ source: build: merge_build_host: True # [win] - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage('r-rspectral', max_pin="x") }} requirements: build: diff --git a/recipes/r-rtassel/meta.yaml b/recipes/r-rtassel/meta.yaml index beb62ea0f7880..9e2ea35bfd8e0 100644 --- a/recipes/r-rtassel/meta.yaml +++ b/recipes/r-rtassel/meta.yaml @@ -13,7 +13,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-rubic/meta.yaml b/recipes/r-rubic/meta.yaml index 1da155221dfae..b81b828cb736b 100644 --- a/recipes/r-rubic/meta.yaml +++ b/recipes/r-rubic/meta.yaml @@ -6,7 +6,7 @@ source: sha256: 36dda0bd2f388e610f551a19b177be08e5a1c2cf68b23a3626dcbd5be1705837 build: noarch: generic - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-saige/meta.yaml b/recipes/r-saige/meta.yaml index ba8176474a80c..58f6f9df95923 100644 --- a/recipes/r-saige/meta.yaml +++ b/recipes/r-saige/meta.yaml @@ -13,7 +13,7 @@ source: - patches/0001-use-shared-libs-in-makevars.patch build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-samr/build_failure.linux-64.yaml b/recipes/r-samr/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..e4f274f9e01af --- /dev/null +++ b/recipes/r-samr/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 98d41c8c7e26405af049a5f7d0bce6c4207827732a0b62c88b419b95136de495 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-impute==1.56.0=r351h9ac9557_0"), MatchSpec("r-base[version='>=3.5.1,<3.5.2.0a0']")} + Encountered problems while solving: + - package bioconductor-impute-1.56.0-r351h9ac9557_0 requires r-base >=3.5.1,<3.5.2.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-impute >=1.56.0 [0m is installable with the potential options + [32mbioconductor-impute [1.56.0|1.58.0][0m would require + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-impute [1.58.0|1.60.0][0m would require + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-impute [1.62.0|1.64.0][0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-impute [1.66.0|1.68.0][0m would require + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-impute 1.72.0[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-impute [1.74.1|1.76.0][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-impute==1.56.0=r351h9ac9557_0"), MatchSpec("r-base[version='>=3.5.1,<3.5.2.0a0']")} + Encountered problems while solving: + - package bioconductor-impute-1.56.0-r351h9ac9557_0 requires r-base >=3.5.1,<3.5.2.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-impute >=1.56.0 [0m is installable with the potential options + [32mbioconductor-impute [1.56.0|1.58.0][0m would require + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-impute [1.58.0|1.60.0][0m would require + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-impute [1.62.0|1.64.0][0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-impute [1.66.0|1.68.0][0m would require + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-impute 1.72.0[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-impute [1.74.1|1.76.0][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-samr/build_failure.osx-64.yaml b/recipes/r-samr/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..cea27afafd927 --- /dev/null +++ b/recipes/r-samr/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 98d41c8c7e26405af049a5f7d0bce6c4207827732a0b62c88b419b95136de495 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + libgfortran5 >=13.2.0 but there are no viable options + libgfortran5 13.2.0 would require + libgfortran 5.0.0 13_2_0_*_1, which conflicts with any installable versions previously reported; + libgfortran5 13.2.0 would require + libgfortran 5.0.0 13_2_0_*_2, which conflicts with any installable versions previously reported; + libgfortran5 13.2.0 would require + libgfortran 5.0.0 13_2_0_*_3, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("4.0.1==hcfea43d_1"), MatchSpec("clang==4.0.1=1")} + Encountered problems while solving: + - nothing provides compiler-rt 4.0.1 hcfea43d_1 needed by clang-4.0.1-1 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-impute >=1.56.0 is installable with the potential options + bioconductor-impute 1.56.0 would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + r-base 3.5.1 would require + libgfortran >=3.0.1,<4.0.0.a0 , which can be installed; + bioconductor-impute [1.58.0|1.60.0] would require + libgfortran >=3.0.1,<4.0.0.a0 , which can be installed; + bioconductor-impute [1.58.0|1.60.0] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-impute [1.62.0|1.64.0] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-impute [1.66.0|1.68.0] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-impute 1.72.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-impute [1.74.1|1.76.0] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it requires + libgfortran5 >=13.2.0 but there are no viable options + libgfortran5 13.2.0 would require + libgfortran 5.0.0 13_2_0_*_1, which conflicts with any installable versions previously reported; + libgfortran5 13.2.0 would require + libgfortran 5.0.0 13_2_0_*_2, which conflicts with any installable versions previously reported; + libgfortran5 13.2.0 would require + libgfortran 5.0.0 13_2_0_*_3, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-samr/meta.yaml b/recipes/r-samr/meta.yaml index b8ea361b5813c..067254a8fb365 100644 --- a/recipes/r-samr/meta.yaml +++ b/recipes/r-samr/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 25f88ac002c2adce8881a562241bc12d683810a05defb553e8e3d4878f037506 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-sartools/meta.yaml b/recipes/r-sartools/meta.yaml index 66fbcd9629aaf..edb5034d4b503 100644 --- a/recipes/r-sartools/meta.yaml +++ b/recipes/r-sartools/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 8cc5b1f4e87a257e5581155f0032d00b7f749d58907654f624fcb1942e63c08a build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-sbpiper/meta.yaml b/recipes/r-sbpiper/meta.yaml index e7f17348aeb0d..8e23315fcdc49 100644 --- a/recipes/r-sbpiper/meta.yaml +++ b/recipes/r-sbpiper/meta.yaml @@ -17,7 +17,7 @@ build: noarch: generic merge_build_host: True # [win] - number: 8 + number: 9 rpaths: - lib/R/lib/ diff --git a/recipes/r-scavenge/meta.yaml b/recipes/r-scavenge/meta.yaml index ae09624aa011a..fc37413e021a4 100644 --- a/recipes/r-scavenge/meta.yaml +++ b/recipes/r-scavenge/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-scbio/meta.yaml b/recipes/r-scbio/meta.yaml index 8b578cd7098b8..1ab5e207d91df 100644 --- a/recipes/r-scbio/meta.yaml +++ b/recipes/r-scbio/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 4f84809c45ef1bcbe991feadf08e6eccd53cbeae35f83d9f556d423aef0f9168 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-scdc/meta.yaml b/recipes/r-scdc/meta.yaml index 0900193d29762..89e162ac7c531 100644 --- a/recipes/r-scdc/meta.yaml +++ b/recipes/r-scdc/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 1362d6303b0ab8aabce25a907b9053a74d00c3508371ba497ac12880a770dc43 build: - number: 9 + number: 10 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-sceasy/meta.yaml b/recipes/r-sceasy/meta.yaml index 6b9b4e5e22767..b3af57e66cf31 100644 --- a/recipes/r-sceasy/meta.yaml +++ b/recipes/r-sceasy/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 noarch: generic source: diff --git a/recipes/r-scimpute/meta.yaml b/recipes/r-scimpute/meta.yaml index 1f566aa102783..71a033ddb138c 100644 --- a/recipes/r-scimpute/meta.yaml +++ b/recipes/r-scimpute/meta.yaml @@ -7,7 +7,7 @@ source: sha256: ed5867415d88e0009ee51249dbab46bdc863a52cc0443baf5706c463f7f9f76d build: - number: 5 + number: 6 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-scopfunctions/build_failure.osx-64.yaml b/recipes/r-scopfunctions/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..e72ac017c942b --- /dev/null +++ b/recipes/r-scopfunctions/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a34b62844e744f9f2f9ffc58425841e38bfd6817d73f0fa5f825f7725354b312 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("bioconductor-mast==1.4.1=r3.4.1_0"), MatchSpec("r-base=3.4.1")} + Encountered problems while solving: + - package bioconductor-mast-1.4.1-r3.4.1_0 requires r-base 3.4.1*, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + bioconductor-mast is installable with the potential options + bioconductor-mast 1.4.1 would require + r-base 3.4.1* , which can be installed; + bioconductor-mast [1.6.1|1.8.1] would require + bioconductor-singlecellexperiment >=1.2.0,<1.4.0 , which requires + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-summarizedexperiment >=1.12.0,<1.13.0 , which requires + bioconductor-genomicranges >=1.34.0,<1.35.0 , which requires + bioconductor-xvector >=0.22.0,<0.23.0 , which requires + bioconductor-zlibbioc >=1.28.0,<1.29.0 , which requires + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed; + bioconductor-mast [1.10.0|1.12.0] would require + bioconductor-summarizedexperiment [>=1.14.0,<1.15.0 |>=1.16.0,<1.17.0 ], which requires + bioconductor-genomicranges [>=1.36.0,<1.37.0 |>=1.38.0,<1.39.0 ], which requires + bioconductor-xvector [>=0.24.0,<0.25.0 |>=0.26.0,<0.27.0 ], which requires + bioconductor-zlibbioc >=1.32.0,<1.33.0 , which requires + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-mast [1.14.0|1.16.0] would require + bioconductor-summarizedexperiment >=1.18.0,<1.19.0 , which requires + bioconductor-genomicranges >=1.40.0,<1.41.0 , which requires + bioconductor-xvector >=0.28.0,<0.29.0 , which requires + bioconductor-zlibbioc >=1.34.0,<1.35.0 , which requires + r-base >=4.0,<4.1.0a0 , which can be installed; + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-mast [1.18.0|1.20.0] would require + bioconductor-summarizedexperiment [>=1.22.0,<1.23.0 |>=1.24.0,<1.25.0 ], which requires + bioconductor-genomicranges >=1.44.0,<1.45.0 , which requires + bioconductor-xvector >=0.32.0,<0.33.0 , which requires + bioconductor-zlibbioc >=1.38.0,<1.39.0 , which requires + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-matrixgenerics >=1.6.0,<1.7.0 , which requires + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-mast 1.24.0 would require + bioconductor-summarizedexperiment >=1.28.0,<1.29.0 , which requires + bioconductor-matrixgenerics >=1.10.0,<1.11.0 , which requires + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-mast [1.26.0|1.28.0] would require + bioconductor-summarizedexperiment [>=1.30.0,<1.31.0 |>=1.32.0,<1.33.0 ], which requires + bioconductor-genomicranges >=1.52.0,<1.53.0 , which requires + bioconductor-xvector >=0.40.0,<0.41.0 , which requires + bioconductor-zlibbioc >=1.46.0,<1.47.0 , which requires + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-scopfunctions/meta.yaml b/recipes/r-scopfunctions/meta.yaml index 34c40cbac9157..33f3d0d83533a 100644 --- a/recipes/r-scopfunctions/meta.yaml +++ b/recipes/r-scopfunctions/meta.yaml @@ -9,7 +9,7 @@ source: sha256: de3f537ddcf9474a3830f101acc28cf6d1f8b33a331f5aff11df8f94c00d713e build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-seamless/meta.yaml b/recipes/r-seamless/meta.yaml index bc06815b02ea7..fa8b930c0f2bc 100644 --- a/recipes/r-seamless/meta.yaml +++ b/recipes/r-seamless/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 8bba2ae29cd9b92fad6e5a1b12aed589ee10b49ef81189524236b07d994ea07b build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-seqmagick/meta.yaml b/recipes/r-seqmagick/meta.yaml index 72e09c9aa4e16..09c3c089905ee 100644 --- a/recipes/r-seqmagick/meta.yaml +++ b/recipes/r-seqmagick/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 95cf80c9c0a266e07cf7b124de105818c58f8f843f70ab25e0877a910211b8e5 build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-seurat-data/meta.yaml b/recipes/r-seurat-data/meta.yaml index da945540fea2a..433409abfc1ef 100644 --- a/recipes/r-seurat-data/meta.yaml +++ b/recipes/r-seurat-data/meta.yaml @@ -9,7 +9,7 @@ build: script: $R CMD INSTALL --build . run_exports: - {{ pin_subpackage("r-seurat-data", max_pin="x.x.x") }} - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-seurat-disk/meta.yaml b/recipes/r-seurat-disk/meta.yaml index 6cda8484ac46d..51db2e4c188d4 100644 --- a/recipes/r-seurat-disk/meta.yaml +++ b/recipes/r-seurat-disk/meta.yaml @@ -9,7 +9,7 @@ build: script: $R CMD INSTALL --build . run_exports: - {{ pin_subpackage("r-seurat-disk", max_pin="x.x.x.x") }} - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-sew/meta.yaml b/recipes/r-sew/meta.yaml index 280796f448f41..0e60a8bb10180 100644 --- a/recipes/r-sew/meta.yaml +++ b/recipes/r-sew/meta.yaml @@ -10,8 +10,10 @@ source: sha256: '{{ sha256 }}' build: - number: 4 + number: 5 script: '$R CMD INSTALL --build --install-tests .' + run_exports: + - {{ pin_subpackage('r-sew', max_pin="x") }} requirements: build: @@ -53,3 +55,7 @@ about: extra: recipe-maintainers: - rwdavies + container: + # SEW can phase a sample at high coverage with long reads ('test-acceptance-sew.R:37:5') - + # Your system is mis-configured /var/db/timezone/localtime’ is not a symlink + extended-base: true diff --git a/recipes/r-sgtr/meta.yaml b/recipes/r-sgtr/meta.yaml index bb816bd750b95..e87029a5cadfa 100644 --- a/recipes/r-sgtr/meta.yaml +++ b/recipes/r-sgtr/meta.yaml @@ -9,7 +9,7 @@ source: sha256: b2305b0275b3078fefe7fdefb983e364187fca235c4bdeb939c2ab2558b75369 build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-shaman/meta.yaml b/recipes/r-shaman/meta.yaml index f082aebe29f2f..f969f98f7b81b 100644 --- a/recipes/r-shaman/meta.yaml +++ b/recipes/r-shaman/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-shinyngs/meta.yaml b/recipes/r-shinyngs/meta.yaml index abf9a23891e2b..de2c97c1f1a65 100644 --- a/recipes/r-shinyngs/meta.yaml +++ b/recipes/r-shinyngs/meta.yaml @@ -14,7 +14,7 @@ source: folder: d3heatmap build: - number: 0 + number: 1 noarch: generic # This is required to make R link correctly on Linux. diff --git a/recipes/r-sigminer/build_failure.linux-64.yaml b/recipes/r-sigminer/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..b5df55715255a --- /dev/null +++ b/recipes/r-sigminer/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 4fee67c82bb519560e137909f381bc47ffed8ede0b50ce3d72c864ab9e838a01 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [32mbioconductor-zlibbioc >=1.28.0,<1.29.0 [0m, which requires + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-maftools [2.10.0|2.10.05|2.8.0][0m would require + [32mbioconductor-zlibbioc >=1.38.0,<1.39.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-maftools 2.14.0[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-maftools [2.16.0|2.18.0][0m would require + [32mbioconductor-zlibbioc >=1.46.0,<1.47.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mbioconductor-maftools [2.0.10|2.2.0][0m would require + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-maftools [2.4.0|2.6.0|2.6.05][0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-base=3.4.1"), MatchSpec("bioconductor-maftools==1.4.27=r3.4.1_0")} + Encountered problems while solving: + - package bioconductor-maftools-1.4.27-r3.4.1_0 requires r-base 3.4.1*, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-maftools[0m is installable with the potential options + [32mbioconductor-maftools [1.4.27|1.6.15][0m would require + [32mr-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ][0m, which can be installed; + [32mbioconductor-maftools [1.6.15|1.8.0|2.0.0][0m would require + [32mbioconductor-bsgenome >=1.50.0,<1.51.0 [0m, which requires + [32mbioconductor-xvector >=0.22.0,<0.23.0 [0m, which requires + [32mbioconductor-zlibbioc >=1.28.0,<1.29.0 [0m, which requires + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-maftools [2.10.0|2.10.05|2.8.0][0m would require + [32mbioconductor-zlibbioc >=1.38.0,<1.39.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-maftools 2.14.0[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-maftools [2.16.0|2.18.0][0m would require + [32mbioconductor-zlibbioc >=1.46.0,<1.47.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mbioconductor-maftools [2.0.10|2.2.0][0m would require + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-maftools [2.4.0|2.6.0|2.6.05][0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-sigminer/build_failure.linux-aarch64.yaml b/recipes/r-sigminer/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..d47f59e8507dc --- /dev/null +++ b/recipes/r-sigminer/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 4fee67c82bb519560e137909f381bc47ffed8ede0b50ce3d72c864ab9e838a01 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec("bioconductor-maftools==1.8.0=r351_0"), MatchSpec(">=2.50.0,<2.51.0")} + Encountered problems while solving: + - nothing provides bioconductor-biostrings >=2.50.0,<2.51.0 needed by bioconductor-maftools-1.8.0-r351_0 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-maftools[0m is installable with the potential options + [32mbioconductor-maftools 2.2.0[0m would require + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-maftools 2.18.0[0m would require + [32mbioconductor-zlibbioc >=1.48.0,<1.49.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mbioconductor-maftools 1.8.0[0m would require + [31mbioconductor-biostrings >=2.50.0,<2.51.0 [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-maftools 2.0.0[0m would require + [31mr-base >=3.5.1,<3.5.2.0a0 [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-maftools 2.0.10[0m would require + [31mr-cometexacttest[0m, which does not exist (perhaps a missing channel); + [32mbioconductor-maftools [2.4.0|2.6.0|2.6.05][0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-aarch64: {MatchSpec("bioconductor-maftools==1.8.0=r351_0"), MatchSpec(">=2.50.0,<2.51.0")} + Encountered problems while solving: + - nothing provides bioconductor-biostrings >=2.50.0,<2.51.0 needed by bioconductor-maftools-1.8.0-r351_0 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-maftools[0m is installable with the potential options + [32mbioconductor-maftools 2.2.0[0m would require + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-maftools 2.18.0[0m would require + [32mbioconductor-zlibbioc >=1.48.0,<1.49.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mbioconductor-maftools 1.8.0[0m would require + [31mbioconductor-biostrings >=2.50.0,<2.51.0 [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-maftools 2.0.0[0m would require + [31mr-base >=3.5.1,<3.5.2.0a0 [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-maftools 2.0.10[0m would require + [31mr-cometexacttest[0m, which does not exist (perhaps a missing channel); + [32mbioconductor-maftools [2.4.0|2.6.0|2.6.05][0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-sigminer/build_failure.osx-64.yaml b/recipes/r-sigminer/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..d7483f6b958b6 --- /dev/null +++ b/recipes/r-sigminer/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 4fee67c82bb519560e137909f381bc47ffed8ede0b50ce3d72c864ab9e838a01 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-maftools [2.4.0|2.6.0|2.6.05] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("r-base=3.4.1"), MatchSpec("bioconductor-maftools==1.4.27=r3.4.1_0")} + Encountered problems while solving: + - package bioconductor-maftools-1.4.27-r3.4.1_0 requires r-base 3.4.1*, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + bioconductor-maftools is installable with the potential options + bioconductor-maftools [1.4.27|1.6.15] would require + r-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ], which can be installed; + bioconductor-maftools [1.6.15|1.8.0|2.0.0] would require + bioconductor-bsgenome >=1.50.0,<1.51.0 , which requires + bioconductor-xvector >=0.22.0,<0.23.0 , which requires + bioconductor-zlibbioc >=1.28.0,<1.29.0 , which requires + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed; + bioconductor-maftools [2.10.0|2.10.05|2.8.0] would require + bioconductor-zlibbioc >=1.38.0,<1.39.0 , which requires + r-base >=4.1,<4.2.0a0 , which can be installed; + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-maftools 2.14.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-maftools [2.16.0|2.18.0] would require + bioconductor-zlibbioc >=1.46.0,<1.47.0 , which requires + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-maftools [2.0.10|2.2.0] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-maftools [2.4.0|2.6.0|2.6.05] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-sigminer/meta.yaml b/recipes/r-sigminer/meta.yaml index b892cc923d1bd..9a1b0eae319ea 100644 --- a/recipes/r-sigminer/meta.yaml +++ b/recipes/r-sigminer/meta.yaml @@ -11,7 +11,7 @@ source: sha256: b2836c76a52f7c7add8756afb09dc50ab31d736b4640b803bee57b6caec1953b build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-signac/meta.yaml b/recipes/r-signac/meta.yaml index 6bc0eb3d6e0cb..b724afa715ee5 100644 --- a/recipes/r-signac/meta.yaml +++ b/recipes/r-signac/meta.yaml @@ -12,7 +12,7 @@ source: sha256: e0aad9e2c27c148fdd376081c2de1e3db46b1835eac83ef41fe562e08363c59e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -51,6 +51,7 @@ requirements: - r-tidyr - r-tidyselect - r-vctrs + - zlib run: - r-base - bioconductor-biocgenerics diff --git a/recipes/r-sigqc/meta.yaml b/recipes/r-sigqc/meta.yaml index 1b32c8487d739..2930e74562513 100644 --- a/recipes/r-sigqc/meta.yaml +++ b/recipes/r-sigqc/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-sigtree/build_failure.linux-64.yaml b/recipes/r-sigtree/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..88fec34471c3a --- /dev/null +++ b/recipes/r-sigtree/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 7a8b563a5dc8e7b449d2674e3cac98e24cdad123be8770b348ea16542963ee46 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-phyloseq==1.16.2=r3.3.1_1"), MatchSpec("3.3.1*")} + Encountered problems while solving: + - nothing provides r 3.3.1* needed by bioconductor-phyloseq-1.16.2-r3.3.1_1 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-phyloseq[0m is installable with the potential options + [32mbioconductor-phyloseq 1.14.0[0m would require + [32mr-biom >=0.3.9 [0m with the potential options + [31mr-biom 0.3.12[0m would require + [31mr 3.2.2* [0m, which does not exist (perhaps a missing channel); + [31mr-biom 0.3.12[0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [32mr-biom 0.3.12[0m would require + [32mr-base 3.3.2* [0m, which can be installed; + [32mr-biom 0.3.12[0m would require + [32mr-base 3.4.1* [0m, which can be installed; + [32mbioconductor-phyloseq 1.16.2[0m would require + [32mbioconductor-biomformat >=1.0.2 [0m with the potential options + [32mbioconductor-biomformat 1.0.2[0m would require + [32mbioconductor-rhdf5 >=2.16.0 [0m with the potential options + [31mbioconductor-rhdf5 2.16.0[0m would require + [31mr 3.2.2* [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-rhdf5 2.16.0[0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [32mbioconductor-rhdf5 2.16.0[0m would require + [32mr-base 3.3.2* [0m, which can be installed; + [32mbioconductor-rhdf5 [2.16.0|2.20.0|2.22.0|2.24.0][0m would require + [32mr-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ][0m, which can be installed; + [32mbioconductor-rhdf5 [2.24.0|2.26.0|2.26.1|2.26.2|2.28.0][0m would require + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.28.0|2.30.0][0m would require + [32mbioconductor-rhdf5lib >=1.8.0,<1.9.0 [0m, which requires + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.32.0|2.34.0][0m would require + [32mbioconductor-rhdf5lib >=1.10.0,<1.11.0 [0m, which requires + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.36.0|2.38.0|2.38.1][0m would require + [32mbioconductor-rhdf5lib >=1.14.0,<1.15.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 2.42.0[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-rhdf5 [2.44.0|2.46.1][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mbioconductor-biomformat [1.0.2|1.2.0][0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [32mbioconductor-biomformat 1.2.0[0m would require + [32mr-base 3.3.2* [0m, which can be installed; + [32mbioconductor-biomformat [1.2.0|1.4.0|1.6.0|1.8.0][0m would require + [32mr-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ][0m, which can be installed; + [32mbioconductor-biomformat [1.10.0|1.10.1|1.12.0|1.8.0][0m would require + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-biomformat [1.12.0|1.14.0][0m would require + [32mbioconductor-rhdf5 >=2.30.0,<2.31.0 [0m, which can be installed (as previously explained); + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-biomformat [1.16.0|1.18.0][0m would require + [32mbioconductor-rhdf5 >=2.32.0,<2.33.0 [0m, which can be installed (as previously explained); + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-biomformat [1.20.0|1.22.0][0m would require + [32mbioconductor-rhdf5 >=2.36.0,<2.37.0 [0m, which can be installed (as previously explained); + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-biomformat 1.26.0[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-biomformat [1.28.0|1.30.0][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mbioconductor-phyloseq [1.16.2|1.19.1][0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [32mbioconductor-phyloseq [1.19.1|1.20.0][0m would require + [32mr-base [3.3.2* |>=3.3,<3.4 ][0m, which can be installed; + [32mbioconductor-phyloseq [1.19.1|1.20.0|1.22.3|1.24.2][0m would require + [32mr-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ][0m, which can be installed; + [32mbioconductor-phyloseq [1.24.2|1.26.0|1.26.1][0m would require + [32mbioconductor-multtest >=2.38.0,<2.39.0 [0m, which requires + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-phyloseq [1.28.0|1.30.0][0m would require + [32mbioconductor-biomformat >=1.14.0,<1.15.0 [0m, which can be installed (as previously explained); + [32mbioconductor-biostrings >=2.52.0,<2.53.0 [0m, which requires + [32mbioconductor-xvector >=0.24.0,<0.25.0 [0m, which requires + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-phyloseq [1.32.0|1.34.0][0m would require + [32mbioconductor-biomformat >=1.16.0,<1.17.0 [0m, which can be installed (as previously explained); + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-phyloseq [1.36.0|1.38.0][0m would require + [32mbioconductor-biomformat [>=1.20.0,<1.21.0 |>=1.22.0,<1.23.0 ][0m, which can be installed (as previously explained); + [32mbioconductor-phyloseq 1.42.0[0m would require + [32mbioconductor-biomformat >=1.26.0,<1.27.0 [0m, which can be installed (as previously explained); + [32mbioconductor-phyloseq [1.44.0|1.46.0][0m would require + [32mbioconductor-biomformat >=1.30.0,<1.31.0 [0m, which can be installed (as previously explained); + [32mbioconductor-biostrings >=2.68.0,<2.69.0 [0m, which requires + [32mbioconductor-xvector >=0.40.0,<0.41.0 [0m, which requires + [32mbioconductor-zlibbioc >=1.46.0,<1.47.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-sigtree/build_failure.osx-64.yaml b/recipes/r-sigtree/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..6316d7d79ca8c --- /dev/null +++ b/recipes/r-sigtree/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 7a8b563a5dc8e7b449d2674e3cac98e24cdad123be8770b348ea16542963ee46 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1 conflicts with any installable versions previously reported; + r-phyext2 0.0.4 would require + r-base >=3.6,<3.7.0a0 but there are no viable options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3] conflicts with any installable versions previously reported; + r-phyext2 0.0.4 would require + r-base >=4.0,<4.1.0a0 , which conflicts with any installable versions previously reported; + r-phyext2 0.0.4 would require + r-base >=4.1,<4.2.0a0 , which conflicts with any installable versions previously reported; + r-phyext2 0.0.4 would require + r-base >=4.2,<4.3.0a0 , which conflicts with any installable versions previously reported; + r-phyext2 0.0.4 would require + r-base >=4.3,<4.4.0a0 , which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("clang==4.0.1=1"), MatchSpec("4.0.1==hcfea43d_1")} + Encountered problems while solving: + - nothing provides compiler-rt 4.0.1 hcfea43d_1 needed by clang-4.0.1-1 + + Could not solve for environment specs + The following packages are incompatible + r-base 4.4.* is requested and can be installed; + r-phyext2 is not installable because there are no viable options + r-phyext2 0.0.4 would require + r-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ], which conflicts with any installable versions previously reported; + r-phyext2 0.0.4 would require + r-base >=3.5.1,<3.5.2.0a0 but there are no viable options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1 conflicts with any installable versions previously reported; + r-phyext2 0.0.4 would require + r-base >=3.6,<3.7.0a0 but there are no viable options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3] conflicts with any installable versions previously reported; + r-phyext2 0.0.4 would require + r-base >=4.0,<4.1.0a0 , which conflicts with any installable versions previously reported; + r-phyext2 0.0.4 would require + r-base >=4.1,<4.2.0a0 , which conflicts with any installable versions previously reported; + r-phyext2 0.0.4 would require + r-base >=4.2,<4.3.0a0 , which conflicts with any installable versions previously reported; + r-phyext2 0.0.4 would require + r-base >=4.3,<4.4.0a0 , which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-sigtree/meta.yaml b/recipes/r-sigtree/meta.yaml index fbd598d711726..cc6f4886e77f3 100644 --- a/recipes/r-sigtree/meta.yaml +++ b/recipes/r-sigtree/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 3ce57e37d1c328720bb3ffc8c1f349c62b22e4d4de132f988ce9a42cbf3af0a1 build: - number: 12 + number: 13 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-singlecellnet/meta.yaml b/recipes/r-singlecellnet/meta.yaml index c1d979092eb50..4808aa23ebbc0 100644 --- a/recipes/r-singlecellnet/meta.yaml +++ b/recipes/r-singlecellnet/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 154b588e0785d0e9e53dc889e03dc99b8c9381d2d6b5f0f0a9adbc47eb8abde2 build: - number: 5 + number: 6 script: R CMD INSTALL --build . noarch: generic rpaths: diff --git a/recipes/r-smartsva/meta.yaml b/recipes/r-smartsva/meta.yaml index 0fed85b49ca9e..dd2736e3d2323 100644 --- a/recipes/r-smartsva/meta.yaml +++ b/recipes/r-smartsva/meta.yaml @@ -11,7 +11,7 @@ source: sha256: d7925743d04bd52dee575a477cc7e8395fedb08f5dbb8427e61e3d6dbfd04881 build: - number: 8 + number: 9 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-soap-nmr/meta.yaml b/recipes/r-soap-nmr/meta.yaml index 777b900859c8f..47226b8e177bf 100644 --- a/recipes/r-soap-nmr/meta.yaml +++ b/recipes/r-soap-nmr/meta.yaml @@ -7,7 +7,7 @@ source: md5: 79c22ee665352c0bd2fa2f429db48d30 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-speaq/meta.yaml b/recipes/r-speaq/meta.yaml index d53df5fc54511..4de140c70140b 100644 --- a/recipes/r-speaq/meta.yaml +++ b/recipes/r-speaq/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 93d665e3310507bd78d14346461eb9f260b945420f1a0612b8f07ee5961d2a7d build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-spieceasi/meta.yaml b/recipes/r-spieceasi/meta.yaml index 18d92982c257d..d806b1ca5143c 100644 --- a/recipes/r-spieceasi/meta.yaml +++ b/recipes/r-spieceasi/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 0f79f5c86a2d28a469116c2f19c29746a7a3495776dcff4d83754137b6158e63 build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-spp/meta.yaml b/recipes/r-spp/meta.yaml index f75be8dc297b9..6695fa806bd3f 100644 --- a/recipes/r-spp/meta.yaml +++ b/recipes/r-spp/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 3c890f3c414183167f9643b556621dcdc14ce6a1b54a04d618c74070fdebfd23 build: - number: 10 + number: 11 run_exports: - {{ pin_subpackage("r-spp", max_pin="x") }} rpaths: @@ -31,6 +31,7 @@ requirements: - r-rcpp - bioconductor-rsamtools - r-catools + - zlib run: - r-base - r-bh >=1.66 diff --git a/recipes/r-spring/meta.yaml b/recipes/r-spring/meta.yaml index b0ea1e39077e8..b192e8994dfdb 100644 --- a/recipes/r-spring/meta.yaml +++ b/recipes/r-spring/meta.yaml @@ -10,7 +10,7 @@ source: sha256: b89d44bf54bb154027ecff9985cfbd27099e25e34c31261946cdca7348d1b047 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-statvisual/meta.yaml b/recipes/r-statvisual/meta.yaml index 8f59c39068425..a91665673cf20 100755 --- a/recipes/r-statvisual/meta.yaml +++ b/recipes/r-statvisual/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 412cb792a1d55169bf7d83904a0e4d682e0cfd39298f74e0a3c07e8a5eba89b1 build: - number: 5 + number: 6 noarch: generic # This is required to make R link correctly on Linux. diff --git a/recipes/r-stitch/meta.yaml b/recipes/r-stitch/meta.yaml index 367acfc76661f..3d71c4a7b9565 100644 --- a/recipes/r-stitch/meta.yaml +++ b/recipes/r-stitch/meta.yaml @@ -11,7 +11,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('r-stitch', max_pin="x") }} diff --git a/recipes/r-structssi/meta.yaml b/recipes/r-structssi/meta.yaml index 0a8f12c6a83ca..5fa48522f3163 100644 --- a/recipes/r-structssi/meta.yaml +++ b/recipes/r-structssi/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-swamp/meta.yaml b/recipes/r-swamp/meta.yaml index 668f761f57668..2f8b2d10d1e92 100644 --- a/recipes/r-swamp/meta.yaml +++ b/recipes/r-swamp/meta.yaml @@ -12,7 +12,7 @@ source: build: noarch: generic - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-syntactic/meta.yaml b/recipes/r-syntactic/meta.yaml index 26f0dde275c31..1c05f545d2b72 100644 --- a/recipes/r-syntactic/meta.yaml +++ b/recipes/r-syntactic/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 0 + number: 1 run_exports: - {{ pin_subpackage('r-syntactic', max_pin="x.x") }} diff --git a/recipes/r-tailfindr/build_failure.osx-64.yaml b/recipes/r-tailfindr/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c68bef7778d5e --- /dev/null +++ b/recipes/r-tailfindr/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 23471799c4b94773a6da3566499dc7ae5c2866460987ce612f9dacf5bc03e54b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("3.2.2*"), MatchSpec("bioconductor-rsamtools==1.22.0=r3.2.2_1")} + Encountered problems while solving: + - nothing provides r 3.2.2* needed by bioconductor-rsamtools-1.22.0-r3.2.2_1 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-rsamtools is installable with the potential options + bioconductor-rsamtools 1.26.1 would require + r-base 3.3.2* , which can be installed; + bioconductor-rsamtools 1.22.0 would require + r 3.2.2* , which does not exist (perhaps a missing channel); + bioconductor-rsamtools [1.24.0|1.26.1] would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-rsamtools [1.26.1|1.28.0|1.30.0] would require + r-base 3.4.1* , which can be installed; + bioconductor-rsamtools 1.32.3 would require + bioconductor-biostrings >=2.48.0,<2.50.0 with the potential options + bioconductor-biostrings 2.48.0 would require + r-base >=3.4.1,<3.4.2.0a0 , which can be installed; + bioconductor-biostrings 2.48.0 would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-rsamtools [1.32.3|1.34.0] would require + bioconductor-genomeinfodb >=1.18.0,<1.19.0 , which requires + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed; + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed; + bioconductor-rsamtools [2.0.0|2.2.0] would require + bioconductor-genomeinfodb [>=1.20.0,<1.21.0 |>=1.22.0,<1.23.0 ], which requires + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-rsamtools [2.10.0|2.8.0] would require + bioconductor-rhtslib >=1.24.0,<1.25.0 , which requires + r-base >=4.1,<4.2.0a0 , which can be installed; + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-rsamtools 2.14.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-rsamtools [2.16.0|2.18.0] would require + bioconductor-rhtslib >=2.2.0,<2.3.0 , which requires + r-base >=4.3,<4.4.0a0 , which can be installed; + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-rsamtools [2.4.0|2.6.0] would require + bioconductor-genomeinfodb >=1.24.0,<1.25.0 , which requires + r-base >=4.0,<4.1.0a0 , which can be installed; + r-base >=4.0,<4.1.0a0 , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-tailfindr/meta.yaml b/recipes/r-tailfindr/meta.yaml index 57dbc3da98763..7d366a36699d8 100644 --- a/recipes/r-tailfindr/meta.yaml +++ b/recipes/r-tailfindr/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 001e9a4f7f1126c3c6e8759c0525b5ca778f3561a1aeae9047938eff76b036c6 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-tcga2stat/meta.yaml b/recipes/r-tcga2stat/meta.yaml index e29188db6b349..5a410f232151e 100644 --- a/recipes/r-tcga2stat/meta.yaml +++ b/recipes/r-tcga2stat/meta.yaml @@ -16,7 +16,7 @@ source: build: noarch: generic merge_build_host: True # [win] - number: 10 + number: 11 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-tcr/meta.yaml b/recipes/r-tcr/meta.yaml index 32c83083fc5c0..c489f4fe99805 100644 --- a/recipes/r-tcr/meta.yaml +++ b/recipes/r-tcr/meta.yaml @@ -13,7 +13,7 @@ source: sha256: 289c4fe8781ee15f9e9dc20c0bf4daea6959361a54d51b2e1236728957355f67 build: - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-tftargets/meta.yaml b/recipes/r-tftargets/meta.yaml index e624638742181..a51cef76d4494 100644 --- a/recipes/r-tftargets/meta.yaml +++ b/recipes/r-tftargets/meta.yaml @@ -11,7 +11,7 @@ source: sha256: e27ed65c283779b4dcda6e0704a37112a81bfedb198b3d7d036c1a80083670ca build: - number: 5 + number: 6 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-tidygenomics/build_failure.osx-64.yaml b/recipes/r-tidygenomics/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..b88e0d2313779 --- /dev/null +++ b/recipes/r-tidygenomics/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 4c94aa73a28490c3e240fb97a1c6895b0377216e48776e3cb104719ab2c0c217 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("4.0.1==hcfea43d_1"), MatchSpec("clang==4.0.1=1")} + Encountered problems while solving: + - nothing provides compiler-rt 4.0.1 hcfea43d_1 needed by clang-4.0.1-1 + + Could not solve for environment specs + The following packages are incompatible + bioconductor-iranges is installable with the potential options + bioconductor-iranges [2.4.6|2.4.7|2.4.8] would require + bioconductor-biocgenerics >=0.15.10 with the potential options + bioconductor-biocgenerics [0.16.1|0.18.0] would require + r 3.2.2* , which does not exist (perhaps a missing channel); + bioconductor-biocgenerics [0.16.1|0.18.0|0.20.0] would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-biocgenerics [0.20.0|0.22.0] would require + r-base 3.3.2* , which can be installed; + bioconductor-biocgenerics [0.22.0|0.22.1|0.24.0|0.26.0] would require + r-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ], which can be installed; + bioconductor-biocgenerics [0.24.0|0.26.0|0.28.0] would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base 3.5.1, which can be installed; + bioconductor-biocgenerics [0.30.0|0.32.0] would require + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.6.1|3.6.2|3.6.3], which can be installed; + bioconductor-biocgenerics [0.34.0|0.36.0] would require + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-biocgenerics [0.38.0|0.40.0] would require + r-base >=4.1,<4.2.0a0 , which can be installed; + bioconductor-biocgenerics 0.44.0 would require + r-base >=4.2,<4.3.0a0 , which can be installed; + bioconductor-biocgenerics [0.46.0|0.48.1] would require + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-iranges [2.10.5|2.12.0|2.14.12|2.8.2] would require + r-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ], which can be installed; + bioconductor-iranges [2.14.12|2.16.0] would require + bioconductor-s4vectors >=0.20.0,<0.21.0 , which requires + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed; + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base 3.5.1, which can be installed; + bioconductor-iranges [2.18.1|2.18.2|2.20.0] would require + bioconductor-biocgenerics [>=0.30.0,<0.31.0 |>=0.32.0,<0.33.0 ], which can be installed (as previously explained); + bioconductor-iranges [2.22.1|2.24.0|2.24.1] would require + bioconductor-biocgenerics >=0.34.0,<0.35.0 , which can be installed (as previously explained); + r-base >=4.0,<4.1.0a0 , which can be installed; + bioconductor-iranges [2.26.0|2.28.0] would require + bioconductor-biocgenerics [>=0.38.0,<0.39.0 |>=0.40.0,<0.41.0 ], which can be installed (as previously explained); + bioconductor-iranges 2.32.0 would require + bioconductor-biocgenerics >=0.44.0,<0.45.0 , which can be installed (as previously explained); + bioconductor-iranges [2.34.1|2.36.0] would require + bioconductor-biocgenerics >=0.46.0,<0.47.0 , which can be installed (as previously explained); + r-base >=4.3,<4.4.0a0 , which can be installed; + bioconductor-iranges [2.6.0|2.6.1|2.8.0] would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-iranges 2.8.2 would require + r-base 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-iranges 2.8.2 would require + r-base 3.3.2* , which can be installed; + r-base 4.4.* is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-tidygenomics/meta.yaml b/recipes/r-tidygenomics/meta.yaml index 838621b9f8441..afb8e145a3181 100644 --- a/recipes/r-tidygenomics/meta.yaml +++ b/recipes/r-tidygenomics/meta.yaml @@ -11,7 +11,7 @@ source: sha256: cc214297f13f043a3c5461df53c4b797d2b684586f0a1fcf246fa6fb6baddcb2 build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-tidyheatmap/meta.yaml b/recipes/r-tidyheatmap/meta.yaml index 296252bcde3ee..04e2d9fd17451 100644 --- a/recipes/r-tidyheatmap/meta.yaml +++ b/recipes/r-tidyheatmap/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 9544d397b4a2c2666d703bbb6c7d49847ed20f447d1be1edc7c0e83a2ebaf7a5 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-tinyarray/build_failure.linux-64.yaml b/recipes/r-tinyarray/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..7848e40ed6d0c --- /dev/null +++ b/recipes/r-tinyarray/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 936f088a0a323e4a5e2694fd10ab7f577f278527fa054c2f76a5f0c5a9418800 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-clusterprofiler==3.0.5=r3.3.1_0"), MatchSpec("3.3.1*")} + Encountered problems while solving: + - nothing provides r 3.3.1* needed by bioconductor-clusterprofiler-3.0.5-r3.3.1_0 + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-clusterprofiler[0m is installable with the potential options + [32mbioconductor-clusterprofiler [2.4.3|3.0.4][0m would require + [32mbioconductor-keggrest[0m with the potential options + [31mbioconductor-keggrest 1.10.1[0m would require + [31mr 3.2.2* [0m, which does not exist (perhaps a missing channel); + [31mbioconductor-keggrest 1.12.3[0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [32mbioconductor-keggrest 1.12.3[0m would require + [32mr-base 3.3.2* [0m, which can be installed; + [32mbioconductor-keggrest [1.12.3|1.14.1|1.16.1|1.18.0|1.20.2][0m would require + [32mr-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ][0m, which can be installed; + [32mbioconductor-keggrest [1.20.2|1.22.0][0m would require + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-keggrest [1.24.0|1.26.0][0m would require + [32mbioconductor-biostrings >=2.52.0,<2.53.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.30.0,<0.31.0 [0m, which requires + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-keggrest [1.28.0|1.30.0|1.30.1][0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-keggrest [1.32.0|1.34.0][0m would require + [32mbioconductor-biostrings >=2.60.0,<2.61.0 [0m, which requires + [32mbioconductor-xvector >=0.32.0,<0.33.0 [0m, which requires + [32mbioconductor-zlibbioc >=1.38.0,<1.39.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-keggrest 1.38.0[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-keggrest [1.40.0|1.42.0][0m would require + [32mbioconductor-biostrings >=2.68.0,<2.69.0 [0m, which requires + [32mbioconductor-xvector >=0.40.0,<0.41.0 [0m, which requires + [32mbioconductor-zlibbioc >=1.46.0,<1.47.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mbioconductor-clusterprofiler 3.0.5[0m would require + [31mr 3.3.1* [0m, which does not exist (perhaps a missing channel); + [32mbioconductor-clusterprofiler [3.0.5|3.4.4][0m would require + [32mr-base [3.3.2* |>=3.3,<3.4 ][0m, which can be installed; + [32mbioconductor-clusterprofiler [3.0.5|3.6.0|3.8.1][0m would require + [32mr-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ][0m, which can be installed; + [32mbioconductor-clusterprofiler [3.10.1|3.8.1][0m would require + [32mbioconductor-dose >=3.8.0,<3.9.0 [0m, which requires + [32mbioconductor-fgsea >=1.8.0,<1.9.0 [0m, which requires + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-clusterprofiler [3.12.0|3.14.0][0m would require + [32mbioconductor-annotationdbi >=1.46.0,<1.47.0 [0m, which requires + [32mbioconductor-biocgenerics >=0.30.0,<0.31.0 [0m, which can be installed (as previously explained); + [32mbioconductor-dose >=3.12.0,<3.13.0 [0m, which requires + [32mbioconductor-fgsea >=1.12.0,<1.13.0 [0m, which requires + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-clusterprofiler [3.16.0|3.18.0|3.18.1][0m would require + [32mbioconductor-dose >=3.14.0,<3.15.0 [0m, which requires + [32mbioconductor-fgsea >=1.14.0,<1.15.0 [0m, which requires + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-clusterprofiler [4.0.0|4.2.0][0m would require + [32mbioconductor-annotationdbi >=1.54.0,<1.55.0 [0m, which requires + [32mbioconductor-keggrest >=1.32.0,<1.33.0 [0m, which can be installed (as previously explained); + [32mbioconductor-enrichplot >=1.14.0,<1.15.0 [0m, which requires + [32mbioconductor-ggtree >=3.2.0,<3.3.0 [0m, which requires + [32mbioconductor-treeio >=1.18.0,<1.19.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [31mbioconductor-clusterprofiler 4.10.0[0m would require + [32mbioconductor-annotationdbi >=1.64.0,<1.65.0 [0m, which can be installed; + [31mbioconductor-dose >=3.28.0,<3.29.0 [0m, which requires + [31mbioconductor-hdo.db >=0.99.0,<0.100.0 [0m but there are no viable options + [31mbioconductor-hdo.db 0.99.1[0m would require + [31mbioconductor-annotationdbi >=1.60.0,<1.61.0 [0m, which conflicts with any installable versions previously reported; + [31mbioconductor-hdo.db 0.99.1[0m would require + [31mbioconductor-annotationdbi >=1.62.0,<1.63.0 [0m, which requires + [32mbioconductor-keggrest >=1.40.0,<1.41.0 [0m, which can be installed (as previously explained); + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mbioconductor-clusterprofiler 4.6.0[0m would require + [32mbioconductor-enrichplot >=1.18.0,<1.19.0 [0m, which requires + [32mbioconductor-ggtree >=3.6.0,<3.7.0 [0m, which requires + [32mbioconductor-treeio >=1.22.0,<1.23.0 [0m, which requires + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [31mbioconductor-clusterprofiler 4.8.1[0m would require + [31mbioconductor-annotationdbi >=1.62.0,<1.63.0 [0m, which cannot be installed (as previously explained); + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-tinyarray/meta.yaml b/recipes/r-tinyarray/meta.yaml index a42ae9556889d..3743a1d3ad480 100644 --- a/recipes/r-tinyarray/meta.yaml +++ b/recipes/r-tinyarray/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 4cd2da08a9f96843ff703cb3280e3af4514bf510c31fde06f71299e551611fa1 build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-tmae/build_failure.linux-64.yaml b/recipes/r-tmae/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..62e6a14710bf5 --- /dev/null +++ b/recipes/r-tmae/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 2b6c5167337f69c0bc6c7a89480021d1b02b9fc13dabf034abe5181bbed46d61 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-genomicscores==1.0.2=0"), MatchSpec("r-base[version='>=3.4,<3.5']")} + Encountered problems while solving: + - package bioconductor-genomicscores-1.0.2-0 requires r-base >=3.4,<3.5, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-genomicscores[0m is installable with the potential options + [32mbioconductor-genomicscores [1.0.2|1.2.0][0m would require + [32mr-base [3.4.1* |>=3.4,<3.5 ][0m, which can be installed; + [32mbioconductor-genomicscores [1.4.1|1.6.0][0m would require + [32mbioconductor-annotationhub >=2.12.1,<2.14.0 [0m, which requires + [32mbioconductor-biocinstaller >=1.30.0,<1.32.0 [0m, which requires + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-bsgenome >=1.50.0,<1.51.0 [0m, which requires + [32mbioconductor-rsamtools >=1.34.0,<1.35.0 [0m, which requires + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-genomicscores [1.10.0|1.8.1][0m would require + [32mbioconductor-bsgenome >=1.54.0,<1.55.0 [0m, which requires + [32mbioconductor-rtracklayer >=1.46.0,<1.47.0 [0m, which requires + [32mbioconductor-genomicalignments >=1.22.0,<1.23.0 [0m, which requires + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-iranges >=2.18.0,<2.19.0 [0m, which requires + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-genomicscores [2.0.0|2.2.0][0m would require + [32mbioconductor-annotationhub >=2.20.0,<2.21.0 [0m, which requires + [32mbioconductor-interactivedisplaybase >=1.26.0,<1.27.0 [0m, which requires + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-s4vectors >=0.28.0,<0.29.0 [0m, which requires + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-genomicscores 2.10.0[0m would require + [32mbioconductor-s4vectors >=0.36.0,<0.37.0 [0m, which requires + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-genomicscores [2.12.0|2.14.1][0m would require + [32mbioconductor-annotationhub >=3.8.0,<3.9.0 [0m, which requires + [32mbioconductor-annotationdbi >=1.62.0,<1.63.0 [0m, which requires + [32mbioconductor-keggrest >=1.40.0,<1.41.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mbioconductor-s4vectors >=0.40.0,<0.41.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mbioconductor-genomicscores [2.4.0|2.6.0][0m would require + [32mbioconductor-annotationhub >=3.0.0,<3.1.0 [0m, which requires + [32mbioconductor-interactivedisplaybase >=1.30.0,<1.31.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-s4vectors >=0.32.0,<0.33.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. +category: |- + dependency issue diff --git a/recipes/r-tmae/meta.yaml b/recipes/r-tmae/meta.yaml index 3846d701b541f..a7058491195f4 100644 --- a/recipes/r-tmae/meta.yaml +++ b/recipes/r-tmae/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 8d11bcf01459dd7f69ecbd22a293b422c218a63d2cf49c1c9bba080bcb58b3aa build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-txrevise/meta.yaml b/recipes/r-txrevise/meta.yaml index 3d1027c55dd5d..f243e40ac3c66 100644 --- a/recipes/r-txrevise/meta.yaml +++ b/recipes/r-txrevise/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ hash }} build: - number: 2 + number: 3 noarch: generic script: R CMD INSTALL --build . rpaths: diff --git a/recipes/r-umi4c/meta.yaml b/recipes/r-umi4c/meta.yaml index 0979267d8ca67..f4eea84ebd36b 100644 --- a/recipes/r-umi4c/meta.yaml +++ b/recipes/r-umi4c/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 54a96756b4fd78c1d62c87a0c51c0c0d9d52210e43648bb9d81a4c12c46f88da build: - number: 2 + number: 3 noarch: generic script: R CMD INSTALL --build . rpaths: diff --git a/recipes/r-umianalyzer/build_failure.linux-64.yaml b/recipes/r-umianalyzer/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..1c88cf476205d --- /dev/null +++ b/recipes/r-umianalyzer/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: b7deaf3d6f2a0c9ad08659369b068bf572894b541e8263ee5eb357d0559f5f0b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-genomeinfodb >=1.28.0,<1.29.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-rsamtools 2.14.0[0m would require + [32mbioconductor-biocgenerics >=0.44.0,<0.45.0 [0m, which requires + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-rsamtools [2.16.0|2.18.0][0m would require + [32mbioconductor-genomeinfodb >=1.36.0,<1.37.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mbioconductor-rsamtools [2.4.0|2.6.0][0m would require + [32mbioconductor-genomeinfodb >=1.24.0,<1.25.0 [0m, which requires + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("r-base[version='>=3.4.1,<3.4.2.0a0']"), MatchSpec("bioconductor-rsamtools==1.32.3=r341hfc679d8_0")} + Encountered problems while solving: + - package bioconductor-rsamtools-1.32.3-r341hfc679d8_0 requires r-base >=3.4.1,<3.4.2.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-rsamtools >=1.32.3 [0m is installable with the potential options + [32mbioconductor-rsamtools 1.32.3[0m would require + [32mr-base >=3.4.1,<3.4.2.0a0 [0m, which can be installed; + [32mbioconductor-rsamtools [1.32.3|1.34.0][0m would require + [32mbioconductor-genomeinfodb >=1.18.0,<1.19.0 [0m, which requires + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-rsamtools [2.0.0|2.2.0][0m would require + [32mbioconductor-genomeinfodb [>=1.20.0,<1.21.0 |>=1.22.0,<1.23.0 ][0m, which requires + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-rsamtools [2.10.0|2.8.0][0m would require + [32mbioconductor-biocgenerics >=0.40.0,<0.41.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-genomeinfodb >=1.28.0,<1.29.0 [0m, which requires + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-rsamtools 2.14.0[0m would require + [32mbioconductor-biocgenerics >=0.44.0,<0.45.0 [0m, which requires + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-rsamtools [2.16.0|2.18.0][0m would require + [32mbioconductor-genomeinfodb >=1.36.0,<1.37.0 [0m, which requires + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [32mbioconductor-rsamtools [2.4.0|2.6.0][0m would require + [32mbioconductor-genomeinfodb >=1.24.0,<1.25.0 [0m, which requires + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/r-umianalyzer/meta.yaml b/recipes/r-umianalyzer/meta.yaml index cd146dfd1384c..ef5c6b926c0aa 100644 --- a/recipes/r-umianalyzer/meta.yaml +++ b/recipes/r-umianalyzer/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 0ebef08a26b5dd3b6b8da9fe84e6b6d1e6928e39288dbfb8b440d6942b22fd90 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-velocyto.r/build_failure.osx-64.yaml b/recipes/r-velocyto.r/build_failure.osx-64.yaml index 2052e04cf3188..10a848bf0bc9f 100644 --- a/recipes/r-velocyto.r/build_failure.osx-64.yaml +++ b/recipes/r-velocyto.r/build_failure.osx-64.yaml @@ -1,104 +1,104 @@ -recipe_sha: 684e911525b5157a20979381a54332c71c824890bd5ad8633058f6d09ff19e31 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 8bcd4b2e7fd10ede81ef840e1c6d6a5da65e5d453130b0f77fafcc72c06fe287 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - In file included from /opt/mambaforge/envs/bioconda/conda-bld/r-velocyto.r_1717694390164/_build_env/bin/../include/c/v1/locale:202: - /opt/mambaforge/envs/bioconda/conda-bld/r-velocyto.r_1717694390164/_build_env/bin/../include/c/v1/__locale:1309:15: error: expected ';' at end of declaration list - int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const - ^ - 12 errors generated. - make: *** [/opt/mambaforge/envs/bioconda/conda-bld/r-velocyto.r_1717694390164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/etc/Makeconf:200: points_within.o] Error 1 - ERROR: compilation failed for package velocyto.R - * removing /opt/mambaforge/envs/bioconda/conda-bld/r-velocyto.r_1717694390164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/R/library/velocyto.R - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/r-velocyto.r_1717694390164/work - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/r-velocyto.r_1717694390164/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/r-velocyto.r_1717694390164/_build_env - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/r-velocyto.r_1717694390164/work - INFO: activate-gfortran_osx-64.sh made the following environmental changes: - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-velocyto.r-0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/r-velocyto.r_1717694390164/work/conda_build.sh']' returned non-zero exit status 1. - DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-velocyto.r-0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments - F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-velocyto.r-0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-velocyto.r-0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-velocyto.r-0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-velocyto.r-0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-velocyto.r-0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-velocyto.r-0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - INFO: activate_clang_osx-64.sh made the following environmental changes: - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang - x86_64-apple-darwin13.4.0-clang -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -fopenmp -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1714471796105/work=/usr/local/src/conda/r-base-4.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o - x86_64-apple-darwin13.4.0-clang -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/RcppArmadillo/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -fopenmp -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1714471796105/work=/usr/local/src/conda/r-base-4.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c points_within.cpp -o points_within.o +log: |2- + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("r-base==4.4.0=ha82e53a_1"), MatchSpec("icu[version='>=73.2,<74.0a0']")} + Encountered problems while solving: + - package r-base-4.4.0-ha82e53a_1 requires icu >=73.2,<74.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + bioconductor-pcamethods is installable with the potential options + bioconductor-pcamethods 1.64.0 would require + r-base 3.3.2* with the potential options + r-base 3.3.2 would require + icu 56.* , which can be installed; + r-base [3.3.2|3.4.1] would require + icu 58.* , which can be installed; + bioconductor-pcamethods 1.64.0 would require + r 3.2.2* , which does not exist (perhaps a missing channel); + bioconductor-pcamethods 1.64.0 would require + r 3.3.1* , which does not exist (perhaps a missing channel); + bioconductor-pcamethods [1.64.0|1.68.0|1.70.0|1.72.0] would require + r-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ] with the potential options + r-base [3.3.2|3.4.1], which can be installed (as previously explained); + r-base [3.4.1|3.5.1] would require + icu >=58.2,<59.0a0 , which can be installed; + bioconductor-pcamethods [1.72.0|1.74.0] would require + r-base >=3.5.1,<3.5.2.0a0 with the potential options + r-base [3.4.1|3.5.1], which can be installed (as previously explained); + r-base [3.5.1|3.6.1] would require + clang_osx-64 4.* , which requires + clang 4.0.1.* but there are no viable options + clang 4.0.1 would require + compiler-rt 4.0.1 hcfea43d_1, which does not exist (perhaps a missing channel); + clang 4.0.1 would require + libcxx 4.0.1 h579ed51_0, which does not exist (perhaps a missing channel); + r-base [3.5.1|3.6.1|...|4.0.2] would require + icu >=64.2,<65.0a0 , which can be installed; + bioconductor-pcamethods [1.76.0|1.78.0] would require + bioconductor-biocgenerics [>=0.30.0,<0.31.0 |>=0.32.0,<0.33.0 ], which requires + r-base >=3.6,<3.7.0a0 with the potential options + r-base [3.5.1|3.6.1], which cannot be installed (as previously explained); + r-base [3.5.1|3.6.1|...|4.0.2], which can be installed (as previously explained); + r-base [3.6.3|4.0.3|4.0.5|4.1.0|4.1.1] would require + icu >=68.1,<69.0a0 , which can be installed; + r-base [3.6.3|4.0.2|4.0.3] would require + icu >=67.1,<68.0a0 , which can be installed; + bioconductor-pcamethods [1.80.0|1.82.0] would require + bioconductor-biocgenerics >=0.34.0,<0.35.0 , which requires + r-base >=4.0,<4.1.0a0 with the potential options + r-base [3.5.1|3.6.1|...|4.0.2], which can be installed (as previously explained); + r-base [3.6.3|4.0.3|4.0.5|4.1.0|4.1.1], which can be installed (as previously explained); + r-base [3.6.3|4.0.2|4.0.3], which can be installed (as previously explained); + r-base [4.0.5|4.1.3|...|4.2.3] would require + icu >=70.1,<71.0a0 , which can be installed; + r-base [4.0.5|4.1.1|4.1.2|4.1.3] would require + icu >=69.1,<70.0a0 , which can be installed; + r-base >=4.0,<4.1.0a0 , which can be installed (as previously explained); + bioconductor-pcamethods [1.84.0|1.86.0] would require + r-base >=4.1,<4.2.0a0 with the potential options + r-base [3.6.3|4.0.3|4.0.5|4.1.0|4.1.1], which can be installed (as previously explained); + r-base [4.0.5|4.1.3|...|4.2.3], which can be installed (as previously explained); + r-base [4.0.5|4.1.1|4.1.2|4.1.3], which can be installed (as previously explained); + r-base [4.1.3|4.2.3|4.3.1|4.3.2|4.3.3] would require + icu >=73.2,<74.0a0 , which conflicts with any installable versions previously reported; + r-base [4.1.3|4.2.3|4.3.0|4.3.1] would require + icu >=72.1,<73.0a0 , which can be installed; + r-base [4.1.3|4.2.3|4.3.3] would require + icu >=75.1,<76.0a0 , which conflicts with any installable versions previously reported; + bioconductor-pcamethods 1.90.0 would require + r-base >=4.2,<4.3.0a0 with the potential options + r-base [4.0.5|4.1.3|...|4.2.3], which can be installed (as previously explained); + r-base [4.1.3|4.2.3|4.3.1|4.3.2|4.3.3], which cannot be installed (as previously explained); + r-base [4.1.3|4.2.3|4.3.0|4.3.1], which can be installed (as previously explained); + r-base [4.1.3|4.2.3|4.3.3], which cannot be installed (as previously explained); + bioconductor-pcamethods [1.92.0|1.94.0] would require + r-base >=4.3,<4.4.0a0 with the potential options + r-base [4.1.3|4.2.3|4.3.1|4.3.2|4.3.3], which cannot be installed (as previously explained); + r-base [4.1.3|4.2.3|4.3.0|4.3.1], which can be installed (as previously explained); + r-base [4.1.3|4.2.3|4.3.3], which cannot be installed (as previously explained); + r-base 4.4.* is not installable because there are no viable options + r-base [4.4.0|4.4.1] would require + icu >=73.2,<74.0a0 , which conflicts with any installable versions previously reported; + r-base [4.4.1|4.4.2] would require + icu >=75.1,<76.0a0 , which conflicts with any installable versions previously reported. # Last 100 lines of the build log. diff --git a/recipes/r-velocyto.r/meta.yaml b/recipes/r-velocyto.r/meta.yaml index cb8389f9e51b0..0e79a2ea2d55b 100644 --- a/recipes/r-velocyto.r/meta.yaml +++ b/recipes/r-velocyto.r/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 8 + number: 9 script: R CMD INSTALL --build . rpaths: - lib/R/lib/ diff --git a/recipes/r-virfinder/meta.yaml b/recipes/r-virfinder/meta.yaml index e1a77084c2921..ba32e22958964 100644 --- a/recipes/r-virfinder/meta.yaml +++ b/recipes/r-virfinder/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-viscorvar/meta.yaml b/recipes/r-viscorvar/meta.yaml index ef22bf4f4573d..47051b97d1612 100644 --- a/recipes/r-viscorvar/meta.yaml +++ b/recipes/r-viscorvar/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 1138d9d36382811a6cfdf25142a663fcd3cfb88b5c97496bdf61f7c6238bcec9 build: - number: 2 + number: 3 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-vision/meta.yaml b/recipes/r-vision/meta.yaml index 73ea22a814fba..48ab8c64abdd7 100644 --- a/recipes/r-vision/meta.yaml +++ b/recipes/r-vision/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 7 + number: 8 # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ diff --git a/recipes/r-wasabi/meta.yaml b/recipes/r-wasabi/meta.yaml index bc24e85ea2c8c..cdefafab85c30 100644 --- a/recipes/r-wasabi/meta.yaml +++ b/recipes/r-wasabi/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 5b80db809bd09bcf8579702d244641caf069c2c04ab88272237dd7e7cdb8ec27 build: - number: 6 + number: 7 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-wgcna/meta.yaml b/recipes/r-wgcna/meta.yaml index 36f76edf48f76..29197eff78d99 100644 --- a/recipes/r-wgcna/meta.yaml +++ b/recipes/r-wgcna/meta.yaml @@ -11,7 +11,7 @@ source: sha256: e8a0a367a93190dd9f738578a82d31856e004b9de46d2775e4ed0f44a95063ce build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("r-wgcna", max_pin="x") }} rpaths: diff --git a/recipes/r-whopgenome/build_failure.osx-64.yaml b/recipes/r-whopgenome/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..f67ff1b06fd2c --- /dev/null +++ b/recipes/r-whopgenome/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 6268e1b59d05ded0a04f6747b576a5cf9971899db8aaccd389c06b14568aae67 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + copy_test_source_files: true + final: true + recipe-maintainers: + - MathiasHaudgaard + - FrodePedersen + - ArneKr + - johanneskoester + - bgruening + - daler + - jdblischak + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/r-whopgenome_1734462100903/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/r-whopgenome_1734462100903/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/r-whopgenome_1734462100903/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/r-whopgenome_1734462100903/work + INFO: activate-gfortran_osx-64.sh made the following environmental changes: + DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-whopgenome-0.9.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-whopgenome-0.9.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-whopgenome-0.9.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-whopgenome-0.9.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-whopgenome-0.9.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-whopgenome-0.9.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-whopgenome-0.9.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-whopgenome-0.9.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + INFO: activate_clang_osx-64.sh made the following environmental changes: + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-whopgenome-0.9.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-whopgenome-0.9.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-whopgenome-0.9.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-whopgenome-0.9.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-whopgenome-0.9.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + -CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + -CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + -DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/r-whopgenome-0.9.7 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + -LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + -OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + -CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + x86_64-apple-darwin13.4.0-clang -std=gnu17 -I"$PREFIX/lib/R/include" -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -mmacosx-version-min=10.13 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1734433510517/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c w_vcf.cpp -o w_vcf.o +# Last 100 lines of the build log. diff --git a/recipes/r-whopgenome/meta.yaml b/recipes/r-whopgenome/meta.yaml index 31369cb0eadf8..c0243803b164d 100644 --- a/recipes/r-whopgenome/meta.yaml +++ b/recipes/r-whopgenome/meta.yaml @@ -11,10 +11,11 @@ source: sha256: 58bb001a831eff64955e424f07de7775d4d463d9674fc7743a0f795b7a6a47f5 build: - number: 9 + number: 10 rpaths: - lib/R/lib/ - lib/ + run_exports: '{{ pin_subpackage("r-whopgenome", max_pin="x.x") }}' requirements: build: @@ -23,6 +24,7 @@ requirements: - make host: - r-base + - zlib run: - r-base diff --git a/recipes/r-wormbase/meta.yaml b/recipes/r-wormbase/meta.yaml index bb2667d5a1a98..0879966c96051 100644 --- a/recipes/r-wormbase/meta.yaml +++ b/recipes/r-wormbase/meta.yaml @@ -10,7 +10,7 @@ source: sha256: dce59a925b8fa24c4de87747e303333eb0a9f79a0f0dde130d8f242cb17809a7 build: - number: 0 + number: 1 noarch: generic run_exports: - {{ pin_subpackage('r-wormbase', max_pin="x.x") }} diff --git a/recipes/r-xcell/meta.yaml b/recipes/r-xcell/meta.yaml index 6c72a5cefde9a..1311565b8c386 100755 --- a/recipes/r-xcell/meta.yaml +++ b/recipes/r-xcell/meta.yaml @@ -13,7 +13,7 @@ source: build: script: $R CMD INSTALL --build . - number: 6 + number: 7 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-xgr/build_failure.linux-64.yaml b/recipes/r-xgr/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..13eca30f458d6 --- /dev/null +++ b/recipes/r-xgr/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 344b50c4db980dd475bc9c0a8b28a032a892c47527e68d60b5896a0c61c2060f # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mr-dnet [1.1.4|1.1.5|1.1.6|1.1.7][0m would require + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mr-dnet 1.1.7[0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-dnet 1.1.7[0m would require + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-dnet 1.1.7[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mr-dnet 1.1.7[0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("bioconductor-suprahex==1.14.0=r3.3.2_0"), MatchSpec("r-base=3.3.2")} + Encountered problems while solving: + - package bioconductor-suprahex-1.14.0-r3.3.2_0 requires r-base 3.3.2*, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mbioconductor-suprahex[0m is installable with the potential options + [32mbioconductor-suprahex 1.14.0[0m would require + [32mr-base [3.3.2* |>=3.3,<3.4 ][0m, which can be installed; + [32mbioconductor-suprahex [1.14.0|1.16.0|1.18.0][0m would require + [32mr-base [3.4.1* |>=3.4.1,<3.4.2.0a0 ][0m, which can be installed; + [32mbioconductor-suprahex [1.18.0|1.20.0|1.22.0][0m would require + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mbioconductor-suprahex [1.22.0|1.24.0][0m would require + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mbioconductor-suprahex [1.26.0|1.28.0|1.28.1][0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mbioconductor-suprahex [1.30.0|1.32.0][0m would require + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mbioconductor-suprahex 1.36.0[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mbioconductor-suprahex [1.38.0|1.40.0][0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed; + [31mr-base 4.4.* [0m is not installable because it conflicts with any installable versions previously reported; + [32mr-dnet[0m is installable with the potential options + [32mr-dnet 1.1.4[0m would require + [32mr-base >=3.5.1,<3.5.2.0a0 [0m, which can be installed; + [32mr-dnet [1.1.4|1.1.5|1.1.6|1.1.7][0m would require + [32mr-base >=3.6,<3.7.0a0 [0m, which can be installed; + [32mr-dnet 1.1.7[0m would require + [32mr-base >=4.0,<4.1.0a0 [0m, which can be installed; + [32mr-dnet 1.1.7[0m would require + [32mr-base >=4.1,<4.2.0a0 [0m, which can be installed; + [32mr-dnet 1.1.7[0m would require + [32mr-base >=4.2,<4.3.0a0 [0m, which can be installed; + [32mr-dnet 1.1.7[0m would require + [32mr-base >=4.3,<4.4.0a0 [0m, which can be installed. +# Last 100 lines of the build log. diff --git a/recipes/r-xgr/meta.yaml b/recipes/r-xgr/meta.yaml index 92178aa08fb47..9fe1dfe5eeb40 100644 --- a/recipes/r-xgr/meta.yaml +++ b/recipes/r-xgr/meta.yaml @@ -11,7 +11,7 @@ source: sha256: db4a4bc452dacba62db4d39a0a65ef19be4adb8030c5676c2642f2631ab1c5e8 build: - number: 5 + number: 6 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/r-xmlrpc/meta.yaml b/recipes/r-xmlrpc/meta.yaml index 2e9ab73a3a7df..5e884ebf0a925 100644 --- a/recipes/r-xmlrpc/meta.yaml +++ b/recipes/r-xmlrpc/meta.yaml @@ -7,7 +7,7 @@ source: - http://download.r-forge.r-project.org/src/contrib/XMLRPC_0.2-4.tar.gz build: - number: 7 + number: 8 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r2r/meta.yaml b/recipes/r2r/meta.yaml index 2983e6fa9ccfe..6b47f025ecbb4 100644 --- a/recipes/r2r/meta.yaml +++ b/recipes/r2r/meta.yaml @@ -8,7 +8,7 @@ about: summary: software to speed depiction of aesthetic consensus RNA secondary structures build: - number: 4 + number: 5 skip: True # [osx] source: diff --git a/recipes/ra/build_failure.linux-64.yaml b/recipes/ra/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..a255eb4fb1114 --- /dev/null +++ b/recipes/ra/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a5ae501719e5440954c389cea8a7b79c75dc6ba0499952b58fdaea09a43f6e94 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + fatal: not a git repository (or any of the parent directories): .git + [CXX] ../src/main.cpp + [LD] to_afg + [CP] ../../bin/debug/to_afg + fatal: not a git repository (or any of the parent directories): .git + [CXX] ../src/main.cpp + [LD] to_afg + [CP] ../../bin/release/to_afg + [MOD] consensus + [MAKE] install + fatal: not a git repository (or any of the parent directories): .git + [CXX] ../src/main.cpp + ../src/main.cpp: In function 'int main(int, char**)': + ../src/main.cpp:38:13: warning: unused variable 'threadLen' [-Wunused-variable] + 38 | const int threadLen = std::max(std::thread::hardware_concurrency(), 1U); + | ^~~~~~~~~ + [LD] consensus + [CP] ../../bin/debug/consensus + fatal: not a git repository (or any of the parent directories): .git + [CXX] ../src/main.cpp + ../src/main.cpp: In function 'int main(int, char**)': + ../src/main.cpp:58:22: warning: unused variable 'part' [-Wunused-variable] + 58 | for (const auto& part: contig->getParts()) { + | ^~~~ + ../src/main.cpp:38:13: warning: unused variable 'threadLen' [-Wunused-variable] + 38 | const int threadLen = std::max(std::thread::hardware_concurrency(), 1U); + | ^~~~~~~~~ + [LD] consensus + [CP] ../../bin/release/consensus + [MOD] unitigger + [MAKE] install + fatal: not a git repository (or any of the parent directories): .git + [CXX] ../src/main.cpp + [LD] unitigger + [CP] ../../bin/debug/unitigger + fatal: not a git repository (or any of the parent directories): .git + [CXX] ../src/main.cpp + [LD] unitigger + [CP] ../../bin/release/unitigger + [MOD] overlap2dot + [MAKE] install + fatal: not a git repository (or any of the parent directories): .git + [CXX] ../src/main.cpp + In file included from ../src/overlap2dot.h:8, + from ../src/main.cpp:6: + ../../include/ra/EdgesSet.hpp:20:7: error: 'uint32_t' does not name a type + 20 | uint32_t size(); + | ^~~~~~~~ + ../../include/ra/EdgesSet.hpp:8:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + 7 | #include + |#include + 8 | + ../../include/ra/EdgesSet.hpp:39:5: error: 'uint32_t' does not name a type + 39 | uint32_t EdgesSet::size() { + | ^~~~~~~~ + ../../include/ra/EdgesSet.hpp:39:5: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + ../src/overlap2dot.h: In function 'int dot_graph(std::ostream&, std::vector&)': + ../src/overlap2dot.h:26:5: error: 'uint32_t' was not declared in this scope + 26 | uint32_t a_id = overlap->a(); + | ^~~~~~~~ + ../src/overlap2dot.h:9:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + 8 | #include "ra/EdgesSet.hpp" + |#include + 9 | + ../src/overlap2dot.h:27:13: error: expected ';' before 'b_id' + 27 | uint32_t b_id = overlap->b(); + | ^~~~~ + | ; + ../src/overlap2dot.h:28:15: error: 'a_id' was not declared in this scope + 28 | output << a_id << " -- " << b_id << " ["; + | ^~~~ + ../src/overlap2dot.h:28:33: error: 'b_id' was not declared in this scope + 28 | output << a_id << " -- " << b_id << " ["; + | ^~~~ + make[2]: *** [../Makefile.rules:50: obj/main.o] Error 1 + make[1]: *** [Makefile:7: install] Error 2 + make: *** [Makefile:43: overlap2dot] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ra_1733981850283/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ra_1733981850283/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/ra/meta.yaml b/recipes/ra/meta.yaml index 30f43eab1ad17..44e748e88eed1 100644 --- a/recipes/ra/meta.yaml +++ b/recipes/ra/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.9" build: - number: 6 + number: 7 skip: True # [osx] source: diff --git a/recipes/rabbitqcplus/meta.yaml b/recipes/rabbitqcplus/meta.yaml index ba6390ac5ee70..3038b08b85808 100644 --- a/recipes/rabbitqcplus/meta.yaml +++ b/recipes/rabbitqcplus/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 9ce239d998582c50c373eefc8d5f83763439693fe348206107f27105a22d4aaf build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage("rabbitqcplus", max_pin="x.x") }} diff --git a/recipes/rabbittclust/build_failure.linux-64.yaml b/recipes/rabbittclust/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..4c88fa2c8fbfe --- /dev/null +++ b/recipes/rabbittclust/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 196d7b658f18846ed84b98eb20d9db2c0089459be1ceb20cb9fe9e1a0d66d7e0 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp: In function 'Reference rabbit::fa::getNextSeq(FastaChunk&, bool&, rabbit::uint64&)': + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:185:21: error: 'struct Reference' has no member named 'length' + 185 | ref.length = ref.seq.size(); + | ^~~~~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:186:21: error: 'struct Reference' has no member named 'gid' + 186 | ref.gid = fachunk.start; + | ^~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:197:21: error: 'struct Reference' has no member named 'length' + 197 | ref.length = ref.seq.size(); + | ^~~~~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:198:21: error: 'struct Reference' has no member named 'gid' + 198 | ref.gid = fachunk.start; + | ^~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp: In function 'void rabbit::fq::print_read(neoReference&)': + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:269:54: error: 'struct neoReference' has no member named 'pname' + 269 | std::cout << std::string((char*)ref.baseref.pname, ref.lname) << std::endl; + | ^~~~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:269:65: error: 'struct neoReference' has no member named 'lname' + 269 | std::cout << std::string((char*)ref.baseref.pname, ref.lname) << std::endl; + | ^~~~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:270:54: error: 'struct neoReference' has no member named 'pseq' + 270 | std::cout << std::string((char*)ref.baseref.pseq, ref.lseq) << std::endl; + | ^~~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:270:64: error: 'struct neoReference' has no member named 'lseq' + 270 | std::cout << std::string((char*)ref.baseref.pseq, ref.lseq) << std::endl; + | ^~~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:271:54: error: 'struct neoReference' has no member named 'pstrand' + 271 | std::cout << std::string((char*)ref.baseref.pstrand, ref.lstrand) << std::endl; + | ^~~~~~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:271:67: error: 'struct neoReference' has no member named 'lstrand' + 271 | std::cout << std::string((char*)ref.baseref.pstrand, ref.lstrand) << std::endl; + | ^~~~~~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:272:54: error: 'struct neoReference' has no member named 'pqual' + 272 | std::cout << std::string((char*)ref.baseref.pqual, ref.lqual) << std::endl; + | ^~~~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:272:65: error: 'struct neoReference' has no member named 'lqual' + 272 | std::cout << std::string((char*)ref.baseref.pqual, ref.lqual) << std::endl; + | ^~~~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp: In function 'int rabbit::fq::chunkFormat(FastqChunk*&, std::vector&, bool)': + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:283:21: error: 'struct neoReference' has no member named 'pname' + 283 | ref.pname = pos_; + | ^~~~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:284:48: error: 'struct neoReference' has no member named 'lname' + 284 | if(neoGetLine(chunk, pos_, ref.lname)){ + | ^~~~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:285:29: error: 'struct neoReference' has no member named 'pseq' + 285 | ref.pseq = pos_; + | ^~~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:288:45: error: 'struct neoReference' has no member named 'lseq' + 288 | neoGetLine(chunk, pos_, ref.lseq); + | ^~~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:289:21: error: 'struct neoReference' has no member named 'pstrand' + 289 | ref.pstrand = pos_; + | ^~~~~~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:290:45: error: 'struct neoReference' has no member named 'lstrand' + 290 | neoGetLine(chunk, pos_, ref.lstrand); + | ^~~~~~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:291:21: error: 'struct neoReference' has no member named 'pqual' + 291 | ref.pqual = pos_; + | ^~~~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/verbos_Formater.cpp:292:45: error: 'struct neoReference' has no member named 'lqual' + 292 | neoGetLine(chunk, pos_, ref.lqual); + | ^~~~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/FastxStream.cpp: In member function 'rabbit::uint64 rabbit::fa::FastaFileReader::FindCutPos_(rabbit::fa::FastaChunk*, rabbit::uchar*, rabbit::uint64, rabbit::uint64, SeqInfos&)': + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/FastxStream.cpp:168:19: error: 'OneSeqInfo' {aka 'struct Reference'} has no member named 'gid' + 168 | seqInfo.gid = this->totalSeqs; + | ^~~ + /opt/conda/conda-bld/rabbittclust_1734129446369/work/RabbitFX/io/FastxStream.cpp:191:19: error: 'OneSeqInfo' {aka 'struct Reference'} has no member named 'gid' + 191 | seqInfo.gid = this->totalSeqs; + | ^~~ + make[2]: *** [CMakeFiles/rabbitfx.dir/build.make:93: CMakeFiles/rabbitfx.dir/io/Formater.cpp.o] Error 1 + make[2]: *** Waiting for unfinished jobs.... + make[2]: *** [CMakeFiles/rabbitfx.dir/build.make:107: CMakeFiles/rabbitfx.dir/io/verbos_Formater.cpp.o] Error 1 + make[2]: *** [CMakeFiles/rabbitfx.dir/build.make:79: CMakeFiles/rabbitfx.dir/io/FastxStream.cpp.o] Error 1 + make[1]: *** [CMakeFiles/Makefile2:87: CMakeFiles/rabbitfx.dir/all] Error 2 + make: *** [Makefile:136: all] Error 2 + cp: cannot stat 'clust-mst': No such file or directory + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/rabbittclust_1734129446369/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/rabbittclust_1734129446369/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/rabbittclust/meta.yaml b/recipes/rabbittclust/meta.yaml index 10eb7fb0f5e1a..ccace89d4dcac 100644 --- a/recipes/rabbittclust/meta.yaml +++ b/recipes/rabbittclust/meta.yaml @@ -10,7 +10,7 @@ source: build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('rabbittclust', max_pin='x.x') }} diff --git a/recipes/racon/build_failure.osx-arm64.yaml b/recipes/racon/build_failure.osx-arm64.yaml new file mode 100644 index 0000000000000..7ee641b1ec408 --- /dev/null +++ b/recipes/racon/build_failure.osx-arm64.yaml @@ -0,0 +1,106 @@ +recipe_sha: a8f6d32492dd923b1c7091f15a19cfdb9732747b7af7851e12469198d50f11d7 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CHECKSYMS=arm64-apple-darwin20.0.0-checksyms + CLANG=arm64-apple-darwin20.0.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=11.0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=arm64-apple-darwin20.0.0 + CONDA_TOOLCHAIN_HOST=arm64-apple-darwin20.0.0 + CPP=arm64-apple-darwin20.0.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang-cpp + DEBUG_CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/racon-1.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=arm64-apple-darwin20.0.0 + INSTALL_NAME_TOOL=arm64-apple-darwin20.0.0-install_name_tool + LD=arm64-apple-darwin20.0.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=arm64-apple-darwin20.0.0-libtool + LIPO=arm64-apple-darwin20.0.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=arm64-apple-darwin20.0.0-nm + NMEDIT=arm64-apple-darwin20.0.0-nmedit + OBJC=arm64-apple-darwin20.0.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang + OTOOL=arm64-apple-darwin20.0.0-otool + PAGESTUFF=arm64-apple-darwin20.0.0-pagestuff + RANLIB=arm64-apple-darwin20.0.0-ranlib + REDO_PREBINDING=arm64-apple-darwin20.0.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk + SEGEDIT=arm64-apple-darwin20.0.0-segedit + SEG_ADDR_TABLE=arm64-apple-darwin20.0.0-seg_addr_table + SEG_HACK=arm64-apple-darwin20.0.0-seg_hack + SIZE=arm64-apple-darwin20.0.0-size + STRINGS=arm64-apple-darwin20.0.0-strings + STRIP=arm64-apple-darwin20.0.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_arm64_apple_darwin20_0_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=arm64-apple-darwin20.0.0 + host_alias=arm64-apple-darwin20.0.0 + INFO: activate_clangxx_osx-arm64.sh made the following environmental changes: + CLANGXX=arm64-apple-darwin20.0.0-clang + CXX=arm64-apple-darwin20.0.0-clang + CXXFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/racon-1.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang + DEBUG_CXXFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/racon-1.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -- The CXX compiler identification is Clang 18.1.8 + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Found ZLIB: $PREFIX/lib/libz.dylib (found suitable version "1.3.1", minimum required is "1.2.8") + -- The C compiler identification is Clang 18.1.8 + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang - skipped + -- Detecting C compile features + -- Detecting C compile features - done + -- Performing Test WOLD_STYLE_CAST + -- Performing Test WOLD_STYLE_CAST - Success + -- Performing Test WSHADOW + -- Performing Test WSHADOW - Success + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success + -- Found Threads: TRUE + -- Found PythonInterp: /opt/mambaforge/envs/bioconda/bin/python (found version "3.10.16") + -- Configuring done (23.6s) + -- Generating done (0.1s) + -- Build files have been written to: $SRC_DIR/build + Change Dir: '$SRC_DIR/build' + + Run Build Command(s): $BUILD_PREFIX/bin/cmake -E env VERBOSE=1 $BUILD_PREFIX/bin/make -f Makefile -j2 install + $BUILD_PREFIX/bin/cmake -S$SRC_DIR -B$SRC_DIR/build --check-build-system CMakeFiles/Makefile.cmake 0 + $BUILD_PREFIX/bin/cmake -E cmake_progress_start $SRC_DIR/build/CMakeFiles $SRC_DIR/build//CMakeFiles/progress.marks + $BUILD_PREFIX/bin/make -f CMakeFiles/Makefile2 all + make[1]: Entering directory '$SRC_DIR/build' + $BUILD_PREFIX/bin/make -f _deps/spoa-build/CMakeFiles/spoa.dir/build.make _deps/spoa-build/CMakeFiles/spoa.dir/depend + $BUILD_PREFIX/bin/make -f _deps/edlib-build/CMakeFiles/edlib.dir/build.make _deps/edlib-build/CMakeFiles/edlib.dir/depend + make[2]: Entering directory '$SRC_DIR/build' + cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR/build/_deps/edlib-src $SRC_DIR/build $SRC_DIR/build/_deps/edlib-build $SRC_DIR/build/_deps/edlib-build/CMakeFiles/edlib.dir/DependInfo.cmake "--color=" + make[2]: Entering directory '$SRC_DIR/build' + cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR/build/_deps/spoa-src $SRC_DIR/build $SRC_DIR/build/_deps/spoa-build $SRC_DIR/build/_deps/spoa-build/CMakeFiles/spoa.dir/DependInfo.cmake "--color=" + make[2]: Leaving directory '$SRC_DIR/build' + $BUILD_PREFIX/bin/make -f _deps/edlib-build/CMakeFiles/edlib.dir/build.make _deps/edlib-build/CMakeFiles/edlib.dir/build + make[2]: Leaving directory '$SRC_DIR/build' + $BUILD_PREFIX/bin/make -f _deps/spoa-build/CMakeFiles/spoa.dir/build.make _deps/spoa-build/CMakeFiles/spoa.dir/build + make[2]: Entering directory '$SRC_DIR/build' + make[2]: Entering directory '$SRC_DIR/build' + [ 4%] Building CXX object _deps/edlib-build/CMakeFiles/edlib.dir/edlib/src/edlib.cpp.o + [ 8%] Building CXX object _deps/spoa-build/CMakeFiles/spoa.dir/src/alignment_engine.cpp.o + cd $SRC_DIR/build/_deps/edlib-build && $BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang -DDLIB_BUILD -I$SRC_DIR/build/_deps/edlib-src/edlib/include -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/racon-1.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -pedantic -Wold-style-cast -Wshadow -Wall -Wextra -pedantic -O3 -DNDEBUG -std=c14 -arch arm64 -isysroot /Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk -mmacosx-version-min=11.0 -MD -MT _deps/edlib-build/CMakeFiles/edlib.dir/edlib/src/edlib.cpp.o -MF CMakeFiles/edlib.dir/edlib/src/edlib.cpp.o.d -o CMakeFiles/edlib.dir/edlib/src/edlib.cpp.o -c $SRC_DIR/build/_deps/edlib-src/edlib/src/edlib.cpp + cd $SRC_DIR/build/_deps/spoa-build && $BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang -I$SRC_DIR/build/_deps/spoa-src/include -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/racon-1.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -pedantic -Wall -Wextra -pedantic -msse4.1 -O3 -DNDEBUG -std=c11 -arch arm64 -isysroot /Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk -mmacosx-version-min=11.0 -MD -MT _deps/spoa-build/CMakeFiles/spoa.dir/src/alignment_engine.cpp.o -MF CMakeFiles/spoa.dir/src/alignment_engine.cpp.o.d -o CMakeFiles/spoa.dir/src/alignment_engine.cpp.o -c $SRC_DIR/build/_deps/spoa-src/src/alignment_engine.cpp + make[2]: Leaving directory '$SRC_DIR/build' + [ 12%] Linking CXX static library ../../lib/libedlib.a + cd $SRC_DIR/build/_deps/edlib-build && $BUILD_PREFIX/bin/cmake -P CMakeFiles/edlib.dir/cmake_clean_target.cmake + cd $SRC_DIR/build/_deps/edlib-build && $BUILD_PREFIX/bin/cmake -E cmake_link_script CMakeFiles/edlib.dir/link.txt --verbose=1 + $BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ar qc ../../lib/libedlib.a CMakeFiles/edlib.dir/edlib/src/edlib.cpp.o + $BUILD_PREFIX/bin/llvm-ranlib ../../lib/libedlib.a + make[2]: Leaving directory '$SRC_DIR/build' + [ 12%] Built target edlib + make[1]: Leaving directory '$SRC_DIR/build' +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/racon/meta.yaml b/recipes/racon/meta.yaml index a853f6be6f209..3092a3ecb7c08 100644 --- a/recipes/racon/meta.yaml +++ b/recipes/racon/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} diff --git a/recipes/rad_haplotyper/meta.yaml b/recipes/rad_haplotyper/meta.yaml index 6a5e5741b553c..e22e49b7a5553 100644 --- a/recipes/rad_haplotyper/meta.yaml +++ b/recipes/rad_haplotyper/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 1a9ca21ec215e6dae7233918daa2f48b9bb2262a630e0acbdde49ab1f2b8984e build: - number: 7 + number: 8 skip: true # [osx] requirements: diff --git a/recipes/radiant/build_failure.linux-64.yaml b/recipes/radiant/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..347c767c74dc6 --- /dev/null +++ b/recipes/radiant/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 84607df2ba99f24cf7424a220475d57e841f32334d393b1043a0c430441d6739 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/radiant-1.1.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/radiant-1.1.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/radiant-1.1.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + -- The CXX compiler identification is GNU 13.3.0 + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Found OpenMP_CXX: -fopenmp (found version "4.5") + -- Found OpenMP: TRUE (found version "4.5") + CMake Warning (dev) at CMakeLists.txt:62 (find_package): + Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake + --help-policy CMP0167" for policy details. Use the cmake_policy command to + set the policy and suppress this warning. + + This warning is for project developers. Use -Wno-dev to suppress it. + + -- Found Boost: $PREFIX/lib/cmake/Boost-1.85.0/BoostConfig.cmake (found suitable version "1.85.0", minimum required is "1.74") found components: system program_options iostreams unit_test_framework + Downloading BioSeqDataLib + CMake Warning (dev) at /opt/conda/conda-bld/radiant_1734124222073/_build_env/share/cmake-3.31/Modules/FetchContent.cmake:1953 (message): + Calling FetchContent_Populate(BioSeqDataLib) is deprecated, call + FetchContent_MakeAvailable(BioSeqDataLib) instead. Policy CMP0169 can be + set to OLD to allow FetchContent_Populate(BioSeqDataLib) to be called + directly for now, but the ability to call it with declared details will be + removed completely in a future version. + Call Stack (most recent call first): + CMakeLists.txt:76 (FetchContent_Populate) + This warning is for project developers. Use -Wno-dev to suppress it. + + Done + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success + -- Found Threads: TRUE + /opt/conda/conda-bld/radiant_1734124222073/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/include + -- Configuring done (2.7s) + -- Generating done (0.0s) + -- Build files have been written to: $SRC_DIR/build + [ 2%] Building CXX object CMakeFiles/makeRadiantDB.dir/src/makeRadiantDb.cpp.o + [ 5%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/utility/Input.cpp.o + [ 7%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/utility/Output.cpp.o + [ 10%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/sequence/IOStrategies/ClustalReader.cpp.o + [ 12%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/sequence/IOStrategies/FASTAReader.cpp.o + [ 15%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/sequence/IOStrategies/FASTAWriter.cpp.o + [ 17%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/sequence/IOStrategies/IndexingFASTAReader.cpp.o + [ 20%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/sequence/IOStrategies/MSFReader.cpp.o + [ 22%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/sequence/IOStrategies/PhylipReader.cpp.o + [ 25%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/sequence/IOStrategies/StockholmReader.cpp.o + [ 27%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/external_interfaces/EI_Manager.cpp.o + In file included from /opt/conda/conda-bld/radiant_1734124222073/work/libs/BioSeqDataLib/src/external_interfaces/EI_Manager.cpp:2: + /opt/conda/conda-bld/radiant_1734124222073/work/libs/BioSeqDataLib/src/external_interfaces/EI_Manager.hpp:32:10: fatal error: boost/filesystem/path_traits.hpp: No such file or directory + 32 | #include // for filesystem + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + compilation terminated. + make[2]: *** [CMakeFiles/makeRadiantDB.dir/build.make:219: CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/external_interfaces/EI_Manager.cpp.o] Error 1 + make[1]: *** [CMakeFiles/Makefile2:90: CMakeFiles/makeRadiantDB.dir/all] Error 2 + make: *** [Makefile:136: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/radiant_1734124222073/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/radiant_1734124222073/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/radiant/build_failure.osx-64.yaml b/recipes/radiant/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..5b92183549100 --- /dev/null +++ b/recipes/radiant/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 84607df2ba99f24cf7424a220475d57e841f32334d393b1043a0c430441d6739 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - bzip2 >=1.0.8,<2.0a0 + - libcxx >=18 + - openmp + - sqlite + test: + commands: + - radiant -h + about: + description: 'This program rapidly annotates protein sequences with Pfam domains + + ' + home: https://domainworld.uni-muenster.de/data/radiant-db/index.html + license: GPL-3.0-or-later + license_file: LICENSE + summary: Annotate proteomes with protein domains + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/radiant_1733978247646/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/radiant_1733978247646/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/radiant_1733978247646/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/radiant_1733978247646/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/radiant-1.1.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/radiant-1.1.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/radiant-1.1.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/radiant-1.1.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -- The CXX compiler identification is Clang 18.1.8 + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.1") + -- Found OpenMP: TRUE (found version "5.1") + -- Found Boost: $PREFIX/lib/cmake/Boost-1.85.0/BoostConfig.cmake (found suitable version "1.85.0", minimum required is "1.74") found components: system program_options iostreams unit_test_framework + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success + -- Found Threads: TRUE + -- Configuring done (5.4s) + -- Generating done (0.0s) + -- Build files have been written to: $SRC_DIR/build + [ 2%] Building CXX object CMakeFiles/makeRadiantDB.dir/src/makeRadiantDb.cpp.o + [ 5%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/utility/Input.cpp.o + [ 7%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/utility/Output.cpp.o + [ 10%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/sequence/IOStrategies/ClustalReader.cpp.o + [ 12%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/sequence/IOStrategies/FASTAReader.cpp.o + [ 15%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/sequence/IOStrategies/FASTAWriter.cpp.o + [ 17%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/sequence/IOStrategies/IndexingFASTAReader.cpp.o + [ 20%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/sequence/IOStrategies/MSFReader.cpp.o + [ 22%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/sequence/IOStrategies/PhylipReader.cpp.o + [ 25%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/sequence/IOStrategies/StockholmReader.cpp.o + [ 27%] Building CXX object CMakeFiles/makeRadiantDB.dir/libs/BioSeqDataLib/src/external_interfaces/EI_Manager.cpp.o +# Last 100 lines of the build log. diff --git a/recipes/radiant/meta.yaml b/recipes/radiant/meta.yaml index d79fe4d62761d..329946d3880ff 100644 --- a/recipes/radiant/meta.yaml +++ b/recipes/radiant/meta.yaml @@ -12,7 +12,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('radiant', max_pin="x") }} diff --git a/recipes/radsex/build_failure.linux-64.yaml b/recipes/radsex/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..da57749bc7196 --- /dev/null +++ b/recipes/radsex/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: b5ec0d8f12dadfd17f5cda0f6fa91520b72d1d2d826912c50ede3a61204d8cdc # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -Wno-unused-function -Wno-unused-but-set-variable -Wno-unused-result -O2 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o bwt.o bwt.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -Wno-unused-function -Wno-unused-but-set-variable -Wno-unused-result -O2 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o bwt_gen.o bwt_gen.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -Wno-unused-function -Wno-unused-but-set-variable -Wno-unused-result -O2 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o bwtindex.o bwtindex.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -Wno-unused-function -Wno-unused-but-set-variable -Wno-unused-result -O2 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o is.o is.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -Wno-unused-function -Wno-unused-but-set-variable -Wno-unused-result -O2 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o kstring.o kstring.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -Wno-unused-function -Wno-unused-but-set-variable -Wno-unused-result -O2 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o ksw.o ksw.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -Wno-unused-function -Wno-unused-but-set-variable -Wno-unused-result -O2 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o kthread.o kthread.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -Wno-unused-function -Wno-unused-but-set-variable -Wno-unused-result -O2 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o malloc_wrap.o malloc_wrap.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -Wno-unused-function -Wno-unused-but-set-variable -Wno-unused-result -O2 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o rle.o rle.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -Wno-unused-function -Wno-unused-but-set-variable -Wno-unused-result -O2 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o rope.o rope.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -Wno-unused-function -Wno-unused-but-set-variable -Wno-unused-result -O2 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -c -o utils.o utils.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -csru libbwa.a ./QSufSort.o ./bntseq.o ./bwa.o ./bwamem.o ./bwamem_extra.o ./bwamem_pair.o ./bwt.o ./bwt_gen.o ./bwtindex.o ./is.o ./kstring.o ./ksw.o ./kthread.o ./malloc_wrap.o ./rle.o ./rope.o ./utils.o + make[1]: Leaving directory '$SRC_DIR/include/bwa' + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/radsex-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -std=c11 -O2 -I ./include -c -o build/analysis.o src/analysis.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/radsex-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -std=c11 -O2 -I ./include -c -o build/depth.o src/depth.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/radsex-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -std=c11 -O2 -I ./include -c -o build/distrib.o src/distrib.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/radsex-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -std=c11 -O2 -I ./include -c -o build/freq.o src/freq.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/radsex-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -std=c11 -O2 -I ./include -c -o build/main.o src/main.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/radsex-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -std=c11 -O2 -I ./include -c -o build/map.o src/map.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/radsex-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -std=c11 -O2 -I ./include -c -o build/marker.o src/marker.cpp + In file included from src/marker.cpp:24: + src/marker.h:43:21: error: 'uint16_t' was not declared in this scope + 43 | std::vector individual_depths; ///< Vector storing marker depth in each individual (in order from the table's header) + | ^~~~~~~~ + src/marker.h:29:1: note: 'uint16_t' is defined in header ''; did you forget to '#include '? + 28 | #include + |#include + 29 | + src/marker.h:43:29: error: template argument 1 is invalid + 43 | std::vector individual_depths; ///< Vector storing marker depth in each individual (in order from the table's header) + | ^ + src/marker.h:43:29: error: template argument 2 is invalid + src/marker.h:63:24: error: expected ')' before 'n_individuals' + 63 | Marker(uint16_t n_individuals); + | ~ ^~~~~~~~~~~~~~ + | ) + src/marker.cpp:27:15: error: expected constructor, destructor, or type conversion before '(' token + 27 | Marker::Marker(uint16_t n_individuals) { + | ^ + src/marker.cpp: In member function 'void Marker::reset(bool)': + src/marker.cpp:47:34: error: 'begin' was not declared in this scope; did you mean 'std::begin'? + 47 | for (auto& individual: this->individual_depths) individual = 0; + | ^~~~~~~~~~~~~~~~~ + | std::begin + In file included from /opt/conda/conda-bld/radsex_1733854357966/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/string:53, + from /opt/conda/conda-bld/radsex_1733854357966/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/locale_classes.h:40, + from /opt/conda/conda-bld/radsex_1733854357966/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/ios_base.h:41, + from /opt/conda/conda-bld/radsex_1733854357966/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/ios:44, + from /opt/conda/conda-bld/radsex_1733854357966/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/istream:40, + from /opt/conda/conda-bld/radsex_1733854357966/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/fstream:40, + from src/marker.h:25: + /opt/conda/conda-bld/radsex_1733854357966/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/range_access.h:95:5: note: 'std::begin' declared here + 95 | begin(_Tp (&__arr)[_Nm]) noexcept + | ^~~~~ + src/marker.cpp:47:34: error: 'end' was not declared in this scope; did you mean 'std::end'? + 47 | for (auto& individual: this->individual_depths) individual = 0; + | ^~~~~~~~~~~~~~~~~ + | std::end + /opt/conda/conda-bld/radsex_1733854357966/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/range_access.h:106:5: note: 'std::end' declared here + 106 | end(_Tp (&__arr)[_Nm]) noexcept + | ^~~ + src/marker.cpp: In member function 'void Marker::output_as_table(std::ofstream&) const': + src/marker.cpp:59:34: error: 'begin' was not declared in this scope; did you mean 'std::begin'? + 59 | for (auto& individual: this->individual_depths) output_file << "\t" << individual; + | ^~~~~~~~~~~~~~~~~ + | std::begin + /opt/conda/conda-bld/radsex_1733854357966/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/range_access.h:95:5: note: 'std::begin' declared here + 95 | begin(_Tp (&__arr)[_Nm]) noexcept + | ^~~~~ + src/marker.cpp:59:34: error: 'end' was not declared in this scope; did you mean 'std::end'? + 59 | for (auto& individual: this->individual_depths) output_file << "\t" << individual; + | ^~~~~~~~~~~~~~~~~ + | std::end + /opt/conda/conda-bld/radsex_1733854357966/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/range_access.h:106:5: note: 'std::end' declared here + 106 | end(_Tp (&__arr)[_Nm]) noexcept + | ^~~ + make: *** [Makefile:90: build/marker.o] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/radsex_1733854357966/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/radsex_1733854357966/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/radsex/meta.yaml b/recipes/radsex/meta.yaml index 24fea4109ebb9..729e481169e7e 100644 --- a/recipes/radsex/meta.yaml +++ b/recipes/radsex/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 source: url: https://github.com/SexGenomicsToolkit/radsex/archive/{{ version }}.tar.gz diff --git a/recipes/radtk/meta.yaml b/recipes/radtk/meta.yaml index b3355c9314349..ce0e91663ed3f 100644 --- a/recipes/radtk/meta.yaml +++ b/recipes/radtk/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("radtk", max_pin="x.x") }} diff --git a/recipes/rainbow/meta.yaml b/recipes/rainbow/meta.yaml index 56388588fbf68..d041329985e26 100644 --- a/recipes/rainbow/meta.yaml +++ b/recipes/rainbow/meta.yaml @@ -6,7 +6,7 @@ source: md5: 1212af13c8a4ca241d9131789cea6a1f build: - number: 9 + number: 10 requirements: build: diff --git a/recipes/randfold/meta.yaml b/recipes/randfold/meta.yaml index 4e34b0a54989e..44a52ae10b9a9 100644 --- a/recipes/randfold/meta.yaml +++ b/recipes/randfold/meta.yaml @@ -3,7 +3,7 @@ package: version: 2.0.1 build: - number: 6 + number: 7 source: url: http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/randfold-2.0.1.tar.gz diff --git a/recipes/rapidnj/meta.yaml b/recipes/rapidnj/meta.yaml index 885e496afe478..9b0604d47bf4e 100644 --- a/recipes/rapidnj/meta.yaml +++ b/recipes/rapidnj/meta.yaml @@ -11,7 +11,7 @@ source: - rapidnj-aarch64.patch # [aarch64 or arm64] build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('rapidnj', max_pin="x") }} diff --git a/recipes/rapidshapes/build_failure.osx-64.yaml b/recipes/rapidshapes/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..fe3671472997b --- /dev/null +++ b/recipes/rapidshapes/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: d2ebf99291b435283b0fade852dd85098387407a1d221b16233db92ec02b006c # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rapidshapes-2.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rapidshapes-2.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + make: Entering directory '$SRC_DIR/Misc/Applications/RapidShapes' + if [ ! -f "x86_64-apple-darwin13.4.0/RapidShapes_pfall_nodangle" ]; then \ + make -C ../RNAshapes pfall_nodangle; \ + install -d $SRC_DIR/Misc/Applications/RapidShapes/x86_64-apple-darwin13.4.0; \ + install ../RNAshapes/x86_64-apple-darwin13.4.0/RNAshapes_pfall_nodangle x86_64-apple-darwin13.4.0/RapidShapes_pfall_nodangle; \ + fi; + if [ ! -f "x86_64-apple-darwin13.4.0/RapidShapes_pfall_overdangle" ]; then \ + make -C ../RNAshapes pfall_overdangle; \ + install -d $SRC_DIR/Misc/Applications/RapidShapes/x86_64-apple-darwin13.4.0; \ + install ../RNAshapes/x86_64-apple-darwin13.4.0/RNAshapes_pfall_overdangle x86_64-apple-darwin13.4.0/RapidShapes_pfall_overdangle; \ + fi; + make[1]: Entering directory '$SRC_DIR/Misc/Applications/RNAshapes' + make[1]: Entering directory '$SRC_DIR/Misc/Applications/RNAshapes' + make compile \ + gapc_product="alg_pfunc" \ + gapc_options="" \ + gapc_file="overdangle.gap" \ + gapc_binaryname="pfall_overdangle"; + make compile \ + gapc_product="alg_pfunc" \ + gapc_options="" \ + gapc_file="nodangle.gap" \ + gapc_binaryname="pfall_nodangle"; + make[2]: Entering directory '$SRC_DIR/Misc/Applications/RNAshapes' + make[2]: Entering directory '$SRC_DIR/Misc/Applications/RNAshapes' + if [ ! -f "x86_64-apple-darwin13.4.0/RNAshapes_pfall_overdangle" ]; then \ + cd /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.AxP1T9xy && gapc -I $SRC_DIR/Misc/Applications/RNAshapes/../../../ -p "alg_pfunc" $SRC_DIR/Misc/Applications/RNAshapes/../../..//overdangle.gap; \ + perl $SRC_DIR/Misc/Applications/RNAshapes/../../..///Misc/Applications/addRNAoptions.pl /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.AxP1T9xy/out.mf 0 'pfall_overdangle' 'alg_pfunc'; \ + cd /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.AxP1T9xy && make -f out.mf CPPFLAGS_EXTRA="-I $SRC_DIR/Misc/Applications/RNAshapes/../../../ -I ./" CXXFLAGS_EXTRA="-O3 -DNDEBUG" LDFLAGS_EXTRA=""; \ + install -d $SRC_DIR/Misc/Applications/RNAshapes/x86_64-apple-darwin13.4.0; \ + install /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.AxP1T9xy/out $SRC_DIR/Misc/Applications/RNAshapes/x86_64-apple-darwin13.4.0/RNAshapes_pfall_overdangle; \ + fi; + if [ ! -f "x86_64-apple-darwin13.4.0/RNAshapes_pfall_nodangle" ]; then \ + cd /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.r1QBeMNz && gapc -I $SRC_DIR/Misc/Applications/RNAshapes/../../../ -p "alg_pfunc" $SRC_DIR/Misc/Applications/RNAshapes/../../..//nodangle.gap; \ + perl $SRC_DIR/Misc/Applications/RNAshapes/../../..///Misc/Applications/addRNAoptions.pl /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.r1QBeMNz/out.mf 0 'pfall_nodangle' 'alg_pfunc'; \ + cd /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.r1QBeMNz && make -f out.mf CPPFLAGS_EXTRA="-I $SRC_DIR/Misc/Applications/RNAshapes/../../../ -I ./" CXXFLAGS_EXTRA="-O3 -DNDEBUG" LDFLAGS_EXTRA=""; \ + install -d $SRC_DIR/Misc/Applications/RNAshapes/x86_64-apple-darwin13.4.0; \ + install /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.r1QBeMNz/out $SRC_DIR/Misc/Applications/RNAshapes/x86_64-apple-darwin13.4.0/RNAshapes_pfall_nodangle; \ + fi; + make[3]: Entering directory '/private/var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.AxP1T9xy' + Including global makefile $PREFIX/share/gapc/config_darwin13.4.0.mf + make[3]: Entering directory '/private/var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.r1QBeMNz' + Including global makefile $PREFIX/share/gapc/config_darwin13.4.0.mf + echo '#include "out.hh"' > out_main.cc + echo '#include "out.hh"' > out_main.cc + cat $PREFIX/include/rtlib/generic_main.cc >> out_main.cc + cat $PREFIX/include/rtlib/generic_main.cc >> out_main.cc + $PREFIX/bin/sed -i 's|gapc::Opts opts;||' out_main.cc + $PREFIX/bin/sed -i 's|gapc::Opts opts;||' out_main.cc + $PREFIX/bin/sed -i 's|\([^_]\)opts\.|\1gapc::Opts::getOpts()->|g' out_main.cc + $PREFIX/bin/sed -i 's|\([^_]\)opts\.|\1gapc::Opts::getOpts()->|g' out_main.cc + $PREFIX/bin/sed -i 's|obj.init(opts);|obj.init(\*gapc::Opts::getOpts());|g' out_main.cc + $PREFIX/bin/sed -i 's|obj.init(opts);|obj.init(\*gapc::Opts::getOpts());|g' out_main.cc + $PREFIX/bin/sed -i 's|#include .rtlib/generic_opts.hh.|#include "Extensions/rnaoptions.hh"|' out_main.cc + $PREFIX/bin/sed -i 's|#include .rtlib/generic_opts.hh.|#include "Extensions/rnaoptions.hh"|' out_main.cc + $PREFIX/bin/sed -i 's%#include .rtlib/generic_opts.hh.%#include "Extensions/rnaoptions.hh"%' out.hh out.cc + $PREFIX/bin/sed -i 's%#include .rtlib/generic_opts.hh.%#include "Extensions/rnaoptions.hh"%' out.hh out.cc + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bellmans-gapc_1721071508431/work=/usr/local/src/conda/bellmans-gapc-2024.01.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -MMD -MP -Wall -Wnon-virtual-dtor -Wno-unused-variable -Wno-parentheses -DNDEBUG -DBISONNEW -O3 -DNDEBUG -DWITH_RNAOPTIONS -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I $SRC_DIR/Misc/Applications/RNAshapes/../../../ -I ./ -I$PREFIX/include -I$PREFIX/include/ -I$PREFIX/include/rtlib -I$PREFIX/include/librna -c -o out.o out.cc + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bellmans-gapc_1721071508431/work=/usr/local/src/conda/bellmans-gapc-2024.01.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -MMD -MP -Wall -Wnon-virtual-dtor -Wno-unused-variable -Wno-parentheses -DNDEBUG -DBISONNEW -O3 -DNDEBUG -DWITH_RNAOPTIONS -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I $SRC_DIR/Misc/Applications/RNAshapes/../../../ -I ./ -I$PREFIX/include -I$PREFIX/include/ -I$PREFIX/include/rtlib -I$PREFIX/include/librna -c -o out.o out.cc + make[3]: Leaving directory '/private/var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.r1QBeMNz' + make[3]: Leaving directory '/private/var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.AxP1T9xy' + make[2]: Leaving directory '$SRC_DIR/Misc/Applications/RNAshapes' + make[2]: Leaving directory '$SRC_DIR/Misc/Applications/RNAshapes' + make[1]: Leaving directory '$SRC_DIR/Misc/Applications/RNAshapes' + make[1]: Leaving directory '$SRC_DIR/Misc/Applications/RNAshapes' + make: Leaving directory '$SRC_DIR/Misc/Applications/RapidShapes' +# Last 100 lines of the build log. diff --git a/recipes/rapidshapes/meta.yaml b/recipes/rapidshapes/meta.yaml index 4d47e3bf59d6d..1f5db9e24584d 100644 --- a/recipes/rapidshapes/meta.yaml +++ b/recipes/rapidshapes/meta.yaml @@ -15,7 +15,7 @@ source: url: https://github.com/jlab/fold-grammars/archive/refs/tags/{{ fold_grammars_version }}.tar.gz build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('rapidshapes', max_pin="x") }} diff --git a/recipes/rapifilt/meta.yaml b/recipes/rapifilt/meta.yaml index 29e5d7fe32456..a5113e6e53a7a 100644 --- a/recipes/rapifilt/meta.yaml +++ b/recipes/rapifilt/meta.yaml @@ -9,7 +9,7 @@ source: sha256: f25f93c278bbbed666351c403e37ee49d67399b0b490adb90546e325c198da3f build: - number: 6 + number: 7 skip: True # [osx] requirements: diff --git a/recipes/rapmap/meta.yaml b/recipes/rapmap/meta.yaml index 0de21af6f9de9..ca3a13f440711 100644 --- a/recipes/rapmap/meta.yaml +++ b/recipes/rapmap/meta.yaml @@ -27,7 +27,7 @@ requirements: - bzip2 build: - number: 5 + number: 6 #skip: True # [osx] about: diff --git a/recipes/raptor/meta.yaml b/recipes/raptor/meta.yaml index cf815b6a65db9..d762f52ad6869 100644 --- a/recipes/raptor/meta.yaml +++ b/recipes/raptor/meta.yaml @@ -10,7 +10,7 @@ source: sha256: be44e7b2635e110c940cf40ff132956200551a2e25765d9f057e844f7a3ccebb build: - number: 2 + number: 3 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin='x') }} diff --git a/recipes/rascaf/meta.yaml b/recipes/rascaf/meta.yaml index b3f2d2c5c4e2d..eeace467d33c6 100644 --- a/recipes/rascaf/meta.yaml +++ b/recipes/rascaf/meta.yaml @@ -7,7 +7,7 @@ package: build: # scaffold.hpp:722:32: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal] skip: True # [osx] - number: 6 + number: 7 source: url: https://github.com/mourisl/Rascaf/archive/ed779e100853977307bbdc01c1644390d8556a7b.tar.gz diff --git a/recipes/rasusa/meta.yaml b/recipes/rasusa/meta.yaml index 33a3a87765c19..071b3202820e0 100644 --- a/recipes/rasusa/meta.yaml +++ b/recipes/rasusa/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 6d6d97f381bea5a4d070ef7bc132224f3c5c97bc366109261182aa9bc5736d69 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('rasusa', max_pin="x.x") }} diff --git a/recipes/ratatosk/meta.yaml b/recipes/ratatosk/meta.yaml index 1a89715c74931..f00696553911f 100644 --- a/recipes/ratatosk/meta.yaml +++ b/recipes/ratatosk/meta.yaml @@ -16,7 +16,7 @@ source: folder: Bifrost build: - number: 1 + number: 2 skip: True # [osx] run_exports: - {{ pin_subpackage('ratatosk', max_pin="x.x") }} diff --git a/recipes/raven-assembler/meta.yaml b/recipes/raven-assembler/meta.yaml index 3e128de7c38a4..82df0bebce548 100644 --- a/recipes/raven-assembler/meta.yaml +++ b/recipes/raven-assembler/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin='x') }} diff --git a/recipes/raxml-ng/meta.yaml b/recipes/raxml-ng/meta.yaml index f86629d2e50cf..82ae46576ed84 100644 --- a/recipes/raxml-ng/meta.yaml +++ b/recipes/raxml-ng/meta.yaml @@ -10,7 +10,7 @@ source: sha256: ad22a51c74f4dbfdbf99c06f652d6dad824f7d072c82782db07587140a7bef82 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('raxml-ng', max_pin="x") }} diff --git a/recipes/raxml/8.2.4/meta.yaml b/recipes/raxml/8.2.4/meta.yaml index b38acc3ef5638..f393d6328d2ae 100644 --- a/recipes/raxml/8.2.4/meta.yaml +++ b/recipes/raxml/8.2.4/meta.yaml @@ -3,7 +3,7 @@ package: version: "8.2.4" build: - number: 7 + number: 8 source: url: https://github.com/stamatak/standard-RAxML/archive/v8.2.4.tar.gz diff --git a/recipes/raxml/8.2.9/meta.yaml b/recipes/raxml/8.2.9/meta.yaml index 39e453e94d5fa..978756723077e 100644 --- a/recipes/raxml/8.2.9/meta.yaml +++ b/recipes/raxml/8.2.9/meta.yaml @@ -3,7 +3,7 @@ package: version: "8.2.9" build: - number: 7 + number: 8 source: url: https://github.com/stamatak/standard-RAxML/archive/v8.2.9.tar.gz diff --git a/recipes/raxml/meta.yaml b/recipes/raxml/meta.yaml index b7e8de64fbd89..3c611473a1a0d 100644 --- a/recipes/raxml/meta.yaml +++ b/recipes/raxml/meta.yaml @@ -3,7 +3,7 @@ package: version: "8.2.13" build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('raxml', max_pin="x") }} diff --git a/recipes/ray/meta.yaml b/recipes/ray/meta.yaml index 8f30c07cc6229..1dc62d971909a 100644 --- a/recipes/ray/meta.yaml +++ b/recipes/ray/meta.yaml @@ -10,7 +10,7 @@ source: md5: 82f693c4db60af4328263c9279701009 build: - number: 6 + number: 7 skip: True # [osx] requirements: diff --git a/recipes/razers3/build_failure.osx-64.yaml b/recipes/razers3/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..7d587f1d06f5c --- /dev/null +++ b/recipes/razers3/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 6e633caca670dbc7499095d9c59de6eabbc8d4d5065a04ac2cf6e300938573fb # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + -- Intel Software Development Emulator not found, not building platform emulated tests. + -- Intel Software Development Emulator not found, not building platform emulated tests. + -- Configuring tests/align_profile + -- Configuring tests/align_split + -- Configuring tests/alignment_free + -- Configuring tests/arg_parse + -- Configuring tests/bam_io + -- Configuring tests/basic + -- Configuring tests/bed_io + -- Configuring tests/blast + -- Configuring tests/consensus + -- Configuring tests/consensus_v2 + -- Configuring tests/find + -- Configuring tests/gff_io + -- Configuring tests/graph_algorithms + -- Configuring tests/graph_align + -- Configuring tests/graph_msa + -- Configuring tests/graph_types + -- Configuring tests/index + -- Configuring tests/journaled_set + -- Configuring tests/journaled_string_tree + -- Configuring tests/map + -- Configuring tests/misc + -- Configuring tests/modifier + -- Configuring tests/modifier_cyclic_shape + -- Configuring tests/multiple_translation_units + -- Configuring tests/parallel + -- Configuring tests/parse_lm + -- Configuring tests/pipe + -- Configuring tests/platform + -- Configuring tests/random + -- Configuring tests/realign + -- Configuring tests/reduced_aminoacid + -- Configuring tests/rna_io + -- Configuring tests/roi_io + -- Configuring tests/score + -- Configuring tests/seeds + -- Configuring tests/seq_io + -- Configuring tests/sequence + -- Configuring tests/sequence_journaled + -- Configuring tests/simd + -- Could NOT find SDE: Intel(R) Software Development Emulator (sde) (missing: SDE_EXECUTABLE SDE_VERSION_STRING) + -- Could NOT find Umesimd (missing: UMESIMD_INCLUDE_DIR) + -- Intel Software Development Emulator not found, not building platform emulated tests. + -- Configuring tests/simple_intervals_io + -- Configuring tests/statistics + -- Configuring tests/store + -- Configuring tests/stream + -- Configuring tests/find_swift + -- Configuring tests/tabix_io + -- Configuring tests/translation + -- Configuring tests/test_ucsc_io + -- Configuring tests/vcf_io + -- Configuring demos + -- Found PythonInterp: /opt/mambaforge/envs/bioconda/bin/python (found suitable version "3.10.16", minimum required is "2.7") + -- Configuring manual + -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE) + -- Sphinx not found, not building sphinx manual as a test. + -- Configuring dox + -- You need Python 2.x for building dox. (skip the tests) + -- Configuring util/py_lib + -- Python nosetests ('import nose' failed), cannot add tests for seqan.dox + -- Configuring apps + -- Configuring apps/alf + -- Configuring apps/bs_tools + -- Boost or zlib not found: Not building bs_tools. + -- Configuring apps/dfi + -- Configuring apps/fiona + -- Boost or OpenMP not found, not building fiona. + -- Configuring apps/fx_tools + -- Configuring apps/gustaf + -- Configuring apps/insegt + -- Configuring apps/mason2 + -- Configuring apps/micro_razers + -- Configuring apps/ngs_roi + -- Configuring apps/pair_align + -- Configuring apps/param_chooser + -- Configuring apps/rabema + -- Configuring apps/razers + -- Configuring apps/razers3 + -- Configuring apps/rep_sep + -- Configuring apps/sak + -- Configuring apps/sam2matrix + -- Configuring apps/samcat + -- Configuring apps/searchjoin + -- Configuring apps/seqan_tcoffee + -- Configuring apps/seqcons2 + -- Configuring apps/sgip + -- Configuring apps/snp_store + -- Boost or zlib not found: Not building snp_store. + -- Configuring apps/splazers + -- Configuring apps/stellar + -- Configuring apps/tree_recon + -- Configuring apps/yara + -- Configuring done (48.2s) + -- Generating done (5.4s) + -- Build files have been written to: $SRC_DIR/build + Built target seqan_library + Building CXX object apps/razers3/CMakeFiles/razers3.dir/param_tabs.cpp.o + Building CXX object apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/razers3/meta.yaml b/recipes/razers3/meta.yaml index 8ad0eed646ccc..8b594931fc896 100644 --- a/recipes/razers3/meta.yaml +++ b/recipes/razers3/meta.yaml @@ -10,7 +10,7 @@ source: sha256: d7084d17729214003e84818e0280a16f223c8f1c6a30eeef040c27e0c0047bd7 build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('razers3', max_pin="x") }} diff --git a/recipes/rcorrector/meta.yaml b/recipes/rcorrector/meta.yaml index 5d667d2952db5..278fafd7f8570 100644 --- a/recipes/rcorrector/meta.yaml +++ b/recipes/rcorrector/meta.yaml @@ -10,7 +10,7 @@ source: sha256: cc1a9e82056bdc717b7ac40729c90573caad371899f9a1c61c25b50f019fbedb build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('rcorrector', max_pin="x") }} diff --git a/recipes/rdeval/build_failure.linux-64.yaml b/recipes/rdeval/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..6d8aeff9481d0 --- /dev/null +++ b/recipes/rdeval/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 42499ee1bbfd0979cef15316f5fd696068587a7666ed575b336ecad5afd7f6c0 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + 2024-12-11T16:57:32 noarch Writing patched repodata + 2024-12-11T16:57:32 noarch Building current_repodata subset + 2024-12-11T16:57:32 noarch Writing current_repodata subset + 2024-12-11T16:57:32 noarch Writing index HTML + /opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (/opt/recipe/meta.yaml). + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml + Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for rdeval + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['rdeval-0.0.2-h077b44d_2.tar.bz2'] + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/rdeval_1733936252875/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libzlib: 1.3.1-hb9d3cd8_2 conda-forge + zlib: 1.3.1-hb9d3cd8_2 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/rdeval_1733936252875/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.43-h4bf12b8_2 conda-forge + binutils_linux-64: 2.43-h4852527_2 conda-forge + gcc_impl_linux-64: 13.3.0-hfea6d02_1 conda-forge + gcc_linux-64: 13.3.0-hc28eda2_7 conda-forge + gxx_impl_linux-64: 13.3.0-hdbfa832_1 conda-forge + gxx_linux-64: 13.3.0-h6834431_7 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libsanitizer: 13.3.0-heb74ff8_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + make: 4.4.1-hb9d3cd8_2 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: rdeval.v0.0.2-with_submodules_56c2f4d7d2.zip + Downloading https://github.com/vgl-hub/rdeval/releases/download/v0.0.2/rdeval.v0.0.2-with_submodules.zip + Success + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 125, in download_to_cache + raise RuntimeError( + RuntimeError: SHA256 mismatch: 'd3cb543a43e6835461535325aacd215960ef616c278bc77cf7f7adeb96bf2446' != '56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d' +# Last 100 lines of the build log. diff --git a/recipes/rdeval/build_failure.linux-aarch64.yaml b/recipes/rdeval/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..7043d8a29e1cb --- /dev/null +++ b/recipes/rdeval/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 42499ee1bbfd0979cef15316f5fd696068587a7666ed575b336ecad5afd7f6c0 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + 2024-12-10T17:23:35 linux-64 Writing current_repodata subset + 2024-12-10T17:23:35 linux-64 Writing index HTML + 2024-12-10T17:23:35 noarch Writing current_repodata subset + 2024-12-10T17:23:35 noarch Writing index HTML + 2024-12-10T17:23:35 linux-aarch64 Writing current_repodata subset + 2024-12-10T17:23:35 linux-aarch64 Writing index HTML + /opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (/opt/recipe/meta.yaml). + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml + Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for rdeval + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['rdeval-0.0.2-h1e84f2d_2.tar.bz2'] + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/rdeval_1733851416889/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + + + The following NEW packages will be INSTALLED: + + _openmp_mutex: 4.5-2_gnu conda-forge + libgcc: 14.2.0-he277a41_1 conda-forge + libgomp: 14.2.0-he277a41_1 conda-forge + libstdcxx: 14.2.0-h3f4de04_1 conda-forge + libzlib: 1.3.1-h86ecc28_2 conda-forge + zlib: 1.3.1-h86ecc28_2 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/rdeval_1733851416889/_build_env + + + The following NEW packages will be INSTALLED: + + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-aarch64: 2.43-h4c662bb_2 conda-forge + binutils_linux-aarch64: 2.43-hf1166c9_2 conda-forge + gcc_impl_linux-aarch64: 13.3.0-hcdea9b6_1 conda-forge + gcc_linux-aarch64: 13.3.0-h1cd514b_7 conda-forge + gxx_impl_linux-aarch64: 13.3.0-h1211b58_1 conda-forge + gxx_linux-aarch64: 13.3.0-h2864abd_7 conda-forge + kernel-headers_linux-aarch64: 4.18.0-h05a177a_18 conda-forge + ld_impl_linux-aarch64: 2.43-h80caac9_2 conda-forge + libgcc: 14.2.0-he277a41_1 conda-forge + libgcc-devel_linux-aarch64: 13.3.0-h0c07274_101 conda-forge + libgomp: 14.2.0-he277a41_1 conda-forge + libsanitizer: 13.3.0-ha58e236_1 conda-forge + libstdcxx: 14.2.0-h3f4de04_1 conda-forge + libstdcxx-devel_linux-aarch64: 13.3.0-h0c07274_101 conda-forge + make: 4.4.1-h2a6d0cb_2 conda-forge + sysroot_linux-aarch64: 2.17-h5b4a56d_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: rdeval.v0.0.2-with_submodules_56c2f4d7d2.zip + Downloading https://github.com/vgl-hub/rdeval/releases/download/v0.0.2/rdeval.v0.0.2-with_submodules.zip + Success + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 125, in download_to_cache + raise RuntimeError( + RuntimeError: SHA256 mismatch: 'd3cb543a43e6835461535325aacd215960ef616c278bc77cf7f7adeb96bf2446' != '56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d' +# Last 100 lines of the build log. diff --git a/recipes/rdeval/build_failure.osx-64.yaml b/recipes/rdeval/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c72468886192c --- /dev/null +++ b/recipes/rdeval/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 42499ee1bbfd0979cef15316f5fd696068587a7666ed575b336ecad5afd7f6c0 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/mambaforge/envs/bioconda/conda_build_config.yaml + Adding in variants from /opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for rdeval + Reloading output folder (local): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (local): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (local): ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['rdeval-0.0.2-h2ec61ea_2.tar.bz2'] + Reloading output folder (local): ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/rdeval_1733868175370/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + + + The following NEW packages will be INSTALLED: + + libcxx: 19.1.5-hf95d169_0 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + zlib: 1.3.1-hd23fc13_2 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (local): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (local): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/rdeval_1733868175370/_build_env + + + The following NEW packages will be INSTALLED: + + ca-certificates: 2024.8.30-h8857fd0_0 conda-forge + cctools_osx-64: 1010.6-h00edd4c_2 conda-forge + clang: 18.1.8-default_h179603d_5 conda-forge + clang-18: 18.1.8-default_h0c94c6a_5 conda-forge + clang_impl_osx-64: 18.1.8-h6a44ed1_23 conda-forge + clang_osx-64: 18.1.8-h7e5c614_23 conda-forge + clangxx: 18.1.8-default_h179603d_5 conda-forge + clangxx_impl_osx-64: 18.1.8-h4b7810f_23 conda-forge + clangxx_osx-64: 18.1.8-h7e5c614_23 conda-forge + compiler-rt: 18.1.8-h1020d70_1 conda-forge + compiler-rt_osx-64: 18.1.8-hf2b8a54_1 conda-forge + ld64_osx-64: 951.9-hc8d1a19_2 conda-forge + libclang-cpp18.1: 18.1.8-default_h0c94c6a_5 conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libcxx-devel: 18.1.8-h7c275be_7 conda-forge + libiconv: 1.17-hd75f5a5_2 conda-forge + libllvm18: 18.1.8-h9ce406d_2 conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libxml2: 2.13.5-he8ee3e7_1 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-tools: 18.1.8-h9ce406d_2 conda-forge + llvm-tools-18: 18.1.8-h9ce406d_2 conda-forge + make: 4.4.1-h00291cd_2 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + sigtool: 0.1.3-h88f4db0_0 conda-forge + tapi: 1300.6.5-h390ca13_0 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache + Downloading source to cache: rdeval.v0.0.2-with_submodules_56c2f4d7d2.zip + Downloading https://github.com/vgl-hub/rdeval/releases/download/v0.0.2/rdeval.v0.0.2-with_submodules.zip + Success + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 125, in download_to_cache + raise RuntimeError( + RuntimeError: SHA256 mismatch: 'd3cb543a43e6835461535325aacd215960ef616c278bc77cf7f7adeb96bf2446' != '56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d' +# Last 100 lines of the build log. diff --git a/recipes/rdeval/build_failure.osx-arm64.yaml b/recipes/rdeval/build_failure.osx-arm64.yaml new file mode 100644 index 0000000000000..92d31a1bd4cfb --- /dev/null +++ b/recipes/rdeval/build_failure.osx-arm64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 42499ee1bbfd0979cef15316f5fd696068587a7666ed575b336ecad5afd7f6c0 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/mambaforge/envs/bioconda/conda_build_config.yaml + Adding in variants from /opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for rdeval + Reloading output folder (local): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (local): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (local): ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['rdeval-0.0.2-hda5e58c_2.tar.bz2'] + Reloading output folder (local): ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/rdeval_1733970186660/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + + + The following NEW packages will be INSTALLED: + + libcxx: 19.1.5-ha82da77_0 conda-forge + libzlib: 1.3.1-h8359307_2 conda-forge + zlib: 1.3.1-h8359307_2 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (local): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (local): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/rdeval_1733970186660/_build_env + + + The following NEW packages will be INSTALLED: + + ca-certificates: 2024.8.30-hf0a4a13_0 conda-forge + cctools_osx-arm64: 1010.6-h908b477_2 conda-forge + clang: 18.1.8-default_h675cc0c_5 conda-forge + clang-18: 18.1.8-default_h5c12605_5 conda-forge + clang_impl_osx-arm64: 18.1.8-h2ae9ea5_23 conda-forge + clang_osx-arm64: 18.1.8-h07b0088_23 conda-forge + clangxx: 18.1.8-default_h675cc0c_5 conda-forge + clangxx_impl_osx-arm64: 18.1.8-h555f467_23 conda-forge + clangxx_osx-arm64: 18.1.8-h07b0088_23 conda-forge + compiler-rt: 18.1.8-h856b3c1_1 conda-forge + compiler-rt_osx-arm64: 18.1.8-h832e737_1 conda-forge + icu: 75.1-hfee45f7_0 conda-forge + ld64_osx-arm64: 951.9-hfc0fa09_2 conda-forge + libclang-cpp18.1: 18.1.8-default_h5c12605_5 conda-forge + libcxx: 19.1.5-ha82da77_0 conda-forge + libcxx-devel: 18.1.8-h6dc3340_7 conda-forge + libiconv: 1.17-h0d3ecfb_2 conda-forge + libllvm18: 18.1.8-h5090b49_2 conda-forge + liblzma: 5.6.3-h39f12f2_1 conda-forge + libxml2: 2.13.5-h178c5d8_1 conda-forge + libzlib: 1.3.1-h8359307_2 conda-forge + llvm-tools: 18.1.8-h5090b49_2 conda-forge + llvm-tools-18: 18.1.8-h5090b49_2 conda-forge + make: 4.4.1-hc9fafa5_2 conda-forge + ncurses: 6.5-h7bae524_1 conda-forge + openssl: 3.4.0-h39f12f2_0 conda-forge + sigtool: 0.1.3-h44b9a77_0 conda-forge + tapi: 1300.6.5-h03f4b80_0 conda-forge + zstd: 1.5.6-hb46c0d2_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache + Downloading source to cache: rdeval.v0.0.2-with_submodules_56c2f4d7d2.zip + Downloading https://github.com/vgl-hub/rdeval/releases/download/v0.0.2/rdeval.v0.0.2-with_submodules.zip + Success + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 125, in download_to_cache + raise RuntimeError( + RuntimeError: SHA256 mismatch: 'd3cb543a43e6835461535325aacd215960ef616c278bc77cf7f7adeb96bf2446' != '56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d' +# Last 100 lines of the build log. diff --git a/recipes/read-it-and-keep/meta.yaml b/recipes/read-it-and-keep/meta.yaml index b17767ca303e5..1034a6c882dc4 100644 --- a/recipes/read-it-and-keep/meta.yaml +++ b/recipes/read-it-and-keep/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 source: url: https://github.com/GenomePathogenAnalysisService/read-it-and-keep/archive/refs/tags/v{{ version }}.tar.gz diff --git a/recipes/readfq/meta.yaml b/recipes/readfq/meta.yaml index 47afdc1db6e42..3f0c9c76a2d1f 100644 --- a/recipes/readfq/meta.yaml +++ b/recipes/readfq/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 5 + number: 6 skip: True # [osx] source: diff --git a/recipes/reads2graph/meta.yaml b/recipes/reads2graph/meta.yaml index 2bc392ca9fd41..23f32e4595b1d 100644 --- a/recipes/reads2graph/meta.yaml +++ b/recipes/reads2graph/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -54,4 +54,4 @@ extra: identifiers: - biotools:reads2graph recipe-maintainers: - - Jappy0 \ No newline at end of file + - Jappy0 diff --git a/recipes/recgraph/meta.yaml b/recipes/recgraph/meta.yaml index 227ff06ebd53e..ab2bb0c27a7d7 100644 --- a/recipes/recgraph/meta.yaml +++ b/recipes/recgraph/meta.yaml @@ -12,7 +12,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} diff --git a/recipes/recon/build_failure.linux-64.yaml b/recipes/recon/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..b8eb8d6b21b55 --- /dev/null +++ b/recipes/recon/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 209414e987db713720eb714953cc3e1520b2e66d0e2c57b836082a65c39da0f8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + 2024-12-15T20:09:49 linux-aarch64 Writing index HTML + 2024-12-15T20:09:49 Subdir: noarch Gathering repodata + 2024-12-15T20:09:49 noarch Writing pre-patch repodata + 2024-12-15T20:09:49 noarch Applying patch instructions + 2024-12-15T20:09:49 noarch Writing patched repodata + 2024-12-15T20:09:49 noarch Building current_repodata subset + 2024-12-15T20:09:49 noarch Writing current_repodata subset + 2024-12-15T20:09:49 noarch Writing index HTML + /opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (/opt/recipe/meta.yaml). + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml + Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for recon + Reloading output folder: ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder: ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['recon-1.08-h7b50bb2_8.tar.bz2'] + Reloading output folder: ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/recon_1734293390366/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder: ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder: ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/recon_1734293390366/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.43-h4bf12b8_2 conda-forge + binutils_linux-64: 2.43-h4852527_2 conda-forge + gcc_impl_linux-64: 13.3.0-hfea6d02_1 conda-forge + gcc_linux-64: 13.3.0-hc28eda2_7 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libsanitizer: 13.3.0-heb74ff8_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + make: 4.4.1-hb9d3cd8_2 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: RECON-1.08_699765fa49.tar.gz + Downloading http://www.repeatmasker.org/RepeatModeler/RECON-1.08.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.242765 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download http://www.repeatmasker.org/RepeatModeler/RECON-1.08.tar.gz +# Last 100 lines of the build log. +category: |- + source download error diff --git a/recipes/recon/build_failure.linux-aarch64.yaml b/recipes/recon/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..232b6ecb5843f --- /dev/null +++ b/recipes/recon/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 209414e987db713720eb714953cc3e1520b2e66d0e2c57b836082a65c39da0f8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + 2024-12-15T13:58:59 linux-aarch64 Writing patched repodata + 2024-12-15T13:58:59 noarch Writing patched repodata + 2024-12-15T13:58:59 linux-aarch64 Building current_repodata subset + 2024-12-15T13:58:59 noarch Building current_repodata subset + 2024-12-15T13:58:59 linux-64 Writing current_repodata subset + 2024-12-15T13:58:59 linux-64 Writing index HTML + 2024-12-15T13:58:59 linux-aarch64 Writing current_repodata subset + 2024-12-15T13:58:59 noarch Writing current_repodata subset + 2024-12-15T13:58:59 linux-aarch64 Writing index HTML + 2024-12-15T13:58:59 noarch Writing index HTML + /opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (/opt/recipe/meta.yaml). + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml + Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for recon + Reloading output folder: ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder: ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['recon-1.08-h661a7b0_8.tar.bz2'] + Reloading output folder: ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/recon_1734271140604/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + + + The following NEW packages will be INSTALLED: + + _openmp_mutex: 4.5-2_gnu conda-forge + libgcc: 14.2.0-he277a41_1 conda-forge + libgomp: 14.2.0-he277a41_1 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder: ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder: ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/recon_1734271140604/_build_env + + + The following NEW packages will be INSTALLED: + + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-aarch64: 2.43-h4c662bb_2 conda-forge + binutils_linux-aarch64: 2.43-hf1166c9_2 conda-forge + gcc_impl_linux-aarch64: 13.3.0-hcdea9b6_1 conda-forge + gcc_linux-aarch64: 13.3.0-h1cd514b_7 conda-forge + kernel-headers_linux-aarch64: 4.18.0-h05a177a_18 conda-forge + ld_impl_linux-aarch64: 2.43-h80caac9_2 conda-forge + libgcc: 14.2.0-he277a41_1 conda-forge + libgcc-devel_linux-aarch64: 13.3.0-h0c07274_101 conda-forge + libgomp: 14.2.0-he277a41_1 conda-forge + libsanitizer: 13.3.0-ha58e236_1 conda-forge + libstdcxx: 14.2.0-h3f4de04_1 conda-forge + make: 4.4.1-h2a6d0cb_2 conda-forge + sysroot_linux-aarch64: 2.17-h5b4a56d_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: RECON-1.08_699765fa49.tar.gz + Downloading http://www.repeatmasker.org/RepeatModeler/RECON-1.08.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.275285 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download http://www.repeatmasker.org/RepeatModeler/RECON-1.08.tar.gz +# Last 100 lines of the build log. +category: |- + source download error diff --git a/recipes/recon/build_failure.osx-64.yaml b/recipes/recon/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..4715d4e4aec9a --- /dev/null +++ b/recipes/recon/build_failure.osx-64.yaml @@ -0,0 +1,88 @@ +recipe_sha: 209414e987db713720eb714953cc3e1520b2e66d0e2c57b836082a65c39da0f8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + /opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (recipes/recon/meta.yaml). + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/mambaforge/envs/bioconda/conda_build_config.yaml + Adding in variants from /opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for recon + Reloading output folder (local): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (local): ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['recon-1.08-h18d8cf3_8.tar.bz2'] + Reloading output folder (local): ...working... done + Solving environment (_build_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/recon_1734296411577/_build_env + + + The following NEW packages will be INSTALLED: + + ca-certificates: 2024.12.14-h8857fd0_0 conda-forge + cctools_osx-64: 1010.6-h00edd4c_2 conda-forge + clang: 18.1.8-default_h179603d_5 conda-forge + clang-18: 18.1.8-default_h0c94c6a_5 conda-forge + clang_impl_osx-64: 18.1.8-h6a44ed1_23 conda-forge + clang_osx-64: 18.1.8-h7e5c614_23 conda-forge + clangxx: 18.1.8-default_h179603d_5 conda-forge + compiler-rt: 18.1.8-h1020d70_1 conda-forge + compiler-rt_osx-64: 18.1.8-hf2b8a54_1 conda-forge + ld64_osx-64: 951.9-hc8d1a19_2 conda-forge + libclang-cpp18.1: 18.1.8-default_h0c94c6a_5 conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libcxx-devel: 18.1.8-h7c275be_7 conda-forge + libiconv: 1.17-hd75f5a5_2 conda-forge + libllvm18: 18.1.8-h9ce406d_2 conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libxml2: 2.13.5-he8ee3e7_1 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-tools: 18.1.8-h9ce406d_2 conda-forge + llvm-tools-18: 18.1.8-h9ce406d_2 conda-forge + make: 4.4.1-h00291cd_2 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + sigtool: 0.1.3-h88f4db0_0 conda-forge + tapi: 1300.6.5-h390ca13_0 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache + Downloading source to cache: RECON-1.08_699765fa49.tar.gz + Downloading http://www.repeatmasker.org/RepeatModeler/RECON-1.08.tar.gz + WARNING: Error: HTTP 404 NOT FOUND for url + Elapsed: 00:00.220142 + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download http://www.repeatmasker.org/RepeatModeler/RECON-1.08.tar.gz +# Last 100 lines of the build log. +category: |- + source download error diff --git a/recipes/recon/meta.yaml b/recipes/recon/meta.yaml index 2c77d6a9ba408..9b31d4de37e8f 100644 --- a/recipes/recon/meta.yaml +++ b/recipes/recon/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 699765fa49d18dbfac9f7a82ecd054464b468cb7521abe9c2bd8caccf08ee7d8 build: - number: 7 + number: 8 run_exports: - {{ pin_subpackage('recon', max_pin="x") }} @@ -30,4 +30,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/red/meta.yaml b/recipes/red/meta.yaml index d7866bff33ce6..8515ce7e9bd37 100644 --- a/recipes/red/meta.yaml +++ b/recipes/red/meta.yaml @@ -14,7 +14,7 @@ source: - makefile.patch build: - number: 2 + number: 3 skip: True # [osx] requirements: diff --git a/recipes/reduce/meta.yaml b/recipes/reduce/meta.yaml index f7b252312ff77..584d9596e42cb 100644 --- a/recipes/reduce/meta.yaml +++ b/recipes/reduce/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 62e61cce221fff76b5834031302d91fe703a19945a42e16620d4fb860604daf4 build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -47,4 +47,4 @@ extra: - linux-aarch64 - osx-arm64 recipe-maintainers: - - eunos-1128 \ No newline at end of file + - eunos-1128 diff --git a/recipes/reffinder/meta.yaml b/recipes/reffinder/meta.yaml index 9f50e1e0a1862..74fb9e28a5130 100644 --- a/recipes/reffinder/meta.yaml +++ b/recipes/reffinder/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 skip: false requirements: diff --git a/recipes/regenie/meta.yaml b/recipes/regenie/meta.yaml index a26632ba592ce..d810a179e52b6 100644 --- a/recipes/regenie/meta.yaml +++ b/recipes/regenie/meta.yaml @@ -14,7 +14,7 @@ source: - patches/0015-update-cmakelist.txt-for-v3.6.patch build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('regenie', max_pin="x") }} diff --git a/recipes/regtools/build_failure.osx-64.yaml b/recipes/regtools/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..73d9073cdfbdd --- /dev/null +++ b/recipes/regtools/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 0a7619a809939f145eb3d8948114ba7fe0e99fbff73276583cfa2b737f0869eb # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/regtools-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/regtools-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + -- The C compiler identification is Clang 18.1.8 + -- The CXX compiler identification is Clang 18.1.8 + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped + -- Detecting C compile features + -- Detecting C compile features - done + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Found ZLIB: $PREFIX/lib/libz.dylib (found version "1.3.1") + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success + -- Found Threads: TRUE + -- Found PythonInterp: /opt/mambaforge/envs/bioconda/bin/python (found version "3.10.16") + -- Configuring done (7.8s) + -- Generating done (0.3s) + -- Build files have been written to: $SRC_DIR/build + [ 1%] Building CXX object src/utils/bedtools/CMakeFiles/bedtools.dir/gzstream/gzstream.C.o + [ 2%] Building CXX object src/variants/CMakeFiles/variants.dir/variants_main.cc.o + [ 3%] Building C object src/utils/samtools/CMakeFiles/samtools.dir/bam_md.c.o + [ 4%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/bgzf.c.o + [ 4%] Building C object src/utils/samtools/CMakeFiles/samtools.dir/bam_aux.c.o + [ 4%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/faidx.c.o + [ 5%] Building C object src/utils/samtools/CMakeFiles/samtools.dir/bam2bcf.c.o + [ 6%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/hts.c.o + [ 6%] Building C object src/utils/samtools/CMakeFiles/samtools.dir/bam2bcf_indel.c.o + [ 6%] Building CXX object src/utils/bedtools/CMakeFiles/bedtools.dir/fileType/fileType.cpp.o + [ 7%] Building C object src/utils/samtools/CMakeFiles/samtools.dir/bamtk.c.o + [ 7%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/hfile.c.o + [ 7%] Building C object src/utils/samtools/CMakeFiles/samtools.dir/bedidx.c.o + [ 8%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/hfile_net.c.o + [ 9%] Building C object src/utils/samtools/CMakeFiles/samtools.dir/errmod.c.o + [ 9%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/kfunc.c.o + [ 10%] Building CXX object src/utils/bedtools/CMakeFiles/bedtools.dir/bedFile/bedFile.cpp.o + [ 10%] Building C object src/utils/samtools/CMakeFiles/samtools.dir/kprobaln.c.o + [ 11%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/kstring.c.o + [ 11%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/knetfile.c.o + [ 12%] Building C object src/utils/samtools/CMakeFiles/samtools.dir/sample.c.o + [ 13%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/md5.c.o + [ 13%] Building C object src/utils/samtools/CMakeFiles/samtools.dir/sam_opts.c.o + [ 13%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/synced_bcf_reader.c.o + [ 14%] Building C object src/utils/samtools/CMakeFiles/samtools.dir/bam_plcmd.c.o + [ 15%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/tbx.c.o + [ 15%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/vcf.c.o + [ 16%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/sam.c.o + [ 16%] Linking C static library libsamtools.a + [ 16%] Built target samtools + [ 16%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/cram/cram_codecs.c.o + [ 17%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/cram/cram_decode.c.o + [ 17%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/cram/cram_encode.c.o + [ 18%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/cram/cram_external.c.o + [ 18%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/cram/cram_index.c.o + [ 19%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/cram/cram_io.c.o + [ 19%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/cram/cram_samtools.c.o + [ 20%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/cram/cram_stats.c.o + [ 20%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/cram/files.c.o + [ 21%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/cram/mFILE.c.o + [ 21%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/cram/md5.c.o + [ 22%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/cram/open_trace_file.c.o + [ 22%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/cram/pooled_alloc.c.o + [ 23%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/cram/sam_header.c.o + [ 23%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/cram/rANS_static.c.o + [ 23%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/cram/string_alloc.c.o + [ 24%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/cram/thread_pool.c.o + [ 24%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/cram/vlen.c.o + [ 25%] Building C object src/utils/htslib/CMakeFiles/htslib.dir/cram/zfio.c.o + [ 25%] Linking C static library libhtslib.a + [ 25%] Built target htslib +# Last 100 lines of the build log. diff --git a/recipes/regtools/meta.yaml b/recipes/regtools/meta.yaml index 0b9aa398da185..f912d62650ac1 100644 --- a/recipes/regtools/meta.yaml +++ b/recipes/regtools/meta.yaml @@ -11,7 +11,7 @@ source: url: https://github.com/griffithlab/{{ name }}/archive/{{ version }}.tar.gz build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/relion/meta.yaml b/recipes/relion/meta.yaml index 9262ba0c65aa6..529511c1c39a1 100644 --- a/recipes/relion/meta.yaml +++ b/recipes/relion/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 7ccc941a6a885bd850efa8867ea908254d8dc260cf72cc24c375bb9f1d56bf91 build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('relion', max_pin='x') }} diff --git a/recipes/renano/meta.yaml b/recipes/renano/meta.yaml index 277968b437690..7837c019c9751 100644 --- a/recipes/renano/meta.yaml +++ b/recipes/renano/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 source: url: https://github.com/guilledufort/RENANO/archive/refs/tags/v{{ version }}.tar.gz diff --git a/recipes/repaq/build_failure.linux-64.yaml b/recipes/repaq/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..47924a0bc8c6f --- /dev/null +++ b/recipes/repaq/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: af07cb44b577e871287b4737d7553a258de581e60d9d429e2203294b23e20a56 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + about: + home: https://github.com/OpenGene/repaq + license: MIT + license_file: LICENSE + summary: A fast lossless FASTQ compressor with ultra-high compression ratio + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/conda/conda-bld/repaq_1734129269531/work + export PREFIX=/opt/conda/conda-bld/repaq_1734129269531/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/conda/conda-bld/repaq_1734129269531/_build_env + export SRC_DIR=/opt/conda/conda-bld/repaq_1734129269531/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/repaq-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/repaq-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/repaq-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/repaq-0.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=c11 -g -I$PREFIX/include -O3 -c src/endian.cpp -o obj/endian.o + src/endian.cpp: In function 'bool isLittleEndian()': + src/endian.cpp:5:9: error: 'uint32_t' does not name a type + 5 | uint32_t i; + | ^~~~~~~~ + src/endian.cpp:2:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + 1 | #include "endian.h" + |#include + 2 | + src/endian.cpp:7:15: error: narrowing conversion of '16909060' from 'int' to 'char' [-Wnarrowing] + 7 | } bint = {0x01020304}; + | ^~~~~~~~~~ + make: *** [Makefile:27: obj/endian.o] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/repaq_1734129269531/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/repaq_1734129269531/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/repaq/meta.yaml b/recipes/repaq/meta.yaml index 810d6b3a59eaa..abccb0e004fc0 100644 --- a/recipes/repaq/meta.yaml +++ b/recipes/repaq/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 97a2f48eb47020aea416df5ff8d5a231db11284622bdcc9816758ac3bbe244d3 build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/repdenovo/build_failure.osx-64.yaml b/recipes/repdenovo/build_failure.osx-64.yaml index b5bb78763b965..ba0484eaa1ac3 100644 --- a/recipes/repdenovo/build_failure.osx-64.yaml +++ b/recipes/repdenovo/build_failure.osx-64.yaml @@ -1,67 +1,67 @@ -recipe_sha: 6b5663fb1507b00dd43bb94c83abab5d45e81696799bada8c2fe933065f90c6d # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: f378451384d542792561f3ec993c8ecf92236b24af069b59adca9d92896cfad0 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- - ^ - ./algorithms/local_alignment.cpp:71:26: warning: ISO C11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] - char *aln_aa_rev_table = "ARNDCQEGHILKMFPSTWYV*X-"; - ^ - ./algorithms/local_alignment.cpp:81:33: warning: ISO C11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] - char *aln_trans_table_eu_char = "KKNNRRSSTTTTIMIIEEDDGGGGAAAAVVVVQQHHRRRRPPPPLLLL**YY*WCCSSSSLLFFX"; - ^ - ./algorithms/local_alignment.cpp:331:2: error: ISO C17 does not allow 'register' storage class specifier [-Wregister] - register int i, j; - ^~~~~~~~~ - ./algorithms/local_alignment.cpp:331:2: error: ISO C17 does not allow 'register' storage class specifier [-Wregister] - register int i, j; - ^~~~~~~~~ - ./algorithms/local_alignment.cpp:515:2: error: ISO C17 does not allow 'register' storage class specifier [-Wregister] - register NT_LOCAL_SCORE *s; - ^~~~~~~~~ - ./algorithms/local_alignment.cpp:516:2: error: ISO C17 does not allow 'register' storage class specifier [-Wregister] - register int i; - ^~~~~~~~~ - ./algorithms/local_alignment.cpp:528:25: warning: variable 'b' set but not used [-Wunused-but-set-variable] - int gap_open, gap_ext, b; - ^ - ./algorithms/local_alignment.cpp:836:23: warning: variable 'tmp_len' set but not used [-Wunused-but-set-variable] - int q, r, qr, tmp_len; - ^ - 6 warnings and 4 errors generated. - make: *** [Makefile:22: local_alignment.o] Error 1 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - Extracting download - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + - llvm-tools 18.1.8 h9ce406d_2 + - libzlib 1.3.1 hd23fc13_2 + - libllvm18 18.1.8 h9ce406d_2 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + host: + - libcxx 19.1.5 hf95d169_0 + - libzlib 1.3.1 hd23fc13_2 + - bamtools 2.5.2 h2ec61ea_6 + - zlib 1.3.1 hd23fc13_2 + run: + - zlib + - bwa + - libzlib >=1.3.1,<2.0a0 + - bamtools >=2.5.2,<2.6.0a0 + - libcxx >=18 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + - python + - velvet + - kmer-jellyfish + test: + commands: + - TERefiner_1 + about: return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + home: https://github.com/Reedwarbler/REPdenovo + license: MIT + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree packages_from_this = build( - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/repdenovo_1717630797899/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/repdenovo_1717630797899/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/repdenovo_1717630797899/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/repdenovo_1717630797899/work + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + summary: 'REPdenovo is designed for constructing repeats directly from sequence + reads. + + ' + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/repdenovo_1734094385701/work + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/repdenovo_1734094385701/work/conda_build.sh']' returned non-zero exit status 2. + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/repdenovo_1734094385701/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/repdenovo_1734094385701/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/repdenovo_1734094385701/work INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as CC=x86_64-apple-darwin13.4.0-clang CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/repdenovo-0.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/repdenovo_1717630797899/work/conda_build.sh']' returned non-zero exit status 2. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/repdenovo-0.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool @@ -70,7 +70,7 @@ log: |2- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -79,7 +79,7 @@ log: |2- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack diff --git a/recipes/repdenovo/meta.yaml b/recipes/repdenovo/meta.yaml index 6736d649752ef..833ccd3d2d2b6 100644 --- a/recipes/repdenovo/meta.yaml +++ b/recipes/repdenovo/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/repeatscout/meta.yaml b/recipes/repeatscout/meta.yaml index c3182a7358a68..765179e0fdf8c 100644 --- a/recipes/repeatscout/meta.yaml +++ b/recipes/repeatscout/meta.yaml @@ -10,7 +10,7 @@ source: sha256: aec393f87aa03efdceb9b664e43de102ed7d83ed1c2cbac3ac53e8cda96e08f9 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('repeatscout', max_pin="x") }} diff --git a/recipes/rerconverge/meta.yaml b/recipes/rerconverge/meta.yaml index 0af09357051c5..6f15f432ad5e2 100644 --- a/recipes/rerconverge/meta.yaml +++ b/recipes/rerconverge/meta.yaml @@ -5,7 +5,7 @@ source: url: 'https://github.com/nclark-lab/RERconverge/archive/refs/tags/v0.3.0.tar.gz' sha256: 636e1baf64321c8bd1cd5e0c7a22b86180532d7e323e2b4d636b0059288e01bf build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/reseek/build_failure.linux-64.yaml b/recipes/reseek/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..011dda36f0442 --- /dev/null +++ b/recipes/reseek/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 8092d3f7c34b107932d4c34ae9a277086ee894e00653f82011524051d7a5d47c # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/msa2cmp.o msa2cmp.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/murmurhash.o murmurhash.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/myss.o myss.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/namedparams.o namedparams.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/prettyaln.o prettyaln.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/scalar_sweep.o scalar_sweep.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/scop40bench.o scop40bench.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/scop40benchroc.o scop40benchroc.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/sweeper.o sweeper.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/swfastpinop.o swfastpinop.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/swfastpinopgapless.o swfastpinopgapless.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/swgapless.o swgapless.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/swgaplessint.o swgaplessint.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/swgaplessprof.o swgaplessprof.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/swgaplessprofb.o swgaplessprofb.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/testmodel.o testmodel.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/testmodel2.o testmodel2.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/test_para.o test_para.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/test_para_cal.o test_para_cal.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/test_para_path.o test_para_path.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/test_xdrop.o test_xdrop.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/timing.o timing.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/trained_features.o trained_features.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/train_features.o train_features.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/userfields.o userfields.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/usort.o usort.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/valuetoint.o valuetoint.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/one2three.o one2three.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/fastaseqsource.o fastaseqsource.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/fileseqsource.o fileseqsource.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/getss.o getss.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/sscluster.o sscluster.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/trainer.o trainer.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/usage.o usage.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/linereader.o linereader.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/lockobj.o lockobj.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/mx.o mx.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/myutils.o myutils.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/objmgr.o objmgr.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/reseek_main.o reseek_main.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/readchains.o readchains.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/pdbchain.o pdbchain.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/quarts.o quarts.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/spher.o spher.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/sw.o sw.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/seqdb.o seqdb.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/seqinfo.o seqinfo.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/seqsource.o seqsource.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/sfasta.o sfasta.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/sort.o sort.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/writelocalaln.o writelocalaln.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/xdropbwd.o xdropbwd.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/xdropfwd.o xdropfwd.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/zscorer.o zscorer.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/adler32.o adler32.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/crc32.o crc32.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/deflate.o deflate.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/gzlib.o gzlib.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/gzread.o gzread.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/infback.o infback.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/inffast.o inffast.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/inflate.o inflate.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/inftrees.o inftrees.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/trees.o trees.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/reseek-2.02 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -ffast-math -march=native -O3 -DNDEBUG -fopenmp -c -o o/zutil.o zutil.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -ffast-math -march=native -O3 -fopenmp -static o/abcxyz.o o/alignselfrev.o o/alpha.o o/alpha2.o o/b62.o o/bcadata.o o/blosum.o o/blosum62.o o/calibrate.o o/calibrate2.o o/calibrate3.o o/calibrate4.o o/calibrate5.o o/calibrate5a.o o/calibrate7.o o/calibratesearcher.o o/calibrate_masm.o o/chainreader2.o o/cif.o o/cigar.o o/cluster.o o/cmprof.o o/cmprof_train.o o/convert.o o/daliscorer.o o/daliscore_msas2.o o/daliscore_msa.o o/daliscore_msas.o o/daliscore_tsv.o o/distmx.o o/evalue_report.o o/explore1.o o/getchains.o o/lddt.o o/lddt_foldmason.o o/lddt_msa.o o/lddt_msas.o o/lddt_msa_foldmason.o o/lddt_muscle.o o/msta_lddtmuw1.o o/msta_lddtmuw.o o/msta_score.o o/msta_scores.o o/mu_mapping.o o/alignpair.o o/pdb.o o/profileloader.o o/md5.o o/pdbchaincal.o o/pdbfilescanner.o o/gumbel.o o/gzipfileio.o o/linereader2.o o/parasail.o o/parasail_cigar.o o/parasail_combo.o o/pdb2mega.o o/readhits.o o/runquery.o o/runself.o o/runthreads.o o/scop40bit.o o/search.o o/combomx.o o/combomx_data.o o/dali.o o/dbsearcher.o o/derepper.o o/dss.o o/dssaligner.o o/dssparams.o o/features.o o/float_feature_bins.o o/getbins.o o/gsw.o o/jiggle.o o/kabsch.o o/kmer_eval.o o/kmer_eval2.o o/logaln.o o/logodds.o o/mergefwdback.o o/msa2cmp.o o/murmurhash.o o/myss.o o/namedparams.o o/prettyaln.o o/scalar_sweep.o o/scop40bench.o o/scop40benchroc.o o/sweeper.o o/swfastpinop.o o/swfastpinopgapless.o o/swgapless.o o/swgaplessint.o o/swgaplessprof.o o/swgaplessprofb.o o/testmodel.o o/testmodel2.o o/test_para.o o/test_para_cal.o o/test_para_path.o o/test_xdrop.o o/timing.o o/trained_features.o o/train_features.o o/userfields.o o/usort.o o/valuetoint.o o/one2three.o o/fastaseqsource.o o/fileseqsource.o o/getss.o o/sscluster.o o/trainer.o o/usage.o o/linereader.o o/lockobj.o o/mx.o o/myutils.o o/objmgr.o o/reseek_main.o o/readchains.o o/pdbchain.o o/quarts.o o/spher.o o/sw.o o/seqdb.o o/seqinfo.o o/seqsource.o o/sfasta.o o/sort.o o/writelocalaln.o o/xdropbwd.o o/xdropfwd.o o/zscorer.o o/adler32.o o/crc32.o o/deflate.o o/gzlib.o o/gzread.o o/infback.o o/inffast.o o/inflate.o o/inftrees.o o/trees.o o/zutil.o -o ../bin/reseek + /opt/conda/conda-bld/reseek_1734188246987/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/conda/conda-bld/reseek_1734188246987/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/libgomp.a(oacc-profiling.o): in function goacc_profiling_initialize': + /home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/work/build/x86_64-conda-linux-gnu/libgomp/../../../libgomp/oacc-profiling.c:137:(.text0x60f): undefined reference to dlopen' + /opt/conda/conda-bld/reseek_1734188246987/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/work/build/x86_64-conda-linux-gnu/libgomp/../../../libgomp/oacc-profiling.c:141:(.text0x62b): undefined reference to dlsym' + /opt/conda/conda-bld/reseek_1734188246987/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/work/build/x86_64-conda-linux-gnu/libgomp/../../../libgomp/oacc-profiling.c:156:(.text0x67b): undefined reference to dlclose' + /opt/conda/conda-bld/reseek_1734188246987/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /home/conda/feedstock_root/build_artifacts/gcc_compilers_1724798720716/work/build/x86_64-conda-linux-gnu/libgomp/../../../libgomp/oacc-profiling.c:152:(.text0x684): undefined reference to dlerror' + collect2: error: ld returned 1 exit status + make: *** [Makefile:259: ../bin/reseek] Error 1 + + + ERROR -- make failed + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/reseek_1734188246987/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/reseek_1734188246987/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/reseek/meta.yaml b/recipes/reseek/meta.yaml index 8b59a2d8fb690..292cd5ae1478d 100644 --- a/recipes/reseek/meta.yaml +++ b/recipes/reseek/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 83296e5edcdccdf4848f52ff34f35b753fa9ae1d383c3347eee41ef7d26888b1 build: - number: 0 + number: 1 skip: True #[osx] run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/reseq/meta.yaml b/recipes/reseq/meta.yaml index 194aa32bf31f2..2a03a6eb5c1dc 100644 --- a/recipes/reseq/meta.yaml +++ b/recipes/reseq/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 4ba3f87d0b6481a23f4af733919a071c1c9684c169f63b68f121b48be0a6c599 build: - number: 4 + number: 5 skip: True # [osx or py2k] requirements: diff --git a/recipes/revbayes/meta.yaml b/recipes/revbayes/meta.yaml index fb669c8bfd642..c9d0fd3bbec02 100644 --- a/recipes/revbayes/meta.yaml +++ b/recipes/revbayes/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 547fc4b9f7d3bd9ebc6ea7dd3e2d7ff824955d49a879b47d0bd6018f6e48b9f7 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('revbayes', max_pin="x") }} @@ -53,7 +53,7 @@ extra: - biotools:revbayes - doi:10.1093/sysbio/syw021 - doi:10.1093/sysbio/syu039 - additional-platforms: + #additional-platforms: # Times out #- osx-arm64 #- linux-aarch64 diff --git a/recipes/revoluzer/meta.yaml b/recipes/revoluzer/meta.yaml index 0938d952509e1..74084698db136 100644 --- a/recipes/revoluzer/meta.yaml +++ b/recipes/revoluzer/meta.yaml @@ -10,7 +10,7 @@ source: sha256: a3c73aa21c1f1d63e40939568bd963690a0df24ccfe7ba6df28ca7ef49dd3b94 build: - number: 1 + number: 2 skip: True # [osx] run_exports: - {{ pin_subpackage('revoluzer', max_pin="x") }} diff --git a/recipes/rfmix/meta.yaml b/recipes/rfmix/meta.yaml index 82ae1cb795f91..73ed51c6390a1 100644 --- a/recipes/rfmix/meta.yaml +++ b/recipes/rfmix/meta.yaml @@ -10,7 +10,7 @@ source: sha256: f15a8fe9bc8e06579f96c727dd91ca07b726e9bde305ce0d8d4ee233b1b299af build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/rgccacmd/meta.yaml b/recipes/rgccacmd/meta.yaml index 24fcdf390ba47..002d0664bb14a 100644 --- a/recipes/rgccacmd/meta.yaml +++ b/recipes/rgccacmd/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 1 + number: 2 rpaths: - lib/ - lib/R/lib/ diff --git a/recipes/rhocall/meta.yaml b/recipes/rhocall/meta.yaml index 0e4786d16e3a8..cd11638069078 100644 --- a/recipes/rhocall/meta.yaml +++ b/recipes/rhocall/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 4d2535c90e14a2a800fa1ddcd32dc252a13e4532edba948ca61b241238bee761 build: - number: 3 + number: 4 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed" diff --git a/recipes/riblast/meta.yaml b/recipes/riblast/meta.yaml index 1ccc6a07472fd..29bb0afa7a594 100644 --- a/recipes/riblast/meta.yaml +++ b/recipes/riblast/meta.yaml @@ -9,7 +9,7 @@ source: sha256: b77ae9cfd131e9ced512749b10349b00c13bd6bf32e0f85500ad5b9ea29c3d5a build: - number: 0 + number: 1 binary_relocation: true script: - cmake -H. -Bbuild_conda -G "${CMAKE_GENERATOR}" -DCMAKE_INSTALL_PREFIX=${PREFIX} diff --git a/recipes/ribotaper/meta.yaml b/recipes/ribotaper/meta.yaml index 719b76d9d487e..020ab5a7f9ffc 100644 --- a/recipes/ribotaper/meta.yaml +++ b/recipes/ribotaper/meta.yaml @@ -8,7 +8,7 @@ source: build: skip: True # [not linux] - number: 8 + number: 9 run_exports: - {{ pin_subpackage('ribotaper', max_pin='x') }} diff --git a/recipes/ribotin/build_failure.linux-64.yaml b/recipes/ribotin/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..a50a0fcd2f54f --- /dev/null +++ b/recipes/ribotin/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 69024fad59c897aaf59b54903ce29be80299ec6d687a784ba7ef8f1b107426d8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']"), MatchSpec("graphaligner==1.0.0=he4d24e2_0")} + Encountered problems while solving: + - package graphaligner-1.0.0-he4d24e2_0 requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mgraphaligner[0m is installable with the potential options + [32mgraphaligner [1.0.0|1.0.1|...|1.0.9][0m would require + [32mprotobuf 3.14.0 [0m, which requires + [32mlibprotobuf 3.14.0.* [0m, which requires + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [32mpypy3.6 [>=7.3.2 |>=7.3.3 ][0m, which requires + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [32mpypy3.7 >=7.3.3 [0m, which requires + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [32mgraphaligner [1.0.14|1.0.15|1.0.16][0m would require + [32mlibzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [32mgraphaligner [1.0.17|1.0.17b|1.0.18|1.0.19][0m would require + [32mlibzlib >=1.2.13,<1.3.0a0 [0m, which can be installed; + [31mlibzlib >=1.3.1,<2.0a0 [0m is not installable because there are no viable options + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_0[0m, which conflicts with any installable versions previously reported; + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_1[0m, which conflicts with any installable versions previously reported; + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_2[0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']"), MatchSpec("graphaligner==1.0.0=he4d24e2_0")} + Encountered problems while solving: + - package graphaligner-1.0.0-he4d24e2_0 requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mgraphaligner[0m is installable with the potential options + [32mgraphaligner [1.0.0|1.0.1|...|1.0.9][0m would require + [32mprotobuf 3.14.0 [0m, which requires + [32mlibprotobuf 3.14.0.* [0m, which requires + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [32mpypy3.6 [>=7.3.2 |>=7.3.3 ][0m, which requires + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [32mpypy3.7 >=7.3.3 [0m, which requires + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [32mgraphaligner [1.0.14|1.0.15|1.0.16][0m would require + [32mlibzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [32mgraphaligner [1.0.17|1.0.17b|1.0.18|1.0.19][0m would require + [32mlibzlib >=1.2.13,<1.3.0a0 [0m, which can be installed; + [31mlibzlib >=1.3.1,<2.0a0 [0m is not installable because there are no viable options + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_0[0m, which conflicts with any installable versions previously reported; + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_1[0m, which conflicts with any installable versions previously reported; + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_2[0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/ribotin/meta.yaml b/recipes/ribotin/meta.yaml index 1acdf0e771f91..6013085e4f0cd 100644 --- a/recipes/ribotin/meta.yaml +++ b/recipes/ribotin/meta.yaml @@ -12,7 +12,7 @@ source: - makefile.patch build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('ribotin', max_pin="x.x") }} diff --git a/recipes/ribowaltz/meta.yaml b/recipes/ribowaltz/meta.yaml index 1725593a487e9..644b28c82ffcc 100755 --- a/recipes/ribowaltz/meta.yaml +++ b/recipes/ribowaltz/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/rmath4/meta.yaml b/recipes/rmath4/meta.yaml index ba2b6e894fa63..dd6bf0ead948c 100644 --- a/recipes/rmath4/meta.yaml +++ b/recipes/rmath4/meta.yaml @@ -11,7 +11,7 @@ source: build: script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation - number: 1 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/rmats/meta.yaml b/recipes/rmats/meta.yaml index b09b14db10e21..c8dc216c2d257 100644 --- a/recipes/rmats/meta.yaml +++ b/recipes/rmats/meta.yaml @@ -13,7 +13,7 @@ source: - rmats_pipeline_setup.patch build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/rmats2sashimiplot/build_failure.linux-64.yaml b/recipes/rmats2sashimiplot/build_failure.linux-64.yaml deleted file mode 100644 index a1e1d2e9d247a..0000000000000 --- a/recipes/rmats2sashimiplot/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: b220de3cd5b023b01e8cbd642ea06cecec2f1f41d179f532b63c91e21cd84dd0 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - [32mpysam 0.7.7[0m would require - [32mpython <3.0.0 [0m, which can be installed; - [31mpython >=3.11,<3.12.0a0 [0m is not installable because it requires - [31mpython_abi 3.11.* *_cp311[0m, which conflicts with any installable versions previously reported; - [31mxz [>=5.2.6,<5.3.0a0 |>=5.2.6,<6.0a0 ][0m, which conflicts with any installable versions previously reported. - - During handling of the above exception, another exception occurred: - - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2409, in build - create_build_envs(top_level_pkg, notest) - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2247, in create_build_envs - raise e - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2220, in create_build_envs - environ.get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions - precs = _install_actions(prefix, index, specs)["LINK"] - File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions - txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction - unlink_precs, link_precs = self.solve_for_diff( - File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff - final_precs = self.solve_final_state( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state - out_state = self._solving_loop(in_state, out_state, index) - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop - solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt - new_conflicts = self._maybe_raise_for_problems( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems - self._maybe_raise_for_conda_build( - File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build - raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("python==3.11.0=h582c2e5_0_cpython"), MatchSpec("xz[version='>=5.2.6,<5.3.0a0']")} - Encountered problems while solving: - - package python-3.11.0-h582c2e5_0_cpython requires xz >=5.2.6,<5.3.0a0, but none of the providers can be installed - - Could not solve for environment specs - The following packages are incompatible - [32mpysam[0m is installable with the potential options - [32mpysam [0.10.0|0.11.0|...|0.9.1.4][0m would require - [32mpython [2.7* |>=2.7,<2.8.0a0 ][0m, which can be installed; - [32mpysam [0.10.0|0.15.2|...|0.9.1][0m would require - [32mpython_abi 2.7.* *_cp27mu[0m, which can be installed; - [32mpysam [0.10.0|0.11.0|...|0.9.1.4][0m would require - [32mpython 3.4* [0m, which can be installed; - [32mpysam [0.10.0|0.11.0|...|0.9.1.4][0m would require - [32mpython [3.5* |>=3.5,<3.6.0a0 ][0m with the potential options - [32mpython [3.5.1|3.5.2][0m would require - [32mxz 5.0.* [0m, which can be installed; - [32mpython [3.5.2|3.5.3|3.5.4|3.5.5][0m, which can be installed; - [32mpysam [0.10.0|0.11.1|...|0.9.1][0m would require - [32mpython 3.6* [0m, which can be installed; - [32mpysam [0.10.0|0.15.2|...|0.9.1][0m would require - [32mpython_abi 3.6.* *_cp36m[0m, which can be installed; - [32mpysam [0.10.0|0.14.1|...|0.9.1][0m would require - [32mpython >=3.6,<3.7.0a0 [0m, which can be installed; - [31mpysam [0.15.1|0.15.2|0.15.3][0m would require - [31mlibdeflate >=1.0,<1.1.0a0 [0m, which conflicts with any installable versions previously reported; - [32mpysam [0.15.2|0.15.4|...|0.9.1][0m would require - [32mpython_abi 3.7.* *_cp37m[0m with the potential options - [32mpython_abi 3.7[0m, which can be installed; - [32mpython_abi 3.7[0m would require - [32mpython 3.7.* *_cpython[0m, which can be installed; - [32mpysam [0.15.2|0.15.3|0.15.4|0.9.1][0m would require - [32mpython >=3.7,<3.8.0a0 [0m, which can be installed; - [32mpysam [0.15.2|0.16.0.1|...|0.9.1][0m would require - [32mpython_abi 3.8.* *_cp38[0m with the potential options - [32mpython_abi 3.8[0m, which can be installed; - [32mpython_abi 3.8[0m would require - [32mpython 3.8.* *_cpython[0m, which can be installed; - [32mpysam [0.16.0.1|0.17.0|...|0.9.1][0m would require - [32mpython_abi 3.9.* *_cp39[0m with the potential options - [32mpython_abi 3.9[0m, which can be installed; - [32mpython_abi 3.9[0m would require - [32mpython 3.9.* *_cpython[0m, which can be installed; - [32mpysam [0.19.1|0.20.0|0.21.0|0.22.0|0.22.1][0m would require - [32mpython_abi 3.10.* *_cp310[0m with the potential options - [32mpython_abi 3.10[0m, which can be installed; - [32mpython_abi 3.10[0m would require - [32mpython 3.10.* *_cpython[0m, which can be installed; - [32mpysam 0.7.7[0m would require - [32mpython <3.0.0 [0m, which can be installed; - [31mpython >=3.11,<3.12.0a0 [0m is not installable because it requires - [31mpython_abi 3.11.* *_cp311[0m, which conflicts with any installable versions previously reported; - [31mxz [>=5.2.6,<5.3.0a0 |>=5.2.6,<6.0a0 ][0m, which conflicts with any installable versions previously reported. -# Last 100 lines of the build log. diff --git a/recipes/rmats2sashimiplot/meta.yaml b/recipes/rmats2sashimiplot/meta.yaml index a98be80a8bb22..7f994db6fc9f4 100644 --- a/recipes/rmats2sashimiplot/meta.yaml +++ b/recipes/rmats2sashimiplot/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 5d8e0fa3e7c5db2e595dc08e4cdb652385c18d7f2b70468d81a0fb3d957d03ce build: - number: 1 + number: 2 entry_points: - rmats2sashimiplot=rmats2sashimiplot.rmats2sashimiplot:main - index_gff=MISO.misopy.index_gff:main diff --git a/recipes/rna-seqc/meta.yaml b/recipes/rna-seqc/meta.yaml index cc91a8ea6f068..1536e4b66f4e2 100644 --- a/recipes/rna-seqc/meta.yaml +++ b/recipes/rna-seqc/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256sum }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("rna-seqc", max_pin="x") }} diff --git a/recipes/rnaalishapes/build_failure.osx-64.yaml b/recipes/rnaalishapes/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c7200600e120c --- /dev/null +++ b/recipes/rnaalishapes/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: b0fa0da505e4f9b3d9448e72638a47f3dc99195e54157b3bff692feb5440db5b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rnaalishapes-2.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rnaalishapes-2.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rnaalishapes-2.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rnaalishapes-2.5.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + make: Entering directory '$SRC_DIR/Misc/Applications/RNAalishapes' + make all_normal + make[1]: Entering directory '$SRC_DIR/Misc/Applications/RNAalishapes' + make compile \ + gapc_product="alg_ali_mfe * (alg_ali_dotBracket * alg_ali_shapeX * alg_ali_pfunc)" \ + gapc_options="--kbacktrace --no-coopt " \ + gapc_file="ali_nodangle.gap" \ + gapc_binaryname="mfe_nodangle"; + make compile \ + gapc_product="alg_ali_mfe * (alg_ali_dotBracket * alg_ali_shapeX * alg_ali_pfunc)" \ + gapc_options="--kbacktrace --no-coopt " \ + gapc_file="ali_overdangle.gap" \ + gapc_binaryname="mfe_overdangle"; + make[2]: Entering directory '$SRC_DIR/Misc/Applications/RNAalishapes' + make[2]: Entering directory '$SRC_DIR/Misc/Applications/RNAalishapes' + if [ ! -f "x86_64-apple-darwin13.4.0/RNAalishapes_mfe_nodangle" ]; then \ + cd /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.qo8MMBUt && gapc -I $SRC_DIR/Misc/Applications/RNAalishapes/../../../ -p "alg_ali_mfe * (alg_ali_dotBracket * alg_ali_shapeX * alg_ali_pfunc)" --kbacktrace --no-coopt $SRC_DIR/Misc/Applications/RNAalishapes/../../..//ali_nodangle.gap; \ + perl $SRC_DIR/Misc/Applications/RNAalishapes/../../..///Misc/Applications/addRNAoptions.pl /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.qo8MMBUt/out.mf 0 'mfe_nodangle' 'alg_ali_mfe * (alg_ali_dotBracket * alg_ali_shapeX * alg_ali_pfunc)'; \ + cd /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.qo8MMBUt && make -f out.mf CPPFLAGS_EXTRA="-I $SRC_DIR/Misc/Applications/RNAalishapes/../../../ -I ./" CXXFLAGS_EXTRA="-O3 -DNDEBUG" LDFLAGS_EXTRA=""; \ + install -d $SRC_DIR/Misc/Applications/RNAalishapes/x86_64-apple-darwin13.4.0; \ + install /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.qo8MMBUt/out $SRC_DIR/Misc/Applications/RNAalishapes/x86_64-apple-darwin13.4.0/RNAalishapes_mfe_nodangle; \ + fi; + if [ ! -f "x86_64-apple-darwin13.4.0/RNAalishapes_mfe_overdangle" ]; then \ + cd /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.npPSJDlv && gapc -I $SRC_DIR/Misc/Applications/RNAalishapes/../../../ -p "alg_ali_mfe * (alg_ali_dotBracket * alg_ali_shapeX * alg_ali_pfunc)" --kbacktrace --no-coopt $SRC_DIR/Misc/Applications/RNAalishapes/../../..//ali_overdangle.gap; \ + perl $SRC_DIR/Misc/Applications/RNAalishapes/../../..///Misc/Applications/addRNAoptions.pl /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.npPSJDlv/out.mf 0 'mfe_overdangle' 'alg_ali_mfe * (alg_ali_dotBracket * alg_ali_shapeX * alg_ali_pfunc)'; \ + cd /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.npPSJDlv && make -f out.mf CPPFLAGS_EXTRA="-I $SRC_DIR/Misc/Applications/RNAalishapes/../../../ -I ./" CXXFLAGS_EXTRA="-O3 -DNDEBUG" LDFLAGS_EXTRA=""; \ + install -d $SRC_DIR/Misc/Applications/RNAalishapes/x86_64-apple-darwin13.4.0; \ + install /var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.npPSJDlv/out $SRC_DIR/Misc/Applications/RNAalishapes/x86_64-apple-darwin13.4.0/RNAalishapes_mfe_overdangle; \ + fi; + make[3]: Entering directory '/private/var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.qo8MMBUt' + Including global makefile $PREFIX/share/gapc/config_darwin13.4.0.mf + make[3]: Entering directory '/private/var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.npPSJDlv' + Including global makefile $PREFIX/share/gapc/config_darwin13.4.0.mf + echo '#include "out.hh"' > out_main.cc + echo '#include "out.hh"' > out_main.cc + cat $PREFIX/include/rtlib/generic_main.cc >> out_main.cc + cat $PREFIX/include/rtlib/generic_main.cc >> out_main.cc + $PREFIX/bin/sed -i 's|gapc::Opts opts;||' out_main.cc + $PREFIX/bin/sed -i 's|gapc::Opts opts;||' out_main.cc + $PREFIX/bin/sed -i 's|\([^_]\)opts\.|\1gapc::Opts::getOpts()->|g' out_main.cc + $PREFIX/bin/sed -i 's|\([^_]\)opts\.|\1gapc::Opts::getOpts()->|g' out_main.cc + $PREFIX/bin/sed -i 's|obj.init(opts);|obj.init(\*gapc::Opts::getOpts());|g' out_main.cc + $PREFIX/bin/sed -i 's|obj.init(opts);|obj.init(\*gapc::Opts::getOpts());|g' out_main.cc + $PREFIX/bin/sed -i 's|#include .rtlib/generic_opts.hh.|#include "Extensions/rnaoptions.hh"|' out_main.cc + $PREFIX/bin/sed -i 's|#include .rtlib/generic_opts.hh.|#include "Extensions/rnaoptions.hh"|' out_main.cc + $PREFIX/bin/sed -i 's%#include .rtlib/generic_opts.hh.%#include "Extensions/rnaoptions.hh"%' out.hh out.cc + $PREFIX/bin/sed -i 's%#include .rtlib/generic_opts.hh.%#include "Extensions/rnaoptions.hh"%' out.hh out.cc + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bellmans-gapc_1721071508431/work=/usr/local/src/conda/bellmans-gapc-2024.01.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -MMD -MP -Wall -Wnon-virtual-dtor -Wno-unused-variable -Wno-parentheses -DNDEBUG -DBISONNEW -O3 -DNDEBUG -DWITH_RNAOPTIONS -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I $SRC_DIR/Misc/Applications/RNAalishapes/../../../ -I ./ -I$PREFIX/include -I$PREFIX/include/ -I$PREFIX/include/rtlib -I$PREFIX/include/librna -c -o out.o out.cc + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bellmans-gapc_1721071508431/work=/usr/local/src/conda/bellmans-gapc-2024.01.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -MMD -MP -Wall -Wnon-virtual-dtor -Wno-unused-variable -Wno-parentheses -DNDEBUG -DBISONNEW -O3 -DNDEBUG -DWITH_RNAOPTIONS -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I $SRC_DIR/Misc/Applications/RNAalishapes/../../../ -I ./ -I$PREFIX/include -I$PREFIX/include/ -I$PREFIX/include/rtlib -I$PREFIX/include/librna -c -o out.o out.cc + make[3]: Leaving directory '/private/var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.npPSJDlv' + make[3]: Leaving directory '/private/var/folders/6y/f6qmctm15g7d62gdx37s226h0000gn/T/tmp.qo8MMBUt' + make[2]: Leaving directory '$SRC_DIR/Misc/Applications/RNAalishapes' + make[2]: Leaving directory '$SRC_DIR/Misc/Applications/RNAalishapes' + make[1]: Leaving directory '$SRC_DIR/Misc/Applications/RNAalishapes' + make: Leaving directory '$SRC_DIR/Misc/Applications/RNAalishapes' +# Last 100 lines of the build log. diff --git a/recipes/rnaalishapes/meta.yaml b/recipes/rnaalishapes/meta.yaml index 17ef0ed23173e..4f4252d01f250 100644 --- a/recipes/rnaalishapes/meta.yaml +++ b/recipes/rnaalishapes/meta.yaml @@ -14,7 +14,7 @@ source: url: https://github.com/jlab/fold-grammars/archive/{{ fold_grammars_version }}.tar.gz build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('rnaalishapes', max_pin="x") }} diff --git a/recipes/rnabridge-align/meta.yaml b/recipes/rnabridge-align/meta.yaml index 82d9d77756a3b..729b8d16181f1 100644 --- a/recipes/rnabridge-align/meta.yaml +++ b/recipes/rnabridge-align/meta.yaml @@ -10,7 +10,7 @@ source: sha256: "85e93e89a06dd27834dd4b3cb46f0b281df163d83259dbc1715d0819de6f98a8" build: - number: 7 + number: 8 requirements: build: diff --git a/recipes/telseq/build_failure.osx-64.yaml b/recipes/rnahybrid/build_failure.osx-64.yaml similarity index 52% rename from recipes/telseq/build_failure.osx-64.yaml rename to recipes/rnahybrid/build_failure.osx-64.yaml index 6536e5d2a079a..81e3fe54207c6 100644 --- a/recipes/telseq/build_failure.osx-64.yaml +++ b/recipes/rnahybrid/build_failure.osx-64.yaml @@ -1,22 +1,21 @@ -recipe_sha: 2fd9750a1a225c0d547b8df2313002147680bfc318a7067da9e42877dba37843 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 23d692e11361309f12c23505992858fd2af30a1564d62991341c7ea56c085f6c # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - utils.check_call_env( +log: |- + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/telseq-0.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rnahybrid-2.1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/telseq_1717627707943/work/conda_build.sh']' returned non-zero exit status 2. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/telseq-0.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rnahybrid-2.1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool LD=x86_64-apple-darwin13.4.0-ld @@ -24,7 +23,7 @@ log: |2- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -33,7 +32,7 @@ log: |2- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -45,60 +44,61 @@ log: |2- ac_cv_func_realloc_0_nonnull=yes build_alias=x86_64-apple-darwin13.4.0 host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/telseq-0.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/telseq-0.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes - checking for a race-free mkdir -p... ./install-sh -c -d + checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes - checking whether make supports nested variables... yes checking for x86_64-apple-darwin13.4.0-gcc... x86_64-apple-darwin13.4.0-clang checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o - checking whether the compiler supports GNU C... yes + checking whether we are using the GNU C compiler... yes checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes - checking for x86_64-apple-darwin13.4.0-clang option to enable C11 features... none needed - checking whether x86_64-apple-darwin13.4.0-clang understands -c and -o together... yes - checking whether make supports the include directive... yes (GNU style) + checking for x86_64-apple-darwin13.4.0-clang option to accept ISO C89... none needed + checking for style of include used by make... GNU checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 - checking whether the compiler supports GNU C... yes - checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes - checking for x86_64-apple-darwin13.4.0-clang option to enable C11 features... none needed - checking dependency style of x86_64-apple-darwin13.4.0-clang... gcc3 - checking for x86_64-apple-darwin13.4.0-ranlib... x86_64-apple-darwin13.4.0-ranlib - checking for stdio.h... yes + checking for log in -lm... yes + checking for g2_open_vd in -lg2... no + checking for gdImageLine in -lgd... yes + checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang-cpp + checking for grep that handles long lines and -e... /usr/bin/grep + checking for egrep... /usr/bin/grep -E + checking for ANSI C header files... yes + checking for sys/types.h... yes + checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes + checking for memory.h... yes + checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes - checking for strings.h... yes - checking for sys/stat.h... yes - checking for sys/types.h... yes checking for unistd.h... yes - checking for api/BamReader.h... yes - checking that generated files are newer than configure... done + checking g2.h usability... no + checking g2.h presence... no + checking for g2.h... no + checking g2_PS.h usability... no + checking g2_PS.h presence... no + checking for g2_PS.h... no + checking for an ANSI C-conforming const... yes + checking for inline... inline + checking for size_t... yes configure: creating ./config.status config.status: creating Makefile - config.status: creating Util/Makefile - config.status: creating Telseq/Makefile + config.status: creating src/Makefile + config.status: creating man/Makefile config.status: creating config.h config.status: executing depfiles commands make all-recursive - make[1]: Entering directory '$SRC_DIR/src' - Making all in Util - make[2]: Entering directory '$SRC_DIR/src/Util' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -g -O0 -std=c11 -MT Util.o -MD -MP -MF .deps/Util.Tpo -c -o Util.o Util.cpp - make[2]: Leaving directory '$SRC_DIR/src/Util' - make[1]: Leaving directory '$SRC_DIR/src' + make[1]: Entering directory '$SRC_DIR' + Making all in src + make[2]: Entering directory '$SRC_DIR/src' + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rnahybrid-2.1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon -MT rnahybrid.o -MD -MP -MF .deps/rnahybrid.Tpo -c -o rnahybrid.o rnahybrid.c + make[2]: Leaving directory '$SRC_DIR/src' + make[1]: Leaving directory '$SRC_DIR' # Last 100 lines of the build log. diff --git a/recipes/rnahybrid/meta.yaml b/recipes/rnahybrid/meta.yaml index 0f3b3a17cafe6..f9568231155e0 100644 --- a/recipes/rnahybrid/meta.yaml +++ b/recipes/rnahybrid/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/rnaredprint/build_failure.osx-64.yaml b/recipes/rnaredprint/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..e866dd33fd6a9 --- /dev/null +++ b/recipes/rnaredprint/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5c5f64c87306d770484c919584695f072df52b1352ac4a4108ebf4bfb261e63c # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + libblas: 3.9.0-25_osx64_openblas conda-forge + libbrotlicommon: 1.1.0-h00291cd_2 conda-forge + libbrotlidec: 1.1.0-h00291cd_2 conda-forge + libbrotlienc: 1.1.0-h00291cd_2 conda-forge + libcblas: 3.9.0-25_osx64_openblas conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libdeflate: 1.22-h00291cd_0 conda-forge + libexpat: 2.6.4-h240833e_0 conda-forge + libffi: 3.4.2-h0d85af4_5 conda-forge + libgfortran: 5.0.0-13_2_0_h97931a8_3 conda-forge + libgfortran5: 13.2.0-h2873a65_3 conda-forge + libjpeg-turbo: 3.0.0-h0dc2134_1 conda-forge + liblapack: 3.9.0-25_osx64_openblas conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libopenblas: 0.3.28-openmp_hbf64a52_1 conda-forge + libpng: 1.6.44-h4b8f8c9_0 conda-forge + libsqlite: 3.47.2-hdb6dae5_0 conda-forge + libtiff: 4.7.0-hf4bdac2_2 conda-forge + libwebp-base: 1.4.0-h10d778d_0 conda-forge + libxcb: 1.17.0-hf1f96e2_0 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-openmp: 19.1.5-ha54dae1_0 conda-forge + matplotlib-base: 3.9.4-py312h535dea3_0 conda-forge + munkres: 1.1.4-pyh9f0ad1d_0 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + numpy: 2.2.0-py312h22eab8f_0 conda-forge + openjdk: 23.0.1-h18c9476_1 conda-forge + openjpeg: 2.5.3-h7fd6d84_0 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + packaging: 24.2-pyhd8ed1ab_2 conda-forge + perl: 5.32.1-7_h10d778d_perl5 conda-forge + pillow: 11.0.0-py312h66fe14f_0 conda-forge + pthread-stubs: 0.4-h00291cd_1002 conda-forge + pyparsing: 3.2.0-pyhd8ed1ab_2 conda-forge + python: 3.12.8-h9ccd52b_1_cpython conda-forge + python-dateutil: 2.9.0.post0-pyhff2d567_1 conda-forge + python_abi: 3.12-5_cp312 conda-forge + qhull: 2020.2-h3c5361c_5 conda-forge + readline: 8.2-h9e318b2_1 conda-forge + rnaredprint: 0.3-py312h5fa12a8_1 local + scipy: 1.14.1-py312h3b0f538_2 conda-forge + six: 1.17.0-pyhd8ed1ab_0 conda-forge + tk: 8.6.13-h1abcd95_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + unicodedata2: 15.1.0-py312h3d0f464_1 conda-forge + viennarna: 2.7.0-py312pl5321h2c65b86_1 bioconda + xorg-libxau: 1.0.11-h00291cd_1 conda-forge + xorg-libxdmcp: 1.1.5-h00291cd_0 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + RNARedPrint --version + design-energyshift.py --version + /opt/mambaforge/envs/bioconda/conda-bld/rnaredprint_1734228393242/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/design-energyshift.py:37: SyntaxWarning: invalid escape sequence '\;' + if re.match(re.compile("^\;"), line, flags=0): + /opt/mambaforge/envs/bioconda/conda-bld/rnaredprint_1734228393242/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/design-energyshift.py:40: SyntaxWarning: invalid escape sequence '\s' + m = re.match(re.compile("^([^\s\;\,\:])[\s\;\,\:]*(.*)$"), line, flags=0) + /opt/mambaforge/envs/bioconda/conda-bld/rnaredprint_1734228393242/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/design-energyshift.py:43: SyntaxWarning: invalid escape sequence '\(' + if re.match(re.compile("^[\(\)\.\{\}\[\]\<\>\\&]$"), line, flags=0): + /opt/mambaforge/envs/bioconda/conda-bld/rnaredprint_1734228393242/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/design-energyshift.py:46: SyntaxWarning: invalid escape sequence '\ ' + elif re.match(re.compile("^[\ ACGTUWSMKRYBDHVN\&\]$", re.IGNORECASE), line, flags=0): + /opt/mambaforge/envs/bioconda/conda-bld/rnaredprint_1734228393242/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/design-energyshift.py:49: SyntaxWarning: invalid escape sequence '\&' + if re.match(re.compile("^[ACGTU\&\]$", re.IGNORECASE), line, flags=0) and sequence == '': + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/conda-bld/rnaredprint_1734228393242/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/design-energyshift.py", line 14, in + from RNARedPrintSampler import RPSampler,gccontent + File "/opt/mambaforge/envs/bioconda/conda-bld/rnaredprint_1734228393242/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/RNARedPrintSampler.py", line 14, in + from distutils.dir_util import copy_tree + ModuleNotFoundError: No module named 'distutils' + WARNING: Tests failed for rnaredprint-0.3-py312h5fa12a8_1.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/rnaredprint_1734228393242/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/rnaredprint_1734228393242/test_tmp + RNARedPrint 0.3 + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/rnaredprint_1734228393242/test_tmp/conda_test_runner.sh']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: rnaredprint-0.3-py312h5fa12a8_1.tar.bz2 +# Last 100 lines of the build log. diff --git a/recipes/rnaredprint/meta.yaml b/recipes/rnaredprint/meta.yaml index 93f3273933725..5bd8bde102d04 100644 --- a/recipes/rnaredprint/meta.yaml +++ b/recipes/rnaredprint/meta.yaml @@ -13,7 +13,7 @@ about: summary: Tree-decomposition based dynamic programming algorithm for multiple target RNA design build: - number: 0 + number: 1 source: url: "https://github.com/yannponty/RNARedPrint/archive/v{{ version }}.tar.gz" diff --git a/recipes/rnashapes/build_failure.osx-64.yaml b/recipes/rnashapes/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..125e83eb2ce29 --- /dev/null +++ b/recipes/rnashapes/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: b6949c7bdfe5591a2e96df8440e7f38ec9ebd06be50c9d2c012606e786a2cda6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rnashapes-3.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rnashapes-3.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rnashapes-3.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rnashapes-3.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + make: Entering directory '$SRC_DIR/Misc/Applications/RNAshapes' + make all_normal + make[1]: Entering directory '$SRC_DIR/Misc/Applications/RNAshapes' + make compile \ + gapc_product="alg_mfe * (alg_dotBracket * alg_shapeX * alg_pfunc)" \ + gapc_options="--kbacktrace --no-coopt " \ + gapc_file="nodangle.gap" \ + gapc_binaryname="mfe_nodangle"; + make compile \ + gapc_product="alg_mfe * (alg_dotBracket * alg_shapeX * alg_pfunc)" \ + gapc_options="--kbacktrace --no-coopt " \ + gapc_file="overdangle.gap" \ + gapc_binaryname="mfe_overdangle"; + make[2]: Entering directory '$SRC_DIR/Misc/Applications/RNAshapes' + make[2]: Entering directory '$SRC_DIR/Misc/Applications/RNAshapes' + if [ ! -f "x86_64-apple-darwin13.4.0/RNAshapes_mfe_overdangle" ]; then \ + cd /var/folders/9f/9p4dh6hs5yddrk7drxq8rc_80000gn/T/tmp.UGKWyIWr && gapc -I $SRC_DIR/Misc/Applications/RNAshapes/../../../ -p "alg_mfe * (alg_dotBracket * alg_shapeX * alg_pfunc)" --kbacktrace --no-coopt $SRC_DIR/Misc/Applications/RNAshapes/../../..//overdangle.gap; \ + perl $SRC_DIR/Misc/Applications/RNAshapes/../../..///Misc/Applications/addRNAoptions.pl /var/folders/9f/9p4dh6hs5yddrk7drxq8rc_80000gn/T/tmp.UGKWyIWr/out.mf 0 'mfe_overdangle' 'alg_mfe * (alg_dotBracket * alg_shapeX * alg_pfunc)'; \ + cd /var/folders/9f/9p4dh6hs5yddrk7drxq8rc_80000gn/T/tmp.UGKWyIWr && make -f out.mf CPPFLAGS_EXTRA="-I $SRC_DIR/Misc/Applications/RNAshapes/../../../ -I ./" CXXFLAGS_EXTRA="-O3 -DNDEBUG" LDFLAGS_EXTRA=""; \ + install -d $SRC_DIR/Misc/Applications/RNAshapes/x86_64-apple-darwin13.4.0; \ + install /var/folders/9f/9p4dh6hs5yddrk7drxq8rc_80000gn/T/tmp.UGKWyIWr/out $SRC_DIR/Misc/Applications/RNAshapes/x86_64-apple-darwin13.4.0/RNAshapes_mfe_overdangle; \ + fi; + if [ ! -f "x86_64-apple-darwin13.4.0/RNAshapes_mfe_nodangle" ]; then \ + cd /var/folders/9f/9p4dh6hs5yddrk7drxq8rc_80000gn/T/tmp.NeNm2ehd && gapc -I $SRC_DIR/Misc/Applications/RNAshapes/../../../ -p "alg_mfe * (alg_dotBracket * alg_shapeX * alg_pfunc)" --kbacktrace --no-coopt $SRC_DIR/Misc/Applications/RNAshapes/../../..//nodangle.gap; \ + perl $SRC_DIR/Misc/Applications/RNAshapes/../../..///Misc/Applications/addRNAoptions.pl /var/folders/9f/9p4dh6hs5yddrk7drxq8rc_80000gn/T/tmp.NeNm2ehd/out.mf 0 'mfe_nodangle' 'alg_mfe * (alg_dotBracket * alg_shapeX * alg_pfunc)'; \ + cd /var/folders/9f/9p4dh6hs5yddrk7drxq8rc_80000gn/T/tmp.NeNm2ehd && make -f out.mf CPPFLAGS_EXTRA="-I $SRC_DIR/Misc/Applications/RNAshapes/../../../ -I ./" CXXFLAGS_EXTRA="-O3 -DNDEBUG" LDFLAGS_EXTRA=""; \ + install -d $SRC_DIR/Misc/Applications/RNAshapes/x86_64-apple-darwin13.4.0; \ + install /var/folders/9f/9p4dh6hs5yddrk7drxq8rc_80000gn/T/tmp.NeNm2ehd/out $SRC_DIR/Misc/Applications/RNAshapes/x86_64-apple-darwin13.4.0/RNAshapes_mfe_nodangle; \ + fi; + make[3]: Entering directory '/private/var/folders/9f/9p4dh6hs5yddrk7drxq8rc_80000gn/T/tmp.UGKWyIWr' + Including global makefile $PREFIX/share/gapc/config_darwin13.4.0.mf + make[3]: Entering directory '/private/var/folders/9f/9p4dh6hs5yddrk7drxq8rc_80000gn/T/tmp.NeNm2ehd' + Including global makefile $PREFIX/share/gapc/config_darwin13.4.0.mf + echo '#include "out.hh"' > out_main.cc + echo '#include "out.hh"' > out_main.cc + cat $PREFIX/include/rtlib/generic_main.cc >> out_main.cc + cat $PREFIX/include/rtlib/generic_main.cc >> out_main.cc + $PREFIX/bin/sed -i 's|gapc::Opts opts;||' out_main.cc + $PREFIX/bin/sed -i 's|gapc::Opts opts;||' out_main.cc + $PREFIX/bin/sed -i 's|\([^_]\)opts\.|\1gapc::Opts::getOpts()->|g' out_main.cc + $PREFIX/bin/sed -i 's|\([^_]\)opts\.|\1gapc::Opts::getOpts()->|g' out_main.cc + $PREFIX/bin/sed -i 's|obj.init(opts);|obj.init(\*gapc::Opts::getOpts());|g' out_main.cc + $PREFIX/bin/sed -i 's|obj.init(opts);|obj.init(\*gapc::Opts::getOpts());|g' out_main.cc + $PREFIX/bin/sed -i 's|#include .rtlib/generic_opts.hh.|#include "Extensions/rnaoptions.hh"|' out_main.cc + $PREFIX/bin/sed -i 's|#include .rtlib/generic_opts.hh.|#include "Extensions/rnaoptions.hh"|' out_main.cc + $PREFIX/bin/sed -i 's%#include .rtlib/generic_opts.hh.%#include "Extensions/rnaoptions.hh"%' out.hh out.cc + $PREFIX/bin/sed -i 's%#include .rtlib/generic_opts.hh.%#include "Extensions/rnaoptions.hh"%' out.hh out.cc + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bellmans-gapc_1721071508431/work=/usr/local/src/conda/bellmans-gapc-2024.01.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -MMD -MP -Wall -Wnon-virtual-dtor -Wno-unused-variable -Wno-parentheses -DNDEBUG -DBISONNEW -O3 -DNDEBUx86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/opt/mambaforge/envs/bioconda/conda-bld/bellmans-gapc_1721071508431/work=/usr/local/src/conda/bellmans-gapc-2024.01.12 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -std=c14 -MMD -MP -Wall -Wnon-virtual-dtor -Wno-unused-variable -Wno-parentheses -DNDEBUG -DBISONNEW -O3 -DNDEBUG -DWITH_RNAOPTIONS -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I $SRC_DIR/Misc/Applications/RNAshapes/../../../ -I ./ -I$PREFIX/include -I$PREFIX/include/ -I/opt/mambaforge/envs/bioconda/coG -DWITH_RNAOPTIONS -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I $SRC_DIR/Misc/Applications/RNAshapes/../../../ -I ./ -I$PREFIX/include -I$PREFIX/include/ -I$PREFIX/include/rtlib -I$PREFIX/include/librna -c -o out.o out.cc + nda-bld/rnashapes_1734535072347/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/rtlib -I$PREFIX/include/librna -c -o out.o out.cc + make[3]: Leaving directory '/private/var/folders/9f/9p4dh6hs5yddrk7drxq8rc_80000gn/T/tmp.UGKWyIWr' + make[3]: Leaving directory '/private/var/folders/9f/9p4dh6hs5yddrk7drxq8rc_80000gn/T/tmp.NeNm2ehd' + make[2]: Leaving directory '$SRC_DIR/Misc/Applications/RNAshapes' + make[2]: Leaving directory '$SRC_DIR/Misc/Applications/RNAshapes' + make[1]: Leaving directory '$SRC_DIR/Misc/Applications/RNAshapes' + make: Leaving directory '$SRC_DIR/Misc/Applications/RNAshapes' +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/rnashapes/meta.yaml b/recipes/rnashapes/meta.yaml index 0ba59f74cfb57..887af96a05dc5 100644 --- a/recipes/rnashapes/meta.yaml +++ b/recipes/rnashapes/meta.yaml @@ -14,7 +14,7 @@ source: url: https://github.com/jlab/fold-grammars/archive/{{ fold_grammars_version }}.tar.gz build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('rnashapes', max_pin="x") }} diff --git a/recipes/rnasnp/meta.yaml b/recipes/rnasnp/meta.yaml index 519fb7736c568..cb3ed03ac21da 100644 --- a/recipes/rnasnp/meta.yaml +++ b/recipes/rnasnp/meta.yaml @@ -9,7 +9,7 @@ source: build: # fails test on OSX skip: True # [osx] - number: 9 + number: 10 requirements: build: diff --git a/recipes/rnastructure/meta.yaml b/recipes/rnastructure/meta.yaml index 10976d6e6a4e0..35ee868eb2bed 100644 --- a/recipes/rnastructure/meta.yaml +++ b/recipes/rnastructure/meta.yaml @@ -11,7 +11,7 @@ source: url: http://rna.urmc.rochester.edu/Releases/{{ version }}/RNAstructureSource.tgz build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name | lower, max_pin="x.x") }} diff --git a/recipes/rnaz/meta.yaml b/recipes/rnaz/meta.yaml index 003d1e4781da3..22d6882df76cd 100644 --- a/recipes/rnaz/meta.yaml +++ b/recipes/rnaz/meta.yaml @@ -9,7 +9,7 @@ source: - "rnaz.patch" build: - number: 6 + number: 7 skip: True # [osx] diff --git a/recipes/rock/build_failure.linux-64.yaml b/recipes/rock/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..8ac8f6666d76f --- /dev/null +++ b/recipes/rock/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 9e0fec9eee6770ae4bcca3476a8d4c00042eb43dda567d02b3d1faf18d1714c3 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + perl: warning: Falling back to the standard locale ("C"). + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + perl: warning: Setting locale failed. + perl: warning: Please check that your locale settings: + LANGUAGE = (unset), + LC_ALL = (unset), + LANG = "C.UTF-8" + are supported and installed on your system. + perl: warning: Falling back to the standard locale ("C"). + checking build system type... x86_64-conda-linux-gnu + checking host system type... x86_64-conda-linux-gnu + checking target system type... x86_64-conda-linux-gnu + checking for a BSD-compatible install... /usr/bin/install -c + checking whether sleep supports fractional seconds... yes + checking filesystem timestamp resolution... 0.01 + checking whether build environment is sane... yes + /opt/conda/conda-bld/rock_1734148590596/work/missing: Unknown --is-lightweight' option + Try /opt/conda/conda-bld/rock_1734148590596/work/missing --help' for more information + configure: WARNING: 'missing' script is too old or missing + checking for a race-free mkdir -p... /usr/bin/mkdir -p + checking for gawk... gawk + checking whether make sets $(MAKE)... yes + checking whether make supports nested variables... yes + checking xargs -n works... yes + checking whether the C compiler works... yes + checking for C compiler default output file name... a.out + checking for suffix of executables... + checking whether we are cross compiling... no + checking for suffix of object files... o + checking whether the compiler supports GNU C... yes + checking whether $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c accepts -g... yes + checking for $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c option to enable C11 features... none needed + checking whether make supports the include directive... yes (GNU style) + checking dependency style of $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c... gcc3 + checking for x86_64-conda-linux-gnu-ranlib... $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + checking for pod2man... pod2man + checking that generated files are newer than configure... done + configure: creating ./config.status + config.status: creating Makefile + config.status: creating src/Makefile + config.status: creating test/Makefile + config.status: creating doc/Makefile + config.status: executing depfiles commands + Making all in . + make[1]: Entering directory '$SRC_DIR' + make[1]: Nothing to be done for 'all-am'. + make[1]: Leaving directory '$SRC_DIR' + Making all in src + make[1]: Entering directory '$SRC_DIR/src' + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DPACKAGE_NAME=\"rock\" -DPACKAGE_TARNAME=\"rock\" -DPACKAGE_VERSION=\"2.0\" -DPACKAGE_STRING=\"rock\ 2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"rock\" -DVERSION=\"2.0\" -I. -DDATADIR=\"$PREFIX/share/rock\" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rock-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT rock.o -MD -MP -MF .deps/rock.Tpo -c -o rock.o rock.cpp + mv -f .deps/rock.Tpo .deps/rock.Po + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DPACKAGE_NAME=\"rock\" -DPACKAGE_TARNAME=\"rock\" -DPACKAGE_VERSION=\"2.0\" -DPACKAGE_STRING=\"rock\ 2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"rock\" -DVERSION=\"2.0\" -I. -DDATADIR=\"$PREFIX/share/rock\" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rock-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT math_utils.o -MD -MP -MF .deps/math_utils.Tpo -c -o math_utils.o math_utils.cpp + mv -f .deps/math_utils.Tpo .deps/math_utils.Po + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DPACKAGE_NAME=\"rock\" -DPACKAGE_TARNAME=\"rock\" -DPACKAGE_VERSION=\"2.0\" -DPACKAGE_STRING=\"rock\ 2.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"rock\" -DVERSION=\"2.0\" -I. -DDATADIR=\"$PREFIX/share/rock\" -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rock-2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT low_level_utils.o -MD -MP -MF .deps/low_level_utils.Tpo -c -o low_level_utils.o low_level_utils.cpp + low_level_utils.cpp: In function 'long unsigned int getNodePhysMemory()': + low_level_utils.cpp:61:5: error: 'uint64_t' was not declared in this scope + 61 | uint64_t mem = 0; + | ^~~~~~~~ + low_level_utils.cpp:34:1: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + 33 | #include "low_level_utils.h" + |#include + 34 | + low_level_utils.cpp:80:9: error: 'mem' was not declared in this scope + 80 | mem=0; + | ^~~ + low_level_utils.cpp:82:5: error: 'mem' was not declared in this scope + 82 | mem=si.totalram; + | ^~~ + make[1]: *** [Makefile:486: low_level_utils.o] Error 1 + make[1]: Leaving directory '$SRC_DIR/src' + make: *** [Makefile:356: all-recursive] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/rock_1734148590596/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/rock_1734148590596/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/rock/meta.yaml b/recipes/rock/meta.yaml index 9ce0f442fe9d9..68974fb5aa829 100644 --- a/recipes/rock/meta.yaml +++ b/recipes/rock/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{sha256}}' build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/roguenarok/meta.yaml b/recipes/roguenarok/meta.yaml index 872c8b9630248..27b080a8a9c56 100644 --- a/recipes/roguenarok/meta.yaml +++ b/recipes/roguenarok/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.0.1" build: - number: 3 + number: 4 source: url: https://github.com/aberer/RogueNaRok/archive/refs/tags/v1.0.1.tar.gz diff --git a/recipes/ropebwt2/meta.yaml b/recipes/ropebwt2/meta.yaml index c8b6fc409490d..b90916f7539d0 100644 --- a/recipes/ropebwt2/meta.yaml +++ b/recipes/ropebwt2/meta.yaml @@ -3,7 +3,7 @@ package: version: "r187" build: - number: 9 + number: 10 run_exports: - {{ pin_subpackage('ropebwt2', max_pin="x.x.x") }} @@ -33,4 +33,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/rosella/build_failure.linux-64.yaml b/recipes/rosella/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..9c11ae0b689a8 --- /dev/null +++ b/recipes/rosella/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5793541e34cb338169217f0505bb9be883619c87ad3ddf4706396ab3ba05e379 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [32mpython [3.8.10|3.9.4|3.9.5|3.9.6|3.9.7][0m, which can be installed (as previously explained); + [31mpython [3.8.12|3.9.10][0m, which cannot be installed (as previously explained); + [31mpython [3.8.12|3.9.7][0m, which cannot be installed (as previously explained); + [32mpython [3.6.11|3.6.12|...|3.9.1][0m, which can be installed (as previously explained); + [32mpython [3.6.12|3.8.6|3.9.1][0m, which can be installed (as previously explained); + [32mpython [3.6.13|3.8.8|3.9.2][0m, which can be installed (as previously explained); + [31mpython [3.9.10|3.9.12|...|3.9.9][0m, which cannot be installed (as previously explained); + [31mpython [3.9.12|3.9.16|3.9.17|3.9.18][0m conflicts with any installable versions previously reported; + [32mmatplotlib-base [3.8.3|3.8.4][0m would require + [32mnumpy >=1.26.4,<2.0a0 [0m, which can be installed; + [32mpython_abi 3.12.* *_cp312[0m, which can be installed; + [32mmatplotlib-base [3.8.3|3.8.4|3.9.1|3.9.2][0m would require + [32mpypy3.9 >=7.3.15 [0m, which can be installed; + [32mpython >=3.9,<3.10.0a0 [0m with the potential options + [32mpython [3.10.0|3.10.1|...|3.9.9][0m, which can be installed (as previously explained); + [32mpython [3.10.4|3.8.13|3.9.12][0m, which can be installed (as previously explained); + [32mpython [3.10.5|3.9.13][0m, which can be installed (as previously explained); + [32mpython [3.10.7|3.10.8|...|3.9.15][0m, which can be installed (as previously explained); + [32mpython [3.8.10|3.9.4|3.9.5|3.9.6|3.9.7][0m, which can be installed (as previously explained); + [31mpython [3.8.12|3.9.10][0m, which cannot be installed (as previously explained); + [31mpython [3.8.12|3.9.7][0m, which cannot be installed (as previously explained); + [32mpython [3.6.11|3.6.12|...|3.9.1][0m, which can be installed (as previously explained); + [32mpython [3.6.12|3.8.6|3.9.1][0m, which can be installed (as previously explained); + [32mpython [3.6.13|3.8.8|3.9.2][0m, which can be installed (as previously explained); + [31mpython [3.9.10|3.9.12|...|3.9.9][0m, which cannot be installed (as previously explained); + [31mpython [3.9.12|3.9.16|3.9.17|3.9.18][0m conflicts with any installable versions previously reported; + [32mpython_abi 3.9 *_pypy39_pp73[0m, which can be installed; + [32mmatplotlib-base [3.8.4|3.9.1|3.9.2|3.9.3|3.9.4][0m would require + [32mpython_abi 3.12.* *_cp312[0m, which can be installed; + [32mmatplotlib-base [3.9.2|3.9.3|3.9.4][0m would require + [32mpython_abi 3.13.* *_cp313[0m, which can be installed; + [32mnumba >=0.53,<=0.57 [0m is installable with the potential options + [31mnumba 0.57.0[0m would require + [31mnumpy >=1.21,!=1.22.0,!=1.22.1,!=1.22.2,<1.25 [0m, which conflicts with any installable versions previously reported; + [31mnumba [0.56.2|0.56.3|0.56.4][0m would require + [31mnumpy >=1.18,!=1.22.0,!=1.22.1,!=1.22.2,<1.24 [0m, which conflicts with any installable versions previously reported; + [32mnumba [0.53.0|0.53.1][0m would require + [32mpython >=3.6,<3.7.0a0 [0m with the potential options + [32mpython [3.10.0|3.10.1|...|3.9.9][0m, which can be installed (as previously explained); + [32mpython [3.6.7|3.6.9|3.8.0|3.8.1][0m, which can be installed (as previously explained); + [32mpython [3.6.10|3.6.9|3.8.2][0m, which can be installed (as previously explained); + [32mpython [3.6.10|3.6.11|...|3.8.5][0m, which can be installed (as previously explained); + [32mpython [3.6.10|3.6.9|3.8.2][0m, which can be installed (as previously explained); + [32mpython [3.6.11|3.6.12|...|3.9.1][0m, which can be installed (as previously explained); + [32mpython [3.6.12|3.8.6|3.9.1][0m, which can be installed (as previously explained); + [32mpython [3.6.13|3.8.8|3.9.2][0m, which can be installed (as previously explained); + [32mpython [3.6.0|3.6.1|...|3.6.5][0m would require + [32mopenssl 1.0.* [0m, which can be installed; + [32mpython 3.6.6[0m would require + [32mopenssl >=1.0.2o,<1.0.3a [0m, which can be installed; + [32mpython [3.6.6|3.6.7][0m would require + [32mopenssl >=1.0.2p,<1.0.3a [0m, which can be installed; + [32mnumba [0.53.0|0.53.1][0m would require + [32mllvmlite >=0.36.0,<0.37.0a0 [0m with the potential options + [32mllvmlite 0.36.0[0m would require + [32mpython >=3.6,<3.7.0a0 [0m, which can be installed (as previously explained); + [32mllvmlite 0.36.0[0m would require + [32mpypy3.6 >=7.3.3 [0m, which can be installed (as previously explained); + [32mllvmlite [0.36.0|0.37.0|0.38.0|0.38.1][0m would require + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [32mnumba [0.54.0|0.54.1|0.55.0|0.55.1|0.55.2][0m would require + [32mllvmlite [>=0.37.0,<0.38.0a0 |>=0.38.0,<0.39.0a0 |>=0.38.1,<0.39.0a0 ][0m, which can be installed (as previously explained); + [32mnumba 0.57.0[0m would require + [32mpython >=3.10,<3.11.0a0 [0m with the potential options + [31mpython 3.10.0[0m, which cannot be installed (as previously explained); + [32mpython [3.10.0|3.10.1|...|3.9.9][0m, which can be installed (as previously explained); + [31mpython [3.10.1|3.10.10|...|3.10.9][0m conflicts with any installable versions previously reported; + [32mpython [3.10.4|3.8.13|3.9.12][0m, which can be installed (as previously explained); + [32mpython [3.10.5|3.9.13][0m, which can be installed (as previously explained); + [32mpython [3.10.6|3.11.0][0m, which can be installed (as previously explained); + [32mpython [3.10.7|3.10.8|...|3.9.15][0m, which can be installed (as previously explained); + [32mpython_abi 3.10.* *_cp310[0m, which can be installed; + [32mnumba 0.57.0[0m would require + [32mpython >=3.11,<3.12.0a0 [0m with the potential options + [32mpython [3.10.6|3.11.0][0m, which can be installed (as previously explained); + [32mpython [3.10.7|3.10.8|...|3.9.15][0m, which can be installed (as previously explained); + [31mpython [3.11.0|3.11.1|...|3.11.9][0m conflicts with any installable versions previously reported; + [32mpython_abi 3.11.* *_cp311[0m, which can be installed; + [31mopenssl >=3.4.0,<4.0a0 [0m is not installable because it conflicts with any installable versions previously reported; + [32mpython >=3.8,<=3.10 [0m is installable with the potential options + [31mpython 3.10.0[0m, which cannot be installed (as previously explained); + [32mpython [3.10.0|3.10.1|...|3.9.9][0m, which can be installed (as previously explained); + [32mpython [3.10.4|3.8.13|3.9.12][0m, which can be installed (as previously explained); + [32mpython [3.10.5|3.9.13][0m, which can be installed (as previously explained); + [32mpython [3.10.7|3.10.8|...|3.9.15][0m, which can be installed (as previously explained); + [32mpython [3.8.13|3.8.16|3.8.5][0m, which can be installed; + [32mpython [3.6.7|3.6.9|3.8.0|3.8.1][0m, which can be installed (as previously explained); + [32mpython [3.8.10|3.9.4|3.9.5|3.9.6|3.9.7][0m, which can be installed (as previously explained); + [31mpython [3.8.12|3.9.10][0m, which cannot be installed (as previously explained); + [31mpython [3.8.12|3.8.13|...|3.8.20][0m conflicts with any installable versions previously reported; + [31mpython [3.8.12|3.9.7][0m, which cannot be installed (as previously explained); + [32mpython 3.8.2[0m, which can be installed (as previously explained); + [32mpython [3.6.10|3.6.9|3.8.2][0m, which can be installed (as previously explained); + [32mpython [3.6.10|3.6.11|...|3.8.5][0m, which can be installed (as previously explained); + [32mpython [3.6.10|3.6.9|3.8.2][0m, which can be installed (as previously explained); + [32mpython [3.6.11|3.6.12|...|3.9.1][0m, which can be installed (as previously explained); + [32mpython [3.6.12|3.8.6|3.9.1][0m, which can be installed (as previously explained); + [32mpython [3.6.13|3.8.8|3.9.2][0m, which can be installed (as previously explained); + [31mpython [3.9.10|3.9.12|...|3.9.9][0m, which cannot be installed (as previously explained); + [31mpython [3.9.12|3.9.16|3.9.17|3.9.18][0m conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/rosella/meta.yaml b/recipes/rosella/meta.yaml index 23f5ba01faa0d..d6dae2b030437 100644 --- a/recipes/rosella/meta.yaml +++ b/recipes/rosella/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ hash }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/rpbp/meta.yaml b/recipes/rpbp/meta.yaml index d4c9bab5756d3..5a7c8e98fbb26 100644 --- a/recipes/rpbp/meta.yaml +++ b/recipes/rpbp/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 skip: True # [py >= 311 ] script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv && compile-rpbp-models" entry_points: diff --git a/recipes/rpsbproc/meta.yaml b/recipes/rpsbproc/meta.yaml index 6f42c04bad539..0f402ea550450 100644 --- a/recipes/rpsbproc/meta.yaml +++ b/recipes/rpsbproc/meta.yaml @@ -24,7 +24,7 @@ source: - update_configsub.patch build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/rrikindp/build_failure.linux-64.yaml b/recipes/rrikindp/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..54a0d2e4d0a04 --- /dev/null +++ b/recipes/rrikindp/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 8b89c931a28d44765d87b183327dbb895343fcf51ef78de4d39cedd291854442 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + 788 | operator=(initializer_list __l) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ + error: command '/opt/conda/conda-bld/rrikindp_1734317151413/_build_env/bin/x86_64-conda-linux-gnu-c' failed with exit code 1 + [1;31merror[0m: [1msubprocess-exited-with-error[0m + + [31m[0m [32mpython setup.py bdist_wheel[0m did not run successfully. + [31m[0m exit code: [1;36m1[0m + [31m>[0m See above for output. + + [1;35mnote[0m: This error originates from a subprocess, and is likely not a problem with pip. + [1;35mfull command[0m: [34m/opt/conda/conda-bld/rrikindp_1734317151413/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python -u -c '[0m + [34m exec(compile('"'"''"'"''"'"'[0m + [34m # This is -- a caller that pip uses to run setup.py[0m + [34m #[0m + [34m # - It imports setuptools before invoking setup.py, to enable projects that directly[0m + [34m # import from distutils.core to work with newer packaging standards.[0m + [34m # - It provides a clear error message when setuptools is not installed.[0m + [34m # - It sets sys.argv[0] to the underlying setup.py, when invoking setup.py so[0m + [34m # setuptools doesn'"'"'t think the script is -c. This avoids the following warning:[0m + [34m # manifest_maker: standard file '"'"'-c'"'"' not found".[0m + [34m # - It generates a shim setup.py, for handling setup.cfg-only projects.[0m + [34m import os, sys, tokenize[0m + [34m [0m + [34m try:[0m + [34m import setuptools[0m + [34m except ImportError as error:[0m + [34m print([0m + [34m "ERROR: Can not execute setup.py since setuptools is not available in "[0m + [34m "the build environment.",[0m + [34m file=sys.stderr,[0m + [34m )[0m + [34m sys.exit(1)[0m + [34m [0m + [34m __file__ = %r[0m + [34m sys.argv[0] = __file__[0m + [34m [0m + [34m if os.path.exists(__file__):[0m + [34m filename = __file__[0m + [34m with tokenize.open(__file__) as f:[0m + [34m setup_py_code = f.read()[0m + [34m else:[0m + [34m filename = ""[0m + [34m setup_py_code = "from setuptools import setup; setup()"[0m + [34m [0m + [34m exec(compile(setup_py_code, filename, "exec"))[0m + [34m '"'"''"'"''"'"' % ('"'"'/opt/conda/conda-bld/rrikindp_1734317151413/work/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-inxq7yuu[0m + [1;35mcwd[0m: /opt/conda/conda-bld/rrikindp_1734317151413/work/ + Building wheel for rrikindp (setup.py): finished with status 'error' + [31m ERROR: Failed building wheel for rrikindp[0m[31m + [0m Running setup.py clean for rrikindp + Running command python setup.py clean + /opt/conda/conda-bld/rrikindp_1734317151413/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + /opt/conda/conda-bld/rrikindp_1734317151413/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.11/site-packages/setuptools/dist.py:330: InformationOnly: Normalizing 'v0.0.2' to '0.0.2' + self.metadata.version = self._normalize_version(self.metadata.version) + running clean + removing 'build/temp.linux-x86_64-cpython-311' (and everything under it) + removing 'build/lib.linux-x86_64-cpython-311' (and everything under it) + 'build/bdist.linux-x86_64' does not exist -- can't clean it + 'build/scripts-3.11' does not exist -- can't clean it + removing 'build' + Failed to build rrikindp + [31mERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (rrikindp)[0m[31m + [0mException information: + Traceback (most recent call last): + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + ^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper + return func(self, options, args) + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/commands/install.py", line 434, in run + raise InstallationError( + pip._internal.exceptions.InstallationError: ERROR: Failed to build installable wheels for some pyproject.toml based projects (rrikindp) + Removed build tracker: '/tmp/pip-build-tracker-jgp1g4jx' + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/rrikindp_1734317151413/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/rrikindp_1734317151413/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/rrikindp/build_failure.osx-64.yaml b/recipes/rrikindp/build_failure.osx-64.yaml index 17f0d029fab2a..222bf13d68d05 100644 --- a/recipes/rrikindp/build_failure.osx-64.yaml +++ b/recipes/rrikindp/build_failure.osx-64.yaml @@ -1,104 +1,104 @@ -recipe_sha: 0e067df3076e62a0e6fa72ecf0654c81ddd7442b0463d16a8d755a789705b475 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 8b89c931a28d44765d87b183327dbb895343fcf51ef78de4d39cedd291854442 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions - precs = _install_actions(prefix, index, specs)["LINK"] - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions - txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction - unlink_precs, link_precs = self.solve_for_diff( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff - final_precs = self.solve_final_state( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state - out_state = self._solving_loop(in_state, out_state, index) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop - solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt - new_conflicts = self._maybe_raise_for_problems( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems - self._maybe_raise_for_conda_build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build - raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("python_abi=3.10[build=*_cp310]"), MatchSpec("viennarna==2.6.2=py310pl5321hb5a725e_0")} - Encountered problems while solving: - - package viennarna-2.6.2-py310pl5321hb5a725e_0 requires python_abi 3.10.* *_cp310, but none of the providers can be installed + - llvm-openmp >=18.1.8 + - matplotlib-base >=3.7.0 + - viennarna >=2.6.0 + - viennarna >=2.7.0,<2.8.0a0 + - python_abi 3.10.* *_cp310 + - pandas >=2.0.0 + - boost-cpp + - python >=3.10,<3.11.0a0 + - intarna >=3.4.1,<3.5.0a0 + - libcxx >=18 + test: + commands: + - RRIkinDP --version + imports: + - rrikindp + about: + description: 'RRIkinDP evaluated thermodynamic and kinetic features of RNA-RNA interactions. + As input, two RNA - Could not solve for environment specs - The following packages are incompatible - python 3.11.* *_cpython is installable and it requires - python_abi 3.11.* *_cp311, which can be installed; - viennarna >=2.6.0 is not installable because there are no viable options - viennarna [2.6.2|2.6.3|2.6.4] would require - python_abi 3.10.* *_cp310, which conflicts with any installable versions previously reported; - viennarna [2.6.2|2.6.3|2.6.4] would require - python_abi 3.8.* *_cp38, which conflicts with any installable versions previously reported; - viennarna [2.6.2|2.6.3|2.6.4] would require - python_abi 3.9.* *_cp39, which conflicts with any installable versions previously reported. + sequences as well as their interaction structure is provided. The tool generates + the state space of - During handling of the above exception, another exception occurred: + all intermediate interactions from single base pair interactions to the full input + interaction. - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2308, in build - output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs - for output_dict, m in deepcopy(_m).get_output_metadata_set( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 2737, in get_output_metadata_set - conda_packages = finalize_outputs_pass( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/metadata.py", line 1095, in finalize_outputs_pass - fm = finalize_metadata( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata - build_unsat, host_unsat = add_upstream_pins( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins - host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files - deps, precs, unsat = get_env_dependencies( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies - precs = environ.get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions - precs = get_package_records( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions - precs = _install_actions(prefix, index, specs)["LINK"] - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions - txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction - unlink_precs, link_precs = self.solve_for_diff( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff - final_precs = self.solve_final_state( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state - out_state = self._solving_loop(in_state, out_state, index) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop - solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt - new_conflicts = self._maybe_raise_for_problems( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems - self._maybe_raise_for_conda_build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build - raise exc - conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("python_abi=3.10[build=*_cp310]"), MatchSpec("viennarna==2.6.2=py310pl5321hb5a725e_0")} - Encountered problems while solving: - - package viennarna-2.6.2-py310pl5321hb5a725e_0 requires python_abi 3.10.* *_cp310, but none of the providers can be installed + On top of this state space it computes the barrier energy for the best direct + path from a given - Could not solve for environment specs - The following packages are incompatible - python 3.11.* *_cpython is installable and it requires - python_abi 3.11.* *_cp311, which can be installed; - viennarna >=2.6.0 is not installable because there are no viable options - viennarna [2.6.2|2.6.3|2.6.4] would require - python_abi 3.10.* *_cp310, which conflicts with any installable versions previously reported; - viennarna [2.6.2|2.6.3|2.6.4] would require - python_abi 3.8.* *_cp38, which conflicts with any installable versions previously reported; - viennarna [2.6.2|2.6.3|2.6.4] would require - python_abi 3.9.* *_cp39, which conflicts with any installable versions previously reported. + start interaction to the full input interaction. + + ' + dev_url: https://github.com/mwaldl/RRIkinDP + doc_url: https://doi.org/10.1101/2023.07.28.548983 + home: https://github.com/mwaldl/RRIkinDP + license: GPL-3.0-only + license_family: GPL + license_file: COPYING + summary: Evaluation of thermodynamic and kinetic features of RNA-RNA interactions. + extra: + copy_test_source_files: true + final: true + recipe-maintainers: + - mwaldl + - s-will + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/rrikindp_1734491721461/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/rrikindp_1734491721461/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/rrikindp_1734491721461/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/rrikindp_1734491721461/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rrikindp-0.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rrikindp-0.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rrikindp-0.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rrikindp-0.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix # Last 100 lines of the build log. diff --git a/recipes/rrikindp/meta.yaml b/recipes/rrikindp/meta.yaml index 426d6c21432a2..d00ae10f9f6c9 100644 --- a/recipes/rrikindp/meta.yaml +++ b/recipes/rrikindp/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 3bdaa7657224b90945d864d0238010cf3337975f58c41106ab60427dd52bc93f build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('rrikindp', max_pin="x.x,x") }} diff --git a/recipes/rscape/0.8.3/meta.yaml b/recipes/rscape/0.8.3/meta.yaml index baedc35a71a2d..f60d407af6148 100644 --- a/recipes/rscape/0.8.3/meta.yaml +++ b/recipes/rscape/0.8.3/meta.yaml @@ -11,7 +11,7 @@ source: - R2R_Makefile.in.patch build: - number: 7 + number: 8 skip: True # [osx] diff --git a/recipes/rscape/build_failure.osx-64.yaml b/recipes/rscape/build_failure.osx-64.yaml index 33470067d516c..95a33ff617e26 100644 --- a/recipes/rscape/build_failure.osx-64.yaml +++ b/recipes/rscape/build_failure.osx-64.yaml @@ -1,104 +1,106 @@ -recipe_sha: 263b6ab291fe5929108bee7c97f59138b2d7979a8c285224feb8b7cb4e507371 # The commit at which this recipe failed to build. +recipe_sha: 03b9560d3961c28788b036484b99757fbadba208ab52a09b9277b3d78afc6fa3 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmscan.o -c hmmscan.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmscan hmmscan.o -lhmmer -leasel -ldivsufsort -lm - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmsearch.o -c hmmsearch.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmsearch hmmsearch.o -lhmmer -leasel -ldivsufsort -lm - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmsim.o -c hmmsim.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmsim hmmsim.o -lhmmer -leasel -ldivsufsort -lm - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmstat.o -c hmmstat.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmstat hmmstat.o -lhmmer -leasel -ldivsufsort -lm - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I../easel -I../libdivsufsort -I../easel -I. -I. -o jackhmmer.o -c jackhmmer.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o jackhmmer jackhmmer.o -lhmmer -leasel -ldivsufsort -lm - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I../easel -I../libdivsufsort -I../easel -I. -I. -o phmmer.o -c phmmer.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o phmmer phmmer.o -lhmmer -leasel -ldivsufsort -lm - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I../easel -I../libdivsufsort -I../easel -I. -I. -o nhmmer.o -c nhmmer.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o nhmmer nhmmer.o -lhmmer -leasel -ldivsufsort -lm - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I../easel -I../libdivsufsort -I../easel -I. -I. -o nhmmscan.o -c nhmmscan.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o nhmmscan nhmmscan.o -lhmmer -leasel -ldivsufsort -lm - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I../easel -I../libdivsufsort -I../easel -I. -I. -o makehmmerdb.o -c makehmmerdb.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o makehmmerdb makehmmerdb.o -lhmmer -leasel -ldivsufsort -lm - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmc2.o -c hmmc2.c - hmmc2.c:524:115: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat] - printf("Hit offset %d did not match expected. Found %d, expected %lu\n", i, (buf_offset-hits_start), stats->hit_offsets[i]); - ~~~ ^~~~~~~~~~~~~~~~~~~~~ - %llu 1 warning generated. - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmc2 hmmc2.o -lhmmer -leasel -ldivsufsort -lm - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmerfm-exactmatch.o -c hmmerfm-exactmatch.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmerfm-exactmatch hmmerfm-exactmatch.o -lhmmer -leasel -ldivsufsort -lm + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmscan hmmscan.o -lhmmer -leasel -ldivsufsort -lm + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmsearch.o -c hmmsearch.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmsearch hmmsearch.o -lhmmer -leasel -ldivsufsort -lm + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmsim.o -c hmmsim.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmsim hmmsim.o -lhmmer -leasel -ldivsufsort -lm + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmstat.o -c hmmstat.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmstat hmmstat.o -lhmmer -leasel -ldivsufsort -lm + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I../easel -I../libdivsufsort -I../easel -I. -I. -o jackhmmer.o -c jackhmmer.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o jackhmmer jackhmmer.o -lhmmer -leasel -ldivsufsort -lm + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I../easel -I../libdivsufsort -I../easel -I. -I. -o phmmer.o -c phmmer.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o phmmer phmmer.o -lhmmer -leasel -ldivsufsort -lm + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I../easel -I../libdivsufsort -I../easel -I. -I. -o nhmmer.o -c nhmmer.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o nhmmer nhmmer.o -lhmmer -leasel -ldivsufsort -lm + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I../easel -I../libdivsufsort -I../easel -I. -I. -o nhmmscan.o -c nhmmscan.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o nhmmscan nhmmscan.o -lhmmer -leasel -ldivsufsort -lm + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I../easel -I../libdivsufsort -I../easel -I. -I. -o makehmmerdb.o -c makehmmerdb.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o makehmmerdb makehmmerdb.o -lhmmer -leasel -ldivsufsort -lm + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmc2.o -c hmmc2.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmc2 hmmc2.o -lhmmer -leasel -ldivsufsort -lm + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I../easel -I../libdivsufsort -I../easel -I. -I. -o hmmerfm-exactmatch.o -c hmmerfm-exactmatch.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -pthread -DHAVE_CONFIG_H -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmerfm-exactmatch hmmerfm-exactmatch.o -lhmmer -leasel -ldivsufsort -lm make[1]: Leaving directory '$SRC_DIR/lib/hmmer/src' make -C lib/R-view/src all make[1]: Entering directory '$SRC_DIR/lib/R-view/src' - x86_64-apple-darwin13.4.0-clang -I../../../lib/hmmer/src -I../../../lib/hmmer/easel -I../../../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o rview_contacts.o -c rview_contacts.c - x86_64-apple-darwin13.4.0-clang -I../../../lib/hmmer/src -I../../../lib/hmmer/easel -I../../../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o rview_cmap.o -c rview_cmap.c - x86_64-apple-darwin13.4.0-clang -I../../../lib/hmmer/src -I../../../lib/hmmer/easel -I../../../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o rview_matrix.o -c rview_matrix.c - x86_64-apple-darwin13.4.0-clang -I../../../lib/hmmer/src -I../../../lib/hmmer/easel -I../../../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o rview_pdbfile.o -c rview_pdbfile.c + x86_64-apple-darwin13.4.0-clang -I../../../lib/hmmer/src -I../../../lib/hmmer/easel -I../../../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o rview_contacts.o -c rview_contacts.c + x86_64-apple-darwin13.4.0-clang -I../../../lib/hmmer/src -I../../../lib/hmmer/easel -I../../../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o rview_cmap.o -c rview_cmap.c + x86_64-apple-darwin13.4.0-clang -I../../../lib/hmmer/src -I../../../lib/hmmer/easel -I../../../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o rview_matrix.o -c rview_matrix.c + x86_64-apple-darwin13.4.0-clang -I../../../lib/hmmer/src -I../../../lib/hmmer/easel -I../../../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o rview_pdbfile.o -c rview_pdbfile.c /opt/mambaforge/envs/bioconda/bin/ar -r librview.a rview_contacts.o rview_cmap.o rview_matrix.o rview_pdbfile.o > /dev/null 2>&1 - x86_64-apple-darwin13.4.0-clang -I../../../lib/hmmer/src -I../../../lib/hmmer/easel -I../../../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o R-view.o -c R-view.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I../../../lib/hmmer/src -I../../../lib/hmmer/easel -I../../../src -L../../../lib/hmmer/src -L../../../lib/hmmer/easel -L../../../src -o R-view R-view.o rview_contacts.o rview_cmap.o rview_matrix.o rview_pdbfile.o -lhmmer -leasel -lm + x86_64-apple-darwin13.4.0-clang -I../../../lib/hmmer/src -I../../../lib/hmmer/easel -I../../../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o R-view.o -c R-view.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I../../../lib/hmmer/src -I../../../lib/hmmer/easel -I../../../src -L../../../lib/hmmer/src -L../../../lib/hmmer/easel -L../../../src -o R-view R-view.o rview_contacts.o rview_cmap.o rview_matrix.o rview_pdbfile.o -lhmmer -leasel -lm make[1]: Leaving directory '$SRC_DIR/lib/R-view/src' make -C src all make[1]: Entering directory '$SRC_DIR/src' - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o e1_bg.o -c e1_bg.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o e1_model.o -c e1_model.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o e1_rate.o -c e1_rate.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o e1_emit.o -c e1_emit.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o e1_simulate.o -c e1_simulate.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o e2_profilesq.o -c e2_profilesq.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o allbranchmsa.o -c allbranchmsa.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o contactmap.o -c contactmap.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o cacofold.o -c cacofold.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o covgrammars.o -c covgrammars.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o correlators.o -c correlators.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o covariation.o -c covariation.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o maxcov.o -c maxcov.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o logsum.o -c logsum.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o minimize.o -c minimize.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o miscellaneous.o -c miscellaneous.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o msamanip.o -c msamanip.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o msatree.o -c msatree.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o plot.o -c plot.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o power.o -c power.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o pottsbuild.o -c pottsbuild.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o pottsscore.o -c pottsscore.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o pottsim.o -c pottsim.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o r2rdepict.o -c r2rdepict.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o ratematrix.o -c ratematrix.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o ratebuilder.o -c ratebuilder.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o ribosum_matrix.o -c ribosum_matrix.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o structure.o -c structure.c - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o cov_simulate.o -c cov_simulate.c - /opt/mambaforge/envs/bioconda/bin/ar -r libsrc.a e1_bg.o e1_model.o e1_rate.o e1_emit.o e1_simulate.o e2_profilesq.o allbranchmsa.o contactmap.o cacofold.o covgrammars.o correlators.o covariation.o maxcov.o logsum.o minimize.o miscellaneous.o msamanip.o msatree.o plot.o power.o pottsbuild.o pottsscore.o pottsim.o r2rdepict.o ratematrix.o ratebuilder.o ribosum_matrix.o structure.o cov_simulate.o > /dev/null 2>&1 - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o msafilter.o -c msafilter.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -L../lib/hmmer/src -L../lib/hmmer/easel -L../lib/R-view/src -L../src -o msafilter msafilter.o e1_bg.o e1_model.o e1_rate.o e1_emit.o e1_simulate.o e2_profilesq.o allbranchmsa.o contactmap.o cacofold.o covgrammars.o correlators.o covariation.o maxcov.o logsum.o minimize.o miscellaneous.o msamanip.o msatree.o plot.o power.o pottsbuild.o pottsscore.o pottsim.o r2rdepict.o ratematrix.o ratebuilder.o ribosum_matrix.o structure.o cov_simulate.o -lhmmer -lrview -leasel -lm - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o appcov.o -c appcov.c - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -L../lib/hmmer/src -L../lib/hmmer/easel -L../lib/R-view/src -L../src -o appcov appcov.o e1_bg.o e1_model.o e1_rate.o e1_emit.o e1_simulate.o e2_profilesq.o allbranchmsa.o contactmap.o cacofold.o covgrammars.o correlators.o covariation.o maxcov.o logsum.o minimize.o miscellaneous.o msamanip.o msatree.o plot.o power.o pottsbuild.o pottsscore.o pottsim.o r2rdepict.o ratematrix.o ratebuilder.o ribosum_matrix.o structure.o cov_simulate.o -lhmmer -lrview -leasel -lm - x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o R-scape.o -c R-scape.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o e1_bg.o -c e1_bg.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o e1_model.o -c e1_model.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o e1_rate.o -c e1_rate.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o e1_emit.o -c e1_emit.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o e1_simulate.o -c e1_simulate.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o e2_profilesq.o -c e2_profilesq.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o allbranchmsa.o -c allbranchmsa.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o contactmap.o -c contactmap.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o cacofold.o -c cacofold.c R-scape.c:739:74: error: incompatible integer to pointer conversion assigning to 'char *' from 'int' [-Wint-conversion] - cfg.treefile = FALSE; if (esl_opt_IsOn(go, "--treefile")) cfg.treefile = TRUE; // input a phylogenetic tree - ^ ~~~~ + 739 | cfg.treefile = FALSE; if (esl_opt_IsOn(go, "--treefile")) cfg.treefile = TRUE; // input a phylogenetic tree + | ^ ~~~~ 1 error generated. make[1]: *** [Makefile:155: R-scape.o] Error 1 - make[1]: Leaving directory '$SRC_DIR/src' make: *** [Makefile:98: all] Error 2 Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o covgrammars.o -c covgrammars.c + utils.check_call_env( + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o correlators.o -c correlators.c + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o covariation.o -c covariation.c raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/rscape_1685392557933/work/conda_build.sh']' returned non-zero exit status 2. + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/rscape_1734474720518/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o maxcov.o -c maxcov.c + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o logsum.o -c logsum.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o minimize.o -c minimize.c + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o miscellaneous.o -c miscellaneous.c + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/rscape_1734474720518/work/conda_build.sh']' returned non-zero exit status 2. + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o msamanip.o -c msamanip.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o msatree.o -c msatree.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o plot.o -c plot.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o power.o -c power.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o pottsbuild.o -c pottsbuild.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o pottsscore.o -c pottsscore.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o pottsim.o -c pottsim.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o r2rdepict.o -c r2rdepict.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o ratematrix.o -c ratematrix.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o ratebuilder.o -c ratebuilder.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o ribosum_matrix.o -c ribosum_matrix.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o structure.o -c structure.c + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o cov_simulate.o -c cov_simulate.c + /opt/mambaforge/envs/bioconda/bin/ar -r libsrc.a e1_bg.o e1_model.o e1_rate.o e1_emit.o e1_simulate.o e2_profilesq.o allbranchmsa.o contactmap.o cacofold.o covgrammars.o correlators.o covariation.o maxcov.o logsum.o minimize.o miscellaneous.o msamanip.o msatree.o plot.o power.o pottsbuild.o pottsscore.o pottsim.o r2rdepict.o ratematrix.o ratebuilder.o ribosum_matrix.o structure.o cov_simulate.o > /dev/null 2>&1 + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o msafilter.o -c msafilter.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -L../lib/hmmer/src -L../lib/hmmer/easel -L../lib/R-view/src -L../src -o msafilter msafilter.o e1_bg.o e1_model.o e1_rate.o e1_emit.o e1_simulate.o e2_profilesq.o allbranchmsa.o contactmap.o cacofold.o covgrammars.o correlators.o covariation.o maxcov.o logsum.o minimize.o miscellaneous.o msamanip.o msatree.o plot.o power.o pottsbuild.o pottsscore.o pottsim.o r2rdepict.o ratematrix.o ratebuilder.o ribosum_matrix.o structure.o cov_simulate.o -lhmmer -lrview -leasel -lm + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o appcov.o -c appcov.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -L../lib/hmmer/src -L../lib/hmmer/easel -L../lib/R-view/src -L../src -o appcov appcov.o e1_bg.o e1_model.o e1_rate.o e1_emit.o e1_simulate.o e2_profilesq.o allbranchmsa.o contactmap.o cacofold.o covgrammars.o correlators.o covariation.o maxcov.o logsum.o minimize.o miscellaneous.o msamanip.o msatree.o plot.o power.o pottsbuild.o pottsscore.o pottsim.o r2rdepict.o ratematrix.o ratebuilder.o ribosum_matrix.o structure.o cov_simulate.o -lhmmer -lrview -leasel -lm + x86_64-apple-darwin13.4.0-clang -I../lib/hmmer/src -I../lib/hmmer/easel -I../lib/R-view/src -I../src -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rscape-1.4.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -o R-scape.o -c R-scape.c + make[1]: Leaving directory '$SRC_DIR/src' # Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/rscape/meta.yaml b/recipes/rscape/meta.yaml index 5a7575ff056ac..400b2e379bf14 100644 --- a/recipes/rscape/meta.yaml +++ b/recipes/rscape/meta.yaml @@ -10,7 +10,7 @@ source: md5: 6b0715b8d60d5650062c055219290bd0 build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/rsem/build_failure.linux-64.yaml b/recipes/rsem/build_failure.linux-64.yaml deleted file mode 100644 index ae01beb6fa0db..0000000000000 --- a/recipes/rsem/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 7daeb20e9af19165bd6db84bfdf8fbed465c24a6206e85df2cd65b129f61263c # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - ./boost/numeric/conversion/detail/converter.hpp:453:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 453 | struct trivial_converter_impl : public std::unary_function< BOOST_DEDUCED_TYPENAME Traits::argument_type - | ^~~~~~~~~~~~~~ - /opt/conda/conda-bld/rsem_1717690589748/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/bits/stl_function.h:117:12: note: declared here - 117 | struct unary_function - | ^~~~~~~~~~~~~~ - ./boost/numeric/conversion/detail/converter.hpp:474:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 474 | struct rounding_converter : public std::unary_function< BOOST_DEDUCED_TYPENAME Traits::argument_type - | ^~~~~~~~~~~~~~ - /opt/conda/conda-bld/rsem_1717690589748/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/bits/stl_function.h:117:12: note: declared here - 117 | struct unary_function - | ^~~~~~~~~~~~~~ - ./boost/numeric/conversion/detail/converter.hpp:504:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] - 504 | struct non_rounding_converter : public std::unary_function< BOOST_DEDUCED_TYPENAME Traits::argument_type - | ^~~~~~~~~~~~~~ - /opt/conda/conda-bld/rsem_1717690589748/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/bits/stl_function.h:117:12: note: declared here - 117 | struct unary_function - | ^~~~~~~~~~~~~~ - In file included from ./boost/iterator/iterator_facade.hpp:10, - from ./boost/range/iterator_range_core.hpp:23, - from ./boost/lexical_cast.hpp:169: - ./boost/iterator.hpp:42:32: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 42 | struct iterator_base : std::iterator {}; - | ^~~~~~~~ - In file included from /opt/conda/conda-bld/rsem_1717690589748/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/bits/stl_algobase.h:65, - from /opt/conda/conda-bld/rsem_1717690589748/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/bits/specfun.h:45, - from /opt/conda/conda-bld/rsem_1717690589748/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/cmath:1935, - from simulation.cpp:1: - /opt/conda/conda-bld/rsem_1717690589748/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ - In file included from ./boost/math/special_functions/lanczos.hpp:1288, - from ./boost/math/special_functions/gamma.hpp:28: - ./boost/math/special_functions/detail/lanczos_sse2.hpp: In static member function 'static T boost::math::lanczos::lanczos13m53::lanczos_sum(const T&) [with T = double]': - ./boost/math/special_functions/detail/lanczos_sse2.hpp:54:21: warning: ISO C17 does not allow 'register' storage class specifier [-Wregister] - 54 | register __m128d vx = _mm_load1_pd(&x); - | ^~ - ./boost/math/special_functions/detail/lanczos_sse2.hpp:55:21: warning: ISO C17 does not allow 'register' storage class specifier [-Wregister] - 55 | register __m128d sum_even = _mm_load_pd(coeff); - | ^~~~~~~~ - ./boost/math/special_functions/detail/lanczos_sse2.hpp:56:21: warning: ISO C17 does not allow 'register' storage class specifier [-Wregister] - 56 | register __m128d sum_odd = _mm_load_pd(coeff2); - | ^~~~~~~ - ./boost/math/special_functions/detail/lanczos_sse2.hpp:57:21: warning: ISO C17 does not allow 'register' storage class specifier [-Wregister] - 57 | register __m128d nc_odd, nc_even; - | ^~~~~~ - ./boost/math/special_functions/detail/lanczos_sse2.hpp:57:29: warning: ISO C17 does not allow 'register' storage class specifier [-Wregister] - 57 | register __m128d nc_odd, nc_even; - | ^~~~~~~ - ./boost/math/special_functions/detail/lanczos_sse2.hpp:58:21: warning: ISO C17 does not allow 'register' storage class specifier [-Wregister] - 58 | register __m128d vx2 = _mm_mul_pd(vx, vx); - | ^~~ - ./boost/math/special_functions/detail/lanczos_sse2.hpp: In static member function 'static T boost::math::lanczos::lanczos13m53::lanczos_sum_expG_scaled(const T&) [with T = double]': - ./boost/math/special_functions/detail/lanczos_sse2.hpp:139:21: warning: ISO C17 does not allow 'register' storage class specifier [-Wregister] - 139 | register __m128d vx = _mm_load1_pd(&x); - | ^~ - ./boost/math/special_functions/detail/lanczos_sse2.hpp:140:21: warning: ISO C17 does not allow 'register' storage class specifier [-Wregister] - 140 | register __m128d sum_even = _mm_load_pd(coeff); - | ^~~~~~~~ - ./boost/math/special_functions/detail/lanczos_sse2.hpp:141:21: warning: ISO C17 does not allow 'register' storage class specifier [-Wregister] - 141 | register __m128d sum_odd = _mm_load_pd(coeff2); - | ^~~~~~~ - ./boost/math/special_functions/detail/lanczos_sse2.hpp:142:21: warning: ISO C17 does not allow 'register' storage class specifier [-Wregister] - 142 | register __m128d nc_odd, nc_even; - | ^~~~~~ - ./boost/math/special_functions/detail/lanczos_sse2.hpp:142:29: warning: ISO C17 does not allow 'register' storage class specifier [-Wregister] - 142 | register __m128d nc_odd, nc_even; - | ^~~~~~~ - ./boost/math/special_functions/detail/lanczos_sse2.hpp:143:21: warning: ISO C17 does not allow 'register' storage class specifier [-Wregister] - 143 | register __m128d vx2 = _mm_mul_pd(vx, vx); - | ^~~ - In file included from Refs.h:15, - from RSPD.h:10, - from SingleModel.h:18: - PolyARules.h: In member function 'int PolyARules::getLenAt(const std::string&)': - PolyARules.h:50:17: warning: control reaches end of non-void function [-Wreturn-type] - 50 | default : assert(false); - | ^~~~~~~ - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o rsem-simulate-reads simulation.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rsem-1.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -I. -O2 -c -o parseIt.o parseIt.cpp - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -pthread -o rsem-parse-alignments parseIt.o $PREFIX/lib/libhts.so -lz - /opt/conda/conda-bld/rsem_1717690589748/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lz: No such file or directory - collect2: error: ld returned 1 exit status - make: *** [Makefile:79: rsem-parse-alignments] Error 1 - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/rsem_1717690589748/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/rsem/build_failure.osx-64.yaml b/recipes/rsem/build_failure.osx-64.yaml deleted file mode 100644 index 87cc138e46c27..0000000000000 --- a/recipes/rsem/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 7daeb20e9af19165bd6db84bfdf8fbed465c24a6206e85df2cd65b129f61263c # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - ^~~~~~~~~ - fatal error: too many errors emitted, stopping now [-ferror-limit=] - 4 warnings and 20 errors generated. - make: *** [Makefile:71: simulation.o] Error 1 - Extracting download - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/rsem/01_fix_cxx_11.patch - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/rsem/01_fix_cxx_11.patch with args: - ['-Np1', '-i', '/tmp/tmpuan6jr1c/01_fix_cxx_11.patch.native', '--binary'] - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/rsem/02_fix_makefile.patch - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/rsem/02_fix_makefile.patch with args: - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - ['-Np1', '-i', '/tmp/tmpsyis2uhu/02_fix_makefile.patch.native', '--binary'] - Patch analysis gives: - [[ RA-MD1LOVE ]] - [[ 01_fix_cxx_11.patch ]] - [[ RA-MD1LOVE ]] - [[ 02_fix_makefile.patch ]] - - Key: - - R :: Reversible A :: Applicable - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - Y :: Build-prefix patch in use M :: Minimal, non-amalgamated - D :: Dry-runnable N :: Patch level (1 is preferred) - L :: Patch level not-ambiguous O :: Patch applies without offsets - V :: Patch applies without fuzz E :: Patch applies without emitting to stderr - - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/rsem_1717693924788/work - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/rsem_1717693924788/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/rsem_1717693924788/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/rsem_1717693924788/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rsem-1.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/rsem_1717693924788/work/conda_build.sh']' returned non-zero exit status 2. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rsem-1.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rsem-1.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rsem-1.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rsem-1.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -I. -O3 -c -o extractRef.o extractRef.cpp - x86_64-apple-darwin13.4.0-clang -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o rsem-extract-reference-transcripts extractRef.o - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rsem-1.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -I. -O3 -c -o synthesisRef.o synthesisRef.cpp - x86_64-apple-darwin13.4.0-clang -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o rsem-synthesis-reference-transcripts synthesisRef.o - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rsem-1.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -I. -O3 -c -o preRef.o preRef.cpp - x86_64-apple-darwin13.4.0-clang -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o rsem-preref preRef.o - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rsem-1.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -I. -O3 -c -o buildReadIndex.o buildReadIndex.cpp - x86_64-apple-darwin13.4.0-clang -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o rsem-build-read-index buildReadIndex.o - x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rsem-1.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -I. -O3 -ffast-math -c -o simulation.o simulation.cpp -# Last 100 lines of the build log. diff --git a/recipes/rsem/meta.yaml b/recipes/rsem/meta.yaml index ce3005ebe91cd..d8616a8663e3a 100644 --- a/recipes/rsem/meta.yaml +++ b/recipes/rsem/meta.yaml @@ -16,7 +16,7 @@ build: rpaths: - lib/R/lib/ - lib/ - number: 9 + number: 10 run_exports: - '{{ pin_subpackage(name, max_pin="x") }}' diff --git a/recipes/rtk/meta.yaml b/recipes/rtk/meta.yaml index 4323e0347ac74..c136603081576 100644 --- a/recipes/rtk/meta.yaml +++ b/recipes/rtk/meta.yaml @@ -9,7 +9,7 @@ source: md5: 0767ad1d59d9041a8f82d547a90abf8d build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/rtk2/meta.yaml b/recipes/rtk2/meta.yaml index 028a06a5a239b..a54e53bd7676c 100644 --- a/recipes/rtk2/meta.yaml +++ b/recipes/rtk2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: ea32bf15f8dfd3245ed82fae8cd3330d1487b506de13c689764161c791a31dcc build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/rukki/meta.yaml b/recipes/rukki/meta.yaml index e4784932e3704..41c776ecfcc81 100644 --- a/recipes/rukki/meta.yaml +++ b/recipes/rukki/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 036360e6287dc2b7e28bfc7b49db4ca79e792417e75f4bcc926c02d4161625b6 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('rukki', max_pin="x.x") }} diff --git a/recipes/rust-bio-tools/build_failure.linux-64.yaml b/recipes/rust-bio-tools/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..adc03df5eecc0 --- /dev/null +++ b/recipes/rust-bio-tools/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c39ae01131b4d24c06e9eeeb5c5c58be8057e8211cd7287875a352555be6b88a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + + --- stderr + clang diag: warning: -Wl,-O2: 'linker' input unused [-Wunused-command-line-argument] + clang diag: warning: -Wl,--sort-common: 'linker' input unused [-Wunused-command-line-argument] + clang diag: warning: -Wl,--as-needed: 'linker' input unused [-Wunused-command-line-argument] + clang diag: warning: -Wl,-z,relro: 'linker' input unused [-Wunused-command-line-argument] + clang diag: warning: -Wl,-z,now: 'linker' input unused [-Wunused-command-line-argument] + clang diag: warning: -Wl,--disable-new-dtags: 'linker' input unused [-Wunused-command-line-argument] + clang diag: warning: -Wl,--gc-sections: 'linker' input unused [-Wunused-command-line-argument] + clang diag: warning: -Wl,--allow-shlib-undefined: 'linker' input unused [-Wunused-command-line-argument] + clang diag: warning: -Wl,-rpath,/opt/conda/conda-bld/rust-bio-tools_1734157928840/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib: 'linker' input unused [-Wunused-command-line-argument] + clang diag: warning: -Wl,-rpath-link,/opt/conda/conda-bld/rust-bio-tools_1734157928840/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib: 'linker' input unused [-Wunused-command-line-argument] + clang diag: warning: argument unused during compilation: '-L/opt/conda/conda-bld/rust-bio-tools_1734157928840/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib' [-Wunused-command-line-argument] + + + error occurred in cc-rs: Command LC_ALL="C" "/opt/conda/conda-bld/rust-bio-tools_1734157928840/_build_env/bin/x86_64-conda-linux-gnu-c" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-m64" "-I" "rocksdb/include/" "-I" "rocksdb/" "-I" "rocksdb/third-party/gtest-1.8.1/fused-src/" "-I" "snappy/" "-I" "lz4/lib/" "-I" "/opt/conda/conda-bld/rust-bio-tools_1734157928840/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/zstd-sys-2.0.13zstd.1.5.6/zstd/lib" "-I" "/opt/conda/conda-bld/rust-bio-tools_1734157928840/work/target/x86_64-unknown-linux-gnu/release/build/libz-sys-4be64253d90217db/out/include" "-I" "/opt/conda/conda-bld/rust-bio-tools_1734157928840/work/target/x86_64-unknown-linux-gnu/release/build/bzip2-sys-46266655033ae2ca/out/include" "-I" "." "-fvisibility-inlines-hidden" "-fmessage-length=0" "-march=nocona" "-mtune=haswell" "-ftree-vectorize" "-fPIC" "-fstack-protector-strong" "-fno-plt" "-O2" "-ffunction-sections" "-pipe" "-isystem" "/opt/conda/conda-bld/rust-bio-tools_1734157928840/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include" "-fdebug-prefix-map=/opt/conda/conda-bld/rust-bio-tools_1734157928840/work=/usr/local/src/conda/rust-bio-tools-0.42.2" "-fdebug-prefix-map=/opt/conda/conda-bld/rust-bio-tools_1734157928840/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol=/usr/local/src/conda-prefix" "-std=c17" "-Wsign-compare" "-Wshadow" "-Wno-unused-parameter" "-Wno-unused-variable" "-Woverloaded-virtual" "-Wnon-virtual-dtor" "-Wno-missing-field-initializers" "-Wno-strict-aliasing" "-Wno-invalid-offsetof" "-msse2" "-std=c17" "-DSNAPPY=1" "-DLZ4=1" "-DZSTD=1" "-DZLIB=1" "-DBZIP2=1" "-DNDEBUG=1" "-DOS_LINUX" "-DROCKSDB_PLATFORM_POSIX" "-DROCKSDB_LIB_IO_POSIX" "-DROCKSDB_SUPPORT_THREAD_LOCAL" "-DHAVE_UINT128_EXTENSION=1" "-DHAVE_UINT128_EXTENSION=1" "-o" "/opt/conda/conda-bld/rust-bio-tools_1734157928840/work/target/x86_64-unknown-linux-gnu/release/build/librocksdb-sys-709f20499f8c56a4/out/3b2529d97c048fcf-string_util.o" "-c" "rocksdb/util/string_util.cc" with args x86_64-conda-linux-gnu-c did not execute successfully (status code exit status: 1). + + + error: failed to compile rust-bio-tools v0.42.2 (/opt/conda/conda-bld/rust-bio-tools_1734157928840/work), intermediate artifacts can be found at /opt/conda/conda-bld/rust-bio-tools_1734157928840/work/target. + To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/rust-bio-tools_1734157928840/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/rust-bio-tools_1734157928840/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. diff --git a/recipes/rust-bio-tools/build_failure.linux-aarch64.yaml b/recipes/rust-bio-tools/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..69d7745904331 --- /dev/null +++ b/recipes/rust-bio-tools/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: c39ae01131b4d24c06e9eeeb5c5c58be8057e8211cd7287875a352555be6b88a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + exit status: 0 + + --- stderr + clang diag: warning: -Wl,-O2: 'linker' input unused [-Wunused-command-line-argument] + clang diag: warning: -Wl,--sort-common: 'linker' input unused [-Wunused-command-line-argument] + clang diag: warning: -Wl,--as-needed: 'linker' input unused [-Wunused-command-line-argument] + clang diag: warning: -Wl,-z,relro: 'linker' input unused [-Wunused-command-line-argument] + clang diag: warning: -Wl,-z,now: 'linker' input unused [-Wunused-command-line-argument] + clang diag: warning: -Wl,--allow-shlib-undefined: 'linker' input unused [-Wunused-command-line-argument] + clang diag: warning: -Wl,-rpath,/opt/conda/conda-bld/rust-bio-tools_1734235956885/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib: 'linker' input unused [-Wunused-command-line-argument] + clang diag: warning: -Wl,-rpath-link,/opt/conda/conda-bld/rust-bio-tools_1734235956885/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib: 'linker' input unused [-Wunused-command-line-argument] + clang diag: warning: argument unused during compilation: '-L/opt/conda/conda-bld/rust-bio-tools_1734235956885/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib' [-Wunused-command-line-argument] + + + error occurred in cc-rs: Command LC_ALL="C" "/opt/conda/conda-bld/rust-bio-tools_1734235956885/_build_env/bin/aarch64-conda-linux-gnu-c" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-I" "rocksdb/include/" "-I" "rocksdb/" "-I" "rocksdb/third-party/gtest-1.8.1/fused-src/" "-I" "snappy/" "-I" "lz4/lib/" "-I" "/opt/conda/conda-bld/rust-bio-tools_1734235956885/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/zstd-sys-2.0.13zstd.1.5.6/zstd/lib" "-I" "/opt/conda/conda-bld/rust-bio-tools_1734235956885/work/target/aarch64-unknown-linux-gnu/release/build/libz-sys-c4c3c58a772cf3f5/out/include" "-I" "/opt/conda/conda-bld/rust-bio-tools_1734235956885/work/target/aarch64-unknown-linux-gnu/release/build/bzip2-sys-ecdb1b3e3f440469/out/include" "-I" "." "-fvisibility-inlines-hidden" "-fmessage-length=0" "-ftree-vectorize" "-fPIC" "-fstack-protector-strong" "-fno-plt" "-O3" "-pipe" "-isystem" "/opt/conda/conda-bld/rust-bio-tools_1734235956885/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include" "-fdebug-prefix-map=/opt/conda/conda-bld/rust-bio-tools_1734235956885/work=/usr/local/src/conda/rust-bio-tools-0.42.2" "-fdebug-prefix-map=/opt/conda/conda-bld/rust-bio-tools_1734235956885/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol=/usr/local/src/conda-prefix" "-std=c17" "-Wsign-compare" "-Wshadow" "-Wno-unused-parameter" "-Wno-unused-variable" "-Woverloaded-virtual" "-Wnon-virtual-dtor" "-Wno-missing-field-initializers" "-Wno-strict-aliasing" "-Wno-invalid-offsetof" "-std=c17" "-DSNAPPY=1" "-DLZ4=1" "-DZSTD=1" "-DZLIB=1" "-DBZIP2=1" "-DNDEBUG=1" "-DOS_LINUX" "-DROCKSDB_PLATFORM_POSIX" "-DROCKSDB_LIB_IO_POSIX" "-DROCKSDB_SUPPORT_THREAD_LOCAL" "-DHAVE_UINT128_EXTENSION=1" "-DHAVE_UINT128_EXTENSION=1" "-o" "/opt/conda/conda-bld/rust-bio-tools_1734235956885/work/target/aarch64-unknown-linux-gnu/release/build/librocksdb-sys-f077a43d31c5fdfb/out/3b2529d97c048fcf-string_util.o" "-c" "rocksdb/util/string_util.cc" with args aarch64-conda-linux-gnu-c did not execute successfully (status code exit status: 1). + + + error: failed to compile rust-bio-tools v0.42.2 (/opt/conda/conda-bld/rust-bio-tools_1734235956885/work), intermediate artifacts can be found at /opt/conda/conda-bld/rust-bio-tools_1734235956885/work/target. + To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/rust-bio-tools_1734235956885/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/rust-bio-tools_1734235956885/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. diff --git a/recipes/rust-bio-tools/meta.yaml b/recipes/rust-bio-tools/meta.yaml index 4df8383242ee8..8bc0de02e557a 100644 --- a/recipes/rust-bio-tools/meta.yaml +++ b/recipes/rust-bio-tools/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 skip: True # [osx] run_exports: - {{ pin_subpackage('rust-bio-tools', max_pin="x.x") }} diff --git a/recipes/rust-mdbg/build_failure.linux-64.yaml b/recipes/rust-mdbg/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..278a966b6d140 --- /dev/null +++ b/recipes/rust-mdbg/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 898894c87946be37bcd22cf6249326da762b21f90c828297a9fc7e86b637d3e8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + error[E0599]: no method named seq found for struct seq_io::fasta::RefRecord in the current scope + --> src/main.rs:731:34 + | + 731 | let seq_str = record.seq(); + | ^^^ method not found in RefRecord<'_> + | + ::: /opt/conda/conda-bld/rust-mdbg_1734152771903/work/.cargo/git/checkouts/seq_io-5c12caa4159d1858/283214f/src/fasta.rs:681:8 + | + 681 | fn seq(&self) -> &[u8]; + | --- the method is available for seq_io::fasta::RefRecord<'_> here + | + = help: items from traits can only be used if the trait is in scope + help: trait Record which provides seq is implemented but not in scope; perhaps you want to import it + | + 5 use seq_io::fasta::Record; + | + + error[E0599]: no method named id found for struct seq_io::fasta::RefRecord in the current scope + --> src/main.rs:732:33 + | + 732 | let seq_id = record.id().unwrap().to_string(); + | ^^ method not found in RefRecord<'_> + | + ::: /opt/conda/conda-bld/rust-mdbg_1734152771903/work/.cargo/git/checkouts/seq_io-5c12caa4159d1858/283214f/src/fasta.rs:695:8 + | + 695 | fn id(&self) -> Result<&str, Utf8Error> { + | -- the method is available for seq_io::fasta::RefRecord<'_> here + | + = help: items from traits can only be used if the trait is in scope + help: trait Record which provides id is implemented but not in scope; perhaps you want to import it + | + 5 use seq_io::fasta::Record; + | + + error[E0599]: no method named seq found for struct seq_io::fastq::RefRecord in the current scope + --> src/main.rs:736:34 + | + 736 | let seq_str = record.seq(); + | ^^^ method not found in RefRecord<'_> + | + ::: /opt/conda/conda-bld/rust-mdbg_1734152771903/work/.cargo/git/checkouts/seq_io-5c12caa4159d1858/283214f/src/fastq.rs:772:8 + | + 772 | fn seq(&self) -> &[u8]; + | --- the method is available for seq_io::fastq::RefRecord<'_> here + | + = help: items from traits can only be used if the trait is in scope + help: trait Record which provides seq is implemented but not in scope; perhaps you want to import it + | + 5 use seq_io::fastq::Record; + | + + error[E0599]: no method named id found for struct seq_io::fastq::RefRecord in the current scope + --> src/main.rs:737:33 + | + 737 | let seq_id = record.id().unwrap().to_string(); + | ^^ method not found in RefRecord<'_> + | + ::: /opt/conda/conda-bld/rust-mdbg_1734152771903/work/.cargo/git/checkouts/seq_io-5c12caa4159d1858/283214f/src/fastq.rs:783:8 + | + 783 | fn id(&self) -> Result<&str, Utf8Error> { + | -- the method is available for seq_io::fastq::RefRecord<'_> here + | + = help: items from traits can only be used if the trait is in scope + help: trait Record which provides id is implemented but not in scope; perhaps you want to import it + | + 5 use seq_io::fastq::Record; + | + + Some errors have detailed explanations: E0432, E0599. + For more information about an error, try rustc --explain E0432. + error: could not compile rust-mdbg (bin "rust-mdbg") due to 8 previous errors + + Caused by: + process didn't exit successfully: rustc --crate-name rust_mdbg --edition=2018 src/main.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=e36b12962408b886 -C extra-filename=-e36b12962408b886 --out-dir /opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps -C linker=/opt/conda/conda-bld/rust-mdbg_1734152771903/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps --extern adler32=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libadler32-47c4a850b0a29bd1.rlib --extern array_tool=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libarray_tool-7c3f8133a5cf9d82.rlib --extern arrayvec=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libarrayvec-9f57a16bdc83a031.rlib --extern bio=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libbio-4002c3d3d24c038a.rlib --extern bio_types=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libbio_types-a9a6479270933408.rlib --extern closure=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libclosure-c6a72f1325c583b6.rlib --extern crossbeam_utils=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libcrossbeam_utils-2ce419ca8692962f.rlib --extern dashmap=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libdashmap-80866b85a8f66677.rlib --extern editdistancewf=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libeditdistancewf-7b74800baccf1466.rlib --extern fasthash=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libfasthash-de7c3759848cd79e.rlib --extern flate2=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libflate2-dd8ab10548ec3c20.rlib --extern glob=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libglob-51a92f4ec7cfd606.rlib --extern itertools=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libitertools-313b36a6be1f8c60.rlib --extern libc=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/liblibc-f6fe57662dfc7b71.rlib --extern lzzzz=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/liblzzzz-2bb3d699d004e13e.rlib --extern nthash=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libnthash-8a710b342ad52ae5.rlib --extern pbr=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libpbr-1cd0e90b87c4f39d.rlib --extern petgraph=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libpetgraph-967b6dd71f25fdc4.rlib --extern petgraph_graphml=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libpetgraph_graphml-603284e913f267f0.rlib --extern rand_core=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/librand_core-a2d2637bf4100142.rlib --extern rand_pcg=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/librand_pcg-3d0690217fde7eed.rlib --extern rayon=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/librayon-c7dc6d7867e2551f.rlib --extern seq_io=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libseq_io-e7a86af8b9c58b92.rlib --extern strsim=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libstrsim-5b0a8a779fa4b0ba.rlib --extern structopt=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libstructopt-27449864fc1ff895.rlib --extern thread_id=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libthread_id-4228a6292133d31f.rlib --extern threadpool=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libthreadpool-926b66b86d5f42ef.rlib --extern xx_bloomfilter=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/deps/libxx_bloomfilter-ddfe4e94760fc20e.rlib -L native=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/build/fasthash-sys-53c8f151d2f64d85/out -L native=/opt/conda/conda-bld/rust-mdbg_1734152771903/work/target/release/build/lzzzz-d269133c6f4f6769/out (exit status: 1) + warning: build failed, waiting for other jobs to finish... + error: failed to compile rust-mdbg v0.1.0 (/opt/conda/conda-bld/rust-mdbg_1734152771903/work), intermediate artifacts can be found at /opt/conda/conda-bld/rust-mdbg_1734152771903/work/target. + To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/rust-mdbg_1734152771903/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/rust-mdbg_1734152771903/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. diff --git a/recipes/hic-straw/build_failure.osx-64.yaml b/recipes/rust-mdbg/build_failure.osx-64.yaml similarity index 52% rename from recipes/hic-straw/build_failure.osx-64.yaml rename to recipes/rust-mdbg/build_failure.osx-64.yaml index a2722ee2e54af..296b35c7491a3 100644 --- a/recipes/hic-straw/build_failure.osx-64.yaml +++ b/recipes/rust-mdbg/build_failure.osx-64.yaml @@ -1,37 +1,72 @@ -recipe_sha: 62985f80bc0c5b45fcb7b19401cd9027e52aca4d404ce5c1ce23e7535f2650b2 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 898894c87946be37bcd22cf6249326da762b21f90c828297a9fc7e86b637d3e8 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- +log: |- + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/rust-mdbg_1733985761678/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + - clangxx_impl_osx-64 18.1.8 h4b7810f_23 + - libllvm18 18.1.8 h9ce406d_2 + - ca-certificates 2024.8.30 h8857fd0_0 + - rust 1.83.0 h34a2095_0 + - clang 18.1.8 default_h179603d_5 + - pkg-config 0.29.2 hf7e621a_1009 + - openssl 3.4.0 hd471939_0 + - rust-std-x86_64-apple-darwin 1.83.0 h38e4360_0 + host: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + - libcxx 19.1.5 hf95d169_0 + run: + - libcxx >=18 + test: + commands: + - rust-mdbg --help + - to_basespace --help + about: + home: https://github.com/ekimb/rust-mdbg + license: MIT + summary: 'An ultra-fast minimizer-space de Bruijn graph (mdBG) implementation, geared + towards the assembly of long and accurate reads. + + ' + extra: + copy_test_source_files: true + final: true + recipe-maintainers: + - thanhleviet + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/rust-mdbg_1733985761678/work api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build return build_tree( - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/hic-straw_1717515448844/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/hic-straw_1717515448844/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/hic-straw_1717515448844/work + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/rust-mdbg_1733985761678/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/rust-mdbg_1733985761678/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/rust-mdbg_1733985761678/work INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as CC=x86_64-apple-darwin13.4.0-clang CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hic-straw-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rust-mdbg-1.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/hic-straw_1717515448844/work/conda_build.sh']' returned non-zero exit status 1. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/rust-mdbg_1733985761678/work/conda_build.sh']' returned non-zero exit status 101. + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hic-straw-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rust-mdbg-1.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool LD=x86_64-apple-darwin13.4.0-ld @@ -39,7 +74,7 @@ log: |2- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -48,7 +83,7 @@ log: |2- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -63,42 +98,7 @@ log: |2- INFO: activate_clangxx_osx-64.sh made the following environmental changes: CLANGXX=x86_64-apple-darwin13.4.0-clang CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hic-straw-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rust-mdbg-1.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hic-straw-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - Using pip 24.0 from $PREFIX/lib/python3.9/site-packages/pip (python 3.9) - Non-user install because user site-packages disabled - Ignoring indexes: https://pypi.org/simple - Created temporary directory: /private/tmp/pip-build-tracker-ylj7gc8f - Initialized build tracking at /private/tmp/pip-build-tracker-ylj7gc8f - Created build tracker: /private/tmp/pip-build-tracker-ylj7gc8f - Entered build tracker: /private/tmp/pip-build-tracker-ylj7gc8f - Created temporary directory: /private/tmp/pip-install-bwo75gax - Created temporary directory: /private/tmp/pip-ephem-wheel-cache-a9wxjigx - Processing $SRC_DIR - Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-ylj7gc8f' - Running setup.py (path:$SRC_DIR/setup.py) egg_info for package from file://$SRC_DIR - Created temporary directory: /private/tmp/pip-pip-egg-info-40p4kwk1 - Preparing metadata (setup.py): started - Preparing metadata (setup.py): finished with status 'done' - Source in $SRC_DIR has version 1.3.1, which satisfies requirement hic-straw==1.3.1 from file://$SRC_DIR - Removed hic-straw==1.3.1 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-ylj7gc8f' - Created temporary directory: /private/tmp/pip-unpack-vo2913rt - Building wheels for collected packages: hic-straw - Created temporary directory: /private/tmp/pip-wheel-tyl3bntg - Building wheel for hic-straw (setup.py): started - Destination directory: /private/tmp/pip-wheel-tyl3bntg - Building wheel for hic-straw (setup.py): finished with status 'error' - Running setup.py clean for hic-straw - Failed to build hic-straw - Exception information: - Traceback (most recent call last): - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper - return func(self, options, args) - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 429, in run - raise InstallationError( - pip._internal.exceptions.InstallationError: Could not build wheels for hic-straw, which is required to install pyproject.toml-based projects - Removed build tracker: '/private/tmp/pip-build-tracker-ylj7gc8f' + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rust-mdbg-1.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix # Last 100 lines of the build log. diff --git a/recipes/rust-mdbg/meta.yaml b/recipes/rust-mdbg/meta.yaml index 9fc9d5c2a7855..734566df8a1bb 100644 --- a/recipes/rust-mdbg/meta.yaml +++ b/recipes/rust-mdbg/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 source: url: https://github.com/ekimb/rust-mdbg/archive/v{{ version }}.tar.gz diff --git a/recipes/rust-ncbitaxonomy/meta.yaml b/recipes/rust-ncbitaxonomy/meta.yaml index 103f0d6352d75..d942300693f2f 100644 --- a/recipes/rust-ncbitaxonomy/meta.yaml +++ b/recipes/rust-ncbitaxonomy/meta.yaml @@ -7,7 +7,7 @@ package: version: "{{ version }}" build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -41,4 +41,4 @@ about: extra: additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 diff --git a/recipes/rust-overlaps/meta.yaml b/recipes/rust-overlaps/meta.yaml index 0b41cd26c49d0..37e82acf3038b 100644 --- a/recipes/rust-overlaps/meta.yaml +++ b/recipes/rust-overlaps/meta.yaml @@ -5,7 +5,7 @@ package: version: {{version}} build: - number: 9 + number: 10 skip: True # [osx] source: diff --git a/recipes/rustybam/build_failure.osx-64.yaml b/recipes/rustybam/build_failure.osx-64.yaml deleted file mode 100644 index be685e4efb964..0000000000000 --- a/recipes/rustybam/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 2888bb7310f298605a52471e1df6b4d045e02b863a07716f06e26d3b93cb96ca # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - = note: env -u IPHONEOS_DEPLOYMENT_TARGET -u TVOS_DEPLOYMENT_TARGET LC_ALL="C" PATH="/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/bin:/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/bin:/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin:/opt/mambaforge/envs/bioconda/condabin:/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/bin:/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin:/opt/mambaforge/envs/bioconda/bin:/opt/mambaforge/condabin:/opt/mambaforge/bin:/usr/local/lib/ruby/gems/3.0.0/bin:/usr/local/opt/ruby@3.0/bin:/usr/local/opt/pipx_bin:/Users/runner/.cargo/bin:/usr/local/opt/curl/bin:/usr/local/bin:/usr/local/sbin:/Users/runner/bin:/Users/runner/.yarn/bin:/Users/runner/Library/Android/sdk/tools:/Users/runner/Library/Android/sdk/platform-tools:/Library/Frameworks/Python.framework/Versions/Current/bin:/Library/Frameworks/Mono.framework/Versions/Current/Commands:/usr/bin:/bin:/usr/sbin:/sbin:/Users/runner/.dotnet/tools" VSLANG="1033" ZERO_AR_DATE="1" "cc" "-arch" "x86_64" "-m64" "/tmp/rustcIyea18/symbols.o" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/target/release/build/syn-83534d4a7b485fa6/build_script_build-83534d4a7b485fa6.build_script_build.9a6b01f912fb026e-cgu.0.rcgu.o" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/target/release/build/syn-83534d4a7b485fa6/build_script_build-83534d4a7b485fa6.build_script_build.9a6b01f912fb026e-cgu.1.rcgu.o" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/target/release/build/syn-83534d4a7b485fa6/build_script_build-83534d4a7b485fa6.build_script_build.9a6b01f912fb026e-cgu.2.rcgu.o" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/target/release/build/syn-83534d4a7b485fa6/build_script_build-83534d4a7b485fa6.7b4qwoeamwdunay.rcgu.o" "-L" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/target/release/deps" "-L" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libstd-2ad7f97be9e16ca5.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libpanic_unwind-8ce93eee8bf4c86e.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libobject-0e1339b212cc7409.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libmemchr-925e672b3deb429c.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libaddr2line-e92d517a950bccd8.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libgimli-de95e5c2a2ace281.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_demangle-37f4c48e230f618e.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libstd_detect-dfeb4bb0652b6b8e.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libhashbrown-0e3ea0ec18336be2.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_std_workspace_alloc-39dd3003e36d7872.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libminiz_oxide-5ea1513e08ee15e0.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libadler-2967159221f4860d.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libunwind-b70656709e3eca11.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcfg_if-cc5626b2e0399737.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/liblibc-8378684dba6ab463.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/liballoc-0ff05b9b25b786cc.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_std_workspace_core-9a6da74aeab39c54.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcore-1638dc700d175798.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcompiler_builtins-7f42af62722c8f43.rlib" "-lSystem" "-lc" "-lm" "-L" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib" "-o" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/target/release/build/syn-83534d4a7b485fa6/build_script_build-83534d4a7b485fa6" "-Wl,-dead_strip" "-nodefaultlibs" "-undefined" "dynamic_lookup" - = note: ld: multiple errors: unsupported mach-o filetype (only MH_OBJECT and MH_DYLIB can be linked) in '/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/lib/libSystem.B.dylib'; unsupported mach-o filetype (only MH_OBJECT and MH_DYLIB can be linked) in '/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/lib/libSystem.B.dylib'; unsupported mach-o filetype (only MH_OBJECT and MH_DYLIB can be linked) in '/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/lib/libSystem.B.dylib' - clang: error: linker command failed with exit code 1 (use -v to see invocation) - - - error: could not compile proc-macro2 (build script) due to 1 previous error - - Caused by: - process didn't exit successfully: rustc --crate-name build_script_build --edition=2021 /opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/proc-macro2-1.0.85/build.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="default"' --cfg 'feature="proc-macro"' -C metadata=acbd332dc98100aa -C extra-filename=-acbd332dc98100aa --out-dir /opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/target/release/build/proc-macro2-acbd332dc98100aa -C strip=debuginfo -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/target/release/deps --cap-lints allow -C link-arg=-undefined -C link-arg=dynamic_lookup (exit status: 1) - warning: build failed, waiting for other jobs to finish... - error: could not compile syn (build script) due to 1 previous error - - Caused by: - process didn't exit successfully: rustc --crate-name build_script_build --edition=2018 /opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/syn-1.0.109/build.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="clone-impls"' --cfg 'feature="default"' --cfg 'feature="derive"' --cfg 'feature="full"' --cfg 'feature="parsing"' --cfg 'feature="printing"' --cfg 'feature="proc-macro"' --cfg 'feature="quote"' -C metadata=83534d4a7b485fa6 -C extra-filename=-83534d4a7b485fa6 --out-dir /opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/target/release/build/syn-83534d4a7b485fa6 -C strip=debuginfo -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/target/release/deps --cap-lints allow -C link-arg=-undefined -C link-arg=dynamic_lookup (exit status: 1) - error: could not compile libc (build script) due to 1 previous error - - Caused by: - process didn't exit successfully: rustc --crate-name build_script_build /opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/libc-0.2.155/build.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="default"' --cfg 'feature="std"' -C metadata=312897ad65048e13 -C extra-filename=-312897ad65048e13 --out-dir /opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/target/release/build/libc-312897ad65048e13 -C strip=debuginfo -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/target/release/deps --cap-lints allow -C link-arg=-undefined -C link-arg=dynamic_lookup (exit status: 1) - error: linking with cc failed: exit status: 1 - | - = note: env -u IPHONEOS_DEPLOYMENT_TARGET -u TVOS_DEPLOYMENT_TARGET LC_ALL="C" PATH="/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/bin:/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/bin:/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin:/opt/mambaforge/envs/bioconda/condabin:/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/bin:/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin:/opt/mambaforge/envs/bioconda/bin:/opt/mambaforge/condabin:/opt/mambaforge/bin:/usr/local/lib/ruby/gems/3.0.0/bin:/usr/local/opt/ruby@3.0/bin:/usr/local/opt/pipx_bin:/Users/runner/.cargo/bin:/usr/local/opt/curl/bin:/usr/local/bin:/usr/local/sbin:/Users/runner/bin:/Users/runner/.yarn/bin:/Users/runner/Library/Android/sdk/tools:/Users/runner/Library/Android/sdk/platform-tools:/Library/Frameworks/Python.framework/Versions/Current/bin:/Library/Frameworks/Mono.framework/Versions/Current/Commands:/usr/bin:/bin:/usr/sbin:/sbin:/Users/runner/.dotnet/tools" VSLANG="1033" ZERO_AR_DATE="1" "cc" "-arch" "x86_64" "-m64" "/tmp/rustcvqN5BT/symbols.o" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/target/release/build/libm-0e90bdf3746d668a/build_script_build-0e90bdf3746d668a.build_script_build.c50687bd71c14a46-cgu.0.rcgu.o" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/target/release/build/libm-0e90bdf3746d668a/build_script_build-0e90bdf3746d668a.4um6vnkueq6nlagc.rcgu.o" "-L" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/target/release/deps" "-L" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libstd-2ad7f97be9e16ca5.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libpanic_unwind-8ce93eee8bf4c86e.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libobject-0e1339b212cc7409.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libmemchr-925e672b3deb429c.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libaddr2line-e92d517a950bccd8.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libgimli-de95e5c2a2ace281.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_demangle-37f4c48e230f618e.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libstd_detect-dfeb4bb0652b6b8e.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libhashbrown-0e3ea0ec18336be2.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_std_workspace_alloc-39dd3003e36d7872.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libminiz_oxide-5ea1513e08ee15e0.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libadler-2967159221f4860d.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libunwind-b70656709e3eca11.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcfg_if-cc5626b2e0399737.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/liblibc-8378684dba6ab463.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/liballoc-0ff05b9b25b786cc.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/librustc_std_workspace_core-9a6da74aeab39c54.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcore-1638dc700d175798.rlib" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib/libcompiler_builtins-7f42af62722c8f43.rlib" "-lSystem" "-lc" "-lm" "-L" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/lib/rustlib/x86_64-apple-darwin/lib" "-o" "/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/target/release/build/libm-0e90bdf3746d668a/build_script_build-0e90bdf3746d668a" "-Wl,-dead_strip" "-nodefaultlibs" "-undefined" "dynamic_lookup" - = note: ld: multiple errors: unsupported mach-o filetype (only MH_OBJECT and MH_DYLIB can be linked) in '/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/lib/libSystem.B.dylib'; unsupported mach-o filetype (only MH_OBJECT and MH_DYLIB can be linked) in '/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/lib/libSystem.B.dylib'; unsupported mach-o filetype (only MH_OBJECT and MH_DYLIB can be linked) in '/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/lib/libSystem.B.dylib' - clang: error: linker command failed with exit code 1 (use -v to see invocation) - - - error: could not compile libm (build script) due to 1 previous error - - Caused by: - process didn't exit successfully: rustc --crate-name build_script_build --edition=2018 /opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/libm-0.2.8/build.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="default"' -C metadata=0e90bdf3746d668a -C extra-filename=-0e90bdf3746d668a --out-dir /opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/target/release/build/libm-0e90bdf3746d668a -C strip=debuginfo -L dependency=/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/target/release/deps --cap-lints allow -C link-arg=-undefined -C link-arg=dynamic_lookup (exit status: 1) - error: failed to compile rustybam v0.1.33 (/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work), intermediate artifacts can be found at /opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/target. - To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rustybam-0.1.33 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/rustybam_1717516737486/work/conda_build.sh']' returned non-zero exit status 101. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rustybam-0.1.33 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rustybam-0.1.33 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/rustybam-0.1.33 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -# Last 100 lines of the build log. diff --git a/recipes/rustybam/meta.yaml b/recipes/rustybam/meta.yaml index dd6ef05dae2cf..c5fb7de0f3521 100644 --- a/recipes/rustybam/meta.yaml +++ b/recipes/rustybam/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 source: url: https://github.com/mrvollger/rustybam/archive/v{{ version }}.tar.gz diff --git a/recipes/rustynuc/meta.yaml b/recipes/rustynuc/meta.yaml index 745871a2ff10f..2b48496665846 100644 --- a/recipes/rustynuc/meta.yaml +++ b/recipes/rustynuc/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{sha256}}' build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/rustyread/meta.yaml b/recipes/rustyread/meta.yaml index 84fe04cb2f7b3..9f9e4067ab6e7 100644 --- a/recipes/rustyread/meta.yaml +++ b/recipes/rustyread/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/sabre/meta.yaml b/recipes/sabre/meta.yaml index a67b4bfe64493..43da1ca30ebe9 100644 --- a/recipes/sabre/meta.yaml +++ b/recipes/sabre/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 8101eda078eded6c755d607a83ad5c659023dad9f0f2dadc11445c0ca305bf02 build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/safesim/build_failure.osx-64.yaml b/recipes/safesim/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c4430cfe3faf4 --- /dev/null +++ b/recipes/safesim/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5d08916a6463a0258a2224a9a7f743698bea389bd5657cc94f2779cd94720841 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - libdeflate 1.22 h00291cd_0 + - libev 4.33 h10d778d_2 + - libzlib 1.2.13 h87427d6_6 + - ncurses 6.5 hf036a51_1 + - xz 5.2.6 h775f41a_0 + - libedit 3.1.20191231 h0678c8f_2 + - openssl 3.4.0 hd471939_0 + - pcre 8.45 he49afe7_0 + - zlib 1.2.13 h87427d6_6 + - zstd 1.5.6 h915ae27_0 + - fastq-tools 0.8.3 h554e40c_4 + - krb5 1.21.3 h37d8d59_0 + - libnghttp2 1.58.0 h64cf6d3_1 + - libssh2 1.11.0 hd019ec5_0 + - libcurl 8.8.0 hf9fcc65_1 + - curl 8.8.0 hea67d85_1 + - htslib 1.8 1 + run: + - zlib + - libdeflate >=1.22,<1.23.0a0 + - openssl >=3.4.0,<4.0a0 + - libzlib >=1.2.13,<2.0a0 + - libcurl >=8.8.0,<9.0a0 + - xz >=5.2.6,<6.0a0 + - fastq-tools + - htslib + - libcxx >=18 + - bzip2 >=1.0.8,<2.0a0 + test: + commands: + - safemut --help 2>&1 | grep version + about: + home: https://github.com/genetronhealth/safesim + license: Apache-2.0 + license_family: APACHE + license_file: LICENSE + summary: SafeSeqS variant simulator + extra: + copy_test_source_files: true + final: true + identifiers: + - doi:TODO-waiting-for-publication + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/safesim_1734413659838/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/safesim_1734413659838/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/safesim_1734413659838/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/safesim_1734413659838/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/safesim-0.1.6.8d44580 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/safesim-0.1.6.8d44580 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/safesim-0.1.6.8d44580 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/safesim-0.1.6.8d44580 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + rm safemut safemut.debug safemix safemix.debug bin/safemut bin/safemix + x86_64-apple-darwin13.4.0-clang -o safemut -O2 safemut.cpp -pthread -lm -lz -lbz2 -llzma -static-libstdc -lhts -ldeflate -fPIE -I $PREFIX/include -L $PREFIX/lib -DCOMMIT_VERSION="\"\"" -DCOMMIT_DIFF_SH="\"\"" -DCOMMIT_DIFF_FULL="\"\"" +# Last 100 lines of the build log. diff --git a/recipes/safesim/meta.yaml b/recipes/safesim/meta.yaml index 9bacc7ac6062a..5a857ee83ef23 100644 --- a/recipes/safesim/meta.yaml +++ b/recipes/safesim/meta.yaml @@ -10,7 +10,7 @@ source: sha256: ed291fed1bd1b74dd953b7a4d9c7cf3e291572a08daf90b53544eed13fb38466 build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/sage-proteomics/meta.yaml b/recipes/sage-proteomics/meta.yaml index 185875e7a26e2..dd1e5d93d7af8 100644 --- a/recipes/sage-proteomics/meta.yaml +++ b/recipes/sage-proteomics/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('sage-proteomics', max_pin="x") }} diff --git a/recipes/salmon/meta.yaml b/recipes/salmon/meta.yaml index b2dcbcab2bfcc..59f054850ac4c 100644 --- a/recipes/salmon/meta.yaml +++ b/recipes/salmon/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage("salmon", max_pin="x") }} diff --git a/recipes/sam2pairwise/meta.yaml b/recipes/sam2pairwise/meta.yaml index fd0995c223f9b..b8fcc1f83f75d 100644 --- a/recipes/sam2pairwise/meta.yaml +++ b/recipes/sam2pairwise/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/sambamba/meta.yaml b/recipes/sambamba/meta.yaml index 4f6491692d307..c0cdbb1b34536 100644 --- a/recipes/sambamba/meta.yaml +++ b/recipes/sambamba/meta.yaml @@ -12,7 +12,7 @@ source: - 0001-fix-osx-compile.patch build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} ignore_run_exports: diff --git a/recipes/samblaster/0.1.20/meta.yaml b/recipes/samblaster/0.1.20/meta.yaml index cde2064c36e95..6af1adf9a3325 100644 --- a/recipes/samblaster/0.1.20/meta.yaml +++ b/recipes/samblaster/0.1.20/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://github.com/GregoryFaust/samblaster/releases/download/v.{{ version }}/samblaster-v.{{ version }}.tar.gz diff --git a/recipes/samblaster/meta.yaml b/recipes/samblaster/meta.yaml index 016234e899fb5..16853f17a68d5 100644 --- a/recipes/samblaster/meta.yaml +++ b/recipes/samblaster/meta.yaml @@ -1,5 +1,5 @@ build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('samblaster', max_pin='x.x') }} @@ -30,4 +30,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/samcut/meta.yaml b/recipes/samcut/meta.yaml index a49634e1887be..bdab43c0dba6e 100644 --- a/recipes/samcut/meta.yaml +++ b/recipes/samcut/meta.yaml @@ -10,7 +10,7 @@ source: sha256: "{{ sha256 }}" build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/samhaplotag/meta.yaml b/recipes/samhaplotag/meta.yaml index cd677ab50568f..7570f58a3d2f3 100644 --- a/recipes/samhaplotag/meta.yaml +++ b/recipes/samhaplotag/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/samsum/meta.yaml b/recipes/samsum/meta.yaml index 44e818532e543..0118f3a9041d8 100644 --- a/recipes/samsum/meta.yaml +++ b/recipes/samsum/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 36b1fc0eaa4da1b7a70d2791357c7547612c9653e4e0ea7db39ba96cdd03ffc5 build: - number: 5 + number: 6 entry_points: - samsum = samsum.__main__:main script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " diff --git a/recipes/samtools/1.1/meta.yaml b/recipes/samtools/1.1/meta.yaml index 167a12069689f..bf761e174951e 100644 --- a/recipes/samtools/1.1/meta.yaml +++ b/recipes/samtools/1.1/meta.yaml @@ -7,7 +7,7 @@ source: url: http://downloads.sourceforge.net/project/samtools/samtools/1.1/samtools-1.1.tar.bz2 build: - number: 8 + number: 9 requirements: build: diff --git a/recipes/samtools/1.3.1/meta.yaml b/recipes/samtools/1.3.1/meta.yaml index dc2cd682af747..5100d0348bf02 100644 --- a/recipes/samtools/1.3.1/meta.yaml +++ b/recipes/samtools/1.3.1/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 11 + number: 12 source: url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2 diff --git a/recipes/samtools/1.3/meta.yaml b/recipes/samtools/1.3/meta.yaml index 1ecea30e8adfe..83e264e260b46 100644 --- a/recipes/samtools/1.3/meta.yaml +++ b/recipes/samtools/1.3/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 8 + number: 9 source: url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2 diff --git a/recipes/samtools/1.6/meta.yaml b/recipes/samtools/1.6/meta.yaml index 9a3bd24371d27..3bb1ffe74c014 100644 --- a/recipes/samtools/1.6/meta.yaml +++ b/recipes/samtools/1.6/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 10 + number: 11 source: url: https://github.com/samtools/samtools/releases/download/{{ version }}/samtools-{{ version }}.tar.bz2 diff --git a/recipes/samtools/meta.yaml b/recipes/samtools/meta.yaml index e0a4803383159..a4611bfe22739 100644 --- a/recipes/samtools/meta.yaml +++ b/recipes/samtools/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("samtools", max_pin="x") }} diff --git a/recipes/sankoff/meta.yaml b/recipes/sankoff/meta.yaml index 1756c57184eae..b50b4b163c098 100644 --- a/recipes/sankoff/meta.yaml +++ b/recipes/sankoff/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '4e0f5308b8b2030a1643c4185ba68a8d99836b87c5cf2bfb6d3a3263b0c1b2e4' build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/sansa/meta.yaml b/recipes/sansa/meta.yaml index 67c87723a5111..fed3c9b7fbdcd 100644 --- a/recipes/sansa/meta.yaml +++ b/recipes/sansa/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('sansa', max_pin="x.x") }} diff --git a/recipes/satrap/meta.yaml b/recipes/satrap/meta.yaml index 3f6ade978ee53..0e9218d5d5ad0 100644 --- a/recipes/satrap/meta.yaml +++ b/recipes/satrap/meta.yaml @@ -3,7 +3,7 @@ package: version: 0.2 build: - number: 6 + number: 7 skip: true # [osx] source: diff --git a/recipes/savvy/meta.yaml b/recipes/savvy/meta.yaml index 05aeea035cc2d..fc7fb66c1db8e 100644 --- a/recipes/savvy/meta.yaml +++ b/recipes/savvy/meta.yaml @@ -14,7 +14,7 @@ source: build: skip: True # [win] - number: 2 + number: 3 requirements: build: diff --git a/recipes/scallop-lr/meta.yaml b/recipes/scallop-lr/meta.yaml index d9d679e72e026..05c6d68bd45f2 100644 --- a/recipes/scallop-lr/meta.yaml +++ b/recipes/scallop-lr/meta.yaml @@ -10,7 +10,7 @@ source: sha256: "6a073587cf82da9fb5c22e11629943293d97bf71e05b0728c6e245d99ef980d5" build: - number: 9 + number: 10 requirements: build: diff --git a/recipes/scallop/meta.yaml b/recipes/scallop/meta.yaml index ae7ec818089d5..7a247b908f774 100644 --- a/recipes/scallop/meta.yaml +++ b/recipes/scallop/meta.yaml @@ -10,7 +10,7 @@ source: sha256: "b09e3c61f1b3b1da2a96d9d8429d80326a3bb14f5fe6af9b5e87570d4b86937a" build: - number: 7 + number: 8 requirements: build: diff --git a/recipes/scallop2/meta.yaml b/recipes/scallop2/meta.yaml index 5b32155b3dad9..e63606a3f4266 100644 --- a/recipes/scallop2/meta.yaml +++ b/recipes/scallop2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: "1edfd369f6c8a6ea979eaf5bc4313137236338c5c98aae4648aac55b802e5fea" build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/scalpel/meta.yaml b/recipes/scalpel/meta.yaml index 8c5bcf4b08822..63c8b2a0fe195 100644 --- a/recipes/scalpel/meta.yaml +++ b/recipes/scalpel/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 506f731b3886def158c15fd8b74fa98390f304a507d2040972e6b09ddefac8f0 build: - number: 7 + number: 8 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/scelestial/meta.yaml b/recipes/scelestial/meta.yaml index 2f367c64e9274..52b2b0ab0db10 100644 --- a/recipes/scelestial/meta.yaml +++ b/recipes/scelestial/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '5c5d51a3d908c92f361219b3a5abe64bc1a0dc5e14d0736fd0e64e1c6df26680' build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage("scelestial", max_pin="x") }} diff --git a/recipes/sciphi/meta.yaml b/recipes/sciphi/meta.yaml index b810932d715b7..af2d59c0753ee 100644 --- a/recipes/sciphi/meta.yaml +++ b/recipes/sciphi/meta.yaml @@ -7,7 +7,7 @@ source: url: https://github.com/cbg-ethz/SCIPhI/releases/download/v{{ version }}/SCIPhI-{{ version }}.tar.bz2 build: - number: 5 + number: 6 skip: True # [osx] package: diff --git a/recipes/sciphin/meta.yaml b/recipes/sciphin/meta.yaml index 8fe756259b851..24fe2f785f80d 100644 --- a/recipes/sciphin/meta.yaml +++ b/recipes/sciphin/meta.yaml @@ -7,7 +7,7 @@ source: url: https://github.com/cbg-ethz/SCIPhIN/releases/download/v{{ version }}/SCIPhIN-{{ version }}.tar.bz2 build: - number: 3 + number: 4 skip: True # [osx] package: diff --git a/recipes/scramble/build_failure.linux-64.yaml b/recipes/scramble/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..920741fe3396c --- /dev/null +++ b/recipes/scramble/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 6b48e6c4ed9720d076ce7ec1f58e9a1fb01ebb14d4ed247c755d81643fbdbb08 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + ' + home: https://github.com/GeneDx/scramble + license: CC + license_file: LICENSE + summary: Soft Clipped Read Alignment Mapper + extra: + copy_test_source_files: true + final: true + identifiers: + - doi:10.1038/s41436-020-0749-x + notes: 'SCRAMble runs as a two-step process. First cluster_identifier is used to + generate soft-clipped + + read cluster consensus sequences. Second, SCRAMble.R analyzes the cluster file + for likely MEIs. + + Custom wrapper script scramble.sh is provided to help setting location of SCRAMble.R + script, + + and values for --install-dir and --mei-refs params. + + ' + + + source tree in: /opt/conda/conda-bld/scramble_1734758260158/work + export PREFIX=/opt/conda/conda-bld/scramble_1734758260158/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + export BUILD_PREFIX=/opt/conda/conda-bld/scramble_1734758260158/_build_env + export SRC_DIR=/opt/conda/conda-bld/scramble_1734758260158/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/scramble-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/scramble-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + mkdir -p /opt/conda/conda-bld/scramble_1734758260158/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin + /opt/conda/conda-bld/scramble_1734758260158/_build_env/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/conda-bld/scramble_1734758260158/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fdebug-prefix-map=/opt/conda/conda-bld/scramble_1734758260158/work=/usr/local/src/conda/scramble-1.0.2 -fdebug-prefix-map=/opt/conda/conda-bld/scramble_1734758260158/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac=/usr/local/src/conda-prefix -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/scramble_1734758260158/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -Wl,-rpath-link,/opt/conda/conda-bld/scramble_1734758260158/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -L/opt/conda/conda-bld/scramble_1734758260158/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -o /opt/conda/conda-bld/scramble_1734758260158/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/cluster_identifier /opt/conda/conda-bld/scramble_1734758260158/work/cluster_identifier/src/cluster_identifier.c -lz -lpthread -llzma -lbz2 -lcurl -lcrypto -lhts + /opt/conda/conda-bld/scramble_1734758260158/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lz: No such file or directory + collect2: error: ld returned 1 exit status + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/scramble_1734758260158/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/scramble_1734758260158/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/scramble/build_failure.osx-64.yaml b/recipes/scramble/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..0b4448897a409 --- /dev/null +++ b/recipes/scramble/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 6b48e6c4ed9720d076ce7ec1f58e9a1fb01ebb14d4ed247c755d81643fbdbb08 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/scramble-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments + F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/scramble-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/scramble-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/scramble-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/scramble_1734758604858/test_tmp/conda_test_runner.sh']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=/opt/mambaforge/envs/bioconda/conda-bld/scramble_1734758604858/_build_env/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: scramble-1.0.2-h18d8cf3_2.tar.bz2 + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/scramble-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/scramble-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/scramble-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + Running sample: $SRC_DIR/validation/test.clusters.txt + Running scramble with options: + blastRef : $SRC_DIR/validation/test.fa + clusterFile : $SRC_DIR/validation/test.clusters.txt + deletions : TRUE + indelScore : 80 + INSTALL.DIR : $PREFIX/share/scramble/bin + mei.refs : $PREFIX/share/scramble/resources/MEI_consensus_seqs.fa + meis : TRUE + meiScore : 50 + minDelLen : 50 + nCluster : 5 + no.vcf : FALSE + outFilePrefix : $SRC_DIR/validation/test_conda + pctAlign : 90 + polyAdist : 100 + polyAFrac : 0.75 + Useful Functions Loaded +# Last 100 lines of the build log. diff --git a/recipes/scramble/meta.yaml b/recipes/scramble/meta.yaml index 9a82ff459ea30..e58ce5efa51de 100644 --- a/recipes/scramble/meta.yaml +++ b/recipes/scramble/meta.yaml @@ -10,7 +10,7 @@ source: sha256: fa4a8a456493efffa16ae8e77aaa43e5ec1c2d38c87f626f462ff02342b18a0f build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/scrappie/meta.yaml b/recipes/scrappie/meta.yaml index 1a58b66f92eb0..b402ce566a82d 100644 --- a/recipes/scrappie/meta.yaml +++ b/recipes/scrappie/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 160f3e462a6e079e55da4de8d3bd232243ff988530cfe649038feccc9bb79797 build: - number: 6 + number: 7 skip: True # [py2k or osx] requirements: diff --git a/recipes/scrm/meta.yaml b/recipes/scrm/meta.yaml index 182a2aa387da4..be7552eff5a80 100644 --- a/recipes/scrm/meta.yaml +++ b/recipes/scrm/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://github.com/scrm/scrm/archive/v{{ version }}.tar.gz diff --git a/recipes/scrubby/build_failure.linux-64.yaml b/recipes/scrubby/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..89310f223c21f --- /dev/null +++ b/recipes/scrubby/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: fc92b752604b46641d0b8a27d54804349c28ffd858a406ed9f6555cef85fd0c1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("minimap2==2.24=h7132678_1"), MatchSpec("kraken2==2.1.2=pl5321h9f5acd7_3")} + Encountered problems while solving: + - package kraken2-2.1.2-pl5321h9f5acd7_3 is excluded by strict repo priority + - package minimap2-2.24-h7132678_1 is excluded by strict repo priority + + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("minimap2==2.24=h7132678_1"), MatchSpec("kraken2==2.1.2=pl5321h9f5acd7_3")} + Encountered problems while solving: + - package kraken2-2.1.2-pl5321h9f5acd7_3 is excluded by strict repo priority + - package minimap2-2.24-h7132678_1 is excluded by strict repo priority + + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("minimap2==2.24=h7132678_1"), MatchSpec("kraken2==2.1.2=pl5321h9f5acd7_3")} + Encountered problems while solving: + - package kraken2-2.1.2-pl5321h9f5acd7_3 is excluded by strict repo priority + - package minimap2-2.24-h7132678_1 is excluded by strict repo priority +# Last 100 lines of the build log. diff --git a/recipes/scrubby/build_failure.osx-64.yaml b/recipes/scrubby/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..33155e01d0c7f --- /dev/null +++ b/recipes/scrubby/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: fc92b752604b46641d0b8a27d54804349c28ffd858a406ed9f6555cef85fd0c1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Encountered problems while solving: + - package kraken2-2.1.2-pl5321he1e422e_1 is excluded by strict repo priority + + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("kraken2==2.1.2=pl5321he1e422e_1")} + Encountered problems while solving: + - package kraken2-2.1.2-pl5321he1e422e_1 is excluded by strict repo priority + + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("kraken2==2.1.2=pl5321he1e422e_1")} + Encountered problems while solving: + - package kraken2-2.1.2-pl5321he1e422e_1 is excluded by strict repo priority + + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("kraken2==2.1.2=pl5321he1e422e_1")} + Encountered problems while solving: + - package kraken2-2.1.2-pl5321he1e422e_1 is excluded by strict repo priority +# Last 100 lines of the build log. diff --git a/recipes/scrubby/meta.yaml b/recipes/scrubby/meta.yaml index 9e5b36b11e7b1..9e1564a58d085 100644 --- a/recipes/scrubby/meta.yaml +++ b/recipes/scrubby/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 88aaf4420393501b1387f45c9291a373a3a01c034c1d1d72555cccb05fea92a2 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/scssim/meta.yaml b/recipes/scssim/meta.yaml index 85f1e05184df1..cf927123dc51d 100644 --- a/recipes/scssim/meta.yaml +++ b/recipes/scssim/meta.yaml @@ -9,7 +9,7 @@ source: sha256: ef6011ac879e1d539f2fe00bda0f98d8a47420aa6a368808556196f642eb8a19 build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/sctools/meta.yaml b/recipes/sctools/meta.yaml index cdf6f57481bec..c1c273e803a66 100644 --- a/recipes/sctools/meta.yaml +++ b/recipes/sctools/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha }} build: - number: 4 + number: 5 skip: True # [osx] requirements: diff --git a/recipes/sdm/meta.yaml b/recipes/sdm/meta.yaml index aa1b42116cce8..b24bd810a9dc2 100644 --- a/recipes/sdm/meta.yaml +++ b/recipes/sdm/meta.yaml @@ -12,7 +12,7 @@ source: - sdm_3.08.patch build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name|lower, max_pin="x.x") }} diff --git a/recipes/sdust/meta.yaml b/recipes/sdust/meta.yaml index f26962300d506..8b2b905323caa 100644 --- a/recipes/sdust/meta.yaml +++ b/recipes/sdust/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 0825a760fae884e65b2b024cc4f511e32e6c1698571c147daf5a61ba0dcac589 build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage("sdust", max_pin="x.x") }} diff --git a/recipes/segemehl/0.2.0/meta.yaml b/recipes/segemehl/0.2.0/meta.yaml index 2eaf3b0e4562a..8fe5987af966a 100644 --- a/recipes/segemehl/0.2.0/meta.yaml +++ b/recipes/segemehl/0.2.0/meta.yaml @@ -3,7 +3,7 @@ package: version: 0.2.0 build: - number: 10 + number: 11 skip: True # [osx] source: diff --git a/recipes/segemehl/0.3.1/meta.yaml b/recipes/segemehl/0.3.1/meta.yaml index 0dbf86f9da19a..6a572958e3d47 100644 --- a/recipes/segemehl/0.3.1/meta.yaml +++ b/recipes/segemehl/0.3.1/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 9 + number: 10 skip: True # [osx] source: diff --git a/recipes/segemehl/meta.yaml b/recipes/segemehl/meta.yaml index 65de611f3a520..85a29255552d4 100644 --- a/recipes/segemehl/meta.yaml +++ b/recipes/segemehl/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 10 + number: 11 skip: True # [osx] source: diff --git a/recipes/segul/meta.yaml b/recipes/segul/meta.yaml index 98e5f7721f857..202559eef590c 100644 --- a/recipes/segul/meta.yaml +++ b/recipes/segul/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 5d33058149e00551f219e6d92a9156d89643551c47fac18ed688aec022b8afdd build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('segul', max_pin="x.x") }} diff --git a/recipes/selam/meta.yaml b/recipes/selam/meta.yaml index befd25c006cac..4537a1f69e2c4 100644 --- a/recipes/selam/meta.yaml +++ b/recipes/selam/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{sha256}} build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage("selam", max_pin="x.x.x") }} diff --git a/recipes/selectfasta/meta.yaml b/recipes/selectfasta/meta.yaml index 04c7c5f0e4848..4a33b50ec6d09 100644 --- a/recipes/selectfasta/meta.yaml +++ b/recipes/selectfasta/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 55018c948ea4eb50a989a94b61e2dba5cb59945ce3845f0ba0044786406f64fa build: - number: 0 + number: 1 skip: True # [osx] requirements: diff --git a/recipes/selene-sdk/meta.yaml b/recipes/selene-sdk/meta.yaml index 74f74604baf55..256a95453bcb2 100644 --- a/recipes/selene-sdk/meta.yaml +++ b/recipes/selene-sdk/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 9eaf17fe0135d05a605403214086ec29d3189c45804fd61de444254c7eb3102d build: - number: 0 + number: 1 script: python setup.py install --single-version-externally-managed --record=record.txt run_exports: - {{ pin_subpackage("selene-sdk", max_pin="x.x") }} diff --git a/recipes/selscan/meta.yaml b/recipes/selscan/meta.yaml index ae02ef6dd7133..868789d6f77c6 100644 --- a/recipes/selscan/meta.yaml +++ b/recipes/selscan/meta.yaml @@ -13,7 +13,7 @@ source: sha256: {{ sha256 }} build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/sensv/build_failure.linux-64.yaml b/recipes/sensv/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..51e88226f0679 --- /dev/null +++ b/recipes/sensv/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: ff35e76fdc4170f77ac39881ee8d85ced2137acb18758878580430c9d4f62852 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("pysam==0.15.3=py27hbcae180_3"), MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']")} + Encountered problems while solving: + - package pysam-0.15.3-py27hbcae180_3 requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mhtslib 1.10.2.* [0m is installable and it requires + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [31mlibzlib >=1.3.1,<2.0a0 [0m is not installable because there are no viable options + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_0[0m, which conflicts with any installable versions previously reported; + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_1[0m, which conflicts with any installable versions previously reported; + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_2[0m, which conflicts with any installable versions previously reported; + [32mpysam 0.15.3.* [0m is installable with the potential options + [31mpysam 0.15.3[0m would require + [31mlibdeflate >=1.0,<1.1.0a0 [0m, which conflicts with any installable versions previously reported; + [32mpysam 0.15.3[0m would require + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("pysam==0.15.3=py27hbcae180_3"), MatchSpec("zlib[version='>=1.2.11,<1.3.0a0']")} + Encountered problems while solving: + - package pysam-0.15.3-py27hbcae180_3 requires zlib >=1.2.11,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mhtslib 1.10.2.* [0m is installable and it requires + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [31mlibzlib >=1.3.1,<2.0a0 [0m is not installable because there are no viable options + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_0[0m, which conflicts with any installable versions previously reported; + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_1[0m, which conflicts with any installable versions previously reported; + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_2[0m, which conflicts with any installable versions previously reported; + [32mpysam 0.15.3.* [0m is installable with the potential options + [31mpysam 0.15.3[0m would require + [31mlibdeflate >=1.0,<1.1.0a0 [0m, which conflicts with any installable versions previously reported; + [32mpysam 0.15.3[0m would require + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed. +# Last 100 lines of the build log. diff --git a/recipes/sensv/meta.yaml b/recipes/sensv/meta.yaml index 47e58c52886a9..ba9b006aaffb3 100644 --- a/recipes/sensv/meta.yaml +++ b/recipes/sensv/meta.yaml @@ -13,7 +13,7 @@ source: folder: data build: - number: 2 + number: 3 skip: True # [osx] requirements: diff --git a/recipes/seq-gen/meta.yaml b/recipes/seq-gen/meta.yaml index 3bd9ce66ecc4a..689becfeb3f92 100644 --- a/recipes/seq-gen/meta.yaml +++ b/recipes/seq-gen/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 7 + number: 8 source: url: https://github.com/rambaut/Seq-Gen/archive/{{ version }}.tar.gz diff --git a/recipes/seqan_tcoffee/meta.yaml b/recipes/seqan_tcoffee/meta.yaml index 7c30ec277d568..d99920efcbe55 100644 --- a/recipes/seqan_tcoffee/meta.yaml +++ b/recipes/seqan_tcoffee/meta.yaml @@ -13,7 +13,7 @@ source: build: skip: True # [osx] - number: 4 + number: 5 requirements: build: diff --git a/recipes/seqcomplexity/meta.yaml b/recipes/seqcomplexity/meta.yaml index 232c118e0156b..bd93e3b8a3529 100644 --- a/recipes/seqcomplexity/meta.yaml +++ b/recipes/seqcomplexity/meta.yaml @@ -6,7 +6,7 @@ package: version: {{version}} build: - number: 1 + number: 2 source: url: https://github.com/stevenweaver/seqcomplexity/archive/v{{ version }}.tar.gz diff --git a/recipes/seqfu/build_failure.osx-64.yaml b/recipes/seqfu/build_failure.osx-64.yaml index c5f5d5bff4d23..2809cb429497a 100644 --- a/recipes/seqfu/build_failure.osx-64.yaml +++ b/recipes/seqfu/build_failure.osx-64.yaml @@ -1,39 +1,106 @@ -recipe_sha: 184967c871fce4a0fd9ae83e451862b416eda8d7124bf15f3c862398b46c3783 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: e3b037c5d4bbdff1fb6a0cdff3b3f282ae4cce30693cf35ef04b66a9ad241a52 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: compiler error log: |2- - 16:20:36 BIOCONDA INFO (ERR) 75706 lines; 4.905s; 167.559MiB peakmem; proj: /opt/mambaforge/envs/bioconda/conda-bld/seqfu_1718122533360/work/src/fu_tabcheck.nim; out: /opt/mambaforge/envs/bioconda/conda-bld/seqfu_1718122533360/work/bin/fu-tabcheck [SuccessX] - 16:20:43 BIOCONDA INFO (ERR) test/byte/count.cpp:1:10: fatal error: 'iostream' file not found - 16:20:43 BIOCONDA INFO (ERR) #include - 16:20:43 BIOCONDA INFO (ERR) ^~~~~~~~~~ - 16:20:43 BIOCONDA INFO (ERR) 1 error generated. - 16:20:44 BIOCONDA INFO (ERR) make: *** [Makefile:35: bin/SeqCountHelper] Error 1 - 16:20:45 BIOCONDA INFO (OUT) Extracting download - 16:20:45 BIOCONDA INFO (ERR) Traceback (most recent call last): - 16:20:45 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - 16:20:45 BIOCONDA INFO (ERR) sys.exit(execute()) - 16:20:45 BIOCONDA INFO (OUT) source tree in: /opt/mambaforge/envs/bioconda/conda-bld/seqfu_1718122533360/work - 16:20:45 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - 16:20:45 BIOCONDA INFO (ERR) api.build( - 16:20:45 BIOCONDA INFO (OUT) export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/seqfu_1718122533360/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol - 16:20:45 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - 16:20:45 BIOCONDA INFO (ERR) return build_tree( - 16:20:45 BIOCONDA INFO (OUT) export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/seqfu_1718122533360/_build_env - 16:20:45 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - 16:20:45 BIOCONDA INFO (ERR) packages_from_this = build( - 16:20:45 BIOCONDA INFO (OUT) export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/seqfu_1718122533360/work - 16:20:45 BIOCONDA INFO (OUT) INFO: activate_clang_osx-64.sh made the following environmental changes: - 16:20:45 BIOCONDA INFO (OUT) +AR=x86_64-apple-darwin13.4.0-ar - 16:20:45 BIOCONDA INFO (OUT) +AS=x86_64-apple-darwin13.4.0-as - 16:20:45 BIOCONDA INFO (OUT) +CC=x86_64-apple-darwin13.4.0-clang - 16:20:45 BIOCONDA INFO (OUT) +CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - 16:20:45 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - 16:20:45 BIOCONDA INFO (ERR) utils.check_call_env( - 16:20:45 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - 16:20:45 BIOCONDA INFO (ERR) return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - 16:20:45 BIOCONDA INFO (OUT) +CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/seqfu-1.20.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - 16:20:45 BIOCONDA INFO (OUT) +CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - 16:20:45 BIOCONDA INFO (OUT) +CLANG=x86_64-apple-darwin13.4.0-clang - 16:20:45 BIOCONDA INFO (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - 16:20:45 BIOCONDA INFO (ERR) raise subprocess.CalledProcessError(proc.returncode, _args) - 16:20:45 BIOCONDA INFO (ERR) subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/seqfu_1718122533360/work/conda_build.sh']' returned non-zero exit status 2. \ No newline at end of file + Verifying dependencies for opencl@1.0.1 + Installing clblast@0.0.2 + Success: clblast installed successfully. + Installing stb_image@any version + Downloading https://gitlab.com/define-private-public/stb_image-Nim.git using git + Verifying dependencies for stb_image@2.5 + Installing stb_image@2.5 + Success: stb_image installed successfully. + Info: Dependency on zip@any version already satisfied + Verifying dependencies for zip@0.3.1 + Installing untar@any version + Downloading https://github.com/dom96/untar using git + Verifying dependencies for untar@0.1.0 + Installing untar@0.1.0 + Success: untar installed successfully. + Installing arraymancer@0.7.33 + Success: arraymancer installed successfully. + Installing datamancer@0.5.0 + Success: datamancer installed successfully. + Installing illwill@#v0.2.0 + Downloading https://github.com/johnnovak/illwill using git + Verifying dependencies for illwill@0.2.0 + Installing illwill@0.2.0 + Success: illwill installed successfully. + ## Automatic build: make + nimble install -y --depsOnly + Verifying dependencies for seqfu@1.22.3 + Info: Dependency on regex@>= 0.23 already satisfied + Verifying dependencies for regex@0.26.0 + Info: Dependency on unicodedb@>= 0.7.2 already satisfied + Verifying dependencies for unicodedb@0.13.0 + Info: Dependency on checksums@any version already satisfied + Verifying dependencies for checksums@0.2.1 + Info: Dependency on docopt@#v0.7.1 already satisfied + Verifying dependencies for docopt@0.7.1 + Info: Dependency on regex@>= 0.11.1 already satisfied + Verifying dependencies for regex@0.26.0 + Info: Dependency on unicodedb@>= 0.7.2 already satisfied + Verifying dependencies for unicodedb@0.13.0 + Info: Dependency on terminaltables@any version already satisfied + Verifying dependencies for terminaltables@0.1.1 + Info: Dependency on readfq@#head already satisfied + Verifying dependencies for readfq@0.1.1 + Info: Dependency on zip@>= 0.2.1 already satisfied + Verifying dependencies for zip@0.3.1 + Info: Dependency on iterutils@any version already satisfied + Verifying dependencies for iterutils@0.4 + Info: Dependency on argparse@any version already satisfied + Verifying dependencies for argparse@4.0.2 + Info: Dependency on colorize@any version already satisfied + Verifying dependencies for colorize@0.2.0 + Info: Dependency on zip@any version already satisfied + Verifying dependencies for zip@0.3.1 + Info: Dependency on datamancer@>= 0.3 already satisfied + Verifying dependencies for datamancer@0.5.0 + Info: Dependency on https://github.com/Vindaar/seqmath@>= 0.2.1 already satisfied + Verifying dependencies for seqmath@0.2.2 + Info: Dependency on arraymancer@>= 0.7.30 already satisfied + Verifying dependencies for arraymancer@0.7.33 + Info: Dependency on nimblas@>= 0.3.1 already satisfied + Verifying dependencies for nimblas@0.3.1 + Info: Dependency on nimlapack@>= 0.3.1 already satisfied + Verifying dependencies for nimlapack@0.3.1 + Info: Dependency on nimcuda@>= 0.2.0 already satisfied + Verifying dependencies for nimcuda@0.2.2 + Info: Dependency on nimcl@>= 0.1.3 already satisfied + Verifying dependencies for nimcl@0.1.3 + Info: Dependency on opencl@>= 1.0 already satisfied + Verifying dependencies for opencl@1.0.1 + Info: Dependency on clblast@>= 0.0.2 already satisfied + Verifying dependencies for clblast@0.0.2 + Info: Dependency on opencl@any version already satisfied + Verifying dependencies for opencl@1.0.1 + Info: Dependency on stb_image@any version already satisfied + Verifying dependencies for stb_image@2.5 + Info: Dependency on zip@any version already satisfied + Verifying dependencies for zip@0.3.1 + Info: Dependency on untar@any version already satisfied + Verifying dependencies for untar@0.1.0 + Info: Dependency on illwill@#v0.2.0 already satisfied + Verifying dependencies for illwill@0.2.0 + touch src/deps.txt + touch src/sfu.nim + nim c --mm:orc -d:NimblePkgVersion=1.22.3 -d:release --opt:speed --passC:"-Wno-error=incompatible-pointer-types" --out:bin/seqfu src/sfu.nim + nim c --mm:orc -d:NimblePkgVersion=1.22.3 -d:release --opt:speed --passC:"-Wno-error=incompatible-pointer-types" --out:bin/fu-msa src/fu_msa.nim + nim c --threads:on --mm:orc -d:NimblePkgVersion=1.22.3 -d:release --opt:speed --passC:"-Wno-error=incompatible-pointer-types" --out:bin/fu-primers src/fu_primers.nim + nim c --mm:orc -d:NimblePkgVersion=1.22.3 -d:release --opt:speed --passC:"-Wno-error=incompatible-pointer-types" --out:bin/dadaist2-mergeseqs src/dadaist2_mergeseqs.nim + nim c --mm:orc -d:NimblePkgVersion=1.22.3 -d:release --opt:speed --passC:"-Wno-error=incompatible-pointer-types" --out:bin/fu-shred src/fu_shred.nim + nim c --threads:on --mm:orc -d:NimblePkgVersion=1.22.3 -d:release --opt:speed --passC:"-Wno-error=incompatible-pointer-types" --out:bin/fu-homocomp src/fu_homocomp.nim + nim c --mm:orc -d:NimblePkgVersion=1.22.3 -d:release --opt:speed --passC:"-Wno-error=incompatible-pointer-types" --out:bin/fu-multirelabel src/fu_multirelabel.nim + nim c --mm:orc -d:NimblePkgVersion=1.22.3 -d:release --opt:speed --passC:"-Wno-error=incompatible-pointer-types" --out:bin/fu-index src/fu_index.nim + nim c --mm:orc -d:NimblePkgVersion=1.22.3 -d:release --opt:speed --passC:"-Wno-error=incompatible-pointer-types" --out:bin/fu-cov src/fu_cov.nim + nim c --threads:on --mm:orc -d:NimblePkgVersion=1.22.3 -d:release --opt:speed --passC:"-Wno-error=incompatible-pointer-types" --out:bin/fu-16Sregion src/dadaist2_region.nim + nim c --threads:on --mm:orc -d:NimblePkgVersion=1.22.3 -d:release --opt:speed --passC:"-Wno-error=incompatible-pointer-types" --out:bin/fu-nanotags src/fu_nanotags.nim + nim c --threads:on --mm:orc -d:NimblePkgVersion=1.22.3 -d:release --opt:speed --passC:"-Wno-error=incompatible-pointer-types" --out:bin/fu-orf src/fu_orf.nim + nim c --threads:on --mm:orc -d:NimblePkgVersion=1.22.3 -d:release --opt:speed --passC:"-Wno-error=incompatible-pointer-types" --out:bin/fu-sw src/fu_sw.nim + nim c --mm:orc -d:NimblePkgVersion=1.22.3 -d:release --opt:speed --passC:"-Wno-error=incompatible-pointer-types" --out:bin/fu-virfilter src/fu_virfilter.nim + nim c --mm:orc -d:NimblePkgVersion=1.22.3 -d:release --opt:speed --passC:"-Wno-error=incompatible-pointer-types" --out:bin/fu-tabcheck src/fu_tabcheck.nim + gcc -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o bin/byteshift test/byte/shifter.c + g -std=c11 -O3 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -o bin/SeqCountHelper test/byte/count.cpp -lz +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/seqfu/meta.yaml b/recipes/seqfu/meta.yaml index 7fc4118201e17..d49a9f87a669f 100644 --- a/recipes/seqfu/meta.yaml +++ b/recipes/seqfu/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/seqhax/build_failure.linux-64.yaml b/recipes/seqhax/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..fb7c056a177c9 --- /dev/null +++ b/recipes/seqhax/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 14840de0be1bf6095fbbcd9a5889e219159d31d69ae19e4ca7ab021277c91493 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + | ^~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:129:13: error: 'seek_pos' was not declared in this scope + 129 | seek_pos = i - ks->begin; if ( i < ks->end ) seek_pos; \ + | ^~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:152:9: note: in expansion of macro '__KS_GETUNTIL' + 152 | __KS_GETUNTIL(SCOPE, __read) \ + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:155:49: note: in expansion of macro 'KSTREAM_INIT2' + 155 | #define KSTREAM_INIT(type_t, __read, __bufsize) KSTREAM_INIT2(static, type_t, __read, __bufsize) + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:239:9: note: in expansion of macro 'KSTREAM_INIT' + 239 | KSTREAM_INIT(type_t, __read, 16384) \ + | ^~~~~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2' + 244 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) + | ^~~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kmseq.hh:24:1: note: in expansion of macro 'KSEQ_INIT' + 24 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:140:13: error: 'kmseq::kstream_t' {aka 'struct kmseq::__kstream_t'} has no member named 'seek_pos' + 140 | ks->seek_pos = seek_pos; \ + | ^~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:152:9: note: in expansion of macro '__KS_GETUNTIL' + 152 | __KS_GETUNTIL(SCOPE, __read) \ + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:155:49: note: in expansion of macro 'KSTREAM_INIT2' + 155 | #define KSTREAM_INIT(type_t, __read, __bufsize) KSTREAM_INIT2(static, type_t, __read, __bufsize) + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:239:9: note: in expansion of macro 'KSTREAM_INIT' + 239 | KSTREAM_INIT(type_t, __read, 16384) \ + | ^~~~~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2' + 244 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) + | ^~~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kmseq.hh:24:1: note: in expansion of macro 'KSEQ_INIT' + 24 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:140:25: error: 'seek_pos' was not declared in this scope + 140 | ks->seek_pos = seek_pos; \ + | ^~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:152:9: note: in expansion of macro '__KS_GETUNTIL' + 152 | __KS_GETUNTIL(SCOPE, __read) \ + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:155:49: note: in expansion of macro 'KSTREAM_INIT2' + 155 | #define KSTREAM_INIT(type_t, __read, __bufsize) KSTREAM_INIT2(static, type_t, __read, __bufsize) + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:239:9: note: in expansion of macro 'KSTREAM_INIT' + 239 | KSTREAM_INIT(type_t, __read, 16384) \ + | ^~~~~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2' + 244 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) + | ^~~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kmseq.hh:24:1: note: in expansion of macro 'KSEQ_INIT' + 24 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kmseq.hh: In function 'int kmseq::ks_getc(kstream_t*)': + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:77:13: error: 'kmseq::kstream_t' {aka 'struct kmseq::__kstream_t'} has no member named 'seek_pos' + 77 | ks->seek_pos; \ + | ^~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:153:9: note: in expansion of macro '__KS_INLINED' + 153 | __KS_INLINED(__read) + | ^~~~~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:155:49: note: in expansion of macro 'KSTREAM_INIT2' + 155 | #define KSTREAM_INIT(type_t, __read, __bufsize) KSTREAM_INIT2(static, type_t, __read, __bufsize) + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:239:9: note: in expansion of macro 'KSTREAM_INIT' + 239 | KSTREAM_INIT(type_t, __read, 16384) \ + | ^~~~~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kseq.h:244:35: note: in expansion of macro 'KSEQ_INIT2' + 244 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) + | ^~~~~~~~~~ + /opt/conda/conda-bld/seqhax_1734240689548/work/src/lib/kmseq.hh:24:1: note: in expansion of macro 'KSEQ_INIT' + 24 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ + make[2]: *** [src/CMakeFiles/seqhax.dir/build.make:107: src/CMakeFiles/seqhax.dir/seqhax/progs/cat.cc.o] Error 1 + make[1]: *** [CMakeFiles/Makefile2:151: src/CMakeFiles/seqhax.dir/all] Error 2 + make: *** [Makefile:166: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/seqhax_1734240689548/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/seqhax_1734240689548/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/seqhax/meta.yaml b/recipes/seqhax/meta.yaml index a6addef9c10bf..76261e144cbac 100644 --- a/recipes/seqhax/meta.yaml +++ b/recipes/seqhax/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 skip: true # [not linux] run_exports: - {{ pin_subpackage('seqhax', max_pin="x") }} diff --git a/recipes/seqprep/meta.yaml b/recipes/seqprep/meta.yaml index dfcd0570cc539..01877e5038b18 100644 --- a/recipes/seqprep/meta.yaml +++ b/recipes/seqprep/meta.yaml @@ -6,7 +6,7 @@ package: version: '{{version}}' build: - number: 8 + number: 9 skip: True # [osx] source: diff --git a/recipes/seqsizzle/build_failure.linux-64.yaml b/recipes/seqsizzle/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..a08354f4915f8 --- /dev/null +++ b/recipes/seqsizzle/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 3d0893c48748a534153d78e99f06506671881bdd968cf69949f1ea3ca00d2f56 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + --> src/search_panel.rs:348:26 + | + 348 | .position(Position::Bottom) + | ^^^^^^^^ + + warning: use of deprecated method ratatui::widgets::block::Title::<'a>::alignment: use Block::title_top() or Block::title_bottom() instead. This will be removed in a future release. + --> src/search_panel.rs:349:26 + | + 349 | .alignment(Alignment::Right), + | ^^^^^^^^^ + + error[E0308]: mismatched types + --> src/tui.rs:68:9 + | + 67 | pub fn size(&self) -> Rect { + | ---- expected Rect because of return type + 68 | self.terminal.size().unwrap() + | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected Rect, found Size + + warning: use of deprecated method ratatui::widgets::block::Title::<'a>::position: use Block::title_top() or Block::title_bottom() instead. This will be removed in a future release. + --> src/ui.rs:19:22 + | + 19 | .position(Position::Bottom), + | ^^^^^^^^ + + warning: use of deprecated method ratatui::Frame::<'_>::size: use .area() as it's the more correct name + --> src/ui.rs:36:15 + | + 36 | frame.size(), + | ^^^^ + + warning: use of deprecated method ratatui::Frame::<'_>::size: use .area() as it's the more correct name + --> src/ui.rs:39:55 + | + 39 | let center_area = centered_rect(80, 80, frame.size()); + | ^^^^ + + warning: use of deprecated method ratatui::Frame::<'_>::size: use .area() as it's the more correct name + --> src/ui.rs:43:67 + | + 43 | let save_file_popup_area = centered_rect(80, 5, frame.size()); + | ^^^^ + + warning: unused variable: tui_rect + --> src/app.rs:300:38 + | + 300 | pub fn resized_update(&mut self, tui_rect: Rect) { + | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: _tui_rect + | + = note: #[warn(unused_variables)] on by default + + warning: unused variable: tui + --> src/control.rs:55:38 + | + 55 | fn handle_input_file_save(app: &App, tui: &Tui, keyevent: KeyEvent) -> Update { + | ^^^ help: if this is intentional, prefix it with an underscore: _tui + + warning: unused variable: app + --> src/control.rs:69:28 + | + 69 | pub fn handle_input_viewer(app: &App, tui: &Tui, keyevent: KeyEvent) -> Update { + | ^^^ help: if this is intentional, prefix it with an underscore: _app + + warning: unused variable: tui + --> src/control.rs:122:45 + | + 122 | pub fn handle_input_search_panel(app: &App, tui: &Tui, keyevent: KeyEvent) -> Update { + | ^^^ help: if this is intentional, prefix it with an underscore: _tui + + For more information about this error, try rustc --explain E0308. + warning: seqsizzle (bin "seqsizzle") generated 14 warnings + error: could not compile seqsizzle (bin "seqsizzle") due to 1 previous error; 14 warnings emitted + + Caused by: + process didn't exit successfully: rustc --crate-name seqsizzle --edition=2021 src/main.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=50dad29e5d213587 -C extra-filename=-50dad29e5d213587 --out-dir /opt/conda/conda-bld/seqsizzle_1734083988989/work/target/release/deps -C linker=/opt/conda/conda-bld/seqsizzle_1734083988989/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=symbols -L dependency=/opt/conda/conda-bld/seqsizzle_1734083988989/work/target/release/deps --extern anyhow=/opt/conda/conda-bld/seqsizzle_1734083988989/work/target/release/deps/libanyhow-7dee469a46e00507.rlib --extern bio=/opt/conda/conda-bld/seqsizzle_1734083988989/work/target/release/deps/libbio-0f318dcf9fc7051e.rlib --extern clap=/opt/conda/conda-bld/seqsizzle_1734083988989/work/target/release/deps/libclap-8e137a9fe8504056.rlib --extern crossterm=/opt/conda/conda-bld/seqsizzle_1734083988989/work/target/release/deps/libcrossterm-e7337446e943d98a.rlib --extern csv=/opt/conda/conda-bld/seqsizzle_1734083988989/work/target/release/deps/libcsv-b2b365e50389e563.rlib --extern gcollections=/opt/conda/conda-bld/seqsizzle_1734083988989/work/target/release/deps/libgcollections-4bdf5b0cecfb0e24.rlib --extern interval=/opt/conda/conda-bld/seqsizzle_1734083988989/work/target/release/deps/libinterval-f8db54941c61351a.rlib --extern num_traits=/opt/conda/conda-bld/seqsizzle_1734083988989/work/target/release/deps/libnum_traits-eca2b94870c48a93.rlib --extern ratatui=/opt/conda/conda-bld/seqsizzle_1734083988989/work/target/release/deps/libratatui-41c84262f613c733.rlib --extern rayon=/opt/conda/conda-bld/seqsizzle_1734083988989/work/target/release/deps/librayon-d5b2d033b8eed27a.rlib --extern shadow_rs=/opt/conda/conda-bld/seqsizzle_1734083988989/work/target/release/deps/libshadow_rs-2ae7e17a343043d8.rlib --extern tui_textarea=/opt/conda/conda-bld/seqsizzle_1734083988989/work/target/release/deps/libtui_textarea-1d8664768a47532c.rlib --extern uuid=/opt/conda/conda-bld/seqsizzle_1734083988989/work/target/release/deps/libuuid-bd19060571a8f0a8.rlib -L native=/opt/conda/conda-bld/seqsizzle_1734083988989/work/target/release/build/libgit2-sys-0aaa02a472c38bb2/out/build -L native=/opt/conda/conda-bld/seqsizzle_1734083988989/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib -L native=/opt/conda/conda-bld/seqsizzle_1734083988989/work/target/release/build/libz-sys-261f8c5cbae2af1f/out/lib -L native=/opt/conda/conda-bld/seqsizzle_1734083988989/work/target/release/build/libz-sys-261f8c5cbae2af1f/out/lib (exit status: 1) + error: failed to compile seqsizzle v0.1.4 (/opt/conda/conda-bld/seqsizzle_1734083988989/work), intermediate artifacts can be found at /opt/conda/conda-bld/seqsizzle_1734083988989/work/target. + To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/seqsizzle_1734083988989/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/seqsizzle_1734083988989/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. diff --git a/recipes/taxonomy/build_failure.osx-64.yaml b/recipes/seqsizzle/build_failure.osx-64.yaml similarity index 54% rename from recipes/taxonomy/build_failure.osx-64.yaml rename to recipes/seqsizzle/build_failure.osx-64.yaml index aac3ff66f31cb..9721c1028754d 100644 --- a/recipes/taxonomy/build_failure.osx-64.yaml +++ b/recipes/seqsizzle/build_failure.osx-64.yaml @@ -1,51 +1,78 @@ -recipe_sha: 20ab377530e681d3bedb6c918d8d0a50b1566558e70e902f8cc131b1d6dba985 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 3d0893c48748a534153d78e99f06506671881bdd968cf69949f1ea3ca00d2f56 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/taxonomy/pyproject.patch with args: - ['-Np1', '-i', '/tmp/tmpg0jtmin3/pyproject.patch.native', '--binary'] - Patch analysis gives: - [[ RA-MD1LOVE ]] - [[ pyproject.patch ]] +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/seqsizzle_1733977664783/work/conda_build.sh']' returned non-zero exit status 101. - Key: + - rust 1.83.0 h34a2095_0 + - pkg-config 0.29.2 hf7e621a_1009 + - clang-18 18.1.8 default_h0c94c6a_5 + host: + - bzip2 1.0.8 hfdf4475_7 + The above exception was the direct cause of the following exception: - R :: Reversible A :: Applicable + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in sys.exit(execute()) - Y :: Build-prefix patch in use M :: Minimal, non-amalgamated - D :: Dry-runnable N :: Patch level (1 is preferred) - L :: Patch level not-ambiguous O :: Patch applies without offsets - V :: Patch applies without fuzz E :: Patch applies without emitting to stderr - - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/taxonomy_1717528041571/work - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute api.build( - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/taxonomy_1717528041571/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/taxonomy_1717528041571/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/taxonomy_1717528041571/work + - liblzma 5.6.3 hd471939_1 + - libzlib 1.3.1 hd23fc13_2 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + - liblzma-devel 5.6.3 hd471939_1 + - xz-gpl-tools 5.6.3 h357f2ed_1 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + - xz-tools 5.6.3 hd471939_1 + raise BuildScriptException(str(exc), caused_by=exc) from exc + - zlib 1.3.1 hd23fc13_2 + - xz 5.6.3 h357f2ed_1 + run: + - bzip2 >=1.0.8,<2.0a0 + - xz + - zlib + - libzlib >=1.3.1,<2.0a0 + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/seqsizzle_1733977664783/work/conda_build.sh']' returned non-zero exit status 101. + - liblzma >=5.6.3,<6.0a0 + run_constrained: + - __osx >=10.13 + test: + commands: + - seqsizzle -h + about: + home: https://github.com/ChangqingW/SeqSizzle + licence_family: AGPL + license: AGPL-3.0-or-later + license_file: LICENSE.md + summary: A pager for viewing FASTQ files with fuzzy adaptor matching and coloring. + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/seqsizzle_1733977664783/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/seqsizzle_1733977664783/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/seqsizzle_1733977664783/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/seqsizzle_1733977664783/work INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as CC=x86_64-apple-darwin13.4.0-clang CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/taxonomy-0.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/seqsizzle-0.1.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/taxonomy_1717528041571/work/conda_build.sh']' returned non-zero exit status 1. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/taxonomy-0.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/seqsizzle-0.1.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool LD=x86_64-apple-darwin13.4.0-ld @@ -53,7 +80,7 @@ log: |- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -62,7 +89,7 @@ log: |- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -74,31 +101,4 @@ log: |- ac_cv_func_realloc_0_nonnull=yes build_alias=x86_64-apple-darwin13.4.0 host_alias=x86_64-apple-darwin13.4.0 - allexport off - braceexpand on - emacs off - errexit on - errtrace off - functrace off - hashall on - histexpand off - history off - ignoreeof off - interactive-comments on - keyword off - monitor off - noclobber off - noexec off - noglob off - nolog off - notify off - nounset on - onecmd off - physical off - pipefail off - posix off - privileged off - verbose off - vi off - xtrace off # Last 100 lines of the build log. diff --git a/recipes/seqstats/meta.yaml b/recipes/seqstats/meta.yaml index 14dbf7d80383f..2541ebe5d750c 100644 --- a/recipes/seqstats/meta.yaml +++ b/recipes/seqstats/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 18503d359b5dc361f46c9a835522a5dca593a3f9a5dc99140bf5152d8f806de8 build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/seqtk/meta.yaml b/recipes/seqtk/meta.yaml index 6425b4714964d..89d5e0afef0a1 100644 --- a/recipes/seqtk/meta.yaml +++ b/recipes/seqtk/meta.yaml @@ -12,7 +12,7 @@ source: - 0001-makefile.patch build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('seqtk', max_pin="x.x") }} diff --git a/recipes/sequali/meta.yaml b/recipes/sequali/meta.yaml index 24533e6037816..75b8dfdfcf708 100644 --- a/recipes/sequali/meta.yaml +++ b/recipes/sequali/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 14ddcfbe91ab4e941c4e20f0e93e3ad83fba80aca40a3c3c499acd19ac0b9f3c build: - number: 0 + number: 1 entry_points: - sequali=sequali.__main__:main - sequali-report=sequali.__main__:sequali_report diff --git a/recipes/sequencetools/meta.yaml b/recipes/sequencetools/meta.yaml index 11d801d5246c7..36122e46e1aa8 100644 --- a/recipes/sequencetools/meta.yaml +++ b/recipes/sequencetools/meta.yaml @@ -13,7 +13,7 @@ source: md5: 4f41008d654e683b7860fc0912376d4e # [osx and arm64] build: - number: 0 + number: 1 script: - "mkdir -p $PREFIX/bin" - "mv pileupCaller* $PREFIX/bin/pileupCaller" diff --git a/recipes/sequenza-utils/build_failure.osx-64.yaml b/recipes/sequenza-utils/build_failure.osx-64.yaml index c23418fdf5dd0..e6d43df9f739b 100644 --- a/recipes/sequenza-utils/build_failure.osx-64.yaml +++ b/recipes/sequenza-utils/build_failure.osx-64.yaml @@ -1,78 +1,54 @@ -recipe_sha: ad01f59bb54fb38b29ef4aeb09c87479685de7020296fce1894dc1cbded9a745 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 22a901ca8432967438dc958f38db77d69f7fe5b8640b1ed214d8cc97380db6e1 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- - Destination directory: /private/tmp/pip-wheel-68a19nc9 - Building wheel for sequenza-utils (setup.py): finished with status 'done' - Created wheel for sequenza-utils: filename=sequenza_utils-3.0.0-cp312-cp312-macosx_10_9_x86_64.whl size=29834 sha256=d937fc6d0ae086acd628fc477b489f38aa978c18e6ee541083cd2953a39a64e7 - Stored in directory: /private/tmp/pip-ephem-wheel-cache-bw95prpo/wheels/ff/a3/eb/ec11dd857897d354eab45aed2e67ffbc0a64b1f49cda5a0739 - Successfully built sequenza-utils - Installing collected packages: sequenza-utils - - changing mode of $PREFIX/bin/sequenza-utils to 755 - Successfully installed sequenza-utils-3.0.0 - Removed build tracker: '/private/tmp/pip-build-tracker-p25sh0bd' - - Resource usage statistics from building sequenza-utils: - Process count: 5 - CPU time: Sys=0:00:00.9, User=0:00:00.9 - Memory: 92.0M - Disk usage: 704B - Time elapsed: 0:00:06.7 - - - compiling .pyc files... - number of files: 50 - INFO: sysroot: '/System/Library/Frameworks/' files: '['vmnet.framework/Versions/Current', 'vmnet.framework/Versions/A/_CodeSignature/CodeResources', 'vmnet.framework/Versions/A/Resources/version.plist', 'vmnet.framework/Versions/A/Resources/InfoPlist.loctable']' - INFO: sysroot: '/usr/lib/' files: '['zsh/5.9/zsh/zselect.so', 'zsh/5.9/zsh/zpty.so', 'zsh/5.9/zsh/zprof.so', 'zsh/5.9/zsh/zleparameter.so']' - INFO: sysroot: '/opt/X11/' files: '[]' INFO (sequenza-utils,lib/python3.12/site-packages/sequenza/c_pileup.cpython-312-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - WARNING (sequenza-utils): interpreter (Python) package conda-forge/osx-64::python==3.12.3=h1411813_0_cpython in requirements/run but it is not used (i.e. it is overdepending or perhaps statically linked? If that is what you want then add it to build/ignore_run_exports) - WARNING (sequenza-utils): dso library package conda-forge/osx-64::libcxx==17.0.6=h88467a6_0 in requirements/run but it is not used (i.e. it is overdepending or perhaps statically linked? If that is what you want then add it to build/ignore_run_exports) + WARNING (sequenza-utils): dso library package conda-forge/osx-64::libcxx==19.1.5=hf95d169_0 in requirements/run but it is not used (i.e. it is overdepending or perhaps statically linked? If that is what you want then add it to build/ignore_run_exports) + WARNING (sequenza-utils): interpreter (Python) package conda-forge/osx-64::python==3.12.8=h9ccd52b_1_cpython in requirements/run but it is not used (i.e. it is overdepending or perhaps statically linked? If that is what you want then add it to build/ignore_run_exports) Fixing permissions INFO :: Time taken to mark (prefix) - 0 replacements in 0 files was 0.09 seconds + 0 replacements in 0 files was 0.12 seconds Files containing CONDA_PREFIX ----------------------------- bin/sequenza-utils (text): Patching - TEST START: /opt/mambaforge/envs/bioconda/conda-bld/osx-64/sequenza-utils-3.0.0-py312h82554b9_7.tar.bz2 - Renaming work directory '/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1717692686269/work' to '/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1717692686269/work_moved_sequenza-utils-3.0.0-py312h82554b9_7_osx-64' - shutil.move(work)=/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1717692686269/work, dest=/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1717692686269/work_moved_sequenza-utils-3.0.0-py312h82554b9_7_osx-64) + TEST START: /opt/mambaforge/envs/bioconda/conda-bld/osx-64/sequenza-utils-3.0.0-py312h692437a_8.tar.bz2 + Renaming work directory '/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1734380101504/work' to '/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1734380101504/work_moved_sequenza-utils-3.0.0-py312h692437a_8_osx-64' + shutil.move(work)=/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1734380101504/work, dest=/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1734380101504/work_moved_sequenza-utils-3.0.0-py312h692437a_8_osx-64) Reloading output folder (local): ...working... done Solving environment (_test_env): ...working... done ## Package Plan ## - environment location: /opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1717692686269/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + environment location: /opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1734380101504/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac The following NEW packages will be INSTALLED: - bzip2: 1.0.8-h10d778d_5 conda-forge - c-ares: 1.28.1-h10d778d_0 conda-forge - ca-certificates: 2024.6.2-h8857fd0_0 conda-forge - htslib: 1.20-hec81eee_1 bioconda - krb5: 1.21.2-hb884880_0 conda-forge - libcurl: 8.8.0-hf9fcc65_0 conda-forge - libcxx: 17.0.6-h88467a6_0 conda-forge - libdeflate: 1.20-h49d49c5_0 conda-forge + bzip2: 1.0.8-hfdf4475_7 conda-forge + c-ares: 1.34.4-hf13058a_0 conda-forge + ca-certificates: 2024.12.14-h8857fd0_0 conda-forge + htslib: 1.21-h9f635df_1 bioconda + krb5: 1.21.3-h37d8d59_0 conda-forge + libcurl: 8.11.1-h5dec5d8_0 conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libdeflate: 1.22-h00291cd_0 conda-forge libedit: 3.1.20191231-h0678c8f_2 conda-forge libev: 4.33-h10d778d_2 conda-forge - libexpat: 2.6.2-h73e2aa4_0 conda-forge + libexpat: 2.6.4-h240833e_0 conda-forge libffi: 3.4.2-h0d85af4_5 conda-forge - libnghttp2: 1.58.0-h64cf6d3_1 conda-forge - libsqlite: 3.45.3-h92b6c6a_0 conda-forge - libssh2: 1.11.0-hd019ec5_0 conda-forge - libzlib: 1.2.13-h87427d6_6 conda-forge - ncurses: 6.5-h5846eda_0 conda-forge - openssl: 3.3.1-h87427d6_0 conda-forge - python: 3.12.3-h1411813_0_cpython conda-forge - python_abi: 3.12-4_cp312 conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libnghttp2: 1.64.0-hc7306c3_0 conda-forge + libsqlite: 3.47.2-hdb6dae5_0 conda-forge + libssh2: 1.11.1-h3dc7d44_0 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + python: 3.12.8-h9ccd52b_1_cpython conda-forge + python_abi: 3.12-5_cp312 conda-forge readline: 8.2-h9e318b2_1 conda-forge - samtools: 1.20-hd510865_0 bioconda - sequenza-utils: 3.0.0-py312h82554b9_7 local + samtools: 1.21-ha21ef43_1 bioconda + sequenza-utils: 3.0.0-py312h692437a_8 local tk: 8.6.13-h1abcd95_1 conda-forge - tzdata: 2024a-h0c530f3_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge zstd: 1.5.6-h915ae27_0 conda-forge Preparing transaction: ...working... done @@ -80,25 +56,49 @@ log: |2- Executing transaction: ...working... done sequenza-utils --help Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1717692686269/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/sequenza-utils", line 11, in + File "/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1734380101504/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/sequenza-utils", line 11, in sys.exit(main()) ^^^^^^ - File "/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1717692686269/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.12/site-packages/sequenza/commands.py", line 30, in main + File "/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1734380101504/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.12/site-packages/sequenza/commands.py", line 30, in main modules = get_modules(sequenza.programs, subparsers, {}) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1717692686269/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.12/site-packages/sequenza/misc.py", line 73, in get_modules + File "/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1734380101504/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.12/site-packages/sequenza/misc.py", line 73, in get_modules __import__(mod) - File "/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1717692686269/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.12/site-packages/sequenza/programs/bam2seqz.py", line 5, in + File "/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1734380101504/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.12/site-packages/sequenza/programs/bam2seqz.py", line 5, in from sequenza.samtools import bam_mpileup, indexed_pileup, tabix_seqz - File "/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1717692686269/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.12/site-packages/sequenza/samtools.py", line 6, in + File "/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1734380101504/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.12/site-packages/sequenza/samtools.py", line 6, in from distutils.spawn import find_executable ModuleNotFoundError: No module named 'distutils' - WARNING: Tests failed for sequenza-utils-3.0.0-py312h82554b9_7.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1717692686269/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1717692686269/test_tmp + WARNING: Tests failed for sequenza-utils-3.0.0-py312h692437a_8.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1734380101504/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1734380101504/test_tmp import: 'sequenza' import: 'sequenza.programs' import: 'sequenza' - TESTS FAILED: sequenza-utils-3.0.0-py312h82554b9_7.tar.bz2 import: 'sequenza.programs' + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/sequenza-utils_1734380101504/test_tmp/conda_test_runner.sh']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: sequenza-utils-3.0.0-py312h692437a_8.tar.bz2 # Last 100 lines of the build log. diff --git a/recipes/sequenza-utils/meta.yaml b/recipes/sequenza-utils/meta.yaml index 4721d77e69dbd..41c912cd8b876 100644 --- a/recipes/sequenza-utils/meta.yaml +++ b/recipes/sequenza-utils/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 0640f3d73e7c320b5234b86f1b94d6315b3248e1b2715c01fe44fbd23ffb2370 build: - number: 7 + number: 8 entry_points: - sequenza-utils = sequenza.commands:main script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " diff --git a/recipes/seqwish/meta.yaml b/recipes/seqwish/meta.yaml index b494ce3617d03..5afd45d9cfe49 100644 --- a/recipes/seqwish/meta.yaml +++ b/recipes/seqwish/meta.yaml @@ -13,7 +13,7 @@ build: skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} - number: 0 + number: 1 requirements: build: diff --git a/recipes/seqyclean/build_failure.osx-64.yaml b/recipes/seqyclean/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..f1f2002b6c8df --- /dev/null +++ b/recipes/seqyclean/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: ce96908b284734884419029df22679c4aae72a72632754b0927eb2128b5e075d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + - clang_impl_osx-64 18.1.8 h6a44ed1_23 + - zstd 1.5.6 h915ae27_0 + raise BuildScriptException(str(exc), caused_by=exc) from exc + - clang-18 18.1.8 default_h0c94c6a_5 + - clang 18.1.8 default_h179603d_5 + - ncurses 6.5 hf036a51_1 + - libxml2 2.13.5 he8ee3e7_1 + - llvm-tools-18 18.1.8 h9ce406d_2 + - libllvm18 18.1.8 h9ce406d_2 + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + - libcxx 19.1.5 hf95d169_0 + - ca-certificates 2024.8.30 h8857fd0_0 + - cctools_osx-64 1010.6 h00edd4c_2 + host: + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/seqyclean_1733860200865/work/conda_build.sh']' returned non-zero exit status 2. + - libcxx 19.1.5 hf95d169_0 + - libzlib 1.3.1 hd23fc13_2 + - zlib 1.3.1 hd23fc13_2 + run: + - libcxx >=18 + - libzlib >=1.3.1,<2.0a0 + - zlib + test: + commands: + - seqyclean -h 2>&1 | grep seqyclean + about: + home: https://github.com/ibest/seqyclean + license: MIT + license_family: MIT + license_file: LICENSE + summary: Main purpose of this software is to pre-process NGS data in order to prepare + for downstream analysis. + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/seqyclean_1733860200865/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/seqyclean_1733860200865/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/seqyclean_1733860200865/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/seqyclean_1733860200865/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/seqyclean-1.10.09 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/seqyclean-1.10.09 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/seqyclean-1.10.09 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/seqyclean-1.10.09 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + rm -rf obj/ + mkdir obj/ + rm -rf bin/ + mkdir bin/ + #x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/seqyclean-1.10.09 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -I src/ -O -Wall -c -o obj/gzstream.o src/gzstream.C + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/seqyclean-1.10.09 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -I src/ -O3 -Wall -c -o obj/gzstream.o src/gzstream.C + x86_64-apple-darwin13.4.0-ar cr obj/libgzstream.a obj/gzstream.o + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/seqyclean-1.10.09 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wall -g -O3 -c -o obj/abi.o src/abi.c +# Last 100 lines of the build log. diff --git a/recipes/seqyclean/meta.yaml b/recipes/seqyclean/meta.yaml index f469c8266cc7b..219b2c1ff1f70 100644 --- a/recipes/seqyclean/meta.yaml +++ b/recipes/seqyclean/meta.yaml @@ -12,7 +12,7 @@ source: - 0001-Replace-explicit-g++-and-gcc.patch build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/sfld/meta.yaml b/recipes/sfld/meta.yaml index 68d8e7e1a5780..51a37ccda655c 100644 --- a/recipes/sfld/meta.yaml +++ b/recipes/sfld/meta.yaml @@ -13,7 +13,7 @@ source: - patch1 build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/sfold/meta.yaml b/recipes/sfold/meta.yaml index b6509c09158c3..a996e95bb921f 100644 --- a/recipes/sfold/meta.yaml +++ b/recipes/sfold/meta.yaml @@ -7,7 +7,7 @@ source: sha256: c25e4d8cf055e13c523ef59f68c8847b66584e36359ce4fb9dc675a97f1a2939 build: - number: 3 + number: 4 skip: True # [osx] run_exports: - {{ pin_subpackage('sfold', max_pin='x') }} diff --git a/recipes/sfs_code/meta.yaml b/recipes/sfs_code/meta.yaml index 49df3de6e1600..f4a5aa2c1c83d 100644 --- a/recipes/sfs_code/meta.yaml +++ b/recipes/sfs_code/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 6 + number: 7 skip: True # [osx] source: diff --git a/recipes/sga/build_failure.osx-64.yaml b/recipes/sga/build_failure.osx-64.yaml index c274b38b8755b..4083bc0c88754 100644 --- a/recipes/sga/build_failure.osx-64.yaml +++ b/recipes/sga/build_failure.osx-64.yaml @@ -1,104 +1,104 @@ -recipe_sha: 5eea4bb110cc9e71d687892aaf69b4c4905565f4be1072f268a508f0853d54f2 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: b023426c6e4e1c81e809161bfb600c567785991efb3279d599104ac5ef123738 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- - /opt/mambaforge/envs/bioconda/conda-bld/sga_1717957120831/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/bamtools/api/algorithms/Sort.h:64:18: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'? - typedef std::binary_function AlignmentSortBase; - ~~~~~^~~~~~~~~~~~~~~ - __binary_function - /opt/mambaforge/envs/bioconda/conda-bld/sga_1717957120831/_build_env/bin/../include/c/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here - using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>; - ^ - 1 error generated. - make[2]: *** [Makefile:924: sga-rewrite-evidence-bam.o] Error 1 - make[1]: *** [Makefile:358: all-recursive] Error 1 - make: *** [Makefile:299: all] Error 2 + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.o -MD -MP -MF .deps/libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.Tpo -c -o libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.o test -f 'PairedDeBruijnHaplotypeBuilder.cpp' || echo './'PairedDeBruijnHaplotypeBuilder.cpp + mv -f .deps/libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.Tpo .deps/libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.Po + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT libgraphdiff_a-HapgenUtil.o -MD -MP -MF .deps/libgraphdiff_a-HapgenUtil.Tpo -c -o libgraphdiff_a-HapgenUtil.o test -f 'HapgenUtil.cpp' || echo './'HapgenUtil.cpp + mv -f .deps/libgraphdiff_a-HapgenUtil.Tpo .deps/libgraphdiff_a-HapgenUtil.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT libgraphdiff_a-VCFTester.o -MD -MP -MF .deps/libgraphdiff_a-VCFTester.Tpo -c -o libgraphdiff_a-VCFTester.o test -f 'VCFTester.cpp' || echo './'VCFTester.cpp + mv -f .deps/libgraphdiff_a-VCFTester.Tpo .deps/libgraphdiff_a-VCFTester.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT libgraphdiff_a-GraphCompare.o -MD -MP -MF .deps/libgraphdiff_a-GraphCompare.Tpo -c -o libgraphdiff_a-GraphCompare.o test -f 'GraphCompare.cpp' || echo './'GraphCompare.cpp + mv -f .deps/libgraphdiff_a-GraphCompare.Tpo .deps/libgraphdiff_a-GraphCompare.Po + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/sga_1734536439375/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + Traceback (most recent call last): + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT libgraphdiff_a-OverlapExtractorWithCorrection.o -MD -MP -MF .deps/libgraphdiff_a-OverlapExtractorWithCorrection.Tpo -c -o libgraphdiff_a-OverlapExtractorWithCorrection.o test -f 'OverlapExtractorWithCorrection.cpp' || echo './'OverlapExtractorWithCorrection.cpp + mv -f .deps/libgraphdiff_a-OverlapExtractorWithCorrection.Tpo .deps/libgraphdiff_a-OverlapExtractorWithCorrection.Po File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build return build_tree( - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT libgraphdiff_a-GraphCompare.o -MD -MP -MF .deps/libgraphdiff_a-GraphCompare.Tpo -c -o libgraphdiff_a-GraphCompare.o test -f 'GraphCompare.cpp' || echo './'GraphCompare.cpp - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - mv -f .deps/libgraphdiff_a-GraphCompare.Tpo .deps/libgraphdiff_a-GraphCompare.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT libgraphdiff_a-OverlapExtractorWithCorrection.o -MD -MP -MF .deps/libgraphdiff_a-OverlapExtractorWithCorrection.Tpo -c -o libgraphdiff_a-OverlapExtractorWithCorrection.o test -f 'OverlapExtractorWithCorrection.cpp' || echo './'OverlapExtractorWithCorrection.cpp - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - mv -f .deps/libgraphdiff_a-OverlapExtractorWithCorrection.Tpo .deps/libgraphdiff_a-OverlapExtractorWithCorrection.Po - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT libgraphdiff_a-DBGPathGuide.o -MD -MP -MF .deps/libgraphdiff_a-DBGPathGuide.Tpo -c -o libgraphdiff_a-DBGPathGuide.o test -f 'DBGPathGuide.cpp' || echo './'DBGPathGuide.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Util -I../StringGraph -I../SQG -I../SuffixTools -I../Thirdparty -I../Algorithm -I../Concurrency -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT libgraphdiff_a-DBGPathGuide.o -MD -MP -MF .deps/libgraphdiff_a-DBGPathGuide.Tpo -c -o libgraphdiff_a-DBGPathGuide.o test -f 'DBGPathGuide.cpp' || echo './'DBGPathGuide.cpp mv -f .deps/libgraphdiff_a-DBGPathGuide.Tpo .deps/libgraphdiff_a-DBGPathGuide.Po rm -f libgraphdiff.a - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/sga_1717957120831/work/conda_build.sh']' returned non-zero exit status 2. - ar cru libgraphdiff.a libgraphdiff_a-DindelUtil.o libgraphdiff_a-DindelRealignWindow.o libgraphdiff_a-DindelHMM.o libgraphdiff_a-OverlapHaplotypeBuilder.o libgraphdiff_a-StringHaplotypeBuilder.o libgraphdiff_a-DeBruijnHaplotypeBuilder.o libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.o libgraphdiff_a-HapgenUtil.o libgraphdiff_a-VCFTester.o libgraphdiff_a-GraphCompare.o libgraphdiff_a-OverlapExtractorWithCorrection.o libgraphdiff_a-DBGPathGuide.o + ar cr libgraphdiff.a libgraphdiff_a-DindelUtil.o libgraphdiff_a-DindelRealignWindow.o libgraphdiff_a-DindelHMM.o libgraphdiff_a-OverlapHaplotypeBuilder.o libgraphdiff_a-StringHaplotypeBuilder.o libgraphdiff_a-DeBruijnHaplotypeBuilder.o libgraphdiff_a-PairedDeBruijnHaplotypeBuilder.o libgraphdiff_a-HapgenUtil.o libgraphdiff_a-VCFTester.o libgraphdiff_a-GraphCompare.o libgraphdiff_a-OverlapExtractorWithCorrection.o libgraphdiff_a-DBGPathGuide.o x86_64-apple-darwin13.4.0-ranlib libgraphdiff.a make[2]: Leaving directory '$SRC_DIR/src/GraphDiff' Making all in SGA make[2]: Entering directory '$SRC_DIR/src/SGA' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-sga.o -MD -MP -MF .deps/sga-sga.Tpo -c -o sga-sga.o test -f 'sga.cpp' || echo './'sga.cpp + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-sga.o -MD -MP -MF .deps/sga-sga.Tpo -c -o sga-sga.o test -f 'sga.cpp' || echo './'sga.cpp mv -f .deps/sga-sga.Tpo .deps/sga-sga.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-index.o -MD -MP -MF .deps/sga-index.Tpo -c -o sga-index.o test -f 'index.cpp' || echo './'index.cpp + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/sga_1734536439375/work/conda_build.sh']' returned non-zero exit status 2. + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-index.o -MD -MP -MF .deps/sga-index.Tpo -c -o sga-index.o test -f 'index.cpp' || echo './'index.cpp mv -f .deps/sga-index.Tpo .deps/sga-index.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-overlap.o -MD -MP -MF .deps/sga-overlap.Tpo -c -o sga-overlap.o test -f 'overlap.cpp' || echo './'overlap.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-overlap.o -MD -MP -MF .deps/sga-overlap.Tpo -c -o sga-overlap.o test -f 'overlap.cpp' || echo './'overlap.cpp mv -f .deps/sga-overlap.Tpo .deps/sga-overlap.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-assemble.o -MD -MP -MF .deps/sga-assemble.Tpo -c -o sga-assemble.o test -f 'assemble.cpp' || echo './'assemble.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-assemble.o -MD -MP -MF .deps/sga-assemble.Tpo -c -o sga-assemble.o test -f 'assemble.cpp' || echo './'assemble.cpp mv -f .deps/sga-assemble.Tpo .deps/sga-assemble.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-correct.o -MD -MP -MF .deps/sga-correct.Tpo -c -o sga-correct.o test -f 'correct.cpp' || echo './'correct.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-correct.o -MD -MP -MF .deps/sga-correct.Tpo -c -o sga-correct.o test -f 'correct.cpp' || echo './'correct.cpp mv -f .deps/sga-correct.Tpo .deps/sga-correct.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-oview.o -MD -MP -MF .deps/sga-oview.Tpo -c -o sga-oview.o test -f 'oview.cpp' || echo './'oview.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-oview.o -MD -MP -MF .deps/sga-oview.Tpo -c -o sga-oview.o test -f 'oview.cpp' || echo './'oview.cpp mv -f .deps/sga-oview.Tpo .deps/sga-oview.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-preprocess.o -MD -MP -MF .deps/sga-preprocess.Tpo -c -o sga-preprocess.o test -f 'preprocess.cpp' || echo './'preprocess.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-preprocess.o -MD -MP -MF .deps/sga-preprocess.Tpo -c -o sga-preprocess.o test -f 'preprocess.cpp' || echo './'preprocess.cpp mv -f .deps/sga-preprocess.Tpo .deps/sga-preprocess.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-rmdup.o -MD -MP -MF .deps/sga-rmdup.Tpo -c -o sga-rmdup.o test -f 'rmdup.cpp' || echo './'rmdup.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-rmdup.o -MD -MP -MF .deps/sga-rmdup.Tpo -c -o sga-rmdup.o test -f 'rmdup.cpp' || echo './'rmdup.cpp mv -f .deps/sga-rmdup.Tpo .deps/sga-rmdup.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-merge.o -MD -MP -MF .deps/sga-merge.Tpo -c -o sga-merge.o test -f 'merge.cpp' || echo './'merge.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-merge.o -MD -MP -MF .deps/sga-merge.Tpo -c -o sga-merge.o test -f 'merge.cpp' || echo './'merge.cpp mv -f .deps/sga-merge.Tpo .deps/sga-merge.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-subgraph.o -MD -MP -MF .deps/sga-subgraph.Tpo -c -o sga-subgraph.o test -f 'subgraph.cpp' || echo './'subgraph.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-subgraph.o -MD -MP -MF .deps/sga-subgraph.Tpo -c -o sga-subgraph.o test -f 'subgraph.cpp' || echo './'subgraph.cpp mv -f .deps/sga-subgraph.Tpo .deps/sga-subgraph.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-scaffold.o -MD -MP -MF .deps/sga-scaffold.Tpo -c -o sga-scaffold.o test -f 'scaffold.cpp' || echo './'scaffold.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-scaffold.o -MD -MP -MF .deps/sga-scaffold.Tpo -c -o sga-scaffold.o test -f 'scaffold.cpp' || echo './'scaffold.cpp mv -f .deps/sga-scaffold.Tpo .deps/sga-scaffold.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-scaffold2fasta.o -MD -MP -MF .deps/sga-scaffold2fasta.Tpo -c -o sga-scaffold2fasta.o test -f 'scaffold2fasta.cpp' || echo './'scaffold2fasta.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-scaffold2fasta.o -MD -MP -MF .deps/sga-scaffold2fasta.Tpo -c -o sga-scaffold2fasta.o test -f 'scaffold2fasta.cpp' || echo './'scaffold2fasta.cpp mv -f .deps/sga-scaffold2fasta.Tpo .deps/sga-scaffold2fasta.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-connect.o -MD -MP -MF .deps/sga-connect.Tpo -c -o sga-connect.o test -f 'connect.cpp' || echo './'connect.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-connect.o -MD -MP -MF .deps/sga-connect.Tpo -c -o sga-connect.o test -f 'connect.cpp' || echo './'connect.cpp mv -f .deps/sga-connect.Tpo .deps/sga-connect.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-walk.o -MD -MP -MF .deps/sga-walk.Tpo -c -o sga-walk.o test -f 'walk.cpp' || echo './'walk.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-walk.o -MD -MP -MF .deps/sga-walk.Tpo -c -o sga-walk.o test -f 'walk.cpp' || echo './'walk.cpp mv -f .deps/sga-walk.Tpo .deps/sga-walk.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-filter.o -MD -MP -MF .deps/sga-filter.Tpo -c -o sga-filter.o test -f 'filter.cpp' || echo './'filter.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-filter.o -MD -MP -MF .deps/sga-filter.Tpo -c -o sga-filter.o test -f 'filter.cpp' || echo './'filter.cpp mv -f .deps/sga-filter.Tpo .deps/sga-filter.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-kmer-count.o -MD -MP -MF .deps/sga-kmer-count.Tpo -c -o sga-kmer-count.o test -f 'kmer-count.cpp' || echo './'kmer-count.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-kmer-count.o -MD -MP -MF .deps/sga-kmer-count.Tpo -c -o sga-kmer-count.o test -f 'kmer-count.cpp' || echo './'kmer-count.cpp mv -f .deps/sga-kmer-count.Tpo .deps/sga-kmer-count.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-stats.o -MD -MP -MF .deps/sga-stats.Tpo -c -o sga-stats.o test -f 'stats.cpp' || echo './'stats.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-stats.o -MD -MP -MF .deps/sga-stats.Tpo -c -o sga-stats.o test -f 'stats.cpp' || echo './'stats.cpp mv -f .deps/sga-stats.Tpo .deps/sga-stats.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-fm-merge.o -MD -MP -MF .deps/sga-fm-merge.Tpo -c -o sga-fm-merge.o test -f 'fm-merge.cpp' || echo './'fm-merge.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-fm-merge.o -MD -MP -MF .deps/sga-fm-merge.Tpo -c -o sga-fm-merge.o test -f 'fm-merge.cpp' || echo './'fm-merge.cpp mv -f .deps/sga-fm-merge.Tpo .deps/sga-fm-merge.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-gmap.o -MD -MP -MF .deps/sga-gmap.Tpo -c -o sga-gmap.o test -f 'gmap.cpp' || echo './'gmap.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-gmap.o -MD -MP -MF .deps/sga-gmap.Tpo -c -o sga-gmap.o test -f 'gmap.cpp' || echo './'gmap.cpp mv -f .deps/sga-gmap.Tpo .deps/sga-gmap.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-filterBAM.o -MD -MP -MF .deps/sga-filterBAM.Tpo -c -o sga-filterBAM.o test -f 'filterBAM.cpp' || echo './'filterBAM.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-filterBAM.o -MD -MP -MF .deps/sga-filterBAM.Tpo -c -o sga-filterBAM.o test -f 'filterBAM.cpp' || echo './'filterBAM.cpp mv -f .deps/sga-filterBAM.Tpo .deps/sga-filterBAM.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-cluster.o -MD -MP -MF .deps/sga-cluster.Tpo -c -o sga-cluster.o test -f 'cluster.cpp' || echo './'cluster.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-cluster.o -MD -MP -MF .deps/sga-cluster.Tpo -c -o sga-cluster.o test -f 'cluster.cpp' || echo './'cluster.cpp mv -f .deps/sga-cluster.Tpo .deps/sga-cluster.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-gen-ssa.o -MD -MP -MF .deps/sga-gen-ssa.Tpo -c -o sga-gen-ssa.o test -f 'gen-ssa.cpp' || echo './'gen-ssa.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-gen-ssa.o -MD -MP -MF .deps/sga-gen-ssa.Tpo -c -o sga-gen-ssa.o test -f 'gen-ssa.cpp' || echo './'gen-ssa.cpp mv -f .deps/sga-gen-ssa.Tpo .deps/sga-gen-ssa.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-bwt2fa.o -MD -MP -MF .deps/sga-bwt2fa.Tpo -c -o sga-bwt2fa.o test -f 'bwt2fa.cpp' || echo './'bwt2fa.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-bwt2fa.o -MD -MP -MF .deps/sga-bwt2fa.Tpo -c -o sga-bwt2fa.o test -f 'bwt2fa.cpp' || echo './'bwt2fa.cpp mv -f .deps/sga-bwt2fa.Tpo .deps/sga-bwt2fa.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-graph-diff.o -MD -MP -MF .deps/sga-graph-diff.Tpo -c -o sga-graph-diff.o test -f 'graph-diff.cpp' || echo './'graph-diff.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-graph-diff.o -MD -MP -MF .deps/sga-graph-diff.Tpo -c -o sga-graph-diff.o test -f 'graph-diff.cpp' || echo './'graph-diff.cpp mv -f .deps/sga-graph-diff.Tpo .deps/sga-graph-diff.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-graph-concordance.o -MD -MP -MF .deps/sga-graph-concordance.Tpo -c -o sga-graph-concordance.o test -f 'graph-concordance.cpp' || echo './'graph-concordance.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-graph-concordance.o -MD -MP -MF .deps/sga-graph-concordance.Tpo -c -o sga-graph-concordance.o test -f 'graph-concordance.cpp' || echo './'graph-concordance.cpp mv -f .deps/sga-graph-concordance.Tpo .deps/sga-graph-concordance.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-gapfill.o -MD -MP -MF .deps/sga-gapfill.Tpo -c -o sga-gapfill.o test -f 'gapfill.cpp' || echo './'gapfill.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-gapfill.o -MD -MP -MF .deps/sga-gapfill.Tpo -c -o sga-gapfill.o test -f 'gapfill.cpp' || echo './'gapfill.cpp mv -f .deps/sga-gapfill.Tpo .deps/sga-gapfill.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-preqc.o -MD -MP -MF .deps/sga-preqc.Tpo -c -o sga-preqc.o test -f 'preqc.cpp' || echo './'preqc.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-preqc.o -MD -MP -MF .deps/sga-preqc.Tpo -c -o sga-preqc.o test -f 'preqc.cpp' || echo './'preqc.cpp mv -f .deps/sga-preqc.Tpo .deps/sga-preqc.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-overlap-long.o -MD -MP -MF .deps/sga-overlap-long.Tpo -c -o sga-overlap-long.o test -f 'overlap-long.cpp' || echo './'overlap-long.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-overlap-long.o -MD -MP -MF .deps/sga-overlap-long.Tpo -c -o sga-overlap-long.o test -f 'overlap-long.cpp' || echo './'overlap-long.cpp mv -f .deps/sga-overlap-long.Tpo .deps/sga-overlap-long.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-variant-detectability.o -MD -MP -MF .deps/sga-variant-detectability.Tpo -c -o sga-variant-detectability.o test -f 'variant-detectability.cpp' || echo './'variant-detectability.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-variant-detectability.o -MD -MP -MF .deps/sga-variant-detectability.Tpo -c -o sga-variant-detectability.o test -f 'variant-detectability.cpp' || echo './'variant-detectability.cpp mv -f .deps/sga-variant-detectability.Tpo .deps/sga-variant-detectability.Po - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-rewrite-evidence-bam.o -MD -MP -MF .deps/sga-rewrite-evidence-bam.Tpo -c -o sga-rewrite-evidence-bam.o test -f 'rewrite-evidence-bam.cpp' || echo './'rewrite-evidence-bam.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -I../Util -I../Bigraph -I../SuffixTools -I../StringGraph -I../Concurrency -I../Algorithm -I../SQG -I../Scaffold -I../GraphDiff -I../Thirdparty -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -I$PREFIX/include -I$PREFIX/include -I$PREFIX/include/bamtools -Wall -Wextra -Wno-unknown-pragmas -I$PREFIX/include -O3 -MT sga-rewrite-evidence-bam.o -MD -MP -MF .deps/sga-rewrite-evidence-bam.Tpo -c -o sga-rewrite-evidence-bam.o test -f 'rewrite-evidence-bam.cpp' || echo './'rewrite-evidence-bam.cpp make[2]: Leaving directory '$SRC_DIR/src/SGA' make[1]: Leaving directory '$SRC_DIR/src' # Last 100 lines of the build log. diff --git a/recipes/sga/meta.yaml b/recipes/sga/meta.yaml index df98ff6102abb..07918eb541a16 100644 --- a/recipes/sga/meta.yaml +++ b/recipes/sga/meta.yaml @@ -14,7 +14,7 @@ source: - configure.patch build: - number: 9 + number: 10 requirements: build: diff --git a/recipes/sgdemux/meta.yaml b/recipes/sgdemux/meta.yaml index 7f412931f8a6c..96016655aa453 100644 --- a/recipes/sgdemux/meta.yaml +++ b/recipes/sgdemux/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 run_exports: '{{ pin_subpackage(name, max_pin="x.x") }}' source: diff --git a/recipes/shapeit4/meta.yaml b/recipes/shapeit4/meta.yaml index 32fb68ad82fb9..e65e0e4775b11 100644 --- a/recipes/shapeit4/meta.yaml +++ b/recipes/shapeit4/meta.yaml @@ -10,7 +10,7 @@ source: build: skip: True # [osx] - number: 4 + number: 5 requirements: build: diff --git a/recipes/sharg/meta.yaml b/recipes/sharg/meta.yaml index edd18ee12069b..cc36e0d8b2dd3 100644 --- a/recipes/sharg/meta.yaml +++ b/recipes/sharg/meta.yaml @@ -13,7 +13,7 @@ source: # osx can be enabled once clangxx_osx-64 17* is available on main channels build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/shark/meta.yaml b/recipes/shark/meta.yaml index bd4515f5c36ed..9ec12731c8133 100644 --- a/recipes/shark/meta.yaml +++ b/recipes/shark/meta.yaml @@ -12,7 +12,7 @@ source: - shark.Makefile.patch build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/shasta/meta.yaml b/recipes/shasta/meta.yaml index 1cfc6b35d6b1e..396c956409280 100644 --- a/recipes/shasta/meta.yaml +++ b/recipes/shasta/meta.yaml @@ -13,7 +13,7 @@ source: sha256: {{ sha256 }} # [linux] build: - number: 0 + number: 1 # As announced with the release of Shasta 0.10.0, macOS versions of Shasta are no longer provided. skip: True # [osx] run_exports: diff --git a/recipes/sherpas/meta.yaml b/recipes/sherpas/meta.yaml index a309c2bb9dff1..028436cedee89 100644 --- a/recipes/sherpas/meta.yaml +++ b/recipes/sherpas/meta.yaml @@ -13,7 +13,7 @@ source: - patch build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/short-read-connector/meta.yaml b/recipes/short-read-connector/meta.yaml index cd9c0537505c8..f3fc07b4ede40 100644 --- a/recipes/short-read-connector/meta.yaml +++ b/recipes/short-read-connector/meta.yaml @@ -7,7 +7,7 @@ source: md5: "2b7a3c9bdb5a3d3e2d3c9fdd9b496323" build: - number: 1 + number: 2 skip: True # [osx] run_exports: - {{ pin_subpackage('short-read-connector', max_pin="x") }} diff --git a/recipes/shustring/meta.yaml b/recipes/shustring/meta.yaml index caac4835a0791..58dd6cdbad5d0 100644 --- a/recipes/shustring/meta.yaml +++ b/recipes/shustring/meta.yaml @@ -15,7 +15,7 @@ source: md5: d57ed4d24f2f3e032a059994f6e9ec8d build: - number: 7 + number: 8 requirements: build: diff --git a/recipes/sibeliaz/meta.yaml b/recipes/sibeliaz/meta.yaml index d812b3a703a60..17da6a68ce2a5 100644 --- a/recipes/sibeliaz/meta.yaml +++ b/recipes/sibeliaz/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 skip: True # [osx] requirements: diff --git a/recipes/sickle-trim/meta.yaml b/recipes/sickle-trim/meta.yaml index 4543169dc404e..a5a7f10c1ec04 100644 --- a/recipes/sickle-trim/meta.yaml +++ b/recipes/sickle-trim/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 10 + number: 11 run_exports: - {{ pin_subpackage('sickle-trim', max_pin="x") }} diff --git a/recipes/sift4g/build_failure.linux-64.yaml b/recipes/sift4g/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..0c681a7dbc594 --- /dev/null +++ b/recipes/sift4g/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: eba7d5807f01f602a0f67558b2268b2c66d44ff3dd39495ff1dd35ba3131f6e4 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [CP] ../swsharpwin/swsharpout/main.c + [LD] swsharpout + [CP] ../bin/swsharpout + >>> sift4g <<< + [CP] src/utils.cpp + [CP] src/select_alignments.cpp + [CP] src/sift_prediction.cpp + In file included from src/select_alignments.cpp:14: + src/utils.hpp:26:6: error: variable or field 'queryLog' declared void + 26 | void queryLog(uint32_t part, uint32_t total); + | ^~~~~~~~ + src/utils.hpp:26:15: error: 'uint32_t' was not declared in this scope + 26 | void queryLog(uint32_t part, uint32_t total); + | ^~~~~~~~ + src/utils.hpp:1:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + |#include + 1 | /*! + src/utils.hpp:26:30: error: 'uint32_t' was not declared in this scope + 26 | void queryLog(uint32_t part, uint32_t total); + | ^~~~~~~~ + src/utils.hpp:26:30: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + src/utils.hpp:28:6: error: variable or field 'databaseLog' declared void + 28 | void databaseLog(uint32_t part, float part_size, float percentage); + | ^~~~~~~~~~~ + src/utils.hpp:28:18: error: 'uint32_t' was not declared in this scope + 28 | void databaseLog(uint32_t part, float part_size, float percentage); + | ^~~~~~~~ + src/utils.hpp:28:18: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + src/utils.hpp:28:33: error: expected primary-expression before 'float' + 28 | void databaseLog(uint32_t part, float part_size, float percentage); + | ^~~~~ + src/utils.hpp:28:50: error: expected primary-expression before 'float' + 28 | void databaseLog(uint32_t part, float part_size, float percentage); + | ^~~~~ + src/select_alignments.cpp: In function 'void selectAlignments(std::vector >&, DbAlignment***, int32_t*, Chain**, int32_t, float)': + src/select_alignments.cpp:66:9: error: 'queryLog' was not declared in this scope + 66 | queryLog(i 1, queries_length); + | ^~~~~~~~ + make[1]: *** [Makefile:41: obj/select_alignments.o] Error 1 + make[1]: *** Waiting for unfinished jobs.... + In file included from src/sift_prediction.cpp:15: + src/utils.hpp:26:6: error: variable or field 'queryLog' declared void + 26 | void queryLog(uint32_t part, uint32_t total); + | ^~~~~~~~ + src/utils.hpp:26:15: error: 'uint32_t' was not declared in this scope + 26 | void queryLog(uint32_t part, uint32_t total); + | ^~~~~~~~ + src/utils.hpp:1:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + |#include + 1 | /*! + src/utils.hpp:26:30: error: 'uint32_t' was not declared in this scope + 26 | void queryLog(uint32_t part, uint32_t total); + | ^~~~~~~~ + src/utils.hpp:26:30: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + src/utils.hpp:28:6: error: variable or field 'databaseLog' declared void + 28 | void databaseLog(uint32_t part, float part_size, float percentage); + | ^~~~~~~~~~~ + src/utils.hpp:28:18: error: 'uint32_t' was not declared in this scope + 28 | void databaseLog(uint32_t part, float part_size, float percentage); + | ^~~~~~~~ + src/utils.hpp:28:18: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + src/utils.hpp:28:33: error: expected primary-expression before 'float' + 28 | void databaseLog(uint32_t part, float part_size, float percentage); + | ^~~~~ + src/utils.hpp:28:50: error: expected primary-expression before 'float' + 28 | void databaseLog(uint32_t part, float part_size, float percentage); + | ^~~~~ + src/sift_prediction.cpp: In function 'void checkData(Chain**, int32_t&, const std::string&)': + src/sift_prediction.cpp:114:9: error: 'queryLog' was not declared in this scope + 114 | queryLog(i 1, queries_length); + | ^~~~~~~~ + src/sift_prediction.cpp: In function 'void siftPredictions(std::vector >&, Chain**, int32_t, const std::string&, int32_t, const std::string&)': + src/sift_prediction.cpp:163:9: error: 'queryLog' was not declared in this scope + 163 | queryLog(i 1, queries_length); + | ^~~~~~~~ + make[1]: *** [Makefile:41: obj/sift_prediction.o] Error 1 + make: *** [Makefile:21: sift4g] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/sift4g_1734124458506/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/sift4g_1734124458506/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/sift4g/meta.yaml b/recipes/sift4g/meta.yaml index 6ac37f0fd8508..26ca4053d51d9 100644 --- a/recipes/sift4g/meta.yaml +++ b/recipes/sift4g/meta.yaml @@ -11,7 +11,7 @@ source: - 0001-Remove-superfluous-use-of-non-imported-function.patch build: - number: 6 + number: 7 skip: True # [osx] requirements: diff --git a/recipes/simba_pbg/meta.yaml b/recipes/simba_pbg/meta.yaml index 7bcb5313f8ca2..7e1e2a72f6ad4 100644 --- a/recipes/simba_pbg/meta.yaml +++ b/recipes/simba_pbg/meta.yaml @@ -10,7 +10,7 @@ source: sha256: df97d748956f3136ace4cd899bb4362b531e568e0ccbe90e5aad3e50666fb316 build: - number: 3 + number: 4 skip: True # [py2k] script: "{{ PYTHON }} -m pip install . --ignore-installed -vv" diff --git a/recipes/simbac/meta.yaml b/recipes/simbac/meta.yaml index a803549a67e53..2ce259f789746 100644 --- a/recipes/simbac/meta.yaml +++ b/recipes/simbac/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 82d42a4aef46c22c3d6472c1f3bf4915f6461bc7ec6eabca2bf1a3e9e3c2a914 build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/simka/build_failure.osx-64.yaml b/recipes/simka/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..0d61b33bfdf2e --- /dev/null +++ b/recipes/simka/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 9925d0a10636e2fe20640885123ce78039f9af65632e0d692dac0ab0be228660 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [ 25%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FDtest.c.o + [ 25%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FDwindows.c.o + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/simka_1733975769628/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + [ 26%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FL.c.o + [ 26%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FO.c.o + [ 26%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FS.c.o + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + [ 26%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FScache.c.o + api.build( + [ 26%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FSdbg.c.o + [ 26%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FSint.c.o + [ 27%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FSsection.c.o + [ 27%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FSstat.c.o + [ 27%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5FStest.c.o + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + [ 27%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5G.c.o + [ 28%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gbtree2.c.o + [ 28%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gcache.c.o + [ 28%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gcompact.c.o + [ 28%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gdense.c.o + [ 28%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gdeprec.c.o + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + [ 29%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gent.c.o + [ 29%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gint.c.o + [ 29%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Glink.c.o + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + [ 29%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gloc.c.o + [ 29%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gname.c.o + [ 30%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gnode.c.o + [ 30%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gobj.c.o + [ 30%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Goh.c.o + [ 30%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Groot.c.o + [ 30%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gstab.c.o + [ 31%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gtest.c.o + [ 31%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Gtraverse.c.o + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/simka_1733975769628/work/conda_build.sh']' returned non-zero exit status 2. + [ 31%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HF.c.o + [ 31%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFbtree2.c.o + [ 32%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFcache.c.o + [ 32%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFdbg.c.o + [ 32%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFdblock.c.o + [ 32%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFdtable.c.o + [ 32%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFhdr.c.o + [ 33%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFhuge.c.o + [ 33%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFiblock.c.o + [ 33%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFiter.c.o + [ 33%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFman.c.o + [ 33%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFsection.c.o + [ 34%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFspace.c.o + [ 34%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFstat.c.o + [ 34%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFtest.c.o + [ 34%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HFtiny.c.o + [ 35%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HG.c.o + [ 35%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HGcache.c.o + [ 35%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HGdbg.c.o + [ 35%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HGquery.c.o + [ 35%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HL.c.o + [ 36%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HLcache.c.o + [ 36%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HLdbg.c.o + [ 36%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HLdblk.c.o + [ 36%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HLint.c.o + [ 36%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HLprfx.c.o + [ 37%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5HP.c.o + [ 37%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5I.c.o + [ 37%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Itest.c.o + [ 37%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5L.c.o + [ 37%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Lexternal.c.o + [ 38%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MF.c.o + [ 38%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MFaggr.c.o + [ 38%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MFdbg.c.o + [ 38%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MFsection.c.o + [ 39%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MM.c.o + [ 39%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MP.c.o + [ 39%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5MPtest.c.o + [ 39%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5O.c.o + [ 39%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Oainfo.c.o + [ 40%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Oalloc.c.o + [ 40%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Oattr.c.o + [ 40%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Oattribute.c.o + [ 40%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Obogus.c.o + [ 40%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Obtreek.c.o + [ 41%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Ocache.c.o + [ 41%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Ocache_image.c.o + [ 41%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Ochunk.c.o + [ 41%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Ocont.c.o + [ 42%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Ocopy.c.o + [ 42%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Odbg.c.o + [ 42%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Odeprec.c.o + [ 42%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/hdf5-static.dir/H5Odrvinfo.c.o +# Last 100 lines of the build log. diff --git a/recipes/simka/meta.yaml b/recipes/simka/meta.yaml index 9e7cebba3f55d..0482530dacd89 100644 --- a/recipes/simka/meta.yaml +++ b/recipes/simka/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://github.com/GATB/simka/releases/download/v{{ version }}/simka-v{{ version }}-Source.tar.gz diff --git a/recipes/simpleaf/meta.yaml b/recipes/simpleaf/meta.yaml index be2283fe7e300..27455ba49377d 100644 --- a/recipes/simpleaf/meta.yaml +++ b/recipes/simpleaf/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("simpleaf", max_pin="x.x") }} diff --git a/recipes/simwalk2/meta.yaml b/recipes/simwalk2/meta.yaml index 1e4999aa5e22f..9661f43ba9c76 100644 --- a/recipes/simwalk2/meta.yaml +++ b/recipes/simwalk2/meta.yaml @@ -7,7 +7,7 @@ source: md5: 2a529d50ca48cd7ea2b67f85c290f203 build: - number: 6 + number: 7 skip: True # [osx] requirements: diff --git a/recipes/ska/meta.yaml b/recipes/ska/meta.yaml index 3a0b57f904f55..0514eebd28e81 100644 --- a/recipes/ska/meta.yaml +++ b/recipes/ska/meta.yaml @@ -10,7 +10,7 @@ source: sha256: fc6110c22c756158b190f50dc11d596265f9b0d09c28725b2b23ed22e2e4fbff build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/skani/meta.yaml b/recipes/skani/meta.yaml index 7894b69a11fe9..3de874bb903cf 100644 --- a/recipes/skani/meta.yaml +++ b/recipes/skani/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('skani', max_pin="x") }} diff --git a/recipes/skc/meta.yaml b/recipes/skc/meta.yaml index 34248e6a791a8..4c112b36058c9 100644 --- a/recipes/skc/meta.yaml +++ b/recipes/skc/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 559362cdc16b4bd7e9cb3d6d3b619e95551b3e29cffd01929cce365a6f4f3f35 build: - number: 0 + number: 1 requirements: build: @@ -29,4 +29,4 @@ about: extra: recipe-maintainers: - - mbhall88 \ No newline at end of file + - mbhall88 diff --git a/recipes/skder/meta.yaml b/recipes/skder/meta.yaml index 678fd77189bf3..ff3bb25e83dbf 100644 --- a/recipes/skder/meta.yaml +++ b/recipes/skder/meta.yaml @@ -10,7 +10,7 @@ source: sha256: d60056e0ebd71f62af562a490b7a4a9761fac207e03a20fe926db571d16d5237 build: - number: 0 + number: 1 skip: True # [py <= 39] run_exports: - {{ pin_subpackage('skder', max_pin='x') }} diff --git a/recipes/skesa/meta.yaml b/recipes/skesa/meta.yaml index b0650797d27fe..d84661ef9d799 100644 --- a/recipes/skesa/meta.yaml +++ b/recipes/skesa/meta.yaml @@ -15,7 +15,7 @@ source: - skesa-aarch64.patch # [linux and aarch64] build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin='x') }} diff --git a/recipes/sketchy/meta.yaml b/recipes/sketchy/meta.yaml index 080eeefb85504..f82c898eff6ca 100644 --- a/recipes/sketchy/meta.yaml +++ b/recipes/sketchy/meta.yaml @@ -10,7 +10,7 @@ source: sha256: eba9431d7c296d0839e56b2ddcf1db69b7a2c82e79cabde50e66e094983aee73 build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/slamem/meta.yaml b/recipes/slamem/meta.yaml index 41e156b3b7b7b..95341299d0acd 100644 --- a/recipes/slamem/meta.yaml +++ b/recipes/slamem/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 source: url: https://github.com/sguizard/slaMEM/archive/refs/tags/v{{ version }}.tar.gz diff --git a/recipes/slclust/meta.yaml b/recipes/slclust/meta.yaml index 3e2f82a2d39e1..a4feeda00c66a 100644 --- a/recipes/slclust/meta.yaml +++ b/recipes/slclust/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 9e21b65288e7fc35647721380cfedffd68608e164b4240c692c511c18c1620f8 build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage("slclust", max_pin=None) }} diff --git a/recipes/slimfastq/meta.yaml b/recipes/slimfastq/meta.yaml index 548a28cdd8b66..41af6111f1d98 100644 --- a/recipes/slimfastq/meta.yaml +++ b/recipes/slimfastq/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 source: url: https://github.com/Infinidat/slimfastq/archive/v{{ version }}.tar.gz diff --git a/recipes/slimm/meta.yaml b/recipes/slimm/meta.yaml index 085be93fa76d7..8cac1be52890a 100644 --- a/recipes/slimm/meta.yaml +++ b/recipes/slimm/meta.yaml @@ -3,7 +3,7 @@ package: version: 0.3.4 build: - number: 5 + number: 6 source: - url: https://github.com/seqan/slimm/archive/v0.3.4.tar.gz diff --git a/recipes/slow5curl/meta.yaml b/recipes/slow5curl/meta.yaml index 3c6270698f1c6..8630443baf2b4 100644 --- a/recipes/slow5curl/meta.yaml +++ b/recipes/slow5curl/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 6c062e59dc3e8bd65612613da7ac9a2518544061f1ef81d159e938e717393d3e build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('slow5curl', max_pin="x") }} diff --git a/recipes/slow5tools/0.2.0/meta.yaml b/recipes/slow5tools/0.2.0/meta.yaml index 6c86c96fa8d03..5f8a40598c881 100644 --- a/recipes/slow5tools/0.2.0/meta.yaml +++ b/recipes/slow5tools/0.2.0/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 47c890e2742576dc1cd5fad9fd7acdcfcbab8264c0dca4b3626877a8dc021b27 build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/slow5tools/0.7.0/meta.yaml b/recipes/slow5tools/0.7.0/meta.yaml index e114983f4d5f8..bdd0cd78b0ae8 100644 --- a/recipes/slow5tools/0.7.0/meta.yaml +++ b/recipes/slow5tools/0.7.0/meta.yaml @@ -10,7 +10,7 @@ source: sha256: a38ea6e0e1c647b6d2b333d15201d9ce5932dda52ec87537e6d982ba1bfbb595 build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/slow5tools/0.8.0/meta.yaml b/recipes/slow5tools/0.8.0/meta.yaml index 57f5e074df82d..a8d1923cf6fb9 100644 --- a/recipes/slow5tools/0.8.0/meta.yaml +++ b/recipes/slow5tools/0.8.0/meta.yaml @@ -10,7 +10,7 @@ source: sha256: f0f6bfdd8bcc633ae0ccd4e61e6d847579882be8bfd6488d1ffdba9d7db794f6 build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/slow5tools/0.9.0/meta.yaml b/recipes/slow5tools/0.9.0/meta.yaml index 64348d550afa5..36f08de414c70 100644 --- a/recipes/slow5tools/0.9.0/meta.yaml +++ b/recipes/slow5tools/0.9.0/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 9a9a4ab2e15fd2ea3275d6d08cfb5d46bdf073207e9430b41d80801cce0de8f6 build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/slow5tools/1.0.0/meta.yaml b/recipes/slow5tools/1.0.0/meta.yaml index 2f375029f4c60..c3c95c2a2d080 100644 --- a/recipes/slow5tools/1.0.0/meta.yaml +++ b/recipes/slow5tools/1.0.0/meta.yaml @@ -10,7 +10,7 @@ source: sha256: a1c188192adfe3ccea6eaa550716f7d784985377dc7dc1e210b2ed5c968fa6b1 build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/slow5tools/meta.yaml b/recipes/slow5tools/meta.yaml index 4941e1c8f1dc6..cd8c52a9dc633 100644 --- a/recipes/slow5tools/meta.yaml +++ b/recipes/slow5tools/meta.yaml @@ -10,7 +10,7 @@ source: sha256: f7221285e0090a5ca05a75f5e70c51d093138b2c8ad658b2756c3c6e51097d5d build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('slow5tools', max_pin="x") }} diff --git a/recipes/smaca/meta.yaml b/recipes/smaca/meta.yaml index 71fa33ffc680f..595232788b154 100644 --- a/recipes/smaca/meta.yaml +++ b/recipes/smaca/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 1a0750ef2c58aeb997806be2c5f5c6952d8c13f95b4f4fff880e184a4fab2d43 build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage(name, max_pin="x") }} skip: true # [osx] diff --git a/recipes/smafa/meta.yaml b/recipes/smafa/meta.yaml index 5a77eb6404adf..f58dabba85bb0 100644 --- a/recipes/smafa/meta.yaml +++ b/recipes/smafa/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('smafa', max_pin="x.x") }} diff --git a/recipes/smartdenovo/meta.yaml b/recipes/smartdenovo/meta.yaml index 2639069dd100b..0cdb9bd6cec10 100644 --- a/recipes/smartdenovo/meta.yaml +++ b/recipes/smartdenovo/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 7 + number: 8 source: url: https://github.com/ruanjue/smartdenovo/archive/3d9c22e25bdf4caf6c08ea1acb41ee58e52f61a8.tar.gz diff --git a/recipes/smartmap/meta.yaml b/recipes/smartmap/meta.yaml index 222f6585fe2ab..c3ccfda6ea36a 100644 --- a/recipes/smartmap/meta.yaml +++ b/recipes/smartmap/meta.yaml @@ -12,7 +12,7 @@ source: - 0001-fix-flags-for-bioconda.patch build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/smashpp/meta.yaml b/recipes/smashpp/meta.yaml index fb814b90e13aa..8fb73013f1851 100644 --- a/recipes/smashpp/meta.yaml +++ b/recipes/smashpp/meta.yaml @@ -7,7 +7,7 @@ package: build: # Passes some invalid flags for clang skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage('smashpp', max_pin="x") }} diff --git a/recipes/smhasher/meta.yaml b/recipes/smhasher/meta.yaml index 8b307e9116885..bff26b89abcae 100644 --- a/recipes/smhasher/meta.yaml +++ b/recipes/smhasher/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.150.1" build: - number: 10 + number: 11 script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv source: diff --git a/recipes/smoothxg/meta.yaml b/recipes/smoothxg/meta.yaml index 5357d1b2094b6..99e98e63aa376 100644 --- a/recipes/smoothxg/meta.yaml +++ b/recipes/smoothxg/meta.yaml @@ -13,7 +13,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage('smoothxg', max_pin="x") }} diff --git a/recipes/smudgeplot/meta.yaml b/recipes/smudgeplot/meta.yaml index 4bff036cc65bd..280d7680e3c2f 100644 --- a/recipes/smudgeplot/meta.yaml +++ b/recipes/smudgeplot/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('smudgeplot', max_pin="x.x") }} @@ -26,6 +26,7 @@ requirements: - r-viridis - python - xorg-libxrender + - zlib run: - python - r-base diff --git a/recipes/smudgeplot_rn/meta.yaml b/recipes/smudgeplot_rn/meta.yaml index 2f541a11ae8d8..8e4ffb3f699ca 100644 --- a/recipes/smudgeplot_rn/meta.yaml +++ b/recipes/smudgeplot_rn/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 6 + number: 7 source: url: https://github.com/RNieuwenhuis/smudgeplot/archive/v{{ version }}.tar.gz diff --git a/recipes/snap-aligner/1.0dev.96/meta.yaml b/recipes/snap-aligner/1.0dev.96/meta.yaml index d655b8dab6b54..577ccfa50f68f 100644 --- a/recipes/snap-aligner/1.0dev.96/meta.yaml +++ b/recipes/snap-aligner/1.0dev.96/meta.yaml @@ -7,7 +7,7 @@ source: sha256: eab1607145065f5bbd47dc9a9428cb21f4eff2300497c828b369a7ccbb70c6b8 build: - number: 3 + number: 4 skip: True # [osx] requirements: diff --git a/recipes/snap-aligner/meta.yaml b/recipes/snap-aligner/meta.yaml index 903a6a8a9ee79..405931fcb710c 100644 --- a/recipes/snap-aligner/meta.yaml +++ b/recipes/snap-aligner/meta.yaml @@ -12,7 +12,7 @@ source: - snap-aligner-aarch64.patch # [linux and aarch64] build: - number: 3 + number: 4 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin='x') }} @@ -39,4 +39,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/snap/build_failure.linux-64.yaml b/recipes/snap/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..7e6056ace7aff --- /dev/null +++ b/recipes/snap/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 8cb84db6d99035c207fba55e0fe0ed8578b4bf22050b93e8e48aeabcfe0ccea1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + 2024-12-15T20:08:51 noarch Applying patch instructions + 2024-12-15T20:08:51 noarch Writing patched repodata + 2024-12-15T20:08:51 noarch Building current_repodata subset + 2024-12-15T20:08:51 noarch Writing current_repodata subset + 2024-12-15T20:08:51 noarch Writing index HTML + /opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (/opt/recipe/meta.yaml). + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml + Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for snap + Reloading output folder: ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder: ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['snap-2013_11_29-h7b50bb2_7.tar.bz2'] + Reloading output folder: ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/snap_1734293332575/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder: ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder: ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/snap_1734293332575/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.43-h4bf12b8_2 conda-forge + binutils_linux-64: 2.43-h4852527_2 conda-forge + gcc_impl_linux-64: 13.3.0-hfea6d02_1 conda-forge + gcc_linux-64: 13.3.0-hc28eda2_7 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libsanitizer: 13.3.0-heb74ff8_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + make: 4.4.1-hb9d3cd8_2 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: snap-2013-11-29_e2a236392d.tar.gz + Downloading http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(, 'Connection to korflab.ucdavis.edu timed out. (connect timeout=9.15)')': /Software/snap-2013-11-29.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(, 'Connection to korflab.ucdavis.edu timed out. (connect timeout=9.15)')': /Software/snap-2013-11-29.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(, 'Connection to korflab.ucdavis.edu timed out. (connect timeout=9.15)')': /Software/snap-2013-11-29.tar.gz + WARNING: Error: HTTP 000 CONNECTION FAILED for url + Elapsed: - + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz +# Last 100 lines of the build log. +category: |- + source download error diff --git a/recipes/snap/meta.yaml b/recipes/snap/meta.yaml index d12d5f1027887..36c6385abe557 100644 --- a/recipes/snap/meta.yaml +++ b/recipes/snap/meta.yaml @@ -7,8 +7,10 @@ source: sha256: e2a236392d718376356fa743aa49a987aeacd660c6979cee67121e23aeffc66a build: - number: 6 + number: 7 skip: True # [osx] + run_exports: + - {{ pin_subpackage('snap') }} requirements: build: diff --git a/recipes/snapatac2/build_failure.osx-64.yaml b/recipes/snapatac2/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..0452021792bf6 --- /dev/null +++ b/recipes/snapatac2/build_failure.osx-64.yaml @@ -0,0 +1,108 @@ +recipe_sha: dac72260205d5dcc339b316fe7a867e18e1f7b6198115d7609a7e4f1c532a47c # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - tomli 2.2.1 pyhd8ed1ab_1 + - wheel 0.45.1 pyhd8ed1ab_1 + - maturin 1.8.1 py311h8462c55_0 + - pip 24.3.1 pyh8b19718_2 + run: + - scipy >=1.4 + - plotly >=5.19.0 + - numpy >=1.16.0 + - pooch >=1.6.0 + - typeguard >=4.0 + - python_abi 3.11.* *_cp311 + - rustworkx + - pyfaidx >=0.7.0,<0.8.0 + - python >=3.11,<3.12.0a0 + - pyarrow + - polars >=1.0 + - pandas >=1.0,<2.1.2 + - python-kaleido + - python-igraph >=0.10.3 + - macs3 + - anndata + - natsort + - multiprocess + - tqdm >=4.62 + - scikit-learn >=1.0 + - typing_extensions + - libzlib >=1.3.1,<2.0a0 + run_constrained: + - __osx >=10.13 + test: + imports: + - snapatac2 + about: + dev_url: https://github.com/kaizhang/SnapATAC2 + doc_url: https://kzhang.org/SnapATAC2 + home: https://github.com/kaizhang/SnapATAC2 + license: MIT + license_family: MIT + license_file: snapatac2-python/LICENSE + summary: 'SnapATAC2: Single-cell epigenomics analysis pipeline.' + extra: + copy_test_source_files: true + final: true + identifiers: + - biotools:snapatac + - doi:10.1038/s41592-023-02139-9 + - usegalaxy-eu:snapatac2_preprocessing + - usegalaxy-eu:snapatac2_clustering + - usegalaxy-eu:snapatac2_peaks_and_motif + - usegalaxy-eu:snapatac2_plotting + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1736270965270/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1736270965270/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1736270965270/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/snapatac2_1736270965270/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/snapatac2-2.8.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/snapatac2-2.8.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 +# Last 100 lines of the build log. +category: |- + compiler error +reason: |- + Library not loaded: @rpath/libLLVM.18.1.dylib diff --git a/recipes/snapatac2/meta.yaml b/recipes/snapatac2/meta.yaml index 51510058d5b0b..c70977e2c8af6 100644 --- a/recipes/snapatac2/meta.yaml +++ b/recipes/snapatac2/meta.yaml @@ -14,7 +14,7 @@ source: - pyproject.toml.patch build: - number: 0 + number: 1 skip: True # [py < 39 or py > 312] run_exports: - {{ pin_subpackage('snapatac2', max_pin="x") }} diff --git a/recipes/sneep/build_failure.osx-64.yaml b/recipes/sneep/build_failure.osx-64.yaml index 7b7f2b4a25dd6..f085d9b029ce3 100644 --- a/recipes/sneep/build_failure.osx-64.yaml +++ b/recipes/sneep/build_failure.osx-64.yaml @@ -1,70 +1,70 @@ -recipe_sha: 2449a710f015e732724a6193b0447a5061f54c4661bdae62ddb48d9371b56483 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 5c16865e8dd3bd6f34a07c16a4b22513e71a222bbbf86eb244cd283fdfb33ff9 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |2- - clang: 14.0.6-h694c41f_1 conda-forge - clang-14: 14.0.6-default_hdb78580_1 conda-forge - clang_osx-64: 14.0.6-h3113cd8_6 conda-forge - clangxx: 14.0.6-default_hdb78580_1 conda-forge - clangxx_osx-64: 14.0.6-h6f97653_6 conda-forge - compiler-rt: 14.0.6-h613da45_0 conda-forge - compiler-rt_osx-64: 14.0.6-hab78ec2_0 conda-forge - ld64_osx-64: 609-hfd63004_13 conda-forge - libclang-cpp14: 14.0.6-default_hdb78580_1 conda-forge - libcxx: 17.0.6-h88467a6_0 conda-forge - libllvm14: 14.0.6-hc8e404f_4 conda-forge - libzlib: 1.3.1-h87427d6_1 conda-forge - llvm-openmp: 16.0.6-hff08bdf_0 conda-forge - llvm-tools: 14.0.6-hc8e404f_4 conda-forge - make: 4.3-h22f3db7_1 conda-forge - openssl: 3.3.1-h87427d6_0 conda-forge - sigtool: 0.1.3-h88f4db0_0 conda-forge - tapi: 1100.0.11-h9ce4665_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - Downloading source to cache: v1.1_663a327abb.tar.gz - Downloading https://github.com/SchulzLab/SNEEP/archive/refs/tags/v1.1.tar.gz - Success - ld: warning: directory not found for option '-L/usr/local/opt/libomp/lib' - ld: library not found for -lomp - clang-14: error: linker command failed with exit code 1 (use -v to see invocation) - make: *** [Makefile:22: all] Error 1 - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/sneep_1717643045632/work - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build return build_tree( - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/sneep_1717643045632/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/sneep_1717643045632/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/sneep_1717643045632/work + - libclang-cpp14 14.0.6 default_hdb78580_1 + - ld64_osx-64 609 hfd63004_13 + host: + - libcxx 19.1.5 hf95d169_0 + - llvm-openmp 19.1.5 ha54dae1_0 + - bzip2 1.0.8 hfdf4475_7 + - ca-certificates 2024.8.30 h8857fd0_0 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + - libffi 3.4.2 h0d85af4_5 + - liblzma 5.6.3 hd471939_1 + - libzlib 1.3.1 hd23fc13_2 + - ncurses 6.5 hf036a51_1 + - tzdata 2024b hc8b5060_0 + - libsqlite 3.47.2 hdb6dae5_0 + - openssl 3.4.0 hd471939_0 + - readline 8.2 h9e318b2_1 + - tk 8.6.13 h1abcd95_1 + - python 3.10.16 h5acdff8_1_cpython + run: + - libcxx >=14.0.6 + - numpy >=1.19 + - python_abi 3.10.* *_cp310 + - matplotlib-base + - python >=3.10,<3.11.0a0 + - llvm-openmp >=19.1.5 + - llvm-openmp >=18.1.8 + - bedtools >=2.27.1 + - scipy + test: + commands: + - differentialBindingAffinity_multipleSNPs -h + about: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + dev_url: https://github.com/SchulzLab/SNEEP + home: https://github.com/SchulzLab/SNEEP + license: MIT + license_family: MIT + summary: Identify regulatory non-coding SNPs (rSNPs) + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/sneep_1733819566783/work + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/sneep_1733819566783/work/conda_build.sh']' returned non-zero exit status 2. + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/sneep_1733819566783/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/sneep_1733819566783/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/sneep_1733819566783/work INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as CC=x86_64-apple-darwin13.4.0-clang CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sneep-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/sneep_1717643045632/work/conda_build.sh']' returned non-zero exit status 2. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sneep-1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool @@ -82,7 +82,7 @@ log: |2- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack diff --git a/recipes/sneep/meta.yaml b/recipes/sneep/meta.yaml index eeae5849ea3dd..0542ea4933d88 100644 --- a/recipes/sneep/meta.yaml +++ b/recipes/sneep/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: True # [py2k] - number: 1 + number: 2 run_exports: - {{ pin_subpackage('sneep', max_pin="x.x") }} diff --git a/recipes/snikt/meta.yaml b/recipes/snikt/meta.yaml index 7c2127467789c..fee888b7962fd 100644 --- a/recipes/snikt/meta.yaml +++ b/recipes/snikt/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 noarch: generic requirements: diff --git a/recipes/snoscan/build_failure.linux-64.yaml b/recipes/snoscan/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..6f16bd24e2667 --- /dev/null +++ b/recipes/snoscan/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: d93188ef5499425c25e428f3e048bf2147d907315f62569fa2f40093ac833d70 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + conn.connect() + File "/opt/conda/lib/python3.10/site-packages/urllib3/connection.py", line 730, in connect + sock_and_verified = _ssl_wrap_socket_and_match_hostname( + File "/opt/conda/lib/python3.10/site-packages/urllib3/connection.py", line 909, in _ssl_wrap_socket_and_match_hostname + ssl_sock = ssl_wrap_socket( + File "/opt/conda/lib/python3.10/site-packages/urllib3/util/ssl_.py", line 469, in ssl_wrap_socket + ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls, server_hostname) + File "/opt/conda/lib/python3.10/site-packages/urllib3/util/ssl_.py", line 513, in _ssl_wrap_socket_impl + return ssl_context.wrap_socket(sock, server_hostname=server_hostname) + File "/opt/conda/lib/python3.10/ssl.py", line 513, in wrap_socket + return self.sslsocket_class._create( + File "/opt/conda/lib/python3.10/ssl.py", line 1104, in _create + self.do_handshake() + File "/opt/conda/lib/python3.10/ssl.py", line 1375, in do_handshake + self._sslobj.do_handshake() + ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007) + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 789, in urlopen + response = self._make_request( + File "/opt/conda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 490, in _make_request + raise new_e + urllib3.exceptions.SSLError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007) + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/requests/adapters.py", line 667, in send + resp = conn.urlopen( + File "/opt/conda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 873, in urlopen + return self.urlopen( + File "/opt/conda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 873, in urlopen + return self.urlopen( + File "/opt/conda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 873, in urlopen + return self.urlopen( + File "/opt/conda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 843, in urlopen + retries = retries.increment( + File "/opt/conda/lib/python3.10/site-packages/urllib3/util/retry.py", line 519, in increment + raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type] + urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='lowelab.ucsc.edu', port=443): Max retries exceeded with url: /software/snoscan-1.0.tar.gz (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007)'))) + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 247, in download_http_errors + yield + File "/opt/conda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 68, in download + download_inner( + File "/opt/conda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 97, in download_inner + resp = session.get( + File "/opt/conda/lib/python3.10/site-packages/requests/sessions.py", line 602, in get + return self.request("GET", url, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/requests/sessions.py", line 589, in request + resp = self.send(prep, **send_kwargs) + File "/opt/conda/lib/python3.10/site-packages/requests/sessions.py", line 724, in send + history = [resp for resp in gen] + File "/opt/conda/lib/python3.10/site-packages/requests/sessions.py", line 724, in + history = [resp for resp in gen] + File "/opt/conda/lib/python3.10/site-packages/requests/sessions.py", line 265, in resolve_redirects + resp = self.send( + File "/opt/conda/lib/python3.10/site-packages/requests/sessions.py", line 703, in send + r = adapter.send(request, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/requests/adapters.py", line 698, in send + raise SSLError(e, request=request) + requests.exceptions.SSLError: HTTPSConnectionPool(host='lowelab.ucsc.edu', port=443): Max retries exceeded with url: /software/snoscan-1.0.tar.gz (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007)'))) + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 103, in download_to_cache + download(url, path) + File "/opt/conda/lib/python3.10/site-packages/conda/common/io.py", line 86, in decorated + return f(*args, **kwds) + File "/opt/conda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 67, in download + with download_http_errors(url): + File "/opt/conda/lib/python3.10/contextlib.py", line 153, in __exit__ + self.gen.throw(typ, value, traceback) + File "/opt/conda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 287, in download_http_errors + raise CondaSSLError( + conda.exceptions.CondaSSLError: Encountered an SSL error. Most likely a certificate verification issue. + + Exception: HTTPSConnectionPool(host='lowelab.ucsc.edu', port=443): Max retries exceeded with url: /software/snoscan-1.0.tar.gz (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007)'))) +# Last 100 lines of the build log. diff --git a/recipes/snoscan/build_failure.osx-64.yaml b/recipes/snoscan/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..198d3fbe73673 --- /dev/null +++ b/recipes/snoscan/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: d93188ef5499425c25e428f3e048bf2147d907315f62569fa2f40093ac833d70 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + conn.connect() + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/connection.py", line 730, in connect + sock_and_verified = _ssl_wrap_socket_and_match_hostname( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/connection.py", line 909, in _ssl_wrap_socket_and_match_hostname + ssl_sock = ssl_wrap_socket( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/util/ssl_.py", line 469, in ssl_wrap_socket + ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls, server_hostname) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/util/ssl_.py", line 513, in _ssl_wrap_socket_impl + return ssl_context.wrap_socket(sock, server_hostname=server_hostname) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/ssl.py", line 513, in wrap_socket + return self.sslsocket_class._create( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/ssl.py", line 1104, in _create + self.do_handshake() + File "/opt/mambaforge/envs/bioconda/lib/python3.10/ssl.py", line 1375, in do_handshake + self._sslobj.do_handshake() + ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007) + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 789, in urlopen + response = self._make_request( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 490, in _make_request + raise new_e + urllib3.exceptions.SSLError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007) + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/requests/adapters.py", line 667, in send + resp = conn.urlopen( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 873, in urlopen + return self.urlopen( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 873, in urlopen + return self.urlopen( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 873, in urlopen + return self.urlopen( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 843, in urlopen + retries = retries.increment( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/util/retry.py", line 519, in increment + raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type] + urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='lowelab.ucsc.edu', port=443): Max retries exceeded with url: /software/snoscan-1.0.tar.gz (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007)'))) + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 247, in download_http_errors + yield + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 68, in download + download_inner( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 97, in download_inner + resp = session.get( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/requests/sessions.py", line 602, in get + return self.request("GET", url, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/requests/sessions.py", line 589, in request + resp = self.send(prep, **send_kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/requests/sessions.py", line 724, in send + history = [resp for resp in gen] + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/requests/sessions.py", line 724, in + history = [resp for resp in gen] + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/requests/sessions.py", line 265, in resolve_redirects + resp = self.send( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/requests/sessions.py", line 703, in send + r = adapter.send(request, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/requests/adapters.py", line 698, in send + raise SSLError(e, request=request) + requests.exceptions.SSLError: HTTPSConnectionPool(host='lowelab.ucsc.edu', port=443): Max retries exceeded with url: /software/snoscan-1.0.tar.gz (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007)'))) + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 103, in download_to_cache + download(url, path) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/common/io.py", line 86, in decorated + return f(*args, **kwds) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 67, in download + with download_http_errors(url): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/contextlib.py", line 153, in __exit__ + self.gen.throw(typ, value, traceback) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 287, in download_http_errors + raise CondaSSLError( + conda.exceptions.CondaSSLError: Encountered an SSL error. Most likely a certificate verification issue. + + Exception: HTTPSConnectionPool(host='lowelab.ucsc.edu', port=443): Max retries exceeded with url: /software/snoscan-1.0.tar.gz (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007)'))) +# Last 100 lines of the build log. diff --git a/recipes/snoscan/meta.yaml b/recipes/snoscan/meta.yaml index 6f908fa168f86..3a1f4e25cd49f 100644 --- a/recipes/snoscan/meta.yaml +++ b/recipes/snoscan/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 5 + number: 6 source: url: http://lowelab.ucsc.edu/software/snoscan-{{ version }}.tar.gz diff --git a/recipes/snostrip/meta.yaml b/recipes/snostrip/meta.yaml index 0eb89d8614b89..f66578894c109 100644 --- a/recipes/snostrip/meta.yaml +++ b/recipes/snostrip/meta.yaml @@ -15,7 +15,7 @@ source: - snostrip.patch # [linux] #adds conda paths libs to @INC for perl scripts and modules build: - number: 5 + number: 6 skip: True # [osx] requirements: diff --git a/recipes/snp-dists/meta.yaml b/recipes/snp-dists/meta.yaml index caa28398f11b4..b071780d57d4d 100644 --- a/recipes/snp-dists/meta.yaml +++ b/recipes/snp-dists/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 run_exports: - {{ pin_subpackage('snp-dists', max_pin="x.x") }} @@ -40,4 +40,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/snp-pileup/meta.yaml b/recipes/snp-pileup/meta.yaml index f601bcf01ad9c..d30ecda56091f 100644 --- a/recipes/snp-pileup/meta.yaml +++ b/recipes/snp-pileup/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{sha256}}' build: - number: 7 + number: 8 skip: True # [osx] run_exports: - {{ pin_subpackage('snp-pileup', max_pin="x.x") }} @@ -36,4 +36,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/snp-sites/meta.yaml b/recipes/snp-sites/meta.yaml index b0e134e4bc456..ab3d9b6709522 100644 --- a/recipes/snp-sites/meta.yaml +++ b/recipes/snp-sites/meta.yaml @@ -7,7 +7,7 @@ package: version: '{{version}}' build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('snp-sites', max_pin="x") }} @@ -44,4 +44,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/snvphyl-tools/meta.yaml b/recipes/snvphyl-tools/meta.yaml index 29b34e88b3b3f..66b31f6af32e3 100644 --- a/recipes/snvphyl-tools/meta.yaml +++ b/recipes/snvphyl-tools/meta.yaml @@ -7,7 +7,7 @@ source: sha256: cf9ea45b221a69a10adc2bc09db6f0891cfeb990cc1d5be2be86d730e985b16c build: - number: 8 + number: 9 skip: True # [osx] requirements: diff --git a/recipes/soapdenovo-trans/1.03/meta.yaml b/recipes/soapdenovo-trans/1.03/meta.yaml index c0920cd36dcc0..2e2f7b078a26c 100644 --- a/recipes/soapdenovo-trans/1.03/meta.yaml +++ b/recipes/soapdenovo-trans/1.03/meta.yaml @@ -10,7 +10,7 @@ source: - 0002-osx-no-rt-link.patch # [osx] build: - number: 2 + number: 3 skip: True [not linux64] requirements: diff --git a/recipes/soapdenovo-trans/meta.yaml b/recipes/soapdenovo-trans/meta.yaml index ee89ef3068736..2d0e6a8c0b834 100644 --- a/recipes/soapdenovo-trans/meta.yaml +++ b/recipes/soapdenovo-trans/meta.yaml @@ -10,7 +10,7 @@ source: - 0002-osx-no-rt-link.patch # [osx] build: - number: 6 + number: 7 skip: True # [osx] requirements: diff --git a/recipes/soapdenovo2-errorcorrection/meta.yaml b/recipes/soapdenovo2-errorcorrection/meta.yaml index 4ba9f5163c0ee..23626b5f3816c 100644 --- a/recipes/soapdenovo2-errorcorrection/meta.yaml +++ b/recipes/soapdenovo2-errorcorrection/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 9f4f38ec0629045d0f2da67c8221636f545f1bdd500b7e4c0ad7e95db1794a8d build: - number: 8 + number: 9 skip: True # [osx] requirements: diff --git a/recipes/soapdenovo2-prepare/meta.yaml b/recipes/soapdenovo2-prepare/meta.yaml index 9ffeec2a9dedc..dc52cd7f5b5cb 100644 --- a/recipes/soapdenovo2-prepare/meta.yaml +++ b/recipes/soapdenovo2-prepare/meta.yaml @@ -9,7 +9,7 @@ source: - Makefile.osx.patch # [osx] build: - number: 8 + number: 9 skip: True # [osx] requirements: diff --git a/recipes/soapec/meta.yaml b/recipes/soapec/meta.yaml index cff5ef7354ee2..c42ad3ceadab4 100644 --- a/recipes/soapec/meta.yaml +++ b/recipes/soapec/meta.yaml @@ -7,7 +7,7 @@ source: sha256: d95faa1ebffc785bca134a72d88b336dd1a4797c526f5d66095db3d4c3ec3d24 build: - number: 8 + number: 9 skip: True # [osx] requirements: diff --git a/recipes/solexaqa/meta.yaml b/recipes/solexaqa/meta.yaml index 53ab33a0a0874..2d2ff7577b702 100644 --- a/recipes/solexaqa/meta.yaml +++ b/recipes/solexaqa/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 6 + number: 7 skip: True # [not linux] source: diff --git a/recipes/somalier/build_failure.linux-64.yaml b/recipes/somalier/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..32cf48a258ae0 --- /dev/null +++ b/recipes/somalier/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 6b040ff7dc602be9fa434be41d8248f87bc0db72ca66a237af89f0461b376cc8 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [1m[0m[32mHint: [0mused config file '/opt/conda/conda-bld/somalier_1734250830932/_build_env/nim/config/nim.cfg'[36m [Conf][0m + [1m[0m[32mHint: [0mused config file '/opt/conda/conda-bld/somalier_1734250830932/_build_env/nim/config/config.nims'[36m [Conf][0m + ..............................CC: stdlib_assertions.nim + CC: stdlib_dollars.nim + CC: stdlib_formatfloat.nim + CC: stdlib_io.nim + CC: stdlib_system.nim + CC: stdlib_math.nim + CC: stdlib_algorithm.nim + CC: stdlib_parseutils.nim + CC: stdlib_unicode.nim + CC: stdlib_strutils.nim + CC: stdlib_strformat.nim + CC: stdlib_hashes.nim + CC: stdlib_sets.nim + CC: stdlib_tables.nim + CC: stdlib_exitprocs.nim + CC: stdlib_streams.nim + CC: stdlib_times.nim + CC: stdlib_os.nim + CC: stdlib_terminal.nim + CC: stdlib_unittest.nim + CC: pedfile.nim + + [1m[0m[32mHint: [0m[36m [Link][0m + [1m[0m[32mHint: [0m78780 lines; 4.674s; 94.027MiB peakmem; Release build; proj: /tmp/nimble_563/githubcom_brentppedfile_0.0.3/src/pedfile.nim; out: /tmp/nimble_563/githubcom_brentppedfile_0.0.3/pedfile[36m [SuccessX][0m + Copying file /tmp/nimble_563/githubcom_brentppedfile_0.0.3/src/pedfile.nim to $SRC_DIR/nimbledeps/pkgs/pedfile-0.0.4/pedfile.nim + Copying file /tmp/nimble_563/githubcom_brentppedfile_0.0.3/pedfile.nimble to $SRC_DIR/nimbledeps/pkgs/pedfile-0.0.4/pedfile.nimble + Copying file /tmp/nimble_563/githubcom_brentppedfile_0.0.3/pedfile to $SRC_DIR/nimbledeps/pkgs/pedfile-0.0.4/pedfile + Creating symlink: $SRC_DIR/nimbledeps/pkgs/pedfile-0.0.4/pedfile -> $SRC_DIR/nimbledeps/bin/pedfile + Success: pedfile installed successfully. + Reading official package list + Checking for https://github.com/brentp/hileup@any version + Installing https://github.com/brentp/hileup@any version + Downloading https://github.com/brentp/hileup using git + Verifying dependencies for hile@0.01 + Reading official package list + Checking for hts@>= 0.2.13 + Info: Dependency on hts@>= 0.2.13 already satisfied + Verifying dependencies for hts@0.3.25 + Installing hile@0.01 + Copying file /tmp/nimble_563/githubcom_brentphileup/src/hilepkg/hiles.nim to $SRC_DIR/nimbledeps/pkgs/hile-0.01/hilepkg/hiles.nim + Copying file /tmp/nimble_563/githubcom_brentphileup/src/hilepkg/utils.nim to $SRC_DIR/nimbledeps/pkgs/hile-0.01/hilepkg/utils.nim + Copying file /tmp/nimble_563/githubcom_brentphileup/src/hilepkg/rcbbc.nim to $SRC_DIR/nimbledeps/pkgs/hile-0.01/hilepkg/rcbbc.nim + Copying file /tmp/nimble_563/githubcom_brentphileup/src/hile.nim to $SRC_DIR/nimbledeps/pkgs/hile-0.01/hile.nim + Copying file /tmp/nimble_563/githubcom_brentphileup/hile.nimble to $SRC_DIR/nimbledeps/pkgs/hile-0.01/hile.nimble + Success: hile installed successfully. + Reading official package list + Checking for argparse@>= 0.10.1 & < 0.10.2 + Installing argparse@>= 0.10.1 & < 0.10.2 + Reading official package list + Downloading https://github.com/iffy/nim-argparse using git + Cloning latest tagged version: v0.10.1 + Verifying dependencies for argparse@0.10.1 + Installing argparse@0.10.1 + Copying file /tmp/nimble_563/githubcom_iffynimargparse_0.10.1_0.10.2/src/argparse.nim to $SRC_DIR/nimbledeps/pkgs/argparse-0.10.1/argparse.nim + Copying file /tmp/nimble_563/githubcom_iffynimargparse_0.10.1_0.10.2/src/argparse/macrohelp.nim to $SRC_DIR/nimbledeps/pkgs/argparse-0.10.1/argparse/macrohelp.nim + Copying file /tmp/nimble_563/githubcom_iffynimargparse_0.10.1_0.10.2/argparse.nimble to $SRC_DIR/nimbledeps/pkgs/argparse-0.10.1/argparse.nimble + Success: argparse installed successfully. + Reading official package list + Checking for lapper@any version + Installing lapper@any version + Reading official package list + Downloading https://github.com/brentp/nim-lapper using git + Cloning latest tagged version: v0.1.7 + Verifying dependencies for lapper@0.1.7 + Installing lapper@0.1.7 + Copying file /tmp/nimble_563/githubcom_brentpnimlapper/src/lapper.nim to $SRC_DIR/nimbledeps/pkgs/lapper-0.1.7/lapper.nim + Copying file /tmp/nimble_563/githubcom_brentpnimlapper/lapper.nimble to $SRC_DIR/nimbledeps/pkgs/lapper-0.1.7/lapper.nimble + Success: lapper installed successfully. + Reading official package list + Checking for arraymancer@#head + Installing arraymancer@#head + Reading official package list + Downloading https://github.com/mratsim/Arraymancer using git + Verifying dependencies for arraymancer@#head + Error: Unsatisfied dependency: nim (>= 1.6.0) + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/somalier_1734250830932/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/somalier_1734250830932/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/somalier/meta.yaml b/recipes/somalier/meta.yaml index 32d5d2be59eec..ad5b16401dc21 100644 --- a/recipes/somalier/meta.yaml +++ b/recipes/somalier/meta.yaml @@ -10,7 +10,7 @@ source: # Skip OSX following https://github.com/bioconda/bioconda-recipes/blob/73a14544ca8ef7926797b39259cb58b83732b7da/recipes/slivar/meta.yaml build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage("somalier", max_pin="x") }} diff --git a/recipes/sonlib/build_failure.linux-64.yaml b/recipes/sonlib/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..35e6016381732 --- /dev/null +++ b/recipes/sonlib/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 9796bdcde3afa9c6dc53a1d80d97a147116adfd5fc126eec60de202c1d9e56e1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + rm -rf externalTools/ + make -j 4 shlib + cd C && make shlib + make[1]: Entering directory '$SRC_DIR/C' + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/avl.o impl/avl.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/bioioC.o impl/bioioC.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/commonC.o impl/commonC.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/fastCMaths.o impl/fastCMaths.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/hashTableC.o impl/hashTableC.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/hashTableC_itr.o impl/hashTableC_itr.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/jsmn.o impl/jsmn.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/lz4.o impl/lz4.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/lz4hc.o impl/lz4hc.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/pairwiseAlignment.o impl/pairwiseAlignment.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibCache.o impl/sonLibCache.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibCommon.o impl/sonLibCommon.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibCompression.o impl/sonLibCompression.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibConnectivity.o impl/sonLibConnectivity.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibEulerTour.o impl/sonLibEulerTour.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibExcept.o impl/sonLibExcept.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibFile.o impl/sonLibFile.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibHash.o impl/sonLibHash.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibKVDatabase.o impl/sonLibKVDatabase.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibKVDatabaseConf.o impl/sonLibKVDatabaseConf.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibKVDatabase_BigRecordFile.o impl/sonLibKVDatabase_BigRecordFile.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibKVDatabase_MySql.o impl/sonLibKVDatabase_MySql.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibKVDatabase_Redis.o impl/sonLibKVDatabase_Redis.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibKVDatabase_TokyoCabinet.o impl/sonLibKVDatabase_TokyoCabinet.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibList.o impl/sonLibList.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibMath.o impl/sonLibMath.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibNaiveConnectivity.o impl/sonLibNaiveConnectivity.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibRandom.o impl/sonLibRandom.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibSet.o impl/sonLibSet.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibSortedSet.o impl/sonLibSortedSet.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibString.o impl/sonLibString.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibTreap.o impl/sonLibTreap.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibTree.o impl/sonLibTree.c + impl/sonLibTreap.c: In function 'stTreap_remove': + impl/sonLibTreap.c:331:18: warning: pointer 'rmnode' used after 'free' [-Wuse-after-free] + 331 | stTreap *p = rmnode->parent; + | ^ + impl/sonLibTreap.c:329:9: note: call to 'free' here + 329 | free(rmnode); + | ^~~~~~~~~~~~ + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibTuples.o impl/sonLibTuples.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/stGraph.o impl/stGraph.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/stJson.o impl/stJson.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/stMatrix.o impl/stMatrix.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/stPhylogeny.o impl/stPhylogeny.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/stPosetAlignment.o impl/stPosetAlignment.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/stSafeC.o impl/stSafeC.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/stThreadPool.o impl/stThreadPool.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/stUnionFind.o impl/stUnionFind.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -shared -fPIC impl/avl.o impl/bioioC.o impl/commonC.o impl/fastCMaths.o impl/hashTableC.o impl/hashTableC_itr.o impl/jsmn.o impl/lz4.o impl/lz4hc.o impl/pairwiseAlignment.o impl/sonLibCache.o impl/sonLibCommon.o impl/sonLibCompression.o impl/sonLibConnectivity.o impl/sonLibEulerTour.o impl/sonLibExcept.o impl/sonLibFile.o impl/sonLibHash.o impl/sonLibKVDatabase.o impl/sonLibKVDatabaseConf.o impl/sonLibKVDatabase_BigRecordFile.o impl/sonLibKVDatabase_MySql.o impl/sonLibKVDatabase_Redis.o impl/sonLibKVDatabase_TokyoCabinet.o impl/sonLibList.o impl/sonLibMath.o impl/sonLibNaiveConnectivity.o impl/sonLibRandom.o impl/sonLibSet.o impl/sonLibSortedSet.o impl/sonLibString.o impl/sonLibTreap.o impl/sonLibTree.o impl/sonLibTuples.o impl/stGraph.o impl/stJson.o impl/stMatrix.o impl/stPhylogeny.o impl/stPosetAlignment.o impl/stSafeC.o impl/stThreadPool.o impl/stUnionFind.o -lquicktree -lz -o libsonLib.so + mv libsonLib.so ../lib/ + make[1]: Leaving directory '$SRC_DIR/C' + mkdir -p /opt/conda/conda-bld/sonlib_1734295487867/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/bin /opt/conda/conda-bld/sonlib_1734295487867/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib /opt/conda/conda-bld/sonlib_1734295487867/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include/sonLib + install sonLib_daemonize.py /opt/conda/conda-bld/sonlib_1734295487867/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/bin/ + cp 'lib/*.h' /opt/conda/conda-bld/sonlib_1734295487867/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include/sonLib/ + cp: cannot stat 'lib/*.h': No such file or directory + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/sonlib_1734295487867/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/sonlib_1734295487867/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/sonlib/build_failure.osx-64.yaml b/recipes/sonlib/build_failure.osx-64.yaml index ad4b54678e4a7..2216a9b609be0 100644 --- a/recipes/sonlib/build_failure.osx-64.yaml +++ b/recipes/sonlib/build_failure.osx-64.yaml @@ -1,103 +1,103 @@ -recipe_sha: b98d13e34ff1057452ff95bc6a9c0f37501cd0ffb3686635e720e8c066868b63 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 9796bdcde3afa9c6dc53a1d80d97a147116adfd5fc126eec60de202c1d9e56e1 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- - cp inc/sonLibString.h ../lib/sonLibString.h - cp inc/sonLibTreap.h ../lib/sonLibTreap.h - cp inc/sonLibTree.h ../lib/sonLibTree.h - cp inc/sonLibTuples.h ../lib/sonLibTuples.h - cp inc/sonLibTypes.h ../lib/sonLibTypes.h - cp inc/stGraph.h ../lib/stGraph.h - cp inc/stJson.h ../lib/stJson.h - cp inc/stMatrix.h ../lib/stMatrix.h - cp inc/stPhylogeny.h ../lib/stPhylogeny.h - cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h - cp inc/stSafeC.h ../lib/stSafeC.h - cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h - cp inc/stThreadPool.h ../lib/stThreadPool.h - cp inc/stUnionFind.h ../lib/stUnionFind.h - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/avl.o impl/avl.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/bioioC.o impl/bioioC.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/commonC.o impl/commonC.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/fastCMaths.o impl/fastCMaths.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/hashTableC.o impl/hashTableC.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/hashTableC_itr.o impl/hashTableC_itr.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/jsmn.o impl/jsmn.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/lz4.o impl/lz4.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/lz4hc.o impl/lz4hc.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/pairwiseAlignment.o impl/pairwiseAlignment.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibCache.o impl/sonLibCache.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibCommon.o impl/sonLibCommon.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibCompression.o impl/sonLibCompression.c + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + cd C && make shlib + make[1]: Entering directory '$SRC_DIR/C' + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/avl.o impl/avl.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/bioioC.o impl/bioioC.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/commonC.o impl/commonC.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/fastCMaths.o impl/fastCMaths.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/hashTableC.o impl/hashTableC.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/hashTableC_itr.o impl/hashTableC_itr.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/jsmn.o impl/jsmn.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/lz4.o impl/lz4.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/lz4hc.o impl/lz4hc.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/pairwiseAlignment.o impl/pairwiseAlignment.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibCache.o impl/sonLibCache.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibCommon.o impl/sonLibCommon.c impl/sonLibTuples.c:16:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] - stIntTuple *stIntTuple_construct0() { - ^ - void - 1 warning generated. + 16 | stIntTuple *stIntTuple_construct0() { + | ^ + | void impl/stGraph.c:83:49: warning: implicit conversion from 'long long' to 'double' changes value from 9223372036854775807 to 9223372036854775808 [-Wimplicit-const-int-float-conversion] - vD->distance = (v == sourceVertex ? 0 : INT64_MAX); - ~ ^~~~~~~~~ - /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/stdint.h:75:26: note: expanded from macro 'INT64_MAX' - #define INT64_MAX 9223372036854775807LL - ^~~~~~~~~~~~~~~~~~~~~ + 83 | vD->distance = (v == sourceVertex ? 0 : INT64_MAX); + | ~ ^~~~~~~~~ + /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/stdint.h:75:26: note: expanded from macro 'INT64_MAX' + 75 | #define INT64_MAX 9223372036854775807LL + | ^~~~~~~~~~~~~~~~~~~~~ + 1 warning generated. 1 warning generated. impl/stSafeC.c:28:9: warning: variable 'nbytes' set but not used [-Wunused-but-set-variable] - int nbytes = write(2, buf, strlen(buf)); - ^ + 28 | int nbytes = write(2, buf, strlen(buf)); + | ^ 1 warning generated. - mkdir -p /opt/mambaforge/envs/bioconda/conda-bld/sonlib_1717959623386/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin /opt/mambaforge/envs/bioconda/conda-bld/sonlib_1717959623386/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib /opt/mambaforge/envs/bioconda/conda-bld/sonlib_1717959623386/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/sonLib - install sonLib_daemonize.py /opt/mambaforge/envs/bioconda/conda-bld/sonlib_1717959623386/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/ - cp lib/avl.h lib/bioioC.h lib/commonC.h lib/fastCMaths.h lib/hashTableC.h lib/hashTableC_itr.h lib/hashTablePrivateC.h lib/jsmn.h lib/pairwiseAlignment.h lib/safesort.h lib/sonLib.h lib/sonLibCache.h lib/sonLibCommon.h lib/sonLibCompression.h lib/sonLibConnectivity.h lib/sonLibEulerTour.h lib/sonLibExcept.h lib/sonLibFile.h lib/sonLibHash.h lib/sonLibKVDatabase.h lib/sonLibKVDatabaseConf.h lib/sonLibList.h lib/sonLibMath.h lib/sonLibNaiveConnectivity.h lib/sonLibRandom.h lib/sonLibSet.h lib/sonLibSortedSet.h lib/sonLibString.h lib/sonLibTreap.h lib/sonLibTree.h lib/sonLibTuples.h lib/sonLibTypes.h lib/stGraph.h lib/stJson.h lib/stMatrix.h lib/stPhylogeny.h lib/stPosetAlignment.h lib/stSafeC.h lib/stSpimapLayer.h lib/stThreadPool.h lib/stUnionFind.h /opt/mambaforge/envs/bioconda/conda-bld/sonlib_1717959623386/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/sonLib/ - cp lib/libsonLib.so /opt/mambaforge/envs/bioconda/conda-bld/sonlib_1717959623386/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/ - /opt/mambaforge/envs/bioconda/conda-bld/sonlib_1717959623386/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/python setup.py install --single-version-externally-managed --record=record.txt + mkdir -p /opt/mambaforge/envs/bioconda/conda-bld/sonlib_1734214757702/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin /opt/mambaforge/envs/bioconda/conda-bld/sonlib_1734214757702/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib /opt/mambaforge/envs/bioconda/conda-bld/sonlib_1734214757702/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/sonLib + install sonLib_daemonize.py /opt/mambaforge/envs/bioconda/conda-bld/sonlib_1734214757702/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/ + cp 'lib/*.h' /opt/mambaforge/envs/bioconda/conda-bld/sonlib_1734214757702/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include/sonLib/ + cp: lib/*.h: No such file or directory Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/conda-bld/sonlib_1717959623386/work/setup.py", line 3, in - from setuptools import setup, find_packages - ModuleNotFoundError: No module named 'setuptools' + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibCompression.o impl/sonLibCompression.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibConnectivity.o impl/sonLibConnectivity.c + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibEulerTour.o impl/sonLibEulerTour.c + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/sonlib_1734214757702/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibExcept.o impl/sonLibExcept.c Traceback (most recent call last): File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree packages_from_this = build( - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibConnectivity.o impl/sonLibConnectivity.c - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/sonlib_1717959623386/work/conda_build.sh']' returned non-zero exit status 1. - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibEulerTour.o impl/sonLibEulerTour.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibExcept.o impl/sonLibExcept.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibFile.o impl/sonLibFile.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibHash.o impl/sonLibHash.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibKVDatabase.o impl/sonLibKVDatabase.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibKVDatabaseConf.o impl/sonLibKVDatabaseConf.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibKVDatabase_BigRecordFile.o impl/sonLibKVDatabase_BigRecordFile.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibKVDatabase_MySql.o impl/sonLibKVDatabase_MySql.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibKVDatabase_Redis.o impl/sonLibKVDatabase_Redis.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibKVDatabase_TokyoCabinet.o impl/sonLibKVDatabase_TokyoCabinet.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibList.o impl/sonLibList.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibMath.o impl/sonLibMath.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibNaiveConnectivity.o impl/sonLibNaiveConnectivity.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibRandom.o impl/sonLibRandom.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibSet.o impl/sonLibSet.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibSortedSet.o impl/sonLibSortedSet.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibString.o impl/sonLibString.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibTreap.o impl/sonLibTreap.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibTree.o impl/sonLibTree.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/sonLibTuples.o impl/sonLibTuples.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/stGraph.o impl/stGraph.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/stJson.o impl/stJson.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/stMatrix.o impl/stMatrix.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/stPhylogeny.o impl/stPhylogeny.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/stPosetAlignment.o impl/stPosetAlignment.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/stSafeC.o impl/stSafeC.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/stThreadPool.o impl/stThreadPool.c - x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c -o impl/stUnionFind.o impl/stUnionFind.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibFile.o impl/sonLibFile.c + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/sonlib_1734214757702/work/conda_build.sh']' returned non-zero exit status 1. + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibHash.o impl/sonLibHash.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibKVDatabase.o impl/sonLibKVDatabase.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibKVDatabaseConf.o impl/sonLibKVDatabaseConf.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibKVDatabase_BigRecordFile.o impl/sonLibKVDatabase_BigRecordFile.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibKVDatabase_MySql.o impl/sonLibKVDatabase_MySql.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibKVDatabase_Redis.o impl/sonLibKVDatabase_Redis.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibKVDatabase_TokyoCabinet.o impl/sonLibKVDatabase_TokyoCabinet.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibList.o impl/sonLibList.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibMath.o impl/sonLibMath.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibNaiveConnectivity.o impl/sonLibNaiveConnectivity.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibRandom.o impl/sonLibRandom.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibSet.o impl/sonLibSet.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibSortedSet.o impl/sonLibSortedSet.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibString.o impl/sonLibString.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibTreap.o impl/sonLibTreap.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibTree.o impl/sonLibTree.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/sonLibTuples.o impl/sonLibTuples.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/stGraph.o impl/stGraph.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/stJson.o impl/stJson.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/stMatrix.o impl/stMatrix.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/stPhylogeny.o impl/stPhylogeny.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/stPosetAlignment.o impl/stPosetAlignment.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/stSafeC.o impl/stSafeC.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/stThreadPool.o impl/stThreadPool.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -c -o impl/stUnionFind.o impl/stUnionFind.c x86_64-apple-darwin13.4.0-clang -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Iinc -Iimpl -fsigned-char -Iinc -Iimpl -fsigned-char -I../externalTools/quicktree_1.1/include/ -I ../externalTools/cutest -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/sonlib-2.0.dev88 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -fPIC -std=c99 -fsigned-char -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -shared -fPIC impl/avl.o impl/bioioC.o impl/commonC.o impl/fastCMaths.o impl/hashTableC.o impl/hashTableC_itr.o impl/jsmn.o impl/lz4.o impl/lz4hc.o impl/pairwiseAlignment.o impl/sonLibCache.o impl/sonLibCommon.o impl/sonLibCompression.o impl/sonLibConnectivity.o impl/sonLibEulerTour.o impl/sonLibExcept.o impl/sonLibFile.o impl/sonLibHash.o impl/sonLibKVDatabase.o impl/sonLibKVDatabaseConf.o impl/sonLibKVDatabase_BigRecordFile.o impl/sonLibKVDatabase_MySql.o impl/sonLibKVDatabase_Redis.o impl/sonLibKVDatabase_TokyoCabinet.o impl/sonLibList.o impl/sonLibMath.o impl/sonLibNaiveConnectivity.o impl/sonLibRandom.o impl/sonLibSet.o impl/sonLibSortedSet.o impl/sonLibString.o impl/sonLibTreap.o impl/sonLibTree.o impl/sonLibTuples.o impl/stGraph.o impl/stJson.o impl/stMatrix.o impl/stPhylogeny.o impl/stPosetAlignment.o impl/stSafeC.o impl/stThreadPool.o impl/stUnionFind.o -lquicktree -lz -o libsonLib.so mv libsonLib.so ../lib/ make[1]: Leaving directory '$SRC_DIR/C' diff --git a/recipes/sonlib/meta.yaml b/recipes/sonlib/meta.yaml index d0c56979f46d8..b1c3679bbe4f9 100644 --- a/recipes/sonlib/meta.yaml +++ b/recipes/sonlib/meta.yaml @@ -17,7 +17,7 @@ source: - patches/0002-Remove-need-for-CuTest-during-build.patch build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/sorted_nearest/build_failure.osx-64.yaml b/recipes/sorted_nearest/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..7923cb25e1de8 --- /dev/null +++ b/recipes/sorted_nearest/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 28bddefe4e1e4d5b8d5c63964d19f9f14f3fb7ba0bb796a4735b4c232cd14cad # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + WARNING: Importing conda-verify failed. Please be sure to test your packages. conda install conda-verify to make this message go away. + compiling .pyc files... + number of files: 57 + INFO: sysroot: '/System/Library/Frameworks/' files: '['vmnet.framework/Versions/Current', 'vmnet.framework/Versions/A/_CodeSignature/CodeResources', 'vmnet.framework/Versions/A/Resources/version.plist', 'vmnet.framework/Versions/A/Resources/InfoPlist.loctable']' + INFO: sysroot: '/usr/lib/' files: '['zsh/5.9/zsh/zselect.so', 'zsh/5.9/zsh/zpty.so', 'zsh/5.9/zsh/zprof.so', 'zsh/5.9/zsh/zleparameter.so']' + INFO: sysroot: '/opt/X11/' files: '[]' + INFO (sorted_nearest,lib/python3.10/site-packages/sorted_nearest/src/max_disjoint_intervals.cpython-310-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT + INFO (sorted_nearest,lib/python3.10/site-packages/sorted_nearest/src/cluster_by.cpython-310-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT + INFO (sorted_nearest,lib/python3.10/site-packages/sorted_nearest/src/clusters.cpython-310-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT + INFO (sorted_nearest,lib/python3.10/site-packages/sorted_nearest/src/k_nearest_ties.cpython-310-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT + INFO (sorted_nearest,lib/python3.10/site-packages/sorted_nearest/src/k_nearest.cpython-310-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT + INFO (sorted_nearest,lib/python3.10/site-packages/sorted_nearest/src/introns.cpython-310-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT + INFO (sorted_nearest,lib/python3.10/site-packages/sorted_nearest/src/annotate_clusters.cpython-310-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT + INFO (sorted_nearest,lib/python3.10/site-packages/sorted_nearest/src/sorted_nearest.cpython-310-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT + INFO (sorted_nearest,lib/python3.10/site-packages/sorted_nearest/src/merge_by.cpython-310-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT + INFO (sorted_nearest,lib/python3.10/site-packages/sorted_nearest/src/tiles.cpython-310-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT + INFO (sorted_nearest,lib/python3.10/site-packages/sorted_nearest/src/windows.cpython-310-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT + WARNING (sorted_nearest): interpreter (Python) package conda-forge/osx-64::python==3.10.16=h5acdff8_1_cpython in requirements/run but it is not used (i.e. it is overdepending or perhaps statically linked? If that is what you want then add it to build/ignore_run_exports) + Fixing permissions + Packaged license file/s. + INFO :: Time taken to mark (prefix) + 0 replacements in 0 files was 0.07 seconds + TEST START: /opt/mambaforge/envs/bioconda/conda-bld/osx-64/sorted_nearest-0.0.39-py310h9735c86_5.tar.bz2 + Renaming work directory '/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1734457261336/work' to '/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1734457261336/work_moved_sorted_nearest-0.0.39-py310h9735c86_5_osx-64' + shutil.move(work)=/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1734457261336/work, dest=/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1734457261336/work_moved_sorted_nearest-0.0.39-py310h9735c86_5_osx-64) + Reloading output folder (local): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1734457261336/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + + + The following NEW packages will be INSTALLED: + + bzip2: 1.0.8-hfdf4475_7 conda-forge + ca-certificates: 2024.12.14-h8857fd0_0 conda-forge + libblas: 3.9.0-26_osx64_openblas conda-forge + libcblas: 3.9.0-26_osx64_openblas conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libffi: 3.4.2-h0d85af4_5 conda-forge + libgfortran: 5.0.0-13_2_0_h97931a8_3 conda-forge + libgfortran5: 13.2.0-h2873a65_3 conda-forge + liblapack: 3.9.0-26_osx64_openblas conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libopenblas: 0.3.28-openmp_hbf64a52_1 conda-forge + libsqlite: 3.47.2-hdb6dae5_0 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-openmp: 19.1.5-ha54dae1_0 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + numpy: 2.2.0-py310h2874b4e_0 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + python: 3.10.16-h5acdff8_1_cpython conda-forge + python_abi: 3.10-5_cp310 conda-forge + readline: 8.2-h9e318b2_1 conda-forge + sorted_nearest: 0.0.39-py310h9735c86_5 local + tk: 8.6.13-h1abcd95_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + /opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py:544: UserWarning: The environment variable 'SETUPTOOLS_SCM_PRETEND_VERSION' is being passed through with value '0.0.39'. If you are splitting build and test phases with --no-test, please ensure that this value is also set similarly at test time. + warnings.warn( + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1734457261336/test_tmp/run_test.py", line 2, in + import sorted_nearest + File "/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1734457261336/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.10/site-packages/sorted_nearest/__init__.py", line 1, in + import pkg_resources + ModuleNotFoundError: No module named 'pkg_resources' + WARNING: Tests failed for sorted_nearest-0.0.39-py310h9735c86_5.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1734457261336/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1734457261336/test_tmp + import: 'sorted_nearest' + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1734457261336/test_tmp/conda_test_runner.sh']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: sorted_nearest-0.0.39-py310h9735c86_5.tar.bz2 +# Last 100 lines of the build log. +category: |- + test failure diff --git a/recipes/sorted_nearest/meta.yaml b/recipes/sorted_nearest/meta.yaml index 24a8e58adac2b..3992c286c78db 100644 --- a/recipes/sorted_nearest/meta.yaml +++ b/recipes/sorted_nearest/meta.yaml @@ -13,7 +13,7 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - number: 4 + number: 5 script_env: - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }} script: "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir" diff --git a/recipes/spacepharer/build_failure.linux-64.yaml b/recipes/spacepharer/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..4c543ee8e64a2 --- /dev/null +++ b/recipes/spacepharer/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 1f9e55db02e0d2a8ff7995bb8d17c501c86cc019b55446fcc90e10aa42c68ef9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [ 33%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/cover.c + [ 33%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/fastcover.c + [ 34%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/divsufsort.c + [ 34%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/zdict.c + [ 35%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/deprecated/zbuff_common.c + [ 35%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/deprecated/zbuff_compress.c + [ 35%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/deprecated/zbuff_decompress.c + [ 36%] Linking C static library libzstd.a + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/cmake -P CMakeFiles/libzstd_static.dir/cmake_clean_target.cmake + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/cmake -E cmake_link_script CMakeFiles/libzstd_static.dir/link.txt --verbose=1 + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar qc libzstd.a CMakeFiles/libzstd_static.dir/__/__/__/lib/common/entropy_common.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/fse_decompress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/threading.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/pool.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/zstd_common.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/error_private.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/xxhash.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/hist.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/fse_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/huf_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstdmt_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_fast.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_double_fast.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_lazy.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_opt.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_ldm.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/huf_decompress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress_block.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_ddict.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib libzstd.a + make[2]: Leaving directory '$SRC_DIR/build' + [ 36%] Built target libzstd_static + make -f lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build.make lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/depend + make[2]: Entering directory '$SRC_DIR/build' + cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR/lib/mmseqs/src $SRC_DIR/build $SRC_DIR/build/lib/mmseqs/src $SRC_DIR/build/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/DependInfo.cmake "--color=" + make[2]: Leaving directory '$SRC_DIR/build' + make -f lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build.make lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build + make[2]: Entering directory '$SRC_DIR/build' + [ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o + [ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o + [ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o + [ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/Alignment.cpp + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/Matcher.cpp + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/CompressedA3M.cpp + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/Main.cpp + [ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/MsaFilter.cpp + [ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/MultipleAlignment.cpp + [ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -msse4.1 -mcx16 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/PSSMCalculator.cpp + In file included from /opt/conda/conda-bld/spacepharer_1734017956308/work/lib/mmseqs/src/commons/Debug.h:5, + from /opt/conda/conda-bld/spacepharer_1734017956308/work/lib/mmseqs/src/alignment/MsaFilter.cpp:5: + /opt/conda/conda-bld/spacepharer_1734017956308/work/lib/mmseqs/src/commons/Util.h:89:12: error: 'uint64_t' does not name a type + 89 | static uint64_t getL2CacheSize(); + | ^~~~~~~~ + /opt/conda/conda-bld/spacepharer_1734017956308/work/lib/mmseqs/src/commons/Util.h:11:1: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + 10 | #include "MMseqsMPI.h" + |#include + 11 | + /opt/conda/conda-bld/spacepharer_1734017956308/work/lib/mmseqs/src/commons/Util.h:330:12: error: 'uint64_t' does not name a type + 330 | static uint64_t revComplement(const uint64_t kmer, const int k); + | ^~~~~~~~ + /opt/conda/conda-bld/spacepharer_1734017956308/work/lib/mmseqs/src/commons/Util.h:330:12: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spacepharer_1734017956308/work/lib/mmseqs/src/commons/Debug.h: In constructor 'Debug::Progress::Progress()': + /opt/conda/conda-bld/spacepharer_1734017956308/work/lib/mmseqs/src/commons/Debug.h:169:69: error: 'SIZE_MAX' was not declared in this scope + 169 | Progress() : currentPos(0), prevPrintedId(0), totalEntries(SIZE_MAX){ + | ^~~~~~~~ + /opt/conda/conda-bld/spacepharer_1734017956308/work/lib/mmseqs/src/commons/Debug.h:12:1: note: 'SIZE_MAX' is defined in header ''; did you forget to '#include '? + 11 | #include + |#include + 12 | + /opt/conda/conda-bld/spacepharer_1734017956308/work/lib/mmseqs/src/commons/Debug.h: In member function 'void Debug::Progress::updateProgress()': + /opt/conda/conda-bld/spacepharer_1734017956308/work/lib/mmseqs/src/commons/Debug.h:184:34: error: 'SIZE_MAX' was not declared in this scope + 184 | if(totalEntries==SIZE_MAX) { + | ^~~~~~~~ + /opt/conda/conda-bld/spacepharer_1734017956308/work/lib/mmseqs/src/commons/Debug.h:184:34: note: 'SIZE_MAX' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spacepharer_1734017956308/work/lib/mmseqs/src/commons/Debug.h:218:34: error: 'SIZE_MAX' was not declared in this scope + 218 | if(totalEntries==SIZE_MAX){ + | ^~~~~~~~ + /opt/conda/conda-bld/spacepharer_1734017956308/work/lib/mmseqs/src/commons/Debug.h:218:34: note: 'SIZE_MAX' is defined in header ''; did you forget to '#include '? + make[2]: *** [lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build.make:135: lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o] Error 1 + make[2]: *** Waiting for unfinished jobs.... + make[2]: Leaving directory '$SRC_DIR/build' + make[1]: *** [CMakeFiles/Makefile2:957: lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/all] Error 2 + make[1]: Leaving directory '$SRC_DIR/build' + make: *** [Makefile:136: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/spacepharer_1734017956308/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/spacepharer_1734017956308/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/spacepharer/build_failure.linux-aarch64.yaml b/recipes/spacepharer/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..43b580d512879 --- /dev/null +++ b/recipes/spacepharer/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 1f9e55db02e0d2a8ff7995bb8d17c501c86cc019b55446fcc90e10aa42c68ef9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [ 33%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/cover.c + [ 33%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/fastcover.c + [ 34%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/divsufsort.c + [ 34%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/dictBuilder/zdict.c + [ 35%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/deprecated/zbuff_common.c + [ 35%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/deprecated/zbuff_compress.c + [ 35%] Building C object lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -I$SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/build/cmake/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/zstd/lib/common -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -MD -MT lib/mmseqs/lib/zstd/build/cmake/lib/CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o -MF CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o.d -o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o -c $SRC_DIR/lib/mmseqs/lib/zstd/lib/deprecated/zbuff_decompress.c + [ 36%] Linking C static library libzstd.a + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/cmake -P CMakeFiles/libzstd_static.dir/cmake_clean_target.cmake + cd $SRC_DIR/build/lib/mmseqs/lib/zstd/build/cmake/lib && $BUILD_PREFIX/bin/cmake -E cmake_link_script CMakeFiles/libzstd_static.dir/link.txt --verbose=1 + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ar qc libzstd.a CMakeFiles/libzstd_static.dir/__/__/__/lib/common/entropy_common.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/fse_decompress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/threading.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/pool.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/zstd_common.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/error_private.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/common/xxhash.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/hist.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/fse_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/huf_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstdmt_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_fast.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_double_fast.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_lazy.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_opt.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/compress/zstd_ldm.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/huf_decompress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_decompress_block.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/decompress/zstd_ddict.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/cover.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/fastcover.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/divsufsort.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/dictBuilder/zdict.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_common.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_compress.c.o CMakeFiles/libzstd_static.dir/__/__/__/lib/deprecated/zbuff_decompress.c.o + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib libzstd.a + make[2]: Leaving directory '$SRC_DIR/build' + [ 36%] Built target libzstd_static + make -f lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build.make lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/depend + make[2]: Entering directory '$SRC_DIR/build' + cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR/lib/mmseqs/src $SRC_DIR/build $SRC_DIR/build/lib/mmseqs/src $SRC_DIR/build/lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/DependInfo.cmake "--color=" + make[2]: Leaving directory '$SRC_DIR/build' + make -f lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build.make lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build + make[2]: Entering directory '$SRC_DIR/build' + [ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o + [ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o + [ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/Alignment.cpp + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/CompressedA3M.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/CompressedA3M.cpp + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/Main.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/Main.cpp + [ 37%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/Matcher.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/Matcher.cpp + [ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/MsaFilter.cpp + [ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/MultipleAlignment.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/MultipleAlignment.cpp + [ 38%] Building CXX object lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o + cd $SRC_DIR/build/lib/mmseqs/src && $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -I$SRC_DIR/build/generated -I$SRC_DIR/build/lib/mmseqs/generated -I$SRC_DIR/lib/mmseqs/src/alignment -I$SRC_DIR/lib/mmseqs/src/clustering -I$SRC_DIR/lib/mmseqs/src/commons -I$SRC_DIR/lib/mmseqs/src/multihit -I$SRC_DIR/lib/mmseqs/src/prefiltering -I$SRC_DIR/lib/mmseqs/src/linclust -I$SRC_DIR/lib/mmseqs/src/taxonomy -I$SRC_DIR/lib/mmseqs/src/util -I$SRC_DIR/lib/mmseqs/src/. -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spacepharer-5.c2e680a -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -fsigned-char -march=armv8-asimd -D_GNU_SOURCE=1 -std=c1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o -MF CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o.d -o CMakeFiles/mmseqs-framework.dir/alignment/PSSMCalculator.cpp.o -c $SRC_DIR/lib/mmseqs/src/alignment/PSSMCalculator.cpp + In file included from /opt/conda/conda-bld/spacepharer_1733933969055/work/lib/mmseqs/src/commons/Debug.h:5, + from /opt/conda/conda-bld/spacepharer_1733933969055/work/lib/mmseqs/src/alignment/MsaFilter.cpp:5: + /opt/conda/conda-bld/spacepharer_1733933969055/work/lib/mmseqs/src/commons/Util.h:89:12: error: 'uint64_t' does not name a type + 89 | static uint64_t getL2CacheSize(); + | ^~~~~~~~ + /opt/conda/conda-bld/spacepharer_1733933969055/work/lib/mmseqs/src/commons/Util.h:11:1: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + 10 | #include "MMseqsMPI.h" + |#include + 11 | + /opt/conda/conda-bld/spacepharer_1733933969055/work/lib/mmseqs/src/commons/Util.h:330:12: error: 'uint64_t' does not name a type + 330 | static uint64_t revComplement(const uint64_t kmer, const int k); + | ^~~~~~~~ + /opt/conda/conda-bld/spacepharer_1733933969055/work/lib/mmseqs/src/commons/Util.h:330:12: note: 'uint64_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spacepharer_1733933969055/work/lib/mmseqs/src/commons/Debug.h: In constructor 'Debug::Progress::Progress()': + /opt/conda/conda-bld/spacepharer_1733933969055/work/lib/mmseqs/src/commons/Debug.h:169:69: error: 'SIZE_MAX' was not declared in this scope + 169 | Progress() : currentPos(0), prevPrintedId(0), totalEntries(SIZE_MAX){ + | ^~~~~~~~ + /opt/conda/conda-bld/spacepharer_1733933969055/work/lib/mmseqs/src/commons/Debug.h:12:1: note: 'SIZE_MAX' is defined in header ''; did you forget to '#include '? + 11 | #include + |#include + 12 | + /opt/conda/conda-bld/spacepharer_1733933969055/work/lib/mmseqs/src/commons/Debug.h: In member function 'void Debug::Progress::updateProgress()': + /opt/conda/conda-bld/spacepharer_1733933969055/work/lib/mmseqs/src/commons/Debug.h:184:34: error: 'SIZE_MAX' was not declared in this scope + 184 | if(totalEntries==SIZE_MAX) { + | ^~~~~~~~ + /opt/conda/conda-bld/spacepharer_1733933969055/work/lib/mmseqs/src/commons/Debug.h:184:34: note: 'SIZE_MAX' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spacepharer_1733933969055/work/lib/mmseqs/src/commons/Debug.h:218:34: error: 'SIZE_MAX' was not declared in this scope + 218 | if(totalEntries==SIZE_MAX){ + | ^~~~~~~~ + /opt/conda/conda-bld/spacepharer_1733933969055/work/lib/mmseqs/src/commons/Debug.h:218:34: note: 'SIZE_MAX' is defined in header ''; did you forget to '#include '? + make[2]: *** [lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/build.make:135: lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/alignment/MsaFilter.cpp.o] Error 1 + make[2]: *** Waiting for unfinished jobs.... + make[2]: Leaving directory '$SRC_DIR/build' + make[1]: *** [CMakeFiles/Makefile2:957: lib/mmseqs/src/CMakeFiles/mmseqs-framework.dir/all] Error 2 + make[1]: Leaving directory '$SRC_DIR/build' + make: *** [Makefile:136: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/spacepharer_1733933969055/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/spacepharer_1733933969055/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/spacepharer/meta.yaml b/recipes/spacepharer/meta.yaml index bdf01d1d23171..688318557c2c3 100644 --- a/recipes/spacepharer/meta.yaml +++ b/recipes/spacepharer/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version|replace("-", ".") }} build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('spacepharer', max_pin="x") }} @@ -52,4 +52,4 @@ extra: - milot-mirdita additional-platforms: - linux-aarch64 - - osx-arm64 \ No newline at end of file + - osx-arm64 diff --git a/recipes/spades/meta.yaml b/recipes/spades/meta.yaml index a9621bd4904de..1e09b0a08a60d 100644 --- a/recipes/spades/meta.yaml +++ b/recipes/spades/meta.yaml @@ -13,7 +13,7 @@ source: - 0001-change-verbosity-remove-expr.patch build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage('spades', max_pin="x") }} diff --git a/recipes/spaln/meta.yaml b/recipes/spaln/meta.yaml index c2a7d7c8260ab..c4f8b1f27bf8a 100644 --- a/recipes/spaln/meta.yaml +++ b/recipes/spaln/meta.yaml @@ -15,7 +15,7 @@ source: - patch-makefile_ldflags # add a LDFLAGS variable to the Makefile build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('spaln', max_pin="x") }} diff --git a/recipes/sparc/meta.yaml b/recipes/sparc/meta.yaml index c02479c5ac882..76d079ced6749 100644 --- a/recipes/sparc/meta.yaml +++ b/recipes/sparc/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 10 + number: 11 source: url: https://github.com/yechengxi/Sparc/archive/ae89503a1613e26432e42febc7f35f6f71152b38.tar.gz diff --git a/recipes/sparseassembler/meta.yaml b/recipes/sparseassembler/meta.yaml index 541b1dd229dad..86c44a93fefe2 100644 --- a/recipes/sparseassembler/meta.yaml +++ b/recipes/sparseassembler/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 9 + number: 10 script: | mkdir -p "${PREFIX}/bin" "${CXX}" ${CPPFLAGS} ${CXXFLAGS} -O3 -o SparseAssembler *.cpp diff --git a/recipes/spclust/meta.yaml b/recipes/spclust/meta.yaml index ce3da49e000ea..c20c3af42084f 100644 --- a/recipes/spclust/meta.yaml +++ b/recipes/spclust/meta.yaml @@ -3,7 +3,7 @@ package: version: "28.5.19" build: - number: 0 + number: 1 source: url: https://github.com/johnymatar/SpCLUST/raw/f582e47f7e85e67dfa85415f6c975ad65eecd183/Linux/install.tar.xz diff --git a/recipes/splicemap/meta.yaml b/recipes/splicemap/meta.yaml index 4184ba6d8c09c..db8eb5d17fd52 100644 --- a/recipes/splicemap/meta.yaml +++ b/recipes/splicemap/meta.yaml @@ -3,7 +3,7 @@ package: version: 3.3.5.2 build: - number: 5 + number: 6 source: url: https://web.stanford.edu/group/wonglab/SpliceMap/SpliceMap3352_linux-64.zip diff --git a/recipes/splitcode/meta.yaml b/recipes/splitcode/meta.yaml index 9bdc34834f81a..3c264a63cac11 100644 --- a/recipes/splitcode/meta.yaml +++ b/recipes/splitcode/meta.yaml @@ -9,7 +9,7 @@ source: sha256: f8bef9a4a27c4805ab54c7218368e50f7aaba2896c223be0db97f508576ce264 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('splitcode', max_pin="x.x") }} diff --git a/recipes/splitmem/meta.yaml b/recipes/splitmem/meta.yaml index 16da691a32a41..2ca91d2263811 100644 --- a/recipes/splitmem/meta.yaml +++ b/recipes/splitmem/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.0" build: - number: 6 + number: 7 source: url: http://downloads.sourceforge.net/project/splitmem/splitmem.1.0.tgz diff --git a/recipes/splitp/meta.yaml b/recipes/splitp/meta.yaml index 4ebe64cb02d6e..597f481506050 100644 --- a/recipes/splitp/meta.yaml +++ b/recipes/splitp/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: url: https://github.com/COMBINE-lab/splitp/archive/refs/tags/v{{ version }}.tar.gz diff --git a/recipes/splitubam/build_failure.osx-64.yaml b/recipes/splitubam/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..671cc5eaeaf0d --- /dev/null +++ b/recipes/splitubam/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 700774915cfc2c1b4bcf1b6e30e4464cbf7058a230928d792d5b1396e1200188 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - clang 18.1.8 default_h179603d_5 + - libcxx-devel 18.1.8 h7c275be_7 + - ncurses 6.5 hf036a51_1 + - cctools_osx-64 1010.6 h00edd4c_2 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + - libclang-cpp18.1 18.1.8 default_h0c94c6a_5 + - ld64_osx-64 951.9 hc8d1a19_2 + - libclang13 18.1.8 default_h9ff962c_5 + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + - libzlib 1.3.1 hd23fc13_2 + - pkg-config 0.29.2 hf7e621a_1009 + - macosx_deployment_target_osx-64 14.5 h5d9aa64_2 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + - clang-18 18.1.8 default_h0c94c6a_5 + - libclang 18.1.8 default_h0c94c6a_5 + - rust 1.83.0 h34a2095_0 + packages_from_this = build( + - llvm-tools-18 18.1.8 h9ce406d_2 + - rust-std-x86_64-apple-darwin 1.83.0 h38e4360_0 + - llvmdev 18.1.8 h9ce406d_2 + - tapi 1300.6.5 h390ca13_0 + - make 4.4.1 h00291cd_2 + - llvm-tools 18.1.8 h9ce406d_2 + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + - libxml2 2.13.5 he8ee3e7_1 + host: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + - libzlib 1.3.1 hd23fc13_2 + - zlib 1.3.1 hd23fc13_2 + run: + - libzlib >=1.3.1,<2.0a0 + run_constrained: + - __osx >=10.13 + test: + commands: + - splitubam --help + about: + dev_url: https://github.com/fellen31/splitubam + home: https://github.com/fellen31/splitubam + license: MIT + license_family: MIT + license_file: LICENSE + summary: Split one ubam into multiple, per line, fast + extra: + copy_test_source_files: true + final: true + + + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/splitubam_1733869809469/work/conda_build.sh']' returned non-zero exit status 101. + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/splitubam_1733869809469/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/splitubam_1733869809469/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/splitubam_1733869809469/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/splitubam_1733869809469/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/splitubam-0.1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/splitubam-0.1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 +# Last 100 lines of the build log. diff --git a/recipes/splitubam/meta.yaml b/recipes/splitubam/meta.yaml index e99a9c167f98a..2c560e8c60ca9 100644 --- a/recipes/splitubam/meta.yaml +++ b/recipes/splitubam/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('splitubam', max_pin="x.x") }} diff --git a/recipes/spoa/meta.yaml b/recipes/spoa/meta.yaml index ca3c358ba60bf..fbac93a382b53 100644 --- a/recipes/spoa/meta.yaml +++ b/recipes/spoa/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/spring/build_failure.linux-64.yaml b/recipes/spring/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..e5f4dc2583ee4 --- /dev/null +++ b/recipes/spring/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5cb0d7d65980f94e1110a51bd5f3319debe2589c45219da8649a0b5bc9932d91 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [ 23%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/config_file.cpp.o + [ 28%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/options_description.cpp.o + [ 28%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/parsers.cpp.o + [ 28%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/variables_map.cpp.o + [ 28%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/value_semantic.cpp.o + [ 33%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/positional_options.cpp.o + [ 33%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/utf8_codecvt_facet.cpp.o + [ 33%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/convert.cpp.o + [ 38%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/winmain.cpp.o + [ 38%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/split.cpp.o + [ 38%] Linking CXX static library libboost_program_options.a + [ 38%] Built target Boost_program_options + [ 38%] Building CXX object CMakeFiles/spring.dir/src/main.cpp.o + [ 38%] Building CXX object CMakeFiles/spring.dir/src/spring.cpp.o + [ 42%] Building CXX object CMakeFiles/spring.dir/src/util.cpp.o + In file included from /opt/conda/conda-bld/spring_1734145147133/work/src/util.cpp:15: + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:43:3: error: 'uint32_t' does not name a type + 43 | uint32_t num_reads; + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:19:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + 18 | #include + |#include + 19 | #include + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:44:3: error: 'uint32_t' does not name a type + 44 | uint32_t num_reads_clean[2]; + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:44:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:45:3: error: 'uint32_t' does not name a type + 45 | uint32_t max_readlen; + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:45:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:46:3: error: 'uint8_t' does not name a type + 46 | uint8_t paired_id_code; + | ^~~~~~~ + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:46:3: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:53:1: error: 'uint32_t' does not name a type + 53 | uint32_t read_fastq_block(std::istream *fin, std::string *id_array, + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:53:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:59:30: error: 'uint32_t' does not name a type + 59 | const uint32_t &num_reads, + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:59:30: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:64:30: error: 'uint32_t' does not name a type + 64 | const uint32_t &num_ids); + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:64:30: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:67:32: error: 'uint32_t' does not name a type + 67 | const uint32_t &num_ids); + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:67:32: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:69:57: error: 'uint32_t' does not name a type + 69 | void quantize_quality(std::string *quality_array, const uint32_t &num_lines, + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:69:57: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:72:61: error: 'uint32_t' does not name a type + 72 | void quantize_quality_qvz(std::string *quality_array, const uint32_t &num_lines, + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:72:61: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:73:27: error: 'uint32_t' has not been declared + 73 | uint32_t *str_len_array, double qv_ratio); + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:82:1: error: 'uint8_t' does not name a type + 82 | uint8_t find_id_pattern(const std::string &id_1, const std::string &id_2); + | ^~~~~~~ + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:82:1: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:85:29: error: 'uint8_t' does not name a type + 85 | const uint8_t paired_id_code); + | ^~~~~~~ + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:85:29: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:87:39: error: 'uint8_t' does not name a type + 87 | void modify_id(std::string &id, const uint8_t paired_id_code); + | ^~~~~~~ + /opt/conda/conda-bld/spring_1734145147133/work/src/util.h:87:39: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + make[2]: *** [CMakeFiles/spring.dir/build.make:107: CMakeFiles/spring.dir/src/util.cpp.o] Error 1 + make[1]: *** [CMakeFiles/Makefile2:134: CMakeFiles/spring.dir/all] Error 2 + make: *** [Makefile:91: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/spring_1734145147133/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/spring_1734145147133/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/spring/build_failure.linux-aarch64.yaml b/recipes/spring/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..b08ee33a62b67 --- /dev/null +++ b/recipes/spring/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5cb0d7d65980f94e1110a51bd5f3319debe2589c45219da8649a0b5bc9932d91 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + [ 23%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/config_file.cpp.o + [ 28%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/options_description.cpp.o + [ 28%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/parsers.cpp.o + [ 28%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/variables_map.cpp.o + [ 28%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/value_semantic.cpp.o + [ 33%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/positional_options.cpp.o + [ 33%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/utf8_codecvt_facet.cpp.o + [ 33%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/convert.cpp.o + [ 38%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/winmain.cpp.o + [ 38%] Building CXX object boost-cmake/CMakeFiles/Boost_program_options.dir/boost/boost_1_67_0/libs/program_options/src/split.cpp.o + [ 38%] Linking CXX static library libboost_program_options.a + [ 38%] Built target Boost_program_options + [ 38%] Building CXX object CMakeFiles/spring.dir/src/main.cpp.o + [ 38%] Building CXX object CMakeFiles/spring.dir/src/spring.cpp.o + [ 42%] Building CXX object CMakeFiles/spring.dir/src/util.cpp.o + In file included from /opt/conda/conda-bld/spring_1734124652823/work/src/util.cpp:15: + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:43:3: error: 'uint32_t' does not name a type + 43 | uint32_t num_reads; + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:19:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + 18 | #include + |#include + 19 | #include + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:44:3: error: 'uint32_t' does not name a type + 44 | uint32_t num_reads_clean[2]; + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:44:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:45:3: error: 'uint32_t' does not name a type + 45 | uint32_t max_readlen; + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:45:3: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:46:3: error: 'uint8_t' does not name a type + 46 | uint8_t paired_id_code; + | ^~~~~~~ + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:46:3: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:53:1: error: 'uint32_t' does not name a type + 53 | uint32_t read_fastq_block(std::istream *fin, std::string *id_array, + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:53:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:59:30: error: 'uint32_t' does not name a type + 59 | const uint32_t &num_reads, + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:59:30: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:64:30: error: 'uint32_t' does not name a type + 64 | const uint32_t &num_ids); + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:64:30: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:67:32: error: 'uint32_t' does not name a type + 67 | const uint32_t &num_ids); + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:67:32: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:69:57: error: 'uint32_t' does not name a type + 69 | void quantize_quality(std::string *quality_array, const uint32_t &num_lines, + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:69:57: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:72:61: error: 'uint32_t' does not name a type + 72 | void quantize_quality_qvz(std::string *quality_array, const uint32_t &num_lines, + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:72:61: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:73:27: error: 'uint32_t' has not been declared + 73 | uint32_t *str_len_array, double qv_ratio); + | ^~~~~~~~ + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:82:1: error: 'uint8_t' does not name a type + 82 | uint8_t find_id_pattern(const std::string &id_1, const std::string &id_2); + | ^~~~~~~ + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:82:1: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:85:29: error: 'uint8_t' does not name a type + 85 | const uint8_t paired_id_code); + | ^~~~~~~ + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:85:29: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:87:39: error: 'uint8_t' does not name a type + 87 | void modify_id(std::string &id, const uint8_t paired_id_code); + | ^~~~~~~ + /opt/conda/conda-bld/spring_1734124652823/work/src/util.h:87:39: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + make[2]: *** [CMakeFiles/spring.dir/build.make:107: CMakeFiles/spring.dir/src/util.cpp.o] Error 1 + make[1]: *** [CMakeFiles/Makefile2:134: CMakeFiles/spring.dir/all] Error 2 + make: *** [Makefile:91: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/spring_1734124652823/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/spring_1734124652823/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/spring/meta.yaml b/recipes/spring/meta.yaml index 8dac430b3ae51..7e97889593ccd 100644 --- a/recipes/spring/meta.yaml +++ b/recipes/spring/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 skip: True # [osx] run_exports: - {{ pin_subpackage('spring', max_pin="x") }} diff --git a/recipes/squeakr/build_failure.linux-64.yaml b/recipes/squeakr/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..aabfa22fd2a54 --- /dev/null +++ b/recipes/squeakr/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: bce6d31ce8752ec4f9c121cd3ee1e42fbd4b8e41cfd4c660cba2015ae4781b1c # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + 126 | first = first | curr; + | ^~~~ + src/kmer.cc:129:25: error: 'first' was not declared in this scope + 129 | first = first >> 2; + | ^~~~~ + src/kmer.cc:130:25: error: 'first_rev' was not declared in this scope + 130 | first_rev = Kmer::reverse_complement(first, kmer_size); + | ^~~~~~~~~ + src/kmer.cc:133:33: error: 'item' was not declared in this scope; did you mean 'tm'? + 133 | item = first; + | ^~~~ + | tm + src/kmer.cc:135:33: error: 'item' was not declared in this scope; did you mean 'tm'? + 135 | item = first_rev; + | ^~~~ + | tm + src/kmer.cc:137:33: error: request for member 'insert' in 'kmerset', which is of non-class type 'int' + 137 | kmerset.insert(item); + | ^~~~~~ + src/kmer.cc:137:40: error: 'item' was not declared in this scope; did you mean 'tm'? + 137 | kmerset.insert(item); + | ^~~~ + | tm + src/kmer.cc:139:33: error: expected ';' before 'next' + 139 | uint64_t next = (first << 2) & BITMASK(2*kmer_size); + | ^~~~~ + | ; + src/kmer.cc:140:33: error: expected ';' before 'next_rev' + 140 | uint64_t next_rev = first_rev >> 2; + | ^~~~~~~~~ + | ; + src/kmer.cc:142:29: error: 'uint32_t' was not declared in this scope + 142 | for(uint32_t i=kmer_size; i'; did you forget to '#include '? + src/kmer.cc:142:51: error: 'i' was not declared in this scope + 142 | for(uint32_t i=kmer_size; i'; did you forget to '#include '? + src/kmer.cc:144:37: error: 'curr' was not declared in this scope + 144 | if (curr > DNA_MAP::G) { // 'N' is encountered + | ^~~~ + src/kmer.cc:151:33: error: 'next' was not declared in this scope; did you mean 'std::next'? + 151 | next |= curr; + | ^~~~ + | std::next + In file included from /opt/conda/conda-bld/squeakr_1733851565652/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/string:47, + from /opt/conda/conda-bld/squeakr_1733851565652/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/locale_classes.h:40, + from /opt/conda/conda-bld/squeakr_1733851565652/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/ios_base.h:41, + from /opt/conda/conda-bld/squeakr_1733851565652/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/ios:44, + from /opt/conda/conda-bld/squeakr_1733851565652/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/istream:40, + from /opt/conda/conda-bld/squeakr_1733851565652/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/fstream:40, + from src/kmer.cc:11: + /opt/conda/conda-bld/squeakr_1733851565652/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_iterator_base_funcs.h:232:5: note: 'std::next' declared here + 232 | next(_InputIterator __x, typename + | ^~~~ + src/kmer.cc:151:41: error: 'curr' was not declared in this scope + 151 | next |= curr; + | ^~~~ + src/kmer.cc:152:41: error: expected ';' before 'tmp' + 152 | uint64_t tmp = Kmer::reverse_complement_base(curr); + | ^~~~ + | ; + src/kmer.cc:153:33: error: 'tmp' was not declared in this scope; did you mean 'tm'? + 153 | tmp <<= (kmer_size*2-2); + | ^~~ + | tm + src/kmer.cc:154:33: error: 'next_rev' was not declared in this scope + 154 | next_rev = next_rev | tmp; + | ^~~~~~~~ + src/kmer.cc:160:41: error: request for member 'insert' in 'kmerset', which is of non-class type 'int' + 160 | kmerset.insert(item); + | ^~~~~~ + make: *** [Makefile:80: obj/kmer.o] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/squeakr_1733851565652/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/squeakr_1733851565652/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/squeakr/meta.yaml b/recipes/squeakr/meta.yaml index b18136c4e98dd..1448477cc712e 100644 --- a/recipes/squeakr/meta.yaml +++ b/recipes/squeakr/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 61f0493e5d27a7d629a87841052d174491018bb81e1876879f402d3b6885a9ff build: - number: 1 + number: 2 skip: True # [osx] run_exports: - {{ pin_subpackage('squeakr', max_pin="x.x") }} diff --git a/recipes/squid/build_failure.linux-64.yaml b/recipes/squid/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..750a0d4f97255 --- /dev/null +++ b/recipes/squid/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 66c28e3228e660cc3d449c9459a228cebbff83eea7fe814f2bba564ccceaebe7 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + src/Config.cpp:115:51: error: 'uint16_t' was not declared in this scope + 115 | Max_LowPhred_Len=(uint16_t)atoi(argv[i1]); + | ^~~~~~~~ + src/Config.cpp:115:51: note: 'uint16_t' is defined in header ''; did you forget to '#include '? + src/Config.cpp:123:33: error: 'Min_Phred' was not declared in this scope + 123 | Min_Phred=(uint8_t)atoi(argv[i1]); + | ^~~~~~~~~ + src/Config.cpp:123:44: error: 'uint8_t' was not declared in this scope + 123 | Min_Phred=(uint8_t)atoi(argv[i1]); + | ^~~~~~~ + src/Config.cpp:123:44: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + src/Config.cpp:131:33: error: 'Min_MapQual' was not declared in this scope + 131 | Min_MapQual=(uint16_t)atoi(argv[i1]); + | ^~~~~~~~~~~ + src/Config.cpp:131:46: error: 'uint16_t' was not declared in this scope + 131 | Min_MapQual=(uint16_t)atoi(argv[i1]); + | ^~~~~~~~ + src/Config.cpp:131:46: note: 'uint16_t' is defined in header ''; did you forget to '#include '? + src/Config.cpp:220:17: error: 'Min_MapQual' was not declared in this scope + 220 | Min_MapQual=255; + | ^~~~~~~~~~~ + In file included from src/ReadRec.h:20, + from src/ReadRec.cpp:7: + src/SingleBamRec.h:32:9: error: 'uint8_t' does not name a type + 32 | uint8_t MapQual; + | ^~~~~~~ + src/SingleBamRec.h:19:1: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + 18 | #include + |#include + 19 | #include + src/SingleBamRec.h:37:109: error: 'uint8_t' has not been declared + 37 | SingleBamRec_t(int32_t RefID, int32_t RefPos, int32_t ReadPos, int32_t MatchRef, int32_t MatchRead, uint8_t MapQual, bool IsReverse, bool IsFirstRead): + | ^~~~~~~ + src/SingleBamRec.h: In constructor 'SingleBamRec_t::SingleBamRec_t(int32_t, int32_t, int32_t, int32_t, int32_t, int, bool, bool)': + src/SingleBamRec.h:38:107: error: class 'SingleBamRec_t' does not have any field named 'MapQual' + 38 | RefID(RefID), RefPos(RefPos), ReadPos(ReadPos), MatchRef(MatchRef), MatchRead(MatchRead), MapQual(MapQual), IsReverse(IsReverse), IsFirstRead(IsFirstRead){}; + | ^~~~~~~ + src/ReadRec.cpp: In member function 'void ReadRec_t::FilterSplitRecord()': + src/ReadRec.cpp:151:41: error: '__gnu_cxx::__alloc_traits, SingleBamRec_t>::value_type' {aka 'class SingleBamRec_t'} has no member named 'MapQual' + 151 | if(FirstRead[i].MapQual > FirstRead[i1].MapQual){ + | ^~~~~~~ + src/ReadRec.cpp:151:66: error: '__gnu_cxx::__alloc_traits, SingleBamRec_t>::value_type' {aka 'class SingleBamRec_t'} has no member named 'MapQual' + 151 | if(FirstRead[i].MapQual > FirstRead[i1].MapQual){ + | ^~~~~~~ + src/ReadRec.cpp:154:46: error: '__gnu_cxx::__alloc_traits, SingleBamRec_t>::value_type' {aka 'class SingleBamRec_t'} has no member named 'MapQual' + 154 | else if(FirstRead[i].MapQual < FirstRead[i1].MapQual){ + | ^~~~~~~ + src/ReadRec.cpp:154:71: error: '__gnu_cxx::__alloc_traits, SingleBamRec_t>::value_type' {aka 'class SingleBamRec_t'} has no member named 'MapQual' + 154 | else if(FirstRead[i].MapQual < FirstRead[i1].MapQual){ + | ^~~~~~~ + src/ReadRec.cpp:161:42: error: '__gnu_cxx::__alloc_traits, SingleBamRec_t>::value_type' {aka 'class SingleBamRec_t'} has no member named 'MapQual' + 161 | if(SecondMate[i].MapQual > SecondMate[i1].MapQual){ + | ^~~~~~~ + src/ReadRec.cpp:161:68: error: '__gnu_cxx::__alloc_traits, SingleBamRec_t>::value_type' {aka 'class SingleBamRec_t'} has no member named 'MapQual' + 161 | if(SecondMate[i].MapQual > SecondMate[i1].MapQual){ + | ^~~~~~~ + src/ReadRec.cpp:164:47: error: '__gnu_cxx::__alloc_traits, SingleBamRec_t>::value_type' {aka 'class SingleBamRec_t'} has no member named 'MapQual' + 164 | else if(SecondMate[i].MapQual < SecondMate[i1].MapQual){ + | ^~~~~~~ + src/ReadRec.cpp:164:73: error: '__gnu_cxx::__alloc_traits, SingleBamRec_t>::value_type' {aka 'class SingleBamRec_t'} has no member named 'MapQual' + 164 | else if(SecondMate[i].MapQual < SecondMate[i1].MapQual){ + | ^~~~~~~ + In file included from src/main.cpp:7: + src/SingleBamRec.h:32:9: error: 'uint8_t' does not name a type + 32 | uint8_t MapQual; + | ^~~~~~~ + src/SingleBamRec.h:20:1: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + 19 | #include + |#include + 20 | + src/SingleBamRec.h:37:109: error: 'uint8_t' has not been declared + 37 | SingleBamRec_t(int32_t RefID, int32_t RefPos, int32_t ReadPos, int32_t MatchRef, int32_t MatchRead, uint8_t MapQual, bool IsReverse, bool IsFirstRead): + | ^~~~~~~ + src/SingleBamRec.h: In constructor 'SingleBamRec_t::SingleBamRec_t(int32_t, int32_t, int32_t, int32_t, int32_t, int, bool, bool)': + src/SingleBamRec.h:38:107: error: class 'SingleBamRec_t' does not have any field named 'MapQual' + 38 | RefID(RefID), RefPos(RefPos), ReadPos(ReadPos), MatchRef(MatchRef), MatchRead(MatchRead), MapQual(MapQual), IsReverse(IsReverse), IsFirstRead(IsFirstRead){}; + | ^~~~~~~ + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/squid_1734161371272/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/squid_1734161371272/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. diff --git a/recipes/squid/meta.yaml b/recipes/squid/meta.yaml index 655d71f8ccdd7..76e5d69f8e1a2 100644 --- a/recipes/squid/meta.yaml +++ b/recipes/squid/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 8 + number: 9 # Test fails on OSX skip: True # [osx] diff --git a/recipes/squigulator/meta.yaml b/recipes/squigulator/meta.yaml index 087ddfe0ea226..649e5ebbbc27e 100644 --- a/recipes/squigulator/meta.yaml +++ b/recipes/squigulator/meta.yaml @@ -10,7 +10,7 @@ source: sha256: b8c895067308fd950581771c5ad80ce3af10a0264c55476145d0ef0a9d437bb7 build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('squigulator', max_pin="x") }} diff --git a/recipes/squizz/meta.yaml b/recipes/squizz/meta.yaml index 72dee1727b56c..ec33a6a00662d 100644 --- a/recipes/squizz/meta.yaml +++ b/recipes/squizz/meta.yaml @@ -7,7 +7,7 @@ source: md5: 12d9b316a7772911ec3baa2e3f6dda12 build: - number: 7 + number: 8 run_exports: - {{ pin_subpackage('squizz', max_pin="x.x") }} diff --git a/recipes/sracat/meta.yaml b/recipes/sracat/meta.yaml index 6e848c4a21365..df7b66a427cd6 100644 --- a/recipes/sracat/meta.yaml +++ b/recipes/sracat/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 6253b52e0d54cc675647ef66227792d24dde315743c14ea688a038a99277391b build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/srax/meta.yaml b/recipes/srax/meta.yaml index 1f96657a6de41..62c9b55b64721 100644 --- a/recipes/srax/meta.yaml +++ b/recipes/srax/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 noarch: generic source: diff --git a/recipes/srnamapper/meta.yaml b/recipes/srnamapper/meta.yaml index 517d9908d7844..e18fd051d8e5d 100644 --- a/recipes/srnamapper/meta.yaml +++ b/recipes/srnamapper/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} diff --git a/recipes/srprism/meta.yaml b/recipes/srprism/meta.yaml index 3028ca551ce4d..a8f005e817dff 100644 --- a/recipes/srprism/meta.yaml +++ b/recipes/srprism/meta.yaml @@ -12,7 +12,7 @@ source: - srprism-fix-compilation.patch build: - number: 5 + number: 6 skip: true # [osx] run_exports: - {{ pin_subpackage('srprism', max_pin="x") }} @@ -42,4 +42,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ssu-align/meta.yaml b/recipes/ssu-align/meta.yaml index af2f229241afd..49dd535d0a4ef 100644 --- a/recipes/ssu-align/meta.yaml +++ b/recipes/ssu-align/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.1.1" build: - number: 6 + number: 7 source: md5: 1a9684bf52ad1dab62706e0d373d1748 diff --git a/recipes/stacks/1.48/meta.yaml b/recipes/stacks/1.48/meta.yaml index cfb5a69e23fa0..6cbd39842a147 100644 --- a/recipes/stacks/1.48/meta.yaml +++ b/recipes/stacks/1.48/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.48" build: - number: 1 + number: 2 skip: True # [osx] source: diff --git a/recipes/stacks/meta.yaml b/recipes/stacks/meta.yaml index 5779690c098d4..8a01979fcba7b 100644 --- a/recipes/stacks/meta.yaml +++ b/recipes/stacks/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage("stacks", max_pin="x") }} diff --git a/recipes/star/meta.yaml b/recipes/star/meta.yaml index 66c86c4a83880..c996eb6466a80 100644 --- a/recipes/star/meta.yaml +++ b/recipes/star/meta.yaml @@ -16,7 +16,7 @@ source: - patches/0003-create-simd-dispatch.patch build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage('star', max_pin="x") }} diff --git a/recipes/starcode/meta.yaml b/recipes/starcode/meta.yaml index 2d1b57415ccf5..4f0881357510a 100644 --- a/recipes/starcode/meta.yaml +++ b/recipes/starcode/meta.yaml @@ -9,7 +9,7 @@ source: sha256: b4f0eae9498f2dcf9c8a7fa2fa88b141c6d5abcf6da44b03d5d85e5f1a8fd5b1 build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('starcode', max_pin='x.x') }} @@ -30,4 +30,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/stare-abc/meta.yaml b/recipes/stare-abc/meta.yaml index 77d7704286449..6f63bd35b8410 100644 --- a/recipes/stare-abc/meta.yaml +++ b/recipes/stare-abc/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 source: url: https://github.com/SchulzLab/STARE/archive/refs/tags/v{{ version }}.tar.gz diff --git a/recipes/stark/meta.yaml b/recipes/stark/meta.yaml index c58f2f649e7d1..e7c2502847acf 100644 --- a/recipes/stark/meta.yaml +++ b/recipes/stark/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{sha256}}' build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/stereogene/meta.yaml b/recipes/stereogene/meta.yaml index 30ab2577bdf6e..cf7af7e5afb9e 100644 --- a/recipes/stereogene/meta.yaml +++ b/recipes/stereogene/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/strainr2/meta.yaml b/recipes/strainr2/meta.yaml index fb508093f4d78..512f6d4c22513 100644 --- a/recipes/strainr2/meta.yaml +++ b/recipes/strainr2/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 4683de73b3a6cb1c764a0e3adfd92e0eca61aa14dee09e87b9a75af5053e1eb0 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("strainr2", max_pin="x") }} diff --git a/recipes/strainseeker/meta.yaml b/recipes/strainseeker/meta.yaml index 76939360e178f..42df3acc80e96 100644 --- a/recipes/strainseeker/meta.yaml +++ b/recipes/strainseeker/meta.yaml @@ -6,7 +6,7 @@ package: build: skip: True # [osx] - number: 4 + number: 5 source: url: https://github.com/jiangweiyao/StrainSeeker/archive/v{{ version }}.tar.gz diff --git a/recipes/straitrazor/meta.yaml b/recipes/straitrazor/meta.yaml index 4184a963e067d..0ae906979f148 100644 --- a/recipes/straitrazor/meta.yaml +++ b/recipes/straitrazor/meta.yaml @@ -9,7 +9,7 @@ source: sha256: ed05625ebd88525fdb29f294083e51079141a71762fe8c193604f790e88ea2a0 build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/strandphaser/meta.yaml b/recipes/strandphaser/meta.yaml index 6295b478cdec7..ebb36c82a3aaf 100644 --- a/recipes/strandphaser/meta.yaml +++ b/recipes/strandphaser/meta.yaml @@ -9,7 +9,7 @@ source: url: https://github.com/weber8thomas/StrandPhaseR/archive/refs/tags/0.1.2.tar.gz sha256: 0aad3b6e73e63b7cefcda86711eed810244f0bbc89d3be75a5ca07fce1f6ebc6 build: - number: 1 + number: 2 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/strangepg/build_failure.linux-64.yaml b/recipes/strangepg/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..e5528fbf2af6c --- /dev/null +++ b/recipes/strangepg/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 8550254c3342c1d8ad7579e92cf608f03a23608c37a936553f87310d79c50d17 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + summary: Strange pangenome-scale interactive graph visualizer + extra: + container: + extended-base: true + copy_test_source_files: true + final: true + recipe-maintainers: + - qwx9 + + + source tree in: /opt/conda/conda-bld/strangepg_1733951292278/work + export PREFIX=/opt/conda/conda-bld/strangepg_1733951292278/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + export BUILD_PREFIX=/opt/conda/conda-bld/strangepg_1733951292278/_build_env + export SRC_DIR=/opt/conda/conda-bld/strangepg_1733951292278/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strangepg-0.8.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strangepg-0.8.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + export C_INCLUDE_PATH=/opt/conda/conda-bld/strangepg_1733951292278/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include + C_INCLUDE_PATH=/opt/conda/conda-bld/strangepg_1733951292278/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include + export LIBRARY_PATH=/opt/conda/conda-bld/strangepg_1733951292278/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib + LIBRARY_PATH=/opt/conda/conda-bld/strangepg_1733951292278/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib + export 'LDLIBS=-ldl -lpthread' + LDLIBS='-ldl -lpthread' + make CC=/opt/conda/conda-bld/strangepg_1733951292278/_build_env/bin/x86_64-conda-linux-gnu-cc PREFIX=/opt/conda/conda-bld/strangepg_1733951292278/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla -j 4 install + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strangepg-0.8.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c99 -Wall -Wformat=2 -Wunused -Wno-parentheses -Wno-unknown-pragmas -Wno-discarded-qualifiers -Wno-incompatible-pointer-types -Wno-ignored-qualifiers -Wno-unused-result -Wno-unused-function -Wno-unused-value -Wno-format-nonliteral -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -MMD -MP -fextended-identifiers -finput-charset=UTF-8 -pthread -D_XOPEN_SOURCE=500 -DVERSION="\"0.8.15\"" -I. -Icmd -Idraw -Ifs -Igraph -Ilayout -Iposix -Irend -Iui -Iutil -Iunix -DSOKOL_GLCORE -c -o sokol/impl_nuklear.o sokol/impl_nuklear.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strangepg-0.8.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c99 -Wall -Wformat=2 -Wunused -Wno-parentheses -Wno-unknown-pragmas -Wno-discarded-qualifiers -Wno-incompatible-pointer-types -Wno-ignored-qualifiers -Wno-unused-result -Wno-unused-function -Wno-unused-value -Wno-format-nonliteral -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -MMD -MP -fextended-identifiers -finput-charset=UTF-8 -pthread -D_XOPEN_SOURCE=500 -DVERSION="\"0.8.15\"" -I. -Icmd -Idraw -Ifs -Igraph -Ilayout -Iposix -Irend -Iui -Iutil -Iunix -DSOKOL_GLCORE -c -o sokol/impl_sokol_gfx.o sokol/impl_sokol_gfx.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strangepg-0.8.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c99 -Wall -Wformat=2 -Wunused -Wno-parentheses -Wno-unknown-pragmas -Wno-discarded-qualifiers -Wno-incompatible-pointer-types -Wno-ignored-qualifiers -Wno-unused-result -Wno-unused-function -Wno-unused-value -Wno-format-nonliteral -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -MMD -MP -fextended-identifiers -finput-charset=UTF-8 -pthread -D_XOPEN_SOURCE=500 -DVERSION="\"0.8.15\"" -I. -Icmd -Idraw -Ifs -Igraph -Ilayout -Iposix -Irend -Iui -Iutil -Iunix -DSOKOL_GLCORE -c -o sokol/impl_sokol_nuklear.o sokol/impl_sokol_nuklear.c + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strangepg-0.8.15 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c99 -Wall -Wformat=2 -Wunused -Wno-parentheses -Wno-unknown-pragmas -Wno-discarded-qualifiers -Wno-incompatible-pointer-types -Wno-ignored-qualifiers -Wno-unused-result -Wno-unused-function -Wno-unused-value -Wno-format-nonliteral -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -MMD -MP -fextended-identifiers -finput-charset=UTF-8 -pthread -D_XOPEN_SOURCE=500 -DVERSION="\"0.8.15\"" -I. -Icmd -Idraw -Ifs -Igraph -Ilayout -Iposix -Irend -Iui -Iutil -Iunix -DSOKOL_GLCORE -c -o lib/chan.o lib/chan.c + In file included from ./lib/sokol_app.h:2156, + from sokol/impl_sokol_gfx.c:6: + /opt/conda/conda-bld/strangepg_1733951292278/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/include/X11/Xlib.h:44:10: fatal error: X11/X.h: No such file or directory + 44 | #include + | ^~~~~~~~~ + compilation terminated. + make: *** [: sokol/impl_sokol_gfx.o] Error 1 + make: *** Waiting for unfinished jobs.... + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/strangepg_1733951292278/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/strangepg_1733951292278/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/strawc/meta.yaml b/recipes/strawc/meta.yaml index b75ed7b4990ed..40b4f2db2dd69 100644 --- a/recipes/strawc/meta.yaml +++ b/recipes/strawc/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 26d798c98bb8a08011e4c233816f6c76c66605ca09ce068d8f1952532cf22ffc build: - number: 4 + number: 5 skip: True # [py2k] requirements: diff --git a/recipes/strdust/build_failure.linux-64.yaml b/recipes/strdust/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..f695efdace5e2 --- /dev/null +++ b/recipes/strdust/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 829c75a5ed265ff1176bc7a6a801dcdb024390bcbfa574de20026a903ab6c624 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + Compiling textwrap v0.16.1 + Running rustc --crate-name textwrap --edition=2021 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/textwrap-0.16.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "hyphenation", "smawk", "terminal_size", "unicode-linebreak", "unicode-width"))' -C metadata=3ef16993d0e8defd -C extra-filename=-3ef16993d0e8defd --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling mime v0.3.17 + Running rustc --crate-name mime --edition=2015 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/mime-0.3.17/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=7dacb0cee2530301 -C extra-filename=-7dacb0cee2530301 --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling bio v1.6.0 (https://github.com/lorewar2/rust-bio.git?branch=reverse_edge_fix#b1d1200f) + Running rustc --crate-name bio --edition=2018 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/git/checkouts/rust-bio-36f8e3e6afd269e3/b1d1200/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("generic-simd", "pest", "pest_derive", "phylogeny", "runtime-dispatch-simd"))' -C metadata=8241997c3d4dea1c -C extra-filename=-8241997c3d4dea1c --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --extern anyhow=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libanyhow-32037a39fec649c9.rmeta --extern approx=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libapprox-7cdbfa23e11610ef.rmeta --extern bio_types=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libbio_types-b7507957b2ed18a3.rmeta --extern bit_set=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libbit_set-a516bbb668e9f0cf.rmeta --extern bv=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libbv-f960c2c8483da76a.rmeta --extern bytecount=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libbytecount-ad8d4626933a08e3.rmeta --extern csv=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libcsv-33ac457a5269e838.rmeta --extern custom_derive=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libcustom_derive-ecccc4d04962aa0b.rmeta --extern editdistancek=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libeditdistancek-6fa342c35d5dc5e6.rmeta --extern enum_map=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libenum_map-6f38a157d8acad5e.rmeta --extern fxhash=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libfxhash-a7f3791b8c50572a.rmeta --extern itertools=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libitertools-429753b1247df1a7.rmeta --extern itertools_num=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libitertools_num-7892e4ab199724b0.rmeta --extern lazy_static=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblazy_static-07a083f8437cbd0b.rmeta --extern multimap=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libmultimap-7fbfd375ac35e9f6.rmeta --extern ndarray=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libndarray-de11d0564b0978f5.rmeta --extern newtype_derive=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libnewtype_derive-7c266ccf05da133c.rmeta --extern num_integer=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libnum_integer-482246d7cd9475a7.rmeta --extern num_traits=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libnum_traits-45cfdbe14cf49886.rmeta --extern ordered_float=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libordered_float-82885c197b16d9c4.rmeta --extern petgraph=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libpetgraph-801a2f1c2908435a.rmeta --extern rand=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/librand-2fe542ff327cb1d6.rmeta --extern regex=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libregex-175f0b512db8628f.rmeta --extern serde=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libserde-9e47180128a2b30f.rmeta --extern serde_derive=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps/libserde_derive-c5359619a68902d0.so --extern statrs=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libstatrs-e960e6105e0125ae.rmeta --extern strum=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libstrum-87785d75ee7baacf.rmeta --extern strum_macros=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps/libstrum_macros-b85342cacd50d113.so --extern thiserror=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libthiserror-ad9d46709d4ae9ce.rmeta --extern triple_accel=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libtriple_accel-778029a81a95050a.rmeta --extern vec_map=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libvec_map-227f8974a6a36df2.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling clap v3.2.25 + Running rustc --crate-name clap --edition=2021 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/clap-3.2.25/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="atty"' --cfg 'feature="clap_derive"' --cfg 'feature="color"' --cfg 'feature="default"' --cfg 'feature="derive"' --cfg 'feature="once_cell"' --cfg 'feature="std"' --cfg 'feature="strsim"' --cfg 'feature="suggestions"' --cfg 'feature="termcolor"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("atty", "backtrace", "cargo", "clap_derive", "color", "debug", "default", "deprecated", "derive", "env", "once_cell", "regex", "std", "strsim", "suggestions", "termcolor", "terminal_size", "unicase", "unicode", "unstable-doc", "unstable-grouped", "unstable-replace", "unstable-v4", "wrap_help", "yaml", "yaml-rust"))' -C metadata=8d88e05f94c2bbba -C extra-filename=-8d88e05f94c2bbba --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --extern atty=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libatty-09a115fde2d9822a.rmeta --extern bitflags=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libbitflags-74580285d8595b2c.rmeta --extern clap_derive=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps/libclap_derive-15d6bbc01bb4409f.so --extern clap_lex=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libclap_lex-8d6eb80e94003ae1.rmeta --extern indexmap=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libindexmap-ce0ee00cc54ec05a.rmeta --extern once_cell=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libonce_cell-14d214d3f0f6a9a9.rmeta --extern strsim=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libstrsim-82fb0eb1e1c13010.rmeta --extern termcolor=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libtermcolor-ea9563cb28a0b668.rmeta --extern textwrap=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libtextwrap-3ef16993d0e8defd.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling env_logger v0.10.2 + Running rustc --crate-name env_logger --edition=2021 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/env_logger-0.10.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="auto-color"' --cfg 'feature="color"' --cfg 'feature="default"' --cfg 'feature="humantime"' --cfg 'feature="regex"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("auto-color", "color", "default", "humantime", "regex"))' -C metadata=558352ae120f12f7 -C extra-filename=-558352ae120f12f7 --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --extern humantime=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libhumantime-09369e586139ed56.rmeta --extern is_terminal=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libis_terminal-a5ec5d81badfa78e.rmeta --extern log=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblog-22c5f274688aa5f4.rmeta --extern regex=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libregex-175f0b512db8628f.rmeta --extern termcolor=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libtermcolor-ea9563cb28a0b668.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling indicatif v0.17.9 + Running rustc --crate-name indicatif --edition=2021 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/indicatif-0.17.9/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="rayon"' --cfg 'feature="unicode-width"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "futures", "improved_unicode", "in_memory", "rayon", "tokio", "unicode-segmentation", "unicode-width", "vt100"))' -C metadata=e5d8c1e3c646b16e -C extra-filename=-e5d8c1e3c646b16e --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --extern console=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libconsole-e33bc999d6ebb70e.rmeta --extern number_prefix=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libnumber_prefix-f7b3c2dd21ffe761.rmeta --extern portable_atomic=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libportable_atomic-598374a642450149.rmeta --extern rayon=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/librayon-9329ab4e7a5bd8e8.rmeta --extern unicode_width=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libunicode_width-a039cb43434fd123.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling flate2 v1.0.35 + Running rustc --crate-name flate2 --edition=2018 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/flate2-1.0.35/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="any_impl"' --cfg 'feature="default"' --cfg 'feature="miniz_oxide"' --cfg 'feature="rust_backend"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("any_impl", "any_zlib", "cloudflare-zlib-sys", "cloudflare_zlib", "default", "libz-ng-sys", "libz-rs-sys", "libz-sys", "miniz-sys", "miniz_oxide", "rust_backend", "zlib", "zlib-default", "zlib-ng", "zlib-ng-compat", "zlib-rs"))' -C metadata=1e2a6a4dee56cec0 -C extra-filename=-1e2a6a4dee56cec0 --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --extern crc32fast=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libcrc32fast-40eb1f8c57f2c347.rmeta --extern miniz_oxide=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libminiz_oxide-8d5ea91c1a82adbb.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling kodama v0.3.0 + Running rustc --crate-name kodama --edition=2018 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/kodama-0.3.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=6380581581cb6c99 -C extra-filename=-6380581581cb6c99 --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling distance v0.4.0 + Running rustc --crate-name distance --edition=2015 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/distance-0.4.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=c29c926233af6ff8 -C extra-filename=-c29c926233af6ff8 --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling levenshtein v1.0.5 + Running rustc --crate-name levenshtein --edition=2015 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/levenshtein-1.0.5/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=d4c28aae9d004cfc -C extra-filename=-d4c28aae9d004cfc --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Compiling human-sort v0.2.2 + Running rustc --crate-name human_sort --edition=2018 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/human-sort-0.2.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=b61230ea5654109f -C extra-filename=-b61230ea5654109f --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib + Running /opt/conda/conda-bld/strdust_1734154771109/work/target/release/build/curl-sys-942b12692fcaa2f3/build-script-build + Running rustc --crate-name openssl_sys --edition=2021 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/openssl-sys-0.9.104/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="openssl-src"' --cfg 'feature="vendored"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("bindgen", "bssl-sys", "openssl-src", "unstable_boringssl", "vendored"))' -C metadata=eb93056c65be8717 -C extra-filename=-eb93056c65be8717 --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --extern libc=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblibc-7bd17ac07d4e6ce6.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/openssl-sys-e4ac35e281568f45/out/openssl-build/install/lib -l static=ssl -l static=crypto --cfg 'osslconf="OPENSSL_NO_IDEA"' --cfg 'osslconf="OPENSSL_NO_CAMELLIA"' --cfg 'osslconf="OPENSSL_NO_COMP"' --cfg 'osslconf="OPENSSL_NO_SSL3_METHOD"' --cfg 'osslconf="OPENSSL_NO_SEED"' --cfg openssl --cfg ossl340 --cfg ossl330 --cfg ossl320 --cfg ossl300 --cfg ossl101 --cfg ossl102 --cfg ossl102f --cfg ossl102h --cfg ossl110 --cfg ossl110f --cfg ossl110g --cfg ossl110h --cfg ossl111 --cfg ossl111b --cfg ossl111c --cfg ossl111d --check-cfg 'cfg(osslconf, values("OPENSSL_NO_OCB", "OPENSSL_NO_SM4", "OPENSSL_NO_SEED", "OPENSSL_NO_CHACHA", "OPENSSL_NO_CAST", "OPENSSL_NO_IDEA", "OPENSSL_NO_CAMELLIA", "OPENSSL_NO_RC4", "OPENSSL_NO_BF", "OPENSSL_NO_PSK", "OPENSSL_NO_DEPRECATED_3_0", "OPENSSL_NO_SCRYPT", "OPENSSL_NO_SM3", "OPENSSL_NO_RMD160", "OPENSSL_NO_EC2M", "OPENSSL_NO_OCSP", "OPENSSL_NO_CMS", "OPENSSL_NO_COMP", "OPENSSL_NO_SOCK", "OPENSSL_NO_STDIO", "OPENSSL_NO_EC", "OPENSSL_NO_SSL3_METHOD", "OPENSSL_NO_KRB5", "OPENSSL_NO_TLSEXT", "OPENSSL_NO_SRP", "OPENSSL_NO_RFC3779", "OPENSSL_NO_SHA", "OPENSSL_NO_NEXTPROTONEG", "OPENSSL_NO_ENGINE", "OPENSSL_NO_BUF_FREELISTS"))' --check-cfg 'cfg(openssl)' --check-cfg 'cfg(libressl)' --check-cfg 'cfg(boringssl)' --check-cfg 'cfg(libressl250)' --check-cfg 'cfg(libressl251)' --check-cfg 'cfg(libressl252)' --check-cfg 'cfg(libressl261)' --check-cfg 'cfg(libressl270)' --check-cfg 'cfg(libressl271)' --check-cfg 'cfg(libressl273)' --check-cfg 'cfg(libressl280)' --check-cfg 'cfg(libressl281)' --check-cfg 'cfg(libressl291)' --check-cfg 'cfg(libressl310)' --check-cfg 'cfg(libressl321)' --check-cfg 'cfg(libressl332)' --check-cfg 'cfg(libressl340)' --check-cfg 'cfg(libressl350)' --check-cfg 'cfg(libressl360)' --check-cfg 'cfg(libressl361)' --check-cfg 'cfg(libressl370)' --check-cfg 'cfg(libressl380)' --check-cfg 'cfg(libressl381)' --check-cfg 'cfg(libressl382)' --check-cfg 'cfg(libressl390)' --check-cfg 'cfg(libressl400)' --check-cfg 'cfg(ossl101)' --check-cfg 'cfg(ossl102)' --check-cfg 'cfg(ossl102f)' --check-cfg 'cfg(ossl102h)' --check-cfg 'cfg(ossl110)' --check-cfg 'cfg(ossl110f)' --check-cfg 'cfg(ossl110g)' --check-cfg 'cfg(ossl110h)' --check-cfg 'cfg(ossl111)' --check-cfg 'cfg(ossl111b)' --check-cfg 'cfg(ossl111c)' --check-cfg 'cfg(ossl111d)' --check-cfg 'cfg(ossl300)' --check-cfg 'cfg(ossl310)' --check-cfg 'cfg(ossl320)' --check-cfg 'cfg(ossl330)' --check-cfg 'cfg(ossl340)' + Running /opt/conda/conda-bld/strdust_1734154771109/work/target/release/build/native-tls-8110408745cb9574/build-script-build + Running /opt/conda/conda-bld/strdust_1734154771109/work/target/release/build/openssl-162b2add0efa118b/build-script-build + Running rustc --crate-name openssl --edition=2021 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/openssl-0.10.68/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("bindgen", "default", "unstable_boringssl", "v101", "v102", "v110", "v111", "vendored"))' -C metadata=6cf6e30a1d0d6db7 -C extra-filename=-6cf6e30a1d0d6db7 --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --extern bitflags=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libbitflags-dd0b9d091b5db6f4.rmeta --extern cfg_if=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libcfg_if-cc1a207a177f0d2d.rmeta --extern foreign_types=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libforeign_types-e5e5612fae1a6ea5.rmeta --extern libc=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblibc-7bd17ac07d4e6ce6.rmeta --extern once_cell=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libonce_cell-14d214d3f0f6a9a9.rmeta --extern openssl_macros=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps/libopenssl_macros-5d52776c30e13744.so --extern ffi=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libopenssl_sys-eb93056c65be8717.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/openssl-sys-e4ac35e281568f45/out/openssl-build/install/lib --cfg 'osslconf="OPENSSL_NO_IDEA"' --cfg 'osslconf="OPENSSL_NO_CAMELLIA"' --cfg 'osslconf="OPENSSL_NO_COMP"' --cfg 'osslconf="OPENSSL_NO_SSL3_METHOD"' --cfg 'osslconf="OPENSSL_NO_SEED"' --cfg ossl101 --cfg ossl102 --cfg ossl110 --cfg ossl110g --cfg ossl110h --cfg ossl111 --cfg ossl111d --cfg ossl300 --cfg ossl310 --cfg ossl320 --cfg ossl330 --check-cfg 'cfg(osslconf, values("OPENSSL_NO_OCB", "OPENSSL_NO_SM4", "OPENSSL_NO_SEED", "OPENSSL_NO_CHACHA", "OPENSSL_NO_CAST", "OPENSSL_NO_IDEA", "OPENSSL_NO_CAMELLIA", "OPENSSL_NO_RC4", "OPENSSL_NO_BF", "OPENSSL_NO_PSK", "OPENSSL_NO_DEPRECATED_3_0", "OPENSSL_NO_SCRYPT", "OPENSSL_NO_SM3", "OPENSSL_NO_RMD160", "OPENSSL_NO_EC2M", "OPENSSL_NO_OCSP", "OPENSSL_NO_CMS", "OPENSSL_NO_EC", "OPENSSL_NO_ARGON2"))' --check-cfg 'cfg(libressl)' --check-cfg 'cfg(boringssl)' --check-cfg 'cfg(libressl250)' --check-cfg 'cfg(libressl251)' --check-cfg 'cfg(libressl261)' --check-cfg 'cfg(libressl270)' --check-cfg 'cfg(libressl271)' --check-cfg 'cfg(libressl273)' --check-cfg 'cfg(libressl280)' --check-cfg 'cfg(libressl291)' --check-cfg 'cfg(libressl310)' --check-cfg 'cfg(libressl321)' --check-cfg 'cfg(libressl332)' --check-cfg 'cfg(libressl340)' --check-cfg 'cfg(libressl350)' --check-cfg 'cfg(libressl360)' --check-cfg 'cfg(libressl361)' --check-cfg 'cfg(libressl370)' --check-cfg 'cfg(libressl380)' --check-cfg 'cfg(libressl382)' --check-cfg 'cfg(libressl390)' --check-cfg 'cfg(libressl400)' --check-cfg 'cfg(ossl101)' --check-cfg 'cfg(ossl102)' --check-cfg 'cfg(ossl110)' --check-cfg 'cfg(ossl110g)' --check-cfg 'cfg(ossl110h)' --check-cfg 'cfg(ossl111)' --check-cfg 'cfg(ossl111d)' --check-cfg 'cfg(ossl300)' --check-cfg 'cfg(ossl310)' --check-cfg 'cfg(ossl320)' --check-cfg 'cfg(ossl330)' + Running rustc --crate-name native_tls --edition=2015 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/native-tls-0.2.12/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alpn", "vendored"))' -C metadata=bea7b0cb621eb7a6 -C extra-filename=-bea7b0cb621eb7a6 --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --extern log=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblog-22c5f274688aa5f4.rmeta --extern openssl=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libopenssl-6cf6e30a1d0d6db7.rmeta --extern openssl_probe=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libopenssl_probe-ec6b75a73933da86.rmeta --extern openssl_sys=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libopenssl_sys-eb93056c65be8717.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/openssl-sys-e4ac35e281568f45/out/openssl-build/install/lib --cfg have_min_max_version + Compiling tokio-native-tls v0.3.1 + Running rustc --crate-name tokio_native_tls --edition=2018 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/tokio-native-tls-0.3.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("vendored"))' -C metadata=e092cda1052fdcad -C extra-filename=-e092cda1052fdcad --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --extern native_tls=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libnative_tls-bea7b0cb621eb7a6.rmeta --extern tokio=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libtokio-368a0fb7a55617c4.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/openssl-sys-e4ac35e281568f45/out/openssl-build/install/lib + Compiling hyper-tls v0.5.0 + Running rustc --crate-name hyper_tls --edition=2018 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/hyper-tls-0.5.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("vendored"))' -C metadata=9b08061cfe7425db -C extra-filename=-9b08061cfe7425db --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --extern bytes=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libbytes-a13d0d504cd35641.rmeta --extern hyper=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libhyper-6ba483352cc5aa54.rmeta --extern native_tls=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libnative_tls-bea7b0cb621eb7a6.rmeta --extern tokio=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libtokio-368a0fb7a55617c4.rmeta --extern tokio_native_tls=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libtokio_native_tls-e092cda1052fdcad.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/openssl-sys-e4ac35e281568f45/out/openssl-build/install/lib + Compiling reqwest v0.11.27 + Running rustc --crate-name reqwest --edition=2021 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/reqwest-0.11.27/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="__tls"' --cfg 'feature="blocking"' --cfg 'feature="default"' --cfg 'feature="default-tls"' --cfg 'feature="hyper-tls"' --cfg 'feature="json"' --cfg 'feature="native-tls-crate"' --cfg 'feature="serde_json"' --cfg 'feature="tokio-native-tls"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("__internal_proxy_sys_no_cache", "__rustls", "__tls", "async-compression", "blocking", "brotli", "cookie_crate", "cookie_store", "cookies", "default", "default-tls", "deflate", "futures-channel", "gzip", "h3", "h3-quinn", "hickory-dns", "hickory-resolver", "http3", "hyper-rustls", "hyper-tls", "json", "mime_guess", "multipart", "native-tls", "native-tls-alpn", "native-tls-crate", "native-tls-vendored", "quinn", "rustls", "rustls-native-certs", "rustls-tls", "rustls-tls-manual-roots", "rustls-tls-native-roots", "rustls-tls-webpki-roots", "serde_json", "socks", "stream", "tokio-native-tls", "tokio-rustls", "tokio-socks", "tokio-util", "trust-dns", "wasm-streams", "webpki-roots"))' -C metadata=b6a35bbacbb97ac8 -C extra-filename=-b6a35bbacbb97ac8 --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --extern base64=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libbase64-861599a43daab6e5.rmeta --extern bytes=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libbytes-a13d0d504cd35641.rmeta --extern encoding_rs=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libencoding_rs-44b557b698cf57da.rmeta --extern futures_core=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libfutures_core-90a74a61ee048f5d.rmeta --extern futures_util=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libfutures_util-38289e698dd5077a.rmeta --extern h2=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libh2-fdfe8b98234c18fc.rmeta --extern http=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libhttp-d3455ff773f3f688.rmeta --extern http_body=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libhttp_body-d6ec5822c01e74dd.rmeta --extern hyper=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libhyper-6ba483352cc5aa54.rmeta --extern hyper_tls=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libhyper_tls-9b08061cfe7425db.rmeta --extern ipnet=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libipnet-59581f7c46bfe7ec.rmeta --extern log=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblog-22c5f274688aa5f4.rmeta --extern mime=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libmime-7dacb0cee2530301.rmeta --extern native_tls_crate=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libnative_tls-bea7b0cb621eb7a6.rmeta --extern once_cell=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libonce_cell-14d214d3f0f6a9a9.rmeta --extern percent_encoding=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libpercent_encoding-bbd2139eab00235e.rmeta --extern pin_project_lite=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libpin_project_lite-77b5986db0d59e3c.rmeta --extern rustls_pemfile=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/librustls_pemfile-8d43ca3e054418ad.rmeta --extern serde=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libserde-9e47180128a2b30f.rmeta --extern serde_json=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libserde_json-f7d9b449b9d6253a.rmeta --extern serde_urlencoded=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libserde_urlencoded-2d465541765abc4d.rmeta --extern sync_wrapper=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libsync_wrapper-624197e59a6a100a.rmeta --extern tokio=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libtokio-368a0fb7a55617c4.rmeta --extern tokio_native_tls=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libtokio_native_tls-e092cda1052fdcad.rmeta --extern tower_service=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libtower_service-e81f1287057cdddb.rmeta --extern url=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liburl-1f7b200e2e72bd4d.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/openssl-sys-e4ac35e281568f45/out/openssl-build/install/lib + Running /opt/conda/conda-bld/strdust_1734154771109/work/target/release/build/hts-sys-bbbce45dec53f53a/build-script-build + Running rustc --crate-name curl_sys --edition=2018 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/curl-sys-0.4.78curl-8.11.0/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="openssl-sys"' --cfg 'feature="protocol-ftp"' --cfg 'feature="ssl"' --cfg 'feature="static-curl"' --cfg 'feature="static-ssl"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "force-system-lib-on-osx", "http2", "libnghttp2-sys", "mesalink", "ntlm", "openssl-sys", "poll_7_68_0", "protocol-ftp", "rustls", "rustls-ffi", "spnego", "ssl", "static-curl", "static-ssl", "upkeep_7_62_0", "windows-static-ssl", "zlib-ng-compat"))' -C metadata=8ec6bd19dc0ea844 -C extra-filename=-8ec6bd19dc0ea844 --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --extern libc=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblibc-7bd17ac07d4e6ce6.rmeta --extern libz_sys=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblibz_sys-5228cf1da53c15c5.rmeta --extern openssl_sys=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libopenssl_sys-eb93056c65be8717.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/curl-sys-61f74625c6ee7558/out/build -l static=curl -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/libz-sys-30a8bb598d5f1016/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/libz-sys-30a8bb598d5f1016/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/openssl-sys-e4ac35e281568f45/out/openssl-build/install/lib --cfg libcurl_vendored --cfg link_libz --cfg link_openssl --check-cfg 'cfg(libcurl_vendored,link_libnghttp2,link_libz,link_openssl,)' + Running rustc --crate-name hts_sys --edition=2018 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/hts-sys-2.2.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="bindgen"' --cfg 'feature="bzip2"' --cfg 'feature="bzip2-sys"' --cfg 'feature="curl"' --cfg 'feature="curl-sys"' --cfg 'feature="default"' --cfg 'feature="lzma"' --cfg 'feature="lzma-sys"' --cfg 'feature="openssl-sys"' --cfg 'feature="s3"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("bindgen", "bzip2", "bzip2-sys", "curl", "curl-sys", "default", "gcs", "libdeflate", "libdeflate-sys", "lzma", "lzma-sys", "openssl-sys", "s3", "static"))' -C metadata=71ed382d55756548 -C extra-filename=-71ed382d55756548 --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --extern bzip2_sys=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libbzip2_sys-586cadb07e7a0eb5.rmeta --extern curl_sys=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libcurl_sys-8ec6bd19dc0ea844.rmeta --extern libz_sys=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblibz_sys-5228cf1da53c15c5.rmeta --extern lzma_sys=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblzma_sys-5978823c44b81597.rmeta --extern openssl_sys=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libopenssl_sys-eb93056c65be8717.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/hts-sys-2921470619e56370/out -l static=hts -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/bzip2-sys-8276af43f608c1dd/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/curl-sys-61f74625c6ee7558/out/build -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/libz-sys-30a8bb598d5f1016/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/libz-sys-30a8bb598d5f1016/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/openssl-sys-e4ac35e281568f45/out/openssl-build/install/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/lzma-sys-3d13704f41d19588/out + Compiling rust-htslib v0.48.0 + Compiling rust-htslib v0.47.1 + Running rustc --crate-name rust_htslib --edition=2018 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/rust-htslib-0.48.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("bindgen", "bzip2", "curl", "default", "gcs", "libdeflate", "lzma", "s3", "serde", "serde_bytes", "serde_feature", "static"))' -C metadata=406624753277a27c -C extra-filename=-406624753277a27c --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --extern bio_types=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libbio_types-b7507957b2ed18a3.rmeta --extern byteorder=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libbyteorder-9d499ed7215ae9be.rmeta --extern custom_derive=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libcustom_derive-ecccc4d04962aa0b.rmeta --extern derive_new=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps/libderive_new-bf41873be31b3a79.so --extern hts_sys=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libhts_sys-71ed382d55756548.rmeta --extern ieee754=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libieee754-c1f63ff7e4e0eabd.rmeta --extern lazy_static=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblazy_static-07a083f8437cbd0b.rmeta --extern libc=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblibc-7bd17ac07d4e6ce6.rmeta --extern libz_sys=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblibz_sys-5228cf1da53c15c5.rmeta --extern linear_map=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblinear_map-1c459daed1e677d6.rmeta --extern newtype_derive=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libnewtype_derive-7c266ccf05da133c.rmeta --extern regex=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libregex-175f0b512db8628f.rmeta --extern thiserror=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libthiserror-edc3cabaf50344c7.rmeta --extern url=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liburl-1f7b200e2e72bd4d.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/hts-sys-2921470619e56370/out -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/bzip2-sys-8276af43f608c1dd/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/curl-sys-61f74625c6ee7558/out/build -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/libz-sys-30a8bb598d5f1016/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/libz-sys-30a8bb598d5f1016/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/openssl-sys-e4ac35e281568f45/out/openssl-build/install/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/lzma-sys-3d13704f41d19588/out + Running rustc --crate-name rust_htslib --edition=2018 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/rust-htslib-0.47.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="bzip2"' --cfg 'feature="curl"' --cfg 'feature="default"' --cfg 'feature="lzma"' --cfg 'feature="s3"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("bindgen", "bzip2", "curl", "default", "gcs", "libdeflate", "lzma", "s3", "serde", "serde_bytes", "serde_feature", "static"))' -C metadata=fbf85506c544d1a0 -C extra-filename=-fbf85506c544d1a0 --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --extern bio_types=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libbio_types-b7507957b2ed18a3.rmeta --extern byteorder=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libbyteorder-9d499ed7215ae9be.rmeta --extern custom_derive=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libcustom_derive-ecccc4d04962aa0b.rmeta --extern derive_new=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps/libderive_new-0fdff38e84213abc.so --extern hts_sys=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libhts_sys-71ed382d55756548.rmeta --extern ieee754=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libieee754-c1f63ff7e4e0eabd.rmeta --extern lazy_static=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblazy_static-07a083f8437cbd0b.rmeta --extern libc=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblibc-7bd17ac07d4e6ce6.rmeta --extern libz_sys=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblibz_sys-5228cf1da53c15c5.rmeta --extern linear_map=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblinear_map-1c459daed1e677d6.rmeta --extern newtype_derive=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libnewtype_derive-7c266ccf05da133c.rmeta --extern regex=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libregex-175f0b512db8628f.rmeta --extern thiserror=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libthiserror-ad9d46709d4ae9ce.rmeta --extern url=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liburl-1f7b200e2e72bd4d.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/hts-sys-2921470619e56370/out -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/bzip2-sys-8276af43f608c1dd/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/curl-sys-61f74625c6ee7558/out/build -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/libz-sys-30a8bb598d5f1016/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/libz-sys-30a8bb598d5f1016/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/openssl-sys-e4ac35e281568f45/out/openssl-build/install/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/lzma-sys-3d13704f41d19588/out + Compiling minimap2 v0.1.22minimap2.2.28 + Running rustc --crate-name minimap2 --edition=2021 /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/minimap2-0.1.22minimap2.2.28/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="htslib"' --cfg 'feature="map-file"' --cfg 'feature="needletail"' --cfg 'feature="rust-htslib"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("curl", "default", "htslib", "map-file", "needletail", "rust-htslib", "simde", "sse2only", "static", "zlib-ng"))' -C metadata=16d4c4dc93cd04c9 -C extra-filename=-16d4c4dc93cd04c9 --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --extern libc=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblibc-7bd17ac07d4e6ce6.rmeta --extern minimap2_sys=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libminimap2_sys-885310bc672de7c6.rlib --extern needletail=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libneedletail-9bfff014e530a6ba.rlib --extern rust_htslib=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/librust_htslib-406624753277a27c.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/libz-sys-30a8bb598d5f1016/out -L native=/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/minimap2-sys-e0b0536bd54c5ee5/out -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/libz-sys-30a8bb598d5f1016/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/libz-sys-30a8bb598d5f1016/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/hts-sys-2921470619e56370/out -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/bzip2-sys-8276af43f608c1dd/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/curl-sys-61f74625c6ee7558/out/build -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/openssl-sys-e4ac35e281568f45/out/openssl-build/install/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/lzma-sys-3d13704f41d19588/out + Compiling STRdust v0.8.2 (/opt/conda/conda-bld/strdust_1734154771109/work) + Running rustc --crate-name STRdust --edition=2021 src/main.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=25553ca2234574a1 -C extra-filename=-25553ca2234574a1 --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --extern bio=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libbio-8241997c3d4dea1c.rlib --extern clap=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libclap-8d88e05f94c2bbba.rlib --extern distance=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libdistance-c29c926233af6ff8.rlib --extern env_logger=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libenv_logger-558352ae120f12f7.rlib --extern flate2=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libflate2-1e2a6a4dee56cec0.rlib --extern hts_sys=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libhts_sys-71ed382d55756548.rlib --extern human_sort=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libhuman_sort-b61230ea5654109f.rlib --extern indicatif=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libindicatif-e5d8c1e3c646b16e.rlib --extern kodama=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libkodama-6380581581cb6c99.rlib --extern levenshtein=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblevenshtein-d4c28aae9d004cfc.rlib --extern libc=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblibc-7bd17ac07d4e6ce6.rlib --extern libz_sys=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblibz_sys-5228cf1da53c15c5.rlib --extern log=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblog-22c5f274688aa5f4.rlib --extern minimap2=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libminimap2-16d4c4dc93cd04c9.rlib --extern petgraph=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libpetgraph-801a2f1c2908435a.rlib --extern rand=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/librand-2fe542ff327cb1d6.rlib --extern rayon=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/librayon-9329ab4e7a5bd8e8.rlib --extern regex=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libregex-175f0b512db8628f.rlib --extern reqwest=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libreqwest-b6a35bbacbb97ac8.rlib --extern rust_htslib=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/librust_htslib-fbf85506c544d1a0.rlib --extern url=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liburl-1f7b200e2e72bd4d.rlib -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/hts-sys-2921470619e56370/out -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/bzip2-sys-8276af43f608c1dd/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/curl-sys-61f74625c6ee7558/out/build -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/libz-sys-30a8bb598d5f1016/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/libz-sys-30a8bb598d5f1016/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/openssl-sys-e4ac35e281568f45/out/openssl-build/install/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/lzma-sys-3d13704f41d19588/out -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/libz-sys-30a8bb598d5f1016/out -L native=/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/minimap2-sys-e0b0536bd54c5ee5/out + error[E0107]: missing generics for struct minimap2::Aligner + --> src/genotype.rs:226:15 + | + 226 | aligner: &Aligner, + | ^^^^^^^ expected 1 generic argument + | + note: struct defined here, with 1 generic parameter: S + --> /opt/conda/conda-bld/strdust_1734154771109/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/minimap2-0.1.22minimap2.2.28/src/lib.rs:300:12 + | + 300 | pub struct Aligner { + | ^^^^^^^ - + help: add missing generic argument + | + 226 | aligner: &Aligner, + | + + warning: unused variable: seq + --> src/motif.rs:4:17 + | + 4 | fn create_motif(seq: &str) -> String { + | ^^^ help: if this is intentional, prefix it with an underscore: _seq + | + = note: #[warn(unused_variables)] on by default + + For more information about this error, try rustc --explain E0107. + warning: STRdust (bin "STRdust") generated 1 warning + error: could not compile STRdust (bin "STRdust") due to 1 previous error; 1 warning emitted + + Caused by: + process didn't exit successfully: rustc --crate-name STRdust --edition=2021 src/main.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=25553ca2234574a1 -C extra-filename=-25553ca2234574a1 --out-dir /opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/strdust_1734154771109/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/strdust_1734154771109/work/target/release/deps --extern bio=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libbio-8241997c3d4dea1c.rlib --extern clap=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libclap-8d88e05f94c2bbba.rlib --extern distance=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libdistance-c29c926233af6ff8.rlib --extern env_logger=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libenv_logger-558352ae120f12f7.rlib --extern flate2=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libflate2-1e2a6a4dee56cec0.rlib --extern hts_sys=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libhts_sys-71ed382d55756548.rlib --extern human_sort=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libhuman_sort-b61230ea5654109f.rlib --extern indicatif=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libindicatif-e5d8c1e3c646b16e.rlib --extern kodama=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libkodama-6380581581cb6c99.rlib --extern levenshtein=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblevenshtein-d4c28aae9d004cfc.rlib --extern libc=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblibc-7bd17ac07d4e6ce6.rlib --extern libz_sys=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblibz_sys-5228cf1da53c15c5.rlib --extern log=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liblog-22c5f274688aa5f4.rlib --extern minimap2=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libminimap2-16d4c4dc93cd04c9.rlib --extern petgraph=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libpetgraph-801a2f1c2908435a.rlib --extern rand=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/librand-2fe542ff327cb1d6.rlib --extern rayon=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/librayon-9329ab4e7a5bd8e8.rlib --extern regex=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libregex-175f0b512db8628f.rlib --extern reqwest=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/libreqwest-b6a35bbacbb97ac8.rlib --extern rust_htslib=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/librust_htslib-fbf85506c544d1a0.rlib --extern url=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/deps/liburl-1f7b200e2e72bd4d.rlib -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/hts-sys-2921470619e56370/out -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/bzip2-sys-8276af43f608c1dd/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/curl-sys-61f74625c6ee7558/out/build -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/libz-sys-30a8bb598d5f1016/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/libz-sys-30a8bb598d5f1016/out/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/openssl-sys-e4ac35e281568f45/out/openssl-build/install/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/lzma-sys-3d13704f41d19588/out -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/libz-sys-30a8bb598d5f1016/out -L native=/opt/conda/conda-bld/strdust_1734154771109/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib -L native=/opt/conda/conda-bld/strdust_1734154771109/work/target/x86_64-unknown-linux-gnu/release/build/minimap2-sys-e0b0536bd54c5ee5/out (exit status: 1) + error: failed to compile STRdust v0.8.2 (/opt/conda/conda-bld/strdust_1734154771109/work), intermediate artifacts can be found at /opt/conda/conda-bld/strdust_1734154771109/work/target. + To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/strdust_1734154771109/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/strdust_1734154771109/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. diff --git a/recipes/strdust/build_failure.osx-64.yaml b/recipes/strdust/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..ce2bf8b6273ac --- /dev/null +++ b/recipes/strdust/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 829c75a5ed265ff1176bc7a6a801dcdb024390bcbfa574de20026a903ab6c624 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - liblzma 5.6.3 hd471939_1 + - libzlib 1.3.1 hd23fc13_2 + - libcxx-devel 19.1.5 h7c275be_0 + - libxml2 2.13.5 he8ee3e7_1 + - zlib 1.3.1 hd23fc13_2 + - zstd 1.5.6 h915ae27_0 + - libllvm19 19.1.5 hc29ff6c_0 + - libclang-cpp19.1 19.1.5 default_h3571c67_0 + - libclang13 19.1.5 default_hf2b7afa_0 + - llvm-tools-19 19.1.5 he90a8e3_0 + - clang-19 19.1.5 default_h3571c67_0 + - clang-format-19 19.1.5 default_h3571c67_0 + - libclang 19.1.5 default_h3571c67_0 + - libclang-cpp 19.1.5 default_h3571c67_0 + - llvm-tools 19.1.5 h3fe3016_0 + - clang 19.1.5 default_h576c50e_0 + raise BuildScriptException(str(exc), caused_by=exc) from exc + - clang-format 19.1.5 default_h3571c67_0 + - llvmdev 19.1.5 he90a8e3_0 + - clang-tools 19.1.5 default_h3571c67_0 + - clangxx 19.1.5 default_heb2e8d1_0 + - clangdev 19.1.5 default_h3571c67_0 + run: + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/strdust_1733986420771/work/conda_build.sh']' returned non-zero exit status 101. + - libcxx >=18 + - libzlib >=1.3.1,<2.0a0 + run_constrained: + - __osx >=10.13 + test: + commands: + - STRdust --help + about: + dev_url: https://github.com/wdecoster/STRdust + doc_url: https://github.com/wdecoster/STRdust/blob/v0.8.2/README.md + home: https://github.com/wdecoster/STRdust + license: MIT + license_family: MIT + license_file: LICENSE + summary: Tandem repeat genotyper for long reads. + extra: + additional-platforms: + - osx-arm64 + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/strdust_1733986420771/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/strdust_1733986420771/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/strdust_1733986420771/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/strdust_1733986420771/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strdust-0.8.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strdust-0.8.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strdust-0.8.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strdust-0.8.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix +# Last 100 lines of the build log. diff --git a/recipes/strdust/build_failure.osx-arm64.yaml b/recipes/strdust/build_failure.osx-arm64.yaml new file mode 100644 index 0000000000000..47a3947231f3e --- /dev/null +++ b/recipes/strdust/build_failure.osx-arm64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 829c75a5ed265ff1176bc7a6a801dcdb024390bcbfa574de20026a903ab6c624 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - llvm-tools 19.1.5 hd2aecb6_0 + - clang 19.1.5 default_h474c9e2_0 + - clang-format 19.1.5 default_hf90f093_0 + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/strdust_1733864211721/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + - llvmdev 19.1.5 h87a4c7e_0 + - clang-tools 19.1.5 default_hf90f093_0 + Traceback (most recent call last): + - clangxx 19.1.5 default_h1ffe849_0 + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + - clangdev 19.1.5 default_hf90f093_0 + run: + - libzlib >=1.3.1,<2.0a0 + sys.exit(execute()) + - libcxx >=18 + run_constrained: + - __osx >=11.0 + test: + commands: + - STRdust --help + about: + dev_url: https://github.com/wdecoster/STRdust + doc_url: https://github.com/wdecoster/STRdust/blob/v0.8.2/README.md + home: https://github.com/wdecoster/STRdust + license: MIT + license_family: MIT + license_file: LICENSE + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + summary: Tandem repeat genotyper for long reads. + extra: + additional-platforms: + - osx-arm64 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/strdust_1733864211721/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/strdust_1733864211721/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/strdust_1733864211721/_build_env + raise BuildScriptException(str(exc), caused_by=exc) from exc + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/strdust_1733864211721/work + INFO: activate_clang_osx-arm64.sh made the following environmental changes: + AR=arm64-apple-darwin20.0.0-ar + AS=arm64-apple-darwin20.0.0-as + CC=arm64-apple-darwin20.0.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang + CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strdust-0.8.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=arm64-apple-darwin20.0.0-checksyms + CLANG=arm64-apple-darwin20.0.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=11.0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=arm64-apple-darwin20.0.0 + CONDA_TOOLCHAIN_HOST=arm64-apple-darwin20.0.0 + CPP=arm64-apple-darwin20.0.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang-cpp + DEBUG_CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strdust-0.8.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=arm64-apple-darwin20.0.0 + INSTALL_NAME_TOOL=arm64-apple-darwin20.0.0-install_name_tool + LD=arm64-apple-darwin20.0.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=arm64-apple-darwin20.0.0-libtool + LIPO=arm64-apple-darwin20.0.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=arm64-apple-darwin20.0.0-nm + NMEDIT=arm64-apple-darwin20.0.0-nmedit + OBJC=arm64-apple-darwin20.0.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang + OTOOL=arm64-apple-darwin20.0.0-otool + PAGESTUFF=arm64-apple-darwin20.0.0-pagestuff + RANLIB=arm64-apple-darwin20.0.0-ranlib + REDO_PREBINDING=arm64-apple-darwin20.0.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk + SEGEDIT=arm64-apple-darwin20.0.0-segedit + SEG_ADDR_TABLE=arm64-apple-darwin20.0.0-seg_addr_table + SEG_HACK=arm64-apple-darwin20.0.0-seg_hack + SIZE=arm64-apple-darwin20.0.0-size + STRINGS=arm64-apple-darwin20.0.0-strings + STRIP=arm64-apple-darwin20.0.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_arm64_apple_darwin20_0_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=arm64-apple-darwin20.0.0 + host_alias=arm64-apple-darwin20.0.0 + INFO: activate_clangxx_osx-arm64.sh made the following environmental changes: + CLANGXX=arm64-apple-darwin20.0.0-clang + CXX=arm64-apple-darwin20.0.0-clang + CXXFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strdust-0.8.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang + DEBUG_CXXFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strdust-0.8.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/strdust_1733864211721/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. diff --git a/recipes/strdust/meta.yaml b/recipes/strdust/meta.yaml index e4f6df68ce9c7..46af07aa74adf 100644 --- a/recipes/strdust/meta.yaml +++ b/recipes/strdust/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 4fd97b05b22870c70a9d41dbcb2f106836f009e3db39bce47921ab6aa9bff100 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('strdust', max_pin="x.x") }} diff --git a/recipes/strike/meta.yaml b/recipes/strike/meta.yaml index 05d3142487db6..1b7783b97eca9 100644 --- a/recipes/strike/meta.yaml +++ b/recipes/strike/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.2 build: - number: 5 + number: 6 skip: True # [osx] source: diff --git a/recipes/stringdecomposer/meta.yaml b/recipes/stringdecomposer/meta.yaml index d09170d075bd7..f6417f644a901 100644 --- a/recipes/stringdecomposer/meta.yaml +++ b/recipes/stringdecomposer/meta.yaml @@ -10,7 +10,7 @@ source: build: skip: True # [py27 or osx] - number: 3 + number: 4 script: {{ PYTHON }} -m pip install . -vv --ignore-installed --no-deps # script: make install PREFIX=${PREFIX} diff --git a/recipes/strobealign/meta.yaml b/recipes/strobealign/meta.yaml index b5830372f63ab..38c7320e22093 100644 --- a/recipes/strobealign/meta.yaml +++ b/recipes/strobealign/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("strobealign", max_pin="x.x") }} diff --git a/recipes/strobemap/meta.yaml b/recipes/strobemap/meta.yaml index a921b8a95c272..6b2af76334630 100644 --- a/recipes/strobemap/meta.yaml +++ b/recipes/strobemap/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 requirements: build: diff --git a/recipes/structure/meta.yaml b/recipes/structure/meta.yaml index 6346d2a2e6495..82857e3662be7 100644 --- a/recipes/structure/meta.yaml +++ b/recipes/structure/meta.yaml @@ -9,7 +9,7 @@ source: md5: 4e0591678cdbfe79347d272b5dceeda1 build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/sts-smctc/meta.yaml b/recipes/sts-smctc/meta.yaml index 3cb31c809a874..528d43f4ba1e8 100644 --- a/recipes/sts-smctc/meta.yaml +++ b/recipes/sts-smctc/meta.yaml @@ -6,7 +6,7 @@ package: build: skip: True # [osx] - number: 11 + number: 12 run_exports: - {{ pin_subpackage('sts-smctc', max_pin='x.x') }} diff --git a/recipes/suma_package/meta.yaml b/recipes/suma_package/meta.yaml index fea29b5aecb08..a9a1bbd916a5b 100644 --- a/recipes/suma_package/meta.yaml +++ b/recipes/suma_package/meta.yaml @@ -9,7 +9,7 @@ source: md5: e528493d05225a605adacd0961b8f50c build: - number: 7 + number: 8 skip: True # [not linux] requirements: diff --git a/recipes/sumaclust/meta.yaml b/recipes/sumaclust/meta.yaml index d151d58a14129..79e21c0f31a03 100644 --- a/recipes/sumaclust/meta.yaml +++ b/recipes/sumaclust/meta.yaml @@ -9,7 +9,7 @@ source: sha256: a7c122ff90671d8589deb05a1a8b008e8f439103bb0b7eca48c3d6da205cf2f2 build: - number: 6 + number: 7 skip: True # [osx] requirements: diff --git a/recipes/super_distance/meta.yaml b/recipes/super_distance/meta.yaml index bbca26a999302..822c9d9a64bf9 100644 --- a/recipes/super_distance/meta.yaml +++ b/recipes/super_distance/meta.yaml @@ -11,7 +11,7 @@ source: md5: unused build: - number: 5 + number: 6 skip: true # [osx] requirements: diff --git a/recipes/superstr/meta.yaml b/recipes/superstr/meta.yaml index 28f42beb07a41..fff35f9793db3 100644 --- a/recipes/superstr/meta.yaml +++ b/recipes/superstr/meta.yaml @@ -12,7 +12,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 # skip: True # [osx] requirements: diff --git a/recipes/survindel2/build_failure.osx-64.yaml b/recipes/survindel2/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..3488c591eb5f1 --- /dev/null +++ b/recipes/survindel2/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 02029b1e505078416e38da23b4f72dbdf3bbf084b2c275ecbd9ecc4b890aa237 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - pysam >=0.16.0.1 + - htslib >=1.21,<1.22.0a0 + - pyfaidx >=0.5.9.1 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + - scikit-learn >=1.2.2 + test: + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/survindel2_1734565177423/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + requires: + - bcftools + source_files: + - demo/reads.bam + - demo/reads.bam.bai + - demo/ref.fa + - demo/ref.fa.fai + about: + Traceback (most recent call last): + description: 'SurVIndel2 is a fast and accurate CNV caller for Illumina paired-end + WGS data. + + ' + home: https://github.com/kensung-lab/SurVIndel2 + license: GPL-3.0-only + license_file: LICENSE.md + summary: A CNV caller for Illumina paired-end WGS data. + extra: + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + copy_test_source_files: true + final: true + recipe-maintainers: + - Mesh89 + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/survindel2_1734565177423/work + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/survindel2_1734565177423/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/survindel2_1734565177423/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/survindel2_1734565177423/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/survindel2-1.1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/survindel2_1734565177423/work/conda_build.sh']' returned non-zero exit status 1. + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/survindel2-1.1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/survindel2-1.1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/survindel2-1.1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/survindel2/meta.yaml b/recipes/survindel2/meta.yaml index 4d5a47805d66d..1c542797acf04 100644 --- a/recipes/survindel2/meta.yaml +++ b/recipes/survindel2/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 8463d4b5f5060f26520d8a57f162f74708e0a3ecb68675dec6af671688a21a3f build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('survindel2', max_pin='x.x') }} diff --git a/recipes/survivor/meta.yaml b/recipes/survivor/meta.yaml index b54e5e2cd021b..64131803582fc 100644 --- a/recipes/survivor/meta.yaml +++ b/recipes/survivor/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('survivor', max_pin="x") }} diff --git a/recipes/svaba/build_failure.linux-64.yaml b/recipes/svaba/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..1752672424468 --- /dev/null +++ b/recipes/svaba/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 0ae7f0d64bdd51d6b6dec0186e7178bfb11703141e12ead29840d5ea6ce73b31 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + 350 | mate.partner = main_region; + | ^~~~~~~~~~~ + In file included from ../../SeqLib/SeqLib/BamRecord.h:22, + from ../../SeqLib/SeqLib/GenomicRegionCollection.h:11, + from ../../SeqLib/SeqLib/ReadFilter.h:12, + from ../../SeqLib/SeqLib/BamReader.h:5, + from svabaBamWalker.h:9, + from svabaBamWalker.cpp:1: + ../../SeqLib/SeqLib/GenomicRegion.h:32:2: note: because 'SeqLib::GenomicRegion' has user-provided 'SeqLib::GenomicRegion::GenomicRegion(const SeqLib::GenomicRegion&)' + 32 | GenomicRegion(const GenomicRegion& gr) : chr(gr.chr), pos1(gr.pos1), pos2(gr.pos2), strand(gr.strand) {} + | ^~~~~~~~~~~~~ + mv -f .deps/svaba-svabaBamWalker.Tpo .deps/svaba-svabaBamWalker.Po + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I../.. -I../../src/SGA/Util -I../../src/SGA/Bigraph -I../../src/SGA/SuffixTools -I../../src/SGA/StringGraph -I../../src/SGA/Algorithm -I../../src/SGA/SQG -I../../src/SGA/SGA -I../../SeqLib -I../../SeqLib/htslib -Wno-sign-compare -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -g -Wall -Wextra -Wno-unknown-pragmas -std=c11 -D_GLIBCXX_USE_CXX11_ABI=0 -fcommon -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/svaba-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -UNDEBUG -L$PREFIX/lib -MT svaba-refilter.o -MD -MP -MF .deps/svaba-refilter.Tpo -c -o svaba-refilter.o test -f 'refilter.cpp' || echo './'refilter.cpp + In file included from BreakPoint.h:14, + from DBSnpFilter.h:13, + from refilter.cpp:2: + DiscordantCluster.h: In constructor 'DiscordantCluster::DiscordantCluster()': + DiscordantCluster.h:24:38: warning: implicitly-declared 'SeqLib::GenomicRegion& SeqLib::GenomicRegion::operator=(const SeqLib::GenomicRegion&)' is deprecated [-Wdeprecated-copy] + 24 | m_reg1 = SeqLib::GenomicRegion(); + | ^ + In file included from ../../SeqLib/SeqLib/BamRecord.h:22, + from ../../SeqLib/SeqLib/GenomicRegionCollection.h:11, + from DBSnpFilter.h:10: + ../../SeqLib/SeqLib/GenomicRegion.h:32:2: note: because 'SeqLib::GenomicRegion' has user-provided 'SeqLib::GenomicRegion::GenomicRegion(const SeqLib::GenomicRegion&)' + 32 | GenomicRegion(const GenomicRegion& gr) : chr(gr.chr), pos1(gr.pos1), pos2(gr.pos2), strand(gr.strand) {} + | ^~~~~~~~~~~~~ + DiscordantCluster.h:25:38: warning: implicitly-declared 'SeqLib::GenomicRegion& SeqLib::GenomicRegion::operator=(const SeqLib::GenomicRegion&)' is deprecated [-Wdeprecated-copy] + 25 | m_reg2 = SeqLib::GenomicRegion(); + | ^ + ../../SeqLib/SeqLib/GenomicRegion.h:32:2: note: because 'SeqLib::GenomicRegion' has user-provided 'SeqLib::GenomicRegion::GenomicRegion(const SeqLib::GenomicRegion&)' + 32 | GenomicRegion(const GenomicRegion& gr) : chr(gr.chr), pos1(gr.pos1), pos2(gr.pos2), strand(gr.strand) {} + | ^~~~~~~~~~~~~ + mv -f .deps/svaba-refilter.Tpo .deps/svaba-refilter.Po + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I../.. -I../../src/SGA/Util -I../../src/SGA/Bigraph -I../../src/SGA/SuffixTools -I../../src/SGA/StringGraph -I../../src/SGA/Algorithm -I../../src/SGA/SQG -I../../src/SGA/SGA -I../../SeqLib -I../../SeqLib/htslib -Wno-sign-compare -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -g -Wall -Wextra -Wno-unknown-pragmas -std=c11 -D_GLIBCXX_USE_CXX11_ABI=0 -fcommon -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/svaba-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -UNDEBUG -L$PREFIX/lib -MT svaba-LearnBamParams.o -MD -MP -MF .deps/svaba-LearnBamParams.Tpo -c -o svaba-LearnBamParams.o test -f 'LearnBamParams.cpp' || echo './'LearnBamParams.cpp + mv -f .deps/svaba-LearnBamParams.Tpo .deps/svaba-LearnBamParams.Po + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I../.. -I../../src/SGA/Util -I../../src/SGA/Bigraph -I../../src/SGA/SuffixTools -I../../src/SGA/StringGraph -I../../src/SGA/Algorithm -I../../src/SGA/SQG -I../../src/SGA/SGA -I../../SeqLib -I../../SeqLib/htslib -Wno-sign-compare -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -g -Wall -Wextra -Wno-unknown-pragmas -std=c11 -D_GLIBCXX_USE_CXX11_ABI=0 -fcommon -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/svaba-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -UNDEBUG -L$PREFIX/lib -MT svaba-STCoverage.o -MD -MP -MF .deps/svaba-STCoverage.Tpo -c -o svaba-STCoverage.o test -f 'STCoverage.cpp' || echo './'STCoverage.cpp + STCoverage.cpp: In constructor 'STCoverage::STCoverage(const SeqLib::GenomicRegion&)': + STCoverage.cpp:19:12: warning: implicitly-declared 'SeqLib::GenomicRegion& SeqLib::GenomicRegion::operator=(const SeqLib::GenomicRegion&)' is deprecated [-Wdeprecated-copy] + 19 | m_gr = gr; + | ^~ + In file included from ../../SeqLib/SeqLib/BamRecord.h:22, + from STCoverage.h:18, + from STCoverage.cpp:1: + ../../SeqLib/SeqLib/GenomicRegion.h:32:2: note: because 'SeqLib::GenomicRegion' has user-provided 'SeqLib::GenomicRegion::GenomicRegion(const SeqLib::GenomicRegion&)' + 32 | GenomicRegion(const GenomicRegion& gr) : chr(gr.chr), pos1(gr.pos1), pos2(gr.pos2), strand(gr.strand) {} + | ^~~~~~~~~~~~~ + mv -f .deps/svaba-STCoverage.Tpo .deps/svaba-STCoverage.Po + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I../.. -I../../src/SGA/Util -I../../src/SGA/Bigraph -I../../src/SGA/SuffixTools -I../../src/SGA/StringGraph -I../../src/SGA/Algorithm -I../../src/SGA/SQG -I../../src/SGA/SGA -I../../SeqLib -I../../SeqLib/htslib -Wno-sign-compare -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -g -Wall -Wextra -Wno-unknown-pragmas -std=c11 -D_GLIBCXX_USE_CXX11_ABI=0 -fcommon -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/svaba-1.1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -UNDEBUG -L$PREFIX/lib -MT svaba-Histogram.o -MD -MP -MF .deps/svaba-Histogram.Tpo -c -o svaba-Histogram.o test -f 'Histogram.cpp' || echo './'Histogram.cpp + In file included from Histogram.cpp:1: + Histogram.h:104:61: error: 'uint32_t' does not name a type + 104 | Histogram(const int32_t& start, const int32_t& end, const uint32_t& width); + | ^~~~~~~~ + Histogram.h:12:1: note: 'uint32_t' is defined in header ''; did you forget to '#include '? + 11 | #include "SeqLib/IntervalTree.h" + |#include + 12 | + Histogram.cpp:14:1: error: no declaration matches 'Histogram::Histogram(const int32_t&, const int32_t&, const uint32_t&)' + 14 | Histogram::Histogram(const int32_t& start, const int32_t& end, const uint32_t& width) + | ^~~~~~~~~ + Histogram.h:85:7: note: candidates are: 'Histogram::Histogram(Histogram&&)' + 85 | class Histogram { + | ^~~~~~~~~ + Histogram.h:85:7: note: 'Histogram::Histogram(const Histogram&)' + Histogram.h:104:3: note: 'Histogram::Histogram(const int32_t&, const int32_t&, const int&)' + 104 | Histogram(const int32_t& start, const int32_t& end, const uint32_t& width); + | ^~~~~~~~~ + Histogram.h:96:3: note: 'Histogram::Histogram()' + 96 | Histogram() {} + | ^~~~~~~~~ + Histogram.h:85:7: note: 'class Histogram' defined here + 85 | class Histogram { + | ^~~~~~~~~ + make[2]: *** [Makefile:743: svaba-Histogram.o] Error 1 + make[2]: Leaving directory '$SRC_DIR/src/svaba' + make[1]: *** [Makefile:358: all-recursive] Error 1 + make[1]: Leaving directory '$SRC_DIR' + make: *** [Makefile:299: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/svaba_1734061095314/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/svaba_1734061095314/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/svaba/meta.yaml b/recipes/svaba/meta.yaml index 347a545338657..a6adcd8ce29d8 100644 --- a/recipes/svaba/meta.yaml +++ b/recipes/svaba/meta.yaml @@ -11,7 +11,7 @@ source: md5: unused build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/svdb/meta.yaml b/recipes/svdb/meta.yaml index 55ca20eaaf5b3..5a9108b0edcb1 100644 --- a/recipes/svdb/meta.yaml +++ b/recipes/svdb/meta.yaml @@ -13,7 +13,7 @@ build: entry_points: - svdb = svdb.__main__:main script: python -m pip install --no-deps --ignore-installed . - number: 3 + number: 4 run_exports: - {{ pin_subpackage('svdb', max_pin="x") }} @@ -41,4 +41,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/svdss/meta.yaml b/recipes/svdss/meta.yaml index 2fe1039f6d6bd..a04cbf6f51cfd 100644 --- a/recipes/svdss/meta.yaml +++ b/recipes/svdss/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage('svdss', max_pin="x") }} diff --git a/recipes/svict/build_failure.osx-64.yaml b/recipes/svict/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..664a510cd9f51 --- /dev/null +++ b/recipes/svict/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 0756df7c993ba5560b545ec7d77a8e45847c7d83a93e19f013a029f84fdfb992 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - libzlib 1.3.1 hd23fc13_2 + sys.exit(execute()) + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + - sigtool 0.1.3 h88f4db0_0 + - make 4.4.1 h00291cd_2 + - libcxx 19.1.5 hf95d169_0 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + - libcxx-devel 18.1.8 h7c275be_7 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + host: + - libcxx 19.1.5 hf95d169_0 + - libzlib 1.3.1 hd23fc13_2 + - zlib 1.3.1 hd23fc13_2 + run: + - zlib + - libcxx >=18 + - libzlib >=1.3.1,<2.0a0 + test: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + commands: + - svict -v + about: + home: https://github.com/vpc-ccg/svict + license: Apache-2.0 + summary: SViCT is a computational tool for detecting structural variations from + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + cell free DNA (cfDNA) containing low dilutions of circulating tumor DNA (ctDNA). + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/svict_1733960021951/work + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/svict_1733960021951/work/conda_build.sh']' returned non-zero exit status 2. + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/svict_1733960021951/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/svict_1733960021951/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/svict_1733960021951/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/svict-1.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/svict-1.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/svict-1.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/svict-1.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + make -C src all + make[1]: Entering directory '$SRC_DIR/src' + x86_64-apple-darwin13.4.0-clang -w -c -O3 -std=c0x partition.cc -o partition.o + x86_64-apple-darwin13.4.0-clang -w -c -O3 -std=c0x svict.cc -o svict.o + x86_64-apple-darwin13.4.0-clang -w -c -O3 -std=c0x assembler.cc -o assembler.o + x86_64-apple-darwin13.4.0-clang -w -c -O3 -std=c0x genome.cc -o genome.o + x86_64-apple-darwin13.4.0-clang -w -c -O3 -std=c0x variant_caller.cc -o variant_caller.o + x86_64-apple-darwin13.4.0-clang -w -c -O3 -std=c0x svict_caller.cc -o svict_caller.o + make[1]: Leaving directory '$SRC_DIR/src' +# Last 100 lines of the build log. diff --git a/recipes/svict/meta.yaml b/recipes/svict/meta.yaml index 326ce90ac76b3..7795a77dae831 100644 --- a/recipes/svict/meta.yaml +++ b/recipes/svict/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/svmlight/meta.yaml b/recipes/svmlight/meta.yaml index bfd083b7eb05b..10c69dcb286b3 100644 --- a/recipes/svmlight/meta.yaml +++ b/recipes/svmlight/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/svtk/meta.yaml b/recipes/svtk/meta.yaml index 92d335a5746ef..d101cb3211341 100644 --- a/recipes/svtk/meta.yaml +++ b/recipes/svtk/meta.yaml @@ -9,7 +9,7 @@ source: sha256: edc661d96edbcae714f9f80546447480d0dac152c5e081c5b01355a5fc423dcd build: - number: 5 + number: 6 skip: True # [py<30] script: | touch svtk/baf/__init__.py diff --git a/recipes/swarm/meta.yaml b/recipes/swarm/meta.yaml index 130ee47b5bc48..efddc02840c7f 100644 --- a/recipes/swarm/meta.yaml +++ b/recipes/swarm/meta.yaml @@ -18,7 +18,7 @@ requirements: - python-igraph build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('swarm', max_pin="x") }} diff --git a/recipes/swipe/meta.yaml b/recipes/swipe/meta.yaml index 6e26e25f982e7..e9e7b93739d64 100644 --- a/recipes/swipe/meta.yaml +++ b/recipes/swipe/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/sword/meta.yaml b/recipes/sword/meta.yaml index 0259952717798..de526b8e39366 100644 --- a/recipes/sword/meta.yaml +++ b/recipes/sword/meta.yaml @@ -6,7 +6,9 @@ package: version: {{ version }} build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage('sword', max_pin="x") }} source: url: https://github.com/rvaser/sword/releases/download/{{ version }}/sword-v{{ version }}.tar.gz diff --git a/recipes/symbiontscreener/build_failure.osx-64.yaml b/recipes/symbiontscreener/build_failure.osx-64.yaml index 97085ff67445d..b63e3c011b7ab 100644 --- a/recipes/symbiontscreener/build_failure.osx-64.yaml +++ b/recipes/symbiontscreener/build_failure.osx-64.yaml @@ -1,6 +1,87 @@ -recipe_sha: 08ef76a497a218150cdaf6227ef3d15db7969a4322608d673ac526ddf830f9bc # The commit at which this recipe failed to build. +recipe_sha: e5c276df5f1db2804283676ff0e20a2e8d696d6762c43087c1802c88b48bb145 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + - cctools_osx-64 949.0.1 h5ba7a2e_0 + - clangxx_osx-64 9.0.1 h05bbb7f_2 + - libllvm9 9.0.1 default_h2671707_7 + - ld64_osx-64 530 h3c32e8a_0 + - clang-9 9.0.1 default_hf139c7e_5 + host: + - libcxx 19.1.5 hf95d169_0 + - libzlib 1.3.1 hd23fc13_2 + - zlib 1.3.1 hd23fc13_2 + run: + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1734033625104/work/conda_build.sh']' returned non-zero exit status 2. + + - zlib + - meryl + - kmer-jellyfish + - plotly + - libcxx >=9.0.1 + - numpy + The above exception was the direct cause of the following exception: + + - libzlib >=1.3.1,<2.0a0 + - pandas + - seqkit + test: + commands: + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + - sysc + about: + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + home: https://github.com/BGI-Qingdao/Symbiont-Screener + license: GPL-3.0-only + license_file: LICENSE + summary: Symbiont-Screener is a reference-free approach to identifying high-confidence + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + host's long reads from symbionts and contaminants and overcoming the low sequencing + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + accuracy according to a trio-based screening model. + extra: + copy_test_source_files: true + final: true + recipe-maintainers: + - cchd0001 + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1734033625104/work + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1734033625104/work/conda_build.sh']' returned non-zero exit status 2. + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1734033625104/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1734033625104/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1734033625104/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar + AS=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/symbiontscreener-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-checksyms + CLANG=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CMAKE_PREFIX_PATH=:$PREFIX + CPPFLAGS=-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/symbiontscreener-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INDR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-indr + INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool + LD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool + LIPO=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-lipo + NM=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-nm + NMEDIT=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-nmedit + OTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-otool + PAGESTUFF=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-pagestuff + RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-redo_prebinding SEGEDIT=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-seg_addr_table @@ -19,86 +100,5 @@ log: |- cd sources && make CC=x86_64-apple-darwin13.4.0-clang CXX=x86_64-apple-darwin13.4.0-clang make[1]: Entering directory '$SRC_DIR/sources' x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -std=c14 -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/symbiontscreener-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -I./gzstream -I./strobemer -c strobemer/strobemer.cpp -L$PREFIX/lib -lz -lpthread -o strobemer.o - clang-9: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] - clang-9: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] - clang-9: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - clang-9: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' [-Wunused-command-line-argument] - In file included from strobemer/strobemer.cpp:1: - In file included from ./strobemer/strobemer.h:5: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/string:545: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/__functional/hash.h:29: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/limits:827: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/type_traits:510: - /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/__type_traits/is_trivially_destructible.h:34:2: error: is_trivially_destructible is not implemented - #error is_trivially_destructible is not implemented - ^ - In file included from strobemer/strobemer.cpp:1: - In file included from ./strobemer/strobemer.h:5: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/string:576: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/string_view:1025: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/algorithm:1747: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/__algorithm/inplace_merge.h:26: - /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/__memory/destruct_n.h:51:41: error: no template named 'is_trivially_destructible'; did you mean 'is_trivially_constructible'? - {__incr(integral_constant::value>());} - ^ - /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/__type_traits/is_trivially_constructible.h:22:29: note: 'is_trivially_constructible' declared here - struct _LIBCPP_TEMPLATE_VIS is_trivially_constructible - ^ - In file included from strobemer/strobemer.cpp:1: - In file included from ./strobemer/strobemer.h:5: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/string:576: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/string_view:1025: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/algorithm:1747: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/__algorithm/inplace_merge.h:26: - /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/__memory/destruct_n.h:55:45: error: no template named 'is_trivially_destructible'; did you mean 'is_trivially_constructible'? - {__set(__s, integral_constant::value>());} - ^ - /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/__type_traits/is_trivially_constructible.h:22:29: note: 'is_trivially_constructible' declared here - struct _LIBCPP_TEMPLATE_VIS is_trivially_constructible - ^ - In file included from strobemer/strobemer.cpp:1: - In file included from ./strobemer/strobemer.h:5: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/string:576: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/string_view:1025: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/algorithm:1747: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/__algorithm/inplace_merge.h:26: - /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/__memory/destruct_n.h:59:49: error: no template named 'is_trivially_destructible'; did you mean 'is_trivially_constructible'? - {__process(__p, integral_constant::value>());} - ^ - /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/__type_traits/is_trivially_constructible.h:22:29: note: 'is_trivially_constructible' declared here - struct _LIBCPP_TEMPLATE_VIS is_trivially_constructible - ^ - In file included from strobemer/strobemer.cpp:1: - In file included from ./strobemer/strobemer.h:5: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/string:576: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/string_view:1027: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/functional:518: - /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/__functional/function.h:590:21: error: no template named 'is_trivially_destructible'; did you mean 'is_trivially_constructible'? - is_trivially_destructible<_Fun>::value> {}; - ^ - /opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/_build_env/bin/../include/c/v1/__type_traits/is_trivially_constructible.h:22:29: note: 'is_trivially_constructible' declared here - struct _LIBCPP_TEMPLATE_VIS is_trivially_constructible - ^ - 5 errors generated. - make[1]: *** [Makefile:20: strobemer.o] Error 1 make[1]: Leaving directory '$SRC_DIR/sources' - make: *** [Makefile:9: symbiontscreenerbinary] Error 2 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/symbiontscreener_1685550230019/work/conda_build.sh']' returned non-zero exit status 2. # Last 100 lines of the build log. diff --git a/recipes/symbiontscreener/meta.yaml b/recipes/symbiontscreener/meta.yaml index e4d634bcac4c8..60a0fc4736d06 100644 --- a/recipes/symbiontscreener/meta.yaml +++ b/recipes/symbiontscreener/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 266e72afe6671e0952c1764c839b07279f38c884591267617854b3a3f165888d build: - number: 1 + number: 2 requirements: diff --git a/recipes/t-coffee/build_failure.osx-64.yaml b/recipes/t-coffee/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..931caae2305e3 --- /dev/null +++ b/recipes/t-coffee/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 7a3d050c624e2d73b122720d6788a44ad8113e280803b23611d66bfd685e6ed9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + !!!!!!!! t_coffee compilation and binary installation failed + + ------- Installing clustalw + + ------- Installing pcma + + ------- Installing dialign-t + + ------- Installing clustalo + + ------- Installing probconsRNA + + ------- Installing dialign-tx + + ------- The installer will now install the t_coffee components for regular multiple sequence alignments + + ------- The installer will now install the trmsd components + + ------- Installing retree + + ------- The installer will now install the expresso components for very accurate structure based multiple sequence alignments + + ------- Installing strike + + ------- Installing mustang + ------- XML::Simple : already processed + + ------- Installing TMalign + ------- t_coffee : already processed + + ------- Installing sap + + ------- The installer will now install the tcoffee components + ------- strike : already processed + ------- t_coffee : already processed + + ------- The installer will now install the rcoffee components for RNA multiple sequence alignments + + ------- Installing RNAplfold + ------- mafft : already processed + ------- famsa : already processed + ------- clustalw2 : already processed + ------- muscle : already processed + ------- t_coffee : already processed + ------- clustalw : already processed + ------- probconsRNA : already processed + + ------- The installer will now install the 3dcoffee components for multiple structure alignments + ------- mustang : already processed + ------- TMalign : already processed + ------- t_coffee : already processed + ------- sap : already processed + + ------- The installer will now install the seq_reformat components + ------- Finishing The installation + + ********************************************************************* + ******** INSTALLATION SUMMARY ***************** + ********************************************************************* + ------- SUMMARY package Installation: + ------- Executable Installed in: $PREFIX/libexec/t-coffee-13.46.0.919e8c6b-2/plugins/macosx + *------ RNAplfold : updated [from binary] + *------ strike : installed [from binary] + *------ mafft : updated [from binary] + *------ prank : updated [from binary] + *------ famsa : previous + *------ kalign : updated [from binary] + *------ retree : updated [from binary] + *------ mustang : updated [from binary] + *------ probcons : updated [from binary] + *------ XML::Simple : updated + *------ poa : installed [from binary] + *------ TMalign : updated [from binary] + *------ proda : installed [from binary] + *------ clustalw2 : updated [from binary] + *------ muscle : updated [from binary] + *------ t_coffee : failed installation + *------ clustalw : updated [from binary] + *------ sap : updated [from binary] + *------ dialign-tx : updated [from binary] + *------ pcma : installed [from binary] + *------ probconsRNA : updated [from binary] + *------ dialign-t : installed [from binary] + *------ clustalo : updated [from binary] + *------ SUMMARY mode Installation: + *------ MODE accurate SUCCESSFULLY installed + *------ MODE psicoffee SUCCESSFULLY installed + *!!!!!! t_coffee : Missing + *!!!!!! MODE mcoffee UNSUCCESSFULLY installed + *------ MODE t_coffee SUCCESSFULLY installed + *------ MODE trmsd SUCCESSFULLY installed + *!!!!!! t_coffee : Missing + *!!!!!! MODE expresso UNSUCCESSFULLY installed + *!!!!!! t_coffee : Missing + *!!!!!! MODE tcoffee UNSUCCESSFULLY installed + *!!!!!! t_coffee : Missing + *!!!!!! MODE rcoffee UNSUCCESSFULLY installed + *!!!!!! t_coffee : Missing + *!!!!!! MODE 3dcoffee UNSUCCESSFULLY installed + *------ MODE seq_reformat SUCCESSFULLY installed +# Last 100 lines of the build log. +category: |- + source download error diff --git a/recipes/t-coffee/meta.yaml b/recipes/t-coffee/meta.yaml index b5cc7ac1818c2..684a61cf83482 100644 --- a/recipes/t-coffee/meta.yaml +++ b/recipes/t-coffee/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 2 run_exports: - {{ pin_subpackage('t-coffee', max_pin="x") }} @@ -31,7 +31,7 @@ requirements: - dialign-tx 1.0.2 - famsa - kalign2 - - mafft 7.310 + - mafft - muscle - mustang 3.2.3 - pasta @@ -54,7 +54,7 @@ requirements: - dialign-tx 1.0.2 - famsa - kalign2 - - mafft 7.310 + - mafft - muscle - mustang 3.2.3 - pasta diff --git a/recipes/t1k/meta.yaml b/recipes/t1k/meta.yaml index 0e4865512483a..b978bd3224370 100644 --- a/recipes/t1k/meta.yaml +++ b/recipes/t1k/meta.yaml @@ -5,7 +5,7 @@ package: version: '{{ version }}' build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('t1k', max_pin="x") }} @@ -48,4 +48,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/tabixpp/meta.yaml b/recipes/tabixpp/meta.yaml index b15f3d0e790dd..fc879eac818ce 100644 --- a/recipes/tabixpp/meta.yaml +++ b/recipes/tabixpp/meta.yaml @@ -17,7 +17,7 @@ source: folder: htslib build: - number: 3 + number: 4 run_exports: # Observed ABI version increase from 1.1.0 to 1.1.2. # Hence, we pin to the patch version even. diff --git a/recipes/table2asn/meta.yaml b/recipes/table2asn/meta.yaml index b337b71f5de5c..790f3c1637fdb 100644 --- a/recipes/table2asn/meta.yaml +++ b/recipes/table2asn/meta.yaml @@ -14,7 +14,7 @@ source: sha256: {{ sha256 }} # [linux] build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('table2asn', max_pin="x") }} diff --git a/recipes/tadarida-d/meta.yaml b/recipes/tadarida-d/meta.yaml index 363b4e43e5296..811b20bf93e65 100644 --- a/recipes/tadarida-d/meta.yaml +++ b/recipes/tadarida-d/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 8 + number: 9 skip: True # [osx] requirements: diff --git a/recipes/takeabreak/build_failure.osx-64.yaml b/recipes/takeabreak/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..e1e9c1f1819a7 --- /dev/null +++ b/recipes/takeabreak/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 0d607074c799d0e8c004305c2fb82ab729472181bd29b7669bb7cbbf7823737b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + -- Looking for alarm + -- Looking for alarm - found + -- Looking for fork + -- Looking for fork - found + -- Looking for frexpf + -- Looking for frexpf - found + -- Looking for frexpl + -- Looking for frexpl - found + -- Looking for gethostname + -- Looking for gethostname - found + -- Looking for getpwuid + -- Looking for getpwuid - found + -- Looking for getrusage + -- Looking for getrusage - found + -- Looking for lstat + -- Looking for lstat - found + -- Looking for rand_r + -- Looking for rand_r - found + -- Looking for random + -- Looking for random - found + -- Looking for setsysinfo + -- Looking for setsysinfo - not found + -- Looking for signal + -- Looking for signal - found + -- Looking for longjmp + -- Looking for longjmp - found + -- Looking for setjmp + -- Looking for setjmp - found + -- Looking for siglongjmp + -- Looking for siglongjmp - found + -- Looking for sigsetjmp + -- Looking for sigsetjmp - found + -- Looking for sigaction + -- Looking for sigaction - found + -- Looking for sigprocmask + -- Looking for sigprocmask - found + -- Looking for snprintf + -- Looking for snprintf - found + -- Looking for srandom + -- Looking for srandom - found + -- Looking for strdup + -- Looking for strdup - found + -- Looking for symlink + -- Looking for symlink - found + -- Looking for system + -- Looking for system - found + -- Looking for vasprintf + -- Looking for vasprintf - found + -- Looking for waitpid + -- Looking for waitpid - found + -- Looking for vsnprintf + -- Looking for vsnprintf - found + -- Performing Other Test VSNPRINTF_WORKS - Success + -- Looking for tzname + -- Looking for tzname - found + -- Performing Other Test LONE_COLON - Failed + -- Performing Other Test HAVE_ATTRIBUTE - Success + -- Performing Other Test HAVE_C99_FUNC - Success + -- Performing Other Test HAVE_FUNCTION - Success + -- Performing Other Test HAVE_C99_DESIGNATED_INITIALIZER - Success + -- Performing Other Test SYSTEM_SCOPE_THREADS - Success + -- Performing Other Test HAVE_SOCKLEN_T - Success + -- Performing Other Test CXX_HAVE_OFFSETOF - Success + -- Performing CXX Test OLD_HEADER_FILENAME - Failed + -- Performing CXX Test H5_NO_NAMESPACE - Failed + -- Performing CXX Test H5_NO_STD - Failed + -- Performing CXX Test BOOL_NOTDEFINED - Failed + -- Performing CXX Test NO_STATIC_CAST - Failed + -- Performing TEST_DIRECT_VFD_WORKS... no + -- Performing Other Test INLINE_TEST_inline - Success + -- Performing Other Test INLINE_TEST___inline__ - Success + -- Performing Other Test INLINE_TEST___inline - Success + -- Checking for appropriate format for 64 bit long: + -- Checking for apropriate format for 64 bit long: found "ll" + -- checking IF converting from long double to integers is accurate... yes + -- Checking IF converting from long double to integers works... no + -- checking IF accurately converting from integers to long double... yes + -- Checking IF accurately converting unsigned long to float values... no + -- Checking IF accurately converting unsigned long long to floating-point values... no + -- Checking IF accurately roundup converting floating-point to unsigned long long values... no + -- Checking IF correctly converting long double to unsigned int values... no + -- Checking IF compiling unsigned long long to floating-point typecasts work... yes + -- Checking IF compiling long long to floating-point typecasts work... yes + -- Checking IF converting unsigned long long to long double with precision... no + -- Checking IF overflows normally converting floating-point to integer values... no + -- Checking IF your system converts long double to (unsigned) long values with special algorithm... no + -- Checking IF your system can convert (unsigned) long to long double values with special algorithm... no + -- Checking IF correctly converting long double to (unsigned) long long values... no + -- Checking IF correctly converting (unsigned) long long to long double values... no + -- Checking IF your system generates wrong code for log2 routine... no + -- Checking IF alignment restrictions are strictly enforced... yes + -- Could NOT find ZLIB (missing: ZLIB_DIR) + -- Found ZLIB: $PREFIX/lib/libz.dylib (found version "1.3.1") + -- Filter ZLIB is ON + -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) + -- Configuring done (67.8s) + -- Generating done (0.2s) + -- Build files have been written to: $SRC_DIR/build + [ 0%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5make_libsettings.dir/H5make_libsettings.c.o + [ 0%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5detect.dir/H5detect.c.o +# Last 100 lines of the build log. diff --git a/recipes/takeabreak/meta.yaml b/recipes/takeabreak/meta.yaml index 13c4417efa7b5..6da0ec57cbf46 100644 --- a/recipes/takeabreak/meta.yaml +++ b/recipes/takeabreak/meta.yaml @@ -10,7 +10,7 @@ source: - 0002-Skip-GATB-tools-compilation.patch build: - number: 7 + number: 8 requirements: build: diff --git a/recipes/tantan/meta.yaml b/recipes/tantan/meta.yaml index 5ddf8f7da345d..d9968c38a8c00 100644 --- a/recipes/tantan/meta.yaml +++ b/recipes/tantan/meta.yaml @@ -10,7 +10,7 @@ source: sha256: f25db9441409d526becfb10df7a610c10d0e5f163d58b21535e4f045bcfc118f build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('tantan', max_pin="None") }} diff --git a/recipes/tatajuba/meta.yaml b/recipes/tatajuba/meta.yaml index 66935f0807c84..8ff9316bafefa 100644 --- a/recipes/tatajuba/meta.yaml +++ b/recipes/tatajuba/meta.yaml @@ -11,7 +11,7 @@ source: md5: unused build: - number: 3 + number: 4 skip: true # [osx] requirements: diff --git a/recipes/taxonomy/meta.yaml b/recipes/taxonomy/meta.yaml index 50482a9b18fb9..7f6920b95fbe7 100644 --- a/recipes/taxonomy/meta.yaml +++ b/recipes/taxonomy/meta.yaml @@ -12,7 +12,7 @@ source: - pyproject.patch build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('taxonomy', max_pin="x.x") }} diff --git a/recipes/taxor/build_failure.linux-64.yaml b/recipes/taxor/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..7b07d74ae1f7e --- /dev/null +++ b/recipes/taxor/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: ff4a9a95285037e1aaa8eb85edf5c3d283e67d797b23ab82f982b38ecaaf9fd6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/taxor_1734147243021/work/build/seqan/seqan3/seqan3-src/include/seqan3/utility/parallel/detail/reader_writer_manager.hpp:310:18: warning: use of 'std::hardware_destructive_interference_size' [-Winterference-size] + 310 | alignas(std::hardware_destructive_interference_size) latch reader_latch; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/taxor_1734147243021/work/build/seqan/seqan3/seqan3-src/include/seqan3/utility/parallel/detail/reader_writer_manager.hpp:312:18: warning: use of 'std::hardware_destructive_interference_size' [-Winterference-size] + 312 | alignas(std::hardware_destructive_interference_size) latch writer_latch; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/taxor_1734147243021/work/build/seqan/seqan3/seqan3-src/include/seqan3/utility/parallel/detail/reader_writer_manager.hpp:314:18: warning: use of 'std::hardware_destructive_interference_size' [-Winterference-size] + 314 | alignas(std::hardware_destructive_interference_size) std::once_flag flag; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + [ 34%] Building CXX object hixf/CMakeFiles/hixf.dir/build/construct_ixf.cpp.o + In file included from /opt/conda/conda-bld/taxor_1734147243021/work/build/hixf/../seqan/lemon/include/lemon/bits/graph_extender.h:30, + from /opt/conda/conda-bld/taxor_1734147243021/work/build/hixf/../seqan/lemon/include/lemon/list_graph.h:28, + from /opt/conda/conda-bld/taxor_1734147243021/work/src/hixf/build/construct_ixf.cpp:2: + /opt/conda/conda-bld/taxor_1734147243021/work/build/hixf/../seqan/lemon/include/lemon/bits/stl_iterators.h:20:31: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 20 | : public T, public std::iterator { + | ^~~~~~~~ + In file included from /opt/conda/conda-bld/taxor_1734147243021/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_algobase.h:65, + from /opt/conda/conda-bld/taxor_1734147243021/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/vector:62, + from /opt/conda/conda-bld/taxor_1734147243021/work/build/hixf/../seqan/lemon/include/lemon/core.h:45, + from /opt/conda/conda-bld/taxor_1734147243021/work/build/hixf/../seqan/lemon/include/lemon/list_graph.h:26: + /opt/conda/conda-bld/taxor_1734147243021/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ + In file included from /opt/conda/conda-bld/taxor_1734147243021/work/src/hixf/build/hierarchical_interleaved_xor_filter.hpp:12, + from /opt/conda/conda-bld/taxor_1734147243021/work/src/hixf/build/build_data.hpp:14, + from /opt/conda/conda-bld/taxor_1734147243021/work/src/hixf/build/construct_ixf.hpp:13, + from /opt/conda/conda-bld/taxor_1734147243021/work/src/hixf/build/construct_ixf.cpp:5: + /opt/conda/conda-bld/taxor_1734147243021/work/build/seqan/seqan3/seqan3-src/include/seqan3/search/dream_index/interleaved_xor_filter.hpp: In member function 'seqan3::interleaved_xor_filter::membership_agent seqan3::interleaved_xor_filter::membership_agent() const': + /opt/conda/conda-bld/taxor_1734147243021/work/build/seqan/seqan3/seqan3-src/include/seqan3/search/dream_index/interleaved_xor_filter.hpp:722:66: error: 'membership_agent' in 'class seqan3::interleaved_xor_filter' does not name a type + 722 | return typename interleaved_xor_filter::membership_agent{*this}; + | ^~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/taxor_1734147243021/work/build/seqan/seqan3/seqan3-src/include/seqan3/search/dream_index/interleaved_xor_filter.hpp: At global scope: + /opt/conda/conda-bld/taxor_1734147243021/work/build/seqan/seqan3/seqan3-src/include/seqan3/search/dream_index/interleaved_xor_filter.hpp:851:48: error: redeclaration of 'template requires (same_as) || (same_as) class seqan3::interleaved_xor_filter' with different constraints + 851 | class interleaved_xor_filter::membership_agent + | ^~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/taxor_1734147243021/work/build/seqan/seqan3/seqan3-src/include/seqan3/search/dream_index/interleaved_xor_filter.hpp:1103:48: error: redeclaration of 'template requires (same_as) || (same_as) class seqan3::interleaved_xor_filter' with different constraints + 1103 | class interleaved_xor_filter::counting_agent_type + | ^~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/taxor_1734147243021/work/build/seqan/seqan3/seqan3-src/include/seqan3/search/dream_index/interleaved_xor_filter.hpp:1113:21: error: 'membership_agent' in 'using seqan3::interleaved_xor_filter::counting_agent_type::ixf_t = class seqan3::interleaved_xor_filter' does not name a type + 1113 | typename ixf_t::membership_agent membership_agent; + | ^~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/taxor_1734147243021/work/build/seqan/seqan3/seqan3-src/include/seqan3/search/dream_index/interleaved_xor_filter.hpp: In member function 'const seqan3::interleaved_xor_filter::counting_agent_type::counting_vector& seqan3::interleaved_xor_filter::counting_agent_type::bulk_count(value_range_t&&) &': + /opt/conda/conda-bld/taxor_1734147243021/work/build/seqan/seqan3/seqan3-src/include/seqan3/search/dream_index/interleaved_xor_filter.hpp:1174:47: error: request for member 'bulk_contains' in '((seqan3::interleaved_xor_filter::counting_agent_type*)this)->seqan3::interleaved_xor_filter::counting_agent_type::membership_agent', which is of non-class type 'int' + 1174 | result_buffer = membership_agent.bulk_contains(value); + | ^~~~~~~~~~~~~ + /opt/conda/conda-bld/taxor_1734147243021/work/build/seqan/seqan3/seqan3-src/include/seqan3/search/dream_index/interleaved_xor_filter.hpp: At global scope: + /opt/conda/conda-bld/taxor_1734147243021/work/build/seqan/seqan3/seqan3-src/include/seqan3/search/dream_index/interleaved_xor_filter.hpp:1233:21: error: 'membership_agent' in 'using seqan3::interleaved_xor_filter::counting_agent_type::counting_vector::ixf_t = class seqan3::interleaved_xor_filter' does not name a type + 1233 | typename ixf_t::membership_agent membership_agent; + | ^~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/taxor_1734147243021/work/src/hixf/build/hierarchical_interleaved_xor_filter.hpp: In member function 'hixf::hierarchical_interleaved_xor_filter::membership_agent hixf::hierarchical_interleaved_xor_filter::membership_agent() const': + /opt/conda/conda-bld/taxor_1734147243021/work/src/hixf/build/hierarchical_interleaved_xor_filter.hpp:131:62: error: 'membership_agent' in 'class hixf::hierarchical_interleaved_xor_filter' does not name a type + 131 | return typename hierarchical_interleaved_xor_filter::membership_agent{*this}; + | ^~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/taxor_1734147243021/work/src/hixf/build/hierarchical_interleaved_xor_filter.hpp: At global scope: + /opt/conda/conda-bld/taxor_1734147243021/work/src/hixf/build/hierarchical_interleaved_xor_filter.hpp:166:61: error: redeclaration of 'template requires (same_as) || (same_as) class hixf::hierarchical_interleaved_xor_filter' with different constraints + 166 | class hierarchical_interleaved_xor_filter::user_bins + | ^~~~~~~~~ + /opt/conda/conda-bld/taxor_1734147243021/work/src/hixf/build/hierarchical_interleaved_xor_filter.hpp:293:61: error: redeclaration of 'template requires (same_as) || (same_as) class hixf::hierarchical_interleaved_xor_filter' with different constraints + 293 | class hierarchical_interleaved_xor_filter::membership_agent + | ^~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/taxor_1734147243021/work/src/hixf/build/hierarchical_interleaved_xor_filter.hpp:422:61: error: redeclaration of 'template requires (same_as) || (same_as) class hixf::hierarchical_interleaved_xor_filter' with different constraints + 422 | class hierarchical_interleaved_xor_filter::counting_agent_type + | ^~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/taxor_1734147243021/work/src/hixf/build/build_data.hpp:22:18: warning: use of 'std::hardware_destructive_interference_size' [-Winterference-size] + 22 | alignas(std::hardware_destructive_interference_size) std::atomic ixf_number{}; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/taxor_1734147243021/work/src/hixf/build/build_data.hpp:22:18: note: its value can vary between compiler versions or with different '-mtune' or '-mcpu' flags + /opt/conda/conda-bld/taxor_1734147243021/work/src/hixf/build/build_data.hpp:22:18: note: if this use is part of a public ABI, change it to instead use a constant variable you define + /opt/conda/conda-bld/taxor_1734147243021/work/src/hixf/build/build_data.hpp:22:18: note: the default value for the current CPU tuning is 64 bytes + /opt/conda/conda-bld/taxor_1734147243021/work/src/hixf/build/build_data.hpp:22:18: note: you can stabilize this value with '--param hardware_destructive_interference_size=64', or disable this warning with '-Wno-interference-size' + /opt/conda/conda-bld/taxor_1734147243021/work/src/hixf/build/build_data.hpp:23:18: warning: use of 'std::hardware_destructive_interference_size' [-Winterference-size] + 23 | alignas(std::hardware_destructive_interference_size) std::atomic user_bin_number{}; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + make[2]: *** [hixf/CMakeFiles/hixf.dir/build.make:107: hixf/CMakeFiles/hixf.dir/build/construct_ixf.cpp.o] Error 1 + make[1]: *** [CMakeFiles/Makefile2:260: hixf/CMakeFiles/hixf.dir/all] Error 2 + make: *** [Makefile:91: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/taxor_1734147243021/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/taxor_1734147243021/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/taxor/meta.yaml b/recipes/taxor/meta.yaml index 767c30ea4dcda..8b485d1412930 100755 --- a/recipes/taxor/meta.yaml +++ b/recipes/taxor/meta.yaml @@ -9,7 +9,7 @@ source: md5: 7bffd64282894433b4db60af8f1052c9 # [linux] build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('taxor', max_pin='x.x.x') }} skip: true # [osx] diff --git a/recipes/tbl2asn-forever/build_failure.osx-64.yaml b/recipes/tbl2asn-forever/build_failure.osx-64.yaml index 8c3e663956812..890edd1345156 100644 --- a/recipes/tbl2asn-forever/build_failure.osx-64.yaml +++ b/recipes/tbl2asn-forever/build_failure.osx-64.yaml @@ -1,57 +1,38 @@ -recipe_sha: 4a43dd506582d708ad4ddfa297b8af9ff3cedc11258e4ec6f1d3d1b4f2a78ea7 # The commit at which this recipe failed to build. +recipe_sha: e1d14ac6074401c5be25ca64d25e775429ecd0309c3da848d1b520cb99e4f70d # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #2 - {} is not a Mach-O file - Can't parse the binary at the index #3 - {} is not a Mach-O file - Can't parse the binary at the index #4 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #2 - {} is not a Mach-O file - Can't parse the binary at the index #3 - {} is not a Mach-O file - Can't parse the binary at the index #4 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - INFO: sysroot: '/System/Library/Frameworks/' files: '['vmnet.framework/Versions/A/_CodeSignature/CodeResources', 'vmnet.framework/Versions/A/Resources/version.plist', 'vmnet.framework/Versions/A/Resources/en.lproj/InfoPlist.strings', 'vmnet.framework/Versions/A/Resources/Info.plist']' - INFO: sysroot: '/usr/lib/' files: '['zsh/5.8.1/zsh/zselect.so', 'zsh/5.8.1/zsh/zpty.so', 'zsh/5.8.1/zsh/zprof.so', 'zsh/5.8.1/zsh/zleparameter.so']' + make -f Makefile.OSX -C man install + make[1]: Entering directory '$SRC_DIR/libfaketime/man' + install -dm0755 "$PREFIX/share/man/man1" + install -m0644 faketime.1 "$PREFIX/share/man/man1/faketime.1" + gzip -f "$PREFIX/share/man/man1/faketime.1" + make[1]: Leaving directory '$SRC_DIR/libfaketime/man' + install -dm0755 "$PREFIX/share/doc/faketime/" + install -m0644 README "$PREFIX/share/doc/faketime/README" + install -m0644 NEWS "$PREFIX/share/doc/faketime/NEWS" + + Resource usage statistics from building tbl2asn-forever: + Process count: 8 + CPU time: Sys=0:00:00.1, User=0:00:00.3 + Memory: 57.7M + Disk usage: 49.4K + Time elapsed: 0:00:16.9 + + + Packaging tbl2asn-forever + Packaging tbl2asn-forever-25.7.2f-h18d8cf3_5 + + + + + + WARNING: Importing conda-verify failed. Please be sure to test your packages. conda install conda-verify to make this message go away. + number of files: 9 + Skipping -add_rpath, file already has LC_RPATH set + Fixing linking of /opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1734476600048/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/faketime/libfaketime.1.dylib in /opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1734476600048/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/faketime/libfaketime.1.dylib + New link location is lib/faketime/libfaketime.1.dylib + INFO: sysroot: '/System/Library/Frameworks/' files: '['vmnet.framework/Versions/Current', 'vmnet.framework/Versions/A/_CodeSignature/CodeResources', 'vmnet.framework/Versions/A/Resources/version.plist', 'vmnet.framework/Versions/A/Resources/InfoPlist.loctable']' + INFO: sysroot: '/usr/lib/' files: '['zsh/5.9/zsh/zselect.so', 'zsh/5.9/zsh/zpty.so', 'zsh/5.9/zsh/zprof.so', 'zsh/5.9/zsh/zleparameter.so']' INFO: sysroot: '/opt/X11/' files: '[]' INFO (tbl2asn-forever,bin/real-tbl2asn): Needed DSO /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices found in $SYSROOT INFO (tbl2asn-forever,bin/real-tbl2asn): Needed DSO /System/Library/Frameworks/libiconv.2.dylib found in $SYSROOT @@ -63,42 +44,63 @@ log: |- INFO (tbl2asn-forever,bin/faketime): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT Fixing permissions INFO :: Time taken to mark (prefix) - 0 replacements in 0 files was 0.21 seconds + 0 replacements in 0 files was 0.05 seconds Files containing CONDA_PREFIX ----------------------------- bin/faketime (binary): Patching - Package verification results: - ----------------------------- - /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/tmps_pseuae/tbl2asn-forever-25.7.2f-h2413b67_4.tar.bz2: C1115 Found invalid license "Public Domain" in info/index.json - TEST START: /opt/mambaforge/envs/bioconda/conda-bld/osx-64/tbl2asn-forever-25.7.2f-h2413b67_4.tar.bz2 - Renaming work directory '/opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1685393999558/work' to '/opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1685393999558/work_moved_tbl2asn-forever-25.7.2f-h2413b67_4_osx-64' - INFO:conda_build.utils:Renaming work directory '/opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1685393999558/work' to '/opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1685393999558/work_moved_tbl2asn-forever-25.7.2f-h2413b67_4_osx-64' - INFO:conda_build.utils:shutil.move(work)=/opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1685393999558/work, dest=/opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1685393999558/work_moved_tbl2asn-forever-25.7.2f-h2413b67_4_osx-64) - shutil.move(work)=/opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1685393999558/work, dest=/opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1685393999558/work_moved_tbl2asn-forever-25.7.2f-h2413b67_4_osx-64) - Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld + TEST START: /opt/mambaforge/envs/bioconda/conda-bld/osx-64/tbl2asn-forever-25.7.2f-h18d8cf3_5.tar.bz2 + Renaming work directory '/opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1734476600048/work' to '/opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1734476600048/work_moved_tbl2asn-forever-25.7.2f-h18d8cf3_5_osx-64' + shutil.move(work)=/opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1734476600048/work, dest=/opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1734476600048/work_moved_tbl2asn-forever-25.7.2f-h18d8cf3_5_osx-64) + Reloading output folder (local): ...working... done + Solving environment (_test_env): ...working... done ## Package Plan ## - environment location: /opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1685393999558/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + environment location: /opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1734476600048/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla The following NEW packages will be INSTALLED: - libiconv: 1.17-hac89ed1_0 conda-forge + libiconv: 1.17-hd75f5a5_2 conda-forge libidn11: 1.34-h112b980_0 conda-forge - libzlib: 1.2.13-hfd90126_4 conda-forge - tbl2asn-forever: 25.7.2f-h2413b67_4 local - zlib: 1.2.13-hfd90126_4 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + tbl2asn-forever: 25.7.2f-h18d8cf3_5 local + zlib: 1.3.1-hd23fc13_2 conda-forge Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1685393999558/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1685393999558/test_tmp tbl2asn-test Failed to alter date for tbl2asn. + WARNING: Tests failed for tbl2asn-forever-25.7.2f-h18d8cf3_5.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1734476600048/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1734476600048/test_tmp [NULL_Caption] This copy of tbl2asn is more than a year old. Please download the current version. - Tests failed for tbl2asn-forever-25.7.2f-h2413b67_4.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken - WARNING:conda_build.build:Tests failed for tbl2asn-forever-25.7.2f-h2413b67_4.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken - TESTS FAILED: tbl2asn-forever-25.7.2f-h2413b67_4.tar.bz2 + utils.check_call_env( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/tbl2asn-forever_1734476600048/test_tmp/conda_test_runner.sh']' returned non-zero exit status 1. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: tbl2asn-forever-25.7.2f-h18d8cf3_5.tar.bz2 # Last 100 lines of the build log. +category: |- + test failure diff --git a/recipes/tbl2asn-forever/meta.yaml b/recipes/tbl2asn-forever/meta.yaml index 7db04f3f27362..a8d5569c17bf7 100644 --- a/recipes/tbl2asn-forever/meta.yaml +++ b/recipes/tbl2asn-forever/meta.yaml @@ -15,7 +15,7 @@ source: - test_makefile.patch build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/tefinder/meta.yaml b/recipes/tefinder/meta.yaml index 5bf3b91c2d4b0..ed446ac3d86c6 100644 --- a/recipes/tefinder/meta.yaml +++ b/recipes/tefinder/meta.yaml @@ -6,7 +6,7 @@ package : version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage( 'tefinder', max_pin="x") }} diff --git a/recipes/telescope/build_failure.linux-64.yaml b/recipes/telescope/build_failure.linux-64.yaml index d3e99a34ae4a5..5364e16ab1249 100644 --- a/recipes/telescope/build_failure.linux-64.yaml +++ b/recipes/telescope/build_failure.linux-64.yaml @@ -1,32 +1,12 @@ -recipe_sha: 6be534f2167e70796d4fae8955f294d9bf6e0fd340c3685f2483e1243bf50465 # The commit at which this recipe failed to build. +recipe_sha: ab2c89fc4f93a45a8dff732e30701a01f7366121317a4be94a9f394014b8c2c9 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- - [34m import os, sys, tokenize[0m - [34m [0m - [34m try:[0m - [34m import setuptools[0m - [34m except ImportError as error:[0m - [34m print([0m - [34m "ERROR: Can not execute setup.py since setuptools is not available in "[0m - [34m "the build environment.",[0m - [34m file=sys.stderr,[0m - [34m )[0m - [34m sys.exit(1)[0m - [34m [0m - [34m __file__ = %r[0m - [34m sys.argv[0] = __file__[0m - [34m [0m - [34m if os.path.exists(__file__):[0m - [34m filename = __file__[0m - [34m with tokenize.open(__file__) as f:[0m - [34m setup_py_code = f.read()[0m - [34m else:[0m - [34m filename = ""[0m [34m setup_py_code = "from setuptools import setup; setup()"[0m [34m [0m [34m exec(compile(setup_py_code, filename, "exec"))[0m - [34m '"'"''"'"''"'"' % ('"'"'/opt/conda/conda-bld/telescope_1685653914752/work/setup.py'"'"',), "", "exec"))' egg_info --egg-base /tmp/pip-pip-egg-info-tdj_wqx2[0m - [1;35mcwd[0m: /opt/conda/conda-bld/telescope_1685653914752/work/ + [34m '"'"''"'"''"'"' % ('"'"'/opt/conda/conda-bld/telescope_1734565157348/work/setup.py'"'"',), "", "exec"))' egg_info --egg-base /tmp/pip-pip-egg-info-hshfejv4[0m + [1;35mcwd[0m: /opt/conda/conda-bld/telescope_1734565157348/work/ + Preparing metadata (setup.py): finished with status 'error' [1;31merror[0m: [1mmetadata-generation-failed[0m [31m[0m Encountered error while generating package metadata. @@ -34,71 +14,93 @@ log: |- [1;35mnote[0m: This is an issue with the package mentioned above, not pip. [1;36mhint[0m: See above for details. - Preparing metadata (setup.py): finished with status 'error' Exception information: Traceback (most recent call last): - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/operations/build/metadata_legacy.py", line 64, in generate_metadata + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/operations/build/metadata_legacy.py", line 64, in generate_metadata call_subprocess( - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/utils/subprocess.py", line 224, in call_subprocess + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/utils/subprocess.py", line 209, in call_subprocess raise error pip._internal.exceptions.InstallationSubprocessError: python setup.py egg_info exited with 1 The above exception was the direct cause of the following exception: Traceback (most recent call last): - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 169, in exc_logging_wrapper - status = run_func(*args) - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 248, in wrapper + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + ^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper return func(self, options, args) - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 377, in run + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/commands/install.py", line 379, in run requirement_set = resolver.resolve( - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 73, in resolve + ^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 76, in resolve collected = self.factory.collect_root_requirements(root_reqs) - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 491, in collect_root_requirements - req = self._make_requirement_from_install_req( - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 453, in _make_requirement_from_install_req - cand = self._make_candidate_from_link( - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 206, in _make_candidate_from_link + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 545, in collect_root_requirements + reqs = list( + ^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 501, in _make_requirements_from_install_req + cand = self._make_base_candidate_from_link( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 233, in _make_base_candidate_from_link self._link_candidate_cache[link] = LinkCandidate( - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 293, in __init__ + ^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 304, in __init__ super().__init__( - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 159, in __init__ self.dist = self._prepare() - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 225, in _prepare + ^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 236, in _prepare dist = self._prepare_distribution() - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 304, in _prepare_distribution + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 315, in _prepare_distribution return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/operations/prepare.py", line 516, in prepare_linked_requirement + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/operations/prepare.py", line 527, in prepare_linked_requirement return self._prepare_linked_requirement(req, parallel_builds) - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/operations/prepare.py", line 631, in _prepare_linked_requirement + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/operations/prepare.py", line 642, in _prepare_linked_requirement dist = _get_prepared_distribution( - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/operations/prepare.py", line 69, in _get_prepared_distribution + ^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/operations/prepare.py", line 72, in _get_prepared_distribution abstract_dist.prepare_distribution_metadata( - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/distributions/sdist.py", line 61, in prepare_distribution_metadata + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/distributions/sdist.py", line 69, in prepare_distribution_metadata self.req.prepare_metadata() - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/req/req_install.py", line 561, in prepare_metadata + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/req/req_install.py", line 581, in prepare_metadata self.metadata_directory = generate_metadata_legacy( - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/operations/build/metadata_legacy.py", line 71, in generate_metadata + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/operations/build/metadata_legacy.py", line 71, in generate_metadata raise MetadataGenerationFailed(package_details=details) from error pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed - Removed file://$SRC_DIR from build tracker '/tmp/pip-build-tracker-n4wkmy4g' - Removed build tracker: '/tmp/pip-build-tracker-n4wkmy4g' + Removed file://$SRC_DIR from build tracker '/tmp/pip-build-tracker-wxrouwo6' + Removed build tracker: '/tmp/pip-build-tracker-wxrouwo6' Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/telescope_1685653914752/work/conda_build.sh']' returned non-zero exit status 1. + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/telescope_1734565157348/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/telescope_1734565157348/work/conda_build.sh']' returned non-zero exit status 1. # Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/telescope/build_failure.osx-64.yaml b/recipes/telescope/build_failure.osx-64.yaml index 31b916c0c7085..c4b8bc590f974 100644 --- a/recipes/telescope/build_failure.osx-64.yaml +++ b/recipes/telescope/build_failure.osx-64.yaml @@ -1,104 +1,106 @@ -recipe_sha: 6be534f2167e70796d4fae8955f294d9bf6e0fd340c3685f2483e1243bf50465 # The commit at which this recipe failed to build. +recipe_sha: ab2c89fc4f93a45a8dff732e30701a01f7366121317a4be94a9f394014b8c2c9 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - import os, sys, tokenize - - try: - import setuptools - except ImportError as error: - print( - "ERROR: Can not execute setup.py since setuptools is not available in " - "the build environment.", - file=sys.stderr, - ) - sys.exit(1) - - __file__ = %r - sys.argv[0] = __file__ - - if os.path.exists(__file__): - filename = __file__ - with tokenize.open(__file__) as f: - setup_py_code = f.read() - else: - filename = "" - setup_py_code = "from setuptools import setup; setup()" - - exec(compile(setup_py_code, filename, "exec")) - '"'"''"'"''"'"' % ('"'"'/opt/mambaforge/envs/bioconda/conda-bld/telescope_1685654772475/work/setup.py'"'"',), "", "exec"))' egg_info --egg-base /private/tmp/pip-pip-egg-info-qctc1yow - cwd: /opt/mambaforge/envs/bioconda/conda-bld/telescope_1685654772475/work/ +log: |- + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + Using pip 24.3.1 from $PREFIX/lib/python3.11/site-packages/pip (python 3.11) + Non-user install because user site-packages disabled + Ignoring indexes: https://pypi.org/simple + Created temporary directory: /private/tmp/pip-build-tracker-l6_doczi + Initialized build tracking at /private/tmp/pip-build-tracker-l6_doczi + Created build tracker: /private/tmp/pip-build-tracker-l6_doczi + Entered build tracker: /private/tmp/pip-build-tracker-l6_doczi + Created temporary directory: /private/tmp/pip-install-w9jn7rl1 + Created temporary directory: /private/tmp/pip-ephem-wheel-cache-a0c_tvqa + Processing $SRC_DIR + Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-l6_doczi' + Running setup.py (path:$SRC_DIR/setup.py) egg_info for package from file://$SRC_DIR + Created temporary directory: /private/tmp/pip-pip-egg-info-678cgsck + Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error' - error: metadata-generation-failed - - Encountered error while generating package metadata. - > See above for output. - - note: This is an issue with the package mentioned above, not pip. - hint: See above for details. Exception information: Traceback (most recent call last): - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/operations/build/metadata_legacy.py", line 64, in generate_metadata + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/operations/build/metadata_legacy.py", line 64, in generate_metadata call_subprocess( - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/utils/subprocess.py", line 224, in call_subprocess + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/utils/subprocess.py", line 209, in call_subprocess raise error pip._internal.exceptions.InstallationSubprocessError: python setup.py egg_info exited with 1 The above exception was the direct cause of the following exception: Traceback (most recent call last): - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/cli/base_command.py", line 169, in exc_logging_wrapper - status = run_func(*args) - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/cli/req_command.py", line 248, in wrapper + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + ^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper return func(self, options, args) - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/commands/install.py", line 377, in run + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/commands/install.py", line 379, in run requirement_set = resolver.resolve( - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 73, in resolve + ^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 76, in resolve collected = self.factory.collect_root_requirements(root_reqs) - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 491, in collect_root_requirements - req = self._make_requirement_from_install_req( - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 453, in _make_requirement_from_install_req - cand = self._make_candidate_from_link( - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 206, in _make_candidate_from_link + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 545, in collect_root_requirements + reqs = list( + ^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 501, in _make_requirements_from_install_req + cand = self._make_base_candidate_from_link( + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 233, in _make_base_candidate_from_link self._link_candidate_cache[link] = LinkCandidate( - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 293, in __init__ + ^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 304, in __init__ super().__init__( - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 159, in __init__ self.dist = self._prepare() - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 225, in _prepare + ^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 236, in _prepare dist = self._prepare_distribution() - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 304, in _prepare_distribution + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 315, in _prepare_distribution return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/operations/prepare.py", line 516, in prepare_linked_requirement + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/operations/prepare.py", line 527, in prepare_linked_requirement return self._prepare_linked_requirement(req, parallel_builds) - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/operations/prepare.py", line 631, in _prepare_linked_requirement + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/operations/prepare.py", line 642, in _prepare_linked_requirement dist = _get_prepared_distribution( - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/operations/prepare.py", line 69, in _get_prepared_distribution + ^^^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/operations/prepare.py", line 72, in _get_prepared_distribution abstract_dist.prepare_distribution_metadata( - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/distributions/sdist.py", line 61, in prepare_distribution_metadata + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/distributions/sdist.py", line 69, in prepare_distribution_metadata self.req.prepare_metadata() - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/req/req_install.py", line 561, in prepare_metadata + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/req/req_install.py", line 581, in prepare_metadata self.metadata_directory = generate_metadata_legacy( - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/operations/build/metadata_legacy.py", line 71, in generate_metadata + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/operations/build/metadata_legacy.py", line 71, in generate_metadata raise MetadataGenerationFailed(package_details=details) from error pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed - Removed file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-v27cfzim' - Removed build tracker: '/private/tmp/pip-build-tracker-v27cfzim' - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/telescope_1685654772475/work/conda_build.sh']' returned non-zero exit status 1. + Removed file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-l6_doczi' + Removed build tracker: '/private/tmp/pip-build-tracker-l6_doczi' # Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/telescope/meta.yaml b/recipes/telescope/meta.yaml index 80c9203115fae..f742b4ddfb829 100644 --- a/recipes/telescope/meta.yaml +++ b/recipes/telescope/meta.yaml @@ -22,6 +22,7 @@ requirements: host: - pip - python + - setuptools - numpy >=1.16.3 - scipy >=1.2.1 - pysam >=0.15.2 diff --git a/recipes/teloscope/meta.yaml b/recipes/teloscope/meta.yaml index caffb2191f6f6..2540e48ccfa5c 100644 --- a/recipes/teloscope/meta.yaml +++ b/recipes/teloscope/meta.yaml @@ -7,7 +7,7 @@ source: url: https://github.com/vgl-hub/teloscope/releases/download/v{{version}}/teloscope.v{{version}}-with_submodules.zip sha256: 1f300bd42c408791bdb7463a37530da2ebe72f64d90e8087cf895a9abc88c8b3 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('teloscope', max_pin="x") }} requirements: diff --git a/recipes/telseq/meta.yaml b/recipes/telseq/meta.yaml index 102fffee130f0..0834309026218 100644 --- a/recipes/telseq/meta.yaml +++ b/recipes/telseq/meta.yaml @@ -9,7 +9,7 @@ source: sha256: aac2477f0d01390d1603afe09cadf0f7ba0fb8864c579289dcbe363ca9bbfa1a build: - number: 7 + number: 8 requirements: build: diff --git a/recipes/tepeaks/meta.yaml b/recipes/tepeaks/meta.yaml index 3f1e556d61e26..da9e19d0e64b8 100644 --- a/recipes/tepeaks/meta.yaml +++ b/recipes/tepeaks/meta.yaml @@ -10,7 +10,7 @@ source: sha256: unused build: - number: 6 + number: 7 skip: True # [osx] requirements: diff --git a/recipes/terminus/meta.yaml b/recipes/terminus/meta.yaml index cff090b695301..ec663cf50b545 100644 --- a/recipes/terminus/meta.yaml +++ b/recipes/terminus/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 7 + number: 8 source: url: https://github.com/COMBINE-lab/terminus/archive/v{{ version }}.tar.gz diff --git a/recipes/tf-comb/build_failure.linux-64.yaml b/recipes/tf-comb/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..4d5cc1dfd321a --- /dev/null +++ b/recipes/tf-comb/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 1856a5db3b7b08a52be037cfd8008cd5ae5ffe0e5b4473a71aa59097a8d62818 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + r-kernsmooth: 2.23_24-r44hc2011d3_1 conda-forge + r-labeling: 0.4.3-r44hc72bb7e_1 conda-forge + r-lambda.r: 1.2.4-r44hc72bb7e_4 conda-forge + r-lattice: 0.22_6-r44hb1dbf0f_1 conda-forge + r-lifecycle: 1.0.4-r44hc72bb7e_1 conda-forge + r-magrittr: 2.0.3-r44hb1dbf0f_3 conda-forge + r-mass: 7.3_60.0.1-r44hb1dbf0f_1 conda-forge + r-matrix: 1.6_5-r44he966344_1 conda-forge + r-mgcv: 1.9_1-r44h0d28552_1 conda-forge + r-munsell: 0.5.1-r44hc72bb7e_1 conda-forge + r-nlme: 3.1_165-r44hbcb9c34_1 conda-forge + r-pillar: 1.10.0-r44hc72bb7e_0 conda-forge + r-pkgconfig: 2.0.3-r44hc72bb7e_4 conda-forge + r-plyr: 1.8.9-r44ha18555a_1 conda-forge + r-purrr: 1.0.2-r44hdb488b9_1 conda-forge + r-r6: 2.5.1-r44hc72bb7e_3 conda-forge + r-rcolorbrewer: 1.1_3-r44h785f33e_3 conda-forge + r-rcpp: 1.0.13_1-r44h93ab643_0 conda-forge + r-rlang: 1.1.4-r44ha18555a_1 conda-forge + r-scales: 1.3.0-r44hc72bb7e_1 conda-forge + r-stringi: 1.8.4-r44h33cde33_3 conda-forge + r-stringr: 1.5.1-r44h785f33e_1 conda-forge + r-tibble: 3.2.1-r44hdb488b9_3 conda-forge + r-tidyr: 1.3.1-r44h0d4f4ea_1 conda-forge + r-tidyselect: 1.2.1-r44hc72bb7e_1 conda-forge + r-upsetr: 1.4.0-r44hc72bb7e_5 conda-forge + r-utf8: 1.2.4-r44hb1dbf0f_1 conda-forge + r-vctrs: 0.6.5-r44h0d4f4ea_1 conda-forge + r-venndiagram: 1.7.3-r44hc72bb7e_3 conda-forge + r-viridislite: 0.4.2-r44hc72bb7e_2 conda-forge + r-withr: 3.0.2-r44hc72bb7e_0 conda-forge + rav1e: 0.6.6-he8a937b_2 conda-forge + readline: 8.2-h8228510_1 conda-forge + reportlab: 4.2.5-py39h8cd3c5a_0 conda-forge + requests: 2.32.3-pyhd8ed1ab_1 conda-forge + rich: 13.9.4-pyhd8ed1ab_1 conda-forge + rlpycairo: 0.2.0-pyhd8ed1ab_0 conda-forge + s3transfer: 0.10.4-pyhd8ed1ab_1 conda-forge + scikit-learn: 1.6.0-py39h4b7350c_0 conda-forge + scipy: 1.13.1-py39haf93ffa_0 conda-forge + seaborn: 0.13.2-hd8ed1ab_3 conda-forge + seaborn-base: 0.13.2-pyhd8ed1ab_3 conda-forge + sed: 4.8-he412f7d_0 conda-forge + setuptools: 75.6.0-pyhff2d567_1 conda-forge + six: 1.17.0-pyhd8ed1ab_0 conda-forge + stack_data: 0.6.3-pyhd8ed1ab_1 conda-forge + statsmodels: 0.14.4-py39hf3d9206_0 conda-forge + svist4get: 1.3.1.1-pyhdfd78af_0 bioconda + svt-av1: 2.3.0-h5888daf_0 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tf-comb: 1.1-py39hff726c5_1 local + threadpoolctl: 3.5.0-pyhc1e730c_0 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tktable: 2.10-h8bc8fbc_6 conda-forge + tobias: 0.17.1-py39hff726c5_0 bioconda + tqdm: 4.67.1-pyhd8ed1ab_0 conda-forge + traitlets: 5.14.3-pyhd8ed1ab_1 conda-forge + typing_extensions: 4.12.2-pyha770c72_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + unicodedata2: 15.1.0-py39h8cd3c5a_1 conda-forge + urllib3: 1.26.19-pyhd8ed1ab_0 conda-forge + uropa: 4.0.3-pyhdfd78af_0 bioconda + wand: 0.6.10-pyhd8ed1ab_0 conda-forge + wcwidth: 0.2.13-pyhd8ed1ab_1 conda-forge + wheel: 0.45.1-pyhd8ed1ab_1 conda-forge + x265: 3.5-h924138e_3 conda-forge + xgboost: 2.1.3-cpu_pyhac85b48_0 conda-forge + xlsxwriter: 3.2.0-pyhd8ed1ab_0 conda-forge + xorg-libice: 1.1.2-hb9d3cd8_0 conda-forge + xorg-libsm: 1.2.5-he73a12e_0 conda-forge + xorg-libx11: 1.8.10-h4f16b4b_1 conda-forge + xorg-libxau: 1.0.12-hb9d3cd8_0 conda-forge + xorg-libxdmcp: 1.1.5-hb9d3cd8_0 conda-forge + xorg-libxext: 1.3.6-hb9d3cd8_0 conda-forge + xorg-libxrender: 0.9.12-hb9d3cd8_0 conda-forge + xorg-libxt: 1.3.1-hb9d3cd8_0 conda-forge + yaml: 0.2.5-h7f98852_2 conda-forge + zipp: 3.21.0-pyhd8ed1ab_1 conda-forge + zlib: 1.3.1-hb9d3cd8_2 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3462, in test + environ.create_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1050, in create_env + _execute_actions(prefix, precs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1338, in _execute_actions + progressive_fetch_extract.execute() + File "/opt/conda/lib/python3.10/site-packages/conda/core/package_cache_data.py", line 900, in execute + raise CondaMultiError(not_cancelled) + conda.CondaMultiError: ('Connection broken: IncompleteRead(34097474 bytes read, 27101542 more expected)', IncompleteRead(34097474 bytes read, 27101542 more expected)) + ('Connection broken: IncompleteRead(34097474 bytes read, 27101542 more expected)', IncompleteRead(34097474 bytes read, 27101542 more expected)) +# Last 100 lines of the build log. diff --git a/recipes/tf-comb/meta.yaml b/recipes/tf-comb/meta.yaml index 032969cfb9cc0..0cd8b06e14649 100644 --- a/recipes/tf-comb/meta.yaml +++ b/recipes/tf-comb/meta.yaml @@ -13,7 +13,7 @@ source: build: skip: True # [py>=311 or py2k] script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation - number: 0 + number: 1 run_exports: - {{ pin_subpackage('tf-comb', max_pin="x") }} diff --git a/recipes/tgsgapcloser/build_failure.osx-64.yaml b/recipes/tgsgapcloser/build_failure.osx-64.yaml index 05550b869388e..4f4410e201a18 100644 --- a/recipes/tgsgapcloser/build_failure.osx-64.yaml +++ b/recipes/tgsgapcloser/build_failure.osx-64.yaml @@ -1,20 +1,98 @@ -recipe_sha: cacb4cd88fd24b850b8c9e75c7eace4f1b14fd99a0c250297dcda83e8b76069f # The commit at which this recipe failed to build. +recipe_sha: c777d5ab57b801fb6169fcedc71981d53a534a3812a453cf49ff028b0c60b10d # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- + about: + home: https://github.com/BGI-Qingdao/TGS-GapCloser + license: GPL-3.0-only + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + license_file: LICENSE + summary: A gap-closing software tool that uses error-prone long reads generated + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + by third-generation-sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled + contigs to fill N-gap in the genome assembly. + extra: + copy_test_source_files: true + final: true + recipe-maintainers: + - cchd0001 + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1734796763069/work + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1734796763069/work/conda_build.sh']' returned non-zero exit status 2. + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1734796763069/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1734796763069/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1734796763069/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar + AS=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-checksyms + CLANG=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CMAKE_PREFIX_PATH=:$PREFIX + CPPFLAGS=-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INDR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-indr + INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool + LD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool + LIPO=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-lipo + NM=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-nm + NMEDIT=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-nmedit + OTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-otool + PAGESTUFF=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-pagestuff + RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-redo_prebinding + SEGEDIT=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-seg_hack + SIZE=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-size + STRINGS=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strings + STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -std=c14 -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -std=c14 -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + cd minimap2 && make + make[1]: Entering directory '$SRC_DIR/minimap2' + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC main.c -o main.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC kthread.c -o kthread.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC kalloc.c -o kalloc.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC misc.c -o misc.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC bseq.c -o bseq.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC sketch.c -o sketch.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC sdust.c -o sdust.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC options.c -o options.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC index.c -o index.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC chain.c -o chain.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC align.c -o align.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC hit.c -o hit.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC map.c -o map.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC format.c -o format.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC pe.c -o pe.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC esterr.c -o esterr.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC splitidx.c -o splitidx.o + x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -msse2 -DHAVE_KALLOC ksw2_ll_sse.c -o ksw2_ll_sse.o x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extz2_sse.c -o ksw2_extz2_sse41.o - clang-9: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib' [-Wunused-command-line-argument] x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extd2_sse.c -o ksw2_extd2_sse41.o - clang-9: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib' [-Wunused-command-line-argument] x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_exts2_sse.c -o ksw2_exts2_sse41.o - clang-9: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib' [-Wunused-command-line-argument] x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extz2_sse.c -o ksw2_extz2_sse2.o - clang-9: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib' [-Wunused-command-line-argument] x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extd2_sse.c -o ksw2_extd2_sse2.o - clang-9: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib' [-Wunused-command-line-argument] x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_exts2_sse.c -o ksw2_exts2_sse2.o - clang-9: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib' [-Wunused-command-line-argument] x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_dispatch.c -o ksw2_dispatch.o - clang-9: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib' [-Wunused-command-line-argument] $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -csru libminimap2.a kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat main.o -o minimap2 -L. -lminimap2 -lm -lz -lpthread make[1]: Leaving directory '$SRC_DIR/minimap2' @@ -22,83 +100,7 @@ log: |- make[1]: Entering directory '$SRC_DIR/main_src_ont' rm -rf tgsgapcloser.o tgsgapcandidate.o tgsseqsplit.o tgsseqgen.o tgsgapcloser tgsgapcandidate tgsseqsplit tgsseqgen ../common/files/file_reader.o ../biocommon/sam_bam/sam_parser.o ../biocommon/pair/pair_sam_parser.o ../biocommon/fasta/fasta.o ../biocommon/fastq/fastq.o ../biocommon/seq/seq.o ../biocommon/paf/PAF.o ../biocommon/align_common/align_result.o ../common/files/file_writer.o ../common/files/gzstream.o ../common/log/log.o ../common/log/logfilter.o ../common/time/timetools.o ../common/string/stringtools.o ../appcommon/contigPairInfo.o ../appcommon/ScaffInfo.o ../appcommon/ONT2Gap.o ../common/args/argsparser.o x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -std=c14 -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -I../ -g -c tgsgapcloser.cpp -o tgsgapcloser.o - clang-9: warning: argument unused during compilation: '-L/opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib' [-Wunused-command-line-argument] - In file included from tgsgapcloser.cpp:1: - In file included from ../common/args/argsparser.h:4: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/string:545: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/__functional/hash.h:29: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/limits:827: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/type_traits:510: - /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/__type_traits/is_trivially_destructible.h:34:2: error: is_trivially_destructible is not implemented - #error is_trivially_destructible is not implemented - ^ - In file included from tgsgapcloser.cpp:1: - In file included from ../common/args/argsparser.h:4: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/string:576: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/string_view:1025: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/algorithm:1747: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/__algorithm/inplace_merge.h:26: - /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/__memory/destruct_n.h:51:41: error: no template named 'is_trivially_destructible'; did you mean 'is_trivially_constructible'? - {__incr(integral_constant::value>());} - ^ - /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/__type_traits/is_trivially_constructible.h:22:29: note: 'is_trivially_constructible' declared here - struct _LIBCPP_TEMPLATE_VIS is_trivially_constructible - ^ - In file included from tgsgapcloser.cpp:1: - In file included from ../common/args/argsparser.h:4: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/string:576: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/string_view:1025: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/algorithm:1747: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/__algorithm/inplace_merge.h:26: - /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/__memory/destruct_n.h:55:45: error: no template named 'is_trivially_destructible'; did you mean 'is_trivially_constructible'? - {__set(__s, integral_constant::value>());} - ^ - /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/__type_traits/is_trivially_constructible.h:22:29: note: 'is_trivially_constructible' declared here - struct _LIBCPP_TEMPLATE_VIS is_trivially_constructible - ^ - In file included from tgsgapcloser.cpp:1: - In file included from ../common/args/argsparser.h:4: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/string:576: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/string_view:1025: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/algorithm:1747: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/__algorithm/inplace_merge.h:26: - /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/__memory/destruct_n.h:59:49: error: no template named 'is_trivially_destructible'; did you mean 'is_trivially_constructible'? - {__process(__p, integral_constant::value>());} - ^ - /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/__type_traits/is_trivially_constructible.h:22:29: note: 'is_trivially_constructible' declared here - struct _LIBCPP_TEMPLATE_VIS is_trivially_constructible - ^ - In file included from tgsgapcloser.cpp:1: - In file included from ../common/args/argsparser.h:4: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/string:576: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/string_view:1027: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/functional:518: - /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/__functional/function.h:590:21: error: no template named 'is_trivially_destructible'; did you mean 'is_trivially_constructible'? - is_trivially_destructible<_Fun>::value> {}; - ^ - /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/_build_env/bin/../include/c/v1/__type_traits/is_trivially_constructible.h:22:29: note: 'is_trivially_constructible' declared here - struct _LIBCPP_TEMPLATE_VIS is_trivially_constructible - ^ - 5 errors generated. - make[1]: *** [Makefile:42: tgsgapcloser.o] Error 1 - make: *** [Makefile:8: all] Error 2 make[1]: Leaving directory '$SRC_DIR/main_src_ont' - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1685394910885/work/conda_build.sh']' returned non-zero exit status 2. # Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/tgsgapcloser/meta.yaml b/recipes/tgsgapcloser/meta.yaml index 9008bafe2bf97..93a0cf69fb67a 100644 --- a/recipes/tgsgapcloser/meta.yaml +++ b/recipes/tgsgapcloser/meta.yaml @@ -7,7 +7,9 @@ source: sha256: bc2cde9397d6dc7776a204cb86e730a5d714d62c2ba60ae38a097cc9799286fe build: - number: 1 + number: 2 + run_exports: + - {{ pin_subpackage('tgsgapcloser', max_pin="x") }} requirements: diff --git a/recipes/thermorawfileparser/meta.yaml b/recipes/thermorawfileparser/meta.yaml index 79cc2bcc2ed53..0989eedf97658 100644 --- a/recipes/thermorawfileparser/meta.yaml +++ b/recipes/thermorawfileparser/meta.yaml @@ -8,7 +8,7 @@ package: build: run_exports: - {{ pin_subpackage('thermorawfileparser', max_pin="x.x.x") }} - number: 0 + number: 1 noarch: generic script: - mkdir $PREFIX/bin diff --git a/recipes/thesias/meta.yaml b/recipes/thesias/meta.yaml index 2a8ef2bb512d9..f42f7694d1e77 100644 --- a/recipes/thesias/meta.yaml +++ b/recipes/thesias/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 0a6d09b832e102cb69a1f0ec240b5cfa1c0f56f7c0e6114401b659880eefb864 build: - number: 5 + number: 6 skip: True # [osx] requirements: diff --git a/recipes/tidehunter/meta.yaml b/recipes/tidehunter/meta.yaml index 227c438e5450b..def57bec83e4d 100644 --- a/recipes/tidehunter/meta.yaml +++ b/recipes/tidehunter/meta.yaml @@ -10,7 +10,7 @@ source: sha256: b4ba87f4500b24f47da98a06a1d1e185ef05764a7d747099148d898b6b6bc054 build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage('tidehunter', max_pin="x") }} diff --git a/recipes/tidk/meta.yaml b/recipes/tidk/meta.yaml index 636b5da45dfd7..30a0284d7c009 100644 --- a/recipes/tidk/meta.yaml +++ b/recipes/tidk/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('tidk', max_pin="x.x") }} diff --git a/recipes/tidyp/meta.yaml b/recipes/tidyp/meta.yaml index 0ff496e43703c..05853c0b391e9 100644 --- a/recipes/tidyp/meta.yaml +++ b/recipes/tidyp/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 5f0965041119bed0ed70a7f0be39e8f0162141eea14d77f472b49f8b3303ab0b build: - number: 6 + number: 7 run_exports: - {{ pin_subpackage('tidyp', max_pin="x") }} diff --git a/recipes/tigmint/meta.yaml b/recipes/tigmint/meta.yaml index f7042d839b8b9..381b85cf81961 100644 --- a/recipes/tigmint/meta.yaml +++ b/recipes/tigmint/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 8e7b5d424ff69d5da7b117bef9996463b02205078ce0fb6e3074ca6c9933efa9 build: - number: 3 + number: 4 skip: True #[(py>38 or py<38) and (arm64 or aarch64)] run_exports: - {{ pin_subpackage("tigmint", max_pin="x") }} diff --git a/recipes/tiny-count/meta.yaml b/recipes/tiny-count/meta.yaml index 297ae04d60448..216faf0334192 100644 --- a/recipes/tiny-count/meta.yaml +++ b/recipes/tiny-count/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: True # [not unix] - number: 1 + number: 2 script: "{{ PYTHON }} -m pip install . -vv" script_env: - tiny_count_only=1 diff --git a/recipes/tinyalign/meta.yaml b/recipes/tinyalign/meta.yaml index f9afc31f9b9f0..c09e0615bf8ba 100644 --- a/recipes/tinyalign/meta.yaml +++ b/recipes/tinyalign/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 9c6dc91ae4a886ab9369a106115add04c71fb62b45f706247d494e43ccf7a588 build: - number: 1 + number: 2 script: "{{ PYTHON }} -m pip install . --no-deps -vv" skip: True # [py < 37] run_exports: diff --git a/recipes/tksm/build_failure.linux-64.yaml b/recipes/tksm/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..6f9f041f5dc22 --- /dev/null +++ b/recipes/tksm/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 6ede4122baa2c6e053a309ae657dae91b0d8d1bb901b7022d882c40ffc9cbe61 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + /opt/conda/conda-bld/tksm_1734158405604/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include/fmt/base.h:737:41: note: 'fmt::v11::throw_format_error' declared here + 737 | FMT_DEPRECATED FMT_NORETURN inline void throw_format_error( + | ^~~~~~~~~~~~~~~~~~ + extern/include/fmtlog/fmtlog.h:649:34: error: 'throw_format_error' is not a member of 'fmt::v11::detail'; did you mean 'fmt::v11::throw_format_error'? + 649 | if (id < 0) fmt::detail::throw_format_error("invalid format string"); + | ^~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/tksm_1734158405604/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include/fmt/base.h:737:41: note: 'fmt::v11::throw_format_error' declared here + 737 | FMT_DEPRECATED FMT_NORETURN inline void throw_format_error( + | ^~~~~~~~~~~~~~~~~~ + In file included from extern/include/fmtlog/fmtlog.h:821: + extern/include/fmtlog/fmtlog-inl.h: In static member function 'static void fmtlogT<__>::setLogFile(const char*, bool)': + extern/include/fmtlog/fmtlog-inl.h:550:18: error: 'throw_format_error' is not a member of 'fmt::v11::detail'; did you mean 'fmt::v11::throw_format_error'? + 550 | fmt::detail::throw_format_error(err.c_str()); + | ^~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/tksm_1734158405604/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include/fmt/base.h:737:41: note: 'fmt::v11::throw_format_error' declared here + 737 | FMT_DEPRECATED FMT_NORETURN inline void throw_format_error( + | ^~~~~~~~~~~~~~~~~~ + In file included from src/util.h:15, + from src/interval.h:19, + from src/head.h:8, + from src/tksm.cpp:10: + extern/include/fmtlog/fmtlog.h: In static member function 'static fmt::v11::string_view fmtlogT<__>::unNameFormat(fmt::v11::string_view, uint32_t*, const Args& ...)': + extern/include/fmtlog/fmtlog.h:636:28: error: 'throw_format_error' is not a member of 'fmt::v11::detail'; did you mean 'fmt::v11::throw_format_error'? + 636 | if (!c) fmt::detail::throw_format_error("invalid format string"); + | ^~~~~~~~~~~~~~~~~~ + In file included from /opt/conda/conda-bld/tksm_1734158405604/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include/fmt/format.h:41, + from /opt/conda/conda-bld/tksm_1734158405604/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include/fmt/core.h:5, + from src/tksm.cpp:1: + /opt/conda/conda-bld/tksm_1734158405604/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include/fmt/base.h:737:41: note: 'fmt::v11::throw_format_error' declared here + 737 | FMT_DEPRECATED FMT_NORETURN inline void throw_format_error( + | ^~~~~~~~~~~~~~~~~~ + extern/include/fmtlog/fmtlog.h:649:34: error: 'throw_format_error' is not a member of 'fmt::v11::detail'; did you mean 'fmt::v11::throw_format_error'? + 649 | if (id < 0) fmt::detail::throw_format_error("invalid format string"); + | ^~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/tksm_1734158405604/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include/fmt/base.h:737:41: note: 'fmt::v11::throw_format_error' declared here + 737 | FMT_DEPRECATED FMT_NORETURN inline void throw_format_error( + | ^~~~~~~~~~~~~~~~~~ + In file included from extern/include/fmtlog/fmtlog.h:821: + extern/include/fmtlog/fmtlog-inl.h: In static member function 'static void fmtlogT<__>::setLogFile(const char*, bool)': + extern/include/fmtlog/fmtlog-inl.h:550:18: error: 'throw_format_error' is not a member of 'fmt::v11::detail'; did you mean 'fmt::v11::throw_format_error'? + 550 | fmt::detail::throw_format_error(err.c_str()); + | ^~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/tksm_1734158405604/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include/fmt/base.h:737:41: note: 'fmt::v11::throw_format_error' declared here + 737 | FMT_DEPRECATED FMT_NORETURN inline void throw_format_error( + | ^~~~~~~~~~~~~~~~~~ + In file included from src/util.h:15, + from src/interval.h:19, + from src/truncate.cpp:16: + extern/include/fmtlog/fmtlog.h: In static member function 'static fmt::v11::string_view fmtlogT<__>::unNameFormat(fmt::v11::string_view, uint32_t*, const Args& ...)': + extern/include/fmtlog/fmtlog.h:636:28: error: 'throw_format_error' is not a member of 'fmt::v11::detail'; did you mean 'fmt::v11::throw_format_error'? + 636 | if (!c) fmt::detail::throw_format_error("invalid format string"); + | ^~~~~~~~~~~~~~~~~~ + In file included from /opt/conda/conda-bld/tksm_1734158405604/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include/fmt/format.h:41, + from /opt/conda/conda-bld/tksm_1734158405604/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include/fmt/compile.h:15, + from src/truncate.cpp:3: + /opt/conda/conda-bld/tksm_1734158405604/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include/fmt/base.h:737:41: note: 'fmt::v11::throw_format_error' declared here + 737 | FMT_DEPRECATED FMT_NORETURN inline void throw_format_error( + | ^~~~~~~~~~~~~~~~~~ + extern/include/fmtlog/fmtlog.h:649:34: error: 'throw_format_error' is not a member of 'fmt::v11::detail'; did you mean 'fmt::v11::throw_format_error'? + 649 | if (id < 0) fmt::detail::throw_format_error("invalid format string"); + | ^~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/tksm_1734158405604/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include/fmt/base.h:737:41: note: 'fmt::v11::throw_format_error' declared here + 737 | FMT_DEPRECATED FMT_NORETURN inline void throw_format_error( + | ^~~~~~~~~~~~~~~~~~ + In file included from extern/include/fmtlog/fmtlog.h:821: + extern/include/fmtlog/fmtlog-inl.h: In static member function 'static void fmtlogT<__>::setLogFile(const char*, bool)': + extern/include/fmtlog/fmtlog-inl.h:550:18: error: 'throw_format_error' is not a member of 'fmt::v11::detail'; did you mean 'fmt::v11::throw_format_error'? + 550 | fmt::detail::throw_format_error(err.c_str()); + | ^~~~~~~~~~~~~~~~~~ + /opt/conda/conda-bld/tksm_1734158405604/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include/fmt/base.h:737:41: note: 'fmt::v11::throw_format_error' declared here + 737 | FMT_DEPRECATED FMT_NORETURN inline void throw_format_error( + | ^~~~~~~~~~~~~~~~~~ + make: *** [Makefile:91: build/obj/tksm.o] Error 1 + make: *** Waiting for unfinished jobs.... + make: *** [Makefile:91: build/obj/tag.o] Error 1 + make: *** [Makefile:97: build/obj/headers.gch] Error 1 + make: *** [Makefile:91: build/obj/truncate.o] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/tksm_1734158405604/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/tksm_1734158405604/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/tksm/meta.yaml b/recipes/tksm/meta.yaml index 33ed879f901ef..e56a76aed48b1 100644 --- a/recipes/tksm/meta.yaml +++ b/recipes/tksm/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 skip: True # [py < 3.8 or osx] run_exports: - {{ pin_subpackage('tksm', max_pin="x.x") }} diff --git a/recipes/tn93/meta.yaml b/recipes/tn93/meta.yaml index 4c2f9e895ef64..f0fe13f999902 100644 --- a/recipes/tn93/meta.yaml +++ b/recipes/tn93/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 0cdd456070a7103cf264a96e2228611bd1188161dec2666e0896bcd655c40f38 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('tn93', max_pin="x") }} diff --git a/recipes/tntblast/2.4/build_failure.osx-64.yaml b/recipes/tntblast/2.4/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..04d123962be66 --- /dev/null +++ b/recipes/tntblast/2.4/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 9782aa7f89643f4df44ad8706a1b85c48775e06f4a5255a530e2e614777fadaa # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tntblast-2.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tntblast-2.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c tntblast.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c degenerate_na.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c primer.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c input.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c nuc_cruc_anchor.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c nuc_cruc.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c nuc_cruc_output.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c nuc_cruc_santa_lucia.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c bind_oligo.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c amplicon_search.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c probe_search.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c padlock_search.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c tntblast_master.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c tntblast_worker.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c tntblast_util.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c options.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c tntblast_local.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c bitmask.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c sequence_data.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c sequence_data_annot.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c annotation.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c annotation_embl.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c annotation_gbk.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c annotation_util.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c sequence_data_fastx.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c tntblast_timer.cpp + x86_64-apple-darwin13.4.0-clang -O3 -Wall -fopenmp -std=c14 -I$BUILD_PREFIX/include -c mpi_util.cpp + x86_64-apple-darwin13.4.0-clang -o tntblast tntblast.o degenerate_na.o primer.o input.o nuc_cruc_anchor.o nuc_cruc.o nuc_cruc_output.o nuc_cruc_santa_lucia.o bind_oligo.o amplicon_search.o probe_search.o padlock_search.o tntblast_master.o tntblast_worker.o tntblast_util.o options.o tntblast_local.o bitmask.o sequence_data.o sequence_data_annot.o annotation.o annotation_embl.o annotation_gbk.o annotation_util.o sequence_data_fastx.o tntblast_timer.o mpi_util.o -lm -lz -L$BUILD_PREFIX/lib -fopenmp + + Resource usage statistics from building tntblast: + Process count: 4 + CPU time: Sys=0:00:02.2, User=0:00:29.2 + Memory: 122.2M + Disk usage: 4.6K + Time elapsed: 0:00:54.4 + + + Packaging tntblast + Packaging tntblast-2.4-he136a0b_1 + number of files: 1 + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2765, in build + newly_built_packages = bundlers[pkg_type]( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1874, in bundle_conda + files = post_process_files(metadata, initial_files) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1653, in post_process_files + post_build(m, new_files, build_python=python) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1759, in post_build + post_process_shared_lib(m, f, prefix_files, host_prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1635, in post_process_shared_lib + mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 477, in mk_relative_osx + names = macho.otool(path, prefix) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 221, in otool + lines = check_output([otool, "-l", path], stderr=STDOUT).decode("utf-8") + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 421, in check_output + return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, + File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 526, in run + raise CalledProcessError(retcode, process.args, + subprocess.CalledProcessError: Command '['/opt/mambaforge/envs/bioconda/conda-bld/tntblast_1733865394964/_build_env/bin/llvm-otool', '-l', '/opt/mambaforge/envs/bioconda/conda-bld/tntblast_1733865394964/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin/tntblast']' died with . +# Last 100 lines of the build log. diff --git a/recipes/tntblast/2.4/meta.yaml b/recipes/tntblast/2.4/meta.yaml index c4f641810f439..95af5d7184253 100644 --- a/recipes/tntblast/2.4/meta.yaml +++ b/recipes/tntblast/2.4/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage( name|lower, max_pin="x") }} diff --git a/recipes/tntblast/build_failure.linux-64.yaml b/recipes/tntblast/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..94b1c1027d090 --- /dev/null +++ b/recipes/tntblast/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 302c59c9daaf35403eb460795564c631a55207f96d6a03a3617bcf3a152fd91b # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + | ^~~~ + compress.h:68:15: error: 'bit' was not declared in this scope + 68 | bit; \ + | ^~~ + compress.h:167:17: note: in expansion of macro 'PACK' + 167 | PACK(HUFFMAN_m, 7); + | ^~~~ + compress.h:68:15: error: 'bit' was not declared in this scope + 68 | bit; \ + | ^~~ + compress.h:170:17: note: in expansion of macro 'PACK' + 170 | PACK(HUFFMAN_r, 7); + | ^~~~ + compress.h:68:15: error: 'bit' was not declared in this scope + 68 | bit; \ + | ^~~ + compress.h:173:17: note: in expansion of macro 'PACK' + 173 | PACK(HUFFMAN_s, 7); + | ^~~~ + compress.h:68:15: error: 'bit' was not declared in this scope + 68 | bit; \ + | ^~~ + compress.h:176:17: note: in expansion of macro 'PACK' + 176 | PACK(HUFFMAN_v, 7); + | ^~~~ + compress.h:68:15: error: 'bit' was not declared in this scope + 68 | bit; \ + | ^~~ + compress.h:179:17: note: in expansion of macro 'PACK' + 179 | PACK(HUFFMAN_w, 7); + | ^~~~ + compress.h:68:15: error: 'bit' was not declared in this scope + 68 | bit; \ + | ^~~ + compress.h:182:17: note: in expansion of macro 'PACK' + 182 | PACK(HUFFMAN_y, 7); + | ^~~~ + compress.h:68:15: error: 'bit' was not declared in this scope + 68 | bit; \ + | ^~~ + compress.h:185:17: note: in expansion of macro 'PACK' + 185 | PACK(HUFFMAN_h, 7); + | ^~~~ + compress.h:68:15: error: 'bit' was not declared in this scope + 68 | bit; \ + | ^~~ + compress.h:188:17: note: in expansion of macro 'PACK' + 188 | PACK(HUFFMAN_k, 7); + | ^~~~ + compress.h:68:15: error: 'bit' was not declared in this scope + 68 | bit; \ + | ^~~ + compress.h:191:17: note: in expansion of macro 'PACK' + 191 | PACK(HUFFMAN_d, 7); + | ^~~~ + compress.h:68:15: error: 'bit' was not declared in this scope + 68 | bit; \ + | ^~~ + compress.h:194:17: note: in expansion of macro 'PACK' + 194 | PACK(HUFFMAN_b, 7); + | ^~~~ + compress.h:68:15: error: 'bit' was not declared in this scope + 68 | bit; \ + | ^~~ + compress.h:197:17: note: in expansion of macro 'PACK' + 197 | PACK(HUFFMAN_i, 7); + | ^~~~ + compress.h:68:15: error: 'bit' was not declared in this scope + 68 | bit; \ + | ^~~ + compress.h:204:5: note: in expansion of macro 'PACK' + 204 | PACK(HUFFMAN_END, 3); + | ^~~~ + compress.h:207:8: error: 'bit' was not declared in this scope + 207 | if(bit != 0){ + | ^~~ + make: *** [Makefile:63: annotation.o] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/tntblast_1734143618259/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/tntblast_1734143618259/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/tntblast/meta.yaml b/recipes/tntblast/meta.yaml index e10695d06f338..f817b572d21d5 100644 --- a/recipes/tntblast/meta.yaml +++ b/recipes/tntblast/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage( name|lower, max_pin="x") }} diff --git a/recipes/tpmcalculator/meta.yaml b/recipes/tpmcalculator/meta.yaml index a4001bdd3824c..f9051f5d86231 100644 --- a/recipes/tpmcalculator/meta.yaml +++ b/recipes/tpmcalculator/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 29aa167a35bb006b2e912d2f7a53f7a9a265308f919906336fc3fe2ee3abece6 build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} diff --git a/recipes/tracy/build_failure.linux-64.yaml b/recipes/tracy/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..c3adf662f4a68 --- /dev/null +++ b/recipes/tracy/build_failure.linux-64.yaml @@ -0,0 +1,4 @@ +recipe_sha: dc5c7200a0e000682c2d92b5260389082b30f811eaf7c583a351c329fb2266f2 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + exists in conda-forge diff --git a/recipes/tracy/build_failure.linux-aarch64.yaml b/recipes/tracy/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..c3adf662f4a68 --- /dev/null +++ b/recipes/tracy/build_failure.linux-aarch64.yaml @@ -0,0 +1,4 @@ +recipe_sha: dc5c7200a0e000682c2d92b5260389082b30f811eaf7c583a351c329fb2266f2 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + exists in conda-forge diff --git a/recipes/tracy/build_failure.osx-64.yaml b/recipes/tracy/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..c3adf662f4a68 --- /dev/null +++ b/recipes/tracy/build_failure.osx-64.yaml @@ -0,0 +1,4 @@ +recipe_sha: dc5c7200a0e000682c2d92b5260389082b30f811eaf7c583a351c329fb2266f2 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +reason: |- + exists in conda-forge diff --git a/recipes/tracy/meta.yaml b/recipes/tracy/meta.yaml index 64b4ec6a20b6f..b2df0a1a4f30d 100644 --- a/recipes/tracy/meta.yaml +++ b/recipes/tracy/meta.yaml @@ -13,7 +13,7 @@ source: git_rev: a654b57 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("tracy", max_pin="x.x") }} diff --git a/recipes/transannot/build_failure.osx-arm64.yaml b/recipes/transannot/build_failure.osx-arm64.yaml new file mode 100644 index 0000000000000..cec1fb7d315b5 --- /dev/null +++ b/recipes/transannot/build_failure.osx-arm64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 30a567096febc083c5156a499f83134e37fccfbfde337d3205374e1ad777e1c3 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + CHECKSYMS=arm64-apple-darwin20.0.0-checksyms + CLANG=arm64-apple-darwin20.0.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=11.0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=arm64-apple-darwin20.0.0 + CONDA_TOOLCHAIN_HOST=arm64-apple-darwin20.0.0 + CPP=arm64-apple-darwin20.0.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=11.0 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang-cpp + DEBUG_CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/transannot-3.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=arm64-apple-darwin20.0.0 + INSTALL_NAME_TOOL=arm64-apple-darwin20.0.0-install_name_tool + LD=arm64-apple-darwin20.0.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=arm64-apple-darwin20.0.0-libtool + LIPO=arm64-apple-darwin20.0.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=arm64-apple-darwin20.0.0-nm + NMEDIT=arm64-apple-darwin20.0.0-nmedit + OBJC=arm64-apple-darwin20.0.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang + OTOOL=arm64-apple-darwin20.0.0-otool + PAGESTUFF=arm64-apple-darwin20.0.0-pagestuff + RANLIB=arm64-apple-darwin20.0.0-ranlib + REDO_PREBINDING=arm64-apple-darwin20.0.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk + SEGEDIT=arm64-apple-darwin20.0.0-segedit + SEG_ADDR_TABLE=arm64-apple-darwin20.0.0-seg_addr_table + SEG_HACK=arm64-apple-darwin20.0.0-seg_hack + SIZE=arm64-apple-darwin20.0.0-size + STRINGS=arm64-apple-darwin20.0.0-strings + STRIP=arm64-apple-darwin20.0.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_arm64_apple_darwin20_0_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=arm64-apple-darwin20.0.0 + host_alias=arm64-apple-darwin20.0.0 + INFO: activate_clangxx_osx-arm64.sh made the following environmental changes: + CLANGXX=arm64-apple-darwin20.0.0-clang + CXX=arm64-apple-darwin20.0.0-clang + CXXFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/transannot-3.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang + DEBUG_CXXFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/transannot-3.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + $SRC_DIR/build $SRC_DIR + -- The CXX compiler identification is Clang 18.1.8 + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- The C compiler identification is Clang 18.1.8 + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang - skipped + -- Detecting C compile features + -- Detecting C compile features - done + -- ZSTD VERSION 1.3.8 + -- Performing Test HAVE_POSIX_FADVISE + -- Performing Test HAVE_POSIX_FADVISE - Failed + -- Performing Test HAVE_POSIX_MADVISE + -- Performing Test HAVE_POSIX_MADVISE - Success + -- Performing Test ATOMIC_LIBRARY_NATIVE + -- Performing Test ATOMIC_LIBRARY_NATIVE - Success + -- Performing Test HAVE_ZLIB_CHECK + -- Performing Test HAVE_ZLIB_CHECK - Success + -- Performing Test HAVE_BZLIB_CHECK + -- Performing Test HAVE_BZLIB_CHECK - Success + -- Configuring done (11.4s) + -- Generating done (0.1s) + -- Build files have been written to: $SRC_DIR/build + Change Dir: '$SRC_DIR/build' + + Run Build Command(s): $BUILD_PREFIX/bin/cmake -E env VERBOSE=1 $BUILD_PREFIX/bin/make -f Makefile -j2 install + $BUILD_PREFIX/bin/cmake -S$SRC_DIR -B$SRC_DIR/build --check-build-system CMakeFiles/Makefile.cmake 0 + $BUILD_PREFIX/bin/cmake -E cmake_progress_start $SRC_DIR/build/CMakeFiles $SRC_DIR/build//CMakeFiles/progress.marks + $BUILD_PREFIX/bin/make -f CMakeFiles/Makefile2 all + make[1]: Entering directory '$SRC_DIR/build' + $BUILD_PREFIX/bin/make -f lib/mmseqs/lib/microtar/CMakeFiles/microtar.dir/build.make lib/mmseqs/lib/microtar/CMakeFiles/microtar.dir/depend + $BUILD_PREFIX/bin/make -f lib/mmseqs/lib/cacode/CMakeFiles/cacode.dir/build.make lib/mmseqs/lib/cacode/CMakeFiles/cacode.dir/depend + make[2]: Entering directory '$SRC_DIR/build' + cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR/lib/mmseqs/lib/cacode $SRC_DIR/build $SRC_DIR/build/lib/mmseqs/lib/cacode $SRC_DIR/build/lib/mmseqs/lib/cacode/CMakeFiles/cacode.dir/DependInfo.cmake "--color=" + make[2]: Entering directory '$SRC_DIR/build' + cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR/lib/mmseqs/lib/microtar $SRC_DIR/build $SRC_DIR/build/lib/mmseqs/lib/microtar $SRC_DIR/build/lib/mmseqs/lib/microtar/CMakeFiles/microtar.dir/DependInfo.cmake "--color=" + make[2]: Leaving directory '$SRC_DIR/build' + $BUILD_PREFIX/bin/make -f lib/mmseqs/lib/cacode/CMakeFiles/cacode.dir/build.make lib/mmseqs/lib/cacode/CMakeFiles/cacode.dir/build + make[2]: Entering directory '$SRC_DIR/build' + Dependee "$SRC_DIR/build/lib/mmseqs/lib/microtar/CMakeFiles/microtar.dir/DependInfo.cmake" is newer than depender "$SRC_DIR/build/lib/mmseqs/lib/microtar/CMakeFiles/microtar.dir/depend.internal". + Dependee "$SRC_DIR/build/lib/mmseqs/lib/microtar/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "$SRC_DIR/build/lib/mmseqs/lib/microtar/CMakeFiles/microtar.dir/depend.internal". + Scanning dependencies of target microtar + make[2]: Leaving directory '$SRC_DIR/build' + $BUILD_PREFIX/bin/make -f lib/mmseqs/lib/microtar/CMakeFiles/microtar.dir/build.make lib/mmseqs/lib/microtar/CMakeFiles/microtar.dir/build + make[2]: Entering directory '$SRC_DIR/build' + [ 0%] Building CXX object lib/mmseqs/lib/cacode/CMakeFiles/cacode.dir/lambda_calculator.cpp.o + cd $SRC_DIR/build/lib/mmseqs/lib/cacode && $BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -I$SRC_DIR/lib/mmseqs/lib/simde -I$SRC_DIR/lib/mmseqs/lib -I$SRC_DIR/lib/mmseqs/lib/simd -I$SRC_DIR/lib/mmseqs/lib/gzstream -I$SRC_DIR/lib/mmseqs/lib/alp -I$SRC_DIR/lib/mmseqs/lib/cacode -I$SRC_DIR/lib/mmseqs/lib/ksw2 -I$SRC_DIR/lib/mmseqs/lib/xxhash -I$SRC_DIR/lib/mmseqs/lib/ips4o -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/transannot-3.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -I$PREFIX/include -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk -mmacosx-version-min=11.0 -fsigned-char -msse4.1 -mcx16 -D__APPLE_API_STRICT_CONFORMANCE -std=c1y -stdlib=libc -w -MD -MT lib/mmseqs/lib/cacode/CMakeFiles/cacode.dir/lambda_calculator.cpp.o -MF CMakeFiles/cacode.dir/lambda_calculator.cpp.o.d -o CMakeFiles/cacode.dir/lambda_calculator.cpp.o -c $SRC_DIR/lib/mmseqs/lib/cacode/lambda_calculator.cpp + [ 0%] Building C object lib/mmseqs/lib/microtar/CMakeFiles/microtar.dir/microtar.c.o + cd $SRC_DIR/build/lib/mmseqs/lib/microtar && $BUILD_PREFIX/bin/arm64-apple-darwin20.0.0-clang -I$SRC_DIR/lib/mmseqs/lib/zstd/lib -I$SRC_DIR/lib/mmseqs/lib/tinyexpr -I$SRC_DIR/lib/mmseqs/lib/microtar -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/transannot-3.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -arch arm64 -isysroot /Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.0.sdk -mmacosx-version-min=11.0 -fsigned-char -msse4.1 -mcx16 -D__APPLE_API_STRICT_CONFORMANCE -o CMakeFiles/microtar.dir/microtar.c.o -c $SRC_DIR/lib/mmseqs/lib/microtar/microtar.c + make[2]: Leaving directory '$SRC_DIR/build' + make[2]: Leaving directory '$SRC_DIR/build' + make[1]: Leaving directory '$SRC_DIR/build' +# Last 100 lines of the build log. diff --git a/recipes/transannot/meta.yaml b/recipes/transannot/meta.yaml index 315da17189512..68bd50dec6cc7 100644 --- a/recipes/transannot/meta.yaml +++ b/recipes/transannot/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('transannot', max_pin="x") }} diff --git a/recipes/transgenescan/build_failure.osx-64.yaml b/recipes/transgenescan/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..dc291a95ddd05 --- /dev/null +++ b/recipes/transgenescan/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: b93aebd5132d98e08a164e3f54fc8f618be5ff95709fb40377c8cc30139511c6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + Traceback (most recent call last): + - libcxx-devel 18.1.8 h7c275be_7 + - libxml2 2.13.5 he8ee3e7_1 + - openssl 3.4.0 hd471939_0 + - tapi 1300.6.5 h390ca13_0 + - zstd 1.5.6 h915ae27_0 + - libllvm18 18.1.8 h9ce406d_2 + - sigtool 0.1.3 h88f4db0_0 + - ld64_osx-64 951.9 hc8d1a19_2 + - libclang-cpp18.1 18.1.8 default_h0c94c6a_5 + - llvm-tools-18 18.1.8 h9ce406d_2 + - clang-18 18.1.8 default_h0c94c6a_5 + - llvm-tools 18.1.8 h9ce406d_2 + - cctools_osx-64 1010.6 h00edd4c_2 + - clang 18.1.8 default_h179603d_5 + - clangxx 18.1.8 default_h179603d_5 + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + - compiler-rt 18.1.8 h1020d70_1 + - clang_impl_osx-64 18.1.8 h6a44ed1_23 + - clang_osx-64 18.1.8 h7e5c614_23 + run: [] + test: + commands: + - TransGeneScan 2>&1 | grep "You missed some parameters for input" + about: + home: https://github.com/COL-IU/TransGeneScan + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + license: GPL-3.0-only + license_file: LICENSE + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + summary: Software tool for finding genes in assembled transcripts from metatranscriptomic + sequences. + extra: + copy_test_source_files: true + final: true + identifiers: + - biotools:TransGeneScan + - doi:10.1186/1471-2105-15-S9-S8 + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/transgenescan_1733964377122/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/transgenescan_1733964377122/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/transgenescan_1733964377122/work/conda_build.sh']' returned non-zero exit status 2. + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/transgenescan_1733964377122/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/transgenescan_1733964377122/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/transgenescan-1.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/transgenescan-1.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/transgenescan-1.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/transgenescan-1.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o util_lib.o util_lib.c + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/transgenescan-1.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/transgenescan-1.3.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o hmm_lib.o hmm_lib.c +# Last 100 lines of the build log. diff --git a/recipes/transgenescan/meta.yaml b/recipes/transgenescan/meta.yaml index c31d6d6651c3a..060d54ceb4fff 100644 --- a/recipes/transgenescan/meta.yaml +++ b/recipes/transgenescan/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.3.0 build: - number: 2 + number: 3 source: url: https://github.com/COL-IU/TransGeneScan/archive/refs/tags/v1.3.0.tar.gz diff --git a/recipes/transrate/build_failure.linux-64.yaml b/recipes/transrate/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..d9cc02aa8947e --- /dev/null +++ b/recipes/transrate/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 168cd945432bedfc8b2f69b7b29d1858f6047af9ac3961d484be57d7ac360b11 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Encountered problems while solving: + - package blast-2.2.31-pl526he19e7b1_5 is excluded by strict repo priority + + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("blast==2.2.31=pl526he19e7b1_5")} + Encountered problems while solving: + - package blast-2.2.31-pl526he19e7b1_5 is excluded by strict repo priority + + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("blast==2.2.31=pl526he19e7b1_5")} + Encountered problems while solving: + - package blast-2.2.31-pl526he19e7b1_5 is excluded by strict repo priority + + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("blast==2.2.31=pl526he19e7b1_5")} + Encountered problems while solving: + - package blast-2.2.31-pl526he19e7b1_5 is excluded by strict repo priority +# Last 100 lines of the build log. diff --git a/recipes/transrate/meta.yaml b/recipes/transrate/meta.yaml index 60e13556ae62d..7694a37793b60 100644 --- a/recipes/transrate/meta.yaml +++ b/recipes/transrate/meta.yaml @@ -11,7 +11,7 @@ source: - patch build: - number: 5 + number: 6 skip: True # [osx] requirements: diff --git a/recipes/treebest/build_failure.osx-64.yaml b/recipes/treebest/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..8ddd7a051835c --- /dev/null +++ b/recipes/treebest/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: bb390c6b2034bcad607b8608ef9b2e87d4ecc7507f5ca103dde48e2d5451c878 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + - clang_osx-64 18.1.8 h7e5c614_23 + - clang-18 18.1.8 default_h0c94c6a_5 + - liblzma 5.6.3 hd471939_1 + - libcxx-devel 18.1.8 h7c275be_7 + - libcxx 19.1.5 hf95d169_0 + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/treebest_1733869567792/work/conda_build.sh']' returned non-zero exit status 2. + - compiler-rt 18.1.8 h1020d70_1 + - ca-certificates 2024.8.30 h8857fd0_0 + - clangxx_impl_osx-64 18.1.8 h4b7810f_23 + - m4 1.4.18 haf1e3a3_1001 + - clangxx_osx-64 18.1.8 h7e5c614_23 + - ncurses 6.5 hf036a51_1 + - libiconv 1.17 hd75f5a5_2 + - libllvm18 18.1.8 h9ce406d_2 + - openssl 3.4.0 hd471939_0 + - clang 18.1.8 default_h179603d_5 + - make 4.4.1 h00291cd_2 + - cctools_osx-64 1010.6 h00edd4c_2 + host: + - libcxx 19.1.5 hf95d169_0 + - libiconv 1.17 hd75f5a5_2 + - m4 1.4.18 haf1e3a3_1001 + - flex 2.6.4 hcc69e7b_1004 + - bison 3.8.2 hd7636e7_0 + run: + - libcxx >=18 + test: + commands: + - treebest 2>&1 | grep 'Usage:' + about: + home: http://treesoft.sourceforge.net/treebest.shtml + license: GPLv2 + summary: 'TreeBeST: Tree Building guided by Species Tree, used in the Ensembl Compara + pipeline.' + extra: + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/treebest_1733869567792/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/treebest_1733869567792/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/treebest_1733869567792/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/treebest_1733869567792/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/treebest-1.9.2.post1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/treebest-1.9.2.post1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/treebest-1.9.2.post1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/treebest-1.9.2.post1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + make[1]: Entering directory '$SRC_DIR' + flex parser.l + bison --yacc -d parser.y + x86_64-apple-darwin13.4.0-clang -c -DUSE_GCC -DHAVE_PHYML -DLH3_ADDON -DYYMAXDEPTH=90000 -DYYINITDEPTH=60000 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/treebest-1.9.2.post1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fcommon lex.yy.c -o lex.yy.o + make[1]: Leaving directory '$SRC_DIR' +# Last 100 lines of the build log. diff --git a/recipes/treebest/meta.yaml b/recipes/treebest/meta.yaml index 574c7eb3d17df..20eac13f602da 100644 --- a/recipes/treebest/meta.yaml +++ b/recipes/treebest/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 660ab25f20a56e94dbeea1db8e5000712d381b59e46cfbd3d75f46ed670f6010 build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/treekin/build_failure.linux-64.yaml b/recipes/treekin/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..173ecb2ee188f --- /dev/null +++ b/recipes/treekin/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 7607422bfc5efa2f78dd3e1f7c2537f79847087909f0cad1c691981b8d4c71a7 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Packaging treekin + Packaging treekin-0.5.1-h80fe1c3_5 + number of files: 2 + Warning: rpath /opt/conda/conda-bld/treekin_1734454448683/_build_env/lib is outside prefix /opt/conda/conda-bld/treekin_1734454448683/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place (removing it) + INFO: sysroot: '/opt/conda/conda-bld/treekin_1734454448683/_build_env/x86_64-conda-linux-gnu/sysroot/' files: '['usr/share/zoneinfo', 'usr/share/locale/zh_TW/LC_MESSAGES/libc.mo', 'usr/share/locale/zh_CN/LC_MESSAGES/libc.mo', 'usr/share/locale/vi/LC_MESSAGES/libc.mo']' + INFO (treekin,bin/treekin): Needed DSO lib/liblapack.so.3 found in conda-forge/linux-64::lapack==3.6.1=ha44fe06_2 + INFO (treekin,bin/treekin): Needed DSO lib/libgfortran.so.5 found in conda-forge/linux-64::libgfortran5==14.2.0=hd5240d6_1 + INFO (treekin,bin/treekin): Needed DSO lib/libquadmath.so.0 found in conda-forge/linux-64::libgcc==14.2.0=h77fa898_1 + INFO (treekin,bin/treekin): Needed DSO lib/libmlapack_dd.so.0 found in conda-forge/linux-64::mlapack==0.8.1=hb70a6f5_1 + INFO (treekin,bin/treekin): Needed DSO lib/libmblas_dd.so.0 found in conda-forge/linux-64::mlapack==0.8.1=hb70a6f5_1 + INFO (treekin,bin/treekin): Needed DSO lib/libmlapack_qd.so.0 found in conda-forge/linux-64::mlapack==0.8.1=hb70a6f5_1 + INFO (treekin,bin/treekin): Needed DSO lib/libmblas_qd.so.0 found in conda-forge/linux-64::mlapack==0.8.1=hb70a6f5_1 + INFO (treekin,bin/treekin): Needed DSO lib/libmlapack_gmp.so.0 found in conda-forge/linux-64::mlapack==0.8.1=hb70a6f5_1 + INFO (treekin,bin/treekin): Needed DSO lib/libmblas_gmp.so.0 found in conda-forge/linux-64::mlapack==0.8.1=hb70a6f5_1 + INFO (treekin,bin/treekin): Needed DSO lib/libmlapack___float128.so.0 found in conda-forge/linux-64::mlapack==0.8.1=hb70a6f5_1 + INFO (treekin,bin/treekin): Needed DSO lib/libmblas___float128.so.0 found in conda-forge/linux-64::mlapack==0.8.1=hb70a6f5_1 + INFO (treekin,bin/treekin): Needed DSO lib/libmlapack_double.so.0 found in conda-forge/linux-64::mlapack==0.8.1=hb70a6f5_1 + INFO (treekin,bin/treekin): Needed DSO lib/libmblas_double.so.0 found in conda-forge/linux-64::mlapack==0.8.1=hb70a6f5_1 + INFO (treekin,bin/treekin): Needed DSO lib/libmlapack_longdouble.so.0 found in conda-forge/linux-64::mlapack==0.8.1=hb70a6f5_1 + INFO (treekin,bin/treekin): Needed DSO lib/libmblas_longdouble.so.0 found in conda-forge/linux-64::mlapack==0.8.1=hb70a6f5_1 + WARNING (treekin,bin/treekin): Needed DSO lib/libqd.so.0 found in ['conda-forge/linux-64::qd==2.3.22=h2cc385e_1004'] + WARNING (treekin,bin/treekin): .. but ['conda-forge/linux-64::qd==2.3.22=h2cc385e_1004'] not in reqs/run, (i.e. it is overlinking) (likely) or a missing dependency (less likely) + WARNING (treekin,bin/treekin): Needed DSO lib/libgmp.so.10 found in ['conda-forge/linux-64::gmp==6.3.0=hac33072_2'] + WARNING (treekin,bin/treekin): .. but ['conda-forge/linux-64::gmp==6.3.0=hac33072_2'] not in reqs/run, (i.e. it is overlinking) (likely) or a missing dependency (less likely) + INFO (treekin,bin/treekin): Needed DSO lib/libstdc.so.6 found in conda-forge/linux-64::libstdcxx==14.2.0=hc0a3c3a_1 + INFO (treekin,bin/treekin): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.17=h4a8ded7_18 + WARNING (treekin,bin/treekin): Needed DSO lib/libgomp.so.1 found in ['conda-forge/linux-64::_openmp_mutex==4.5=2_gnu'] + WARNING (treekin,bin/treekin): .. but ['conda-forge/linux-64::_openmp_mutex==4.5=2_gnu'] not in reqs/run, (i.e. it is overlinking) (likely) or a missing dependency (less likely) + INFO (treekin,bin/treekin): Needed DSO lib/libgcc_s.so.1 found in conda-forge/linux-64::libgcc==14.2.0=h77fa898_1 + INFO (treekin,bin/treekin): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libpthread.so.0 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.17=h4a8ded7_18 + INFO (treekin,bin/treekin): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-64==2.17=h4a8ded7_18 + Fixing permissions + Packaged license file/s. + INFO :: Time taken to mark (prefix) + 0 replacements in 0 files was 0.02 seconds + WARNING: Importing conda-verify failed. Please be sure to test your packages. conda install conda-verify to make this message go away. + TEST START: /opt/conda/conda-bld/linux-64/treekin-0.5.1-h80fe1c3_5.tar.bz2 + Renaming work directory '/opt/conda/conda-bld/treekin_1734454448683/work' to '/opt/conda/conda-bld/treekin_1734454448683/work_moved_treekin-0.5.1-h80fe1c3_5_linux-64' + shutil.move(work)=/opt/conda/conda-bld/treekin_1734454448683/work, dest=/opt/conda/conda-bld/treekin_1734454448683/work_moved_treekin-0.5.1-h80fe1c3_5_linux-64) + Reloading output folder (local): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/treekin_1734454448683/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + gmp: 6.3.0-hac33072_2 conda-forge + lapack: 3.6.1-ha44fe06_2 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-ng: 14.2.0-h69a702a_1 conda-forge + libgfortran: 14.2.0-h69a702a_1 conda-forge + libgfortran-ng: 14.2.0-h69a702a_1 conda-forge + libgfortran5: 14.2.0-hd5240d6_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-ng: 14.2.0-h4852527_1 conda-forge + mlapack: 0.8.1-hb70a6f5_1 conda-forge + mpc: 1.3.1-h24ddda3_1 conda-forge + mpfr: 4.2.1-h90cbb55_3 conda-forge + qd: 2.3.22-h2cc385e_1004 conda-forge + treekin: 0.5.1-h80fe1c3_5 local + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + export PREFIX=/opt/conda/conda-bld/treekin_1734454448683/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ + export SRC_DIR=/opt/conda/conda-bld/treekin_1734454448683/test_tmp + treekin --version + treekin: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory + WARNING: Tests failed for treekin-0.5.1-h80fe1c3_5.tar.bz2 - moving package to /opt/conda/conda-bld/broken + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3523, in test + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/treekin_1734454448683/test_tmp/conda_test_runner.sh']' returned non-zero exit status 127. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3727, in build_tree + test(pkg, config=metadata.config.copy(), stats=stats) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3537, in test + tests_failed( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3584, in tests_failed + raise CondaBuildUserError("TESTS FAILED: " os.path.basename(pkg)) + conda_build.exceptions.CondaBuildUserError: TESTS FAILED: treekin-0.5.1-h80fe1c3_5.tar.bz2 +# Last 100 lines of the build log. +category: |- + test failure diff --git a/recipes/treekin/meta.yaml b/recipes/treekin/meta.yaml index bde0d1e1da203..48f2dc6ba1d1d 100644 --- a/recipes/treekin/meta.yaml +++ b/recipes/treekin/meta.yaml @@ -8,7 +8,9 @@ package: build: skip: True # [osx] - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage('treekin', max_pin="x.x") }} source: url: https://github.com/ViennaRNA/Treekin/releases/download/v{{ version }}/Treekin-{{ version }}.tar.gz diff --git a/recipes/treemix/build_failure.osx-64.yaml b/recipes/treemix/build_failure.osx-64.yaml index 6b120cb1a7881..6d305b04b6209 100644 --- a/recipes/treemix/build_failure.osx-64.yaml +++ b/recipes/treemix/build_failure.osx-64.yaml @@ -1,27 +1,13 @@ -recipe_sha: 3cdff620ea62dbf5a358af7054630871b262837c1810d1a11593c4faa7cf88ea # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 0848cf6f7c9f61bc71cfd5922c84ab786035012b80b7a75ead3e4964c2406d90 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/treemix_1717518490688/work - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/treemix_1717518490688/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/treemix_1717518490688/_build_env - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/treemix_1717518490688/work/conda_build.sh']' returned non-zero exit status 2. - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/treemix_1717518490688/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/treemix-1.13 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/treemix-1.13 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool @@ -30,7 +16,7 @@ log: |- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -39,7 +25,7 @@ log: |- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -96,9 +82,23 @@ log: |- make[1]: Entering directory '$SRC_DIR' Making all in src make[2]: Entering directory '$SRC_DIR/src' - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/treemix-1.13 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT TreeMix.o -MD -MP -MF .deps/TreeMix.Tpo -c -o TreeMix.o TreeMix.cpp - x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/treemix-1.13 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT gzstream.o -MD -MP -MF .deps/gzstream.Tpo -c -o gzstream.o gzstream.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/treemix-1.13 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT TreeMix.o -MD -MP -MF .deps/TreeMix.Tpo -c -o TreeMix.o TreeMix.cpp + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/treemix-1.13 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT gzstream.o -MD -MP -MF .deps/gzstream.Tpo -c -o gzstream.o gzstream.cpp + mv -f .deps/gzstream.Tpo .deps/gzstream.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/treemix-1.13 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT PopGraph.o -MD -MP -MF .deps/PopGraph.Tpo -c -o PopGraph.o PopGraph.cpp mv -f .deps/TreeMix.Tpo .deps/TreeMix.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/treemix-1.13 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT nnls.o -MD -MP -MF .deps/nnls.Tpo -c -o nnls.o nnls.cpp + mv -f .deps/nnls.Tpo .deps/nnls.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/treemix-1.13 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT PhyloPop_params.o -MD -MP -MF .deps/PhyloPop_params.Tpo -c -o PhyloPop_params.o PhyloPop_params.cpp + mv -f .deps/PopGraph.Tpo .deps/PopGraph.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/treemix-1.13 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT CountData.o -MD -MP -MF .deps/CountData.Tpo -c -o CountData.o CountData.cpp + mv -f .deps/PhyloPop_params.Tpo .deps/PhyloPop_params.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/treemix-1.13 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT CmdLine.o -MD -MP -MF .deps/CmdLine.Tpo -c -o CmdLine.o CmdLine.cpp + mv -f .deps/CmdLine.Tpo .deps/CmdLine.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/treemix-1.13 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT GraphState2.o -MD -MP -MF .deps/GraphState2.Tpo -c -o GraphState2.o GraphState2.cpp + mv -f .deps/CountData.Tpo .deps/CountData.Po + x86_64-apple-darwin13.4.0-clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/treemix-1.13 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT three_pop.o -MD -MP -MF .deps/three_pop.Tpo -c -o three_pop.o three_pop.cpp + mv -f .deps/three_pop.Tpo .deps/three_pop.Po make[2]: Leaving directory '$SRC_DIR/src' make[1]: Leaving directory '$SRC_DIR' # Last 100 lines of the build log. diff --git a/recipes/treemix/meta.yaml b/recipes/treemix/meta.yaml index ea21b86229cca..ddccaed024be3 100644 --- a/recipes/treemix/meta.yaml +++ b/recipes/treemix/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.13 build: - number: 9 + number: 10 source: url: https://bitbucket.org/nygcresearch/treemix/downloads/treemix-1.13.tar.gz diff --git a/recipes/trf/meta.yaml b/recipes/trf/meta.yaml index 2eac35360b473..44d28624f015f 100644 --- a/recipes/trf/meta.yaml +++ b/recipes/trf/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a build: - number: 6 + number: 7 run_exports: - {{ pin_subpackage(name, max_pin='x') }} diff --git a/recipes/trimadap/meta.yaml b/recipes/trimadap/meta.yaml index 7255cf9012664..bc6eb1e72b228 100644 --- a/recipes/trimadap/meta.yaml +++ b/recipes/trimadap/meta.yaml @@ -3,7 +3,7 @@ package: version: "r11" build: - number: 5 + number: 6 source: url: https://github.com/lh3/trimadap/archive/ddfef210563830d9193b40949da3523b6fb93003.tar.gz diff --git a/recipes/trimadap/r2/meta.yaml b/recipes/trimadap/r2/meta.yaml index d2417fb61e44c..b663134be4d66 100644 --- a/recipes/trimadap/r2/meta.yaml +++ b/recipes/trimadap/r2/meta.yaml @@ -3,7 +3,7 @@ package: version: "r2" build: - number: 4 + number: 5 source: url: https://github.com/lh3/trimadap/archive/3fe26d3a3ddbedfe1be4abb4a6844331015ca6b6.tar.gz diff --git a/recipes/trimal/meta.yaml b/recipes/trimal/meta.yaml index 49ab7cd5dc61d..eb620c4876417 100644 --- a/recipes/trimal/meta.yaml +++ b/recipes/trimal/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 3fba2e07bffb7290c34e713a052d0f0ff1ce0792861740a8cec46f40685c6d73 build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('trimal', max_pin='x') }} diff --git a/recipes/trinity/meta.yaml b/recipes/trinity/meta.yaml index c448dfbc9bb83..b90c9b3ca55aa 100644 --- a/recipes/trinity/meta.yaml +++ b/recipes/trinity/meta.yaml @@ -13,7 +13,7 @@ source: - makefile.patch build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('trinity', max_pin="x") }} diff --git a/recipes/trnascan-se/1.3.1/build_failure.linux-64.yaml b/recipes/trnascan-se/1.3.1/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..13bceb19e6f53 --- /dev/null +++ b/recipes/trnascan-se/1.3.1/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 6d05b49e3d456650e19825d66bada3426610f033740fcf065849acb77696d2a9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + conn.connect() + File "/opt/conda/lib/python3.10/site-packages/urllib3/connection.py", line 730, in connect + sock_and_verified = _ssl_wrap_socket_and_match_hostname( + File "/opt/conda/lib/python3.10/site-packages/urllib3/connection.py", line 909, in _ssl_wrap_socket_and_match_hostname + ssl_sock = ssl_wrap_socket( + File "/opt/conda/lib/python3.10/site-packages/urllib3/util/ssl_.py", line 469, in ssl_wrap_socket + ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls, server_hostname) + File "/opt/conda/lib/python3.10/site-packages/urllib3/util/ssl_.py", line 513, in _ssl_wrap_socket_impl + return ssl_context.wrap_socket(sock, server_hostname=server_hostname) + File "/opt/conda/lib/python3.10/ssl.py", line 513, in wrap_socket + return self.sslsocket_class._create( + File "/opt/conda/lib/python3.10/ssl.py", line 1104, in _create + self.do_handshake() + File "/opt/conda/lib/python3.10/ssl.py", line 1375, in do_handshake + self._sslobj.do_handshake() + ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007) + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 789, in urlopen + response = self._make_request( + File "/opt/conda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 490, in _make_request + raise new_e + urllib3.exceptions.SSLError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007) + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/requests/adapters.py", line 667, in send + resp = conn.urlopen( + File "/opt/conda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 873, in urlopen + return self.urlopen( + File "/opt/conda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 873, in urlopen + return self.urlopen( + File "/opt/conda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 873, in urlopen + return self.urlopen( + File "/opt/conda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 843, in urlopen + retries = retries.increment( + File "/opt/conda/lib/python3.10/site-packages/urllib3/util/retry.py", line 519, in increment + raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type] + urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='lowelab.ucsc.edu', port=443): Max retries exceeded with url: /software/tRNAscan-SE-1.3.1.tar.gz (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007)'))) + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 247, in download_http_errors + yield + File "/opt/conda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 68, in download + download_inner( + File "/opt/conda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 97, in download_inner + resp = session.get( + File "/opt/conda/lib/python3.10/site-packages/requests/sessions.py", line 602, in get + return self.request("GET", url, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/requests/sessions.py", line 589, in request + resp = self.send(prep, **send_kwargs) + File "/opt/conda/lib/python3.10/site-packages/requests/sessions.py", line 724, in send + history = [resp for resp in gen] + File "/opt/conda/lib/python3.10/site-packages/requests/sessions.py", line 724, in + history = [resp for resp in gen] + File "/opt/conda/lib/python3.10/site-packages/requests/sessions.py", line 265, in resolve_redirects + resp = self.send( + File "/opt/conda/lib/python3.10/site-packages/requests/sessions.py", line 703, in send + r = adapter.send(request, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/requests/adapters.py", line 698, in send + raise SSLError(e, request=request) + requests.exceptions.SSLError: HTTPSConnectionPool(host='lowelab.ucsc.edu', port=443): Max retries exceeded with url: /software/tRNAscan-SE-1.3.1.tar.gz (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007)'))) + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 103, in download_to_cache + download(url, path) + File "/opt/conda/lib/python3.10/site-packages/conda/common/io.py", line 86, in decorated + return f(*args, **kwds) + File "/opt/conda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 67, in download + with download_http_errors(url): + File "/opt/conda/lib/python3.10/contextlib.py", line 153, in __exit__ + self.gen.throw(typ, value, traceback) + File "/opt/conda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 287, in download_http_errors + raise CondaSSLError( + conda.exceptions.CondaSSLError: Encountered an SSL error. Most likely a certificate verification issue. + + Exception: HTTPSConnectionPool(host='lowelab.ucsc.edu', port=443): Max retries exceeded with url: /software/tRNAscan-SE-1.3.1.tar.gz (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007)'))) +# Last 100 lines of the build log. +category: |- + source download error diff --git a/recipes/trnascan-se/1.3.1/build_failure.osx-64.yaml b/recipes/trnascan-se/1.3.1/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..7148bb4098446 --- /dev/null +++ b/recipes/trnascan-se/1.3.1/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 6d05b49e3d456650e19825d66bada3426610f033740fcf065849acb77696d2a9 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + conn.connect() + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/connection.py", line 730, in connect + sock_and_verified = _ssl_wrap_socket_and_match_hostname( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/connection.py", line 909, in _ssl_wrap_socket_and_match_hostname + ssl_sock = ssl_wrap_socket( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/util/ssl_.py", line 469, in ssl_wrap_socket + ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls, server_hostname) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/util/ssl_.py", line 513, in _ssl_wrap_socket_impl + return ssl_context.wrap_socket(sock, server_hostname=server_hostname) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/ssl.py", line 513, in wrap_socket + return self.sslsocket_class._create( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/ssl.py", line 1104, in _create + self.do_handshake() + File "/opt/mambaforge/envs/bioconda/lib/python3.10/ssl.py", line 1375, in do_handshake + self._sslobj.do_handshake() + ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007) + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 789, in urlopen + response = self._make_request( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 490, in _make_request + raise new_e + urllib3.exceptions.SSLError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007) + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/requests/adapters.py", line 667, in send + resp = conn.urlopen( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 873, in urlopen + return self.urlopen( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 873, in urlopen + return self.urlopen( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 873, in urlopen + return self.urlopen( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/connectionpool.py", line 843, in urlopen + retries = retries.increment( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/urllib3/util/retry.py", line 519, in increment + raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type] + urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='lowelab.ucsc.edu', port=443): Max retries exceeded with url: /software/tRNAscan-SE-1.3.1.tar.gz (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007)'))) + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 247, in download_http_errors + yield + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 68, in download + download_inner( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 97, in download_inner + resp = session.get( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/requests/sessions.py", line 602, in get + return self.request("GET", url, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/requests/sessions.py", line 589, in request + resp = self.send(prep, **send_kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/requests/sessions.py", line 724, in send + history = [resp for resp in gen] + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/requests/sessions.py", line 724, in + history = [resp for resp in gen] + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/requests/sessions.py", line 265, in resolve_redirects + resp = self.send( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/requests/sessions.py", line 703, in send + r = adapter.send(request, **kwargs) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/requests/adapters.py", line 698, in send + raise SSLError(e, request=request) + requests.exceptions.SSLError: HTTPSConnectionPool(host='lowelab.ucsc.edu', port=443): Max retries exceeded with url: /software/tRNAscan-SE-1.3.1.tar.gz (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007)'))) + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 103, in download_to_cache + download(url, path) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/common/io.py", line 86, in decorated + return f(*args, **kwds) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 67, in download + with download_http_errors(url): + File "/opt/mambaforge/envs/bioconda/lib/python3.10/contextlib.py", line 153, in __exit__ + self.gen.throw(typ, value, traceback) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/gateways/connection/download.py", line 287, in download_http_errors + raise CondaSSLError( + conda.exceptions.CondaSSLError: Encountered an SSL error. Most likely a certificate verification issue. + + Exception: HTTPSConnectionPool(host='lowelab.ucsc.edu', port=443): Max retries exceeded with url: /software/tRNAscan-SE-1.3.1.tar.gz (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007)'))) +# Last 100 lines of the build log. +category: |- + source download error diff --git a/recipes/trnascan-se/1.3.1/meta.yaml b/recipes/trnascan-se/1.3.1/meta.yaml index 57510bf54bde2..3f78764f39cd7 100644 --- a/recipes/trnascan-se/1.3.1/meta.yaml +++ b/recipes/trnascan-se/1.3.1/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 10 + number: 11 source: url: http://lowelab.ucsc.edu/software/tRNAscan-SE-1.3.1.tar.gz diff --git a/recipes/trnascan-se/meta.yaml b/recipes/trnascan-se/meta.yaml index 48596fa090ce3..8dbebe988bda2 100644 --- a/recipes/trnascan-se/meta.yaml +++ b/recipes/trnascan-se/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('trnascan-se', max_pin="x") }} diff --git a/recipes/trumicount/meta.yaml b/recipes/trumicount/meta.yaml index 2e8b10e602cc5..5b289c60621d8 100644 --- a/recipes/trumicount/meta.yaml +++ b/recipes/trumicount/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: generic - number: 2 + number: 3 script: | install -d "${PREFIX}/bin" install trumicount "${PREFIX}/bin/" diff --git a/recipes/tssar/meta.yaml b/recipes/tssar/meta.yaml index 1c82fdc3dc84b..e1725d12396d0 100644 --- a/recipes/tssar/meta.yaml +++ b/recipes/tssar/meta.yaml @@ -7,7 +7,7 @@ source: md5: 22f3c1fe591a566b0c31877fff6c31b9 build: - number: 8 + number: 9 skip: True # [osx] rpaths: diff --git a/recipes/tssv/meta.yaml b/recipes/tssv/meta.yaml index 7315d9a6e4479..fc01204fd4ef6 100644 --- a/recipes/tssv/meta.yaml +++ b/recipes/tssv/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 28b0b5071bcb50362841a053e94d860be371bc0fc1420c28678399b3abb22383 build: - number: 4 + number: 5 skip: True # [py2k] script: "{{ PYTHON }} -m pip install . -vv" diff --git a/recipes/tttrlib/meta.yaml b/recipes/tttrlib/meta.yaml index daf00affe224d..8263df3e3039a 100644 --- a/recipes/tttrlib/meta.yaml +++ b/recipes/tttrlib/meta.yaml @@ -10,7 +10,7 @@ source: sha256: a224214e50d7a202ef1d264c64641ab0b26f29bf756a96659489847953b698a6 build: - number: 0 + number: 1 run_exports: '{{ pin_subpackage("tttrlib", max_pin="x.x") }}' requirements: diff --git a/recipes/twopaco/meta.yaml b/recipes/twopaco/meta.yaml index e08f4d023ef9d..0158d6fd72cf4 100644 --- a/recipes/twopaco/meta.yaml +++ b/recipes/twopaco/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/ucsc-addcols/meta.yaml b/recipes/ucsc-addcols/meta.yaml index 63fadaf3b0f19..d4e7de9a464a7 100644 --- a/recipes/ucsc-addcols/meta.yaml +++ b/recipes/ucsc-addcols/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-ameme/meta.yaml b/recipes/ucsc-ameme/meta.yaml index 7b92909aa8ed1..03f1885404e59 100644 --- a/recipes/ucsc-ameme/meta.yaml +++ b/recipes/ucsc-ameme/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-autodtd/meta.yaml b/recipes/ucsc-autodtd/meta.yaml index 597fe094769b6..daf85ca5539b1 100644 --- a/recipes/ucsc-autodtd/meta.yaml +++ b/recipes/ucsc-autodtd/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-autosql/meta.yaml b/recipes/ucsc-autosql/meta.yaml index b2a651b3b5a58..b72b8abdd61d6 100644 --- a/recipes/ucsc-autosql/meta.yaml +++ b/recipes/ucsc-autosql/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-autoxml/meta.yaml b/recipes/ucsc-autoxml/meta.yaml index c5328653b9315..f7f42950f2fc1 100644 --- a/recipes/ucsc-autoxml/meta.yaml +++ b/recipes/ucsc-autoxml/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-avecols/meta.yaml b/recipes/ucsc-avecols/meta.yaml index 1845792fc30ac..0e8df3fa80de7 100644 --- a/recipes/ucsc-avecols/meta.yaml +++ b/recipes/ucsc-avecols/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-axtchain/meta.yaml b/recipes/ucsc-axtchain/meta.yaml index 8bdb49a164a0d..802a117f6a5da 100644 --- a/recipes/ucsc-axtchain/meta.yaml +++ b/recipes/ucsc-axtchain/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-axtsort/meta.yaml b/recipes/ucsc-axtsort/meta.yaml index 41b575334e20f..5dc43881d7130 100644 --- a/recipes/ucsc-axtsort/meta.yaml +++ b/recipes/ucsc-axtsort/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-axtswap/meta.yaml b/recipes/ucsc-axtswap/meta.yaml index af74691f328d2..332140210b4bd 100644 --- a/recipes/ucsc-axtswap/meta.yaml +++ b/recipes/ucsc-axtswap/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-axttomaf/meta.yaml b/recipes/ucsc-axttomaf/meta.yaml index 9fad27f9b6c48..2abd56bf2186f 100644 --- a/recipes/ucsc-axttomaf/meta.yaml +++ b/recipes/ucsc-axttomaf/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-axttopsl/meta.yaml b/recipes/ucsc-axttopsl/meta.yaml index b6873169ffcc3..9b377045c4e20 100644 --- a/recipes/ucsc-axttopsl/meta.yaml +++ b/recipes/ucsc-axttopsl/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bamtopsl/build_failure.linux-aarch64.yaml b/recipes/ucsc-bamtopsl/build_failure.linux-aarch64.yaml index 94614dba9e19b..a85bdb6091a87 100644 --- a/recipes/ucsc-bamtopsl/build_failure.linux-aarch64.yaml +++ b/recipes/ucsc-bamtopsl/build_failure.linux-aarch64.yaml @@ -1,13 +1,6 @@ -recipe_sha: cabd65b4a582750389dddd801a4cb10eeace0ae27e187a087c070a8ab41e7a12 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: b113b5fc5fda524181b7b44bf768ea08f97dd16388be22c34a149259bf696a47 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. log: |- - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o rmskOut.o -c rmskOut.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o rmskOut2.o -c rmskOut2.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o rnaGene.o -c rnaGene.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o sage.o -c sage.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o sageCounts.o -c sageCounts.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o samAlignment.o -c samAlignment.c - $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o sample.o -c sample.c $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o sanger22extra.o -c sanger22extra.c $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o scoredRef.o -c scoredRef.c $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o seqWindow.o -c seqWindow.c @@ -70,35 +63,42 @@ log: |- $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o web.o -c web.c ar rcus ../../lib/aarch64/jkhgap.a adjacency.o affyPairs.o agpFrag.o agpGap.o alignSeqSizes.o altGraphX.o asmAlias.o asmEquivalent.o asmSummary.o autoUpgrade.o axtInfo.o barChartBed.o barChartCategory.o barChartUi.o bed.o bed12Source.o bedDetail.o bigBedFind.o bigBedLabel.o bigChain.o bigDbSnp.o bigGenePred.o bigLink.o bigPsl.o blastTab.o borf.o botDelay.o cart.o cartDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cgapSage/cgapSage.o cgapSage/cgapSageLib.o cgiApoptosis.o chainCart.o chainDb.o chainLink.o chainNet.o chainNetDbLoad.o chromAlias.o chromBins.o chromGraph.o chromGraphFactory.o chromInfo.o chromInserts.o chromKeeper.o clonePos.o cpgIsland.o ctgPos.o customAdjacency.o customComposite.o customFactory.o customPp.o customTrack.o cv.o cytoBand.o dbDb.o decoration.o decoratorUi.o defaultDb.o dnaMotifSql.o dupTrack.o encode/encodeErge.o encode/encodeErgeHssCellLines.o encode/encodeExp.o encode/encodeHapMapAlleleFreq.o encode/encodeIndels.o encode/encodePeak.o encode/encodeRegionInfoCustom.o encode/encodeRna.o encode/encodeStanfordPromoters.o encode/encodeStanfordPromotersAverage.o encode/peptideMapping.o encode/wgEncodeGencodeAnnotationRemark.o encode/wgEncodeGencodeAttrs.o encode/wgEncodeGencodeEntrezGene.o encode/wgEncodeGencodeExonSupport.o encode/wgEncodeGencodeGeneSource.o encode/wgEncodeGencodeGeneSymbol.o encode/wgEncodeGencodePdb.o encode/wgEncodeGencodePubMed.o encode/wgEncodeGencodeRefSeq.o encode/wgEncodeGencodeTag.o encode/wgEncodeGencodeTranscriptSource.o encode/wgEncodeGencodeTranscriptSupport.o encode/wgEncodeGencodeTranscriptionSupportLevel.o encode/wgEncodeGencodeUniProt.o encode3/encode3Valid.o estOrientInfo.o expData.o exportedDataHubs.o expRecord.o facetField.o facetedTable.o featureBits.o findKGAlias.o fakeCurl.o findKGProtAlias.o gbSeq.o gbExtFile.o gcPercent.o genark.o genbank.o genbankBlackList.o gencodeTracksCommon.o gencodeAttrs.o gencodeToRefSeq.o geneGraph.o genePred.o genePredReader.o geoMirror.o ggCluster.o ggDump.o ggGraph.o ggMrnaAli.o ggTypes.o glDbRep.o googleAnalytics.o gpFx.o grp.o gtexAse.o gtexDonor.o gtexGeneBed.o gtexInfo.o gtexSample.o gtexSampleData.o gtexTissue.o gtexTissueMedian.o gtexUi.o hCommon.o hPrint.o hVarSubst.o hapmapAllelesOrtho.o hapmapPhaseIIISummary.o hapmapSnps.o hdb.o hgColors.o hgConfig.o hgFind.o hgFindSpec.o hgFindSpecCustom.o hgHgvs.o hgHgvsParse.o hgMaf.o hgRelate.o hic.o hicUi.o hubConnect.o hubPublic.o hubSearchText.o hui.o imageClone.o indelShift.o interact.o interactUi.o itemAttr.o jksql.o joiner.o jsHelper.o kgAlias.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o lav.o lfs.o liftOver.o liftOverChain.o liftUp.o longRange.o lrg.o lsSnpPdb.o mafFrames.o mafGene.o mafSummary.o makeItemsItem.o mdb.o microarray.o minChromSize.o namedSessionDb.o netAlign.o netCart.o pepPred.o pgPhenoAssoc.o pgSnp.o pslReader.o qaSeq.o quickLift.o quickLiftChain.o rankProp.o refLink.o refSeqStatus.o rikenCluster.o rmskAlign.o rmskJoined.o rmskOut.o rmskOut2.o rnaGene.o sage.o sageCounts.o samAlignment.o sample.o sanger22extra.o scoredRef.o seqWindow.o snakeUi.o snp.o snpExceptions.o soTerm.o spDb.o sqlProg.o sqlSanity.o stanMad.o stsAlias.o stsInfo2.o stsMap.o stsMarker.o tableStatus.o tablesTables.o tagRepo.o tfbsCons.o tigrCmrGene.o traceInfo.o trackDb.o trackDbCache.o trackDbCustom.o trackHub.o trackVersion.o trashDir.o txAliDiff.o txCluster.o txCommon.o txEdgeBed.o txGraph.o txInfo.o txRnaAccs.o variantProjector.o vcfUi.o vegaInfo.o web.o wigAsciiToBinary.o wigDataStream.o wiggle.o wiggleCart.o wiggleUtils.o wikiLink.o bigRmskAlignBed.o bigRmskBed.o cd kent/src/utils/bamToPsl - make CC=/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_build_env/bin/aarch64-conda-linux-gnu-cc CXX= 'CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/include -fdebug-prefix-map=/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/work=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -Wl,-rpath-link,/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -L/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -L/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib' 'CXXFLAGS= -I/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -Wl,-rpath-link,/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -L/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -L/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib' -j 4 + make CC=/opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_build_env/bin/aarch64-conda-linux-gnu-cc CXX= 'CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem /opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/include -fdebug-prefix-map=/opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/work=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=/opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -Wl,-rpath-link,/opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -L/opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -L/opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib' 'CXXFLAGS= -I/opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/include -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -Wl,-rpath-link,/opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -L/opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib -L/opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib' -j 4 $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-bamtopsl-469 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_aarch64 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I$PREFIX/include -I$BUILD_PREFIX/include -I$PREFIX/include/libpng16 -o bamToPsl.o -c bamToPsl.c $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc -O -g -o $SRC_DIR/bin/bamToPsl bamToPsl.o ../../lib/aarch64/jkweb.a -L$PREFIX/lib -lmysqlclient -lstdc -lrt -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -lpthread $PREFIX/lib/libssl.a $PREFIX/lib/libcrypto.a -ldl ../../htslib/libhts.a -L$PREFIX/lib -lpng16 -lm -lz - /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.4.0/../../../../aarch64-conda-linux-gnu/bin/ld: ../../lib/aarch64/jkweb.a(bamFile.o): in function bamFetchAlreadyOpen': - /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:207: undefined reference to cram_get_Md5' - /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.4.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:207: undefined reference to cram_get_Md5' - /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.4.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:214: undefined reference to cram_get_ref_url' - /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.4.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:214: undefined reference to cram_get_ref_url' - /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.4.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:215: undefined reference to cram_get_cache_dir' - /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.4.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:215: undefined reference to cram_get_cache_dir' - /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.4.0/../../../../aarch64-conda-linux-gnu/bin/ld: ../../lib/aarch64/jkweb.a(bamFile.o): in function bamAndIndexFetchPlus': - /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:257: undefined reference to cram_set_cache_url' - /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/12.4.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:257: undefined reference to cram_set_cache_url' + /opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: ../../lib/aarch64/jkweb.a(bamFile.o): in function bamFetchAlreadyOpen': + /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:207:(.text0x930): undefined reference to cram_get_Md5' + /opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:207:(.text0x934): undefined reference to cram_get_Md5' + /opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:214:(.text0x950): undefined reference to cram_get_ref_url' + /opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:214:(.text0x954): undefined reference to cram_get_ref_url' + /opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:215:(.text0x968): undefined reference to cram_get_cache_dir' + /opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:215:(.text0x96c): undefined reference to cram_get_cache_dir' + /opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: ../../lib/aarch64/jkweb.a(bamFile.o): in function bamAndIndexFetchPlus': + /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:257:(.text0xca8): undefined reference to cram_set_cache_url' + /opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: /usr/local/src/conda/ucsc-bamtopsl-469/kent/src/lib/bamFile.c:257:(.text0xcac): undefined reference to cram_set_cache_url' collect2: error: ld returned 1 exit status - make: *** [../../inc/userApp.mk:32: /opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/work/bin/bamToPsl] Error 1 + make: *** [../../inc/userApp.mk:32: /opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/work/bin/bamToPsl] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + Traceback (most recent call last): File "/opt/conda/bin/conda-build", line 11, in sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ucsc-bamtopsl_1724787806460/work/conda_build.sh']' returned non-zero exit status 1. + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ucsc-bamtopsl_1734125967701/work/conda_build.sh']' returned non-zero exit status 1. # Last 100 lines of the build log. diff --git a/recipes/ucsc-bamtopsl/meta.yaml b/recipes/ucsc-bamtopsl/meta.yaml index 24249d39cd741..f7415e7824ba1 100644 --- a/recipes/ucsc-bamtopsl/meta.yaml +++ b/recipes/ucsc-bamtopsl/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bedclip/meta.yaml b/recipes/ucsc-bedclip/meta.yaml index 3dcd15559784f..22ec136f8b3a8 100644 --- a/recipes/ucsc-bedclip/meta.yaml +++ b/recipes/ucsc-bedclip/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bedcommonregions/meta.yaml b/recipes/ucsc-bedcommonregions/meta.yaml index 7e61e49095f09..a974ceed51d75 100644 --- a/recipes/ucsc-bedcommonregions/meta.yaml +++ b/recipes/ucsc-bedcommonregions/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bedcoverage/meta.yaml b/recipes/ucsc-bedcoverage/meta.yaml index 237bcd0ba115c..c9a53db272f99 100644 --- a/recipes/ucsc-bedcoverage/meta.yaml +++ b/recipes/ucsc-bedcoverage/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-bedextendranges/meta.yaml b/recipes/ucsc-bedextendranges/meta.yaml index b0278a6067f83..d009d129e8e89 100644 --- a/recipes/ucsc-bedextendranges/meta.yaml +++ b/recipes/ucsc-bedextendranges/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-bedgeneparts/meta.yaml b/recipes/ucsc-bedgeneparts/meta.yaml index de9f72681bcd3..28337229be05e 100644 --- a/recipes/ucsc-bedgeneparts/meta.yaml +++ b/recipes/ucsc-bedgeneparts/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bedgraphpack/meta.yaml b/recipes/ucsc-bedgraphpack/meta.yaml index d950f7ed9e88e..a9ca2cdeea765 100644 --- a/recipes/ucsc-bedgraphpack/meta.yaml +++ b/recipes/ucsc-bedgraphpack/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bedgraphtobigwig/meta.yaml b/recipes/ucsc-bedgraphtobigwig/meta.yaml index fa8e2af63aaa1..8f7033757f07b 100644 --- a/recipes/ucsc-bedgraphtobigwig/meta.yaml +++ b/recipes/ucsc-bedgraphtobigwig/meta.yaml @@ -15,7 +15,7 @@ source: - include.macos.patch # [osx] build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bedintersect/meta.yaml b/recipes/ucsc-bedintersect/meta.yaml index 5ed61c6ad927f..3b68cd2e20610 100644 --- a/recipes/ucsc-bedintersect/meta.yaml +++ b/recipes/ucsc-bedintersect/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-beditemoverlapcount/meta.yaml b/recipes/ucsc-beditemoverlapcount/meta.yaml index bdb5fb822e3a5..67a50dafaa445 100644 --- a/recipes/ucsc-beditemoverlapcount/meta.yaml +++ b/recipes/ucsc-beditemoverlapcount/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-bedpileups/meta.yaml b/recipes/ucsc-bedpileups/meta.yaml index f75c721a2889f..f492944dc57e9 100644 --- a/recipes/ucsc-bedpileups/meta.yaml +++ b/recipes/ucsc-bedpileups/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bedremoveoverlap/meta.yaml b/recipes/ucsc-bedremoveoverlap/meta.yaml index 40e11ffca0e67..5ffad03a8134e 100644 --- a/recipes/ucsc-bedremoveoverlap/meta.yaml +++ b/recipes/ucsc-bedremoveoverlap/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bedrestricttopositions/meta.yaml b/recipes/ucsc-bedrestricttopositions/meta.yaml index ab068a46f57fb..515ea4a9bf778 100644 --- a/recipes/ucsc-bedrestricttopositions/meta.yaml +++ b/recipes/ucsc-bedrestricttopositions/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bedsort/meta.yaml b/recipes/ucsc-bedsort/meta.yaml index 416d0f783723e..71f96c2dedf64 100644 --- a/recipes/ucsc-bedsort/meta.yaml +++ b/recipes/ucsc-bedsort/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bedtobigbed/meta.yaml b/recipes/ucsc-bedtobigbed/meta.yaml index f2e33534cc625..024c6e2f68e58 100644 --- a/recipes/ucsc-bedtobigbed/meta.yaml +++ b/recipes/ucsc-bedtobigbed/meta.yaml @@ -15,7 +15,7 @@ source: - include.macos.patch # [osx] build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bedtogenepred/meta.yaml b/recipes/ucsc-bedtogenepred/meta.yaml index 1fc76c92ba6db..a82376f2cf0c1 100644 --- a/recipes/ucsc-bedtogenepred/meta.yaml +++ b/recipes/ucsc-bedtogenepred/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-bedtopsl/meta.yaml b/recipes/ucsc-bedtopsl/meta.yaml index bf6d5446c806b..11d04a327e06e 100644 --- a/recipes/ucsc-bedtopsl/meta.yaml +++ b/recipes/ucsc-bedtopsl/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bedweedoverlapping/meta.yaml b/recipes/ucsc-bedweedoverlapping/meta.yaml index e372114ed5e4b..67cc3726a8e6f 100644 --- a/recipes/ucsc-bedweedoverlapping/meta.yaml +++ b/recipes/ucsc-bedweedoverlapping/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bigbedinfo/meta.yaml b/recipes/ucsc-bigbedinfo/meta.yaml index 964aa7c634c8e..4a9552ae1f3aa 100644 --- a/recipes/ucsc-bigbedinfo/meta.yaml +++ b/recipes/ucsc-bigbedinfo/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bigbednameditems/meta.yaml b/recipes/ucsc-bigbednameditems/meta.yaml index eb9e9631ab382..37139948d1fb6 100644 --- a/recipes/ucsc-bigbednameditems/meta.yaml +++ b/recipes/ucsc-bigbednameditems/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bigbedsummary/meta.yaml b/recipes/ucsc-bigbedsummary/meta.yaml index 528d9716a3817..b76927bdc16e0 100644 --- a/recipes/ucsc-bigbedsummary/meta.yaml +++ b/recipes/ucsc-bigbedsummary/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bigbedtobed/meta.yaml b/recipes/ucsc-bigbedtobed/meta.yaml index 708bb43118bd2..727d2fb802e4f 100644 --- a/recipes/ucsc-bigbedtobed/meta.yaml +++ b/recipes/ucsc-bigbedtobed/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bigmaftomaf/meta.yaml b/recipes/ucsc-bigmaftomaf/meta.yaml index f59a7e70f7d81..69b9dcf9f7e8c 100644 --- a/recipes/ucsc-bigmaftomaf/meta.yaml +++ b/recipes/ucsc-bigmaftomaf/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bigpsltopsl/meta.yaml b/recipes/ucsc-bigpsltopsl/meta.yaml index 515aa553be985..33d41225fd320 100644 --- a/recipes/ucsc-bigpsltopsl/meta.yaml +++ b/recipes/ucsc-bigpsltopsl/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bigwigaverageoverbed/meta.yaml b/recipes/ucsc-bigwigaverageoverbed/meta.yaml index e2e1bb8da3cce..89741abc24324 100644 --- a/recipes/ucsc-bigwigaverageoverbed/meta.yaml +++ b/recipes/ucsc-bigwigaverageoverbed/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bigwigcat/meta.yaml b/recipes/ucsc-bigwigcat/meta.yaml index f314a3ed65b9a..bb03c1771f4f3 100644 --- a/recipes/ucsc-bigwigcat/meta.yaml +++ b/recipes/ucsc-bigwigcat/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bigwigcluster/meta.yaml b/recipes/ucsc-bigwigcluster/meta.yaml index b385ad7c28da7..ceaf370ed894f 100644 --- a/recipes/ucsc-bigwigcluster/meta.yaml +++ b/recipes/ucsc-bigwigcluster/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bigwigcorrelate/meta.yaml b/recipes/ucsc-bigwigcorrelate/meta.yaml index 0b51d8e1375da..0a1d091ab6420 100644 --- a/recipes/ucsc-bigwigcorrelate/meta.yaml +++ b/recipes/ucsc-bigwigcorrelate/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bigwiginfo/meta.yaml b/recipes/ucsc-bigwiginfo/meta.yaml index 844216cdcde7e..50b2a1da05fc8 100644 --- a/recipes/ucsc-bigwiginfo/meta.yaml +++ b/recipes/ucsc-bigwiginfo/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bigwigmerge/meta.yaml b/recipes/ucsc-bigwigmerge/meta.yaml index 96f88d832b3ee..2d7524dcfcf96 100644 --- a/recipes/ucsc-bigwigmerge/meta.yaml +++ b/recipes/ucsc-bigwigmerge/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bigwigsummary/meta.yaml b/recipes/ucsc-bigwigsummary/meta.yaml index 390d49e449180..7536d28fa8b81 100644 --- a/recipes/ucsc-bigwigsummary/meta.yaml +++ b/recipes/ucsc-bigwigsummary/meta.yaml @@ -15,7 +15,7 @@ source: - include.macos.patch # [osx] build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bigwigtobedgraph/meta.yaml b/recipes/ucsc-bigwigtobedgraph/meta.yaml index 3cc5185b0c350..10f58efb785ba 100644 --- a/recipes/ucsc-bigwigtobedgraph/meta.yaml +++ b/recipes/ucsc-bigwigtobedgraph/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-bigwigtowig/meta.yaml b/recipes/ucsc-bigwigtowig/meta.yaml index af93e4083efd4..4a8877c576f38 100644 --- a/recipes/ucsc-bigwigtowig/meta.yaml +++ b/recipes/ucsc-bigwigtowig/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-blasttopsl/meta.yaml b/recipes/ucsc-blasttopsl/meta.yaml index 905368c1cacaa..d057b4d81d2d0 100644 --- a/recipes/ucsc-blasttopsl/meta.yaml +++ b/recipes/ucsc-blasttopsl/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-blat/meta.yaml b/recipes/ucsc-blat/meta.yaml index ae226831c18f2..705a9f14cca3b 100644 --- a/recipes/ucsc-blat/meta.yaml +++ b/recipes/ucsc-blat/meta.yaml @@ -15,7 +15,7 @@ source: - include.macos.patch # [osx] build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-catdir/meta.yaml b/recipes/ucsc-catdir/meta.yaml index 9443ff4922d67..44578869a8579 100644 --- a/recipes/ucsc-catdir/meta.yaml +++ b/recipes/ucsc-catdir/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-catuncomment/meta.yaml b/recipes/ucsc-catuncomment/meta.yaml index 4e34d400fbd36..6adf394322215 100644 --- a/recipes/ucsc-catuncomment/meta.yaml +++ b/recipes/ucsc-catuncomment/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-chainantirepeat/meta.yaml b/recipes/ucsc-chainantirepeat/meta.yaml index 0ecd147dd4112..6bad571c8b6bc 100644 --- a/recipes/ucsc-chainantirepeat/meta.yaml +++ b/recipes/ucsc-chainantirepeat/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-chaincleaner/meta.yaml b/recipes/ucsc-chaincleaner/meta.yaml index 4417d84ba8197..e9cf1447c1be1 100644 --- a/recipes/ucsc-chaincleaner/meta.yaml +++ b/recipes/ucsc-chaincleaner/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage("ucsc-chaincleaner", max_pin=None) }} diff --git a/recipes/ucsc-chainfilter/meta.yaml b/recipes/ucsc-chainfilter/meta.yaml index 950b6e95f0bba..3f9febd1bf41d 100644 --- a/recipes/ucsc-chainfilter/meta.yaml +++ b/recipes/ucsc-chainfilter/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-chainmergesort/meta.yaml b/recipes/ucsc-chainmergesort/meta.yaml index ae45368e76907..72df6c8cc6fa3 100644 --- a/recipes/ucsc-chainmergesort/meta.yaml +++ b/recipes/ucsc-chainmergesort/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-chainnet/meta.yaml b/recipes/ucsc-chainnet/meta.yaml index 55b46b9d727b0..83ed801be7098 100644 --- a/recipes/ucsc-chainnet/meta.yaml +++ b/recipes/ucsc-chainnet/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-chainprenet/meta.yaml b/recipes/ucsc-chainprenet/meta.yaml index 02c19c160aef0..b84ed90d24990 100644 --- a/recipes/ucsc-chainprenet/meta.yaml +++ b/recipes/ucsc-chainprenet/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-chainscore/meta.yaml b/recipes/ucsc-chainscore/meta.yaml index 1902cceb93c8d..3ec5bbce61265 100644 --- a/recipes/ucsc-chainscore/meta.yaml +++ b/recipes/ucsc-chainscore/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage("ucsc-chainscore", max_pin=None) }} diff --git a/recipes/ucsc-chainsort/meta.yaml b/recipes/ucsc-chainsort/meta.yaml index 93c9d98b79b37..735d8a3c31c5d 100644 --- a/recipes/ucsc-chainsort/meta.yaml +++ b/recipes/ucsc-chainsort/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-chainsplit/meta.yaml b/recipes/ucsc-chainsplit/meta.yaml index 8904f36ce5819..52678c332357f 100644 --- a/recipes/ucsc-chainsplit/meta.yaml +++ b/recipes/ucsc-chainsplit/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-chainstitchid/meta.yaml b/recipes/ucsc-chainstitchid/meta.yaml index ef2cfd4aeacd6..253db7650a2d8 100644 --- a/recipes/ucsc-chainstitchid/meta.yaml +++ b/recipes/ucsc-chainstitchid/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-chainswap/meta.yaml b/recipes/ucsc-chainswap/meta.yaml index 4e91525fb6b79..404aad6ee6693 100644 --- a/recipes/ucsc-chainswap/meta.yaml +++ b/recipes/ucsc-chainswap/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-chaintoaxt/meta.yaml b/recipes/ucsc-chaintoaxt/meta.yaml index 77d4ae748c889..b31b3fa38f6c4 100644 --- a/recipes/ucsc-chaintoaxt/meta.yaml +++ b/recipes/ucsc-chaintoaxt/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-chaintopsl/meta.yaml b/recipes/ucsc-chaintopsl/meta.yaml index ced6ca5ebea90..691f3c82f6581 100644 --- a/recipes/ucsc-chaintopsl/meta.yaml +++ b/recipes/ucsc-chaintopsl/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-chaintopslbasic/meta.yaml b/recipes/ucsc-chaintopslbasic/meta.yaml index 9a9683eff74f7..3d85eff0ceb13 100644 --- a/recipes/ucsc-chaintopslbasic/meta.yaml +++ b/recipes/ucsc-chaintopslbasic/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-checkagpandfa/meta.yaml b/recipes/ucsc-checkagpandfa/meta.yaml index 5a739b8c2d0db..75473fe8e853d 100644 --- a/recipes/ucsc-checkagpandfa/meta.yaml +++ b/recipes/ucsc-checkagpandfa/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-checkcoveragegaps/meta.yaml b/recipes/ucsc-checkcoveragegaps/meta.yaml index cc86c26c9b7a9..88a239e2edb65 100644 --- a/recipes/ucsc-checkcoveragegaps/meta.yaml +++ b/recipes/ucsc-checkcoveragegaps/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-checktablecoords/meta.yaml b/recipes/ucsc-checktablecoords/meta.yaml index adb7ea668615a..e0b660df3952c 100644 --- a/recipes/ucsc-checktablecoords/meta.yaml +++ b/recipes/ucsc-checktablecoords/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-chopfalines/meta.yaml b/recipes/ucsc-chopfalines/meta.yaml index 55a8833c00e82..2c515413418a3 100644 --- a/recipes/ucsc-chopfalines/meta.yaml +++ b/recipes/ucsc-chopfalines/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-chromgraphfrombin/meta.yaml b/recipes/ucsc-chromgraphfrombin/meta.yaml index 81ed418950a54..0599ecca92249 100644 --- a/recipes/ucsc-chromgraphfrombin/meta.yaml +++ b/recipes/ucsc-chromgraphfrombin/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-chromgraphtobin/meta.yaml b/recipes/ucsc-chromgraphtobin/meta.yaml index 3ca7a67b56d0a..2ee28945ae1bf 100644 --- a/recipes/ucsc-chromgraphtobin/meta.yaml +++ b/recipes/ucsc-chromgraphtobin/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-coltransform/meta.yaml b/recipes/ucsc-coltransform/meta.yaml index 46a6ce6c314fa..2fa3d601ea989 100644 --- a/recipes/ucsc-coltransform/meta.yaml +++ b/recipes/ucsc-coltransform/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-countchars/meta.yaml b/recipes/ucsc-countchars/meta.yaml index 3191991de187e..e0881ea2472ba 100644 --- a/recipes/ucsc-countchars/meta.yaml +++ b/recipes/ucsc-countchars/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-crtreeindexbed/meta.yaml b/recipes/ucsc-crtreeindexbed/meta.yaml index 59945d6280836..948f41bce0919 100644 --- a/recipes/ucsc-crtreeindexbed/meta.yaml +++ b/recipes/ucsc-crtreeindexbed/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-crtreesearchbed/meta.yaml b/recipes/ucsc-crtreesearchbed/meta.yaml index cf88771bb980d..68c8baa4e4e82 100644 --- a/recipes/ucsc-crtreesearchbed/meta.yaml +++ b/recipes/ucsc-crtreesearchbed/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-dbsnoop/meta.yaml b/recipes/ucsc-dbsnoop/meta.yaml index b20c4a5c34f80..c679aa2461674 100644 --- a/recipes/ucsc-dbsnoop/meta.yaml +++ b/recipes/ucsc-dbsnoop/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-dbtrash/meta.yaml b/recipes/ucsc-dbtrash/meta.yaml index 4270a211766bf..e02a8b78e875d 100644 --- a/recipes/ucsc-dbtrash/meta.yaml +++ b/recipes/ucsc-dbtrash/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-estorient/meta.yaml b/recipes/ucsc-estorient/meta.yaml index 5c3d11569e838..09c3541363f18 100644 --- a/recipes/ucsc-estorient/meta.yaml +++ b/recipes/ucsc-estorient/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -58,4 +58,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-expmatrixtobarchartbed/meta.yaml b/recipes/ucsc-expmatrixtobarchartbed/meta.yaml index ad965a7733d42..4179adba01b07 100644 --- a/recipes/ucsc-expmatrixtobarchartbed/meta.yaml +++ b/recipes/ucsc-expmatrixtobarchartbed/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-faalign/meta.yaml b/recipes/ucsc-faalign/meta.yaml index e5bb10fb1e460..481ce20de0edc 100644 --- a/recipes/ucsc-faalign/meta.yaml +++ b/recipes/ucsc-faalign/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-facmp/meta.yaml b/recipes/ucsc-facmp/meta.yaml index 7a45c7f7ff32d..575f79e0b908d 100644 --- a/recipes/ucsc-facmp/meta.yaml +++ b/recipes/ucsc-facmp/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-facount/meta.yaml b/recipes/ucsc-facount/meta.yaml index e09912d257d02..d8d2b3a0d497d 100644 --- a/recipes/ucsc-facount/meta.yaml +++ b/recipes/ucsc-facount/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-fafilter/meta.yaml b/recipes/ucsc-fafilter/meta.yaml index ee67056366443..76c5b15664bad 100644 --- a/recipes/ucsc-fafilter/meta.yaml +++ b/recipes/ucsc-fafilter/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-fafiltern/meta.yaml b/recipes/ucsc-fafiltern/meta.yaml index 64f3693d3df25..4375b0e3af053 100644 --- a/recipes/ucsc-fafiltern/meta.yaml +++ b/recipes/ucsc-fafiltern/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-fafrag/meta.yaml b/recipes/ucsc-fafrag/meta.yaml index 63fbd2a2bc5cf..ce1e36a9bece3 100644 --- a/recipes/ucsc-fafrag/meta.yaml +++ b/recipes/ucsc-fafrag/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-fanoise/meta.yaml b/recipes/ucsc-fanoise/meta.yaml index 6ba0418b05532..96a301c9c7ffd 100644 --- a/recipes/ucsc-fanoise/meta.yaml +++ b/recipes/ucsc-fanoise/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-faonerecord/meta.yaml b/recipes/ucsc-faonerecord/meta.yaml index d52e42e40b317..372dac53e0efa 100644 --- a/recipes/ucsc-faonerecord/meta.yaml +++ b/recipes/ucsc-faonerecord/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-fapolyasizes/meta.yaml b/recipes/ucsc-fapolyasizes/meta.yaml index 6dac4793b6b2e..b999951e808c9 100644 --- a/recipes/ucsc-fapolyasizes/meta.yaml +++ b/recipes/ucsc-fapolyasizes/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-farandomize/build_failure.linux-64.yaml b/recipes/ucsc-farandomize/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..ae940ec251556 --- /dev/null +++ b/recipes/ucsc-farandomize/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5677ab6b22e1267bc633bb491b5d8a6429ab05cce89ec304e232fc350ff6170e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Encountered problems while solving: + - nothing provides requested gcc_linux-64 13.* + - nothing provides requested make + + Could not solve for environment specs + The following packages are incompatible + [31mgcc_linux-64 13.* [0m does not exist (perhaps a typo or a missing channel); + [31mmake[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("gcc_linux-64=13"), MatchSpec("make")} + Encountered problems while solving: + - nothing provides requested gcc_linux-64 13.* + - nothing provides requested make + + Could not solve for environment specs + The following packages are incompatible + [31mgcc_linux-64 13.* [0m does not exist (perhaps a typo or a missing channel); + [31mmake[0m does not exist (perhaps a typo or a missing channel). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 465, in add_upstream_pins + build_deps, build_unsat, extra_run_specs_from_build = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 444, in _read_upstream_pin_files + deps, precs, unsat = get_env_dependencies( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 156, in get_env_dependencies + precs = environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("gcc_linux-64=13"), MatchSpec("make")} + Encountered problems while solving: + - nothing provides requested gcc_linux-64 13.* + - nothing provides requested make + + Could not solve for environment specs + The following packages are incompatible + [31mgcc_linux-64 13.* [0m does not exist (perhaps a typo or a missing channel); + [31mmake[0m does not exist (perhaps a typo or a missing channel). +# Last 100 lines of the build log. diff --git a/recipes/ucsc-farandomize/meta.yaml b/recipes/ucsc-farandomize/meta.yaml index 7a357380b6102..28624131554fa 100644 --- a/recipes/ucsc-farandomize/meta.yaml +++ b/recipes/ucsc-farandomize/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-farc/meta.yaml b/recipes/ucsc-farc/meta.yaml index 59ad4f779fb2c..8bed179b20e4d 100644 --- a/recipes/ucsc-farc/meta.yaml +++ b/recipes/ucsc-farc/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-fasize/meta.yaml b/recipes/ucsc-fasize/meta.yaml index e5ca815518a66..95c6c9d02bc56 100644 --- a/recipes/ucsc-fasize/meta.yaml +++ b/recipes/ucsc-fasize/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-fasomerecords/meta.yaml b/recipes/ucsc-fasomerecords/meta.yaml index 86fe4dda5cbc4..147dded4a909e 100644 --- a/recipes/ucsc-fasomerecords/meta.yaml +++ b/recipes/ucsc-fasomerecords/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-fasplit/meta.yaml b/recipes/ucsc-fasplit/meta.yaml index 9b811fc0a565c..5e71c177c37fc 100644 --- a/recipes/ucsc-fasplit/meta.yaml +++ b/recipes/ucsc-fasplit/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-fastqstatsandsubsample/meta.yaml b/recipes/ucsc-fastqstatsandsubsample/meta.yaml index ccdb6bfc69d23..af8861e3bfdeb 100644 --- a/recipes/ucsc-fastqstatsandsubsample/meta.yaml +++ b/recipes/ucsc-fastqstatsandsubsample/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-fastqtofa/meta.yaml b/recipes/ucsc-fastqtofa/meta.yaml index 5bc623ded2330..ab99da60abb15 100644 --- a/recipes/ucsc-fastqtofa/meta.yaml +++ b/recipes/ucsc-fastqtofa/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-fatofastq/meta.yaml b/recipes/ucsc-fatofastq/meta.yaml index e2ecba2ff9675..363e8d494e4bc 100644 --- a/recipes/ucsc-fatofastq/meta.yaml +++ b/recipes/ucsc-fatofastq/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-fatotab/meta.yaml b/recipes/ucsc-fatotab/meta.yaml index c7901931785a1..526c85423cc66 100644 --- a/recipes/ucsc-fatotab/meta.yaml +++ b/recipes/ucsc-fatotab/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-fatotwobit/meta.yaml b/recipes/ucsc-fatotwobit/meta.yaml index c129b57df25c7..af933201619c3 100644 --- a/recipes/ucsc-fatotwobit/meta.yaml +++ b/recipes/ucsc-fatotwobit/meta.yaml @@ -15,7 +15,7 @@ source: - include.macos.patch # [osx] build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-fatovcf/meta.yaml b/recipes/ucsc-fatovcf/meta.yaml index c2f215b62fb08..f43f1791db061 100644 --- a/recipes/ucsc-fatovcf/meta.yaml +++ b/recipes/ucsc-fatovcf/meta.yaml @@ -15,7 +15,7 @@ source: - include.macos.patch # [osx] build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-fatrans/meta.yaml b/recipes/ucsc-fatrans/meta.yaml index 51811a6159fa7..6f4ff53dc44ad 100644 --- a/recipes/ucsc-fatrans/meta.yaml +++ b/recipes/ucsc-fatrans/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-featurebits/meta.yaml b/recipes/ucsc-featurebits/meta.yaml index 8dd37713562a8..fa926496627b3 100644 --- a/recipes/ucsc-featurebits/meta.yaml +++ b/recipes/ucsc-featurebits/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-fetchchromsizes/meta.yaml b/recipes/ucsc-fetchchromsizes/meta.yaml index cfe061d194d38..a4d582fee8548 100644 --- a/recipes/ucsc-fetchchromsizes/meta.yaml +++ b/recipes/ucsc-fetchchromsizes/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-findmotif/meta.yaml b/recipes/ucsc-findmotif/meta.yaml index 7a216c91b07df..da0e65732228e 100644 --- a/recipes/ucsc-findmotif/meta.yaml +++ b/recipes/ucsc-findmotif/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-gaptolift/meta.yaml b/recipes/ucsc-gaptolift/meta.yaml index d966465836968..bb1fae2b66ca0 100644 --- a/recipes/ucsc-gaptolift/meta.yaml +++ b/recipes/ucsc-gaptolift/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-genepredcheck/meta.yaml b/recipes/ucsc-genepredcheck/meta.yaml index db9f5b2a78bcd..3c0291e6535d9 100644 --- a/recipes/ucsc-genepredcheck/meta.yaml +++ b/recipes/ucsc-genepredcheck/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-genepredfilter/meta.yaml b/recipes/ucsc-genepredfilter/meta.yaml index 555cc71621d1a..9f17373639d7d 100644 --- a/recipes/ucsc-genepredfilter/meta.yaml +++ b/recipes/ucsc-genepredfilter/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-genepredhisto/meta.yaml b/recipes/ucsc-genepredhisto/meta.yaml index 26ea81c76bb67..13d96ead2f2e7 100644 --- a/recipes/ucsc-genepredhisto/meta.yaml +++ b/recipes/ucsc-genepredhisto/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-genepredsinglecover/meta.yaml b/recipes/ucsc-genepredsinglecover/meta.yaml index 7da1658b06ae8..4d8b937871988 100644 --- a/recipes/ucsc-genepredsinglecover/meta.yaml +++ b/recipes/ucsc-genepredsinglecover/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-genepredtobed/meta.yaml b/recipes/ucsc-genepredtobed/meta.yaml index 3bec9a4e9fa8e..ed9f6b1f2f89c 100644 --- a/recipes/ucsc-genepredtobed/meta.yaml +++ b/recipes/ucsc-genepredtobed/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-genepredtobiggenepred/meta.yaml b/recipes/ucsc-genepredtobiggenepred/meta.yaml index a1246916eef6c..181f301326a58 100644 --- a/recipes/ucsc-genepredtobiggenepred/meta.yaml +++ b/recipes/ucsc-genepredtobiggenepred/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-genepredtofakepsl/meta.yaml b/recipes/ucsc-genepredtofakepsl/meta.yaml index db76e2c25d187..a1f8b1ec94a02 100644 --- a/recipes/ucsc-genepredtofakepsl/meta.yaml +++ b/recipes/ucsc-genepredtofakepsl/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-genepredtogtf/meta.yaml b/recipes/ucsc-genepredtogtf/meta.yaml index 63feeb7475766..5e9756277470c 100644 --- a/recipes/ucsc-genepredtogtf/meta.yaml +++ b/recipes/ucsc-genepredtogtf/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-genepredtomafframes/meta.yaml b/recipes/ucsc-genepredtomafframes/meta.yaml index a2198b27e22c8..c7c13593c1c30 100644 --- a/recipes/ucsc-genepredtomafframes/meta.yaml +++ b/recipes/ucsc-genepredtomafframes/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-genepredtoprot/meta.yaml b/recipes/ucsc-genepredtoprot/meta.yaml index 415939a3f7ac5..b40a083dbfc1e 100644 --- a/recipes/ucsc-genepredtoprot/meta.yaml +++ b/recipes/ucsc-genepredtoprot/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-gensub2/meta.yaml b/recipes/ucsc-gensub2/meta.yaml index 5b1d1ebc67a8d..0568782e2de0b 100644 --- a/recipes/ucsc-gensub2/meta.yaml +++ b/recipes/ucsc-gensub2/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-getrna/meta.yaml b/recipes/ucsc-getrna/meta.yaml index a513246dfff19..1097490f1adeb 100644 --- a/recipes/ucsc-getrna/meta.yaml +++ b/recipes/ucsc-getrna/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-getrnapred/meta.yaml b/recipes/ucsc-getrnapred/meta.yaml index 511717e689efd..8e0ab8468670c 100644 --- a/recipes/ucsc-getrnapred/meta.yaml +++ b/recipes/ucsc-getrnapred/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-gff3togenepred/meta.yaml b/recipes/ucsc-gff3togenepred/meta.yaml index c16b7d914188d..a4c56712643c5 100644 --- a/recipes/ucsc-gff3togenepred/meta.yaml +++ b/recipes/ucsc-gff3togenepred/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-gff3topsl/meta.yaml b/recipes/ucsc-gff3topsl/meta.yaml index 6b6d7a265cea8..f2b4543c48e74 100644 --- a/recipes/ucsc-gff3topsl/meta.yaml +++ b/recipes/ucsc-gff3topsl/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-gmtime/meta.yaml b/recipes/ucsc-gmtime/meta.yaml index be7f2efb84739..26c39daeee2a3 100644 --- a/recipes/ucsc-gmtime/meta.yaml +++ b/recipes/ucsc-gmtime/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-gtftogenepred/meta.yaml b/recipes/ucsc-gtftogenepred/meta.yaml index 813e6c2d6a6b6..399297a3acf1e 100644 --- a/recipes/ucsc-gtftogenepred/meta.yaml +++ b/recipes/ucsc-gtftogenepred/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-headrest/meta.yaml b/recipes/ucsc-headrest/meta.yaml index 5544ab7e8edc7..734bf4f8be742 100644 --- a/recipes/ucsc-headrest/meta.yaml +++ b/recipes/ucsc-headrest/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-hgbbidblink/meta.yaml b/recipes/ucsc-hgbbidblink/meta.yaml index 45c299a6c87ee..d859a255fd5d8 100644 --- a/recipes/ucsc-hgbbidblink/meta.yaml +++ b/recipes/ucsc-hgbbidblink/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-hgfakeagp/meta.yaml b/recipes/ucsc-hgfakeagp/meta.yaml index 457365f7fa59a..cbc29def98fba 100644 --- a/recipes/ucsc-hgfakeagp/meta.yaml +++ b/recipes/ucsc-hgfakeagp/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-hgfindspec/meta.yaml b/recipes/ucsc-hgfindspec/meta.yaml index 02d2bf103bd22..f5f5cccd8febd 100644 --- a/recipes/ucsc-hgfindspec/meta.yaml +++ b/recipes/ucsc-hgfindspec/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-hggcpercent/meta.yaml b/recipes/ucsc-hggcpercent/meta.yaml index 8e1740f1de060..e05b3a38fbb20 100644 --- a/recipes/ucsc-hggcpercent/meta.yaml +++ b/recipes/ucsc-hggcpercent/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-hgloadbed/meta.yaml b/recipes/ucsc-hgloadbed/meta.yaml index d10d7a94dec54..135a1cd439d6d 100644 --- a/recipes/ucsc-hgloadbed/meta.yaml +++ b/recipes/ucsc-hgloadbed/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-hgloadchain/meta.yaml b/recipes/ucsc-hgloadchain/meta.yaml index b251f71789efa..5de213973c39f 100644 --- a/recipes/ucsc-hgloadchain/meta.yaml +++ b/recipes/ucsc-hgloadchain/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-hgloadmaf/meta.yaml b/recipes/ucsc-hgloadmaf/meta.yaml index b16d0a55d7962..13b8529e96a99 100644 --- a/recipes/ucsc-hgloadmaf/meta.yaml +++ b/recipes/ucsc-hgloadmaf/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-hgloadnet/meta.yaml b/recipes/ucsc-hgloadnet/meta.yaml index 34ae43d661357..88b223a015574 100644 --- a/recipes/ucsc-hgloadnet/meta.yaml +++ b/recipes/ucsc-hgloadnet/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-hgloadout/meta.yaml b/recipes/ucsc-hgloadout/meta.yaml index f1abed39bf9f8..1d181f0e7bfef 100644 --- a/recipes/ucsc-hgloadout/meta.yaml +++ b/recipes/ucsc-hgloadout/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-hgloadoutjoined/meta.yaml b/recipes/ucsc-hgloadoutjoined/meta.yaml index 530efb471e395..0c5467c6dbc12 100644 --- a/recipes/ucsc-hgloadoutjoined/meta.yaml +++ b/recipes/ucsc-hgloadoutjoined/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-hgloadsqltab/meta.yaml b/recipes/ucsc-hgloadsqltab/meta.yaml index 1ae390c3c6a3f..8d09108d75f31 100644 --- a/recipes/ucsc-hgloadsqltab/meta.yaml +++ b/recipes/ucsc-hgloadsqltab/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-hgloadwiggle/meta.yaml b/recipes/ucsc-hgloadwiggle/meta.yaml index e8e2571e9013b..02fac6e345b75 100644 --- a/recipes/ucsc-hgloadwiggle/meta.yaml +++ b/recipes/ucsc-hgloadwiggle/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-hgspeciesrna/meta.yaml b/recipes/ucsc-hgspeciesrna/meta.yaml index 26e0337c640e6..d32d9a95805e6 100644 --- a/recipes/ucsc-hgspeciesrna/meta.yaml +++ b/recipes/ucsc-hgspeciesrna/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-hgsqldump/meta.yaml b/recipes/ucsc-hgsqldump/meta.yaml index cf837117dbedc..f256973d457b1 100644 --- a/recipes/ucsc-hgsqldump/meta.yaml +++ b/recipes/ucsc-hgsqldump/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-htmlcheck/meta.yaml b/recipes/ucsc-htmlcheck/meta.yaml index edc5c0b821f24..0b0483c1c5edd 100644 --- a/recipes/ucsc-htmlcheck/meta.yaml +++ b/recipes/ucsc-htmlcheck/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-hubpubliccheck/meta.yaml b/recipes/ucsc-hubpubliccheck/meta.yaml index f0a4cc1d4f97e..13f60feaa2230 100644 --- a/recipes/ucsc-hubpubliccheck/meta.yaml +++ b/recipes/ucsc-hubpubliccheck/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-ixixx/meta.yaml b/recipes/ucsc-ixixx/meta.yaml index 12e29c5de07c1..5915353eab582 100644 --- a/recipes/ucsc-ixixx/meta.yaml +++ b/recipes/ucsc-ixixx/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-lavtoaxt/meta.yaml b/recipes/ucsc-lavtoaxt/meta.yaml index 06c0cafe88b92..ddc5489fcd6a1 100644 --- a/recipes/ucsc-lavtoaxt/meta.yaml +++ b/recipes/ucsc-lavtoaxt/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-lavtopsl/meta.yaml b/recipes/ucsc-lavtopsl/meta.yaml index cfc2c04b24fa7..f8ac609b7d0e6 100644 --- a/recipes/ucsc-lavtopsl/meta.yaml +++ b/recipes/ucsc-lavtopsl/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-ldhggene/meta.yaml b/recipes/ucsc-ldhggene/meta.yaml index aec3b9faa2050..0d9c7e02227ff 100644 --- a/recipes/ucsc-ldhggene/meta.yaml +++ b/recipes/ucsc-ldhggene/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-liftover/meta.yaml b/recipes/ucsc-liftover/meta.yaml index a38bea325585b..ffa3b45488bdf 100644 --- a/recipes/ucsc-liftover/meta.yaml +++ b/recipes/ucsc-liftover/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-liftup/meta.yaml b/recipes/ucsc-liftup/meta.yaml index b61c25d8102ca..bc5fe418e2e9e 100644 --- a/recipes/ucsc-liftup/meta.yaml +++ b/recipes/ucsc-liftup/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-linestora/meta.yaml b/recipes/ucsc-linestora/meta.yaml index 8929fdad5aeff..5727a9ef6cb5c 100644 --- a/recipes/ucsc-linestora/meta.yaml +++ b/recipes/ucsc-linestora/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-localtime/meta.yaml b/recipes/ucsc-localtime/meta.yaml index 9a5bb720eea6a..b4c93e47fe2e7 100644 --- a/recipes/ucsc-localtime/meta.yaml +++ b/recipes/ucsc-localtime/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-mafaddirows/meta.yaml b/recipes/ucsc-mafaddirows/meta.yaml index 1678cf8b45d74..20ab933b218d2 100644 --- a/recipes/ucsc-mafaddirows/meta.yaml +++ b/recipes/ucsc-mafaddirows/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-mafaddqrows/meta.yaml b/recipes/ucsc-mafaddqrows/meta.yaml index 852353ae2d074..3ec01bb6898b6 100644 --- a/recipes/ucsc-mafaddqrows/meta.yaml +++ b/recipes/ucsc-mafaddqrows/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-mafcoverage/meta.yaml b/recipes/ucsc-mafcoverage/meta.yaml index e4a133f4200cc..5070575aa6380 100644 --- a/recipes/ucsc-mafcoverage/meta.yaml +++ b/recipes/ucsc-mafcoverage/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-maffetch/meta.yaml b/recipes/ucsc-maffetch/meta.yaml index 9090dbba9ad87..52dccb9004ae1 100644 --- a/recipes/ucsc-maffetch/meta.yaml +++ b/recipes/ucsc-maffetch/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-maffilter/meta.yaml b/recipes/ucsc-maffilter/meta.yaml index fe2bdf5d06413..f98e4dd99b49b 100644 --- a/recipes/ucsc-maffilter/meta.yaml +++ b/recipes/ucsc-maffilter/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-maffrag/meta.yaml b/recipes/ucsc-maffrag/meta.yaml index be0547277cd93..44f48904d5bb5 100644 --- a/recipes/ucsc-maffrag/meta.yaml +++ b/recipes/ucsc-maffrag/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-maffrags/meta.yaml b/recipes/ucsc-maffrags/meta.yaml index 34d81f233584a..4df74caf8d99c 100644 --- a/recipes/ucsc-maffrags/meta.yaml +++ b/recipes/ucsc-maffrags/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-mafgene/meta.yaml b/recipes/ucsc-mafgene/meta.yaml index 00c8dcbf6fd3c..3430d04b36b9c 100644 --- a/recipes/ucsc-mafgene/meta.yaml +++ b/recipes/ucsc-mafgene/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-mafmefirst/meta.yaml b/recipes/ucsc-mafmefirst/meta.yaml index 4ee6e4b03ce1e..f65469fd7bbf7 100644 --- a/recipes/ucsc-mafmefirst/meta.yaml +++ b/recipes/ucsc-mafmefirst/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-maforder/meta.yaml b/recipes/ucsc-maforder/meta.yaml index ad84eab22d85c..8cae5508b0f92 100644 --- a/recipes/ucsc-maforder/meta.yaml +++ b/recipes/ucsc-maforder/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-mafranges/meta.yaml b/recipes/ucsc-mafranges/meta.yaml index 66d3c977d9dc7..1fcbb03eaeda4 100644 --- a/recipes/ucsc-mafranges/meta.yaml +++ b/recipes/ucsc-mafranges/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-mafsinregion/meta.yaml b/recipes/ucsc-mafsinregion/meta.yaml index 48415aa8bb4dc..594d67a99283a 100644 --- a/recipes/ucsc-mafsinregion/meta.yaml +++ b/recipes/ucsc-mafsinregion/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-mafspecieslist/meta.yaml b/recipes/ucsc-mafspecieslist/meta.yaml index 39fea6c3f3bcf..7694326f5479c 100644 --- a/recipes/ucsc-mafspecieslist/meta.yaml +++ b/recipes/ucsc-mafspecieslist/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-mafspeciessubset/meta.yaml b/recipes/ucsc-mafspeciessubset/meta.yaml index 566864c8adf9a..a23bcb7c44ad1 100644 --- a/recipes/ucsc-mafspeciessubset/meta.yaml +++ b/recipes/ucsc-mafspeciessubset/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-mafsplit/meta.yaml b/recipes/ucsc-mafsplit/meta.yaml index 8fb771c78e0c5..e380421fd208b 100644 --- a/recipes/ucsc-mafsplit/meta.yaml +++ b/recipes/ucsc-mafsplit/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-mafsplitpos/meta.yaml b/recipes/ucsc-mafsplitpos/meta.yaml index 77c67139a4334..2d91c225bdf8f 100644 --- a/recipes/ucsc-mafsplitpos/meta.yaml +++ b/recipes/ucsc-mafsplitpos/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-maftoaxt/meta.yaml b/recipes/ucsc-maftoaxt/meta.yaml index 2e31d3a08bf55..452a6dad3b4ee 100644 --- a/recipes/ucsc-maftoaxt/meta.yaml +++ b/recipes/ucsc-maftoaxt/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-maftobigmaf/meta.yaml b/recipes/ucsc-maftobigmaf/meta.yaml index e99a1f9fec06f..e73e9701daede 100644 --- a/recipes/ucsc-maftobigmaf/meta.yaml +++ b/recipes/ucsc-maftobigmaf/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-maftopsl/meta.yaml b/recipes/ucsc-maftopsl/meta.yaml index ede1d2177c11c..b627b8fd0b1fb 100644 --- a/recipes/ucsc-maftopsl/meta.yaml +++ b/recipes/ucsc-maftopsl/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-maftosnpbed/meta.yaml b/recipes/ucsc-maftosnpbed/meta.yaml index 46d27f2eb21d2..72d7276beefae 100644 --- a/recipes/ucsc-maftosnpbed/meta.yaml +++ b/recipes/ucsc-maftosnpbed/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-maketablelist/meta.yaml b/recipes/ucsc-maketablelist/meta.yaml index b11002a961035..019546b7ede33 100644 --- a/recipes/ucsc-maketablelist/meta.yaml +++ b/recipes/ucsc-maketablelist/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-maskoutfa/meta.yaml b/recipes/ucsc-maskoutfa/meta.yaml index fa8cc7eb1593a..e6f48df715be3 100644 --- a/recipes/ucsc-maskoutfa/meta.yaml +++ b/recipes/ucsc-maskoutfa/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-mktime/meta.yaml b/recipes/ucsc-mktime/meta.yaml index e52b1b0b0c71b..671a80933d648 100644 --- a/recipes/ucsc-mktime/meta.yaml +++ b/recipes/ucsc-mktime/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-mrnatogene/meta.yaml b/recipes/ucsc-mrnatogene/meta.yaml index b867c1e781a84..f53ad47785f6f 100644 --- a/recipes/ucsc-mrnatogene/meta.yaml +++ b/recipes/ucsc-mrnatogene/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-netchainsubset/meta.yaml b/recipes/ucsc-netchainsubset/meta.yaml index 2f921aa504a60..4045a389b7777 100644 --- a/recipes/ucsc-netchainsubset/meta.yaml +++ b/recipes/ucsc-netchainsubset/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-netclass/meta.yaml b/recipes/ucsc-netclass/meta.yaml index bd64db2ff8c0e..511840f17d73a 100644 --- a/recipes/ucsc-netclass/meta.yaml +++ b/recipes/ucsc-netclass/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-netfilter/meta.yaml b/recipes/ucsc-netfilter/meta.yaml index 59415265530ab..09dd008afb76a 100644 --- a/recipes/ucsc-netfilter/meta.yaml +++ b/recipes/ucsc-netfilter/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-netsplit/meta.yaml b/recipes/ucsc-netsplit/meta.yaml index feca545a7efbc..6777b5466df1f 100644 --- a/recipes/ucsc-netsplit/meta.yaml +++ b/recipes/ucsc-netsplit/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-netsyntenic/meta.yaml b/recipes/ucsc-netsyntenic/meta.yaml index 87b26bea97f27..5a877a22f063f 100644 --- a/recipes/ucsc-netsyntenic/meta.yaml +++ b/recipes/ucsc-netsyntenic/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-nettoaxt/meta.yaml b/recipes/ucsc-nettoaxt/meta.yaml index aeef00d707002..40b6e57b2d148 100644 --- a/recipes/ucsc-nettoaxt/meta.yaml +++ b/recipes/ucsc-nettoaxt/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-nettobed/meta.yaml b/recipes/ucsc-nettobed/meta.yaml index 78ef0cc414f73..1e43554c47188 100644 --- a/recipes/ucsc-nettobed/meta.yaml +++ b/recipes/ucsc-nettobed/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-newprog/meta.yaml b/recipes/ucsc-newprog/meta.yaml index 4f06ccbc16664..5ac810768b6b7 100644 --- a/recipes/ucsc-newprog/meta.yaml +++ b/recipes/ucsc-newprog/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-newpythonprog/meta.yaml b/recipes/ucsc-newpythonprog/meta.yaml index 361d9f8b5f4fd..f1539b35811ce 100644 --- a/recipes/ucsc-newpythonprog/meta.yaml +++ b/recipes/ucsc-newpythonprog/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-nibfrag/meta.yaml b/recipes/ucsc-nibfrag/meta.yaml index d62bed526b13b..d537c27323825 100644 --- a/recipes/ucsc-nibfrag/meta.yaml +++ b/recipes/ucsc-nibfrag/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-nibsize/meta.yaml b/recipes/ucsc-nibsize/meta.yaml index c137ff3bace8e..d2e97571cc67e 100644 --- a/recipes/ucsc-nibsize/meta.yaml +++ b/recipes/ucsc-nibsize/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-oligomatch/meta.yaml b/recipes/ucsc-oligomatch/meta.yaml index f34d627ba9455..b00c8c84db023 100644 --- a/recipes/ucsc-oligomatch/meta.yaml +++ b/recipes/ucsc-oligomatch/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-overlapselect/meta.yaml b/recipes/ucsc-overlapselect/meta.yaml index 00978ce2ec5d1..6c40c2cb35d75 100644 --- a/recipes/ucsc-overlapselect/meta.yaml +++ b/recipes/ucsc-overlapselect/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -59,4 +59,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-para/meta.yaml b/recipes/ucsc-para/meta.yaml index 51ddc57dd7308..6b3568b185c55 100644 --- a/recipes/ucsc-para/meta.yaml +++ b/recipes/ucsc-para/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-parafetch/meta.yaml b/recipes/ucsc-parafetch/meta.yaml index 027e9eb2c2a9f..f2d7bbea6bce8 100644 --- a/recipes/ucsc-parafetch/meta.yaml +++ b/recipes/ucsc-parafetch/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-parahub/build_failure.linux-aarch64.yaml b/recipes/ucsc-parahub/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..bae4fa0bb937a --- /dev/null +++ b/recipes/ucsc-parahub/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: be414f7cf31d27150bc38d37d07ac334f2f45051e05b9d90f09e93127238913e # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml + Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for ucsc-parahub + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['ucsc-parahub-469-hd4000eb_1.tar.bz2'] + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/ucsc-parahub_1733853560038/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ + + + The following NEW packages will be INSTALLED: + + _openmp_mutex: 4.5-2_gnu conda-forge + ca-certificates: 2024.8.30-hcefe29a_0 conda-forge + libgcc: 14.2.0-he277a41_1 conda-forge + libgcc-ng: 14.2.0-he9431aa_1 conda-forge + libgomp: 14.2.0-he277a41_1 conda-forge + libopenssl-static: 3.4.0-h86ecc28_0 conda-forge + libpng: 1.6.44-hc4a20ef_0 conda-forge + libstdcxx: 14.2.0-h3f4de04_1 conda-forge + libstdcxx-ng: 14.2.0-hf1166c9_1 conda-forge + libuuid: 2.38.1-hb4cce97_0 conda-forge + libzlib: 1.3.1-h86ecc28_2 conda-forge + mysql-connector-c: 6.1.11-h8945da3_1008 conda-forge + openssl: 3.4.0-h86ecc28_0 conda-forge + zlib: 1.3.1-h86ecc28_2 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/ucsc-parahub_1733853560038/_build_env + + + The following NEW packages will be INSTALLED: + + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-aarch64: 2.43-h4c662bb_2 conda-forge + binutils_linux-aarch64: 2.43-hf1166c9_2 conda-forge + gcc_impl_linux-aarch64: 13.3.0-hcdea9b6_1 conda-forge + gcc_linux-aarch64: 13.3.0-h1cd514b_7 conda-forge + kernel-headers_linux-aarch64: 4.18.0-h05a177a_18 conda-forge + ld_impl_linux-aarch64: 2.43-h80caac9_2 conda-forge + libgcc: 14.2.0-he277a41_1 conda-forge + libgcc-devel_linux-aarch64: 13.3.0-h0c07274_101 conda-forge + libgomp: 14.2.0-he277a41_1 conda-forge + libsanitizer: 13.3.0-ha58e236_1 conda-forge + libstdcxx: 14.2.0-h3f4de04_1 conda-forge + make: 4.4.1-h2a6d0cb_2 conda-forge + sysroot_linux-aarch64: 2.17-h5b4a56d_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: userApps.v469.src_3f95b26ccc.tgz + Downloading http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v469.src.tgz + WARNING:urllib3.connectionpool:Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(, 'Connection to hgdownload.cse.ucsc.edu timed out. (connect timeout=9.15)')': /admin/exe/userApps.archive/userApps.v469.src.tgz + WARNING:urllib3.connectionpool:Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(, 'Connection to hgdownload.cse.ucsc.edu timed out. (connect timeout=9.15)')': /admin/exe/userApps.archive/userApps.v469.src.tgz + WARNING:urllib3.connectionpool:Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(, 'Connection to hgdownload.cse.ucsc.edu timed out. (connect timeout=9.15)')': /admin/exe/userApps.archive/userApps.v469.src.tgz + WARNING: Error: HTTP 000 CONNECTION FAILED for url + Elapsed: - + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v469.src.tgz +# Last 100 lines of the build log. diff --git a/recipes/ucsc-parahub/meta.yaml b/recipes/ucsc-parahub/meta.yaml index 5643cd381a146..5b182b224f063 100644 --- a/recipes/ucsc-parahub/meta.yaml +++ b/recipes/ucsc-parahub/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-parahubstop/meta.yaml b/recipes/ucsc-parahubstop/meta.yaml index 58351f6cdbfed..ec026d7c41586 100644 --- a/recipes/ucsc-parahubstop/meta.yaml +++ b/recipes/ucsc-parahubstop/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-paranode/meta.yaml b/recipes/ucsc-paranode/meta.yaml index bebf62ba576af..199169924fc9a 100644 --- a/recipes/ucsc-paranode/meta.yaml +++ b/recipes/ucsc-paranode/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-paranodestart/meta.yaml b/recipes/ucsc-paranodestart/meta.yaml index fc403349abe12..52d970c592398 100644 --- a/recipes/ucsc-paranodestart/meta.yaml +++ b/recipes/ucsc-paranodestart/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-paranodestatus/meta.yaml b/recipes/ucsc-paranodestatus/meta.yaml index 8f02ac48eb5c0..d85b464b0a546 100644 --- a/recipes/ucsc-paranodestatus/meta.yaml +++ b/recipes/ucsc-paranodestatus/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-paranodestop/meta.yaml b/recipes/ucsc-paranodestop/meta.yaml index f7128debc7d61..c4b84f6ee4281 100644 --- a/recipes/ucsc-paranodestop/meta.yaml +++ b/recipes/ucsc-paranodestop/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-parasol/meta.yaml b/recipes/ucsc-parasol/meta.yaml index 0b01fffa4b53f..ed7156043df03 100644 --- a/recipes/ucsc-parasol/meta.yaml +++ b/recipes/ucsc-parasol/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-parasync/meta.yaml b/recipes/ucsc-parasync/meta.yaml index ef74648b0d782..e1ec0f8009808 100644 --- a/recipes/ucsc-parasync/meta.yaml +++ b/recipes/ucsc-parasync/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-paratestjob/meta.yaml b/recipes/ucsc-paratestjob/meta.yaml index edbd7f5781f3d..f34efff5a4e86 100644 --- a/recipes/ucsc-paratestjob/meta.yaml +++ b/recipes/ucsc-paratestjob/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-positionaltblcheck/meta.yaml b/recipes/ucsc-positionaltblcheck/meta.yaml index d71f3a86bf615..27312d2d740e7 100644 --- a/recipes/ucsc-positionaltblcheck/meta.yaml +++ b/recipes/ucsc-positionaltblcheck/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-pslcat/meta.yaml b/recipes/ucsc-pslcat/meta.yaml index 84be38fe0d48b..23d2aa7f21d69 100644 --- a/recipes/ucsc-pslcat/meta.yaml +++ b/recipes/ucsc-pslcat/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslcdnafilter/meta.yaml b/recipes/ucsc-pslcdnafilter/meta.yaml index bb1f6757f31f7..0850903e42f3b 100644 --- a/recipes/ucsc-pslcdnafilter/meta.yaml +++ b/recipes/ucsc-pslcdnafilter/meta.yaml @@ -15,7 +15,7 @@ source: - include.macos.patch # [osx] build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslcheck/meta.yaml b/recipes/ucsc-pslcheck/meta.yaml index 58ac61563cab6..3292a5a11741e 100644 --- a/recipes/ucsc-pslcheck/meta.yaml +++ b/recipes/ucsc-pslcheck/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-psldropoverlap/meta.yaml b/recipes/ucsc-psldropoverlap/meta.yaml index 6e34ccd565410..25d539e9ec23b 100644 --- a/recipes/ucsc-psldropoverlap/meta.yaml +++ b/recipes/ucsc-psldropoverlap/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslfilter/meta.yaml b/recipes/ucsc-pslfilter/meta.yaml index 3069b7da5417d..52c8b3843a936 100644 --- a/recipes/ucsc-pslfilter/meta.yaml +++ b/recipes/ucsc-pslfilter/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslhisto/meta.yaml b/recipes/ucsc-pslhisto/meta.yaml index 3f78d33a190b3..7af34694e7cb2 100644 --- a/recipes/ucsc-pslhisto/meta.yaml +++ b/recipes/ucsc-pslhisto/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslliftsubrangeblat/meta.yaml b/recipes/ucsc-pslliftsubrangeblat/meta.yaml index 79dce984359ef..fe6e416db00b8 100644 --- a/recipes/ucsc-pslliftsubrangeblat/meta.yaml +++ b/recipes/ucsc-pslliftsubrangeblat/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-pslmap/meta.yaml b/recipes/ucsc-pslmap/meta.yaml index df0c23ae1a8c3..9544ea6016f98 100644 --- a/recipes/ucsc-pslmap/meta.yaml +++ b/recipes/ucsc-pslmap/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslmappostchain/meta.yaml b/recipes/ucsc-pslmappostchain/meta.yaml index 7c51187e06db4..46db46dda770c 100644 --- a/recipes/ucsc-pslmappostchain/meta.yaml +++ b/recipes/ucsc-pslmappostchain/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslmrnacover/meta.yaml b/recipes/ucsc-pslmrnacover/meta.yaml index a50e026a5250b..3ed3ec80494fc 100644 --- a/recipes/ucsc-pslmrnacover/meta.yaml +++ b/recipes/ucsc-pslmrnacover/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslpairs/meta.yaml b/recipes/ucsc-pslpairs/meta.yaml index 73161b3ec6fb7..126a4494859a6 100644 --- a/recipes/ucsc-pslpairs/meta.yaml +++ b/recipes/ucsc-pslpairs/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslpartition/meta.yaml b/recipes/ucsc-pslpartition/meta.yaml index 377e85b51ecf5..ba83d83de1ac6 100644 --- a/recipes/ucsc-pslpartition/meta.yaml +++ b/recipes/ucsc-pslpartition/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslpostarget/meta.yaml b/recipes/ucsc-pslpostarget/meta.yaml index 8172abd6a6979..3116d968cf0b3 100644 --- a/recipes/ucsc-pslpostarget/meta.yaml +++ b/recipes/ucsc-pslpostarget/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslpretty/meta.yaml b/recipes/ucsc-pslpretty/meta.yaml index e2db3fedad559..2ebc3ed24f71c 100644 --- a/recipes/ucsc-pslpretty/meta.yaml +++ b/recipes/ucsc-pslpretty/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslrc/meta.yaml b/recipes/ucsc-pslrc/meta.yaml index 3ac6f82f47dfe..ab5c5b6d72ad8 100644 --- a/recipes/ucsc-pslrc/meta.yaml +++ b/recipes/ucsc-pslrc/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslrecalcmatch/meta.yaml b/recipes/ucsc-pslrecalcmatch/meta.yaml index 3a6b62e0f316b..40c294bc85b90 100644 --- a/recipes/ucsc-pslrecalcmatch/meta.yaml +++ b/recipes/ucsc-pslrecalcmatch/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslreps/meta.yaml b/recipes/ucsc-pslreps/meta.yaml index a6430c181ea3c..cebc949f6d870 100644 --- a/recipes/ucsc-pslreps/meta.yaml +++ b/recipes/ucsc-pslreps/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslscore/meta.yaml b/recipes/ucsc-pslscore/meta.yaml index 1476a30e87a17..0ee1af4a59d0a 100644 --- a/recipes/ucsc-pslscore/meta.yaml +++ b/recipes/ucsc-pslscore/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslselect/meta.yaml b/recipes/ucsc-pslselect/meta.yaml index 58d456a600295..994050d06187c 100644 --- a/recipes/ucsc-pslselect/meta.yaml +++ b/recipes/ucsc-pslselect/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslsomerecords/meta.yaml b/recipes/ucsc-pslsomerecords/meta.yaml index 5af9a55a1dad2..bec5726108303 100644 --- a/recipes/ucsc-pslsomerecords/meta.yaml +++ b/recipes/ucsc-pslsomerecords/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslsort/meta.yaml b/recipes/ucsc-pslsort/meta.yaml index 5e7ae26baeb3f..eed9497cc3ab0 100644 --- a/recipes/ucsc-pslsort/meta.yaml +++ b/recipes/ucsc-pslsort/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslsortacc/meta.yaml b/recipes/ucsc-pslsortacc/meta.yaml index 0041b30f4489a..0a3cb441da82c 100644 --- a/recipes/ucsc-pslsortacc/meta.yaml +++ b/recipes/ucsc-pslsortacc/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage("ucsc-pslsortacc", max_pin=None) }} diff --git a/recipes/ucsc-pslstats/meta.yaml b/recipes/ucsc-pslstats/meta.yaml index df4dcdf568dde..d1ac83796d15a 100644 --- a/recipes/ucsc-pslstats/meta.yaml +++ b/recipes/ucsc-pslstats/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslswap/meta.yaml b/recipes/ucsc-pslswap/meta.yaml index 034f5d8fb55c0..a8ba54a12e713 100644 --- a/recipes/ucsc-pslswap/meta.yaml +++ b/recipes/ucsc-pslswap/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-psltobed/meta.yaml b/recipes/ucsc-psltobed/meta.yaml index 470ba825d07d8..e22a15f38451c 100644 --- a/recipes/ucsc-psltobed/meta.yaml +++ b/recipes/ucsc-psltobed/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-psltobigpsl/meta.yaml b/recipes/ucsc-psltobigpsl/meta.yaml index 79c71bdbe2174..01d3cf00ac29e 100644 --- a/recipes/ucsc-psltobigpsl/meta.yaml +++ b/recipes/ucsc-psltobigpsl/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-psltochain/meta.yaml b/recipes/ucsc-psltochain/meta.yaml index 87146c0c41407..75e8bbe2a9abb 100644 --- a/recipes/ucsc-psltochain/meta.yaml +++ b/recipes/ucsc-psltochain/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-psltopslx/meta.yaml b/recipes/ucsc-psltopslx/meta.yaml index cefae969c7fcd..706c165911dcd 100644 --- a/recipes/ucsc-psltopslx/meta.yaml +++ b/recipes/ucsc-psltopslx/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-pslxtofa/meta.yaml b/recipes/ucsc-pslxtofa/meta.yaml index 25bb9bac1eb2d..4d5ed950da955 100644 --- a/recipes/ucsc-pslxtofa/meta.yaml +++ b/recipes/ucsc-pslxtofa/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-qacagplift/meta.yaml b/recipes/ucsc-qacagplift/meta.yaml index d801311aa1b38..dfd310cc5a715 100644 --- a/recipes/ucsc-qacagplift/meta.yaml +++ b/recipes/ucsc-qacagplift/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-qactoqa/meta.yaml b/recipes/ucsc-qactoqa/meta.yaml index 510d12750220f..d6609525b79b8 100644 --- a/recipes/ucsc-qactoqa/meta.yaml +++ b/recipes/ucsc-qactoqa/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-qactowig/meta.yaml b/recipes/ucsc-qactowig/meta.yaml index 86bbbe0154949..35b571c96f6e1 100644 --- a/recipes/ucsc-qactowig/meta.yaml +++ b/recipes/ucsc-qactowig/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-qatoqac/meta.yaml b/recipes/ucsc-qatoqac/meta.yaml index 2cdd1b678e576..950db2803241a 100644 --- a/recipes/ucsc-qatoqac/meta.yaml +++ b/recipes/ucsc-qatoqac/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-randomlines/meta.yaml b/recipes/ucsc-randomlines/meta.yaml index b186f57343ca7..0c000b9475a32 100644 --- a/recipes/ucsc-randomlines/meta.yaml +++ b/recipes/ucsc-randomlines/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-rasqlquery/meta.yaml b/recipes/ucsc-rasqlquery/meta.yaml index 8b9fca2d654b4..b137ed0103a0a 100644 --- a/recipes/ucsc-rasqlquery/meta.yaml +++ b/recipes/ucsc-rasqlquery/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-ratolines/meta.yaml b/recipes/ucsc-ratolines/meta.yaml index 2b95786fa9a09..e31ad442d2887 100644 --- a/recipes/ucsc-ratolines/meta.yaml +++ b/recipes/ucsc-ratolines/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-ratotab/meta.yaml b/recipes/ucsc-ratotab/meta.yaml index a0318e0be1bf6..0d369913872fa 100644 --- a/recipes/ucsc-ratotab/meta.yaml +++ b/recipes/ucsc-ratotab/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-rmfadups/meta.yaml b/recipes/ucsc-rmfadups/meta.yaml index 3219c579197fb..8947b478386fe 100644 --- a/recipes/ucsc-rmfadups/meta.yaml +++ b/recipes/ucsc-rmfadups/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-rowstocols/meta.yaml b/recipes/ucsc-rowstocols/meta.yaml index 3b9bf1fc1db8b..59172ac8bb96b 100644 --- a/recipes/ucsc-rowstocols/meta.yaml +++ b/recipes/ucsc-rowstocols/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-spacedtotab/meta.yaml b/recipes/ucsc-spacedtotab/meta.yaml index 1f7c293aafb21..096b3c59f4d11 100644 --- a/recipes/ucsc-spacedtotab/meta.yaml +++ b/recipes/ucsc-spacedtotab/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-splitfile/meta.yaml b/recipes/ucsc-splitfile/meta.yaml index e893afcb87139..df3d5270a510c 100644 --- a/recipes/ucsc-splitfile/meta.yaml +++ b/recipes/ucsc-splitfile/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-splitfilebycolumn/meta.yaml b/recipes/ucsc-splitfilebycolumn/meta.yaml index 4bab401fc02c4..92b7eb7d5db8a 100644 --- a/recipes/ucsc-splitfilebycolumn/meta.yaml +++ b/recipes/ucsc-splitfilebycolumn/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-sqltoxml/meta.yaml b/recipes/ucsc-sqltoxml/meta.yaml index 690ca5a345e3b..aaf4fbe24bfac 100644 --- a/recipes/ucsc-sqltoxml/meta.yaml +++ b/recipes/ucsc-sqltoxml/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-stringify/meta.yaml b/recipes/ucsc-stringify/meta.yaml index c2ff5e46c9cff..15abcd8fb35d3 100644 --- a/recipes/ucsc-stringify/meta.yaml +++ b/recipes/ucsc-stringify/meta.yaml @@ -15,7 +15,7 @@ source: - include.macos.patch # [osx] build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-subchar/meta.yaml b/recipes/ucsc-subchar/meta.yaml index 58f2a5ab8d6c0..338f211fe9e3b 100644 --- a/recipes/ucsc-subchar/meta.yaml +++ b/recipes/ucsc-subchar/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-subcolumn/meta.yaml b/recipes/ucsc-subcolumn/meta.yaml index f481ad2ca4aba..af55d9e032e32 100644 --- a/recipes/ucsc-subcolumn/meta.yaml +++ b/recipes/ucsc-subcolumn/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-taillines/meta.yaml b/recipes/ucsc-taillines/meta.yaml index 5b2df04b6411d..f16f7e5a89562 100644 --- a/recipes/ucsc-taillines/meta.yaml +++ b/recipes/ucsc-taillines/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-tdbquery/meta.yaml b/recipes/ucsc-tdbquery/meta.yaml index 212fa54971621..c45bbec35f6af 100644 --- a/recipes/ucsc-tdbquery/meta.yaml +++ b/recipes/ucsc-tdbquery/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-texthistogram/meta.yaml b/recipes/ucsc-texthistogram/meta.yaml index 756b419e8949d..81d476d9e44d2 100644 --- a/recipes/ucsc-texthistogram/meta.yaml +++ b/recipes/ucsc-texthistogram/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-ticktodate/meta.yaml b/recipes/ucsc-ticktodate/meta.yaml index ac0059144d920..e723c89627d99 100644 --- a/recipes/ucsc-ticktodate/meta.yaml +++ b/recipes/ucsc-ticktodate/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-tolower/meta.yaml b/recipes/ucsc-tolower/meta.yaml index 332473fb2342b..2dba7ba24283f 100644 --- a/recipes/ucsc-tolower/meta.yaml +++ b/recipes/ucsc-tolower/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-toupper/meta.yaml b/recipes/ucsc-toupper/meta.yaml index 321ceb63c29a7..0e2558f88b099 100644 --- a/recipes/ucsc-toupper/meta.yaml +++ b/recipes/ucsc-toupper/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-transmappsltogenepred/meta.yaml b/recipes/ucsc-transmappsltogenepred/meta.yaml index 293cafa31d030..4bce732abe6ba 100644 --- a/recipes/ucsc-transmappsltogenepred/meta.yaml +++ b/recipes/ucsc-transmappsltogenepred/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-trfbig/meta.yaml b/recipes/ucsc-trfbig/meta.yaml index 0025de973200c..73da998701fba 100644 --- a/recipes/ucsc-trfbig/meta.yaml +++ b/recipes/ucsc-trfbig/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-twobitdup/meta.yaml b/recipes/ucsc-twobitdup/meta.yaml index 18ea0f188ccfd..784b0af1975ff 100644 --- a/recipes/ucsc-twobitdup/meta.yaml +++ b/recipes/ucsc-twobitdup/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-twobitinfo/meta.yaml b/recipes/ucsc-twobitinfo/meta.yaml index efd408cb42f7b..0a6e9009e734a 100644 --- a/recipes/ucsc-twobitinfo/meta.yaml +++ b/recipes/ucsc-twobitinfo/meta.yaml @@ -15,7 +15,7 @@ source: - include.macos.patch # [osx] build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-twobitmask/meta.yaml b/recipes/ucsc-twobitmask/meta.yaml index cfef8cf9866cd..32bccff1d8af3 100644 --- a/recipes/ucsc-twobitmask/meta.yaml +++ b/recipes/ucsc-twobitmask/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-twobittofa/meta.yaml b/recipes/ucsc-twobittofa/meta.yaml index b7543b173d7f9..47a269a6cf5a9 100644 --- a/recipes/ucsc-twobittofa/meta.yaml +++ b/recipes/ucsc-twobittofa/meta.yaml @@ -15,7 +15,7 @@ source: - include.macos.patch # [osx] build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-validatefiles/meta.yaml b/recipes/ucsc-validatefiles/meta.yaml index 67e9b60320e72..7c041a541835c 100644 --- a/recipes/ucsc-validatefiles/meta.yaml +++ b/recipes/ucsc-validatefiles/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -53,4 +53,4 @@ extra: identifiers: - biotools:UCSC_Genome_Browser_Utilities - doi:10.1093/bib/bbs038 - \ No newline at end of file + diff --git a/recipes/ucsc-validatemanifest/meta.yaml b/recipes/ucsc-validatemanifest/meta.yaml index a3b17fc4ab953..a187738f42b2b 100644 --- a/recipes/ucsc-validatemanifest/meta.yaml +++ b/recipes/ucsc-validatemanifest/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-websync/meta.yaml b/recipes/ucsc-websync/meta.yaml index 91c8888cce901..63e2805635c03 100644 --- a/recipes/ucsc-websync/meta.yaml +++ b/recipes/ucsc-websync/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-wigcorrelate/meta.yaml b/recipes/ucsc-wigcorrelate/meta.yaml index dfa59e07f8970..85079b7198610 100644 --- a/recipes/ucsc-wigcorrelate/meta.yaml +++ b/recipes/ucsc-wigcorrelate/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-wigtobigwig/meta.yaml b/recipes/ucsc-wigtobigwig/meta.yaml index c9deee8b43399..3f5624b3c4e0f 100644 --- a/recipes/ucsc-wigtobigwig/meta.yaml +++ b/recipes/ucsc-wigtobigwig/meta.yaml @@ -15,7 +15,7 @@ source: - include.macos.patch # [osx] build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-wordline/meta.yaml b/recipes/ucsc-wordline/meta.yaml index a4f886851f2d7..ce02113e8960e 100644 --- a/recipes/ucsc-wordline/meta.yaml +++ b/recipes/ucsc-wordline/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-xmlcat/meta.yaml b/recipes/ucsc-xmlcat/meta.yaml index fdfb1b545ec90..9ccc22ff089ed 100644 --- a/recipes/ucsc-xmlcat/meta.yaml +++ b/recipes/ucsc-xmlcat/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ucsc-xmltosql/meta.yaml b/recipes/ucsc-xmltosql/meta.yaml index d66247fc304ce..43a7102bae3bb 100644 --- a/recipes/ucsc-xmltosql/meta.yaml +++ b/recipes/ucsc-xmltosql/meta.yaml @@ -15,7 +15,7 @@ source: build: skip: True # [osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage(package, max_pin=None) }} diff --git a/recipes/ultraplex/meta.yaml b/recipes/ultraplex/meta.yaml index 49c1dae9563dc..60a93aa6e5115 100644 --- a/recipes/ultraplex/meta.yaml +++ b/recipes/ultraplex/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 7b1efa09a421590907c7e5177eb9e4837deade89c237b961bcf2f7edfa9f2e90 build: - number: 2 + number: 3 skip: True # [py < 37 or py > 39] script: - "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --use-pep517 -vvv" diff --git a/recipes/umi-transfer/meta.yaml b/recipes/umi-transfer/meta.yaml index acf6e68d657d7..145f7a8fedc28 100644 --- a/recipes/umi-transfer/meta.yaml +++ b/recipes/umi-transfer/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('umi-transfer', max_pin="x") }} diff --git a/recipes/umi_tools/meta.yaml b/recipes/umi_tools/meta.yaml index 257127fa2a822..3fda933bcb753 100644 --- a/recipes/umi_tools/meta.yaml +++ b/recipes/umi_tools/meta.yaml @@ -24,6 +24,7 @@ requirements: host: - python - pip + - setuptools run: - python - matplotlib-base diff --git a/recipes/umis/build_failure.osx-64.yaml b/recipes/umis/build_failure.osx-64.yaml deleted file mode 100644 index 156eb183093d2..0000000000000 --- a/recipes/umis/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: db16a0980e9904f8ba53514b8333744e1c9d1e29c19bfa250e06ecc2916beea4 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/umis-1.0.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - running install - running build - running build_py - creating build - post_process_shared_lib(m, f, prefix_files, host_prefix) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1603, in post_process_shared_lib - mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 470, in mk_relative_osx - names = macho.otool(path, prefix) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 221, in otool - lines = check_output([otool, "-l", path], stderr=STDOUT).decode("utf-8") - File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 421, in check_output - return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, - File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 526, in run - raise CalledProcessError(retcode, process.args, - subprocess.CalledProcessError: Command '['/opt/mambaforge/envs/bioconda/conda-bld/umis_1717900414497/_build_env/bin/llvm-otool', '-l', '/opt/mambaforge/envs/bioconda/conda-bld/umis_1717900414497/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/python3.9/site-packages/utils.cpython-39-darwin.so']' died with . - creating build/lib.macosx-10.9-x86_64-cpython-39 - creating build/lib.macosx-10.9-x86_64-cpython-39/umis - copying umis/__init__.py -> build/lib.macosx-10.9-x86_64-cpython-39/umis - copying umis/umis.py -> build/lib.macosx-10.9-x86_64-cpython-39/umis - copying umis/barcodes.py -> build/lib.macosx-10.9-x86_64-cpython-39/umis - running build_ext - Compiling umis/utils.pyx because it changed. - [1/1] Cythonizing umis/utils.pyx - building 'utils' extension - creating build/temp.macosx-10.9-x86_64-cpython-39 - creating build/temp.macosx-10.9-x86_64-cpython-39/umis - x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/umis-1.0.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include/python3.9 -c umis/utils.c -o build/temp.macosx-10.9-x86_64-cpython-39/umis/utils.o - x86_64-apple-darwin13.4.0-clang -bundle -undefined dynamic_lookup -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/umis-1.0.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 build/temp.macosx-10.9-x86_64-cpython-39/umis/utils.o -o build/lib.macosx-10.9-x86_64-cpython-39/utils.cpython-39-darwin.so - running install_lib - creating $PREFIX/lib/python3.9/site-packages/umis - copying build/lib.macosx-10.9-x86_64-cpython-39/umis/__init__.py -> $PREFIX/lib/python3.9/site-packages/umis - copying build/lib.macosx-10.9-x86_64-cpython-39/umis/umis.py -> $PREFIX/lib/python3.9/site-packages/umis - copying build/lib.macosx-10.9-x86_64-cpython-39/umis/barcodes.py -> $PREFIX/lib/python3.9/site-packages/umis - copying build/lib.macosx-10.9-x86_64-cpython-39/utils.cpython-39-darwin.so -> $PREFIX/lib/python3.9/site-packages - byte-compiling $PREFIX/lib/python3.9/site-packages/umis/__init__.py to __init__.cpython-39.pyc - byte-compiling $PREFIX/lib/python3.9/site-packages/umis/umis.py to umis.cpython-39.pyc - byte-compiling $PREFIX/lib/python3.9/site-packages/umis/barcodes.py to barcodes.cpython-39.pyc - running install_egg_info - running egg_info - creating umis.egg-info - writing umis.egg-info/PKG-INFO - writing dependency_links to umis.egg-info/dependency_links.txt - writing entry points to umis.egg-info/entry_points.txt - writing requirements to umis.egg-info/requires.txt - writing top-level names to umis.egg-info/top_level.txt - writing manifest file 'umis.egg-info/SOURCES.txt' - reading manifest file 'umis.egg-info/SOURCES.txt' - reading manifest template 'MANIFEST.in' - adding license file 'LICENSE.md' - writing manifest file 'umis.egg-info/SOURCES.txt' - Copying umis.egg-info to $PREFIX/lib/python3.9/site-packages/umis-1.0.9-py3.9.egg-info - running install_scripts - Installing umis script to $PREFIX/bin - writing list of installed files to 'record.txt' - - Resource usage statistics from building umis: - Process count: 3 - CPU time: Sys=0:00:00.2, User=0:00:00.6 - Memory: 162.6M - Disk usage: 3.8K - Time elapsed: 0:00:04.4 - - - compiling .pyc files... - number of files: 14 -# Last 100 lines of the build log. diff --git a/recipes/umis/meta.yaml b/recipes/umis/meta.yaml index 5a028eaffa3c6..3b49a8297d616 100644 --- a/recipes/umis/meta.yaml +++ b/recipes/umis/meta.yaml @@ -6,7 +6,7 @@ package: version: "{{ version }}" build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage('umis', max_pin='x') }} diff --git a/recipes/unicycler/0.4.4/meta.yaml b/recipes/unicycler/0.4.4/meta.yaml index 4e471674d0a6b..f6cff0905e282 100644 --- a/recipes/unicycler/0.4.4/meta.yaml +++ b/recipes/unicycler/0.4.4/meta.yaml @@ -13,7 +13,7 @@ source: - misc.py.patch build: - number: 7 + number: 8 skip: True # [py<34] requirements: diff --git a/recipes/unicycler/meta.yaml b/recipes/unicycler/meta.yaml index 5e1fa962a312d..fba7edbe6bad6 100644 --- a/recipes/unicycler/meta.yaml +++ b/recipes/unicycler/meta.yaml @@ -13,7 +13,7 @@ source: - misc.py.patch build: - number: 2 + number: 3 entry_points: - unicycler = unicycler.unicycler:main script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir diff --git a/recipes/unifrac-binaries/build_failure.osx-64.yaml b/recipes/unifrac-binaries/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..69ae244ea10ef --- /dev/null +++ b/recipes/unifrac-binaries/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 5bbf0149c08eb3e6ec185fe312cc0b076c6ec670e58b37b88f77f939789dd83f # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - faithpd --help + about: + description: 'UniFrac is a commonly phylogenetic diversity distance metric used + in + + microbiome research. The metric relates two microbiome samples together + + within the context of an evolutionary history, and produces a distance + + that corresponds to how similar two samples by the amount of overlapping + + branch length. This package contains command line utilities and + + a shared library. + + ' + dev_url: https://github.com/biocore/unifrac-binaries + doc_url: https://github.com/biocore/unifrac-binaries + home: https://github.com/biocore/unifrac-binaries + license: BSD-3-Clause + license_family: BSD + license_file: LICENSE + summary: Fast phylogenetic diversity calculations + extra: + copy_test_source_files: true + final: true + recipe-maintainers: + - sfiligoi + - wasade + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/unifrac-binaries_1733951831011/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/unifrac-binaries_1733951831011/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/unifrac-binaries_1733951831011/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/unifrac-binaries_1733951831011/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/unifrac-binaries-1.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/unifrac-binaries-1.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/unifrac-binaries-1.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/unifrac-binaries-1.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + === PREIX === + CONDA_PREFIX_1=/opt/mambaforge/envs/bioconda + CONDA_PREFIX_2=$PREFIX + CONDA_PREFIX=$BUILD_PREFIX + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + BUILD_PREFIX=$BUILD_PREFIX + SYS_PREFIX=/opt/mambaforge/envs/bioconda + PREFIX=$PREFIX + CMAKE_PREFIX_PATH=:$PREFIX + Arch: Darwin + $SRC_DIR + $BUILD_PREFIX/bin/clang + $BUILD_PREFIX/bin/h5c + cd src && make api + make[1]: Entering directory '$SRC_DIR/src' + h5c -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -fopenmp -mpopcnt -Wall -std=c17 -pedantic -I. -O3 -fPIC -L$PREFIX/lib -c tree.cpp -o tree.o + make[1]: Leaving directory '$SRC_DIR/src' +# Last 100 lines of the build log. diff --git a/recipes/unifrac-binaries/meta.yaml b/recipes/unifrac-binaries/meta.yaml index c51e9178b420c..4a9c313a35094 100644 --- a/recipes/unifrac-binaries/meta.yaml +++ b/recipes/unifrac-binaries/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 7067a3bcee8702caa8c3ea6e5fd8f1bb059f84a791b237762730fbf232ae785f build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/unimap/meta.yaml b/recipes/unimap/meta.yaml index 86e5b2fbf5e29..0b429ed41a261 100644 --- a/recipes/unimap/meta.yaml +++ b/recipes/unimap/meta.yaml @@ -16,7 +16,7 @@ source: - 0001-gh-4-Consider-LDFLAGS-while-linking.patch build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/unmerge/meta.yaml b/recipes/unmerge/meta.yaml index ffe257e0e348e..7510b60a284ce 100644 --- a/recipes/unmerge/meta.yaml +++ b/recipes/unmerge/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 9e94ddae669762523c5873e68fb3b6d5d6ac9c8b4d4b7d19aed91cb31275d4cc build: - number: 4 + number: 5 skip: True # [osx] requirements: diff --git a/recipes/usalign/meta.yaml b/recipes/usalign/meta.yaml index b3e5a789aa3d8..526dbea1c7fb1 100644 --- a/recipes/usalign/meta.yaml +++ b/recipes/usalign/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 21b510507e9258c1a2e03c6d32680282981a54e27778a3f3f739861ca7c7b38a build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name|lower|replace("-", ""), max_pin=None) }} diff --git a/recipes/ushuffle/meta.yaml b/recipes/ushuffle/meta.yaml index 60cc87d270dce..cce3e47eb8984 100644 --- a/recipes/ushuffle/meta.yaml +++ b/recipes/ushuffle/meta.yaml @@ -8,7 +8,7 @@ about: summary: uShuffle---a useful tool for shuffling biological sequences while preserving the k-let counts build: - number: 8 + number: 9 source: url: https://github.com/s-will/ushuffle/archive/v1.2.2.tar.gz diff --git a/recipes/uvaia/meta.yaml b/recipes/uvaia/meta.yaml index 68aeef746cd99..d3e3382e255fc 100644 --- a/recipes/uvaia/meta.yaml +++ b/recipes/uvaia/meta.yaml @@ -11,7 +11,7 @@ source: md5: unused build: - number: 2 + number: 3 skip: true # [osx] requirements: diff --git a/recipes/vadr/build_failure.linux-64.yaml b/recipes/vadr/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..1df98c2efcbc6 --- /dev/null +++ b/recipes/vadr/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: ed1ff9fba826bf33dee5fcfe068df4a8cbe2f34ffd876c52b673f62f73f614a2 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + [32mperl-net-ssleay [1.88|1.92][0m would require + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [31mperl-net-ssleay [1.72|1.74|1.84|1.85|1.86][0m conflicts with any installable versions previously reported; + [31mperl-io-socket-ssl [2.024|2.056|2.060|2.066|2.074][0m conflicts with any installable versions previously reported; + [32mperl-net-ssleay >=1.88 [0m is installable with the potential options + [32mperl-net-ssleay 1.92[0m, which can be installed (as previously explained); + [31mperl-net-ssleay 1.88[0m, which cannot be installed (as previously explained); + [32mperl-net-ssleay [1.88|1.92][0m, which can be installed (as previously explained). + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("perl-net-ssleay==1.92=pl5321haa6b8db_0"), MatchSpec("perl-io-socket-ssl"), MatchSpec("zlib[version='>=1.2.12,<1.3.0a0']"), MatchSpec("perl-lwp-protocol-https==6.07=pl526_4")} + Encountered problems while solving: + - package perl-net-ssleay-1.92-pl5321haa6b8db_0 requires zlib >=1.2.12,<1.3.0a0, but none of the providers can be installed + - package perl-lwp-protocol-https-6.07-pl526_4 requires perl-io-socket-ssl, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [31mblast >=2.15.0 [0m is not installable because there are no viable options + [31mblast 2.16.0[0m would require + [32mentrez-direct >=22.4,<23.0a0 [0m, which requires + [32mwget[0m with the potential options + [32mwget 1.21.4[0m would require + [32mzlib[0m with the potential options + [32mzlib [1.2.12|1.2.13][0m, which can be installed; + [32mzlib 1.2.11[0m, which can be installed; + [31mzlib [1.2.8|1.3|1.3.1][0m conflicts with any installable versions previously reported; + [32mwget [1.20.1|1.20.3][0m would require + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [31mlibzlib >=1.3.1,<2.0a0 [0m but there are no viable options + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_0[0m, which conflicts with any installable versions previously reported; + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_1[0m, which conflicts with any installable versions previously reported; + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_2[0m, which conflicts with any installable versions previously reported; + [31mblast [2.15.0|2.16.0][0m conflicts with any installable versions previously reported; + [31mminimap2 >=2.26 [0m is not installable because there are no viable options + [31mminimap2 2.28[0m would require + [31mlibzlib >=1.3.1,<2.0a0 [0m, which cannot be installed (as previously explained); + [31mminimap2 [2.26|2.27|2.28][0m conflicts with any installable versions previously reported; + [32mperl-lwp-protocol-https >=6.07 [0m is installable and it requires + [32mperl-io-socket-ssl[0m with the potential options + [32mperl-io-socket-ssl 2.075[0m would require + [32mperl-net-ssleay[0m with the potential options + [32mperl-net-ssleay 1.92[0m would require + [32mzlib >=1.2.12,<1.3.0a0 [0m, which can be installed; + [31mperl-net-ssleay 1.88[0m would require + [32mperl >=5.26.2,<5.26.3.0a0 [0m, which can be installed; + [31mperl-mime-base64[0m but there are no viable options + [31mperl-mime-base64 3.16[0m would require + [31mperl >=5.32.1,<5.33.0a0 *_perl5[0m, which conflicts with any installable versions previously reported; + [31mperl-mime-base64 [3.15|3.16][0m conflicts with any installable versions previously reported; + [32mperl-net-ssleay [1.88|1.92][0m would require + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [31mperl-net-ssleay [1.72|1.74|1.84|1.85|1.86][0m conflicts with any installable versions previously reported; + [31mperl-io-socket-ssl [2.024|2.056|2.060|2.066|2.074][0m conflicts with any installable versions previously reported; + [32mperl-net-ssleay >=1.88 [0m is installable with the potential options + [32mperl-net-ssleay 1.92[0m, which can be installed (as previously explained); + [31mperl-net-ssleay 1.88[0m, which cannot be installed (as previously explained); + [32mperl-net-ssleay [1.88|1.92][0m, which can be installed (as previously explained). +# Last 100 lines of the build log. diff --git a/recipes/vadr/meta.yaml b/recipes/vadr/meta.yaml index 655160c155e81..2a1c6fc9a0347 100644 --- a/recipes/vadr/meta.yaml +++ b/recipes/vadr/meta.yaml @@ -16,7 +16,7 @@ source: folder: fasta build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/vamos/build_failure.osx-64.yaml b/recipes/vamos/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..81858346f8cbd --- /dev/null +++ b/recipes/vamos/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 901cfb86929ae21ae1327a433e54109d151749c45e40ec7a15574b71dfb3eb3d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - openssl 3.4.0 hd471939_0 + - readline 8.2 h9e318b2_1 + - tk 8.6.13 h1abcd95_1 + - xz-gpl-tools 5.6.3 h357f2ed_1 + - xz-tools 5.6.3 hd471939_1 + - zlib 1.2.13 h87427d6_6 + - zstd 1.5.6 h915ae27_0 + - krb5 1.21.3 h37d8d59_0 + - libgfortran 5.0.0 13_2_0_h97931a8_3 + - libnghttp2 1.58.0 h64cf6d3_1 + - libssh2 1.11.0 hd019ec5_0 + - xz 5.6.3 h357f2ed_1 + - libboost 1.85.0 h739af76_2 + - libcurl 8.8.0 hf9fcc65_1 + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/vamos_1734325675938/work/conda_build.sh']' returned non-zero exit status 1. + - libopenblas 0.3.28 openmp_hbf64a52_1 + - python 3.12.3 h1411813_0_cpython + - htslib 1.21 hec81eee_0 + - libblas 3.9.0 25_osx64_openblas + - libboost-devel 1.85.0 h2b186f8_2 + - libcblas 3.9.0 25_osx64_openblas + - liblapack 3.9.0 25_osx64_openblas + - numpy 2.2.0 py312h22eab8f_0 + - libboost-python 1.85.0 py312h44e70fa_2 + - libboost-python-devel 1.85.0 py312h0be7463_2 + - boost 1.85.0 h0be7463_2 + run: + - htslib >=1.21,<1.22.0a0 + - libzlib >=1.2.13,<2.0a0 + - zlib 1.2.* + - libcxx >=17 + test: + commands: + - vamos | grep 'Usage' + about: + home: https://github.com/ChaissonLab/vamos + license: USC-RL v1.0 + license_file: LICENSE.txt + summary: VNTR annotation using efficient motif selection + extra: + additional-platforms: + - linux-aarch64 + copy_test_source_files: true + final: true + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/vamos_1734325675938/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/vamos_1734325675938/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/vamos_1734325675938/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/vamos_1734325675938/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/vamos-2.1.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/vamos-2.1.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 + INFO: activate_clangxx_osx-64.sh made the following environmental changes: + CLANGXX=x86_64-apple-darwin13.4.0-clang + CXX=x86_64-apple-darwin13.4.0-clang + CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/vamos-2.1.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/vamos-2.1.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/vamos-2.1.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fPIE -O3 -DNDEBUG -c main.cpp -I $BUILD_PREFIX/include + x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/vamos-2.1.5 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$PREFIX/lib -fPIE -O3 -DNDEBUG -c io.cpp -I $BUILD_PREFIX/include -I ../abPOA-1.4.1/include -I $BUILD_PREFIX/include +# Last 100 lines of the build log. diff --git a/recipes/vamos/meta.yaml b/recipes/vamos/meta.yaml index f8d8a23b86ccc..0a247e303dc02 100644 --- a/recipes/vamos/meta.yaml +++ b/recipes/vamos/meta.yaml @@ -12,7 +12,7 @@ source: - vamos-aarch64.patch # [linux and aarch64] build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin='x') }} diff --git a/recipes/varfish-server-worker/build_failure.linux-64.yaml b/recipes/varfish-server-worker/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..77c71747cc89a --- /dev/null +++ b/recipes/varfish-server-worker/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: fb32764e52097b62723f0f36945f29853bd98236d3a8875014414d36b780fa90 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + Running rustc --crate-name unicode_width --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/unicode-width-0.2.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="cjk"' --cfg 'feature="default"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("cjk", "compiler_builtins", "core", "default", "no_std", "rustc-dep-of-std", "std"))' -C metadata=a039cb43434fd123 -C extra-filename=-a039cb43434fd123 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling rustc-demangle v0.1.24 + Running rustc --crate-name rustc_demangle --edition=2015 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/rustc-demangle-0.1.24/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("compiler_builtins", "core", "rustc-dep-of-std", "std"))' -C metadata=2c5cf5dee47f2cc9 -C extra-filename=-2c5cf5dee47f2cc9 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling urlencoding v2.1.3 + Running rustc --crate-name urlencoding --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/urlencoding-2.1.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=54038e9180cb8a6f -C extra-filename=-54038e9180cb8a6f --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling option-ext v0.2.0 + Running rustc --crate-name option_ext --edition=2015 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/option-ext-0.2.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=42b7a04d8a355747 -C extra-filename=-42b7a04d8a355747 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Running rustc --crate-name minimal_lexical --edition=2018 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/minimal-lexical-0.2.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "compact", "default", "lint", "nightly", "std"))' -C metadata=7f12a2b8dd876f1f -C extra-filename=-7f12a2b8dd876f1f --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling rustc-hash v2.1.0 + Running rustc --crate-name rustc_hash --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/rustc-hash-2.1.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "nightly", "rand", "std"))' -C metadata=553df341db1d07e6 -C extra-filename=-553df341db1d07e6 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling arrayvec v0.7.6 + Running rustc --crate-name arrayvec --edition=2018 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/arrayvec-0.7.6/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("borsh", "default", "serde", "std", "zeroize"))' -C metadata=99a4590ec8c12a16 -C extra-filename=-99a4590ec8c12a16 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Running rustc --crate-name urlencoding --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/urlencoding-2.1.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C embed-bitcode=no -C debug-assertions=off --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=a6df050112548230 -C extra-filename=-a6df050112548230 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --cap-lints allow + Compiling procfs v0.16.0 + Running rustc --crate-name build_script_build --edition=2018 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/procfs-0.16.0/build.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="chrono"' --cfg 'feature="default"' --cfg 'feature="flate2"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("backtrace", "chrono", "default", "flate2", "serde", "serde1"))' -C metadata=5a93100a8fbdf05b -C extra-filename=-5a93100a8fbdf05b --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/build/procfs-5a93100a8fbdf05b -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --cap-lints allow + Compiling impl-more v0.1.8 + Running rustc --crate-name impl_more --edition=2018 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/impl-more-0.1.8/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --warn=missing_docs --deny=rust_2018_idioms --deny=nonstandard-style --deny=future_incompatible --forbid=unsafe_code --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=3fe0aa7ade294f9b -C extra-filename=-3fe0aa7ade294f9b --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling actix-web v4.9.0 + Running rustc --crate-name actix_web --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/actix-web-4.9.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --deny=rust_2018_idioms --deny=nonstandard_style --deny=future_incompatible --cfg 'feature="__compress"' --cfg 'feature="compat"' --cfg 'feature="compat-routing-macros-force-pub"' --cfg 'feature="compress-brotli"' --cfg 'feature="compress-gzip"' --cfg 'feature="compress-zstd"' --cfg 'feature="cookies"' --cfg 'feature="default"' --cfg 'feature="http2"' --cfg 'feature="macros"' --cfg 'feature="unicode"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("__compress", "__tls", "actix-tls", "compat", "compat-routing-macros-force-pub", "compress-brotli", "compress-gzip", "compress-zstd", "cookies", "default", "experimental-io-uring", "http2", "macros", "openssl", "rustls", "rustls-0_20", "rustls-0_21", "rustls-0_22", "rustls-0_23", "secure-cookies", "unicode"))' -C metadata=d0c10dfba41b4553 -C extra-filename=-d0c10dfba41b4553 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --extern actix_codec=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libactix_codec-f367c6751e3f4d1a.rmeta --extern actix_http=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libactix_http-6bb9ee93399af9e3.rmeta --extern actix_macros=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps/libactix_macros-ea59f919fd637798.so --extern actix_router=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libactix_router-a163c7038f62156e.rmeta --extern actix_rt=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libactix_rt-ad27050e3be0d5cf.rmeta --extern actix_server=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libactix_server-116bd94b04d1a6d2.rmeta --extern actix_service=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libactix_service-4bb03674bf1285c2.rmeta --extern actix_utils=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libactix_utils-57573256d4d8c341.rmeta --extern actix_web_codegen=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps/libactix_web_codegen-95f843c2135459f6.so --extern ahash=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libahash-945e758b82a99d43.rmeta --extern bytes=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libbytes-a13d0d504cd35641.rmeta --extern bytestring=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libbytestring-03babfd90072b2d6.rmeta --extern cfg_if=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libcfg_if-cc1a207a177f0d2d.rmeta --extern cookie=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libcookie-0abb36e7e99911a7.rmeta --extern derive_more=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps/libderive_more-1e1534e81e18ac9e.so --extern encoding_rs=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libencoding_rs-44b557b698cf57da.rmeta --extern futures_core=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libfutures_core-90a74a61ee048f5d.rmeta --extern futures_util=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libfutures_util-6baf884906957a10.rmeta --extern impl_more=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libimpl_more-3fe0aa7ade294f9b.rmeta --extern itoa=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libitoa-790a0b83dfbc78a7.rmeta --extern language_tags=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/liblanguage_tags-7bc106e6b4ee9985.rmeta --extern log=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/liblog-22c5f274688aa5f4.rmeta --extern mime=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libmime-7dacb0cee2530301.rmeta --extern once_cell=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libonce_cell-14d214d3f0f6a9a9.rmeta --extern pin_project_lite=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libpin_project_lite-77b5986db0d59e3c.rmeta --extern regex=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libregex-175f0b512db8628f.rmeta --extern regex_lite=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libregex_lite-155b427abd1b770c.rmeta --extern serde=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libserde-bd72b630b6c57b93.rmeta --extern serde_json=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libserde_json-93a9b1d2428615cf.rmeta --extern serde_urlencoded=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libserde_urlencoded-eb7f6b53a3801ab6.rmeta --extern smallvec=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libsmallvec-6633be87dc610e5a.rmeta --extern socket2=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libsocket2-c6523bbf030e93e2.rmeta --extern time=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libtime-40f89bf71c14e180.rmeta --extern url=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/liburl-1f7b200e2e72bd4d.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -L native=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/build/zstd-sys-b67db1b4a9204acf/out + Running /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/build/procfs-5a93100a8fbdf05b/build-script-build + Compiling nutype_macros v0.4.3 + Running rustc --crate-name nutype_macros --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/nutype_macros-0.4.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type proc-macro --emit=dep-info,link -C prefer-dynamic -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="serde"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("arbitrary", "new_unchecked", "regex", "schemars08", "serde", "std"))' -C metadata=545932bf35db9c98 -C extra-filename=-545932bf35db9c98 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --extern cfg_if=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps/libcfg_if-8d05f4d140599acd.rlib --extern kinded=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps/libkinded-ab35ae17237cd3dc.rlib --extern proc_macro2=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps/libproc_macro2-e9917080d209ed18.rlib --extern quote=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps/libquote-fb1f1222afc14bf4.rlib --extern syn=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps/libsyn-67391e00b515bd0a.rlib --extern urlencoding=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps/liburlencoding-a6df050112548230.rlib --extern proc_macro --cap-lints allow + Compiling backtrace v0.3.74 + Running rustc --crate-name backtrace --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/backtrace-0.3.74/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --allow=unexpected_cfgs --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("coresymbolication", "cpp_demangle", "dbghelp", "default", "dl_iterate_phdr", "dladdr", "kernel32", "libunwind", "serde", "serialize-serde", "std", "unix-backtrace"))' -C metadata=94d7834775d6da7a -C extra-filename=-94d7834775d6da7a --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --extern addr2line=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libaddr2line-fb6ea6f787f8ff59.rmeta --extern cfg_if=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libcfg_if-cc1a207a177f0d2d.rmeta --extern libc=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/liblibc-7bd17ac07d4e6ce6.rmeta --extern miniz_oxide=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libminiz_oxide-8d5ea91c1a82adbb.rmeta --extern object=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libobject-214a510aa55fe7ff.rmeta --extern rustc_demangle=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/librustc_demangle-2c5cf5dee47f2cc9.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Running rustc --crate-name rust_decimal --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/rust_decimal-1.36.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("borsh", "c-repr", "db-diesel-mysql", "db-diesel-postgres", "db-diesel2-mysql", "db-diesel2-postgres", "db-postgres", "db-tokio-postgres", "default", "diesel", "legacy-ops", "maths", "maths-nopanic", "ndarray", "proptest", "rand", "rkyv", "rkyv-safe", "rocket-traits", "rust-fuzz", "serde", "serde-arbitrary-precision", "serde-bincode", "serde-float", "serde-str", "serde-with-arbitrary-precision", "serde-with-float", "serde-with-str", "serde_json", "std", "tokio-pg", "tokio-postgres"))' -C metadata=df07e56347e4379e -C extra-filename=-df07e56347e4379e --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --extern arrayvec=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libarrayvec-99a4590ec8c12a16.rmeta --extern num_traits=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libnum_traits-45cfdbe14cf49886.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Running rustc --crate-name nom --edition=2018 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/nom-7.1.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="alloc"' --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "default", "docsrs", "std"))' -C metadata=338fc54054b05009 -C extra-filename=-338fc54054b05009 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --extern memchr=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libmemchr-869b0042e8600ae7.rmeta --extern minimal_lexical=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libminimal_lexical-7f12a2b8dd876f1f.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling dirs-sys v0.4.1 + Running rustc --crate-name dirs_sys --edition=2015 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/dirs-sys-0.4.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=1e2f5ca590efe328 -C extra-filename=-1e2f5ca590efe328 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --extern libc=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/liblibc-7bd17ac07d4e6ce6.rmeta --extern option_ext=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/liboption_ext-42b7a04d8a355747.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling aws-smithy-query v0.60.7 + Running rustc --crate-name aws_smithy_query --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/aws-smithy-query-0.60.7/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=5173523b8da8bb5a -C extra-filename=-5173523b8da8bb5a --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --extern aws_smithy_types=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libaws_smithy_types-1ca95f68fc4819ed.rmeta --extern urlencoding=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/liburlencoding-54038e9180cb8a6f.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Running rustc --crate-name thiserror --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/thiserror-2.0.6/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "std"))' -C metadata=897679c44298139f -C extra-filename=-897679c44298139f --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --extern thiserror_impl=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps/libthiserror_impl-1be922c140ef926a.so --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib --check-cfg 'cfg(error_generic_member_access)' --check-cfg 'cfg(thiserror_nightly_testing)' --check-cfg 'cfg(thiserror_no_backtrace_type)' + Compiling indicatif v0.17.9 + Running rustc --crate-name indicatif --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/indicatif-0.17.9/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="rayon"' --cfg 'feature="unicode-width"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "futures", "improved_unicode", "in_memory", "rayon", "tokio", "unicode-segmentation", "unicode-width", "vt100"))' -C metadata=45b9b542b93f94ba -C extra-filename=-45b9b542b93f94ba --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --extern console=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libconsole-6cb446f01e00956b.rmeta --extern number_prefix=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libnumber_prefix-f7b3c2dd21ffe761.rmeta --extern portable_atomic=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libportable_atomic-598374a642450149.rmeta --extern rayon=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/librayon-9329ab4e7a5bd8e8.rmeta --extern unicode_width=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libunicode_width-a039cb43434fd123.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling cached v0.54.0 + Running rustc --crate-name cached --edition=2018 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/cached-0.54.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="ahash"' --cfg 'feature="cached_proc_macro"' --cfg 'feature="cached_proc_macro_types"' --cfg 'feature="default"' --cfg 'feature="proc_macro"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("ahash", "async", "async-trait", "async_tokio_rt_multi_thread", "cached_proc_macro", "cached_proc_macro_types", "default", "directories", "disk_store", "futures", "proc_macro", "r2d2", "redis", "redis_ahash", "redis_async_std", "redis_connection_manager", "redis_store", "redis_tokio", "rmp-serde", "serde", "serde_json", "sled", "tokio", "wasm"))' -C metadata=9329b40faa42eb71 -C extra-filename=-9329b40faa42eb71 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --extern ahash=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libahash-945e758b82a99d43.rmeta --extern cached_proc_macro=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps/libcached_proc_macro-00b596f139fdc3f3.so --extern cached_proc_macro_types=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libcached_proc_macro_types-f15d37d66dc671cb.rmeta --extern hashbrown=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libhashbrown-d6f1826ec4ce9075.rmeta --extern once_cell=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libonce_cell-14d214d3f0f6a9a9.rmeta --extern thiserror=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libthiserror-ad9d46709d4ae9ce.rmeta --extern web_time=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libweb_time-5e8cf884c468639c.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling env_logger v0.11.5 + Running rustc --crate-name env_logger --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/env_logger-0.11.5/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no '--warn=clippy::zero_sized_map_values' '--warn=clippy::wildcard_imports' '--warn=clippy::verbose_file_reads' --warn=unused_qualifications --warn=unused_macro_rules --warn=unused_lifetimes --warn=unsafe_op_in_unsafe_fn --warn=unreachable_pub '--warn=clippy::trait_duplication_in_bounds' '--warn=clippy::todo' '--warn=clippy::string_to_string' '--warn=clippy::string_lit_as_bytes' '--warn=clippy::string_add_assign' '--warn=clippy::string_add' '--warn=clippy::str_to_string' '--warn=clippy::single_match_else' '--warn=clippy::semicolon_if_nothing_returned' '--warn=clippy::self_named_module_files' '--warn=clippy::same_functions_in_if_condition' --warn=rust_2018_idioms '--warn=clippy::rest_pat_in_fully_bound_structs' '--warn=clippy::ref_option_ref' '--warn=clippy::redundant_feature_names' '--warn=clippy::rc_mutex' '--warn=clippy::ptr_as_ptr' '--warn=clippy::path_buf_push_overwrite' '--warn=clippy::negative_feature_names' '--warn=clippy::needless_for_each' '--warn=clippy::needless_continue' '--warn=clippy::mutex_integer' '--warn=clippy::mem_forget' '--warn=clippy::match_wildcard_for_single_variants' '--warn=clippy::macro_use_imports' '--warn=clippy::lossy_float_literal' '--warn=clippy::linkedlist' '--allow=clippy::let_and_return' '--warn=clippy::large_types_passed_by_value' '--warn=clippy::large_stack_arrays' '--warn=clippy::large_digit_groups' '--warn=clippy::invalid_upcast_comparisons' '--warn=clippy::infinite_loop' '--warn=clippy::inefficient_to_string' '--warn=clippy::inconsistent_struct_constructor' '--warn=clippy::imprecise_flops' '--warn=clippy::implicit_clone' '--allow=clippy::if_same_then_else' '--warn=clippy::from_iter_instead_of_collect' '--warn=clippy::fn_params_excessive_bools' '--warn=clippy::float_cmp_const' '--warn=clippy::flat_map_option' '--warn=clippy::filter_map_next' '--warn=clippy::fallible_impl_from' '--warn=clippy::explicit_into_iter_loop' '--warn=clippy::explicit_deref_methods' '--warn=clippy::expl_impl_clone_on_copy' '--warn=clippy::enum_glob_use' '--warn=clippy::empty_enum' '--warn=clippy::doc_markdown' '--warn=clippy::debug_assert_with_mut_call' '--warn=clippy::dbg_macro' '--warn=clippy::create_dir' '--allow=clippy::collapsible_else_if' '--warn=clippy::checked_conversions' '--allow=clippy::branches_sharing_code' '--allow=clippy::bool_assert_comparison' --cfg 'feature="auto-color"' --cfg 'feature="color"' --cfg 'feature="default"' --cfg 'feature="humantime"' --cfg 'feature="regex"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("auto-color", "color", "default", "humantime", "regex", "unstable-kv"))' -C metadata=348f8d1876b7c1b2 -C extra-filename=-348f8d1876b7c1b2 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --extern anstream=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libanstream-d6af3b43a6258433.rmeta --extern anstyle=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libanstyle-3c6bf311dc731e52.rmeta --extern env_filter=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libenv_filter-39c727e1eb9e57e9.rmeta --extern humantime=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libhumantime-09369e586139ed56.rmeta --extern log=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/liblog-22c5f274688aa5f4.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling tracing-subscriber v0.3.19 + Running rustc --crate-name tracing_subscriber --edition=2018 /opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/tracing-subscriber-0.3.19/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --warn=unexpected_cfgs --check-cfg 'cfg(flaky_tests)' --check-cfg 'cfg(tracing_unstable)' --cfg 'feature="alloc"' --cfg 'feature="ansi"' --cfg 'feature="default"' --cfg 'feature="fmt"' --cfg 'feature="nu-ansi-term"' --cfg 'feature="registry"' --cfg 'feature="sharded-slab"' --cfg 'feature="smallvec"' --cfg 'feature="std"' --cfg 'feature="thread_local"' --cfg 'feature="tracing-log"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "ansi", "chrono", "default", "env-filter", "fmt", "json", "local-time", "matchers", "nu-ansi-term", "once_cell", "parking_lot", "regex", "registry", "serde", "serde_json", "sharded-slab", "smallvec", "std", "thread_local", "time", "tracing", "tracing-log", "tracing-serde", "valuable", "valuable-serde", "valuable_crate"))' -C metadata=5b20c75171dc5d12 -C extra-filename=-5b20c75171dc5d12 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps --target x86_64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/bin/x86_64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/deps --extern nu_ansi_term=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libnu_ansi_term-d4a01ad48e7b248c.rmeta --extern sharded_slab=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libsharded_slab-66787fc62a5161d1.rmeta --extern smallvec=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libsmallvec-6633be87dc610e5a.rmeta --extern thread_local=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libthread_local-562ba3de0c899e1d.rmeta --extern tracing_core=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libtracing_core-3077905bdfbf0aed.rmeta --extern tracing_log=/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/x86_64-unknown-linux-gnu/release/deps/libtracing_log-5b5536484d0d4762.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734125361611/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Running /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/build/annonars-7b04b8937e8c01fe/build-script-build + error: failed to run custom build command for annonars v0.40.0 + + Caused by: + process didn't exit successfully: /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target/release/build/annonars-7b04b8937e8c01fe/build-script-build (exit status: 1) + --- stdout + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/class_by_freq.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/clinvar_public.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/extracted_vars.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/gene_impact.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/phenotype_link.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar/minimal.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar/per_gene.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar/sv.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/cons/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/dbsnp/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/functional/refseq.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/genes/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/exac_cnv.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad2.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad3.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad_cnv4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad_sv2.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad_sv4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/mtdna.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/vep_common.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/vep_gnomad2.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/vep_gnomad3.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/vep_gnomad4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/helixmtdb/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734125361611/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/regions/clingen.proto + + --- stderr + Error: Could not find protoc. If protoc is installed, try setting the PROTOC environment variable to the path of the protoc binary. To install it on Debian, run apt-get install protobuf-compiler. It is also available at https://github.com/protocolbuffers/protobuf/releases For more information: https://docs.rs/prost-build/#sourcing-protoc + warning: build failed, waiting for other jobs to finish... + error: failed to compile varfish-server-worker v0.13.0 (/opt/conda/conda-bld/varfish-server-worker_1734125361611/work), intermediate artifacts can be found at /opt/conda/conda-bld/varfish-server-worker_1734125361611/work/target. + To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/varfish-server-worker_1734125361611/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. diff --git a/recipes/varfish-server-worker/build_failure.linux-aarch64.yaml b/recipes/varfish-server-worker/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..7f7a365186d32 --- /dev/null +++ b/recipes/varfish-server-worker/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: fb32764e52097b62723f0f36945f29853bd98236d3a8875014414d36b780fa90 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + Compiling cached_proc_macro_types v0.1.1 + Running rustc --crate-name cached_proc_macro_types --edition=2018 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/cached_proc_macro_types-0.1.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=dddfa4df852b11da -C extra-filename=-dddfa4df852b11da --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Running rustc --crate-name urlencoding --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/urlencoding-2.1.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C embed-bitcode=no -C debug-assertions=off --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=8d90e9c616cc71d3 -C extra-filename=-8d90e9c616cc71d3 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --cap-lints allow + Running rustc --crate-name minimal_lexical --edition=2018 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/minimal-lexical-0.2.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "compact", "default", "lint", "nightly", "std"))' -C metadata=3c0cd5399d09f6b0 -C extra-filename=-3c0cd5399d09f6b0 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling rustc-hash v2.1.0 + Running rustc --crate-name rustc_hash --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/rustc-hash-2.1.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "nightly", "rand", "std"))' -C metadata=4d2f5041a39f116f -C extra-filename=-4d2f5041a39f116f --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling impl-more v0.1.8 + Running rustc --crate-name impl_more --edition=2018 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/impl-more-0.1.8/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --warn=missing_docs --deny=rust_2018_idioms --deny=nonstandard-style --deny=future_incompatible --forbid=unsafe_code --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=70350bcee1568121 -C extra-filename=-70350bcee1568121 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling rustc-demangle v0.1.24 + Running rustc --crate-name rustc_demangle --edition=2015 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/rustc-demangle-0.1.24/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("compiler_builtins", "core", "rustc-dep-of-std", "std"))' -C metadata=3be13422140c9c47 -C extra-filename=-3be13422140c9c47 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling number_prefix v0.4.0 + Running rustc --crate-name number_prefix --edition=2015 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/number_prefix-0.4.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "std"))' -C metadata=fbce956ab9832b91 -C extra-filename=-fbce956ab9832b91 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling option-ext v0.2.0 + Running rustc --crate-name option_ext --edition=2015 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/option-ext-0.2.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=ae19d540ece13ea5 -C extra-filename=-ae19d540ece13ea5 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling dirs-sys v0.4.1 + Running rustc --crate-name dirs_sys --edition=2015 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/dirs-sys-0.4.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=f0859eb73f95fe89 -C extra-filename=-f0859eb73f95fe89 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --extern libc=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/liblibc-2a24f77235633cff.rmeta --extern option_ext=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/liboption_ext-ae19d540ece13ea5.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling indicatif v0.17.9 + Running rustc --crate-name indicatif --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/indicatif-0.17.9/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="rayon"' --cfg 'feature="unicode-width"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "futures", "improved_unicode", "in_memory", "rayon", "tokio", "unicode-segmentation", "unicode-width", "vt100"))' -C metadata=0559d6f0b2b1074d -C extra-filename=-0559d6f0b2b1074d --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --extern console=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libconsole-8ef364442257e21c.rmeta --extern number_prefix=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libnumber_prefix-fbce956ab9832b91.rmeta --extern portable_atomic=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libportable_atomic-254892da6b69e040.rmeta --extern rayon=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/librayon-3b4afb0543006396.rmeta --extern unicode_width=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libunicode_width-351adfbce60e77c5.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Running rustc --crate-name nom --edition=2018 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/nom-7.1.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="alloc"' --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "default", "docsrs", "std"))' -C metadata=839bb4e849218885 -C extra-filename=-839bb4e849218885 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --extern memchr=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libmemchr-a83414d2b225da05.rmeta --extern minimal_lexical=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libminimal_lexical-3c0cd5399d09f6b0.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling backtrace v0.3.74 + Running rustc --crate-name backtrace --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/backtrace-0.3.74/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --allow=unexpected_cfgs --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("coresymbolication", "cpp_demangle", "dbghelp", "default", "dl_iterate_phdr", "dladdr", "kernel32", "libunwind", "serde", "serialize-serde", "std", "unix-backtrace"))' -C metadata=7eb81647a2221da0 -C extra-filename=-7eb81647a2221da0 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --extern addr2line=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libaddr2line-4a2c198e5d9e681a.rmeta --extern cfg_if=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libcfg_if-986e17e20ae237e0.rmeta --extern libc=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/liblibc-2a24f77235633cff.rmeta --extern miniz_oxide=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libminiz_oxide-946b1b3df8e023d5.rmeta --extern object=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libobject-3a03f4ac841fc0d8.rmeta --extern rustc_demangle=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/librustc_demangle-3be13422140c9c47.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling actix-web v4.9.0 + Running rustc --crate-name actix_web --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/actix-web-4.9.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --deny=rust_2018_idioms --deny=nonstandard_style --deny=future_incompatible --cfg 'feature="__compress"' --cfg 'feature="compat"' --cfg 'feature="compat-routing-macros-force-pub"' --cfg 'feature="compress-brotli"' --cfg 'feature="compress-gzip"' --cfg 'feature="compress-zstd"' --cfg 'feature="cookies"' --cfg 'feature="default"' --cfg 'feature="http2"' --cfg 'feature="macros"' --cfg 'feature="unicode"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("__compress", "__tls", "actix-tls", "compat", "compat-routing-macros-force-pub", "compress-brotli", "compress-gzip", "compress-zstd", "cookies", "default", "experimental-io-uring", "http2", "macros", "openssl", "rustls", "rustls-0_20", "rustls-0_21", "rustls-0_22", "rustls-0_23", "secure-cookies", "unicode"))' -C metadata=39434269e348f937 -C extra-filename=-39434269e348f937 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --extern actix_codec=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libactix_codec-eff912c4c47333cc.rmeta --extern actix_http=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libactix_http-b6e624a8b6cfb463.rmeta --extern actix_macros=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps/libactix_macros-7079fcecb2d8d11b.so --extern actix_router=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libactix_router-92b67ed6ec586605.rmeta --extern actix_rt=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libactix_rt-631a39149bd61943.rmeta --extern actix_server=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libactix_server-ff59e967eddc3d2e.rmeta --extern actix_service=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libactix_service-f0129079f0ceb915.rmeta --extern actix_utils=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libactix_utils-be09f7c3165f426d.rmeta --extern actix_web_codegen=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps/libactix_web_codegen-3a3d90d2d79ca052.so --extern ahash=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libahash-c67be8aae5d28708.rmeta --extern bytes=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libbytes-a64b2f4eb8883c85.rmeta --extern bytestring=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libbytestring-308943d7d9dbf679.rmeta --extern cfg_if=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libcfg_if-986e17e20ae237e0.rmeta --extern cookie=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libcookie-6d819976896ff112.rmeta --extern derive_more=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps/libderive_more-e549714e340da729.so --extern encoding_rs=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libencoding_rs-03c4df22df2f39bd.rmeta --extern futures_core=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libfutures_core-35fb8fb190be09eb.rmeta --extern futures_util=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libfutures_util-d828d688d194ca82.rmeta --extern impl_more=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libimpl_more-70350bcee1568121.rmeta --extern itoa=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libitoa-314b234d6fede382.rmeta --extern language_tags=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/liblanguage_tags-afdb9a7de534831b.rmeta --extern log=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/liblog-53bb487e5c58e460.rmeta --extern mime=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libmime-dd2a5e7879e8966f.rmeta --extern once_cell=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libonce_cell-2dde76b2e89f1c14.rmeta --extern pin_project_lite=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libpin_project_lite-4b27d065cc848bf8.rmeta --extern regex=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libregex-c7c83881d15aa531.rmeta --extern regex_lite=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libregex_lite-4a676ebd889848bc.rmeta --extern serde=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libserde-0299858dcdb32ecc.rmeta --extern serde_json=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libserde_json-4e7929e6007d452c.rmeta --extern serde_urlencoded=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libserde_urlencoded-77ee262dd8863d94.rmeta --extern smallvec=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libsmallvec-10e76c4da428a6a7.rmeta --extern socket2=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libsocket2-7c0fc4a4424d031c.rmeta --extern time=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libtime-e8e3c4374f171ba7.rmeta --extern url=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/liburl-8af5f061a98c22e1.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -L native=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/build/zstd-sys-cc5ce4b4bfb4b187/out + Running rustc --crate-name rust_decimal --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/rust_decimal-1.36.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("borsh", "c-repr", "db-diesel-mysql", "db-diesel-postgres", "db-diesel2-mysql", "db-diesel2-postgres", "db-postgres", "db-tokio-postgres", "default", "diesel", "legacy-ops", "maths", "maths-nopanic", "ndarray", "proptest", "rand", "rkyv", "rkyv-safe", "rocket-traits", "rust-fuzz", "serde", "serde-arbitrary-precision", "serde-bincode", "serde-float", "serde-str", "serde-with-arbitrary-precision", "serde-with-float", "serde-with-str", "serde_json", "std", "tokio-pg", "tokio-postgres"))' -C metadata=80aa6af21271c5f3 -C extra-filename=-80aa6af21271c5f3 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --extern arrayvec=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libarrayvec-4b64f37000c5a530.rmeta --extern num_traits=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libnum_traits-97a05ca6f5fd89f5.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling nutype_macros v0.4.3 + Running rustc --crate-name nutype_macros --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/nutype_macros-0.4.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type proc-macro --emit=dep-info,link -C prefer-dynamic -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="serde"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("arbitrary", "new_unchecked", "regex", "schemars08", "serde", "std"))' -C metadata=8d35f3b942e00c99 -C extra-filename=-8d35f3b942e00c99 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --extern cfg_if=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps/libcfg_if-f219c80e14ea1fcf.rlib --extern kinded=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps/libkinded-889e479530584bc0.rlib --extern proc_macro2=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps/libproc_macro2-046790e841f2f24c.rlib --extern quote=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps/libquote-e0e603d463a4e85d.rlib --extern syn=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps/libsyn-7c54b5261e2e1147.rlib --extern urlencoding=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps/liburlencoding-8d90e9c616cc71d3.rlib --extern proc_macro --cap-lints allow + Compiling cached v0.54.0 + Running rustc --crate-name cached --edition=2018 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/cached-0.54.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="ahash"' --cfg 'feature="cached_proc_macro"' --cfg 'feature="cached_proc_macro_types"' --cfg 'feature="default"' --cfg 'feature="proc_macro"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("ahash", "async", "async-trait", "async_tokio_rt_multi_thread", "cached_proc_macro", "cached_proc_macro_types", "default", "directories", "disk_store", "futures", "proc_macro", "r2d2", "redis", "redis_ahash", "redis_async_std", "redis_connection_manager", "redis_store", "redis_tokio", "rmp-serde", "serde", "serde_json", "sled", "tokio", "wasm"))' -C metadata=3dace2be72882d5e -C extra-filename=-3dace2be72882d5e --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --extern ahash=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libahash-c67be8aae5d28708.rmeta --extern cached_proc_macro=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps/libcached_proc_macro-60228eeafa2ae5fa.so --extern cached_proc_macro_types=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libcached_proc_macro_types-dddfa4df852b11da.rmeta --extern hashbrown=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libhashbrown-ab6324b2f43027d9.rmeta --extern once_cell=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libonce_cell-2dde76b2e89f1c14.rmeta --extern thiserror=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libthiserror-44843e01280f39e3.rmeta --extern web_time=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libweb_time-ef3ddc3113160f04.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Running /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/build/procfs-19d51930f89d46f0/build-script-build + Compiling env_logger v0.11.5 + Running rustc --crate-name env_logger --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/env_logger-0.11.5/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no '--warn=clippy::zero_sized_map_values' '--warn=clippy::wildcard_imports' '--warn=clippy::verbose_file_reads' --warn=unused_qualifications --warn=unused_macro_rules --warn=unused_lifetimes --warn=unsafe_op_in_unsafe_fn --warn=unreachable_pub '--warn=clippy::trait_duplication_in_bounds' '--warn=clippy::todo' '--warn=clippy::string_to_string' '--warn=clippy::string_lit_as_bytes' '--warn=clippy::string_add_assign' '--warn=clippy::string_add' '--warn=clippy::str_to_string' '--warn=clippy::single_match_else' '--warn=clippy::semicolon_if_nothing_returned' '--warn=clippy::self_named_module_files' '--warn=clippy::same_functions_in_if_condition' --warn=rust_2018_idioms '--warn=clippy::rest_pat_in_fully_bound_structs' '--warn=clippy::ref_option_ref' '--warn=clippy::redundant_feature_names' '--warn=clippy::rc_mutex' '--warn=clippy::ptr_as_ptr' '--warn=clippy::path_buf_push_overwrite' '--warn=clippy::negative_feature_names' '--warn=clippy::needless_for_each' '--warn=clippy::needless_continue' '--warn=clippy::mutex_integer' '--warn=clippy::mem_forget' '--warn=clippy::match_wildcard_for_single_variants' '--warn=clippy::macro_use_imports' '--warn=clippy::lossy_float_literal' '--warn=clippy::linkedlist' '--allow=clippy::let_and_return' '--warn=clippy::large_types_passed_by_value' '--warn=clippy::large_stack_arrays' '--warn=clippy::large_digit_groups' '--warn=clippy::invalid_upcast_comparisons' '--warn=clippy::infinite_loop' '--warn=clippy::inefficient_to_string' '--warn=clippy::inconsistent_struct_constructor' '--warn=clippy::imprecise_flops' '--warn=clippy::implicit_clone' '--allow=clippy::if_same_then_else' '--warn=clippy::from_iter_instead_of_collect' '--warn=clippy::fn_params_excessive_bools' '--warn=clippy::float_cmp_const' '--warn=clippy::flat_map_option' '--warn=clippy::filter_map_next' '--warn=clippy::fallible_impl_from' '--warn=clippy::explicit_into_iter_loop' '--warn=clippy::explicit_deref_methods' '--warn=clippy::expl_impl_clone_on_copy' '--warn=clippy::enum_glob_use' '--warn=clippy::empty_enum' '--warn=clippy::doc_markdown' '--warn=clippy::debug_assert_with_mut_call' '--warn=clippy::dbg_macro' '--warn=clippy::create_dir' '--allow=clippy::collapsible_else_if' '--warn=clippy::checked_conversions' '--allow=clippy::branches_sharing_code' '--allow=clippy::bool_assert_comparison' --cfg 'feature="auto-color"' --cfg 'feature="color"' --cfg 'feature="default"' --cfg 'feature="humantime"' --cfg 'feature="regex"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("auto-color", "color", "default", "humantime", "regex", "unstable-kv"))' -C metadata=13dc49d2c79ec331 -C extra-filename=-13dc49d2c79ec331 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --extern anstream=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libanstream-91c5757d0034c133.rmeta --extern anstyle=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libanstyle-d6accd4b074e0980.rmeta --extern env_filter=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libenv_filter-0ccd5f184616fe72.rmeta --extern humantime=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libhumantime-414cf61819ba5aee.rmeta --extern log=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/liblog-53bb487e5c58e460.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Running rustc --crate-name thiserror --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/thiserror-2.0.6/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "std"))' -C metadata=f0908152080e3144 -C extra-filename=-f0908152080e3144 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --extern thiserror_impl=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps/libthiserror_impl-6ef9a680803f03b1.so --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib --check-cfg 'cfg(error_generic_member_access)' --check-cfg 'cfg(thiserror_nightly_testing)' --check-cfg 'cfg(thiserror_no_backtrace_type)' + Compiling aws-smithy-query v0.60.7 + Running rustc --crate-name aws_smithy_query --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/aws-smithy-query-0.60.7/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=5310ba2a01b622b1 -C extra-filename=-5310ba2a01b622b1 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --extern aws_smithy_types=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libaws_smithy_types-e96a61e6877e2f05.rmeta --extern urlencoding=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/liburlencoding-b32cd9b609dcfbaf.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling tracing-subscriber v0.3.19 + Running rustc --crate-name tracing_subscriber --edition=2018 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/tracing-subscriber-0.3.19/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --warn=unexpected_cfgs --check-cfg 'cfg(flaky_tests)' --check-cfg 'cfg(tracing_unstable)' --cfg 'feature="alloc"' --cfg 'feature="ansi"' --cfg 'feature="default"' --cfg 'feature="fmt"' --cfg 'feature="nu-ansi-term"' --cfg 'feature="registry"' --cfg 'feature="sharded-slab"' --cfg 'feature="smallvec"' --cfg 'feature="std"' --cfg 'feature="thread_local"' --cfg 'feature="tracing-log"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "ansi", "chrono", "default", "env-filter", "fmt", "json", "local-time", "matchers", "nu-ansi-term", "once_cell", "parking_lot", "regex", "registry", "serde", "serde_json", "sharded-slab", "smallvec", "std", "thread_local", "time", "tracing", "tracing-log", "tracing-serde", "valuable", "valuable-serde", "valuable_crate"))' -C metadata=fced7c7ec6f4f787 -C extra-filename=-fced7c7ec6f4f787 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --extern nu_ansi_term=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libnu_ansi_term-f49656fa7f230019.rmeta --extern sharded_slab=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libsharded_slab-d810b7c320f4d25d.rmeta --extern smallvec=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libsmallvec-10e76c4da428a6a7.rmeta --extern thread_local=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libthread_local-909261e8f28f24ea.rmeta --extern tracing_core=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libtracing_core-1e8205cce6148317.rmeta --extern tracing_log=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libtracing_log-7edc3f9cf6cfecec.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Running rustc --crate-name pbjson_types --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/pbjson-types-0.7.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=43e3f71e21f41816 -C extra-filename=-43e3f71e21f41816 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --extern bytes=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libbytes-a64b2f4eb8883c85.rmeta --extern chrono=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libchrono-f62e18a27b5b534e.rmeta --extern pbjson=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libpbjson-f7dea76f1ac7d4f4.rmeta --extern prost=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libprost-b4be563f15b904a8.rmeta --extern serde=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libserde-0299858dcdb32ecc.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Compiling noodles v0.77.0 + Running rustc --crate-name noodles --edition=2021 /opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-0.77.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="async"' --cfg 'feature="bcf"' --cfg 'feature="bed"' --cfg 'feature="bgzf"' --cfg 'feature="core"' --cfg 'feature="csi"' --cfg 'feature="default"' --cfg 'feature="fasta"' --cfg 'feature="gff"' --cfg 'feature="tabix"' --cfg 'feature="vcf"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("async", "bam", "bcf", "bed", "bgzf", "core", "cram", "csi", "default", "fasta", "fastq", "gff", "gtf", "htsget", "refget", "sam", "tabix", "vcf"))' -C metadata=49d34305ad646234 -C extra-filename=-49d34305ad646234 --out-dir /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/deps --extern noodles_bcf=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libnoodles_bcf-93484ae851c94d9b.rmeta --extern noodles_bed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libnoodles_bed-86411346d504e7cf.rmeta --extern noodles_bgzf=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libnoodles_bgzf-6aa00e93a37fed71.rmeta --extern noodles_core=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libnoodles_core-e645eca308bd6031.rmeta --extern noodles_csi=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libnoodles_csi-9f5932bf64c8cb33.rmeta --extern noodles_fasta=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libnoodles_fasta-02ea14c6d9570734.rmeta --extern noodles_gff=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libnoodles_gff-2c8013281ab730b0.rmeta --extern noodles_tabix=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libnoodles_tabix-c4b66d1c709049ab.rmeta --extern noodles_vcf=/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/aarch64-unknown-linux-gnu/release/deps/libnoodles_vcf-1880acb647ee3eff.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/varfish-server-worker_1734016617113/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib + Running /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/build/annonars-0406b57362b0299a/build-script-build + error: failed to run custom build command for annonars v0.40.0 + + Caused by: + process didn't exit successfully: /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target/release/build/annonars-0406b57362b0299a/build-script-build (exit status: 1) + --- stdout + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/class_by_freq.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/clinvar_public.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/extracted_vars.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/gene_impact.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar_data/phenotype_link.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar/minimal.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar/per_gene.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/clinvar/sv.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/cons/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/dbsnp/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/functional/refseq.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/genes/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/exac_cnv.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad2.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad3.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad_cnv4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad_sv2.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/gnomad_sv4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/mtdna.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/vep_common.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/vep_gnomad2.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/vep_gnomad3.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/gnomad/vep_gnomad4.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/helixmtdb/base.proto + cargo:rerun-if-changed=/opt/conda/conda-bld/varfish-server-worker_1734016617113/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/annonars-0.40.0/protos/annonars/regions/clingen.proto + + --- stderr + Error: Could not find protoc. If protoc is installed, try setting the PROTOC environment variable to the path of the protoc binary. To install it on Debian, run apt-get install protobuf-compiler. It is also available at https://github.com/protocolbuffers/protobuf/releases For more information: https://docs.rs/prost-build/#sourcing-protoc + warning: build failed, waiting for other jobs to finish... + error: failed to compile varfish-server-worker v0.13.0 (/opt/conda/conda-bld/varfish-server-worker_1734016617113/work), intermediate artifacts can be found at /opt/conda/conda-bld/varfish-server-worker_1734016617113/work/target. + To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/varfish-server-worker_1734016617113/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. diff --git a/recipes/varfish-server-worker/meta.yaml b/recipes/varfish-server-worker/meta.yaml index e7c4ceb6229c5..55d2aca67e184 100644 --- a/recipes/varfish-server-worker/meta.yaml +++ b/recipes/varfish-server-worker/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 skip: True # [osx] run_exports: - {{ pin_subpackage("varfish-server-worker", max_pin="x.x") }} diff --git a/recipes/vargeno/meta.yaml b/recipes/vargeno/meta.yaml index f86b7b97756c8..c12cc2d6cc197 100644 --- a/recipes/vargeno/meta.yaml +++ b/recipes/vargeno/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 525af31c7f70423f669d703928325510669282ad2acbce6f2613ee20a04bc98e build: - number: 5 + number: 6 requirements: build: diff --git a/recipes/variantbam/build_failure.linux-64.yaml b/recipes/variantbam/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..6eefc92f2103a --- /dev/null +++ b/recipes/variantbam/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: ad5a5a602481e30f3309017a12cf9b1023354785e0563f1af3054dbdf93afa7f # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + 102 | Histogram(const int32_t& start, const int32_t& end, const uint32_t& width); + | ^~~~~~~~~ + Histogram.h:98:3: note: 'Histogram::Histogram()' + 98 | Histogram() {} + | ^~~~~~~~~ + Histogram.h:87:7: note: 'class Histogram' defined here + 87 | class Histogram { + | ^~~~~~~~~ + Histogram.cpp:115:59: error: 'S' was not declared in this scope + 115 | void Histogram::initialSpans(size_t num_bins, std::vector* pspanv, size_t min_bin_width) { + | ^ + Histogram.cpp:115:60: error: template argument 1 is invalid + 115 | void Histogram::initialSpans(size_t num_bins, std::vector* pspanv, size_t min_bin_width) { + | ^ + Histogram.cpp:115:60: error: template argument 2 is invalid + Histogram.cpp: In member function 'void Histogram::initialSpans(size_t, int*, size_t)': + Histogram.cpp:118:21: error: request for member 'begin' in '* pspanv', which is of non-class type 'int' + 118 | std::sort(pspanv->begin(), pspanv->end()); + | ^~~~~ + Histogram.cpp:118:38: error: request for member 'end' in '* pspanv', which is of non-class type 'int' + 118 | std::sort(pspanv->begin(), pspanv->end()); + | ^~~ + Histogram.cpp:125:19: error: 'begin' was not declared in this scope; did you mean 'std::begin'? + 125 | for (auto& i : *pspanv) + | ^~~~~~ + | std::begin + In file included from /opt/conda/conda-bld/variantbam_1734138412892/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/string:53, + from /opt/conda/conda-bld/variantbam_1734138412892/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/locale_classes.h:40, + from /opt/conda/conda-bld/variantbam_1734138412892/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/ios_base.h:41, + from /opt/conda/conda-bld/variantbam_1734138412892/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/ios:44, + from /opt/conda/conda-bld/variantbam_1734138412892/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/ostream:40, + from /opt/conda/conda-bld/variantbam_1734138412892/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/iostream:41, + from Histogram.h:4: + /opt/conda/conda-bld/variantbam_1734138412892/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/range_access.h:95:5: note: 'std::begin' declared here + 95 | begin(_Tp (&__arr)[_Nm]) noexcept + | ^~~~~ + Histogram.cpp:125:19: error: 'end' was not declared in this scope; did you mean 'std::end'? + 125 | for (auto& i : *pspanv) + | ^~~~~~ + | std::end + /opt/conda/conda-bld/variantbam_1734138412892/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/range_access.h:106:5: note: 'std::end' declared here + 106 | end(_Tp (&__arr)[_Nm]) noexcept + | ^~~ + Histogram.cpp:136:40: error: request for member 'size' in '* pspanv', which is of non-class type 'int' + 136 | std::cerr << "Events: " << pspanv->size() << " Num Bins " << num_bins << " quantile count (hist height) " << bin_cut << std::endl; + | ^~~~ + Histogram.cpp:141:3: error: 'S' was not declared in this scope + 141 | S last_span = 0; + | ^ + Histogram.cpp:145:22: error: 'begin' was not declared in this scope; did you mean 'std::begin'? + 145 | for (auto& span : *pspanv) { + | ^~~~~~ + | std::begin + /opt/conda/conda-bld/variantbam_1734138412892/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/range_access.h:95:5: note: 'std::begin' declared here + 95 | begin(_Tp (&__arr)[_Nm]) noexcept + | ^~~~~ + Histogram.cpp:145:22: error: 'end' was not declared in this scope; did you mean 'std::end'? + 145 | for (auto& span : *pspanv) { + | ^~~~~~ + | std::end + /opt/conda/conda-bld/variantbam_1734138412892/_build_env/lib/gcc/x86_64-conda-linux-gnu/13.3.0/include/c/bits/range_access.h:106:5: note: 'std::end' declared here + 106 | end(_Tp (&__arr)[_Nm]) noexcept + | ^~~ + Histogram.cpp:151:47: error: 'last_span' was not declared in this scope + 151 | if (bin.getCount() > bin_cut && span != last_span && (last_span - bin.bounds.first) >= min_bin_width) { + | ^~~~~~~~~ + Histogram.cpp:164:9: error: 'last_span' was not declared in this scope + 164 | last_span = span; + | ^~~~~~~~~ + Histogram.cpp:177:25: error: request for member 'size' in '* pspanv', which is of non-class type 'int' + 177 | bin.m_count = pspanv->size() - intra; + | ^~~~ + make[2]: *** [Makefile:437: variant-Histogram.o] Error 1 + make[2]: Leaving directory '$SRC_DIR/src' + make[1]: *** [Makefile:358: all-recursive] Error 1 + make[1]: Leaving directory '$SRC_DIR' + make: *** [Makefile:299: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/variantbam_1734138412892/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/variantbam_1734138412892/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/variantbam/meta.yaml b/recipes/variantbam/meta.yaml index e264d5b78604f..830f8bcfae17c 100644 --- a/recipes/variantbam/meta.yaml +++ b/recipes/variantbam/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 8 + number: 9 skip: True # [osx] source: diff --git a/recipes/vartrix/meta.yaml b/recipes/vartrix/meta.yaml index dc51ecd4f4926..f1f6eafede0e5 100644 --- a/recipes/vartrix/meta.yaml +++ b/recipes/vartrix/meta.yaml @@ -14,7 +14,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 binary_has_prefix_files: - vartrix run_exports: diff --git a/recipes/vcf-validator/meta.yaml b/recipes/vcf-validator/meta.yaml index 66ac7e00d8d62..25a84034a3444 100644 --- a/recipes/vcf-validator/meta.yaml +++ b/recipes/vcf-validator/meta.yaml @@ -10,7 +10,7 @@ source: sha256: b46117700445644e6fc5a6d2655b477902c67aba0e7abe8a62df6cb49f923fff build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage("vcf-validator", max_pin="x.x") }} @@ -51,4 +51,4 @@ extra: recipe-maintainers: - apriltuesday - tcezard - - ebi-variation \ No newline at end of file + - ebi-variation diff --git a/recipes/vcf2parquet/meta.yaml b/recipes/vcf2parquet/meta.yaml index ad6addc3938bc..6d9b199ef8f7e 100644 --- a/recipes/vcf2parquet/meta.yaml +++ b/recipes/vcf2parquet/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('vcf2parquet', max_pin="x.x") }} diff --git a/recipes/vcfbub/meta.yaml b/recipes/vcfbub/meta.yaml index 4cdeb5b6cc0ea..ca73439d7018e 100644 --- a/recipes/vcfbub/meta.yaml +++ b/recipes/vcfbub/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 7a952b52a98a7f3508c77a8851501b5185c9bff6cd456587ed5a5eba23f83099 build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} diff --git a/recipes/vcfdist/build_failure.linux-64.yaml b/recipes/vcfdist/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..8f9831da4fb9a --- /dev/null +++ b/recipes/vcfdist/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 226330896e7042f3ec655419703d18c447cc1020f46da748dd667b6547721864 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/vcfdist-2.5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/vcfdist-2.5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -std=c17 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include globals.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/vcfdist-2.5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -std=c17 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include print.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/vcfdist-2.5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -std=c17 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include variant.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/vcfdist-2.5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -std=c17 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include dist.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/vcfdist-2.5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -std=c17 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include bed.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/vcfdist-2.5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -std=c17 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include cluster.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/vcfdist-2.5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -std=c17 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include phase.cpp + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/vcfdist-2.5.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -std=c17 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include edit.cpp + In file included from edit.cpp:1: + edit.h:19:54: error: 'uint8_t' has not been declared + 19 | void add_edits(const std::string & ctg, int pos, uint8_t hap, + | ^~~~~~~ + edit.h:21:53: error: 'uint8_t' has not been declared + 21 | void add_edit(const std::string & ctg, int pos, uint8_t hap, + | ^~~~~~~ + edit.h:22:13: error: 'uint8_t' has not been declared + 22 | uint8_t type, int len, int sc, int min_qual, int max_qual); + | ^~~~~~~ + edit.h:34:17: error: 'uint8_t' was not declared in this scope + 34 | std::vector haps; // edit haplotype + | ^~~~~~~ + edit.h:9:1: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + 8 | #include "defs.h" + |#include + 9 | + edit.h:34:24: error: template argument 1 is invalid + 34 | std::vector haps; // edit haplotype + | ^ + edit.h:34:24: error: template argument 2 is invalid + edit.h:35:17: error: 'uint8_t' was not declared in this scope + 35 | std::vector types; // edit type: SUB, INS, DEL + | ^~~~~~~ + edit.h:35:17: note: 'uint8_t' is defined in header ''; did you forget to '#include '? + edit.h:35:24: error: template argument 1 is invalid + 35 | std::vector types; // edit type: SUB, INS, DEL + | ^ + edit.h:35:24: error: template argument 2 is invalid + edit.cpp:4:6: error: no declaration matches 'void editData::add_edits(const std::string&, int, uint8_t, const std::vector&, int, int, int)' + 4 | void editData::add_edits(const std::string & ctg, int pos, uint8_t hap, + | ^~~~~~~~ + edit.h:19:10: note: candidate is: 'void editData::add_edits(const std::string&, int, int, const std::vector&, int, int, int)' + 19 | void add_edits(const std::string & ctg, int pos, uint8_t hap, + | ^~~~~~~~~ + edit.h:12:7: note: 'class editData' defined here + 12 | class editData { + | ^~~~~~~~ + edit.cpp:79:6: error: no declaration matches 'void editData::add_edit(const std::string&, int, uint8_t, uint8_t, int, int, int, int)' + 79 | void editData::add_edit(const std::string & ctg, int pos, uint8_t hap, + | ^~~~~~~~ + edit.h:21:10: note: candidate is: 'void editData::add_edit(const std::string&, int, int, int, int, int, int, int)' + 21 | void add_edit(const std::string & ctg, int pos, uint8_t hap, + | ^~~~~~~~ + edit.h:12:7: note: 'class editData' defined here + 12 | class editData { + | ^~~~~~~~ + edit.cpp: In member function 'int editData::get_ed(int, int) const': + edit.cpp:110:36: error: invalid types 'const int[int]' for array subscript + 110 | is_type(this->types[i], type)) { + | ^ + edit.cpp: In member function 'int editData::get_de(int, int) const': + edit.cpp:121:36: error: invalid types 'const int[int]' for array subscript + 121 | is_type(this->types[i], type)) { + | ^ + edit.cpp: In member function 'int editData::get_score(int) const': + edit.cpp:132:32: error: invalid types 'const int[int]' for array subscript + 132 | switch (this->types[i]) { + | ^ + edit.cpp: In member function 'void editData::write_edits()': + edit.cpp:275:64: error: invalid types 'int[int]' for array subscript + 275 | this->ctgs[i].data(), this->poss[i], this->haps[i], + | ^ + edit.cpp:276:38: error: invalid types 'int[int]' for array subscript + 276 | type_strs[this->types[i]].data(), this->lens[i], + | ^ + make: *** [Makefile:37: edit.o] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/vcfdist_1734240545792/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/vcfdist_1734240545792/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/vcfdist/meta.yaml b/recipes/vcfdist/meta.yaml index c2947a9c708d7..40c72710fe65c 100644 --- a/recipes/vcfdist/meta.yaml +++ b/recipes/vcfdist/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("vcfdist", max_pin="x.x") }} diff --git a/recipes/vcflib/build_failure.linux-64.yaml b/recipes/vcflib/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..baeadea29eb30 --- /dev/null +++ b/recipes/vcflib/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 039cbc49702ddc83f23305256c8b8c53a7212ce68ecc7fa8163e54a912e152e6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + menu menu - ncurses 6.5 add-on library + mit-krb5-gssapi mit-krb5-gssapi - Kerberos implementation of the GSSAPI + ncurses ncurses - ncurses 6.5 add-on library + libcurl libcurl - Library to transfer files with HTTP, FTP, etc. + libssh2 libssh2 - Library for SSH-based communication + libedit libedit - command line editor library provides generic line editing, history, and tokenization functions. + panelw panelw - ncurses 6.5 add-on library + ncursesw ncursesw - ncurses 6.5 add-on library + libkeyutils libkeyutils - keyutils library + gssrpc gssrpc - GSSAPI RPC implementation + krb5 krb5 - An implementation of Kerberos network authentication + tinfo tinfo - ncurses 6.5 terminal interface library + openssl OpenSSL - Secure Sockets Layer and cryptography libraries and tools + panel panel - ncurses 6.5 add-on library + libdeflate libdeflate - Fast implementation of DEFLATE, zlib, and gzip + libzstd zstd - fast lossless compression algorithm library + libcrypto OpenSSL-libcrypto - OpenSSL cryptography library + kadm-server kadm-server - Kerberos administration server library + mit-krb5 mit-krb5 - An implementation of Kerberos network authentication + libcares c-ares - asynchronous DNS lookup library + kdb kdb - Kerberos database access libraries + htslib htslib - C library for high-throughput sequencing data formats + krb5-gssapi krb5-gssapi - Kerberos implementation of the GSSAPI + tinfow tinfow - ncurses 6.5 terminal interface library + libssl OpenSSL-libssl - Secure Sockets Layer and cryptography libraries + libnghttp2 libnghttp2 - HTTP/2 C library + form form - ncurses 6.5 add-on library + cmake -S . -B build -DZIG=ON -DOPENMP=ON -DWFA_GITMODULE=OFF -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_INSTALL_PREFIX=/opt/conda/conda-bld/vcflib_1734305501767/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh -DCMAKE_CXX_COMPILER=/opt/conda/conda-bld/vcflib_1734305501767/_build_env/bin/x86_64-conda-linux-gnu-c '-DCMAKE_CXX_FLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/conda-bld/vcflib_1734305501767/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include -fdebug-prefix-map=/opt/conda/conda-bld/vcflib_1734305501767/work=/usr/local/src/conda/vcflib-1.0.10 -fdebug-prefix-map=/opt/conda/conda-bld/vcflib_1734305501767/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh=/usr/local/src/conda-prefix -O3 -D_FILE_OFFSET_BITS=64 -I/opt/conda/conda-bld/vcflib_1734305501767/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include' '' + zlib zlib - zlib compression library + menuw menuw - ncurses 6.5 add-on library + kadm-client kadm-client - Kerberos administration client library + formw formw - ncurses 6.5 add-on library + CMake Warning: + Ignoring empty string ("") provided on the command line. + + + -- The C compiler identification is GNU 13.3.0 + -- The CXX compiler identification is GNU 13.3.0 + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - failed + -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CMake Error at /opt/conda/conda-bld/vcflib_1734305501767/_build_env/share/cmake-3.31/Modules/CMakeTestCCompiler.cmake:67 (message): + The C compiler + + "/opt/conda/conda-bld/vcflib_1734305501767/_build_env/bin/x86_64-conda-linux-gnu-cc" + + is not able to compile a simple test program. + + It fails with the following output: + + Change Dir: '/opt/conda/conda-bld/vcflib_1734305501767/work/build/CMakeFiles/CMakeScratch/TryCompile-VhJlJD' + + Run Build Command(s): /opt/conda/conda-bld/vcflib_1734305501767/_build_env/bin/cmake -E env VERBOSE=1 /opt/conda/conda-bld/vcflib_1734305501767/_build_env/bin/make -f Makefile cmTC_215fb/fast + /opt/conda/conda-bld/vcflib_1734305501767/_build_env/bin/make -f CMakeFiles/cmTC_215fb.dir/build.make CMakeFiles/cmTC_215fb.dir/build + make[1]: Entering directory '/opt/conda/conda-bld/vcflib_1734305501767/work/build/CMakeFiles/CMakeScratch/TryCompile-VhJlJD' + Building C object CMakeFiles/cmTC_215fb.dir/testCCompiler.c.o + /opt/conda/conda-bld/vcflib_1734305501767/_build_env/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/conda-bld/vcflib_1734305501767/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include -fdebug-prefix-map=/opt/conda/conda-bld/vcflib_1734305501767/work=/usr/local/src/conda/vcflib-1.0.10 -fdebug-prefix-map=/opt/conda/conda-bld/vcflib_1734305501767/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh=/usr/local/src/conda-prefix -o CMakeFiles/cmTC_215fb.dir/testCCompiler.c.o -c /opt/conda/conda-bld/vcflib_1734305501767/work/build/CMakeFiles/CMakeScratch/TryCompile-VhJlJD/testCCompiler.c + Linking C executable cmTC_215fb + /opt/conda/conda-bld/vcflib_1734305501767/_build_env/bin/cmake -E cmake_link_script CMakeFiles/cmTC_215fb.dir/link.txt --verbose=1 + /opt/conda/conda-bld/vcflib_1734305501767/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -llzma: No such file or directory + collect2: error: ld returned 1 exit status + /opt/conda/conda-bld/vcflib_1734305501767/_build_env/bin/x86_64-conda-linux-gnu-cc -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/conda-bld/vcflib_1734305501767/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include -fdebug-prefix-map=/opt/conda/conda-bld/vcflib_1734305501767/work=/usr/local/src/conda/vcflib-1.0.10 -fdebug-prefix-map=/opt/conda/conda-bld/vcflib_1734305501767/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh=/usr/local/src/conda-prefix -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/vcflib_1734305501767/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -Wl,-rpath-link,/opt/conda/conda-bld/vcflib_1734305501767/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -L/opt/conda/conda-bld/vcflib_1734305501767/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -L/opt/conda/conda-bld/vcflib_1734305501767/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -lhts -ltabixpp -lpthread -lz -lm -llzma -lbz2 -fopenmp -lwfa2 CMakeFiles/cmTC_215fb.dir/testCCompiler.c.o -o cmTC_215fb + make[1]: *** [CMakeFiles/cmTC_215fb.dir/build.make:102: cmTC_215fb] Error 1 + make[1]: Leaving directory '/opt/conda/conda-bld/vcflib_1734305501767/work/build/CMakeFiles/CMakeScratch/TryCompile-VhJlJD' + make: *** [Makefile:133: cmTC_215fb/fast] Error 2 + + + + + + CMake will not be able to correctly generate this project. + Call Stack (most recent call first): + CMakeLists.txt:10 (project) + + -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - broken + + -- Configuring incomplete, errors occurred! + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/vcflib_1734305501767/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/vcflib_1734305501767/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/vcflib/build_failure.linux-aarch64.yaml b/recipes/vcflib/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..ddd2534ae48be --- /dev/null +++ b/recipes/vcflib/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 039cbc49702ddc83f23305256c8b8c53a7212ce68ecc7fa8163e54a912e152e6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + libcurl libcurl - Library to transfer files with HTTP, FTP, etc. + zlib zlib - zlib compression library + libnghttp2 libnghttp2 - HTTP/2 C library + kadm-server kadm-server - Kerberos administration server library + libcrypto OpenSSL-libcrypto - OpenSSL cryptography library + openssl OpenSSL - Secure Sockets Layer and cryptography libraries and tools + libssh2 libssh2 - Library for SSH-based communication + panel panel - ncurses 6.5 add-on library + panelw panelw - ncurses 6.5 add-on library + libedit libedit - command line editor library provides generic line editing, history, and tokenization functions. + ncursesw ncursesw - ncurses 6.5 add-on library + gssrpc gssrpc - GSSAPI RPC implementation + menuw menuw - ncurses 6.5 add-on library + kadm-client kadm-client - Kerberos administration client library + tinfow tinfow - ncurses 6.5 terminal interface library + formw formw - ncurses 6.5 add-on library + libdeflate libdeflate - Fast implementation of DEFLATE, zlib, and gzip + libkeyutils libkeyutils - keyutils library + ncurses ncurses - ncurses 6.5 library + ncurses ncurses - ncurses 6.5 add-on library + mit-krb5 mit-krb5 - An implementation of Kerberos network authentication + libcares c-ares - asynchronous DNS lookup library + cmake -S . -B build -DZIG=ON -DOPENMP=ON -DWFA_GITMODULE=OFF -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_INSTALL_PREFIX=/opt/conda/conda-bld/vcflib_1734561516831/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh -DCMAKE_CXX_COMPILER=/opt/conda/conda-bld/vcflib_1734561516831/_build_env/bin/aarch64-conda-linux-gnu-c '-DCMAKE_CXX_FLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem /opt/conda/conda-bld/vcflib_1734561516831/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include -fdebug-prefix-map=/opt/conda/conda-bld/vcflib_1734561516831/work=/usr/local/src/conda/vcflib-1.0.10 -fdebug-prefix-map=/opt/conda/conda-bld/vcflib_1734561516831/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh=/usr/local/src/conda-prefix -O3 -D_FILE_OFFSET_BITS=64 -I/opt/conda/conda-bld/vcflib_1734561516831/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include' '' + krb5-gssapi krb5-gssapi - Kerberos implementation of the GSSAPI + ncursesw ncursesw - ncurses 6.5 library + tinfo tinfo - ncurses 6.5 terminal interface library + libssl OpenSSL-libssl - Secure Sockets Layer and cryptography libraries + libzstd zstd - fast lossless compression algorithm library + mit-krb5-gssapi mit-krb5-gssapi - Kerberos implementation of the GSSAPI + menu menu - ncurses 6.5 add-on library + form form - ncurses 6.5 add-on library + kdb kdb - Kerberos database access libraries + CMake Warning: + Ignoring empty string ("") provided on the command line. + + + -- The C compiler identification is GNU 13.3.0 + -- The CXX compiler identification is GNU 13.3.0 + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - failed + -- Check for working C compiler: $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc + CMake Error at /opt/conda/conda-bld/vcflib_1734561516831/_build_env/share/cmake-3.31/Modules/CMakeTestCCompiler.cmake:67 (message): + The C compiler + + "/opt/conda/conda-bld/vcflib_1734561516831/_build_env/bin/aarch64-conda-linux-gnu-cc" + + is not able to compile a simple test program. + + It fails with the following output: + + Change Dir: '/opt/conda/conda-bld/vcflib_1734561516831/work/build/CMakeFiles/CMakeScratch/TryCompile-siIDRM' + + Run Build Command(s): /opt/conda/conda-bld/vcflib_1734561516831/_build_env/bin/cmake -E env VERBOSE=1 /opt/conda/conda-bld/vcflib_1734561516831/_build_env/bin/make -f Makefile cmTC_8fe13/fast + /opt/conda/conda-bld/vcflib_1734561516831/_build_env/bin/make -f CMakeFiles/cmTC_8fe13.dir/build.make CMakeFiles/cmTC_8fe13.dir/build + make[1]: Entering directory '/opt/conda/conda-bld/vcflib_1734561516831/work/build/CMakeFiles/CMakeScratch/TryCompile-siIDRM' + Building C object CMakeFiles/cmTC_8fe13.dir/testCCompiler.c.o + /opt/conda/conda-bld/vcflib_1734561516831/_build_env/bin/aarch64-conda-linux-gnu-cc -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem /opt/conda/conda-bld/vcflib_1734561516831/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include -fdebug-prefix-map=/opt/conda/conda-bld/vcflib_1734561516831/work=/usr/local/src/conda/vcflib-1.0.10 -fdebug-prefix-map=/opt/conda/conda-bld/vcflib_1734561516831/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh=/usr/local/src/conda-prefix -o CMakeFiles/cmTC_8fe13.dir/testCCompiler.c.o -c /opt/conda/conda-bld/vcflib_1734561516831/work/build/CMakeFiles/CMakeScratch/TryCompile-siIDRM/testCCompiler.c + Linking C executable cmTC_8fe13 + /opt/conda/conda-bld/vcflib_1734561516831/_build_env/bin/cmake -E cmake_link_script CMakeFiles/cmTC_8fe13.dir/link.txt --verbose=1 + /opt/conda/conda-bld/vcflib_1734561516831/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: cannot find -llzma: No such file or directory + collect2: error: ld returned 1 exit status + /opt/conda/conda-bld/vcflib_1734561516831/_build_env/bin/aarch64-conda-linux-gnu-cc -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem /opt/conda/conda-bld/vcflib_1734561516831/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include -fdebug-prefix-map=/opt/conda/conda-bld/vcflib_1734561516831/work=/usr/local/src/conda/vcflib-1.0.10 -fdebug-prefix-map=/opt/conda/conda-bld/vcflib_1734561516831/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh=/usr/local/src/conda-prefix -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/vcflib_1734561516831/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -Wl,-rpath-link,/opt/conda/conda-bld/vcflib_1734561516831/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -L/opt/conda/conda-bld/vcflib_1734561516831/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -L/opt/conda/conda-bld/vcflib_1734561516831/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -lhts -ltabixpp -lpthread -lz -lm -llzma -lbz2 -fopenmp -lwfa2 CMakeFiles/cmTC_8fe13.dir/testCCompiler.c.o -o cmTC_8fe13 + make[1]: *** [CMakeFiles/cmTC_8fe13.dir/build.make:102: cmTC_8fe13] Error 1 + make[1]: Leaving directory '/opt/conda/conda-bld/vcflib_1734561516831/work/build/CMakeFiles/CMakeScratch/TryCompile-siIDRM' + make: *** [Makefile:133: cmTC_8fe13/fast] Error 2 + + + + + + CMake will not be able to correctly generate this project. + Call Stack (most recent call first): + CMakeLists.txt:10 (project) + + -- Check for working C compiler: $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc - broken + + -- Configuring incomplete, errors occurred! + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/vcflib_1734561516831/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/vcflib_1734561516831/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/vcflib/build_failure.osx-64.yaml b/recipes/vcflib/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..1df4ebbffcd9d --- /dev/null +++ b/recipes/vcflib/build_failure.osx-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: 039cbc49702ddc83f23305256c8b8c53a7212ce68ecc7fa8163e54a912e152e6 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped + -- Detecting C compile features + -- Detecting C compile features - done + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Found PkgConfig: $BUILD_PREFIX/bin/pkg-config (found version "0.29.2") + -- Found PythonInterp: $BUILD_PREFIX/bin/python (found suitable version "3.13.1", minimum required is "3.7") + -- Found PythonLibs: $BUILD_PREFIX/lib/libpython3.13.dylib + -- Performing Test HAS_FLTO_THIN + -- Performing Test HAS_FLTO_THIN - Success + -- Found pybind11: $BUILD_PREFIX/include (found version "2.13.6") + -- Found BZip2: $PREFIX/lib/libbz2.dylib (found version "1.0.8") + -- Looking for BZ2_bzCompressInit + -- Looking for BZ2_bzCompressInit - found + -- Looking for lzma_auto_decoder in /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/lib/liblzma.tbd + -- Looking for lzma_auto_decoder in /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/lib/liblzma.tbd - found + -- Looking for lzma_easy_encoder in /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/lib/liblzma.tbd + -- Looking for lzma_easy_encoder in /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/lib/liblzma.tbd - found + -- Looking for lzma_lzma_preset in /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/lib/liblzma.tbd + -- Looking for lzma_lzma_preset in /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/lib/liblzma.tbd - found + -- Found LibLZMA: /Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/lib/liblzma.tbd (found version "5.6.3") + -- Found ZLIB: $PREFIX/lib/libz.dylib (found version "1.3.1") + -- Found CURL: $PREFIX/lib/libcurl.dylib (found version "8.11.1") + -- + + -- Found OpenMP_C: -fopenmp=libomp (found version "5.1") + -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.1") + -- Found OpenMP: TRUE (found version "5.1") + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success + -- Found Threads: TRUE + -- Checking for module 'htslib' + -- Package 'bzip2', required by 'htslib', not found + -- Checking for module 'tabixpp' + -- No package 'tabixpp' found + -- Using included htslib + -- Using included tabixpp + -- WFA using include $PREFIX/include/wfa2lib + -- Configuring done (16.7s) + -- Generating done (0.9s) + -- Build files have been written to: $SRC_DIR/build + Change Dir: '$SRC_DIR/build' + + Run Build Command(s): $BUILD_PREFIX/bin/cmake -E env VERBOSE=1 $BUILD_PREFIX/bin/make -f Makefile -j2 install + $BUILD_PREFIX/bin/cmake -S$SRC_DIR -B$SRC_DIR/build --check-build-system CMakeFiles/Makefile.cmake 0 + $BUILD_PREFIX/bin/cmake -E cmake_progress_start $SRC_DIR/build/CMakeFiles $SRC_DIR/build//CMakeFiles/progress.marks + $BUILD_PREFIX/bin/make -f CMakeFiles/Makefile2 all + make[1]: Entering directory '$SRC_DIR/build' + $BUILD_PREFIX/bin/make -f CMakeFiles/ZIG-EXT.dir/build.make CMakeFiles/ZIG-EXT.dir/depend + $BUILD_PREFIX/bin/make -f CMakeFiles/htslib-EXT.dir/build.make CMakeFiles/htslib-EXT.dir/depend + make[2]: Entering directory '$SRC_DIR/build' + cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR $SRC_DIR/build $SRC_DIR/build $SRC_DIR/build/CMakeFiles/ZIG-EXT.dir/DependInfo.cmake "--color=" + make[2]: Entering directory '$SRC_DIR/build' + cd $SRC_DIR/build && $BUILD_PREFIX/bin/cmake -E cmake_depends "Unix Makefiles" $SRC_DIR $SRC_DIR $SRC_DIR/build $SRC_DIR/build $SRC_DIR/build/CMakeFiles/htslib-EXT.dir/DependInfo.cmake "--color=" + make[2]: Leaving directory '$SRC_DIR/build' + $BUILD_PREFIX/bin/make -f CMakeFiles/ZIG-EXT.dir/build.make CMakeFiles/ZIG-EXT.dir/build + make[2]: Entering directory '$SRC_DIR/build' + make[2]: Leaving directory '$SRC_DIR/build' + $BUILD_PREFIX/bin/make -f CMakeFiles/htslib-EXT.dir/build.make CMakeFiles/htslib-EXT.dir/build + make[2]: Entering directory '$SRC_DIR/build' + [ 0%] Creating directories for 'ZIG-EXT' + $BUILD_PREFIX/bin/cmake -Dcfgdir= -P $SRC_DIR/build/ZIG-EXT-prefix/tmp/ZIG-EXT-mkdirs.cmake + [ 1%] Creating directories for 'htslib-EXT' + $BUILD_PREFIX/bin/cmake -Dcfgdir= -P $SRC_DIR/build/htslib-EXT-prefix/tmp/htslib-EXT-mkdirs.cmake + $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/build/htslib-EXT-prefix/src/htslib-EXT-stamp/htslib-EXT-mkdir + $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/build/ZIG-EXT-prefix/src/ZIG-EXT-stamp/ZIG-EXT-mkdir + [ 2%] No download step for 'ZIG-EXT' + [ 2%] No download step for 'htslib-EXT' + $BUILD_PREFIX/bin/cmake -E echo_append + $BUILD_PREFIX/bin/cmake -E echo_append + $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/build/ZIG-EXT-prefix/src/ZIG-EXT-stamp/ZIG-EXT-download + $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/build/htslib-EXT-prefix/src/htslib-EXT-stamp/htslib-EXT-download + [ 3%] Performing update step for 'htslib-EXT' + cd $SRC_DIR/contrib/tabixpp/htslib && autoreconf -i + [ 3%] No update step for 'ZIG-EXT' + cd $SRC_DIR/src/zig && $BUILD_PREFIX/bin/cmake -E echo_append + cd $SRC_DIR/src/zig && $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/build/ZIG-EXT-prefix/src/ZIG-EXT-stamp/ZIG-EXT-update + [ 4%] No patch step for 'ZIG-EXT' + $BUILD_PREFIX/bin/cmake -E echo_append + $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/build/ZIG-EXT-prefix/src/ZIG-EXT-stamp/ZIG-EXT-patch + [ 5%] No configure step for 'ZIG-EXT' + cd $SRC_DIR/src/zig && $BUILD_PREFIX/bin/cmake -E echo_append + cd $SRC_DIR/src/zig && $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/build/ZIG-EXT-prefix/src/ZIG-EXT-stamp/ZIG-EXT-configure + [ 5%] Performing build step for 'ZIG-EXT' + cd $SRC_DIR/src/zig && $SRC_DIR/src/zig/compile.sh + make[2]: Leaving directory '$SRC_DIR/build' + [ 6%] No install step for 'ZIG-EXT' + cd $SRC_DIR/src/zig && $BUILD_PREFIX/bin/cmake -E echo_append + [ 6%] Completed 'ZIG-EXT' + $BUILD_PREFIX/bin/cmake -E make_directory $SRC_DIR/build/CMakeFiles + $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/build/CMakeFiles/ZIG-EXT-complete + $BUILD_PREFIX/bin/cmake -E touch $SRC_DIR/build/ZIG-EXT-prefix/src/ZIG-EXT-stamp/ZIG-EXT-done + make[2]: Leaving directory '$SRC_DIR/build' + [ 6%] Built target ZIG-EXT + make[1]: Leaving directory '$SRC_DIR/build' +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/vcflib/meta.yaml b/recipes/vcflib/meta.yaml index cdb515fec7db1..653d7ef2669fe 100644 --- a/recipes/vcflib/meta.yaml +++ b/recipes/vcflib/meta.yaml @@ -31,7 +31,7 @@ source: folder: zig-macos-aarch64-0.10.1 # [osx and arm64] build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('vcflib', max_pin="x") }} diff --git a/recipes/vcftools/meta.yaml b/recipes/vcftools/meta.yaml index 9b96a1085272c..47eec81ef51a2 100644 --- a/recipes/vcftools/meta.yaml +++ b/recipes/vcftools/meta.yaml @@ -13,7 +13,7 @@ source: - patch build: - number: 11 + number: 12 run_exports: - {{ pin_subpackage('vcftools', max_pin='x.x') }} diff --git a/recipes/vdjer/meta.yaml b/recipes/vdjer/meta.yaml index 0f72f27b8f633..1fb13f7a6eb55 100644 --- a/recipes/vdjer/meta.yaml +++ b/recipes/vdjer/meta.yaml @@ -11,7 +11,7 @@ source: build: - number: 7 + number: 8 skip: True # [osx] diff --git a/recipes/vechat/build_failure.linux-64.yaml b/recipes/vechat/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..6d7cfbabd377e --- /dev/null +++ b/recipes/vechat/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: bac7c6de77bec92e64252974c2d0c039ae8599fd39305f694034841215166663 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/graph.cpp: In member function 'void spoa::Graph::AddWeights(const spoa::Alignment&, const char*, uint32_t, const std::vector&)': + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/graph.cpp:1106:19: warning: unused parameter 'sequence' [-Wunused-parameter] + 1106 | const char *sequence, + | ~~~~~~~~~~~~^~~~~~~~ + [ 50%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/sisd_alignment_engine.cpp: In member function 'void spoa::SisdAlignmentEngine::Initialize(const char*, uint32_t, const spoa::Graph&)': + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/sisd_alignment_engine.cpp:156:7: warning: this statement may fall through [-Wimplicit-fallthrough=] + 156 | } + | ^ + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/sisd_alignment_engine.cpp:157:5: note: here + 157 | case AlignmentSubtype::kAffine: + | ^~~~ + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/sisd_alignment_engine.cpp:173:7: warning: this statement may fall through [-Wimplicit-fallthrough=] + 173 | } + | ^ + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/sisd_alignment_engine.cpp:174:5: note: here + 174 | case AlignmentSubtype::kLinear: + | ^~~~ + [ 50%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/dispatcher.cpp.o + In file included from /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/dispatcher.cpp:3: + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/simd_alignment_engine_implementation.hpp:315:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__m128i []'} [-Wignored-attributes] + 315 | std::unique_ptr<__mxxxi[]> sequence_profile_storage; + | ^ + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/simd_alignment_engine_implementation.hpp:320:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__m128i []'} [-Wignored-attributes] + 320 | std::unique_ptr<__mxxxi[]> M_storage; + | ^ + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/simd_alignment_engine_implementation.hpp:328:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__m128i []'} [-Wignored-attributes] + 328 | std::unique_ptr<__mxxxi[]> masks_storage; + | ^ + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/simd_alignment_engine_implementation.hpp:332:28: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__m128i []'} [-Wignored-attributes] + 332 | std::unique_ptr<__mxxxi[]> penalties_storage; + | ^ + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/simd_alignment_engine_implementation.hpp: In member function 'void spoa::SimdAlignmentEngine::Realloc(uint64_t, uint64_t, uint8_t)': + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/simd_alignment_engine_implementation.hpp:432:65: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__m128i []'} [-Wignored-attributes] + 432 | pimpl_->sequence_profile_storage = std::unique_ptr<__mxxxi[]>(storage); + | ^ + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/simd_alignment_engine_implementation.hpp:446:52: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__m128i []'} [-Wignored-attributes] + 446 | pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage); + | ^ + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/simd_alignment_engine_implementation.hpp:462:52: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__m128i []'} [-Wignored-attributes] + 462 | pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage); + | ^ + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/simd_alignment_engine_implementation.hpp:480:52: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__m128i []'} [-Wignored-attributes] + 480 | pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage); + | ^ + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/simd_alignment_engine_implementation.hpp:491:54: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__m128i []'} [-Wignored-attributes] + 491 | pimpl_->masks_storage = std::unique_ptr<__mxxxi[]>(storage); + | ^ + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/simd_alignment_engine_implementation.hpp:501:58: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__m128i []'} [-Wignored-attributes] + 501 | pimpl_->penalties_storage = std::unique_ptr<__mxxxi[]>(storage); + | ^ + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/simd_alignment_engine_implementation.hpp: In member function 'void spoa::SimdAlignmentEngine::Initialize(const char*, const spoa::Graph&, uint64_t, uint64_t, uint64_t) [with T = spoa::InstructionSet; spoa::Architecture A = spoa::Architecture::kAutomatic]': + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/simd_alignment_engine_implementation.hpp:557:7: warning: this statement may fall through [-Wimplicit-fallthrough=] + 557 | for (std::uint32_t i = 1; i < matrix_height; i) { + | ^~~ + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/simd_alignment_engine_implementation.hpp:566:5: note: here + 566 | case AlignmentSubtype::kAffine: + | ^~~~ + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/simd_alignment_engine_implementation.hpp: In member function 'void spoa::SimdAlignmentEngine::Initialize(const char*, const spoa::Graph&, uint64_t, uint64_t, uint64_t) [with T = spoa::InstructionSet; spoa::Architecture A = spoa::Architecture::kAutomatic]': + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/simd_alignment_engine_implementation.hpp:557:7: warning: this statement may fall through [-Wimplicit-fallthrough=] + 557 | for (std::uint32_t i = 1; i < matrix_height; i) { + | ^~~ + /opt/conda/conda-bld/vechat_1734155536549/work/vendor/spoa/src/simd_alignment_engine_implementation.hpp:566:5: note: here + 566 | case AlignmentSubtype::kAffine: + | ^~~~ + [ 50%] Linking CXX static library lib/libspoa.a + [ 50%] Built target spoa + [ 50%] Building CXX object CMakeFiles/racon.dir/src/main.cpp.o + [ 50%] Building CXX object CMakeFiles/racon.dir/src/logger.cpp.o + [ 75%] Building CXX object CMakeFiles/racon.dir/src/polisher.cpp.o + In file included from /opt/conda/conda-bld/vechat_1734155536549/work/src/polisher.cpp:13: + /opt/conda/conda-bld/vechat_1734155536549/work/src/window.hpp:51:14: error: 'std::uint32_t' has not been declared + 51 | std::uint32_t num_prune); + | ^~~~~~~~ + make[2]: *** [CMakeFiles/racon.dir/build.make:107: CMakeFiles/racon.dir/src/polisher.cpp.o] Error 1 + make[1]: *** [CMakeFiles/Makefile2:560: CMakeFiles/racon.dir/all] Error 2 + make: *** [Makefile:156: all] Error 2 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/vechat_1734155536549/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/vechat_1734155536549/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/vechat/meta.yaml b/recipes/vechat/meta.yaml index c957d0b0e3ba0..b874cbbf32d55 100644 --- a/recipes/vechat/meta.yaml +++ b/recipes/vechat/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 skip: True # [osx] source: diff --git a/recipes/velocyto.py/build_failure.linux-64.yaml b/recipes/velocyto.py/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..dd5ebda8c512e --- /dev/null +++ b/recipes/velocyto.py/build_failure.linux-64.yaml @@ -0,0 +1,4 @@ +recipe_sha: e173b84fee301079bf166c8b14b8008d011e849bc926090870321d31dca82abb # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +category: |- + test failure diff --git a/recipes/velocyto.py/meta.yaml b/recipes/velocyto.py/meta.yaml index d562d51c97a22..1173ef01f1516 100644 --- a/recipes/velocyto.py/meta.yaml +++ b/recipes/velocyto.py/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 2461eabf2ec6b152240c95f7ad8a0a5768a83c72822d9398beec2981732b890d build: - number: 7 + number: 8 run_exports: - {{ pin_subpackage("velocyto.py", max_pin="x.x") }} script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv" @@ -24,7 +24,8 @@ requirements: host: - python - pip - - numpy + - setuptools + - numpy <2 - cython run: - python diff --git a/recipes/velvet/meta.yaml b/recipes/velvet/meta.yaml index 445a544f7f3da..976da9170d76c 100644 --- a/recipes/velvet/meta.yaml +++ b/recipes/velvet/meta.yaml @@ -4,7 +4,7 @@ package: name: velvet version: {{ version }} build: - number: 7 + number: 8 skip: True # [osx] run_exports: - {{ pin_subpackage("velvet", max_pin="x") }} diff --git a/recipes/verifybamid/meta.yaml b/recipes/verifybamid/meta.yaml index d00d1fb773097..10d4ff69c76ac 100644 --- a/recipes/verifybamid/meta.yaml +++ b/recipes/verifybamid/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 8 + number: 9 source: url: https://github.com/statgen/verifyBamID/releases/download/v{{ version }}/verifyBamIDLibStatGen.{{ version }}.tgz diff --git a/recipes/verifybamid2/build_failure.osx-64.yaml b/recipes/verifybamid2/build_failure.osx-64.yaml deleted file mode 100644 index c211e26887045..0000000000000 --- a/recipes/verifybamid2/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 719e48692e845e21d83868b9c295678d5c3c8132b4b4e2502617109015fae933 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - libexpat: 2.6.2-h73e2aa4_0 conda-forge - libiconv: 1.17-hd75f5a5_2 conda-forge - libllvm16: 16.0.6-hbedff68_3 conda-forge - libnghttp2: 1.58.0-h64cf6d3_1 conda-forge - libssh2: 1.11.0-hd019ec5_0 conda-forge - libuv: 1.48.0-h67532ce_0 conda-forge - libxml2: 2.12.7-h3e169fe_1 conda-forge - libzlib: 1.3.1-h87427d6_1 conda-forge - llvm-tools: 16.0.6-hbedff68_3 conda-forge - m4: 1.4.18-haf1e3a3_1001 conda-forge - make: 4.3-h22f3db7_1 conda-forge - ncurses: 6.5-h5846eda_0 conda-forge - openssl: 3.3.1-h87427d6_0 conda-forge - perl: 5.32.1-7_h10d778d_perl5 conda-forge - rhash: 1.4.4-h0dc2134_0 conda-forge - sigtool: 0.1.3-h88f4db0_0 conda-forge - tapi: 1100.0.11-h9ce4665_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - zstd: 1.5.6-h915ae27_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - Downloading source to cache: 2.0.1_03c85fa871.tar.gz - Downloading https://github.com/Griffan/VerifyBamID/archive/2.0.1.tar.gz - Success - dyld[65511]: Library not loaded: @rpath/librhash.1.dylib - Referenced from: <35DD3714-1FE0-3722-8243-CAF393FEE8B7> /opt/mambaforge/envs/bioconda/pkgs/cmake-3.29.5-h749d262_0/bin/cmake - Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/cmake-3.29.5-h749d262_0/bin/../lib/librhash.1.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/cmake-3.29.5-h749d262_0/bin/../lib/librhash.1.dylib' (no such file), '/usr/local/lib/librhash.1.dylib' (no such file), '/usr/lib/librhash.1.dylib' (no such file, not in dyld cache) - /opt/mambaforge/envs/bioconda/conda-bld/verifybamid2_1718297263210/work/conda_build.sh: line 15: 65511 Abort trap: 6 cmake -DCMAKE_INSTALL_PREFIX=${PREFIX} .. - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/verifybamid2_1718297263210/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/verifybamid2_1718297263210/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/verifybamid2_1718297263210/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/verifybamid2_1718297263210/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/verifybamid2-2.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/verifybamid2_1718297263210/work/conda_build.sh']' returned non-zero exit status 134. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/verifybamid2-2.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/verifybamid2-2.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/verifybamid2-2.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -# Last 100 lines of the build log. diff --git a/recipes/verifybamid2/meta.yaml b/recipes/verifybamid2/meta.yaml index 10426dc8cce54..0d67a737a4f40 100644 --- a/recipes/verifybamid2/meta.yaml +++ b/recipes/verifybamid2/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 11 + number: 12 source: url: https://github.com/Griffan/VerifyBamID/archive/{{ version }}.tar.gz diff --git a/recipes/verifyidintensity/meta.yaml b/recipes/verifyidintensity/meta.yaml index 6b34fdce99fe1..e41c5d6a1c880 100644 --- a/recipes/verifyidintensity/meta.yaml +++ b/recipes/verifyidintensity/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 5 + number: 6 source: url: https://github.com/gjun/verifyIDintensity/archive/master.zip diff --git a/recipes/verkko/build_failure.linux-64.yaml b/recipes/verkko/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..1f7cfe2bd6035 --- /dev/null +++ b/recipes/verkko/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a44f98a0764fffabe291868d9f87ecef4b520c4267830a972c9d424391bfb34a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("libzlib[version='>=1.2.13,<1.3.0a0']"), MatchSpec("graphaligner==1.0.19=h21ec9f0_0")} + Encountered problems while solving: + - package graphaligner-1.0.19-h21ec9f0_0 requires libzlib >=1.2.13,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mgraphaligner >=1.0.19 [0m is installable with the potential options + [32mgraphaligner 1.0.19[0m would require + [32mlibzlib >=1.2.13,<1.3.0a0 [0m, which can be installed; + [32mgraphaligner [1.0.19|1.0.20][0m would require + [32mprotobuf 3.14.0 [0m, which requires + [32mlibprotobuf 3.14.0.* [0m, which requires + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [32mpypy3.6 [>=7.3.2 |>=7.3.3 ][0m, which requires + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [32mpypy3.7 >=7.3.3 [0m, which requires + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [31mlibzlib >=1.3.1,<2.0a0 [0m is not installable because there are no viable options + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_0[0m, which conflicts with any installable versions previously reported; + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_1[0m, which conflicts with any installable versions previously reported; + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_2[0m, which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/conda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/conda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("libzlib[version='>=1.2.13,<1.3.0a0']"), MatchSpec("graphaligner==1.0.19=h21ec9f0_0")} + Encountered problems while solving: + - package graphaligner-1.0.19-h21ec9f0_0 requires libzlib >=1.2.13,<1.3.0a0, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + [32mgraphaligner >=1.0.19 [0m is installable with the potential options + [32mgraphaligner 1.0.19[0m would require + [32mlibzlib >=1.2.13,<1.3.0a0 [0m, which can be installed; + [32mgraphaligner [1.0.19|1.0.20][0m would require + [32mprotobuf 3.14.0 [0m, which requires + [32mlibprotobuf 3.14.0.* [0m, which requires + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [32mpypy3.6 [>=7.3.2 |>=7.3.3 ][0m, which requires + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [32mpypy3.7 >=7.3.3 [0m, which requires + [32mzlib >=1.2.11,<1.3.0a0 [0m, which can be installed; + [31mlibzlib >=1.3.1,<2.0a0 [0m is not installable because there are no viable options + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_0[0m, which conflicts with any installable versions previously reported; + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_1[0m, which conflicts with any installable versions previously reported; + [31mlibzlib 1.3.1[0m would require + [31mzlib 1.3.1 *_2[0m, which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/verkko/build_failure.osx-64.yaml b/recipes/verkko/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..2f0b2e0f729ca --- /dev/null +++ b/recipes/verkko/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: a44f98a0764fffabe291868d9f87ecef4b520c4267830a972c9d424391bfb34a # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("minimap2==2.28=h10309d6_2"), MatchSpec("k8")} + Encountered problems while solving: + - package minimap2-2.28-h10309d6_2 requires k8, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + libzlib >=1.3.1,<2.0a0 is installable with the potential options + libzlib 1.3.1 would require + zlib 1.3.1 *_0, which can be installed; + libzlib 1.3.1 would require + zlib 1.3.1 *_1, which can be installed; + libzlib 1.3.1 would require + zlib 1.3.1 *_2, which can be installed; + minimap2 >=2.28 is not installable because there are no viable options + minimap2 2.28 would require + k8 but there are no viable options + k8 0.2.5 would require + zlib >=1.2.11,<1.3.0a0 , which conflicts with any installable versions previously reported; + k8 0.2.5 would require + zlib >=1.2.13,<1.3.0a0 , which conflicts with any installable versions previously reported; + k8 [0.2.5|1.0|1.1|1.2] would require + libzlib >=1.2.13,<1.3.0a0 , which conflicts with any installable versions previously reported; + minimap2 2.28 would require + libzlib >=1.2.13,<1.3.0a0 , which conflicts with any installable versions previously reported. + + During handling of the above exception, another exception occurred: + + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2439, in build + create_build_envs(top_level_pkg, notest) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2277, in create_build_envs + raise e + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2250, in create_build_envs + environ.get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 938, in get_install_actions + precs = get_package_records( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions + _actions = _install_actions(prefix, index, specs, subdir=subdir) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1307, in install_actions + txn = solver.solve_for_transaction(prune=False, ignore_pinned=False) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 152, in solve_for_transaction + unlink_precs, link_precs = self.solve_for_diff( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 221, in solve_for_diff + final_precs = self.solve_final_state( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state + out_state = self._solving_loop(in_state, out_state, index) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop + solved = self._solve_attempt(in_state, out_state, index, attempt=attempt) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt + new_conflicts = self._maybe_raise_for_problems( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems + self._maybe_raise_for_conda_build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build + raise exc + conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("minimap2==2.28=h10309d6_2"), MatchSpec("k8")} + Encountered problems while solving: + - package minimap2-2.28-h10309d6_2 requires k8, but none of the providers can be installed + + Could not solve for environment specs + The following packages are incompatible + libzlib >=1.3.1,<2.0a0 is installable with the potential options + libzlib 1.3.1 would require + zlib 1.3.1 *_0, which can be installed; + libzlib 1.3.1 would require + zlib 1.3.1 *_1, which can be installed; + libzlib 1.3.1 would require + zlib 1.3.1 *_2, which can be installed; + minimap2 >=2.28 is not installable because there are no viable options + minimap2 2.28 would require + k8 but there are no viable options + k8 0.2.5 would require + zlib >=1.2.11,<1.3.0a0 , which conflicts with any installable versions previously reported; + k8 0.2.5 would require + zlib >=1.2.13,<1.3.0a0 , which conflicts with any installable versions previously reported; + k8 [0.2.5|1.0|1.1|1.2] would require + libzlib >=1.2.13,<1.3.0a0 , which conflicts with any installable versions previously reported; + minimap2 2.28 would require + libzlib >=1.2.13,<1.3.0a0 , which conflicts with any installable versions previously reported. +# Last 100 lines of the build log. diff --git a/recipes/verkko/meta.yaml b/recipes/verkko/meta.yaml index bc812c97aaa3a..1b266116aee65 100644 --- a/recipes/verkko/meta.yaml +++ b/recipes/verkko/meta.yaml @@ -12,7 +12,7 @@ source: - osx_availability.patch # [osx] build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('verkko', max_pin="x.x") }} diff --git a/recipes/verse/meta.yaml b/recipes/verse/meta.yaml index b317a6c3384a6..fdc7cef682b2f 100644 --- a/recipes/verse/meta.yaml +++ b/recipes/verse/meta.yaml @@ -9,7 +9,7 @@ source: - 0001-Inject-our-CC.patch build: - number: 8 + number: 9 requirements: build: diff --git a/recipes/veryfasttree/build.sh b/recipes/veryfasttree/build.sh index 8cf6516043503..42e58a7fb096f 100644 --- a/recipes/veryfasttree/build.sh +++ b/recipes/veryfasttree/build.sh @@ -23,6 +23,7 @@ fi if [[ "$(uname)" == "Darwin" ]]; then export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" export LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib" + export CFLAGS="${CFLAGS} -fno-define-target-os-macros" else export CONFIG_ARGS="" fi diff --git a/recipes/veryfasttree/meta.yaml b/recipes/veryfasttree/meta.yaml index 1f3718f2aba7f..f1ba34cf096a8 100644 --- a/recipes/veryfasttree/meta.yaml +++ b/recipes/veryfasttree/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('veryfasttree', max_pin="x") }} diff --git a/recipes/viennarna/meta.yaml b/recipes/viennarna/meta.yaml index feb2a8c2bf757..7d5dffddcd774 100644 --- a/recipes/viennarna/meta.yaml +++ b/recipes/viennarna/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: # Ronny said VRNA is stable in x.x releases - {{ pin_subpackage('viennarna', max_pin='x.x') }} diff --git a/recipes/viewbs/meta.yaml b/recipes/viewbs/meta.yaml index 8846a008427da..c6e5b27e9df38 100644 --- a/recipes/viewbs/meta.yaml +++ b/recipes/viewbs/meta.yaml @@ -12,7 +12,7 @@ source: build: skip: True # [ osx ] - number: 3 + number: 4 requirements: build: diff --git a/recipes/viguno/build_failure.linux-64.yaml b/recipes/viguno/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..7fed891a83f17 --- /dev/null +++ b/recipes/viguno/build_failure.linux-64.yaml @@ -0,0 +1,92 @@ +recipe_sha: f9fdadf3017cae87c9fc872cc53d4f6e2fe3d1d50100b1ee5552616e86ea1c61 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + 2024-12-13T11:16:54 Subdir: linux-64 Gathering repodata + 2024-12-13T11:16:54 linux-64 Writing pre-patch repodata + 2024-12-13T11:16:54 linux-64 Applying patch instructions + 2024-12-13T11:16:54 linux-64 Writing patched repodata + 2024-12-13T11:16:54 linux-64 Building current_repodata subset + 2024-12-13T11:16:54 linux-64 Writing current_repodata subset + 2024-12-13T11:16:54 linux-64 Writing index HTML + 2024-12-13T11:16:54 Subdir: linux-aarch64 Gathering repodata + 2024-12-13T11:16:54 linux-aarch64 Writing pre-patch repodata + 2024-12-13T11:16:54 linux-aarch64 Applying patch instructions + 2024-12-13T11:16:54 linux-aarch64 Writing patched repodata + 2024-12-13T11:16:54 linux-aarch64 Building current_repodata subset + 2024-12-13T11:16:54 linux-aarch64 Writing current_repodata subset + 2024-12-13T11:16:54 linux-aarch64 Writing index HTML + 2024-12-13T11:16:54 Subdir: noarch Gathering repodata + 2024-12-13T11:16:54 noarch Writing pre-patch repodata + 2024-12-13T11:16:54 noarch Applying patch instructions + 2024-12-13T11:16:54 noarch Writing patched repodata + 2024-12-13T11:16:54 noarch Building current_repodata subset + 2024-12-13T11:16:54 noarch Writing current_repodata subset + 2024-12-13T11:16:54 noarch Writing index HTML + 2024-12-13T11:16:55 Subdir: linux-64 Gathering repodata + 2024-12-13T11:16:55 linux-64 Writing pre-patch repodata + 2024-12-13T11:16:55 linux-64 Applying patch instructions + 2024-12-13T11:16:55 linux-64 Writing patched repodata + 2024-12-13T11:16:55 linux-64 Building current_repodata subset + 2024-12-13T11:16:55 linux-64 Writing current_repodata subset + 2024-12-13T11:16:55 linux-64 Writing index HTML + 2024-12-13T11:16:55 Subdir: linux-aarch64 Gathering repodata + 2024-12-13T11:16:55 linux-aarch64 Writing pre-patch repodata + 2024-12-13T11:16:55 linux-aarch64 Applying patch instructions + 2024-12-13T11:16:55 linux-aarch64 Writing patched repodata + 2024-12-13T11:16:55 linux-aarch64 Building current_repodata subset + 2024-12-13T11:16:55 linux-aarch64 Writing current_repodata subset + 2024-12-13T11:16:55 linux-aarch64 Writing index HTML + 2024-12-13T11:16:55 Subdir: noarch Gathering repodata + 2024-12-13T11:16:55 noarch Writing pre-patch repodata + 2024-12-13T11:16:55 noarch Applying patch instructions + 2024-12-13T11:16:55 noarch Writing patched repodata + 2024-12-13T11:16:55 noarch Building current_repodata subset + 2024-12-13T11:16:55 noarch Writing current_repodata subset + 2024-12-13T11:16:55 noarch Writing index HTML + /opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (/opt/recipe/meta.yaml). + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml + Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for viguno + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2338, in build + output_metas = expand_outputs([(m, need_source_download, need_reparse_in_env)]) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 916, in expand_outputs + for output_dict, m in deepcopy(_m).get_output_metadata_set( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 2658, in get_output_metadata_set + conda_packages = finalize_outputs_pass( + File "/opt/conda/lib/python3.10/site-packages/conda_build/metadata.py", line 1025, in finalize_outputs_pass + fm = finalize_metadata( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 650, in finalize_metadata + build_unsat, host_unsat = add_upstream_pins( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 491, in add_upstream_pins + host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 453, in _read_upstream_pin_files + extra_run_specs = get_upstream_pins(m, precs, env) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 425, in get_upstream_pins + loc, dist = execute_download_actions( + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 392, in execute_download_actions + pfe.execute() + File "/opt/conda/lib/python3.10/site-packages/conda/core/package_cache_data.py", line 900, in execute + raise CondaMultiError(not_cancelled) + conda.CondaMultiError: Failed to write to /opt/conda/pkgs/clangdev-19.1.5-default_hb5137d0_0.conda.partial + errno: 28 + Failed to write to /opt/conda/pkgs/clangdev-19.1.5-default_hb5137d0_0.conda.partial + errno: 28 +# Last 100 lines of the build log. diff --git a/recipes/viguno/build_failure.linux-aarch64.yaml b/recipes/viguno/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..022290893c30a --- /dev/null +++ b/recipes/viguno/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: f9fdadf3017cae87c9fc872cc53d4f6e2fe3d1d50100b1ee5552616e86ea1c61 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + Running rustc --crate-name allocator_api2 --edition=2018 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/allocator-api2-0.2.16/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="alloc"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "default", "nightly", "serde", "std"))' -C metadata=a6d831398f16df6d -C extra-filename=-a6d831398f16df6d --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + Compiling scopeguard v1.2.0 + Running rustc --crate-name scopeguard --edition=2015 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/scopeguard-1.2.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "use_std"))' -C metadata=d17dfe74cbdea182 -C extra-filename=-d17dfe74cbdea182 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + Running rustc --crate-name bytes --edition=2018 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/bytes-1.5.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "serde", "std"))' -C metadata=c7d161ec1cfef0e0 -C extra-filename=-c7d161ec1cfef0e0 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --cap-lints allow + Compiling paste v1.0.14 + Running rustc --crate-name build_script_build --edition=2018 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/paste-1.0.14/build.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C embed-bitcode=no -C debug-assertions=off --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=e367352717e6e1f5 -C extra-filename=-e367352717e6e1f5 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/release/build/paste-e367352717e6e1f5 -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --cap-lints allow + Compiling anyhow v1.0.79 + Running rustc --crate-name build_script_build --edition=2018 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/anyhow-1.0.79/build.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("backtrace", "default", "std"))' -C metadata=b559790219e1e303 -C extra-filename=-b559790219e1e303 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/release/build/anyhow-b559790219e1e303 -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --cap-lints allow + Compiling futures-core v0.3.30 + Running rustc --crate-name futures_core --edition=2018 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/futures-core-0.3.30/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="alloc"' --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "cfg-target-has-atomic", "default", "portable-atomic", "std", "unstable"))' -C metadata=176ca2b680ef1303 -C extra-filename=-176ca2b680ef1303 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + Running /opt/conda/conda-bld/viguno_1733976374700/work/target/release/build/paste-e367352717e6e1f5/build-script-build + Running rustc --crate-name lock_api --edition=2018 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/lock_api-0.4.11/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="atomic_usize"' --cfg 'feature="default"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("arc_lock", "atomic_usize", "default", "nightly", "owning_ref", "serde"))' -C metadata=4a63c0d1e03325a8 -C extra-filename=-4a63c0d1e03325a8 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern scopeguard=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libscopeguard-d17dfe74cbdea182.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib --cfg has_const_fn_trait_bound + Running rustc --crate-name hashbrown --edition=2021 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/hashbrown-0.14.3/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="ahash"' --cfg 'feature="allocator-api2"' --cfg 'feature="default"' --cfg 'feature="inline-more"' --cfg 'feature="raw"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("ahash", "alloc", "allocator-api2", "compiler_builtins", "core", "default", "equivalent", "inline-more", "nightly", "raw", "rayon", "rkyv", "rustc-dep-of-std", "rustc-internal-api", "serde"))' -C metadata=6682795449dd8644 -C extra-filename=-6682795449dd8644 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern ahash=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libahash-ad70461c301afbb5.rmeta --extern allocator_api2=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/liballocator_api2-a6d831398f16df6d.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + Running rustc --crate-name generic_array --edition=2015 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/generic-array-0.14.7/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="more_lengths"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("more_lengths", "serde", "zeroize"))' -C metadata=80454acf9a69a709 -C extra-filename=-80454acf9a69a709 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern typenum=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libtypenum-560e6c6d1854511b.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib --cfg relaxed_coherence + Running rustc --crate-name thiserror --edition=2021 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/thiserror-1.0.56/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C embed-bitcode=no -C debug-assertions=off --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=4bb2903833202197 -C extra-filename=-4bb2903833202197 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern thiserror_impl=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps/libthiserror_impl-48fd3361c0ea893f.so --cap-lints allow + Running rustc --crate-name parking_lot_core --edition=2018 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/parking_lot_core-0.9.9/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("backtrace", "deadlock_detection", "nightly", "petgraph", "thread-id"))' -C metadata=eaf12c11a0f270c7 -C extra-filename=-eaf12c11a0f270c7 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern cfg_if=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libcfg_if-986e17e20ae237e0.rmeta --extern libc=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/liblibc-ec074d56dfa3058f.rmeta --extern smallvec=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libsmallvec-6e91d5a0959d7dfa.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + Compiling tracing-attributes v0.1.27 + Running rustc --crate-name tracing_attributes --edition=2018 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/tracing-attributes-0.1.27/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type proc-macro --emit=dep-info,link -C prefer-dynamic -C embed-bitcode=no -C debug-assertions=off --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("async-await"))' -C metadata=972df0ddbf0268ae -C extra-filename=-972df0ddbf0268ae --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern proc_macro2=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps/libproc_macro2-06f0cd92858008f8.rlib --extern quote=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps/libquote-388a27b5796448f9.rlib --extern syn=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps/libsyn-a41cf051db8ae11f.rlib --extern proc_macro --cap-lints allow + Running /opt/conda/conda-bld/viguno_1733976374700/work/target/release/build/typenum-4b7e2c0aa846ee3a/build-script-main + Compiling powerfmt v0.2.0 + Running rustc --crate-name powerfmt --edition=2021 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/powerfmt-0.2.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "default", "macros", "std"))' -C metadata=97b0607a1e543e7d -C extra-filename=-97b0607a1e543e7d --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + Compiling crossbeam-utils v0.8.20 + Running rustc --crate-name build_script_build --edition=2021 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/crossbeam-utils-0.8.20/build.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type bin --emit=dep-info,link -C embed-bitcode=no --warn=unexpected_cfgs -C debug-assertions=off --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "loom", "nightly", "std"))' -C metadata=d7c0e864ac308112 -C extra-filename=-d7c0e864ac308112 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/release/build/crossbeam-utils-d7c0e864ac308112 -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --cap-lints allow + Compiling time-core v0.1.2 + Running rustc --crate-name time_core --edition=2021 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/time-core-0.1.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C embed-bitcode=no -C debug-assertions=off --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=199d1e0af0b85f6a -C extra-filename=-199d1e0af0b85f6a --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --cap-lints allow + Running /opt/conda/conda-bld/viguno_1733976374700/work/target/release/build/crossbeam-utils-d7c0e864ac308112/build-script-build + Running rustc --crate-name typenum --edition=2018 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/typenum-1.17.0/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C embed-bitcode=no -C debug-assertions=off --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("const-generics", "force_unix_path_separator", "i128", "no_std", "scale-info", "scale_info", "strict"))' -C metadata=39d2ceb508e87dc2 -C extra-filename=-39d2ceb508e87dc2 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --cap-lints allow + Compiling time-macros v0.2.16 + Running rustc --crate-name time_macros --edition=2021 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/time-macros-0.2.16/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type proc-macro --emit=dep-info,link -C prefer-dynamic -C embed-bitcode=no --warn=variant-size-differences '--warn=clippy::use-debug' '--warn=clippy::unwrap-used' '--warn=clippy::unwrap-in-result' --warn=unused-tuple-struct-fields --warn=unused-qualifications --warn=unused-lifetimes --warn=unused-import-braces --warn=unused --deny=unstable-syntax-pre-expansion --deny=unsafe-op-in-unsafe-fn --warn=unreachable-pub '--warn=clippy::unnested-or-patterns' --deny=unnameable-test-items '--warn=clippy::uninlined-format-args' '--warn=clippy::unimplemented' '--warn=rustdoc::unescaped-backticks' '--deny=clippy::undocumented-unsafe-blocks' --deny=unconditional-recursion --warn=trivial-numeric-casts --warn=trivial-casts '--warn=clippy::todo' --deny=temporary-cstring-as-ptr --deny=suspicious-double-ref-op '--deny=clippy::std-instead-of-core' --warn=single-use-lifetimes '--warn=clippy::semicolon-outside-block' '--warn=rustdoc::private-doc-tests' '--warn=clippy::print-stdout' --deny=overlapping-range-endpoints --deny=opaque-hidden-inferred-bound '--warn=clippy::obfuscated-if-else' '--warn=clippy::nursery' --warn=noop-method-call --deny=non-ascii-idents --deny=named-arguments-used-positionally '--warn=clippy::missing-enforced-import-renames' '--warn=clippy::missing-docs-in-private-items' --warn=missing-docs --warn=missing-debug-implementations --warn=missing-copy-implementations --warn=missing-abi --warn=meta-variable-misuse '--warn=clippy::manual-let-else' --warn=macro-use-extern-crate --warn=let-underscore --warn=keyword-idents --deny=invalid-value --deny=invalid-reference-casting --deny=invalid-nan-comparisons --deny=invalid-macro-export-arguments --deny=invalid-from-utf8 --deny=improper-ctypes-definitions --deny=improper-ctypes --deny=hidden-glob-reexports '--warn=clippy::get-unwrap' --deny=future-incompatible '--warn=clippy::explicit-auto-deref' --deny=drop-bounds --deny=deref-nullptr '--warn=clippy::decimal-literal-representation' '--warn=clippy::dbg-macro' --deny=const-item-mutation --deny=clashing-extern-declarations --deny=ambiguous-glob-reexports '--deny=clippy::alloc-instead-of-core' '--warn=clippy::all' --warn=unstable-name-collisions '--allow=clippy::redundant-pub-crate' '--allow=clippy::option-if-let-else' -C debug-assertions=off --cfg 'feature="formatting"' --cfg 'feature="parsing"' --cfg 'feature="serde"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("formatting", "large-dates", "parsing", "serde"))' -C metadata=d071eeb11aa08855 -C extra-filename=-d071eeb11aa08855 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern time_core=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps/libtime_core-199d1e0af0b85f6a.rlib --extern proc_macro --cap-lints allow + Compiling parking_lot v0.12.1 + Running rustc --crate-name parking_lot --edition=2018 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/parking_lot-0.12.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("arc_lock", "deadlock_detection", "default", "hardware-lock-elision", "nightly", "owning_ref", "send_guard", "serde"))' -C metadata=41225c4132ae8d22 -C extra-filename=-41225c4132ae8d22 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern lock_api=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/liblock_api-4a63c0d1e03325a8.rmeta --extern parking_lot_core=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libparking_lot_core-eaf12c11a0f270c7.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + Compiling deranged v0.3.10 + Running rustc --crate-name deranged --edition=2021 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/deranged-0.3.10/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="alloc"' --cfg 'feature="powerfmt"' --cfg 'feature="serde"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "default", "num", "powerfmt", "quickcheck", "rand", "serde", "std"))' -C metadata=58426a89c8939ff7 -C extra-filename=-58426a89c8939ff7 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern powerfmt=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libpowerfmt-97b0607a1e543e7d.rmeta --extern serde=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libserde-9b82cf4ab88b9921.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + Compiling tracing v0.1.40 + Running rustc --crate-name tracing --edition=2018 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/tracing-0.1.40/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="attributes"' --cfg 'feature="default"' --cfg 'feature="log"' --cfg 'feature="std"' --cfg 'feature="tracing-attributes"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("async-await", "attributes", "default", "log", "log-always", "max_level_debug", "max_level_error", "max_level_info", "max_level_off", "max_level_trace", "max_level_warn", "release_max_level_debug", "release_max_level_error", "release_max_level_info", "release_max_level_off", "release_max_level_trace", "release_max_level_warn", "std", "tracing-attributes", "valuable"))' -C metadata=528b773c520af566 -C extra-filename=-528b773c520af566 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern log=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/liblog-34439240624e14af.rmeta --extern pin_project_lite=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libpin_project_lite-5c31e549c0f92c50.rmeta --extern tracing_attributes=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps/libtracing_attributes-972df0ddbf0268ae.so --extern tracing_core=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libtracing_core-0e29d5b655035162.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + Running rustc --crate-name paste --edition=2018 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/paste-1.0.14/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type proc-macro --emit=dep-info,link -C prefer-dynamic -C embed-bitcode=no -C debug-assertions=off --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=5ddd0d20007d965c -C extra-filename=-5ddd0d20007d965c --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern proc_macro --cap-lints allow + Compiling mio v0.8.10 + Running rustc --crate-name mio --edition=2018 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/mio-0.8.10/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="default"' --cfg 'feature="log"' --cfg 'feature="net"' --cfg 'feature="os-ext"' --cfg 'feature="os-poll"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "log", "net", "os-ext", "os-poll"))' -C metadata=dc3676ffeaa57a19 -C extra-filename=-dc3676ffeaa57a19 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern libc=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/liblibc-ec074d56dfa3058f.rmeta --extern log=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/liblog-34439240624e14af.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + Running /opt/conda/conda-bld/viguno_1733976374700/work/target/release/build/generic-array-c382c9c5240df74a/build-script-build + Compiling rand_core v0.6.4 + Running rustc --crate-name rand_core --edition=2018 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/rand_core-0.6.4/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="alloc"' --cfg 'feature="getrandom"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "getrandom", "serde", "serde1", "std"))' -C metadata=02bcacb07e8f335a -C extra-filename=-02bcacb07e8f335a --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern getrandom=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libgetrandom-efa3f2a703280fbb.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + Compiling socket2 v0.5.5 + Running rustc --crate-name socket2 --edition=2021 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/socket2-0.5.5/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="all"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("all"))' -C metadata=b5002db1498f6dfc -C extra-filename=-b5002db1498f6dfc --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern libc=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/liblibc-ec074d56dfa3058f.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + Compiling signal-hook-registry v1.4.1 + Running rustc --crate-name signal_hook_registry --edition=2015 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/signal-hook-registry-1.4.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=f621bd917a7b5b59 -C extra-filename=-f621bd917a7b5b59 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern libc=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/liblibc-ec074d56dfa3058f.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + Running rustc --crate-name time_core --edition=2021 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/time-core-0.1.2/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values())' -C metadata=208d788887c4ec4b -C extra-filename=-208d788887c4ec4b --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + Compiling ppv-lite86 v0.2.17 + Running rustc --crate-name ppv_lite86 --edition=2018 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/ppv-lite86-0.2.17/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="simd"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "no_simd", "simd", "std"))' -C metadata=f623adcbb87e0765 -C extra-filename=-f623adcbb87e0765 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + Compiling bitflags v2.4.1 + Running rustc --crate-name bitflags --edition=2021 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/bitflags-2.4.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("arbitrary", "bytemuck", "compiler_builtins", "core", "example_generated", "rustc-dep-of-std", "serde", "std"))' -C metadata=81233c65a23ea8e6 -C extra-filename=-81233c65a23ea8e6 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + Compiling rand_chacha v0.3.1 + Running rustc --crate-name rand_chacha --edition=2018 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/rand_chacha-0.3.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "serde", "serde1", "simd", "std"))' -C metadata=212add80515c634f -C extra-filename=-212add80515c634f --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern ppv_lite86=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libppv_lite86-f623adcbb87e0765.rmeta --extern rand_core=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/librand_core-02bcacb07e8f335a.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + Compiling tokio v1.35.1 + Running rustc --crate-name tokio --edition=2021 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/tokio-1.35.1/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --cfg 'feature="bytes"' --cfg 'feature="default"' --cfg 'feature="io-util"' --cfg 'feature="libc"' --cfg 'feature="mio"' --cfg 'feature="net"' --cfg 'feature="parking_lot"' --cfg 'feature="rt"' --cfg 'feature="signal"' --cfg 'feature="signal-hook-registry"' --cfg 'feature="socket2"' --cfg 'feature="sync"' --cfg 'feature="time"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("bytes", "default", "fs", "full", "io-std", "io-util", "libc", "macros", "mio", "net", "num_cpus", "parking_lot", "process", "rt", "rt-multi-thread", "signal", "signal-hook-registry", "socket2", "sync", "test-util", "time", "tokio-macros", "tracing", "windows-sys"))' -C metadata=bd69097fbdaff290 -C extra-filename=-bd69097fbdaff290 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern bytes=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libbytes-4449d9e38e2ec426.rmeta --extern libc=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/liblibc-ec074d56dfa3058f.rmeta --extern mio=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libmio-dc3676ffeaa57a19.rmeta --extern parking_lot=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libparking_lot-41225c4132ae8d22.rmeta --extern pin_project_lite=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libpin_project_lite-5c31e549c0f92c50.rmeta --extern signal_hook_registry=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libsignal_hook_registry-f621bd917a7b5b59.rmeta --extern socket2=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libsocket2-b5002db1498f6dfc.rmeta --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + Compiling time v0.3.31 + Running rustc --crate-name time --edition=2021 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/time-0.3.31/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --warn=variant-size-differences '--warn=clippy::use-debug' '--warn=clippy::unwrap-used' '--warn=clippy::unwrap-in-result' --warn=unused-tuple-struct-fields --warn=unused-qualifications --warn=unused-lifetimes --warn=unused-import-braces --warn=unused --deny=unstable-syntax-pre-expansion --deny=unsafe-op-in-unsafe-fn --warn=unreachable-pub '--warn=clippy::unnested-or-patterns' --deny=unnameable-test-items '--warn=clippy::uninlined-format-args' '--warn=clippy::unimplemented' '--warn=rustdoc::unescaped-backticks' '--deny=clippy::undocumented-unsafe-blocks' --deny=unconditional-recursion --warn=trivial-numeric-casts --warn=trivial-casts '--warn=clippy::todo' --deny=temporary-cstring-as-ptr --deny=suspicious-double-ref-op '--deny=clippy::std-instead-of-core' --warn=single-use-lifetimes '--warn=clippy::semicolon-outside-block' '--warn=rustdoc::private-doc-tests' '--warn=clippy::print-stdout' --deny=overlapping-range-endpoints --deny=opaque-hidden-inferred-bound '--warn=clippy::obfuscated-if-else' '--warn=clippy::nursery' --warn=noop-method-call --deny=non-ascii-idents --deny=named-arguments-used-positionally '--warn=clippy::missing-enforced-import-renames' '--warn=clippy::missing-docs-in-private-items' --warn=missing-docs --warn=missing-debug-implementations --warn=missing-copy-implementations --warn=missing-abi --warn=meta-variable-misuse '--warn=clippy::manual-let-else' --warn=macro-use-extern-crate --warn=let-underscore --warn=keyword-idents --deny=invalid-value --deny=invalid-reference-casting --deny=invalid-nan-comparisons --deny=invalid-macro-export-arguments --deny=invalid-from-utf8 --deny=improper-ctypes-definitions --deny=improper-ctypes --deny=hidden-glob-reexports '--warn=clippy::get-unwrap' --deny=future-incompatible '--warn=clippy::explicit-auto-deref' --deny=drop-bounds --deny=deref-nullptr '--warn=clippy::decimal-literal-representation' '--warn=clippy::dbg-macro' --deny=const-item-mutation --deny=clashing-extern-declarations --deny=ambiguous-glob-reexports '--deny=clippy::alloc-instead-of-core' '--warn=clippy::all' --warn=unstable-name-collisions '--allow=clippy::redundant-pub-crate' '--allow=clippy::option-if-let-else' --cfg 'feature="alloc"' --cfg 'feature="default"' --cfg 'feature="formatting"' --cfg 'feature="macros"' --cfg 'feature="parsing"' --cfg 'feature="serde"' --cfg 'feature="serde-well-known"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "default", "formatting", "large-dates", "local-offset", "macros", "parsing", "quickcheck", "rand", "serde", "serde-human-readable", "serde-well-known", "std", "wasm-bindgen"))' -C metadata=f012a617b8ed950a -C extra-filename=-f012a617b8ed950a --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern deranged=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libderanged-58426a89c8939ff7.rmeta --extern itoa=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libitoa-67dbbcec1ea07cfe.rmeta --extern powerfmt=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libpowerfmt-97b0607a1e543e7d.rmeta --extern serde=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libserde-9b82cf4ab88b9921.rmeta --extern time_core=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libtime_core-208d788887c4ec4b.rmeta --extern time_macros=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps/libtime_macros-d071eeb11aa08855.so --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + Running rustc --crate-name generic_array --edition=2015 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/generic-array-0.14.7/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C embed-bitcode=no -C debug-assertions=off --cfg 'feature="more_lengths"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("more_lengths", "serde", "zeroize"))' -C metadata=53c3478d463ae182 -C extra-filename=-53c3478d463ae182 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern typenum=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps/libtypenum-39d2ceb508e87dc2.rmeta --cap-lints allow --cfg relaxed_coherence + error[E0282]: type annotations needed for Box<_> + --> /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/time-0.3.31/src/format_description/parse/mod.rs:83:9 + | + 83 | let items = format_items + | ^^^^^ + ... + 86 | Ok(items.into()) + | ---- type must be known at this point + | + = note: this is an inference error on crate time caused by an API change in Rust 1.80.0; update time to version >=0.3.35 by calling cargo update + + Running rustc --crate-name crossbeam_utils --edition=2021 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/crossbeam-utils-0.8.20/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --warn=unexpected_cfgs --cfg 'feature="default"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("default", "loom", "nightly", "std"))' -C metadata=f0c848798ba22ca2 -C extra-filename=-f0c848798ba22ca2 --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib --check-cfg 'cfg(crossbeam_no_atomic,crossbeam_sanitize_thread)' + For more information about this error, try rustc --explain E0282. + error: could not compile time (lib) due to 1 previous error + + Caused by: + process didn't exit successfully: rustc --crate-name time --edition=2021 /opt/conda/conda-bld/viguno_1733976374700/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/time-0.3.31/src/lib.rs --error-format=json --json=diagnostic-rendered-ansi,artifacts,future-incompat --crate-type lib --emit=dep-info,metadata,link -C opt-level=3 -C embed-bitcode=no --warn=variant-size-differences '--warn=clippy::use-debug' '--warn=clippy::unwrap-used' '--warn=clippy::unwrap-in-result' --warn=unused-tuple-struct-fields --warn=unused-qualifications --warn=unused-lifetimes --warn=unused-import-braces --warn=unused --deny=unstable-syntax-pre-expansion --deny=unsafe-op-in-unsafe-fn --warn=unreachable-pub '--warn=clippy::unnested-or-patterns' --deny=unnameable-test-items '--warn=clippy::uninlined-format-args' '--warn=clippy::unimplemented' '--warn=rustdoc::unescaped-backticks' '--deny=clippy::undocumented-unsafe-blocks' --deny=unconditional-recursion --warn=trivial-numeric-casts --warn=trivial-casts '--warn=clippy::todo' --deny=temporary-cstring-as-ptr --deny=suspicious-double-ref-op '--deny=clippy::std-instead-of-core' --warn=single-use-lifetimes '--warn=clippy::semicolon-outside-block' '--warn=rustdoc::private-doc-tests' '--warn=clippy::print-stdout' --deny=overlapping-range-endpoints --deny=opaque-hidden-inferred-bound '--warn=clippy::obfuscated-if-else' '--warn=clippy::nursery' --warn=noop-method-call --deny=non-ascii-idents --deny=named-arguments-used-positionally '--warn=clippy::missing-enforced-import-renames' '--warn=clippy::missing-docs-in-private-items' --warn=missing-docs --warn=missing-debug-implementations --warn=missing-copy-implementations --warn=missing-abi --warn=meta-variable-misuse '--warn=clippy::manual-let-else' --warn=macro-use-extern-crate --warn=let-underscore --warn=keyword-idents --deny=invalid-value --deny=invalid-reference-casting --deny=invalid-nan-comparisons --deny=invalid-macro-export-arguments --deny=invalid-from-utf8 --deny=improper-ctypes-definitions --deny=improper-ctypes --deny=hidden-glob-reexports '--warn=clippy::get-unwrap' --deny=future-incompatible '--warn=clippy::explicit-auto-deref' --deny=drop-bounds --deny=deref-nullptr '--warn=clippy::decimal-literal-representation' '--warn=clippy::dbg-macro' --deny=const-item-mutation --deny=clashing-extern-declarations --deny=ambiguous-glob-reexports '--deny=clippy::alloc-instead-of-core' '--warn=clippy::all' --warn=unstable-name-collisions '--allow=clippy::redundant-pub-crate' '--allow=clippy::option-if-let-else' --cfg 'feature="alloc"' --cfg 'feature="default"' --cfg 'feature="formatting"' --cfg 'feature="macros"' --cfg 'feature="parsing"' --cfg 'feature="serde"' --cfg 'feature="serde-well-known"' --cfg 'feature="std"' --check-cfg 'cfg(docsrs)' --check-cfg 'cfg(feature, values("alloc", "default", "formatting", "large-dates", "local-offset", "macros", "parsing", "quickcheck", "rand", "serde", "serde-human-readable", "serde-well-known", "std", "wasm-bindgen"))' -C metadata=f012a617b8ed950a -C extra-filename=-f012a617b8ed950a --out-dir /opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps --target aarch64-unknown-linux-gnu -C linker=/opt/conda/conda-bld/viguno_1733976374700/_build_env/bin/aarch64-conda-linux-gnu-cc -C strip=debuginfo -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps -L dependency=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps --extern deranged=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libderanged-58426a89c8939ff7.rmeta --extern itoa=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libitoa-67dbbcec1ea07cfe.rmeta --extern powerfmt=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libpowerfmt-97b0607a1e543e7d.rmeta --extern serde=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libserde-9b82cf4ab88b9921.rmeta --extern time_core=/opt/conda/conda-bld/viguno_1733976374700/work/target/aarch64-unknown-linux-gnu/release/deps/libtime_core-208d788887c4ec4b.rmeta --extern time_macros=/opt/conda/conda-bld/viguno_1733976374700/work/target/release/deps/libtime_macros-d071eeb11aa08855.so --cap-lints allow -C link-arg=-Wl,-rpath-link,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib -C link-arg=-Wl,-rpath,/opt/conda/conda-bld/viguno_1733976374700/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib (exit status: 1) + warning: build failed, waiting for other jobs to finish... + error: failed to compile viguno v0.3.2 (/opt/conda/conda-bld/viguno_1733976374700/work), intermediate artifacts can be found at /opt/conda/conda-bld/viguno_1733976374700/work/target. + To reuse those artifacts with a future compilation, set the environment variable CARGO_TARGET_DIR to that path. + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/viguno_1733976374700/work/conda_build.sh']' returned non-zero exit status 101. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/viguno_1733976374700/work/conda_build.sh']' returned non-zero exit status 101. +# Last 100 lines of the build log. diff --git a/recipes/viguno/meta.yaml b/recipes/viguno/meta.yaml index 2ac8badcffa71..9c5777a8e5f9e 100644 --- a/recipes/viguno/meta.yaml +++ b/recipes/viguno/meta.yaml @@ -7,7 +7,7 @@ package: build: skip: True # [osx] - number: 1 + number: 2 run_exports: - {{ pin_subpackage("viguno", max_pin="x.x") }} diff --git a/recipes/viral_consensus/build_failure.linux-64.yaml b/recipes/viral_consensus/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..d098d1cd2b9bd --- /dev/null +++ b/recipes/viral_consensus/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: f71a1e5fc2f6a5423c5dc6905f8425c18107d31ab3f8ae869a5f2ddb6ce2a8c1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + summary: Fast viral consensus genome reconstruction + extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + copy_test_source_files: true + final: true + identifiers: + - biotools:viral_consensus + - doi:10.1093/bioinformatics/btad317 + - doi:10.1093/bioinformatics/btae018 + maintainers: + - niemasd + + + source tree in: /opt/conda/conda-bld/viral_consensus_1734162603766/work + export PREFIX=/opt/conda/conda-bld/viral_consensus_1734162603766/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/conda/conda-bld/viral_consensus_1734162603766/_build_env + export SRC_DIR=/opt/conda/conda-bld/viral_consensus_1734162603766/work + INFO: activate-binutils_linux-64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip + INFO: activate-gcc_linux-64.sh made the following environmental changes: + BUILD=x86_64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc + CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/viral_consensus-0.0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/viral_consensus-0.0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/viral_consensus-0.0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/viral_consensus-0.0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + make -j4 CXX=/opt/conda/conda-bld/viral_consensus_1734162603766/_build_env/bin/x86_64-conda-linux-gnu-c 'INCLUDE=-I/opt/conda/conda-bld/viral_consensus_1734162603766/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include -Ihtslib' 'RELEASEFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/conda-bld/viral_consensus_1734162603766/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/conda-bld/viral_consensus_1734162603766/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include -fdebug-prefix-map=/opt/conda/conda-bld/viral_consensus_1734162603766/work=/usr/local/src/conda/viral_consensus-0.0.6 -fdebug-prefix-map=/opt/conda/conda-bld/viral_consensus_1734162603766/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/viral_consensus_1734162603766/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib -Wl,-rpath-link,/opt/conda/conda-bld/viral_consensus_1734162603766/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib -L/opt/conda/conda-bld/viral_consensus_1734162603766/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' + $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/viral_consensus-0.0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -I$PREFIX/include -Ihtslib -o viral_consensus main.cpp common.cpp argparse.cpp count.cpp fasta.cpp primer.cpp -lhts -llzma -lbz2 -lz -lcurl -pthread + /opt/conda/conda-bld/viral_consensus_1734162603766/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -llzma: No such file or directory + collect2: error: ld returned 1 exit status + make: *** [Makefile:22: viral_consensus] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/viral_consensus_1734162603766/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/viral_consensus_1734162603766/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/viral_consensus/build_failure.linux-aarch64.yaml b/recipes/viral_consensus/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..185eee5afad1f --- /dev/null +++ b/recipes/viral_consensus/build_failure.linux-aarch64.yaml @@ -0,0 +1,104 @@ +recipe_sha: f71a1e5fc2f6a5423c5dc6905f8425c18107d31ab3f8ae869a5f2ddb6ce2a8c1 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE + summary: Fast viral consensus genome reconstruction + extra: + additional-platforms: + - linux-aarch64 + - osx-arm64 + copy_test_source_files: true + final: true + identifiers: + - biotools:viral_consensus + - doi:10.1093/bioinformatics/btad317 + - doi:10.1093/bioinformatics/btae018 + maintainers: + - niemasd + + + source tree in: /opt/conda/conda-bld/viral_consensus_1734391606751/work + export PREFIX=/opt/conda/conda-bld/viral_consensus_1734391606751/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho + export BUILD_PREFIX=/opt/conda/conda-bld/viral_consensus_1734391606751/_build_env + export SRC_DIR=/opt/conda/conda-bld/viral_consensus_1734391606751/work + INFO: activate-binutils_linux-aarch64.sh made the following environmental changes: + ADDR2LINE=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-addr2line + AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ar + AS=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-as + CXXFILT=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cfilt + DWP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-dwp + ELFEDIT=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-elfedit + GPROF=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gprof + LD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld + LD_GOLD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld.gold + NM=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-nm + OBJCOPY=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-objcopy + OBJDUMP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-objdump + RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib + READELF=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-readelf + SIZE=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-size + STRINGS=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strings + STRIP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strip + INFO: activate-gcc_linux-aarch64.sh made the following environmental changes: + BUILD=aarch64-conda-linux-gnu + CC=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc + CC_FOR_BUILD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc + CFLAGS=-ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/viral_consensus-0.0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot/usr + CONDA_BUILD_SYSROOT=$BUILD_PREFIX/aarch64-conda-linux-gnu/sysroot + CONDA_TOOLCHAIN_BUILD=aarch64-conda-linux-gnu + CONDA_TOOLCHAIN_HOST=aarch64-conda-linux-gnu + CPP=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cpp + CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include + DEBUG_CFLAGS=-ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/viral_consensus-0.0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib + HOST=aarch64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_aarch64_conda_cos7_linux_gnu + build_alias=aarch64-conda-linux-gnu + host_alias=aarch64-conda-linux-gnu + -BUILD=aarch64-conda_cos7-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-aarch64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/viral_consensus-0.0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/viral_consensus-0.0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-g + make -j4 CXX=/opt/conda/conda-bld/viral_consensus_1734391606751/_build_env/bin/aarch64-conda-linux-gnu-c 'INCLUDE=-I/opt/conda/conda-bld/viral_consensus_1734391606751/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include -Ihtslib' 'RELEASEFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/conda-bld/viral_consensus_1734391606751/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem /opt/conda/conda-bld/viral_consensus_1734391606751/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/include -fdebug-prefix-map=/opt/conda/conda-bld/viral_consensus_1734391606751/work=/usr/local/src/conda/viral_consensus-0.0.6 -fdebug-prefix-map=/opt/conda/conda-bld/viral_consensus_1734391606751/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/conda-bld/viral_consensus_1734391606751/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib -Wl,-rpath-link,/opt/conda/conda-bld/viral_consensus_1734391606751/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib -L/opt/conda/conda-bld/viral_consensus_1734391606751/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib' + $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/viral_consensus-0.0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -I$PREFIX/include -Ihtslib -o viral_consensus main.cpp common.cpp argparse.cpp count.cpp fasta.cpp primer.cpp -lhts -llzma -lbz2 -lz -lcurl -pthread + /opt/conda/conda-bld/viral_consensus_1734391606751/_build_env/bin/../lib/gcc/aarch64-conda-linux-gnu/13.3.0/../../../../aarch64-conda-linux-gnu/bin/ld: cannot find -llzma: No such file or directory + collect2: error: ld returned 1 exit status + make: *** [Makefile:22: viral_consensus] Error 1 + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/viral_consensus_1734391606751/work/conda_build.sh']' returned non-zero exit status 2. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/viral_consensus_1734391606751/work/conda_build.sh']' returned non-zero exit status 2. +# Last 100 lines of the build log. diff --git a/recipes/viral_consensus/meta.yaml b/recipes/viral_consensus/meta.yaml index 216948ec4fd42..e0bdb4c052689 100644 --- a/recipes/viral_consensus/meta.yaml +++ b/recipes/viral_consensus/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage('viral_consensus', max_pin="x.x.x") }} diff --git a/recipes/virdig/build_failure.linux-64.yaml b/recipes/virdig/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..6b027670e5653 --- /dev/null +++ b/recipes/virdig/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 7bdb9a5679a56f7b7a59e7dc1c3fd0bab701a8cc2c800bd4b9d8a061fc3e2e9d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/virdig_1734148156309/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.43-h4bf12b8_2 conda-forge + binutils_linux-64: 2.43-h4852527_2 conda-forge + boost: 1.85.0-h9cebb41_4 conda-forge + bzip2: 1.0.8-h4bc722e_7 conda-forge + ca-certificates: 2024.8.30-hbcca054_0 conda-forge + gcc_impl_linux-64: 13.3.0-hfea6d02_1 conda-forge + gcc_linux-64: 13.3.0-hc28eda2_7 conda-forge + gxx_impl_linux-64: 13.3.0-hdbfa832_1 conda-forge + gxx_linux-64: 13.3.0-h6834431_7 conda-forge + icu: 75.1-he02047a_0 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libblas: 3.9.0-25_linux64_openblas conda-forge + libboost: 1.85.0-h0ccab89_4 conda-forge + libboost-devel: 1.85.0-h00ab1b0_4 conda-forge + libboost-headers: 1.85.0-ha770c72_4 conda-forge + libboost-python: 1.85.0-py312hf74af30_4 conda-forge + libboost-python-devel: 1.85.0-py312h9cebb41_4 conda-forge + libcblas: 3.9.0-25_linux64_openblas conda-forge + libexpat: 2.6.4-h5888daf_0 conda-forge + libffi: 3.4.2-h7f98852_5 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libgcc-ng: 14.2.0-h69a702a_1 conda-forge + libgfortran: 14.2.0-h69a702a_1 conda-forge + libgfortran5: 14.2.0-hd5240d6_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + liblapack: 3.9.0-25_linux64_openblas conda-forge + liblzma: 5.6.3-hb9d3cd8_1 conda-forge + liblzma-devel: 5.6.3-hb9d3cd8_1 conda-forge + libnsl: 2.0.1-hd590300_0 conda-forge + libopenblas: 0.3.28-pthreads_h94d23a6_1 conda-forge + libsanitizer: 13.3.0-heb74ff8_1 conda-forge + libsqlite: 3.47.2-hee588c1_0 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + libstdcxx-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libstdcxx-ng: 14.2.0-h4852527_1 conda-forge + libuuid: 2.38.1-h0b41bf4_0 conda-forge + libxcrypt: 4.4.36-hd590300_1 conda-forge + libzlib: 1.3.1-hb9d3cd8_2 conda-forge + make: 4.4.1-hb9d3cd8_2 conda-forge + ncurses: 6.5-he02047a_1 conda-forge + numpy: 2.2.0-py312h7e784f5_0 conda-forge + openssl: 3.4.0-hb9d3cd8_0 conda-forge + pip: 24.3.1-pyh8b19718_0 conda-forge + python: 3.12.8-h9e4cc4f_1_cpython conda-forge + python_abi: 3.12-5_cp312 conda-forge + readline: 8.2-h8228510_1 conda-forge + setuptools: 75.6.0-pyhff2d567_1 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tk: 8.6.13-noxft_h4845f30_101 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + wheel: 0.45.1-pyhd8ed1ab_1 conda-forge + xz: 5.6.3-hbcc6ac9_1 conda-forge + xz-gpl-tools: 5.6.3-hbcc6ac9_1 conda-forge + xz-tools: 5.6.3-hb9d3cd8_1 conda-forge + zstd: 1.5.6-ha6fb4c9_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: v1.0.0_9ffd628fd1.tar.gz + Downloading https://github.com/Limh616/VirDiG/archive/refs/tags/v1.0.0.tar.gz + Success + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 125, in download_to_cache + raise RuntimeError( + RuntimeError: SHA256 mismatch: 'cb9ce7fc5ced952f7af21776ea7b68bd2866af05b0f0727e8237966888c131c4' != '9ffd628fd1c22dd86a1e9e0e4c5b543334a99f0fc6dec56bb1f741e2fe8a32b1' +# Last 100 lines of the build log. diff --git a/recipes/virdig/build_failure.osx-64.yaml b/recipes/virdig/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..7218ae61a5817 --- /dev/null +++ b/recipes/virdig/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: 7bdb9a5679a56f7b7a59e7dc1c3fd0bab701a8cc2c800bd4b9d8a061fc3e2e9d # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (local): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (local): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/virdig_1734189202733/_build_env + + + The following NEW packages will be INSTALLED: + + boost: 1.85.0-h0be7463_4 conda-forge + bzip2: 1.0.8-hfdf4475_7 conda-forge + ca-certificates: 2024.8.30-h8857fd0_0 conda-forge + cctools_osx-64: 1010.6-h00edd4c_2 conda-forge + clang: 18.1.8-default_h179603d_5 conda-forge + clang-18: 18.1.8-default_h0c94c6a_5 conda-forge + clang_impl_osx-64: 18.1.8-h6a44ed1_23 conda-forge + clang_osx-64: 18.1.8-h7e5c614_23 conda-forge + clangxx: 18.1.8-default_h179603d_5 conda-forge + clangxx_impl_osx-64: 18.1.8-h4b7810f_23 conda-forge + clangxx_osx-64: 18.1.8-h7e5c614_23 conda-forge + compiler-rt: 18.1.8-h1020d70_1 conda-forge + compiler-rt_osx-64: 18.1.8-hf2b8a54_1 conda-forge + icu: 75.1-h120a0e1_0 conda-forge + ld64_osx-64: 951.9-hc8d1a19_2 conda-forge + libblas: 3.9.0-25_osx64_openblas conda-forge + libboost: 1.85.0-hcca3243_4 conda-forge + libboost-devel: 1.85.0-h2b186f8_4 conda-forge + libboost-headers: 1.85.0-h694c41f_4 conda-forge + libboost-python: 1.85.0-py312h44e70fa_4 conda-forge + libboost-python-devel: 1.85.0-py312h0be7463_4 conda-forge + libcblas: 3.9.0-25_osx64_openblas conda-forge + libclang-cpp18.1: 18.1.8-default_h0c94c6a_5 conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libcxx-devel: 18.1.8-h7c275be_7 conda-forge + libexpat: 2.6.4-h240833e_0 conda-forge + libffi: 3.4.2-h0d85af4_5 conda-forge + libgfortran: 5.0.0-13_2_0_h97931a8_3 conda-forge + libgfortran5: 13.2.0-h2873a65_3 conda-forge + libiconv: 1.17-hd75f5a5_2 conda-forge + liblapack: 3.9.0-25_osx64_openblas conda-forge + libllvm18: 18.1.8-h9ce406d_2 conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + liblzma-devel: 5.6.3-hd471939_1 conda-forge + libopenblas: 0.3.28-openmp_hbf64a52_1 conda-forge + libsqlite: 3.47.2-hdb6dae5_0 conda-forge + libxml2: 2.13.5-hebb159f_1 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-openmp: 19.1.5-ha54dae1_0 conda-forge + llvm-tools: 18.1.8-h9ce406d_2 conda-forge + llvm-tools-18: 18.1.8-h9ce406d_2 conda-forge + make: 4.4.1-h00291cd_2 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + numpy: 2.2.0-py312h22eab8f_0 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + python: 3.12.8-h9ccd52b_1_cpython conda-forge + python_abi: 3.12-5_cp312 conda-forge + readline: 8.2-h9e318b2_1 conda-forge + sigtool: 0.1.3-h88f4db0_0 conda-forge + tapi: 1300.6.5-h390ca13_0 conda-forge + tk: 8.6.13-h1abcd95_1 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + xz: 5.6.3-h357f2ed_1 conda-forge + xz-gpl-tools: 5.6.3-h357f2ed_1 conda-forge + xz-tools: 5.6.3-hd471939_1 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache + Downloading source to cache: v1.0.0_9ffd628fd1.tar.gz + Downloading https://github.com/Limh616/VirDiG/archive/refs/tags/v1.0.0.tar.gz + Success + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 125, in download_to_cache + raise RuntimeError( + RuntimeError: SHA256 mismatch: 'cb9ce7fc5ced952f7af21776ea7b68bd2866af05b0f0727e8237966888c131c4' != '9ffd628fd1c22dd86a1e9e0e4c5b543334a99f0fc6dec56bb1f741e2fe8a32b1' +# Last 100 lines of the build log. diff --git a/recipes/virulign/meta.yaml b/recipes/virulign/meta.yaml index ca6ccce4ff6b3..c1384db8cb4c9 100644 --- a/recipes/virulign/meta.yaml +++ b/recipes/virulign/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/vphaser2/meta.yaml b/recipes/vphaser2/meta.yaml index 564a6bc38b562..c9a9b7aba0bd5 100644 --- a/recipes/vphaser2/meta.yaml +++ b/recipes/vphaser2/meta.yaml @@ -7,7 +7,7 @@ source: md5: fd22b1c4403903576e62defb51b6ae32 build: - number: 14 + number: 15 skip: True # [osx] requirements: diff --git a/recipes/vsearch/meta.yaml b/recipes/vsearch/meta.yaml index 90efe2074a3db..f9faf5f9b8b84 100644 --- a/recipes/vsearch/meta.yaml +++ b/recipes/vsearch/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('vsearch', max_pin="x") }} diff --git a/recipes/vt/meta.yaml b/recipes/vt/meta.yaml index 2132b3ae295e9..08316db36c687 100644 --- a/recipes/vt/meta.yaml +++ b/recipes/vt/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 8f06d464ec5458539cfa30f81a034f47fe7f801146fe8ca80c14a3816b704e17 build: - number: 11 + number: 12 run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} diff --git a/recipes/vtools/meta.yaml b/recipes/vtools/meta.yaml index 8b2dcd71211c4..93e49576afbe7 100644 --- a/recipes/vtools/meta.yaml +++ b/recipes/vtools/meta.yaml @@ -12,7 +12,7 @@ source: - patch build: - number: 6 + number: 7 entry_points: - vtools-filter = vtools.cli:filter_cli - vtools-stats = vtools.cli:stats_cli diff --git a/recipes/w4mclassfilter/meta.yaml b/recipes/w4mclassfilter/meta.yaml index 7f78f51857138..321b56ebaebb0 100644 --- a/recipes/w4mclassfilter/meta.yaml +++ b/recipes/w4mclassfilter/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: generic - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/wally/meta.yaml b/recipes/wally/meta.yaml index 26a0beaba7985..527143d6c11f1 100644 --- a/recipes/wally/meta.yaml +++ b/recipes/wally/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("wally", max_pin="x.x") }} diff --git a/recipes/weeder/meta.yaml b/recipes/weeder/meta.yaml index 5cbce18083ea8..3d30ffe65b68c 100644 --- a/recipes/weeder/meta.yaml +++ b/recipes/weeder/meta.yaml @@ -7,7 +7,7 @@ source: md5: 3401675b24ca928b7cc54ce9ebf18b6a build: - number: 9 + number: 10 skip: True # [osx] run_exports: - {{ pin_subpackage('weeder', max_pin="x") }} diff --git a/recipes/wfa2-lib/meta.yaml b/recipes/wfa2-lib/meta.yaml index 3be8971631094..7b0e7970c515c 100644 --- a/recipes/wfa2-lib/meta.yaml +++ b/recipes/wfa2-lib/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 2 + number: 3 run_exports: - {{ pin_subpackage(name, max_pin="x") }} diff --git a/recipes/wfmash/build_failure.linux-64.yaml b/recipes/wfmash/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..afeae617bbc19 --- /dev/null +++ b/recipes/wfmash/build_failure.linux-64.yaml @@ -0,0 +1,106 @@ +recipe_sha: a0554d730328a219aff2b4054d736ec2e7a6ee068a1ba4733eee1353ee6aefcb # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wfmash-0.21.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib + HOST=x86_64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu + build_alias=x86_64-conda-linux-gnu + host_alias=x86_64-conda-linux-gnu + -BUILD=x86_64-conda_cos6-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wfmash-0.21.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wfmash-0.21.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g + export LIBRARY_PATH=/opt/conda/conda-bld/wfmash_1734534553159/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + LIBRARY_PATH=/opt/conda/conda-bld/wfmash_1734534553159/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + export LD_LIBRARY_PATH=/opt/conda/conda-bld/wfmash_1734534553159/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + LD_LIBRARY_PATH=/opt/conda/conda-bld/wfmash_1734534553159/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + export CPATH=/opt/conda/conda-bld/wfmash_1734534553159/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + CPATH=/opt/conda/conda-bld/wfmash_1734534553159/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + export C_INCLUDE_PATH=/opt/conda/conda-bld/wfmash_1734534553159/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + C_INCLUDE_PATH=/opt/conda/conda-bld/wfmash_1734534553159/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + export CPLUS_INCLUDE_PATH=/opt/conda/conda-bld/wfmash_1734534553159/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + CPLUS_INCLUDE_PATH=/opt/conda/conda-bld/wfmash_1734534553159/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + export CPP_INCLUDE_PATH=/opt/conda/conda-bld/wfmash_1734534553159/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + CPP_INCLUDE_PATH=/opt/conda/conda-bld/wfmash_1734534553159/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + export CXX_INCLUDE_PATH=/opt/conda/conda-bld/wfmash_1734534553159/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + CXX_INCLUDE_PATH=/opt/conda/conda-bld/wfmash_1734534553159/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + case $(uname -m) in + uname -m + EXTRA_FLAGS='-march=sandybridge -Ofast' + MARCH=sandybridge + sed -i s/-march=x86-64-v3/-march=sandybridge/g src/common/wflign/deps/WFA2-lib/Makefile + cmake -H. -Bbuild -DCMAKE_BUILD_TYPE=Generic '-DEXTRA_FLAGS=-march=sandybridge -Ofast' + CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): + Compatibility with CMake < 3.10 will be removed from a future version of + CMake. + + Update the VERSION argument value. Or, use the ... syntax + to tell CMake that the project requires at least but has been updated + to work with policies introduced by or earlier. + + + -- The C compiler identification is GNU 13.3.0 + -- The CXX compiler identification is GNU 13.3.0 + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - skipped + -- Detecting C compile features + -- Detecting C compile features - done + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1") + -- Found CURL: $PREFIX/lib/libcurl.so (found version "8.11.1") + -- Found ZLIB: $PREFIX/lib/libz.so (found version "1.3.1") + -- Found BZip2: $PREFIX/lib/libbz2.so (found version "1.0.8") + -- Looking for BZ2_bzCompressInit + -- Looking for BZ2_bzCompressInit - found + CMake Error at /opt/conda/conda-bld/wfmash_1734534553159/_build_env/share/cmake-3.31/Modules/FindPackageHandleStandardArgs.cmake:233 (message): + Could NOT find LibLZMA (missing: LIBLZMA_LIBRARY LIBLZMA_INCLUDE_DIR + LIBLZMA_HAS_AUTO_DECODER LIBLZMA_HAS_EASY_ENCODER LIBLZMA_HAS_LZMA_PRESET) + Call Stack (most recent call first): + /opt/conda/conda-bld/wfmash_1734534553159/_build_env/share/cmake-3.31/Modules/FindPackageHandleStandardArgs.cmake:603 (_FPHSA_FAILURE_MESSAGE) + /opt/conda/conda-bld/wfmash_1734534553159/_build_env/share/cmake-3.31/Modules/FindLibLZMA.cmake:108 (find_package_handle_standard_args) + CMakeLists.txt:31 (find_package) + + + -- Configuring incomplete, errors occurred! + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/wfmash_1734534553159/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/wfmash_1734534553159/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/wfmash/build_failure.linux-aarch64.yaml b/recipes/wfmash/build_failure.linux-aarch64.yaml new file mode 100644 index 0000000000000..f6f5b4b8d1387 --- /dev/null +++ b/recipes/wfmash/build_failure.linux-aarch64.yaml @@ -0,0 +1,106 @@ +recipe_sha: a0554d730328a219aff2b4054d736ec2e7a6ee068a1ba4733eee1353ee6aefcb # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + DEBUG_CFLAGS=-ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wfmash-0.21.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include + GCC=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc + GCC_AR=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ar + GCC_NM=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-nm + GCC_RANLIB=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-gcc-ranlib + HOST=aarch64-conda-linux-gnu + LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_aarch64_conda_cos7_linux_gnu + build_alias=aarch64-conda-linux-gnu + host_alias=aarch64-conda-linux-gnu + -BUILD=aarch64-conda_cos7-linux-gnu + -CONDA_BUILD_SYSROOT= + INFO: activate-gxx_linux-aarch64.sh made the following environmental changes: + CXX=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c + CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wfmash-0.21.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CXX_FOR_BUILD=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c + DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wfmash-0.21.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + GXX=$BUILD_PREFIX/bin/aarch64-conda-linux-gnu-g + export LIBRARY_PATH=/opt/conda/conda-bld/wfmash_1734536002953/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + LIBRARY_PATH=/opt/conda/conda-bld/wfmash_1734536002953/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + export LD_LIBRARY_PATH=/opt/conda/conda-bld/wfmash_1734536002953/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + LD_LIBRARY_PATH=/opt/conda/conda-bld/wfmash_1734536002953/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib + export CPATH=/opt/conda/conda-bld/wfmash_1734536002953/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + CPATH=/opt/conda/conda-bld/wfmash_1734536002953/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + export C_INCLUDE_PATH=/opt/conda/conda-bld/wfmash_1734536002953/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + C_INCLUDE_PATH=/opt/conda/conda-bld/wfmash_1734536002953/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + export CPLUS_INCLUDE_PATH=/opt/conda/conda-bld/wfmash_1734536002953/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + CPLUS_INCLUDE_PATH=/opt/conda/conda-bld/wfmash_1734536002953/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + export CPP_INCLUDE_PATH=/opt/conda/conda-bld/wfmash_1734536002953/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + CPP_INCLUDE_PATH=/opt/conda/conda-bld/wfmash_1734536002953/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + export CXX_INCLUDE_PATH=/opt/conda/conda-bld/wfmash_1734536002953/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + CXX_INCLUDE_PATH=/opt/conda/conda-bld/wfmash_1734536002953/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/include + case $(uname -m) in + uname -m + EXTRA_FLAGS='-march=native -Ofast' + MARCH=native + sed -i s/-march=x86-64-v3/-march=native/g src/common/wflign/deps/WFA2-lib/Makefile + cmake -H. -Bbuild -DCMAKE_BUILD_TYPE=Generic '-DEXTRA_FLAGS=-march=native -Ofast' + CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): + Compatibility with CMake < 3.10 will be removed from a future version of + CMake. + + Update the VERSION argument value. Or, use the ... syntax + to tell CMake that the project requires at least but has been updated + to work with policies introduced by or earlier. + + + -- The C compiler identification is GNU 13.3.0 + -- The CXX compiler identification is GNU 13.3.0 + -- Detecting C compiler ABI info + -- Detecting C compiler ABI info - done + -- Check for working C compiler: $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-cc - skipped + -- Detecting C compile features + -- Detecting C compile features - done + -- Detecting CXX compiler ABI info + -- Detecting CXX compiler ABI info - done + -- Check for working CXX compiler: $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c - skipped + -- Detecting CXX compile features + -- Detecting CXX compile features - done + -- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1") + -- Found CURL: $PREFIX/lib/libcurl.so (found version "8.11.1") + -- Found ZLIB: $PREFIX/lib/libz.so (found version "1.3.1") + -- Found BZip2: $PREFIX/lib/libbz2.so (found version "1.0.8") + -- Looking for BZ2_bzCompressInit + -- Looking for BZ2_bzCompressInit - found + CMake Error at /opt/conda/conda-bld/wfmash_1734536002953/_build_env/share/cmake-3.31/Modules/FindPackageHandleStandardArgs.cmake:233 (message): + Could NOT find LibLZMA (missing: LIBLZMA_LIBRARY LIBLZMA_INCLUDE_DIR + LIBLZMA_HAS_AUTO_DECODER LIBLZMA_HAS_EASY_ENCODER LIBLZMA_HAS_LZMA_PRESET) + Call Stack (most recent call first): + /opt/conda/conda-bld/wfmash_1734536002953/_build_env/share/cmake-3.31/Modules/FindPackageHandleStandardArgs.cmake:603 (_FPHSA_FAILURE_MESSAGE) + /opt/conda/conda-bld/wfmash_1734536002953/_build_env/share/cmake-3.31/Modules/FindLibLZMA.cmake:108 (find_package_handle_standard_args) + CMakeLists.txt:31 (find_package) + + + -- Configuring incomplete, errors occurred! + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/wfmash_1734536002953/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/wfmash_1734536002953/work/conda_build.sh']' returned non-zero exit status 1. +# Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/wfmash/meta.yaml b/recipes/wfmash/meta.yaml index 980acc916dbe1..8abce4182ece1 100644 --- a/recipes/wfmash/meta.yaml +++ b/recipes/wfmash/meta.yaml @@ -13,7 +13,7 @@ build: skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} - number: 0 + number: 1 requirements: build: @@ -28,6 +28,7 @@ requirements: - jemalloc - htslib - libblas + - liblzma run: - llvm-openmp # [osx] - python >=3.7 diff --git a/recipes/wgatools/build_failure.osx-64.yaml b/recipes/wgatools/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..de21351a795b6 --- /dev/null +++ b/recipes/wgatools/build_failure.osx-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: d7b6dcf2733a58312ce6237bb795ccf87d16adc35608942b065ccc0a4c16aeea # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |2- + - llvm-tools 18.1.8 h9ce406d_2 + - ca-certificates 2024.8.30 h8857fd0_0 + - clangxx 18.1.8 default_h179603d_5 + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + - libzlib 1.3.1 hd23fc13_2 + - zstd 1.5.6 h915ae27_0 + - compiler-rt_osx-64 18.1.8 hf2b8a54_1 + - rust 1.83.0 h34a2095_0 + - libuv 1.49.2 hd79239c_0 + - libiconv 1.17 hd75f5a5_2 + - llvm-tools-18 18.1.8 h9ce406d_2 + - c-ares 1.34.3 hf13058a_1 + - libllvm18 18.1.8 h9ce406d_2 + - libclang-cpp18.1 18.1.8 default_h0c94c6a_5 + - krb5 1.21.3 h37d8d59_0 + - make 4.4.1 h00291cd_2 + - rhash 1.4.5 ha44c9a9_0 + - compiler-rt 18.1.8 h1020d70_1 + - liblzma 5.6.3 hd471939_1 + - libcxx-devel 18.1.8 h7c275be_7 + - libssh2 1.11.1 h3dc7d44_0 + - libexpat 2.6.4 h240833e_0 + - ld64_osx-64 951.9 hc8d1a19_2 + host: + - ca-certificates 2024.8.30 h8857fd0_0 + - openssl 3.4.0 hd471939_0 + run: + - openssl >=3.4.0,<4.0a0 + - perl + run_constrained: + - __osx >=10.13 + test: + commands: + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + - wgatools --help + about: + raise BuildScriptException(str(exc), caused_by=exc) from exc + dev_url: https://github.com/wjwei-handsome/wgatools + home: https://github.com/wjwei-handsome/wgatools + license: MIT + license_family: MIT + license_file: LICENSE + summary: A Rust library and tools for whole genome alignment files + extra: + copy_test_source_files: true + final: true + recipe-maintainers: + - AndreaGuarracino + + + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/wgatools_1734204863139/work/conda_build.sh']' returned non-zero exit status 101. + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/wgatools_1734204863139/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/wgatools_1734204863139/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/wgatools_1734204863139/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/wgatools_1734204863139/work + INFO: activate_clang_osx-64.sh made the following environmental changes: + AR=x86_64-apple-darwin13.4.0-ar + AS=x86_64-apple-darwin13.4.0-as + CC=x86_64-apple-darwin13.4.0-clang + CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wgatools-0.1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms + CLANG=x86_64-apple-darwin13.4.0-clang + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_PREFIX_PATH=:$PREFIX + CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 + CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp + DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wgatools-0.1.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix + HOST=x86_64-apple-darwin13.4.0 + INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool + LD=x86_64-apple-darwin13.4.0-ld + LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib + LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib + LIBTOOL=x86_64-apple-darwin13.4.0-libtool + LIPO=x86_64-apple-darwin13.4.0-lipo + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib + NM=x86_64-apple-darwin13.4.0-nm + NMEDIT=x86_64-apple-darwin13.4.0-nmedit + OBJC=x86_64-apple-darwin13.4.0-clang + OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang + OTOOL=x86_64-apple-darwin13.4.0-otool + PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff + RANLIB=x86_64-apple-darwin13.4.0-ranlib + REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SEGEDIT=x86_64-apple-darwin13.4.0-segedit + SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table + SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack + SIZE=x86_64-apple-darwin13.4.0-size + STRINGS=x86_64-apple-darwin13.4.0-strings + STRIP=x86_64-apple-darwin13.4.0-strip + _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 + ac_cv_func_malloc_0_nonnull=yes + ac_cv_func_realloc_0_nonnull=yes + build_alias=x86_64-apple-darwin13.4.0 + host_alias=x86_64-apple-darwin13.4.0 +# Last 100 lines of the build log. diff --git a/recipes/wgatools/meta.yaml b/recipes/wgatools/meta.yaml index 656097287727a..e5b2a265e8c71 100644 --- a/recipes/wgatools/meta.yaml +++ b/recipes/wgatools/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 07e15a7e7e918318f781805b670294601481b5009c922b140c71ee5f298c2390 build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin='x.x') }} diff --git a/recipes/wgsim/meta.yaml b/recipes/wgsim/meta.yaml index 357c3118b9a22..0c55bdcc35df7 100644 --- a/recipes/wgsim/meta.yaml +++ b/recipes/wgsim/meta.yaml @@ -9,7 +9,7 @@ source: - 0001-Fix-shebang-in-perl-script.patch build: - number: 7 + number: 8 requirements: build: diff --git a/recipes/whatshap/meta.yaml b/recipes/whatshap/meta.yaml index 60ae860a8702e..901b1aaa7ede1 100644 --- a/recipes/whatshap/meta.yaml +++ b/recipes/whatshap/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 1f7ac47b18784b213492e4b92dddc63132d371b2f353660462536bcadc15e62e build: - number: 2 + number: 3 script_env: - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }} script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv diff --git a/recipes/wiggletools/meta.yaml b/recipes/wiggletools/meta.yaml index de7d1be501ac1..a67f13faae583 100644 --- a/recipes/wiggletools/meta.yaml +++ b/recipes/wiggletools/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 8 + number: 9 run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} @@ -40,4 +40,4 @@ about: extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/winnowmap/meta.yaml b/recipes/winnowmap/meta.yaml index 5bfe83e16eb65..b008be33c1ac3 100644 --- a/recipes/winnowmap/meta.yaml +++ b/recipes/winnowmap/meta.yaml @@ -12,7 +12,7 @@ source: - 0001-Un-vendor-meryl.patch build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/wise2/build_failure.osx-64.yaml b/recipes/wise2/build_failure.osx-64.yaml index 0594df5aa47e9..60d460d350c66 100644 --- a/recipes/wise2/build_failure.osx-64.yaml +++ b/recipes/wise2/build_failure.osx-64.yaml @@ -1,104 +1,106 @@ -recipe_sha: 74de50cceedff44a49438c42df39aa023ee20290ea56636487500240dca82461 # The commit at which this recipe failed to build. +recipe_sha: a1adcd76bce12f58d228e0969c0ab4533fcda42547200860e944b96ead6df480 # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - ca-certificates: 2023.5.7-h8857fd0_0 conda-forge - gettext: 0.21.1-h8a4c099_0 conda-forge - glib: 2.76.3-h7d26f99_0 conda-forge - glib-tools: 2.76.3-h7d26f99_0 conda-forge - libcxx: 16.0.4-hd57cbcb_0 conda-forge - libexpat: 2.5.0-hf0c8a7f_1 conda-forge - libffi: 3.4.2-h0d85af4_5 conda-forge - libglib: 2.76.3-hc62aa5d_0 conda-forge - libiconv: 1.17-hac89ed1_0 conda-forge - libsqlite: 3.42.0-h58db7d2_0 conda-forge - libzlib: 1.2.13-hfd90126_4 conda-forge - ncurses: 6.3-h96cf925_1 conda-forge - openssl: 3.1.0-h8a1eda9_3 conda-forge - pcre2: 10.40-h1c4e4bc_0 conda-forge - python: 3.11.3-h99528f9_0_cpython conda-forge - readline: 8.2-h9e318b2_1 conda-forge - tk: 8.6.12-h5dbffcc_0 conda-forge - tzdata: 2023c-h71feb2d_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge +log: |- + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ aln.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ dnamatrix.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ probability.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ alnrange.c + The above exception was the direct cause of the following exception: - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld - Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld - - ## Package Plan ## - - environment location: /opt/mambaforge/envs/bioconda/conda-bld/wise2_1685393236374/_build_env - - - The following NEW packages will be INSTALLED: - - ca-certificates: 2023.5.7-h8857fd0_0 conda-forge - cctools_osx-64: 973.0.1-h48a5a9d_13 conda-forge - clang: 15.0.7-h694c41f_2 conda-forge - clang-15: 15.0.7-default_hdb78580_2 conda-forge - clang_osx-64: 15.0.7-h03d6864_3 conda-forge - clangxx: 15.0.7-default_hdb78580_2 conda-forge - clangxx_osx-64: 15.0.7-h2133e9c_3 conda-forge - compiler-rt: 15.0.7-he1888fc_1 conda-forge - compiler-rt_osx-64: 15.0.7-he1888fc_1 conda-forge - icu: 72.1-h7336db1_0 conda-forge - ld64_osx-64: 609-h8ce0179_13 conda-forge - libclang-cpp15: 15.0.7-default_hdb78580_2 conda-forge - libcxx: 16.0.4-hd57cbcb_0 conda-forge - libiconv: 1.17-hac89ed1_0 conda-forge - libllvm15: 15.0.7-he4b1e75_2 conda-forge - libxml2: 2.11.4-hd95e348_0 conda-forge - libzlib: 1.2.13-hfd90126_4 conda-forge - llvm-tools: 15.0.7-he4b1e75_2 conda-forge - make: 4.3-h22f3db7_1 conda-forge - openssl: 3.1.0-h8a1eda9_3 conda-forge - pkg-config: 0.29.2-ha3d46e9_1008 conda-forge - sigtool: 0.1.3-h88f4db0_0 conda-forge - tapi: 1100.0.11-h9ce4665_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - zstd: 1.5.2-hbc0c0cd_6 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - INFO:conda_build.source:Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - INFO:conda_build.source:Downloading source to cache: wise2.4.1_240e2b12d6.tar.gz - INFO:conda_build.source:Downloading https://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz - Downloading source to cache: wise2.4.1_240e2b12d6.tar.gz - Downloading https://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz - Error: HTTP 403 FORBIDDEN for url - Elapsed: 00:00.405409 - - An HTTP error occurred when trying to retrieve this URL. - HTTP errors are often intermittent, and a simple retry will get you on your way. - WARNING:conda_build.source:Error: HTTP 403 FORBIDDEN for url - Elapsed: 00:00.405409 - - An HTTP error occurred when trying to retrieve this URL. - HTTP errors are often intermittent, and a simple retry will get you on your way. Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ alnconvert.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ basematrix.c + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ shattermatrix.c return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2125, in build - try_download(m, no_download_source=False, raise_error=True) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/render.py", line 650, in try_download - source.provide(metadata) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/source.py", line 871, in provide - unpack(source_dict, src_dir, metadata.config.src_cache, recipe_path=metadata.path, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/source.py", line 146, in unpack - src_path, unhashed_fn = download_to_cache(cache_folder, recipe_path, source_dict, verbose) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/source.py", line 102, in download_to_cache - raise RuntimeError("Could not download %s" % url) - RuntimeError: Could not download https://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ matrixdebug.c + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ dpenvelope.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ dbsearchimpl.c + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ dprunimpl.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ complexsequence.c + raise BuildScriptException(str(exc), caused_by=exc) from exc + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ complexevalset.c + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/wise2_1734476928941/work/conda_build.sh']' returned non-zero exit status 2. + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ complexconsensi.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ sequence.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ sequencestream.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ seqalign.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ hitlist.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ hsp.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ hspstream.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ codon.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ compmat.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ codonmatrix.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ codonmapper.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ sequencedb.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ hscore.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ seqlookup.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ arrayseqlookup.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ genericindexresult.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ linkedlist_lookpos.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ singlenumberspace.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ histogram.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ searchstatinterface.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ searchstatlookup.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ proteindb.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ protein.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ pairbase.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ pairbaseseq.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ genomicdb.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ randommodel.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ randomdb.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ genomic.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ cdna.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ cdnadb.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ dna.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ embl.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ genomicregion.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ gene.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ transcript.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ translation.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ btcanvas.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ asciibtcanvas.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ dynlibcross.c + ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o + if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi + if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi + make[1]: Leaving directory '$SRC_DIR/src/dynlibsrc' + (cd dynlibsrc ; make CC="x86_64-apple-darwin13.4.0-clang" CFLAGS="-c -O3 pkg-config --cflags glib-2.0" libdyna_glib.a ) + make[1]: Entering directory '$SRC_DIR/src/dynlibsrc' + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ subseqhash.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ intallocator.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ proteinstreamedindex.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ shadowseq.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ shadowseqindex.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ hsphandler.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ hspscaninterface.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ hsp2hitscan.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ hsplookupscan.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ hsplookupthreaded.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ hspthreadeddb.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ hspscanruntime.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ hsptwohitscan.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ proteinindexcons.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ dnaindexcons.c + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -I../base/ staticseq.c + ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o + if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi + if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi + make[1]: Leaving directory '$SRC_DIR/src/dynlibsrc' + (cd external ; make CC="x86_64-apple-darwin13.4.0-clang" CFLAGS="-c -O3 pkg-config --cflags glib-2.0" all ) + make[1]: Entering directory '$SRC_DIR/src/external' + (cd mott; make CC="x86_64-apple-darwin13.4.0-clang" CFLAGS="-c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include" all) + make[2]: Entering directory '$SRC_DIR/src/external/mott' + x86_64-apple-darwin13.4.0-clang -c -O3 -I$PREFIX/include/glib-2.0 -I$PREFIX/lib/glib-2.0/include -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 -c -o mott_api.o mott_api.c + make[2]: Leaving directory '$SRC_DIR/src/external/mott' + make[1]: Leaving directory '$SRC_DIR/src/external' # Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/wise2/meta.yaml b/recipes/wise2/meta.yaml index 0852d41a13f5b..25504fdbc30d2 100644 --- a/recipes/wise2/meta.yaml +++ b/recipes/wise2/meta.yaml @@ -11,7 +11,7 @@ source: - patch build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage("wise2", max_pin='x.x') }} diff --git a/recipes/wtdbg/meta.yaml b/recipes/wtdbg/meta.yaml index d95306e935b52..3723795b58bc3 100644 --- a/recipes/wtdbg/meta.yaml +++ b/recipes/wtdbg/meta.yaml @@ -9,7 +9,7 @@ source: sha256: a2ffc8503d29f491a9a38ef63230d5b3c96db78377b5d25c91df511d0df06413 build: - number: 4 + number: 5 skip: true # [osx] requirements: diff --git a/recipes/xatlas/meta.yaml b/recipes/xatlas/meta.yaml index 09cbbc7ed87ed..7c6b201b82094 100644 --- a/recipes/xatlas/meta.yaml +++ b/recipes/xatlas/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 4 + number: 5 skip: True # [osx] source: diff --git a/recipes/xbioc/meta.yaml b/recipes/xbioc/meta.yaml index 5f3edc9d14928..e056a542ca207 100644 --- a/recipes/xbioc/meta.yaml +++ b/recipes/xbioc/meta.yaml @@ -10,7 +10,7 @@ source: sha256: '00b0854a26acfcca063a3ad719b5133f9d02aa775598b4790ea8778e94a598b4' build: - number: 3 + number: 4 noarch: generic rpaths: - lib/R/lib/ diff --git a/recipes/xs-sim/meta.yaml b/recipes/xs-sim/meta.yaml index 22e322034f5d4..18f1517bbc952 100644 --- a/recipes/xs-sim/meta.yaml +++ b/recipes/xs-sim/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 3882f88dd757bee2d44cf2393af02084c572dd490dd8cbe55925cb2788777174 build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/xtandem/meta.yaml b/recipes/xtandem/meta.yaml index a7cf61d10183c..3b15140744de6 100644 --- a/recipes/xtandem/meta.yaml +++ b/recipes/xtandem/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: true # [osx] - number: 9 + number: 10 run_exports: - {{ pin_subpackage('xtandem', max_pin="x") }} diff --git a/recipes/yacrd/0.4.1/meta.yaml b/recipes/yacrd/0.4.1/meta.yaml index bf4c343d491d1..44a1606be26db 100644 --- a/recipes/yacrd/0.4.1/meta.yaml +++ b/recipes/yacrd/0.4.1/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 7 + number: 8 requirements: build: diff --git a/recipes/yacrd/0.5.1/meta.yaml b/recipes/yacrd/0.5.1/meta.yaml index 1c74c03151f7f..68f877a0dc78f 100644 --- a/recipes/yacrd/0.5.1/meta.yaml +++ b/recipes/yacrd/0.5.1/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 7 + number: 8 requirements: build: diff --git a/recipes/yacrd/meta.yaml b/recipes/yacrd/meta.yaml index be40c2a3e3184..c4d1e1f07d0ff 100644 --- a/recipes/yacrd/meta.yaml +++ b/recipes/yacrd/meta.yaml @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage('yacrd', max_pin="x") }} diff --git a/recipes/yaha/meta.yaml b/recipes/yaha/meta.yaml index 8b921d975c38a..adee28a5bf13e 100644 --- a/recipes/yaha/meta.yaml +++ b/recipes/yaha/meta.yaml @@ -9,7 +9,7 @@ source: - 0001-2caff3fbc92c091d9b154fa247889529a44f90ce.patch build: - number: 6 + number: 7 skip: true # [not linux] requirements: diff --git a/recipes/yahmm/build_failure.linux-64.yaml b/recipes/yahmm/build_failure.linux-64.yaml index da1376670b799..13c9876ba1844 100644 --- a/recipes/yahmm/build_failure.linux-64.yaml +++ b/recipes/yahmm/build_failure.linux-64.yaml @@ -1,44 +1,14 @@ -recipe_sha: 89d6a965f4a9b74d87364eade30096aa1b7c2a66a546356f7a99730acf50cf71 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 5270553cf7c144e518ed02eb2b63fbeeac38ce449aef132499010fdf816b979a # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: compiler error log: |2- - 6:03:41 BIOCONDA INFO (OUT) Error compiling Cython file: - 16:03:41 BIOCONDA INFO (OUT) ------------------------------------------------------------ - 16:03:41 BIOCONDA INFO (OUT) ... - 16:03:41 BIOCONDA INFO (OUT) if self.in_edge_count[i] == 0: - 16:03:41 BIOCONDA INFO (OUT) merge_count += 1 - 16:03:41 BIOCONDA INFO (OUT) self.graph.remove_node( prestates[i] ) - 16:03:41 BIOCONDA INFO (OUT) - 16:03:41 BIOCONDA INFO (OUT) if verbose: - 16:03:41 BIOCONDA INFO (OUT) print "Orphan state {} removed due to no edges \ - 16:03:41 BIOCONDA INFO (OUT) ^ - 16:03:41 BIOCONDA INFO (OUT) ------------------------------------------------------------ - 16:03:41 BIOCONDA INFO (OUT) - 16:03:41 BIOCONDA INFO (OUT) yahmm/yahmm.pyx:2348:12: Syntax error in simple statement list - 16:03:41 BIOCONDA INFO (OUT) Traceback (most recent call last): - 16:03:41 BIOCONDA INFO (OUT) File "", line 2, in - 16:03:41 BIOCONDA INFO (OUT) File "", line 34, in - 16:03:41 BIOCONDA INFO (OUT) File "/opt/conda/conda-bld/yahmm_1718121715058/work/setup.py", line 24, in - cmd_obj.run() - File "/opt/conda/conda-bld/yahmm_1718121715058/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.8/site-packages/setuptools/_distutils/command/build.py", line 132, in run - self.run_command(cmd_name) - File "/opt/conda/conda-bld/yahmm_1718121715058/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.8/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command - self.distribution.run_command(command) - File "/opt/conda/conda-bld/yahmm_1718121715058/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.8/site-packages/setuptools/dist.py", line 968, in run_command - super().run_command(command) - File "/opt/conda/conda-bld/yahmm_1718121715058/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 988, in run_command - cmd_obj.run() - File "/opt/conda/conda-bld/yahmm_1718121715058/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.8/site-packages/setuptools/_distutils/command/build_ext.py", line 359, in run - self.build_extensions() - File "/opt/conda/conda-bld/yahmm_1718121715058/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.8/site-packages/setuptools/_distutils/command/build_ext.py", line 479, in build_extensions - self._build_extensions_serial() - File "/opt/conda/conda-bld/yahmm_1718121715058/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.8/site-packages/setuptools/_distutils/command/build_ext.py", line 505, in _build_extensions_serial + File "/opt/conda/conda-bld/yahmm_1734733076981/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.12/site-packages/setuptools/_distutils/command/build_ext.py", line 502, in _build_extensions_serial self.build_extension(ext) - File "/opt/conda/conda-bld/yahmm_1718121715058/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.8/site-packages/Cython/Distutils/build_ext.py", line 130, in build_extension + File "/opt/conda/conda-bld/yahmm_1734733076981/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.12/site-packages/Cython/Distutils/build_ext.py", line 130, in build_extension new_ext = cythonize( - File "/opt/conda/conda-bld/yahmm_1718121715058/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize + ^^^^^^^^^^ + File "/opt/conda/conda-bld/yahmm_1734733076981/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.12/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize cythonize_one(*args) - File "/opt/conda/conda-bld/yahmm_1718121715058/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one + File "/opt/conda/conda-bld/yahmm_1734733076981/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.12/site-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: yahmm/yahmm.pyx [1;31merror[0m: [1msubprocess-exited-with-error[0m @@ -48,7 +18,7 @@ log: |2- [31m>[0m See above for output. [1;35mnote[0m: This error originates from a subprocess, and is likely not a problem with pip. - [1;35mfull command[0m: [34m/opt/conda/conda-bld/yahmm_1718121715058/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/python -u -c '[0m + [1;35mfull command[0m: [34m/opt/conda/conda-bld/yahmm_1734733076981/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/python -u -c '[0m [34m exec(compile('"'"''"'"''"'"'[0m [34m # This is -- a caller that pip uses to run setup.py[0m [34m #[0m @@ -83,40 +53,54 @@ log: |2- [34m setup_py_code = "from setuptools import setup; setup()"[0m [34m [0m [34m exec(compile(setup_py_code, filename, "exec"))[0m - [34m '"'"''"'"''"'"' % ('"'"'/opt/conda/conda-bld/yahmm_1718121715058/work/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-72fnr0kj[0m - [1;35mcwd[0m: /opt/conda/conda-bld/yahmm_1718121715058/work/ + [34m '"'"''"'"''"'"' % ('"'"'/opt/conda/conda-bld/yahmm_1734733076981/work/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-0nv1y7ns[0m + [1;35mcwd[0m: /opt/conda/conda-bld/yahmm_1734733076981/work/ Building wheel for yahmm (setup.py): finished with status 'error' [31m ERROR: Failed building wheel for yahmm[0m[31m [0m Running setup.py clean for yahmm Running command python setup.py clean 'build/bdist.linux-x86_64' does not exist -- can't clean it - 'build/scripts-3.8' does not exist -- can't clean it + 'build/scripts-3.12' does not exist -- can't clean it Failed to build yahmm - [31mERROR: Could not build wheels for yahmm, which is required to install pyproject.toml-based projects[0m[31m + [31mERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (yahmm)[0m[31m [0mException information: Traceback (most recent call last): - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + ^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper return func(self, options, args) - File "$PREFIX/lib/python3.8/site-packages/pip/_internal/commands/install.py", line 429, in run + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 434, in run raise InstallationError( - pip._internal.exceptions.InstallationError: Could not build wheels for yahmm, which is required to install pyproject.toml-based projects - Removed build tracker: '/tmp/pip-build-tracker-dk6gx091' + pip._internal.exceptions.InstallationError: ERROR: Failed to build installable wheels for some pyproject.toml based projects (yahmm) + Removed build tracker: '/tmp/pip-build-tracker-j6zd5112' + Traceback (most recent call last): + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build + utils.check_call_env( + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env + return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) + File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ + raise subprocess.CalledProcessError(proc.returncode, _args) + subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/yahmm_1734733076981/work/conda_build.sh']' returned non-zero exit status 1. + + The above exception was the direct cause of the following exception: + Traceback (most recent call last): File "/opt/conda/bin/conda-build", line 11, in sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/yahmm_1718121715058/work/conda_build.sh']' returned non-zero exit status 1. + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build + raise BuildScriptException(str(exc), caused_by=exc) from exc + conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/yahmm_1734733076981/work/conda_build.sh']' returned non-zero exit status 1. # Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/yahmm/build_failure.osx-64.yaml b/recipes/yahmm/build_failure.osx-64.yaml index 3cb29bb5d53aa..366ffff3fe006 100644 --- a/recipes/yahmm/build_failure.osx-64.yaml +++ b/recipes/yahmm/build_failure.osx-64.yaml @@ -1,29 +1,22 @@ -recipe_sha: 89d6a965f4a9b74d87364eade30096aa1b7c2a66a546356f7a99730acf50cf71 # The hash of the recipe's meta.yaml at which this recipe failed to build. +recipe_sha: 5270553cf7c144e518ed02eb2b63fbeeac38ce449aef132499010fdf816b979a # The hash of the recipe's meta.yaml at which this recipe failed to build. skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: compiler error log: |2- - 'build/scripts-3.9' does not exist -- can't clean it - ERROR: Could not build wheels for yahmm, which is required to install pyproject.toml-based projects - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/yahmm_1718122048816/work - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/yahmm_1718122048816/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/yahmm_1718122048816/_build_env - return build_tree( - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/yahmm_1718122048816/work - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) + license: MIT + license_file: LICENSE.txt + summary: YAHMM is a HMM package for Python, implemented in Cython for speed. + extra: + container: + extended-base: true + copy_test_source_files: true + final: true + skip-lints: + - cython_must_be_in_host + + + source tree in: /opt/mambaforge/envs/bioconda/conda-bld/yahmm_1734714151065/work + export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/yahmm_1734714151065/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/yahmm_1734714151065/_build_env + export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/yahmm_1734714151065/work INFO: activate_clang_osx-64.sh made the following environmental changes: AR=x86_64-apple-darwin13.4.0-ar AS=x86_64-apple-darwin13.4.0-as @@ -32,12 +25,13 @@ log: |2- CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/yahmm-1.1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms CLANG=x86_64-apple-darwin13.4.0-clang - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/yahmm_1718122048816/work/conda_build.sh']' returned non-zero exit status 1. - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin + CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.15 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin CMAKE_PREFIX_PATH=:$PREFIX CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 + CPP=x86_64-apple-darwin13.4.0-clang-cpp + CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.15 + CPP_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang-cpp DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/yahmm-1.1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix HOST=x86_64-apple-darwin13.4.0 INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool @@ -46,7 +40,7 @@ log: |2- LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib LIBTOOL=x86_64-apple-darwin13.4.0-libtool LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib + MESON_ARGS=-Dbuildtype=release --prefix=$PREFIX -Dlibdir=lib NM=x86_64-apple-darwin13.4.0-nm NMEDIT=x86_64-apple-darwin13.4.0-nmedit OBJC=x86_64-apple-darwin13.4.0-clang @@ -55,7 +49,7 @@ log: |2- PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff RANLIB=x86_64-apple-darwin13.4.0-ranlib REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk + SDKROOT=/Applications/Xcode_15.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk SEGEDIT=x86_64-apple-darwin13.4.0-segedit SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack @@ -67,39 +61,46 @@ log: |2- ac_cv_func_realloc_0_nonnull=yes build_alias=x86_64-apple-darwin13.4.0 host_alias=x86_64-apple-darwin13.4.0 - Using pip 24.0 from $PREFIX/lib/python3.9/site-packages/pip (python 3.9) + Using pip 24.3.1 from $PREFIX/lib/python3.11/site-packages/pip (python 3.11) Non-user install because user site-packages disabled Ignoring indexes: https://pypi.org/simple - Created temporary directory: /private/tmp/pip-build-tracker-3ipzv77c - Initialized build tracking at /private/tmp/pip-build-tracker-3ipzv77c - Created build tracker: /private/tmp/pip-build-tracker-3ipzv77c - Entered build tracker: /private/tmp/pip-build-tracker-3ipzv77c - Created temporary directory: /private/tmp/pip-install-gxe18bl5 - Created temporary directory: /private/tmp/pip-ephem-wheel-cache-54ja9u3k + Created temporary directory: /private/tmp/pip-build-tracker-_d4xc6vs + Initialized build tracking at /private/tmp/pip-build-tracker-_d4xc6vs + Created build tracker: /private/tmp/pip-build-tracker-_d4xc6vs + Entered build tracker: /private/tmp/pip-build-tracker-_d4xc6vs + Created temporary directory: /private/tmp/pip-install-us1qv8n5 + Created temporary directory: /private/tmp/pip-ephem-wheel-cache-xjw71gd0 Processing $SRC_DIR - Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-3ipzv77c' + Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-_d4xc6vs' Running setup.py (path:$SRC_DIR/setup.py) egg_info for package from file://$SRC_DIR - Created temporary directory: /private/tmp/pip-pip-egg-info-l2q6h51q + Created temporary directory: /private/tmp/pip-pip-egg-info-gnbiqcgq Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Source in $SRC_DIR has version 1.1.3, which satisfies requirement yahmm==1.1.3 from file://$SRC_DIR - Removed yahmm==1.1.3 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-3ipzv77c' - Created temporary directory: /private/tmp/pip-unpack-dsefgft3 + Removed yahmm==1.1.3 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-_d4xc6vs' + Created temporary directory: /private/tmp/pip-unpack-gua39h9y Building wheels for collected packages: yahmm - Created temporary directory: /private/tmp/pip-wheel-kvbv_9y_ + Created temporary directory: /private/tmp/pip-wheel-piivg19k Building wheel for yahmm (setup.py): started - Destination directory: /private/tmp/pip-wheel-kvbv_9y_ + Destination directory: /private/tmp/pip-wheel-piivg19k Building wheel for yahmm (setup.py): finished with status 'error' Running setup.py clean for yahmm Failed to build yahmm Exception information: Traceback (most recent call last): - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper + status = _inner_run() + ^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run + return self.run(options, args) + ^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper return func(self, options, args) - File "$PREFIX/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 429, in run + ^^^^^^^^^^^^^^^^^^^^^^^^^ + File "$PREFIX/lib/python3.11/site-packages/pip/_internal/commands/install.py", line 434, in run raise InstallationError( - pip._internal.exceptions.InstallationError: Could not build wheels for yahmm, which is required to install pyproject.toml-based projects - Removed build tracker: '/private/tmp/pip-build-tracker-3ipzv77c' + pip._internal.exceptions.InstallationError: ERROR: Failed to build installable wheels for some pyproject.toml based projects (yahmm) + Removed build tracker: '/private/tmp/pip-build-tracker-_d4xc6vs' # Last 100 lines of the build log. +category: |- + compiler error diff --git a/recipes/yahmm/meta.yaml b/recipes/yahmm/meta.yaml index 7086a95db96b5..00bba2e58fa50 100644 --- a/recipes/yahmm/meta.yaml +++ b/recipes/yahmm/meta.yaml @@ -17,6 +17,7 @@ requirements: host: - python - pip + - setuptools - cython >=0.20.1 - numpy >=1.8.0 - scipy >=0.13.3 diff --git a/recipes/yahs/meta.yaml b/recipes/yahs/meta.yaml index b4cc5e55f410f..80cdf8d0a7aca 100644 --- a/recipes/yahs/meta.yaml +++ b/recipes/yahs/meta.yaml @@ -11,7 +11,7 @@ source: - Makefile.patch build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage('yahs', max_pin="x") }} diff --git a/recipes/yak/meta.yaml b/recipes/yak/meta.yaml index f44283997a96a..f4d2180569c30 100644 --- a/recipes/yak/meta.yaml +++ b/recipes/yak/meta.yaml @@ -11,7 +11,7 @@ source: - yak.patch build: - number: 5 + number: 6 run_exports: - {{ pin_subpackage('yak', max_pin="x.x") }} diff --git a/recipes/yass/build_failure.linux-64.yaml b/recipes/yass/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..95af2be54713b --- /dev/null +++ b/recipes/yass/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +recipe_sha: ad6c5b85566ff3bc7307b185d468146696a31c34c7cc9efe6bea95dc68012a35 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + 2024-12-11T22:32:50 noarch Applying patch instructions + 2024-12-11T22:32:50 noarch Writing patched repodata + 2024-12-11T22:32:50 noarch Building current_repodata subset + 2024-12-11T22:32:50 noarch Writing current_repodata subset + 2024-12-11T22:32:50 noarch Writing index HTML + /opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (/opt/recipe/meta.yaml). + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml + Adding in variants from /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for yass + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['yass-1.14-h7b50bb2_7.tar.bz2'] + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_h_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/yass_1733956370936/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_build_env): ...working... done + Reloading output folder (file:///opt/host-conda-bld): ...working... done + Solving environment (_test_env): ...working... done + + ## Package Plan ## + + environment location: /opt/conda/conda-bld/yass_1733956370936/_build_env + + + The following NEW packages will be INSTALLED: + + _libgcc_mutex: 0.1-conda_forge conda-forge + _openmp_mutex: 4.5-2_gnu conda-forge + binutils_impl_linux-64: 2.43-h4bf12b8_2 conda-forge + binutils_linux-64: 2.43-h4852527_2 conda-forge + gcc_impl_linux-64: 13.3.0-hfea6d02_1 conda-forge + gcc_linux-64: 13.3.0-hc28eda2_7 conda-forge + kernel-headers_linux-64: 3.10.0-he073ed8_18 conda-forge + ld_impl_linux-64: 2.43-h712a8e2_2 conda-forge + libgcc: 14.2.0-h77fa898_1 conda-forge + libgcc-devel_linux-64: 13.3.0-h84ea5a7_101 conda-forge + libgomp: 14.2.0-h77fa898_1 conda-forge + libsanitizer: 13.3.0-heb74ff8_1 conda-forge + libstdcxx: 14.2.0-hc0a3c3a_1 conda-forge + make: 4.4.1-hb9d3cd8_2 conda-forge + sysroot_linux-64: 2.17-h4a8ded7_18 conda-forge + tzdata: 2024b-hc8b5060_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/conda/conda-bld/src_cache + Downloading source to cache: yass-1.14_2ea4d2a32b.tar.gz + Downloading https://bioinfo.lifl.fr/yass/files/yass-1.14/yass-1.14.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NameResolutionError(": Failed to resolve 'bioinfo.lifl.fr' ([Errno -2] Name or service not known)")': /yass/files/yass-1.14/yass-1.14.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NameResolutionError(": Failed to resolve 'bioinfo.lifl.fr' ([Errno -2] Name or service not known)")': /yass/files/yass-1.14/yass-1.14.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NameResolutionError(": Failed to resolve 'bioinfo.lifl.fr' ([Errno -2] Name or service not known)")': /yass/files/yass-1.14/yass-1.14.tar.gz + WARNING: Error: HTTP 000 CONNECTION FAILED for url + Elapsed: - + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/conda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/conda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/conda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download https://bioinfo.lifl.fr/yass/files/yass-1.14/yass-1.14.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/yass/build_failure.osx-64.yaml b/recipes/yass/build_failure.osx-64.yaml new file mode 100644 index 0000000000000..4d80777e14c6c --- /dev/null +++ b/recipes/yass/build_failure.osx-64.yaml @@ -0,0 +1,89 @@ +recipe_sha: ad6c5b85566ff3bc7307b185d468146696a31c34c7cc9efe6bea95dc68012a35 # The hash of the recipe's meta.yaml at which this recipe failed to build. +skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. +log: |- + /opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py:501: UserWarning: RECIPE_PATH received is a file (recipes/yass/meta.yaml). + It should be a path to a folder. + Forcing conda-build to use the recipe file. + warnings.warn( + WARNING: No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.22 + Adding in variants from internal_defaults + Adding in variants from /opt/mambaforge/envs/bioconda/conda_build_config.yaml + Adding in variants from /opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml + Attempting to finalize metadata for yass + Reloading output folder (local): ...working... done + Getting pinned dependencies: ...working... done + Reloading output folder (local): ...working... done + Getting pinned dependencies: ...working... done + BUILD START: ['yass-1.14-h18d8cf3_7.tar.bz2'] + Reloading output folder (local): ...working... done + Solving environment (_build_env): ...working... done + + ## Package Plan ## + + environment location: /opt/mambaforge/envs/bioconda/conda-bld/yass_1733974505222/_build_env + + + The following NEW packages will be INSTALLED: + + ca-certificates: 2024.8.30-h8857fd0_0 conda-forge + cctools_osx-64: 1010.6-h00edd4c_2 conda-forge + clang: 18.1.8-default_h179603d_5 conda-forge + clang-18: 18.1.8-default_h0c94c6a_5 conda-forge + clang_impl_osx-64: 18.1.8-h6a44ed1_23 conda-forge + clang_osx-64: 18.1.8-h7e5c614_23 conda-forge + clangxx: 18.1.8-default_h179603d_5 conda-forge + compiler-rt: 18.1.8-h1020d70_1 conda-forge + compiler-rt_osx-64: 18.1.8-hf2b8a54_1 conda-forge + ld64_osx-64: 951.9-hc8d1a19_2 conda-forge + libclang-cpp18.1: 18.1.8-default_h0c94c6a_5 conda-forge + libcxx: 19.1.5-hf95d169_0 conda-forge + libcxx-devel: 18.1.8-h7c275be_7 conda-forge + libiconv: 1.17-hd75f5a5_2 conda-forge + libllvm18: 18.1.8-h9ce406d_2 conda-forge + liblzma: 5.6.3-hd471939_1 conda-forge + libxml2: 2.13.5-he8ee3e7_1 conda-forge + libzlib: 1.3.1-hd23fc13_2 conda-forge + llvm-tools: 18.1.8-h9ce406d_2 conda-forge + llvm-tools-18: 18.1.8-h9ce406d_2 conda-forge + make: 4.4.1-h00291cd_2 conda-forge + ncurses: 6.5-hf036a51_1 conda-forge + openssl: 3.4.0-hd471939_0 conda-forge + sigtool: 0.1.3-h88f4db0_0 conda-forge + tapi: 1300.6.5-h390ca13_0 conda-forge + zstd: 1.5.6-h915ae27_0 conda-forge + + Preparing transaction: ...working... done + Verifying transaction: ...working... done + Executing transaction: ...working... done + Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache + Downloading source to cache: yass-1.14_2ea4d2a32b.tar.gz + Downloading https://bioinfo.lifl.fr/yass/files/yass-1.14/yass-1.14.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NameResolutionError(": Failed to resolve 'bioinfo.lifl.fr' ([Errno 8] nodename nor servname provided, or not known)")': /yass/files/yass-1.14/yass-1.14.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NameResolutionError(": Failed to resolve 'bioinfo.lifl.fr' ([Errno 8] nodename nor servname provided, or not known)")': /yass/files/yass-1.14/yass-1.14.tar.gz + WARNING:urllib3.connectionpool:Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NameResolutionError(": Failed to resolve 'bioinfo.lifl.fr' ([Errno 8] nodename nor servname provided, or not known)")': /yass/files/yass-1.14/yass-1.14.tar.gz + WARNING: Error: HTTP 000 CONNECTION FAILED for url + Elapsed: - + + An HTTP error occurred when trying to retrieve this URL. + HTTP errors are often intermittent, and a simple retry will get you on your way. + Traceback (most recent call last): + File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in + sys.exit(execute()) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute + api.build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build + return build_tree( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree + packages_from_this = build( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2449, in build + try_download(m, no_download_source=False, raise_error=True) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/render.py", line 762, in try_download + source.provide(metadata) + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 1035, in provide + unpack( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 169, in unpack + src_path, unhashed_fn = download_to_cache( + File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/source.py", line 116, in download_to_cache + raise RuntimeError(f"Could not download {url}") + RuntimeError: Could not download https://bioinfo.lifl.fr/yass/files/yass-1.14/yass-1.14.tar.gz +# Last 100 lines of the build log. diff --git a/recipes/yass/meta.yaml b/recipes/yass/meta.yaml index e6f2b4388c926..e04a30b826b5d 100644 --- a/recipes/yass/meta.yaml +++ b/recipes/yass/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 2ea4d2a32bb17fb6de590b0e8bce5231e2506b490b3456700b4bc029544a1982 build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/zagros/meta.yaml b/recipes/zagros/meta.yaml index a85768f195b09..de515bf7accb9 100644 --- a/recipes/zagros/meta.yaml +++ b/recipes/zagros/meta.yaml @@ -7,7 +7,7 @@ source: sha256: 3d8495d4217e75059a49673c8eaf524f933e2f35be325502fdbaf107e933c028 build: - number: 9 + number: 10 skip: True # [osx] requirements: diff --git a/recipes/zerone/meta.yaml b/recipes/zerone/meta.yaml index 63f737c6dcc9e..2a944240435cf 100644 --- a/recipes/zerone/meta.yaml +++ b/recipes/zerone/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 2d06066135c988f6b528a87b0fbad87cb93e82afce6a67d24e6efd828165a130 build: - number: 6 + number: 7 requirements: build: diff --git a/recipes/zorro/meta.yaml b/recipes/zorro/meta.yaml index 4b66063f8fdab..595a3a4320908 100644 --- a/recipes/zorro/meta.yaml +++ b/recipes/zorro/meta.yaml @@ -13,7 +13,7 @@ source: sha256: {{ sha256 }} build: - number: 4 + number: 5 skip: true # [osx] requirements: diff --git a/virdig/build.sh b/virdig/build.sh deleted file mode 100644 index e3e9aee0cf205..0000000000000 --- a/virdig/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash -set -xe -make -j"${CPU_COUNT}" CXX="${CXX}" INCLUDES="-I$PREFIX/include" CFLAGS+="${CFLAGS} -g -Wall -O2 -L$PREFIX/lib" diff --git a/virdig/meta.yaml b/virdig/meta.yaml deleted file mode 100644 index cc9ba09166410..0000000000000 --- a/virdig/meta.yaml +++ /dev/null @@ -1,38 +0,0 @@ -{% set name = "virdig" %} -{% set version = "1.0.0" %} - -package: - name: {{ name }} - version: {{ version }} - -source: - url: "https://github.com/Limh616/VirDiG/archive/refs/tags/v{{ version }}.tar.gz" - sha256: "9ffd628fd1c22dd86a1e9e0e4c5b543334a99f0fc6dec56bb1f741e2fe8a32b1" - -build: - number: 0 - - run_exports: - - {{ pin_subpackage("virdig", max_pin="x") }} - -requirements: - build: - - make - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - boost >= 1.80.0 - host: - - zlib - - boost >= 1.80.0 - -test: - commands: - - virdig -h - -about: - home: "https://github.com/Limh616/VirDiG" - license: MIT - license_family: MIT - license_file: LICENSE - summary: "A de novo transcriptome assembler for coronavirus." - dev_url: "https://github.com/Limh616/VirDiG"